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 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 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 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 (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.545)DS(0.455)WDADAFSVEDPVRK;AAAAAAAGDS(0.914)DS(0.086)WDADAFSVEDPVRK 113.4 5.19E-25 594660000 569150 438639 546255 580230 467452 541250 674670 611530 525690 TRUE FALSE 542247.4074 483336.8128 571301.3321 521904.178 548975.4808 522506.3768 571736.7003 557981.1913 607211.3203 0.893012678 0.795994404 0.940860806 0.859509961 0.904092961 0.860501706 0.941577802 0.918924224 1 19.21183916 0.999657706 0.351043684 1.013096677 0.849707144 0.498153681 0.039382862 1.174616126 0.416672299 0.069856925 0.038799514 9.992121503 -0.999657706 -0.163389534 (ac)AAAAAAAGDSDS(ph)WDADAFSVEDPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.054)DS(0.946)WDADAFSVEDPVRK;AAAAAAAGDS(0.203)DS(0.797)WDADAFSVEDPVRK 127.67 4.27E-34 594890000 407230 348130 375760 438360 368570 438170 467400 448710 407350 TRUE FALSE 387981.045 383604.8428 392988.9677 394295.22 432848.4913 422996.063 396089.5456 409418.5736 470519.7575 0.824579709 0.815278926 0.835223094 0.837999284 0.919936909 0.898997452 0.841812781 0.870141088 1 18.84389578 -4.999999998 0.119259362 1.482094651 0.777549837 0.744739898 0.028330239 81.09189457 0.628199223 9.450406777 0.290906636 1.00E-05 4.999999998 -0.704544814 (ac)AAAAKPNNLSLVVHGPGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAAAKPNNLSLVVHGPGDLR 20 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2;A0A6I8PRA7 Q00796 SORD Sorbitol dehydrogenase 0 62.739 1.09E-11 132880000 112150 89041 100550 114500 96871 94545 108980 120550 118290 FALSE TRUE 106848.8918 98114.37913 105160.317 102990.2425 113765.2717 91270.88294 92353.09944 109994.0029 136633.8091 0.782009171 0.718082734 0.769650774 0.753768362 0.832628999 0.66799633 0.675916891 0.805027714 1 17.05995499 0.963575937 13.15241449 0.999999998 0.740328332 0.734619106 0.048502887 3.966624932 1432.781866 0.047898553 0.011975771 9.195512464 -0.963575937 -0.259671666 (ac)AAAITDMADLEELSRLS(ph)PLPPGS(ph)PGSAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 2 AAAIT(0.005)DMADLEELS(0.018)RLS(0.965)PLPPGS(0.809)PGS(0.202)AAR 44.811 0.0010065 11673000 5441.9 6369.2 7188.1 6073 5903.8 4947.8 8390 5781.2 6005.5 TRUE FALSE 5184.672172 7018.228721 7517.681495 5462.530502 6933.420851 4776.456445 7109.951407 5274.96748 6936.802268 0.747415303 1.011738327 1.083738761 0.787470983 0.999512539 0.688567478 1.024960945 0.760432152 1 12.76005505 (ac)AAAS(ph)VTPPGSLELLQPGFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAASVTPPGSLELLQPGFSK 20 0 Q12933-4;Q12933-3;Q12933;Q12933-2;B1AMX7;B1AMX8;B1AMY1 Q12933-4 TRAF2 TNF receptor-associated factor 2 1 AAAS(0.333)VT(0.333)PPGS(0.333)LELLQPGFSK 46.3 0.0055623 55059000 93729 87111 98480 110480 101090 103770 125770 112220 104500 TRUE FALSE 89298.61592 95987.70994 102995.4054 99374.3405 118720.064 100176.4189 106581.4766 102393.4219 120705.3263 0.739806756 0.795223483 0.853279707 0.823280493 0.983552819 0.829925422 0.88298901 0.848292491 1 16.88112981 8 0.136549165 0.995510813 0.121172743 0.582996948 0.051138474 51.55931704 0.471562225 0.219610919 8.76307464 100000000 -8 -0.87433807 (ac)AAASVT(ph)PPGSLELLQPGFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAASVTPPGSLELLQPGFSK 20 0 Q12933-4;Q12933-3;Q12933;Q12933-2;B1AMX7;B1AMX8;B1AMY1 Q12933-4 TRAF2 TNF receptor-associated factor 2 1 AAAS(0.178)VT(0.812)PPGS(0.009)LELLQPGFSK;AAAS(0.102)VT(0.869)PPGS(0.029)LELLQPGFSK 94.728 3.94E-11 61161000 300670 276030 305940 340460 277540 302350 357230 323330 287000 TRUE FALSE 286457.925 304157.7708 319967.6516 306236.314 325942.8881 291879.5437 302728.0025 295017.5111 331506.4942 0.864109542 0.917501696 0.96519271 0.923771689 0.983217203 0.880464029 0.913188754 0.889929809 1 18.33867761 4.374622623 2.380337206 0.930390456 0.866238042 0.244395293 0.038582638 0.443471183 4.587344449 0.009268835 0.042138933 23693.14013 -4.374622623 -0.064152414 (ac)AADVSVTHRPPLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.001)HRPPLS(0.998)PK;AADVSVT(0.004)HRPPLS(0.996)PK;AADVSVT(0.002)HRPPLS(0.998)PK;AADVSVT(0.002)HRPPLS(0.998)PK;AADVSVTHRPPLS(1)PK;AADVS(0.001)VT(0.003)HRPPLS(0.997)PK;AADVSVTHRPPLS(1)PK 105.79 1.72E-06 8763930000 7602400 6370540 6630400 7817830 5193750 7531950 8516230 8726920 5906990 TRUE FALSE 7243049.619 7019705.269 6934410.398 7031966.875 6099538.356 7271116.683 7216922.702 7962744.62 6823015.84 1.061561308 1.028827345 1.016326293 1.030624439 0.893965147 1.065674894 1.057732075 1.16704179 1 22.70197814 2.027622332 24.99994794 1.07643049 1.012921213 0.233951006 0.059157104 321.9570686 291390.0845 0.021189117 0.015648931 106.5669 -2.027622332 -0.063509276 (ac)AAGGDHGS(ph)PDSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGGDHGSPDSYR 13 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 1 AAGGDHGS(0.951)PDS(0.049)YR;AAGGDHGS(0.975)PDS(0.025)YR 68.14 6.37E-06 224270000 16889 22622.6 35433 20287.7 26512 19459.1 21336.1 27127 89540 TRUE FALSE 16090.69044 24927.86866 37057.6381 18248.34185 31135.68441 18785.22649 18080.88608 24751.61607 103425.4059 0.155577735 0.241022681 0.358303047 0.176439645 0.301044836 0.181630677 0.174820547 0.23931853 1 16.65823109 0.921552674 21.30230566 1 0.223098367 0.937181607 0.06277263 2939.798844 798301.4343 0.058344067 0.014586017 8.347427856 -0.921552674 -0.776901633 (ac)AAHEWDWFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAHEWDWFQR 10 0 Q96JQ2;G3V3D8 Q96JQ2 CLMN Calmin 0 ; 51.066 0.0052949 26437000 8723.9 6492.3 8663.7 8656.4 9290.8 7419.3 7971.2 7706 9776 FALSE TRUE 8311.538536 7153.872751 9060.939215 7786.242226 10911.11258 7162.367781 6755.047039 7031.221788 11292.01215 0.736054693 0.633533923 0.80242025 0.68953541 0.966268229 0.634286227 0.598214645 0.622672177 1 13.46301497 (ac)AALHTTPDS(ph)PAAQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER;AALHT(0.006)T(0.033)PDS(0.961)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER 170.35 1.47E-88 4306540000 131549 121957.7 101841.3 146148.1 151149.2 116291.4 133800 126700 136183 TRUE FALSE 125330.9395 134385.3283 106510.8243 131457.0153 177509.5726 112264.1997 113386.3526 115605.4763 157301.5641 0.796755838 0.854316542 0.677112303 0.835700624 1.128466672 0.713687752 0.72082152 0.734928969 1 17.26317349 -1.6625126 6.48705896 1.001247457 0.807102694 0.185054379 0.126800891 0.002250382 0.000117075 0.120772252 0.0282932 0.021751409 1.6625126 -0.194144763 (ac)AARDS(ph)DS(ph)EEDLVSYGTGLEPLEEGERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AARDSDSEEDLVSYGTGLEPLEEGERPK 28 2 Q9BRR8;K7EQ19 Q9BRR8 GPATCH1 G patch domain-containing protein 1 2 AARDS(0.994)DS(0.984)EEDLVS(0.016)Y(0.004)GT(0.001)GLEPLEEGERPK 48.115 0.014209 23120000 27980 25944 22431 30141 19879 25281 27981 28851 22900 TRUE FALSE 26657.44085 28587.7231 23459.48354 27111.16942 23345.89131 24405.51263 23711.98454 26324.65349 26451.21504 1.007796459 1.080771641 0.886896254 1.02494987 0.882601849 0.922661307 0.896442167 0.995215284 1 14.69104637 2.752136934 24.68513209 0.928658843 1.008113713 0.182514611 0.060526265 840.2230152 1527733.457 0.01786866 0.018855407 565.1151289 -2.752136934 0.079454869 (ac)AAS(ph)DTERDGLAPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASDTERDGLAPEK 14 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AAS(0.976)DT(0.024)ERDGLAPEK 45.864 0.021492 133070000 295270 295430 283170 328810 226470 313220 338900 366190 253300 TRUE FALSE 281313.1723 325534.6529 296153.6246 295757.3941 265966.2963 302373.1129 287194.5807 334124.4623 292580.4703 0.961489917 1.112632885 1.012212552 1.010858291 0.909036396 1.033469912 0.981591766 1.141991678 1 18.15847395 -0.962893771 4.65601827 0.999999717 1.019083895 0.008610819 0.067505348 1.84E-07 4.09E-08 0.060618156 0.014287625 0.108919648 0.962893771 0.019084178 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 AASAAAASAAAASAASGS(0.992)PGPGEGS(0.008)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAASGS(0.998)PGPGEGS(0.002)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR 207.53 7.03E-137 4407360000 6669620 5790020 6537120 7086470 5585150 7123140 8259120 7677080 7038410 TRUE FALSE 6354360.281 6380029.621 6836853.418 6374124.572 6559198.392 6876463.876 6999039.555 7004834.176 8129890.676 0.781604641 0.784762044 0.840952688 0.784035706 0.806800319 0.845824889 0.860902051 0.861614806 1 22.95480452 -0.307996224 0.24397049 1.090068741 0.766666907 0.923658835 0.017770636 2.176559057 0.1804455 0.188989545 0.033457182 0.492043813 0.307996224 -0.323401834 (ac)AASDTERDGLAPEKT(ph)SPDRDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASDTERDGLAPEKTSPDRDK 21 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AASDTERDGLAPEKT(0.5)S(0.5)PDRDK 53.865 0.00017973 218370000 79255 56823 73058 74894 57633 93116 102330 78346 78544 TRUE FALSE 75508.77322 62613.3283 76407.78156 67365.51283 67684.17695 89891.36957 86717.67908 71485.6089 90724.20237 0.832289193 0.690150221 0.842198438 0.742530781 0.74604323 0.990820169 0.955838429 0.787944198 1 16.46919985 2.245865453 24.97090466 0.934915329 0.767245156 0.560491255 0.071687867 112.2921711 383860.965 0.02345686 0.019254495 176.1430259 -2.245865453 -0.167670173 (ac)AASDTERDGLAPEKTS(ph)PDRDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASDTERDGLAPEKTSPDRDK 21 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AASDTERDGLAPEKT(0.193)S(0.807)PDRDK 67.31 4.45E-06 152310000 58914 33611 50777 51026 35084 55188 63847 60939 45572 TRUE FALSE 56129.25198 37035.99911 53105.17568 45896.76954 41202.63849 53276.82572 54105.96752 55602.8581 52639.07301 1.06630396 0.703583802 1.00885469 0.871914472 0.782738679 1.012115576 1.027867028 1.0563039 1 15.68384646 2.112007995 8.289862078 1.028275312 0.88311219 0.310397976 0.10187926 0.284462681 19.63737562 0.036203459 0.02671536 129.4219667 -2.112007995 -0.145163122 (ac)AATDLERFS(ph)NAEPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATDLERFSNAEPEPR 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599 A0A087X142 8-Sep Septin-8 1 AAT(0.036)DLERFS(0.964)NAEPEPR 43.791 0.0046224 37446000 7502.1 6410.7 7779 9488.1 8641.9 7670.2 10747 9389.9 6292.1 TRUE FALSE 7147.490601 7063.957618 8135.674844 8534.338162 10149.04462 7404.579051 9107.347768 8567.670577 7267.846732 0.983439919 0.971946421 1.119406496 1.174259513 1.396430745 1.018813319 1.253101242 1.178845797 1 12.82731228 3.591788327 2.806555586 1.186396396 0.975764844 0.324446245 0.111529503 0.244718674 3.71565616 0.028212131 0.046742044 3906.504485 -3.591788327 -0.210631551 (ac)AATLGAGT(ph)PPRPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AATLGAGTPPRPQAR 15 1 A0A075B730 A0A075B730 EPPK1 1 AAT(0.001)LGAGT(0.999)PPRPQAR;AATLGAGT(1)PPRPQAR 64.842 2.65E-06 717030000 59199 50551 48088 68204 51890 55534 70529 63375 68181 TRUE FALSE 56400.78059 55702.20437 50292.88237 61348.00434 60939.59957 53610.84366 59768.5057 57825.54903 78754.16126 0.716162545 0.707292205 0.638606031 0.778981115 0.773795297 0.680736647 0.758925049 0.734253887 1 16.26506854 -4.999999989 0.277842 3.012271762 0.703923017 0.819353448 0.041120409 86.61686321 0.831854601 100.3319573 0.044696875 1.00E-05 4.999999989 -2.308348745 (ac)ACPLDQAIGLLVAIFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ACPLDQAIGLLVAIFHK 17 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 147.72 1.71E-19 4370500000 14557000 12178000 11342000 14729000 11399000 12061000 12907000 15349000 7991200 FALSE TRUE 13868919.46 13418952.05 11862041.92 13248412.94 13386981.99 11643324.55 10937800.1 14004960.19 9230434.483 1.502520763 1.453772525 1.285101145 1.435296785 1.450308977 1.261405903 1.184971316 1.517259043 1 23.13796713 -4.13697119 0.102867296 6.02E-15 1.644977429 0.55026603 0.109682655 101.8293165 0.855129505 23.26330418 1.696610377 7.30E-05 4.13697119 1.644977429 (ac)ACRPRS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ACRPRSPPR 9 2 F8W8D3;Q14493;E7EUV9;Q14493-2 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 ACRPRS(1)PPR;ACRPRS(1)PPR;ACRPRS(1)PPR 61.435 0.0082995 415993000 46809.2 48540.3 54062 50338.1 66337.2 41381.8 50804.3 45887.9 92946 TRUE FALSE 44596.62188 53486.61176 56540.79617 45278.01855 77906.38668 39948.73789 43053.17095 41869.71221 107359.591 0.415394856 0.498200592 0.526648767 0.42174172 0.725658378 0.37210218 0.401018396 0.389995079 1 16.71209155 -0.963710527 4.425332354 1.000012864 0.467011654 0.724323614 0.102975507 52469235 115625536.8 11174.16473 0.023607147 0.108715001 0.963710527 -0.533001211 (ac)ADANKAEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADANKAEVPGATGGDSPHLQPAEPPGEPR 29 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 ADANKAEVPGAT(0.006)GGDS(0.994)PHLQPAEPPGEPR;ADANKAEVPGAT(0.027)GGDS(0.973)PHLQPAEPPGEPR 70.605 8.89E-25 665740000 531770 325630 509120 475170 456860 485220 657980 523400 491610 TRUE FALSE 506634.286 358812.0672 532463.6556 427405.0088 536536.2394 468416.7097 557593.0664 477568.3213 567846.368 0.892203093 0.631882297 0.937689639 0.75267719 0.94486162 0.824900424 0.981943529 0.841016775 1 19.11514113 2.492530156 0.662483689 0.951798668 0.77430071 0.225843205 0.098760442 0.907614217 0.81222277 0.072990087 0.059930672 310.8351733 -2.492530156 -0.177497958 (ac)ADDKVAILT(ph)DDEEEQKRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADDKVAILTDDEEEQKRK 18 3 C9JAZ7;C9J134;C9JJH2;Q6ZSS7 C9JAZ7 MFSD6 Major facilitator superfamily domain-containing protein 6 1 ADDKVAILT(1)DDEEEQKRK;ADDKVAILT(1)DDEEEQKRK;ADDKVAILT(1)DDEEEQKRK 101.71 2.65E-09 221593000 213898 167074 175762 255378 126145 273008 258590 274573 150992 TRUE FALSE 203787.4654 184099.0305 183820.8616 229706.9183 148144.6481 263553.6645 219137.3462 250529.9325 174407.0682 1.168458753 1.055570926 1.053975985 1.317073446 0.849418831 1.51114096 1.256470557 1.436466624 1 17.41209898 2.228598792 24.99999958 1.322070033 1.100371506 0.261438915 0.174991907 243.2614818 610479.7089 0.056530928 0.042243474 169.2773269 -2.228598792 -0.221698526 (ac)ADEAALALQPGGS(ph)PSAAGADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADEAALALQPGGSPSAAGADR 21 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 ADEAALALQPGGS(0.832)PS(0.168)AAGADR;ADEAALALQPGGS(0.837)PS(0.163)AAGADR;ADEAALALQPGGS(0.939)PS(0.061)AAGADR 101.38 5.73E-25 280626000 13993.5 10871.3 17836.3 16668.4 14389 13622.4 19802.1 14264.5 24065.5 TRUE FALSE 13332.05499 11979.09783 18654.112 14992.86076 16898.43704 13150.65287 16780.92595 13015.42476 27797.45483 0.479614233 0.430942254 0.671072662 0.539360918 0.607913104 0.47308838 0.603685699 0.468223614 1 14.76266517 -5 0.353659519 6.53860684 0.516124532 0.779229631 0.077298726 202.6788428 1.642863403 852.580912 0.056214248 1.00E-05 5 -6.022482308 (ac)ADEDGEGIHPSAPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADEDGEGIHPSAPHR 15 0 Q96L92-3;Q96L92;A0A2R8Y8A7;H7C603;A0A2R8Y871 Q96L92-3 SNX27 Sorting nexin-27 0 81.311 3.93E-06 0 8703.7 9995.6 10113 7947.9 12294 9310.7 9319.6 9371.9 18889 FALSE TRUE 8292.29335 11014.163 10576.69105 7148.961992 14438.06971 8988.268124 7897.723854 8551.246752 21818.20965 0.38006296 0.50481516 0.484764388 0.32766034 0.661744018 0.411961764 0.361978548 0.391931643 1 14.4132451 -1.690076285 2.977401843 1.066873219 0.440177378 0.774957885 0.094733824 53899911.05 52670631.48 27224298.27 0.0211728 0.020413793 1.690076285 -0.626695841 (ac)ADEELEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADEELEALRR 10 1 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ;;; 82.279 1.74E-05 1654660000 230306 210507 207576 222586 215457 218170 234104 239791 211514 FALSE TRUE 219419.8918 231957.9026 217093.5649 200211.2324 253032.6326 210614.7182 198387.1352 218793.6288 244314.5109 0.898104214 0.949423355 0.888582361 0.819481543 1.035684011 0.862063892 0.812015359 0.895540867 1 17.89838003 (ac)ADFDDRVSDEEKVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADFDDRVSDEEKVR 14 2 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;; 143.25 1.02E-05 944813000 687870 463936 652130 618460 519580 701270 836610 771080 618210 FALSE TRUE 655355.7483 511211.6059 682030.8055 556291.2258 610194.5875 676984.8441 708969.7791 703560.1474 714078.8494 0.917763842 0.715903582 0.955119741 0.779033333 0.854519901 0.948053348 0.992845229 0.985269551 1 19.44572386 2.170009691 2.763504314 0.98939547 0.833745534 0.524802439 0.065753535 0.195861379 3.025166378 0.026715186 0.018127742 147.9141392 -2.170009691 -0.155649936 (ac)ADGDS(ph)GS(ph)ERGGGGGPCGFQPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 2 ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR;ADGDS(1)GS(1)ERGGGGGPCGFQPASR 122.53 5.93E-08 5087320000 38150.4 29564.9 34244 49175.6 34573 41665.3 31875.4 48175.2 31400 TRUE FALSE 36347.1062 32577.59692 35814.12127 44232.37526 40602.52025 40222.42021 27012.2223 43956.7241 36269.35163 1.002143809 0.898212829 0.987448622 1.219552412 1.119471907 1.108991984 0.744767168 1.211952299 1 15.14646333 3.470288736 24.9164882 1.044420246 0.948953691 0.106386242 0.135691429 418.8049301 1527269.531 0.03911594 0.053086824 2953.17196 -3.470288736 -0.095466555 (ac)ADGDS(ph)GSERGGGGGPCGFQPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 ADGDS(0.912)GS(0.088)ERGGGGGPCGFQPASR;ADGDS(0.913)GS(0.087)ERGGGGGPCGFQPASR;ADGDS(0.5)GS(0.5)ERGGGGGPCGFQPASR;ADGDS(0.5)GS(0.5)ERGGGGGPCGFQPASR;ADGDS(0.992)GS(0.008)ERGGGGGPCGFQPASR;ADGDS(0.989)GS(0.011)ERGGGGGPCGFQPASR 175.21 6.52E-32 2785530000 27676.4 15984.1 31242.4 24798 20807.6 30635.1 23562.9 22521.6 25170 TRUE FALSE 26368.19142 17612.89796 32674.89494 22305.25793 24436.43885 29574.19881 19967.94684 20549.48931 29073.23505 0.906957598 0.605811425 1.123882323 0.767209356 0.840513235 1.017231098 0.686815444 0.706818119 1 14.82740399 -1.417717882 7.971026674 1.000004078 0.821432095 0.09998705 0.155700024 1.04E-05 7.61E-07 0.139172967 0.032802634 0.038219246 1.417717882 -0.178571982 (ac)ADHS(ph)FSDGVPSDSVEAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.985)FS(0.015)DGVPSDSVEAAK;ADHS(0.998)FS(0.002)DGVPSDSVEAAK;ADHS(0.996)FS(0.004)DGVPSDSVEAAK 100.22 4.32E-148 369560000 733910 698600 762210 894250 646610 856860 952350 918290 730360 TRUE FALSE 699219.5288 769788.1342 797158.0824 804358.291 759378.5793 827186.7233 807051.5164 837879.6594 843620.4986 0.828831838 0.912481543 0.94492498 0.95345987 0.900142399 0.980519943 0.956652331 0.993194998 1 19.68623463 7.693299226 0.274359292 0.989310754 2.67E-10 0.801243385 0.022658061 17.00651067 0.278557981 0.024507079 7.758300446 49351371.43 -7.693299226 -0.989310754 (ac)ADILSQSETLASQDLSGDFKKPALPVS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADILSQSETLASQDLSGDFKKPALPVSPAAR 31 2 A0A087X0M4;A0A087WWF4 A0A087X0M4 SLC4A1AP 1 ADILSQSETLASQDLSGDFKKPALPVS(1)PAAR;ADILSQSETLASQDLS(0.002)GDFKKPALPVS(0.998)PAAR;ADILSQSETLASQDLSGDFKKPALPVS(1)PAAR;ADILS(0.001)QS(0.001)ET(0.001)LAS(0.002)QDLS(0.071)GDFKKPALPVS(0.926)PAAR 188.96 1.62E-105 523119000 507219 336158 519421 448664 410382 541084 706309 622428 570547 TRUE FALSE 483243.7631 370412.8824 543236.9666 403563.4423 481952.4909 522346.1254 598548.5898 567924.9046 659024.5148 0.733271301 0.562062373 0.824304642 0.612364841 0.731311932 0.792605 0.90823418 0.861765977 1 19.32997261 1.829563971 0.852760881 0.975338096 0.665757063 0.673323505 0.074716393 0.303723312 0.413537351 0.059993157 0.027197516 67.54045323 -1.829563971 -0.309581034 (ac)ADKEAAFDDAVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADKEAAFDDAVEER 14 1 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 65.695 0.0046455 166470000 231610 194790 204780 254590 194900 206120 246980 233240 192200 FALSE TRUE 220662.2543 214639.3225 214169.3656 228998.1295 228890.4983 198982.0127 209298.6649 212816.2691 222005.3944 0.993949967 0.966820302 0.964703431 1.031498042 1.031013228 0.896293594 0.942763871 0.95860855 1 17.76023521 2.244495291 24.99999 0.94271818 0.993114414 0.325752769 0.03349602 158.5862372 668050.198 0.011580714 0.009450667 175.5881857 -2.244495291 0.050396234 (ac)ADLEEQLS(ph)DEEKVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADLEEQLSDEEKVR 14 1 P47755;F8W9N7;C9JUG7;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 1 ADLEEQLS(1)DEEKVR;ADLEEQLS(1)DEEKVR 96.734 1.04E-05 318760000 632250 500930 531520 617740 404780 605900 693380 625750 467990 TRUE FALSE 602364.7955 551975.3365 555890.7177 555643.6016 475373.5038 584917.5311 587592.1462 570956.0127 540563.499 1.114327543 1.021111003 1.02835415 1.027897005 0.879403631 1.082051474 1.086999302 1.056223762 1 19.04410457 -0.837064359 7.723842666 1 1.040481165 0.03013801 0.063438286 0 0 0.061101992 0.014401878 0.145524341 0.837064359 0.040481164 (ac)ADRDS(ph)GSEQGGAALGSGGSLGHPGSGSGSGGGGGGGGGGGGSGGGGGGAPGGLQHETQELASKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADRDSGSEQGGAALGSGGSLGHPGSGSGSGGGGGGGGGGGGSGGGGGGAPGGLQHETQELASKR 64 2 Q00577;A0A494C0H6 Q00577 PURA Transcriptional activator protein Pur-alpha 1 ADRDS(0.349)GS(0.103)EQGGAALGS(0.103)GGS(0.103)LGHPGS(0.114)GS(0.114)GS(0.114)GGGGGGGGGGGGSGGGGGGAPGGLQHETQELASKR 57.399 5.72E-11 41945000 16464 6844.3 14587 13639 19229 13906 21514 16506 20309 TRUE FALSE 15685.77935 7541.741951 15255.82838 12267.98181 22582.53151 13424.43173 18231.64417 15060.64714 23458.416 0.668663193 0.321494084 0.650334975 0.522967186 0.962662249 0.572265056 0.777189908 0.642014667 1 14.51781798 2.785770957 23.87516542 0.759098227 0.524584355 0.369797362 0.158547116 254.7565591 128834.5223 0.043885158 0.04654706 610.6199049 -2.785770957 -0.234513872 (ac)ADSRDPASDQMQHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADSRDPASDQMQHWK 15 1 P04040 P04040 CAT Catalase 0 56.482 0.00047204 203880000 111520 92288 96876 107470 89264 93372 119410 114330 99264 FALSE TRUE 106248.6706 101692.2521 101317.8604 96666.91142 104831.6133 90138.50423 101191.8114 104318.6591 114657.3541 0.926662501 0.886923066 0.883657757 0.843093861 0.91430344 0.786155453 0.882558403 0.909829639 1 16.80696937 -1.985245993 6.397895157 1.097444301 0.878898078 0.472804461 0.040104489 0.031700773 7.31E-05 0.022083128 0.008779539 0.01034556 1.985245993 -0.218546223 (ac)ADVLDLHEAGGEDFAMDEDGDES(ph)IHKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADVLDLHEAGGEDFAMDEDGDESIHKLK 28 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK 264.56 1.30E-146 167677000 169628 156112 172490 182813 107000 209199 225284 212619 115387 TRUE FALSE 161610.0206 172019.9903 180398.8371 164436.2899 125660.7661 201954.3862 190912.7882 194000.9532 133280.6266 1.212554478 1.290660125 1.353526328 1.23375988 0.942828446 1.515256878 1.432412144 1.455582541 1 17.02410756 2.168416374 25 1.396314645 1.226524715 0.114782807 0.175437423 77.52692759 27629.61125 0.059991745 0.044306849 147.372474 -2.168416374 -0.169789929 (ac)ADVLDLHEAGGEDFAMDEDGDESIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADVLDLHEAGGEDFAMDEDGDESIHK 26 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 142.94 3.30E-61 300205000 147353 128671 150264 157230 152744 146524 187192 166416 144301 FALSE TRUE 140387.9157 141782.7212 157153.753 141424.9417 179382.5052 141449.8371 158632.4224 151843.7328 166678.4621 0.842267885 0.850636125 0.94285579 0.8484896 1.076218865 0.848638962 0.951727178 0.910997923 1 17.34670817 8 0.210860169 0.974550857 0.211797862 0.255944289 0.066484936 60.98626423 0.76118843 0.098853744 15.63235571 100000000 -8 -0.762752995 (ac)AEPPS(ph)PVHCVAAAAPTATVSEKEPFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AEPPSPVHCVAAAAPTATVSEKEPFGK 27 1 Q6PCB5 Q6PCB5 RSBN1L Round spermatid basic protein 1-like protein 1 AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK 150.68 8.51E-34 2355120000 3696040 3264580 3656740 4015760 2621980 3841350 4463980 4409840 2941990 TRUE FALSE 3521335.514 3597244.414 3824405.146 3612088.175 3079252.482 3708323.086 3782917.864 4023691.032 3398218.784 1.036229783 1.058567633 1.125414633 1.062935734 0.906137208 1.091254955 1.113206096 1.184058852 1 21.69634731 2.017526987 24.99971159 1.10930777 1.041740007 0.145884344 0.069684577 403.550077 575603.4585 0.024917026 0.018398565 104.1182804 -2.017526987 -0.067567763 (ac)AETLSGLGDSGAAGAAALS(ph)SASSETGTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AETLSGLGDSGAAGAAALSSASSETGTRR 29 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7ES42 Q15424 SAFB Scaffold attachment factor B1 1 AETLSGLGDS(0.001)GAAGAAALS(0.167)S(0.167)AS(0.167)S(0.167)ET(0.167)GT(0.167)RR 44.264 0.0006848 30987000 18877 18009 18961 17977 9936.6 20718 20492 29552 10686 TRUE FALSE 17984.72162 19844.13757 19830.3806 16169.91781 11669.53989 20000.53047 17365.56904 26964.27021 12343.1303 1.457063255 1.607707047 1.606592503 1.310033793 0.945427911 1.620377487 1.406901541 2.184556879 1 13.5914207 (ac)AEYLASIFGTEKDKVNCSFYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEYLASIFGTEKDKVNCSFYFK 22 2 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 0 135.73 7.87E-30 116840000 318690 181520 267680 237110 255740 283230 442900 379060 339080 FALSE TRUE 303626.1553 200017.0944 279953.3928 213275.2523 300340.975 273421.6741 375327.4706 345867.4969 391662.7946 0.77522338 0.510686992 0.714781686 0.544537942 0.766835602 0.698104793 0.958292377 0.88307468 1 18.57925256 1.874469878 1.390891683 0.96851958 0.639299999 0.6773027 0.090174965 0.216880365 0.782978186 0.060952436 0.026105428 74.89794087 -1.874469878 -0.329219581 (ac)AGS(ph)YPEGAPAILADKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSYPEGAPAILADKR 16 1 Q6P1Q9;F8WAS9 Q6P1Q9 METTL2B Methyltransferase-like protein 2B 1 AGS(0.54)Y(0.46)PEGAPAILADKR 42.095 0.072781 12776000 37407 27055 30642 37327 29188 37216 44359 40318 38931 TRUE FALSE 35638.84524 29811.93526 32046.96601 33574.81904 34278.37796 35927.20059 37591.21984 36787.54218 44968.22065 0.792534032 0.662955635 0.712658085 0.746634369 0.762280061 0.798946458 0.835950796 0.818078671 1 15.45661818 0.907414219 0.466027793 1.008563048 0.715374466 0.83815748 0.035935677 0.45133054 0.242098859 0.047352736 0.02210326 8.080053171 -0.907414219 -0.293188582 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.999)PVQS(0.001)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK 124.1 7.72E-28 1883228000 2206600 1902379 2101336 2401261 1861389 2174911 2485880 2419230 1902387 TRUE FALSE 2102298.391 2096233.583 2197684.334 2159881.682 2186014.652 2099593.287 2106613.35 2207389.396 2197399.46 0.956721083 0.95396109 1.000129642 0.982926282 0.994818963 0.955490035 0.958684749 1.004546254 1 21.06736573 (ac)AKPLTDSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKPLTDSEKR 10 2 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 70.496 0.00041811 368840000 617470 475260 528730 597710 454450 557690 722360 643910 504340 FALSE TRUE 588283.4168 523689.5343 552972.7935 537627.0552 533705.9361 538377.0555 612150.7149 587525.8268 582550.4714 1.009841114 0.898959936 0.94922727 0.922884937 0.916153985 0.92417238 1.050811466 1.008540643 1 19.15202352 1.750368751 13.86422577 1.021826489 0.937251205 0.598941627 0.031965403 0.110094537 122.125924 0.014516501 0.007996475 56.28190009 -1.750368751 -0.084575284 (ac)ALVTVSRS(ph)PPGSGASTPVGPWDQAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.01)VS(0.147)RS(0.593)PPGS(0.183)GAS(0.059)T(0.008)PVGPWDQAVQR;ALVT(0.012)VS(0.086)RS(0.582)PPGS(0.115)GAS(0.181)T(0.023)PVGPWDQAVQR;ALVT(0.015)VS(0.026)RS(0.634)PPGS(0.114)GAS(0.169)T(0.042)PVGPWDQAVQR;ALVT(0.034)VS(0.037)RS(0.58)PPGS(0.277)GAS(0.057)T(0.015)PVGPWDQAVQR;ALVT(0.009)VS(0.098)RS(0.855)PPGS(0.027)GAS(0.009)T(0.002)PVGPWDQAVQR 81.904 5.79E-61 1280710000 20921.5 6907.54 13527.8 5652.5 18474.4 12572.3 15241.3 21737.2 20865 TRUE FALSE 19932.58216 7611.426179 14148.06301 5084.299961 21696.32951 12136.9181 12915.95976 19833.77553 24100.63764 0.827056216 0.315818457 0.587041025 0.210961222 0.900238817 0.503593236 0.535917761 0.822956464 1 14.5567837 1.078515447 3.215064356 0.996520971 0.545927662 0.361942155 0.203972172 0.221546535 4.532589152 0.176025292 0.046390527 11.98161738 -1.078515447 -0.450593308 (ac)ALVTVSRSPPGSGAS(ph)TPVGPWDQAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.001)VS(0.036)RS(0.254)PPGS(0.314)GAS(0.349)T(0.047)PVGPWDQAVQR 55.985 2.78E-26 626090000 2774.2 2751.7 3639.7 2947.7 2855.8 3218.4 3716.8 2820.1 3095.1 TRUE FALSE 2643.069064 3032.101358 3806.583845 2651.391596 3353.850616 3106.946001 3149.733896 2573.157094 3575.0723 0.739305066 0.848123088 1.064757164 0.741633 0.93812106 0.869058229 0.881026629 0.719749666 1 11.8037567 4.315909018 2.993455747 0.882127467 0.752054762 0.160967221 0.104044135 0.415729196 7.222861738 0.023555639 0.080668264 20697.07711 -4.315909018 -0.130072705 (ac)AS(ph)ESDTEEFYDAPEDVHLGGGYPVGSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASESDTEEFYDAPEDVHLGGGYPVGSPGK 29 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 AS(0.332)ES(0.332)DT(0.332)EEFY(0.003)DAPEDVHLGGGYPVGSPGK;AS(0.333)ES(0.333)DT(0.333)EEFYDAPEDVHLGGGYPVGSPGK 86.131 4.00E-18 106428000 131841 106711 113446 121003 96134 111478 129056 117847 107290 TRUE FALSE 125609.1372 117584.9722 118647.6113 108839.5485 112899.7392 107617.4889 109366.1369 107527.6919 123927.9852 1.013565556 0.948816944 0.957391594 0.87824835 0.91101085 0.868387303 0.882497498 0.867662713 1 16.91914249 3.873213641 0.970965386 0.89184331 1.011864948 0.409471955 0.041116319 0.549356079 0.888397953 0.013020302 0.051722581 7468.160474 -3.873213641 0.120021638 (ac)AS(ph)FVTEVLAHSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASFVTEVLAHSGR 13 0 O43264;O43264-2;F5H3C1 O43264 ZW10 Centromere/kinetochore protein zw10 homolog 1 AS(0.986)FVT(0.014)EVLAHSGR 61.353 0.0097545 1711600 2010.2 2975.8 2472 2302.9 1880.9 3148.7 3017.7 2202.5 2359.4 TRUE FALSE 1915.18183 3279.037403 2585.343645 2071.408117 2208.928364 3039.659729 2557.294441 2009.637424 2725.283702 0.702745857 1.203191213 0.948651197 0.760070636 0.810531529 1.11535534 0.938358982 0.737404852 1 11.41219071 4.751140751 23.97427328 0.945322711 0.702745632 0.202800716 0.146883653 50.63727987 1063740.217 0.034319893 0.211380319 56382.03554 -4.751140751 -0.242577079 (ac)AS(ph)GADSKGDDLSTAILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASGADSKGDDLSTAILK 17 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 AS(0.989)GADS(0.011)KGDDLSTAILK 90.731 2.32E-07 20124000 117980 105010 118070 150390 74391 150600 150200 146390 98160 TRUE FALSE 112403.3192 115710.6384 123483.6263 135272.5115 87364.76685 145384.6842 127284.2314 133571.3155 113382.1515 0.991366963 1.020536627 1.089092284 1.193067072 0.770533684 1.282253709 1.122612596 1.178062983 1 16.79083402 (ac)AS(ph)GVAVSDGVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.994)GVAVS(0.006)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK 87.149 1.22E-28 86907435000 25104932 21888411 24407655 26411451 21296161 28513036 30527084 28003851 23404257 TRUE FALSE 23918271.62 24118864.97 25526770.12 23756521.77 25010204.74 27525622.41 25869616.67 25551685.35 27033669.64 0.884758597 0.892178727 0.944258418 0.878775323 0.925150195 1.01819778 0.956940623 0.945180055 1 24.68825403 2.436285024 7.307779154 0.975700777 0.899659975 0.669565539 0.02664071 0.121560807 17.42129039 0.008768172 0.007356454 273.0769379 -2.436285024 -0.076040803 (ac)AS(ph)GVQVADEVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 ASGVQVADEVCR 12 0 P60981;F6RFD5 P60981 DSTN Destrin 1 AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR;AS(1)GVQVADEVCR 87.258 6.42E-16 36395287000 362496.9 224249.5 273308.4 296354.7 283052.2 241512.6 308080.19 288778.7 321152.9 TRUE FALSE 345362.3899 247100.779 285839.8605 266564.5625 332416.4141 233148.9581 261076.8987 263491.7061 370955.6515 0.93100722 0.666119462 0.770549955 0.718588762 0.896108235 0.62850898 0.703795447 0.71030514 1 18.50088719 -1.159494639 4.970475328 1.000016562 0.75063393 0.400567688 0.094867329 1.66E-05 2.80E-06 0.087352413 0.020587795 0.069263648 1.159494639 -0.249382633 (ac)AS(ph)GVTVNDEVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASGVTVNDEVIK 12 0 Q9Y281;G3V2U0;F8WDN3 Q9Y281 CFL2 Cofilin-2 1 AS(0.996)GVT(0.004)VNDEVIK;AS(0.983)GVT(0.017)VNDEVIK;AS(0.996)GVT(0.004)VNDEVIK;AS(0.986)GVT(0.014)VNDEVIK 85.807 1.08E-21 944650000 1921110 1792580 1829140 2060030 1647180 2128580 2288590 2218170 1859300 TRUE FALSE 1830302.938 1975245.94 1913007.878 1852951.871 1934447.67 2054866.741 1939423.563 2023935.276 2147630.748 0.852242844 0.919732567 0.890752696 0.862788853 0.900735693 0.956806352 0.903052615 0.942403752 1 21.03431453 -5 0.086977483 1.346546926 0.809897761 0.695953003 0.024203295 126.6467897 0.769946338 8.077218558 0.618241267 1.00E-05 5 -0.536649165 (ac)AS(ph)LSLAPVNIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLSLAPVNIFK 12 0 P78371;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 1 AS(0.903)LS(0.097)LAPVNIFK;AS(0.848)LS(0.152)LAPVNIFK 56.563 5.86E-05 77256000 278140 238732 266750 307170 289380 323090 373150 324590 313340 TRUE FALSE 264992.8734 263059.0622 278980.7514 276292.688 339847.7804 311901.3123 316219.1141 296167.1788 361931.1669 0.732163731 0.726820695 0.770811626 0.763384625 0.938984568 0.861769698 0.873699596 0.818296975 1 18.46535582 2.852800084 5.24210903 0.886040216 0.741586281 0.688147645 0.049935721 0.126294968 4.995566062 0.014044605 0.014952768 712.5249624 -2.852800084 -0.144453935 (ac)AS(ph)PGKDNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASPGKDNYR 9 1 O15131;Q5TD90 O15131 KPNA5 Importin subunit alpha-6 1 AS(1)PGKDNYR;AS(1)PGKDNYR;AS(1)PGKDNYR;AS(1)PGKDNYR 62.463 0.0017754 2128920000 2257100 1770500 1953190 2332010 1613010 2161670 2516290 2397210 1798430 TRUE FALSE 2150411.356 1950915.963 2042745.693 2097591.924 1894318.433 2086810.826 2132383.746 2187297.584 2077321.339 1.035184743 0.93914982 0.983355658 1.00975804 0.911904383 1.004568136 1.026506446 1.052941373 1 20.98629297 2.004736977 24.99590394 1.025955157 0.976477629 0.296896877 0.035849559 156.6981082 826854.3022 0.012766357 0.009396268 101.0966993 -2.004736977 -0.049477528 (ac)AS(ph)PSLERPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPSLERPEK 10 1 Q13601-2;Q13601 Q13601-2 KRR1 KRR1 small subunit processome component homolog 1 AS(0.962)PS(0.038)LERPEK 50.473 0.042584 97980000 86643 73357 76363 94388 78134 85428 94211 92803 97404 TRUE FALSE 82547.5571 80832.1617 79864.31908 84899.93891 91760.54486 82469.60694 79837.38165 84676.67734 112508.9148 0.733697923 0.718451172 0.709848808 0.754606326 0.815584658 0.733005087 0.709609383 0.752621936 1 16.77967979 0.945504356 21.94369846 1 0.736863298 0.877455814 0.030456413 1444.08283 581488.3367 0.03024857 0.007562143 8.820726491 -0.945504356 -0.263136702 (ac)AS(ph)PSRQPPPGGSGLLQGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPSRQPPPGGSGLLQGSR 19 1 Q96S90 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 AS(0.991)PS(0.009)RQPPPGGSGLLQGSR 62.287 0.0049998 158980000 50326 50525 51268 66416 58009 51785 58251 58423 63981 TRUE FALSE 47947.18972 55673.55494 53618.68851 59739.7375 68125.75123 49991.67247 49363.7401 53307.1724 73902.84671 0.648786777 0.753334376 0.725529406 0.808355025 0.921828512 0.676451242 0.667954515 0.721314195 1 16.17334232 -2.068285667 2.484025567 1.391349757 0.735236525 0.514806291 0.079046129 5956065.991 1535616.766 13247965.17 0.020127739 0.008545045 2.068285667 -0.656113231 (ac)AS(ph)PSSFTYYCPPSSSPVWSEPLYSLRPEHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASPSSFTYYCPPSSSPVWSEPLYSLRPEHAR 31 1 P49356 P49356 FNTB Protein farnesyltransferase subunit beta 1 AS(0.995)PS(0.004)S(0.001)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.997)PS(0.003)SFTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.972)PS(0.024)S(0.004)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.991)PS(0.008)S(0.001)FTYYCPPSSSPVWSEPLYSLRPEHAR 162.45 4.39E-58 1853030000 15308.8 4580.1 22670.4 14352.2 13775.3 18274.5 21816.3 12986.1 23202 TRUE FALSE 14585.18336 5046.817397 23709.86026 12909.48959 16177.70796 17641.64948 18487.82275 11848.96824 26800.04766 0.544222292 0.188313747 0.884694705 0.481696516 0.603644746 0.658269332 0.689842906 0.442124894 1 14.70994795 -4.999999999 0.088430282 2.407914864 0.174565803 0.338264504 0.18452461 216.4222675 1.333946917 58.36299675 4.285717021 1.00E-05 4.999999999 -2.233349061 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.487)PT(0.487)DGT(0.025)DLEASLLSFEK;AS(0.444)PT(0.444)DGT(0.111)DLEASLLSFEK 87.498 4.55E-90 104792000 248080 235509 229063 277930 196566 255600 266310 277210 222328 TRUE FALSE 236353.75 259507.6349 239565.7651 249991.9484 230847.0482 246748.5079 225679.5184 252936.0228 256805.4907 0.920360968 1.010522143 0.932868547 0.973468081 0.898917883 0.960838132 0.878795534 0.984932301 1 17.97031652 2.780036097 24.98901542 0.933816486 0.962045341 0 0.043509673 1175.928214 708495.7908 0.012069798 0.012801926 602.6096714 -2.780036097 0.028228856 (ac)ASAVS(ph)PANLPAVLLQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.098)AVS(0.902)PANLPAVLLQPR;AS(0.098)AVS(0.902)PANLPAVLLQPR;AS(0.133)AVS(0.867)PANLPAVLLQPR 78.653 2.05E-09 193166000 123581 98401 157477 115606 95016 137729 175862 96688 39933.7 TRUE FALSE 117739.571 108428.1738 164697.4762 103985.0652 111586.7603 132959.4102 149031.022 88221.48614 46126.41424 2.552541163 2.350674241 3.570567514 2.254349638 2.419150982 2.882500458 3.230925803 1.912602304 1 15.49330552 (ac)ASCAS(ph)IDIEDATQHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASCASIDIEDATQHLR 16 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 AS(0.05)CAS(0.95)IDIEDATQHLR;AS(0.143)CAS(0.857)IDIEDATQHLR 82.259 2.69E-12 56217000 31896 25693 30756 29646 25765 24688 31193 30906 24171 TRUE FALSE 30388.33929 28311.14591 32166.19302 26665.92776 30258.40784 23833.04837 26433.93495 28199.7068 27919.31523 1.088434263 1.014034394 1.152112534 0.955106797 1.083780443 0.853640147 0.946797396 1.010042924 1 14.76897594 2.260723827 24.99936677 0.944661028 1.054845304 0.389566992 0.065545798 215.3370009 242892.3197 0.02071424 0.017318233 182.2736235 -2.260723827 0.110184276 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASEDNRVPSPPPTGDDGGGGGR 22 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.029)EDNRVPS(0.964)PPPT(0.007)GDDGGGGGR;ASEDNRVPS(0.979)PPPT(0.021)GDDGGGGGR;AS(0.001)EDNRVPS(0.977)PPPT(0.023)GDDGGGGGR 112.74 1.70E-18 505620000 23791.7 14767 20416.8 18976.8 25780.6 17295.1 16226.6 18470 26650.1 TRUE FALSE 22667.11349 16271.77409 21352.93047 17069.21601 30276.72848 16696.16635 13750.93415 16852.66888 30782.8614 0.736354987 0.528598491 0.693662951 0.554503878 0.983557964 0.542385132 0.44670747 0.547469212 1 14.90983972 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.007)EDNRVPS(0.967)PPPT(0.021)GDDGGGGGREET(0.002)PT(0.002)EGGALSLKPGLPIR;AS(0.015)EDNRVPS(0.754)PPPT(0.23)GDDGGGGGREET(0.001)PTEGGALSLKPGLPIR;ASEDNRVPS(0.991)PPPT(0.009)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.999)PPPT(0.001)GDDGGGGGREETPTEGGALSLKPGLPIR 117.32 1.49E-36 2690910000 311330 286690 303655 327531 290279 338777 362454 331582 338373 TRUE FALSE 296614.0479 315904.0369 317577.8821 294606.9616 340903.5657 327045.0675 307154.9854 302546.9223 390846.1567 0.758902302 0.808256731 0.81253935 0.753767068 0.872219312 0.836761631 0.785871833 0.774081866 1 18.57624133 -1.263265399 3.542556945 1.000484054 0.800225634 0.755219601 0.035729912 11764087.34 17614480.21 61426.35213 0.008332596 0.054542445 1.263265399 -0.20025842 (ac)ASGEHS(ph)PGSGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGEHSPGSGAAR 13 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 1 AS(0.001)GEHS(0.991)PGS(0.008)GAAR;AS(0.029)GEHS(0.95)PGS(0.021)GAAR 85.271 3.13E-32 3262100000 0 0 0 0 0 0 13018 0 0 TRUE FALSE 0 0 0 0 0 0 11031.86501 0 0 0 (ac)ASGRPEELWEAVVGAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGRPEELWEAVVGAAER 18 1 Q96B36;H9KV91;M0R2V8 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 50.563 6.61E-07 9882600 5267.9 4782.2 4206.6 4243.4 3998.4 4596.1 5103.1 4726.8 6298.8 FALSE TRUE 5018.896807 5269.511617 4399.476771 3816.84537 4695.719694 4436.935905 4324.52837 4312.896334 7275.585734 0.689827182 0.72427318 0.604690389 0.524610046 0.645407788 0.609838997 0.594389033 0.592790257 1 12.82884768 -1.248385144 4.46996636 1.000161546 0.630149828 0.820467654 0.055304539 9778461.229 2730968.497 15496.5358 0.014828399 0.05644362 1.248385144 -0.370011717 (ac)ASGVQVADEVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGVQVADEVCR 12 0 P60981;F6RFD5 P60981 DSTN Destrin 0 ; 42.743 0.00030275 83743000 47390 34155 35305 43137 40773 29470 47520 48439 48194 FALSE TRUE 45149.96862 37635.43333 36923.76917 38800.78681 47883.79829 28449.44651 40269.95124 44197.42437 55667.67938 0.811062525 0.676073329 0.663289176 0.697007442 0.860172345 0.511058604 0.723399137 0.793951263 1 15.76455232 0.886678627 2.785282702 0.999474082 0.705153481 0.506980313 0.091809335 0.354401079 5.735939704 0.081751256 0.021634858 7.703332209 -0.886678627 -0.2943206 (ac)ASHLRPPS(ph)PLLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASHLRPPSPLLVR 13 1 Q8TDB6;Q8TDB6-2 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR 73.498 0.00026842 64922000 9806.2 6856.9 8988.1 9244.1 11537.3 7460.6 9081.5 9015 11890.8 TRUE FALSE 9342.68036 7555.625906 9400.213275 8314.865505 13549.40147 7202.237551 7695.950382 8225.598808 13734.76453 0.680221371 0.550109606 0.684410224 0.605388282 0.986504096 0.524380126 0.560326343 0.598888957 1 13.74554456 -0.998231161 4.372618433 1.000013722 0.640142978 0.414065168 0.130945033 36367349.93 72850949.57 7813.730786 0.030106438 0.100408121 0.998231161 -0.359870744 (ac)ASLEVSRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASLEVSRSPR 10 1 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.008)RS(0.992)PR;ASLEVS(0.027)RS(0.973)PR;ASLEVS(0.002)RS(0.998)PR;ASLEVS(0.001)RS(0.999)PR;ASLEVS(0.001)RS(0.999)PR;ASLEVS(0.001)RS(0.999)PR 136.94 2.33E-12 5225050000 301848 296455 300446 348710 279879 322195 312146 308648 375857 TRUE FALSE 287580.2432 326664.1015 314221.7463 313657.0083 328689.809 311037.3064 264522.3947 281621.1449 434142.9839 0.662409054 0.752434368 0.723774788 0.722473977 0.757100359 0.716439786 0.609297869 0.648682935 1 18.72781074 -1.151204365 4.315316669 1.00006282 0.698922614 0.804044259 0.046687099 3.20E-05 6.29E-06 0.049142723 0.011580539 0.070598526 1.151204365 -0.301140206 (ac)ASLEVSRS(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLEVSRSPRR 11 2 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.288)RS(0.712)PRR;ASLEVS(0.289)RS(0.711)PRR 98.592 3.71E-05 1310500000 51310 54802 76398 54147 57193 63682 77723 53236 102874 TRUE FALSE 48884.67799 60386.3861 79900.92387 48704.04069 67167.44109 61476.67637 65864.92887 48574.37362 118827.1745 0.411393086 0.50818667 0.67241289 0.409872917 0.565253204 0.517362099 0.554291804 0.408781693 1 16.85850528 -2.001172301 2.95861272 1.495636167 0.50831447 0.779513885 0.082568066 25191410.43 30214886.93 85096380.51 0.018454343 0.009973043 2.001172301 -0.987321696 (ac)AT(ph)PPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATPPKR 6 1 D6RCP9;D6RFG8;P27707;D6R9C6;D6RG38;Q9UBK9 D6RCP9 DCK;UXT Deoxycytidine kinase;Protein UXT 1 AT(1)PPKR 50.966 0.087689 987670000 342710 366960 340500 373530 305090 414450 421680 432880 368220 TRUE FALSE 326510.7775 404353.6412 356112.2618 335982.0547 358297.5994 400097.4926 357344.9713 394974.7324 425321.677 0.767679606 0.950700759 0.83727748 0.78994811 0.842415562 0.940693866 0.840175779 0.928649429 1 18.69819486 0.707996071 0.63738777 1.003211965 0.847228529 0.432387453 0.05668171 1.223787776 0.996761059 0.059920785 0.022393788 5.105003819 -0.707996071 -0.155983436 (ac)AT(ph)TGTPTADRGDAAATDDPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATTGTPTADRGDAAATDDPAAR 22 1 Q86TI2;Q86TI2-4 Q86TI2 DPP9 Dipeptidyl peptidase 9 1 AT(0.327)T(0.327)GT(0.327)PT(0.018)ADRGDAAATDDPAAR;AT(0.328)T(0.328)GT(0.328)PT(0.017)ADRGDAAATDDPAAR 51.643 0.0032698 189513000 23805 25697.5 24443.3 28691.3 22531.5 24406 24359 24134.5 27829.6 TRUE FALSE 22679.78483 28316.10447 25564.04948 25807.19601 26460.98647 23560.8141 20642.58717 22021.15523 32145.27223 0.705540294 0.880879286 0.795266231 0.802830221 0.82316884 0.732948034 0.642165573 0.685051135 1 14.97231895 2.189710895 7.437046046 0.724674402 0.803362024 0 0.105551158 0.474057687 59.7258429 0.03573646 0.02650304 154.7785932 -2.189710895 0.078687622 (ac)ATLKDQLIYNLLKEEQTPQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATLKDQLIYNLLKEEQTPQNK 21 2 F5GZQ4;P00338;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 89.831 1.14E-16 255015000 241240 124186 229092 203047 218221 224359 305190 258080 270950 FALSE TRUE 229837.0633 136840.6946 239596.0948 182636.3298 256278.6733 216589.3916 258627.6603 235481.147 312967.5422 0.734379871 0.437236059 0.765562119 0.583563166 0.81886662 0.692050652 0.826372149 0.752413958 1 18.25565352 1.284244876 0.329471476 1.025060393 0.573428269 0.510995362 0.104317779 1.007323416 0.366802351 0.17436508 0.125962011 19.24176367 -1.284244876 -0.451632124 (ac)ATSPQKS(ph)PSVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSPQKSPSVPK 12 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 AT(0.045)S(0.086)PQKS(0.866)PS(0.003)VPK 79.492 0.00090093 193180000 522340 501980 484640 575960 326880 600390 610700 628960 392640 TRUE FALSE 497650.0234 553132.3327 506861.2234 518063.4065 383887.7685 579598.3438 517526.4987 573884.9281 453528.6059 1.097284751 1.219619503 1.117594826 1.142294885 0.846446649 1.277975273 1.141111039 1.265377576 1 18.79083402 -0.320783788 7.271564485 1 1.140350511 0.116032286 0.120005664 0 0 0.106694321 0.025148092 0.477767069 0.320783788 0.140350511 (ac)AVPETRPNHTIYINNLNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVPETRPNHTIYINNLNEK 19 1 P09012;M0R221;M0R2B8;M0R268;M0QXK2;M0R0G9 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 ; 108.25 4.62E-19 1192390000 470530 409850 362810 493650 374700 448180 534810 488050 467640 FALSE TRUE 448288.9794 451614.181 379445.1974 444027.3641 440047.5614 432659.4142 453214.912 445313.7547 540159.2228 0.829920069 0.836076034 0.702469163 0.822030515 0.814662682 0.800984961 0.839039477 0.824412018 1 19.04302521 -0.063942871 0.671400544 1.009644892 0.804490275 0.718130748 0.038143176 2.885840226 1.351807482 0.110092648 0.013962129 0.863092076 0.063942871 -0.205154617 (ac)AVTLDKDAYYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVTLDKDAYYRR 12 2 Q9Y5B9;G3V5A4;G3V401;G3V2X0 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 110.66 0.00047568 350710000 135640 88585 129040 106920 210030 124440 198230 143580 261850 FALSE TRUE 129228.566 97611.91221 134956.6116 96172.19847 246659.1655 120130.6116 167986.3728 131007.374 302456.3607 0.427263509 0.322730565 0.446201929 0.317970494 0.815519849 0.397183287 0.555406976 0.433144715 1 18.20636748 -4.999999999 0.180033477 3.219041508 0.343542867 0.600070456 0.139072277 84.93710295 0.817722993 67.39005541 0.392467409 1.00E-05 4.999999999 -2.87549864 (ac)AYHSFLVEPISCHAWNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYHSFLVEPISCHAWNK 17 0 C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6;C9JM51;F8WEB3 C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 125.89 3.85E-46 610860000 728840 597020 638530 745460 835910 602270 906510 748780 605430 FALSE TRUE 694389.1776 657857.0168 667807.2321 670524.9445 981692.4393 581413.2389 768205.2503 683212.8537 699316.9923 0.992953389 0.940713616 0.954942093 0.958828331 1.403787481 0.831401561 1.098507914 0.976971618 1 19.41558704 (ac)AYHSFLVEPISCHAWNKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYHSFLVEPISCHAWNKDR 19 1 C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6;C9JM51;F8WEB3 C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 95.814 3.50E-10 312410000 320970 137993 334720 254810 491910 267110 578190 392080 490850 FALSE TRUE 305798.3842 152054.6436 350067.2431 229196.0147 577698.9483 257859.9137 489976.4963 357747.3967 566968.5111 0.53935691 0.268188869 0.617436835 0.404248226 1.018925984 0.454804647 0.864204073 0.630982832 1 19.11290909 2.766963552 24.98028396 0.763859456 0.443800504 0.438304354 0.187304234 629.5793036 553711.7839 0.050639545 0.053702242 584.7410078 -2.766963552 -0.320058952 (ac)DDDIAALVVDNGSGMCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DDDIAALVVDNGSGMCK 17 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7 C9JTX5;P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 ;;;;;;;;;;; 155.48 6.48E-105 1038541000 1962908 1694656 1770706 1972879 1663629 1813244 2149527 2073751 1889394 FALSE TRUE 1870125.229 1867343.373 1851894.622 1774561.455 1953765.371 1750450.906 1821577.177 1892162.369 2182391.572 0.856915529 0.855640847 0.84856203 0.813126974 0.895240522 0.802079209 0.834670185 0.867013231 1 21.05747855 0.820961135 4.252698803 0.999994732 0.844317983 0.787868879 0.025283344 0.717342265 16.61903434 0.022434778 0.005712383 6.621572445 -0.820961135 -0.155676749 (ac)GDKKS(ph)PTRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GDKKSPTRPK 10 3 Q8IY57;Q8IY57-5;G3V1X5;A0A0B4J255;F8VRE5;G3V219;G3V212;Q8IY57-4 Q8IY57 YAF2 YY1-associated factor 2 1 GDKKS(0.939)PT(0.061)RPK;GDKKS(0.823)PT(0.177)RPK;GDKKS(0.881)PT(0.119)RPK;GDKKS(0.903)PT(0.097)RPK;GDKKS(0.98)PT(0.02)RPK 51.875 0.00067701 5024630000 5581970 5101230 4892610 5793230 2719720 6295130 6179960 6521380 2972460 TRUE FALSE 5318121.34 5621051.137 5116941.008 5210883.514 3194038.307 6077128.07 5237093.599 5950333.395 3433413.916 1.548931026 1.637160935 1.490336188 1.517697441 0.930280585 1.769995759 1.525331267 1.733066138 1 21.71121236 3.505666715 3.029338205 1.448063664 1.592056922 0.058724591 0.272626312 0.852479816 15.7634877 0.072586964 0.112536581 3203.809726 -3.505666715 0.143993258 (ac)GDREQLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDREQLLQR 9 1 Q04917;F8WEB6;A2IDB1 Q04917 YWHAH 14-3-3 protein eta 0 ; 91.906 0.00027509 433170000 94849 75811 91991 103816 91245 79447 117937 102024 121413 FALSE TRUE 90365.67574 83536.22709 96208.87834 93380.21844 107158.0991 76695.73047 99943.54459 93090.2377 140241.1079 0.644359397 0.595661488 0.686024802 0.665854825 0.764099063 0.546884801 0.712655127 0.663787095 1 17.09754977 -5 0.308001093 4.019375621 0.63919778 0.766776902 0.058997801 126.400042 1.149671769 247.2999545 0.051110887 1.00E-05 5 -3.380177841 (ac)GDS(ph)DDEYDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;GDS(1)DDEYDRR;GDS(1)DDEYDRR 89.827 3.96E-07 16851390000 17250 13137 20727 16101 59896 11052 20169 14365 46595 TRUE FALSE 16434.62669 14475.67524 21677.35345 14482.49689 70341.84344 10669.26647 17091.84862 13107.12445 53820.71463 0.30535876 0.268961037 0.402769707 0.269087785 1.306965987 0.198237176 0.317570079 0.243533081 1 15.71587393 (ac)GS(ph)ASPGLS(ph)SVSPSHLLLPPDTVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 2 GS(0.473)AS(0.473)PGLS(0.356)S(0.356)VS(0.288)PS(0.055)HLLLPPDTVSR 44.807 0.058386 26184000 4547.2 3239.9 4908.7 4494.8 3445.8 5886.1 4488 4736.2 5805.1 TRUE FALSE 4332.262868 3570.049493 5133.76875 4042.974164 4046.746429 5682.262881 3803.273172 4321.47322 6705.32526 0.646092874 0.532420033 0.765625611 0.602949746 0.603512324 0.847425391 0.567201892 0.644483758 1 12.7110916 -5 0.313155286 4.217901623 0.627118305 0.575823385 0.093520379 207.4930923 1.866305287 441.2045688 0.080056815 1.00E-05 5 -3.590783318 (ac)GS(ph)ASPGLSSVS(ph)PSHLLLPPDTVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 2 GS(0.498)AS(0.498)PGLS(0.127)S(0.09)VS(0.697)PS(0.089)HLLLPPDTVSR 88.73 4.53E-05 18391000 10361 9287.2 10115 10790 8223 10773 9948.8 12456 9046.1 TRUE FALSE 9871.256064 10233.57624 10578.78276 9705.3687 9657.088597 10399.92831 8430.927838 11365.28661 10448.92299 0.944715171 0.979390532 1.012428053 0.928839146 0.924218564 0.995311031 0.806870512 1.087699337 1 13.35106663 3.200205547 24.99286722 0.939235315 0.974086076 0 0.073856712 533.6002865 347702.0162 0.019920638 0.023810049 1585.643484 -3.200205547 0.034850761 (ac)GS(ph)ASPGLSSVSPSHLLLPPDTVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.496)AS(0.496)PGLS(0.003)S(0.004)VSPSHLLLPPDTVSR;GS(0.498)AS(0.498)PGLS(0.003)S(0.001)VSPSHLLLPPDTVSR;GS(0.499)AS(0.499)PGLS(0.001)S(0.001)VSPSHLLLPPDTVSR 114.59 1.33E-38 197392000 8933.4 7875.1 11395.8 9820.2 8682 5409.3 10247.9 9389.1 13891.6 TRUE FALSE 8511.135886 8677.581643 11918.3087 8833.054839 10196.13805 5221.974585 8684.394639 8566.940629 16045.83838 0.530426375 0.540799517 0.742766344 0.550488833 0.635438162 0.325441056 0.541224113 0.533904208 1 13.96991155 -1.223224733 3.416663064 1.00100563 0.545962008 0.652359636 0.103184709 23870459.05 34652690.57 251513.4112 0.023632818 0.059810202 1.223224733 -0.455043622 (ac)GT(ph)PQKDVIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTPQKDVIIK 10 1 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 1 GT(1)PQKDVIIK 57.598 0.001099 367800000 610140 663530 627060 770360 482400 766440 816000 881340 629510 TRUE FALSE 581299.8914 731144.4614 655811.3212 692921.9492 566530.4073 739897.9906 691504.2131 804165.1973 727131.1957 0.799442927 1.005519314 0.901916085 0.95295313 0.779130933 1.01755776 0.951003364 1.105942369 1 19.47185617 1.731505744 1.82938421 1.039555093 0.902306202 0.359362115 0.079370785 0.35979959 2.42029654 0.053069104 0.021359196 53.88969731 -1.731505744 -0.137248891 (ac)GTRDDEYDYLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 91.867 1.06E-05 1173367000 2017900 1506820 1651690 2287580 1805920 1998170 2331400 2074850 2040770 FALSE TRUE 1922517.866 1660366.671 1727421.62 2057628.112 2120871.876 1928972.872 1975702.111 1893165.135 2357242.189 0.815579271 0.704368299 0.732814655 0.872896354 0.899725911 0.818317643 0.838141333 0.803127122 1 21.16866856 -4.999999998 0.111011562 1.630272436 0.693804727 0.553100955 0.055457761 125.1204193 0.921231119 17.88877618 0.693561534 1.00E-05 4.999999998 -0.936467709 (ac)MAAPEEHDS(ph)PTEAS(ph)QPIVEEEET(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MAAPEEHDSPTEASQPIVEEEETK 24 0 Q9H0S4;Q9H0S4-2;F5H1N9 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 3 MAAPEEHDS(0.966)PT(0.205)EAS(0.83)QPIVEEEET(1)K;MAAPEEHDS(0.966)PT(0.228)EAS(0.806)QPIVEEEET(1)K 44.258 0.035895 942640000 684800 730070 610530 748960 549960 698600 657470 796300 512500 TRUE FALSE 652430.8611 804464.963 638523.4044 673673.1179 645872.8499 674407.3068 557160.8762 726571.7505 591975.8825 1.102124057 1.358948881 1.078630774 1.138007709 1.091045884 1.139247944 0.941188472 1.227367148 1 19.17517888 3.694361929 24.10604853 1.08220611 1.230536505 0.264902725 0.098405941 313.2681248 170856.849 0.024534525 0.038009002 4947.228039 -3.694361929 0.148330395 (ac)MDDREDLVYQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 MDDREDLVYQAK 12 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;;;;; 95.502 3.73E-05 2389790000 4703045 3914602 4049653 4932394 4091596 4407071 5117636 4997083 4609092 FALSE TRUE 4480741.383 4313504.394 4235333.596 4436580.384 4805169.047 4254453.026 4336846.636 4559511.921 5323846.447 0.841636104 0.810223292 0.795540149 0.833341162 0.902574688 0.79913143 0.814607761 0.856431899 1 22.34403753 0.833846966 4.102842147 0.999990504 0.827028018 0.759775265 0.030142659 0.613116759 14.57423365 0.028270532 0.007213395 6.820982977 -0.833846966 -0.172962486 (ac)MDEET(ph)RHSLECIQANQIFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.5)RHS(0.5)LECIQANQIFPR;MDEET(0.5)RHS(0.5)LECIQANQIFPR 79.027 1.01E-24 129788000 15780.7 10676.9 10989.2 15988.2 18049.2 5776.9 14908.1 15858.8 17579.3 TRUE FALSE 15034.77759 11764.88825 11493.06569 14381.03576 21196.97477 5576.844504 12633.59554 14470.1194 20305.40806 0.740432181 0.57939679 0.566010082 0.708236728 1.043907845 0.274648236 0.622178855 0.712623916 1 14.3095764 0.860178968 4.236639896 0.999945182 0.641141719 0.252852094 0.188784199 1.29570636 37.33767226 0.170099532 0.043326713 7.247345534 -0.860178968 -0.358803464 (ac)MDFEDDYTHSACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDFEDDYTHSACR 13 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2;E2QRN4 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 83.397 5.84E-06 0 24272 19816 22866 21743 21839 22186 28924 23526 24247 FALSE TRUE 23124.71066 21835.27293 23914.42872 19557.35233 25647.71469 21417.69326 24511.11257 21465.93872 28007.10092 0.825673129 0.779633458 0.853870195 0.698299777 0.91575757 0.764723679 0.875174929 0.766446294 1 14.77350503 -5 0.332403423 2.933026521 0.804668365 0.469625971 0.062861724 288.7927795 2.480779255 394.8798539 0.044187767 1.00E-05 5 -2.128358156 (ac)MDFQHRPGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDFQHRPGGK 10 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 59.426 0.017155 108980000 169580 128040 133350 153750 134760 146380 169850 162460 145500 FALSE TRUE 161564.2895 141087.4216 139464.2294 138294.7579 158262.1013 141310.8239 143936.263 148234.1411 168063.3969 0.96132943 0.839489289 0.829831076 0.822872562 0.941680962 0.840818563 0.856440282 0.88201324 1 17.35864602 -1.190747407 5.458926502 1.000004925 0.87114628 0.42944754 0.046430034 2.70E-06 4.01E-07 0.043628295 0.010282895 0.064454403 1.190747407 -0.128858645 (ac)MDLAAAAEPGAGS(ph)QHLEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MDLAAAAEPGAGSQHLEVR 19 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 MDLAAAAEPGAGS(1)QHLEVR;MDLAAAAEPGAGS(1)QHLEVR 101.49 5.96E-16 69575000 35108.2 25951.4 36541.9 37260.1 45605 35305.7 46928.4 39814.9 54186.1 TRUE FALSE 33448.70496 28595.87716 38217.38226 33514.64396 53558.49756 34083.05476 39768.61068 36328.49628 62589.00364 0.534418237 0.456883406 0.610608574 0.53547176 0.85571737 0.5445534 0.635392934 0.580429375 1 15.93362159 -5 0.157040416 2.506098721 0.467831618 0.614145884 0.102546292 84.80205584 0.772761253 39.89740635 0.433315562 1.00E-05 5 -2.038267103 (ac)MDLFGDLPEPERS(ph)PRPAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;MDLFGDLPEPERS(1)PRPAAGK 141.36 3.83E-25 1920194000 2513198 2226762 2354355 2619212 2088961 2488681 2838122 2853300 2727232 TRUE FALSE 2394404.111 2453671.579 2462304.506 2355923.834 2453275.137 2402497.353 2405114.363 2603449.926 3150157.21 0.760090355 0.778904485 0.78164496 0.747875003 0.778778637 0.76265951 0.763490265 0.826450794 1 21.5869924 0.822975051 2.561618174 0.999925687 0.767870191 0.979422548 0.010581204 0.086292351 0.9817425 0.009688689 0.002586976 6.652349391 -0.822975051 -0.232055496 (ac)MDPQRS(ph)PLLEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MDPQRSPLLEVK 12 1 Q9BW19;A2AB20;A0A140T9E6 Q9BW19 KIFC1 Kinesin-like protein KIFC1 1 MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK 65.563 0.00075083 723820000 1836930 1690870 1735040 1993220 1427070 1906230 2129890 2021240 1741280 TRUE FALSE 1750101.959 1863171.575 1814593.3 1792857.739 1675950.556 1840216.777 1804936.162 1844249.51 2011308.809 0.870130907 0.926347842 0.902195273 0.891388598 0.833263668 0.914934976 0.897393853 0.916940005 1 20.93970317 0.613727877 1.227345566 0.999980303 0.891293621 0.650937526 0.025165404 0.847061212 1.894258965 0.023330354 0.007076091 4.108921806 -0.613727877 -0.108686682 (ac)MDRGEQGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MDRGEQGLLR 10 1 P55327-2;P55327-4;E5RFR7 P55327-2 TPD52 0 ;;;;; 101.6 1.65E-06 2270482000 399820 436123 414172 488346 568873 450219 573872 488545 624883 FALSE TRUE 380921.301 480564.4295 433162.1959 439256.5323 668084.2711 434627.8031 486317.2865 445765.4099 721786.6642 0.527747768 0.665798432 0.600124964 0.608568368 0.92559797 0.602155491 0.673768733 0.617586098 1 19.46121296 -5 0.199090902 2.541032303 0.5938946 0.524936059 0.104387289 111.6410096 1.10332279 68.69438019 0.240033489 1.00E-05 5 -1.947137704 (ac)MDRNPS(ph)PPPPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR 86.772 0.00010001 2446150000 195631.7 201953.6 189305.7 215939.9 224985.9 213558.8 251435.5 217749 244385.8 TRUE FALSE 186384.5772 222532.9014 197985.5536 194233.211 264223.3697 206163.2052 213074.3965 198681.7432 282283.9017 0.660273491 0.788330118 0.701370331 0.688077534 0.936019972 0.730339931 0.754823053 0.703836606 1 18.10678733 -5 0.33002856 3.544016846 0.736796269 0.516778812 0.076962161 286.2055012 2.473418938 511.1587881 0.06070059 1.00E-05 5 -2.807220578 (ac)MDSAGQDINLNS(ph)PNKGLLSDSMTDVPVDTGVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 MDS(0.001)AGQDINLNS(0.998)PNKGLLS(0.001)DSMTDVPVDTGVAAR;MDSAGQDINLNS(0.994)PNKGLLS(0.002)DS(0.003)MT(0.001)DVPVDTGVAAR;MDSAGQDINLNS(0.997)PNKGLLS(0.002)DSMTDVPVDTGVAAR 101.11 5.38E-60 306503000 210554 183322 200443 208408 156881 211166 258578 238599 188801 TRUE FALSE 200601.5297 202002.7202 209633.5098 187458.4319 184240.9967 203853.2685 219127.177 217706.0067 218079.2948 0.919855917 0.926281059 0.961271954 0.859588399 0.844834889 0.934766726 1.004805051 0.998288292 1 17.73449328 1.837971854 3.964526633 1.000887451 0.906875968 0.64750507 0.032986384 0.157879901 4.052467502 0.0173329 0.009452317 68.86076679 -1.837971854 -0.094011483 (ac)MEAERGPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEAERGPER 9 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 54.611 0.018759 0 24174 19915 26933 31459 28811 17378 31017 12947 18352 FALSE TRUE 23031.34293 21944.36114 28167.90469 28296.68155 33835.62928 16776.1955 26284.78698 11813.29204 21197.93443 1.08648996 1.035212238 1.328804218 1.33487919 1.596175768 0.791407085 1.239969256 0.557285054 1 14.37163607 1.253490745 24.99968429 0.778642481 1.182011091 0.355063836 0.235950218 228.6537118 382871.6878 0.15170725 0.05490501 17.92630351 -1.253490745 0.40336861 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 1 MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQS(0.001)PLVS(0.04)S(0.035)S(0.067)DS(0.856)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.004)DS(0.996)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSS(0.005)S(0.017)DS(0.977)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.002)DS(0.997)PPRPQPAFK 170.44 1.02E-62 2183462000 2284935 1777692 2167150 2794482 2407528 2424973 2871459 2336754 2724394 TRUE FALSE 2176930.651 1958840.836 2266515.971 2513575.36 2827400.121 2340995.577 2433365.192 2132135.432 3146879.107 0.691774478 0.622470953 0.720242467 0.798751803 0.898477515 0.743910235 0.773263004 0.67753967 1 21.58549033 -5 0.09884488 1.77398143 0.561904589 0.524720981 0.076158286 152.1084236 1.025622457 24.87645427 1.358824682 1.00E-05 5 -1.212076841 (ac)MEDS(ph)MDMDMSPLRPQNYLFGCELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.495)MDMDMS(0.495)PLRPQNY(0.01)LFGCELK;MEDS(0.654)MDMDMS(0.346)PLRPQNYLFGCELK;MEDS(0.932)MDMDMS(0.068)PLRPQNYLFGCELK;MEDS(0.539)MDMDMS(0.46)PLRPQNYLFGCELK;MEDS(0.6)MDMDMS(0.4)PLRPQNYLFGCELK;MEDS(0.826)MDMDMS(0.174)PLRPQNYLFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.001)LFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.002)LFGCELK;MEDS(0.501)MDMDMS(0.499)PLRPQNYLFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.002)LFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.002)LFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.002)LFGCELK;MEDS(0.917)MDMDMS(0.082)PLRPQNYLFGCELK;MEDS(0.821)MDMDMS(0.179)PLRPQNYLFGCELK;MEDS(0.557)MDMDMS(0.44)PLRPQNY(0.002)LFGCELK;MEDS(0.686)MDMDMS(0.314)PLRPQNYLFGCELK;MEDS(0.99)MDMDMS(0.01)PLRPQNYLFGCELK;MEDS(0.835)MDMDMS(0.164)PLRPQNYLFGCELK;MEDS(0.915)MDMDMS(0.085)PLRPQNYLFGCELK;MEDS(0.974)MDMDMS(0.026)PLRPQNYLFGCELK;MEDS(0.964)MDMDMS(0.035)PLRPQNYLFGCELK;MEDS(0.993)MDMDMS(0.007)PLRPQNYLFGCELK 92.336 2.50E-26 2171970000 2070908 1847293 1913739 2257113 1736928 2059696 2363723 2315332 2004345 TRUE FALSE 1973020.283 2035534.257 2001485.826 2030223.713 2039847.693 1988368.211 2003093.644 2112589.256 2315168.586 0.852214519 0.879216429 0.864509755 0.876922625 0.881079549 0.858843811 0.865204226 0.912499102 1 21.14268582 0.900848522 2.743882752 0.999876492 0.868240251 0.953868837 0.009222512 0.075846806 1.236992396 0.008728681 0.002315702 7.958817059 -0.900848522 -0.131636242 (ac)MEDSMDMDMS(ph)PLRPQNYLFGCELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 31 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.384)MDMDMS(0.605)PLRPQNY(0.01)LFGCELK;MEDS(0.468)MDMDMS(0.523)PLRPQNY(0.009)LFGCELK;MEDS(0.47)MDMDMS(0.522)PLRPQNY(0.008)LFGCELK;MEDS(0.01)MDMDMS(0.982)PLRPQNY(0.008)LFGCELK;MEDS(0.003)MDMDMS(0.996)PLRPQNY(0.001)LFGCELK;MEDS(0.028)MDMDMS(0.971)PLRPQNY(0.001)LFGCELK;MEDS(0.034)MDMDMS(0.885)PLRPQNY(0.081)LFGCELK;MEDS(0.006)MDMDMS(0.994)PLRPQNYLFGCELK;MEDS(0.01)MDMDMS(0.989)PLRPQNY(0.001)LFGCELK;MEDS(0.01)MDMDMS(0.986)PLRPQNY(0.005)LFGCELK;MEDS(0.189)MDMDMS(0.811)PLRPQNYLFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDS(0.003)MDMDMS(0.997)PLRPQNYLFGCELK;MEDS(0.042)MDMDMS(0.957)PLRPQNYLFGCELK;MEDS(0.012)MDMDMS(0.988)PLRPQNYLFGCELK;MEDS(0.001)MDMDMS(0.999)PLRPQNYLFGCELK;MEDS(0.033)MDMDMS(0.966)PLRPQNY(0.001)LFGCELK;MEDS(0.334)MDMDMS(0.664)PLRPQNY(0.002)LFGCELK;MEDS(0.186)MDMDMS(0.812)PLRPQNY(0.002)LFGCELK;MEDS(0.01)MDMDMS(0.989)PLRPQNY(0.001)LFGCELK;MEDS(0.337)MDMDMS(0.663)PLRPQNYLFGCELK;MEDS(0.002)MDMDMS(0.996)PLRPQNY(0.001)LFGCELK;MEDS(0.119)MDMDMS(0.881)PLRPQNYLFGCELK;MEDS(0.127)MDMDMS(0.871)PLRPQNY(0.002)LFGCELK;MEDS(0.002)MDMDMS(0.923)PLRPQNY(0.076)LFGCELK;MEDS(0.155)MDMDMS(0.825)PLRPQNY(0.02)LFGCELK;MEDS(0.023)MDMDMS(0.975)PLRPQNY(0.002)LFGCELK;MEDS(0.105)MDMDMS(0.868)PLRPQNY(0.027)LFGCELK;MEDS(0.132)MDMDMS(0.866)PLRPQNY(0.002)LFGCELK;MEDS(0.009)MDMDMS(0.99)PLRPQNY(0.002)LFGCELK;MEDS(0.374)MDMDMS(0.624)PLRPQNY(0.001)LFGCELK 124.86 4.37E-38 3168395000 3040593 2729012 2720630 3202526 2562068 2972384 3376647 3280905 2966711 TRUE FALSE 2896870.195 3007101.425 2845373.577 2880602.002 3008891.848 2869449.597 2861477.484 2993611.565 3426773.39 0.845363806 0.877531451 0.830336078 0.840616427 0.878053932 0.837361935 0.835035515 0.873594844 1 21.70841936 0.860692373 5.293394995 0.999998062 0.850562212 0.891002348 0.016452113 0.537268797 20.20530478 0.015754955 0.003974868 7.255918111 -0.860692373 -0.149435851 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHK 32 2 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPT(0.001)SQKPGVGAGHGGDPKLS(0.999)PHK;MEFDLGAALEPT(0.001)S(0.001)QKPGVGAGHGGDPKLS(0.997)PHK;MEFDLGAALEPTS(0.003)QKPGVGAGHGGDPKLS(0.997)PHK 146.06 3.25E-37 892980000 1336540 1454170 1182410 1706290 636810 1589120 1473640 1661250 420270 TRUE FALSE 1273364.403 1602351.576 1236624.668 1534770.487 747869.4624 1534088.376 1248809.153 1515782.143 485443.3252 2.623095915 3.300800512 2.547413063 3.161585314 1.54059068 3.160180183 2.572512769 3.122469843 1 18.88894335 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHKVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHKVQGR 36 3 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPTS(0.001)QKPGVGAGHGGDPKLS(0.999)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(0.999)PHKVQGR 145.17 2.24E-50 6232040000 4670500 3743900 4611410 4689710 2742570 5317530 6216660 5724110 1937230 TRUE FALSE 4449734.721 4125407.666 4822847.71 4218291.441 3220873.34 5133382.603 5268194.34 5222876.583 2237645.734 1.988578734 1.843637535 2.155322282 1.885147133 1.439402712 2.294099787 2.354346919 2.334094492 1 21.09355022 3.802917162 24.98830923 2.001495398 1.916108303 0 0.432998416 1786.851515 693789.775 0.105230133 0.189706203 6352.097597 -3.802917162 -0.085387095 (ac)MEGS(ph)PIPVLTVPTAPYEDQRPAGGGGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEGSPIPVLTVPTAPYEDQRPAGGGGLR 28 1 Q15124;Q15124-2 Q15124 PGM5 Phosphoglucomutase-like protein 5 1 MEGS(0.986)PIPVLT(0.013)VPT(0.001)APYEDQRPAGGGGLR;MEGS(0.999)PIPVLT(0.001)VPTAPYEDQRPAGGGGLR 56.303 0.00019889 93581000 5245.7 3186.1 3464.5 3869.2 4939.2 4098.2 4519.9 5633.5 5909.5 TRUE FALSE 4997.746157 3510.767212 3623.350752 3480.260665 5800.594916 3956.278306 3830.306241 5140.200875 6825.915078 0.732172331 0.514329166 0.530822712 0.509859942 0.849790079 0.579596766 0.561141795 0.753042019 1 12.73680675 0.94295369 3.795934887 0.999644414 0.608388218 0.578876939 0.106248645 0.18687572 7.197933898 0.097827511 0.025120249 8.769073083 -0.94295369 -0.391256196 (ac)MEITIRNS(ph)PYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 MEIT(0.204)IRNS(0.796)PYRR 73.887 0.00032903 93233000 13554 7492.3 8014.6 9515.7 15165 7960.2 10396 9322.4 16807 TRUE FALSE 12913.32928 8255.773888 8382.077338 8559.163757 17809.7712 7684.536278 8809.899264 8506.081235 19413.34372 0.665178007 0.42526285 0.431768863 0.440890754 0.917398438 0.395837852 0.453806381 0.438156423 1 14.24476101 -1.381878654 5.776968982 1.000129612 0.517482613 0.471330863 0.15937691 0.000251066 2.69E-05 0.145621383 0.034314175 0.041507 1.381878654 -0.482646999 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.486)PPHLS(0.167)S(0.176)S(0.185)PEDLCPAPGT(0.782)PPGT(0.189)PRPPDT(0.015)PLPEEVKR;MELDLS(0.964)PPHLS(0.022)S(0.007)S(0.007)PEDLCPAPGT(0.959)PPGT(0.04)PRPPDT(0.001)PLPEEVKR;MELDLS(0.762)PPHLS(0.076)S(0.079)S(0.083)PEDLCPAPGT(0.943)PPGT(0.052)PRPPDT(0.005)PLPEEVKR 102.93 1.60E-13 325541000 103314 61042.8 89253 105187 106937 85312 132425 106493 141687 TRUE FALSE 98430.55197 67263.13072 93345.33833 94613.40292 125586.7789 82357.62405 112221.1341 97167.90837 163659.0963 0.601436487 0.410995369 0.570364498 0.578112705 0.767368156 0.503226682 0.685700561 0.593721404 1 17.32033427 -4.999999998 0.168220561 2.647769484 0.476036198 0.67591578 0.091224022 71.71489848 0.673551828 39.2917475 0.314877859 1.00E-05 4.999999998 -2.171733286 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLS(0.26)PPHLS(0.239)S(0.239)S(0.239)PEDLCPAPGT(0.022)PPGT(0.001)PRPPDTPLPEEVKR 57.509 0.00011742 105900000 17261 12797 21534 17958 19430 19216 24692 19594 25247 TRUE FALSE 16445.10674 14101.02885 22521.3552 16152.82772 22818.58585 18550.5451 20924.7819 17878.24549 29162.17582 0.563919059 0.483538298 0.772279659 0.553896521 0.782471994 0.636116633 0.717531574 0.613062811 1 14.83181074 -5 0.114366509 2.169086981 0.436025779 0.60563132 0.092958268 97.32193106 0.73211088 26.61281173 0.93922358 1.00E-05 5 -1.733061202 (ac)MELDLSPPHLSSS(ph)PEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.004)PPHLS(0.302)S(0.331)S(0.363)PEDLCPAPGT(0.956)PPGT(0.043)PRPPDT(0.001)PLPEEVKR;MELDLS(0.156)PPHLS(0.263)S(0.281)S(0.301)PEDLCPAPGT(0.954)PPGT(0.045)PRPPDT(0.001)PLPEEVKR 87.627 5.16E-20 140778000 51064 33037 40761 45367 53287 39839 63128 53532 70249 TRUE FALSE 48650.30592 36403.50786 42629.93217 40806.62297 62580.23593 38459.36544 53496.66417 48844.45429 81142.85614 0.599563637 0.448634786 0.525368889 0.502898529 0.771235311 0.473971059 0.659289884 0.60195631 1 16.30817646 -4.999999998 0.204518789 3.053199595 0.498600609 0.697318117 0.090385831 72.96310459 0.724440255 61.10645866 0.184776006 1.00E-05 4.999999998 -2.554598986 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLSSSPEDLCPAPGT(0.985)PPGT(0.015)PRPPDT(0.001)PLPEEVKR;MELDLS(0.003)PPHLS(0.016)S(0.016)S(0.016)PEDLCPAPGT(0.908)PPGT(0.039)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.852)PPGT(0.145)PRPPDT(0.003)PLPEEVKR;MELDLSPPHLS(0.064)S(0.064)S(0.186)PEDLCPAPGT(0.651)PPGT(0.032)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.949)PPGT(0.05)PRPPDT(0.001)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.938)PPGT(0.06)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.964)PPGT(0.036)PRPPDT(0.001)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.998)PPGT(0.002)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.995)PPGT(0.005)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.951)PPGT(0.049)PRPPDTPLPEEVKR;MELDLSPPHLS(0.001)S(0.001)S(0.001)PEDLCPAPGT(0.791)PPGT(0.203)PRPPDT(0.003)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.843)PPGT(0.154)PRPPDT(0.003)PLPEEVKR 201.18 7.17E-97 7343960000 1765380 1018978 1532916 1741142 2267170 1454532 2708827 2093441 2856088 TRUE FALSE 1681933.986 1122813.017 1603201.715 1566119.098 2662563.73 1404161.192 2295545.69 1910128.208 3298995.54 0.509832149 0.340349965 0.485966621 0.474726043 0.807083155 0.425632946 0.695831705 0.579002968 1 21.6535954 -5 0.112184415 2.598376858 0.254182334 0.629181427 0.119470246 93.80876666 0.695984411 33.96421786 1.274215505 1.00E-05 5 -2.344194524 (ac)MENGYTYEDYKNTAEWLLSHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MENGYTYEDYKNTAEWLLSHTK 22 1 P00491;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 146.89 1.19E-54 838760000 1307220 1047345 1110840 1292810 987610 1224780 1456750 1308460 974120 FALSE TRUE 1245430.301 1154070.646 1161773.113 1162854.283 1159848.871 1182365.561 1234496.032 1193884.306 1125181.554 1.106870528 1.025675049 1.032520581 1.033481466 1.03081042 1.050822027 1.097152746 1.061059258 1 20.10172638 1.975832072 24.65469197 1.06614591 1.046936448 0 0.033425909 1958.053833 1997488.053 0.013306095 0.008637824 94.5871353 -1.975832072 -0.019209462 (ac)MESYHKPDQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ;;;;;;;;;;;;;;; 101.93 1.86E-07 18122660000 16486740 11387850 13009890 14903850 12388280 13804740 19391900 16417010 12804920 FALSE TRUE 15707444.47 12548284.86 13606406.33 13405686.68 14548792.11 13326678.39 16433309.5 14979449.57 14790641.6 1.061985335 0.848393545 0.919933475 0.906362756 0.983648479 0.901020981 1.111061301 1.012765368 1 23.8181813 1.747048802 25 1.048863361 0.936274068 0.376925755 0.063011823 1.8737503 5532.259717 0.027737909 0.015382088 55.85329538 -1.747048802 -0.112589294 (ac)MET(ph)PSQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 METPSQRR 8 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 MET(0.685)PS(0.315)QRR;MET(0.91)PS(0.09)QRR 73.233 0.00048294 171551000 13709 13689.6 13527.7 9287.7 13986.4 12788.9 17111.3 11765.2 15270.2 TRUE FALSE 13061.00274 15084.5858 14147.95843 8354.082751 16425.62373 12346.01719 14500.65691 10734.97672 17638.22463 0.740494183 0.855221323 0.802119189 0.473635126 0.931251533 0.699958043 0.822115447 0.608620025 1 14.10641773 -0.319842775 5.981428674 0.999999995 0.754420236 0.276848018 0.129763051 2450648.689 546279.4335 0.111756201 0.02710486 0.478803399 0.319842775 -0.245579759 (ac)METMAS(ph)PGKDNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 METMASPGKDNYR 13 1 O60684;S4R3E5 O60684 KPNA6 Importin subunit alpha-7 1 METMAS(1)PGKDNYR;MET(0.008)MAS(0.992)PGKDNYR;METMAS(1)PGKDNYR;MET(0.002)MAS(0.998)PGKDNYR 120.84 7.29E-11 260090000 1474340 1340360 1246810 1509170 869110 1567250 1456200 1376810 892380 TRUE FALSE 1404650.87 1476944.208 1303977.472 1357465.364 1020682.509 1512975.74 1234029.945 1256249.217 1030765.733 1.362725618 1.432861184 1.265057064 1.316948479 0.990217735 1.467817266 1.197197293 1.218753377 1 19.97528505 -3.582500923 0.055735762 1.80E-08 1.855606258 0.390335268 0.125376049 323.3858858 1.72407547 53.75545923 14.57501975 0.000261516 3.582500923 1.85560624 (ac)MEVAEPSS(ph)PTEEEEEEEEHSAEPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.134)S(0.616)PT(0.134)EEEEEEEEHS(0.116)AEPRPR;MEVAEPS(0.152)S(0.736)PT(0.113)EEEEEEEEHSAEPRPR;MEVAEPS(0.065)S(0.761)PT(0.174)EEEEEEEEHSAEPRPR;MEVAEPS(0.018)S(0.806)PT(0.176)EEEEEEEEHSAEPRPR;MEVAEPS(0.024)S(0.795)PT(0.181)EEEEEEEEHSAEPRPR 118.55 2.43E-11 5565980000 236980 204780 225390 241440 160630 227050 271860 253090 159310 TRUE FALSE 225778.425 225647.3148 235724.3544 217169.9925 188643.8211 219187.2016 230382.7639 230928.0979 184014.9812 1.22695676 1.226244262 1.281006323 1.180175609 1.025154691 1.191137809 1.251978304 1.254941834 1 17.4894637 -1.180040476 3.660029994 0.999795478 1.206900616 0.454803798 0.070397531 17561138.72 38230408.11 45331.41771 0.017368939 0.066063187 1.180040476 0.207105139 (ac)MEVKPPPGRPQPDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 59.261 0.0026516 775460000 396030 329860 333820 396070 326190 364950 408070 355470 359240 FALSE TRUE 377310.4468 363473.109 349125.9772 356256.2911 383077.4327 352311.69 345811.4268 324343.1623 414949.1045 0.909293315 0.875946243 0.8413706 0.858554187 0.923191371 0.849047958 0.833382752 0.78164565 1 18.66257487 (ac)MEVKPPPGRPQPDSGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 47.548 0.0035598 340111000 178418 128262 159556 191023 144644 179094 198791 190957 188984 FALSE TRUE 169984.5347 141332.0436 166871.8004 171821.0051 169869.8678 172891.9299 168461.7819 174235.7928 218290.6735 0.778707271 0.647448841 0.764447687 0.78712023 0.778181977 0.792026187 0.771731468 0.798182487 1 17.73589097 -5 0.171509156 1.974081485 0.6992465 0.795186513 0.038680906 56.14225549 0.531313772 18.52036541 0.135771634 1.00E-05 5 -1.274834985 (ac)MEVS(ph)PLQPVNENMQVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MEVSPLQPVNENMQVNK 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK 156.17 2.03E-27 394555000 771143 806099 813169 961739 719074 862851 1027365 962326 971703 TRUE FALSE 734692.5986 888241.4046 850453.603 865063.1685 844480.2779 832970.2535 870621.6004 878059.6338 1122389.738 0.654578863 0.79138411 0.757716837 0.770733319 0.752394867 0.74213994 0.775685638 0.782312599 1 20.09814229 -5 0.220499944 2.269283773 0.720279695 0.849134712 0.033526934 56.1817692 0.561854798 31.64591248 0.062661158 1.00E-05 5 -1.549004077 (ac)MHGHGGYDS(ph)DFS(ph)DDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MHGHGGYDSDFSDDER 16 0 Q70Z53;Q70Z53-2;Q70Z53-4;Q70Z53-5;Q70Z53-3 Q70Z53 FRA10AC1 Protein FRA10AC1 2 MHGHGGY(0.085)DS(0.922)DFS(0.993)DDER;MHGHGGY(0.033)DS(0.968)DFS(0.999)DDER 96.444 1.21E-35 349830000 61314 70673 68582 91399 91895 68277 85906 64628 107035 TRUE FALSE 58415.80873 77874.65905 71726.55254 82211.39887 107921.4589 65912.55037 72799.46193 58968.82971 123633.4411 0.472491975 0.629883455 0.580154947 0.664960856 0.872914787 0.533128818 0.588833096 0.476965044 1 16.9157095 -2.136981834 2.477902886 1.86906427 0.602289995 0.547912612 0.113497434 15815592.3 2687349.018 77710101.07 0.028251901 0.00729488 2.136981834 -1.266774275 (ac)MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK 32 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 119.18 2.18E-15 12050000 12156 14050 12280 13445 10054 13227 14395 14167 7786.8 FALSE TRUE 11581.40997 15481.71097 12843.05015 12093.48306 11807.41442 12768.94567 12198.77837 12926.46238 8994.337175 1.287633513 1.721273138 1.427904013 1.344566345 1.312760928 1.419664999 1.35627319 1.437177874 1 13.13480125 -3.48013388 0.212312866 8.64E-18 1.496681435 0.52901243 0.1213653 55.09227548 0.981108861 24.3265335 0.259642586 0.000331029 3.48013388 1.496681435 (ac)MNTAPS(ph)RPSPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNT(0.001)APS(0.405)RPS(0.297)PT(0.297)RR 48.899 0.029198 376930000 5923.3 4629.1 9890.7 8359.8 8145.2 9357.1 12152 6567.5 12615 TRUE FALSE 5643.317348 5100.810553 10344.19838 7519.457021 9565.720301 9033.061281 10297.98921 5992.414883 14571.26977 0.387290705 0.350059441 0.709903704 0.516046792 0.656478155 0.619922726 0.706732452 0.41124864 1 13.83083898 -5 0.071972071 2.537371806 3.63E-17 0.566465244 0.12745771 195.3651508 1.009109803 49.6976928 5.854889544 1.00E-05 5 -2.537371806 (ac)MNTAPSRPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.024)RPS(0.83)PT(0.146)R;MNTAPS(0.104)RPS(0.688)PT(0.208)R;MNTAPS(0.013)RPS(0.946)PT(0.041)R;MNTAPS(0.244)RPS(0.635)PT(0.121)R;MNTAPS(0.063)RPS(0.751)PT(0.186)R;MNTAPS(0.026)RPS(0.817)PT(0.157)R;MNTAPS(0.031)RPS(0.723)PT(0.246)R 97.957 4.60E-07 9158230000 308989.8 292781.6 309659.7 332344.4 301521.5 328678.7 381754 309983.7 367965 TRUE FALSE 294384.4645 322616.3779 323857.9035 298936.5095 354106.7541 317296.4742 323510.4159 282839.8839 425027.1329 0.69262511 0.7590489 0.761969951 0.70333512 0.833139173 0.746532279 0.761152385 0.665463125 1 18.69719542 -1.717970203 2.854633373 1.040219162 0.743147741 0.756954868 0.046204478 7991233.126 7173035.745 2297791.591 0.010148382 0.019143873 1.717970203 -0.297071421 (ac)MNTAPSRPS(ph)PTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.096)RPS(0.452)PT(0.452)RR;MNT(0.001)APS(0.145)RPS(0.427)PT(0.427)RR 55.011 0.0023853 1105220000 66182.2 52775.5 67476.2 76850 96469 66874.1 100563.4 59663.9 120206 TRUE FALSE 63053.89857 58153.38345 70570.05051 69124.89199 113293.1631 64558.23315 85220.60636 54439.41262 138846.9326 0.454125254 0.418830884 0.508257901 0.497849616 0.815957263 0.464959736 0.613773778 0.392082213 1 17.08313578 -5 0.223856356 3.446849887 0.46125926 0.5840119 0.124463222 106.976932 1.070221795 118.5989354 0.214946995 1.00E-05 5 -2.985590627 (ac)MNTAPSRPSPT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.009)RPS(0.38)PT(0.611)R 45.825 0.00049783 364630000 20468 21890 27060 20782 25881 25257 28850 22955 25084 TRUE FALSE 19500.5182 24120.61589 28300.72777 18692.95388 30394.63821 24382.34376 24448.40263 20944.93851 28973.89861 0.673037428 0.832494661 0.976766301 0.645165296 1.049035155 0.84152789 0.843807834 0.722889894 1 14.8224662 4.4181491 2.363017074 0.860272702 0.675402477 0.194755083 0.122440491 0.494060722 4.917443532 0.027812615 0.140540601 26190.82026 -4.4181491 -0.184870225 (ac)MNVDHEVNLLVEEIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 MNVDHEVNLLVEEIHR 16 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 ;;;;;;;;;;;;;;; 164.09 2.73E-35 1508226000 73221.23 74152.6 95634.6 75628 157452.31 67730.9 104687.92 76820.42 179129.91 FALSE TRUE 69760.20757 81708.83424 100019.541 68025.72976 184911.943 65385.36195 88715.85508 70093.61677 206908.4616 0.337154929 0.3949033 0.483399955 0.328772102 0.893689613 0.316011058 0.428768618 0.338766314 1 17.65863312 -1.684779038 2.540920727 1.089272993 0.435422695 0.518400441 0.1695186 11383180.42 9127549.134 6537438.165 0.040824696 0.020664313 1.684779038 -0.653850299 (ac)MQPQSVLHSGYFHPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQPQSVLHSGYFHPLLR 17 0 P13716 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 78.069 0.025063 120170000 19929 19675 20725 17831 27239 18360 29182 22585 33162 FALSE TRUE 18986.99567 21679.90487 21675.26175 16038.594 31989.47298 17724.1886 24729.74994 20607.33767 38304.59359 0.495684561 0.565987075 0.565865859 0.418712026 0.835134118 0.462717051 0.645607945 0.537986067 1 15.22522979 -4.999999998 0.260784409 3.813556756 0.530966727 0.592348611 0.113481536 124.7333981 1.224012359 188.0895428 0.130019375 1.00E-05 4.999999998 -3.282590029 (ac)MS(ph)PTPPLFSLPEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 MS(0.814)PT(0.186)PPLFSLPEAR 66.289 0.0013986 9751300 4885.6 5242.1 6560.2 5048.4 5338.7 4377.2 6957.7 4846.2 6186.2 TRUE FALSE 4654.66737 5776.27595 6860.991659 4540.925241 6269.76759 4225.616466 5896.175078 4421.841037 7145.524301 0.651410194 0.808376783 0.960180299 0.63549224 0.877439825 0.591365488 0.825156396 0.618826674 1 12.80282416 -1.026983325 4.131671903 1.000022812 0.751548501 0.297523816 0.122380938 22954436.14 59465023.52 8234.267079 0.026007668 0.093975939 1.026983325 -0.248474311 (ac)MT(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 32 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 MT(0.667)T(0.667)S(0.667)QKHRDFVAEPMGEKPVGSLAGIGEVLGK;MT(0.685)T(0.685)S(0.629)QKHRDFVAEPMGEKPVGSLAGIGEVLGK 62.284 4.69E-08 236700000 278810 196060 306650 238590 174014 288230 334440 259840 198684 TRUE FALSE 265631.2038 216038.7369 320710.2058 214606.4799 204361.9865 278248.5228 283415.0356 237087.0321 229494.9 1.157460161 0.941366178 1.397461146 0.935125268 0.890485961 1.212438807 1.234951346 1.033081921 1 17.80810257 (ac)MTT(ph)SQKHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTTSQKHR 8 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 MT(0.001)T(0.499)S(0.499)QKHR 67.726 0.026858 67280000 61210 20546 38898 44523 62470 38693 76764 51601 64699 TRUE FALSE 58316.72461 22639.66076 40681.51178 40047.46345 73364.74822 37353.05171 65052.24193 47082.54289 74732.19048 0.780342771 0.302943894 0.544363968 0.535879695 0.981702098 0.499825463 0.8704715 0.630016899 1 16.18944219 2.863343701 10.60470515 0.770586832 0.527090966 0.309355676 0.18706321 0.520770724 42.403864 0.051916533 0.055084546 730.0350324 -2.863343701 -0.243495866 (ac)MTTS(ph)QKHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MTTSQKHR 8 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 MT(0.001)T(0.022)S(0.977)QKHR;MTT(0.019)S(0.981)QKHR;MTT(0.017)S(0.983)QKHR;MTT(0.019)S(0.981)QKHR;MTT(0.032)S(0.968)QKHR 106.29 0.001819 390969000 404275 170043 281167 315233 443267 278909 508563 369188 479528 TRUE FALSE 385165.7219 187370.575 294058.7851 283545.1799 520572.6245 269250.3114 430972.3739 336859.9415 553890.7532 0.695382112 0.338280742 0.530896722 0.511915352 0.939847112 0.486107251 0.778081908 0.608170365 1 19.07924193 0.005645922 0.232029501 1.171172401 0.467648758 0.388012496 0.161557185 7.203627954 0.672148325 1.393030941 0.354120096 1.013085086 -0.005645922 -0.703523643 (ac)MVDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MVDYSVWDHIEVSDDEDETHPNIDTASLFR 30 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 MVDYSVWDHIEVS(0.902)DDEDET(0.064)HPNIDT(0.017)AS(0.017)LFR;MVDY(0.001)S(0.001)VWDHIEVS(0.998)DDEDETHPNIDTASLFR;MVDYS(0.009)VWDHIEVS(0.991)DDEDETHPNIDTASLFR 86.507 1.08E-18 82645000 51083.8 42957.8 47955 48962.3 53302.1 44259.7 52385.3 48951.1 55153.1 TRUE FALSE 48669.17001 47335.24866 50153.78418 44040.51658 62597.96936 42726.97549 44392.96036 44664.68218 63705.96106 0.763965714 0.743026993 0.787269878 0.691309194 0.982607723 0.670690384 0.696841545 0.701106795 1 15.95914075 -2.296134841 2.299219469 2.188869655 0.752133147 0.431119311 0.088549662 6716436.541 1304977.863 41243815.34 0.019881531 0.005056676 2.296134841 -1.436736509 (ac)MVNPTVFFDIAVDGEPLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 59.898 0.001765 58301000 2167.7 1104.4 2086 1807.4 1763.3 1129.4 2996.4 1480.9 2300 FALSE TRUE 2065.237117 1216.939616 2181.645163 1625.716718 2070.818962 1090.288595 2539.244147 1351.224545 2656.672253 0.777377456 0.458069156 0.821194696 0.611937252 0.779478522 0.41039635 0.955798798 0.508615447 1 11.37540454 -5 0.275957113 3.364042028 0.646685452 0.250429339 0.175342466 286.427817 2.758328379 386.8838209 0.180894497 1.00E-05 5 -2.717356576 (ac)S(ph)AIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 1 S(0.81)AIQNLHS(0.176)FDPFADAS(0.013)KGDDLLPAGTEDYIHIR 58.861 5.02E-06 20254000 17590 13878 15901 19938 16242 21133 26031 20842 12552 TRUE FALSE 16758.55556 15292.18398 16630.07658 17933.79436 19074.59966 20401.15891 22059.49286 19016.96399 14498.50005 1.155882022 1.054742485 1.147020486 1.236941359 1.315625726 1.407122036 1.521501726 1.311650441 1 13.82361603 2.976654595 1.801884559 1.370231238 1.10563698 0.239801646 0.138062569 0.31676162 2.075802013 0.044642577 0.051796566 947.6644639 -2.976654595 -0.264594258 (ac)S(ph)DAAVDTSSEITTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.912)DAAVDT(0.075)S(0.01)S(0.002)EITTK;S(0.999)DAAVDT(0.001)S(0.001)SEITTK;S(0.999)DAAVDTSSEITTK 94.82 7.82E-70 919890000 949450 825910 963120 1113120 780270 1004470 1159800 1069240 974550 TRUE FALSE 904571.3801 910071.168 1007280.005 1001227.063 916348.841 969684.952 982851.2088 975611.6772 1125678.237 0.80357899 0.808464744 0.894820537 0.889443386 0.814041536 0.861422848 0.873119135 0.866687874 1 20.10236308 -5 0.134580243 1.516804398 0.787649744 0.724808023 0.029921599 75.46007429 0.632295195 10.48536968 0.210948138 1.00E-05 5 -0.729154654 (ac)S(ph)DNDDIEVES(ph)DADKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 2 S(1)DNDDIEVES(1)DADKR;S(1)DNDDIEVES(1)DADKR 59.198 5.13E-07 712900000 1517420 1283760 1391950 1511650 956980 1568310 1651670 1824990 1078010 TRUE FALSE 1445694.564 1414576.604 1455772.284 1359696.07 1123877.009 1513999.031 1399677.406 1665184.201 1245182.285 1.161030462 1.136039775 1.169123832 1.091965479 0.902580307 1.215885457 1.124074301 1.337301551 1 20.24792553 -0.41643652 7.169566424 1 1.137274092 0.144778738 0.108053126 0 0 0.097090718 0.022884502 0.383321766 0.41643652 0.137274092 (ac)S(ph)DNDDIEVESDADKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 1 S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR 153.34 5.35E-56 2341700000 2581900 2248700 2282750 2710700 1711180 2728300 2967200 2795300 1975050 TRUE FALSE 2459858.704 2477845.087 2387416.345 2438215.286 2009609.25 2633818.287 2514499.144 2550528.713 2281330.667 1.078256098 1.086140261 1.046501667 1.068768908 0.880893454 1.154509658 1.102207225 1.11800045 1 21.12144414 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)DNGELEDKPPAPPVR 57.019 0.00027668 117170000 130440 134500 129920 144220 105320 145420 151190 142510 120240 TRUE FALSE 124274.3597 148205.7029 135876.9605 129722.7316 123687.7747 140384.0689 128123.1887 130031.0689 138886.2051 0.89479268 1.067101681 0.97833302 0.934021716 0.890569186 1.010784828 0.922504785 0.936241787 1 17.08354378 3.338202347 6.070003256 0.94536699 0.987419542 0.063027077 0.053701233 0.450219493 23.27059626 0.014240407 0.019315092 2178.72465 -3.338202347 0.042052552 (ac)S(ph)DQDHSMDEMTAVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(1)DQDHSMDEMTAVVK 108.37 3.18E-07 55157000 84146 76398 68075 83850 67666 78576 91853 93480 77653 TRUE FALSE 80168.58534 84183.04306 71196.30609 75421.2387 79466.92898 75854.89342 77839.13785 85294.39563 89695.03064 0.893790712 0.938547459 0.793759761 0.840863068 0.885968023 0.845697837 0.867819959 0.950937806 1 16.45274044 1.08228825 3.404994711 0.998713286 0.871535702 0.599105845 0.03794637 0.166622466 3.731855993 0.038840427 0.010167575 12.08615751 -1.08228825 -0.127177584 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SDQEAKPSTEDLGDKK 16 2 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.994)DQEAKPS(0.004)T(0.001)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.996)DQEAKPS(0.003)T(0.001)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK 116.78 5.30E-15 28803806000 11223350 11712010 9171090 12577560 3921765 13100870 10723620 12691970 3680680 TRUE FALSE 10692844.49 12905477.13 9591593.548 11313239.77 4605719.574 12647183.59 9087534.816 11580593.82 4251461.056 2.515098774 3.035539304 2.256069954 2.661023969 1.0833263 2.974785237 2.137508658 2.723909185 1 22.01952729 2.902008745 21.65981662 2.11544281 2.655771742 0.175731328 0.644853561 27.21900027 6007.861537 0.177891444 0.188682651 798.0107565 -2.902008745 0.540328932 (ac)S(ph)DQEAKPSTEDLGDKKEGEYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.9)DQEAKPS(0.088)T(0.012)EDLGDKKEGEYIK;S(0.894)DQEAKPS(0.053)T(0.053)EDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK 121.26 1.63E-17 1327960000 1453930 822183 1407760 1230261 657951 1699490 1974430 1861030 696928 TRUE FALSE 1385205.61 905964.3824 1472307.188 1106592.827 772697.4461 1640636.235 1673194.441 1698068.347 805004.0348 1.720743686 1.125415952 1.828943862 1.374642584 0.959867793 2.03804722 2.078491993 2.109391101 1 19.61863649 2.211246031 24.99859538 1.920931942 1.411370843 0.173659281 0.405411634 270.3053683 247384.6666 0.137201589 0.101354247 162.64699 -2.211246031 -0.509561099 (ac)S(ph)DSGEQNYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSGEQNYGER 11 0 P62995;P62995-2 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.986)DS(0.014)GEQNYGER 56.209 0.00026221 168280000 9382.9 10130 7992 9821.1 13137 12796 12060 13672 14633 TRUE FALSE 8939.388912 11162.25852 8358.441105 8833.864369 15428.08864 12352.87131 10220.0255 12474.8072 16902.2109 0.528888733 0.660402274 0.49451762 0.522645494 0.91278524 0.73084352 0.604656134 0.738057717 1 14.04492435 2.763793461 24.97681595 0.753718544 0.564048001 0.495975607 0.118328115 783.9677327 776011.7465 0.035163573 0.037283417 580.4882865 -2.763793461 -0.189670542 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_SK-BR-3_Trastuzumab_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 50.358 0.00016066 2351100000 28404.4 28143 43503 39784 35823 40676 38798 18641 48740 TRUE FALSE 27061.7803 31010.8037 45497.65558 35784.83674 42070.51986 39267.37992 32878.65253 17008.69522 56298.35027 0.480685139 0.550829705 0.808152554 0.635628514 0.747278022 0.697487222 0.584007389 0.302117116 1 15.78080503 3.98203114 22.7678396 0.663291114 0.506989263 0.1310192 0.176625963 446.4742676 565718.6641 0.041750037 0.076077869 9594.694253 -3.98203114 -0.156301851 (ac)S(ph)EGESQTVLSSGSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.725)EGES(0.212)QT(0.057)VLS(0.004)S(0.003)GSDPK;S(0.995)EGES(0.004)QTVLSSGSDPK 80.469 3.94E-35 254980000 1069500 1160760 910100 1325710 706580 1146180 1085200 1168640 666410 TRUE FALSE 1018946.855 1279042.764 951828.9852 1192447.112 829807.3283 1106487.499 919632.8089 1066307.686 769753.4592 1.323731439 1.661626522 1.236537457 1.549128617 1.078017017 1.437457001 1.194710849 1.385258713 1 19.55403692 -1.778228322 0.118922108 0.415099217 1.639087823 0.334674962 0.165580861 53.30693446 0.973914194 10.72552941 1.875059587 0.016663709 1.778228322 1.223988607 (ac)S(ph)ESGHS(ph)QPGLYGIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 2 S(0.616)ES(0.616)GHS(0.764)QPGLY(0.004)GIER 45.764 4.54E-07 95594000 21090 16191 17498 23665 20125 16448 24624 19957 22106 TRUE FALSE 20093.1175 17840.88131 18300.30061 21286.14924 23634.79363 15878.40164 20867.15655 18209.45928 25534.08558 0.786913533 0.698708448 0.716700841 0.833636637 0.925617389 0.621851195 0.817227485 0.713143192 1 14.64013677 -1.409240961 3.545686084 1.001904497 0.762865248 0.437025532 0.08408654 12797463.28 5249665.199 185626.0071 0.018222204 0.038972569 1.409240961 -0.239039249 (ac)S(ph)ESGHSQPGLYGIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 S(0.43)ES(0.43)GHS(0.139)QPGLY(0.001)GIER 40.113 2.60E-05 99109000 40889 46730 43051 41094 31070 46952 47642 46893 33224 TRUE FALSE 38956.258 51491.84013 45024.93093 36963.15305 36488.59816 45326.04047 40373.33789 42786.80032 38376.20824 1.015114828 1.341764663 1.173251163 0.963178874 0.950813013 1.181097418 1.052040828 1.114930377 1 15.22792455 3.364073788 8.000158078 1.052035653 1.191281006 0.266761446 0.102837062 0.301944818 20.01734576 0.028014595 0.037959017 2312.457653 -3.364073788 0.139245352 (ac)S(ph)GDEMIFDPTMSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 SGDEMIFDPTMSK 13 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 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;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK 87.184 2.16E-62 7000334000 18161570 16190580 15988515 19408480 15185420 17275100 20040100 18587940 16876603 TRUE FALSE 17303108.58 17840418.51 16721604.23 17457502.72 17833752.44 16676858.96 16982614.68 16960281.43 19493740.4 0.887623833 0.915187037 0.857793522 0.895544024 0.914845077 0.855498155 0.871182971 0.870037309 1 24.2165076 -1.230872671 6.573230439 1.000001013 0.884814773 0.753652688 0.020926094 3.15E-07 3.68E-08 0.02052249 0.004837155 0.058766162 1.230872671 -0.11518624 (ac)S(ph)GDEMIFDPTMSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 SGDEMIFDPTMSKK 14 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK 126.67 2.27E-09 4917343000 10929950 7007250 10326290 9608540 8498490 10774800 14312540 12711170 11167080 TRUE FALSE 10413312.92 7721296.742 10799760.61 8642671.304 9980623.965 10401665.97 12128899.16 11598112.57 12898813.73 0.807307799 0.598605182 0.837267739 0.670036135 0.773762934 0.806404852 0.940311211 0.899161179 1 23.62073506 1.892274975 1.215796094 0.96909065 0.718530653 0.650860789 0.070240791 0.254572412 0.695473245 0.050301025 0.021647957 78.0324019 -1.892274975 -0.250559997 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.998)GEDEQQEQT(0.002)IAEDLVVTK;S(0.989)GEDEQQEQT(0.011)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.965)GEDEQQEQT(0.035)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.992)GEDEQQEQT(0.008)IAEDLVVTK 150.26 9.53E-215 6821168000 3215449 2697421 2965088 3259208 2598249 3064177 3593841 3475476 3131503 TRUE FALSE 3063461.098 2972291.267 3101040.218 2931586.22 3051382.803 2958063.782 3045534.55 3171144.897 3617120.492 0.84693366 0.821728575 0.857322897 0.810475135 0.843594459 0.817795202 0.841977633 0.876704247 1 21.78641023 0.774606483 1.852448556 0.999906264 0.832933531 0.931663622 0.014128182 0.165559178 0.949934757 0.011665226 0.003269307 5.951226541 -0.774606483 -0.166972733 (ac)S(ph)KGPAVGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 103.26 1.14E-17 26429000 71456 60128 66768 74028 42637 73199 80364 83342 49279 TRUE FALSE 68078.41649 66255.11156 69829.37884 66586.5648 50072.8793 70664.10028 68102.99581 76044.13266 56920.93564 1.196017172 1.163984935 1.226778479 1.169807981 0.879691782 1.241443056 1.196448988 1.335960694 1 15.79667176 -0.503314255 7.130179178 1.000003176 1.173443158 0.185092299 0.116099569 0 0 0.106259844 0.025045685 0.313823704 0.503314255 0.173439983 (ac)S(ph)KS(ph)ESPKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_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(0.974)KS(0.943)ES(0.083)PKEPEQLRK 41.996 0.016265 169830000 416190 349130 360540 417210 138350 471380 439030 491940 146500 TRUE FALSE 396517.5235 384706.7439 377071.1156 375271.2582 162478.1962 455055.9924 372047.9102 448863.1257 169218.4718 2.343228368 2.273432326 2.228309425 2.217673131 0.960168204 2.689162641 2.198624691 2.652565769 1 17.36852754 2.979158422 24.86849858 2.010485636 2.280478149 0.072935089 0.581112192 2487.060945 2967604.187 0.165202088 0.177001173 953.1437892 -2.979158422 0.269992513 (ac)S(ph)KSES(ph)PKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_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(0.754)KS(0.356)ES(0.89)PKEPEQLRK 49.298 0.0027098 117530000 366300 329950 341390 388480 120590 446530 381810 469690 150040 TRUE FALSE 348985.7249 363572.2801 357043.0692 349429.2523 141620.8578 431066.5541 323557.8721 428561.4536 173307.4369 2.013680031 2.097845809 2.060171655 2.016239225 0.817165497 2.487294036 1.86695896 2.472839373 1 17.40297404 2.971636915 24.94508621 1.808225935 2.057025454 0.071047484 0.531797691 2327.613688 2047117.085 0.149872383 0.15927607 936.7785003 -2.971636915 0.248799519 (ac)S(ph)LDIQSLDIQCEELSDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLDIQSLDIQCEELSDAR 18 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9;E9PR82;E9PMI1 P13489 RNH1 Ribonuclease inhibitor 1 S(1)LDIQSLDIQCEELSDAR;S(0.976)LDIQS(0.024)LDIQCEELSDAR 126.95 1.51E-49 97269000 11078.2 13047.4 7044 12311 12284.8 10895.7 11169.2 9399.8 8532.7 TRUE FALSE 10554.55544 14376.94489 7366.974367 11073.47489 14427.26523 10518.37918 9465.133404 8576.703681 9855.907537 1.070886207 1.458713451 0.747467886 1.123536808 1.463819052 1.067215691 0.960351278 0.87020943 1 13.26677301 1.882739714 3.80125379 0.941603598 1.185793814 0.202261546 0.203670225 0.359645118 8.53217999 0.098081152 0.054474042 76.33781305 -1.882739714 0.244190215 (ac)S(ph)LPLNPKPFLNGLTGKPVMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLPLNPKPFLNGLTGKPVMVK 21 2 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 1 S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK;S(0.998)LPLNPKPFLNGLT(0.002)GKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK 117.66 2.02E-11 999474000 3352870 2278350 2361160 3135920 2489560 2909800 4003460 3411250 3382150 TRUE FALSE 3194386.48 2510516.455 2469421.522 2820691.364 2923738.476 2809032.896 3392658.648 3112542.866 3906636.548 0.817682024 0.64262862 0.632109358 0.72202554 0.748402991 0.719041268 0.868434677 0.796732132 1 21.89749561 1.110236645 0.680420927 0.994302564 0.701106743 0.69032276 0.060434911 0.398070074 0.437018984 0.058654847 0.024255107 12.88951703 -1.110236645 -0.293195822 (ac)S(ph)QERPTFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQERPTFYR 9 1 Q16539-2;Q16539;Q16539-5;Q16539-3;Q16539-4;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 1 S(0.996)QERPT(0.004)FYR;S(1)QERPTFYR 58.596 0.00094651 306960000 59398 37929 52050 57436 54826 47572 65703 63334 70766 TRUE FALSE 56590.37426 41794.00822 54436.54398 51662.42416 64387.63704 45924.56971 55678.80063 57788.13921 81740.02986 0.692321429 0.511304049 0.665971667 0.632033341 0.787712424 0.561836958 0.681169321 0.706974775 1 16.31875515 -5 0.233651479 2.975218361 0.606124537 0.689691194 0.073859332 87.64223019 0.875830983 81.8274247 0.11464755 1.00E-05 5 -2.369093824 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDR 22 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 S(0.813)QGDS(0.187)NPAAIPHAAEDIQGDDR;S(1)QGDSNPAAIPHAAEDIQGDDR 135.47 1.60E-55 342780000 2224.5 4252.9 2657.2 3237.1 12879.5 10484.2 1914.2 1658.6 9707.3 TRUE FALSE 2119.352294 4686.275345 2779.035248 2911.700558 15125.68072 10121.12953 1622.153633 1513.364191 11212.65851 0.189014255 0.41794507 0.247848023 0.259679768 1.348982555 0.90265208 0.144671635 0.134969257 1 13.45284076 VKQLPLVKPYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKQLPLVKPYLR 12 2 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 99.5 0.0021155 116690000 173070 108650 170630 161130 196800 181330 278490 227760 294490 FALSE TRUE 164889.3241 119721.5585 178453.5543 144932.9063 231121.8577 175050.4966 236001.2357 207816.127 340158.0052 0.48474333 0.351958668 0.524619593 0.426075248 0.679454413 0.514615249 0.693798858 0.610939986 1 18.37584552 0.12319999 0.221814544 1.216284267 0.343772846 0.80920738 0.078653764 2.636015137 0.248888557 0.639590815 0.188654261 1.328005855 -0.12319999 -0.872511421 (ac)S(ph)REMQDVDLAEVKPLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SREMQDVDLAEVKPLVEK 18 2 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RJ98 Q92597 NDRG1 Protein NDRG1 1 S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK 95.094 1.46E-11 1076031000 2954333 1887989 2743280 3408640 2170672 3928840 4593780 3492370 2600220 TRUE FALSE 2814687.534 2080377.226 2869062.101 3065997.031 2549236.51 3792783.286 3892914.49 3186559.569 3003448.838 0.937151817 0.692662781 0.95525586 1.020825457 0.848769747 1.262809354 1.296148095 1.060966822 1 21.51818866 2.242900868 24.99996541 1.195110571 0.876925887 0.520176984 0.122958865 72.4022593 417040.9336 0.043389443 0.035132522 174.9447316 -2.242900868 -0.318184684 (ac)S(ph)SPPEGKLETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSPPEGKLETK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 1 S(0.5)S(0.5)PPEGKLETK;S(0.5)S(0.5)PPEGKLETK;S(0.5)S(0.5)PPEGKLETK;S(0.5)S(0.5)PPEGKLETK 89.247 0.00080925 6856910000 6231740 3109260 6063370 5025380 4340940 6522180 8854700 7412800 5602090 TRUE FALSE 5937178 3426097.129 6341381.512 4520219.255 5097998.562 6296315.271 7503752.887 6763695.934 6470833.506 0.917529093 0.529467668 0.979994541 0.69855286 0.787842641 0.973030022 1.159626945 1.045258842 1 22.62552013 2.132876218 3.208805866 1.083214813 0.763649709 0.519106992 0.126817888 0.169555346 3.457250691 0.05040023 0.034477037 135.7926359 -2.132876218 -0.319565104 (ac)S(ph)SSPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.333)S(0.333)S(0.333)PVKR 49.211 0.038628 23908000000 16888000 14456000 13846000 17227000 12449000 16253000 18564000 17491000 14120000 TRUE FALSE 16089737.71 15929082.84 14480852.8 15495309.23 14620101.66 15690154.53 15731720.85 15959395.31 16309657.49 0.986515978 0.976665687 0.887869829 0.950069567 0.896407645 0.962016189 0.964564759 0.978524247 1 23.95922315 1.272045576 1.537144605 0.997419175 0.947036979 0.27956311 0.031172404 0.580527784 2.53663793 0.030625536 0.009352796 18.70878463 -1.272045576 -0.050382196 (ac)S(ph)SSPVNVKK ddPTM_SK-BR-3_Trastuzumab_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 41.984 0.02134 10117000000 15491000 13190000 14862000 15835000 11085000 16758000 19343000 17005000 13332000 TRUE FALSE 14758771.13 14534076 15543437.4 14243235.72 13018220.49 16177666.26 16391870.09 15515952.05 15399458.47 0.958395463 0.943804357 1.00934961 0.92491796 0.84536872 1.05053475 1.064444579 1.007564784 1 23.87637628 2.19054167 24.99999891 1.03957241 0.942180642 0.520013819 0.044443566 89.83286092 46768.91593 0.016293421 0.012033517 155.0749572 -2.19054167 -0.097391768 (ac)S(ph)TGGDFGNPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 61.679 0.011349 59684000 146010 128200 163010 195040 130060 182760 195710 168670 161380 TRUE FALSE 139108.3967 141263.7258 170484.1697 175434.2086 152742.4228 176430.9754 165850.845 153900.3606 186405.9862 0.746265716 0.757828269 0.914585273 0.941140423 0.819407284 0.946487712 0.889729179 0.825619197 1 17.50808867 3.743646952 22.86256513 0.900596522 0.752046945 0.581052101 0.053980227 76.28417582 342884.2352 0.012520999 0.021673861 5541.750285 -3.743646952 -0.148549577 (ac)SAADEVDGLGVARPHYGSVLDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 151.01 7.11E-73 1087090000 37302.2 28991.8 22722.7 25845.5 34163.2 16827.6 21032.3 19852.2 40645.6 FALSE TRUE 35538.99893 31946.09738 23764.55827 23247.46124 40121.25126 16244.85599 17823.43635 18113.83612 46948.71206 0.756974949 0.680446725 0.506181261 0.495167177 0.854576185 0.346012814 0.379636322 0.38582179 1 15.51879796 -1.177377222 4.817981614 1.000048071 0.558160456 0.411964347 0.168520198 9.31E-05 1.59E-05 0.174654799 0.041162065 0.066469556 1.177377222 -0.441887615 (ac)SAEVPEAASAEEQKEMEDKVT(ph)SPEKAEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 SAEVPEAASAEEQKEMEDKVT(0.551)S(0.449)PEKAEEAK 98.342 4.37E-09 99511000 189410 208010 184000 212660 52514 236930 205780 267320 53938 TRUE FALSE 180456.9647 229206.4555 192436.582 191283.0128 61672.42497 228725.0547 174384.4816 243912.0436 62302.42956 2.896467537 3.678932862 3.088749241 3.070233603 0.989887961 3.671206024 2.798999699 3.914968411 1 15.9270008 2.984388734 24.81208252 2.634480893 3.248823094 0.106121333 0.969106112 1613.454312 2564381.635 0.269800539 0.294542171 964.692127 -2.984388734 0.614342201 (ac)SAEVPEAASAEEQKEMEDKVTS(ph)PEKAEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 SAEVPEAASAEEQKEMEDKVT(0.21)S(0.79)PEKAEEAK 117.8 3.05E-18 106370000 280190 259370 253040 313110 77482 374920 288660 361300 58967 TRUE FALSE 266945.974 285800.0979 264642.1343 281635.5879 90994.83627 361936.4264 244619.6154 329662.6566 68111.3012 3.919261111 4.196074555 3.885436479 4.134931839 1.33597266 5.313896813 3.591468833 4.840058123 1 16.05560657 -0.925796905 8.264609135 0.999999998 3.899552928 0.435713554 1.037930325 5.31E-08 9.64E-09 0.891392974 0.210103334 0.11863234 0.925796905 2.89955293 (ac)SAHLQWMVVR ddPTM_SK-BR-3_Trastuzumab_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 ; 75.854 0.00013794 96053000 39412 46062 49354 47857 61680 49004 52209 40799 71977 FALSE TRUE 37549.07287 50755.77017 51616.92972 43046.32344 72436.97247 47306.97919 44243.55817 37226.42327 83138.82555 0.451643051 0.610494192 0.620852284 0.517764392 0.871277312 0.569011877 0.53216482 0.447762198 1 16.34323475 -2.114977669 2.561869694 1.832568788 0.577541749 0.55404983 0.119089427 14536082.78 2893110.676 70810719.07 0.027319648 0.007674009 2.114977669 -1.255027039 (ac)SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 ;;; 89.297 2.57E-58 906823000 544701 436035 479541 544118 445713 541308 693148 624781 349587 FALSE TRUE 518954.0632 480467.4622 501528.4292 489422.2249 523445.2061 522562.3682 587395.5421 570071.8635 403799.1665 1.285178639 1.189867395 1.242024429 1.212043673 1.296300858 1.294114529 1.454672498 1.411770778 1 18.62327841 2.420367841 2.436736672 1.34172462 1.232231124 0 0.125443967 0.552270136 6.698715566 0.044694463 0.036060991 263.2496736 -2.420367841 -0.109493497 (ac)SCESS(ph)MVLGYWDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCESSMVLGYWDIR 14 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 1 S(0.22)CES(0.316)S(0.463)MVLGYWDIR 58.676 3.53E-17 29729000 3322.4 3665.6 3688.7 4476.8 4363 4645 4256.3 2614.2 5481.9 TRUE FALSE 3165.356736 4039.128807 3857.830544 4026.783559 5123.905819 4484.142485 3606.923263 2385.286789 6332.005054 0.499898012 0.637890964 0.609258917 0.635941305 0.809207475 0.708171021 0.569633668 0.376703235 1 12.62844669 4.73057774 1.020308366 0.658653167 0.416360101 0.099240757 0.160353049 4.601163834 3.886406854 0.045728678 1.220622945 53774.66828 -4.73057774 -0.242293066 (ac)SCINLPTVLPGS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SCINLPTVLPGSPSK 15 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.815)PS(0.185)K;SCINLPTVLPGS(0.872)PS(0.128)K;SCINLPTVLPGS(0.845)PS(0.155)K;SCINLPTVLPGS(0.791)PS(0.209)K;SCINLPTVLPGS(0.794)PS(0.206)K;SCINLPTVLPGS(0.818)PS(0.182)K 94.339 6.32E-13 2862830000 6047740 6662900 5921960 7144770 4266350 7030010 6986130 7761270 5287930 TRUE FALSE 5761875.316 7341857.085 6193487.724 6426564.145 5010400.089 6786558.991 5920267.559 7081652.054 6107955.177 0.943339489 1.202015547 1.014003467 1.052162951 0.820307279 1.111101636 0.969271612 1.159414542 1 22.54225804 3.549537863 24.99999689 1.013041982 1.078566202 0.040107974 0.108181783 392.9691624 135660.1066 0.026525085 0.041092477 3544.360299 -3.549537863 0.06552422 SSSHSSPGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHSSPGS(1)PK 87.447 0.0088357 61924000 115260 75254 100720 133170 125850 94076 181420 165050 197370 TRUE FALSE 109811.8882 82922.46816 105338.1116 119783.4986 147798.2002 90818.12453 153741.047 150597.347 227977.1316 0.481679401 0.363731518 0.462055606 0.525418921 0.648302745 0.398365064 0.674370477 0.660580936 1 17.79852959 0.264267992 0.303990579 1.123877871 0.39698318 0.809104068 0.080138561 1.617611844 0.269522705 0.349867768 0.094537976 1.837671973 -0.264267992 -0.72689469 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 SDEFSLADALPEHS(1)PAK 130.77 5.06E-27 449140000 676600 604930 615990 719710 526230 730800 853490 847690 567840 TRUE FALSE 644618.4589 666573.0547 644233.7508 647363.3834 618004.3454 705492.2128 723274.4251 773461.7697 655897.7271 0.982803313 1.016275903 0.982216776 0.986988301 0.942226692 1.075613139 1.102724396 1.179241424 1 19.32311135 2.099050597 5.525944623 1.10156435 0.987364305 0.567903497 0.046375135 0.135144117 6.270149194 0.016109023 0.011760585 125.6176305 -2.099050597 -0.114200045 (ac)SDQDHS(ph)MDEMTAVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(0.007)DQDHS(0.991)MDEMT(0.001)AVVK;S(0.015)DQDHS(0.985)MDEMTAVVK;S(0.109)DQDHS(0.883)MDEMT(0.008)AVVK 98.582 6.94E-25 180270000 205130 183713 202642 210287 200891 198043 234930 213650 196778 TRUE FALSE 195433.9114 202433.5636 211933.3361 189148.5512 235926.3268 191184.7213 199087.1137 194941.6734 227293.3272 0.859831275 0.890626953 0.932422164 0.832178197 1.037981755 0.841136533 0.875903909 0.857665624 1 17.79419581 4.30151975 2.414814519 0.902482176 0.862213602 0.044963841 0.066873506 1.083029974 11.96556667 0.015670889 0.060830357 20022.56675 -4.30151975 -0.040268574 (ac)SDSGEQNYGERES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 124.62 1.06E-16 3858863000 7286 16436.5 6653.5 12852.6 13305.7 15483.6 30515.8 18022.2 33936.9 TRUE FALSE 6941.605219 18111.39804 6958.569556 11560.63223 15626.20987 14947.39905 25860.05425 16444.08063 39199.66113 0.177083297 0.462029454 0.177516064 0.294916637 0.398631249 0.381314497 0.659700964 0.419495479 1 15.25855356 0.330978659 0.319887843 1.131829059 0.236772752 0.791125682 0.110591586 1.583797331 0.300319985 0.426274076 0.1209646 2.142785303 -0.330978659 -0.895056307 (ac)SELDQLRQEAEQLKNQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SELDQLRQEAEQLKNQIR 18 2 P62873-2;P62873;F6X3N5;F6UT28;B1AKQ8 P62873-2 GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 147.7 1.17E-48 70494000 82403 32711 85892 51128 93673 51472 111710 81506 129970 FALSE TRUE 78507.9735 36044.28809 89830.23316 45988.5163 110009.5415 49689.51173 94666.58781 74368.90255 150125.0838 0.522950406 0.240095041 0.598369246 0.306334659 0.732785879 0.330987404 0.630584746 0.495379591 1 17.19580553 -5 0.184489819 3.259428378 0.364679073 0.545235269 0.150940851 89.05557803 0.863889589 73.49333312 0.379647761 1.00E-05 5 -2.894749305 (ac)SES(ph)GHS(ph)QPGLYGIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 2 S(0.5)ES(0.602)GHS(0.896)QPGLY(0.002)GIER 44.294 0.0041747 0 60598 37165 48456 55236 47585 42486 53232 47656 52527 TRUE FALSE 57733.65263 40952.15575 50677.75553 49683.57234 55883.80893 41014.69917 45110.48073 43482.988 60672.61889 0.951560254 0.674969311 0.835265668 0.81887964 0.921071316 0.676000145 0.743506405 0.716682233 1 15.88875797 2.23203268 24.99970294 0.757523773 0.826700559 0.027895533 0.113018214 402.0120686 1539550.202 0.038342905 0.028989119 170.6210775 -2.23203268 0.069176786 (ac)SES(ph)GHSQPGLYGIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 S(0.027)ES(0.654)GHS(0.319)QPGLYGIER 66.797 3.14E-06 137190000 97976 79488 74702 83760 54968 78848 95936 85046 64706 TRUE FALSE 93344.86865 87587.91757 78127.16059 75340.28567 64554.4018 76117.47399 81299.20121 77598.92138 74740.27601 1.248923253 1.171897165 1.045315388 1.008027929 0.863716396 1.01842645 1.087756235 1.038247723 1 16.18959827 3.80292845 2.072221329 1.007348388 1.2304496 0.700149844 0.056512896 0.183633277 1.539795192 0.017443268 0.037760645 6352.262694 -3.80292845 0.223101212 (ac)SESSSKS(ph)SQPLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESSSKSSQPLASK 14 1 P17096;P17096-3;A0A669KAX1;A0A1W2PRV2;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 SESS(0.007)S(0.007)KS(0.699)S(0.287)QPLASK 92.65 3.84E-06 133580000 709120 546330 648260 682470 531270 713290 807370 776870 569900 TRUE FALSE 675601.3029 602001.6481 677983.3622 613866.819 623923.3198 688588.5884 684190.8781 708843.1444 658277.1814 1.026317366 0.914510886 1.029935993 0.932535467 0.947812468 1.046046571 1.039365935 1.07681561 1 19.32833566 2.229861877 24.97183092 1.043437338 0.968726154 0.42564466 0.040516299 160.7878175 461576.3605 0.013840335 0.010376974 169.7703627 -2.229861877 -0.074711185 (ac)SETAPAAPAAPAPAEKT(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK 100.39 3.52E-11 312140000 474450 533040 431060 642780 272540 586820 511620 577150 323220 TRUE FALSE 452023.6888 587357.382 450824.5274 578166.5332 320070.8897 566498.2763 433562.9725 526611.6863 373343.3068 1.210745393 1.573236673 1.207533439 1.548618986 0.857309838 1.517365561 1.161298367 1.410529335 1 18.51014334 -4.417063794 0.176294664 3.03E-10 1.390611449 0.154045754 0.219504632 175.2526015 2.018980137 62.35067208 0.641054798 3.83E-05 4.417063794 1.390611449 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVKK 63.491 3.93E-05 354240000 675760 743650 670260 932500 383840 936200 828960 910150 435910 TRUE FALSE 643818.164 819428.7805 700992.084 838763.3284 450781.5745 903779.1593 702486.9271 830452.441 503508.6965 1.278663444 1.627437195 1.392214452 1.665836825 0.895280613 1.794962362 1.395183305 1.649330879 1 18.94165717 -1.02880958 4.719383334 1.000003992 1.463058316 0.247097797 0.253639324 14335913.33 3125180.924 1798.062204 0.051266964 0.09358159 1.02880958 0.463054324 (ac)SETAPAETATPAPVEKS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETAT(0.002)PAPVEKS(0.998)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETAT(0.02)PAPVEKS(0.98)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAET(0.002)AT(0.052)PAPVEKS(0.946)PAK;SETAPAETAT(0.005)PAPVEKS(0.995)PAK 182.47 2.75E-66 2227770000 3131760 3279270 3211120 3967150 1718540 4183150 3474390 3882800 2022130 TRUE FALSE 2983727.911 3613431.341 3358353.028 3568364.545 2018252.832 4038286.467 2944307.994 3542801.448 2335711.593 1.277438499 1.547036609 1.437828642 1.527741934 0.864084777 1.728931979 1.260561451 1.516797476 1 21.15543071 -1.268589886 3.867285064 0.99941357 1.395880774 0.223236219 0.231585334 196.2937205 37925973.76 37522.54917 0.04871126 0.053877832 1.268589886 0.396467205 (ac)SETAPAETATPAPVEKS(ph)PAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK 99.387 1.13E-07 610910000 669260 724350 614680 798300 330049 867010 687910 822840 323304 TRUE FALSE 637625.4061 798162.0885 642863.686 718053.3673 387609.4411 836985.2263 582956.6952 750787.7675 373440.3331 1.707435833 2.137321595 1.721462919 1.922806145 1.037942093 2.241282347 1.561043742 2.010462451 1 18.51051823 -1.724641723 2.518251817 0.837999447 1.799801448 0.353432134 0.336722231 17761425.21 13360510.11 18057758.08 0.076918421 0.018852037 1.724641723 0.961802001 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 SETAPLAPT(0.001)IPAPAEKT(0.999)PVK;SETAPLAPT(0.002)IPAPAEKT(0.997)PVK;S(0.001)ET(0.001)APLAPT(0.002)IPAPAEKT(0.995)PVK 55.536 0.00016988 0 306290 339655 286490 390510 172496 369062 322381 350708 187911 TRUE FALSE 291812.2787 374266.2307 299625.8499 351255.1929 202579.2478 356281.2904 273195.8575 319998.1483 217051.2782 1.344439347 1.724321708 1.380438081 1.618305111 0.933324372 1.641461379 1.258669656 1.474297461 1 17.72767639 -3.639603396 0.154259908 1.24E-15 1.581011445 0.258901104 0.22453965 100.6183481 1.343064699 32.93514407 0.999233254 0.000229296 3.639603396 1.581011445 (ac)SETAPLAPTIPAPAEKT(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SETAPLAPTIPAPAEKTPVKK 21 2 P16402 P16402 HIST1H1D Histone H1.3 1 SETAPLAPT(0.007)IPAPAEKT(0.993)PVKK 45.546 0.00072523 109250000 207160 221360 209360 255890 116970 262320 233200 269430 133400 TRUE FALSE 197367.9574 243916.8357 218959.3631 230167.451 137369.531 253235.7926 197621.057 245837.2809 154086.9907 1.280886572 1.58298137 1.421011353 1.493750056 0.891506352 1.643459915 1.282529149 1.595444753 1 17.23338554 (ac)SGDHLHNDS(ph)QIEADFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGDHLHNDSQIEADFR 16 0 P11387 P11387 TOP1 DNA topoisomerase 1 1 SGDHLHNDS(1)QIEADFR;SGDHLHNDS(1)QIEADFR 110.32 1.67E-45 446180000 23344.8 29578.7 32772.9 39621 26219.6 33202.7 38074.1 27838.5 28797.5 TRUE FALSE 22241.33757 32592.80316 34275.56988 35638.22181 30792.28994 32052.88217 32265.19677 25400.81336 33263.26922 0.668645569 0.979843651 1.030432988 1.071398652 0.925714479 0.963611904 0.969994758 0.763629491 1 15.02164235 4.543642531 2.508223359 0.967048616 0.65735512 0.559909029 0.081608057 0.241946154 2.542723647 0.019719826 0.133168985 34965.72443 -4.543642531 -0.309693497 (ac)SGDHLHNDSQIEADFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGDHLHNDSQIEADFR 16 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 41.367 0.00046061 0 20823 16418 19354 15763 19374 19776 27073 20697 19664 FALSE TRUE 19838.73806 18091.01287 20241.40004 14178.47329 22752.81947 19091.15216 22942.51662 18884.66096 22713.39269 0.873437902 0.796491 0.891165856 0.624234058 1.001735838 0.840524021 1.010087614 0.831432856 1 14.4712556 2.673136122 24.99995768 0.935408101 0.810190502 0.351854616 0.093859989 223.3842838 85358.87028 0.026975055 0.025432328 471.1249689 -2.673136122 -0.125217599 (ac)SHQTGIQASEDVKEIFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHQTGIQASEDVKEIFAR 18 1 Q12792;Q12792-3;F8VRG3 Q12792 TWF1 Twinfilin-1 0 41.422 0.080731 110290000 39150 22472 32308 32887 47839 37873 50337 37984 54206 FALSE TRUE 37299.45709 24761.92235 33789.35376 29581.13628 56182.10645 36561.44851 42657.16615 34657.91959 62611.98963 0.595723875 0.395482119 0.539662674 0.472451626 0.89730588 0.583936858 0.681293893 0.553534871 1 15.93415133 2.776029383 24.81905311 0.707075307 0.495973155 0.402587388 0.142947423 535.767296 354887.6165 0.039162714 0.041537477 597.0756811 -2.776029383 -0.211102153 (ac)SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 151.28 1.16E-246 10089146000 2987402 2626178 2726467 3307577 2911478 2972951 3597905 3309825 1211990 FALSE TRUE 2846193.428 2893788.524 2851478.209 2975093.076 3419238.841 2869996.961 3048978.512 3019999.177 1399939.219 2.033083572 2.067081545 2.036858579 2.125158746 2.442419495 2.050086834 2.177936349 2.157235925 1 20.41693276 -0.396110227 7.183720292 1.000001533 2.129483413 0.898824134 0.119784845 0 0 0.114297954 0.026940286 0.401688846 0.396110227 1.12948188 (ac)SKS(ph)ESPKEPEQLR ddPTM_SK-BR-3_Trastuzumab_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" 1 S(0.148)KS(0.704)ES(0.148)PKEPEQLR 61.11 1.34E-05 293620000 457090 167260 496280 317450 352010 485910 792150 562680 509240 TRUE FALSE 435484.2616 184303.9842 519034.9289 285539.3229 413400.4325 469082.8149 671292.9687 513408.7562 588210.3384 0.740354654 0.313330066 0.882396815 0.485437443 0.702810552 0.797474618 1.141246464 0.872831915 1 19.16597262 2.119024929 2.355324016 1.015396107 0.590361087 0.520677815 0.164742923 0.203372503 2.223277492 0.074720339 0.045914233 131.5300331 -2.119024929 -0.42503502 (ac)SKS(ph)ESPKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSESPKEPEQLRK 14 3 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.073)KS(0.49)ES(0.436)PKEPEQLRK;S(0.153)KS(0.728)ES(0.119)PKEPEQLRK 51.888 2.74E-06 761160000 1223590 398040 1409970 761190 722210 1291670 2066220 1423590 1027470 TRUE FALSE 1165753.326 438600.7285 1474618.519 684673.735 848163.1953 1246939.144 1750980.19 1298932.913 1186804.8 0.982262058 0.369564337 1.242511422 0.576905094 0.714661076 1.050669111 1.475373364 1.094478985 1 20.17865124 2.074471702 4.334985984 1.247962422 0.754317791 0.341227608 0.260544497 0.187684085 6.798840782 0.096877991 0.068133353 118.7057353 -2.074471702 -0.493644631 (ac)SKSES(ph)PKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSESPKEPEQLR 13 2 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.318)KS(0.318)ES(0.365)PKEPEQLR;SKS(0.002)ES(0.998)PKEPEQLR;SKS(0.001)ES(0.998)PKEPEQLR;S(0.003)KS(0.026)ES(0.972)PKEPEQLR 89.911 1.70E-05 2315040000 2467140 867118 2848050 1647550 1885520 2552050 4074290 2905350 2696940 TRUE FALSE 2350523.182 955478.31 2978635.91 1481935.144 2214354.091 2463671.869 3452682.231 2650942.152 3115167.681 0.754541464 0.306718099 0.956171935 0.475716011 0.710829823 0.790863324 1.108345548 0.850978959 1 21.57087839 2.110630377 2.384016212 0.993727417 0.605800454 0.42432548 0.181310524 0.243704262 2.723323746 0.082389118 0.050409265 129.0120801 -2.110630377 -0.387926963 (ac)SKSES(ph)PKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_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" 1 S(0.087)KS(0.115)ES(0.798)PKEPEQLRK 40.602 1.48E-05 995450000 1401700 511020 1785300 948630 968390 1734100 2719700 1836800 1391300 TRUE FALSE 1335444.419 563093.519 1867157.771 853271.9101 1137276.909 1674047.682 2304759.814 1675960.055 1607055.698 0.83098826 0.350388303 1.161850067 0.530953539 0.707677345 1.041686162 1.43415055 1.042876147 1 20.6159885 2.139007558 3.796871007 1.213001671 0.687404386 0.422853807 0.238146118 0.175360618 4.8126364 0.089649727 0.06371706 137.7233436 -2.139007558 -0.525597284 (ac)SLVIPEKFQHILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLVIPEKFQHILR 13 1 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 ; 63.76 0.00044828 392980000 844920 320520 866350 532380 1250830 706240 1474750 923390 1666010 FALSE TRUE 804982.3061 353181.3524 906073.0044 478864.1509 1468974.356 681782.7317 1249749.802 842533.0764 1924366.322 0.418310327 0.183531248 0.470842268 0.248842513 0.763354845 0.354289474 0.649434459 0.437823644 1 20.87595203 -4.999999998 0.114697803 2.931336893 0.112434127 0.576730346 0.158986877 98.26581855 0.740735836 43.84804906 1.533211682 1.00E-05 4.999999998 -2.818902766 (ac)SQGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;;; 63.901 0.00089307 1141080000 20573.5 16573.5 20424.5 14119.5 26711.4 12939.9 31786.4 19967 34005.7 FALSE TRUE 19601.03143 18262.35849 21360.98353 12700.18103 31369.8597 12491.78802 26936.80088 18218.58363 39279.13028 0.499018977 0.464937955 0.543825267 0.323331523 0.798639366 0.318026085 0.685778954 0.463823499 1 15.26147537 -5 0.25933653 4.139643903 0.474111625 0.525142329 0.145788518 136.298423 1.339494679 227.7286256 0.163429633 1.00E-05 5 -3.665532278 (ac)SQPGQKPAAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR 80.312 0.00022399 612515000 859288 853728 718641 908572 644645 779377 815389 849833 698806 TRUE FALSE 818671.1592 940723.8538 751591.4007 817240.6164 757070.8839 752386.9791 690986.4324 775417.1173 807173.2655 1.014244641 1.165454673 0.931140107 1.012472354 0.937928591 0.932125742 0.856057134 0.960657582 1 19.62251887 3.721341058 24.69273973 0.937687564 1.089849655 0.524065779 0.055949239 437.4393497 627285.4903 0.014951656 0.023225599 5264.305177 -3.721341058 0.152162091 (ac)SQPGQKPAAS(ph)PRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;S(0.003)QPGQKPAAS(0.997)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR 127.32 1.62E-06 49803670000 12498220 10335690 11780880 12251950 9655080 11229530 13165350 12602470 11840270 TRUE FALSE 11907453.91 11388908.56 12321045 11020360.71 11338922.9 10840648.56 11156734.06 11498930.92 13676398.6 0.870657127 0.832741783 0.900898355 0.805794057 0.829086898 0.792653744 0.815765494 0.840786471 1 23.70518504 -0.998911521 7.59779842 1.000000004 0.835246252 0.73303209 0.031091417 2.24E-09 2.95E-10 0.030086001 0.007091338 0.100250946 0.998911521 -0.164753753 (ac)SQQHTLPVT(ph)LSPALSQELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVT(0.591)LS(0.373)PALS(0.036)QELLK 54.805 0.00019209 6491200 18348 15648 17736 20467 14148 19328 20557 20361 16792 TRUE FALSE 17480.7264 17242.54899 18549.21314 18409.61828 16615.40672 18658.66651 17420.65209 18578.0829 19396.0176 0.901253379 0.888973672 0.956341324 0.949144234 0.856640114 0.961984408 0.89815613 0.957829761 1 14.24347285 -4.999999972 0.16255727 1.320822537 0.894706047 0.375438651 0.034005097 132.2225101 1.224047469 13.59521638 0.12705762 1.00E-05 4.999999972 -0.426116489 (ac)SQQHTLPVTLS(ph)PALSQELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVT(0.03)LS(0.949)PALS(0.021)QELLK;SQQHTLPVT(0.137)LS(0.844)PALS(0.018)QELLK 72.21 1.65E-08 57064000 104915 75595 95028 111155 92287 97408 131485 119819 109154 TRUE FALSE 99955.87587 83298.21644 99385.1278 99981.48822 108381.8236 94034.73654 111424.5484 109327.0132 126081.0448 0.792790669 0.660672003 0.788263834 0.792993811 0.859620284 0.745827707 0.883753371 0.867116967 1 16.94399187 1.173437257 0.329985884 1.024073925 0.715551028 0.686159739 0.050662353 0.797855814 0.28090436 0.093391983 0.061565179 14.90861355 -1.173437257 -0.308522897 (ac)SQQHTLPVTLSPALS(ph)QELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVTLS(0.02)PALS(0.979)QELLK;SQQHTLPVT(0.001)LS(0.03)PALS(0.97)QELLK;SQQHTLPVTLS(0.004)PALS(0.996)QELLK 115.63 7.66E-30 72188000 142875 109557 129279 211083 123648 198267 218391 157739 131076 TRUE FALSE 136121.5819 120720.9829 135206.57 189864.5358 145212.1721 191400.9641 185071.4419 143926.5369 151402.5966 0.899070326 0.797350809 0.893026758 1.254037513 0.959112824 1.264185479 1.222379576 0.950621324 1 17.20803042 3.351294438 6.370921274 1.129447655 0.848299013 0.485323039 0.118173176 0.146777466 7.661207607 0.030703549 0.041659062 2245.403723 -3.351294438 -0.281148643 (ac)SS(ph)SPLSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPLSKK 8 1 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 S(0.194)S(0.401)S(0.401)PLS(0.005)KK;S(0.021)S(0.596)S(0.38)PLS(0.004)KK 56.563 0.032528 2702300000 5105200 4013000 4851000 4691100 3165200 5445200 6421600 5733500 4096600 TRUE FALSE 4863887.314 4421929.262 5073423.148 4219541.715 3717209.878 5256631.359 5441866.979 5231444.345 4731879.805 1.027897477 0.934497376 1.072179209 0.891726309 0.785567265 1.110897059 1.150043366 1.105574224 1 22.173982 2.112050385 23.07295849 1.10934961 0.952287587 0.421654732 0.085311244 4.244427028 852.0126478 0.031137757 0.022996765 129.4345996 -2.112050385 -0.157062024 (ac)SS(ph)SPVNVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.128)S(0.503)S(0.37)PVNVKK;S(0.113)S(0.444)S(0.444)PVNVKK;S(0.128)S(0.503)S(0.37)PVNVKK;S(0.11)S(0.445)S(0.445)PVNVKK 47.938 0.017465 20953100000 14372300 12198200 13669500 14315900 9690900 15072300 17112900 15312700 11904500 TRUE FALSE 13692949.86 13441210.45 14296260.1 12876838.53 11380989.89 14550342.47 14502012.81 13971838.81 13750589.06 0.995808238 0.977500701 1.039683466 0.936457229 0.827672898 1.058161393 1.054646659 1.016090202 1 23.71299009 (ac)SSEPPPPPQPPTHQASVGLLDTPRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSEPPPPPQPPTHQASVGLLDTPRSR 26 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 SSEPPPPPQPPT(0.031)HQAS(0.027)VGLLDT(0.103)PRS(0.839)R 48.798 0.0061968 171800000 2440.2 1467.2 2902.1 2949.6 1989.3 2716.5 2613.3 1387.9 2810 TRUE FALSE 2324.856582 1616.709348 3035.164156 2653.100604 2336.23329 2622.426924 2214.593088 1266.368118 3245.760449 0.716274851 0.498098789 0.935116502 0.817404934 0.719779949 0.80795455 0.682303307 0.390160684 1 11.66434081 3.758937995 24.97704187 0.750501358 0.607186842 0.12370087 0.17105876 1645.271898 2016643.065 0.041336376 0.074413307 5740.345004 -3.758937995 -0.143314516 (ac)SSILPFT(ph)PPVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.009)S(0.009)ILPFT(0.982)PPVVK 44.318 0.027387 21238000 113850 124520 105210 129320 98538 118100 124970 129770 109640 TRUE FALSE 108468.5361 137208.7296 110033.9826 116320.5079 115722.996 114010.1674 105903.5313 118406.6508 126642.4112 0.856494559 1.083434279 0.868855713 0.918495682 0.91377758 0.900252658 0.836240642 0.934968386 1 16.9504011 (ac)SSILPFT(ph)PPVVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSILPFTPPVVKR 13 1 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(0.99)PPVVKR;S(0.002)S(0.002)ILPFT(0.996)PPVVKR;S(0.005)S(0.005)ILPFT(0.99)PPVVKR 59.871 0.0021418 207048000 539560 329001 555830 466990 550860 543620 718700 597510 732310 TRUE FALSE 514056.0681 362526.5759 581315.3553 420047.278 646929.8096 524794.3031 609049.1152 545188.8568 845872.8947 0.607722592 0.428582803 0.687237242 0.496584393 0.764807353 0.620417449 0.72002439 0.644528108 1 19.69008137 -5 0.119419482 2.327567154 0.410615733 0.661765067 0.090020253 79.67947388 0.617827881 25.30378991 0.775441444 1.00E-05 5 -1.916951421 (ac)SSS(ph)PVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.109)S(0.109)S(0.781)PVKR 61.999 0.044447 29677000000 15655000 13086000 12835000 14887000 11789000 15089000 17613000 16102000 13304000 TRUE FALSE 14915019.18 14419478.28 13423497.45 13390530.48 13844997.87 14566464.15 14925813.37 14692023.52 15367116.37 0.970580219 0.938333382 0.873520908 0.871375615 0.900949634 0.947898343 0.97128264 0.956068996 1 23.87334313 1.997037752 3.497095528 0.971313224 0.916721215 0.472246478 0.031002428 0.288152935 7.241934461 0.016569045 0.010088769 99.32023809 -1.997037752 -0.054592009 (ac)SSS(ph)PVNVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(0.051)S(0.2)S(0.75)PVNVKK;S(0.015)S(0.061)S(0.924)PVNVKK;S(0.313)S(0.313)S(0.373)PVNVKK 59.757 0.022271 56221900000 39119800 32497400 36678800 38928200 25658400 40451900 46207800 41241200 31220400 TRUE FALSE 37270684.58 35808922.01 38360559.26 35015063.38 30133216.84 39051040.56 39157951.45 37629901.89 36061900.18 1.033519709 0.992984891 1.06374204 0.970971114 0.835597034 1.082889154 1.085853803 1.04348084 1 25.10397208 (ac)STNENANT(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STNENANTPAAR 12 0 P52292;J3QLL0;J3KS65;J3QL07 P52292 KPNA2 Importin subunit alpha-1 1 STNENANT(1)PAAR 51.927 0.00058209 16429000 9888.3 10366 9753 11067 11715 10350 10253 12930 15075 TRUE FALSE 9420.899656 11422.30719 10200.1847 9954.524134 13758.09229 9991.576905 8688.716541 11797.78065 17412.75401 0.541034442 0.655973615 0.585788135 0.571680053 0.790115813 0.573807963 0.498985774 0.677536744 1 14.08785678 0.972526169 22.7428566 1.000000003 0.601042461 0.717647296 0.077902544 470.262745 389284.8621 0.073664045 0.018416011 9.386985977 -0.972526169 -0.398957542 (ac)SVCTLSVPVS(ph)SLSPGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVCTLSVPVSSLSPGRR 17 1 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SVCTLS(0.003)VPVS(0.376)S(0.376)LS(0.244)PGRR 55.656 0.0013755 35764000 15760 9509.2 14244 14857 8975.5 15885 15635 12095 24378 TRUE FALSE 15015.05603 10478.19829 14897.10149 13363.54613 10540.82436 15334.89847 13249.59359 11035.89768 28158.41573 0.533235114 0.372116045 0.529046152 0.474584446 0.374340107 0.544593794 0.470537608 0.391921825 1 14.78127855 -1.544100081 3.122191228 1.020293855 0.461809696 0.873682744 0.064373135 30488026.23 36070068.16 5217759.701 0.014301372 0.028569321 1.544100081 -0.558484159 (ac)SYGRPPPDVEGMTSLKVDNLT(ph)YRTSPDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLR 30 3 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.003)Y(0.003)GRPPPDVEGMTSLKVDNLT(0.894)YRT(0.081)S(0.016)PDT(0.003)LR;SYGRPPPDVEGMT(0.009)S(0.009)LKVDNLT(0.362)Y(0.036)RT(0.309)S(0.265)PDT(0.01)LR 99.774 1.14E-34 1015760000 648320 259651 698430 443680 733850 587510 1006380 719520 1001040 TRUE FALSE 617675.1984 286109.7321 730453.7063 399080.4435 861833.2077 567164.3814 852838.2476 656515.0144 1156276.171 0.534193486 0.247440654 0.631729447 0.345142842 0.74535239 0.490509444 0.737573141 0.567783918 1 20.14105459 0.409196561 0.220190446 1.189336541 0.323313948 0.554585834 0.141846218 3.681235889 0.419192256 0.953460706 0.365111238 2.565644981 -0.409196561 -0.866022593 (ac)SYGRPPPDVEGMTSLKVDNLTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYGRPPPDVEGMTSLKVDNLTYR 23 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ; 115.54 3.20E-36 312860000 297230 191093 288480 251450 316320 283670 431780 336620 407170 FALSE TRUE 283180.527 210565.594 301707.0933 226173.7683 371486.1078 273846.4368 365904.0308 307143.7683 470311.8441 0.602112259 0.447714844 0.641504349 0.480901706 0.789871896 0.582265661 0.778003011 0.653064073 1 18.84325814 0.218011498 0.229714619 1.15712574 0.47094162 0.649495245 0.095294634 3.413539395 0.360925804 0.670352542 0.209753341 1.652005536 -0.218011498 -0.68618412 (ac)SYGRPPPDVEGMTSLKVDNLTYRTS(ph)PDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLR 30 3 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 SYGRPPPDVEGMTSLKVDNLT(0.1)Y(0.001)RT(0.401)S(0.469)PDT(0.028)LR;SYGRPPPDVEGMT(0.005)S(0.005)LKVDNLT(0.217)YRT(0.196)S(0.554)PDT(0.023)LR;SYGRPPPDVEGMTS(0.003)LKVDNLT(0.024)YRT(0.231)S(0.736)PDT(0.005)LR;SYGRPPPDVEGMT(0.001)S(0.001)LKVDNLT(0.051)Y(0.02)RT(0.213)S(0.65)PDT(0.065)LR;SYGRPPPDVEGMT(0.003)S(0.007)LKVDNLT(0.127)Y(0.027)RT(0.296)S(0.528)PDT(0.011)LR;SYGRPPPDVEGMT(0.001)S(0.005)LKVDNLT(0.015)Y(0.004)RT(0.208)S(0.723)PDT(0.044)LR;SYGRPPPDVEGMT(0.001)S(0.002)LKVDNLT(0.029)Y(0.002)RT(0.279)S(0.686)PDT(0.002)LR 72.792 7.04E-13 3773840000 1461226 636404 1673860 1044372 1686870 1371201 2217080 1488575 2483900 TRUE FALSE 1392156.743 701254.2911 1750608.137 939389.7424 1981059.594 1323715.966 1878823.727 1358227.482 2869090.526 0.485225799 0.244416928 0.610161346 0.327417254 0.690483474 0.461371279 0.654849929 0.473400009 1 21.45216206 -4.999999987 0.134456896 2.800056423 0.27498338 0.605511386 0.132028708 81.87061802 0.685628489 39.35226415 0.794404693 1.00E-05 4.999999987 -2.525073043 (ac)T(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.667)T(0.667)S(0.667)QKHRDFVAEPMGEKPVGSLAGIGEVLGK;T(0.781)T(0.88)S(0.331)QKHRDFVAEPMGEKPVGS(0.008)LAGIGEVLGK 75.717 1.08E-12 1279560000 666000 637840 1019580 646000 459870 953640 942360 877460 652710 TRUE FALSE 634519.4999 702836.6212 1066328.752 581062.8527 540071.1824 920615.2077 798585.6744 800624.9507 753928.9332 0.841617123 0.932231926 1.414362421 0.77071303 0.716342295 1.221090168 1.05923203 1.061936895 1 19.52406901 2.212978822 24.9999496 1.091814369 0.940490961 0.128103761 0.194525681 495.7963427 484516.5742 0.072225459 0.053361018 163.2972317 -2.212978822 -0.151323407 (ac)T(ph)TS(ph)QKHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.572)T(0.479)S(0.949)QKHR 44.135 0.037206 172760000 67524 102590 81259 95936 61561 87235 80112 84231 79540 TRUE FALSE 64332.27434 113044.0376 84984.80553 86292.33101 72297.21891 84214.03008 67889.44304 76855.2871 91874.65697 0.700217845 1.230415888 0.92500814 0.939239763 0.786911443 0.916618716 0.738935472 0.836523255 1 16.48737934 2.933988214 3.308175533 0.836731641 0.973584226 0.076179135 0.144781972 0.457160637 9.819840404 0.043957082 0.048675868 858.9902088 -2.933988214 0.136852585 (ac)TDRYTIHSQLEHLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDRYTIHSQLEHLQSK 16 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 81.632 1.98E-13 152440000 224990 131770 219930 201010 242960 200380 297010 234380 47180 FALSE TRUE 214355.1686 145197.5128 230014.008 180804.0929 285332.1471 193440.7904 251695.6695 213856.4447 54496.43344 3.933379766 2.664348906 4.220716725 3.317723409 5.235794878 3.549604592 4.618571412 3.924228269 1 15.73387419 3.717366224 24.78043959 3.92401044 3.298864166 0 1.162088586 1975.783362 2310081.853 0.269209316 0.417536921 5216.344006 -3.717366224 -0.625146274 (ac)TECFLPPT(ph)SSPSEHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TECFLPPTSSPSEHRR 16 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.351)S(0.351)S(0.249)PS(0.048)EHRR 81.723 9.84E-05 71896000 8314.7 7400.4 6981.1 10789 10220 6151.3 8367.8 11779 31982 TRUE FALSE 7921.680609 8154.509174 7301.19034 9704.469222 12002.36476 5938.278939 7091.138425 10747.56832 36941.60522 0.21443791 0.220740521 0.197641394 0.262697551 0.324901008 0.160747723 0.191955341 0.290933982 1 15.17295894 0.757596174 4.187414424 0.999995497 0.223214177 0.967727632 0.044176643 0.630554598 10.76085921 0.042533438 0.010837488 5.722636678 -0.757596174 -0.77678132 (ac)TECFLPPTSS(ph)PSEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.036)S(0.145)S(0.614)PS(0.205)EHR;TECFLPPT(0.05)S(0.348)S(0.508)PS(0.094)EHR;TECFLPPT(0.177)S(0.177)S(0.515)PS(0.131)EHR 64.675 0.00038152 511740000 106829 91791 106321 103176 125051 96235 141737 112353 148090 TRUE FALSE 101779.4049 101144.6073 111195.923 92804.55246 146859.8548 92902.35782 120112.4175 102514.7757 171055.0409 0.595009679 0.591298606 0.650059317 0.54254205 0.858553212 0.543113827 0.702185781 0.599308709 1 17.38410109 -5 0.262428607 3.393606645 0.604706172 0.604000505 0.092567634 122.940378 1.204298099 158.8923284 0.105265329 1.00E-05 5 -2.788900473 (ac)TEKAPEPHVEEDDDDELDSKLNYKPPPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEKAPEPHVEEDDDDELDSKLNYKPPPQK 29 3 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 71.974 0.00018034 135970000 88549 59257 81455 77665 68747 99485 113780 103500 84278 FALSE TRUE 84363.46426 65295.35567 85189.79232 69857.96665 80736.45503 96039.8095 96420.77129 94436.99131 97347.40181 0.86662266 0.670745746 0.875111105 0.717615112 0.829364251 0.986567774 0.990481199 0.970102844 1 16.57085485 2.314689066 3.778657352 0.987931854 0.777966226 0.720921629 0.060741691 0.107967645 3.031502927 0.020672496 0.016537182 206.3901973 -2.314689066 -0.209965628 (ac)TT(ph)SQKHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 T(0.029)T(0.646)S(0.325)QKHR;T(0.027)T(0.598)S(0.375)QKHR 57.598 0.015658 1553960000 789560 425538 602890 662290 721500 608290 979410 873280 974840 TRUE FALSE 752239.0636 468900.806 630533.1028 595715.3509 847329.3716 587224.7648 829983.0164 796810.9737 1126013.208 0.668055275 0.416425671 0.559969544 0.52904828 0.752503936 0.521507883 0.737098828 0.7076391 1 20.10279232 0.706825703 0.455202055 1.025015996 0.533135101 0.680205354 0.091930903 0.846495848 0.383832287 0.132329466 0.052591858 5.091265001 -0.706825703 -0.491880895 (ac)TT(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 T(0.038)T(0.48)S(0.48)QKHRDFVAEPMGEKPVGS(0.001)LAGIGEVLGK 60.728 5.38E-05 216460000 180500 110850 275330 158410 174090 202570 391560 243870 257410 TRUE FALSE 171968.1227 122145.741 287954.1528 142486.3258 204451.2409 195554.9501 331820.3305 222515.45 297327.8281 0.578378835 0.410811668 0.968473603 0.479222973 0.687629013 0.657708198 1.116008322 0.748384204 1 18.18169497 1.868226171 6.19776109 0.957411085 0.606546344 0.442198324 0.171261086 0.197204801 8.94969444 0.071614845 0.043367409 73.82886146 -1.868226171 -0.350864741 (ac)TTS(ph)QKHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 T(0.004)T(0.091)S(0.905)QKHR 67.563 0.026053 1440900000 1208200 582540 954920 1049500 1005300 894520 1499300 1403500 1475900 TRUE FALSE 1151090.78 641901.4883 998704.0265 944002.2661 1180624.002 863542.5481 1270554.248 1280602.1 1704775.034 0.675215649 0.376531493 0.585827459 0.553740081 0.692539472 0.506543404 0.745291445 0.75118539 1 20.70114994 1.010021282 0.620434094 1.005937415 0.533394164 0.696520605 0.09233903 0.428589394 0.393263615 0.088096433 0.03751017 10.23343138 -1.010021282 -0.472543251 (ac)VDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.001)S(0.001)VWDHIEVS(0.999)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.999)DDEDETHPNIDTASLFR;VDY(0.004)S(0.004)VWDHIEVS(0.986)DDEDET(0.006)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.995)DDEDET(0.005)HPNIDTASLFR;VDY(0.001)S(0.001)VWDHIEVS(0.998)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.996)DDEDET(0.004)HPNIDTASLFR;VDY(0.101)S(0.111)VWDHIEVS(0.786)DDEDET(0.002)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR 193.03 1.56E-92 1526271000 217717.6 186518.59 200638.8 205975.9 201174.6 205107.4 241419.9 205750 229719.7 TRUE FALSE 207426.5205 205525.0464 209838.2874 185270.8112 236259.3865 198004.4793 204586.8603 187733.4393 265343.4578 0.781728414 0.774562328 0.790817641 0.698230183 0.890390848 0.746219564 0.771026585 0.707511091 1 18.01750145 -1.497113849 5.79098736 1.000278979 0.772081618 0.654967569 0.052430561 0.000165647 1.44E-05 0.044528967 0.010482893 0.031833629 1.497113849 -0.228197361 (ac)VNPTVFFDIAVDGEPLGR ddPTM_SK-BR-3_Trastuzumab_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 ; 65.563 0.0012678 183007000 3578.9 6073.3 4866.2 4562.8 3189.4 4248.3 5263.9 3464.7 4996.7 FALSE TRUE 3409.73249 6692.176175 5089.320083 4104.138675 3745.63035 4101.180306 4460.795377 3161.3125 5771.562716 0.590781502 1.159508525 0.88179239 0.711096609 0.648980273 0.710584032 0.772892126 0.547739435 1 12.49474628 3.257638303 6.989636015 0.71896041 0.897732727 0.125783819 0.17611662 0.260346902 52.3966695 0.04654307 0.061247601 1809.832169 -3.257638303 0.178772317 (ac)VSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VSVINTVDTSHEDMIHDAQMDYYGTR 26 0 P55735 P55735 SEC13 Protein SEC13 homolog 0 ;;; 152.35 6.89E-53 263446000 21769.6 18582.7 25431 30305.7 20904.4 21778.6 31452.8 26213.5 28193.8 FALSE TRUE 20740.59415 20476.29826 26597.0365 27259.31346 24550.12074 21024.40162 26654.09769 23918.10697 32565.95051 0.636879742 0.628764029 0.816713042 0.837049527 0.753858566 0.645594595 0.818465215 0.73445137 1 14.99107672 -5 0.097836569 1.837087281 0.537663895 0.569444032 0.074564666 141.2863819 0.945000122 24.51215337 1.377697165 1.00E-05 5 -1.299423385 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 AAAAAATAPPS(1)PGPAQPGPR;AAAAAATAPPS(1)PGPAQPGPR 351.47 4.16E-95 456010000 422770 411550 447780 493060 478730 435820 522870 484970 587780 TRUE FALSE 402786.4999 453487.4129 468311.1559 443496.672 562220.3604 420727.4441 443096.5783 442503.4558 678929.9204 0.59326668 0.667944363 0.689778344 0.65322894 0.828097781 0.619692006 0.652639639 0.651766025 1 19.37290314 -1.82199066 2.523014588 1.118585091 0.666440274 0.735933938 0.062182692 7517453.703 4751776.427 5409734.142 0.014395795 0.015066395 1.82199066 -0.452144817 AAAAPGAS(ph)PSPGGDAAWSEAGPGPRPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.5)PS(0.5)PGGDAAWS(0.001)EAGPGPRPLAR;AAAAPGAS(0.947)PS(0.053)PGGDAAWSEAGPGPRPLAR 113.33 7.12E-11 0 72470 67338 86257 77786 84696 78124 84194 78264 98011 TRUE FALSE 69044.48672 74199.81876 90211.96877 69966.8035 99466.95558 75418.54629 71348.65897 71410.78926 113210.0453 0.609879508 0.655417269 0.796854807 0.61802646 0.878605386 0.666182458 0.63023258 0.630781386 1 16.78864245 -1.926847983 2.46612777 1.210615416 0.680897003 0.564869498 0.086586632 8384746.487 4522388.919 10188381.65 0.01988428 0.011834557 1.926847983 -0.529718413 AAAAPGASPS(ph)PGGDAAWSEAGPGPRPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.118)PS(0.882)PGGDAAWSEAGPGPRPLAR;AAAAPGAS(0.077)PS(0.923)PGGDAAWSEAGPGPRPLAR 173.04 9.40E-13 285450000 124576 98437 124696 133300 137669 113895 157183 128353 205910 TRUE FALSE 118687.5394 108467.8422 130413.4349 119900.4307 161678.43 109950.7876 133201.8465 117113.7309 237841.4712 0.499019531 0.456051006 0.548320839 0.50411911 0.679773923 0.462286022 0.560044663 0.492402483 1 17.85964077 -5 0.379695257 7.722078082 0.510459683 0.840522134 0.064794583 210.9476585 1.578067854 1167.617982 0.040539958 1.00E-05 5 -7.211618399 AAAEEGHIIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAAEEGHIIPR 11 0 X6R5A3;O95551-3;O95551;O95551-2 X6R5A3 TDP2 Tyrosyl-DNA phosphodiesterase 2 0 141.71 3.80E-05 116780000 113350 104290 99970 97505 149560 104090 133870 117880 143720 FALSE TRUE 107992.1701 114917.2696 104553.7234 87703.61215 175643.2166 100485.3372 113445.6728 107557.8023 166007.3636 0.650526385 0.692242001 0.629813769 0.528311578 1.058044733 0.605306506 0.683377354 0.647909827 1 17.34088771 -1.33530145 2.809090566 1.004257026 0.686026341 0.331447137 0.139724312 10375159.93 12262951.7 366055.5752 0.032081678 0.046206019 1.33530145 -0.318230685 AAAFQVAPHSHGEEAVAQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAAFQVAPHSHGEEAVAQDR 20 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 123.14 1.69E-05 148980000 134060 141990 119590 160810 111350 133960 125730 128510 70722 FALSE TRUE 127723.2495 156458.9424 125073.3198 144645.0733 130769.4047 129320.9316 106547.5793 117256.9831 81689.20656 1.563526626 1.915295166 1.53108746 1.770675458 1.600816194 1.583084682 1.30430425 1.435403624 1 16.31785785 1.274166392 0.574420831 1.006514712 1.734223521 0.750304099 0.124159975 0.331853511 0.273293065 0.115274339 0.056676217 18.80036982 -1.274166392 0.727708809 AAAIGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 336.06 6.02E-81 317979000 684053 573523 639120 690446 619022 608670 787137 699757 687936 FALSE TRUE 651719.1704 631965.6457 668424.2842 621041.0563 726979.2408 587591.6053 667044.7939 638482.5674 794617.6014 0.820167045 0.795307887 0.841189879 0.781559652 0.914879358 0.739464623 0.839453836 0.803509218 1 19.59990123 -1.092099407 4.647186014 1.000011104 0.816064241 0.615472472 0.045468126 4.43E-06 8.65E-07 0.03725389 0.008780296 0.080891072 1.092099407 -0.183946863 AAALEFLNRFEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAALEFLNRFEEAK 14 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 173.44 2.46E-06 188152000 389130 325100 354560 404440 319320 376960 444750 426110 321160 FALSE TRUE 370736.5961 358228.0596 370816.9267 363784.9228 375009.3069 363905.7807 376895.2191 388797.5494 370963.8525 0.999387389 0.965668372 0.999603935 0.9806479 1.010905252 0.980973694 1.015989069 1.048073948 1 18.50091909 1.606696766 4.596873865 1.026324474 0.988485828 0.441813267 0.016892899 0.121981312 5.721999115 0.008723772 0.003974772 40.42935068 -1.606696766 -0.037838646 AAALEFLNRFEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAALEFLNRFEEAKR 15 2 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 214.53 1.38E-12 343920000 574770 341733 543640 473880 575060 516470 765900 643410 720970 FALSE TRUE 547601.7612 376555.9812 568566.4317 426244.6821 675350.2819 498584.5144 649047.8883 587069.6095 832774.3454 0.657563197 0.452170487 0.682737689 0.511836951 0.810964321 0.598703019 0.779380263 0.704956406 1 19.6675661 0.548339362 0.287198841 1.081849186 0.531273748 0.60790771 0.097157647 1.966915286 0.369259987 0.344619522 0.130615793 3.534592584 -0.548339362 -0.550575438 AAAPRPPVSAASGRPQDDTDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAAPRPPVSAASGRPQDDTDSSR 23 2 Q8TF74 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ;;; 207.13 7.02E-25 864808000 383285 345521 378124 394931 412614 345031 445238 401328 494711 FALSE TRUE 365167.8776 380729.9827 395461.3594 355231.7856 484573.751 333082.49 377308.7657 366185.5927 571428.2552 0.639044139 0.666277838 0.692057762 0.621655969 0.848004533 0.58289468 0.660290705 0.640825142 1 19.12421285 -1.681019445 2.746414026 1.044254077 0.667135031 0.688759377 0.069943303 16790990.02 14798937.42 5182479.001 0.015054271 0.020843976 1.681019445 -0.377119046 AAAS(ph)SPVTTLTQTMHDLAGLGSETPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAASSPVTTLTQTMHDLAGLGSETPK 26 0 P30305;P30305-3 P30305 CDC25B M-phase inducer phosphatase 2 1 AAAS(0.462)S(0.462)PVT(0.006)T(0.006)LT(0.054)QT(0.008)MHDLAGLGSETPK 145.29 1.47E-07 51089000 61431 48315 64532 69276 53205 68213 75280 74125 59803 TRUE FALSE 58527.27837 53238.35343 67490.85603 62312.24486 62483.93515 65850.76671 63794.65339 67634.22204 69076.94381 0.847276604 0.770710899 0.977038825 0.902070089 0.904555583 0.953295891 0.92353034 0.979114279 1 16.07591663 3.906941314 0.320682811 0.990682102 0.72612938 0.530944787 0.046980011 2.868287463 0.35774111 0.051336688 0.284499125 8071.259557 -3.906941314 -0.264552722 AAAT(ph)PAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAATPAKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAAT(1)PAKK;AAAT(1)PAKK 71.349 0.028698 1193400000 3850300 4982500 4555400 5471000 2460000 4622900 5125700 7264800 3946500 TRUE FALSE 3668303.95 5490222.415 4764269.596 4921044.686 2889023.221 4462807.814 4343680.325 6628655.599 4558503.064 0.804716789 1.204391516 1.045139057 1.07953085 0.633765774 0.979007308 0.95287428 1.454129899 1 22.12012871 1.278549035 24.99853182 1.22706565 0.968035562 0.262575835 0.187414254 177.1712486 110757.4495 0.117214996 0.042802086 18.99105251 -1.278549035 -0.259030089 AAAT(ph)PESQEPQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 AAAT(0.997)PES(0.003)QEPQAK 249.82 1.35E-16 470580000 541480 448340 515650 576050 448030 567910 640680 578340 500810 TRUE FALSE 515885.3135 494026.3557 539293.0625 518144.3596 526166.2901 548243.1343 542932.4991 527697.4836 578473.057 0.891805257 0.854017918 0.932269975 0.895710445 0.909577868 0.947741866 0.938561429 0.912224826 1 19.14189024 -4.999590406 0.028780221 1.620415432 0.486620324 0.674394657 0.022158745 782.6607991 1.696579268 51.20184944 21.52304735 1.00E-05 4.999590406 -1.133795108 AAATGNAS(ph)PGKLEHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAATGNASPGKLEHSK 16 1 H0Y6H0;Q8NB78 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AAATGNAS(1)PGKLEHSK;AAAT(0.001)GNAS(0.999)PGKLEHSK;AAATGNAS(0.995)PGKLEHS(0.005)K;AAATGNAS(1)PGKLEHSK 156.15 1.16E-07 881590000 1177170 1098420 1099630 1274060 743782 1291490 1265020 1370430 837714 TRUE FALSE 1121527.507 1210350.247 1150049.123 1145989.068 873497.3453 1246765.377 1072017.965 1250427.884 967622.4087 1.159054913 1.250849749 1.188530891 1.184334982 0.90272542 1.288483365 1.107888734 1.292268423 1 19.88408465 -2.339189999 2.258049668 7.29E-05 1.171419628 0.190465656 0.111286787 2844007.617 454514.5074 14636820.94 0.024329605 0.004579415 2.339189999 1.1713467 AAATQPDAKDTPDEPWAFPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAATQPDAKDTPDEPWAFPAR 21 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 84.499 0.0024159 0 57907 50832 86341 69052 52803 73756 82424 55595 46780 FALSE TRUE 55169.85087 56011.83859 90299.82025 62110.76177 62011.82648 71201.81123 69848.70498 50726.80707 54034.40348 1.021013416 1.036595853 1.671154199 1.149466965 1.147635996 1.317712543 1.292670974 0.938787213 1 15.72159064 -0.710890953 6.993215089 1 1.195928591 0.083799204 0.204565823 0 0 0.193894765 0.045701435 0.194584861 0.710890953 0.195928591 AAAYDIS(ph)EDEED ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAAYDISEDEED 12 0 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 AAAYDIS(1)EDEED;AAAYDIS(1)EDEED 377.14 7.48E-87 1386860000 1233680 1082360 1053350 1247820 1105020 1094990 1202470 1129430 1163100 TRUE FALSE 1175366.391 1192653.715 1101647.139 1122386.763 1297735.138 1057070.222 1019011.117 1030531.122 1343467.608 0.874875125 0.887742814 0.820002755 0.835440137 0.965959381 0.786822262 0.758493253 0.767068082 1 20.35753011 AAAYNLVQHGITNLCVIGGDGSLTGANIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAAYNLVQHGITNLCVIGGDGSLTGANIFR 30 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 221.29 3.46E-45 0 47981 52168 51088 54678 49815 48061 49388 55132 45995 FALSE TRUE 45713.03322 57483.97851 53430.43533 49181.66356 58502.72023 46396.63552 41852.95353 50304.34981 53127.66969 0.860437386 1.081996987 1.005698832 0.92572597 1.101172338 0.873304547 0.787780713 0.946857826 1 15.69717581 2.182573836 24.65622012 0.873566136 0.991972054 0.184252064 0.088583878 91.63838164 40356.07669 0.031257387 0.023085126 152.2557967 -2.182573836 0.118405917 AADAEAEVASLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 236.92 4.49E-17 821910000 578230 375550 522320 524910 599210 533510 638670 595130 691130 FALSE TRUE 550898.2138 413818.972 546268.8886 472145.0495 703712.0343 515034.4149 541229.1615 543017.2622 798306.9106 0.690083233 0.518370775 0.684284304 0.591432998 0.881505628 0.645158407 0.677971284 0.680211151 1 19.60658397 -5 0.194552003 2.492991155 0.602668364 0.57142392 0.090349227 95.50279367 0.939306098 55.28835952 0.218085363 1.00E-05 5 -1.890322792 AADCEVEQWDSDEPIPAKELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AADCEVEQWDSDEPIPAKELER 22 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 ; 225.05 5.83E-26 391430000 334110 160147 311740 257810 317510 305350 420400 350680 415950 FALSE TRUE 318317.2824 176466.1614 326033.5874 231894.449 372883.6435 294775.6529 356260.2588 319972.6001 480453.4016 0.662535183 0.367290898 0.678595648 0.482657524 0.776107823 0.613536405 0.741508454 0.665980507 1 18.87403699 0.323286708 0.260033155 1.120101527 0.488689338 0.572250625 0.110119593 3.090902901 0.422066131 0.583106598 0.185139556 2.105167751 -0.323286708 -0.631412189 AADEEAFEDNSEEYIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AADEEAFEDNSEEYIRR 17 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 342.97 1.31E-72 4160240000 1249470 899900 1306030 1262640 1386470 1252040 1635680 1469060 1707870 FALSE TRUE 1190410.029 991600.8331 1365912.767 1135717.028 1628269.929 1208681.541 1386126.975 1340421.318 1972717.757 0.603436566 0.502657225 0.692401517 0.57571187 0.825394268 0.612698667 0.7026484 0.679479522 1 20.91175313 -5 0.129430083 2.223270599 0.483515998 0.682546718 0.078859821 75.41168037 0.616753492 23.86447064 0.553652298 1.00E-05 5 -1.739754601 AADESER ddPTM_SK-BR-3_Trastuzumab_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 295970000 373490 345510 302640 420710 307710 310040 316770 426490 414760 FALSE TRUE 355835.8679 380717.8618 316516.3434 378419.4315 361374.5266 299303.2371 268440.9186 389144.2746 479078.8625 0.742750089 0.794687246 0.660676912 0.789889643 0.754311148 0.624747323 0.560327202 0.812276026 1 18.86990364 0.989864069 24.41044299 1.00000001 0.706083028 0.626225985 0.073383811 250.0786302 602268.3731 0.080055931 0.020013983 9.769314016 -0.989864069 -0.293916982 AADIS(ph)LDNLVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK 167.71 3.30E-05 66135000 161228 176301 163666 208068 135519 187617 200290 195781 172213 TRUE FALSE 153607.072 194266.2723 171170.248 187152.6093 159153.4707 181119.7762 169732.0819 178637.3777 198918.9125 0.77220949 0.976610368 0.860502633 0.940848746 0.800092202 0.910520644 0.853272722 0.898041194 1 17.60182092 0.963421012 18.67224739 1.000000003 0.876907838 0.29883596 0.060414302 214.3152264 109401.9409 0.052288388 0.013072097 9.192232747 -0.963421012 -0.123092165 AADKLIQNLDANHDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;; 276.67 1.59E-35 9053110000 11805590 8679030 12156830 10959560 11922810 10670040 14597500 12941760 13628530 FALSE TRUE 11247563.16 9563433.024 12714232.68 9857884.207 14002144.29 10300533.84 12370383.27 11808510.89 15741972.83 0.714495145 0.607511722 0.807664504 0.626216569 0.889478367 0.654335638 0.785821663 0.750129035 1 23.90811302 -5 0.15898799 2.050349992 0.643348526 0.523116558 0.083563731 92.04513598 0.84361845 30.3688071 0.312774776 1.00E-05 5 -1.407001466 AADPPAENSS(ph)APEAEQGGAE ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 AADPPAENS(0.066)S(0.934)APEAEQGGAE;AADPPAENS(0.113)S(0.887)APEAEQGGAE 302.02 6.58E-55 721840000 466560 391060 444460 475730 507310 479430 536600 498300 530340 TRUE FALSE 444506.6334 430909.4586 464838.9306 427908.7166 595784.7034 462827.2189 454731.8147 454666.2103 612582.4186 0.725627475 0.703430992 0.758818596 0.698532481 0.972578849 0.75553461 0.742319402 0.742212307 1 19.22454444 -5 0.218655868 2.197980063 0.726256616 0.477659629 0.077744772 133.0425948 1.330034167 70.37843086 0.146306336 1.00E-05 5 -1.471723448 AADRLPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.173)S(0.501)PS(0.326)AEGPPGPPSGPAPR;AADRLPNLS(0.096)S(0.809)PS(0.096)AEGPPGPPSGPAPR;AADRLPNLS(0.445)S(0.524)PS(0.031)AEGPPGPPSGPAPR;AADRLPNLS(0.186)S(0.626)PS(0.189)AEGPPGPPSGPAPR;AADRLPNLS(0.074)S(0.911)PS(0.015)AEGPPGPPSGPAPR 178.06 1.51E-17 4431430000 836118 616138 745824 788349 791666 737256 853804 787245 795805 TRUE FALSE 796596.3592 678923.1627 780020.7681 709102.6608 929732.2997 711724.6399 723540.5186 718309.6544 919214.375 0.866605637 0.738590672 0.848573292 0.77142251 1.011442298 0.774274923 0.787129247 0.781438665 1 19.81004183 -0.917500922 4.19288385 1.000005092 0.818002462 0.34294881 0.077023736 3883946.865 1852709.956 173.0825636 0.016744945 0.120920262 0.917500922 -0.18200263 AADS(ph)DDGAVSAPAASDGGVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AADSDDGAVSAPAASDGGVSK 21 0 Q96GM8 Q96GM8 TOE1 Target of EGR1 protein 1 1 AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK 428.65 5.63E-174 1366630000 2263970 2070050 2203190 2510880 1693480 2400670 2764410 2571340 1993140 TRUE FALSE 2156956.625 2280990.448 2304208.441 2258481.572 1988822.376 2317534.196 2342648.483 2346179.838 2302225.972 0.936900483 0.990776091 1.00086111 0.980999085 0.863869316 1.006649314 1.017558012 1.019091899 1 21.13459802 2.033266464 24.99989155 1.013651761 0.959113595 0.347147992 0.038035747 216.3890927 162616.3137 0.014043552 0.010371821 107.9608919 -2.033266464 -0.054538167 AADTEEMDIEMDS(ph)GDEA ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AADTEEMDIEMDSGDEA 17 0 Q9UBB5 Q9UBB5 MBD2 Methyl-CpG-binding domain protein 2 1 AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA 392.51 3.58E-122 848601000 1730914 1447425 1612923 1758685 1725734 1569646 1915451 1753813 1951154 TRUE FALSE 1649097.126 1594919.253 1686877.115 1581898.643 2026701.463 1515288.765 1623213.77 1600239.836 2253728.997 0.731719354 0.70768014 0.748482678 0.701902777 0.899265824 0.672347371 0.720234674 0.710040931 1 21.10388262 -1.466600166 3.322078902 1.004497448 0.733896094 0.645882802 0.061300219 172935155.8 287964018 7541295.15 0.013566331 0.034150718 1.466600166 -0.270601353 AAEACARPHGPPPDLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAEACARPHGPPPDLAAR 18 1 Q3KQV9;A0A087X226 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ;; 119.38 4.54E-05 454120000 362380 322922 326866 374802 394570 327665 372820 336739 384770 FALSE TRUE 345251.0156 355828.1189 341853.1294 337126.1909 463382.8831 316317.8789 315939.4617 307252.348 444438.1665 0.776825758 0.800624577 0.769180406 0.758544644 1.042626214 0.711725281 0.71087383 0.691327548 1 18.76162319 -0.547778795 7.312094135 1.00000134 0.782106494 0.324806397 0.098450213 0 0 0.09218448 0.02172809 0.283283451 0.547778795 -0.217894846 AAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AAEAHVDAHYYEQNEQPTGTCAACITGDNR 30 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ;;;; 310.65 1.81E-92 793750000 265769 262355 295086 303986 308932 285612 313465 290286 72946.4 FALSE TRUE 253206.6261 289089.2728 308615.985 273428.7497 362809.643 275721.1848 265640.1571 264867.0189 84258.55515 3.00511474 3.430978282 3.662725814 3.245115576 4.305908668 3.272322725 3.152678759 3.143502977 1 16.36253556 0.31535569 0.998214031 0.989815799 3.452952163 0.827648654 0.348540716 1.181182275 1.380043846 0.350461726 0.104471756 2.067072408 -0.31535569 2.463136364 AAEDDEDDDVDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;;;; 372.05 6.05E-91 19472172000 7198772 6130265 6186520 7185889 3976326 7185067 7463950 7611213 4478430 FALSE TRUE 6858500.314 6754945.973 6470178.061 6463549.785 4669795.995 6936246.328 6325187.343 6944734.84 5172922.052 1.325846445 1.305827906 1.250778186 1.249496845 0.90273852 1.340875865 1.222749401 1.342516816 1 22.30254802 -5 0.189560799 0.022095535 1.289070719 0.237728638 0.129793075 202.2237303 1.976473941 75.75514473 0.341533731 1.00E-05 5 1.266975184 AAEDDEDDDVDTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;; 286.74 1.22E-33 80211700000 24977950 22387230 20808430 25308540 10143810 27902090 24435320 26902800 9883540 FALSE TRUE 23797291.81 24668514.19 21762517.1 22764477.48 11912887.25 26935833.63 20707263.15 24547048.21 11416228.91 2.084514247 2.160828623 1.906278972 1.99404529 1.043504589 2.359433562 1.813844425 2.15018886 1 23.44458283 3.409076085 2.241145204 1.778491475 2.117883044 0.120581393 0.430571849 0.664863651 6.756328332 0.117490063 0.178983577 2564.933353 -3.409076085 0.33939157 AAEEAEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 189.82 8.79E-05 770547000 1071800 974260 968350 1089110 1104440 983980 1137740 1096680 1193350 FALSE TRUE 1021138.138 1073538.202 1012749.805 979630.5936 1297053.986 949904.5259 964156.867 1000648.885 1378408.623 0.740809453 0.778824351 0.734723933 0.710696797 0.940979304 0.6891313 0.699471006 0.725945027 1 20.3945722 -1.111616603 4.552898581 1.000013729 0.751350278 0.542063819 0.071462756 1.54E-05 3.01E-06 0.065594845 0.015459459 0.077336301 1.111616603 -0.248663451 AAEEAFVNDIDESSPGTEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAEEAFVNDIDESSPGTEWER 21 0 P09496-2;P09496-5 P09496-2 CLTA Clathrin light chain A 0 295.09 1.77E-54 65351000 154980 131830 147170 163860 159000 136590 174560 166330 183840 FALSE TRUE 147654.4025 145263.6269 153917.8901 147388.4815 186729.5497 131859.8541 147927.666 151765.2634 212348.9683 0.69533845 0.684079739 0.72483465 0.694086167 0.879352281 0.620958299 0.696625311 0.714697437 1 17.69607757 0.905771498 18.24218009 1 0.709256235 0.655624781 0.065140113 2274.911393 440414.9991 0.058081773 0.014520443 8.049548065 -0.905771498 -0.290743765 AAEEEDEADPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 ;;;;;; 177.1 3.80E-05 13950680000 10626980 8846960 8908270 10319160 6741170 10265220 11155550 11089850 7455570 FALSE TRUE 10124663.72 9748475.282 9316722.991 9281858.432 7916827.914 9909732.857 9453565.962 10118763.94 8611741.718 1.175681302 1.131998102 1.081862798 1.077814307 0.919306242 1.150723417 1.097753076 1.174996217 1 23.03787362 3.935105717 2.027670401 1.075184661 1.166999269 0.195652554 0.071703472 0.5320637 4.267854319 0.019311195 0.048850319 8612.033633 -3.935105717 0.091814608 AAEEQGDDQDS(ph)EK ddPTM_SK-BR-3_Trastuzumab_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 251.05 3.94E-18 226320000 398410 502580 289460 476520 184131 432740 293500 405250 143637 TRUE FALSE 379577.9489 553793.4734 302732.0273 428619.3043 216243.3881 417754.1053 248721.1845 369764.1616 165911.4924 2.287833974 3.33788495 1.824659781 2.583421426 1.303365939 2.517933504 1.499119687 2.228683236 1 17.3400543 2.312919711 0.145422171 0.43111233 3.722315728 0.38001585 0.541902289 6.670995162 0.597283341 4.639463543 7.370324516 205.5510552 -2.312919711 3.291203398 AAEEQGDDQDS(ph)EKSKPAGSDGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(0.959)EKS(0.032)KPAGS(0.009)DGER 199.43 1.36E-24 729990000 931021 922445 703090 986846 345197 996417 800987 959192 311259 TRUE FALSE 887013.4824 1016443.194 735327.372 887646.3652 405399.2475 961910.8294 678781.722 875200.0635 359527.456 2.467164795 2.827164316 2.045260688 2.468925114 1.127589119 2.675486429 1.887982992 2.434306612 1 18.45574242 -0.925399142 0.150498407 9.54E-17 2.885506236 0.392812704 0.482169515 25.72041674 0.843657054 15.09336174 3.065723326 0.118741043 0.925399142 2.885506236 AAEEQGDDQDS(ph)EKSKPAGSDGERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAEEQGDDQDSEKSKPAGSDGERR 24 3 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(0.996)EKS(0.004)KPAGSDGERR 173.68 2.76E-12 212760000 47667 41391 48364 53781 25839 52696 53780 59299 24703 TRUE FALSE 45413.87538 45608.78996 50581.53724 48374.8317 30345.31342 50871.12431 45574.87326 54106.4652 28533.81507 1.591580911 1.598411914 1.772687497 1.695350992 1.06348602 1.782836406 1.597223265 1.896222607 1 14.80038503 -1.210730441 3.651170627 0.999195483 1.615850936 0.438313047 0.222050428 28961578.93 49678096.97 269330.0678 0.049173204 0.061555882 1.210730441 0.616655453 AAEHAWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAEHAWQK 8 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 72.547 0.045871 22482000 102050 92671 81072 93751 97909 83008 106710 99220 96220 FALSE TRUE 97226.29874 102114.2803 84789.23139 84326.97136 114984.2986 80133.41215 90429.42964 90531.7708 111141.3062 0.874798957 0.918778839 0.762895761 0.758736551 1.034577535 0.721004772 0.813643754 0.814564575 1 16.76203558 3.770233542 24.90404183 0.831738422 0.896788903 0.035185718 0.101858109 1648.651622 1296309.525 0.02387483 0.043036565 5891.603921 -3.770233542 0.065050481 AAEINGEVDDDDAGGEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAEINGEVDDDDAGGEWR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ;;; 341.27 4.28E-75 340227000 277886 231315 239006 274309 281914 244962 309217 253319 297584 FALSE TRUE 264750.8795 254886.2615 249964.6615 246734.9382 331079.7123 236478.9045 262040.2675 231137.0454 343731.8069 0.770225141 0.741526552 0.727208412 0.717812356 0.963191959 0.687975043 0.762339307 0.672434267 1 18.39092383 -1.461746276 3.490955989 1.003212439 0.756644239 0.481471246 0.079783416 12293935.74 5427934.179 296107.0143 0.016981904 0.034534544 1.461746276 -0.2465682 AAELEMELNEHSLVIDTLKEVDETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAELEMELNEHSLVIDTLKEVDETR 25 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 101.5 0.0032262 10270000 14286 10606 14519 11819 12141 14403 15158 14766 12869 FALSE TRUE 13610.72909 11686.76346 15184.71051 10630.93167 14258.38656 13904.2205 12845.3687 13473.01076 14864.65879 0.91564356 0.78621135 1.02153105 0.715181681 0.959213848 0.935387801 0.864154965 0.906378744 1 13.85959873 AAELEMELNEHSLVIDTLKEVDETRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAELEMELNEHSLVIDTLKEVDETRK 26 2 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 252.02 9.85E-53 44105000 30649 19349 28566 27184 23026 27792 43233 35476 28682 FALSE TRUE 29200.28251 21320.6851 29875.77936 24451.41267 27041.72711 26829.55607 36637.01182 32369.53337 33129.85807 0.881388699 0.643548942 0.901778066 0.738047613 0.816234318 0.809830094 1.105860814 0.977050167 1 15.0158444 1.752999107 24.99945366 1.03125515 0.789306419 0.652577936 0.078619425 2.517211311 4364.296053 0.033398091 0.018520982 56.62381242 -1.752999107 -0.241948732 AAESET(ph)PGKSPEKKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAESETPGKSPEKKPK 16 3 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAES(0.005)ET(0.835)PGKS(0.16)PEKKPK 82.36 0.0054086 490410000 1761000 1868800 1599100 2097000 682540 2305400 1924900 2327000 628280 TRUE FALSE 1677761.02 2059232.845 1672420.317 1886205.576 801574.7599 2225563.42 1631221.152 2123235.544 725710.4536 2.311887629 2.837540557 2.304528353 2.599115896 1.104537982 3.066737442 2.247757551 2.925733718 1 19.46903453 AAESETPGKS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAESETPGKSPEK 13 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAES(0.005)ET(0.378)PGKS(0.617)PEK;AAES(0.001)ET(0.319)PGKS(0.68)PEK 105.9 0.0008579 528690000 775360 1093290 662120 993340 343430 929400 661150 880250 343730 TRUE FALSE 738710.2694 1204697.494 692478.8569 893487.576 403324.0833 897214.645 560279.4246 803170.6435 397033.8929 1.860572316 3.034243463 1.744130336 2.250406305 1.015842956 2.259793587 1.411162711 2.022927155 1 18.59890264 3.265977106 1.879761342 1.630535567 2.414416989 0.256102326 0.528756317 0.385054519 2.800653469 0.150502224 0.214010634 1844.91816 -3.265977106 0.783881423 AAESETPGKS(ph)PEKKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAESETPGKSPEKKPK 16 3 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAESET(0.018)PGKS(0.982)PEKKPK;AAES(0.002)ET(0.034)PGKS(0.964)PEKKPK 136.68 1.15E-05 935990000 2271600 2436700 2116310 2649980 889560 2931990 2449820 2946750 828810 TRUE FALSE 2164225.97 2685002.5 2213344.907 2383598.976 1044698.982 2830454.451 2076054.965 2688716.948 957337.6218 2.260671596 2.804655786 2.311979448 2.489820646 1.091254494 2.956589595 2.168571377 2.808535763 1 19.86866828 2.918439812 25 2.125613052 2.491959255 0.097748222 0.639385161 260.2745983 79777.33447 0.177155488 0.187901818 828.7810493 -2.918439812 0.366346203 AAESLTAIPEPAS(ph)PQLLETPIHASQIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAESLTAIPEPASPQLLETPIHASQIQK 28 0 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLT(0.002)AIPEPAS(0.975)PQLLET(0.017)PIHAS(0.005)QIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK 271.39 1.29E-61 241225000 204525 177962 225131 257849 362673 220404 402063 293798 503246 TRUE FALSE 194857.5086 196096.5301 235453.479 231929.5286 425923.0564 212771.3542 340720.905 268071.4896 581286.8195 0.33521749 0.337349005 0.405055596 0.39899327 0.732724435 0.366035057 0.586149373 0.461169049 1 19.14889067 -5 0.132294858 2.884300023 0.216932785 0.725832571 0.110688399 67.91969637 0.56316495 33.82256733 0.724835784 1.00E-05 5 -2.667367238 AAEWQLDQPSWSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAEWQLDQPSWSGR 14 0 Q9NVZ3;Q9NVZ3-2;D6RAN6;F6SKB8;Q9NVZ3-3;H0Y970 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 0 132.86 4.49E-05 0 74202 71637 67240 80245 77089 76362 87716 71420 80992 FALSE TRUE 70694.61851 78936.89174 70323.02051 72178.62014 90533.29719 73717.56479 74333.31319 65166.08618 93551.82571 0.755673318 0.843777138 0.751701209 0.7715362 0.967734157 0.787986383 0.794568279 0.696577386 1 16.51347819 -2.102889176 2.483581114 1.359687671 0.800297558 0.444099479 0.071529247 3704723.102 1726565.752 7491053.12 0.016518268 0.007890614 2.102889176 -0.559390113 AAFDDAIAELDTLSEESYKDSTLIMQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAFDDAIAELDTLSEESYKDSTLIMQLLR 29 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 367.29 1.92E-136 476290000 982730 807510 867300 967530 843290 773360 1234500 1043100 917500 FALSE TRUE 936278.3005 889796.1871 907066.5629 870272.0462 990359.509 746578.3493 1046154.352 951760.6342 1059781.214 0.883463764 0.839603661 0.855899832 0.821180858 0.934494305 0.7044646 0.987141816 0.898072755 1 20.01533503 1.617336285 25 0.956955663 0.846643899 0.447161257 0.063513121 0.624542368 1644.295932 0.025921593 0.014135466 41.4320369 -1.617336285 -0.110311764 AAFNSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAFNSGK 7 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 133.7 0.0075516 3142860000 4553740 3823880 3490910 4495840 3812920 4021790 5262370 4308650 4274180 FALSE TRUE 4338493.735 4213537.719 3650971.676 4043909.622 4477892.041 3882514.404 4459498.806 3931361.764 4936998.005 0.87877162 0.853461499 0.739512488 0.819102948 0.907007059 0.786411986 0.903281468 0.796306128 1 22.23520263 -2.212689151 2.344317556 1.501542284 0.840914929 0.482341159 0.053298985 4149335.043 761258.6013 11068900.69 0.012120955 0.006127888 2.212689151 -0.660627355 AAFTTPDHAPLS(ph)PQSSVASSGSEQTEEQGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAFTTPDHAPLSPQSSVASSGSEQTEEQGSSR 32 0 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3 M0QZ22 SAMD4B Protein Smaug homolog 2 1 AAFTTPDHAPLS(0.995)PQS(0.004)S(0.001)VASSGSEQTEEQGSSR;AAFTTPDHAPLS(0.999)PQSS(0.001)VASSGSEQTEEQGSSR 220.74 4.12E-36 211330000 76678 63637 71439 75094 79443 68895 79439 72259 75348 TRUE FALSE 73053.5829 70121.68265 74714.54881 67545.40845 93297.83405 66509.14887 67319.12155 65931.61889 87032.58302 0.839381992 0.805694606 0.858466407 0.776093345 1.071987419 0.764186774 0.77349332 0.757550984 1 16.40926799 -0.302270996 6.889209958 1.000000037 0.828415916 0.250941067 0.091753284 11268965.9 1635740.83 0.08331397 0.020206606 0.498573285 0.302270996 -0.171584121 AAGALGSAS(ph)SGSMPNLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.476)S(0.362)GS(0.163)MPNLAAR;AAGALGSAS(0.359)S(0.297)GS(0.343)MPNLAAR 144.33 5.33E-07 179135000 272400 230199 260721 273210 287380 250770 315640 285110 332980 TRUE FALSE 259524.1918 253656.5398 272675.3157 245746.4117 337498.981 242085.772 267483.3209 260144.2569 384616.8378 0.674760349 0.659504512 0.708953142 0.638938256 0.877494035 0.629420629 0.695454007 0.676372513 1 18.5530624 -2.183657998 2.303643518 1.815420327 0.692191051 0.657390978 0.069143381 7733044.497 1704775.734 32862071.99 0.01660094 0.006551519 2.183657998 -1.123229276 AAGALGSASS(ph)GSMPNLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.191)S(0.636)GS(0.172)MPNLAAR;AAGALGSAS(0.009)S(0.639)GS(0.353)MPNLAAR 305.63 2.03E-50 241120000 272890 228111 242970 260940 282360 241510 279470 276340 324500 TRUE FALSE 259991.0305 251355.7702 254110.4148 234709.8154 331603.4946 233146.4481 236831.7187 252142.2046 374821.8027 0.693639027 0.670600719 0.67794993 0.626190402 0.884696387 0.622019441 0.631851501 0.672698874 1 18.51584535 -0.982916901 5.146222332 1.000001221 0.681653158 0.634830536 0.075054622 1.49E-06 2.95E-07 0.067759816 0.015971049 0.104011917 0.982916901 -0.318348063 AAGALGSASSGS(ph)MPNLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.043)S(0.043)GS(0.915)MPNLAAR;AAGALGSAS(0.017)S(0.122)GS(0.861)MPNLAAR;AAGALGSAS(0.008)S(0.012)GS(0.98)MPNLAAR;AAGALGS(0.001)AS(0.022)S(0.241)GS(0.736)MPNLAAR;AAGALGSASS(0.009)GS(0.991)MPNLAAR;AAGALGSAS(0.001)S(0.062)GS(0.937)MPNLAAR 317.81 9.34E-62 1518414000 942510 833670 877550 1006390 985380 928340 1082790 997550 1108460 TRUE FALSE 897959.4202 918621.9208 917786.5355 905225.7652 1157229.96 896191.353 917590.4987 910199.2337 1280354.316 0.701336661 0.717474772 0.716822308 0.707011922 0.903835716 0.69995574 0.716669197 0.710896369 1 20.28811168 -1.297865129 3.268042164 1.001357438 0.731843951 0.653595623 0.060778786 38846836.37 56329944.37 521669.4469 0.013990817 0.0503657 1.297865129 -0.269513488 AAGDGDCGTTHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 196.57 1.41E-07 640886000 777477 616082 693704 792831 761900 651458 853242 743597 763881 FALSE TRUE 740727.203 678861.4562 725511.0146 713134.1216 894775.1188 628897.8461 723064.262 678483.7046 882339.7641 0.839503367 0.769387807 0.822258096 0.808230741 1.014093612 0.712761537 0.819485068 0.768959682 1 19.75097478 -2.377688351 2.26398308 2.310679693 0.817045759 0.345418097 0.078103762 5036361.009 535541.9004 33900264.9 0.018164117 0.004190942 2.377688351 -1.493633934 AAGDVDIGDAAYYFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAGDVDIGDAAYYFER 16 0 P09758 P09758 TACSTD2 Tumor-associated calcium signal transducer 2 0 78.705 0.047446 17341000 28817 28113 32716 36129 32533 23338 30767 34904 41521 FALSE TRUE 27454.87752 30977.74666 34216.06096 32497.24428 38206.7449 22529.79921 26072.92908 31847.62072 47959.86462 0.572455276 0.645909802 0.713431141 0.677592494 0.796639966 0.469763611 0.54364059 0.664047344 1 15.54953997 0.958183757 22.40216884 1.000000001 0.625188126 0.61637636 0.090643197 1598.604932 856420.5097 0.089588849 0.022397212 9.082047255 -0.958183757 -0.374811875 AAGGAPS(ph)PPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;AAGGAPS(1)PPPPVR 177.81 1.59E-05 2304913000 1198049 1021817 1096628 1220098 1110705 1155897 1447225 1307975 1405313 TRUE FALSE 1141419.598 1125941.314 1146909.479 1097451.431 1304411.6 1115867.997 1226424.246 1193441.775 1623241.763 0.703172888 0.693637473 0.706554935 0.676086247 0.803584303 0.687431794 0.755540101 0.735221211 1 20.63044646 -5 0.247306256 2.696105753 0.691577941 0.868825911 0.034621667 53.17922457 0.527978956 45.47203761 0.044595053 1.00E-05 5 -2.004527811 AAGGAPS(ph)PPPPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGGAPSPPPPVRR 14 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR 73.279 0.01108 286960000 487080 425240 470370 528920 417070 457160 538990 501760 425850 TRUE FALSE 464056.6937 468572.4395 491936.9298 475751.9567 489806.876 441328.4346 456757.1763 457823.2344 491888.6431 0.943418191 0.952598614 1.000098166 0.967194432 0.995767808 0.897212084 0.928578414 0.93074569 1 18.90797222 2.244470591 24.99991145 0.931404332 0.967688926 0.193553409 0.030801719 194.5395775 822927.6915 0.010251707 0.008367573 175.5781993 -2.244470591 0.036284594 AAGGGAGS(ph)S(ph)EDDAQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGGGAGSSEDDAQSR 16 0 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 2 AAGGGAGS(1)S(1)EDDAQSR;AAGGGAGS(1)S(1)EDDAQSR 189.56 1.46E-09 80394000 248370 255220 267520 292440 236300 261150 300420 266210 264250 TRUE FALSE 236630.0423 281227.2082 279786.0566 263043.3756 277510.6452 252106.31 254585.4114 242899.2411 305228.5404 0.775255296 0.921366029 0.91664448 0.861791546 0.9091897 0.825959164 0.834081279 0.795794655 1 18.21953034 2.220853108 24.97031743 0.84754916 0.87480846 0 0.068107354 961.1298984 1355332.505 0.023634814 0.017495005 166.2850127 -2.220853108 0.027259301 AAGGIILTAS(ph)HCPGGPGGEFGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AAGGIILTASHCPGGPGGEFGVK 23 0 Q15124;Q15124-2;Q5JTY7 Q15124 PGM5 Phosphoglucomutase-like protein 5 1 AAGGIILT(0.001)AS(0.999)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILT(0.001)AS(0.999)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILT(0.002)AS(0.998)HCPGGPGGEFGVK 357.53 3.94E-102 13890000000 12644780 10722360 11342450 14402050 10448160 14236840 15024730 14520720 11048450 TRUE FALSE 12047086.31 11814980.67 11862512.55 12954328.57 12270315.8 13743814.66 12732431.49 13249208.78 12761787.2 0.943996802 0.925809253 0.9295338 1.015087336 0.961488826 1.076950622 0.997699718 1.038193834 1 23.60532705 3.086273684 1.594750706 1.021307553 0.931235773 0.588164373 0.031239891 0.222032102 1.164116155 0.009795721 0.012435078 1219.758024 -3.086273684 -0.09007178 AAGIDEQENWHEGKENIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGIDEQENWHEGKENIR 18 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 189.87 1.83E-14 139796000 213515 148925 200726 217823 199109 210167 283610 245744 229005 FALSE TRUE 203422.5691 164100.6268 209929.4856 195927.0182 233833.5466 202888.8641 240340.0856 224225.3526 264517.9258 0.769031318 0.620376204 0.793630469 0.740694672 0.883998866 0.767013666 0.908596591 0.847675453 1 18.01300597 1.918051531 0.356638325 1.003004834 0.67167592 0.644704182 0.061908203 0.695250506 0.24942156 0.073783647 0.078755795 82.80404091 -1.918051531 -0.331328913 AAGISLIVPGKS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.841)PT(0.159)R;AAGISLIVPGKS(0.5)PT(0.5)R 155.49 1.39E-06 3636300000 2428310 1888950 2027400 2267280 1841070 2085100 2392070 2077460 1776120 TRUE FALSE 2313528.599 2081436.153 2120358.295 2039368.707 2162152.025 2012892.464 2027115.788 1895546.589 2051551.618 1.127696997 1.014566796 1.033538848 0.994061611 1.053910614 0.981156139 0.988089098 0.923957541 1 20.96828402 8 0.355205454 0.976635524 2.775533066 0.662365676 0.030834805 34.55411905 0.484996317 0.023559151 41.8327225 100000000 -8 1.798897542 AAGLATMISTMRPDIDNMDEYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAGLATMISTMRPDIDNMDEYVR 23 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 218.74 2.00E-32 199782000 244700 217450 231120 252390 257270 243990 294030 258050 287200 FALSE TRUE 233133.5159 239608.4022 241717.0806 227019.2777 302137.8065 235540.5651 249170.3233 235453.774 331737.5092 0.702765016 0.722283117 0.728639584 0.684334064 0.910773724 0.710020901 0.751106873 0.709759275 1 18.33968262 -5 0.330845479 3.645396139 0.728594072 0.619244188 0.063774064 228.8715375 1.973854096 426.1477447 0.049581089 1.00E-05 5 -2.916802068 AAHLCAEAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAHLCAEAALR 11 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 152.54 3.29E-05 815990000 645890 457840 438490 592110 663900 543040 753380 575560 610370 FALSE TRUE 615360.0597 504494.4165 458595.2002 532589.9779 779683.9498 524234.3886 638438.0442 525160.9152 705023.0623 0.872822596 0.715571509 0.650468367 0.755422065 1.105898504 0.743570553 0.905556255 0.744884733 1 19.42731093 2.941388154 24.99910242 0.887014899 0.750925995 0.281316432 0.11925564 360.7200554 153853.779 0.033900403 0.035956876 873.751942 -2.941388154 -0.136088904 AAHSEGNTTAGLDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 AAHSEGNTTAGLDMR 15 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;;;;;;;;;; 195.2 8.96E-09 4686897000 3326552 2646325 2940383 3197767 3354073 2846489 3669333 3349606 3669687 FALSE TRUE 3169312.48 2915988.526 3075202.469 2876321.386 3939022.269 2747914.372 3109508.859 3056296.741 4238763.318 0.74769744 0.687933793 0.725495207 0.678575606 0.929285731 0.648282097 0.733588697 0.721035008 1 22.01521198 -2.151723636 2.214101121 1.583165364 0.730961894 0.551084134 0.07540958 6429087.508 1410904.903 18826836.61 0.016392224 0.007051416 2.151723636 -0.85220347 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AAHVPENSDTEQDVLTVKPVR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(0.996)DT(0.004)EQDVLTVKPVR;AAHVPENS(0.999)DT(0.001)EQDVLTVKPVR;AAHVPENS(0.999)DT(0.001)EQDVLTVKPVR 248.58 9.50E-31 1466840000 818531 794200 721557 905249 634852 820215 885258 882777 664587 TRUE FALSE 779840.6618 875129.8829 754641.1022 814251.6507 745569.9878 791810.7489 750195.6332 805476.366 767647.7577 1.015883462 1.140014902 0.983056479 1.060709997 0.971239713 1.031476665 0.977265452 1.049278602 1 19.55008494 3.718439117 24.99247849 1.009284963 1.077949193 0.311022133 0.041750106 763.2037048 947958.0514 0.010068818 0.015621215 5229.246532 -3.718439117 0.06866423 AAHVPENS(ph)DTEQDVLTVKPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAHVPENSDTEQDVLTVKPVRK 22 2 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(0.999)DT(0.001)EQDVLTVKPVRK;AAHVPENS(0.994)DT(0.006)EQDVLTVKPVRK 239.34 7.23E-31 533100000 624250 474240 684920 628670 498920 707820 836880 749080 625720 TRUE FALSE 594742.9396 522565.5952 716324.2595 565474.8972 585931.49 683308.0159 709198.5856 683486.5841 722753.4619 0.822884941 0.723020536 0.991104571 0.782389746 0.81069344 0.945423373 0.981245505 0.94567044 1 19.46314409 2.183800688 4.527098213 0.970752441 0.816853215 0.51540618 0.068469679 0.160972915 6.801747377 0.025790085 0.019038917 152.6865169 -2.183800688 -0.153899226 AAHVTLLTSLVEGEAVHLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAHVTLLTSLVEGEAVHLAR 20 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 126.8 1.31E-05 9713200 8807.3 6625.7 4897.9 8324.2 7184.7 5200.3 7907.7 6885 6165.2 FALSE TRUE 8390.996383 7300.866363 5122.47356 7487.435601 8437.709405 5020.212307 6701.23513 6282.1129 7121.267729 1.178300929 1.025220037 0.719320457 1.051418917 1.184860579 0.704960479 0.94101716 0.882162157 1 12.79791838 4.155051714 3.13669512 0.924439441 1.1477833 0.231324231 0.143639225 0.316292958 6.051309618 0.035136424 0.092686395 14290.64115 -4.155051714 0.223343859 AAIDWFDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 135.79 0.00049067 115983000 426820 461260 332590 482740 283450 400970 396890 424830 282400 FALSE TRUE 406645.0645 508262.9184 347839.5805 434214.0581 332883.5903 387084.3084 336337.1411 387629.633 326193.1497 1.246638885 1.558165519 1.066360777 1.331156275 1.020510672 1.186672095 1.031098113 1.18834388 1 18.31536696 3.377593097 1.430863607 1.099651319 1.390412679 0.363590979 0.136456322 0.345909889 1.460419243 0.041243959 0.069171873 2385.575119 -3.377593097 0.290761361 AAIDWFDGKEFSGNPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAIDWFDGKEFSGNPIK 17 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 244.97 1.38E-20 1340680000 2553690 1869140 2491670 2509550 1992550 2509700 3340600 2961090 2346310 FALSE TRUE 2432982.135 2059607.491 2605915.534 2257285.266 2340050.089 2422788.46 2830930.116 2701801.262 2710163.772 0.897725134 0.759956838 0.96153434 0.832896259 0.863434938 0.893963858 1.044560534 0.99691439 1 21.3699486 1.871122581 3.945787193 1.01580829 0.856576755 0.636875893 0.052007309 0.135361565 3.374153927 0.024319622 0.013523163 74.32288875 -1.871122581 -0.159231534 AAIELPSLEVLS(ph)DQEEDREQCGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAIELPSLEVLSDQEEDREQCGVK 24 1 Q9BQI3-2;Q9BQI3 Q9BQI3-2 EIF2AK1 Eukaryotic translation initiation factor 2-alpha kinase 1 1 AAIELPS(0.313)LEVLS(0.687)DQEEDREQCGVK;AAIELPS(0.001)LEVLS(0.999)DQEEDREQCGVK 202.98 7.56E-25 42349000 59015 61488 49657 62711 33672 56911 59984 64807 38687 TRUE FALSE 56225.47791 67753.69711 51933.82257 56407.17114 39544.38614 54940.1578 50832.33912 59132.15552 44686.38237 1.258223981 1.516204569 1.162184536 1.262289945 0.884931472 1.229460853 1.137535339 1.323270141 1 15.44754763 3.652650577 7.58946767 1.14658699 1.386705493 0.346821172 0.139423521 0.265233039 20.74320936 0.034200756 0.053139369 4494.181185 -3.652650577 0.240118503 AAIPPPVYEEQDRPRS(ph)PTGPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 AAIPPPVYEEQDRPRS(0.911)PT(0.088)GPS(0.001)NSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.986)PT(0.014)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.966)PT(0.034)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.996)PT(0.004)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.392)PT(0.392)GPS(0.099)NS(0.113)FLANMGGT(0.005)VAHK;AAIPPPVY(0.002)EEQDRPRS(0.925)PT(0.073)GPSNSFLANMGGTVAHK 296.53 1.64E-90 2550010000 1263772 834171 1278091 1207787 1241723 1153057 1608053 1380106 1435975 TRUE FALSE 1204036.002 919173.9733 1336692.737 1086377.956 1458279.098 1113126.347 1362714.981 1259256.602 1658658.669 0.72590945 0.554167045 0.80588777 0.654973791 0.879191798 0.67110031 0.821576498 0.759201773 1 20.6615856 -5 0.099058841 1.930933588 0.522458707 0.5126474 0.087085919 129.3467626 0.873626677 24.63643687 1.337590278 1.00E-05 5 -1.408474881 AAISQLRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAISQLRSPR 10 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 AAIS(0.003)QLRS(0.997)PR;AAIS(0.009)QLRS(0.991)PR;AAIS(0.023)QLRS(0.977)PR 69.602 0.03421 564210000 962890 1030990 828790 935960 991720 812340 1026080 982180 1008870 TRUE FALSE 917376.098 1136049.053 866790.8413 841875.5226 1164675.654 784208.4621 869532.6507 896175.1123 1165320.407 0.787230784 0.974881283 0.743821902 0.722441242 0.999446716 0.67295523 0.746174739 0.769037517 1 20.15229525 2.207867612 24.99820892 0.7690299 0.847674599 0.015396888 0.121307019 496.8004456 404620.8598 0.04202597 0.031041554 161.3866521 -2.207867612 0.078644699 AAKLS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;AAKLS(1)EGS(1)QPAEEEEDQETPSR;AAKLS(1)EGS(1)QPAEEEEDQETPSR 224.49 3.90E-26 580120000 1501050 1116800 1390660 1567100 1033600 1578570 1790220 1573260 1114450 TRUE FALSE 1430098.341 1230603.19 1454423.137 1409572.131 1213859.513 1523903.725 1517089.059 1435497.014 1287273.214 1.110951681 0.955976693 1.129848054 1.095006185 0.942969604 1.183823067 1.178529191 1.115145564 1 20.29588686 2.212318329 24.99874717 1.140766283 1.046315576 0.148971041 0.078965053 298.6503866 284496.5853 0.027471121 0.020294866 163.049071 -2.212318329 -0.094450707 AAKNS(ph)EEEEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AAKNS(1)EEEEEEK 227 8.47E-12 2417860000 2296600 2911210 1844670 2882420 993540 2847550 2181000 2650780 855757 TRUE FALSE 2188044.269 3207865.609 1929249.944 2592673.665 1166813.061 2748938.629 1848248.393 2418663.651 988463.425 2.213581418 3.245305317 1.951766647 2.622933333 1.180431194 2.7810221 1.869819709 2.446892408 1 19.91482806 3.713402365 24.84365536 2.046463148 2.729443439 0.196603449 0.619115179 949.7232851 937847.1846 0.144495916 0.22395597 5168.950399 -3.713402365 0.682980291 AAKNS(ph)EEEEEEKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AAKNS(1)EEEEEEKKK;AAKNS(1)EEEEEEKKK;AAKNS(1)EEEEEEKKK 181.14 1.19E-06 7600820000 7470930 7038770 6915030 7977650 1939350 9422190 7613710 9322440 1696380 TRUE FALSE 7117793.945 7756028.665 7232090.965 7175721.465 2277572.026 9095897.198 6452098.704 8506117.732 1959445.946 3.632554375 3.958276409 3.69088567 3.662117589 1.162355119 4.6420761 3.292817909 4.341083125 1 20.90201434 2.971990507 24.96228744 3.116731562 3.771131379 0.099083382 1.165119218 1951.266401 1738985.572 0.324765212 0.345214614 937.5415131 -2.971990507 0.654399817 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 AAKPGPAEAPS(0.976)PT(0.024)AS(0.001)PS(0.013)GDAS(0.976)PPAT(0.01)APYDPR;AAKPGPAEAPS(0.986)PT(0.013)ASPS(0.018)GDAS(0.981)PPATAPYDPR 162.31 1.03E-12 494160000 189775 184366 201892 214080 181100 219740 252220 227850 214950 TRUE FALSE 180804.7118 203153.105 211148.9479 192560.2717 212683.7827 212130.3487 213739.2067 207898.2461 248283.3482 0.728219243 0.81823089 0.850435397 0.775566598 0.856617184 0.854388143 0.86086807 0.837342688 1 17.92162798 -5 0.064857095 1.635759012 0.570533031 0.802694725 0.030953038 141.9675077 0.667973619 13.93223439 2.017633895 1.00E-05 5 -1.065225981 AAKPGPAEAPSPTASPSGDAS(ph)PPATAPYDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPSPTASPS(0.001)GDAS(0.998)PPAT(0.001)APYDPR;AAKPGPAEAPSPTASPS(0.008)GDAS(0.965)PPAT(0.025)APY(0.001)DPR;AAKPGPAEAPSPTAS(0.013)PS(0.115)GDAS(0.851)PPAT(0.019)APY(0.002)DPR;AAKPGPAEAPSPTASPS(0.013)GDAS(0.973)PPAT(0.013)APYDPR 109.59 6.76E-05 2290190000 573147 532455 539650 601959 473987 566160 661710 614400 593895 TRUE FALSE 546055.4772 586712.7699 564393.4863 541448.9377 556650.1827 546553.7372 560753.9864 560599.8789 685993.2034 0.796007124 0.855274902 0.822739181 0.789291986 0.811451455 0.796733458 0.817433735 0.817209086 1 19.38783476 0.290575626 2.544559693 1.000000212 0.814740823 0.910451597 0.018401233 12.40890018 43.77555682 0.018068898 0.004805703 1.952430691 -0.290575626 -0.185259388 AALAPAKES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;AALAPAKES(1)PR;AALAPAKES(1)PR 139.74 0.0001024 46874780000 42942910 38652850 37898490 41780760 29881160 42061460 47419850 44796440 35842410 TRUE FALSE 40913083.75 42591619.36 39636173.25 37580878.63 35092424.84 40604861.09 40185080.96 40873826.23 41400667.89 0.988222795 1.02876648 0.957380044 0.907736047 0.847629438 0.980777924 0.970638471 0.987274562 1 25.30315071 -0.137432455 8.28941072 1 0.963292525 0.056871352 0.049824834 0 0 0.052118572 0.012284465 0.728731504 0.137432455 -0.036707475 AALAPAKES(ph)PRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 96.673 0.0027926 336780000 802690 723220 713650 830130 483270 898940 837050 921940 508580 TRUE FALSE 764748.4345 796916.9402 746371.5584 746683.7553 567552.135 867809.4824 709342.649 841210.0461 587447.9889 1.301814712 1.356574463 1.270532153 1.271063599 0.966131718 1.477253304 1.207498642 1.431973659 1 19.1641016 -1.511669924 2.900647695 0.989077158 1.285117601 0.296110891 0.138264906 21466411.04 22848176.89 1847111.257 0.029653866 0.030784356 1.511669924 0.296040442 AALAPAKES(ph)PRKGAAPTPPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AALAPAKESPRKGAAPTPPGK 21 3 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AALAPAKES(0.999)PRKGAAPT(0.001)PPGK 104.53 0.00029418 239580000 917530 215680 1336800 547510 1037700 1056500 2314600 1399100 1986600 TRUE FALSE 874160.1753 237658.0372 1398093.602 492473.2546 1218674.551 1019913.14 1961465.259 1276587.387 2294671.782 0.380952162 0.103569512 0.609278248 0.214615989 0.53108883 0.444470163 0.854791206 0.55632679 1 21.12985638 1.729155581 0.476490649 0.988354833 0.243849785 0.611026798 0.166779178 0.512409522 0.285202934 0.157391809 0.111859921 53.59886343 -1.729155581 -0.744505047 AALCAVHVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AALCAVHVIR 10 0 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9 O43747 AP1G1 AP-1 complex subunit gamma-1 0 112.84 0.0025019 0 155860 180800 190520 295670 212130 276330 294110 318660 219890 FALSE TRUE 148492.8067 199223.7256 199255.5305 265948.6899 249125.4048 266760.6228 249238.1178 290756.4411 253989.4182 0.584641706 0.784378054 0.784503275 1.047085709 0.980849543 1.050282428 0.981293314 1.144758089 1 17.95440887 3.770548601 0.818806494 1.045666164 0.568810821 0.85996848 0.061872739 0.264738425 0.309726388 0.023982016 0.0896186 5895.879528 -3.770548601 -0.476855343 AALEAIDELDLFGAHGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AALEAIDELDLFGAHGGR 18 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 0 147.24 7.80E-08 19113000 14604 15024 13122 16534 16914 10780 16962 13986 14563 FALSE TRUE 13913.69786 16554.96268 13723.65668 14871.97091 19863.79624 10406.6859 14374.13537 12761.3117 16821.35566 0.827144859 0.984163406 0.815847245 0.884112506 1.18086774 0.618659168 0.854517059 0.758637529 1 14.03800636 2.214975899 24.99999409 0.79579041 0.92650691 0.176996536 0.137374497 382.8509765 405822.5659 0.04660894 0.034442327 164.049873 -2.214975899 0.1307165 AALEEVYPDLTPEETRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AALEEVYPDLTPEETRR 17 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;;;; 231.23 8.57E-16 542291000 488613 411517 445037 494921 567512 463386 594886 505803 579567 FALSE TRUE 465517.2318 453451.0502 465442.3867 445170.6008 666485.9131 447338.8266 504125.2149 461512.2079 669443.2903 0.695379636 0.677355434 0.695267834 0.664986276 0.995582333 0.668225125 0.753051412 0.689397018 1 19.35260232 -5 0.221904994 2.378154966 0.693063029 0.42406819 0.098227684 145.8668422 1.459051291 90.17169696 0.172050509 1.00E-05 5 -1.685091937 AALLELWELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AALLELWELRR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 137.89 0.0001104 80529000 95971 75897 61125 107063 88732 67175 101023 96459 92343 FALSE TRUE 91434.64103 83630.99059 63927.64171 96300.82383 104206.8327 64848.71291 85610.08594 88012.5386 106663.0808 0.857228577 0.784066895 0.599341789 0.902850575 0.9769719 0.607977122 0.802621538 0.825145289 1 16.70270138 0.784686535 3.03451266 0.999930185 0.789848124 0.240609227 0.116368801 1.817963023 23.46396496 0.105774031 0.027651277 6.090971044 -0.784686535 -0.210082061 AALLKAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AALLKASPK 9 1 P50914 P50914 RPL14 60S ribosomal protein L14 1 AALLKAS(1)PK;AALLKAS(1)PK 66.568 0.038373 5204200000 7921300 8152400 7486700 8383600 4665600 10123600 10439300 10360900 5689600 TRUE FALSE 7546875.848 8983138.829 7829972.6 7540864.6 5479279.163 9773017.194 8846593.054 9453644.669 6571914.11 1.148352782 1.366898392 1.191429539 1.147438094 0.833741749 1.487088393 1.346121222 1.438491817 1 22.64788219 AALLNQHYQVNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AALLNQHYQVNFK 13 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 119.39 0.00035277 442170000 690050 656820 570980 658640 525070 628740 691170 694370 569970 FALSE TRUE 657432.704 723750.7047 597159.9978 592432.2559 616642.0418 606966.5761 585719.3223 633567.2817 658358.0366 0.998594484 1.099326908 0.907044442 0.899863331 0.93663631 0.921939951 0.889666853 0.96234457 1 19.32851286 3.728794773 24.97183423 0.922925499 1.048960697 0.590885397 0.040341629 336.3920875 860174.0045 0.009770943 0.015340228 5355.435258 -3.728794773 0.126035198 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR ddPTM_SK-BR-3_Trastuzumab_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 ; 502.74 0 583230000 197141 161689 157887 163511 207454 124961 195247 178683 143796 FALSE TRUE 187822.5356 178165.2929 165126.2751 147074.5636 243633.9119 120633.5692 165458.4842 163036.5693 166095.1493 1.130812889 1.072670055 0.994166752 0.885483798 1.466833396 0.726291946 0.996166865 0.981585374 1 17.34165042 AALQEELQLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AALQEELQLCK 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 ;; 218.52 2.46E-11 303977000 499650 421002 452190 522260 405595 472360 567680 517350 501900 FALSE TRUE 476032.5347 463902.5824 472923.3588 469761.4326 476330.6396 456002.0548 481069.9898 472048.0914 579732.0887 0.82112504 0.800201665 0.815761915 0.810307799 0.821639252 0.78657377 0.829814322 0.814252136 1 19.14502682 -0.637771029 0.796587757 1.01556058 0.810638601 0.960888883 0.011895752 3.873205376 1.522965828 0.185009495 0.003492236 0.230265552 0.637771029 -0.204921979 AALQSQAEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AALQSQAEALRR 12 1 Q8WZA9 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 93.766 0.011205 169140000 151380 112910 103450 121750 399330 98496 171000 103410 272880 FALSE TRUE 144224.5674 124415.6574 108193.2848 109511.4587 468973.0256 95085.05882 144910.8094 94354.87219 315196.8367 0.457569844 0.394723687 0.343256252 0.347438318 1.487873516 0.301668823 0.459747029 0.299352218 1 18.26589353 AALRDYETVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AALRDYETVVK 11 1 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 86.996 0.012817 193750000 613470 449520 507600 504320 708770 558360 855630 654340 813070 FALSE TRUE 584472.4889 495326.5991 530873.9621 453624.7955 832379.2636 539023.8532 725087.9288 597042.5207 939156.743 0.622337531 0.527416326 0.565266625 0.483012872 0.886304943 0.573944506 0.772062741 0.635721912 1 19.84100643 -1.347787501 0.186931202 1.368308019 0.50278808 0.551549374 0.110465747 17.1276127 0.606608042 3.359915136 0.350028956 0.044896501 1.347787501 -0.865519939 AALSEEELEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 179.6 1.13E-05 918910000 1058710 1031030 982010 1217820 598090 1288080 1287750 1392690 813880 FALSE TRUE 1008666.876 1136093.129 1027036.13 1095402.42 702396.7066 1243473.467 1091280.086 1270738.68 940092.3537 1.072944453 1.208490979 1.092484292 1.165207243 0.747157132 1.322714159 1.160822213 1.351716856 1 19.84244297 AALSRDEILRYS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AALSRDEILRYSR 13 2 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 AALSRDEILRY(0.442)S(0.558)R;AALSRDEILRY(0.445)S(0.555)R;AALSRDEILRY(0.387)S(0.613)R;AALSRDEILRY(0.448)S(0.552)R 70.622 0.035037 5875730000 1656110 1302027 1490760 1460202 4591340 882991 1719280 1049236 4277270 TRUE FALSE 1577828.962 1434705.032 1559112.821 1313419.721 5392068.242 852412.8003 1456972.259 957359.3335 4940567.186 0.319361908 0.290392778 0.31557365 0.265843915 1.091386482 0.172533389 0.294899797 0.193775188 1 22.23624524 -1.515214421 3.21490039 1.017577396 0.361390475 0.364257989 0.262279001 167653016.2 205314871.7 25941888.39 0.059598857 0.030534132 1.515214421 -0.656186921 AALTGLLHR ddPTM_SK-BR-3_Trastuzumab_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 ; 183.65 4.49E-05 965810000 1676340 1111930 1040020 1057450 1727970 935630 1479080 1168270 1518510 FALSE TRUE 1597102.73 1225236.931 1087705.946 951153.117 2029327.421 903228.8985 1253419.181 1065970.085 1753992.775 0.910552628 0.698541607 0.620131372 0.542278811 1.156975929 0.514955883 0.71460909 0.607739154 1 20.74221137 4.552731679 2.786228245 0.715174665 0.914034082 0.065655851 0.202060564 0.758969746 10.24991438 0.045294371 0.282414923 35705.21719 -4.552731679 0.198859416 AAMIWIVGEYAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 136.33 1.16E-05 0 69874 60610 70040 66411 67634 53674 77409 64446 67160 FALSE TRUE 66571.1945 66786.22791 73251.40328 59735.24011 79429.34819 51815.25592 65598.83534 58802.76659 77574.82979 0.858154567 0.860926516 0.944267664 0.770033789 1.023906187 0.667939022 0.8456201 0.758013479 1 16.24330101 2.235737681 24.99999905 0.804481296 0.881148001 0.09872176 0.104547187 150.6304362 1333966.668 0.033017241 0.025467764 172.0828861 -2.235737681 0.076666705 AAMYDIISS(ph)PSKDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.126)S(0.784)PS(0.079)KDS(0.004)T(0.006)K;AAMYDIIS(0.132)S(0.867)PS(0.001)KDSTK 145.62 7.28E-07 197673000 418420 383130 393750 468770 235009 528690 507810 499730 284787 TRUE FALSE 398642.1158 422171.3826 411803.827 421648.349 275994.4952 510381.3327 430334.2579 455970.992 328950.3135 1.211861182 1.283389513 1.251872426 1.281799505 0.839015754 1.551545361 1.308204432 1.386139406 1 18.32751016 AANCNLHVPGPMAVNQFS(ph)PSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AANCNLHVPGPMAVNQFSPSLAR 23 0 Q99990;H0Y5G3 Q99990 VGLL1 Transcription cofactor vestigial-like protein 1 1 AANCNLHVPGPMAVNQFS(0.996)PS(0.004)LAR;AANCNLHVPGPMAVNQFS(0.955)PS(0.045)LAR;AANCNLHVPGPMAVNQFS(0.992)PS(0.008)LAR;AANCNLHVPGPMAVNQFS(0.988)PS(0.012)LAR 172 3.55E-12 2053310000 1753000 1622560 1726310 1844070 1785310 1663560 1901220 1887530 1933880 TRUE FALSE 1670139.164 1787900.709 1805463.021 1658700.58 2096667.499 1605950.5 1611153.971 1722247.867 2233776.234 0.747675232 0.800393827 0.80825599 0.742554494 0.938620202 0.718939738 0.721269188 0.771002861 1 21.09105324 -2.303260986 2.21158967 2.039383225 0.778157769 0.540607537 0.063368057 4189787.197 460861.812 21856190.54 0.016049717 0.004974381 2.303260986 -1.261225455 AANFENHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AANFENHSGK 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 83.397 0.015631 98783000 329990 194970 170780 310490 304460 246440 534630 278010 433790 FALSE TRUE 314392.0267 214837.6647 178610.4319 279278.9553 357557.7276 237905.721 453062.3743 253665.9706 501059.9377 0.627453929 0.428766398 0.356465202 0.557376342 0.713602706 0.474804915 0.904207941 0.506258736 1 18.93462367 1.004726336 0.404052049 1.013235096 0.474186938 0.474619816 0.148534169 1.071737807 0.476475331 0.212101499 0.112606275 10.10942223 -1.004726336 -0.539048158 AAPAQVRPPS(ph)PGNIRPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 191.73 1.10E-14 1934420000 898860 1132840 753720 1106300 741530 951320 800060 988580 747710 TRUE FALSE 856372.6692 1248277.684 788278.8075 995092.6222 870852.5972 918375.5499 677996.1529 902014.6944 863661.048 0.991561066 1.44533285 0.912717795 1.152179578 1.008326819 1.063351823 0.785025739 1.044408216 1 19.7201057 2.824814277 0.996172799 0.933909658 1.187571561 0.165176765 0.156309366 0.646429926 1.371803838 0.078487513 0.079380051 668.058166 -2.824814277 0.253661903 AAPAQVRPPS(ph)PGNIRPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAPAQVRPPSPGNIRPVKR 19 3 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIRPVKR 101.94 0.00028689 154880000 121080 111560 119700 122960 115730 129420 148380 136600 129300 TRUE FALSE 115356.7884 122928.0908 125188.3634 110599.8272 135913.2754 124938.1529 125741.9058 124638.5798 149351.1836 0.772386168 0.823080794 0.838214739 0.740535324 0.910024762 0.836539423 0.841921053 0.834533593 1 17.18834915 -4.999999997 0.161680248 1.669361347 0.775322988 0.660746209 0.041254032 75.21252157 0.694614123 16.11253874 0.154218692 1.00E-05 4.999999997 -0.894038359 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.553)S(0.447)PPASPLQHLLPGK;AAPEAS(0.88)S(0.12)PPASPLQHLLPGK;AAPEAS(0.856)S(0.144)PPASPLQHLLPGK 249.85 1.07E-30 1996110000 842690 671110 780100 877640 746640 757010 913290 778490 680330 TRUE FALSE 802857.7138 739496.872 815868.3566 789417.9598 876853.7796 730794.5539 773950.8368 710321.2886 785832.1018 1.021665712 0.941036731 1.038222229 1.004563135 1.115828404 0.929962714 0.984880657 0.903909737 1 19.58386158 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.441)S(0.56)PPAS(0.999)PLQHLLPGK;AAPEAS(0.087)S(0.914)PPAS(0.999)PLQHLLPGK;AAPEAS(0.44)S(0.56)PPAS(1)PLQHLLPGK;AAPEAS(0.111)S(0.889)PPAS(1)PLQHLLPGK;AAPEAS(0.125)S(0.875)PPAS(1)PLQHLLPGK;AAPEAS(0.089)S(0.911)PPAS(1)PLQHLLPGK;AAPEAS(0.455)S(0.554)PPAS(0.991)PLQHLLPGK;AAPEAS(0.472)S(0.541)PPAS(0.987)PLQHLLPGK;AAPEAS(0.366)S(0.634)PPAS(1)PLQHLLPGK;AAPEAS(0.088)S(0.912)PPAS(1)PLQHLLPGK;AAPEAS(0.474)S(0.542)PPAS(0.983)PLQHLLPGK 192.12 6.41E-18 3105946000 2801230 2300920 2571450 3007610 2455147 2553900 2864390 2534000 2182577 TRUE FALSE 2668821.409 2535386.364 2689353.526 2705279.329 2883323.859 2465457.803 2427374.697 2312109.526 2521039.894 1.058619269 1.005690695 1.066763573 1.07308073 1.143704178 0.977952712 0.962846603 0.917125323 1 21.26558752 2.027599467 23.4709233 0.959496767 1.059974556 0.640970114 0.038907524 72.36671458 61540.97447 0.014853089 0.010969378 106.5612895 -2.027599467 0.100477789 AAPEASS(ph)PPASPLQHLLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.408)S(0.592)PPASPLQHLLPGK;AAPEAS(0.425)S(0.575)PPASPLQHLLPGK 256.33 2.24E-36 2688600000 1564400 1185160 1278670 1652690 1318090 1258520 1607840 1421090 1209570 TRUE FALSE 1490453.912 1305929.151 1337298.284 1486558.461 1547964.479 1214937.137 1362534.478 1296651.826 1397143.938 1.066786229 0.934713393 0.957165721 1.063998076 1.107949179 0.869586235 0.975228422 0.928073186 1 20.41404923 2.229223025 24.99999286 0.942252004 1.015941561 0.30687047 0.060842494 281.9197972 754791.6764 0.022568887 0.016884988 169.5208123 -2.229223025 0.073689557 AAPFSLEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AAPFSLEYR 9 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 221.7 9.54E-07 1730870000 2221540 1592681 1156925 1349739 2542690 1284389 2388070 1738260 2423480 FALSE TRUE 2116532.207 1754977.005 1209971.156 1214060.671 2986134.331 1239910.287 2023726.062 1586048.739 2799300.901 0.75609314 0.626934033 0.432240477 0.433701383 1.066742889 0.442935694 0.72293981 0.566587443 1 21.41663514 -1.812035597 2.516991537 1.121962196 0.637276409 0.266481858 0.192137634 17307716.77 11520785.23 12846511.36 0.046165097 0.015415741 1.812035597 -0.484685787 AAPGAEFAPNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 172.11 5.87E-05 1473410000 2218450 1822240 1810870 2073890 2009480 1963470 2487680 2182860 2191270 FALSE TRUE 2113588.265 2007928.328 1893900.181 1865418.637 2359932.676 1895474.542 2108138.727 1991717.206 2531080.96 0.835053599 0.793308614 0.748257448 0.737004729 0.932381347 0.74887946 0.832900551 0.786903792 1 21.27132222 -4.99999651 0.452578803 5.536432381 0.800796301 0.542725982 0.057108503 1010.862503 5.786383327 4599.116612 0.027443023 1.00E-05 4.99999651 -4.735636079 AAPGYHMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAPGYHMAK 9 0 P11216;H0Y4Z6;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, muscle form;Glycogen phosphorylase, liver form" 0 86.011 0.014427 75418000 174270 160080 117380 143990 161920 134680 184580 162210 150240 FALSE TRUE 166032.6025 176392.334 122761.9891 129515.8516 190158.7967 130015.9978 156418.931 148006.0325 173538.4519 0.956748206 1.016445244 0.707405118 0.746323655 1.095773269 0.749205703 0.901350273 0.852871688 1 17.40489584 3.817621473 24.99988637 0.860689059 0.986597089 0.15315168 0.11887089 171.7069779 54293.77651 0.028149799 0.050747771 6570.848782 -3.817621473 0.12590803 AAPHKAEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAPHKAEGLEEADTGASGCHSHPEEQPTSISPSR 34 1 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AAPHKAEGLEEADTGASGCHSHPEEQPTS(0.001)IS(0.991)PS(0.007)R 241.06 2.14E-47 211990000 113700 70439 111270 106250 114310 100630 159530 117850 15133 TRUE FALSE 108325.6263 77616.81418 116371.8396 95569.54814 134245.6278 97145.15787 135190.7685 107530.4292 17479.74835 6.197207429 4.440385103 6.657523737 5.467444166 7.680066389 5.55758332 7.734137003 6.151714949 1 14.09339679 3.720846321 24.55372505 6.175562924 5.318796073 0 1.947606358 2173.763573 3013045.888 0.451459762 0.701195118 5258.311629 -3.720846321 -0.856766851 AAPLDSIHSLAAYYIDCIR ddPTM_SK-BR-3_Trastuzumab_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 ; 296.17 1.06E-49 8154700000 4922500 4606100 5201700 5419500 5821800 4652600 6141000 5923200 6525300 FALSE TRUE 4689823.18 5075466.827 5440203.09 4874721.564 6837120.077 4491479.295 5204077.663 5404533.207 7537210.197 0.622222687 0.67338799 0.721779405 0.646754095 0.907115484 0.595907395 0.690451444 0.7170469 1 22.8455992 -5 0.298204101 3.534512886 0.674237817 0.564803619 0.083964927 187.9281639 1.743437964 297.5543186 0.078828308 1.00E-05 5 -2.860275069 AAPQS(ph)PSVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AAPQSPSVPK 10 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 1 AAPQS(0.938)PS(0.062)VPK;AAPQS(0.898)PS(0.102)VPK;AAPQS(0.991)PS(0.009)VPK;AAPQS(1)PSVPK;AAPQS(0.998)PS(0.002)VPK;AAPQS(0.99)PS(0.01)VPK;AAPQS(0.999)PS(0.001)VPK;AAPQS(0.991)PS(0.009)VPK;AAPQS(0.923)PS(0.077)VPK 220.25 6.22E-09 3409416000 4972180 4735220 4328600 5561110 3487860 4949430 4993890 5195890 3517900 TRUE FALSE 4737154.905 5217744.301 4527070.592 5002096.657 4096141.68 4778029.998 4231980.361 4740910.326 4063437.965 1.165799736 1.284071357 1.114098611 1.231001113 1.008048287 1.175858974 1.041477783 1.166723934 1 21.95426944 2.75475175 24.79360719 1.085767211 1.204601372 0.404633733 0.072062523 682.2188337 1044685.386 0.019615853 0.020749486 568.5278573 -2.75475175 0.118834161 AAPTRGS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAPTRGSPTK 10 1 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 AAPTRGS(0.853)PT(0.146)K 62.528 0.051175 43559000 121390 106190 105000 135090 82325 118120 136580 126110 96621 TRUE FALSE 115652.1353 117010.8817 109814.3539 121510.4965 96682.45393 114029.4748 115742.2125 115067.1398 111604.4912 1.036267752 1.04844241 0.983959988 1.088759917 0.866295369 1.021728369 1.037074864 1.031026069 1 16.76803556 3.689018552 1.635652405 1.00492458 1.043066301 0.057576505 0.05702171 1.130602204 5.908385719 0.016355794 0.035278238 4886.732342 -3.689018552 0.038141722 AAQAGRQS(ph)SAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAQAGRQSSAKR 12 2 Q99986 Q99986 VRK1 Serine/threonine-protein kinase VRK1 1 AAQAGRQS(0.97)S(0.03)AKR 79.81 0.011495 9460100 18278 10674 18339 18736 19414 19565 23574 18397 23321 TRUE FALSE 17414.03516 11761.69274 19179.86129 16852.62168 22799.79545 18887.45914 19977.35333 16786.06115 26937.50157 0.646460664 0.436628939 0.712013371 0.62561933 0.846396069 0.701158535 0.741618642 0.623148405 1 14.71732843 -4.99999998 0.074463418 2.15241138 0.270176875 0.531956853 0.101180747 197.2289346 1.049749471 38.31297064 4.200199194 1.00E-05 4.99999998 -1.882234505 AAQDRDQIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AAQDRDQIYR 10 1 P62995;P62995-3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;;;;; 201.75 2.15E-07 11747770000 6226640 4882830 4880270 5684260 6570790 5202220 6878400 5890510 6689210 FALSE TRUE 5932319.067 5380395.928 5104035.207 5112867.385 7716733.696 5022065.817 5828973.75 5374705.717 7726538.523 0.76778483 0.696352696 0.660584968 0.661728065 0.998731019 0.649976157 0.754409459 0.695616245 1 22.8813908 -1.886001069 2.490529126 1.137777424 0.735061387 0.40255801 0.101206686 18373140.8 10345969.57 14891562.43 0.022537715 0.013001664 1.886001069 -0.402716036 AAQEEYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAQEEYVK 8 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 146.81 0.0012734 495761000 811151 828480 644571 917700 641790 771150 819140 818854 744920 FALSE TRUE 772809.4998 912903.0539 674125.2179 825451.0525 753717.9728 744444.8821 694165.1485 747150.8027 860438.3891 0.898157857 1.060974342 0.783467156 0.959337778 0.875969718 0.865192548 0.806757529 0.868337364 1 19.71471237 3.740279042 24.99764055 0.870276017 0.979566095 0.229867222 0.074272261 172.3627775 2507315.831 0.017839878 0.030147715 5498.940775 -3.740279042 0.109290078 AAQEEYVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 AAQEEYVKR 9 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;;;;; 192.64 5.53E-05 79960200000 39906900 30044900 37466300 40391200 36745600 41275500 53457900 45152200 43818500 FALSE TRUE 38020579.92 33106509.47 39184166.91 36330999.84 43154021.01 39846119.09 45301915.53 41198434 50613649.19 0.751192229 0.654102401 0.774181817 0.717810322 0.852616274 0.787260348 0.895053336 0.813978732 1 25.59302316 1.592820255 0.323205944 1.013673827 0.673480846 0.736971249 0.049255715 0.596785741 0.212854268 0.073552707 0.067808016 39.15797774 -1.592820255 -0.34019298 AAQLQHSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAQLQHSEK 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 93.111 0.0096207 322841000 304810 236610 215970 265030 252830 225930 334360 298820 253090 FALSE TRUE 290402.2354 260720.828 225872.4381 238388.6809 296923.472 218105.9874 283347.2411 272653.7367 292337.9046 0.993378658 0.891847495 0.77264164 0.81545594 1.015685846 0.74607495 0.969245646 0.932666385 1 18.15727738 1.600037259 25 0.963232169 0.881665864 0.205052473 0.086617189 1.247538465 3971.633978 0.044234407 0.021064269 39.81413266 -1.600037259 -0.081566305 AAQMHSGYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AAQMHSGYQR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;;;; 133.23 0.00020274 732419000 306287 218951 194259 234248 321350 202059 324959 245144 312417 FALSE TRUE 291809.4205 241262.3558 203165.9673 210700.946 377393.3383 195061.6462 275380.5363 223677.8918 360865.0328 0.808638671 0.668566733 0.562997101 0.583877425 1.045801904 0.540539062 0.763112275 0.619838088 1 18.46109983 AAQQQQPSAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAQQQQPSASPR 12 0 Q86U86-8;Q86U86 Q86U86-8 PBRM1 Protein polybromo-1 1 AAQQQQPS(0.01)AS(0.99)PR;AAQQQQPS(0.044)AS(0.956)PR 110.92 0.0015078 26878000 48582.6 38721.1 48629.8 47155.1 53091.4 42330.2 52904.9 46530.5 56245.9 TRUE FALSE 46286.19678 42666.82411 50859.52443 42414.97976 62350.52335 40864.29456 44833.28584 42456.04275 64968.22691 0.712443589 0.656733701 0.782836886 0.652857278 0.959707942 0.628988915 0.690080182 0.653489325 1 15.98744671 -1.602706738 3.086313387 1.017039826 0.71307188 0.459066582 0.096405009 43333488.37 57731197.65 6146119.485 0.021895117 0.024962798 1.602706738 -0.303967946 AAQSPFSIPNSSSGPYGS(ph)QDSVHSSPEDGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAQSPFSIPNSSSGPYGSQDSVHSSPEDGGGGR 33 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AAQSPFSIPNSSSGPYGS(0.988)QDS(0.012)VHSSPEDGGGGR 217.39 3.85E-36 122340000 49351 34382 48961 51537 79502 42331 72502 66267 95576 TRUE FALSE 47018.27603 37885.56489 51205.91028 46356.40285 93367.12363 40865.06686 61440.48831 60464.31018 110397.4379 0.425900065 0.343174313 0.463832415 0.419904698 0.845736327 0.370163181 0.556539078 0.547696679 1 16.75234717 -4.999999998 0.151609162 2.872376852 0.323360199 0.605373277 0.133229979 86.0191471 0.770417839 48.39842134 0.609702838 1.00E-05 4.999999998 -2.549016654 AAREPNIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAREPNIDR 9 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 132.32 0.00028125 174690000 212680 112860 223180 159400 267300 192540 314430 226120 380810 FALSE TRUE 202627.0379 124360.5623 233413.0238 143376.8092 313917.0354 185872.2915 266457.9286 206319.7341 439864.0699 0.460658307 0.282724984 0.530648079 0.325957083 0.713668283 0.422567571 0.605773344 0.469053392 1 18.74669823 -5 0.159829524 3.017218902 0.319346059 0.666274838 0.119176495 69.12807907 0.635116014 44.03046165 0.443202881 1.00E-05 5 -2.697872843 AARPEIADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AARPEIADR 9 1 Q96GM8;Q96GM8-2 Q96GM8 TOE1 Target of EGR1 protein 1 0 74.944 0.036169 229930000 153840 134240 142460 173880 164450 147420 188130 165580 203860 FALSE TRUE 146568.2881 147919.2086 148991.9319 156401.252 193130.0279 142314.8084 159427.3133 151080.9374 235473.5676 0.622440512 0.628177549 0.632733149 0.664198762 0.8201771 0.604377 0.677049721 0.641604656 1 17.8452056 -5 0.343958663 4.776962289 0.647039521 0.75411314 0.060617485 196.0241145 1.633027069 544.715834 0.045693691 1.00E-05 5 -4.129922769 AAS(ph)ALLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 129.38 0.0011466 419067000 818987 834432 701988 829920 716648 748653 800224 802328 723949 TRUE FALSE 780275.1076 919461.5695 734174.8442 746494.8649 841631.1843 722726.9589 678135.1317 732071.9069 836215.3135 0.933103108 1.099551222 0.877973451 0.892706523 1.006476646 0.864283334 0.810957562 0.875458623 1 19.67351494 3.716510472 24.61775613 0.892560394 1.016327171 0.287765664 0.071753096 641.0109525 715652.9836 0.01900644 0.029472416 5206.075616 -3.716510472 0.123766776 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;AAS(1)LNYLNQPSAAPLQVSR 342.85 4.91E-76 1099093000 636212 643346 638342 748989 652385 668215 760248 660161 719675 TRUE FALSE 606139.5196 708903.6888 667610.6121 673699.2027 766160.7374 645074.547 644258.2047 602353.8031 831278.5234 0.729165379 0.852787205 0.803113028 0.810437397 0.921665502 0.776002903 0.77502087 0.72461129 1 19.66497241 4.654113776 3.276416148 0.821021802 0.72428118 0.128122791 0.079644237 0.583583023 10.21049809 0.017575852 0.125477144 45093.48245 -4.654113776 -0.096740622 AAS(ph)LRGGVGAPGSPSTPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AASLRGGVGAPGSPSTPPTR 20 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 AAS(0.783)LRGGVGAPGS(0.204)PS(0.009)T(0.003)PPTR;AAS(1)LRGGVGAPGSPSTPPTR;AAS(1)LRGGVGAPGSPSTPPTR;AAS(0.801)LRGGVGAPGS(0.114)PS(0.073)T(0.012)PPTR 202.61 3.01E-21 667599000 310171 207137 326688 296561 351489 318352 424323 338711 451448 TRUE FALSE 295509.8315 228244.4958 341666.9679 266750.1249 412788.5703 307327.3904 359584.7331 309051.6692 521456.2502 0.566701102 0.437705935 0.655216939 0.511548428 0.791607292 0.58936371 0.689577952 0.592670371 1 18.99218669 -5 0.132276406 2.372638554 0.429836941 0.663362368 0.091177925 76.33154533 0.632858326 27.68140621 0.593530654 1.00E-05 5 -1.942801614 AAS(ph)LTEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.994)LT(0.006)EDR;AAS(0.999)LT(0.001)EDR;AAS(1)LTEDR;AAS(0.999)LT(0.001)EDR 170.85 0.00030714 852330000 1558340 1978380 1357870 1954080 1377820 1663180 1455120 1585890 1292600 TRUE FALSE 1484680.357 2179979.171 1420129.683 1757652.166 1618111.372 1605583.66 1233114.719 1447021.064 1493049.806 0.994394393 1.460084695 0.951160287 1.177222728 1.083762487 1.075371801 0.825903271 0.969171328 1 20.50983086 2.13223168 1.923890858 0.91684636 1.167797087 0.26584582 0.144905639 0.365007422 2.631423062 0.074687714 0.043405628 135.5912549 -2.13223168 0.250950727 AAS(ph)LTEDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.998)LT(0.002)EDRDR;AAS(0.5)LT(0.5)EDRDR;AAS(0.832)LT(0.168)EDRDR;AAS(1)LTEDRDR;AAS(0.982)LT(0.018)EDRDR 193.81 3.22E-07 10920600000 8650390 7701683 7480456 8721760 7589299 7860901 9030420 8337372 9046618 TRUE FALSE 8241503.208 8486493.254 7823442.307 7845032.115 8912870.343 7588676.027 7652663.574 7607307.508 10449521.32 0.788696722 0.812141819 0.748689061 0.750755166 0.852945324 0.72622236 0.73234585 0.728005358 1 23.31693352 -1.240922759 5.404511804 1.000018198 0.769605878 0.763046862 0.040706449 9.15E-06 1.28E-06 0.040390145 0.009519297 0.057421858 1.240922759 -0.23041232 AAS(ph)PAKPSSLDLVPNLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AASPAKPSSLDLVPNLPK 18 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 AAS(1)PAKPSSLDLVPNLPK;AAS(1)PAKPSSLDLVPNLPK 237.95 4.39E-24 3056100000 4696800 4294500 4144300 4979600 2594500 4875100 5513300 5497000 3064300 TRUE FALSE 4474791.572 4732114.432 4334320.254 4479041.147 3046979.979 4706274.065 4672144.826 5015653.539 3539495.994 1.264245412 1.336945837 1.224558599 1.265446028 0.860851371 1.329645258 1.320002858 1.417053035 1 21.75511251 -1.815825604 2.516922553 0.911762345 1.256691793 0.220688686 0.148826082 14450035.26 9822649.595 7758622.369 0.035077519 0.015281796 1.815825604 0.344929448 AAS(ph)PERPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASPERPPR 9 1 A0A1B0GV45 A0A1B0GV45 1 AAS(1)PERPPR 120.77 0.00038312 100940000 167790 114640 123500 160070 156370 136470 165130 127400 187650 TRUE FALSE 159858.8992 126321.9463 129162.5972 143979.4595 183640.8785 131744.0097 139936.3857 116244.1806 216749.8036 0.737527308 0.582800742 0.595906409 0.664265698 0.847248189 0.607816051 0.645612514 0.536305817 1 17.72567116 -1.02735228 4.506286412 1.000014359 0.653030019 0.609451456 0.087499746 0.240638383 50192943.12 1614.676471 0.019560401 0.093896136 1.02735228 -0.34698434 AAS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AASPFR 6 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 AAS(1)PFR;AAS(1)PFR;AAS(1)PFR;AAS(1)PFR 99.755 0.040319 3293740000 1416230 1171310 1236180 1407510 1477190 1257730 1538110 1420620 1591060 TRUE FALSE 1349287.615 1290667.821 1292860.076 1266024.421 1734811.468 1214174.495 1303443.07 1296222.982 1837793.459 0.734188931 0.702292096 0.70348497 0.688882864 0.943964329 0.660669723 0.709243503 0.70531483 1 20.80954321 -1.175346471 4.541684131 1.000048835 0.728328427 0.539479355 0.078071042 3.58E-05 6.49E-06 0.070014082 0.016499516 0.066781094 1.175346471 -0.271720407 AAS(ph)PPASASDLIEQQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.999)PPAS(0.001)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.998)PPAS(0.002)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK 380.17 1.92E-105 2599190000 1526885 1416125 1428915 1702445 1192874 1566755 1679633 1655391 1354820 TRUE FALSE 1454712.172 1560429.748 1494432.166 1531311.994 1400910.848 1512497.881 1423374.137 1510436.188 1564918.566 0.929576914 0.997131596 0.954958423 0.978525035 0.895197283 0.966502612 0.909551569 0.965185167 1 20.57765615 AAS(ph)PPASASDLIEQQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AASPPASASDLIEQQQKR 18 1 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQKR;AAS(1)PPASASDLIEQQQKR;AAS(1)PPASASDLIEQQQKR;AAS(1)PPASASDLIEQQQKR;AAS(1)PPASASDLIEQQQKR 205.21 6.05E-16 1765600000 1226060 594201 1339100 931890 1198780 1249050 1993350 1483540 1905620 TRUE FALSE 1168106.574 654750.7575 1400499.06 838214.6467 1407846.852 1205795.085 1689227.847 1353633.373 2201133.817 0.530684034 0.297460678 0.63626257 0.380810399 0.639600756 0.547806351 0.767435325 0.614970958 1 21.06981543 1.09403849 0.34432138 1.042693335 0.394721267 0.671760856 0.111064036 0.767908523 0.277787249 0.185823382 0.112794923 12.41762355 -1.09403849 -0.647972068 AAS(ph)PS(ph)PQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 155.86 1.75E-05 2202160000 2657150 2263850 2268600 2732900 2548860 2367270 2833260 2266500 2589260 TRUE FALSE 2531551.785 2494538.889 2372617.554 2458183.7 2993380.377 2285290.846 2400994.151 2068033.245 2990789.217 0.846449416 0.834073787 0.793308181 0.82191807 1.00086638 0.764109632 0.802796177 0.6914674 1 21.51209481 -0.500875485 6.576774714 1.000021325 0.823037079 0.34700806 0.077725289 9555894.667 1452975.372 0.070790656 0.017169256 0.315590931 0.500875485 -0.176984246 AAS(ph)PSPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASPSPAR 8 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AAS(0.921)PS(0.079)PAR 106.68 0.0043514 123770000 167800 167580 308030 204940 163040 276550 245760 173590 230680 TRUE FALSE 159868.4265 184656.5925 322153.4802 184339.0418 191474.1244 266973.0042 208264.7983 158389.5393 266452.6762 0.599988068 0.693018344 1.209045766 0.691826573 0.718604621 1.001952797 0.781620216 0.594437787 1 18.0235198 3.982820003 24.88642918 0.848640651 0.634874338 0.198656405 0.178927057 1005.632194 1456732.471 0.042827136 0.078006296 9612.138127 -3.982820003 -0.213766313 AAS(ph)PSPQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.937)PS(0.063)PQSVR;AAS(0.998)PS(0.002)PQSVR;AAS(0.977)PS(0.023)PQSVR;AAS(0.728)PS(0.272)PQSVR;AAS(0.999)PS(0.001)PQSVR;AAS(0.954)PS(0.046)PQSVR 154.94 1.43E-05 5259020000 3941240 3396140 3264950 3891490 4071040 3412110 4053320 3410460 4264590 TRUE FALSE 3754945.396 3742210.527 3414651.187 3500310.032 4781028.087 3293947.775 3434911.59 3111822.042 4925920.837 0.762282936 0.759697659 0.693200581 0.710589989 0.970585652 0.668696856 0.6973136 0.631723924 1 22.23196201 3.968053923 24.51801054 0.749883399 0.76131355 0 0.124428539 8855.088121 6796133.226 0.029577474 0.053343074 9290.817356 -3.968053923 0.011430151 AAS(ph)QDHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AASQDHVR 8 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 1 AAS(1)QDHVR;AAS(1)QDHVR;AAS(1)QDHVR;AAS(1)QDHVR;AAS(1)QDHVR 109.11 0.0023709 267365000 259736.7 185811.2 206548.4 347570 282368 296849.5 332987 213979.1 295940 TRUE FALSE 247459.4609 204745.5725 216018.8484 312631.6033 331612.8898 286569.5274 282183.7174 195241.9556 341832.8637 0.723919457 0.59896398 0.631942892 0.91457445 0.970102424 0.83833229 0.825502014 0.57116204 1 18.38293158 3.247218274 24.99751973 0.847744345 0.650657804 0.387846354 0.119299076 190.0895476 548848.0411 0.03198594 0.042647725 1766.925645 -3.247218274 -0.197086541 AAS(ph)VIPGSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AASVIPGSTSR 11 0 J3KPJ3;Q8N5S9;Q8N5S9-2 J3KPJ3 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 1 AAS(0.995)VIPGS(0.004)TSR;AAS(1)VIPGSTSR 129.04 0.00026578 254110000 222930 223470 229830 290290 280250 298540 364400 322220 404430 TRUE FALSE 212392.5407 246241.8471 240367.9328 261109.4977 329125.5113 288201.4849 308804.0873 294004.7086 467146.9389 0.454658959 0.527118614 0.514544596 0.558945111 0.704543868 0.616939684 0.661042729 0.629362379 1 18.83351689 -5 0.104448686 2.391961692 0.301127049 0.910971631 0.044844569 45.54664757 0.320469197 13.61270246 0.63473016 1.00E-05 5 -2.090834643 AASAPAKES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR 170.26 1.75E-05 51152050000 48873930 44217900 43534350 50936670 34979950 49491870 54007230 50725220 40059760 TRUE FALSE 46563756.19 48723754.28 45530443.01 45816419.16 41080442.2 47777954.13 45767435.15 46283450.83 46272022.98 1.006304743 1.052985176 0.98397347 0.990153795 0.88780303 1.032545176 0.989095185 1.000246971 1 25.46363684 3.715746245 22.13878603 0.98272942 1.029644941 0.200098675 0.038419455 245.5074517 238237.3345 0.009779928 0.015170823 5196.922552 -3.715746245 0.046915521 AASAPAKES(ph)PRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 138.19 4.12E-05 885370000 1056750 997490 970440 1100570 567753 1168700 1130150 1158470 667429 TRUE FALSE 1006799.522 1099135.365 1014935.634 989938.6127 666768.9434 1128227.626 957724.8609 1057028.225 770930.4806 1.305953711 1.425725656 1.316507337 1.284082855 0.864888547 1.463462211 1.242297308 1.371107061 1 19.55624124 -4.531352211 0.200568268 4.06E-30 1.337739599 0.212135216 0.164903269 178.9958418 2.101093202 73.13620849 0.377123727 2.94E-05 4.531352211 1.337739599 AASDPLLSSVS(ph)PAVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.217)S(0.16)VS(0.623)PAVSK;AASDPLLS(0.27)S(0.148)VS(0.582)PAVSK;AASDPLLS(0.001)SVS(0.999)PAVSK 202.63 3.13E-11 151086000 388370 363460 320690 396180 269815 356050 426240 424670 351350 TRUE FALSE 370012.5198 400496.9872 335393.9537 356355.2337 316870.6506 343719.8992 361209.2596 387483.6435 405835.5636 0.911730151 0.986845469 0.826428199 0.878077886 0.780785813 0.846943763 0.890038459 0.954779912 1 18.63053577 -0.905660986 5.420109709 1.000000131 0.888658038 0.268736437 0.059542788 1.00E-07 2.00E-08 0.0611151 0.01440495 0.124262193 0.905660986 -0.111342093 AASEQQADTSGGDS(ph)PKDESKPPFSYAQLIVQAISSAQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASEQQADTSGGDSPKDESKPPFSYAQLIVQAISSAQDR 39 2 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 AAS(0.113)EQQADT(0.142)S(0.142)GGDS(0.483)PKDES(0.098)KPPFS(0.019)Y(0.004)AQLIVQAISSAQDR 47.231 0.026924 103320000 102830 85102 92413 94304 48530 96830 96771 97226 55611 TRUE FALSE 97969.42969 93773.99055 96650.22746 84824.38275 56993.61663 93476.75282 82006.80663 88712.37601 64234.86986 1.525175188 1.459861143 1.504638021 1.320534827 0.887269123 1.455233785 1.276671173 1.381062594 1 15.97106906 8 0.088399272 0.847664886 2.765459879 0.36280716 0.170117713 174.3840531 1.110557976 3.222148788 40.58769612 100000000 -8 1.917794993 AASGEAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AASGEAKPK 9 1 P10412;P16401;P16403 P10412;P16401;P16403 HIST1H1E;HIST1H1B;HIST1H1C Histone H1.4;Histone H1.5;Histone H1.2 0 86.898 0.01261 88715000 137180 118150 119930 149670 97255 134880 133740 148150 128970 FALSE TRUE 130695.7733 130189.6193 125428.9091 134624.8872 114216.2412 130209.0718 113335.5067 135177.2006 148970.0089 0.877329432 0.873931742 0.841974234 0.903704633 0.766706279 0.874062321 0.760794119 0.90741218 1 17.18466239 0.993269315 24.68772929 1.000000006 0.844259949 0.547545134 0.046406655 161.1842723 591216.2571 0.043094317 0.010773579 9.846214999 -0.993269315 -0.155740057 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK 134.37 1.63E-08 70481000 44963 45809 42634 51557 39609 43187 53263 45346 40397 TRUE FALSE 42837.6881 50476.98918 44588.81107 46374.39241 46516.79706 41691.42336 45136.75111 41375.26385 46661.56044 0.918050912 1.081768134 0.955579082 0.993845726 0.996897588 0.893485408 0.967321939 0.88670982 1 15.50994693 2.268557576 24.59974515 0.936257067 0.994057096 0.197456184 0.051930908 239.2054256 196165.4424 0.016616133 0.01390019 185.5912839 -2.268557576 0.057800029 AASLT(ph)EDRDR ddPTM_SK-BR-3_Trastuzumab_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 1 AAS(0.475)LT(0.525)EDRDR;AAS(0.373)LT(0.627)EDRDR;AAS(0.072)LT(0.928)EDRDR 179.72 1.32E-05 1030217000 1547590 1433059 1389016 1594520 1423384 1511200 1733600 1551750 1653640 TRUE FALSE 1474438.488 1579089.341 1452703.758 1434235.82 1671621.719 1458866.765 1469107.48 1415870.544 1910078.046 0.771925781 0.826714565 0.760546806 0.750878124 0.875158857 0.76377338 0.769134792 0.741263189 1 20.86520016 -2.141998321 2.45875164 1.480579087 0.78492396 0.744628178 0.040019464 2146068.81 603857.1079 5768792.968 0.009663159 0.007211103 2.141998321 -0.695655127 AASLTEDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 95.483 0.0067409 582570000 250160 231370 269710 248300 371740 233680 291330 242240 379320 FALSE TRUE 238335.4326 254946.866 282076.4703 223340.4123 436571.3383 225587.603 246882.2579 221028.1814 438143.0083 0.543967216 0.581880485 0.643800004 0.509743184 0.996412884 0.514872082 0.563474147 0.504465842 1 18.74104231 -1.196723584 3.706949705 1.000414017 0.603899249 0.421414951 0.144548374 49985056.15 89638967.23 246751.7458 0.032352526 0.063573543 1.196723584 -0.396514768 AASPS(ph)PQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.496)PS(0.504)PQSVR;AAS(0.395)PS(0.605)PQSVR 101.71 0.0032991 1151960000 556560 461840 483980 550850 535170 482770 624500 537710 577930 TRUE FALSE 530252.5118 508902.0211 506170.9617 495477.5115 628503.4786 466051.5538 529221.0553 490625.2618 667552.4327 0.794323391 0.762340149 0.758248996 0.742230104 0.941504289 0.698149735 0.792778259 0.734961387 1 19.34852163 -0.942541908 4.193996319 1.000007768 0.778345272 0.539551271 0.064431093 3106712.006 1481593.483 214.882177 0.013392636 0.114145315 0.942541908 -0.221662496 AASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK 180.26 4.24E-17 8829470000 5295190 4102650 4825350 4902170 2801970 5127640 5527400 6188050 3563320 TRUE FALSE 5044896.863 4520714.699 5046597.07 4409394.558 3290632.681 4950068.541 4684093.612 5646191.537 4115901.467 1.225708852 1.09835348 1.226121935 1.071307123 0.79949258 1.20266935 1.138048044 1.371799491 1 21.97277701 -0.409371687 7.278644733 1.00000973 1.135917402 0.082665289 0.147221406 0 0 0.135171068 0.031860126 0.389608401 0.409371687 0.135907672 AAT(ph)PLPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AATPLPSLR 9 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AAT(0.758)PLPS(0.242)LR;AAT(1)PLPSLR;AAT(0.999)PLPS(0.001)LR;AAT(0.997)PLPS(0.003)LR 136.27 0.0022069 824510000 2540130 2190070 2364090 2607410 2272300 2234380 2794660 2454450 2453390 TRUE FALSE 2420063.089 2413240.623 2472485.865 2345308.193 2668588.401 2157002.86 2368283.29 2239525.346 2833849.191 0.853984431 0.85157694 0.872483219 0.827605153 0.94168328 0.761156545 0.835712534 0.790276827 1 21.43433155 2.229780226 24.9999054 0.830806986 0.863853964 0 0.068991308 594.9454447 1693938.837 0.022253919 0.016689293 169.7384476 -2.229780226 0.033046978 AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AATAARPPAPPPAPQPPS(0.999)PT(0.003)PS(0.984)PPRPT(0.013)LAR;AATAARPPAPPPAPQPPS(0.925)PT(0.076)PS(0.993)PPRPT(0.005)LAR;AATAARPPAPPPAPQPPS(0.989)PT(0.012)PS(0.998)PPRPTLAR;AATAARPPAPPPAPQPPS(0.912)PT(0.159)PS(0.854)PPRPT(0.075)LAR;AATAARPPAPPPAPQPPS(0.917)PT(0.172)PS(0.859)PPRPT(0.053)LAR;AAT(0.001)AARPPAPPPAPQPPS(0.775)PT(0.228)PS(0.99)PPRPT(0.007)LAR 122.96 8.23E-05 6464040000 1120388 953399 1072218 1121217 1116268 1020672 1182380 1078380 1167889 TRUE FALSE 1067429.48 1050551.442 1121380.256 1008510.137 1310944.786 985325.8727 1001986.215 983951.3303 1348999.261 0.791275066 0.778763541 0.83126825 0.747598732 0.971790588 0.730412463 0.742762612 0.729393528 1 20.36345813 -2.228413874 2.374735973 1.736965807 0.788661608 0.458137728 0.071612305 3027441.637 763847.9707 11962138.76 0.016818592 0.005909982 2.228413874 -0.948304199 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.881)PT(0.115)PS(0.004)PPRPTLAR 190.22 1.30E-18 205370000 98002 68491 103830 84387 85168 88916 108690 103940 100850 TRUE FALSE 93369.63968 75470.31077 108590.7082 75904.25844 100021.2722 85836.81662 92107.34427 94838.46258 116489.3029 0.801529731 0.647873314 0.932194678 0.651598529 0.858630533 0.736864368 0.790693583 0.814138811 1 16.82983795 -4.999999337 0.227813598 2.235626541 0.743592943 0.399914994 0.085729889 141.7415935 1.417920905 80.46344665 0.13140813 1.00E-05 4.999999337 -1.492033598 AATAARPPAPPPAPQPPSPT(ph)PSPPRPTLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.365)PT(0.496)PS(0.138)PPRPTLAR 144.55 2.01E-06 208570000 60652 61831 74915 68636 50207 63399 70813 66539 69503 TRUE FALSE 57785.10016 68131.6492 78349.92685 61736.57888 58963.0849 61203.47673 60009.17628 60712.49241 80281.17027 0.719783979 0.84866288 0.975944005 0.769004471 0.734457217 0.762364033 0.747487563 0.756248224 1 16.29277403 -1.557281881 3.093796465 1.00898613 0.78941901 0.440352924 0.074668541 18449451.66 20944760.35 1369590.134 0.018441091 0.027715207 1.557281881 -0.21956712 AATEALGEKS(ph)PDSATVSGYDIMK ddPTM_SK-BR-3_Trastuzumab_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(0.997)PDS(0.003)ATVSGYDIMK;AATEALGEKS(1)PDSATVSGYDIMK 306 1.01E-62 696180000 1039990 762500 854460 1018100 533940 1007280 1098260 1049270 559850 TRUE FALSE 990831.7338 840199.6169 893637.8362 915758.6537 627058.9669 972397.641 930700.2661 957390.3563 646668.6787 1.532209254 1.299273716 1.38190988 1.416117223 0.969675798 1.503703014 1.439222738 1.480495945 1 19.30266721 4.612021178 2.730147081 1.336505055 1.544842658 0.10687251 0.187725637 0.810028581 9.674564103 0.043067699 0.332694894 40928.06178 -4.612021178 0.208337603 AATFGLILDDVSLTHLTFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AATFGLILDDVSLTHLTFGK 20 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ; 305.33 2.64E-55 252270000 1536360 1151280 1316850 1541040 1470510 1141160 1670700 1451530 1361360 FALSE TRUE 1463739.308 1268596.741 1377228.875 1386131.731 1726966.478 1101641.343 1415804.03 1324426.338 1572472.756 0.930851935 0.806752763 0.875836398 0.88149809 1.098248903 0.70057897 0.900367924 0.842257097 1 20.58460359 3.229702431 4.836715589 0.894286297 0.865472565 0.015325209 0.105912966 1.139915226 69.63362292 0.028725703 0.036631037 1697.080452 -3.229702431 -0.028813732 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK 31 0 O00764;O00764-2 O00764 PDXK Pyridoxal kinase 0 255.96 1.16E-58 97106000 103490 100940 102220 93794 113320 82149 135040 127710 24087 FALSE TRUE 98598.2328 111225.9008 106906.8881 84365.64892 133082.9721 79304.15953 114437.1678 116527.0354 27822.28894 3.543857697 3.997726463 3.842490758 3.032304391 4.783322192 2.850382285 4.113147127 4.188261994 1 14.76395349 -0.715376424 6.362225636 0.999999986 3.787553669 0.711499572 0.559106758 1.10E-07 2.82E-08 0.463391854 0.109222508 0.192585496 0.715376424 2.787553683 AATGEEVSAEDLGGADLHCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AATGEEVSAEDLGGADLHCR 20 0 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;D6RD67 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 233.37 1.73E-29 375730000 298140 221841 223798 278870 257430 234690 294070 269810 270700 FALSE TRUE 284047.5131 244446.8501 234059.3597 250837.4578 302325.7105 226562.6265 249204.2205 246184.006 312678.7735 0.90843235 0.781782682 0.748561717 0.802220934 0.96688914 0.724585887 0.796997563 0.787338403 1 18.25432176 -1.773444118 7.509973698 1.00369586 0.81415787 0.39525502 0.072068576 0.00430783 0.000129956 0.067404501 0.01564112 0.016848292 1.773444118 -0.18953799 AATSDLEHYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AATSDLEHYDK 11 0 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 146.16 3.59E-05 143280000 932620 794470 759170 894330 797810 813150 991620 888370 669100 FALSE TRUE 888536.9009 875427.3962 793978.6954 804430.2493 936947.8114 784990.4116 840330.1566 810579.6133 772860.6107 1.149672902 1.132710587 1.027324571 1.040847778 1.212311507 1.015694681 1.087298466 1.048804405 1 19.55984871 3.153268469 0.015252185 3.21E-06 2.196168569 0.273103069 0.057548509 1650.689185 7.563427903 513.9626201 574.7757432 1423.208304 -3.153268469 2.196165361 AATTATPAATT(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATTATPAATTSPK 14 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 AATTATPAAT(0.057)T(0.471)S(0.471)PK 89.629 0.067888 57585000 74737 85390 70856 82430 56052 75382 69599 79711 61822 TRUE FALSE 71204.33012 94091.33808 74104.81769 74143.97979 65827.45105 72771.50244 58980.39428 72731.08227 71409.04002 0.997133278 1.317639028 1.03775121 1.03829963 0.921836381 1.019079691 0.825951368 1.018513654 1 16.1238191 3.219882306 2.028879545 0.943705438 1.155297552 0.35710478 0.099089579 0.268154107 2.268967575 0.029882237 0.040627453 1659.137218 -3.219882306 0.211592114 AATTATPAATTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AATTATPAATTSPK 14 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 AATTATPAAT(0.002)T(0.079)S(0.919)PK 131.86 5.64E-05 59362000 155380 198190 139020 182190 87847 173060 147030 172940 96718 TRUE FALSE 148035.4953 218385.7863 145394.2045 163875.9151 103167.489 167066.8888 124597.8731 157796.4568 111716.5335 1.325099256 1.954820648 1.301456463 1.466890441 0.923475566 1.49545357 1.115303789 1.412471833 1 16.76948319 3.569039149 8.459132118 1.248238426 1.640270569 0.320988197 0.240138267 0.328481769 27.65945763 0.05765909 0.089371879 3707.14138 -3.569039149 0.392032143 AAVAGEDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 143.89 0.00023467 525690000 434820 329030 360810 457530 536010 374410 428730 396340 527910 FALSE TRUE 414266.9203 362558.5311 377353.4954 411538.2151 629489.9743 361444.0878 363319.3643 361634.3685 609775.5866 0.679376035 0.594576987 0.618839953 0.674901102 1.032330562 0.592749359 0.595824714 0.593061409 1 19.21791887 -1.650903751 2.857899294 1.033485902 0.666450578 0.376233549 0.13222249 57764025.41 56292539.61 14261197.45 0.031217056 0.022340673 1.650903751 -0.367035324 AAVEEGIVLGGGCALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAVEEGIVLGGGCALLR 17 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 174.84 3.03E-09 18018000 37998 24841 33113 28608 31558 27938 36229 40428 40597 FALSE TRUE 36201.90984 27372.32614 34631.2638 25732.26949 37061.70521 26970.50005 30701.60066 36887.91 46892.57542 0.772017948 0.583724095 0.738523391 0.548749333 0.790353374 0.575155018 0.654721998 0.786647133 1 15.5170719 0.931865571 3.032782568 0.999449299 0.663088871 0.626774752 0.082437682 0.181112229 3.965866912 0.068779649 0.018044417 8.548020811 -0.931865571 -0.336360428 AAVENLPTFLVELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAVENLPTFLVELSR 15 0 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 92.856 0.011821 29679000 128200 95266 121660 113580 103350 130750 167230 133600 108450 FALSE TRUE 122140.2401 104973.7137 127238.2313 102162.7226 121374.2073 126222.0947 141715.9921 121901.2757 125267.8721 0.975032449 0.837993908 1.015729167 0.815554067 0.968917291 1.007617457 1.131303579 0.973124822 1 16.93465692 2.29071558 2.97493052 1.051292563 0.91100259 0.353229822 0.071800653 0.217009403 3.93854121 0.025761571 0.019621455 195.3059976 -2.29071558 -0.140289974 AAVEWFDGKDFQGSK ddPTM_SK-BR-3_Trastuzumab_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 ; 218.98 1.70E-12 2388300000 3206920 2767340 2939630 3475140 2417030 3399860 3855460 3780280 2657000 FALSE TRUE 3055335.247 3049335.092 3074414.943 3125812.325 2838559.267 3282121.996 3267238.767 3449258.643 3069033.99 0.995536464 0.993581401 1.001753305 1.018500393 0.92490317 1.069431621 1.064582138 1.123890662 1 21.54935319 2.196420401 24.81552482 1.069277608 0.990677053 0.503131432 0.038092168 98.96878375 58280.08584 0.012707004 0.009384823 157.1883667 -2.196420401 -0.078600555 AAVGQES(ph)PGGLEAGNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAVGQESPGGLEAGNAK 17 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK 233.59 4.31E-20 468370000 932110 870040 962600 1103110 777130 1081550 1151890 1082920 993860 TRUE FALSE 888051.0076 958698.0652 1006736.162 992223.287 912661.226 1044095.652 976148.0246 988093.7839 1147982.733 0.773575231 0.835115405 0.876961067 0.864318999 0.795013026 0.909504666 0.850315947 0.860721817 1 20.13066951 -5 0.117703571 1.504554984 0.763554548 0.689185283 0.034612765 86.84844901 0.666702754 10.48754135 0.33715959 1.00E-05 5 -0.741000436 AAVGRPLDKHEGALETLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAVGRPLDKHEGALETLLR 19 2 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 208.13 1.71E-16 1251400000 672990 643030 601450 724320 584940 634420 725210 743030 667210 FALSE TRUE 641179.0964 708555.4881 629027.0774 651509.9775 686953.3508 612449.8763 614565.8951 677966.3542 770677.5192 0.831968081 0.919392963 0.816200112 0.845373014 0.891362903 0.794690206 0.797435866 0.879701739 1 19.55576778 0.976574293 23.04203255 1.000000002 0.844989618 0.619874007 0.038695783 527.1876913 518554.6536 0.039405492 0.009851373 9.474892547 -0.976574293 -0.155010384 AAVHLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAVHLEGK 8 0 P18206;P18206-2 P18206 VCL Vinculin 0 100.15 0.0063088 244370000 894670 910610 592960 999500 656960 792600 936960 905090 677310 FALSE TRUE 852380.7222 1003402.194 620147.8025 899028.3611 771533.616 765152.0633 794009.5435 825835.5214 782343.7756 1.089521958 1.282559184 0.79267941 1.149147458 0.986182341 0.978025373 1.014911307 1.055591605 1 19.57744317 3.763679632 24.99978322 1.002663759 1.186040563 0.386892495 0.098893757 671.8378258 668646.4798 0.0225858 0.040696296 5803.361597 -3.763679632 0.183376804 AAVHYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAVHYDR 7 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 92.677 0.036046 109489000 133373 117727 118257 124942 174224 116724 142591 123159 146852 FALSE TRUE 127068.7226 129723.5151 123679.2004 112382.5928 204608.6104 112681.8186 120836.1241 112374.5451 169625.0581 0.749115278 0.764766224 0.72913284 0.662535324 1.206240473 0.664299366 0.712371895 0.662487879 1 17.37198978 AAVLS(ph)DS(ph)EDEEKASAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAVLSDSEDEEKASAK 16 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 AAVLS(1)DS(1)EDEEKASAK;AAVLS(1)DS(1)EDEEKASAK 178.72 1.56E-09 1285510000 3087300 2747600 2538700 3221300 1392390 3233800 3074600 3498300 1536110 TRUE FALSE 2941369.447 3027583.564 2655101.906 2897488.804 1635222.375 3121812.695 2605513.301 3191970.306 1774322.093 1.657742672 1.706332562 1.496403565 1.633011737 0.921604021 1.759439679 1.468455649 1.798980195 1 20.7588365 3.519722645 2.051732945 1.452236443 1.682637799 0.110982498 0.28581985 0.711803177 5.955663806 0.07764992 0.131192322 3309.197177 -3.519722645 0.230401356 AAVPSGAS(ph)TGIYEALELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.009)GAS(0.951)T(0.039)GIYEALELR;AAVPSGAS(0.968)T(0.032)GIYEALELR;AAVPSGAS(0.925)T(0.075)GIYEALELR;AAVPSGAS(0.964)T(0.036)GIYEALELR 257.15 1.36E-30 283131000 32869.1 27538.6 29595.7 35732.6 31191.3 28963.1 36639.2 30473 40636.8 TRUE FALSE 31315.44278 30344.81465 30952.69212 32140.69116 36631.05284 27960.10058 31049.21711 27804.62257 46938.5474 0.667158328 0.646479628 0.659430124 0.684739792 0.780404484 0.595674603 0.661486536 0.592362229 1 15.51848558 -1.463494822 3.114814775 1.007220514 0.661354593 0.809446495 0.051695929 15110977.87 18361951.17 946192.0049 0.012022492 0.034395781 1.463494822 -0.345865922 AAVPSGASTGIYEALELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 266.35 9.05E-31 1100862000 104833.5 71092.2 74862.5 98310.5 102027.6 88691.9 120115.2 102575.6 114529.8 FALSE TRUE 99878.22821 78336.57601 78295.01967 88428.14176 119821.1811 85620.47726 101789.4202 93593.53668 132290.4964 0.754991711 0.592155734 0.591841604 0.66843911 0.905742925 0.647215632 0.769438644 0.707484961 1 17.0133499 -5 0.180959383 2.258497937 0.637062239 0.526131353 0.090251432 103.751711 1.000508004 46.73583525 0.265477775 1.00E-05 5 -1.621435698 AAVPSGASTGIYEALELRDNDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAVPSGASTGIYEALELRDNDK 22 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 265.9 1.19E-37 690870000 853940 259896 804660 505543 949730 771090 1522810 983350 1428150 FALSE TRUE 813575.9485 286379.6979 841554.4569 454724.8572 1115362.611 744386.96 1290477.366 897242.6609 1649620.208 0.493189853 0.173603413 0.510150429 0.275654272 0.67613297 0.451247479 0.782287559 0.543908626 1 20.65370248 1.376065963 0.394290794 1.011590004 0.306100884 0.608829651 0.147960873 0.635700269 0.297628268 0.175998045 0.12304937 23.7720132 -1.376065963 -0.70548912 AAVPSGASTGIYEALELRDNDKTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AAVPSGASTGIYEALELRDNDKTR 24 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ; 243.23 6.42E-38 364350000 329550 118889 264090 210407 249940 257540 622500 216423 423490 FALSE TRUE 313972.8246 131003.9243 276198.7877 189256.4886 293529.4569 248621.3252 527526.192 197471.8548 489162.6663 0.641857701 0.267812598 0.56463587 0.386898882 0.600065126 0.508258995 1.078426929 0.403693635 1 18.89995477 1.872083795 8.879059675 0.82934436 0.480698004 0.371042054 0.203796497 0.297714906 20.02294495 0.07698426 0.048522458 74.48756809 -1.872083795 -0.348646356 AAVS(ph)PQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AAVSPQKR 8 1 E9PJF5;G5E9I4;Q9HCU9 E9PJF5 BRMS1 Breast cancer metastasis-suppressor 1 1 AAVS(1)PQKR;AAVS(1)PQKR;AAVS(1)PQKR 121.9 0.0008658 715870000 818960 767590 721170 903700 625040 859970 959340 928760 747650 TRUE FALSE 780249.3838 845808.2937 754236.3578 812858.3591 734046.7781 830189.0233 812975.0635 847432.8507 863591.7435 0.903493334 0.979407573 0.873371432 0.941253046 0.849992816 0.961321168 0.941388184 0.981288736 1 19.71998992 1.356519921 1.446454338 0.998429769 0.919798771 0.394849126 0.037665356 0.406410855 1.591743374 0.032307647 0.010211349 22.72583874 -1.356519921 -0.078630998 AAVT(ph)PGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AAVTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK 82.029 0.0125 7876350000 14125800 14222800 14240400 16362100 7790700 17105800 17287000 17497900 10345800 TRUE FALSE 13458101.43 15672119.49 14893336.43 14717350.62 9149395.613 16513421.86 14649550.65 15965691.11 11950173.82 1.126184575 1.311455358 1.246286175 1.231559544 0.765628663 1.381856205 1.225885989 1.336021664 1 23.51052827 -2.354791476 1.929533796 7.80E-05 1.206731771 0.122485247 0.170606512 2029051.766 241842.5906 8821655.723 0.038787715 0.004417825 2.354791476 1.206653753 AAVVT(ph)SPPPTTAPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 131.56 0.0001945 122150000 230940 206020 201100 230620 186300 196440 227450 215490 190590 TRUE FALSE 220023.9239 227013.6722 210320.6339 207437.6395 218790.661 189637.2335 192748.3251 196620.5532 220145.7238 0.99944673 1.031197283 0.955370063 0.942274217 0.993844701 0.861416839 0.875548804 0.89313819 1 17.7480993 3.007752881 0.985739517 0.899434321 1.014166725 0.33986171 0.047042983 0.434605147 0.920584541 0.02157298 0.026756258 1018.011962 -3.007752881 0.114732404 AAWEAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AAWEAGK 7 0 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 110.63 0.015726 158130000 175450 175970 154510 149020 272670 132940 180460 141980 249160 FALSE TRUE 167156.8262 193901.5431 161594.4363 134040.2265 320223.5617 128336.2545 152927.5126 129547.4785 287798.4603 0.580812093 0.673740724 0.561484715 0.465743376 1.112666 0.445924048 0.531370156 0.450132632 1 18.13469935 -2.151039637 2.469097617 1.932001851 0.605157587 0.292603519 0.194089736 8483686.61 2424477.77 44258337.3 0.04334388 0.007062531 2.151039637 -1.326844264 AAWEVDSGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AAWEVDSGRR 10 1 B7Z9I1;Q5T4U5;P11310;P11310-2 B7Z9I1 ACADM "Medium-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;;; 173.24 5.57E-06 1190650000 1006044 669365 735272 745454 1201620 627188 1039343 770543 1219850 FALSE TRUE 958490.2939 737574.0545 768984.9485 670519.5476 1411182.148 605468.3223 880772.1365 703070.17 1409018.108 0.680254064 0.523466697 0.545759451 0.475877169 1.001535849 0.429709398 0.625096393 0.498978804 1 20.42625872 -1.095275142 5.184551252 1.00000821 0.597317201 0.383228369 0.160438814 1.36E-05 2.37E-06 0.13827253 0.032590484 0.080301722 1.095275142 -0.402691009 AAWGEETDYTPVWCMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AAWGEETDYTPVWCMR 16 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494C007;A0A494C0P4 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ;;; 248.41 4.86E-20 139228000 74705 59845 61853 63972 85517 67206 89902 72244 77507 FALSE TRUE 71173.8427 65943.27354 64689.02123 57541.41302 100431.1377 64878.63937 76185.79874 65917.93237 89526.38971 0.795004053 0.736579167 0.722569305 0.642731302 1.121804845 0.724687319 0.850987055 0.736296109 1 16.45002539 AAYEAELGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AAYEAELGDAR 11 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 223.36 1.63E-11 3283130000 3630230 2965030 2775590 3672280 3425810 3085840 3576650 3347240 3513760 FALSE TRUE 3458636.222 3267169.928 2902853.547 3303135.438 4023270.179 2978976.587 3030966.353 3054137.921 4058655.955 0.852162948 0.804988145 0.715225331 0.813849578 0.991281405 0.733981057 0.746790658 0.752499831 1 21.95257062 -2.131419939 2.30667954 1.399732453 0.801109214 0.384528167 0.078983065 5225985.273 1386663.658 10931635.75 0.019294726 0.007388905 2.131419939 -0.598623239 AAYEAELGDARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AAYEAELGDARK 12 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 208.95 9.76E-08 4217470000 3963800 2981060 3496530 3618130 3334300 3714430 4547450 4091180 3939520 FALSE TRUE 3776439.029 3284833.403 3656849.359 3254428.698 3915800.864 3585798.358 3853652.983 3732934.59 4550440.641 0.829906228 0.721871498 0.803625329 0.715189793 0.860532237 0.788011237 0.846874685 0.820345739 1 22.11757482 0.049521535 0.400253267 1.033686268 0.769440931 0.688827554 0.044301493 2.155002713 0.479983893 0.159613139 0.027866609 1.120783 -0.049521535 -0.264245336 ACDEGHCTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ACDEGHCTAK 10 0 A0A0A0MT83;P26440;A0A0S2Z4K7;P26440-2;H0YLC3 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 ;;;;;; 120.09 0.00060585 860257000 2692958 2358006 2415350 2444915 1951011 2117757 2460039 2624214 2130975 FALSE TRUE 2565667.212 2598289.492 2526096.187 2199147.499 2291266.701 2044418.544 2084714.869 2394423.91 2461435.719 1.042345811 1.055599166 1.026269411 0.893440963 0.930865951 0.830579701 0.846950766 0.972775316 1 21.23106863 3.279430206 4.362751346 0.895628239 1.047619252 0.56073594 0.052603492 0.12222027 5.040394396 0.014371691 0.019152155 1902.962394 -3.279430206 0.151991014 ACDHCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ACDHCLR 7 0 C9IYN9;Q6GMV2 C9IYN9 SMYD5 SET and MYND domain-containing protein 5 0 68.915 0.061157 30566000 60317 61745 54188 70276 57949 51668 53924 57045 47219 FALSE TRUE 57465.93495 68036.8857 56672.5734 63211.72296 68055.28725 49878.7242 45696.90342 52049.83739 54541.48136 1.053618888 1.24743377 1.039072867 1.158966009 1.247771156 0.914509892 0.837837592 0.954316533 1 15.73506626 2.222095895 24.96126251 0.905131387 1.149462078 0.656253523 0.079415083 125.5050093 190270.0623 0.027879124 0.020648355 166.7615391 -2.222095895 0.244330691 ACESASHDNQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ACESASHDNQSVR 13 0 Q8TBZ6 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 0 ; 162.93 3.96E-05 106151000 81130 70775 78500 81589 93297 65870 90930 89511 107284 FALSE TRUE 77295.14568 77987.05296 82099.30265 73387.51871 109567.9673 63588.90538 77056.95846 81672.94231 123921.0548 0.623745059 0.629328512 0.662512943 0.592211863 0.884175554 0.513140446 0.621822971 0.659072362 1 16.9190618 0.920663486 16.48790488 1.000000001 0.642309558 0.581855994 0.093710324 359.8556877 74787.71154 0.081757417 0.020439826 8.33035456 -0.920663486 -0.357690442 ACFHCETCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ACFHCETCK 9 0 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 161.79 6.43E-05 532590000 1763910 1184000 760310 982930 1476290 1088160 2231000 1663290 1624860 FALSE TRUE 1680533.47 1304650.946 795170.9655 884124.009 1733754.509 1050476.746 1890619.975 1517643.51 1876834.99 0.895408216 0.695133538 0.423676546 0.471071785 0.923765018 0.559706502 1.007344804 0.808618508 1 20.83987038 1.72267413 9.962461134 0.927827516 0.677053176 0.372639372 0.168410253 0.124155778 37.86474766 0.081076265 0.043839574 52.80488849 -1.72267413 -0.250774341 ACGNFGIPCELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ACGNFGIPCELR 12 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 188.28 2.19E-05 454980000 689530 610740 622710 714180 725130 578292 749870 676880 836800 FALSE TRUE 656937.2834 672975.1004 651261.8694 642389.2695 851592.4424 558265.603 635463.5592 617608.7988 966566.6702 0.6796606 0.696253162 0.673788875 0.664609374 0.881048839 0.577575888 0.657444105 0.638971752 1 19.88250972 -1.319581043 3.679226996 1.000994236 0.682932213 0.624235575 0.077128894 905203630.6 1245454962 9569741.102 0.017275667 0.047909204 1.319581043 -0.318062023 ACHQLHQEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ACHQLHQEGK 10 0 A0A499FJT0;Q8NHP1;Q8NHP1-3;O95154 A0A499FJT0;O95154 AKR7L;AKR7A3 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 3 0 ; 139.43 2.38E-05 305627000 409786 345197 316449 343721 293482 336497 407792 361779 34002 FALSE TRUE 390416.2279 380372.9668 330958.4997 309169.5121 344665.1679 324844.0245 345575.8408 330099.7128 39274.8565 9.940615006 9.684897684 8.426727152 7.871945046 8.775720616 8.271042938 8.798907789 8.40486108 1 15.26131838 -0.551866617 0.570362568 1.15E-18 9.105489841 0.941769627 0.608374136 2.783998736 0.710426381 7.184833709 0.289234116 0.280629539 0.551866617 9.105489841 ACIAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ACIAEK 6 0 P60981;P60981-2 P60981 DSTN Destrin 0 109.88 0.067884 266230000 459170 454800 394180 465640 404210 466400 524660 477430 441280 FALSE TRUE 437465.9441 501144.6371 412253.5429 418832.9825 474704.096 450248.4511 444613.481 435623.6982 509711.4487 0.858261954 0.983192821 0.808797887 0.821706053 0.931319273 0.883339882 0.872284666 0.854647663 1 18.95932123 -1.486247838 6.247415761 1.000072439 0.88261938 0.363936155 0.050694915 5.05E-05 4.16E-06 0.048506551 0.011426065 0.032640151 1.486247838 -0.117453059 ACLISLGYDVENDRQGEAEFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ACLISLGYDVENDRQGEAEFNR 22 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;; 339.55 3.38E-81 2220058000 905211 503336 584138 794244 995679 595536 1054442 806543 1241166 FALSE TRUE 862423.47 554626.5106 610921.3051 714405.0842 1169325.102 574912.439 893567.5067 735917.8192 1433639.684 0.601562219 0.386866042 0.426133088 0.498315645 0.815633883 0.401015991 0.623285974 0.513321323 1 20.45125105 -5 0.247234914 3.826083639 0.484125122 0.575019614 0.126363313 123.7963404 1.229145415 176.4104607 0.173329491 1.00E-05 5 -3.341958517 ACNQLGQFLQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ACNQLGQFLQHR 12 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 ; 142.72 6.16E-05 781080000 3074000 2364200 1998580 2370270 2488820 2265500 3268100 2752200 2664200 FALSE TRUE 2928698.112 2605114.668 2090216.87 2132005.956 2922869.42 2187045.167 2769491.322 2511202.778 3077350.529 0.951694675 0.846544663 0.679226123 0.69280569 0.949800613 0.710690949 0.899959656 0.816027539 1 21.55325735 -0.46488627 15.70060417 1 0.825584474 0.243867654 0.09980384 0 0 0.094125851 0.022185676 0.34285756 0.46488627 -0.174415526 ACQSIYPLHDVFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ACQSIYPLHDVFVR 14 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 173.54 2.68E-06 6267160000 7204000 6280210 6481160 7527410 7726760 6790000 7898150 7441800 7719490 FALSE TRUE 6863481.197 6920170.539 6778327.597 6770740.446 9074304.498 6554860.597 6693142.158 6790156.541 8916589.084 0.769742906 0.776100645 0.760192887 0.759341984 1.017687864 0.735130949 0.750639297 0.761519509 1 23.0880605 -2.076258574 2.09253813 1.305820662 0.7882048 0.392903119 0.081450513 5928680.894 1673842.811 8646384.122 0.019773244 0.008389603 2.076258574 -0.517615862 ACRPPGS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ACRPPGSPGR 10 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR;ACRPPGS(1)PGR 98.368 0.0032851 4196559000 3477977 3780595 2722179 4013892 3292561 3027992 3105911 3051810 2785817 TRUE FALSE 3313579.92 4165841.929 2846993.6 3610407.95 3866782.596 2923131.878 2632047.233 2784577.338 3217827.272 1.029756926 1.294613283 0.884756501 1.122001787 1.201675003 0.908417895 0.817957898 0.865359481 1 21.61765546 2.1452552 6.21651572 0.872443681 1.115352618 0.441053535 0.11540617 0.16860137 9.303797566 0.041656756 0.030674432 139.7189135 -2.1452552 0.242908937 ACRPPGS(ph)PGRAPPPTPAPSGCDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ACRPPGSPGRAPPPTPAPSGCDPR 24 2 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR;ACRPPGS(1)PGRAPPPTPAPSGCDPR 105.02 0.001537 8231520000 1682290 1130050 1625740 1563830 1946000 1443480 1949870 1563180 1984250 TRUE FALSE 1602771.486 1245203.38 1700281.787 1406630.837 2285381.784 1393491.926 1652381.52 1426299.672 2291957.356 0.69930249 0.54329256 0.741847043 0.613724699 0.997131023 0.607992082 0.720947759 0.622306374 1 21.12814877 -5 0.260608748 2.996902374 0.661847427 0.362159186 0.124930691 205.3616763 2.015590575 220.076278 0.152823532 1.00E-05 5 -2.335054948 ACRT(ph)PESFLGPSASSLVNLDSLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(0.995)PES(0.005)FLGPSASSLVNLDSLVK;ACRT(0.973)PES(0.026)FLGPSASSLVNLDSLVK;ACRT(0.967)PES(0.033)FLGPSASSLVNLDSLVK 310.83 3.00E-73 538098000 493188 405920 426375 481307 384404 484005 570248 547678 491700 TRUE FALSE 469875.9806 447283.7095 445924.7155 432925.1059 451443.9359 467243.7855 483246.1943 499720.4109 567950.3247 0.827318799 0.787540195 0.785147391 0.762258752 0.794865178 0.822684247 0.850859966 0.879866406 1 19.11540523 0.944603904 0.861443917 0.99919191 0.792306903 0.935106787 0.017264425 0.1695092 0.270769067 0.017721081 0.006230794 8.802456841 -0.944603904 -0.206885007 ACS(ph)TLSLSGPELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ACSTLSLSGPELK 13 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ACS(0.981)T(0.018)LSLSGPELK;ACS(0.977)T(0.021)LS(0.002)LSGPELK;ACS(0.493)T(0.493)LS(0.015)LSGPELK;ACS(0.96)T(0.027)LS(0.013)LSGPELK 199.13 1.26E-07 927220000 2026480 1668864 1888649 2142690 1641962 2016470 2321360 2174350 1660570 TRUE FALSE 1930692.306 1838923.139 1975245.425 1927302.73 1928319.653 1946639.138 1967193.897 1983952.387 1918082.715 1.006574061 0.958729843 1.029802005 1.004806892 1.005337068 1.014888004 1.025604309 1.034341414 1 20.87123351 3.726922161 24.98870253 1.016954839 0.98265195 0.4389866 0.015849903 556.7795064 1195450.804 0.004040197 0.006317723 5332.393142 -3.726922161 -0.034302889 ACTGLSGPGSGS(ph)KSPPATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGS(0.001)GS(0.575)KS(0.418)PPAT(0.006)R 126.04 1.58E-05 236640000 259090 159770 237500 261270 200280 246780 304270 269830 257170 TRUE FALSE 246843.3292 176050.7446 248389.6099 235006.6432 235208.7686 238233.9467 257848.0232 246202.2547 297050.6102 0.830980718 0.592662458 0.836186163 0.791133346 0.791813787 0.801997837 0.868027246 0.828822586 1 18.18034923 0.970823755 0.309286652 1.030471993 0.710264558 0.518544777 0.068859778 1.426628475 0.409486648 0.16569342 0.09309397 9.350261463 -0.970823755 -0.320207435 ACTGLSGPGSGSKS(ph)PPATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGS(0.001)GS(0.065)KS(0.931)PPAT(0.003)R;ACTGLSGPGSGS(0.018)KS(0.975)PPAT(0.007)R 176.27 5.77E-13 297434000 395910 314426 398940 409740 353356 411690 499030 479430 435150 TRUE FALSE 377196.1189 346466.3669 417231.7936 368552.1567 414981.1745 397433.0721 422893.8082 437448.5676 502630.8396 0.750443644 0.689305828 0.830095889 0.733246207 0.825618211 0.790705704 0.841360647 0.870317802 1 18.93913967 0.714135777 0.248200601 1.064971054 0.694111753 0.814870629 0.036722618 1.26694639 0.216427885 0.157386936 0.074673823 5.177686813 -0.714135777 -0.370859301 ADAAEFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADAAEFWR 8 0 Q13191;A0A2R8Y8D8;A0A2R8Y5E1;A0A2R8YFD4;Q13191-3;Q13191-2;A0A2R8YDW4;C9JU85;A0A2R8Y7I2;P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 Q13191;P22681 CBLB;CBL E3 ubiquitin-protein ligase CBL-B;E3 ubiquitin-protein ligase CBL 0 79.474 0.057313 0 52234 43990 41212 46683 49363 42095 57152 51746 56246 FALSE TRUE 49765.00234 48472.63101 43101.61096 41990.33615 57971.89157 40637.23959 48432.41273 47214.84592 64968.34242 0.765988487 0.746096163 0.663424821 0.646319955 0.892309845 0.625492941 0.745477119 0.726736194 1 15.98744928 -1.920186786 1.92664686 1.190861281 0.728049594 0.568664772 0.074852354 691533.8924 263118.5227 594754.1278 0.017878003 0.012017475 1.920186786 -0.462811686 ADAASSLTVDVT(ph)PPTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(0.992)PPT(0.008)AK;ADAASSLTVDVT(0.996)PPT(0.004)AK;ADAAS(0.024)S(0.019)LT(0.064)VDVT(0.886)PPT(0.007)AK;ADAASSLTVDVT(1)PPTAK 281.61 6.18E-35 490620000 974959 889222 923225 1081780 772715 967770 1129270 1016560 938614 TRUE FALSE 928874.6203 979834.7328 965555.7794 973037.4192 907476.2513 934255.8822 956979.121 927544.6173 1084169.465 0.856761466 0.903765291 0.890594884 0.897495687 0.837024359 0.861724954 0.882684074 0.855534718 1 20.04815885 -1.775298489 3.252471534 1.023200454 0.875166324 0.782212262 0.021004436 18103.48286 8942014.659 104192.5155 0.004828094 0.016776506 1.775298489 -0.148034131 ADAETLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADAETLRK 8 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 144.09 0.00094763 3437050000 4625180 3425070 3702580 4048660 3185160 4023500 4547420 4342050 3769160 FALSE TRUE 4406556.908 3774088.527 3872346.955 3641681.005 3740650.896 3884165.186 3853627.56 3961837.083 4353662.083 1.012149502 0.866876771 0.889445915 0.836463863 0.859196425 0.892160465 0.885146226 0.910001054 1 22.053798 0.833926637 4.470985429 0.999997458 0.89387026 0.346850331 0.046329142 2.05443992 54.09506376 0.046144164 0.011719461 6.822234396 -0.833926637 -0.106127198 ADAGSHTEGS(ph)PSQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADAGSHTEGSPSQPR 15 0 Q86V15;Q86V15-2 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 ADAGSHTEGS(0.992)PS(0.008)QPR;ADAGS(0.001)HT(0.004)EGS(0.937)PS(0.058)QPR 166.6 8.75E-07 238611000 166749 197503 197956 194147 165168 179841 173678 175121 182392 TRUE FALSE 158867.1052 217628.7802 207032.4784 174630.9747 193973.2469 173613.0611 147180.2313 159786.4769 210676.4198 0.754081094 1.033000183 0.98270361 0.828906125 0.920716457 0.82407448 0.698607995 0.758444998 1 17.68466932 2.103800833 4.566736519 0.780208784 0.907692815 0.091093615 0.109025878 0.309512647 11.14027464 0.040477964 0.02909137 126.9991554 -2.103800833 0.127484031 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR 300.2 8.93E-71 2349770000 669382 675438 681337 773198 783991 712099 918031 809812 894400 TRUE FALSE 637741.6394 744265.9001 712576.9754 695474.6681 920718.7822 687438.8331 777968.5102 738900.5682 1033098.984 0.617309328 0.720420707 0.689747049 0.673192674 0.891220296 0.665414296 0.753043534 0.715227272 1 19.97854706 -5 0.17318076 2.122002716 0.647990155 0.638034991 0.069111449 81.05665625 0.769899713 31.31411516 0.219413676 1.00E-05 5 -1.474012562 ADATNVNNWHWTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADATNVNNWHWTER 14 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;;; 249.6 3.81E-18 6475340000 2556550 2107950 2299470 2714870 2633680 2360260 3025840 2793050 2611070 FALSE TRUE 2435706.948 2322752.502 2404902.974 2441966.11 3092992.958 2278523.604 2564192.535 2548475.735 3015981.4 0.807600122 0.770148152 0.79738654 0.809675454 1.025534494 0.755483308 0.850201707 0.844990534 1 21.5241961 -4.999999999 0.129491573 1.568824854 0.754459668 0.364391605 0.072694073 154.0547242 1.260314755 22.83302566 0.528820819 1.00E-05 4.999999999 -0.814365186 ADCILYYGFGDIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADCILYYGFGDIFR 14 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ; 123.26 0.00024186 130910000 155853 165265 156200 165042 140499 134211 167767 166316 136123 FALSE TRUE 148486.1376 182105.6914 163361.9245 148451.6646 165001.9811 129563.2394 142171.0629 151752.4893 157232.2596 0.944374506 1.158195474 1.038984779 0.944155258 1.049415569 0.824024534 0.904210518 0.965148562 1 17.26253772 2.819310605 1.462823338 0.918833969 1.052742286 0.230996625 0.079134538 0.440522614 1.910700512 0.030897201 0.031646709 659.6455007 -2.819310605 0.133908317 ADDADEFGYS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 ADDADEFGYS(1)R 83.615 0.017387 129960000 266320 258150 296650 291410 244150 300300 333530 323420 286620 TRUE FALSE 253731.5814 284455.7785 310251.6959 262116.9132 286729.6827 289900.5357 282643.8728 295099.6302 331067.5657 0.766404226 0.85920763 0.93712501 0.791732384 0.866076029 0.87565369 0.853734712 0.891357719 1 18.33676615 -5 0.12160803 1.48342658 0.780499389 0.564814735 0.0435004 113.937989 0.894480622 13.54662835 0.390572409 1.00E-05 5 -0.702927191 ADDADEFGYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;; 333.24 3.40E-57 15773950000 4804848 4069683 4299605 5053098 4345142 4422872 5055285 4609704 4650860 FALSE TRUE 4577732.357 4484388.325 4496746.142 4545150.989 5102933.389 4269706.834 4284008.427 4206053.88 5372091.615 0.852132221 0.834756487 0.837056861 0.846067289 0.94989694 0.794794121 0.797456323 0.7829453 1 22.35705248 -2.210448728 2.399970172 1.52325739 0.836463989 0.550230368 0.046344418 11298578.76 2157198.901 32137250.1 0.01231294 0.006159582 2.210448728 -0.686793401 ADDGRPFPQVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ADDGRPFPQVIK 12 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;; 177.83 2.08E-05 62490110000 43340860 33725850 36078390 41599210 34219820 39905560 48568200 42562570 39428750 FALSE TRUE 41292223.44 37162552.46 37732619.87 37417578.38 40187745.77 38523620.45 41158229.07 38835565.73 45543159.18 0.906661378 0.815985389 0.82850247 0.821585043 0.882410147 0.845870624 0.903719237 0.852720067 1 25.44073103 -0.192418155 0.482024155 1.019824829 0.847905347 0.672260989 0.031539112 3.316279057 0.838567315 0.152122982 0.0158408 0.642069212 0.192418155 -0.171919482 ADDLGKGGNEESTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADDLGKGGNEESTK 14 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 162.87 3.99E-06 4013680000 1884010 1023900 1755910 1541160 1178870 1773950 2406140 2136230 1562300 FALSE TRUE 1794956.581 1128236.574 1836420.21 1386239.669 1384464.555 1712517.667 2039039.151 1949170.376 1804573.505 0.994670805 0.625209542 1.017647774 0.768181327 0.767197651 0.948987482 1.129928565 1.080128003 1 20.78322648 1.991675886 4.293836564 1.077930293 0.826687284 0.460425449 0.116159482 0.163113891 7.171116616 0.047559718 0.030117169 98.10155368 -1.991675886 -0.251243009 ADDTDSQSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADDTDSQSWR 10 0 O75369-8 O75369-8 FLNB Filamin-B 0 ;;;;; 236.56 8.83E-12 1125570000 1819540 1627360 1539560 1975750 1790280 1729780 2066450 1839030 1972260 FALSE TRUE 1733533.95 1793189.834 1610150.349 1777143.856 2102504.265 1669877.285 1751175.1 1677994.784 2278108.008 0.760953363 0.787139955 0.706792805 0.7800964 0.922916849 0.733010586 0.768697135 0.736573849 1 21.11940472 -1.146788271 4.557734963 1.000029061 0.775081505 0.599549537 0.057910235 1.61E-05 3.02E-06 0.052937635 0.012475909 0.071320065 1.146788271 -0.224947556 ADDTDSQSWRS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADDTDSQSWRSPLK 14 1 O75369-8 O75369-8 FLNB Filamin-B 1 ADDTDSQS(0.004)WRS(0.996)PLK;ADDTDSQSWRS(1)PLK;ADDTDSQSWRS(1)PLK 225.11 1.76E-12 1191550000 2683840 1908490 2656370 2920290 2019130 2783910 3352870 2936860 2301080 TRUE FALSE 2556980.202 2102967.301 2778167.192 2626736.901 2371265.633 2687502.499 2841328.102 2679692.969 2657919.734 0.962023107 0.791207979 1.045241192 0.988267955 0.892150956 1.011130044 1.069004479 1.008191833 1 21.34186611 3.033006507 0.705177063 1.030301459 0.885737591 0.21092124 0.071177453 0.854773815 0.947066574 0.046053018 0.064442244 1078.962887 -3.033006507 -0.144563868 ADEASELACPT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK;ADEASELACPT(1)PK 293.29 1.49E-39 44251970000 48905780 35412730 35993970 47960470 23244370 38979530 38386410 38843070 20331230 TRUE FALSE 46594100.7 39021327.45 37644329.13 43139392.44 27298180.77 37629659.1 32529858.14 35441764.87 23484093.31 1.984070668 1.661606728 1.602971366 1.836962231 1.162411527 1.602346687 1.385186888 1.509181743 1 24.48518056 8 0.076001667 0.496158647 4.25726216 0.664368072 0.168975067 114.7080464 0.638765715 5.050979105 45.58433253 100000000 -8 3.761103513 ADEASELACPT(ph)PKEDGLAQQQTQLNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADEASELACPTPKEDGLAQQQTQLNLR 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 1 ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR;ADEASELACPT(1)PKEDGLAQQQTQLNLR 274.67 1.22E-60 4095780000 4201560 990257 3993430 2564760 3558300 3044470 5575800 3360590 4071610 TRUE FALSE 4002960.585 1091165.314 4176532.716 2306945.452 4178866.393 2939039.241 4725109.303 3066318.924 4703014.484 0.851147833 0.232014024 0.888054402 0.490524845 0.888550611 0.624926683 1.004698012 0.651990109 1 22.16515434 2.457762618 0.844937216 0.88717699 0.574214695 0.165741309 0.222733041 0.879679223 1.25783494 0.146131656 0.103303065 286.9211863 -2.457762618 -0.312962295 ADEDPIMGFHQMFLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADEDPIMGFHQMFLLK 16 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 203.04 2.88E-11 501560000 1078820 892930 861100 1013340 812790 906420 1131140 1055670 744390 FALSE TRUE 1027826.317 983920.5822 900582.2867 911477.138 954540.3187 875030.4481 958563.8182 963229.9383 859826.1994 1.19538846 1.144324961 1.047400379 1.060071371 1.110154958 1.017682933 1.114834392 1.12026121 1 19.71368555 3.943583175 3.298874554 1.073031737 1.180322463 0.531412463 0.040841247 0.167867529 3.649868994 0.009937695 0.020783384 8781.792584 -3.943583175 0.107290727 ADEGISFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;;;;; 211.39 7.32E-05 31116340000 15771230 13529310 13666350 15948480 14642390 14027250 16608510 14790420 15014550 FALSE TRUE 15025755.21 14907962.07 14292965.67 14345308.49 17196018.18 13541482.82 14074576.76 13495292.42 17342929.73 0.866390826 0.859598828 0.824137899 0.827156006 0.991529023 0.780807108 0.811545511 0.778143752 1 24.0478443 ADEHVIDQGDDGDNFYVIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADEHVIDQGDDGDNFYVIER 20 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ;;;;; 285.61 4.11E-45 2067430000 1439871 1207646 1258950 1437588 1367646 1296694 1534874 1392723 1247400 FALSE TRUE 1371811.151 1330706.5 1316674.103 1293078.923 1606163.029 1251789.162 1300700.781 1270768.791 1440840.421 0.952090968 0.923562721 0.913823685 0.897447701 1.114740401 0.86879098 0.902737571 0.88196359 1 20.45847913 -0.59560095 5.070097803 1.000000003 0.931288476 0.0879007 0.068921286 7432314.759 2931823.355 0.400466745 0.015083005 0.25374591 0.59560095 -0.068711527 ADEICIAGS(ph)PLTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADEICIAGSPLTPR 14 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 ADEICIAGS(0.998)PLT(0.002)PR 142.85 8.39E-06 0 54518 45793 46218 54493 49078 49298 60238 52080 60122 TRUE FALSE 51941.04218 50459.35876 48337.14102 49015.26011 57637.18766 47590.7979 51047.58675 47519.59911 69445.4127 0.747940579 0.726604635 0.696045126 0.705809905 0.82996393 0.685297935 0.735075 0.684272686 1 16.08359178 -1.173190115 4.978416138 1.000020818 0.727949384 0.805216656 0.042287425 8.84E-06 1.47E-06 0.037036211 0.008728851 0.067113499 1.173190115 -0.272071434 ADEVAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 111.65 0.0033513 803370000 2267320 1956440 1885110 2295420 1382500 2145270 2397220 2328050 1589210 FALSE TRUE 2160148.277 2155803.46 1971544.158 2064680.021 1623607.562 2070978.762 2031480.061 2124193.6 1835656.57 1.176771468 1.174404567 1.074026694 1.124763779 0.88448329 1.128195108 1.106677629 1.157184647 1 20.80786474 3.738822264 6.042452122 1.072643008 1.176124901 0.246066965 0.078025542 0.199919125 33.88752505 0.019722955 0.033287365 5480.526268 -3.738822264 0.103481893 ADEVVWVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADEVVWVR 8 0 P14868;C9J7S3;H7C278;C9JLC1;C9JQM9 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;; 161.12 0.0008128 285973000 586522 605953 527281 636460 525639 561726 554592 595514 508271 FALSE TRUE 558798.2674 667700.2996 551457.3554 572481.8316 617310.2752 542273.2878 469978.8046 543367.6371 587091.0708 0.951808493 1.137302768 0.93930462 0.975115889 1.051472771 0.923661276 0.800521125 0.925525296 1 19.16322479 2.087714106 5.255553009 0.880843299 1.017328068 0.27409666 0.074926815 0.191206675 8.776517634 0.02756395 0.020007849 122.3810306 -2.087714106 0.136484769 ADFCIIHYAGK ddPTM_SK-BR-3_Trastuzumab_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 ; 135.66 0.00011535 4321200000 11319600 10083600 9724400 11263500 8967000 10386400 11842200 11207000 8996000 FALSE TRUE 10784544.94 11111130.3 10170273.36 10131271.58 10530841.96 10026716.36 10035454.89 10225655.67 10391053.73 1.037868268 1.069297743 0.978752841 0.974999441 1.013452748 0.964937399 0.965778366 0.984082647 1 23.30883863 3.731859797 24.89176148 0.980627479 1.053583006 0.757214439 0.016534481 192.2160124 714032.374 0.004286755 0.006813933 5393.364814 -3.731859797 0.072955527 ADFDNTVAIHPTSSEELVTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;; 278.36 7.06E-45 561520000 800862 553727 358065 388853 1034641 345262 1110081 470347 1105418 FALSE TRUE 763006.8404 610152.4108 374482.6344 349764.7577 1215082.063 333305.4904 940717.7554 429160.9232 1276840.578 0.597574085 0.477861075 0.293288482 0.273929858 0.951631773 0.261039237 0.736754276 0.336111595 1 20.28414698 -5 0.34516369 6.538809048 0.487603263 0.33170268 0.224287987 469.714743 3.900094807 1921.50584 0.156427857 1.00E-05 5 -6.051205785 ADFS(ph)PFGNSQGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADFSPFGNSQGPSR 14 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 1 ADFS(0.993)PFGNS(0.005)QGPS(0.002)R 63.462 0.072262 64927000 84862 73155 78057 90442 78047 89193 99900 88927 88640 TRUE FALSE 80850.74144 80609.57767 81635.99066 81350.59833 91658.37209 86104.22405 84658.42021 81140.08045 102385.8385 0.78966723 0.787311789 0.79733674 0.79454932 0.895225096 0.840977867 0.826856736 0.792493197 1 16.64365666 -5 0.201894378 1.841468694 0.78498284 0.752704518 0.033208475 69.9794168 0.693355966 23.81343632 0.077218094 1.00E-05 5 -1.056485854 ADGIVPETWIDGPKDTSVEDALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADGIVPETWIDGPKDTSVEDALER 24 1 Q96A35 Q96A35 MRPL24 "39S ribosomal protein L24, mitochondrial" 0 90.475 0.0088067 22393000 42205 20665 38187 30858 30515 31976 46070 40894 40466 FALSE TRUE 40210.05329 22770.78699 39937.91172 27756.09521 35836.80634 30868.6631 39041.17537 37313.10457 46741.26061 0.86026891 0.487166728 0.854446611 0.593824275 0.76670603 0.660415716 0.835261498 0.798290506 1 15.51240902 0.970513236 0.767080108 0.998129953 0.688776771 0.38239374 0.115882492 0.673511303 0.884713662 0.100400034 0.037520278 9.343578439 -0.970513236 -0.309353182 ADGYEPPVQES(ph)V ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADGYEPPVQESV 12 0 P61247;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 ADGYEPPVQES(1)V;ADGYEPPVQES(1)V 95.573 0.0062631 136212000 189267 187065 166322 194064 139895 182692 199185 193150 163563 TRUE FALSE 180320.724 206127.1362 173948.0282 174556.318 164292.6437 176365.3302 168795.67 176236.762 188927.5147 0.954443953 1.091038203 0.92071305 0.923932749 0.869606759 0.933507915 0.893441436 0.932827399 1 17.5274733 3.666878585 10.25154335 0.917192042 1.022681396 0.42532255 0.046644913 0.413990139 57.7787447 0.011265885 0.017463178 4643.854295 -3.666878585 0.105489353 ADGYVLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADGYVLEGK 9 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 138.98 0.00028267 317162000 745940 681460 660020 781120 636660 705500 868320 795860 744300 FALSE TRUE 710680.8945 750901.5488 690282.5698 702600.3336 747693.3024 681068.3581 735841.8362 726170.2793 859722.2426 0.826640116 0.873423429 0.802913471 0.817241079 0.869691704 0.79219581 0.855906477 0.844656848 1 19.71351111 0.220338391 1.315720722 1.000180492 0.83551609 0.793173307 0.026500163 2.730608217 4.169296488 0.02416216 0.006934913 1.660880517 -0.220338391 -0.164664402 ADHDFVVQEDFMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADHDFVVQEDFMK 13 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 176.25 1.69E-05 499657000 1599620 1398630 1375910 1611320 1186276 1552190 1775660 1692860 1134130 FALSE TRUE 1524009.133 1541151.987 1438996.834 1449347.052 1393162.159 1498437.271 1504750.455 1544624.204 1310005.088 1.163361232 1.176447329 1.0984666 1.106367498 1.063478433 1.143840802 1.148660008 1.179097866 1 20.32114098 -1.498968814 3.017254399 0.995782364 1.13752632 0.572450004 0.036596807 6792986.109 7853247.98 237467.0651 0.009406608 0.031697951 1.498968814 0.141743956 ADHGEPIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;; 153.24 7.85E-05 3768141000 1060787 982790 960030 1095376 1060788 994615 1148503 1082506 960974 FALSE TRUE 1010645.701 1082937.418 1004048.325 985266.7234 1245789.091 960171.2332 973277.7736 987716.0359 1109996.94 0.910494132 0.975621985 0.904550534 0.887630126 1.122335609 0.865021514 0.87682924 0.88983672 1 20.08212427 -0.828194141 5.132624092 1.000000046 0.929137096 0.081335301 0.074946527 5.55E-08 1.28E-08 0.068961332 0.016254326 0.148527154 0.828194141 -0.07086295 ADHLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADHLLK 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 116.35 0.023648 342370000 1021800 904070 902910 1034700 807240 965410 1179600 1061300 849580 FALSE TRUE 973501.539 996195.7608 944309.3166 930689.9902 948022.4004 931977.6096 999630.3552 968366.9457 981328.5273 0.99202409 1.015150108 0.962276435 0.948397977 0.966060166 0.949710096 1.018650052 0.986791802 1 19.90437667 1.715085032 17.35282919 1.00198421 0.977196219 0.280477874 0.02135513 0.360113372 251.9298017 0.011317537 0.006260766 51.89016264 -1.715085032 -0.024787991 ADHPPAEVTSHAASGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADHPPAEVTSHAASGAK 17 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 84.874 0.0029931 125290000 95542 79070 79118 102660 84310 94232 99683 114720 47520 FALSE TRUE 91025.91901 87127.3229 82745.63856 92340.42176 99013.63731 90968.72221 84474.52755 104674.5086 54889.1589 1.658358788 1.587332082 1.507504218 1.6823071 1.803883304 1.657316746 1.53900204 1.90701608 1 15.74423361 -0.288054695 10.24076231 1.000000019 1.650945825 0.756035461 0.118881141 0 0 0.107595642 0.025360536 0.515163761 0.288054695 0.650945805 ADHQPLTEASYVNLPTIALCNTDSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADHQPLTEASYVNLPTIALCNTDSPLR 27 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;; 227.96 1.10E-34 1672750000 1264534 1100213 1110718 1333050 1297249 1206795 1461580 1266435 1256130 FALSE TRUE 1204761.984 1212325.956 1161645.519 1199049.281 1523488.815 1165003.387 1238589.127 1155539.238 1450924.225 0.830341077 0.835554286 0.800624525 0.826403792 1.050012667 0.802938821 0.853655281 0.796415979 1 20.46854075 ADHWMLYECESPWAGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADHWMLYECESPWAGGSR 18 0 A0A494C0N6;O14734 A0A494C0N6 ACOT8 Acyl-coenzyme A thioesterase 8 0 198.96 1.68E-15 69179000 72805 75437 74726 90259 79493 69446 75957 76503 64910 FALSE TRUE 69363.65194 83124.11606 78152.26101 81185.99384 93356.55403 67041.06761 64368.3646 69803.99175 74975.91129 0.925145833 1.108677636 1.042364937 1.082827704 1.245153976 0.894168093 0.858520603 0.931018917 1 16.19413953 ADIDLTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADIDLTKR 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ; 104.2 0.0074175 359720000 544180 548690 470950 488370 489470 544220 615900 590020 517720 FALSE TRUE 518457.6899 604602.1348 492543.5233 439278.1198 574833.413 525373.5249 521933.1432 538354.7209 598005.3735 0.866978313 1.011031274 0.823643976 0.734572195 0.96125125 0.878543151 0.872790056 0.900250641 1 19.18979892 0.908977293 9.371379525 0.99999999 0.886258862 0.204719389 0.073586062 13.91227279 1433.34833 0.070701562 0.017689284 8.109186575 -0.908977293 -0.113741129 ADIDVSGPKVDIDTPDIDIHGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADIDVSGPKVDIDTPDIDIHGPEGK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 199.46 4.29E-25 500743000 1420580 963690 1306560 1271540 887632 1403510 1707790 1652800 853961 FALSE TRUE 1353431.999 1061891.107 1366467.068 1143722.383 1042434.74 1354906.097 1447235.27 1508072.07 986388.9105 1.372107882 1.076544044 1.385322821 1.159504503 1.056819201 1.373602321 1.467205536 1.528881817 1 19.91179705 2.077486511 11.88617569 1.393046863 1.212317197 0.094160804 0.176164271 0.872809012 130.0652601 0.059630358 0.044037482 119.53264 -2.077486511 -0.180729666 ADIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 113.25 0.061181 774790000 1660650 1441400 1546620 1797360 1598740 1554240 1850360 1714870 1706750 FALSE TRUE 1582154.366 1588280.299 1617534.057 1616685.958 1877559.75 1500416.279 1568053.598 1564706.892 1971424.073 0.802543901 0.805651265 0.820490162 0.820059966 0.952387553 0.761082458 0.795391321 0.793693713 1 20.91080672 -2.175223024 2.317863585 1.467197665 0.816638395 0.560347092 0.050374276 2590190.579 657374.7495 6342730.918 0.012140439 0.006680008 2.175223024 -0.65055927 ADIIYPGHGPVIHNAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADIIYPGHGPVIHNAEAK 18 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 231.44 4.55E-20 566220000 791470 765090 612080 797300 560550 732070 896080 864790 178916 FALSE TRUE 754058.7816 843053.5408 640144.4734 717153.8892 658309.7425 706718.2323 759366.5384 789064.4031 206661.3795 3.648764871 4.07939569 3.097552503 3.470188242 3.185451215 3.419691836 3.674448221 3.818151243 1 17.65690928 -1.415726056 6.068684355 0.999266495 3.57737496 0.885689557 0.287654218 0.002981923 0.00028709 0.29092603 0.068559681 0.038394936 1.415726056 2.578108465 ADIKGPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADIKGPEDK 9 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ;;; 100.72 0.0040746 1204910000 4100450 3209450 3391420 3586480 1967690 3359480 3696360 4147990 2226390 FALSE TRUE 3906629.855 3536496.604 3546919.962 3225960.217 2310854.513 3243140.365 3132412.394 3784770.006 2571647.19 1.519115791 1.375187318 1.379240502 1.254433434 0.898589247 1.261114035 1.218056818 1.471729878 1 21.2942613 3.266632794 2.939239556 1.184948671 1.437965657 0.358780183 0.15548219 0.277557877 4.913788981 0.044359605 0.059620849 1847.705681 -3.266632794 0.253016986 ADIKSPS(ph)LDVTVPEAELNLETPEISVGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ADIKS(0.004)PS(0.896)LDVT(0.101)VPEAELNLETPEISVGGK;ADIKS(0.002)PS(0.996)LDVT(0.003)VPEAELNLETPEISVGGK 338.1 1.16E-105 344840000 396720 228384 312180 434640 391030 421990 575300 341330 351920 TRUE FALSE 377967.8318 251656.5893 326493.7618 390949.1614 459225.5082 407376.3805 487527.4189 311441.3357 406493.9562 0.929823989 0.619090605 0.803194628 0.961758854 1.129722844 1.002170818 1.199347275 0.766164739 1 18.63287438 3.17049336 3.303941047 1.044055731 0.765957448 0.384465747 0.134104273 0.197431703 4.340397476 0.037576319 0.047350396 1480.789615 -3.17049336 -0.278098283 ADILEDKDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;; 140.39 3.59E-05 5742950000 9888260 8705970 8126320 10033210 4881450 10348700 10567140 10210420 5255440 FALSE TRUE 9420861.546 9593118.241 8498919.81 9024652.669 5732773.334 9990321.924 8954928.714 9316341.496 6070426.794 1.551927379 1.580303752 1.400053093 1.486658677 0.944377311 1.645736332 1.475172837 1.534709471 1 22.53336652 -2.028550047 2.459604294 0.455057486 1.463589119 0.351356564 0.192626808 9621553.393 2604821.982 29605093.2 0.044465077 0.009363753 2.028550047 1.008531633 ADKDES(ph)T(ph)MINEIT(ph)LAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;ADKDES(1)T(1)MINEIT(1)LAK 55.656 0.053985 13226120000 8626550 7347560 8473170 7906030 5906000 10220270 10346480 10368660 6260630 TRUE FALSE 8218790.078 8096284.717 8861673.226 7111300.844 6936004.53 9866339.487 8767934.45 9460725.163 7231496.526 1.136526865 1.119586339 1.225427295 0.983378865 0.959138196 1.364356527 1.212464726 1.308266571 1 22.78586281 2.235390386 24.99924915 1.240614515 1.096035988 0.233379501 0.119696653 109.6664558 864775.5619 0.040662987 0.03129214 171.9453304 -2.235390386 -0.144578527 ADKDYHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ADKDYHFK 8 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 96.331 0.0054176 35502720000 59411680 60965270 49745160 65193120 34196100 60015270 57708590 60463530 29827880 FALSE TRUE 56603407.63 67177700.32 52026024.79 58639783.72 40159889.01 57936926.15 48904084.7 55169022.78 34453435.29 1.642895901 1.949811383 1.510038821 1.70200107 1.165628004 1.681600852 1.419425503 1.601263337 1 25.0381445 -1.919381765 0.104583698 2.88E-11 2.107934936 0.500537582 0.19309609 53.46126992 0.815212325 16.88390331 3.361301863 0.012039771 1.919381765 2.107934936 ADKDYHFKVDNDENEHQLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADKDYHFKVDNDENEHQLSLR 21 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;; 252.01 1.41E-36 19064220000 15113540 6726455 14340440 11913360 11070880 14495830 21529320 15974050 6980800 FALSE TRUE 14399152.92 7411888.412 14997963.36 10715806.42 13001637.97 13993835.77 18244626.82 14575277.5 8063346.811 1.785753888 0.919207444 1.86001715 1.328952688 1.612436904 1.735487274 2.262661801 1.807596503 1 22.94294734 2.338383013 2.853868645 1.859077239 1.439369919 0.002599802 0.407571655 0.432262369 7.160653191 0.147599037 0.115314881 217.9631184 -2.338383013 -0.41970732 ADKLAEEHSS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADKLAEEHSS 10 1 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 133.91 0.00016835 1798560000 3726200 1846350 3336200 2608800 3303700 2629800 4269500 3466600 3873500 FALSE TRUE 3550069.911 2034495.164 3489168.07 2346558.468 3879864.234 2538729.367 3618109.36 3163046.126 4474182.597 0.793456645 0.45471885 0.779844808 0.524466406 0.867167164 0.567417469 0.808663769 0.706955082 1 22.09319271 0.076205043 0.380913813 1.057227954 0.633651429 0.364548345 0.132565715 3.994949427 0.836691331 0.480891313 0.089650668 1.19180456 -0.076205043 -0.423576526 ADKNEVAAEVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADKNEVAAEVAK 12 1 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 124.45 0.00029443 462960000 914460 799170 806420 1014520 547330 1018930 1058720 995220 687570 FALSE TRUE 871235.2881 880606.3316 843395.1547 912538.5221 642784.1787 983644.1986 897192.8193 908073.2608 794194.844 1.097004463 1.108803889 1.061949925 1.149010887 0.809353251 1.238542665 1.129688547 1.143388512 1 19.59913347 ADLAEEYSKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 151.26 3.06E-05 604950000 1004200 793060 773650 1020400 640040 909560 1014900 942640 768180 FALSE TRUE 956733.4561 873873.7156 809122.6177 917827.4534 751662.7734 878061.7091 860058.3651 860097.4444 887305.4311 1.078245915 0.984862354 0.911887372 1.034398552 0.847129688 0.989582255 0.969292348 0.969336391 1 19.75907127 4.374912083 2.088796851 0.959212738 1.077903391 0.338570213 0.051085991 0.363656265 2.780022926 0.011861093 0.06126131 23708.93704 -4.374912083 0.118690653 ADLASKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADLASKR 7 1 P51148;P51148-2;K7ERI8;K7ERQ8;K7ENY4 P51148 RAB5C Ras-related protein Rab-5C 0 ; 107.29 0.012041 812440000 1578790 987390 1256690 1419710 1650670 1412990 2135480 1603880 1944630 FALSE TRUE 1504163.726 1088006.164 1314310.48 1276998.054 1938546.325 1364057.802 1809673.305 1463435.764 2246193.289 0.669650174 0.4843778 0.585127952 0.568516548 0.863036291 0.607275344 0.805662324 0.651518181 1 21.09905065 0.102699167 0.2209914 1.156248548 0.516614065 0.564921243 0.102214934 5.010644292 0.464366399 0.886616518 0.257509623 1.266774076 -0.102699167 -0.639634484 ADLDVSGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADLDVSGPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 93.178 0.022276 111740000 208310 212460 172890 230820 141090 210360 198210 226920 158870 FALSE TRUE 198463.5991 234109.9155 180817.1775 207617.5351 165696.0513 203075.1805 167969.4241 207049.6818 183506.7482 1.081505727 1.275756439 0.985343478 1.131389102 0.902942551 1.106636036 0.915331048 1.128294648 1 17.48547359 3.723818663 24.80855331 1.018939377 1.178631087 0.324204092 0.092399036 637.3735155 1072606.781 0.021895959 0.034086067 5294.423318 -3.723818663 0.159691711 ADLIPYQDS(ph)PEGPDHSSASSGVPNPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADLIPYQDSPEGPDHSSASSGVPNPPK 27 0 Q8WUA4;H0Y4Q6;H7C318 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 ADLIPYQDS(1)PEGPDHSSASSGVPNPPK 158.13 1.02E-11 150430000 76921 60629 75228 88501 82924 76082 111950 100010 103160 TRUE FALSE 73285.09677 66807.16403 78677.27821 79604.71134 97385.91935 73447.26126 94869.9714 91252.59421 119157.5259 0.615027009 0.560662564 0.660279555 0.668062808 0.817287188 0.616387934 0.796172719 0.765814778 1 16.86251055 -4.999994487 0.074487425 2.186180281 0.287227438 0.776713978 0.060826425 111.4234719 0.593218789 21.84304081 2.392968427 1.00E-05 4.999994487 -1.898952844 ADLLLSTQPGREEGSPLELER ddPTM_SK-BR-3_Trastuzumab_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 ;; 197.72 8.16E-22 261910000 177218 132933 142881 197957 214093 156413 192568 171206 209302 FALSE TRUE 168841.2564 146479.0238 149432.2352 178057.9863 251430.7514 150996.3786 163188.2148 156214.295 241759.4852 0.698385241 0.605887391 0.618102885 0.736508791 1.040003668 0.624572717 0.675002326 0.646155806 1 17.88321297 -2.429913237 2.162643695 3.560033251 0.699090813 0.351073082 0.125522654 6604423.963 325959.9151 83472027.13 0.030447561 0.003716095 2.429913237 -2.860942438 ADLNQGIGEPQS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(0.98)PS(0.02)R;ADLNQGIGEPQS(0.998)PS(0.002)R;ADLNQGIGEPQS(0.993)PS(0.007)R;ADLNQGIGEPQS(0.99)PS(0.01)R 309.1 4.36E-56 849790000 1086730 1080180 1026570 1226020 1062880 1037660 1129700 1105720 1170860 TRUE FALSE 1035362.427 1190251.57 1073639.25 1102778.14 1248245.935 1001725.574 957343.5166 1008897.295 1352430.989 0.765556568 0.880083036 0.793858806 0.815404371 0.922964607 0.740685168 0.707868664 0.745988005 1 20.36712355 ADLSIPDLHEIVTEELEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ADLSIPDLHEIVTEELEER 19 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ;;;; 217.4 3.61E-19 33428100 81908 68179.6 77665 91228 81429 76162 87379 83143 76601 FALSE TRUE 78036.37117 75127.17875 81226.01707 82057.58812 95630.19182 73524.49084 74047.72872 75862.55815 88479.89186 0.881967298 0.849087597 0.918016686 0.927415104 1.080812711 0.830974013 0.83688765 0.857398857 1 16.433062 2.409134414 0.007602747 1.79988298 2.16E-06 0.054185264 0.077050424 14043.41253 54.49685606 6352.729014 6544.365955 256.5277868 -2.409134414 -1.799880822 ADLVWQPWEDLESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADLVWQPWEDLESSR 15 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 0 113.65 0.0015549 6489300 23586 17999 19504 21424 13243 22484 20102 25028 14362 FALSE TRUE 22471.13652 19833.11856 20398.27769 19270.41882 15552.57501 21705.37344 17035.0707 22836.41564 16589.18561 1.354565381 1.195545039 1.229612964 1.161625367 0.93751287 1.308405003 1.026878058 1.376584492 1 14.01795544 4.523384485 0.834672525 1.13596916 1.432968326 0.198240702 0.13454288 2.615897222 1.745197572 0.042538604 0.674381765 33372.1729 -4.523384485 0.296999166 ADPSLLGFSVNAS(ph)SER ddPTM_SK-BR-3_Trastuzumab_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(0.957)S(0.043)ER;ADPSLLGFSVNAS(0.961)S(0.039)ER;ADPSLLGFSVNAS(0.912)S(0.088)ER 184.8 1.85E-09 221319000 137111 107161 110225 153104 131439 130228 145935 123156 134843 TRUE FALSE 130630.0348 118080.8277 115278.9253 137713.695 154361.92 125718.1717 123669.9355 112371.8077 155753.7638 0.838695847 0.758125036 0.740135728 0.884175712 0.991063819 0.807159767 0.794009291 0.721470898 1 17.2489075 -1.967228713 2.49468578 1.152610268 0.815761478 0.353894405 0.077757801 16710628.38 7655906.986 14737408.59 0.018862209 0.010783787 1.967228713 -0.33684879 ADQCYEDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADQCYEDVR 9 0 P31146;H3BRY3;H3BTU6;H3BRJ0;H3BNA2;H3BU76;H3BSL1 P31146 CORO1A Coronin-1A;Coronin 0 ;;; 125.71 0.0011489 2917890000 2080530 1736020 1748750 2116050 1966690 1848440 2276830 1899960 2184860 FALSE TRUE 1982187.47 1912922.412 1828931.917 1903340.634 2309680.113 1784428.059 1929457.767 1733589.43 2523676.93 0.7854363 0.757990212 0.724709211 0.754193459 0.915204354 0.707074681 0.764542301 0.686930014 1 21.2670958 -1.077335109 4.505611086 1.000015171 0.763865545 0.595532357 0.061621385 9.37E-06 1.92E-06 0.054920338 0.012943947 0.083688328 1.077335109 -0.236149626 ADQDRLDLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADQDRLDLEER 11 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 150.21 3.10E-05 311610000 704320 550220 596030 699840 733820 615280 760360 674440 721710 FALSE TRUE 671028.1894 606288.0435 623358.5651 629490.7536 861797.9757 593972.6993 644353.117 615382.4582 833629.1008 0.804948134 0.727287523 0.747764881 0.755120896 1.033790657 0.712514353 0.772949404 0.738196948 1 19.66904612 -1.489318861 3.131080779 1.005443962 0.783536075 0.348524112 0.091620311 25641136.53 32280769.94 1212704.29 0.02079673 0.032410157 1.489318861 -0.221907887 ADQEEQIHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADQEEQIHPR 10 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;;;;; 203.02 2.13E-07 3954897000 3330099 2761651 2880287 3277546 3181307 3048728 3617900 3295425 3195440 FALSE TRUE 3172691.82 3043066.377 3012351.008 2948080.849 3736125.934 2943149.785 3065922.908 3006860.117 3690972.515 0.859581535 0.824461944 0.816140189 0.798727392 1.012233475 0.797391412 0.830654494 0.814652535 1 21.81556956 -1.331458506 5.354718321 1.000041266 0.843163951 0.381358461 0.062337086 2.83E-05 3.53E-06 0.055583243 0.013097653 0.046616697 1.331458506 -0.156877315 ADQELLMYSHDNIICGITSVAFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADQELLMYSHDNIICGITSVAFSR 24 0 P62879;E7EP32;P62879-2 P62879 GNB2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 0 ;; 294.31 6.64E-62 533472000 488839 532440 491680 530877 483458 411684 512994 541346 452144 FALSE TRUE 465732.5493 586696.2413 514224.0143 477512.2354 567772.9221 397427.2799 434727.3435 493942.8744 522260.1823 0.891763464 1.12337923 0.984612712 0.91431867 1.08714572 0.760975646 0.832396109 0.945779309 1 18.99440919 2.242861848 24.99989864 0.862780808 1.002557057 0.258973611 0.093773905 117.8769544 685135.8847 0.031330193 0.025356167 174.9290137 -2.242861848 0.139776249 ADRDESSPYAAMLAAQDVAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;;;;;;; 257.37 1.62E-36 6463380000 3087167 3064639 2875998 3445778 3065959 3032921 3419776 3165083 3074633 FALSE TRUE 2941242.734 3376929.198 3007865.353 3099401.849 3600661.279 2927890.185 2898026.363 2887931.553 3551431.383 0.828185151 0.950864267 0.846944522 0.872719057 1.013861987 0.824425385 0.816016431 0.813173969 1 21.75996918 -1.70296409 8.642347135 1.000344897 0.872715004 0.281725216 0.064780445 0.000426441 1.47E-05 0.062132841 0.014605962 0.019816909 1.70296409 -0.127629894 ADRDQS(ph)PFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.996)PFS(0.004)K;ADRDQS(1)PFSK;ADRDQS(1)PFSK;ADRDQS(0.999)PFS(0.001)K;ADRDQS(0.631)PFS(0.369)K;ADRDQS(0.999)PFS(0.001)K;ADRDQS(0.998)PFS(0.002)K 149.32 1.43E-05 4537139000 13649140 11980263 11898290 14313560 9227966 13358890 14255220 13936870 10300127 TRUE FALSE 13003972.2 13201065.42 12443838.37 12874733.75 10837320.35 12896268.29 12080324.37 12716483.78 11897418.09 1.09300792 1.10957397 1.045927635 1.08214519 0.910896824 1.083955207 1.015373612 1.068843986 1 23.50414519 3.398526857 1.842261691 1.023406658 1.100503287 0.277355204 0.049750066 0.389445537 2.688121873 0.01406295 0.02223328 2503.380455 -3.398526857 0.077096629 ADREEGKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADREEGKER 9 2 O60828-2;O60828;A0A5H1ZRR1;O60828-3 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 54.539 0.07558 29715000 81613 47729 66767 65024 73974 69928 105870 85513 105290 FALSE TRUE 77755.31523 52592.63936 69828.33299 58487.66398 86875.04218 67506.37583 89717.58706 78025.02839 121617.8355 0.639341384 0.43244183 0.574161945 0.480913542 0.71432814 0.555069703 0.737700903 0.641559094 1 16.89199529 0.369043259 0.378565277 1.056955679 0.519330268 0.723523487 0.083060829 1.379968725 0.354768188 0.218797931 0.060771331 2.339070215 -0.369043259 -0.537625411 ADREVQAEQPSSS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADREVQAEQPSSSSPR 16 1 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 ADREVQAEQPS(0.02)S(0.136)S(0.709)S(0.136)PR 85.974 0.00537 0 52446 39909 51028 53425 56510 54996 68837 54041 80320 TRUE FALSE 49966.98152 43975.77247 53367.68427 48054.6175 66365.32611 53091.47473 58334.65137 49308.88355 92775.61538 0.538578821 0.47400141 0.575233956 0.517966033 0.715331565 0.572256778 0.628771376 0.531485384 1 16.50145804 -5 0.214903082 3.137530519 0.506483282 0.809175109 0.065761364 58.40598035 0.583243751 53.92889879 0.123802974 1.00E-05 5 -2.631047237 ADREVQAEQPSSSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADREVQAEQPSSSSPR 16 1 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 ADREVQAEQPS(0.005)S(0.079)S(0.384)S(0.532)PR;ADREVQAEQPS(0.003)S(0.026)S(0.144)S(0.827)PR;ADREVQAEQPS(0.026)S(0.072)S(0.379)S(0.523)PR 114.3 0.00035986 1022337000 465884 316438 464294 429470 553522 411763 621077 461265 670645 TRUE FALSE 443862.5866 348683.392 485582.3391 386298.8597 650056.0615 397503.5441 526320.2968 420874.1913 774645.2014 0.572988235 0.450120121 0.626844829 0.498678439 0.839166189 0.513142718 0.679434012 0.543312203 1 19.56317616 -4.999999999 0.190237636 2.780194845 0.508704069 0.577678506 0.109775035 88.90966355 0.869773313 60.00130904 0.26564722 1.00E-05 4.999999999 -2.271490776 ADRGEAERGS(ph)GGS(ph)S(ph)GDELREDDEPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADRGEAERGSGGSSGDELREDDEPVK 26 3 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 3 ADRGEAERGS(1)GGS(1)S(1)GDELREDDEPVK 78.909 0.039119 125440000 160840 105430 142030 149860 96944 129330 190730 144760 120270 TRUE FALSE 153237.412 116173.4369 148542.216 134795.7881 113851.0029 124851.2697 161630.6355 132084.047 138920.8573 1.103055473 0.836256262 1.069257841 0.970306336 0.819538585 0.89872228 1.163472776 0.950786293 1 17.08390369 -0.887948406 5.153848969 1.000000038 0.979581539 0.003728274 0.110911845 4.71E-08 1.04E-08 0.105337499 0.024828241 0.12943496 0.887948406 -0.020418499 ADS(ph)LLAVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;ADS(1)LLAVVK 141.88 0.00011083 74923000 312671 324584 252870 346160 195469 308243 329332 327852 212396 TRUE FALSE 297891.6615 357659.4786 264464.3396 311363.3391 229558.7317 297568.4676 279086.3548 299143.5408 245333.2869 1.214232546 1.457851412 1.077979849 1.269144286 0.935701529 1.212915179 1.137580466 1.219335316 1 17.90438347 3.726520392 24.97201986 1.131774597 1.336041983 0.367778571 0.116205267 649.400835 1346889.347 0.027786895 0.043413071 5327.46239 -3.726520392 0.204267386 ADS(ph)PVNGLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ADSPVNGLPK 10 0 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 ADS(1)PVNGLPK;ADS(1)PVNGLPK;ADS(1)PVNGLPK;ADS(1)PVNGLPK;ADS(1)PVNGLPK 191.31 8.45E-07 2233450000 5572880 4972810 4897900 5799770 3068040 5412800 5776150 5928740 3367560 TRUE FALSE 5309461.007 5479544.993 5122473.56 5216766.101 3603105.205 5225353.379 4894892.231 5409588.095 3889784.006 1.364975793 1.40870161 1.316904371 1.341145445 0.926299558 1.343353094 1.258396925 1.390716833 1 21.89125862 -5 0.077481941 0.140010323 1.581713586 0.295467228 0.138752289 328.9471661 1.812559658 50.67419108 5.092442036 1.00E-05 5 1.441703263 ADSEQPSKRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADSEQPSKRPR 11 2 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 0 ; 101.95 0.0016499 57341000 91487 59569 93265 92211 92409 89093 125756 106700 129448 FALSE TRUE 87162.59082 65639.14882 97541.2925 82941.77509 108525.1003 86007.68707 106569.6125 97356.78235 149522.1347 0.582941054 0.438992855 0.652353531 0.554712352 0.725812941 0.575217089 0.712734691 0.651119532 1 17.18999955 -5 0.127588427 2.378491265 0.421454209 0.766763464 0.071209554 59.79280662 0.484547776 20.92830164 0.510975115 1.00E-05 5 -1.957037056 ADSGPTQPPLSLS(ph)PAPETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK;ADSGPTQPPLSLS(1)PAPETK 314.08 1.34E-61 1903820000 3411430 3321520 3117000 3830680 2286359 3473830 3594220 3709280 2513260 TRUE FALSE 3250178.465 3659986.664 3259917.533 3445612.769 2685099.286 3353530.396 3045855.727 3384475.779 2903003.525 1.119591636 1.260758602 1.122946461 1.18691305 0.924938348 1.15519336 1.049208415 1.165853141 1 21.46911489 ADTLDPALLRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADTLDPALLRPGR 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 140.91 3.61E-05 1034200000 2126750 2082020 1782880 2376190 1949660 1971190 2113590 2080660 1895640 FALSE TRUE 2026222.742 2294180.205 1864626.812 2137330.867 2289680.087 1902927.196 1791123.027 1898466.38 2189606.17 0.925382277 1.04775929 0.851580909 0.976125705 1.045704072 0.869072814 0.8180115 0.867035546 1 21.06223997 2.186467706 15.80119951 0.867263007 0.970970243 0.209326119 0.072944797 3.455333891 1046.728788 0.025452981 0.018799666 153.6270552 -2.186467706 0.103707236 ADTLDPALLRPGRLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADTLDPALLRPGRLDR 16 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 126.77 3.93E-05 410520000 377580 188684 392920 313500 467300 324600 530360 402670 576070 FALSE TRUE 359732.5417 207911.1141 410935.7707 281986.3844 548796.972 313359.0206 449443.8413 367410.0801 665403.9934 0.540622757 0.312458471 0.617573346 0.423782224 0.824757557 0.470930478 0.675445061 0.552160918 1 19.343871 -5 0.124707085 2.552058056 0.325808069 0.542848006 0.133845657 99.63743715 0.795486332 38.62637509 1.021652684 1.00E-05 5 -2.226249987 ADTQTYQPYNKDWIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ADTQTYQPYNKDWIK 15 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ;; 254.68 9.62E-25 3012260000 3559340 2708210 3287770 3619100 3026260 3621220 4423370 4136570 3442730 FALSE TRUE 3391097.052 2984179.678 3438517.507 3255301.192 3554038.786 3495816.243 3748503.666 3774350.001 3976610.985 0.85276057 0.750432891 0.864685412 0.81861193 0.893735595 0.879094348 0.942637759 0.949137347 1 21.92310801 1.983219843 0.609588085 0.996924337 0.802512214 0.785083753 0.032677991 0.300909603 0.225173056 0.027867531 0.017367182 96.20991768 -1.983219843 -0.194412123 ADTSS(ph)QGALVFLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADTSSQGALVFLSK 14 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 ADT(0.001)S(0.027)S(0.972)QGALVFLSK 123.02 0.00055955 0 64424 51529 52705 65751 52263 64846 75927 66477 91495 TRUE FALSE 61378.8052 56779.86368 55121.57638 59141.58456 61377.65065 62600.36676 64342.94165 60655.92146 105683.5773 0.580779027 0.537262885 0.521571826 0.55960998 0.580768102 0.592337697 0.608826303 0.573938951 1 16.68939168 -5 0.303318217 4.677684232 0.546998661 0.974260448 0.022088672 39.92068534 0.366635171 93.45167524 0.021744823 1.00E-05 5 -4.130685571 ADVFHAYLSLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADVFHAYLSLLK 12 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 203.51 1.24E-07 194331000 1905700 1616030 1155830 1344610 1705690 1400620 2211100 1751690 1542660 FALSE TRUE 1815621.338 1780705.294 1208825.949 1209447.248 2003161.796 1352116.178 1873756.085 1598302.737 1781887.834 1.018931328 0.999336356 0.678396208 0.678744882 1.124179512 0.75881105 1.051556697 0.896971575 1 20.76497509 -1.472818407 8.64349088 1.000002386 0.914030096 0.032813048 0.155143008 6.87E-06 4.19E-07 0.144608181 0.034083529 0.033665231 1.472818407 -0.08597229 ADVIQATGDAICIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADVIQATGDAICIFR 15 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 77.593 0.05915 29524000 79627 64528 95585 91175 79042 87381 121420 73677 84025 FALSE TRUE 75863.18952 71103.47656 99967.6668 82009.91578 92826.89977 84354.97406 102895.149 67225.45129 97055.16786 0.781650181 0.732608867 1.030008695 0.844982473 0.956434385 0.86914459 1.060171769 0.69265195 1 16.56651741 3.755850555 24.82433993 0.927528646 0.757129504 0.294257727 0.105817539 751.8130704 1079425.755 0.024127466 0.043361805 5699.681075 -3.755850555 -0.170399142 ADVLEAHEAEAEEPEAGKS(ph)EAEDDEDEVDDLPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADVLEAHEAEAEEPEAGKSEAEDDEDEVDDLPSSR 35 1 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5 A8MY87 KSR1 Kinase suppressor of Ras 1 1 ADVLEAHEAEAEEPEAGKS(0.946)EAEDDEDEVDDLPS(0.027)S(0.027)R 56.933 0.024197 94972000 31645 28171 28688 33246 24886 29877 39847 32740 28208 TRUE FALSE 30149.20356 31041.65693 30003.37318 29904.04892 29226.11052 28842.352 33767.60831 29873.11203 32582.35257 0.925323102 0.9527138 0.920847355 0.917798948 0.896992028 0.885213919 1.03637723 0.91684945 1 14.99180316 1.74681536 25 0.98568651 0.920811078 0.467091298 0.033984785 1.659369771 5038.219442 0.014752943 0.008181308 55.82328118 -1.74681536 -0.064875433 ADVVPQQADPEFPRAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;ADVVPQQADPEFPRAS(1)PR 226.75 2.03E-19 1818720000 1354286 1082821 1217910 1303435 1376000 1178794 1455810 1331946 1532373 TRUE FALSE 1290271.585 1193161.691 1273752.378 1172411.237 1615973.964 1137972.068 1233699.447 1215313.747 1770005.579 0.7289647 0.674100526 0.719631844 0.662377143 0.912976763 0.642920046 0.69700314 0.686615772 1 20.75532248 -1.254950139 5.327695128 1.000030831 0.712663179 0.588456314 0.074716803 2.48E-05 3.47E-06 0.065687592 0.015481055 0.055596808 1.254950139 -0.287367652 ADWLSHYWMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADWLSHYWMPK 11 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 117.52 0.00084366 191729000 718410 747160 512900 711900 606450 619170 849920 736100 568440 FALSE TRUE 684452.1831 823296.4535 536416.9723 640338.4595 712214.688 597727.9876 720249.0941 671643.1817 656590.772 1.042433449 1.253895864 0.81697306 0.975247425 1.084716262 0.910350881 1.096952813 1.022925101 1 19.32463495 3.756695439 24.99935246 0.995744935 1.148164641 0.330547994 0.094836516 881.8709251 1215679.578 0.02319934 0.041719255 5710.780114 -3.756695439 0.152419706 ADWWTNTAHYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ADWWTNTAHYNR 12 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 245.69 1.75E-16 223870000 184430 153780 113320 134860 201540 116260 214080 164530 189350 FALSE TRUE 175712.3594 169450.3568 118515.8341 121303.6166 236688.5122 112233.887 181418.1642 150122.881 218713.4309 0.803390805 0.774759721 0.541877257 0.554623537 1.082185539 0.513154984 0.829478845 0.686390773 1 17.73868229 -1.534681096 2.692430704 1.014983804 0.730854473 0.208643775 0.168815909 20149733.21 20207407.9 2203382.546 0.036697383 0.029195701 1.534681096 -0.284129332 ADYDTLS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 ADYDTLS(1)LR;ADYDTLS(1)LR;ADYDTLS(1)LR;ADYDTLS(1)LR;ADYDTLS(1)LR;ADYDTLS(1)LR 177.44 5.47E-05 2899360000 4772100 3547990 4482350 4799870 4659290 4420290 5464290 4867150 4637270 TRUE FALSE 4546532.29 3909534.215 4687870.181 4317377.948 5471868.701 4267214.249 4630612.202 4440956.544 5356394.148 0.848804656 0.729881728 0.875191416 0.806023199 1.021558263 0.796658 0.864501766 0.829094428 1 22.35283069 -5 0.116768451 1.49782086 0.759743397 0.290281498 0.074708306 186.0777224 1.420507732 22.18089427 0.73195631 1.00E-05 5 -0.738077463 ADYDTLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;;; 176.6 0.00012337 354296000 650610 587840 507668 553959 742380 527709 732020 645920 737640 FALSE TRUE 619856.9547 647741.5643 530945.08 498273.9889 871850.837 509434.305 620336.9045 589359.8206 852029.4439 0.727506495 0.760233779 0.623153441 0.584808415 1.023263742 0.597906925 0.728069797 0.691712974 1 19.70054376 -1.354307342 5.206604567 1.000122015 0.719276153 0.3416262 0.123397467 0.000156883 1.95E-05 0.107249161 0.025267942 0.044227527 1.354307342 -0.280845862 ADYEIASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 78.934 0.058627 0 64732 56638 62454 66544 51666 65728 76386 73349 96928 FALSE TRUE 61672.24665 62409.47659 65317.57768 59854.87069 60676.53404 63451.82288 64731.91277 66926.17271 111959.0992 0.550846221 0.557431035 0.583405709 0.534613722 0.541952682 0.566741099 0.578174648 0.597773412 1 16.77261226 -0.149491116 0.817325232 1.013668268 0.554525098 0.990899296 0.013202162 0.660764176 0.386320229 0.041562461 0.004243919 0.708775805 0.149491116 -0.459143169 ADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ADYQAVDDEIEANLEEFDISEDDIDDGFRR 30 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 71.974 0.0091122 29017900 14966.2 15105.9 12201.7 13223.4 14928.5 15092.9 18063.7 18160.4 14537.4 FALSE TRUE 14258.77739 16645.20838 12761.16001 11894.15871 17532.02567 14570.22909 15307.7508 16570.1791 16791.78575 0.849151937 0.991270889 0.759964438 0.708331972 1.044083455 0.867699797 0.911621375 0.986802676 1 14.03546804 2.719475181 24.97975255 0.945068043 0.853235459 0.339853526 0.088465219 1386.946478 1815286.622 0.02974085 0.028077965 524.1736443 -2.719475181 -0.091832584 AEADDPQDMACTPS(ph)GDSLETKEDQKMSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEADDPQDMACTPSGDSLETKEDQKMSPK 29 2 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AEADDPQDMACT(0.048)PS(0.311)GDS(0.311)LET(0.311)KEDQKMS(0.019)PK 55.101 0.054852 29243000 41083 23732 36859 39349 18244 52011 48634 52869 23588 TRUE FALSE 39141.08801 26150.31778 38549.02161 35393.56376 21425.74782 50209.84603 41213.99008 48239.51008 27245.90657 1.436586003 0.959788866 1.414855531 1.299041516 0.786384104 1.842839984 1.512667232 1.770523215 1 14.73375187 2.225759439 24.99986628 1.577227024 1.188927386 0.253821199 0.295206574 268.7727759 524892.1807 0.098352163 0.073104331 168.1742265 -2.225759439 -0.388299638 AEAEAGS(ph)PRPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR 140.27 0.00010333 12256240000 9527880 7857010 8319290 9839600 9429270 8730080 10322800 8907040 9493400 TRUE FALSE 9077515.995 8657648.252 8700737.675 8850504.714 11073731.7 8427755.141 8747867.269 8127092.358 10965587.99 0.827818445 0.789528866 0.79345838 0.807116292 1.009862099 0.768563907 0.797756334 0.74114515 1 23.38647984 -2.338461563 2.411173429 2.202739005 0.816323483 0.387018004 0.072412681 2316361.738 804072.9097 15482136.78 0.017516952 0.004587102 2.338461563 -1.386415523 AEAEAGSPRPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 73.435 0.033595 10316160000 4921900 4410200 4516200 5010600 5143900 4727200 5650200 5035400 5600100 FALSE TRUE 4689251.541 4859604.394 4723272.237 4506924.968 6040994.531 4563495.879 4788158.217 4594473.682 6468534.907 0.724932556 0.751268172 0.730191969 0.696745868 0.933904604 0.70549142 0.740222985 0.710280419 1 22.62500755 -1.634377442 2.867044529 1.022482784 0.748678351 0.575111746 0.067765175 16880650.68 16245062.7 2812814.773 0.015040728 0.02320719 1.634377442 -0.273804433 AEAGDNLGALVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEAGDNLGALVR 12 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 81.625 0.039881 122498000 234090 182169 203890 222280 302170 196418 253470 315120 326570 FALSE TRUE 223025.0296 200732.2282 213238.5582 199935.9921 354868.3523 189615.9954 214798.4962 287526.4222 377212.8077 0.591244584 0.532145845 0.565300419 0.530035004 0.940764325 0.502676451 0.569435851 0.762239289 1 18.52501914 -5 0.199688305 2.800205871 0.544050529 0.489106651 0.127069962 117.8210435 1.165062444 84.34639418 0.290066649 1.00E-05 5 -2.256155342 AEAGVPAEFSIWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEAGVPAEFSIWTR 14 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ; 110.98 0.0015781 81927000 145899 114249 131078 138203 146643 128421 170879 147855 168024 FALSE TRUE 139002.6434 125891.103 137088.056 124310.5719 172217.4928 123973.7486 144808.2701 134908.0324 194080.3038 0.716212005 0.648654709 0.706347081 0.640511012 0.887351727 0.638775528 0.746125533 0.695114495 1 17.56629419 -5 0.29103437 3.298155905 0.690170508 0.614194982 0.072172308 153.0576712 1.438837056 213.644172 0.067925985 1.00E-05 5 -2.607985397 AEAPAGPALGLPS(ph)PEAESGVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEAPAGPALGLPSPEAESGVDR 22 0 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDR 248.52 3.65E-31 97483000 63002 71954 58362 80045 56508 58556 61179 60119 57827 TRUE FALSE 60024.02032 79286.1944 61037.95543 71998.72452 66362.97731 56528.19104 51845.01992 54854.66165 66794.51582 0.898636955 1.18701653 0.913816871 1.077913713 0.993539312 0.846299885 0.776186776 0.821244993 1 16.02744203 2.273982022 4.082853213 0.833440358 1.028374075 0.357322014 0.099371979 0.178692686 6.442216957 0.034094525 0.026855791 187.9239022 -2.273982022 0.194933717 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.994)PEAES(0.006)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.98)PEAES(0.02)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.863)PEAES(0.137)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.972)PEAES(0.028)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.996)PEAES(0.004)GVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.78)PEAES(0.22)GVDRGEPEPMEVEEGELEIVPVRR 341.03 6.05E-134 1269832000 126210.7 82417.8 108752.7 106718.8 138262.2 99139.2 134935.8 124736.6 161873 TRUE FALSE 120244.9703 90816.26752 113739.1189 95991.22347 162375.0839 95705.98465 114348.8654 113814.002 186975.4381 0.643105702 0.485712286 0.608310482 0.513389483 0.868430022 0.511863941 0.611571587 0.608710979 1 17.51248924 -5 0.329378448 5.036458751 0.583447324 0.57261416 0.10673719 241.4246585 2.089830119 682.137129 0.082333805 1.00E-05 5 -4.453011427 AEAPLPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEAPLPSPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK 158.06 7.04E-05 453789000 2039550 1614190 1652170 2232380 1246700 1663390 1833880 1693820 1004300 TRUE FALSE 1943144.513 1778677.796 1727923.629 2007976.921 1464124.085 1605786.387 1554087.924 1545500.141 1160041.715 1.675064344 1.533287789 1.48953577 1.73095234 1.262130548 1.384248831 1.339682793 1.332279798 1 20.14574525 0.905764609 0.134254787 0.619435681 1.94443752 0.75779133 0.10323955 3.974338327 0.357930661 1.857754531 1.283571368 8.04942039 -0.905764609 1.325001839 AEAPSS(ph)PDVAPAGKEDSPSASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEAPSSPDVAPAGKEDSPSASGR 23 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 AEAPS(0.191)S(0.809)PDVAPAGKEDSPSASGR 107.19 0.00083022 133760000 61254 51208 54909 65568 48479 58908 60413 60253 53535 TRUE FALSE 58358.64481 56426.15342 57426.63196 58976.98007 56933.72225 56868.00119 51195.88729 54976.9279 61836.93438 0.943750614 0.912499204 0.928678508 0.953750063 0.920707387 0.919644574 0.827917616 0.88906296 1 15.91618118 1.977792153 24.06342375 0.883350213 0.930247372 0 0.044541822 718.8359559 778896.6987 0.016269776 0.010611184 95.01499578 -1.977792153 0.04689716 AEASS(ph)PVPYLSPETNPASSTSAVNHNVNLTNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEASSPVPYLSPETNPASSTSAVNHNVNLTNVR 33 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 AEAS(0.12)S(0.88)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.043)S(0.957)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.052)S(0.948)PVPYLSPETNPASSTSAVNHNVNLTNVR 309.5 2.64E-104 967630000 261340 195948 244262 271314 309469 194866 314003 251919 299324 TRUE FALSE 248986.9761 215915.324 255461.6543 244041.0013 363440.2956 188117.7416 266096.0753 229859.6369 345741.6372 0.720153286 0.62449905 0.738880212 0.705847879 1.051190417 0.544099181 0.769638501 0.664830648 1 18.39933483 -2.020154202 2.761485931 1.315517071 0.722427355 0.29742775 0.131475837 44924422.27 11339869.96 89990558.67 0.028891898 0.009546536 2.020154202 -0.593089716 AEASSGDHPTDTEMKEEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 AEASSGDHPTDTEMKEEQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;;;;;;;; 326.62 2.25E-75 6619612000 6937318 5458511 6005838 7106551 3766527 7201125 7947658 8157779 3847918 FALSE TRUE 6609404.727 6014739.477 6281211.613 6392186.992 4423408.116 6951748.236 6735096.803 7443440.624 4444633.471 1.487052818 1.353258827 1.413212508 1.438180906 0.995224498 1.564076831 1.515332332 1.674702914 1 22.08363302 AECRPAASENYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AECRPAASENYMR 13 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 113.25 0.00076289 63777000 75491 60181 65095 66577 50959 64530 73234 68213 83414 FALSE TRUE 71922.69004 66313.51232 68079.67014 59884.55347 59846.23347 62295.30992 62060.80827 62239.9081 96349.4171 0.746477687 0.688260649 0.706591406 0.621535192 0.621137473 0.646556168 0.644122301 0.645981159 1 16.55598832 -1.230345206 4.427354775 1.000129886 0.66803132 0.877341648 0.039341658 5.67E-05 9.85E-06 0.042811464 0.010086831 0.058837579 1.230345206 -0.332098566 AEDEKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEDEKQR 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 87.323 0.017717 211780000 639800 577500 674850 685530 928620 578870 746520 812130 1197970 FALSE TRUE 609557.922 636347.9066 705792.54 616619.222 1090571.034 558823.5868 632624.6632 741015.5918 1383745.069 0.440513166 0.459873658 0.51005966 0.445616202 0.788130024 0.403848656 0.457182958 0.535514531 1 20.40014675 0.860842721 7.550685128 0.999999908 0.494202876 0.680446127 0.106771585 4.72579168 256.5991199 0.096889695 0.024277346 7.258430468 -0.860842721 -0.505797032 AEDGATPS(ph)PSNETPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGAT(0.002)PS(0.976)PS(0.022)NETPK 232.6 4.03E-14 59262000 167010 149840 156940 188950 121180 165590 179250 183210 108060 TRUE FALSE 159115.7683 165108.8664 164135.8542 169956.387 142313.7536 159855.5768 151902.1203 167167.1611 124817.3929 1.27478843 1.322803357 1.315007872 1.361640258 1.140175662 1.280715556 1.216994818 1.339293806 1 16.92945946 -4.061316678 0.253290616 3.64E-11 1.306546596 0.644135494 0.065097024 65.99325353 1.009961944 34.15030187 0.084970734 8.68E-05 4.061316678 1.306546596 AEDGATPSPSNET(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 393.42 1.38E-113 2749990000 2640124 3042600 2437916 3110410 1374217 2911610 2582292 3076090 1472272 TRUE FALSE 2515330.571 3352644.399 2549696.86 2797745.677 1613880.01 2810780.216 2188315.928 2806731.252 1700584.422 1.479097737 1.971466018 1.499306254 1.645167179 0.949014932 1.65283192 1.28680229 1.650450995 1 20.6975992 2.96197338 24.85878495 1.345386742 1.679167488 0.284583241 0.263573285 625.664596 409009.7636 0.072645795 0.077069521 916.1643325 -2.96197338 0.333780746 AEDGATPSPSNET(ph)PKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK 242.22 3.60E-20 758220000 343490 389370 355180 412100 197258 379000 425810 474180 232611 TRUE FALSE 327253.9084 429047.2457 371465.3543 370674.9251 231659.7327 365875.135 360844.864 432658.2854 268683.1259 1.217992039 1.596852219 1.38254069 1.379598826 0.862204249 1.361734697 1.343012751 1.61029199 1 18.03554619 -2.182018517 2.428307444 0.038009876 1.347602798 0.214277554 0.207098147 2292216.153 1286204.869 12095042.65 0.049989934 0.006576298 2.182018517 1.309592921 AEDGENYDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEDGENYDIKK 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 124.86 0.00054581 613360000 901300 816150 765490 941360 518470 829360 894710 927670 634390 FALSE TRUE 858697.3352 899316.6129 800588.4737 846732.7043 608891.0038 800639.0552 758205.557 846438.2969 732767.9612 1.171854367 1.227287027 1.092553873 1.155526373 0.830946543 1.092622901 1.034714394 1.155124598 1 19.4829969 3.297609449 1.983519206 1.033429006 1.194634291 0.333904863 0.091081755 0.323834543 2.614025996 0.026484803 0.038164309 1984.30967 -3.297609449 0.161205285 AEDGHAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDGHAVAK 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 66.435 0.063739 179500000 178750 168250 168850 224190 185150 181830 200760 197030 167470 FALSE TRUE 170300.8417 185394.8663 176591.9395 201653.9953 217440.1014 175533.1815 170130.3748 179777.0087 193440.3923 0.88037891 0.958408242 0.912901062 1.042460641 1.124067723 0.907427758 0.879497673 0.92936644 1 17.56152955 -0.785929306 4.534904448 1.00000013 0.949411754 0.030765422 0.076299667 10103763.24 2228007.106 15.73114268 0.018606164 0.163708298 0.785929306 -0.050588376 AEDGSVIDYELIDQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEDGSVIDYELIDQDAR 17 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ; 262.64 5.49E-27 25874000 66236 40823 42961 61269 61218 39867 51264 42953 57521 FALSE TRUE 63105.15555 44982.91011 44930.80434 55110.12372 71894.39982 38486.39579 43442.73527 39191.80761 66441.0629 0.949791481 0.677034776 0.676250535 0.829458791 1.08207781 0.579256172 0.653853707 0.589873279 1 16.01978753 AEDKEWMPVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEDKEWMPVTK 11 1 P15880;E9PQD7;E9PPT0;E9PMM9 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 169.62 1.52E-05 4296780000 9912530 9292640 7876350 10487330 6011550 9770910 10626380 11105480 6938930 FALSE TRUE 9443984.352 10239570.58 8237488.438 9433123.664 7059962.417 9432540.937 9005130.564 10133025.3 8014983.825 1.17829113 1.277553493 1.027761081 1.176936082 0.880845498 1.176863378 1.12353696 1.26426023 1 22.93426818 3.744563761 24.92307535 1.099328028 1.227922312 0.207121192 0.109276643 664.4466794 2758555.943 0.026207391 0.045815513 5553.461447 -3.744563761 0.128594284 AEDMAELTCLNEASVLHNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDMAELTCLNEASVLHNLR 20 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 0 69.148 0.020206 124950000 27396 30020 38442 32941 93659 24257 39753 28383 82563 FALSE TRUE 26101.04537 33079.07213 40204.60372 29629.7081 109993.0999 23416.97401 33687.94974 25897.63405 95366.44837 0.273692119 0.346862788 0.421580172 0.310693211 1.153373139 0.245547301 0.353247398 0.271559175 1 16.54119417 -2.033612482 2.61181749 1.719201965 0.412631238 0.318361762 0.265443948 25915908.14 9471074.096 111563443 0.060549082 0.009255236 2.033612482 -1.306570728 AEDNFEDIITKPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDNFEDIITKPPVR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 168.07 1.16E-06 100960000 143910 133010 116280 154310 109740 147370 153510 150440 120980 FALSE TRUE 137107.6595 146563.8702 121611.553 138798.4656 128878.6213 142266.5399 130089.2301 137266.6761 139740.9605 0.98115584 1.04882541 0.870264184 0.993255414 0.922268036 1.018073294 0.930931272 0.982293778 1 17.09239544 3.807195855 25 0.958506396 1.014990589 0.198963526 0.046179848 222.8994216 81188.69981 0.01035537 0.018668408 6414.988103 -3.807195855 0.056484193 AEDQTES(ph)SCESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.891)S(0.109)CESHR;AEDQTES(0.871)S(0.129)CESHR;AEDQTES(0.956)S(0.044)CESHR 188.58 3.86E-06 539020000 661250 545190 607610 754190 712420 670850 756990 641770 685070 TRUE FALSE 629994.023 600745.4808 635469.5195 678377.3883 836665.8224 647618.2963 641497.2724 585573.2166 791307.1567 0.796143467 0.759181155 0.803063026 0.857287063 1.057321187 0.818415821 0.810680489 0.740007482 1 19.59387828 AEDQTES(ph)SCESHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDQTESSCESHRK 14 1 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.669)S(0.266)CES(0.064)HRK 99.663 0.00098357 199870000 147560 147250 144770 183930 144630 173020 183720 193200 163060 TRUE FALSE 140585.1312 162254.9424 151407.8477 165441.007 169853.4262 167028.274 155690.1398 176282.3838 188346.512 0.746417493 0.861470386 0.803879223 0.878386359 0.901813495 0.886813736 0.826615466 0.935947164 1 17.52302979 8 0.0389622 1.389724958 1.45E-12 0.720530441 0.037047109 453.7390913 1.347486583 13.37110068 42.18148262 100000000 -8 -1.389724958 AEDQTESS(ph)CESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.258)S(0.742)CESHR 149.09 2.81E-05 164110000 201750 168240 192170 230060 215080 214380 239500 208170 226220 TRUE FALSE 192213.6773 185383.8473 200981.1846 206933.9317 252589.8839 206955.9668 202959.8763 189941.5312 261301.0422 0.735602414 0.70946463 0.769155694 0.791936878 0.966662367 0.792021207 0.776728154 0.726906902 1 17.99535335 -5 0.15355341 1.743445569 0.716981449 0.453500783 0.072500379 128.2255243 1.155799355 29.52445863 0.352681708 1.00E-05 5 -1.02646412 AEDREQLVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AEDREQLVAK 10 1 Q13268;C9JZP6;Q13268-2;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;; 183 1.57E-06 30471800000 23596655 16802602 19949090 17870299 17087003 17496601 22708964 21033719 20235463 FALSE TRUE 22481287.88 18514806.25 20863775.51 16073942.59 20066970.91 16890689.32 19244294.46 19191895.06 23373475.25 0.961829066 0.792128943 0.892626162 0.687700157 0.858536041 0.722643472 0.823339031 0.821097199 1 24.47836892 -1.577396212 2.411551376 1.01711435 0.821136666 0.345039144 0.077928973 4579227.589 3832845.914 499019.5571 0.018334891 0.02646085 1.577396212 -0.195977684 AEDS(ph)DS(ph)EPEPEDNVR ddPTM_SK-BR-3_Trastuzumab_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 205.52 6.37E-09 343730000 480320 468880 544750 653300 408960 608310 553310 543280 462440 TRUE FALSE 457616.2255 516659.4051 569727.3263 587629.0428 480282.4945 587244.0722 468892.3973 495707.5231 534152.8334 0.856714028 0.967250144 1.066599839 1.100114061 0.89914808 1.099393349 0.877824413 0.928025636 1 19.02689306 4.379491589 2.498559161 0.991681215 0.862176541 0.232089968 0.078135313 0.438169822 5.03764255 0.0194808 0.08560322 23960.26348 -4.379491589 -0.129504674 AEEAEAQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 123.86 0.00087512 559200000 665140 613530 596110 692250 559740 659900 751190 720220 635990 FALSE TRUE 633700.1504 676049.4045 623442.2331 622663.7148 657358.4788 637047.4975 636582.1689 657153.7187 734616.081 0.862627659 0.920275804 0.848664015 0.847604253 0.894832683 0.867184253 0.866550822 0.894553952 1 19.48663095 0.820870903 4.073453932 0.9999954 0.875178143 0.772360462 0.021561231 0.734038943 16.15920561 0.020675918 0.005277567 6.620196838 -0.820870903 -0.124817257 AEEAQKTES(ph)VDNEGE ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEEAQKTESVDNEGE 15 1 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 AEEAQKT(0.019)ES(0.981)VDNEGE;AEEAQKT(0.059)ES(0.941)VDNEGE;AEEAQKT(0.069)ES(0.931)VDNEGE 130.21 0.00016074 276440000 616800 663672 509300 723545 368247 626672 602792 602187 361927 TRUE FALSE 587645.0864 731300.9313 532651.9088 650812.882 432469.1602 604970.1915 510825.0094 549456.3139 418052.7907 1.405671962 1.749302834 1.274125949 1.556772007 1.034484567 1.447114348 1.22191508 1.314322799 1 18.67332561 2.233142433 0.207023436 0.926767226 1.737585403 0.391941013 0.175875914 3.169565261 0.468437176 0.558243275 0.924014751 171.057623 -2.233142433 0.810818177 AEEDEILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEEDEILNR 9 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 154.12 0.00017788 188303000 358590 306220 327750 483620 436910 366280 441110 357290 351180 FALSE TRUE 341640.1614 337424.1661 342777.6617 435005.5988 513106.9657 353595.6318 373810.568 326003.7935 405639.2008 0.84222669 0.831833229 0.845030907 1.072395365 1.264934367 0.871699853 0.921534623 0.803679213 1 18.62983756 3.307876697 9.818037533 0.985336444 0.83789362 0.246578176 0.122949119 0.56008051 74.98561482 0.03531388 0.047801703 2031.780077 -3.307876697 -0.147442824 AEEDEILNRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 245.5 4.74E-16 1.39952E+11 44900783 32022699 38999952 59329893 57696247 47704502 59695553 44104584 51005779 TRUE FALSE 42778411.97 35285848.43 40788138.38 53365939.44 67758454.21 46052483.13 50587900.01 40242552.81 58915494.71 0.726097815 0.598923061 0.692315979 0.905804826 1.150095651 0.781670142 0.858651875 0.683055502 1 25.81214378 3.279154806 5.584114408 0.891453572 0.661473657 0.411015045 0.126470229 0.178739356 13.51806772 0.034877667 0.046574186 1901.756047 -3.279154806 -0.229979915 AEEDKLEQIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEEDKLEQIKK 11 2 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 106.49 0.0013072 235660000 235400 207130 209430 261290 135870 275920 289270 300550 139770 FALSE TRUE 224273.1085 228236.7825 219032.5727 235024.6328 159565.685 266364.8212 245136.5487 274232.2487 161444.8178 1.389162635 1.413713897 1.356702406 1.455758296 0.988360526 1.649881519 1.518392179 1.698612891 1 17.30068161 AEEDTQFNYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEEDTQFNYHR 11 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 150.09 3.41E-05 93354000 131660 121310 100900 146020 127340 117890 122320 133190 115650 FALSE TRUE 125436.6927 133671.6269 105526.3648 131341.7922 149548.0557 113807.4397 103657.8374 121527.1775 133584.4113 0.939006965 1.000652887 0.789960174 0.98321197 1.1195023 0.851951501 0.775972558 0.909740712 1 17.02739214 AEEFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 101.52 0.05841 12401000000 17446000 14792400 15247200 22708700 11749040 21603500 22460500 22031700 13239420 FALSE TRUE 16621362.15 16299762.38 15946299.2 20425978.33 13798068.86 20855365.38 19033738.21 20102487.55 15292521.64 1.086894794 1.065864922 1.042751456 1.335684122 0.902275582 1.363762359 1.244643536 1.314530594 1 23.86632298 2.219195311 24.9999844 1.254449922 1.093192315 0.196043617 0.141020945 323.1934821 417229.783 0.04648236 0.034379677 165.6514765 -2.219195311 -0.161257608 AEEGDADEKLFEES(ph)DDKEDEDADGKEVEDADEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEEGDADEKLFEESDDKEDEDADGKEVEDADEK 33 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 AEEGDADEKLFEES(1)DDKEDEDADGKEVEDADEK 58.087 0.025834 88204000 49762 54832 38154 51131 15370 58202 48122 72995 10830 TRUE FALSE 47409.84888 60419.44314 39903.39864 45991.21474 18050.52313 56186.45015 40780.10508 66603.17083 12509.46109 3.789919369 4.829899763 3.189857529 3.676514473 1.442949701 4.491516441 3.259940999 5.32422383 1 13.61073202 3.723279941 23.91396499 3.31390763 4.309909579 0.108876034 1.289847129 900.516271 1409291.084 0.308318995 0.47988232 5287.859911 -3.723279941 0.996001949 AEEILEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEEILEK 7 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 114.93 0.013479 249010000 796340 760690 635280 762940 758250 705020 982090 857850 806520 FALSE TRUE 758698.5864 838205.1758 664408.2164 686247.8217 890488.5599 680604.9806 832254.1332 782732.1063 931591.0025 0.814411672 0.899756625 0.713197331 0.736640672 0.955879305 0.730583463 0.893368582 0.840210032 1 19.82933718 0.3593834 0.740125043 1.002767259 0.818734454 0.3467947 0.078438444 2.589533296 2.012968359 0.088284244 0.025870968 2.287617447 -0.3593834 -0.184032805 AEEKS(ph)PISINVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AEEKSPISINVK 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 AEEKS(0.999)PIS(0.001)INVK;AEEKS(0.997)PIS(0.003)INVK;AEEKS(0.948)PIS(0.052)INVK;AEEKS(0.916)PIS(0.084)INVK;AEEKS(0.993)PIS(0.007)INVK;AEEKS(0.982)PIS(0.018)INVK;AEEKS(0.958)PIS(0.042)INVK 210.08 2.89E-08 4619990000 6700110 5774800 5506760 6780580 3411180 6879350 6870330 7013580 3742369 TRUE FALSE 6383409.079 6363258.685 5759250.393 6098983.216 4006088.712 6641116.385 5822134.976 6399433.754 4322716.471 1.476712415 1.472050903 1.332322032 1.410914469 0.926752596 1.536329396 1.346869501 1.480419499 1 22.04350678 -2.20249838 2.078536022 2.68E-05 1.379398544 0.319774238 0.170633779 2112874.081 445179.3664 9907266.205 0.04224273 0.00627338 2.20249838 1.379371751 AEELS(ph)PAALSPLLEPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(1)PAALSPLLEPIR;AEELS(0.996)PAALS(0.004)PLLEPIR 79.771 0.013462 20009500 35271 31974 32917 35671 33725 29260 40853 35630 34745 TRUE FALSE 33603.80973 35232.18695 34426.27701 32085.28331 39606.62932 28246.71886 34620.12453 32510.04831 40133.07715 0.837309574 0.877884016 0.857803076 0.799472295 0.986882446 0.703826391 0.862633194 0.810056209 1 15.29250416 -1.068291247 4.601209426 1.000008073 0.843676477 0.330471423 0.070647748 5.09E-06 1.03E-06 0.059505637 0.014024889 0.085449348 1.068291247 -0.156331596 AEELSPAALS(ph)PSLEPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AEELSPAALS(0.976)PS(0.024)LEPIR;AEELSPAALS(1)PSLEPIR;AEELSPAALS(0.991)PS(0.009)LEPIR;AEELSPAALS(0.713)PS(0.287)LEPIR 314.42 3.32E-58 267873000 378687 284279 293689 354211 368791 299076 373994 327585 350979 TRUE FALSE 360787.216 313247.3533 307154.9311 318605.0373 433108.0336 288718.9231 316934.3464 298899.9208 405407.0308 0.889938231 0.772673707 0.757645793 0.785889275 1.068328866 0.712170488 0.781768254 0.737283515 1 18.62901158 -1.01247204 7.291556807 1.000000012 0.812487008 0.249216408 0.101880353 1.84E-08 2.46E-09 0.092626058 0.02183217 0.097169051 1.01247204 -0.187513004 AEENKKEPLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEENKKEPLCR 11 2 H3BUM8;H3BRL3;O14562 H3BUM8 UBFD1 Ubiquitin domain-containing protein UBFD1 0 81.431 0.0122 204720000 378050 240860 374250 419210 263790 389980 461750 502190 317340 FALSE TRUE 360180.3257 265403.9078 391409.7327 377070.2144 309794.8925 376474.8948 391301.5569 458215.5813 366551.4665 0.982618701 0.724056325 1.067816578 1.02869651 0.845160696 1.027072401 1.067521461 1.250071609 1 18.48365625 1.862438119 2.238837094 1.125011628 0.917604295 0.322868497 0.114307369 0.317734014 2.958103482 0.067721343 0.032357828 72.85143636 -1.862438119 -0.207407333 AEENTDQAS(ph)PQEDYAGFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEENTDQASPQEDYAGFER 19 0 Q9NU22 Q9NU22 MDN1 Midasin 1 AEENTDQAS(1)PQEDYAGFER;AEENTDQAS(1)PQEDYAGFER 306.28 1.40E-50 313610000 497080 446750 491220 604760 556140 602840 622980 516190 629890 TRUE FALSE 473584.0135 492274.3329 513742.9229 543968.3758 653130.6399 581963.4996 527932.9592 470989.6671 727570.1242 0.650911847 0.676600532 0.706107777 0.747650787 0.897687547 0.799872727 0.725611101 0.647346079 1 19.47272678 -5 0.144596475 1.873152242 0.64276856 0.530176123 0.07711575 114.3952396 0.999217296 29.28086911 0.447044402 1.00E-05 5 -1.230383682 AEEQQLPPPLSPPS(ph)PSTPNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AEEQQLPPPLS(0.006)PPS(0.846)PS(0.121)T(0.027)PNHR;AEEQQLPPPLS(0.006)PPS(0.69)PS(0.228)T(0.076)PNHR;AEEQQLPPPLS(0.042)PPS(0.608)PS(0.248)T(0.102)PNHR;AEEQQLPPPLSPPS(0.877)PS(0.093)T(0.03)PNHR 145.16 7.78E-08 536090000 660330 630550 603230 725550 716740 612630 722120 710410 692530 TRUE FALSE 629117.5095 694803.7619 630888.6922 652616.3355 841739.2291 591414.4695 611947.3314 648202.7343 799924.0154 0.786471587 0.868587201 0.788685775 0.815847909 1.052273982 0.73933831 0.765006825 0.810330384 1 19.60950344 4.699835467 3.788051362 0.840328018 0.783092526 0.026080673 0.1006978 1.098800199 28.035356 0.023005515 0.161242886 50099.73943 -4.699835467 -0.057235492 AEEYEFLTPVEEAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEEYEFLTPVEEAPK 15 0 P52565;J3KTF8;J3QQX2;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 203.11 1.30E-08 103986000 304434 251716 270428 314302 218510 304345 328543 333307 261902 FALSE TRUE 290044.0082 277366.1466 282827.3913 282707.7658 256618.0748 293805.4563 278417.7312 304120.8721 302516.4245 0.95877111 0.916863099 0.934915821 0.934520386 0.848278156 0.971204974 0.920339223 1.005303671 1 18.20665395 1.236506438 24.99616658 1.00265188 0.927432512 0.488859191 0.032396638 43.99012035 535223.4555 0.024245798 0.007202765 17.23877645 -1.236506438 -0.075219368 AEFAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 137.59 0.029481 8228420000 7177280 6431590 6405140 7369350 9110640 6372660 7961570 6913610 7770450 FALSE TRUE 6838024.198 7086976.333 6698822.005 6628568.937 10699532.73 6151973.186 6746886.272 6308217.657 8975451.7 0.761858503 0.789595507 0.74634929 0.738522044 1.192088497 0.685422126 0.751704371 0.702830105 1 23.09755312 AEFEDQDDEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEFEDQDDEAR 11 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ; 334.63 3.01E-57 454260000 661930 556550 575950 670660 622340 606850 682360 599590 654560 FALSE TRUE 630641.8807 613263.0777 602357.8772 603243.9826 730875.899 585834.6323 578253.4496 547086.721 756065.8218 0.834109759 0.811123926 0.796700313 0.797872309 0.966682897 0.774846072 0.764818926 0.723596683 1 19.52815231 -0.088307014 7.517067786 0.999999999 0.809622664 0.473252647 0.063414073 2704526.949 359784.8154 0.05978737 0.014500567 0.816005312 0.088307014 -0.190377335 AEFEVHEVYAVDVLVSSGEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 AEFEVHEVYAVDVLVSSGEGK 21 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;;;;;;;;;; 181.4 5.04E-17 463210500 859333 751929 730467.5 947366 612102.6 825823 923159 869168 545526.5 FALSE TRUE 818714.0321 828551.42 763960.1574 852134.9698 718853.0996 797224.5424 782314.1396 793059.0422 630123.9635 1.299290425 1.314902254 1.21239661 1.352329096 1.140812191 1.265186834 1.241524184 1.25857623 1 19.26527615 -4.58247806 0.202188114 5.10E-11 1.308324875 0.685917453 0.056136635 61.38758494 0.709278825 24.91671771 0.117807897 2.62E-05 4.58247806 1.308324875 AEFFQHLIEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AEFFQHLIEDR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;;;; 174.73 1.07E-05 321569000 524402 570776 472955 585769 492604 498867 534083 530896 430146 FALSE TRUE 499614.5567 628938.7233 494640.4546 526886.3872 578513.9816 481591.1107 452598.8292 484407.9318 496850.8448 1.005562458 1.265850164 0.9955512 1.060451829 1.164361473 0.969287092 0.91093501 0.974956442 1 18.92245329 2.155302804 6.652415435 0.949857612 1.106107504 0.403660393 0.0803861 0.189352059 12.38283756 0.029436257 0.021712477 142.9890575 -2.155302804 0.156249892 AEFTS(ph)PPSLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.002)S(0.985)PPS(0.012)LFK;AEFT(0.001)S(0.986)PPS(0.013)LFK;AEFT(0.001)S(0.998)PPS(0.001)LFK 126.34 0.00032458 177722000 1222350 1408420 1267130 1525440 1031110 1415350 1561350 1536600 1286610 TRUE FALSE 1164571.938 1551939.599 1325229.164 1372099.873 1210935.258 1366336.075 1323137.381 1402047.158 1486130.908 0.783626753 1.044281894 0.89173111 0.923269859 0.814824085 0.919391466 0.890323574 0.943421034 1 20.50312977 0.967453226 3.453925654 0.9998663 0.901572566 0.194670975 0.069004687 0.408797986 12.8731133 0.062478147 0.016185891 9.277975605 -0.967453226 -0.098293734 AEGDVAALNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEGDVAALNRR 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 193.52 1.47E-06 734380000 1157530 735340 915460 951570 1260870 940320 1387920 1135050 1404680 FALSE TRUE 1102815.851 810271.982 957434.7465 855916.3757 1480765.329 907756.4826 1176167.313 1035659.005 1622510.6 0.679697162 0.499393953 0.590094602 0.527525907 0.912638308 0.559476457 0.724905781 0.638306464 1 20.62979647 -5 0.175833484 2.487175776 0.553532839 0.499170499 0.11526089 102.8630452 0.982411649 53.18714723 0.346900725 1.00E-05 5 -1.933642937 AEGEPQEES(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 194.13 2.01E-06 217370000 456940 533090 352100 530710 256290 482440 418120 490490 240190 TRUE FALSE 435341.3518 587412.4771 368244.1333 477362.0225 300986.8949 465732.9818 354328.1147 447540.0953 277437.4385 1.569151424 2.117279053 1.327305123 1.720611411 1.084882042 1.678695508 1.277146 1.613120773 1 18.08180296 4.731374069 0.057269735 1.61E-07 3.5558686 0.314818935 0.273094811 174.6909335 1.576089342 31.5651362 72.10993292 53873.36084 -4.731374069 3.555868439 AEGEPQEES(ph)PLKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(1)PLKSK;AEGEPQEES(0.999)PLKS(0.001)K 146.88 4.96E-06 805600000 598060 498020 587970 659840 287720 646900 649400 675810 320900 TRUE FALSE 569790.889 548768.8042 614929.0061 593511.6296 337898.2769 624497.6908 550322.103 616632.4937 370663.5331 1.537218631 1.480503894 1.658995157 1.601213976 0.911603777 1.684810172 1.484694484 1.663590935 1 18.49975066 -1.701580346 2.610348955 0.916866644 1.49985018 0.335668301 0.222275404 17632794.98 14164016.17 9620729.166 0.049903659 0.01988015 1.701580346 0.582983536 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(0.999)DKES(0.001)GK;AEGEWEDQEALDYFS(0.989)DKES(0.011)GK 285.02 1.60E-45 9180299000 3688311 3440577 3077481 3917758 1664463 4027566 3748395 4157523 1697529 TRUE FALSE 3513971.849 3791175.708 3218586.548 3523937.523 1954744.82 3888090.38 3176508.499 3793468.246 1960773.128 1.792135867 1.933510642 1.641488504 1.79721839 0.996925546 1.982937406 1.620028577 1.934679843 1 20.90299119 3.469883213 2.205277853 1.58922102 1.859505174 0.113570376 0.338241108 0.670311005 6.532506368 0.091250457 0.145750651 2950.415717 -3.469883213 0.270284154 AEGFVDALHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;;; 174.41 3.11E-06 820393000 1508793 1229050 1178286 1378537 1486522 1255845 1627205 1413453 1429455 FALSE TRUE 1437475.345 1354291.592 1232311.579 1239963.842 1745770.966 1212354.773 1378944.992 1289683.562 1651127.581 0.870602225 0.820222258 0.746345463 0.750980031 1.057320456 0.734258689 0.835153508 0.781092616 1 20.65502017 AEGGGGGGRPGAPAAGDGKTEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGGGGGGRPGAPAAGDGKTEQK 23 2 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 55.734 0.053063 23666000 58781 49498 55320 62306 41338 66774 66130 69228 41865 FALSE TRUE 56002.53862 54541.90247 57856.47672 56042.88251 48547.33411 64461.59964 56040.65394 63166.02932 48357.21038 1.158101102 1.127895965 1.196439502 1.158935391 1.003931652 1.333029741 1.158889305 1.306238073 1 15.5614434 2.233780069 24.99999471 1.211300636 1.135962544 0.098863544 0.101870614 244.0464612 1276233.55 0.032833174 0.025037602 171.3089563 -2.233780069 -0.075338092 AEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.001)S(0.031)IS(0.961)PS(0.008)R;AEGLEEADTGASGCHSHPEEQPT(0.001)S(0.001)IS(0.994)PS(0.005)R 322.68 1.95E-92 492230000 347080 324130 308770 373820 397510 372730 383960 324050 35253 TRUE FALSE 330674.2162 357159.2155 322927.4099 336242.9034 466835.6181 359822.2666 325379.8501 295674.4641 40719.85519 8.120711989 8.771131769 7.930465577 8.257468053 11.4645697 8.836531096 7.990692711 7.261186532 1 15.31344481 0.605985756 1.342156997 1.00434787 8.815218387 0.857250137 0.994108531 0.514956248 1.313514108 0.942216017 0.27975869 4.036321542 -0.605985756 7.810870517 AEGLGDGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGLGDGYR 9 0 Q9BX68 Q9BX68 HINT2 "Histidine triad nucleotide-binding protein 2, mitochondrial" 0 103.8 0.0087538 0 185170 163760 160690 156860 200870 148900 184910 164400 200270 FALSE TRUE 176417.3811 180447.3302 168057.7954 141092.1348 235901.6644 143743.5557 156698.5834 150004.2645 231326.8488 0.762632535 0.780053553 0.726494985 0.609925461 1.019776414 0.621387255 0.677390386 0.648451597 1 17.8195732 3.740613774 23.83812079 0.73713604 0.771343041 0 0.145397084 671.2231681 7793098.733 0.034711754 0.058720421 5503.180705 -3.740613774 0.034207001 AEGNDHIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 113.46 0.0017969 246882000 394373 327296 345389 401646 372810 331070 471697 402182 402073 FALSE TRUE 375731.7699 360647.8345 361225.4273 361271.781 437827.946 319604.9629 399730.9593 366964.812 464424.4273 0.809026717 0.776547945 0.777791619 0.777891428 0.942732381 0.688174317 0.86070184 0.790149679 1 18.82508433 -4.999999994 0.322898304 2.908969615 0.794261225 0.47391561 0.065209748 268.3536983 2.360118437 350.4525883 0.049762151 1.00E-05 4.999999994 -2.11470839 AEGPLDS(ph)PSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Trastuzumab_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(0.587)PS(0.129)EGHS(0.09)Y(0.013)QNS(0.09)GLDHFQNS(0.09)NIDQSFWETFGSAEPTK;AEGPLDS(0.232)PS(0.054)EGHS(0.177)Y(0.163)QNS(0.177)GLDHFQNS(0.177)NIDQS(0.015)FWET(0.005)FGSAEPTK 59.31 0.020688 357162000 46656 36550 43357 49693 43939 43602 56488 50341 21159 TRUE FALSE 44450.66334 40274.48655 45344.96134 44697.76523 51601.94769 42092.05181 47869.71813 45932.87517 24440.22965 1.818749822 1.647876764 1.855341049 1.828860279 2.111352815 1.722244529 1.958644366 1.879396217 1 14.57697022 -1.080445593 6.167125167 0.999998205 1.842334981 0.821357605 0.1249065 3.08E-06 4.60E-07 0.12082531 0.028478739 0.083091081 1.080445593 0.842336776 AEGPLDSPS(ph)EGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK 42 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;F8W1U7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 AEGPLDS(0.107)PS(0.405)EGHS(0.37)Y(0.008)QNS(0.107)GLDHFQNS(0.003)NIDQSFWETFGSAEPTK 85.244 0.00045102 283050000 39615 29098 33027 41211 31444 36879 44866 38272 15921 TRUE FALSE 37742.47746 32063.11928 34541.32062 37068.39198 36927.82364 35601.87098 38020.86768 34920.70079 18389.94737 2.052342876 1.743513379 1.878271858 2.015687769 2.008044009 1.935941973 2.067481049 1.898901617 1 14.16662973 0.945433386 22.76414089 1 1.950370459 0.909695898 0.094223195 2113.165747 881573.2446 0.094726465 0.023681616 8.819285175 -0.945433386 0.950370459 AEGPLDSPSEGHS(ph)YQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK 42 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;F8W1U7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 AEGPLDS(0.111)PS(0.101)EGHS(0.375)Y(0.3)QNS(0.101)GLDHFQNS(0.012)NIDQSFWETFGSAEPTK 87.473 0.00039253 99281000 54739 45344 45959 60628 46958 51097 57778 51736 17314 TRUE FALSE 52151.59595 49964.60515 48066.26561 54533.55825 55147.46033 49327.49808 48962.90493 47205.72157 19998.96669 2.607714526 2.498359336 2.403437455 2.726818795 2.757515485 2.466502337 2.448271738 2.36040803 1 14.28763784 0.172194704 0.885232084 0.981612176 2.576041493 0.952949278 0.108301736 0.779286913 0.668967855 0.14189416 0.035086009 1.486601969 -0.172194704 1.594429317 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK 42 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;F8W1U7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 94.406 7.29E-05 22791000 12648 10196 10661 13372 13045 12493 19252 12625 6345.9 FALSE TRUE 12050.15411 11234.98399 11149.8174 12027.82115 15320.04387 12060.36428 16314.75381 11519.48807 7329.989762 1.643952379 1.532742113 1.521123188 1.640905587 2.090049832 1.64534531 2.22575397 1.57155582 1 12.83959547 2.983043837 23.94093423 1.818073668 1.571350752 0 0.334881298 874.6681873 1234973.824 0.089704108 0.097396834 961.7093472 -2.983043837 -0.246722916 AEGS(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEGSPNQGK 9 0 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGK;AEGS(1)PNQGK 114.86 0.0016462 338620000 550490 653010 640570 899680 434810 603510 741330 1009970 616700 TRUE FALSE 524469.4287 719552.4614 669940.7681 809242.4571 510640.7263 582610.2974 628226.493 921531.6726 712334.6863 0.736268272 1.010132562 0.940485955 1.136042471 0.716855063 0.817888429 0.881926017 1.293677944 1 19.44219572 1.259335386 24.9941323 1.14683895 0.892651063 0.361210387 0.14123155 214.1810747 257682.6098 0.089162658 0.032482203 18.16918245 -1.259335386 -0.254187887 AEGS(ph)PNQGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGSPNQGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGKK 82.925 0.010139 270110000 415270 421720 432820 488310 203000 450780 449560 580750 314230 TRUE FALSE 395641.0101 464693.7475 452665.2251 439224.1511 238403.1357 435169.3756 380971.3653 529896.4513 362959.1835 1.090042705 1.280292023 1.247151872 1.210119956 0.656831805 1.198948519 1.049625915 1.459933996 1 18.46944779 AEGSEKEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGSEKEESR 10 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 69.672 0.051326 270080000 349810 296000 330980 362080 264010 333860 368830 355680 314770 FALSE TRUE 333275.1746 326162.7365 346155.7604 325683.0305 310053.2604 322298.3445 312558.2095 324534.7736 363582.924 0.916641439 0.897079359 0.952068256 0.895759974 0.852771789 0.886450719 0.859661411 0.892601803 1 18.47192492 -0.995503004 6.030893308 1.000000093 0.89341819 0.592875374 0.02756588 3.60E-08 6.07E-09 0.027938915 0.00658526 0.101040851 0.995503004 -0.106581903 AEGSEKEESRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGSEKEESRR 11 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 70.488 0.029038 32782000 35494 29369 35604 37436 27157 38587 37776 38378 38377 FALSE TRUE 33816.26896 32361.73449 37236.47862 33672.86216 31893.1722 37250.72251 32012.5774 35017.41887 44328.30916 0.762859437 0.73004667 0.840015767 0.75962433 0.719476398 0.840337094 0.722170054 0.789956115 1 15.43594071 0.958897032 22.56314235 1.000000001 0.765130923 0.741331051 0.042765598 1104.065398 606068.9549 0.037090455 0.009272614 9.096975651 -0.958897032 -0.234869077 AEGSPS(ph)EGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGSPSEGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(0.45)PS(0.55)EGKK 63.76 0.046851 214280000 150200 149780 140410 165350 68364 155930 153240 185480 98578 TRUE FALSE 143100.3437 165042.7523 146847.9374 148728.7039 80286.65996 150530.105 129860.4236 169238.3879 113864.9728 1.256754735 1.449460253 1.289667347 1.306184863 0.705104107 1.322005366 1.14047736 1.486307719 1 16.79696449 2.972547557 24.99636202 1.140358719 1.340336973 0.179940848 0.206366628 1184.187815 1078242.842 0.058666907 0.062375563 938.7448278 -2.972547557 0.199978254 AEGT(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEGTPNQGK 9 0 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGT(1)PNQGK 106.67 0.032401 21616000 95499 118880 112140 136100 69531 113520 118400 154960 120300 TRUE FALSE 90984.95153 130994.0072 117281.7299 122418.9694 81657.18439 109588.7739 100335.9054 141390.8809 138955.5096 0.654777574 0.942704665 0.844023603 0.880993994 0.58764985 0.788660876 0.722072163 1.017526267 1 17.08426351 1.230854881 24.9844668 1.008763321 0.780596383 0.467297184 0.103861155 172.0501736 557818.8891 0.09086213 0.024428264 17.01589829 -1.230854881 -0.228166938 AEGTNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEGTNFR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 111.73 0.015154 231201000 535470 475010 586870 622470 547560 570530 582330 586120 597680 FALSE TRUE 510159.3943 523414.059 613778.57 559898.133 643054.2906 550772.403 493484.8633 534796.2256 690365.1619 0.738970363 0.758169861 0.889063649 0.811017363 0.931469788 0.797798663 0.714817158 0.77465703 1 19.39700014 -2.407685014 2.213774434 2.638975889 0.79487871 0.468418665 0.065903095 4942495.439 208634.5659 41147306.76 0.01792748 0.003911245 2.407685014 -1.84409718 AEGYEVAHGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AEGYEVAHGGR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ;;; 115.91 0.0010592 1186130000 1059600 817130 854990 982940 1033780 864280 1175510 986330 1052830 FALSE TRUE 1009514.808 900396.476 894192.1372 884133.0037 1214070.905 834349.7669 996164.3598 899961.7163 1216097.499 0.830126539 0.740398263 0.73529642 0.727024769 0.998333526 0.68608789 0.819148432 0.740040759 1 20.21382747 -1.064575441 4.194625635 1.00002502 0.784679869 0.376456387 0.087138518 8792747.679 4463112.842 1932.770813 0.018241523 0.086183586 1.064575441 -0.215345151 AEHIPAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEHIPAGK 8 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ; 86.011 0.016336 457480000 956530 817930 787540 976360 831120 850060 1001720 937720 803080 FALSE TRUE 911316.7226 901277.9969 823649.488 878214.4378 976067.0649 820622.2091 848889.2162 855608.2656 927617.5448 0.982427217 0.971605164 0.887919264 0.946741944 1.05223006 0.884655765 0.915128461 0.922371801 1 19.82317058 AEIIDQDLYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEIIDQDLYER 11 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 219.35 2.31E-11 1476918000 1431007 1180848 1210849 1392661 1370655 1189751 1522380 1347301 1528880 FALSE TRUE 1363366.135 1301177.754 1266367.624 1252668.07 1609696.798 1148549.625 1290112.971 1229324.182 1765970.902 0.772020724 0.736805885 0.717094275 0.709336756 0.911508109 0.650378567 0.730540333 0.696118028 1 20.75203014 -1.141859457 4.610255237 1.000028677 0.740714582 0.587929208 0.06828147 1.83E-05 3.41E-06 0.060168026 0.014180173 0.072134088 1.141859457 -0.259314094 AEIIDQDLYERLEHGQATAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEIIDQDLYERLEHGQATAK 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 211.03 1.87E-22 62039000 65541 23083 66810 37729 82887 54239 124820 78586 138260 FALSE TRUE 62443.00682 25435.18394 69873.30458 33936.40924 97342.46656 52360.68983 105776.4165 71704.59323 159700.6547 0.391000318 0.159267875 0.437526726 0.212500126 0.609530792 0.327867722 0.662341784 0.448993734 1 17.2850107 0.198683518 0.270022761 1.189639566 0.226244321 0.684996845 0.135957667 2.563016963 0.339517746 0.721577087 0.196304994 1.58009616 -0.198683518 -0.963395244 AEIIHHLADLLTDQRDEILLANKK ddPTM_SK-BR-3_Trastuzumab_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 0 213.15 3.69E-26 32579000 182260 139960 158640 159360 123570 140890 175100 176000 27170 FALSE TRUE 173644.931 154222.0831 165913.8009 143340.83 145120.5689 136010.944 148385.2791 160588.507 31383.38483 5.533021117 4.9141316 5.286676431 4.567411412 4.624121 4.333851963 4.728147708 5.116991294 1 14.93771334 -0.929323368 0.518922046 9.67E-23 4.999304478 0.915586053 0.369676147 5.025881459 0.861632912 8.881756717 0.172570116 0.117672948 0.929323368 4.999304478 AEITFDDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;; 205.83 1.43E-05 2724510000 4019600 3923630 3204680 4380280 2454550 3755370 3788170 4105100 2167840 FALSE TRUE 3829601.474 4323452.358 3351617.748 3939965.932 2882622.743 3625320.595 3210215.092 3745635.681 2504017.555 1.529382838 1.726606249 1.338496106 1.573457791 1.151199095 1.447801589 1.282025793 1.495850408 1 21.25581325 0.816304209 0.057561524 2.99E-09 2.551571479 0.499075398 0.149996887 36.16019694 1.191768763 28.35087408 23.3549303 6.550948852 -0.816304209 2.551571476 AEITGPDGTRLPVPVVDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEITGPDGTRLPVPVVDHK 19 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 144.27 8.23E-08 120640000 351870 302170 308020 350910 294920 339460 403030 341370 329610 FALSE TRUE 335237.8024 332961.4665 322143.0217 315635.8601 346353.9546 327704.4151 341540.3713 311477.8331 380724.2354 0.880526563 0.874547601 0.846132165 0.82904063 0.909723948 0.860739571 0.89708072 0.818119269 1 18.53838688 -1.255523841 3.521630173 1.000314344 0.86808709 0.688792654 0.028534874 1447515.506 1034286.989 3140.360516 0.006106864 0.055523414 1.255523841 -0.132227254 AEKDEPGAWEETFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AEKDEPGAWEETFK 14 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 177.58 1.90E-06 1189733000 1490690 1354580 1187560 1569260 770571 1531790 1535620 1589280 809593 FALSE TRUE 1420228.038 1492613.242 1242010.801 1411515.003 904958.3384 1478743.728 1301332.965 1450114.218 935140.5476 1.518732175 1.59613787 1.328154152 1.509414822 0.967724414 1.581306395 1.391590781 1.5506912 1 19.83482369 -3.370355026 0.253665482 7.47E-34 1.48394192 0.326801603 0.187399541 86.17535402 1.797297073 46.31950643 0.25377908 0.000426231 3.370355026 1.48394192 AEKDNAEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AEKDNAEIR 9 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 91.549 0.0097381 1615180000 5377260 5555570 4946520 5870400 3590800 5556120 5388210 5941120 4085360 FALSE TRUE 5123087.577 6121688.899 5173322.835 5280296.239 4217034.383 5363710.171 4566139.603 5420884.037 4718896.764 1.085653667 1.297271207 1.096299219 1.118968374 0.893648366 1.136644949 0.967628628 1.148760888 1 22.17001818 3.274196578 2.38218935 1.032173227 1.189058634 0.288252986 0.093542241 0.289581939 3.362123003 0.02560763 0.035322199 1880.167657 -3.274196578 0.156885407 AEKEEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEKEEENR 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;;;; 128.28 0.0010399 1928410000 5191900 4560450 4192070 5215860 3190470 4741170 5097660 5439190 4217930 FALSE TRUE 4946489.176 5025165.04 4384280.556 4691551.843 3746886.958 4576982.094 4319918.342 4962905.689 4872025.042 1.015284021 1.031432514 0.899888756 0.962957251 0.769061515 0.939441414 0.886678189 1.018653567 1 22.21609012 3.740809182 24.80793782 0.914919939 1.023358274 0.247192057 0.069391618 188.1555757 2075867.617 0.016504726 0.028038627 5505.657388 -3.740809182 0.108438336 AEKEEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEKEEENRR 9 2 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;; 74.841 0.022469 306224000 652490 544320 561000 659190 467465 667730 720980 659490 521450 FALSE TRUE 621648.0908 599786.8268 586722.4049 592926.9688 548990.748 644606.3427 610981.2593 601741.5594 602313.8028 1.032100025 0.995804552 0.974114161 0.984415376 0.911469645 1.070216787 1.014390267 0.999049925 1 19.20015579 2.203641352 24.99994425 1.023003854 0.986538591 0.237396732 0.035531168 303.9337668 217595.1466 0.013329947 0.009845213 159.8237631 -2.203641352 -0.036465263 AEKPPLSAS(ph)SPQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLS(0.015)AS(0.489)S(0.489)PQQRPPEPET(0.003)GES(0.001)AGT(0.001)S(0.001)R 46.772 0.060155 194680000 27846 29973 27530 26907 25501 26027 30002 34324 33450 TRUE FALSE 26529.77477 33027.28278 28792.27773 24202.25724 29948.36633 25125.67846 25424.64388 31318.4086 38637.25516 0.68663715 0.854804065 0.745194699 0.62639691 0.775116302 0.650296672 0.658034422 0.810575401 1 15.23770499 0.942947603 5.592447082 0.999961044 0.72033376 0.648386144 0.067068441 0.239980069 21.31692938 0.067424373 0.016985338 8.768950186 -0.942947603 -0.279627284 AEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLS(0.012)AS(0.171)S(0.796)PQQRPPEPET(0.009)GES(0.002)AGT(0.005)S(0.005)R;AEKPPLSAS(0.167)S(0.819)PQQRPPEPET(0.003)GES(0.001)AGT(0.004)S(0.004)R 122.63 2.38E-05 442710000 279550 244960 223980 277400 207223 269020 279430 276640 267320 TRUE FALSE 266336.2255 269921.7025 234249.7045 249515.225 243362.6256 259703.7699 236797.8214 252415.935 308774.6203 0.862558669 0.874170624 0.758643001 0.80808204 0.788156181 0.841078744 0.766895353 0.817476303 1 18.23619465 -1.223111737 3.073629159 1.000744702 0.817570823 0.704604737 0.037676731 5338199.144 7469960.878 38189.15923 0.010312208 0.059825765 1.223111737 -0.183173879 AELAESR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 137.18 0.0067653 1407550000 2130230 1863020 1757000 1990900 2269950 1859150 2254560 2116420 2478130 FALSE TRUE 2029538.25 2052863.856 1837560.188 1790770.95 2665828.561 1794767.169 1910585.464 1931095.045 2862425.744 0.709027388 0.717176283 0.641959077 0.625613067 0.93131798 0.627009163 0.667470752 0.674635857 1 21.44880684 -1.305362687 6.015960459 1.000019944 0.69889703 0.535195309 0.088073709 2.18E-05 2.51E-06 0.078738004 0.018557498 0.04950366 1.305362687 -0.301122914 AELEIQKDALEPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELEIQKDALEPGQR 15 1 H3BQB1;P07741-2;P07741;H3BQZ9 H3BQB1 APRT Adenine phosphoribosyltransferase 0 145.46 3.70E-06 77584000 123280 67263 111340 95237 103780 102770 141120 136910 139690 FALSE TRUE 117452.7987 74117.17617 116445.0491 85663.59582 121879.1991 99211.04913 119589.5522 124921.4346 161352.4118 0.727927134 0.459349664 0.721681491 0.530909919 0.755360257 0.614871808 0.741169908 0.774214858 1 17.29985562 0.801323406 0.560403846 1.010108886 0.604214557 0.621314313 0.090626235 0.674374216 0.468021677 0.093510316 0.038166066 6.328829644 -0.801323406 -0.405894329 AELELELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 194.29 7.58E-05 103654000 227730 203481 197097 227140 233510 203073 244390 229450 260400 FALSE TRUE 216965.6542 224215.9452 206134.0924 204307.4557 274234.0701 196040.5311 207103.817 209358.1416 300781.5021 0.721339752 0.745444596 0.685328356 0.679255387 0.911738482 0.65177057 0.688552373 0.696047264 1 18.19835632 -1.894479471 2.555040487 1.149383724 0.722022295 0.595859695 0.071838553 14047319.77 8346406.262 12649638.39 0.01856983 0.012750304 1.894479471 -0.427361429 AELEQHLEQEQEFQVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELEQHLEQEQEFQVNK 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 177.56 1.02E-09 67847000 97312 85712 87088 93779 75481 84754 115030 100120 76383 FALSE TRUE 92712.25461 94446.15025 91081.07094 84352.15675 88644.8625 81818.94773 97480.06083 91352.96203 88228.08553 1.050824735 1.070477158 1.032336476 0.956069218 1.004723858 0.92735717 1.104864287 1.035418161 1 16.42895036 3.480003448 24.96808661 1.009651005 1.059110265 0.192869803 0.046771399 195.347299 1692276.544 0.013204734 0.018208091 3019.975696 -3.480003448 0.04945926 AELESDPPY(ph)MEMKGKLSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELESDPPYMEMKGKLSAK 19 2 Q1MSJ5-1;Q1MSJ5;E5RI67;F2Z2M5 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 AELES(0.478)DPPY(0.516)MEMKGKLS(0.006)AK 48.883 0.050163 690590000 723700 811270 643210 785740 523170 724040 738890 737320 99320 TRUE FALSE 689492.1352 893939.3353 672701.8147 706755.9224 614410.6824 698966.3133 626158.7599 672756.352 114722.0383 6.01011057 7.792219771 5.86375403 6.160594186 5.355646493 6.092694336 5.458051207 5.864229417 1 16.80778304 -0.389931278 0.393107877 2.39E-14 6.635996548 0.866054439 0.632009338 2.500389563 0.400815066 4.859218365 0.430903339 0.407444746 0.389931278 6.635996548 AELGFLESCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELGFLESCLR 11 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 98.943 0.011968 12465000 17454 13122 13406 16377 20777 13630 17586 18288 20065 FALSE TRUE 16628.98401 14459.14672 14020.67836 14730.75285 24400.50222 13157.98968 14902.93271 16686.60577 23176.57772 0.717490917 0.623868929 0.604950331 0.635587921 1.052808681 0.567727895 0.643016967 0.719977124 1 14.50037993 0.95128511 18.72999192 1.000000003 0.685747052 0.334734641 0.135141591 458.4319712 176260.764 0.122855336 0.030713834 8.938921215 -0.95128511 -0.314252951 AELGMGDSTSQS(ph)PPIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.009)QS(0.99)PPIKR;AELGMGDSTS(0.019)QS(0.981)PPIKR;AELGMGDSTS(0.008)QS(0.992)PPIKR;AELGMGDSTS(0.021)QS(0.979)PPIKR;AELGMGDSTS(0.001)QS(0.999)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.001)QS(0.999)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR 271.92 7.81E-36 4883140000 3075070 3019370 3161900 3504610 2453760 3463020 3774710 3646710 3097480 TRUE FALSE 2929717.535 3327047.236 3306876.243 3152319.944 2881694.967 3343094.749 3198808.662 3327384.74 3577821.379 0.818855171 0.929908702 0.924270916 0.881072477 0.805432877 0.934393978 0.89406606 0.930003035 1 21.77064993 0.860682116 0.971262778 0.999763105 0.88056024 0.443470674 0.042675369 0.694965559 1.316860516 0.039377892 0.013041904 7.255746751 -0.860682116 -0.119202865 AELGS(ph)WSSQEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Trastuzumab_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(0.364)WS(0.332)S(0.304)QEHLEWEPACQTPQPSAR 69.873 0.020215 242230000 11639 16467 16528 19769 22949 14890 19300 14849 20452 TRUE FALSE 11088.84754 18145.00602 17285.82515 17781.78256 26951.29833 14374.35557 16355.43053 13548.74284 23623.59171 0.469397189 0.768088369 0.731718757 0.752712914 1.140863704 0.608474602 0.692334626 0.573525949 1 14.52794071 4.585276056 1.775895468 0.771610457 0.417233056 0.246703877 0.170951993 0.907283108 3.710011833 0.042980362 0.491492971 38483.63228 -4.585276056 -0.354377402 AELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.007)WS(0.55)S(0.443)QEHLEWEPACQTPQPSAR;AELGS(0.003)WS(0.55)S(0.447)QEHLEWEPACQTPQPSAR 227.58 8.22E-35 287282000 135307 144981 132105 151689 144566 133854 156018 131845 120007 TRUE FALSE 128911.3063 159754.7287 138162.1449 136440.9335 169778.2646 129218.6024 132214.5886 120299.9528 138617.0726 0.92998145 1.152489558 0.996718097 0.984301074 1.224800534 0.932198321 0.953811721 0.867858126 1 17.08074543 AELLRFPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AELLRFPER 9 1 P23919-2;P23919;H7C312;G5E9E9;H7C3A4 P23919-2 DTYMK Thymidylate kinase 0 ; 83.883 0.014471 527830000 432460 226880 88142 116742 1746120 100758 525510 186818 1264120 FALSE TRUE 412018.4729 249999.3299 92183.39788 105006.8724 2050642.775 97268.7252 445333.7978 170459.2255 1460153.273 0.28217481 0.171214443 0.063132686 0.071914966 1.404402409 0.066615421 0.304991131 0.116740639 1 20.47768839 AELNEFLTR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 231.81 9.24E-08 1843023000 1467090 1354390 1249280 1420310 1436840 1342730 1584100 1420630 1473610 FALSE TRUE 1397743.563 1492403.881 1306560.724 1277537.74 1687424.441 1296230.923 1342416.451 1296232.106 1702129.913 0.821173256 0.876786119 0.767603409 0.750552429 0.991360547 0.761534659 0.788668621 0.761535354 1 20.69890972 3.781967852 24.96020704 0.819986497 0.848979662 0 0.093511359 2443.639435 1405144.816 0.021963051 0.039594001 6052.960672 -3.781967852 0.028993166 AELNNEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELNNEKK 8 1 P63010;P63010-2;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7ERB2;K7EN71;A0A087WXS3;K7EKZ5;K7EJX1 P63010 AP2B1 AP-2 complex subunit beta 0 90.15 0.021486 166650000 157750 133170 147160 143410 149550 139970 178880 143870 181890 FALSE TRUE 150293.4701 146740.1744 153907.4316 128994.1543 175631.4727 135122.8038 151588.5706 131271.9801 210096.5722 0.715354223 0.698441544 0.732555652 0.61397553 0.835955917 0.643146161 0.721518533 0.624817334 1 17.6806931 -1.052287903 4.709223767 1.000010298 0.700953623 0.688697478 0.063739519 5.83E-06 1.17E-06 0.052200494 0.012303351 0.088656809 1.052287903 -0.299056675 AELNPWPEYIYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AELNPWPEYIYTR 13 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;; 193.73 3.76E-06 191294000 198198 174288 158219 195508 193971 181683 204821 171300 213481 FALSE TRUE 188829.5733 192048.1453 165473.4976 175855.1644 227799.481 175391.2722 173571.7947 156300.0639 246586.5432 0.76577404 0.778826545 0.67105648 0.713157994 0.923811486 0.711276738 0.703898081 0.6338548 1 17.91173454 -1.318858588 3.882610433 1.000584783 0.741880069 0.526261792 0.078119991 11917821.23 4048444.848 58622.68663 0.017700234 0.047988968 1.318858588 -0.258704714 AELRDDPIISTHLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AELRDDPIISTHLAK 15 1 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 89.484 0.0038344 391680000 694090 538660 611230 713580 671670 622300 894320 791020 709780 FALSE TRUE 661281.7413 593550.0664 639255.5001 641849.5827 788809.0353 600749.595 757875.0587 721754.0953 819849.0573 0.806589622 0.723974811 0.779723407 0.782887505 0.962139345 0.73275634 0.924408038 0.880349973 1 19.64499879 1.450666035 0.347439659 1.013015185 0.745579004 0.51034335 0.066844183 0.930435878 0.368649233 0.094385044 0.075350633 28.22708527 -1.450666035 -0.267436181 AELSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AELSYR 6 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 158.53 0.021857 1087696000 1375941 1095555 1027151 1135064 1560900 1038880 1464380 1270171 1741140 FALSE TRUE 1310902.996 1207193.3 1074246.889 1020965.21 1833120.466 1002903.325 1240961.936 1158948.094 2011147.099 0.651818555 0.600251121 0.534146354 0.507653175 0.911480054 0.498672288 0.617041855 0.576262221 1 20.93958718 -1.261858889 3.579671996 1.000873982 0.612229444 0.521848691 0.116669952 35482028.83 50984623.04 334539.2279 0.025469596 0.054719373 1.261858889 -0.388644538 AEMDMVAWGVDLASVEQHINSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEMDMVAWGVDLASVEQHINSHR 23 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 160.67 1.08E-11 97547300 78301.9 65936.6 70478.2 89312.6 88567.6 68704.2 88318.9 82124.8 5267.6 FALSE TRUE 74600.72437 72655.6145 73709.69518 80334.72777 104013.7614 66324.95633 74844.22972 74933.51714 6084.472505 12.2608368 11.94115257 12.11439367 13.20323622 17.09495134 10.90069127 12.30085758 12.31553221 1 12.57091648 -0.253102682 0.903156849 0.688934907 12.80666203 0.838356393 1.626277092 4.865659062 3.012868901 7.106988446 0.502390573 0.558338169 0.253102682 12.11772712 AEMDQILHGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEMDQILHGLDK 12 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ; 116.84 0.00079845 223472000 730900 705070 661570 804620 591180 734370 819980 779300 522080 FALSE TRUE 696351.8055 776917.4346 691903.6389 723738.0689 694281.6048 708938.5828 694876.991 711060.3607 603041.5 1.154732809 1.288331623 1.14735659 1.200146373 1.151299877 1.175604967 1.152287183 1.179123428 1 19.20189776 -5 0.180230802 0.22513465 1.225383679 0.664177386 0.040796271 73.64226095 0.709234942 20.35421336 0.117910972 1.00E-05 5 1.000249029 AENGERS(ph)DLEEDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER 175.19 2.29E-06 268060000 429020 467140 370510 450210 354030 454250 399320 402750 319320 TRUE FALSE 408741.0748 514742.0971 387498.25 404954.0355 415772.7199 438519.2086 338396.4 367483.0749 368838.5147 1.108184364 1.395575778 1.050590528 1.097916891 1.127248656 1.188919245 0.917464924 0.996325113 1 18.49262979 2.393570908 0.642613646 0.96195919 1.230103496 0.350813297 0.10490176 0.719270907 0.596020899 0.087566747 0.067849897 247.497552 -2.393570908 0.268144306 AENGKLVINGNPITIFQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AENGKLVINGNPITIFQER 19 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 226.71 1.31E-19 482020000 673450 668520 959290 583580 615850 825050 773960 959790 824750 FALSE TRUE 641617.3531 736642.948 1003274.395 524917.4297 723254.045 796478.3116 655878.1872 875745.6994 952648.0178 0.673509356 0.773258259 1.053142794 0.551008788 0.759203852 0.836067778 0.688479034 0.919275202 1 19.86158374 1.06666832 4.964990764 0.998548314 0.760602467 0.299929064 0.128445334 0.20923354 9.218624735 0.113375581 0.028717112 11.65918839 -1.06666832 -0.237945848 AENLQLLTENELHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AENLQLLTENELHR 14 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 208.15 8.44E-09 205443000 425930 391310 368760 417710 399210 385520 456900 406560 394390 FALSE TRUE 405797.133 431184.9339 385668.0108 375720.9972 468832.0976 372169.3457 387191.5135 370959.4511 455549.9869 0.890785083 0.946515083 0.846598665 0.82476349 1.029156209 0.816967087 0.84994298 0.814311188 1 18.79724984 AENNS(ph)EVGASGYGVPGPTWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AENNSEVGASGYGVPGPTWDR 21 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 AENNS(0.964)EVGAS(0.019)GY(0.016)GVPGPTWDR 62.966 0.038659 42245000 42452 34120 46434 45263 38284 45351 51136 43903 62160 TRUE FALSE 40445.37809 37596.86679 48563.04483 40713.07725 44960.71748 43780.4835 43334.26402 40058.62058 71799.45533 0.563310375 0.523637214 0.676370658 0.567038804 0.626198587 0.609760663 0.60354586 0.557923739 1 16.13168528 -5 0.421244957 8.667882636 0.581336086 0.897026689 0.04341281 274.8876972 1.777548697 1951.451965 0.024683909 1.00E-05 5 -8.08654655 AENSHNAGQVDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 84.468 0.0097302 45747000 38886 37662 35876 42299 38778 37704 36005 41400 38929 FALSE TRUE 37047.93584 41499.80062 37520.95009 38047.02416 45540.87092 36398.30103 30511.77597 37774.79652 44965.9105 0.823911613 0.922916942 0.834431009 0.846130407 1.012786585 0.809464339 0.678553501 0.840076318 1 15.45654406 2.022584841 24.99081501 0.788872412 0.884996514 0 0.097144812 364.7570746 403613.0949 0.033362735 0.024638464 105.3379449 -2.022584841 0.096124102 AENYDIPSADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 245.08 1.50E-15 1644740000 2482750 2147380 2196640 2550100 2492190 2314620 2769420 2483570 2698650 FALSE TRUE 2365395.328 2366200.463 2297358.117 2293759.103 2926827.147 2234464.129 2346894.115 2266095.445 3117142.859 0.758834431 0.759092724 0.737007645 0.735853057 0.938945464 0.716830838 0.75289912 0.726978373 1 21.57179284 -1.752417421 4.126289213 1.022350493 0.765099228 0.576071777 0.063134948 0.012623568 0.00075743 0.059445585 0.013370336 0.017684084 1.752417421 -0.257251265 AEPAKIEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 137.89 7.21E-05 6801620000 8004260 4212880 7777460 6379580 7423640 7542750 11145800 8714920 9779950 FALSE TRUE 7625914.493 4642177.262 8134064.234 5738292.498 8718320.466 7281542.676 9445303.503 7951795.404 11296574.7 0.675064318 0.410936712 0.720046957 0.507967473 0.771766726 0.644579695 0.836121015 0.703912081 1 23.42938205 1.326498075 0.375120047 1.014397002 0.531654017 0.56515149 0.107263404 0.745178577 0.325526988 0.139501285 0.097469206 21.20791992 -1.326498075 -0.482742985 AEPDESNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AEPDESNAR 9 0 P61088;F8VSD4;F8VV71;Q5JXB2;F8VZ29 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;; 159.28 0.00015395 115441000 336866 308427 306107 351745 308167 306135 372664 319330 339910 FALSE TRUE 320943.0118 339856.062 320142.3087 316386.9243 361911.2272 295533.4682 315807.2624 291367.7723 392621.5068 0.817436147 0.86560735 0.815396771 0.805831873 0.921781464 0.752718491 0.804355485 0.742108538 1 18.58277968 2.207017408 24.9999062 0.806056897 0.842322181 0 0.077519201 636.6997799 504619.6357 0.025361119 0.018732308 161.0710196 -2.207017408 0.036265284 AEPDHMVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEPDHMVLGK 10 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 65.305 0.052616 136420000 99060 124470 102650 122660 384810 70958 123800 86117 372140 FALSE TRUE 94377.63012 137153.6345 107356.604 110329.9838 451920.7422 68500.70667 104912.0363 78576.13895 429849.5706 0.219559671 0.319073564 0.249753894 0.25667115 1.051346269 0.159359719 0.244066863 0.182799157 1 18.71347234 -1.137041931 4.040749537 1.000172569 0.329200249 0.394325197 0.258782932 101908138.9 203142564.1 294795.02 0.058395845 0.072938708 1.137041931 -0.67097232 AEPYCSVLPGFTFIQHLPLSER ddPTM_SK-BR-3_Trastuzumab_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 ; 225.3 6.20E-26 534760000 694060 544070 570630 727760 716740 606000 764630 701260 714030 FALSE TRUE 661253.1593 599511.3516 596793.9499 654604.1821 841739.2291 585014.068 647971.6501 639853.9568 824758.1256 0.80175404 0.726893538 0.723598751 0.79369231 1.020589192 0.709315919 0.78565052 0.775808006 1 19.65361156 -2.149801039 2.188723053 1.451470535 0.787835438 0.358102811 0.0872782 6366538.016 1459075.377 14258604.96 0.020727977 0.007082702 2.149801039 -0.663635097 AEQEAQAPHWWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEQEAQAPHWWR 12 0 Q96DV4 Q96DV4 MRPL38 "39S ribosomal protein L38, mitochondrial" 0 80.469 0.013918 0 71775 69243 73117 81055 72402 67434 63965 67088 66160 FALSE TRUE 68382.33799 76298.94042 76469.48677 72907.19741 85028.88588 65098.74367 54205.96445 61213.41906 76419.7549 0.894825403 0.998419067 1.000650772 0.954036002 1.112655831 0.85185753 0.709318743 0.801015642 1 16.22165801 2.018052452 21.5735511 0.798507188 0.982744812 0.383550417 0.09101735 37.70402826 45057.23086 0.031235269 0.023058547 104.2443324 -2.018052452 0.184237623 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 32 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 304.42 2.79E-90 2099520000 1225962 800458 1080282 1135970 686897 1151905 1437365 1395810 762112 TRUE FALSE 1168013.206 882025.5802 1129813.998 1021780.137 806691.6193 1112014.241 1218068.57 1273585.477 880296.4366 1.326840775 1.001964274 1.283447202 1.160722792 0.916386328 1.263227016 1.383702716 1.446768865 1 19.7476299 2.013375245 24.99480906 1.320459385 1.139643398 0.124596204 0.165869431 333.2426253 622739.9751 0.057004349 0.042078988 103.1276794 -2.013375245 -0.180815987 AERPDVDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AERPDVDEKR 10 2 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 98.353 0.0030566 60299000 65343 76778 69641 83214 63819 65469 84935 87351 66438 FALSE TRUE 62254.36589 84601.76549 72834.10873 74849.17062 74949.01339 63201.79211 71976.60581 79702.08336 76740.86572 0.81122835 1.102434338 0.94909157 0.975349573 0.976650611 0.823574135 0.937917564 1.038587233 1 16.22770742 AES(ph)GDSLGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.989)GDS(0.009)LGS(0.002)EDRDLLYSIDAYR 170.53 4.27E-12 50686000 47627 36800 41623 57306 46545 49098 62291 37378 43665 TRUE FALSE 45375.7661 40549.96184 43531.45572 51545.49201 54662.43326 47397.72395 52787.3639 34104.98417 50436.34519 0.89966404 0.803982955 0.86309695 1.021991023 1.08379053 0.939753342 1.046613582 0.676198564 1 15.62217612 3.316240103 7.081405497 0.973231391 0.84949164 0.157979582 0.112909569 0.332803153 25.22512659 0.029186334 0.039503512 2071.286157 -3.316240103 -0.123739751 AES(ph)GPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AES(1)GPDLR 109.02 0.0038796 6813080000 12410060 11467730 11096390 13136300 10437740 12019090 13551860 13087630 10863920 TRUE FALSE 11823461.06 12636304.72 11605170.46 11815814.17 12258078.55 11602865.9 11484274.86 11941607.74 12548641.23 0.942210463 1.006985896 0.924814906 0.941601083 0.976845088 0.924631256 0.915180748 0.95162556 1 23.58102782 3.721090436 24.90943816 0.942209264 0.974598184 0.099953795 0.029941547 1158.599743 1651960.841 0.007531427 0.011690788 5261.268139 -3.721090436 0.032388921 AES(ph)PAEKVPEESVLPLVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 255.67 3.72E-31 699800000 1624830 1846920 1271460 1829210 691410 1632190 1414540 1716060 666690 TRUE FALSE 1548027.506 2035123.248 1329757.699 1645334.336 811991.6851 1575666.851 1198725.943 1565792.689 770076.8802 2.010224623 2.642753341 1.72678564 2.136584512 1.054429377 2.046116292 1.556631518 2.033293986 1 19.55464296 3.765092436 0.076508913 5.34E-15 4.153948879 0.367652899 0.396997788 64.68141607 1.130492292 20.08215066 42.93355332 5822.271269 -3.765092436 4.153948879 AES(ph)PDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AES(1)PDLR;AES(1)PDLR;AES(1)PDLR 114.99 0.0060646 4452430000 11830260 9947210 10243720 12348660 10799320 11302730 13102690 11582490 12167080 TRUE FALSE 11271067.06 10960842.01 10713404.69 11107349.24 12682717.99 10911313.63 11103633.99 10568265.77 14053888.63 0.801989211 0.779915246 0.762308922 0.790339922 0.902434787 0.77639107 0.790075565 0.751981608 1 23.74446603 -1.019830816 4.642716927 1.000004231 0.794580342 0.712898485 0.040998317 2.34E-06 4.95E-07 0.037906546 0.008934407 0.095536469 1.019830816 -0.20542389 AES(ph)PEEVACR ddPTM_SK-BR-3_Trastuzumab_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 266.68 9.94E-18 2410367000 1693420 1441080 1554910 1740000 1422028 1584520 1752350 1609650 1505800 TRUE FALSE 1613375.393 1587927.69 1626204.162 1565091.894 1670029.233 1529647.675 1484996.823 1468700.513 1739311.773 0.927594131 0.912963228 0.934969904 0.899834014 0.960166693 0.879455713 0.85378415 0.844414748 1 20.73008513 2.191353983 20.20982568 0.879081401 0.924339246 0.069833955 0.045460982 27.41862481 11736.92635 0.014969237 0.011055763 155.365284 -2.191353983 0.045257845 AES(ph)PESSAIESTQST(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(0.994)PES(0.006)SAIESTQS(0.169)T(0.831)PQK 361.79 1.86E-90 121770000 185570 214850 182250 235610 134860 215180 217940 224770 138670 TRUE FALSE 176798.4739 236743.4593 190606.3428 211926.0352 158379.5413 207728.2626 184689.2503 205087.9472 160174.2354 1.103788468 1.478037081 1.189993774 1.323096906 0.988795364 1.296889367 1.153052174 1.280405346 1 17.28928258 AES(ph)PESSAIESTQST(ph)PQKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AESPESSAIESTQSTPQKGR 20 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(0.995)PES(0.002)S(0.003)AIES(0.019)T(0.009)QS(0.134)T(0.839)PQKGR;AES(0.998)PES(0.001)S(0.001)AIESTQS(0.102)T(0.898)PQKGR 186.44 7.51E-17 384340000 616840 422540 712690 630220 524600 743850 936830 793140 777270 TRUE FALSE 587683.1957 465597.3064 745367.5414 566869.0883 616090.0739 718090.288 793899.3774 723688.4569 897805.0619 0.654577726 0.518595101 0.830210892 0.6313944 0.686218089 0.799828736 0.884266988 0.806064131 1 19.7760427 1.938708322 0.393797898 1.004817128 0.574103946 0.658010801 0.081069787 0.616914142 0.24930001 0.089719918 0.087874802 86.83770189 -1.938708322 -0.430713182 AES(ph)PESSAIESTQSTPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.97)PES(0.029)SAIESTQSTPQK;AES(0.975)PES(0.021)S(0.004)AIESTQSTPQK;AES(0.953)PES(0.047)SAIESTQSTPQK;AES(0.814)PES(0.185)S(0.001)AIESTQSTPQK;AES(0.965)PES(0.031)S(0.004)AIESTQSTPQK;AES(0.898)PES(0.101)S(0.001)AIESTQSTPQK;AES(0.995)PES(0.005)SAIESTQSTPQK;AES(0.99)PES(0.01)SAIESTQSTPQK;AES(0.587)PES(0.411)S(0.002)AIESTQSTPQK;AES(1)PESSAIESTQSTPQK 446.06 9.95E-191 6066040000 4451814 3776917 4124388 4568252 3138288 4619262 5109963 4563786 3661977 TRUE FALSE 4241385.575 4161789.136 4313495.269 4109042.63 3685604.434 4459295.799 4330344.293 4164156.704 4229857.69 1.00272536 0.983907602 1.019773143 0.971437559 0.871330599 1.054242512 1.023756497 0.984467329 1 22.0121777 AES(ph)PGPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AESPGPGSR 9 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 AES(0.998)PGPGS(0.002)R;AES(0.999)PGPGS(0.001)R 134.57 0.00025732 458450000 3348700 2863410 2998700 3377200 2952100 3123600 3781600 3571700 3576700 TRUE FALSE 3190413.587 3155194.734 3136193.361 3037717.44 3466945.305 3015428.949 3204647.466 3258943.013 4131356.369 0.772243618 0.76371885 0.759119544 0.735283323 0.839178467 0.729888366 0.775688946 0.788831251 1 21.97818408 0.513618142 1.949154002 0.999992393 0.767177513 0.859094275 0.029335854 1.229283629 4.558236886 0.02474792 0.006837287 3.263008028 -0.513618142 -0.23281488 AES(ph)PMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AESPMSR 7 0 Q6ZUT6 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 AES(1)PMSR;AES(1)PMSR;AES(1)PMSR 123.35 0.015798 569743000 1360370 924510 1104890 1288920 799500 1177010 1404130 885450 979240 TRUE FALSE 1296068.006 1018718.62 1155550.299 1159355.313 938932.5469 1136249.849 1189904.18 807915.3039 1131095.538 1.145851931 0.900647722 1.021620421 1.024984428 0.830108965 1.004556919 1.051992639 0.714276802 1 20.10928936 4.638556403 3.064140871 0.95524867 1.156578869 0.259413645 0.105421198 0.408893451 6.218006589 0.023738634 0.174977753 43506.72603 -4.638556403 0.201330199 AES(ph)PSPAPPPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 AES(1)PSPAPPPGLR;AES(0.635)PS(0.365)PAPPPGLR 200.82 1.12E-07 315440000 493550 446360 501340 556000 452470 491590 600150 580550 561620 TRUE FALSE 470220.8696 491844.5915 524326.9349 500109.8237 531380.6247 474566.115 508586.095 529713.9643 648713.1612 0.724851749 0.758185005 0.808256971 0.770925971 0.819130328 0.731550003 0.783992256 0.816561149 1 19.30722118 -5 0.242003749 2.326209907 0.749457468 0.857218306 0.029234291 60.70688635 0.604643953 39.61491548 0.044610497 1.00E-05 5 -1.576752439 AES(ph)PTSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AESPTSAR 8 0 C9J6N8 C9J6N8 TFAP2A 1 AES(0.999)PT(0.001)SAR;AES(1)PTSAR;AES(0.983)PT(0.017)SAR;AES(0.89)PT(0.11)SAR;AES(0.994)PT(0.006)SAR 157.34 0.00039692 389522000 742336 591188 641470 720868 690603 610918 801430 701027 824690 TRUE FALSE 707247.2484 651430.7293 670882.034 648404.9791 811043.9445 589761.7565 679157.1342 639641.3595 952578.7133 0.742455441 0.683860263 0.704279893 0.680683885 0.851419345 0.619121284 0.712966944 0.671483995 1 19.86147878 -1.019495381 5.030475122 1.000003413 0.707855202 0.700391515 0.059960508 2.04E-06 3.97E-07 0.051488359 0.012135781 0.095610286 1.019495381 -0.292148212 AESFMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AESFMFR 7 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ;; 97.602 0.02763 93195000 274482 213485 201309 201386 299327 210586 345656 241866 267828 FALSE TRUE 261507.7798 235239.3642 210539.2168 181142.2967 351529.534 203293.354 292919.8288 220686.9308 309361.3984 0.845314836 0.760403093 0.680560722 0.585536197 1.136307037 0.657138722 0.946853196 0.713362856 1 18.23893367 2.77899639 24.99987059 0.87299087 0.737102518 0.239117225 0.149598682 877.8187452 542719.8394 0.041619284 0.044143313 601.16874 -2.77899639 -0.135888353 AESGDS(ph)LGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.003)GDS(0.498)LGS(0.498)EDRDLLYSIDAYR;AESGDS(0.995)LGS(0.005)EDRDLLYSIDAYR 189.39 1.30E-17 122135000 126725 130624 137637 146073 129774 144917 179588 141809 129836 TRUE FALSE 120734.9604 143934.7341 143947.7926 131389.4645 152406.5445 139898.488 152188.5522 129391.4522 149970.3038 0.805059117 0.959754901 0.959841975 0.87610321 1.016244821 0.932841265 1.014791251 0.86278049 1 17.19431733 4.56704005 2.124369237 0.955676951 0.789893939 0.435602318 0.052516256 0.380280251 2.545740226 0.012015015 0.105594016 36901.16264 -4.56704005 -0.165783013 AESGDSLGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 174 2.84E-12 105740000 144280 121540 126240 146390 151140 140850 164310 145420 175210 FALSE TRUE 137460.1703 133925.0642 132028.2289 131674.5991 177498.7681 135972.3292 139241.4917 132686.2539 202380.672 0.6792159 0.661748293 0.652375682 0.650628332 0.877053952 0.671864205 0.688017736 0.655627104 1 17.62671199 -1.346832969 3.225013888 1.002416189 0.690588025 0.676122659 0.066971812 20454232.82 26642503.95 464701.3054 0.015828791 0.044995288 1.346832969 -0.311828164 AESLQQEVEALKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AESLQQEVEALKER 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;; 201.3 1.64E-08 280871000 247792 188223 245784 250371 215574 247142 286533 270424 253380 FALSE TRUE 236079.3632 207403.1377 257053.4395 225203.2314 253170.0373 238583.4106 242817.1283 246744.241 292672.8763 0.80663219 0.708651722 0.878296078 0.769470797 0.865027332 0.815187979 0.829653678 0.843071774 1 18.15892952 -5 0.141044109 1.684008633 0.736856685 0.64495076 0.045095946 76.9260341 0.662636054 14.69953708 0.247449636 1.00E-05 5 -0.947151949 AESPES(ph)SAIESTQSTPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.069)PES(0.927)S(0.003)AIESTQSTPQK 440.34 1.49E-190 811520000 335230 298270 318490 378900 238650 386860 408710 370790 286980 TRUE FALSE 319384.3423 328664.0521 333093.0815 340812.2521 280270.4844 373462.9412 346353.783 338321.6619 331483.3927 0.963500282 0.991494776 1.004856016 1.028142766 0.845503849 1.126641483 1.044860137 1.020629297 1 18.33857707 2.208170549 24.99999193 1.053704489 0.974316902 0.320984074 0.057937693 234.9094252 193243.7941 0.019913602 0.014708882 161.4992647 -2.208170549 -0.079387587 AESSQTCHSEQGDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AESSQTCHSEQGDKK 15 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ;;;; 170.11 7.52E-07 189762400 350174 279765 306463 356716 186677 346151 381809 370349 204770 FALSE TRUE 333621.969 308273.3716 320514.6317 320858.23 219233.4097 334163.7041 323557.0246 337919.2782 236524.6858 1.410516488 1.303345444 1.355100127 1.356552822 0.926894413 1.412806883 1.367963025 1.428685032 1 17.85163124 -1.781930724 2.715124154 0.917688646 1.322064646 0.326096328 0.144654053 26474840.79 21622132.44 14524957.73 0.033168356 0.016522253 1.781930724 0.404376001 AESSSGGGTVPSSAGILEQGPSPGDGS(ph)PPKPKDPVSAAVPAPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESSSGGGTVPSSAGILEQGPSPGDGSPPKPKDPVSAAVPAPGR 44 2 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7 Q68EM7 ARHGAP17 Rho GTPase-activating protein 17 1 AESSSGGGTVPSSAGILEQGPS(0.006)PGDGS(0.986)PPKPKDPVS(0.008)AAVPAPGR 94.695 3.26E-05 353050000 49352 42434 50196 50043 33185 59180 65685 59724 37057 TRUE FALSE 47019.22877 46758.07284 52497.53625 45012.58256 38972.45349 57130.58176 55663.54686 54494.24994 42803.6103 1.098487451 1.092386192 1.226474493 1.051607148 0.910494541 1.33471409 1.300440465 1.273122747 1 15.38544487 2.215585188 24.99999024 1.260235013 1.085934672 0.265468004 0.118771651 256.3256007 278910.8316 0.041192448 0.030442369 164.2801869 -2.215585188 -0.17430034 AESVVLEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AESVVLEHR 9 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2;E9PKF1;E9PI70;E9PIP0;E9PRL3;E9PPH0;E9PPA0 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 110.14 0.002336 182720000 318140 318710 271630 322200 611100 225080 321520 248690 525370 FALSE TRUE 303102.1527 351186.9113 284084.5042 289811.8439 717675.6465 217285.4232 272466.2189 226913.3852 606841.6964 0.499474829 0.57871256 0.468136099 0.477574045 1.182640631 0.358059482 0.448990602 0.373925171 1 19.21096069 AET(ph)PPLPIPPPPPDIQPLER ddPTM_SK-BR-3_Trastuzumab_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 155.03 3.87E-07 122724000 154837 133143 142678 152578 118722 153776 163369 159492 130082 TRUE FALSE 147518.1619 146710.4231 149219.9274 137240.5696 139427.0792 148450.6986 138444.0586 145526.035 150254.4522 0.981788957 0.976413151 0.993114848 0.913387707 0.927939753 0.98799534 0.92139738 0.968530601 1 17.19704821 3.270494391 24.99309395 0.948689894 0.981912025 0.19533709 0.028183435 258.4577519 202281.3074 0.007058001 0.009555794 1864.208101 -3.270494391 0.033222131 AET(ph)PTESVSEPEVATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AET(0.661)PT(0.339)ESVSEPEVATK 205.52 5.25E-12 0 125000 138000 116540 143760 72990 133180 127400 146970 83563 TRUE FALSE 119091.4977 152062.3569 121883.4743 129308.9717 85719.43289 128567.9432 107962.7901 134100.5277 96521.52326 1.233833592 1.575424338 1.26275954 1.339690541 0.888086201 1.332013201 1.118535913 1.389332898 1 16.55856306 3.135331361 2.6181644 1.16471812 1.39442542 0.235175017 0.172442787 0.344201536 4.794853101 0.048374242 0.060824332 1365.624693 -3.135331361 0.2297073 AETEQGEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 131.52 0.00057706 59886000 94270 92575 99271 99045 109246 94729 112189 98314 114701 FALSE TRUE 89814.04393 102008.4977 103822.6735 89088.80843 128298.4678 91448.51098 95072.50756 89705.10496 132488.2453 0.677901981 0.76994376 0.783636868 0.67242802 0.968376233 0.690238676 0.71759202 0.677079727 1 17.01550484 -2.267939718 2.31823185 2.069300298 0.744194618 0.452431021 0.088282765 2748006.115 546918.8439 15394205.97 0.020350537 0.005395855 2.267939718 -1.325105679 AEVLGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEVLGHK 7 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 0 60.76 0.095567 61932000 148130 148060 145990 180320 142710 158310 184770 177590 146340 FALSE TRUE 141128.1885 163147.4823 152683.7859 162193.891 167598.5788 152827.685 156579.943 162039.2781 169033.6598 0.834911749 0.965177483 0.903274449 0.959536055 0.991510087 0.904125753 0.926324042 0.958621368 1 17.36695103 4.615497472 2.615618113 0.945081113 0.826210488 0.540306513 0.033101116 0.27384257 2.930533999 0.007691324 0.06321118 41256.98353 -4.615497472 -0.118870625 AEVLGHKT(ph)PEPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEVLGHKTPEPAPR 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 1 AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR 145.48 1.26E-05 191969000 650530 571920 643240 747550 427130 694680 723340 814120 532200 TRUE FALSE 619780.7361 630199.2982 672733.1903 672404.8537 501621.3368 670623.0574 612981.1979 742831.3369 614730.8579 1.008214779 1.025162948 1.094354028 1.093819913 0.816001556 1.090921415 0.997153779 1.208384657 1 19.22959538 1.308083992 24.99998338 1.104227562 1.018908969 0.126293771 0.094280839 82.66991735 29725.86958 0.056681761 0.020698335 20.32750104 -1.308083992 -0.085318593 AEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.002)GGDS(0.998)PHLQPAEPPGEPR;AEVPGAT(0.023)GGDS(0.977)PHLQPAEPPGEPR;AEVPGAT(0.045)GGDS(0.955)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR 251.47 1.13E-39 2545070000 1345560 1361920 1142770 1464940 1219800 1229870 1228320 1177540 1011734 TRUE FALSE 1281958.045 1500701.196 1195167.135 1317681.448 1432532.734 1187279.294 1040917.224 1074428.355 1168628.541 1.096976498 1.284155866 1.022709178 1.127545153 1.225823846 1.015959521 0.890716928 0.919392533 1 20.156385 2.046082863 4.715061818 0.929933437 1.156942151 0.637711236 0.074754227 0.113632766 5.615608003 0.029019332 0.020299045 111.1943866 -2.046082863 0.227008714 AEVVETTQVYTEEETRR ddPTM_SK-BR-3_Trastuzumab_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 0 238.81 4.68E-20 132110000 60696 59182 75481 70319 65645 60833 68499 66108 78815 FALSE TRUE 57827.02037 65212.71308 78941.87851 63250.40052 77093.46722 58726.33796 58048.21948 60319.23306 91037.22767 0.635201904 0.716330173 0.867138428 0.694775117 0.846834522 0.645080474 0.63763167 0.662577658 1 16.474169 -2.26700348 2.259944783 2.169729799 0.708515335 0.544264573 0.082379178 4403348.929 654235.3888 26352117.59 0.020023255 0.0054075 2.26700348 -1.461214464 AEVWDLDMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AEVWDLDMLR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 99.013 0.011597 21933000 48416 38744 30156 36800 42247 31826 45580 49140 47757 FALSE TRUE 46127.47163 42692.05765 31538.68243 33100.79408 49614.86342 30723.85764 38625.93387 44837.04109 55162.91165 0.83620444 0.773926835 0.571737087 0.600055238 0.899424304 0.556965844 0.700215647 0.812811357 1 15.75141099 0.929541099 3.426040354 0.999582266 0.712199777 0.418547517 0.111019733 0.319278236 9.221262861 0.105320407 0.027274657 8.502391513 -0.929541099 -0.287382488 AEVYGS(ph)ENESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AEVYGSENESER 12 0 Q9BVS4-2;Q9BVS4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 AEVYGS(1)ENESER;AEVYGS(1)ENESER 201.06 1.60E-07 158893000 183818 272910 195184 229860 219580 220870 191087 204135 178805 TRUE FALSE 175129.2874 300719.8393 204133.3795 206754.0361 257874.6825 213221.2165 161933.1686 186259.8572 206533.1662 0.847947527 1.456036552 0.988380623 1.001069416 1.248587272 1.032382452 0.784054065 0.901839935 1 17.65601395 1.962464003 6.722299519 0.878881077 1.123474093 0.242593636 0.16985158 0.261289341 35.36141469 0.069300175 0.043929577 91.71999085 -1.962464003 0.244593016 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.21)PGPAAS(0.79)PEQLSFR 256.34 1.67E-59 169430000 94963 59626 74599 93569 101900 70634 93590 83523 80744 TRUE FALSE 90474.28719 65701.95719 78019.43794 84163.26635 119671.3277 68187.92687 79311.1266 76209.28334 93265.36714 0.970073779 0.704462537 0.836531719 0.902406423 1.283127182 0.731117337 0.850381326 0.817123072 1 16.50905383 4.768096305 22.37594925 0.877541493 0.970074378 0.01751247 0.16247404 2343.144226 2896926.105 0.037523076 1.009523187 58626.8155 -4.768096305 0.092532886 AFAHITGGGLLENIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFAHITGGGLLENIPR 16 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 136.57 1.67E-05 263810000 104080 98811 98437 110080 106330 93416 121970 114790 176860 FALSE TRUE 99160.34467 108879.9532 102950.4338 99014.54926 124873.9183 90180.9805 103361.2364 104738.3791 204286.5455 0.485398313 0.532976623 0.503951122 0.484684633 0.611268442 0.441443563 0.505962035 0.512703266 1 17.64023466 0.705381639 7.195160127 1 0.509009027 0.927163669 0.043179911 40.01084335 977.6652331 0.037240257 0.009336119 5.074364252 -0.705381639 -0.490990973 AFCGFEDPR ddPTM_SK-BR-3_Trastuzumab_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 75.189 0.090649 253910000 514210 457380 474730 503420 543260 466900 587770 532430 599220 FALSE TRUE 489904.3124 503987.542 496496.8401 452815.2652 638004.372 450731.1359 498094.8914 485807.6066 692143.9772 0.707806943 0.728154197 0.717331735 0.654221203 0.921779851 0.651210082 0.719640577 0.701888079 1 19.40071265 -1.140266876 5.269863306 1.000008123 0.724317329 0.572440943 0.07461802 6.33E-06 1.03E-06 0.064221914 0.015136805 0.072399093 1.140266876 -0.275690794 AFDIIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AFDIIER 7 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BV15;H3BRD9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;; 139.31 0.0062827 176109000 383122 376447 362213 423889 427685 393636 446915 416396 446659 FALSE TRUE 365012.5823 414807.3773 378820.8243 381278.8724 502273.1286 380004.2866 378729.9086 379934.1588 515924.5965 0.707492112 0.804007756 0.734256182 0.739020537 0.9735398 0.736550049 0.734079963 0.736414122 1 18.9768007 -1.751809911 2.747983841 1.047883517 0.769720293 0.472079459 0.07620903 17008768.34 14525442.64 5549502.758 0.018613723 0.017708839 1.751809911 -0.278163224 AFDQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AFDQLR 6 0 Q9H0I9 Q9H0I9 TKTL2 Transketolase-like protein 2 0 ;;;;; 177.57 0.0084773 2251530000 4294060 3134430 1954850 2347890 4464850 2412770 4215090 3067790 3803940 FALSE TRUE 4091088.294 3453831.981 2044481.806 2111875.637 5243518.426 2329215.17 3572000.605 2799158.044 4393835.587 0.931097264 0.78606309 0.465306852 0.480645121 1.193380663 0.530109769 0.812957275 0.637064812 1 22.06704946 AFDSGIIPMEFVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFDSGIIPMEFVNK 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 117.94 0.00063843 20511000 170000 145500 134760 165380 137820 152420 170450 158710 159770 FALSE TRUE 161964.4369 160326.6154 140938.8793 148755.6882 161855.7644 147141.6572 144444.722 144812.511 184546.3156 0.877635711 0.868760858 0.76370465 0.806061545 0.877046848 0.797315604 0.782701738 0.784694674 1 17.49362341 3.95869432 23.27591495 0.81795986 0.874307684 0.041713834 0.068720085 406.1718748 228879.4601 0.01560599 0.028136026 9092.730526 -3.95869432 0.056347824 AFDTAGNGYCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 271.62 1.12E-26 3885740000 2229700 2161980 1836680 2193840 2250950 1989530 2366160 2124760 2220760 FALSE TRUE 2124306.5 2382288.22 1920893.595 1973311.035 2643514.967 1920632.077 2005158.834 1938704.75 2565144.119 0.828143138 0.928715156 0.748844317 0.769278818 1.03055222 0.748742366 0.781694416 0.755787847 1 21.29060845 3.75397822 24.86554811 0.822380017 0.878429135 0.022146605 0.105241242 2401.857083 3873708.187 0.025256206 0.04530919 5675.161441 -3.75397822 0.056049118 AFEDDDITHVEGSVDPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 206.74 8.19E-16 146953000 168626 198995 133244 214601 143640 154352 139422 170325 107744 FALSE TRUE 160655.3832 219272.8167 139353.3692 193028.8998 168690.7705 149006.7515 118150.6132 155410.4401 124452.3892 1.290898344 1.761901222 1.119732374 1.551026067 1.355464299 1.197299244 0.949363961 1.24875417 1 16.9252344 2.201352306 2.552282889 1.061850713 1.452925047 0.4394751 0.182108967 0.228566501 3.029390175 0.075317307 0.051404145 158.9835924 -2.201352306 0.391074334 AFEDDDITHVEGSVDPIRDIEIIHEELQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFEDDDITHVEGSVDPIRDIEIIHEELQLK 30 1 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 144.58 2.72E-08 37637000 63506 78371 50324 74771 39758 65140 60761 67299 29079.2 FALSE TRUE 60504.19724 86357.094 52631.40518 67254.87702 46691.78261 62884.18547 51490.7935 61405.94279 33588.65382 1.801328436 2.571019799 1.566939999 2.002309392 1.390105804 1.872185346 1.532981755 1.828175166 1 15.03568636 -0.232753329 0.112443378 1.41E-11 2.682273005 0.442396855 0.307908067 23.60971113 0.768530521 12.91599247 5.345420057 0.585122328 0.232753329 2.682273005 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK 41 2 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 81.988 0.00020488 52970000 57498 61414 48861 64324 27222 59329 61272 71219 20591 FALSE TRUE 54780.18349 67672.15642 51101.32518 57858.02931 31969.50818 57274.42185 51923.83106 64982.6868 23784.14712 2.30322253 2.845263111 2.148545623 2.43262998 1.344151969 2.408092314 2.183127728 2.732184866 1 14.53771267 3.414952086 2.273667772 2.06859504 2.563722242 0.142745117 0.531433722 0.554308025 5.79262199 0.14373171 0.219245032 2599.872712 -3.414952086 0.495127202 AFEDEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AFEDEKK 7 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 98.392 0.018113 2130820000 5069900 4505200 4312960 5287400 2501780 5150400 5124000 5651900 2763130 FALSE TRUE 4830255.875 4964285.002 4510713.482 4755900.507 2938089.64 4972040.357 4342239.691 5156989.673 3191622.088 1.513417235 1.555411281 1.413298115 1.490120188 0.920563136 1.557841191 1.360511856 1.615789567 1 21.60585841 -2.169333592 2.155269211 3.08E-05 1.431554145 0.322904856 0.194894679 4234856.377 894961.5489 20669998.66 0.044818652 0.006771212 2.169333592 1.43152335 AFEDWLNDDLGSYQGAQGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 76.588 0.02575 13980000 11675 13704 11455 12577 9825.8 10840 12537 12607 9584.5 FALSE TRUE 11123.14589 15100.45318 11980.22308 11312.73607 11539.41641 10464.60808 10624.25039 11503.06425 11070.81531 1.004726895 1.363987453 1.082144607 1.021852117 1.042327605 0.945242766 0.95966287 1.039044002 1 13.43447385 3.438780963 4.156129793 0.996080776 1.190098899 0.403214619 0.090775313 0.173119892 6.574818434 0.024809933 0.035326455 2746.508597 -3.438780963 0.194018123 AFEEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFEEAEK 7 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 101.28 0.021339 50969000 94241 76400 82502 94434 71884 93699 106590 105470 77546 FALSE TRUE 89786.4147 84185.24686 86284.79831 84941.31491 84420.54684 90454.18014 90327.73784 96234.48767 89571.43763 1.002400063 0.939867095 0.963307061 0.948308045 0.942494048 1.009855178 1.008443542 1.074388111 1 16.45075114 1.946375009 2.157793011 1.03187811 0.960562541 0.582811244 0.026615233 0.214792632 1.842673244 0.01453566 0.007364965 88.3842761 -1.946375009 -0.071315569 AFELLHLHLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AFELLHLHLDLR 12 0 Q9H4A4;A6NKB8;A0A087WU27 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 210.15 2.71E-08 684979100 1047468 898296 703560 820062 1096088 761748 1238253 932978 628104.7 FALSE TRUE 997956.2635 989833.3837 735818.9219 737627.8097 1287245.4 735368.4758 1049334.763 851281.5003 725507.969 1.375527639 1.364331511 1.014212046 1.016705317 1.774267762 1.013591176 1.446344916 1.173359269 1 19.46863194 0.99302255 22.90225437 0.999999969 1.293346631 0.133267774 0.235512639 167.9474291 551264.4502 0.20521636 0.05130409 9.840621994 -0.99302255 0.293346662 AFELMHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFELMHSGK 9 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 145.72 9.65E-05 1529420000 2769500 2539800 2084500 2504200 2194900 2385400 2866000 2579100 2078800 FALSE TRUE 2638591.224 2798608.508 2180076.387 2252473.058 2577689.865 2302793 2428739.062 2353260.331 2401169.687 1.09887745 1.16551884 0.907922667 0.938073253 1.073514246 0.959029681 1.011481644 0.980047493 1 21.19530593 3.748941624 24.99946399 0.984193964 1.132198153 0.640808059 0.046889909 388.9213342 936595.0562 0.011575287 0.020583321 5609.725677 -3.748941624 0.148004189 AFENDVDALCNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFENDVDALCNLR 13 0 F8WBI9;E7ETT4;E7EUY3;E7ETT1;E9PDR0;C9JQS9;E7EX59;P05166;P05166-2;E9PEC3;E7ENC1 F8WBI9 PCCB "Propionyl-CoA carboxylase beta chain, mitochondrial" 0 72.652 0.090652 16937000 22147 20128 17222 18201 24161 16923 19022 16879 21286 FALSE TRUE 21100.1552 22179.06608 18011.64573 16371.4009 28374.67075 16336.95227 16119.84454 15400.98528 24586.92417 0.858186045 0.902067535 0.73257011 0.66585803 1.154055325 0.664456935 0.655626724 0.626389262 1 14.58560364 AFESDVFHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFESDVFHNR 10 0 O14545;F8VNX8 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ; 131.52 0.0027105 83336000 261065 202600 208677 257128 332371 194028 288946 218606 293706 FALSE TRUE 248724.9748 223245.1703 218245.0469 231281.0049 390336.3972 187308.7617 244861.9808 199463.6997 339252.4264 0.733156067 0.658050328 0.643311675 0.681737217 1.150578056 0.552122099 0.721769284 0.587950695 1 18.37199961 -2.108504616 2.467860594 1.528425932 0.71485341 0.228219841 0.164068435 19287216.62 4493548.57 57337779.41 0.038302785 0.007789245 2.108504616 -0.813572522 AFEVMDEFDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 188.04 7.73E-06 145812000 319990 269600 270260 309440 323210 260070 325850 305920 302730 FALSE TRUE 304864.7069 297072.5465 282651.6883 278334.5033 379577.7217 251063.7107 276135.5979 279132.023 349675.8223 0.871849546 0.849565591 0.808324941 0.795978691 1.085513202 0.717989906 0.78969028 0.798259431 1 18.41565852 -0.277656016 7.566148961 1.000000003 0.838470501 0.214833709 0.096317577 0 0 0.087371054 0.020593555 0.52764762 0.277656016 -0.161529502 AFFESHPAPSAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFFESHPAPSAER 13 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 208.27 4.72E-08 929650000 1180030 1003036 1014047 1139370 1409890 988830 1382410 1197880 1312170 FALSE TRUE 1124252.32 1105246.509 1060542.058 1024838.363 1655774.37 954586.5692 1171497.965 1092987.277 1515654.622 0.74176023 0.729220558 0.699725414 0.676168797 1.092448336 0.629818004 0.772932004 0.72113215 1 20.53150961 -2.155593683 2.159213388 1.529504864 0.75572772 0.269537749 0.125206709 7475080.869 1717075.669 19353466.91 0.029505075 0.00698886 2.155593683 -0.773777144 AFFSEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AFFSEVER 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;;; 215.1 1.99E-05 2678190000 3112108 2626645 2706772 3138578 3520469 2688794 3494205 2988792 3524443 FALSE TRUE 2965004.822 2894303.112 2830880.174 2823082.177 4134437.679 2595680.39 2961099.852 2727077.528 4070995.62 0.728324248 0.710957068 0.695377848 0.693462347 1.015583917 0.637603336 0.72736503 0.66987975 1 21.95695024 -2.0928586 2.537303267 1.458590375 0.733456167 0.393189632 0.103518601 12622221.48 3534798.748 33494971.18 0.023152066 0.008074979 2.0928586 -0.725134208 AFGFSHLEALLDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AFGFSHLEALLDDSK 15 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;; 236.55 1.04E-17 452207000 1995906 2176942 1630684 2362369 1356854 2063299 1948064 2136264 1215998 FALSE TRUE 1901563.479 2398774.865 1705452.474 2124899.18 1593488.908 1991846.438 1650851.058 1949201.399 1404568.759 1.353841502 1.707837262 1.214217861 1.512848101 1.134504023 1.418119565 1.175343711 1.387757905 1 20.42169582 0.874884025 0.133021411 0.714517611 1.733794107 0.361890104 0.162367238 8.319595835 0.720800464 2.932637779 1.996325365 7.496939817 -0.874884025 1.019276496 AFGFSHLEALLDDSKELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFGFSHLEALLDDSKELQR 19 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 214.19 2.62E-19 357260000 2058200 1193420 1992180 1822460 1919930 2059600 2861800 2397700 2250000 FALSE TRUE 1960912.965 1315030.855 2083523.424 1639262.858 2254765.184 1988275.536 2425179.849 2187744.677 2598918.509 0.754511139 0.505991569 0.801688632 0.63074808 0.867578255 0.765039584 0.933149632 0.84179041 1 21.30947997 2.236256014 0.602466226 0.968756802 0.632762088 0.554455461 0.094743917 0.509630808 0.369638088 0.07647835 0.055976831 172.2883904 -2.236256014 -0.335994714 AFGPGLQGGSAGS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 312.05 1.14E-57 1418520000 984870 970250 982960 1152320 1199330 1004600 1241120 1067610 1341490 TRUE FALSE 938317.1469 1069119.578 1028029.688 1036486.604 1408492.772 969810.4501 1051764.349 974124.4086 1549521.418 0.605552873 0.689967603 0.663449809 0.668907569 0.908985675 0.625877409 0.678767223 0.628661468 1 20.56339127 -1.953413047 2.560256428 1.241261326 0.682460962 0.581589495 0.084287535 40612063.09 22153342.63 58337631.7 0.019720381 0.011132353 1.953413047 -0.558800364 AFGSGIDIKPGT(ph)PPIAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;AFGSGIDIKPGT(1)PPIAGR 101.16 0.001159 1899730000 5070200 4605700 4580200 5252900 3445980 5064500 5577900 5473600 4208340 TRUE FALSE 4830541.694 5075026.066 4790206.7 4724868.512 4046957.821 4889115.095 4726888.91 4994302.567 4860947.874 0.993744804 1.044040421 0.985447041 0.972005591 0.832544994 1.005794594 0.97242123 1.027433887 1 22.21280623 3.48980948 3.935885133 0.964288282 1.018889876 0.125753661 0.053512448 0.381118854 13.26877215 0.014520291 0.021712625 3088.940055 -3.48980948 0.054601594 AFGSGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFGSGYR 7 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 117.62 0.012074 491696000 566584 533529 440214 506904 637992 446925 569412 518740 605475 FALSE TRUE 539802.6972 587896.2117 460398.2473 455949.0469 749257.6028 431447.8752 482537.7414 473316.3756 699368.9707 0.771842503 0.840609516 0.658305225 0.651943489 1.07133378 0.616910234 0.689961611 0.676776345 1 19.41569426 3.814646522 24.99999611 0.748811999 0.806225956 0.001307656 0.153877952 561.5951027 184521.8266 0.036767742 0.066283983 6525.991778 -3.814646522 0.057413957 AFGYYGPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFGYYGPLR 9 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 155.73 0.00016891 326820000 721710 212918 259160 178441 930620 187860 723010 263930 684670 FALSE TRUE 687596.1986 234614.5863 271042.7423 160503.7717 1092919.833 181354.3611 612701.5455 240818.89 790845.1268 0.86944482 0.296663124 0.342725438 0.202952217 1.381964428 0.229317163 0.774742772 0.304508281 1 19.59303567 AFHNEAQVNPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 201.48 1.48E-07 5174030000 3769220 3658970 3187140 4235590 3671150 3266930 3639190 3548330 3161980 FALSE TRUE 3591056.44 4031823.203 3333273.522 3809820.446 4311397.398 3153795.395 3083964.727 3237619.414 3652323.709 0.983225126 1.103906314 0.912644603 1.043122338 1.180453251 0.863503798 0.84438428 0.886454672 1 21.80038321 2.203759 24.98822194 0.880409916 1.041090578 0.437713549 0.081062883 146.7131672 105342.0336 0.028469693 0.021027248 159.8670643 -2.203759 0.160680662 AFHNEAQVNPERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFHNEAQVNPERK 13 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 215.51 1.88E-11 3276250000 3371710 2437700 3181650 2973330 2578390 3256720 4063260 3572740 3015460 FALSE TRUE 3212335.95 2686104.401 3327531.8 2674445.219 3028060.4 3143938.97 3443335.06 3259891.945 3483082.136 0.922268217 0.771186064 0.955341181 0.767838689 0.86936233 0.902631304 0.988588533 0.93592164 1 21.73193306 1.993337963 2.602968385 0.972812663 0.85154872 0.445140941 0.05963394 0.239372012 3.052148667 0.027945586 0.015618429 98.47771507 -1.993337963 -0.121263943 AFHPFIAGPYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFHPFIAGPYNR 12 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 73.499 0.039033 221920000 803250 637240 624700 709420 773480 677320 985340 812310 862790 FALSE TRUE 765281.9644 702175.4805 653343.1129 638107.7538 908374.6671 653864.2386 835008.286 741179.8301 996587.0667 0.767902765 0.704580166 0.655580566 0.640293031 0.911485506 0.656103476 0.837867873 0.74371809 1 19.92663633 -0.386544292 0.361805128 1.074116759 0.709865047 0.508342286 0.082757408 5.797056949 0.819694126 0.617187035 0.060865075 0.410634759 0.386544292 -0.364251712 AFKPEETSSNSDPPS(ph)PPVLNNSHPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFKPEETSSNSDPPSPPVLNNSHPVPR 27 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR 193.47 1.45E-18 592380000 1165540 1042200 1090670 1261000 928910 1275150 1329590 1251020 912010 TRUE FALSE 1110447.234 1148401.365 1140678.298 1134241.884 1090911.61 1230991.236 1126736.626 1141474.057 1053439.853 1.054115459 1.090144218 1.082812934 1.076703033 1.035570856 1.168544395 1.069578508 1.083568325 1 20.00667651 0.198393827 2.604780655 0.999999902 1.082928505 0.362453595 0.03443681 101.6631612 326.1495679 0.030296487 0.008034418 1.57904253 -0.198393827 0.082928603 AFLDFHALPYQVVEVNPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFLDFHALPYQVVEVNPVRR 20 1 Q9H7Z7 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 122.44 1.98E-05 151118000 282090 214404 276390 258030 329210 218400 310220 262400 285090 FALSE TRUE 268756.1647 236252.0114 289062.7549 232092.3342 386624.1198 210836.7532 262890.2414 239422.8649 329300.3012 0.816143088 0.717436366 0.87780896 0.7048045 1.174077638 0.640256788 0.798329793 0.72706543 1 18.32904431 -2.141691801 2.283667801 1.417552109 0.801812881 0.145770751 0.146360104 12683786.23 2846733.308 27464676.35 0.03158435 0.007216194 2.141691801 -0.615739228 AFLEENNLDYIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFLEENNLDYIIR 13 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 161.99 9.59E-05 44917000 43900 28047 39344 38016 45446 35168 54896 44401 52226 FALSE TRUE 41824.934 30905.02119 41147.96132 34194.55945 53371.76801 33950.12334 46520.60697 40513.01306 60324.94135 0.693327388 0.512309179 0.682105285 0.566839498 0.884738001 0.562787507 0.771167048 0.671579817 1 15.88046699 -5 0.162369925 2.308478471 0.569504412 0.509093406 0.104948713 95.54042794 0.884014597 40.02998005 0.376020814 1.00E-05 5 -1.73897406 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR 31 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532-3;P51532-5;A0A2R8YF58;A0A2R8YF80;A0A2R8Y440;A0A2R8Y4C5 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ; 100.95 0.00021338 21285000 10089.4 9921 7967.8 10966.5 12829.4 9987.6 12715.5 10840.5 9804.5 FALSE TRUE 9612.494057 10931.96118 8333.131511 9864.126585 15066.8433 9641.726908 10775.51694 9891.248351 11324.93179 0.84879046 0.9653004 0.735821784 0.871009801 1.330413603 0.851371742 0.951486256 0.873404674 1 13.46721474 2.945726368 24.99999484 0.993861214 0.865626224 0.208970791 0.140230539 552.5581655 254523.7758 0.041138323 0.043634021 882.5236819 -2.945726368 -0.128234991 AFLS(ph)PPTLLEGPLR ddPTM_SK-BR-3_Trastuzumab_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(0.942)PPT(0.058)LLEGPLR;AFLS(0.993)PPT(0.007)LLEGPLR;AFLS(0.993)PPT(0.007)LLEGPLR 135.14 3.64E-05 148439000 337098 297536 277517 363263 423656 319658 378765 314158 332951 TRUE FALSE 321164.0456 327855.2567 290241.429 326747.1131 497541.4723 308588.1633 320977.4428 286648.6601 384583.3406 0.835096094 0.852494692 0.754690592 0.849613279 1.293715613 0.802396076 0.834610886 0.745348614 1 18.55293674 2.982715415 24.9782616 0.92308317 0.822426476 0.121244954 0.150155351 1883.53627 2721935.87 0.045211593 0.048957904 960.9823588 -2.982715415 -0.100656693 AFMGT(ph)PVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFMGTPVQK 9 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMGT(1)PVQK 104.43 0.034 83088000 329510 350290 345250 386990 288450 347210 394880 386120 371780 TRUE FALSE 313934.7153 385984.9492 361080.054 348089.03 338755.5887 335186.0306 334633.8035 352309.2858 429433.7436 0.731043426 0.898823055 0.840828322 0.810576801 0.788842502 0.780530258 0.779244315 0.820404291 1 18.71207603 0.945001495 20.31617807 1.000000001 0.806699411 0.661709259 0.04364998 1027.92129 379710.6677 0.042623854 0.010655964 8.810519057 -0.945001495 -0.19330059 AFNADFH ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFNADFH 7 0 A0A0A0MT83;P26440;A0A0S2Z4K7;P26440-2 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 ; 104.11 0.019134 245460000 566880 480580 477140 478280 607500 393620 507680 488320 529560 FALSE TRUE 540084.7058 529551.6484 499017.341 430202.3857 713447.8077 379988.8407 430224.0918 445560.1121 611681.4602 0.882950916 0.865731075 0.815812434 0.703311141 1.166371476 0.621220137 0.703346627 0.728418533 1 19.22242102 AFPMPGFDEH ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFPMPGFDEH 10 0 P34897-3;P34897-2;P34897 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 ; 173.59 7.83E-06 140421000 91721 85407 84176 79510 107033 73279 83120 89869 88721 FALSE TRUE 87385.5301 94110.0704 88035.55286 71517.50374 125699.5213 70741.32986 70438.5174 81999.59393 102479.3996 0.852713135 0.918331595 0.859056096 0.697872002 1.226583312 0.690298052 0.68734319 0.800156854 1 16.6449744 AFQGLLDTYSVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFQGLLDTYSVWR 13 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 206.1 1.50E-07 206000000 135340 118810 111880 121430 129530 122520 141550 136000 130270 FALSE TRUE 128942.7464 130916.8741 117009.8087 109223.6257 152119.991 118277.1017 119953.9478 124091.119 150471.6063 0.856924104 0.870043707 0.77762052 0.725875322 1.010954789 0.78604266 0.797186597 0.824681294 1 17.19913175 -1.677267303 2.555007673 1.025131615 0.832179093 0.328857302 0.075787119 12993400.78 10562286.86 2118412.104 0.017277065 0.02102484 1.677267303 -0.192952522 AFQLEEGEET(ph)EPDCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFQLEEGEETEPDCK 15 0 P38432 P38432 COIL Coilin 1 AFQLEEGEET(1)EPDCK 121.82 0.00126 34808000 54525 47063 50286 57462 41592 56315 60776 56176 30795 TRUE FALSE 51947.71131 51858.77321 52591.66284 51685.81059 48845.63163 54364.79743 51503.50497 51256.93163 35570.53132 1.460414264 1.457913933 1.478517775 1.453051407 1.373205005 1.52836619 1.44792622 1.440994265 1 15.1183949 0.435645453 2.426806253 1.000001415 1.457928354 0.93562169 0.037536569 2.631047337 10.99583072 0.032690278 0.008748637 2.726750821 -0.435645453 0.457926939 AFREEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AFREEAIK 8 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 138.4 0.0006449 1544230000 2077590 1371390 1252960 1375730 1796010 1645660 2371330 1973860 2084910 FALSE TRUE 1979386.438 1511136.2 1310409.455 1237439.007 2109233.575 1588670.382 2009540.056 1801018.354 2408227.195 0.821926786 0.627489052 0.544138634 0.51383815 0.875844929 0.659684595 0.834447871 0.74786065 1 21.19954007 0.950960474 0.621698133 0.996187767 0.662094565 0.44593057 0.113765913 0.842349426 0.759292131 0.11607267 0.048388503 8.932241849 -0.950960474 -0.334093201 AFREEFGAEPELAVSAPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFREEFGAEPELAVSAPGR 19 1 P51570;P51570-2;K7ERJ9 P51570 GALK1 Galactokinase 0 ; 190.83 1.00E-14 209000000 100377 84774 95359 107109 114172 98992 119377 112664 128560 FALSE TRUE 95632.37814 93412.56698 99731.30447 96342.19983 134083.5607 95563.88222 101163.8461 102798.5429 148496.4282 0.644004568 0.629055985 0.67160743 0.648784627 0.902941318 0.643543305 0.681254407 0.692262731 1 17.1800687 -5 0.233672595 2.730443804 0.648515485 0.614055812 0.077846882 109.2618076 1.091874818 89.65860469 0.125550296 1.00E-05 5 -2.081928319 AFS(ph)DPFVEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 1 AFS(1)DPFVEAEK;AFS(1)DPFVEAEK 190.1 2.54E-06 67412000 315170 267660 260170 317870 188911 295730 311120 323880 193435 TRUE FALSE 300272.5387 294934.8583 272099.0518 285917.1037 221857.0186 285488.7959 263652.9299 295519.3502 223431.9119 1.343910707 1.320021191 1.217816424 1.279661 0.99295135 1.27774405 1.180014653 1.322637164 1 17.76947573 7.999999754 0.024914502 1.54E-11 2.904348473 0.370316509 0.100413544 1986.560246 3.806991374 152.7329756 319.2238975 99999943.3 -7.999999754 2.904348473 AFS(ph)FSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.996)FS(0.004)K;AFS(0.999)FS(0.001)K;AFS(0.993)FS(0.007)K;AFS(0.791)FS(0.209)K 136.75 0.01367 938110000 3323690 2887460 3004520 4494770 2555080 4494200 4536030 3466210 2984720 TRUE FALSE 3166585.761 3181695.457 3142280.214 4042947.18 3000685.143 4338564.727 3843975.314 3162690.277 3447575.134 0.918496519 0.922879222 0.911446478 1.172692987 0.870375562 1.2584395 1.114979417 0.917366599 1 21.71715056 3.264170386 24.9749697 1.070320255 0.918864004 0.240489584 0.113652688 268.8870353 262220.1084 0.029303707 0.039663317 1837.259011 -3.264170386 -0.151456251 AFS(ph)IDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFSIDIIR 8 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" 1 AFS(1)IDIIR 63.816 0.074391 4904300 32782 23701 33287 33537 26510 28614 36786 34184 35540 TRUE FALSE 31232.45983 26116.15885 34813.24188 30165.79704 31133.33561 27623.09001 31173.62008 31190.66774 41051.36169 0.760814223 0.636182523 0.848041099 0.734830607 0.758399584 0.672890956 0.759380902 0.759796179 1 15.32514246 0.435465682 1.461899284 1.000021424 0.731370267 0.678432373 0.056073444 1.817550483 4.128169302 0.050532707 0.014663093 2.725622352 -0.435465682 -0.268651157 AFS(ph)LASADLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AFSLASADLLR 11 0 Q9P219;Q9P219-2;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 AFS(0.999)LAS(0.001)ADLLR;AFS(1)LASADLLR;AFS(1)LASADLLR;AFS(1)LASADLLR;AFS(1)LASADLLR;AFS(0.997)LAS(0.003)ADLLR 228.74 3.20E-12 149698400 239170.3 182534.9 196849 228158 316122 249376 322170 228455 302927 TRUE FALSE 227865.1939 201135.4138 205874.7214 205223.1244 371253.5767 240740.0466 273017.0494 208450.2691 349903.372 0.651223201 0.57483131 0.588375928 0.586513709 1.061017431 0.688018653 0.780264128 0.595736668 1 18.41659704 AFS(ph)WLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AFSWLR 6 0 Q9P206-2 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AFS(1)WLR;AFS(1)WLR;AFS(1)WLR;AFS(1)WLR;AFS(1)WLR;AFS(1)WLR;AFS(1)WLR 96.492 0.044211 630974000 591729 523427 548546 651621 504770 574270 676009 567561 464914 TRUE FALSE 563759.1429 576764.8064 573697.3767 586118.8191 592801.7282 554382.8859 572871.4113 517862.35 537010.4887 1.049810301 1.074028941 1.068316893 1.091447619 1.103892272 1.032350201 1.066778812 0.964343083 1 19.03459074 1.246590901 24.9884462 0.982171536 1.068560412 0.742957063 0.021353528 76.10236345 236818.8268 0.014384629 0.005047679 17.64375022 -1.246590901 0.086388876 AFSNLSALRKHEIIHT(ph)GQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFSNLSALRKHEIIHTGQK 19 2 A0A0A0MS76;A8MXY4 A0A0A0MS76 ZNF99 Zinc finger protein 99 1 AFS(0.005)NLS(0.073)ALRKHEIIHT(0.922)GQK 69.979 0.022259 1499700000 1103600 688250 872250 872080 1156400 789850 1410700 992810 1689900 TRUE FALSE 1051435.015 758383.4575 912243.5253 784416.8616 1358075.794 762497.2964 1195471.806 905874.2932 1951961.061 0.538655732 0.388523866 0.467347194 0.401860917 0.695749429 0.390631407 0.612446544 0.464084203 1 20.89649284 -5 0.266850653 4.428820985 0.455193368 0.719936059 0.099067937 97.90325379 0.954185329 184.5384271 0.109066624 1.00E-05 5 -3.973627617 AFTHTAQYDEAISDYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;; 276.18 9.58E-36 1102590000 558170 499670 491296 560130 568840 484410 616610 549380 551300 FALSE TRUE 531786.4103 550586.9411 513822.4076 503824.6682 668045.5159 467634.7602 522534.8197 501273.3748 636792.7883 0.835101182 0.864624963 0.806891059 0.791190914 1.049078331 0.734359385 0.820572766 0.78718444 1 19.28046447 2.386248094 0.009468668 1.696107611 4.73E-06 0.088053773 0.093295565 8303.788539 40.96066814 3600.527072 3732.604753 243.3593821 -2.386248094 -1.696102881 AFTKPEEACSFILSADFPALVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFTKPEEACSFILSADFPALVVK 23 1 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;H7C366 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 58.914 0.015443 0 185460 164860 174110 196290 130930 175800 221610 197450 147550 FALSE TRUE 176693.6733 181659.4214 182093.1157 176558.5563 153764.1505 169712.0019 187799.3244 180160.2313 170431.3004 1.036744265 1.065880627 1.068425314 1.03595147 0.902206051 0.99577954 1.101906304 1.057084179 1 17.37883079 -0.435510013 6.25673539 0.999999028 1.036613377 0.031797901 0.054041114 0 0 0.05412496 0.012757376 0.366851236 0.435510013 0.03661435 AFTMDCITLEGDQVSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFTMDCITLEGDQVSHR 17 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 161.8 2.92E-09 77398000 51500 46403 49266 56164 76284 46740 60625 51354 76633 FALSE TRUE 49065.69706 51131.51846 51524.89483 50518.28802 89587.90545 45121.38208 51375.5428 46857.17152 88516.85425 0.554309091 0.577647262 0.582091346 0.570719423 1.012099969 0.509749047 0.580404074 0.529358752 1 16.43366456 -2.065274008 2.386460604 1.557826036 0.610312258 0.415523807 0.143589566 13219280.41 4310646.26 40160635.25 0.032762997 0.008604507 2.065274008 -0.947513779 AFVAIGDYNGHVGLGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFVAIGDYNGHVGLGVK 17 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 111.7 0.00049685 11636000 22809 25066 21864 27437 20362 24295 26138 24541 23591 FALSE TRUE 21730.86377 27620.2539 22866.48603 24678.98063 23913.12635 23453.65806 22150.16804 22392.05994 27249.37179 0.797481275 1.013610666 0.839156447 0.905671544 0.877566152 0.860704542 0.812868943 0.821745914 1 14.73393535 2.399445978 2.897731442 0.853302932 0.89672983 0 0.075354825 0.769686822 13.17231928 0.026634398 0.02167531 250.8684107 -2.399445978 0.043426898 AFVDFLSDEIKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 AFVDFLSDEIKEER 14 1 Q07021 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;;;;;;;;; 284.67 1.33E-33 3199876900 7030633 6905754 5573627 6807705 4206025 5459021 5470476 6394587 4123204 FALSE TRUE 6698308.911 7609458.184 5829183.311 6123381.56 4939554.428 5269973.734 4635854.414 5834643.062 4762609.418 1.40643675 1.597749787 1.223947378 1.28571987 1.037152954 1.106530742 0.973385388 1.225093756 1 22.18332081 3.27140258 1.365928697 1.061366021 1.500532893 0.716742952 0.102778345 0.178203435 0.695401928 0.033077783 0.050800037 1868.110578 -3.27140258 0.439166871 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AFVEDSEDEDGAGEGGSSLLQK 22 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK 309.99 2.33E-67 371409000 442393 376780 420018 458726 322353 437677 492588 467028 389420 TRUE FALSE 421481.9596 415174.3104 439276.2408 412613.991 378571.2611 422520.1357 417434.6536 426132.5524 449809.2647 0.93702374 0.923000798 0.976583355 0.917308787 0.841626198 0.939331777 0.928025913 0.947362773 1 18.77895385 0.820745694 1.635009532 0.999863342 0.923149449 0.349260285 0.033316538 0.763300595 3.739040287 0.031113923 0.00893851 6.618288488 -0.820745694 -0.076713893 AFVHWYVGEGMEEGEFSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 29 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 324.46 3.67E-67 7669286900 10307717 11788536 10185491.9 11842372.6 10502496 10238350.6 10194035 10849456 8042397.9 FALSE TRUE 9820491.645 12989801.22 10652506.78 10651954.81 12334127.98 9883793.952 8638747.734 9899420.116 9289571.891 1.05715223 1.398320759 1.146716652 1.146657234 1.327739117 1.063966571 0.92994035 1.06564869 1 23.14718068 2.054514773 6.35676622 0.991989862 1.218972747 0.505745805 0.100045557 0.14556811 12.52474183 0.036259447 0.026448654 113.3743404 -2.054514773 0.226982885 AFVHWYVGEGMEEGEFSEAREDMAALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFVHWYVGEGMEEGEFSEAREDMAALEK 28 1 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 0 269.95 2.30E-55 50973000 47933 18641 46094 36400 48870 42361 74360 53769 55508 FALSE TRUE 45667.30208 20540.53909 48207.45549 32741.00284 57392.91253 40894.02795 63015.01628 49060.70131 64115.89714 0.712261765 0.320365775 0.751879918 0.510653431 0.89514325 0.637814174 0.98282983 0.765187785 1 15.96839449 2.444547699 0.749250105 0.930673779 0.526849701 0.426334179 0.157774793 0.546098528 0.614187196 0.110073198 0.080527651 278.3221039 -2.444547699 -0.403824078 AFYAELYHIISSNLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AFYAELYHIISSNLEK 16 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 268.59 1.52E-27 641420000 1569040 1465550 1238500 1333230 1351080 1341130 1658370 1613480 1032850 FALSE TRUE 1494874.589 1614891.211 1295286.45 1199211.187 1586707.924 1294686.332 1405355.198 1472195.138 1193019.103 1.25301815 1.353617228 1.085721467 1.005190264 1.329993728 1.085218442 1.177982142 1.234008017 1 20.18618571 8 0.024794827 0.144882037 2.601677457 0.217132418 0.110635536 2740.274436 5.226453714 178.5476932 371.8671309 100000000 -8 2.45679542 AFYVNVLNEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AFYVNVLNEEQR 12 0 P04040 P04040 CAT Catalase 0 80.737 0.045445 25451000 32621 26264 28710 35294 29510 27616 37462 34837 38039 FALSE TRUE 31079.06998 28940.33146 30026.3819 31746.18007 34656.53466 26659.651 31746.48386 31786.4876 43937.89384 0.707340914 0.658664513 0.683382367 0.722523938 0.788761855 0.606757599 0.722530852 0.723441313 1 15.4231781 0.477432218 1.719740196 0.999979316 0.695010773 0.802943962 0.046619331 1.465526446 4.372180735 0.041536738 0.011710161 3.00214883 -0.477432218 -0.304968544 AGAAAGDS(ph)DEESRADDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGAAAGDSDEESRADDK 17 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDK;AGAAAGDS(1)DEESRADDK 234.23 2.40E-20 222740000 334680 417870 317660 395400 199996 333990 324080 354800 201580 TRUE FALSE 318860.3397 460451.4281 332225.0252 355653.6408 234875.2391 322423.8426 274635.6439 323731.8311 232839.9969 1.369439718 1.977544384 1.4268383 1.527459395 1.008740948 1.384744232 1.179503726 1.390361774 1 17.82897938 3.098868081 2.126888664 1.220317931 1.65939789 0.43334494 0.210084321 0.255007165 2.352353938 0.062323828 0.077805155 1255.648497 -3.098868081 0.439079959 AGAAAGDS(ph)DEESRADDKGVMDYYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(0.932)DEES(0.068)RADDKGVMDYYLK;AGAAAGDS(0.987)DEES(0.013)RADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(0.984)DEES(0.016)RADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK 287.01 3.72E-54 2301303000 1818814 1544637 1577407 1734776 1004556 1597875 1926977 1986830 1113701 TRUE FALSE 1732842.267 1702037.266 1649732.671 1560393.021 1179750.248 1542540.188 1632981.267 1812852.632 1286408.063 1.347039339 1.323092816 1.282433404 1.212984484 0.917088661 1.199106436 1.269411561 1.409236062 1 20.29491692 3.320057937 3.093064173 1.176909089 1.330870845 0.222418053 0.134542521 0.401140034 7.709618382 0.039330884 0.054244523 2089.574874 -3.320057937 0.153961756 AGADEERAETAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGADEERAETAR 12 1 P78371;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 186.13 1.11E-05 114690000 179660 62908 186190 110290 283160 155790 330820 183970 426890 FALSE TRUE 171167.8279 69318.39672 194726.9957 99203.43966 332543.0143 150394.9532 280347.3331 167860.6115 493089.9209 0.34713309 0.140579626 0.394911734 0.20118732 0.674406432 0.305005126 0.568552147 0.340425964 1 18.91149124 -4.999999991 0.143663221 3.275380172 0.139462513 0.650662815 0.148813537 73.54615731 0.64011586 47.59690885 0.745555956 1.00E-05 4.999999991 -3.135917659 AGAES(ph)PTMSVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.5)PT(0.5)MS(0.001)VDGR;AGAES(0.755)PT(0.244)MS(0.001)VDGR;AGAES(0.5)PT(0.5)MSVDGR;AGAES(0.756)PT(0.244)MSVDGR;AGAES(0.5)PT(0.5)MSVDGR;AGAES(0.969)PT(0.03)MSVDGR 226.54 1.11E-11 3175150000 2114980 1866050 1724060 2074000 2019390 1818100 2000150 1916050 2082010 TRUE FALSE 2015009.087 2056202.617 1803109.856 1865517.58 2371570.977 1755138.741 1694990.382 1748270.504 2404877.477 0.837884302 0.855013462 0.749772025 0.775722504 0.986150438 0.729824599 0.704813612 0.726968638 1 21.19753196 AGAGMITQHSSNAS(ph)PINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGAGMITQHSSNASPINR 18 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 AGAGMITQHSSNAS(1)PINR;AGAGMITQHSS(0.001)NAS(0.999)PINR;AGAGMITQHSS(0.005)NAS(0.995)PINR;AGAGMITQHS(0.032)S(0.096)NAS(0.872)PINR 256.9 8.49E-31 825987000 422390 288330 410010 425983 726515 347890 636324 471952 883632 TRUE FALSE 402424.4618 317711.1548 428809.3641 383162.3795 853218.986 335842.4821 539241.0869 430625.3809 1020661.138 0.394278225 0.311279761 0.420129021 0.375406063 0.835947362 0.329044058 0.528325285 0.421908276 1 19.96107254 -5 0.193016171 3.415526187 0.344945074 0.579723157 0.147544485 93.46516656 0.917592025 86.95337436 0.357371068 1.00E-05 5 -3.070581112 AGAHLQGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 AGAHLQGGAK 10 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;; 174.27 7.34E-06 55763026400 97443234 80640162 68837453 85603390 75733257 82182325 103096060 87010315 74903304 FALSE TRUE 92837285.44 88857486.19 71993718.31 76998374.6 88941113.04 79336330.48 87366862.56 79391230.55 86518925.83 1.073028641 1.027029466 0.832115258 0.8899599 1.027996039 0.916982379 1.009800592 0.917616924 1 26.36651242 3.981116246 24.10690136 0.945017457 1.055778984 0.372525689 0.059365091 449.486509 573814.1635 0.014783611 0.026863092 9574.50315 -3.981116246 0.110761527 AGAHLQGGAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGAHLQGGAKR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 137.98 4.36E-05 2272544000 4196660 2132650 4016690 3160840 4865600 4023630 6705050 4726190 6669800 FALSE TRUE 3998292.199 2349969.46 4200859.21 2843106.358 5714159.099 3884290.684 5682071.476 4312339.748 7704118.519 0.518981138 0.305027688 0.545274479 0.369037204 0.741701868 0.504183662 0.737536872 0.559744731 1 22.87719847 0.463683778 0.236759143 1.161027269 0.342666105 0.640970717 0.119529442 2.669692296 0.351284062 0.670976278 0.258364249 2.908598514 -0.463683778 -0.818361164 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 AGAPGALS(0.991)PS(0.009)YDGGLHGLQSK 181.81 2.31E-18 0 141180 112260 123650 158290 111410 147100 164310 141370 113920 TRUE FALSE 134506.7012 123699.4216 129319.4748 142378.3885 130839.8687 142005.8901 139241.4917 128990.8934 131586.1318 1.022195116 0.940064275 0.982774348 1.082016673 0.99432871 1.07918584 1.058177559 0.980277265 1 17.00564792 3.353961514 9.073055653 1.038143312 0.977925658 0.257730599 0.039624207 0.287566145 21.64140839 0.0102269 0.013850454 2259.235554 -3.353961514 -0.060217655 AGASCVCCSQPQQSST(ph)SPPPSDALQWVVVEVSGTPNQLETHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHR 42 0 Q13952-3;Q13952 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 1 AGASCVCCSQPQQS(0.009)S(0.109)T(0.409)S(0.409)PPPS(0.027)DALQWVVVEVS(0.017)GT(0.017)PNQLET(0.004)HR 47.522 0.063279 27296000 17092 13067 13736 15932 19485 13794 16785 17587 20941 TRUE FALSE 16284.09503 14398.54216 14365.80919 14330.48509 22883.17783 13316.31032 14224.13997 16046.98905 24188.42333 0.67321854 0.595265841 0.593912592 0.59245222 0.946038422 0.550524114 0.58805569 0.663416082 1 14.56202911 0.942724219 21.03792444 1.000000001 0.642422986 0.493177752 0.111358299 2424.039509 890374.6923 0.101410051 0.025352513 8.76444094 -0.942724219 -0.357577014 AGASCVCCSQPQQSSTS(ph)PPPSDALQWVVVEVSGTPNQLETHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHR 42 0 Q13952-3;Q13952 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 1 AGASCVCCSQPQQSS(0.009)T(0.153)S(0.831)PPPS(0.007)DALQWVVVEVSGTPNQLETHR;AGASCVCCSQPQQS(0.001)S(0.014)T(0.191)S(0.784)PPPS(0.01)DALQWVVVEVSGTPNQLETHR 172.17 5.80E-20 62569000 89315 80297 88266 95324 101098 84218 110038 95521 102022 TRUE FALSE 85093.25696 88479.35559 92313.08341 85741.85042 118729.4592 81301.50954 93249.68211 87156.67485 117843.0507 0.722089732 0.750823702 0.783356192 0.727593608 1.007521941 0.689913483 0.79130404 0.739599614 1 16.84650716 AGAVTSTPNRNS(ph)SKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGAVTSTPNRNSSKR 15 2 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 AGAVTSTPNRNS(0.834)S(0.166)KR 116.06 0.00024961 73759000 51649 35626 45317 63988 38186 47275 53070 45769 42432 TRUE FALSE 49207.65413 39256.3299 47394.82927 57555.80467 44845.62631 45637.8549 44973.1968 41761.22372 49012.13785 1.00398914 0.800951185 0.967001877 1.174317367 0.91499021 0.931154137 0.917593045 0.852058807 1 15.58085146 -0.333168972 7.36906459 0.999999999 0.940111734 0.027110739 0.098878758 0 0 0.093978792 0.022151014 0.464334581 0.333168972 -0.059888266 AGCECLNESDEHGFDNCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGCECLNESDEHGFDNCLR 19 0 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 135.49 7.67E-06 137620000 51795 50418 46765 60476 48553 58347 55724 56881 47552 FALSE TRUE 49346.753 55555.65152 48909.22151 54396.83758 57020.62783 56326.42876 47222.28036 51900.19809 54926.1213 0.898420493 1.0114614 0.890454675 0.990363716 1.038133159 1.025494381 0.859741763 0.944909214 1 15.7452048 -1.241017745 3.642776167 1.00006863 0.955964142 0.046448792 0.060399777 8862891.66 3023239.599 5225.65332 0.013989828 0.0574093 1.241017745 -0.044104487 AGDEFVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGDEFVEK 8 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 119.27 0.0086777 0 505720 379560 413640 412160 344430 361550 433950 441090 386210 FALSE TRUE 481815.6178 418237.5955 432605.8031 370728.8937 404498.4829 349029.4328 367742.9575 402465.8212 446101.4743 1.08005834 0.937539147 0.969747531 0.831041624 0.906740969 0.782399192 0.824348223 0.902184468 1 18.76701239 4.24568517 0.808604523 0.8574273 1.119449827 0.462250126 0.065158524 0.967965206 0.772769058 0.022820131 0.20008943 17606.99213 -4.24568517 0.262022527 AGDGS(ph)SVKEVETYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGDGSSVKEVETYHR 15 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 AGDGS(0.7)S(0.3)VKEVETYHR 156.73 1.25E-06 244570000 173710 146750 167810 181320 145370 188810 215430 217430 185130 TRUE FALSE 165499.0726 161703.9918 175504.2545 163093.3691 170722.482 182271.4624 182562.1969 198390.6765 213839.0149 0.773942363 0.756194991 0.820730747 0.762692295 0.798369194 0.85237702 0.853736616 0.927757157 1 17.70616557 1.320067519 0.65241515 1.002939547 0.769749173 0.929838168 0.020343695 0.145775057 0.14627702 0.018134302 0.008184506 20.89620975 -1.320067519 -0.233190374 AGDGSS(ph)VKEVETYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGDGSSVKEVETYHR 15 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 AGDGS(0.261)S(0.739)VKEVETYHR;AGDGS(0.033)S(0.967)VKEVETYHR;AGDGS(0.224)S(0.776)VKEVETYHR 193.85 4.59E-08 806430000 841890 738570 787570 863900 738460 856370 1015030 1006380 840890 TRUE FALSE 802095.5282 813831.1227 823680.8635 777059.1307 867247.1902 826713.6922 860168.5312 918256.032 971290.9265 0.825803584 0.837886055 0.848026931 0.800027169 0.892880976 0.851149403 0.885593088 0.945397519 1 19.88954396 1.184090384 0.799381691 1.002665544 0.833023618 0.866159236 0.021716394 0.18278694 0.264712241 0.018590801 0.007083763 15.27884003 -1.184090384 -0.169641926 AGDKDDITEPAVCALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGDKDDITEPAVCALR 16 1 P14923 P14923 JUP Junction plakoglobin 0 ; 80.638 0.013686 584590000 393130 362200 369400 427300 292890 390070 448180 446240 328870 FALSE TRUE 374547.524 399108.5918 386337.3554 384346.9922 343969.9233 376561.7781 379801.9096 407164.8599 379869.48 0.985990041 1.050646637 1.017026573 1.011786975 0.905495022 0.991292531 0.999822122 1.071854627 1 18.53514428 -1.467303668 4.287179677 0.999978833 1.004068507 0.000913478 0.043737585 8.68E-06 1.08E-06 0.041548945 0.009742486 0.034095443 1.467303668 0.004089674 AGDLLEDS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK 204 2.05E-07 31040720000 40661630 45099760 31500300 46070100 17802090 41685220 34830410 42031600 16139500 TRUE FALSE 38739635.33 49695476.82 32944619.91 41439046.02 20906768.86 40241650.38 29516391.25 38351090.28 18642331.23 2.078046724 2.66573296 1.767194215 2.222846784 1.121467514 2.158616853 1.583299368 2.057204638 1 24.15207895 1.482478173 0.093851874 4.58E-15 3.438468926 0.397479653 0.39459953 9.669431178 0.924249409 16.06155607 15.59629308 30.3723344 -1.482478173 3.438468926 AGDLLEDS(ph)PKRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK 206.43 3.23E-08 1.31229E+11 55816195 40896105.01 48144624.5 52549276.2 26628051.61 55023496.4 62066559.7 63310027.4 29441199 TRUE FALSE 53177874.08 45063464.61 50352103.15 47266923.12 31271975.38 53118018.92 52597166.09 57766265.77 34006789.78 1.563742842 1.32513139 1.480648526 1.389926054 0.919580342 1.561982747 1.546666605 1.698668594 1 25.01931949 AGDPGEMPQS(ph)PTGLGQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGDPGEMPQSPTGLGQPK 18 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9;H0YHL2 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 AGDPGEMPQS(0.981)PT(0.019)GLGQPK 104.44 0.001981 81951000 98403 79186 84846 104360 61517 95124 103240 96773 68142 TRUE FALSE 93751.68521 87255.14343 88736.27302 93869.53453 72245.54532 91829.83203 87488.84187 88299.04309 78709.11334 1.191116012 1.10857739 1.127395155 1.192613289 0.91788031 1.16669885 1.111546531 1.121840145 1 16.26424307 -4.999896091 0.017468367 3.24E-06 1.930964433 0.222196306 0.075393791 6560.074165 8.680826236 622.9382268 367.7357481 1.00E-05 4.999896091 1.930961196 AGDRNS(ph)EDDGVVMTFSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGDRNSEDDGVVMTFSSVK 19 1 Q9NY61 Q9NY61 AATF Protein AATF 1 AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK 245.62 8.22E-25 537138000 1052790 1302191 742435 1206087 556458 972889 873926 1111794 577076 TRUE FALSE 1003026.703 1434885.743 776476.3791 1084848.843 653504.099 939197.61 740592.5379 1014439.423 666565.9988 1.504767277 2.15265367 1.164890469 1.627519023 0.980404191 1.409009178 1.111056578 1.521888943 1 19.3463882 3.724048673 24.99197204 1.267053197 1.828710484 0.451148685 0.261015988 564.9268325 972897.7897 0.062201949 0.096835218 5297.228087 -3.724048673 0.561657287 AGDSAVLVLPPS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR 260.24 9.31E-27 8388788000 4472810 3783360 4090120 4580410 4611540 3983420 4757320 4133480 4769450 TRUE FALSE 4261389.136 4168888.685 4277656.048 4119978.485 5415791.116 3845473.167 4031503.46 3771530.578 5509071.947 0.773522142 0.756731574 0.776474892 0.747853454 0.983067778 0.698025585 0.731793576 0.684603616 1 22.39337787 AGDTETLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGDTETLK 8 0 C9JNG9;P12111 C9JNG9 COL6A3 Collagen alpha-3(VI) chain 0 75.311 0.090077 1830100000 1157200 976060 1203900 1011600 945050 1350500 1426900 1287300 1276100 FALSE TRUE 1102501.449 1075521.624 1259100.006 909912.0461 1109866.421 1303731.846 1209200.198 1174577.188 1473991.071 0.747970236 0.729666309 0.85421142 0.617311776 0.752966855 0.884491007 0.820357886 0.796868591 1 20.49129635 0.364671259 0.354498311 1.036193975 0.729813633 0.544863423 0.068851748 2.347312498 0.53937444 0.214970605 0.060703421 2.315641155 -0.364671259 -0.306380342 AGDWQCPNPGCGNQNFAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGDWQCPNPGCGNQNFAWR 19 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2 B0QYK0 EWSR1 RNA-binding protein EWS 0 278.27 6.56E-34 0 113000 105890 88276 120750 98496 115460 108730 109430 116240 FALSE TRUE 107658.7139 116680.3114 92323.54192 108611.9806 115673.6712 111461.5912 92141.24154 99847.72908 134265.9055 0.801832107 0.869024127 0.687617169 0.808931949 0.861526765 0.830155584 0.686259413 0.743656617 1 17.03473348 AGEAGKLEEVMQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGEAGKLEEVMQELR 15 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 161.24 1.52E-06 1347092000 1883060 1577985 1727507 1949610 1394530 1901907 2239803 2106981 1558964 FALSE TRUE 1794051.486 1738783.466 1806714.905 1753631.499 1637735.59 1836043.484 1898079.916 1922482.574 1800720.175 0.996296654 0.965604478 1.003329073 0.973850087 0.909489222 1.019616212 1.054067113 1.067618723 1 20.78014258 2.011359913 24.91970302 1.044137476 0.972558319 0.546802594 0.030066901 144.5666428 317127.9028 0.010660496 0.007866808 102.6502268 -2.011359913 -0.071579156 AGELTEDEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 265.58 1.35E-20 2922160000 2436240 2200590 2215510 2662490 2194870 2297350 2699350 2600020 2434200 FALSE TRUE 2321083.763 2424832.623 2317093.325 2394851.447 2577654.633 2217792.193 2287514.581 2372348.465 2811683.304 0.82551394 0.862413139 0.824094706 0.851750069 0.916765636 0.788777381 0.813574764 0.843746684 1 21.42300267 0.927441543 21.46626457 1 0.839423424 0.685696963 0.03386888 6091.33525 1802111.36 0.032007223 0.008001806 8.461386698 -0.927441543 -0.160576576 AGEPDGES(ph)LDEQPSSSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGEPDGESLDEQPSSSSSK 19 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGEPDGES(0.999)LDEQPS(0.001)SSSSK;AGEPDGES(1)LDEQPSSSSSK;AGEPDGES(0.999)LDEQPSSS(0.001)SSK;AGEPDGES(0.997)LDEQPS(0.003)SSSSK;AGEPDGES(1)LDEQPSSSSSK 365.07 8.43E-108 811940000 1780650 1881910 1570560 2096820 1106280 1879610 1740650 1873750 1061640 TRUE FALSE 1696482.203 2073678.769 1642571.729 1886043.67 1299214.882 1814518.634 1475081.873 1709674.517 1226273.709 1.383444977 1.691040714 1.339482138 1.538028301 1.059481967 1.479701164 1.20289774 1.394203027 1 20.2258496 0.557824046 0.143438854 0.709088214 1.720370134 0.395109007 0.163919565 9.343952301 0.677584697 2.770226653 1.514675719 3.612634671 -0.557824046 1.01128192 AGEPDGES(ph)LDEQPSSSSSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGEPDGESLDEQPSSSSSKR 20 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGEPDGES(1)LDEQPSSSSSKR;AGEPDGES(1)LDEQPSSSSSKR 144.29 9.69E-08 1036240000 1298920 894490 1188690 1212110 821520 1236870 1560530 1418620 1001680 TRUE FALSE 1237522.626 985639.548 1243192.612 1090266.4 964792.8279 1194036.882 1322442.487 1294398.112 1157015.419 1.069581793 0.851881083 1.074482321 0.942309309 0.833863415 1.031997381 1.142977411 1.118738862 1 20.14197666 2.002609175 24.94874886 1.099215715 0.953908868 0.33890457 0.084992359 75.5702578 722590.0325 0.029992431 0.022022767 100.6025931 -2.002609175 -0.145306847 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_SK-BR-3_Trastuzumab_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 239.12 8.14E-46 2903190000 875320 685318 788120 843640 771370 793350 962280 809060 705695 TRUE FALSE 833945.3583 755152.6833 824256.0816 758835.7044 905896.6838 765876.0906 815466.5125 738214.4173 815130.5764 1.023081924 0.926419282 1.011195145 0.930937602 1.111351617 0.939574729 1.000412126 0.905639463 1 19.63667166 0.030167454 0.004360412 0.827148659 1.133813641 0.001826839 0.060726247 488538.963 659.4811414 23547.49199 22831.88178 1.071932539 -0.030167454 0.306664982 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 215.62 1.17E-34 1532350000 322866 263024 308175 335879 298494 326117 364132 326480 285492 TRUE FALSE 307604.764 289826.4446 322305.1286 302115.8048 350551.2591 314823.4865 308576.9757 297891.6804 329764.6413 0.93280093 0.878888784 0.977379283 0.916155849 1.063034708 0.954691459 0.935749128 0.903346336 1 18.33107719 3.731485529 24.95292075 0.961602726 0.905844857 0.211548735 0.046714687 750.8648791 2648203.942 0.011887072 0.018855396 5388.718896 -3.731485529 -0.055757869 AGEPNSPDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNS(0.001)PDAEEANS(0.999)PDVTAGCDPAGVHPPR 146.57 2.31E-08 482180000 24892 20292 21109 26877 19625 23357 26928 24395 25557 TRUE FALSE 23715.40449 22359.77787 22076.86853 24175.2729 23047.59379 22548.14123 22819.63903 22258.84447 29520.24903 0.803360584 0.75743866 0.747855091 0.81893865 0.780738461 0.763819479 0.773016481 0.754019536 1 14.84941727 -2.213462899 2.478514079 1.76057247 0.775066683 0.911329042 0.022066483 2283138.334 835569.8452 9614980.888 0.005186793 0.006116981 2.213462899 -0.985505787 AGEQQLS(ph)EPEDMEMEAGDTDDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGEQQLSEPEDMEMEAGDTDDPPR 24 0 Q93009;H3BMF6 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 1 AGEQQLS(1)EPEDMEMEAGDTDDPPR 180.23 1.92E-17 132220000 140860 117060 141480 138060 136640 110390 159390 126980 158530 TRUE FALSE 134201.827 128988.5471 147966.9979 124181.9465 160469.9727 106567.1666 135072.1281 115860.958 183114.0227 0.732886673 0.704416544 0.808059349 0.678167322 0.876339072 0.581971632 0.737639456 0.632725754 1 17.48238275 -1.587918432 2.977323736 1.01660152 0.719868395 0.53359612 0.082551735 18490265.6 20870269.8 2433525.105 0.018134398 0.025827452 1.587918432 -0.296733125 AGETRFT(ph)DTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGETRFTDTR 10 1 P13639 P13639 EEF2 Elongation factor 2 1 AGETRFT(0.999)DT(0.001)R;AGET(0.07)RFT(0.887)DT(0.043)R;AGETRFT(1)DTR;AGETRFT(0.999)DTR;AGETRFT(0.999)DT(0.001)R;AGETRFT(0.999)DT(0.001)R 131.32 0.00040934 5605460000 6477620 2389689 2996070 7104340 10906650 5940310 5823440 2546240 7570730 TRUE FALSE 6171435.74 2633201.026 3133442.773 6390198.246 12808766.31 5734595.575 4934967.273 2323277.727 8744760.142 0.705729561 0.301117582 0.358322324 0.730745971 1.46473615 0.655775056 0.564334206 0.265676553 1 23.05998738 3.172884783 7.265807099 0.770044958 0.458435395 0.183290272 0.323535731 0.410360909 37.82220166 0.095512561 0.114845157 1488.966006 -3.172884783 -0.311609563 AGETRFT(ph)DTRKDEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGETRFTDTRKDEQER 16 3 P13639 P13639 EEF2 Elongation factor 2 1 AGET(0.025)RFT(0.699)DT(0.276)RKDEQER 103.45 0.0014792 620760000 417330 93166 234940 352850 585380 381800 477770 163360 468880 TRUE FALSE 397603.638 102659.7213 245712.2314 317380.8476 687470.0867 368578.1703 404877.4117 149055.3324 541591.5157 0.73413934 0.189551938 0.453685525 0.586015176 1.269351655 0.680546426 0.747569709 0.275217259 1 19.04684561 2.993191658 23.92209632 0.783158269 0.450547715 0.235486812 0.279236459 251.2220293 882713.304 0.078762143 0.090763064 984.4454546 -2.993191658 -0.332610554 AGETRFTDT(ph)RKDEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGETRFTDTRKDEQER 16 3 P13639 P13639 EEF2 Elongation factor 2 1 AGETRFT(0.043)DT(0.957)RKDEQER;AGETRFT(0.067)DT(0.933)RKDEQER 148.38 9.64E-07 2227100000 1318610 310550 774580 1238070 1987460 1305000 1609250 598810 1736760 TRUE FALSE 1256281.919 342195.3981 810095.2592 1113616.851 2334072.395 1259807.523 1363729.357 546375.0219 2006087.871 0.626234741 0.170578469 0.403818432 0.55511868 1.163494595 0.627992194 0.679795425 0.272358469 1 20.93595337 2.997297583 13.19106515 0.729543554 0.395258983 0.280887396 0.25542352 0.349694722 1661.06371 0.071900559 0.082953016 993.7967741 -2.997297583 -0.334284571 AGFADPDDFTLGAGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGFADPDDFTLGAGPR 16 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ; 138.24 5.78E-05 19220000 110521 102860 102867 111238 103507 102004 121999 113971 116942 FALSE TRUE 105296.8914 113341.5509 107583.5537 100056.1449 121558.588 98471.5759 103385.8119 103991.095 135076.7681 0.779533689 0.839089893 0.796462302 0.740735408 0.899922242 0.72900453 0.76538559 0.769866621 1 17.04342004 -0.749885143 6.100560274 1.000000005 0.791123017 0.64242914 0.049230501 5970451.091 978672.5757 0.433962024 0.010766543 0.177874977 0.749885143 -0.208876988 AGFAGDDAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 194.9 9.61E-07 45760150000 82959940 71179620 74022110 83876540 83964830 73743820 90964990 82068900 89808210 FALSE TRUE 79038588.05 78432904.2 77416096.96 75445110.84 98608269.77 71190053.02 77086610.09 74882512.04 103735208.5 0.761926343 0.756087594 0.746285645 0.727285479 0.950576677 0.686267026 0.743109415 0.721862067 1 26.6283304 -2.189616884 2.255046973 1.6406549 0.76065661 0.530032489 0.070521086 6443036.268 1307918.452 21069938.83 0.016939405 0.00646224 2.189616884 -0.87999829 AGFDSDYDQALADIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 98.105 0.0071109 32387000 55827 61462 49236 65779 51602 56491 58959 59705 55374 FALSE TRUE 53188.16835 67725.04768 51493.5193 59166.76995 60601.37246 54534.70251 49963.72169 54476.91368 63961.11711 0.831570347 1.058847167 0.805075359 0.925042786 0.947472077 0.852622733 0.78115774 0.851719234 1 15.96490752 2.177558924 7.516895466 0.844852512 0.921468275 0.012210617 0.087817633 0.438577546 45.78410107 0.030794735 0.022775451 150.507771 -2.177558924 0.076615763 AGFESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGFESER 7 0 Q13946-3;Q13946-2;Q13946;E5RG23 Q13946-3 PDE7A "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A" 0 101.33 0.021262 116650000 191670 146550 155050 173090 178540 160950 187830 167890 201920 FALSE TRUE 182610.139 161483.6116 162159.1959 155690.6644 209677.3195 155376.2611 159173.0838 153188.6616 233232.7223 0.782952483 0.692371165 0.695267775 0.667533538 0.899004725 0.666185515 0.682464631 0.656806043 1 17.83141069 -1.073793036 4.012506898 1.000053178 0.717722833 0.593909664 0.073328807 20137465.61 40387420.61 14679.21283 0.016677105 0.084373675 1.073793036 -0.282330345 AGFNYES(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.991)PS(0.009)K;AGFNYES(0.97)PS(0.03)K;AGFNYES(0.997)PS(0.003)K;AGFNYES(0.939)PS(0.061)K 215.93 8.35E-09 1036060000 1268810 1869220 1237610 1650660 751090 1533630 1319520 1649670 974730 TRUE FALSE 1208835.866 2059695.643 1294355.643 1484732.521 882079.8582 1480520.009 1118202.989 1505216.149 1125886.15 1.073675048 1.829399574 1.149632796 1.318723497 0.783453867 1.314981988 0.993175899 1.336916836 1 20.10262952 3.520192084 24.64244731 1.122873982 1.457867307 0.227542898 0.248068629 476.8959727 272848.7701 0.060301911 0.093411479 3312.776098 -3.520192084 0.334993325 AGFNYES(ph)PSKGGNFPSFPHDEVTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGFNYESPSKGGNFPSFPHDEVTDR 25 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.973)PS(0.027)KGGNFPSFPHDEVTDR;AGFNYES(0.982)PS(0.018)KGGNFPSFPHDEVTDR;AGFNYES(0.976)PS(0.024)KGGNFPSFPHDEVTDR;AGFNYES(0.968)PS(0.032)KGGNFPSFPHDEVTDR;AGFNYES(0.988)PS(0.012)KGGNFPSFPHDEVTDR;AGFNYES(0.955)PS(0.045)KGGNFPSFPHDEVTDR 237.79 1.07E-38 1361042000 957627 970978 996168 1044422 713562 1138193 1248269 1285885 799841 TRUE FALSE 912361.8695 1069921.762 1041843.288 939434.7163 838006.9869 1098777.091 1057822.638 1173286.092 923876.2573 0.987536872 1.158079076 1.127687047 1.016840414 0.907055442 1.189311969 1.144983032 1.269960217 1 19.81734011 AGFQTEDFSLYACAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGFQTEDFSLYACASPK 17 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 AGFQTEDFS(0.004)LY(0.003)ACAS(0.993)PK;AGFQTEDFSLYACAS(1)PK 141.78 6.41E-07 74497000 70061 72699 63872 81334 50750 75155 75696 82345 54816 TRUE FALSE 66749.35538 80107.11075 66800.59438 73158.1518 59600.78393 72552.36351 64147.18495 75134.43526 63316.58532 1.05421597 1.265183685 1.05502522 1.155434258 0.941313933 1.14586665 1.0131182 1.186646988 1 15.95029583 3.637021954 24.99669421 1.070790302 1.159809584 0.142032013 0.090570924 58.51392374 14390.33249 0.021517641 0.033334987 4335.327931 -3.637021954 0.089019282 AGGAAVVITEPEHTKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGGAAVVITEPEHTKER 17 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 70.197 0.019916 128310000 107210 57460 109580 91365 114300 97448 163750 123270 154540 FALSE TRUE 102142.3958 63315.23933 114604.3514 82180.81662 134233.8838 94073.35133 138766.93 112475.8253 178505.2739 0.5722094 0.354696743 0.642022215 0.460383129 0.751988335 0.527006005 0.777382802 0.630098052 1 17.44560717 0.531066861 0.233678032 1.144446771 0.407424719 0.622499494 0.110655299 2.615400907 0.35514425 0.60385951 0.249157978 3.396775627 -0.531066861 -0.737022053 AGGAS(ph)PAASSTAQPPTQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AGGASPAASSTAQPPTQHR 19 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(0.976)PAASS(0.017)T(0.006)AQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(0.999)PAAS(0.001)STAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR 212.05 6.46E-17 5039466000 1328230 1112258 1202900 1363876 1256893 1139701 1468301 1332501 1320933 TRUE FALSE 1265447.2 1225598.355 1258054.155 1226776.593 1476094.741 1100232.869 1244284.715 1215820.148 1525776.543 0.829379116 0.803262024 0.824533684 0.804034247 0.96743835 0.721096987 0.815509139 0.796853349 1 20.54111226 -0.85011795 4.296225495 1.000001962 0.818646934 0.467079962 0.060313757 12219494.11 22731580.6 373.7557131 0.013141095 0.141215397 0.85011795 -0.181355028 AGGGDLLLPPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK 177.84 1.58E-05 1172568000 5633480 4847750 5243400 6285760 3470340 6145500 6260970 6453450 4089350 TRUE FALSE 5367196.565 5341741.236 5483815.076 5653903.463 4075566.197 5932679.794 5305744.036 5888351.706 4723505.512 1.136274013 1.130884938 1.160962989 1.19697192 0.862826599 1.255990869 1.123264072 1.246606295 1 22.17142651 -0.225725703 7.369674569 1.000033218 1.136651553 0.139724412 0.108399589 6325852.08 858362.4327 0.093293396 0.022626972 0.594667628 0.225725703 0.136618335 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AGGGGGLGAGSPALSGGQGR 20 0 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 1 AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR 344.48 3.97E-81 2658235000 2818841 2606252 2519504 3193813 2856372 2660940 3103648 2920265 3027073 TRUE FALSE 2685599.972 2871832.042 2635025.751 2872764.849 3354522.372 2568790.981 2630129.495 2664551.115 3496496.021 0.768083234 0.82134572 0.753618976 0.821612504 0.95939545 0.734675791 0.752218644 0.762063248 1 21.73747843 -2.121477735 2.49784604 1.411387933 0.795456432 0.495585071 0.06447132 4923727.211 1627592.174 11493456.76 0.015710935 0.007560008 2.121477735 -0.615931501 AGGIETIANEFSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGGIETIANEFSDR 14 0 Q92598-2;Q92598;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 156.46 1.29E-05 295760000 271320 227640 338930 276020 582680 228840 316330 232730 543030 FALSE TRUE 258495.2413 250836.7748 354470.2757 248273.9452 684299.2075 220915.2134 268068.0487 212350.9274 627240.319 0.412115155 0.399905375 0.565126739 0.395819493 1.090968145 0.35220187 0.427376941 0.338547955 1 19.25865877 -1.990676124 3.091310912 1.477791782 0.489410861 0.339167305 0.220046307 331961815.2 399537079.3 1133066720 0.051768583 0.010217011 1.990676124 -0.988380922 AGGIETIANEYSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGGIETIANEYSDR 14 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 128.08 0.00017638 109680000 98091 87882 82276 93135 88484 94436 111950 100240 108900 FALSE TRUE 93454.43283 96837.27571 86048.43598 83772.89286 103915.5816 91165.65764 94869.9714 91462.45419 125787.6558 0.742953927 0.769847209 0.68407695 0.665986597 0.826119073 0.72475838 0.754207325 0.727117885 1 16.94063082 -1.914188603 2.493467851 1.159029292 0.739708054 0.778333125 0.044105525 3750904.047 1971607.246 3486260.765 0.010699153 0.012184603 1.914188603 -0.419321238 AGGLDWPEATEVS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 AGGLDWPEATEVSPSR 16 0 Q9Y446;Q9Y446-2;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 AGGLDWPEATEVS(0.99)PS(0.01)R;AGGLDWPEATEVS(0.998)PS(0.002)R;AGGLDWPEATEVS(0.994)PS(0.006)R;AGGLDWPEATEVS(0.883)PS(0.117)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.999)PS(0.001)R;AGGLDWPEATEVS(0.988)PS(0.012)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.997)PS(0.003)R;AGGLDWPEATEVS(0.997)PS(0.003)R 335.61 1.07E-71 8215964000 6073406 5448104 5680044 6587103 6277130 5870315 7126400 6466362 6886730 TRUE FALSE 5786328.135 6003271.992 5940479.636 5924954.892 7371859.485 5667024.52 6039136.795 5900133.063 7954688.916 0.727410989 0.75468344 0.746789686 0.744838039 0.926731336 0.712413091 0.759192076 0.741717637 1 22.92337408 -2.268770179 2.323625482 2.00103368 0.762365555 0.608472738 0.059421681 3173686.811 482943.6609 16742030.6 0.013744994 0.005385547 2.268770179 -1.238668124 AGGPAT(ph)PLSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPAT(0.997)PLS(0.003)PTR;AGGPAT(0.961)PLS(0.039)PTR 156 0.00081396 339340000 295930 234390 238980 280400 288080 254330 287340 254940 282300 TRUE FALSE 281941.9754 258274.6075 249937.4694 252213.6593 338321.0608 245522.4883 243501.0056 232616.1021 326077.6422 0.864646755 0.792064754 0.7664968 0.773477315 1.037547556 0.752957138 0.746757748 0.713376423 1 18.314856 -0.638578157 4.989779673 1.000000025 0.806147583 0.309306059 0.091146294 5399937.74 1623300.126 1.815853214 0.020679788 0.229838005 0.638578157 -0.193852442 AGGPATPLS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPATPLS(0.999)PT(0.001)R 180.31 2.06E-05 198360000 239900 212350 240780 265310 239930 232260 271920 252060 268210 TRUE FALSE 228560.4024 233988.7064 251820.0012 238640.5347 281773.716 224216.778 230433.6098 229988.2901 309802.637 0.73776132 0.755283134 0.812840083 0.770298591 0.909526526 0.723740702 0.743807774 0.742370344 1 18.2409899 -2.324458483 2.310401502 2.285157969 0.771279253 0.633888643 0.053820921 2487987.197 263736.2256 16892301.36 0.012663293 0.004737416 2.324458483 -1.513878716 AGGPS(ph)DDDNADKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGGPSDDDNADKPK 14 1 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 AGGPS(1)DDDNADKPK;AGGPS(1)DDDNADKPK;AGGPS(1)DDDNADKPK 184.01 8.13E-07 1483510000 1278410 1197300 1133030 1437450 521080 1443280 1330000 1454310 485660 TRUE FALSE 1217982.093 1319306.231 1184980.546 1292954.795 611956.187 1393298.852 1127084.073 1326962.907 560973.6724 2.171192968 2.351814882 2.112363921 2.304840421 1.090882188 2.483715226 2.009156808 2.365463785 1 19.09757354 AGGPT(ph)TPLSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPT(0.5)T(0.5)PLSPTR 116.82 0.0089486 56960000 261590 209150 234730 269160 200510 245650 287560 256410 221070 TRUE FALSE 249225.1591 230462.6228 245492.6027 242103.5254 235478.8805 237143.0789 243687.4406 233957.3811 255352.4065 0.97600474 0.90252771 0.961387465 0.948115307 0.922172161 0.928689422 0.954318167 0.916213731 1 17.96213013 -1.877607678 2.735952296 1.028286545 0.938843978 0.430213989 0.022177574 6640064.182 4529895.48 1208136.052 0.00487261 0.013255384 1.877607678 -0.089442567 AGGPTTPLS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPT(0.001)T(0.028)PLS(0.775)PT(0.196)R 98 0.004831 251320000 164620 187010 177110 178560 175580 173770 200630 187040 194200 TRUE FALSE 156838.7388 206066.5316 185230.6687 160610.8096 206201.0964 167752.3013 170020.2087 170661.786 224315.5442 0.69918801 0.918645796 0.825759398 0.716003923 0.919245687 0.747840735 0.757951079 0.760811234 1 17.77517007 -1.125733148 5.086617913 1.000007275 0.796341633 0.422266367 0.075946381 5.89E-06 1.01E-06 0.069078865 0.016281463 0.074862935 1.125733148 -0.203665642 AGGSAALS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.99)PS(0.01)K;AGGSAALS(0.989)PS(0.011)K;AGGSAALS(0.987)PS(0.013)K;AGGSAALS(0.995)PS(0.005)K 248.67 3.04E-16 2159700000 3723440 3561570 2921380 3463450 2414580 3587080 3786080 3816980 2881420 TRUE FALSE 3547440.37 3924498.032 3055328.163 3115297.426 2835681.988 3462858.52 3208443.96 3482744.996 3328255.897 1.065855655 1.17914552 0.91799677 0.936014995 0.852002393 1.04044239 0.964001585 1.046417434 1 21.66633493 3.735952469 24.99946081 0.96266583 1.12250059 0.517381747 0.063094676 154.4579821 1480503.114 0.016037555 0.026161449 5444.430639 -3.735952469 0.15983476 AGGSAALS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGGSAALSPSKK 12 1 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.974)PS(0.026)KK;AGGSAALS(0.98)PS(0.02)KK 96.489 0.0033415 724450000 1525570 1459740 1317450 1574850 801740 1624070 1561310 1602360 958810 TRUE FALSE 1453459.329 1608489.166 1377856.386 1416543.086 941563.2022 1567828.049 1323103.484 1462048.864 1107497.358 1.312381758 1.452363885 1.244117086 1.279048727 0.850171962 1.415649471 1.194678682 1.320137564 1 20.07887183 7.999996785 0.027402371 2.43E-07 3.010353601 0.203117421 0.162938652 2386.271097 5.022885351 182.892619 411.2984592 99999259.81 -7.999996785 3.010353358 AGHCAVAINTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 108.7 0.0020282 123840000 113820 99813 84006 116950 106250 96445 105030 88914 67886 FALSE TRUE 108439.9542 109984.0582 87857.75819 105193.9638 124779.9664 93105.08547 89005.74449 81128.2188 78413.41417 1.382926063 1.402617898 1.120442964 1.341530208 1.591308932 1.187361709 1.135083142 1.034621686 1 16.25881286 1.796707344 2.32637978 1.043054465 1.360711668 0.578660978 0.120139845 0.207215363 2.177198663 0.073218269 0.033508312 62.61917535 -1.796707344 0.317657203 AGHSENGVEEDTEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGHSENGVEEDTEGR 15 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 0 178.85 6.95E-07 479790000 351690 356440 396030 436190 284740 370650 301080 347040 220450 FALSE TRUE 335066.3107 392761.6412 414188.3672 392343.3525 334398.5658 357814.2976 255144.7163 316651.3378 254636.2601 1.315862519 1.542441917 1.626588323 1.540799226 1.313240171 1.405197741 1.001996794 1.243543782 1 17.95807835 1.991524098 1.615434337 1.074956784 1.488302093 0.678938447 0.120581977 0.21744616 1.058195851 0.076035531 0.036823844 98.0672729 -1.991524098 0.413345308 AGHYAASIIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGHYAASIIIR 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 146.11 3.59E-05 581320000 501550 439460 358590 400000 532190 394060 526560 445670 474010 FALSE TRUE 477842.7255 484241.4736 375031.7062 359791.24 625003.7675 380413.6034 446223.6011 406644.7722 547517.0499 0.872744923 0.88443177 0.684968087 0.657132486 1.141523844 0.69479773 0.814994896 0.742707049 1 19.06254437 -1.049342757 4.176674658 1.000019072 0.817833216 0.150323953 0.140037249 17007922.61 4273050.168 3006.085026 0.030260106 0.089260074 1.049342757 -0.182185856 AGIIQDTWHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGIIQDTWHK 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 100.88 0.0037132 41562000 95744 81269 86467 95971 80385 90984 99545 97852 90668 FALSE TRUE 91218.37087 89550.4035 90431.59748 86323.81275 94404.11855 87833.20127 84357.58198 89283.56013 104728.3304 0.870999953 0.855073342 0.863487436 0.824264193 0.901419112 0.838676612 0.80548961 0.852525385 1 16.67629224 -1.837445968 5.256434252 1.020956558 0.850109349 0.763488977 0.025966135 0.006957549 0.000215161 0.027430224 0.006035068 0.014539653 1.837445968 -0.17084721 AGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTVK 42 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 15.975 0.090515 15150000 14573 17328 15476 21833 16431 17203 22967 15601 5127.8 FALSE TRUE 13884.16317 19093.7429 16185.58991 19638.30536 19296.5612 16607.2558 19462.96233 14234.89373 5922.993035 2.344112696 3.223664588 2.732670765 3.315605007 3.257907123 2.803862118 3.286001219 2.403327785 1 12.53211067 0.915045261 4.408738061 1.000448796 2.986866568 0.809593606 0.305929228 0.170790319 7.66789066 0.282475577 0.071817665 8.223283465 -0.915045261 1.986417772 AGKDLVSSLTSGLLTIGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGKDLVSSLTSGLLTIGDR 19 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 186.06 1.95E-14 256260000 450120 248381 502700 357010 499240 439430 689460 508180 669250 FALSE TRUE 428843.7197 273691.3063 525749.2922 321122.6765 586307.2979 424212.4289 584270.2142 463681.0652 773033.8719 0.554754113 0.354048272 0.680111585 0.4154057 0.758449687 0.548763055 0.755814506 0.599819855 1 19.5601721 -1.518647572 0.135117034 1.582604644 0.312055697 0.585433617 0.118938814 24.29939259 0.557669009 5.608392216 0.923059684 0.030293708 1.518647572 -1.270548946 AGKEPAKPS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.621)PS(0.379)R;AGKEPAKPS(0.5)PS(0.5)R;AGKEPAKPS(0.628)PS(0.372)R;AGKEPAKPS(0.5)PS(0.5)R 113.59 0.00059991 1858340000 3043670 2583690 2763040 3108420 1885240 3224560 3350000 3349380 2134120 TRUE FALSE 2899801.751 2846970.948 2889728.117 2795955.716 2214025.259 3112892.679 2838895.973 3056090.531 2465068.43 1.176357506 1.154925727 1.172270953 1.134230467 0.898159756 1.26280173 1.151649966 1.239758902 1 21.23319627 -1.281755035 3.456939984 0.999513964 1.149054053 0.186767182 0.097558706 5015698.746 3743411.736 16537.29842 0.021292409 0.052269093 1.281755035 0.149540089 AGKEPAKPS(ph)PSRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGKEPAKPSPSRDR 14 3 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.5)PS(0.5)RDR 80.316 0.091929 141020000 274050 233460 257230 289640 202780 301710 347530 336580 237670 TRUE FALSE 261096.1996 257249.8394 269024.2499 260524.8369 238144.7678 291261.707 294507.9157 307107.2709 274526.6497 0.951077791 0.93706691 0.979956774 0.948996526 0.867474134 1.060959682 1.072784431 1.118679265 1 18.06658668 2.154801953 8.421806174 1.07019542 0.940861858 0.708936378 0.040041935 0.131751319 11.78558214 0.013812277 0.010199082 142.8242501 -2.154801953 -0.129333562 AGKFPSLLTHNENMVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGKFPSLLTHNENMVAK 17 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 242.48 1.25E-20 2293340000 2560900 2095260 2398600 2741700 2085890 2637500 3235700 2906000 2399700 FALSE TRUE 2439851.332 2308769.376 2508578.183 2466099.107 2449668.556 2546162.714 2742034.537 2651535.234 2771833.22 0.880230208 0.8329395 0.905024936 0.889699672 0.883771988 0.918584385 0.989249468 0.956599847 1 21.40240902 2.002547447 1.026382886 0.993848649 0.866693066 0.818134417 0.022063202 0.197665561 0.383293719 0.017241865 0.008114236 100.588295 -2.002547447 -0.127155583 AGKPVICATQMLESMIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGKPVICATQMLESMIK 17 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 211.29 2.38E-12 484250000 1268230 1098690 1140230 1313110 959850 1239420 1461000 1343190 1138430 FALSE TRUE 1208283.281 1210647.76 1192510.673 1181113.688 1127247.536 1196498.575 1238097.617 1225573.163 1314971.91 0.91886623 0.920664351 0.906871595 0.898204501 0.857240773 0.909904284 0.941539213 0.93201471 1 20.32660055 0.926385574 1.067833242 0.998262051 0.904942846 0.699576348 0.019758077 0.37611216 0.878731647 0.020027132 0.006453621 8.440838175 -0.926385574 -0.093319204 AGLESGAEPGDGDS(ph)DTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(0.999)DT(0.001)TK;AGLESGAEPGDGDS(0.996)DT(0.004)TK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(0.988)DT(0.011)T(0.001)K 438.08 4.55E-170 5072350000 9835020 9095960 8041280 11402730 5531400 10637120 9888570 10153880 6008450 TRUE FALSE 9370138.096 10022848.67 8409980.642 10256505.92 6496074.409 10268753.87 8379887.03 9264752.438 6940209.739 1.350123188 1.44417086 1.211776151 1.477838034 0.936005489 1.479602815 1.207440026 1.334938393 1 22.72654783 -4.95878386 0.128473207 1.56E-10 1.445224587 0.264553209 0.161667421 175.0414329 1.439245807 45.52466602 1.110962725 1.10E-05 4.95878386 1.445224587 AGLESGAEPGDGDS(ph)DTTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.994)DT(0.002)T(0.004)KK;AGLESGAEPGDGDS(0.982)DT(0.009)T(0.009)KK;AGLESGAEPGDGDS(0.998)DT(0.001)T(0.001)KK 211.92 6.51E-17 1589360000 1523550 1377970 1350970 1718940 763370 1636370 1581670 1687690 837920 TRUE FALSE 1451534.811 1518386.71 1412913.311 1546148.885 896501.4863 1579702.097 1340357.192 1539906.917 967860.3541 1.499735788 1.568807631 1.459831788 1.597491703 0.926271525 1.632159113 1.384866305 1.591042458 1 19.88443938 -2.139191187 2.371977829 0.014944178 1.460569804 0.334727713 0.202668103 4426054.722 1432246.544 23388507.04 0.044302006 0.007257864 2.139191187 1.445625625 AGLESGAEPGDGDS(ph)DTTKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLESGAEPGDGDSDTTKKK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.98)DT(0.01)T(0.01)KKK 98.376 0.00042179 424550000 139660 86750 148270 138750 77079 155890 184490 181760 92626 TRUE FALSE 133058.5486 95589.92363 155068.3262 124802.5864 90521.5532 150491.4902 156342.6621 165844.1308 106989.967 1.24365445 0.893447547 1.449372595 1.166488689 0.846075158 1.406594416 1.461283394 1.550090494 1 16.70711599 2.179252206 24.99167709 1.400744899 1.117300764 0.205892914 0.220839263 93.17857929 39263.16113 0.076542931 0.056530722 151.095735 -2.179252206 -0.283444134 AGLGS(ph)PERPPK ddPTM_SK-BR-3_Trastuzumab_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 77.644 0.019411 2841240000 3368340 3012070 2985180 3416270 2363630 3238180 3465080 3448080 2719490 TRUE FALSE 3209125.244 3319003.357 3122053.456 3072860.049 2775846.324 3126041.015 2936418.405 3146147.836 3141214.62 1.021619224 1.056598723 0.993900078 0.978239446 0.883685663 0.99516951 0.934803495 1.00157048 1 21.58289109 3.438290769 2.649037739 0.958493487 1.03865122 0.393192486 0.036702581 0.213229005 3.024913189 0.009663715 0.014577971 2743.410327 -3.438290769 0.080157733 AGLGSGLSLSGLVHPELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLGSGLSLSGLVHPELSR 19 0 P49748;P49748-3;P49748-2;G3V1M7 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 241.08 2.39E-24 416110000 254900 218670 209500 210600 195270 223780 220410 241560 174840 FALSE TRUE 242851.3822 240952.7216 219105.7822 189430.0879 229325.0262 216030.4425 186782.4064 220407.7258 201953.2942 1.202512606 1.193111123 1.084932945 0.937989591 1.135534961 1.06970497 0.924879226 1.091379701 1 17.62366215 3.620741381 3.427709996 1.023348095 1.198892521 0.537616613 0.064535788 0.163603162 3.545854494 0.017178456 0.028014428 4175.816264 -3.620741381 0.175544425 AGLIPS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLIPSK 7 0 S4R337;Q5T2T1-2;Q5T2T1;K7EPM7;A0A0C4DGP3;D3DX46;Q13368 S4R337 MPP7;MPP3 MAGUK p55 subfamily member 7;MAGUK p55 subfamily member 3 1 AGLIPS(1)K 79.906 0.032889 247160000 1049200 965760 883870 1238600 586870 1107100 1098400 1088400 613650 TRUE FALSE 999606.3953 1064172.042 924396.3138 1114093.575 689219.9422 1068760.849 930818.9065 993093.926 708811.7079 1.410256609 1.501346592 1.30414933 1.571776485 0.972359704 1.507820536 1.3132104 1.401068739 1 19.43504291 -3.897848517 0.191541872 3.69E-17 1.456244488 0.336224647 0.164894896 91.20391631 1.308288137 36.02490752 0.40233925 0.000126518 3.897848517 1.456244488 AGLLAGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGLLAGDR 8 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 135.35 0.0019485 317530000 420030 344350 294190 305480 468750 297720 456930 352030 499910 FALSE TRUE 400176.0143 379439.6565 307678.9025 274772.57 550499.8516 287409.8817 387216.9364 321204.387 577433.4896 0.693025295 0.657114046 0.532838687 0.475851462 0.953356294 0.497736773 0.670582748 0.556262137 1 19.13929526 -1.815087028 3.16368358 1.094956211 0.634800098 0.421239213 0.136325549 10143480.15 16921294.75 6332358.086 0.028599509 0.015307807 1.815087028 -0.460156113 AGLQFPVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 186.11 9.79E-05 10270720000 10649760 8759450 6669720 8327590 11818330 7906220 11051690 9289620 11199490 FALSE TRUE 10146366.95 9652047.914 6975533.259 7490484.832 13879443.01 7632425.619 9365551.712 8476171.625 12936249.71 0.784336046 0.746124119 0.539223764 0.579030631 1.072910876 0.59000296 0.723977344 0.655226346 1 23.6249161 AGLQS(ph)LEASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGLQSLEASGR 11 0 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AGLQS(1)LEASGR;AGLQS(1)LEASGR 165.02 2.32E-05 680370000 408770 369490 382590 450960 402360 419110 464060 416580 483160 TRUE FALSE 389448.2522 407141.4511 400132.1299 405628.644 472531.4566 404596.1156 393259.124 380102.0468 558085.9852 0.697828404 0.72953176 0.716972188 0.726821054 0.846700095 0.72497093 0.704656871 0.681081512 1 19.09012789 -1.080706518 4.60177668 1.000013108 0.728042568 0.785519519 0.04457258 7.22E-06 1.44E-06 0.042602022 0.010040803 0.083041174 1.080706518 -0.27197054 AGLQSLEAS(ph)GRLEDEFDMFALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLQSLEASGRLEDEFDMFALTR 23 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AGLQS(0.178)LEAS(0.822)GRLEDEFDMFALTR 66.294 0.017112 6722400 6725.6 3411.1 6445 6788.5 9522.7 6120.1 10829 7287.4 10178 TRUE FALSE 6407.694217 3758.694968 6740.509625 6106.107083 11183.45587 5908.159402 9176.837162 6649.276623 11756.35226 0.545041019 0.319716089 0.57335043 0.519387898 0.951269205 0.502550389 0.78058542 0.565590115 1 13.52115287 2.944855266 10.62908742 0.728950834 0.465922904 0.395215992 0.164209054 0.73626098 140.2836229 0.044743451 0.047546754 880.7553019 -2.944855266 -0.26302793 AGLS(ph)PAEPLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLSPAEPLLSR 12 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 AGLS(1)PAEPLLSR 96.067 0.0059714 27380000 44514 31905 38634 43790 40547 35665 51092 43183 47982 TRUE FALSE 42409.91144 35156.15577 40405.40711 39388.146 47618.38396 34429.91211 43296.97703 39401.66759 55422.8035 0.765206896 0.634326551 0.729039395 0.710684836 0.859183963 0.621222853 0.781212322 0.710928807 1 15.75819207 -5 0.322825825 3.672320839 0.711781408 0.607515807 0.068843025 207.4656755 1.824933554 379.1885289 0.053940256 1.00E-05 5 -2.960539431 AGLS(ph)PANCQSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGLSPANCQSDR 12 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 AGLS(1)PANCQSDR;AGLS(1)PANCQSDR 175.66 2.84E-05 324290000 260480 269950 236100 302320 220610 288140 273460 273060 254060 TRUE FALSE 248167.6266 297458.2119 246925.4185 271930.2192 259084.3142 278161.6396 231738.6546 249149.4188 293458.3272 0.845665649 1.013630162 0.841432652 0.926639983 0.882865777 0.947874413 0.789681645 0.849011242 1 18.16279612 1.762567886 25 0.857456858 0.913749538 0.005260562 0.072348788 28.25688373 29446.59419 0.030228446 0.01676404 57.88524632 -1.762567886 0.056292679 AGLS(ph)PANCQSDRVNLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGLSPANCQSDRVNLEK 17 1 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 AGLS(1)PANCQSDRVNLEK 217.73 2.95E-15 230880000 170440 87501 154180 139780 138420 151720 191120 165120 163180 TRUE FALSE 162383.639 96417.45138 161249.3055 125729.0488 162560.4042 146465.8984 161961.1338 150661.2174 188485.121 0.861519669 0.511538793 0.855501509 0.667050259 0.862457489 0.777068755 0.859278085 0.799326847 1 17.52409112 1.123391354 0.360581976 1.014076687 0.691809981 0.337496678 0.107053151 1.387498902 0.54470551 0.168348536 0.102917776 13.28591148 -1.123391354 -0.322266707 AGLTMNDIDAFEFHEAFSGQILANFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AGLTMNDIDAFEFHEAFSGQILANFK 26 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;;;;; 323.36 1.90E-82 260970400 408400.3 291836.5 331989.1 350269.9 353631 288781.8 413475.2 363208.1 346928 FALSE TRUE 389096.0272 321574.9711 347211.1286 315060.1042 415304.1344 278781.2139 350391.9642 331403.6733 400727.8224 0.970973328 0.802477276 0.866451265 0.78621969 1.036374595 0.695687193 0.874388911 0.827004402 1 18.61226315 2.227753068 24.99998144 0.837504184 0.881342651 0.030212909 0.103035135 781.3153304 1807321.563 0.034488117 0.025720995 168.9480051 -2.227753068 0.043838467 AGLTVSDVDIFEINEAFASQAAYCVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGLTVSDVDIFEINEAFASQAAYCVEK 27 0 P09110;C9JDE9;H7C131 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 148.87 1.16E-07 30118000 79884 63616 74489 86511 67607 67758 98977 77125 85544 FALSE TRUE 76108.04163 70098.54273 77904.39433 77814.74992 79397.63939 65411.52347 83876.24081 70371.52613 98809.72662 0.770248479 0.709429579 0.788428397 0.787521154 0.803540725 0.661994782 0.848866237 0.712192297 1 16.59236544 -4.999999998 0.419088122 5.380534202 0.757345871 0.655510154 0.054286434 527.8748037 3.441031217 2128.49667 0.028360849 1.00E-05 4.999999998 -4.623188331 AGLVGPEFHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 199.68 4.94E-08 1841540000 2545380 2249050 2198140 2648420 2103230 2379530 2883440 2592560 2055550 FALSE TRUE 2425064.932 2478230.752 2298926.893 2382195.79 2470032.646 2297126.279 2443518.27 2365541.702 2374314.196 1.021374903 1.043766978 0.968248809 1.003319525 1.040314147 0.967490437 1.029146974 0.996305252 1 21.17907943 3.777362222 24.99893422 1.003161986 1.032570943 0.240628103 0.023225068 706.4850983 455168.0199 0.005451223 0.009827147 5989.109065 -3.777362222 0.029408957 AGLYGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 153.67 0.0010173 2403630000 4060840 3318380 2739820 3344580 4320090 3290360 4833690 3889610 4540360 FALSE TRUE 3868892.141 3656526.695 2865443.457 3008376.464 5073512.328 3176414.008 4096221.814 3549015.128 5244455.84 0.737710882 0.697217558 0.546375743 0.573629859 0.96740491 0.605670847 0.781057547 0.676717516 1 22.32236166 -4.999999566 0.260909386 2.952710282 0.677209229 0.392259579 0.118923675 201.5536866 1.97759257 210.8256645 0.145265808 1.00E-05 4.999999566 -2.275501053 AGMSSNQS(ph)IS(ph)SPVLDAVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.003)S(0.022)NQS(0.968)IS(0.92)S(0.088)PVLDAVPR;AGMSSNQS(0.944)IS(0.728)S(0.328)PVLDAVPR 190.83 2.45E-14 81438000 137412 149770 125328 161014 112438 132909 136772 142007 133306 TRUE FALSE 130916.8071 165031.7333 131074.4128 144828.5668 132047.1516 128306.328 115904.9194 129572.1143 153978.4136 0.850228314 1.071784865 0.851251871 0.940577081 0.857569243 0.833274775 0.752734859 0.841495319 1 17.23236859 2.760159343 1.641845342 0.827242572 0.947040039 0.088085011 0.08789002 0.487428037 2.6263984 0.032369725 0.031927809 575.6511051 -2.760159343 0.119797467 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.002)IS(0.648)S(0.349)PVLDAVPR;AGMSSNQSIS(0.5)S(0.5)PVLDAVPR;AGMS(0.006)S(0.006)NQS(0.316)IS(0.446)S(0.226)PVLDAVPR 340.57 9.75E-76 1927213000 1003225 1124710 884116 1158075 939801 1012335 1041840 1031848 957972 TRUE FALSE 955804.5425 1239319.228 924653.5931 1041663.101 1103701.997 977277.5851 882888.1733 941493.9189 1106529.405 0.86378594 1.120005688 0.835634 0.941378599 0.997444796 0.883191699 0.797889481 0.85085305 1 20.07761036 2.094583893 5.770081795 0.855773476 0.960456098 0.092800313 0.092110586 0.304078382 15.18776714 0.033231714 0.024304259 124.3322787 -2.094583893 0.104682621 AGMSSNQSIS(ph)SPVLDAVPRT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.017)S(0.019)NQS(0.02)IS(0.484)S(0.46)PVLDAVPRT(0.852)PS(0.148)R 68.326 0.013173 212740000 124900 97806 103350 112820 116230 114670 127850 119780 145200 TRUE FALSE 118996.2245 107772.5426 108088.6997 101479.1193 136500.4752 110698.9491 108344.1344 109291.4282 167716.8744 0.709506571 0.642586162 0.644471226 0.60506207 0.813874428 0.660034654 0.645994237 0.65164241 1 17.35566832 -1.111453868 4.531669722 1.000031001 0.670409228 0.768387776 0.056650916 1.66E-05 3.26E-06 0.051323769 0.012095992 0.077365285 1.111453868 -0.329621773 AGMSSNQSISS(ph)PVLDAVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.008)IS(0.119)S(0.874)PVLDAVPR;AGMSSNQS(0.007)IS(0.06)S(0.932)PVLDAVPR;AGMSSNQSIS(0.209)S(0.791)PVLDAVPR;AGMSSNQSIS(0.004)S(0.995)PVLDAVPR;AGMSSNQS(0.003)IS(0.024)S(0.974)PVLDAVPR;AGMSSNQS(0.004)IS(0.247)S(0.749)PVLDAVPR;AGMSSNQS(0.044)IS(0.113)S(0.842)PVLDAVPR;AGMSSNQS(0.016)IS(0.063)S(0.921)PVLDAVPR;AGMSSNQSIS(0.264)S(0.736)PVLDAVPR;AGMSSNQSIS(0.03)S(0.97)PVLDAVPR;AGMSSNQSIS(0.169)S(0.831)PVLDAVPR;AGMSSNQSIS(0.008)S(0.992)PVLDAVPR;AGMSSNQSIS(0.138)S(0.861)PVLDAVPR;AGMSSNQSIS(0.02)S(0.98)PVLDAVPR;AGMSSNQSIS(0.25)S(0.75)PVLDAVPR;AGMSSNQS(0.003)IS(0.135)S(0.861)PVLDAVPR 363.91 8.99E-108 4743985000 3701970 3807412 3225390 4097615 3349189 3467923 3723029 3638460 3474017 TRUE FALSE 3526985.215 4195391.611 3373277.322 3685714.955 3933286.501 3347827.957 3155012.548 3319857.154 4012749.814 0.878944708 1.045515371 0.84063983 0.918501059 0.980197292 0.834297704 0.786247011 0.827327221 1 21.93615978 2.224547726 24.92721939 0.837598693 0.93840778 0.133486069 0.078765962 285.6680784 508165.269 0.027378331 0.02032008 167.7056624 -2.224547726 0.100809086 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQSIS(0.065)S(0.935)PVLDAVPRT(0.667)PS(0.333)R;AGMS(0.003)S(0.003)NQS(0.009)IS(0.077)S(0.908)PVLDAVPRT(0.764)PS(0.236)R;AGMS(0.048)S(0.048)NQS(0.036)IS(0.352)S(0.517)PVLDAVPRT(0.784)PS(0.216)R;AGMSSNQSIS(0.02)S(0.98)PVLDAVPRT(0.976)PS(0.024)R;AGMSSNQSIS(0.009)S(0.991)PVLDAVPRT(0.893)PS(0.107)R;AGMS(0.003)S(0.003)NQS(0.009)IS(0.148)S(0.837)PVLDAVPRT(0.849)PS(0.151)R 162 3.93E-11 2410020000 924581 764232 895840 912413 1024730 856999 1033270 896824 1038940 TRUE FALSE 880877.8885 842108.1097 936915.1501 820695.5118 1203442.588 827320.9097 875625.6842 818293.3362 1200053.509 0.734032176 0.701725468 0.780727812 0.683882432 1.002824106 0.68940335 0.729655534 0.681880708 1 20.1946673 -1.580270995 2.832173803 1.016334555 0.747536492 0.406672973 0.094643284 31306286.05 33241955.97 3862265.956 0.021031128 0.026286272 1.580270995 -0.268798063 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPRTPSRER 25 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.075)S(0.075)NQS(0.095)IS(0.36)S(0.395)PVLDAVPRT(0.924)PS(0.076)RER 52.268 0.088768 204390000 54397 33281 62521 50888 85713 49652 76053 58298 86100 TRUE FALSE 51825.76161 36672.37174 65387.64969 45772.64156 100661.3201 47932.53879 64449.71804 53193.11806 99451.94826 0.521113588 0.368744629 0.657479827 0.460248817 1.012160363 0.481966815 0.648048823 0.534862504 1 16.60171201 -5 0.106304038 2.298810258 0.31985874 0.365287254 0.172900545 174.4117642 1.24360649 50.27410744 2.224822273 1.00E-05 5 -1.978951519 AGMSSNQSISSPVLDAVPRT(ph)PSRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPRTPSRER 25 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSISSPVLDAVPRT(0.847)PS(0.153)RER 157.11 9.85E-07 81195000 14081 8058.5 12582 11306 12979 9900.7 17866 14779 20037 TRUE FALSE 13415.41904 8879.670312 13158.89715 10169.4994 15242.53349 9557.836276 15140.21357 13484.87241 23144.23563 0.579644074 0.383666605 0.568560455 0.439396641 0.658588762 0.412968327 0.654167794 0.582644967 1 14.4983653 -0.312293915 0.416456126 1.101375924 0.485971345 0.734581627 0.089897515 2.970179317 0.548315504 0.525051518 0.049711136 0.48719866 0.312293915 -0.615404578 AGMSYYNS(ph)PGLHVQHMGTSHGITRPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 AGMS(0.016)Y(0.004)Y(0.014)NS(0.965)PGLHVQHMGT(0.092)S(0.087)HGIT(0.061)RPS(0.761)PR 54.389 0.095833 116220000 28979 30745 35579 33447 40418 33941 43971 35730 10050 TRUE FALSE 27609.2201 33877.95045 37210.33234 30084.84401 47466.8864 32765.61466 37262.41637 32601.29178 11608.50267 2.378361868 2.918373834 3.205437721 2.591621406 4.088975792 2.822553053 3.209924434 2.808397664 1 13.50289428 4.468249976 2.270888044 2.971879139 2.366810284 0.004235843 0.777678782 1.068854697 9.369402991 0.171338729 1.027286654 29393.41026 -4.468249976 -0.605068855 AGMTHIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 AGMTHIVR 8 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;;;;;; 167.24 0.00031378 3357940000 5077081 4307589 3914478 4071968 5422906 4038653 5830329 4750867 4857992 FALSE TRUE 4837097.443 4746537.216 4093960.688 3662646.04 6368659.089 3898793.434 4940805.23 4334855.9 5611344.588 0.862021102 0.845882327 0.729586398 0.65272164 1.134961325 0.694805563 0.880502908 0.772516432 1 22.41991508 AGNFIGWLHIDGANLSVLLVEHALSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGNFIGWLHIDGANLSVLLVEHALSK 26 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 261.58 4.53E-53 50576000 33981 28624 24279 32125 24696 29408 41036 32290 15521 FALSE TRUE 32374.78547 31540.81814 25392.21617 28895.73397 29002.97458 28389.59359 34775.20452 29462.51642 17927.91741 1.805830802 1.759312999 1.416350577 1.611773041 1.617754808 1.583541074 1.939723601 1.643387558 1 14.12992029 -1.192219095 2.629873635 0.994840656 1.691475728 0.688060845 0.141715445 733851.4221 868413.0053 31460.73051 0.037523707 0.064236357 1.192219095 0.696635072 AGNLGGGVVTIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGNLGGGVVTIER 13 0 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 ; 138.99 9.92E-05 232070000 215006 199029 190978 205365 202459 193920 222150 202782 240540 FALSE TRUE 204843.0925 219310.2814 199734.5302 184721.32 237767.7855 187204.5018 188256.9374 185025.3331 277841.7147 0.737265434 0.789335329 0.718878842 0.664843723 0.855767053 0.67378112 0.677569017 0.665937918 1 18.08390369 -0.943794018 5.343276319 1.000000622 0.726021 0.670820125 0.060963948 4.44E-07 8.78E-08 0.058029126 0.013677565 0.113816698 0.943794018 -0.273979622 AGNNMLLVGVHGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGNNMLLVGVHGPR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 109.22 0.00078023 248720000 386710 323150 315780 370810 418500 357770 439610 344350 396330 FALSE TRUE 368430.9847 356079.3524 330258.8253 333535.4743 491486.2675 345380.3352 372539.4205 314196.8885 457790.8322 0.804802016 0.777821064 0.721418609 0.728576133 1.073604434 0.754450091 0.813776499 0.686332854 1 18.80432905 AGNS(ph)DS(ph)EEDDANGRVELILEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;AGNS(1)DS(1)EEDDANGRVELILEPK 213.84 2.37E-24 130486000 457500 372300 438050 467870 282730 476980 536080 499240 318330 TRUE FALSE 435874.8817 410237.7933 458135.0258 420838.8187 332038.0225 460462.063 454291.1502 455523.899 367694.9906 1.185425129 1.115701339 1.245964828 1.144532369 0.90302569 1.252293544 1.23551085 1.238863489 1 18.48815 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGPDLPSLPSHALEDEGWAAAAPS(0.965)PGS(0.035)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.957)PGS(0.043)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.999)PGS(0.001)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.999)PGS(0.001)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.698)PGS(0.302)AR 358.7 1.51E-120 5159086000 1889088 1644739 1819979 2026531 2026003 1664563 2166315 1972664 1995482 TRUE FALSE 1799794.554 1812339.774 1903426.837 1822820.254 2379337.282 1606918.766 1835803.86 1799927.082 2304931.157 0.780845254 0.786288028 0.825806372 0.79083501 1.032281279 0.697165623 0.796467979 0.780902751 1 21.13629223 -2.207599413 2.273867033 1.570238852 0.807727013 0.3257261 0.085172512 4594241.624 850940.6563 13497475.14 0.019013277 0.006200127 2.207599413 -0.762511839 AGPGS(ph)SPLFSLLPGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.5)S(0.5)PLFSLLPGYR 85.457 0.0074919 15429000 26917 26910 26608 32088 28576 26280 34931 33749 29500 TRUE FALSE 25644.68675 29652.15959 27828.00312 28862.45328 33559.64535 25369.91701 29601.6344 30793.75865 34074.70933 0.752601776 0.870210199 0.81667617 0.847034468 0.984884274 0.744538031 0.868727422 0.903713025 1 15.05641373 -5 0.102547746 1.490330989 0.742963017 0.412261711 0.064617568 183.789316 1.275133833 19.25701643 0.94736421 1.00E-05 5 -0.747367971 AGPGSS(ph)PLFSLLPGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.017)S(0.983)PLFS(0.001)LLPGYR;AGPGS(0.09)S(0.91)PLFSLLPGYR;AGPGS(0.054)S(0.946)PLFSLLPGYR 171.11 5.29E-09 228109000 388601 375425 418266 436725 398313 418685 531128 453396 485950 TRUE FALSE 370232.6009 413681.2343 437443.9098 392824.5733 467778.6611 404185.8335 450094.6688 413694.2426 561308.6441 0.659588276 0.736994234 0.779328654 0.699837028 0.833371561 0.720077693 0.801866626 0.737017409 1 19.09843475 -5 0.166721366 1.975920034 0.680798939 0.752388004 0.046809205 59.11390126 0.553178193 19.09025091 0.159334157 1.00E-05 5 -1.295121095 AGPIWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 121.52 0.0033265 3898444000 7647490 6001140 5755390 6647710 7950590 6252480 8446290 6941940 8199780 FALSE TRUE 7286008.304 6612662.989 6019280.324 5979469.561 9337170.379 6035955.05 7157653.334 6334066.932 9471360.004 0.769267381 0.698174601 0.635524394 0.631321115 0.985832064 0.637284936 0.755715476 0.668760023 1 23.17514017 -1.309467654 3.162783551 1.001802395 0.724349783 0.40762722 0.105026089 19178224.48 26610286.42 328304.8181 0.022950068 0.049037954 1.309467654 -0.277452613 AGPLT(ph)PPKPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGPLTPPKPPR 11 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 AGPLT(1)PPKPPR;AGPLT(1)PPKPPR 116.24 0.0016422 1315660000 1510270 1348220 1420340 1570140 1081950 1496250 1697070 1592300 1255450 TRUE FALSE 1438882.53 1485605.151 1485463.994 1412306.544 1270641.737 1444434.487 1438150.803 1452869.771 1450138.774 0.992237816 1.024457229 1.024359889 0.973911304 0.876220787 0.996066386 0.991733225 1.001883266 1 20.46775954 3.223802526 20.63708241 0.971322542 1.012929409 0.205291479 0.037309431 45.76158592 63990.14586 0.010882184 0.013097356 1674.181452 -3.223802526 0.041606867 AGPPPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 94.302 0.016765 279273000 341530 307462 290759 340300 354133 262027 373127 332931 432853 FALSE TRUE 325386.5537 338792.7274 304090.5877 306092.3975 415893.6831 252952.9393 316199.6232 303777.7967 499977.6325 0.650802221 0.677615768 0.608208384 0.612212182 0.831824578 0.505928511 0.632427538 0.607582773 1 18.93150403 -1.30453309 3.273424471 1.001878962 0.641846232 0.659513876 0.081101752 17293597.45 25251221.72 323467.2563 0.017624486 0.049598314 1.30453309 -0.36003273 AGPTLTDENGDDLGLPPS(ph)PGDTSYYQDQVDDFHEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGPTLTDENGDDLGLPPSPGDTSYYQDQVDDFHEAR 36 0 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 1 AGPTLTDENGDDLGLPPS(0.547)PGDT(0.118)S(0.118)Y(0.109)Y(0.109)QDQVDDFHEAR;AGPTLTDENGDDLGLPPS(0.775)PGDT(0.047)S(0.059)Y(0.053)Y(0.066)QDQVDDFHEAR 87.203 0.0015017 65012000 44378 31589.4 35145.3 44953 37498 31743.7 45426 38875 37790 TRUE FALSE 42280.33989 34808.39577 36756.74677 40434.23903 44037.63933 30644.40771 38495.42939 35470.89891 43650.2802 0.968615544 0.797438083 0.842073558 0.926322554 1.00887415 0.70204378 0.881905665 0.812615606 1 15.41370329 2.254487147 24.99904297 0.838962868 0.896723272 0.078964645 0.093502629 613.6332466 963186.2177 0.030342091 0.025310355 179.6747903 -2.254487147 0.057760404 AGQATEGHCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGQATEGHCPR 11 0 C9J8T0;P57772-2;P57772 C9J8T0 EEFSEC Selenocysteine-specific elongation factor 0 ;; 113.61 0.0013687 61718000 52843 43497 48514 57857 64502 45548 57169 49102 55982 FALSE TRUE 50345.21611 47929.39375 50738.41489 52041.10444 75751.12838 43970.66134 48446.81907 44802.36857 64663.40264 0.778573568 0.741213604 0.784654268 0.804799969 1.171468331 0.679993003 0.749215431 0.692855104 1 15.9806618 3.227913602 4.282224631 0.835305763 0.762500633 0.06082263 0.146636981 0.724169265 30.90027393 0.042196639 0.054069357 1690.10467 -3.227913602 -0.07280513 AGQDMGLEHGFEKPLDSAMS(ph)AEEDTDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGQDMGLEHGFEKPLDSAMSAEEDTDVR 28 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 AGQDMGLEHGFEKPLDS(0.008)AMS(0.936)AEEDT(0.055)DVR 84.408 0.0024051 54057000 25194 25648 25090 30835 23826 27697 30832 28705 23705 TRUE FALSE 24003.12955 28261.56036 26240.40132 27735.40722 27981.24686 26737.84595 26128.01213 26191.43803 27381.05033 0.8766329 1.032157642 0.958341663 1.012941683 1.021920142 0.976509141 0.954237029 0.956553445 1 14.74089017 4.673931285 3.474981944 0.986383864 0.87035305 0.610327457 0.028100404 0.177875759 3.559000021 0.006836556 0.048400229 47198.83565 -4.673931285 -0.116030814 AGQEHLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGQEHLLR 8 0 Q3KQV9;A0A087X226;Q16222;Q16222-3;Q16222-2 Q3KQV9;Q16222 UAP1L1;UAP1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1;UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 108.98 0.0037068 179150000 170210 154390 171090 189950 170590 158300 170320 166790 168640 FALSE TRUE 162164.5106 170122.5165 178934.6457 170855.8651 200340.842 152818.0313 144334.5559 152184.9834 194791.8299 0.832501603 0.873355503 0.918594203 0.877120284 1.028486883 0.784519717 0.740968222 0.781269848 1 17.57157364 AGQTQPNPGILPIQPALT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGQTQPNPGILPIQPALTPR 20 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 AGQTQPNPGILPIQPALT(1)PR 160.71 2.64E-10 90374000 64596 62733 68719 75245 63444 69758 74432 68994 60165 TRUE FALSE 61542.6751 69125.56402 71869.83412 67681.22964 74508.61351 67342.26297 63076.03136 62952.5196 69495.08092 0.885568795 0.994682834 1.034171529 0.973899573 1.072142266 0.96902201 0.907633037 0.905855764 1 16.08462324 -0.705972134 7.926068653 1 0.966303958 0.028786048 0.058015921 0 0 0.057703933 0.013600948 0.196801256 0.705972134 -0.033696042 AGQVVTIWAAGAGATHSPPTDLVWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGQVVTIWAAGAGATHSPPTDLVWK 25 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 ; 206.47 3.74E-25 674370000 1188320 972350 1042810 1221830 1048230 1025020 1310540 1174790 1061970 FALSE TRUE 1132150.469 1071433.57 1090623.87 1099009.327 1231040.98 989523.3004 1110593.053 1071919.16 1226654.884 0.922957617 0.87345967 0.889104087 0.895940123 1.003575656 0.806684352 0.905383468 0.873855535 1 20.22629798 -1.390060485 4.315830684 1.000243412 0.895591134 0.308219891 0.048778785 0.000102487 1.45E-05 0.042369064 0.009963314 0.040732355 1.390060485 -0.104652277 AGRPQYDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGRPQYDTK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 128.86 0.00036988 799840000 862430 719340 648980 850060 721790 813060 919920 903310 810410 FALSE TRUE 821664.6431 792641.5638 678736.3749 764610.3538 847669.9475 784903.5283 779569.3085 824211.3877 936084.2438 0.877767838 0.846763065 0.72508044 0.816817887 0.905548783 0.838496678 0.832798238 0.880488474 1 19.83627885 0.828772842 2.464922898 0.999959566 0.836704106 0.55627782 0.04648386 0.530830849 5.746511247 0.044962288 0.012071409 6.741753075 -0.828772842 -0.163255461 AGS(ph)EECVFYTDETASPLAPDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGSEECVFYTDETASPLAPDLAK 23 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 AGS(0.879)EECVFY(0.107)T(0.013)DETASPLAPDLAK;AGS(0.997)EECVFY(0.003)TDETASPLAPDLAK;AGS(0.995)EECVFY(0.005)TDETASPLAPDLAK;AGS(0.998)EECVFY(0.002)TDETASPLAPDLAK 188.26 1.40E-17 144103000 543409 462076 487249 565704 298154 555761 578871 614982 336841 TRUE FALSE 517723.1335 509162.0697 509589.8486 508838.3592 350151.9632 536514.8572 490553.5973 561130.9159 389076.5819 1.330645836 1.308642291 1.309741764 1.307810294 0.899956408 1.3789441 1.260815017 1.442212001 1 18.56969462 -2.021476411 2.75623277 0.680355543 1.278930107 0.272365474 0.143741184 36694919.12 24612424.87 74064406.18 0.032272619 0.009517515 2.021476411 0.598574564 AGS(ph)FTGTSDPEAAPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGSFTGTSDPEAAPAR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 AGS(0.95)FT(0.043)GT(0.005)S(0.002)DPEAAPAR;AGS(0.997)FT(0.002)GTSDPEAAPAR 115.09 0.00055857 616740000 269820 223790 236790 282120 192153 276350 286260 271430 197278 TRUE FALSE 257066.1433 246594.4554 247647.0557 253760.7616 225664.4224 266779.9302 242585.7795 247662.1503 227870.8647 1.128122034 1.08216755 1.086786835 1.11361653 0.990317137 1.170750506 1.064575675 1.086853076 1 17.79785695 -5 0.23006557 0.510783817 1.101679354 0.282966351 0.045912931 199.9448395 1.999626274 45.57012769 0.070146698 1.00E-05 5 0.590895538 AGS(ph)ISTLDSLDFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.874)IS(0.126)T(0.001)LDSLDFAR 245.5 1.22E-17 71361000 164840 131470 131270 170660 132760 161400 166710 144110 125900 TRUE FALSE 157048.3399 144866.9425 137288.8593 153504.9326 155913.302 155810.6775 141275.3277 131490.9644 145423.929 1.07993465 0.996169911 0.944059621 1.055568596 1.072129622 1.07142393 0.971472361 0.904190702 1 17.14990515 1.577444859 5.55327833 0.947932172 1.033573652 0.38443696 0.046722505 0.145769833 9.449052845 0.026121157 0.01203969 37.79591461 -1.577444859 0.085641479 AGS(ph)PAPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSPAPSNR 9 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AGS(0.953)PAPS(0.047)NR 96.009 0.0080335 37104000 191970 177940 182130 212430 156790 173950 223310 191550 222490 TRUE FALSE 182895.9585 196072.2883 190480.8407 191076.1328 184134.1264 167926.0679 189239.9581 174776.8665 256992.6129 0.711677882 0.762949122 0.741191891 0.743508269 0.716495795 0.653427606 0.736363415 0.680085177 1 17.97136736 -0.855256988 5.13459018 1.000000369 0.721431847 0.883699272 0.032107618 1.34E-07 2.98E-08 0.030611007 0.007215074 0.139554232 0.855256988 -0.278568522 AGS(ph)PDVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGSPDVLR 8 0 Q8NDX6 Q8NDX6 ZNF740 Zinc finger protein 740 1 AGS(1)PDVLR;AGS(1)PDVLR;AGS(1)PDVLR;AGS(1)PDVLR;AGS(1)PDVLR 99.815 0.0068662 1129200000 4363780 4348140 3652400 4587780 3087800 4179980 4334710 4287400 3162150 TRUE FALSE 4157512.768 4791220.409 3819866.153 4126607.638 3626311.342 4035226.244 3673370.377 3911972.527 3652520.072 1.138258705 1.311757448 1.045816608 1.129797388 0.99282448 1.104778664 1.005708471 1.07103382 1 21.80046077 3.720986339 24.9965194 1.051689965 1.225008074 0.593427093 0.060212649 439.1004658 624548.123 0.01460464 0.022681696 5260.007208 -3.720986339 0.17331811 AGS(ph)PFS(ph)PPPSSSSLTGEAAISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 AGS(1)PFS(0.896)PPPS(0.095)S(0.007)S(0.001)SLTGEAAISR;AGS(1)PFS(0.626)PPPS(0.265)S(0.095)S(0.011)S(0.002)LT(0.001)GEAAISR 142.23 1.70E-07 222590000 542420 418860 502880 549200 422430 488850 541090 461170 407890 TRUE FALSE 516780.8816 461542.3102 525937.5454 493993.3726 496101.6583 471921.0019 458536.7827 420787.51 471143.498 1.096865146 0.979621521 1.116300124 1.048498758 1.052973585 1.001650249 0.973242302 0.893119637 1 18.84580701 1.907669808 1.90736003 0.946707746 1.054068573 0.535778902 0.044096421 0.256700304 1.736148937 0.026033195 0.012309538 80.84809814 -1.907669808 0.107360827 AGS(ph)PFSPPPSSSSLTGEAAISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.97)PFS(0.029)PPPSSSSLTGEAAISR;AGS(0.999)PFS(0.001)PPPSSSSLTGEAAISR;AGS(0.999)PFS(0.001)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.932)PFS(0.068)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.712)PFS(0.288)PPPSSSSLTGEAAISR 332.26 8.95E-81 3499780000 1011773 907466 943510 1064566 746564 1014632 1189952 1136724 856121 TRUE FALSE 963948.4954 999937.8171 986770.8668 957553.8031 876764.5252 979495.0394 1008402.967 1037186.42 988883.8722 0.974784323 1.011178203 0.997863242 0.968317747 0.88662031 0.990505627 1.019738511 1.048845521 1 19.91544159 1.774768608 3.937372938 1.026136797 0.973378099 0.330607197 0.034851175 0.27227984 8.301979234 0.018999486 0.009791309 59.5344859 -1.774768608 -0.052758698 AGS(ph)PLCNSNLQDSEEDIEPSYSLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(0.989)PLCNS(0.011)NLQDSEEDIEPSYSLFR;AGS(0.99)PLCNS(0.01)NLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR 187.32 8.96E-18 401742000 409096 314951 345473 401937 280290 370999 430148 416169 335169 TRUE FALSE 389758.8428 347044.865 361313.2788 361533.5291 329172.4873 358151.2116 364521.0224 379727.0361 387145.2967 1.006750815 0.896420202 0.933275651 0.93384456 0.850255679 0.925108001 0.941561283 0.980838562 1 18.56251559 1.22904562 2.336410652 0.99905164 0.925638101 0.336168333 0.038385816 0.34770497 3.230437625 0.035430011 0.010145652 16.94515791 -1.22904562 -0.07341354 AGS(ph)SSPEPWARPSCTPQEGGCPRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSSSPEPWARPSCTPQEGGCPRPK 25 2 Q86VE0 Q86VE0 MYPOP "Myb-related transcription factor, partner of profilin" 1 AGS(0.358)S(0.333)S(0.309)PEPWARPSCTPQEGGCPRPK 43.612 0.095778 81286000 74409 66940 74930 69037 66919 75444 77246 68786 41578 TRUE FALSE 70891.83403 73761.2621 78365.61462 62097.2696 78589.65241 72831.35536 65460.70398 62762.73318 48025.70389 1.476122749 1.535870505 1.631743176 1.293000718 1.636408132 1.516507817 1.363034764 1.306857122 1 15.55151914 0.95371161 1.064149816 1.003066255 1.516504545 0.737584966 0.097507733 0.272152875 0.639104079 0.083330473 0.026955316 8.989004752 -0.95371161 0.513438289 AGSATVLSGS(ph)IAGLEGGSQLALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AGSATVLSGSIAGLEGGSQLALR 23 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 AGSATVLSGS(1)IAGLEGGSQLALR;AGSATVLS(0.003)GS(0.997)IAGLEGGSQLALR;AGSATVLS(0.052)GS(0.948)IAGLEGGSQLALR;AGSATVLSGS(1)IAGLEGGSQLALR;AGSATVLS(0.011)GS(0.989)IAGLEGGSQLALR;AGSATVLS(0.003)GS(0.997)IAGLEGGSQLALR 328.75 1.87E-86 815260000 894237 814999 846704 955219 920406 837842 961741 922263 937091 TRUE FALSE 851968.1892 898048.3247 885526.2159 859198.5713 1080924.515 808827.3215 815009.7469 841504.7625 1082410.286 0.78710282 0.829674603 0.818105876 0.793782711 0.998627349 0.747246522 0.752958243 0.777436036 1 20.04581602 -2.245785318 2.340234355 1.711217515 0.810883702 0.407746346 0.070737942 4741805.467 853631.0932 17872315.38 0.017512571 0.005678252 2.245785318 -0.900333813 AGSES(ph)PHPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSESPHPGR 10 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 AGS(0.004)ES(0.996)PHPGR 64.224 0.047327 77266000 85653 78244 81698 79365 117460 52870 85111 68352 101490 TRUE FALSE 81604.35244 86217.15256 85443.93411 71387.07942 137944.9868 51039.09864 72125.75378 62366.73652 117228.5509 0.696113292 0.735462069 0.728866249 0.608956427 1.176718349 0.435381127 0.615257574 0.532009788 1 16.83896445 AGSES(ph)PHPGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSESPHPGRR 11 1 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 AGSES(1)PHPGRR 147.26 1.66E-05 17193000 11255 11455 13509 9173.1 12329 11182 15215 12738 16840 TRUE FALSE 10722.99846 12622.27752 14128.40101 8251.00256 14479.1737 10794.76454 12893.67231 11622.59319 19451.46119 0.55126956 0.648911534 0.726341372 0.424184203 0.744374603 0.554959056 0.662863945 0.597517743 1 14.24759091 -5 0.437354443 8.992316156 0.610165899 0.632224723 0.092530754 665.4075222 4.046064893 5134.40114 0.044088542 1.00E-05 5 -8.382150257 AGSGKNDHAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGSGKNDHAEK 11 1 P43487;F6WQW2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 78.096 0.018515 158275000 518890 339580 513050 453900 352104 487190 627560 699720 520260 FALSE TRUE 494363.098 374183.5881 536573.85 408273.1096 413510.8261 470318.4881 531814.1961 638448.8074 600939.2637 0.822650687 0.62266457 0.892891982 0.679391636 0.68810752 0.782638973 0.884971624 1.062418194 1 19.19685966 1.542707848 2.250555621 1.031051253 0.737475356 0.691372598 0.078098558 0.144461519 1.534446682 0.056455178 0.019742125 34.89055259 -1.542707848 -0.293575896 AGSIS(ph)TLDSLDFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.011)IS(0.988)TLDSLDFAR;AGS(0.014)IS(0.986)TLDSLDFAR;AGS(0.179)IS(0.821)TLDSLDFAR 374.66 2.81E-97 256038000 514540 391640 403440 510880 398200 472140 502710 423710 353070 TRUE FALSE 490218.7139 431548.5613 421938.1231 459525.3718 467645.9539 455789.6734 426012.3566 386607.7062 407822.2924 1.202040014 1.05817796 1.0346127 1.126778453 1.146690514 1.11761834 1.044602918 0.947980808 1 18.63758111 1.51238487 3.154505414 0.97571727 1.11301647 0.600706099 0.047273539 0.159846781 3.350476843 0.03436924 0.012729066 32.53755162 -1.51238487 0.1372992 AGSISTLDSLDFARYS(ph)DDGNRETDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGSISTLDSLDFARYSDDGNRETDEK 26 2 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.002)IS(0.002)T(0.002)LDS(0.08)LDFARYS(0.915)DDGNRETDEK;AGS(0.001)IS(0.001)T(0.001)LDS(0.032)LDFARYS(0.964)DDGNRETDEK 92.817 0.0047764 53032000 70552 53255 62337 64038 49886 68015 72606 74263 54343 TRUE FALSE 67217.14678 58681.74505 65195.21311 57600.77858 58586.10261 65659.6235 61528.6212 67760.13803 62770.23489 1.070844277 0.934865787 1.038632613 0.917644783 0.933342096 1.04603119 0.980219706 1.079494734 1 15.93779299 1.693781444 1.789721137 1.030537636 0.984249404 0.099907757 0.055508636 0.782030236 5.088151188 0.039497053 0.01529299 49.40619909 -1.693781444 -0.046288232 AGSMKDPLLDDHGDFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 185.33 3.52E-10 148290000 447520 370900 385600 442990 340550 393510 472660 444630 333550 FALSE TRUE 426366.6165 408695.1317 403280.1414 398459.8036 399941.8122 379882.65 400547.036 405695.8401 385275.2305 1.106654627 1.060787456 1.046732594 1.03422118 1.038067803 0.986003304 1.03963869 1.053002654 1 18.55552991 4.405531457 0.692315079 1.022990689 1.137566398 0.657030919 0.019165946 1.172963328 0.571757197 0.007896187 0.098225415 25440.84064 -4.405531457 0.11457571 AGSNEDPILAPS(ph)GTPPPTIPPDETFGGRVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSNEDPILAPSGTPPPTIPPDETFGGRVPR 31 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.5)GT(0.5)PPPTIPPDETFGGRVPR 106.19 8.68E-05 163950000 55436 23792 56650 34400 72589 41019 95715 56481 111190 TRUE FALSE 52815.65014 26216.43185 59247.45853 30942.04664 85248.49862 39598.50174 81111.91882 51535.22422 128432.7773 0.411231862 0.20412571 0.461311044 0.240920171 0.663759676 0.30832084 0.631551544 0.401262242 1 16.97065391 -4.99999997 0.15351896 3.214173905 0.226454825 0.641816223 0.141226619 71.87698614 0.647812857 48.15814462 0.575810696 1.00E-05 4.99999997 -2.98771908 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.144)GT(0.856)PPPTIPPDETFGGR;AGSNEDPILAPS(0.019)GT(0.981)PPPTIPPDETFGGR;AGSNEDPILAPS(0.28)GT(0.709)PPPT(0.011)IPPDETFGGR;AGSNEDPILAPS(0.04)GT(0.96)PPPTIPPDETFGGR 104.48 0.0036823 339178000 531561 489163 482409 556485 535876 515865 612480 538979 579710 TRUE FALSE 506435.165 539009.2658 504527.9298 500546.0705 629332.6047 498000.4657 519034.927 491783.1415 669608.4661 0.756315355 0.804961844 0.753467071 0.747520523 0.939851625 0.743718891 0.775131966 0.734433876 1 19.35295824 -1.123794034 4.288275611 1.000030859 0.782999088 0.569934643 0.059527189 18732100340 3827620209 7309352.946 0.012835798 0.075197944 1.123794034 -0.217031771 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGRVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGSNEDPILAPSGTPPPTIPPDETFGGRVPR 31 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.212)GT(0.788)PPPTIPPDETFGGRVPR;AGSNEDPILAPS(0.024)GT(0.97)PPPT(0.006)IPPDETFGGRVPR 156.12 4.47E-09 238350000 107731 38256 126187 66796 153260 105136 193189 122843 251140 TRUE FALSE 102638.7691 42154.32989 131972.7988 60081.53918 179988.4955 101495.114 163714.4699 112086.2157 290085.5086 0.353822463 0.145316911 0.454944473 0.207116651 0.620467035 0.349879987 0.564366247 0.386390262 1 18.1461187 -5 0.138985151 3.215464131 0.138277924 0.696359388 0.132413272 66.5228194 0.568187816 40.56208091 0.72265074 1.00E-05 5 -3.077186206 AGSPFS(ph)PPPSSSSLTGEAAISR ddPTM_SK-BR-3_Trastuzumab_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 AGSPFS(0.998)PPPS(0.001)S(0.001)SSLTGEAAISR;AGSPFS(1)PPPSSSSLTGEAAISR;AGSPFS(1)PPPSSSSLTGEAAISR;AGSPFS(1)PPPSSSSLTGEAAISR 212.85 1.68E-23 216915000 296194 226343 280816 293246 288816 263142 324698 275027 244753 TRUE FALSE 282193.4966 249407.609 293691.6914 263768.3549 339185.419 254029.3266 275159.3566 250944.1779 282708.0452 0.998179929 0.882209096 1.038851551 0.933006186 1.199772786 0.898557119 0.973298642 0.887644275 1 18.10895341 -1.615591504 8.032313723 1.000022012 0.973062742 0.005060803 0.09372706 3.37E-05 1.61E-06 0.082667887 0.019469101 0.024233073 1.615591504 -0.02695927 AGSRLS(ph)AEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSRLSAEER 10 1 Q86Y82;B1AJQ6 Q86Y82 STX12 Syntaxin-12 1 AGS(0.001)RLS(0.999)AEER 94.023 0.005079 118460000 141740 116710 143500 164570 156590 134270 167110 162470 170760 TRUE FALSE 135040.2311 128602.8817 150079.6169 148027.1109 183899.2464 129620.1962 141614.3003 148243.2655 197240.5887 0.684647273 0.65201023 0.760896213 0.750490109 0.932360057 0.657167965 0.717977477 0.751586002 1 17.58959694 -5 0.225616391 2.398923178 0.697215665 0.521595817 0.078743994 129.7421781 1.298015781 82.87906844 0.143406706 1.00E-05 5 -1.701707513 AGSSPCLGSSSAAS(ph)SPPPPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.548)S(0.451)PPPPASR 93.152 0.0020608 63118000 57408 47835 51311 60487 53940 57750 62733 57415 54578 TRUE FALSE 54694.43761 52709.44088 53663.6601 54406.73184 63347.11892 55750.10302 53161.92868 52387.43822 63041.67749 0.867591723 0.836104669 0.851240992 0.863027984 1.004845071 0.884337239 0.843282266 0.830996895 1 15.9440183 -2.141151052 2.256330963 1.269398638 0.870600097 0.393500013 0.049616529 5077708.295 1243105.884 6999806.607 0.013209086 0.007225185 2.141151052 -0.398798541 AGSST(ph)PGDAPPAVAEVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.001)S(0.016)T(0.983)PGDAPPAVAEVQGR;AGS(0.027)S(0.197)T(0.777)PGDAPPAVAEVQGR;AGS(0.016)S(0.101)T(0.883)PGDAPPAVAEVQGR 218.63 3.71E-18 486070000 643580 536260 619670 663250 625330 664590 762610 662440 716250 TRUE FALSE 613159.2489 590905.5037 648082.4824 596578.8499 734387.354 641575.0817 646259.8382 604433.2418 827322.3919 0.741137016 0.714238499 0.78334938 0.721095979 0.887667687 0.775483763 0.781146316 0.730589729 1 19.6580901 -5 0.236001752 2.29747535 0.739742242 0.673368803 0.050514229 95.55512374 0.954219258 59.4843055 0.078366 1.00E-05 5 -1.557733108 AGTEDEEEEEEGRRETPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGTEDEEEEEEGRRETPEDR 20 2 O95456;O95456-2;F8WBH7 O95456 PSMG1 Proteasome assembly chaperone 1 0 ; 245.61 3.19E-30 673680000 293030 162513 290138 258615 323883 269013 384980 321330 388170 FALSE TRUE 279179.0526 179073.2595 303441.1143 232618.5289 380368.0927 259697.0124 326244.2304 293192.6417 448365.4211 0.622659642 0.399391325 0.676771892 0.518814605 0.848343951 0.579208387 0.727630221 0.653914481 1 18.77431549 -5 0.104977939 2.28757905 0.364222606 0.554528885 0.111439762 114.097744 0.805882878 31.53849325 1.448801799 1.00E-05 5 -1.923356444 AGTEKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGTEKLR 7 1 A0A0G2JR78;Q9NY99-2;Q9NY99 A0A0G2JR78 SNTG2 Gamma-2-syntrophin 0 114.72 0.0053274 175120000 312360 224400 272400 323470 252190 296430 358760 343150 291970 FALSE TRUE 297595.3618 247266.6151 284889.8094 290954.181 296171.8562 286164.5548 304024.5729 313101.9668 337247.2164 0.882424961 0.733190974 0.844750662 0.862732639 0.878204005 0.848530517 0.901488754 0.928404896 1 18.36344701 1.334662056 0.461229347 1.004966514 0.809555461 0.6471134 0.040152276 0.556363141 0.325373616 0.045510683 0.027539407 21.61036269 -1.334662056 -0.195411053 AGTFIAPPVYSNITPYQSHLRS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.01)PY(0.005)QS(0.092)HLRS(0.893)PVR;AGTFIAPPVYSNIT(0.002)PYQS(0.003)HLRS(0.996)PVR 162.02 1.20E-11 2591000000 1801250 1445150 1846210 1857980 2292500 1801180 2370800 1933730 2405600 TRUE FALSE 1716108.482 1592412.428 1930860.555 1671212.32 2692311.274 1738804.685 2009090.917 1764402.35 2778648.162 0.617605534 0.573088903 0.694892063 0.601447979 0.968928456 0.625773608 0.723046172 0.634985881 1 21.40595174 -5 0.137420483 2.072040707 0.554349394 0.451505749 0.111242266 121.6338474 1.032027356 36.0785751 0.671105861 1.00E-05 5 -1.517691312 AGTFQAFEQFGQQLLAHGHYAS(ph)PEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 AGTFQAFEQFGQQLLAHGHYAS(1)PEIK;AGTFQAFEQFGQQLLAHGHYAS(1)PEIK 189.39 1.45E-17 74149000 177915 160134 174099 185905 149127 179623 208504 185370 69145 TRUE FALSE 169505.3105 176451.8367 182081.6114 167217.4762 175134.7016 173402.6105 176692.8854 169138.0201 79867.65346 2.122327416 2.209302878 2.279791674 2.093682097 2.192811407 2.171124391 2.21232098 2.117728677 1 16.28532371 0.683517036 3.891885034 1.000001561 2.18260045 0.981750675 0.050416222 0.855048027 10.40960788 0.045191285 0.011563807 4.825219077 -0.683517036 1.182598889 AGTGYAS(ph)PDRTHVLAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGTGYASPDRTHVLAAGK 18 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 AGT(0.006)GYAS(0.984)PDRT(0.009)HVLAAGK;AGT(0.108)GYAS(0.887)PDRT(0.005)HVLAAGK;AGT(0.461)GYAS(0.539)PDRTHVLAAGK 214.95 5.92E-19 2252370000 2910540 2458560 2673550 3070300 2418930 2938750 3372890 3237580 2659890 TRUE FALSE 2772964.542 2709090.059 2796134.912 2761667.611 2840790.626 2836980.351 2858293.683 2954080.332 3072372.156 0.90254839 0.881758433 0.910089914 0.898871449 0.924624519 0.923384345 0.930321438 0.961498211 1 21.55092155 1.169791312 0.457000613 1.004386117 0.890882626 0.930497235 0.008901224 0.221676755 0.126783698 0.010130465 0.00564691 14.78397815 -1.169791312 -0.113503491 AGTLSITEFADMLS(ph)GNAGGFRSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AGTLSITEFADMLSGNAGGFRSR 23 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 AGTLSITEFADMLS(0.666)GNAGGFRS(0.334)R 67.31 0.016368 6287500 6615.9 1746.1 5994.7 4152.8 8948.1 6423.7 10729 6356.9 11573 TRUE FALSE 6303.179518 1924.029575 6269.562925 3735.352654 10508.64581 6201.245658 9092.093998 5800.256136 13367.68173 0.471523757 0.143931432 0.469008991 0.279431597 0.78612328 0.463898362 0.680154882 0.433901424 1 13.70646167 -0.753886584 0.142722685 1.567428476 0.112239144 0.534583973 0.167328223 17.82630691 0.59270779 5.241167602 1.274387786 0.176243625 0.753886584 -1.455189332 AGTLSITEFADMLSGNAGGFRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGTLSITEFADMLSGNAGGFRSR 23 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 AGTLSITEFADMLSGNAGGFRS(1)R;AGTLSITEFADMLSGNAGGFRS(1)R;AGTLSITEFADMLS(0.014)GNAGGFRS(0.986)R 151.19 4.58E-08 795996000 438324 157657.6 434802 316995 738868 446776 843953 497034 1060862 TRUE FALSE 417605.2932 173723.0887 454738.1018 285130.0603 867726.3453 431304.0351 715192.4696 453511.068 1225375.061 0.340797937 0.14177136 0.371101156 0.23268799 0.708131227 0.351977161 0.583651889 0.370099803 1 20.22479196 -4.999999998 0.114794668 3.084205556 0.034242703 0.655738365 0.14676097 85.84804923 0.647518277 41.4860516 1.446694544 1.00E-05 4.999999998 -3.049962853 AGTQIENIDEDFRDGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGTQIENIDEDFRDGLK 17 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;; 304.13 4.63E-46 1034460000 1084240 886700 556867 731630 813680 691430 1046800 802220 615210 FALSE TRUE 1032990.124 977055.7381 582399.9028 658085.1624 955585.5344 667485.6057 887091.4342 731973.364 710613.6247 1.453659328 1.374946531 0.819573229 0.926080136 1.34473292 0.939308764 1.24834566 1.030058162 1 19.43870582 3.891249107 7.395946189 1.066739011 1.424233042 0.497131907 0.154270655 0.195448714 11.72600105 0.037974767 0.068901276 7784.82953 -3.891249107 0.357494031 AGTQIENIEEDFRDGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AGTQIENIEEDFRDGLK 17 1 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;; 226.65 1.83E-15 232304000 241805 208181 197605 263168 164072 221659 256479 267336 191962 FALSE TRUE 230375.3569 229394.8806 206665.3847 236713.8527 192686.1049 213982.8933 217348.418 243926.6426 221730.4866 1.03898819 1.034566262 0.932056696 1.067574677 0.869010427 0.965058511 0.98023696 1.100104214 1 17.75844762 1.267335126 24.97785138 1.050052203 0.988460464 0.16369838 0.061475616 342.2145243 297061.5496 0.039629447 0.014464624 18.50696168 -1.267335126 -0.061591739 AGVHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGVHIK 6 0 P12532;P12532-2;P12277;H0YJG0;H0YJK0 P12532;P12277 CKMT1A;CKB "Creatine kinase U-type, mitochondrial;Creatine kinase B-type" 0 ; 72.054 0.086609 652110000 2384400 2037510 1906940 2525000 2015360 2012350 2283600 2206620 1686840 FALSE TRUE 2271694.137 2245134.585 1994375.085 2271182.203 2366838.146 1942661.815 1935194.879 2013396.655 1948426.532 1.165912135 1.152280853 1.023582389 1.165649392 1.214743336 0.997041347 0.993209057 1.033344918 1 20.8938781 2.220934669 24.99980368 1.003737752 1.142927403 0.663864937 0.048966086 147.8888697 209757.2784 0.018305845 0.013549055 166.3162443 -2.220934669 0.139189652 AGVLAGHDNR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 163.64 6.40E-06 7021450000 8345910 6141510 5142650 6226000 9161520 4869590 8082020 7075870 8625650 FALSE TRUE 7951415.374 6767336.851 5378445.589 5600150.651 10759286.19 4700954.877 6848959.413 6456269.311 9963271.748 0.798072719 0.679228372 0.53982725 0.562079485 1.079894884 0.471828431 0.687420717 0.648006947 1 23.24818814 -1.266858927 4.230675407 1.000249664 0.684472306 0.261506102 0.167248848 8137230018 1410110558 20384865.4 0.03578929 0.054093001 1.266858927 -0.315777357 AGVLAHLEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;; 198.62 5.30E-08 4193390000 5377850 4891160 4826320 5084930 4341420 5275110 5510960 5387260 3712260 FALSE TRUE 5123649.688 5389574.765 5047611.546 4573783.176 5098562.273 5092431.618 4670161.836 4915522.955 4287938.321 1.194898178 1.25691518 1.177165147 1.066662539 1.189047484 1.18761774 1.089139229 1.146360462 1 22.03185272 -5 0.061566481 0.347075433 1.435977439 0.579330383 0.048386108 251.6155526 1.129008897 24.25278442 3.865689675 1.00E-05 5 1.088902007 AGVVGPELHEQLLSAEK ddPTM_SK-BR-3_Trastuzumab_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 ; 250.41 2.72E-21 426280000 1294190 1129390 1124700 1382430 964510 1257120 1501600 1420720 1109520 FALSE TRUE 1233016.204 1244476.125 1176268.607 1243465.51 1132720.239 1213585.619 1272503.341 1296314.225 1281578.695 0.962107289 0.971049324 0.917827842 0.970260753 0.883847588 0.946945844 0.992918614 1.011497952 1 20.28949064 1.672154202 3.920518746 1.004322335 0.944717511 0.536244739 0.026164472 0.151384186 5.456233316 0.014960651 0.0069381 47.00609807 -1.672154202 -0.059604824 AGWGS(ph)PCHLSGESVILLGPTVGTESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AGWGSPCHLSGESVILLGPTVGTESK 26 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 AGWGS(0.937)PCHLS(0.055)GES(0.008)VILLGPTVGTESK;AGWGS(0.985)PCHLS(0.013)GES(0.002)VILLGPTVGTESK 232 1.37E-35 168426000 344640 252700 316570 335700 319700 310600 441480 359750 394690 TRUE FALSE 328349.5502 278450.4173 331085.0476 301954.7982 375455.5788 299843.8441 374124.1177 328248.3828 455896.5094 0.720228261 0.610775497 0.726228521 0.662331893 0.823554406 0.657701557 0.820633872 0.720006352 1 18.79834684 -5 0.154883744 2.080356979 0.627158731 0.680890489 0.062687116 66.54606013 0.602382904 21.9314877 0.25263144 1.00E-05 5 -1.453198248 AGYTDKVVIGMDVAASEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 AGYTDKVVIGMDVAASEFFR 20 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;;;;;;;;;;; 197.31 1.52E-21 8923218000 7913981 4620754 6948160 6584779 7920454 6936261 10179691 8553815 9762734 FALSE TRUE 7539902.802 5091614.086 7266740.009 5922864.505 9301778.67 6696056.542 8626592.175 7804797.612 11276688.93 0.668627365 0.451516763 0.644403695 0.525230814 0.824867896 0.593796334 0.764993362 0.692117843 1 23.42684019 0.248189272 0.27070377 1.110032797 0.531814545 0.606610279 0.097056902 2.967986852 0.408476874 0.506421322 0.144896362 1.770880567 -0.248189272 -0.578218252 AHALSDETWGLVECHPHLALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHALSDETWGLVECHPHLALER 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 234.04 6.89E-31 337630000 95473 79266 96635 97819 117259 86419 121811 76943 8081.4 FALSE TRUE 90960.1805 87343.29552 101065.8103 87986.04828 137708.9325 83426.28836 103226.4947 70205.46302 9334.622238 9.744387955 9.356918072 10.82698451 9.425774931 14.75249121 8.937296683 11.05845444 7.520975271 1 13.18837592 0.882423998 2.82910948 1.003442098 10.46721642 0.774045384 1.642281193 0.204173018 3.36551445 1.458751123 0.38523479 7.628233841 -0.882423998 9.463774326 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 AHAS(1)PFSGALTPSAPPGPEMNR;AHAS(0.994)PFS(0.006)GALTPSAPPGPEMNR 190.8 1.06E-17 363140000 261190 237308 254222 294812 271392 235626 294441 273854 267037 TRUE FALSE 248844.0663 261489.955 265878.3302 265176.9377 318722.6789 227466.2125 249518.6177 249873.892 308447.7341 0.806762504 0.847760985 0.861988275 0.859714332 1.033311785 0.737454639 0.808949427 0.81010124 1 18.23466652 -2.336761346 2.276303598 1.918839659 0.842736317 0.290037056 0.075710045 5745154.398 530675.5775 27400311.81 0.018737075 0.004605096 2.336761346 -1.076103342 AHATGAGPAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AHATGAGPAGR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 115.78 0.0010771 51148500 27697.4 17305.3 26748.5 32049.4 31373.7 22191.4 31411 29708.3 32693.7 FALSE TRUE 26388.19879 19068.72974 27974.94518 28827.73342 36845.26335 21422.90625 26618.67505 27106.88376 37763.67202 0.698772057 0.504949035 0.740789857 0.763372095 0.975680101 0.567288749 0.704875178 0.717803177 1 15.20471143 -5 0.16780721 2.142670701 0.621007652 0.346733321 0.124100092 150.2753903 1.409994362 57.50373199 0.466019023 1.00E-05 5 -1.52166305 AHCGDPVSLAAAGDGS(ph)PDIGPTGELSGSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHCGDPVSLAAAGDGSPDIGPTGELSGSLK 30 0 Q5JSP0-2;Q5JSP0-3;Q5JSP0 Q5JSP0-2 FGD3 "FYVE, RhoGEF and PH domain-containing protein 3" 1 AHCGDPVSLAAAGDGS(1)PDIGPTGELSGSLK;AHCGDPVSLAAAGDGS(1)PDIGPTGELSGSLK 203.66 1.10E-25 258970000 282960 277430 256270 322530 277690 268330 305270 293210 233610 TRUE FALSE 269585.0416 305700.4324 268020.233 290108.6716 326119.0481 259037.6648 258695.4548 267534.978 269837.0457 0.999066088 1.132907573 0.993267 1.075125437 1.208577745 0.959978139 0.958709929 0.991468674 1 18.0417289 AHEAQDAGYR ddPTM_SK-BR-3_Trastuzumab_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 ; 112.13 0.0016622 453950000 282500 276090 265380 282840 221923 259300 308540 303890 256880 FALSE TRUE 269146.7849 304223.8849 277547.9355 254408.3858 260626.3009 250320.376 261466.5563 277279.7806 296715.6384 0.907086618 1.025304519 0.935400429 0.85741482 0.878370626 0.843637286 0.881202479 0.934496685 1 18.17872144 3.453237919 7.3144243 0.888327148 0.968569893 0.204418923 0.052396402 0.181712124 39.0177065 0.013287339 0.018300044 2839.474146 -3.453237919 0.080242745 AHEEQLK ddPTM_SK-BR-3_Trastuzumab_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 ; 143.85 0.0023936 473580000 1076220 1093060 889890 1290950 779020 1032080 1148700 1195880 571870 FALSE TRUE 1025349.213 1204444.057 930692.3367 1161181.253 914880.8414 996338.8108 973444.7177 1091162.407 660552.6789 1.552259564 1.823388346 1.408960052 1.757893489 1.385023285 1.508341186 1.473682189 1.651893092 1 19.3333141 -2.869179112 0.22019869 6.24E-12 1.674504939 0.602506633 0.143883426 32.57189345 0.753330171 15.71154476 0.26421549 0.001351515 2.869179112 1.674504939 AHFLDADPGFVHSDGTISHHDMYDYLHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHFLDADPGFVHSDGTISHHDMYDYLHLSR 30 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 94.006 0.0002627 64603000 24282 19038 22063 20864 32711 19006 32558 26811 20654 FALSE TRUE 23134.23798 20977.99384 23074.61037 18766.71108 38415.78804 18347.81745 27590.67913 24463.28671 23856.91683 0.969707785 0.879325438 0.967208401 0.786636061 1.610257868 0.769077479 1.156506489 1.025416942 1 14.54211999 AHFNAMFQPS(ph)SPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.625)S(0.331)PT(0.044)R 95.761 0.0023446 297750000 90182 102550 89158 94399 84441 101120 110490 107710 89698 TRUE FALSE 85919.27558 112999.9616 93245.98249 84909.83317 99167.48366 97618.18904 93632.72121 98278.34139 103607.9077 0.829273339 1.090649971 0.89998905 0.81953043 0.957142035 0.942188595 0.903721765 0.948560236 1 16.66077459 0.979720586 19.7468293 1.000000008 0.928111479 0.097174942 0.074836304 242.3640918 236003.5152 0.069986428 0.017496607 9.543783668 -0.979720586 -0.071888528 AHFNAMFQPSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.07)S(0.892)PT(0.038)R;AHFNAMFQPS(0.254)S(0.714)PT(0.032)R;AHFNAMFQPS(0.109)S(0.877)PT(0.014)R 151.41 4.47E-06 1159520000 492250 535230 429790 553010 488670 496180 482940 475040 412180 TRUE FALSE 468982.318 589770.5455 449496.2966 497420.3841 573893.8933 478997.1622 409258.6332 433442.9793 476098.7693 0.985052574 1.238756711 0.944124047 1.044784016 1.205409319 1.006087798 0.859608677 0.910405586 1 18.86090137 1.998224157 24.99242636 0.914016333 1.089215029 0.374816066 0.094343094 61.03097961 858932.3482 0.033979287 0.024723198 99.59193183 -1.998224157 0.175198695 AHFNLDESGVLSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AHFNLDESGVLSLDR 15 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;; 222.57 1.38E-12 319863000 267178 295246 229484 318909 258103 261183 272249 276306 201166 FALSE TRUE 254549.0254 325331.9031 240006.0684 286851.6614 303116.0815 252138.1672 230712.4149 252111.1818 232361.7959 1.095485704 1.400109264 1.032898147 1.234504409 1.304500511 1.085110254 0.992901669 1.084994118 1 17.82601336 2.066962414 5.823408744 1.028240499 1.220375884 0.417263429 0.103135414 0.178806587 11.27014556 0.037331022 0.02717266 116.6708641 -2.066962414 0.192135385 AHGCFQDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHGCFQDGR 9 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 105.4 0.0031047 31580000 31439 22635 25973 29419 31187 25511 33726 28428 35257 FALSE TRUE 29952.94078 24941.53223 27163.88774 26461.74623 36626.00293 24627.54767 28580.47928 25938.69361 40724.47549 0.735502187 0.612445757 0.66701627 0.649775004 0.899360949 0.604735785 0.701801041 0.636931312 1 15.3136085 -2.058542809 2.5069444 1.439795824 0.686355696 0.572870013 0.084527836 11842633.67 2732089.294 29906602.65 0.020407908 0.008738908 2.058542809 -0.753440128 AHGFTFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHGFTFTR 8 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU0;Q5JPT9;Q5JPU1 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 ; 117.4 0.0045947 0 102567 80892 66402 67780 99507 64118 89419 76154 87701 FALSE TRUE 97718.86118 89134.98677 69446.59738 60966.62563 116860.9893 61897.57758 75776.48926 69485.55204 101301.2232 0.964636538 0.8799004 0.685545497 0.601835039 1.153598996 0.611024977 0.748031336 0.68593004 1 16.62829207 3.953304691 4.866516243 0.769276372 0.935516902 0.103101856 0.173028094 0.356909059 19.45039509 0.041064556 0.079122555 8980.586316 -3.953304691 0.16624053 AHGGYSVFAGVGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AHGGYSVFAGVGER 14 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;; 157.38 5.31E-06 2379870000 1426890 1280430 1254910 1256850 1637960 1086530 1428390 1294230 1505950 FALSE TRUE 1359443.738 1410907.273 1312448.865 1130509.05 1923619.705 1048903.194 1210462.871 1180900.36 1739485.035 0.781520801 0.811106301 0.754504258 0.64991019 1.105855852 0.602996388 0.695874266 0.678879287 1 20.73022884 AHGLLAEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHGLLAEENR 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 95.573 0.0073299 427940000 271486 203857 205102 259671 375240 237430 329430 251359 379650 FALSE TRUE 258653.3948 224630.2601 214506.1296 233568.3777 440681.7372 229207.7396 279169.4031 229348.6734 438524.183 0.589826981 0.512241442 0.489154619 0.532623711 1.004920035 0.522679817 0.636611193 0.523001199 1 18.74229688 2.913358462 24.99761457 0.698736523 0.531934633 0.254321213 0.168594227 121.459254 35040.56747 0.047512782 0.050394929 819.1406183 -2.913358462 -0.16680189 AHGNSGMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHGNSGMVR 9 0 C9K025;P18077 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 122.44 0.00058567 54746000 38305.7 26197.6 14946.3 16987 56423 18717.1 49226 30507.9 38893 FALSE TRUE 36495.06548 28867.16522 15631.60264 15279.43449 66263.15334 18068.92213 41715.6696 27836.46654 44924.3278 0.812367536 0.642573114 0.347954069 0.340114927 1.474994876 0.402207958 0.928576378 0.619630118 1 15.4552093 AHGNVQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHGNVQDR 8 0 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 67.507 0.058915 20257000 16517 11936 15821 15301 28799 11768 20901 10418 32399 FALSE TRUE 15736.27414 13152.29197 16546.4085 13762.91441 33821.53648 11360.47121 17712.16858 9505.744691 37423.27145 0.420494348 0.351446879 0.442142225 0.36776353 0.903756812 0.303567026 0.473292897 0.254006246 1 15.19164806 -1.194813323 3.772727708 1.000482441 0.438805127 0.496758359 0.177273875 789993131.4 1328411812 4797473.467 0.039207473 0.06385379 1.194813323 -0.561677314 AHGVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AHGVDK 6 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;; 121.68 0.019546 1473130000 4772140 3933200 3804410 5202170 3204060 4043090 5033290 6053900 3934240 FALSE TRUE 4546570.4 4333997.552 3978845.962 4679237.988 3762847.05 3903076.78 4265369.168 5523788.422 4544341.846 1.000490402 0.953712924 0.875560443 1.029684418 0.828029047 0.858887142 0.938610983 1.215531007 1 22.11563993 1.311148069 9.859150926 1.107239878 0.929299845 0.472238761 0.079673751 0.268113227 34.05289259 0.049761116 0.018172416 20.47142474 -1.311148069 -0.177940034 AHIAQLCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 153.05 7.90E-05 789530000 2797060 1928990 1316260 1512580 2413480 1782720 3104080 2461370 2031350 FALSE TRUE 2664848.517 2125556.274 1376611.823 1360532.585 2834390.148 1720983.959 2630495.586 2245839.394 2346361.383 1.135736607 0.905894671 0.586700682 0.579847842 1.207993861 0.733469265 1.121095669 0.957158352 1 21.1619938 1.719157883 15.9968192 1.028823232 0.877413269 0.123171978 0.206852209 0.395768547 296.7309653 0.097542517 0.05388549 52.37908208 -1.719157883 -0.151409963 AHINNSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHINNSEK 8 0 Q9NVM9-2;Q9NVM9;H0YH12 Q9NVM9-2 ASUN Protein asunder homolog 0 87.308 0.015416 33883000 49296 41584 46927 47621 55073 47225 63109 55477 53321 FALSE TRUE 46965.87578 45821.45688 49078.64937 42834.04661 64677.71376 45589.58641 53480.56297 50619.13978 61589.74835 0.762559956 0.743978634 0.796863937 0.695473642 1.050137653 0.740213877 0.868335468 0.821876061 1 15.91040261 -4.999999698 0.067371564 1.703809677 0.541233902 0.342300627 0.092896828 338.143456 1.646606665 37.32618426 5.024503327 1.00E-05 4.999999698 -1.162575775 AHLDHIPDYTPPLLTTIS(ph)PEQESDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 AHLDHIPDYTPPLLTTIS(0.999)PEQESDER;AHLDHIPDYTPPLLTT(0.002)IS(0.997)PEQES(0.001)DER 195.51 1.21E-24 127465000 41628 44602 42115 50053 45074 46845 51875 41739 10625.3 TRUE FALSE 39660.32694 49146.99451 44046.01441 45021.57735 52934.89133 45222.7459 43960.516 38084.11189 12273.01726 3.23150584 4.004475304 3.588849709 3.668338144 4.313111456 3.684729269 3.581883336 3.103076537 1 13.58320235 0.677106411 1.496982523 1.00089582 3.746805152 0.904880289 0.277336431 0.315902042 1.065130916 0.254415225 0.073966232 4.754517065 -0.677106411 2.745909333 AHLLAEVIENLECDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHLLAEVIENLECDPR 16 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ; 192.4 5.40E-10 92652000 89119 73483 79662 85610 87671 77960 97745 87222 64132 FALSE TRUE 84906.52149 80971.00124 83314.5815 77004.32015 102960.7946 75260.22565 82832.20504 79584.37929 74077.26302 1.146188696 1.09306146 1.124698431 1.03951357 1.389910891 1.015969308 1.118186629 1.074342869 1 16.17674317 1.053883423 1.15500956 1.003254566 1.135554346 0.165014587 0.099818584 0.881205155 2.453578768 0.085314346 0.027140787 11.32096435 -1.053883423 0.13229978 AHLMEIQVNGGTVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHLMEIQVNGGTVAEK 16 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 142.32 1.52E-06 253030000 405250 427640 365480 451140 258753 408670 388620 410470 223333 FALSE TRUE 386094.6356 471217.0022 382237.6195 405790.5501 303879.4413 394517.6554 329328.8815 374527.0708 257966.341 1.496686095 1.826660797 1.48173447 1.57303681 1.177980973 1.529337719 1.276635084 1.451844722 1 17.97682331 1.023337323 0.164613839 0.746110983 1.864936784 0.546044052 0.153453085 3.612023625 0.460624652 1.539399823 1.079791179 10.55206173 -1.023337323 1.118825801 AHLMEIQVNGGTVAEKLDWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHLMEIQVNGGTVAEKLDWAR 21 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 215.98 3.82E-25 222830000 385190 205570 386020 350430 415200 373210 541180 444670 364550 FALSE TRUE 366982.8321 226517.8167 403719.3988 315204.1106 487610.7485 360285.6441 458613.0515 405732.3375 421082.5521 0.871522295 0.537941588 0.958765441 0.748556569 1.157993239 0.855617603 1.089128603 0.963545831 1 18.68374357 3.136304401 1.558474623 1.008428403 0.721518812 0.368930925 0.139078248 0.31926757 1.607259988 0.043643233 0.057849292 1368.687816 -3.136304401 -0.286909592 AHPEPGTWDSFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHPEPGTWDSFLEK 14 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;H3BPL6;P0DMM9-2 A0A0A6YYL2 SULT1A4;SULT1A3 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3 0 175.74 2.34E-06 64700000 92231 102740 75426 102570 60309 85748 90061 95298 67542 FALSE TRUE 87871.42341 113209.3228 78884.35671 92259.46873 70826.87051 82778.52526 76320.54037 86953.20191 78016.0684 1.126324682 1.45110264 1.011129609 1.182570086 0.90784978 1.061044564 0.978266938 1.114555036 1 16.25148368 3.717033348 24.78136665 1.034380832 1.288713667 0.490600234 0.106833636 471.9721883 543316.2978 0.026243904 0.040699645 5212.347336 -3.717033348 0.254332835 AHPPELK ddPTM_SK-BR-3_Trastuzumab_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 ;; 94.407 0.014223 773820000 1647770 1267260 1085490 1495280 1450070 1324050 1695740 1484810 1214410 FALSE TRUE 1569883.178 1396395.235 1135260.79 1344971.614 1702961.749 1278197.817 1437023.719 1354792.165 1402734.5 1.119159169 0.99548078 0.809319789 0.958821226 1.214029988 0.911218635 1.024444553 0.965822231 1 20.41981054 4.448381202 2.904821156 0.985085503 1.113529874 0.148228892 0.100973884 0.502982147 7.953429805 0.024547492 0.109362584 28078.9719 -4.448381202 0.128444371 AHQLVHEGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 110.84 0.00106 78991000 560190 593120 383960 510450 438380 523430 613440 596730 441410 FALSE TRUE 533710.9289 653559.6023 401564.9458 459138.5962 514833.3332 505303.4879 519848.4614 544477.1577 509861.6084 1.046776066 1.281837251 0.787595966 0.900516118 1.009751126 0.991060083 1.01958738 1.067892049 1 18.95974618 3.75120062 24.99967734 0.972116686 1.164306649 0.425357954 0.094739716 679.141614 1343217.35 0.02413442 0.043151635 5638.98085 -3.75120062 0.192189963 AHQLVMEGYNWCHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 185.86 2.35E-07 266340000 111320 140240 116600 121810 122170 106010 125560 110660 55417 FALSE TRUE 106058.1242 154530.6154 121946.2253 109565.4274 143476.4093 102338.8471 106403.5159 100970.0238 64010.78533 1.656878972 2.414134035 1.905088724 1.711671351 2.241441166 1.598775059 1.662274809 1.577390798 1 15.96602739 1.018899253 0.572055645 0.991768685 2.024510217 0.60220323 0.243331224 0.565669434 0.452364737 0.243752262 0.109355471 10.44477895 -1.018899253 1.032741532 AHQSES(ph)YLPIGCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHQSESYLPIGCK 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 AHQS(0.355)ES(0.597)Y(0.048)LPIGCK 113.65 0.00051869 95980000 221560 165100 188430 221980 189880 193090 245280 227760 182840 TRUE FALSE 211087.2979 181923.8777 197069.7019 199666.1487 222995.0119 186403.2449 207858.0311 207816.127 211193.8934 0.999495272 0.861406903 0.93312216 0.945416297 1.055878124 0.882616642 0.984204741 0.984006325 1 17.68820859 2.990618977 24.28544849 0.975292433 0.927738902 0.156786028 0.053152371 573.1404243 1483744.307 0.014882412 0.016885407 978.631019 -2.990618977 -0.04755353 AHQVVEDGYEFFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 168.5 3.48E-06 1324610000 1749030 2165840 1699290 2186740 1321140 1891190 1703890 1933900 982540 FALSE TRUE 1666356.818 2386541.558 1777204.127 1966924.741 1551546.398 1825697.616 1443930.286 1764557.464 1134907.285 1.468275726 2.102851563 1.565946532 1.733114913 1.367112907 1.608675563 1.272289204 1.554803187 1 20.11414301 1.361998719 0.358996813 0.979797197 1.813166701 0.493821618 0.205945424 0.916237872 0.378326342 0.293756216 0.21594456 23.0143503 -1.361998719 0.833369504 AHQVVEDGYEFFAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHQVVEDGYEFFAKR 15 1 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 98.312 0.0019324 128870000 366950 233720 387750 325750 367180 340760 554050 409250 322070 FALSE TRUE 349605.0007 257536.3337 405528.721 293004.9911 431216.0757 328959.3958 469519.4967 373413.9004 372014.9707 0.93976057 0.692274113 1.090087101 0.787616129 1.159136351 0.884263865 1.262098393 1.003760412 1 18.50500115 2.883806163 1.070485367 1.090814875 0.838585999 0.21025515 0.14968476 0.547489045 1.336675226 0.065190061 0.070082741 765.2549772 -2.883806163 -0.252228875 AHS(ph)HEEASRPAATSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AHSHEEASRPAATSTR 16 1 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 AHS(1)HEEASRPAATSTR;AHS(1)HEEASRPAATSTR;AHS(1)HEEASRPAATSTR;AHS(1)HEEASRPAATSTR;AHS(1)HEEASRPAATSTR 236.95 5.79E-20 850023000 296135.8 288959.1 288205.2 333577.2 321732.8 307307 369835.8 270680.3 81850.3 TRUE FALSE 282138.0476 318404.3608 301419.6935 300045.3861 377842.8985 296664.8815 313410.5562 246978.098 94543.22649 2.984222753 3.367817798 3.188168044 3.173631758 3.996509454 3.137875579 3.314997466 2.612329906 1 16.52868648 0.83733193 2.151637115 1.000786059 3.308028291 0.880410722 0.269279809 0.183449162 1.577561444 0.244004465 0.066878632 6.875937645 -0.83733193 2.307242232 AHS(ph)IAGFSPECPEDPVGQNVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHSIAGFSPECPEDPVGQNVVK 22 0 E7EV07 E7EV07 ARHGEF4 1 AHS(0.805)IAGFS(0.195)PECPEDPVGQNVVK;AHS(1)IAGFSPECPEDPVGQNVVK 206.94 5.59E-23 136334000 131138 114521 123813 143568 100029 136348 155591 133212 90231 TRUE FALSE 124939.3666 126190.8201 129489.9485 129136.2719 117474.0259 131626.2346 131852.7353 121547.2511 104223.5626 1.198763154 1.210770548 1.242424892 1.239031449 1.127135006 1.262922042 1.265095262 1.166216621 1 16.66932195 0.925779519 6.513327515 1.000004467 1.220720163 0.75712488 0.039300644 0.407659857 35.33288272 0.037415805 0.009393835 8.429067252 -0.925779519 0.220715696 AHS(ph)IQIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 AHS(1)IQIMK 81.017 0.015427 181240000 322160 289640 310690 349060 201800 344490 371180 345410 173960 TRUE FALSE 306932.1353 319154.6453 324935.4438 313971.8256 236993.8561 332560.2249 314549.6738 315164.0693 200936.8283 1.527505624 1.588333249 1.617102482 1.56253997 1.179444595 1.655048642 1.56541574 1.568473395 1 17.61638248 -1.302966975 3.748385461 0.998689029 1.537966707 0.621830412 0.130572641 9565399.341 3325617.107 101331.1005 0.028900297 0.049777494 1.302966975 0.539277677 AHS(ph)PAEGASVESSSPGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHSPAEGASVESSSPGPK 18 0 C9J4C4;Q8NFG4-3;Q8NFG4-2;Q8NFG4 C9J4C4 FLCN Folliculin 1 AHS(0.959)PAEGAS(0.038)VES(0.001)S(0.001)S(0.001)PGPK 57.499 0.027625 0 73052 57464 64881 68082 43114 81043 74496 68269 35954 TRUE FALSE 69598.97674 63319.64693 67855.85803 61238.26801 50633.06795 78236.46059 63130.26699 62291.00444 41529.56269 1.67588995 1.524688507 1.633916989 1.4745705 1.219205421 1.883873933 1.520128383 1.499919585 1 15.34185106 0.672795942 2.492574131 1.000101017 1.566339509 0.52501838 0.166649273 1.74646949 12.34190465 0.147687052 0.039458307 4.70756085 -0.672795942 0.566238492 AHS(ph)SPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_SK-BR-3_Trastuzumab_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 1 AHS(0.967)S(0.033)PAS(0.001)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR 152.96 2.60E-13 240880000 40817 28418 38672 38139 49953 33709 58410 49508 38167 TRUE FALSE 38887.6613 31313.82651 40445.14945 34305.19526 58664.78738 32541.64888 49498.48173 45172.81706 44085.74343 0.88209154 0.710293716 0.917420152 0.778147142 1.330697473 0.738144496 1.122777521 1.024658167 1 15.42802457 AHSAPSSGTSSRPGS(ph)IR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHSAPSSGTSSRPGSIR 17 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AHSAPS(0.006)S(0.029)GT(0.025)S(0.033)S(0.023)RPGS(0.883)IR;AHSAPSS(0.006)GT(0.006)S(0.001)S(0.001)RPGS(0.984)IR 102.07 0.00058488 275230000 86287 71518 75152 95621 96549 73252 106393 85903 93954 TRUE FALSE 82208.38451 78805.76551 78597.79354 86008.99541 113387.115 70715.26487 90160.79381 78380.87792 108523.9065 0.757514056 0.72616042 0.72424405 0.792535011 1.044812325 0.65161002 0.830792005 0.722245268 1 16.72765336 -5 0.265224897 2.445311784 0.762572569 0.28845069 0.105852132 257.5307158 2.514780286 203.81933 0.125621715 1.00E-05 5 -1.682739215 AHSIQIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;; 101.54 0.005321 1956480000 4840200 3875320 3730690 4336150 4678180 3947740 5329890 4365690 4500880 FALSE TRUE 4611413.338 4270219.514 3901745.827 3900271.964 5494053.111 3811028.774 4516717.39 3983407.04 5198853.483 0.887005828 0.821377161 0.750501209 0.750217712 1.056781679 0.733051775 0.868791053 0.766208752 1 22.30976207 AHSNPMADHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHSNPMADHTLR 12 0 Q9UBP6;F8VSD9;H0YHX0;Q9UBP6-2 Q9UBP6 METTL1 tRNA (guanine-N(7)-)-methyltransferase 0 ; 67.252 0.039104 35980000 16942.1 15496.5 16914.8 15571.3 21070.9 14960 21167.6 15575.7 17637.9 FALSE TRUE 16141.28051 17075.61097 17690.36031 14006.04334 24745.65829 14441.93145 17938.09385 14211.80914 20373.09545 0.792284145 0.838145141 0.868319709 0.687477432 1.214624373 0.708872713 0.880479547 0.697577311 1 14.31437758 4.147446353 0.960566916 0.863554386 0.788008442 0.023440562 0.157836069 4.969091971 6.516449447 0.049164944 0.321300766 14042.56211 -4.147446353 -0.075545945 AHSSMVGVNLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHSSMVGVNLPQK 13 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 128.08 0.00016945 1513020000 960010 759150 821120 786910 1412060 809140 1455280 1159870 1575800 FALSE TRUE 914632.2299 836508.2481 858769.1642 707808.3118 1658322.817 781119.2789 1233250.308 1058305.634 1820167.016 0.502499068 0.459577742 0.471807893 0.38886998 0.911082776 0.429147035 0.677547883 0.581433256 1 20.79563941 -4.999999993 0.14096991 2.617766287 0.379880488 0.522381169 0.142474223 100.5500875 0.865872176 45.36809748 0.765280345 1.00E-05 4.999999993 -2.237885799 AHSSPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_SK-BR-3_Trastuzumab_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 AHSSPASLQLGAVS(0.999)PGT(0.001)LTPTGVVSGPAATPTAQHLR;AHS(0.067)S(0.18)PAS(0.284)LQLGAVS(0.469)PGTLTPTGVVSGPAATPTAQHLR 151.67 3.27E-13 480170000 59585 37854 53847 53716 83882 47246 65396 53039 77313 TRUE FALSE 56768.53514 41711.36564 56315.93821 48316.36563 98510.99424 45609.85917 55418.63912 48394.62398 89302.30518 0.635689471 0.467080503 0.630621327 0.54104276 1.103118156 0.510735519 0.620573444 0.54191909 1 16.4464098 AHT(ph)PLNTPDPSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AHT(1)PLNTPDPSTK 110.12 0.0039861 130220000 213450 220000 197330 262280 146870 237050 268270 200050 96200 TRUE FALSE 203360.6415 242418.2501 206377.7757 235915.1161 172484.0815 228840.8991 227340.4844 182532.5615 111118.2047 1.830128934 2.181624972 1.857281408 2.123100502 1.552257634 2.059436613 2.045933743 1.642688181 1 16.76173567 0.918344554 3.511370094 1.000703653 1.962168507 0.739031705 0.179177172 0.160425429 4.695697572 0.157762787 0.040753032 8.285992851 -0.918344554 0.961464854 AHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AHTPTPGIYMGR 12 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(1)PTPGIYMGR;AHT(0.999)PT(0.001)PGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR 174.94 0.00010679 3994190000 2421670 3543880 2040370 3353170 1709510 2606870 2228680 2131900 837080 TRUE FALSE 2307202.458 3905005.401 2133922.983 3016102.981 2007648.003 2516593.438 1888653.933 1945219.534 966890.0912 2.386209642 4.038727293 2.206996433 3.119385552 2.076397329 2.602770947 1.953328461 2.011831078 1 19.88299238 1.475946644 0.401845118 0.951679337 3.206255366 0.548766399 0.534199008 0.704092816 0.335107895 0.622133866 0.456024039 29.91897039 -1.475946644 2.254576028 AHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.991)PT(0.009)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.818)PT(0.182)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.971)PT(0.029)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.985)PT(0.015)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.987)PT(0.013)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.82)PT(0.18)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.948)PT(0.052)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.973)PT(0.027)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.939)PT(0.061)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.948)PT(0.052)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.968)PT(0.032)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.877)PT(0.123)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.953)PT(0.047)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.419)PT(0.419)PGIY(0.157)MGRPT(0.006)HSGGGGGGGGGGGGGGGGR;AHT(0.787)PT(0.213)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.817)PT(0.183)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.838)PT(0.162)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 334.24 4.60E-117 16269779000 1958110 1949772 2144963 2302207 1787293 2249746 2589388 1836891 871376 TRUE FALSE 1865554.021 2148455.984 2243311.675 2070784.778 2098996.333 2171836.732 2194329.303 1676043.086 1006504.54 1.85349787 2.134571578 2.228814264 2.057402323 2.085431561 2.157801228 2.180148441 1.665211651 1 19.94092225 0.949525073 3.314625369 1.001537126 2.09488922 0.923094804 0.102389072 0.071114311 1.988530332 0.104353238 0.027128633 8.902768345 -0.949525073 1.093352094 AHTDFFEAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHTDFFEAFK 10 0 P61201;P61201-2;B4DIH5;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 137.98 7.69E-05 323550000 936530 860780 779780 1014700 771500 856730 1056160 970780 694680 FALSE TRUE 892262.0829 948494.4606 815533.6843 912700.4282 906049.3557 827061.2253 895023.3943 885773.3568 802407.4265 1.111981337 1.18206092 1.016358595 1.137452618 1.129163721 1.030724789 1.11542262 1.103894764 1 19.61397543 -4.999999984 0.118923539 0.652371704 1.161550277 0.311574559 0.048370414 170.6033743 1.319055533 14.32283397 0.445041888 1.00E-05 4.999999984 0.509178573 AHTMTDDVTFWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHTMTDDVTFWK 12 0 A0A087WVQ6;Q00610-2;Q00610;J3KSQ2 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 82.362 0.015157 332550000 1508300 1463700 1161200 1346700 2129900 1317800 1500500 1339600 1610600 FALSE TRUE 1437005.648 1612852.694 1214442.169 1211327.157 2501353.886 1272164.256 1271571.166 1222297.522 1860363.622 0.772432674 0.866955618 0.652798278 0.651123868 1.344551063 0.683825592 0.683506789 0.657020761 1 20.8271532 AHTPTPGIY(ph)MGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.322)PT(0.322)PGIY(0.339)MGRPT(0.008)HS(0.009)GGGGGGGGGGGGGGGGR 61.958 0.036943 116670000 17943 10793 18076 16728 14567 18407 19757 19898 25055 TRUE FALSE 17094.86995 11892.81897 18904.80248 15046.46966 17107.48019 17769.56097 16742.70679 18155.62563 28940.40144 0.590692219 0.410941742 0.653232213 0.519912265 0.59112795 0.614005338 0.578523654 0.627345328 1 14.82079731 -5 0.218492696 3.231941829 0.504830578 0.825348601 0.062721989 54.76182339 0.547436384 53.6234845 0.111956743 1.00E-05 5 -2.727111251 AHVDEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHVDEFK 7 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 120.65 0.0045151 338680000 907600 884080 805320 983680 650090 906130 933430 991690 488180 FALSE TRUE 864699.5467 974168.7571 842244.7186 884798.6175 763465.4902 874750.4909 791018.1099 904852.3663 563884.4611 1.533469365 1.72760348 1.493647683 1.569113318 1.353939579 1.55129384 1.402801752 1.604676895 1 19.10504006 -3.044653568 0.21054608 1.39E-16 1.631717668 0.712563379 0.104876963 28.67651073 0.597620272 13.06382795 0.218381626 0.000902291 3.044653568 1.631717668 AHVIVMAATNRPNSIDPALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AHVIVMAATNRPNSIDPALRR 21 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 145.05 7.32E-08 1190140000 388380 287870 372760 365000 422300 354400 472240 393170 362950 FALSE TRUE 370022.0471 317204.2803 389851.4147 328309.5065 495948.9863 342127.0391 400191.1147 358741.9505 419234.4323 0.882613685 0.756627452 0.929912681 0.783116751 1.182987245 0.816075715 0.95457597 0.855707267 1 18.67739769 AHYNSSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AHYNSSNK 8 0 Q92947-2;Q92947 Q92947-2 GCDH "Glutaryl-CoA dehydrogenase, mitochondrial" 0 101.54 0.005321 25465000 72893 56851 49611 51000 78935 39172 67998 61058 93625 FALSE TRUE 69447.49235 62644.18153 51885.71342 45873.38311 92701.23901 37815.46382 57623.65623 55711.43783 108143.8868 0.642176774 0.579266969 0.479784063 0.424188407 0.857202767 0.349677313 0.532842474 0.515160306 1 16.72259259 -1.415166579 3.000976154 1.007906982 0.549468028 0.522757526 0.135852926 27547331.12 33528519.71 1864737.349 0.030423326 0.03844443 1.415166579 -0.458438954 AIAGDEHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIAGDEHKR 9 1 H0YDU8;P53041;A8MU39;M0R196;A0A087WY80;E7EU14 H0YDU8 PPP5C;PPP5D1 Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5;Protein PPP5D1 0 ; 138.66 8.46E-05 196872000 645380 544290 566440 660090 517310 608000 694830 663830 564990 FALSE TRUE 614874.1664 599753.7698 592411.8343 593736.4991 607528.7002 586944.8075 588820.9221 605701.526 652605.7636 0.942183169 0.919013903 0.907763718 0.909793527 0.930927574 0.899386491 0.902261296 0.928127761 1 19.3158522 -1.660589885 6.049068384 1.000734206 0.917027726 0.788966232 0.013418784 0.000141989 7.97E-06 0.013884543 0.003244247 0.021847921 1.660589885 -0.08370648 AICDHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 AICDHVR 7 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;;;;;;;; 183.89 0.000636 3601453000 5931245 3982563 2427226 2955478 6472540 3283094 6277240 4628202 5947800 FALSE TRUE 5650886.803 4388390.697 2538516.713 2658387.736 7601348.927 3169399.632 5319531.749 4222932.097 6870154.447 0.822526895 0.638761578 0.369499221 0.386947303 1.106430574 0.461328731 0.774295802 0.614677898 1 22.7119111 2.805578688 24.99999949 0.749899659 0.588002749 0.203262415 0.220495343 415.5372409 155008.0435 0.065457849 0.069428525 639.1145256 -2.805578688 -0.16189691 AICGLT(ph)PGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AICGLTPGRR 10 1 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 AICGLT(1)PGRR;AICGLT(1)PGRR 107.09 0.0013653 135390000 427450 412830 467220 430880 444450 448840 528750 489370 491850 TRUE FALSE 407245.2856 454897.8463 488642.4991 387567.1238 521961.9393 433296.5583 448079.4763 446518.1685 568123.586 0.716825169 0.800702272 0.860098949 0.682188054 0.918747174 0.762680109 0.788700711 0.785952528 1 19.11584527 -5 0.317902422 2.977696888 0.778269173 0.500867805 0.06608063 247.8822696 2.205803604 329.5820167 0.053061165 1.00E-05 5 -2.199427714 AIDALREFNEEGALSVLQQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIDALREFNEEGALSVLQQFK 21 1 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 167.16 1.14E-11 29835000 56319 31474 64968 36640 83982 55169 105970 58143 119470 FALSE TRUE 53656.91248 34681.23638 67946.84706 32956.87759 98628.43421 53258.4837 89802.33023 53051.69068 137996.7974 0.38882723 0.251319139 0.492379884 0.238823496 0.714715385 0.385939998 0.650756626 0.384441463 1 17.07427526 -5 0.132006522 2.951273261 0.196946388 0.609156698 0.145525459 82.44777069 0.682701525 42.28545439 0.91345885 1.00E-05 5 -2.754326874 AIDDNMSLDEIEKLTYIDKWFLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIDDNMSLDEIEKLTYIDKWFLYK 24 2 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 212.07 1.32E-25 230560000 524770 255100 479110 348420 386490 353010 573490 450200 420650 FALSE TRUE 499965.1621 281094.98 501077.6674 313396.1596 453893.7336 340785.1752 485993.5676 410778.1013 485882.2536 1.0289842 0.578524896 1.03127386 0.645004335 0.93416405 0.701373991 1.000229097 0.845427258 1 18.89024721 1.702418143 11.42934372 0.940940565 0.813979858 0.128938553 0.156608852 0.227210487 54.83627705 0.06542722 0.035676748 50.39856173 -1.702418143 -0.126960707 AIEALHGHELRPGR ddPTM_SK-BR-3_Trastuzumab_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 89.466 0.0036879 70681000 81898 67037 76321 72849 80059 60688 75323 59978 14602 FALSE TRUE 78026.84385 73868.14651 79820.39334 65526.08012 94021.26425 58586.35934 63831.09295 54726.00836 16866.40358 4.626169619 4.379602691 4.732508205 3.885006059 5.574470206 3.473553746 3.784511181 3.244675611 1 14.04186476 0.752515722 0.694754328 0.968987336 4.574949404 0.821374255 0.513226518 0.380356991 0.371554112 0.465153877 0.172394632 5.656082319 -0.752515722 3.605962068 AIEALKEFNEDGALAVLQQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIEALKEFNEDGALAVLQQFK 21 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 311.77 1.36E-66 946800000 2652100 2025830 2433300 2596500 1907450 2762400 3218200 3012400 2276700 FALSE TRUE 2526740.489 2232264.38 2544869.212 2335494.887 2240108.676 2666737.395 2727204.484 2748618.286 2629759.008 0.960825871 0.848847508 0.967719553 0.888102248 0.851830403 1.014061512 1.037054907 1.045197783 1 21.32649917 2.148265667 6.686757527 1.029583106 0.903681352 0.689368693 0.04024493 0.114395813 7.07724766 0.014279135 0.01052756 140.6907897 -2.148265667 -0.125901754 AIEEGTLEEIEEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 137.16 4.29E-05 9848600 9508.8 7720.1 10085 9281.2 8228.6 7075.9 10513 8251.8 10493 FALSE TRUE 9059.337869 8506.786967 10547.40723 8348.236143 9663.665235 6830.859809 8909.048766 7529.228646 12120.20085 0.747457735 0.701868482 0.8702337 0.688786947 0.797318902 0.563592955 0.735057849 0.621213191 1 13.56512599 -1.125962798 4.920840019 1.000014145 0.71712455 0.525270652 0.084932626 1.19E-05 2.11E-06 0.074278197 0.017506664 0.074823359 1.125962798 -0.282889594 AIEKVDDLLESYMGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIEKVDDLLESYMGIR 16 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 125.18 7.16E-05 40683000 138240 88097 132820 118380 105740 126530 148960 139150 118080 FALSE TRUE 131705.6692 97074.18446 138909.9284 106480.2175 124181.0225 122148.2344 126233.4162 126965.2883 136391.2433 0.965646078 0.711733262 1.018466618 0.780696875 0.910476505 0.895572409 0.925524345 0.930890321 1 17.0573915 1.293115689 0.604371981 0.998817253 0.858816987 0.165223371 0.08591835 1.107529132 0.987005452 0.077325628 0.03673612 19.63883355 -1.293115689 -0.140000266 AIELDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIELDKK 7 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 73.248 0.079221 791450000 774940 744540 674040 907190 567220 853150 984150 960790 634980 FALSE TRUE 738310.122 820409.4725 704945.4007 815997.5377 666142.9884 823605.2016 833999.8423 876658.1341 733449.4554 1.006627132 1.118563067 0.961136988 1.112547745 0.908232985 1.12292019 1.137092456 1.195253644 1 19.48433802 2.053599977 24.99989537 1.127014004 1.033129266 0.239247555 0.078867922 118.0670154 55067.73294 0.026377927 0.019481388 113.1357804 -2.053599977 -0.093884739 AIEMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIEMER 6 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 111.28 0.065105 138290000 238110 192750 196880 253880 252890 198100 246020 222740 252490 FALSE TRUE 226855.0122 212391.4441 205907.1427 228359.5001 296993.9359 191239.7473 208485.1305 203235.7048 291644.8597 0.77784677 0.728253686 0.706020133 0.7830054 1.018341061 0.65572816 0.71485961 0.696860233 1 18.15385312 -2.061029707 2.678793869 1.353725036 0.757258545 0.366056675 0.099147229 24935312.86 11407649.61 53866949.54 0.023150486 0.00868901 2.061029707 -0.596466491 AIEPNDYTGKVSEEIEDIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIEPNDYTGKVSEEIEDIIK 20 1 O75223;M0QZK8;O75223-3 O75223 GGCT Gamma-glutamylcyclotransferase 0 112.56 0.00013833 26301000 42456 28935 47350 39325 33372 49288 76658 56314 52567 FALSE TRUE 40449.18902 31883.5094 49521.04434 35371.97629 39192.06623 47581.1442 64962.41418 51382.84762 60718.82188 0.666172165 0.525100923 0.815579795 0.582553732 0.64546816 0.783630886 1.06988924 0.8462425 1 15.88985618 1.99755195 3.594480453 0.974179884 0.638254624 0.72228824 0.091665445 0.109433745 2.950822502 0.039130839 0.024009798 99.4379013 -1.99755195 -0.33592526 AIEPPPLDAVIEAEHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AIEPPPLDAVIEAEHTLR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;; 290.2 3.76E-49 1009898800 660497 627896 675557 798718 827408 659945 720007 670366 820305 FALSE TRUE 629276.6158 691879.3163 706531.9567 718429.3492 971707.6932 637090.9392 610156.7083 611665.1992 947513.7099 0.664134576 0.730205072 0.745669376 0.758225809 1.025534178 0.672381763 0.643955546 0.645547598 1 19.85378729 4.207373179 1.53156325 0.764838542 0.664829168 0.066266902 0.133741486 1.62764698 6.525680286 0.037305144 0.181669974 16120.30221 -4.207373179 -0.100009374 AIEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AIEVGR 6 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 126.68 0.040453 939330000 1014920 877500 856170 1002550 1057240 869920 1038940 960700 1118120 FALSE TRUE 966946.743 966918.2476 895426.2414 901771.7693 1241622.321 839794.4523 880430.6216 876576.015 1291512.339 0.748693384 0.74867132 0.693316056 0.69822931 0.961370855 0.650241137 0.681705157 0.678720589 1 20.30063 -1.43576749 3.441658927 1.003035283 0.732188471 0.483607924 0.08683042 21005822.41 33836905.47 637381.0262 0.020156736 0.036663381 1.43576749 -0.270846812 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK 31 0 Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 197.54 4.45E-26 619812000 531374 404331 429340 510397 488200 436048 636392 558752 192661.5 FALSE TRUE 506257.0041 445532.7886 449025.6637 459090.9239 573341.9254 420947.5484 539298.7123 509824.7127 222538.4614 2.274919135 2.002048481 2.017744082 2.062973388 2.57637229 1.891572116 2.423395528 2.290951009 1 17.76369517 -0.787142675 5.53789774 0.999999772 2.18691246 0.763462236 0.208580344 6.58E-05 35639373 22.63247499 0.045206302 0.163251554 0.787142675 1.186912688 AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK;AIGGIILT(0.053)AS(0.947)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILT(0.014)AS(0.986)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK 277.82 5.29E-52 29943290000 3719540 3509540 3348530 3747350 2692050 3661920 3532100 3766530 2297420 TRUE FALSE 3543724.716 3867166.116 3502063.413 3370659.259 3161542.668 3535106.792 2993213.274 3436712.666 2653692.16 1.335394048 1.45727759 1.319694675 1.270177193 1.191375064 1.332146526 1.127942916 1.295068327 1 21.33956959 0.245733908 0.097035393 0.597926714 1.682946399 0.655076727 0.07440181 15.30923258 0.561711763 3.868607023 2.201817716 1.760896814 -0.245733908 1.085019686 AIGPHDVLATLLNNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIGPHDVLATLLNNLK 16 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 229.97 2.69E-15 102090000 377940 363110 308170 380380 323630 358060 436350 400220 333880 FALSE TRUE 360075.5252 400111.3218 322299.8993 342143.4797 380070.9695 345660.2924 369776.7934 365174.6151 385656.4052 0.933669246 1.037481334 0.83571774 0.887171781 0.985517068 0.896290812 0.958824457 0.946891093 1 18.55695655 0.5984524 1.439324959 0.999896587 0.939480029 0.118257941 0.055234987 4.052033417 11.3900303 0.052651186 0.015394619 3.966910483 -0.5984524 -0.060416558 AIGSASEGAQSSLQEVYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AIGSASEGAQSSLQEVYHK 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 331.4 2.78E-75 1109970000 1251530 1018330 1156970 1385740 1089250 1201270 1393710 1275870 1186950 FALSE TRUE 1192372.657 1122098.985 1210018.219 1246442.782 1279214.855 1159669.719 1181073.942 1164148.059 1371016.144 0.869699939 0.818443306 0.882570365 0.909137932 0.933041424 0.845846873 0.861458815 0.849113312 1 20.38681413 AIGSTSKPQES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AIGSTSKPQESPK 13 1 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGSTSKPQES(1)PK;AIGS(0.001)T(0.008)S(0.008)KPQES(0.983)PK;AIGSTSKPQES(1)PK;AIGSTSKPQES(1)PK 154.88 2.36E-05 1574960000 1705440 1792090 1541080 2057500 753841 1976920 1746910 2090110 871670 TRUE FALSE 1624827.231 1974706.008 1611740.042 1850676.191 885310.6317 1908458.765 1480386.795 1907088.888 1006844.132 1.613782292 1.961282731 1.600784065 1.83809602 0.879292637 1.89548581 1.470323706 1.894125245 1 19.94140893 -2.695215555 0.260743704 4.11E-18 1.720162714 0.269766585 0.318555356 64.30814768 1.844854496 37.59810632 0.401319861 0.002017365 2.695215555 1.720162714 AIGSTSKPQES(ph)PKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIGSTSKPQESPKGK 15 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGSTSKPQES(1)PKGK 100.67 0.0010784 366070000 792800 737140 804840 885350 369830 967600 932570 985210 362870 TRUE FALSE 755325.9152 812255.4041 841742.7101 796352.9359 434328.2349 934091.7694 790289.3187 898939.7895 419142.0263 1.802076308 1.93790017 2.008251755 1.899959646 1.036231653 2.228580554 1.885492909 2.144714042 1 18.67707966 2.953498211 24.99891644 1.743892769 1.910673977 0.066553842 0.407137349 1605.743355 863231.508 0.116003376 0.123043495 898.4588919 -2.953498211 0.166781208 AIGTEPDSDVLSEIMHSFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIGTEPDSDVLSEIMHSFAK 20 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 228.49 3.01E-25 167445000 503090 619340 481300 631950 456360 561640 577470 594420 418220 FALSE TRUE 479309.9327 682451.4501 503368.0811 568425.1854 535949.0395 542190.266 489366.3455 542369.4336 483075.4216 0.992205174 1.412722361 1.042007228 1.176679996 1.109452097 1.122371873 1.013022654 1.122742763 1 18.88188893 2.313985156 0.889996073 1.038591226 1.183455386 0.128676077 0.114917217 0.983172898 1.505463554 0.081375898 0.049983858 206.0559481 -2.313985156 0.14486416 AIGVKPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIGVKPPR 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 112.17 0.0028202 2260200000 2770400 2310800 2393300 2956000 2340400 2508500 2960500 2699500 2872800 FALSE TRUE 2639448.682 2546273.147 2503035.172 2658857.264 2748565.019 2421630.016 2508821.352 2463117.469 3318299.152 0.795422161 0.767342856 0.754312694 0.801271116 0.828305374 0.729780501 0.756056412 0.742283127 1 21.66201252 -2.290087138 2.420089034 2.148966893 0.77183046 0.85527131 0.02949541 4048794.261 598969.7346 25514370.31 0.007316158 0.005127585 2.290087138 -1.377136433 AIHSWLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIHSWLTR 8 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 170.66 0.00029388 3940400000 1878030 1478460 1314930 1452530 1931400 1443380 1994940 1565770 1704080 FALSE TRUE 1789259.244 1629116.755 1375220.841 1306518.925 2268235.548 1393395.389 1690575.263 1428662.878 1968340.023 0.909019388 0.827660229 0.698670364 0.663766884 1.152359614 0.707903803 0.858883752 0.72582118 1 20.90854803 4.448237108 2.970613179 0.8211185 0.904958941 0.0241147 0.150874813 1.053696657 17.52763756 0.034476864 0.15049589 28069.65712 -4.448237108 0.083840441 AIHVLDVEQGQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIHVLDVEQGQLER 14 0 Q9H6Y2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ; 210.07 5.75E-09 369300000 366230 307720 312110 366200 330200 314080 369650 355440 334530 FALSE TRUE 348919.0337 339077.0178 326420.5522 329388.8803 387786.7755 303203.3308 313253.1034 324315.7893 386407.2039 0.902982735 0.877512154 0.844757937 0.852439802 1.003570253 0.78467308 0.810681323 0.839310929 1 18.55976247 AIIEEYLHLNDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 216.84 2.68E-11 358707000 1677891 1512314 1530654 1816577 1310570 1695789 1903620 1891358 1236022 FALSE TRUE 1598580.418 1666420.516 1600836 1633971.229 1539132.993 1637063.402 1613187.807 1725740.667 1427697.979 1.119690888 1.167208009 1.121270761 1.144479612 1.078052232 1.146645457 1.129922316 1.208757519 1 20.44525939 -1.242882589 5.059189823 0.999979568 1.13826841 0.627890333 0.033738634 7.02E-06 1.05E-06 0.029506798 0.006953792 0.057163316 1.242882589 0.138288842 AIIESDQEQGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIIESDQEQGRK 12 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 93.623 0.011333 94656000 137510 112010 132430 163210 125310 156210 195350 174020 165100 FALSE TRUE 131010.1748 123423.9463 138502.0465 146803.8207 147164.0243 150800.4085 165545.7697 158781.8863 190702.8648 0.686985877 0.647205518 0.726271452 0.769803961 0.771692782 0.790761107 0.868082238 0.832614059 1 17.54096699 1.803119203 0.262377661 1.035580812 0.601709942 0.929133598 0.026291772 0.416448106 0.10915343 0.058435814 0.068783637 63.55053376 -1.803119203 -0.43387087 AIIVEFAQQGLNAALFYENKDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIIVEFAQQGLNAALFYENKDPR 23 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 149 9.11E-08 240742000 662580 590070 647960 692890 576140 648650 773450 728180 602470 FALSE TRUE 631261.1565 650198.8039 677669.6069 623239.3808 676618.6336 626187.0879 655445.9971 664416.6989 695897.9706 0.907117398 0.934330651 0.973805982 0.895590169 0.972295742 0.899826001 0.941870827 0.954761656 1 19.40851627 -5 0.209885684 1.325091417 0.923377186 0.384183321 0.027012711 143.5528367 1.430272241 19.58978979 0.051365561 1.00E-05 5 -0.401714231 AIKVEQATKPSFESGR ddPTM_SK-BR-3_Trastuzumab_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 ; 112.91 0.00039509 2805000000 4212600 2888720 3751300 3869300 3263650 4101700 5191800 4288100 3737800 FALSE TRUE 4013478.747 3183083.852 3923300.816 3480350.613 3832829.527 3959657.101 4399695.556 3912611.231 4317438.934 0.929597108 0.737262044 0.908710204 0.806114612 0.887755353 0.917131003 1.01905218 0.906234296 1 22.04174434 2.20784491 2.171078655 0.975951026 0.840840679 0.45732159 0.060593094 0.245092032 2.329877495 0.026606059 0.017369648 161.3782161 -2.20784491 -0.135110347 AILDAEPGPRPALQPS(ph)PSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AILDAEPGPRPALQPSPSIR 20 1 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.595)PS(0.405)IR;AILDAEPGPRPALQPS(0.893)PS(0.107)IR 97.509 0.0005642 120056000 240430 235160 229510 274230 252840 232780 293110 264450 240260 TRUE FALSE 229065.3504 259123.0714 240033.2605 246663.8794 296935.2159 224718.7702 248390.6862 241293.3561 277518.2937 0.825406309 0.93371528 0.864927704 0.888820251 1.069966278 0.809743989 0.895042568 0.869468289 1 18.08222335 AILDAEPGPRPALQPS(ph)PSIRLPLDAPLPGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AILDAEPGPRPALQPSPSIRLPLDAPLPGSK 31 2 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.842)PS(0.158)IRLPLDAPLPGSK 103.4 8.84E-05 107180000 137020 90956 129450 128130 131230 134180 175970 136750 156710 TRUE FALSE 130543.3361 100224.5198 135385.4105 115250.129 154116.4705 129533.313 149122.5446 124775.445 181011.7864 0.721186939 0.553690573 0.747936989 0.636699583 0.85141677 0.715607064 0.823827815 0.689322212 1 17.46572411 -5 0.106294344 1.960871674 0.52827431 0.563143758 0.081038807 109.8282041 0.783053323 22.91548102 1.014374743 1.00E-05 5 -1.432597363 AILELHYSQELSLLYLLQDDVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AILELHYSQELSLLYLLQDDVDR 23 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 208.46 1.01E-24 17929000 24806 23192 19217 24210 22916 18234 25087 23969 22868 FALSE TRUE 23633.46954 25555.29117 20098.11846 21776.3648 26912.54314 17602.55201 21259.5174 21870.14729 26414.25265 0.894724142 0.967481136 0.760881586 0.824417223 1.018864456 0.66640356 0.804850233 0.827967673 1 14.68902897 2.243222875 24.99999966 0.80307085 0.894377072 0.077358598 0.106269557 217.6607211 1167147.063 0.03507594 0.028450228 175.0744921 -2.243222875 0.091306222 AILILDNDGDR ddPTM_SK-BR-3_Trastuzumab_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 492462000 767846 897018 642081 893605 716418 721644 708062 735829 663733 FALSE TRUE 731551.4413 988425.154 671521.049 803778.1277 841361.0724 696653.2873 600034.1374 671395.9119 766661.3238 0.954204182 1.289259186 0.875903125 1.04841356 1.097435134 0.908684533 0.782658677 0.875739901 1 19.54822988 2.138840369 4.727387665 0.858701594 1.067778146 0.300354316 0.11858606 0.206851653 7.839559252 0.044205107 0.032180284 137.6703351 -2.138840369 0.209076553 AILILDNDGDRLFAK ddPTM_SK-BR-3_Trastuzumab_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 ; 235.22 1.03E-17 2890700000 1126090 817340 1100850 1200170 1138170 1115820 1395000 1340010 1437830 FALSE TRUE 1072861.957 900627.8752 1151325.061 1079526.631 1336666.488 1077178.874 1182167.129 1222671.621 1660801.333 0.645990544 0.542285135 0.693234668 0.650003471 0.804832258 0.648589842 0.711805263 0.736193786 1 20.66344808 -4.999999999 0.135661975 2.157774157 0.536950762 0.771459126 0.058214103 61.31614552 0.516270902 19.12268726 0.373392584 1.00E-05 4.999999999 -1.620823395 AILVDLEPGTMDS(ph)VR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.008)MDS(0.992)VR;AILVDLEPGT(0.001)MDS(0.999)VR 153.24 2.82E-06 17382200 56065 46767 48150 55193 63121 50789 58643 47052 62700 TRUE FALSE 53414.91856 51532.61047 50357.72513 49644.89478 74129.28242 49030.16419 49695.9333 42931.87744 72423.19577 0.737538823 0.711548419 0.695325919 0.685483349 1.023557185 0.676995314 0.686188075 0.592791812 1 16.14416422 -2.181902355 2.459950069 1.764937186 0.7270372 0.370553656 0.112151329 5368287.637 1903661.135 22729562.3 0.026253361 0.006578057 2.181902355 -1.037899985 AILVDLEPGTMDSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 246.26 8.55E-18 679671000 1215050 1051863 1040183 1214717 1277765 1073594 1335473 1220149 1317613 FALSE TRUE 1157616.994 1159049.036 1087876.419 1092611.339 1500606.811 1036415.171 1131722.066 1113306.285 1521941.695 0.760618491 0.761559421 0.71479507 0.717906174 0.9859818 0.680982178 0.743604088 0.7315039 1 20.53748166 -1.071823987 4.957639373 1.000005982 0.760998199 0.447121948 0.08312291 5.06E-06 9.47E-07 0.074046086 0.017452393 0.084757085 1.071823987 -0.239007783 AIMEMPSFYSHGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 248.64 2.03E-18 406580000 1217660 1276310 1148260 1341930 915820 1261100 1099210 1002060 687430 FALSE TRUE 1160103.625 1406367.44 1200908.857 1207036.647 1075538.718 1217427.791 931505.3261 914314.3141 794033.1335 1.46102672 1.771169717 1.512416556 1.520133853 1.354526244 1.53322039 1.173131557 1.151481312 1 19.59883968 1.693691755 0.68348302 0.989253117 1.605022331 0.780655762 0.10587351 0.274183133 0.262713419 0.093129881 0.04598837 49.39599696 -1.693691755 0.615769214 AIMTYVSSFYHAFSGAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 146.78 8.14E-08 167557000 500040 334160 253815 265509 545060 233511 648610 403780 401790 FALSE TRUE 476404.1002 368211.2839 265452.6688 238819.5309 640118.2914 225424.4555 549652.632 368422.8826 464097.5411 1.026517182 0.793392016 0.571976029 0.514589089 1.379275335 0.485726459 1.184347218 0.793847952 1 18.82406853 2.789698913 24.99992794 0.956616699 0.762478494 0.160731308 0.268540885 773.2941293 378037.9978 0.076725544 0.081379628 616.1676784 -2.789698913 -0.194138205 AINEAYKEDYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AINEAYKEDYHK 12 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;; 164.33 3.46E-05 3217790000 4420730 2860080 3048360 6364750 3885800 4459320 5100250 3774100 2818010 FALSE TRUE 4211770.854 3151525.404 3188130.321 5724953.238 4563482.29 4304892.63 4322113.19 3443619.796 3255012.598 1.29393381 0.968206822 0.979452529 1.758811392 1.401986061 1.32254254 1.327833014 1.057943615 1 21.6342317 5.074118249 19.35462145 1.241122103 2.731744115 0.004397904 0.245555024 1693.265584 527484.3463 0.056933826 20934.80714 118609.165 -5.074118249 1.490622013 AINVLLEGNPDTHSWEMVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AINVLLEGNPDTHSWEMVGK 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 121.63 3.19E-05 132310000 222430 145520 257240 182910 190240 266490 332930 287430 238080 FALSE TRUE 211916.1747 160348.6534 269034.7084 164523.5393 223417.7958 257261.3845 282135.4138 262261.1054 275000.2305 0.770603626 0.583085524 0.978307211 0.598266914 0.812427667 0.93549516 1.0259461 0.953675948 1 18.0690733 2.279636655 2.749539655 0.992488052 0.723964736 0.535025106 0.109078703 0.185367836 2.880054611 0.041205538 0.030640419 190.3867213 -2.279636655 -0.268523317 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AIPGDQHPES(0.986)PVHT(0.014)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.999)PVHT(0.001)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.982)PVHT(0.018)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.993)PVHT(0.007)EPMGIQGR 219.26 9.17E-26 3037120000 2431460 2359480 2325360 2597810 2521110 2343240 2767010 2569650 1529389 TRUE FALSE 2316529.704 2599913.695 2431980.056 2336673.203 2960790.786 2262093.011 2344851.805 2344637.823 1766558.835 1.311323268 1.471739091 1.376676512 1.322725944 1.676021612 1.280508164 1.327355624 1.327234495 1 20.75251037 0.543171703 0.811606316 0.998396651 1.410995505 0.559598835 0.111061157 1.072022571 1.142598202 0.10473885 0.03474051 3.492783794 -0.543171703 0.412598854 AIQDHLLEVEQSKDQMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AIQDHLLEVEQSKDQMEK 18 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 171.21 8.32E-12 166261000 406053 354629 355578 449800 222582 405996 427450 445690 246598 FALSE TRUE 386859.6794 390766.0983 371881.603 404585.2494 261400.2303 391936.2567 362234.6518 406663.0208 284839.1584 1.358168875 1.371883348 1.305584545 1.420398978 0.917711707 1.375991486 1.27171648 1.427693521 1 18.11978797 -2.232898532 2.199335831 0.000150138 1.307400235 0.302778008 0.145988309 2130523.297 415265.0744 10588312.09 0.032746531 0.005849267 2.232898532 1.307250097 AIQEGANSIVSSLHQAAAAACLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIQEGANSIVSSLHQAAAAACLSR 24 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 AIQEGANSIVSSLHQAAAAACLS(1)R;AIQEGANSIVSSLHQAAAAACLS(1)R 240.52 9.74E-38 292540000 238840 202007 234990 249040 307760 216500 298300 248060 311760 TRUE FALSE 227550.5065 222591.743 245764.5239 224006.0261 361433.2466 209002.5507 252788.8563 226338.5514 360106.1486 0.631898421 0.618128138 0.682478 0.622055544 1.003685297 0.580391508 0.701984283 0.628532871 1 18.45806271 -5 0.306759184 3.75778138 0.663534153 0.402101806 0.119841308 281.8880804 2.570620418 502.0565406 0.107073719 1.00E-05 5 -3.094247227 AIQNKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIQNKDR 7 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 62.714 0.076419 52001000 100710 23228 66998 45310 153660 69705 201910 103780 273660 FALSE TRUE 95949.63789 25594.95961 70069.92457 40755.35272 180458.2553 67291.09837 171104.9212 94692.47303 316097.7951 0.303544154 0.080971649 0.221671665 0.128932733 0.570893749 0.212880632 0.541303748 0.299567015 1 18.27001145 -2.06270803 0.198816559 1.912008151 0.105180501 0.718354745 0.144173732 16.55538406 0.473037036 7.263314331 0.357745402 0.008655496 2.06270803 -1.806827649 AIQWGEDGRPFHYLFYTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIQWGEDGRPFHYLFYTGK 19 1 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 177.6 2.39E-14 310568000 884440 871260 740110 764080 703550 664330 779460 796420 651920 FALSE TRUE 842634.274 960042.3845 774044.7756 687273.2267 826248.8972 641324.0855 660539.0612 726681.2427 753016.4241 1.119011813 1.274928878 1.027925489 0.912693541 1.097252159 0.851673436 0.877190776 0.965027082 1 19.52232181 3.54181076 4.289839178 0.941211355 1.19533429 0.625619052 0.077438748 0.122218211 4.414592701 0.02089674 0.032367717 3481.855632 -3.54181076 0.254122935 AIS(ph)SANLLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AISSANLLVR 10 0 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 AIS(0.5)S(0.5)ANLLVR;AIS(0.5)S(0.5)ANLLVR;AIS(0.909)S(0.091)ANLLVR;AIS(0.988)S(0.012)ANLLVR 172.13 4.00E-06 456430000 530320 471877 404260 573160 618920 508080 591230 499200 598940 TRUE FALSE 505252.8246 519961.8028 422795.7209 515544.8679 726859.452 490485.0622 501027.0048 455487.4016 691820.5562 0.730323521 0.751584783 0.61113495 0.745200274 1.050647376 0.708977289 0.724215261 0.658389517 1 19.40003836 -1.570808084 3.192134055 1.010728005 0.748272416 0.319245682 0.115845521 51257027.29 47716770.8 4537819.5 0.027011932 0.026865314 1.570808084 -0.262455589 AIS(ph)SDMFFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.937)S(0.063)DMFFGR;AIS(0.978)S(0.022)DMFFGR;AIS(0.819)S(0.181)DMFFGR;AIS(0.938)S(0.062)DMFFGR;AIS(0.928)S(0.072)DMFFGR;AIS(0.916)S(0.084)DMFFGR;AIS(0.937)S(0.063)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.933)S(0.067)DMFFGR;AIS(0.95)S(0.05)DMFFGR;AIS(0.729)S(0.271)DMFFGR;AIS(0.976)S(0.024)DMFFGR;AIS(0.988)S(0.012)DMFFGR 193.28 6.19E-07 1617062000 1531464 796909 879893 1956484 2452695 1651183 1875158 858403 1767366 TRUE FALSE 1459074.732 878114.9331 920236.9644 1759814.511 2880444.231 1594002.119 1589068.207 783236.6826 2041440.093 0.714728165 0.430144845 0.450778334 0.86204563 1.410986412 0.780822383 0.778405506 0.383668708 1 20.9611558 3.228155773 24.30846597 0.871637355 0.536203221 0.270814344 0.260967493 196.0024222 457912.7363 0.075346265 0.091033425 1691.047371 -3.228155773 -0.335434134 AIS(ph)TGSLASSTLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.949)T(0.042)GS(0.003)LAS(0.002)S(0.004)T(0.001)LNK;AIS(0.991)T(0.009)GSLASSTLNK 281.54 2.63E-33 203172000 461780 419360 401820 479860 429320 430940 524800 511180 503150 TRUE FALSE 439952.5746 462093.2608 420243.8445 431623.5611 504193.2721 416016.4397 444732.1214 466418.3693 581175.9323 0.757004119 0.795100477 0.723092305 0.742672807 0.867539834 0.715818424 0.765228043 0.802542472 1 19.14861543 0.757760108 3.026350556 0.999977478 0.767590957 0.746816772 0.042375155 0.7558025 8.822435716 0.037303691 0.009751473 5.724797223 -0.757760108 -0.232386521 AIST(ph)GSLASSTLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.257)T(0.742)GS(0.001)LASSTLNK 218.6 5.95E-11 142860000 297790 262530 256640 300720 249730 284750 351110 332480 316760 TRUE FALSE 283714.0569 289282.1055 268407.1979 270491.0543 293282.8329 274889.0361 297541.7209 303366.2886 365881.523 0.77542603 0.790644204 0.733590468 0.739285909 0.801578693 0.751306144 0.813218767 0.829138039 1 18.48101704 0.604706642 0.915355463 1.000660026 0.766900064 0.912418227 0.022507027 0.344633999 0.473861833 0.021347986 0.006998953 4.024450985 -0.604706642 -0.233759962 AIT(ph)PPQQPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK 149.23 0.00026516 1384403000 3117310 2762970 2528990 3086380 2572940 2915430 3586590 3203560 2946010 TRUE FALSE 2969960.934 3044519.784 2644946.693 2776131.219 3021659.921 2814467.928 3039389.823 2923039.303 3402862.185 0.872783196 0.894693825 0.777271176 0.815822407 0.887975991 0.827088426 0.893186282 0.858994324 1 21.69831729 0.000522414 0.724227095 1.00505666 0.852623309 0.607675245 0.037275259 3.576484745 1.977431007 0.08788989 0.013364935 1.001203627 -0.000522414 -0.152433352 AIT(ph)PPQQPYKK ddPTM_SK-BR-3_Trastuzumab_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 81.865 0.012016 168830000 460170 389520 451660 471950 336920 471400 540680 512120 447690 TRUE FALSE 438418.6761 429212.5308 472369.0578 424508.6894 395678.7413 455075.2998 458189.3357 467276.0579 517115.4787 0.847815805 0.830012925 0.913469191 0.820916617 0.765165147 0.880026452 0.886048387 0.903620327 1 18.98012696 0.986983113 1.016427172 0.997878223 0.840356683 0.630272731 0.038315434 0.371205188 0.810359541 0.035427295 0.011691764 9.704722318 -0.986983113 -0.15752154 AITGAS(ph)LADIMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AITGASLADIMAK 13 0 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 1 AITGAS(1)LADIMAK;AITGAS(1)LADIMAK 183.41 1.09E-05 96494000 153550 120159 145077 161439 152559 144913 202556 164091 130937 TRUE FALSE 146291.9958 132403.3387 151728.924 145210.845 179165.2413 139894.6265 171652.362 149722.3221 151242.0412 0.967270705 0.875440041 1.003219229 0.960122224 1.184625914 0.924971822 1.134951371 0.989951742 1 17.2064997 3.244497373 2.055157104 1.050612238 0.925706206 0.232992164 0.080497034 0.338993322 2.941665425 0.0222798 0.03075072 1755.890273 -3.244497373 -0.124906032 AITHLNNNFMFGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AITHLNNNFMFGQK 14 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 220.4 4.65E-12 635000000 1946000 1767800 1683100 2027300 1739300 1920500 2230700 1999800 1900500 FALSE TRUE 1854016.437 1947940.83 1760271.8 1823511.952 2042633.369 1853992.603 1890365.745 1824686.91 2195219.834 0.844569828 0.887355699 0.801865842 0.83067396 0.930491488 0.844558971 0.861128219 0.831209195 1 21.06593399 -2.028664712 2.716237368 1.171829098 0.856373796 0.63177142 0.034991578 15676279.27 9658341.366 16740777.57 0.00789106 0.009361281 2.028664712 -0.315455302 AITSLLGGGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AITSLLGGGSPK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AITSLLGGGS(1)PK;AITSLLGGGS(1)PK;AITSLLGGGS(1)PK 209.84 5.29E-08 3044500000 2987260 2790470 2844940 3327760 2014190 3359760 3353860 3468890 2161100 TRUE FALSE 2846058.14 3074822.066 2975383.313 2993247.242 2365464.098 3243410.669 2842167.059 3165135.602 2496232.351 1.140141517 1.2317852 1.191949665 1.199106021 0.94761375 1.299322424 1.138582736 1.26796514 1 21.2513208 AITVFSPDGHLFQVEYAQEAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AITVFSPDGHLFQVEYAQEAVKK 23 1 O14818;O14818-4;Q8TAA3-2;Q8TAA3-5;Q8TAA3;F5GY34 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 169.56 5.42E-12 181650000 283450 220870 239760 293070 247970 267780 338320 345760 250040 FALSE TRUE 270051.8802 243376.9041 250753.2332 263610.0468 291215.8895 258506.7115 286703.0703 315483.4214 288814.9262 0.935034362 0.84267426 0.868214245 0.912729997 1.008313155 0.895060082 0.992687858 1.092337663 1 18.13978578 2.069261312 0.809321966 1.037247508 0.883922836 0.551188063 0.050342174 0.463741594 0.56750296 0.041184615 0.021894852 117.290088 -2.069261312 -0.153324672 AIVDALPPPCESACTVPTDVDKWFHHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIVDALPPPCESACTVPTDVDKWFHHQK 28 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 160.47 6.30E-12 1685330000 4593000 4414400 3975500 5272700 3241600 4697800 5038200 5100600 401790 FALSE TRUE 4375897.992 4864232.379 4157780.607 4742678.179 3806934.014 4535114.008 4269530.057 4653964.424 464097.5411 9.428832529 10.48105613 8.958850756 10.21914093 8.202874776 9.771898375 9.199639469 10.02798768 1 18.82406853 -1.423015028 3.429433808 0.910097311 9.561374671 0.943238289 0.658069164 9972233.623 15717224.61 8934517.92 0.149355087 0.037755913 1.423015028 8.651277361 AIVICPTDEDLKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIVICPTDEDLKDR 14 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 154.07 5.67E-06 816340000 869250 691200 756800 882570 662600 862790 978540 917820 641590 FALSE TRUE 828162.2752 761634.0658 791500.0286 793852.3868 778157.2302 832911.366 829245.7509 837450.8151 741084.5004 1.117500467 1.027729045 1.068029392 1.071203603 1.05002497 1.123908765 1.118962481 1.130034179 1 19.49927853 2.240294452 24.99688224 1.105576919 1.066403795 0.052821036 0.043025095 78.23739629 1127968.975 0.013880964 0.011051022 173.8979457 -2.240294452 -0.039173124 AIVQQWLEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AIVQQWLEYR 10 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;D6RCQ0 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 211.45 1.37E-07 457780000 338810 301510 227000 275160 399120 241570 393600 333800 372420 FALSE TRUE 322795.1228 332234.2118 237408.1745 247500.394 468726.4016 233204.3703 333549.091 304570.7024 430172.9915 0.750384448 0.77232699 0.551890005 0.575350845 1.089623037 0.542117648 0.775383619 0.708019119 1 18.71455742 -1.806038876 2.123026014 1.106724525 0.724487089 0.235805993 0.157915321 3003986.039 1598788.507 1643656.327 0.038206087 0.015630077 1.806038876 -0.382237436 AIWHAFTALDQDHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIWHAFTALDQDHSGK 16 0 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 168.41 3.46E-09 492400000 612360 530890 546110 601850 488330 567470 669750 669650 217920 FALSE TRUE 583414.9564 584988.2946 571149.6837 541350.8946 573494.5974 547818.3716 567567.3367 611011.896 251713.9206 2.317769931 2.324020432 2.269042897 2.150659341 2.278358686 2.176353101 2.254811078 2.427406059 1 17.94142548 -1.393440991 3.341309567 0.988066185 2.272291223 0.964507129 0.076852095 8371605.053 12679656.58 981877.9538 0.018721959 0.040416529 1.393440991 1.284225038 AIWNVINWENVTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AIWNVINWENVTER 14 0 P04179-3;P04179-4;P04179-2;P04179 P04179-3 SOD2 "Superoxide dismutase [Mn], mitochondrial" 0 184.03 3.12E-06 36789000 164990 124220 117320 95535 126810 137430 122800 196780 156520 FALSE TRUE 157191.2497 136878.1592 122699.238 85931.6403 148925.6239 132670.7646 104064.6046 179548.9 180792.3222 0.869457551 0.757101616 0.678675049 0.475305805 0.823738652 0.73382964 0.575603009 0.993122373 1 17.46397389 1.220485304 24.92519752 0.996561668 0.709163211 0.538892976 0.113141577 223.982409 308855.0295 0.110865289 0.027944721 16.61442454 -1.220485304 -0.287398457 AIYHDLEQSIR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 244.27 7.24E-16 1008054000 1416520 1116321 1103223 1328443 1581776 1141270 1487499 1304886 1460755 FALSE TRUE 1349563.907 1230075.379 1153806.866 1194905.386 1857637.234 1101747.534 1260553.708 1190623.264 1687281.425 0.799845175 0.729027986 0.683825975 0.708183809 1.100964668 0.652972004 0.747091558 0.705645926 1 20.68626919 -1.848804524 2.401250362 1.102210318 0.764155746 0.255778589 0.125437054 21548243.93 12595376.88 12627034.15 0.0296808 0.014164312 1.848804524 -0.338054572 AKADS(ph)PVNGLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 AKADS(1)PVNGLPK;AKADS(1)PVNGLPK;AKADS(1)PVNGLPK;AKADS(1)PVNGLPK;AKADS(1)PVNGLPK 186.72 6.91E-06 3068100000 9322050 8014870 8385310 9638020 4795510 10300130 10437170 11040020 5700070 TRUE FALSE 8881415.171 8831594.365 8769784.758 8669187.919 5631845.426 9943433.915 8844788.025 10073297.32 6584007.744 1.348937534 1.341370592 1.331982753 1.316703785 0.855382564 1.510240313 1.343374487 1.529964379 1 22.6505346 2.989999785 24.90009494 1.275638442 1.339846664 0.034215132 0.204680307 2449.644467 6099536.917 0.058177644 0.065799894 977.2367373 -2.989999785 0.064208222 AKAEKPPLS(ph)ASSPQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.328)AS(0.328)S(0.328)PQQRPPEPET(0.006)GES(0.005)AGT(0.002)S(0.002)R 80.667 0.0134 145100000 35691 33215 30464 34689 27867 36346 38543 42046 28333 TRUE FALSE 34003.95716 36599.64626 31860.80453 31201.99582 32726.99598 35087.32891 32662.55746 38364.22934 32726.73694 1.039026813 1.118340834 0.973540521 0.953409925 1.000007915 1.07213038 0.998038928 1.172259533 1 14.99818214 -0.629791819 7.598848777 1.000000252 1.040099776 0.035698601 0.066613906 0 0 0.062041902 0.014623416 0.23453528 0.629791819 0.040099524 AKAEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.022)AS(0.173)S(0.804)PQQRPPEPETGESAGTSR;AKAEKPPLSAS(0.171)S(0.759)PQQRPPEPET(0.051)GES(0.012)AGT(0.003)S(0.003)R 129.01 5.84E-05 419408000 231165 176709 184227 225276 149882 217160 242136 242762 184385 TRUE FALSE 220238.2886 194715.848 192673.9902 202630.8285 176021.3733 209639.6947 205193.7061 221504.4723 212978.4841 1.034087032 0.914251263 0.904664107 0.951414549 0.826474909 0.984323349 0.963448054 1.040032158 1 17.70034817 1.563090165 2.185550185 1.016810455 0.935204508 0.283299183 0.054357898 0.392208282 3.973611604 0.041807096 0.014838382 36.56707014 -1.563090165 -0.081605947 AKAGLESGAEPGDGDS(ph)DTTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKAGLESGAEPGDGDSDTTKK 21 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AKAGLESGAEPGDGDS(0.997)DT(0.002)T(0.002)KK;AKAGLESGAEPGDGDS(0.991)DT(0.004)T(0.004)KK 117.82 5.07E-05 172471000 463960 332128 463530 462230 226818 549720 548600 547910 278899 TRUE FALSE 442029.5303 365972.2208 484783.309 415765.7622 266374.9874 530683.0586 464900.9943 499932.0957 322149.2325 1.372126598 1.136033192 1.504840801 1.290599884 0.826868297 1.647320574 1.443123085 1.551864929 1 18.29736963 AKDDATLSGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKDDATLSGKR 11 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 64.121 0.039544 89425000 228950 143780 172400 175560 170820 179910 245780 200330 191210 FALSE TRUE 218127.9872 158431.3455 180304.7105 157912.3753 200610.9539 173679.6716 208281.7469 182788.0432 220861.8702 0.987621752 0.717332264 0.816368667 0.714982514 0.908309586 0.786372367 0.943040764 0.827612494 1 17.75278485 1.732569866 10.6603977 0.912921952 0.821548424 0.214704985 0.090906701 0.151151904 75.50539159 0.040419439 0.021978043 54.02190147 -1.732569866 -0.091373528 AKDDDDDDDDDAEM ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKDDDDDDDDDAEM 14 1 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 0 ; 195.25 1.10E-07 753810000 1989170 1757760 1718760 2072570 1144920 2047190 2134330 2275730 1246250 FALSE TRUE 1895145.876 1936877.742 1797566.846 1864231.326 1344593.686 1976295.297 1808698.759 2076455.017 1439512.085 1.316519601 1.345509887 1.248733418 1.295043887 0.934062103 1.372892466 1.256466533 1.442471403 1 20.45714847 -1.923777422 2.644142917 0.825688933 1.277305867 0.295464125 0.13415892 9557342.251 6375899.242 10328150.12 0.03056994 0.011918527 1.923777422 0.451616933 AKDNFNFLHLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKDNFNFLHLNR 12 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 198.57 1.09E-07 168290000 1643000 1294500 1236600 1350400 1579400 1397400 1944200 1657400 1758100 FALSE TRUE 1565338.646 1426411.022 1293299.333 1214655.226 1854846.86 1349007.688 1647576.582 1512269.27 2030737.169 0.770822867 0.702410456 0.636861999 0.598135123 0.91338598 0.664294577 0.81131946 0.744689807 1 20.9535721 -0.187222803 0.416931716 1.050450956 0.704715409 0.49801576 0.087717608 4.601992335 0.92667233 0.447822463 0.052305302 0.649796244 0.187222803 -0.345735547 AKDPFAHLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKDPFAHLPK 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 91.937 0.0058935 8109900000 38331000 32940000 30849000 38550000 27939000 36769000 45946000 41634000 30873000 FALSE TRUE 36519169.59 36296623.45 32263457.16 34674880.76 32811552.75 35495680.31 38936093.84 37988306.24 35660627.16 1.02407536 1.017834692 0.904736112 0.97235757 0.92010588 0.995374539 1.091851068 1.065273083 1 25.08782874 1.893683184 5.929956542 1.059837861 0.975646115 0.432815301 0.043358454 0.229773619 10.72269389 0.020173538 0.012205165 78.28583425 -1.893683184 -0.084191745 AKDQDILDLVGVLHDPETLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKDQDILDLVGVLHDPETLLR 21 1 F5H345;A0A3B3IRR1;A0A3F2YNY7;P08397-2;P08397 F5H345 HMBS Porphobilinogen deaminase 0 126.55 1.28E-05 79818000 287840 176710 247670 274570 264750 248410 345320 289520 255830 FALSE TRUE 274234.3736 194716.9499 259025.9145 246969.702 310922.3162 239807.4994 292635.0918 264168.094 295502.8098 0.928026281 0.658934343 0.876559904 0.835760926 1.052180574 0.811523584 0.990295463 0.893961361 1 18.17281232 3.101297299 2.429969427 0.940491521 0.797345248 0.27498037 0.095173781 0.323370558 3.884118836 0.02747622 0.034037831 1262.691621 -3.101297299 -0.143146274 AKDSIDAGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKDSIDAGSK 10 1 E7EQY1;Q96C01 E7EQY1 FAM136A Protein FAM136A 0 64.64 0.06508 58940000 125910 95798 103630 122310 80960 109530 126380 120010 95464 FALSE TRUE 119958.4838 105559.9251 108381.538 110015.1664 95079.39837 105736.9486 107098.4099 109501.2882 110268.0696 1.087880511 0.95730274 0.982891407 0.99770647 0.86225685 0.958908132 0.971254963 0.993046207 1 16.75065556 4.629796804 1.758567336 0.961697864 1.115645919 0.476466286 0.039939122 0.569000278 2.125325932 0.010070435 0.137018261 42637.9979 -4.629796804 0.153948055 AKEAAEQDVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AKEAAEQDVEK 11 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ;;;;;; 188.09 3.01E-06 2839050000 5205860 3932850 4526190 5362970 3568000 5634720 6726440 6173270 4298400 FALSE TRUE 4959789.315 4333611.886 4733720.289 4823874.067 4190258.07 5439588.234 5700198.038 5632705.752 4964973.919 0.998955764 0.872836788 0.953422992 0.971580948 0.843963763 1.095592509 1.148082172 1.134488488 1 22.24335471 2.156712703 7.587865798 1.112613198 0.930410861 0.651425516 0.05989002 0.124181117 9.883429585 0.020532375 0.015157981 143.4540134 -2.156712703 -0.182202338 AKEALELTDTGLLSGSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKEALELTDTGLLSGSEER 19 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 139.7 1.66E-07 175856000 194333 149175 185758 178500 171069 168125 215420 214840 204990 FALSE TRUE 185147.2642 164376.1021 194275.188 160556.8409 200903.3794 162302.7891 182553.7225 196027.4707 236778.8023 0.78194189 0.694217981 0.820492317 0.6780879 0.848485496 0.685461653 0.770988453 0.827892821 1 17.8531804 0.855508432 2.028538165 0.999620889 0.749453512 0.657744654 0.056160694 0.284936366 2.260022809 0.045581282 0.012623167 7.169822954 -0.855508432 -0.250167377 AKEAQDDLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKEAQDDLVK 10 1 P15311;E7EQR4 P15311 EZR Ezrin 0 95.417 0.0067819 311340000 1122400 905690 837990 1126200 667110 1018700 1089400 1140800 783980 FALSE TRUE 1069346.376 997980.8407 876412.6704 1012992.236 783453.7728 983422.1636 923192.0218 1040905.504 905555.6144 1.180873222 1.10206466 0.96781761 1.118641661 0.865163619 1.085987595 1.019475786 1.149466126 1 19.78844372 4.071136996 2.776955696 1.029907153 1.164174505 0.269797877 0.080522337 0.298811779 4.585177474 0.018893475 0.048087176 11779.77502 -4.071136996 0.134267351 AKEEDREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKEEDREK 8 2 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 50.123 0.088617 42647000 90467 74534 71781 93068 53439 84011 101340 112350 85310 FALSE TRUE 86190.8042 82129.09934 75072.22985 83712.62782 62758.74468 81101.678 85878.72176 102512.0384 98539.4391 0.874683325 0.833464246 0.761849576 0.849534243 0.636889607 0.823037748 0.871516243 1.040314815 1 16.58841364 1.406500514 2.820106487 1.021546492 0.80235134 0.651999381 0.066331552 0.16853127 2.339143893 0.054200765 0.01745616 25.49767104 -1.406500514 -0.219195152 AKEEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 1611220000 4546500 3688600 3729500 4701000 3375110 4207800 4794800 4510000 3777600 FALSE TRUE 4331595.955 4064472.534 3900501.264 4228446.549 3963728.115 4062082.831 4063265.197 4115080.491 4363410.915 0.992708695 0.931489748 0.893911057 0.969069068 0.908401293 0.93094208 0.931213053 0.943088004 1 22.05702491 0.942655824 18.28637476 1 0.938000188 0.335074615 0.027721853 639.7935044 204024.8424 0.026130238 0.006532559 8.763060774 -0.942655824 -0.061999812 AKEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 93053000 233980 204650 226080 276600 332530 201000 289350 308240 462180 FALSE TRUE 222920.2291 225504.0677 236445.9916 248795.6425 390523.1267 194039.3196 245204.3432 281248.8715 533852.5139 0.417568941 0.422408927 0.442905082 0.466038159 0.731518756 0.3634699 0.459311021 0.526828785 1 19.0260817 -5 0.313159519 5.806012974 0.445053958 0.740118279 0.097578358 150.9478047 1.357694224 479.2084883 0.086943704 1.00E-05 5 -5.360959017 AKEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKEELER 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 109.48 0.0064015 1870860000 2959300 2332190 2297710 2812970 2144670 2469530 3064820 2594200 2338980 FALSE TRUE 2819419.754 2569842.812 2403062.276 2530204.911 2518699.769 2384009.557 2597225.42 2367038.095 2701697.073 1.043573605 0.951195765 0.889463997 0.936524282 0.932265795 0.882411867 0.9613311 0.876130089 1 21.36543449 4.364844797 2.02689964 0.92405233 1.043477684 0.484289923 0.037781258 0.26885092 1.925758601 0.008595677 0.044703838 23165.66633 -4.364844797 0.119425354 AKEFTNVYIK ddPTM_SK-BR-3_Trastuzumab_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 ; 133.05 0.00018918 1095070000 3194100 2507900 1934390 2203400 2902400 2331800 3684800 2972400 2993700 FALSE TRUE 3043121.223 2763457.861 2023083.695 1981910.046 3408577.641 2251049.181 3122616.084 2712120.898 3457947.706 0.880036797 0.799161264 0.585053294 0.573146332 0.985722726 0.650978376 0.903025826 0.784315186 1 21.72148462 1.642581468 10.11722836 0.882636448 0.75895947 0.205066879 0.136667454 0.211272851 41.38657747 0.064577336 0.034390004 43.9118231 -1.642581468 -0.123676978 AKEIGFSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKEIGFSDK 9 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 112.13 0.0018361 437010000 1108700 731130 918150 884840 777710 923750 1150000 1076200 908310 FALSE TRUE 1056293.948 805632.9782 960248.0857 795894.2021 913342.3778 891760.3059 974546.3788 981962.2227 1049166.076 1.006793846 0.767879363 0.915248889 0.758596966 0.870541279 0.849970588 0.928877135 0.935945457 1 20.00081163 1.312299267 1.392338575 0.992080451 0.85999191 0.298654954 0.070675558 0.472540915 1.73458099 0.061150784 0.019255833 20.52576098 -1.312299267 -0.13208854 AKESWEMNSEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKESWEMNSEEK 12 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 68.283 0.048414 220490000 175080 199910 145990 170240 76179 184960 133410 169540 73810 FALSE TRUE 166804.3154 220281.0563 152683.7859 153127.1518 89464.59348 178554.7888 113055.8543 154694.1788 85256.07783 1.956509373 2.583757802 1.790884472 1.796084873 1.049363233 2.094335012 1.326073837 1.814465112 1 16.37951507 4.101731075 0.153849408 0.813815577 3.346676886 0.394781036 0.374416971 16.14358985 0.544105834 1.775408533 8.663304477 12639.53437 -4.101731075 2.532861309 AKEVELVS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKEVELVSE 9 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AKEVELVS(1)E;AKEVELVS(1)E 110.93 0.0058054 1167600000 3135360 2333860 2864440 3330310 2574270 3052820 3612420 3024680 3089050 TRUE FALSE 2987157.746 2571682.987 2995777.407 2995540.912 3023221.873 2947100.078 3061278.982 2759822.984 3568084.097 0.837188156 0.720746181 0.839603923 0.839537643 0.847295577 0.825961496 0.857961556 0.773474758 1 21.76671819 -5 0.212594668 1.889811017 0.789845831 0.624703005 0.043217871 93.53098032 0.933134873 35.57151499 0.086807157 1.00E-05 5 -1.099965186 AKFAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKFAGR 6 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 114.6 0.022937 1843600000 2370300 1272240 1908700 1653720 2351400 1990170 3202200 2313300 3223500 FALSE TRUE 2258260.616 1401882.702 1996215.783 1487484.924 2761483.416 1921249.914 2713645.578 2110735.188 3723383.917 0.606507593 0.376507697 0.536129453 0.399498133 0.741659597 0.515995653 0.72881165 0.566886261 1 21.82818295 -0.020445393 0.302423695 1.129640696 0.461606152 0.632158291 0.110455616 3.265227855 0.443790657 0.625950498 0.121557563 0.95401369 0.020445393 -0.668034544 AKFDLSEGPSKPTTLAVQFLSEGSTLSGVDFELVGTGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKFDLSEGPSKPTTLAVQFLSEGSTLSGVDFELVGTGYR 39 2 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 0 42.661 0.051843 10167000 13112 11490 11396 13671 10435 11781 15111 13537 13839 FALSE TRUE 12492.22175 12660.84406 11918.51787 12296.76511 12254.8607 11373.02102 12805.53942 12351.62852 15985.08144 0.781492531 0.792041261 0.745602574 0.76926509 0.76664362 0.711477202 0.801093161 0.772697253 1 13.96443847 0.041179732 1.241428383 1.000662141 0.768023039 0.897264407 0.0247377 3.253638624 3.86293624 0.02968312 0.006905133 1.099460756 -0.041179732 -0.232639101 AKFEELNMDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AKFEELNMDLFR 12 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 176.91 2.18E-05 3976558000 3559610 2661740 2202810 2610300 3057430 2545520 3738250 2978880 3081910 FALSE TRUE 3391354.29 2932974.332 2303811.017 2347907.685 3590644.824 2457368.004 3167911.305 2718033.475 3559836.863 0.952671266 0.82390695 0.647167583 0.659554855 1.008654318 0.690303545 0.889903506 0.763527538 1 21.7633797 -0.781550219 6.102165092 1.000000007 0.812770081 0.20168957 0.121261217 1.08E-08 2.04E-09 0.111399929 0.026257214 0.165367355 0.781550219 -0.187229926 AKFENLCK ddPTM_SK-BR-3_Trastuzumab_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 ; 136.57 0.00071634 9595400000 8205600 6381400 4573700 5001500 6315800 5764200 9687700 7405700 7299400 FALSE TRUE 7817737.55 7031671.915 4783408.669 4498739.718 7417273.52 5564584.309 8209663.438 6757217.648 8431353.672 0.927222111 0.833990862 0.567335787 0.53357265 0.879725108 0.659987058 0.973706448 0.801439236 1 23.00733285 1.720427846 10.66131619 0.913804963 0.751688674 0.297067617 0.136493047 0.162370238 55.07463582 0.06787535 0.03687576 52.53247294 -1.720427846 -0.162116288 AKFFPEDVSEELIQEITQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKFFPEDVSEELIQEITQR 19 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3;A0A2R8Y5P0;E9PNV3;E9PQ82 A0A2R8Y5S7 RDX Radixin 0 117.55 4.18E-05 0 108380 104220 120270 114190 94387 118630 119590 118570 72300 FALSE TRUE 103257.0922 114840.1365 125784.4985 102711.4043 110848.0629 114521.8134 101344.3491 108187.3822 83511.91474 1.236435454 1.375134756 1.506186259 1.229901201 1.327332312 1.371323047 1.213531619 1.295472419 1 16.34969442 0.269787449 0.580744874 0.984893267 1.341886011 0.603670624 0.083444387 1.799034292 0.876795636 0.143546998 0.034416542 1.861176021 -0.269787449 0.356992744 AKFFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKFFSR 6 1 P46776;E9PJD9;E9PLX7 P46776 RPL27A 60S ribosomal protein L27a 0 ; 107.43 0.028522 670790000 1147170 624050 706510 745950 1332050 830920 1528540 1061280 1661110 FALSE TRUE 1092945.548 687641.4045 738904.1823 670965.6888 1564359.098 802145.0321 1295333.149 968348.697 1918706.455 0.569626242 0.358388018 0.385105382 0.349696895 0.815319662 0.418065531 0.675107516 0.504688299 1 20.87170258 -1.142426894 0.253596269 1.350050589 0.413012503 0.554165044 0.142627728 12.08271387 0.681201937 3.110170197 0.212957344 0.072039901 1.142426894 -0.937038086 AKGPS(ph)PPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AKGPSPPGAK 10 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 AKGPS(1)PPGAK;AKGPS(1)PPGAK;AKGPS(1)PPGAK 74.475 0.025363 562640000 3937460 3381090 3487240 4458180 2180120 4432320 4424110 4629140 2505080 TRUE FALSE 3751344.069 3725626.915 3647133.403 4010035.276 2560332.238 4278827.647 3749130.765 4223787.961 2893555.012 1.296448159 1.287560423 1.260433407 1.385850713 0.884839662 1.478744185 1.295683251 1.459722709 1 21.46441164 AKGPSES(ph)SKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.01)ES(0.495)S(0.495)KER 53.754 0.070964 327930000 506990 432270 476390 559650 286260 528140 550100 566610 282310 TRUE FALSE 483025.5875 476318.8045 498232.9527 503392.9187 336183.6534 509850.3794 466172.1417 516994.6246 326089.193 1.481268309 1.460700982 1.527903909 1.543727697 1.030956133 1.56353044 1.429584763 1.585439309 1 18.3149071 -1.230650423 3.771075192 0.999436026 1.450994986 0.449603967 0.157464479 8276494.541 5402041.082 35266.3922 0.033683369 0.058796243 1.230650423 0.45155896 AKGPSESS(ph)KER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.001)ES(0.07)S(0.928)KER;AKGPSES(0.037)S(0.962)KER 103.6 0.0021358 565970000 656250 570850 603260 671750 335930 728710 742170 737940 403670 TRUE FALSE 625230.3631 629020.264 630920.0677 604224.4138 394516.0856 703474.59 628938.3356 673322.0615 466269.0819 1.340921771 1.349049912 1.353124391 1.29587064 0.846112472 1.508730939 1.348874202 1.444063284 1 18.83080324 3.00599648 23.68795029 1.261030443 1.344204856 0.059275778 0.195215183 327.1186438 1292192.038 0.054812012 0.065312438 1013.903168 -3.00599648 0.083174413 AKGPSESSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKGPSESSK 9 1 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 0 85.813 0.01328 83802000 28849 25157 29336 32601 25577 27694 36008 32272 35004 FALSE TRUE 27485.36494 27720.5269 30681.08462 29323.88554 30037.6207 26734.94984 30514.31827 29446.0926 40432.24154 0.679788305 0.685604504 0.758827199 0.725259952 0.742912576 0.661228485 0.754702611 0.728282466 1 15.30321857 -5 0.290118745 3.237351508 0.697501001 0.889292772 0.031501061 73.49814729 0.692040852 99.47580738 0.032374231 1.00E-05 5 -2.539850507 AKHDELTYF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKHDELTYF 9 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 87.913 0.011983 371460000 1077800 671240 635760 1000600 750140 722600 1233400 980940 826260 FALSE TRUE 1026854.53 739640.1191 664910.2249 900017.787 880964.1785 697576.1808 1045222.177 895043.6933 954392.1808 1.075925129 0.774985519 0.696684485 0.943027201 0.923063072 0.730911458 1.095170516 0.937815409 1 19.8642227 1.716704476 14.21167515 1.011571496 0.864372277 0.279354301 0.115894031 0.180889724 99.50068121 0.053301763 0.029358124 52.08401749 -1.716704476 -0.147199219 AKHHAISAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKHHAISAK 9 1 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 119.68 0.00047338 626630000 1077250 575050 457360 635960 1364440 697870 1542410 836330 270130 FALSE TRUE 1026330.527 633648.2488 478330.4084 572032.0926 1602397.904 673702.5869 1307087.026 763096.5115 312020.3808 3.289306054 2.030791217 1.533010143 1.833316436 5.135555248 2.15916212 4.189107849 2.445662394 1 18.25128074 AKIDDPTDSKPEDWDKPEHIPDPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKIDDPTDSKPEDWDKPEHIPDPDAK 26 3 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 138.02 6.44E-06 896640000 2810600 2540200 2150400 2957300 892440 3172100 2510500 3313400 644970 FALSE TRUE 2677748.508 2799049.268 2248997.967 2660026.585 1048081.253 3062249.382 2127477.117 3023261.131 744988.6535 3.594348042 3.757170334 3.018835195 3.570559864 1.406841901 4.110464457 2.855717475 4.058130437 1 19.50685893 3.543735772 1.889398418 2.933439072 3.68236532 0.097126051 1.009020203 0.807881654 5.72356143 0.270090753 0.477346837 3497.323228 -3.543735772 0.748926248 AKKDDTDDEIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKKDDTDDEIAK 12 2 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 ; 115.12 0.0005535 650210000 813790 671470 647060 1112070 438440 1000280 891280 925400 345380 FALSE TRUE 775323.7595 739893.5564 676728.341 1000282.611 514903.7972 965640.0528 755298.8665 844367.0701 398939.7664 1.943460704 1.854649796 1.696317083 2.507352475 1.29068055 2.420515912 1.893265425 2.11652771 1 18.60581141 -0.519274159 7.542227226 0.999913876 1.957707425 0.436270955 0.344762663 0 0 0.282293767 0.066537279 0.302500322 0.519274159 0.95779355 AKLAEQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AKLAEQAER 9 1 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947 P27348;P31946-2;P63104;P31947-2 YWHAQ;YWHAB;YWHAZ;SFN "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" 0 ;;; 145.46 8.86E-05 1653860000 1893220 848280 1456080 1004460 2064720 1447950 2763250 1915180 2911900 FALSE TRUE 1803731.243 934720.6964 1522842.708 903489.7725 2424806.514 1397807.128 2341665.462 1747476.686 3363462.58 0.53627213 0.277904295 0.452760413 0.268618946 0.72092567 0.415585753 0.696206783 0.519546938 1 21.68151578 0.431272267 0.35494647 1.07801823 0.374803042 0.611047873 0.13703386 1.746510893 0.422671575 0.372425864 0.11396288 2.699431227 -0.431272267 -0.703215188 AKLEEHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKLEEHFK 8 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 76.716 0.021079 356210000 1145200 1070400 931210 1181700 969810 1171500 1360400 1398700 959740 FALSE TRUE 1091068.666 1179474.977 973906.8996 1062913.271 1138944.557 1130930.661 1152845.995 1276222.413 1108571.578 0.984211293 1.063959243 0.878524147 0.958813389 1.027398302 1.020169274 1.039938257 1.151231403 1 20.08027049 1.915986941 1.61098437 1.072883514 0.986754281 0.288068619 0.059464347 0.52414446 2.538075284 0.040043981 0.018208062 82.41133344 -1.915986941 -0.086129233 AKLEQLFQDEVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 138.19 4.74E-05 264740000 347010 296760 301270 362850 246040 348940 386090 410070 285420 FALSE TRUE 330607.525 327000.1814 315083.5275 326375.6286 288949.2981 336856.1203 327184.8795 374162.0969 329681.4759 1.002808921 0.991867015 0.955721054 0.989972602 0.876449905 1.021762352 0.992427247 1.134919989 1 18.3307133 1.40731479 5.632073193 1.068678214 0.976687785 0.364357008 0.050427567 0.204796607 10.37993923 0.031446351 0.011578268 25.54552251 -1.40731479 -0.091990429 AKLNWLSVDFNNWKDWEDDS(ph)DEDMSNFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AKLNWLSVDFNNWKDWEDDSDEDMSNFDR 29 2 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 AKLNWLSVDFNNWKDWEDDS(0.999)DEDMS(0.001)NFDR;AKLNWLSVDFNNWKDWEDDS(0.999)DEDMS(0.001)NFDR;AKLNWLSVDFNNWKDWEDDS(0.999)DEDMS(0.001)NFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR 407.23 5.69E-175 11563272000 2488666 1428059 2188245 2066653 1602870 2355532 3093260 2551609 1919302 TRUE FALSE 2371031.69 1573579.836 2288578.198 1858909.114 1882410.021 2273959.336 2621326.375 2328176.589 2216937.552 1.069507659 0.7097989 1.032315139 0.838503147 0.849103764 1.02572097 1.182408757 1.050176893 1 21.0801367 2.069915895 4.872319768 1.0995429 0.893551725 0.357335112 0.109809179 0.180706587 8.19267524 0.040130321 0.028702739 117.4670047 -2.069915895 -0.205991175 AKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 36 2 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 184.15 2.90E-23 242860000 275950 150090 244430 265150 241970 244760 424030 292300 213240 FALSE TRUE 262906.3904 165384.3416 255637.3573 238496.6182 284169.4914 236283.8998 359336.4357 266704.6624 246308.1701 1.067388021 0.671452926 1.037876077 0.968285454 1.153715247 0.959301917 1.458889632 1.082808834 1 17.91010496 2.792434131 1.211342167 1.195653204 0.882225495 0.21848148 0.17179873 0.474718901 1.444436899 0.075452688 0.074228414 620.0605923 -2.792434131 -0.313427709 AKLTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 253.26 6.30E-58 565993000 725660 504003 760648 684004 717315 771546 923191 874289 799770 FALSE TRUE 691359.4899 555361.4787 795524.4632 615246.6184 842414.5089 744827.1686 782341.2574 797731.6203 923794.2469 0.748391205 0.601174429 0.861148969 0.665999621 0.911907074 0.806269547 0.846878252 0.863538199 1 19.81721204 2.08007298 0.246470489 1.0295302 0.612474814 0.532933737 0.079391928 1.609849436 0.332340121 0.170591275 0.251016174 120.2466483 -2.08007298 -0.417055386 AKNS(ph)PPQAPSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AKNSPPQAPSTR 12 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 AKNS(1)PPQAPSTR;AKNS(0.999)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR 111.22 0.00085101 492336000 493460 528000 522090 579990 385081 578630 631480 635340 526210 TRUE FALSE 470135.1237 581803.8003 546028.3429 521688.3033 452239.0045 558591.898 535136.1281 579706.2615 607811.9593 0.773487781 0.957210189 0.898350772 0.858305427 0.744044268 0.919020907 0.880430403 0.953759222 1 19.21326554 1.173699111 1.515055433 0.999903257 0.86014034 0.389225368 0.062465764 0.404890524 1.782866724 0.057130738 0.01718519 14.91760525 -1.173699111 -0.139762917 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 AKNWEDEDFYDS(0.999)DDDT(0.001)FLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(0.999)DDDT(0.001)FLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR 216.51 6.79E-25 2399650000 1906930 1645000 1856460 1954200 1535300 1895080 2256650 2127900 1864670 TRUE FALSE 1816793.198 1812627.37 1941580.527 1757760.103 1803055.834 1829452.904 1912356.596 1941569.795 2153833.5 0.843516083 0.841581938 0.901453398 0.8161077 0.837137984 0.849393839 0.887885065 0.901448415 1 21.0384753 0.857434185 0.993830919 0.9994186 0.846891241 0.820865575 0.022241826 0.274185916 0.540354801 0.020015794 0.006571543 7.201686055 -0.857434185 -0.152527359 AKNWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKNWVK 6 1 P20339-2;P20339;P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;K7ENY4 P20339-2;P51148 RAB5A;RAB5C Ras-related protein Rab-5A;Ras-related protein Rab-5C 0 ; 91.26 0.043863 678430000 908230 666470 716030 794970 919260 824280 1071670 854390 1031760 FALSE TRUE 865299.7678 734384.0507 748860.6838 715058.1053 1079578.653 795734.9769 908167.0589 779575.0822 1191760.071 0.726068769 0.616218036 0.628365308 0.600001731 0.905869125 0.667697296 0.762038502 0.654137608 1 20.18466239 -5 0.211639772 2.485225505 0.650780321 0.535220509 0.089373891 110.0995183 1.09794985 69.40089356 0.17370281 1.00E-05 5 -1.834445183 AKPAMPQDSVPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 AKPAMPQDS(0.15)VPS(0.85)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDS(0.374)VPS(0.626)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDS(0.006)VPS(0.994)PR;AKPAMPQDS(0.004)VPS(0.996)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.05)VPS(0.95)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.249)VPS(0.751)PR;AKPAMPQDS(0.003)VPS(0.997)PR;AKPAMPQDS(0.004)VPS(0.996)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.002)VPS(0.998)PR;AKPAMPQDS(0.429)VPS(0.571)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDS(0.013)VPS(0.987)PR;AKPAMPQDSVPS(1)PR 195.77 1.56E-08 40906070000 15483110 13828540 14633830 16651690 13805040 15560360 17756230 16386950 15680930 TRUE FALSE 14751254.07 15237683.95 15304805.58 14977830.49 16212634.61 15021500.83 15047191 14952021.79 18112648.54 0.814417287 0.841273098 0.844978886 0.826926579 0.89510016 0.82933762 0.830755975 0.825501679 1 24.11049419 -1.502710778 3.976827086 1.00170637 0.837928603 0.843992972 0.021814841 0.000316946 3.96E-05 0.02028431 0.004732404 0.031426008 1.502710778 -0.163777767 AKPAMPQDSVPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 0 118.19 0.00023688 114110000 159390 134500 155740 178300 152160 149850 180410 162230 165650 FALSE TRUE 151855.9506 148205.7029 162880.833 160376.9453 178696.6558 144660.6569 152885.141 148024.2812 191338.156 0.793652211 0.774574743 0.851272096 0.838185904 0.933931107 0.756047095 0.79903112 0.773626569 1 17.54576507 -2.127757261 2.447630408 1.386559523 0.811861909 0.562268735 0.051219349 18898354.7 5789581.424 40515607.55 0.012250361 0.007451483 2.127757261 -0.574697614 AKPDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKPDFK 6 1 P13489;E9PMJ3;E9PLZ3;E9PIM9 P13489 RNH1 Ribonuclease inhibitor 0 ; 66.258 0.092919 2075530000 5539300 4377700 4276300 5974400 3764200 5200100 5942500 6081400 4224500 FALSE TRUE 5277468.267 4823792.607 4472372.585 5373841.961 4420675.288 5020019.233 5035862.483 5548880.376 4879613.884 1.081533989 0.988560309 0.916542311 1.101284259 0.905947764 1.028773865 1.032020689 1.137155625 1 22.21833556 1.562687652 3.47419813 1.071991941 1.004829325 0.122993309 0.069398926 0.368620806 10.11389582 0.041116285 0.016688402 36.53319478 -1.562687652 -0.067162616 AKPPADPAAAAS(ph)PCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR 123.6 6.16E-05 3570050000 4857920 4298100 4592350 5106900 4386100 5082360 5995800 5886620 5899860 TRUE FALSE 4628295.749 4736081.277 4802913.79 4593544.71 5151034.451 4906356.599 5081030.59 5371156.346 6814780.156 0.679155548 0.694971983 0.704778977 0.674056184 0.75586216 0.719958162 0.745589802 0.78816282 1 22.70023569 -0.714196267 0.312190018 1.128727536 0.676083263 0.964589139 0.017825054 1.644066156 0.153597284 0.218446209 0.016872859 0.193109542 0.714196267 -0.452644274 AKPPVKPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKPPVKPKPR 10 3 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 94.692 0.0034743 537840000 1017770 885280 814380 960850 693150 895000 998000 1041810 734040 FALSE TRUE 969662.0291 975491.0385 851720.1285 864263.5325 814035.1405 864005.9256 845736.7705 950583.5934 847871.1742 1.143643113 1.150517989 1.004539551 1.019333548 0.960092954 1.01902972 0.997482632 1.121141539 1 19.69348555 3.740162498 24.97326753 1.014097594 1.147080559 0.634738831 0.04084719 71.90214821 1120946.636 0.009903741 0.016709518 5497.465322 -3.740162498 0.132982966 AKPS(ph)PHPIKDK ddPTM_SK-BR-3_Trastuzumab_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 73.834 0.022163 1311470000 2371500 1981070 2028550 2404900 1273710 2395800 2700300 2668400 918040 TRUE FALSE 2259403.895 2182943.285 2121561.024 2163154.883 1495844.621 2312832.845 2288319.641 2434740.75 1060404.955 2.130699112 2.058594008 2.000708328 2.039932833 1.410635262 2.181084533 2.1579677 2.296048071 1 20.01618389 3.542641779 1.909755457 1.925818406 2.100930987 0.044689281 0.393201099 1.389329302 10.05440903 0.109358549 0.192407539 3488.524515 -3.542641779 0.175112581 AKPVATAPIPGTPWCVVWTGDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKPVATAPIPGTPWCVVWTGDER 23 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 164.66 1.28E-11 480980000 783720 674000 723070 798390 720890 758100 862760 789110 812870 FALSE TRUE 746675.1088 742681.3663 756223.4747 718134.3204 846612.9878 731846.8069 731130.1163 720011.3451 938925.728 0.795244061 0.790990537 0.805413519 0.764846781 0.901682596 0.779451223 0.778687914 0.7668459 1 19.84065152 -1.060983337 4.451080434 1.000011362 0.797244079 0.726724761 0.038946975 4.80E-06 1.01E-06 0.034924986 0.008231354 0.086899377 1.060983337 -0.202767283 AKQEQEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKQEQEAK 8 1 P05455 P05455 SSB Lupus La protein 0 98.249 0.0069828 40011000 65097 64199 57197 78505 43047 64170 76588 105850 64449 FALSE TRUE 62019.99382 70740.95109 59819.53903 70613.52825 50554.38317 61947.77681 64903.09396 96581.21285 74443.42176 0.83311584 0.950264636 0.803557086 0.948552963 0.679098058 0.832145747 0.871844583 1.297377398 1 16.18385675 1.313518274 8.235597049 1.147097471 0.850943004 0.597266794 0.103473664 0.14645076 14.00175315 0.062809876 0.0228329 20.58345496 -1.313518274 -0.296154467 AKQGYVIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKQGYVIYR 9 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 112.11 0.0018388 298950000 351320 225660 263080 267890 424760 271680 459570 369530 475670 FALSE TRUE 334713.7998 248655.0106 275142.4782 240961.1882 498838.0095 262271.6535 389454.1559 337171.9942 549434.4742 0.609196939 0.45256536 0.500773961 0.438562194 0.90791174 0.477348375 0.708827302 0.613670984 1 19.06758791 -2.293615366 0.19291399 1.595469069 0.472249981 0.503405342 0.134736963 30.72535679 0.780171818 8.272935107 0.361366683 0.005086097 2.293615366 -1.123219087 AKQTLENER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AKQTLENER 9 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 169.58 5.32E-05 768670000 1506270 1053500 882560 1147040 1336190 1194930 1635920 1367050 1447740 FALSE TRUE 1435071.602 1160852.848 923026.249 1031737.36 1569221.113 1153549.274 1386330.358 1247343.855 1672248.125 0.85816906 0.694186963 0.55196728 0.61697624 0.938390116 0.689819446 0.829021924 0.745908359 1 20.6733575 2.751164358 24.98652052 0.817594645 0.695264722 0.303932247 0.116743552 1238.378281 2455044.256 0.035393408 0.037306243 563.8510039 -2.751164358 -0.122329923 AKREEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKREEELR 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 104.89 0.0025273 164263000 233536 135901 211568 204835 303590 200264 296414 249490 351830 FALSE TRUE 222497.2161 149749.4664 221268.6021 184244.5966 356535.9999 193328.8075 251190.6003 227643.333 406389.9995 0.54749678 0.368487085 0.544473541 0.453368924 0.877324738 0.475722355 0.618102317 0.560159781 1 18.63250537 -5 0.158498612 2.694574179 0.416666555 0.548443788 0.129641747 93.96375781 0.859973005 49.99326744 0.521802781 1.00E-05 5 -2.277907624 AKREELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKREELER 8 2 Q9NWB6 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 117.01 0.0012152 78215000 76552 49172 69379 57023 113350 68980 109440 88940 129840 FALSE TRUE 72933.53867 54182.6827 72560.09578 51290.9397 133118.2041 66591.2053 92742.918 81151.9421 149974.9241 0.486304888 0.361278281 0.483814853 0.341996771 0.887603077 0.444015596 0.618389498 0.541103405 1 17.19436178 -5 0.137741627 2.712412908 0.323578266 0.5433882 0.145045465 97.53559883 0.828701652 45.66592046 0.841952283 1.00E-05 5 -2.388834643 AKS(ph)LDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AKS(1)LDRR;AKS(1)LDRR 103.26 0.0066288 3627320000 7026340 5443660 6102010 6982560 5209240 6680180 7772010 7072000 6103440 TRUE FALSE 6694218.833 5998375.143 6381793.194 6280659.803 6117729.807 6448843.692 6586247.132 6452738.189 7049930.303 0.949543974 0.850841765 0.905227842 0.890882538 0.867771672 0.914738645 0.934228687 0.915291061 1 22.74917756 0.72050826 0.702847851 0.999931654 0.893473281 0.565025819 0.027640227 0.793260182 0.772119107 0.027377196 0.00999613 5.254220076 -0.72050826 -0.106458372 AKS(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 29 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(0.983)PQPPVEEEDEHFDDT(0.017)VVCLDTYNCDLHFK;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(0.984)PQPPVEEEDEHFDDT(0.016)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDT(0.001)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDT(0.001)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.974)PQPPVEEEDEHFDDT(0.026)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 326.45 3.45E-108 65501410000 4989996.4 5423263.1 4775655.3 5135509.1 2911359.8 5220255.9 4738629.1 5590901.2 2003862.1 TRUE FALSE 4754129.159 5975899.776 4994623.819 4619277.968 3419100.027 5039477.129 4015664.2 5101332.252 2314610.8 2.053964822 2.58181625 2.157867672 1.995703972 1.477181402 2.17724601 1.73491984 2.203969778 1 21.1423382 -1.42901466 0.17556926 2.38E-13 2.444326819 0.562455577 0.290900851 19.83242091 0.631848518 10.52145579 1.158629638 0.037237914 1.42901466 2.444326819 AKS(ph)PT(ph)PDGSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.998)PT(0.999)PDGS(0.003)ER;AKS(1)PT(1)PDGS(0.001)ER 162.96 0.00061482 1771500000 3428500 2819900 2985500 3454800 1976990 3494900 3706200 3776000 2371060 TRUE FALSE 3266441.6 3107251.016 3122388.128 3107516.94 2321776.43 3373870.737 3140751.121 3445353.422 2738751.875 1.192675258 1.134550028 1.140077039 1.134647125 0.847749828 1.23190084 1.146781915 1.258001301 1 21.38508714 4.308932547 1.354580172 1.113903045 1.197100985 0.050321225 0.115721797 2.373970755 6.501533459 0.032020192 0.21985387 20367.25715 -4.308932547 0.08319794 AKS(ph)PTPDGS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.791)PT(0.342)PDGS(0.867)ER 100.18 0.050446 193760000 694510 568340 574770 668260 408200 722970 752860 769780 480150 TRUE FALSE 661681.8887 626254.4921 601123.773 601085.2352 479389.9508 697933.3676 637997.3798 702373.9823 554609.2097 1.193059684 1.129181559 1.083869078 1.083799592 0.864374306 1.258423689 1.150354824 1.266430434 1 19.08111205 -0.144862095 7.528252012 1.000000002 1.129380809 0.114059701 0.11269774 0 5.46E-18 0.104353943 0.02459646 0.716370849 0.144862095 0.129380807 AKSEDS(ph)DVELS(ph)D ddPTM_SK-BR-3_Trastuzumab_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(0.003)EDS(0.997)DVELS(1)D;AKSEDS(1)DVELS(1)D 147.51 0.00071183 586960000 2094000 1787470 2000110 2230000 1380330 2229200 2459700 2198100 1616130 TRUE FALSE 1995020.77 1969615.225 2091817.022 2005836.163 1621059.115 2152002.245 2084427.59 2005622.711 1866751.186 1.068712737 1.05510324 1.120565524 1.074506436 0.868385207 1.152806148 1.116607079 1.074392091 1 20.83209822 AKSEENQGDNSS(ph)ENGNGKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKSEENQGDNSSENGNGKEK 20 2 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 AKSEENQGDNS(0.391)S(0.609)ENGNGKEK 52.321 0.064712 46730000 16117 10850 16105 15059 8177 15903 15908 16494 9849.4 TRUE FALSE 15355.18135 11955.62734 16843.43018 13545.24071 9603.066211 15352.27512 13480.94243 15049.69792 11376.79465 1.34969311 1.050878363 1.480507533 1.190602549 0.844092427 1.349437658 1.184950845 1.32284166 1 13.47380652 -2.356640332 1.882399723 7.68E-05 1.213132521 0.131489202 0.177817732 2510905.813 284101.8956 10651333.75 0.039870658 0.004399058 2.356640332 1.213055684 AKSEENTKEEKPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKSEENTKEEKPDSK 15 3 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ; 104.45 0.00061001 501500000 1295830 885730 1149220 1365050 604320 1424940 1495620 1657520 599700 FALSE TRUE 1234578.684 975986.894 1201912.874 1227832.581 709713.2167 1375593.971 1267435.7 1512378.762 692698.4132 1.782274451 1.408963664 1.735117117 1.772535576 1.024563076 1.985848306 1.829707815 2.183314893 1 19.40186784 AKSEGTYLNSVIESHTEFIFTTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKSEGTYLNSVIESHTEFIFTTIK 24 1 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 253.13 5.38E-44 29815000 73876 68489 74997 82360 56015 82006 83018 93616 49762 FALSE TRUE 70384.02789 75468.10697 78435.68663 74081.01633 65783.99826 79166.11166 70352.07937 85418.48675 57478.83681 1.224520742 1.312972063 1.364601147 1.288839866 1.144490771 1.377308868 1.223964911 1.486085862 1 15.81074325 -0.822808309 5.347693781 0.999999851 1.293892159 0.498691111 0.095049159 1.50E-07 3.26E-08 0.081285722 0.019159219 0.150380558 0.822808309 0.293892308 AKSPT(ph)PDGS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.419)PT(0.638)PDGS(0.943)ER;AKS(0.166)PT(0.917)PDGS(0.917)ER 149.71 0.00085837 688980000 1521810 1275380 1286510 1493580 815490 1562340 1669570 1682470 1065200 TRUE FALSE 1449877.057 1405342.672 1345497.756 1343442.501 957711.1978 1508235.774 1414846.433 1535144.007 1230385.776 1.178392246 1.142196781 1.093557633 1.091887217 0.778382859 1.225823481 1.149920993 1.247693234 1 20.2306793 -0.277667223 7.436378874 1.000000027 1.116230655 0.07046228 0.129191564 0 0 0.120361655 0.028369514 0.527634005 0.277667223 0.116230628 AKT(ph)GGAYGEDLGADYNLSQVCDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AKTGGAYGEDLGADYNLSQVCDGK 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 1 AKT(1)GGAYGEDLGADYNLSQVCDGK;AKT(0.998)GGAY(0.002)GEDLGADYNLSQVCDGK;AKT(1)GGAYGEDLGADYNLSQVCDGK 190.23 1.99E-17 361246000 317953 214039 271783 276972 175561 275242 305228 285754 217139 TRUE FALSE 302923.9918 235849.8174 284244.5194 249130.2483 206178.7828 265710.3005 258659.8627 260731.8649 250811.8071 1.207774049 0.940345752 1.133298 0.993295536 0.822045761 1.059401085 1.031290615 1.039551797 1 17.93624574 4.650742922 3.132600336 1.005600684 1.220155291 0.384747319 0.081244745 0.305315786 4.836521799 0.019104862 0.142677686 44744.83611 -4.650742922 0.214554607 AKT(ph)PVTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.954)PVT(0.046)LK;AKT(0.966)PVT(0.034)LK;AKT(0.995)PVT(0.005)LK;AKT(0.997)PVT(0.003)LK 97.911 0.012765 5618780000 11733550 10594650 10931310 17249290 10563620 15647280 17018280 14574980 9530190 TRUE FALSE 11178928.35 11674256.88 11432521.38 15515358.6 12405911.98 15105410.77 14421828.82 13298717.48 11008083.19 1.015519973 1.060516775 1.038556956 1.40945143 1.126982034 1.372210812 1.31011263 1.208086572 1 23.39205994 3.266564618 24.91661914 1.260959543 1.039740635 0.376352775 0.118653476 168.7468251 150141.6971 0.028908477 0.039134039 1847.415648 -3.266564618 -0.221218908 AKT(ph)QTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.5)QT(0.5)PPVS(0.614)PAPQPT(0.255)EERLPS(0.069)S(0.062)PVYEDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPTEERLPSSPVYEDAASFK;AKT(0.5)QT(0.5)PPVS(0.994)PAPQPT(0.004)EERLPS(0.001)S(0.001)PVYEDAASFK 167.64 7.99E-14 2153370000 306883 207165 295642 284092 202722 288191 353437 314299 234974 TRUE FALSE 292377.2488 228275.349 309197.4781 255534.5324 238076.6526 278210.8734 299513.6943 286777.3134 271412.5678 1.077242852 0.841064033 1.139215772 0.941498525 0.877176228 1.025047866 1.103536571 1.056610295 1 18.050128 2.00556667 24.97293342 1.064737829 0.97038368 0.135956559 0.089399911 226.2695604 1015072.926 0.031562575 0.023238966 101.2900231 -2.00556667 -0.094354149 AKT(ph)QTPPVSPAPQPTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.622)QT(0.378)PPVSPAPQPTEER 76.417 0.024683 332710000 166840 171120 168730 212750 105570 186260 166320 175900 116820 TRUE FALSE 158953.8038 188557.3225 176466.4374 191363.9658 123981.3746 179809.7695 140944.8293 160497.2635 134935.849 1.177995359 1.397384935 1.307780243 1.418184769 0.918817168 1.33255744 1.044532127 1.189433829 1 17.04191416 2.756622601 24.93208445 1.114788214 1.319997869 0.439614316 0.127128875 750.4430102 1035881.932 0.034790615 0.036832177 570.9822407 -2.756622601 0.205209655 AKT(ph)QTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.5)QT(0.5)PPVS(0.262)PAPQPT(0.211)EERLPS(0.285)S(0.242)PVYEDAASFK 190 1.19E-19 1805400000 306500 211800 294120 272900 200390 286490 355610 300460 210480 TRUE FALSE 292012.3524 233382.6608 307605.6929 245467.5735 235337.9526 276568.7795 301355.1633 274150.1296 243120.1634 1.201102979 0.959947779 1.265241388 1.009655349 0.96799027 1.137580592 1.239531757 1.12763222 1 17.89131002 2.01804771 24.70035169 1.15889106 1.078097086 0.006291768 0.112371846 460.7936931 630646.0902 0.039274993 0.029000815 104.2431942 -2.01804771 -0.080793975 AKT(ph)QTPPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.534)QT(0.448)PPVS(0.018)PAPQPTEERLPSSPVYEDAASFK 80.816 0.038775 1470300000 21879 20515 22754 21059 19563 25325 26492 29654 22966 TRUE FALSE 20844.82303 22605.50182 23797.29341 18942.10931 22974.78101 24447.9889 22450.15884 27057.33855 26527.44999 0.785783143 0.852155101 0.897081831 0.714056923 0.866075745 0.92161097 0.846299168 1.019975104 1 14.69519838 1.406584345 1.045281395 1.013908727 0.824071015 0.562062528 0.06021051 0.342925889 0.749030076 0.051704989 0.018215977 25.50259328 -1.406584345 -0.189837712 AKTGGAYGEDLGADYNLSQVCDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AKTGGAYGEDLGADYNLSQVCDGK 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 ;; 260.48 4.67E-44 806720000 701060 362502 745900 566590 634910 712890 1062240 839790 867640 FALSE TRUE 667922.2832 399441.3659 780100.2528 509635.2967 745638.103 688202.4405 900175.7786 766253.5356 1002189.18 0.666463275 0.398568827 0.778396203 0.50852205 0.744009333 0.686699133 0.898209437 0.764579733 1 19.93472344 1.862948438 0.533361979 0.983243652 0.541271119 0.563266055 0.114042707 0.519247464 0.324966719 0.100429511 0.067433741 72.93709101 -1.862948438 -0.441972533 AKTQT(ph)PPVS(ph)PAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.473)QT(0.539)PPVS(0.988)PAPQPT(0.495)EERLPS(0.254)S(0.238)PVY(0.012)EDAASFK 81.128 0.0040226 180410000 43174 32334 46762 45098 34421 43810 50204 45214 40344 TRUE FALSE 41133.25058 35628.87136 48906.08395 40564.66336 40424.0115 42292.84871 42544.45774 41254.82247 46600.34147 0.882681313 0.764562452 1.04947909 0.87047996 0.867461701 0.90756521 0.912964506 0.885290132 1 15.50805291 -4.999999911 0.061698218 1.39402214 0.721224334 0.172661163 0.069916946 570.5961562 2.565304506 34.03675474 5.404358938 1.00E-05 4.999999911 -0.672797806 AKTQT(ph)PPVS(ph)PAPQPTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.076)QT(0.924)PPVS(1)PAPQPTEER;AKT(0.04)QT(0.96)PPVS(1)PAPQPTEER;AKT(0.169)QT(0.831)PPVS(1)PAPQPTEER;AKT(0.046)QT(0.954)PPVS(1)PAPQPTEER;AKT(0.05)QT(0.95)PPVS(0.999)PAPQPT(0.001)EER 110.91 0.00073319 3454580000 4234320 4331720 3940130 4863440 3084830 4299730 3864600 3905940 2684170 TRUE FALSE 4034172.085 4773127.193 4120788.858 4374557.771 3622823.375 4150829.272 3274984.292 3563915.187 3100417.375 1.301170648 1.539511174 1.329107781 1.410957701 1.168495379 1.338796933 1.056304328 1.149495296 1 21.56403101 2.024592319 0.687417837 1.017076782 1.42243675 0.673058012 0.093961024 0.35835151 0.326282395 0.075497651 0.043394264 105.8259848 -2.024592319 0.405359967 AKTQT(ph)PPVSPAPQPTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.173)QT(0.827)PPVSPAPQPTEER;AKT(0.04)QT(0.96)PPVSPAPQPTEER;AKT(0.023)QT(0.977)PPVSPAPQPTEER;AKTQT(1)PPVSPAPQPTEER;AKT(0.008)QT(0.992)PPVSPAPQPTEER;AKT(0.001)QT(0.999)PPVSPAPQPTEER;AKT(0.002)QT(0.998)PPVSPAPQPTEER;AKT(0.379)QT(0.62)PPVSPAPQPTEER 195.36 4.13E-15 5533940000 4889573 5215698 4504251 5740530 3251421 4824080 4756304 4895115 3313794 TRUE FALSE 4658452.574 5747183.556 4710775.364 5163481.018 3818467.793 4657020.9 4030642.469 4466472.78 3827680.249 1.217043293 1.501479534 1.230712875 1.348984419 0.997593201 1.216669261 1.053024863 1.166887642 1 21.86803889 2.752047112 24.89804813 1.097782832 1.336883262 0.571152887 0.101862832 497.7804698 918974.9608 0.028581298 0.030161282 564.9982619 -2.752047112 0.239100431 AKTQT(ph)PPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.164)QT(0.836)PPVS(0.006)PAPQPT(0.218)EERLPS(0.293)S(0.483)PVYEDAASFK 216.71 1.61E-35 236470000 305570 190440 309120 268080 211590 296430 353480 307370 225490 TRUE FALSE 291126.3117 209846.0525 323293.4578 241132.0891 248491.229 286164.5548 299550.1339 280455.0533 260457.8376 1.117748325 0.805681466 1.241250641 0.925800856 0.954055487 1.09869819 1.150090689 1.07677717 1 17.99069032 2.221207511 23.77520656 1.100091082 0.997872871 0.068866738 0.120516669 260.7684703 357270.3434 0.042134993 0.031206315 166.4207639 -2.221207511 -0.102218212 AKTQT(ph)PPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.34)QT(0.66)PPVSPAPQPTEERLPSSPVYEDAASFK;AKT(0.21)QT(0.789)PPVS(0.001)PAPQPTEERLPSSPVYEDAASFK 240.8 4.42E-45 1057159000 327466 246112 329090 335209 215448 327350 430114 351086 292078 TRUE FALSE 311987.3312 271191.0926 344179.102 301513.1545 253022.063 316013.7874 364492.2097 320343.0486 337371.9645 0.924757727 0.803834109 1.020176951 0.893711352 0.749979517 0.936692496 1.080386778 0.949524804 1 18.36398057 1.995104767 24.99717025 1.016311717 0.87662321 0.37728382 0.077017796 196.7652696 1004770.876 0.028078005 0.020187848 98.8791597 -1.995104767 -0.139688507 AKTQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPT(0.02)EERLPS(0.447)S(0.447)PVY(0.085)EDAASFK;AKTQTPPVSPAPQPT(0.004)EERLPS(0.528)S(0.458)PVY(0.009)EDAASFK 93.36 5.35E-05 2414880000 289201 186055 312182 246594 228937 314359 409123 333399 316072 TRUE FALSE 275531.0419 205014.216 326495.8535 221805.9026 268863.5403 303472.669 346703.7723 304204.8161 365086.8315 0.754700028 0.561549194 0.894296439 0.607542873 0.736437245 0.831234224 0.949647433 0.833239629 1 18.47788011 2.123985354 2.418238502 0.920454551 0.695029173 0.51241756 0.096880683 0.219055154 2.534289088 0.042839402 0.02669115 133.0409551 -2.123985354 -0.225425378 AKVDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AKVDEFPLCGHMVSDEYEQLSSEALEAAR 29 1 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;; 313.05 2.49E-92 726340000 450777 371727 422928 491670 389927 443450 547873 503044 417873 FALSE TRUE 429469.6646 409606.4039 442319.6671 442246.3975 457930.1453 428093.2153 464284.9115 458994.8006 482674.6106 0.889770572 0.848618085 0.916393068 0.916241268 0.948734686 0.88691886 0.961900422 0.950940427 1 18.88069142 2.261206929 0.24442928 1.013604683 0.837321222 0.676953524 0.024626397 1.423213621 0.256706929 0.053417372 0.090006248 182.4764942 -2.261206929 -0.176283461 AKVEEAR ddPTM_SK-BR-3_Trastuzumab_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 ; 87.476 0.017614 438168000 1172910 1011180 926990 1148040 924310 1077600 1331400 1177930 1065080 FALSE TRUE 1117468.869 1114220.392 969493.4084 1032636.838 1085509.371 1040282.442 1128270.477 1074784.205 1230247.167 0.908328748 0.90568824 0.788047666 0.839373474 0.882350637 0.845588163 0.917108779 0.873632741 1 20.23051676 0.237114955 0.786171327 1.001886284 0.869549184 0.536847244 0.038227351 2.664651659 2.037491769 0.052834126 0.013623627 1.726294769 -0.237114955 -0.132337099 AKVEFNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKVEFNIR 8 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 129.38 0.00099688 2236300000 1611830 1061900 505670 616100 1448390 842410 1673370 1116640 1462010 FALSE TRUE 1535641.99 1170108.817 528855.4697 554168.4575 1700988.757 813237.1305 1418066.673 1018861.082 1688731.044 0.909346693 0.692892347 0.313167376 0.32815673 1.007258535 0.481566993 0.839723222 0.603329397 1 20.68750814 -0.131472081 0.621640894 1.022810373 0.649824938 0.184772201 0.231382051 10.63274519 4.20020795 0.839568208 0.090146661 0.738801755 0.131472081 -0.372985436 AKVS(ph)PVNDVDVGVYQLMQSEQLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKVSPVNDVDVGVYQLMQSEQLLSR 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 AKVS(1)PVNDVDVGVYQLMQSEQLLSR 107.91 0.0021208 26828000 13464 13013 13990 20672 11356 16238 18433 14505 11827 TRUE FALSE 12827.5834 14339.03949 14631.45534 18594.01129 13336.4828 15675.67399 15620.7073 13234.8653 13661.07076 0.938988139 1.049627789 1.071032835 1.361094721 0.976239933 1.147470375 1.143446775 0.968801461 1 13.73778295 4.171638472 1.882152224 1.111073905 0.94916899 0.146100501 0.114244834 0.567133118 3.755778055 0.028534677 0.10747252 14846.99191 -4.171638472 -0.161904915 AKVYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKVYGR 6 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 ; 106.84 0.028984 553350000 810240 613620 682730 714710 761420 702840 986470 761240 939870 FALSE TRUE 771941.5609 676148.5756 714033.8458 642865.9929 894211.4069 678500.4746 835965.8837 694581.79 1085620.239 0.711060399 0.622822375 0.657719725 0.592164709 0.823687119 0.624988785 0.770035279 0.639801806 1 20.05008809 -5 0.265009335 3.129843721 0.656846383 0.660431373 0.071816775 111.6957335 1.090978497 129.7678194 0.080427196 1.00E-05 5 -2.472997338 AKWDAWNELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKWDAWNELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 138.45 5.87E-05 594450000 1937220 1638630 1017350 1832810 981620 1461400 1660740 1748880 1043070 FALSE TRUE 1845651.45 1805608.26 1063996.504 1648572.457 1152814.217 1410791.352 1407363.611 1595738.796 1204823.968 1.531884739 1.49864902 0.88311366 1.368309811 0.956832075 1.170952262 1.168107249 1.324458043 1 20.20039095 3.835747167 8.641477933 1.139345024 1.518159593 0.532535227 0.151758191 0.216255967 17.6027747 0.034159524 0.061735914 6850.892722 -3.835747167 0.378814569 AKYAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AKYAYR 6 1 J3KS46 J3KS46 HEXDC 0 ;;;; 81.455 0.056391 484652000 1390500 1071700 746970 915630 1197560 991270 1573690 1255740 1433230 FALSE TRUE 1324773.821 1180907.448 781219.3134 823589.1328 1406414.085 956942.0713 1333594.688 1145780.749 1655487.988 0.800231611 0.713328914 0.471896697 0.49749025 0.849546535 0.578042292 0.805559869 0.692110578 1 20.65882511 0.363518426 0.700866055 1.005552638 0.665877936 0.404934189 0.126076785 2.386769506 1.707850415 0.15923576 0.04616111 2.309502445 -0.363518426 -0.339674702 AKYHGNVMLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKYHGNVMLLR 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 ; 167.09 1.18E-05 1759140000 1465650 1021770 775690 797250 1656700 940240 1912200 1414940 1711000 FALSE TRUE 1396371.629 1125889.525 811256.1538 717108.9153 1945627.955 907679.253 1620458.77 1291040.353 1976333.141 0.706546685 0.569686103 0.410485528 0.362848196 0.984463558 0.459274418 0.819931992 0.653250368 1 20.91439473 0.763822063 0.519425968 1.007983452 0.568050884 0.33183098 0.182290312 1.499827951 0.889650276 0.216225111 0.087974985 5.80526518 -0.763822063 -0.439932568 AKYPDYEVTWANDGY ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AKYPDYEVTWANDGY 15 1 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 252.37 9.88E-24 351060000 933290 728870 767020 908170 819050 834160 1064960 944970 917390 FALSE TRUE 889175.2313 803142.6817 802188.6257 816879.0262 961892.0607 805272.83 902480.7927 862223.4172 1059654.156 0.839118335 0.757929063 0.757028717 0.770892108 0.907741507 0.759939293 0.851674849 0.813683797 1 20.01516205 -1.892621649 0.294336257 1.198027427 0.786293978 0.623360108 0.04783098 18.77022783 0.881682953 2.612609596 0.048804537 0.012804964 1.892621649 -0.411733449 AKYPS(ph)LGQKPGGSDFLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AKYPSLGQKPGGSDFLMK 18 2 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 1 AKYPS(1)LGQKPGGSDFLMK 127.38 1.33E-05 227350000 368450 292320 271460 379990 193910 368810 415050 384460 203500 TRUE FALSE 351034.0987 322107.7403 283906.7095 341792.6833 227727.8426 356038.0172 351726.4996 350794.6442 235057.7407 1.493395188 1.370334537 1.207816891 1.454079675 0.968816606 1.514683227 1.49634085 1.492376483 1 17.84265567 4.352080013 2.623600591 1.337521039 1.4843988 0.063661819 0.200411427 0.882752816 11.41124323 0.048360107 0.193121356 22494.69005 -4.352080013 0.146877761 ALAAFLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALAAFLKK 8 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 151.75 0.0012891 0 379900 228970 210590 195040 324560 250340 464040 318380 351140 FALSE TRUE 361942.8799 252302.3033 220245.7598 175434.2086 381163.1612 241670.663 393242.1753 290500.9594 405592.9978 0.892379508 0.622057838 0.543021603 0.432537567 0.939767608 0.595845255 0.969548728 0.71623761 1 18.62967322 1.740005841 15.52505982 0.881335858 0.67858217 0.283487065 0.167334767 0.088534323 313.7573899 0.075052136 0.04144001 54.95482655 -1.740005841 -0.202753688 ALAAGADS(ph)PKTEEARPSPAPGPGTPTGTPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALAAGADSPKTEEARPSPAPGPGTPTGTPTR 31 2 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(0.966)PKT(0.034)EEARPSPAPGPGTPTGTPTR;ALAAGADS(0.999)PKT(0.001)EEARPSPAPGPGTPTGTPTR;ALAAGADS(1)PKTEEARPSPAPGPGTPTGTPTR;ALAAGADS(1)PKTEEARPSPAPGPGTPTGTPTR 268.75 1.14E-59 674594000 395967 299494 375262 374596 279395 403291 472238 425461 331282 TRUE FALSE 377250.4246 330012.7791 392468.1339 336940.8984 328121.3995 389324.9315 400189.4199 388205.3793 382655.5206 0.985874773 0.862427853 1.025643465 0.880533222 0.85748508 1.017429282 1.045821629 1.014503538 1 18.54568669 2.134242993 8.223953339 1.026591402 0.922914619 0.449054929 0.053228209 0.209158786 14.89824628 0.018870511 0.01392795 136.2206641 -2.134242993 -0.103676783 ALADYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALADYIR 7 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 107.43 0.0174 46112000 110370 69816 40548 54264 141410 54671 125380 76873 133600 FALSE TRUE 105153.0288 76930.32977 42407.16591 48809.27963 166071.8592 52777.72956 106250.9782 70141.59259 154318.0057 0.681404794 0.49851817 0.274803745 0.316290244 1.076166443 0.342006296 0.688519643 0.454526303 1 17.23554688 -5 0.329391963 5.551557409 0.530637711 0.270125688 0.235685574 477.9385603 4.137008597 1522.705339 0.18372707 1.00E-05 5 -5.020919698 ALAEEAS(ph)EEELPS(ph)DVDLNDPYFAEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 2 ALAEEAS(1)EEELPS(1)DVDLNDPYFAEEVK;ALAEEAS(1)EEELPS(1)DVDLNDPYFAEEVK 130.56 2.47E-05 88090000 285116 238229 251276 282600 185321 288233 306810 309060 227276 TRUE FALSE 271639.1317 262504.8059 262797.2531 254192.5111 217640.9237 278251.4189 260000.4995 281997.068 262520.8013 1.034733744 0.99993907 1.001053066 0.968275694 0.829042585 1.059921414 0.990399611 1.074189423 1 18.00207222 -0.740464246 7.489442545 0.999999538 0.994616695 0.000617759 0.067000892 0 0 0.061363799 0.014463586 0.18177567 0.740464246 -0.005382843 ALAEEASEEELPS(ph)DVDLNDPYFAEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 ALAEEASEEELPS(1)DVDLNDPYFAEEVK;ALAEEASEEELPS(1)DVDLNDPYFAEEVK 165.37 6.26E-12 55589000 151248 146338 150458 171951 109454 161056 167815 168270 121361 TRUE FALSE 144098.8068 161250.0086 157356.6481 154666.1588 128542.7429 155478.5903 142211.7396 153535.3867 140181.0441 1.027947878 1.150298242 1.122524441 1.10333148 0.916976641 1.109127068 1.014486235 1.095264968 1 17.09693175 ALAMPGRPES(ph)PPVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 122.87 6.43E-05 1251404000 972590 876345 891889 992000 1014510 884209 1050610 995960 1131060 TRUE FALSE 926617.5982 965645.5518 932782.9928 892282.2753 1191440.223 853588.6206 890320.1487 908748.4625 1306459.008 0.709258838 0.739131917 0.713978002 0.682977629 0.911961428 0.653360431 0.681475762 0.695581306 1 20.31723043 -1.588998933 2.758029924 1.020436682 0.721992679 0.600661376 0.070851964 38057661.03 36718163.59 5650535.266 0.016859607 0.025763275 1.588998933 -0.298444003 ALANECSQGDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALANECSQGDKR 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;;; 158.11 9.97E-05 864350000 535040 503830 565310 653820 499050 611950 721430 686330 624070 FALSE TRUE 509749.7195 555170.8498 591230.0227 588096.7714 586084.162 590758.0181 611362.6035 626231.3067 720847.5883 0.707153257 0.770163983 0.82018728 0.815840659 0.813048655 0.819532489 0.84811632 0.868743014 1 19.45933473 -5 0.030844292 2.212324018 5.28E-11 0.945970083 0.017340684 297.0967922 0.689223534 39.02045168 15.41961624 1.00E-05 5 -2.212324018 ALANSLACQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALANSLACQGK 11 0 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 153.12 0.0035697 0 151840 123650 125410 139330 127230 130190 167870 150940 144880 FALSE TRUE 144662.8241 136250.0756 131160.1725 125324.2837 149418.8717 125681.4877 142258.3484 137722.8934 167347.2505 0.864446973 0.814175765 0.783760547 0.748887618 0.892867205 0.751022125 0.850078791 0.822976733 1 17.35248532 0.053826316 1.023492492 1.001427676 0.814949148 0.613660774 0.046012386 4.42919526 4.167998435 0.060128379 0.012778024 1.131947581 -0.053826316 -0.186478529 ALAPEYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALAPEYAK 8 0 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ; 98.299 0.017729 136243000 802580 624730 645670 751280 612600 711720 900820 755220 780510 FALSE TRUE 764643.634 688390.6973 675274.6082 675759.9071 719437.246 687072.9579 763383.3643 689088.9331 901547.5045 0.848145694 0.76356564 0.749017223 0.749555518 0.798002593 0.762103998 0.846747798 0.764340126 1 19.78204399 -1.169392723 0.528891516 1.078522328 0.783729754 0.769368695 0.036835446 13.08807789 1.964388146 1.551810984 0.016378009 0.067702901 1.169392723 -0.294792574 ALAPS(ph)PPAEFIYYCVDEDELQPYTNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALAPSPPAEFIYYCVDEDELQPYTNRR 27 1 Q9UIS9-6;Q9UIS9-5;Q9UIS9;Q9UIS9-9;Q9UIS9-12 Q9UIS9-6 MBD1 Methyl-CpG-binding domain protein 1 1 ALAPS(0.55)PPAEFIY(0.225)Y(0.225)CVDEDELQPYTNRR;ALAPS(0.97)PPAEFIY(0.015)Y(0.015)CVDEDELQPYTNRR 54.324 0.052681 40424000 10785.9 8144.9 9695.7 10968.9 10285 8158.1 10462.3 11307.8 15499.7 TRUE FALSE 10276.07188 8974.87457 10140.25744 9866.285332 12078.70074 7875.582951 8866.083982 10317.62909 17903.31431 0.573975952 0.501296822 0.566389958 0.551087087 0.674662832 0.439895251 0.495220261 0.576297154 1 14.12793907 0.947285607 20.01448364 1.000000001 0.53899283 0.844514796 0.0611777 414.0984614 157224.7991 0.057149628 0.014287407 8.856978848 -0.947285607 -0.46100717 ALAPTWEQLALGLEHSETVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALAPTWEQLALGLEHSETVK 20 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 318.13 1.54E-66 529270000 1102950 916450 925220 1105740 868390 1065860 1277570 1154470 844440 FALSE TRUE 1050815.739 1009837.297 967642.2522 994588.9144 1019836.941 1028949.001 1082653.232 1053378.487 975391.4424 1.077327208 1.035314903 0.992055302 1.019681813 1.045566833 1.054908785 1.109967942 1.079954612 1 19.89562179 2.110544434 3.516792177 1.076664947 1.035406142 0.088786269 0.03505679 0.35989312 8.633632478 0.01430512 0.00984302 128.9865521 -2.110544434 -0.041258805 ALASEKS(ph)PTADAKPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALASEKSPTADAKPAPK 17 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 ALASEKS(0.735)PT(0.265)ADAKPAPK;ALASEKS(0.967)PT(0.033)ADAKPAPK 167.51 1.15E-09 1495970000 1766680 1555570 1637240 1802890 808575 1855540 1906890 1982780 827940 TRUE FALSE 1683172.538 1714084.352 1712309.073 1621660.072 949590.224 1791282.185 1615958.908 1809157.272 956332.7067 1.760028206 1.79235149 1.79049515 1.695707007 0.992949648 1.873074268 1.689745521 1.891765553 1 19.86715309 2.989868897 24.70987505 1.553261864 1.77574616 0.146699638 0.308451564 957.0575689 2334283.205 0.086161538 0.097320592 976.9422614 -2.989868897 0.222484296 ALASEKSPT(ph)ADAKPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALASEKSPTADAKPAPK 17 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 ALASEKS(0.319)PT(0.681)ADAKPAPK 129.32 0.0016202 1270900000 1775600 1511500 1682400 2016500 796360 2126000 2069200 2265800 922210 TRUE FALSE 1691670.907 1665523.568 1759539.704 1813797.589 935244.9319 2052376.087 1753505.537 2067394.54 1065221.617 1.588092919 1.563546535 1.651806231 1.702742002 0.877981555 1.926712765 1.646141525 1.940811666 1 20.02272218 ALAT(ph)PPKLHTCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALATPPKLHTCEK 13 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 ALAT(1)PPKLHTCEK;ALAT(1)PPKLHTCEK;ALAT(1)PPKLHTCEK 168.32 4.46E-05 1376090000 2717510 2320480 2423330 2864100 1892620 2844450 3180100 3143070 1991250 TRUE FALSE 2589058.688 2556939.55 2534442.078 2576195.227 2222692.329 2745945.983 2694917.338 2867846.128 2300042.88 1.125656704 1.111692122 1.101910795 1.120063999 0.966369952 1.1938673 1.171681346 1.246866375 1 21.13322933 ALDDKNCWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALDDKNCWEK 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 128.08 0.00030922 1552760000 1822270 1442880 1665640 1898030 1158810 1833190 2031630 1961800 1411880 FALSE TRUE 1736134.908 1589911.112 1742011.242 1707236.418 1360906.097 1769706.171 1721667.53 1790014.392 1630827.14 1.064573226 0.974910874 1.06817651 1.046853083 0.834488257 1.085158646 1.055702035 1.097611358 1 20.63717244 ALDEYYDKHFTEFVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALDEYYDKHFTEFVPLR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 232.78 2.05E-17 904940000 1394130 1091030 1351500 1412710 1349320 1358700 1730010 1563080 1319510 FALSE TRUE 1328232.238 1202207.197 1413467.612 1270701.707 1584640.981 1311647.878 1466065.201 1426208.429 1524132.872 0.871467483 0.788781096 0.927391331 0.833721082 1.039700022 0.860586306 0.961901175 0.935750718 1 20.53955725 3.153574746 1.517413447 0.947726584 0.836232757 0.355888198 0.06154456 0.367950662 1.760811855 0.019189742 0.025907469 1424.212347 -3.153574746 -0.111493827 ALDIAENEMPGLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDIAENEMPGLMR 14 0 P23526 P23526 AHCY Adenosylhomocysteinase 0 97.214 0.0071268 16617000 15323 18093 18488 20265 17481 16392 19217 17182 19880 FALSE TRUE 14598.71216 19936.69727 19335.69309 18227.9237 20529.68087 15824.34093 16285.09371 15677.45299 22962.88887 0.63575242 0.868213812 0.842040964 0.793799239 0.894037374 0.689126748 0.709191853 0.682729995 1 14.48701653 2.208314715 24.99974128 0.740049244 0.800614604 0 0.113844343 613.2942366 506914.4722 0.039514204 0.029186742 161.552884 -2.208314715 0.060565359 ALDIDS(ph)DEESEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALDIDSDEESEPK 13 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 ALDIDS(1)DEESEPK;ALDIDS(1)DEESEPK 275.66 3.46E-32 136548000 224613 216273 185741 235631 121899 221384 207062 240199 119236 TRUE FALSE 213995.9886 238311.4646 194257.4086 211944.9242 143158.147 213717.4166 175470.8889 219165.9022 137726.5099 1.55377486 1.730323848 1.410457643 1.53888256 1.039437848 1.551752213 1.274053115 1.591312394 1 17.07144675 1.169121 0.054017322 6.34E-09 2.645600443 0.380675411 0.188573365 37.67781036 1.643433961 41.2515254 37.49513234 14.76117741 -1.169121 2.645600437 ALDKLDGTEINGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDKLDGTEINGR 13 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 94.09 0.0048471 354300000 352070 354850 341600 403290 290550 381980 416740 399330 361800 FALSE TRUE 335428.3488 391009.6184 357262.6979 362750.523 341221.828 368751.9368 353158.659 364362.5482 417906.0962 0.802640478 0.935639901 0.8548875 0.868019218 0.81650359 0.882379894 0.845067019 0.871876605 1 18.67281928 0.944521658 19.33068296 1 0.861033451 0.599769438 0.036141606 609.661458 212429.8387 0.03253789 0.008134472 8.800790003 -0.944521658 -0.138966549 ALDLDSSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDLDSSCK 9 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 151.97 0.00018979 75294000 221040 197100 172160 232200 143180 201340 232880 224840 173670 FALSE TRUE 210591.8773 217184.7141 180053.7063 208858.8148 168150.5467 194367.5453 197349.8789 205151.8176 200601.8566 1.04980024 1.082665523 0.897567497 1.041160926 0.838230261 0.968921966 0.983788895 1.02268155 1 17.61397543 3.756915831 24.8027528 0.963434601 1.066232894 0.334823769 0.059523749 719.9189777 972797.8033 0.014012076 0.025200358 5713.678916 -3.756915831 0.102798293 ALDLDSSCKEAADGYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALDLDSSCKEAADGYQR 17 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 117.53 0.00019424 509370000 266461 119863 353033 182146 303207 292777 470980 315297 491190 FALSE TRUE 253865.9166 132077.176 369219.9122 163836.338 356086.2048 282638.0591 399123.3509 287687.9232 567361.2365 0.447450231 0.232792033 0.650766899 0.288769002 0.627618141 0.498162442 0.70347307 0.507063057 1 19.11390806 -2.369546162 0.123440551 1.928536738 0.15400279 0.614416883 0.135117914 36.71003065 0.5783896 10.7048213 1.270485236 0.004270255 2.369546162 -1.774533948 ALDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALDLLDR 7 0 P27361;E9PBK7;E9PQW4;P27361-3;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;; 143.85 0.0055686 160123000 429389 370891 374137 439412 468856 374573 491336 418840 500220 FALSE TRUE 409092.6329 408685.2146 391291.5515 395241.4709 550624.338 361601.4431 416373.6692 382164.1492 577791.5628 0.708028049 0.707322919 0.67721922 0.684055456 0.952980925 0.62583372 0.720629542 0.66142217 1 19.14018961 -1.462218074 4.555209477 1.001005477 0.716807802 0.504084186 0.088155935 0.000822797 9.71E-05 0.078018264 0.018326082 0.034497047 1.462218074 -0.284197674 ALDMSYDHKPEDEVELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALDMSYDHKPEDEVELAR 18 1 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 161.51 5.10E-11 292340000 280800 245736 254876 292340 209146 282240 307150 299010 201967 FALSE TRUE 267527.1405 270776.7778 266562.3167 262953.4278 245620.9962 272465.958 260288.6263 272827.0992 233287.0109 1.146772551 1.160702333 1.142636771 1.127167033 1.052870433 1.167943114 1.115744187 1.16949117 1 17.83174646 -1.30551836 3.628159077 0.999590591 1.135821785 0.612537884 0.033845652 2475156.148 890648.9282 7902.939888 0.007521107 0.049485919 1.30551836 0.136231194 ALDQASEEIWNDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALDQASEEIWNDFR 14 0 F8VQZ7;P50579-3;P50579;F8VRR3;P50579-2;F8VY03;G3V1U3;F8VZX9 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 ;; 165.7 9.13E-06 38828600 42891.5 42625.6 42671.6 48489.7 44697.5 41370 49621.5 50638.1 39410.2 FALSE TRUE 40864.1038 46969.1971 44628.13507 43615.42323 52492.72985 39937.34653 42050.82881 46203.95951 45521.73254 0.897683404 1.03179722 0.980369871 0.958123094 1.153135589 0.877324836 0.92375282 1.014986841 1 15.47426785 -2.172170941 8.98070313 1.860503752 0.975535482 0.004220371 0.078157871 0.148145741 0.002840134 0.008325502 0.016801675 0.006727118 2.172170941 -0.88496827 ALDSGYQVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDSGYQVELR 11 0 Q02846 Q02846 GUCY2D Retinal guanylyl cyclase 1 0 61.344 0.087907 32793000 11868 9458.4 18358 11087 67363 10518 24825 14596 80419 FALSE TRUE 11307.02316 10422.22171 19199.73246 9972.513696 79111.08587 10153.75902 21037.49031 13317.89686 92889.9678 0.121724912 0.112199648 0.206693284 0.10735835 0.851664477 0.109309533 0.226477528 0.143372822 1 16.50323517 -5 0.328506479 8.709083645 0.194399332 0.528980623 0.225306016 274.2240504 2.378926301 1476.193948 0.182108483 1.00E-05 5 -8.514684313 ALDVMVSTFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ALDVMVSTFHK 11 0 P26447 P26447 S100A4 Protein S100-A4 0 ;;;;; 220.1 9.40E-12 19737670000 31374340 21920740 19063260 24853650 29525370 23141580 35256630 27810150 27406060 FALSE TRUE 29891337.13 24154488.33 19937329.33 22355313.88 34674585.18 22340181.28 29877583.56 25374945.84 31656051.81 0.944253481 0.763029087 0.62981099 0.706194001 1.09535407 0.705715969 0.943819012 0.801582774 1 24.915978 ALDVS(ph)ASDDEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDVSASDDEIAR 13 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 1 ALDVS(0.519)AS(0.481)DDEIAR 233.52 1.29E-16 241650000 408310 329360 249270 328910 483900 329350 443620 396900 485400 TRUE FALSE 389009.9955 362922.1585 260699.2761 295847.3419 568292.0068 317944.5269 375937.6214 362145.3319 560673.3529 0.693826438 0.647296963 0.464975328 0.527664353 1.0135884 0.567076222 0.670510948 0.645911438 1 19.09680098 ALDYYMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALDYYMLR 8 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 89.55 0.032166 28790000 83692 62352 43869 49832 102370 47969 81772 66911 73022 FALSE TRUE 79736.04502 68705.73969 45880.43704 44822.79269 120223.2956 46307.8215 69296.17955 61051.91812 84345.87882 0.94534607 0.814571389 0.543955884 0.531416512 1.425360637 0.54902293 0.821571611 0.723828111 1 16.36402996 ALEAASLSQHPPSLCIS(ph)DS(ph)EEEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALEAASLSQHPPSLCISDSEEEEEER 26 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 ALEAASLSQHPPSLCIS(1)DS(1)EEEEEER 193.03 1.84E-18 160570000 173140 134200 174350 203790 222990 175140 234440 201690 236010 TRUE FALSE 164956.0153 147875.1326 182344.12 183304.642 261879.3854 169074.8579 198671.8722 184028.9544 272609.2254 0.605100635 0.542443611 0.668884627 0.672408066 0.960640217 0.620209597 0.728778976 0.675065028 1 18.05647486 -4.999999994 0.070191558 2.062914267 0.287481008 0.496795096 0.105206735 249.750712 1.26164436 43.53429867 5.400009855 1.00E-05 4.999999994 -1.775433259 ALEAELDAQHLS(ph)ETFDNIDNLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.333)ET(0.333)FDNIDNLS(0.333)PK;ALEAELDAQHLS(0.333)ET(0.333)FDNIDNLS(0.333)PK 108.17 0.0039717 59591000 89942 93270 82185 93919 83468 77644 72352 67540 49223 TRUE FALSE 85690.61991 102774.319 85953.26354 84478.08369 98024.79277 74955.16881 61313.37356 61625.83955 56856.25144 1.507145085 1.807616866 1.511764518 1.485818737 1.724081175 1.318327658 1.078392824 1.083888543 1 15.79503136 1.970301589 2.662323275 1.060028725 1.616028644 0.851612708 0.105242339 0.098354269 1.296564661 0.05380559 0.029590297 93.39026099 -1.970301589 0.555999919 ALEAELDAQHLSETFDNIDNLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLSETFDNIDNLS(1)PK 144.4 1.47E-07 43430000 51935 41764 45472 51673 39539 45300 58480 56526 40504 TRUE FALSE 49480.13548 46019.79908 47556.93618 46478.73187 46434.58908 43731.24964 49557.80194 51576.28378 46785.15345 1.05760336 0.983641084 1.016496317 0.993450452 0.992506931 0.934724938 1.059263426 1.102407067 1 15.51376316 1.605365717 25 1.060636768 0.999921255 0.319351818 0.038926946 0.269102378 2656.39019 0.018636313 0.00925056 40.3056303 -1.605365717 -0.060715513 ALEATTEHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 168.74 4.85E-06 623290000 613950 529943 507874 589482 684480 531704 664690 589944 627600 FALSE TRUE 584929.8002 583944.7942 531160.5253 530226.1494 803853.0953 513290.9572 563279.3326 538285.3759 724925.0027 0.806883192 0.805524423 0.732711002 0.731422075 1.108877597 0.708060772 0.777017389 0.742539399 1 19.46747222 -1.038710289 4.132600162 1.000020304 0.801308125 0.230186147 0.114006012 11656593.48 5861457.182 2072.763752 0.024685407 0.091472324 1.038710289 -0.198712179 ALEDAFLAIDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEDAFLAIDAK 12 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 170.52 9.52E-05 18216900 66368 69033 59635 71544 59371 62511 72602 73575 60130 FALSE TRUE 63230.91617 76067.54118 62369.32374 64352.2612 69725.2836 60346.2284 61525.23147 67132.38295 69454.6533 0.910391358 1.095211589 0.897986251 0.926536353 1.003896504 0.86885796 0.885833109 0.966564222 1 16.08378373 3.696518051 24.99947539 0.926820218 1.002801683 0.152825899 0.06309247 649.4104 386154.0418 0.016049775 0.024864363 4971.850383 -3.696518051 0.075981464 ALEEGDGSVSGSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALEEGDGSVSGSSPR 15 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 ALEEGDGSVS(0.004)GS(0.386)S(0.61)PR 142.17 4.86E-06 364780000 579240 525970 893650 598390 545840 574600 647330 633650 703250 TRUE FALSE 551860.4731 579566.941 934624.7364 538238.7003 641034.3232 554701.4579 548567.9195 578164.2468 812306.4183 0.679374754 0.713483149 1.150581499 0.6626055 0.78915334 0.682872184 0.675321415 0.711756344 1 19.63166452 ALEEGLTPQEICDKYHIIHADIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEEGLTPQEICDKYHIIHADIYR 24 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 159.46 1.41E-11 417752000 770430 699410 740870 827600 733440 785770 877090 802490 58239 FALSE TRUE 734013.3007 770680.6742 774839.6223 744408.0757 861351.7038 758558.5879 743273.8116 732219.7213 67270.40668 10.91138492 11.45645927 11.5182836 11.06590717 12.80431837 11.27625988 11.04904591 10.88472268 1 16.03768436 -0.067805299 1.073618636 0.912141235 11.45908009 0.975787811 0.514352215 1.490056947 1.34149909 0.9757463 0.147812198 0.855450138 0.067805299 10.54693886 ALEELQEALAEKEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ALEELQEALAEKEELR 16 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ;;;;;; 208.2 1.41E-11 326998000 636278 576013 585940.2 678523 497887 670479 707861 701754 577582 FALSE TRUE 606202.3999 634709.3796 612806.1377 610316.5789 584718.3352 647260.1441 599863.8037 640304.6995 667150.4667 0.908644197 0.951373657 0.91854262 0.91481099 0.876441469 0.970186152 0.899143197 0.959760551 1 19.34765265 0.995881125 5.124657694 0.999933002 0.922116315 0.512986144 0.025907093 0.111209371 10.72211828 0.022432193 0.005668291 9.905607719 -0.995881125 -0.077816687 ALEENNNFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEENNNFSK 10 0 E5RGX5;Q93045;Q93045-2 E5RGX5 STMN2 Stathmin;Stathmin-2 0 ; 169.76 0.0053611 0 78898 61270 72020 77979 72229 75558 84238 83517 82582 FALSE TRUE 75168.6479 67513.48266 75322.18824 70140.40277 84825.71473 72941.40751 71385.94596 76203.80873 95388.39479 0.788027182 0.707774597 0.789636815 0.735313797 0.889266613 0.764678006 0.748371394 0.798879244 1 16.54152613 -5 0.312420436 3.056857355 0.761263017 0.680581467 0.047945265 169.7459288 1.529265597 230.0066404 0.04251583 1.00E-05 5 -2.295594339 ALEESESSQLIS(ph)PPLAQAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALEESESSQLISPPLAQAIR 20 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 ALEESESSQLIS(1)PPLAQAIR 128.14 2.13E-05 10740000 33171 33419 30189 32181 37835 31846 37512 35390 45562 TRUE FALSE 31603.07257 36824.43409 31573.19551 28946.10474 44433.41202 30743.16503 31788.85544 32291.06399 52627.52226 0.600504664 0.69971818 0.599936956 0.550018384 0.844299905 0.584165161 0.604034811 0.613577508 1 15.68352985 -1.679337631 2.985370572 1.039930446 0.638042238 0.655238302 0.082740018 33930309.8 30387530.58 10206585.78 0.018601817 0.020924851 1.679337631 -0.401888207 ALEFAPACHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 102.06 0.002997 174890000 215940 189610 148220 144900 249410 144300 239820 158270 217510 FALSE TRUE 205732.9442 208931.4746 155016.0336 130334.3767 292907.025 139302.8548 203231.0544 144411.0398 251240.3399 0.818869073 0.831600031 0.617002961 0.518763733 1.165843929 0.554460541 0.80891092 0.574792407 1 17.9387086 ALEHAFQLEHIMDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEHAFQLEHIMDLTR 16 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 176.46 1.83E-09 290700000 154357 145534 148177 180852 185655 147081 190944 169659 49942 FALSE TRUE 147060.8505 160364.0801 154971.062 162672.4134 218033.1732 141987.5481 161811.9859 154802.7585 57686.75029 2.549300312 2.779911838 2.686423854 2.819926804 3.779605752 2.461354598 2.80501129 2.683506312 1 15.81595237 0.152994556 1.165978761 0.994511567 2.831522847 0.722963724 0.355576383 3.377457541 4.13021403 0.367726055 0.099392278 1.422310957 -0.152994556 1.837011279 ALEHFTDLYDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEHFTDLYDIK 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 221.09 2.80E-11 157738000 456930 518600 388980 549190 323750 453710 454540 507230 310770 FALSE TRUE 435331.8244 571445.9296 406815.1178 493984.3778 380211.8975 437997.9089 385191.5748 462814.2522 358962.6244 1.212749726 1.591937129 1.133307732 1.376144323 1.059196339 1.220176919 1.07306875 1.28931042 1 18.45347411 3.097109116 1.377117294 1.135963299 1.382541576 0.272470581 0.147974334 0.442634597 1.754344193 0.050162906 0.065369935 1250.573195 -3.097109116 0.246578277 ALEHFTDLYDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALEHFTDLYDIKR 13 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 184.34 6.22E-06 1407940000 2568200 1940530 2347300 2617300 2433200 2550200 3381500 3080400 2863000 FALSE TRUE 2446806.276 2138272.213 2454926.027 2354204.031 2857549.31 2461885.935 2865590.069 2810663.846 3306979.418 0.739891595 0.646593747 0.742346933 0.711889532 0.864096491 0.744451544 0.866527942 0.84991876 1 21.65708264 1.428664828 0.359552876 1.015087191 0.672372028 0.773974893 0.048123593 0.494866932 0.204934788 0.064861533 0.049939575 26.83272799 -1.428664828 -0.342715162 ALEHSALAINHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 118.28 0.00037173 129710000 45353 44897 39178 48123 39183 43381 42284 49583 18877 FALSE TRUE 43209.25357 49472.05534 40974.35005 43285.58461 46016.50279 41878.70509 35832.7992 45241.24966 21804.34875 1.981680538 2.268907726 1.879182475 1.985181264 2.110427756 1.920658378 1.643378558 2.074872778 1 14.41232828 -1.816843345 0.249257861 2.20E-17 2.140857565 0.788820065 0.160323006 11.58930578 0.468569666 7.173454849 0.243022821 0.015246026 1.816843345 2.140857565 ALEIIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALEIIPR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 100.74 0.022265 153961000 352650 321680 323551 358130 445530 302946 398080 339565 444140 FALSE TRUE 335980.9334 354459.5577 338386.1334 322130.092 523230.2909 292454.9041 337345.5848 309830.8885 513014.9628 0.654914491 0.690934151 0.659602854 0.627915588 1.019912339 0.570070905 0.657574553 0.603941232 1 18.96864138 -2.299565225 2.314640022 2.557376055 0.684547314 0.389757385 0.123624747 4896646.142 1040935.118 39595788.15 0.028884731 0.005016892 2.299565225 -1.87282874 ALELDHK ddPTM_SK-BR-3_Trastuzumab_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 ;; 114.6 0.005868 418819000 825390 732928 699877 846080 647730 826640 887650 858130 645055 FALSE TRUE 786375.4505 807614.1965 731967.0527 761030.431 760693.9069 798013.2495 752222.6897 782987.588 745086.8349 1.055414502 1.083919563 0.982391606 1.021398306 1.020946648 1.071033888 1.009577212 1.050867565 1 19.50704905 3.763920192 24.99518237 1.024672476 1.069667036 0.369271214 0.025583646 725.5293845 715101.7295 0.006099988 0.010989522 5806.577028 -3.763920192 0.04499456 ALELDSNLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALELDSNLYR 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 258.47 7.19E-17 960340000 1746920 1686270 1339660 1587750 1761200 1449330 1820100 1607000 1670180 FALSE TRUE 1664346.554 1858102.83 1401084.736 1428146.353 2068352.722 1399139.339 1542410.317 1466282.561 1929182.984 0.862720938 0.963155307 0.726258083 0.740285585 1.072139211 0.725249678 0.799514784 0.760053646 1 20.87955856 3.757918138 24.59218898 0.821907268 0.912938116 0.068698771 0.119655728 1466.106111 1862563.855 0.028479117 0.051240196 5726.880726 -3.757918138 0.091030847 ALELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALELFR 6 0 B0QYF8;P02144;Q8WVH6 B0QYF8 MB Myoglobin 0 103.28 0.080999 17238000 50318 29854 29283 41656 53133 33704 59370 39058 50229 FALSE TRUE 47939.56786 32896.15654 30625.65451 37468.65974 62399.37838 32536.82203 50312.0161 35637.87446 58018.25679 0.826284182 0.566996638 0.52786237 0.645808092 1.07551281 0.560803165 0.867175591 0.614252762 1 15.82421933 2.929316982 24.99964896 0.80418496 0.643159138 0.213386906 0.171226927 259.1722726 91665.04133 0.047836357 0.050738138 849.8004991 -2.929316982 -0.161025822 ALELPLAASSIPRPRT(ph)PS(ph)PESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALELPLAASSIPRPRTPSPESHR 23 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 ALELPLAAS(0.037)S(0.041)IPRPRT(0.921)PS(0.866)PES(0.135)HR;ALELPLAASS(0.045)IPRPRT(0.951)PS(0.985)PES(0.018)HR;ALELPLAAS(0.001)S(0.037)IPRPRT(0.963)PS(0.992)PES(0.008)HR;ALELPLAASS(0.005)IPRPRT(0.994)PS(0.996)PES(0.004)HR;ALELPLAASSIPRPRT(1)PS(0.992)PES(0.008)HR 179.17 9.33E-17 382438000 260121 123151 263303 242138 354320 224687 357468 225518 389049 TRUE FALSE 247825.5958 135700.2269 275375.703 217797.8282 416113.2958 216906.0329 302929.6912 205770.4484 449380.7319 0.55148247 0.301971618 0.612789297 0.484662142 0.925970488 0.482677644 0.674104762 0.4578978 1 18.77757874 -5 0.124429389 2.427164755 0.351287146 0.401987802 0.164936212 137.4519957 1.095773917 49.55812846 1.320951667 1.00E-05 5 -2.075877608 ALEMAIEAGAEDVKETEDEEERNVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALEMAIEAGAEDVKETEDEEERNVFK 26 2 Q9BSH4 Q9BSH4 TACO1 Translational activator of cytochrome c oxidase 1 0 256.12 7.15E-53 71493000 219620 163350 186040 196720 116130 180690 202020 222300 121490 FALSE TRUE 209238.9978 179995.5507 194570.118 176945.3319 136383.0352 174432.66 171198.1386 202834.2335 140330.0487 1.491049136 1.282658649 1.386517854 1.260922614 0.971873355 1.24301717 1.219967785 1.445408417 1 17.09846444 4.295974772 0.733922005 1.199565674 1.55084317 0.307937013 0.14047525 2.116107431 1.292031039 0.055643056 0.554514077 19768.548 -4.295974772 0.351277496 ALEQKPDDAQYYCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALEQKPDDAQYYCQR 15 1 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 ;; 174.39 8.35E-07 1083150000 790860 695150 696060 858480 623470 770490 936070 924810 801710 FALSE TRUE 753477.6151 765986.5753 727975.0395 772183.9594 732202.9706 743807.7381 793255.3294 843828.7337 926035.0922 0.813659894 0.827167979 0.786120359 0.833860364 0.790685987 0.803217658 0.856614761 0.911227599 1 19.82070734 1.083558097 1.482823602 0.998669587 0.810723904 0.941957678 0.015674935 0.078756969 0.347050348 0.013830847 0.004132041 12.12154833 -1.083558097 -0.187945682 ALEQSQSLPLPAPT(ph)STSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 ALEQSQSLPLPAPT(0.246)S(0.246)T(0.246)S(0.246)PS(0.014)R 77.871 0.012157 0 48737 46392 43643 46847 49468 40191 51544 46327 49833 TRUE FALSE 46433.2986 51119.39754 45644.07472 42137.85056 58095.20354 38799.17559 43680.01613 42270.36229 57560.84713 0.806681988 0.888093211 0.792970865 0.732057512 1.009283331 0.674054979 0.758849432 0.734359628 1 15.8128002 ALERPYTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ALERPYTSK 9 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 123.79 0.00049957 1869110000 3136290 2360010 2929420 3836610 3449750 3692600 4667660 4066750 4077220 FALSE TRUE 2988043.787 2600497.702 3063736.805 3450946.674 4051385.308 3564724.336 3955522.74 3710643.811 4709494.454 0.634472302 0.552181923 0.650544731 0.73276372 0.860259068 0.756922929 0.839903896 0.787907035 1 22.16714077 2.750928945 0.23370103 1.023473145 0.437311034 0.793744824 0.057927623 1.643892193 0.201088934 0.127296083 0.307852806 563.5454461 -2.750928945 -0.586162111 ALES(ph)PERPFLAILGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 1 ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK 234.73 2.33E-20 1142191300 1215428 1008166 1012044 1228597 924734 1113063 1307823 1229196 1090963 TRUE FALSE 1157977.127 1110899.262 1058447.218 1105096.095 1086007.317 1074517.349 1108290.582 1121561.082 1260143.97 0.918924468 0.881565351 0.839941502 0.87696019 0.861812096 0.852694116 0.879495207 0.890026147 1 20.26515714 0.630933343 2.216774269 0.999986157 0.874814643 0.783738465 0.020781073 1.232613516 6.779491106 0.021476747 0.005828175 4.274972674 -0.630933343 -0.125171515 ALESPERPFLAILGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 208.2 4.92E-12 2600400000 2542300 1949770 2096470 2435000 2076020 2251800 2681900 2384700 2166700 FALSE TRUE 2422130.517 2148453.78 2192595.223 2190229.174 2438077.231 2173819.601 2272726.899 2175883.026 2502700.77 0.967806678 0.858454117 0.87609164 0.875146242 0.974178479 0.868589496 0.908109721 0.869413975 1 21.25505438 -1.291992431 4.720010324 1.000045482 0.900081157 0.373295626 0.040830102 1.81E-05 2.71E-06 0.036541937 0.0086091 0.05105139 1.291992431 -0.099964325 ALFAGDIEEMEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALFAGDIEEMEERR 14 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 208.97 1.17E-08 45700000 59655 36132 57454 48427 79733 52038 82490 61225 91770 FALSE TRUE 56835.22637 39813.89188 60088.32273 43559.02595 93638.40996 50235.91101 69904.63547 55863.81443 106001.2229 0.536175195 0.37559842 0.566864429 0.410929466 0.883371035 0.473918221 0.659470085 0.527011037 1 16.69372138 -4.999999996 0.147358517 2.616629558 0.396755339 0.516161947 0.138383025 98.48291593 0.869085896 46.56379826 0.659015354 1.00E-05 4.999999996 -2.219874219 ALFDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALFDYDR 7 0 Q92796-2;Q5JUW8;Q92796-3;Q92796 Q92796-2 DLG3 Disks large homolog 3 0 79.116 0.077928 38108000 126020 100000 74088 84511 153950 79724 138880 102870 140350 FALSE TRUE 120063.2843 110190.1137 77485.00808 76015.79372 180798.8313 76963.13789 117691.3053 93862.15745 162114.7612 0.740606737 0.679704383 0.477963928 0.468901124 1.115252121 0.474744788 0.725975256 0.578985879 1 17.30665593 ALFEEVPELLTEAEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 198.15 6.65E-11 48494000 112108 97051 101192 124199 67735 114941 118978 134084 76345 FALSE TRUE 106808.877 106940.6072 105831.7533 111714.2806 79547.96255 110960.5643 100825.7209 122342.8941 88184.19268 1.211202073 1.212695881 1.200121587 1.266828863 0.902066007 1.258281796 1.143353677 1.387356287 1 16.42823245 -2.140684425 2.5907253 0.554914534 1.192250934 0.203100857 0.122667285 12144637 5217344.423 32822898.07 0.026496593 0.007232952 2.140684425 0.6373364 ALFPGDSEIDQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALFPGDSEIDQLFR 14 0 G3V5T9;P24941;P24941-2;E7ESI2;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 0 107.06 0.0021075 14594000 19245 19627 19050 20199 25197 22897 21418 21410 27048 FALSE TRUE 18335.32699 21627.01361 19923.46134 18168.55814 29591.34882 22104.07115 18150.29073 19535.2269 31242.4657 0.586871957 0.692231331 0.637704512 0.581534067 0.947151518 0.707500854 0.580949369 0.625278014 1 14.9312207 -2.033662738 2.495116004 1.404196693 0.666892154 0.480845284 0.107752549 30567468.59 12289371.45 70598241.82 0.026024203 0.009254165 2.033662738 -0.737304539 ALGALVDSCAPGLCPDWESWDPQKPVDNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALGALVDSCAPGLCPDWESWDPQKPVDNAR 30 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 143.9 4.03E-08 82004000 209180 147660 109620 129350 153690 117790 231650 154740 186270 FALSE TRUE 199292.476 162706.7219 114646.1854 116347.4923 180493.4873 113710.9028 196307.538 141190.1453 215155.8003 0.926270524 0.756227449 0.532851939 0.540759264 0.838896684 0.528504937 0.912397145 0.656222817 1 17.71502221 -0.855619696 5.278389299 1.000000248 0.727329829 0.260494481 0.150675264 4.31E-07 9.31E-08 0.142494525 0.033586251 0.13943773 0.855619696 -0.27267042 ALGFPLERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALGFPLERPK 10 1 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 126.71 0.00034241 1706710000 4673200 4258600 3866100 4630200 3379300 4423300 4570900 4586000 2629700 FALSE TRUE 4452307.097 4692556.182 4043364.509 4164763.499 3968648.85 4270120.012 3873525.255 4184425.528 3037500.445 1.465779899 1.544874237 1.331148614 1.371115354 1.30655087 1.405800621 1.275234465 1.377588449 1 21.53445319 -3.941773222 0.108455493 8.04E-12 1.649862459 0.787584477 0.066160266 52.3106942 0.481052177 12.58394238 0.881993529 0.000114348 3.941773222 1.649862459 ALGHQLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALGHQLGR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 139.31 0.0014978 0 110860 92929 89170 105140 119210 107190 116210 112800 124600 FALSE TRUE 105619.8675 102398.5708 93258.5327 94571.12745 140000.1863 103477.9834 98480.03016 102922.634 143922.3316 0.733867123 0.711484935 0.647978195 0.657098356 0.972748181 0.718984901 0.684258162 0.715126227 1 17.13493094 -1.533632704 3.6167214 1.00560375 0.727604855 0.466919645 0.090562958 11774.03999 42018221.31 252299.0254 0.020402178 0.029266265 1.533632704 -0.277998895 ALGKHPVSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALGKHPVSCK 10 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 88.681 0.0072275 1449000000 2946000 1553500 2445400 1992490 2566800 2076950 3237600 2753300 2723700 FALSE TRUE 2806748.418 1711803.416 2557524.009 1792201.12 3014449.107 2005024.701 2743644.657 2512206.456 3146077.485 0.892142178 0.544107201 0.812924672 0.569662104 0.958161114 0.637309383 0.872084261 0.798520211 1 21.58512277 0.81508633 0.550992493 1.004823696 0.716877137 0.260035517 0.135224435 1.405490382 0.955190387 0.139586653 0.057758402 6.532603958 -0.81508633 -0.287946559 ALGNICYDSHEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALGNICYDSHEGR 13 0 P52306-4;P52306;P52306-5;D6RHH8 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ;;; 186.94 7.39E-06 1612210000 1365040 1211430 1228220 1420630 1607240 1310620 1522470 1424850 1573160 FALSE TRUE 1300517.264 1334876.094 1284535.102 1277825.573 1887542.147 1265232.901 1290189.239 1300082.58 1817117.618 0.715703404 0.734611827 0.706908066 0.703215665 1.038756175 0.696285638 0.710019663 0.715464188 1 20.79322037 -1.89121766 2.695828512 1.12768272 0.749069269 0.364752505 0.102502688 31385365.63 16341383.12 25398528.91 0.023540009 0.012846427 1.89121766 -0.378613451 ALGS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ALGSPTK 7 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 1 ALGS(0.962)PT(0.038)K;ALGS(0.992)PT(0.008)K;ALGS(0.998)PT(0.002)K;ALGS(0.997)PT(0.003)K;ALGS(0.985)PT(0.015)K;ALGS(0.984)PT(0.016)K;ALGS(0.993)PT(0.007)K;ALGS(0.991)PT(0.009)K 150.27 0.0020563 6946950000 12211800 10840700 10457700 12518800 7534850 12131500 12503000 12505200 8826500 TRUE FALSE 11634572.42 11945379.65 10937195.89 11260386.44 8848925.454 11711383.11 10595437.72 11410178.39 10195268.54 1.141173709 1.171659148 1.072771732 1.104471785 0.867944323 1.148707664 1.039250479 1.119164086 1 23.28139644 3.531240679 2.268802945 1.046424376 1.156715839 0.249095115 0.07736797 0.378165301 3.851550985 0.020819302 0.034570372 3398.135396 -3.531240679 0.110291463 ALGYFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALGYFHR 7 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YB83;H0YC27;H0YBD9 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ; 77.748 0.037205 446710000 1255210 854990 606800 679370 1631500 566460 1258760 855760 1188740 FALSE TRUE 1195878.711 942114.453 634622.3802 611078.4369 1916033.083 546843.3482 1066713.043 780825.1177 1373083.728 0.870943764 0.686130375 0.462187678 0.445040914 1.395423341 0.398259288 0.776873997 0.568665335 1 20.38898817 ALHHGIDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALHHGIDLEK 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 73.721 0.025526 127300000 159200 157220 143740 166230 118660 152190 155270 161760 13230 FALSE TRUE 151674.9315 173240.8967 150330.6212 149520.2446 139354.2664 146919.6221 131580.7098 147595.4369 15281.64083 9.925304042 11.33653766 9.837335064 9.784305641 9.119064371 9.614126112 8.610378377 9.658350075 1 13.89951184 -0.350407265 0.49340348 2.69E-16 10.27807172 0.944628922 0.666074407 1.539965481 0.361437273 4.37427136 0.326603403 0.446264906 0.350407265 10.27807172 ALHSLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALHSLLLR 8 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 190.08 0.0001883 1104300000 1196920 850860 544370 701840 1425210 642500 1298810 1005220 1184510 FALSE TRUE 1140343.964 937563.6013 569329.903 631289.7098 1673766.173 620250.0639 1100652.68 917197.6078 1368197.761 0.833464281 0.685254448 0.416116675 0.461402385 1.223336436 0.453333635 0.804454379 0.670369177 1 20.38384534 ALHSVLQAVPLNELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALHSVLQAVPLNELR 15 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 108.63 0.0010633 690690000 626210 510300 533680 580610 620860 531300 687780 603820 648280 FALSE TRUE 596610.2943 562300.1502 558149.7559 522245.9797 729137.7874 512900.9478 582846.5291 550946.3197 748811.9514 0.796742484 0.750923044 0.745380405 0.697432752 0.973726162 0.68495294 0.778361681 0.735760585 1 19.51424394 -1.241888795 5.162316769 1.000028042 0.770165755 0.451458353 0.079533333 2.27E-05 3.34E-06 0.068203932 0.016073862 0.057294272 1.241888795 -0.229862286 ALIEHEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALIEHEMK 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;; 105.57 0.0043629 623750000 949010 787530 815810 974900 759590 888540 994120 999460 725960 FALSE TRUE 904152.1781 867780.2023 853215.6954 876901.1998 892062.2555 857769.637 842448.7357 911941.9839 838538.1691 1.078248089 1.034872632 1.017503707 1.045749892 1.063830233 1.022934517 1.004663552 1.087537834 1 19.67751693 ALIEILATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALIEILATR 9 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 133.57 0.00063549 53739000 164234 114538 113325 209310 228760 130893 185540 126048 169326 FALSE TRUE 156470.9843 126209.5524 118521.0633 188269.7611 268655.6716 126360.1426 157232.4653 115010.5689 195584.2113 0.800018484 0.645295198 0.605984821 0.962602042 1.37360613 0.646065149 0.803911851 0.588036059 1 17.57743039 3.236980368 24.99972531 0.885233966 0.692129859 0.171081816 0.218850663 82.4082892 1303716.686 0.062766874 0.078868845 1725.759879 -3.236980368 -0.193104107 ALIEVLQPLIAEHQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALIEVLQPLIAEHQAR 16 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 143.97 1.36E-06 38487000 95242 73330 83622 98250 101470 83040 115950 83279 99400 FALSE TRUE 90740.09941 80802.41037 87456.15141 88373.72334 119166.3359 80164.30398 98259.69793 75986.64927 114814.4443 0.790319545 0.7037652 0.761717325 0.769709106 1.037903694 0.698207481 0.855813034 0.661821339 1 16.80894463 -2.560460363 2.226242052 4.791040145 0.785718858 0.293271664 0.104928117 4794606.684 292977.1947 92867190.04 0.024057008 0.002751311 2.560460363 -4.005321287 ALIQTCLNSPDS(ph)PPRSDPTTDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALIQTCLNSPDSPPRSDPTTDQR 23 1 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(0.995)PPRS(0.005)DPTTDQR;ALIQTCLNS(0.002)PDS(0.996)PPRS(0.003)DPTTDQR 177.6 3.28E-17 606050000 237850 197225 220940 249030 246710 212492 263130 244690 284370 TRUE FALSE 226607.3019 217322.4517 231070.3175 223997.0313 289736.1459 205133.3488 222984.6858 223263.6464 328468.6472 0.689890203 0.661623122 0.703477545 0.681943416 0.882081588 0.624514244 0.6788614 0.679710676 1 18.32539614 -1.037713827 4.630720413 1.00001062 0.696455105 0.656421607 0.068100303 8423572.049 1887666.848 909.4369771 0.014971039 0.091682442 1.037713827 -0.303555516 ALIRS(ph)PSLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALIRSPSLAK 10 1 Q5SW96 Q5SW96 LDLRAP1 Low density lipoprotein receptor adapter protein 1 1 ALIRS(0.989)PS(0.011)LAK 79.974 0.015381 131980000 360380 286090 342040 342570 337210 402440 422130 401240 416860 TRUE FALSE 343345.5516 315242.8963 357722.8723 308134.2128 396019.3172 388503.4019 357726.3156 366105.2985 481504.5198 0.71306818 0.654703919 0.742927341 0.639940437 0.822462305 0.806853074 0.742934491 0.760336162 1 18.87718981 -5 0.146634323 1.978176801 0.638499109 0.749837851 0.050507328 62.86297914 0.553287784 17.82728804 0.257370405 1.00E-05 5 -1.339677692 ALIVLAHSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALIVLAHSER 10 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 178.22 2.24E-06 871130000 1147680 989330 557060 576890 1138430 624070 1129460 886860 861020 FALSE TRUE 1093431.441 1090143.852 582601.752 518899.9212 1336971.832 602458.2994 957140.133 809201.8369 994542.5841 1.099431496 1.096125866 0.585798699 0.521747313 1.344308281 0.605764207 0.962392308 0.813642221 1 19.92367362 3.848718088 14.24087965 0.83391673 1.098147048 0.174044747 0.23945968 1.707736683 214.5105895 0.056897702 0.102584619 7058.592141 -3.848718088 0.264230319 ALKDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 96.711 0.011429 6091480000 12572200 12660400 9832940 14175900 5813370 13177100 11946130 13326800 6083450 FALSE TRUE 11977937.02 13950509.15 10283790.03 12750911.6 6827219.887 12720773.72 10123528.46 12159834.74 7026840.356 1.704597858 1.985317504 1.463501304 1.814601009 0.971591717 1.810312043 1.440694245 1.730483991 1 22.74444469 -2.03774185 0.101047323 1.03E-12 2.150741521 0.323259622 0.27966417 85.31224166 1.210178806 26.64956644 5.292267133 0.009167653 2.03774185 2.150741521 ALKDEEKMELQEIQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALKDEEKMELQEIQLK 16 2 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 0 104.21 0.00077579 235630000 545600 265340 561980 433200 383470 577290 738100 609950 420160 FALSE TRUE 519810.5693 292378.4477 587747.3389 389653.913 450347.0466 557298.3025 625489.2889 556539.5445 485316.2669 1.071075925 0.602449305 1.211060455 0.80288657 0.927945501 1.148319849 1.288828196 1.146756419 1 18.88856569 2.231272033 4.378270925 1.186250579 0.898209396 0.274911833 0.173638398 0.201796078 9.222830697 0.061341637 0.046878547 170.3225037 -2.231272033 -0.288041183 ALKDEIDVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALKDEIDVLR 10 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 65.179 0.063607 204180000 319180 294890 290420 364170 363000 309100 403870 349370 340570 FALSE TRUE 304092.994 324939.6263 303736.0443 327562.9397 426307.0851 298395.7895 342252.2139 318777.3107 393383.8562 0.773018489 0.826011594 0.772111106 0.832680179 1.083692374 0.758535931 0.870020995 0.810346702 1 18.58557823 -5 0.047557731 1.581514834 0.528207668 0.241333855 0.091661565 898.3938508 3.167116883 70.22717244 16.88779618 1.00E-05 5 -1.053307166 ALKEDDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALKEDDPK 8 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 81.338 0.021086 214940000 1144940 1073210 1029870 1314340 648850 1403350 1340460 1486120 718180 FALSE TRUE 1090820.955 1182571.319 1077090.558 1182220.046 762009.2346 1354751.638 1135948.208 1355987.454 829551.6864 1.314952369 1.425554716 1.298400782 1.425131267 0.918579574 1.633112993 1.369351936 1.634602734 1 19.66197235 ALKEPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALKEPPR 7 1 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 91.9 0.014651 998650000 4326200 4355000 3526950 4697200 3268540 4027940 4183680 4286100 3578160 FALSE TRUE 4121709.1 4798779.451 3688664.146 4225028.532 3838572.341 3888451.428 3545382.777 3910786.362 4133042.778 0.997257788 1.161076647 0.892481483 1.022256182 0.928752144 0.940820513 0.857814198 0.946224506 1 21.97877287 3.728531741 24.9682092 0.933531601 1.07916722 0.46674273 0.060885811 471.6808169 1174311.268 0.015629778 0.024518775 5352.192698 -3.728531741 0.145635619 ALKEPPRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ALKEPPRDR 9 2 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;;; 103.7 0.0019009 8994740000 23218600 17514900 21696500 22347400 22427100 22138500 28877500 24249700 26563600 FALSE TRUE 22121102.79 19299688.22 22691305.99 20100996.89 26338379.14 21371838.19 24471707 22126267.71 30682947.42 0.720957556 0.629003725 0.739541273 0.655119491 0.858404467 0.696537979 0.797567022 0.721125888 1 24.87093374 -4.999999991 0.158532525 2.043911399 0.644515609 0.664650756 0.062335506 70.06463675 0.641307833 22.90728355 0.238873057 1.00E-05 4.999999991 -1.399395791 ALLADAQLMLDHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLADAQLMLDHLK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 201.44 1.78E-08 96328000 250604 201676 193341 222010 204469 192634 263250 244504 197897 FALSE TRUE 238758.4456 222227.0137 202205.8761 199693.133 240128.3289 185963.0363 223086.3776 223093.9336 228585.856 1.04450227 0.972181821 0.884594872 0.873602315 1.050495131 0.813536933 0.9759413 0.975974356 1 17.80237661 4.221898283 2.547384411 0.934807379 1.035115659 0.181590717 0.068712457 0.395396732 5.021334025 0.016125514 0.052421494 16668.5677 -4.221898283 0.10030828 ALLDFEDKDGDKVVAGDEWLFEGPGTYIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALLDFEDKDGDKVVAGDEWLFEGPGTYIPR 30 2 Q14764;H3BQK6 Q14764 MVP Major vault protein 0 168.72 1.22E-12 36542000 97625 89204 89520 98825 55264 106700 96763 101090 50975 FALSE TRUE 93010.45972 98293.98902 93624.58055 88890.92324 64902.0241 103004.9522 82000.02718 92238.02369 58879.94266 1.579662879 1.66939682 1.59009293 1.509697857 1.102277298 1.749406463 1.392664861 1.566544048 1 15.84548865 -3.129259068 0.203434994 1.55E-11 1.628591613 0.465467312 0.175184349 51.47631131 1.011359091 22.71015938 0.397985008 0.000742576 3.129259068 1.628591613 ALLDSLQLGPDSLTVHLIHEVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLDSLQLGPDSLTVHLIHEVTK 23 0 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 252.6 1.04E-43 496860000 904440 926490 862370 1006970 735490 895160 944740 942210 26714 FALSE TRUE 861688.9136 1020900.384 901910.5175 905747.4625 863759.2231 864160.3847 800602.5617 859705.0974 30856.67068 27.925531 33.08524094 29.22902885 29.35337619 27.99262539 28.00562619 25.94585041 27.86123967 1 14.91329479 -0.190540372 0.62149494 1.35E-20 29.82264539 0.962593713 1.718554776 1.100925205 0.415741841 7.137463642 0.662377272 0.644851371 0.190540372 29.82264539 ALLDSQFSYQHAIEESVVLIYDPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALLDSQFSYQHAIEESVVLIYDPIK 25 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;; 239.13 1.59E-38 1287160000 1246750 1230500 1234365 1561100 956523 1332146 1311983 1558891 904422 FALSE TRUE 1187818.598 1355889.349 1290961.856 1404175.262 1123340.308 1286013.45 1111815.897 1422386.24 1044675.145 1.137021977 1.297905244 1.235754352 1.344126228 1.075301077 1.231017562 1.064269503 1.361558421 1 19.99462296 2.730487127 24.99502424 1.150202215 1.247107637 0.1857826 0.111054865 1078.531064 3339055.553 0.032043374 0.030672635 537.6344973 -2.730487127 0.096905422 ALLELQLEPEELYQTFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 281.51 5.85E-39 120607000 441446 558886 446527 530986 448543 445904 459477 498946 398808 FALSE TRUE 420579.7224 615837.1188 467000.7046 477610.2785 526768.7572 430462.2327 389375.3448 455255.6432 460653.1078 0.913007457 1.336878246 1.013779559 1.03681115 1.143525895 0.934460715 0.84526803 0.988283017 1 18.81332122 2.202958758 8.54901728 0.919760317 1.100841068 0.271336391 0.11613231 0.284192874 61.22647155 0.042157985 0.031370954 159.5727605 -2.202958758 0.181080751 ALLENMEGLFLAVDEIVDGGVILESDPQQVVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALLENMEGLFLAVDEIVDGGVILESDPQQVVHR 33 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8W651;F8VYK5;F8VYE0;P61923-2;P61923-3 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 142.37 4.32E-10 138300000 27381 25587 26904 32477 30341 26967 31306 29293 30473 FALSE TRUE 26086.75439 28194.34439 28137.57501 29212.35026 35632.46079 26033.12603 26529.69473 26727.94963 35198.59721 0.741130513 0.801007615 0.799394784 0.829929389 1.012326161 0.739606919 0.753714546 0.759347012 1 15.10323031 -2.42928681 2.17270859 2.706047295 0.800833381 0.373231272 0.079465084 5715267.985 417367.6309 48132407.8 0.019242257 0.003721459 2.42928681 -1.905213914 ALLEPELRPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLEPELRPEDR 12 1 P0DPD7;P0DPD8 P0DPD7 0 ; 123.31 0.00031277 127587000 221032 224338 218886 238273 235895 222681 256315 228241 263097 FALSE TRUE 210584.2554 247198.2973 228922.1396 214321.3454 277035.0133 214969.5011 217209.4392 208255.0081 303896.739 0.692946743 0.813428594 0.753289227 0.705243979 0.911609036 0.707376795 0.714747515 0.685282141 1 18.21322167 -1.369286663 5.516356183 1.000082964 0.749889655 0.569487592 0.068842887 6.58E-05 7.52E-06 0.062411205 0.014705601 0.042728076 1.369286663 -0.250193309 ALLFIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLFIPR 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 143.22 0.0056673 933560000 717590 763200 619920 679290 737250 601520 782400 732100 686880 FALSE TRUE 683670.9428 840970.9477 648343.9452 611006.4786 865826.1666 580689.2116 663030.5102 667993.4429 793397.8423 0.861700028 1.059961224 0.81717382 0.770113613 1.091288784 0.731901677 0.835684791 0.84194008 1 19.59768495 3.716184482 24.91762743 0.858183661 0.960830653 0.090574883 0.115594582 1350.558348 1503955.56 0.028445688 0.044104621 5202.169304 -3.716184482 0.102646992 ALLFVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLFVPR 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 148.62 0.0048189 1376200000 957430 996780 841790 946950 977960 801770 957600 925240 851290 FALSE TRUE 912174.1813 1098353.015 880386.9041 851760.7869 1148515.914 774004.5039 811500.5325 844221.0806 983303.7054 0.927662711 1.117002823 0.895335693 0.86622351 1.168017478 0.787146941 0.825279645 0.858555781 1 19.90727755 2.203710117 24.99999674 0.847837099 0.995028482 0.249296389 0.107150557 211.6296486 151811.2925 0.03749151 0.027690461 159.8490712 -2.203710117 0.147191383 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR 43 1 A0A1B0GUA3;Q96EK5;A0A1B0GUH6;A0A1B0GTE6;A0A0D9SFK7;A0A1B0GU96;A0A1B0GVY9 A0A1B0GUA3 KIAA1279;KIF1BP KIF1-binding protein 0 121.92 4.44E-09 36227000 39463 37713 38658 41005 37814 39255 36701 41302 40191 FALSE TRUE 37597.6622 41555.99758 40430.50754 36883.0995 44408.74963 37895.58951 31101.58839 37685.37792 46423.61501 0.809882259 0.895147816 0.870903904 0.794490035 0.956598266 0.81629984 0.669951885 0.811771723 1 15.50257125 2.003980269 24.88948847 0.778708352 0.863523621 0 0.093838886 189.0383949 1182089.902 0.031792218 0.023382002 100.9207033 -2.003980269 0.084815269 ALLLLCGEDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLLLCGEDD 10 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 130.77 0.00062335 34022000 58526 48387 53107 54960 62384 47275 63582 55908 73752 FALSE TRUE 55759.59197 53317.69031 55542.00848 49435.31638 73263.74985 45637.8549 53881.39814 51012.39913 85189.08349 0.65453917 0.625874679 0.651985046 0.580301071 0.860013359 0.535724215 0.632491816 0.598813804 1 16.37838095 -1.535273149 3.125269693 1.012658851 0.641195755 0.635676422 0.085058628 81200479.36 85052294.29 8549830.214 0.018290879 0.029155927 1.535273149 -0.371463096 ALLLVGDVAQAADVAIEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLLVGDVAQAADVAIEHR 19 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 ; 84.829 0.003134 14946100 15114.7 13461.9 16017 16135.6 20864.1 15960.3 18733.6 12903.2 16430.2 FALSE TRUE 14400.25809 14833.68291 16751.39529 14513.61883 24502.79243 15407.59081 15875.44525 11773.3274 18978.1115 0.758782458 0.781620601 0.882669242 0.764755694 1.291108045 0.811861117 0.836513436 0.620363486 1 14.21204882 3.724832096 1.896472283 0.888353268 0.762170153 0.073426845 0.173300044 0.931705044 6.53912428 0.048680973 0.101339656 5306.792366 -3.724832096 -0.126183115 ALLPHVLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLPHVLCK 9 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 157.54 6.83E-05 521280000 2767300 2106580 2120980 2490500 2589200 2382400 3164100 2588000 2874400 FALSE TRUE 2636495.213 2321242.897 2218229.031 2240150.208 3040755.66 2299896.891 2681358.432 2361381 3320147.272 0.794089839 0.699138534 0.668111638 0.674714109 0.915849633 0.692709299 0.807602258 0.711227788 1 21.66281581 -5 0.283689447 2.902304135 0.730659821 0.520615172 0.076528405 182.7766124 1.739638239 205.0349162 0.078635622 1.00E-05 5 -2.171644314 ALLQQQPEDDSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLQQQPEDDSKR 13 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 93.958 0.0086188 219588000 103894 97475 95378 122253 100310 101710 122585 123857 125242 FALSE TRUE 98983.13652 107407.8133 99751.17564 109963.8962 117804.0322 98187.7572 103882.4068 113011.4245 144663.8897 0.684228364 0.742464574 0.689537492 0.760133689 0.814329218 0.678730244 0.718094937 0.781199957 1 17.14234532 -4.999999997 0.317344377 3.524393701 0.717641244 0.80412871 0.041800249 132.9086843 1.18421869 224.9678764 0.036731114 1.00E-05 4.999999997 -2.806752457 ALLQSS(ph)ASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALLQSSASR 9 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 ALLQS(0.002)S(0.998)ASR 147.3 9.73E-05 65129000 147680 146440 135010 152590 181510 155540 166070 168900 219590 TRUE FALSE 140699.4591 161362.4025 141200.342 137251.3633 213165.2865 150153.6108 140732.9714 154110.2206 253642.8957 0.554714764 0.636179468 0.556689521 0.541120471 0.84041497 0.591988238 0.554846888 0.607587373 1 17.95243923 -1.788509247 2.469303044 1.117820453 0.607831038 0.665268569 0.086823183 10914013.92 7353422.873 7733335.745 0.020824505 0.016273867 1.788509247 -0.509989414 ALLYEDALYTVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALLYEDALYTVLHR 14 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 ; 200.21 1.96E-08 206145000 593580 514200 535110 618290 704590 470210 716870 650950 720910 FALSE TRUE 565522.6498 566597.5646 559645.3228 556138.3145 827470.2729 453926.5098 607498.3153 593949.3671 832705.0409 0.679139217 0.680430088 0.672081104 0.667869518 0.993713539 0.545122808 0.729548022 0.713277016 1 19.66744603 -4.999999998 0.387895291 5.369073861 0.699404692 0.397477387 0.112124668 631.7359336 4.599366969 2328.480864 0.066152486 1.00E-05 4.999999998 -4.669669169 ALMDEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALMDEVVK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 143.85 0.0013838 182152000 351030 292050 317440 376060 316200 321360 395230 378840 352770 FALSE TRUE 334437.5076 321810.227 331994.938 338257.7343 371345.1799 310231.2226 334930.4046 345666.7612 407475.7699 0.820754342 0.789765308 0.81475995 0.830129689 0.911330703 0.761348884 0.821963978 0.848312432 1 18.63635475 0.75150461 2.740710672 0.999966275 0.818732973 0.684087749 0.03781263 0.788207897 7.902844853 0.034463594 0.00910908 5.642929312 -0.75150461 -0.181233302 ALNHSVEDIEPDLLT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALNHSVEDIEPDLLTPR 17 0 Q8IWR0;I3L2K5 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR 196.81 5.76E-11 168969000 254923 199723 209971 236557 260576 208287 252192 225953 239708 TRUE FALSE 242873.295 220075.0008 219598.378 212777.8409 306020.3719 201073.969 213715.4786 206167.3575 276880.6924 0.877176711 0.794836935 0.793115533 0.768482046 1.105242728 0.726211594 0.771868478 0.744607201 1 18.07890493 -0.52971699 6.641912871 0.999999741 0.821369911 0.209491852 0.108215639 0 0 0.098133255 0.02313023 0.295313302 0.52971699 -0.17862983 ALNSIIDVYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALNSIIDVYHK 11 0 P05109 P05109 S100A8 "Protein S100-A8;Protein S100-A8, N-terminally processed" 0 101.6 0.0031662 552170000 938920 680030 752980 859390 824130 867650 1102000 912740 820180 FALSE TRUE 894539.1124 749325.8301 787504.8778 773002.4845 967858.0111 837603.0629 933869.6604 832815.6469 947369.3255 0.944234828 0.790954288 0.831254355 0.815946288 1.021626925 0.884135722 0.985750367 0.879082344 1 19.85356743 2.753147749 24.81432118 0.950131424 0.846653117 0.448521835 0.059698486 666.5293726 1133838.757 0.016984918 0.017942319 566.4319597 -2.753147749 -0.103478307 ALPAAHIPAPPHEGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR 92.932 0.0053266 69134000 71257 67678 76269 80724 96735 54196 76147 73157 75349 TRUE FALSE 67888.82283 74574.46514 79766.00909 72609.47015 113605.5534 52319.17893 64529.37661 66750.98525 87033.73809 0.780028806 0.856845481 0.916495268 0.834268087 1.305304769 0.601136755 0.741429451 0.766955283 1 16.40928714 -1.489910718 7.607167608 1.000020676 0.843037018 0.061411599 0.181950376 6.08E-05 4.08E-06 0.16796787 0.039585197 0.032366019 1.489910718 -0.156983658 ALPAVQQNNLDEDLIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALPAVQQNNLDEDLIRK 17 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 332.07 7.79E-72 497080000 507610 389140 417300 481000 411230 439070 540900 545650 490460 FALSE TRUE 483616.2813 428793.8084 436433.6178 432648.9662 482948.3818 423864.8958 458375.7707 497869.9933 566518.0319 0.85366441 0.756893487 0.77037904 0.763698491 0.852485454 0.748193124 0.809110646 0.878824619 1 19.11176235 0.956791143 2.159572588 0.999381863 0.7912781 0.771915542 0.036518698 0.152248535 1.54738969 0.032561197 0.008980257 9.052971295 -0.956791143 -0.208103763 ALPESLGQHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALPESLGQHALR 12 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ;;; 198.55 1.82E-07 1186430000 846029 682056 740262 798166 1019941 739133 948621 837070 1036298 FALSE TRUE 806038.8858 751558.2818 774203.7449 717932.8373 1197818.387 713536.6389 803891.4438 763771.7132 1197001.801 0.673381515 0.627867294 0.646785781 0.599775904 1.000682193 0.596103229 0.671587497 0.638070647 1 20.19099389 -1.710949939 2.403149217 1.06497056 0.678152619 0.424102494 0.116469009 5863849.461 4272265.053 2294103.687 0.028357737 0.019455843 1.710949939 -0.386817941 ALPLALVLHELGAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALPLALVLHELGAGR 15 0 C9JGI3;P19971;A0A494C0L6;P19971-2 C9JGI3 TYMP Thymidine phosphorylase 0 ; 217.12 2.11E-12 256800000 366000 275050 311660 322160 372160 288990 363610 327170 360080 FALSE TRUE 348699.9053 303077.9077 325949.9193 289775.8647 437064.5862 278982.2038 308134.6163 298521.2604 415919.3674 0.838383429 0.728693904 0.78368536 0.69671164 1.050839707 0.67076031 0.740851811 0.717738302 1 18.66594434 -1.658589048 2.968116189 1.021723379 0.775981907 0.295854826 0.107350961 43007286.85 38868886.73 7043287.196 0.024012466 0.021948809 1.658589048 -0.245741472 ALPLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 116.05 0.0058141 247312000 475740 472800 472640 536780 519500 482130 585500 575760 703910 TRUE FALSE 453252.713 520978.8575 494311.0115 482821.8546 610100.6355 465433.7172 496171.2216 525343.4021 813068.7677 0.557459259 0.640756204 0.6079572 0.593826591 0.750367816 0.572440777 0.610245088 0.646124194 1 19.63301785 -4.999999987 0.403756846 7.298696329 0.612297133 0.838216475 0.052255114 279.3460426 1.925277041 1553.031042 0.029988544 1.00E-05 4.999999987 -6.686399196 ALPNNT(ph)SSSPQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.501)S(0.146)S(0.082)S(0.271)PQPK 101.32 0.02232 131620000 179750 185890 186440 212200 140170 196140 205860 225730 190150 TRUE FALSE 171253.5737 204832.4023 194988.4584 190869.2528 164615.6036 189347.6226 174452.2761 205963.8845 219637.4908 0.779710117 0.932593072 0.887774021 0.869019456 0.749487726 0.86209154 0.794273671 0.937744662 1 17.74476481 1.039924445 5.080805434 0.999478091 0.843311865 0.514257393 0.054067277 0.133932152 7.938502691 0.051214065 0.012951569 10.96287456 -1.039924445 -0.156166226 ALPNNTSSS(ph)PQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ALPNNTSS(0.013)S(0.986)PQPK;ALPNNTS(0.001)S(0.014)S(0.986)PQPK;ALPNNTS(0.001)S(0.014)S(0.985)PQPK;ALPNNT(0.001)S(0.045)S(0.344)S(0.61)PQPK;ALPNNTS(0.003)S(0.072)S(0.925)PQPK 264.43 3.21E-24 1272498000 1807177 1911327 1836556 2008890 1297626 2094316 2201300 2226500 1743101 TRUE FALSE 1721755.325 2106093.394 1920763.909 1806952.561 1523931.564 2021789.312 1865451.255 2031535.857 2013412.201 0.855142988 1.046031902 0.953984439 0.897457838 0.756890002 1.004160654 0.926512343 1.009001463 1 20.94121113 1.368154229 1.833965608 1.005889142 0.922710199 0.158311259 0.078935549 0.720045548 4.320701313 0.070851454 0.021726643 23.3428688 -1.368154229 -0.083178943 ALPQT(ph)PRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;ALPQT(1)PRPR;ALPQT(1)PRPR 125.72 0.00079807 33253250000 6734230 5001890 5864610 6137900 6946410 5360690 6795870 5969290 7340710 TRUE FALSE 6415916.294 5511588.278 6133508.169 5520906.631 8157861.705 5175047.961 5759035.217 5446587.322 8479069.816 0.756676904 0.65002275 0.723370405 0.651121733 0.96211753 0.610332038 0.679206015 0.642356702 1 23.01547457 -1.078192272 4.031178133 1.000053947 0.706643251 0.458728683 0.099163279 5068376.041 2711210.278 2329.59775 0.02123474 0.083523316 1.078192272 -0.293410695 ALPSLNTGSSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGSS(0.003)S(0.997)PR;ALPSLNTGSS(0.005)S(0.995)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.063)S(0.937)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.015)S(0.985)PR;ALPSLNTGSS(0.015)S(0.985)PR;ALPSLNTGS(0.002)S(0.144)S(0.854)PR;ALPSLNTGS(0.001)S(0.127)S(0.872)PR 282.69 1.64E-32 23601710000 11182390 8400620 9115980 10730270 11378340 9429370 11594810 9662040 11491890 TRUE FALSE 10653820.59 9256652.729 9533956.7 9651642.873 13362718.89 9102828.553 9825808.781 8815980.556 13273993.61 0.802608537 0.697352508 0.718243279 0.7271092 1.006684144 0.68576412 0.740230037 0.664154347 1 23.66209915 -1.984128594 2.758042554 1.22209597 0.75430475 0.38694975 0.096801751 23286589.09 9655888.389 32916081.76 0.022632757 0.010372213 1.984128594 -0.46779122 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.558)S(0.441)PVGPSSSK 88.001 0.0016601 214440000 395280 355270 367030 407510 311480 405270 475960 485930 339170 TRUE FALSE 376595.8978 391472.4169 383858.6885 366546.3206 365802.0134 391235.3983 403343.5604 443379.3931 391766.7514 0.961275801 0.9992487 0.979814359 0.935623861 0.933723988 0.9986437 1.029550259 1.131743293 1 18.57963544 1.685989084 2.686754236 1.06787295 0.967442483 0.548557387 0.037858166 0.16509575 2.667041755 0.022447408 0.009635318 48.5276303 -1.685989084 -0.100430467 ALPTSKPEGSLHSS(ph)PVGPSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGS(0.001)LHS(0.1)S(0.899)PVGPSSSK 88.917 0.0015758 276960000 371030 323300 378450 428030 336090 405370 461310 437880 362570 TRUE FALSE 353492.1472 356244.6376 395802.3068 385003.6112 394703.9896 391331.9353 390928.687 399536.9059 418795.5038 0.84406863 0.850641027 0.945096839 0.919311711 0.942474277 0.934422485 0.933459608 0.954014315 1 18.67588643 8 0.187766147 0.992540229 0.250389777 0.803205466 0.020621436 21.22714504 0.245889932 0.042840821 4.553874884 100000000 -8 -0.742150451 ALQALEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALQALEELR 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 ;;; 134.77 0.00055763 201828000 411180 297395 205221 245309 465534 267867 456930 353795 471260 FALSE TRUE 391744.3363 327699.8886 214630.5858 220650.0733 546722.9822 258590.6986 387216.9364 322814.8342 544340.5939 0.719667687 0.602012586 0.394294653 0.405352964 1.00437665 0.475053122 0.711350468 0.593038325 1 19.0541501 -2.298902868 0.355658944 1.511327175 0.598963319 0.321567379 0.177456621 61.43098625 2.833159088 24.90116917 0.126220791 0.00502455 2.298902868 -0.912363856 ALQDEWDAVMLHSFTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ALQDEWDAVMLHSFTLR 17 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;;;; 234.48 3.90E-20 445662100 722751.3 673505 646664.6 746070.4 738389.5 651036.8 829086.7 706972.9 722553.2 FALSE TRUE 688588.2784 742135.9252 676314.8115 671073.986 867164.395 628491.2324 702594.2967 645066.605 834603.06 0.82504883 0.889208249 0.810343077 0.804063654 1.039014157 0.75304209 0.841830483 0.772902276 1 19.67073068 -2.314858044 2.339774533 1.846686563 0.844767808 0.281495869 0.079249408 10407456.77 1993298.507 46300878.7 0.018622325 0.004843307 2.314858044 -1.001918755 ALQEFDLALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALQEFDLALR 10 0 B7Z6D5;Q96GQ7 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 ; 126.29 0.00089898 29839000 155170 150801 138116 163623 146605 148761 181183 175100 156979 FALSE TRUE 147835.4216 166167.7933 144448.7552 147175.3052 172172.8656 143609.3693 153540.2057 159767.3157 181322.5016 0.815317571 0.916421249 0.796639987 0.811677006 0.949539434 0.792010743 0.846779657 0.881122389 1 17.46819844 0.828847876 3.256891767 0.999959021 0.849701961 0.470701691 0.050784461 0.755505369 12.86421754 0.044773656 0.011628675 6.742917972 -0.828847876 -0.15025706 ALQEGEGDLSIS(ph)ADRLSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALQEGEGDLSISADRLSEKR 20 2 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 ALQEGEGDLS(0.166)IS(0.818)ADRLS(0.016)EKR 96.303 0.00057552 35248000 49466 30741 39252 40453 35823 41359 60083 50459 48549 TRUE FALSE 47127.84021 33873.54285 41051.74303 36386.58758 42070.51986 39926.72746 50916.23485 46040.54246 56077.73097 0.840402053 0.604046246 0.732050715 0.648859841 0.750217941 0.711988998 0.907958185 0.821012934 1 15.77514036 1.453915056 0.951712494 0.976604009 0.702724682 0.609257974 0.073983056 0.313417036 0.571855856 0.063315782 0.023520155 28.43904814 -1.453915056 -0.273879327 ALQEVGSGGTLGLSS(ph)PKS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALQEVGSGGTLGLSSPKS 18 1 A0A0M3HER3 A0A0M3HER3 1 ALQEVGSGGTLGLSS(1)PKS;ALQEVGSGGTLGLS(0.001)S(0.998)PKS(0.001) 240.68 6.14E-24 123602000 267180 231980 254920 289240 185019 283290 313160 295740 222150 TRUE FALSE 254550.9309 255619.0257 266608.3342 260165.0457 217286.255 273479.5963 265381.6904 269843.4378 256599.8874 0.992014975 0.996177466 1.039004096 1.013893842 0.846790142 1.065782215 1.034223721 1.051611676 1 17.96916101 ALQHTES(ph)PSETNKPHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALQHTESPSETNKPHSK 17 1 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 ALQHTES(0.99)PS(0.01)ETNKPHSK;ALQHT(0.007)ES(0.984)PS(0.004)ET(0.004)NKPHS(0.001)K 231.93 1.86E-16 131638000 182210 210268 193028 220133 140300 218814 251671 255344 107010 TRUE FALSE 173597.2944 231694.5483 201878.5247 198004.8126 164768.2756 211236.4163 213273.9667 232984.7257 123604.5643 1.404456991 1.874482141 1.633261085 1.601921529 1.333027438 1.708969386 1.725453813 1.884920084 1 16.91537249 -0.922660621 5.394221821 0.999998998 1.649364902 0.571346567 0.175773122 2.04E-06 4.07E-07 0.16361184 0.038563621 0.119492151 0.922660621 0.649365904 ALQKYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALQKYEK 7 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 96.253 0.011735 901200000 1012670 557870 953430 761820 932080 901730 1396310 1074210 1188000 FALSE TRUE 964803.096 614717.5872 997145.7086 685240.4062 1094634.457 870502.864 1183277.265 980146.4777 1372228.973 0.703091915 0.447970127 0.726661314 0.499363022 0.797705397 0.634371436 0.862303076 0.714273272 1 20.3880898 1.326766174 0.442025075 1.001772093 0.570097872 0.524341689 0.111225903 0.665306655 0.365927294 0.11760178 0.073317775 21.22101603 -1.326766174 -0.431674221 ALQLEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALQLEEER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 234.91 3.31E-08 2175450000 2778570 2281170 2324690 2610170 2993570 2147180 2862950 2502420 3065790 FALSE TRUE 2647232.503 2513623.816 2431279.336 2347790.753 3515647.66 2072822.618 2426154.396 2283294.839 3541217.055 0.747548784 0.709819188 0.68656603 0.66298979 0.992779489 0.585341871 0.685118805 0.644776867 1 21.75581384 -1.167235454 4.417683018 1.000057021 0.713958965 0.409912935 0.107700615 5.83E-05 1.10E-05 0.095630077 0.022535514 0.068040038 1.167235454 -0.286098056 ALQLLHCFPLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALQLLHCFPLDIR 13 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 127.76 0.00017323 109664000 243300 216330 201616 237550 265430 197359 256020 236610 229080 FALSE TRUE 231799.6912 238374.2729 210860.293 213671.0227 311720.908 190524.4083 216959.4469 215891.1741 264604.5564 0.876023052 0.900869872 0.796888368 0.807510746 1.178063266 0.720034496 0.819938439 0.815901196 1 18.01347838 -0.710228499 6.973486843 0.999999997 0.864241785 0.109570025 0.121479112 8.12E-10 0 0.109019914 0.02569624 0.194881898 0.710228499 -0.135758212 ALQS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 86.205 0.056477 3469700000 11365400 11426400 10665000 12611200 6825200 12367100 12811700 13847100 9350100 TRUE FALSE 10828180.07 12590763.15 11154000.8 11343498.22 8015512.719 11938824.23 10857039.86 12634574.52 10800065.75 1.002603161 1.165804305 1.032771564 1.050317514 0.742172585 1.105439957 1.005275348 1.169860888 1 23.36453676 3.384911674 3.277382261 1.005985407 1.085289048 0.054590614 0.116507443 0.625260542 13.3586288 0.03197837 0.045337802 2426.116625 -3.384911674 0.079303641 ALQTS(ph)PQPPEGPGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.04)S(0.96)PQPPEGPGLPR 191.93 6.47E-10 43438000 155190 136360 134410 163900 157950 148040 169900 171330 178220 TRUE FALSE 147854.4763 150255.239 140572.8314 147424.4606 185496.43 142913.3377 143978.6346 156327.4369 205857.4474 0.718237198 0.729899457 0.68286493 0.716148298 0.901091665 0.694234479 0.699409404 0.759396558 1 17.65128612 0.952124716 19.83213275 1.000000001 0.732388377 0.645150442 0.061397516 460.5259477 190772.1248 0.05682115 0.014205287 8.956219227 -0.952124716 -0.267611624 ALRDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALRDFLR 7 1 O75828;P16152;E9PQ63;A8MTM1;P16152-2 O75828;P16152 CBR3;CBR1 Carbonyl reductase [NADPH] 3;Carbonyl reductase [NADPH] 1 0 136.11 0.0027466 197250000 148430 54581 32044 29116 235710 56885 203420 98608 229240 FALSE TRUE 141414.0081 60142.86595 33513.2491 26189.20436 276817.7494 54915.05819 172384.5429 89973.36077 264789.3684 0.534062258 0.227134746 0.12656569 0.0989058 1.045426223 0.207391477 0.651025168 0.339792195 1 18.01448567 -1.258769672 0.248036489 1.453809383 0.290794254 0.314739499 0.282674814 22.12627681 1.147377289 7.028673377 0.444362881 0.055109989 1.258769672 -1.163015129 ALRPDLADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALRPDLADK 9 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 93.096 0.0087833 87072000 446250 365730 366670 485630 304060 403350 458250 458680 312210 FALSE TRUE 425156.6469 402998.3028 383482.1822 436813.5498 357087.9677 389381.8884 388335.5462 418515.5476 360625.9323 1.17894086 1.117496738 1.063379385 1.211264944 0.990189379 1.079739014 1.076837552 1.160525381 1 18.46014362 8 0.080799561 0.948615775 1.512353153 0.254634797 0.062306907 248.8177761 1.463674081 1.522060368 15.65049471 100000000 -8 0.563737379 ALRPGDLPPS(ph)PDDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 125.03 4.14E-05 230840000 202960 184130 202940 209760 156326 200343 222720 223990 180882 TRUE FALSE 193366.483 202893.0563 212244.9997 188674.5263 183589.2049 193405.0717 188739.9735 204376.2482 208932.2567 0.925498466 0.971094935 1.015855584 0.903041633 0.878702062 0.92568316 0.903354879 0.978193848 1 17.67267572 1.052276205 6.207452775 0.999830213 0.933742726 0.286673729 0.038261577 0.237837206 18.55023136 0.038406695 0.009654246 11.27914566 -1.052276205 -0.066087487 ALRPPMSQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALRPPMSQAR 10 1 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 104.79 0.0024026 333550000 189510 97691 47168 43097 261700 69961 201330 120900 200710 FALSE TRUE 180552.2379 107645.824 49330.69946 38764.80768 307340.3971 67538.23303 170613.4108 110313.3551 231835.0817 0.778796015 0.464320685 0.212783583 0.167208549 1.325685461 0.29132016 0.735925769 0.475826843 1 17.82273937 ALRPPTS(ph)PGVFGALQNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.164)S(0.836)PGVFGALQNFK 109.85 0.00021226 94695000 160760 201610 147390 212590 133320 167580 171420 185360 137980 TRUE FALSE 153161.1934 222154.2882 154147.9773 191220.0493 156570.9658 161776.6626 145266.7307 169128.8957 159377.2337 0.960997941 1.393889724 0.967189439 1.199795259 0.982392291 1.015055029 0.911464751 1.061186042 1 17.28208604 2.726573136 23.90123231 0.983974356 1.146470641 0.217861211 0.126071503 524.3839155 1045540.5 0.038294267 0.036392169 532.8109432 -2.726573136 0.162496285 ALRTDYNASVSVPDSSGPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALRTDYNASVSVPDSSGPER 20 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 93.804 0.0013299 211420000 41210 28942 60916 33695 88148 45997 74688 49249 113010 FALSE TRUE 39262.08497 31891.2227 63709.05885 30307.91458 103520.9833 44404.11236 63292.97386 44936.49647 130535.0136 0.300778189 0.244311636 0.488061073 0.232182261 0.793051461 0.340170128 0.484873538 0.344248606 1 16.99407731 -5 0.174543945 3.375945535 0.259299895 0.573568811 0.162104782 88.92686374 0.847081019 73.39458828 0.495664106 1.00E-05 5 -3.11664564 ALS(ph)GHSAADRNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSGHSAADRNER 13 1 A0A0U1RQE4 A0A0U1RQE4 1 ALS(1)GHSAADRNER;ALS(1)GHSAADRNER 174.59 1.19E-05 410070000 327580 205911 291963 274350 349140 288390 359760 321420 361760 TRUE FALSE 312095.9426 226893.565 305349.7923 246771.8168 410029.9055 278402.982 304872.0046 293274.7608 417859.8932 0.746891357 0.542989573 0.73074683 0.590561145 0.981261691 0.666259161 0.729603414 0.701849509 1 18.67265977 -5 0.176374243 2.194093037 0.636857248 0.385022027 0.115131254 129.6408223 1.239493449 54.20423943 0.348411376 1.00E-05 5 -1.557235789 ALS(ph)GRAS(ph)PVPAPSSGLHAAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSGRASPVPAPSSGLHAAVR 21 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 ALS(1)GRAS(1)PVPAPSSGLHAAVR 74.65 0.017451 61137000 40907 37499 42593 43569 49875 38055 56016 45277 57275 TRUE FALSE 38973.40718 41320.19073 44545.93118 39189.36134 58573.18421 36737.14581 47469.7304 41312.30585 66156.91448 0.589105576 0.624578565 0.673337497 0.592369848 0.885367534 0.555303192 0.717532412 0.624459381 1 16.01360433 -5 0.244183495 3.004450197 0.622204763 0.57118427 0.092976341 118.1359277 1.175213028 117.9390983 0.125469195 1.00E-05 5 -2.382245435 ALS(ph)HDSIFIPESGQDATRPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(0.996)HDS(0.004)IFIPESGQDATRPVR 184.3 2.43E-17 309160000 53709 42646 53459 63900 65144 43455 62824 60274 55674 TRUE FALSE 51170.28201 46991.67588 55910.14803 57476.6506 76505.09297 41950.14245 53239.04496 54996.08903 64307.63958 0.795710779 0.730732401 0.86941689 0.8937764 1.189673474 0.652335286 0.827880565 0.855203043 1 15.97270252 7.999785969 0.030486513 1.431744598 2.32E-06 0.09499526 0.139640426 3301.222072 7.717032453 114.6440478 282.2581122 99950729.62 -7.999785969 -1.431742274 ALS(ph)IESLSPTDSSNGVNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)IESLSPTDSSNGVNWR;ALS(0.999)IES(0.001)LSPTDSSNGVNWR;ALS(0.989)IES(0.011)LSPTDSSNGVNWR;ALS(0.844)IES(0.156)LSPTDSSNGVNWR 382.82 9.46E-127 959880000 669642 513591 591702 650403 629720 625122 698242 644527 633276 TRUE FALSE 637989.3498 565926.5068 618832.122 585023.2548 739542.9686 603473.8684 591712.3588 588088.799 731481.2078 0.872188298 0.77367197 0.845998661 0.799778926 1.011021146 0.825002559 0.808923527 0.803969798 1 19.48046128 -1.982078698 2.423510172 1.145673725 0.838990792 0.360635987 0.065723265 7312438.635 3308125.843 5964274.925 0.015576463 0.010421286 1.982078698 -0.306682933 ALS(ph)MPDLDKLCSEDYSAGPSAVLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSMPDLDKLCSEDYSAGPSAVLFK 25 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ALS(1)MPDLDKLCSEDYSAGPSAVLFK;ALS(1)MPDLDKLCSEDYSAGPSAVLFK 200.48 4.02E-25 155540000 335600 232390 261360 314210 208750 316510 350740 324340 207486 TRUE FALSE 319736.8531 256070.8052 273343.6145 282625.0138 245155.9339 305549.1793 297228.1712 295939.0702 239661.8692 1.334116496 1.068467028 1.140538607 1.179265666 1.022924234 1.274917785 1.240198002 1.234819169 1 17.87064087 ALS(ph)PEGALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSPEGALRR 10 1 I3L100;I3L2W2;Q96JN8-2;Q96JN8;K7EPS7;I3L2Z9 I3L100 NEURL4 Neuralized-like protein 4 1 ALS(1)PEGALRR 64.121 0.045413 91460000 44816 37375 41297 48452 53410 40580 52287 43159 53655 TRUE FALSE 42697.6365 41183.55499 43190.5083 43581.51291 62724.68709 39174.70442 44309.65783 39379.76916 61975.54337 0.688943318 0.664513012 0.696896 0.703205015 1.012087731 0.63209941 0.714953923 0.635408211 1 15.91941139 -2.106879247 2.455866075 1.520420219 0.715651894 0.400952884 0.108079191 16593144.21 4379153.518 48278494.54 0.026668901 0.007818452 2.106879247 -0.804768325 ALS(ph)PGLEESGLGLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;ALS(1)PGLEESGLGLLAR 336.23 9.96E-72 862094000 237458 227474 194973 241013 230690 214584 247065 218063 231545 TRUE FALSE 226233.8309 250653.8592 203912.7049 216785.9153 270922.263 207152.9023 209370.6966 198968.2477 267451.816 0.845886314 0.937192586 0.762427819 0.810560641 1.012975971 0.774542889 0.782835203 0.743940537 1 18.02891947 ALS(ph)PVIPLIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR 196.24 6.42E-08 2016741900 1750248 1462903 1545509 1757527 1718376 1536349 1950524 1715032 1805291 TRUE FALSE 1667517.246 1611974.479 1616372.116 1580857.047 2018060.23 1483144.849 1652935.74 1564854.706 2085246.308 0.799673995 0.773037925 0.775146854 0.75811526 0.967780268 0.711256432 0.792681293 0.750441183 1 20.99178637 -1.122644982 4.950485592 1.00000951 0.79034699 0.486376721 0.067488544 6.37E-06 1.13E-06 0.058764744 0.013850355 0.075397165 1.122644982 -0.209662519 ALS(ph)SDS(ph)ILSPAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 ALS(0.986)S(0.015)DS(0.509)ILS(0.49)PAPDAR 139.66 7.42E-06 16722000 66232 58226 68528 75476 64167 64676 85981 61831 69699 TRUE FALSE 63101.34462 64159.2956 71670.07658 67889.00908 75357.70448 62436.2539 72863.0193 56416.74985 80507.56495 0.783793978 0.796934992 0.890227852 0.843262483 0.936032589 0.775532758 0.905045623 0.700763337 1 16.29683673 -2.457233575 2.327794465 2.949586208 0.831905831 0.372805977 0.06963096 2900804.27 779971.5136 29024567.01 0.016008 0.003489526 2.457233575 -2.117680376 ALS(ph)SDSILSPAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.983)S(0.017)DSILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.993)S(0.007)DSILSPAPDAR;ALS(0.994)S(0.006)DSILSPAPDAR;ALS(0.876)S(0.124)DSILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.99)S(0.009)DSILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR 422.24 3.90E-153 3185195000 1345608 1214282 1152768 1437752 1366712 1223390 1433123 1183276 1306068 TRUE FALSE 1282003.777 1338018.716 1205623.553 1293226.437 1605066.14 1181023.698 1214473.765 1079662.08 1508606.355 0.849793435 0.886923691 0.799163777 0.857232527 1.063939665 0.782857432 0.805030259 0.715668522 1 20.52478498 -0.847732817 4.815220841 1.000000427 0.84859399 0.222394197 0.090829883 4.02E-07 9.61E-08 0.084603173 0.019941102 0.141993081 0.847732817 -0.151406437 ALS(ph)TDCTPSGDLSPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSTDCTPSGDLSPLSR 17 0 J3KNM6;F8VVT9;Q99490-2;Q99490 J3KNM6 AGAP2 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2" 1 ALS(0.961)T(0.039)DCTPSGDLSPLSR 107.82 0.00071902 35051000 38973 36562 33267 41114 48820 39252 47746 44766 46074 TRUE FALSE 37130.82353 40287.70937 34792.32486 36981.14261 57334.19254 37892.6934 40461.47078 40846.05172 53218.92061 0.697699673 0.757018536 0.653758559 0.694887123 1.077327234 0.712015444 0.760283567 0.767509962 1 15.69965163 ALS(ph)YAS(ph)LDKEDLLSPINQNTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 2 ALS(0.995)Y(0.006)AS(0.999)LDKEDLLSPINQNTLQR 175.39 8.96E-13 77507000 296680 215180 224700 280930 188020 282090 299390 252640 192640 TRUE FALSE 282656.5244 237107.0866 235002.7173 252690.3827 220810.6285 272321.1526 253712.5568 230517.5023 222513.6273 1.270288601 1.065584564 1.056127304 1.135617561 0.992346541 1.223840337 1.14021132 1.035970269 1 17.76353417 4.591487828 2.844183092 1.094251812 1.27706145 0.396925435 0.071350513 0.322082862 4.355581206 0.016731649 0.115441622 39038.02411 -4.591487828 0.182809638 ALSAIADLLTNEHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 296.04 4.57E-44 604992000 1403754 1277212 1377756 1525364 1619959 1291587 1633578 1489945 1588858 FALSE TRUE 1337401.33 1407361.355 1440927.475 1372031.513 1902479.337 1246859.018 1384345.673 1359477.517 1835249.984 0.728729787 0.766849948 0.78513962 0.747599251 1.036632259 0.679394649 0.754309051 0.740758768 1 20.80754516 -1.918352421 2.319954405 1.144516364 0.776402362 0.343309909 0.095544384 10256328.73 4867435.202 8051402.624 0.021908258 0.012068341 1.918352421 -0.368114002 ALSAS(ph)HTDLAH ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ALSASHTDLAH 11 0 Q07866-6;Q07866-4;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ALSAS(0.999)HTDLAH;ALS(0.006)AS(0.994)HTDLAH;ALSAS(0.901)HT(0.099)DLAH;ALSAS(0.979)HT(0.021)DLAH;ALS(0.001)AS(0.957)HT(0.042)DLAH;ALSAS(0.999)HT(0.001)DLAH 179.19 4.64E-06 3044010000 4145590 3549350 3755690 4581760 5057870 4070670 4839890 4019310 693621 TRUE FALSE 3949636.176 3911032.8 3927892.101 4121192.78 5939960.927 3929701.677 4101475.89 3667357.909 801184.2022 4.929747948 4.881565051 4.902608028 5.143876738 7.413976599 4.904866654 5.119267053 4.577421645 1 19.61177445 0.561126837 1.481596732 1.000626793 5.304172102 0.762618106 0.754371936 0.934521342 2.592851361 0.713395876 0.207140713 3.640213344 -0.561126837 4.303545309 ALSCHPDKNPDNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSCHPDKNPDNPR 14 1 H0YLQ7;Q9NVM6;S4R343;H0YK99 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 0 ; 160.48 2.85E-06 154330000 132417 94997 107108 134268 144626 115319 173203 141038 165690 FALSE TRUE 126157.9108 104677.3023 112019.0077 120771.1255 169848.7286 111325.4741 146777.7013 128687.965 191384.359 0.659186109 0.546948052 0.585309104 0.631039685 0.887474449 0.581685331 0.766926315 0.672405863 1 17.5461134 -5 0.137082497 2.192915119 0.5288157 0.578937258 0.093604541 92.52280229 0.783885003 30.00140877 0.563290153 1.00E-05 5 -1.664099419 ALSDHHIYLEGTLLKPNMVTPGHACTQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ALSDHHIYLEGTLLKPNMVTPGHACTQK 28 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;; 294.31 1.90E-71 9260240000 8430250 5311090 7147660 8696380 8667020 7753080 12139260 9616510 2123310 FALSE TRUE 8031768.79 5852296.109 7475387.281 7822203.36 10178545.54 7484588.896 10287192.93 8774437.404 2452582.07 3.27482162 2.386177482 3.047966211 3.189374763 4.150134532 3.051718018 4.194433719 3.577632533 1 21.22586998 3.216582409 3.098416944 3.456135286 2.826571454 0 0.923877759 0.586888501 11.6087738 0.243378936 0.316270281 1646.57838 -3.216582409 -0.629563832 ALSFLVNDCSLIHNNVCMAAVFVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSFLVNDCSLIHNNVCMAAVFVDR 25 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 ; 236.77 1.89E-38 51946000 28586 29100.4 29305.6 35068 30719.7 29345.2 30594 30392.7 29881.6 FALSE TRUE 27234.79643 32065.76384 30649.29075 31542.89802 36077.20595 28328.96837 25926.3234 27731.35407 34515.48591 0.789060206 0.929025421 0.887986651 0.91387669 1.045246938 0.820761105 0.751150468 0.803446723 1 15.07495617 -0.40059796 7.388348856 1.000011277 0.865082983 0.195428681 0.084312005 0 0 0.085910592 0.020249321 0.397559412 0.40059796 -0.134928293 ALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCR 39 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 307.38 2.70E-94 74585000 183900 103220 154680 147840 207220 119840 211330 168270 234040 FALSE TRUE 175207.4115 113738.2354 161772.231 132978.8423 243359.1024 115689.9108 179087.7272 153535.3867 270333.7279 0.648115249 0.420732686 0.598416751 0.49190622 0.900217314 0.42795219 0.662469047 0.567947581 1 18.04438199 -5 0.263676817 3.758769527 0.550002533 0.464741626 0.137863898 165.3008726 1.617017065 247.4371775 0.15872404 1.00E-05 5 -3.208766995 ALSS(ph)AGPIPIRPPIVPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSSAGPIPIRPPIVPVK 18 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 ALS(0.329)S(0.671)AGPIPIRPPIVPVK;ALS(0.364)S(0.636)AGPIPIRPPIVPVK 195.18 2.10E-15 590660000 850860 707250 689530 867190 667730 789200 882870 791150 658840 TRUE FALSE 810641.534 779319.5791 721145.6325 780018.4136 784181.9006 761869.8061 748171.9665 721872.7119 761009.5423 1.065218619 1.024060193 0.94761707 1.024978493 1.030449498 1.001130424 0.983130861 0.948572484 1 19.53755502 4.116664554 3.053100782 0.992844392 1.056493182 0.420623222 0.027779727 0.225589619 4.093411933 0.007077831 0.018165573 13081.7111 -4.116664554 0.06364879 ALSS(ph)DSILSPAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.109)S(0.891)DSILSPAPDAR;ALS(0.022)S(0.978)DSILSPAPDAR;ALS(0.317)S(0.683)DSILSPAPDAR 392.31 1.48E-114 3735210000 620300 580070 509840 661440 612960 585680 646380 534560 550600 TRUE FALSE 590979.6483 639179.7925 533216.6683 594950.7945 719860.0299 565397.7547 547762.8594 487751.0925 635984.2359 0.929236316 1.005024585 0.838411769 0.935480411 1.131883448 0.889012216 0.861283706 0.766923243 1 19.27863148 2.01976783 24.99842108 0.864278955 0.966185159 0.185329143 0.091594378 343.7004701 434642.1667 0.032260203 0.023822849 104.6568912 -2.01976783 0.101906203 ALSSDSILS(ph)PAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR 388.32 2.13E-114 870500000 1177230 1153510 1213500 1327830 1374410 1066820 1290660 1202940 1286730 TRUE FALSE 1121584.671 1271053.98 1269140.175 1194354.006 1614106.669 1029875.756 1093746.112 1097604.196 1486269.517 0.754630744 0.855197504 0.853909847 0.803591806 1.086012093 0.692926649 0.735900252 0.73849607 1 20.50326432 -0.302150701 7.450136435 1.000000883 0.812763979 0.220326893 0.109243083 0 0 0.1023827 0.024131834 0.498711404 0.302150701 -0.187236904 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.107)S(0.893)PPLS(1)PALPK;ALSSGGSIT(0.011)S(0.989)PPLS(1)PALPK;ALSSGGSIT(0.004)S(0.996)PPLS(1)PALPK;ALSSGGSIT(0.027)S(0.973)PPLS(1)PALPK 237.16 4.79E-24 378289000 810000 638570 752950 876340 668140 639850 792310 632870 616650 TRUE FALSE 771712.9053 703641.009 787473.5023 788248.6383 784663.4045 617691.8341 671428.5577 577452.5477 712276.9326 1.083445034 0.98787561 1.105572097 1.106660348 1.101626865 0.86720741 0.942650993 0.810713532 1 19.44207874 2.23919056 24.99999963 0.903710486 1.068104065 0.67474268 0.059118652 9.932204469 394192.4165 0.020256548 0.016012036 173.4564924 -2.23919056 0.164393579 ALSSGGSITS(ph)PPLSPALPK ddPTM_SK-BR-3_Trastuzumab_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 ALSSGGSIT(0.479)S(0.521)PPLSPALPK;ALSSGGSIT(0.01)S(0.99)PPLSPALPK;ALSSGGSIT(0.023)S(0.977)PPLSPALPK;ALSSGGSIT(0.052)S(0.948)PPLSPALPK;ALSSGGSIT(0.004)S(0.996)PPLSPALPK 326.98 3.86E-75 1177444000 2911430 2363560 2586030 2879720 2311910 2610780 2967450 2672070 2358280 TRUE FALSE 2773812.474 2604409.451 2704602.033 2590245.074 2715106.372 2520368.034 2514711.002 2438089.385 2723990.018 1.018290249 0.956100953 0.992882505 0.950901089 0.996738738 0.925248631 0.923171886 0.895043436 1 21.37728999 2.230653589 24.99776638 0.92863898 0.981518526 0.330260901 0.032589835 169.5719294 536090.5456 0.010823925 0.008135632 170.0801338 -2.230653589 0.052879546 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.005)S(0.005)LHGDDQDS(0.99)EDEVLTIPEVK 261.86 5.52E-44 1726581000 2551700 2245660 2436710 3031860 2209070 2805980 3292910 3095820 2546420 TRUE FALSE 2431086.198 2474495.307 2548435.564 2727091.673 2594331.109 2708808.209 2790516.101 2824733.589 2941305.808 0.826532961 0.841291409 0.866429991 0.927170397 0.88203379 0.920954292 0.948733754 0.960367188 1 21.48802536 3.006377701 0.273739936 1.010831455 0.767325886 0.910542741 0.016348605 0.829219825 0.114367308 0.024060994 0.067067756 1014.793557 -3.006377701 -0.243505569 ALSSQHQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ALSSQHQAR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 163.88 6.27E-05 653971000 711386 381061 249943 355794 1019585 357774 867628 534339 959405 FALSE TRUE 677760.1936 419891.5491 261403.1338 320028.9112 1197400.301 345384.1967 735255.4135 487549.4445 1108184.627 0.611595015 0.378900355 0.2358841 0.288786636 1.080506146 0.311666656 0.663477362 0.439953264 1 20.07976683 ALSTGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 140.98 0.0060195 3425060000 3701000 2702300 2936730 3494800 2672500 3409300 3977000 3672300 3144800 FALSE TRUE 3526061.065 2977667.442 3071381.975 3143496.064 3138583.154 3291235.086 3370235.607 3350733.944 3632479.523 0.970703632 0.81973413 0.845533184 0.865385763 0.864033268 0.906057437 0.92780581 0.922437119 1 21.79252323 1.150781942 0.84041559 0.995903932 0.873556269 0.486269179 0.040093191 0.511073439 0.809396199 0.038291072 0.014101455 14.15083094 -1.150781942 -0.122347663 ALSVGNIDDALQCYSEAIKLDPHNHVLYSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALSVGNIDDALQCYSEAIKLDPHNHVLYSNR 31 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 198.28 7.89E-26 416340000 233063 83671 279030 164460 299400 236317 420360 242650 37273 FALSE TRUE 222046.5739 92197.17003 291823.8015 147928.1683 351615.2652 228133.283 356226.3616 221402.2796 43053.10648 5.157504116 2.141475437 6.77822869 3.43594645 8.16701265 5.298880887 8.274115174 5.142539012 1 15.39382972 2.76337787 24.85604351 6.1822922 4.225395938 0.024920751 2.342463893 1309.666169 1311710.871 0.639061166 0.677558429 579.9330642 -2.76337787 -1.956896263 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 ALS(0.002)YAS(0.998)LDKEDLLSPINQNTLQR 237.97 2.19E-37 138270000 97489 80448 81978 97096 80813 95997 113920 101540 86843 TRUE FALSE 92880.88817 88645.74266 85736.77239 87335.72561 94906.76161 92672.59982 96539.41172 92648.6193 100310.1689 0.925936913 0.883716413 0.854716659 0.87065675 0.946133006 0.92386047 0.962409024 0.923621407 1 16.61410834 2.727634923 23.92119294 0.947771396 0.88682333 0.590928038 0.027751773 307.9503669 674238.4601 0.008739037 0.008321963 534.1151818 -2.727634923 -0.060948066 ALT(ph)TPTHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALTTPTHYK 9 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4;H0YCR0 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 ALT(0.566)T(0.427)PT(0.007)HYK;ALT(0.494)T(0.494)PT(0.011)HYK;ALT(0.492)T(0.492)PT(0.016)HYK 83.397 0.059595 481200000 1538000 1289500 1315550 1542820 1233580 1503340 1627950 1506980 1116460 TRUE FALSE 1465301.788 1420901.516 1375869.269 1387732.802 1448715.961 1451278.959 1379576.328 1375020.842 1289594.915 1.136249664 1.101820037 1.066900352 1.076099779 1.123388395 1.125375839 1.069774944 1.066242451 1 20.29848653 -5 0.15654746 0.627695896 1.126799369 0.658617124 0.023231764 86.27075606 0.784969527 9.898912101 0.108964898 1.00E-05 5 0.499103472 ALTAHLYSLLQTQHALGDAFADLSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALTAHLYSLLQTQHALGDAFADLSQK 26 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 130.16 4.26E-05 142290000 303030 252830 280320 315560 231240 281270 304460 314330 198130 FALSE TRUE 288706.3724 278593.6644 293172.9493 283839.3093 271568.1828 271529.5494 258009.0352 286805.5988 228854.9885 1.261525363 1.217337084 1.281042424 1.240258345 1.186638686 1.186469874 1.127390916 1.253219782 1 17.80407421 -4.999999999 0.139488959 0.236112507 1.297040828 0.752759637 0.040769124 64.59261372 0.552861945 13.63902217 0.239642124 1.00E-05 4.999999999 1.060928321 ALTDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALTDSFR 7 0 C9J0K6;P30626-3;P30626-2;P30626;B4DHQ6 C9J0K6 SRI Sorcin 0 ;; 143.37 0.005645 240530000 951320 771370 694840 828710 978760 741780 1040730 887100 1040290 FALSE TRUE 906352.9889 849973.48 726699.1013 745406.4964 1149455.434 716091.9726 881947.5242 809420.8212 1201612.86 0.754280367 0.707360505 0.604769744 0.620338315 0.956593818 0.595942334 0.733969778 0.673611983 1 20.19654073 -1.089320902 4.335807497 1.000032894 0.707827295 0.442916657 0.103650283 36537874820 7674650380 12527985.16 0.022000731 0.081410252 1.089320902 -0.292205599 ALTGGIAHLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALTGGIAHLFK 11 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 99.522 0.004712 1025990000 3899400 2486500 1711490 1725550 3487700 1677090 3701300 2558100 3151500 FALSE TRUE 3715083.09 2739877.177 1789963.509 1552094.436 4095953.776 1619011.953 3136598.706 2334099.203 3640218.524 1.020565954 0.752668324 0.491718697 0.426373973 1.125194476 0.444756803 0.861651213 0.641197551 1 21.79559363 -1.139922103 4.994762307 1.000013413 0.734890784 0.119882147 0.235136593 3.28E-05 5.64E-06 0.212309641 0.050039331 0.072456591 1.139922103 -0.265122629 ALTHIDHSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALTHIDHSLSR 11 0 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 254.34 1.13E-20 1330130000 710573 614657 513470 602467 900788 566999 829209 641495 54057.2 FALSE TRUE 676985.6225 677291.2471 537013.1074 541905.8725 1057885.142 547363.6825 702697.9376 585322.297 62440.11449 10.84215857 10.84705325 8.600450396 8.67880972 16.94239594 8.766218431 11.25395018 9.374138754 1 15.93018556 0.662436075 2.25501565 0.999815625 10.83385244 0.622096051 2.39228616 1.270912038 7.685078219 2.100719853 0.568947719 4.596593247 -0.662436075 9.83403681 ALTHNGT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALTHNGTPR 9 0 Q9HB90 Q9HB90 RRAGC Ras-related GTP-binding protein C 1 ALTHNGT(1)PR 84.289 0.057371 129730000 235930 197560 197560 219940 254030 233450 292010 241820 275640 TRUE FALSE 224778.0565 217691.5886 206618.3214 197831.2133 298332.7516 225365.568 247458.5114 220644.9588 318384.8434 0.70599484 0.683737286 0.648957781 0.621358766 0.937019327 0.707840127 0.777230815 0.693013387 1 18.28041213 2.769582749 24.97219477 0.797230509 0.671794738 0.381423301 0.096773404 792.7772295 638168.4518 0.026695313 0.028311593 588.2781916 -2.769582749 -0.125435771 ALTLDQWLEQHKGDFNLL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALTLDQWLEQHKGDFNLL 18 1 I3L1Y8;Q9HBL8;I3L3Z0 I3L1Y8 NMRAL1 NmrA-like family domain-containing protein 1 0 ; 162.41 3.25E-11 153268000 247817 229675 267801 265380 242091 249338 308120 282065 234870 FALSE TRUE 236103.1815 253079.1436 280079.9407 238703.4982 284311.5938 240703.3625 261110.635 257365.8933 271292.4401 0.870290309 0.932864711 1.032391248 0.87987523 1.047989372 0.887246849 0.962469264 0.948665924 1 18.04948932 4.261172623 2.719540232 0.96025745 0.878044724 0.225072054 0.054530251 0.353013373 5.132453139 0.012164407 0.040394946 18246.20806 -4.261172623 -0.082212726 ALTNLPHTDFTLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALTNLPHTDFTLCK 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 161.84 4.53E-06 239930000 380270 341840 295050 363770 309960 329300 398450 373420 275900 FALSE TRUE 362295.3907 376673.8846 308578.3343 327203.1485 364016.9259 317896.2584 337659.1345 340721.3652 318685.1629 1.136844237 1.181962415 0.968285852 1.026728529 1.14224623 0.997524502 1.059538296 1.069147249 1 18.28177233 3.755075003 24.94397152 1.042481507 1.159403336 0.515159111 0.048935092 565.2823494 853821.8445 0.011784236 0.021164206 5689.511811 -3.755075003 0.116921829 ALTSFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ALTSFER 7 0 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ;; 147.69 0.0049651 265376000 262231 199665 195298 223534 276624 188007 230225 215001 302566 FALSE TRUE 249835.8603 220011.0905 204252.6065 201063.9376 324867.138 181496.2704 195099.9479 196174.3726 349486.39 0.714865779 0.62952692 0.584436511 0.57531264 0.929555906 0.519322857 0.558247627 0.561321923 1 18.41487675 -1.918421737 2.751279907 1.218613814 0.633333089 0.4897752 0.117373593 12293502.84 9289055.681 17392083.67 0.027595746 0.012066415 1.918421737 -0.585280725 ALTVPELTQQMFDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALTVPELTQQMFDAK 15 0 Q13509;A0A0B4J269;Q13509-2;P68371;P04350 Q13509;P68371;P04350 TUBB3;TUBB4B;TUBB4A Tubulin beta-3 chain;Tubulin beta-4B chain;Tubulin beta-4A chain 0 ; 161.48 3.84E-06 36959000 236760 196032 208453 244650 183206 228830 261380 269110 231960 FALSE TRUE 225568.824 216007.8837 218010.7762 220057.3172 215157.0684 220905.5597 221501.6804 245545.3018 267931.1721 0.841890931 0.806206616 0.813682016 0.821320324 0.803031117 0.824486222 0.826711124 0.916449175 1 18.03150291 1.041417739 2.274449935 0.999675876 0.817918228 0.969095009 0.010874638 0.042294457 0.461424698 0.009982202 0.00275233 11.00063458 -1.041417739 -0.181757648 ALTVPELTQQVFDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALTVPELTQQVFDAK 15 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 ; 183.06 1.21E-06 113062000 195951 174472 192475 215581 153051 227031 242206 228682 188694 FALSE TRUE 186688.7846 192250.8952 201300.1691 193910.3883 179743.0459 219168.8595 205253.0263 208657.3918 217955.7018 0.856544624 0.882064078 0.923582946 0.889677979 0.824676962 1.005566075 0.941719003 0.957338533 1 17.73367542 2.232266884 24.99992426 0.969353673 0.877371916 0.720709574 0.031052001 85.21864108 338501.9122 0.011098592 0.00840044 170.7131139 -2.232266884 -0.091981757 ALVAT(ph)PGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ALVATPGKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK 122.7 0.00033898 11966700000 30328500 30390000 30388600 34659500 16924650 36795000 37073300 36319000 19907870 TRUE FALSE 28894931.91 33486775.55 31781947.37 31175461.21 19876303.6 35520779.92 31417087.19 33138715.82 22995080.8 1.25657014 1.456258225 1.382119404 1.355744799 0.864371983 1.544712116 1.366252524 1.441121956 1 24.45482193 2.969795722 24.99531588 1.280109649 1.369039114 0.062270296 0.204147763 2549.177014 2109552.149 0.05964614 0.063349426 932.8154312 -2.969795722 0.088929465 ALVDHENVISCPHLGASTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVDHENVISCPHLGASTK 19 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 172.84 4.38E-12 245630000 158140 149450 144910 171110 150100 138370 183370 185610 92052 FALSE TRUE 150665.0356 164679.1249 151554.2668 153909.6977 176277.3925 133578.2122 155393.5387 169357.0044 106326.954 1.416997571 1.548799422 1.425360749 1.447513466 1.657880583 1.256296801 1.46146892 1.592794658 1 16.69814784 -1.605570861 3.03736177 0.97016266 1.471405617 0.651663027 0.109300685 23126292.36 25142650.31 5510774.168 0.024106532 0.024798713 1.605570861 0.501242958 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEETREPGS(0.974)PPS(0.026)VQR;ALVEFESNPEETREPGS(0.998)PPS(0.002)VQR;ALVEFESNPEETREPGS(0.996)PPS(0.004)VQR;ALVEFESNPEETREPGS(0.999)PPS(0.001)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(0.997)PPS(0.003)VQR;ALVEFESNPEETREPGS(0.999)PPS(0.001)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEET(0.008)REPGS(0.836)PPS(0.157)VQR 220.38 1.17E-32 10131540000 2189062 2123138 2078895 2306778 2283187 2062550 2386939 2179248 2403242 TRUE FALSE 2085589.378 2339488.176 2174214.392 2074896.293 2681374.09 1991123.376 2022767.616 1988421.492 2775924.495 0.751313438 0.842778029 0.783239744 0.747461358 0.965939129 0.717282974 0.728682506 0.716309646 1 21.4045369 -0.401147729 8.11917758 0.999998697 0.7828959 0.453714143 0.075293314 0 0 0.069890985 0.016473463 0.397056465 0.401147729 -0.217102797 ALVFQPVAELKDQTDFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVFQPVAELKDQTDFEHR 19 1 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 56.936 0.054673 127000000 182530 150770 185630 223350 162570 188390 206160 219560 165010 FALSE TRUE 173902.1686 166133.6344 194141.3191 200898.4337 190922.1565 181866.0071 174706.5056 200334.1624 190598.908 0.912398557 0.871640012 1.018585684 1.054037695 1.001695962 0.954181789 0.916618607 1.051077178 1 17.54018033 3.741079231 24.98787104 0.991043986 0.89201928 0.517901719 0.042495754 184.8735258 1834169.817 0.01205345 0.020500947 5509.081932 -3.741079231 -0.099024705 ALVHERDEAAYGELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALVHERDEAAYGELR 15 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;; 197.47 5.05E-09 1282970000 1365180 1024040 1287910 1299090 1550780 1265000 1637210 1354830 1415420 FALSE TRUE 1300650.647 1128390.84 1346961.947 1168503.005 1821235.541 1221192.733 1387423.545 1236193.903 1634916.105 0.795545804 0.690182718 0.823872212 0.714717411 1.113962689 0.746945198 0.848620636 0.756120696 1 20.64078518 ALVLDCHYPEDEVGQEDEAES(ph)DIFSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 1 ALVLDCHYPEDEVGQEDEAES(0.997)DIFS(0.003)IR 221.72 1.61E-34 62482000 75703 53620 66795 63137 81493 56454 72480 62102 73432 TRUE FALSE 72124.66922 59083.93896 69857.61682 56790.34881 95705.3534 54498.98382 61421.84481 56664.01966 84819.45952 0.850331629 0.696584714 0.823603654 0.669543866 1.128341939 0.642529251 0.724148033 0.668054477 1 16.37210767 -0.292088102 7.89553804 1.000011198 0.772096764 0.197537601 0.142132592 0 0 0.124587861 0.02936564 0.510401449 0.292088102 -0.227914434 ALVLDCHYPEDEVGQEDEAESDIFS(ph)IR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 1 ALVLDCHYPEDEVGQEDEAES(0.056)DIFS(0.944)IR 125.02 4.91E-05 55689000 25319 18687 21972 15524 24262 19916 24498 24464 23210 TRUE FALSE 24122.22105 20591.22655 22979.43793 13963.49803 28493.28512 19226.30393 20760.38016 22321.80247 26809.28826 0.899771035 0.768063156 0.857144647 0.520845533 1.062813934 0.717150852 0.774372671 0.832614512 1 14.7104453 -1.319424617 7.744507677 1.000001064 0.801514518 0.167124908 0.137332374 2.19E-06 1.93E-07 0.115641992 0.027256933 0.047926463 1.319424617 -0.198486547 ALVLDCHYPEDEVGQEDEAESDIFSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;;;;;;;;;;;; 352.86 2.89E-110 3095247000 1266054 947770 1100131 1038309 1294749 900543.6 1176343.8 1077632.5 1196706 FALSE TRUE 1206210.136 1044348.841 1150573.095 933936.2067 1520552.816 869357.5493 996870.9483 983269.2854 1382285.055 0.872620399 0.755523499 0.83237035 0.675646607 1.100028399 0.628927837 0.721176103 0.711336119 1 20.39862373 ALVNQLHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALVNQLHER 9 0 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;A0A0G2JM88 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 160.59 6.52E-05 124090000 145490 109930 83272 81778 156610 89887 127620 106710 154040 FALSE TRUE 138612.976 121131.992 87090.10357 73557.52007 183922.7344 86774.19065 108149.2251 97365.90669 177927.7365 0.779040855 0.680793194 0.489468957 0.41341233 1.033693442 0.487693444 0.607826679 0.547221634 1 17.4409319 -2.058284705 2.434393954 1.504365274 0.636266513 0.300746743 0.177119103 7600893.488 2823877.388 21303354.47 0.041321163 0.008744104 2.058284705 -0.86809876 ALVTGYFMQVAHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALVTGYFMQVAHLER 15 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 170.49 1.14E-06 112216600 216023.7 229938.2 166623.9 201936.8 203783.5 176449.1 197419.2 209607.1 147727.1 FALSE TRUE 205812.6878 253369.164 174263.7706 181637.7292 239323.2779 170338.6234 167299.2752 191252.7911 170635.8642 1.206151408 1.484852936 1.021261102 1.06447569 1.402537966 0.998258041 0.980446145 1.120824113 1 17.38056138 2.947980696 0.535338759 1.002505959 1.345549301 0.2382533 0.15325675 1.185185078 0.714575222 0.12522306 0.187815784 887.1165799 -2.947980696 0.343043342 ALVVPEPEPDSDS(ph)NQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.005)DS(0.995)NQER;ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDS(0.001)DS(0.999)NQER;ALVVPEPEPDS(0.001)DS(0.999)NQER;ALVVPEPEPDS(0.057)DS(0.943)NQER;ALVVPEPEPDS(0.002)DS(0.998)NQER;ALVVPEPEPDS(0.001)DS(0.999)NQER;ALVVPEPEPDS(0.004)DS(0.996)NQER 376.05 5.18E-105 3043590000 2851080 2439111 2588669 2838880 3025500 2516592 2906370 2748208 3180270 TRUE FALSE 2716315.099 2687659.184 2707362.034 2553510.389 3553146.242 2429441.788 2462949.877 2507560.338 3673450.029 0.739445229 0.731644411 0.737007993 0.695125936 0.967250463 0.661351528 0.670473222 0.682617245 1 21.80870422 -1.749458943 2.823569717 1.052320193 0.733226847 0.477496367 0.086884095 23524697.68 18429939.88 8555126.708 0.021064648 0.017804962 1.749458943 -0.319093346 ALWEDEGVR ddPTM_SK-BR-3_Trastuzumab_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 ; 190.26 8.67E-05 482550000 678360 570030 592250 678660 736420 538230 695760 641620 748620 FALSE TRUE 646295.2672 628116.7051 619405.2483 610439.8074 864851.4148 519590.9601 589609.0335 585436.3514 864712.1662 0.747410864 0.72638819 0.716313789 0.705945668 1.000161035 0.600883138 0.681855832 0.677030316 1 19.72186046 -2.241852265 2.389593992 2.02271036 0.729731598 0.39957812 0.103211253 8360742.401 1411101.589 46317376.14 0.024504902 0.005729909 2.241852265 -1.292978761 ALWFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ALWFER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 132.8 0.034289 664739000 792682 638788 556749 629122 991170 546958 867606 702585 929030 FALSE TRUE 755213.4928 703881.2234 582276.4923 565881.4613 1164029.734 528016.7073 735236.77 641062.9328 1073099.228 0.703768555 0.655933026 0.542611976 0.52733377 1.084736345 0.492048353 0.685152641 0.5973939 1 20.03335206 -2.184169572 2.260935587 1.880667711 0.662441889 0.292832613 0.165488256 7481815.497 1498466.675 33750425.28 0.037166509 0.006543806 2.184169572 -1.218225821 ALWFQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALWFQGR 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 166.22 0.0026321 1023610000 1188960 950710 620310 680640 1360690 687880 1208510 907310 1148890 FALSE TRUE 1132760.217 1047588.43 648751.8271 612220.7741 1597993.905 664058.5431 1024129.604 827861.1264 1327053.993 0.85359015 0.789409048 0.488866188 0.461338255 1.204166457 0.500400546 0.771731677 0.623833793 1 20.33979564 ALYDTFSAFGNILSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALYDTFSAFGNILSCK 16 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E5RGH3;B1ANR1;E5RJB9;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEQ8 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 167.98 1.43E-08 18895000 63230 53540 53660 55504 54017 51476 62483 61755 63043 FALSE TRUE 60241.24321 58995.78687 56120.36408 49924.63247 63437.5477 49693.37321 52950.07077 56347.40482 72819.38646 0.827269305 0.810165943 0.770678892 0.685595346 0.871162897 0.682419554 0.727142501 0.773796753 1 16.15203496 -1.012430963 3.376062756 1.000105402 0.769407019 0.599881668 0.059406308 9803181.683 16339251.63 12111.42318 0.015258484 0.097178242 1.012430963 -0.230698383 ALYDYEGQEHDELSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ALYDYEGQEHDELSFK 16 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;H0Y923 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;;; 303.9 3.62E-46 806591000 2017470 1789100 1806050 2171360 1667240 1942010 2266380 2183810 1551510 FALSE TRUE 1922108.191 1971411.324 1888859.179 1953090.767 1958006.128 1874757.707 1920602.106 1992584.019 1792110.247 1.072539033 1.100050249 1.053986038 1.089827354 1.092570132 1.046117397 1.071698635 1.111864643 1 20.77322796 -1.470455222 3.119483341 0.998239856 1.07905543 0.609533925 0.020071768 969816.4547 956161.5107 10220.18237 0.004397743 0.033848917 1.470455222 0.080815574 ALYETELADAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALYETELADAR 11 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 167.67 4.41E-05 118211000 226726 231130 197023 236999 212290 216337 246430 230577 219390 FALSE TRUE 216009.1113 254682.4098 206056.6994 213175.4103 249313.3088 208845.1954 208832.5775 210386.4555 253411.8807 0.852403252 1.005013692 0.813129593 0.841221057 0.983826441 0.824133402 0.82408361 0.830215438 1 17.95112464 ALYETELADARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ALYETELADARR 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 194.29 2.75E-06 529340000 408650 219780 363110 330790 483710 373310 467450 430910 581090 FALSE TRUE 389333.9244 242175.8319 379758.9527 297538.3607 568068.8709 360382.1811 396131.9172 393177.236 671202.4694 0.580054368 0.360808911 0.565788968 0.443291517 0.846345025 0.536920225 0.590182449 0.585780378 1 19.3563885 -5 0.167165515 2.742745405 0.438687861 0.577932111 0.119983932 89.19517709 0.835587776 51.42245476 0.424050471 1.00E-05 5 -2.304057544 ALYHTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALYHTEER 8 0 A0A0C4DGB9 A0A0C4DGB9 PPA2 0 144.38 0.00058641 212260000 160110 106090 129590 130620 139430 115920 132250 161940 131080 FALSE TRUE 152541.9176 116900.6916 135531.8297 117489.8294 163746.5479 111905.6613 112072.8336 147759.6751 151407.2169 1.007494363 0.77209458 0.895147751 0.775985662 1.08149764 0.739103879 0.740208002 0.975909062 1 17.20807445 ALYYLQIHPQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ALYYLQIHPQELR 13 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 164.68 3.66E-05 511430000 237800 175170 145480 155950 263550 164600 273860 225790 203260 FALSE TRUE 226559.6653 193020.0222 152150.4019 140273.6097 309513.0366 158899.8607 232077.6272 206018.6306 234780.5227 0.964984926 0.822129621 0.648053766 0.597466979 1.31830798 0.676801716 0.988487565 0.877494556 1 17.8409532 AMAATLGAGT(ph)PPRPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AMAATLGAGTPPRPQAR 17 1 P58107 P58107 EPPK1 Epiplakin 1 AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAAT(0.003)LGAGT(0.997)PPRPQAR 244.52 2.61E-20 14474400000 936479 655547 732943 839904 924012 786044 892757 887376 866788 TRUE FALSE 892213.4936 722347.9846 766549.1615 755475.2542 1085159.4 758823.0992 756550.523 809672.6532 1001205.056 0.89113962 0.721478562 0.765626539 0.75456596 1.083853296 0.757909775 0.755639935 0.808698127 1 19.93330605 AMASVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 AMASVAR 7 0 H7C2G2;Q93070 H7C2G2 ART4 NAD(P)(+)--arginine ADP-ribosyltransferase;Ecto-ADP-ribosyltransferase 4 0 ;;;;;;;;;; 148.28 0.007443 3104836000 4097614 3003903 2502442 2371014 5211310 2987093 5432954 3687446 5169499 FALSE TRUE 3903927.907 3310004.131 2617181.441 2132675.168 6120160.814 2883649.22 4604057.084 3364553.68 5971158.503 0.6537974 0.554331983 0.438303796 0.357162713 1.024953669 0.482929606 0.771049216 0.563467488 1 22.50957943 2.762989839 24.99337696 0.732178821 0.5233157 0.33234421 0.183292815 1064.035028 1088605.548 0.051400863 0.054495761 579.4151394 -2.762989839 -0.208863121 AMDDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMDDKR 6 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 72.021 0.09098 41195000 115100 103080 89848 125490 70391 102650 98299 115860 85079 FALSE TRUE 109659.4511 113583.9692 93967.61967 112875.5068 82667.16811 99095.20476 83301.68217 105714.6842 98272.6168 1.11586986 1.155804871 0.95619332 1.148595717 0.841202471 1.00837047 0.847659143 1.0757288 1 16.58450185 3.305258909 1.119310815 0.946861577 1.135800922 0.274098136 0.095657343 0.467500427 1.241856966 0.033237971 0.056263186 2019.569993 -3.305258909 0.188939345 AMDDKRFDEATQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AMDDKRFDEATQLR 14 2 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 164.93 2.27E-06 1047070000 646110 310420 655180 528030 703820 605930 1012400 746770 922550 FALSE TRUE 615569.6608 342052.1509 685220.6511 474951.4212 826565.9852 584946.4922 857939.786 681378.8599 1065614.342 0.577666456 0.320990566 0.643028743 0.445706671 0.775670852 0.548928884 0.805112837 0.639423507 1 20.02325397 1.291374154 0.286530668 1.055332332 0.401434921 0.583540936 0.12300452 1.040821135 0.316472922 0.263908502 0.201263318 19.56023887 -1.291374154 -0.653897411 AMDSDWFAENYMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AMDSDWFAENYMGR 14 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;;;; 357.56 7.37E-82 915799000 895742 643493 732482 718836 944417 562383 853240 734690 931694 FALSE TRUE 853402.0508 709065.6683 766067.0242 646577.2396 1109123.026 542907.5357 723062.5672 670356.6488 1076176.347 0.792994618 0.658874979 0.711841536 0.600809748 1.030614572 0.504478227 0.671881118 0.622905949 1 20.03748307 -1.260351172 5.648023663 1.00002007 0.697930622 0.315185468 0.139283166 3.15E-05 4.13E-06 0.120843173 0.028481118 0.054909669 1.260351172 -0.302089448 AMEVDERPTEQYSDIGGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AMEVDERPTEQYSDIGGLDK 20 1 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 193.27 7.28E-18 652654000 1581440 1334530 1395610 1691730 1137740 1513050 1669870 1698980 1319890 FALSE TRUE 1506688.465 1470520.124 1459600.099 1521674.086 1336161.496 1460652.699 1415100.662 1550208.304 1524571.8 0.988269929 0.964546323 0.95738364 0.998099326 0.876417559 0.958074063 0.928195486 1.016815544 1 20.53997267 1.226557843 24.99831175 1.008407811 0.954513832 0.320449343 0.033489301 310.0295075 645682.0065 0.030097156 0.007761293 16.84836814 -1.226557843 -0.053893978 AMGDS(ph)DDEYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMGDSDDEYDR 11 0 C9JUL9 C9JUL9 SRRT 1 AMGDS(1)DDEYDR 99.5 0.0024189 0 66266 53568 57497 75716 54050 58723 66543 68583 55240 TRUE FALSE 63133.73751 59026.6401 60133.29432 68104.88383 63476.30289 56689.40779 56390.6432 62577.50894 63806.33707 0.989458734 0.92509056 0.942434515 1.067368649 0.994827564 0.888460463 0.883778098 0.980741284 1 15.9614121 2.249671002 24.99304886 0.922329641 0.978251475 0.123301625 0.052205929 340.8592071 766769.5799 0.01827031 0.015153043 177.6932792 -2.249671002 0.055921834 AMGDS(ph)DDEYDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMGDSDDEYDRR 12 1 C9JUL9 C9JUL9 SRRT 1 AMGDS(1)DDEYDRR 82.529 0.0063111 53825000 48819 47086 39160 46084 46301 47597 53610 43915 40679 TRUE FALSE 46511.42262 51884.11693 40955.52473 41451.54877 54375.87974 45948.70396 45430.80988 40069.56979 46987.29156 0.98987239 1.104215953 0.871629825 0.882186383 1.157246522 0.977896415 0.966874412 0.852774622 1 15.51998299 1.591245718 3.362281919 0.923266063 1.005820411 0.08049874 0.093180569 0.431681847 11.36753613 0.058173647 0.024085785 39.01626733 -1.591245718 0.082554348 AMGIMNSFVNDIFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 359.14 1.98E-82 14596567000 1858269 1598555 1616495 1809114 2053717 1444254 2220913 1925668 2229972 FALSE TRUE 1770432.307 1761449.572 1690612.895 1627258.424 2411884.595 1394239.122 1882071.932 1757046.301 2575784.669 0.687337078 0.6838497 0.656348691 0.631752508 0.936368876 0.541287142 0.730679064 0.682140213 1 21.29658056 -2.088146612 2.082229936 1.468919086 0.692739186 0.483697254 0.09944109 3267651.803 892058.6241 7261326.077 0.023196311 0.008163068 2.088146612 -0.7761799 AMKDEEK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 107.47 0.0068139 1521790000 2898230 2755320 2118890 3140960 1301840 2744110 2769830 3244640 1461730 FALSE TRUE 2761236.412 3036090.241 2216043.202 2825224.733 1528880.484 2649080.783 2347241.562 2960522.121 1688407.623 1.635408638 1.798197425 1.312504855 1.67330726 0.905516217 1.568981771 1.390210237 1.75344039 1 20.68723182 3.738471154 24.9999998 1.393065532 1.716803041 0.21825418 0.269011593 10.63780279 2972959.983 0.063010599 0.104929251 5476.097267 -3.738471154 0.32373751 AMKEENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMKEENVK 8 1 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 88.496 0.013292 97052000 347220 287510 376090 456620 390430 420890 497570 497450 445620 FALSE TRUE 330807.5987 316807.5959 393334.0985 410719.6901 458520.8684 406314.4738 421656.558 453890.6409 514724.4737 0.642688692 0.615489669 0.764164361 0.797940862 0.890808368 0.789382465 0.819188866 0.881812822 1 18.97344085 5.95441266 0.147504974 1.045576092 1.38E-11 0.819757905 0.048094675 15.14465342 0.258273327 0.219055777 3.102350862 900352.6764 -5.95441266 -1.045576092 AMKENGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMKENGR 7 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 62.2 0.079245 26351000 66483 44951 59562 55583 62026 57578 83725 72159 85418 FALSE TRUE 63340.48035 49531.55801 62292.97661 49995.69124 72843.31476 55584.05942 70951.21353 65840.37542 98664.18719 0.641980461 0.50202165 0.631363602 0.506725821 0.738295392 0.563366111 0.719118209 0.667317872 1 16.59023889 -0.26326515 0.350893586 1.106044712 0.563385063 0.750224925 0.071481303 2.81062527 0.410254111 0.440224758 0.053866138 0.54542476 0.26326515 -0.542659648 AMKEYEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AMKEYEEEER 10 1 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 115.33 0.0011287 1102070000 3357930 2409780 3394360 3155770 2931020 3553830 4461160 3936970 3498510 FALSE TRUE 3199207.304 2655339.322 3549994.763 2838546.004 3442188.96 3430759.976 3780528.107 3592228.036 4041041.063 0.791678989 0.657092883 0.878485199 0.702429389 0.851807469 0.848979241 0.935533207 0.888936286 1 21.94629558 2.02990733 0.589999943 0.987577609 0.730863126 0.613910633 0.063344713 0.449010699 0.317029199 0.052923138 0.03490016 107.1290689 -2.02990733 -0.256714483 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;AMKPPGGESS(0.001)NLFGS(0.999)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGES(0.002)S(0.002)NLFGS(0.992)PEEAT(0.001)PS(0.001)S(0.001)RPNR 239.45 2.07E-45 1198310000 888783 955699 941889 1089094 789191 994612 1180632 1078375 1069154 TRUE FALSE 846771.989 1053085.815 985075.5423 979616.202 926825.6605 960168.337 1000504.905 983946.7682 1234952.942 0.685671462 0.852733557 0.797662412 0.793241725 0.750494719 0.777493866 0.810156299 0.79674839 1 20.23602464 -4.999999999 0.285147392 2.635263243 0.771133855 0.73097983 0.041822358 124.8665564 1.185652533 121.0972922 0.044744149 1.00E-05 4.999999999 -1.864129388 AMKPPGGESSNLFGSPEEATPSSRPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 0 ; 106.99 0.0010435 249550000 116755 99405 111200 116572 80591 105759 125890 124038 106248 FALSE TRUE 111236.2225 109534.4825 116298.63 104853.9611 94646.04488 102096.5393 106683.1684 113176.5752 122724.3972 0.906390458 0.892524103 0.94764067 0.854385627 0.771208065 0.83191722 0.869290628 0.922201109 1 16.90506255 0.955125211 2.970056546 0.999655668 0.869942072 0.461030127 0.046362781 0.283830517 6.097644973 0.047623403 0.012538685 9.018311064 -0.955125211 -0.129713595 AMLDQLMGT(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMLDQLMGTSR 11 0 Q9Y383;V9GZ75;F8WEU3 Q9Y383 LUC7L2;C7orf55-LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.635)S(0.365)R 114.56 0.013868 87426000 168620 135180 113080 225870 194050 207440 228560 198680 249570 TRUE FALSE 160649.6668 148954.9957 118264.8299 203165.1185 227892.2586 200256.3008 193688.9742 181282.5259 288272.041 0.557284939 0.516716762 0.41025425 0.704768724 0.790545825 0.694678194 0.671896496 0.628859203 1 18.13707139 3.153063297 7.223419001 0.728151468 0.508926863 0.546949242 0.107665855 0.174083618 12.43651943 0.028389428 0.034080279 1422.536102 -3.153063297 -0.219224605 AMLDQLMGT(ph)SRDGDTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AMLDQLMGTSRDGDTTR 17 1 Q9Y383 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.5)S(0.5)RDGDTTR;AMLDQLMGT(0.5)S(0.5)RDGDTTR 86.539 0.007703 103283000 77237 34905 70766 82782 143258 79093 141473 86891 217502 TRUE FALSE 73586.16008 38461.85918 74010.6911 74460.59608 168242.1498 76353.98958 119888.6955 79282.3634 251231.0993 0.292902273 0.153093543 0.294592076 0.296382877 0.669670874 0.303919339 0.477204836 0.315575435 1 17.93865554 -5 0.156773403 3.426196279 0.151881904 0.714812129 0.131381452 67.06071613 0.610598777 50.57333375 0.553278591 1.00E-05 5 -3.274314375 AMLDQLMGTS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AMLDQLMGTSR 11 0 Q9Y383;V9GZ75;F8WEU3 Q9Y383 LUC7L2;C7orf55-LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.266)S(0.734)R;AMLDQLMGT(0.192)S(0.808)R;AMLDQLMGT(0.148)S(0.852)R;AMLDQLMGT(0.142)S(0.858)R;AMLDQLMGT(0.131)S(0.869)R 155.08 3.33E-05 283238000 655101 537223 524394 908060 776114 809563 912593 761450 1019770 TRUE FALSE 624135.674 591966.6345 548437.9836 816780.0836 911468.0359 781527.6303 773360.1769 694773.4013 1177910.723 0.529866705 0.502556452 0.465602335 0.693414252 0.77380061 0.663486302 0.656552455 0.589835365 1 20.16779877 -5 0.102861062 2.250481984 0.345824866 0.70143894 0.08418931 101.829535 0.708151495 27.27845012 1.330172243 1.00E-05 5 -1.904657119 AMLPGS(ph)PLFTR ddPTM_SK-BR-3_Trastuzumab_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(1)PLFTR;AMLPGS(1)PLFTR 153.74 3.39E-05 482146000 919157 742555 857048 971124 967507 792322 1015426 924739 1053727 TRUE FALSE 875710.2702 818222.1987 896344.4985 873504.7705 1136239.914 764883.6905 860504.1141 843763.9508 1217133.601 0.71948574 0.672253397 0.736438874 0.717673696 0.933537545 0.628430346 0.706992324 0.693238565 1 20.21505611 -1.503904478 2.670024685 1.013180873 0.721601651 0.537479846 0.079785069 9302386.709 9424203.329 895955.4373 0.018770303 0.03133975 1.503904478 -0.291579222 AMS(ph)LNTLNVDAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(0.999)LNT(0.001)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.996)LNT(0.004)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.995)LNT(0.005)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.994)LNT(0.006)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.866)LNT(0.134)LNVDAPR;AMS(0.679)LNT(0.321)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.993)LNT(0.007)LNVDAPR;AMS(1)LNTLNVDAPR 315.88 9.85E-51 5529017000 7120793 6166480 6380855 7623921 7357800 6663178 7898218 6734423 7717628 TRUE FALSE 6784207.227 6794851.323 6673423.513 6857549.977 8640997.99 6432430.475 6693199.783 6144721.221 8914438.334 0.761035858 0.762229887 0.748608411 0.769263269 0.969326128 0.721574398 0.750826865 0.689299874 1 23.08771247 -2.28222754 2.292189184 2.013867001 0.771441167 0.483666554 0.07418932 5208856.515 814298.0239 27365787.84 0.018270994 0.005221226 2.28222754 -1.242425834 AMS(ph)TTSISSPQPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.81)T(0.09)T(0.09)S(0.01)ISSPQPGK;AMS(0.937)T(0.053)T(0.01)SISSPQPGK;AMS(0.993)T(0.007)TSISSPQPGK;AMS(0.989)T(0.011)TSISSPQPGK;AMS(0.833)T(0.154)T(0.014)SISSPQPGK;AMS(0.99)T(0.01)TSISSPQPGK;AMS(0.957)T(0.041)T(0.002)SISSPQPGK;AMS(0.99)T(0.01)TSISSPQPGK;AMS(0.982)T(0.018)TSISSPQPGK 286.74 8.01E-34 6290780000 4244142 2882991 3216155 5820880 4848460 5584770 6096270 3373849 3778009 TRUE FALSE 4043529.819 3176771.061 3363618.888 5235754.083 5694029.889 5391368.015 5166172.046 3078416.896 4363883.34 0.926589806 0.727968833 0.770785703 1.199792404 1.304807999 1.235451912 1.183847423 0.705430612 1 22.0571811 3.241303882 24.99383003 1.136617992 0.808079891 0.385333356 0.173435223 63.63269367 579750.3497 0.047357836 0.061361305 1743.026066 -3.241303882 -0.328538101 AMST(ph)TSISSPQPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.026)T(0.913)T(0.061)SISSPQPGK;AMS(0.001)T(0.404)T(0.404)S(0.191)ISSPQPGK;AMS(0.006)T(0.49)T(0.49)S(0.014)ISSPQPGK;AMS(0.096)T(0.9)T(0.004)SISSPQPGK;AMS(0.263)T(0.627)T(0.11)SISSPQPGK 317.91 5.81E-55 6485710000 3578870 2291670 2601160 4664840 3902720 4479000 4854940 2611550 3062100 TRUE FALSE 3409703.908 2525193.778 2720425.759 4195921.421 4583353.132 4323891.107 4114229.736 2382868.837 3536954.829 0.964022464 0.713945725 0.769143484 1.186309021 1.295847234 1.222489773 1.163212406 0.673706324 1 21.75407636 3.240761369 24.99921033 1.121013978 0.815086898 0.328812467 0.181401606 58.1150321 660143.718 0.049810314 0.064302368 1740.850068 -3.240761369 -0.305927079 AMSTTSISS(ph)PQPGK ddPTM_SK-BR-3_Trastuzumab_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(0.005)S(0.995)PQPGK;AMSTTSIS(0.039)S(0.961)PQPGK;AMSTTS(0.009)IS(0.067)S(0.924)PQPGK;AMSTTS(0.007)IS(0.068)S(0.925)PQPGK;AMSTTS(0.018)IS(0.099)S(0.883)PQPGK;AMSTT(0.001)S(0.004)IS(0.043)S(0.952)PQPGK;AMSTTS(0.014)IS(0.174)S(0.812)PQPGK;AMST(0.001)T(0.005)S(0.019)IS(0.051)S(0.924)PQPGK 312.66 9.44E-56 2494140000 5555740 5833170 5761170 6004560 4335290 5562620 6726230 6890790 6297360 TRUE FALSE 5293131.181 6427576.655 6025325.343 5400970.221 5091363.203 5369985.075 5700020.078 6287395.897 7273922.426 0.727685954 0.883646577 0.82834611 0.742511386 0.699947416 0.738251628 0.783623985 0.86437489 1 22.79430211 0.941176774 2.530344597 0.999462421 0.776799349 0.660711862 0.052835667 0.225273656 3.275737369 0.054174512 0.014564777 8.733267722 -0.941176774 -0.222663071 AMT(ph)PEQEETASLLSSVTQGMESAYVSPSGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AMTPEQEETASLLSSVTQGMESAYVSPSGYR 31 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AMT(0.798)PEQEET(0.168)AS(0.033)LLSSVTQGMESAYVSPSGYR 79.898 0.0065568 12198000 7151.2 6514.6 5460.8 7100.7 7849.8 7342.4 9761.8 8879.1 6085.5 TRUE FALSE 6813.176948 7178.445146 5711.183081 6386.924146 9218.802635 7088.130847 8272.458122 8101.598933 7029.20826 0.969266622 1.021230967 0.812493082 0.908626393 1.311499431 1.008382535 1.176869118 1.152562086 1 12.77914648 2.772850778 24.98677702 1.133482611 0.941642772 0.493262889 0.101253889 515.5633598 375683.1111 0.028773516 0.030517871 592.7216323 -2.772850778 -0.191839838 AMTGVEQWPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AMTGVEQWPYR 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 152.17 7.69E-05 699040000 530013 433100 382647 458077 481683 418678 524634 484064 464472 FALSE TRUE 504960.3359 477233.3824 400191.7434 412030.2297 565688.3627 404179.0759 444591.4477 441676.79 536499.9456 0.941212278 0.889531092 0.745930632 0.767996778 1.054405256 0.753362753 0.82868871 0.823255983 1 19.0332185 3.992808262 23.10535709 0.842162503 0.921831898 0.060836191 0.101937227 355.0389177 1140677.869 0.023908732 0.046134165 9835.767676 -3.992808262 0.079669395 AMTLS(ph)PQEEVAAGQMASSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AMTLSPQEEVAAGQMASSSR 20 0 Q9Y6A5;A0A494BZT8 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 AMTLS(1)PQEEVAAGQMASSSR;AMT(0.002)LS(0.998)PQEEVAAGQMASSSR 309.21 3.34E-66 197057000 168362 134824 172393 186958 178885 167558 189454 179527 197359 TRUE FALSE 160403.8619 148562.7189 180297.3896 168164.6266 210082.4874 161755.4244 160549.3127 163806.6641 227964.4257 0.703635497 0.651692554 0.790901427 0.73767925 0.921558207 0.709564327 0.704273538 0.718562397 1 17.79844918 -2.380019345 2.206261903 2.828674609 0.734753315 0.551065737 0.072839473 2551421.451 307336.7949 23264718.75 0.018426247 0.004168508 2.380019345 -2.093921294 ANAS(ph)PQKPLDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANASPQKPLDLK 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK 136.01 7.11E-05 630470000 2158910 2390750 2237550 2681200 1289090 2847350 2778360 3035010 1623340 TRUE FALSE 2056862.603 2634370.143 2340143.881 2411680.682 1513906.888 2748745.556 2354470.154 2769248.435 1875079.276 1.096947008 1.404938008 1.248023969 1.286175317 0.80738287 1.465935649 1.255664325 1.476870055 1 20.83852016 ANCDASLIVTEELHLITFETEVYHQGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANCDASLIVTEELHLITFETEVYHQGLK 28 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;;; 349.64 4.67E-111 415509000 647923 734577 589685 787672 465260 676769 733203 717083 308716 FALSE TRUE 617296.9638 809431.2314 616722.6405 708493.7141 546401.1967 653332.3198 621339.4162 654291.411 356590.1006 1.731110771 2.269920646 1.729500173 1.986857495 1.532294912 1.832166173 1.742447183 1.834855791 1 18.44390713 -2.103168307 0.243430372 3.43E-17 1.984002929 0.653485849 0.191268272 19.27716501 0.670383873 11.19040625 0.297051856 0.007885545 2.103168307 1.984002929 ANEHQGIGFLNDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANEHQGIGFLNDPR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 73.279 0.036278 194221000 557370 625900 499970 568320 513690 522250 539060 577240 485490 FALSE TRUE 531024.2247 689679.9216 522894.119 511191.3939 603277.3734 504164.3515 456816.4965 526693.8055 560777.3097 0.946943137 1.229864172 0.932445215 0.911576458 1.075787773 0.899045562 0.814613018 0.939220964 1 19.09706845 3.609777295 10.6412766 0.92609023 1.088306181 0.29220573 0.095125156 0.443632704 35.81774586 0.025307457 0.039214335 4071.714274 -3.609777295 0.162215951 ANESS(ph)PKPVGPPPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANESSPKPVGPPPER 15 1 Q9BQI0-3;Q9BQI0;Q9BQI0-2;A6PVM9 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 1 ANES(0.248)S(0.752)PKPVGPPPER;ANES(0.434)S(0.566)PKPVGPPPER 125.23 5.56E-05 674330000 280420 274469 277050 291000 186300 309140 342450 358910 243201 TRUE FALSE 267165.1023 302437.7031 289753.0165 261748.1271 218790.661 298434.4043 290202.963 327481.9377 280915.369 0.951051925 1.076615011 1.031460178 0.931768625 0.778849024 1.062364104 1.033061893 1.165767252 1 18.09977603 2.065591595 25 1.064407293 0.968567719 0.278281694 0.087361652 90.33448009 34429.58616 0.03358092 0.02480115 116.3031814 -2.065591595 -0.095839575 ANFDKESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANFDKESER 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 106.62 0.0026507 1560480000 3034300 2196480 2544690 2721700 2498280 2806800 3492900 3130900 2902300 FALSE TRUE 2890874.652 2420303.809 2661366.554 2448109.545 2933979.241 2709599.812 2959993.953 2856741.798 3352373.861 0.862336593 0.721967152 0.793875225 0.730261494 0.875194523 0.808263017 0.88295461 0.852154896 1 21.67675162 0.945357367 0.528745507 1.002145209 0.780214948 0.629391471 0.049004912 0.62079049 0.421382187 0.052361281 0.023705606 8.817741584 -0.945357367 -0.221930261 ANGMELDGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 196.88 5.22E-07 1768480000 1731420 1204320 1493710 1436160 1953360 1473540 2014300 1676410 2135310 FALSE TRUE 1649579.208 1327041.577 1562198.081 1291794.468 2294025.366 1422510.94 1706981.54 1529614.653 2466442.969 0.668808981 0.538038622 0.633380987 0.523747958 0.930094632 0.576745928 0.692082307 0.620170291 1 21.2340005 -4.999999999 0.234402712 2.967161898 0.60461458 0.487085664 0.113428803 132.4949489 1.323775891 123.9149402 0.170231162 1.00E-05 4.999999999 -2.362547317 ANGQENGHVKS(ph)NGDLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANGQENGHVKSNGDLSPK 18 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 ANGQENGHVKS(1)NGDLSPK;ANGQENGHVKS(1)NGDLSPK 234.39 5.52E-24 495490000 928550 720120 1007540 942530 724930 1103830 1292660 1113890 751190 TRUE FALSE 884659.2817 793501.0467 1053736.706 847785.0937 851357.5625 1065604.09 1095440.976 1016351.886 867680.7087 1.019567766 0.914508112 1.214429104 0.97707035 0.981187612 1.228106237 1.262493178 1.171343187 1 19.72680473 2.238379705 24.99999999 1.196865296 1.013383995 0.301095113 0.103965521 4.473788826 618075.007 0.035422288 0.027829769 173.1329405 -2.238379705 -0.1834813 ANHEEVLAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANHEEVLAAGK 11 0 P00491 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 142.08 3.78E-05 1906840000 3385130 3156140 2808740 3317080 2522590 3125480 3484370 3314150 2336280 FALSE TRUE 3225121.614 3477754.254 2937523.507 2983640.816 2962528.897 3017243.844 2952765.362 3023945.457 2698578.37 1.195118752 1.288735689 1.08854482 1.105634303 1.097810955 1.118086425 1.094192925 1.120569812 1 21.36376816 8 0.134922808 0.980161572 1.912472938 0.554894516 0.050114316 50.86104602 0.460801854 0.235803504 9.087171131 99999999.97 -8 0.932311365 ANKLDHVVTIIK ddPTM_SK-BR-3_Trastuzumab_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 ; 137.16 5.84E-05 707690000 1304330 1337060 1300480 1487200 1042830 1390420 1478500 1616230 1113630 FALSE TRUE 1242676.906 1473307.934 1360108.294 1337703.831 1224699.222 1342269.407 1252927.67 1474704.333 1286326.053 0.96606681 1.145361187 1.057358895 1.039941489 0.952090816 1.043490804 0.974035835 1.146446758 1 20.29482495 2.997380261 15.7904032 1.017027886 1.060744251 0.043426052 0.066616584 2.349403935 14162.87113 0.018372601 0.021306722 993.9859849 -2.997380261 0.043716365 ANKTPLRPLDPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANKTPLRPLDPTR 13 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 92.265 0.0034602 479020000 1736300 1055600 1531300 1452700 1590400 1400700 2143000 1753000 2030300 FALSE TRUE 1654228.54 1163166.84 1601511.62 1306671.836 1867765.256 1352193.408 1816045.991 1599498.027 2345148.555 0.705383263 0.495988554 0.682904124 0.557180838 0.796437928 0.576591792 0.774384202 0.682045504 1 21.16124788 -0.444574318 0.302376483 1.135508364 0.593602215 0.605479017 0.089474737 5.137799136 0.535669708 0.793568021 0.091340961 0.359273911 0.444574318 -0.541906149 ANLQQAIVT(ph)PLKPVDNTYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANLQQAIVTPLKPVDNTYYK 20 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ANLQQAIVT(1)PLKPVDNTYYK;ANLQQAIVT(1)PLKPVDNTYYK 192.47 9.45E-22 0 657450 651090 704100 759600 474790 724350 817880 844680 642010 TRUE FALSE 626373.6414 717436.8112 736383.6814 683243.5649 557593.2257 699265.5779 693097.3846 770715.3413 741569.6319 0.84465924 0.967457108 0.993006792 0.921347822 0.751909466 0.942953362 0.934635609 1.039302728 1 19.50022264 1.418524172 2.728206189 1.019243808 0.905297945 0.320807924 0.068077439 0.337584733 4.472066694 0.055669704 0.017996684 26.21344931 -1.418524172 -0.113945862 ANNIDYTVHSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANNIDYTVHSVR 12 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 172.76 3.49E-05 353140000 332060 292390 309010 344420 336660 308150 341550 330810 351350 FALSE TRUE 316364.1819 322184.8734 323178.4142 309798.2472 395373.3974 297478.6882 289440.2745 301842.5227 405835.5636 0.779537848 0.793880336 0.796328472 0.763359043 0.974220677 0.733003007 0.713195936 0.743755722 1 18.63053577 -2.22992311 2.436420047 1.782120023 0.784693399 0.466031074 0.071555555 3034006.063 1092452.475 12972410.04 0.016966587 0.005889479 2.22992311 -0.997426625 ANNPEQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANNPEQNR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 139.88 0.001532 192688000 227517 197186 190439 223644 291543 195784 256120 218034 302109 FALSE TRUE 216762.7223 217279.4776 199170.8165 201162.8802 342388.0069 189003.951 217044.19 198941.7871 348958.5208 0.621170453 0.622651303 0.570757854 0.576466452 0.981171075 0.541622972 0.621977046 0.570101531 1 18.41269603 -1.361676041 3.087887324 1.003865311 0.636772869 0.452439853 0.125062346 20199481.76 26837762.87 710607.4025 0.028343545 0.043483446 1.361676041 -0.367092441 ANPELCGSLHLNGS(ph)PSSCIASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANPELCGSLHLNGSPSSCIASR 22 0 Q9NXR5 Q9NXR5 ANKRD10 Ankyrin repeat domain-containing protein 10 1 ANPELCGSLHLNGS(0.939)PS(0.051)S(0.01)CIASR;ANPELCGSLHLNGS(0.733)PS(0.222)S(0.045)CIASR 126.93 1.22E-05 209240000 228530 148213 231560 192189 202441 226370 325970 326460 159541 TRUE FALSE 217727.8398 163316.0732 242177.255 172869.7966 237746.6463 218530.7501 276237.2897 297873.4317 184281.8035 1.181493971 0.886230057 1.314168032 0.938073067 1.290125459 1.185850942 1.498993848 1.616401762 1 17.4915541 2.256638344 1.68096274 1.407306132 1.074495981 0.2250857 0.205436572 0.399604117 2.254868409 0.097348618 0.061274766 180.566984 -2.256638344 -0.332810151 ANPFGGASHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 169.89 1.64E-05 2461280000 6098430 4664100 4399290 5140990 5104330 5152670 6465700 5566000 5306570 FALSE TRUE 5810169.3 5139377.093 4601001.798 4624207.918 5994523.536 4974231.746 5479238.714 5078611.533 6129485.773 0.947904851 0.838467905 0.750634224 0.754420206 0.977981475 0.811525131 0.893914908 0.828554257 1 22.54733461 2.744423817 24.99475524 0.888222348 0.835340518 0.180521488 0.079183235 1224.186034 5218698.164 0.024462004 0.025318926 555.1672226 -2.744423817 -0.052881831 ANRDQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANRDQDSSDDERALEDWVSSETSALPRPR 29 3 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 ANRDQDS(0.5)S(0.5)DDERALEDWVSSETSALPRPR 100.1 0.0042534 20160000 7342.2 2266.6 6362.8 5135.6 6668.8 5906 7655.2 6422.8 8885.4 TRUE FALSE 6995.148757 2497.569117 6654.540674 4619.359731 7831.836609 5701.473739 6487.258643 5860.385583 10263.30245 0.681568997 0.243349461 0.64838201 0.450085122 0.76309128 0.555520386 0.632082965 0.571003886 1 13.32520741 -5 0.170494414 2.781741972 0.445585016 0.484025567 0.140999605 102.9158091 0.971742415 61.73128994 0.465150094 1.00E-05 5 -2.336156956 ANRDQDSS(ph)DDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANRDQDSSDDERALEDWVSSETSALPRPR 29 3 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 ANRDQDS(0.144)S(0.856)DDERALEDWVSSETSALPRPR 119.36 0.00038159 28227000 4779.9 3367.7 5559.5 4611.4 7568.1 6291 7250.7 6552.4 9459.5 TRUE FALSE 4553.9636 3710.872459 5814.408574 4147.853311 8887.974244 6073.141093 6144.472547 5978.63712 10926.43095 0.416784183 0.339623476 0.532141612 0.379616485 0.81343801 0.555821121 0.56234946 0.547172004 1 13.41553461 -5 0.097889196 2.592356175 0.149103845 0.661801178 0.116170463 107.8687052 0.721790406 35.20736555 1.975869804 1.00E-05 5 -2.44325233 ANS(ph)FQSPTPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSFQSPTPSK 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 ANS(0.994)FQS(0.006)PTPSK 187.63 3.67E-06 80257000 165800 149250 136190 178850 102140 203390 189420 190500 113840 TRUE FALSE 157962.9626 164458.7447 142434.4462 160871.6582 119953.1837 196346.5533 160520.5001 173818.8101 131493.7258 1.201296576 1.250696516 1.083203365 1.22341699 0.912235036 1.493200927 1.220746458 1.321879117 1 17.00463444 2.229322514 24.99999544 1.27899605 1.157902189 0.125832005 0.152633528 386.0242989 1044643.957 0.051045621 0.038219883 169.559651 -2.229322514 -0.121093861 ANS(ph)FVGTAQYVSPELLTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.785)FVGT(0.215)AQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.69)FVGT(0.308)AQY(0.002)VSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.987)FVGT(0.013)AQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK 432.38 1.91E-169 2006603000 2952320 2592426 2756611 3151347 1743656 3132149 3339850 3343830 2008752 TRUE FALSE 2812769.685 2856597.157 2883004.341 2834567.612 2047749.054 3023681.895 2830294.542 3051026.518 2320259.001 1.212265391 1.231154434 1.24253557 1.221660001 0.882551928 1.303165678 1.219818365 1.314950838 1 21.14585443 2.960094805 24.99955677 1.16349839 1.227503896 0.081072828 0.12985071 1718.114311 1076353.796 0.038076452 0.040392672 912.2099499 -2.960094805 0.064005506 ANS(ph)GGVDLDSSGEFASIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSGGVDLDSSGEFASIEK 19 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 ANS(1)GGVDLDSSGEFASIEK 266.01 1.60E-33 0 287190 249710 260630 292230 189380 300290 317020 295490 206860 TRUE FALSE 273615.0979 275155.7329 272580.1433 262854.4852 222407.812 289890.882 268652.7765 269615.3291 238938.7923 1.145126311 1.151574134 1.140794848 1.100091294 0.930815 1.213243271 1.124358142 1.12838659 1 17.86628157 -1.975087841 2.378161579 0.894581615 1.120850145 0.203041642 0.072327164 8365957.717 3426301.361 4850354.168 0.01678516 0.010590395 1.975087841 0.22626853 ANS(ph)GQAHKDEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSGQAHKDEALK 13 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 ANS(1)GQAHKDEALK 199.01 7.32E-08 120870000 278900 278300 241480 317820 119030 313930 285100 316940 115570 TRUE FALSE 265716.9497 306659.0864 252552.0969 285872.1298 139788.7943 303058.5254 241602.7588 289187.0534 133492.0054 1.990508338 2.297209377 1.891889302 2.141492511 1.047169783 2.270237267 1.809866877 2.166324887 1 17.02639382 ANS(ph)LDNER ddPTM_SK-BR-3_Trastuzumab_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 81.431 0.023997 197340000 205540 185020 173990 210400 174310 185580 185140 195580 165070 TRUE FALSE 195824.5315 203873.7484 181967.6136 189250.1923 204709.6088 179153.3181 156893.4927 178453.9784 190668.2125 1.027043412 1.069259242 0.954367858 0.992562891 1.07364309 0.939607686 0.822861297 0.935939851 1 17.54070482 2.05419592 6.187263811 0.895312467 1.024725592 0.416181761 0.056048214 0.140940052 11.55642227 0.02025617 0.014747252 113.2911329 -2.05419592 0.129413124 ANS(ph)LGDLYAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANSLGDLYAQK 11 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 ANS(1)LGDLYAQK;ANS(1)LGDLYAQK 166.79 2.10E-05 154589000 499510 468810 465160 526830 363630 509260 566520 551150 374890 TRUE FALSE 475899.1522 516582.272 486488.0461 473872.0475 427046.9569 491624.1985 480086.9691 502888.3842 433026.0265 1.099008196 1.192958946 1.123461446 1.094326942 0.986192355 1.135322517 1.108679247 1.161335239 1 18.72409421 1.107976766 0.011548837 7.12E-07 2.174181242 0.192683414 0.057814091 1618.405251 14.04011808 1336.141474 1304.420569 12.82261981 -1.107976766 2.174180531 ANS(ph)LVTLGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANSLVTLGSHR 11 0 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ANS(1)LVTLGSHR;ANS(1)LVTLGSHR 118.16 0.00048784 222184000 472370 339120 347820 426820 422050 381770 509660 424580 375230 TRUE FALSE 450042.0062 373676.7135 363767.891 383915.2427 495655.3864 368549.2092 431902.0065 387401.5244 433418.752 1.038353796 0.862160928 0.839298921 0.885783647 1.143594697 0.850330558 0.996500508 0.893827327 1 18.72540205 ANS(ph)PEKPPEAGAAHKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSPEKPPEAGAAHKPR 17 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 ANS(1)PEKPPEAGAAHKPR 85.248 0.0026524 469930000 407890 372640 375220 425780 173780 428770 428060 432670 169670 TRUE FALSE 388609.8481 410612.4397 392424.2081 382979.7855 204087.177 413921.5874 362751.5851 394783.1211 195981.557 1.98288989 2.095158574 2.002352742 1.954162378 1.041359095 2.11204357 1.850947562 2.014389145 1 17.58035837 2.977924856 24.88448449 1.692358706 2.028061012 0.213034331 0.36747697 1261.837463 1422423.694 0.103753743 0.110931648 950.4403292 -2.977924856 0.335702306 ANS(ph)RDGEAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANSRDGEAGR 10 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ANS(1)RDGEAGR;ANS(1)RDGEAGR;ANS(1)RDGEAGR;ANS(1)RDGEAGR 143.25 2.08E-05 202755000 265304 192812 243920 287329 256627 210016 302287 243740 286792 TRUE FALSE 252763.6057 212459.762 255103.9733 258446.143 301382.6675 202743.0933 256167.5663 222396.8335 331266.2386 0.763022537 0.64135652 0.770087451 0.780176525 0.909789868 0.612024618 0.77329814 0.671353756 1 18.33763165 -1.532748606 2.871709277 1.011965441 0.736799416 0.484007339 0.084259128 20992295.71 22658962.36 1954765.677 0.01895197 0.029325903 1.532748606 -0.275166025 ANS(ph)TSDSVFTETPSPVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANSTSDSVFTETPSPVLK 18 0 C9JEZ4;Q9UKI2 C9JEZ4 CDC42EP3 Cdc42 effector protein 3 1 ANS(0.912)T(0.081)S(0.007)DSVFTETPSPVLK;ANS(0.456)T(0.133)S(0.411)DSVFTETPSPVLK 277.07 4.20E-39 131406000 322250 233140 256590 358250 230500 331030 362980 310360 287040 TRUE FALSE 307017.8811 256897.2311 268354.9053 322238.0294 270699.127 319566.3481 307600.7344 283183.2331 331552.6972 0.926000252 0.774830768 0.809388395 0.971905921 0.816458829 0.963847831 0.927758203 0.854112289 1 18.33887867 3.250865234 24.99947379 0.917448881 0.836225069 0.272220584 0.065658189 293.8918661 597100.8677 0.01699346 0.022847144 1781.825763 -3.250865234 -0.081223813 ANSALT(ph)PPKPESGLTLQESNTPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANSALTPPKPESGLTLQESNTPGLR 25 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 ANS(0.003)ALT(0.997)PPKPESGLTLQESNTPGLR;ANS(0.01)ALT(0.989)PPKPESGLTLQESNTPGLR;ANS(0.003)ALT(0.981)PPKPES(0.014)GLT(0.002)LQESNTPGLR;ANSALT(1)PPKPESGLTLQESNTPGLR 161.26 3.39E-11 1284700000 2085170 1866850 1924850 2131190 1438740 2154830 2409090 2296830 1570430 TRUE FALSE 1986608.147 2057084.137 2013106.276 1916958.732 1689655.8 2080207.697 2041539.075 2095707.389 1813964.264 1.095174908 1.134026827 1.109782765 1.056778665 0.931471382 1.146774354 1.125457163 1.155319005 1 20.7907146 -0.284880049 7.145485235 1 1.096906188 0.174283475 0.064325291 4199027.165 587647.4998 0.06199843 0.015036828 0.518943349 0.284880049 0.096906188 ANSFQS(ph)PTPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSFQSPTPSK 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 ANS(0.166)FQS(0.834)PTPSK 199.41 5.28E-08 56008000 189780 164030 182010 199870 113300 205530 209760 206190 123670 TRUE FALSE 180809.4755 180744.8435 190355.3385 179778.6879 133059.4841 198412.4446 177757.2595 188134.9105 142848.112 1.265746344 1.265293891 1.33257161 1.258530375 0.931475273 1.388974918 1.244379481 1.317027631 1 17.12412244 -1.42710399 2.955367146 0.994907339 1.251565592 0.295942533 0.121415768 15538635.78 18779000.18 665364.5559 0.027971777 0.037402102 1.42710399 0.256658253 ANSFTVSSVAAPSWLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANSFTVSSVAAPSWLHR 17 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 143.67 5.40E-07 251260000 217670 175260 190970 219380 217160 194480 240510 198920 210160 FALSE TRUE 207381.1705 193119.1933 199726.1634 197327.5056 255032.6352 187745.1088 203815.7822 181501.5103 242750.5395 0.854297465 0.795545887 0.822763005 0.812881842 1.050595545 0.773407586 0.839610007 0.747687361 1 17.88911498 -2.244502266 2.366576545 1.61790149 0.836971541 0.280675253 0.081957095 10129252.28 1298605.968 33714317.65 0.019980278 0.005695053 2.244502266 -0.780929948 ANSWQLVET(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 135.72 0.0013724 151316000 394500 372780 461460 443550 261320 434620 472570 466560 309910 TRUE FALSE 375852.7668 410766.7058 482618.3974 398963.5113 306894.1253 419569.0004 400470.7672 425705.533 357969.26 1.049958219 1.147491563 1.348211848 1.114518915 0.857319775 1.17208109 1.118729489 1.189223714 1 18.44947618 -2.493657512 1.847144439 5.87E-05 1.122499762 0.093169701 0.122084485 1272075.671 100932.9703 5305277.426 0.029054086 0.003208799 2.493657512 1.122441018 ANSWQLVET(ph)PEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 155.03 2.49E-05 1548630000 1122500 1384180 1064560 1364970 807140 1339540 1423670 1540760 1084860 TRUE FALSE 1069441.65 1525229.516 1113371.129 1227760.622 947904.9605 1293151.394 1206462.994 1405842.886 1253094.548 0.853440509 1.217170339 0.888497305 0.97978291 0.756451268 1.03196634 0.962786883 1.121896898 1 20.25706384 -0.962862971 7.266902989 1.000000001 0.9826116 0.001245783 0.130786626 1.77E-09 0 0.11854969 0.027942429 0.108927373 0.962862971 -0.017388401 ANT(ph)PELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 113.42 0.0016714 1635610000 2403580 2343790 2356510 2621920 980780 2918470 2592140 3040640 1098810 TRUE FALSE 2289967.537 2582624.866 2464558.314 2358359.62 1151827.721 2817402.652 2196661.435 2774385.442 1269207.843 1.804249438 2.034832104 1.941808293 1.858135083 0.907517022 2.219811883 1.730734211 2.185918924 1 20.27549691 2.983614125 24.96576464 1.677707616 1.928475599 0.099745911 0.426141651 1927.886758 2937361.7 0.118757969 0.129109053 962.9730322 -2.983614125 0.250767983 ANTIPIIGS(ph)PSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANTIPIIGSPSSK 13 0 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 ANTIPIIGS(0.999)PS(0.001)SK;ANTIPIIGS(0.874)PS(0.107)S(0.019)K 162.61 4.21E-05 409780000 800040 673220 672420 816790 548910 770560 885460 878320 732470 TRUE FALSE 762223.6947 741821.8834 703251.1221 734684.7174 644639.7302 743875.314 750366.8144 801409.6445 846057.7067 0.900912182 0.876798211 0.831209404 0.86836242 0.761933524 0.879225268 0.886897913 0.947228112 1 19.69039654 1.171705985 1.685764574 0.99862216 0.856114472 0.648431917 0.03737152 0.227616045 1.211729579 0.035615512 0.010492164 14.84930013 -1.171705985 -0.142507688 ANVS(ph)SPHREFPPATAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ANVSSPHREFPPATAR 16 1 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.5)S(0.5)PHREFPPATAR;ANVS(0.5)S(0.5)PHREFPPATAR;ANVS(0.5)S(0.5)PHREFPPATAR 78.012 0.01352 653890000 165961 143656 156765 168485 175273 168490 214001 197751 199630 TRUE FALSE 158116.3524 158294.7097 163952.8303 151548.5677 205840.5557 162655.1491 181351.2171 180434.8741 230587.6008 0.685710558 0.686484048 0.711021884 0.65722774 0.892678336 0.705394169 0.786474279 0.782500332 1 17.81495541 -5 0.126282076 1.918942898 0.609852469 0.699602826 0.058568176 74.2831847 0.597968738 17.18324737 0.435030617 1.00E-05 5 -1.309090429 ANVSS(ph)PHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.011)S(0.989)PHR;ANVS(0.047)S(0.953)PHR;ANVS(0.054)S(0.946)PHR;ANVS(0.013)S(0.987)PHR;ANVS(0.019)S(0.981)PHR;ANVS(0.06)S(0.94)PHR 93.096 0.0072859 970980000 1691690 1986570 1330820 2045020 1591330 1642180 1730420 1652140 1384320 TRUE FALSE 1611727.166 2189003.742 1391839.413 1839450.704 1868857.448 1585310.895 1466412.648 1507469.863 1598993.275 1.007963693 1.36898871 0.870447321 1.150380513 1.168771299 0.991443128 0.917084937 0.942761853 1 20.60873244 2.117055496 4.761770324 0.946478446 1.128840156 0.255209722 0.127006994 0.253588208 9.487455173 0.047411301 0.034353103 130.9349228 -2.117055496 0.18236171 ANVSS(ph)PHREFPPATAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ANVSSPHREFPPATAR 16 1 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.182)S(0.818)PHREFPPATAR 75.608 0.017576 263420000 85008 87251 83577 82038 91955 95543 104130 106580 97378 TRUE FALSE 80989.84031 96141.9761 87409.08812 73791.38438 107991.9229 92234.32195 88243.05602 97247.29018 112478.8829 0.720044849 0.854755787 0.777115543 0.656046562 0.960108423 0.820014562 0.784529982 0.864582646 1 16.77929465 -4.999999998 0.158666126 1.750972965 0.745536559 0.431582173 0.077390678 129.2187828 1.18321367 30.38669979 0.315715473 1.00E-05 4.999999998 -1.005436406 ANVSSPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ;;; 90.657 0.013041 62708000 151905 101672 77880 93266 169613 86239 161068 122168 170354 FALSE TRUE 144724.7517 112032.4924 81450.87503 83890.72449 199193.4535 83252.52181 136494.1184 111470.3223 196771.6283 0.735496031 0.569352876 0.413936073 0.426335469 1.012307797 0.423092102 0.693667678 0.566495908 1 17.58616269 -4.99999455 0.452305427 9.999985462 0.604051206 0.318842659 0.181172418 1621.873717 9.294111968 14629.69797 0.087861248 1.00E-05 4.99999455 -9.395934256 ANWEAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ANWEAQQR 8 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ; 117.89 0.0046364 202117000 242360 228800 206165 242770 294740 209310 258410 236190 287400 FALSE TRUE 230904.1231 252114.9801 215617.8692 218366.2984 346142.5627 202061.5422 218984.8085 215507.9515 331968.5242 0.695560291 0.759454472 0.649512991 0.657792177 1.042696935 0.60867681 0.659655336 0.649181883 1 18.34068693 -2.285943604 2.239110906 2.243872972 0.715256452 0.3462795 0.122927071 7378349.631 1113683.569 46426027.6 0.02872697 0.005176741 2.285943604 -1.52861652 APAASEGNHTDGAEEAAGSCAQAPS(ph)HSPPNKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGS(0.014)CAQAPS(0.493)HS(0.493)PPNKPK 50.057 0.037578 103350000 19823 15076 17798 24806 12829 19729 18813 22329 12687 TRUE FALSE 18886.00608 16612.26154 18614.0559 22312.45375 15066.37354 19045.77978 15942.73133 20373.75439 14654.43516 1.288757012 1.13359958 1.270199479 1.52257344 1.02811015 1.299659766 1.08791169 1.390279063 1 13.83904974 APAPLGTVADSLRAS(ph)DGQLQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 APAPLGT(0.001)VADS(0.083)LRAS(0.916)DGQLQAK;APAPLGTVADSLRAS(1)DGQLQAK;APAPLGTVADSLRAS(1)DGQLQAK 248.02 2.45E-31 697498000 632769 543549 588020 677449 533408 614235 735599 739354 646106 TRUE FALSE 602859.2634 598937.2611 614981.2986 609350.5395 626434.1863 592963.8879 623369.8623 674612.2442 746300.8186 0.807796599 0.802541343 0.824039427 0.816494534 0.839385635 0.794537368 0.835279618 0.90394145 1 19.50939774 1.006621912 1.901028024 0.999495331 0.813314931 0.959539124 0.012466568 0.058301064 0.441405417 0.011383226 0.003219854 10.15364352 -1.006621912 -0.1861804 APAPQPPSLPDRS(ph)PRPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APAPQPPSLPDRSPRPQR 18 2 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 APAPQPPS(0.03)LPDRS(0.97)PRPQR;APAPQPPS(0.167)LPDRS(0.833)PRPQR;APAPQPPS(0.011)LPDRS(0.989)PRPQR;APAPQPPS(0.004)LPDRS(0.996)PRPQR;APAPQPPS(0.006)LPDRS(0.994)PRPQR;APAPQPPS(0.001)LPDRS(0.999)PRPQR 116.35 8.51E-05 1700884000 883468 842106 871437 926582 984469 824636 999021 944785 1107320 TRUE FALSE 841708.2185 927917.5588 911393.2484 833440.217 1156160.082 796078.6485 846601.9982 862054.6168 1279037.53 0.658079375 0.725481103 0.712561772 0.651615138 0.903929755 0.622404448 0.661905517 0.67398696 1 20.28662717 -0.973471808 4.340722027 1.00000998 0.699415872 0.592016123 0.077928864 6511387.49 4500210.558 572.823391 0.016896697 0.106298758 0.973471808 -0.300594108 APDFVFYAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APDFVFYAPR 10 0 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 87.639 0.029636 50076000 51764 34281 32840 32976 49716 29859 50028 39436 41268 FALSE TRUE 49317.21831 37774.27287 34345.74648 29661.18983 58386.45466 28824.97534 42395.30977 35982.77478 47667.63067 1.034606034 0.792451237 0.720525564 0.622250139 1.224865886 0.604707533 0.889394106 0.754868121 1 15.5407223 4.567543908 2.845905957 0.817954743 1.039382797 0.110968316 0.183214051 0.61198892 8.547462557 0.040560991 0.259376669 36943.99934 -4.567543908 0.221428054 APDWVDAEECHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APDWVDAEECHR 12 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ;; 182.08 1.73E-05 790740000 678620 623820 636548 721720 700840 627310 750860 684000 713440 FALSE TRUE 646542.9775 687387.9672 665734.3554 649171.3344 823066.2741 605586.0974 636302.5165 624105.3339 824076.6315 0.784566572 0.834131124 0.807854913 0.787756029 0.998773952 0.734866242 0.772139983 0.757338954 1 19.65241898 -2.400797058 2.242522725 2.511627729 0.809190112 0.405422843 0.072431504 3095604.588 362133.0845 23780110.26 0.016645503 0.003973772 2.400797058 -1.702437617 APELPNTSS(ph)SPSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNT(0.001)S(0.001)S(0.499)S(0.499)PSLK;APELPNT(0.012)S(0.029)S(0.633)S(0.325)PS(0.001)LK 148.72 8.06E-06 150109000 449730 373760 409110 457380 375770 430060 538730 483750 477280 TRUE FALSE 428472.1542 411846.5689 427868.0982 411403.2934 441304.169 415166.9144 456536.844 441390.2855 551294.1448 0.777211509 0.747054132 0.776115804 0.746250069 0.800487676 0.753076952 0.828118434 0.800643884 1 19.07246275 -0.299478404 0.433762297 1.043819981 0.758964523 0.920361246 0.0209672 1.433198067 0.284520314 0.116029663 0.01078884 0.501789531 0.299478404 -0.284855458 APELPNTSSS(ph)PSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNTSS(0.016)S(0.983)PS(0.001)LK;APELPNTSS(0.087)S(0.91)PS(0.003)LK 208.79 7.92E-09 251570000 684850 637360 636500 731230 519480 683880 789910 776260 673050 TRUE FALSE 652478.4977 702307.7086 665684.1546 657725.3712 610077.1475 660197.0641 669394.7218 708286.5592 777423.1565 0.83928359 0.903378942 0.856270036 0.846032647 0.784742701 0.849211988 0.861042942 0.911069542 1 19.56834056 0.934731344 1.99256291 0.999677837 0.850647934 0.748121208 0.028557115 0.21457015 1.800260804 0.028776431 0.008029617 8.604613041 -0.934731344 -0.149029903 APEPQLS(ph)PGSDASEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APEPQLSPGSDASEVR 16 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 APEPQLS(0.985)PGS(0.014)DASEVR 126.88 0.00043971 0 33400 30438 36963 34491 33644 33771 32932 32601 36747 TRUE FALSE 31821.24819 33539.66681 38657.79011 31023.89915 39511.50295 32601.5018 27907.61856 29746.28361 42445.53708 0.749695972 0.790181232 0.910762185 0.730910745 0.930875321 0.768078438 0.657492412 0.700810631 1 15.37332525 -0.198527186 9.094867092 0.999996524 0.776520928 0.398828207 0.084855156 0 0 0.082762153 0.019507226 0.63310073 0.198527186 -0.223475596 APEVNLNAPDVDVHGPDWNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APEVNLNAPDVDVHGPDWNLK 21 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 268.09 3.04E-37 271240000 457210 465250 420980 541300 354270 442370 482130 503710 341760 FALSE TRUE 435598.5894 512659.5039 440282.3494 486887.4956 416054.5758 427050.616 408572.2136 459602.4821 394758.3953 1.103456176 1.298666501 1.115321054 1.233380978 1.053947378 1.081802492 1.034993096 1.164262717 1 18.59061042 2.730932052 24.92431523 1.067511302 1.192817058 0.433311089 0.068479358 479.7335671 1567398.198 0.020089565 0.019282902 538.185573 -2.730932052 0.125305756 APEYLHR ddPTM_SK-BR-3_Trastuzumab_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 0.0023274 161560000 202010 205150 173260 214430 228730 190110 240070 218920 221220 FALSE TRUE 192461.3876 226055.0182 181204.1424 192875.089 268620.4396 183526.443 203442.9123 199750.2042 255525.6678 0.753197866 0.884666579 0.709142623 0.754816887 1.051246405 0.71823095 0.796174076 0.781722658 1 17.96310869 -1.526879083 2.778112833 1.009275251 0.808082697 0.271510148 0.099745462 13985520.05 14213696.94 976232.7581 0.021952546 0.029724935 1.526879083 -0.201192554 APFDLFENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APFDLFENR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 129.42 0.0009067 332345000 227107 231016 167294 199612 214487 166472 222553 207994 229540 FALSE TRUE 216372.1022 254556.793 174964.5954 179546.6225 251893.4649 160707.0329 188598.4524 189780.9427 265135.8909 0.816080016 0.960099337 0.659905359 0.677187166 0.950054193 0.606130812 0.711327507 0.715787448 1 18.01637245 3.740808572 24.96840997 0.74138207 0.888089676 0.132165504 0.129704274 281.8219678 3130228.734 0.030607112 0.051994183 5505.649652 -3.740808572 0.146707606 APGFGDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APGFGDNR 8 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 98.457 0.017469 1393660000 1923920 1707450 1640230 1755680 1947780 1397460 1770960 1587430 2006330 FALSE TRUE 1832980.114 1881441.096 1715436.168 1579195.711 2287472.215 1349065.61 1500767.526 1448426.214 2317461.409 0.790943101 0.811854337 0.740222107 0.681433445 0.987059463 0.582130776 0.647591162 0.625005537 1 21.14411388 APGFGDNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 APGFGDNRK 9 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;; 123.86 0.00087528 9871210000 5740150 4037040 4646600 4284650 4364520 4092890 5256160 4978570 4902740 FALSE TRUE 5468824.485 4448418.966 4859651.206 3853948.842 5125690.906 3951152.193 4454236.256 4542620.018 5663031.879 0.96570611 0.785518969 0.858135944 0.680545143 0.90511426 0.697709686 0.786546209 0.802153354 1 22.43314322 4.609361657 2.075456184 0.799510263 0.989448691 0.185808443 0.094260825 0.670324938 3.988387277 0.020697711 0.217711033 40678.19341 -4.609361657 0.189938428 APGPGLAQGLPQLHSLVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APGPGLAQGLPQLHSLVLR 19 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 161.86 2.87E-11 83196000 84513 66150 61531 79454 94103 68951 80748 77939 101760 FALSE TRUE 80518.23798 72890.76021 64352.25721 71467.13297 110514.5334 66563.20958 68428.40956 71114.24798 117540.4211 0.685025945 0.620133564 0.547490443 0.608021754 0.940225774 0.566300588 0.582169172 0.60501951 1 16.84279745 -1.102806238 3.975240542 1.00009581 0.641506239 0.500781357 0.111580741 4630256.78 1712695.367 3777.86185 0.025146219 0.078921215 1.102806238 -0.358589571 APGT(ph)PHSHTKPYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 1 APGT(1)PHSHTKPYVR;APGT(1)PHSHTKPYVR 163.7 6.21E-06 284290000 292960 304440 308420 345470 289330 332710 379290 308730 27095 TRUE FALSE 279112.3614 335462.7821 322561.3621 310742.6992 339789.0604 321188.1693 321422.3444 281695.9645 31296.75422 8.918252655 10.7187723 10.30654361 9.928911384 10.85700639 10.26266708 10.27014949 9.000804446 1 14.93372542 0.664798381 2.438772863 1.000356753 10.17809585 0.967658634 0.523210051 0.365195567 2.459535633 0.492098776 0.131841714 4.621664137 -0.664798381 9.177739098 APGTPHSHTKPYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 182.89 9.49E-07 3223400000 3088900 2464900 2596100 2854200 2872300 2849800 3600500 2905500 166820 FALSE TRUE 2942893.819 2716076.112 2715133.753 2567290.393 3373228.211 2751110.711 3051177.597 2651079.017 192689.5936 15.27271797 14.09560351 14.09071296 13.32345118 17.50602172 14.27742236 15.83467763 13.75828849 1 17.55591913 0.844782227 6.811362514 1.000004459 14.875763 0.93401176 1.154185629 1.535292527 67.39625791 1.030636978 0.258569327 6.99491155 -0.844782227 13.87575854 APGYPSS(ph)PVTTASGTTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APGYPSSPVTTASGTTLR 18 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 APGYPS(0.001)S(0.998)PVT(0.001)TASGTTLR;APGYPSS(1)PVTTASGTTLR;APGYPS(0.003)S(0.997)PVTTASGTTLR 239.86 6.54E-24 628150000 480923 463622 478585 512392 501109 462671 547460 494070 587450 TRUE FALSE 458190.7229 510865.6089 500528.5956 460885.3827 588502.2509 446648.5873 463934.9222 450806.6116 678548.7457 0.675251006 0.752879748 0.737645746 0.679222216 0.867295466 0.658240974 0.683716424 0.664368794 1 19.37209293 -1.701285216 5.542209619 1.006295911 0.71516162 0.675243045 0.062152205 0.004576452 0.000246662 0.056960218 0.013220183 0.019893664 1.701285216 -0.29113429 APIDTS(ph)DVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APIDTSDVEEK 11 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2 D6RIY6 EXOSC9 Exosome complex component RRP45 1 APIDT(0.171)S(0.829)DVEEK 149.69 3.59E-05 258920000 642630 947420 559350 867510 361120 801820 596830 738310 392280 TRUE FALSE 612254.1535 1043963.175 584996.7508 780306.2466 424099.2137 774052.7723 505772.622 673659.6624 453112.7789 1.351218023 2.303980871 1.291062133 1.722101611 0.935968336 1.708300468 1.116217961 1.486737284 1 18.78951065 3.311260603 1.894828123 1.300038835 1.803656449 0.212011961 0.36028159 0.412107585 3.036612006 0.102229763 0.150111757 2047.672998 -3.311260603 0.503617614 APIQDIWYHEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 APIQDIWYHEDR 12 0 J3QLR8;Q9Y3D9 J3QLR8 MRPS23 "28S ribosomal protein S23, mitochondrial" 0 ;;;; 233.37 5.39E-16 431821000 838062 651559 697352 673405 846419 562796 738969 723724 695269 FALSE TRUE 798448.4701 717953.6029 729326.279 605713.05 994034.2056 543306.2334 626225.707 660350.8899 803087.7656 0.994223178 0.893991459 0.908152646 0.754230205 1.237765345 0.676521617 0.779772441 0.822264911 1 19.61519814 APIRPDIVNFVHTNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APIRPDIVNFVHTNLR 16 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 270.51 2.38E-35 4557800000 6275700 6276200 5411300 7110800 6604500 5805400 6800600 6220300 6150700 FALSE TRUE 5979060.098 6915751.915 5659413.458 6396008.874 7756322.709 5604357.542 5763043.568 5675617.556 7104519.143 0.841585472 0.973429978 0.796593456 0.900273297 1.091744924 0.788844034 0.811179962 0.798874272 1 22.76030558 APIRPDIVNFVHTNLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APIRPDIVNFVHTNLRK 17 2 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 182.17 4.58E-10 1322960000 2120600 1276620 1978640 1863670 2043600 2023350 2696600 2299800 2531400 FALSE TRUE 2020363.441 1406709.029 2069362.601 1676330.351 2400003.193 1953280.882 2285184.144 2098417.32 2923956.583 0.690969029 0.481097783 0.707726856 0.573308906 0.820806713 0.668026637 0.781538329 0.717663638 1 21.47949046 0.184841986 0.223948467 1.141255302 0.544331602 0.617660405 0.086093133 3.985932515 0.397406798 0.672229598 0.208078215 1.530530493 -0.184841986 -0.596923701 APKPDGPGGGPGGSHMGGNYGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 APKPDGPGGGPGGSHMGGNYGDDR 24 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;;;;;;;;; 256.89 4.20E-44 5353980000 3224880 3067690 2948490 4045660 2715450 3475050 3961700 3537870 2682700 FALSE TRUE 3072446.313 3380291.099 3083681.183 3638982.571 3189023.62 3354708.147 3357269.903 3228075.347 3098719.415 0.991521304 1.090867112 0.995146953 1.17435046 1.029142427 1.082611136 1.083437851 1.041744965 1 21.5632407 4.650191503 3.005835326 1.067514125 0.98610592 0.145766265 0.052082419 0.498668048 7.179957242 0.011079662 0.087000514 44688.06021 -4.650191503 -0.081408205 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;; 214.11 1.45E-27 389998000 462196 378689 435872 469266 342476 453080 514286 507182 394647 FALSE TRUE 440348.9111 417277.8396 455857.1623 422094.4901 402203.706 437389.726 435822.2252 462770.4553 455846.8412 0.966001892 0.915390438 1.000022642 0.925956817 0.882322021 0.959510271 0.956071614 1.015188466 1 18.79818965 1.386795069 2.617802072 1.00831563 0.940048457 0.413496349 0.031720013 0.263151791 3.100534749 0.025602014 0.008015287 24.36660758 -1.386795069 -0.068267173 APLDLDKYVEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 155.43 4.26E-05 543190000 389310 332500 369940 422570 337070 384620 462110 426270 405500 FALSE TRUE 370908.0878 366382.128 386902.1149 380092.4608 395854.9013 371300.513 391606.6323 388943.539 468382.869 0.791890806 0.782227857 0.826038142 0.811499493 0.84515239 0.792728636 0.836082313 0.830396594 1 18.83732878 -5 0.220508415 1.967179409 0.78751545 0.919569573 0.017536813 37.18731774 0.371898348 15.95312969 0.031581285 1.00E-05 5 -1.179663959 APLEHELAGEPQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APLEHELAGEPQLR 14 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 122.64 0.00010756 70827000 93815 85564 92833 107640 99392 86426 104180 102980 109370 FALSE TRUE 89380.55087 94283.06888 97089.48487 96819.8227 116725.9333 83433.04595 88285.4276 93962.52527 126330.541 0.707513402 0.746320471 0.768535337 0.76640076 0.923972401 0.660434486 0.698844689 0.74378313 1 16.94684393 -2.329484942 2.172816732 2.314588552 0.747168722 0.555942065 0.069545119 2231809.629 277652.8063 14421619.19 0.016642151 0.004682902 2.329484942 -1.567419829 APLS(ph)PSLLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APLSPSLLIR 10 0 O75807 O75807 PPP1R15A Protein phosphatase 1 regulatory subunit 15A 1 APLS(0.989)PS(0.011)LLIR 69.01 0.061113 7722600 21602 15854 15229 20413 23493 14953 18296 17159 16455 TRUE FALSE 20580.91627 17469.54062 15927.26471 18361.04646 27590.17176 14435.17386 15504.60917 15656.46699 19006.75736 1.082821014 0.91912262 0.837979063 0.966027298 1.451598042 0.759475885 0.815741943 0.823731618 1 14.2142248 APLS(ph)PSLNSRPS(ph)PISATPPALVPETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APLSPSLNSRPSPISATPPALVPETR 26 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 2 APLS(0.968)PS(0.032)LNS(0.016)RPS(0.878)PIS(0.084)AT(0.022)PPALVPETR 82.946 0.0085369 38796000 25342 24695 26773 26962 30794 21836 34815 25008 31770 TRUE FALSE 24144.13388 27211.44858 28000.56853 24251.72854 36164.46385 21079.81384 29503.33233 22818.16694 36696.72934 0.657936942 0.741522448 0.763026271 0.660868938 0.98549556 0.574433041 0.803977162 0.621803832 1 15.16336387 -2.070118366 2.402423614 1.399239512 0.729128251 0.361151658 0.114409561 19282190.14 6260979.664 42181875.11 0.025475041 0.008509061 2.070118366 -0.670111261 APLS(ph)PSLNSRPSPISATPPALVPETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APLSPSLNSRPSPISATPPALVPETR 26 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 APLS(0.847)PS(0.131)LNS(0.021)RPS(0.001)PISATPPALVPETR 122.11 8.37E-05 141790000 55687 43756 51296 58485 55632 49912 69584 58213 60680 TRUE FALSE 53054.78587 48214.78615 53647.97234 52605.97669 65334.20319 48183.53492 58967.6828 53115.56111 70089.94449 0.756952888 0.687898763 0.765416105 0.750549556 0.932148023 0.68745289 0.841314446 0.757819991 1 16.09691986 -4.999999999 0.156729946 1.851389628 0.702128618 0.51605895 0.070193258 97.97335413 0.891945572 25.92423305 0.283950657 1.00E-05 4.999999999 -1.149261011 APLYDLAAHEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APLYDLAAHEDK 12 0 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 90.926 0.0047553 0 326750 302460 288100 335140 238440 329510 354040 321160 122490 FALSE TRUE 311305.1751 333281.0179 301309.67 301451.0905 280023.8605 318098.9861 300024.6956 293037.5278 141485.1236 2.200267895 2.355590534 2.129620855 2.130620399 1.97917529 2.248285742 2.12053881 2.07115434 1 17.11029084 -1.78499733 0.384050889 1.60E-13 2.224528885 0.937964523 0.093780718 7.909870003 0.531795878 7.355807405 0.064588143 0.016405999 1.78499733 2.224528885 APPCEYKDWLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APPCEYKDWLTK 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 147.18 5.96E-05 713440000 1513720 1317160 1405390 2018800 1299260 1956840 2124160 1716930 1501610 FALSE TRUE 1442169.456 1451380.101 1469828.522 1815866.389 1525850.533 1889074.14 1800080.379 1566586.507 1734472.01 0.83147462 0.836784966 0.847421298 1.046927468 0.879720471 1.089134982 1.037826133 0.903206566 1 20.72606513 3.253903336 21.29266407 0.999019714 0.837167136 0.57166832 0.062780909 26.36135564 36582.86169 0.016490875 0.022194129 1794.334206 -3.253903336 -0.161852579 APPHELTEEEKQQILHSEEFLSFFDHSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 254.43 2.21E-58 62310000 32017 34479 28970 40188 25645 31714 36919 34381 6890.8 FALSE TRUE 30503.61986 37992.4493 30298.30316 36148.22589 30117.47988 30615.73623 31286.32849 31370.41737 7959.390071 3.832406703 4.773286516 3.806611171 4.541582404 3.783892938 3.846492753 3.930744468 3.941309208 1 12.95844217 -0.927375884 0.457476075 1.30E-18 4.223657115 0.897779795 0.325289625 4.21231726 0.601499433 6.155775335 0.159463326 0.118201807 0.927375884 4.223657115 APPQTHLPSGAS(ph)SGTGSASATHGGGSPPGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.157)S(0.157)GT(0.157)GS(0.157)AS(0.157)AT(0.132)HGGGS(0.08)PPGTR 71.735 0.0071676 155420000 29537 32390 36810 41328 42824 27817 48814 32479 23721 TRUE FALSE 28140.84455 35690.57782 38497.77491 37173.63092 50292.49204 26853.69032 41366.52777 29634.96658 27399.53153 1.027055682 1.302598104 1.405052304 1.356725055 1.835523793 0.980078447 1.509753104 1.081586616 1 14.74186361 1.073548014 6.806558116 1.001023267 1.328958877 0.222031308 0.237961348 0.292212104 20.17110968 0.214529568 0.053837337 11.84535318 -1.073548014 0.327935611 APPQTHLPSGASS(ph)GTGSASATHGGGSPPGTR ddPTM_SK-BR-3_Trastuzumab_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 APPQTHLPSGAS(0.051)S(0.198)GT(0.198)GS(0.198)AS(0.198)AT(0.106)HGGGS(0.048)PPGT(0.001)R;APPQTHLPSGAS(0.017)S(0.397)GT(0.092)GS(0.308)AS(0.056)AT(0.022)HGGGS(0.107)PPGT(0.002)R 108.15 0.00020907 1533180000 238131 209703 202292 278714 231547 227067 261176 246619 199608 TRUE FALSE 226875.0196 231071.9741 211567.2883 250697.1392 271928.7235 219203.6129 221328.8044 225023.733 230562.1892 0.984007917 1.002211052 0.917614848 1.087329801 1.17941595 0.950735303 0.959952736 0.975978471 1 17.81479641 APPQTHLPSGASSGTGSASAT(ph)HGGGSPPGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.013)S(0.072)GT(0.089)GS(0.089)AS(0.156)AT(0.318)HGGGS(0.258)PPGT(0.005)R 111.23 0.00017989 477410000 44798 34625 43472 49501 59726 43166 56182 50508 35711 TRUE FALSE 42680.48732 38153.32687 45465.2342 44525.06543 70142.19549 41671.1506 47610.40405 46085.25176 41248.87949 1.034706587 0.924954261 1.102217436 1.079424847 1.700463051 1.010237153 1.154222966 1.117248573 1 15.33206731 3.358828132 2.656474055 1.196674131 0.984454452 0.138957808 0.198448025 0.451696825 6.450313969 0.055754834 0.079898185 2284.694479 -3.358828132 -0.21221968 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.003)GAS(0.085)S(0.031)GT(0.017)GS(0.017)AS(0.017)AT(0.075)HGGGS(0.722)PPGT(0.035)R;APPQTHLPSGAS(0.019)S(0.005)GT(0.005)GS(0.019)AS(0.015)AT(0.04)HGGGS(0.826)PPGT(0.071)R;APPQTHLPSGASSGTGSAS(0.002)AT(0.066)HGGGS(0.909)PPGT(0.023)R;APPQTHLPSGAS(0.024)S(0.083)GT(0.07)GS(0.07)AS(0.059)AT(0.05)HGGGS(0.566)PPGT(0.078)R;APPQTHLPSGASSGTGSASAT(0.001)HGGGS(0.98)PPGT(0.019)R;APPQTHLPSGASSGTGSAS(0.002)AT(0.016)HGGGS(0.981)PPGTR;APPQTHLPS(0.002)GAS(0.033)S(0.107)GT(0.107)GS(0.107)AS(0.107)AT(0.09)HGGGS(0.335)PPGT(0.111)R 219.54 1.13E-34 5506910000 550838 481621 513533 590243 615975 530688 617976 614851 490794 TRUE FALSE 524800.9794 530698.7275 537078.996 530910.6523 723400.845 512310.1415 523692.4113 561011.3869 566903.8269 0.92573194 0.936135377 0.947389964 0.936509205 1.276055674 0.903698506 0.923776462 0.989605927 1 19.11274448 2.925175498 24.99999989 1.007847916 0.935702827 0.137523996 0.100266915 308.8551005 103191.9057 0.030607191 0.03246384 841.7352177 -2.925175498 -0.072145089 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTRGPGASVHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APPQTHLPSGASSGTGSASATHGGGSPPGTRGPGASVHDR 40 1 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 APPQTHLPSGASSGTGSASATHGGGS(0.994)PPGT(0.002)RGPGAS(0.003)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.995)PPGT(0.002)RGPGAS(0.004)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.996)PPGT(0.001)RGPGAS(0.003)VHDR 204.76 1.32E-31 673790000 50246 15597.8 62410 36640.4 119166 39414.7 101179 62969 76141 TRUE FALSE 47870.97116 17187.23355 65271.56023 32957.23738 139948.5127 38049.75906 85742.28527 57455.10054 87948.55741 0.544306497 0.195423712 0.742156121 0.374733121 1.591254215 0.432636534 0.974914061 0.653280761 1 16.42437229 APPQTHLPSGASSGTGSASATHGGGSPPGTR ddPTM_SK-BR-3_Trastuzumab_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 ; 133.94 1.48E-06 49686000 21892.8 14049.7 20000.1 18524.4 24145 15915.9 27924 19769 23694 FALSE TRUE 20857.97073 15481.3804 20917.12437 16662.29212 28355.88036 15364.72839 23663.68094 18037.92156 27368.34451 0.762120293 0.565667404 0.764281682 0.608816222 1.036083142 0.561405108 0.864636914 0.659079746 1 14.74022055 -4.999999996 0.158047361 2.018456703 0.64638748 0.248303954 0.145939817 165.427578 1.512009714 52.82169873 0.558146702 1.00E-05 4.999999996 -1.372069223 APQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APQSPR 6 0 P12270 P12270 TPR Nucleoprotein TPR 1 APQS(1)PR;APQS(1)PR 69.716 0.097313 696340000 876330 913510 782850 997700 835210 720310 853600 1031140 1139770 TRUE FALSE 834907.6176 1006597.708 818744.4468 897409.3005 980870.3596 695365.4841 723367.6426 940847.9152 1316519.71 0.634177833 0.764589926 0.621900637 0.681652765 0.745047987 0.528184636 0.549454472 0.7146478 1 20.32829769 0.971590179 22.46432604 1.000000004 0.649009178 0.691046882 0.073871147 516.7641117 408618.9444 0.076827356 0.019206839 9.366776957 -0.971590179 -0.350990826 APQT(ph)SS(ph)SPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.727)S(0.366)S(0.83)S(0.077)PPPVR 99.991 0.018489 308460000 218120 183590 191840 214330 215530 194280 243470 195950 249230 TRUE FALSE 207809.8999 202298.0297 200636.0538 192785.1412 253118.3638 187552.0349 206324.1799 178791.5792 287879.3155 0.721864645 0.702718184 0.696945015 0.669673474 0.879251652 0.651495348 0.716703732 0.621064347 1 18.13510461 -1.026348983 4.649846101 1.000008016 0.709608487 0.644167613 0.068312359 8001176.457 1766079.715 704.5811155 0.01435729 0.094113303 1.026348983 -0.290399529 APQTS(ph)S(ph)SPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.129)S(0.707)S(0.733)S(0.431)PPPVR;APQT(0.406)S(0.582)S(0.524)S(0.488)PPPVR 100.69 0.0045183 350900000 317510 267010 293430 317090 330630 308840 353700 329830 386190 TRUE FALSE 302501.9315 294218.6226 306884.0557 285215.5108 388291.7673 298144.7934 299736.5689 300948.3367 446078.3728 0.678136287 0.659567109 0.687959952 0.639384306 0.870456384 0.668368635 0.671937012 0.674653503 1 18.76693768 -2.207692835 2.328005488 1.941574223 0.690737763 0.691263386 0.064279455 4327600.281 847030.0828 21471535.93 0.014710483 0.006198793 2.207692835 -1.25083646 APQTS(ph)SSPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.23)S(0.412)S(0.229)S(0.13)PPPVR;APQT(0.067)S(0.364)S(0.364)S(0.205)PPPVR 88.092 0.010679 1569394000 277940 241750 246360 286750 269010 258150 310230 273740 296900 TRUE FALSE 264802.327 266384.5998 257655.8497 257925.3452 315925.2588 249210.2008 262898.7157 249769.8744 342941.7356 0.772149609 0.776763433 0.751310858 0.752096693 0.92122138 0.726683792 0.766598779 0.72831577 1 18.38760396 -1.842617955 2.660277895 1.085873021 0.7747545 0.625736002 0.054833297 16043844.34 10740568.22 8774239.01 0.012197493 0.014367528 1.842617955 -0.311118521 APQTSS(ph)SPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.296)S(0.184)S(0.336)S(0.184)PPPVR 84.169 0.012995 278530000 89991 83843 88572 93960 102440 94248 100730 103720 116050 TRUE FALSE 85737.30377 92386.69702 92633.11381 84514.96229 120305.5036 90984.16813 85361.78847 94637.72695 134046.4413 0.639608952 0.689214097 0.691052391 0.63049016 0.897491216 0.67875109 0.636807569 0.706007008 1 17.03237339 -1.420328583 2.221098334 1.015922922 0.691230638 0.610438223 0.076185192 335893.346 288039.2009 33479.98717 0.018982978 0.037990186 1.420328583 -0.324692284 APQTSS(ph)SPPPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.236)S(0.021)S(0.372)S(0.372)PPPVRR 73.857 0.037806 72511000 43493 30318 39950 44003 46995 40888 50977 46050 54711 TRUE FALSE 41437.17208 33407.43867 41781.74702 39579.73484 55190.91312 39472.03831 43199.52239 42017.61787 63195.30245 0.655700194 0.528638006 0.661152734 0.62630818 0.873338856 0.624603994 0.683587557 0.664885146 1 15.9475297 -4.999999999 0.182892131 2.420698292 0.586784552 0.615379684 0.084090304 86.87994662 0.840589475 44.89691191 0.242105947 1.00E-05 4.999999999 -1.83391374 APQTSSS(ph)PPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.02)S(0.061)S(0.061)S(0.859)PPPVR;APQT(0.002)S(0.038)S(0.038)S(0.922)PPPVR;APQT(0.002)S(0.028)S(0.028)S(0.943)PPPVR;APQT(0.003)S(0.087)S(0.087)S(0.823)PPPVR;APQT(0.008)S(0.286)S(0.286)S(0.419)PPPVR;APQT(0.013)S(0.174)S(0.174)S(0.638)PPPVR 164.06 6.12E-05 15125396000 2724870 2330290 2408410 2671840 2757000 2425080 2824300 2526260 2865840 TRUE FALSE 2596070.795 2567749.2 2518837.981 2403261.567 3237819.927 2341098.872 2393401.163 2305047.282 3310259.831 0.784249856 0.775694154 0.760918511 0.726003906 0.978116551 0.70722511 0.723025166 0.696334246 1 21.65851303 -2.365219728 2.380680027 2.710510792 0.768992339 0.453736257 0.079673784 7987473.999 1592663.275 72744983.24 0.018496806 0.004313008 2.365219728 -1.941518453 APRPFGSVSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APRPFGSVSSPK 12 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 APRPFGSVS(0.032)S(0.968)PK;APRPFGSVS(0.005)S(0.995)PK 113.67 0.00069051 759200000 1329680 1192690 1186710 1525960 807370 1337800 1314840 1318700 899450 TRUE FALSE 1266828.662 1314226.467 1241121.827 1372567.602 948175.0724 1291471.651 1114237.009 1203227.637 1038932.112 1.219356536 1.264978194 1.194613019 1.3211331 0.912643917 1.243076073 1.072482981 1.158138846 1 19.98666996 2.7691685 24.99931724 1.094713647 1.246027954 0.453513876 0.093096858 627.7260489 512700.888 0.024917976 0.026427163 587.7173345 -2.7691685 0.151314307 APRPTRPDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APRPTRPDK 9 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 118.67 0.00053536 12597160000 6164130 5682570 5901750 7335690 5523350 7055820 8054800 7994130 6452040 FALSE TRUE 5872763.791 6261630.344 6172351.075 6598292.504 6486620.491 6811475.184 6825892.323 7294121.598 7452589.411 0.788016549 0.840195266 0.828215636 0.885369117 0.870384793 0.913974299 0.915908813 0.978736543 1 22.82931035 2.410678023 0.319878482 1.014053386 0.767393951 0.93515509 0.016614354 0.374752536 0.09182521 0.020240095 0.033028049 257.4411831 -2.410678023 -0.246659435 APS(ph)DS(ph)SLGTPSDGRPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 2 APS(1)DS(0.722)S(0.278)LGTPSDGRPELR;APS(1)DS(0.729)S(0.267)LGT(0.003)PS(0.001)DGRPELR;APS(1)DS(0.554)S(0.442)LGT(0.004)PSDGRPELR 179.14 2.73E-13 1013450000 935190 832860 912240 1010550 978070 877700 1086840 950290 1077380 TRUE FALSE 890985.4221 917729.3809 954067.1063 908967.5941 1148645.098 847305.0289 921022.5968 867077.5698 1244454.588 0.715964593 0.737455099 0.766654819 0.730414434 0.923010859 0.680864563 0.740101411 0.696753082 1 20.24708215 -1.910649097 2.475929834 1.15171488 0.747488375 0.585720968 0.066356614 6138947.488 3177611.106 5408562.005 0.014977259 0.012284314 1.910649097 -0.404226506 APS(ph)DSS(ph)LGTPSDGRPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 2 APS(0.998)DS(0.234)S(0.767)LGTPSDGRPELR 166.21 1.49E-11 316530000 382130 357990 385220 463370 436410 382390 440410 461740 444610 TRUE FALSE 364067.4722 394469.588 402882.718 416791.1673 512519.7658 369147.7384 373217.3658 421307.5978 513557.848 0.708912294 0.768111303 0.784493353 0.811575889 0.997978646 0.71880459 0.72672897 0.820370284 1 18.97016727 -3.120372441 1.332207973 7.716485027 0.783946349 0.381930315 0.082527667 587106.3747 7938.781274 11958822.91 0.022766361 0.000757927 3.120372441 -6.932538678 APS(ph)DSSLGTPSDGRPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 1 APS(0.889)DS(0.085)S(0.025)LGTPSDGRPELR;APS(0.995)DS(0.004)S(0.001)LGTPSDGRPELR;APS(0.934)DS(0.033)S(0.033)LGTPSDGRPELR;APS(0.91)DS(0.045)S(0.045)LGTPSDGRPELR;APS(0.993)DS(0.007)SLGTPSDGRPELR;APS(0.84)DS(0.08)S(0.08)LGTPSDGRPELR 205.21 5.98E-16 4407810000 2012270 1732230 1830840 2042650 2058310 1874940 2301960 2037450 2170860 TRUE FALSE 1917153.985 1908746.206 1914785.825 1837318.941 2417278.612 1810010.358 1950753.724 1859040.077 2507505.882 0.764566097 0.761213053 0.763621668 0.73272767 0.964017126 0.721836934 0.777965762 0.741390116 1 21.25782165 -1.801994435 2.741688552 1.063798536 0.777300636 0.510586318 0.068169821 17593106.36 13222161.82 7468248.044 0.015901108 0.015776315 1.801994435 -0.2864979 APS(ph)IDGKEELDLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;APS(1)IDGKEELDLAEK 164.98 8.79E-07 186048000 264310 308870 239855 332180 198077 300130 275290 306700 190592 TRUE FALSE 251816.5901 340344.2042 250852.589 298788.6353 232621.5661 289736.4228 233289.4545 279843.7221 220148.034 1.143851188 1.545978849 1.139472311 1.357216914 1.056659748 1.316098162 1.059693563 1.271161577 1 17.74811443 1.583185877 0.339199738 0.998962739 1.346056289 0.21161796 0.147720335 1.62324653 0.614117264 0.205879834 0.183164695 38.29886263 -1.583185877 0.347093549 APS(ph)LTDLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APSLTDLVK 9 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 APS(1)LTDLVK;APS(0.998)LT(0.002)DLVK;APS(1)LTDLVK;APS(1)LTDLVK 160.61 6.84E-05 381487000 1076400 968460 951700 1137690 839440 1012600 1153980 1139680 905430 TRUE FALSE 1025520.705 1067147.175 995336.3864 1023327.24 985838.0702 977533.4081 977919.1567 1039883.577 1045839.46 0.980571822 1.020373791 0.951710491 0.978474497 0.942628489 0.934687823 0.935056664 0.994305165 1 19.99622998 3.725907508 24.48494468 0.956590989 1.000472807 0.260008481 0.025254119 549.4713517 1063279.336 0.006378719 0.009963293 5319.949485 -3.725907508 0.043881818 APS(ph)LTNDEVEEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APSLTNDEVEEFR 13 0 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 APS(0.996)LT(0.004)NDEVEEFR;APS(0.999)LT(0.001)NDEVEEFR 147.83 4.51E-05 42268000 199618 173508 205762 214164 195507 205736 259412 209018 191762 TRUE FALSE 190182.4527 191188.6625 215196.3912 192635.8278 229603.3589 198611.3107 219833.935 190715.2758 221499.4716 0.858613573 0.863156292 0.971543587 0.869689785 1.036586486 0.896667199 0.992480629 0.861019101 1 17.75694373 3.750802324 23.10773631 0.946786114 0.860884899 0.280990237 0.057173027 288.0393684 543705.099 0.012735262 0.022701682 5633.811652 -3.750802324 -0.085901215 APS(ph)PAPSSVPLGSEKPSNVSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 APS(1)PAPSSVPLGSEKPSNVSQDR;APS(0.996)PAPS(0.003)S(0.001)VPLGSEKPSNVSQDR;APS(1)PAPSSVPLGSEKPSNVSQDR 218.22 1.38E-32 3520560000 2353810 2121240 2172690 2320530 1802290 2285560 2622570 2413550 2089030 TRUE FALSE 2242550.066 2337396.768 2272309.986 2087265.916 2116608.805 2206410.484 2222448.78 2202206.767 2412986.103 0.92936717 0.968673945 0.941700403 0.86501365 0.877174055 0.91439005 0.921036709 0.912647928 1 21.20238818 -1.14923626 3.605308273 1.000068279 0.919800913 0.438312334 0.029552848 2049991.573 981150.3378 1036.973076 0.007695171 0.070919186 1.14923626 -0.080267366 APS(ph)PARPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;APS(1)PARPK;APS(1)PARPK 86.344 0.0097501 847160000 2248210 2154990 2033842 2344230 1628910 2117770 2387780 2333890 2003220 TRUE FALSE 2141941.569 2374585.931 2127095.667 2108583.547 1912991.388 2044431.094 2023480.306 2129522.219 2313869.127 0.925696939 1.02624038 0.919280889 0.911280384 0.826750038 0.883555198 0.874500759 0.920329588 1 21.14187584 3.507225216 4.239492199 0.891445038 0.97638197 0.239756891 0.050242537 0.209325586 8.552039172 0.012656351 0.019142352 3215.327511 -3.507225216 0.084936932 APS(ph)PEPAAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 APS(1)PEPAAPR;APS(1)PEPAAPR;APS(1)PEPAAPR 92.611 0.0098071 1318460000 698310 640350 653670 803440 742980 673150 770400 673110 818050 TRUE FALSE 665302.2702 705602.393 683641.4161 722676.6848 872555.4768 649838.6467 652861.3306 614168.92 944909.016 0.704091356 0.746741095 0.723499728 0.764810868 0.923428036 0.687726157 0.690925073 0.64997678 1 19.8498159 -2.328638162 2.434595084 2.666953429 0.735906774 0.55755215 0.073795439 3686339.309 804487.0433 33895853.79 0.018143309 0.004692041 2.328638162 -1.931046655 APS(ph)PGAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APSPGAYK 8 0 P54259 P54259 ATN1 Atrophin-1 1 APS(1)PGAYK;APS(1)PGAYK 114.86 0.0027014 374540000 794450 709200 753060 908610 533130 834730 863840 844300 639130 TRUE FALSE 756897.9229 781468.2863 787588.5459 817274.7966 626107.7032 805823.0908 732045.3425 770368.6161 738243.0162 1.025269331 1.058551546 1.066841851 1.107053882 0.848105149 1.091541773 0.991604833 1.043516294 1 19.49373628 APS(ph)PHVVQENLHSEVVEVCTSSTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.759)PHVVQENLHS(0.241)EVVEVCTSSTLK 138.93 7.40E-06 80630000 71494 88471 74365 96570 62210 91516 94086 82899 48439 TRUE FALSE 68114.62031 97486.29548 77774.70881 86862.60013 73059.4043 88346.77797 79731.45269 75639.92408 55950.67273 1.217404849 1.742361454 1.390058511 1.552485357 1.30578241 1.579011899 1.425031171 1.351903747 1 15.77186786 0.756408046 1.691723358 1.000384802 1.473372491 0.492873102 0.145869776 0.67125365 3.172155985 0.126380256 0.035976136 5.707002285 -0.756408046 0.472987689 APS(ph)PLGPTRDPVATFLETCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 APSPLGPTRDPVATFLETCR 20 1 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.938)PLGPT(0.062)RDPVATFLETCR;APS(0.996)PLGPT(0.004)RDPVATFLETCR;APS(0.954)PLGPT(0.046)RDPVATFLETCR 145.52 8.72E-08 150881000 93965 96450 76903 99335 76225 85041 83210 87020 87833 TRUE FALSE 89523.46067 106278.3647 80429.07862 89349.65708 89518.61587 82096.00885 70514.78624 79400.06748 101453.6931 0.882407116 1.047555406 0.792766396 0.880693984 0.882359362 0.80919685 0.695044055 0.782623728 1 16.63046186 3.216190891 1.048366192 0.797197006 0.957123858 0.105187261 0.097893919 0.635352635 1.505318415 0.039422049 0.061413724 1645.094653 -3.216190891 0.159926852 APS(ph)PLGPTRDPVATFLETCREPGSQPAGPASLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPLGPTRDPVATFLETCREPGSQPAGPASLR 33 2 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.8)PLGPT(0.197)RDPVAT(0.003)FLETCREPGSQPAGPASLR 84.529 0.00022716 125920000 7208.8 6119.4 10406 8648.7 10661 9674.5 10662 9640.5 11483 TRUE FALSE 6868.05431 6742.973817 10883.12539 7779.316245 12520.27502 9339.469639 9035.316079 8796.326712 13263.72499 0.517807352 0.508377083 0.820518022 0.586510671 0.943948629 0.704136255 0.681205022 0.663186753 1 13.69519838 4.177186804 0.095975562 1.177348331 2.16E-22 0.448886851 0.122933692 46.24253408 0.871111092 2.8669366 8.725288142 15037.88654 -4.177186804 -1.177348331 APS(ph)PPLSQVFQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 APSPPLSQVFQTR 13 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 APS(0.992)PPLS(0.008)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(0.981)PPLS(0.019)QVFQTR;APS(0.958)PPLS(0.042)QVFQTR;APS(1)PPLSQVFQTR 170.78 2.75E-05 1088244000 316756 261552 272759 313269 303189 306233 333774 305209 321920 TRUE FALSE 301783.5716 288204.4462 285265.2699 281778.6049 356065.0656 295628.0744 282850.6461 278483.2819 371841.7095 0.811591502 0.775072938 0.767168563 0.757791818 0.957571613 0.795037423 0.760674876 0.748929652 1 18.50432908 -1.121397457 4.642163376 1.000014564 0.795741453 0.530133931 0.060134574 1.02E-05 1.94E-06 0.056257684 0.013258957 0.075614057 1.121397457 -0.204273112 APS(ph)PPVEHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APSPPVEHPR 10 0 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR 115.57 0.00077603 3158030000 1232791 1038845 1018778 1205866 1187116 1079028 1353238 1109343 1213198 TRUE FALSE 1174519.413 1144704.487 1065489.979 1084650.059 1394148.655 1041660.99 1146776.689 1012203.046 1401334.55 0.838143477 0.816867383 0.760339477 0.774012215 0.994872106 0.74333498 0.818346118 0.72231363 1 20.41836999 -1.105178834 4.350490489 1.000020846 0.811713023 0.389061718 0.075310309 36352263499 7477382957 9144831.713 0.016058634 0.078491236 1.105178834 -0.188307823 APS(ph)PRPGPGPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;APS(1)PRPGPGPLR 118.51 0.00037431 5612570000 2113200 1800420 1876690 2107730 2010080 1911640 2265690 1943230 2191510 TRUE FALSE 2013313.224 1983884.845 1962738.093 1895856.976 2360637.316 1845439.427 1920017.378 1773070.479 2531358.178 0.795349011 0.783723482 0.775369566 0.748948526 0.932557603 0.729031333 0.758492968 0.700442353 1 21.27148023 -1.127592422 4.596392101 1.000021556 0.779451892 0.563799003 0.061358202 1.26E-05 2.38E-06 0.055064639 0.012977592 0.074543122 1.127592422 -0.220569664 APS(ph)PSGLMS(ph)PSRLPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.998)PS(0.002)GLMS(0.982)PS(0.018)RLPGSR;APS(0.992)PS(0.06)GLMS(0.868)PS(0.077)RLPGS(0.004)R;APS(0.997)PS(0.224)GLMS(0.72)PS(0.057)RLPGS(0.001)R;APS(0.999)PS(0.037)GLMS(0.931)PS(0.034)RLPGSR 116.51 0.0011053 412085000 522122 423734 463761 509048 480588 481673 551770 474041 497651 TRUE FALSE 497442.3278 466912.9763 485024.9006 457877.5279 564402.395 464992.5432 467587.3525 432531.457 574824.1754 0.86538171 0.812270945 0.843779579 0.796552315 0.981869621 0.80893004 0.813444132 0.752458709 1 19.13276121 -2.168588705 2.477629517 1.431686929 0.835023453 0.428561047 0.060114028 5001927.792 1332271.524 12154380.6 0.013916448 0.006782836 2.168588705 -0.596663476 APS(ph)PSGLMSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 APSPSGLMSPSR 12 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.714)PS(0.286)GLMSPSR;APS(0.641)PS(0.359)GLMSPSR;APS(0.859)PS(0.141)GLMSPSR;APS(0.771)PS(0.229)GLMSPSR;APS(0.963)PS(0.037)GLMSPSR;APS(0.741)PS(0.259)GLMSPSR;APS(0.985)PS(0.015)GLMSPSR;APS(0.99)PS(0.01)GLMSPSR;APS(0.999)PS(0.001)GLMSPSR;APS(0.999)PS(0.001)GLMSPSR;APS(0.938)PS(0.062)GLMSPSR 196.02 2.22E-07 3236300000 2112415 1945506 1722512 2043310 1928371 1819205 2060386 1877142 1900315 TRUE FALSE 2012565.329 2143755.273 1801490.879 1837912.597 2264678.292 1756205.475 1746036.274 1712769.495 2195006.145 0.916883688 0.976651149 0.820722476 0.837315468 1.031741208 0.800091371 0.79545849 0.780302825 1 21.06579355 2.162293896 25 0.822588667 0.91690981 0.129184424 0.086183242 53.29326421 17467.19375 0.029968724 0.022133365 145.3094624 -2.162293896 0.094321143 APS(ph)PSGLMSPSRLPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.965)PS(0.034)GLMSPSRLPGSR 53.454 0.081778 222110000 227890 151780 260670 205330 223440 272720 319390 264410 284190 TRUE FALSE 217118.0913 167246.5546 272621.9773 184689.8383 262407.8653 263275.638 270661.1895 241256.8587 328260.7338 0.661419625 0.509493026 0.830504381 0.562631528 0.79938853 0.802032077 0.824531117 0.734954973 1 18.32448266 1.884672011 0.17688834 1.101880479 0.443198257 0.54320147 0.09575101 2.478046343 0.398002758 0.536741217 0.678042819 76.67821795 -1.884672011 -0.658682222 APS(ph)PSINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.999)PS(0.001)INR 157.99 0.00038601 182930000 188290 166410 169120 186000 197020 159670 200070 200130 251310 TRUE FALSE 179389.9049 183367.3682 176874.3193 167302.9266 231380.2256 154140.5879 169545.647 182605.5562 290281.8713 0.617985216 0.631687289 0.609319206 0.576346452 0.797088101 0.531003149 0.584072461 0.629062902 1 18.14709495 0.92024542 19.57849864 1 0.618883548 0.748101709 0.068926098 2100.218521 515572.7978 0.061338322 0.015334581 8.322339331 -0.92024542 -0.381116453 APS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.918)PS(0.081)SR;APS(0.864)PS(0.132)S(0.003)R;APS(0.971)PS(0.026)S(0.002)R;APS(0.994)PS(0.005)SR;APS(0.556)PS(0.408)S(0.036)R;APS(0.926)PS(0.074)SR;APS(0.893)PS(0.107)SR;APS(0.965)PS(0.035)SR;APS(0.957)PS(0.042)S(0.001)R;APS(0.992)PS(0.008)SR 130.31 0.0037507 11634392000 3578610 3133342 3190260 3553340 3281945 3331303 3513577 3073546 3321364 TRUE FALSE 3409456.197 3452633.112 3336536.577 3196151.512 3854315.169 3215939.142 2977516.297 2804410.018 3836424.166 0.888706788 0.899961256 0.869699604 0.833106918 1.004663458 0.838264749 0.776117595 0.730995817 1 21.87133081 2.012451797 24.99871134 0.809919258 0.89631026 0.10116617 0.081660883 327.9965989 658496.1138 0.027266573 0.020125048 102.9086301 -2.012451797 0.086391002 APS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.978)PT(0.022)K;APS(0.983)PT(0.017)K;APS(0.578)PT(0.422)K;APS(0.993)PT(0.007)K;APS(0.809)PT(0.191)K;APS(0.867)PT(0.133)K 104.75 0.035211 24150870000 54787620 53497780 47980000 59057800 33090960 51633620 56029780 68976900 46859750 TRUE FALSE 52197917.78 58949264.6 50179930.46 53121197.74 38862012.95 49845534.79 47481408 62936916.97 54126520.7 0.964368615 1.08910131 0.927085832 0.981426426 0.717984686 0.920907794 0.877230005 1.162774111 1 25.68983232 3.70503134 19.43529399 0.924464092 1.026734696 0.074207788 0.114700333 78.05925376 45246.58148 0.028763599 0.044576214 5070.27296 -3.70503134 0.102270603 APS(ph)PTKPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPTKPLR 9 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.982)PT(0.018)KPLR 108.3 0.001595 375230000 352400 407590 258330 437330 262060 343600 360360 342990 244840 TRUE FALSE 335742.7504 449123.8844 270174.686 393368.7575 307763.181 331701.0458 305380.4635 312955.9773 282808.5367 1.187173323 1.588084609 0.955327195 1.390936646 1.088238653 1.172882013 1.079813456 1.106600179 1 18.10946614 2.747003393 0.557312866 1.038574804 1.367267967 0.234772393 0.164319713 1.085111479 0.712866486 0.127287535 0.150983764 558.4745576 -2.747003393 0.328693163 APS(ph)PTKPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPTKPLRR 10 2 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.998)PT(0.002)KPLRR 103.46 0.0014669 188210000 280710 293590 381300 349780 216220 408810 291720 363620 228220 TRUE FALSE 267441.3946 323507.1548 398782.9822 314619.4499 253928.6995 394652.8072 247212.7562 331779.5051 263611.192 1.014529742 1.227213277 1.512769542 1.193498074 0.963269797 1.497101865 0.937793097 1.258594154 1 18.0080521 1.663916377 25 1.073372173 1.215854103 0.142697666 0.191569948 0.776793459 328.9172061 0.084220637 0.046704087 46.12287563 -1.663916377 0.14248193 APS(ph)PTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.999)PT(0.001)KR;APS(0.981)PT(0.019)KR;APS(0.917)PT(0.083)KR;APS(0.999)PT(0.001)KR;APS(0.993)PT(0.007)KR;APS(0.846)PT(0.154)KR;APS(0.981)PT(0.019)KR;APS(0.668)PT(0.332)KR;APS(0.997)PT(0.003)KR;APS(0.974)PT(0.026)KR 115.13 0.0035212 7809980000 11223550 9639010 9854480 11218660 7635340 10916180 11598280 11272640 8829480 TRUE FALSE 10693035.03 10621236.08 10306317.66 10090938.98 8966940.879 10538149.95 9828749.369 10285547.88 10198710.66 1.0484693 1.041429297 1.010551039 0.989432813 0.879222989 1.033282568 0.963724699 1.008514529 1 23.28188344 3.470494777 2.40258542 0.975505226 1.045148369 0.315313042 0.040254824 0.298323761 3.452568401 0.010978456 0.017230069 2954.573357 -3.470494777 0.069643143 APS(ph)RQDVYGPQPQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 234.12 7.29E-18 1437820000 308794 271906 301792 324817 374628 300563 352736 308284 390756 TRUE FALSE 294197.9196 299613.5305 315629.4617 292165.778 439963.0046 290154.4279 298919.6448 281289.0186 451352.4448 0.651814171 0.663812801 0.699297113 0.647311832 0.974765972 0.642855558 0.662275453 0.623213681 1 18.7838949 -1.951982682 2.665107502 1.228913372 0.692568149 0.470899291 0.101333232 61745758.6 21076035.38 87281210.4 0.024807906 0.011169078 1.951982682 -0.536345223 APS(ph)VATVGSICDLNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APSVATVGSICDLNLK 16 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-5;O75369-4;A0A0C4DGA1 O75369-8 FLNB Filamin-B 1 APS(1)VATVGSICDLNLK;APS(1)VATVGSICDLNLK 278.72 2.31E-35 232840000 430190 389340 308550 496360 286880 425410 467670 456450 311900 TRUE FALSE 409855.7713 429014.1886 322697.3227 446464.9498 336911.7812 410677.945 396318.3522 416480.8182 360267.859 1.137641788 1.190820046 0.895714993 1.239258342 0.935170243 1.139923906 1.100065804 1.156031013 1 18.45871042 APSEEELHGDQTDFGQGSQS(ph)PQKQEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.023)QS(0.977)PQKQEEQR;APSEEELHGDQTDFGQGSQS(1)PQKQEEQR;APSEEELHGDQTDFGQGS(0.037)QS(0.963)PQKQEEQR;APSEEELHGDQTDFGQGS(0.012)QS(0.988)PQKQEEQR 284.44 3.14E-62 1148170000 735840 869480 668820 882690 465525 800370 760080 847640 405319 TRUE FALSE 701058.3015 958081.0005 699486.0586 793960.3242 546712.4126 772652.9862 644115.8362 773416.148 468173.8004 1.497431725 2.046421649 1.494073478 1.695866628 1.167755248 1.650355029 1.375804959 1.651985112 1 18.83668468 -2.422195716 0.125058723 7.12E-14 1.940636572 0.391714177 0.226312232 59.46151651 0.934351923 19.132574 2.148379263 0.003782721 2.422195716 1.940636572 APSPS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.46)PS(0.538)S(0.002)R 103.87 0.0086838 3348500000 1112600 959350 772400 1008600 932240 879720 1024800 1090800 1011400 TRUE FALSE 1060009.603 1057108.856 807815.304 907213.6118 1094822.361 849255.0758 868447.9383 995283.7693 1168242.746 0.907353892 0.904870892 0.691478981 0.776562589 0.937153142 0.726950866 0.743379696 0.851949453 1 20.15590865 3.927075259 24.98420688 0.801477197 0.906423901 0.109270224 0.095462278 199.5450086 68364.08742 0.022516414 0.040592054 8454.25336 -3.927075259 0.104946704 APSPT(ph)SSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_SK-BR-3_Trastuzumab_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(0.386)PT(0.428)S(0.14)S(0.039)AGEEGT(0.007)KKPEPLSPASYHQPEGVAR 65.058 0.0048079 474270000 130280 103570 134040 141730 92737 147260 172870 187580 109710 TRUE FALSE 124121.9226 114123.9007 140185.8666 127483.0311 108910.3034 142160.3493 146495.5065 171154.5008 126723.2665 0.979472247 0.90057575 1.106236214 1.005995463 0.859434155 1.121817273 1.156026913 1.350616233 1 16.9513219 2.070242233 6.175940904 1.1750508 0.969755072 0.443679672 0.104860071 0.170390687 11.42945733 0.037186279 0.027189394 117.5553052 -2.070242233 -0.205295728 APSRPYQDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APSRPYQDTR 10 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 0 ; 94.465 0.0073738 165583000 412690 398780 259650 369260 399470 304430 363930 345020 344040 FALSE TRUE 393182.9616 439416.1354 271555.2093 332141.2833 469137.4415 293887.5128 308405.7945 314808.2197 397391.9661 0.989408431 1.105749922 0.683343481 0.835802713 1.18054083 0.73954065 0.776074558 0.792185667 1 18.60020318 3.759837916 24.98429372 0.849550166 1.047579189 0.22756223 0.144361726 1038.666061 1219621.662 0.036120788 0.065040006 5752.252167 -3.759837916 0.198029023 APSS(ph)PVAKPGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APSSPVAKPGPVK 13 1 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 APS(0.172)S(0.828)PVAKPGPVK;APS(0.181)S(0.819)PVAKPGPVK 86.641 0.0069285 83236000 578390 553110 551210 626750 401300 559220 639970 593320 481290 TRUE FALSE 551050.651 609472.5378 576483.5237 563747.8993 471286.5929 539854.0712 542330.8226 541365.7554 555925.9951 0.991230228 1.096319552 1.036978894 1.014070046 0.847750595 0.971089814 0.975544996 0.973809032 1 19.08453332 2.986814261 23.98814131 0.953095055 1.043503406 0.42931572 0.047280497 321.2469732 584430.455 0.013653771 0.015111752 970.0949881 -2.986814261 0.09040835 APTTVEDRVGDST(ph)PVSEKPVSAAVDANASESP ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APTTVEDRVGDSTPVSEKPVSAAVDANASESP 32 2 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 APTTVEDRVGDS(0.118)T(0.881)PVSEKPVSAAVDANASESP 191.25 7.84E-20 191900000 256540 185030 278970 252080 263930 259790 383530 314270 346560 TRUE FALSE 244413.8626 203884.7674 291761.0504 226740.4395 309959.3084 250793.4072 325015.4545 286750.8527 400302.7548 0.610572522 0.509326416 0.728850968 0.566422381 0.774312204 0.626509321 0.811924101 0.716334947 1 18.61073202 -0.204056925 0.153823326 1.290350632 0.443798177 0.701052496 0.076574399 7.736925645 0.370332296 1.508564709 0.481751644 0.625090754 0.204056925 -0.846552455 APVDEDRLS(ph)PLVAADSLLEHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR 311.55 1.98E-67 226121900 189855.9 180609.8 181207.7 200936 213439.8 182969.9 210476.9 208747.1 223801.3 TRUE FALSE 180881.7879 199014.144 189516.2523 180737.5315 250663.6335 176633.6065 178364.7832 190468.0973 258507.2626 0.699716465 0.769859005 0.73311771 0.699158429 0.969657993 0.683282956 0.689979776 0.736799792 1 17.97984529 -1.526340181 2.574042307 1.015394223 0.74459817 0.475603123 0.083202907 5938353.222 5600796.81 636717.3494 0.01955589 0.029761843 1.526340181 -0.270796053 APVPEPGLDLSLS(ph)PRPDSPQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLS(0.147)LS(0.853)PRPDSPQPR 69.248 0.011381 75072000 24222 17962 23632 26022 28381 23727 30399 26688 33285 TRUE FALSE 23077.07406 19792.34822 24715.55058 23406.21912 33330.63741 22905.32804 25761.07423 24351.05724 38446.6678 0.600235999 0.514800095 0.642852866 0.608797081 0.866931761 0.595768875 0.670046995 0.633372373 1 15.23057094 -5 0.167345865 2.396247901 0.542872241 0.625525238 0.088160549 83.936819 0.786674415 38.98027961 0.319878916 1.00E-05 5 -1.85337566 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLS(0.042)LS(0.027)PRPDS(0.931)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLS(0.002)PRPDS(0.997)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR 191.65 8.17E-18 2172334000 1227063 997765 1156413 1253435 1287238 1096190 1254031 1190337 1442212 TRUE FALSE 1169062.164 1099438.388 1209435.68 1127437.332 1511731.9 1058228.665 1062705.539 1086104.782 1665862.871 0.701775749 0.659981327 0.726011547 0.676788799 0.907476795 0.635243563 0.637930983 0.651977303 1 20.66783822 -1.093615363 3.895037007 1.000083903 0.695361767 0.586785162 0.079137552 28137108.28 61720323.61 34173.71783 0.018457847 0.080609205 1.093615363 -0.304722136 APVPGT(ph)PDSLSSGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 APVPGTPDSLSSGSSR 16 0 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 1 APVPGT(0.973)PDS(0.026)LS(0.001)SGSSR;APVPGT(0.999)PDS(0.001)LSSGSSR 119.54 0.0020804 194997000 195591 148656 171052 165574 191995 143674 177748 166489 203790 TRUE FALSE 186345.8011 163804.2154 178894.9034 148930.1869 225478.8672 138698.5334 150629.278 151910.3405 235392.7124 0.791637936 0.695876324 0.759984885 0.632688181 0.957883806 0.589221867 0.639906293 0.645348528 1 17.84471013 -1.042975276 4.819197225 1.000007028 0.712297325 0.419911995 0.105598396 7.46E-06 1.48E-06 0.095659498 0.022546609 0.090578416 1.042975276 -0.287709703 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_SK-BR-3_Trastuzumab_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(0.997)PPS(0.003)HQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK 253.7 1.09E-43 5177180000 1480100 1391540 1516280 1622200 1233220 1602920 1783270 1639660 1256520 TRUE FALSE 1410138.606 1533339.508 1585802.938 1459133.374 1448293.178 1547410.478 1511199.409 1496082.678 1451374.704 0.971588248 1.05647391 1.092621315 1.005345739 0.997876822 1.066168836 1.041219339 1.030803881 1 20.4689886 4.620809274 3.21386935 1.03890353 0.969542212 0.303304913 0.030480494 0.325110987 5.586230274 0.00719015 0.047546976 41764.69113 -4.620809274 -0.069361318 APVPTGEVYFADSFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APVPTGEVYFADSFDR 16 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8;D6RHJ3;D6RD16 P27824 CANX Calnexin 0 ;;; 182.25 5.06E-09 322529000 99017 79143 81286 114235 124228 94717 110269 91408 100527 FALSE TRUE 94336.66264 87207.76168 85013.0435 102751.8808 145893.3239 91436.92654 93445.43882 83403.83094 116116.2137 0.812433162 0.751038626 0.732137578 0.88490554 1.25644231 0.787460455 0.804757887 0.71827894 1 16.82520991 3.183202805 7.486136608 0.900805483 0.769071382 0.172753778 0.147364924 0.44581437 50.77958327 0.043360521 0.052186344 1524.764617 -3.183202805 -0.131734101 APVS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APVSPLK 7 0 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 APVS(1)PLK;APVS(1)PLK;APVS(1)PLK;APVS(1)PLK 95.502 0.014076 580470000 1615980 1749060 1432210 2007170 1059750 1694920 1599400 1751030 1096730 TRUE FALSE 1539595.828 1927291.203 1497878.245 1805405.458 1244570.064 1636224.495 1355382.155 1597700.53 1266805.287 1.215337387 1.521379191 1.182406058 1.425164133 0.982447798 1.29161483 1.069921454 1.261204501 1 20.27276336 2.75101786 24.99984429 1.134877308 1.345004375 0.378035865 0.136201056 754.0972608 1513360.695 0.037163958 0.039164636 563.6608353 -2.75101786 0.210127066 APVSGSRS(ph)PDREASGSGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 APVSGSRSPDREASGSGGR 19 2 Q8N5F7 Q8N5F7 NKAP NF-kappa-B-activating protein 1 APVS(0.09)GS(0.09)RS(0.672)PDREAS(0.105)GS(0.042)GGR;APVS(0.095)GS(0.095)RS(0.717)PDREAS(0.079)GS(0.014)GGR;APVS(0.049)GS(0.049)RS(0.592)PDREAS(0.241)GS(0.069)GGR;APVS(0.19)GS(0.19)RS(0.614)PDREAS(0.002)GS(0.003)GGR 97.825 0.00083042 344375000 143952.3 102639.2 157338 140007.8 194015 137274 187651 150281 222302 TRUE FALSE 137147.9601 113098.2512 164552.1029 125933.9499 227851.1546 132520.167 159021.3935 137121.599 256775.4588 0.534116308 0.440455843 0.640840459 0.490443871 0.887355652 0.516093585 0.61930137 0.534013646 1 17.9701478 -5 0.199697537 2.894228655 0.505931445 0.524329598 0.123833309 106.1856428 1.050015871 80.47411598 0.276681671 1.00E-05 5 -2.38829721 APVSGSRSPDREAS(ph)GSGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APVSGSRSPDREASGSGGR 19 2 Q8N5F7 Q8N5F7 NKAP NF-kappa-B-activating protein 1 APVS(0.026)GS(0.023)RS(0.335)PDREAS(0.479)GS(0.137)GGR 85.387 0.0023979 223480000 83438 48857 80596 70134 99145 67993 113270 85045 109910 TRUE FALSE 79494.0511 53835.58385 84291.40632 63083.99707 116435.8566 65638.38536 95988.58115 77598.00895 126954.2815 0.626162822 0.42405489 0.663950875 0.496903266 0.917147931 0.517023803 0.756087783 0.61122798 1 16.95394952 -4.999999995 0.122236735 2.285672125 0.432024789 0.446484222 0.135066503 121.4529851 0.956802532 38.30579507 1.085253067 1.00E-05 4.999999995 -1.853647336 APYFS(ph)GSSTFSPTILSSDKETIEIIDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 APYFSGSSTFSPTILSSDKETIEIIDLAK 29 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 APYFS(0.212)GS(0.212)S(0.196)T(0.181)FS(0.196)PT(0.003)ILSSDKETIEIIDLAK 87.893 0.0010973 10007000 15557 15099 14405 17513 11646 16984 17860 14422 14028 TRUE FALSE 14821.65144 16637.60527 15065.4835 15752.55997 13677.05871 16395.83982 15135.12898 13159.13322 16203.39059 0.914725307 1.026797766 0.929773519 0.972176772 0.84408622 1.011877096 0.934071723 0.8121222 1 13.98400811 AQAEAQQPTFDALRDELR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 274.68 4.38E-39 3867240000 2402670 2032920 2136060 2437100 2474030 2229820 2598940 2384310 2713930 FALSE TRUE 2289100.551 2240076.859 2234000.464 2192118.078 2905500.049 2152600.774 2202423.97 2175527.176 3134792.404 0.730223969 0.714585392 0.71264702 0.699286522 0.926855649 0.686680487 0.702574106 0.693994018 1 21.57993848 -1.22958407 4.893379921 1.000045623 0.731388633 0.588879351 0.070000243 3.28E-05 5.17E-06 0.063891754 0.015056877 0.058940787 1.22958407 -0.26865699 AQAGEGVRPSPMQLELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQAGEGVRPSPMQLELR 17 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;; 224.15 2.57E-15 1222700000 1033500 860684 847363 1004850 983310 807275 1105850 961670 1052780 FALSE TRUE 984648.5032 948388.6781 886215.4317 903840.5689 1154798.953 779318.8643 937132.2722 877461.0767 1216039.746 0.809717369 0.779899408 0.728771765 0.743265648 0.949639152 0.640866277 0.770642798 0.721572695 1 20.21375895 -1.78408227 4.150964317 1.029269307 0.769495591 0.463362424 0.078434398 0.020109235 0.001046007 0.071881706 0.016207756 0.016440603 1.78408227 -0.259773716 AQALDRDGNLVEDFVFDAGVGDIGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQALDRDGNLVEDFVFDAGVGDIGNR 26 1 Q9H9P8 Q9H9P8 L2HGDH "L-2-hydroxyglutarate dehydrogenase, mitochondrial" 0 133.95 3.96E-05 8942300 8815 6170 8688.9 8171.4 8602.9 6270.3 9385.3 7139.7 8856 FALSE TRUE 8398.33242 6798.730015 9087.294659 7349.995347 10103.24304 6053.157939 7953.400112 6514.510018 10229.34325 0.821004068 0.664630157 0.888355629 0.718520746 0.987672697 0.591744532 0.777508381 0.636845383 1 13.3204259 -2.139577926 2.451550251 1.530207102 0.758907785 0.286421099 0.118628379 6253519.096 1954284.942 18423699.42 0.025127122 0.007251404 2.139577926 -0.771299318 AQATGS(ph)PHTS(ph)PTHGGGRPMPMPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQATGSPHTSPTHGGGRPMPMPVR 24 1 E9PEY4;E7EVB6;O60941-5;O60941-6 E9PEY4 DTNB Dystrobrevin;Dystrobrevin beta 2 AQAT(0.443)GS(0.556)PHT(0.035)S(0.949)PT(0.018)HGGGRPMPMPVR;AQAT(0.458)GS(0.542)PHT(0.182)S(0.786)PT(0.033)HGGGRPMPMPVR 60.527 0.066972 79478000 36698 34495 36339 37688 43534 36640 45354 39793 28976 TRUE FALSE 34963.35827 38010.07972 38005.17909 33899.53064 51126.31582 35371.14761 38434.41432 36308.51396 33469.45009 1.044634978 1.135664901 1.13551848 1.012849944 1.527551713 1.056818905 1.148343167 1.084825531 1 15.03055723 0.935562688 1.788098101 1.000305753 1.147848205 0.107866503 0.142095263 1.013811563 6.695585014 0.125427883 0.035665179 8.621100109 -0.935562688 0.147542453 AQAVS(ph)EEEEEEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQAVSEEEEEEEGK 14 0 G3V529;Q9GZR7;Q9GZR7-2 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 AQAVS(1)EEEEEEEGK;AQAVS(1)EEEEEEEGK 257.02 2.60E-24 311620000 361670 497740 344510 479030 231140 432940 373100 428110 232680 TRUE FALSE 344574.5759 548460.2719 360306.1243 430876.9943 271450.7428 417947.1792 316176.7425 390622.4188 268762.826 1.28207677 2.040685016 1.34060997 1.603186723 1.010001074 1.555078079 1.176415456 1.453409404 1 18.03597408 3.113200557 1.959955521 1.27451621 1.640858796 0.224836346 0.271535078 0.415237976 3.264216575 0.081139689 0.102964517 1297.778447 -3.113200557 0.366342586 AQCPIVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQCPIVER 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 91.853 0.028365 115390000 98967 93684 72200 103260 107100 87161 102320 81616 122700 FALSE TRUE 94289.02604 103230.5061 75510.44142 92880.10862 125778.2061 84142.59271 86709.20476 74469.27037 141727.6893 0.665283026 0.72837218 0.532785384 0.655342009 0.887463887 0.593691981 0.611801442 0.525439106 1 17.11276212 -1.540736486 3.092112662 1.013044227 0.655884792 0.528331578 0.103790789 27257992.57 34847857.04 3018252.944 0.024947417 0.028791448 1.540736486 -0.357159436 AQCYMDTEQYEEAVRDYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQCYMDTEQYEEAVRDYEK 19 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PRZ0;Q99615-2 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 165.74 1.94E-11 167249000 93300 81421 101928 103827 87709 98232 122041 124353 113151 FALSE TRUE 88889.8939 89717.89247 106601.4996 93390.1127 103005.4218 94830.20121 103421.404 113463.9921 130697.8792 0.68011734 0.68645255 0.815632972 0.714549565 0.788118541 0.725568018 0.791301318 0.868139505 1 16.99587621 -4.999999998 0.104973601 1.866108089 0.580288156 0.819807797 0.040845738 65.54970092 0.462969123 12.11255749 0.556489605 1.00E-05 4.999999998 -1.285819933 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR 33 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 131.23 5.57E-08 295910000 98238 77654 79056 105742 92762 92005 98675 102442 110807 FALSE TRUE 93594.48443 85567.03089 82680.7958 95112.61326 108939.6634 88818.84378 83620.31646 93471.6354 127990.3836 0.731261848 0.668542655 0.645992249 0.74312312 0.851155066 0.693949352 0.653332806 0.730302018 1 16.96567589 0.95273164 22.93168083 1 0.708089748 0.701472701 0.058547525 2736.846517 1327750.352 0.057639837 0.014409959 8.968744249 -0.95273164 -0.291910252 AQDGSHPLSLQDLIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 173.37 4.24E-09 86930000 191330 180740 176940 201470 136660 185480 201690 209080 141360 FALSE TRUE 182286.2101 199157.6115 185052.874 181217.8528 160493.4607 179056.7811 170918.4862 190771.8468 163281.3868 1.116393078 1.219720235 1.133337226 1.109850035 0.982925634 1.096614774 1.046772627 1.168362485 1 17.31700082 3.188432644 2.830039314 1.062973441 1.167378718 0.374435716 0.057131463 0.240487626 3.929377532 0.015833947 0.020392503 1543.237058 -3.188432644 0.104405278 AQDITLPHLCSVLLAFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQDITLPHLCSVLLAFAR 18 0 Q969Z0;Q969Z0-2;H7C4R5 Q969Z0 TBRG4 Protein TBRG4 0 ; 192.55 1.69E-14 106062000 334831 296590 305150 297535 364890 266544 359122 327531 320650 FALSE TRUE 319004.2022 326812.8582 319141.4293 267626.2165 428526.7005 257313.5144 304331.3432 298850.6493 370374.7643 0.861301128 0.882384249 0.861671637 0.722582212 1.157008365 0.694738247 0.821684878 0.80688718 1 18.49862628 -0.34931125 7.53245465 1 0.850891957 0.124619571 0.124079015 0 0 0.106771603 0.025166308 0.447392552 0.34931125 -0.149108042 AQEDEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQEDEVKR 8 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ; 67.563 0.094237 145834000 192957 188497 180641 244504 186020 185448 228944 189655 221383 FALSE TRUE 183836.305 207705.0586 188923.5685 219925.9934 218461.8291 179025.8893 194014.388 173047.8028 255713.945 0.718913883 0.812255501 0.738808236 0.86004693 0.85432114 0.700102176 0.758716495 0.676724153 1 17.96417131 -2.351956127 2.333867207 2.540466246 0.767621684 0.58945694 0.061603226 2969806.791 445331.5621 24183897.74 0.014273859 0.004446762 2.351956127 -1.772844562 AQEEAERLEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AQEEAERLEADR 12 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 224.42 1.83E-11 9186820000 8975670 5852010 8088960 7900690 9907120 7277540 10211230 8472200 11135260 FALSE TRUE 8551407.867 6448336.472 8459846.817 7106497.631 11634918.59 7025516.965 8653319.321 7730329.254 12862059.25 0.664855269 0.501345574 0.657736576 0.552516319 0.904592209 0.54622023 0.672778686 0.60101801 1 23.6166183 -5 0.282905369 3.734908839 0.608292391 0.508315812 0.111087265 179.770403 1.713168238 289.2280339 0.113172984 1.00E-05 5 -3.126616448 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK 34 0 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2;E9PJ74;E9PRQ5 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ;; 230.11 3.99E-37 236587000 115559 86313 114626 127683 123271 111109 151585 133748 80449 FALSE TRUE 110096.7551 95108.39283 119881.7155 114848.0623 144769.4234 107261.2675 128457.9242 122036.3161 92924.62004 1.184796398 1.023500476 1.290096375 1.235927166 1.557923221 1.154282551 1.382388479 1.313282917 1 16.50377326 3.717813877 20.84920347 1.2993443 1.104148546 0.173546849 0.14971048 111.2211018 111770.3111 0.035178325 0.054639407 5221.723573 -3.717813877 -0.195195755 AQELGHSQSALASAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQELGHSQSALASAQR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 233.52 1.18E-19 558255000 374524 303786 334367 363980 396075 328055 418751 381770 464593 FALSE TRUE 356820.9928 334742.1388 349698.0577 327392.0389 465150.3546 316694.3731 354862.8441 348340.1949 536639.7096 0.664917237 0.623774448 0.65164402 0.610077922 0.86678333 0.590143382 0.661268329 0.649113714 1 19.03359429 -1.753821176 2.456408859 1.084051729 0.661700443 0.65950474 0.075684112 6215568.894 4339020.881 3161758.047 0.018552904 0.017627017 1.753821176 -0.422351286 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(ph)PHSHL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFT(0.006)ET(0.023)S(0.006)PT(0.021)S(0.07)APWDPLPGPPPVLPHS(0.849)PHS(0.025)HL 142.1 1.36E-14 52968000 12715 9397.4 11303 16489 19708 8776.6 16941 10904 1735.2 TRUE FALSE 12113.98715 10355.00574 11821.25373 14831.49439 23145.06896 8472.664141 14356.33931 9949.187954 2004.285954 6.044041333 5.166431329 5.897987614 7.399889404 11.54778784 4.227273122 7.162819896 4.963956333 1 10.96887264 3.463215265 23.32274449 6.541617114 5.593064875 0 2.689989413 467.7818375 784544.4741 0.681237358 0.92301225 2905.462437 -3.463215265 -0.948552239 AQEQQQQMAELHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQEQQQQMAELHSK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 162.76 4.39E-06 575470000 460831 435931 442224 534428 416279 483566 524312 513144 430073 FALSE TRUE 439048.4319 480352.8645 462500.4078 480706.2821 488877.9258 466819.9882 444318.5747 468210.391 496766.5243 0.883812436 0.966959006 0.931021688 0.967670442 0.984120108 0.939717081 0.894421329 0.942515987 1 18.92220843 AQEQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQEQSPR 7 0 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 AQEQS(1)PR;AQEQS(1)PR 129.63 0.0038206 259410000 304240 379030 336780 429050 329290 306460 370800 488150 486600 TRUE FALSE 289859.1781 417653.5879 352221.6961 385921.0789 386718.0717 295847.2134 314227.6498 445404.9982 562059.4428 0.515709116 0.743077255 0.626662714 0.686619687 0.688037674 0.526362856 0.5590648 0.792451766 1 19.10036319 0.983121148 4.248763865 0.999366967 0.623738125 0.743092614 0.073093148 0.093386397 5.159541913 0.071348703 0.018191773 9.618805602 -0.983121148 -0.375628841 AQFEGIVTDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQFEGIVTDLIR 12 0 P38646;H0YBG6 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 178.71 0.00029303 10571000 226604 157308 152165 149412 241237 133868 187350 169288 211407 FALSE TRUE 215892.878 173337.864 159141.9158 134392.8219 283308.6564 129232.1176 158766.3166 154464.2453 244190.9178 0.884115101 0.709845663 0.651711035 0.550359625 1.160193257 0.529225733 0.650172897 0.632555243 1 17.89765002 AQFSVAGVHTVPGS(ph)PQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AQFSVAGVHTVPGSPQAR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHT(0.002)VPGS(0.998)PQAR;AQFSVAGVHT(0.024)VPGS(0.976)PQAR 160.57 5.58E-10 2136460000 915170 847640 915110 1001140 1042480 863670 1076760 1014370 1085790 TRUE FALSE 871911.7278 934015.4797 957068.6987 900503.5052 1224288.182 833760.8913 912480.4859 925546.3853 1254168.768 0.695210844 0.744728703 0.763109976 0.718008236 0.976174988 0.664791624 0.727557973 0.737975948 1 20.25830007 -1.505552374 2.881472919 1.009397299 0.749462728 0.45985425 0.083878696 16250875.09 17802296.65 1206545.769 0.0196867 0.031221059 1.505552374 -0.259934571 AQGAGVTLPPT(ph)PSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQGAGVTLPPTPSGSR 16 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 AQGAGVTLPPT(0.823)PS(0.149)GS(0.027)R;AQGAGVTLPPT(0.999)PS(0.001)GSR 171.71 5.40E-08 173031000 205282 183709 202976 236350 247360 211780 259930 227061 284380 TRUE FALSE 195578.7267 202429.156 212282.6504 212591.649 290499.5057 204446.0055 220272.9046 207178.3351 328480.198 0.595404922 0.616259845 0.64625707 0.647197762 0.884374484 0.622399788 0.670581989 0.630717883 1 18.32544688 -5 0.248813096 3.023519565 0.62878076 0.62258149 0.081730777 119.6335204 1.186502893 123.2490622 0.116223234 1.00E-05 5 -2.394738805 AQGEPVAGHES(ph)PKIPYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;AQGEPVAGHES(1)PKIPYEK 232.87 6.68E-22 16285060000 13327040 10380310 10916620 12744700 6686720 13055330 13505790 13386580 6277940 TRUE FALSE 12697097.23 11438075.39 11417157.83 11463578.54 7852881.851 12603220.65 11445233.68 12214380.09 7251490.872 1.750963692 1.577341211 1.574456622 1.580858164 1.082933426 1.73801786 1.578328359 1.684395706 1 22.78984621 -1.719677721 2.669019519 0.897255558 1.575748114 0.4815377 0.186112145 16821401.48 13732830.55 11537608.65 0.042472859 0.019068752 1.719677721 0.678492556 AQGGQT(ph)QSPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.5)QS(0.5)PTK 168.76 0.00019772 37640000 130430 144230 121710 155670 75825 132840 124420 154640 102750 TRUE FALSE 124264.8324 158927.201 127290.5239 140021.7558 89048.85599 128239.7175 105437.4439 141098.9018 118683.9452 1.047023101 1.339079188 1.072516789 1.179786833 0.750302459 1.080514447 0.888388431 1.188862584 1 16.85676526 AQGGQTQS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.03)QS(0.962)PT(0.008)K;AQGGQT(0.068)QS(0.932)PTK;AQGGQT(0.026)QS(0.974)PTK;AQGGQT(0.004)QS(0.996)PTK;AQGGQT(0.033)QS(0.966)PT(0.001)K;AQGGQT(0.028)QS(0.972)PTK;AQGGQT(0.022)QS(0.977)PT(0.001)K;AQGGQT(0.032)QS(0.961)PT(0.007)K;AQGGQT(0.028)QS(0.958)PT(0.013)K 231.32 1.21E-12 2131525000 3995154 4371644 3705199 4740404 2558951 4194324 4182265 4808245 3354418 TRUE FALSE 3806310.988 4817119.494 3875086.039 4263889.584 3005231.244 4049073.508 3544183.662 4387209.578 3874604.011 0.982374193 1.24325466 1.000124407 1.10047106 0.775622808 1.045028988 0.914721518 1.132298827 1 21.88561744 AQGGQTQS(ph)PTKSHTPSPTSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQGGQTQSPTKSHTPSPTSPK 21 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.138)QS(0.853)PT(0.007)KS(0.002)HTPSPTSPK;AQGGQT(0.275)QS(0.721)PT(0.004)KSHTPSPTSPK 130.78 8.63E-06 228349000 280576 136752 312787 223924 226682 294261 464730 374297 326002 TRUE FALSE 267313.7285 150687.1843 327128.5933 201414.7341 266215.269 284070.6678 393826.9031 341521.5704 376556.7252 0.709889668 0.400171274 0.868736558 0.534885505 0.706972552 0.754390106 1.045863417 0.906959158 1 18.52250769 2.015198614 2.086557865 0.989866624 0.616304248 0.592931125 0.127140196 0.199813147 1.63065653 0.06688839 0.035670397 103.5615672 -2.015198614 -0.373562376 AQGPRPHQENNHQESYPLS(ph)VSPMENNHCPASSESHPKPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQES(0.002)Y(0.002)PLS(0.245)VS(0.245)PMENNHCPAS(0.245)S(0.245)ES(0.112)HPKPS(0.453)S(0.453)PR 49.366 0.016512 86411000 41536 38461 42569 53299 41588 46646 59757 47592 14762 TRUE FALSE 39572.6756 42380.21963 44520.83076 47941.28326 48840.93403 45030.63732 50639.97214 43424.59218 17051.21557 2.32081258 2.485466181 2.61100627 2.811605019 2.864366698 2.640904817 2.969874608 2.546715336 1 14.05758697 4.044234836 2.100093565 2.630184077 2.349068236 0 0.564680812 1.232343376 10.61908707 0.132890992 0.378631174 11072.2233 -4.044234836 -0.281115841 AQGVRS(ph)PLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AQGVRS(1)PLLR 142.77 2.13E-05 2856490000 2334750 1584260 1828720 1983460 2594160 1912320 2841020 2246350 2762980 TRUE FALSE 2224390.995 1745697.895 1912568.621 1784078.832 3046580.683 1846095.879 2407570.22 2049647.685 3191448.827 0.696984697 0.546992288 0.599279113 0.559018468 0.954607405 0.578450722 0.754381584 0.642231098 1 21.60578008 -5 0.177114582 2.376093556 0.588232862 0.44344903 0.119058036 115.8474485 1.109225663 55.92020976 0.352331549 1.00E-05 5 -1.787860693 AQHEDQVEQYKK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 229.75 4.84E-12 12661240000 8790590 6787340 7335900 8300350 5130670 8100240 9383300 8546090 5273330 FALSE TRUE 8375076.232 7478977.663 7672258.271 7465983.048 6025457.224 7819726.658 7951705.249 7797749.054 6091091.084 1.374971432 1.227855167 1.259586857 1.225721787 0.989224614 1.283797361 1.30546484 1.280189205 1 22.53826925 -2.31299208 1.933161428 3.37E-05 1.248273188 0.368794082 0.099868576 2180148.505 289046.1651 9496806.786 0.02559848 0.004864161 2.31299208 1.248239484 AQHQQALSSLELLNVLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQHQQALSSLELLNVLFR 18 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 95.954 0.0016826 39028000 33342 31076 31718 30037 39705 34632 51867 36834 36588 FALSE TRUE 31765.98974 34242.67973 33172.30167 27017.62369 46629.53943 33432.68516 43953.73655 33608.61969 42261.88017 0.751646392 0.810249795 0.784922524 0.639290623 1.10334749 0.791083715 1.040032681 0.795246675 1 15.36706933 2.746206523 24.99798553 0.943102166 0.759849599 0.464399174 0.105962745 511.5339023 1672439.924 0.02868973 0.029916222 557.450774 -2.746206523 -0.183252567 AQIEDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQIEDTLRR 9 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 111.06 0.003506 762700000 371500 276940 317490 350120 398850 309790 427040 361850 437820 FALSE TRUE 353939.9312 305160.5009 332047.2305 314925.2724 468409.3137 299061.8946 361887.2049 330164.4957 505714.8895 0.699880384 0.603423999 0.656589785 0.622732846 0.926232 0.591364622 0.715595313 0.652866867 1 18.94796473 -5 0.325933451 4.14010194 0.667271147 0.519836098 0.095085959 261.6172682 2.284028187 568.285301 0.074775274 1.00E-05 5 -3.472830794 AQIHDLVLVGGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 174.59 2.52E-06 2702060000 2752870 2463810 2396400 2664000 2743320 2344700 2831930 2522150 2683300 FALSE TRUE 2622747.291 2714875.04 2506277.31 2396209.659 3221754.139 2263502.451 2399867.067 2301297.175 3099412.46 0.846207894 0.875932157 0.808629811 0.773117386 1.039472539 0.730300494 0.774297419 0.742494652 1 21.56356333 AQKLPDLS(ph)PVENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQKLPDLSPVENK 13 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 AQKLPDLS(1)PVENK 190.24 2.77E-06 262770000 1468700 1205400 1164800 1465400 720460 1512900 1465200 1641900 883710 TRUE FALSE 1399277.462 1328231.63 1218207.232 1318095.208 846107.9959 1460507.894 1241656.83 1498126.532 1020751.233 1.370831027 1.301229513 1.193441842 1.291299158 0.82890715 1.430816683 1.216414724 1.467670557 1 19.96119988 3.991383558 2.19507195 1.214530584 1.357962068 0.08204618 0.186404833 0.795607055 7.536309032 0.0467494 0.121191331 9803.554295 -3.991383558 0.143431484 AQLADSFHLQQFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQLADSFHLQQFFR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 167.55 3.63E-06 95205000 289750 248710 195900 260500 274810 220780 298620 255530 252710 FALSE TRUE 276054.0917 274053.8318 204882.2088 234314.0451 322736.777 213134.3332 253060.0345 233154.4386 291898.9761 0.945717917 0.938865341 0.701894236 0.80272308 1.105645457 0.730164717 0.866943892 0.79875045 1 18.15510962 3.947551552 24.99924342 0.851075003 0.943149151 0.076667017 0.119811499 677.3014994 322831.7188 0.028503024 0.051384742 8862.404172 -3.947551552 0.092074148 AQLEPVAS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 183.81 5.44E-06 759230000 2951480 4018120 2681080 3513430 1853620 3143820 3120540 3446530 2330870 TRUE FALSE 2811969.39 4427570.996 2804010.17 3160253.341 2176890.741 3034948.725 2644444.31 3144733.562 2692329.415 1.044437346 1.644513101 1.041481089 1.173798913 0.808552894 1.127257574 0.982214247 1.16803447 1 21.36042351 3.60448684 17.27865312 1.03957593 1.344472781 0.334936877 0.176534296 1.747050317 232.3569841 0.043432549 0.067285431 4022.414667 -3.60448684 0.304896851 AQLGGPEAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQLGGPEAAK 10 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;; 123.63 0.0010634 179904000 535630 434340 432350 518510 354755 478800 531080 502210 375946 FALSE TRUE 510311.8314 478599.7398 452173.6752 466388.3897 416624.1597 462219.0359 450053.992 458233.83 434245.7856 1.175168184 1.102140206 1.04128512 1.074019381 0.959420157 1.064418012 1.036403822 1.055240707 1 18.72815232 4.123306192 1.137919538 1.031192514 1.184820089 0.678670787 0.032612029 0.356840524 0.723332295 0.009383192 0.050999357 13283.30646 -4.123306192 0.153627574 AQLGGPEAAKS(ph)DETAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(0.999)DET(0.001)AAK;AQLGGPEAAKS(1)DETAAK 235.99 2.16E-20 1376490000 988420 704330 762710 981420 407020 1014010 1013900 1019170 430480 TRUE FALSE 941699.3455 776102.0278 797681.0079 882765.797 478004.1591 978894.5794 859210.9334 929926.0718 497236.6398 1.893865556 1.560830328 1.604228136 1.775343421 0.961321272 1.968669444 1.727971884 1.870188151 1 18.92357308 4.590741948 2.625296839 1.600821546 1.911039992 0.076333009 0.337777692 0.976177539 10.88063876 0.076513488 0.574506181 38971.03569 -4.590741948 0.310218446 AQLGLGHSYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQLGLGHSYSR 11 0 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ; 127.17 0.00029214 271590000 308230 275830 246130 319570 351100 270360 322740 293930 329520 FALSE TRUE 293660.5788 303937.3906 257415.304 287446.2165 412331.7288 260997.3654 273500.0855 268191.931 380620.2786 0.771531616 0.798531785 0.676304754 0.755204682 1.083315188 0.68571587 0.718564146 0.704618083 1 18.5379929 -2.214492615 2.342187364 1.7191116 0.773884049 0.2710379 0.116362943 9295711.654 1655666.89 35495724.64 0.028099189 0.006102494 2.214492615 -0.94522755 AQLLHALS(ph)LDEGGPEPEPSLSDSSSGGSFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AQLLHALSLDEGGPEPEPSLSDSSSGGSFGR 31 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR 235.13 6.48E-46 1185137000 371421 313058.6 340361 411424 418126 376693 443923 351447.3 390704.8 TRUE FALSE 353864.6654 344959.6273 355966.8885 370066.8779 491047.042 363648.027 376194.3931 320672.7113 451293.3049 0.784112376 0.764380113 0.788770595 0.82001411 1.088088471 0.805790875 0.833591788 0.710563857 1 18.78370585 2.994158475 24.85331128 0.875743659 0.780121164 0.188437465 0.102644489 443.4516712 1886720.357 0.029053823 0.033678222 986.6394466 -2.994158475 -0.095622495 AQLS(ph)PGIYDDTSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR 283.22 2.04E-33 2021952000 1258406 1200645 1126791 1291632 1333381 1166964 1392729 1290792 1424719 TRUE FALSE 1198923.642 1322992.091 1178455.482 1161794.697 1565922.224 1126551.744 1180242.612 1177763.41 1645657.146 0.728537925 0.803929357 0.716100243 0.705976151 0.951548278 0.684560418 0.71718621 0.715679698 1 20.65023237 -1.031167235 4.293826148 1.00001661 0.753690266 0.503255162 0.077136482 9363780.575 2248722.595 1492.115939 0.016866588 0.09307494 1.031167235 -0.246326344 AQLSVQT(ph)SPVPTPDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AQLS(0.008)VQT(0.623)S(0.37)PVPTPDPK 103.79 0.01578 51104000 51381 46030 48856 51986 35622 49049 55059 58045 41386 TRUE FALSE 48952.32196 50720.50933 51096.09593 46760.26851 41834.46552 47350.42083 46658.73832 52962.27208 47803.92951 1.024022972 1.061011299 1.068868113 0.978167883 0.875126082 0.990513151 0.976043995 1.107906246 1 15.54484159 3.230015392 24.93586939 0.981103528 1.049484785 0.210808996 0.056712592 247.5759485 722452.4514 0.015937402 0.019337956 1698.303841 -3.230015392 0.068381257 AQLTFEYLHTNSTTHEFLFGALAELVDNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQLTFEYLHTNSTTHEFLFGALAELVDNAR 30 0 Q9Y6X9 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 0 107.76 0.00016078 45751000 30775 36779 38218 32282 31274 30043 37762 30873 22763 FALSE TRUE 29320.32674 40526.82191 39970.3331 29036.95203 36728.1757 29002.60338 32000.71335 28169.59645 26292.96978 1.115139407 1.541355817 1.520190889 1.104361823 1.39688198 1.103055441 1.217082498 1.071373705 1 14.68238948 1.761908526 0.723549768 1.014063437 1.35979122 0.376423313 0.151741727 0.675371794 0.697429494 0.133231179 0.064791011 57.79742977 -1.761908526 0.345727782 AQLYLPS(ph)TSPPHEGLDGFAQELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLY(0.006)LPS(0.331)T(0.331)S(0.331)PPHEGLDGFAQELSR;AQLY(0.001)LPS(0.43)T(0.324)S(0.245)PPHEGLDGFAQELSR 103.9 0.0020269 155315000 57614 61510 58121 63955 72033 59387 70949 62150 65686 TRUE FALSE 54890.7004 67777.93893 60785.90534 57526.12189 84595.53239 57330.4133 60124.42698 56707.81652 75872.2494 0.723462146 0.893316588 0.801161239 0.758197132 1.114973301 0.755617683 0.792442922 0.747411827 1 16.21128469 -2.484183478 2.229084594 3.108963988 0.824319114 0.193017148 0.11351542 3493001.909 410390.9574 37423617.75 0.025666813 0.003279567 2.484183478 -2.284644874 AQLYLPST(ph)SPPHEGLDGFAQELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLYLPS(0.081)T(0.459)S(0.459)PPHEGLDGFAQELSR 185.3 8.81E-17 155010000 89177 81751 80460 85573 100240 86254 93237 91321 91522 TRUE FALSE 84961.77994 90081.51984 84149.17059 76971.03946 117721.8243 83267.00235 79011.98324 83324.44912 105714.7643 0.803688874 0.852118627 0.796002064 0.728101131 1.113579782 0.787657267 0.747407268 0.78820068 1 16.68981735 2.650157681 0.012952443 1.668668011 3.32E-06 0.088232739 0.114763526 5247.801744 28.46965663 1772.853359 1891.917557 446.8458012 -2.650157681 -1.668664693 AQNDLIWNIKDELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQNDLIWNIKDELKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 161.14 9.39E-07 1706560000 1462370 1255640 1315260 1556970 818340 1574760 1670120 1537500 829430 FALSE TRUE 1393246.668 1383591.144 1375565.972 1400460.418 961058.2369 1520225.666 1415312.52 1402868.349 958053.7683 1.454246843 1.444168573 1.435792038 1.46177643 1.003136013 1.586785332 1.477278799 1.464289788 1 19.8697471 -2.014965468 2.508754194 0.539705139 1.422152788 0.421349153 0.15303018 7088337.679 2586766.294 18808299.41 0.035018235 0.009661277 2.014965468 0.882447649 AQNGRT(ph)PEDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQNGRTPEDER 11 1 A0A0A0MRJ2;Q5VTZ4;P18847-5;P18847 A0A0A0MRJ2 ATF3 Cyclic AMP-dependent transcription factor ATF-3 1 AQNGRT(1)PEDER;AQNGRT(1)PEDER;AQNGRT(1)PEDER 124.51 0.00056184 510720000 966870 894490 780260 1036900 835700 844550 855880 805990 732180 TRUE FALSE 921167.9713 985639.548 816035.6928 932668.842 981445.8154 815303.0217 725299.7867 735413.2428 845722.7349 1.089208003 1.165440525 0.964897429 1.10280687 1.160481769 0.964031104 0.857609423 0.869567782 1 19.68982524 2.066395832 4.915191092 0.896730462 1.098888946 0.634738456 0.066235986 0.113019011 5.321204453 0.024826393 0.017746825 116.5187541 -2.066395832 0.202158483 AQNGRT(ph)PEDERNLFIQQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQNGRTPEDERNLFIQQIK 19 2 A0A0A0MRJ2;Q5VTZ4;P18847-5;P18847 A0A0A0MRJ2 ATF3 Cyclic AMP-dependent transcription factor ATF-3 1 AQNGRT(1)PEDERNLFIQQIK;AQNGRT(1)PEDERNLFIQQIK;AQNGRT(1)PEDERNLFIQQIK;AQNGRT(1)PEDERNLFIQQIK 274.11 1.02E-37 1434690000 1752710 988620 1591110 1476930 1338980 1538190 1980600 1668690 1510910 TRUE FALSE 1669862.872 1089361.502 1664063.967 1328466.19 1572497.688 1484922.095 1678423.094 1522570.657 1745214.206 0.95682402 0.624199309 0.953501273 0.761205235 0.901034201 0.850853775 0.961728989 0.872426234 1 20.73497269 1.840970859 0.632557874 0.980201325 0.805632448 0.19458431 0.100612735 0.977789103 0.796194431 0.086212476 0.048408718 69.33792796 -1.840970859 -0.174568877 AQNTWGCGNSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 312.64 5.69E-46 1536100000 573931 425612 435376 462123 592700 471391 573400 531486 583110 FALSE TRUE 546802.4191 468982.3467 455338.4202 415669.5181 696066.6923 455066.6115 485917.2988 484946.2683 673535.7207 0.811838782 0.696299145 0.676041977 0.617145469 1.033451784 0.675638422 0.721442507 0.720000816 1 19.36139493 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.995)DT(0.005)DAEEERIPATPVVIPMK;AQPFGFIDS(0.985)DT(0.015)DAEEERIPATPVVIPMK;AQPFGFIDS(0.888)DT(0.112)DAEEERIPATPVVIPMK;AQPFGFIDS(0.966)DT(0.034)DAEEERIPATPVVIPMK;AQPFGFIDS(0.999)DT(0.001)DAEEERIPATPVVIPMK 256.93 8.66E-54 797555000 676610 635406 643845 769367 510183 633016 733484 687382 620830 TRUE FALSE 644627.9862 700154.5938 673365.9301 692028.7675 599158.7537 611094.4972 621577.5444 627191.188 717105.1456 0.898930917 0.976362529 0.939005855 0.9650311 0.83552427 0.852168613 0.866787176 0.874615378 1 19.45182514 2.747779887 24.74388145 0.874028176 0.944663695 0.247421293 0.048791184 604.2550739 1621777.663 0.013363868 0.014000437 559.4739714 -2.747779887 0.070635519 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQPFGFIDSDTDAEEERIPATPVVIPMKK 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.999)DT(0.001)DAEEERIPATPVVIPMKK 221.65 9.44E-35 212810000 133570 120700 143820 145400 129420 145540 163660 181800 152260 TRUE FALSE 127256.4108 132999.4672 150414.2893 130784.1158 151990.807 140499.9133 138690.6612 165880.6282 175871.7032 0.723575246 0.756230052 0.855250086 0.743633645 0.864214108 0.798877311 0.78858997 0.943191117 1 17.42416385 -4.999998704 0.083097148 1.719044114 0.593316972 0.691031388 0.049171573 127.7084734 0.747199327 16.36747866 1.399866802 1.00E-05 4.999998704 -1.125727142 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR 36 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 124.48 6.82E-09 37048000 21473 20606 15279 16387 26695 18032 22635 18652 1736.2 FALSE TRUE 20458.01385 22705.77483 15979.55726 14739.74763 31350.59955 17407.54732 19181.61503 17018.732 2005.441029 10.20125426 11.32208552 7.968101297 7.349878364 15.6327706 8.680159162 9.564786376 8.486278956 1 10.96970383 0.498225867 1.110879216 0.990949598 10.28751004 0.612354471 2.266165359 1.196328152 1.992785616 2.033181541 0.626956712 3.149385816 -0.498225867 9.296560444 AQPSMS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQPSMSPK 8 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 1 AQPS(0.131)MS(0.869)PK;AQPS(0.1)MS(0.9)PK;AQPS(0.049)MS(0.951)PK 101.38 0.021248 642680000 1613030 1479340 1354180 1627180 1009370 1653390 1803490 1789410 1178280 TRUE FALSE 1536785.269 1630086.428 1416270.492 1463612.775 1185403.808 1596132.69 1528334.477 1632719.774 1361001.645 1.12915754 1.197710844 1.04060895 1.075393833 0.870978968 1.172763234 1.122948296 1.199645703 1 20.37623738 3.738756068 24.99812103 1.075380975 1.163434192 0.148192935 0.093219588 32.70951292 4183451.994 0.024124212 0.040211555 5479.690984 -3.738756068 0.088053217 AQPYDPNFYDETYDYGGFTMMFDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 AQPYDPNFYDETYDYGGFTMMFDDRR 26 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;; 194.52 2.17E-18 3144494000 1113321 935067 1047936 1140724 1243113 1027166 1313025 1126144 1356387 FALSE TRUE 1060696.523 1030351.39 1095984.902 1026056.256 1459911.514 991594.9839 1112698.921 1027532.861 1566728.568 0.677013584 0.657645115 0.699537191 0.654903649 0.931821595 0.632907961 0.710205292 0.655846125 1 20.57932383 -2.155564783 2.456751879 1.723465219 0.699937267 0.548760589 0.084757851 11008053.94 1247900.823 44769014.59 0.019984173 0.006989325 2.155564783 -1.023527952 AQQELVPPQQQAS(ph)PPQLPK ddPTM_SK-BR-3_Trastuzumab_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 141.53 1.06E-07 489453000 1031060 890170 1073070 1076460 984270 1045390 1295360 1113150 1248350 TRUE FALSE 982323.8372 980879.335 1122271.321 968252.1957 1155926.376 1009187.882 1097729.041 1015676.685 1441937.742 0.681252601 0.680250822 0.778307751 0.67149376 0.801647909 0.699883117 0.761287404 0.704383175 1 20.45957744 -5 0.249854574 2.694324515 0.694701893 0.791684373 0.044707276 72.20146522 0.715531364 62.4739479 0.057338163 1.00E-05 5 -1.999622621 AQQLEQIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQQLEQIRR 9 1 Q9NPH2-2;Q9NPH2-3;Q9NPH2 Q9NPH2-2 ISYNA1 Inositol-3-phosphate synthase 1 0 83.869 0.025458 114050000 191370 187840 152120 173970 171210 182320 257960 187860 114610 FALSE TRUE 182324.3194 206981.1096 159094.8525 156482.2051 201068.9698 176006.2127 218603.4642 171409.9825 132383.1335 1.377247347 1.563500607 1.201775848 1.182040348 1.518841295 1.329521428 1.651293926 1.294802276 1 17.0143598 0.984376232 24.08332399 0.999999982 1.418753997 0.420923258 0.148264774 543.6604987 838029.822 0.141149394 0.035287348 9.646643561 -0.984376232 0.418754015 AQQMHTGPVLDVCWSDDGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQQMHTGPVLDVCWSDDGSK 20 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 216.44 1.13E-24 108800000 183360 173060 166030 201030 140000 192390 193990 206740 162590 FALSE TRUE 174692.9362 190695.0108 173642.6397 180822.0825 164415.9557 185727.4861 164393.2626 188636.7496 187803.6268 0.930189364 1.015395783 0.924596839 0.962825295 0.875467415 0.988945151 0.875346581 1.004436138 1 17.5188654 AQQNNVEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AQQNNVEHK 9 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;;;; 155.15 7.40E-05 2161896000 3815380 4106960 3072680 4496090 2398453 3474770 3645710 3835220 2586659 FALSE TRUE 3635034.549 4525463.893 3213565.417 4044134.491 2816742.444 3354437.844 3089489.981 3499387.805 2987784.867 1.216631957 1.514655203 1.075567874 1.35355612 0.942752765 1.122717328 1.034040307 1.171231518 1 21.51064484 3.127723479 1.389886108 1.063917343 1.345677917 0.375029409 0.135333305 0.349741847 1.412937945 0.044869403 0.060035152 1341.910276 -3.127723479 0.281760573 AQQNNVEHKVETFSGVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQQNNVEHKVETFSGVYK 18 1 P62081;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 287.54 2.98E-40 1473610000 2033730 1531180 1943330 2027620 1533840 2065620 2512860 2356840 1707300 FALSE TRUE 1937599.613 1687208.983 2032433.603 1823799.785 1801341.21 1994087.061 2129477.055 2150462.595 1972059.364 0.982526007 0.855556893 1.030614818 0.924819921 0.913431534 1.011169896 1.079824012 1.090465446 1 20.91127155 2.040499749 3.910782132 1.062607732 0.937056659 0.519843516 0.050893561 0.153004821 4.981876608 0.020356163 0.013537246 109.7740656 -2.040499749 -0.125551074 AQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYS(ph)PSTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEK 40 3 Q96F24-3;Q96F24 Q96F24-3 NRBF2 Nuclear receptor-binding factor 2 1 AQQNTDKDAAAHLQTSHKPSAEDAEGQSPLS(0.03)QKY(0.001)S(0.632)PS(0.153)T(0.184)EK 120.91 6.90E-09 103920000 148790 116830 127050 155040 64192 156520 141640 146910 13355 TRUE FALSE 141756.9916 128735.1098 132875.3682 139455.0846 75387.06448 151099.6732 120030.2166 134045.7816 15426.02519 9.189469731 8.345319564 8.613713936 9.040247433 4.887005145 9.795113859 7.781020393 8.689586586 1 13.91307875 -1.256522634 3.946531439 0.991522819 8.309042122 0.750130483 1.322721197 27210244.66 53716805.27 2852495.478 0.286833399 0.055395867 1.256522634 7.317519303 AQREPLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQREPLTR 8 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 108.98 0.0061038 0 31226 25764 33677 37611 32706 27651 36126 30556 41347 FALSE TRUE 29750.00886 28389.38089 35221.12376 33830.27082 38409.91604 26693.43894 30614.3152 27880.35465 47758.88159 0.62292097 0.594431443 0.737477985 0.708355592 0.804246556 0.558920939 0.641018261 0.58377319 1 15.54348143 -1.166363422 4.024880223 1.000145107 0.652043841 0.671539584 0.075466934 8763985.989 5079414.44 10973.92114 0.017627829 0.068176795 1.166363422 -0.348101266 AQS(ph)AYLQPGPAALEGSGLASAS(ph)SLSSLREPSLQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSAYLQPGPAALEGSGLASASSLSSLREPSLQPR 35 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 AQS(1)AYLQPGPAALEGS(0.003)GLAS(0.187)AS(0.491)S(0.308)LS(0.01)S(0.002)LREPSLQPR 197.72 1.18E-27 106420000 87509 61921 85777 93298 98684 84845 106230 80819 93266 TRUE FALSE 83372.623 68230.8203 89709.9603 83919.50779 115894.4584 81906.79638 90022.66245 73742.05991 107729.2149 0.77390913 0.633354846 0.832735673 0.778985606 1.075794142 0.760302546 0.835638341 0.68451311 1 16.71705002 3.633617919 6.375451977 0.846780053 0.704135683 0.216467364 0.11757913 0.323745255 16.78783489 0.029115028 0.045364308 4301.480113 -3.633617919 -0.14264437 AQS(ph)PGAVEEILDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQSPGAVEEILDR 13 0 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PHY4 H7BXT7 BET1L BET1-like protein 1 AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR 210.57 3.02E-08 211973000 337920 333610 291148 398673 316288 356845 388924 342329 301305 TRUE FALSE 321947.1913 367605.2383 304497.4238 358597.6326 371448.5271 344487.3682 329586.5007 312352.858 348029.8405 0.925056285 1.05624632 0.874917574 1.030364615 1.067289306 0.989821354 0.947006441 0.897488725 1 18.40885148 1.707418587 4.729265273 0.940965111 0.99327222 0.089909777 0.062242178 0.346238855 18.31665207 0.0313082 0.015421599 50.98220173 -1.707418587 0.052307109 AQS(ph)PVSGPNVAHLTDGATLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSPVSGPNVAHLTDGATLNDR 22 0 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 AQS(0.928)PVS(0.072)GPNVAHLTDGATLNDR 80.117 0.004413 138180000 83826 54537 64045 71809 99336 61861 73849 74600 74056 TRUE FALSE 79863.71111 60094.3823 66981.5266 64590.62289 116660.1669 59718.73806 62581.97872 68067.62852 85540.22625 0.933639232 0.702527746 0.783041261 0.755090625 1.363804751 0.698136312 0.731608758 0.795738233 1 16.3843154 -1.521900334 3.705238114 1.002800237 0.834549596 0.055215938 0.196366467 0.004380163 0.000565188 0.183342765 0.042519409 0.030067662 1.521900334 -0.168250641 AQS(ph)TDSLGTSGSLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQS(0.904)T(0.072)DS(0.024)LGTSGSLQSK 358.1 1.51E-87 122590000 313970 295610 275550 372080 204970 298660 315820 292740 227160 TRUE FALSE 299129.2603 325732.9951 288184.2401 334677.8115 240716.7031 288317.3293 267635.8586 267106.1337 262386.8126 1.14003161 1.241422889 1.098318308 1.27551308 0.917411591 1.098825533 1.020004991 1.017986121 1 18.00133569 2.741534417 24.99994005 1.020051972 1.187139324 0.647930536 0.06498857 155.3030092 1305593.312 0.017940997 0.018295182 551.4859049 -2.741534417 0.167087352 AQS(ph)YDIQAWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQSYDIQAWK 10 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 AQS(1)YDIQAWK;AQS(1)YDIQAWK 148.68 2.59E-05 259150000 720550 863970 673380 948960 557880 674600 705190 699030 502520 TRUE FALSE 686491.0295 952009.5253 704255.1391 853568.7379 655174.0954 651238.4328 597600.3138 637819.2274 580448.2351 1.182691217 1.640128211 1.213295341 1.470533781 1.128738199 1.121957814 1.029549713 1.098839119 1 19.14680789 2.619188659 4.213196159 1.069150921 1.389588787 0.567353604 0.131005506 0.158604478 4.715913826 0.041004876 0.038398843 416.091323 -2.619188659 0.320437866 AQS(ph)YPDNHQEFSDYDNPIFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AQSYPDNHQEFSDYDNPIFEK 21 0 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK 334.35 2.12E-80 654014000 717401 668628 684167 806171 602910 724840 830096 816509 617523 TRUE FALSE 683490.8765 736761.9534 715536.7337 725133.1595 708057.3131 699738.6091 703449.6094 745011.1434 713285.313 0.958229286 1.032913394 1.00315641 1.016610249 0.992670535 0.981008015 0.986210702 1.044478457 1 19.44411974 4.715783563 4.160498829 1.004519542 0.955495209 0.364685707 0.020007804 0.231782217 8.014799672 0.004717478 0.031822848 51973.69132 -4.715783563 -0.049024333 AQSDGIWGEHEIDYILLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQSDGIWGEHEIDYILLVR 19 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;;; 229.37 8.20E-20 213665000 277927 262272 266541 293956 293088 260127 295456 285926 239540 FALSE TRUE 264789.9415 288997.815 278762.1685 264406.9844 344202.4544 251118.7368 250378.7608 260888.8037 276686.6398 0.95700299 1.044495011 1.007501369 0.955618907 1.244015449 0.907592564 0.904918145 0.942903509 1 18.07789346 AQSEGRPCEYNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSEGRPCEYNSR 13 1 O00622 O00622 CYR61 Protein CYR61 0 123.76 0.00020036 43348000 36472 39857 38127 43790 40252 34130 36989 35746 37813 FALSE TRUE 34748.04084 43918.47361 39875.16066 39388.146 47271.93606 32948.06954 31345.6487 32615.89074 43676.84692 0.795571185 1.005532146 0.912958775 0.901808367 1.082311096 0.754360076 0.717671968 0.7467547 1 15.41458109 2.198279872 24.99996164 0.773408397 0.93259339 0.259902469 0.107169341 162.6573056 100951.1835 0.03683321 0.02720347 157.8628254 -2.198279872 0.159184993 AQSELAAHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AQSELAAHQK 10 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;;; 123.67 0.00045588 1107833000 2407140 2253410 1795480 2348060 1807050 2074390 2512490 2272690 1788840 FALSE TRUE 2293359.263 2483035.041 1877804.534 2112028.548 2122198.948 2002553.354 2129163.505 2073681.215 2066244.171 1.10991687 1.201714239 0.908800886 1.022158261 1.027080428 0.969175561 1.030451064 1.003599306 1 20.97857932 3.748519041 24.99992902 0.998574084 1.15581556 0.721977314 0.041565402 306.5048731 769456.9666 0.009911555 0.017606098 5604.269883 -3.748519041 0.157241476 AQSGSDS(ph)SPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGS(0.001)DS(0.693)S(0.306)PEPK;AQSGS(0.006)DS(0.806)S(0.189)PEPK 157.86 6.41E-05 185278000 915460 704740 774960 893470 531820 852260 947880 907130 625340 TRUE FALSE 872188.0201 776553.8072 810492.6825 803656.6981 624569.2396 822746.0225 803263.497 827696.8882 722314.5334 1.207490615 1.075090935 1.122077219 1.112613219 0.864677659 1.139041213 1.112068856 1.145895382 1 19.46226767 4.94036709 1.035033538 1.072964237 1.326447368 0.206071226 0.084188318 4.234078694 2.802798758 0.024513898 1.306598005 87170.00889 -4.94036709 0.253483131 AQSGSDSS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGSDS(0.245)S(0.755)PEPK;AQSGS(0.002)DS(0.262)S(0.736)PEPK;AQSGS(0.004)DS(0.272)S(0.724)PEPK 203.76 1.27E-07 364420000 1733070 1395780 1426240 1707660 1050390 1657930 1799170 1757150 1233130 TRUE FALSE 1651151.216 1538011.569 1491634.515 1536002.772 1233577.683 1600515.468 1524673.572 1603284.631 1424357.502 1.159225274 1.079793216 1.047233235 1.078382899 0.866059035 1.123675387 1.070428997 1.125619536 1 20.44187987 4.336232197 1.489053385 1.047260512 1.166291177 0.195261615 0.073494628 0.928082532 3.162610009 0.019682702 0.131300932 21688.63383 -4.336232197 0.119030665 AQSLLSTDREAS(ph)IDILHSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSLLSTDREASIDILHSIVK 21 1 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 AQS(0.213)LLS(0.324)T(0.059)DREAS(0.403)IDILHSIVK 65.901 0.014078 9442400 7753.7 5646 10103 7910.6 9773.7 9791.2 11928 9177.2 10199 TRUE FALSE 7387.197967 6221.333819 10566.23254 7115.411459 11478.23019 9452.128289 10108.16453 8373.595717 11780.60883 0.627064193 0.528099516 0.896917358 0.603993525 0.974332511 0.802346332 0.858034137 0.710794819 1 13.52412648 3.74162427 24.99648428 0.825622576 0.577581844 0.448030153 0.118508903 203.9559922 1664079.072 0.027255806 0.046612399 5516.000153 -3.74162427 -0.248040732 AQSLVISPPAPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQSLVISPPAPSPR 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AQSLVIS(0.005)PPAPS(0.995)PR 78.228 0.023565 64533000 147100 167340 157600 163000 160440 170590 175110 156380 122630 TRUE FALSE 140146.8745 184392.1362 164826.1159 146614.9303 188420.6852 164682.4255 148393.7534 142686.5382 141646.8341 0.989410568 1.301773791 1.163641369 1.035073825 1.330214589 1.162626942 1.047631981 1.007340115 1 17.11193883 1.650632075 3.588976643 1.010603347 1.167972488 0.315418127 0.102213011 0.227929723 6.927913065 0.058350612 0.02605189 44.73341719 -1.650632075 0.157369141 AQSNGSGNGS(ph)DSEMDTSSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AQSNGSGNGS(0.997)DS(0.003)EMDTSSLER;AQSNGSGNGS(1)DSEMDTSSLER;AQSNGSGNGS(0.999)DS(0.001)EMDTSSLER;AQSNGSGNGS(0.825)DS(0.175)EMDTSSLER 342.82 7.49E-81 417489000 491755 458043 485663 546477 499711 468326 569850 509070 585891 TRUE FALSE 468510.7157 504718.1025 507931.1289 491544.0937 586860.4402 452107.7532 482908.9165 464493.1321 676747.984 0.692297172 0.745799196 0.750546941 0.726332557 0.867177227 0.668059254 0.713572745 0.68636057 1 19.36825916 -1.478370897 3.755012453 1.002962329 0.730625177 0.704486995 0.054696829 263971695.2 36669717.81 6891577.029 0.012066682 0.033237558 1.478370897 -0.272337151 AQSTDS(ph)LGTSGSLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQSTDS(0.436)LGT(0.436)S(0.127)GSLQSK;AQSTDS(1)LGTSGSLQSK;AQSTDS(1)LGTSGSLQSK 387.29 2.58E-121 378640000 745200 799130 767430 876480 608820 821540 862840 939550 790570 TRUE FALSE 709975.8728 880562.2555 802617.4246 788374.5652 714998.0152 793089.8638 731197.9109 857278.0211 913167.5579 0.777486965 0.964294283 0.878937735 0.863340532 0.782986659 0.868504205 0.800726991 0.938795968 1 19.80052008 1.029148615 5.487264924 0.99970517 0.853040291 0.478124092 0.054569316 0.134470623 11.0161836 0.051918187 0.013091471 10.69420772 -1.029148615 -0.146664879 AQT(ph)PPGPSLSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AQTPPGPSLSGSK 13 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(1)PPGPSLSGSK;AQT(0.999)PPGPS(0.001)LSGSK;AQT(0.999)PPGPS(0.001)LSGSK;AQT(1)PPGPSLSGSK;AQT(1)PPGPSLSGSK 189.04 6.26E-05 3629600000 2600290 2324450 2110120 2593700 1516050 2509650 2643280 2520790 1689930 TRUE FALSE 2477379.445 2561314.098 2206871.089 2332976.348 1780448.64 2422740.191 2239999.089 2300056.264 1951995.713 1.269152093 1.312151497 1.130571688 1.195174934 0.912117085 1.24116061 1.147543037 1.1783101 1 20.89651845 3.732348327 22.9845522 1.125097014 1.290651804 0.361061034 0.09642573 153.520867 568007.693 0.023529064 0.037577494 5399.435122 -3.732348327 0.16555479 AQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(1)PPGPS(0.001)LS(0.007)GS(0.03)KS(0.962)PCPQEK;AQT(0.788)PPGPS(0.19)LS(0.032)GS(0.072)KS(0.917)PCPQEK 111.5 0.0003832 5189600000 4129100 3301700 3600500 3854300 2157340 4222300 4280100 4332700 2252390 TRUE FALSE 3933925.626 3638146.984 3765586.486 3466858.441 2533579.413 4076080.692 3627092.136 3953305.819 2601679.138 1.512071788 1.398384194 1.447367753 1.332546505 0.973824703 1.566711526 1.394135073 1.519520898 1 21.31101162 -1.390703603 3.170016939 0.995381465 1.395614651 0.361232422 0.164236199 35883651.09 49785699.14 1536466.874 0.038778955 0.040672081 1.390703603 0.400233186 AQTAPNKDVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQTAPNKDVQR 11 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 124.21 0.0003228 251193000 464930 282320 382360 379220 452080 395640 592750 440210 578520 FALSE TRUE 442953.6803 311088.729 399891.5842 341100.0851 530922.6089 381938.8876 502315.1009 401662.8787 668233.9269 0.662872181 0.465538663 0.598430532 0.510450115 0.794516093 0.571564646 0.751705474 0.601081242 1 19.34999371 -2.79011275 0.195144501 1.670148275 0.525860449 0.617190979 0.096149443 30.362196 0.65082602 8.731412137 0.239363407 0.001621389 2.79011275 -1.144287826 AQTAPTKTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPT(0.034)KT(0.239)S(0.727)PR;AQT(0.011)APT(0.044)KT(0.171)S(0.773)PR;AQTAPT(0.003)KT(0.021)S(0.976)PR;AQTAPT(0.004)KT(0.015)S(0.982)PR 97.69 0.0036814 2203780000 2560250 2170070 2376350 2561240 2060170 2557270 2988990 2586770 2347640 TRUE FALSE 2439232.056 2391202.6 2485307.998 2303779.289 2419462.996 2468711.099 2532964.679 2360258.705 2711700.021 0.899521347 0.881809412 0.916512881 0.849570111 0.892231064 0.910392403 0.934087347 0.870398159 1 21.37076616 -5 0.249495845 1.633543745 0.886515808 0.645962938 0.024310003 111.5175242 1.105457413 35.9760768 0.033328059 1.00E-05 5 -0.747027937 AQTEGINISEEALNHLGEIGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AQTEGINISEEALNHLGEIGTK 22 0 Q9Y265;H7C4G5;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 211.92 2.71E-23 41900000 93139 88119 88199 92937 73930 92647 114140 101050 89159 FALSE TRUE 88736.50405 97098.42628 92243.01139 83594.79619 86823.36859 89438.61116 96725.84668 92201.5263 102985.3224 0.861642242 0.942837523 0.895690855 0.811715634 0.843065464 0.868459787 0.93921973 0.895288029 1 16.65207921 0.792858048 0.951194473 0.998030761 0.878588426 0.495512525 0.038700296 0.803222441 1.397097011 0.039352284 0.013042268 6.206661324 -0.792858048 -0.119442335 AQTLPTSVVTITSESS(ph)PGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AQTLPTSVVTITSESSPGKR 20 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 AQTLPTSVVTITSES(0.301)S(0.699)PGKR;AQTLPTSVVTITSES(0.071)S(0.929)PGKR;AQTLPTSVVTITSES(0.057)S(0.943)PGKR;AQTLPTSVVTITSES(0.042)S(0.958)PGKR;AQTLPTSVVTITS(0.001)ES(0.202)S(0.798)PGKR 297.95 6.58E-55 2026480000 1217470 1174160 1226770 1346900 865573 1324950 1353990 1485230 1024890 TRUE FALSE 1159922.606 1293808.239 1283018.618 1211507.053 1016528.657 1279066.649 1147413.958 1355175.388 1183824.707 0.979809426 1.092905252 1.083791047 1.023383822 0.858681738 1.080452741 0.969243125 1.144743288 1 20.17502404 -1.247882556 3.560421512 0.99994486 1.026305818 0.011719412 0.080432025 3.25E-05 6.87E-06 0.071802387 0.016888526 0.056508977 1.247882556 0.026360958 AQTPPGPSLSGS(ph)KSPCPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQTPPGPS(0.005)LS(0.049)GS(0.694)KS(0.252)PCPQEK;AQTPPGPSLSGS(0.875)KS(0.125)PCPQEK 225.95 2.88E-25 3348080000 3887730 3395540 3508620 3849060 1981420 4118580 4150370 4190310 2419760 TRUE FALSE 3703964.708 3741549.386 3669493.697 3462145.176 2326979.021 3975952.542 3517154.83 3823384.242 2795004.022 1.325209079 1.338656172 1.312875999 1.238690588 0.832549435 1.422521224 1.25837201 1.367935148 1 21.41441893 -2.193871838 2.423945042 0.211408201 1.267240098 0.205933293 0.161467131 9480808.428 2987690.416 40752418.4 0.038336426 0.006399237 2.193871838 1.055831897 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQTPPGPSLSGS(0.009)KS(0.991)PCPQEK;AQTPPGPSLSGS(0.005)KS(0.995)PCPQEK;AQTPPGPSLSGS(0.001)KS(0.999)PCPQEK 241.84 5.60E-30 3953130000 3984830 3399500 3478130 4102560 2122880 4107100 4439250 4271330 2556220 TRUE FALSE 3796474.983 3745912.915 3637605.701 3690162.874 2493109.6 3964870.097 3761960.88 3897309.701 2952625.542 1.285796295 1.268671852 1.231990189 1.249790338 0.844370397 1.342828625 1.274107003 1.319947161 1 21.49356697 -2.306865616 2.067063433 2.88E-05 1.232104872 0.205517484 0.140083687 1587866.819 227902.2692 7413774.394 0.034884423 0.004933264 2.306865616 1.232076035 AQVADVVVSR ddPTM_SK-BR-3_Trastuzumab_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 ;; 147.74 6.13E-05 523628000 736858 752390 706538 853040 772680 729114 815740 788130 784290 FALSE TRUE 702028.1827 829059.3964 738933.4662 767290.7985 907435.1474 703864.5994 691283.8809 719117.1591 905913.6876 0.77493937 0.915163782 0.81567756 0.846980026 1.001679475 0.776966513 0.763079188 0.793803172 1 19.78901408 -0.034581533 7.800278222 0.999999999 0.836047837 0.329802686 0.073455592 3099269.439 397328.0535 0.070845928 0.017494155 0.923460806 0.034581533 -0.163952162 AQVARPGGDTIFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQVARPGGDTIFGK 14 1 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 163.23 3.93E-06 3202500000 3097100 2524700 2917000 3318200 2965000 3208600 3854400 3468000 3563900 FALSE TRUE 2950706.221 2781969.8 3050747.335 2984648.232 3482095.061 3097485.377 3266340.489 3164323.535 4116571.41 0.716787328 0.675797775 0.741089375 0.725032542 0.845872624 0.752443009 0.793461394 0.768679374 1 21.97301182 -4.999999999 0.132324453 1.867746559 0.642536889 0.825504566 0.037671963 52.36040841 0.434213272 11.9800189 0.256528077 1.00E-05 4.999999999 -1.22520967 AQVLATIHGHAGAFPAAGDAGEGAPGGGSS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.006)S(0.994)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.189)S(0.811)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.202)S(0.798)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.084)S(0.916)PER 152.95 2.34E-10 1380120000 678190 612150 692000 712040 793440 665330 789560 724450 165844 TRUE FALSE 646133.3027 674528.781 723728.8845 640464.3864 931815.6848 642289.4553 669098.1207 661013.3174 191562.2405 3.372967977 3.521199059 3.778035184 3.343374899 4.864297277 3.352902188 3.492849734 3.450645157 1 17.54745369 0.153198367 1.069043398 0.987287471 3.669442542 0.780322947 0.44352278 2.414116007 2.638150763 0.476613974 0.125090608 1.422978594 -0.153198367 2.682155071 AQVWLEQVCAHLGLGVQEPHPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQVWLEQVCAHLGLGVQEPHPGER 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ; 287.14 4.11E-53 204760000 111479 110911 110517 117072 122325 102232 136719 115435 59081.4 FALSE TRUE 106209.6086 122212.957 115584.3138 105303.7001 143658.4413 98691.68021 115860.0055 105326.8994 68243.44177 1.556334292 1.790838121 1.693705809 1.543059632 2.105087867 1.446170909 1.697745637 1.543399581 1 16.05840279 0.440757137 0.972524701 0.997323762 1.70222496 0.599841321 0.176647804 1.285704064 1.645554333 0.154864861 0.048492171 2.759034538 -0.440757137 0.704901198 AQYDELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;; 210.05 9.83E-05 49557840000 37179480 34261780 32233840 38133210 39013570 34122020 41738430 36283680 40381830 FALSE TRUE 35422079.66 37753094.33 33711793.45 34299987.28 45817524.26 32940365.89 35370465.92 33106488.63 46644037.95 0.759412804 0.809387351 0.722746034 0.735356302 0.9822804 0.706207424 0.758306259 0.709768924 1 25.47518935 -1.212537744 4.923756391 1.000025289 0.774801213 0.441448538 0.080244522 2.43E-05 3.88E-06 0.071626473 0.016880284 0.061300251 1.212537744 -0.225224076 AQYDELARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AQYDELARK 9 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 121.9 0.00096357 1632390000 2078650 548530 2231600 1058590 2582670 1757840 4167320 2308300 4641760 FALSE TRUE 1980396.334 604425.8306 2333921.067 952178.522 3033086.83 1696965.56 3531518.796 2106173.015 5361580.434 0.369368017 0.112732773 0.435304682 0.177592882 0.565707606 0.316504729 0.658671233 0.392826899 1 22.3542269 -0.032161705 0.248668811 1.255672821 0.183950574 0.671748132 0.14483399 3.63297851 0.365630389 1.081723459 0.248285524 0.92862056 0.032161705 -1.071722247 AQYSLPGILHFLQHEWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AQYSLPGILHFLQHEWAR 18 0 O43815-2;O43815 O43815-2 STRN Striatin 0 ; 101.67 0.00035994 26812000 74650 55303 31842 36763 85248 46576 94226 49803 24681 FALSE TRUE 71121.44244 60938.43857 33301.9872 33067.51339 100115.2242 44963.06144 79850.09312 45441.9853 28508.40343 2.494753613 2.137560552 1.168146343 1.159921617 3.511779412 1.577186234 2.800931779 1.593985627 1 14.79909962 ARAEEAEAQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARAEEAEAQKR 11 2 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 ;;; 71.888 0.026884 682192000 850352 640323 713013 773267 898373 713137 884154 795709 1008827 FALSE TRUE 810157.5462 705572.6417 745705.3513 695536.732 1055048.967 688440.8869 749260.0687 726032.5016 1165270.739 0.69525263 0.605501038 0.639941712 0.596888525 0.905411019 0.590799086 0.642992262 0.623059069 1 20.15223376 -1.552349123 2.956657122 1.016138077 0.659512914 0.573386263 0.091462646 21535766.95 24113332.3 2770896.501 0.020274391 0.028031793 1.552349123 -0.356625163 ARAHS(ph)HEEASRPAATSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARAHSHEEASRPAATSTR 18 2 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 ARAHS(0.999)HEEASRPAATSTR;ARAHS(0.999)HEEAS(0.001)RPAATSTR;ARAHS(1)HEEASRPAATSTR;ARAHS(1)HEEASRPAATSTR 71.527 0.011099 88537000 18205.7 17920.2 18678.5 17458.8 29579.1 14916.5 23175.9 17314.6 23146.5 TRUE FALSE 17345.15264 19746.28875 19534.9277 15703.80825 34737.68567 14399.93786 19639.9908 15798.44183 26735.941 0.648757889 0.738567188 0.730661685 0.587366955 1.299287939 0.538598505 0.734591343 0.590906519 1 14.70649283 4.024862711 1.06441772 0.77523512 0.655100047 0.038003246 0.224159799 3.198526057 5.867126407 0.069338699 0.332146324 10589.18927 -4.024862711 -0.120135073 ARASPSVTCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARASPSVTCK 10 1 O15014 O15014 ZNF609 Zinc finger protein 609 0 59.067 0.097589 3805300000 194730 198180 228210 171510 664900 116040 244280 106620 364090 FALSE TRUE 185525.4988 218374.7673 238673.6542 154269.489 780858.3495 112021.5057 207010.5995 97283.78757 420551.2177 0.441148405 0.519258435 0.567525771 0.366826875 1.856749705 0.266368283 0.492236357 0.23132447 1 18.68192199 ARDAAEFELFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARDAAEFELFFR 12 1 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;; 134.61 0.0001298 129449000 87638 58786 76643 66470 95312 74715 112149 94995 117852 FALSE TRUE 83495.52542 64776.36023 80157.15736 59788.30932 111934.3826 72127.60082 95038.61029 86676.7342 136127.8863 0.613360919 0.475849306 0.588837156 0.439206918 0.822273714 0.529851765 0.698156806 0.636730185 1 17.05460311 -1.794671492 0.227119491 1.435396466 0.512023268 0.619329859 0.102567636 16.50929316 0.607281467 4.067799653 0.181752113 0.016044586 1.794671492 -0.923373198 ARDCLIPMGITSENVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARDCLIPMGITSENVAER 18 1 P09110;C9JDE9;H0Y4D4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ;; 203.06 1.12E-15 448940000 287381 187749 258807 229037 333348 269257 362062 313607 440210 FALSE TRUE 273797.0697 206880.8366 270673.5569 206013.7656 391483.7857 259932.5626 306822.7922 286145.9085 508475.5185 0.538466573 0.406864891 0.532323676 0.405159655 0.769916685 0.511199759 0.60341704 0.562752577 1 18.95581879 -5 0.184347567 2.979592527 0.439652923 0.699189597 0.09695419 68.3053139 0.662449661 49.40884955 0.256211285 1.00E-05 5 -2.539939604 ARDDLITDLLNEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ARDDLITDLLNEAK 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ;;;;;; 288.12 2.76E-34 1286740000 2552267 2234427 2279911 2645427 1901897 2477494 2833876 2743321 2170806 FALSE TRUE 2431626.397 2462117.652 2384447.174 2379503.652 2233587.235 2391697.762 2401516.168 2503101.27 2507443.508 0.969763183 0.981923479 0.950947516 0.948975977 0.890782675 0.953839141 0.957754845 0.998268261 1 21.25778577 1.254622403 4.016893435 1.001005363 0.952788258 0.422249869 0.023579732 0.238569473 7.576520623 0.021811312 0.00649627 17.97307569 -1.254622403 -0.048217105 ARDYDAMGSQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARDYDAMGSQTK 12 1 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ;; 124.42 0.00029492 140227000 232244 155975 205657 194962 190237 207697 287839 225023 262748 FALSE TRUE 221266.2864 171869.0298 215086.5769 175364.0494 223414.2726 200504.4008 243923.874 205318.7932 303493.6179 0.729064051 0.566301957 0.708702141 0.577817914 0.736141584 0.660654422 0.803719945 0.676517663 1 18.21130665 -0.170047141 0.365102483 1.075085313 0.638853067 0.688633816 0.068361616 2.948622016 0.486783198 0.368959225 0.049653636 0.676009593 0.170047141 -0.436232245 AREEAERELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AREEAERELER 11 2 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 0 112.51 0.00085309 294750000 112650 105140 105250 163820 164160 131330 168040 189520 211070 FALSE TRUE 107325.2578 115853.8855 110075.8166 147352.5024 192789.452 126782.0092 142402.4117 172924.6241 243801.6576 0.440215455 0.475197284 0.451497409 0.604394998 0.7907635 0.520021112 0.584091237 0.709284038 1 17.89534841 -5 0.099910558 2.460624917 0.243143585 0.758477458 0.08586573 92.33578497 0.627837057 27.9349737 1.480576752 1.00E-05 5 -2.217481332 AREEEEQKEGGDGAAGDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AREEEEQKEGGDGAAGDPK 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 123.53 1.75E-05 1215480000 2542140 2362590 2325700 2940970 1219240 2882000 2564900 2917090 1188970 FALSE TRUE 2421978.08 2603340.607 2432335.645 2645338.108 1431875.07 2782195.617 2173577.397 2661654.135 1373349.395 1.763555646 1.895614194 1.771097475 1.926194541 1.042615284 2.025846902 1.582683478 1.938075004 1 20.38926728 -1.792725098 2.628017138 0.787735554 1.74406633 0.414909448 0.277361702 10702696.36 7749415.789 14528189 0.059806761 0.016116655 1.792725098 0.956330776 AREES(ph)WGPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 AREES(1)WGPPR;AREES(1)WGPPR;AREES(1)WGPPR 133.88 0.00011235 567120000 843568 671644 609000 716960 798770 719891 957980 818240 851900 TRUE FALSE 803694.2124 740085.2872 636923.2524 644889.8187 938075.2351 694960.9942 811822.5565 746590.5678 984008.3011 0.816755521 0.752112849 0.647274268 0.655370303 0.953320449 0.706255215 0.825015963 0.758723851 1 19.90831096 -1.346271894 0.361517765 1.144098122 0.750335097 0.418178193 0.088310314 20.60429346 1.652254951 2.875475251 0.063564091 0.045053455 1.346271894 -0.393763024 AREESWGPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 188.49 1.02E-06 577830000 389161 341259 373968 434730 643663 336660 439188 346425 623770 FALSE TRUE 370766.1308 376033.6801 391114.8027 391030.1145 755917.6234 325001.3798 372181.8044 316090.1905 720501.0658 0.51459484 0.521905793 0.54283723 0.542719689 1.049155455 0.45107689 0.516559686 0.438708845 1 19.45864104 -2.13034581 2.347574863 1.874954415 0.567508589 0.37501386 0.173470417 10953518.21 2991224.053 51026319.55 0.040610432 0.007407202 2.13034581 -1.307445826 AREETDKEEPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AREETDKEEPASK 13 2 P05455 P05455 SSB Lupus La protein 0 ;;;;;; 225.09 7.33E-12 3689810000 4503470 3987620 3966360 4855210 2632230 4971910 5191510 5309950 2884460 FALSE TRUE 4290599.898 4393963.012 4148221.529 4367155.067 3091290.079 4799731.51 4399449.801 4844982.628 3331767.325 1.287784974 1.318808483 1.245051387 1.310762319 0.927822917 1.440596249 1.320455293 1.454177965 1 21.66785622 ARENIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 122.13 0.0039863 728700000 685140 591370 593220 663160 514960 632920 761820 756760 680130 FALSE TRUE 652754.79 651631.2753 620419.7238 596497.8969 604768.861 611001.8217 645590.3672 690494.0826 785601.0868 0.830898532 0.829468399 0.789738882 0.759288533 0.769816732 0.777750734 0.821778862 0.87893728 1 19.5834374 0.933386055 1.817030103 0.999388459 0.797831138 0.886930444 0.023596642 0.157058088 1.073252856 0.026659759 0.007557794 8.578000257 -0.933386055 -0.201557322 AREQAEAEVASLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 294.97 1.25E-43 1187500000 839710 640650 761420 785750 815010 745200 911250 820150 938480 FALSE TRUE 800018.5724 705932.9634 796331.8601 706764.9172 957147.486 719393.5371 772222.0762 748333.3181 1084014.685 0.738014515 0.651220849 0.734613535 0.651988323 0.882965424 0.663638184 0.712372338 0.690335037 1 20.04795287 -1.792311163 2.763650863 1.076642257 0.712530322 0.639391108 0.067075843 14013141.85 10628744.02 7223240.449 0.015389167 0.016132023 1.792311163 -0.364111935 AREQAEAEVASLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AREQAEAEVASLNRR 15 2 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 159.18 1.00E-06 306100000 112270 60940 132580 85805 151040 100340 182610 140610 207640 FALSE TRUE 106963.2196 67149.85528 138658.9241 77179.71838 177381.3282 96865.20064 154749.4906 128297.443 239839.7507 0.445977863 0.279978006 0.578131539 0.321797026 0.739582691 0.403874672 0.645220361 0.534929855 1 17.87171126 -5 0.124765022 2.781895372 0.236381603 0.630850226 0.128996072 81.20206323 0.648500772 36.01343998 0.951008895 1.00E-05 5 -2.545513769 AREQEELLAPADGTVELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AREQEELLAPADGTVELVR 19 1 C9JGI3;P19971;A0A494C0L6 C9JGI3 TYMP Thymidine phosphorylase 0 ; 93.371 0.0016117 95436000 92649 70376 73608 85948 93956 74433 103931 83186 99403 FALSE TRUE 88269.66538 77547.39441 76982.99961 77308.34375 110341.8967 71855.36655 88074.41713 75901.79284 114817.9096 0.76877959 0.675394585 0.670479021 0.673312587 0.961016422 0.625820195 0.767079086 0.661062313 1 16.80898817 -1.901757587 2.498787692 1.155716563 0.725939176 0.45156253 0.095115175 8537345.771 4501919.926 7806822.853 0.020816683 0.012538408 1.901757587 -0.429777388 AREWDDWKDTHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AREWDDWKDTHPR 13 2 A0A1W2PR95;P78318 A0A1W2PR95 IGBP1 Immunoglobulin-binding protein 1 0 56.569 0.072765 57219000 134220 83035 110040 109860 99510 121580 149570 133940 118160 FALSE TRUE 127875.6866 91496.3609 115085.4428 98816.66408 116864.5125 117369.6541 126750.3495 122211.5035 136483.6493 0.936930447 0.670383312 0.843217802 0.724018332 0.856252841 0.859953956 0.928685231 0.895429629 1 17.0583686 1.795787459 0.968487299 0.969816448 0.791962477 0.428815103 0.073947858 0.477612979 0.831413473 0.059934415 0.02533685 62.48668119 -1.795787459 -0.177853971 ARFEELCSDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 237.07 3.91E-16 6688078000 5245944 3968748 3329285 3594506 5857019 3570950 6018786 4629485 6574783 FALSE TRUE 4997978.624 4373167.933 3481936.01 3233179.428 6878481.259 3447287.106 5100509.653 4224102.751 7594366.768 0.658116572 0.575843657 0.458489314 0.425733906 0.905734667 0.453926866 0.671617504 0.556215268 1 22.85649824 -5 0.384886598 6.956194333 0.5823887 0.462015024 0.139559511 546.4631819 4.018760162 2721.377644 0.083212565 1.00E-05 5 -6.373805633 ARFEELNADLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 209.25 5.24E-08 29550624000 20979715 15339732 13558122 14634861 22824458 14796246 23656608 18974507 25772538 FALSE TRUE 19988045.45 16902868.13 14179775.3 13163736.97 26805036.25 14283848.29 20047357.97 17312998.58 29769211.57 0.671433484 0.56779697 0.476323509 0.442193 0.900428155 0.479819503 0.673425896 0.581573971 1 24.82731768 -4.99997095 0.336431583 5.222278252 0.586286518 0.478451954 0.1317661 319.5338751 2.716391013 967.3615303 0.09789168 1.00E-05 4.99997095 -4.635991734 ARFFGS(ph)SQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARFFGSSQR 9 1 Q6ZVH7-3;Q6ZVH7-2;Q6ZVH7 Q6ZVH7-3 ESPNL Espin-like protein 1 ARFFGS(1)SQR;ARFFGS(1)SQR 83.456 0.042503 1098290000 65934 71736 67504 67313 117859 62787 78775 62585 87796 TRUE FALSE 62817.43049 79045.97996 70599.12517 60546.56935 138413.5723 60612.67045 66756.42695 57104.72562 101410.9553 0.619434363 0.77946194 0.696168624 0.597041702 1.364877906 0.597693516 0.658276285 0.563102137 1 16.62985399 5.145857782 0.966772177 0.770315059 0.408109628 0.040945228 0.241995905 16.36874173 7.138847457 0.071105901 7.446567937 139912.9078 -5.145857782 -0.36220543 ARFPAFEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARFPAFEL 8 1 O43813 O43813 LANCL1 LanC-like protein 1 0 95.352 0.079197 63840000 276060 208350 118650 134280 295840 158770 310290 227180 334300 FALSE TRUE 263011.1909 229581.1019 124090.2199 120781.9193 347434.4023 153271.7551 262949.5616 207286.9148 386141.5366 0.68112639 0.594551687 0.321359419 0.312791834 0.899759206 0.396931541 0.680966787 0.536815896 1 18.55877023 -0.870771123 0.531975651 1.112580809 0.54969973 0.380584112 0.179530772 18.72670223 3.462806158 3.619182664 0.076243102 0.134656982 0.870771123 -0.562881078 ARGDS(ph)EALDEES ddPTM_SK-BR-3_Trastuzumab_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 191.84 1.28E-05 4941001000 3192690 2624510 2852000 3329620 3054340 2951150 3486750 3020570 3018680 TRUE FALSE 3041777.871 2891950.553 2982767.021 2994920.272 3587015.929 2848950.936 2954782.249 2756072.878 3486801.477 0.872369101 0.829399257 0.855445038 0.858930539 1.028741083 0.817067147 0.847419123 0.790430111 1 21.7334728 -2.394111029 2.380710846 2.200370862 0.861655706 0.315972672 0.063580819 2814078.981 795782.3629 18621307.85 0.015087146 0.004035422 2.394111029 -1.338715156 ARHDS(ph)PDLAPNVTYSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR 254.87 9.18E-31 1427680000 518984 441231 491302 562430 553703 494884 597986 501876 505617 TRUE FALSE 494452.6548 486192.9405 513828.6827 505893.4679 650268.6279 477746.043 506752.2529 457929.0768 584025.502 0.846628534 0.832485806 0.879805215 0.866218112 1.113425057 0.818022572 0.86768857 0.784090892 1 19.15567184 ARHDT(ph)PDPS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARHDTPDPSPLR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 ARHDT(1)PDPS(1)PLR 98.281 0.010191 333180000 283700 264630 251390 316370 315490 275920 320580 263810 261490 TRUE FALSE 270290.0632 291596.0979 262916.4802 284567.8865 370511.3561 266364.8212 271669.6331 240709.3979 302040.5337 0.894880101 0.965420417 0.870467539 0.942151317 1.226694151 0.881884355 0.8994476 0.796944022 1 18.20438265 ARIEAENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARIEAENR 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 ; 95.502 0.0097348 174410000 261560 238710 226240 246000 278430 229220 312960 302700 383970 FALSE TRUE 249196.5772 263034.8204 236613.3278 221271.6126 326988.1038 221282.0539 265212.2041 276193.9833 443514.1066 0.561868435 0.593069795 0.533496735 0.498905467 0.737266524 0.49892901 0.597979185 0.622740019 1 18.75862047 0.460275634 1.556617601 1.000035597 0.573379133 0.796924912 0.067024984 1.293152328 3.304388847 0.057172496 0.01640442 2.885862497 -0.460275634 -0.426656464 ARIPS(ph)GK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARIPSGK 7 1 Q9NTM9;A0A0B4J226 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 1 ARIPS(1)GK;ARIPS(1)GK;ARIPS(1)GK;ARIPS(1)GK 81.338 0.016638 1488083000 2150280 1699580 1780060 1961430 1624990 1966040 2297180 2167440 1982820 TRUE FALSE 2048640.526 1872769.134 1861677.512 1764263.33 1908387.742 1897955.542 1946703 1977647.463 2290305.599 0.894483482 0.817693995 0.812851138 0.77031787 0.833245896 0.828690958 0.849975218 0.863486281 1 21.12710868 0.527978362 1.074767969 1.000158598 0.828303172 0.758326295 0.030269248 0.867025801 1.420706543 0.030524758 0.009512012 3.372705041 -0.527978362 -0.171855427 ARLEIEPEWAYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 155.43 3.57E-05 380530000 1054200 922220 880300 1040530 845660 938760 1115060 1085440 966830 FALSE TRUE 1004370.055 1016195.266 920662.6257 935933.9475 993142.8363 906250.5058 944937.1175 990393.1193 1116761.059 0.899359847 0.909948694 0.824404306 0.838078961 0.889306471 0.811499021 0.84614082 0.886844246 1 20.09088911 -1.346277322 7.544229534 1.000001583 0.864713978 0.627787969 0.033085987 9.53E-07 8.26E-08 0.034658133 0.008168905 0.045052892 1.346277322 -0.135287605 ARLS(ph)YSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.993)Y(0.001)S(0.006)DK;ARLS(0.998)YS(0.002)DK;ARLS(1)YSDK;ARLS(0.999)YS(0.001)DK;ARLS(0.997)YS(0.003)DK;ARLS(1)YSDK;ARLS(1)YSDK;ARLS(0.998)YS(0.002)DK;ARLS(0.997)YS(0.003)DK 186.24 0.00012629 12676110000 9606380 11379560 8056640 11708980 5932600 10441100 9133780 10360970 6470400 TRUE FALSE 9152305.455 12539150.1 8426044.913 10531971.08 6967243.562 10079522.09 7740254.108 9453708.54 7473796.586 1.224585838 1.677748378 1.127411593 1.40918621 0.932222798 1.34864817 1.035652231 1.264913813 1 22.83340987 3.279824821 1.659002181 1.139522323 1.434025236 0.240382999 0.192162035 0.411967233 2.343219824 0.056375501 0.08310227 1904.692276 -3.279824821 0.294502913 ARLS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.427)Y(0.142)S(0.427)DKNLIDS(0.004)MDQS(0.001)AFAGFSFVNPK;ARLS(0.472)Y(0.029)S(0.472)DKNLIDS(0.025)MDQS(0.001)AFAGFSFVNPK;ARLS(0.74)YS(0.253)DKNLIDS(0.007)MDQSAFAGFSFVNPK;ARLS(0.5)YS(0.5)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.294)Y(0.273)S(0.294)DKNLIDS(0.069)MDQS(0.069)AFAGFS(0.001)FVNPK;ARLS(0.993)YS(0.005)DKNLIDS(0.002)MDQSAFAGFSFVNPK;ARLS(0.886)YS(0.114)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.499)Y(0.002)S(0.499)DKNLIDS(0.001)MDQSAFAGFSFVNPK;ARLS(0.497)Y(0.002)S(0.497)DKNLIDS(0.004)MDQSAFAGFSFVNPK 288.7 1.94E-63 8909638000 3921587 3122386 3957708 4022328 2662407 4077218 4813754 4684773 3727786 TRUE FALSE 3736221.354 3440560.683 4139172.827 3617995.948 3126729.938 3936022.918 4079327.417 4274549.441 4305872.014 0.867703764 0.799039236 0.961285615 0.840246978 0.726154871 0.914105878 0.947387057 0.992725614 1 22.03787401 1.79293442 2.539891898 0.98505123 0.841505429 0.526131098 0.060507185 0.213258755 2.663330313 0.035117439 0.016450523 62.07752885 -1.79293442 -0.143545801 ARLSYS(ph)DKNLIDSMDQSAFAGFS(ph)FVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 2 ARLS(0.392)Y(0.111)S(0.47)DKNLIDS(0.025)MDQS(0.005)AFAGFS(0.998)FVNPK 66.479 0.0074999 28869000 33436 16153 40015 37958 33760 61655 70540 40886 38841 TRUE FALSE 31855.54654 17799.00906 41849.72733 34142.38972 39647.73331 59519.87189 59777.82744 37305.80509 44864.26391 0.710042777 0.396730215 0.932807622 0.761015266 0.883726375 1.326665517 1.332415206 0.831526071 1 15.45327912 2.902296168 1.203430532 1.166213738 0.586743049 0.478848064 0.200337876 0.310637081 0.942741136 0.086506843 0.094683483 798.5390665 -2.902296168 -0.579470689 ARLSYS(ph)DKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.4)Y(0.001)S(0.496)DKNLIDS(0.04)MDQS(0.045)AFAGFS(0.017)FVNPK 51.868 0.06809 1119700000 171220 149410 171160 180540 104330 181760 192390 186510 137140 TRUE FALSE 163126.7699 164635.0489 179007.8553 162391.7762 122525.119 175465.6056 163037.372 170178.1956 158406.9708 1.029795401 1.039316945 1.130050366 1.025155493 0.773483126 1.107688663 1.029231045 1.074310018 1 17.2732763 -0.22752897 6.635723276 0.999989751 1.026889656 0.007134776 0.09649729 0 0 0.088112395 0.020768291 0.592203582 0.22752897 0.026899905 ARNDEYENLFNMIVEIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARNDEYENLFNMIVEIPR 18 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;D6RGV9;D6RGI1;D6RAD3 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;; 249.86 8.41E-25 153694000 195001 140295 187352 170918 175040 177896 183647 179927 191863 FALSE TRUE 185783.6892 154591.22 195942.2745 153736.9979 205566.9206 171735.4169 155628.2772 164171.638 221616.1341 0.838313013 0.697563021 0.884151667 0.693708509 0.927581024 0.774922898 0.702242541 0.740792807 1 17.75770339 -1.076162044 4.426385176 1.000016787 0.776960373 0.41881831 0.08032608 9957728.007 2420966.197 1749.607997 0.017209859 0.083914682 1.076162044 -0.223056414 ARNS(ph)GTQS(ph)DGEEKQPGLVMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 2 ARNS(0.991)GT(0.009)QS(1)DGEEKQPGLVMER;ARNS(0.992)GT(0.03)QS(0.978)DGEEKQPGLVMER;ARNS(0.932)GT(0.135)QS(0.932)DGEEKQPGLVMER 137.5 8.53E-06 833280000 1446320 1367900 1283340 1516310 996510 1525210 1717240 1554720 1041730 TRUE FALSE 1377955.32 1507290.565 1342182.408 1363887.638 1170301.028 1472391.595 1455243.499 1418580.475 1203276.168 1.145169627 1.252655546 1.115440033 1.133478477 0.972595535 1.223652254 1.209401081 1.178931747 1 20.19853637 3.716940463 24.66828636 1.133290478 1.198912597 0.114525054 0.08545675 1480.163407 1688845.879 0.022589825 0.035038991 5211.232664 -3.716940463 0.065622119 ARNS(ph)GTQSDGEEKQPGLVMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.81)GT(0.188)QS(0.002)DGEEKQPGLVMER;ARNS(0.726)GT(0.274)QSDGEEKQPGLVMER;ARNS(0.856)GT(0.144)QSDGEEKQPGLVMER;ARNS(0.966)GT(0.034)QSDGEEKQPGLVMER;ARNS(1)GTQSDGEEKQPGLVMER;ARNS(0.878)GT(0.122)QSDGEEKQPGLVMER 226.89 1.18E-25 3980770000 1451476 1199561 1374639 1500908 1137281 1399233 1685267 1562941 1312973 TRUE FALSE 1382867.606 1321797.63 1437667.558 1350033.876 1335622.446 1350777.21 1428148.567 1426081.6 1516582.147 0.911831653 0.87156349 0.947965503 0.890181833 0.880679262 0.890671971 0.941688896 0.940325984 1 20.53239221 1.09674445 1.127229045 0.997714473 0.897658646 0.667992702 0.022538982 0.268191226 0.713699966 0.020100292 0.006478625 12.49523563 -1.09674445 -0.100055827 ARNSGT(ph)QSDGEEKQPGLVMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.344)GT(0.656)QS(0.001)DGEEKQPGLVMER 110.68 0.00035749 203890000 77317 64076 75218 94333 84451 73100 77020 87281 106960 TRUE FALSE 73662.37864 70605.41725 78666.8197 84850.46762 99179.22766 70568.52867 65269.18443 79638.21293 123546.8105 0.596230516 0.571487171 0.636736953 0.686788006 0.802766395 0.571188591 0.528295179 0.644599505 1 16.91469824 -1.241235128 2.312043629 1.006684355 0.620139011 0.697836314 0.076331602 182288.9442 182679.5229 8624.586855 0.020946729 0.057380572 1.241235128 -0.386545344 ARPATDS(ph)FDDYPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ARPAT(0.014)DS(0.986)FDDYPPR;ARPAT(0.125)DS(0.875)FDDYPPR;ARPAT(0.034)DS(0.966)FDDYPPR;ARPAT(0.013)DS(0.987)FDDYPPR;ARPAT(0.047)DS(0.953)FDDYPPR 139.04 7.19E-06 326260000 1064910 846526 942728 1445600 1011540 1432940 1548520 974232 1008350 TRUE FALSE 1014573.815 932787.9618 985953.0113 1300285.542 1187952.256 1383316.928 1312264.833 888923.0814 1164719.768 0.871088345 0.800869005 0.846515221 1.116393468 1.019946848 1.187682193 1.126678596 0.763207688 1 20.15155145 3.250506043 23.75742536 1.057267854 0.83572852 0.383682942 0.115010773 104.6241238 208077.2149 0.030446813 0.040865186 1780.352681 -3.250506043 -0.221539334 ARPATDSFDDYPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 125.22 8.44E-05 360000000 341120 276480 287600 344390 333490 300120 385300 345470 401490 FALSE TRUE 324995.9336 304653.6263 300786.7445 309771.2629 391650.5504 289726.7691 326515.4085 315218.8153 463751.0187 0.700798318 0.6569336 0.648595329 0.667968911 0.844527634 0.624746378 0.704074806 0.679715629 1 18.82299093 -1.931001326 2.182513499 1.219683348 0.689246586 0.727079809 0.059503534 2629781.674 1126221.733 2942682.873 0.014182003 0.011721918 1.931001326 -0.530436762 ARPDAEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARPDAEKK 8 2 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 100.02 0.003601 1020400000 3061440 2576120 2596140 2931790 2038430 3092150 3751180 3411840 2734690 FALSE TRUE 2916731.798 2838629.557 2715175.587 2637080.899 2393931.547 2985068.07 3178868.596 3113081.202 3158771.758 0.923375293 0.898649784 0.859566881 0.834843762 0.757867845 0.945009104 1.006362232 0.985535341 1 21.59093227 2.009065625 24.98984112 0.992426009 0.865120745 0.691158409 0.043802054 129.4476416 356827.184 0.018088572 0.0133405 102.1093767 -2.009065625 -0.127305263 ARPEDVISEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARPEDVISEGR 11 1 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 ;;; 176.87 7.51E-06 461013000 661091 523593 566114 637133 709864 543086 661081 612688 769876 FALSE TRUE 629842.5386 576947.722 592070.8869 573087.1804 833664.0568 524278.7956 560220.9519 559037.7907 889264.4381 0.708273615 0.648792077 0.665798453 0.644450802 0.937475987 0.589564558 0.629982408 0.628651914 1 19.76225297 -0.970205782 4.306662758 1.000011154 0.678581139 0.520598643 0.095976019 8134957.685 5667662.64 793.7496076 0.02121783 0.107101171 0.970205782 -0.321430014 ARPELEELLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARPELEELLAK 11 1 F5H8D0;Q96GC5-3;Q96GC5;F5H702 F5H8D0 MRPL48 "39S ribosomal protein L48, mitochondrial" 0 116.24 0.00084518 0 98588 78766 79238 83770 80897 73558 88601 90964 81829 FALSE TRUE 93927.94062 86792.34495 82871.14068 75349.28045 95005.41119 71010.66802 75083.29018 82998.70993 94518.6234 0.99375062 0.918256549 0.8767705 0.797189778 1.005150179 0.751287582 0.794375621 0.878120173 1 16.528311 4.142661531 1.199310962 0.852121302 1.001760168 0.152655674 0.08360106 0.898994987 2.049200332 0.024061681 0.129598023 13888.6979 -4.142661531 0.149638866 ARPEYMLPVHFYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARPEYMLPVHFYGR 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 174.83 1.49E-06 3067900000 2109290 1739470 1598330 1921590 2401330 1756990 2337740 2074490 2174250 FALSE TRUE 2009588.042 1916723.971 1671615.011 1728428.122 2820121.192 1696144.996 1981074.827 1892836.658 2511421.585 0.800179489 0.763202794 0.665605098 0.688226992 1.122918274 0.675372469 0.788826073 0.753691323 1 21.2600728 ARPFPDGLAEDIDKGEVSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 255.98 2.01E-36 5129760000 3602940 3219483 3232893 3849520 2892272 3756879 4305130 3968350 3284663 FALSE TRUE 3432636.167 3547551.978 3381124.342 3462558.936 3396683.321 3626777.338 3648303.349 3620860.236 3794031.762 0.904746291 0.935034865 0.891169224 0.912633091 0.895270133 0.955916441 0.961590091 0.954356859 1 21.85530033 2.137454948 5.322234706 0.965479621 0.910782332 0.754964051 0.01703406 0.10851282 4.766190307 0.006130149 0.004490405 137.2318593 -2.137454948 -0.054697289 ARPPS(ph)GSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(0.875)GS(0.039)S(0.086)K;ARPPS(0.97)GS(0.026)S(0.003)K 89.356 0.031995 256855000 305266 284715 280710 312670 208125 296200 353750 314030 279640 TRUE FALSE 290836.6812 313727.7822 293580.8312 281239.8176 244421.9341 285942.5197 299778.9404 286531.8684 323005.143 0.900408825 0.971277978 0.90890451 0.870697646 0.756712205 0.885256863 0.928093397 0.887081443 1 18.30119761 -0.459026114 6.305637568 1.000000037 0.895121759 0.283572039 0.054793066 7587788.359 1203333.695 0.056322386 0.013660185 0.347515265 0.459026114 -0.104878278 ARPPSEGEFIDCFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARPPSEGEFIDCFQK 15 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 124.43 8.81E-05 637970000 235921 253649 201552 271347 192341 223380 241933 252440 232885 FALSE TRUE 224769.4819 279496.1215 210793.3586 244070.684 225885.2095 215644.2946 205021.6774 230335.0153 268999.6164 0.835575474 1.039020521 0.783619551 0.907327257 0.839723166 0.801652796 0.762163457 0.856265219 1 18.03724459 3.719802496 24.98315286 0.834892024 0.937298016 0.139966834 0.083470402 1044.648792 1391323.801 0.020687677 0.032108305 5245.688478 -3.719802496 0.102405992 ARPPSGS(ph)SK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(0.274)GS(0.638)S(0.088)K 55.232 0.078632 202000000 132430 107220 122410 131890 98140 119630 155120 136930 121520 TRUE FALSE 126170.2964 118145.8399 128022.6196 118632.1666 115255.5849 115487.1831 131453.595 124939.6833 140364.701 0.898874827 0.841706206 0.912071331 0.845170943 0.821115167 0.822765142 0.936514623 0.890107573 1 17.09882065 0.91295962 1.079110422 0.996924213 0.861682846 0.572832078 0.036613582 0.443688606 1.050044152 0.033651603 0.01079256 8.183886922 -0.91295962 -0.135241368 ARPS(ph)AHSPGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARPSAHSPGKK 11 2 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ARPS(0.667)AHS(0.333)PGKK 63.212 0.039691 52078000 76834 72881 67244 87369 49313 73744 78550 83913 62280 TRUE FALSE 73202.20909 80307.65676 70327.20391 78586.50213 57913.17159 71190.22679 66565.75483 76565.13287 71938.06432 1.017572683 1.116344421 0.977607677 1.092418914 0.805042117 0.989604425 0.92532035 1.06432017 1 16.13446772 ARPTILSSGLPEEPDQNLS(ph)SPEEVFHSGHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARPTILSSGLPEEPDQNLSSPEEVFHSGHSR 31 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 ARPTILSSGLPEEPDQNLS(0.497)S(0.497)PEEVFHS(0.003)GHS(0.003)R 52.345 0.041728 69452000 15066 10158 14014 15543 24989 14648 19006 14576 23678 TRUE FALSE 14353.86004 11193.11175 14656.55576 13980.58811 29347.07369 14140.73609 16106.28563 13299.64817 27349.86331 0.524823831 0.409256588 0.535891372 0.511175795 1.07302451 0.517031326 0.588898213 0.486278415 1 14.739246 2.967515631 24.99895485 0.691384509 0.48339983 0.259764884 0.192594025 961.5948806 740013.5926 0.055509542 0.058922061 927.9308869 -2.967515631 -0.207984678 ARQEEGADAS(ph)EEDPTPAGEEDVKDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARQEEGADASEEDPTPAGEEDVKDAR 26 2 E5RHA3;Q86X53;H0YB25 E5RHA3 ERICH1 Glutamate-rich protein 1 1 ARQEEGADAS(1)EEDPTPAGEEDVKDAR 75.343 0.0128 97790000 95645 89619 80806 95434 73572 113670 105040 105120 60747 TRUE FALSE 91124.0504 98751.27799 84511.03503 85840.79301 86402.93351 109733.5794 89014.21881 95915.13552 70167.33451 1.298667693 1.407368239 1.20442134 1.223372579 1.231384007 1.563884109 1.26859912 1.366948541 1 16.09851194 -1.282647247 3.953031106 0.999525988 1.324718858 0.469429496 0.107028723 7828197.899 2540099.124 31786.33981 0.023692595 0.052161822 1.282647247 0.32519287 ARQEELYSELQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 246.64 3.07E-17 1202820000 483670 466340 462210 477580 834350 435250 534290 529490 664000 FALSE TRUE 460807.8776 513860.5762 483402.7857 429572.7511 979860.3758 420177.1834 452774.2476 483125.0486 766969.7288 0.600816252 0.66998808 0.630276225 0.560090881 1.277573728 0.547840635 0.590341744 0.629914103 1 19.54881011 -2.386411919 2.03093513 2.946578806 0.680491042 0.173722081 0.212985376 6127617.667 605893.5817 54742211.77 0.050198655 0.004107599 2.386411919 -2.266087764 ARQEFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARQEFEER 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 60.892 0.081553 129110000 66701 50690 50913 62638 278020 63293 59623 67790 92837 FALSE TRUE 63548.17592 55855.36863 53247.41141 56341.50924 326506.6 61101.14754 50526.4163 61853.94822 107233.6878 0.592613918 0.5208752 0.496554884 0.525408669 3.044813683 0.569794332 0.471180441 0.576814521 1 16.71039868 2.907315255 22.00940258 1.079516867 0.535638161 0.141229692 0.726982768 47.14915393 11189.61284 0.223595803 0.237159469 807.8212162 -2.907315255 -0.543878706 ARQPLSEASNQQPLS(ph)GGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARQPLSEASNQQPLSGGEEK 20 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEASNQQPLS(1)GGEEK 158.29 1.65E-11 439020000 418790 400910 416470 491940 318180 540870 576130 546950 403080 TRUE FALSE 398994.6267 441763.1848 435565.5614 442489.2566 373670.4913 522139.5363 488230.7871 499056.1584 465587.5878 0.856970068 0.948829386 0.935517984 0.95038886 0.802578293 1.121463609 1.048633598 1.071884585 1 18.82869307 2.228045341 24.99999983 1.064875807 0.905872217 0.693721317 0.053219685 112.7276151 268007.1876 0.018314384 0.01366755 169.0617427 -2.228045341 -0.15900359 ARQPQS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARQPQSPPR 9 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 ARQPQS(1)PPR;ARQPQS(1)PPR;ARQPQS(1)PPR 116.84 0.00075645 126616000 170253 154573 135152 143273 157422 130738 169988 166213 201543 TRUE FALSE 162205.4781 170324.1644 141348.8529 128870.9258 184876.347 126210.5103 144053.2086 151658.5086 232797.2591 0.69676713 0.731641623 0.607175761 0.553575787 0.794151734 0.54214775 0.618792546 0.651461745 1 17.82871455 -0.604771513 7.092714083 1 0.652519656 0.671298223 0.077060094 0 0 0.072797446 0.017158522 0.248443985 0.604771513 -0.347480344 ARS(ph)DPTHQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARSDPTHQHR 10 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 ARS(0.999)DPT(0.001)HQHR;ARS(0.999)DPT(0.001)HQHR;ARS(0.997)DPT(0.003)HQHR;ARS(0.965)DPT(0.035)HQHR 145.43 1.84E-05 531601000 48268.6 36592.9 44541.5 45691.8 55450.6 48473.7 62054.8 47444.2 14761.08 TRUE FALSE 45987.03894 40321.75811 46583.77183 41098.77346 65121.16708 46795.04361 52587.20055 43289.73433 17050.1529 2.697162847 2.364891292 2.73216153 2.410463631 3.819389039 2.744552726 3.084265629 2.538964582 1 14.05749706 ARS(ph)LAIPDDDRFEDLEEANPFSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARSLAIPDDDRFEDLEEANPFSFR 24 2 Q96C92-4 Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 1 ARS(1)LAIPDDDRFEDLEEANPFSFR;ARS(1)LAIPDDDRFEDLEEANPFSFR 177.92 2.16E-17 31229000 6372.1 3661.07 4828.4 6448.7 6747.7 5688.6 9321.7 5097.5 10587.2 TRUE FALSE 6070.903461 4034.137195 5049.786916 5800.464424 7924.496744 5491.602356 7899.50346 4651.135876 12229.0089 0.496434626 0.329882595 0.412935092 0.474320075 0.648008093 0.449063567 0.645964323 0.38033629 1 13.57801987 -4.999999999 0.194159604 3.294321909 0.387917463 0.708466065 0.104124646 69.99644537 0.688127732 62.13330044 0.247670359 1.00E-05 4.999999999 -2.906404446 ARS(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARSMDSSDLSDGAVTLQEYLELKK 24 2 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.997)MDS(0.003)SDLSDGAVTLQEYLELKK;ARS(1)MDSSDLSDGAVTLQEYLELKK;ARS(0.993)MDS(0.003)S(0.004)DLSDGAVTLQEYLELKK;ARS(0.593)MDS(0.127)S(0.127)DLS(0.151)DGAVT(0.002)LQEYLELKK 263.16 1.94E-44 518959000 1131616 869057 971554 1059955 726126 1096861 1299967 1232805 922789 TRUE FALSE 1078126.754 957614.8963 1016100.712 953406.3096 852762.1445 1058876.429 1101633.159 1124854.059 1065890.405 1.011479932 0.898417785 0.953288168 0.894469361 0.800046741 0.993419608 1.033533235 1.055318683 1 20.02362768 2.013353728 24.99798478 1.028376543 0.918022616 0.50737719 0.054153116 197.2431549 369234.7568 0.020593819 0.015201609 103.1225701 -2.013353728 -0.110353927 ARS(ph)PDLGPQEQMNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 126.22 0.00012991 365870000 211440 168110 185530 217030 154720 213770 219800 226830 195630 TRUE FALSE 201445.6502 185240.6001 194036.734 195213.7321 181703.119 206367.0913 186265.4731 206967.5627 225967.3013 0.891481418 0.819767281 0.858693859 0.863902569 0.804112445 0.913260857 0.824302773 0.915918195 1 17.7857545 0.972220555 4.256213296 0.99987134 0.85346477 0.679093356 0.032727759 0.099563063 5.57472146 0.027440091 0.006994418 9.380382663 -0.972220555 -0.146406571 ARS(ph)PGREEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ARSPGREEVAR 11 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 ARS(1)PGREEVAR;ARS(1)PGREEVAR;ARS(1)PGREEVAR;ARS(1)PGREEVAR;ARS(1)PGREEVAR 120.49 0.00035043 4352060000 1593286 1368912 1483088 1772137 1722682 1380532 1797253 1620450 1864639 TRUE FALSE 1517974.528 1508405.689 1551089.052 1593998.422 2023117.195 1332723.831 1523049.046 1478554.807 2153797.693 0.704789746 0.70034697 0.720164692 0.740087348 0.939325547 0.618778558 0.707145825 0.686487321 1 21.03845131 -1.02140557 3.973078603 1.000034694 0.723822456 0.52274971 0.081880057 21284974.67 41215732.52 10247.52734 0.018745694 0.09519068 1.02140557 -0.276212238 ARS(ph)PSVAAMASPQLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.997)PS(0.003)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(0.858)PS(0.142)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.972)PS(0.028)VAAMASPQLCR;ARS(0.965)PS(0.035)VAAMASPQLCR;ARS(0.989)PS(0.011)VAAMASPQLCR;ARS(0.991)PS(0.009)VAAMASPQLCR;ARS(0.996)PS(0.004)VAAMASPQLCR 201.9 2.73E-11 8971050000 1956861 1485451 1514271 1738905 2081846 1537996 2167739 1822977 2281705 TRUE FALSE 1864364.059 1636820.146 1583701.823 1564106.966 2444919.283 1484734.813 1837010.602 1663347.47 2635540.158 0.707393531 0.621056803 0.600902179 0.593467324 0.927672939 0.563351239 0.69701484 0.631122036 1 21.32966724 -1.423602247 2.775680016 1.008332128 0.667041845 0.509667613 0.102414992 9599682.613 10625799.56 631145.0665 0.023639478 0.037704897 1.423602247 -0.341290283 ARS(ph)PTDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARSPTDDK 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.999)PT(0.001)DDK;ARS(0.998)PT(0.002)DDK 75.378 0.023343 512310000 513720 594380 422750 579140 307910 488940 472250 571190 353280 TRUE FALSE 489437.4737 654947.9978 442133.5057 520923.7469 361609.4065 472007.8852 400199.589 521173.5755 408064.8581 1.199410986 1.605009559 1.083488315 1.276570958 0.886156696 1.156698196 0.980725444 1.277183186 1 18.63843895 3.712030997 24.22350646 1.089694451 1.402210262 0.402883431 0.155708043 388.7054562 354916.7039 0.037845836 0.05865329 5152.654192 -3.712030997 0.312515811 ARS(ph)PTDDKVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.978)PT(0.022)DDKVK;ARS(0.974)PT(0.026)DDKVK;ARS(0.996)PT(0.004)DDKVK;ARS(0.993)PT(0.007)DDKVK;ARS(0.993)PT(0.007)DDKVK;ARS(0.996)PT(0.004)DDKVK;ARS(0.997)PT(0.003)DDKVK;ARS(0.997)PT(0.003)DDKVK 142.85 1.83E-05 7514780000 13686930 12625740 10760620 13641350 6935960 13790070 13780880 14360000 6672600 TRUE FALSE 13039975.94 13912317.26 11254005.07 12270095.58 8145589.228 13312516.42 11678353.65 13102562.27 7707352.729 1.691887786 1.805070788 1.460164789 1.591998707 1.056859536 1.727248886 1.51522242 1.700008126 1 22.87780399 -3.117328079 0.188145998 3.75E-30 1.708496204 0.392406278 0.2139329 62.69659926 1.160615129 26.589316 0.620825485 0.000763259 3.117328079 1.708496204 ARS(ph)PTDDKVKIEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ARSPTDDKVKIEDK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.975)PT(0.025)DDKVKIEDK;ARS(0.971)PT(0.029)DDKVKIEDK;ARS(0.996)PT(0.004)DDKVKIEDK;ARS(0.995)PT(0.005)DDKVKIEDK;ARS(0.981)PT(0.019)DDKVKIEDK 146.78 4.54E-05 3135000000 2002100 959060 2090540 1501850 1046430 2201860 2738470 2623830 1312620 TRUE FALSE 1907464.701 1056789.304 2186393.327 1350881.185 1228927.061 2125609.036 2320666.106 2394073.535 1516174.406 1.258077365 0.697010384 1.442046059 0.890980074 0.810544655 1.401955493 1.530606306 1.579022523 1 20.53200429 2.166208803 8.102519567 1.435885069 1.011165391 0.304577271 0.262514958 0.255932453 25.26347653 0.090638131 0.066954163 146.6252625 -2.166208803 -0.424719679 ARS(ph)PVRLPHEGSPSPGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARSPVRLPHEGSPSPGEK 18 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ARS(1)PVRLPHEGSPSPGEK;ARS(1)PVRLPHEGSPSPGEK;ARS(1)PVRLPHEGSPSPGEK;ARS(1)PVRLPHEGSPSPGEK 204.82 5.38E-16 726543000 663480 475156 598938 662740 559383 551601 759880 684620 660420 TRUE FALSE 632118.6153 523574.9366 626399.8997 596120.1161 656939.2181 532498.9191 643946.3498 624671.0434 762834.5606 0.828644437 0.686354504 0.821147772 0.781453996 0.861181771 0.698052955 0.844149417 0.818881414 1 19.54101068 -0.483375631 0.412184652 1.054697825 0.769767404 0.575069694 0.056992468 5.48827777 0.890707438 0.465960627 0.033265756 0.328567323 0.483375631 -0.284930421 ARS(ph)PYSPAEEDALFMDLPTGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.878)PY(0.055)S(0.067)PAEEDALFMDLPTGPR;ARS(0.953)PYS(0.047)PAEEDALFMDLPTGPR;ARS(0.988)PY(0.005)S(0.007)PAEEDALFMDLPTGPR;ARS(0.978)PY(0.009)S(0.013)PAEEDALFMDLPTGPR;ARS(0.971)PY(0.003)S(0.026)PAEEDALFMDLPTGPR;ARS(0.9)PYS(0.1)PAEEDALFMDLPTGPR;ARS(0.977)PYS(0.023)PAEEDALFMDLPTGPR 177.73 9.52E-17 346578000 242341 212051 226459 243148 248235 220585 263509 247876 272080 TRUE FALSE 230886.0212 233659.238 236842.3691 218706.3011 291527.1054 212946.0861 223305.8624 226170.6634 314272.7768 0.734667583 0.743491817 0.753620379 0.695912332 0.92762443 0.677583621 0.710547903 0.719663554 1 18.26165778 -2.258804885 2.334770561 2.032009205 0.743306882 0.576230814 0.06859863 4722538.661 1029734.197 25590869.18 0.015397281 0.005510552 2.258804885 -1.288702323 ARS(ph)RT(ph)PPSAPSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARSRTPPSAPSQSR 14 2 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ARS(0.995)RT(0.983)PPS(0.019)APS(0.002)QS(0.001)R 79.511 0.020841 1373300000 120900 92140 115850 119360 129390 117080 149070 118520 143810 TRUE FALSE 115185.2966 101529.1708 121161.8371 107361.706 151955.575 113025.4902 126326.6336 108141.7605 166111.3203 0.693422317 0.611211629 0.729401445 0.646323838 0.914781574 0.680420155 0.760493827 0.651019812 1 17.34179087 -5 0.193407339 2.258315381 0.656484639 0.523308874 0.085369574 103.3170635 1.014793264 50.28006538 0.204495523 1.00E-05 5 -1.601830743 ARS(ph)VS(ph)PPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;ARS(1)VS(1)PPPKR 94.551 0.0043047 5500740000 334477 268573 303773 304931 330032 284179 356746 310343 356307 TRUE FALSE 318666.9351 295940.894 317701.2925 274278.7565 387589.4763 274337.81 302317.8456 283167.7217 411561.2698 0.774287958 0.719068862 0.771941667 0.66643481 0.94175401 0.666578296 0.7345634 0.688032967 1 18.6507477 -1.860095806 2.675680686 1.107780805 0.744727079 0.504372292 0.079335344 24818000.15 15934727.11 17035002.24 0.016956667 0.013800798 1.860095806 -0.363053726 ARSDEGQLS(ph)PATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;ARSDEGQLS(1)PATR;ARSDEGQLS(0.938)PAT(0.062)R;ARSDEGQLS(0.994)PAT(0.006)R;ARSDEGQLS(0.945)PAT(0.055)R 172.93 1.37E-05 2015590000 1540040 1300370 1642290 1544380 1699840 1561230 1960260 1780600 2092220 TRUE FALSE 1467245.361 1432879.181 1717590.621 1389135.988 1996291.558 1507164.214 1661186.334 1624681.224 2416670.792 0.607134975 0.592914511 0.71072594 0.57481391 0.826050269 0.623653093 0.687386275 0.672280738 1 21.20458953 -5 0.20433073 2.599308904 0.602539127 0.703282617 0.069974963 72.09161361 0.715685904 47.13317545 0.143237868 1.00E-05 5 -1.996769777 ARSMDSSDLS(ph)DGAVTLQEYLELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ARSMDSSDLSDGAVTLQEYLELK 23 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.167)MDS(0.209)S(0.209)DLS(0.415)DGAVTLQEYLELK;ARS(0.199)MDS(0.247)S(0.247)DLS(0.307)DGAVTLQEYLELK;ARS(0.047)MDS(0.057)S(0.057)DLS(0.839)DGAVTLQEYLELK 100.7 0.0034306 103120000 100997 91750 86922 97918 73859 93636 108737 113333 94346 TRUE FALSE 96223.07197 101099.4293 90907.45968 88075.09661 86739.98622 90393.36184 92147.17356 103408.9617 108976.6958 0.882969255 0.927716046 0.834191742 0.808201202 0.795949864 0.829474239 0.845567696 0.948908947 1 16.73366013 1.099858881 3.593381298 0.998214939 0.852114201 0.674441102 0.03767769 0.15652991 3.680561547 0.043001009 0.01121731 12.58516406 -1.099858881 -0.146100738 ARSPS(ph)VAAMASPQLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.358)PS(0.642)VAAMASPQLCR 117.07 0.0013406 93155000 140420 109240 116190 122340 151400 121330 163990 147830 186070 TRUE FALSE 133782.6249 120371.6802 121517.4264 110042.1508 177804.1121 117128.3117 138970.3136 134885.2215 214924.7853 0.622462527 0.560064211 0.565395128 0.512003074 0.827285284 0.544973496 0.646599756 0.627592678 1 17.71347234 -5 0.270906257 3.707339229 0.581666567 0.675417416 0.08496495 116.310335 1.127832634 176.1167539 0.093762839 1.00E-05 5 -3.125672663 ART(ph)PATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ARTPATK 7 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 ART(1)PATK;ART(1)PATK 89.247 0.029121 289010000 769490 931750 658780 991350 526340 785020 813250 1087270 775870 TRUE FALSE 733117.7327 1026696.384 688985.7146 891697.6146 618133.5294 757834.5606 689173.7761 992062.8748 896187.957 0.818040152 1.145626178 0.768795998 0.994989508 0.689736483 0.845620112 0.769005844 1.106980815 1 19.77344181 ART(ph)PLTAAQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ARTPLTAAQQK 11 1 I3L2J0 I3L2J0 CIC 1 ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(0.999)PLT(0.001)AAQQK;ART(1)PLTAAQQK 163.62 3.84E-05 1279280000 1376220 1020040 1050410 1135060 1189480 1141440 1515030 1281620 1187230 TRUE FALSE 1311168.808 1123983.236 1098572.337 1020961.612 1396924.935 1101911.647 1283884.348 1169394.559 1371339.565 0.956122642 0.819624303 0.801094321 0.744499494 1.01865721 0.803529392 0.936226432 0.852738876 1 20.38715442 2.744811599 24.9997251 0.909961994 0.84090194 0.22699956 0.081527318 977.5335906 3909478.919 0.024044693 0.024936821 555.6631528 -2.744811599 -0.069060053 ARTDEVPAGGS(ph)RS(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARTDEVPAGGSRSEAEDEDDEDYVPYVPLR 30 2 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 2 ART(0.003)DEVPAGGS(0.998)RS(0.999)EAEDEDDEDYVPYVPLR 79.534 0.0015284 57106000 27578 18378 18693 24612 32572 19939 29742 26835 42076 TRUE FALSE 26274.44259 20250.73909 19550.09254 22137.955 38252.54649 19248.50743 25204.31165 24485.18514 48600.93119 0.540616033 0.416673891 0.402257571 0.45550475 0.787074353 0.396052235 0.518597299 0.503800741 1 15.56869634 -4.999999987 0.355351398 7.010184777 0.482395094 0.660009845 0.112258678 271.145597 2.187048287 1244.213525 0.078670885 1.00E-05 4.999999987 -6.527789683 ARTDEVPAGGSRS(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ARTDEVPAGGSRSEAEDEDDEDYVPYVPLR 30 2 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 ARTDEVPAGGS(0.203)RS(0.796)EAEDEDDEDYVPYVPLR 127.72 9.36E-06 71446000 66790 39942 63383 61888 64942 60355 90841 72015 105980 TRUE FALSE 63632.96907 44012.13521 66289.17324 55666.90066 76267.86424 58264.89122 76981.53704 65708.98482 122414.8371 0.519814187 0.359532686 0.541512572 0.454739817 0.623027944 0.475962658 0.628857897 0.536773045 1 16.9014189 -5 0.182804808 3.07553285 0.409270768 0.826186914 0.071136069 46.4164985 0.449027939 34.8510476 0.188375653 1.00E-05 5 -2.666262081 AS(ph)DKDITVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASDKDITVSK 10 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 AS(1)DKDITVSK;AS(1)DKDITVSK;AS(1)DKDITVSK;AS(0.999)DKDIT(0.001)VSK 161.84 4.21E-06 2771830000 4347050 4258270 3770070 4843000 1982340 4671400 4171950 4921210 2009280 TRUE FALSE 4141573.562 4692192.554 3942931.439 4356172.439 2328059.468 4509628.247 3535442.404 4490282.763 2320868.88 1.784492694 2.021739614 1.698903144 1.876957581 1.003098231 1.943077562 1.523327076 1.934742114 1 21.14623359 -2.531898701 0.182619683 3.13E-18 1.920946146 0.35209472 0.298019425 49.67667686 1.096664595 22.04585309 0.919955386 0.002938335 2.531898701 1.920946146 AS(ph)DLEDEESAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 403.23 2.15E-120 1786800000 1252900 1512670 1007100 1461230 790760 1293070 992630 1251750 722960 TRUE FALSE 1193677.9 1666812.793 1053276.531 1314344.384 928668.2936 1248290.662 841186.0626 1142140.134 835072.9444 1.429429498 1.996008617 1.261298834 1.573927635 1.112080447 1.49482829 1.00732046 1.367713014 1 19.6715427 3.069524833 1.07614774 1.183572077 1.68951712 0.365333605 0.237297986 0.43788281 1.093506888 0.094878287 0.124486623 1173.612787 -3.069524833 0.505945043 AS(ph)DPGLPAEEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 201.48 1.79E-06 259989000 815100 948280 611680 1069940 402027 783810 684460 842070 385590 TRUE FALSE 776571.8384 1044910.81 639726.133 962387.5984 472140.3815 756666.4632 580033.056 768333.8867 445385.3279 1.743595466 2.346082694 1.436343079 2.160797714 1.0600717 1.698902985 1.302317386 1.725099231 1 18.76469451 2.746486464 24.98910564 1.397962322 1.945679945 0.414238068 0.331014644 556.6885905 1755162.833 0.091458506 0.095425559 557.810216 -2.746486464 0.547717623 AS(ph)DPGLPAEEPKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASDPGLPAEEPKEK 14 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPKEK 151.04 4.27E-06 131570000 640110 486260 542600 656970 318950 654070 655370 735940 325410 TRUE FALSE 609853.2689 535810.4468 567478.7467 590930.1274 374574.779 631419.3919 555381.2698 671497.1921 375872.9208 1.62249855 1.425509573 1.50976225 1.57215403 0.996546328 1.679874651 1.477577232 1.786500583 1 18.51988546 4.615408261 2.549014104 1.45447212 1.636988126 0.044742309 0.257304333 1.387444845 13.92172734 0.057371051 0.485836183 41248.50957 -4.615408261 0.182516007 AS(ph)ESPARGPSGSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASESPARGPSGSPR 14 1 O43237;O43237-2;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 AS(0.666)ES(0.334)PARGPSGSPR 105.9 0.0005893 168170000 213860 166360 199010 240550 218970 208080 244230 224500 275430 TRUE FALSE 203751.2616 183312.2731 208134.8053 216369.457 257158.2987 200874.1374 206968.2279 204841.5899 318142.2777 0.640440696 0.576195891 0.65421926 0.68010281 0.808312245 0.631397181 0.650552418 0.643867867 1 18.27931258 -5 0.327959056 4.432089917 0.64107011 0.759932143 0.059646361 175.2432474 1.522327861 419.0640277 0.052411178 1.00E-05 5 -3.791019807 AS(ph)FSRPTFLQLS(ph)PGGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASFSRPTFLQLSPGGLR 17 1 S4R3C3;S4R3I3;Q5JR12 S4R3C3 PPM1J Protein phosphatase 1J 2 AS(1)FSRPTFLQLS(1)PGGLR 214.16 1.19E-14 57394000 120840 96115 110390 124910 115040 108820 133260 115570 126840 TRUE FALSE 115128.1327 105909.2278 115451.4907 112353.8095 135102.9396 105051.5361 112928.7395 105450.0781 146509.6994 0.785805535 0.722882022 0.788012611 0.766869429 0.922143313 0.717027859 0.770793606 0.719748102 1 17.16063665 -1.385294988 2.969908858 1.003400615 0.772212658 0.592378788 0.058855355 17785949.96 21407916.97 517046.091 0.013874941 0.04118177 1.385294988 -0.231187957 AS(ph)GEMASAQYITAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR 307.46 2.70E-47 535194000 604408 1136515 570160 898432 428481 693903 498193 687291 391104 TRUE FALSE 575838.8317 1252327.171 596302.4 808119.9085 503207.9507 669872.9651 422184.5079 627108.1565 451754.4108 1.274672295 2.772141545 1.319970288 1.788847854 1.11389715 1.482825511 0.934544296 1.388161668 1 18.78517916 3.020634758 1.406504003 1.16679169 1.973972409 0.307076494 0.438418114 0.406685262 1.667558166 0.156866458 0.190611538 1048.660134 -3.020634758 0.807180719 AS(ph)GQAFELILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;AS(1)GQAFELILS(1)PR 198.24 1.86E-07 205842000 632600 661390 677080 724210 566610 698770 740820 656330 611130 TRUE FALSE 602698.2517 728786.3929 708124.7877 651411.0349 665426.6046 674571.4197 627794.3029 598858.2658 705900.9192 0.853800066 1.032420235 1.003150398 0.922808028 0.942662896 0.95561771 0.889351871 0.848360229 1 19.42910617 1.757469156 9.628083989 0.90208001 0.954047929 0.077123326 0.05995417 0.29316133 108.6330186 0.027153621 0.014818886 57.20963226 -1.757469156 0.051967919 AS(ph)GQAFELILSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR 232.01 1.54E-12 1140407000 567385 504569 488481 544455 538266 492903 614509 557578 540648 TRUE FALSE 540565.8355 555985.1547 510878.337 489725.349 632139.42 475833.6455 520754.3658 508753.5144 624488.9306 0.865613158 0.890304259 0.818074288 0.784201809 1.012250801 0.761956893 0.833888865 0.814671789 1 19.25231647 AS(ph)GVAVSDGVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK 152.02 7.28E-05 219630000 872410 725680 834300 892390 651530 880830 986490 924350 750270 TRUE FALSE 831172.9083 799627.617 872553.4802 802685.2618 765156.6257 850326.6362 835982.8324 843409.0137 866618.0398 0.959099476 0.922699021 1.006848969 0.926227271 0.882922569 0.981201172 0.9646497 0.973218852 1 19.72503674 AS(ph)HSSERPPPR ddPTM_SK-BR-3_Trastuzumab_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(0.995)HS(0.005)SERPPPR 69.314 0.033211 108690000 23459 19041 24218 22290 25432 21463 22622 24284 23390 TRUE FALSE 22350.13956 20981.29955 25328.41925 20049.36685 29867.33275 20719.73093 19170.59842 22157.56422 27017.20174 0.827255901 0.776590402 0.937492324 0.742096352 1.105493198 0.766908843 0.709570095 0.820128022 1 14.72159064 -0.292829917 7.324558798 0.999999998 0.826396089 0.166048223 0.114042728 0 0 0.10452933 0.024637799 0.509530379 0.292829917 -0.173603909 AS(ph)LADALPLHIAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLADALPLHIAPR 14 0 H3BRB6;Q8ND25;Q8ND25-2 H3BRB6 ZNRF1 E3 ubiquitin-protein ligase ZNRF1 1 AS(1)LADALPLHIAPR 115.8 0.00025662 20520000 22732 24561 23270 26471 22813 24762 24287 16997 8083.8 TRUE FALSE 21657.50341 27063.79382 24336.95252 23810.08479 26791.57998 23904.48573 20581.57209 15508.65257 9337.394418 2.319437569 2.898431041 2.606396542 2.549970979 2.869277957 2.560080967 2.204209351 1.660918655 1 13.18880431 1.160172049 1.392755381 1.010169232 2.653730954 0.91950731 0.164185154 0.09553111 0.364852385 0.147079404 0.045000311 14.46012506 -1.160172049 1.643561722 AS(ph)LEDAPVDDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR 243.49 5.77E-17 1121545000 2421400 2722860 1907860 2756360 1734810 2313280 2263000 2362480 1651020 TRUE FALSE 2306945.221 3000322.53 1995337.268 2479285.456 2037360.315 2233170.534 1917737.787 2155608.727 1907051.749 1.209691987 1.573277983 1.046294244 1.300061971 1.068329853 1.171006783 1.005603434 1.130335728 1 20.86291256 3.195157833 1.076366728 1.069583902 1.374145538 0.362383559 0.136810532 0.434854814 1.084336004 0.052632648 0.07946972 1567.320567 -3.195157833 0.304561637 AS(ph)LSEIGFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLSEIGFGK 10 0 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 AS(1)LSEIGFGK;AS(0.999)LS(0.001)EIGFGK 102.4 0.0030966 47087000 202952 190060 182694 220761 201897 188990 227331 202203 198817 TRUE FALSE 193358.8612 209427.3301 191070.7006 198569.6849 237107.7729 182445.2289 192647.4807 184497.0334 229648.5249 0.841977371 0.911947203 0.83201362 0.8646678 1.032481149 0.794454173 0.838879678 0.803388715 1 17.80906799 -0.277191651 7.554763955 0.999999999 0.866590792 0.281314921 0.067780704 0 0 0.061983364 0.014609619 0.528212104 0.277191651 -0.133409207 AS(ph)LSSAPVVLVGDHA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLSSAPVVLVGDHA 15 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 AS(1)LSSAPVVLVGDHA;AS(1)LSSAPVVLVGDHA 146.59 4.05E-06 112805000 122310 117041 111872 130873 118207 121963 139172 134049 129570 TRUE FALSE 116528.6487 128967.611 117001.4419 117717.3974 138822.2634 117739.3907 117938.7553 122310.9589 149663.0538 0.778606648 0.861719761 0.781765699 0.786549481 0.927565353 0.786696434 0.788028523 0.81724217 1 17.19135859 -0.763964679 4.718430631 1.00000027 0.815913647 0.605318212 0.046687427 4944654.828 2095899.555 12.93706659 0.010243494 0.172200862 0.763964679 -0.184086624 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR 236.65 3.41E-37 2588290000 298594 238248 287737 449527 443271 282663 428557 256200 110924 TRUE FALSE 284480.0534 262525.7421 300930.0261 404339.6919 520577.3221 272874.3094 363172.7587 233765.7698 128125.5274 2.220322984 2.048972967 2.348712487 3.155808995 4.063025789 2.129741941 2.834507424 1.824505815 1 16.96719842 1.002254961 3.499398999 1.003321258 2.624033095 0.466403562 0.598812489 0.203814068 6.295575884 0.59819591 0.154997901 10.05205743 -1.002254961 1.620711836 AS(ph)PEPELQLRPYQMEVAQPALEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASPEPELQLRPYQMEVAQPALEGK 24 1 A0A3B3IRK8;Q9BYX4 A0A3B3IRK8 IFIH1 Interferon-induced helicase C domain-containing protein 1 1 AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK 241.22 8.58E-38 540390000 419189 467312 392078 504768 268632 475185 446494 529304 317406 TRUE FALSE 399374.7667 514931.6241 410055.1641 454027.7616 315481.3357 458729.2243 378373.1399 482955.3357 366627.7014 1.08931967 1.40450823 1.118451122 1.238389134 0.860495087 1.251212668 1.032036419 1.317290903 1 18.48395627 3.217147576 2.361056163 1.103099004 1.240416158 0.093564408 0.154027502 0.548530117 6.264717517 0.042941924 0.057209363 1648.722545 -3.217147576 0.137317153 AS(ph)PEPPGPESSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 218.58 2.51E-11 9421965000 2851240 3180619 2605173 3264502 2219049 2757310 2842563 2992091 2139196 TRUE FALSE 2716467.536 3504727.692 2724622.759 2936348.057 2606050.443 2661823.663 2408877.807 2730087.65 2470931.59 1.099369787 1.418383134 1.102670252 1.188356678 1.054683365 1.077255102 0.974886483 1.104881924 1 21.23662364 2.93990814 1.309550588 1.029135939 1.247578132 0.419754601 0.093575531 0.343540975 1.223266569 0.036247875 0.041100814 870.7793864 -2.93990814 0.218442193 AS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASPEPQRENASPAPGTTAEEAMSR 24 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 AS(1)PEPQRENASPAPGTTAEEAMSR;AS(1)PEPQRENASPAPGTTAEEAMSR 153.25 4.86E-08 310800000 55889 47503 41871 52505 39153 48452 57676 51175 49809 TRUE FALSE 53247.23773 52343.60971 43790.82677 47227.09765 45981.2708 46774.09509 48876.46691 46693.8457 57533.12533 0.92550574 0.909799518 0.761141108 0.820867933 0.799213854 0.812994163 0.8495361 0.811599325 1 15.81210522 3.882277961 7.95066532 0.828137922 0.919589433 0.215108933 0.063173299 0.300711848 18.50448455 0.0140375 0.025417362 7625.669179 -3.882277961 0.091451511 AS(ph)PGLLPVANGNSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK 343.31 2.06E-72 2311154000 3502740 2973700 3017360 3458410 2280030 3193270 3583250 3473730 2826570 TRUE FALSE 3337172.422 3276723.411 3155708.941 3110764.056 2677666.51 3082686.259 3036559.402 3169551.786 3264900.039 1.02213617 1.003621358 0.966556067 0.952789984 0.820137363 0.944190089 0.930061982 0.970795965 1 21.63860739 3.527005131 2.019608674 0.927911931 1.015094198 0.310230688 0.046477138 0.32214684 2.609475877 0.013136254 0.022424029 3365.155454 -3.527005131 0.087182267 AS(ph)PIKMDLAPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPIKMDLAPSK 12 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 AS(1)PIKMDLAPSK 98.281 0.0067461 163220000 380690 493980 299330 484590 188990 395020 382150 448220 198960 TRUE FALSE 362695.5382 544317.1236 313054.5766 435878.0925 221949.7962 381340.3584 323845.9988 408971.4806 229813.7007 1.578215472 2.36851468 1.362210241 1.896658429 0.965781394 1.659345623 1.409167504 1.779578326 1 17.81010528 3.7157678 24.9599482 1.465100036 1.973365133 0.282799335 0.351901038 814.6009494 892052.9105 0.083834847 0.129974285 5197.180496 -3.7157678 0.508265097 AS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.773)PIT(0.191)NDGEDEFVPS(0.036)DGLDKDEYTFSPGK;AS(0.977)PIT(0.023)NDGEDEFVPSDGLDKDEYTFSPGK 93.392 7.96E-08 0 145865 119227 119147 153475 74337 140811 152312 146928 77467 TRUE FALSE 138970.2505 131376.3668 124610.0078 138047.4014 87301.34926 135934.6798 129074.007 134062.2054 89480.18671 1.553084047 1.468217397 1.39259888 1.542770601 0.975650057 1.519159545 1.44248701 1.498233412 1 16.44928065 -2.033932828 2.583294282 0.473729575 1.430094432 0.389603041 0.166643473 54715043.71 47988813.44 169309721.3 0.038843248 0.009248412 2.033932828 0.956364857 AS(ph)PNLIGATGANSLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 87.323 0.0068273 24015000 78524 70305 71248 76383 55188 78742 88219 73420 77959 TRUE FALSE 74812.32614 77469.15943 74514.79127 68704.83572 64812.76973 76015.1448 74759.5713 66990.95558 90048.48356 0.830800511 0.860304986 0.827496348 0.762976044 0.71975415 0.844157967 0.830214661 0.743943184 1 16.45841436 -1.943841865 8.37591889 1.064386184 0.809818324 0.636736995 0.04659778 0.030327512 0.000203337 0.024422824 0.010912901 0.011380416 1.943841865 -0.25456786 AS(ph)PPAESMSVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASPPAESMSVYR 12 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 AS(1)PPAESMSVYR;AS(1)PPAESMSVYR;AS(1)PPAESMSVYR;AS(1)PPAESMSVYR 234.49 5.30E-16 1027960000 127941 101537 98021 116831 94846 107698 121306 113233 115346 TRUE FALSE 121893.4825 111883.7357 102515.3598 105086.9259 111387.1124 103968.3913 102798.5418 103317.7182 133233.2686 0.914887729 0.839758245 0.769442654 0.788743885 0.836030772 0.780348575 0.771568114 0.775464862 1 17.02359485 4.252670341 2.176007097 0.803528083 0.909106928 0.132405287 0.069741925 0.447194881 3.993741922 0.015914972 0.061411145 17892.47177 -4.252670341 0.105578844 AS(ph)PPGDLQNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASPPGDLQNPK 11 0 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK 180.17 7.11E-06 605080000 966130 1089060 740373 1156080 542957 970200 874910 967390 545180 TRUE FALSE 920462.9496 1200036.452 774319.8344 1039868.642 637648.5289 936601.7307 741426.4107 882680.2031 629723.73 1.461693288 1.905655441 1.229618319 1.651309284 1.012584564 1.48732164 1.177383629 1.401694364 1 19.26435951 3.254420878 1.355242883 1.252911399 1.661002178 0.300787498 0.234976173 0.428688888 1.649506884 0.074291358 0.112476233 1796.473759 -3.254420878 0.408090779 AS(ph)PPPQGPLPGPPGALHR ddPTM_SK-BR-3_Trastuzumab_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 174.26 4.05E-12 1709040000 1260590 996381 1072470 1264040 1136040 1183970 1398660 1216220 1224210 TRUE FALSE 1201004.409 1097913.357 1121643.81 1136976.298 1334165.016 1142968.822 1185268.729 1109721.329 1414054.234 0.849334049 0.776429454 0.793211309 0.804054236 0.943503427 0.808292068 0.83820599 0.784779892 1 20.43140602 -2.336096188 2.331517869 2.068478 0.824169716 0.570975406 0.04774544 2050738.556 456428.6494 11482851.54 0.011021072 0.004612154 2.336096188 -1.244308283 AS(ph)PSCSSPTRDSSGVPVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPSCSSPTRDSSGVPVSK 19 1 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 AS(0.25)PS(0.25)CS(0.25)S(0.25)PT(0.001)RDSSGVPVSK 82.007 0.013336 39051000 35696 21575 36058 27456 32190 38159 50440 40218 45374 TRUE FALSE 34008.72082 23773.51703 37711.29497 24696.07072 37803.92581 36837.54426 42744.45161 36696.29871 52410.36818 0.648892996 0.45360332 0.719538829 0.471205824 0.721306244 0.702867496 0.815572435 0.700172504 1 15.67756462 1.296217204 0.403197561 1.008764622 0.539076262 0.632420171 0.09465591 0.615278604 0.296468006 0.113929645 0.074530899 19.77958632 -1.296217204 -0.46968836 AS(ph)PVSFQELNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASPVSFQELNR 11 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 AS(1)PVSFQELNR;AS(1)PVSFQELNR 192.65 1.36E-06 178547000 124284 130792 107899 142165 94051 112474 120568 125786 118450 TRUE FALSE 118409.3416 144119.8535 112846.2759 127874.3041 110453.4646 108578.9972 102173.1372 114771.511 136818.621 0.865447559 1.053364318 0.824787408 0.934626465 0.807298479 0.793598096 0.746778008 0.838858849 1 17.06190507 3.061669257 1.478868077 0.812723432 0.948149849 0.111650265 0.090268079 0.469220549 2.123950037 0.030450423 0.038167949 1152.575164 -3.061669257 0.135426417 AS(ph)QSRPNS(ph)SALETLGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 2 AS(0.594)QS(0.594)RPNS(0.665)S(0.146)ALETLGGEK 99.387 0.00059496 607690000 270230 239250 245220 274230 236170 286370 318980 305960 253940 TRUE FALSE 257456.7634 263629.847 256463.5796 246663.8794 277357.9732 276452.9351 270313.7425 279168.5204 293319.7183 0.877734252 0.898779832 0.87434824 0.840938621 0.945582434 0.942496934 0.921566897 0.951755041 1 18.16211453 2.717231904 24.50221132 0.944548152 0.877864394 0.71286867 0.024661286 376.0769435 432032.8344 0.00756383 0.007138226 521.4730924 -2.717231904 -0.066683757 AS(ph)S(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.587)S(0.587)HS(0.479)S(0.341)QT(0.006)QGGGSVTK 123.19 4.71E-05 929500000 1015800 904630 978280 982100 836890 1030200 1134400 936690 768440 TRUE FALSE 967785.1471 996812.8255 1023135.106 883377.4421 982843.351 994523.9157 961326.4453 854668.4579 887605.7506 1.090332218 1.123035565 1.152690939 0.995236276 1.107297187 1.120456819 1.083055675 0.962891979 1 19.75955949 1.298946148 5.493892945 0.981566636 1.098658199 0.56705252 0.041690053 0.125812767 7.115400415 0.028599576 0.009831711 19.90426515 -1.298946148 0.117091563 AS(ph)SDIVSLAGPSAGPGSSEGGCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AS(0.5)S(0.5)DIVSLAGPSAGPGSSEGGCSR 183.54 2.95E-17 73191000 22876 16938 20522 22781 20596 23968 25019 24400 20988 TRUE FALSE 21794.69682 18664.00146 21462.954 20491.0106 24187.93588 23137.98215 21201.89204 22263.40665 24242.71185 0.899020578 0.769880926 0.885336349 0.845244159 0.997740518 0.954430441 0.874567671 0.918354629 1 14.56526347 2.77098158 22.17627603 0.936296902 0.843970263 0.481226625 0.050030208 151.9176075 103912.4127 0.01515367 0.016070325 590.1760483 -2.77098158 -0.092326639 AS(ph)SHSS(ph)QTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_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(0.514)S(0.487)HS(0.298)S(0.675)QT(0.025)QGGGSVTKK 88.836 0.0042805 108910000 248300 170710 220190 235540 173260 268610 301860 251080 171080 TRUE FALSE 236563.3511 188105.5431 230285.9293 211863.0717 203476.4891 259307.9683 255805.713 229094.1041 197610.2126 1.19712108 0.951901931 1.165354392 1.072126126 1.0296861 1.312219469 1.294496421 1.1593232 1 17.59229798 2.246904326 24.99992751 1.22789058 1.078908965 0.160309093 0.109661066 211.8881049 634872.5491 0.035444593 0.029202664 176.564881 -2.246904326 -0.148981615 AS(ph)SHSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.243)S(0.243)HS(0.243)S(0.136)QT(0.136)QGGGSVTK;AS(0.56)S(0.372)HS(0.014)S(0.055)QTQGGGSVTK;AS(0.482)S(0.482)HS(0.015)S(0.02)QTQGGGSVTK 232.6 1.69E-16 2404740000 1048700 774310 995920 1069890 1324940 933526 1387100 1085812 1373880 TRUE FALSE 999130.0293 853213.0693 1041583.917 962342.6245 1556009.117 901197.7605 1175472.419 990732.545 1586934.294 0.629597604 0.537648643 0.656349744 0.606416175 0.980512629 0.567885995 0.740719023 0.624305965 1 20.59781096 -5 0.138810751 2.133951876 0.538638227 0.421515742 0.122979544 126.2742416 1.077750628 39.85580542 0.713488493 1.00E-05 5 -1.59531365 AS(ph)SHSSQTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.496)S(0.496)HS(0.008)SQTQGGGSVTKK;AS(0.573)S(0.423)HS(0.004)SQTQGGGSVTKK;AS(0.482)S(0.482)HS(0.035)S(0.001)QTQGGGSVTKK 189.51 1.65E-10 572608000 664830 348864 643820 630050 709850 609428 1056680 837870 950970 TRUE FALSE 633404.8035 384413.6382 673339.7838 566716.177 833647.6153 588323.3555 895464.0587 764501.661 1098441.571 0.576639505 0.349962755 0.61299554 0.515927467 0.758936695 0.535598225 0.815213192 0.695987553 1 20.0670267 1.429260943 0.328328207 1.033432258 0.427817112 0.665816959 0.104055424 0.702482897 0.259481293 0.161374226 0.130715422 26.86958401 -1.429260943 -0.605615146 AS(ph)SKGGGGYTCQSGSGWDEFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSKGGGGYTCQSGSGWDEFTK 22 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AS(0.496)S(0.496)KGGGGYT(0.008)CQSGSGWDEFTK 129.8 8.84E-06 120150000 93609 73888 100400 96515 87871 92639 115500 105780 89388 TRUE FALSE 89184.28809 81417.2712 105003.4393 86813.12883 103195.6746 89430.8882 97878.3537 96517.34242 103249.8345 0.863771729 0.788546263 1.016984093 0.84080647 0.999475448 0.866160112 0.947975889 0.934794161 1 16.65577994 8 0.141929024 1.010533169 0.351902741 0.252521009 0.066148473 80.38157619 0.757745926 0.241228088 10.77947689 99999999.96 -8 -0.658630428 AS(ph)SMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSMLR 6 0 Q8IUX7 Q8IUX7 AEBP1 Adipocyte enhancer-binding protein 1 1 AS(0.632)S(0.368)MLR 91.906 0.049679 135520000 309140 336350 288540 358880 297480 306930 322640 297410 281680 TRUE FALSE 294527.5649 370624.4474 301769.8444 322804.7006 349360.4178 296300.9371 273415.3423 271367.2037 325361.4958 0.905231777 1.139115883 0.927490955 0.992141679 1.073760793 0.910682244 0.840343267 0.834048304 1 18.311684 2.077110196 6.063755292 0.874090247 1.011406053 0.317291988 0.079964245 0.195614693 11.89172749 0.028364361 0.020744862 119.4291101 -2.077110196 0.137315806 AS(ph)SPCPEFEQFQIVPAVETPYLAR ddPTM_SK-BR-3_Trastuzumab_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(0.541)S(0.459)PCPEFEQFQIVPAVETPYLAR;AS(0.541)S(0.459)PCPEFEQFQIVPAVETPYLAR 130.65 3.98E-05 249940000 275160 243400 255410 284780 274480 255640 313160 288520 293000 TRUE FALSE 262153.7321 268202.7367 267120.8011 256153.3734 322349.2251 246787.1227 265381.6904 263255.6593 338436.9436 0.774601405 0.792474763 0.789277903 0.756871784 0.95246465 0.72919676 0.784139248 0.777857336 1 18.36852754 -1.074224767 4.589246591 1.000009827 0.793056562 0.54361781 0.059127072 6.39E-06 1.29E-06 0.051797969 0.01220821 0.084289841 1.074224767 -0.206953265 AS(ph)SPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSPFR 6 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.844)S(0.156)PFR 85.265 0.057599 806810000 943760 964960 780400 994280 979780 897140 939090 796250 803960 TRUE FALSE 899150.3352 1063290.521 816182.1119 894333.0854 1150653.322 866071.8168 795814.5729 726526.1288 928634.0107 0.968250489 1.145004931 0.878906116 0.963063031 1.239081606 0.93262987 0.856973322 0.782360026 1 19.82475059 2.009878095 24.98510121 0.871614812 1.040338129 0.304423912 0.111726859 221.9215408 561313.453 0.039627681 0.029234904 102.3005797 -2.009878095 0.168723317 AS(ph)SPIKQSHEPVPDTSVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSPIKQSHEPVPDTSVEK 19 1 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 AS(0.489)S(0.489)PIKQS(0.021)HEPVPDTSVEK 105.16 0.00020468 263760000 206690 149090 203950 206920 126080 198450 254410 228380 144800 TRUE FALSE 196920.1733 164282.4405 213301.3092 186120.0085 148068.3121 191577.6267 215595.0819 208381.8365 167254.8445 1.177366037 0.982228294 1.275307211 1.11279293 0.88528564 1.145423484 1.289021449 1.245894175 1 17.35168847 1.998531664 24.99702872 1.21211966 1.084131947 0.079813295 0.128251312 91.37370979 1555563.825 0.045621791 0.033225048 99.6624741 -1.998531664 -0.127987713 AS(ph)SPPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.797)S(0.203)PPDR;AS(0.64)S(0.36)PPDR;AS(0.658)S(0.342)PPDR 76.827 0.041648 346733000 1060360 1204610 831350 1229710 777143 949000 937240 1030130 897800 TRUE FALSE 1010238.884 1327361.129 869468.2198 1106097.215 912676.4931 916135.892 794246.8244 939926.3561 1037026.239 0.974169068 1.279968702 0.838424514 1.066604849 0.880090068 0.883425952 0.765888841 0.906366995 1 19.98402097 3.179217467 1.176824385 0.861886771 1.109713474 0.25177755 0.123312489 0.442722229 1.306377339 0.045578002 0.066188765 1510.836497 -3.179217467 0.247826703 AS(ph)SPPDRIDIFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.561)S(0.439)PPDRIDIFGR;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;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR 197.15 8.24E-08 26862430000 5265390 3815150 4771240 4750210 5056090 4757660 5926340 5170100 5945860 TRUE FALSE 5016505.45 4203918.122 4990006.073 4272709.866 5937870.495 4592901.041 5022167.988 4717378.636 6867913.602 0.730426406 0.612109931 0.726567974 0.622126327 0.86458142 0.668747644 0.731250898 0.686872158 1 22.71144046 -5 0.281473657 3.203745858 0.682293972 0.630238698 0.070677329 136.898269 1.307545514 176.373024 0.071589712 1.00E-05 5 -2.521451886 AS(ph)SPSEHGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSPSEHGPR 10 0 C9J052;Q9NSU2-2;Q9NSU2;Q9NSU2-1 C9J052 TREX1 Three-prime repair exonuclease 1 1 AS(0.497)S(0.497)PS(0.005)EHGPR 128.85 0.00020532 147740000 150000 142660 155220 168010 199670 129290 174870 150290 215080 TRUE FALSE 142909.7973 157197.2162 162336.9905 151121.3156 234492.3848 124812.6549 148190.3698 137129.8109 248433.5079 0.575243648 0.632753679 0.653442412 0.608296831 0.943883886 0.502398633 0.596499124 0.55197792 1 17.92250025 -1.489889529 3.226491684 1.008350319 0.630352934 0.486971894 0.11833337 33228965.6 39403632.52 2446146.177 0.02635225 0.032367598 1.489889529 -0.377997385 AS(ph)SREDGRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSREDGRPR 10 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 AS(0.5)S(0.5)REDGRPR 68.515 0.047051 384930000 186330 131780 176310 173590 186570 177450 224670 196910 230340 TRUE FALSE 177522.5502 145208.5318 184393.9879 156140.4034 219107.7489 171304.862 190392.4652 179667.5165 266059.9508 0.667227629 0.54577373 0.693054281 0.586861731 0.823527736 0.643858129 0.715599866 0.675289595 1 18.02139184 -5 0.179999067 2.396346012 0.59056966 0.688591915 0.071241359 68.83401596 0.662650978 34.28796428 0.199871965 1.00E-05 5 -1.805776352 AS(ph)TFCGTPDYIAPEILQGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTFCGTPDYIAPEILQGLK 20 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 AS(0.355)T(0.355)FCGT(0.289)PDYIAPEILQGLK;AS(0.488)T(0.488)FCGT(0.023)PDYIAPEILQGLK 208.27 3.76E-22 434235000 315440 422182 338802 478223 222374 490317 398987 424920 222781 TRUE FALSE 300529.7763 465202.8258 354336.4068 430151.1155 261155.9552 473337.1993 338114.2053 387711.7522 257328.7397 1.167882673 1.807815273 1.376979529 1.671601532 1.014872865 1.839426097 1.313938761 1.506678782 1 17.97325307 -2.362497707 0.519761776 0.264842339 1.476433249 0.231456565 0.263583767 186.1394802 11.45814183 156.9009718 0.104388866 0.004340126 2.362497707 1.21159091 AS(ph)TPDWVSEGPQPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.547)T(0.453)PDWVSEGPQPGLR;AS(0.5)T(0.5)PDWVSEGPQPGLR 117.08 0.00039626 142255000 128087 116280 116136 134607 108222 120002 138510 128240 123820 TRUE FALSE 122032.5814 128129.0642 121460.9505 121076.0486 127095.8825 115846.3007 117377.7556 117010.6258 143021.3732 0.853247166 0.895873542 0.849250345 0.846559125 0.888649575 0.809992927 0.820700801 0.818133843 1 17.12587123 2.257403641 24.99136461 0.843087919 0.867757433 0 0.056833087 828.2294267 1098471.591 0.017423368 0.014554814 180.8854526 -2.257403641 0.024669514 AS(ph)TPQPAPAGVPALASQHPPEEEVHYHLPVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTPQPAPAGVPALASQHPPEEEVHYHLPVAR 32 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 AS(0.5)T(0.5)PQPAPAGVPALASQHPPEEEVHYHLPVAR;AS(0.776)T(0.224)PQPAPAGVPALASQHPPEEEVHYHLPVAR 51.533 0.031587 283890000 156257 116031 145972 153550 148115 139985 172303 126370 20153.9 TRUE FALSE 148871.0413 127854.6908 152664.9606 138114.8623 173946.2091 135137.2843 146015.0128 115304.3729 23279.26388 6.395006391 5.492213649 6.557980586 5.9329566 7.47215247 5.805049723 6.272320875 4.953093597 1 14.50675782 0.765121017 2.030978316 1.000610929 6.239736101 0.90732146 0.529432635 0.23698088 1.563170035 0.472281947 0.130295533 5.822654448 -0.765121017 5.239125172 ASAAFSS(ph)VGSVITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASAAFSSVGSVITK 14 0 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 ASAAFS(0.007)S(0.993)VGSVITK;ASAAFS(0.011)S(0.989)VGSVITK;ASAAFS(0.064)S(0.93)VGS(0.006)VITK;ASAAFS(0.058)S(0.941)VGS(0.001)VITK 276.75 5.30E-18 552950000 2404650 2064530 2423680 4205390 2177640 3785300 3984350 2783760 2034160 TRUE FALSE 2290986.96 2274907.954 2534808.125 3782656.207 2557419.727 3654214.112 3376464.23 2539999.217 2349607.144 0.97505107 0.968207796 1.078822105 1.609910073 1.088445672 1.555244723 1.437033522 1.08103145 1 21.16398813 3.459811816 23.87782774 1.334067852 0.980276974 0.306473706 0.203235509 125.4688912 173079.4317 0.050675128 0.068633539 2882.782097 -3.459811816 -0.353790879 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 203.83 5.93E-27 303560000 317191 309558 306519 362430 268244 323060 370060 397550 325531 FALSE TRUE 302198.01 341102.3121 320573.1993 325997.8478 315025.6687 311872.3512 313600.5504 362738.4145 376012.6849 0.803690998 0.907156396 0.852559534 0.866986304 0.837805961 0.829419761 0.83401588 0.96469728 1 18.52042181 1.150595112 4.558532506 0.996225591 0.849228512 0.810183317 0.02734253 0.086234721 2.957340423 0.025861408 0.00667151 14.14474464 -1.150595112 -0.146997079 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR 35 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 179.01 2.52E-20 99280000 14019 8248.2 13313 10632 14582 12585 21068 15131 19010 FALSE TRUE 13356.34965 9088.700957 13923.41422 9563.251161 17125.09618 12149.17829 17853.68966 13806.04943 21957.97371 0.60826877 0.413913464 0.634093765 0.435525212 0.779903301 0.553292324 0.813084572 0.628748791 1 14.42245731 0.848601385 0.319870962 1.054373896 0.482435927 0.58405073 0.113650204 1.277799326 0.355524611 0.254461976 0.126012048 7.056695616 -0.848601385 -0.571937969 ASAGRLT(ph)PESQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASAGRLTPESQSK 13 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2;H7BZ56;H7BZC2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AS(0.004)AGRLT(0.996)PESQSK 76.158 0.04758 258490000 496850 422680 481160 583080 448740 541350 610760 602660 554470 TRUE FALSE 473364.8852 465751.5725 503221.6619 524467.6906 527000.1139 522602.9138 517577.3446 549887.8955 640454.3758 0.739107894 0.727220533 0.785726011 0.818899379 0.822853483 0.815987732 0.808140852 0.85859027 1 19.28873627 -5 0.090508408 1.707815398 0.610866302 0.928458259 0.020011911 54.46670635 0.342192325 7.378941975 0.51068562 1.00E-05 5 -1.096949097 ASALLFS(ph)SDEEDQWNIPASQTHLASDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.56)S(0.44)DEEDQWNIPASQTHLASDSR;AS(0.001)ALLFS(0.538)S(0.461)DEEDQWNIPASQTHLASDSR 193.94 9.73E-19 448287000 73105 58683 78264 74685 81680 68880 79299 74253 92506 TRUE FALSE 69649.47153 64662.86442 81852.48181 67177.52191 95924.96614 66494.66833 67200.48112 67751.01368 106851.358 0.651835155 0.605166519 0.766040632 0.628700684 0.897742134 0.622309997 0.628915555 0.634067876 1 16.70524572 -1.938668142 2.662372126 1.224597841 0.67282619 0.557662038 0.089581661 14872776.49 8623316.719 20749670.78 0.020298507 0.011516801 1.938668142 -0.551771651 ASALLFSS(ph)DEEDQWNIPASQTHLASDSR ddPTM_SK-BR-3_Trastuzumab_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(0.16)S(0.84)DEEDQWNIPASQTHLASDSR;ASALLFS(0.028)S(0.972)DEEDQWNIPASQTHLASDSR;ASALLFS(0.03)S(0.97)DEEDQWNIPASQTHLASDSR;ASALLFS(0.037)S(0.963)DEEDQWNIPASQTHLASDSR;ASALLFS(0.15)S(0.85)DEEDQWNIPASQTHLASDSR 273.73 1.12E-61 1008335000 266512 218569 243703 285741 297920 254038 334467 286311 323137 TRUE FALSE 253914.5059 240841.4296 254877.0236 257017.7718 349877.1537 245240.6004 283437.9162 261240.091 373247.4356 0.680284663 0.645259435 0.682863429 0.688598895 0.937386624 0.65704564 0.759383426 0.699911282 1 18.50977282 -5 0.168134409 2.089223373 0.644799867 0.540533252 0.082388243 98.55944954 0.925486696 35.89116507 0.288298663 1.00E-05 5 -1.444423506 ASAPS(ph)PNAQVACDHCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASAPSPNAQVACDHCLK 17 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 AS(0.001)APS(0.999)PNAQVACDHCLK;AS(0.193)APS(0.807)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;AS(0.002)APS(0.998)PNAQVACDHCLK 275.37 6.56E-36 2010690000 2503970 2212560 2378160 2502020 2063310 2674040 3160300 2771910 2308820 TRUE FALSE 2385612.3 2438022.379 2487200.988 2250512.196 2423150.611 2581437.324 2678138.192 2529186.866 2666860.014 0.894539754 0.914192109 0.93263275 0.843880888 0.9086156 0.967968814 1.00422901 0.948376312 1 21.34671067 2.208977117 3.920590425 0.984670446 0.898886227 0.700302534 0.026668573 0.115618615 3.841316591 0.009824416 0.007310583 161.7994783 -2.208977117 -0.085784219 ASAS(ph)PSTSSTSSRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASASPSTSSTSSRPK 15 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;F5H858 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASAS(0.746)PS(0.2)T(0.054)SSTSSRPK;ASAS(0.958)PS(0.035)T(0.007)SSTSSRPK 193.27 6.04E-08 244964000 314669 272902 293102 326490 245975 314114 360150 313580 303160 TRUE FALSE 299795.22 300711.0241 306541.0166 293670.6049 288872.9621 303236.1534 305202.5029 286121.2728 350172.5045 0.856135808 0.858751102 0.875400018 0.838645528 0.82494473 0.865962203 0.871577577 0.817086633 1 18.41770628 -1.911250639 2.53062028 1.087255501 0.853636478 0.853931641 0.019332474 2974191.434 1605106.201 1540529.9 0.004437066 0.012267311 1.911250639 -0.233619023 ASAVSELS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR 183.37 1.76E-06 44665170000 6756170 5934620 6132150 7020860 6897190 6327940 7290630 6504630 7441640 TRUE FALSE 6436819.234 6539364.525 6413315.143 6315109.814 8100057.752 6108801.851 6178310.492 5935050.114 8595651.525 0.748845997 0.7607759 0.74611158 0.734686579 0.942343664 0.710685145 0.718771634 0.690471234 1 23.03517557 -1.163116496 4.106522817 1.000088778 0.756227598 0.550048801 0.069187088 9484595.634 2686385.274 7536.90303 0.015469022 0.068688416 1.163116496 -0.24386118 ASDADRPCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASDADRPCR 9 1 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 ;; 87.308 0.012357 100285000 251159 238814 236856 272244 266558 239776 285232 246133 289637 FALSE TRUE 239287.2118 263149.4181 247716.0819 244877.5159 313045.6308 231472.497 241714.6198 224580.2897 334552.4267 0.715245781 0.786571542 0.740440248 0.731955581 0.935714722 0.691887066 0.722501469 0.671285789 1 18.35187278 -2.238554053 2.324130378 1.893261294 0.750811322 0.538576382 0.072872719 4291077.45 667273.8773 20215780.8 0.017070397 0.00577359 2.238554053 -1.142449972 ASDPQS(ph)PPQVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASDPQSPPQVSR 12 0 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 ASDPQS(0.999)PPQVS(0.001)R;ASDPQS(1)PPQVSR;AS(0.022)DPQS(0.978)PPQVS(0.001)R 182.02 0.00012044 344287000 610360 501420 550400 621530 651150 563080 675190 596730 713720 TRUE FALSE 581509.4924 552515.2681 575636.3844 559052.6236 764710.3538 543580.3984 572177.3648 544477.1577 824400.0524 0.705372944 0.670202854 0.698248845 0.678132688 0.927596197 0.659364828 0.694053043 0.6604526 1 19.65298507 -1.515204968 3.257468079 1.007663529 0.709160667 0.571311018 0.078463215 20198282.68 26601396.38 1383156.63 0.017776918 0.030534797 1.515204968 -0.298502862 ASDSSS(ph)PSCSSGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASDSSSPSCSSGPR 14 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 ASDSS(0.024)S(0.964)PS(0.009)CS(0.002)SGPR;ASDSS(0.001)S(0.537)PS(0.073)CS(0.358)S(0.031)GPR 153.2 6.77E-06 60998000 154841 134512 150764 167454 158378 150905 172201 152046 174809 TRUE FALSE 147521.9728 148218.9257 157676.6785 150621.2058 185999.0731 145679.122 145928.5748 138732.0462 201917.4869 0.730605234 0.734056906 0.780896598 0.745954241 0.921163768 0.721478482 0.722713902 0.687072964 1 17.62340633 -2.105704398 2.457493323 1.448010388 0.753672904 0.594682715 0.063422128 15024119.44 5336045.007 37508560.26 0.01494957 0.007839631 2.105704398 -0.694337484 ASDVHEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASDVHEVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 152.47 0.00045665 13153670000 22982400 19898300 20008600 26140000 26161800 20938300 26763600 23222900 24808400 FALSE TRUE 21896067.5 21925959.39 20926014.1 23512357.54 30724409.64 20213201.42 22680321.27 21189379.76 28655559.97 0.764112358 0.765155503 0.73026017 0.820516422 1.072197147 0.705384974 0.791480651 0.739450905 1 24.77231175 -2.535171892 2.147267187 3.879134429 0.795808845 0.275649964 0.102530927 3260920.351 278667.3498 45642460.66 0.024139515 0.002916273 2.535171892 -3.083325584 ASDVHEVRK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 138.08 9.52E-05 1250430000 2508100 1338420 2303760 2066840 2555830 2256970 3585840 2612200 3120330 FALSE TRUE 2389547.084 1474806.52 2409389.675 1859077.316 3001565.943 2178810.563 3038754.25 2383461.92 3604214.84 0.662986861 0.409189403 0.668492246 0.515806465 0.832793292 0.604517394 0.843111297 0.661298515 1 21.78125358 1.217278142 0.299427802 1.040551373 0.499876654 0.522187804 0.117134883 1.159878313 0.363480033 0.240717108 0.170132542 16.49218286 -1.217278142 -0.540674719 ASEDGESVGHCPSCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASEDGESVGHCPSCQR 16 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 69.485 0.046081 208640000 140380 123200 136820 150240 144030 123160 167520 132580 124350 FALSE TRUE 133744.5156 135754.2201 143093.3323 135137.5898 169148.7864 118894.9383 141961.7473 120970.5923 143633.5629 0.93115086 0.945142746 0.996238828 0.940849667 1.177641096 0.827765711 0.98836055 0.842216749 1 17.13203338 -0.175478068 7.836468016 1 0.957586336 0.020172269 0.095546669 11113161.47 1418133.942 0.081776969 0.019833828 0.667608615 0.175478068 -0.042413663 ASEDTTS(ph)GSPPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTT(0.004)S(0.638)GS(0.358)PPKK;ASEDT(0.001)T(0.084)S(0.579)GS(0.335)PPKK;ASEDT(0.002)T(0.103)S(0.595)GS(0.3)PPKK;ASEDT(0.001)T(0.013)S(0.493)GS(0.493)PPKK 139.3 4.14E-05 303929000 671428 595623 635123 723817 349865 769025 771559 782847 397770 TRUE FALSE 639690.9291 656317.6609 664244.0178 651057.54 410881.3452 742393.4714 653843.5039 714296.7665 459454.1401 1.392284612 1.428472624 1.445724306 1.417023993 0.894281517 1.615816263 1.423087631 1.554663903 1 18.80956134 2.94708415 24.99601382 1.337815029 1.420764243 0.054732526 0.222089577 1405.113156 663736.3509 0.064315898 0.068217848 885.287128 -2.94708415 0.082949214 ASEDTTSGS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ASEDTTSGS(0.999)PPK;ASEDTTSGS(1)PPK;ASEDTTS(0.001)GS(0.999)PPK 228.93 9.86E-12 1109882000 2349010 2180920 2176040 2622790 1382320 2678800 2647800 2813950 1693370 TRUE FALSE 2237976.953 2403158.228 2275813.586 2359142.166 1623396.17 2586032.484 2243829.48 2567545.62 1955969.171 1.14417803 1.228627865 1.163522217 1.206124412 0.829970224 1.322123335 1.147170167 1.312671824 1 20.8994522 -2.33683336 2.225290411 0.049642323 1.16911475 0.133693837 0.135435713 2142079.458 412274.7298 10451828.25 0.029831839 0.004604332 2.33683336 1.119472427 ASEDTTSGS(ph)PPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDT(0.001)T(0.002)S(0.014)GS(0.982)PPKK;ASEDTTS(0.001)GS(0.999)PPKK;ASEDTT(0.001)S(0.026)GS(0.973)PPKK;ASEDTT(0.007)S(0.205)GS(0.788)PPKK;ASEDTT(0.001)S(0.025)GS(0.974)PPKK;ASEDTTS(0.039)GS(0.961)PPKK 227.47 9.58E-12 9643755000 6410059 5881062 5959598 7021795 3295891 7472478 7425615 7446680 3899323 TRUE FALSE 6107068.215 6480348.904 6232851.463 6315950.826 3870693.347 7213704.213 6292701.051 6794609.222 4504010.096 1.355917967 1.438795377 1.383844914 1.402294997 0.859388248 1.601618127 1.397132981 1.508568826 1 22.10277863 ASEEHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 ASEEHLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;;;;;;;;;; 113.7 0.0060716 16816330000 24254230 23109313 21106593 24879850 18524210 22955948 26885440 24178250 18797479 FALSE TRUE 23107780.62 25464178.27 22074351.17 22378880.21 21754826.36 22160977.76 22783572.34 22061074.25 21712496.04 1.064261823 1.172789081 1.016665754 1.030691274 1.001949583 1.020655466 1.049329948 1.016054267 1 24.37202225 3.71928172 24.91374331 1.022807217 1.118525452 0.664114888 0.029245814 385.2746856 497882.8614 0.007437687 0.011543667 5239.401976 -3.71928172 0.095718234 ASEENLLSSSSVPSADRDSS(ph)PTTNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.271)S(0.568)PT(0.154)T(0.007)NSK;ASEENLLSSSSVPSADRDS(0.21)S(0.786)PT(0.004)T(0.001)NSK 229.95 4.27E-35 532940000 484530 443710 447540 525700 360390 512840 554650 572730 461670 TRUE FALSE 461627.2271 488924.5535 468060.1517 472855.6372 423241.9019 495080.2222 470027.9557 522578.725 533263.4257 0.865664519 0.916853716 0.877727834 0.886720548 0.793682599 0.928397108 0.88141795 0.97996356 1 19.02448886 1.1921404 3.05514029 1.0017997 0.88002383 0.62585297 0.035830329 0.153817268 2.527190493 0.030995065 0.008562331 15.56468731 -1.1921404 -0.121775871 ASEHKDQLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASEHKDQLSR 10 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 ;; 165.63 3.48E-06 180126000 192223 151854 179844 203149 188995 189491 251575 217232 233386 FALSE TRUE 183136.9997 167328.0952 188090.0253 182728.0766 221955.6682 182928.8792 213192.6133 198210.0145 269578.3089 0.6793462 0.620703112 0.697719435 0.677829301 0.823343944 0.678574177 0.790837416 0.735259507 1 18.04034489 -5 0.129809733 2.01295221 0.580044008 0.789689236 0.04936358 56.09027947 0.459586791 14.6702314 0.336785314 1.00E-05 5 -1.432908202 ASEKPVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;ASEKPVS(1)PK 108.68 0.0015572 1482740000 3926830 3452970 3483270 4222060 1862040 3999150 4017900 4184140 2133750 TRUE FALSE 3741216.528 3804831.569 3642981.375 3797650.507 2186779.186 3860658.433 3404895.561 3817754.52 2464641.052 1.517955941 1.543767018 1.478098148 1.540853385 0.887260717 1.566418132 1.381497544 1.549010359 1 21.23294612 -3.750696206 0.183252838 5.51E-15 1.532774413 0.297665431 0.203684372 101.1486115 1.481813726 39.35352099 0.594739374 0.000177543 3.750696206 1.532774413 ASELS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASELSPGR 8 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T196 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 1 ASELS(1)PGR 92.201 0.012531 119370000 135950 116420 117270 138590 149880 110210 134010 132250 134340 TRUE FALSE 129523.9129 128283.3304 122646.9455 124658.6699 176019.0245 106393.4001 113564.3132 120669.4889 155172.7611 0.834707793 0.826712945 0.790389658 0.803354075 1.134342286 0.685644821 0.73185727 0.777646077 1 17.2435158 -0.572047026 7.273639973 1.00000312 0.819158767 0.178029913 0.119204664 15080608.47 2073323.26 0.111257524 0.026983913 0.267887823 0.572047026 -0.180844353 ASEPLLS(ph)PPPFGESR ddPTM_SK-BR-3_Trastuzumab_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 284.53 5.73E-34 286029000 246981 253702 223564 255485 256634 235568 255204 276073 275486 TRUE FALSE 235306.6976 279554.5222 233814.6305 229803.1624 301390.8883 227410.2211 216267.9427 251898.5846 318206.9619 0.7394769 0.878530503 0.734787916 0.722181441 0.947153659 0.714661363 0.679645541 0.79161871 1 18.27960587 ASES(ph)PARGPSGSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASESPARGPSGSPR 14 1 O43237;O43237-2;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 AS(0.053)ES(0.947)PARGPSGSPR;AS(0.001)ES(0.999)PARGPSGSPR 105.02 0.0006201 323536000 307590 226779 304450 298610 332500 308410 391390 332270 427770 TRUE FALSE 293050.8303 249888.0379 318409.3336 268593.1555 390487.8947 297729.6844 331676.2671 303174.6773 494106.3869 0.593092577 0.505737316 0.644414527 0.543593774 0.79029113 0.602561902 0.671264885 0.613581782 1 18.91446218 -4.999999998 0.182078021 2.598798026 0.535088281 0.729381412 0.07360079 63.70756457 0.615543084 36.8271086 0.202987225 1.00E-05 4.999999998 -2.063709746 ASES(ph)SSEEKDDYEIFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASESSSEEKDDYEIFVK 17 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 AS(0.003)ES(0.8)S(0.132)S(0.066)EEKDDYEIFVK 144.92 2.99E-07 88662000 168250 138980 150670 163560 90378 179720 179020 189440 97598 TRUE FALSE 160297.1559 153142.22 157578.3685 147118.6381 106139.8946 173496.2513 151707.2111 172851.6293 112732.9994 1.421918665 1.358450683 1.397801614 1.305018396 0.941515751 1.539001466 1.345721412 1.533283336 1 16.78255036 3.230160686 15.06352695 1.300357931 1.389550396 0.065414361 0.192743387 5.142784781 9216.302806 0.052259114 0.064305615 1698.872109 -3.230160686 0.089192465 ASESS(ph)SEEKDDYEIFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASESSSEEKDDYEIFVK 17 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 ASES(0.35)S(0.525)S(0.125)EEKDDYEIFVK 246.67 6.80E-21 89396000 199050 175740 182030 221010 108470 222320 213290 236640 114720 TRUE FALSE 189641.301 193648.1058 190376.2556 198793.6549 127387.1337 214621.0027 180748.6932 215918.5471 132510.1917 1.43114502 1.461382731 1.436691421 1.500214077 0.961338385 1.619656571 1.364036161 1.629448606 1 17.0157438 -1.647587012 2.893353123 0.959711058 1.422111008 0.344791259 0.184280521 152002961.8 144236643.7 45570421.62 0.039516277 0.022511943 1.647587012 0.46239995 ASESSKPWPDATYGTGSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 190.37 1.69E-17 546810000 532180 461390 469210 524370 436330 436190 527680 508490 471750 FALSE TRUE 507024.9061 508406.1656 490723.7426 471659.3314 512425.8139 421084.6309 447172.7245 463963.9199 544906.5806 0.930480424 0.933015279 0.900564904 0.865578336 0.940392045 0.772764811 0.820641079 0.851455894 1 19.05564939 3.115751312 1.127228497 0.849997651 0.932434166 0.059383293 0.063740478 0.704309687 1.918438151 0.024594282 0.033669664 1305.423156 -3.115751312 0.082436515 ASET(ph)PPPVAQPKPEAPHPGLETTLQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 AS(0.001)ET(0.999)PPPVAQPKPEAPHPGLETTLQER;AS(0.001)ET(0.999)PPPVAQPKPEAPHPGLETTLQER;AS(0.101)ET(0.899)PPPVAQPKPEAPHPGLETTLQER;AS(0.006)ET(0.994)PPPVAQPKPEAPHPGLETTLQER 192.63 5.01E-18 998180000 776340 720033 710280 823000 565881 766620 827450 775820 578734 TRUE FALSE 739643.9468 793405.1813 742847.0406 740270.4764 664570.4672 740071.7572 701207.3053 707885.0879 668481.113 1.106454517 1.186877484 1.111246116 1.10739176 0.994149953 1.107094491 1.048956046 1.058945532 1 19.35052727 3.100865212 2.518296006 1.050620757 1.144250186 0.540975975 0.038959778 0.196729569 2.535605467 0.011127728 0.013751579 1261.435975 -3.100865212 0.093629429 ASEYS(ph)PASLDAFGAFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASEYSPASLDAFGAFLK 17 0 P17029;E9PC66;B3KRF7 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ASEYS(1)PASLDAFGAFLK;ASEYS(1)PASLDAFGAFLK 319.33 1.97E-58 45538000 157046 124841 135421 158704 122965 131524 156108 141493 145148 TRUE FALSE 149622.7468 137562.4398 141630.1868 142750.7724 144410.0571 126969.2909 132290.8575 129103.1228 167656.8105 0.892434649 0.82050016 0.844762502 0.851446308 0.86134322 0.757316631 0.789057462 0.770044011 1 17.35515156 2.290634246 24.99993709 0.807182044 0.852456376 0 0.070025177 227.9289562 109424.905 0.021348051 0.017861045 195.2694245 -2.290634246 0.045274332 ASFNNPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASFNNPDR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 121.53 0.0033248 772700000 1133140 964780 970240 1136940 1261530 1076370 1139330 1063730 1335670 FALSE TRUE 1079578.718 1063092.179 1014726.464 1022652.631 1481540.433 1039095.037 965504.2833 970584.162 1542798.882 0.699753371 0.689067247 0.657717915 0.66285544 0.96029395 0.673512957 0.625813445 0.629106083 1 20.55711857 -2.198861834 2.429204569 1.919617786 0.697687225 0.4931819 0.095629654 4777590.162 1338769.635 24076486.41 0.022699374 0.006326131 2.198861834 -1.221930562 ASFSRPTFLQLS(ph)PGGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASFSRPTFLQLSPGGLR 17 1 S4R3C3;S4R3I3;Q5JR12 S4R3C3 PPM1J Protein phosphatase 1J 1 ASFSRPTFLQLS(1)PGGLR;ASFSRPTFLQLS(1)PGGLR 172.81 9.42E-10 398380000 354110 295719 322180 328900 368640 300752 386500 307710 365560 TRUE FALSE 337371.9221 325853.1023 336952.2717 295838.3471 432930.6993 290336.8828 327532.3264 280765.2811 422249.1778 0.798987754 0.77170808 0.797993908 0.70062504 1.025296725 0.687596088 0.775684936 0.664927952 1 18.68773509 -2.262642486 2.308339892 1.889109238 0.779891205 0.32993838 0.099453497 5907379.521 779460.1162 27550240.44 0.022817469 0.005462073 2.262642486 -1.109218034 ASGDPGASGMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ASGDPGASGMSPR 13 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.201)GMS(0.799)PR;ASGDPGAS(0.073)GMS(0.927)PR;ASGDPGASGMS(1)PR 187.77 9.01E-07 1424327000 1916772 1639014 1650713 1988210 1806973 1743218 1949644 1843177 1943381 TRUE FALSE 1826169.986 1806031.39 1726399.824 1788351.353 2122108.519 1682849.924 1652190 1681778.651 2244750.6 0.813529123 0.804557705 0.769083133 0.796681535 0.945364941 0.749682358 0.736023859 0.749205124 1 21.09812373 -2.141397691 2.351400725 1.441470311 0.794689651 0.542408441 0.059020886 9626685.035 2272288.266 22686550.73 0.014326881 0.007221083 2.141397691 -0.64678066 ASGGAQS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASGGAQSPLR 10 0 H7BZV9;C9JU48;D3YTC9;Q6NXT1 H7BZV9 ANKRD54 Ankyrin repeat domain-containing protein 54 1 ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR;ASGGAQS(1)PLR 106.11 0.0025807 537086000 748160 621270 569270 792350 711970 728600 873530 703810 732560 TRUE FALSE 712795.9595 684578.1193 595371.5926 712701.4726 836137.3426 703368.3993 740256.955 642180.6653 846161.6634 0.842387442 0.809039394 0.703614473 0.842275777 0.988153185 0.831245883 0.874841046 0.758933775 1 19.6905738 3.003311774 24.99807683 0.881196107 0.795181698 0.273106244 0.077346727 147.7601396 1115309.991 0.021020136 0.025003167 1007.65479 -3.003311774 -0.086014408 ASGGLPQFGDEYDFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASGGLPQFGDEYDFYR 16 0 Q01780;Q01780-2;K7EJ37 Q01780 EXOSC10 Exosome component 10 0 128.96 0.00013483 48006000 18727 19167 20873 21360 13913 19785 22354 26148 15912 FALSE TRUE 17841.81182 21120.13909 21830.0477 19212.85222 16339.42279 19099.84049 18943.48674 23858.3425 18379.55169 0.970742493 1.149110677 1.187735591 1.045338458 0.889000073 1.039189683 1.030682742 1.298091646 1 14.16581396 -1.081003119 4.377118786 0.999994701 1.068779349 0.038473374 0.114501833 6.95E-06 1.46E-06 0.10561344 0.024890964 0.082984481 1.081003119 0.068784648 ASGQAFELILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 160.93 4.42E-05 5864550000 1158423 1041003 1161742 1350863 1365050 1098521 1277469 1091699 1321875 TRUE FALSE 1103666.641 1147082.389 1215009.02 1215071.685 1603114.288 1060478.942 1082567.642 996104.0481 1526864.624 0.72283202 0.751266596 0.795754254 0.795795296 1.049938719 0.694546803 0.709013507 0.652385308 1 20.54214072 -2.407387841 2.354618161 3.106822191 0.768608434 0.305201255 0.108301775 10660752.18 1050125.949 120186219.8 0.028165287 0.003913922 2.407387841 -2.338213758 ASGQPAGPDNKENCPVPGKPGEAVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASGQPAGPDNKENCPVPGKPGEAVAAR 27 2 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 197.89 3.26E-25 153970000 101180 91151 100180 106760 71035 106170 135260 124440 98914 FALSE TRUE 96397.42192 100439.3905 104773.3521 96028.28197 83423.48151 102493.3063 114623.6028 113543.3739 114253.0779 0.843718381 0.879095709 0.917028705 0.840487484 0.730163975 0.897072605 1.003243018 0.993788316 1 16.80187351 1.845880958 3.981374338 0.998084309 0.848394348 0.690866512 0.047519719 0.139064107 3.550572302 0.024070903 0.013208839 70.12630523 -1.845880958 -0.149689961 ASGSLSPPILAPLS(ph)PGAEISPHDLSLESCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASGSLSPPILAPLSPGAEISPHDLSLESCR 30 0 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 ASGSLSPPILAPLS(1)PGAEISPHDLSLESCR;ASGSLSPPILAPLS(1)PGAEISPHDLSLESCR;ASGSLSPPILAPLS(1)PGAEISPHDLSLESCR;ASGSLSPPILAPLS(1)PGAEISPHDLSLESCR 273.54 1.80E-71 267294000 206043 160983 168328 213725 232675 174732 246848 207778 254430 TRUE FALSE 196303.7557 177387.3507 176046.0053 192240.9569 273253.4463 168680.987 209186.8039 189583.8568 293885.705 0.667959524 0.603592988 0.599028814 0.654135107 0.929794957 0.573967989 0.711796458 0.645093836 1 18.16489566 -5 0.262298708 3.151273923 0.643628662 0.513903987 0.099595431 157.7574176 1.545576928 183.202398 0.121778935 1.00E-05 5 -2.507645261 ASGTNDKPGGPHYILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGTNDKPGGPHYILR 16 1 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 162.41 4.86E-09 493480000 1428820 1047320 1233950 1220350 1229130 1106450 1524650 1373580 1190800 FALSE TRUE 1361282.51 1154043.099 1290527.828 1097678.099 1443489.883 1068133.359 1292036.64 1253302.053 1375463.182 0.989690257 0.839021439 0.938249635 0.798042517 1.049457304 0.776562668 0.939346583 0.911185461 1 20.39148609 -1.110350064 3.905168048 1.000031317 0.903335343 0.112705469 0.083453519 23203309248 40804808783 9478890.854 0.017127357 0.077562167 1.110350064 -0.096695975 ASGYFTRPWQWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGYFTRPWQWEK 13 1 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 166.86 3.00E-05 1006840000 571610 376340 387090 475730 760670 472240 868400 673520 793530 FALSE TRUE 544591.1281 414689.4739 404838.4594 427908.7166 893330.6072 455886.2104 735909.6307 614543.0182 916586.5796 0.594151322 0.452428045 0.441680544 0.466850297 0.974627632 0.497373866 0.802880652 0.670469143 1 19.80591164 1.265464752 0.321088194 1.033091458 0.456966002 0.465484548 0.152927725 1.252530355 0.438436238 0.276578143 0.198793656 18.42742921 -1.265464752 -0.576125456 ASGYQS(ph)SQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 ASGYQS(0.987)S(0.013)QKK;ASGYQS(0.956)S(0.043)QKK 147.26 0.0026266 0 223957 212186 216922 269230 131399 246920 276650 283640 173376 TRUE FALSE 213370.9965 233807.9946 226868.0883 242166.4889 154314.944 238369.0985 234441.9615 258802.9779 200262.2646 1.065457823 1.167508992 1.132854903 1.209246731 0.770564261 1.190284645 1.170674675 1.29232024 1 17.61153107 ASGYQSSQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 108.37 0.0034634 681680000 702510 396990 507570 493420 502270 534160 840980 627770 730160 FALSE TRUE 669303.7445 437443.7323 530842.5866 443820.4842 589865.729 515661.9053 712673.0553 572799.1308 843389.4837 0.793587966 0.518673449 0.629415705 0.526234311 0.699398961 0.611416096 0.845010602 0.679163236 1 19.68583951 0.861888133 0.641355335 0.996710493 0.621341012 0.56388251 0.097486678 0.667649855 0.60845418 0.095391282 0.037940496 7.275923647 -0.861888133 -0.375369481 ASHEEVEGLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASHEEVEGLVEK 12 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 184.03 1.48E-05 2020550000 7746230 6685640 3226010 3702040 5914590 3685110 7266480 3944110 2802020 FALSE TRUE 7380081.059 7366914.317 3373925.749 3329903.906 6946092.623 3557493.717 6157845.018 3598742.819 3236542.951 2.280235786 2.276167636 1.042447389 1.028845888 2.146145665 1.099164686 1.902599506 1.111909489 1 21.62602222 3.754632597 24.21092525 1.406675984 2.278201918 0.488560041 0.396515073 413.1942254 622435.4008 0.094530502 0.169676945 5683.718983 -3.754632597 0.871525934 ASHGYGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASHGYGGK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 120.46 0.0014981 1650330000 4093380 3612890 3473910 4239340 3256020 3730740 4504200 4335600 3692520 FALSE TRUE 3899894.04 3981047.599 3633192.21 3813193.489 3823868.857 3601543.538 3817001.565 3955951.88 4265137.143 0.914365449 0.933392636 0.851834792 0.894037721 0.896540657 0.844414474 0.894930558 0.927508717 1 22.0241607 0.902445313 2.897828654 0.999830016 0.892929443 0.64158124 0.026171857 0.281622953 5.180199743 0.026772586 0.007054295 7.988133473 -0.902445313 -0.106900573 ASHPEDPASVVEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASHPEDPASVVEAR 14 0 Q9UHL4;R4GMR2 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 78.191 0.013291 0 53326 43241 49948 53308 72724 44836 52034 58901 109760 FALSE TRUE 50805.38566 47647.30706 52238.16521 47949.37856 85407.04257 43283.31808 44095.25763 53743.31619 126781.0202 0.400733371 0.37582366 0.412034586 0.378206284 0.673657953 0.341402191 0.347806458 0.423906639 1 16.95197926 -1.694096143 2.309520965 1.115550963 0.412088006 0.788586886 0.094445233 1808553.423 1265673.481 1214421.21 0.023429754 0.020225714 1.694096143 -0.703462956 ASHS(ph)SERPPPR ddPTM_SK-BR-3_Trastuzumab_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(0.138)HS(0.856)S(0.006)ERPPPR 91.28 0.0061457 0 22317 21721 19712 23425 30232 21288 28524 25002 33079 TRUE FALSE 21262.11964 23934.39459 20615.8147 21070.2745 35504.45123 20550.79122 24172.13992 22812.69234 38208.72238 0.556472929 0.626411801 0.539557813 0.551451951 0.929223722 0.537856017 0.63263408 0.597054571 1 15.2216144 -5 0.320791651 4.606669188 0.603283326 0.517815584 0.114742722 257.7108032 2.27788174 631.4603304 0.094536644 1.00E-05 5 -4.003385862 ASHTAPQVLFSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASHTAPQVLFSHR 13 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 125.03 0.00011848 349673000 254567 321991 228343 272266 315678 223277 303921 243586 225257 FALSE TRUE 242534.1224 354802.249 238812.7524 244897.3044 370732.1433 215544.8615 257552.2696 222256.3185 260188.7051 0.932147006 1.363634324 0.917844425 0.941229575 1.424858712 0.828417442 0.989867218 0.854212017 1 17.98919881 ASIGQS(ph)PGLPSTTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.999)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK 255.49 1.05E-24 354988000 886790 823720 745650 950880 646150 822020 920680 914530 751390 TRUE FALSE 844873.1941 907658.0045 779838.79 855295.7358 758838.3554 793553.2413 780213.3566 834448.905 867911.7236 0.973455216 1.045795304 0.898523166 0.985463974 0.874326656 0.914324832 0.898954738 0.961444444 1 19.72718879 3.734961426 24.99905562 0.92606839 1.00962526 0.336258831 0.043679055 258.6112658 1796250.215 0.010441668 0.01688187 5432.020823 -3.734961426 0.08355687 ASIHEAWTDGK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 172.17 1.37E-05 3091080000 6093200 2934330 2873090 5067100 5425100 3757840 7107800 5214600 5477400 FALSE TRUE 5805186.512 3233341.563 3004824.018 4557745.481 6371235.722 3627705.059 6023374.566 4757981.98 6326807.217 0.91755388 0.511054226 0.47493529 0.720386338 1.007022263 0.573386375 0.952040162 0.752035239 1 22.59304621 2.992443335 24.8919997 0.841052043 0.642138886 0.260933027 0.171817565 484.9494749 1597453.907 0.048193823 0.055348352 982.7506401 -2.992443335 -0.198913156 ASIHEAWTDGKEAMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASIHEAWTDGKEAMLK 16 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 157.8 1.92E-08 65884000 330060 228080 254250 339920 358680 242590 425110 351230 462830 FALSE TRUE 314458.7179 251321.6113 265907.614 305750.5958 421233.6784 234189.0475 360251.6618 320474.4392 534603.3126 0.588209445 0.470108593 0.49739238 0.571920504 0.787936903 0.438061347 0.673867246 0.599462128 1 19.02810925 -4.999999995 0.208267577 3.056868394 0.508896024 0.656931792 0.097542947 82.85392806 0.82473702 70.95594844 0.194214159 1.00E-05 4.999999995 -2.547972369 ASKEEERPS(ph)SEDEIALHFEPPNAPLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASKEEERPSSEDEIALHFEPPNAPLNR 27 2 P41182-2;P41182 P41182-2 BCL6 B-cell lymphoma 6 protein 1 AS(0.169)KEEERPS(0.416)S(0.416)EDEIALHFEPPNAPLNR 53.123 0.048555 17701000 25027 18191 21930 24564 21036 23477 28583 20787 25359 TRUE FALSE 23844.02331 20044.68358 22935.51219 22094.78005 24704.67174 22663.9856 24222.13839 18966.78008 29291.5442 0.814024114 0.684316383 0.783007957 0.754305744 0.84340626 0.773738163 0.826932791 0.647517248 1 14.83819663 -1.225121495 4.33584802 1.000101045 0.76865007 0.593895846 0.060797749 5.48E-05 9.80E-06 0.05434008 0.012802501 0.059549553 1.225121495 -0.231450974 ASKETS(ph)CKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASKETSCKR 9 2 A0A3B3ISA2;Q8WWF3 A0A3B3ISA2 SSMEM1 Serine-rich single-pass membrane protein 1 1 AS(0.001)KET(0.001)S(0.998)CKR 78.653 0.015217 104540000 107740 100960 90910 123870 65944 112370 129410 115690 76519 TRUE FALSE 102647.3437 111247.9388 95078.31342 111418.3523 77444.61272 108478.5987 109666.1277 105559.5703 88385.17572 1.161363802 1.25867192 1.075726927 1.260599997 0.876217217 1.227339289 1.240775128 1.194313067 1 16.4315168 3.748236241 24.67020698 1.142487647 1.210017853 0.063659881 0.121970277 1769.80893 4512513.518 0.029874873 0.053030837 5600.621732 -3.748236241 0.067530206 ASLENSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ASLENSLR 8 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;; 247.1 8.93E-09 14691960000 9107400 7846670 6879300 7619370 9488470 7212530 9758010 8064110 9535390 FALSE TRUE 8676911.251 8646254.594 7194722.71 6853456.452 11143256.16 6962758.278 8269246.356 7357973.778 11014089.58 0.787801042 0.785017639 0.653228999 0.622244481 1.011727395 0.632168299 0.750788006 0.66805102 1 23.39284691 -1.446324121 3.355399796 1.003510937 0.743782194 0.341214261 0.113844877 394020838.7 674719398.9 13876473.9 0.0249875 0.035782928 1.446324121 -0.259728743 ASLENSLREVEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASLENSLREVEAR 13 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 175.15 1.71E-05 240868000 443750 236267 568230 372235 690630 410086 732750 469920 1008350 FALSE TRUE 422774.8169 260342.8759 594283.9076 334817.2306 811075.6533 395884.619 620955.5296 428771.3136 1164719.768 0.362984152 0.223524047 0.510237676 0.287465912 0.696369784 0.339896883 0.53313728 0.368132598 1 20.15155145 -5 0.181567014 3.440312526 0.284479045 0.651203844 0.134910731 74.26726977 0.716940919 65.40476454 0.365496559 1.00E-05 5 -3.15583348 ASLGLADHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLGLADHR 9 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 82.749 0.017571 49781000 102080 103220 81301 93020 126010 82402 118960 105230 130160 FALSE TRUE 97254.8807 113738.2354 85028.73127 83669.45287 147986.1041 79548.39808 100810.4671 96015.50334 150344.548 0.646879996 0.756517192 0.565559127 0.556518038 0.984313073 0.529107301 0.670529583 0.638636416 1 17.19791303 -0.949906817 5.374601634 1.000000745 0.671774137 0.391790173 0.129743666 1.04E-06 2.04E-07 0.113085576 0.026654465 0.112225922 0.949906817 -0.328226608 ASLGQAS(ph)IQNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASLGQASIQNGK 12 0 E9PC69;Q7KZI7-14;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 ASLGQAS(1)IQNGK;ASLGQAS(1)IQNGK;ASLGQAS(1)IQNGK 168.45 4.88E-05 151220000 476966 427594 400309 516363 393889 410355 460207 501952 367221 TRUE FALSE 454420.7624 471166.3147 418663.5636 464457.2102 462583.1169 396144.3035 389993.9699 457998.4219 424167.7572 1.071323208 1.110801815 0.987023546 1.094984714 1.090566431 0.933933088 0.919433322 1.079757747 1 18.69427543 2.244628405 24.99931525 0.968923019 1.073689067 0.379088945 0.054319904 123.9809469 510803.5202 0.01841907 0.015041283 175.6420127 -2.244628405 0.104766048 ASLGS(ph)LEGEAEAEASS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(0.004)LGS(0.996)LEGEAEAEAS(0.101)S(0.899)PK 207.1 1.14E-15 74861000 239490 252020 206850 274330 129930 237810 222080 240990 126440 TRUE FALSE 228169.7823 277701.1245 216334.2771 246753.8272 152589.7509 229574.5801 188197.6172 219887.638 146047.6694 1.562296634 1.90144167 1.481257989 1.689543066 1.044794151 1.571915396 1.288604042 1.505588134 1 17.15607981 2.181483914 0.126956687 0.679184022 2.202808082 0.436300333 0.207201818 7.359077432 0.632593532 2.847417348 4.015550956 151.8741686 -2.181483914 1.52362406 ASLGS(ph)LEGEAEAEASS(ph)PKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(0.007)LGS(0.993)LEGEAEAEAS(0.093)S(0.907)PKGK 152.12 3.87E-08 93574000 578850 366360 649920 540860 372850 618640 800940 690700 438840 TRUE FALSE 551488.9077 403692.5005 679719.4749 486491.7252 437874.922 597216.3417 678741.8927 630218.6464 506893.0659 1.087978796 0.796405648 1.340952403 0.95975218 0.86384082 1.178190001 1.339023826 1.243297036 1 18.9513219 2.06558261 7.429525873 1.23842857 1.001232466 0.207547739 0.167511177 0.264940162 25.36539362 0.059606101 0.043851338 116.3007752 -2.06558261 -0.237196104 ASLGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.001)LGS(0.999)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK 498.44 1.05E-266 6877741000 5762850 5126840 4917270 5842110 3654793 5199210 5912290 5808750 4045980 TRUE FALSE 5490451.501 5649270.825 5142731.693 5254850.004 4292187.742 5019160.054 5010261.574 5300105.056 4673409.914 1.174827717 1.208811324 1.100423842 1.124414528 0.918427405 1.073982412 1.072078347 1.134098047 1 22.15604415 3.422134463 1.949348743 1.050783052 1.191375578 0.465865925 0.060983327 0.264328891 2.032560069 0.017796183 0.028245677 2643.227007 -3.422134463 0.140592525 ASLGSLEGEAEAEAS(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.5)S(0.5)PK 82.102 0.0061317 47827000 41224 43524 42370 52287 29542 42124 40243 40515 31582 TRUE FALSE 39275.42322 47959.14508 44312.70641 47031.01142 34694.11545 40665.23532 34103.19124 36967.29182 36479.57526 1.076641461 1.314684854 1.21472649 1.289242297 0.951055905 1.114739824 0.934857136 1.013369579 1 15.15480131 2.736126041 24.99978334 1.002851102 1.222108296 0.666810325 0.077628943 126.4673058 1298641.359 0.023458027 0.023102082 544.6607013 -2.736126041 0.219257194 ASLGSLEGEAEAEAS(ph)SPKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.557)S(0.443)PKGK 116.35 5.83E-05 83983000 109670 68872 118170 95723 74074 110140 142420 123520 95063 TRUE FALSE 104486.1164 75890.1351 123588.2114 86100.74218 86992.48215 106325.8242 120691.2133 112703.934 109804.8845 0.951561644 0.691136241 1.125525626 0.784124883 0.792246015 0.968315978 1.099142482 1.026401826 1 16.74458271 2.023535031 5.465522183 1.049152157 0.860603769 0.314429426 0.117016577 0.181593703 16.00305108 0.043758099 0.030616057 105.5686652 -2.023535031 -0.188548388 ASLGSLEGEAEAEASS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.01)S(0.99)PK;ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.002)S(0.998)PK 407.35 3.18E-147 717020000 2061210 2235930 1902130 2570520 1283840 2093270 2129010 2271140 1218450 TRUE FALSE 1963780.688 2463773.809 1989344.542 2312126.446 1507741.29 2020779.535 1804190.423 2072266.942 1407401.003 1.395324207 1.750584093 1.41348808 1.642834161 1.071294739 1.435823572 1.281930607 1.472406895 1 20.42460202 2.756668465 24.95634809 1.285718282 1.559032252 0.40941015 0.175343892 789.3367779 1087867.725 0.048004083 0.050824581 571.0425432 -2.756668465 0.27331397 ASLGSLEGEAEAEASS(ph)PKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.176)S(0.824)PKGK;ASLGSLEGEAEAEAS(0.03)S(0.97)PKGK;ASLGSLEGEAEAEAS(0.118)S(0.882)PKGK;ASLGSLEGEAEAEAS(0.023)S(0.977)PKGK 240.2 6.54E-30 1173368000 1093160 650393 1222250 1027350 771022 1110250 1502310 1260060 831859 TRUE FALSE 1041488.493 716668.7861 1278291.371 924078.8262 905487.9927 1071801.764 1273105.018 1149722.466 960859.4452 1.083913468 0.745862248 1.330362498 0.961721125 0.942372995 1.115461548 1.324964878 1.196556346 1 19.87396588 2.022932911 5.866090706 1.212928317 0.996620628 0.153101307 0.164762294 0.216105175 24.03295568 0.061630995 0.043529377 105.4224029 -2.022932911 -0.216307688 ASLLT(ph)DEEDVDMALDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLLTDEEDVDMALDQR 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 AS(0.111)LLT(0.889)DEEDVDMALDQR 90.367 0.042702 15025000 10771 9389.5 10010 13763 10742 12004 13518 11306 12276 TRUE FALSE 10261.87618 10346.30072 10468.9684 12379.51709 12615.4014 11588.29847 11455.58082 10315.9867 14179.69938 0.723701956 0.729655858 0.738306795 0.873045102 0.889680455 0.817245709 0.807886015 0.727518012 1 13.79153933 -5 0.087493043 1.609692094 0.617781808 0.530447528 0.061414684 181.2838509 1.107541741 21.49131298 1.620934379 1.00E-05 5 -0.991910286 ASLPQAATFGELSGPLKPGS(ph)PYRPPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 ASLPQAATFGELSGPLKPGS(1)PYRPPVPR 190.22 2.71E-18 174540000 392580 277580 317460 348610 340360 337190 456240 417670 378870 TRUE FALSE 374023.5214 305865.7176 332015.855 313567.0605 399718.6762 325513.0258 386632.2086 381096.6006 437623.2246 0.854670183 0.698924784 0.758679696 0.716522897 0.913385428 0.743820272 0.883481924 0.870832669 1 18.73932978 1.100738172 0.610472479 1.000655985 0.764523677 0.546552539 0.064846814 0.556475358 0.506720958 0.060567808 0.026840984 12.61067032 -1.100738172 -0.236132308 ASLQVLGTVGEPINPEAWLWYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLQVLGTVGEPINPEAWLWYHR 23 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 260.01 1.04E-43 307420000 463270 383780 388890 465780 490930 437670 513710 420930 397140 FALSE TRUE 441372.1452 422887.6183 406720.9912 418958.9095 576548.0366 422513.3782 435334.1046 384071.1377 458726.4429 0.962168526 0.92187321 0.886630796 0.913308827 1.256845001 0.921057386 0.949005908 0.837255283 1 18.80727455 -2.749201232 2.058560366 2.50576743 0.956813267 0.014851743 0.112408135 3848719.13 559290.6717 28039073.59 0.026398764 0.001781553 2.749201232 -1.548954163 ASLVALPEQTAS(ph)EEETPPPLLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASLVALPEQTASEEETPPPLLTK 23 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ASLVALPEQT(0.208)AS(0.792)EEETPPPLLTK;ASLVALPEQT(0.004)AS(0.996)EEETPPPLLTK 177.14 3.58E-17 61146000 170282 166469 163453 195303 140736 171149 205730 205836 182005 TRUE FALSE 162233.1073 183432.3804 170947.4817 175670.7714 165280.3138 165222.0672 174342.11 187811.9086 210229.4058 0.771695599 0.872534361 0.813147338 0.83561465 0.786190272 0.78591321 0.829294595 0.893366501 1 17.68160495 0.962606267 2.192565165 0.999396373 0.81450454 0.819528153 0.028589851 0.136652292 1.439622825 0.026774753 0.00736966 9.175004103 -0.962606267 -0.184891833 ASMSEFLES(ph)EDGEVEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR 439.83 1.54E-190 390346000 982123 922144 920999 1041781 1018856 947749 1066807 979510 1070728 TRUE FALSE 935699.9922 1016111.522 963227.7151 937059.1946 1196544.164 914928.2145 904045.9989 893738.9117 1236771.03 0.756566874 0.821584188 0.77882461 0.757665867 0.967474282 0.739771706 0.730972813 0.722638945 1 20.238147 -2.216760325 2.4739389 1.740511176 0.784595514 0.478143535 0.070773587 4111125.775 1016404.54 17207501.12 0.017141513 0.006070713 2.216760325 -0.955915662 ASNEDGDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASNEDGDIKR 10 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 136.49 0.00018654 1676040000 2025150 1798030 1830640 2193120 1500780 2035950 2300170 2226260 1722420 FALSE TRUE 1929425.173 1981251.301 1914576.655 1972663.411 1762515.557 1965444.541 1949236.821 2031316.872 1989524.097 0.969792312 0.995841822 0.96232896 0.991525267 0.88589807 0.987896826 0.979750295 1.021006418 1 20.92399194 1.482290889 2.580008623 1.00959012 0.967282218 0.25043903 0.031248515 0.394248565 5.168361919 0.023709872 0.008033058 30.35923958 -1.482290889 -0.042307902 ASNGDAWVEAHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 167.56 3.17E-05 3809900000 7055090 5485390 6095820 5891830 5226260 5213790 6515480 6332670 5499240 FALSE TRUE 6721609.878 6044357.477 6375319.377 5299572.055 6137718.089 5033235.145 5521423.861 5778147.843 6352034.053 1.05818228 0.951562512 1.003665806 0.834311027 0.966260262 0.792381638 0.869237132 0.909653159 1 22.59878722 3.883888086 0.884147751 0.882399165 1.055301573 0.337958145 0.066828349 0.763509615 0.98950138 0.02321008 0.09988953 7653.993454 -3.883888086 0.172902408 ASNTS(ph)TPTKGNTETSASASQTNHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 AS(0.251)NT(0.187)S(0.28)T(0.28)PT(0.002)KGNTETSASASQTNHVK 105.56 0.0024848 120280000 62541 54096 62047 68749 44876 69526 88755 80615 59839 TRUE FALSE 59584.81087 59608.4439 64891.91632 61838.21991 52702.36019 67118.29719 75213.79465 73555.92323 69118.5265 0.862067146 0.862409066 0.938849822 0.894669245 0.762492531 0.97106088 1.088185736 1.064199817 1 16.07678484 2.011470955 7.045231164 1.053431467 0.868004302 0.758689608 0.048458332 0.063158114 16.40437744 0.01808885 0.01280972 102.676476 -2.011470955 -0.185427166 ASNTST(ph)PTKGNTETSASASQTNHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ASNT(0.003)S(0.036)T(0.954)PT(0.006)KGNTETSASASQTNHVK;ASNT(0.016)S(0.034)T(0.947)PT(0.003)KGNTETSASASQTNHVK;AS(0.003)NT(0.064)S(0.403)T(0.528)PT(0.001)KGNTETSASASQTNHVK 281.12 4.09E-53 1057170000 492149 441846 496977 547488 372199 516009 593683 626938 459147 TRUE FALSE 468886.0921 486870.6097 519763.887 492453.4661 437110.3878 498139.4789 503105.7546 572039.9851 530349.1718 0.884108276 0.918018988 0.980040914 0.928545744 0.82419359 0.939267006 0.948631169 1.078610122 1 19.01658299 1.443048564 3.206293602 1.03801054 0.911489375 0.568200621 0.044594501 0.168171789 3.17675953 0.032778822 0.011259456 27.73630244 -1.443048564 -0.126521165 ASPDQNASTHT(ph)PQSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(0.999)PQSSVK 135.98 4.35E-05 319650000 225750 221351 225240 270380 185215 246390 279370 260900 226540 TRUE FALSE 215079.2449 243906.9186 235567.4768 243200.8887 217516.4374 237857.4525 236746.9755 238054.2129 261670.6662 0.821946334 0.932114104 0.900244113 0.929415942 0.831260303 0.908995479 0.904751683 0.909747418 1 17.99739268 -5 0.189235871 1.464131413 0.872274204 0.494413871 0.035747858 117.2965131 1.145909144 20.4790129 0.093135298 1.00E-05 5 -0.591857208 ASPITNDGEDEFVPSDGLDKDEYTFS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 ASPITNDGEDEFVPS(0.021)DGLDKDEY(0.269)T(0.292)FS(0.418)PGK 52.777 0.045845 0 84935 82933 79408 90337 41397 99589 95238 96515 39690 TRUE FALSE 80920.29087 91383.96699 83048.93535 81256.15313 48616.62369 96140.20796 80707.69393 88063.63494 45844.92249 1.765087309 1.993327985 1.811518721 1.77241336 1.060458194 2.097074283 1.760450003 1.92090269 1 15.48447434 3.113101793 4.39213767 1.649347207 1.871914566 0.103773734 0.347912008 0.560118719 18.89961068 0.095592303 0.115900472 1297.48335 -3.113101793 0.222567359 ASPS(ph)PQPSSQPLQIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.159)PS(0.841)PQPSSQPLQIHR;AS(0.054)PS(0.946)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.001)PS(0.999)PQPSSQPLQIHR;AS(0.04)PS(0.96)PQPSSQPLQIHR;AS(0.028)PS(0.972)PQPSSQPLQIHR;AS(0.133)PS(0.867)PQPSSQPLQIHR 227.57 3.16E-15 3092080000 2302343 1941525 2043063 2333986 2244372 2142434 2584242 2393915 2313713 TRUE FALSE 2193515.809 2139368.605 2136739.459 2099369.293 2635789.766 2068240.973 2189968.42 2184291.112 2672511.795 0.820769365 0.800508573 0.7995248 0.785541638 0.986259358 0.773894049 0.819442004 0.817317669 1 21.34976488 -1.335723449 2.699650722 1.002844081 0.823155791 0.461500042 0.059225754 3450594.312 3895394.631 78003.33123 0.013859794 0.046161143 1.335723449 -0.179688291 ASPSCSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASPSCSSPTR 10 0 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 ASPS(0.001)CS(0.085)S(0.913)PT(0.001)R;ASPSCS(0.005)S(0.995)PTR;ASPSCS(0.03)S(0.969)PT(0.001)R;ASPSCS(0.002)S(0.998)PTR;ASPS(0.012)CS(0.171)S(0.813)PT(0.004)R;ASPS(0.001)CS(0.031)S(0.968)PTR 217.74 7.45E-09 1189158000 2083230 2271210 1932240 2525240 1973330 2016720 2177820 2145690 2109560 TRUE FALSE 1984759.846 2502648.881 2020835.115 2271398.078 2317478.127 1946880.481 1845553.561 1957802.009 2436699.791 0.814527852 1.027064922 0.829332823 0.932161642 0.951072486 0.798982496 0.757398826 0.803464594 1 21.21649709 2.230822258 24.99937348 0.812323271 0.915192007 0.102568247 0.088249463 237.820299 768290.4783 0.029866223 0.022467716 170.1462015 -2.230822258 0.102868735 ASPSCSS(ph)PTRDSSGVPVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPSCSSPTRDSSGVPVSK 19 1 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 ASPS(0.013)CS(0.094)S(0.872)PT(0.02)RDS(0.001)S(0.001)GVPVSK 106.36 0.00083026 36560000 23107 14989 28126 25274 25241 27977 38223 29559 38122 TRUE FALSE 22014.7779 16516.39614 29415.60492 22733.4095 29643.02241 27008.14947 32391.37934 26970.65726 44033.76506 0.499952204 0.375084804 0.668023842 0.516272217 0.673188458 0.613350901 0.735603219 0.612499459 1 15.42632259 -4.943004257 0.068793728 2.568392847 6.03E-11 0.75795444 0.081455696 127.6168946 0.639700157 31.69363157 4.167623367 1.14E-05 4.943004257 -2.568392847 ASPSS(ph)PGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.226)PS(0.364)S(0.41)PGRQDS(1)DEDDGPQRVEEVDQGR 86.145 0.0044323 166730000 79149 68651 67294 83149 78975 73995 86045 77149 81526 TRUE FALSE 75407.78363 75646.61495 70379.49646 74790.70455 92748.215 71432.5346 72917.25493 70393.42457 94168.6357 0.800773878 0.803310087 0.747377255 0.794220963 0.984916202 0.758559727 0.774326339 0.747525161 1 16.52295901 -1.170923331 4.96501112 1.000015204 0.80124102 0.454299239 0.068413079 1.10E-05 1.84E-06 0.063399467 0.014942255 0.067464712 1.170923331 -0.198774184 ASPSSPGRQDS(ph)DEDDGPQR ddPTM_SK-BR-3_Trastuzumab_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 199.85 4.09E-16 822620000 933190 1142130 1026140 1077950 769890 971200 878270 939580 753850 TRUE FALSE 889079.9581 1258514.345 1073189.534 969592.418 904158.5722 937567.1005 744273.781 857305.3942 870753.2079 1.021047009 1.445316921 1.232484158 1.113510016 1.038363757 1.076731147 0.854747102 0.984556114 1 19.73190436 2.719124788 1.361914719 0.951847261 1.245674925 0.485108849 0.114474117 0.320036116 1.208081647 0.050644882 0.047140601 523.7509071 -2.719124788 0.293827664 ASPSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 AS(0.001)PS(0.009)S(0.009)PGRQDS(0.982)DEDDGPQRVEEVDQGR;ASPS(0.001)S(0.001)PGRQDS(0.999)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR 216.16 1.95E-34 4021130000 807171 586876 760216 748593 836216 714328 946390 789382 966400 TRUE FALSE 769017.6265 646679.3316 795072.6556 673343.0094 982051.8056 689590.6422 802000.8239 720259.5273 1116264.376 0.688920692 0.579324527 0.712261963 0.603211053 0.879766323 0.617766415 0.718468528 0.645240986 1 20.09024733 -5 0.27725685 3.317599299 0.654759539 0.578576175 0.084996838 147.5668766 1.418423727 196.6049828 0.088910292 1.00E-05 5 -2.66283976 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 AS(0.009)QEPS(0.991)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(0.999)PKPGTEVIPAAPR 204.65 2.72E-16 448930000 537730 505220 523670 615720 345833 600730 603690 649650 453030 TRUE FALSE 512312.5686 556702.4924 547680.7875 553826.6558 406146.1657 579926.5695 511586.003 592763.202 523283.5786 0.979034293 1.063863869 1.046623303 1.058368117 0.776149266 1.108245305 0.977645819 1.132776235 1 18.99723346 -0.821517036 5.277082751 0.999999991 1.015705611 0.00280736 0.098626632 1.02E-08 2.17E-09 0.085200746 0.020081996 0.150828344 0.821517036 0.015705621 ASQPDLVDT(ph)PTSSKPQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASQPDLVDTPTSSKPQPK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ASQPDLVDT(0.883)PT(0.083)S(0.013)S(0.021)KPQPK 191.99 3.19E-14 120660000 183960 192810 203060 225090 130470 231170 245790 251620 169340 TRUE FALSE 175264.5754 212457.5582 212370.5019 202463.5256 153223.9267 223164.5249 208290.2213 229586.8189 195600.3823 0.89603391 1.086181712 1.08573664 1.035087576 0.783351877 1.140920699 1.06487635 1.173754448 1 17.57754966 ASQS(ph)RPNS(ph)SALETLGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 2 AS(0.004)QS(0.996)RPNS(0.976)S(0.024)ALETLGGEK;AS(0.022)QS(0.979)RPNS(0.97)S(0.029)ALETLGGEK;AS(0.022)QS(0.978)RPNS(0.588)S(0.412)ALETLGGEK 244.77 2.07E-24 1106140000 2200650 1879670 2007550 2260310 1805180 2208880 2530710 2467440 2022760 TRUE FALSE 2096629.636 2071210.51 2099598.153 2033099.344 2120002.82 2132385.932 2144603.71 2251377.873 2336439.29 0.897361059 0.88648163 0.89863159 0.870169986 0.907364822 0.912664815 0.917894045 0.963593568 1 21.15588012 1.175782097 0.979502334 1.001098217 0.890621584 0.928167095 0.010193932 0.112893944 0.232759688 0.008810499 0.003030356 14.98932571 -1.175782097 -0.110476633 ASQSRPNSS(ph)ALETLGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 ASQSRPNS(0.357)S(0.643)ALETLGGEK 203.45 7.16E-16 428130000 380210 321530 314390 363720 290920 371960 427070 412740 319740 TRUE FALSE 362238.2268 354294.2725 328805.0925 327158.1746 341656.3559 359078.9319 361912.6278 376598.2975 369323.6462 0.980815148 0.959305683 0.890289847 0.885830566 0.925086599 0.972260876 0.979933539 1.019697226 1 18.49452611 1.80139164 1.875906899 1.005916284 0.934405106 0.546859578 0.029806202 0.321974924 2.197277138 0.023615906 0.010172028 63.29824076 -1.80139164 -0.071511178 ASQSTQAHENSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASQSTQAHENSR 12 0 A0A0A6YYL4;P57737;P57737-3;I3L167;P57737-2;P57737-4;E7EP81;I3L0X8;I3L212 A0A0A6YYL4 CORO7-PAM16;CORO7 Coronin;Coronin-7 0 69.229 0.050538 5844200 1740.1 690.23 1984.6 2634.9 3699.4 1753.5 1761.1 2304.5 3640.3 FALSE TRUE 1657.848922 760.5652217 2075.595873 2370.034846 4344.574189 1692.775855 1492.41185 2102.705763 4204.819132 0.394273539 0.180879414 0.493623104 0.563647275 1.033236877 0.402579945 0.354928905 0.500070442 1 12.03782803 3.534792614 4.016662071 0.592016485 0.288904826 0.265605193 0.232433884 0.316250011 10.25340808 0.063635772 0.098395228 3426.04146 -3.534792614 -0.303111659 ASREEILAQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASREEILAQAK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 167.83 1.71E-05 1631830000 1574240 910760 1533600 1186650 1508240 1477940 2138580 1708310 2046610 FALSE TRUE 1499828.795 1003567.479 1603917.077 1067365.688 1771276.578 1426758.567 1812300.343 1558721.32 2363987.826 0.634448612 0.424523117 0.678479415 0.451510653 0.749274831 0.603538881 0.766628459 0.659360976 1 21.17279118 0.517580119 0.31146112 1.074447008 0.511532497 0.625687786 0.099481434 1.746524269 0.364305905 0.309347051 0.109653524 3.292911957 -0.517580119 -0.562914512 ASRVPS(ph)S(ph)DEEVVEEPQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASRVPSSDEEVVEEPQSR 18 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 AS(0.005)RVPS(0.998)S(0.997)DEEVVEEPQSR;AS(0.001)RVPS(0.999)S(1)DEEVVEEPQSR;AS(0.022)RVPS(0.979)S(0.999)DEEVVEEPQSR 167.99 1.24E-11 1292460000 775880 448802 792260 682550 972710 722840 1175520 846380 1387270 TRUE FALSE 739205.69 494535.434 828585.9047 613938.7772 1142350.316 697807.8696 996172.8341 772266.4803 1602400.746 0.461311374 0.30862157 0.517090314 0.383136852 0.712899266 0.435476501 0.621675218 0.48194341 1 20.61180357 -4.999999998 0.152146773 2.900478187 0.321493555 0.701824134 0.107204014 64.94685559 0.582729894 37.13741227 0.46101239 1.00E-05 4.999999998 -2.578984632 ASRVPS(ph)SDEEVVEEPQS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASRVPSSDEEVVEEPQSR 18 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 AS(0.004)RVPS(0.847)S(0.149)DEEVVEEPQS(1)R 262.24 9.48E-30 247840000 248940 123980 282310 201860 297090 213280 360260 249270 419340 TRUE FALSE 237173.0996 136613.703 295254.1927 181568.6493 348902.4019 205894.0601 305295.7204 227442.5973 484369.1055 0.489653648 0.282044625 0.609564461 0.374855967 0.720323402 0.425076781 0.630295609 0.469564625 1 18.88574732 -4.999999995 0.16634907 2.966440997 0.362162728 0.610424059 0.126452129 77.73707707 0.726777711 50.33410843 0.424371684 1.00E-05 4.999999995 -2.604278269 ASS(ph)DIVSLAGPSAGPGSSEGGCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AS(0.14)S(0.859)DIVSLAGPSAGPGSSEGGCSR 211.13 3.56E-25 69061000 17821 13751 15127 14953 13866 15678 18276 15683 16102 TRUE FALSE 16978.63665 15152.24253 15820.58791 13449.89603 16284.22601 15135.06693 15487.66054 14309.71338 18599.01592 0.912878225 0.814679798 0.850614246 0.72315095 0.875542345 0.813756329 0.832713978 0.769380135 1 14.18293867 -0.347092298 7.018004864 1.000000006 0.82776829 0.52494529 0.052487106 0 0 0.047196446 0.011124309 0.449684276 0.347092298 -0.172231717 ASS(ph)ESQGLGAGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASSESQGLGAGVR 13 0 Q9BV36-2;H7C2D8;Q9BV36-3 Q9BV36-2;Q9BV36-3 MLPH Melanophilin 1 AS(0.052)S(0.947)ESQGLGAGVR;AS(0.007)S(0.977)ES(0.016)QGLGAGVR;AS(0.015)S(0.985)ESQGLGAGVR;ASS(0.999)ES(0.001)QGLGAGVR 179.55 5.14E-06 575710000 1177300 862543 1083256 1223040 1318130 1055704 1266880 1116530 1199890 TRUE FALSE 1121651.362 950437.1123 1132924.359 1100097.696 1548011.455 1019144.706 1073594.188 1018760.714 1385962.813 0.809293981 0.685759462 0.817427674 0.793742578 1.116921349 0.73533337 0.774619765 0.735056312 1 20.40245712 -2.358947931 2.304856794 2.335037288 0.801332524 0.207634384 0.116807289 6341942.832 781870.2219 44352415.14 0.02933251 0.004375746 2.358947931 -1.533704764 ASS(ph)ESQIFELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSESQIFELNK 12 0 Q9BV36;Q9BV36-4 Q9BV36 MLPH Melanophilin 1 ASS(1)ESQIFELNK;ASS(1)ESQIFELNK;ASS(1)ESQIFELNK 331.39 3.74E-58 140765000 697260 549490 585040 725980 523830 685460 788040 773190 619400 TRUE FALSE 664301.9016 605483.6557 611864.6627 653003.1111 615185.7861 661722.3483 667810.0247 705485.3847 715453.3885 0.928504795 0.846293645 0.855212474 0.912712305 0.859854459 0.924899314 0.933408151 0.986067571 1 19.44849825 1.522240994 1.198054591 1.001357155 0.880141653 0.734232353 0.026743601 0.214369017 0.590871407 0.02279877 0.007991458 33.28442003 -1.522240994 -0.121215503 ASS(ph)FADMMGILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 AS(0.027)S(0.973)FADMMGILK;AS(0.138)S(0.862)FADMMGILK 127.56 0.00028069 32866000 186243 128166 138976 152046 148025 148084 195286 165815 157124 TRUE FALSE 177439.6625 141226.2611 145348.1871 136762.0472 173840.5131 142955.8139 165491.534 151295.3596 181489.9874 0.977682929 0.778149049 0.800860638 0.753551472 0.957851811 0.787678791 0.911849388 0.833629236 1 17.46953043 -0.410088201 0.585433906 1.017703645 0.846674288 0.271802204 0.076721911 12.17225534 3.571606893 0.536636156 0.029814314 0.388966141 0.410088201 -0.171029357 ASS(ph)FSGISILTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSFSGISILTR 12 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 AS(0.001)S(0.998)FS(0.001)GISILTR;AS(0.002)S(0.998)FSGISILTR;ASS(0.999)FS(0.001)GISILTR 244.47 2.21E-16 304229000 379508 278888 276075 454050 578160 355518 433096 285518 442949 TRUE FALSE 361569.409 307307.0043 288733.3118 408408.0314 678990.9209 343206.3225 367019.2508 260516.5303 511639.2687 0.706688151 0.60063217 0.56432985 0.798234335 1.327089148 0.670797461 0.717339879 0.509180093 1 18.96476747 3.158247658 6.913955402 0.828563387 0.6312771 0.174833637 0.218252203 0.419125875 29.78001613 0.063325784 0.076118234 1439.619292 -3.158247658 -0.197286287 ASS(ph)FSGISVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASSFSGISVLTR 12 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C1X4;H7BZ47;H7C207 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 AS(0.021)S(0.933)FS(0.045)GISVLTR;AS(0.003)S(0.995)FS(0.003)GISVLTR;AS(0.003)S(0.988)FS(0.009)GISVLTR;AS(0.003)S(0.997)FSGISVLTR;AS(0.01)S(0.957)FS(0.033)GISVLTR 194.06 2.11E-06 307104000 575995 416401 453920 657500 762601 557645 714129 490295 671886 TRUE FALSE 548768.8579 458832.7353 474732.681 591406.8508 895598.373 538333.6138 605175.5052 447362.1706 776078.6494 0.707104697 0.591219377 0.611706921 0.762044995 1.154004654 0.69365858 0.779786309 0.576439219 1 19.56584334 3.1045596 5.370267645 0.824444347 0.638533737 0.249989537 0.159286762 0.302468724 13.32081897 0.044763512 0.053898494 1272.212328 -3.1045596 -0.18591061 ASS(ph)HS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.466)S(0.532)HS(0.53)S(0.465)QT(0.007)QGGGSVTK 62.617 0.039832 274610000 65704 53256 59355 67158 48119 67918 74743 62722 49553 TRUE FALSE 62598.30213 58682.84695 62076.48546 60407.15025 56510.93836 65565.98263 63339.5826 57229.72917 57237.42616 1.093660326 1.025253071 1.084543622 1.055378522 0.987307469 1.145508927 1.106611301 0.999865525 1 15.80467118 1.21870631 24.3775729 0.999932595 1.070727482 0.31893456 0.043280913 260.5069236 319844.6829 0.041159498 0.010350289 16.54650634 -1.21870631 0.070794886 ASS(ph)HSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.02)S(0.947)HS(0.034)S(0.646)QT(0.353)QGGGSVTK;ASS(1)HSS(0.983)QT(0.017)QGGGSVTK;ASS(1)HSS(0.973)QT(0.027)QGGGSVTK;ASS(1)HSS(0.994)QT(0.006)QGGGSVTK;AS(0.001)S(0.999)HSS(0.935)QT(0.065)QGGGSVTK;AS(0.085)S(0.903)HS(0.049)S(0.96)QT(0.003)QGGGSVTK;AS(0.006)S(0.993)HS(0.002)S(0.998)QTQGGGSVTK;ASS(1)HSS(0.98)QT(0.02)QGGGSVTK 372.59 3.16E-104 21623352000 13037068 10751401 12099367 13348975 9748367 13631540 15865279 13046421 8830531 TRUE FALSE 12420831.63 11846980.99 12654134.94 12007110.67 11448479.12 13159476.35 13444739.3 11904007.21 10199924.65 1.217737587 1.161477304 1.24061063 1.177176409 1.122408205 1.290154271 1.318121434 1.167068152 1 23.28205516 0.978952517 24.17149941 0.999999996 1.218845974 0.586460742 0.05748737 852.3759206 978893.3178 0.060222223 0.015055556 9.526919979 -0.978952517 0.218845978 ASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.257)S(0.739)HS(0.023)S(0.968)QT(0.014)QGGGSVTKK;AS(0.437)S(0.533)HS(0.03)S(0.999)QTQGGGSVTKK;AS(0.114)S(0.886)HS(0.002)S(0.998)QTQGGGSVTKK;AS(0.124)S(0.876)HS(0.003)S(0.997)QTQGGGSVTKK;AS(0.027)S(0.973)HS(0.011)S(0.983)QT(0.006)QGGGSVTKK;AS(0.083)S(0.85)HS(0.08)S(0.983)QT(0.002)QGGGSVTKK;AS(0.452)S(0.534)HS(0.094)S(0.902)QT(0.019)QGGGSVTKK 166.21 2.42E-09 2269395000 2788210 1999140 2647950 2685010 1885450 2892080 3621260 2938830 1941060 TRUE FALSE 2656416.839 2202854.639 2769361.127 2415107.694 2214271.883 2791926.544 3068770.278 2681490.465 2242069.671 1.184805661 0.98250945 1.235180674 1.077177808 0.987601729 1.245245222 1.368722086 1.195988911 1 21.09639968 2.203553612 21.07820279 1.248165225 1.092333106 0.121146879 0.120677265 41.8379466 25189.84517 0.041766056 0.030850783 159.7914772 -2.203553612 -0.155832119 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.002)S(0.998)HSS(0.472)QT(0.528)QGGGSVTK 272.21 1.91E-34 3556500000 3410100 3071700 3197000 3542600 2655200 3523500 4045700 3553200 2483000 TRUE FALSE 3248911.331 3384709.722 3343585.612 3186491.117 3118266.039 3401480.312 3428454.161 3242062.971 2868050.959 1.132794144 1.180142812 1.165804116 1.111030161 1.087242202 1.185990194 1.195395134 1.130406335 1 21.45163923 0.967716191 22.8794004 0.999999999 1.154210855 0.658972887 0.033864091 920.6116997 652435.1345 0.03413232 0.00853308 9.283595117 -0.967716191 0.154210856 ASS(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.018)S(0.96)HS(0.018)S(0.003)QTQGGGSVTK;AS(0.022)S(0.764)HS(0.106)S(0.106)QT(0.002)QGGGSVTK;AS(0.09)S(0.567)HS(0.114)S(0.114)QT(0.114)QGGGSVTK;AS(0.016)S(0.764)HS(0.122)S(0.097)QT(0.001)QGGGSVTK 186.72 1.53E-09 825508000 285192.3 208931 273004.5 305179.5 294633 254630.6 374366.3 325315.2 338817 TRUE FALSE 271711.8252 230221.3064 285522.0264 274502.2769 346016.9019 245812.6785 317249.8452 296828.8765 391359.0099 0.694277679 0.588261163 0.729565486 0.701407838 0.884141908 0.628100216 0.810636365 0.758456734 1 18.57813313 -5 0.107696618 1.948873702 0.538637152 0.595747297 0.076685082 105.1494348 0.757081125 21.90373117 0.932084535 1.00E-05 5 -1.41023655 ASS(ph)HSSQTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_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(0.115)S(0.675)HS(0.204)S(0.006)QTQGGGSVTKK;AS(0.119)S(0.879)HS(0.001)SQTQGGGSVTKK 150.91 1.27E-07 444470000 380310 245490 357540 393540 406870 351850 603750 470640 587360 TRUE FALSE 362333.5 270505.7101 373933.5627 353980.6115 477827.9992 339665.3463 511636.8489 429428.2666 678444.789 0.534064829 0.398714405 0.551162849 0.521753011 0.704299019 0.500652893 0.754131887 0.632959783 1 19.37187189 0.093501 0.220970012 1.202077369 0.400334414 0.767355115 0.081127803 3.091723526 0.284783686 0.684389693 0.197142576 1.24022648 -0.093501 -0.801742956 ASS(ph)KGGGGYTCQSGSGWDEFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSKGGGGYTCQSGSGWDEFTK 22 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AS(0.014)S(0.986)KGGGGYTCQSGSGWDEFTK 182.87 2.70E-17 122560000 153140 121610 133850 166260 119810 155270 167380 154900 107760 TRUE FALSE 145901.3757 134002.1973 139987.1549 149547.2289 140704.8261 149892.961 141843.1069 141336.1348 124470.8704 1.172172856 1.076574758 1.124657957 1.201463671 1.130423733 1.204241285 1.139568691 1.135495673 1 16.92544863 -0.502629897 10.32826836 1 1.145547055 0.602222538 0.0377707 0 0 0.035968379 0.008477828 0.314318616 0.502629897 0.145547055 ASS(ph)LEDLVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 AS(0.001)S(0.999)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;AS(0.015)S(0.985)LEDLVLK;ASS(1)LEDLVLK;AS(0.017)S(0.983)LEDLVLK;AS(0.001)S(0.999)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK 307.97 8.51E-42 6850657800 8195718 7071562 7385843 8513591 5478749 8218785 9194611 8857369 6403016 TRUE FALSE 7808322.652 7792162.207 7724491.207 7657788.658 6434241.091 7934166.415 7791804.221 8081770.814 7395963.019 1.055754691 1.053569655 1.044419934 1.035401156 0.869966639 1.072769887 1.053521252 1.092727315 1 22.81830658 -0.212413758 6.8238644 1.000000002 1.036093212 0.030934076 0.060751029 0 0 0.056672401 0.013357813 0.613177545 0.212413758 0.03609321 ASS(ph)LGEIDESSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 AS(0.01)S(0.99)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;AS(0.001)S(0.999)LGEIDESSELR 326.12 2.24E-57 1106580000 1364860 1138310 1247410 1411140 1259820 1209060 1431150 1295680 2007660 TRUE FALSE 1300345.773 1254305.083 1304604.982 1269289.526 1479532.209 1167189.949 1212801.783 1182223.39 2318997.659 0.56073613 0.540882427 0.56257279 0.547344031 0.638005046 0.503316571 0.522985341 0.509799303 1 21.14506993 -1.819236975 2.590676505 1.153906849 0.547539013 0.935008256 0.037433534 4160544.184 2786200.493 3998067.814 0.009398317 0.015162228 1.819236975 -0.606367836 ASS(ph)LNENVDHSALLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.13)S(0.87)LNENVDHSALLK 211.96 7.20E-10 248220000 219990 172490 179140 253500 204300 218420 265830 233690 184310 TRUE FALSE 209591.5087 190066.9271 187353.7462 228017.6984 239929.8553 210856.0606 225272.7512 213226.8647 212891.8535 0.984497552 0.892786286 0.880041876 1.07104943 1.127003459 0.990437432 1.058155808 1.001573622 1 17.69976122 3.233633093 24.99967687 1.045577663 0.92280936 0.585879521 0.04833586 80.59588073 408901.547 0.013492767 0.016617445 1712.509909 -3.233633093 -0.122768303 ASS(ph)LNFLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 ASS(1)LNFLNK;ASS(1)LNFLNK;AS(0.001)S(0.999)LNFLNK;AS(0.001)S(0.999)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK 226.33 2.52E-07 5629014000 13835090 11856750 11662550 14160650 11095640 13463290 16328600 13955360 12544480 TRUE FALSE 13181132.71 13064966.31 12197289.45 12737194.56 13030716.1 12997052.89 13837372.17 12733354.7 14489813.89 0.909682679 0.90166557 0.841783721 0.879044731 0.899301827 0.896978594 0.954972388 0.878779727 1 23.78853573 0.202798121 0.454007165 1.009669434 0.887435555 0.57771472 0.02822331 2.396522403 0.736230808 0.078284363 0.016563737 1.595137486 -0.202798121 -0.122233878 ASS(ph)LNVLNVGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ASSLNVLNVGGK 12 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 AS(0.005)S(0.995)LNVLNVGGK;AS(0.001)S(0.999)LNVLNVGGK;AS(0.034)S(0.966)LNVLNVGGK;AS(0.006)S(0.994)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.014)S(0.986)LNVLNVGGK;ASS(1)LNVLNVGGK 309.49 3.15E-46 5033860000 12032630 10760128 10670022 13029220 9155310 12169710 13816210 12780430 10622793 TRUE FALSE 11463871.43 11856597.28 11159253.06 11719498.05 10751993.17 11748269.89 11708293.41 11661307.8 12270121.48 0.934291599 0.966298279 0.909465573 0.955124859 0.876274386 0.957469729 0.954211694 0.950382424 1 23.5486462 0.779671578 0.962482588 0.999307374 0.935758666 0.380929443 0.026162389 0.924345173 1.624392394 0.023535924 0.007757053 6.021040904 -0.779671578 -0.063548708 ASS(ph)LSESSPPK ddPTM_SK-BR-3_Trastuzumab_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 AS(0.001)S(0.997)LS(0.001)ESSPPK;ASS(0.5)LS(0.5)ESSPPK 213.63 1.95E-09 228050000 608680 370050 433700 767580 526580 677600 765640 456150 463820 TRUE FALSE 579908.9027 407758.5157 453585.574 690421.4001 618415.3853 654134.5421 648827.5561 416207.0878 535746.8367 1.082430848 0.761102983 0.846641628 1.288708309 1.154305248 1.220976956 1.211071184 0.776872693 1 19.0311919 3.255012713 24.99957075 1.134966005 0.89419259 0.263792528 0.16297747 270.5693983 411137.6953 0.043064841 0.058143984 1798.923574 -3.255012713 -0.240773415 ASS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSPFR 6 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.057)S(0.943)PFR;AS(0.028)S(0.972)PFR;AS(0.049)S(0.951)PFR 123.45 0.019702 1594730000 1966930 2135030 1733590 2261880 1836160 1904700 2016590 1911690 1736770 TRUE FALSE 1873957.117 2352591.984 1813076.816 2034511.525 2156385.723 1838739.761 1708922.158 1744292.289 2006099.421 0.934129733 1.172719537 0.903782134 1.014162859 1.074914683 0.916574593 0.851863143 0.869494438 1 20.93596168 2.122730527 5.743222636 0.889388264 1.027057756 0.295216185 0.082791206 0.210279568 9.778477562 0.029813021 0.021865386 132.6571086 -2.122730527 0.137669492 ASS(ph)PFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.249)S(0.751)PFRR;AS(0.168)S(0.832)PFRR 100.84 0.0058197 596200000 700580 680290 701690 730090 707830 714810 817980 743440 803670 TRUE FALSE 667464.9718 749612.3244 733863.1806 656699.9661 831275.3279 690055.9505 693182.1278 678340.4524 928299.039 0.71901935 0.807511688 0.790546095 0.707422865 0.895482267 0.743355235 0.746722876 0.730734843 1 19.8242301 -0.988295795 4.388751359 1.000008118 0.768284742 0.641382993 0.054610914 6327873.739 1441839.073 509.6144618 0.011689436 0.102731636 0.988295795 -0.231723376 ASS(ph)PPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.186)S(0.814)PPDR;AS(0.047)S(0.953)PPDR;AS(0.35)S(0.65)PPDR 91.085 0.017479 1074229000 1245000 1371410 1043650 1413710 961320 1131150 1121330 1196850 1086070 TRUE FALSE 1186151.317 1511158.238 1091502.385 1271601.185 1128973.904 1091977.992 950250.5139 1092047.469 1254492.189 0.945523079 1.204597567 0.870075075 1.013638185 0.899944945 0.870454198 0.757478223 0.870509581 1 20.25867206 2.980762455 1.15733326 0.846040129 1.058393152 0.260595315 0.102728684 0.433754566 1.23296706 0.042201418 0.050009151 956.6706606 -2.980762455 0.212353023 ASS(ph)PPDRIDIFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.01)S(0.99)PPDRIDIFGR;AS(0.477)S(0.523)PPDRIDIFGR;AS(0.092)S(0.908)PPDRIDIFGR;AS(0.248)S(0.752)PPDRIDIFGR 207.79 3.09E-08 7305090000 1326580 964300 1243350 1266730 1358870 1226760 1566220 1342280 1596830 TRUE FALSE 1263875.192 1062563.266 1300358.827 1139395.894 1595856.498 1184276.994 1327264.373 1224742.847 1844458.241 0.685228413 0.576084209 0.705008549 0.617740141 0.865216931 0.642073085 0.719595784 0.66401224 1 20.8147657 -5 0.222288536 2.646287223 0.639126816 0.624466046 0.076783342 94.07389545 0.941025044 69.43531792 0.131151817 1.00E-05 5 -2.007160407 ASS(ph)RS(ph)PVFTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 2 AS(0.463)S(0.561)RS(0.976)PVFTPR;AS(0.478)S(0.559)RS(0.963)PVFTPR 57.328 0.064502 760860000 861890 837810 807060 991580 864600 907280 1134310 993880 1033270 TRUE FALSE 821150.1678 923183.7915 844064.4993 891904.4945 1015385.966 875860.6661 961250.1765 906850.5983 1193504.234 0.688016133 0.773506926 0.707215337 0.747298978 0.850760255 0.733856354 0.805401564 0.759821852 1 20.18677225 -4.999999999 0.178756212 1.987423859 0.706043371 0.774811467 0.042215111 57.7504328 0.554685032 20.22568303 0.121915462 1.00E-05 4.999999999 -1.281380488 ASS(ph)SLGLQDFDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSSLGLQDFDLLR 14 0 P41743 P41743 PRKCI Protein kinase C iota type 1 AS(0.039)S(0.922)S(0.039)LGLQDFDLLR;ASS(0.999)S(0.001)LGLQDFDLLR;ASS(0.988)S(0.012)LGLQDFDLLR 242.01 1.92E-17 119902000 276549 232713 221823 263972 252732 236575 282046 266017 267385 TRUE FALSE 263477.0768 256426.7193 231993.804 237437.033 296808.3808 228382.3484 239014.7026 242723.1412 308849.7002 0.853091574 0.830263779 0.751154376 0.768778577 0.961012365 0.73946113 0.773886788 0.785894048 1 18.2365454 -1.77076361 4.809212437 1.015111771 0.808679344 0.469344174 0.064174873 0.010480434 0.000499561 0.062628813 0.014063022 0.016952603 1.77076361 -0.206432427 ASS(ph)VTTFTGEPNTCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 AS(0.001)S(0.893)VT(0.107)TFTGEPNTCPR;AS(0.002)S(0.98)VT(0.018)TFTGEPNTCPR;AS(0.008)S(0.975)VT(0.017)TFTGEPNTCPR;ASS(0.791)VT(0.208)TFTGEPNTCPR;AS(0.015)S(0.924)VT(0.06)T(0.001)FTGEPNTCPR;AS(0.057)S(0.886)VT(0.057)T(0.001)FTGEPNTCPR;ASS(1)VTTFTGEPNTCPR;ASS(1)VTTFTGEPNTCPR 379.99 5.91E-105 15085700000 5052140 3603550 4436990 7353250 6417460 6772030 7420510 4293450 5222450 TRUE FALSE 4813335.355 3970755.842 4640430.38 6614087.34 7536662.992 6537512.903 6288374.912 3917492.757 6032320.873 0.797924291 0.658246788 0.769261198 1.096441565 1.249380321 1.083747539 1.042447019 0.649417171 1 22.52428174 3.298407144 5.975151019 1.038241983 0.727823228 0.418138868 0.153970075 0.172370325 12.17201052 0.042342869 0.057088231 1987.957723 -3.298407144 -0.310418756 ASSGDIGS(ph)LDYQEFVVDIESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSGDIGSLDYQEFVVDIESR 21 0 J3KN59 J3KN59 BNIP2 1 AS(0.009)S(0.009)GDIGS(0.981)LDYQEFVVDIESR 113.54 0.00020829 10269000 13679 12719 12087 14371 12354 17549 17169 12900 15932 TRUE FALSE 13032.42078 14015.08056 12641.20091 12926.39978 14508.53369 16941.27373 14549.55372 11770.40761 18402.65319 0.708181622 0.761579345 0.686922737 0.702420441 0.788393583 0.920588654 0.790622611 0.639603838 1 14.16762616 2.573332389 4.952312506 0.824297883 0.721067972 0.270977813 0.093612868 0.33410257 13.16773913 0.02878619 0.026824396 374.3970248 -2.573332389 -0.103229911 ASSGDQGS(ph)PPCFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSGDQGSPPCFLR 14 0 A6NN50;O75147-2;O75147-1;O75147-4;O75147 A6NN50 OBSL1 Obscurin-like protein 1 1 ASSGDQGS(1)PPCFLR;ASSGDQGS(1)PPCFLR 194.19 1.80E-07 185229000 477200 420430 423440 475120 470900 435100 545450 455870 493890 TRUE FALSE 454643.7017 463272.295 442855.1428 427360.0349 553024.8109 420032.3779 462231.5846 415951.6061 570479.9388 0.7969495 0.812074647 0.776285217 0.749123687 0.969402732 0.736278963 0.810250376 0.729125738 1 19.12181663 -1.199322157 4.225191411 1.000080593 0.799818098 0.469353689 0.067646617 8912751.243 2529890.372 6799.291756 0.014102079 0.063194291 1.199322157 -0.200262495 ASSHS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.082)HS(0.901)S(0.014)QT(0.002)QGGGSVTK;ASS(0.018)HS(0.49)S(0.49)QT(0.001)QGGGSVTK;ASS(0.001)HS(0.952)S(0.047)QTQGGGSVTK;AS(0.004)S(0.09)HS(0.767)S(0.127)QT(0.013)QGGGSVTK;AS(0.002)S(0.04)HS(0.479)S(0.479)QT(0.001)QGGGSVTK 297.55 1.01E-45 10025800000 1585948 1129154 1487148 1706870 1744430 1453668 2212530 1860890 2001700 TRUE FALSE 1510983.381 1244216.076 1555335.207 1535292.185 2048658.04 1403327.113 1874967.913 1697940.606 2312113.413 0.653507468 0.538129345 0.672689842 0.66402114 0.886054304 0.606945622 0.810932501 0.734367353 1 21.14078074 -4.999999538 0.076734744 2.12047927 0.330094964 0.605067693 0.086183748 158.486021 0.865970613 30.06121282 3.086671272 1.00E-05 4.999999538 -1.790384306 ASSHS(ph)SQTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_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 AS(0.307)S(0.307)HS(0.379)S(0.006)QTQGGGSVTKK 123.43 2.52E-05 334460000 150410 93894 155370 135440 157300 140320 209330 156840 195800 TRUE FALSE 143300.4174 103461.9053 162493.8682 121825.3139 184733.0702 135460.6832 177392.8639 143106.2581 226163.664 0.633613795 0.457464756 0.718479111 0.538659976 0.816811449 0.598949808 0.784356164 0.632755305 1 17.78700764 -5 0.111108296 2.204115882 0.428618739 0.561065906 0.102047681 103.1922406 0.760261837 27.99897111 1.082599799 1.00E-05 5 -1.775497143 ASSHSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.052)S(0.197)HS(0.197)S(0.554)QTQGGGSVTK;AS(0.028)S(0.153)HS(0.244)S(0.575)QTQGGGSVTK 262.17 4.62E-27 17465800000 3284220 2186020 2986910 3479120 3191320 2783850 4330340 3716880 3863890 TRUE FALSE 3128981.429 2408777.923 3123862.778 3129392.248 3747885.198 2687444.576 3669667.101 3391410.283 4463082.327 0.701080823 0.539711739 0.699933936 0.701172871 0.839752647 0.6021499 0.822227069 0.759880736 1 22.08960899 -0.983380415 0.165802009 1.297648458 0.556528054 0.608611694 0.080347255 14.31960006 0.513521558 2.265346328 0.38401747 0.103900966 0.983380415 -0.741120404 ASSHSSQTQGGGS(ph)VTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(1)VTK;ASSHSSQTQGGGS(0.993)VT(0.007)K;ASSHSSQT(0.001)QGGGS(0.998)VT(0.002)K;ASSHSSQTQGGGS(1)VTK;ASSHSS(0.001)QT(0.132)QGGGS(0.866)VT(0.001)K;ASSHSSQT(0.002)QGGGS(0.939)VT(0.058)K;ASSHSSQTQGGGS(1)VTK;ASSHSSQTQGGGS(0.997)VT(0.003)K;ASSHSSQTQGGGS(0.997)VT(0.003)K 231.37 9.01E-16 3053959000 2644879 1837341 2653977 2971892 3588962 2451009 4570393 3558314 5476690 TRUE FALSE 2519860.811 2024568.137 2775664.471 2673151.77 4214875.836 2366129.944 3873095.607 3246729.162 6325987.114 0.3983348 0.320039877 0.438771755 0.422566743 0.666279548 0.374033317 0.61225158 0.513236765 1 22.59285919 -5 0.140370564 2.926114467 0.258101881 0.793229556 0.08993565 53.11819019 0.45630501 28.42449726 0.487447808 1.00E-05 5 -2.668012586 GKTESEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKTESEAR 8 1 P82930 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 85.676 0.015115 63231000 202310 110090 190170 151890 198520 164400 279840 271040 371620 FALSE TRUE 192747.2072 121308.2962 198889.4826 136621.7286 233141.8251 158706.7868 237145.2684 247306.3007 429248.9316 0.449033633 0.282605936 0.463342988 0.318280882 0.543138976 0.36973135 0.5524656 0.576137254 1 18.71145502 0.382524457 0.501965316 1.039833353 0.370426181 0.85815867 0.075456489 0.703154005 0.294271975 0.12297199 0.033796839 2.412817406 -0.382524457 -0.669407171 ASSHSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 202.34 3.06E-11 305185000 327397 218783 305472 340079 513985 257202 528823 380267 716314 FALSE TRUE 311921.5926 241077.2364 319478.1934 305893.6128 603623.8213 248295.0302 448141.3388 346968.8056 827396.3167 0.376991759 0.291368515 0.386124747 0.369706278 0.729546179 0.300092018 0.541628395 0.419350194 1 19.65821901 -4.999999999 0.188077722 3.484452978 0.308858286 0.686103842 0.12369424 71.78300379 0.700129661 66.6900462 0.312863605 1.00E-05 4.999999999 -3.175594692 ASSIIDELFQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 120.96 0.00089511 30665000 28008 27299 23885 30735 35187 22836 29517 24613 33937 FALSE TRUE 26684.11735 30080.79914 24980.15088 27645.45941 41323.60166 22045.18359 25013.63953 22457.75524 39199.77663 0.680721158 0.767371697 0.637252378 0.70524533 1.054179519 0.562380337 0.638106685 0.572905184 1 15.25855781 ASSKT(ph)SPHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSKTSPHWK 10 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 AS(0.032)S(0.261)KT(0.622)S(0.085)PHWK 85.837 0.022581 264710000 481570 337440 463440 482390 385110 511870 677620 565860 510030 TRUE FALSE 458807.1405 371825.5196 484689.1824 433899.2407 452273.0621 494143.8136 574236.6237 516310.2986 589122.8475 0.778797058 0.631151077 0.822730241 0.736517422 0.76770586 0.838778899 0.974731545 0.876405152 1 19.16820898 2.067000976 1.754713765 0.952563373 0.731574207 0.717742614 0.057848879 0.177780636 1.037224687 0.032528298 0.017238843 116.6812239 -2.067000976 -0.220989166 ASSNKDFT(ph)PNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASSNKDFTPNR 11 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 AS(0.007)S(0.006)NKDFT(0.987)PNR;AS(0.004)S(0.004)NKDFT(0.992)PNR;AS(0.001)S(0.001)NKDFT(0.998)PNR 81.703 0.033867 1265450000 2872800 2264230 2648100 2892210 1997800 2837510 3254800 3095960 2491330 TRUE FALSE 2737008.437 2494957.611 2769518.004 2601479.556 2346215.687 2739246.317 2758220.481 2824861.33 2877672.732 0.951118731 0.867005335 0.962415904 0.904022034 0.815317065 0.951896401 0.958489981 0.981647877 1 21.4564711 2.017425114 24.99605711 0.970373621 0.90152258 0.432584908 0.042088406 240.6244199 345170.6483 0.015154275 0.011189886 104.0938602 -2.017425114 -0.068851041 ASSPHGLGSPLVAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSPHGLGSPLVASPR 16 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 ASSPHGLGS(0.002)PLVAS(0.998)PR 62.684 0.048217 93043000 75383 48648 71299 57448 79929 57132 70376 78102 96415 TRUE FALSE 71819.79498 53605.28651 74568.12967 51673.2179 93868.59229 55153.50451 59638.84866 71262.97484 111366.5458 0.644895597 0.481341018 0.669573876 0.463992284 0.842879625 0.49524302 0.535518528 0.63989571 1 16.76495639 0.881333886 6.762079613 0.999999124 0.583199188 0.56366317 0.112200116 1.994825228 113.5933246 0.096066549 0.024104189 7.609110413 -0.881333886 -0.416799935 ASSPS(ph)PLTIGTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR 315.08 9.01E-58 322560000 499160 522110 442950 570070 477160 460180 526260 519170 533200 TRUE FALSE 475565.696 575313.6026 463259.6956 512765.4805 560376.5529 444243.8512 445969.3716 473708.7225 615885.9328 0.772165219 0.934123629 0.752184245 0.832565664 0.909870681 0.721308651 0.724110339 0.769150093 1 19.23230365 2.230348018 24.99962206 0.772474114 0.842462709 0 0.095958038 390.9089554 1189938.969 0.032236359 0.024205979 169.960507 -2.230348018 0.069988595 ASSRPGS(ph)PTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.107)S(0.107)RPGS(0.636)PT(0.14)ADPNS(0.009)IPLVLCADLNSLPDSGVVEYLSNGGVADNHK 184.67 1.33E-28 41443000 18935 24063 15527 21377 12635 21954 16049 22696 11013 TRUE FALSE 18039.98008 26515.04706 16238.92831 19228.14335 14838.54 21193.72748 13600.43029 20708.61792 12720.83979 1.418143799 2.084378664 1.276561027 1.511546695 1.166474874 1.666063548 1.069145631 1.627928522 1 13.6349063 2.426069484 0.189053791 0.907433833 1.965809093 0.221276822 0.284845905 5.894077435 0.667251111 1.106581312 2.06501103 266.7285378 -2.426069484 1.05837526 ASSRS(ph)PVFTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 AS(0.237)S(0.036)RS(0.727)PVFTPR;AS(0.128)S(0.128)RS(0.744)PVFTPR;AS(0.14)S(0.176)RS(0.684)PVFTPR;AS(0.052)S(0.068)RS(0.88)PVFTPR;AS(0.035)S(0.027)RS(0.937)PVFTPR;AS(0.035)S(0.024)RS(0.941)PVFTPR 116.96 0.00055637 1687340000 506172 393376 466568 515418 510517 450533 572222 520672 572465 TRUE FALSE 482246.2527 433461.4616 487960.6043 463607.2034 599551.0032 434930.9292 484919.0243 475079.1994 661239.9485 0.729305986 0.655528243 0.737947859 0.70111796 0.906707171 0.657750534 0.733348046 0.718467178 1 19.33481436 -2.139868474 2.184765053 1.555182985 0.725319006 0.599247271 0.069290375 3655107.717 842811.3076 10058125.13 0.015926441 0.007246554 2.139868474 -0.829863979 ASSSGPRS(ph)PLDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASSSGPRSPLDQR 13 1 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 AS(0.053)S(0.053)S(0.046)GPRS(0.847)PLDQR;AS(0.007)S(0.006)S(0.005)GPRS(0.983)PLDQR;AS(0.002)S(0.002)S(0.002)GPRS(0.994)PLDQR;AS(0.064)S(0.064)S(0.072)GPRS(0.8)PLDQR;AS(0.311)S(0.264)S(0.045)GPRS(0.38)PLDQR 108.34 0.00074137 1291630000 2366840 2079580 2199860 2491920 2520720 2334070 2716640 2461100 2790200 TRUE FALSE 2254964.164 2291491.566 2300725.757 2241427.467 2960332.77 2253240.571 2302166.673 2245593.037 3222889.966 0.699671471 0.711005213 0.713870402 0.695471298 0.918533615 0.699136674 0.714317491 0.696763793 1 21.6199235 -1.486395839 3.194406398 1.006195511 0.728917847 0.612676742 0.067172598 19794020.04 25989939.13 1092036.06 0.015838309 0.03262903 1.486395839 -0.277277664 ASSTS(ph)TPEPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASS(0.003)T(0.023)S(0.592)T(0.382)PEPTR 127.87 0.00029129 843380000 776160 733810 739720 853250 823210 805460 955680 894840 1017700 TRUE FALSE 739472.455 808586.0733 773636.8937 767479.6889 966777.5634 777566.7182 809873.4637 816483.0658 1175519.718 0.629060018 0.687854113 0.658123281 0.652885423 0.822425646 0.661466334 0.68894928 0.694571986 1 20.16486731 -5 0.283295783 3.355255503 0.664535049 0.79050758 0.050953612 100.2118577 0.954401303 139.0169995 0.053855825 1.00E-05 5 -2.690720454 ASSTST(ph)PEPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASS(0.001)T(0.008)S(0.121)T(0.871)PEPTR;ASS(0.003)T(0.01)S(0.237)T(0.75)PEPTR;ASSTS(0.004)T(0.996)PEPTR;ASST(0.001)S(0.439)T(0.56)PEPTR;ASST(0.003)S(0.034)T(0.963)PEPTR 202.27 4.54E-07 1805020000 2190160 2082300 2081740 2384490 2280790 2169020 2522240 2385740 2697420 TRUE FALSE 2086635.477 2294488.737 2177189.838 2144796.535 2678559.054 2093906.294 2137425.964 2176831.958 3115722.117 0.669711675 0.736422778 0.698775358 0.688378634 0.859691254 0.672045264 0.686013028 0.698660495 1 21.57113514 -1.242991495 5.280580935 1.000028926 0.712437024 0.726879319 0.055145809 1.76E-05 2.53E-06 0.050095508 0.011806438 0.057148983 1.242991495 -0.287591902 ASSVST(ph)KESPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.168)T(0.721)KES(0.111)PAR 154.72 0.00045686 23330000 72080 62891 64005 81425 51620 66897 80685 83637 60726 TRUE FALSE 68672.92125 69299.6644 66939.69256 73240.0043 60622.51166 64580.34012 68375.02137 76313.30089 70143.07793 0.979040602 0.987975812 0.954330698 1.044151561 0.86426934 0.920694415 0.97479357 1.087966242 1 16.09801312 1.36589286 7.196616817 1.042896837 0.961799539 0.322635957 0.050458 0.258570298 14.89709669 0.032750811 0.011916 23.22163853 -1.36589286 -0.081097297 ASSVSTKES(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.001)T(0.034)KES(0.965)PAR;AS(0.001)S(0.001)VS(0.006)T(0.326)KES(0.666)PAR;ASSVSTKES(1)PAR;ASSVS(0.005)T(0.135)KES(0.86)PAR;ASSVST(0.001)KES(0.999)PAR;ASSVS(0.004)T(0.091)KES(0.906)PAR;ASSVS(0.029)T(0.17)KES(0.801)PAR;ASSVST(0.001)KES(0.999)PAR;ASSVSTKES(1)PAR 221.99 6.81E-11 3152164000 6747840 6021128 5835607 7340558 4708693 6614768 7670830 7474210 5978168 TRUE FALSE 6428882.976 6634687.789 6103175.353 6602671.164 5529887.568 6385696.926 6500503.999 6819728.549 6905231.761 0.931016249 0.960820436 0.88384801 0.956183861 0.800825774 0.924762144 0.941388244 0.987617619 1 22.71925841 1.351107231 2.282757457 0.998746313 0.914273509 0.370997692 0.044863791 0.344302421 3.053143488 0.038981891 0.011789189 22.44436028 -1.351107231 -0.084472805 ASSVSTKES(ph)PARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ASSVSTKESPARK 13 2 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AS(0.002)S(0.002)VS(0.007)T(0.006)KES(0.983)PARK;ASSVS(0.001)T(0.001)KES(0.997)PARK;ASSVS(0.024)T(0.024)KES(0.952)PARK;ASSVS(0.002)T(0.04)KES(0.958)PARK;ASSVS(0.002)T(0.002)KES(0.997)PARK;AS(0.002)S(0.009)VS(0.032)T(0.024)KES(0.933)PARK;ASSVSTKES(1)PARK;ASSVS(0.001)T(0.001)KES(0.998)PARK 141.36 3.14E-05 9246690000 1691110 1391389 1572091 1645274 1044339 1737053 1824453 1860791 1367288 TRUE FALSE 1611174.582 1533173.121 1644172.927 1479887.932 1226471.391 1676898.419 1546099.186 1697850.275 1579320.04 1.020169783 0.970780515 1.041063803 0.937041191 0.776581921 1.061785057 0.978965091 1.075051435 1 20.59087212 -0.643419322 7.056760607 1.000000292 0.981438286 0.003937778 0.084545381 0 0 0.077122119 0.018177858 0.227290183 0.643419322 -0.018562007 ASSVT(ph)TFTGEPNTCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 AS(0.028)S(0.192)VT(0.771)T(0.008)FTGEPNTCPR;ASS(0.189)VT(0.804)T(0.006)FTGEPNTCPR 358.55 1.49E-86 1910470000 693920 468600 618320 990410 854890 930750 985990 586070 736630 TRUE FALSE 661119.7768 516350.8728 646670.5836 890852.1051 1003982.545 898517.8941 835559.1166 534750.6038 850862.8182 0.776999256 0.606855608 0.760017443 1.046998513 1.179958183 1.056007943 0.982013902 0.628480399 1 19.69856702 3.341060143 4.83763562 0.994910657 0.691342333 0.431033362 0.145526101 0.178159971 6.899060094 0.040489375 0.055122464 2193.108624 -3.341060143 -0.303568325 AST(ph)PDWVSEGPQPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.003)T(0.997)PDWVSEGPQPGLR;AS(0.028)T(0.972)PDWVSEGPQPGLR;AS(0.001)T(0.999)PDWVSEGPQPGLR;AS(0.443)T(0.557)PDWVSEGPQPGLR;AS(0.002)T(0.998)PDWVSEGPQPGLR 292.26 1.63E-44 1459920000 1448810 1421930 1304340 1533330 1180540 1317790 1438070 1488780 1264090 TRUE FALSE 1380327.623 1566826.284 1364145.279 1379196.755 1386425.802 1272154.602 1218666.01 1358414.531 1460118.621 0.945353071 1.073081502 0.934270175 0.944578567 0.949529567 0.87126798 0.834634934 0.930345323 1 20.47765415 3.064265627 1.299827696 0.8935498 1.004712065 0.205558418 0.057414277 0.426068457 1.511361034 0.021617342 0.027521249 1159.486316 -3.064265627 0.111162265 AST(ph)PDWVSEGPQPGLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTPDWVSEGPQPGLRR 17 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.16)T(0.836)PDWVS(0.003)EGPQPGLRR;AS(0.079)T(0.921)PDWVSEGPQPGLRR 176.42 6.49E-10 502690000 332451 226143 354807 307456 338559 300481 464030 385617 466840 TRUE FALSE 316736.7001 249187.2288 371075.2519 276549.9388 397603.5824 290075.2676 393233.701 351850.3312 539235.1629 0.587381391 0.462112351 0.688151065 0.512855907 0.737347283 0.537938339 0.729243432 0.652498864 1 19.04055505 -5 0.14606566 2.447063546 0.469072533 0.700672278 0.083191736 63.64683596 0.559014296 26.52097733 0.388900964 1.00E-05 5 -1.977991012 ASTAS(ph)PCNNNINAATAVALQEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASTASPCNNNINAATAVALQEPR 23 0 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 AS(0.128)T(0.128)AS(0.743)PCNNNINAATAVALQEPR 190.6 9.49E-18 90969000 45921 45612 51081 52145 53872 45751 55278 50153 58865 TRUE FALSE 43750.40534 50259.91466 53423.11438 46903.28553 63267.25974 44166.6314 46844.32585 45761.33744 67993.48356 0.643449976 0.739187228 0.785709329 0.689820304 0.930490047 0.649571534 0.688953167 0.673025341 1 16.05310887 -2.144890252 2.308991312 1.599675666 0.722440062 0.513030169 0.084159083 7839621.999 1811164.732 24635287.16 0.019195665 0.007163244 2.144890252 -0.877235604 ASTASASAAVS(ph)AARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASTASASAAVSAARPR 16 1 E9PC69;Q7KZI7-14;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 E9PC69;Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 AS(0.013)T(0.096)AS(0.293)AS(0.066)AAVS(0.531)AARPR 102.5 0.003399 0 53161 51161 48737 57595 54367 51228 54947 55395 53358 TRUE FALSE 50648.18488 56374.36407 50971.63966 51805.44118 63848.58759 49453.96151 46563.82598 50544.32013 61632.48613 0.821777411 0.914685868 0.827025533 0.840554137 1.035956711 0.802400887 0.755507832 0.820092184 1 15.91140337 -0.238608444 7.566989872 1 0.851042261 0.270733512 0.076185312 0 0 0.074548748 0.017571309 0.577286705 0.238608444 -0.148957739 ASTFCGT(ph)PDYIAPEILQGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTFCGTPDYIAPEILQGLK 20 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 AS(0.296)T(0.296)FCGT(0.408)PDYIAPEILQGLK;AS(0.204)T(0.154)FCGT(0.642)PDYIAPEILQGLK 214.52 4.63E-24 434217000 415447 522738 437009 632410 280948 614900 469879 565575 267264 TRUE FALSE 395809.6436 576005.5965 457046.2949 568838.9453 329945.2422 593605.8588 398190.3286 516050.2547 308709.9361 1.282140927 1.865847286 1.480503999 1.842632448 1.068787245 1.922859582 1.289852648 1.671634743 1 18.23589239 -2.639054436 0.380330562 1.59E-15 1.573420652 0.269534283 0.28300752 96.16810096 3.833350447 78.96508173 0.165215143 0.002295861 2.639054436 1.573420652 ASTRS(ph)PTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASTRSPTQR 9 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 AS(0.026)T(0.026)RS(0.866)PT(0.083)QR 55.452 0.077758 84862000 17255 17111 15807 18441 25934 17681 25873 16174 26259 TRUE FALSE 16439.39035 18854.63035 16531.76659 16587.27564 30456.88139 17068.70254 21925.59866 14757.71882 30331.11161 0.541997621 0.621626751 0.545043215 0.546873318 1.00414656 0.562745697 0.72287488 0.48655384 1 14.88851075 ASTS(ph)KSESSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AST(0.025)S(0.703)KS(0.268)ES(0.002)S(0.002)QK 103.14 0.0016804 203740000 227770 203570 240650 315290 139450 246070 274660 378900 214310 TRUE FALSE 217003.7635 224314.0144 251684.0405 283596.4502 163770.0358 237548.5342 232755.5725 345721.5073 247544.1003 0.876626683 0.906157788 1.016724051 1.14564011 0.661579232 0.959621069 0.940259018 1.396605724 1 17.91732604 1.341218972 9.407364435 1.197293739 0.926125205 0.349715623 0.152412937 0.270464092 22.10180299 0.092385952 0.033758519 21.93910832 -1.341218972 -0.271168533 ASTSKS(ph)ESSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.002)T(0.007)S(0.237)KS(0.724)ES(0.029)S(0.001)QK;AS(0.003)T(0.002)S(0.06)KS(0.926)ES(0.008)S(0.001)QK 96.464 0.018396 64044000 189775 167690 199915 273140 114526 217840 251250 326880 163412 TRUE FALSE 180804.7118 184777.8016 209081.3005 245683.4483 134499.2981 210296.1462 212917.198 298256.6543 188753.0984 0.957890034 0.978939171 1.107697316 1.301612797 0.712567366 1.114133479 1.128019618 1.580141767 1 17.5261408 1.540024303 3.642956507 1.305238558 1.0205403 0.207082948 0.202869835 0.247776904 7.292828785 0.119221573 0.047927158 34.67562541 -1.540024303 -0.284698258 ASTVS(ph)PGGYMVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 ASTVS(1)PGGYMVPK;ASTVS(1)PGGYMVPK 234.04 1.25E-16 220120000 507020 474580 438820 555970 401080 485230 550220 526560 505140 TRUE FALSE 483054.1694 522940.2416 458940.3311 500082.8393 471028.225 468426.3634 466273.8335 480451.6149 583474.5313 0.827892467 0.896252044 0.786564462 0.857077409 0.807281552 0.802822297 0.799133139 0.823432025 1 19.15431016 -0.761115204 7.678329891 0.999999213 0.827747138 0.748391015 0.03184457 0 0 0.032410326 0.007639187 0.173334414 0.761115204 -0.172252075 ASVEVEAPPS(ph)VVLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASVEVEAPPSVVLNR 15 0 Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 AS(0.089)VEVEAPPS(0.911)VVLNR 58.752 0.071709 122240000 139050 114040 142610 124620 115790 143570 166330 152450 141900 TRUE FALSE 132477.3821 125660.8057 149148.8096 112092.9608 135983.7393 138598.1349 140953.3036 139100.6698 163905.1273 0.808256485 0.766667936 0.909970372 0.683889288 0.829649088 0.845599752 0.859968849 0.848665762 1 17.32250146 0.471183589 0.467926901 1.013307833 0.791722752 0.528227295 0.056943371 1.547063864 0.615989957 0.096233013 0.029558391 2.959263168 -0.471183589 -0.22158508 ASVITQVFHVPLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ASVITQVFHVPLEER 15 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62 Q00341 HDLBP Vigilin 0 ;; 146.76 3.83E-06 755199000 651559 592087 569346 694553 707089 592647 735544 627969 624645 FALSE TRUE 620761.0973 652421.3384 595451.0773 624735.2129 830405.0977 572123.4858 623323.2536 572980.7053 721511.7564 0.860361722 0.904242145 0.825282571 0.865869762 1.150923863 0.792951024 0.863912817 0.794139112 1 19.46066338 -0.603525882 18.67061804 1 0.883271769 0.117292436 0.101513592 0 0 0.091504612 0.021567844 0.249157588 0.603525882 -0.116728231 ASVLDTSMSAGSGS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.008)GS(0.985)PS(0.008)K;ASVLDTSMSAGS(0.058)GS(0.911)PS(0.031)K 162.77 2.56E-09 95145000 257693 269177 217498 299288 163250 266416 275732 291884 183058 TRUE FALSE 245512.3626 296606.4423 227470.4984 269203.0016 191720.7483 257189.9471 233664.0192 266325.0896 211445.6997 1.161113056 1.402754668 1.075786827 1.273154299 0.906713868 1.216340401 1.105078134 1.259543656 1 17.68992769 3.72153597 24.90003442 1.1260356 1.281933875 0.220788705 0.126389948 951.2035888 1391218.255 0.030100983 0.046755408 5266.668333 -3.72153597 0.155898275 ASVSQTS(ph)PQSASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.078)S(0.911)PQS(0.003)AS(0.009)SPR;ASVSQT(0.249)S(0.748)PQS(0.002)ASSPR 244.54 5.10E-18 70541000 195938 165555 175555 213095 197498 194082 213479 179088 208322 TRUE FALSE 186676.3991 182425.2427 183604.3704 191674.2857 231941.5887 187360.8917 180908.8577 163406.1053 240627.5118 0.775789924 0.758122965 0.763023185 0.796560145 0.963903034 0.778634539 0.751821171 0.679083219 1 17.87644207 -2.187658721 2.516998459 1.64318682 0.783270956 0.476833798 0.071311977 6784220.142 1905716.391 24885907.02 0.017133979 0.006491443 2.187658721 -0.859915864 ASVSQTSPQSASS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.005)S(0.033)PQS(0.017)AS(0.114)S(0.831)PR 143.43 4.63E-06 57156000 205920 186980 176120 219730 200680 192130 214640 196040 205060 TRUE FALSE 196186.5697 206033.4746 184195.2762 197642.3229 235678.5285 185476.4899 181892.7259 178873.6983 236859.6575 0.828281911 0.86985465 0.777655757 0.834427969 0.99501338 0.783064925 0.767934598 0.755188537 1 17.85367297 -0.350017608 7.519584191 1.000000056 0.827831221 0.382837428 0.069238498 0 0 0.066724015 0.015727001 0.446665482 0.350017608 -0.172168836 ASWES(ph)LDEEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.011)WES(0.989)LDEEWR 152.4 3.46E-05 15067000 52488 43290 36259 75369 57560 54825 51200 39320 41926 TRUE FALSE 50006.99626 47701.30022 37921.51102 67792.76493 67598.44578 52926.3965 43388.49965 35876.93235 48427.66995 1.032612065 0.985000936 0.783054627 1.399876661 1.395864097 1.092895788 0.895944399 0.740835402 1 15.56354397 1.687357427 4.385204659 0.857002434 1.102923195 0.251046236 0.19130234 0.259992259 11.69567532 0.109921531 0.052651208 48.68076862 -1.687357427 0.245920761 ASWES(ph)LDEEWRAPQAGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASWESLDEEWRAPQAGSR 18 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 ASWES(1)LDEEWRAPQAGSR 158.73 2.71E-11 106820000 56352 36339 39888 73079 82811 57272 77213 35975 61161 TRUE FALSE 53688.35264 40041.98541 41716.90425 65732.96008 97253.21218 55288.65628 65432.73874 32824.83828 70645.53551 0.759968089 0.566801357 0.590510129 0.930461629 1.37663635 0.782620669 0.926211943 0.464641368 1 16.10831077 3.233180872 24.78187619 0.923082456 0.640869911 0.244320774 0.22700859 157.3787712 724967.5015 0.063092923 0.077524562 1710.727639 -3.233180872 -0.282212545 ASYDDPYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 76.221 0.057794 463790000 2888700 2449950 2437500 3064800 1637920 2864600 3024100 3076200 1743930 FALSE TRUE 2752156.876 2699602.69 2549261.786 2756720.481 1923572.729 2765398.184 2562718.004 2806831.62 2014369.758 1.366262011 1.340172369 1.265538155 1.368527536 0.954925342 1.372835436 1.272218268 1.393404368 1 20.9418971 -2.262531944 2.025160429 3.11E-05 1.293985613 0.342335175 0.127043291 1767597.783 304759.9374 8060625.638 0.030828881 0.005463464 2.262531944 1.293954516 ASYDTLCVLDGDKDSVNCAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ASYDTLCVLDGDKDSVNCAR 20 1 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 72.883 0.0086852 0 45863 36453 47707 46710 45340 41037 48129 43059 46843 FALSE TRUE 43695.14688 40167.60214 49894.41314 42014.62206 53247.28164 39615.8784 40786.0371 39288.52569 54107.1732 0.807566618 0.742371108 0.922140452 0.776507431 0.984107624 0.73217424 0.753800923 0.72612416 1 15.72353225 -2.169893531 2.454704946 1.519477531 0.80117065 0.340214921 0.084880682 11599134.49 1458784.158 33834945.35 0.020317311 0.006762487 2.169893531 -0.718306881 ASYHFSPEELDENTS(ph)PLLGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.137)S(0.863)PLLGDAR;ASYHFSPEELDENT(0.367)S(0.633)PLLGDAR;ASYHFSPEELDENT(0.251)S(0.749)PLLGDAR;ASYHFSPEELDENT(0.206)S(0.794)PLLGDAR 229.69 1.68E-26 730030000 300023 195845 301383 303176 480636 219073 328752 250466 404897 TRUE FALSE 285841.5074 215801.8282 315201.7087 272700.1725 564458.7662 211486.4471 278594.8445 228533.8692 467686.3588 0.61118205 0.461424252 0.673959594 0.583083443 1.206917319 0.452197168 0.595687343 0.488647712 1 18.83518182 3.615667452 5.588715715 0.69256284 0.536893026 0.085914917 0.233616385 0.585324194 24.274127 0.059541522 0.093045316 4127.31344 -3.615667452 -0.155669814 ASYNNPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ASYNNPHR 8 0 P54725-2;P54725;A0A494C0B4;K7ELU6;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;;;;; 134.15 0.00088892 396180000 633087 512483 502169 563688 699981 505954 708487 597519 696309 FALSE TRUE 603162.2322 564705.6003 525193.9454 507025.0113 822057.4648 488432.6861 600394.2959 545197.0687 804289.0435 0.749932176 0.702117734 0.652991545 0.63040149 1.022092084 0.607285018 0.746490706 0.677862111 1 19.61735454 -1.800135569 2.718438745 1.079047839 0.723788209 0.361179654 0.115503328 25278002.89 20497450.06 13251287.16 0.025531706 0.015843985 1.800135569 -0.35525963 AT(ph)NESEDEIPQLVPIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.5)NES(0.5)EDEIPQLVPIGK 102.48 0.0034795 294830000 296510 293940 286380 336260 231920 312750 320660 295320 278140 TRUE FALSE 282494.5599 323892.8202 299510.8063 302458.5059 272366.7746 301919.3891 271737.4277 269460.2152 321272.5307 0.879298829 1.008155971 0.932263974 0.94143905 0.84777486 0.939760983 0.84581594 0.838727839 1 18.29343811 2.832573479 8.345863562 0.88563399 0.944643172 0.124431892 0.057436905 0.498337252 40.25192326 0.016071968 0.017059881 680.101102 -2.832573479 0.059009182 AT(ph)PAQTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATPAQTPR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3ITP6;E5RFR3;E5RG53 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 AT(1)PAQTPR 86.18 0.050369 0 173670 176130 168910 206000 165230 174140 185660 172850 206240 TRUE FALSE 165460.9633 194077.8472 176654.6906 185292.4886 194046.0597 168109.4881 157334.1571 157714.3377 238222.6459 0.694564376 0.814691007 0.741552886 0.777812235 0.814557571 0.705682231 0.660450045 0.662045949 1 17.86195104 -1.062047836 4.697954195 1.000009919 0.735856717 0.692349024 0.055728642 0.093807812 37406246.51 836.966268 0.013982644 0.086686639 1.062047836 -0.264153201 AT(ph)PPPSPLLSELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATPPPSPLLSELLK 14 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 AT(0.999)PPPS(0.001)PLLSELLK 84.753 0.089518 65669000 42061 43031 31601 46129 27452 39036 41719 39635 28474 TRUE FALSE 40072.85989 47415.90782 33049.93711 41492.02528 32239.62011 37684.17353 35354.00033 36164.34928 32889.60249 1.218405114 1.441668619 1.004874933 1.261554477 0.980237451 1.145777713 1.074929389 1.099567843 1 15.00534395 3.73475148 24.99998303 1.090331052 1.330036869 0.529404299 0.097308613 207.5459627 1362159.933 0.02277887 0.036851417 5429.395521 -3.73475148 0.239705817 AT(ph)SLPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.333)S(0.333)LPS(0.333)IPNPFPELCS(0.032)PPS(0.143)QS(0.825)PILGGPSSAR 92.121 0.00087227 35002000 54290 48277 48028 55568 54380 60110 62222 56443 58727 TRUE FALSE 51723.81929 53196.48119 50230.13131 49982.19907 63863.85478 58028.37563 52728.89111 51500.5517 67834.08322 0.762504877 0.78421464 0.74048515 0.73683017 0.941471481 0.855445712 0.777321497 0.759213499 1 16.04972272 2.781112621 24.99874626 0.845935039 0.760569061 0.348490712 0.072043115 657.6498961 386359.6003 0.021049969 0.022326718 604.1052652 -2.781112621 -0.085365978 AT(ph)SLPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 AT(0.539)S(0.46)LPS(0.001)IPNPFPELCSPPSQSPILGGPSSAR;AT(0.494)S(0.494)LPS(0.012)IPNPFPELCSPPSQSPILGGPSSAR;AT(0.5)S(0.5)LPSIPNPFPELCSPPSQSPILGGPSSAR 207.16 1.99E-25 303893000 370836 377762 360602 442681 371449 382413 439793 398453 402361 TRUE FALSE 353307.3172 416256.3773 377135.9584 398181.8648 436229.588 369169.9419 372694.5005 363562.343 464757.0889 0.760197801 0.895642879 0.811468975 0.856752644 0.938618471 0.794328803 0.80191246 0.782263147 1 18.82611735 4.700187466 3.81962423 0.84882798 0.754763917 0.150622537 0.07006882 0.44484705 11.60814895 0.015516944 0.107760272 50140.36214 -4.700187466 -0.094064063 AT(ph)SNVFAMFDQSQIQEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 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(0.606)S(0.394)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.571)S(0.429)NVFAMFDQSQIQEFK;AT(0.784)S(0.216)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.583)S(0.417)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQS(0.001)QIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.593)S(0.407)NVFAMFDQSQIQEFK;AT(0.58)S(0.42)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.599)S(0.401)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.579)S(0.421)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.588)S(0.412)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.58)S(0.42)NVFAMFDQSQIQEFK 316.24 6.98E-61 7480798000 12458386 10507106 10605417 12654245 7999241 11529897 12574589 12317342 8331635 TRUE FALSE 11869502.78 11577792.05 11091685.86 11382216.25 9394306.098 11130613.78 10656104.5 11238770.24 9623662.404 1.233366497 1.203054675 1.152543117 1.182732288 0.976167461 1.156588138 1.10728162 1.167826734 1 23.1981546 8 0.136502088 1.005270944 1.82385001 0.442805571 0.06221386 66.76383929 0.610457325 0.266395667 10.6192408 100000000 -8 0.818579066 AT(ph)SNVFAMFDQSQIQEFKEAFNMIDQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSNVFAMFDQSQIQEFKEAFNMIDQNR 28 1 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(0.794)S(0.206)NVFAMFDQSQIQEFKEAFNMIDQNR;AT(0.821)S(0.179)NVFAMFDQSQIQEFKEAFNMIDQNR 70.249 0.0063531 77613000 202001 75792 233183 131681 203964 179405 301070 216929 333640 TRUE FALSE 192452.8131 83515.29097 243874.6712 118444.1757 239535.257 173192.1599 255136.242 197933.5467 385379.1872 0.499385591 0.216709396 0.632817441 0.307344505 0.621557326 0.449407144 0.662039494 0.513607256 1 18.55591913 -1.857400459 0.182068988 1.648519949 0.305159407 0.617880601 0.132059472 19.01110153 0.534329952 5.711542073 0.415467283 0.013886716 1.857400459 -1.343360542 AT(ph)TPASTANSDVATIPTDTPLKEENEGFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATTPASTANSDVATIPTDTPLKEENEGFVK 30 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 AT(0.499)T(0.499)PAS(0.001)T(0.001)ANS(0.001)DVATIPTDTPLKEENEGFVK 99.357 0.00087845 78089000 93946 89247 81674 104350 54778 94872 105220 106590 61455 TRUE FALSE 89505.35876 98341.37077 85418.83369 93860.53975 64331.26586 91586.55885 89166.7565 97256.41453 70985.12753 1.260902979 1.385379927 1.203334229 1.322256408 0.906264003 1.290221798 1.256132934 1.370095651 1 16.11522917 -2.214192248 2.455362211 0.144865773 1.25470081 0.255533526 0.133460671 7325367.463 1500597.387 35039149 0.030850473 0.006106716 2.214192248 1.109835037 ATAAVIFLHGLGDTGHGWAEAFAGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATAAVIFLHGLGDTGHGWAEAFAGIR 26 0 B4DP64;E5RGR0;O75608-2;O75608 B4DP64 LYPLA1 Acyl-protein thioesterase 1 0 ; 229.66 4.48E-35 102527000 82798 47610 67989 91067 88466 75706 103097 72033 47109 FALSE TRUE 78884.30263 52461.51313 71106.3629 81912.77214 103894.4424 73084.28224 87367.65914 65725.40865 54414.42312 1.449694734 0.964110435 1.306755798 1.505350373 1.909318089 1.343104972 1.605597453 1.207867416 1 15.73170148 3.393965736 4.635668683 1.482684603 1.19652231 0.083363664 0.267682686 0.321605078 12.53033776 0.069083918 0.095272191 2477.22661 -3.393965736 -0.286162293 ATAGDTHLGGEDFDNR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 204.72 2.45E-11 38311000000 34365500 28889600 28749900 33820000 32915400 29246900 34774400 30465600 31594700 FALSE TRUE 32741110.92 31833483.08 30068111.35 30420349.35 38655835.34 28234072.52 29468926.6 27797870.56 36494244.71 0.897158201 0.872287763 0.823913787 0.833565665 1.059231 0.773658223 0.807495177 0.7617056 1 25.12116563 ATALPLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATALPLLK 8 0 Q9Y2P8 Q9Y2P8 RCL1 RNA 3-terminal phosphate cyclase-like protein 0 101.99 0.0050516 71161000 78083 93674 91449 99582 397960 57638 130820 72817 482770 FALSE TRUE 74392.17134 103219.4871 95642.02711 89571.82817 467364.098 55641.98161 110861.0063 66440.75745 557635.506 0.133406447 0.185102071 0.171513517 0.160627914 0.838117539 0.099781992 0.198805501 0.119147287 1 19.0889629 -1.969923492 2.612732324 1.640629375 0.232182544 0.551377854 0.215858033 44446951.03 20296289.9 172214705.2 0.050770654 0.010717081 1.969923492 -1.408446831 ATAPQTQHVS(ph)PMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 32 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;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.021)QHVS(0.979)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 228.51 7.67E-12 1.76417E+11 39096314 36014554 36743632 39965238 41919918 37216130 43975214 38951948 38211768 TRUE FALSE 37248308.72 39684478 38428363.87 35947856.35 49230738.43 35927326.09 37265987.44 35541108.94 44137453.82 0.843916119 0.899111176 0.870652032 0.814452426 1.115395977 0.813987282 0.844316657 0.805236955 1 25.39550007 -2.352687531 2.319677141 1.815363172 0.876073463 0.158776072 0.089782232 5103889.929 1028989.721 21748009.27 0.020212989 0.004439279 2.352687531 -0.939289709 ATAPQTQHVS(ph)PMRQVEPPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ATAPQTQHVSPMRQVEPPAK 20 1 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)PMRQVEPPAK;ATAPQTQHVS(1)PMRQVEPPAK;ATAPQTQHVS(1)PMRQVEPPAK;ATAPQTQHVS(1)PMRQVEPPAK;ATAPQT(0.001)QHVS(0.998)PMRQVEPPAK;ATAPQTQHVS(0.999)PMRQVEPPAK;ATAPQTQHVS(1)PMRQVEPPAK 168.65 7.21E-12 1875770000 717611 322395 870073 500869 934343 719668 1395580 826171 1308630 TRUE FALSE 683690.9502 355247.417 909966.7077 450520.6965 1097292.123 694745.7167 1182658.639 753827.0874 1511565.657 0.452306486 0.235019508 0.602002767 0.298049042 0.725930838 0.45961994 0.782406397 0.498706149 1 20.52761222 0.717819707 0.18952355 1.228428278 0.205776883 0.556525823 0.152505196 3.501828264 0.411688432 1.178990136 0.630570365 5.221793664 -0.717819707 -1.022651395 ATAPQTQHVSPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 152.16 4.21E-05 1144276000 461370 341946 421866 481519 780712 383679 676181 527705 974126 FALSE TRUE 439561.9544 376790.6862 441208.9734 433115.7953 916867.9256 370392.1 573017.1695 481496.3527 1125188.485 0.390656286 0.33486895 0.392120057 0.384927326 0.814857189 0.32918227 0.509263272 0.427925062 1 20.10173526 -5 0.213405827 3.722991468 0.362925687 0.613364609 0.138561814 95.15947753 0.94971304 111.1340959 0.265441886 1.00E-05 5 -3.36006578 ATDAEADVASLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATDAEADVASLNRR 14 1 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKX5;H0YKP3 P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ; 187.63 1.48E-06 482340000 610260 412020 566320 547600 675100 555530 726290 608890 770920 FALSE TRUE 581414.2192 454005.3064 592286.3322 492554.2076 792837.2263 536291.8568 615481.1213 555572.3637 890470.3363 0.652929352 0.509848883 0.665138756 0.553139378 0.890357819 0.602256847 0.691186552 0.623908895 1 19.76420803 -4.999999998 0.194416885 2.5718483 0.579347001 0.545947705 0.100809972 98.28594744 0.966528576 59.91870073 0.237205255 1.00E-05 4.999999998 -1.992501298 ATDCVGHDVVTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ATDCVGHDVVTLLR 14 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;; 198.48 2.20E-08 1847521000 3011673 2441214 2413733 3148165 2867254 2271109 2704301 2339522 2557989 FALSE TRUE 2869317.186 2689976.482 2524405.046 2831705.473 3367302.19 2192459.926 2291710.215 2134661.051 2954668.87 0.971112944 0.910415549 0.854378327 0.958383358 1.139654675 0.742032364 0.775623366 0.722470485 1 21.49456503 2.1959597 24.99999942 0.78788939 0.954003718 0.34562192 0.104417642 141.9895053 83324.54057 0.036257787 0.026778349 157.0217089 -2.1959597 0.166114327 ATDFVADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ATDFVADR 8 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;; 201.3 0.00026257 2695040000 4284890 3699300 3388270 3733130 3805950 3136950 4051610 3652540 3904600 FALSE TRUE 4082351.742 4076262.876 3543625.531 3357868.68 4469706.475 3028316.635 3433462.482 3332704.234 4510105.426 0.905156611 0.903806561 0.785707915 0.744521106 0.991042571 0.671451407 0.761282089 0.738941537 1 22.10472973 3.742772472 23.2706678 0.797107147 0.904481608 0.09810131 0.106525241 225.1783381 1244102.325 0.025284932 0.043528061 5530.602832 -3.742772472 0.107374461 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ATDIPASASPPPVAGVPFFK 20 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.012)AS(0.988)PPPVAGVPFFK;ATDIPAS(0.003)AS(0.997)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK 289.61 2.09E-54 1454041000 3586940 3584190 2958947 3946190 2592054 3461770 3621990 3684830 2914211 TRUE FALSE 3417392.455 3949423.036 3094617.647 3549511.484 3044107.397 3341888.037 3069388.903 3362166.751 3366131.958 1.015228309 1.173282297 0.919339374 1.054477818 0.904333946 0.992797691 0.911844497 0.998822029 1 21.6826603 3.729240106 24.99823464 0.964325599 1.094255305 0.429990247 0.059877945 475.9424368 1276510.194 0.014410226 0.022656144 5360.929628 -3.729240106 0.129929706 ATDKSFVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATDKSFVEK 9 1 P35579;P35579-2;A0A494C024;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 P35579;P35749;Q7Z406 MYH9;MYH11;MYH14 Myosin-9;Myosin-11;Myosin-14 0 ;; 93.258 0.0086833 479100000 1029170 542160 1064060 957870 1033320 1159580 1758480 1328360 1657600 FALSE TRUE 980523.1737 597406.7204 1112848.203 861583.0878 1213530.681 1119423.454 1490191.579 1212041.756 1914652.142 0.51211557 0.312018412 0.581227357 0.449994581 0.633812615 0.584661532 0.778309306 0.633034967 1 20.86865087 1.380715458 0.331852494 1.034968306 0.372330506 0.767462712 0.089057887 0.552130029 0.206181402 0.139715563 0.108505671 24.0278802 -1.380715458 -0.6626378 ATDS(ph)FSGRFEDVYQLQEDVLGEGAHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATDSFSGRFEDVYQLQEDVLGEGAHAR 27 1 Q9HBH9;Q9HBH9-2 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 AT(0.29)DS(0.36)FS(0.335)GRFEDVY(0.014)QLQEDVLGEGAHAR;AT(0.012)DS(0.974)FS(0.014)GRFEDVYQLQEDVLGEGAHAR;AT(0.17)DS(0.786)FS(0.043)GRFEDVY(0.002)QLQEDVLGEGAHAR 217.62 2.06E-34 67959000 55853.8 34758 58286.4 49234 80236 51968.2 86158.7 61837.4 87979 TRUE FALSE 53213.70157 38299.87972 60958.88909 44284.90478 94229.133 50168.5282 73013.6079 56422.58944 101622.334 0.523641797 0.376884472 0.599857204 0.435779253 0.927248266 0.493676205 0.718479935 0.555218398 1 16.63285798 -5 0.088920281 2.413724671 0.200727036 0.475795819 0.147019468 164.6742893 1.019635323 44.23885275 3.203463711 1.00E-05 5 -2.212997635 ATDSDLSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLS(0.01)S(0.99)PR;ATDSDLS(0.002)S(0.998)PR;ATDSDLS(0.001)S(0.999)PR;ATDSDLS(0.005)S(0.995)PR 132.69 0.00022762 1391130000 3556520 2775790 2931090 3479030 3506780 3091680 3803810 3260970 3719150 TRUE FALSE 3388410.348 3058646.157 3065483.376 3129311.295 4118361.322 2984614.346 3223468.923 2975422.179 4295896.787 0.788755065 0.711992468 0.713584038 0.728441918 0.958673247 0.694759324 0.750359956 0.692619569 1 22.0345279 -1.063040815 4.60172575 1.000009664 0.754160621 0.495164047 0.077773542 8.91E-06 1.81E-06 0.070081471 0.016517556 0.086488663 1.063040815 -0.245849043 ATEDGEEDEEMIESIENLEDLKGHSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 272.18 5.31E-61 56457000 77273 69217 77981 84151 67449 84342 107072 102114 67275 FALSE TRUE 73620.45843 76270.29099 81556.50598 75691.9816 79212.08424 81421.21539 90736.19989 93172.35682 77707.66341 0.947402807 0.981502823 1.049529768 0.974060708 1.019360006 1.047788749 1.167660896 1.199011175 1 16.24576926 2.019737178 2.619570944 1.138162696 0.988994508 0.490149744 0.058313853 0.192304505 2.521867718 0.027169119 0.015627479 104.649505 -2.019737178 -0.149168188 ATEETGQAQSGQANCQGLS(ph)PVSVASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATEETGQAQSGQANCQGLSPVSVASK 26 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 ATEETGQAQSGQANCQGLS(0.985)PVS(0.015)VASK;ATEETGQAQSGQANCQGLS(0.97)PVS(0.03)VASK;ATEETGQAQSGQANCQGLS(0.999)PVS(0.001)VASK 263.16 4.13E-53 568310000 576030 590630 567700 686700 501180 609820 671340 673600 573560 TRUE FALSE 548802.2035 650815.8685 593729.6065 617671.6114 588585.6333 588701.7805 568914.753 614616.013 662504.7555 0.828374738 0.982356524 0.8961892 0.932327815 0.888424767 0.888600083 0.858733086 0.927715625 1 19.33757128 0.982875031 23.08201451 1.000000003 0.898624345 0.393366442 0.040666351 417.4461211 562659.9183 0.038143929 0.009535982 9.61335612 -0.982875031 -0.101375658 ATENDIANFFS(ph)PLNPIR ddPTM_SK-BR-3_Trastuzumab_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 237.09 3.47E-20 215730000 177908 141702 153053 180968 165448 156357 176056 169590 179140 TRUE FALSE 169498.6414 156141.5949 160070.6314 162776.7528 194302.0788 150942.3179 149195.4237 154739.8005 206920.1163 0.819150136 0.75459843 0.773586611 0.786664708 0.939019764 0.729471453 0.721029093 0.747823862 1 17.65871438 -0.922222752 5.010938604 0.999999993 0.780893854 0.545153823 0.061974163 6.01E-07 1.29E-07 0.059794956 0.01409375 0.119612687 0.922222752 -0.21910614 ATENDIYNFFS(ph)PLNPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 1 ATENDIYNFFS(1)PLNPMR 112.43 0.00048385 11060000 29149 30157 28247 28749 33281 23470 31501 30682 36219 TRUE FALSE 27771.18454 33230.03259 29542.15289 25859.0959 39085.19586 22657.22802 26694.94389 27995.32142 41835.65754 0.663816136 0.794299278 0.706147689 0.618111377 0.934255565 0.541576955 0.638090697 0.669173692 1 15.35244549 -2.347736204 2.222007252 2.798563395 0.696473639 0.447669288 0.106227056 5400227.51 744908.1394 48652036.49 0.02506696 0.00449018 2.347736204 -2.102089757 ATENDIYNFFS(ph)PLNPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 287.54 1.16E-36 508294000 467159 371267 341957 444770 431982 386660 479780 416607 470316 TRUE FALSE 445077.3199 409099.5294 357636.0667 400060.8746 507319.524 373269.8672 406580.7492 380126.6825 543250.2032 0.819286062 0.753059137 0.658326614 0.736421031 0.933859796 0.687104883 0.748422636 0.699726719 1 19.05125728 -0.984032831 4.471554009 1.000006516 0.756574765 0.49986246 0.077142108 13423626.09 43749978.22 1543.326055 0.017680117 0.103744998 0.984032831 -0.243431752 ATENDIYNFFSPLNPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 206.2 1.67E-11 18782000 43825 29579 31985 34591 40238 32101 41957 39072 39769 FALSE TRUE 41753.4791 32593.13373 33451.54389 31113.84696 47255.49446 30989.33432 35555.68906 35650.64855 45936.17341 0.908945522 0.709530884 0.728217903 0.677327793 1.028720743 0.674617236 0.774023747 0.776090952 1 15.48734306 -1.157758145 3.188834496 1.000441012 0.782226657 0.276494525 0.109395877 21913617.55 32538561.87 100567.333 0.025198749 0.069541148 1.157758145 -0.218214355 ATENDIYNFFSPLNPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 322.26 2.57E-58 50400000 69342 61088 58568 71577 68980 63342 72202 73623 65257 FALSE TRUE 66064.34108 67312.93665 61253.40073 64381.94397 81010.09016 61148.45066 61186.25882 67176.17982 75376.72227 0.876455477 0.893020214 0.812630198 0.854135627 1.074736175 0.811237857 0.811739447 0.891205903 1 16.20183144 2.336504242 0.008158291 1.768213031 3.08E-06 0.084788151 0.081921883 11114.32322 49.41258678 5274.433005 5430.582784 217.0222401 -2.336504242 -1.768209951 ATEPPS(ph)PDAGELSLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATEPPSPDAGELSLASR 17 0 Q8IYB8 Q8IYB8 SUPV3L1 "ATP-dependent RNA helicase SUPV3L1, mitochondrial" 1 ATEPPS(1)PDAGELSLASR;ATEPPS(1)PDAGELSLASR 194.19 9.23E-11 168282000 131358 95973 106864 99265 113044 97602 117780 106236 125039 TRUE FALSE 125148.9677 105752.7578 111763.8201 89286.69361 132758.8378 94222.01827 99810.49782 96933.41265 144429.4095 0.866506123 0.732210692 0.77383007 0.618202996 0.919195324 0.652374185 0.691067686 0.671147331 1 17.14000502 4.587285865 2.092069484 0.73924572 0.881883879 0.056694805 0.12061121 1.082355042 6.780942529 0.027127245 0.260614625 38662.13786 -4.587285865 0.14263816 ATFIKVPQNQNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATFIKVPQNQNGK 13 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 115.12 0.00062864 1026720000 799790 551730 768150 754420 749770 742810 1058110 840300 902300 FALSE TRUE 761985.5117 607951.9143 803370.4373 678584.2683 880529.6506 717086.3034 896675.886 766718.8773 1042224.076 0.731114862 0.583321695 0.770823143 0.65109249 0.844856371 0.688034675 0.860348467 0.735656463 1 19.99123406 -0.380938128 0.186723495 1.189744126 0.608635707 0.5776195 0.076469376 8.43523268 0.468328523 1.180598155 0.269622824 0.415969867 0.380938128 -0.581108419 ATGAALT(ph)PTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATGAALTPTEER 12 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 ATGAALT(1)PTEER;ATGAALT(1)PTEER;ATGAALT(0.964)PT(0.036)EER;ATGAALT(0.986)PT(0.014)EER 238.93 1.42E-06 795930000 1791450 1528970 1639070 1920170 1890200 1726770 2023500 1954800 2256900 TRUE FALSE 1706771.709 1684773.781 1714222.981 1727150.864 2219850.282 1666971.522 1714777.911 1783627.349 2606888.525 0.654716031 0.646277647 0.657574332 0.662533456 0.851532492 0.639448717 0.657787203 0.684197783 1 21.31389746 -2.368859841 1.797814978 2.485477474 0.677381782 0.723816705 0.06172681 994054.934 104478.1019 5981012.363 0.016081252 0.004277009 2.368859841 -1.808095692 ATGDGS(ph)S(ph)PELPSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATGDGSSPELPSLER 15 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 2 ATGDGS(1)S(1)PELPSLER 186.77 1.38E-11 0 118710 117480 120870 130320 110970 126500 133910 123930 100640 TRUE FALSE 113098.8136 129451.3456 126412.0091 117219.986 130323.1329 122119.2733 113479.5701 113078.0322 116246.7372 0.972920327 1.113591217 1.087445653 1.008372268 1.121090673 1.050517857 0.976195744 0.972741558 1 16.8268307 1.771337635 5.0706416 0.980973868 1.060663978 0.389816806 0.044862005 0.190128324 10.50651267 0.021474977 0.011518329 59.06601012 -1.771337635 0.07969011 ATGDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATGDWK 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;; 127.95 0.039173 1198410000 2645440 2268230 2216610 2702680 2121820 2484310 2944480 2579090 2405560 FALSE TRUE 2520395.294 2499365.216 2318243.761 2431001.472 2491864.736 2398277.722 2495245.497 2353251.207 2778601.959 0.907073172 0.89950459 0.834320207 0.874900942 0.896805218 0.863123886 0.898021931 0.846919149 1 21.40592775 -1.967667285 2.777630397 1.096656475 0.881123179 0.71514674 0.024188834 9123346.654 5358437.771 5673261.619 0.005707298 0.010772902 1.967667285 -0.215533296 ATGEADVEFVTHEDAVAAMSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATGEADVEFVTHEDAVAAMSK 21 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ; 170.53 8.09E-12 161263000 251560 211747 201262 248220 233020 222620 274150 246550 246620 FALSE TRUE 239669.2573 233324.26 210490.0618 223268.454 273658.6142 214910.6136 232323.3824 224960.775 284864.57 0.841344564 0.819070831 0.738912746 0.783770526 0.960662164 0.754430828 0.81555731 0.789711318 1 18.11991667 -1.230063665 5.294558354 1.000015597 0.814004651 0.485334788 0.060531054 1.03E-05 1.50E-06 0.054330041 0.01280464 0.058875734 1.230063665 -0.186010946 ATGEPGTFVCTSHLPAAASAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ATGEPGTFVCTSHLPAAAS(0.001)AS(0.999)PK;ATGEPGTFVCTSHLPAAAS(0.001)AS(0.999)PK;ATGEPGTFVCTSHLPAAAS(0.336)AS(0.664)PK 173.11 2.72E-12 945729000 1248330 1138880 1185740 1396930 833370 1346450 1368370 1390240 901690 TRUE FALSE 1189323.915 1254933.167 1240107.352 1256507.942 978709.4641 1299822.099 1159600.025 1268503.215 1041519.48 1.14191231 1.204906092 1.190671299 1.206418091 0.939693864 1.248005557 1.113373342 1.21793518 1 19.99025839 ATGHSGGGCISQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATGHSGGGCISQGR 14 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 130.24 6.32E-05 93530000 59699.2 52045.2 55352.6 59690 69424.6 47670.1 69865.1 55007.1 71544 FALSE TRUE 56877.33713 57348.66505 57890.57146 53689.8478 81532.22826 46019.27248 59205.89583 50190.38671 82638.67812 0.688265331 0.693968809 0.700526349 0.649693933 0.986610993 0.556873289 0.71644292 0.607347405 1 16.33452956 -1.176534989 3.765867726 1.000220728 0.700579797 0.412004648 0.112642033 39591793.59 77997724.36 116333.6312 0.024167282 0.066598586 1.176534989 -0.299640931 ATGNDLRPPPPS(ph)PSSDLTHPMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATGNDLRPPPPSPSSDLTHPMK 22 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 ATGNDLRPPPPS(0.956)PS(0.022)S(0.022)DLTHPMK;ATGNDLRPPPPS(0.806)PS(0.082)S(0.112)DLTHPMK 141.5 7.36E-08 555080000 532790 468900 513150 538940 457024 531230 560170 566800 481510 TRUE FALSE 507606.0726 516681.4431 536678.4351 484764.7273 536728.8409 512833.3719 474705.7783 517167.9872 556180.1116 0.912664912 0.928982235 0.964936401 0.871596659 0.965027029 0.922063485 0.853510883 0.929857031 1 19.08519263 1.981413639 24.94719543 0.905581351 0.927730078 0 0.04517913 2430.024576 3261650.987 0.016546274 0.010896056 95.81061744 -1.981413639 0.022148727 ATGSAGLLGDPECEGS(ph)PPEHSPEQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATGSAGLLGDPECEGSPPEHSPEQGR 26 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 ATGSAGLLGDPECEGS(1)PPEHSPEQGR;ATGSAGLLGDPECEGS(1)PPEHSPEQGR 189.23 5.75E-18 170040000 197144 172196 199663 236930 254330 199159 286810 242320 270210 TRUE FALSE 187825.3938 189742.9682 208817.746 213113.3463 298685.0715 192262.0739 243051.8669 221101.1762 312112.7868 0.601786924 0.607930774 0.66904579 0.682808764 0.956978003 0.616001914 0.778730886 0.708401532 1 18.25170794 -4.999999988 0.054000137 2.158980103 0.149263343 0.530663655 0.096139705 353.5082388 1.404818378 57.24800498 11.38751414 1.00E-05 4.999999988 -2.00971676 ATHGS(ph)NSLPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATHGSNSLPSSAR 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 AT(0.008)HGS(0.903)NS(0.086)LPS(0.001)S(0.001)AR 75.669 0.032267 23490000 37292 36589 34679 44116 40181 35375 48687 37701 47493 TRUE FALSE 35529.28107 40317.4607 36269.06645 39681.37587 47188.55368 34149.95488 41258.90395 34399.70057 54857.97188 0.647659398 0.734942604 0.661144866 0.723347483 0.86019501 0.622515811 0.752104071 0.627068399 1 15.74341367 -1.606161921 3.172427873 1.016507738 0.7068278 0.630587947 0.071252827 25339417.32 31490632.87 3521192.935 0.015903827 0.024764986 1.606161921 -0.309679938 ATHGSNS(ph)LPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATHGSNSLPSSAR 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 AT(0.001)HGS(0.015)NS(0.981)LPS(0.001)S(0.001)AR;ATHGS(0.011)NS(0.988)LPSSAR;ATHGS(0.004)NS(0.996)LPSSAR;ATHGS(0.38)NS(0.619)LPSSAR 109.65 0.00056335 620940000 784193 729339 716727 882809 1202494 662529 906345 748614 1154050 TRUE FALSE 747125.751 803659.4733 749589.6419 794067.3621 1412208.573 639585.4546 768065.4241 683061.3895 1333014.18 0.560478472 0.602888916 0.562326833 0.59569311 1.059410015 0.479803939 0.576186987 0.512418697 1 20.3462607 -2.261712864 2.333966286 2.569912621 0.615412442 0.355649367 0.161262858 4463672.166 896313.1936 36924615.08 0.040000964 0.005473777 2.261712864 -1.954500179 ATIAGGGVIPHIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATIAGGGVIPHIHK 14 0 Q71UI9;P0C0S5;Q71UI9-4;Q71UI9-3 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z 0 ; 143.86 5.21E-06 6659900000 5484400 5063100 5035900 5608200 5344500 5594200 6607600 4651100 193569 FALSE TRUE 5225163.281 5579035.646 5266800.996 5044453.081 6276579.108 5400471.451 5599489.263 4243825.027 223586.6919 23.3697419 24.95244953 23.55596816 22.56150864 28.07223925 24.15381437 25.04392911 18.98066916 1 17.77047479 0.804291018 2.524720553 1.005448449 24.5339902 0.960761974 1.490842344 0.135333687 1.41898258 1.341638004 0.35874606 6.372223771 -0.804291018 23.52854175 ATIS(ph)DEEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 AT(0.001)IS(0.999)DEEIER;AT(0.001)IS(0.999)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;AT(0.001)IS(0.999)DEEIER;ATIS(1)DEEIER 251.24 9.39E-14 8033150000 2303980 2038880 2059880 2296170 2285300 2215140 2516720 2295000 2466350 TRUE FALSE 2195075.431 2246644.19 2154327.535 2065354.629 2683855.596 2138429.146 2132748.141 2094037.633 2848818.962 0.770521209 0.788623012 0.756217775 0.724986269 0.942094121 0.75063708 0.748642918 0.735054653 1 21.44193251 -1.945343761 2.885942311 1.154956053 0.777169546 0.566261784 0.061308848 12648554.14 7977130.634 13106018.72 0.014298988 0.011341128 1.945343761 -0.377786508 ATISNPITGDLETVHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATISNPITGDLETVHYR 17 0 P13674 P13674 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 109.38 0.0006097 123160000 114710 70479 95244 110620 111860 94515 128240 96772 106720 FALSE TRUE 109287.8856 77660.89023 99611.03161 99500.26744 131368.3486 91241.92185 108674.6327 88298.13066 123269.5925 0.886576189 0.630008493 0.80807464 0.807176088 1.065699544 0.740181905 0.881601297 0.716300986 1 16.91145744 3.221201125 3.196554691 0.866875095 0.75619546 0.127319027 0.121335742 0.450193922 9.522081436 0.033362481 0.043371147 1664.183168 -3.221201125 -0.110679635 ATLENITNLRPVGEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATLENITNLRPVGEDFR 17 1 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ;;; 127.97 3.51E-05 1165200000 2025170 1778600 1802730 2147530 2173300 1888010 2262730 2086020 2305600 FALSE TRUE 1929444.228 1959841.362 1885386.954 1931656.204 2552322.832 1822627.74 1917508.981 1903357.03 2663140.673 0.724499553 0.735913571 0.707956201 0.725330143 0.958388289 0.684390336 0.72001791 0.714703902 1 21.34469721 -1.601590689 2.566902383 1.024265949 0.744129009 0.518555185 0.076766321 11290214.13 9924398.755 1841515.228 0.018023266 0.02502703 1.601590689 -0.280136941 ATLLPEAGRS(ph)PEEAGFPGDPHEDKQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATLLPEAGRSPEEAGFPGDPHEDKQ 25 2 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 AT(0.001)LLPEAGRS(0.999)PEEAGFPGDPHEDKQ;ATLLPEAGRS(1)PEEAGFPGDPHEDKQ;AT(0.036)LLPEAGRS(0.964)PEEAGFPGDPHEDKQ 173.03 2.63E-12 683030000 724680 632070 645690 728980 528800 760860 802660 781010 493020 TRUE FALSE 690425.8126 696478.6516 675295.5252 655701.5454 621022.5526 734511.2274 680199.4751 712620.624 569475.0236 1.21238998 1.223018785 1.185821146 1.151414054 1.090517629 1.289804113 1.194432498 1.251364141 1 19.11927304 -1.834075471 2.69292117 0.928135049 1.201073989 0.577369448 0.053724955 10477636.02 6560376.268 4846692.74 0.012711334 0.014652932 1.834075471 0.27293894 ATLPDADKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATLPDADKER 10 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8 P12814-3 ACTN1 Alpha-actinin-1 0 94.465 0.0073738 252470000 496650 360070 286250 425330 387230 371070 534070 437250 410610 FALSE TRUE 473174.3388 396761.5424 299374.8456 382575.0203 454762.7894 358219.7529 452587.8126 398962.072 474285.3017 0.997657606 0.836546148 0.631212573 0.806634781 0.958838041 0.755283268 0.954252242 0.841185823 1 18.85539563 1.667323441 11.10802968 0.922736333 0.840908656 0.156678991 0.107822676 0.277820742 46.06854379 0.051843897 0.028135419 46.4861352 -1.667323441 -0.081827677 ATLPSPDKLPGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 113.25 0.00076289 412200000 851170 769130 759210 939810 617160 859210 948420 959290 771730 FALSE TRUE 810936.881 847505.2214 794020.5295 845338.5133 724792.5086 829455.3423 803721.1101 875289.4821 891405.9469 0.909727923 0.950751141 0.890750765 0.948320478 0.813089155 0.930502366 0.901633103 0.981920173 1 19.76572306 1.167938098 4.53421712 0.99811178 0.909444453 0.453467812 0.038633227 0.185972922 6.787548215 0.033647913 0.008773533 14.72102661 -1.167938098 -0.088667327 ATLYVTAIEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATLYVTAIEDR 11 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 91.855 0.024266 40967000 29520 28919 24392 26858 38071 23887 35877 30564 32916 FALSE TRUE 28124.6481 31865.87898 25510.39733 24158.18281 44710.57035 23059.7872 30403.30472 27887.65413 38020.44517 0.739724324 0.838124826 0.670965246 0.635399788 1.175961253 0.606510184 0.799656727 0.733490994 1 15.2144878 -1.795481629 2.601108498 1.065398086 0.777348792 0.165283207 0.158841354 28088027.68 21295649.76 11658063.91 0.034001745 0.016014684 1.795481629 -0.288049294 ATNES(ph)EDEIPQLVPIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.003)NES(0.997)EDEIPQLVPIGK;AT(0.167)NES(0.833)EDEIPQLVPIGK;AT(0.003)NES(0.997)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.003)NES(0.997)EDEIPQLVPIGK;AT(0.002)NES(0.998)EDEIPQLVPIGK;AT(0.004)NES(0.996)EDEIPQLVPIGK;AT(0.044)NES(0.956)EDEIPQLVPIGK;AT(0.117)NES(0.883)EDEIPQLVPIGK;AT(0.006)NES(0.994)EDEIPQLVPIGK;AT(0.163)NES(0.837)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK 343.59 6.14E-73 11823780000 5742660 5704730 5522300 6453000 4539520 6001380 6218000 5802380 5135160 TRUE FALSE 5471215.843 6286048.473 5775502.917 5804332.18 5331210.851 5793550.706 5269329.899 5294292.847 5931494.386 0.922400914 1.059774833 0.973701152 0.978561523 0.898797251 0.976743857 0.888364644 0.892573187 1 22.49996419 2.879582815 4.886344758 0.925454176 0.990577543 0.216232803 0.048433989 0.281308911 10.07460119 0.014090032 0.015064607 757.8492331 -2.879582815 0.065123368 ATNES(ph)EDEIPQLVPIGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATNESEDEIPQLVPIGKK 18 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 ATNES(1)EDEIPQLVPIGKK;AT(0.001)NES(0.999)EDEIPQLVPIGKK;AT(0.003)NES(0.997)EDEIPQLVPIGKK;AT(0.067)NES(0.933)EDEIPQLVPIGKK 188.23 2.38E-14 475796000 1086530 546309 1299970 783190 1036370 1163670 1826320 1323970 1780410 TRUE FALSE 1035171.88 601978.5082 1359574.91 704462.2532 1217112.6 1123371.816 1547681.341 1208036.168 2056506.89 0.503364168 0.292718936 0.661108853 0.342552829 0.591834925 0.546252396 0.752577757 0.587421406 1 20.97176447 0.910173148 0.327288135 1.061361709 0.380202608 0.65836203 0.116657244 1.008440921 0.303409832 0.243701815 0.127237869 8.131546461 -0.910173148 -0.6811591 ATNVTYQAHHVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATNVTYQAHHVSR 13 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 63.037 0.041692 77750000 83796 65490 74551 86590 132476 69805 122081 95247 40614 FALSE TRUE 79835.12915 72163.50546 77969.23709 77885.80869 155579.7725 67387.63535 103455.3013 86906.66774 46912.21169 1.70179845 1.538266964 1.662024328 1.660245933 3.316402422 1.436462552 2.205295754 1.852538275 1 15.5176759 2.956579079 24.99510478 2.053833752 1.627931168 0.056126463 0.592912905 973.4995739 560391.5274 0.161441254 0.171244726 904.855184 -2.956579079 -0.425902584 ATQCLVKS(ph)PEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATQCLVKSPEVK 12 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 ATQCLVKS(1)PEVK;ATQCLVKS(1)PEVK;ATQCLVKS(1)PEVK 171.46 2.32E-05 1278800000 1187030 953891 1090810 1277290 720694 1345480 1357480 1411190 746598 TRUE FALSE 1130921.444 1051093.577 1140824.717 1148894.383 846382.8054 1298885.69 1150371.494 1287618.722 862376.6047 1.311400887 1.218833595 1.322884586 1.332242058 0.981453811 1.506169907 1.333954896 1.493104886 1 19.71795851 ATQQQHDFTLTQTADGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATQQQHDFTLTQTADGR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 267.39 8.98E-28 1896310000 737275 655490 725669 933296 894245 864637 919177 838357 949616 FALSE TRUE 702425.4719 722285.1762 758941.6414 839479.3129 1050201.045 834694.4039 778939.6668 764946.0167 1096877.599 0.640386377 0.658492048 0.691910968 0.765335452 0.957445977 0.760973152 0.710142743 0.697385029 1 20.06497111 -5 0.066203804 1.820535405 0.402378133 0.483555353 0.087055274 317.9609667 1.524123749 42.22040029 5.8794328 1.00E-05 5 -1.418157273 ATS(ph)FEESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSFEESER 9 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 AT(0.01)S(0.99)FEESER;AT(0.076)S(0.924)FEESER 104.95 0.0033323 697350000 1507760 981380 1393070 1457860 1153880 1602180 1757190 1581860 1304810 TRUE FALSE 1436491.173 1081383.738 1456943.637 1311313.143 1355116.307 1546696.105 1489098.392 1443343.952 1507153.271 0.95311552 0.71750084 0.966685782 0.870059581 0.899123091 1.02623677 0.988020543 0.957662356 1 20.52339471 2.38199872 4.497193802 0.992355024 0.865361044 0.392469673 0.068675293 0.201006792 7.223395619 0.023938462 0.019817079 240.9898326 -2.38199872 -0.12699398 ATS(ph)LPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.453)S(0.507)LPS(0.04)IPNPFPELCS(0.971)PPS(0.025)QS(0.005)PILGGPSSAR 99.725 0.00013305 31493000 69756 53897 60436 68253 64287 64929 72203 66930 71142 TRUE FALSE 66458.77212 59389.16558 63207.05038 61392.07877 75498.63245 62680.49245 61187.10625 61069.25438 82174.33802 0.808753362 0.722721558 0.769182349 0.747095508 0.918761675 0.762774535 0.744601146 0.743166977 1 16.32640031 -1.101624884 4.046766943 1.000041591 0.774376304 0.616184312 0.055240417 6024574.991 3282538.681 2576.967731 0.012448305 0.079136186 1.101624884 -0.225665288 ATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 AT(0.174)S(0.826)LPSIPNPFPELCSPPSQSPILGGPSSAR 195.74 9.14E-26 185190000 336700 304140 319320 355620 319290 306970 342880 299800 356520 TRUE FALSE 320784.8583 335132.2118 333961.1379 319872.402 374974.0749 296339.5519 290567.3586 273547.9227 411807.3007 0.778968361 0.81380833 0.810964588 0.776752625 0.910557132 0.719607329 0.705590596 0.664261955 1 18.65160988 2.139594171 19.53868976 0.742290701 0.812159769 0.009897459 0.097986093 6.19519538 1207.738307 0.032304984 0.023858831 137.9094958 -2.139594171 0.069869068 ATS(ph)PEAGGGGGALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATSPEAGGGGGALK 14 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 AT(0.001)S(0.999)PEAGGGGGALK;ATS(1)PEAGGGGGALK;AT(0.003)S(0.997)PEAGGGGGALK;AT(0.158)S(0.842)PEAGGGGGALK 233.52 3.62E-17 346978000 1777390 1571280 1660970 1966050 1427200 1858300 2089320 1957810 1729400 TRUE FALSE 1693376.297 1731395.218 1737127.117 1768418.919 1676103.228 1793946.605 1770555.861 1786373.777 1997586.519 0.847711116 0.866743544 0.869612956 0.88527776 0.839064147 0.898057024 0.886347522 0.894266036 1 20.92982656 -5 0.184823564 1.549957762 0.84625006 0.88795759 0.014759959 37.5441162 0.364392268 7.550269029 0.038654506 1.00E-05 5 -0.703707702 ATS(ph)PESTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATSPESTSR 9 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 AT(0.161)S(0.839)PESTSR;AT(0.021)S(0.979)PES(0.001)TSR;AT(0.001)S(0.994)PES(0.005)TSR 206.73 1.35E-05 1676300000 2354640 2022590 2056150 2393770 2264570 2050510 2523710 2289690 2459620 TRUE FALSE 2243340.834 2228694.22 2150426.511 2153143.692 2659510.291 1979500.325 2138671.688 2089192.605 2841045.308 0.789618113 0.784462752 0.756913839 0.757870241 0.936102738 0.696750706 0.75277634 0.735360538 1 21.43799041 -1.601640204 6.164249604 1.000784216 0.776115111 0.559415695 0.06240901 0.000628501 4.06E-05 0.056464314 0.013263957 0.025024177 1.601640204 -0.224669104 ATS(ph)PLVSLYPALECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.239)S(0.761)PLVSLYPALECR;AT(0.076)S(0.924)PLVSLYPALECR;AT(0.021)S(0.979)PLVSLYPALECR;ATS(1)PLVSLYPALECR;ATS(1)PLVSLYPALECR;AT(0.147)S(0.853)PLVSLYPALECR;AT(0.012)S(0.988)PLVSLYPALECR 266.63 2.61E-25 1420090000 1235761 933120 1001451 1148004 1250467 1008837 1272921 1160488 1433459 TRUE FALSE 1177349.027 1028205.989 1047368.519 1032604.457 1468548.049 973900.7217 1078713.523 1058869.519 1655752.501 0.71106583 0.620990147 0.632563453 0.623646624 0.886936936 0.58819221 0.651494425 0.639509539 1 20.65905561 -1.369659362 5.459517469 1.000120622 0.666735305 0.607727044 0.083475524 0.000113036 1.31E-05 0.07454392 0.017563854 0.042691424 1.369659362 -0.333385317 ATS(ph)SSSGSLSATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.333)S(0.333)S(0.333)SGSLSATGR;AT(0.036)S(0.909)S(0.05)S(0.003)S(0.001)GS(0.001)LSATGR;AT(0.001)S(0.895)S(0.101)S(0.003)SGSLSATGR;AT(0.007)S(0.971)S(0.021)S(0.001)SGSLSATGR 278.84 3.57E-33 527293000 883770 865630 862380 1056200 867320 919110 1034490 940650 881940 TRUE FALSE 841995.9436 953838.6811 901920.976 950028.7694 1018580.333 887280.9902 876659.5508 858281.6993 1018706.751 0.826534175 0.936323118 0.88535879 0.932583168 0.999875904 0.870987641 0.860561246 0.842520871 1 19.95830738 ATSAGSS(ph)PSCSLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSAGSSPSCSLAGR 15 0 Q9BXB5;Q9BXB5-2 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 ATSAGS(0.183)S(0.774)PS(0.034)CS(0.008)LAGR 93.909 0.0049039 55406000 147580 142380 150690 164150 175340 172710 162780 162950 157570 TRUE FALSE 140604.1859 156888.6839 157599.2856 147649.3301 205919.2405 166729.0094 137944.9213 148681.2341 182005.1508 0.772528608 0.86200134 0.865905634 0.811237097 1.131392378 0.916067532 0.757917678 0.816906738 1 17.47361975 4.449411006 1.073008993 0.891348317 0.746356786 0.127653676 0.105377008 2.674980847 3.523848381 0.033364744 0.395555665 28145.63209 -4.449411006 -0.144991531 ATSCFPRPMT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSCFPRPMTPR 12 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 ATSCFPRPMT(1)PR;ATSCFPRPMT(1)PR 71.344 0.072492 509710000 779270 686190 684950 812050 843770 706230 862630 784830 853510 TRUE FALSE 742435.4515 756113.5411 716355.635 730421.1912 990923.2209 681773.078 731019.9502 716106.1246 985867.9717 0.753077971 0.76695213 0.72662431 0.740891491 1.005127714 0.691546026 0.741498833 0.726371223 1 19.91103493 -1.700234416 2.909363171 1.031195412 0.767416418 0.413674682 0.086405235 25521826.93 21111388.96 5786818.355 0.02058146 0.019941856 1.700234416 -0.263778994 ATSFS(ph)SAGEVPKPRPPSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSFSSAGEVPKPRPPSTR 19 2 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H7BZT5 O15231-3 ZNF185 Zinc finger protein 185 1 AT(0.085)S(0.244)FS(0.643)S(0.028)AGEVPKPRPPSTR 111.45 0.0001127 255920000 37620 41315 35090 48184 37428 41731 52818 47022 48708 TRUE FALSE 35841.77716 45525.04547 36698.91121 43340.45278 43955.43135 40285.84501 44759.64403 42904.5044 56261.38787 0.637058176 0.809170324 0.652293031 0.770340982 0.781271721 0.716047835 0.795565942 0.762592357 1 15.77985752 -5 0.183108821 2.0851229 0.689235598 0.727940481 0.052073977 66.38154741 0.642492896 26.15192625 0.140204261 1.00E-05 5 -1.395887302 ATSILSYLS(ph)DSDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ATSILSYLSDSDLR 14 0 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILS(0.02)YLS(0.968)DS(0.011)DLR;ATSILS(0.078)YLS(0.922)DSDLR;ATSILSYLS(1)DSDLR;ATSILSYLS(1)DSDLR 232.17 2.79E-13 66412000 116722 104688 105859 123041 121967 96789 109189 109820 114008 TRUE FALSE 111204.7824 115355.8262 110712.7399 110672.6849 143238.0062 93437.17266 92530.21266 100203.5786 131687.7784 0.844457882 0.875979743 0.840721449 0.840417283 1.087709186 0.709535644 0.702648445 0.76091783 1 17.00676193 ATSILSYLS(ph)DSDLRGPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSILSYLSDSDLRGPSLR 19 1 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILSYLS(1)DSDLRGPSLR;ATSILSYLS(0.999)DS(0.001)DLRGPSLR 160.57 1.89E-11 56317000 27869 22309.4 33174 30266 39064 30362 41153 32240 45772 TRUE FALSE 26551.6876 24582.75322 34695.06071 27223.60418 45876.74923 29310.55633 34874.35402 29416.89469 52870.08799 0.502206231 0.464965241 0.656232324 0.514915053 0.867725986 0.554388265 0.659623529 0.556399579 1 15.69016411 -5 0.128511518 2.323557111 0.416166193 0.565806608 0.112355528 100.0189626 0.814296282 34.41072721 0.818915317 1.00E-05 5 -1.907390918 ATSLPS(ph)IPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.295)S(0.295)LPS(0.407)IPNPFPELCS(0.488)PPS(0.412)QS(0.098)PILGGPS(0.002)S(0.002)AR 49.525 0.044183 321950000 11167 9846.8 10334 12863 11267 11336 13761 10918 12218 TRUE FALSE 10639.15804 10850.20011 10807.82412 11569.9868 13231.96123 10943.43148 11661.50671 9961.96204 14112.70504 0.753870928 0.768824976 0.765822292 0.81982772 0.937592134 0.775431177 0.826312651 0.70588608 1 13.78470692 -2.39020567 2.395470324 2.76232804 0.795196978 0.529219855 0.060995958 6948515.05 581101.9495 67392927.68 0.014498377 0.004071874 2.39020567 -1.967131062 ATSLPS(ph)IPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.151)S(0.163)LPS(0.686)IPNPFPELCS(0.045)PPS(0.153)QS(0.714)PILGGPS(0.044)S(0.044)AR 75.717 0.0016193 31675000 26742 26931 28378 31339 30799 30230 35035 29805 39635 TRUE FALSE 25477.95866 29675.29952 29679.15937 28188.74418 36170.33585 29183.12752 29689.76729 27195.11619 45781.39337 0.556513395 0.648195639 0.648279949 0.615724907 0.790066295 0.637445158 0.648511657 0.594021156 1 15.48247375 -2.024321027 2.895714845 1.421252714 0.641816839 0.778417274 0.059968685 392892.2351 5349450.788 1229721.983 0.013658465 0.00945538 2.024321027 -0.779435875 ATSLPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 ATSLPSIPNPFPELCS(0.899)PPS(0.551)QS(0.548)PILGGPS(0.001)S(0.001)AR 83.59 0.00040165 245950000 26022 23409 22803 24981 25067 22107 26527 26279 31400 TRUE FALSE 24791.99163 25794.40371 23848.54011 22469.86242 29438.67686 21341.42905 22479.81895 23977.87145 36269.35163 0.683552104 0.711190097 0.657539742 0.619527546 0.811668131 0.588414959 0.619802063 0.661105599 1 15.14646333 -2.030358374 2.64638354 1.398396831 0.668887173 0.741661395 0.061374818 8628006.653 2746275.368 20877341.91 0.014234806 0.009324845 2.030358374 -0.729509658 ATSS(ph)SSGSLSATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.203)S(0.369)S(0.369)S(0.04)GS(0.02)LSATGR 201.97 1.79E-08 117000000 153770 141910 145670 170520 156820 142060 168900 161420 175630 TRUE FALSE 146501.5968 156370.7903 152349.1136 153379.0056 184169.3583 137140.4266 143131.2029 147285.2091 202865.8034 0.722160139 0.770809016 0.750984695 0.756061411 0.90783836 0.676015495 0.705546231 0.726022851 1 17.63016617 -1.309451563 5.489738815 1.000040477 0.749884312 0.615247238 0.061632566 2.97E-05 3.73E-06 0.058024072 0.013674196 0.049039771 1.309451563 -0.250156165 ATSSHFS(ph)AS(ph)EESMDFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSSHFSASEESMDFLDK 18 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 2 AT(0.008)S(0.01)S(0.01)HFS(0.971)AS(1)EESMDFLDK 137.09 2.59E-06 20724000 59737 47692 58721 63807 39856 62213 66907 61603 45811 TRUE FALSE 56913.3504 52551.86902 61413.41593 57392.99913 46806.87378 60058.54821 56699.10832 56208.71474 52915.13591 1.075558995 0.993134915 1.160602064 1.084623485 0.884564935 1.134997523 1.071510209 1.06224266 1 15.69139283 ATSSHFS(ph)ASEESMDFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSSHFSASEESMDFLDK 18 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 ATSSHFS(1)ASEESMDFLDK 225.83 2.48E-19 37225000 86605 72906 79766 90461 69458 85133 96199 94760 72308 TRUE FALSE 82511.35328 80335.20429 83423.35 81367.68842 81571.45321 82184.82286 81522.07573 86462.31205 83521.15534 0.987909625 0.961854562 0.998828975 0.974216509 0.976656188 0.984000072 0.976064991 1.035214512 1 16.34985405 1.252428054 24.99538601 1.017607255 0.979055463 0.603364491 0.012683564 116.3334105 209687.56 0.007512014 0.002713722 17.88249259 -1.252428054 -0.038551792 ATSSS(ph)SGSLSATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.14)S(0.077)S(0.779)S(0.002)GS(0.002)LSATGR 200.9 1.95E-08 226410000 334180 305230 313420 344920 346500 316870 351380 318020 401680 TRUE FALSE 318383.9737 336333.284 327790.617 310247.9863 406929.4903 305896.7124 297770.5275 290172.4829 463970.4829 0.68621601 0.72490233 0.706490238 0.668680439 0.877059005 0.659302097 0.641787653 0.625411516 1 18.8236735 -2.016716889 2.721562836 1.334343672 0.698953857 0.648239183 0.069744781 8757247.197 2560495.003 18356502.99 0.016350784 0.009622393 2.016716889 -0.635389815 ATSSSS(ph)GSLSATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AT(0.001)S(0.021)S(0.019)S(0.193)S(0.484)GS(0.282)LSATGR;ATSSS(0.038)S(0.744)GS(0.218)LSATGR 175.6 1.25E-07 0 98548 75876 89584 101886 95023 88778 99685 94146 109777 TRUE FALSE 93889.83134 83607.85066 93691.51501 91644.22571 111594.9811 85703.5956 84476.22241 85902.07714 126800.6565 0.74045225 0.659364494 0.738888249 0.722742518 0.880082045 0.675892365 0.666212816 0.677457669 1 16.95220269 -1.600833231 3.698211597 1.00949843 0.71564885 0.653095975 0.06402679 0.005088342 0.00054921 0.062909611 0.014443182 0.025070718 1.600833231 -0.29384958 ATSSSSGS(ph)LSATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSSS(0.035)S(0.336)GS(0.61)LS(0.018)ATGR;ATSSS(0.005)S(0.228)GS(0.765)LS(0.001)ATGR 174.68 2.63E-06 254860000 324543 255144 288255 342743 316544 311763 340696 318562 315347 TRUE FALSE 309202.4956 281143.4637 301471.7769 308289.8225 371749.1734 300966.5691 288716.5679 290667.0225 364249.4022 0.84887578 0.771843308 0.827652084 0.846370154 1.02058966 0.826265101 0.792634294 0.797989017 1 18.47456708 -2.475135909 2.210300023 2.831918718 0.836820415 0.345860342 0.068219789 4395198.648 337847.9846 40487836.93 0.017138883 0.003348606 2.475135909 -1.995098302 ATST(ph)SPNSQSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.651)S(0.348)PNS(0.001)QSSK 135.58 0.0013987 59924000 201740 199410 188790 220930 141780 212210 233750 240500 205010 TRUE FALSE 192204.15 219730.1057 197446.2082 198721.6967 166506.3871 204861.1145 198087.1444 219440.545 236801.9038 0.811666405 0.927906838 0.833803298 0.839189607 0.70314632 0.865115995 0.836509932 0.926684041 1 17.85332115 1.044647327 2.491756979 0.999745265 0.835928349 0.517087676 0.055445073 0.228078758 3.016087749 0.05277205 0.014353576 11.08274464 -1.044647327 -0.163816916 ATSTS(ph)PNSQSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.024)S(0.969)PNS(0.007)QSSK;ATST(0.022)S(0.973)PNS(0.005)QSSK;ATST(0.022)S(0.975)PNS(0.003)QSSK;ATST(0.021)S(0.979)PNSQSSK;ATST(0.001)S(0.999)PNSQSSK;ATST(0.002)S(0.998)PNSQSSK;ATST(0.002)S(0.995)PNS(0.002)QSSK;ATSTS(0.999)PNSQSSK;AT(0.002)S(0.007)T(0.034)S(0.955)PNS(0.002)QSSK 303.29 1.12E-36 3348642000 9699160 9359340 9405300 10450020 6489940 9746280 11022180 11394460 9794170 TRUE FALSE 9240699.929 10313067.39 9836542.308 9399564.136 7621783.481 9408763.88 9340544.005 10396700.68 11312999.86 0.81682136 0.911612085 0.869490182 0.830863984 0.673719047 0.831677185 0.825646965 0.919004756 1 23.4314782 1.031693689 2.853337198 0.999303239 0.827881983 0.494133914 0.060358372 0.222402909 4.020746384 0.059835373 0.015929593 10.75706243 -1.031693689 -0.171421256 ATSVALPGWSPSETRSS(ph)FMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATSVALPGWSPSETRSSFMSR 21 1 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWSPSET(0.001)RS(0.249)S(0.75)FMSR 146.15 5.94E-09 0 39428 26035 37433 45181 46911 40535 57191 37753 52209 TRUE FALSE 37564.31658 28687.9961 39149.34008 40639.32004 55092.26355 39131.26279 48465.46257 34447.14718 60305.30507 0.622902355 0.475712644 0.649185673 0.673892952 0.913555839 0.64888591 0.803668309 0.571212551 1 15.8799973 3.272964013 2.355892818 0.766364467 0.552218581 0.347930046 0.127586801 0.287552535 3.266141663 0.03451798 0.047642519 1874.839146 -3.272964013 -0.214145887 ATT(ph)PADGEEPAPEAEALAAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATTPADGEEPAPEAEALAAAR 21 0 Q96S44;Q5JZ02 Q96S44 TP53RK TP53-regulating kinase 1 AT(0.206)T(0.794)PADGEEPAPEAEALAAAR 106.34 0.0041283 93780000 104730 100970 101520 113230 102420 109730 119820 121860 107920 TRUE FALSE 99779.62045 111258.9578 106174.7924 101847.9053 120282.0156 105930.0226 101539.2584 111189.2924 124655.6824 0.800441813 0.892530173 0.851744504 0.817033795 0.964914019 0.849780937 0.814557799 0.89197131 1 16.92758912 -5 0.425460973 3.730741491 0.85528141 0.459989601 0.047779251 887.4093546 5.648180252 2268.634463 0.025924432 1.00E-05 5 -2.875460081 ATTPPNQGRPDS(ph)PVYANLQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 ATTPPNQGRPDS(1)PVYANLQELK 151.95 2.72E-08 104370000 45004 38655 39655 48070 33297 43719 50744 47646 46647 TRUE FALSE 42876.75011 42593.98845 41473.22097 43237.91227 39103.98626 42205.00007 43002.07082 43473.86365 53880.77852 0.795770798 0.790522884 0.769722007 0.802473785 0.725750209 0.783303457 0.798096687 0.806852923 1 15.71748308 0.341666672 1.176483889 1.000328094 0.780469544 0.911697738 0.021311 0.88697951 1.339948943 0.019969981 0.005967489 2.19617363 -0.341666672 -0.21985855 ATVHDPETGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATVHDPETGK 10 0 P13674-2;P13674-3 P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 109.42 0.0020212 97617000 328240 252040 203560 323140 259090 277130 281940 288410 221050 FALSE TRUE 312724.7457 277723.1625 212893.4273 290657.3533 304275.214 267532.9186 238924.8748 263155.2914 255329.305 1.224789868 1.087705786 0.833799424 1.138362685 1.191697185 1.047795585 0.935751871 1.030650561 1 17.9619996 4.250173922 2.959109851 1.026664545 1.2048035 0.278573942 0.09903271 0.315103687 5.532388318 0.025578577 0.079328485 17789.917 -4.250173922 0.178138954 ATVHDPETGKLTTAQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ATVHDPETGKLTTAQYR 17 1 P13674-2;P13674-3 P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 66.826 0.024213 61706000 119560 68195 117340 88057 123720 109130 167990 118290 134610 FALSE TRUE 113908.6357 75144.14803 122720.1551 79205.34306 145296.7288 105350.8007 142360.0402 107931.9005 155484.6313 0.732603826 0.483289875 0.789275146 0.509409466 0.934476466 0.677564077 0.915589142 0.69416443 1 17.24641246 2.736421978 24.9980959 0.831705628 0.624893743 0.389685406 0.133587047 187.3363437 2189722.034 0.037170721 0.036664106 545.031971 -2.736421978 -0.206811885 ATVMDVKPVDYR ddPTM_SK-BR-3_Trastuzumab_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 62.14 0.072849 162290000 474830 475130 412190 516020 446710 463880 505750 519540 488170 FALSE TRUE 452385.7269 523546.2872 431089.3192 464148.6892 524616.0826 447815.7193 428588.5488 474046.3233 563872.9104 0.802283136 0.92848278 0.764515037 0.823144153 0.930380007 0.794178459 0.760080048 0.840697105 1 19.10501051 ATVT(ph)PS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVK;AT(0.002)VT(0.998)PS(1)PVK 111.52 0.0050113 85863000 1236660 1465040 1027470 1564940 832740 1313780 1275310 1374690 943240 TRUE FALSE 1178205.533 1614329.242 1074580.516 1407629.258 977969.5923 1268283.469 1080738.037 1254314.856 1089512.842 1.081405824 1.481698223 0.986294493 1.291980419 0.897620987 1.164083084 0.991946121 1.151262113 1 20.05525177 3.33904145 1.651898018 1.05806188 1.265220689 0.164146469 0.156231358 0.485701372 2.726264863 0.04549612 0.070524067 2182.938244 -3.33904145 0.207158809 ATVT(ph)PS(ph)PVKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVKGK;AT(0.202)VT(0.798)PS(1)PVKGK;AT(0.028)VT(0.972)PS(1)PVKGK 125.47 0.00075088 2430100000 8120500 8283400 7687400 9676100 4680860 9643500 9680300 9775400 5742600 TRUE FALSE 7736660.058 9127487.877 8039874.894 8703440.045 5497200.502 9309543.177 8203392.444 8919414.153 6633133.079 1.166365874 1.376044739 1.212078033 1.312116 0.828748713 1.40349109 1.236729664 1.344675894 1 22.66125904 -2.054621959 2.783965041 0.658924579 1.240322765 0.17111751 0.162193882 47069503.59 46509573.31 100953454.4 0.036704538 0.008818161 2.054621959 0.581398185 ATVTPS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.061)PS(0.939)PVK;ATVT(0.016)PS(0.984)PVK;ATVT(0.008)PS(0.992)PVK;ATVT(0.106)PS(0.894)PVK;ATVT(0.048)PS(0.952)PVK;ATVT(0.088)PS(0.912)PVK;ATVT(0.012)PS(0.988)PVK;ATVT(0.161)PS(0.839)PVK;ATVT(0.046)PS(0.954)PVK;ATVT(0.022)PS(0.978)PVK;ATVT(0.003)PS(0.997)PVK;ATVT(0.006)PS(0.994)PVK 211.64 5.05E-06 14540030000 26753100 34509640 17506950 29176280 15838280 25891410 26253210 28575500 16061660 TRUE FALSE 25488533.98 38026211.55 18309660.97 26243424.9 18600471.02 24994783.98 22247800.64 26073277.73 18552420.2 1.373865712 2.049663124 0.986914956 1.414555331 1.002590003 1.347251933 1.199185896 1.405384174 1 24.14510407 3.730562146 24.9998692 1.211678264 1.711764424 0.471941089 0.227208356 424.49079 1326780.78 0.054302081 0.085795356 5377.27374 -3.730562146 0.500086161 ATVTPS(ph)PVKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.002)PS(0.998)PVKGK;ATVTPS(0.999)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVTPS(1)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.008)PS(0.992)PVKGK;ATVTPS(1)PVKGK;ATVT(0.019)PS(0.981)PVKGK 164.88 1.35E-05 62325780000 33048100 32445300 30240400 36011400 18643430 37386300 38631700 39077300 23362700 TRUE FALSE 31485981.81 35751512.96 31626952.25 32391465.65 21894838.29 36091603.06 32737724.65 35655484.45 26985668.2 1.166766803 1.324833341 1.171990703 1.200321053 0.811350608 1.33743596 1.213152271 1.321274841 1 24.68569007 -1.530849893 2.926271246 0.991575899 1.199225204 0.140196375 0.149893616 20402370.89 24487979.59 1382426.263 0.03520971 0.029454395 1.530849893 0.207649306 ATVWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 92.491 0.036363 187131000 1023870 875110 624620 797210 1089610 705880 1071600 913690 1026280 FALSE TRUE 975473.6942 964284.7039 653259.4448 717072.9362 1279637.639 681435.1986 908107.7387 833682.4598 1185430.261 0.822885771 0.813447012 0.551073704 0.604905206 1.079471042 0.574842081 0.766057497 0.703274151 1 20.17697936 -1.122494077 4.344155726 1.000037637 0.745745522 0.221378819 0.153139125 19906666.48 5143720.037 7397.487831 0.033222908 0.075423368 1.122494077 -0.254292115 AVAAPRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVAAPRPDR 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 113.18 0.0016807 741510000 785380 718408 693450 768810 941520 691750 892420 814130 991950 FALSE TRUE 748256.6439 791614.592 725245.3684 691527.7582 1105720.79 667794.524 756264.9386 742840.4612 1145776.54 0.653056349 0.690897888 0.632972786 0.603545049 0.965040522 0.582831382 0.660045753 0.648329264 1 20.12789427 -1.206169319 4.473346191 1.000090473 0.678191199 0.474597899 0.105938659 8.70E-05 1.54E-05 0.093400697 0.022008588 0.062205771 1.206169319 -0.321899274 AVAFNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVAFNKR 7 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 119.22 0.0077453 806240000 931580 667780 357800 436390 924720 520330 1006140 725090 965030 FALSE TRUE 887546.0596 735827.5412 374205.4839 392523.2481 1085990.875 502310.8416 852634.864 661597.2757 1114681.924 0.796232576 0.660123328 0.335706066 0.352139242 0.974260775 0.450631549 0.764913152 0.593530102 1 20.08820066 -0.425921551 0.585847309 1.045440176 0.61516503 0.266713979 0.200237384 13.33900918 3.874271391 1.491782053 0.079613513 0.375040742 0.425921551 -0.430275146 AVAGVMITAS(ph)HNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVAGVMITASHNR 13 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 1 AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR 181.58 7.68E-06 931820000 1305180 944910 1080680 1355340 1488920 1216420 1460300 1219840 1216700 TRUE FALSE 1243486.728 1041197.403 1130230.247 1219098.648 1748587.177 1174295.07 1237504.415 1113024.343 1405379.622 0.884804866 0.74086559 0.804217045 0.867451491 1.244209856 0.835571437 0.880548142 0.791974158 1 20.42252845 2.995767741 24.85274164 0.941164969 0.809596061 0.20754576 0.125958208 279.1648701 1639334.432 0.036292292 0.042403862 990.3021942 -2.995767741 -0.131568908 AVAHHTDCTFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVAHHTDCTFIR 12 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QRR3 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 78.692 0.014482 438020000 239340 226452 212130 262990 263170 237090 294180 267670 195942 FALSE TRUE 228026.8725 249527.7163 221856.3703 236553.7456 309066.7647 228879.5139 249297.438 244231.3958 226327.6846 1.007507645 1.10250638 0.980244068 1.045182546 1.365572069 1.011274932 1.101488925 1.079105264 1 17.78805354 2.958143974 24.99915331 1.11768561 1.038670558 0.119559135 0.103725815 1016.574942 607164.9973 0.029581897 0.031378878 908.1215335 -2.958143974 -0.079015052 AVALYFEDKLTEIYSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVALYFEDKLTEIYSDR 17 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 0 73.887 0.0113 0 18335 18052 20795 23960 17941 20434 22920 21520 15334 FALSE TRUE 17468.34089 19891.51932 21748.47132 21551.49528 21069.90472 19726.36546 19423.13305 19635.59472 17711.9184 0.986247818 1.123058433 1.227900379 1.216779277 1.18958908 1.113733984 1.096613738 1.108609145 1 14.11243286 -0.878392605 6.92401441 0.999999998 1.12710196 0.262082638 0.069452974 3.29E-09 3.96E-10 0.073516161 0.017327925 0.132314486 0.878392605 0.127101962 AVASS(ph)PAATNSEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AVASSPAATNSEVK 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVAS(0.007)S(0.929)PAAT(0.059)NS(0.005)EVK;AVAS(0.005)S(0.995)PAATNSEVK;AVAS(0.035)S(0.953)PAAT(0.008)NS(0.003)EVK 212.43 2.56E-09 164590000 748610 581710 672950 777240 562700 738670 831900 794490 663340 TRUE FALSE 713224.6889 640986.9103 703805.4231 699110.3585 660834.7018 713089.6727 704978.3761 724920.2437 766207.3793 0.930850718 0.836571048 0.918557354 0.912429686 0.86247499 0.930674504 0.92008821 0.946114934 1 19.54737539 1.05053203 0.709025498 1.000297945 0.889064921 0.570843078 0.028959467 0.482617262 0.564404692 0.026546422 0.010544791 11.23393819 -1.05053203 -0.111233024 AVCMLSNTTAIAEAWAR ddPTM_SK-BR-3_Trastuzumab_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 ; 238.43 6.99E-20 79977000 73446 71375 71394 77718 78032 64120 75504 77981 73912 FALSE TRUE 69974.35314 78648.19365 74667.48552 69905.63899 91640.75609 61899.50832 63984.47807 71152.57024 85373.89547 0.819622354 0.921220629 0.874593869 0.818817492 1.073404881 0.725040224 0.749461855 0.833423025 1 16.38150739 AVCS(ph)TYLQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.371)T(0.371)Y(0.256)LQS(0.002)R;AVCS(0.562)T(0.287)Y(0.151)LQSR 151.44 0.0055426 176740000 295147 272147 284975 283390 327188 260441 297474 290030 431756 TRUE FALSE 281195.9862 299879.0887 298041.3856 254903.0988 384249.4836 251421.8629 252088.8778 264633.4357 498710.5154 0.563846114 0.601308935 0.597624025 0.511124372 0.770486027 0.504143897 0.505481377 0.530635364 1 18.9278431 -1.283792468 4.968888219 1.000118275 0.571797863 0.745066498 0.078477647 9.75E-05 1.41E-05 0.072081611 0.016985139 0.052024454 1.283792468 -0.428320412 AVDDLNLHSYSNLPIWVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVDDLNLHSYSNLPIWVNK 19 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 149.36 8.63E-08 132550000 214420 253810 189830 275180 183160 218010 215340 243580 159710 FALSE TRUE 204284.7915 279673.5276 198533.8933 247518.3836 215103.046 210460.259 182485.928 222250.8439 184477.0111 1.107372622 1.516034577 1.076198558 1.341730236 1.166015455 1.140848162 0.989206877 1.204761735 1 17.49308152 2.358132773 1.899158956 1.064873223 1.277129585 0.272176187 0.135069554 0.381054804 2.805803598 0.057447404 0.04154193 228.1039329 -2.358132773 0.212256362 AVDFAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AVDFAER 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ;;;; 162.31 0.0029707 1339525000 2362180 2223860 2191350 2499730 2364420 2243210 2554100 2362870 2290800 FALSE TRUE 2250524.433 2450473.862 2291825.565 2248452.391 2776774.099 2165527.075 2164425.136 2155964.576 2646045.564 0.850523688 0.926089065 0.866132313 0.849740617 1.049405247 0.818401279 0.817984832 0.814787397 1 21.33540647 -1.697860344 8.02603475 1.000470196 0.874898613 0.240645752 0.070254634 0.000575605 2.17E-05 0.066241322 0.015555937 0.020051167 1.697860344 -0.125571583 AVDHATNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AVDHATNR 8 0 P49748;P49748-3;P49748-2;J3KSR4 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;;;;;; 133.23 0.00092812 361144500 610429 425062.8 436227.4 458020.6 665473 363972 583843 498532 682810 FALSE TRUE 581575.2309 468377.1826 456228.8578 411979.4991 781531.2805 351367.5584 494767.0273 454877.8952 788696.6875 0.737387693 0.593862241 0.578459204 0.522354798 0.990914876 0.445504037 0.627322309 0.576746299 1 19.58911106 -1.390206411 3.297699109 1.003571388 0.633397422 0.380123445 0.146853892 124451362.4 169432970.2 4228550.177 0.03190674 0.04071867 1.390206411 -0.370173966 AVDIPHMDIEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AVDIPHMDIEALK 13 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;;; 210.41 3.02E-08 1564638000 6461150 5941070 5708010 6874330 5082570 6607110 7319730 6942960 4676380 FALSE TRUE 6155744.244 6546471.787 5969727.904 6183309.288 5968968.599 6378304.124 6202970.752 6334997.615 5401569.127 1.139621488 1.211957421 1.105184024 1.144724643 1.105043453 1.180824308 1.148364597 1.172806913 1 22.36494713 -1.234063025 3.347425195 0.999581456 1.153827663 0.679738326 0.032538401 5200299.31 7246068.58 22143.00538 0.007530756 0.058336044 1.234063025 0.154246207 AVDIPHMDIEALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVDIPHMDIEALKK 14 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 194.85 6.25E-08 1504860000 7288400 6678000 6613000 8177300 5122400 8404200 9291500 8927400 5271000 FALSE TRUE 6943891.776 7358495.792 6916212.591 7355302.268 6015744.938 8113160.447 7873911.025 8145669.529 6088399.759 1.140511801 1.208609172 1.135965584 1.208084646 0.98806668 1.332560405 1.29326446 1.337899916 1 22.53763166 2.197795161 24.99998902 1.27075825 1.149754578 0.14693298 0.113249501 214.3305018 131439.9705 0.037469809 0.027673615 157.6867349 -2.197795161 -0.121003672 AVDLGPPKPSDQETGEQVS(ph)SPSSHPALHTTTEDSAGVQTEF ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPS(0.001)DQET(0.018)GEQVS(0.44)S(0.44)PS(0.017)S(0.017)HPALHT(0.021)T(0.021)T(0.021)EDS(0.004)AGVQT(0.001)EF;AVDLGPPKPSDQET(0.002)GEQVS(0.547)S(0.438)PS(0.007)S(0.007)HPALHTTTEDSAGVQTEF 117.97 9.33E-07 188642000 127493 112374 133952 150783 141149 138487 192934 157105 19408 TRUE FALSE 121466.6586 123825.0384 140093.8317 135626.0064 165765.3409 133691.1605 163498.3748 143348.0533 22417.69352 5.418338798 5.523540513 6.249252698 6.049953634 7.394397679 5.963644759 7.293273712 6.394415787 1 14.45235023 3.767987738 6.201918181 6.17956633 5.464992306 0 1.815472369 0.764602689 100.2385004 0.407347001 0.722190131 5861.216155 -3.767987738 -0.714574023 AVDLMTHNYYELLYAFHIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVDLMTHNYYELLYAFHIYR 20 0 Q12769;G3V198;E9PR16 Q12769 NUP160 Nuclear pore complex protein Nup160 0 156.73 8.71E-09 10648000 13399 10660 8545 13279 15086 8916 17308 15783 5190.8 FALSE TRUE 12765.65582 11746.26612 8936.796702 11944.16969 17716.99362 8607.236684 14667.34672 14400.95685 5995.762753 2.1291129 1.959094548 1.490518733 1.992101786 2.954919058 1.435553246 2.446285372 2.401855684 1 12.54972758 -0.820403721 7.056267222 0.999999995 2.090844897 0.375910402 0.445728024 2.95E-08 5.86E-09 0.396299029 0.093408576 0.151215489 0.820403721 1.090844902 AVDPDGDGHVSWDEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVDPDGDGHVSWDEYK 16 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 159.13 9.24E-09 82574000 249360 192110 204730 245350 226010 216070 302930 276770 226400 FALSE TRUE 237573.247 211686.2274 214117.073 220686.9519 265426.0724 208587.4417 256712.4648 252534.5515 261508.9557 0.908470788 0.809479839 0.818775297 0.843898257 1.014978901 0.797630204 0.981658407 0.96568223 1 17.99650083 1.751166702 0.692847006 1.003516073 0.848720158 0.38387184 0.065416534 0.656473278 0.632631177 0.05612903 0.028072685 56.38540465 -1.751166702 -0.154795915 AVDTWSWGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVDTWSWGER 10 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 280.9 1.05E-23 3687830000 2149050 1844740 849910 894810 2190290 917900 1939290 1033280 1149630 FALSE TRUE 2047468.666 2032721.103 888879.2142 804861.9988 2572275.883 886112.8928 1643415.693 942800.5254 1327908.749 1.541874521 1.530768665 0.669382753 0.60611243 1.937087834 0.667299537 1.237596856 0.70998894 1 20.34072458 3.767609031 22.72088073 1.004636459 1.536322168 0.25730085 0.393791985 286.3466192 223970.0399 0.0934331 0.168376147 5856.107373 -3.767609031 0.531685709 AVDVFFPPEAQNDFPVAMQISEKHDVVFLITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVDVFFPPEAQNDFPVAMQISEKHDVVFLITK 32 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 174.02 7.61E-15 73511000 68402 60518 65203 80092 57264 79197 84539 90731 56286 FALSE TRUE 65168.77302 66684.853 68192.62204 72041 67250.82347 76454.38803 71641.02288 82786.11264 65014.54541 1.002372202 1.025691291 1.048882548 1.108075117 1.034396581 1.175958204 1.101922999 1.273347558 1 15.9884749 3.061738033 0.827616194 1.140212041 1.005929157 0.272140567 0.073058327 0.674761221 1.029624699 0.035810249 0.04914154 1152.757704 -3.061738033 -0.134282884 AVDWIFSHIDDLDAEAAMDISEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVDWIFSHIDDLDAEAAMDISEGR 24 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 148.89 1.16E-07 42776000 29944 24711 30682 32263 36251 26389 35028 32325 32012 FALSE TRUE 28528.60646 27229.07899 32088.80005 29019.86194 42573.16292 25475.14231 29683.83527 29494.45163 36976.25747 0.771538507 0.73639359 0.867821739 0.784824207 1.151364844 0.688959458 0.802780955 0.797659191 1 15.17431159 AVEDIHGLFSLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVEDIHGLFSLSK 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 151.74 4.49E-05 135810000 509020 498790 434600 524900 451640 467800 572660 590710 451000 FALSE TRUE 484959.6334 549617.2681 454526.8399 472136.0548 530405.873 451599.9687 485290.1994 538984.3008 520938.7766 0.930934027 1.055051558 0.872514891 0.90631774 1.018173146 0.866896436 0.931568586 1.034640394 1 18.9907543 1.240054968 24.99780099 1.017320215 0.945815472 0.223597924 0.059023376 63.22573347 1057807.492 0.044596032 0.014303739 17.38020793 -1.240054968 -0.071504743 AVEEKIEWLESHQDADIEDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEEKIEWLESHQDADIEDFK 21 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 171.06 4.44E-12 206983000 238844 128661 197461 201629 172202 219911 277294 243450 155200 FALSE TRUE 227554.3175 141771.7022 206514.7822 181360.8698 202233.9743 212295.4269 234987.7074 222132.2274 179267.6233 1.269355354 0.790838298 1.151991521 1.011676657 1.128112096 1.184237415 1.310820677 1.239109568 1 17.45175543 2.411152105 2.454420212 1.221849317 1.040771456 0.12280124 0.143949083 0.399483261 4.919790454 0.053857918 0.043211276 257.7223634 -2.411152105 -0.181077861 AVEES(ph)S(ph)DEERQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEESSDEERQR 12 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR 116.19 0.010386 857400000 376090 299360 359290 371840 367470 340480 432100 362530 455690 TRUE FALSE 358312.971 329865.1243 375763.8019 334461.9368 431556.6517 328689.0922 366175.2089 330784.9513 526356.0779 0.680742536 0.626695764 0.713896576 0.635429039 0.819894877 0.624461474 0.695679644 0.628443301 1 19.00567958 -1.840393217 2.542985447 1.126960174 0.676733715 0.744906537 0.059184685 7507090.87 4779142.81 5803575.771 0.013082077 0.014441316 1.840393217 -0.450226459 AVEESLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVEESLRK 8 1 Q6GMR7 Q6GMR7 FAAH2 Fatty-acid amide hydrolase 2 0 151.04 0.00076898 971040000 1008400 700200 741480 652120 779130 623720 936540 760730 837830 FALSE TRUE 960734.9305 771551.1761 775477.5914 586567.6587 915010.0253 602120.42 793653.6223 694116.4483 967756.3974 0.992744593 0.797257634 0.80131487 0.606110856 0.94549623 0.622181803 0.820096488 0.717242945 1 19.88428441 4.498243561 1.724330873 0.772571435 1.017355838 0.204544665 0.123878551 0.720612463 3.047440245 0.028234254 0.250354653 31495.14132 -4.498243561 0.244784403 AVEFSSGAKS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVEFSSGAKSPSK 13 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 AVEFSS(0.004)GAKS(0.966)PS(0.029)K 132.51 7.15E-05 133300000 352350 332180 302380 414930 184620 383380 372820 415090 185600 TRUE FALSE 335695.1138 366029.5197 316244.4221 373220.4481 216817.6695 370103.4545 315939.4617 378742.5191 214381.9001 1.565874328 1.707371376 1.475145159 1.740913985 1.011361824 1.726374542 1.473722649 1.766672088 1 17.70982358 -1.768169659 2.790153333 0.873834197 1.559929446 0.386201192 0.221239637 28411608.25 22394084.53 24545610.35 0.051662321 0.01705416 1.768169659 0.686095249 AVEHINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 AVEHINK 7 0 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;;;;;; 167.24 0.0010938 53328170000 89554720 69999640 64949210 74250890 70260120 76364330 94263040 85774230 70921160 FALSE TRUE 85321645.87 77132682.9 67927195.52 66787049.47 82513462.68 73719814.1 79881481.99 78263383.7 81919251.28 1.041533517 0.941569676 0.829196977 0.815279051 1.007253623 0.899908299 0.975124659 0.955372302 1 26.28769919 1.278249411 1.189868434 0.994812671 0.929014348 0.111002044 0.069812867 1.202533338 3.391951073 0.068345817 0.022295061 18.97795495 -1.278249411 -0.065798324 AVEHMFETEDGSKDEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVEHMFETEDGSKDEWR 17 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 0 183.58 4.11E-10 40390000 73688 57459 61967 73243 53998 64383 75610 73578 51128 FALSE TRUE 70204.91428 63314.13743 64808.24824 65880.47449 63415.2341 62153.40057 64074.30583 67135.12026 59056.66911 1.188771994 1.072091237 1.097390849 1.115546736 1.073803095 1.052436609 1.084963084 1.136791513 1 15.84981237 8 0.033075233 0.71799147 1.662203133 0.477042028 0.03636351 1005.757022 2.546371395 22.11027821 58.73028654 100000000 -8 0.944211663 AVEQHNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AVEQHNGK 8 0 Q9BRA2;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;;; 101.64 0.0052489 631748000 1272937 1167270 1137652 1413566 983130 1131148 1380714 1713248 1355470 FALSE TRUE 1212767.791 1286216.14 1189814.469 1271471.66 1154587.561 1091976.061 1170060.721 1563226.923 1565669.365 0.774600192 0.82151198 0.759939804 0.812094615 0.73744022 0.697449976 0.747322996 0.998440001 1 20.57834815 1.235505029 24.99999999 0.99922016 0.766920296 0.884420692 0.035291104 28.07127781 229651.7315 0.032491217 0.009467651 17.19907256 -1.235505029 -0.232299864 AVEVQGPSLESGDHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEVQGPSLESGDHGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 243.83 5.08E-20 446240000 695320 532600 601560 680970 586670 605260 791380 734770 606340 FALSE TRUE 662453.6016 586872.5455 629142.121 612517.6018 688985.0623 584299.6944 670640.4463 670429.6435 700368.1104 0.945864884 0.837948697 0.898302067 0.874565236 0.98374705 0.834275127 0.957554229 0.957253241 1 19.41775387 1.578373736 7.326172037 0.971285065 0.895415488 0.382242351 0.045782688 0.124461439 13.57578361 0.022662867 0.010672854 37.8768397 -1.578373736 -0.075869576 AVEYLLMGIPGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEYLLMGIPGDR 13 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 158.41 0.00010165 144967000 317190 320180 255910 326400 303740 268310 302220 282630 263510 FALSE TRUE 302197.0573 352806.706 267643.7266 293589.6519 356712.1598 259018.3574 256110.7883 257881.4189 304373.785 0.992848505 1.159123168 0.879325815 0.964569442 1.171954279 0.850987734 0.841435107 0.847252397 1 18.21548458 2.208427124 24.99980224 0.867721836 1.036837556 0.362801995 0.096646861 193.2035166 160287.3358 0.034670161 0.025608671 161.5947041 -2.208427124 0.16911572 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAAGENPLEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEY(0.01)LLT(0.01)GIPGS(0.294)PEPEHGS(0.294)VQES(0.294)QVS(0.097)EQPATEAAGENPLEFLR;AVEYLLTGIPGS(0.999)PEPEHGS(0.001)VQESQVSEQPATEAAGENPLEFLR;AVEYLLT(0.005)GIPGS(0.414)PEPEHGS(0.414)VQES(0.121)QVS(0.044)EQPAT(0.003)EAAGENPLEFLR;AVEY(0.003)LLT(0.015)GIPGS(0.933)PEPEHGS(0.029)VQES(0.017)QVS(0.003)EQPATEAAGENPLEFLR 229.4 1.24E-44 163278000 49591.4 34007.8 46461.8 51369.6 68059 44851.7 60160.1 58093 74006.7 TRUE FALSE 47247.3128 37473.23348 48592.11949 46205.83021 79928.46805 43298.47438 50981.57183 53006.06895 85483.28106 0.552708228 0.438369153 0.568440037 0.540524763 0.93501872 0.50651395 0.596392314 0.620075274 1 16.38335466 -5 0.162893004 2.561865831 0.472426391 0.509911803 0.127822756 106.8233825 0.989810436 54.0016863 0.500100789 1.00E-05 5 -2.089439439 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAGENPLEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.971)PEPEHGS(0.028)VQES(0.001)QVSEQPATEAGENPLEFLR;AVEYLLT(0.002)GIPGS(0.818)PEPEHGS(0.126)VQES(0.053)QVS(0.001)EQPATEAGENPLEFLR;AVEYLLTGIPGS(0.852)PEPEHGS(0.144)VQES(0.003)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.872)PEPEHGS(0.057)VQES(0.071)QVSEQPATEAGENPLEFLR;AVEYLLT(0.007)GIPGS(0.44)PEPEHGS(0.44)VQES(0.106)QVS(0.007)EQPATEAGENPLEFLR;AVEYLLT(0.001)GIPGS(0.335)PEPEHGS(0.335)VQES(0.322)QVS(0.007)EQPATEAGENPLEFLR 208.18 1.69E-35 251707600 44229.2 37227.6 42504.2 45617.5 58628 34205.9 52181.9 44246 53215.1 TRUE FALSE 42138.57337 41021.13476 44453.05961 41031.94223 68852.70464 33021.34111 44220.59277 40371.58568 61467.42592 0.685543159 0.667363797 0.723197026 0.667539621 1.120149471 0.537216918 0.719415074 0.656796426 1 15.90753445 -1.684860141 2.777189141 1.037634597 0.71722476 0.250806234 0.150702669 46420919.41 41035405.33 12307573.26 0.033121636 0.020660454 1.684860141 -0.320409838 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAAGENPLEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.402)PEPEHGS(0.596)VQESQVSEQPATEAAGENPLEFLR;AVEYLLTGIPGS(0.062)PEPEHGS(0.934)VQES(0.004)QVSEQPATEAAGENPLEFLR 160.23 1.52E-19 90343000 28970 19267.1 26340 29171 34654 24534 35086 34072 37546 TRUE FALSE 27600.64551 21230.43939 27547.71505 26238.67566 40697.64663 23684.38143 29732.9863 31088.47505 43368.44192 0.636422345 0.489536595 0.635201862 0.605017716 0.938416158 0.546120183 0.685590374 0.71684556 1 15.40435799 -4.999999998 0.135807357 2.233250041 0.503329946 0.503647897 0.113193834 110.6052954 0.931876122 36.86397875 0.716928739 1.00E-05 4.999999998 -1.729920095 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAGENPLEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.118)PEPEHGS(0.881)VQES(0.001)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.458)PEPEHGS(0.525)VQES(0.017)QVSEQPATEAGENPLEFLR 158.6 2.30E-19 24422900 12473.9 9838.4 12063.4 13047.1 14870 9141 17184.7 11888.9 14413 TRUE FALSE 11884.28347 10840.94415 12616.51882 11735.58072 17463.32329 8824.444878 14562.8584 10847.84489 16648.09443 0.713852478 0.651182283 0.757835612 0.70492036 1.048968299 0.530057354 0.874746264 0.65159679 1 14.02306943 -5 0.192320222 2.098960854 0.69496434 0.235629765 0.141256508 185.1852136 1.816491436 78.39071118 0.328236268 1.00E-05 5 -1.403996513 AVFHEEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVFHEEEQR 9 0 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 113.62 0.0022233 0 78149 60949 87218 85379 99152 76043 104390 88492 90056 FALSE TRUE 74455.05165 67159.77239 91217.03157 76796.54071 116444.0774 73409.61184 88463.38825 80743.17135 104021.4245 0.715766507 0.645634038 0.876906195 0.738276187 1.119423983 0.705716271 0.850434309 0.776216743 1 16.66652117 3.735823501 24.86303823 0.855510827 0.680700268 0.280298594 0.122900148 249.6049956 2267333.477 0.029165918 0.047534423 5442.814101 -3.735823501 -0.174810559 AVFPS(ph)IVGRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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" 1 AVFPS(1)IVGRPR;AVFPS(1)IVGRPR;AVFPS(1)IVGRPR;AVFPS(1)IVGRPR 110.15 0.0011101 836030000 1074070 708990 682120 929110 1101370 775510 1092750 838980 1005640 TRUE FALSE 1023300.84 781236.8871 713395.8767 835714.0976 1293448.579 748653.8942 926030.9178 765514.4635 1161589.515 0.880948757 0.672558487 0.614154886 0.719457336 1.113516059 0.644508137 0.797210121 0.659023221 1 20.14766891 4.740649381 5.4360693 0.766431286 0.885268819 0.034725755 0.162131684 0.507831118 50.63081285 0.035705818 0.22251825 55036.31926 -4.740649381 0.118837533 AVFPSIVGR ddPTM_SK-BR-3_Trastuzumab_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 ; 180.18 0.00011387 475560000 494380 559850 359810 497920 482490 387790 462030 462590 417200 FALSE TRUE 471011.6372 616899.3515 376307.6444 447868.1356 566636.1032 374360.7351 391538.8377 422083.1673 481897.2452 0.977410935 1.28014708 0.780887727 0.929385134 1.175844247 0.776847635 0.812494451 0.875877942 1 18.87836603 3.733403469 24.99646814 0.898298015 1.128779008 0.307417787 0.137665665 439.3713225 2129614.491 0.035955869 0.057563661 5412.569294 -3.733403469 0.230480993 AVFPSIVGRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 227.94 3.31E-12 70995619200 5280731 4309854 3668071 4109472 6181511 3885008 6391783 4853533 6815637 FALSE TRUE 5031121.311 4749033.022 3836255.684 3696380.067 7259564.561 3750469.199 5416599.11 4428531.92 7872571.177 0.639069651 0.603237864 0.487293871 0.469526408 0.922133874 0.476396988 0.688034314 0.562526755 1 22.90840347 -4.99999954 0.37150805 6.203922338 0.599240439 0.462472301 0.133217663 468.8966562 3.600985942 1959.931402 0.083192295 1.00E-05 4.99999954 -5.604681899 AVFVDLEPTVIDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 301.48 5.68E-44 1876665000 1493348 1294790 1332069 1532514 1579472 1269326 1631538 1465770 1655838 FALSE TRUE 1422760.4 1426730.573 1393145.681 1378462.781 1854931.417 1225368.922 1382616.913 1337419.408 1912616.9 0.743881537 0.745957318 0.728397663 0.720720799 0.969839499 0.640676615 0.722892762 0.699261524 1 20.8671165 -1.172734312 3.786505622 1.000171156 0.745214527 0.468244976 0.084904895 4433045.242 2749531.297 6275.036898 0.018366317 0.067183974 1.172734312 -0.254956629 AVGESVQKPLDYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVGESVQKPLDYYR 14 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 91.812 0.0047489 162110000 454480 421950 415320 489700 345300 501610 545970 537050 421660 FALSE TRUE 432997.6311 464947.1847 434362.8328 440474.4256 405520.2107 484239.1199 462672.2491 490023.0549 487048.8793 0.889022949 0.954621198 0.891825957 0.904374169 0.832606804 0.994231053 0.949950341 1.006106524 1 18.89370704 2.207068454 24.99998921 0.980203983 0.902520995 0.649989668 0.033461956 145.1611839 115235.0666 0.012372047 0.009138216 161.0899526 -2.207068454 -0.077682989 AVGHPFVIQLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVGHPFVIQLGR 12 0 O14980 O14980 XPO1 Exportin-1 0 ; 117.02 0.00077851 999430000 1779480 1692690 1529100 1853890 2099370 1768210 2155500 1941250 1946270 FALSE TRUE 1695367.507 1865177.035 1599210.747 1667533.455 2465499.463 1706976.444 1826638.887 1771263.859 2248087.611 0.754137649 0.829672752 0.711364957 0.741756436 1.096709688 0.759301566 0.812530115 0.787898056 1 21.10026683 -5 0.185367381 1.76725718 0.774698178 0.24019772 0.106624674 203.6190285 1.977953333 57.98485984 0.292554658 1.00E-05 5 -0.992559002 AVGIWHCGSCMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVGIWHCGSCMK 12 0 Q6P4E4;E9PEL3;P61513;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 164.04 5.84E-05 1844000000 3675700 2785500 2022880 2448700 3684000 2507400 4322000 3165700 3263300 FALSE TRUE 3501956.946 3069345.617 2115631.049 2202552.024 4326488.434 2420568.109 3662599.521 2888494.526 3769355.897 0.929059776 0.814289152 0.561271237 0.584331139 1.147805766 0.642170221 0.97167782 0.766309843 1 21.84588659 2.767607551 24.99442936 0.887574635 0.751617382 0.209975366 0.170617016 1480.027373 1273537.518 0.050909775 0.053989748 585.6087421 -2.767607551 -0.135957253 AVGMPSPVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPS(0.001)PVS(0.999)PK;AVGMPSPVS(1)PK 133.32 0.0011709 71326000 348390 310790 310370 364710 226703 373920 389190 402890 283960 TRUE FALSE 331922.2951 342459.8543 324600.7715 328048.6579 266239.9314 360971.0566 329811.9175 367610.8157 327995.0665 1.011973438 1.044100626 0.989651384 1.000163391 0.811719317 1.100538067 1.005539263 1.12078154 1 18.32331459 AVGNIVTGTDEQTQVVLNCDVLSHFPNLLSHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVGNIVTGTDEQTQVVLNCDVLSHFPNLLSHPK 33 0 O00505 O00505 KPNA3 Importin subunit alpha-4 0 154.51 5.62E-11 34606000 90286 66611 86712 87574 57129 89977 97987 94784 31100 FALSE TRUE 86018.35971 73398.73663 90687.83097 78770.89514 67092.27951 86861.07393 83037.2835 86484.21048 35922.82916 2.394531882 2.043233741 2.524518059 2.192780941 1.86767805 2.417990897 2.311546318 2.40749998 1 15.13261336 3.004688108 24.82975417 2.12402283 2.282682171 0.065486778 0.429393895 515.2749133 2729027.252 0.11157836 0.132889334 1010.853242 -3.004688108 0.158659341 AVGS(ph)PLCVPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVGSPLCVPAR 11 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 AVGS(1)PLCVPAR;AVGS(1)PLCVPAR 119.74 0.00057185 167257000 143158 154864 137051 150264 188753 144682 193117 145942 198271 TRUE FALSE 136391.2051 170644.8177 143334.9239 135159.1772 221671.4634 139671.6261 163653.4548 133162.5448 229017.8541 0.59554835 0.745115783 0.625867902 0.590168735 0.967922193 0.609872216 0.714588194 0.581450496 1 17.80510055 -1.7386472 2.89741663 1.055317165 0.683424536 0.430141418 0.116072863 25881733.72 24763400.52 10375396.08 0.024909377 0.018253779 1.7386472 -0.371892629 AVHS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVHSPIR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 AVHS(1)PIR;AVHS(1)PIR 111.46 0.0084891 0 454570 501550 408750 490390 2035540 359080 524360 480870 1098420 TRUE FALSE 433083.377 552658.5152 427491.5918 441095.0655 2390537.532 346644.9696 444359.2515 438762.4735 1268757.364 0.341344523 0.43559039 0.33693723 0.347659118 1.884156577 0.273216124 0.35023186 0.345820632 1 20.27498476 AVIFCLSADKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVIFCLSADKK 11 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 174.1 1.83E-05 3961100000 2335390 1940500 1786820 2426440 2125780 2699550 3807200 2973970 2406850 FALSE TRUE 2225000.743 2138239.156 1868747.464 2182529.641 2496515.359 2606063.907 3226341.716 2713553.421 2780092.006 0.800333492 0.769125321 0.672189072 0.785056623 0.897997388 0.937402036 1.160516166 0.976066049 1 21.4067012 2.351733598 1.766764562 1.058221538 0.758573914 0.791258594 0.063907023 0.140659915 0.892654463 0.029511258 0.020754986 224.7675428 -2.351733598 -0.299647624 AVIFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AVIFDR 6 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;; 106.84 0.073935 676720000 849910 652320 544340 697720 1165710 485010 730680 621220 902520 FALSE TRUE 809736.4387 718792.1496 569298.5274 627583.86 1369009.455 468213.9821 619201.3461 566822.6835 1042478.192 0.776741849 0.689503296 0.546101138 0.6020115 1.313225989 0.449135517 0.593970551 0.543726178 1 19.99158577 4.525901891 3.161488704 0.694760928 0.774754304 0 0.258145962 2.02717029 38.47335803 0.060383876 0.309371554 33566.17783 -4.525901891 0.079993376 AVIVPGNGGGDVTTHGWYGWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVIVPGNGGGDVTTHGWYGWVK 22 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 231.76 9.24E-27 184610000 424260 368910 382270 488540 380570 407630 485850 492520 372200 FALSE TRUE 404206.0706 406502.3484 399797.4576 439431.031 446941.2875 393513.6709 411724.6593 449392.3378 429918.8751 0.940191497 0.945532685 0.929936974 1.022125467 1.039594476 0.915320759 0.957679886 1.045295668 1 18.71370493 3.256880623 24.98360621 0.988492009 0.940283169 0.319076602 0.038786873 345.0737707 470585.5931 0.011037873 0.014918283 1806.677447 -3.256880623 -0.04820884 AVIVSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVIVSSPK 8 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 AVIVS(0.105)S(0.895)PK;AVIVS(0.243)S(0.757)PK;AVIVS(0.193)S(0.807)PK;AVIVS(0.026)S(0.974)PK 160.53 0.00037008 1948440000 4450830 4337630 4169670 4859500 2837620 4974900 5195900 5382700 3495940 TRUE FALSE 4240448.087 4779639.428 4360853.494 4371013.828 3332500.03 4802617.966 4403170.026 4911362.253 4038072.52 1.050116873 1.183643782 1.079934417 1.082450552 0.82526998 1.189334253 1.090413806 1.216264004 1 21.94523539 -0.380394289 7.244832174 1 1.091698349 0.062664064 0.108751496 0 0 0.098347317 0.023180685 0.416491087 0.380394289 0.091698349 AVKEERS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVKEERSPK 9 2 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 AVKEERS(1)PK 54.7 0.069568 75788000 178860 138210 186180 198580 129290 221400 236280 226360 159680 TRUE FALSE 170405.6423 152293.7561 194716.5372 178618.3611 151838.1351 213732.8625 200231.1464 206538.7184 184442.3589 0.923896459 0.825698376 1.055704006 0.968423752 0.823228113 1.158805731 1.085602828 1.119800894 1 17.4928105 2.232359599 24.99999979 1.099002747 0.915448539 0.550969307 0.076810848 104.4681753 421169.3809 0.027520351 0.020833805 170.7495623 -2.232359599 -0.183554208 AVLDYHDDNFAIVFAAMGVNMETAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVLDYHDDNFAIVFAAMGVNMETAR 25 0 P15313;C9JL73 P15313 ATP6V1B1 "V-type proton ATPase subunit B, kidney isoform" 0 ; 145.89 2.71E-07 15636500 18258.9 26431 22160 25365 20347.5 21837 25301 24545 17474.6 FALSE TRUE 17395.83798 29124.34895 23176.05792 22815.26201 23896.09756 21080.77921 21440.86777 22395.70968 20184.47172 0.86184262 1.442908655 1.148212261 1.130337337 1.183885211 1.044405794 1.062245674 1.109551441 1 14.30095821 2.237197042 24.90139736 1.059030403 1.165114508 0.106689025 0.140337725 77.42490657 1413879.294 0.04983702 0.038838132 172.6621093 -2.237197042 0.106084104 AVLFCLS(ph)EDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 AVLFCLS(1)EDKK 65.495 0.03999 292610000 222120 180320 198830 209100 113970 227130 243810 216980 154410 TRUE FALSE 211620.8278 198694.813 207946.5522 188080.8707 133846.3319 219264.4311 206612.3066 197980.0809 178355.1142 1.186513932 1.114040458 1.165913033 1.054530293 0.750448522 1.229370025 1.158432196 1.110033103 1 17.44439306 3.236241517 24.92376811 1.063592104 1.1510394 0.127348387 0.126344897 149.4573577 1606254.741 0.036851864 0.046072301 1722.826395 -3.236241517 0.087447295 AVLFCLSEDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 184.88 7.56E-06 9488000000 10913400 9538900 9837900 11567900 6464200 12469000 13219800 12951100 6992100 FALSE TRUE 10397545.21 10510924.75 10288977.45 10405072.71 7591554.433 12037195.4 11202876.71 11817033.03 8076399.157 1.28739863 1.301437008 1.273956035 1.288330667 0.939967712 1.490416109 1.387112808 1.463156141 1 22.94528078 AVLPVTCHRDS(ph)FSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVLPVTCHRDSFSR 14 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 AVLPVTCHRDS(0.942)FS(0.058)R 148.44 4.69E-06 150950000 156350 120140 134080 160620 164950 139770 168760 147990 172110 TRUE FALSE 148959.6454 132382.4026 140227.7006 144474.1724 193717.2278 134929.7299 143012.5625 135031.2111 198799.9398 0.749294218 0.665907659 0.705370941 0.72673147 0.97443303 0.678721181 0.719379305 0.67923165 1 17.60095779 -1.50198341 3.214798366 1.006666294 0.733794035 0.467067996 0.088085534 23061927.59 32068829.13 1380550.215 0.020477788 0.031478686 1.50198341 -0.272872259 AVLPVTCHRDSFS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVLPVTCHRDSFSR 14 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 AVLPVTCHRDS(0.362)FS(0.637)R 78.597 0.012981 286600000 102800 85902 98482 100580 112350 107890 125560 105560 128010 TRUE FALSE 97940.84773 94655.51146 102997.4971 90469.50731 131943.8044 104153.7422 106403.5159 96316.60679 147861.137 0.662383975 0.64016491 0.696582613 0.611854536 0.892349451 0.704402417 0.719617866 0.651399068 1 17.17388339 -5 0.21853036 2.516134417 0.655543121 0.600239352 0.077122464 100.7849513 1.007523499 67.34796672 0.140471244 1.00E-05 5 -1.860591297 AVLSAEQLRDEEVHAGLGELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVLSAEQLRDEEVHAGLGELLR 22 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 116.94 8.85E-05 25966000 24885 16729 21219 21023 30536 21795 26940 25698 27349 FALSE TRUE 23708.73537 18433.70412 22191.91214 18909.7281 35861.46873 21040.23369 22829.80821 23447.74689 31590.14324 0.750510537 0.583527082 0.702494825 0.598595833 1.135210704 0.666037932 0.722687708 0.742248831 1 14.94718686 AVLVDLEPGTMDSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVLVDLEPGTMDSVR 15 0 P68371;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;A0A075B724;Q3ZCM7;P04350;M0R278 P68371;Q3ZCM7;P04350 TUBB4B;TUBB4A;TUBB8 Tubulin beta-4B chain;Tubulin beta-8 chain;Tubulin beta-4A chain 0 ;;; 199.12 1.76E-08 186522000 382513 312607 313641 362709 384109 340239 386793 395838 419547 FALSE TRUE 364432.3686 344462.0087 328021.7501 326248.8022 451097.488 328456.4381 327780.6239 361176.3263 484608.206 0.75201444 0.71080515 0.676880305 0.673221787 0.930849875 0.677777293 0.676382735 0.745295523 1 18.88645931 0.949153619 21.77499849 1.000000001 0.725414981 0.550666678 0.076650527 2240.769543 959613.2825 0.070116911 0.017529228 8.895157017 -0.949153619 -0.27458502 AVNENHKDYMFLECILFITEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVNENHKDYMFLECILFITEMK 22 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ; 169.84 4.71E-12 497070000 1319880 1502990 1330170 1578300 857900 1664370 1723990 1448030 608540 FALSE TRUE 1257491.888 1656146.39 1391159.61 1419646.285 1007517.488 1606732.45 1460963.662 1321232.817 702909.2752 1.788981783 2.35613108 1.979145331 2.019672148 1.433353526 2.285831908 2.078452673 1.87966337 1 19.42297897 2.976883057 24.75885725 1.855490495 2.063621908 0.088492387 0.382052775 1981.047446 2121755.246 0.108012831 0.115286558 948.1631156 -2.976883057 0.208131412 AVNPTPSSWS(ph)LDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVNPTPSSWSLDSGK 15 0 C9J637;A0A590UJ51;H0Y599;Q8N1I0-4;Q8N1I0;Q8N1I0-3 C9J637 DOCK4 Dedicator of cytokinesis protein 4 1 AVNPTPS(0.044)S(0.028)WS(0.924)LDS(0.003)GK 115.26 0.001379 0 22062 18369 23564 30573 21123 28174 26776 24141 24495 TRUE FALSE 21019.17298 20240.82198 24644.43271 27499.74396 24806.84451 27198.32732 22690.82943 22027.08606 28293.5595 0.742896029 0.715386199 0.871026239 0.971943596 0.876766478 0.961290407 0.801978607 0.778519439 1 14.78818607 3.704131726 5.861643375 0.888359525 0.728868602 0.4850018 0.07071133 0.146203733 15.19292203 0.018348524 0.029397623 5059.78107 -3.704131726 -0.159490923 AVPEHAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AVPEHAAR 8 0 X6RA56;X6RLR1;O75935-2;O75935 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 103.83 0.0046967 66348000 175417 197076 170554 194182 234107 176639 220472 212173 208604 FALSE TRUE 167125.3861 217158.2685 178374.0696 174662.4564 274935.1867 170521.9471 186834.9472 193594.0073 240953.2429 0.6936009 0.901246507 0.740284992 0.724881119 1.141031278 0.707697249 0.775399181 0.803450516 1 17.87839369 -2.524653756 2.031535328 3.211706429 0.80999882 0.169822874 0.131346775 3729027.364 217594.6365 38063888.26 0.030778903 0.002987764 2.524653756 -2.401707609 AVPIAVADEGES(ph)ESEDDDLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVPIAVADEGESESEDDDLKPR 22 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 AVPIAVADEGES(0.999)ES(0.001)EDDDLKPR;AVPIAVADEGES(0.999)ES(0.001)EDDDLKPR 211.49 1.96E-23 186474000 169929 136802 159507 181899 115259 171326 202481 189475 146596 TRUE FALSE 161896.7929 150742.2793 166820.5537 163614.1669 135360.1331 165392.9377 171588.8046 172883.5645 169329.359 0.956105863 0.890231205 0.985183873 0.966248074 0.799389627 0.976752872 1.013343496 1.020989896 1 17.36947261 2.009835352 24.99169341 1.008457375 0.920914821 0.410711266 0.050975317 198.2616767 503781.9991 0.018283826 0.013486376 102.2905118 -2.009835352 -0.087542553 AVPKEDIYSGGGGGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVPKEDIYSGGGGGGSR 17 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 128.26 3.42E-05 654200000 306063 249825 313028 332148 315845 308775 403363 353090 381903 FALSE TRUE 291596.0085 275282.4515 327380.6434 298759.852 370928.268 298082.0443 341822.5661 322171.5678 441126.5667 0.661025725 0.624044146 0.74214674 0.677265607 0.840865856 0.675729069 0.774885468 0.730338166 1 18.75083312 -5 0.130930089 1.98387411 0.587457053 0.7382081 0.055619181 65.44406501 0.539141159 16.85178631 0.375046048 1.00E-05 5 -1.396417057 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(0.993)PGS(0.006)S(0.002)NDSSAR;AVPMAPAPAS(0.919)PGS(0.036)S(0.044)NDS(0.001)S(0.001)AR 287.75 1.62E-45 999691000 1372900 1131280 1196940 1469770 1155530 1367450 1440730 1314400 1188910 TRUE FALSE 1308005.738 1246558.718 1251820.883 1322025.927 1357054.066 1320094.864 1220920.178 1199304.168 1373280.091 0.952468289 0.907723578 0.9115554 0.96267756 0.988184476 0.961271391 0.889054015 0.873313591 1 20.38919447 -0.494986696 5.883060156 1 0.93038366 0.267500665 0.035991863 0 4.55E-11 0.035935305 0.008470033 0.31989931 0.494986696 -0.06961634 AVPPVS(ph)PELR ddPTM_SK-BR-3_Trastuzumab_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 121.36 0.0005424 844160000 795013 742253 695110 856580 867150 755230 876790 779570 919160 TRUE FALSE 757434.3111 817889.4246 726981.4811 770474.951 1018380.685 729076.1957 743019.5821 711306.718 1061698.638 0.713417427 0.770359304 0.684734307 0.725700235 0.959199389 0.686707291 0.699840383 0.669970453 1 20.01794289 -2.038076661 2.812674001 1.333535603 0.739360971 0.493437286 0.083188483 20486494.87 7394196.334 44275687 0.019545321 0.009160588 2.038076661 -0.594174632 AVPREELFVTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVPREELFVTSK 12 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 208.27 6.27E-08 342180000 515290 271430 488780 398920 507630 433160 659140 507460 644990 FALSE TRUE 490933.2629 299089.0256 511191.0465 358819.8037 596160.5113 418159.5606 558576.0871 463024.1122 745011.755 0.658960425 0.401455445 0.686151652 0.481629721 0.800202825 0.561279145 0.74975473 0.621499069 1 19.50690366 -2.90237031 0.167049127 1.721892686 0.484780498 0.537200592 0.114249371 38.97655571 0.698635793 10.42423343 0.421151815 0.001252073 2.90237031 -1.237112188 AVPSWFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVPSWFVR 8 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 147.69 0.0012404 242710000 171110 125610 107070 121940 255140 108420 190740 139090 244070 FALSE TRUE 163021.9694 138409.8018 111979.2654 109682.3595 299636.3352 104665.3882 161639.1098 126910.5422 281919.1291 0.578257921 0.490955695 0.397203502 0.389056109 1.062844995 0.371260328 0.573352757 0.450166481 1 18.10492185 -2.196719925 2.266099515 2.286594791 0.539112587 0.345237611 0.199460498 7840739.815 1660321.055 51679229.06 0.047861571 0.006357408 2.196719925 -1.747482203 AVPVWDVLASGYVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVPVWDVLASGYVSR 15 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 180.2 1.49E-06 341190000 54814 52672 49972 62553 60413 49193 78052 56278 67631 FALSE TRUE 52223.05085 58039.33668 52263.26563 56265.0536 70949.00807 47489.43408 66143.73388 51349.99997 78118.87007 0.668507504 0.742961805 0.669022294 0.720249199 0.908218565 0.607912455 0.846706229 0.657331576 1 16.25338346 -5 0.23173532 2.446620076 0.701801661 0.462132816 0.091220379 135.2197385 1.351905017 91.92152025 0.135427793 1.00E-05 5 -1.744818415 AVQALCAVYEHWVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVQALCAVYEHWVPR 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 171.91 1.06E-06 312640000 365710 287260 370470 352740 424830 326480 438600 360640 392720 FALSE TRUE 348423.6131 316532.1206 387456.4159 317281.905 498920.2175 315173.9157 371683.5146 329060.4497 453621.0119 0.768094078 0.697789812 0.854141245 0.699442699 1.099861348 0.694795672 0.819370146 0.725408306 1 18.79112794 -5 0.235314956 2.125738038 0.768316334 0.205493858 0.122008474 251.8537437 2.51560075 136.0679514 0.182512377 1.00E-05 5 -1.357421704 AVQGMLDFDYVCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVQGMLDFDYVCSR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 229.97 2.53E-12 104049000 120394 108696 110012 129388 134759 118272 135404 125340 132392 FALSE TRUE 114703.2142 119772.246 115056.159 116381.6724 158260.9269 114176.211 114745.6329 114364.5651 152922.6752 0.750073291 0.78322097 0.752381286 0.761049153 1.034908177 0.746627084 0.750350677 0.747858779 1 17.22244282 -2.517064809 2.22170165 3.984222077 0.788149267 0.35966219 0.087657126 2922800.374 289636.3712 44038999.99 0.021308759 0.003040431 2.517064809 -3.19607281 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR 367.94 1.51E-126 2963360000 499775 484374 503239 582588 534079 536669 604847 533976 288504 TRUE FALSE 476151.6262 533732.2613 526313.0059 524025.1474 627222.2085 518084.018 512566.4814 487218.2307 333243.7268 1.428838978 1.601627332 1.579363581 1.57249816 1.88217259 1.554669979 1.538112919 1.462047719 1 18.34621819 -0.645830661 13.1489502 0.999999477 1.575885361 0.693526875 0.120626413 0 0 0.114583062 0.027007487 0.226031693 0.645830661 0.575885884 AVQTLAGSQPTSDKPSQRPS(ph)ESTNCSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.01)QRPS(0.355)ES(0.26)T(0.26)NCS(0.105)PT(0.012)R 171.95 1.05E-12 172520000 182880 164310 168180 197880 149020 170190 199450 174410 176170 TRUE FALSE 174235.6248 181053.3758 175891.2194 177988.7265 175009.0408 164296.2776 169020.2393 159137.7358 203489.5438 0.856238712 0.889742895 0.864374729 0.874682419 0.860039477 0.807394201 0.830608965 0.782043798 1 17.63459514 2.465937216 24.42533428 0.837987122 0.871795953 0 0.058685337 439.5223859 959883.6114 0.017652138 0.014781577 292.3729674 -2.465937216 0.033808831 AVQTLAGSQPTSDKPSQRPSESTNCS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPSQRPS(0.006)ES(0.004)T(0.004)NCS(0.981)PT(0.005)R 208.34 7.60E-26 162790000 61837 60397 58944 69523 51792 59540 74325 64273 62773 TRUE FALSE 58914.08756 66551.52297 61646.6407 62534.41595 60824.5084 57478.11487 62985.35618 58644.91539 72507.51624 0.812523868 0.917856885 0.850210349 0.862454256 0.838871769 0.792719401 0.868673476 0.808811533 1 16.14584293 -1.777476428 6.468769481 1.005506261 0.848535616 0.651311883 0.035732328 0.002802213 9.64E-05 0.034166996 0.007822809 0.016692584 1.777476428 -0.156970646 AVQTRPVLQPQPGS(ph)LNSSIWDGSEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVQTRPVLQPQPGSLNSSIWDGSEVLR 27 1 Q86TB9-4;Q86TB9 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVQTRPVLQPQPGS(0.998)LNS(0.001)S(0.001)IWDGSEVLR 112.15 0.00072104 60649000 20650 16449 21123 23430 24916 22013 26220 22629 27283 TRUE FALSE 19673.91542 18125.1718 22091.51044 21074.77189 29261.34251 21250.68429 22219.65744 20647.4848 31513.9083 0.624293097 0.575148332 0.701008273 0.668745104 0.928521535 0.67432716 0.705074636 0.655186421 1 14.94370107 -5 0.126541804 1.99124247 0.549085169 0.528349609 0.091916494 116.4648785 0.93878118 29.75068687 0.74778967 1.00E-05 5 -1.442157301 AVRPEVNTVASSDEVCDGDREKEEPPS(ph)PIEATPPQSLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVRPEVNTVASSDEVCDGDREKEEPPSPIEATPPQSLLEK 40 3 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 AVRPEVNTVASSDEVCDGDREKEEPPS(1)PIEATPPQSLLEK 189.19 1.78E-24 100800000 56942 46966 53694 55464 32628 59092 67889 65193 41913 TRUE FALSE 54250.46451 51751.8888 56155.92301 49888.65335 38318.31287 57045.62922 57531.28618 59484.35531 48412.65398 1.120584394 1.068974422 1.159943081 1.030487884 0.791493746 1.178320636 1.188352248 1.228694369 1 15.56309656 AVS(ph)EEQQPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;AVS(1)EEQQPALK 190.03 3.19E-05 377120000 882860 543920 658750 1325090 739310 1258270 1226730 731620 694170 TRUE FALSE 841128.9575 599346.0664 688954.3391 1191889.436 868245.4299 1214695.794 1039569.808 667555.4742 801818.3383 1.04902684 0.74748361 0.859239938 1.486483133 1.082845563 1.514926432 1.296515381 0.832552016 1 19.61291589 3.264722998 24.99653601 1.238022342 0.879125183 0.308181281 0.219484836 219.0827046 209318.4705 0.056611111 0.076627722 1839.598293 -3.264722998 -0.358897159 AVS(ph)LDSPVSVGSSPPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.5)LDS(0.5)PVS(0.001)VGSSPPVK;AVS(0.969)LDS(0.031)PVSVGSSPPVK 337.68 2.91E-72 395686000 857210 627872 650640 894950 886950 833620 980370 781780 963760 TRUE FALSE 816691.3821 691852.8706 680472.4876 804987.9257 1041633.799 804751.5304 830796.5508 713323.1987 1113214.979 0.733633124 0.621490803 0.611267815 0.723119919 0.935698692 0.722907566 0.746303784 0.640777579 1 20.0863008 2.999619095 24.98911558 0.787300113 0.660331329 0.290598008 0.107418341 19.06929573 1251186.148 0.029074455 0.034396693 999.1233175 -2.999619095 -0.126968784 AVS(ph)PAPQSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AVSPAPQSSSR 11 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR 164.53 2.38E-05 8272750000 6433314 5444025 5463970 6128378 6656921 5521362 6514805 5717696 6852333 TRUE FALSE 6129223.997 5998777.337 5714498.429 5512341.8 7817885.915 5330155.849 5520851.845 5217024.227 7914957.805 0.774384924 0.757903893 0.721987226 0.696446139 0.98773564 0.673428208 0.697521324 0.659134812 1 22.91615023 4.497324599 3.241567918 0.758158211 0.773709547 0 0.123366501 4.435628996 91.43815312 0.027936002 0.128785835 31428.56844 -4.497324599 0.015551336 AVS(ph)PAVPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR 186.27 1.42E-06 642903000 1230160 998261 1062290 1147210 1257920 1043285 1299720 1137060 1353510 TRUE FALSE 1172012.775 1099984.931 1110997.047 1031890.271 1477300.85 1007155.779 1101423.843 1037492.998 1563405.418 0.749653776 0.703582652 0.710626325 0.660027309 0.94492499 0.644206402 0.704503023 0.663610978 1 20.57626051 -1.149276952 4.835545844 1.000021386 0.722127991 0.514454319 0.084679486 1.77E-05 3.12E-06 0.0743676 0.017527264 0.070912541 1.149276952 -0.277893396 AVS(ph)PPHLDGPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 132.14 2.86E-05 130440000 577710 676410 562920 660120 504720 667790 582030 669660 457100 TRUE FALSE 550402.7932 745336.948 588730.4388 593763.4835 592743.0082 644664.2649 493230.6338 611021.0203 527984.7335 1.042459674 1.411663824 1.115052011 1.124584568 1.122651794 1.220990351 0.934175938 1.157270242 1 19.01013669 2.215079081 0.758652542 1.021402506 1.210988949 0.173091412 0.117937229 0.922036919 1.014018201 0.093448143 0.056675523 164.0888538 -2.215079081 0.189586443 AVS(ph)PSNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.786)PS(0.214)NPK;AVS(0.996)PS(0.004)NPK;AVS(0.987)PS(0.013)NPK;AVS(0.993)PS(0.007)NPK;AVS(0.986)PS(0.014)NPK;AVS(0.981)PS(0.019)NPK;AVS(0.994)PS(0.006)NPK 150.15 0.00051793 4589450000 9036270 8122204 8159839 9156681 6174477 9259572 9757526 9862025 7828567 TRUE FALSE 8609143.425 8949865.822 8533975.689 8236234.029 7251303.834 8938910.7 8268836.199 8998453.809 9042581.188 0.952067031 0.989746803 0.94375439 0.910827767 0.801906412 0.988535299 0.914433172 0.995120046 1 23.10830322 -0.288361766 6.522674474 1 0.93855338 0.109322774 0.05632377 7130423.465 1093174.782 0.052842499 0.012816189 0.51479964 0.288361766 -0.06144662 AVSDWIDEQEKGSSEQAES(ph)DNMDVPPEDDSKEGAGEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSDWIDEQEKGSSEQAESDNMDVPPEDDSKEGAGEQK 38 2 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 AVSDWIDEQEKGS(0.049)S(0.049)EQAES(0.902)DNMDVPPEDDSKEGAGEQK 115.37 3.29E-06 89414000 59191 43370 49760 59549 28223 62035 60705 61559 26892 TRUE FALSE 56393.15874 47789.45231 52041.54522 53563.02138 33145.08226 59886.7124 51443.33733 56168.56762 31062.27401 1.815487131 1.538504627 1.675393926 1.724375407 1.067052665 1.927956478 1.656135584 1.808256781 1 14.92287583 4.624837356 2.816885971 1.589780978 1.830529291 0.057198583 0.30112574 1.057751944 13.41007412 0.066251959 0.51569483 42153.86066 -4.624837356 0.240748313 AVSEDVSNGSSGS(ph)PSPGDTLPWNLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVSEDVSNGSSGS(0.765)PS(0.234)PGDTLPWNLGK 188.26 6.64E-18 54308000 78934 84921 95206 94931 84727 100810 119240 107810 99343 TRUE FALSE 75202.94625 93574.54645 99571.28927 85388.35552 99503.36197 97318.92442 101047.748 98369.58486 114748.6051 0.655371333 0.81547437 0.867734202 0.744134149 0.867142236 0.848105512 0.880601101 0.857261705 1 16.80811709 7.881596685 0.110475837 1.052777264 7.47E-15 0.735096698 0.04633223 51.76096951 0.409257248 0.398255178 8.290317909 76137162.01 -7.881596685 -1.052777264 AVSEDVSNGSSGSPS(ph)PGDTLPWNLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVS(0.001)EDVS(0.008)NGS(0.007)S(0.006)GS(0.434)PS(0.53)PGDT(0.015)LPWNLGK 87.102 0.0080175 48544000 125310 112860 119280 138910 112420 134360 153850 135890 131730 TRUE FALSE 119386.8446 124360.5623 124749.106 124946.5029 132026.0124 129707.0795 130377.3569 123990.7512 152158.0156 0.784624091 0.817311936 0.81986549 0.821162805 0.867690157 0.852449863 0.856855002 0.814881495 1 17.21521081 -5 0.162680821 1.640843783 0.78376104 0.860318386 0.021989661 44.415547 0.411313098 9.194684494 0.085642975 1.00E-05 5 -0.857082743 AVSEGCAS(ph)EDEVEGEA ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSEGCASEDEVEGEA 16 0 Q9BYX2-4;Q9BYX2-2;Q9BYX2;Q9BYX2-6;Q9BYX2-5 Q9BYX2-4 TBC1D2 TBC1 domain family member 2A 1 AVSEGCAS(1)EDEVEGEA 166.05 7.15E-09 125220000 167000 143800 147130 160510 163100 146980 163500 160880 188030 TRUE FALSE 159106.241 158453.3835 153876.056 144375.2299 191544.5884 141890.0457 138555.0721 146792.4943 217188.7321 0.732571342 0.729565397 0.708490052 0.664745489 0.881926915 0.653302979 0.637947792 0.675875276 1 17.72858973 -1.500343404 3.138665168 1.007831876 0.709363917 0.638915678 0.068378702 19164258.9 25067377.81 1313247.432 0.016692326 0.031597782 1.500343404 -0.298467959 AVSGKEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSGKEPR 8 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 86.011 0.014899 272670000 951240 689730 814020 837050 860380 885210 1119900 967310 1098800 FALSE TRUE 906276.7704 760014.2712 851343.6222 752908.1437 1010430 854554.9557 949038.6866 882607.2084 1269196.292 0.71405564 0.598815389 0.670773802 0.59321647 0.796117989 0.673304012 0.747747762 0.695406387 1 20.27548378 -3.013228598 0.233256394 1.622656354 0.63738308 0.752165065 0.057713409 25.55471508 0.584871374 7.869019589 0.091728813 0.000969999 3.013228598 -0.985273274 AVSPPHLDGPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 171.71 1.91E-06 600640000 536660 467610 458810 537800 557670 501240 562260 493400 556890 TRUE FALSE 511293.1454 515259.9906 479846.8923 483739.3222 654927.4714 483881.9331 476476.9104 450195.2803 643249.657 0.794859569 0.801026452 0.745973025 0.752024221 1.018154404 0.752245925 0.740734029 0.699876441 1 19.29501926 -2.335839291 2.242551975 2.195418268 0.788995454 0.371406294 0.08662349 8459393.112 792517.2863 51521194.82 0.02075505 0.004614883 2.335839291 -1.406422814 AVSRLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVSRLSR 7 1 O43665 O43665 RGS10 Regulator of G-protein signaling 10 1 AVSRLS(1)R;AVSRLS(1)R;AVSRLS(1)R;AVSRLS(1)R 90.696 0.028935 875680000 474351 363977 345997 512120 545380 431357 612890 364313 606330 TRUE FALSE 451929.3683 401066.6701 361861.3047 460640.7246 640494.0993 416418.9989 519382.374 332411.8224 700356.5597 0.645284694 0.572660689 0.516681538 0.657723153 0.914525738 0.594581422 0.741597072 0.474632268 1 19.41773008 3.001026251 24.9075829 0.724706156 0.586677284 0.201388097 0.149109792 56.82051493 1378984.792 0.038947581 0.046188682 1002.365825 -3.001026251 -0.138028872 AVSTCAHLFWSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVSTCAHLFWSGR 13 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 96.866 0.004041 753680000 278000 238320 249440 291000 319540 283830 358900 302000 371250 FALSE TRUE 264859.4909 262605.0789 260877.0707 261748.1271 375267.6748 274000.8959 304143.2133 275555.279 428821.5539 0.617645005 0.612387779 0.608358112 0.610389391 0.875113836 0.638962509 0.709253559 0.642587287 1 18.7100179 -5 0.181943365 2.39086486 0.592184522 0.648656874 0.078694383 80.6150852 0.77872432 40.57598618 0.224462571 1.00E-05 5 -1.798680338 AVSTVVVTTAPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVSTVVVTTAPSPK 14 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 AVSTVVVTTAPS(1)PK;AVSTVVVTTAPS(1)PK 204.52 1.42E-08 116418000 383290 325660 375520 399150 257580 428940 418630 430550 316370 TRUE FALSE 365172.6413 358845.1242 392737.9634 359026.6837 302501.8704 414085.7002 354760.3048 392848.7595 365431.0438 0.999292883 0.981977668 1.074725232 0.982474504 0.82779467 1.133143194 0.970799583 1.075028425 1 18.47923967 AVT(ph)PSSEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.507)PS(0.192)S(0.301)EAK;AVT(0.911)PS(0.035)S(0.054)EAK;AVT(0.874)PS(0.126)S(0.001)EAK 147.19 0.0010396 823570000 2381570 2158940 1975550 2545500 1637460 2321770 2433190 2516830 1755980 TRUE FALSE 2268997.906 2378938.441 2066130.922 2289621.504 1923032.506 2241366.523 2061962.177 2296443.023 2028288.41 1.118676168 1.172879768 1.018657362 1.128844149 0.948106046 1.105053163 1.01660206 1.132207339 1 20.95183138 3.740460585 24.99994968 1.050940209 1.145777971 0.305584813 0.060057066 167.4659233 2203518.02 0.013610297 0.023077232 5501.23991 -3.740460585 0.094837762 AVT(ph)PVPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AVTPVPTK 8 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.999)PVPT(0.001)K;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK 128.81 0.012492 6366100000 10519600 12352100 8715500 12844300 7106900 10685500 10376100 10991500 7541300 TRUE FALSE 10022359.36 13610793.03 9115114.296 11553166.56 8346341.11 10315458.46 8793035.375 10029025.99 8710766.288 1.150571491 1.562525337 1.046419338 1.326308866 0.958163821 1.184219403 1.009444529 1.151336824 1 23.05436821 3.19798564 1.425308532 1.071559447 1.336627182 0.273764963 0.153513819 0.417576906 1.772945093 0.049417078 0.070146444 1577.559107 -3.19798564 0.265067734 AVT(ph)PVPTKTEEVSNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.998)PVPT(0.002)KTEEVSNLK;AVT(1)PVPTKTEEVSNLK;AVT(0.997)PVPT(0.003)KTEEVSNLK;AVT(1)PVPTKTEEVSNLK;AVT(0.993)PVPT(0.006)KTEEVSNLK;AVT(0.993)PVPT(0.007)KTEEVSNLK 187.43 2.17E-09 11260820000 13395580 11144400 12446490 13683230 8929200 14684300 16956310 15890450 11525180 TRUE FALSE 12762397.48 12280027.03 13017173.88 12307765.72 10486449.65 14175779.01 14369313.49 14498997.96 13312446.05 0.95868163 0.922447083 0.977819841 0.924530749 0.78771772 1.064851565 1.079389425 1.089131021 1 23.66627234 2.128765814 14.68635381 1.066762427 0.922764471 0.621774674 0.055456993 0.462754876 59.33543023 0.019779479 0.014608209 134.5134818 -2.128765814 -0.143997956 AVT(ph)TPGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.5)T(0.5)PGKK;AVT(0.5)T(0.5)PGKK;AVT(0.5)T(0.5)PGKK 95.642 0.018387 2498620000 7579290 7787680 7491210 9069260 4511840 8469090 9099460 8739440 6071760 TRUE FALSE 7221031.982 8581253.446 7834689.388 8157600.754 5298703.467 8175803.29 7711170.254 7974168.303 7013337.531 1.02961421 1.223562021 1.117112837 1.163155305 0.755518103 1.165750722 1.099500804 1.137000503 1 22.74166973 AVTDKFLSAIVSSVDKIPYGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVTDKFLSAIVSSVDKIPYGMR 22 2 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 98.269 0.0006669 43108000 91122 66097 92784 83623 88276 92914 109100 96342 94322 FALSE TRUE 86814.84365 72832.35945 97038.23818 75217.05717 103671.3065 89696.36488 92454.79124 87905.78374 108948.974 0.796839478 0.668499727 0.890676016 0.690387935 0.951558354 0.823287834 0.84860635 0.806852791 1 16.73329309 -4.999994832 0.071769162 1.696529939 0.559620427 0.38414685 0.080607029 261.9857226 1.349843363 29.79042918 3.530274199 1.00E-05 4.999994832 -1.136909511 AVTEQGAELSNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AVTEQGAELSNEER 14 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 385.3 1.63E-113 1541040000 729742 627187 646035 741941 786109 665016 782932 728378 850020 FALSE TRUE 695248.5419 691098.0684 675656.3438 667359.6811 923206.1607 641986.3292 663481.3439 664597.3609 981836.7603 0.708110116 0.703882861 0.688155477 0.679705332 0.940284779 0.653862592 0.675755248 0.676891911 1 19.90512366 -1.844713084 2.721883329 1.108209145 0.713503926 0.545959322 0.08141703 17179973.45 11034507.94 12077491.79 0.018360258 0.014298383 1.844713084 -0.394705218 AVTEQGHELSNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 278.79 3.43E-33 29018696000 8763437 7530477 7886256 8739643 9267413 7793919 9451683 8451065 8689347 FALSE TRUE 8349206.7 8297841.168 8247848.638 7861117.481 10883646.89 7524013.631 8009655.166 7711044.947 10036846.55 0.831855569 0.826737873 0.821756973 0.783225831 1.084369163 0.749639201 0.798025069 0.768273671 1 23.25880273 -2.455099356 2.216978249 2.717357478 0.83179023 0.240642769 0.093216625 3362315.096 331565.2165 29205040.29 0.021369561 0.003506716 2.455099356 -1.885567248 AVTFS(ph)PDLGPVPHEGLGEYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVT(0.027)FS(0.973)PDLGPVPHEGLGEYNR;AVT(0.019)FS(0.981)PDLGPVPHEGLGEYNR;AVT(0.12)FS(0.88)PDLGPVPHEGLGEYNR;AVT(0.004)FS(0.996)PDLGPVPHEGLGEYNR 208.97 1.83E-22 367131000 202541 185887 198173 222310 259825 187845 241354 223787 248358 TRUE FALSE 192967.2883 204829.0966 207259.4281 199962.9764 305138.3977 181339.8805 204531.0145 204191.0239 286872.0902 0.67265968 0.714008451 0.72248028 0.697045768 1.063674049 0.632128 0.712969374 0.711784209 1 18.13004809 -2.394907012 2.137195967 2.84631816 0.735594707 0.32153621 0.118088977 6237981.1 565583.4269 55753215.41 0.027304641 0.004028033 2.394907012 -2.110723453 AVTGYKDPYSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 87.18 0.0097529 775150000 1956650 1698160 1826200 2031800 1431590 1924300 2309870 2120550 1809130 FALSE TRUE 1864163.032 1871204.435 1909933.076 1827559.604 1681258.843 1857661.008 1957456.908 1934863.4 2089680.641 0.892080348 0.895449955 0.913983237 0.874564069 0.804553007 0.888968856 0.936725387 0.925913445 1 20.99485105 1.159562543 1.227481842 0.994060158 0.881031265 0.598077165 0.031389025 0.319521863 0.978427166 0.030467453 0.009641741 14.4398454 -1.159562543 -0.113028893 AVTGYRDPYTEQTISLFQAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 224.97 2.72E-25 359380000 456280 418790 392600 479090 408030 463170 495940 481360 412090 FALSE TRUE 434712.5487 461465.1771 410601.0983 430930.963 479190.3028 447130.3068 420275.2444 439209.5666 475994.8125 0.91327161 0.969475223 0.86261675 0.905327015 1.006713288 0.939359621 0.882940808 0.922719229 1 18.86058633 AVTGYRDPYTGQSVSLFQALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVTGYRDPYTGQSVSLFQALKK 22 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 0 146.6 4.74E-08 202800000 247740 171740 225370 221880 202580 219860 297820 250770 256840 FALSE TRUE 236029.8212 189240.5013 235703.4374 199576.2009 237909.8879 212246.1931 252382.0892 228811.2494 296669.4354 0.795598714 0.637883377 0.794498554 0.672722488 0.801935958 0.715429929 0.850718204 0.771266676 1 18.17849677 0.317081966 0.426568258 1.02716262 0.717364377 0.634626424 0.060527438 1.589988169 0.480153586 0.138026754 0.034820157 2.075305159 -0.317081966 -0.309798244 AVTIANS(ph)PSKPSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.981)PS(0.019)KPSEK;AVTIANS(0.986)PS(0.014)KPSEK 172.97 1.68E-06 376060000 580860 743580 494190 700580 283220 674730 555130 705640 317790 TRUE FALSE 553403.899 819351.6474 516849.1003 630156.3674 332613.4783 651363.9309 470434.7228 643850.4208 367071.2502 1.507619839 2.232132446 1.408034816 1.716714036 0.906127838 1.774489096 1.281589671 1.75402029 1 18.4857006 3.701029726 24.00916244 1.423518212 1.86987621 0.240945129 0.341285029 402.3733711 257405.0134 0.08071936 0.125054316 5023.769741 -3.701029726 0.446357998 AVTIANS(ph)PSKPSEKDSVVSLESQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVTIANSPSKPSEKDSVVSLESQK 24 2 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVT(0.012)IANS(0.543)PS(0.406)KPS(0.039)EKDSVVSLESQK;AVTIANS(0.896)PS(0.104)KPSEKDSVVSLESQK 289.53 4.70E-62 671480000 916650 626420 975570 813430 1229260 951520 1318670 1035780 1534380 TRUE FALSE 873321.7711 690252.9102 1020300.849 731662.471 1443642.555 918568.6238 1117482.672 945081.6122 1772323.814 0.492755198 0.389462075 0.575685347 0.412826632 0.814547852 0.518284874 0.630518342 0.533244323 1 20.75721079 -4.999999997 0.140127551 2.603358592 0.368765033 0.627772469 0.113126449 80.87092014 0.694019605 36.16855269 0.624413916 1.00E-05 4.999999997 -2.234593559 AVTLHDQGTAQWADLSSQFYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AVTLHDQGTAQWADLSSQFYLR 22 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 309.66 3.70E-67 1809053000 977733 963985 889737 1061220 989632 961141 1042532 961417 952281 FALSE TRUE 931517.4988 1062216.167 930532.3215 954544.1494 1162223.507 927856.4462 883474.596 877230.2307 1099955.874 0.846868062 0.9656898 0.84597241 0.86780222 1.05660921 0.843539698 0.803190943 0.79751402 1 20.06901422 2.050278585 24.99996055 0.839614723 0.914731427 0.073575447 0.083721926 182.7567445 90871.04273 0.028769354 0.021247572 112.2738421 -2.050278585 0.075116704 AVTNHSVYCSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AVTNHSVYCSTK 12 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ;;;; 150.21 6.79E-05 1647140000 2797190 2497310 2357120 2641290 2256480 2529240 2973560 2842790 2616670 FALSE TRUE 2664972.372 2751788.728 2465196.284 2375782.511 2650009.398 2441651.785 2519888.809 2593860.237 3022449.82 0.881725928 0.910449765 0.815628523 0.786045312 0.876775317 0.807838651 0.833723952 0.858197949 1 21.52728696 0.939932308 19.72279272 1 0.848943478 0.624958558 0.037445709 1164.202934 382259.5992 0.039604224 0.009901056 8.708278457 -0.939932308 -0.151056522 AVTPS(ph)SEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.244)PS(0.727)S(0.029)EAK 120.65 0.00066705 175840000 464960 431580 415550 515510 319250 461330 493960 490600 350320 TRUE FALSE 442982.2623 475558.4927 434603.3785 463689.9554 374927.0989 445354.0264 418597.3298 447640.4632 404645.8364 1.09474069 1.175246227 1.074033981 1.145915548 0.926556176 1.100602024 1.034478282 1.106252488 1 18.62630023 AVTPSS(ph)EAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.142)PS(0.324)S(0.534)EAK 130.98 0.00036284 325680000 666720 654130 607570 717520 451270 692610 682880 716660 508140 TRUE FALSE 635205.4669 720786.5907 635427.6855 645393.5264 529971.3451 668624.742 578694.114 653905.4511 586939.756 1.082232819 1.228041862 1.082611425 1.09959075 0.902939935 1.139170989 0.985951468 1.114092962 1 19.16285291 3.292183466 2.437204741 1.033271445 1.153206184 0.270393314 0.076802088 0.305377129 3.704713755 0.0207814 0.028907423 1959.672353 -3.292183466 0.119934739 AVTT(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AVTTPGK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.23)T(0.77)PGK;AVT(0.055)T(0.945)PGK 128.6 0.041826 621050000 2665100 2584400 2760600 3171800 2042370 3086100 3500900 3352200 2862300 TRUE FALSE 2539126.005 2847753.298 2887176.241 2852964.638 2398558.681 2979227.583 2966773.407 3058663.597 3306170.865 0.767996001 0.861344865 0.873268914 0.862921111 0.725479347 0.901111196 0.897344247 0.925137787 1 21.65672986 1.357974182 1.040043255 0.992725516 0.825176858 0.572661233 0.050191819 0.339894273 0.745160757 0.044879379 0.015638685 22.80206513 -1.357974182 -0.167548658 AVTT(ph)PGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.014)T(0.986)PGKK 121.6 0.0027587 110770000 502660 528200 507420 589730 274950 590080 622640 624060 346070 TRUE FALSE 478900.258 582024.1805 530685.7089 530449.22 322901.1929 569645.3816 527644.8324 569413.998 399736.7681 1.19803905 1.456018628 1.327587931 1.326996319 0.807784569 1.425051251 1.319980734 1.424472412 1 18.60869075 2.956331763 24.99885227 1.225208906 1.335229338 0.089052299 0.19637163 1343.35981 769036.1842 0.057960907 0.061480015 904.3400468 -2.956331763 0.110020432 AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 156.78 3.94E-09 144727000 80646 73373 77874 85660 85087 75716 83573 78380 105651 TRUE FALSE 76834.0234 80849.79212 81444.59993 77049.29406 99926.14586 73093.93593 70822.40393 71516.63168 122034.8175 0.629607394 0.66251414 0.667388223 0.631371404 0.818833083 0.598959686 0.580345883 0.586034651 1 16.89693329 -1.59534909 2.969808578 1.022253508 0.645522709 0.728931651 0.067668979 18378558.34 19341221.36 3199944.132 0.016094569 0.025389311 1.59534909 -0.376730799 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR 30 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 309.37 1.96E-92 422440000 223300 247980 222800 270550 243320 234730 254300 236100 69186 FALSE TRUE 212745.0515 273249.4439 233015.6004 243353.8 285754.931 226601.2412 215501.8645 215425.8324 79915.01153 2.662141286 3.41925051 2.915792614 3.045157541 3.575735341 2.835527855 2.696638095 2.695686683 1 16.28617891 0.392248459 0.763022621 0.972978788 3.0992398 0.846505527 0.271644531 0.739819041 0.621555718 0.296039936 0.090065853 2.467450555 -0.392248459 2.126261012 AVVIVDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 158.36 0.0008502 3212758000 4871331 4107630 4141650 5031496 5335250 4209777 5410964 4620228 5815347 FALSE TRUE 4641072.838 4526202.167 4331548.749 4525720.463 6265715.911 4063991.367 4585422.063 4215656.343 6717161.312 0.690927703 0.67382663 0.644848106 0.673754917 0.932792235 0.605016193 0.682642838 0.627594924 1 22.67942024 -1.255141332 4.333606629 1.000183037 0.690640905 0.538018193 0.089859484 0.000147633 2.54E-05 0.080831776 0.019041032 0.055572338 1.255141332 -0.309542132 AVVLPGGTAT(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVVLPGGTATSPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 AVVLPGGT(0.122)AT(0.494)S(0.384)PK 86.772 0.09695 56687000 119180 105770 114920 134020 97808 133950 146490 137100 101420 TRUE FALSE 113546.5976 116548.0833 120189.1957 120548.055 114865.6842 129311.2779 124140.26 125094.7972 117147.6956 0.969260189 0.994881569 1.025962952 1.029026259 0.98052022 1.10383117 1.059690158 1.067838309 1 16.83796905 2.250473204 24.99998463 1.063944282 0.998959444 0.459502901 0.030885068 169.727182 356192.4738 0.01022282 0.008488015 178.0218065 -2.250473204 -0.064984838 AVVLPGGTATS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVVLPGGTATSPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 AVVLPGGT(0.001)AT(0.218)S(0.781)PK 104.7 0.0015854 43676000 277270 240610 256540 299380 194460 291890 293230 291560 239110 TRUE FALSE 264163.9966 265128.4326 268302.6128 269285.7536 228373.7624 281781.7761 248492.378 266029.4607 276189.9576 0.956457646 0.959949575 0.971442318 0.975001973 0.826872072 1.020246277 0.899715472 0.963211925 1 18.07530134 0.986596205 23.20096501 1.000000011 0.945235483 0.107368624 0.05123353 600.027132 1038607.499 0.043518481 0.01087962 9.696080329 -0.986596205 -0.054764528 AVVMPLQLIQEQAAS(ph)PNAEIHILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVVMPLQLIQEQAASPNAEIHILK 24 0 H3BRB3;Q14807-2;Q14807;I3L306 H3BRB3 KIF22 Kinesin-like protein;Kinesin-like protein KIF22 1 AVVMPLQLIQEQAAS(1)PNAEIHILK 177.06 2.79E-17 66647000 99619 110880 112390 123280 94313 121000 145120 122530 108030 TRUE FALSE 94910.2073 122178.7981 117543.1927 110887.6602 110761.1573 116809.7397 122979.2787 111800.6236 124782.7407 0.760603644 0.979132189 0.941982778 0.888645814 0.88763203 0.936104938 0.985547184 0.895962238 1 16.92905888 4.618871533 2.994407016 0.937547884 0.752453003 0.65526715 0.040560018 0.182427167 2.686978362 0.009770943 0.069485987 41578.75996 -4.618871533 -0.185094881 AVVS(ph)PPKFVFGSESVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;AVVS(1)PPKFVFGSESVK 220.28 7.05E-15 651580000 1580270 1722340 1694320 1941920 974010 2038400 2000920 2224570 1213140 TRUE FALSE 1505573.769 1897848.404 1772006.248 1746714.512 1143877.036 1967809.697 1695642.905 2029774.858 1401267.555 1.074437043 1.354379752 1.264573808 1.246524624 0.816315936 1.4043069 1.210077903 1.448527692 1 20.41830102 AVVSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVVSQR 6 0 P14625 P14625 HSP90B1 Endoplasmin 0 101.33 0.085259 30767000 58142 47538 57018 52349 66710 48192 72365 59457 64709 FALSE TRUE 55393.74289 52382.17625 59632.3317 47086.77906 78344.20288 46523.09896 61324.39018 54250.62988 74743.74123 0.74111547 0.700823579 0.797823747 0.629976213 1.048170744 0.622434711 0.820461876 0.725821707 1 16.18966516 -5 0.243891923 2.402740903 0.734723824 0.278165336 0.120095137 211.8351535 2.10768964 147.8304558 0.158469455 1.00E-05 5 -1.668017079 AVVVS(ph)PKEENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 180.97 3.90E-06 1967530000 4983620 4235370 4237490 5132420 2176890 5543510 5151590 5687920 2394730 TRUE FALSE 4748054.159 4666959.018 4431783.108 4616499.391 2556538.927 5351536.859 4365620.33 5189855.571 2766092.498 1.716520385 1.687202804 1.602181818 1.668960598 0.924242023 1.934691939 1.578262597 1.876240789 1 21.39941797 2.941196573 24.99979662 1.519060711 1.673976261 0.077381733 0.322180845 844.7975964 359158.0293 0.091010679 0.096531567 873.3665879 -2.941196573 0.15491555 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;;;;; 301 6.24E-71 869604000 345352 297047 308002 357087 368196 296019 382848 359596 399054 FALSE TRUE 329027.8954 327316.427 322124.1964 321191.9363 432409.2658 285767.7878 324437.5061 328107.8679 460937.2562 0.713823608 0.71011059 0.698846084 0.696823552 0.938108734 0.619971122 0.703864792 0.711827615 1 18.81421086 -0.952346575 4.760011554 1.000002874 0.721152898 0.533973177 0.080937965 2.27E-06 4.99E-07 0.072024888 0.016976254 0.111597233 0.952346575 -0.278849977 AVYHNMPLIWKPGYLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVYHNMPLIWKPGYLDR 17 1 Q92552;Q92552-2;G5EA06;D6RH20 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 117.37 0.00013248 307220000 247010 219680 212620 208520 234050 186830 239560 230330 213890 FALSE TRUE 235334.3268 242065.6418 222368.8373 187559.1734 274868.2459 180360.0303 203010.7222 210161.0841 247058.9688 0.952543144 0.979788926 0.900063812 0.759167637 1.112561293 0.730028265 0.821709583 0.850651507 1 17.9144959 2.20818204 24.99985687 0.830461254 0.937093897 0.134872159 0.108112022 325.3209424 267718.9151 0.037025856 0.027348658 161.5035377 -2.20818204 0.106632643 AVYQARPQLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AVYQARPQLHK 11 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 94.692 0.0049956 240570000 273680 203340 240920 229430 241580 234740 324500 270250 253890 FALSE TRUE 260743.6888 224060.5772 251966.4203 206367.2605 283711.4755 226610.8949 274991.5651 246585.4773 293261.9645 0.889115263 0.764028767 0.859185475 0.703695963 0.967433591 0.772725148 0.93769939 0.840836887 1 18.16183044 0.724036035 0.492163298 1.004959489 0.816800971 0.303434498 0.078514992 1.586921956 0.833930867 0.095093987 0.037906607 5.297073933 -0.724036035 -0.188158518 AWALLQLDGT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWALLQLDGTPR 12 0 A0A499FJE4;Q96MK2 A0A499FJE4 FAM65C Protein FAM65C 1 AWALLQLDGT(1)PR;AWALLQLDGT(1)PR 115.14 0.01098 45391000 92868 65798 83040 87199 96929 67608 90902 91014 107357 TRUE FALSE 88478.31369 72502.89101 86847.46614 78433.59085 113833.3869 65266.71801 77033.23037 83044.33166 124005.3753 0.713503858 0.584675389 0.700352432 0.63250154 0.917971392 0.526321685 0.6212088 0.669683322 1 16.92004313 0.9157867 19.91788437 1 0.662754499 0.498443738 0.103535454 5824.977456 1377711.465 0.092445439 0.02311136 8.237334465 -0.9157867 -0.337245501 AWDDFFPGSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 AWDDFFPGSDR 11 0 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ;;;;;; 218.93 2.38E-11 438511000 503831 404682 436018 624929 681547 488369 593654 495893 707601 FALSE TRUE 480015.9071 445919.5559 456009.8566 562109.9496 800408.581 471456.6591 503081.1791 452469.98 817332.1492 0.587296006 0.545579366 0.557924776 0.687737476 0.979294136 0.576823828 0.615516201 0.553593763 1 19.64056296 3.202478729 5.768375846 0.71113732 0.562804344 0.211193503 0.15221507 0.313918667 27.20768281 0.042424129 0.05216847 1593.96481 -3.202478729 -0.148332975 AWEEYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 157.79 0.0033786 1549060000 2031790 2024460 1532840 2026920 1606750 1859430 2015840 1903780 1547510 FALSE TRUE 1935751.313 2230754.776 1603122.23 1823170.151 1886966.691 1795037.473 1708286.585 1737074.931 1787489.947 1.082943888 1.247981718 0.896856641 1.019961065 1.055651638 1.004222416 0.955690177 0.971795636 1 20.7695037 3.740216479 24.99999742 0.987834788 1.165462803 0.630621123 0.056993259 82.17121264 1240601.44 0.014367494 0.024280378 5498.148674 -3.740216479 0.177628015 AWEVDTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AWEVDTCR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 151.56 0.0010961 1238900000 2349270 1918470 1716030 2028130 2410150 2054590 2697240 2290180 2589620 FALSE TRUE 2238224.663 2113964.274 1794711.673 1824258.519 2830479.397 1983439.033 2285726.5 2089639.698 2991205.044 0.748268551 0.706726635 0.599996204 0.609874112 0.946267259 0.663090294 0.764149052 0.698594602 1 21.51229538 -5 0.282711544 3.1002878 0.700761841 0.461351312 0.096443057 208.3643955 1.986271672 257.0293554 0.101073871 1.00E-05 5 -2.399525959 AWGGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AWGGKK 6 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 92.279 0.07526 5886400000 3384400 2228400 2735100 3056600 2461400 2891100 4082100 3045200 2929400 FALSE TRUE 3224426.119 2455476.493 2860507.04 2749344.761 2890667.381 2790980.482 3459300.672 2778546.144 3383676.391 0.952935726 0.725683018 0.845384342 0.812531827 0.854297825 0.824836704 1.022349738 0.821161903 1 21.69016017 1.761733691 25 0.947646889 0.832390027 0.327173597 0.075526062 13.45239413 14523.91104 0.03202602 0.017760604 57.77416682 -1.761733691 -0.115256862 AWGPGLHGGIVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWGPGLHGGIVGR 13 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 ; 161.67 4.18E-05 2187400000 1558650 1034360 1074680 1501220 1784520 1161260 1738840 1479870 1648520 FALSE TRUE 1484975.703 1139762.46 1123955.141 1350314.513 2095739.723 1121045.275 1473548.022 1350284.738 1904164.062 0.779857016 0.598563161 0.590261713 0.709137695 1.1006088 0.588733554 0.7738556 0.709122057 1 20.86072636 2.987914241 24.87556905 0.807222286 0.660053013 0.223287448 0.150819258 919.2597468 1892075.822 0.042414023 0.047267285 972.5551577 -2.987914241 -0.147169273 AWLDEDS(ph)NLSPSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.95)NLS(0.047)PS(0.003)PLR;AWLDEDS(0.996)NLS(0.004)PSPLR 93.909 0.0049039 21414000 53440 41603 56742 52267 68097 52863 69988 58024 99685 TRUE FALSE 50913.99711 45842.393 59343.67683 47013.02186 79973.09524 51032.34105 59310.04518 52943.11096 115143.6407 0.442178107 0.398132218 0.515388227 0.4082989 0.694550691 0.443205901 0.515096143 0.459800564 1 16.81307521 -5 0.283304572 4.882477961 0.446476105 0.785748232 0.084441501 98.12441477 0.934507631 224.4231999 0.086922951 1.00E-05 5 -4.436001856 AWLDEDSNLS(ph)PSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.151)NLS(0.829)PS(0.02)PLR;AWLDEDSNLS(0.994)PS(0.006)PLR 153.75 2.73E-06 51995000 47310 44759 49176 49943 62228 42655 48802 44873 63140 TRUE FALSE 45073.75006 49319.99299 51430.76824 44922.63475 73080.5435 41177.84665 41356.35859 40943.68223 72931.42873 0.618029166 0.676251567 0.705193483 0.615957147 1.002044589 0.564610448 0.567058116 0.5613997 1 16.15425304 4.42153142 1.794388419 0.689959787 0.613996387 0.016699903 0.165535308 2.710657852 13.75120304 0.041618348 0.28371076 26395.59278 -4.42153142 -0.0759634 AWLDEDSNLS(ph)PSPLRDLSGGLGGQEEEEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.027)NLS(0.565)PS(0.409)PLRDLSGGLGGQEEEEEQR 158.49 1.39E-12 28353000 21688 18580 22146 23193 20744 17794 24129 22714 23585 TRUE FALSE 20662.85122 20473.32312 23161.41601 20861.59558 24361.74703 17177.78932 20447.67789 20725.04175 27242.44134 0.758480158 0.751523069 0.850196049 0.765775553 0.894257116 0.630552493 0.750581698 0.760763013 1 14.73356838 -1.192991911 3.536344123 1.000325847 0.766400796 0.524689313 0.068629559 16531704.58 29299078.23 61763.51782 0.0159011 0.064122152 1.192991911 -0.23392505 AWLDEDSNLSPS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDSNLS(0.004)PS(0.996)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR 243.09 2.05E-14 161075000 270644 331392 239279 329949 275446 264656 275432 256961 248339 TRUE FALSE 257851.1945 365161.2216 250250.1788 296781.8997 323483.6952 255490.8964 233409.7897 234460.1326 286850.1438 0.898905579 1.273003446 0.872407368 1.0346235 1.12770972 0.890677247 0.8136994 0.817361043 1 18.12993772 2.124850025 6.022127252 0.855737628 1.051485097 0.29173645 0.12239469 0.219351782 10.76577438 0.043937534 0.032280162 133.3061005 -2.124850025 0.195747468 AWLDEDSNLSPS(ph)PLRDLSGGLGGQEEEEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.014)NLS(0.039)PS(0.946)PLRDLSGGLGGQEEEEEQR;AWLDEDS(0.071)NLS(0.063)PS(0.856)PLRDLS(0.009)GGLGGQEEEEEQR 115.77 3.27E-05 59943000 45520 35911 47101 44182 40558 41261 49972 44029 45396 TRUE FALSE 43368.35981 39570.37173 49260.62744 39740.74142 47631.30236 39832.12122 42347.8536 40173.58735 52435.77983 0.82707571 0.754644479 0.939446836 0.75789359 0.908374063 0.759636289 0.807613689 0.766148372 1 15.67826396 -1.050357349 4.569182135 1.000007516 0.812355197 0.451641546 0.063963557 0.05811276 34193488.46 642.6224313 0.013141923 0.089051789 1.050357349 -0.18765232 AWMAFMSEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWMAFMSEAER 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 195.7 1.47E-07 109909000 207584 144980 142185 153059 226120 149370 245730 176963 216868 FALSE TRUE 197771.9157 159753.6268 148704.3229 137673.2185 265555.2564 144197.2794 208239.3754 161467.1816 250498.7818 0.789512485 0.637742131 0.593632918 0.549596359 1.060105979 0.575640641 0.831298954 0.644582702 1 17.93444406 AWNAYPYCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AWNAYPYCR 9 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L471;I3L4C0;I3L4U7;I3L459;I3L3W1;A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 F5GWE5;A0A0A0MSW4 PITPNA;PITPNB Phosphatidylinositol transfer protein alpha isoform;Phosphatidylinositol transfer protein beta isoform 0 104.37 0.0084913 0 158370 109330 92831 92048 195770 93338 167440 110670 164830 FALSE TRUE 150884.164 120470.8513 97087.39317 82795.16016 229912.226 90105.68166 141893.9528 100979.1481 190390.9946 0.792496327 0.632754987 0.509936898 0.434869098 1.207579311 0.473266511 0.745276598 0.530377754 1 17.53860572 AWNDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWNDIK 6 0 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ; 114.02 0.059648 292450000 896780 933290 774470 996210 687850 846970 956510 969350 748250 FALSE TRUE 854390.9866 1028393.312 809980.2156 896069.0781 807810.8222 817639.2165 810576.832 884468.5752 864284.7885 0.988552614 1.189877834 0.937168195 1.036775251 0.934658151 0.946029859 0.937858496 1.023353167 1 19.72114724 3.715833059 24.97988996 0.968563603 1.089215242 0.387706554 0.060087648 620.090551 681542.3826 0.015028304 0.023297313 5197.961512 -3.715833059 0.120651639 AWNDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AWNDIKK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 92.439 0.025123 1526800000 3550300 2848300 2767000 3272600 2097300 3060400 3635200 3408100 2701800 FALSE TRUE 3382484.355 3138545.008 2893869.687 2943632.03 2463068.456 2954417.581 3080583.475 3109668.697 3120781.345 1.083858169 1.005692056 0.927290113 0.943235589 0.789247366 0.946691631 0.987119293 0.996439145 1 21.57347585 4.086839967 1.949504427 0.937894464 1.074317445 0.368514163 0.060172163 0.353769544 2.585133364 0.016780923 0.05348152 12213.49522 -4.086839967 0.136422981 AWNPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AWNPFR 6 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;; 109.88 0.067884 2032555000 1065825 848537 706498 814191 1170324 773293 1162335 912101 1036372 FALSE TRUE 1015445.565 935003.885 738891.6321 732346.9738 1374428.135 746513.6695 984999.448 832232.6011 1197087.277 0.848263601 0.781065761 0.617241238 0.611774085 1.148143633 0.62360839 0.822830104 0.695214641 1 20.19109691 AWRDPDEPVLLEEPVVLALAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 AWRDPDEPVLLEEPVVLALAEK 22 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;;;;;; 187.62 2.53E-17 1176463300 920620.6 737654.3 811504 887198 742866.4 821502.3 1004878 955640 839815 FALSE TRUE 877104.6887 812822.1118 848712.2611 798015.1715 872422.065 793053.4694 851565.4052 871959.0954 970049.221 0.904185756 0.837918421 0.874916698 0.822654309 0.899358554 0.817539412 0.877857934 0.89888129 1 19.88769843 0.809062375 1.865247075 0.999773586 0.860726182 0.69236734 0.029049249 0.348542584 2.159919943 0.02443115 0.00684826 6.442617906 -0.809062375 -0.139047404 AWTVEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AWTVEQLR 8 0 Q00688;G3V5F2 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 192.58 0.00040747 753300000 1089740 790590 778550 863340 1227170 816020 1201900 956540 1256400 FALSE TRUE 1038230.15 871152.0198 814247.2876 776555.423 1441188.059 787761.0228 1018528.081 872780.2867 1451236.095 0.71541092 0.600282768 0.561071552 0.535099303 0.993076223 0.54282072 0.701834859 0.601404754 1 20.46885081 -2.304733501 2.234104825 2.646288757 0.656742741 0.393494463 0.134070391 7899809.896 1246386.457 65480191.66 0.029344338 0.004957543 2.304733501 -1.989546017 AWVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AWVESR 6 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;; 119.7 0.04836 4157670000 5502330 4784750 4633550 5414990 5994290 4599610 5961140 5310650 6326670 FALSE TRUE 5242245.765 5272321.465 4846002.851 4870664.917 7039692.278 4440324.352 5051658.609 4845621.332 7307777.671 0.717351567 0.721467141 0.663129486 0.666504256 0.963315059 0.607616235 0.691271524 0.663077279 1 22.80100131 -1.366205136 3.040326927 1.003411126 0.71146817 0.475593647 0.095134198 20812802.33 26016478.06 626970.329 0.020861572 0.04303233 1.366205136 -0.291942956 AWVWNTHADFADECPKPELLAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AWVWNTHADFADECPKPELLAIR 23 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 202.95 1.19E-24 619560900 233750 210150 207820 230812 172401 232047 260052 237158 164196 FALSE TRUE 222701.1007 231564.5239 217348.7526 207610.3392 202467.6798 224011.1542 220376.2912 216391.1883 189658.6771 1.174220469 1.220954018 1.145999518 1.09465247 1.06753713 1.181127896 1.161962609 1.140950636 1 17.53304585 -5 0.17438821 0.402992492 1.188826761 0.539766984 0.043058995 112.1762749 1.068198753 23.31651206 0.158129365 1.00E-05 5 0.785834269 AYCAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYCAWR 6 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 117.67 0.052398 152680000 329630 222590 162480 201510 391600 203820 404450 267720 385630 FALSE TRUE 314049.0432 245272.1741 169929.8687 181253.832 459894.916 196761.6623 342743.7243 244277.0175 445431.5309 0.705044482 0.550639452 0.381494926 0.406917381 1.032470501 0.441732676 0.769464442 0.548405312 1 18.76484416 AYDATHLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AYDATHLVK 9 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ;; 120.12 0.0007167 492100000 1889090 1596700 1557980 1807720 1599190 1815220 1984810 1914650 1549670 FALSE TRUE 1799796.46 1759405.545 1629414.924 1626004.551 1878088.23 1752358.476 1681990.781 1746993.096 1789984.909 1.005481359 0.982916413 0.910295342 0.908390089 1.049220147 0.978979469 0.939667576 0.975982025 1 20.77151599 AYDPDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 93.992 0.024837 787350000 1339490 1091910 1115070 1208750 1416290 1073420 1417220 1204430 1614630 FALSE TRUE 1276174.962 1203176.87 1166197.062 1087244.154 1663290.528 1036247.196 1200997.06 1098963.724 1865018.574 0.684269304 0.645128626 0.625300508 0.582966931 0.891835905 0.55562299 0.643959839 0.58925082 1 20.83075857 -1.099326431 4.398762146 1.000037903 0.652843519 0.58137728 0.092724561 3.10E-05 6.35E-06 0.080812593 0.019045634 0.079556115 1.099326431 -0.347194384 AYEDGCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYEDGCK 7 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 94.887 0.032269 296040000 663960 564090 571310 626670 450590 591100 719430 640600 550950 FALSE TRUE 632575.9266 621571.4123 597505.1286 563675.941 529172.7533 570630.0588 609667.7403 584505.668 636388.5121 0.994009028 0.976716896 0.938899929 0.885741855 0.831524679 0.896669327 0.958011857 0.918473003 1 19.27954827 3.647687835 2.857720504 0.911165308 0.987143635 0.293899225 0.044148458 0.296778759 4.700136083 0.012300297 0.021065151 4443.117877 -3.647687835 0.075978327 AYEFAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 116.54 0.012638 1632720000 2437360 2169460 2314760 2526710 2602540 2323820 2636850 2271380 2685870 FALSE TRUE 2322150.823 2390530.44 2420894.036 2272720.31 3056422.152 2243345.531 2234550.103 2072485.926 3102381.002 0.748506009 0.770547021 0.780334212 0.73257292 0.985185943 0.723104457 0.7202694 0.668030756 1 21.56494444 3.961933299 1.397461756 0.787077901 0.751519236 0.014460661 0.110678218 3.246527102 11.60717243 0.031367824 0.107139861 9160.797832 -3.961933299 -0.035558665 AYEKPPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYEKPPEKK 9 2 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 74.944 0.022305 501890000 1483800 1212500 1405700 1661400 898510 1686400 1844000 1994500 1140700 FALSE TRUE 1413663.715 1336055.128 1470152.735 1494392.916 1055209.86 1627999.545 1562663.933 1819851.006 1317593.93 1.072913044 1.014011296 1.115785905 1.134183212 0.800861203 1.235585189 1.185998127 1.381192615 1 20.32947438 AYEVLKDEDLR ddPTM_SK-BR-3_Trastuzumab_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 96.64 0.0062576 74448000 291960 276160 278020 339210 261960 310760 363030 357460 290930 FALSE TRUE 278159.6294 304301.018 290767.492 305111.9663 307645.7411 299998.3033 307643.106 326158.9074 336045.9385 0.827742869 0.905533985 0.86526114 0.907947192 0.915487158 0.892730037 0.915479316 0.970578335 1 18.35829894 7.99999995 0.030628375 1.422951705 0.144571002 0.80902551 0.021062722 530.4580245 1.245626184 16.41072294 40.57374163 99999988.53 -7.99999995 -1.278380702 AYFETEKK ddPTM_SK-BR-3_Trastuzumab_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 ; 84.213 0.028239 313910000 771160 666390 726180 862430 616910 918080 1070780 1009740 771980 FALSE TRUE 734708.7951 734295.8986 759476.0713 775736.8979 724498.9087 886286.6594 907412.8448 921321.8126 891694.7157 0.823946562 0.823483515 0.851722073 0.86995794 0.812496582 0.993935081 1.017627254 1.033225606 1 19.76619034 2.192083967 5.78455506 1.014687058 0.83559754 0.956664332 0.018510945 0.035329896 2.726071426 0.00705494 0.005249453 155.6266493 -2.192083967 -0.179089519 AYFHLLNQIAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYFHLLNQIAPK 12 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2;Q14651;C9JAM8 P13797;Q14651 PLS3;PLS1 Plastin-3;Plastin-1 0 ; 131.82 0.00019196 482840000 860920 390710 483440 692530 764230 610150 1135550 880590 911710 FALSE TRUE 820226.0178 430523.7932 505606.2022 622915.5687 897511.47 589020.3525 962300.9917 803480.8713 1053093.33 0.778873053 0.40881827 0.480115283 0.591510316 0.85226204 0.55932398 0.913785098 0.762972139 1 20.00620187 1.729907688 0.66618218 0.971620327 0.559356765 0.47940912 0.138894954 0.559479045 0.50896533 0.123907008 0.063391113 53.69176596 -1.729907688 -0.412263562 AYGDRIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 AYGDRIER 8 1 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 ;;;; 169.44 0.00027453 2555090000 1940430 985950 1960230 1478580 2608890 1688440 2702230 2025280 3539380 FALSE TRUE 1848709.719 1086419.426 2050108.484 1329950.329 3063879.59 1629968.899 2289955.184 1847935.747 4088248.974 0.452200864 0.265741992 0.501463707 0.325310503 0.749435665 0.398696095 0.560131048 0.452011548 1 21.96305163 -4.999999999 0.175261625 3.200755977 0.330385565 0.640967261 0.128110102 75.52089095 0.720442182 57.7170571 0.38230384 1.00E-05 4.999999999 -2.870370412 AYGELPEHAK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 145.34 3.06E-05 3465340000 5566760 4944890 5089610 5791260 4403660 5562840 6082140 6176370 4626140 FALSE TRUE 5303630.287 5448779.913 5322973.653 5209111.542 5171656.91 5370197.456 5154197.837 5635534.3 5343538.164 0.992531563 1.019695143 0.996151518 0.974843144 0.967833812 1.004989071 0.964566487 1.054644718 1 22.34936389 1.239782151 24.99998962 1.027322351 0.990598207 0.363514718 0.02114874 35.74870805 731782.4295 0.015887571 0.005048135 17.36929339 -1.239782151 -0.036724144 AYGENIGYSEKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYGENIGYSEKDR 13 1 P05026-2;P05026 P05026-2 ATP1B1 Sodium/potassium-transporting ATPase subunit beta-1 0 79.614 0.018268 352660000 127240 79278 87000 152360 144150 94916 163040 143730 153900 FALSE TRUE 121225.6174 87356.51833 90989.03605 137044.4833 169289.7144 91629.03512 138165.2536 131144.2392 177766.026 0.681939176 0.4914129 0.511847163 0.77092618 0.952317595 0.515447396 0.777230929 0.737735113 1 17.4396201 -5 0.094588589 2.129661231 0.403043998 0.400582963 0.135884132 193.4051966 1.259312133 43.08463919 2.655173921 1.00E-05 5 -1.726617233 AYGVPVKPMT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYGVPVKPMTPK 12 1 H3BT74;F8W872;Q15131-4;Q15131-3;Q15131-2;Q15131 H3BT74 CDK10 Cyclin-dependent kinase 10 1 AYGVPVKPMT(1)PK;AYGVPVKPMT(1)PK 123.38 0.00055245 291000000 1270570 1136910 1195720 1466340 672220 1463660 1446380 1550480 802030 TRUE FALSE 1210512.674 1252762.422 1250544.945 1318940.717 789454.9552 1412973.087 1225708.166 1414711.752 926404.7162 1.306678013 1.352284158 1.349890521 1.423719778 0.8521707 1.525222252 1.323080663 1.527099039 1 19.82128307 AYHEQLSVAEITNACFEPANQMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AYHEQLSVAEITNACFEPANQMVK 24 0 P68363;P68363-2;C9JDS9;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ;; 299.25 4.20E-62 774500000 711120 593620 704070 773270 595190 702490 805070 766620 663880 FALSE TRUE 677506.7669 654110.5529 736352.3059 695539.4305 698990.9476 678162.5952 682241.7854 699490.6887 766831.1198 0.883514961 0.853004705 0.960253551 0.907030782 0.911531796 0.884370206 0.889689748 0.912183492 1 19.54854936 -5 0.27655233 1.742932265 0.888929311 0.559306193 0.027678696 169.2947614 1.628934679 72.08167343 0.033192036 1.00E-05 5 -0.854002954 AYHEQLTVAEITNACFEPANQMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYHEQLTVAEITNACFEPANQMVK 24 0 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 131.37 5.67E-05 61313000 56163 47985 56003 56787 51032 64081 63754 66768 51491 FALSE TRUE 53508.28629 52874.72605 58570.79294 51078.66287 59931.96464 61861.8589 54027.15638 60921.43996 59475.9613 0.899662404 0.889010029 0.984780938 0.858811892 1.007667019 1.040115326 0.908386434 1.024303578 1 15.86001906 2.725040145 24.78376118 0.987364233 0.908218422 0.460826428 0.0467874 686.2528858 1257936.973 0.014505557 0.013744543 530.93352 -2.725040145 -0.079145811 AYHLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AYHLQK 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ;; 142.27 0.011547 2857830000 6391800 5345600 4237560 4770900 5991000 4672300 7017200 5575600 6050700 FALSE TRUE 6089672.281 5890322.717 4431856.318 4291320.068 7035828.503 4510497.079 5946597.26 5087370.906 6989011.653 0.871320951 0.842797667 0.634117746 0.614009574 1.006698637 0.645369804 0.850849527 0.727909919 1 22.73665702 -1.903336863 8.390122353 1.033478195 0.783340579 0.243507206 0.124173225 0.058755123 0.000676921 0.090844709 0.026292528 0.012492896 1.903336863 -0.250137615 AYHPHCFTCVMCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYHPHCFTCVMCHR 14 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 145.81 2.95E-06 194040000 149660 86135 133760 117690 153290 118460 175950 159270 127680 FALSE TRUE 142585.8684 94912.25443 139893.0283 105859.5776 180023.7275 114357.7005 149105.596 145323.4745 147479.9623 0.966815194 0.643560338 0.948556171 0.717789562 1.220665673 0.775411783 1.011022743 0.985377757 1 17.17015943 2.782602896 24.99977332 0.981562065 0.813501756 0.278929028 0.141686923 586.0884196 332681.0709 0.038859498 0.041216483 606.1818039 -2.782602896 -0.168060309 AYIDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYIDSFR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 146.21 0.0051989 157554000 377070 363290 331620 373090 402760 314040 397800 355660 365540 FALSE TRUE 359246.6484 400309.664 346825.105 335586.2844 473001.2165 303164.7161 337108.3039 324516.5249 422226.0763 0.850839559 0.948093182 0.821420382 0.794802366 1.120255813 0.718015142 0.798407116 0.768584754 1 18.68765616 AYILVT(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYILVTPLK 9 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 AYILVT(1)PLK;AYILVT(1)PLK 131.82 0.0036043 163325000 714880 651450 703530 769110 606930 724440 782920 787850 674930 TRUE FALSE 681089.0392 717833.4956 735787.5464 691797.6016 712778.3998 699352.4612 663471.1747 718861.6773 779594.6973 0.873645038 0.920777807 0.943807787 0.887381102 0.914293545 0.897071855 0.85104629 0.922096674 1 19.57236475 0.979450909 24.3520736 1.000000002 0.897485187 0.612298116 0.025381615 796.3199429 943694.9471 0.02527459 0.006318648 9.537859243 -0.979450909 -0.102514815 AYINKVEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYINKVEELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 174.1 2.93E-06 1016410000 2177760 1747320 1444410 2331650 1174350 1923930 2218270 2405530 1440460 FALSE TRUE 2074821.601 1925373.895 1510637.627 2097268.112 1379156.268 1857303.822 1879832.17 2194889.041 1663839.18 1.2470085 1.157187496 0.90792286 1.260499294 0.828899983 1.116276046 1.129816026 1.319171388 1 20.66608456 3.994936911 23.19362403 1.083615026 1.213325725 0.117763614 0.146761186 235.721224 1079850.782 0.034135108 0.067190855 9884.095008 -3.994936911 0.129710699 AYINKVEELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYINKVEELKK 11 2 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 105.25 0.0014009 720480000 2514090 1892880 1566890 2533200 1149750 2152470 2515540 2737520 1306290 FALSE TRUE 2395253.948 2085766.624 1638733.456 2278557.923 1350266.036 2077929.424 2131748.172 2497808.236 1508862.782 1.587456446 1.382343477 1.086071892 1.510116063 0.894889882 1.377149367 1.412817784 1.655424381 1 20.52503018 4.275926054 2.624662225 1.297756127 1.564965792 0.143070683 0.233722638 0.520871317 6.974889357 0.055730139 0.194254534 18876.69915 -4.275926054 0.267209665 AYLGYQAVPSGSSGSLSTSSS(ph)SSPPGTPSPADAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYLGYQAVPSGSSGSLSTSSSSSPPGTPSPADAK 34 0 P17676-3;P17676-2;P17676 P17676-3 CEBPB CCAAT/enhancer-binding protein beta 1 AYLGYQAVPSGSSGSLS(0.001)T(0.005)S(0.015)S(0.069)S(0.37)S(0.269)S(0.269)PPGT(0.001)PSPADAK 116.82 2.66E-06 132830000 239480 182790 208270 247370 182980 226500 259090 232940 208210 TRUE FALSE 228160.255 201416.5088 217819.3855 222503.8976 214891.6541 218656.2482 219561.062 212542.5387 240498.1434 0.948698613 0.837497146 0.905700902 0.925179274 0.893527289 0.909180608 0.912942856 0.883759582 1 17.87566623 -2.287924851 2.189861807 1.423583596 0.900830081 0.532321701 0.028829478 1979622.09 293020.2345 4152636.839 0.006699129 0.005153178 2.287924851 -0.522753515 AYLPVNESFGFTADLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 262.48 1.60E-26 354340000 193914 156361 166802 179611 192800 162675 198877 174325 216834 FALSE TRUE 184748.0695 172294.3637 174450.0367 161556.161 226424.259 157041.524 168534.661 159060.1788 250459.5093 0.737636475 0.687913045 0.696519917 0.645039038 0.904035385 0.627013622 0.672901826 0.635073427 1 17.93421786 -1.025753766 4.60214857 1.000007921 0.700716101 0.584847388 0.079230996 9489903.514 2115165.548 941.7181065 0.017054095 0.094242378 1.025753766 -0.29929182 AYLQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYLQAR 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 ; 152.49 0.028846 0 996760 764300 567040 714370 1022940 743650 1156520 904960 1165810 FALSE TRUE 949645.1302 842183.0389 593039.3449 642560.1704 1201340.412 717897.214 980071.6331 825716.9049 1346597.861 0.705218059 0.625415399 0.440398253 0.477173022 0.892130047 0.53311923 0.727813152 0.613187447 1 20.36088765 -1.364514376 0.385176935 1.220698489 0.610666056 0.453903781 0.129561974 20.67425373 1.78203493 4.678259794 0.08381539 0.043200187 1.364514376 -0.610032433 AYMCPFMQFIEGGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYMCPFMQFIEGGRR 15 1 O94855;O94855-2;P53992;G5EA31 O94855;P53992 SEC24D;SEC24C Protein transport protein Sec24D;Protein transport protein Sec24C 0 148.62 5.61E-06 93303000 39525 35089 35967 31896 31679 37465 47233 36820 35768 FALSE TRUE 37656.73158 38664.60899 37616.12253 28689.75348 37203.80757 36167.57766 40026.73836 33595.8456 41314.71876 0.911460436 0.935855553 0.910477516 0.694419673 0.90049766 0.875416286 0.968825144 0.813168929 1 15.33436823 -0.005433656 7.752944768 0.999999997 0.886150924 0.195022674 0.076700165 2454118.184 316540.1114 0.072260267 0.017525689 0.987566487 0.005433656 -0.113849073 AYNMVDIIHSVVDEREFFEIMPNYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYNMVDIIHSVVDEREFFEIMPNYAK 26 1 F8WBI9;E7ETT4;E7EUY3;E7ETT1;E9PDR0;C9JQS9;E7EX59;P05166;P05166-2;E9PEC3 F8WBI9 PCCB "Propionyl-CoA carboxylase beta chain, mitochondrial" 0 83.693 0.0086593 36245000 91750 48165 99658 62741 108460 63833 124410 84830 100970 FALSE TRUE 87413.15933 53073.06826 104227.4179 56434.15548 127375.3897 61622.4472 105428.9696 77401.83549 116627.9119 0.749504625 0.455063178 0.893674732 0.48388207 1.092151849 0.52836792 0.903977168 0.663664763 1 16.83155358 -4.999999926 0.079709046 1.989679923 0.411384236 0.159269146 0.202334806 371.8076257 2.099462205 64.31254755 6.062038025 1.00E-05 4.999999926 -1.578295687 AYNYVAQEVDDYHAFQTLTHIYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYNYVAQEVDDYHAFQTLTHIYNK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 223.97 4.17E-33 210140000 359000 360090 325630 391040 310850 338800 387030 381810 178764 FALSE TRUE 342030.7815 396783.5804 340560.4576 351731.9163 365062.1416 327067.271 327981.4652 348376.6923 206485.8081 1.656437237 1.921602187 1.649316535 1.703419327 1.767976913 1.583969736 1.588397131 1.687170152 1 17.6556831 -2.415138731 0.253159867 1.41E-10 1.794788345 0.853599759 0.091364494 13.77818212 0.435411748 7.824904816 0.128965357 0.003844689 2.415138731 1.794788345 AYPLADAHLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AYPLADAHLTK 11 0 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 ;;; 170.89 1.52E-05 1059230000 2478350 2145060 2035520 2372730 2186210 2142940 2869880 2519270 2338380 FALSE TRUE 2361203.307 2363644.053 2128850.605 2134218.673 2567484.332 2068729.45 2432027.097 2298669.363 2701004.028 0.874194664 0.875098307 0.788170097 0.790157531 0.950566643 0.765911279 0.900415946 0.851042553 1 21.36506436 -0.057772165 0.798128924 1.004170483 0.848963042 0.418408922 0.055979078 5.990077035 3.64276112 0.126850408 0.017084156 0.875442921 0.057772165 -0.155207441 AYQHGGVTGLS(ph)QY ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYQHGGVTGLSQY 13 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 AYQHGGVTGLS(1)QY;AYQHGGVTGLS(1)QY 124.55 0.0002208 369240000 435160 333610 385350 428630 529990 390260 495070 452350 480900 TRUE FALSE 414590.8492 367605.2383 403018.6787 385543.2981 622420.0882 376745.1983 419537.9789 412739.8359 555475.5159 0.746371059 0.661784773 0.725538151 0.694077933 1.120517593 0.678239072 0.755277176 0.743038755 1 19.0833638 AYRNS(ph)IK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYRNSIK 7 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 AYRNS(1)IK 74.376 0.028069 152980000 141600 128690 86909 161010 98393 152250 137600 124380 81540 TRUE FALSE 134906.8486 141803.6573 90893.86361 144824.9689 115552.708 146977.5443 116606.5928 113488.6278 94184.80675 1.432363173 1.505589513 0.965058662 1.537668058 1.226872062 1.560522863 1.238061603 1.204956847 1 16.52320673 -4.173174673 0.15224496 2.56E-18 1.470092713 0.279161925 0.179983604 121.8597845 1.380713271 37.69690275 0.826455968 6.71E-05 4.173174673 1.470092713 AYRNS(ph)IKDAQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AYRNSIKDAQSR 12 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 AYRNS(1)IKDAQSR;AYRNS(1)IKDAQSR;AYRNS(1)IKDAQSR 94.461 0.0034421 253136000 282081 166039 248213 251442 274477 236630 344250 242233 272004 TRUE FALSE 268747.5902 182958.5629 259593.8116 226166.5725 322345.7019 228435.4438 291728.3399 221021.7944 314184.9911 0.855380103 0.582327508 0.826245107 0.719851612 1.025974222 0.727073063 0.928524112 0.703476616 1 18.26125474 AYS(ph)FCGTVEYMAPEVVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR 331.48 6.79E-75 3150103000 2453507 2150310 2376467 2624446 2281678 2414410 2679112 2495552 2498465 TRUE FALSE 2337534.586 2369429.034 2485430.363 2360631.702 2679601.921 2330798.376 2270364.259 2277028.237 2885914.192 0.809980627 0.821032393 0.861228088 0.817984023 0.928510601 0.807646458 0.786705393 0.789014533 1 21.46059697 -2.199594626 2.35791085 1.514359891 0.825981129 0.631927511 0.041290805 3726549.552 722631.2662 10250161.31 0.009987428 0.006315466 2.199594626 -0.688378762 AYS(ph)GSDLPSSSSGGANGTAGGGGGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.981)GS(0.019)DLPSSSSGGANGTAGGGGGAR;AYS(0.846)GS(0.153)DLPS(0.001)SSSGGANGTAGGGGGAR;AYS(0.999)GS(0.001)DLPSSSSGGANGTAGGGGGAR 345.28 1.56E-98 213156000 192839 175706 189235 207521 189737 199334 230625 202994 206645 TRUE FALSE 183723.8826 193610.6412 197911.6119 186660.5948 222827.0727 192431.0136 195438.9205 185218.7692 238690.4512 0.769716098 0.811136936 0.829155967 0.782019531 0.933539954 0.806194855 0.818796561 0.775978965 1 17.86478133 -2.487042347 2.295817365 3.423676308 0.815373853 0.613245259 0.045966407 4178090.355 653705.827 51871317.16 0.011252429 0.003258049 2.487042347 -2.608302455 AYS(ph)PEYR ddPTM_SK-BR-3_Trastuzumab_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 140.14 0.002774 15001920000 8110000 7653200 7073970 8592970 7501940 7258010 8116040 7791880 7263870 TRUE FALSE 7726656.372 8433069.781 7398318.522 7729188.33 8810275.961 7006663.294 6877789.037 7109581.68 8390313.861 0.920901947 1.005095867 0.881768983 0.921203719 1.050053205 0.835089534 0.819729649 0.847355867 1 23.00029335 2.203856208 24.99977456 0.855242367 0.954415341 0.231981367 0.068234126 196.6939604 141689.9533 0.023369659 0.017260401 159.9028515 -2.203856208 0.099172974 AYS(ph)PEYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AYSPEYRR 8 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 AYS(1)PEYRR;AY(0.004)S(0.996)PEYRR;AYS(1)PEYRR;AYS(1)PEYRR;AYS(1)PEYRR;AYS(1)PEYRR 134.84 0.00052627 3775260000 3005380 1326830 2722220 2261650 3413130 2580460 3912500 2932920 4686810 TRUE FALSE 2863321.643 1462035.485 2847036.48 2034304.645 4008378.791 2491098.023 3315576.267 2676097.976 5413616.558 0.528911055 0.270066317 0.525902869 0.375775533 0.740425324 0.460154131 0.612451257 0.494327211 1 22.36816128 -5 0.160496181 2.938454344 0.350130294 0.63465025 0.121424797 75.8444285 0.698142814 46.59563359 0.460587248 1.00E-05 5 -2.58832405 AYSEAHEISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYSEAHEISK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 81.017 0.022273 1047740000 4638400 3456400 3858100 4609400 3765700 3975000 5060700 4750800 4209000 FALSE TRUE 4419152.024 3808611.09 4034997.701 4146054.355 4422436.888 3837344.753 4288597.269 4334794.766 4861710.223 0.908970675 0.78338916 0.829954381 0.852797506 0.909646335 0.789299357 0.882117007 0.891619321 1 22.21303248 0.80085513 1.338274484 0.999629795 0.845377815 0.555248537 0.042460377 0.516214616 1.682352294 0.037793127 0.011321347 6.322009288 -0.80085513 -0.15425198 AYSLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYSLGR 6 0 P18754-2;C9JW69;P18754 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 112.56 0.06256 387020000 409090 363100 362110 396510 388950 374680 430160 390310 419460 FALSE TRUE 389753.1264 400100.3028 378713.1017 356652.0615 456782.7569 361704.7377 364531.1916 356132.3872 484507.7145 0.804431209 0.82578727 0.781645143 0.736112245 0.942777056 0.746540719 0.752374381 0.735039663 1 18.88616011 -1.071436872 4.334235558 1.00001805 0.792267466 0.532895447 0.061597554 38087796816 8159944517 7803620.785 0.013704322 0.084832668 1.071436872 -0.207750585 AYSNS(ph)IVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYSNSIVR 8 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 AYS(0.159)NS(0.841)IVR 76.143 0.038356 81496000 46710 42703 44488 47733 44009 40899 53932 48922 58890 TRUE FALSE 44502.11087 47054.48425 46527.8188 42934.78815 51684.15567 39482.65737 45703.68287 44638.13033 68022.36043 0.654227677 0.691750241 0.684007707 0.63118639 0.759811264 0.580436449 0.671892045 0.656227306 1 16.05372145 -1.859338763 2.606005623 1.143323825 0.666603151 0.84196297 0.045449457 10260262.75 6557604.374 9129207.668 0.009700819 0.013824876 1.859338763 -0.476720674 AYSPELIVHPVLDSPNAVHEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYSPELIVHPVLDSPNAVHEVEK 23 0 Q8IW45-2;Q8IW45 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 183.09 2.17E-17 108419000 154856 124622 136271 156840 117757 141388 170281 155322 69956 FALSE TRUE 147536.2638 137321.1235 142519.1601 141074.1452 138293.7835 136491.6981 144301.506 141721.1823 80804.41919 1.825843998 1.699425908 1.763754527 1.745871657 1.711463122 1.689161304 1.785812057 1.753879103 1 16.30214658 -1.107494086 4.186228639 0.999864247 1.747082282 0.970783661 0.040720898 2693115.075 712483.2775 3358.98434 0.009138549 0.078073907 1.107494086 0.747218035 AYSSFGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYSSFGGGR 9 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 153.04 0.00018389 656730000 763930 648570 512840 595090 756060 579430 775750 642050 323150 FALSE TRUE 727820.5429 714660.0204 536354.2213 535270.4226 887916.6246 559364.1938 657395.0899 585828.6983 373262.4516 1.949889521 1.914631427 1.436935912 1.434032329 2.378799745 1.498581471 1.761214092 1.569481998 1 18.50983086 -2.26777099 0.248103944 1.83E-14 1.872041709 0.417323972 0.284073717 35.72431411 1.180051662 20.33486216 0.423849747 0.005397952 2.26777099 1.872041709 AYSSFGGGRGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 AYSSFGGGRGSR 12 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 1 AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R 110.55 0.00089506 1119380000 677700 546460 550750 756370 676020 655630 859910 628150 699400 TRUE FALSE 645666.4641 602144.8953 576002.4323 680338.2506 793917.674 632925.3687 728714.9362 573145.856 807859.38 0.799231252 0.745358549 0.712998384 0.842149349 0.98274241 0.783459825 0.902031906 0.709462402 1 19.62374467 3.095252044 6.287660282 0.869132259 0.758395313 0.292973517 0.086867746 0.261249225 14.46813104 0.02274161 0.027292094 1245.23708 -3.095252044 -0.110736947 AYT(ph)PPPPLGPHPNLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 AY(0.005)T(0.995)PPPPLGPHPNLGK;AY(0.001)T(0.999)PPPPLGPHPNLGK 125.18 0.00028877 516970000 1598480 1469230 1466460 1713430 1027710 1659840 1788010 1813580 1079320 TRUE FALSE 1522923.018 1618946.207 1533698.642 1541192.761 1206942.299 1602359.325 1515216.235 1654773.321 1246695.433 1.221567817 1.298589988 1.230211165 1.236222352 0.968113195 1.285285309 1.215386048 1.327327651 1 20.24967763 -2.327432078 1.980429573 4.57E-05 1.224665458 0.339664807 0.097615047 1365026.179 172103.855 6098281.643 0.023541956 0.00470509 2.327432078 1.224619783 AYT(ph)PVVVTLWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 110.31 0.016814 17789000 45904 43270 33955 41778 26185 36339 37871 37327 32441 TRUE FALSE 43734.20889 47679.26219 35511.87034 37578.39607 30751.65571 35080.57132 32093.0834 34058.45 37471.78459 1.167123727 1.272404363 0.947696266 1.002845113 0.820661627 0.936186299 0.856459967 0.908909206 1 15.19351707 3.673152157 4.965683364 0.912206717 1.219728513 0.796912294 0.061782897 0.072717108 3.565270746 0.015651062 0.024951449 4711.423646 -3.673152157 0.307521796 AYT(ph)PVVVTQWYR ddPTM_SK-BR-3_Trastuzumab_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 179.46 0.00023128 427810000 375605 374110 271119 346783 259908 310707 392028 355409 279270 TRUE FALSE 357850.896 412232.2343 283550.0743 311923.714 305235.8729 299947.1387 332216.9285 324287.5038 322577.7653 1.109347682 1.277931335 0.879013078 0.966972146 0.946239654 0.929844431 1.029881673 1.005300237 1 18.29928747 3.739201838 24.99975744 0.967478318 1.193639512 0.727991716 0.058009892 25.68175995 1001256.259 0.014774708 0.024759573 5485.31835 -3.739201838 0.226161194 AYTNFDAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 AYTNFDAER 9 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 81.338 0.050172 185910000 140950 108840 70120 118340 171320 102200 135570 99975 151550 FALSE TRUE 134287.5728 119930.9197 73335.07136 106444.2384 201198.1538 98660.78837 114886.3066 91220.659 175051.6 0.767131365 0.68511753 0.418934025 0.608073496 1.149364837 0.563609749 0.656299666 0.521107256 1 17.41742072 AYVHEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 AYVHEFK 7 0 Q9H4A4;A6NKB8;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 129.29 0.0036753 1679010000 6581330 6558700 5682940 7345010 5232940 6637270 6898040 7162000 5192340 FALSE TRUE 6270243.574 7227038.987 5943508.42 6606675.64 6145563.079 6407419.676 5845617.307 6534857.312 5997541.568 1.045468965 1.205000233 0.990990784 1.10156396 1.024680364 1.06834102 0.974668911 1.089589332 1 22.51593982 3.724047103 24.9977294 1.035189664 1.125234606 0.306975802 0.055930576 774.0400487 1333187.862 0.013716307 0.02134931 5297.208933 -3.724047103 0.090044942 AYWQVHLDQVEVASGLTLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 295.21 1.37E-54 382004000 567939 406959 402468 584764 479842 469024 617352 519962 447611 FALSE TRUE 541093.649 448428.5848 420921.5559 525982.4117 563526.2929 452781.5813 523163.614 474431.3708 517024.2278 1.046553759 0.867326057 0.814123465 1.01732643 1.089941752 0.875745385 1.011874465 0.917619224 1 18.97987236 AYYEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 AYYEFR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;;; 166.22 0.016361 5068190000 6665960 5234120 4956810 5718370 6839430 5096840 6959600 5932520 6979970 FALSE TRUE 6350873.281 5767482.779 5184084.641 5143548.583 8032224.427 4920335.153 5897785.198 5413037.099 8062388.099 0.787716146 0.71535663 0.642996167 0.637968369 0.996258717 0.610282598 0.731518395 0.671393765 1 22.9427758 -1.219480205 4.526524079 1.000080401 0.725650491 0.384989327 0.109541869 8.06E-05 1.39E-05 0.096168162 0.022660429 0.06032812 1.219480205 -0.27442991 CAAPRPPSS(ph)SPEQR ddPTM_SK-BR-3_Trastuzumab_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(0.09)S(0.455)S(0.455)PEQR 111.22 0.00040222 168800000 145260 123710 139270 154490 119920 148350 175240 141450 159790 TRUE FALSE 138393.8477 136316.1896 145655.6673 138960.3717 140834.01 143212.6023 148503.9195 129063.8881 184569.4171 0.74982004 0.738563256 0.789164692 0.752889476 0.763040878 0.775928128 0.804596568 0.699270172 1 17.49380399 -2.035266801 2.819834663 1.299815603 0.761545226 0.873738615 0.028759758 10210445.9 10438534.8 19630129.12 0.006689313 0.009220048 2.035266801 -0.538270377 CAGCDELIFSNEYTQAENQNWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CAGCDELIFSNEYTQAENQNWHLK 24 0 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ; 218.44 1.17E-32 365350000 246177 191377 216013 246398 176003 221209 251786 252367 180874 FALSE TRUE 234540.7011 210878.5339 225917.4097 221629.6049 206697.8675 213548.4769 213371.4213 230268.4076 208923.0161 1.122617821 1.009359992 1.08134285 1.060819478 0.989349433 1.022139546 1.021292078 1.102168693 1 17.67261191 4.645478528 3.090097168 1.03586308 1.127829388 0.362519161 0.036041124 0.311689489 4.803856884 0.008263793 0.061677364 44205.72605 -4.645478528 0.091966308 CAGNEDIITLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CAGNEDIITLR 11 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;; 157.38 7.12E-05 107196000 214490 224872 214627 250476 220598 226006 257313 247270 238502 FALSE TRUE 204351.4828 247786.7125 224467.8602 225297.6766 259070.2214 218179.3556 218055.176 225617.7279 275487.6721 0.741780862 0.899447553 0.814801833 0.817814006 0.940405861 0.791975023 0.791524261 0.818975769 1 18.07162823 -2.323492978 2.089898349 1.820596935 0.826996514 0.485573996 0.055931197 4091481.847 553472.447 15820663 0.013090611 0.00474796 2.323492978 -0.99360042 CAHIEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CAHIEAK 7 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 108.09 0.0073318 311410000 925090 793160 811000 1001700 611090 912140 1066770 989760 625040 FALSE TRUE 881362.8291 873983.9057 848185.1522 901007.2129 717663.9025 880552.3631 904014.6439 903091.3674 721968.0109 1.220778228 1.21055766 1.174823731 1.247987721 0.994038367 1.219655649 1.252153323 1.25087449 1 19.46157539 3.645203999 1.574811039 1.175119058 1.218273724 0.039820241 0.095653379 1.728304621 8.42070158 0.028169552 0.059173306 4417.779125 -3.645203999 0.043154667 CAIKVEQSAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 84.169 0.01474 128010000 256560 209960 277510 243910 250200 272620 332600 292610 276300 FALSE TRUE 244432.9173 231355.1627 290234.108 219391.7034 293834.8008 263179.101 281855.7614 266987.5172 319147.1929 0.765893991 0.724916803 0.909405173 0.687431092 0.920687405 0.824632354 0.883152876 0.836565457 1 18.28386243 -4.999996721 0.038134141 1.99139266 0.226730957 0.47109476 0.069012912 659.6524225 1.881456823 76.30295072 24.26106134 1.00E-05 4.999996721 -1.764661703 CALGWDHQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CALGWDHQEK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 166.86 5.42E-06 1061600000 2872250 2617360 2574880 3116090 1909270 2925150 3238180 3044000 1742840 FALSE TRUE 2736484.435 2884071.96 2692940.795 2802854.713 2242246.084 2823851.322 2744136.168 2777451.223 2013110.726 1.359331307 1.432644475 1.33770128 1.392300322 1.113821537 1.402730255 1.363132257 1.3796813 1 20.9409951 -1.474101373 3.107359018 0.991814631 1.353232595 0.609508397 0.08735379 37190525.43 47609748.79 2654792.798 0.020067195 0.033565926 1.474101373 0.361417964 CALSS(ph)PSLAFTPPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 CALS(0.255)S(0.642)PS(0.102)LAFTPPIK;CALS(0.309)S(0.69)PS(0.001)LAFTPPIK 253.15 1.22E-24 167844000 896160 596570 703290 851570 606290 734070 855200 755570 593140 TRUE FALSE 853800.2928 657361.1612 735536.5421 765968.5657 712026.784 708648.9718 724723.5332 689408.2853 685121.1219 1.246203431 0.959481675 1.073586142 1.1180046 1.039271395 1.034341154 1.057803518 1.006257526 1 19.38599954 4.671348979 3.454414908 1.042549791 1.257650943 0.692746358 0.04368628 0.141743381 2.79412868 0.010043884 0.071008686 46919.02506 -4.671348979 0.215101152 CAPSAGS(ph)PAAAVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CAPSAGSPAAAVGR 14 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPS(0.001)AGS(0.999)PAAAVGR;CAPSAGS(1)PAAAVGR;CAPS(0.006)AGS(0.994)PAAAVGR;CAPS(0.057)AGS(0.943)PAAAVGR 220.46 4.86E-12 955410000 844200 741560 813740 988950 719090 852090 916150 836390 770440 TRUE FALSE 804296.339 817125.8071 851050.7839 889538.8671 844499.0683 822581.9096 776374.4913 763151.2576 889915.9003 0.903789154 0.918205649 0.956327203 0.999576327 0.948965029 0.924336681 0.872413327 0.857554357 1 19.76330948 -0.221559583 7.586378416 0.999999999 0.921614037 0.262851393 0.040678015 0 0 0.042216191 0.009950452 0.600399632 0.221559583 -0.078385962 CAPSAGSPAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR 275.17 8.42E-74 2708650000 743623 565135 768733 744632 605878 769300 894125 803894 747163 TRUE FALSE 708473.4145 622722.899 803980.1684 669780.1767 711542.9314 742658.9481 757709.8095 733500.7796 863029.2221 0.820914746 0.721554825 0.931579311 0.776080531 0.824471424 0.860525842 0.877965415 0.849914187 1 19.71904988 -4.999999703 0.104104979 1.587987325 0.71064916 0.52280237 0.053255049 122.9001324 0.862568348 15.35917239 0.723135871 1.00E-05 4.999999703 -0.877338164 CATITPDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CATITPDEKR 10 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 133.81 0.00030042 284460000 194170 153490 180660 237730 142610 205020 224110 217100 169290 FALSE TRUE 184991.9689 169130.8055 188943.4397 213832.9287 167481.1388 197920.106 189917.9034 198089.5731 195542.6286 0.946044196 0.864930612 0.966251917 1.093536127 0.856494259 1.012158359 0.971235299 1.013025009 1 17.57712363 3.495366473 24.25094042 0.98758146 0.907171358 0.24649883 0.060899224 626.6262476 832889.1011 0.014855611 0.022529491 3128.718379 -3.495366473 -0.080410102 CAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CAVSDVEMQEHYDEFFEEVFTEMEEK 26 0 P0DN76;Q01081 P0DN76 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 146.5 1.57E-07 24724000 78617 59606 61151 81033 53374 66793 84821 73809 49566 FALSE TRUE 74900.93021 65679.91917 63954.83384 72887.40889 62682.4087 64479.94166 71879.99861 67345.89267 57252.44213 1.308257385 1.14719856 1.11706735 1.273088207 1.094842532 1.126239148 1.255492271 1.176297293 1 15.80504961 -4.146042987 0.330394523 1.95E-38 1.198750739 0.407802116 0.071071652 195.8381212 2.924457234 135.2617133 0.058078228 7.14E-05 4.146042987 1.198750739 CCLTYCFNKPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CCLTYCFNKPEDK 13 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 162.48 3.68E-05 2032800000 2189400 1690100 1818400 2161400 1061500 2179900 2269900 2371500 995040 FALSE TRUE 2085911.401 1862323.111 1901775.439 1944131.966 1246625.264 2104409.516 1923585.065 2163838.888 1149345.721 1.814868549 1.620333271 1.654659171 1.691511901 1.084639061 1.830963023 1.67363486 1.882670156 1 20.13238139 4.679872561 0.935558599 1.577423494 1.929489778 0.073456071 0.290516185 5.690079688 4.1860596 0.086183865 2.00307779 47848.96646 -4.679872561 0.352066285 CDDSPRT(ph)PSNTPSAEADWSPGLELHPDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CDDSPRTPSNTPSAEADWSPGLELHPDYK 29 1 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 CDDS(0.214)PRT(0.763)PS(0.021)NT(0.001)PSAEADWSPGLELHPDYK 85.925 0.0029025 48462000 76443 54989 62084 64276 49408 70363 79237 70305 47590 TRUE FALSE 72829.69089 60592.44162 64930.61281 57814.85436 58024.73956 67926.31167 67147.94036 64148.72149 54970.01414 1.324898529 1.102281718 1.181200584 1.051752583 1.055570759 1.235697548 1.221537622 1.166976623 1 15.74635723 4.615858676 2.858817762 1.141491974 1.335067757 0.374994608 0.078017451 0.366201646 4.860949645 0.019256407 0.142947075 41291.31136 -4.615858676 0.193575783 CDENILWLDYK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 183.08 1.28E-05 2400624000 1780920 1329213 1390198 1758348 1211260 1511377.1 2018559 1675501 1355577 FALSE TRUE 1696739.441 1464661.316 1453939.953 1581595.518 1422503.361 1459037.732 1710590.751 1528785.25 1565792.958 1.083629501 0.935411868 0.928564627 1.010092369 0.90848752 0.931820344 1.092475696 0.976364878 1 20.57846203 1.752549682 25 1.031113173 0.969794357 0.168010182 0.058114579 7.461901499 13353.93764 0.026572335 0.014735524 56.56524622 -1.752549682 -0.061318816 CDEPILSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CDEPILSNR 9 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 98.582 0.011194 0 288370 209230 261500 299550 294070 246000 290470 252620 332900 FALSE TRUE 274739.3216 230550.7749 273490.0337 269438.6649 345355.7149 237480.9583 246153.4667 230499.2536 384524.4318 0.714491197 0.5995738 0.71124228 0.70070623 0.898137248 0.617596539 0.640150394 0.599439813 1 18.55271574 -1.020687157 4.199702695 1.000023492 0.680793691 0.561960661 0.087278769 7580438.336 5527003.164 1497.767579 0.019975741 0.095348276 1.020687157 -0.319229801 CDFITQVEEEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CDFITQVEEEISR 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 79.693 0.046099 10250000 12214 10325 11392 11826 11230 11351 12849 11428 12467 FALSE TRUE 11636.66843 11377.12924 11914.33447 10637.22801 13188.50844 10957.91202 10888.64906 10427.30374 14400.31869 0.80808409 0.790060934 0.827366028 0.738680042 0.915848373 0.760949272 0.756139451 0.72410229 1 13.81381312 -1.269314469 3.662442933 1.000422479 0.790658595 0.596016985 0.054293082 11252222.33 22155886.86 57581.91248 0.012286701 0.053788017 1.269314469 -0.209763884 CDGETDKHWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CDGETDKHWR 10 1 Q9NXV6;J3KNE1;D6RGD2 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ; 129.7 0.00017791 75807000 153113 130565 150951 161743 120173 158192 183034 161763 121873 FALSE TRUE 145875.6519 143869.7219 157872.2527 145484.2863 141131.1332 152713.7714 155108.8016 147598.1742 140772.4424 1.036251481 1.02200203 1.121471291 1.033471352 1.002548018 1.084827178 1.101840666 1.048487699 1 17.10300541 CDILVQEELLAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CDILVQEELLASPK 14 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK 254.59 3.08E-24 245753000 425868 543960 356226 553480 183548 507350 395984 510620 197041 TRUE FALSE 405738.0636 599390.1424 372559.3145 497843.1389 215558.7131 489780.3423 335569.3681 465907.4058 227597.1119 1.782703041 2.633557769 1.636924613 2.187387769 0.94710654 2.151962027 1.474400818 2.047070817 1 17.79612273 3.231648973 1.855442985 1.613209126 2.173142925 0.182486803 0.478190364 0.488732836 3.46772131 0.13714903 0.190577157 1704.70397 -3.231648973 0.559933799 CDKTVYFAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CDKTVYFAEK 10 1 P52943;H0YHD8 P52943 CRIP2 Cysteine-rich protein 2 0 ; 101.89 0.0027585 925910000 1762340 1094040 1612800 1408010 1279470 1659210 2452800 2005880 1617450 FALSE TRUE 1679037.681 1205523.92 1686748.475 1266474.16 1502609.163 1601751.142 2078580.311 1830234.513 1868275.885 0.898709711 0.645260119 0.902836936 0.677883909 0.804275843 0.85734187 1.112566044 0.979638247 1 20.83327608 1.929045913 4.084034936 1.037264825 0.779814987 0.617616158 0.087765339 0.131868666 4.0251043 0.037854946 0.021987024 84.92702531 -1.929045913 -0.257449838 CDLEDER ddPTM_SK-BR-3_Trastuzumab_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 ; 117.16 0.012315 232650000 1059310 1077660 642420 993360 922250 792200 927590 755390 588390 FALSE TRUE 1009238.516 1187474.779 671875.5924 893505.5655 1083090.108 764765.9154 786069.1091 689244.047 679634.5161 1.484972425 1.747225532 0.988583682 1.314685385 1.593636112 1.125260559 1.156605632 1.014139263 1 19.3743996 3.01942619 0.314276231 0.951968637 1.742760582 0.396781623 0.205823517 2.326971457 0.414807737 0.254836314 0.658087537 1045.745947 -3.01942619 0.790791945 CDNFTSSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 173.37 0.00012908 1222700000 841810 709400 604750 701970 688200 694280 826140 671490 643350 FALSE TRUE 802019.3096 781688.6665 632478.3857 631406.6419 808221.8621 670236.9095 700097.1699 612690.7758 743117.4322 1.079263216 1.051904629 0.85111499 0.849672763 1.087609881 0.901925968 0.942108393 0.824487153 1 19.50323069 3.848696734 6.484372533 0.923924266 1.068530041 0.371049153 0.077676894 0.223508159 11.48055653 0.018827693 0.034262737 7058.245074 -3.848696734 0.144605775 CDRVDQLTAQLADLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CDRVDQLTAQLADLAAR 17 1 P18206;P18206-2 P18206 VCL Vinculin 0 ;; 216.17 4.90E-15 314706000 282162 237495 196346 299237 180992 222558 297549 248796 226854 FALSE TRUE 268824.7615 261696.0105 205348.6583 269157.1282 212556.9475 214850.7607 252152.4352 227010.1033 262033.3597 1.025918081 0.998712572 0.783673722 1.027186495 0.811182774 0.819936671 0.962291349 0.866340467 1 17.99939097 3.967017842 23.77204644 0.895293662 1.015716048 0.265992199 0.080968117 359.3033374 258969.9384 0.018609996 0.033561906 9268.679019 -3.967017842 0.120422386 CDVDIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 92.925 0.024552 78102070000 72387900 50748800 65026400 63966100 45202600 68169700 82885300 71497600 57361400 FALSE TRUE 68966267.43 55920160.42 68007924.76 57536106.1 53085919.13 65808966.2 70239625.19 65236891.11 66256712.95 1.040894792 0.843992373 1.026430708 0.868381535 0.801215707 0.993242243 1.060113339 0.984608022 1 25.9815633 2.016063854 24.99943736 1.022859259 0.918574248 0.273209792 0.075882725 286.4458724 445780.7915 0.027370786 0.020209036 103.7680973 -2.016063854 -0.104285011 CEAFGWHAIIVDGHSVEELCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 CEAFGWHAIIVDGHSVEELCK 21 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;;; 343.27 3.32E-81 833028000 2438521 2168643 1941122 2170238 1451994 1890470 2287926 2013723 640545 FALSE TRUE 2323256.945 2389630.187 2030124.364 1952081.553 1705221.294 1825002.55 1938860.868 1837390.739 739877.4471 3.140056443 3.22976487 2.743865719 2.638384993 2.304734791 2.466628165 2.620516243 2.483371734 1 19.4969268 -0.427261555 0.184293921 1.49E-18 3.453258189 0.881872161 0.208845935 5.098577937 0.271615465 4.190794031 0.936996641 0.373885347 0.427261555 3.453258189 CEDKFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CEDKFTK 7 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 78.334 0.032482 371990000 828360 671720 766360 925260 557970 889370 891200 952880 639770 FALSE TRUE 789205.0645 740169.0317 801498.364 832251.1069 655279.7913 858570.8939 755231.072 869440.7757 738982.2641 1.067962119 1.001605949 1.084597565 1.126212559 0.886732772 1.161828823 1.021988089 1.176538082 1 19.49518021 CEFEEVQGFLDQVAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CEFEEVQGFLDQVAHK 16 0 E9PI14;Q9NX20 E9PI14 MRPL16 "39S ribosomal protein L16, mitochondrial" 0 ; 144.97 1.26E-06 48382000 82772 69327 70084 73874 63055 59250 67077 65225 62968 FALSE TRUE 78859.5316 76391.50012 73297.42072 66448.04517 74051.77204 57198.15764 56843.1717 59513.55322 72732.75584 1.084236816 1.050303941 1.007763557 0.913591743 1.018135105 0.786415377 0.781534689 0.818249667 1 16.15031762 2.906578941 0.964621036 0.827856721 1.070833246 0.501412884 0.078589368 0.34739488 0.701219815 0.0384192 0.042613731 806.4527757 -2.906578941 0.242976525 CEFQDAYVLLSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CEFQDAYVLLSEK 13 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 198.57 2.90E-07 169288000 655421 569896 515940 548067 415501 455878 569092 599911 434998 FALSE TRUE 624440.5482 627969.0503 539596.3593 492974.2639 487964.2428 440090.8306 482266.5633 547379.6125 502455.2682 1.242778388 1.249800908 1.073919199 0.98113065 0.971159571 0.875880617 0.959819896 1.089409639 1 18.93863564 3.555179543 2.300432418 0.967895901 1.250955263 0.809305252 0.052707494 0.107168317 1.116416844 0.015117171 0.025466311 3590.70348 -3.555179543 0.283059362 CEFQDAYVLLSEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CEFQDAYVLLSEKK 14 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 171.46 4.83E-06 1046550000 1533730 831910 1422450 1197440 931360 1249580 1648030 1573440 1100480 FALSE TRUE 1461233.622 916682.5748 1487670.739 1077071.056 1093788.889 1206306.731 1396592.755 1435661.252 1271136.818 1.149548657 0.721151777 1.170346668 0.847328974 0.86048085 0.948998341 1.098695857 1.129430941 1 20.27768789 1.760458195 5.896715264 1.084805224 0.93933861 0.155021953 0.137166812 0.270873377 23.574975 0.062332978 0.033404284 57.60473653 -1.760458195 -0.145466614 CEGFELHFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CEGFELHFWR 10 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 173.24 3.47E-06 662230000 1374560 1078635 1023611 1178840 2424060 921447 1447860 1103640 1625699 FALSE TRUE 1309587.273 1188549.133 1070544.577 1060340.764 2846815.297 889537.0593 1226962.365 1006999.431 1877804.098 0.697403565 0.632946288 0.570104506 0.564670598 1.516034234 0.473711321 0.653402752 0.53626437 1 20.84061513 CEGINISGNFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CEGINISGNFYR 12 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ;; 236.69 1.02E-15 338450000 428681 414409 334680 418896 282706 386560 421178 395900 273449 FALSE TRUE 408418.0987 456637.7482 350025.409 376787.7782 332009.8369 373173.3303 356919.5606 361232.8972 315854.0743 1.29305946 1.445723786 1.108187095 1.192917264 1.051149451 1.181473853 1.13001411 1.143670215 1 18.26889866 3.729985003 24.99905405 1.125521097 1.369391624 0.707216973 0.067710902 268.8836833 783831.7407 0.015961798 0.025162252 5370.132517 -3.729985003 0.243870527 CELLYEGPPDDEAAMGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CELLYEGPPDDEAAMGIK 18 0 P13639 P13639 EEF2 Elongation factor 2 0 81.431 0.010759 0 24962 26922 23271 27353 18740 26504 29796 28444 55640 FALSE TRUE 23782.09573 29665.38241 24337.99837 24603.42447 22008.25007 25586.15983 25250.07296 25953.29257 64268.36703 0.370043566 0.461586061 0.378693275 0.38282324 0.342442964 0.39811436 0.392884931 0.403826856 1 15.9718212 0.206026213 2.203951861 1.000008277 0.393562306 0.975845894 0.030098875 5.60240582 15.19916654 0.02952328 0.00799381 1.607038246 -0.206026213 -0.606445971 CESAPGCGVWQRPVIDNPNYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CESAPGCGVWQRPVIDNPNYK 21 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 172.57 4.95E-12 262040000 417700 318978 377576 533560 401030 452497 537060 429730 360176 FALSE TRUE 397956.1488 351482.2208 394888.2331 479925.5351 470969.505 436826.9154 455121.6332 392100.5631 416030.2546 0.95655579 0.844847741 0.949181529 1.153583255 1.132055902 1.049988338 1.093962827 0.942480886 1 18.66632892 3.413049185 6.401406974 1.070300813 0.899989309 0.523676606 0.06609134 0.131676042 10.06248156 0.017415624 0.023739144 2588.506052 -3.413049185 -0.170311504 CETS(ph)PPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CETSPPSSPR 10 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;O75335;H0YD72;B1APN9;M0QZB5;O75335-1;O75335-2 Q13136-2 PPFIA1;PPFIA4 Liprin-alpha-1;Liprin-alpha-4 2 CET(0.446)S(0.554)PPS(0.5)S(0.5)PR 75.695 0.05588 102850000 136530 113230 133150 139240 131070 130420 142920 119250 133590 TRUE FALSE 130076.4975 124768.2657 139255.0592 125243.3307 153928.5665 125903.5227 121114.9291 108807.8378 154306.4549 0.842975088 0.808574507 0.90245777 0.811653218 0.997551052 0.815931665 0.784898656 0.705141194 1 17.23543889 -0.581287904 7.319792556 0.999982774 0.83380637 0.32111886 0.076013893 0 0 0.070417386 0.016597537 0.262247947 0.581287904 -0.166176404 CFLAQPVTLLDIYTHWQQTSELGR ddPTM_SK-BR-3_Trastuzumab_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 ; 278.19 4.09E-52 352240000 480730 386460 403120 463710 395680 409000 554070 479290 381710 FALSE TRUE 458006.8456 425840.7134 421603.4507 417096.9898 464686.4667 394836.2274 469536.4453 437320.8267 440903.6373 1.038791262 0.965836245 0.95622584 0.946004874 1.053941105 0.895515922 1.064941193 0.991873937 1 18.75010385 1.674766609 24.97910692 1.021718223 0.98067037 0.142369841 0.048588785 0.598191557 228.4113467 0.020432523 0.011330784 47.28970544 -1.674766609 -0.041047853 CFSEENHEPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CFSEENHEPLR 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 174.23 1.13E-05 988040000 784360 656630 625650 813660 648390 722730 844660 796120 625280 FALSE TRUE 747284.8573 723541.3435 654336.6714 731869.3509 761469.0107 697701.6789 715791.6038 726407.5123 722245.2289 1.03466915 1.001794563 0.905975762 1.013325283 1.054308122 0.966017706 0.991064496 1.005762978 1 19.46212924 4.281253661 3.474839112 0.990248037 1.029425818 0.111219076 0.037656378 0.466356504 11.62662769 0.009239556 0.027879346 19109.69083 -4.281253661 0.039177781 CGAQDKEHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGAQDKEHPR 10 1 Q96GX9 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 0 115.18 0.00075569 46548000 125410 93477 99736 113180 66119 106140 127920 108810 69449 FALSE TRUE 119482.1178 103002.4126 104308.9943 101802.9314 77650.13267 102464.3452 108403.4546 99282.01956 80218.79622 1.48945289 1.284018427 1.300306152 1.269065807 0.967979281 1.27731093 1.351347311 1.237640357 1 16.2916527 4.614486923 0.852047072 1.211891221 1.613435087 0.365742001 0.122807049 2.287145059 1.459747154 0.042228388 0.832766029 41161.09534 -4.614486923 0.401543865 CGCLDEDTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGCLDEDTQR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 142.56 0.011283 0 89610 73389 82759 103710 82342 80383 98381 92294 89225 FALSE TRUE 85374.31289 80867.42254 86553.58201 93284.87376 96702.41873 77599.31655 83371.17156 84212.24808 103061.5573 0.828381747 0.784651665 0.839824123 0.905137436 0.938297667 0.752941432 0.808945389 0.817106303 1 16.65314677 -2.35075334 2.213932537 2.017689839 0.829766959 0.481176701 0.053845532 4548868.584 593981.1703 23131164.68 0.013844246 0.004459094 2.35075334 -1.18792288 CGDLEEELKNVTNNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGDLEEELKNVTNNLK 16 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 77.192 0.0072744 0 37251 29786 31465 39011 26621 38906 43647 39055 30966 FALSE TRUE 35490.21905 32821.22726 32907.70137 35089.54016 31263.69397 37558.67546 36987.84852 35635.13716 35768.04913 0.992232451 0.917613011 0.920030647 0.981030306 0.874067631 1.050062175 1.034103045 0.996284059 1 15.12638381 2.219838952 24.99999932 1.025116909 0.940603943 0.561836542 0.03627663 167.6499592 223870.1606 0.012659866 0.009365704 165.8971602 -2.219838952 -0.084512966 CGEDDETIPSEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGEDDETIPSEYR 13 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RAA8;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 159.83 2.38E-06 0 78700 73116 74105 83636 62154 78547 94780 69478 64820 FALSE TRUE 74980.00697 80566.60353 77502.78755 75228.75038 72993.63792 75826.89769 80319.57025 63394.13799 74871.95455 1.001443163 1.076058506 1.035137763 1.004765414 0.974912948 1.01275435 1.072759096 0.846700722 1 16.1921378 1.24958772 24.99998993 0.923350331 1.028363808 0.441412573 0.047637788 157.3311335 356696.9949 0.030025215 0.010737063 17.76592071 -1.24958772 0.105013478 CGESGHLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 90.629 0.011301 122630000 205910 199670 177960 224440 137890 198490 216010 223710 152010 FALSE TRUE 196177.0424 220016.6 186119.642 201878.8648 161937.9723 191616.2415 183053.7072 204120.7664 175582.9344 1.117289918 1.253063692 1.060009862 1.149763589 0.922287652 1.091314723 1.042548399 1.162531923 1 17.42179311 3.716990541 24.13559662 1.061567783 1.185176799 0.316486182 0.0757394 489.0000645 547160.9173 0.01843645 0.028593734 5211.833593 -3.716990541 0.123609015 CGESGHLAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 168.74 5.90E-05 1001630000 1658590 1427220 1475460 1733170 1269260 1505400 1802260 1668650 1285780 FALSE TRUE 1580191.738 1572655.341 1543111.3 1558948.459 1490618.542 1453267.621 1527292.136 1522534.16 1485172.196 1.063978805 1.058904378 1.039011709 1.049675225 1.003667148 0.978517929 1.028360308 1.025156655 1 20.50219878 2.788087337 4.908439947 1.008052874 1.054885313 0.696100737 0.015008472 0.122217707 6.709482464 0.004864762 0.005091451 613.8854455 -2.788087337 0.046832438 CGETGHVAINCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 94.551 0.005103 147340000 369496 380250 301832 394240 200418 349205 382940 403560 243143 FALSE TRUE 352030.6564 418997.9073 315671.2958 354610.2462 235370.8357 337111.9433 324515.4698 368222.147 280848.3746 1.253454491 1.491900773 1.123991891 1.262639482 0.838070849 1.200334322 1.155482813 1.311106562 1 18.09943193 3.720707258 24.14788604 1.133261385 1.372677625 0.333274191 0.144056499 501.188358 677891.4436 0.035761414 0.055547758 5256.628167 -3.720707258 0.23941624 CGGVEQASSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CGGVEQASSSPR 12 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 CGGVEQASS(0.024)S(0.975)PR;CGGVEQASS(0.068)S(0.932)PR;CGGVEQASS(0.022)S(0.978)PR;CGGVEQAS(0.002)S(0.25)S(0.748)PR 142.1 6.41E-05 756254000 1376150 1154800 1324770 1492430 1027290 1360300 1496130 1353720 1113810 TRUE FALSE 1311102.117 1272475.433 1385512.015 1342408.101 1206449.051 1313192.47 1267867.89 1235181.1 1286533.966 1.019096387 0.989072552 1.076933879 1.043429972 0.937751418 1.020721181 0.985491191 0.960084329 1 20.29505812 2.767045878 24.99675307 0.983719659 1.025996816 0.39642526 0.030945342 896.1435771 786394.2009 0.009435381 0.01000629 584.8518631 -2.767045878 0.042277157 CGHTNNLRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 CGHTNNLRPK 10 1 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ;;;;; 175.65 1.65E-06 2007693000 2504109 2315315 2117602 2722671 1832333 2637838 3030515 2452538 1377911 FALSE TRUE 2385744.73 2551248.231 2214696.146 2448982.938 2151891.295 2546489.009 2568154.278 2237780.771 1591590.4 1.498969037 1.602955277 1.391498809 1.538701752 1.352038373 1.599965046 1.613577386 1.406002933 1 20.60203767 0.913652451 6.310917329 1.000008742 1.521528167 0.774357934 0.086744066 0.461191211 33.37137006 0.081034445 0.020356395 8.196953122 -0.913652451 0.521519425 CGIIHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGIIHVR 7 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 69.432 0.081525 0 357890 343070 362190 441750 355340 366330 402580 391410 197520 FALSE TRUE 340973.249 378029.223 378796.7698 397344.4507 417311.1835 353643.9002 341159.0271 357136.0654 228150.3928 1.4945109 1.656929968 1.660294182 1.741590036 1.829105698 1.550047299 1.49532518 1.565353717 1 17.79962561 0.35662248 0.764789912 0.991983146 1.649344434 0.804428115 0.098534851 1.045841109 0.853749131 0.122752145 0.036178952 2.273120611 -0.35662248 0.657361287 CGLGQENS(ph)DNEHLVENEVSLLLEESDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(1)DNEHLVENEVSLLLEESDLR 144.55 6.57E-08 96866000 101513 92358 91079 106682 95333 108346 110648 96913 87646 TRUE FALSE 96714.68167 101769.3852 95255.06224 95958.12268 111959.045 104593.9509 93766.61541 88426.78395 101237.694 0.955322843 1.005251909 0.940905096 0.947849747 1.105902758 1.033152245 0.9262026 0.873457113 1 16.62738703 CGQEEHDVLLSNEEDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CGQEEHDVLLSNEEDRK 17 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 172.97 9.97E-10 1227040000 1505970 1266630 1314690 1586270 841470 1473600 1560240 1506830 796150 FALSE TRUE 1434785.783 1395701.037 1374969.837 1426815.126 988222.1016 1422568.863 1322196.732 1374883.977 919612.8758 1.560206278 1.517704975 1.495161576 1.551538874 1.074606639 1.546921427 1.437775358 1.495068211 1 19.81066714 -3.291054856 0.234893234 4.69E-15 1.526076161 0.509425185 0.141779796 54.55235935 1.120315714 27.15032088 0.229139786 0.000511617 3.291054856 1.526076161 CGS(ph)GPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGS(0.333)GPVHIS(0.333)GQHLVAVEEDAES(0.333)EDEEEEDVKLLSISGK;CGS(0.382)GPVHIS(0.34)GQHLVAVEEDAES(0.278)EDEEEEDVKLLSISGK;CGS(0.376)GPVHIS(0.341)GQHLVAVEEDAES(0.283)EDEEEEDVKLLSISGK 88.744 0.0002864 569596000 189122 112326 185683 177890 180186 162522 246560 205486 70811 TRUE FALSE 180182.5779 123772.1471 194196.7492 160008.1592 211610.3814 156893.8224 208942.7436 187492.5565 81792.00823 2.202936225 1.513254776 2.374275353 1.956281093 2.587176742 1.918204795 2.554561847 2.292308999 1 16.31967227 3.720438374 24.98335945 2.186753691 1.85809544 0.015594977 0.484582132 1783.980456 2459399.42 0.112658375 0.174915126 5253.374649 -3.720438374 -0.328658251 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 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(0.028)GPVHIS(0.027)GQHLVAVEEDAES(0.945)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGS(0.063)GPVHIS(0.063)GQHLVAVEEDAES(0.874)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.013)GPVHIS(0.012)GQHLVAVEEDAES(0.976)EDEEEEDVK;CGS(0.019)GPVHIS(0.019)GQHLVAVEEDAES(0.961)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.997)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.997)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 354.77 2.01E-120 24891977000 4821736 4468523 4073648 5565895 3637999.4 5012581 5412181 5695105 1850011 TRUE FALSE 4593822.095 4923870.574 4260428.79 5006400.66 4272465.344 4838994.063 4586453.387 5196411.415 2136901.257 2.149758712 2.304210621 1.993741534 2.342832006 1.999374248 2.264491186 2.146310397 2.431750834 1 21.02708881 -0.623743787 6.560151469 0.999999999 2.200222735 0.87903814 0.140362364 3.44E-09 5.25E-10 0.115501769 0.027224028 0.237824292 0.623743787 1.200222736 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGS(0.171)GPVHIS(0.137)GQHLVAVEEDAES(0.692)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.147)GPVHIS(0.147)GQHLVAVEEDAES(0.706)EDEEEEDVKLLS(0.001)ISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.002)GPVHIS(0.001)GQHLVAVEEDAES(0.997)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(0.999)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(0.997)EDEEEEDVKLLS(0.002)IS(0.001)GK;CGS(0.027)GPVHIS(0.027)GQHLVAVEEDAES(0.945)EDEEEEDVKLLS(0.001)ISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.006)GPVHIS(0.006)GQHLVAVEEDAES(0.975)EDEEEEDVKLLS(0.013)IS(0.001)GK;CGSGPVHISGQHLVAVEEDAES(0.999)EDEEEEDVKLLS(0.001)ISGK;CGSGPVHISGQHLVAVEEDAES(0.997)EDEEEEDVKLLS(0.002)ISGK 430.06 6.03E-221 9457877000 2670725 1499198 2423013 2424476 2288098 2371333 3726475 3114873 1323381 TRUE FALSE 2544485.122 1651967.981 2534110.543 2180763.066 2687141.567 2289213.144 3157932.797 2842118.207 1528604.167 1.664580784 1.08070357 1.657793821 1.426636872 1.757905431 1.497584001 2.065893098 1.859289847 1 20.54378344 2.89714034 1.472043691 1.730011871 1.398664892 0.014147744 0.32597789 0.696615985 3.075106225 0.117411022 0.128360214 789.1150743 -2.89714034 -0.331346979 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGKR 39 2 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(0.805)EDEEEEDVKLLS(0.092)IS(0.103)GKR;CGSGPVHISGQHLVAVEEDAES(0.575)EDEEEEDVKLLS(0.212)IS(0.212)GKR;CGSGPVHISGQHLVAVEEDAES(0.656)EDEEEEDVKLLS(0.172)IS(0.172)GKR 68.108 0.0018383 714490000 74688 40927 64076 57830 65681 65757 125924 98002 68001 TRUE FALSE 71157.64626 45097.50783 67013.94798 52016.81853 77135.7456 63479.8186 106711.981 89420.42534 78546.24778 0.905933107 0.574152287 0.853178221 0.662244474 0.982042399 0.808183973 1.35858789 1.138442992 1 16.26125474 1.755959917 25 1.193317648 0.784191799 0.589924362 0.143753453 3.935906892 5661.357531 0.061772611 0.034256214 57.01116511 -1.755959917 -0.409125849 CGYAGSNFPEHIFPALVGRPIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CGYAGSNFPEHIFPALVGRPIIR 23 1 P61160;P61160-2;A0A1B0GWD0;A0A1B0GWH0 P61160 ACTR2 Actin-related protein 2 0 141.47 1.10E-07 135580000 59777 50454 61497 61830 52489 63528 73710 69860 57245 FALSE TRUE 56951.45968 55595.31996 64316.69828 55614.73093 61643.06498 61328.00943 62464.18572 63742.68805 66122.26223 0.861305372 0.840795794 0.972693554 0.841089356 0.932258863 0.92749412 0.944677082 0.964012511 1 16.01284846 2.907677147 0.227150692 1.017128514 0.79382252 0.5569527 0.037041631 2.990784339 0.318532889 0.075765722 0.205279919 808.494644 -2.907677147 -0.223305995 CHDCS(ph)QPCPWPMIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CHDCSQPCPWPMIEK 15 0 O75509 O75509 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 1 CHDCS(1)QPCPWPMIEK;CHDCS(1)QPCPWPMIEK 73.464 0.02428 956960000 1091790 1074717 1169880 1232850 1155180 1107700 1305100 1026720 1409040 TRUE FALSE 1040183.25 1184231.884 1223520.155 1108921.576 1356643.026 1069340.071 1105983.025 936814.9538 1627546.727 0.639111144 0.727617748 0.751757314 0.681345462 0.833550892 0.657025727 0.679539952 0.575599421 1 20.63426753 -1.509349415 3.581676425 1.005315871 0.695798907 0.661660853 0.068926229 8140.32529 30943982.56 185581.4727 0.015172033 0.030949282 1.509349415 -0.309516964 CHELSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CHELSPR 7 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ; 146.21 0.0022347 336040000 485200 424550 464330 470900 461220 497880 648460 490700 284270 FALSE TRUE 462265.5576 467812.1277 485619.9898 423564.2373 541656.622 480638.2908 549525.5172 447731.7066 328353.1398 1.407830478 1.424722566 1.478956437 1.289965546 1.649616088 1.463784665 1.673580821 1.363567612 1 18.32488872 0.97991122 24.09329865 0.999999993 1.482850987 0.652727047 0.110944903 584.2367519 700700.4516 0.105874936 0.026468734 9.547973822 -0.97991122 0.482850994 CHQPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CHQPLAR 7 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 63.148 0.081181 38219000 35134 37681 36195 44027 38680 37706 48218 40087 27153 FALSE TRUE 33473.28545 41520.73674 37854.57655 39601.32231 45425.77975 36400.23177 40861.45852 36576.76977 31363.74856 1.067260356 1.323844841 1.206953196 1.262646339 1.448353014 1.160582948 1.302824451 1.166211676 1 14.93681038 -0.4639191 6.989560911 1 1.245499272 0.348073368 0.104147376 0 0 0.093168676 0.021960067 0.343621952 0.4639191 0.245499272 CHTPPLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CHTPPLYR 8 0 Q02543;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 63.565 0.072507 314960000 156200 153410 152560 182340 124550 185020 193810 147340 87395 FALSE TRUE 148816.7356 169042.6534 159555.0269 164010.8368 146271.4806 178612.711 164240.7249 134438.1285 100947.7702 1.47419537 1.674555594 1.580570096 1.624709851 1.448981787 1.769357665 1.626987149 1.331759267 1 16.62324952 0.984510655 3.2129759 1.001936046 1.60308484 0.82046433 0.091822528 0.087570866 2.268781002 0.083294847 0.021760203 9.649629865 -0.984510655 0.601148795 CHWTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CHWTQR 6 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 103.71 0.034451 44370000 52322 67361 55213 70407 56286 59576 66657 51710 45226 FALSE TRUE 49848.84275 74225.16248 57744.57066 63329.5546 66102.26058 57512.86818 56487.25041 47181.99827 52239.4171 0.954238112 1.42086506 1.105383135 1.212294434 1.265371328 1.10094774 1.081314715 0.903187686 1 15.67285118 1.622917321 1.877086872 0.956417029 1.195669001 0.362271694 0.122269665 0.322207773 2.359356911 0.090062289 0.032972102 41.967908 -1.622917321 0.239251973 CIACQAAKLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CIACQAAKLSPR 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 CIACQAAKLS(1)PR;CIACQAAKLS(1)PR;CIACQAAKLS(1)PR 130.72 0.00012809 737630000 913340 817360 915190 890960 723430 948540 1153490 1135480 1067560 TRUE FALSE 870168.2283 900649.9133 957152.3667 801399.0081 849595.963 915691.822 977503.9152 1036051.352 1233111.752 0.705668587 0.730387908 0.77620894 0.649899741 0.688985375 0.742586242 0.792713161 0.840192586 1 20.23387212 0.996263266 1.027589414 0.998053141 0.712854346 0.884156697 0.033237293 0.176636371 0.394308882 0.031181128 0.010259446 9.914327612 -0.996263266 -0.285198795 CIDHYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CIDHYTK 7 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 90.777 0.01689 425240000 902450 858610 848820 1009450 703070 940940 1057670 988780 758020 FALSE TRUE 859792.977 946103.3352 887739.2366 907978.1682 825685.1854 908355.0119 896303.0161 902197.1813 875569.8702 0.981981 1.080557209 1.013898795 1.037013948 0.943026038 1.037444347 1.023679602 1.030411406 1 19.73986278 CIESLIAVFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CIESLIAVFQK 11 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 253.98 4.67E-20 200571000 985490 766390 798840 887560 746990 822150 1073950 929050 832690 FALSE TRUE 938907.8408 844486.0123 835467.6042 798340.7825 877264.8195 793678.7394 910099.2031 847697.4568 961819.3124 0.976179027 0.878009 0.868632594 0.830031974 0.912089005 0.825184865 0.946226793 0.881347927 1 19.87540637 -1.012497545 4.94072782 1.000001412 0.893155179 0.353000883 0.0467175 7.03E-07 1.40E-07 0.043748052 0.010311378 0.097163344 1.012497545 -0.106846232 CIIKHPNGTQETILLNHTFNETQIEWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CIIKHPNGTQETILLNHTFNETQIEWFR 28 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 138.78 1.04E-06 410920000 125140 61311 112780 88562 137420 85865 128880 105130 112390 FALSE TRUE 119224.8802 67558.6606 117951.0746 79659.5795 161386.0045 82891.47352 109216.989 95924.25987 129818.8672 0.918394088 0.520407103 0.908581912 0.613620972 1.243162939 0.638516383 0.841302896 0.738908465 1 16.98614055 CIIPNHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 138.78 0.00069046 1788660000 3397830 3141520 2954160 3730300 2326290 3320260 3666750 3468270 2412760 FALSE TRUE 3237221.31 3461644.46 3089611.158 3355323.157 2731994.239 3205278.564 3107319.943 3164569.892 2786918.498 1.161577316 1.242104662 1.108611953 1.203954532 0.980292119 1.150115644 1.114966206 1.135508589 1 21.41023938 7.895564055 0.018512113 1.29E-06 2.5545594 0.352500444 0.065082327 3414.165978 4.956323635 260.4154525 446.6261569 78625614.95 -7.895564055 2.554558109 CIIPNHEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CIIPNHEKK 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 120.12 0.00046525 634580000 1893280 1424900 1652030 1770760 1182610 1984380 2200100 2188200 1404020 FALSE TRUE 1803788.407 1570098.93 1727777.21 1592759.841 1388856.81 1915660.423 1864434.337 1996589.608 1621748.251 1.112249331 0.968152072 1.065379419 0.982125209 0.856394825 1.181231687 1.149644735 1.231134121 1 20.62911845 2.197844093 24.9991354 1.15362581 1.005879813 0.391459918 0.0879233 144.1848197 88525.76872 0.030758952 0.022717223 157.7045027 -2.197844093 -0.147745997 CIIVEEGKEILVGDVGVTITDPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CIIVEEGKEILVGDVGVTITDPFK 24 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 258.46 5.63E-44 1441273000 1703470 1272290 1574460 1741120 1057185 1837770 2152270 1909080 1240720 FALSE TRUE 1622950.349 1401937.797 1646650.548 1566099.31 1241557.729 1774127.564 1823901.682 1741910.835 1433124.521 1.132455921 0.978238651 1.148993353 1.092786626 0.866329276 1.237943764 1.272674953 1.215463701 1 20.45073254 2.165368701 24.99999994 1.212780214 1.049889547 0.262796775 0.108939821 44.03753011 15040.53367 0.037336253 0.027574656 146.341904 -2.165368701 -0.162890667 CIIVEEGKEILVGDVGVTITDPFKHFVGMLPEKDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CIIVEEGKEILVGDVGVTITDPFKHFVGMLPEKDCR 36 3 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 145.16 2.57E-13 70352000 40726 12514 57822 22183 59116 42653 113520 56614 88314 FALSE TRUE 38800.96269 13789.19083 60473.19589 19953.1227 69425.81168 41175.91591 96200.43906 51656.57803 102009.2841 0.380366974 0.135175842 0.592820511 0.195601046 0.680583266 0.40364871 0.943055722 0.506390948 1 16.63834094 1.966932186 0.458639647 0.971820696 0.236730394 0.512769245 0.198011362 0.65523795 0.322129681 0.181289359 0.152097383 92.66851125 -1.966932186 -0.735090303 CILQDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CILQDGR 7 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 ; 108.09 0.017056 214296000 1038100 798410 814910 985800 974000 830820 1227910 999690 1124310 FALSE TRUE 989031.0703 879768.8867 852274.4296 886705.5111 1143865.292 802048.4951 1040569.777 912151.8439 1298662.253 0.761576821 0.67744241 0.656271042 0.682783772 0.880802756 0.61759591 0.801262819 0.702378037 1 20.30859484 -5 0.295340351 3.244354782 0.707605532 0.567442972 0.076144859 177.3579652 1.654304261 245.7516829 0.070020746 1.00E-05 5 -2.53674925 CKDDEFTHLYTLIVRPDNTYEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CKDDEFTHLYTLIVRPDNTYEVK 23 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 275.15 6.11E-52 695680000 1263500 992000 1062600 1309400 647270 1231700 1336400 1286400 575750 FALSE TRUE 1203776.859 1093085.928 1111321.261 1177776.624 760153.6831 1189045.92 1132507.635 1173755.996 665034.3695 1.810097213 1.643653288 1.671073424 1.771001137 1.14302917 1.78794657 1.702930987 1.764955392 1 19.34306938 -1.630216701 2.904743937 0.943893124 1.665543526 0.539827571 0.192010168 35911050.42 37035711.66 15244974.71 0.042622998 0.023430594 1.630216701 0.721650402 CKDGVVFGVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CKDGVVFGVEK 11 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 85.457 0.013864 240370000 800890 756490 583670 722190 549250 711280 757770 787690 525680 FALSE TRUE 763033.5169 833577.1911 610431.8468 649594.0891 645039.0261 686648.1953 642158.2691 718715.6878 607199.7696 1.256643291 1.372821982 1.005322922 1.069819393 1.06231764 1.130843965 1.057573308 1.183656061 1 19.21181172 3.740542242 24.99996133 1.07695908 1.314732644 0.73531901 0.060306792 73.02962759 921327.3352 0.014329338 0.024294666 5502.274362 -3.740542242 0.237773565 CKELGITALHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CKELGITALHIK 12 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 121.24 0.0002282 1247330000 1690700 1143320 1360950 1407880 1196270 1495630 2116180 1883590 1378590 FALSE TRUE 1610783.962 1259825.608 1423350.904 1266357.228 1404899.109 1443835.958 1793317.875 1718652.874 1592374.696 1.011560888 0.791161534 0.893854259 0.795263345 0.882266663 0.906718727 1.126190889 1.079301799 1 20.60274842 1.83358622 5.119190673 1.077446364 0.875076486 0.633725412 0.067630375 0.130000571 5.052877605 0.030307083 0.017456547 68.16888964 -1.83358622 -0.202369878 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 36 3 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 210.48 6.67E-31 368900000 529980 371990 394590 553240 287630 479090 602250 600760 292670 FALSE TRUE 504928.8957 409896.2039 412682.3418 497627.2641 337792.5809 462498.9932 510365.7014 548154.2696 338055.7688 1.493626029 1.212510602 1.220752254 1.472027133 0.999221466 1.368114482 1.5097086 1.621490654 1 18.36690174 2.003426902 24.99956476 1.435003449 1.286638002 0.024160521 0.210619082 228.3604407 1665896.829 0.071938631 0.052878146 100.7921948 -2.003426902 -0.148365447 CKHFELGGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CKHFELGGDK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;R4GN19;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 106.01 0.0014863 317830000 573360 456890 422390 535630 322300 562720 704190 605360 310290 FALSE TRUE 546258.4091 503447.6104 441756.9993 481787.4548 378509.018 543232.8653 596752.8822 552351.4692 358408.1885 1.524123685 1.404676641 1.232552753 1.34424232 1.056083622 1.515682071 1.665009063 1.541124023 1 18.45124407 CLAFHDISPQAPTHFLVIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLAFHDISPQAPTHFLVIPK 20 0 P49773;D6REP8;D6RE99;D6RD60 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 204.29 5.65E-22 971120000 2172660 1609420 1828740 2211700 1528770 2080350 2496300 2323000 981910 FALSE TRUE 2069962.668 1773421.728 1912589.538 1989375.714 1795387.004 2008306.958 2115443.587 2119585.805 1134179.588 1.825074873 1.563616333 1.686319837 1.754021793 1.582982998 1.770713368 1.865175154 1.868827325 1 20.11321767 -0.792354417 6.488969109 0.999999989 1.734264621 0.830034954 0.105153707 1.74E-08 3.17E-09 0.10606306 0.024999303 0.161304165 0.792354417 0.734264631 CLAGYYGDPIIGSGDHCRPCPCPDGPDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLAGYYGDPIIGSGDHCRPCPCPDGPDSGR 30 1 P07942;G3XAI2 P07942 LAMB1 Laminin subunit beta-1 0 ; 165.87 1.76E-12 162192000 117794 89532 110180 118196 105445 117384 141728 116822 119828 FALSE TRUE 112226.1111 98655.41259 115231.862 106314.7135 123834.5746 113318.9626 120104.7906 106592.4464 138410.3142 0.810821879 0.712775006 0.832538114 0.768112652 0.89469181 0.818717617 0.867744512 0.770119243 1 17.07859193 -4.999999999 0.134003063 1.653196876 0.73023493 0.570010294 0.051801426 92.05104396 0.769299114 16.10701492 0.32925597 1.00E-05 4.999999999 -0.922961946 CLATHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 94.401 0.033099 141053000 141107 119455 125011 138992 104104 123657 147030 133457 106965 FALSE TRUE 134437.1518 131627.6003 130742.878 125020.2601 122259.7046 119374.7271 124597.8731 121770.7976 123552.5859 1.088096625 1.065356903 1.058196209 1.011878944 0.989535781 0.966185582 1.008460262 0.985578705 1 16.91476568 3.245838513 1.814268615 0.989641845 1.07767224 0.907624982 0.011882493 0.086375966 0.586287781 0.003748674 0.005284559 1761.321001 -3.245838513 0.088030395 CLEELVFGDVENDEDALLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLEELVFGDVENDEDALLRR 20 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ; 82.007 0.0070775 11251400 12214.5 10407.5 10830.5 9445.8 10653.5 10878.1 15652.5 12363.9 15078.3 FALSE TRUE 11637.14479 11468.03608 11327.08914 8496.290238 12511.46703 10501.38867 13264.42365 11281.25137 17416.56575 0.668165295 0.658455648 0.650362953 0.487828103 0.718365905 0.602954039 0.761598115 0.647731104 1 14.08817256 -0.158361132 0.543609979 1.035498203 0.635104216 0.715499034 0.070063013 2.834585652 0.889465662 0.277268876 0.029055084 0.694446619 0.158361132 -0.400393987 CLELFSELAEDKENYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLELFSELAEDKENYK 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 210.09 9.64E-12 156360000 309100 360260 264910 389000 133810 325830 279350 338680 150860 FALSE TRUE 294489.4556 396970.9036 277056.3855 349896.9809 157146.4216 314546.4254 236730.0269 309023.3837 174254.5983 1.68999532 2.278108626 1.589951647 2.007964119 0.901820802 1.805096844 1.358529584 1.773401602 1 17.4108372 2.78521177 24.9878627 1.423361349 1.916796104 0.366879432 0.336785018 428.840679 229700.1187 0.092067963 0.097652552 609.8341917 -2.78521177 0.493434755 CLELFSELAEDKENYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLELFSELAEDKENYKK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 217.11 2.86E-15 3589100000 1518100 1463340 1371220 1682510 680340 1683940 1558340 1780040 707730 FALSE TRUE 1446342.422 1612456.01 1434091.793 1513380.898 798991.0806 1625624.736 1320586.612 1624170.261 817481.1538 1.769266991 1.972468726 1.754281168 1.851273135 0.977381652 1.98857763 1.615433709 1.986798415 1 19.64082595 CLFTLLGHLDYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLFTLLGHLDYIR 13 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 159.08 4.23E-05 117930000 183402 172014 96585 104595 158122 110259 190020 163766 114376 FALSE TRUE 174732.9509 189542.4222 101013.5178 94080.91188 185698.4267 106440.7032 161028.959 149425.7809 132112.8459 1.322603791 1.434700924 0.764600271 0.71212539 1.405604621 0.805680193 1.218874349 1.131046567 1 17.01141123 3.760116029 24.94009954 1.01873962 1.378652406 0.34285201 0.21420624 807.3686486 934140.6859 0.052452846 0.094447722 5755.936959 -3.760116029 0.359912787 CLHNFLTDGVPAEGAFTEDFQGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLHNFLTDGVPAEGAFTEDFQGLR 24 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 0 152.07 1.00E-07 32193000 34774 42062 33143 41367 26866 33848 34351 31322 25950 FALSE TRUE 33130.30194 46348.16562 34662.63933 37208.71057 31551.42189 32675.83527 29110.12405 28579.27963 29974.19347 1.105294192 1.546268982 1.156416081 1.241358191 1.052619545 1.09013226 0.971172889 0.95346284 1 14.87143331 2.734898486 1.15801828 0.983894947 1.314853036 0.530531538 0.118134809 0.32691747 0.90971054 0.055924073 0.051762329 543.1233649 -2.734898486 0.330958089 CLIKS(ph)PDRLADINYEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLIKSPDRLADINYEGR 17 2 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 CLIKS(1)PDRLADINYEGR 138.66 1.52E-06 96527000 215200 196850 227820 239390 162070 251290 287660 277950 210510 TRUE FALSE 205027.9225 216909.2388 238265.7723 215326.0624 190334.9567 242587.7643 243772.1838 253611.2245 243154.8157 0.843199103 0.892062278 0.97989329 0.885551297 0.782772721 0.997667941 1.002538992 1.043003092 1 17.89151564 2.104504922 8.951031356 1.011592444 0.880962718 0.643254914 0.049681006 0.17767146 13.84078487 0.018686447 0.013793646 127.2052166 -2.104504922 -0.130629726 CLKDEDPYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 97.734 0.0053416 576220000 2200780 1969890 1950370 2477000 1545340 2151410 2468200 2301500 1805230 FALSE TRUE 2096753.491 2170624.031 2039796.394 2228007.254 1814846.807 2076906.132 2091630.758 2099968.459 2085175.849 1.005552358 1.040978885 0.978237109 1.068498494 0.870356717 0.996034044 1.003095619 1.007094179 1 20.99173762 CLKDEDPYVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLKDEDPYVRK 11 2 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 48.741 0.09436 162710000 491400 370030 481880 493560 319420 518990 591460 598460 362640 FALSE TRUE 468172.4959 407736.4777 503974.6746 443946.4111 375126.7469 501017.2462 501221.9141 546055.6698 418876.3591 1.117686605 0.973405323 1.203158554 1.059850721 0.895554831 1.196098169 1.196586781 1.303620168 1 18.67616494 CLS(ph)PGGHPTYRPAYLLENEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 115.54 0.00034029 64271000 74475 62513 68763 80988 81598 69753 75421 71236 67198 TRUE FALSE 70954.71435 68883.14577 71915.85157 72846.93237 95828.66537 67337.43612 63914.14125 64998.19819 77618.72264 0.914144319 0.887455287 0.92652712 0.93852269 1.234607606 0.867541153 0.823437169 0.837403606 1 16.24411707 -0.877683377 4.003224791 1.000002373 0.923309262 0.034764351 0.114979353 4.34858E+11 8.70377E+11 15427247.42 0.027850041 0.13253074 0.877683377 -0.076693111 CLSSLKDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CLSSLKDER 9 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 87.258 0.012388 2459210000 9667900 7845500 7782100 9410600 6678000 8693500 10894500 9721700 7432300 FALSE TRUE 9210917.527 8644965.37 8138916.983 8464628.609 7842641.086 8392441.915 9232343.934 8870416.41 8584863.125 1.07292538 1.007000955 0.948054368 0.985994591 0.913542938 0.97758599 1.075421215 1.033262416 1 23.0333637 -0.675637668 7.544869113 0.999999351 1.00585392 0 0.050713032 0 0 0.052333933 0.012335226 0.211038811 0.675637668 0.005854569 CLTQSGIAGGYKPFNLETCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLTQSGIAGGYKPFNLETCR 20 1 C9J0K6;P30626-3;P30626-2;P30626;B4DHQ6 C9J0K6 SRI Sorcin 0 257.73 2.86E-36 257560000 247860 173190 171050 226860 171190 203340 257560 250490 239060 FALSE TRUE 236144.149 190838.2579 178892.8117 204055.6018 201045.4818 196298.2848 218264.4916 228555.7677 276132.2039 0.85518511 0.691111921 0.64785204 0.738977921 0.72807691 0.710885156 0.790434757 0.827704138 1 18.07499963 0.865936772 1.221602231 0.999023916 0.731419691 0.719257793 0.053237291 0.352155427 1.022410975 0.051637217 0.015894027 7.344069402 -0.865936772 -0.267604225 CLTTDEYDGHSTYPSHQYQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CLTTDEYDGHSTYPSHQYQ 19 0 P30043;M0R192;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;; 205.78 3.95E-16 1589270000 1185510 805480 989690 1256110 1259210 1062530 1502160 1238590 414780 FALSE TRUE 1129473.292 887559.3278 1035068.265 1129843.436 1478815.825 1025734.32 1272977.903 1130132.493 479101.964 2.357479987 1.85254788 2.160434194 2.358252567 3.086641125 2.140952024 2.657008317 2.358855898 1 18.8699732 3.268892105 4.607961508 2.398840125 2.093137623 0 0.547158582 0.556590177 27.45405741 0.137746561 0.182254143 1857.342964 -3.268892105 -0.305702502 CLVAGLLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CLVAGLLSPR 10 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 CLVAGLLS(1)PR;CLVAGLLS(1)PR 143.97 3.46E-05 45933000 116063 103362 97480 117843 113758 104608 130749 108651 122642 TRUE FALSE 110576.932 113894.7053 101949.5544 105997.1978 133597.3592 100985.3987 110800.8387 99136.94244 141660.695 0.780575953 0.803996517 0.71967425 0.748247054 0.943079936 0.712868158 0.782156537 0.699819681 1 17.11208 -1.721957383 3.028624916 1.032044919 0.777224737 0.516156572 0.068755044 18006789.87 23899294.29 4499725.327 0.015226642 0.018968921 1.721957383 -0.254820182 CLWEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CLWEESR 7 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;;; 154.09 0.0039591 1047450000 929157 889640 909490 966244 1108700 824287 1001550 912615 1164450 FALSE TRUE 885237.59 980295.3274 951191.0161 869115.3174 1302056.929 795741.7345 848745.1528 832701.5925 1345026.959 0.65815602 0.728829501 0.707191042 0.64616944 0.968052663 0.591617684 0.63102464 0.619096582 1 20.35920366 -1.154541285 3.676906912 1.000236675 0.69276707 0.454273418 0.105478085 20958129.49 37391577.89 59728.51066 0.023651178 0.070058158 1.154541285 -0.307469605 CLYASVLTAQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CLYASVLTAQPR 12 0 P13639 P13639 EEF2 Elongation factor 2 0 138.22 0.00058758 0 80870 66899 48216 72254 69368 65545 80833 73841 72457 FALSE TRUE 77047.43537 73716.08416 50426.75129 64990.89065 81465.75724 63275.16021 68500.44125 67375.09058 83693.2615 0.920593056 0.880788762 0.602518654 0.776536718 0.973384903 0.756036497 0.818470209 0.805024077 1 16.35282385 -1.207126167 4.029628757 1.000112575 0.822674488 0.245265875 0.100579468 12235680850 2407519244 13347127.35 0.023436558 0.062068869 1.207126167 -0.177438087 CMIDQAHQEERPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CMIDQAHQEERPIR 14 1 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ;; 128.95 4.25E-05 308682000 285721 285031 302951 330392 354314 266057 311890 290793 381930 FALSE TRUE 272215.5346 314075.983 316841.603 297180.3685 416106.2494 256843.3794 264305.4522 265329.6233 441157.7538 0.617048056 0.711935765 0.71820477 0.673637414 0.943214181 0.582203026 0.599117776 0.601439329 1 18.75093512 4.55813451 2.459073952 0.706535127 0.612335142 0.037552897 0.142007246 1.438054184 14.1537542 0.033455785 0.24197107 36152.18158 -4.55813451 -0.094199985 CNAEEHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CNAEEHVR 8 0 P11279-2;P11279 P11279-2 LAMP1 Lysosome-associated membrane glycoprotein 1 0 ;; 118.18 0.0019367 254792000 344852 313146 312585 411273 301243 312901 366218 394508 292726 FALSE TRUE 328551.5294 345055.9334 326917.3314 369931.0567 353779.6838 302065.1599 310344.718 359962.7881 338120.453 0.97169966 1.020511863 0.966866478 1.094080684 1.046312581 0.893365536 0.917852544 1.064599272 1 18.36717776 2.258381626 24.9989962 0.954911837 1.016558901 0.138492017 0.058326525 375.7433209 473900.2048 0.019867626 0.016601531 181.2932463 -2.258381626 0.061647064 CNEIINWLDKNQTAEKEEFEHQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CNEIINWLDKNQTAEKEEFEHQQK 24 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 304.49 9.66E-63 2817100000 1458500 994980 1137120 1623770 731280 1526110 1750470 1589870 658940 FALSE TRUE 1389559.595 1096369.593 1189258.077 1460545.555 858815.0005 1473260.428 1483403.652 1450652.554 761125.0498 1.825665304 1.440459217 1.562500245 1.91892982 1.128349409 1.935635187 1.948961806 1.905931955 1 19.53777398 CPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 348.66 8.63E-111 1288904000 2452744 2036215 2145227 2635594 1888989 2247557 2865230 2699483 2070940 FALSE TRUE 2336807.652 2243707.623 2243587.78 2370659.084 2218428.084 2169723.538 2428086.54 2463101.958 2392090.798 0.976889194 0.937969255 0.937919155 0.991040593 0.927401286 0.907040627 1.015047816 1.029685813 1 21.18984072 1.630415684 7.447163112 1.017754832 0.948575803 0.630246805 0.024666849 0.075225732 8.860801547 0.012288386 0.006159914 42.6988014 -1.630415684 -0.06917903 CPFPAGAALACCS(ph)EDEEDDEEHEGGGS(ph)RSPAGGESATVAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPFPAGAALACCSEDEEDDEEHEGGGSRSPAGGESATVAAK 41 1 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 2 CPFPAGAALACCS(1)EDEEDDEEHEGGGS(0.545)RS(0.455)PAGGESATVAAK 113.95 5.15E-06 47410000 18426 16059 19442 19058 25845 19165 19379 18612 23477 TRUE FALSE 17555.0395 17695.43036 20333.43493 17142.25363 30352.35982 18501.31124 16422.37763 16982.23461 27117.69326 0.647364779 0.652541873 0.749821703 0.632142766 1.119282512 0.682259773 0.605596408 0.626241858 1 14.72694684 3.633009001 1.865966179 0.756449866 0.646080504 0.079718054 0.167205444 1.036756014 7.085855192 0.048770401 0.093660866 4295.453297 -3.633009001 -0.110369362 CPFPAGAALACCS(ph)EDEEDDEEHEGGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPFPAGAALACCSEDEEDDEEHEGGGSR 28 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(0.999)EDEEDDEEHEGGGS(0.001)R 167.87 3.43E-12 123600000 115421 91328 91564 120886 85705 131458 137193 112836 88844 TRUE FALSE 109965.2781 100634.427 95762.29997 108734.3096 100651.9249 126905.5765 116261.6881 102955.4817 102621.4738 1.071562062 0.980637125 0.933160443 1.05956683 0.980807634 1.236637634 1.13291774 1.003254756 1 16.64697312 2.297673592 24.99996186 1.112078199 1.007043713 0.225834887 0.077545153 88.97434277 37628.24566 0.025532677 0.021362158 198.4602766 -2.297673592 -0.105034486 CPGESSHICDFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 CPGESSHICDFIR 13 0 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2;A0A286YFL6 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;;;; 194.06 1.34E-06 3125690000 2414660 1838599 1808398 2073100 2559710 1890689 2835500 2352080 2467460 FALSE TRUE 2300523.807 2025954.328 1891314.837 1864708.049 3006122.614 1825213.966 2402892.397 2146119.406 2850101.095 0.807172704 0.710835953 0.663595702 0.654260318 1.054742451 0.640403237 0.843090233 0.752997643 1 21.44258166 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 37 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 258.43 2.43E-62 80004000 53870 52956 47639 57645 52004 50205 60701 57211 28978 FALSE TRUE 51323.67186 58352.27661 49823.29527 51850.41508 61073.48113 48466.38826 51439.9476 52201.30155 33471.76024 1.53334248 1.743328591 1.488517333 1.549079424 1.824627109 1.447978472 1.536816326 1.559562484 1 15.0306568 -1.140075423 0.403286903 0.719893209 1.623654077 0.728901599 0.112761601 8.865370917 0.92804203 2.852621275 0.066723101 0.072431016 1.140075423 0.903760868 CPLLKPWALTFS(ph)YGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 CPLLKPWALT(0.001)FS(0.999)YGR 130.27 3.68E-05 70063000 68254 54108 40283 54526 53263 40894 61770 55749 43481 TRUE FALSE 65027.76869 59621.66672 42130.0154 49044.94289 62552.05034 39477.83053 52345.85202 50867.32202 50223.81141 1.294759734 1.187119516 0.838845444 0.976527697 1.245466017 0.786038125 1.042251684 1.012812859 1 15.6160839 3.925713823 5.845945998 0.98921994 1.255902616 0.437936806 0.12243525 0.170771073 10.2983806 0.029326504 0.05416016 8427.792275 -3.925713823 0.266682676 CPLLKPWALTFSYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 96.673 0.0032914 1653660000 3846100 3344000 2937400 3515900 2517200 3180500 4182100 3897600 2445800 FALSE TRUE 3664302.475 3684757.402 3072082.695 3162475.052 2956198.883 3070358.488 3544043.835 3556305.482 2825082.173 1.297060493 1.304300964 1.08743127 1.119427634 1.046411645 1.086820949 1.254492301 1.258832581 1 21.4298614 3.748018272 24.4541915 1.134328869 1.300680751 0.445956564 0.081934092 458.8980195 1186545.047 0.021710663 0.038483726 5597.811522 -3.748018272 0.166351882 CPPGVVPACHNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 164.11 3.76E-05 1345110000 1382370 1015960 1260430 1608230 1661270 1310040 2167760 1881260 2412400 FALSE TRUE 1317028.11 1119487.479 1318221.962 1446567.665 1950994.962 1264672.986 1837028.398 1716526.901 2786502.671 0.472645558 0.4017536 0.473073999 0.51913378 0.700159014 0.453856729 0.659259515 0.616014806 1 21.41002411 -5 0.126525082 2.646359052 0.307542676 0.820289167 0.073713889 53.16856932 0.428535604 22.02283932 0.553805387 1.00E-05 5 -2.338816377 CPQIVIAFYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CPQIVIAFYEER 12 0 Q13185;P45973 Q13185;P45973 CBX3;CBX5 Chromobox protein homolog 3;Chromobox protein homolog 5 0 ;; 186.87 2.61E-05 402150000 331396 268338 290708 350233 288220 292490 364698 348597 294612 FALSE TRUE 315731.5678 295681.9473 304037.2493 315026.9134 338485.4767 282360.998 309056.622 318071.9987 340298.9243 0.927806541 0.868888868 0.8934417 0.925735849 0.994671016 0.829744022 0.908191592 0.934684114 1 18.37644307 0.905082714 3.020232789 0.999821106 0.904255427 0.324883532 0.042330403 0.440681576 8.918143204 0.038321497 0.010048834 8.036791723 -0.905082714 -0.095565679 CPS(ph)PTMSLPSSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPSPTMSLPSSWK 13 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 CPS(0.729)PT(0.097)MS(0.174)LPSSWK;CPS(0.585)PT(0.315)MS(0.1)LPSSWK 132.06 0.00048171 272610000 762740 784510 671870 829350 498030 763800 762740 787090 555550 TRUE FALSE 726686.7918 864452.4609 702675.9041 745982.1623 584886.2743 737349.4145 646370.0043 718168.227 641701.8566 1.132436792 1.347124762 1.095019278 1.16250585 0.911461091 1.149052955 1.007274636 1.119161834 1 19.29154363 3.345081926 2.088559752 1.04853138 1.235539362 0.379069462 0.092085554 0.263754711 2.347907635 0.025297512 0.037346484 2213.512232 -3.345081926 0.187007982 CPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.843)QS(0.041)S(0.058)S(0.058)RPAAMISQPPTPPTGQPVREDAK;CPS(0.776)QS(0.067)S(0.09)S(0.067)RPAAMISQPPTPPTGQPVREDAK;CPS(0.985)QS(0.006)S(0.006)S(0.002)RPAAMISQPPTPPTGQPVREDAK;CPS(0.997)QS(0.002)SSRPAAMISQPPTPPTGQPVREDAK;CPS(0.993)QS(0.004)S(0.001)S(0.001)RPAAMISQPPTPPTGQPVREDAK;CPS(0.981)QS(0.01)S(0.004)S(0.004)RPAAMISQPPTPPTGQPVREDAK 158.99 2.50E-12 1332570000 438980 374248 425264 472542 331547 452871 496456 479190 384750 TRUE FALSE 418230.2854 412384.2967 444762.775 425041.1804 389368.6918 437187.9637 420712.5192 437229.5833 444415.065 0.941080351 0.927926007 1.000782399 0.956405878 0.876137473 0.983737947 0.946665746 0.983831597 1 18.7615482 1.165146597 1.425608539 1.000432486 0.94420046 0.240626794 0.033047612 0.543966912 2.160359166 0.029281668 0.00891602 14.6267082 -1.165146597 -0.056232026 CPSIILHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPSIILHDR 9 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 103.7 0.0033798 157590000 74803 49108 62938 78634 76756 54201 72876 67972 64982 FALSE TRUE 71267.21044 54112.16103 65823.76955 70729.56093 90142.2221 52324.00578 61757.42774 62020.01134 75059.07668 0.949481576 0.720927614 0.876959489 0.942318558 1.200950319 0.697104309 0.822784272 0.826282631 1 16.19573892 -0.220675293 24.95872516 1 0.86930605 0.063512296 0.140432003 0 0 0.13201466 0.031116154 0.601623383 0.220675293 -0.13069395 CPSPT(ph)MSLPSSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPSPTMSLPSSWK 13 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 CPS(0.329)PT(0.525)MS(0.145)LPSSWK 111.53 0.010866 194330000 362080 346670 312900 379400 266260 312590 343620 349210 270970 TRUE FALSE 344965.196 381996.0671 327246.7745 341261.9912 312695.6597 301764.9299 291194.458 318631.3211 312990.6437 1.102158173 1.220471202 1.045548105 1.090326494 0.999057531 0.964134028 0.930361542 1.018021872 1 18.25576001 3.03868701 1.235448216 0.966866205 1.155691379 0.674371095 0.046794451 0.210780682 0.678893463 0.01807268 0.022570734 1093.168252 -3.03868701 0.188825174 CPSQS(ph)SSRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.12)QS(0.523)S(0.145)S(0.213)RPAAMISQPPTPPTGQPVREDAK 157.8 3.94E-10 777140000 181900 148610 167660 195370 123730 181870 200090 205150 148710 TRUE FALSE 173301.9475 163753.528 175347.3768 175731.0364 145308.4728 175571.7963 169562.5956 187185.9784 171771.1873 1.008911624 0.953323608 1.020819496 1.023053046 0.845942065 1.022125998 0.987142246 1.089740261 1 17.39012854 1.385710443 5.973683266 1.04507685 0.97910041 0.183429399 0.056672254 0.329997851 16.19512099 0.035897489 0.013027637 24.30582926 -1.385710443 -0.06597644 CPSQSSSRPAAMISQPPT(ph)PPTGQPVREDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPSQSSSRPAAMIS(0.001)QPPT(0.999)PPTGQPVREDAK 115.77 0.0055588 122710000 122830 104080 127730 133080 82431 144250 166800 153220 94128 TRUE FALSE 117024.0693 114685.8703 133586.5468 119702.5456 96806.9403 139254.5863 141351.5965 139803.2445 108724.8895 1.076331922 1.054826276 1.22866574 1.100967277 0.890384352 1.280797681 1.300084987 1.285843979 1 16.73032272 2.18679993 24.99998006 1.24934256 1.077285287 0.255096069 0.11831346 110.9245562 53574.8511 0.040910351 0.030214331 153.7446208 -2.18679993 -0.172057273 CPSSSGKPNHADILLINLQYVSEVEIINDRTET(ph)PPPLASLNVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSK 44 2 K7ELG9;Q3MHD2 K7ELG9 LSM12 Protein LSM12 homolog 1 CPSSSGKPNHADILLINLQYVSEVEIINDRT(0.011)ET(0.987)PPPLAS(0.003)LNVSK;CPS(0.001)S(0.001)S(0.001)GKPNHADILLINLQYVS(0.001)EVEIINDRT(0.312)ET(0.685)PPPLASLNVSK 83.058 0.00016926 43702000 42358 29741 33188 40096 25684.4 40810 53414 47369 30304 TRUE FALSE 40355.82129 32771.64171 34709.70263 36065.4739 30163.75123 39396.73947 45264.71328 43221.11924 35003.38955 1.152911812 0.936241951 0.991609758 1.030342329 0.861738009 1.125512128 1.293152288 1.234769541 1 15.09520701 2.006986461 24.65465329 1.208742879 1.001761774 0.384001794 0.104902957 118.418439 417886.7095 0.036567442 0.026944217 101.6217013 -2.006986461 -0.206981105 CPT(ph)PEIQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPTPEIQKK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQKK;CPT(1)PEIQKK 107.97 0.0015751 974950000 2710000 2208950 2474200 2858700 1634470 2943900 3126700 3095200 1847920 TRUE FALSE 2581903.671 2434044.516 2587644.517 2571338.045 1919521.051 2841952.005 2649664.489 2824167.879 2134485.996 1.209613779 1.140342228 1.212303347 1.204663816 0.899289597 1.331445608 1.24135951 1.323113801 1 21.02545727 CPTQFPLILWHPYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CPTQFPLILWHPYAR 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 105.14 0.0013387 160439000 476540 427510 411050 466970 405360 469770 535180 458660 377890 FALSE TRUE 454014.8986 471073.755 429897.0491 420029.2884 476054.6557 453501.7471 453528.4617 418497.2989 436491.2512 1.040146618 1.079228401 0.984892705 0.962285698 1.090639628 1.038970989 1.039032192 0.958775915 1 18.73559321 7.999999999 0.109221644 0.983082692 1.196084964 0.080818166 0.043251016 264.9689041 2.021939796 0.39782426 8.505635881 99999999.85 -7.999999999 0.213002272 CPVTVCGDVHGQFHDLMELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 141.1 9.19E-08 64201000 39470 34749 40085 42453 40136 33836 42282 35883 11317 FALSE TRUE 37604.33132 38289.96261 41922.9369 38185.54378 47135.70569 32664.25084 35831.10434 32740.89429 13071.98256 2.87671217 2.929162614 3.207083295 2.921174627 3.605857449 2.498798532 2.74106121 2.504661718 1 13.67419034 0.508591213 0.763842473 0.98016252 3.033753741 0.846330133 0.267175158 0.568998875 0.532409478 0.26508749 0.087176933 3.225456676 -0.508591213 2.05359122 CQEHSKES(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CQEHSKESPAR 11 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 CQEHS(0.27)KES(0.73)PAR;CQEHSKES(1)PAR;CQEHSKES(1)PAR 173.36 7.42E-06 125661000 177208 193981 167457 216001 106744 194499 196292 185505 111264 TRUE FALSE 168831.729 213747.8844 175135.0691 194288.1691 125360.1198 187763.4509 166344.0503 169261.1988 128518.2529 1.313678993 1.663171415 1.362725256 1.511755449 0.97542658 1.460986643 1.294322375 1.317020696 1 16.97161375 -3.401661058 0.11132614 0.104435285 1.637591872 0.338970892 0.170982356 108.7278955 1.16749636 24.83845703 2.136690613 0.000396587 3.401661058 1.533156588 CQEVISWLDANTLAEKDEFEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 354.52 2.14E-96 1066440000 2870310 2140470 2365910 2858460 1308650 2809860 3075770 3038320 1173490 FALSE TRUE 2734636.135 2358586.327 2474389.314 2571122.17 1536878.146 2712553.844 2606504.796 2772268.594 1355468.836 2.017483591 1.74005205 1.825485949 1.896850818 1.133835102 2.001192334 1.922954425 2.045247017 1 20.37036051 5.055071848 0.974415182 1.737096668 2.342067248 0.064636211 0.355811834 10.48838507 5.263693098 0.100668719 7.697297509 113519.8603 -5.055071848 0.60497058 CQHAAEIITDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CQHAAEIITDLLR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;; 172.1 2.40E-05 469673000 545839 470075 448630 501735 458738 476518 592219 511605 401591 FALSE TRUE 520038.2722 517976.1769 469200.1293 451299.6446 538741.762 460016.0622 501865.1147 466806.154 463867.6812 1.12109184 1.116646401 1.011495623 0.972905988 1.161412583 0.991696729 1.08191438 1.006334722 1 18.82335381 3.753033991 23.0023401 1.038612683 1.118869158 0.298579829 0.054519469 311.8953967 495686.4168 0.012763163 0.022837708 5662.836092 -3.753033991 0.080256475 CQHGEEECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CQHGEEECK 9 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 ; 117.02 0.001219 227150000 522220 564760 512770 612040 434030 576070 492580 522730 360580 FALSE TRUE 497535.6955 622309.6861 536281.0117 550516.5764 509724.6946 556120.5515 417427.8741 476956.99 416496.9048 1.194572372 1.494152007 1.287599033 1.321778313 1.223837893 1.335233336 1.002235237 1.145163348 1 18.66794625 1.751697245 8.743298276 1.058039105 1.318405578 0.655963376 0.088605981 0.073552121 21.95918261 0.040678588 0.022000327 56.45432835 -1.751697245 0.260366473 CQHLQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CQHLQAEK 8 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 120.15 0.0015563 1396040000 5942600 4739030 3932500 4931100 3581910 4960480 6327450 5258450 3378410 FALSE TRUE 5661705.075 5221942.545 4112809.015 4435416.46 4206593.97 4788697.334 5362081.291 4797992.241 3902316.568 1.450857453 1.338164768 1.053940382 1.136611134 1.077973531 1.227142199 1.374076448 1.229524094 1 21.89589939 3.950140614 5.496600095 1.184050824 1.410974812 0.45104723 0.108584722 0.188259015 13.35859154 0.029973137 0.056495325 8915.395498 -3.950140614 0.226923988 CQSLQEELDFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CQSLQEELDFRK 12 1 Q03252 Q03252 LMNB2 Lamin-B2 0 103.21 0.0018608 0 67970 70276 71734 73690 56467 73674 79623 71687 53956 FALSE TRUE 64757.1928 77437.2043 75023.07485 66282.5412 66314.82692 71122.65091 67475.04897 65409.70624 62323.22091 1.039054013 1.242509664 1.203774031 1.063528814 1.06404685 1.141190232 1.082663059 1.049523842 1 15.92748217 1.3355961 0.522975173 0.998425699 1.148284583 0.32707058 0.062317784 0.982943414 0.693300031 0.066612528 0.036262332 21.65689046 -1.3355961 0.149858884 CQSLTEDLEFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CQSLTEDLEFRK 12 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 83.869 0.020134 169020000 96267 74744 94331 107870 76623 117660 137950 125300 104550 FALSE TRUE 91716.64969 82360.49858 98656.16966 97026.70266 89986.02694 113585.4047 116903.1939 114328.0677 120763.08 0.759475907 0.682000646 0.816939827 0.803446737 0.745145179 0.940563992 0.968037531 0.946713745 1 16.88181993 2.20426361 5.123173433 0.964043178 0.754322471 0.870661737 0.03877934 0.066001533 4.22864561 0.015586236 0.011688639 160.0529232 -2.20426361 -0.209720707 CQYVTEK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 134.81 0.0073009 1879760000 2557960 1905570 2128420 2679320 2060290 2328350 2963270 2532750 2220390 FALSE TRUE 2437050.3 2099749.749 2226010.162 2409989.663 2419603.924 2247718.656 2511168.737 2310968.983 2564716.741 0.950222011 0.818706298 0.867936067 0.93967089 0.943419554 0.876400352 0.97912128 0.901062073 1 21.29036807 1.325694363 0.388702243 1.00043663 0.87891673 0.298522674 0.045851507 1.296952901 0.594884217 0.061604956 0.042080366 21.16870854 -1.325694363 -0.1215199 CRDDSFFGETSHNYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CRDDSFFGETSHNYHK 16 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 169.64 3.58E-09 288970000 204740 228600 175820 230680 130220 187360 211810 201700 20329 FALSE TRUE 195062.346 251894.5999 183881.5209 207491.6081 152930.3268 180871.6762 179494.4943 184038.0787 23481.51749 8.307058775 10.7273561 7.830904496 8.836379855 6.512795726 7.702725187 7.644075575 7.837571774 1 14.51923803 -0.204200564 0.373694481 3.55E-15 9.140425955 0.82697217 1.039714198 2.412019037 0.403730234 6.327331701 0.792159689 0.624884045 0.204200564 9.140425955 CRDDSFFGETSHNYHKFDSEYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CRDDSFFGETSHNYHKFDSEYER 23 2 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 308.05 1.37E-73 1036820000 872010 664148 952750 832940 749620 913570 1191980 923520 57265 FALSE TRUE 830791.8155 731825.4363 996434.5299 749211.2887 880353.4907 881932.8418 1010121.559 842651.6929 66145.36373 12.56009142 11.06389617 15.06431402 11.32673927 13.30937561 13.33325258 15.2712375 12.73939163 1 16.01335242 0.932450089 22.76055679 0.999999999 13.0798935 0.88872631 1.344319546 5779.711921 1947443.302 1.34866519 0.337166297 8.559533355 -0.932450089 12.0798935 CREMDEQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CREMDEQIR 9 1 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 175.07 4.94E-05 596290000 318029 227354 298814 288415 332484 292522 389303 320539 401721 FALSE TRUE 302996.3994 250521.6311 312514.9175 259422.9762 390469.1043 282391.8898 329907.6773 292470.9059 464017.841 0.652984374 0.539896549 0.673497633 0.559079745 0.841495886 0.608579811 0.710980588 0.630300993 1 18.82382075 -4.999999999 0.205305791 2.650947032 0.59331401 0.633096577 0.083491767 83.44326254 0.828975276 56.58552993 0.167561299 1.00E-05 4.999999999 -2.057633021 CRHENLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CRHENLLLR 9 1 Q6ZMV8 Q6ZMV8 ZNF730 Putative zinc finger protein 730 0 ; 68.735 0.052194 1644170000 81173 70514.9 111240 114579.9 116267 80471 108762 73446.3 154581 FALSE TRUE 77336.11316 77700.44848 116340.464 103062.1108 136543.928 77684.26909 92168.35935 67014.95261 178552.632 0.433127825 0.435168318 0.651575184 0.577208578 0.764726493 0.435077704 0.516197148 0.375323241 1 17.44598987 -2.094371439 2.608609067 1.848521544 0.518710938 0.62018 0.117124458 4855572.908 1600611.962 24633574.42 0.028027966 0.008046899 2.094371439 -1.329810605 CRS(ph)PGMLEPLGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR 191.97 2.59E-07 13600620000 3053700 2633900 2873610 3202680 2729180 3022520 3235430 3013140 3212580 TRUE FALSE 2909357.653 2902297.404 3005367.861 2880740.522 3205148.128 2917849.375 2741805.731 2749293.488 3710770.499 0.784030609 0.782127972 0.809903998 0.776318698 0.863741945 0.786319007 0.738877743 0.740895587 1 21.82328735 -1.070770012 4.755661969 1.000008215 0.78438137 0.788593312 0.034936547 3.09E-06 6.04E-07 0.034363617 0.008099274 0.084963029 1.070770012 -0.215626845 CRSPGMLEPLGSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CRSPGMLEPLGSSR 14 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 CRS(0.014)PGMLEPLGS(0.116)S(0.869)R 122.75 0.00028131 169690000 120360 84907 95258 125470 98423 102620 116240 114650 112880 TRUE FALSE 114670.8213 93559.11983 99625.67352 112857.5172 115587.94 99066.24367 98505.45311 104610.6382 130384.8539 0.879479617 0.717561258 0.764089314 0.865572295 0.886513553 0.759798709 0.755497668 0.802322011 1 16.99241676 0.912697015 19.44363803 1 0.798356486 0.531909096 0.05763514 5085.882861 1132704.5 0.056086964 0.014021741 8.178939872 -0.912697015 -0.201643514 CS(ph)PTVAFVEFPSSPQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.999)PT(0.001)VAFVEFPSSPQLK;CS(0.998)PT(0.002)VAFVEFPSSPQLK;CS(0.842)PT(0.158)VAFVEFPSSPQLK 278.95 7.88E-36 220506000 304159 230708 264423 309388 182800 300715 323341 295856 233927 TRUE FALSE 289782.0069 254217.4075 276547.0561 278287.7304 214680.2621 290301.1641 274009.3919 269949.2802 270203.2044 1.072459549 0.940837871 1.023478077 1.029920171 0.794514123 1.074380908 1.014086389 0.999060247 1 18.04368526 -1.005259383 7.130927919 1 0.994676234 0.0004683 0.080162456 5.27E-10 7.43E-11 0.071098768 0.016758139 0.098796286 1.005259383 -0.005323766 CSATPSAQVKPIVSAS(ph)PPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 CSATPSAQVKPIVSAS(1)PPSR 241.62 5.73E-30 348550000 625960 548270 617900 665770 426730 641480 727360 698540 513090 TRUE FALSE 596372.1113 604139.3363 646231.3262 598845.5347 501151.5769 619265.3868 616387.8731 637372.1344 592657.3767 1.006267929 1.019373689 1.090396157 1.010441375 0.845600842 1.044896109 1.040040835 1.075447905 1 19.17683878 -0.638285776 5.055669635 0.999999999 1.016164891 0.006077583 0.066377205 1.86E-09 3.67E-10 0.062305535 0.014685553 0.229992791 0.638285776 0.016164892 CSCSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CSCSFR 6 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;; 122.98 0.044171 577770000 653700 579550 536440 653380 495310 566510 740360 625220 462420 FALSE TRUE 622800.8965 638606.8039 561036.3046 587701.0011 581691.9072 546891.6167 627404.4844 570472.4223 534129.7319 1.166010539 1.195602427 1.050374602 1.100296362 1.089046111 1.023892856 1.174629396 1.068040943 1 19.02683067 8 0.120584327 0.9968646 1.58754104 0.382964845 0.051275368 97.39187226 0.806340411 0.345626847 9.675846894 100000000 -8 0.59067644 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(ph)ISPLDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYS(0.015)IQGQHT(0.555)IS(0.43)PLDLAK;CSDAAGYPHATHDLEGPPLDAYS(0.296)IQGQHT(0.581)IS(0.123)PLDLAK;CSDAAGYPHATHDLEGPPLDAY(0.022)S(0.024)IQGQHT(0.515)IS(0.439)PLDLAK 162.52 2.30E-17 538215000 175846 155573 200963 206939 133843 203752 239703 200723 43404 TRUE FALSE 167534.1081 171426.0656 210177.3523 186137.0986 157185.1768 196696.0172 203131.9049 183146.63 50134.87064 3.341668302 3.419298053 4.192238848 3.712727213 3.135246482 3.923337482 4.051708966 3.653078739 1 15.61352678 2.855983027 16.77655333 3.457521419 3.618390151 0.015390459 0.894805357 16.36311427 2270.494178 0.247695958 0.262725161 717.7662391 -2.855983027 0.160868732 CSDAAGYPHATHDLEGPPLDAYSIQGQHTIS(ph)PLDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYS(0.002)IQGQHT(0.16)IS(0.838)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.004)IS(0.996)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.004)IS(0.996)PLDLAK;CSDAAGYPHATHDLEGPPLDAYS(0.001)IQGQHT(0.018)IS(0.981)PLDLAK 350.8 8.09E-145 799407000 302640 315397 355320 406664 212723 356881 395185 394056 28476.3 TRUE FALSE 288334.807 347536.3129 371611.7735 365785.3621 249821.8238 344522.1215 334892.2702 359550.3676 32892.25917 8.766038402 10.56589975 11.29784888 11.12071263 7.595155522 10.47426143 10.1814919 10.93115452 1 15.00546048 -0.477948315 12.76252813 1.000000169 10.089064 0.86439451 1.134746412 0 0 1.047060517 0.24679452 0.332699145 0.477948315 9.089063833 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 163.82 3.90E-18 260130000 41924 39889 47963 47544 32673 44038 50254 49714 10339 FALSE TRUE 39942.33561 43953.73445 50162.15099 42764.78679 38371.16086 42512.95302 42586.82932 45360.77861 11942.31932 3.344604557 3.680502362 4.200369264 3.580944845 3.213040938 3.559857335 3.566043429 3.79832237 1 13.54379543 2.83281785 4.749724865 3.259685391 3.694510278 0.111544279 0.814115506 0.663582299 25.01813074 0.225049191 0.238935187 680.4838938 -2.83281785 0.434824886 CSDFTEEICRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CSDFTEEICRR 11 1 H0YL72;P50213;P50213-2;H0YM46;H0YNF5 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 ;;; 172.61 2.11E-05 606400000 744950 458422 679810 566560 669870 536139 770750 659030 769120 FALSE TRUE 709737.6898 505135.723 710979.9609 509608.3124 786695.1159 517572.372 653157.9317 601321.8395 888391.2015 0.798902205 0.568596044 0.800300543 0.573630526 0.885527811 0.582595113 0.735214318 0.676866046 1 19.76083558 -1.262774443 2.994391559 1.001866501 0.698329933 0.431866569 0.107057806 7633127.383 10031840.76 130290.7707 0.022473255 0.054604138 1.262774443 -0.303536568 CSDIVFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CSDIVFAR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 132.57 0.0022257 36652000 155296 133482 123406 159311 156247 128554 171065 152475 177776 FALSE TRUE 147955.4658 147083.9676 129064.2872 143296.7556 183496.4273 124102.1427 144965.8924 139123.4807 205344.5941 0.720522819 0.716278742 0.628525371 0.697835539 0.893602425 0.604360408 0.705964007 0.677512263 1 17.64768744 -1.594400604 3.453820445 1.011681532 0.705975015 0.5937418 0.076537722 102381132.4 32520611.3 9525828.504 0.017014712 0.025444821 1.594400604 -0.305706516 CSDS(ph)QSWEDIAPEIEPCAENRLDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSDSQSWEDIAPEIEPCAENRLDTK 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 CS(0.128)DS(0.868)QS(0.005)WEDIAPEIEPCAENRLDTK 131.1 5.10E-05 31084000 29928 16709 28453 28524 20504 28417 40736 29506 32037 TRUE FALSE 28513.36275 18411.6661 29757.59819 25656.71333 24079.89111 27432.91216 34520.97503 26922.29822 37005.13434 0.770524503 0.497543555 0.804147822 0.693328474 0.65071757 0.741327188 0.932869875 0.727528725 1 15.17543783 1.47164855 0.525414713 0.988419724 0.646793235 0.451049106 0.103658338 0.65025605 0.448526067 0.101653866 0.058280307 29.62433093 -1.47164855 -0.341626489 CSDVSELSSS(ph)PPGPYHQEPYVCKPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.003)S(0.166)S(0.831)PPGPYHQEPYVCKPEER;CSDVSELS(0.081)S(0.437)S(0.481)PPGPY(0.001)HQEPYVCKPEER;CSDVSELSS(0.037)S(0.962)PPGPYHQEPYVCKPEER 171.02 2.96E-12 711977000 496382 393793 442451 539272 331312 494044 553020 505986 328688 TRUE FALSE 472919.0066 433920.9544 462737.816 485063.354 389092.7079 476935.1324 468646.6421 461679.1834 379659.2563 1.24564066 1.1429221 1.218824007 1.277628152 1.024847153 1.256218897 1.234387505 1.216035631 1 18.53434566 -1.011800481 4.370954865 0.999992698 1.201698785 0.435890529 0.072239701 6.22E-06 1.41E-06 0.063902225 0.015061177 0.097319421 1.011800481 0.201706088 CSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR 38 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 86.944 0.00038811 128550000 136950 95972 124040 138280 92659 141120 184260 152620 107720 FALSE TRUE 130476.6449 105751.6559 129727.3567 124379.8317 108818.7003 136232.979 156147.7528 139255.7837 124424.6674 1.048639692 0.849925164 1.042617669 0.999639655 0.874574974 1.0949033 1.254958169 1.119197556 1 16.92491301 2.054825249 6.502335465 1.1585006 0.961582101 0.410812874 0.089245474 0.147070453 13.15452333 0.031391337 0.022930801 113.4554204 -2.054825249 -0.196918499 CSGPGLS(ph)PGMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;CSGPGLS(1)PGMVR;CSGPGLS(1)PGMVR 285.31 2.28E-28 2778050000 3312334 2848789 3045269 3525832 2739848 3223385 3604485 3218535 2903496 TRUE FALSE 3155766.536 3139083.838 3184897.596 3171408.669 3217676.624 3111758.369 3054554.612 2936703.013 3353755.331 0.940965045 0.935990711 0.949651147 0.94562911 0.959424975 0.927842989 0.910786361 0.875646171 1 21.67734601 2.033192701 8.33065566 0.918987818 0.944518402 0.042836792 0.03134757 0.448485944 99.6232352 0.01047665 0.007676773 107.9425567 -2.033192701 0.025530585 CSLVFY(ph)ILS(ph)PLNLNSIPDIEALQLHADVENQSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSLVFYILSPLNLNSIPDIEALQLHADVENQSGK 34 0 Q5T370 Q5T370 ARRDC1 2 CS(0.434)LVFY(0.745)ILS(0.665)PLNLNS(0.156)IPDIEALQLHADVENQSGK 43.951 0.061561 437290000 182860 130140 158760 198260 213940 133210 225120 142690 264210 TRUE FALSE 174216.5702 143401.414 166039.303 178330.5281 251251.0683 128596.9043 190773.8094 130195.3072 305182.3374 0.570860593 0.469887659 0.5440659 0.584340921 0.823281814 0.421377283 0.625114189 0.426614817 1 18.21931194 -1.559681981 2.779154194 1.02637628 0.558182046 0.591908147 0.11528876 26792457.63 27029678.32 5248606.128 0.027673713 0.027562463 1.559681981 -0.468194234 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPS(ph)PTEIAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPSPTEIAGQK 47 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 CSNNVVHVHSCADSCALLVNLLQYVMS(0.005)T(0.005)GDLHPPPRPPS(0.824)PT(0.165)EIAGQK 97.424 4.32E-06 60415000 21635 21571 26433 25976 21331 26307 28755 26061 5392.5 TRUE FALSE 20612.35643 23769.10942 27644.9792 23364.84313 25051.11965 25395.98199 24367.89663 23778.96068 6228.741359 3.309232996 3.816037311 4.438293004 3.751133942 4.021859025 4.077225322 3.912170248 3.817618891 1 12.60472495 0.636930606 4.511919031 1.000000256 3.881855542 0.912051731 0.282382392 7.733311426 95.85977139 0.283678994 0.072000966 4.334416154 -0.636930606 2.881855286 CSPT(ph)VAFVEFPSSPQLK ddPTM_SK-BR-3_Trastuzumab_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(0.371)PT(0.629)VAFVEFPSSPQLK 266.28 1.38E-26 134450000 378170 287630 329020 364150 231940 372790 412530 364410 251960 TRUE FALSE 360294.6536 316939.824 344105.8924 327544.9502 272390.2626 359880.1888 349590.9719 332500.3285 291032.67 1.237986971 1.089018027 1.182361734 1.125457668 0.935943936 1.236562853 1.201208689 1.142484548 1 18.15082159 4.657679565 3.25362168 1.127866985 1.2443717 0.138282305 0.091374922 0.603863698 10.38977854 0.02152838 0.156876749 45465.24809 -4.657679565 0.116504715 CSS(ph)PTVGPPPLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.108)S(0.892)PTVGPPPLPQK 128.54 0.00019917 0 69453 63395 69773 90634 58716 73523 86042 76399 71858 TRUE FALSE 66170.09433 69855.02257 72972.16106 81523.29813 68956.05181 70976.88007 72914.71263 69709.09854 83001.37164 0.797216878 0.84161287 0.879168134 0.98219218 0.830782076 0.855129002 0.878475996 0.839854778 1 16.34084756 -5 0.198492627 1.601433623 0.838684576 0.421109847 0.049307663 142.4802986 1.407276521 34.20239287 0.121433519 1.00E-05 5 -0.762749047 CSSVAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSSVAAK 7 0 F5H3V4;F5GZH5;Q9ULI2-2;Q9ULI2 F5H3V4 RIMKLB Beta-citrylglutamate synthase B 0 86.512 0.046579 597000000 386150 331390 345960 341280 313360 399670 503440 426840 370290 FALSE TRUE 367897.4548 365159.0178 361822.6082 306973.886 368009.8848 385829.3277 426630.9817 389463.6268 427712.682 0.860150915 0.8537484 0.845947814 0.717710507 0.860413778 0.902075959 0.997470965 0.910573016 1 18.70628246 2.096275325 2.723339192 0.966892002 0.828925154 0.651733102 0.047577904 0.174385142 2.55487117 0.021874866 0.013792931 124.8174556 -2.096275325 -0.137966848 CSVS(ph)AVNLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CSVSAVNLPK 10 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 CS(0.002)VS(0.998)AVNLPK;CSVS(1)AVNLPK 158.04 8.51E-06 405320000 589930 440810 516160 569590 367560 555030 612340 574160 428420 TRUE FALSE 562045.178 485729.0402 539826.4466 512333.731 431662.3476 535809.1719 518916.2866 523883.5066 494857.1855 1.13577249 0.98155398 1.09087321 1.035316342 0.872296817 1.082755162 1.048618272 1.058655955 1 18.9166527 4.668072105 3.363127121 1.02487889 1.142367135 0.245312607 0.062676351 0.390781517 7.240123723 0.014557024 0.105334413 46566.33998 -4.668072105 0.117488244 CSWQDLKDFMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CSWQDLKDFMR 11 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 79.283 0.025143 140110000 326830 162680 266520 220950 292330 276730 474000 334280 366430 FALSE TRUE 311381.3936 179257.277 278740.2056 198739.6862 343312.2594 267146.7707 401682.5944 305008.6711 423254.0929 0.735684306 0.423521662 0.658564702 0.469551717 0.811125669 0.631173508 0.949034164 0.720627812 1 18.69116449 1.99184026 0.870329559 0.926862187 0.569196061 0.48432273 0.131319802 0.444945585 0.623294656 0.098801045 0.048448172 98.1386907 -1.99184026 -0.357666126 CTHWAEGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 111.61 0.0020974 1442670000 3817930 3367130 3573520 4290760 2576720 3961690 4252110 3852070 2301390 FALSE TRUE 3637464.015 3710244.375 3737369.427 3859444.653 3026099.152 3824495.682 3603372.524 3514762.33 2658277.807 1.368353603 1.395732367 1.405936361 1.451859035 1.138368286 1.438711812 1.35552895 1.322195265 1 21.34206045 -3.342319211 0.309943817 1.08E-16 1.385763492 0.639996767 0.08569608 56.10945054 1.318838518 36.22703178 0.074842512 0.000454654 3.342319211 1.385763492 CTKEEHLCTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 CTKEEHLCTQR 11 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 132.69 0.00010652 5900360000 7361490 5070520 6598980 6576680 5252720 7012400 8617830 7412240 5798580 FALSE TRUE 7013526.957 5587211.753 6901549.76 5915579.632 6168792.705 6769558.83 7303021.756 6763184.971 6697794.171 1.047139816 0.83418684 1.030421297 0.883213112 0.921018554 1.010714671 1.090362225 1.009763035 1 22.67525461 2.092916689 4.737888651 1.045038569 0.939422671 0.281979736 0.066578772 0.21972666 8.550218357 0.024155077 0.01737483 123.8558971 -2.092916689 -0.105615898 CTLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CTLAEK 6 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 110.61 0.066431 873050000 1392120 1160300 1181210 1399390 952370 1302040 1489040 1392290 1114190 FALSE TRUE 1326317.247 1278535.889 1235369.647 1258720.659 1118463.026 1256950.028 1261859.6 1270373.707 1286972.895 1.030571236 0.993444302 0.959903392 0.978047528 0.869064944 0.976671718 0.980486539 0.987102146 1 20.29555024 4.098682412 1.70997482 0.961818028 1.027751476 0.259273288 0.035937575 0.497667646 2.709739287 0.009828656 0.035391394 12551.11799 -4.098682412 0.065933448 CTLPEHES(ph)PSQDISDACEAESTER ddPTM_SK-BR-3_Trastuzumab_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(0.983)PS(0.017)QDISDACEAESTER;CTLPEHES(0.981)PS(0.019)QDISDACEAESTER;CT(0.003)LPEHES(0.889)PS(0.108)QDISDACEAESTER 343.29 6.73E-88 869950000 735830 996360 699440 1061590 609420 998970 848660 951940 575850 TRUE FALSE 701048.7742 1097890.217 731510.0158 954876.9563 715702.6551 964375.4184 719181.3303 868583.087 665149.877 1.05397114 1.650590724 1.099767197 1.435581648 1.076002086 1.449861831 1.081231998 1.30584567 1 19.34331993 0.44969375 0.405683118 0.972051279 1.325076542 0.143382767 0.199744218 4.112441329 1.262562417 0.427798852 0.12946372 2.816396205 -0.44969375 0.353025263 CTLPEHESPS(ph)QDISDACEAESTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CTLPEHESPSQDISDACEAESTER 24 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 CTLPEHES(0.246)PS(0.754)QDISDACEAESTER 301.51 1.98E-62 287070000 196080 172480 192470 209890 179580 183600 208340 211170 184490 TRUE FALSE 186811.687 190055.9081 201294.9399 188791.4584 210898.6951 177241.886 176553.9066 192678.8353 213099.767 0.876639565 0.891863519 0.944604223 0.885929915 0.989671167 0.831731956 0.828503518 0.904171966 1 17.70116949 CTMHCNDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CTMHCNDK 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ; 67.563 0.04458 141720000 190069 145410 142959 170100 129960 152215 167863 163074 110342 FALSE TRUE 181084.8151 160227.4443 149513.8116 153001.2248 152624.9829 146943.7564 142252.4163 148794.3761 127453.2738 1.420793752 1.257146557 1.173087258 1.200449547 1.197497548 1.152922573 1.11611426 1.167442558 1 16.95960891 8 0.207563031 1.045462607 2.858975819 0.870708821 0.038204406 15.75841095 0.194812054 0.062916511 9.408030969 100000000 -8 1.813513212 CTVDVPEDLREACANENAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CTVDVPEDLREACANENAHK 20 1 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;C9J5B4;C9IZ22;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 111.77 9.81E-05 84098000 213290 178870 181440 217520 160940 204106 245260 212410 177005 FALSE TRUE 203208.2044 197097.0564 189759.2035 195654.4763 189007.885 197037.758 207841.0825 193810.2543 204454.0314 0.993906567 0.964016483 0.928126495 0.956960716 0.92445174 0.963726451 1.016566321 0.947940488 1 17.64141698 1.976561442 23.89641098 0.990043837 0.956479751 0.273424258 0.025522888 595.1030538 606726.8829 0.01054864 0.006864439 94.74612164 -1.976561442 -0.033564086 CTVFHGAQVEDAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 241.42 1.94E-17 53881120000 26642110 23549460 22887680 28625980 22387020 24951120 29385660 27314460 23777790 FALSE TRUE 25382790.26 25949176.75 23937102.77 25748442.1 26291309.2 24087056.46 24902337.86 24922661.08 27465128.23 0.924182478 0.9448045 0.871545276 0.937495791 0.957261476 0.877005061 0.906689299 0.907429263 1 24.71109769 -1.006773484 4.919794088 1.000001078 0.916959757 0.483190899 0.027342722 3.14E-07 6.34E-08 0.025694653 0.006056209 0.098452447 1.006773484 -0.083041321 CTYLVLDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CTYLVLDEADR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 121.9 0.00093525 116240000 220970 200310 186730 231170 153730 216540 243260 214690 186850 FALSE TRUE 210525.186 220721.8167 195291.7552 207932.3524 180540.4633 209041.1655 206146.2192 195890.6055 215825.7437 0.975440568 1.022685306 0.904858484 0.963427017 0.836510326 0.968564555 0.955151205 0.907633177 1 17.71950743 3.740748818 24.99956041 0.932657557 0.999062938 0.258331535 0.045990789 220.9626643 2524416.389 0.011001778 0.018675776 5504.892191 -3.740748818 0.066405381 CVELVHEEMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 122.86 0.00038195 238935000 261700 242240 221650 264090 251900 239260 255790 260580 238060 FALSE TRUE 249329.9596 266924.5314 231812.8717 237543.1715 295831.2802 230974.3662 216764.5376 237762.2338 274977.129 0.906729809 0.970715392 0.84302601 0.863865196 1.075839585 0.839976645 0.788300243 0.864661853 1 18.0689521 CVFELPAENDKPHDVEINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CVFELPAENDKPHDVEINK 19 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 259.56 2.71E-31 367080000 500010 413670 460560 661800 368290 610670 618180 564320 336080 FALSE TRUE 476375.5182 455823.4433 481677.1316 595274.6067 432519.6594 589522.3448 523865.2873 514905.1492 388197.5699 1.22714709 1.174204783 1.240804088 1.533432079 1.114174052 1.518614207 1.349481109 1.326399723 1 18.56643156 3.461592129 24.99139757 1.33609741 1.201813959 0.053249885 0.161981481 428.0533393 688874.5433 0.039105329 0.052964991 2894.623803 -3.461592129 -0.134283451 CVFS(ph)YNSNCQEK ddPTM_SK-BR-3_Trastuzumab_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 494130000 350340 428070 299750 417680 283080 456000 417470 447460 173690 TRUE FALSE 333780.1225 471690.8197 313493.834 375694.0129 332449.0624 440208.6057 353777.2841 408278.0303 200624.9581 1.663701893 2.35110738 1.562586415 1.872618524 1.657067324 2.194186655 1.763376239 2.035031105 1 17.61414157 -1.32750481 3.707558414 0.997114057 1.901992927 0.556388785 0.248735807 9272992.319 9966417.395 184599.3053 0.052858064 0.04704302 1.32750481 0.90487887 CVFSYNS(ph)NCQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.129)Y(0.107)NS(0.764)NCQEK 59.57 0.063188 1741100000 2057300 2257700 1706500 2308300 1639400 2797300 2559800 2684800 1084800 TRUE FALSE 1960055.506 2487762.197 1784744.713 2076265.299 1925310.841 2700428.8 2169255.496 2449704.679 1253025.244 1.564258594 1.985404691 1.424348569 1.657001971 1.536529971 2.155127212 1.73121452 1.955032184 1 20.25698405 -0.686287046 8.737379952 1 1.758058111 0.522973077 0.225358251 0 0 0.201933838 0.047596262 0.205926839 0.686287046 0.75805811 CVGAELEYDS(ph)EHSDWHGFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 1 CVGAELEYDS(1)EHSDWHGFD;CVGAELEYDS(1)EHSDWHGFD 267.36 7.97E-32 263170000 213310 220370 238450 238390 217760 219370 243170 222070 103308 TRUE FALSE 203227.259 242825.9535 249383.1684 214426.5843 255737.2751 211773.1619 206069.9504 202624.3735 119328.477 1.703091032 2.034937172 2.089888136 1.796943945 2.143137007 1.774707657 1.726913437 1.698038713 1 16.86457885 0.572551331 0.744842135 0.992226162 1.9380136 0.806011098 0.140570278 0.582737381 0.553947167 0.140623143 0.047807862 3.737242945 -0.572551331 0.945787439 CVGAELEYDSEHSDWHGFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ; 270.75 2.62E-39 157635000 177610 143512 169437 191201 181988 159566 210392 187013 21202.4 FALSE TRUE 169214.7273 158136.036 177205.854 171981.1122 213726.6496 154040.1894 178292.8363 170637.1503 24490.35991 6.909442244 6.457072765 7.235739072 7.02240036 8.726970547 6.28982955 7.280123158 6.967523179 1 14.57992636 0.90858953 19.09319053 1 7.074780127 0.896669649 0.651971095 1750.555161 365645.6317 0.593419385 0.148354846 8.101949464 -0.90858953 6.074780127 CVGHALEVEEALLCMDGAGPPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVGHALEVEEALLCMDGAGPPDLR 24 0 C9JGI3;P19971;A0A494C0L6;P19971-2;A0A494C1N7 C9JGI3 TYMP Thymidine phosphorylase 0 130.87 6.03E-05 17806000 24548 16731 19556 22724 22137 21267 25035 20252 18494 FALSE TRUE 23387.66469 18435.90792 20452.66194 20439.74035 25997.68579 20530.51846 21215.45095 18478.62752 21361.95507 1.094827913 0.863025311 0.957433993 0.956829105 1.217008729 0.961078628 0.993141821 0.865025109 1 14.38275607 -3.960408184 0.002512328 0.259643988 1.689801782 0.005373957 0.103734041 3556386.892 806.3211821 236934.966 222278.723 0.000109545 3.960408184 1.430157793 CVLFTYFQGDISSVVDEHFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVLFTYFQGDISSVVDEHFSR 21 0 Q99990;Q8N8G2-2;Q8N8G2 Q99990 VGLL1;VGLL2 Transcription cofactor vestigial-like protein 1;Transcription cofactor vestigial-like protein 2 0 216.04 6.33E-25 23162000 27640 22199 28026 28135 28952 23434 35841 31533 34264 FALSE TRUE 26333.51198 24461.10334 29311.01982 25306.81635 34001.21963 22622.4747 30372.79718 28771.80335 39577.48612 0.665365958 0.618056015 0.740598322 0.639424552 0.859105086 0.571599587 0.767426134 0.726973999 1 15.27239236 -4.999999974 0.193823348 2.367921529 0.637602697 0.600292587 0.079148953 84.29430345 0.828360443 44.44226022 0.178752152 1.00E-05 4.999999974 -1.730318832 CVLLSNLS(ph)STSHVPEVDPGSAELQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVLLSNLSSTSHVPEVDPGSAELQK 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 CVLLS(0.081)NLS(0.629)S(0.071)T(0.094)S(0.125)HVPEVDPGSAELQK 138.52 5.53E-06 80780000 63873 59024 62335 78022 57641 66946 85960 75090 62937 TRUE FALSE 60853.84987 65038.6127 65193.12141 70179.08033 67693.57215 64627.64323 72845.22324 68514.72152 72696.94852 0.837089467 0.894653958 0.896779339 0.965364871 0.931174878 0.88900077 1.002039628 0.942470391 1 16.14960719 8 0.183478584 1.002948845 0.269736479 0.665975861 0.029937633 29.1159759 0.331967181 0.060780727 5.990456009 100000000 -8 -0.733212366 CVLLSNLSSTSHVPEVDPGSAELQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVLLSNLSSTSHVPEVDPGSAELQK 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 0 218 1.47E-33 183990000 476390 385830 420260 519830 337560 457310 606900 574390 414630 FALSE TRUE 453871.9888 425146.5157 439529.3367 467575.7008 396430.3571 441473.24 514306.2585 524093.3666 478928.7028 0.947681745 0.887703145 0.917734381 0.976295006 0.827743994 0.921793239 1.073868105 1.094303523 1 18.86945138 1.757407542 5.658631623 1.062481551 0.911703267 0.689825562 0.045085074 0.086113125 6.77915387 0.020624434 0.010960793 57.20151639 -1.757407542 -0.150778284 CVMDDDNEVRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 CVMDDDNEVRDR 12 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 200.44 1.46E-07 802560000 896030 580166 765047 756386 888500 755667 978077 902385 1094270 FALSE TRUE 853676.4377 639285.575 800125.1617 680352.6422 1043454.119 729498.0623 828853.39 823367.3856 1263963.803 0.67539627 0.505778388 0.633028541 0.538269087 0.82554114 0.577151071 0.65575722 0.651416903 1 20.26952372 -5 0.249315325 3.276013198 0.591307233 0.647470537 0.085782349 104.7148344 1.038162332 121.2830031 0.112884914 1.00E-05 5 -2.684705965 CVPAPGAGASGGTS(ph)PSATQPNPAVFIFEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CVPAPGAGASGGTSPSATQPNPAVFIFEHK 30 0 O60343-2;O60343-3;O60343 O60343-2 TBC1D4 TBC1 domain family member 4 1 CVPAPGAGAS(0.003)GGT(0.053)S(0.908)PS(0.036)ATQPNPAVFIFEHK;CVPAPGAGASGGT(0.027)S(0.915)PS(0.058)AT(0.001)QPNPAVFIFEHK 176.98 5.67E-18 97751000 166082 142467 167464 188478 123162 158735 175373 185759 108877 TRUE FALSE 158231.633 156984.5493 175142.39 169531.8334 144641.4138 153237.9671 148616.6279 169492.9572 125761.0891 1.258192293 1.248276 1.392659616 1.348046797 1.150128508 1.218484734 1.181737761 1.34773767 1 16.94032609 2.736831305 24.99482883 1.193129862 1.29974424 0.320436875 0.093788437 220.4896876 3186861.903 0.027674203 0.027397836 545.5459111 -2.736831305 0.106614378 CVPASGELS(ph)PELQEWAPYS(ph)PGHSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 2 CVPAS(0.022)GELS(0.978)PELQEWAPY(0.002)S(0.958)PGHS(0.022)S(0.019)R 107.91 0.0018497 35453000 53174 44423 51319 58050 64109 47119 71442 53553 67973 TRUE FALSE 50660.5704 48949.7542 53672.02691 52214.70371 75289.5893 45487.25722 60542.21078 48863.61542 78513.90568 0.645243285 0.623453308 0.683598994 0.665037655 0.958933181 0.579352878 0.771101759 0.622356193 1 16.26066057 -5 0.207506208 2.427630809 0.646371804 0.432864445 0.108303945 130.0860149 1.294278897 77.49156354 0.21643479 1.00E-05 5 -1.781259005 CVPASGELS(ph)PELQEWAPYSPGHSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 CVPAS(0.003)GELS(0.997)PELQEWAPYSPGHSSR;CVPAS(0.037)GELS(0.963)PELQEWAPYSPGHSSR 131.5 5.16E-05 81894000 40816 28300 39659 44178 64793 33109 64920 45556 83865 TRUE FALSE 38886.70857 31183.80217 41477.40438 39737.14351 76092.87869 31962.42703 55015.26166 41566.87513 96870.35588 0.40143043 0.321912745 0.428174378 0.410209534 0.785512534 0.329950548 0.567926701 0.429097991 1 16.56376762 -5 0.184030439 3.279661928 0.342905465 0.628136216 0.131945605 81.48222949 0.789840839 67.99168702 0.355591486 1.00E-05 5 -2.936756463 CVPDPDTGLYMLQLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CVPDPDTGLYMLQLAGR 17 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 64.55 0.09645 0 30938 21207 25087 28461 45100 26301 37210 31027 61577 FALSE TRUE 29475.62205 23368.01741 26237.26376 25600.04621 52965.42572 25390.18978 31532.93109 28310.1114 71126.04667 0.414413895 0.32854374 0.368884045 0.359925054 0.744669895 0.356974568 0.443338728 0.398027343 1 16.11809036 -5 0.311946193 6.190676892 0.393937261 0.697990797 0.118243628 163.4708882 1.474268602 558.1663841 0.104417328 1.00E-05 5 -5.796739631 CYEMASHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 CYEMASHLR 9 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;;;;; 226.47 2.36E-07 20441670000 22119830 14473800 12582600 16080210 18047030 14910737 22525150 17095910 16463900 FALSE TRUE 21074269.47 15948696.68 13159524.66 14463796.74 21194426.32 14394374.44 19088524.66 15598901.49 19017037.53 1.108178361 0.838653058 0.691986049 0.760570447 1.11449674 0.756919916 1.00375911 0.820259279 1 24.18078918 CYEMASHLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CYEMASHLRR 10 1 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 63.283 0.037986 22738000 21688 16235 19298 17989 21812 19213 26438 24318 28193 FALSE TRUE 20662.85122 17889.36496 20182.83239 16180.71154 25616.00589 18547.64899 22404.39753 22188.587 32565.02645 0.6345105 0.549342866 0.619770183 0.496873895 0.786610935 0.569557314 0.687989539 0.681362474 1 14.99103578 -1.014998423 0.315500827 1.205497126 0.578422622 0.725386253 0.074387511 6.761267628 0.542707757 1.300002086 0.065517726 0.096605439 1.014998423 -0.627074504 CYFKHT(ph)LQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 CYFKHTLQQK 10 1 Q9P109 Q9P109 GCNT4 "Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4" 1 CY(0.448)FKHT(0.552)LQQK 72.79 0.068797 689360000 1869600 1744200 1431400 1654700 752500 1700800 1378700 1439700 490930 TRUE FALSE 1781227.713 1921935.963 1497031.106 1488366.412 883735.7617 1641900.87 1168353.993 1313632.236 567060.9171 3.141157607 3.389293646 2.639982867 2.624702863 1.558449428 2.895457649 2.060367693 2.316562817 1 19.1131442 3.781824803 0.103048286 4.49E-16 5.825099746 0.669761283 0.414042754 20.72076108 0.497209266 7.869827122 21.57263671 6050.967258 -3.781824803 5.825099746 CYQSEFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 CYQSEFGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 168.08 0.00071867 1030258000 1608260 1621920 1471740 1699910 1236390 1582040 1577180 1542370 1220410 FALSE TRUE 1532240.737 1787195.492 1539220.735 1529031.817 1452016.025 1527253.558 1336552.224 1407311.906 1409664.95 1.086953845 1.267815797 1.091905374 1.084677474 1.030043362 1.083415998 0.948134679 0.998330778 1 20.42692087 2.895243187 1.002892047 0.991788036 1.174833394 0.569098078 0.056473157 0.328643879 0.71213778 0.027810048 0.03035951 785.6754571 -2.895243187 0.183045358 CYYSNTDAVIYVVDSCDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 CYYSNTDAVIYVVDSCDRDR 20 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 163.45 1.79E-11 226379000 329680 280436 331490 352540 245103 377630 363950 395220 280165 FALSE TRUE 314096.6798 309012.7472 346689.1444 317102.0094 287848.8856 364552.5784 308422.7431 360612.4416 323611.5573 0.970597844 0.954887859 1.071312617 0.979884687 0.889488892 1.126512852 0.953064673 1.114337339 1 18.30390361 2.240263723 24.99997871 1.037690179 0.975253298 0.234944983 0.066153949 76.25231106 1119332.566 0.021882453 0.017427319 173.8856421 -2.240263723 -0.062436881 CYYYHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 CYYYHAR 7 0 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 132.8 0.0033333 284550000 222408 180375 120877 144864 236435 144688 250167 178207 215342 FALSE TRUE 211895.2146 198755.4176 126419.33 130301.9955 277669.1891 139677.4183 211999.4295 162602.2503 248736.1375 0.851887533 0.799061285 0.508246736 0.523856311 1.116320258 0.561548554 0.852306511 0.653713819 1 17.9242566 DAADKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DAADKPR 7 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;;;;; 120.49 0.0041458 8483630000 21977500 19587970 18614490 23128390 13244540 19555560 22124440 26483490 19613180 FALSE TRUE 20938667.13 21584006.41 19467982.78 20803480.3 15554383.58 18878346.05 18748950.33 24164455.22 22654691.78 0.924253013 0.952738912 0.859335583 0.918285735 0.686585531 0.833308448 0.827596796 1.066642418 1 24.43330653 1.237793078 24.99998089 1.033321267 0.864643729 0.486034499 0.074906904 19.55869758 636855.4531 0.063304076 0.019370538 17.28992376 -1.237793078 -0.168677538 DAAEFELFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAAEFELFFR 10 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;; 169.09 1.10E-05 466066000 863958 748127 683060 830015 682091 642562 769232 808330 676721 FALSE TRUE 823120.4175 824361.9918 714378.9766 746580.3153 801047.4544 620309.9168 651871.5305 737548.34 781663.4365 1.053036869 1.054625243 0.913921444 0.955117357 1.02479842 0.793576734 0.833954232 0.943562543 1 19.57618803 3.505151543 0.820417628 0.887097747 1.073748962 0.297062569 0.073360675 0.682234961 0.924584027 0.033589951 0.083857681 3200.011527 -3.505151543 0.186651215 DADADAGGGADGGDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DADADAGGGADGGDGR 16 0 Q14657 Q14657 LAGE3 EKC/KEOPS complex subunit LAGE3 0 156.14 4.46E-07 33395000 46701 37078 41877 50262 36435 43846 49012 45800 36665 FALSE TRUE 44493.53628 40856.29035 43797.10187 45209.56827 42789.25246 42327.60203 41534.31923 41789.5092 42350.82094 1.050594423 0.964710706 1.034150009 1.06750158 1.010352374 0.999451748 0.980720522 0.986746143 1 15.37010232 2.212414545 3.08949548 0.988000825 1.02229159 0.282691973 0.027072839 0.375701045 7.408161122 0.011497535 0.008299855 163.085198 -2.212414545 0.034290765 DADAGDEDEESEEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 385.3 5.83E-114 1244780000 787170 693470 761520 845240 645780 775030 824720 784000 676170 FALSE TRUE 749962.0341 764135.3814 796436.4452 760274.8693 758403.8275 748190.5168 698893.817 715348.8038 781026.9902 0.960225502 0.978372567 1.019729734 0.973429701 0.971034083 0.957957313 0.89483952 0.915907917 1 19.57501288 1.992201615 4.724287268 0.925140378 0.979127962 0.264900702 0.031164948 0.187064273 11.13327247 0.012388652 0.007993853 98.22038111 -1.992201615 0.053987583 DADDAVYELNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 234.92 1.15E-15 128554000 548170 646070 424220 670520 303000 545250 461390 571670 254170 FALSE TRUE 522259.0905 711905.2675 443670.9066 603118.0557 355843.1041 526367.8558 390996.4815 521611.5442 293585.3855 1.778900164 2.424866164 1.511215914 2.054319069 1.212060006 1.792895293 1.331798178 1.776694515 1 18.16342063 2.178201246 0.192671813 0.828313869 2.43951094 0.3951296 0.322930163 3.370071578 0.475006411 1.264014207 1.989527907 150.7305367 -2.178201246 1.611197071 DADKSIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DADKSIIR 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 81.548 0.02059 97289000 206920 119240 194970 158840 180540 178620 267630 206980 215220 FALSE TRUE 197139.3017 131390.6916 203909.5674 142873.1014 212026.1188 172434.3446 226798.1281 188855.7339 248595.2184 0.793013248 0.528532658 0.820247343 0.57472184 0.852897011 0.693635001 0.912318948 0.75969174 1 17.92343902 1.369872363 0.474421147 0.995658365 0.663109515 0.396659406 0.111501458 0.774261734 0.470151551 0.109830366 0.06604756 23.43539962 -1.369872363 -0.33254885 DADPILISLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DADPILISLR 10 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 204.42 4.36E-07 358197700 803423 703402 595708 685126 710373 611116 855113 754187 734634 FALSE TRUE 765446.787 775079.4635 623021.801 616255.8328 834261.8263 589952.8997 724649.8066 688146.3881 848557.2887 0.902056699 0.913408527 0.73421301 0.726239514 0.983153215 0.695242275 0.853978649 0.810960435 1 19.69465254 -1.525521218 2.305745637 1.013361014 0.833986418 0.258560449 0.091248215 2091701.788 1734703.381 173791.0653 0.022707024 0.029818019 1.525521218 -0.179374596 DADSQNPDAPEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DADSQNPDAPEGKR 14 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 147.51 1.29E-05 317600000 390710 230563 375000 354550 294291 374130 533610 452620 412800 FALSE TRUE 372241.9126 254057.6318 392194.1209 318909.9604 345615.2572 361173.7843 452197.9941 412986.1933 476814.9157 0.780684287 0.532822325 0.822529053 0.66883386 0.724841539 0.757471657 0.948372165 0.866135223 1 18.86306984 1.884880189 2.053127653 0.941542184 0.690492698 0.617828237 0.083001928 0.196201768 1.53728247 0.048434668 0.022970027 76.71498219 -1.884880189 -0.251049486 DADVQFLASVLPPDTDPAFFEHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DADVQFLASVLPPDTDPAFFEHLR 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31;H0YDA6 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;;;;;; 163.71 1.64E-11 1199689000 1332638.1 1249290 1090248 1470768 1051820.4 1211835.1 1293491 1399586 1001380.8 FALSE TRUE 1269646.938 1376594.071 1140236.949 1322923.606 1235257.545 1169868.947 1096145.191 1277030.83 1156669.82 1.097674475 1.190135722 0.985792946 1.14373487 1.067943093 1.011411317 0.947673374 1.104058226 1 20.14154566 2.385799275 3.233135372 1.004249142 1.111279108 0.290187928 0.063698903 0.254215365 5.337085054 0.022754249 0.018558779 243.1080135 -2.385799275 0.107029966 DAEDAIYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAEDAIYGR 9 0 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ; 119.21 0.0020101 390030000 777340 710750 689980 817520 727140 706040 801130 815390 775100 FALSE TRUE 740596.6787 783176.2331 721616.2655 735341.3364 853952.9858 681589.6578 678902.9047 743990.1289 895298.5493 0.827206388 0.874765444 0.806006294 0.821336455 0.953819244 0.76129874 0.758297783 0.830996688 1 19.77200932 DAEDALHNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 147.24 3.54E-05 828340000 3711040 4197190 2769670 4337050 2793720 3300240 3105490 3458480 2225130 FALSE TRUE 3535626.494 4624888.433 2896662.109 3901081.494 3280943.883 3185951.861 2631690.464 3155637.157 2570191.796 1.375627492 1.799433194 1.127021771 1.51781727 1.276536595 1.239577477 1.023927657 1.227782752 1 21.29344459 2.560784535 0.656319669 1.041469491 1.561430319 0.456281991 0.174969708 0.570482991 0.508606872 0.130869183 0.114836579 363.734533 -2.560784535 0.519960828 DAEDALHNLDRK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 255.54 2.50E-21 950870000 2568457 2235601 2049211 2629737 1422632 2442705 2431417 2630559 1125880 FALSE TRUE 2447051.128 2463411.284 2143169.351 2365390.841 1670738.57 2358113.513 2060459.681 2400213.308 1300475.72 1.88165845 1.894238582 1.647988746 1.818865823 1.284713389 1.813269926 1.584389196 1.845642538 1 20.31060803 -2.512479014 0.198629481 1.12E-21 1.888337408 0.589042218 0.187059724 29.87866561 0.720278457 14.12054572 0.467951103 0.003072706 2.512479014 1.888337408 DAEDAMDAMDGAVLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAEDAMDAMDGAVLDGR 17 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;; 276.71 2.14E-35 499802000 849950 749920 771770 844280 630081 816073 975860 892810 683771 FALSE TRUE 809774.5479 826337.7006 807156.4179 759411.3704 739966.9269 787812.1874 826974.6341 814630.8233 789806.7145 1.025281924 1.046253071 1.021967024 0.961515465 0.936896222 0.997474664 1.047059513 1.031430613 1 19.59114011 -3.126239365 9.347914798 1.000103398 1.011242054 0 0.035814869 0 0 0 0.008695792 0.000747757 3.126239365 0.011138656 DAEDAVYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAEDAVYGR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 160.88 0.00021636 854120000 1978550 2275210 1624530 2326260 1363190 1845110 1741660 1945010 1344440 FALSE TRUE 1885027.863 2507056.486 1699016.307 2092419.925 1600929.904 1781213.378 1475937.779 1774694.613 1552928.889 1.213853304 1.614405208 1.094072188 1.34740228 1.03090999 1.147002539 0.950421999 1.142804816 1 20.56656034 2.98044485 1.140680632 1.036185367 1.391696512 0.426763653 0.145935271 0.363389353 1.00569778 0.058971039 0.069926781 955.9712913 -2.98044485 0.355511145 DAEDDGEEEDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAEDDGEEEDD 11 0 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ; 257.96 3.53E-20 377430000 999940 859570 898160 1024410 756450 952930 1045190 965790 669830 FALSE TRUE 952674.8179 947161.1602 939341.5244 921434.3605 888374.6405 919929.7952 885727.0693 881220.3076 773703.8154 1.231317203 1.224190887 1.214084131 1.190939404 1.148210236 1.188994777 1.144788292 1.138963373 1 19.56142186 -5 0.107262182 0.351909164 1.310747811 0.956461798 0.013936829 28.96583078 0.207927685 4.084661794 0.175954148 1.00E-05 5 0.958838647 DAEGILEDLQSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAEGILEDLQSYR 13 0 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8;E5RK61;E5RFS4;E5RHU5 E5RI16 FAM49B Protein FAM49B 0 ; 209.19 9.28E-08 76857000 149067 147232 129257 171103 140835 141009 160732 149347 134716 FALSE TRUE 142020.8983 162235.1082 135183.5613 153903.4014 165396.5794 136125.823 136209.3814 136269.3849 155607.0692 0.912689244 1.042594716 0.868749485 0.989051475 1.062911732 0.874804876 0.87534186 0.875727469 1 17.24754808 2.193447238 24.99999856 0.89309846 0.974498205 0.196273355 0.066707247 169.5067671 93932.73078 0.023148115 0.017096082 156.1159362 -2.193447238 0.081399745 DAEILRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DAEILRK 7 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 123.69 0.0067652 1092350000 2427140 1722620 2115660 2133720 1813710 2166590 2731210 2457790 2007940 FALSE TRUE 2312413.902 1898156.936 2212665.104 1919234.412 2130020.45 2091560.445 2314513.752 2242572.878 2319321.08 0.997021897 0.818410591 0.954014139 0.827498369 0.918381016 0.901798575 0.997927269 0.966909195 1 21.14527113 1.757636232 6.496395014 0.986273506 0.899850109 0.364176476 0.053038101 0.163067669 18.93519296 0.023793 0.012776135 57.23164536 -1.757636232 -0.086423397 DAELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAELLR 6 0 A0A087WYM3 A0A087WYM3 SIRT2 0 ; 106.85 0.073919 280140000 683830 664530 552520 754460 590550 584740 672440 651040 555100 FALSE TRUE 651506.7111 732246.3625 577853.5885 678620.2474 693541.733 564490.3072 569846.9278 594031.4862 641182.0729 1.016102506 1.142025633 0.901231667 1.058389303 1.081661142 0.880390034 0.888744324 0.92646303 1 19.29037456 2.237219143 24.99970203 0.910631987 1.046187898 0.407564084 0.068427143 29.80169092 555367.0183 0.023758277 0.018519312 172.6708963 -2.237219143 0.135555911 DAELQDQEFGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAELQDQEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 99.941 0.0056328 205873000 494190 453750 427090 515320 303190 460920 520130 520500 345510 FALSE TRUE 470830.6181 499987.6409 446672.4989 463519.0546 356066.24 444958.2248 440774.6157 474922.2607 399089.9262 1.179760719 1.252819498 1.119227697 1.161440127 0.892195509 1.114932239 1.104449365 1.190013151 1 18.60635434 3.39326679 2.143307403 1.075282726 1.214009354 0.309702517 0.084875463 0.345241417 3.216970163 0.024471929 0.037197502 2473.243008 -3.39326679 0.138726628 DAELQDQEFGKRDS(ph)LGTYSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DAELQDQEFGKRDSLGTYSSR 21 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR;DAELQDQEFGKRDS(0.999)LGTYSSR;DAELQDQEFGKRDS(0.984)LGT(0.015)YS(0.001)SR;DAELQDQEFGKRDS(0.993)LGT(0.007)YSSR;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(1)LGTYSSR 292.25 4.87E-55 9490350000 4761830 3456186 4510920 4501860 3068104 4576700 5760150 5173230 3589430 TRUE FALSE 4536747.733 3808375.283 4717750.144 4049324.48 3603180.366 4418207.731 4881333.325 4720234.556 4146060.472 1.094230961 0.918552758 1.137887442 0.976667974 0.869061219 1.065639964 1.17734253 1.138486664 1 21.98330973 2.002202023 24.98511647 1.124108668 0.999274075 0.226005295 0.088604215 80.64658776 915040.7594 0.031325119 0.022986685 100.5083222 -2.002202023 -0.124834594 DAENHEAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAENHEAQLK 10 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 149.96 2.24E-05 572700000 2129770 2004810 1918250 2341500 1583920 2153200 2424100 2283100 1591800 FALSE TRUE 2029099.993 2209102.418 2006203.66 2106127.971 1860155.147 2078634.144 2054259.023 2083179.661 1838648.214 1.1035825 1.201481828 1.091129692 1.14547631 1.011697144 1.130523027 1.117265939 1.132995232 1 20.81021405 -5 0.186002712 0.501521249 1.14422524 0.354453659 0.048240579 143.411598 1.394462176 26.5662452 0.131768101 1.00E-05 5 0.642703991 DAESIHQYLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAESIHQYLLQR 12 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 208.95 6.09E-08 1622260000 1538680 1211410 1301090 1572300 1769970 1376950 1916560 1610980 1845730 FALSE TRUE 1465949.646 1334854.056 1360746.263 1414249.417 2078652.208 1329265.876 1624153.572 1469914.051 2131956.382 0.68760771 0.626116964 0.638261775 0.663357576 0.974997531 0.623495812 0.761813697 0.689467225 1 21.02374649 -4.999999997 0.165795591 2.125267339 0.628944605 0.456068265 0.101767461 115.6206213 1.079456557 42.82755572 0.366548073 1.00E-05 4.999999997 -1.496322734 DAEVERDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAEVERDEER 10 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ;;; 174.4 2.84E-06 2987150000 2693590 2062520 2187650 2619770 2125210 2441750 2824520 2540040 2293470 FALSE TRUE 2566269.339 2272693.133 2287955.916 2356425.742 2495845.951 2357191.585 2393587.598 2317620.632 2649129.614 0.968721698 0.857901826 0.863663259 0.889509418 0.942138104 0.889798511 0.903537368 0.874861169 1 21.337087 -1.435426354 3.043527631 1.001928117 0.899177636 0.465966667 0.034056623 8521177.964 9811440.462 139543.5528 0.00841282 0.036692191 1.435426354 -0.102750481 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK 30 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 271.47 3.16E-71 98419000 172970 184610 159980 192080 104150 171730 153320 172440 95395 FALSE TRUE 164794.0509 203421.9689 167315.2412 172771.7535 122313.727 165782.947 129928.2181 157340.2394 110188.3694 1.495566654 1.846129224 1.518447384 1.56796724 1.110042083 1.50454125 1.179146391 1.427920572 1 16.74961243 2.891445211 4.751051147 1.271268878 1.639961302 0.519610471 0.172068576 0.169179387 6.005374577 0.048058615 0.051520182 778.8345535 -2.891445211 0.368692425 DAFPEAIIVKPSDIFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAFPEAIIVKPSDIFGR 17 1 Q16795;A0A3B3ISG8 Q16795 NDUFA9 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial" 0 ; 92.977 0.0028963 215060000 239620 234980 242700 258060 222300 219640 277750 221110 228030 FALSE TRUE 228293.6375 258924.7292 253828.0351 232119.3185 261069.0496 212033.8117 235374.1363 201748.4362 263391.7278 0.866745662 0.983040475 0.963690231 0.881270344 0.991181659 0.805013178 0.893627671 0.765963449 1 18.00685051 2.238022393 24.99999978 0.859313481 0.935698108 0.191672473 0.07184322 20.76649733 964515.7909 0.023009483 0.018039845 172.9905553 -2.238022393 0.076384626 DAGDKDKEQELSEEDKQLQDELEMLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAGDKDKEQELSEEDKQLQDELEMLVER 28 3 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 161.72 3.95E-12 73141300 103592 90210 90127 112660 34927.6 134722 106215 126226 36912 FALSE TRUE 98695.41146 99402.50156 94259.4121 101335.2028 41018.96238 130056.5434 90009.95098 115172.9823 42636.12444 2.314830739 2.331415035 2.210787527 2.376745168 0.962070613 3.050383802 2.111119436 2.701300453 1 15.37978868 DAGGPRPES(ph)PVPAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAGGPRPESPVPAGR 15 1 Q9BVG9;E9PS47;E9PLE4 Q9BVG9 PTDSS2 Phosphatidylserine synthase 2 1 DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR 157.14 1.21E-06 928110000 847960 728150 821810 1144270 1142340 950870 1134310 949830 1043230 TRUE FALSE 807878.6113 802349.3128 859490.8014 1029245.806 1341563.734 917941.1335 961250.1765 866657.8498 1205008.78 0.670433796 0.6658452 0.713265177 0.854139673 1.113322788 0.761771324 0.797712176 0.719212892 1 20.20061223 3.2998777 4.032924502 0.863710964 0.672015127 0.387003711 0.113874055 0.232169866 7.566976019 0.032451801 0.043753054 1994.700515 -3.2998777 -0.191695838 DAGHPLYPFNDPY ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DAGHPLYPFNDPY 13 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;;; 169.21 6.72E-05 2263740000 3272030 2671390 2821080 3179560 2993300 2846530 3452340 3097040 3404730 FALSE TRUE 3117367.626 2943607.678 2950429.308 2859944.588 3515330.572 2747953.952 2925622.126 2825846.759 3932718.139 0.79267507 0.748491901 0.750226486 0.727218297 0.893867917 0.698741648 0.743918588 0.718548001 1 21.90709536 -1.073784449 4.491917525 1.000013588 0.759197534 0.664545387 0.053764264 8.21E-06 1.69E-06 0.047682581 0.011238116 0.084375343 1.073784449 -0.240816054 DAGQISGLNVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAGQISGLNVLR 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 154.94 0.00016455 233020000 147000 118919 113159 114053 141936 110155 158658 126743 154573 FALSE TRUE 140051.6013 131036.9813 118347.4521 102588.1758 166689.5935 106340.3047 134451.8081 115644.711 178543.3914 0.784412127 0.733922327 0.662849805 0.574583999 0.933608308 0.59559922 0.75304836 0.647712078 1 17.44591521 -1.408999951 3.045045519 1.004498809 0.715968381 0.436593954 0.103122225 16393301.33 20196394.15 641509.1567 0.022581232 0.038994203 1.408999951 -0.288530428 DAGRPGERGS(ph)GGLFSPSTAHVPDGALGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.999)GGLFS(0.001)PSTAHVPDGALGQR;DAGRPGERGS(1)GGLFSPSTAHVPDGALGQR;DAGRPGERGS(0.692)GGLFS(0.308)PSTAHVPDGALGQR;DAGRPGERGS(0.926)GGLFS(0.069)PS(0.004)T(0.001)AHVPDGALGQR 120.23 2.17E-05 2631264000 770150 465443 683165 654563 766962 639274 905204 779883 836408 TRUE FALSE 733746.5358 512872.1709 714488.791 588765.0837 900719.93 617135.7811 767098.5046 711592.3101 966113.8809 0.759482449 0.53086099 0.739549245 0.609415821 0.932312378 0.638781611 0.794004226 0.736551171 1 19.88183373 -3.783612715 0.149853633 1.730491739 0.601457416 0.430453842 0.106193418 74.35977041 0.93056084 16.97141199 0.512662296 0.000164584 3.783612715 -1.129034323 DAGTIAGLNVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 216.26 9.19E-11 1619939000 1011840 838232 779521 857329 961780 796322 1096780 932689 956945 FALSE TRUE 964012.3285 923648.7938 815262.8089 771148.6601 1129514.127 768745.1695 929446.0673 851017.8067 1105343.143 0.872138516 0.83562177 0.737565356 0.697655443 1.021867403 0.695481013 0.840866543 0.769912775 1 20.07606288 -2.061491216 2.6017133 1.270347856 0.812970691 0.280165829 0.096073639 18043382.59 6252840.169 29002273.13 0.020831621 0.008679781 2.061491216 -0.457377165 DAHNALLDIQSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 147.83 7.93E-06 720180000 532368 560026 528989 669599 583556 544143 637531 564009 376977 FALSE TRUE 507204.0197 617093.2861 553243.6689 602289.6364 685327.9816 525299.1915 540263.9369 514621.382 435436.6678 1.164816969 1.417182639 1.270549106 1.383185388 1.573886703 1.20637335 1.240740564 1.181851277 1 18.73210338 1.133848009 1.125210193 1.009894216 1.341373723 0.487286612 0.112825498 0.403823923 1.06689639 0.103219709 0.033456064 13.60968298 -1.133848009 0.331479507 DAIAQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAIAQAVR 8 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 133.81 0.0021016 1161290000 1502600 1004360 742130 855690 1397890 817920 1443830 1034740 1226240 FALSE TRUE 1431575.076 1106705.426 776157.3946 769674.4155 1641681.573 789595.2253 1223547.216 944132.6801 1416399.036 1.010714523 0.781351439 0.54797933 0.543402244 1.159053015 0.55746665 0.863843581 0.666572524 1 20.43379634 4.432029025 2.671368347 0.753121841 1.002202652 0.124452188 0.202901327 0.535301188 7.015684015 0.046653072 0.216153447 27041.39083 -4.432029025 0.249080811 DAIHFYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAIHFYNK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 111.04 0.0037001 692220000 2447360 2103070 1327910 1592630 1774490 1515270 2361950 1997250 1583180 FALSE TRUE 2331678.143 2317375.224 1388795.987 1432535.807 2083960.494 1462795.82 2001591.147 1822360.202 1828691.469 1.275052781 1.267231386 0.75944795 0.783366594 1.139591085 0.799913952 1.094548305 0.996537816 1 20.80238026 3.762897493 23.78768918 0.945362185 1.271142239 0.537149842 0.128052968 289.2546402 282725.5928 0.031585032 0.056895933 5792.919497 -3.762897493 0.325780054 DAINQGMDEELERDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAINQGMDEELERDEK 16 1 F8WF02;C9J634;P11177-3;P11177-2;P11177 F8WF02 PDHB "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial" 0 ; 250.95 3.88E-21 1206610000 523700 501380 592500 494350 362680 469850 472660 524600 295410 FALSE TRUE 498945.7389 552471.192 619666.7111 444656.9988 425931.2772 453578.9767 400547.036 478663.2429 341220.6741 1.462237715 1.619102341 1.81602921 1.30313616 1.248257534 1.329283397 1.173865086 1.402796722 1 18.38034553 3.10495906 7.187851556 1.247204615 1.60418152 0.650810381 0.134582325 0.136435711 8.344421774 0.036316934 0.043532339 1273.383037 -3.10495906 0.356976905 DAKLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAKLDK 6 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652;P17066;P48741 A0A0G2JIW1;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA8;HSPA2;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;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 ;; 84.244 0.051138 2745000000 4123000 2222670 4217600 3236130 2565220 4150900 5313000 5037600 3689300 FALSE TRUE 3928113.961 2449162.6 4410981.132 2910828.064 3012593.556 4007153.292 4502404.27 4596481.038 4261417.802 0.921785693 0.574729518 1.035097082 0.683065637 0.706946302 0.940333354 1.056550772 1.078627173 1 22.02290207 2.038354911 3.943303051 1.043124488 0.775643444 0.468875023 0.127559939 0.17772468 5.928941033 0.050672687 0.033687512 109.2332641 -2.038354911 -0.267481044 DALDGPAAEAEPEHSFDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 242.59 8.53E-30 320360000 454890 485000 382680 493160 363190 391250 415940 437280 276360 FALSE TRUE 433388.2512 534422.0514 400226.2565 443586.6199 426530.221 377700.9144 352480.7137 398989.445 319216.4973 1.357662448 1.67416802 1.253776856 1.389610573 1.336178501 1.183212389 1.104205819 1.249902334 1 18.28417569 2.442414036 0.586575834 1.056588741 1.512790519 0.591657038 0.116033141 0.507330413 0.356660201 0.096068377 0.08360907 276.9580773 -2.442414036 0.456201777 DALDGPAAEAEPEHSFDGLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 245.95 1.91E-30 703080000 424350 318490 368938 401770 390839 391339 473641 418639 395586 FALSE TRUE 404291.8165 350944.4931 385854.1722 361383.3163 459001.1979 377786.8323 401378.3664 381980.7498 456931.4565 0.884797513 0.768046253 0.844446507 0.790891743 1.004529654 0.826791036 0.878421393 0.835969475 1 18.80161824 DALGDSLQVPVS(ph)PSSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 DALGDSLQVPVS(0.985)PS(0.008)S(0.001)T(0.001)T(0.001)S(0.001)S(0.001)R;DALGDSLQVPVS(0.941)PS(0.052)S(0.005)T(0.001)TSSR;DALGDSLQVPVS(0.978)PS(0.02)S(0.002)TTSSR 236.27 1.52E-29 124642000 335480 231548 275262 310371 274268 279333 335993 293757 278038 TRUE FALSE 319622.5253 255143.0044 287883.035 279171.9174 322100.2524 269659.6282 284731.0969 268034.0798 321154.713 0.995229129 0.794455115 0.896399845 0.86927548 1.002944186 0.839656456 0.886585454 0.834594882 1 18.29290894 4.740511773 5.422202686 0.884801358 0.999419899 0.190496467 0.066941457 0.211952284 20.89680615 0.014327545 0.089331675 55018.88344 -4.740511773 0.114618541 DALHSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DALHSEK 7 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 111.01 0.0066756 137050000 258790 287240 222700 318840 173540 244130 239440 275770 159350 FALSE TRUE 246557.5096 316510.0826 232911.0153 286789.5974 203805.3211 235675.7169 202909.0304 251622.1169 184061.1842 1.339541037 1.719591689 1.265399961 1.558121006 1.107269422 1.280420519 1.102399897 1.367056927 1 17.48982589 2.738701172 24.99999994 1.180448374 1.486178793 0.474638086 0.155894813 10.19464138 1813381.658 0.044537663 0.044598728 547.8998385 -2.738701172 0.30573042 DALKTEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DALKTEFK 8 1 Q5VTU8;P56381 Q5VTU8 ATP5EP2;ATP5E "ATP synthase subunit epsilon-like protein, mitochondrial;ATP synthase subunit epsilon, mitochondrial" 0 ; 114.5 0.0040091 603940000 1567800 1107900 1407890 1408160 1153840 1544700 2075230 1880580 1319170 FALSE TRUE 1493693.201 1220796.27 1472443.149 1266609.081 1355069.331 1491206.652 1758615.549 1715906.446 1523740.146 0.980280794 0.801184029 0.966334813 0.831250056 0.889304737 0.978648922 1.154144001 1.126114876 1 20.53918546 1.973939748 3.580606523 1.106123408 0.890429541 0.650510306 0.066428438 0.123594562 3.194431246 0.028644396 0.017025644 94.17589325 -1.973939748 -0.215693867 DALSDLALHFLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DALSDLALHFLNK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 256.31 7.29E-24 1941390000 3422800 3523300 2850100 3308400 2411980 3239700 3696100 3689400 2134040 FALSE TRUE 3261011.027 3882328.276 2980779.904 2975833.346 2832628.548 3127508.377 3132192.061 3366336.577 2464976.024 1.322938234 1.574996364 1.209253102 1.207246366 1.149150548 1.268778417 1.27067851 1.365667067 1 21.23314218 1.256627316 0.036698073 2.07E-11 2.441625189 0.361244704 0.119049986 83.50534333 2.673329967 90.24763385 85.77909871 18.05623989 -1.256627316 2.441625189 DAMEQCHNYNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DAMEQCHNYNAR 12 0 Q92785;J3KMZ8;Q92785-2;E9PN04 Q92785 DPF2 Zinc finger protein ubi-d4 0 105.65 0.0015225 28542000 11185 7652.3 11092 13303 10167 9479.7 12983 10972 12199 FALSE TRUE 10656.30722 8432.07807 11600.57917 11965.75717 11940.12158 9151.415612 11002.2049 10011.23351 14090.75862 0.756262137 0.598411931 0.823275701 0.849191835 0.847372516 0.649462237 0.780809976 0.710482224 1 13.78246166 -2.321852396 2.14361906 2.251635099 0.744433996 0.471824126 0.082154654 3731791.343 441886.5374 22655477.19 0.021253155 0.004765929 2.321852396 -1.507201103 DANDPVDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DANDPVDDR 9 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 103.88 0.0077957 141460000 342610 324610 329780 367740 339060 347230 378900 369300 347940 FALSE TRUE 326415.5043 357688.1281 344900.7392 330774.0765 398191.9566 335205.338 321091.846 336962.1342 401896.7582 0.812187453 0.890000033 0.858182437 0.823032458 0.990781708 0.834058328 0.79894112 0.83842959 1 18.61646541 4.670952716 3.451611384 0.86750566 0.809088478 0.064288875 0.068313951 0.808600227 15.90735873 0.015550127 0.109900893 46876.23425 -4.670952716 -0.058417182 DANEVEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DANEVEKK 8 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ; 96.89 0.013822 497450000 1118380 835550 885880 1067790 693300 1120420 1242790 1279980 866530 FALSE TRUE 1065516.394 920693.4949 926498.4743 960453.7205 814211.3005 1081619.574 1053179.56 1167898.166 1000907.047 1.064550796 0.91985914 0.925658858 0.959583334 0.813473442 1.080639384 1.052225143 1.166839787 1 19.93287657 2.148374033 24.99999993 1.076431626 0.946499055 0.468972839 0.072699172 18.02684559 4991.726614 0.026270786 0.019402265 140.7258995 -2.148374033 -0.12993257 DANQVHSTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DANQVHSTTR 10 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;; 86.014 0.013847 177417000 134921 101998 112627 132984 145161 113707 155043 138821 142459 FALSE TRUE 128543.5517 112391.7122 117791.0594 119616.1957 170477.0324 109769.2981 131388.3428 126665.0973 164550.8141 0.781178461 0.683021307 0.715833951 0.726925578 1.036014518 0.667084503 0.798466683 0.769762811 1 17.32817364 -4.999999999 0.193456704 2.017099766 0.725498955 0.333935452 0.102041614 155.5227366 1.527654442 61.04913592 0.247966908 1.00E-05 4.999999999 -1.291600811 DANVS(ph)GTLVSSSTLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DANVSGTLVSSSTLEK 16 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 DANVS(0.996)GT(0.003)LVS(0.001)SSTLEK 96.012 0.0037316 36986000 120320 99438 113180 125950 102000 114880 125330 127700 110350 TRUE FALSE 114632.7121 109570.8453 118369.415 113289.2667 119788.7677 110901.6768 106208.6067 116517.911 127462.5144 0.899344506 0.859631914 0.928660599 0.888804581 0.939796051 0.870072878 0.83325366 0.914134729 1 16.9597135 0.980456838 24.15197093 1.000000002 0.88517402 0.557575772 0.031028302 690.6330272 853504.7125 0.030455018 0.007613755 9.559976788 -0.980456838 -0.114825982 DAPAPRPLPASEGHLQPPAQTSGPT(ph)GSPPCIQTSPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQTS(0.001)GPT(0.757)GS(0.228)PPCIQT(0.013)S(0.001)PDPR 150.57 3.09E-13 358280000 96253 73425 91800 102920 107540 94042 111250 103140 105500 TRUE FALSE 91703.31145 80907.09098 96009.1208 92574.28606 126294.942 90785.30196 94276.76925 94108.51482 121860.4012 0.752527569 0.663932583 0.787861519 0.759674883 1.036390335 0.744994281 0.77364565 0.772264935 1 16.89486987 -5 0.099202239 1.652958184 0.632061415 0.337305514 0.094773959 216.6168726 1.464720284 29.94992213 1.61949274 1.00E-05 5 -1.02089677 DAPAPRPLPASEGHLQPPAQTSGPTGS(ph)PPCIQTSPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQTSGPT(0.002)GS(0.998)PPCIQTSPDPR;DAPAPRPLPASEGHLQPPAQTSGPT(0.015)GS(0.979)PPCIQT(0.006)SPDPR;DAPAPRPLPASEGHLQPPAQTSGPT(0.011)GS(0.987)PPCIQT(0.003)SPDPR 207.35 6.63E-31 1377600000 273612 205327 267101 278218 287390 267028 320635 276958 310286 TRUE FALSE 260678.903 226250.0547 279347.845 250250.9981 337510.725 257780.7534 271716.2419 252706.0893 358403.5682 0.727333448 0.63127177 0.779422611 0.698238021 0.941705817 0.719247174 0.758129288 0.705088095 1 18.45122547 -5 0.189841898 2.093966098 0.691678526 0.483533657 0.081417652 113.8411525 1.113076056 47.29513485 0.211624924 1.00E-05 5 -1.402287572 DAPQDFHPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAPQDFHPDR 10 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 122.86 0.00047732 2671660000 3080750 1627900 2164760 2785300 2896480 2444010 3447270 2925780 3027950 FALSE TRUE 2935129.053 1793784.861 2264016.387 2505316.352 3401625.195 2359373.321 2921325.648 2669583.193 3497509.021 0.83920557 0.512874978 0.64732253 0.716314479 0.97258511 0.674586772 0.835258931 0.763281289 1 21.73789635 2.986360648 21.98771227 0.826303206 0.661180036 0.32413818 0.121343556 155.1703738 250149.0313 0.033900516 0.037467767 969.0822708 -2.986360648 -0.16512317 DAPT(ph)SPASVASSSSTPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 DAPT(0.572)S(0.428)PASVASSSSTPSSK 98.942 0.0097887 141660000 136130 113130 131220 144150 87740 139760 154190 144340 114100 TRUE FALSE 129695.4047 124658.0756 137236.5668 129659.7681 103041.8282 134920.0762 130665.4836 131700.8244 131794.0453 0.984076363 0.945855144 1.041295656 0.983805967 0.781839787 1.02371906 0.99143693 0.999292678 1 17.00792566 DAPTS(ph)PASVASSSSTPSSK ddPTM_SK-BR-3_Trastuzumab_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(1)PASVASSSSTPSSK;DAPTS(0.999)PAS(0.001)VASSSSTPSSK;DAPT(0.016)S(0.984)PASVASSSSTPSSK;DAPT(0.007)S(0.992)PAS(0.002)VASSSSTPSSK;DAPT(0.032)S(0.968)PASVASSSSTPSSK;DAPTS(0.997)PAS(0.002)VASSSSTPSSK 415.31 5.06E-148 2544280000 2564150 2085560 2312070 2520230 1693650 2466080 2806950 2633480 2011230 TRUE FALSE 2442947.711 2298080.935 2418080.696 2266891.692 1989022.024 2380679.031 2378698.224 2402878.53 2323121.276 1.051579931 0.989221251 1.040875791 0.975795674 0.856185187 1.024776044 1.023923395 1.034331937 1 21.14763304 -0.130405318 6.756957894 1.000000001 1.000853346 0 0.055869282 0 0 0.053368183 0.012579001 0.740618715 0.130405318 0.000853345 DAQELYAAGENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAQELYAAGENR 12 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 211.46 3.30E-05 144170000 229991 179792 178709 247283 234190 174138 233147 201938 190247 FALSE TRUE 219119.7812 198113.0092 186902.9844 222425.643 275032.6619 168107.5574 197576.1431 184255.2382 219749.5331 0.997134229 0.901540069 0.850527333 1.012178 1.251573362 0.764996198 0.899096987 0.838478406 1 17.74550057 DAQHYGGWEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DAQHYGGWEHR 11 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;;;;;; 148.62 2.01E-05 8183560000 3739298 3689356 3611366 3992512 3543227 3667701 3909346 3655285 539641 FALSE TRUE 3562548.794 4065305.571 3776950.703 3591177.108 4161164.667 3540687.595 3312903.468 3335208.868 623325.7702 5.715388268 6.521959729 6.059352724 5.761316603 6.675746241 5.6803164 5.314882885 5.350667383 1 19.24962683 -0.111850765 0.569257445 0.568862095 6.16404585 0.953972014 0.342738744 0.938788701 0.328026656 1.213937467 0.138727091 0.772946144 0.111850765 5.595183756 DAQIGWIQTVEDLHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DAQIGWIQTVEDLHER 16 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 213.24 2.42E-12 50806000 88610 93377 72795 98270 82226 82806 103790 86369 66674 FALSE TRUE 84421.58091 102892.2225 76132.72275 88391.7129 96566.18837 79938.40746 87954.92927 78806.07249 77013.4634 1.096192499 1.336029026 0.988563809 1.147743641 1.253887101 1.037979646 1.142072118 1.023276568 1 16.23282306 1.408486237 0.632116621 0.994105439 1.178380352 0.221094996 0.099262651 0.937497972 0.872895121 0.09099794 0.043280662 25.61452091 -1.408486237 0.184274913 DAQNSSDS(ph)SFEKNVEITEQLANGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAQNSSDSSFEKNVEITEQLANGR 24 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 DAQNS(0.002)S(0.002)DS(0.498)S(0.498)FEKNVEITEQLANGR;DAQNSSDS(0.5)S(0.5)FEKNVEITEQLANGR 143.07 1.52E-07 104232000 102545 96302 112228 111857 71367 124498 126175 141077 86206 TRUE FALSE 97697.90107 106115.2833 117373.7648 100612.9218 83813.3822 120186.603 106924.6864 128723.55 99574.3862 0.981154942 1.06568855 1.17875459 1.010429747 0.841716283 1.207003203 1.073817178 1.292737569 1 16.60348706 DAQRLS(ph)PIPEEVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 177 1.30E-06 714090000 1266380 1377150 1031770 1504900 773910 1269230 1169180 1412300 728690 TRUE FALSE 1206520.727 1517483.151 1079077.675 1353624.593 908879.659 1225276.247 990800.1175 1288631.525 841691.5236 1.433447639 1.802897033 1.282034623 1.608219348 1.07982513 1.455730767 1.177153494 1.531002141 1 19.68293206 3.154163159 1.414673872 1.274528143 1.596321779 0.254386251 0.212934495 0.466931536 1.953008138 0.068147833 0.093115106 1426.143277 -3.154163159 0.321793635 DAS(ph)DDLDDLNFFNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 DAS(1)DDLDDLNFFNQK 191.37 1.14E-11 0 32830 28859 25001 34239 18639 32780 33087 29204 22675 TRUE FALSE 31278.19096 31799.76491 26147.32058 30797.23067 21889.6357 31644.82038 28038.97047 26646.74294 26191.32319 1.194219579 1.214133577 0.998319955 1.175856235 0.835759062 1.208217704 1.070544251 1.017388192 1 14.67680133 3.750005201 24.2724031 1.054559949 1.204176601 0.294045979 0.102291835 558.3400128 1184157.435 0.023674046 0.042195218 5623.480601 -3.750005201 0.149616651 DAS(ph)PSKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.972)PS(0.028)KEER;DAS(0.597)PS(0.403)KEER;DAS(0.975)PS(0.025)KEER;DAS(0.93)PS(0.07)KEER;DAS(0.982)PS(0.018)KEER;DAS(0.714)PS(0.286)KEER;DAS(0.678)PS(0.322)KEER;DAS(0.5)PS(0.5)KEER;DAS(0.93)PS(0.07)KEER 169.65 3.53E-05 15706238000 17515900 15070440 15110170 18205630 8909832 17950610 18570640 18161460 9766656 TRUE FALSE 16687958.12 16606134.97 15802986.24 16375565.48 10463703.88 17328975.87 15737347.79 16571146.28 11281219.13 1.479269033 1.472015992 1.400822558 1.451577644 0.927533076 1.536090707 1.395004176 1.468914493 1 23.42741965 -2.183591251 2.176643854 0.000113202 1.398329145 0.342704001 0.170112119 1839852.384 462148.3827 9032750.105 0.040096861 0.006552526 2.183591251 1.398215943 DAS(ph)PTPSTDAEYPANGSGADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DASPTPSTDAEYPANGSGADR 21 0 O43639;E9PEE2;E7EPF5 O43639 NCK2 Cytoplasmic protein NCK2 1 DAS(1)PTPSTDAEYPANGSGADR;DAS(1)PTPSTDAEYPANGSGADR;DAS(1)PTPSTDAEYPANGSGADR;DAS(1)PTPSTDAEYPANGSGADR 360.21 6.74E-96 648870000 278413 224667 231334 258470 205524 236671 252008 249409 206882 TRUE FALSE 265252.9693 247560.8227 241940.8927 232488.1045 241367.3205 228475.0239 213559.5512 227569.4258 238964.204 1.110011311 1.035974504 1.01245663 0.972899291 1.010056387 0.956105643 0.893688459 0.952315962 1 17.866435 4.01669393 0.566797533 0.939770279 1.148822462 0.70044626 0.031353628 0.934485584 0.398093573 0.018981609 0.116849944 10391.87539 -4.01669393 0.209052183 DASDDLDDLNFFNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 283.24 1.64E-33 169809000 400460 384700 344370 456010 274082 381580 416760 445260 288701 FALSE TRUE 381531.0494 423901.3674 360159.7051 410171.0084 321881.814 368365.7889 353175.6077 406270.6739 333471.2766 1.144119677 1.271178051 1.080032166 1.230004013 0.965245995 1.104640234 1.059088541 1.21830785 1 18.34720298 2.762277482 24.90707662 1.07480718 1.186544857 0.309384975 0.082681205 867.6533728 911194.6567 0.023057898 0.024443118 578.4655266 -2.762277482 0.111737678 DASDDLDDLNFFNQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DASDDLDDLNFFNQKK 16 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 115.91 0.00075176 143235000 315780 253472 272425 298832 185905 315250 355980 354110 216474 FALSE TRUE 300853.7052 279301.085 284915.9557 268792.8396 218326.7731 304332.8135 301668.713 323102.2511 250043.6823 1.203204586 1.117009166 1.139464725 1.074983527 0.873154527 1.217118588 1.206464047 1.292183222 1 17.93182063 DASIVGFFDDSFSEAHSEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DASIVGFFDDSFSEAHSEFLK 21 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 362.51 2.40E-96 561664000 1252313 1399278 1045758 1464451 803661 1122943 1060225 1264245 647368 FALSE TRUE 1193118.646 1541866.019 1093707.039 1317241.603 943819.224 1084055.202 898468.2039 1153541.006 747758.5231 1.59559351 2.061983878 1.462647372 1.761586879 1.262197882 1.44973968 1.201548596 1.542665138 1 19.51221292 2.879910369 1.151030894 1.280311151 1.804690306 0.481469298 0.213591738 0.349226816 0.974307944 0.088039068 0.094215937 758.4210342 -2.879910369 0.524379155 DASPS(ph)KEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.187)PS(0.813)KEER;DAS(0.387)PS(0.613)KEER 132.5 0.00018365 3279740000 4840213 4315749 4508286 4888019 2560123 4739065 5156111 5059246 2841892 TRUE FALSE 4611425.724 4755528.73 4714995.372 4396666.043 3006607.641 4574949.991 4369451.568 4616231.599 3282598.097 1.404809723 1.448708794 1.436360844 1.339386033 0.915923166 1.393697875 1.331095504 1.406273769 1 21.64640669 -5 0.112821365 0.001315034 1.517218655 0.314460745 0.154095347 204.2647893 1.521685751 48.12468828 1.773523348 1.00E-05 5 1.515903622 DASRPHVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DASRPHVVK 9 1 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 63.426 0.045749 821111000 2129460 1717650 1728930 2043860 1498240 1809620 2174630 2119200 1602960 FALSE TRUE 2028804.646 1892680.488 1808203.151 1838407.31 1759532.582 1746952.406 1842850.254 1933631.613 1851538.85 1.095739712 1.02222024 0.976594766 0.99290777 0.950308216 0.943513773 0.995307365 1.044337586 1 20.82029339 4.266325884 1.531746263 0.982444544 1.099157109 0.59771013 0.028252277 0.32257258 1.246216194 0.007896535 0.043564271 18464.00393 -4.266325884 0.116712565 DASVPLIDVTNLPT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 DASVPLIDVT(0.052)NLPT(0.948)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR 261.31 8.86E-26 129519000 97906 100847 104405 115350 100833 105465 123123 112171 114936 TRUE FALSE 93278.17741 111123.424 109192.0725 103754.7988 118418.2433 101812.7206 104338.325 102348.7126 132759.6879 0.702609195 0.837026855 0.82247913 0.781523371 0.891974403 0.766894848 0.785918728 0.770932157 1 17.01845762 -2.620540971 2.07373993 4.976053469 0.794596965 0.628518741 0.04954851 1773452.002 73165.35776 33370151.81 0.012325057 0.002395847 2.620540971 -4.181456503 DATLLIHEATLEDGLEEEAVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DATLLIHEATLEDGLEEEAVEK 22 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 168.27 9.62E-12 16773000 16241 17079 18085 18256 12485 17445 16338 18662 13611 FALSE TRUE 15473.32012 18819.36952 18914.21514 16420.8722 14662.38005 16840.87528 13845.33803 17027.85635 15721.72436 0.984199936 1.197029606 1.20306238 1.044470175 0.932619076 1.071184998 0.880650094 1.083078163 1 13.94047184 3.005591324 20.31358783 0.984404388 1.122493868 0.350017436 0.08308587 14.96271442 54352.77897 0.023215121 0.027588795 1012.957733 -3.005591324 0.13808948 DATMEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DATMEVQR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 118.32 0.0044398 554520000 865410 802100 708080 863610 850400 688460 874750 803560 884430 FALSE TRUE 824503.7844 883834.9019 740546.1684 776798.282 998709.4908 664618.4576 741290.8216 733196.0265 1021582.887 0.807084569 0.865162204 0.724900718 0.760386936 0.977609848 0.650577125 0.725629639 0.717705862 1 19.96237483 2.202326043 24.99999478 0.744364475 0.822744957 0.024580028 0.112889828 386.9652789 266983.9845 0.038014804 0.02807662 159.3404512 -2.202326043 0.078380482 DATNRS(ph)PTQIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DATNRSPTQIVK 12 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 DAT(0.001)NRS(0.991)PT(0.009)QIVK;DATNRS(0.994)PT(0.006)QIVK;DAT(0.144)NRS(0.58)PT(0.276)QIVK;DAT(0.014)NRS(0.964)PT(0.022)QIVK 170.95 2.41E-05 2947660000 2070210 1695860 1802990 2043920 1403310 1922600 2153690 2047400 1572400 TRUE FALSE 1972355.276 1868670.062 1885658.875 1838461.278 1648046.82 1856019.88 1825105.035 1868118.802 1816239.761 1.085955345 1.0288675 1.038221338 1.012234903 0.907394968 1.02190246 1.004881114 1.028563982 1 20.79252323 4.079269129 1.023866139 0.996262912 1.087801575 0.395854473 0.034669884 0.790833277 1.274460482 0.011478833 0.062692772 12002.42855 -4.079269129 0.091538664 DATNVGDEGGFAPNILENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DATNVGDEGGFAPNILENK 19 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 358.82 8.46E-91 470363000 1246041 1202025 942332 1253068 790032 1189875 1187324 1305155 848277 FALSE TRUE 1187143.111 1324512.714 985538.8543 1127107.224 927813.3307 1148669.33 1006175.917 1190868.709 979823.4648 1.211588775 1.351787094 1.005833081 1.150316628 0.946918873 1.172322742 1.026895102 1.21539109 1 19.90216232 3.738572008 25 1.075999611 1.281687938 0.476111834 0.090573066 0.709864262 1556333.62 0.020710785 0.034518207 5477.369104 -3.738572008 0.205688328 DATNVGDEGGFAPNILENKEGLELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DATNVGDEGGFAPNILENKEGLELLK 26 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 173.36 3.46E-12 867969000 369935 185370 329874 293785 282118 350355 506781 447615 348407 FALSE TRUE 352448.9057 204259.4137 344999.0492 264253.1736 331319.2899 338222.1185 429462.2508 408419.4576 402436.1781 0.875788323 0.507557284 0.857276428 0.656633742 0.823284058 0.840436663 1.067156171 1.014867648 1 18.61840048 2.069664788 1.650580738 1.038010214 0.71420425 0.58609801 0.10786965 0.233220516 1.202098284 0.061344603 0.032005611 117.3991055 -2.069664788 -0.323805964 DAVDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAVDFLR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;; 142.64 0.0057599 816390000 1964280 1746380 1733740 1922760 1827850 1731790 2279260 1987160 2140240 FALSE TRUE 1871432.377 1924338.107 1813233.694 1729480.512 2146626.461 1671817.678 1931517.026 1813153.736 2472137.488 0.757009829 0.778410633 0.733467982 0.699589129 0.868328105 0.676264037 0.781314565 0.733435638 1 21.23732755 -2.126559066 2.413693541 1.493839271 0.755604971 0.689560029 0.051965635 3343359.073 1208899.98 9007590.947 0.010825632 0.00747207 2.126559066 -0.7382343 DAVFDGSSCIS(ph)PTIVQQFGYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAVFDGSSCISPTIVQQFGYQR 22 0 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 DAVFDGSSCIS(0.946)PT(0.054)IVQQFGYQR;DAVFDGS(0.002)S(0.002)CIS(0.988)PT(0.008)IVQQFGYQR 82.342 0.0028391 64092000 73194 74193 75198 87811 64605 73903 80585 84432 57972 TRUE FALSE 69734.26468 81753.35105 78645.90268 78984.07145 75872.09155 71343.72058 68290.2782 77038.68648 66962.00168 1.04140054 1.220891685 1.17448554 1.179535699 1.13306188 1.065435901 1.019836273 1.150483626 1 16.03105503 2.277214833 3.745230109 1.05516236 1.153879903 0.371630726 0.059308303 0.234754822 6.921253334 0.021719679 0.016973328 189.3279938 -2.277214833 0.098717543 DAVLLVFANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 164.96 1.40E-05 42576000 428880 472130 365750 529050 285390 409400 392880 428420 257950 FALSE TRUE 408607.6924 520240.5838 382519.9993 475868.8889 335161.9256 395222.3753 332938.9403 390905.2736 297951.5686 1.371389633 1.746057543 1.283832809 1.597135035 1.124887267 1.326465161 1.117426372 1.311975887 1 18.18471832 2.736707787 24.9991648 1.190307089 1.514446102 0.519520739 0.153940627 123.4105346 1665095.774 0.044235104 0.043667317 545.390774 -2.736707787 0.324139013 DAVSGMGVIVHIIEKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DAVSGMGVIVHIIEKDK 17 1 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 121.27 3.65E-05 19057000 99383 102360 95731 114970 61774 117290 120260 129240 52473 FALSE TRUE 94685.36255 112790.6004 100120.361 103412.9972 72547.36604 113228.2179 101912.1283 117923.0605 60610.24485 1.562200628 1.860916429 1.651871912 1.706196658 1.196948902 1.868136619 1.68143403 1.945596174 1 15.88727405 DAVTYTEHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DAVTYTEHAK 10 0 P62805 P62805 HIST1H4A Histone H4 0 ; 152.04 0.0043822 0 2318300 2400900 2095080 2920400 2036870 2545500 2582800 3030300 1731870 FALSE TRUE 2208718.553 2645554.44 2191141.49 2626835.844 2392099.483 2457348.697 2188746.424 2764950.867 2000439.554 1.104116617 1.322486567 1.095330017 1.313129326 1.195786935 1.228404373 1.094132746 1.382171664 1 20.93188561 -1.311610256 4.374427144 0.999795275 1.210126455 0.312442512 0.100689011 0.00017612 2.77E-05 0.085408568 0.020111485 0.04879662 1.311610256 0.210331179 DAWAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAWAIR 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 126.04 0.041095 255253000 472062 501530 324325 436109 459288 385345 438603 436165 396877 FALSE TRUE 449748.5648 552636.4772 339195.6221 392270.4948 539387.6818 372000.406 371686.0569 397972.0803 458422.6582 0.981078393 1.20551737 0.739918972 0.855696131 1.17661654 0.8114791 0.810793381 0.86813353 1 18.80631883 3.744507701 24.99952374 0.887093374 1.093297877 0.280631301 0.131783831 549.2279124 2308760.766 0.033324036 0.058137091 5552.744636 -3.744507701 0.206204503 DAYREFDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DAYREFDRK 9 2 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 94.309 0.0049546 501170000 401835 213649 439859 359016 343538 402684 543933 452420 429336 FALSE TRUE 382841.0559 235420.076 460026.9702 322927.0296 403450.9184 388738.9521 460946.0308 412803.7064 495915.2341 0.7719889 0.474718379 0.927632262 0.651173845 0.813548144 0.783881852 0.929485523 0.832407795 1 18.91973402 2.16691559 0.439889166 0.990003598 0.631026556 0.383960375 0.117954908 0.927621928 0.407430946 0.113168352 0.111970215 146.8640804 -2.16691559 -0.358977042 DAYSGGAVNLYHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DAYSGGAVNLYHVR 14 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 251.91 3.43E-24 2960600000 2831140 2553940 1797610 2128950 2677040 2151120 3081490 2560580 2374950 FALSE TRUE 2697317.623 2814189.39 1880032.197 1914943.901 3143914.928 2076626.175 2611352.105 2336362.041 2743245.116 0.983257969 1.025861442 0.685331466 0.698057891 1.146056876 0.756996217 0.951920807 0.851678192 1 21.38745211 DCDHADEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 155.84 7.23E-05 212887000 449050 544400 390680 541690 258120 440880 440690 510400 235000 FALSE TRUE 427824.2964 599874.9789 408593.0644 487238.2921 303136.0463 425612.2151 373454.6467 465706.6702 271442.5998 1.576113317 2.209951494 1.505265072 1.794995673 1.116759295 1.567963965 1.375814434 1.715672745 1 18.05028763 3.166687586 1.805979865 1.403422173 1.868531995 0.310602918 0.283019966 0.359468471 2.415454946 0.084437951 0.112307149 1467.86997 -3.166687586 0.465109822 DCDPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DCDPGSPR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 1 DCDPGS(1)PR;DCDPGS(1)PR 118.03 0.0020606 1228620000 2733600 2814600 2706200 3056800 2420800 2745200 3141900 2926700 2823700 TRUE FALSE 2604388.145 3101410.94 2830281.947 2749524.656 2842986.754 2650133.036 2662545.45 2670422.633 3261584.975 0.798503846 0.950890737 0.86776275 0.843002613 0.871658036 0.812529202 0.816334841 0.81874998 1 21.63714179 3.375972334 5.366385122 0.8464745 0.879950898 0 0.06560705 0.660445337 29.28452537 0.016818787 0.02294522 2376.688877 -3.375972334 0.033476398 DCEQAENWMAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DCEQAENWMAAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 156.58 0.00017053 111050000 73655 68558 75527 76014 63081 62452 81228 79016 80290 FALSE TRUE 70173.47412 75544.13814 78989.98766 68372.9283 74082.30643 60289.27158 68835.17675 72096.94015 92740.96314 0.756661045 0.814571421 0.851727058 0.737246261 0.798808897 0.65008244 0.742230557 0.777401244 1 16.50091909 0.934438669 19.07864236 1.000000001 0.764908897 0.6550625 0.053422467 913.5495966 265848.7826 0.052543658 0.013135915 8.59881626 -0.934438669 -0.235091103 DCFGCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DCFGCLR 7 0 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;;;; 129.96 0.0083975 3668130000 3901420 2556650 2289780 2659190 3801820 2585540 4248580 3132450 3829520 FALSE TRUE 3717007.608 2817175.542 2394768.678 2391883.169 4464856.204 2496002.101 3600381.09 2858156.072 4423382.403 0.840308902 0.636882658 0.541388571 0.54073624 1.009376038 0.564274547 0.813942988 0.646147181 1 22.07671854 2.810411752 25 0.776819636 0.656144862 0.198025395 0.159268081 316.1569799 110002.8227 0.045722136 0.048495644 646.2666608 -2.810411752 -0.120674774 DCGATWVVLGHSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DCGATWVVLGHSER 14 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;;;;;;;; 234.63 7.53E-17 39162860000 19588740 12627240 13733010 16788940 19013230 14816700 22751540 17456200 18998160 FALSE TRUE 18662819.08 13913970.11 14362682.09 15101283.85 22329131.29 14303593.96 19280374.71 15927642.59 21944297.62 0.850463268 0.634058576 0.654506348 0.688164375 1.017536841 0.651813706 0.878605232 0.72582148 1 24.38734276 DCGEYAHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DCGEYAHTR 9 0 Q5T8A0;Q9Y399 Q5T8A0 MRPS2 "28S ribosomal protein S2, mitochondrial" 0 86.624 0.014012 67583000 53365 52856 50916 40252 45732 43150 42656 52103 53371 FALSE TRUE 50842.54221 58242.08649 53250.54896 36205.79249 53707.64632 41655.70468 36148.04377 47540.5851 61647.5021 0.824729964 0.944759877 0.863790862 0.58730348 0.871205556 0.675707908 0.586366723 0.771168068 1 15.91175482 3.397691155 9.835196635 0.719497969 0.887977884 0.160953431 0.128544549 0.417566048 48.21789233 0.032648283 0.044218777 2498.567891 -3.397691155 0.168479915 DCHEEVYAGSHQYPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DCHEEVYAGSHQYPGR 16 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ; 136.63 9.48E-06 187673000 124185 83509 133688 125490 221803 118998 217413 119968 288362 FALSE TRUE 118315.0212 92018.66204 139817.727 112875.5068 260485.373 114877.0694 184242.6538 109462.9659 333079.7062 0.35521534 0.276266192 0.419772578 0.338884371 0.782051167 0.344893631 0.553148842 0.328638953 1 18.34550793 -5 0.17764493 3.311755466 0.295808445 0.596930534 0.147847273 85.65137864 0.820942324 70.02122603 0.434909674 1.00E-05 5 -3.015947021 DCKEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 68.915 0.086532 94397000 142990 167720 116930 170150 65633 139750 113100 178690 74097 FALSE TRUE 136231.1461 184810.8587 122291.3562 153046.1987 77079.37442 134910.4225 95844.51778 163042.9563 85587.58432 1.591716219 2.159318552 1.428844582 1.788182246 0.900590606 1.576284966 1.119841371 1.904983738 1 16.38511391 3.210049943 1.796587324 1.326302486 1.848310911 0.243680171 0.349645685 0.393218483 2.61874419 0.10194751 0.140137207 1621.996614 -3.210049943 0.522008426 DCLFRPLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DCLFRPLNK 9 1 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJM8 A0A590UJ56 CUL1 Cullin-1 0 86.136 0.014549 0 245760 228780 203510 229900 205210 223380 258060 244690 208360 FALSE TRUE 234143.4118 252092.9421 212841.1348 206790.0152 240998.559 215644.2946 218688.2074 223263.6464 240671.4046 0.97287591 1.047456978 0.884364036 0.859221375 1.00135934 0.896011285 0.908658873 0.927670019 1 17.87670521 3.737750648 24.99915096 0.919542292 1.010166445 0.337041939 0.048947799 65.34377429 2016808.19 0.01182509 0.019558808 5467.019812 -3.737750648 0.090624152 DCLHGIEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DCLHGIEAK 9 0 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ;; 125.97 0.00048667 657345000 1642940 1484250 1475930 1777190 1134800 1588130 1774690 1785160 1062640 FALSE TRUE 1565281.482 1635496.762 1543602.85 1598543.485 1332708.761 1533132.66 1503928.446 1628841.927 1227428.784 1.275252383 1.33245756 1.257590559 1.30235131 1.085772778 1.249060377 1.225267377 1.327035791 1 20.22720789 -4.614683166 0.210499551 2.78E-17 1.295945295 0.547243573 0.071639237 91.85732571 1.061439789 39.10270408 0.146054443 2.43E-05 4.614683166 1.295945295 DCLIPMGITSENVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DCLIPMGITSENVAER 16 0 P09110;C9JDE9;H0Y4D4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 220.37 2.69E-14 120840000 180981 168911 153950 195019 166956 166539 187262 179243 163276 FALSE TRUE 172426.3868 186123.2229 161008.7598 175415.3196 196073.0735 160771.7127 158691.7426 163547.5327 188596.0082 0.914263183 0.986888454 0.853723052 0.930111519 1.039645936 0.852466148 0.841437441 0.867184487 1 17.52493961 DCMEHAVLPVDGATLAEVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DCMEHAVLPVDGATLAEVMR 20 0 K7EIG1;A0A494C0R8;O75153 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;; 214.26 1.28E-24 150561000 281513 274339 260216 328344 269980 284520 317865 314019 253073 FALSE TRUE 268206.4384 302294.456 272147.161 295338.2373 317064.4265 274667.0011 269368.8563 286521.8316 292318.2683 0.917515145 1.034127828 0.930996077 1.010331099 1.084654847 0.93961627 0.921491694 0.980170802 1 18.15718047 -2.100996449 10.65561725 1.286923079 0.975923909 0.016524674 0.053875585 0.094453974 0.000895257 0.01341716 0.012096279 0.007925078 2.100996449 -0.31099917 DCQLNAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DCQLNAHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 146.03 0.00055986 1321070000 1845950 1954010 1339200 1840990 1136340 1667330 1728940 1715790 1064170 FALSE TRUE 1758695.602 2153125.841 1400603.645 1655930.188 1334517.336 1609589.944 1465158.449 1565546.332 1229196.049 1.430769 1.751653728 1.139446914 1.347165238 1.085683067 1.309465602 1.191964822 1.273634367 1 20.2292836 3.7300941 24.99668655 1.20842456 1.591211368 0.622765681 0.128551437 320.5418575 946373.3011 0.030199255 0.047618213 5371.481689 -3.7300941 0.382786807 DCQLNAHKDHQYQFLEDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DCQLNAHKDHQYQFLEDAVR 20 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 233.89 1.08E-29 2519310000 2077055 1451718 2140596 2104881 1947706 2134519 2863799 2241409 122595 FALSE TRUE 1978876.726 1599649.715 2238744.444 1893294.363 2287385.31 2060600.072 2426873.865 2045139.346 141606.4065 13.97448587 11.29645017 15.80962684 13.37011799 16.15312023 14.55160203 17.13816434 14.44242105 1 17.11152701 -1.311862765 7.83305124 0.999945027 14.50144352 0.876040153 1.606488231 0.001692381 0.000148653 1.706751518 0.402283959 0.048768257 1.311862765 13.50149849 DCS(ph)PSSPLKLDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.377)PS(0.377)S(0.246)PLKLDAR 73.834 0.021651 168380000 244720 227380 249050 292350 171840 250460 254810 270530 145130 TRUE FALSE 233152.5706 250550.2805 260469.1888 262962.4226 201808.8416 241786.5074 215934.0546 246840.959 167636.0192 1.390826218 1.494608866 1.55377818 1.56865108 1.203851312 1.442330285 1.288112517 1.472481632 1 17.35497264 2.744430549 24.99369918 1.311339108 1.491269458 0.374803106 0.138301608 573.5818003 2442267.346 0.03846255 0.039791226 555.1758277 -2.744430549 0.17993035 DCVGPEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DCVGPEVEK 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 114.5 0.0037886 1014340000 2179500 1910010 1909520 2268370 1459370 2174820 2386720 2306550 1502640 FALSE TRUE 2076479.354 2104642.191 1997073.381 2040349.138 1713883.666 2099505.438 2022582.029 2104576.254 1735661.737 1.196361774 1.212587767 1.150612091 1.175545381 0.987452583 1.209628232 1.165308877 1.212549778 1 20.72705438 -1.934212872 2.614446283 0.887830168 1.166720858 0.376246539 0.066164915 9763763.358 5451173.649 6682891.098 0.015898608 0.011635556 1.934212872 0.27889069 DDAMLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDAMLLK 7 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 108.09 0.017057 154186000 509630 459800 371520 450070 302120 371960 407320 445780 316000 FALSE TRUE 485540.7999 506654.1427 388554.5595 404828.1085 354809.6323 359078.9319 345175.8531 406745.14 365003.6661 1.330235406 1.3880796 1.064522348 1.109106966 0.972071421 0.983768015 0.94567777 1.114359054 1 18.47755143 3.657738023 3.400140187 1.012315317 1.36183515 0.850651318 0.057786441 0.075994301 1.692301797 0.015877595 0.026462452 4547.136831 -3.657738023 0.349519833 DDAT(ph)PVRDEPMDAESITFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDATPVRDEPMDAESITFK 19 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 DDAT(1)PVRDEPMDAESITFK;DDAT(1)PVRDEPMDAESITFK 233.45 6.66E-24 113284000 373990 411180 287830 443730 213240 367770 326170 398810 184355 TRUE FALSE 356312.2339 453079.7095 301027.2902 399125.4174 250428.9885 355034.0327 276406.776 363888.0822 212943.8318 1.67326863 2.12769586 1.413646442 1.87432251 1.176033071 1.667266103 1.298026684 1.708845375 1 17.70011342 1.986282364 0.071709789 3.09E-10 3.031049903 0.389688933 0.262678892 19.92432525 1.119593567 21.20576791 24.37734905 96.89076042 -1.986282364 3.031049903 DDAYWPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDAYWPEAK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 131.44 0.00077488 79159000 305260 266390 273440 326850 194110 285240 325600 324200 221640 FALSE TRUE 290830.9648 293535.4439 285977.4945 293994.417 227962.7225 275362.0673 275923.7399 295811.3293 256010.7992 1.136010534 1.14657446 1.117052466 1.148367248 0.890441822 1.075587702 1.077781644 1.155464262 1 17.96584514 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR 228.18 1.08E-25 241387000 513490 567230 423709 566870 243038 560700 474780 533870 174638 TRUE FALSE 489218.3453 625031.3819 443136.4768 509887.1506 285423.7503 541282.8184 402343.5911 487121.5126 201719.9691 2.42523508 3.0985102 2.196790326 2.527697941 1.414950396 2.683337801 1.994565004 2.414840309 1 17.62199438 -0.891399427 0.179175722 2.08E-11 2.90504451 0.494760388 0.43324021 15.98075676 0.655541818 10.41593645 1.681315324 0.128410511 0.891399427 2.90504451 DDDFPSLQAIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDDFPSLQAIAR 12 0 Q86UK7-2;H3BQQ2;H3BPG6;Q86UK7-3;Q86UK7 Q86UK7-2 ZNF598 Zinc finger protein 598 0 78.342 0.060459 14134000 26747 25098 22064 29638 23186 21247 29733 25137 31338 FALSE TRUE 25482.72232 27655.51473 23075.65622 26658.73193 27229.63106 20511.21106 25196.68477 22935.87102 36197.73699 0.703986615 0.764012257 0.637488919 0.736475099 0.752246779 0.566643464 0.696084531 0.633627208 1 15.14361189 -1.023117141 5.755467094 1.000000736 0.691335887 0.725655961 0.06054394 5.51E-07 9.36E-08 0.056508263 0.013319094 0.094816268 1.023117141 -0.308664849 DDDKNNDGYIDYAEFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDDKNNDGYIDYAEFAK 17 1 Q8NI22-2;Q8NI22-3;Q8NI22 Q8NI22-2 MCFD2 Multiple coagulation factor deficiency protein 2 0 ; 164.2 2.39E-09 285000000 501930 541970 370810 567840 202208 511650 423410 523280 216970 FALSE TRUE 478204.7636 597197.3592 387812.0053 510759.6444 237473.0112 493931.4322 358811.028 477458.8291 250616.5995 1.908112889 2.382912227 1.547431439 2.038012029 0.947554997 1.970864792 1.431712938 1.905136492 1 17.93512245 7.999999298 0.058439218 3.53E-08 5.305780771 0.318962644 0.377943193 354.915238 1.55219011 29.21344786 161.4837285 99999838.47 -7.999999298 5.305780736 DDDRTPGLHGDCDDDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDDRTPGLHGDCDDDKYR 18 2 O95159 O95159 ZFPL1 Zinc finger protein-like 1 0 70.942 0.01462 150770000 117290 98340 106110 137670 91289 121600 145020 122910 88224 FALSE TRUE 111745.9341 108360.9578 110975.2485 123831.15 107209.7727 117388.9615 122894.5355 112147.3488 101905.3273 1.096566167 1.063349293 1.089003405 1.215158749 1.05205268 1.151941361 1.205967723 1.100505261 1 16.63686995 3.4494843 24.99938378 1.136496823 1.079327431 0.036777961 0.065711915 380.9587727 344600.421 0.016636454 0.022526356 2815.038248 -3.4494843 -0.057169391 DDDVPLMWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDDVPLMWR 9 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 167.24 0.00013989 142199000 273480 263760 235830 289920 207550 254710 293600 279830 212350 FALSE TRUE 260553.1424 290637.4439 246643.0388 260776.6908 243746.6543 245889.3288 248805.9277 255326.6017 245280.1535 1.062267528 1.184920344 1.005556443 1.063178929 0.993747969 1.00248359 1.014374478 1.040959075 1 17.90407098 3.72105757 24.9934563 1.017595762 1.123593938 0.606899717 0.035602056 436.9142119 623891.2688 0.008905242 0.013829002 5260.869993 -3.72105757 0.105998176 DDDYRGGGDRYEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDDYRGGGDRYEDR 14 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 83.729 0.0047327 76384000 98667 51919 94393 75454 80825 87862 109470 96070 97451 FALSE TRUE 94003.20645 57209.60513 98721.01242 67869.22057 94920.85441 84819.31691 92768.34095 87657.6015 112563.2034 0.835114883 0.508244288 0.87702739 0.602943222 0.843267174 0.753526147 0.824144464 0.778741177 1 16.78037577 0.503275099 0.330144236 1.042986088 0.681435746 0.34320834 0.112265212 2.881110567 0.653307682 0.324922549 0.110856486 3.186215157 -0.503275099 -0.361550342 DDDYRGGGDRYEDRYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDDYRGGGDRYEDRYDR 17 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 150.68 1.22E-07 6100030000 2609690 1210412 2517540 1946820 2618520 2390020 3683220 2810380 3249840 FALSE TRUE 2486335.126 1333754.359 2632971.699 1751121.955 3075189.059 2307253.008 3121277.142 2564288.228 3753808.589 0.662350002 0.355306971 0.701413414 0.466492074 0.819218398 0.614643223 0.831496084 0.683116405 1 21.83992366 1.465230107 0.352897819 1.014025258 0.488221602 0.501223889 0.129107445 0.87370026 0.352677869 0.174159148 0.139166518 29.18973196 -1.465230107 -0.525803656 DDEAAAVALSSLIHALDDLDMVAIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDEAAAVALSSLIHALDDLDMVAIVR 26 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 108.4 0.0019798 128510000 10950 10884 9705.1 11584 9049.1 9861.9 13339 11256 9166.7 FALSE TRUE 10432.4152 11993.09197 10150.08843 10419.55431 10627.26017 9520.37993 11303.89056 10270.36497 10588.22502 0.985284614 1.132682008 0.958620394 0.984069973 1.003686657 0.899147866 1.0675907 0.969979855 1 13.37017314 3.712735785 24.99250987 0.986720827 1.058983339 0.249097402 0.054378365 901.6343672 872575.5767 0.013621736 0.021109579 5161.02289 -3.712735785 0.072262512 DDEENYLDLFSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;; 230.36 4.23E-12 165001000 351322 345781 309405 395374 198033 356228 353811 376636 174621 FALSE TRUE 334715.7053 381016.477 323591.5253 355630.2544 232569.8925 343891.735 299830.6338 343655.7552 201700.3328 1.659470268 1.88902255 1.604318251 1.763161465 1.153046647 1.704963647 1.486515315 1.703793694 1 17.62185394 -2.712459391 0.164335301 7.13E-14 1.837697281 0.500850816 0.19520431 42.46288126 0.797251343 16.45278528 0.80195169 0.001938834 2.712459391 1.837697281 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 DDEKEAEEGEDDRDS(0.996)ANGEDDS(0.004);DDEKEAEEGEDDRDS(1)ANGEDDS 201.1 1.23E-22 2983100000 2687400 3185900 2215400 3484800 1155240 2959900 2325300 2905400 979680 TRUE FALSE 2560371.928 3510546.832 2316978.281 3134501.283 1356713.49 2857397.921 1970532.778 2650987.774 1131603.771 2.262604627 3.102275657 2.047517286 2.769963625 1.198929807 2.525086956 1.741362859 2.34268199 1 20.10993746 -0.188252452 0.14908359 5.30E-13 3.089568072 0.3952274 0.510074074 15.51147274 0.720814837 10.94974842 3.639210124 0.648257496 0.188252452 3.089568072 DDEVQVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 173.28 0.00073472 324580000 1138600 911540 934100 1066830 987970 1027970 1068480 1043450 853330 FALSE TRUE 1084780.634 1004426.962 976929.409 959590.2216 1160271.655 992371.1411 905463.752 952079.9863 985660.0582 1.100562639 1.019039936 0.991142332 0.973550885 1.177151946 1.00680872 0.918636952 0.965931386 1 19.91073064 1.996705377 24.99125107 0.955042527 1.049635087 0.321771035 0.060060658 145.2830385 1102042.188 0.022162748 0.016048835 99.24425521 -1.996705377 0.09459256 DDEYDYLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 122.13 0.0013826 17835000 34262 41250 32446 47283 23154 37479 37325 37891 26860 FALSE TRUE 32642.50316 45453.4219 33933.68119 42530.02301 27192.05027 36181.09283 31630.38573 34573.06317 31025.31162 1.052124909 1.465043203 1.093741833 1.370816949 0.876447289 1.166179837 1.019502596 1.114350231 1 14.92115808 2.747309496 24.99524829 1.045970337 1.252127882 0.357266449 0.139517185 670.8231955 1916519.085 0.038862815 0.040685122 558.8683256 -2.747309496 0.206157545 DDFNSGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDFNSGFR 8 0 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 ; 211.79 6.56E-05 297870000 406010 593210 385220 565910 323550 437400 372380 427100 278060 FALSE TRUE 386818.7119 653658.7734 402882.718 509023.6516 379977.0176 422252.7283 315566.5918 389700.8598 321180.1247 1.204366903 2.035178155 1.25438247 1.584854144 1.183065166 1.31469134 0.982522166 1.213340521 1 18.29302309 2.573095943 1.086684717 1.072414958 1.587303776 0.375047964 0.242154657 0.453889739 1.09624696 0.129151269 0.100715652 374.1932451 -2.573095943 0.514888818 DDFNSGFRDDFLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDFNSGFRDDFLGGR 15 1 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 138.91 7.02E-06 61485000 31967 27670 29329 35165 31729 30703 37693 32713 33754 FALSE TRUE 30455.98326 30489.60446 30673.76366 31630.14739 37262.52755 29639.74741 31942.24057 29848.4763 38988.39793 0.781155033 0.782017371 0.786740807 0.811270764 0.955733745 0.76021968 0.819275535 0.765573296 1 15.25075725 -2.596763149 2.241083659 5.206913893 0.806571792 0.540648336 0.055681985 2637894.668 214065.6385 56756542.48 0.012850775 0.002530678 2.596763149 -4.400342101 DDFTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DDFTEER 7 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ;;; 152.63 0.0041887 2063930000 4713980 3313730 3671660 3899700 3432920 3257170 3804110 3754100 3463840 FALSE TRUE 4491159.508 3651402.854 3840009.243 3507694.747 4031620.161 3144373.386 3223723.152 3425371.102 4000994.616 1.12251076 0.912623786 0.959763662 0.87670569 1.007654483 0.78589793 0.80573044 0.856129895 1 21.93192726 7.999999766 0.458435557 0.861634934 7.278719412 0.455646141 0.075192645 68.00787253 0.80252187 0.041974279 410.6761361 99999946.14 -7.999999766 6.417084477 DDFTEFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ;; 114.93 0.0059582 378866000 792680 729270 716480 845290 477770 766190 838440 832110 440430 FALSE TRUE 755211.5873 803583.4421 749331.3167 760319.8433 561092.9367 739656.6482 710520.579 759246.0371 508729.635 1.484504804 1.579588423 1.47294607 1.494546004 1.102929529 1.453928762 1.396656554 1.492435244 1 18.95653961 -3.701649205 0.167868528 9.84E-15 1.562102553 0.537659915 0.126540305 62.35124527 0.87167984 22.24231739 0.483870207 0.00019877 3.701649205 1.562102553 DDGLFSGDPNWFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDGLFSGDPNWFPK 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 243.53 3.58E-17 1018381000 3419039 2241896 2373077 3368931 2140290 2809781 4010768 3694947 2778103 FALSE TRUE 3257427.802 2470347.751 2481884.928 3030279.655 2513555.898 2712477.579 3398851.679 3371397.853 3208917.025 1.015117492 0.769838463 0.773433812 0.944330948 0.783303488 0.845293773 1.059189643 1.050634163 1 21.61365505 1.739065463 6.73806775 1.039614139 0.855044789 0.543682384 0.07819876 0.102767145 13.40871332 0.037931783 0.01995006 54.83596146 -1.739065463 -0.18456935 DDGLFSGDPNWFPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 221.91 2.36E-12 3308100000 11336400 6917100 8432200 10399300 7058500 9697600 14826600 12292100 9128900 FALSE TRUE 10800550.84 7621960.354 8818824.711 9353942.607 8289500.165 9361769.68 12564529.86 11215738.56 10544563.19 1.024276743 0.7228332 0.836338552 0.88708678 0.78613974 0.887829065 1.191564756 1.063651321 1 23.329996 1.849598525 6.080252056 1.098946571 0.849953058 0.589870721 0.089549804 0.14392095 6.636282996 0.03796197 0.022789809 70.72916399 -1.849598525 -0.248993513 DDGSWEVIEGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDGSWEVIEGYR 12 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;; 358.92 1.40E-71 1122841000 1644586 1177717 1346315 1282187 1301482 1160032 1465372 1322879 1334681 FALSE TRUE 1566849.679 1297727.701 1408044.874 1153299.127 1528460.049 1119859.801 1241802.588 1207040.702 1541656.513 1.016341621 0.841774864 0.91333242 0.748090847 0.991440075 0.726400331 0.805498876 0.782950477 1 20.55604993 6.009374143 0.685471158 0.83016811 1.948920778 0.212215172 0.094931397 18.04917972 1.671814647 0.031901118 23.305669 1021819.398 -6.009374143 1.118752668 DDGVFVQEVTQNS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR 402.21 3.58E-140 1137320000 916285 858853 941193 964701 762119 929691 1076102 958207 919503 TRUE FALSE 872974.024 946371.0971 984347.63 867727.4227 895032.3123 897495.5676 911922.8759 874301.3153 1062094.829 0.821936046 0.891041997 0.926798251 0.816996184 0.842704708 0.84502395 0.858607773 0.823185738 1 20.01848115 -1.721228513 6.379893895 1.002406943 0.85545657 0.650013177 0.033799361 0.001136316 4.97E-05 0.032136902 0.007459949 0.019000783 1.721228513 -0.146950373 DDGYSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 124.08 0.0097275 428100000 898990 854920 783400 925730 505890 819040 952110 956600 715000 FALSE TRUE 856496.5243 942037.32 819319.6649 832673.8616 594117.0558 790676.4394 806848.1328 872835.0327 825878.5483 1.037073219 1.140648733 0.992058295 1.008227981 0.719375818 0.957376168 0.976957368 1.056856404 1 19.65557011 3.438442878 2.626009473 0.942707828 1.087470507 0.253815554 0.092964046 0.326681027 4.552341185 0.026605855 0.040196473 2744.371359 -3.438442878 0.144762678 DDILNGSHPVSFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 173.03 2.76E-06 660130000 1337090 1259780 1288210 1503650 946350 1353510 1577670 1478020 925990 FALSE TRUE 1273888.406 1388153.014 1347275.703 1352500.245 1111393.14 1306637.609 1336967.466 1348596.733 1069587.8 1.191008728 1.297839237 1.259621419 1.264506051 1.039085469 1.221627256 1.24998384 1.260856503 1 20.02862348 DDIPVFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDIPVFLR 8 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 97.798 0.018556 15323000 96469 91507 90174 106600 91579 90328 101900 95087 91886 FALSE TRUE 91909.10155 100831.6673 94308.56709 95884.36547 107550.3486 87199.91871 86353.28348 86760.67819 106135.2116 0.865962391 0.950030304 0.88857002 0.903417104 1.013333341 0.821592734 0.813615785 0.817454235 1 16.69554384 2.17939472 24.99999819 0.843058708 0.919908384 0.140075872 0.067010545 102.3586996 43249.756 0.022591475 0.016684916 151.1453253 -2.17939472 0.076849676 DDIVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDIVDR 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;; 128.38 0.038736 2348710000 3946980 3401990 3427160 3992440 2954850 3496460 4064270 3768890 3081890 FALSE TRUE 3760414.078 3748656.649 3584298.676 3591112.346 3470174.904 3375376.713 3444190.966 3438866.011 3559813.761 1.056351351 1.05304853 1.006878145 1.008792197 0.974819229 0.94818913 0.967519988 0.966024136 1 21.76337033 3.334921953 1.118629044 0.96648076 1.058997043 0.822030121 0.015148317 0.157483023 0.416008479 0.005371826 0.009411932 2162.329897 -3.334921953 0.092516283 DDKCANLFEALVGTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDKCANLFEALVGTLK 16 1 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 ; 186.68 1.33E-09 109303000 607200 358630 598530 541410 447000 570490 877980 722230 595320 FALSE TRUE 578498.8594 395174.8047 625973.1925 486986.4382 524956.6585 550733.7883 744028.0258 658987.7124 687639.1851 0.841282568 0.574683371 0.910322166 0.708200534 0.763418766 0.800905184 1.08200353 0.958333566 1 19.39129223 1.859446551 4.662823263 1.015889492 0.748954324 0.618718111 0.091489108 0.134229957 4.2684907 0.040617677 0.023269486 72.35133533 -1.859446551 -0.266935168 DDKEEEEDGTGS(ph)PQLNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.005)GS(0.995)PQLNNR 203.25 7.29E-16 752200000 855670 825360 658070 896280 369000 891980 784170 844510 319570 TRUE FALSE 815224.1749 909465.1224 688243.1604 806184.2316 433353.4832 861090.5089 664530.4642 770560.2274 369127.2835 2.208517797 2.463825252 1.864514468 2.184027753 1.173994724 2.332773944 1.800274577 2.087519026 1 18.49375885 -1.458400974 0.156822951 8.21E-17 2.478290056 0.451017681 0.354864401 28.56219059 0.791139722 14.22286881 1.887697045 0.034801585 1.458400974 2.478290056 DDKGNLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDKGNLNR 8 1 E9PM90;Q9UK41;Q9UK41-2;E9PQR7 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 58.433 0.09574 47713000 129770 127650 101180 148660 96165 122950 126510 145820 124810 FALSE TRUE 123636.0293 140657.6801 105819.2031 133716.4144 112936.1456 118692.2107 107208.576 133051.2278 144164.8974 0.85760148 0.975672183 0.734015041 0.927524084 0.783381722 0.823308675 0.743652428 0.922910016 1 17.1373604 3.755268976 24.89382701 0.831129832 0.916636823 0.069366905 0.089831679 1314.90405 1959072.909 0.020597188 0.037014547 5692.053528 -3.755268976 0.085506991 DDKHGS(ph)YEDAVHSGALND ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 1 DDKHGS(1)YEDAVHSGALND 141.36 7.28E-08 119280000 157460 115100 134110 149330 101910 153810 152850 133160 61144 TRUE FALSE 150017.1779 126828.8209 140259.0762 134319.0647 119683.0717 148483.5211 129529.9252 121499.8045 70625.89924 2.124109986 1.795783448 1.985943934 1.901838648 1.694605988 2.102394769 1.834028687 1.72032931 1 16.10790971 0.681789016 1.554065354 1.00042505 1.92611878 0.834040501 0.128816732 0.415220516 1.499564553 0.112583702 0.032490676 4.806058095 -0.681789016 0.925693729 DDKHGSYEDAVHSGALND ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;; 252.83 1.03E-30 3235090000 6000110 3664890 5298370 5460540 5275440 5376640 7806740 6854930 2465766 FALSE TRUE 5716496.691 4038346.458 5541305.505 4911636.145 6195475.066 5190445.609 6615678.432 6254675.989 2848144.398 2.007095109 1.417886839 1.945584469 1.724503908 2.175267192 1.822395526 2.322803028 2.196052979 1 21.44159086 2.762657491 23.22198521 2.005008738 1.749924722 0 0.397936899 755.974795 728524.9497 0.10860192 0.115114846 578.9719064 -2.762657491 -0.255084016 DDNGKPYVLPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDNGKPYVLPSVR 13 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ;;;;; 151.56 3.63E-05 7178120000 7972860 7139400 6555130 7165430 5047440 5982820 6411970 6715620 4475280 FALSE TRUE 7595998.708 7866912.977 6855689.194 6445147.363 5927711.938 5775633.443 5433706.213 6127564.711 5169283.566 1.469449027 1.521857502 1.326235852 1.246816368 1.146718276 1.117298629 1.051152668 1.185379876 1 22.30153291 3.215777973 1.130818979 1.086505618 1.508897279 0.901163736 0.05328785 0.114583444 0.313135104 0.019368774 0.029549878 1643.531275 -3.215777973 0.422391661 DDNGVPFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDNGVPFVR 9 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 83.623 0.037324 69957000 174090 159350 154640 218970 159840 166110 193380 194570 152350 FALSE TRUE 165861.1107 175587.9462 161730.397 196958.7196 187716.0454 160357.569 163876.3293 177532.4193 175975.6599 0.942523022 0.997796776 0.919049811 1.11923842 1.066715962 0.911248573 0.931244295 1.008846447 1 17.42501637 -2.199591282 8.915746805 2.055930335 0.982455947 0 0.066707566 0.185983105 0.004163489 0.008579558 0.01516892 0.006315514 2.199591282 -1.073474388 DDNMFQIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDNMFQIGK 9 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 115.86 0.0032741 277950000 615990 549900 518720 638070 361510 567490 599910 631610 358700 FALSE TRUE 586873.3735 605935.4352 542503.8251 573929.9913 424557.2295 547837.679 508382.7114 576302.88 414325.364 1.416455338 1.462462808 1.309366677 1.385215681 1.024695243 1.322240265 1.22701325 1.390942795 1 18.66040462 7.999999995 0.032385013 5.00E-10 3.246879667 0.450529085 0.117018534 964.5234999 2.392121943 73.71469028 191.884136 99999998.8 -7.999999995 3.246879666 DDPDGKQEAKPQQAAGMLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;DDPDGKQEAKPQQAAGMLS(1)PK;DDPDGKQEAKPQQAAGMLS(1)PK;DDPDGKQEAKPQQAAGMLS(1)PK 155.8 1.10E-08 2262466000 4192640 4414250 3555440 4867620 1298141 5019130 3846440 5058640 1102931 TRUE FALSE 3994462.216 4864067.094 3718460.441 4378317.59 1524536.379 4845316.27 3259594.933 4615678.664 1273967.906 3.135449642 3.818045234 2.918802288 3.436756583 1.196683505 3.803326791 2.558616207 3.623072952 1 20.2808975 DDPSKPVHLTAFLGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDPSKPVHLTAFLGYK 16 1 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 152.71 3.13E-07 1284520000 2709000 2463700 2019230 2948800 1878810 2350400 2898200 3076900 1964620 FALSE TRUE 2580950.939 2714753.831 2111813.693 2652381.022 2206473.869 2269005.059 2456026.361 2807470.324 2269283.236 1.137341914 1.196304537 0.930608246 1.16881885 0.972321936 0.999877416 1.082291678 1.237161708 1 21.11380526 3.791170554 24.99942164 1.058458395 1.166823283 0.19870711 0.092517223 473.2403949 224874.7459 0.021896736 0.039474859 6182.591527 -3.791170554 0.108364887 DDQRS(ph)S(ph)VLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDQRSSVLK 9 1 H0YK95 H0YK95 AP4E1 2 DDQRS(1)S(1)VLK 69.721 0.030977 11126000 20591 22022 19220 27376 18697 23649 28153 30361 22045 TRUE FALSE 19617.70424 24266.06684 20101.25601 24624.11247 21957.75088 22830.0292 23857.74278 27702.42989 25463.62601 0.770420687 0.95296981 0.789410589 0.967030872 0.862318307 0.896574164 0.936934228 1.087921645 1 14.63615025 1.47456103 2.886699557 1.042647053 0.874542277 0.530843363 0.065163088 0.179569172 2.921392787 0.044996755 0.015546786 29.82366622 -1.47456103 -0.168104777 DDQVTVIGAGVTLHEALAAAELLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDQVTVIGAGVTLHEALAAAELLKK 25 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 126.46 8.54E-05 10590000 17447 15156 15935 19137 13066 14979 24744 19520 11681 FALSE TRUE 16622.31489 16700.41363 16665.63551 17213.3124 15344.70626 14460.27347 20968.84835 17810.72532 13492.42982 1.231973418 1.237761756 1.235184154 1.275775574 1.137282644 1.071732347 1.554119504 1.320053212 1 13.71986256 1.757271957 24.99999998 1.348946263 1.20748438 0.034136117 0.147195522 13.11842792 17544.6441 0.061380272 0.034038415 57.18366109 -1.757271957 -0.141461883 DDREDLVYQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDREDLVYQAK 11 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 174.9 9.54E-06 1027300000 1497730 1196410 2874810 2692040 1240330 1989980 2391700 2033820 2146440 FALSE TRUE 1426935.271 1318325.539 3006622.882 2421431.025 1456643.159 1921066.494 2026802.238 1855727.939 2479298.953 0.575539819 0.531733189 1.21269074 0.97665956 0.587522194 0.774842619 0.817490055 0.748488978 1 21.24150081 DDREQFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDREQFYK 8 1 P60604-2;P60604 P60604-2 UBE2G2 Ubiquitin-conjugating enzyme E2 G2 0 128.86 0.0010174 111790000 377470 324200 337070 390040 232450 405200 373270 397440 237800 FALSE TRUE 359627.7412 357236.3486 352524.9929 350832.4382 272989.2064 391167.8224 316320.8059 362638.0466 274676.8095 1.309275952 1.300569747 1.283417386 1.2772554 0.993856041 1.424102104 1.151610893 1.320235397 1 18.06737559 -4.881770625 0.185877659 2.10E-17 1.307393635 0.322913197 0.115384628 144.0981624 1.458010119 53.69981905 0.295402048 1.31E-05 4.881770625 1.307393635 DDRGPPQRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DDRGPPQRPK 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 141.08 2.15E-05 1080200000 1233100 974140 1033250 1143210 911099 1157230 1420560 1237750 1079942 FALSE TRUE 1174813.807 1073405.974 1080625.535 1028292.359 1069994.377 1117154.835 1203827.482 1129366.048 1247413.89 0.941799523 0.860505068 0.86629269 0.824339353 0.857770132 0.895576716 0.965058584 0.90536594 1 20.2505088 1.884198173 4.040232137 0.951393873 0.873230901 0.531559613 0.036928832 0.20620095 5.402590983 0.01805757 0.010167508 76.59460361 -1.884198173 -0.078162972 DDRNEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDRNEEKR 8 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 147.2 0.00030434 595530000 449902 487127 288611 511172 241538 371670 366775 485664 251744 FALSE TRUE 428636.0241 536765.7951 301844.0998 459788.0194 283662.1507 358798.9747 310816.7375 443136.6855 290783.1738 1.474074371 1.845931414 1.038038398 1.581205726 0.975510883 1.233905559 1.068895196 1.52394198 1 18.14958426 3.737151852 24.99949533 1.205550235 1.660002897 0.416823618 0.224681779 98.9790476 1756458.307 0.052853189 0.087042902 5459.487195 -3.737151852 0.454452663 DDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 79.635 0.059111 92614000 195220 208590 135440 229230 80633 226520 189480 194690 41253 TRUE FALSE 185992.3375 229845.5581 141650.058 206187.3649 94695.36967 218675.5556 160571.346 177641.9115 47650.30455 3.903276994 4.823590538 2.97269995 4.327094377 1.987298309 4.589174354 3.369786352 3.728033077 1 15.54019781 3.735025428 24.82650339 3.3286492 4.363433773 0.165105305 1.081102031 442.6037287 3108270.84 0.24839117 0.402460047 5432.821398 -3.735025428 1.034784573 DDS(ph)HSAEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.966)HS(0.034)AEDS(1)EDEKEDHKNVR 161.68 3.91E-11 8690900000 2816900 2280500 2218900 2688400 902710 2743200 2590100 2532100 515160 TRUE FALSE 2683750.72 2512885.543 2320638.76 2418156.924 1060142.338 2648202.296 2194932.675 2310375.9 595048.3817 4.510138674 4.222993659 3.899916093 4.063798842 1.78160696 4.450398283 3.688662539 3.882668992 1 19.18264745 2.971242677 24.59087566 3.25763346 4.222007926 0.23134115 1.025316749 953.9687505 815755.2554 0.286189876 0.30412449 935.9285099 -2.971242677 0.964374466 DDS(ph)QNAIDHKIESDTEETQDTSVDHNETGNTGESSVEENEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDSQNAIDHKIESDTEETQDTSVDHNETGNTGESSVEENEK 41 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 DDS(0.153)QNAIDHKIES(0.153)DT(0.153)EET(0.153)QDT(0.153)S(0.153)VDHNET(0.048)GNT(0.016)GES(0.007)S(0.008)VEENEK 50.513 0.015395 114120000 84174 72494 67886 89976 32095 89371 91276 102310 30466 TRUE FALSE 80195.26184 79881.22102 70998.64025 80931.44154 37692.35784 86276.05986 77350.1698 93351.19402 35190.51168 2.278888769 2.269964749 2.017550665 2.299808604 1.071094339 2.451685291 2.198040497 2.652737615 1 15.10289887 3.685388894 2.028121737 2.014544344 2.285208227 0.047591818 0.541086134 1.215726534 9.778777606 0.144813458 0.28234838 4846.061191 -3.685388894 0.270663883 DDSFFGETSHNYHKFDSEYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DDSFFGETSHNYHKFDSEYER 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 111.57 0.00015826 128870000 231530 179200 214500 231640 144830 231470 248530 251350 60441 FALSE TRUE 220586.0357 197460.6837 224335.0372 208355.1071 170088.3061 223454.1359 210612.1839 229340.4615 69813.88159 3.159630015 2.828387124 3.213329958 2.984436653 2.436310692 3.200712104 3.016766568 3.285026649 1 16.09122631 2.975353288 23.71553871 2.779008984 3.037889419 0.06921952 0.655084602 1505.312286 1448440.843 0.176404066 0.188105223 944.8291583 -2.975353288 0.258880435 DDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.013)HS(0.987)AEDS(1)EDEKEDHK;DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.01)HS(0.99)AEDS(1)EDEKEDHK;DDS(0.046)HS(0.954)AEDS(1)EDEKEDHK;DDS(0.012)HS(0.988)AEDS(1)EDEKEDHK;DDS(0.011)HS(0.989)AEDS(1)EDEKEDHK 210.34 4.59E-12 10526700000 3772490 4608160 2706460 4489440 1387250 4406850 3059060 3790010 583679 TRUE FALSE 3594171.874 5077736.743 2830553.868 4038152.962 1629185.961 4254239.68 2592344.214 3458136.632 674192.9583 5.331072996 7.531577838 4.198432857 5.989610114 2.416498038 6.310121794 3.845107223 5.129298059 1 19.36280203 3.382878693 1.666547366 4.188056072 6.357338651 0.221947625 1.681586409 0.489591937 2.781274815 0.473290517 0.759574356 2414.786245 -3.382878693 2.169282579 DDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.089)HS(0.911)AEDS(1)EDEKEDHKNVR;DDS(0.386)HS(0.614)AEDS(1)EDEKEDHKNVR;DDS(0.014)HS(0.986)AEDS(1)EDEKEDHKNVR;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDS(0.01)HS(0.99)AEDS(1)EDEKEDHKNVR;DDS(0.004)HS(0.996)AEDS(1)EDEKEDHKNVR 253.39 7.43E-36 16343780000 7136994 5766969 5714561 7028192 2436548 7407037 7053092 6962742 1647074 TRUE FALSE 6799642.438 6354629.698 5976579.274 6321704.787 2861481.2 7150529.451 5977013.276 6353047.399 1902493.824 3.574068075 3.340157859 3.141444771 3.322851674 1.504068588 3.758503372 3.141672894 3.339326162 1 20.85946034 2.954453309 24.98978213 2.777478611 3.362497542 0.154243186 0.835719817 954.0111949 523430.2919 0.234766375 0.249016132 900.4369506 -2.954453309 0.585018931 DDSHSAEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK 302.11 1.12E-46 997280000 885980 1011060 656900 985800 364070 964180 693030 903050 262890 TRUE FALSE 844101.4812 1114088.163 687019.5148 886705.5111 427563.6927 930790.2048 587295.5451 823974.1546 303657.6385 2.779780167 3.668895565 2.262480595 2.92008301 1.408045241 3.065261949 1.93407137 2.713497209 1 18.21208614 0.674113585 0.137948094 9.50E-12 3.947490809 0.430918992 0.602612284 8.83051986 0.670995078 10.77413626 6.435356637 4.721865208 -0.674113585 3.947490809 DDSHSAEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR 339.42 1.51E-80 7520409000 6545003 5223632 5010268 6196209 2215540 6399335 5648522 6427909 1909330 TRUE FALSE 6235633.679 5755926.04 5239993.744 5573354.299 2601929.475 6177724.424 4786736.227 5865047.211 2205419.145 2.827414323 2.609901185 2.375962753 2.527117946 1.179789103 2.801156614 2.170442856 2.659379839 1 21.07262144 -1.535757449 0.242309317 1.07E-33 2.640872052 0.440727312 0.482091767 22.09421379 0.980287948 16.03130599 0.794370606 0.029123432 1.535757449 2.640872052 DDTSRYDERPGPS(ph)PLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDTSRYDERPGPSPLPHR 18 2 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 DDTSRYDERPGPS(1)PLPHR;DDTSRYDERPGPS(1)PLPHR;DDTSRYDERPGPS(1)PLPHR;DDTSRYDERPGPS(1)PLPHR;DDTSRYDERPGPS(1)PLPHR 158.05 2.43E-11 1677930000 1254815 693248 1320803 953451 1591306 1068601 1928408 1291624 2067390 TRUE FALSE 1195502.382 763890.7594 1381363.124 857608.294 1868829.263 1031595.079 1634193.942 1178522.555 2387990.282 0.500631175 0.319888554 0.578462624 0.359133913 0.782595003 0.431992997 0.684338606 0.493520666 1 21.18736554 -4.999999999 0.139571623 2.722307726 0.329072318 0.571510059 0.134491926 86.2694542 0.73865195 41.12171032 0.720878504 1.00E-05 4.999999999 -2.393235408 DDWEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DDWEEKR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 143.61 0.0038644 4719540000 5106900 4413130 4529790 5544710 3219140 5472420 5970640 5765210 3437470 FALSE TRUE 4865506.958 4862832.964 4737485.352 4987345.217 3780556.997 5282908.723 5059709.21 5260377.649 3970535.291 1.225403277 1.224729818 1.193160369 1.256088877 0.952152977 1.330528086 1.274314126 1.324853518 1 21.92090209 DDYPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 109.63 0.068384 478300000 292840 279020 236010 281080 236180 253890 247570 245390 213172 FALSE TRUE 278998.0336 307452.4552 246831.2919 252825.3044 277369.7172 245097.7256 209798.6496 223902.3507 246229.625 1.133080691 1.248641203 1.00244352 1.026786701 1.126467691 0.995403074 0.85204471 0.909323363 1 17.90964482 2.823947846 0.68719384 0.907691119 1.187849337 0.518581815 0.079031863 0.496017212 0.511909033 0.057400935 0.063728319 666.7266979 -2.823947846 0.280158218 DDYSRDDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DDYSRDDYR 9 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 116.77 0.0011497 2588320000 2216920 1638770 1942360 2014490 2011610 2058330 2644910 2225570 2251920 FALSE TRUE 2112130.585 1805762.526 2031419.127 1811989.638 2362434.147 1987049.516 2241380.402 2030687.292 2601136.252 0.812003056 0.69422066 0.780973748 0.696614657 0.908231603 0.763915967 0.861692808 0.780692396 1 21.31071054 -1.285758183 0.220714269 1.183219729 0.731635048 0.545126563 0.062989819 14.16230743 0.628198919 1.619105631 0.127794279 0.051789512 1.285758183 -0.451584681 DDYSRDDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DDYSRDDYRR 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 67.776 0.034848 1280560000 1789410 887940 1867230 1294420 1831020 1630850 2568330 1987840 2548030 FALSE TRUE 1704828.136 978422.0955 1952844.342 1164302.442 2150349.308 1574373.256 2176484.088 1813774.191 2943165.479 0.579249841 0.332438697 0.663518364 0.395595304 0.730624671 0.534925157 0.73950449 0.616266467 1 21.48893723 0.275913243 0.256404677 1.144045895 0.424105051 0.596769058 0.118752831 3.062712136 0.395989747 0.650690443 0.198824316 1.88761423 -0.275913243 -0.719940845 DEAAYGELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DEAAYGELR 9 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;; 101.64 0.0089423 1718780000 3471250 3926020 2947350 3961170 2190630 3543870 3193130 4006480 1941890 FALSE TRUE 3307170.892 4326085.902 3082488.913 3562985.666 2572675.178 3421144.893 2705959.373 3655651.372 2243028.383 1.474422221 1.928680856 1.374253191 1.588471056 1.146965057 1.525234776 1.206386594 1.629783822 1 21.09701645 3.310988078 1.761417473 1.332743462 1.688160252 0.264241315 0.229249254 0.387185262 2.471305603 0.065180194 0.097200939 2046.388461 -3.310988078 0.35541679 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 33 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 159.75 2.35E-14 89299000 120033 122983 102435 135393 70061.6 118909 112518 119803 42006.9 FALSE TRUE 114359.278 135515.1075 107131.7461 121783.0384 82280.32086 114791.1515 95351.31257 109312.4142 48521.11551 2.356897132 2.792909975 2.207940707 2.509897745 1.695763174 2.365797866 1.965150874 2.25288337 1 15.5663251 -1.089107348 0.200544923 2.73E-11 2.687934633 0.69564621 0.273044803 10.19455585 0.439161295 6.510774078 0.740868555 0.081450293 1.089107348 2.687934633 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 206.73 7.77E-26 148240000 21849 21851 22851 25088 21424 19412 20316 27598 30824 TRUE FALSE 20816.24107 24077.64174 23898.74095 22566.10658 25160.33882 18739.75757 17216.42107 25181.37281 35604.02849 0.584659713 0.676261725 0.671236991 0.633807677 0.706671124 0.526338124 0.483552615 0.707261899 1 15.11975287 0.979590167 23.59505289 1.000000004 0.610678072 0.762552522 0.068043537 388.2094352 448795.639 0.072190029 0.018047507 9.540918083 -0.979590167 -0.389321932 DEATAAVIDLNDRPIGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEATAAVIDLNDRPIGSR 18 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 246.49 2.47E-24 346910000 273850 288910 269170 318320 247210 293410 289450 308180 268980 FALSE TRUE 260905.6532 318350.2575 281511.7107 286321.8688 290323.3457 283249.1381 245289.0864 281194.1254 310692.0446 0.839756465 1.024648886 0.906079559 0.921561636 0.934440874 0.911671679 0.789492652 0.905057372 1 18.24512578 1.984084266 24.06334658 0.868740766 0.929444827 0 0.068774189 811.5497485 1226998.623 0.025665431 0.017127924 96.40160534 -1.984084266 0.060704061 DECSFHIFYQLLGGAGEQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DECSFHIFYQLLGGAGEQLK 20 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3 Q7Z406 MYH14 Myosin-14 0 106.39 0.00024212 48603000 155620 136550 163750 187790 105130 143360 174540 179050 101370 FALSE TRUE 148264.151 150464.6002 171258.0995 168912.9924 123464.6387 138395.4073 147910.7174 163371.4328 117089.9419 1.266241563 1.285034375 1.462620074 1.442591821 1.054442736 1.181958117 1.263223083 1.395264445 1 16.83725763 2.750923859 24.97884216 1.200869996 1.345537206 0.345901849 0.123333728 1091.373551 2205023.343 0.037583667 0.039611555 563.5388475 -2.750923859 0.144667211 DEDGESGGQRS(ph)EAEEGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEDGESGGQRSEAEEGEVR 19 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DEDGES(0.139)GGQRS(0.861)EAEEGEVR;DEDGES(0.093)GGQRS(0.907)EAEEGEVR 169.6 8.37E-12 396890000 177354 195166 140246 194517 132009 174529 153719 178753 112831 TRUE FALSE 168970.8279 215053.6373 146676.4178 174963.7816 155031.3278 168485.017 130266.3433 163100.4397 130328.2552 1.29650188 1.650092199 1.12543836 1.342485414 1.189545026 1.292774285 0.999524954 1.251458783 1 16.99179037 2.728398189 0.522375788 1.050794961 1.475157386 0.37337729 0.148298148 0.854021184 0.488131069 0.121366054 0.150077562 535.0547073 -2.728398189 0.424362425 DEDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 114.54 0.058621 201870000 514840 436810 444400 536720 457950 430220 546630 527110 464410 FALSE TRUE 490504.5335 481321.4356 464776.1796 482767.8859 537816.335 415321.3735 463231.554 480953.454 536428.3309 0.914389687 0.897270722 0.866427354 0.899967168 1.002587492 0.774234599 0.863547891 0.896584737 1 19.03302591 2.239682109 24.99999762 0.86779207 0.910405135 0.030519279 0.064814228 71.71680999 1598739.613 0.021261607 0.016871954 173.6529275 -2.239682109 0.042613065 DEDYKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 154.35 0.0015363 5988534000 10252317 6472519 8970591 9618087 6701227 9538689 11734920 10052607 7893149 FALSE TRUE 9767710.294 7132076.045 9381901.47 8651258.622 7869918.867 9208361.808 9944542.427 9172347.439 9117178.234 1.071352346 0.782267919 1.029035654 0.948896512 0.863196777 1.010001293 1.090747836 1.006051127 1 23.12015595 2.032908584 10.46146233 1.044364161 0.934303737 0.215291968 0.082817324 0.570589592 177.3495801 0.029460697 0.021698892 107.8719635 -2.032908584 -0.110060424 DEEVLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 124.08 0.0067044 757640000 885040 756500 741670 965500 459820 885450 913240 974950 548620 FALSE TRUE 843205.9132 833588.2101 775676.3031 868446.1057 540012.4624 854786.6445 773908.4652 889578.2095 633697.1876 1.330613311 1.315436184 1.224048833 1.370443364 0.852161684 1.348888177 1.221259113 1.403790686 1 19.27343409 -2.267642766 2.190631411 0.000176211 1.259183147 0.213930605 0.155614549 1503841.081 420041.5864 7365366.605 0.037206793 0.005399546 2.267642766 1.259006936 DEFEGLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DEFEGLFK 8 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 159.2 0.00083884 1054611000 2416101 2097155 2071374 2423010 1410212 2178682 2370862 2490212 1532453 FALSE TRUE 2301896.694 2310857.479 2166348.547 2179444.431 1656152.526 2103233.696 2009143.458 2272155.836 1770097.985 1.300434617 1.305496927 1.223857982 1.231256377 0.935627598 1.188201848 1.135046464 1.283632802 1 20.75539779 3.199122542 2.384849851 1.124159975 1.295207222 0.371916749 0.098745482 0.288505561 3.359407612 0.028409304 0.037388991 1581.694274 -3.199122542 0.171047246 DEFSYQEMIANLPLCSHPNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEFSYQEMIANLPLCSHPNPR 21 0 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ; 168.05 1.13E-11 106747000 103815 124409 82625 106693 73068 96932 84390 101560 64621 FALSE TRUE 98907.87069 137086.4185 86413.43798 95968.01694 85811.03607 93575.22053 71514.75557 92666.868 74642.09464 1.325095058 1.83658322 1.157703818 1.285709055 1.14963328 1.253652125 0.958102206 1.241482684 1 16.18770185 3.710802643 22.34271436 1.148073847 1.580838997 0.559658717 0.159072236 114.8687129 92459.00274 0.040214505 0.062329014 5138.101067 -3.710802643 0.432765149 DEGGNQQDEAITWFNVIYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEGGNQQDEAITWFNVIYPR 20 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 ; 189.69 2.17E-21 10292000 24833 25875 26600 26844 25297 26043 28044 27307 31775 FALSE TRUE 23659.1933 28511.69192 27819.63631 24145.59012 29708.78879 25141.12438 23765.37274 24915.85432 36702.50472 0.644620673 0.776832321 0.757976507 0.657873088 0.809448538 0.684997511 0.647513648 0.678859781 1 15.1635909 -1.68643877 5.241938219 1.006647147 0.707380084 0.72364443 0.056852288 0.004384548 0.000262274 0.054648957 0.012675969 0.020585491 1.68643877 -0.299267063 DEHLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEHLLK 6 0 O00505;O00629 O00505;O00629 KPNA3;KPNA4 Importin subunit alpha-4;Importin subunit alpha-3 0 ; 100.82 0.037225 441290000 1973070 2023100 1689500 2276400 1442680 1993520 2152700 2035080 834570 FALSE TRUE 1879806.891 2229256.19 1766965.246 2047571.947 1694282.935 1924483.903 1824266.078 1856877.607 963990.8532 1.950025651 2.312528363 1.832968892 2.124057443 1.757571589 1.996371538 1.892410153 1.92623986 1 19.87865993 -1.906218808 0.290520239 3.47E-13 2.094687979 0.811124711 0.148949251 11.480095 0.528018503 8.052949157 0.154174413 0.012410269 1.906218808 2.094687979 DEILEWESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DEILEWESR 9 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 137.84 0.00035664 300514000 632368 610434 579146 650028 657260 572684 653773 605467 624830 FALSE TRUE 602477.2179 672637.9186 605700.417 584685.9505 771885.9359 552851.8095 554027.9215 552449.0997 721725.4452 0.83477342 0.931985872 0.839239382 0.810122401 1.069500793 0.76601402 0.767643603 0.765456038 1 19.46109059 DEILPTT(ph)PISEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DEILPTTPISEQK 13 0 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 DEILPT(0.23)T(0.77)PISEQK;DEILPT(0.013)T(0.987)PISEQK;DEILPT(0.211)T(0.789)PISEQK;DEILPT(0.183)T(0.817)PISEQK;DEILPT(0.001)T(0.999)PISEQK;DEILPT(0.013)T(0.987)PISEQK;DEILPT(0.015)T(0.985)PISEQK;DEILPT(0.014)T(0.986)PISEQK;DEILPT(0.063)T(0.937)PISEQK;DEILPT(0.003)T(0.997)PISEQK;DEILPT(0.005)T(0.994)PIS(0.001)EQK;DEILPT(0.017)T(0.983)PISEQK 358.01 2.99E-75 15795750000 21740820 19992680 17620200 22424020 10679730 20765930 19326400 20571960 10097210 TRUE FALSE 20713174.52 22029956.82 18428103.6 20169914.91 12542271.53 20046800.64 16377802.73 18770570.12 11663033.76 1.775967982 1.888870193 1.58004375 1.729388367 1.075386713 1.718832429 1.404248934 1.609407167 1 23.47543977 2.669909885 0.062676355 1.97E-14 3.161629137 0.506214256 0.206455005 42.18987668 1.115450772 23.29498757 31.9644893 467.6380971 -2.669909885 3.161629137 DEKDEHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DEKDEHGR 8 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 110.76 0.0020216 391488000 1662660 1709600 1398710 1893070 815792 1576290 1474020 2008360 888872 FALSE TRUE 1584069.357 1883810.184 1462842.237 1702775.007 958065.8665 1521702.682 1249131.177 1832497.351 1026713.73 1.542853972 1.83479594 1.424781021 1.658471059 0.933138263 1.482109996 1.21663044 1.7848182 1 19.96960255 2.859384592 18.76835334 1.305157777 1.633269301 0.288781546 0.256833702 3.573650431 540.3146706 0.07057057 0.074851786 723.4101406 -2.859384592 0.328111525 DEKKEES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DEKKEESEESDDDMGFGLFD 20 2 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 2 DEKKEES(1)EES(1)DDDMGFGLFD;DEKKEES(1)EES(1)DDDMGFGLFD 112.23 8.70E-05 142533000 480200 396840 417960 482510 185018 535950 498840 576920 205824 TRUE FALSE 457501.8977 437278.4472 437123.8794 434007.1781 217285.0806 517389.9171 422732.7962 526401.8264 237742.1347 1.924361865 1.839297219 1.83864707 1.825537482 0.913952762 2.176265127 1.778114749 2.214171363 1 17.85903809 -1.983496699 2.835075627 0.272189011 1.810707782 0.345223265 0.352196606 100242008.2 83067849.35 478583270.9 0.078136959 0.010387315 1.983496699 1.538518772 DELEVIHLIEEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DELEVIHLIEEHR 13 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ; 230.14 2.65E-12 60266000 125079 147131 116165 141088 88517 119476 120061 129645 3753.6 FALSE TRUE 119166.7636 162123.8162 121491.2802 126905.5662 103954.3368 115338.5162 101743.4894 118292.5965 4335.689117 27.4850803 37.39286 28.02121574 29.26998748 23.97642773 26.60211861 23.46650939 27.28345906 1 12.0820456 0.102682078 0.404976572 4.73E-26 31.47238555 0.843951958 3.663991916 1.480432129 0.349313616 13.02486552 2.4483251 1.26672423 -0.102682078 31.47238555 DELHHSGWNTCSSCFGDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DELHHSGWNTCSSCFGDSTK 20 0 Q13228;Q13228-4;Q13228-2;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 88.264 0.0012987 115760000 62818 36222 50232 63263 46074 52301 76122 65060 19217 FALSE TRUE 59848.71763 39913.06298 52535.18689 56903.68305 54109.29101 50489.80326 64508.19082 59363.0015 22197.07421 2.696243526 1.798122698 2.36676178 2.563566824 2.437676718 2.274615239 2.90615737 2.674361536 1 14.43808191 3.48900195 24.35131213 2.442268976 2.219726333 0 0.557460461 1628.464482 3337785.557 0.135341439 0.197583336 3083.201791 -3.48900195 -0.222542643 DELHIVEAEAMNYEGS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK 296.06 6.90E-50 678793000 852367 1246222 593718 1056538 571843 1179256 671906 853349 270623 TRUE FALSE 812077.3011 1373213.439 620940.5576 950332.7929 671572.2381 1138418.069 569394.3993 778625.2377 312589.8327 2.597900559 4.393020166 1.986438753 3.04019099 2.148413569 3.641890906 1.82153845 2.490884719 1 18.25391133 0.30019993 0.224662025 0.227335615 3.582237633 0.38685103 0.749421826 5.574677265 0.604305421 5.440642871 1.865304439 1.996181055 -0.30019993 3.354902018 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;DELHIVEAEAMNY(0.003)EGS(0.965)PIKVT(0.032)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.467)EGS(0.522)PIKVT(0.01)LAT(0.001)LK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;DELHIVEAEAMNY(0.014)EGS(0.98)PIKVT(0.006)LATLK;DELHIVEAEAMNY(0.47)EGS(0.527)PIKVT(0.002)LAT(0.001)LK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;DELHIVEAEAMNY(0.001)EGS(0.999)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK 313.05 1.04E-81 10717566000 6423681 7317312 5405958 7618830 3247055.8 7110206 6430813 7366849 2573444.5 TRUE FALSE 6120046.33 8062954.412 5653826.522 6852970.734 3813341.303 6863977.783 5449674.367 6721768.647 2972521.13 2.058873953 2.712496921 1.902030726 2.305440545 1.282864322 2.309143479 1.833350926 2.261302226 1 21.50325563 3.30423808 1.883745294 1.852474867 2.36333146 0.184960669 0.457127326 0.510765153 3.722338156 0.12845622 0.187856215 2014.828473 -3.30423808 0.510856593 DELHIVEAEAMNYEGSPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;; 274.6 2.06E-39 2366336000 3277622 3886134 2595472 4027684 1862564 3317984 2891616 3331638 1495730 FALSE TRUE 3122695.304 4282135.473 2714476.958 3622813.552 2187394.572 3203081.382 2450446.871 3039902.115 1727680.169 1.807449874 2.478546405 1.571168673 2.096923734 1.266087677 1.853978207 1.418345198 1.759528279 1 20.72040474 1.612850486 0.180985269 0.717578899 2.459500869 0.436323728 0.31421818 2.580591422 0.485710794 1.836078693 1.920187377 41.00629065 -1.612850486 1.74192197 DELHIVEAEAMNYEGSPIKVT(ph)LATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNY(0.065)EGS(0.404)PIKVT(0.531)LATLK 91.729 0.014338 89041000 24975 24644 16667 30025 13952 25751 20911 28497 10295 TRUE FALSE 23794.48125 27155.25162 17431.19844 27006.82996 16385.22438 24859.23641 17720.64289 26001.65161 11891.49602 2.00096617 2.283585814 1.46585412 2.271104486 1.377894283 2.090505381 1.490194578 2.186575311 1 13.53764261 -2.002255595 0.187738153 4.75E-16 2.145650114 0.37516712 0.349128798 33.3066851 0.916258576 16.47082959 0.988932524 0.009948198 2.002255595 2.145650114 DELLAQHAAGALGLPDLVAVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DELLAQHAAGALGLPDLVAVLTR 23 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 159.66 1.98E-11 404070000 746150 860410 565740 924240 489070 680090 614950 813800 446620 FALSE TRUE 710880.9682 948086.7572 591679.7386 831333.6393 574363.6532 656538.3128 521128.0832 742539.3578 515879.5486 1.377997965 1.837806441 1.146933892 1.611487878 1.113367752 1.272658152 1.010173954 1.439365759 1 18.97667473 2.939553352 1.093361719 1.147351856 1.571462308 0.30774368 0.222466489 0.476705004 1.216378094 0.093219369 0.106199834 870.068313 -2.939553352 0.424110451 DENGELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DENGELR 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 115.46 0.013204 173320000 412300 373600 397120 455170 366460 441900 511090 452390 435070 FALSE TRUE 392811.3961 411670.2647 415328.3448 409415.4468 430370.508 426596.8922 433113.8337 412776.3333 502538.4336 0.781654436 0.819181653 0.826460858 0.814694796 0.856393221 0.848884113 0.861852158 0.821382616 1 18.93887441 -5 0.157460206 1.634390126 0.779347744 0.890639292 0.019371056 37.74667168 0.344402132 7.475251588 0.080262656 1.00E-05 5 -0.855042382 DENQSINHQMAQEDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DENQSINHQMAQEDAQR 17 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 205.18 8.11E-12 1214860000 622616 699116 488867 713281 460327 580432 548941 579003 384240 FALSE TRUE 593186.1756 770356.7152 511282.0355 641580.6387 540607.8831 560331.4943 465189.9685 528302.4278 443825.9768 1.336528745 1.735717952 1.151987631 1.445568021 1.218062735 1.262502701 1.048135965 1.190336879 1 18.75963458 2.574848305 0.599028471 1.039970177 1.523413498 0.479432614 0.151554996 0.600068539 0.447628858 0.118173721 0.112626946 375.7061507 -2.574848305 0.483443321 DEPDWESLIFLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DEPDWESLIFLAR 13 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;;;; 185.77 1.95E-05 301198100 290677.3 300050.5 242414.8 336431.1 293839.3 254734.2 309545 299149.8 268744 FALSE TRUE 276937.5601 330625.9871 253529.7584 302612.4067 345084.7809 245912.6908 262318.2251 272954.6576 310419.447 0.892139854 1.065094311 0.816732846 0.974850028 1.111672559 0.792194861 0.845044431 0.879309142 1 18.24385942 2.211091433 24.99997057 0.861311019 0.970573522 0.177082535 0.096194535 307.9892706 280302.1336 0.033604619 0.02482433 162.5891021 -2.211091433 0.109262503 DEPLLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEPLLFR 7 0 Q70Z35-3;Q70Z35-4;Q70Z35 Q70Z35-3 PREX2 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein" 0 79.454 0.075798 51431000 46472 53910 39502 54795 42073 40428 45316 51960 36771 FALSE TRUE 44275.36066 59403.49029 41313.20577 49286.9025 49410.51788 39027.96822 38402.21191 47410.10694 42473.25888 1.042429091 1.398609192 0.972687448 1.160421964 1.163332393 0.918883299 0.904150351 1.116234266 1 15.37426719 2.247522978 24.81716501 0.966972947 1.164828922 0.291482969 0.123019408 179.90324 498159.958 0.041764924 0.034461263 176.8165766 -2.247522978 0.197855975 DEPSVAAMVYPFTGDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DEPSVAAMVYPFTGDHK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;;;; 236.78 3.38E-20 2321977000 4664611 4056425 4051528 4872597 3002128 4515384 4770841 4952653 2886073 FALSE TRUE 4444124.082 4469779.319 4237294.566 4382794.292 3525698.173 4359015.12 4042961.583 4518972.448 3333630.461 1.333118393 1.340814278 1.271075068 1.314721096 1.057615178 1.30758798 1.21278037 1.355570901 1 21.66866276 -5 0.155765158 0.037464776 1.352788692 0.473404411 0.088806882 111.3248069 1.010501323 33.44899173 0.376141646 1.00E-05 5 1.315323916 DEQGACAVLAVHLNTLLGERPVQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEQGACAVLAVHLNTLLGERPVQHR 25 1 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 100.08 0.0041477 7885700 7524.7 8958.1 5495.5 10015 8123.7 8027.1 10405 8940.2 4334.7 FALSE TRUE 7169.022344 9870.940575 5747.474111 9008.273173 9540.470708 7749.119514 8817.526149 8157.348693 5006.903137 1.431827648 1.971466254 1.147909986 1.79917065 1.905463406 1.547687123 1.761073843 1.629220392 1 12.28970283 0.939374063 20.14669457 0.999999998 1.666995018 0.420471153 0.239183441 1869.839388 621371.6664 0.207256092 0.051814023 8.697091978 -0.939374063 0.66699502 DEQLESLFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEQLESLFQR 10 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 125.75 0.00093265 15068000 22712 23288 17462 24911 16532 20363 18990 20998 14193 FALSE TRUE 21638.44877 25661.07368 18262.64997 22406.89895 19415.17557 19657.8242 16092.72672 19159.3038 16393.97795 1.319902274 1.56527438 1.113985271 1.366776204 1.184287037 1.19908812 0.981624275 1.168679369 1 14.00087834 2.685789501 0.624013104 1.022299428 1.436623435 0.521074796 0.120049409 0.528474731 0.436371434 0.089058053 0.091019787 485.0533419 -2.685789501 0.414324007 DESETEKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DESETEKEK 9 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 113.93 0.0015697 935970000 1420560 1134390 1112270 1472400 707440 1364050 1480440 1586810 774730 FALSE TRUE 1353412.944 1249985.631 1163268.68 1324391.555 830817.312 1316812.606 1254571.688 1447860.504 894871.1716 1.512410934 1.396833053 1.299928656 1.479980132 0.928421139 1.471510814 1.401957877 1.617954126 1 19.77132048 4.272288335 1.584926726 1.334277179 1.517086218 0.077430502 0.211717782 1.359524472 5.693728045 0.054252705 0.293128305 18719.24527 -4.272288335 0.182809039 DETEFYLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DETEFYLGK 9 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 201.39 5.02E-05 923171000 1688230 1780030 1275620 1865220 1099830 1638670 1695330 1672070 1181749 FALSE TRUE 1608430.714 1961417.081 1334108.439 1677724.542 1291640.004 1581922.447 1436676.272 1525654.687 1365008.599 1.178330096 1.436926538 0.977362662 1.229094485 0.946250452 1.158910243 1.052503458 1.1176887 1 20.38047861 3.7340079 24.99963861 1.076553805 1.307628318 0.472823979 0.104581793 268.6991462 1475467.728 0.024403699 0.039230985 5420.107502 -3.7340079 0.231074512 DETEFYLGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DETEFYLGKR 10 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 169.37 7.46E-06 2260202000 3661680 2321924 3366520 3014090 3176050 3529510 5219570 4046910 4153650 FALSE TRUE 3488599.643 2558530.695 3520878.272 2711107.947 3729952.114 3407282.184 4423228.733 3692541.106 4797776.828 0.72712837 0.53327422 0.7338562 0.565075877 0.777433434 0.710179382 0.921932989 0.769635862 1 22.19393462 1.745500819 0.666768824 0.970597872 0.62712295 0.610798831 0.087419785 0.393549588 0.356948668 0.072475769 0.037292858 55.65456839 -1.745500819 -0.343474922 DETNYGIPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 213.98 2.88E-08 1234466000 1505100 1821160 1491910 1731040 1176190 1509220 1462630 1590140 1212760 FALSE TRUE 1433956.906 2006738.274 1560315.549 1557032.57 1381317.164 1456955.333 1239478.93 1450898.912 1400828.627 1.023649059 1.432536597 1.113851844 1.111508246 0.986071484 1.04006679 0.88481839 1.035743334 1 20.41784904 3.039652376 1.734598711 0.975048687 1.225650784 0.416660848 0.109660272 0.285389714 1.751696955 0.036837885 0.044810298 1095.600889 -3.039652376 0.250602097 DETVSDCSPHIANIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DETVSDCSPHIANIGR 16 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 195.2 9.08E-11 284690000 246150 284560 214108 310810 220156 254610 263330 267230 196982 FALSE TRUE 234514.9773 313556.9875 223925.0636 279566.7883 258551.1367 245792.7919 223154.1721 243829.9245 227528.9625 1.030703849 1.37809703 0.984160702 1.228708579 1.136343848 1.08027035 0.9807726 1.071643459 1 17.79569067 2.141663752 2.549157947 1.016876067 1.169704871 0.236177194 0.108552332 0.354094248 4.596238217 0.04709299 0.030378098 138.5682564 -2.141663752 0.152828805 DETYKPHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DETYKPHLER 10 1 A0A0A6YYC7;Q96JP5-2;Q96JP5;H3BTR0 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 0 ;; 113.22 0.00091116 199086000 373080 405480 367192 473810 269291 388025 387820 393120 272619 FALSE TRUE 355445.2478 446798.873 384028.1164 426181.7186 316255.2651 374587.597 328650.9362 358696.3287 314895.3622 1.128772572 1.418880449 1.219541989 1.353407417 1.004318587 1.189562127 1.043683 1.139096893 1 18.26451298 2.740312919 24.99980045 1.084640694 1.283085322 0.535360257 0.094576786 118.5637263 1691536.901 0.027016138 0.027334762 549.9369735 -2.740312919 0.198444628 DEVQEVVYFSAADHEPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEVQEVVYFSAADHEPESK 19 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 225.23 1.78E-19 79358000 187600 158430 161690 195450 111170 188840 206850 203520 102790 FALSE TRUE 178732.5198 174574.1971 169103.6464 175802.9947 130558.0128 182300.4234 175291.2334 185698.7099 118730.1482 1.505367613 1.470344304 1.424268806 1.480693803 1.099619724 1.535418141 1.476383514 1.564040075 1 16.85732679 -2.157341582 2.223022727 1.81E-05 1.446912352 0.541544624 0.128518447 2569989.749 645840.6743 12925050.77 0.030355589 0.006960788 2.157341582 1.446894203 DEVVS(ph)PLPSALQGPSGSLSAPPAASVISAPPSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEVVSPLPSALQGPSGSLSAPPAASVISAPPSSSSR 36 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DEVVS(0.96)PLPS(0.04)ALQGPSGSLSAPPAASVISAPPSSSSR 124.18 1.46E-08 190860000 41792 38535 39379 45589 36019 42909 42157 39150 32123 TRUE FALSE 39816.57498 42461.76031 41184.5661 41006.30711 42300.7022 41423.05057 35725.17538 35721.81845 37104.47078 1.073093731 1.144383936 1.109962364 1.105158118 1.14004327 1.116389742 0.962826706 0.962736234 1 15.17930541 1.741168987 5.960049395 0.97270794 1.115693544 0.897777584 0.022176372 0.041246352 3.861191282 0.010642203 0.005554183 55.1022061 -1.741168987 0.142985604 DEWLRPEDLPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DEWLRPEDLPIK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 207.66 6.92E-08 595980000 1531920 1629150 1318140 1793980 956990 1555170 1460800 1640420 935480 FALSE TRUE 1459509.178 1795162.237 1378578.023 1613645.722 1123888.753 1501314.073 1237928.131 1496776.128 1080549.461 1.3507102 1.661342033 1.27581205 1.493356649 1.040108569 1.389398753 1.145646891 1.385199089 1 20.04333368 2.760968475 24.8527646 1.212737507 1.461384541 0.37910635 0.159235165 727.8892884 807307.4867 0.043733427 0.046353902 576.724598 -2.760968475 0.248647035 DEYRQDYDAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DEYRQDYDAGR 11 1 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 164.81 2.04E-05 220290000 229960 173230 199250 204690 208120 204500 240160 219040 214060 FALSE TRUE 219090.2465 190882.3339 208385.8096 184114.1723 244416.0621 197418.1137 203519.1812 199859.6964 247255.3315 0.886089069 0.772004926 0.842796021 0.744631758 0.988516853 0.798438248 0.823113418 0.80831299 1 17.9156421 -1.11957246 4.76646847 1.000010757 0.83086912 0.378997108 0.067137395 6.83E-06 1.26E-06 0.057829292 0.013629628 0.075932472 1.11957246 -0.169141637 DFAKS(ph)SGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFAKSSGLK 9 1 Q8NC26-2;Q8NC26 Q8NC26-2 ZNF114 Zinc finger protein 114 1 DFAKS(0.982)S(0.018)GLK 67.563 0.036667 399170000 350960 293590 357490 344840 288450 326180 424340 381750 397200 TRUE FALSE 334370.8163 323507.1548 373881.2701 310176.028 338755.5887 314884.3048 359599.1395 348321.9462 458795.7474 0.728801037 0.705122392 0.814918779 0.676065613 0.738358171 0.686327863 0.783789173 0.759209187 1 18.80749249 0.243313025 0.858784775 1.003030446 0.726389278 0.809171777 0.040615619 1.201272233 1.053422763 0.043670364 0.011801032 1.751108373 -0.243313025 -0.276641168 DFAYGETDPLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFAYGETDPLIR 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 134.68 0.00032855 56682000 166710 142320 135810 187320 147290 155360 160950 177480 170900 FALSE TRUE 158829.9487 156822.5698 142037.0228 168490.2377 172977.3294 149979.8442 136394.1215 161938.9103 197402.2992 0.804600298 0.794431324 0.719530742 0.853537362 0.876268058 0.759767464 0.690944949 0.820349667 1 17.59077927 0.971710967 24.16676587 1.000000002 0.783130428 0.595725634 0.055085117 1581.432313 1350988.432 0.055642952 0.013910738 9.36938245 -0.971710967 -0.216869575 DFDFESANAQFNKEEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFDFESANAQFNKEEIDR 18 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 268.55 1.58E-31 367900000 539483 520574 486579 593751 343711 541847 561847 579794 372348 FALSE TRUE 513982.7077 573621.0824 508889.1284 534066.0214 403654.0896 523082.7025 476126.9211 529024.1637 430089.8261 1.195058977 1.333723905 1.183215918 1.241754603 0.938534383 1.216217336 1.107040651 1.230031802 1 18.71427848 2.944385641 24.99922384 1.112384393 1.247016538 0.341148749 0.095331644 320.7835515 144195.1935 0.026416292 0.028018794 879.8034106 -2.944385641 0.134632145 DFDPAVTEYIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DFDPAVTEYIQR 12 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;; 272.58 2.23E-27 2067719000 2398050 1853330 1791590 2121150 2195130 1992620 2445210 2252650 2660710 FALSE TRUE 2284698.929 2042186.434 1873736.174 1907927.972 2577959.977 1923615.07 2072148.305 2055396.024 3073319.318 0.743397836 0.664488855 0.609678325 0.62080369 0.838819436 0.625907975 0.674237881 0.668787006 1 21.55136624 -1.216257314 3.992933741 1.000221759 0.680899538 0.688350908 0.067505701 9395940.221 2862047.193 19237.45373 0.014825273 0.06077748 1.216257314 -0.319322221 DFDS(ph)S(ph)EDEKHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 131.72 0.00011024 688020000 2540910 2268550 2267250 2790240 951050 2815540 2639360 2396850 834530 TRUE FALSE 2420806.22 2499717.824 2371205.655 2509759.774 1116912.819 2718037.144 2236677.157 2186969.107 963944.6502 2.511353966 2.593217177 2.459898143 2.603634735 1.158689784 2.819702504 2.320337746 2.268770419 1 19.87859078 DFDTALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFDTALK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 143 0.005702 442281000 1229710 1071190 1054060 1277610 927970 1154340 1340610 1314680 995150 FALSE TRUE 1171584.045 1180345.479 1102389.694 1149182.215 1089807.674 1114364.916 1136075.323 1199559.65 1149472.779 1.019236007 1.026858139 0.959039408 0.99974722 0.948093503 0.969457421 0.988344694 1.043573777 1 20.13254087 1.264624206 24.58985429 1.0217869 0.990467456 0.217427714 0.026701155 291.8628906 275360.542 0.019332878 0.007053686 18.39179876 -1.264624206 -0.031319444 DFDWNLK ddPTM_SK-BR-3_Trastuzumab_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 ; 126.67 0.0091423 278020000 1062120 1072580 963620 1150920 739710 1128040 1123710 1217110 771080 FALSE TRUE 1011915.693 1181877.121 1007802.93 1035227.335 868715.1898 1088975.692 952267.4011 1110533.396 890655.1483 1.136147581 1.326975007 1.131529899 1.162321171 0.975366495 1.222668161 1.069176328 1.246872483 1 19.76450742 -4.999999992 0.042416371 0.302003351 1.558706599 0.174525032 0.09837188 1066.158827 3.36945572 92.97374223 26.03146354 1.00E-05 4.999999992 1.256703248 DFESHITSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 150.1 2.22E-05 725820000 2601300 2372310 2362700 2779300 1996650 2620800 2986800 3026800 1976370 FALSE TRUE 2478341.704 2614051.086 2471032.132 2499919.484 2344865.128 2530041.039 2531108.804 2761757.346 2282855.366 1.08563238 1.14507959 1.082430437 1.095084481 1.027163246 1.108279165 1.108746897 1.209782007 1 21.12240803 -0.652085158 6.72082358 0.999995034 1.106446175 0.344665797 0.04667182 0 4.70E-11 0.042428831 0.010000571 0.222799823 0.652085158 0.106451141 DFFELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFFELR 6 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 114.59 0.058529 52241000 165670 341520 147740 252670 115170 176950 142230 198950 100950 FALSE TRUE 157839.1074 376321.2763 154514.0251 227271.1316 135255.6115 170822.1771 120530.2013 181528.8833 116604.8104 1.353624322 3.227322054 1.325108497 1.949071661 1.159948814 1.46496681 1.033664056 1.55678726 1 16.83126778 3.173655819 1.557537449 1.252114385 2.232994497 0.289489089 0.546902607 0.384688933 1.937548427 0.177227526 0.242307665 1491.611831 -3.173655819 0.980880111 DFFHGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 116.54 0.0054322 106030000 117390 103110 89801 109760 110280 90756 131000 112740 102350 FALSE TRUE 111841.2073 113617.0262 93918.46468 98726.71627 129512.7971 87613.09696 111013.544 102867.8879 118221.9153 0.946027706 0.96104877 0.794425166 0.835096573 1.095505827 0.74109015 0.939026777 0.870125371 1 16.85113797 DFFQSYGNVVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFFQSYGNVVELR 13 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 240.65 1.73E-16 238669000 202089 224910 178315 220314 162039 186628 190749 212478 173461 FALSE TRUE 192536.6535 247828.5847 186490.9191 198167.6182 190298.5503 180165.0256 161646.7367 193872.2999 200360.446 0.960951412 1.236913721 0.930777121 0.989055585 0.949781028 0.899204555 0.806779681 0.96761763 1 17.6122382 3.613745808 8.738166297 0.919705617 1.098684424 0.38097779 0.085458125 0.263567063 17.48947704 0.022753709 0.035280025 4109.091458 -3.613745808 0.178978808 DFGEEHPFYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFGEEHPFYDR 11 0 Q68CQ4 Q68CQ4 DIEXF Digestive organ expansion factor homolog 0 138.75 5.09E-05 185800000 220770 183680 194160 226110 199450 213770 248950 217570 164840 FALSE TRUE 210334.6396 202397.2008 203062.4281 203380.9932 234234.0169 206367.0913 210968.1052 198518.4174 190402.5453 1.10468397 1.062996298 1.066490092 1.068163206 1.230204231 1.083846285 1.108010951 1.042624809 1 17.53869324 -1.462390644 6.665554629 0.999974921 1.096113075 0.254276082 0.051599272 1.82E-05 1.47E-06 0.047226549 0.011128502 0.034483343 1.462390644 0.096138154 DFGLLVFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFGLLVFVR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 86.794 0.032331 9284700 37525 35474 25244 35113 36840 33293 46760 32975 34728 FALSE TRUE 35751.26762 39088.84093 26401.46237 31583.37453 43264.88434 32140.05506 39625.90319 30087.53419 40113.44087 0.891254074 0.974457441 0.658169975 0.787351417 1.078563279 0.801229073 0.987846027 0.750061165 1 15.2917981 DFIDNLDRPPGSSYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFIDNLDRPPGSSYFR 16 1 Q3YEC7;G3V154;F2Z2T0;Q3YEC7-4;Q3YEC7-6;Q3YEC7-3 Q3YEC7 RABL6 Rab-like protein 6 0 ; 154.47 3.21E-07 143040000 205249 195361 141589 170293 213569 145615 224189 185939 190776 FALSE TRUE 195547.2865 215268.508 148080.9957 153174.8241 250815.366 140572.316 189984.8505 169657.1954 220360.5677 0.887396908 0.976892146 0.671994074 0.695109954 1.138204392 0.637919558 0.862154479 0.769907235 1 17.74950656 3.78783455 24.99970531 0.818132363 0.932144549 0.076040725 0.153752279 836.857079 424586.4725 0.035895492 0.064711368 6135.282294 -3.78783455 0.114012186 DFIEDYVDILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFIEDYVDILR 11 0 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ; 132.91 0.00040156 38658000 105514 96796 87478 106364 94867 86793 114326 103799 101034 FALSE TRUE 100526.5623 106659.6224 91488.95283 95672.08864 111411.7748 83787.33665 96883.46896 94709.80929 116701.8367 0.861396574 0.913949818 0.783954695 0.819799339 0.954670277 0.717960737 0.83017947 0.811553716 1 16.83246774 3.755182098 24.67295154 0.833892847 0.887673193 0.02964944 0.081789177 1718.911826 2551545.289 0.018857043 0.033865329 5690.914985 -3.755182098 0.053780347 DFIGVDSTGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFIGVDSTGKR 11 1 Q9NR50-3;Q9NR50-2;Q9NR50 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ; 139.31 6.33E-05 393190000 920310 716820 839080 946550 691660 935960 1024820 980580 777360 FALSE TRUE 876808.7702 789864.773 877552.648 851400.9957 812285.285 903547.4705 868464.8869 894715.2168 897909.0186 0.976500683 0.879671277 0.977329139 0.948204081 0.904640969 1.006279536 0.967208112 0.996443067 1 19.77620974 2.230284422 24.9998134 0.98792516 0.935299402 0.435468429 0.031000796 178.7024775 539800.6077 0.010953277 0.00822707 169.9356208 -2.230284422 -0.052625758 DFIHTASISFLTPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFIHTASISFLTPLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 204.28 4.98E-09 68512000 91945 85054 83119 88142 99981 73957 113070 90350 82274 FALSE TRUE 87598.94207 93721.0993 86930.08837 79281.7987 117417.6547 71395.85055 95819.09483 82438.47502 95032.63172 0.921777504 0.986199136 0.914739356 0.834258688 1.235550911 0.751277211 1.008275716 0.867475451 1 16.53613536 -0.846754071 5.103290486 1.000000073 0.944249122 0.02033316 0.127941823 9.06E-08 2.04E-08 0.105786753 0.024934144 0.142313444 0.846754071 -0.05575095 DFIIFEAAPQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFIIFEAAPQETR 13 0 P60510;H3BTA2 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ;;; 146.16 9.54E-05 83238000 195728 171167 162383 202569 154645 165747 178294 190542 168726 FALSE TRUE 186476.3253 188609.1119 169828.4212 182206.3793 181615.039 160007.1398 151091.9757 173857.1324 194891.1663 0.956822871 0.967766346 0.871401328 0.934913484 0.931879276 0.821007657 0.775263336 0.892072923 1 17.57230917 2.250214514 23.00130042 0.843835289 0.936891402 0.114019897 0.064640898 92.23424546 182042.4457 0.021165283 0.017540465 177.9157984 -2.250214514 0.093056113 DFISVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFISVLR 7 0 Q9Y3B9 Q9Y3B9 RRP15 RRP15-like protein 0 94.539 0.052684 0 121910 118740 116680 115370 135510 113360 135290 132160 120360 FALSE TRUE 116147.5559 130839.741 122029.8934 103772.7884 159142.9011 109434.3148 114649.0257 120587.3698 139024.8141 0.835444785 0.941125092 0.877756206 0.746433571 1.144708606 0.787156706 0.824665917 0.867380191 1 17.08498288 4.75039389 20.55428009 0.887792846 0.835444864 0.021976913 0.113555165 9.150443505 473255.3296 0.024675107 0.144472476 56285.15801 -4.75039389 -0.052347982 DFKPGDLIFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFKPGDLIFAK 11 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 150.21 3.10E-05 435190000 2701700 2495300 2422100 2960800 1848820 2779800 3216700 3250100 2068000 FALSE TRUE 2573995.995 2749573.907 2533155.681 2663174.759 2171253.623 2683534.829 2725933.336 2965504.014 2388694.878 1.07757421 1.15107791 1.060476875 1.114907887 0.908970686 1.123431399 1.141181053 1.241474598 1 21.18779115 2.018767375 24.99972256 1.140505649 1.073133005 0.110178367 0.084909586 488.096326 650182.4049 0.030111235 0.022234522 104.4160776 -2.018767375 -0.067372644 DFKPGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFKPGDR 7 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 61.679 0.082108 275770000 601230 540160 510690 650070 444310 515650 616960 620090 526870 FALSE TRUE 572811.0494 595202.9181 534105.6416 584723.7285 521797.5233 497792.9112 522831.4208 565791.6323 608574.3087 0.941234359 0.978028335 0.877634225 0.960809091 0.857409713 0.817965701 0.859108597 0.92970016 1 19.21507391 3.734860403 24.96758109 0.888493126 0.959631349 0.142321033 0.054731632 405.3475204 2735131.988 0.013834634 0.022379868 5430.75741 -3.734860403 0.071138223 DFLEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFLEKR 6 1 H0YNS7;H0YM05;A0A087WUZ7;Q6P656-2;Q6P656;Q9Y5W8-2;Q9Y5W8 H0YNS7 C15orf26;SNX13 Uncharacterized protein C15orf26;Sorting nexin-13 0 97.473 0.065792 283130000 374800 275160 323780 319870 313060 312330 371950 343350 344280 FALSE TRUE 357083.9468 303199.1168 338625.6333 287716.0599 367657.5649 301513.9338 315202.1962 313284.4538 397669.1841 0.897942212 0.762440564 0.851525959 0.723506048 0.924531192 0.758202913 0.792624143 0.787801686 1 18.60120924 -1.614545451 6.124922185 1.000823182 0.811037728 0.466671461 0.063040043 0.000626043 3.94E-05 0.053925175 0.012656861 0.024291512 1.614545451 -0.189785455 DFLFPHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFLFPHLR 8 0 Q9H2M9;F8WDJ2;Q9H2M9-2 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 119.27 0.0017256 140970000 458620 414630 403910 472950 439100 399430 473740 467490 411650 FALSE TRUE 436941.9415 456881.2684 422429.673 425408.1675 515678.901 385597.6389 401462.2622 426554.0973 475486.5796 0.918936433 0.960871007 0.888415554 0.894679652 1.084528824 0.81095378 0.844318808 0.897089667 1 18.8590451 DFLHLFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFLHLFEK 8 0 C9JEQ8;A4D1E9-2;A4D1E9 C9JEQ8 GTPBP10 GTP-binding protein 10 0 95.502 0.0096049 40594000 175590 134850 135030 135890 141680 110740 155010 151430 125250 FALSE TRUE 167290.2087 148591.3683 141221.2591 122230.079 166388.9471 106905.046 131360.3775 138169.9864 144673.1303 1.156332267 1.027083384 0.976140205 0.844870632 1.150102626 0.738941957 0.907980475 0.955049401 1 17.14243747 4.298762163 0.85392282 0.916928095 1.213743732 0.301905819 0.105828897 1.367120228 1.186665277 0.035262276 0.336663159 19895.83463 -4.298762163 0.296815636 DFLLKPELLR ddPTM_SK-BR-3_Trastuzumab_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 ; 125.72 0.00036625 4415300000 5161100 3798300 3563600 4102100 3900600 3777800 5471200 4521300 4291300 FALSE TRUE 4917145.031 4185351.088 3726994.585 3689749.115 4580863.405 3646973.839 4636467.955 4125391.003 4956772.887 0.992005311 0.844370154 0.751899405 0.744385349 0.924162456 0.735755687 0.935380349 0.832273557 1 22.24096973 -1.490913937 6.440756513 1.000078038 0.851676375 0.237809155 0.086465833 9.46E-05 7.48E-06 0.081724677 0.019252587 0.03229134 1.490913937 -0.148401663 DFLLPFLEEPMDTEADLQFRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFLLPFLEEPMDTEADLQFRPR 22 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 96.848 0.0012787 224806500 198539.1 163991 189805.7 192970.7 206641.6 170741.1 232439.7 197827.3 190797 FALSE TRUE 189154.5502 180701.8693 198508.4791 173572.9186 242679.8296 164828.2929 196976.7547 180504.4929 220384.8243 0.858292084 0.819937897 0.9007357 0.787590158 1.101163977 0.747911266 0.893785474 0.819042298 1 17.74966536 -2.577470496 2.129943639 3.308114693 0.864099856 0.162900825 0.095330151 3429047.24 355849.7305 37905077.02 0.020888189 0.002645632 2.577470496 -2.444014837 DFLLQQTMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFLLQQTMLR 10 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 115.78 0.0056235 0 74209 82268 66628 80623 72820 69861 83344 74583 70185 FALSE TRUE 70701.28764 90651.20273 69682.9597 72518.62287 85519.78494 67441.69605 70628.34208 68052.11713 81068.93134 0.872113231 1.118199059 0.859551971 0.894530391 1.054902088 0.831905576 0.871213434 0.839435231 1 16.30686151 2.218755287 24.98079425 0.872974936 0.965945311 0.131684794 0.091450479 386.8970759 487996.7428 0.032431272 0.02398402 165.4837245 -2.218755287 0.092970375 DFLRPFEHIMK ddPTM_SK-BR-3_Trastuzumab_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 ; 88.338 0.0078431 119207000 633660 562570 563310 710810 531500 651480 814160 715640 550800 FALSE TRUE 603708.1476 619896.5226 589138.3207 639358.0283 624193.4317 628919.0842 689944.9389 652974.7678 636215.2509 0.948905495 0.974350303 0.926004713 1.004939802 0.981104164 0.988531921 1.084452059 1.026342526 1 19.27915543 1.934668683 5.899915413 1.044831758 0.967589715 0.540182601 0.029129408 0.14476861 9.732041492 0.01195795 0.007324843 86.03371634 -1.934668683 -0.077242043 DFLTHVSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFLTHVSAR 9 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 88.681 0.01262 34888000 42111 32238 39703 50536 57179 39127 56634 46610 69869 FALSE TRUE 40120.49649 35523.08885 41523.42182 45456.02527 67150.9995 37772.02218 47993.44315 42528.5813 80703.92768 0.497131895 0.440165552 0.514515501 0.563244275 0.832066065 0.468032019 0.594685346 0.526970403 1 16.30035127 -5 0.203616853 3.07235177 0.476825704 0.6281226 0.107805107 91.88587251 0.911690366 77.71545879 0.240706481 1.00E-05 5 -2.595526066 DFMHVLEHECQHHHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFMHVLEHECQHHHSK 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 203.99 8.11E-12 383800000 218140 217055 219401 303800 249500 229210 329540 184581 7805.2 FALSE TRUE 207828.9545 239173.1513 229460.7529 273261.4468 293012.721 221272.4002 279262.6206 168418.1091 9015.590553 23.05217315 26.52883911 25.4515499 30.30987768 32.50066862 24.54330628 30.97552168 18.68076286 1 13.13820628 0.925075209 3.983402342 1.011843199 27.36750277 0.889604703 2.985706654 0.10360456 4.09869218 2.911022495 0.744686635 8.415408629 -0.925075209 26.35565957 DFMIQGGDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFMIQGGDFTR 11 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 298.77 2.38E-35 616110000 683960 716910 489863 752520 575136 610474 691540 681670 624139 FALSE TRUE 651630.5663 789963.9441 512323.7031 676875.2599 675439.5363 589333.1323 586032.872 621979.361 720927.2885 0.903878348 1.095760913 0.710645458 0.938895324 0.936903828 0.817465425 0.812887626 0.862749089 1 19.45949423 3.752747527 24.98996173 0.860494479 0.999819619 0.256530446 0.092155713 883.2913093 1555895.892 0.021912613 0.039271708 5659.102062 -3.752747527 0.13932514 DFNCWESLGEAYLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFNCWESLGEAYLSR 15 0 Q6PGP7;D6RCE2 Q6PGP7 TTC37 Tetratricopeptide repeat protein 37 0 ; 160.27 4.00E-06 40380000 36058 36770 40926 44618 40771 35159 39124 34685 44980 FALSE TRUE 34353.6098 40516.9048 42802.49758 40132.91387 47881.44949 33941.43501 33154.91524 31647.79752 51955.26867 0.661215131 0.77984208 0.82383363 0.772451282 0.921589874 0.653281869 0.638143466 0.60913548 1 15.66498244 DFNDIRQDFLPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFNDIRQDFLPWK 13 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;O94776;O94776-2 Q9BTC8;O94776 MTA3;MTA2 Metastasis-associated protein MTA3;Metastasis-associated protein MTA2 0 113.07 0.00077615 93954000 256710 202750 240930 219690 227150 242380 309650 297750 235150 FALSE TRUE 244575.8271 223410.4555 251976.8788 197606.3438 266764.8881 233986.3198 262407.2054 271677.4315 271615.861 0.900447515 0.822523599 0.927695746 0.727521372 0.982140318 0.861460443 0.966096768 1.000226682 1 18.0512082 1.721361223 1.135332188 1.008793882 0.858674463 0.419027682 0.066401061 0.411336187 0.99283038 0.049792593 0.019427082 52.64549613 -1.721361223 -0.150119419 DFNGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFNGDFR 7 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 124.83 0.0095567 1001890000 4105570 4544310 4096170 4717890 3726290 4336550 4414670 4522120 3841290 FALSE TRUE 3911507.843 5007380.355 4283983.446 4243638.734 4376153.796 4186374.186 3741131.011 4126139.2 4436977.635 0.881570331 1.128556591 0.965518377 0.956425541 0.986291606 0.943519335 0.843171032 0.929943655 1 22.08114585 2.094801787 3.931722192 0.904172589 0.992019009 0.098960133 0.071956927 0.322550383 9.441956222 0.028355518 0.019799751 124.3946743 -2.094801787 0.08784642 DFNHINVELSLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFNHINVELSLLGK 14 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 183.6 1.39E-06 1107993000 2409060 2282414 1980640 2480332 1810681 2285795 2661544 2531893 1808528 FALSE TRUE 2295188.508 2514994.581 2071454.303 2231004.315 2126463.193 2206637.346 2255476.58 2310187.027 2088985.286 1.098709753 1.20393121 0.991607896 1.067984696 1.017940724 1.056320196 1.079699601 1.105889564 1 20.9943709 3.740941123 24.99996994 1.05107626 1.151320481 0.503686141 0.043354106 153.6160612 1613259.497 0.010686107 0.018193157 5507.330288 -3.740941123 0.100244221 DFNLDGAPYGYTPFCDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFNLDGAPYGYTPFCDSR 18 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 171.81 2.87E-11 109407000 148883 134417 124745 148032 130933 146021 159091 156687 145855 FALSE TRUE 141845.5956 148114.2451 130464.6816 133151.5421 153767.6737 140964.2562 134818.746 142966.6556 168473.4485 0.841946294 0.879154825 0.774393133 0.790341406 0.912711618 0.836714969 0.800237351 0.848600518 1 17.36216171 -2.162592015 1.866576315 1.32926422 0.836299094 0.614195056 0.040965803 1255943.544 252699.625 1746228.107 0.011052475 0.006877142 2.162592015 -0.492965126 DFNVGDYIQAVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFNVGDYIQAVLDR 14 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;;; 175.28 5.60E-06 448679000 182846 156880 164715 176317 156056 153575 189564 170942 175295 FALSE TRUE 174203.2319 172866.2504 172267.3457 158593.2802 183272.117 148256.6592 160642.5302 155973.4123 202478.8533 0.860352719 0.853749651 0.850791788 0.783258486 0.905142014 0.732208114 0.793379297 0.770319516 1 17.62741172 3.392963496 9.642016745 0.815470182 0.856256891 0 0.076458075 0.935109408 98.73926216 0.018891077 0.025586404 2471.516395 -3.392963496 0.040786709 DFPDEVLQLIHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFPDEVLQLIHER 13 0 Q96SZ6-5;Q96SZ6-2;Q96SZ6-6;Q96SZ6-3;Q96SZ6 Q96SZ6-5 CDK5RAP1 CDK5 regulatory subunit-associated protein 1 0 ; 85.554 0.0092319 8980000 31566 28181 33459 29716 41396 26427 37680 31929 33657 FALSE TRUE 30073.93774 31052.67594 34993.12825 26728.89122 48615.44929 25511.82636 31931.22396 29133.12749 38876.35566 0.773579139 0.798754806 0.900113389 0.687535927 1.250514573 0.656229884 0.821353324 0.749379076 1 15.24660536 -2.545065822 2.093704881 3.41070946 0.825880423 0.095510472 0.164346987 5927415.635 264532.0175 68393090.93 0.035432178 0.002850586 2.545065822 -2.584829037 DFPLSGYVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFPLSGYVELR 11 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;; 157.78 7.08E-05 226129000 214745 180856 183912 189949 196767 145723 201536 184401 211064 FALSE TRUE 204594.4294 199285.432 192344.5471 170854.9656 231083.1025 140676.576 170787.9817 168253.8709 243794.7272 0.83920777 0.817431264 0.788961063 0.700814852 0.947859313 0.577028788 0.700540097 0.690145652 1 17.8953074 2.238263256 24.99999999 0.710214901 0.813786713 0.062830538 0.12212212 14.3272754 1204365.307 0.038935491 0.030565236 173.0865237 -2.238263256 0.103571812 DFPWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFPWLR 6 0 Q96DT7-3;Q96DT7-2;Q96DT7 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 0 99.511 0.090068 99658000 205170 185900 226660 202670 397600 173270 252060 198240 363030 FALSE TRUE 195472.0207 204843.4214 237052.5852 182297.2266 466941.3141 167269.6165 213603.6176 180881.0547 419326.8383 0.466156713 0.488505392 0.565316988 0.434737799 1.113549793 0.398900335 0.509396485 0.431360548 1 18.67771564 -2.133427609 2.501788195 1.982207794 0.544640223 0.31962433 0.205693806 40443968.7 9554941.524 225972358.4 0.048020677 0.007354826 2.133427609 -1.437567571 DFPYEEDSRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ;; 153.34 2.97E-05 196852000 223095 194271 208855 233104 200096 198408 225737 211753 212103 FALSE TRUE 212549.7415 214067.4358 218431.2083 209671.9431 234992.679 191537.0812 191296.6747 193210.7847 244994.85 0.867568202 0.873763003 0.891574694 0.855821839 0.959173954 0.781800439 0.780819167 0.788632025 1 17.9023919 2.213701221 24.99959847 0.814050218 0.883978548 0.074073519 0.070116005 348.9426535 350908.4635 0.023199462 0.017141133 163.5690838 -2.213701221 0.06992833 DFQDYMEPEEGCQGS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFQDYMEPEEGCQGSPQR 18 0 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR 215.59 9.89E-19 121718000 177581 198871 157629 216415 175183 199592 187881 186153 192446 TRUE FALSE 169187.0981 219136.181 164856.4456 194660.553 205734.8597 192680.079 159216.3028 169852.4565 222289.5428 0.761111368 0.985814169 0.741629334 0.8757072 0.925526487 0.866797765 0.716256378 0.764104574 1 17.76208056 DFQDYMEPEEGCQGS(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_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 201.16 3.75E-16 1469476000 1590570 1652340 1619470 1778290 1484017 1597610 1893130 1746510 1773300 TRUE FALSE 1515386.908 1820715.325 1693724.301 1599532.911 1742829.095 1542284.365 1604298.249 1593576.326 2048294.307 0.739828697 0.888893416 0.82689499 0.780909709 0.850868495 0.752960334 0.7832362 0.778001638 1 20.96599159 -0.949913448 5.076065663 1.000000922 0.802703396 0.660352325 0.04500067 4.58E-07 9.47E-08 0.042465026 0.010009056 0.112224209 0.949913448 -0.197297526 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DFQEYVEPGEDFPASPQRR 19 1 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEY(0.003)VEPGEDFPAS(0.997)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR 221.21 1.67E-19 5396450000 1872818 1683442 1769826 1964348 1765680 1792574 2059669 1922477 1981190 TRUE FALSE 1784293.605 1854986.654 1850974.273 1766888.007 2073614.033 1730496.713 1745428.666 1754134.722 2288422.827 0.779704513 0.810596115 0.808842776 0.772098577 0.906132385 0.756196229 0.762721227 0.766525618 1 21.12592221 -1.177191774 5.058830739 1.000014126 0.79466169 0.687688154 0.043339691 6.56E-06 1.07E-06 0.039874577 0.009397882 0.066497945 1.177191774 -0.205352436 DFQSGQHVIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFQSGQHVIVR 11 0 I3L0N3;P46459;I3L338;I3L4Q9;I3L0L3 I3L0N3 NSF Vesicle-fusing ATPase 0 111.94 0.00093045 0 350500 276120 259740 299490 289420 258590 354710 285790 291220 FALSE TRUE 333932.5596 304256.9419 271649.3359 269384.6962 339894.7564 249634.9635 300592.4748 260764.7125 336380.9103 0.992721494 0.904501215 0.807564661 0.800832295 1.010446033 0.742119888 0.893607412 0.775206632 1 18.35973631 4.210896381 2.37769565 0.855854982 0.982219646 0.171128938 0.089207732 0.423122089 4.640862027 0.020526975 0.068771208 16251.60959 -4.210896381 0.126364664 DFS(ph)PEALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFSPEALKK 9 1 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 DFS(1)PEALKK;DFS(1)PEALKK;DFS(1)PEALKK 112.43 0.0012029 333480000 516110 548100 510010 612530 275865 567680 590570 657200 281513 TRUE FALSE 491714.5031 603952.0131 533394.463 550957.3207 323975.7687 548021.0993 500467.6999 599652.084 325168.5983 1.512183236 1.85735036 1.640362771 1.694374314 0.996331658 1.685344471 1.539102185 1.844126669 1 18.31082842 DFSAFINLVEFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSAFINLVEFCR 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 164.11 2.01E-06 0 56369 66801 65870 59308 58684 59972 86076 66688 72683 FALSE TRUE 53704.54908 73608.09785 68890.20465 53346.24716 68918.47102 57895.1546 72943.52531 60848.44518 83954.30843 0.639687826 0.876763792 0.82056783 0.635420006 0.820904517 0.689603139 0.868847909 0.724780495 1 16.35731674 -5 0.282274192 2.735307131 0.752009037 0.42436689 0.087765296 224.6038196 2.142556071 228.5093487 0.090870178 1.00E-05 5 -1.983298093 DFSALESQLQDTQELLQEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFSALESQLQDTQELLQEENR 21 0 P35579 P35579 MYH9 Myosin-9 0 ; 163.91 1.67E-11 31528000 17704.9 15136.6 13199.7 17570.9 13177.6 14401 16206 16549.6 17173.4 FALSE TRUE 16868.02446 16679.03675 13804.9193 15804.63975 15475.76927 13902.28976 13733.47706 15100.42929 19836.56316 0.85035015 0.840822909 0.69593302 0.796742844 0.780163839 0.700841655 0.692331476 0.761242215 1 14.27587447 3.839993031 8.172618076 0.755482921 0.846478744 0.063659838 0.089865268 0.488280369 35.47343865 0.020547354 0.037165779 6918.198691 -3.839993031 0.090995822 DFSAPTLEDHFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFSAPTLEDHFNK 13 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ;; 194.24 4.34E-07 485250000 499690 428480 471000 521860 368660 502580 577070 545620 318923 FALSE TRUE 476070.644 472142.5991 492595.8159 469401.6413 432954.1873 485175.5286 489027.3729 497842.6203 368379.95 1.292335926 1.281672901 1.337194969 1.274232328 1.175292486 1.317051942 1.327508115 1.351437884 1 18.49083502 -0.996847887 5.11142784 0.999997809 1.29391495 0.782371729 0.048827275 1.21E-06 2.37E-07 0.046830336 0.011037934 0.100728441 0.996847887 0.293917141 DFSASYFSGEQEVT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 DFSASYFSGEQEVT(0.997)PS(0.003)R 218.79 5.07E-14 53827000 26746 31176 36393 38724 36753 32284 37028 34797 42129 TRUE FALSE 25481.76959 34352.86984 38061.65505 34831.38995 43162.71156 31165.99698 31378.69853 31749.99021 48662.15015 0.523646602 0.705946403 0.782161391 0.71577992 0.886987349 0.640456636 0.644827621 0.65245761 1 15.57051245 -2.510325326 2.128774393 4.802991212 0.688322374 0.503116843 0.095408701 5293651.545 229518.2287 97751256.02 0.02530529 0.003087981 2.510325326 -4.114668838 DFSCADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSCADR 7 0 A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60;A0A0D9SFU1 A0A0D9SFD6 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 0 85.272 0.079675 0 143890 133980 130300 168210 141830 124380 175290 150240 153610 FALSE TRUE 137088.6049 147632.7143 136274.3839 151301.2112 166565.1071 120072.6894 148546.2911 137084.1891 177431.0543 0.772630278 0.832056795 0.768041336 0.852732414 0.938759609 0.676728715 0.837205706 0.772605391 1 17.43689901 -1.485188533 2.821614775 1.00679494 0.807259787 0.443336553 0.068189435 14042307.25 15303166.9 743429.8473 0.015727657 0.032719862 1.485188533 -0.199535153 DFSDITKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFSDITKK 8 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 82.287 0.033132 845410000 2343560 2272380 2337760 2711820 1814580 2837300 2934200 2849180 1979740 FALSE TRUE 2232784.563 2503938.105 2444948.608 2439222.701 2131042.177 2739043.59 2486533.9 2599690.695 2286747.968 0.976401682 1.094977733 1.069181494 1.066677542 0.93190951 1.197789887 1.087366835 1.136850554 1 21.12486594 2.229654615 24.99999908 1.113095244 1.035956335 0.238150627 0.067571973 266.4937588 748067.0807 0.022946733 0.017197533 169.6893611 -2.229654615 -0.07713891 DFSDKINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFSDKINR 8 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 149.94 0.00045346 2033430000 2918530 1788750 2597870 2525840 2391260 2571010 3537750 2922830 3063150 FALSE TRUE 2780576.871 1971025.659 2716984.909 2271937.764 2808294.987 2481975.279 2998001.262 2666891.51 3538167.658 0.785880473 0.557075257 0.767907339 0.642122699 0.793714504 0.701486057 0.8473316 0.753749333 1 21.75457098 0.661786953 0.396316789 1.024791356 0.670532822 0.574599119 0.077056989 1.240947434 0.4295327 0.140024075 0.054352833 4.589728046 -0.661786953 -0.354258534 DFSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFSELR 6 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;; 114.67 0.058367 482470000 1419900 1341160 1195420 1417560 1943510 1151290 1578760 1323280 1914030 FALSE TRUE 1352784.141 1477825.729 1250231.189 1275064.176 2282457.529 1111420.539 1337891.166 1207406.588 2210847.997 0.611884735 0.668442937 0.565498483 0.576730819 1.032390075 0.502712326 0.605148417 0.546128268 1 21.07616841 -1.796335039 2.848804654 1.094950538 0.638818482 0.374389385 0.146811432 25650167.28 22405609.11 16960076.33 0.033453011 0.015983245 1.796335039 -0.456132055 DFSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DFSESR 6 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;; 122.78 0.044374 4370790000 6767060 7052220 5660620 7865310 5580580 6225130 6122430 6484600 5340240 FALSE TRUE 6447194.485 7770849.236 5920165.026 7074674.096 6553831.385 6009552.187 5188340.857 5916774.047 6168377.145 1.045201085 1.25978828 0.959760548 1.146926319 1.06248876 0.974251743 0.841119266 0.959210812 1 22.55645955 2.236561952 2.71043185 0.91460343 1.113885989 0.432340718 0.086028903 0.204712777 3.090057745 0.034380715 0.024598083 172.4098017 -2.236561952 0.199282559 DFSGGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFSGGWR 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ; 116.11 0.012861 516450000 480720 490290 443580 512220 514120 422350 476570 494830 521080 FALSE TRUE 457997.3183 540251.1084 463918.5818 460730.6724 603782.3652 407723.9136 403860.4937 451500.0619 601886.4251 0.760936448 0.897596433 0.77077429 0.76547776 1.003149996 0.67741005 0.670991198 0.750141627 1 19.19913175 DFSHDDTLDVPTQVELLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSHDDTLDVPTQVELLIK 19 0 P42345;B1AKP8 P42345 MTOR Serine/threonine-protein kinase mTOR 0 63.691 0.032004 0 22262 17586 19542 25267 18389 20889 24249 25125 23786 FALSE TRUE 21209.71938 19378.03339 20438.02003 22727.11316 21596.03578 20165.60869 20549.36969 22924.9218 27474.6114 0.771975227 0.705306915 0.743887502 0.827204171 0.786036078 0.733972481 0.747940322 0.83440386 1 14.74581146 0.895303143 2.886573038 0.999799532 0.756015696 0.844499562 0.032681912 0.160288366 2.863703149 0.03277059 0.008636627 7.857839309 -0.895303143 -0.243783835 DFSHPCTWQVLDGAEDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSHPCTWQVLDGAEDTLR 19 0 Q9BSH5 Q9BSH5 HDHD3 Haloacid dehalogenase-like hydrolase domain-containing protein 3 0 149.53 8.47E-08 81424000 149740 113400 96821 123790 109420 88165 119960 113340 103980 FALSE TRUE 142662.087 124955.5889 101260.3386 111346.394 128502.8134 85111.82394 101657.8988 103415.3487 120104.6873 1.187814482 1.040388945 0.843100639 0.927077839 1.069923383 0.70864698 0.846410752 0.861043403 1 16.87393293 4.24651376 0.97563794 0.872747911 1.248818096 0.467893127 0.100247621 0.761216928 0.957053204 0.032292817 0.255364 17640.61657 -4.24651376 0.376070185 DFSNSPLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 166.19 6.09E-05 730240000 718820 547015 551572 662950 848640 584577 882950 703240 834960 FALSE TRUE 684842.8032 602756.4504 576862.1218 596309.0065 996642.5473 564332.9519 748239.761 641660.5775 964441.3324 0.710092755 0.624979903 0.598130858 0.618294744 1.033388464 0.585139741 0.77582714 0.665318414 1 19.87933396 DFSSMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFSSMKK 7 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 73.26 0.07917 973880000 1130900 881590 1028800 1081800 750440 1220800 1460900 1281300 948590 FALSE TRUE 1077444.598 971425.0233 1075971.498 973055.4087 881316.4984 1178523.39 1238012.874 1169102.579 1095692.492 0.983345789 0.886585452 0.982001342 0.888073447 0.80434657 1.075596847 1.129890806 1.066998804 1 20.06341153 2.151235283 9.239195083 1.085262568 0.915113959 0.628104809 0.060171401 0.17708616 17.0725106 0.021608078 0.015956898 141.6561008 -2.151235283 -0.170148609 DFSSVFQFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFSSVFQFLR 10 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 ; 201.07 5.78E-07 366370000 587700 398940 236870 234083 551490 256700 529670 361490 496860 FALSE TRUE 559920.5857 439592.4396 247730.7238 210552.5321 647669.6814 247810.4146 448859.1134 329836.0192 573910.5112 0.975623507 0.765959903 0.431653923 0.366873455 1.128520333 0.431792779 0.782106452 0.574716812 1 19.13046627 -0.469143192 6.839468749 0.999999996 0.698635316 0.139410371 0.245159664 30292349.67 4429048.472 0.224025541 0.054334174 0.339513313 0.469143192 -0.30136468 DFSWSPGGNIIAFWVPEDKDIPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFSWSPGGNIIAFWVPEDKDIPAR 24 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 202.73 1.16E-24 466360000 718700 634730 651080 806690 555280 757790 817680 811090 560330 FALSE TRUE 684728.4753 699409.7086 680932.662 725599.9886 652120.6562 731547.5423 692927.8983 740066.6597 647223.1146 1.057948117 1.080631536 1.052083349 1.121097149 1.007567007 1.13028649 1.070616736 1.143449056 1 19.30390361 DFT(ph)PVCTTELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 1 DFT(0.994)PVCT(0.003)T(0.003)ELGR 90.861 0.012106 0 98136 79814 75571 78877 68469 82890 90862 79530 92472 TRUE FALSE 93497.30577 87947.13734 79036.0051 70948.1341 80409.97192 80019.49852 76999.3331 72565.93158 106812.0855 0.875343884 0.823381895 0.739953768 0.664233207 0.75281717 0.749161466 0.720885963 0.67937941 1 16.70471537 3.889688464 2.937660459 0.740761676 0.859792871 0.132407809 0.092969824 0.350946928 5.842286238 0.021530422 0.044547417 7756.904854 -3.889688464 0.119031195 DFTNEAPPAPLPDAS(ph)ASPLSPHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR;DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR 82.477 0.006846 533416000 317249 304952 289204 341287 309840 302842 335167 332150 254555 TRUE FALSE 302253.2685 336026.9555 302464.2895 306980.1824 363875.9979 292354.5056 284031.1184 303065.1852 294030.0893 1.027967135 1.142831866 1.02868482 1.044043428 1.237546806 0.994301319 0.965993375 1.030728474 1 18.16560427 2.06096404 24.99999998 0.991378778 1.093009684 0.369516219 0.06360144 68.67038541 28159.65215 0.022313265 0.016479437 115.0705106 -2.06096404 0.101630906 DFTNEAPPAPLPDASASPLS(ph)PHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.009)AS(0.023)PLS(0.969)PHR;DFTNEAPPAPLPDAS(0.001)AS(0.039)PLS(0.961)PHR;DFTNEAPPAPLPDASAS(0.024)PLS(0.976)PHR;DFTNEAPPAPLPDASAS(0.008)PLS(0.992)PHR 188.8 1.30E-17 451691000 873940 871520 800550 1018180 766550 820390 894160 842140 669050 TRUE FALSE 832630.5882 960328.8788 837256.0094 915830.612 900236.0773 791979.6886 757739.4696 768397.7571 772802.857 1.07741655 1.242656999 1.083401804 1.185076639 1.16489745 1.024814649 0.980508111 0.99429984 1 19.5597409 2.164905766 4.260054684 0.992639023 1.155356458 0.715558155 0.047467205 0.10586747 3.696395653 0.017359064 0.012654366 146.1859943 -2.164905766 0.162717435 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASASPLS(1)PHRR;DFTNEAPPAPLPDASASPLS(1)PHRR;DFTNEAPPAPLPDASAS(0.001)PLS(0.999)PHRR 256.87 4.29E-44 1030010000 377844 345472 336894 400320 350196 330839 391363 384693 289655 TRUE FALSE 359984.0629 380675.9896 352340.9231 360079.073 411270.0715 319381.9625 331653.3865 351007.2415 334573.218 1.075950027 1.137795762 1.053105581 1.076234001 1.229237875 0.954595124 0.991272967 1.049119363 1 18.35196244 2.209161346 24.9999454 0.995745861 1.109618136 0.540916027 0.052836068 156.3516507 132954.1751 0.018560557 0.013709992 161.8681288 -2.209161346 0.113872275 DFTPAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFTPAELR 8 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ;; 117.93 0.0046146 291059000 506490 409130 383060 572260 706830 461094 634100 474140 621990 FALSE TRUE 482549.2215 450820.8121 400623.6799 514735.3376 830100.9282 445126.1992 537356.399 432621.788 718445.0325 0.671657816 0.627495204 0.55762607 0.716457508 1.155413275 0.619568901 0.747943649 0.602164074 1 19.45451826 3.00024289 24.99991709 0.80231764 0.629388849 0.238989169 0.165700558 13.76642784 1416628.99 0.045861959 0.054320642 1000.559431 -3.00024289 -0.172928791 DFTPVCTTELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 140.49 0.00013892 2716520000 699243 539983 578771 644919 596720 621404 718110 660008 670927 FALSE TRUE 666191.1692 595007.8816 605308.2228 580090.5169 700787.7791 599884.6237 608549.1305 602214.2006 774970.9325 0.85963375 0.767780902 0.781072163 0.748531967 0.904276212 0.774073708 0.785254137 0.777079727 1 19.56378267 -1.159751725 4.827690118 1.000017626 0.799273449 0.641909934 0.047011631 8.27E-06 1.44E-06 0.042193292 0.009944182 0.069222659 1.159751725 -0.200744177 DFTSEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 86.086 0.047307 408290000 753360 717990 676870 796290 764530 751900 769180 728390 766440 FALSE TRUE 717750.1658 791153.9973 707905.159 716245.4163 897863.7899 725861.5145 651827.464 664608.3102 885295.6008 0.810746337 0.893660825 0.79962575 0.809046623 1.014196602 0.819908643 0.736282281 0.750719093 1 19.75579973 -0.837912553 5.611133363 1.000000051 0.83051309 0.320549247 0.078096672 5.08E-08 1.04E-08 0.076537987 0.018040171 0.145240404 0.837912553 -0.169486961 DFTVSALHGDMDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DFTVSALHGDMDQK 14 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;; 182.02 1.57E-06 1435550000 2118790 1905040 1774770 2284420 1344050 2033180 2153700 2269360 1333140 FALSE TRUE 2018638.996 2099165.742 1856144.96 2054785.761 1578451.894 1962770.467 1825113.51 2070642.808 1539876.542 1.310909635 1.363203922 1.205385567 1.334383442 1.025050938 1.274628461 1.185233659 1.344681051 1 20.55438326 -5 0.087613124 0.237565778 1.466533464 0.372267601 0.101519994 214.7379608 1.31342226 31.58286766 2.373914395 1.00E-05 5 1.228967686 DFTVSALHGDMDQKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFTVSALHGDMDQKER 16 1 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 118.55 0.00015843 257770000 256394 123737 288606 185304 270154 223455 413720 282645 333944 FALSE TRUE 244274.7637 136345.941 301838.8706 166676.8899 317268.7721 215716.6973 350599.4155 257895.1054 385730.33 0.633278601 0.353474773 0.78251267 0.432107296 0.822514455 0.559242249 0.90892364 0.668589129 1 18.55723306 1.665427007 0.36609285 1.007460755 0.479931444 0.409982803 0.155829807 0.962199239 0.390611572 0.183643117 0.163291987 46.2835867 -1.665427007 -0.527529311 DFTVSAMHGDMDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 DFTVSAMHGDMDQK 14 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;;;;;;;;;;;; 261.67 1.61E-24 9549240000 12660816 12067575 11401845 14025929 8571477 13279420 14031113 14941230 8564027 FALSE TRUE 12062364.32 13297274.61 11924630.87 12616015.97 10066339.87 12819550.36 11890409.01 13632896.69 9892092.568 1.219394606 1.344232731 1.205471015 1.275363719 1.017614808 1.295939182 1.202011499 1.378161051 1 23.23784431 -1.207372052 3.994157308 0.999834422 1.242595564 0.375402145 0.09821028 0.000132614 2.63E-05 0.087085851 0.020512381 0.062033737 1.207372052 0.242761142 DFTVSAMHGDMDQKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DFTVSAMHGDMDQKER 16 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;; 208.39 9.00E-12 386880000 443640 143770 465750 296784 467160 399860 775360 514970 648540 FALSE TRUE 422670.0164 158420.3265 487105.0982 266950.7085 548632.5561 386012.7479 657064.5915 469876.4968 749112.2709 0.564227864 0.211477415 0.650243117 0.356356075 0.732376945 0.515293585 0.87712432 0.627244427 1 19.51482243 1.783031582 0.45545497 0.983286674 0.380337353 0.519894423 0.159073003 0.636490338 0.327870964 0.1512757 0.116003777 60.67804531 -1.783031582 -0.60294932 DFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFVAEPMGEKPVGSLAGIGEVLGK 24 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ; 192.47 6.42E-18 201301000 646970 528020 488590 681990 408880 603700 711350 718870 464800 FALSE TRUE 616389.0103 581825.8383 510992.3348 613435.0695 480188.5425 582793.7176 602820.4927 655921.9318 536878.8101 1.14809711 1.083719132 0.951783392 1.142595047 0.894407701 1.085521922 1.122824148 1.221731831 1 19.03423694 1.833187611 4.398712177 1.127829958 1.054711481 0.092956426 0.093784109 0.500626606 15.34331134 0.043046846 0.023970736 68.10635086 -1.833187611 -0.073118477 DFVDDDDDDDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 ; 339.22 1.94E-62 936410000 1145720 1171850 1121110 1331060 996740 1218580 1234610 1201870 1001480 FALSE TRUE 1091564.086 1291262.847 1172514.002 1197259.32 1170571.14 1176380.269 1046247.569 1096627.891 1156784.404 0.943619297 1.116251951 1.013597693 1.034989162 1.011918156 1.016939946 0.90444474 0.947996781 1 20.14168858 1.856109954 6.448918444 0.942705019 1.028011185 0.333686725 0.047405921 0.228464377 11.05792028 0.019884725 0.012075924 71.7976044 -1.856109954 0.085306167 DFVDHIDLVDPVDGVVLVDPEYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DFVDHIDLVDPVDGVVLVDPEYLK 24 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;;; 175.86 1.12E-12 364143000 694376 639195 601035 721980 439577 672728 668148 725612 356231 FALSE TRUE 661554.2226 704329.6972 628593.0493 649405.1987 516239.0896 649431.2607 566209.7512 662073.5666 411473.4841 1.607768783 1.711725602 1.527663564 1.578243128 1.254610831 1.578306466 1.376054043 1.609030939 1 18.65043994 -3.10785875 0.145253358 4.10E-15 1.750529282 0.638451973 0.126701191 41.38151391 0.613307738 13.76684237 0.715868566 0.000780084 3.10785875 1.750529282 DFVDHLDKVDPVDGVVLVDPDYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFVDHLDKVDPVDGVVLVDPDYLK 24 1 P32121;P32121-3;P32121-4;I3L412;K7ENA6 P32121 ARRB2 Beta-arrestin-2 0 99.366 0.0029266 11476000 34145 39500 34132 40344 19316 38942 33822 43669 14234 FALSE TRUE 32531.03352 43525.09491 35696.98596 36288.54447 22684.70428 37593.42878 28661.83272 39845.11086 16441.33602 1.978612533 2.647296719 2.171173067 2.207153021 1.379736066 2.286519096 1.743278811 2.423471596 1 14.00503992 2.972912357 23.36205642 1.843693968 2.291793209 0.223723194 0.435687189 472.2978878 407338.927 0.117866349 0.125431165 939.533688 -2.972912357 0.448099241 DFVNYLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DFVNYLVR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 102.41 0.011565 438980000 566790 404160 277020 295970 598740 313050 582420 419660 504610 FALSE TRUE 539998.96 445344.3635 289721.641 266218.5333 703160.0664 302209 493561.1321 382912.3456 582862.3416 0.92646054 0.764064397 0.497067009 0.45674341 1.206391314 0.518491209 0.846788507 0.656951596 1 19.15279567 DFYELEPEKFQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFYELEPEKFQNK 13 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 204.13 7.32E-08 290540000 595930 531210 504590 602760 368340 553730 560130 652350 419760 FALSE TRUE 567761.5699 585340.9029 527725.9506 542169.4196 432578.3794 534554.1913 474671.881 595226.7757 484854.237 1.170994346 1.20725129 1.08842186 1.118211162 0.892182323 1.10250494 0.97899914 1.22764066 1 18.88719157 3.448856292 1.959311239 1.040717637 1.189068248 0.271774313 0.089816147 0.349707169 2.704633234 0.024639562 0.039876602 2810.970529 -3.448856292 0.148350612 DFYFGK ddPTM_SK-BR-3_Trastuzumab_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 ; 103.71 0.080148 734790000 1909070 1621220 1610830 1777070 1437010 1567260 1999900 1680130 1633500 FALSE TRUE 1818832.045 1786424.161 1684688.149 1598435.547 1687624.089 1512985.393 1694778.524 1533008.91 1886814.837 0.963969547 0.946793573 0.892874126 0.84716079 0.894430156 0.801872745 0.898221962 0.812485083 1 20.84752142 3.685762121 2.690306055 0.86831694 0.958370769 0.254936322 0.05477996 0.278815209 3.97520241 0.013129191 0.023467055 4850.227631 -3.685762121 0.090053829 DFYFSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DFYFSVK 7 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 ; 98.299 0.026439 168316000 536620 506410 464210 527530 410420 514680 613290 553460 449250 FALSE TRUE 511255.0361 558013.7547 485494.4877 474501.6822 481997.1181 496856.5025 519721.3467 504996.1083 518917.3955 0.985233951 1.075342163 0.935591082 0.914406968 0.92885134 0.957486696 1.001549285 0.973172441 1 18.98514537 3.727401401 24.96103817 0.958328268 1.030288059 0.415620637 0.035277227 626.9638676 1402400.544 0.009759907 0.015279897 5338.280633 -3.727401401 0.071959791 DFYLATS(ph)PPDSFLDDHHLTRPHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.009)S(0.991)PPDSFLDDHHLTRPHPER;DFYLAT(0.003)S(0.997)PPDSFLDDHHLTRPHPER;DFYLAT(0.003)S(0.997)PPDSFLDDHHLTRPHPER;DFYLAT(0.004)S(0.996)PPDSFLDDHHLTRPHPER;DFYLAT(0.013)S(0.987)PPDSFLDDHHLTRPHPER 179.81 1.34E-17 1055029000 449706 416854 476717 527739 541854 468065 596425 504255 99747.9 TRUE FALSE 428449.2886 459331.8965 498574.946 474689.6731 636353.166 451855.7917 505429.4122 460099.759 115216.2949 3.718651854 3.986692134 4.327295427 4.119987312 5.523117773 3.921804569 4.386787586 3.993356664 1 16.81398524 0.751442773 4.337880578 1.000006859 4.241836434 0.816030977 0.486112921 2.0203629 34.94651505 0.459992904 0.1169842 5.642125901 -0.751442773 3.241829575 DGADFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 142.64 0.0057599 8238060000 15436950 12963840 12650650 15553400 10476260 14687040 16468340 15465130 12109260 FALSE TRUE 14707275.97 14284870.03 13230694.82 13989942.68 12303316.43 14178424.12 13955792.27 14110921.23 13987102.2 1.051488418 1.021288744 0.94592108 1.000203079 0.879618684 1.013678453 0.997761515 1.008852372 1 23.73759376 3.944296524 5.031040065 0.978208803 1.040984273 0.280480485 0.040045182 0.231768113 12.62789022 0.00993536 0.018885688 8796.228945 -3.944296524 0.06277547 DGAGFLINLIDSPGHVDFSSEVTAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGAGFLINLIDSPGHVDFSSEVTAALR 27 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 303.02 4.79E-71 2605588000 1154744 1083375 1128453 1223264 1139390 1083278 1246956 1274228 979924 FALSE TRUE 1100161.54 1193772.144 1180193.686 1100299.179 1338099.255 1045763.811 1056709.96 1162649.841 1131885.609 0.971972371 1.054675609 1.042679293 0.972093973 1.182185942 0.923912984 0.933583705 1.02717963 1 20.11029673 DGAHVVISSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 DGAHVVISSR 10 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;;;;;;;;; 190.57 8.87E-07 67441343100 13362775 10610876 11155169 11225768 12126165 9720607.5 12477379 11324851 11431943 FALSE TRUE 12731143.11 11692136.33 11666644.53 10097332.47 14240964.34 9383980.425 10573725.67 10333187.01 13204750.33 0.964133572 0.885449254 0.883518752 0.764674244 1.07847282 0.710651863 0.800751654 0.782535584 1 23.65455369 2.204324875 24.99999931 0.802787415 0.907343804 0.140941294 0.106305653 288.0820579 210364.8166 0.03558839 0.026285109 160.0755028 -2.204324875 0.104556389 DGASS(ph)SPESASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.028)S(0.658)S(0.314)PESASR 122.46 0.00037566 81215000 209940 209710 220430 232910 277200 194600 224390 211460 293910 TRUE FALSE 200016.5523 231079.6874 230536.9335 209497.4443 325543.5922 187860.9532 190155.1843 192943.4414 339488.0617 0.589171093 0.680671026 0.679072284 0.617098119 0.958925008 0.553365418 0.560123332 0.568336455 1 18.37300132 -1.662568164 2.664423384 1.044388504 0.647947091 0.461924267 0.118391882 28847406.23 24572319.42 8708075.565 0.029802814 0.021748627 1.662568164 -0.396441413 DGASSS(ph)PESASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.023)S(0.977)PESASR 178.22 2.34E-05 94039000 192610 150780 177620 195400 224460 166090 219330 186270 212470 TRUE FALSE 183505.707 166144.6534 185764.0527 175758.0208 263605.7529 160338.2617 185867.1802 169959.2113 245418.7625 0.747724849 0.676984318 0.756926858 0.716155599 1.07410595 0.653325198 0.757347068 0.692527375 1 17.90488602 -2.238798161 2.332927888 1.8846175 0.754784395 0.293041198 0.117256697 10490134.71 1853329.615 48976472.98 0.026408316 0.005770346 2.238798161 -1.129833106 DGAWGAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 217.5 1.72E-05 25431700000 14352100 10398860 5317601 5989941 15159220 6592030 15492620 9844780 13350510 FALSE TRUE 13673704.68 11458515.66 5561418.266 5387820.751 17802983.17 6363746.348 13128936.28 8982718.873 15420838.91 0.886703036 0.743053976 0.360643043 0.34938571 1.15447566 0.412671865 0.851376268 0.582505201 1 23.87837792 -1.452082297 11.28008413 1.000000208 0.684360143 0.138990416 0.257008469 1.25E-06 6.05E-08 0.230317355 0.054286286 0.035311625 1.452082297 -0.315640065 DGDILGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGDILGK 7 0 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;;;; 117.93 0.01191 1941020000 7103000 5649420 5928280 5813580 4281880 5781020 6587730 6462320 4290670 FALSE TRUE 6767255.267 6225102.321 6200097.502 5229187.893 5028638.516 5580821.828 5582650.797 5896445.002 4956045.19 1.365454714 1.256062462 1.251017145 1.055113037 1.01464743 1.126063547 1.126432585 1.18974803 1 22.24075791 3.379272932 3.689816886 1.093628934 1.304630857 0.712139708 0.062023398 0.122918868 3.224442604 0.017725032 0.024762884 2394.820305 -3.379272932 0.211001923 DGDKPEETQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DGDKPEETQGK 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;; 166.04 1.91E-05 2595019000 4595500 4669350 4066530 5722350 2043360 5305110 4708770 5765200 2107190 FALSE TRUE 4378279.822 5145162.074 4252984.423 5147128.506 2399721.337 5121392.71 3990360.654 5260368.525 2433962.263 1.798828145 2.113903799 1.74735019 2.114711713 0.985932023 2.104138091 1.639450502 2.161236682 1 21.21487537 DGDKS(ph)PMSSLQISNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGDKSPMSSLQISNEK 16 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 DGDKS(0.973)PMS(0.014)S(0.014)LQISNEK;DGDKS(0.965)PMS(0.035)SLQISNEK;DGDKS(0.999)PMS(0.001)SLQISNEK;DGDKS(0.995)PMS(0.003)S(0.003)LQISNEK 260.56 5.20E-27 1347010000 1738450 1900410 1427590 2033100 682526 1897440 1602880 2005840 686640 TRUE FALSE 1656276.914 2094063.94 1493046.414 1828728.925 801558.3183 1831731.177 1358331.217 1830198.016 793120.6243 2.088303926 2.640284309 1.882496014 2.30573871 1.010638601 2.309524076 1.712641401 2.307591002 1 19.59718077 3.252222557 1.9478649 1.77541685 2.335929691 0.191608237 0.493878617 0.48861098 3.813714156 0.139781428 0.195591109 1787.403307 -3.252222557 0.560512841 DGDSYDPYDFS(ph)DTEEEMPQVHT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.004)DFS(0.978)DT(0.023)EEEMPQVHT(0.995)PK 239.31 2.98E-37 1997760000 2153410 2090090 2021820 2348290 1319840 2412640 2508940 2214560 1076130 TRUE FALSE 2051622.577 2303072.547 2114522.447 2112235.428 1550019.678 2329089.672 2126155.123 2020641.386 1243010.744 1.650526825 1.852817892 1.701129662 1.699289759 1.246988158 1.873748624 1.71048813 1.62560251 1 20.24540734 0.756506703 4.035855795 1.000007711 1.689536958 0.607356624 0.169533392 2.317087352 37.82399494 0.155181054 0.039624432 5.708298865 -0.756506703 0.689529247 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.993)DT(0.007)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.996)DT(0.004)EEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK 292.47 4.86E-62 5162400000 5835890 5548230 5488020 6467980 3883720 6384340 6744460 6663840 3449110 TRUE FALSE 5560039.045 6113600.945 5739651.145 5817806.362 4561039.538 6163248.705 5715468.756 6080318.842 3983980.363 1.395599009 1.534545953 1.440682589 1.460299959 1.144844884 1.547007802 1.434612683 1.526191971 1 21.92577911 -1.840104085 2.777442436 0.842157886 1.438862814 0.589585076 0.114152048 137381348.7 94124477.05 144148819.1 0.025533257 0.014450934 1.840104085 0.596704928 DGDSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGDSYR 6 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 114.59 0.058529 256250000 673130 602310 571710 700160 516090 548190 652110 677620 601220 FALSE TRUE 641312.4789 663686.0738 597923.469 629778.5866 606095.9326 529206.0428 552618.6427 618284.0005 694454.127 0.923477094 0.955694621 0.860997791 0.90686852 0.872765974 0.762046077 0.79575975 0.890316547 1 19.40551987 3.239269595 1.251713038 0.840209236 0.937550417 0.06469776 0.067633236 0.591717859 1.957459209 0.023759647 0.036182535 1734.880617 -3.239269595 0.097341181 DGDVIKTEGATLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGDVIKTEGATLR 13 1 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 150.12 4.02E-05 560590000 837020 480710 691460 644200 591690 764190 1050820 901780 774530 FALSE TRUE 797455.7234 529694.8955 723164.1249 579443.7921 694880.5487 737725.9087 890498.1094 822815.3626 894640.1566 0.891370365 0.592075922 0.808329606 0.647683639 0.776715133 0.824606299 0.995370153 0.919716555 1 19.77094799 1.979458187 2.2793135 0.972214336 0.733027873 0.601781967 0.084460991 0.194203551 1.871687961 0.043636613 0.023139839 95.38019082 -1.979458187 -0.239186463 DGEEAGAYDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DGEEAGAYDGPR 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 218.94 7.70E-11 4143820000 4000830 3768690 3364720 4232250 2724100 3812290 3817030 3975100 2758720 FALSE TRUE 3811718.695 4152723.796 3518995.74 3806816.189 3199182.178 3680269.441 3234671.969 3627019.171 3186528.208 1.196198008 1.303212627 1.104335349 1.194659498 1.003971083 1.15494645 1.015108531 1.138235388 1 21.603554 3.278286417 1.320048354 1.067819775 1.246615963 0.472546809 0.070789792 0.30115665 1.099950333 0.022301641 0.034813614 1897.957212 -3.278286417 0.178796188 DGEIVGLSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGEIVGLSGR 10 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 110.53 0.0043582 32321000 101760 70710 71000 92485 80019 81579 90888 95845 96645 FALSE TRUE 96950.00647 77915.42939 74255.42023 83188.23209 93974.28827 78753.89877 77021.36633 87452.30369 111632.213 0.868476973 0.697965464 0.665179147 0.745199167 0.841820526 0.705476463 0.689956458 0.783396668 1 16.76839387 0.966517146 22.05791017 1.000000002 0.743875704 0.601196433 0.064810066 702.008195 462471.9352 0.062979544 0.015747254 9.25799936 -0.966517146 -0.256124298 DGEKEESKKEETPGT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGEKEESKKEETPGTPK 17 3 Q99442 Q99442 SEC62 Translocation protein SEC62 1 DGEKEES(0.001)KKEET(0.023)PGT(0.976)PK 76.186 0.010826 98797000 301520 204300 262880 387720 114720 411050 352280 372770 77809 TRUE FALSE 287267.7472 225118.4023 274933.308 348745.649 134727.1317 396815.2354 298533.2159 340128.2826 89875.22233 3.19629526 2.504788266 3.059055665 3.880331419 1.499046436 4.415179458 3.321640917 3.784449972 1 16.45563581 3.48935588 24.46409274 3.169468685 2.839105087 0 1.064306605 2272.864445 4544765.339 0.257019625 0.376205773 3085.715487 -3.48935588 -0.330363598 DGELLFVHSAEGSEFWSALLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGELLFVHSAEGSEFWSALLEK 22 0 P17655;P17655-2;C9JWY7 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 330.38 9.77E-81 929937000 1305998 1419332 1231670 1599716 762707 1371173 1313136 1519749 631316 FALSE TRUE 1244266.063 1563963.544 1288143.288 1438909.508 895722.8593 1323688.935 1112792.986 1386671.721 729217.261 1.706303635 2.144715475 1.76647394 1.973224696 1.228334692 1.815218874 1.52601021 1.901589273 1 19.47598919 2.770972165 24.99353356 1.552850647 1.910298984 0.322229264 0.283498216 780.1240344 601576.1606 0.076720216 0.081368779 590.163254 -2.770972165 0.357448337 DGELPVEDDIDLSDVELDDLGKDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DGELPVEDDIDLSDVELDDLGKDEL 25 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;;; 201.15 5.76E-25 226863200 400938.1 375992.7 325384 432867 193251.9 385630.8 354351.1 420535 174840.3 FALSE TRUE 381986.5506 414306.7836 340303.1782 389354.3868 226954.9702 372276.3087 300288.3316 383710.726 201953.6408 1.891456619 2.051494502 1.685055922 1.927939429 1.123797369 1.84337508 1.486917148 1.8999941 1 17.62366463 -1.300376663 0.105171113 3.60E-12 2.382758175 0.447256629 0.262674671 47.12741933 0.891388253 18.00237088 4.757103355 0.050075274 1.300376663 2.382758175 DGETPDPEDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGETPDPEDPSR 12 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 78.655 0.058493 109970000 195840 170610 160710 192110 144520 196050 192500 224220 165930 FALSE TRUE 186583.0313 187995.353 168078.7125 172798.7378 169724.2422 189260.7393 163130.5895 204586.1081 191661.5769 0.973502537 0.980871367 0.8769557 0.901582574 0.885541301 0.987473558 0.851138721 1.067434127 1 17.54820162 1.223731675 24.99898873 1.033717102 0.927587945 0.468299202 0.049057306 259.1689202 436900.9932 0.046650209 0.011858055 16.73908347 -1.223731675 -0.106129157 DGFIDKEDLHDMLASLGK ddPTM_SK-BR-3_Trastuzumab_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 ;; 223.5 3.07E-19 1362563000 6392470 7975600 5174940 8341820 3300960 7015610 5804470 7021270 2479880 FALSE TRUE 6090310.612 8788322.708 5412216.118 7503284.405 3876646.379 6772657.667 4918891.495 6406450.377 2864447.125 2.126173166 3.068069447 1.889445286 2.619452927 1.35336636 2.364385646 1.717221956 2.236539932 1 21.44982528 -0.391053125 0.152043759 1.17E-12 2.923473033 0.413258503 0.458448628 16.28233333 0.695316907 10.500824 2.997627426 0.406393614 0.391053125 2.923473033 DGFNPADVEAGLYGSHLYVWDWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DGFNPADVEAGLYGSHLYVWDWQR 24 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;;; 325.46 1.18E-74 2393579000 2617308 2742401 2375918 2708288 2166627 2399173 2471449 2608880 1884645 FALSE TRUE 2493593.038 3021854.78 2484856.19 2436045.745 2544486.063 2316089.037 2094384.064 2380432.637 2176906.121 1.145475688 1.388141983 1.141462264 1.11904033 1.168854292 1.063936113 0.962092046 1.093493474 1 21.05384776 2.73309986 0.882788058 1.009519658 1.258320967 0.526375844 0.078994462 0.394779145 0.656548273 0.047577849 0.044011057 540.8786757 -2.73309986 0.248801309 DGFQHPAR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 99.442 0.0068105 635468000 657970 558101 551847 612206 644435 572472 695150 645421 611855 FALSE TRUE 626869.0621 614972.1264 577149.7308 550665.8898 756824.26 552647.1511 589092.1002 588904.5156 706738.3485 0.886988888 0.87015531 0.81663848 0.779165148 1.070869101 0.781968535 0.833536345 0.833270923 1 19.43081667 4.226920456 3.778636306 0.862450838 0.883692083 0 0.094043885 1.814024863 56.18561863 0.02185835 0.058288377 16862.44148 -4.226920456 0.021241244 DGGAAS(ph)PATEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGGAASPATEGR 12 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 DGGAAS(1)PATEGR 89.747 0.0051989 0 80285 96279 96774 95986 163440 66029 81845 72181 154640 TRUE FALSE 76490.08716 106089.9396 101211.1836 86337.30492 191943.8843 63742.39917 69358.04206 65860.44898 178620.7814 0.428226137 0.593939511 0.566626027 0.48335532 1.074588761 0.356858808 0.388297719 0.36871661 1 17.44654041 4.598461475 2.715709822 0.570809796 0.420336012 0.031563844 0.250844895 1.499598505 17.98650202 0.05896309 0.437638363 39669.93373 -4.598461475 -0.150473784 DGGFCEVCKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 129.89 0.00046686 1187090000 2207050 1543620 1961960 2255780 1512680 2348480 2741940 2664350 1848110 FALSE TRUE 2102727.12 1700916.633 2051917.807 2029024.709 1776490.913 2267151.549 2323606.694 2431045.389 2134705.46 0.985019788 0.796792187 0.961218231 0.950493989 0.832194861 1.062044198 1.088490538 1.138820055 1 21.02560559 2.15740033 6.829645387 1.082227362 0.902513253 0.614164681 0.065731338 0.132213062 9.159644742 0.023327005 0.017212698 143.681327 -2.15740033 -0.179714109 DGGNPFAEPSELDNPFQDPAVIQHRPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGGNPFAEPSELDNPFQDPAVIQHRPSR 28 1 O14828 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R 183.93 6.90E-18 210876000 138613 122245 133232 162584 135012 146232 172529 161544 142363 TRUE FALSE 132061.0382 134701.9045 139340.819 146240.7474 158558.0501 141167.9492 146206.5323 147398.351 164439.927 0.803095943 0.819155706 0.847366096 0.889326273 0.964230847 0.858477328 0.889118203 0.896365948 1 17.32720111 8 0.077069368 1.099426206 0.299428879 0.688478627 0.03371015 119.7296801 0.675149523 1.102536038 10.24480419 99999999.99 -8 -0.799997327 DGGQTES(ph)NEEGKENR ddPTM_SK-BR-3_Trastuzumab_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(0.016)ES(0.984)NEEGKENR;DGGQT(0.024)ES(0.976)NEEGKENR;DGGQT(0.002)ES(0.998)NEEGKENR;DGGQTES(1)NEEGKENR 212.83 4.10E-10 786010000 532205 549578 492040 595849 272506 592540 553638 591791 314885 TRUE FALSE 507048.7244 605580.623 514600.5207 535953.1265 320030.9601 572020.1912 469170.3548 539970.6428 363715.7576 1.394079618 1.664983192 1.414842525 1.473549373 0.87989303 1.57271215 1.28993684 1.484595131 1 18.4724519 -4.088782503 0.107681554 4.10E-15 1.660512596 0.254709306 0.210559218 174.3106091 1.539256797 41.97875737 2.788696569 8.15E-05 4.088782503 1.660512596 DGGQTESNEEGKENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 242.19 5.91E-18 3071540000 1563332 1443622 1516080 1702103 994854 1684647 1730282 1731434 1030377 FALSE TRUE 1489436.395 1590728.723 1585593.768 1531004.373 1168356.223 1626307.252 1466295.702 1579820.46 1190162.603 1.251456222 1.336564197 1.332249698 1.286382524 0.981677814 1.366458035 1.232012919 1.327398841 1 20.18272726 -1.330066697 3.26191211 0.99826663 1.266256533 0.369544936 0.108453147 34914044.62 52579109.03 596556.7401 0.02439476 0.046766331 1.330066697 0.267989903 DGGS(ph)GNS(ph)TIIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 DGGS(1)GNS(0.985)T(0.015)IIVSR;DGGS(1)GNS(0.981)T(0.019)IIVSR 218.45 3.53E-11 157735000 443730 423520 432500 536350 346950 477650 547240 463090 367780 TRUE FALSE 422755.7623 466677.1695 452330.5528 482435.079 407457.9702 461108.8607 463748.4872 422539.3846 424813.444 0.99515627 1.098546141 1.064774571 1.135639857 0.959145658 1.085438484 1.091652098 0.994646922 1 18.6964699 -1.078416973 8.849424819 1 1.057716639 0.078903032 0.055092684 6.67E-10 9.07E-20 0.048276031 0.01137877 0.083480113 1.078416973 0.05771664 DGGT(ph)SYSPQENSHNHSALHSSNSHSSNPSNNPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 DGGT(0.382)S(0.295)Y(0.009)S(0.277)PQENS(0.005)HNHS(0.005)ALHS(0.005)S(0.005)NS(0.005)HS(0.005)S(0.005)NPS(0.002)NNPSK 49.193 0.061937 23347000 7352 5334.8 7811.4 6524.2 17338 4715.7 16043 12223 1052.5 TRUE FALSE 7004.48553 5878.422185 8169.560417 5868.375021 20361.74171 4552.394127 13595.3457 11152.68932 1215.716325 5.761611808 4.83535679 6.71995617 4.827092392 16.74876063 3.744618736 11.18299181 9.173759615 1 10.24759091 DGHADAAQDTEQFVATVLQAASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGHADAAQDTEQFVATVLQAASR 23 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ; 156.29 1.93E-08 29437000 24661.7 28416 29317 33768 30942 30272 30775 35472 21240.5 FALSE TRUE 23495.99032 31311.62271 30661.21345 30373.57648 36338.275 29223.67305 26079.70853 32365.88363 24534.36826 0.957676598 1.276235132 1.249725003 1.238001165 1.481117208 1.191132078 1.062986756 1.319205911 1 14.5825165 -1.361099017 3.644445653 0.999023961 1.207925181 0.191518911 0.140731751 17619893.72 34387017.79 181773.9404 0.03410034 0.043541259 1.361099017 0.20890122 DGHRYS(ph)RS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGHRYSRSPAR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 2 DGHRY(0.054)S(0.973)RS(0.973)PAR 53.995 0.072122 307330000 57354 60595 57641 62484 82067 39356 57705 40055 56091 TRUE FALSE 54642.99008 66769.69939 60283.89686 56202.98961 96379.45882 37993.09185 48901.04242 36547.57186 64789.30581 0.843395209 1.030566674 0.930460608 0.867473249 1.487582829 0.586409923 0.754770279 0.564098834 1 15.98346808 DGIDDESYEAIFKPVMSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGIDDESYEAIFKPVMSK 18 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 180.62 7.08E-14 64888000 121530 127380 102070 150860 82736 129460 115950 136380 79857 FALSE TRUE 115785.5177 140360.1668 106750.0105 135695.2662 97165.1322 124976.7677 98259.69793 124437.8442 92240.81571 1.255252535 1.521670919 1.157296904 1.471097856 1.05338544 1.354896602 1.065251832 1.34905403 1 16.49311765 1.237600704 0.218393658 0.929326959 1.443129601 0.25596964 0.154130216 3.060536401 0.647463726 0.636478851 0.492459117 17.28226675 -1.237600704 0.513802642 DGIDDESYGQIFKPIISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGIDDESYGQIFKPIISK 18 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ; 203.56 1.07E-15 345230000 765420 775580 654550 897680 440820 849480 806580 866180 443730 FALSE TRUE 729240.1135 854612.4838 684561.7649 807443.5009 517698.8684 820062.2946 683521.4071 790332.6873 512541.3821 1.422792654 1.667401918 1.335622427 1.57537231 1.010062575 1.599992358 1.333592625 1.541988052 1 18.96730897 -3.441619838 0.22247045 2.52E-13 1.508396725 0.329320891 0.189545348 77.27338354 1.440744919 36.23387533 0.330135575 0.000361726 3.441619838 1.508396725 DGIEPMWEDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGIEPMWEDEK 11 0 D6RBW1;P06730;P06730-3;P06730-2;H0Y8J7 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 172.56 3.07E-05 84894000 183280 192820 154720 205890 100690 186760 164890 195230 95941 FALSE TRUE 174616.7176 212468.5772 161814.065 185193.546 118250.3041 180292.4544 139733.0021 178134.6262 110819.0403 1.575692383 1.917256968 1.460164829 1.671134722 1.067057645 1.626908642 1.260911498 1.607437005 1 16.75784625 1.596087311 0.064030036 3.12E-16 2.796871932 0.391467508 0.220953957 19.70064064 1.289711764 27.12078495 27.43574576 39.45366121 -1.596087311 2.796871932 DGIEPMWEDEKNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGIEPMWEDEKNK 13 1 D6RBW1;P06730;P06730-3;P06730-2;H0Y8J7 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 114.87 0.00064671 145890000 125360 112180 105320 126480 70787 118300 125220 128920 52301 FALSE TRUE 119434.4812 123611.2695 110149.0262 113765.9901 83132.23039 114203.2413 106115.3892 117631.0814 60411.57196 1.9770133 2.046152178 1.823310048 1.883182086 1.376097785 1.890419958 1.756540771 1.947161405 1 15.88253731 -2.231788853 0.242179212 1.99E-17 1.971937429 0.660181558 0.186683266 22.27830654 0.729426085 12.9875076 0.304785537 0.005864232 2.231788853 1.971937429 DGISCEASNPHGNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGISCEASNPHGNKR 15 1 P50895;A0A087WXM8 P50895 BCAM Basal cell adhesion molecule 0 ;; 177.21 4.95E-07 131573000 176923 127618 151206 239240 180006 174334 221942 204488 176442 FALSE TRUE 168560.2004 140622.4193 158138.9447 215191.1407 211398.9894 168296.7699 188080.6717 186581.9467 203803.7242 0.827071247 0.689989449 0.775937463 1.055874428 1.037267549 0.825778678 0.922851986 0.91549822 1 17.63682089 3.34317823 7.564513693 0.947617685 0.754794802 0.608417449 0.073436842 0.15617932 10.11758192 0.020678429 0.028016162 2203.830707 -3.34317823 -0.192822883 DGIVLGADTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGIVLGADTR 10 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ;;; 150.61 4.95E-05 473660000 1256800 1114340 896440 1129170 1074450 1007970 1250190 1130790 1067680 FALSE TRUE 1197393.555 1227892.513 937542.6607 1015663.686 1261833.74 973063.7462 1059450.554 1031772.033 1233250.361 0.970924957 0.995655506 0.760220868 0.823566502 1.023177271 0.789023686 0.859071756 0.836628202 1 20.23403428 3.773384548 24.85245863 0.863577815 0.983290275 0.237070025 0.083650911 661.4984562 472083.0737 0.019725455 0.035558496 5934.50565 -3.773384548 0.11971246 DGKPMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGKPMLR 7 1 Q9Y3F4 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 73.26 0.045031 149580000 335190 278440 284950 322120 245050 309600 365960 342300 262830 FALSE TRUE 319346.233 306813.3526 298015.2394 289739.8856 287786.6424 298878.4744 310126.0807 312326.3974 303588.3341 1.051905482 1.010622999 0.981642593 0.954384122 0.947950267 0.984486032 1.021534907 1.028782606 1 18.21175683 1.701710915 7.321507428 1.018668686 0.9928226 0.155854455 0.0297371 0.304961 35.72132199 0.017297789 0.009016338 50.31655689 -1.701710915 -0.025846087 DGKS(ph)PTVPCLQEEAGEPLGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGKSPTVPCLQEEAGEPLGGK 21 1 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 DGKS(0.906)PT(0.094)VPCLQEEAGEPLGGK;DGKS(0.856)PT(0.144)VPCLQEEAGEPLGGK 109.68 0.00017568 60694000 154310 137576 127065 166510 85277 150695 147232 153390 69758 TRUE FALSE 147016.0721 151595.1508 132891.0559 149772.0985 100149.2818 145476.3944 124769.0543 139958.3584 80575.71437 1.824570508 1.881400022 1.649269348 1.85877469 1.242921426 1.805462049 1.548469725 1.73697943 1 16.29805745 -2.456861855 0.17545844 5.97E-16 1.912693958 0.591787504 0.18415827 29.95792034 0.652829587 12.69878333 0.628786293 0.003492514 2.456861855 1.912693958 DGLAFNALIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DGLAFNALIHR 11 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 210.87 1.13E-08 1705189000 3551860 2215554 1186910 1630373 3716590 1468578 3484780 1940651 2123510 FALSE TRUE 3383970.617 2441321.471 1241330.998 1466484.809 4364762.119 1417720.776 2953112.809 1770717.31 2452813.085 1.37962841 0.995314925 0.506084628 0.597878745 1.779492349 0.577997885 1.203969771 0.72191286 1 21.22600587 4.400789627 2.744563952 0.92919573 1.357131882 0.128587152 0.374452488 0.550336525 7.699105132 0.088028468 0.371875669 25164.57658 -4.400789627 0.427936152 DGLAPEKT(ph)SPDRDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.631)S(0.369)PDRDK;DGLAPEKT(0.703)S(0.297)PDRDK;DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.893)S(0.107)PDRDK 230.29 1.56E-12 1427020000 1753870 1868760 1309370 1924320 596984 1789210 1448070 1835010 592901 TRUE FALSE 1670968.041 2059188.769 1369405.91 1730883.698 701097.8206 1727249.209 1227140.326 1674326.796 684845.059 2.439921292 3.006795102 1.999585004 2.527409193 1.023732027 2.52210217 1.791851032 2.444825694 1 19.3854181 1.98758452 0.095113764 4.34E-14 4.073384812 0.360414605 0.525688752 13.37332616 1.007445944 18.37875099 22.07956427 97.18170634 -1.98758452 4.073384812 DGLAPEKTS(ph)PDRDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.088)S(0.912)PDRDK 167.28 1.92E-06 190200000 595080 683960 442530 647870 205690 561070 481270 639900 214730 TRUE FALSE 566951.7477 753656.3016 462820.4382 582744.8767 241562.2709 541640.0052 407843.4224 583866.9637 248029.2317 2.285826327 3.038578543 1.8659915 2.349500794 0.973926618 2.183774878 1.644336111 2.354024804 1 17.92015064 3.437295083 2.007492372 1.743572382 2.645869133 0.321935524 0.522858769 0.322660136 2.623355567 0.140880803 0.224558846 2737.127847 -3.437295083 0.902296752 DGLGFCALIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 161380000 258210 180900 137850 174860 278640 172100 293570 207140 226300 FALSE TRUE 246004.925 199333.9157 144170.5589 157282.7406 327234.7278 166140.1338 248780.5047 189001.7235 261393.4482 0.941128887 0.762581913 0.551546184 0.60170881 1.25188573 0.635594101 0.951747285 0.723054555 1 17.99586346 DGLGGLPDIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGLGGLPDIVR 11 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 127.76 0.00065101 66769000 121590 96126 91511 105231 118004 96641 132800 108536 127991 FALSE TRUE 115842.6817 105921.3487 95706.86987 94652.97995 138583.8602 93294.29794 112538.921 99032.01245 147839.1906 0.783572213 0.716463262 0.647371441 0.640242818 0.937395962 0.631052548 0.761225224 0.669863059 1 17.17366924 -1.306191651 3.563626705 1.000915666 0.726465164 0.475080656 0.091322866 839109787.3 1138378199 8021293.142 0.020479934 0.04940926 1.306191651 -0.274450503 DGLILTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGLILTSR 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 161.02 0.00081417 1062450000 1113300 890430 901440 1011810 1067720 921470 1140410 1073190 1092930 FALSE TRUE 1060676.515 981165.8293 942771.9156 910100.9365 1253930.03 889559.2628 966419.5094 979215.7943 1262416.002 0.840195715 0.777212763 0.746799719 0.720919994 0.99327799 0.704648278 0.765531732 0.775668078 1 20.26775597 -1.254877033 3.252943855 1.000788728 0.789349777 0.398954299 0.080788687 22156548.59 31160322.13 174138.1303 0.01838159 0.055606168 1.254877033 -0.211438952 DGLIPLEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGLIPLEIR 9 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;; 103.87 0.007798 698426000 725340 798328 641230 786188 538828 650458 626176 701809 497850 FALSE TRUE 691054.6157 879678.5308 670631.0298 707158.8886 632799.4326 627932.4764 530641.3507 640354.8834 575054.0353 1.201721183 1.52973195 1.166205241 1.229725982 1.100417341 1.091953865 0.922767806 1.113556021 1 19.133338 2.895123157 1.105019157 1.009639271 1.353985803 0.578763841 0.104825989 0.288260263 0.747028415 0.04692667 0.05101632 785.4583422 -2.895123157 0.344346533 DGLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGLKPR 6 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 79.939 0.060035 217010000 783250 659970 679370 924560 865700 761050 960750 886890 876690 FALSE TRUE 746227.3248 727221.6933 710519.7865 831621.4723 1016677.806 734694.6477 814169.9421 809229.2099 1012642.608 0.73691085 0.718142499 0.701649112 0.821238871 1.00398482 0.725522156 0.80400522 0.799126171 1 19.94969366 -5 0.087557608 1.674380694 0.599855222 0.425185455 0.082520438 218.5373399 1.335957658 28.08540974 2.114378162 1.00E-05 5 -1.074525473 DGLLENQTPEFFQDVCKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 288.57 5.88E-41 6997750000 4477608 4149867 4112483 4841120 2537677 4636104 4964030 4887650 2886398 FALSE TRUE 4265960.344 4572743.165 4301044.413 4354481.42 2980247.065 4475554.556 4206676.053 4459661.455 3334005.86 1.279529948 1.371546229 1.290053045 1.306080914 0.893893769 1.342395528 1.261748248 1.337628559 1 21.66882521 -4.332145621 0.239490336 2.69E-32 1.293994684 0.252339894 0.136094703 170.8527489 2.286046651 83.87505573 0.209462326 4.65E-05 4.332145621 1.293994684 DGLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGLLLR 6 0 O14746-3;O14746 REV__O43296 TERT Telomerase reverse transcriptase 0 ; 114.6 0.058509 1358420000 1277120 1142740 1101620 1304450 1160820 1118380 1315990 1234810 1201100 FALSE TRUE 1216753.069 1259186.505 1152130.367 1173324.208 1363266.64 1079650.22 1115211.556 1126683.49 1387360.454 0.877027355 0.907613088 0.83044775 0.845724126 0.982633343 0.778204552 0.803836921 0.812105814 1 20.40391124 2.198159315 24.9999894 0.827224102 0.885609716 0.0348158 0.072751561 293.1403854 181391.0702 0.024450658 0.01805821 157.8190101 -2.198159315 0.058385614 DGLLPENTFIVGYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DGLLPENTFIVGYAR 15 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 199.27 1.75E-08 433977000 350526 308860 312057 360207 335531 306015 368623 336963 346497 FALSE TRUE 333957.3307 340333.1851 326365.1221 323998.308 394047.5002 295417.6238 312382.7911 307456.7334 400229.9851 0.83441357 0.850344047 0.815443955 0.80953032 0.984552669 0.738119668 0.780508215 0.768200147 1 18.61046973 DGLNDDDFEPYLS(ph)PQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGLNDDDFEPYLSPQAR 17 0 Q9Y5A9;S4R3J8 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 DGLNDDDFEPYLS(1)PQAR 191.47 2.53E-10 57016000 139980 166020 115280 160110 102480 143930 132820 148600 84446 TRUE FALSE 133363.4228 182937.6267 120565.702 144015.4386 120352.4796 138945.668 112555.8696 135587.7962 97541.45439 1.36724866 1.875485945 1.236045769 1.476453673 1.233859802 1.424478125 1.153928556 1.39005305 1 16.57372786 2.141570927 0.278512472 0.985302983 1.685870901 0.366494292 0.185145216 1.807957401 0.42049923 0.311799718 0.461862819 138.5386423 -2.141570927 0.700567918 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGLNQTTIPVSPPSTTKPSR 20 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DGLNQTTIPVS(0.999)PPSTTKPSR;DGLNQTTIPVS(0.957)PPS(0.013)T(0.013)T(0.013)KPS(0.004)R;DGLNQTTIPVS(0.995)PPS(0.002)T(0.002)T(0.002)KPSR;DGLNQTTIPVS(0.993)PPS(0.002)T(0.002)T(0.002)KPSR 138.08 1.48E-06 1611040000 849130 757540 739640 903280 556660 830330 833740 809980 542130 TRUE FALSE 808993.3077 834734.1873 773553.2256 812480.5783 653741.3278 801575.4639 706537.6503 739053.8572 626200.7516 1.291907277 1.33301371 1.235311877 1.297476211 1.043980427 1.280061485 1.128292562 1.180218732 1 19.25626571 2.639258242 0.059536868 0.527706369 1.905469266 0.5822753 0.072472905 37.50548673 0.961908072 9.352752092 12.5324536 435.7709163 -2.639258242 1.377762897 DGLPRT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.999)PS(0.001)R;DGLPRT(0.999)PS(0.001)R;DGLPRT(0.997)PS(0.003)R;DGLPRT(0.993)PS(0.007)R;DGLPRT(0.998)PS(0.002)R 112.5 0.003157 1674030000 797842 861919 755722 973270 735506 806789 806881 814908 719557 TRUE FALSE 760129.5898 949749.526 790372.6012 875435.0505 863778.0135 778849.6946 683776.4841 743550.3354 831142.2246 0.914560189 1.142703978 0.950947477 1.053291512 1.039266191 0.937083536 0.822694918 0.894612635 1 19.66473585 2.083725863 4.364475846 0.884561287 1.025133405 0.326655175 0.074554445 0.189078689 6.710383903 0.027527036 0.019487264 121.2623171 -2.083725863 0.140572117 DGLPRTPS(ph)RR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGLPRTPSRR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.267)PS(0.733)RR;DGLPRT(0.061)PS(0.939)RR;DGLPRT(0.104)PS(0.896)RR;DGLPRT(0.065)PS(0.935)RR;DGLPRT(0.056)PS(0.944)RR 107.99 0.0011532 7616530000 3619980 2992740 3199240 3653630 3051720 3373340 3703570 3483080 3250550 TRUE FALSE 3448870.72 3297703.608 3345928.318 3286360.171 3583939.002 3256520.39 3138522.376 3178083.05 3754628.692 0.918565057 0.878303523 0.891147592 0.875282336 0.954538863 0.86733487 0.835907525 0.846444032 1 21.84023881 DGLTDVYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGLTDVYNK 9 0 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7;H0YEL7;A0A5F9ZHH9 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ; 150.36 0.00063549 173800000 439300 335880 338160 368390 263870 316860 353690 358540 282880 FALSE TRUE 418535.1596 370106.5539 353664.9705 331358.7373 309888.8445 305887.0587 299728.0945 327144.3369 326747.5856 1.280912784 1.132698664 1.082379751 1.014112275 0.948404389 0.936157059 0.917307756 1.001214244 1 18.31781705 3.877502247 0.809750824 0.945904679 1.303523532 0.917610994 0.031177847 0.218010952 0.231904303 0.012633259 0.056529214 7542.272985 -3.877502247 0.357618852 DGMALDEVWDSSHFALQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGMALDEVWDSSHFALQPGR 20 0 A6NN50;O75147-2;O75147-1;O75147-4;O75147 A6NN50 OBSL1 Obscurin-like protein 1 0 175.51 1.83E-12 30497000 55663 52821 56749 64159 55970 62787 67523 66050 56359 FALSE TRUE 53031.9203 58203.51995 59350.99778 57709.61543 65731.15028 60612.67045 57221.12621 60266.31185 65098.86588 0.814636624 0.894078862 0.911705557 0.886491871 1.009712679 0.931086427 0.878988066 0.925765926 1 15.99034479 4.651409056 0.766937105 0.932836347 0.751748087 0.475686729 0.041221287 2.145915413 1.045836832 0.015253465 0.326966763 44813.51974 -4.651409056 -0.181088261 DGMDNQGGYGSVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGMDNQGGYGSVGR 14 0 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 124.45 0.00022563 435310000 280290 222780 240510 302160 261600 250510 271960 257300 275370 FALSE TRUE 267041.2472 245481.5353 251537.6214 271786.3027 307222.9572 241834.7759 230467.5071 234769.448 318072.9732 0.839559691 0.771777409 0.790817336 0.854477826 0.965888281 0.760312244 0.724574316 0.738099329 1 18.27899827 -0.287422686 7.515237689 1.000000019 0.802612736 0.433021431 0.069797504 0 0 0.070242138 0.016556231 0.515914001 0.287422686 -0.197387283 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DGMEYPFIGEGEPHVDGEPGDLR 23 0 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;;;;; 284.88 3.04E-52 467490000 502873 463124 435802 538816 431285 470845 512505 500393 359172 FALSE TRUE 479103.1899 510316.8621 455783.9528 484653.192 506500.9675 454539.5196 434312.9494 456575.9362 414870.5594 1.154825714 1.230062849 1.098617249 1.168203386 1.220865053 1.09561768 1.04686375 1.100526239 1 18.66230176 2.063040509 5.11823804 1.057911659 1.176242248 0.641258196 0.04322008 0.122222905 6.346651025 0.015910146 0.011415684 115.6220085 -2.063040509 0.118330589 DGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 3308900000 4815900 5346100 4073300 5862800 3069500 4879000 4561300 4929000 3216300 FALSE TRUE 4588261.951 5890873.668 4260064.834 5273460.205 3604819.828 4710039.007 3865389.911 4497390.63 3715067.377 1.235041383 1.585670748 1.146699212 1.419479021 0.970324213 1.267820615 1.040462936 1.210581175 1 21.82495695 2.750417819 24.79574693 1.109469724 1.36302586 0.420452919 0.144276179 598.9201536 1252459.392 0.040375441 0.04250146 562.8825937 -2.750417819 0.253556136 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 206.47 1.02E-30 4255700000 282340 189890 259070 247960 211330 297400 334380 311620 240490 FALSE TRUE 268994.3477 209240.0069 270948.6158 223034.5897 248185.8851 287100.9634 283364.1897 284332.9008 277783.9609 0.968358097 0.753247258 0.975393305 0.802906651 0.893449299 1.033540462 1.020088376 1.023575659 1 18.08360378 2.292692803 5.103578866 1.021589804 0.868983477 0.524191906 0.066493553 0.138955846 7.562827312 0.021864527 0.017801755 196.1971992 -2.292692803 -0.152606327 DGNDLHMTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGNDLHMTYK 10 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 133.07 0.00020691 1170370000 3493860 2885730 3201620 3617010 2870160 3288940 4270100 3803070 2839130 FALSE TRUE 3328712.162 3179789.168 3348417.444 3253421.283 3370714.995 3175043.183 3618617.819 3470053.029 3279407.78 1.015034538 0.969622987 1.021043331 0.992075857 1.027842593 0.968175779 1.103436371 1.058134048 1 21.64500388 1.744449337 25 1.062398385 0.998510812 0.391260285 0.031680861 0.917491494 3908.881409 0.012915003 0.007161982 55.5199846 -1.744449337 -0.063887573 DGNLHEGDIILK ddPTM_SK-BR-3_Trastuzumab_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 79.875 0.021857 147120000 266810 264190 283050 303940 367590 247610 336470 301340 306580 FALSE TRUE 254198.4201 291111.2614 296028.1225 273387.3738 431697.5796 239035.2036 285135.3218 274953.0721 354122.8606 0.717825502 0.822062888 0.835947507 0.772012779 1.219061596 0.675006418 0.805187559 0.776434121 1 18.43389046 4.410589827 1.189467344 0.858424287 0.694637544 0.092035997 0.149385058 2.367325548 4.215892067 0.042052848 0.417726015 25738.89077 -4.410589827 -0.163786744 DGNVLLHEMQIQHPTASLIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGNVLLHEMQIQHPTASLIAK 21 0 P40227 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 264.64 4.49E-37 1635860000 2034300 1616180 1709200 1931350 1647370 1845960 2356300 2189000 780340 FALSE TRUE 1938142.671 1780870.579 1787568.511 1737207.029 1934670.806 1782033.942 1996803.159 1997319.555 901351.1418 2.150263733 1.975778913 1.983209903 1.927336582 2.146411889 1.977069601 2.215344349 2.215917263 1 19.78172972 -0.744676618 7.720311022 0.999999019 2.07118846 0.911091143 0.105427037 0 0 0.10191331 0.024021197 0.180021088 0.744676618 1.071189441 DGPLNMILDDGGDLTNLIHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGPLNMILDDGGDLTNLIHTK 21 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 221.14 4.42E-25 423140000 880740 850940 890820 971970 547790 959760 998180 1014880 483650 FALSE TRUE 839109.1657 937651.7534 931664.9781 874265.729 643324.4026 926523.2705 845889.3082 926011.727 558651.9719 1.502024888 1.678418408 1.667701942 1.564955953 1.151565617 1.658498166 1.514161501 1.657582491 1 19.09159027 -1.592390434 2.977346782 0.966234892 1.55226129 0.5535437 0.155032062 24225695.49 26623801.53 6450076.082 0.035538992 0.025562867 1.592390434 0.586026398 DGQAMLWDLNEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 179.67 3.15E-05 387076000 1169390 1124670 1028830 1309120 767591 1191370 1209380 1284030 815120 FALSE TRUE 1114115.252 1239275.152 1076002.873 1177524.77 901458.6274 1150112.558 1024866.869 1171593.526 941524.6465 1.183309705 1.316242922 1.142830278 1.250657404 0.957445597 1.221542699 1.088518365 1.244357788 1 19.84463934 -2.542702221 0.028290286 4.02E-08 2.003447586 0.235679932 0.099242081 1203.174649 4.120644049 189.2290859 111.069723 0.002866143 2.542702221 2.003447546 DGQDAIAQS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_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 290.69 4.31E-36 486110000 4160610 4951300 3430670 5258380 1965239 4565510 3696620 4529210 1681075 TRUE FALSE 3963946.211 5455843.099 3587969.613 4729797.652 2307976.059 4407405.244 3132632.726 4132608.362 1941767.525 2.041411322 2.809730325 1.847785364 2.435820762 1.188595457 2.269790377 1.613289276 2.128271437 1 20.88893906 -0.347190589 0.134661383 5.96E-13 2.840009346 0.3903757 0.429113377 20.41525138 0.771096016 12.28174462 4.075792635 0.449582514 0.347190589 2.840009346 DGQDAIAQS(ph)PEKESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DGQDAIAQSPEKESK 15 1 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK 258.37 4.88E-25 6673600000 6004800 5924520 5051020 6656800 2174218 6756060 5589310 6694720 1936032 TRUE FALSE 5720965.004 6528235.324 5282614.263 5987645.817 2553400.931 6522095.948 4736558.105 6108494.826 2236261.955 2.558271401 2.919262348 2.362251995 2.677524341 1.141816559 2.916516974 2.118069439 2.731564973 1 21.09265776 DGQDAIAQS(ph)PEKESKDYEMNANHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGQDAIAQSPEKESKDYEMNANHK 24 2 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(0.999)PEKES(0.001)KDYEMNANHK;DGQDAIAQS(0.976)PEKES(0.024)KDYEMNANHK 98.002 0.0036776 488570000 207579 119649 196429 188333 111255 233824 263383 244214 105701 TRUE FALSE 197767.1521 131841.3691 205435.4639 169401.409 130657.8368 225726.6162 223199.086 222829.3275 122092.5712 1.619813147 1.079847593 1.682620506 1.387483344 1.070153863 1.848815321 1.828113568 1.825085058 1 16.8976159 2.220994507 24.99992547 1.71433812 1.36677395 0.115346447 0.314130216 343.2030383 488440.3524 0.106066876 0.07850691 166.3391612 -2.220994507 -0.347564169 DGQDAIAQS(ph)PEKESKDYEMNANHKDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGQDAIAQSPEKESKDYEMNANHKDGK 27 3 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEKESKDYEMNANHKDGK 188.26 6.21E-18 161830000 187750 75808 175260 134900 75366 201460 262550 242170 74229 TRUE FALSE 178875.4296 83532.92139 183295.8444 121339.5957 88509.80654 194483.3897 222493.1754 220964.311 85740.05421 2.086252817 0.974257856 2.137808823 1.415203161 1.032304066 2.268290958 2.59497358 2.577142189 1 16.38768171 3.691684253 24.99338555 1.939020989 1.530252662 0.034284798 0.630868538 1092.278845 582377.456 0.172385496 0.267059359 4916.819363 -3.691684253 -0.408768327 DGQPCMDHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGQPCMDHDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;; 114.72 0.00099974 462966000 637343 521672 525973 616043 560586 528856 644981 604833 542471 FALSE TRUE 607217.0595 574830.9699 550089.3823 554117.1872 658352.0209 510541.5841 546577.3026 551870.6161 626594.6321 0.969074787 0.917388915 0.87790312 0.884331207 1.05068251 0.814787676 0.872298093 0.880745841 1 19.25717288 DGQS(ph)SPQPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 2 DGQS(0.763)S(0.237)PQPS(1)PR 94.551 0.012308 78718000 207020 154150 193700 215780 196190 162430 192970 155000 162030 TRUE FALSE 197234.5749 169858.0603 202581.3366 194089.3844 230405.4739 156805.0084 163528.8824 141427.3783 187156.7849 1.053846779 0.907570946 1.082415135 1.037041668 1.231082667 0.837827004 0.873753428 0.755662577 1 17.51388782 2.179270284 24.99999303 0.857501192 1.040262444 0.484925896 0.098499639 67.37957253 28410.18992 0.03555086 0.02625606 151.1020249 -2.179270284 0.182761253 DGQS(ph)SPQPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.5)S(0.5)PQPSPR 145.81 3.78E-05 132760000 214660 180020 206190 225080 166600 205330 230120 214020 179130 TRUE FALSE 204513.4472 198364.2427 215644.0154 202454.5308 195654.9873 198219.3706 195010.9676 195279.2742 206908.5655 0.988424267 0.958704837 1.04221889 0.978473415 0.945610863 0.958004663 0.942498282 0.943795022 1 17.65863385 2.889231783 5.411647923 0.953760109 0.989774802 0.292777809 0.026222777 0.278402291 11.54786464 0.007699511 0.008223037 774.8752391 -2.889231783 0.036014693 DGQSS(ph)PQPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 2 DGQS(0.128)S(0.872)PQPS(1)PR 95.264 0.0046365 0 125720 98495 124890 126630 124030 96024 112250 90400 93393 TRUE FALSE 119777.4648 108531.7525 130616.33 113900.9118 145660.7927 92698.6648 95124.20089 82484.09676 107875.9095 1.11032635 1.006079606 1.210801658 1.055851231 1.350262477 0.859308304 0.881792806 0.764620175 1 16.7190132 2.193978545 24.99922386 0.867949522 1.122977774 0.600094949 0.108568077 90.06212786 50501.44605 0.037835275 0.02794333 156.3070422 -2.193978545 0.255028252 DGQSS(ph)PQPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.104)S(0.896)PQPSPR;DGQS(0.067)S(0.933)PQPSPR;DGQS(0.006)S(0.994)PQPSPR;DGQS(0.019)S(0.981)PQPSPR;DGQS(0.057)S(0.939)PQPS(0.004)PR 174.72 1.12E-05 1302581000 1631265 1379027 1526613 1666284 1381322 1536009 1801145 1609299 1343509 TRUE FALSE 1554158.336 1519551.419 1596609.716 1498785.967 1622224.119 1482816.623 1526347.25 1468380.248 1551853.514 1.001485206 0.97918483 1.028840481 0.965803765 1.045346165 0.955513268 0.983564 0.946210602 1 20.56556095 DGQWFTDWDAVPHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGQWFTDWDAVPHSR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;; 211.12 1.54E-09 1400570000 1485430 1228810 1272740 1457430 1471940 1238540 1627480 1435800 1307430 FALSE TRUE 1415216.668 1354027.136 1331096.388 1310926.367 1728645.87 1195649.049 1379178.035 1310073.74 1510179.567 0.937118141 0.89660009 0.88141597 0.868059929 1.144662468 0.791726411 0.913254334 0.867495342 1 20.52628867 3.66067628 0.004098501 1.82450685 1.73E-07 0.018956319 0.094029056 215526.9445 204.5956664 44638.03311 46446.3915 4578.005181 -3.66067628 -1.824506677 DGRHPQGEQMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 132.79 0.00023497 381078000 115955.2 107355.8 119105.6 109569.5 112862.3 97869.4 108675.2 114454.5 115263.6 FALSE TRUE 110474.2275 118295.4781 124566.7096 98555.36569 132545.4494 94480.15814 92094.80228 104432.2572 133138.0904 0.829771759 0.888517161 0.935620371 0.740249206 0.995548674 0.709640328 0.691723924 0.784390529 1 17.02256386 2.210845895 24.98784582 0.760099594 0.871367657 0.081692104 0.107563624 319.5206294 288080.7468 0.03588011 0.026505061 162.497205 -2.210845895 0.111268063 DGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR 33 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 ; 185.38 8.55E-20 298750000 370750 303890 273950 430300 300920 333940 372590 387220 267730 FALSE TRUE 353225.3823 334856.7365 286510.8785 387045.4265 353400.3527 322375.5741 315744.5524 353312.964 309248.201 1.142206749 1.082809004 0.92647549 1.251568886 1.142772542 1.042449311 1.021006917 1.142489957 1 18.23840568 -4.999999994 0.158525041 0.662225112 1.115419767 0.093561114 0.087435521 331.1625485 3.03109395 35.06177452 0.365692766 1.00E-05 4.999999994 0.453194655 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR 32 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 65.893 0.0027484 97004000 127530 108320 114720 143820 72036 123620 130400 148220 58682 FALSE TRUE 121501.9096 119357.9311 119980.0255 129362.9404 84599.05559 119339.0084 110505.085 135241.071 67782.10485 1.792536687 1.760906236 1.770084091 1.908511703 1.248103106 1.760627066 1.630298812 1.995232685 1 16.04861682 DGSGDSHPDFPEDADIDLKDVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGSGDSHPDFPEDADIDLKDVDK 23 1 Q08752 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 ; 145.55 8.30E-08 75874000 181573 178441 161239 217402 86450 201491 201429 216773 65828 FALSE TRUE 172990.4041 196624.3408 168631.9676 195548.3379 101526.8526 194513.3161 170697.3066 197791.2069 76036.27004 2.275103764 2.585928277 2.21778327 2.571777098 1.335242412 2.558164887 2.24494582 2.601274455 1 16.21440014 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_SK-BR-3_Trastuzumab_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(0.999)DEES(0.001)PRK 209.25 7.54E-26 300670000 105053 91189 92807 109661 69569 107073 119580 109578 81149 TRUE FALSE 100087.3529 100481.2628 97062.29275 98637.66794 81701.81157 103365.0352 101335.8748 99982.76941 93733.17247 1.067790092 1.071992552 1.035516991 1.05232401 0.871642444 1.102758313 1.08111005 1.066674335 1 16.51627209 -0.756207736 6.252352513 0.999999999 1.047705007 0.041130982 0.063829463 8.89E-10 1.42E-10 0.059640826 0.014057477 0.175304177 0.756207736 0.047705008 DGTGVVEFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 176.78 5.58E-06 510450000 777560 664160 636770 759730 632910 669230 850610 781330 737420 FALSE TRUE 740806.2798 731838.6591 665966.5344 683360.497 743289.3036 646054.3973 720833.822 712912.6031 851775.3274 0.869720284 0.859192131 0.781857038 0.802277872 0.8726354 0.75847982 0.846272249 0.836972591 1 19.70011342 0.421820874 2.109463801 0.999995909 0.829997062 0.673599224 0.037564869 5.266144626 18.38487199 0.035552299 0.009697561 2.641319114 -0.421820874 -0.169998846 DGTS(ph)PEEEIEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGTSPEEEIEIER 13 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 DGT(0.001)S(0.999)PEEEIEIER;DGT(0.025)S(0.975)PEEEIEIER 268.21 1.15E-24 770330000 1002200 870030 796050 974910 746220 954330 976320 950490 669410 TRUE FALSE 954827.9922 958687.0461 832549.6799 876910.1946 876360.5317 921281.3128 827364.4527 867260.0567 773218.6839 1.234874444 1.23986534 1.076732491 1.134103731 1.133392855 1.191488685 1.070026462 1.121623255 1 19.56051697 8 0.090397395 0.912074054 1.843253775 0.612116225 0.04649899 93.69602901 0.608456987 0.815019692 10.82043554 99999999.99 -8 0.931179721 DGTSLWDLLSSCHFTEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGTSLWDLLSSCHFTEEQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 270.94 2.59E-39 267150000 461880 424970 402770 547060 456240 447200 520220 532630 428480 FALSE TRUE 440047.8478 468274.9262 421237.4029 492068.4895 535808.1115 431713.3519 440850.8845 485990.0936 494926.49 0.889117589 0.94615046 0.851111047 0.994225404 1.082601401 0.872277723 0.890740127 0.981943992 1 18.91685474 3.225947197 24.99986027 0.958328823 0.905415978 0.218750799 0.063134246 480.2592061 951874.0825 0.019131719 0.023012304 1682.469489 -3.225947197 -0.052912845 DGTSLWDLLSSCHFTEEQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGTSLWDLLSSCHFTEEQRR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 232.15 3.28E-26 769924000 882856 549993 915476 884810 1171690 859330 1342890 1037255 1271370 FALSE TRUE 841125.1465 606037.912 957451.4801 795867.2178 1376032.365 829571.1866 1138007.467 946427.4534 1468527.566 0.572767693 0.412684056 0.651980597 0.541949117 0.937015005 0.564899976 0.774930953 0.64447374 1 20.48593892 -0.359264749 0.074507854 1.724776971 5.67E-10 0.499426933 0.12803534 50.02588537 0.971996864 14.85388723 7.804656892 0.43725547 0.359264749 -1.72477697 DGTTHQTSLELFMYLNEVAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGTTHQTSLELFMYLNEVAGK 21 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;; 177.08 6.59E-17 633566000 1027946 916646 869849 1069826 738947 942146 1121264 1095888 740715 FALSE TRUE 979357.0298 1010053.27 909732.437 962285.0579 867819.1228 909519.2478 950194.5834 999926.2371 855581.2992 1.144668579 1.180546221 1.063291633 1.124714926 1.014303519 1.063042459 1.110583628 1.168709786 1 19.70654542 3.739093999 24.99984032 1.082460732 1.162607403 0.325667623 0.050385756 50.89680166 2385508.551 0.012405467 0.020748853 5483.95647 -3.739093999 0.08014667 DGTVLCELINALYPEGQAPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGTVLCELINALYPEGQAPVKK 22 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 212.74 2.78E-23 415820000 940910 593920 703480 868550 545180 807930 1169380 1043000 745490 FALSE TRUE 896435.049 654441.1232 735735.2538 781241.7039 640259.2194 779951.1815 990969.6039 951669.3907 861096.7818 1.041038671 0.76000879 0.854416448 0.907263528 0.743539208 0.905764832 1.150822561 1.105182845 1 19.71581587 1.835238616 5.326442244 1.096059002 0.86301915 0.569526739 0.089131303 0.149104492 6.111441576 0.0395066 0.022968408 68.42875145 -1.835238616 -0.233039853 DGVLALDNFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGVLALDNFHR 11 0 Q70J99;Q70J99-3;K7EMK8 Q70J99 UNC13D Protein unc-13 homolog D 0 ;;; 181.31 6.28E-06 478770000 1017210 1038690 927570 1124790 871300 1037730 1035580 1090070 822660 FALSE TRUE 969128.4992 1144533.692 970100.002 1011723.972 1023254.444 1001793.15 877583.2513 994617.692 950233.9112 1.019884144 1.204475738 1.020906527 1.064710447 1.076844798 1.054259523 0.923544446 1.046708269 1 19.85792317 1.949335663 6.793326863 0.982765149 1.084775758 0.310011798 0.05867551 0.244085426 26.6388735 0.02443854 0.015291794 88.98886406 -1.949335663 0.102010609 DGVLEEQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGVLEEQIER 10 0 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 125.97 0.0073611 0 59640 56322 41735 63945 42514 52823 56496 59982 55974 FALSE TRUE 56820.9354 62061.27583 43648.59103 57517.12711 49928.42814 50993.72626 47876.49758 54729.6581 64654.16204 0.878844201 0.959896067 0.675108758 0.889612135 0.772238423 0.788715292 0.740501401 0.846498607 1 15.98045562 3.770514777 24.99993144 0.801315384 0.919370145 0.17058937 0.090202749 799.6408372 625611.3339 0.02019289 0.036399016 5895.420358 -3.770514777 0.118054761 DGVTVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGVTVAK 7 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JCQ4;C9JL25;C9JL19 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 105.39 0.018466 163735000 577380 500030 495710 548410 515260 467240 575290 553010 561450 FALSE TRUE 550088.3917 550983.6255 518438.7938 493282.7849 605121.1809 451059.3616 487518.9446 504585.5127 648516.7985 0.848225355 0.849605788 0.799422305 0.76063224 0.933084821 0.695524561 0.751744513 0.778060821 1 19.30678442 2.229492931 24.99998786 0.77879384 0.835374285 0 0.090303266 481.2493258 1326814.397 0.029969622 0.022444807 169.626199 -2.229492931 0.056580445 DGVVEITGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGVVEITGK 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ; 152.34 0.00018775 336690000 1331940 1037450 943620 1278260 811160 1124820 1152840 1242130 793370 FALSE TRUE 1268981.836 1143167.334 986885.9104 1149766.876 952626.0472 1085867.201 976953.0846 1133362.512 916401.7676 1.384743985 1.247452127 1.076914019 1.254653709 1.039528819 1.184924822 1.066075077 1.236752866 1 19.80562072 7.999999999 0.378480372 1.096899138 5.510227389 0.511663454 0.083720746 44.25078313 0.605662389 0.054603909 143.0314105 99999999.7 -7.999999999 4.413328251 DGVVEITGKHEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DGVVEITGKHEER 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 200.13 6.75E-08 4476800000 9590474 3459480 8573170 6443928 7765704 8120821 12617789 9315832 8373376 FALSE TRUE 9137151.301 3812004.945 8966258.325 5796172.115 9120040.319 7839594.933 10692713.55 8500088.364 9671876.385 0.944713408 0.394132927 0.927044347 0.599281038 0.94294426 0.810555741 1.105546961 0.878845844 1 23.20536438 2.448235388 1.410641052 0.99169615 0.695170101 0.278053264 0.175546235 0.446229859 1.793630421 0.082993055 0.060122868 280.6954596 -2.448235388 -0.296526048 DGVVRPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 133.86 0.00082194 18903970000 22175220 27882190 20424700 29556730 15342480 27002890 23069330 27797740 15445690 FALSE TRUE 21127041.3 30723416.86 21361192.7 26585631.35 18018203.65 26067773.15 19549680.01 25363622.52 17840928.72 1.184189547 1.722074974 1.197313942 1.490148398 1.009936419 1.461121983 1.095777037 1.421653711 1 24.08868738 2.766524771 24.95094228 1.216477337 1.41739437 0.17501876 0.21265043 1149.423975 1025568.38 0.058444625 0.061979022 584.1505247 -2.766524771 0.200917033 DGVYFLYEALHGPPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGVYFLYEALHGPPKK 16 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 146.78 7.08E-07 72580000 352290 322260 328990 383200 241330 385880 419890 409080 237410 FALSE TRUE 335637.9499 355098.6604 344074.5169 344680.008 283417.8756 372516.8788 355828.0687 373258.7865 274226.3303 1.223945015 1.294910886 1.254709993 1.25691799 1.033518099 1.35842856 1.297570763 1.361134017 1 18.06500757 2.968546738 24.98187765 1.236198042 1.26030941 0.01179964 0.12189958 5284.665494 4197362.065 0.035203008 0.037383178 930.1366098 -2.968546738 0.024111368 DGWGGYGSDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGWGGYGSDKR 11 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 129.84 0.00037947 2100140000 2917880 2251000 2292260 2800260 2391280 2554920 3486270 2952760 2604070 FALSE TRUE 2779957.595 2480379.459 2397362.388 2518772.545 2808318.475 2466442.48 2954375.482 2694200.681 3007895.876 0.924220023 0.82462278 0.797023064 0.837386881 0.933648833 0.819989315 0.9822067 0.895709423 1 21.5203232 1.53568369 0.855713555 0.986443881 0.852033644 0.421324545 0.053368226 0.512218734 0.754757954 0.046424899 0.018653643 34.33078148 -1.53568369 -0.134410237 DGWPAMCIHGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGWPAMCIHGDK 12 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 154.07 7.12E-05 1406940000 4304540 3483240 3626370 4265150 3004630 3962580 4720940 4374450 2852240 FALSE TRUE 4101072.925 3838186.116 3792642.651 3836409.019 3528636.521 3825354.861 4000673.897 3991399.968 3294550.812 1.244804879 1.165010448 1.151186571 1.164471043 1.07105239 1.161115757 1.21433061 1.21151568 1 21.65165035 -2.053467229 2.79097441 0.753291777 1.174980928 0.576200598 0.046580866 726221.5404 3999808.636 1272920.672 0.011309058 0.008841639 2.053467229 0.42168915 DGWPAMGIHGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGWPAMGIHGDK 12 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;; 117.03 0.00058997 1041230000 2010180 1886480 1701250 2027040 1414140 1929270 2170750 2123700 1381920 FALSE TRUE 1915162.775 2078714.457 1779253.995 1823278.088 1660765.568 1862458.896 1839562.219 1937737.57 1596221.096 1.199810465 1.302272262 1.114666383 1.14224658 1.040435797 1.166792558 1.152448257 1.213953114 1 20.60622907 7.937345568 0.019181687 1.98E-06 2.633355195 0.350953326 0.068899014 3473.416121 5.18897766 268.0645694 470.5085501 86565644.7 -7.937345568 2.633353212 DGWQVEEADDWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGWQVEEADDWLR 13 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;;; 240.12 1.81E-16 252764000 664410 674100 566650 713460 583310 562270 679610 677310 580450 FALSE TRUE 633004.656 742791.5564 592631.463 641741.6453 685039.0793 542798.4489 575923.0126 618001.1458 670463.2215 0.94413032 1.107878154 0.883913456 0.957161593 1.021739981 0.80958721 0.8589927 0.921752493 1 19.35479867 2.251619139 24.9979172 0.880233746 0.990792766 0.223934444 0.075209519 254.1995198 486613.3385 0.025219947 0.020978194 178.4921576 -2.251619139 0.11055902 DGWSLWYSEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 155.06 7.38E-05 48307000 55859 130940 53846 75930 50502 60730 44832 62855 37937 FALSE TRUE 53218.65577 144282.9349 56314.89236 68297.37214 59309.53281 58626.90487 37992.055 57351.08298 43820.0762 1.214481132 3.292621724 1.285139079 1.558586339 1.353478541 1.337900569 0.867001117 1.30878556 1 15.41930437 3.529237427 24.78377195 1.235366888 2.259440625 0.389594853 0.52544363 266.9765946 126959.4986 0.133822643 0.207314931 3382.497055 -3.529237427 1.024073737 DGYAQILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGYAQILR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;; 94.114 0.024634 539144000 765681 567503 486558 500505 818815 457617 736670 653117 788595 FALSE TRUE 729488.7766 625332.2009 508867.1656 450193.2865 961616.0768 441769.6085 624277.4616 595926.6131 910886.285 0.800856033 0.686509624 0.558650596 0.494236541 1.055692782 0.484988759 0.685351697 0.654227232 1 19.79691143 -1.25158794 3.705711312 1.000538717 0.679783973 0.274827649 0.164567304 3344625101 4933997460 19986177.32 0.036096033 0.056028895 1.25158794 -0.320754744 DGYDYDGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGYDYDGYR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 163.04 0.00014732 9503900000 10028700 8149430 8421600 9616700 8633330 8553890 10573700 9675600 8980700 FALSE TRUE 9554663.226 8979866.182 8807738.69 8650011.045 10138980.02 8257666.644 8960487.866 8828353.17 10373381.09 0.921075119 0.865664349 0.849071158 0.833866121 0.9774036 0.796043891 0.863796267 0.851058406 1 23.30638287 -1.141915035 5.062956453 1.000005873 0.870193817 0.409161374 0.049187321 2.99E-06 5.07E-07 0.043681228 0.010295298 0.072124857 1.141915035 -0.129812056 DGYGGS(ph)RDSYSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DGYGGSRDSYSSSR 14 1 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" 1 DGYGGS(0.634)RDS(0.333)YS(0.004)S(0.004)S(0.025)R 107.74 0.0022793 161820000 210460 169300 205500 226420 205540 190490 225790 209870 234930 TRUE FALSE 200511.9729 186551.8625 214922.3783 203659.8314 241386.1109 183893.2835 191341.5886 191492.6702 271361.7445 0.738910244 0.687465592 0.792014286 0.750510474 0.889536258 0.677668416 0.705116297 0.705673051 1 18.04985782 -1.573827754 2.993958488 1.013838678 0.738673764 0.629839403 0.06173775 18636334.32 18031054.26 2022340.278 0.015087857 0.026679166 1.573827754 -0.275164914 DGYGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGYGGSR 7 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 ;;;; 121.99 0.0102 950439000 1208589 1091513 1055487 1237121 1008430 1106707 1284699 1177559 1189513 FALSE TRUE 1151461.393 1202739.416 1103882.123 1112763.247 1184299.873 1068381.459 1088694.572 1074445.691 1373976.601 0.83805022 0.875371105 0.803421341 0.809885151 0.86195054 0.777583445 0.792367622 0.781997081 1 20.389926 3.735910142 24.72866441 0.819259441 0.856710662 0 0.066142413 536.8015339 5008302.409 0.015281385 0.024944686 5443.900032 -3.735910142 0.037451221 DGYGGSRDS(ph)YSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DGYGGSRDSYSSSR 14 1 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" 1 DGYGGSRDS(0.986)YS(0.01)S(0.003)S(0.001)R;DGYGGSRDS(1)YSSSR;DGYGGSRDS(1)YSSSR 189.8 9.64E-08 423030000 745900 609880 636260 708020 706120 623390 759820 699410 770650 TRUE FALSE 710642.7852 672027.4654 665433.1503 636848.4844 829267.1044 601801.848 643895.5039 638165.9526 890158.4661 0.798332895 0.754952619 0.747544595 0.715432711 0.931594919 0.676061478 0.723349301 0.716912749 1 19.76370266 -1.177097906 4.374973453 1.000060881 0.757530698 0.545876772 0.069359932 3.84E-05 7.22E-06 0.062573357 0.014744985 0.06651232 1.177097906 -0.242530182 DGYNYTLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DGYNYTLSK 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;;;; 192.26 8.13E-05 5179580000 4122190 3495517 2484692 3441614 2812781 3222618 3842850 3418206 2793390 FALSE TRUE 3927342.248 3851714.156 2598617.586 3095656.422 3303329.116 3111017.931 3256552.654 3118889.762 3226574.655 1.217186233 1.193747106 0.805379656 0.959425011 1.023788218 0.964185944 1.009290967 0.966625631 1 21.62157198 3.839882773 8.383377097 0.967042237 1.207644967 0.740508006 0.060061074 0.138369626 10.38283121 0.014838162 0.026828797 6916.442532 -3.839882773 0.240602729 DGYRDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DGYRDGPR 8 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 97.431 0.0075121 74918000 106784 63910 104364 90854 134103 89200 138813 102607 171345 FALSE TRUE 101736.5319 70422.50166 109149.1926 81721.18331 157490.5207 86110.98163 117634.5274 93622.18713 197916.3075 0.514038147 0.355819601 0.551491658 0.412907781 0.795743023 0.435087855 0.594365006 0.473039278 1 17.59453096 -4.999999999 0.218141079 3.455498613 0.445605577 0.610438932 0.12096979 93.56298423 0.93524028 100.8932697 0.212613617 1.00E-05 4.999999999 -3.009893035 DGYRDGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DGYRDGYR 8 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 96.331 0.0082232 396828000 257863 157033 272872 232249 395740 213319 366882 272618 490182 FALSE TRUE 245674.327 173034.8412 285383.4511 208902.8893 464756.9307 205931.7095 310907.4126 248746.1227 566196.9211 0.433902619 0.305608941 0.504035682 0.36895801 0.820839735 0.363710402 0.549115336 0.439327932 1 19.11094438 -5 0.196649949 3.374461565 0.373216236 0.578757039 0.141518623 92.61693196 0.913045522 86.37733115 0.32214045 1.00E-05 5 -3.001245329 DGYSYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DGYSYGSR 8 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;; 129.68 0.002513 3218440000 1988710 1700970 1720130 1876900 1779020 1780130 2050170 1954730 1941460 FALSE TRUE 1894707.62 1874300.777 1798999.662 1688230.446 2089280.525 1718483.652 1737378.913 1783563.479 2242531.701 0.844896694 0.835796781 0.802218163 0.752823447 0.931661534 0.766314095 0.774739956 0.79533479 1 21.09669695 -0.651680927 7.295867963 0.999997086 0.813376786 0.571496814 0.050894094 0 0 0.047061899 0.011092596 0.223007297 0.651680927 -0.1866203 DHAISLSEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHAISLSEPR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 115.18 0.0026962 0 86278 87786 84215 95683 119450 91678 115050 83037 111240 FALSE TRUE 82199.80993 96731.4932 88076.34105 86064.76305 140282.0422 88503.16787 97497.00946 75765.84007 128490.5311 0.639734378 0.752829741 0.685469508 0.66981405 1.091769495 0.688791362 0.758787505 0.589660884 1 16.97130252 DHALLEEQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHALLEEQSK 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 150.04 2.23E-05 511510000 1515690 1033980 1004730 1511450 1297540 1149780 1857510 1340850 1073370 FALSE TRUE 1444046.338 1139343.738 1050797.864 1359516.174 1523830.565 1109962.83 1574112.734 1223438.066 1239822.738 1.164719999 0.918956963 0.847538791 1.096540766 1.229071317 0.895259295 1.269627251 0.986784666 1 20.24170244 3.063798994 24.9999929 1.099242691 0.989001951 0.099190703 0.135722951 123.3937862 48351.04596 0.037024006 0.044252148 1158.24116 -3.063798994 -0.11024074 DHASIQMNVAEVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHASIQMNVAEVDK 14 0 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 127.88 7.70E-05 188890000 207250 185250 187260 259830 195690 202290 254760 249570 155910 FALSE TRUE 197453.7032 204127.1856 195846.0562 233711.3948 229818.274 195284.6466 215891.683 227716.3277 180087.7265 1.096430651 1.133487493 1.08750363 1.297764147 1.276146234 1.084386206 1.198813974 1.264474443 1 17.45834034 3.310367316 24.9999997 1.193850402 1.11039886 0.148610007 0.090305714 76.14721253 26509.26955 0.022988891 0.031127098 2043.465529 -3.310367316 -0.083451542 DHASIQMNVAEVDKVTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DHASIQMNVAEVDKVTGR 18 1 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 241.74 3.15E-24 2274380000 1480790 1037770 1351680 1544000 2031460 1367720 2274100 2092030 1687700 FALSE TRUE 1410795.991 1143519.943 1413655.865 1388794.187 2385745.981 1320355.513 1927144.278 1908840.763 1949419.896 0.723700417 0.586594989 0.725167455 0.712414082 1.223823551 0.677306883 0.988573207 0.979183995 1 20.89461344 2.968470651 24.46846376 0.951514752 0.671947195 0.520747359 0.136066799 380.9130864 295609.0257 0.037432067 0.039744768 929.973667 -2.968470651 -0.279567556 DHAVVVGVYRPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHAVVVGVYRPPPK 14 1 P22087 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 104.41 0.00063654 512540000 1340000 1327500 1261900 1559500 1677200 1336500 1709100 1350700 1288900 FALSE TRUE 1276660.856 1462773.759 1319759.363 1402736.097 1969703.149 1290216.67 1448345.405 1232425.547 1488776.029 0.857523785 0.982534465 0.886472738 0.942207605 1.323035239 0.866629127 0.972843045 0.827811251 1 20.5056953 4.956302948 0.933564177 0.98142347 0.747650855 0.070918433 0.134960938 8.379288459 4.406703904 0.041065104 2.181613157 90428.00467 -4.956302948 -0.233772614 DHCMEITIRNS(ph)PYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHCMEITIRNSPYRR 15 2 Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 Q5QPR3 CDK11A Cyclin-dependent kinase 11A 1 DHCMEIT(0.163)IRNS(0.833)PY(0.004)RR 79.511 0.010293 105170000 235870 156240 244970 195830 238550 225720 357670 258850 297730 TRUE FALSE 224720.8925 172161.0336 256202.1168 176144.7963 280153.0445 217903.2598 303100.8724 236183.7217 343900.4478 0.653447514 0.500612996 0.744989192 0.512197054 0.814634137 0.633623077 0.88136225 0.686779338 1 18.39163147 1.221822061 0.312356353 1.034573121 0.548725899 0.528254827 0.106900685 1.053585597 0.350217737 0.195873631 0.137103796 16.66564247 -1.221822061 -0.485847222 DHEKAEFEVHEVYAVDVLVSSGEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHEKAEFEVHEVYAVDVLVSSGEGK 25 1 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 87.659 0.01016 90466000 213460 145881 285140 231080 195836 301530 415020 234430 66589 FALSE TRUE 203370.1688 160746.4398 298213.951 207851.3994 229989.7364 291087.9405 351701.0766 213902.0664 76915.28203 2.644080129 2.089915495 3.877174252 2.70234203 2.990169578 3.784526726 4.572577352 2.781008673 1 16.23098265 3.747961291 24.89426104 3.343236193 2.366997781 0.048006038 0.971076926 1068.077319 2828405.026 0.234861017 0.416361684 5597.077124 -3.747961291 -0.976238412 DHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEK 34 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 156.44 1.83E-11 100220000 123560 108580 159210 154950 102010 183140 231030 127160 19292 FALSE TRUE 117719.5637 119644.4254 166509.936 139374.1316 119800.5117 176797.8159 195782.1303 116025.1963 22283.70483 5.282764449 5.36914424 7.47227345 6.254531402 5.376148743 7.933950715 8.785887797 5.206728287 1 14.44370149 2.290222726 24.9998972 6.693701701 5.893834753 0 2.213169764 434.8554683 210429.4617 0.708281867 0.592590488 195.0844827 -2.290222726 -0.799866948 DHENIVIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DHENIVIAK 9 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 123.75 0.000549 1960420000 6069110 9547800 5996440 9992300 3917510 7540540 6394280 5735140 1374610 FALSE TRUE 5782235.198 10520731.67 6271382.705 8987855.02 4600722.504 7279409.209 5418715.147 5232940.738 1587777.498 3.641716301 6.6260743 3.949786864 5.660651464 2.897586412 4.584653213 3.412767313 3.295764516 1 20.59857733 0.875832276 0.41476422 0.770760161 5.139478982 0.564149675 1.010531968 0.956193935 0.413570066 1.454531865 0.687833966 7.513326744 -0.875832276 4.36871882 DHFEEAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DHFEEAMR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;;; 199.29 9.79E-05 6489140000 7578910 6941020 6411860 7366540 7508740 6990240 9034800 6936920 4512330 FALSE TRUE 7220669.944 7648317.829 6705850.123 6626041.404 8818261.879 6748166.236 7656375.325 6329486.51 5212079.091 1.38537229 1.467421675 1.286597921 1.271285659 1.691889498 1.294716776 1.468967602 1.21438804 1 22.31342755 0.995174387 3.628563881 1.000776527 1.410990168 0.547890999 0.122701563 0.14052688 4.851933381 0.10612668 0.027394624 9.889501181 -0.995174387 0.410213641 DHGDMTNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHGDMTNRK 9 1 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 67.113 0.029504 35815000 42656.7 31465.9 38249 41371.1 46024 39463.2 51441 38035.3 33793 FALSE TRUE 40640.40233 34672.31098 40002.75448 37212.39843 54050.57103 38096.57949 43592.73067 34704.72749 39033.44585 1.041168707 0.888271846 1.024832771 0.953346486 1.384724557 0.975998369 1.116804569 0.889102326 1 15.25242321 DHGLLIYHIPQVEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHGLLIYHIPQVEPR 15 0 Q9Y676 Q9Y676 MRPS18B "28S ribosomal protein S18b, mitochondrial" 0 151.8 1.70E-06 50877000 56754 59299 59604 64091 55023 53352 68355 48418 10101 FALSE TRUE 54071.3509 65341.63552 62336.90236 57648.45092 64618.99378 51504.40686 57926.18932 44178.26324 11667.41149 4.63439135 5.600354077 5.342821962 4.94098035 5.538417311 4.414381622 4.96478498 3.786466542 1 13.5101969 0.631633723 0.969503204 0.984822657 5.177809283 0.926363384 0.363910061 0.268702746 0.417093665 0.317652494 0.102838616 4.281872418 -0.631633723 4.192986626 DHIMEIFSTYGK ddPTM_SK-BR-3_Trastuzumab_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 ; 174.24 3.09E-05 711540000 2776630 2758480 2625560 3263700 2371430 2967900 3424600 2867000 1203530 FALSE TRUE 2645384.203 3039572.248 2745944.523 2935626.675 2785006.641 2865120.879 2902114.373 2615950.281 1390167.286 1.902925087 2.186479483 1.975261935 2.111707494 2.003360797 2.060990003 2.087600825 1.881752152 1 20.40682707 0.764377095 2.9891162 1.000071136 2.051259334 0.946645243 0.077507561 0.275631105 3.240111442 0.06734578 0.017629048 5.812689098 -0.764377095 1.051188199 DHINDIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHINDIIK 8 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 102.61 0.0049323 762710000 1805880 1769350 1266680 1747000 1339530 1614180 2068560 1683860 674780 FALSE TRUE 1720519.631 1949648.777 1324758.531 1571388.241 1573143.608 1558280.542 1752963.18 1536412.292 779421.4361 2.207431759 2.501405127 1.6996691 2.016095745 2.018347886 1.999278529 2.249056927 1.971221499 1 19.57204408 -1.845072455 0.368575832 2.99E-18 2.176618816 0.723039566 0.210173947 19.24684043 1.192386197 17.17058648 0.158286725 0.014286556 1.845072455 2.176618816 DHINLPGFSGQNPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DHINLPGFSGQNPLR 15 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 194.01 6.91E-08 1132840000 1342230 1715250 1203560 1704480 1154910 1301500 1363280 1270160 550735 FALSE TRUE 1278785.448 1890035.925 1258744.416 1533142.432 1356325.938 1256428.729 1155286.598 1158938.057 636140.171 2.0102259 2.971099785 1.978721788 2.410070142 2.132118046 1.975081571 1.816088105 1.821828128 1 19.27898517 1.062305543 0.415994356 0.939720949 2.481916908 0.681022011 0.278849205 0.635352474 0.30360125 0.369239369 0.202291287 11.54265042 -1.062305543 1.542195959 DHINLPGFSGQNPLRGPNDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DHINLPGFSGQNPLRGPNDER 21 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;;; 119.16 3.94E-05 1842940000 960413 706718 936109 884846 1005215 912811 1320300 949682 542629 FALSE TRUE 915016.1808 778733.3677 979030.5236 795899.599 1180524.178 881200.1262 1118863.986 866522.8095 626777.134 1.45987486 1.242440615 1.562007404 1.269828709 1.883483161 1.405922581 1.78510658 1.382505459 1 19.25759302 DHLYGTLDPNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHLYGTLDPNTR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 132.79 0.00017471 582790000 572110 674020 640740 777050 667080 642270 742410 649610 490810 FALSE TRUE 545067.4941 742703.4043 670118.5628 698939.4577 783418.5408 620028.0289 629141.7192 592726.7046 566922.3081 0.961450072 1.310062056 1.182028919 1.232866387 1.381879897 1.093673719 1.109749449 1.045516636 1 19.11279151 1.675249 1.954476389 1.031971588 1.20158041 0.300295319 0.11185206 0.417118101 3.332197742 0.082187579 0.031892195 47.34226147 -1.675249 0.169608822 DHNS(ph)EDEDEDKYADDIDMPGQNFDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHNSEDEDEDKYADDIDMPGQNFDSK 26 1 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 DHNS(1)EDEDEDKYADDIDMPGQNFDSK 256.03 7.73E-53 143290000 176880 283330 190700 294540 81757 293420 197240 206830 33734 TRUE FALSE 168519.2329 312201.6491 199443.7836 264932.2796 96015.39491 283258.7918 167147.4154 188718.8687 38965.29643 4.32485438 8.012300116 5.118497789 6.799185529 2.464125869 7.269514614 4.289648245 4.84325505 1 15.24990217 2.776127292 24.9510467 4.457110805 6.142756753 0.208679264 1.894153077 945.4351173 627937.6647 0.519739511 0.551256631 597.2103038 -2.776127292 1.685645948 DHNVEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHNVEFR 7 0 E7ESL0;J3KQY1;Q9NWU5-2;Q9NWU5-3;Q9NWU5 E7ESL0 MRPL22 "39S ribosomal protein L22, mitochondrial" 0 85.212 0.039007 0 239790 203090 197880 210660 238670 201040 256850 234050 228660 FALSE TRUE 228455.6019 223785.1019 206952.9937 189484.0566 280293.9724 194077.9344 217662.8151 213555.3412 264119.425 0.864970844 0.847287555 0.783558399 0.717418102 1.061239522 0.734811286 0.824107561 0.808555983 1 18.01083088 -1.517377972 2.991683207 1.006068363 0.831176499 0.243899816 0.093918988 65757624.89 73019426.74 3244628.696 0.020150442 0.030382397 1.517377972 -0.174891864 DHNVGSPPKS(ph)PTHASPQHTQTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DHNVGSPPKSPTHASPQHTQTEK 23 1 A0A0C4DGH6;A0JNW5;F8W665;A0JNW5-2 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 DHNVGSPPKS(0.995)PT(0.005)HASPQHTQTEK 218.98 1.08E-32 82978000 35225 43752 37641 56768 31132 42825 53621 43158 5427.5 TRUE FALSE 33559.98406 48210.37854 39366.87708 51061.57279 36561.41094 41341.95951 45440.13163 39378.85673 6269.16898 5.353179052 7.690074824 6.279441056 8.144871027 5.831938979 6.594487984 7.248190594 6.281351938 1 12.6140585 0.938529233 16.99768175 0.999999992 6.757442161 0.824927923 0.824563639 106.3517784 29408.66998 0.716967283 0.179243094 8.680190039 -0.938529233 5.757442169 DHPESYHSFMWNNFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHPESYHSFMWNNFFK 16 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 ; 131.86 2.44E-05 203404000 922410 771550 871260 1046930 930960 934120 1321210 1005540 342060 FALSE TRUE 878809.5073 850171.8222 911208.1328 941690.6074 1093319.129 901771.1902 1119635.149 917489.5869 395104.9178 2.224243404 2.151762187 2.30624346 2.38339379 2.767161531 2.28235881 2.833766674 2.322141653 1 18.59187628 3.462949775 3.077678407 2.410230081 2.189573914 0 0.508079198 0.946549374 18.40390097 0.127392614 0.191251799 2903.686833 -3.462949775 -0.220656168 DHQFLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHQFLEGK 8 0 Q96RS6-2;Q96RS6;Q96RS6-3 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 ; 101.65 0.0086672 160010000 659150 808590 616230 852000 482500 736920 685280 623890 234650 FALSE TRUE 627993.2858 890986.2403 644484.755 766355.3413 566647.8472 711400.2756 580727.95 569258.8842 271038.3236 2.31699074 3.287307229 2.377836265 2.827479639 2.090655815 2.624722092 2.142604567 2.100289275 1 18.04813733 0.426362074 0.374957496 0.784178342 2.80188154 0.714864742 0.31654699 1.331101328 0.351626489 0.804215772 0.240599194 2.669082967 -0.426362074 2.017703198 DHQPCIIFMDEIDAIGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DHQPCIIFMDEIDAIGGR 18 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;;;;; 179.78 8.19E-14 186666800 242552.6 240550.2 222651.3 288333 216958.2 245988.9 278524 241580.3 133074.3 FALSE TRUE 231087.6193 265062.5389 232860.0823 259349.219 254795.6414 237470.2427 236030.0484 220426.2482 153710.7828 1.503392378 1.724423844 1.514923534 1.687254559 1.657630237 1.544915967 1.53554646 1.434032436 1 17.22985885 0.611807757 0.894996534 0.99771779 1.618257409 0.878094953 0.07050408 0.375155042 0.500535913 0.062844033 0.020756021 4.090795381 -0.611807757 0.62053962 DHQPCIIFMDEIDAIGGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHQPCIIFMDEIDAIGGRR 19 1 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ; 147.25 6.97E-08 54878000 22765 14639.1 24869 22381 27798 23328 30295 23266 21020.1 FALSE TRUE 21688.94357 16130.84093 26009.26825 20131.21936 32645.9624 22520.14551 25672.94134 21228.7057 24279.78975 0.893292067 0.664373172 1.071231197 0.82913483 1.344573521 0.927526381 1.057379063 0.874336471 1 14.56746831 3.729182581 24.87457055 1.020038081 0.778832617 0.29962061 0.149878929 598.5507784 1587613.422 0.036024726 0.056638903 5360.219588 -3.729182581 -0.241205464 DHQYQFLEDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DHQYQFLEDAVR 12 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;; 234.04 5.19E-16 2429350000 2726350 3230500 2276610 3142250 2361060 2710640 2849100 2409370 1146160 FALSE TRUE 2597480.839 3559691.623 2380994.82 2826385.06 2772828.116 2616769.857 2414417.468 2198392.79 1323900.639 1.961990773 2.688790622 1.798469425 2.134892134 2.094438234 1.976560612 1.82371501 1.660542132 1 20.33636342 0.759390491 0.416743169 0.909436915 2.276625357 0.716347375 0.225132537 0.808774114 0.326923694 0.364594523 0.154829205 5.746329045 -0.759390491 1.367188443 DHRDNLEFFLAGIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 151.9 1.76E-06 2362407000 3701952 3032769 4134975 4063237 4253739 3731039 5004517 4312806 3350394 FALSE TRUE 3526968.066 3341811.609 4324567.694 3654792.697 4995589.735 3601832.184 4240986.017 3935153.843 3869955.99 0.911371621 0.863527032 1.11747206 0.944401618 1.29086474 0.930716575 1.095874482 1.016847182 1 21.88388573 3.745414376 24.97431919 1.059982978 0.887449315 0.3196142 0.102508347 501.6712262 1828027.658 0.023262014 0.040778234 5564.349185 -3.745414376 -0.172533662 DHRPPCAQEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DHRPPCAQEAPR 12 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;;;; 160.56 4.07E-05 350176000 309646 256898 273416 311746 307689 280860 315296 267500 194255 FALSE TRUE 295009.6472 283076.1983 285952.394 280408.6998 361349.8642 271133.7478 267191.8044 244076.2819 224379.0733 1.314782359 1.261598036 1.274416504 1.24970968 1.610443696 1.208373597 1.190805366 1.087785409 1 17.7755786 1.451862501 1.669823792 1.023103468 1.321121741 0.539340505 0.108169083 0.27726379 1.455541158 0.092137206 0.029610549 28.30495709 -1.451862501 0.298018273 FRCPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FRCPEALFQPSFLGMESCGIHETTFNSIMK 30 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 ;;; 401.33 6.12E-175 1456011000 1368091 562235 1496081 879195 1659403 1212458 2704315 1978441 3097954 FALSE TRUE 1303424.05 619527.3857 1564677.794 790816.6482 1948802.358 1170470.275 2291722.079 1805198.218 3578368.884 0.36425089 0.173131224 0.43726006 0.220999197 0.544606333 0.327096035 0.640437628 0.504475161 1 21.77087069 0.611968239 0.346611003 1.088874006 0.24580227 0.770023685 0.11297393 0.967042122 0.257712187 0.260791032 0.098867213 4.092307301 -0.611968239 -0.843071736 DHS(ph)PTPSVFNSDEERYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHSPTPSVFNSDEERYR 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.895)PT(0.051)PS(0.051)VFNS(0.002)DEERYR;DHS(1)PTPSVFNSDEERYR 118.37 0.00010396 693980000 140948 91898 151678 135411 134914 130787 216849 79471 102512 TRUE FALSE 134285.6674 101262.5107 158632.5863 121799.229 158442.9589 126257.8134 183764.7023 72512.09794 118409.0374 1.134082924 0.855192415 1.339699991 1.02863119 1.33809853 1.066285278 1.551948283 0.612386517 1 16.85341967 3.742560136 24.98580389 1.179122218 0.994637681 0.024967669 0.261958819 788.0438059 4923051.944 0.061439398 0.105875254 5527.899471 -3.742560136 -0.184484537 DHSDSKDQSDKHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHSDSKDQSDKHDR 14 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 ;; 184.76 4.04E-07 157728000 164610 121236 183168 167113 119126 195046 248207 175462 25517.5 FALSE TRUE 156829.2115 133590.0862 191566.434 150314.4837 139901.5367 188291.5081 210338.4635 160097.6171 29474.62357 5.320821524 4.53237633 6.499368295 5.099793162 4.746508003 6.38825828 7.136256142 5.431710322 1 14.84718577 2.255269637 24.9608568 5.707389198 5.201569962 0 1.7354 1237.955064 1849321.988 0.543647285 0.453684717 179.9988112 -2.255269637 -0.505819236 DHSFFIPDIEYLSDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHSFFIPDIEYLSDIK 16 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 ;; 140.96 1.65E-06 106676000 209699 209392 215782 250862 163865 217977 271245 220063 114816 FALSE TRUE 199786.9439 230729.2829 225675.8181 225644.8752 192443.0041 210428.4018 229861.5935 200793.1171 132621.0789 1.506449394 1.739763277 1.701658741 1.701425422 1.451074035 1.586688961 1.733220657 1.514036221 1 17.01695057 0.901609093 6.385698052 1.000005338 1.6348181 0.809893486 0.095559181 0.595899221 38.47020246 0.090405219 0.0227053 7.972767385 -0.901609093 0.634812762 DHSGGIGDICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHSGGIGDICK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 156.01 3.13E-05 1396270000 2087880 1587710 1633830 1867930 1677060 1869200 2712640 2096000 1472050 FALSE TRUE 1989190.05 1749499.454 1708742.722 1680162.128 1969538.733 1804469.135 2298776.947 1912463.128 1700327.996 1.169886078 1.028918808 1.004948884 0.988140013 1.158328709 1.061247677 1.351960888 1.124761301 1 20.69738164 DHSVAESLNYVASWNMSMLQTQDLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DHSVAESLNYVASWNMSMLQTQDLVK 26 0 Q13011 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;;; 259.33 1.57E-52 294326500 369927.5 303991.7 294085.9 358328 320099.7 300204.6 460466 341048.4 233095.8 FALSE TRUE 352441.7602 334968.7998 307570.0294 322308.1887 375924.9863 289808.4394 390213.4547 311184.3941 269243.1062 1.309009412 1.244112819 1.142350621 1.197089847 1.396228827 1.076382023 1.449297849 1.155774788 1 18.03854988 0.993374191 24.8220343 0.999999977 1.262442159 0.367818109 0.109863386 221.5506909 829991.3728 0.094997972 0.023749493 9.848593014 -0.993374191 0.262442182 DHVFLCEGEEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DHVFLCEGEEPK 12 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ; 111.79 0.0013434 355420000 836520 824530 771270 903910 1657080 568090 885770 645480 1392570 FALSE TRUE 796979.3574 908550.5444 806633.4924 813047.2495 1946074.227 548416.9009 750629.5182 588958.3493 1608522.643 0.495472887 0.564835409 0.501474751 0.50546211 1.209851932 0.34094447 0.466657726 0.366148622 1 20.61730481 DHYEATAMHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DHYEATAMHR 10 0 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ;; 148.32 1.77E-05 129332000 164248 120972 91176 85100 120738 85046 111869 156315 38871.7 FALSE TRUE 156484.3225 133299.1843 95356.50979 76545.58632 141794.669 82100.8357 94801.32943 142627.2299 44899.72471 3.48519559 2.968819635 2.123766023 1.70481193 3.158029808 1.828537619 2.111401129 3.176572481 1 15.45441898 8 0.310018074 1.984710011 16.68682101 0.323693627 0.649171343 58.25632346 0.833497156 0.577085843 480.3231341 100000000 -8 14.702111 DIAAHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DIAAHIK 7 0 P63167;F8VXL2;F8VRV5 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 ;;;;;;; 116.54 0.0054322 6399670000 9552880 8962990 7620740 9512700 6995570 8579210 9593250 9283280 6758170 FALSE TRUE 9101334.294 9876328.871 7970158.467 8556465.323 8215595.193 8282109.807 8129623.52 8470386.789 7806192.488 1.165912102 1.265191563 1.021004604 1.09611252 1.052445889 1.060966639 1.041432623 1.085085565 1 22.89618761 3.735048839 24.99881814 1.054412822 1.215551835 0.779365302 0.036362475 108.2680728 770714.9851 0.008628029 0.013995363 5433.114269 -3.735048839 0.161139013 DIAAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 138.38 0.028678 5961470000 8116560 6559580 6511780 8067450 8506480 6660770 8462220 7257590 8781750 FALSE TRUE 7732906.294 7228008.66 6810351.554 7256494.599 9990007.419 6430105.865 7171152.92 6622076.945 10143578.94 0.762344961 0.712569863 0.671395332 0.715378136 0.984860223 0.633908988 0.706964767 0.652834368 1 23.27406343 -1.641676618 2.714859353 1.028735711 0.729807736 0.430587722 0.09756541 20101811.61 18449628.62 4051885.515 0.022057693 0.022820407 1.641676618 -0.298927975 DIAWTEDSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIAWTEDSKR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 170.89 6.72E-06 257020000 280510 264880 206590 269420 154790 242450 227080 244140 182930 FALSE TRUE 267250.8482 291871.5731 216062.3558 242337.3897 181785.327 234053.8957 192434.7754 222761.8073 211297.8501 1.264806282 1.381327699 1.022548766 1.146899458 0.860327386 1.107696532 0.91072756 1.054254964 1 17.68891856 3.730288956 24.24267212 1.009729 1.323066993 0.679975662 0.087917692 177.6950123 520790.8292 0.021090854 0.033305657 5373.892274 -3.730288956 0.313337993 DICNDVLSLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DICNDVLSLLEK 12 0 P63104;E7EX29;B0AZS6;E7ESK7 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 184.03 3.45E-05 290457000 1012986 1117221 917792 1124981 654268 1042588 984786 1075409 709515 FALSE TRUE 965104.1593 1231067.09 959873.671 1011895.773 768372.1321 1006482.916 834538.8089 981240.4869 819542.9625 1.177612649 1.502138566 1.171230448 1.234707415 0.937561747 1.228102689 1.018297816 1.197302072 1 19.64446006 3.267362554 2.090388583 1.088578827 1.334206839 0.368298959 0.125440039 0.272077767 2.439951173 0.035223271 0.049256623 1850.813053 -3.267362554 0.245628012 DIDAFWLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIDAFWLQR 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 168.66 0.00013739 434333000 849190 726860 662730 842880 875730 673470 944190 866500 971550 FALSE TRUE 809050.4716 800927.8604 693116.826 758152.101 1028457.035 650147.565 800136.4743 790624.6664 1122213.012 0.720941981 0.713703951 0.617633924 0.675586625 0.916454384 0.579344169 0.71299875 0.704522812 1 20.09791512 -1.217788342 2.562360608 1.00290329 0.704659518 0.526861642 0.08781051 794713.7891 902799.4803 18463.72204 0.02056036 0.060563597 1.217788342 -0.298243772 DIDEVSSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;;;;; 309.22 1.76E-41 1825632000 2107749 1931222 1676251 2049317 1841000 1797703 2146464 1991668 1882305 FALSE TRUE 2008119.882 2128015.717 1753108.766 1843315.762 2162069.817 1735448.094 1818981.494 1817266.991 2174203.246 0.92361185 0.978756573 0.806322394 0.847812073 0.994419368 0.798199569 0.836619804 0.835831238 1 21.05205538 3.751714588 24.89593468 0.864949754 0.951184214 0.156949033 0.071769967 1037.96752 1964509.007 0.017111968 0.030605627 5645.658284 -3.751714588 0.08623446 DIDFLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIDFLAEK 8 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9;C9J029;H7C5T1;H7C511 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ; 112.84 0.0068939 89753000 324600 350610 251092 332880 198641 284161 302820 318460 191741 FALSE TRUE 309256.8013 386337.5576 262604.8166 299418.27 233283.9275 274320.4333 256619.2473 290573.9541 221475.215 1.39634948 1.744382809 1.185707469 1.351926761 1.053318438 1.238605563 1.158681559 1.311993101 1 17.75678573 3.72207928 24.84659709 1.19463675 1.570366138 0.58892546 0.133431787 410.5922681 618992.4236 0.032055439 0.049820465 5273.261153 -3.72207928 0.375729387 DIDFLKEEEHDCFLEEIMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DIDFLKEEEHDCFLEEIMTK 20 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;;; 214.74 7.47E-25 774415000 2901140 2498340 2560050 3132070 1691074 2968340 3249330 3345310 1364869 FALSE TRUE 2764008.862 2752923.686 2677430.825 2817228.373 1985996.77 2865545.642 2753585.03 3052376.922 1576525.914 1.753227675 1.74619628 1.698310698 1.786985135 1.259729861 1.817633073 1.746615775 1.936141293 1 20.58831745 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;DIDHETVVEEQIIGENS(0.995)PPDY(0.004)S(0.001)EYMTGK;DIDHETVVEEQIIGENS(0.998)PPDY(0.002)S(0.001)EYMTGK 261.87 5.81E-54 996805000 750896 706961 656227 809005 510263 709404 741234 763189 525185 TRUE FALSE 715402.6342 779001.1296 686315.657 727682.2804 599252.7056 684837.1616 628145.1396 696360.1252 606628.0075 1.179310262 1.284149627 1.131361639 1.199552726 0.987842134 1.128924404 1.03547006 1.14791951 1 19.21045258 3.064808795 1.819902137 1.066683419 1.222846602 0.493323129 0.06574038 0.242257571 1.637799373 0.019755356 0.02438867 1160.937381 -3.064808795 0.156163183 DIDIEDLEELDPDFIMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIDIEDLEELDPDFIMAK 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 146.5 1.65E-06 0 100759 94336 85527 100430 65706 96829 101555 97690 65940 FALSE TRUE 95996.32176 103948.9457 89448.49755 90334.5856 77165.1056 93475.78745 86060.91956 89135.74571 76165.63843 1.260362596 1.364774822 1.174394378 1.186028076 1.013122284 1.227269795 1.129917918 1.170288171 1 16.21685266 8 0.115371264 0.948057454 2.140445995 0.48655841 0.077312846 75.1854354 0.600370872 0.578969008 14.34830892 100000000 -8 1.192388542 DIDIHEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 194.22 0.00016651 10972060000 25834010 30388790 25027330 28477780 20968190 25152570 23450020 26228720 17024510 FALSE TRUE 24612887.55 33485442.25 26174857.84 25615139.45 24625035.7 24281530.19 19872288.76 23931994.23 19664584.06 1.251635299 1.702829927 1.331065928 1.302602657 1.252253067 1.234784835 1.010562374 1.217009938 1 24.22909634 2.596656464 0.898966572 1.071276442 1.469406987 0.531589296 0.132090538 0.401124396 0.670947269 0.082581129 0.066024783 395.0540002 -2.596656464 0.398130545 DIDISS(ph)PEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDIS(0.073)S(0.927)PEFK;DIDIS(0.023)S(0.977)PEFK;DIDISS(1)PEFK;DIDIS(0.047)S(0.953)PEFK;DIDIS(0.001)S(0.999)PEFK;DIDIS(0.16)S(0.84)PEFK;DIDIS(0.062)S(0.938)PEFK;DIDIS(0.012)S(0.988)PEFK 299.09 2.22E-32 5573640000 12921760 12294800 12167160 15021510 8213100 13208800 14233830 15078690 8825490 TRUE FALSE 12310974.01 13547654.1 12725036.32 13511519.28 9645462.04 12751375.94 12062197.81 13758319.97 10194101.91 1.207656556 1.328969851 1.248274387 1.325425171 0.946180656 1.250858197 1.183252621 1.349635317 1 23.28123135 -4.475136192 0.251394252 3.11E-23 1.250845476 0.261012306 0.116133523 186.8374139 2.363277655 96.31511397 0.155294223 3.35E-05 4.475136192 1.250845476 DIDLICSNALEYNPDRDPGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIDLICSNALEYNPDRDPGDR 21 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;;; 144.88 1.13E-07 1038090000 1442090 1361810 1360920 1503110 1334460 1404420 1636420 1486980 1486050 FALSE TRUE 1373925.264 1500579.987 1423319.528 1352014.527 1567189.401 1355784.583 1386754.074 1356772.148 1716499.044 0.80042297 0.874209626 0.829199138 0.787658188 0.913015015 0.789854552 0.807896794 0.790429889 1 20.71103762 -1.596995292 2.987328471 1.010879263 0.825998041 0.647949705 0.040729033 10133743.1 9746711.504 854726.5236 0.009461885 0.025293254 1.596995292 -0.184881222 DIDPQNDLTFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DIDPQNDLTFLR 12 0 Q9NP97;B1AKR6;Q8TF09;H3BQI1 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 ;; 151.79 0.00015851 313809000 334983 266664 266094 320806 287281 278045 336970 308777 310547 FALSE TRUE 319149.0175 293837.3648 278294.6731 288557.9714 337382.7154 268416.2319 285559.0376 281738.849 358705.0427 0.889725483 0.819161511 0.775831505 0.804443587 0.940557492 0.748292329 0.796083142 0.785433198 1 18.4524385 DIDTHTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIDTHTHR 8 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 106.91 0.0071454 32409000 272980 231968 241384 273657 262471 261688 303078 242275 84811 FALSE TRUE 260076.7764 255605.8029 252451.6952 246148.4784 308245.8593 252625.6789 256837.8847 221060.1166 97963.05673 2.65484546 2.609206077 2.577009167 2.512666373 3.146552074 2.578785181 2.621783081 2.256566138 1 16.57995017 0.728199444 1.685602214 1.00043214 2.675661228 0.900979253 0.174184024 0.2683147 1.199792891 0.156366884 0.044497455 5.34809907 -0.728199444 1.675229088 DIEDVFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIEDVFYK 8 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 157.54 0.0008731 329711000 977040 867692 826083 1055120 651728 891814 990280 1000150 677649 FALSE TRUE 930857.2555 956110.8013 863959.7227 949057.333 765389.1569 860930.2576 839194.5983 912571.5639 782735.346 1.18923626 1.221499459 1.10376991 1.212488152 0.977839011 1.099899554 1.072130705 1.16587499 1 19.57816507 2.761331479 24.99185726 1.070967151 1.184873459 0.489368068 0.059866505 660.9713861 725439.5088 0.01689012 0.017903057 577.2068533 -2.761331479 0.113906308 DIEEHLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DIEEHLQR 8 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;; 166.3 0.00031929 786790000 1384850 1208610 1197890 1367540 1294960 1271070 1472940 1393270 1239120 FALSE TRUE 1319390.885 1331768.733 1252814.441 1230072.281 1520800.614 1227052.527 1248215.951 1271267.893 1431276.401 0.921828156 0.930476274 0.875312721 0.859423295 1.062548515 0.857313463 0.872099861 0.888205724 1 20.44887087 -0.839458609 9.685199705 1 0.908339265 0.187783515 0.059868654 0 0 0.054561515 0.012860272 0.144724278 0.839458609 -0.091660735 DIEEIIDELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DIEEIIDELK 10 0 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ;;;; 205.14 4.05E-07 42969100 246980 229000 199396 233506 135078.5 191416 203924 238126 138820 FALSE TRUE 235305.7449 252335.3604 208538.5038 210033.5332 158636.1476 184787.2159 172811.6485 217274.4251 160347.4966 1.467473767 1.573678203 1.300541064 1.309864748 0.989327249 1.152417218 1.077732126 1.355022246 1 17.2908423 3.322910816 1.696460541 1.123186834 1.519237123 0.649499527 0.114869485 0.183768024 1.088448783 0.033619 0.051069611 2103.346464 -3.322910816 0.396050289 DIEIS(ph)T(ph)EEEKDTGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIEISTEEEKDTGDLK 16 1 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 2 DIEIS(1)T(1)EEEKDTGDLK 125.88 0.00017104 52148000 236390 259240 180290 263150 113200 284310 203710 257700 84331 TRUE FALSE 225216.3132 285656.8507 188556.4748 236697.662 132942.0442 274464.2734 172630.2981 235134.4218 97408.62078 2.312077836 2.932562318 1.93572677 2.429945729 1.364787255 2.817658963 1.772228133 2.413897456 1 16.57176184 -1.308218586 0.201047655 1.33E-13 2.625548778 0.402985557 0.471040692 20.96071023 0.822735467 13.09635091 1.223891152 0.049179195 1.308218586 2.625548778 DIEIS(ph)TEEEKDTGDLKDSSLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 DIEIS(0.554)T(0.446)EEEKDTGDLKDSSLLK;DIEIS(0.909)T(0.091)EEEKDTGDLKDSSLLK 204.79 5.88E-23 120296000 324022 302319 291350 323307 122660 383312 361858 400148 132920 TRUE FALSE 308706.1222 333125.6498 304708.6857 290807.5661 144051.8652 370037.8093 306649.9161 365108.9198 153532.5547 2.01068837 2.169739508 1.98465196 1.894110123 0.938249646 2.410158614 1.997295731 2.378055393 1 17.22818507 3.363159849 3.576906511 1.836869145 2.087592423 0.061722989 0.491192217 0.787312117 19.42125109 0.133142994 0.185243509 2307.596381 -3.363159849 0.250723278 DIEREDIEFICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DIEREDIEFICK 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;; 239.87 3.16E-16 3836486000 5900890 5462110 5240990 6013480 4059790 5606020 5863740 6255520 4370490 FALSE TRUE 5621966.624 6018705.219 5481294.576 5408993.566 4767816.091 5411882.122 4969118.768 5707753.506 5048243.268 1.11364812 1.192237557 1.085782575 1.071460561 0.944450542 1.072032752 0.98432633 1.130641533 1 22.26735 3.352584029 2.361751585 1.026004121 1.151743016 0.442606052 0.054887169 0.215014857 2.438640677 0.014788914 0.02147703 2252.081114 -3.352584029 0.125738895 DIFDCLEGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIFDCLEGAAR 11 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1;E9PL88;C9JDU0 Q9Y5U2-2 TSSC4 Protein TSSC4 0 ; 119.16 0.001452 41836000 32769 28644 32498 34436 42182 28080 38150 28459 63827 FALSE TRUE 31220.07431 31562.85617 33988.06544 30974.42786 49538.52744 27107.58256 32329.51683 25966.97909 73724.96518 0.42346679 0.428116257 0.461011617 0.420134859 0.671936939 0.367685254 0.438515186 0.352214193 1 16.16986562 -1.076998685 4.185245546 1.000073392 0.445039581 0.801412625 0.086764278 34667516.33 89447946.04 39753.23191 0.019310125 0.083753182 1.076998685 -0.555033811 DIFQEIFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIFQEIFDK 9 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 97.456 0.01172 0 18042 17316 14663 20824 11177 11495 14460 16087 13190 FALSE TRUE 17189.19042 19080.52009 15335.31305 18730.73196 13126.26526 11096.92527 12253.86142 14678.337 15235.43783 1.128237377 1.252377535 1.006555454 1.229418686 0.861561407 0.728362741 0.804299919 0.963433881 1 13.89514334 2.726898824 21.38681142 0.843125794 1.159440539 0.6533243 0.101095749 55.13195752 101106.8303 0.030476764 0.029045359 533.2106604 -2.726898824 0.316314745 DIFQEIYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIFQEIYDK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 123.63 0.0034739 0 51325 55528 34547 54364 43553 45444 57803 50635 47170 FALSE TRUE 48898.96897 61186.36633 36131.01412 48899.22744 51148.62941 43870.26289 48984.09073 46201.13097 54484.88269 0.897477732 1.12299712 0.66313833 0.897482476 0.938767359 0.805182295 0.899040033 0.847962383 1 15.73356838 3.762375578 24.99940444 0.863320812 1.010237401 0.256084064 0.103244477 905.9816779 951037.5265 0.024039032 0.043307637 5785.962016 -3.762375578 0.146916589 DIGKPEVEYDCDNLQHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIGKPEVEYDCDNLQHSK 18 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 0 131.71 9.82E-06 127610000 212070 178690 169100 227520 133560 196680 218100 221130 116830 FALSE TRUE 202045.8714 196898.7142 176853.4023 204649.2573 156852.8217 189868.9223 184824.8393 201766.6849 134947.3997 1.497219449 1.459077497 1.310535828 1.516511306 1.162325632 1.406984667 1.369606526 1.495150595 1 17.04203765 -3.26129146 0.303241636 3.35E-31 1.429590821 0.567176406 0.108496339 60.5523398 1.470166076 38.66845926 0.100525216 0.000547909 3.26129146 1.429590821 DIGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIGRPK 6 1 Q8TBC4;F8W8D4;Q8TBC4-2;S4R3U2;Q8IZ07;H0YIN8 Q8TBC4;Q8IZ07 UBA3;ANKRD13A NEDD8-activating enzyme E1 catalytic subunit;Ankyrin repeat domain-containing protein 13A 0 69.39 0.085391 96750000 229810 189310 193640 241580 189780 205180 239530 243030 220230 FALSE TRUE 218947.3367 208600.9042 202518.5855 217295.9194 222877.5719 198074.5652 202985.2992 221749.0048 254382.1436 0.86070246 0.820029666 0.796119502 0.854210584 0.876152582 0.778649642 0.797954197 0.871716079 1 17.95663788 0.912876647 5.104011176 0.999981772 0.826043236 0.760200414 0.03070541 0.283174158 15.66164906 0.030224336 0.007635413 8.182323524 -0.912876647 -0.173938536 DIHLDLPSNNNLVSKDTEEPLPVKESDQTLAALLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIHLDLPSNNNLVSKDTEEPLPVKESDQTLAALLSPK 37 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 DIHLDLPSNNNLVSKDTEEPLPVKESDQTLAALLS(1)PK 143.78 2.08E-13 134610000 294240 129450 325730 223940 188300 316900 458710 387090 164730 TRUE FALSE 280331.8583 142641.1022 340665.0427 201429.1257 221139.4604 305925.6735 388725.3647 353194.3475 190275.4871 1.473294656 0.749655693 1.790377983 1.058618369 1.162206776 1.607803918 2.042960818 1.856226217 1 17.53773019 2.127845137 4.57709955 1.765035117 1.216644841 0.165252156 0.382364403 0.244679961 8.732857295 0.136403621 0.098757091 134.2286237 -2.127845137 -0.548390277 DIHTLAQLISAYSLVDPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIHTLAQLISAYSLVDPEK 19 0 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 156.73 1.30E-08 131760000 393230 403690 345350 443160 286050 410810 424420 425320 233370 FALSE TRUE 374642.7972 444826.47 361184.6391 398612.7149 335937.0294 396583.5467 359666.934 388076.726 269559.8277 1.389831713 1.650195705 1.33990529 1.478754154 1.24624293 1.471226444 1.334274981 1.439668252 1 18.04024598 -3.565415936 0.190377642 3.71E-13 1.521048671 0.599336132 0.107623947 46.25959564 0.740856401 18.3866152 0.280495975 0.000272009 3.565415936 1.521048671 DIHTLAQLISAYSLVDPEKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIHTLAQLISAYSLVDPEKAK 21 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 76.768 0.0064203 17234000 46886 36958 44039 40803 40511 49846 61921 50707 36852 FALSE TRUE 44669.7917 40724.06222 46058.23171 36701.40492 47576.10557 48119.82052 52473.81419 46266.82627 42566.81995 1.049404014 0.956709058 1.082021907 0.862206878 1.117680523 1.130453733 1.232739826 1.08692231 1 15.37744169 2.508775798 23.26909554 1.140347424 0.994093443 0.345098832 0.0821707 246.1273835 180926.6296 0.024176093 0.022764549 322.6827862 -2.508775798 -0.146253981 DIHYSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIHYSVK 7 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 136.11 0.0030116 463790000 1076500 772360 841520 1083060 1378260 841460 1667520 1275840 1433850 FALSE TRUE 1025615.978 851064.3621 880104.5244 974188.7511 1618628.108 812320.0292 1413109.198 1164120.686 1656204.135 0.619256985 0.513864411 0.531398579 0.588205723 0.977311959 0.490470958 0.853221634 0.702884784 1 20.65944907 1.082460387 0.237143313 1.08668569 0.480882894 0.439457583 0.140360746 2.311959742 0.490991545 0.537020512 0.358724437 12.09094892 -1.082460387 -0.605802796 DIICQIAYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIICQIAYAR 10 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 81.95 0.045305 215220000 308760 277370 245720 290600 209990 287880 309110 300960 241370 FALSE TRUE 294165.5267 305634.3183 256986.5051 261388.3359 246612.1895 277910.6434 261949.5923 274606.3469 278800.4269 1.055111465 1.09624767 0.921757933 0.937546398 0.884547389 0.996808529 0.93955951 0.984956695 1 18.08887324 3.740256711 24.99990701 0.948528257 1.075679573 0.660223948 0.036764558 72.28089692 1065395.879 0.008872081 0.014994527 5498.658032 -3.740256711 0.127151316 DIIHDPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DIIHDPGR 8 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;;;;;;;;; 135.79 0.00081866 16620200000 21261520 18499450 19873660 23468100 20449890 20786980 24378210 22063400 19891230 FALSE TRUE 20256530.09 20384564.99 20784886.97 21109042 24016344.34 20067121.67 20658866.33 20131411.73 22975860.36 0.881644029 0.887216612 0.904640203 0.918748707 1.045285964 0.873400228 0.899155288 0.876198385 1 24.45361555 DIIHFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIIHFFR 7 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 134.66 0.0031526 244300000 638410 513800 469340 550950 605140 465180 673310 567890 553590 FALSE TRUE 608233.6245 566156.8041 490859.7032 495567.4593 710676.2244 449070.7 570584.1933 518162.541 639437.9099 0.951200445 0.885397621 0.76764248 0.775004815 1.111407712 0.702289766 0.892321498 0.810340665 1 19.28644475 4.260032173 3.012604114 0.858038341 0.941643341 0.042651167 0.119039499 0.711988618 12.98396657 0.027336779 0.085299432 18198.35668 -4.260032173 0.083605 DIILREDLEELQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIILREDLEELQAR 14 1 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ; 140.03 9.17E-06 63081000 79833 60717 64552 87146 82541 63762 81072 68824 76959 FALSE TRUE 76059.4523 66904.13133 67511.77305 78385.91851 96936.12427 61553.90595 68702.97741 62797.4057 88893.40867 0.855625332 0.752633208 0.75946883 0.881796746 1.09047595 0.692446233 0.772869197 0.706434894 1 16.43978883 -1.630141321 7.596487398 1.000292505 0.811305148 0.207040274 0.114310306 0.000551826 2.69E-05 0.107854931 0.025382969 0.023434661 1.630141321 -0.188987357 DIINMLFYHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIINMLFYHDR 11 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 132.47 0.00018178 166060000 378070 362060 246952 307670 294410 253415 336220 309340 217732 FALSE TRUE 360199.3804 398954.3256 258274.9935 276742.4271 345755.0108 244639.175 284923.4639 282252.5497 251496.7665 1.432222709 1.5863199 1.026951547 1.100381651 1.37478909 0.972732884 1.132911042 1.122290968 1 17.94018033 3.739414549 24.99999466 1.113719965 1.50927132 0.677784057 0.115944486 37.35946995 1093737.2 0.028271311 0.047447756 5488.005642 -3.739414549 0.395551354 DIIRQPS(ph)EEEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK 274.08 2.23E-32 6626570000 4433149 2158935 4311347 4148901 4015119 5016769 6985050 4105266 4695089 TRUE FALSE 4223602.832 2378932.931 4509026.524 3731845.589 4715354.482 4843037.032 5919352.333 3745787.146 5423179.423 0.77880566 0.438660193 0.831435985 0.688128734 0.869481556 0.893025411 1.091491148 0.690699469 1 22.37070747 2.835495741 1.256007721 0.946776262 0.629383912 0.377530083 0.142639102 0.372044563 1.215103333 0.059136417 0.060787455 684.692769 -2.835495741 -0.317392351 DIISDTSGDFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 198.55 2.92E-07 583030000 1021820 756210 548220 1148820 688030 785450 779830 762160 567940 FALSE TRUE 973520.5937 833268.6587 573356.4293 1033338.431 808022.2142 758249.6696 660852.6109 695421.2299 656013.2346 1.483995356 1.270200988 0.874001314 1.575179244 1.231716331 1.15584508 1.007376949 1.060071952 1 19.32336539 7.999999999 0.163143891 0.941707519 2.918282741 0.311859624 0.181328104 70.22587757 0.735947818 0.493523595 33.55369624 99999999.87 -7.999999999 1.976575223 DIISIAEDEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIISIAEDEDLR 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 268.73 9.55E-22 986260000 1202200 1494520 1109570 1450510 971830 1187500 1129170 1266130 914040 FALSE TRUE 1145374.389 1646813.287 1160444.882 1304701.979 1141316.844 1146376.577 956894.3779 1155260.945 1055784.655 1.084856067 1.559800362 1.099130279 1.235765241 1.081012912 1.085805303 0.906334804 1.094220246 1 20.00988417 2.770561294 1.165655343 0.995494784 1.302174707 0.375682121 0.137211667 0.40415934 1.142437853 0.063028566 0.060491479 589.6051849 -2.770561294 0.306679923 DIISIAEDEDLRVHFEESSKLEDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DIISIAEDEDLRVHFEESSKLEDLLR 26 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;;;;;;; 206.46 1.80E-25 467436500 320815.2 172558.8 295860.8 289628.3 259717.1 285091 424393.9 362545.5 247930.6 FALSE TRUE 305650.9013 190142.7379 309426.3103 260514.313 305011.68 275218.2272 359644.816 330799.094 286378.4112 1.067297287 0.663956257 1.080480575 0.909685587 1.065065201 0.96102994 1.255837738 1.155111842 1 18.12756321 2.500833351 1.086687742 1.146295976 0.893508302 0.23788906 0.137897616 0.535605212 1.278437399 0.077487833 0.056155343 316.835146 -2.500833351 -0.252787674 DIKDTTVGTLSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DIKDTTVGTLSQR 13 1 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;; 118.19 0.0004077 741470000 1028470 791190 896190 1039940 859890 1019770 1259200 1130060 1019020 FALSE TRUE 979856.2613 871813.1605 937281.198 935403.2554 1009854.544 984455.1092 1067085.913 1031105.956 1177044.417 0.83247178 0.740679916 0.796300619 0.794705146 0.857957889 0.836378895 0.906580837 0.876012783 1 20.16673733 1.369375319 0.478464679 0.999888149 0.777674375 0.818736552 0.030043947 0.330760422 0.203355613 0.031508842 0.018805174 23.40859347 -1.369375319 -0.222213775 DIKEES(ph)DEEEEDDEESGR ddPTM_SK-BR-3_Trastuzumab_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 240.75 3.49E-24 1366560000 848020 747350 665450 877500 449230 867590 773090 912590 384560 TRUE FALSE 807935.7752 823505.8147 695961.5407 789292.0329 527575.5698 837545.1408 655140.9217 832678.7817 444195.6007 1.818873879 1.853926093 1.56679071 1.776901958 1.187710029 1.885532273 1.474892864 1.874576831 1 18.76083558 -2.656267124 0.222382824 7.50E-19 1.794347224 0.45510025 0.226475616 39.98679824 1.014052706 20.41391551 0.409717853 0.002206647 2.656267124 1.794347224 DIKEES(ph)DEEEEDDEESGRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIKEESDEEEEDDEESGRLR 20 2 Q96EV2;A8MTF7;Q96EV2-2;H7BXM6;H7C0H2 Q96EV2 RBM33 RNA-binding protein 33 1 DIKEES(1)DEEEEDDEESGRLR;DIKEES(1)DEEEEDDEESGRLR 163.46 1.02E-11 347740000 285750 154003 235915 219416 180658 237597 352750 298540 246570 TRUE FALSE 272243.1638 169696.0808 246731.9361 197359.8868 212164.698 229368.9563 298931.5088 272398.2549 284806.8163 0.955887107 0.59582872 0.866313311 0.692960546 0.744942487 0.805349251 1.049593941 0.956431656 1 18.11962415 1.828889396 4.878332269 1.002338856 0.765990367 0.542523759 0.097600997 0.155940001 5.733359786 0.043212608 0.024553057 67.43562644 -1.828889396 -0.23634849 DIKWDFTPCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIKWDFTPCK 10 1 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 121.02 0.00047978 518640000 1654550 1054370 1166800 1151790 1438160 1291400 2222080 1886150 1657880 FALSE TRUE 1576342.701 1161811.502 1220298.934 1036009.881 1688974.649 1246678.494 1883060.885 1720988.707 1914975.563 0.823165961 0.606697821 0.637239951 0.54100423 0.881982351 0.651015354 0.983334159 0.898700088 1 20.86889455 1.792464324 1.40834936 0.982823615 0.676674087 0.557429506 0.108696912 0.286894296 1.077327729 0.07890333 0.03186567 62.01037023 -1.792464324 -0.306149527 DILETHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DILETHLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 167.33 0.00031328 517900000 643890 691680 432260 704590 573710 610020 657630 581560 498150 FALSE TRUE 613454.5958 762162.9784 452079.5486 633763.2746 673764.8424 588894.8544 557296.4653 530635.5234 575400.5578 1.066134865 1.324578101 0.785677981 1.101429719 1.170949234 1.023452005 0.96853654 0.922201962 1 19.13420709 3.168861094 0.445611567 0.960678579 1.189107306 0.096806101 0.137401822 2.593127532 0.965491281 0.122082687 0.267539224 1475.234616 -3.168861094 0.228428727 DILGEAGLHFDELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DILGEAGLHFDELNK 15 0 J3QRH2;A0A087X2B4;J3KRU2;J3QR43;J3QRC6;Q8IY31-4;Q8IY31;Q8IY31-3;Q8IY31-2 J3QRH2 IFT20 Intraflagellar transport protein 20 homolog 0 ; 124.45 9.65E-05 79376000 143247 120453 146388 153874 118319 154445 169498 169101 127694 FALSE TRUE 136475.9982 132727.2976 153100.0346 138406.2932 138953.7961 149096.5309 143637.9671 154293.62 147496.1333 0.925285261 0.899869675 1.037993547 0.938372349 0.942084331 1.010850437 0.973842255 1.046085863 1 17.17031761 3.921462974 0.353105028 1.013387173 0.868785978 0.341796562 0.039629278 3.56612907 0.546256233 0.038095216 0.210187884 8345.703936 -3.921462974 -0.144601195 DILIQYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DILIQYDR 8 0 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;; 190.26 0.0004359 3737460000 4043970 4258250 3132070 4121260 3642670 3351840 3933980 3785260 3495980 FALSE TRUE 3852819.552 4692170.516 3275678.508 3706983.115 4277950.495 3235764.94 3333779.099 3453802.567 4038118.723 0.9541125 1.161969431 0.811189252 0.917997555 1.059391956 0.801305054 0.825577287 0.855299907 1 21.9452519 3.732753399 24.99860965 0.886752821 1.058040967 0.327292831 0.096003821 450.5718357 1939599.19 0.024895275 0.039737626 5404.473593 -3.732753399 0.171288146 DILKPEIMEEIVMETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DILKPEIMEEIVMETR 16 1 A3KFL2;Q13868-3;Q13868-2;Q13868 A3KFL2 EXOSC2 Exosome complex component RRP4 0 ;; 150.59 6.61E-07 54628900 67096 71283 55308 79886 50016 66164 70572 72008 52393 FALSE TRUE 63924.50505 78546.81874 57843.92651 71855.70751 58738.77456 63872.72409 59804.94526 65702.59778 60517.83885 1.056291934 1.297911826 0.95581613 1.187347547 0.970602647 1.055436303 0.988220108 1.085673233 1 15.88507285 3.2871907 1.306747335 1.024837862 1.162943076 0.168389173 0.096483828 0.555733774 1.989227744 0.031480218 0.049728731 1937.27244 -3.2871907 0.138105213 DILLRPELEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 149.69 6.15E-05 278319000 509996 467432 411095 662009 584098 456138 557039 473279 499165 FALSE TRUE 485889.4998 515063.8522 429944.1124 595462.5976 685964.5063 440341.8267 472052.4698 431836.1818 576572.9588 0.842719889 0.893319474 0.745688999 1.032761923 1.189727156 0.763722648 0.818721139 0.748970577 1 19.13714365 -0.942464652 4.0414403 1.000006255 0.878690515 0.069333203 0.13877251 1.9964E+11 4.03382E+11 18333820.03 0.03314241 0.114165622 0.942464652 -0.12131574 DILLVNDHLLNFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DILLVNDHLLNFVR 14 0 Q9NTI5-2;Q9NTI5;Q9NTI5-3 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 179.12 1.90E-06 49313000 125520 120080 106050 121830 123320 101830 126620 118820 111670 FALSE TRUE 119586.9184 132316.2885 110912.4974 109583.4169 144826.969 98303.60157 107301.7935 108415.4909 128987.2133 0.927122273 1.025809343 0.859872034 0.849568063 1.122800976 0.762118966 0.831879306 0.840513475 1 16.97686853 2.201272585 24.99999973 0.84030671 0.954392852 0.190097029 0.097646882 228.205578 153000.5987 0.033686586 0.024879801 158.9544115 -2.201272585 0.114086142 DILQDVHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DILQDVHDK 9 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 89.9 0.011794 282900000 193730 190950 171830 248590 145120 218300 231510 231030 131050 FALSE TRUE 184572.7668 210408.0221 179708.5755 223601.2609 170428.8821 210740.2163 196188.8975 210799.7884 151372.5647 1.219327738 1.390001038 1.187193834 1.477158436 1.125890166 1.392195585 1.296066417 1.392589132 1 17.20774422 -0.850029317 6.762080171 0.999999995 1.310239652 0.447941418 0.10817313 7.83E-09 1.16E-09 0.087598229 0.0206471 0.14124422 0.850029317 0.310239658 DILQDYTHEFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DILQDYTHEFHK 12 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 78.287 0.015113 31932000 56709 51506 48388 70448 52869 60381 64634 54398 12490 FALSE TRUE 54028.47796 56754.51996 50606.63766 63366.4332 62089.33686 58289.99083 54772.89622 49634.62274 14426.88541 3.744985589 3.933941273 3.507800625 4.39224624 4.303724269 4.040372483 3.796584963 3.440425381 1 13.81647225 0.586884459 1.514353583 1.000442922 3.967099782 0.930980454 0.251920522 0.421105329 1.255164086 0.242814976 0.070243061 3.862642007 -0.586884459 2.96665686 DILYIGDHIFGDILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DILYIGDHIFGDILK 15 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 100.42 0.0021637 23171000 181980 176760 147550 177520 118240 156530 176830 167080 98919 FALSE TRUE 173378.166 194772.045 154315.3134 159675.3523 138861.0186 151109.3269 149851.3358 152449.5895 114258.8533 1.517415596 1.704656045 1.350576423 1.397487789 1.215319553 1.322517446 1.311507436 1.334247501 1 16.80194643 7.999999999 0.077573562 0.656770082 3.260567419 0.688911209 0.101693237 105.24691 0.59696719 3.129287406 29.48001347 99999999.87 -7.999999999 2.603797337 DIMEDTIEDKLDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIMEDTIEDKLDTK 14 1 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 171.46 2.75E-06 69736000 174270 170050 140930 196190 77424 174990 169440 207860 88641 FALSE TRUE 166032.6025 187378.2883 147391.7799 176468.6085 90926.72109 168930.0524 143588.816 189658.6765 102386.9936 1.621618105 1.830098549 1.439555697 1.723545172 0.88806906 1.649917109 1.40241266 1.852370793 1 16.64367293 3.397836607 1.874894259 1.41826102 1.716583667 0.14123078 0.302193897 0.600392089 4.290529513 0.084751312 0.133307954 2499.404842 -3.397836607 0.298322647 DIMLATGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIMLATGK 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 ; 98.392 0.019671 0 427940 387000 333070 411940 345580 379370 473460 434570 381150 FALSE TRUE 407712.1243 426435.74 348341.589 370531.0086 405849.0426 366232.3218 401224.9813 396516.747 440256.7954 0.926077981 0.968606832 0.791223651 0.841624735 0.921846174 0.83186069 0.911343074 0.900648783 1 18.74798575 -1.021512987 5.270998702 1.00000075 0.892180986 0.311544493 0.052382869 4.75E-07 8.82E-08 0.052216936 0.012307564 0.095167139 1.021512987 -0.107819764 DIMLATGKLS(ph)PDAIPGK ddPTM_SK-BR-3_Trastuzumab_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 DIMLAT(0.031)GKLS(0.969)PDAIPGK 76.704 0.011713 87412000 181270 183420 164720 199210 121340 193120 175180 211680 115090 TRUE FALSE 172701.7263 202110.7065 172272.5749 179185.0323 142501.6576 186432.206 148453.0736 193144.177 132937.5694 1.299119031 1.520343026 1.295890813 1.347888585 1.071944208 1.402404202 1.116712712 1.45289385 1 17.02038936 -4.999999998 0.092630194 0.003774313 1.560052755 0.313739794 0.139769187 210.2584305 1.346143608 41.34566812 2.693805589 1.00E-05 4.999999998 1.556278441 DINAVLIDMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 165.66 4.96E-05 170810200 254653 222446 223526 264470 253410 218515 257817 244400 266513 FALSE TRUE 242616.0574 245113.5003 233774.8882 237884.9731 297604.6238 210947.7708 218482.2815 222999.0404 307842.4749 0.788117551 0.796230281 0.759397768 0.772749028 0.966743215 0.685245825 0.70972104 0.724393346 1 18.23183278 DINAYNCEEPTEKLPFPIIDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DINAYNCEEPTEKLPFPIIDDR 22 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 281.24 1.02E-45 10098751000 6691384 4940418 5982541 6365313 4982783 6616802 7690664 6733344 6075820 FALSE TRUE 6375095.539 5443852.211 6256846.422 5725459.644 5851778.778 6387660.488 6517311.958 6143736.704 7018027.135 0.908388557 0.77569552 0.891539218 0.815821816 0.833821053 0.910178938 0.928653001 0.875422193 1 22.7426341 1.176304631 0.560358351 0.995541897 0.839204427 0.503975533 0.044373579 0.620670545 0.492932093 0.043924809 0.021242275 15.00737143 -1.176304631 -0.15633747 DINKAMY(ph)VS(ph)EKLEAGTVFINTY(ph)NK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DINKAMYVSEKLEAGTVFINTYNK 24 2 A0A494C1M4;Q3SY69 A0A494C1M4 ALDH1L2 Mitochondrial 10-formyltetrahydrofolate dehydrogenase 3 DINKAMY(0.993)VS(0.991)EKLEAGT(0.104)VFINT(0.084)Y(0.828)NK 44.555 0.068499 793150000 288160 312270 274330 331010 272880 270050 311460 276760 286000 TRUE FALSE 274539.2479 344090.668 286908.3018 297736.2459 320470.1856 260698.1008 263941.0566 252525.4272 330351.4193 0.831052122 1.041589798 0.868494231 0.901271278 0.97008872 0.789153869 0.798970554 0.764414537 1 18.33364202 2.233948987 24.99989198 0.817830005 0.927005802 0.176790194 0.085307121 143.2113821 776348.0622 0.028542877 0.021785739 171.3755993 -2.233948987 0.109175797 DINLDVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DINLDVNR 8 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ;; 160.88 0.00081608 444380000 1515330 1232690 1015380 1131210 1472250 1116170 1614830 1418220 1501580 FALSE TRUE 1443703.354 1358302.512 1061936.177 1017498.622 1729009.934 1077516.753 1368458.025 1294033.138 1734437.357 0.83237561 0.783137256 0.612265512 0.58664478 0.996870787 0.621248584 0.788992476 0.746082372 1 20.72603631 -0.653787536 1.041749561 1.009904308 0.749802922 0.301575479 0.121374424 77.90584904 43.61096449 3.187570788 0.034006136 0.221928187 0.653787536 -0.260101386 DINTFVGT(ph)PVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DINTFVGTPVEK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 DINT(0.001)FVGT(0.999)PVEK;DINTFVGT(1)PVEK 235.35 5.37E-15 112543000 385810 611790 355450 584230 272450 499710 379860 488580 315300 TRUE FALSE 367573.5259 674132.0965 371747.7341 525502.0904 319965.1937 482404.9174 321905.3804 445797.3451 364195.1137 1.00927638 1.851019059 1.020737841 1.442913622 0.878554329 1.324578225 0.883881657 1.224061851 1 18.47435204 3.013885796 1.607225188 1.064557129 1.395352609 0.140952287 0.277655295 0.551522546 2.912732062 0.091824644 0.110055298 1032.489863 -3.013885796 0.330795481 DINWDSSQWQPLIQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DINWDSSQWQPLIQDR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 143.38 3.30E-06 63014000 82429 58246 69949 77661 77266 69406 97219 81888 92146 FALSE TRUE 78532.74453 64181.33362 73156.23084 69854.36873 90741.16594 67002.45282 82386.456 74717.4526 106435.5311 0.73784331 0.603006656 0.687329035 0.656306856 0.852545809 0.629512083 0.774050312 0.701997273 1 16.69962032 -5 0.218242783 2.516725979 0.662096866 0.634547302 0.070842561 88.43269324 0.883980762 58.79723428 0.123571761 1.00E-05 5 -1.854629113 DIPGLTDTTVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIPGLTDTTVPR 12 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 228.64 2.35E-11 79243000 61722 62228 56996 64491 63119 65894 68366 70679 75579 FALSE TRUE 58804.52338 68569.10395 59609.32298 58008.24216 74126.93362 63612.07426 57935.51107 64489.97207 87299.40532 0.673595922 0.785447549 0.682814766 0.664474654 0.849111553 0.728665608 0.663641532 0.73872178 1 16.41368421 -1.29141381 2.177502706 1.007945159 0.722540254 0.686384018 0.058775708 109246.0794 99421.16815 5642.022914 0.014663335 0.051119452 1.29141381 -0.285404905 DIPGLTDTTVPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIPGLTDTTVPRR 13 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 146.79 6.81E-05 90773000 74448 35389 70450 56247 99078 64144 106120 74757 134900 FALSE TRUE 70928.99058 38995.17933 73680.20218 50592.9447 116357.1718 61922.6772 89929.44497 68210.88077 155819.603 0.455199405 0.250258495 0.472855794 0.324689216 0.746742833 0.397399788 0.577138198 0.437755452 1 17.24951722 -4.999999999 0.164740303 3.121377975 0.305620732 0.637568372 0.130695023 75.5780802 0.703711853 52.24558337 0.460151066 1.00E-05 4.999999999 -2.815757243 DIPRT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.989)PS(0.011)R;DIPRT(0.999)PS(0.001)R;DIPRT(0.757)PS(0.243)R;DIPRT(1)PSR;DIPRT(0.995)PS(0.005)R 140.48 0.001049 7008890000 2211580 1947020 1751350 2203050 1890650 1735070 2054630 2084260 1964660 TRUE FALSE 2107042.996 2145423.552 1831651.13 1981595.228 2220378.761 1674984.091 1741158.458 1901751.145 2269329.439 0.92848705 0.94539978 0.807133199 0.873207387 0.978429453 0.738096489 0.767256806 0.838023388 1 21.11383463 2.238437905 25 0.808380029 0.907794752 0.114643708 0.083258948 4.445280817 905272.2144 0.028045918 0.022051186 173.1561435 -2.238437905 0.099414723 DIPSFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DIPSFER 7 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;; 200.12 0.0008406 91436000 320597 359626 320873 381222 305598 327181 318803 318234 303245 FALSE TRUE 305443.0152 396272.2983 335585.3444 342900.8403 358894.1944 315850.6399 270163.7471 290367.7439 350270.6858 0.872019919 1.131331608 0.958074307 0.978959571 1.024619556 0.90173301 0.771299906 0.828981001 1 18.41811073 2.062418956 4.701083574 0.839927645 0.997857466 0.302987892 0.08626024 0.186019988 8.265270096 0.031899065 0.022591651 115.4566511 -2.062418956 0.157929821 DIPVTIHNLEEYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIPVTIHNLEEYLR 14 0 Q14669-3;Q14669;Q14669-2;Q14669-4;H7C2Y1 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 0 ; 166.9 3.73E-06 44781000 46204 43197 39385 46489 47045 41810 47524 46961 39868 FALSE TRUE 44020.02849 47598.82341 41190.84121 41815.8374 55249.63311 40362.10922 40273.34096 42848.84588 46050.52582 0.955907185 1.033621714 0.894470594 0.908042561 1.199761178 0.876474448 0.874546821 0.930474628 1 15.49093001 DIPVVIDADGLWLVAQQPALIHGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIPVVIDADGLWLVAQQPALIHGYR 25 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 141.08 3.78E-07 52411000 69892 48926 55242 67438 58564 59929 69734 63936 55801 FALSE TRUE 66588.34367 53911.61502 57774.90034 60659.00412 68777.54306 57853.6437 59094.79755 58337.42489 64454.33409 1.033108861 0.836431185 0.896369517 0.941115985 1.067073984 0.89759121 0.916847538 0.905097007 1 15.97598975 4.744555844 6.051113987 0.928174537 1.036037229 0.198554522 0.062932655 0.200230132 32.35819852 0.014648868 0.08904405 55533.60211 -4.744555844 0.107862692 DIQDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIQDLK 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 97.068 0.09653 190980000 559470 628860 488610 691730 519860 533430 578870 600510 397550 FALSE TRUE 533024.9619 692941.549 511013.2518 622195.9862 610523.4194 514957.1853 490552.7498 547926.1609 459200.0236 1.160768586 1.509018975 1.112833679 1.354956346 1.329536995 1.121422384 1.068276839 1.19321893 1 18.80876319 2.193859822 5.824444426 1.09613068 1.305449899 0.413991749 0.116575367 0.174136038 13.94205533 0.040891144 0.030453981 156.2643186 -2.193859822 0.209319219 DIQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 135.82 0.031258 332871000 371302 321935 338119 428086 473697 364762 430974 426666 474244 FALSE TRUE 353751.2903 354740.5425 353622.0906 385053.982 556309.6068 352130.2005 365221.0009 389304.8631 547787.3374 0.645782161 0.647588066 0.645546303 0.702926037 1.015557624 0.642822819 0.666720415 0.71068613 1 19.06325639 -5 0.218096979 2.465227294 0.662895647 0.403024162 0.111337649 159.4699114 1.594017543 102.94355 0.217187026 1.00E-05 5 -1.802331647 DIQNTQCLLNVEHLSAGCPHVTLQFADSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIQNTQCLLNVEHLSAGCPHVTLQFADSK 29 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 181.95 5.76E-18 447080000 344900 254270 317270 425090 379180 320190 459600 455990 114280 FALSE TRUE 328597.2605 280180.4021 331817.1433 382359.1456 445308.8719 309101.74 389479.5789 416061.0982 132001.9587 2.489336247 2.122547307 2.513728936 2.896617211 3.373502001 2.341645101 2.950559087 3.151931246 1 17.01019981 3.46772451 5.941113202 2.744036562 2.306320098 0.013562133 0.658257601 0.367710183 49.15681675 0.158938785 0.225357543 2935.786774 -3.46772451 -0.437716464 DIQRPDSEHGLS(ph)PDSENFDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIQRPDSEHGLSPDSENFDWK 21 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 DIQRPDS(0.01)EHGLS(0.99)PDSENFDWK 153.87 2.36E-08 74275000 129920 102710 111070 138120 94505 120880 128310 134520 82148 TRUE FALSE 123778.9391 113176.2658 116162.6694 124235.9152 110986.6421 116693.8953 108733.9529 122740.7157 94887.09229 1.304486586 1.192746696 1.224219929 1.309302585 1.169670599 1.229818435 1.145929866 1.293544914 1 16.53392423 -4.793983193 0.213124905 1.90E-11 1.260672005 0.623032166 0.056586227 84.12806493 0.909815833 36.06511635 0.10604817 1.61E-05 4.793983193 1.260672005 DIREEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DIREEAEK 8 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 147.75 0.00048539 3255260000 5868320 4833000 5140610 5837190 4388050 5658300 6188370 6118150 4734260 FALSE TRUE 5590936.143 5325488.195 5376312.053 5250424.571 5153324.531 5462351.652 5244220.499 5582412.352 5468424.862 1.022403395 0.973861455 0.983155514 0.96013472 0.942378228 0.998889404 0.959000193 1.020844666 1 22.3826939 1.228570474 24.99363676 1.010422341 0.978386335 0.270456449 0.022666365 327.6753619 819759.4693 0.020751967 0.005436451 16.92662895 -1.228570474 -0.032036006 DIREEAEKYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIREEAEKYAK 11 2 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 93.959 0.0049836 209356000 295900 82403 319950 185331 279740 264530 512210 334920 418480 FALSE TRUE 281913.3934 90799.95938 334620.024 166701.1758 328526.5674 255369.2598 434062.9571 305592.6293 483375.7411 0.583217918 0.187845503 0.692256552 0.344868726 0.679650507 0.528303839 0.897982501 0.632205142 1 18.88278555 1.794399431 0.528189773 0.973608038 0.395929405 0.492973021 0.168284997 0.5868262 0.369149161 0.149323982 0.098030081 62.28728929 -1.794399431 -0.577678633 DIRPVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIRPVCR 7 1 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 128.57 0.0034156 2527360000 185857 130621 134946 164561 150653 130791 150350 141982 184637 FALSE TRUE 177071.9079 143931.4284 141133.4076 148019.0156 176926.8355 126261.6749 127411.3461 129549.3034 213269.563 0.830272757 0.674880308 0.661760664 0.694046603 0.829592526 0.592028572 0.597419268 0.607443939 1 17.70231856 -0.964465 4.743967722 1.000003834 0.686514199 0.574037688 0.085023068 3.61E-06 7.88E-07 0.086222828 0.020322667 0.108526301 0.964465 -0.313489635 DIS(ph)ENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;DIS(1)ENKR 125.71 0.0024638 2075390000 3376740 2914930 3023000 3423390 1925396 3497800 3528390 3635890 2164811 TRUE FALSE 3217128.192 3211964.681 3161607.54 3079264.333 2261184.453 3376670.309 2990069.302 3317512.197 2500518.834 1.286584268 1.284519292 1.264380615 1.231450166 0.904286112 1.350387873 1.195779557 1.326729538 1 21.25379604 -2.320600167 1.975519317 3.99E-05 1.232617414 0.254160504 0.124052854 1883186.224 215042.9595 8411085.634 0.028720762 0.004779691 2.320600167 1.232577518 DISDIEGEKDGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DISDIEGEKDGIR 13 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;;; 119.87 0.00028716 553600000 1853650 1690560 1728360 2081900 1277250 1751460 1881210 1980290 1368600 FALSE TRUE 1766031.638 1862829.986 1807607.016 1872623.457 1500001.996 1690806.501 1594196.864 1806885.309 1580835.498 1.117150798 1.178383196 1.143450421 1.184578319 0.948866595 1.069565115 1.008452091 1.142993886 1 20.59225582 2.75645136 24.9643414 1.035283938 1.154643883 0.567118728 0.052915186 550.1927086 767725.7004 0.014519556 0.015369476 570.7571491 -2.75645136 0.119359945 DISDIEGEKDGIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DISDIEGEKDGIRK 14 2 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 108.71 0.00045541 539420000 610880 465300 536090 648770 371800 618910 682700 706230 442330 FALSE TRUE 582004.913 512714.599 560670.2568 583554.407 436641.8023 597476.9915 578541.5764 644388.7572 510924.2773 1.139121664 1.003504084 1.097364681 1.142154391 0.854611577 1.169404192 1.132343093 1.261221645 1 18.96274996 DISENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;; 187.55 0.00093429 47635860000 23577380 19365280 18957210 22745600 16619840 21509180 24789370 22438120 19275980 FALSE TRUE 22462923.97 21338624.05 19826416.83 20459169.07 19518334.83 20764311.7 21007296.32 20473319.26 22265200.53 1.00888038 0.958384544 0.890466574 0.918885462 0.876629645 0.932590375 0.943503576 0.919520991 1 24.40828727 4.145190065 2.542296671 0.923051896 1.000637217 0.377562453 0.033338103 0.242657329 3.079471327 0.00801025 0.023301441 13969.79602 -4.145190065 0.077585321 DISGPS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DISGPSPSK 9 0 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DISGPS(1)PSK;DISGPS(0.989)PS(0.011)K;DISGPS(0.999)PS(0.001)K 199.21 2.63E-05 682164000 1715950 1817240 1457390 2018750 965610 1859960 1709760 1900940 1034730 TRUE FALSE 1634840.444 2002418.822 1524212.773 1815821.415 1134012.078 1795549.119 1448904.71 1734483.616 1195190.644 1.367849098 1.675397003 1.275288408 1.519273452 0.948812714 1.502311893 1.21227916 1.451219205 1 20.18880933 -3.212232616 0.072838431 1.38E-11 1.875129689 0.261574886 0.196782174 225.3104044 1.690242901 45.74094241 9.502014715 0.000613433 3.212232616 1.875129689 DISGPS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DISGPSPSKK 10 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DIS(0.004)GPS(0.97)PS(0.026)KK;DISGPS(0.863)PS(0.137)KK;DISGPS(0.983)PS(0.017)KK;DIS(0.036)GPS(0.841)PS(0.122)KK;DISGPS(0.834)PS(0.166)KK;DISGPS(0.989)PS(0.01)KK 142.51 3.77E-05 2312400000 4554530 4790690 3892580 5209470 2193030 4977220 4266090 5076960 2046980 TRUE FALSE 4339246.393 5278866.758 4071058.643 4685804.178 2575493.738 4804857.623 3615219.618 4632394.468 2364415.204 1.835230287 2.232631032 1.721803614 1.981802591 1.08927304 2.032154765 1.529012169 1.959213619 1 21.17305197 -1.955649404 0.149696161 8.05E-15 2.164390398 0.382908647 0.315405766 41.52238118 0.912611772 17.26005856 1.786315397 0.011075175 1.955649404 2.164390398 DISILQCHGDCDPLVPLMFGSLTVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DISILQCHGDCDPLVPLMFGSLTVEK 26 0 B4DP64;E5RGR0;O75608-2;O75608;A0A087X1K9 B4DP64 LYPLA1 Acyl-protein thioesterase 1 0 215.37 4.21E-34 78109000 208150 95300 159360 191160 175990 164060 246810 213120 191870 FALSE TRUE 198311.162 105011.1783 166666.8136 171944.2336 206682.6003 158378.5611 209154.6015 194458.083 221624.2197 0.894808168 0.473825372 0.752024368 0.775836837 0.932581288 0.714626593 0.943735309 0.877422528 1 17.75775603 2.169633069 0.595715817 0.971835005 0.68416658 0.33425045 0.123672259 0.840573652 0.597517299 0.108574958 0.076964291 147.7859233 -2.169633069 -0.287668425 DISLDSELHDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;; 242.82 2.59E-16 141818000 293544 243302 264798 301034 296257 262494 331061 289531 264038 FALSE TRUE 279668.7569 268094.7504 276939.2502 270773.4904 347924.127 253403.767 280551.5641 264178.1307 304983.6645 0.916995857 0.879046262 0.908046176 0.887829487 1.140795942 0.830876524 0.919890462 0.866204199 1 18.21837245 DISLSDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DISLSDYK 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 182.39 0.00053234 7287600000 16562000 13723970 11820600 14221410 11246800 14157000 17237400 14973520 11656990 FALSE TRUE 15779147.08 15122458.15 12362586.2 12791846.85 13208238.36 13666739.54 14607518.04 13662359.21 13464696.47 1.171890292 1.123119127 0.918148153 0.950028608 0.980953294 1.015005393 1.084875405 1.014680074 1 23.68267837 3.902455622 6.029397632 1.002443948 1.15402247 0.67300173 0.044487729 0.13950177 7.084132761 0.013065754 0.023953845 7988.323098 -3.902455622 0.151578522 DISMEIDS(ph)PENMMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR 268.2 4.14E-25 173348000 252770 254670 237496 281710 253850 244610 287730 269090 272080 TRUE FALSE 240822.063 280621.1625 248385.4265 253391.9756 298121.3596 236139.0944 243831.504 245527.0531 314272.7768 0.766283563 0.892922274 0.790349801 0.806280385 0.948607012 0.751382594 0.775859451 0.781254602 1 18.26165778 -2.231291555 2.230709963 1.60489307 0.81561424 0.4766008 0.061200285 2994014.967 478897.2797 9157982.384 0.015185299 0.005870951 2.231291555 -0.78927883 DISPVLKDPASFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DISPVLKDPASFR 13 1 H3BQB1;P07741-2;P07741;H3BQZ9;H3BQF1;H3BSW3 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;; 176.89 1.45E-05 3031330000 8600650 7709980 7525440 8960150 7272980 8456210 9767120 9321500 8431750 FALSE TRUE 8194114.319 8495635.728 7870488.868 8059458.699 8541385.409 8163369.327 8276966.459 8505260.044 9739302.727 0.841345068 0.872304308 0.808116257 0.827519066 0.877001737 0.838188272 0.849852057 0.873292502 1 23.21538706 0.625179766 1.732409002 0.999993686 0.845957068 0.857202691 0.019771931 0.592600207 2.295536118 0.018288208 0.005163338 4.218710913 -0.625179766 -0.154036618 DISQNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 137.18 0.0046628 9823890000 7705150 5905220 5384660 6238220 5537360 5827670 7992090 6668420 6586830 FALSE TRUE 7340942.83 6506968.632 5631551.987 5611142.274 6503073.831 5625856.327 6772749.886 6084497.793 7608281.956 0.96486209 0.855248093 0.740187078 0.737504512 0.854736177 0.739438464 0.890181243 0.799720335 1 22.85913928 -0.25034083 11.15053112 0.999999734 0.830781682 0.359247178 0.073707146 0 0 0.073963472 0.017433358 0.561900178 0.25034083 -0.169218052 DISSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DISSALR 7 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 ; 133.47 0.0076042 406300000 260705 198750 201091 225301 259070 190465 288150 251183 273350 FALSE TRUE 248381.9913 219002.851 210311.2213 202653.3154 304251.726 183869.1493 244187.4253 229188.0849 315739.7219 0.78666691 0.693618306 0.666090475 0.641836618 0.963615614 0.582344053 0.773382024 0.725876629 1 18.26837625 DISTNKVEQIPYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DISTNKVEQIPYGER 15 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 80.534 0.015219 180940000 127200 106300 131240 126280 106790 117030 141230 125840 105570 FALSE TRUE 121187.5081 117132.0909 137257.4838 113586.0945 125414.1422 112977.2218 119682.7696 114820.7825 121941.2564 0.993818759 0.96056162 1.125603326 0.931482074 1.02847999 0.92648891 0.981478895 0.941607343 1 16.89582679 2.246428624 24.99959132 0.961833365 1.002102046 0.144911443 0.053986345 372.3126306 1182978.088 0.017429157 0.014332387 176.3715875 -2.246428624 0.040268681 DISTNYYASQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DISTNYYASQK 11 0 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 149.96 0.0039558 0 73091 49848 60597 63753 77676 66176 81121 70027 91712 FALSE TRUE 69636.13328 54927.56787 63375.43239 57344.42732 91222.66981 63884.30853 68744.50156 63895.06464 105934.2286 0.657352531 0.518506328 0.598252645 0.541321045 0.86112554 0.603056343 0.648935689 0.603157879 1 16.69280929 -5 0.259408182 3.411379872 0.593492929 0.609888896 0.093023874 126.635391 1.244439128 162.7181195 0.116558263 1.00E-05 5 -2.817886943 DISTNYYASQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DISTNYYASQKK 12 1 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 179.41 3.33E-05 484980000 777240 422560 855440 786300 782320 922500 1402200 1152800 1109100 FALSE TRUE 740501.4055 465619.3444 894662.7701 707259.6301 918756.3603 890553.5937 1188268.637 1051854.721 1281093.564 0.578022891 0.363454597 0.698358649 0.552074923 0.717165698 0.695151095 0.92754243 0.821060031 1 20.28894441 2.220958246 0.577004864 0.986104582 0.471000315 0.75387958 0.09154675 0.344613828 0.231994301 0.076650816 0.057905781 166.3252734 -2.220958246 -0.515104267 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 289.23 5.90E-62 2522230000 2790600 3090600 2609670 3298110 1678140 3082070 3001420 3262140 1636700 TRUE FALSE 2658693.868 3405535.654 2729325.951 2966577.717 1970807.085 2975337.143 2543498.254 2976489.728 1890511.077 1.406336044 1.801383602 1.443697413 1.569193512 1.042473175 1.573826876 1.34540246 1.574436545 1 20.85034487 -3.457834408 0.153717759 2.76E-16 1.644868104 0.345795624 0.198196122 80.52246848 1.130747213 27.05592552 0.941892477 0.00034847 3.457834408 1.644868104 DITDTLVAVTISEGAHHLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DITDTLVAVTISEGAHHLDLR 21 0 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ;; 233.49 5.45E-30 140587000 214357 165479 171705 204494 222046 157166 239231 196080 28081.5 FALSE TRUE 204224.7694 182341.4982 179577.8441 183937.8746 260770.7521 151723.302 202731.9172 178910.1957 32436.2356 6.296192072 5.62153699 5.536334312 5.670752823 8.039488778 4.677586631 6.250167858 5.5157509 1 14.98531878 0.095661726 1.135791547 0.9790606 6.006907352 0.770154084 0.853573877 3.209795155 3.591354879 0.913950655 0.225602269 1.246412299 -0.095661726 5.027846751 DITLFHAMDTLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DITLFHAMDTLYR 13 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 ; 136.3 7.40E-05 329650000 177927 173987 171963 184713 175280 153196 198270 172919 152439 FALSE TRUE 169516.7433 191716.4731 179847.6736 166145.2983 205848.7765 147890.7841 168020.27 157777.2957 176078.4616 0.962734123 1.088812745 1.021406435 0.943586722 1.169074143 0.839914109 0.954235223 0.896062439 1 17.42585892 2.219287015 24.99999257 0.919727205 1.032442878 0.370656815 0.074002208 246.98759 320368.1704 0.024825355 0.01836204 165.6864584 -2.219287015 0.112715673 DITSSIHFEAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DITSSIHFEAYR 12 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 206.69 8.72E-08 408390000 478150 316030 225260 279760 632090 269850 612500 404790 619170 FALSE TRUE 455548.7971 348233.8163 235588.3938 251637.9933 742326.2959 260505.0268 519051.8757 369344.4417 715187.7213 0.636963952 0.486912465 0.329407772 0.351848872 1.037946086 0.364247063 0.725756134 0.516430065 1 19.44796244 -2.891161723 0.239567016 1.815278569 0.498035084 0.311287533 0.210466619 64.37055868 1.582313714 26.90767354 0.321560598 0.001284808 2.891161723 -1.317243485 DIVEAHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIVEAHYR 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;; 160.88 0.00035078 2032490000 2909510 2879280 2272690 2580140 3122760 2359510 3447800 2741880 3078620 FALSE TRUE 2771983.228 3172681.905 2376895.084 2320779.425 3667368.355 2277799.577 2921774.787 2501786.452 3556036.666 0.779514805 0.892196061 0.668411298 0.652630904 1.031307801 0.640544457 0.821637981 0.703532243 1 21.76183877 -1.179844018 4.84070172 1.000023292 0.78256128 0.254111971 0.120994662 2.73E-05 4.63E-06 0.105281698 0.024812478 0.066093079 1.179844018 -0.217462012 DIVENYFMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DIVENYFMR 9 0 Q13263;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;; 248.99 1.26E-10 2402261000 1319828 1047823 942397 1073751 1300837 981971 1406825 1104650 1366734 FALSE TRUE 1257442.346 1154597.355 985606.8346 965815.5095 1527702.561 947965.098 1192188.008 1007920.99 1578680.128 0.796514964 0.731368777 0.62432333 0.611786702 0.967708742 0.600479528 0.755180221 0.638458021 1 20.59028745 -1.675448182 2.649425653 1.038499173 0.721030158 0.39330351 0.110784252 24843884.1 20628461.24 6431221.864 0.025963489 0.021113091 1.675448182 -0.317469016 DIVHSGLAYTMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIVHSGLAYTMER 13 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 192.65 2.54E-06 240950000 363830 338460 302670 294350 295490 283400 330410 326100 282220 FALSE TRUE 346632.4769 372949.4588 316547.7189 264761.3788 347023.3624 273585.7869 279999.8861 297544.9552 325985.2362 1.063337963 1.144068557 0.971049249 0.812188251 1.064537052 0.839258213 0.858934255 0.912755923 1 18.3144471 3.568319961 4.540218935 0.904926832 1.10181819 0.497405847 0.076940586 0.148543299 5.248202363 0.01930298 0.03016647 3701.007465 -3.568319961 0.196891357 DIVNGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIVNGLR 7 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 92.319 0.036657 252330000 156030 124080 112380 122060 143950 124670 163850 122300 150680 FALSE TRUE 148654.7711 136723.8931 117532.7342 109790.2969 169054.8344 120352.6466 138851.6732 111590.7636 174046.6848 0.854108605 0.785558732 0.6752943 0.630809469 0.9713189 0.691496346 0.797784073 0.641154204 1 17.40911481 DIVNMLMHHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 92.925 0.0055701 162405000 311430 359160 217104 297470 273980 239840 283900 271110 59125 FALSE TRUE 296709.3211 395758.8123 227058.4331 267567.7504 321762.0253 231534.2807 240585.8408 247370.1712 68293.80303 4.344600944 5.794944706 3.324729669 3.917892086 4.711438095 3.39026779 3.522806318 3.622146669 1 16.05946705 0.166956823 0.243677378 8.14E-15 5.17749171 0.709451935 0.658380773 3.213102135 0.357484817 4.760643137 1.355713303 1.468780248 -0.166956823 5.17749171 DIVQETQREEDHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIVQETQREEDHRR 14 2 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 60.401 0.055997 107990000 73332 53444 66218 63825 82869 60620 80373 77883 72233 FALSE TRUE 69865.74169 58890.00436 69254.1608 57409.18974 97321.32736 58520.7142 68110.6227 71063.15164 83434.52472 0.837372082 0.705822974 0.830042012 0.68807475 1.166439525 0.701396866 0.816336198 0.851723575 1 16.34835687 DIVQFVPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIVQFVPYR 9 0 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 101.54 0.0091025 25949000 56842 51849 43983 46942 65613 46756 69313 53473 55550 FALSE TRUE 54155.19131 57132.47205 45999.66406 42223.30098 77055.88643 45136.828 58738.02883 48790.62064 64164.41029 0.844006686 0.890407498 0.716903091 0.65804861 1.200913187 0.703455822 0.915430042 0.760400048 1 15.96948569 DIVQFVPYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIVQFVPYRR 10 1 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 ; 115.57 0.0019319 790420000 732380 443140 513130 532050 718160 541800 885160 684250 913170 FALSE TRUE 697761.8488 488296.4698 536657.5181 478567.3232 843406.8766 523037.3301 750112.5849 624333.4426 1054779.74 0.66152375 0.462936907 0.508786335 0.453713041 0.799604737 0.495873508 0.711155663 0.591908831 1 20.00851033 -0.773372008 0.332381859 1.179652987 0.53500241 0.596400316 0.109287932 7.379412015 0.728884605 1.438920545 0.091710266 0.168510898 0.773372008 -0.644650577 DIWAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DIWAELR 7 0 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 ;;; 98.457 0.026169 121979000 379897 361945 320526 345323 341249 266841 321365 327196 311000 FALSE TRUE 361940.0217 398827.607 335222.4341 310610.476 400762.7176 257600.2293 272334.867 298544.9837 359228.2916 1.007548765 1.1102344 0.933173812 0.864660393 1.115621255 0.717093378 0.758110854 0.831073138 1 18.45454145 2.234644286 24.99940629 0.798046845 1.010788676 0.410287717 0.104504974 81.41930126 519723.2678 0.036572693 0.028024659 171.6501892 -2.234644286 0.21274183 DIWDFLR ddPTM_SK-BR-3_Trastuzumab_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 ; 105.39 0.018466 25974000 219760 277350 220920 238880 212934 185152 260851 221360 197794 FALSE TRUE 209372.3803 305612.2803 231049.4005 214867.3286 250069.6222 178740.1398 221053.3891 201976.5449 228466.8833 0.916423323 1.337665555 1.011303683 0.940474722 1.094555231 0.782345945 0.967551121 0.884051736 1 17.80162553 3.4885489 22.87114363 0.943569378 1.134951156 0.256697801 0.12690711 196.7442189 393760.331 0.032387074 0.047120098 3079.98712 -3.4885489 0.191381777 DIWSWVPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIWSWVPER 9 0 Q9ULP9-2;Q9ULP9;H3BV07;A0A2R8Y518 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 0 120.15 0.0016539 16592000 28910 26604 22437 30223 29215 18565 27032 28933 25541 FALSE TRUE 27543.48159 29314.97785 23465.75864 27184.92662 34310.08675 17922.08939 22907.77192 26399.47314 29501.76783 0.933621393 0.993668515 0.79540178 0.921467716 1.162984094 0.607492049 0.776488109 0.89484377 1 14.84851379 2.23316723 24.99999955 0.791531346 0.953934009 0.204572445 0.133378926 176.4826271 818042.2366 0.045933359 0.0349026 171.0673901 -2.23316723 0.162402663 DIYDKDNYELDEDTD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIYDKDNYELDEDTD 15 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 135.6 0.00022848 40457000 125470 126030 128730 142960 97095 135140 154540 142260 113560 FALSE TRUE 119539.2818 138872.6003 134632.3978 128589.3892 114028.3373 130460.0679 130962.0847 129802.9602 131170.3048 0.91132884 1.058719811 1.026393878 0.980323934 0.869315181 0.994585383 0.998412597 0.989575807 1 17.00108162 2.045343093 24.99993218 0.995991021 0.975320103 0.05188344 0.052687861 566.2140408 312179.7197 0.020474039 0.015121074 111.0051412 -2.045343093 -0.020670918 DIYLS(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIYLSPDR 8 0 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(1)PDR 79.07 0.030408 98315000 93533 89228 82120 110080 83563 85398 97147 103550 88957 TRUE FALSE 89111.88045 98320.43464 85885.28323 99014.54926 98136.36074 82440.64585 82325.44092 94482.61305 102751.9972 0.867252052 0.956871275 0.835850256 0.963626518 0.955079837 0.802326457 0.801205263 0.91952094 1 16.64880691 2.246368357 24.99961926 0.855238166 0.915483382 0.002468999 0.070768617 325.1748653 1041178.305 0.023024738 0.018929744 176.3471143 -2.246368357 0.060245216 DIYLS(ph)PDRTGSSFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DIYLSPDRTGSSFGK 15 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(1)PDRTGSSFGK;DIYLS(0.786)PDRT(0.143)GS(0.057)S(0.014)FGK 200.99 4.02E-09 264960000 470330 387610 440430 483680 380650 482320 579460 515200 464740 TRUE FALSE 448098.433 427107.8997 460624.1511 435059.5675 447035.2395 465617.1375 491052.7345 470086.3568 536809.5056 0.834743849 0.795641462 0.858077486 0.810454291 0.83276327 0.867378712 0.914761623 0.875704234 1 19.03405069 1.060954755 0.461618064 1.004299753 0.812287101 0.842198793 0.023165861 0.368493182 0.208245488 0.027411219 0.01423559 11.50680505 -1.060954755 -0.192012652 DIYQDLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIYQDLNR 8 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 115.49 0.0057067 69749000 148090 123080 101380 117310 156430 107770 162270 143860 154950 FALSE TRUE 141090.0792 135621.9919 106028.3733 105517.7759 183711.3425 104037.8979 137512.7312 131262.8558 178978.8546 0.788305856 0.757754273 0.592407262 0.589554426 1.026441603 0.581285974 0.768318311 0.73339868 1 17.44942963 0.081986789 1.639934758 1.000100746 0.731508392 0.296231235 0.130937714 28.63174628 48.92615878 0.12009789 0.032512542 1.207777095 -0.081986789 -0.268592354 DIYQFLCNASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DIYQFLCNASER 12 0 O75509 O75509 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 0 73.985 0.087764 68619000 34627 32473 32885 38949 32760 31892 31722 34196 35571 FALSE TRUE 32990.25033 35782.03562 34392.80978 35033.77252 38473.33363 30787.57204 26882.22629 31201.61696 41087.16901 0.802933157 0.870881019 0.837069348 0.852669419 0.936383172 0.749323275 0.654273023 0.759400506 1 15.32640031 2.202045622 24.28386146 0.749952289 0.85491165 0.045197408 0.095269103 180.0130862 119714.1279 0.032361201 0.023901199 159.2375996 -2.202045622 0.104959362 DKADKDEQIR ddPTM_SK-BR-3_Trastuzumab_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 ;; 95.401 0.0041887 339544000 436640 378395 385790 440630 261660 440460 476870 491080 300894 FALSE TRUE 416000.8925 416953.8807 403478.8531 396337.0353 307293.4212 425206.7598 404114.7232 448078.4318 347555.1048 1.196935067 1.199677044 1.160906134 1.140357399 0.88415741 1.223422571 1.162735686 1.289229897 1 18.40688221 3.458670632 2.985652182 1.124413998 1.197448329 0.083361062 0.111488514 0.709254291 12.9126029 0.031099271 0.046736277 2875.217032 -3.458670632 0.073034331 DKAIT(ph)PPLPESTVPFSNGVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKAITPPLPESTVPFSNGVLK 21 1 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 DKAIT(1)PPLPESTVPFSNGVLK 92.833 0.0029257 65486000 197630 177460 168570 229300 129020 223850 220600 223710 159120 TRUE FALSE 188288.4216 195543.3758 176299.1012 206250.3284 151521.0472 216098.0184 186943.4184 204120.7664 183795.5169 1.024445126 1.063918092 0.959213283 1.122172792 0.824400125 1.17575239 1.017127194 1.110586209 1 17.48774205 DKALQDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKALQDYR 8 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;H0YJT1;H0YJD2;H0YJY8;H0YJE9 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 77.677 0.029725 455240000 1392870 1007490 1055680 1116820 1167000 1158360 1508390 1318030 1293180 FALSE TRUE 1327031.796 1110154.376 1104083.972 1004555.132 1370524.431 1118245.703 1278257.402 1202616.306 1493719.75 0.888407478 0.743214634 0.739150682 0.672519147 0.917524476 0.748631531 0.855754503 0.805115087 1 20.51047807 0.093623555 0.573713319 1.012783314 0.784238023 0.437210392 0.073909479 3.39435878 1.407230632 0.171220229 0.030021819 1.240576515 -0.093623555 -0.228545291 DKANMQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 138.4 0.00042487 1904743000 2944620 2077779 1753122 2212775 2236198 2154303 3098277 2486184 2242127 FALSE TRUE 2805433.648 2289507.042 1833504.378 1990342.653 2626190.223 2079698.947 2625577.94 2268480.549 2589824.604 1.083252373 0.884039421 0.707964692 0.768524112 1.014041731 0.803026948 1.013805312 0.875920534 1 21.30442296 1.722640289 24.99992966 0.959157697 0.888141824 0.10565037 0.115246291 2.747951955 4297.823044 0.05530996 0.030672166 52.80077401 -1.722640289 -0.071015873 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK 241.4 6.79E-39 4395560000 5201040 5221540 4787030 5941820 2554049 5994710 5573470 6055050 2690581 TRUE FALSE 4955197.147 5753620.862 5006520.061 5344536.965 2999474.337 5787111.69 4723134.788 5524837.722 3107822.56 1.594427304 1.851335059 1.610941411 1.719704668 0.965136934 1.862111359 1.519756903 1.777719807 1 21.56747271 -1.873987 2.658622105 0.713156308 1.620405624 0.362202294 0.255305871 11082417.91 8095391.22 20120117.27 0.056139655 0.013366355 1.873987 0.907249317 DKAS(ph)PEPEKDFSEK ddPTM_SK-BR-3_Trastuzumab_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(0.998)PEPEKDFS(0.002)EK;DKAS(0.999)PEPEKDFS(0.001)EK;DKAS(1)PEPEKDFSEK;DKAS(0.999)PEPEKDFS(0.001)EK;DKAS(0.997)PEPEKDFS(0.003)EK 120.92 6.14E-05 2506470000 7029830 6656110 5647610 7403620 2603460 7820790 6958210 8081800 2235910 TRUE FALSE 6697543.868 7334375.176 5906558.505 6659394.052 3057502.6 7549954.081 5896607.268 7374114.748 2582643.503 2.593290115 2.839871305 2.287020449 2.5785185 1.183865522 2.923343493 2.283167329 2.855258474 1 21.30041708 3.523376402 2.283871781 2.213842832 2.713865022 0.110836049 0.635314761 0.667904288 6.903675904 0.167856198 0.276675965 3337.155178 -3.523376402 0.50002219 DKASDASDKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKASDASDKQR 11 2 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 ; 67.519 0.033606 145248000 132563 77215 117776 116630 94567 132862 165319 152470 126952 FALSE TRUE 126297.0097 85083.29629 123176.1461 104906.1308 111059.4549 128260.9556 140096.5503 139118.9185 146639.0678 0.861278046 0.580222567 0.839995425 0.715403694 0.757366073 0.874671106 0.95538353 0.948716605 1 17.16190999 2.047414051 1.797046121 0.971411985 0.736020466 0.628783126 0.07656959 0.216423962 1.318103639 0.042974286 0.022531553 111.5357395 -2.047414051 -0.235391519 DKASGDVK ddPTM_SK-BR-3_Trastuzumab_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 73.887 0.038673 142220000 262700 251860 294310 264450 281140 294070 345900 352350 276370 FALSE TRUE 250282.6916 277524.8203 307804.4046 237866.9836 330170.727 283886.2822 293126.6021 321496.3661 319228.0481 0.784024753 0.869362269 0.964214788 0.745131842 1.034278563 0.88928991 0.918235737 1.007105635 1 18.28422789 8 0.158130287 1.020221521 0.146259609 0.382176663 0.074596364 61.89158193 0.633701817 0.203537494 12.57515291 99999999.9 -8 -0.873961912 DKAVESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 144.77 0.00052903 1488080000 2128010 1711520 1892310 2090800 1595230 1982240 2417430 2195780 1947140 FALSE TRUE 2027423.185 1885925.834 1979074.285 1880628.812 1873437.607 1913594.532 2048606.654 2003505.863 2249092.527 0.901440541 0.838527456 0.879943471 0.836172274 0.832974893 0.850829616 0.910859215 0.890806331 1 21.10091158 0.765119328 0.935698201 0.998992085 0.858392055 0.754867076 0.024799565 0.433483531 0.716438845 0.023410196 0.007781408 5.822631801 -0.765119328 -0.14060003 DKDAVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKDAVDK 7 1 P25815 P25815 S100P Protein S100-P 0 ;;; 88.37 0.017016 2813430000 4989470 4716610 3306420 5231280 1657960 4202380 3903130 5672920 2140340 FALSE TRUE 4753627.641 5197237.921 3458022.627 4705421.796 1947107.699 4056850.527 3307635.833 5176169.051 2472252.996 1.922791741 2.102227373 1.398733315 1.90329299 0.787584322 1.640952821 1.337903458 2.093705239 1 21.23739496 3.736815063 24.86349007 1.460906975 2.012509574 0.268740661 0.384339003 158.4930955 2257570.422 0.090342115 0.148347985 5455.255093 -3.736815063 0.551602599 DKDAVDKLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKDAVDKLLK 10 2 P25815 P25815 S100P Protein S100-P 0 ; 125.54 0.00022853 1095070000 4866500 3309220 4340000 4261500 2598500 5213600 6111300 6089300 3128030 FALSE TRUE 4636470.189 3646433.28 4538993.293 3833125.924 3051677.577 5033051.725 5178908.943 5556088.611 3613108.917 1.283235656 1.009223183 1.256256979 1.060894098 0.844612672 1.39299751 1.433366406 1.537758407 1 21.78480931 2.189182652 24.99679533 1.383735106 1.103361557 0.299201406 0.184653784 115.175135 58304.76217 0.063347777 0.046785507 154.5904465 -2.189182652 -0.280373548 DKDAYSSFGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 199.96 4.42E-08 5985230000 8375070 6449450 7657210 7854940 6623020 7786640 10278500 8996090 8264830 FALSE TRUE 7979197.039 7106656.287 8008300.653 7065346.508 7778072.591 7516986.704 8710326.047 8208344.668 9546497.625 0.835824545 0.744425502 0.838873162 0.740098284 0.814756667 0.787407801 0.912410644 0.859827865 1 23.18654011 1.172038856 0.780670449 0.994246388 0.786550569 0.705893873 0.041889113 0.294738939 0.41019976 0.035744969 0.013772391 14.86068595 -1.172038856 -0.207695818 DKDDDGGEDDDANCNLICGDEYGPETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DKDDDGGEDDDANCNLICGDEYGPETR 27 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 341.46 7.51E-96 4532690000 3057476 2525048 2820065 3270161 1698753 3431718 3305551 3502967 1910033 FALSE TRUE 2912955.169 2782353.262 2949367.77 2941438.203 1995014.985 3312876.745 2801228.484 3196228.639 2206231.163 1.320330897 1.261134059 1.336835332 1.333241164 0.904263805 1.501600014 1.269689474 1.4487279 1 21.07315253 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 DKDDQEWES(0.014)PS(0.984)PPKPT(0.002)VFISGVIAR;DKDDQEWES(0.06)PS(0.938)PPKPT(0.002)VFIS(0.001)GVIAR;DKDDQEWES(0.044)PS(0.956)PPKPTVFISGVIAR 199.59 3.69E-25 7508350000 5229070 5007640 4204890 5716450 2829530 5631380 4912520 5681600 2762740 TRUE FALSE 4981902.224 5517924.209 4397688.366 5141821.585 3322999.136 5436363.899 4163024.849 5184088.984 3191171.609 1.561151462 1.729121741 1.37807956 1.611264518 1.041310071 1.703563633 1.304544336 1.624509622 1 21.60565476 -3.44411016 0.138125063 1.01E-14 1.707861631 0.34015602 0.2107555 86.74889473 1.116958606 27.09048466 1.307808752 0.000359658 3.44411016 1.707861631 DKDFAIDIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKDFAIDIIK 10 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;; 112.51 0.0014699 4724050000 23932090 21669990 18902450 22636190 14274000 22421850 24398910 25185300 14628710 FALSE TRUE 22800867.53 23878186.62 19769146.03 20360757.18 16763381.08 21645375.71 20676408.16 22979941.62 16897255.63 1.349382884 1.413139928 1.169961943 1.204974205 0.992077142 1.280999482 1.223654812 1.359980704 1 24.01028561 3.735935332 24.67559305 1.187408936 1.381261413 0.358325526 0.11341958 186.3526503 1751570.625 0.027980453 0.045591964 5444.215807 -3.735935332 0.193852477 DKDNFWMTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKDNFWMTR 9 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 138.76 0.00011626 2495330000 2549850 2306640 2139300 2626080 1852100 2206350 2646310 2400110 1981840 FALSE TRUE 2429323.644 2541689.238 2237389.021 2362101.449 2175105.654 2129943.546 2242566.807 2189943.645 2289173.625 1.061222974 1.110308633 0.977378472 1.031857708 0.950170677 0.930442114 0.97964033 0.956652488 1 21.12639546 3.490525825 1.528621317 0.964940798 1.08668902 0.632747868 0.033227781 0.199950866 0.942887793 0.009783128 0.017843338 3094.039298 -3.490525825 0.121748222 DKDPILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKDPILR 7 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 107.66 0.006773 1003670000 1277950 1232690 1080480 1589330 979150 1419470 1397280 1469950 1061770 FALSE TRUE 1217543.836 1358302.512 1130021.077 1429567.529 1149913.45 1370313.398 1184099.273 1341233.385 1226423.869 0.99275941 1.107531048 0.921395209 1.16563903 0.937615028 1.117324469 0.965489423 1.093613244 1 20.22602625 DKDPPIPVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKDPPIPVAK 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 89.548 0.010431 186370000 592690 487280 503590 653710 365810 619900 696440 707070 452510 FALSE TRUE 564674.7183 536934.386 526680.0996 587997.8288 429607.1482 598432.7076 590185.287 645155.2024 522682.9397 1.080338912 1.027265949 1.007647389 1.124960821 0.821926861 1.144924891 1.129145878 1.234314636 1 18.99557655 DKDPVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKDPVNK 7 1 P62851;E9PQK3;E9PK60 P62851 RPS25 40S ribosomal protein S25 0 ; 111.95 0.0058957 1849840000 8608300 7686400 7432700 9416700 4954800 9443000 9953400 9794800 5562100 FALSE TRUE 8201402.719 8469652.899 7773496.647 8470115.425 5818915.551 9115986.542 8434826.023 8937115.386 6424642.061 1.276554031 1.318307358 1.209950153 1.31837935 0.905718248 1.418909638 1.31288653 1.391068219 1 22.61518465 3.746375317 23.97767288 1.242515955 1.297430686 0.024284895 0.162640936 1704.717152 5230509.326 0.039415361 0.069383796 5576.674761 -3.746375317 0.054914731 DKDQSDGFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DKDQSDGFGK 10 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ;;;;; 138.63 5.45E-05 2891170000 6300800 5083100 4347280 6529690 3165670 5723970 6403690 6480790 3394520 FALSE TRUE 6002973.671 5601073.669 4546607.088 5873313.156 3717761.846 5525747.484 5426689.479 5913297.671 3920924.825 1.531009631 1.428508303 1.159575175 1.497940771 0.948184934 1.409296972 1.384033033 1.508138497 1 21.90276255 3.960339368 7.034002833 1.297171154 1.493483451 0.165234886 0.193047087 0.359623455 52.94176268 0.045193097 0.08370488 9127.23785 -3.960339368 0.196312297 DKDTDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKDTDKFK 8 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 61.56 0.047917 2173700000 10703000 9384400 8514500 9954900 5197700 12185000 13192000 13037000 5204000 FALSE TRUE 10197090.4 10340681.03 8904898.247 8954214.539 6104177.234 11763030.39 11179318.11 11895411.17 6011009.742 1.696402242 1.72029018 1.481431345 1.489635673 1.015499475 1.956914212 1.85980702 1.978937263 1 22.51917593 DKDVTLS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKDVTLSPVK 10 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 DKDVTLS(1)PVK;DKDVT(0.001)LS(0.999)PVK 136.17 0.0017896 322140000 825810 1014010 597780 993190 399590 866300 720670 896530 325980 TRUE FALSE 786775.5979 1117338.772 625188.8043 893352.6543 469278.3695 836299.8138 610718.5555 818025.0804 376531.3135 2.089535637 2.967452458 1.660389938 2.372585286 1.246319636 2.221063119 1.621959538 2.172528688 1 18.52241032 1.027646752 0.105404247 4.38E-12 3.396645262 0.357733005 0.458128152 11.71166965 0.898765811 15.02456396 11.77906679 10.65728923 -1.027646752 3.396645262 DKEADEEGGENGPADQGFQPQEEEEREDS(ph)DTEEQVPEALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKEADEEGGENGPADQGFQPQEEEEREDSDTEEQVPEALER 41 2 Q9NU22 Q9NU22 MDN1 Midasin 1 DKEADEEGGENGPADQGFQPQEEEEREDS(0.822)DT(0.178)EEQVPEALER;DKEADEEGGENGPADQGFQPQEEEEREDS(0.942)DT(0.058)EEQVPEALER 183.05 7.74E-28 198135000 61331 66496 59784 77696 36586 83389 64868 73335 41677 TRUE FALSE 58432.00518 73272.018 62525.15553 69885.85047 42966.58682 80501.21802 54971.19522 66913.39863 48140.0563 1.213791791 1.52205925 1.298817665 1.451719334 0.892532957 1.672229411 1.141901349 1.389973418 1 15.55495021 -3.61775642 0.28424155 3.00E-08 1.350812909 0.17706935 0.21507988 157.1748127 3.088215883 92.27386245 0.21042578 0.000241126 3.61775642 1.350812879 DKEEIVICDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKEEIVICDR 10 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ;; 155.02 1.23E-05 378186000 963470 925870 829810 1131770 635380 935380 1018950 1072430 707520 FALSE TRUE 917928.6825 1020217.206 867857.6093 1018002.329 746190.0708 902987.5561 863490.4632 978522.3439 817238.5881 1.123207709 1.248371309 1.061939098 1.245661113 0.913062699 1.104925256 1.056595315 1.197352105 1 19.6403978 2.767523583 24.99864572 1.061926731 1.171722553 0.289341498 0.089418377 893.9605664 771597.8226 0.024729012 0.026224851 585.4955289 -2.767523583 0.109795822 DKEEKES(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEEKESSR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 DKEEKES(0.5)S(0.5)R 89.301 0.0096081 103100000 186940 194410 167720 233910 95310 197140 198330 278200 108460 TRUE FALSE 178103.7167 214220.6 175410.1279 210396.9224 111932.0338 190312.9924 168071.1159 253839.3332 125279.4229 1.421651797 1.709942424 1.400151149 1.67942123 0.893459048 1.519108151 1.341570005 2.026185365 1 16.93478995 DKEEKES(ph)SREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKEEKESSREK 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 DKEEKES(0.893)S(0.107)REK;DKEEKES(0.754)S(0.246)REK 119.54 0.0031603 316250000 433730 330980 348050 398300 128670 432320 432130 465410 138836 TRUE FALSE 413228.4425 364707.2383 364008.4368 358262.1273 151110.0073 417348.65 366200.6319 424656.2331 160365.9778 2.57678373 2.274218281 2.269860738 2.234028266 0.942282206 2.602476259 2.28353069 2.648044423 1 17.29100858 3.867518061 1.332683232 2.045302662 2.523164347 0.099563193 0.586725188 1.275690084 4.214659051 0.171496407 0.528312101 7370.858274 -3.867518061 0.477861685 DKEEKESS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEEKESSR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 DKEEKES(0.078)S(0.922)R 76.563 0.027625 121480000 206210 193320 176910 232240 81876 196450 193930 268170 99152 TRUE FALSE 196462.862 213019.5278 185021.4985 208894.794 96155.14848 189646.8872 164342.4167 244687.6131 114527.9858 1.715413579 1.859977947 1.615513425 1.823962873 0.839577749 1.655899962 1.434954222 2.136487528 1 16.80534065 DKEEKESS(ph)REK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEEKESSREK 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 DKEEKES(0.362)S(0.638)REK 103.88 0.014785 179970000 343770 265980 267380 316630 114860 346030 307570 393100 125090 TRUE FALSE 327520.6734 293083.6644 279639.6375 284801.7508 134891.5476 334046.8943 260644.5476 358678.08 144488.3183 2.266762304 2.028424635 1.935378865 1.971105721 0.933580993 2.311930114 1.803914327 2.482401928 1 17.14059333 3.91583942 1.366746125 1.800377065 2.236699363 0.104964762 0.488999279 1.128864341 3.890898536 0.136324613 0.441923434 8238.334465 -3.91583942 0.436322298 DKEGAALREDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEGAALREDLER 13 2 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 92.935 0.0032875 61015000 71172 57899 63614 67458 56343 67550 86675 78835 70278 FALSE TRUE 67807.84061 63798.97393 66530.76482 60676.99368 66169.20136 65210.72656 73451.13685 71931.78947 81176.35331 0.835315185 0.785930524 0.81958307 0.747471292 0.815129021 0.803321705 0.904834153 0.886117527 1 16.30877191 1.241031976 0.951271531 0.992979414 0.797751962 0.824571186 0.029833043 0.188106142 0.364251611 0.026143896 0.009219088 17.41935123 -1.241031976 -0.195227452 DKEGDRAS(ph)EEGKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEGDRASEEGKQK 14 3 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DKEGDRAS(1)EEGKQK 88.551 0.035925 45088000 92398 64187 77065 89302 30606 99747 92111 100430 30769 TRUE FALSE 88030.52966 70727.72827 80598.50648 80325.1933 35943.67671 96292.73638 78057.77522 91635.81679 35540.49937 2.476907506 1.990060059 2.267793303 2.260103114 1.011344166 2.709380512 2.196304965 2.578349162 1 15.11717633 4.625403973 2.599987958 2.070934534 2.513084749 0.050335377 0.58052861 1.291009257 13.43687389 0.130141744 1.116657099 42208.89409 -4.625403973 0.442150214 DKEPEVVFIGDSLVQLMHQCEIWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 242.44 7.51E-38 893070000 528650 505890 455650 559680 323470 513090 562440 570800 279770 FALSE TRUE 503661.7622 557440.7661 476542.0032 503419.9031 379883.0656 495321.5646 476629.4481 520817.726 323155.3027 1.558574957 1.724993405 1.474653206 1.557826527 1.175543345 1.532766322 1.474923803 1.611663871 1 18.30186814 -3.207350083 0.2033627 7.70E-15 1.620545823 0.545929315 0.143940875 47.53417782 0.907456169 21.01639459 0.343284356 0.000620369 3.207350083 1.620545823 DKEPFTFSS(ph)PASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKEPFTFSSPASGR 14 1 Q6P1X5;H0YEX2 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 1 DKEPFT(0.006)FS(0.174)S(0.82)PASGR 93.226 0.0028137 246910000 173370 134240 152910 160570 112290 180070 187010 176720 141560 TRUE FALSE 165175.1437 147919.2086 159921.0747 144429.1985 131873.3404 173834.1307 158478.1898 161245.4599 163512.4018 1.010168904 0.904636021 0.978036363 0.883292013 0.806503598 1.063125052 0.969212048 0.986135964 1 17.31904054 2.206003522 24.99998591 1.000715072 0.924703613 0.349660108 0.059008614 256.1789198 196713.5106 0.021972048 0.016228642 160.6954284 -2.206003522 -0.076011459 DKEQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKEQWK 6 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;; 91.626 0.043483 2744630000 4400190 5412700 3475580 5401760 2368660 4707610 3907570 4515750 2157790 FALSE TRUE 4192201.739 5964260.284 3634938.781 4858764.822 2781753.554 4544584.285 3311398.429 4120326.991 2492409.053 1.681987848 2.392970077 1.458403779 1.949425122 1.116090295 1.823370157 1.328593485 1.653150387 1 21.24910943 2.152862367 0.20363189 0.862755093 2.305003831 0.352886186 0.328213662 3.275164347 0.504467663 1.122154525 1.74884977 142.1878107 -2.152862367 1.442248738 DKEVS(ph)DDEAEEKEDKEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKEVSDDEAEEKEDKEEEK 19 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDKEEEK;DKEVS(1)DDEAEEKEDKEEEK 218.29 2.43E-19 2199020000 2636420 3631350 1733690 2975580 502440 3322170 2006020 3115530 282070 TRUE FALSE 2511801.651 4001388.694 1813181.401 2676469.045 590065.3769 3207122.42 1699964.806 2842717.677 325811.975 7.709359521 12.28128185 5.565115897 8.214765726 1.811061048 9.843476195 5.217625307 8.725025152 1 18.3136801 3.721070719 24.25531494 6.075627139 9.995320779 0.250495265 3.003487948 634.1718406 879481.2856 0.701372528 1.089617867 5261.029278 -3.721070719 3.919693639 DKFESSFSHKPSLFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKFESSFSHKPSLFNK 16 2 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 137.61 6.65E-06 273290000 355550 283040 321520 386650 257800 369160 431030 444910 302090 FALSE TRUE 338743.8561 311882.0978 336262.01 347783.2074 302760.2384 356375.8966 365268.4571 405951.3218 348936.5743 0.970789195 0.893807416 0.963676596 0.996694623 0.867665532 1.021319984 1.046804732 1.163395733 1 18.4126053 1.897174543 2.607611141 1.079440425 0.939452053 0.535575041 0.055493264 0.192046923 2.355160533 0.027794862 0.014263381 78.91772239 -1.897174543 -0.139988373 DKFNECGHVLYADIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKFNECGHVLYADIK 15 1 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 149.44 2.02E-06 2688560000 7704110 6799990 6538010 7854210 4663980 7542440 8653240 8326170 4798400 FALSE TRUE 7339951.988 7492916.712 6837784.225 7064689.889 5477376.635 7281243.412 7333029.31 7597086.415 5542511.365 1.324300756 1.351899206 1.233697827 1.274636969 0.988248156 1.313708341 1.323051741 1.370693881 1 22.40210839 -2.265659213 2.090801742 2.31E-05 1.278327359 0.38403154 0.108249415 1702891.369 267523.1806 8041613.715 0.026238725 0.005424264 2.265659213 1.278304245 DKFPEVIINFPDPAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKFPEVIINFPDPAQK 16 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 84.14 0.0057324 0 239980 233110 239280 300360 160320 261380 289190 287310 188080 FALSE TRUE 228636.621 256864.174 250251.2247 270167.2422 188279.7572 252328.3451 245068.7542 262151.6133 217246.4858 1.052429549 1.18236285 1.151923005 1.243597755 0.866664225 1.161484128 1.128067749 1.206701283 1 17.72897331 DKFQETSDEFEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKFQETSDEFEAAR 14 1 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ;; 229.54 1.14E-12 742240000 523040 436470 463900 534640 381550 504680 556840 523000 482800 FALSE TRUE 498316.9358 480946.7892 485170.2739 480896.9715 448092.1992 487202.8051 471883.8309 477203.3474 557670.1582 0.893569305 0.862421598 0.869995044 0.862332266 0.80350758 0.873639728 0.846170131 0.855708953 1 19.08905255 -1.123014263 4.486864205 1.000016334 0.859393251 0.787263993 0.023124793 3.73E-06 7.28E-07 0.022079552 0.005203596 0.075333082 1.123014263 -0.140623083 DKFS(ph)PFPVQDRPESSLVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKFS(1)PFPVQDRPESSLVFK;DKFS(1)PFPVQDRPESSLVFK 93.093 0.00094527 611098000 1579810 1468940 1258410 1586750 824648 1511100 1556900 1715730 881317 TRUE FALSE 1505135.512 1618626.656 1316109.343 1427246.875 968466.3501 1458770.228 1319366.311 1565491.586 1017987.139 1.478540793 1.590026626 1.292854588 1.402028395 0.951354209 1.432994752 1.296054007 1.537830416 1 19.9572879 3.728821025 22.46352137 1.287782986 1.534283707 0.258969258 0.182261793 198.5185645 457867.2371 0.043915961 0.069189568 5355.75898 -3.728821025 0.246500721 DKFSFDLGK ddPTM_SK-BR-3_Trastuzumab_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 ; 143.24 9.34E-05 2574300000 10541000 13270200 8095300 12549200 5039100 10345500 8832200 11560500 5653300 FALSE TRUE 10042747.82 14622448.47 8466477.512 11287730.57 5917917.445 9987232.741 7484685.676 10548201.33 6529984.891 1.5379435 2.239277535 1.296553921 1.7285998 0.906268168 1.529441937 1.146202602 1.615348505 1 22.63864822 3.715307434 24.26236084 1.325453097 1.888610517 0.373948812 0.307085674 448.3037715 467759.9168 0.073282946 0.113619696 5191.674243 -3.715307434 0.56315742 DKFSPFPVQDRPESSLVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 140.63 9.74E-08 225770000 193310 180690 154310 190330 113620 178170 176770 166520 128480 FALSE TRUE 184172.6194 199102.5164 161385.2661 171197.6668 133435.292 171999.9282 149800.4899 151938.626 148404.0222 1.24102175 1.341624799 1.087472319 1.153591825 0.89913528 1.158997753 1.009409905 1.023817439 1 17.17917067 3.520126892 2.044369014 1.036899084 1.292109812 0.610601684 0.08032133 0.176364713 1.465104112 0.021263118 0.035972715 3312.278852 -3.520126892 0.255210729 DKGATKES(ph)SEKDR ddPTM_SK-BR-3_Trastuzumab_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(0.003)KES(0.499)S(0.499)EKDR 101.67 0.010151 120560000 287760 274060 241500 312850 116500 349830 313900 338890 120480 TRUE FALSE 274158.1551 301987.0256 252573.0139 281401.7236 136817.5631 337715.2994 266008.7898 309214.995 139163.4231 1.970044636 2.170017228 1.814938209 2.022095443 0.983143128 2.426753323 1.911484957 2.221955944 1 17.08642055 3.724571918 23.05777406 1.829430508 2.070030918 0.055112461 0.468933228 853.8393504 1407396.738 0.11360389 0.177186863 5303.614117 -3.724571918 0.24060041 DKGETIQGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKGETIQGLR 10 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 ; 113.22 0.001383 871700000 1231710 1106490 1053210 1234670 949030 1144810 1297450 1227520 1024980 FALSE TRUE 1173489.509 1219242.589 1101500.72 1110558.626 1114540.532 1105164.943 1099500.173 1120031.841 1183928.664 0.991182616 1.029827748 0.93037761 0.938028329 0.941391628 0.933472579 0.928687857 0.946029838 1 20.17515072 3.734006041 24.99426275 0.940588921 1.010505183 0.582222415 0.022631722 190.492344 1045371.13 0.005257143 0.008447065 5420.0843 -3.734006041 0.069916262 DKGLQTSQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKGLQTSQDAR 11 1 P27797 P27797 CALR Calreticulin 0 ;;; 164.48 2.07E-05 754538000 2953370 2705950 2597630 3136780 2522690 2845690 3108320 3176310 2517170 FALSE TRUE 2813770.053 2981689.381 2716733.905 2821464.915 2962646.337 2747143.042 2634088.696 2898175.458 2907519.868 0.967756088 1.025509547 0.934381889 0.970402626 1.018959963 0.944840678 0.905957247 0.996786123 1 21.47135762 2.196746148 24.99667632 0.948576065 0.984902573 0.023656282 0.037512032 247.0695005 147696.6195 0.013457054 0.009938788 157.3063115 -2.196746148 0.036326508 DKGLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKGLVEK 7 1 H0YFD6;P40939;A0A2R8YG21;A0A2R8Y688 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 84.213 0.0198 275330000 757290 587940 582850 611660 457000 562620 759400 706990 596370 FALSE TRUE 721494.4025 647851.7544 609574.249 550174.7747 536700.6553 543136.3283 643539.5827 645082.2076 688852.0138 1.047386649 0.940480309 0.884913213 0.798683554 0.779123302 0.788465908 0.934220369 0.936459783 1 19.39383456 4.119656592 1.708033437 0.863540335 1.038923049 0.365277075 0.071945556 0.390825753 2.109271621 0.020081586 0.075015019 13172.14771 -4.119656592 0.175382714 DKGQS(ph)FNDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKGQSFNDKR 10 2 A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25 A0A590UJ08 DLG1 Disks large homolog 1 1 DKGQS(1)FNDKR;DKGQS(1)FNDKR 68.83 0.046308 158282000 305260 270070 260290 366710 186511 315120 325330 303430 165286 TRUE FALSE 290830.9648 297590.44 272224.554 329847.6141 219038.4593 304207.3154 275694.9334 276860.0606 190917.7087 1.523331527 1.558736704 1.425873775 1.727695227 1.147292521 1.593394963 1.444051132 1.450153904 1 17.5425914 -3.026554003 0.268073232 6.29E-11 1.538563795 0.527277868 0.146039594 45.11459205 1.138691305 25.60231699 0.163699575 0.000940689 3.026554003 1.538563795 DKGS(ph)FNDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKGSFNDKR 9 2 A0A590UJD9;A0A0C4DFT3;A0A590UK02;A0A590UK70 A0A590UJD9 DLG1 1 DKGS(1)FNDKR;DKGS(1)FNDKR 74.76 0.020965 284310000 575600 595640 558190 742150 339770 632670 715810 658190 332680 TRUE FALSE 548392.5287 656336.3932 583783.5636 667547.672 399025.7804 610760.4793 606600.0377 600555.3943 384270.3153 1.427100941 1.708007012 1.519200262 1.737182513 1.03839866 1.589403227 1.578576366 1.56284618 1 18.55176201 DKGVLQEEEDVLVNVNLVDKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKGVLQEEEDVLVNVNLVDKER 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 99.366 0.00057294 19035000 47769 33230 34424 49294 27229 39889 45481 45526 32534 FALSE TRUE 45511.05404 36616.17478 36002.37445 44338.87347 31977.72898 38507.63393 38542.03813 41539.50209 37579.20656 1.211070116 0.974373281 0.958039771 1.179877851 0.850942101 1.02470588 1.025621392 1.105385289 1 15.19764699 4.60674239 2.985969915 1.01518093 1.218421954 0.333133311 0.086856448 0.323007462 4.797212397 0.01937388 0.133107404 40433.59807 -4.60674239 0.203241024 DKHIEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 ;;;;; 128.27 0.0006854 3328030000 4235056 4115713 3848380 5018228 3388410 4184762 4811773 4179976 2094152 FALSE TRUE 4034873.296 4535108.834 4024832.03 4513786.187 3979347.631 4039842.643 4077648.655 3813955.142 2418902.397 1.668059572 1.874862268 1.663908405 1.866047259 1.645104671 1.670113953 1.68574336 1.576729655 1 21.20592113 -0.285283497 0.462793341 0.876299206 1.769955043 0.896055748 0.077713119 1.69037787 0.375329562 0.419811982 0.037755271 0.51846149 0.285283497 0.893655837 DKHIEEVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKHIEEVRK 9 2 P16949 P16949 STMN1 Stathmin 0 83.397 0.0097276 341970000 316640 303580 308820 370570 259910 344850 421870 369760 155150 FALSE TRUE 301673.0547 334515.1471 322979.7025 333319.5996 305238.2217 332907.758 357505.9833 337381.8542 179209.8696 1.683350674 1.866611185 1.802242829 1.85993997 1.703244483 1.857641874 1.994901197 1.882607554 1 17.45129057 -0.864884818 5.518870394 0.999999546 1.834924925 0.895864394 0.089065821 5.31E-07 1.09E-07 0.092056381 0.021697885 0.136494509 0.864884818 0.834925379 DKHKEEDKNSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKHKEEDKNSER 12 3 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 83.729 0.0055352 62600000 178760 162270 181720 198080 90546 217850 218530 226790 55978 FALSE TRUE 170310.3691 178805.4975 190052.0417 178168.6221 106337.1937 210305.7999 185189.2349 206931.0653 64658.78234 2.633986643 2.765370627 2.939307467 2.755520837 1.644590106 3.252548103 2.864100254 3.200355123 1 15.98055872 -0.552168053 9.616940346 1 2.753053162 0.611990966 0.439649021 0 0 0.398502469 0.093927933 0.280434827 0.552168053 1.753053162 DKIIVNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKIIVNDR 8 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 136.63 0.00071367 4650310000 5511300 4335040 4984420 5500650 4840650 5453400 6537870 5787200 5535260 FALSE TRUE 5250791.771 4776785.505 5212960.587 4947714.211 5684857.827 5264547.391 5540397.855 5280442.088 6393639.851 0.821252353 0.747115198 0.81533535 0.773849376 0.889142642 0.823403807 0.866548318 0.825889824 1 22.60820605 -5 0.137137782 1.650838823 0.745384523 0.730045361 0.035979031 64.39114012 0.545674347 11.36628836 0.213082084 1.00E-05 5 -0.9054543 DKKS(ph)PLIESTANMDNNQSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKKSPLIESTANMDNNQSQK 20 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 DKKS(1)PLIESTANMDNNQSQK;DKKS(0.989)PLIES(0.006)T(0.006)ANMDNNQSQK;DKKS(1)PLIESTANMDNNQSQK;DKKS(0.997)PLIES(0.002)T(0.002)ANMDNNQSQK;DKKS(0.978)PLIES(0.011)T(0.011)ANMDNNQSQK 252.21 2.35E-36 3257090000 3352570 2613250 2924340 3394070 1576810 3499040 3577160 3709910 1575390 TRUE FALSE 3194100.66 2879543.146 3058423.882 3052891.635 1851805.165 3377867.367 3031398.543 3385050.613 1819693.435 1.755296029 1.582433112 1.680735789 1.677695581 1.01764678 1.856283758 1.6658842 1.860231261 1 20.79526399 5.102948147 0.769723136 1.56749628 1.97594528 0.043606549 0.302938338 17.33061876 5.324605852 0.099952083 6.916653224 126750.0524 -5.102948147 0.408449 DKLCGPYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKLCGPYEK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 75.695 0.03423 164510000 634170 427530 495830 510390 395290 595740 826410 697330 472370 FALSE TRUE 604194.0409 471095.7931 518564.2959 459084.6275 464228.4508 575109.3744 700325.9764 636268.0884 545622.7271 1.107347643 0.863409403 0.950408167 0.84139572 0.850823156 1.05404219 1.283535201 1.166131939 1 19.05754421 2.001384782 6.269663145 1.17920489 0.930129987 0.505517074 0.102020634 0.104598845 18.43092522 0.039682598 0.027184964 100.3193668 -2.001384782 -0.249074903 DKLCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKLCSK 6 1 Q9Y2B0;F8VXJ7;F8W031;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 85.064 0.050287 279140000 854060 704810 809420 1098800 700660 866800 1058400 1024900 983100 FALSE TRUE 813690.2764 776630.9403 846532.7076 988346.5364 822854.8822 836782.4987 896921.6412 935154.3227 1135554.127 0.716557896 0.683922432 0.745479839 0.870364972 0.724628499 0.736893538 0.789853711 0.823522455 1 20.11496504 -5 0.146122498 1.893642518 0.66980838 0.741380125 0.047150058 68.00667604 0.597432792 17.54174444 0.256829563 1.00E-05 5 -1.223834139 DKLDETGNSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKLDETGNSLK 11 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 167.98 1.70E-05 915760000 1146590 1326450 1146630 1440160 633020 1359530 1230240 1458250 638040 FALSE TRUE 1092392.963 1461616.763 1199204.12 1295392.381 743418.4876 1312449.135 1042544.293 1330557.899 736983.9845 1.482247899 1.983240876 1.627177991 1.757694072 1.008730859 1.780838068 1.414609157 1.805409517 1 19.49127374 DKLEEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKLEEILR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 107.21 0.0036916 195712000 382240 324670 294880 356380 268870 336060 429800 395770 289800 FALSE TRUE 364172.2727 357754.2421 308400.5397 320556.0053 315760.8429 324422.1579 364226.1162 361114.2807 334740.7039 1.087923484 1.068750343 0.921311738 0.957624817 0.943299811 0.969174511 1.088084335 1.078788078 1 18.35268447 -1.237793964 5.287848683 0.999998127 1.020088287 0 0.06427883 1.55E-06 2.23E-07 0.067836091 0.015987629 0.057837037 1.237793964 0.020090159 DKLESEMEDAYHEHQANLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKLESEMEDAYHEHQANLLR 20 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 330.68 5.18E-80 2605700000 2916933 2581005 2547283 3217044 1948217 2953304 3181113 2847119 66139 FALSE TRUE 2779055.358 2844012.344 2664078.445 2893660.625 2287985.428 2851030.342 2695775.787 2597810.167 76395.49833 36.37721356 37.22748599 34.87219147 37.8773709 29.94921793 37.31935002 35.28710259 34.00475452 1 16.22120001 -0.377817242 0.928121129 2.79E-15 35.83481213 0.959783272 2.212778486 3.150129454 1.842655374 14.88031077 0.632752973 0.418969837 0.377817242 35.83481213 DKLFDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKLFDQR 7 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;; 80.219 0.027822 3706170000 14288900 11433800 10946700 13099800 11149200 12271900 15588000 13849900 12206400 FALSE TRUE 13613492.01 12598917.22 11448617.02 11782983.22 13093616.95 11846921.03 13209764.31 12637129.33 14099306.17 0.9655434 0.8935842 0.811998611 0.835713692 0.928671013 0.840248512 0.93690882 0.896294412 1 23.74912083 0.507051947 0.929502928 0.999955053 0.887219253 0.35641633 0.047816272 2.057340748 2.62953212 0.048243734 0.01546672 3.214044955 -0.507051947 -0.112735799 DKLNNLVLFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKLNNLVLFDK 11 1 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 196.5 5.50E-08 3354500000 17710100 15900400 14803400 18039000 12057300 17994500 19666300 19448900 13476800 FALSE TRUE 16872978.67 17520668.84 15482150.53 16225685.45 14160089.3 17371345.95 16665844.74 17745851.21 15566713.31 1.083914011 1.125521392 0.994567718 1.04233213 0.909638985 1.115928944 1.070607803 1.139987026 1 23.89196104 -0.150666083 7.167465769 0.999991732 1.063578833 0.070052691 0.068141997 4366888.701 609265.3379 0.064469312 0.015636105 0.706860831 0.150666083 0.063587101 DKLPLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKLPLEK 7 1 Q92831 Q92831 KAT2B Histone acetyltransferase KAT2B 0 ; 109.21 0.0064555 715020000 1160970 1112430 1354780 1357420 973380 1732680 1815890 1829610 1080870 FALSE TRUE 1106093.249 1225787.882 1416898.003 1220969.563 1143137.164 1672676.857 1538842.629 1669399.649 1248485.799 0.885947801 0.981819643 1.134893167 0.977960313 0.915618876 1.339764424 1.232567187 1.337139477 1 20.25174798 2.242261879 24.99995457 1.248550972 0.978133047 0.539592105 0.11313437 63.18615489 426789.628 0.03719219 0.030000066 174.6875201 -2.242261879 -0.270417925 DKLSGEYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKLSGEYEK 9 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 141.71 9.67E-05 2120480000 3930030 3302210 3568220 4688550 2674710 4955950 5169870 5183410 3142470 FALSE TRUE 3744265.27 3638708.953 3731826.416 4217248.046 3141178.577 4784324.209 4381111.38 4729523.141 3629788.198 1.031538224 1.002457652 1.028111342 1.161844112 0.865388944 1.318072556 1.206988161 1.302974963 1 21.79145394 2.226699554 24.99999522 1.22575812 1.024019335 0.41348888 0.110805638 184.6527135 389196.5628 0.036082051 0.026858093 168.5386669 -2.226699554 -0.201738785 DKLTPWEQFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKLTPWEQFLEK 12 1 Q9H501;A0A087WX71 Q9H501 ESF1 ESF1 homolog 0 117.79 0.00063452 36686000 212910 179840 185130 196300 139220 193470 222310 236430 165330 FALSE TRUE 202846.1662 198165.9005 193618.3936 176567.5511 163499.9239 186770.0854 188392.5265 215726.9358 190968.532 1.062196814 1.037688767 1.013875907 0.92458977 0.8561616 0.978014982 0.986510838 1.129646511 1 17.5429754 1.285366763 21.96594342 1.064822902 0.986124444 0.222114459 0.065288172 55.2343892 25920.96234 0.047070767 0.017189682 19.29153399 -1.285366763 -0.078698458 DKLYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKLYER 6 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ; 85.064 0.050287 387830000 657550 518240 521490 618770 485910 587630 680410 653150 541950 FALSE TRUE 626468.9146 571049.2452 545400.8323 556570.064 570652.5502 567280.2258 576600.9579 595956.7234 625992.8381 1.000760514 0.912229678 0.871257304 0.889099731 0.911595973 0.906208811 0.92109833 0.952018437 1 19.25578663 0.955038056 2.450248308 0.999788748 0.918108678 0.39942846 0.033493796 0.378678113 5.151810823 0.03472095 0.009387879 9.016501426 -0.955038056 -0.08168007 DKMMNGGHYTYSENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKMMNGGHYTYSENR 15 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 184.31 2.82E-07 391220000 478540 374410 420030 501690 439560 403760 535470 487240 431400 FALSE TRUE 455920.3626 412562.8047 439288.791 451259.1681 516219.1248 389777.69 453774.2169 444574.6826 498299.3087 0.91495283 0.827941756 0.88157616 0.905598623 1.035961953 0.782215996 0.910645889 0.892184024 1 18.92665305 -5 0.40509216 2.835398002 0.887883703 0.204727737 0.065146802 1216.344507 8.34345248 1978.023284 0.036977773 1.00E-05 5 -1.947514299 DKMMNGGHYTYSENRVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKMMNGGHYTYSENRVEK 18 2 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 178.88 5.19E-14 477686000 1050550 575020 1050480 877290 900790 993760 1501730 1165370 1122300 FALSE TRUE 1000892.583 633615.1917 1098645.547 789103.1425 1057887.491 959345.842 1272613.507 1063324.025 1296340.552 0.772090777 0.488772175 0.847497631 0.608715928 0.816056775 0.740041527 0.981696905 0.82025053 1 20.30601334 2.078515424 0.759806018 0.969700147 0.65108561 0.462514597 0.112528374 0.494376832 0.538127898 0.087125304 0.048238975 119.8161674 -2.078515424 -0.318614537 DKNEFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKNEFHK 7 1 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 81.548 0.016165 108290000 801480 800050 717620 888660 499040 748950 826320 887550 451470 FALSE TRUE 763595.6288 881576.0046 750523.5868 799330.2085 586072.418 723013.6737 700249.7076 809831.4168 521481.6618 1.464280884 1.690521583 1.439213767 1.532805978 1.123860072 1.386460401 1.342807924 1.552943231 1 18.99225699 2.872258908 9.227779314 1.314285492 1.547168283 0.35969095 0.162313841 0.372187514 26.04948662 0.045234661 0.048012637 745.1760847 -2.872258908 0.232882791 DKNNMQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 DKNNMQHR 8 1 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;;;;;;;;;; 183.65 0.0001335 2514127000 5503981 4115330 3664677 4680416 3883967 4140745 5697539 5011236 4326917 FALSE TRUE 5243818.726 4534686.806 3832706.065 4209931.691 4561329.615 3997349.962 4828274.783 4572425.61 4997913.19 1.049201642 0.90731604 0.766861272 0.842337898 0.912646827 0.7998038 0.966058153 0.914866953 1 22.25289441 0.979589256 1.401553944 0.99622277 0.894278307 0.160304468 0.079511682 1.009803512 4.044168503 0.079442257 0.023809265 9.540898074 -0.979589256 -0.101944464 DKNRHDKDQQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKNRHDKDQQHR 12 3 E9PM95;J3KQL8;Q9BQE5 E9PM95 APOL2 Apolipoprotein L2 0 52.928 0.063597 5537900 12062 4799.9 9331.8 10174 9342.9 8520.4 10812 9402.7 2189.8 FALSE TRUE 11491.85316 5289.015267 9759.67226 9151.290191 10972.2988 8225.336412 9162.430824 8579.349741 2529.383 4.543342453 2.091029815 3.858518959 3.61799308 4.337934904 3.251914167 3.622397566 3.391874517 1 11.30456979 0.659974948 3.50324215 1.000002101 3.544965938 0.602573702 0.661272648 4.664692464 47.3177601 0.603726803 0.155642165 4.570618235 -0.659974948 2.544963837 DKNSVNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKNSVNFK 8 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 140.45 0.00059228 2978000000 4860800 4407000 3891500 4596100 2906000 4497400 4734700 4678200 2950300 FALSE TRUE 4631039.617 4856078.31 4069929.124 4134091.296 3412805.48 4341653.91 4012334.556 4268552.007 3407817.456 1.358945917 1.424981934 1.194292 1.213119937 1.0014637 1.274027722 1.17739128 1.252576484 1 21.70041663 3.677503381 4.934719035 1.167613973 1.392095836 0.515892849 0.093698254 0.144349362 7.250430844 0.022866859 0.036557113 4758.864953 -3.677503381 0.224481863 DKPAQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DKPAQIR 7 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;; 133.6 0.0029694 5167786000 4809360 4180470 4186220 4781860 3475664 4484160 5182410 4712520 4027030 FALSE TRUE 4582031.084 4606464.646 4378162.328 4301178.348 4081818.701 4328872.415 4391738.173 4299866.766 4651521.245 0.985060767 0.990313578 0.941232362 0.924682082 0.877523392 0.930635847 0.944150944 0.924400113 1 22.14927119 3.659817507 3.727788477 0.929261625 0.9880594 0.349040573 0.0297977 0.204476825 5.433502969 0.007523166 0.012361995 4568.961592 -3.659817507 0.058797775 DKPEEQWWNAEDSEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKPEEQWWNAEDSEGKR 17 2 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 109.38 0.00034292 119610000 57347 52338 58105 64393 33702 56977 59317 58532 36188 FALSE TRUE 54636.32096 57671.3017 60769.17172 57920.0933 39579.61813 55003.8722 50267.10222 53406.62778 41799.85022 1.307093702 1.379701157 1.453813145 1.38565313 0.946884209 1.315886825 1.202566563 1.277675099 1 15.35121015 DKPHNIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPHNIFK 8 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 114.89 0.0015432 1664800000 5002500 4665800 3686000 4814400 3304700 4274700 4995300 4869400 3273300 FALSE TRUE 4766041.739 5141250.325 3855006.746 4330447.365 3881038.634 4126666.067 4233175.24 4443009.522 3780906.646 1.260555254 1.359792982 1.0195985 1.145346281 1.026483592 1.091448812 1.119619085 1.175117488 1 21.8503008 3.741855908 24.99999452 1.090034309 1.310174127 0.707260469 0.060741688 130.0574617 986688.1109 0.014437628 0.024761637 5518.942992 -3.741855908 0.220139818 DKPHNIFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPHNIFKR 9 2 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 152.97 4.76E-05 597100000 1322880 972310 1191390 1200320 1066250 1174700 1509300 1363950 1207060 FALSE TRUE 1260350.084 1071389.494 1246016.41 1079661.553 1252203.662 1134019.844 1279028.565 1244515.307 1394244.7 0.903966201 0.768437201 0.893685599 0.774370204 0.898123308 0.813357831 0.917363046 0.892608957 1 20.41105236 0.975406863 0.754259429 0.998941495 0.836354276 0.48255128 0.050703793 0.552293414 0.705450571 0.04301045 0.016232034 9.449457219 -0.975406863 -0.16258722 DKPHVNVGTIGHVDHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DKPHVNVGTIGHVDHGK 17 1 P49411;H3BNU3 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;; 257.15 1.36E-27 4484281000 5084674 3991405 3997595 4030440 3014575 3871615 4596180 4108292 93729.3 FALSE TRUE 4844331.537 4398133.707 4180888.685 3625292.514 3540315.926 3737540.002 3894948.326 3748548.173 108264.3611 44.74539438 40.62402125 38.61740503 33.48555772 32.70065872 34.52234847 35.97627405 34.62402709 1 16.72419888 -0.144149333 0.487486268 2.91E-25 39.71464833 0.912737611 3.503167413 1.661321567 0.442821077 17.30430565 1.964196582 0.717547519 0.144149333 39.71464833 DKPLIIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPLIIYK 8 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ; 105.4 0.0070687 0 5403300 4295700 3303300 3602500 3152900 3444800 4735400 4154000 3401000 FALSE TRUE 5147896.717 4733436.714 3454759.572 3240369.856 3702764.762 3325505.712 4012927.758 3790253.738 3928409.71 1.310427653 1.2049244 0.879429547 0.824855373 0.94256074 0.84652721 1.021514571 0.964831578 1 21.90551397 3.834784249 4.125736369 0.924288913 1.272134999 0.821846677 0.064799096 0.08186242 2.472729616 0.017215385 0.032251828 6835.719739 -3.834784249 0.347846086 DKPLKDVIIADCGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPLKDVIIADCGK 14 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 198.15 1.26E-08 3444900000 13662800 11123600 11175800 13753600 7481000 14075800 16564300 16822900 9202000 FALSE TRUE 13016986.52 12257107.49 11688221.48 12371062 8785684.031 13588351.52 14037111.81 15349797.69 10628999.16 1.224667188 1.15317607 1.099654004 1.163897166 0.826576792 1.278422484 1.320642856 1.444143278 1 23.34150242 2.042555102 24.99999299 1.29280138 1.111721885 0.213850616 0.152046365 184.3710672 108312.3384 0.05298286 0.03913041 110.2948165 -2.042555102 -0.181079494 DKPRS(ph)PFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKPRSPFSK 9 2 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 DKPRS(0.968)PFS(0.032)K 60.157 0.076838 120760000 372120 323370 319320 411350 192430 356090 400860 378470 230010 TRUE FALSE 354530.6251 356321.7706 333961.1379 370000.3165 225989.7311 343758.514 339701.4447 345329.1604 265678.7761 1.334433372 1.341175144 1.257010977 1.392660422 0.850612662 1.293887751 1.27861717 1.299799576 1 18.01932346 -5 0.079883855 0.247008583 1.500998057 0.229149566 0.148812346 380.137358 2.150540801 52.34591795 4.909359506 1.00E-05 5 1.253989474 DKPSGDTAAVFEEGGDVDDLLDMI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPSGDTAAVFEEGGDVDDLLDMI 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 135.68 2.74E-05 9560300 44974 36575 40417 51495 33736 42696 48973 49541 37576 FALSE TRUE 42848.16815 40302.03408 42270.15943 46318.62477 39619.54772 41217.42681 41501.2694 45202.92741 43403.09417 0.987214598 0.928552096 0.973897374 1.067173335 0.912827725 0.949642591 0.956182277 1.041467856 1 15.40551027 1.245797072 24.99102942 1.020733932 0.965599722 0.209608803 0.042444442 218.147422 753389.3181 0.02838212 0.009883305 17.61152941 -1.245797072 -0.055134211 DKPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DKPSLR 6 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ;;;;;; 130.77 0.014246 5332110000 11768340 9749290 9921360 12026970 9042510 10892450 12528990 12002390 10338740 FALSE TRUE 11212073.89 10742753.74 10376264.17 10817996.13 10619520.88 10515241.73 10617462.46 10951397.1 11942019 0.938875905 0.899576005 0.868886925 0.905876647 0.88925674 0.880524619 0.889084372 0.917047369 1 23.50954343 0.849617877 4.107928988 0.999991692 0.897381321 0.757941715 0.018361844 0.551071232 14.32831429 0.018916138 0.00482657 7.07323158 -0.849617877 -0.102610371 DKPSVEPVEEYDYEDLKESS(ph)NSVSNHQLSGFDQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.088)S(0.454)NS(0.454)VS(0.003)NHQLSGFDQAR 209.83 2.60E-28 165180000 63589 54373 60468 77230 61698 87455 107990 95767 72395 TRUE FALSE 60583.27399 59913.67052 63240.51761 69466.69367 72458.11167 84426.41142 91514.14213 87381.13379 83621.64686 0.724492715 0.716485178 0.756269698 0.830726209 0.866499458 1.009623878 1.094383399 1.044958298 1 16.35158884 2.535476123 1.202458374 1.065512574 0.725297105 0.94277567 0.033023737 0.088494707 0.259791323 0.017365447 0.013231449 343.1437736 -2.535476123 -0.340215469 DKPSVEPVEEYDYEDLKESSNS(ph)VSNHQLSGFDQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.001)S(0.024)NS(0.952)VS(0.024)NHQLSGFDQAR;DKPSVEPVEEYDYEDLKES(0.128)S(0.128)NS(0.722)VS(0.023)NHQLSGFDQAR 189.89 6.73E-21 310860000 139525 91784 121416 144668 106977 140245 196703 201242 134999 TRUE FALSE 132929.9298 101136.8939 126983.0437 130125.6978 125633.7549 135388.2805 166692.3447 183620.1836 155933.9554 0.852475841 0.648588011 0.81433863 0.834492381 0.80568568 0.868241174 1.068993243 1.17755099 1 17.25057559 1.837162726 2.251532249 1.103288115 0.779657709 0.783714247 0.069758964 0.122823189 1.172160813 0.041928191 0.019656727 68.73259257 -1.837162726 -0.323630405 DKPTYDEIFYTLS(ph)PVNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 DKPTYDEIFYT(0.209)LS(0.791)PVNGK;DKPTYDEIFYTLS(1)PVNGK 309.82 2.43E-61 523310000 540027 596510 569606 693450 368486 671740 720150 736870 460515 TRUE FALSE 514500.9939 657295.0472 595722.9985 623743.0885 432749.8417 648477.4754 610277.891 672345.7564 531929.3142 0.967235646 1.235681188 1.119928875 1.172605216 0.813547647 1.219104603 1.147291331 1.263975755 1 19.02087502 DKPTYDEIFYTLSPVNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 181.41 6.71E-14 303540000 1168350 1059490 1003310 1296320 801550 1118760 1295850 1327470 894010 FALSE TRUE 1113124.411 1167453.236 1049312.756 1166011.451 941340.0662 1080017.061 1098144.283 1211229.689 1032648.505 1.077931557 1.130542707 1.016137389 1.129146506 0.911578395 1.045870938 1.063425045 1.172935112 1 19.97791784 3.743027266 24.95536278 1.049437464 1.104237131 0.095583056 0.071301879 815.8209637 4558009.167 0.017354062 0.029994281 5533.848515 -3.743027266 0.054799667 DKPVYDELFYTLS(ph)PINGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 1 DKPVYDELFYT(0.005)LS(0.995)PINGK;DKPVYDELFYTLS(1)PINGK 163.64 1.98E-11 102912000 159109 163440 172055 204741 117877 193789 212137 211494 139991 TRUE FALSE 151588.2329 180094.7218 179943.8919 184160.0457 138434.7115 187078.0383 179771.6045 192974.4642 161700.0893 0.937465363 1.113757714 1.112824938 1.13889885 0.856120192 1.156944558 1.111759463 1.193409756 1 17.30296095 DKPVYDELFYTLSPINGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 125.12 2.77E-05 36626000 140870 118710 117340 162130 102640 140560 160270 151400 124120 FALSE TRUE 134211.3543 130806.684 122720.1551 145832.3844 120540.3835 135692.372 135817.8679 138142.6134 143367.8957 0.936132554 0.912384766 0.855980723 1.017189962 0.840776681 0.946462744 0.947338086 0.963553331 1 17.12936247 1.268582056 1.161514657 0.997303874 0.916651123 0.25142083 0.048009408 0.578001048 1.567812875 0.039405535 0.012928923 18.56017454 -1.268582056 -0.080652752 DKQDEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DKQDEEQR 8 1 P27797;K7EL50 P27797 CALR Calreticulin 0 ;;;;;;;; 153.05 0.00040799 8029317000 15972670 13919430 12894340 16131760 8319330 14605190 15390380 17236820 10999730 FALSE TRUE 15217673.54 15337835.74 13485558.24 14510164.84 9770218.518 14099408.61 13042294.87 15727472.66 12705511.95 1.197722186 1.207179672 1.061394322 1.142037007 0.768974801 1.109708028 1.026506836 1.237846434 1 23.59895117 3.623352885 2.058849002 1.038652751 1.206837366 0.214634874 0.120325368 0.429033956 3.565310751 0.032840195 0.060299281 4201.001967 -3.623352885 0.168184615 DKQFVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKQFVAK 7 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 105.57 0.0072026 2466580000 6211450 5659200 5578440 6821240 4580210 6529470 6968510 6790340 4912010 FALSE TRUE 5917847.068 6235878.914 5834216.992 6135555.996 5378997.174 6303352.817 5905335.814 6195741.832 5673739.424 1.04302412 1.099077425 1.028284268 1.08139545 0.9480515 1.110969741 1.040819004 1.09200324 1 22.43586846 DKQLNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKQLNEK 7 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 108.98 0.0065041 495950000 702880 518910 593130 689130 415380 616980 715540 676750 508920 FALSE TRUE 669656.2554 571787.519 620325.5972 619857.3431 487822.1405 595613.8279 606371.2312 617490.1823 587840.7144 1.139179779 0.972691249 1.055261369 1.054464803 0.829854293 1.013223163 1.031523024 1.050437929 1 19.16506576 4.622277225 2.753593372 1.00203673 1.148859291 0.29804172 0.066330374 0.431211371 5.191444433 0.015981781 0.126651255 41906.0981 -4.622277225 0.146822561 DKQPYEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKQPYEQK 8 1 P26583 P26583 HMGB2 High mobility group protein B2 0 147.95 0.00048256 497080000 347790 300510 297440 353100 235000 365380 371500 397040 252000 FALSE TRUE 331350.656 331132.3107 311077.9182 317605.7172 275983.9256 352726.799 314820.8519 362273.0728 291078.873 1.138353507 1.137603383 1.068706619 1.091132839 0.948141384 1.211791139 1.081565449 1.244587314 1 18.1510506 DKQS(ph)PSQANGCSDHRPIDILEMLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(0.981)PS(0.019)QANGCSDHRPIDILEMLSR;DKQS(0.938)PS(0.062)QANGCSDHRPIDILEMLSR;DKQS(0.923)PS(0.076)QANGCS(0.001)DHRPIDILEMLSR 178.85 1.35E-17 162656000 136395 108100 120217 139598 112427 120403 162498 143276 132165 TRUE FALSE 129947.8787 119115.5129 125729.0684 125565.3438 132034.2332 116233.4139 137705.9456 130729.9939 152660.4732 0.851221511 0.780264271 0.823586261 0.822513786 0.864888143 0.761385128 0.902040605 0.856344744 1 17.21996704 0.601710358 0.670593034 1.002612932 0.816220028 0.684308842 0.037281047 0.726118027 0.593409031 0.036814441 0.012878262 3.99678105 -0.601710358 -0.186392903 DKQVYR ddPTM_SK-BR-3_Trastuzumab_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 ; 125.86 0.016181 390670000 891810 697090 720520 838020 768030 665850 885080 883290 854060 FALSE TRUE 849655.9087 768124.2635 753556.5547 753780.6375 901974.1888 642791.4475 750044.7904 805944.445 986503.2629 0.861280384 0.778633272 0.763866257 0.764093405 0.914314451 0.651585729 0.760306447 0.816970886 1 19.9119643 0.876586628 6.083050911 0.999998465 0.784563101 0.491748844 0.068213057 1.793910972 88.08921008 0.062670097 0.015754374 7.526388432 -0.876586628 -0.215435364 DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 DKRPLS(0.836)GPDVGT(0.164)PQPAGLASGAK;DKRPLS(0.995)GPDVGT(0.005)PQPAGLASGAK;DKRPLS(0.95)GPDVGT(0.05)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.966)GPDVGT(0.034)PQPAGLASGAK;DKRPLS(0.5)GPDVGT(0.5)PQPAGLASGAK 201.6 1.16E-24 9969190000 4591940 4111070 4466400 5122760 3189210 5051780 5511610 5262810 3801840 TRUE FALSE 4374888.097 4529992.707 4671188.858 4607810.432 3745407.214 4876835.592 4670712.667 4801970.456 4391409.93 0.996237693 1.031557695 1.063710501 1.049278137 0.852894008 1.11053982 1.063602064 1.093491733 1 22.06625278 DKS(ph)HSHTPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKSHSHTPSRR 11 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.99)HS(0.009)HT(0.001)PSRR;DKS(0.499)HS(0.499)HT(0.002)PSRR 69.716 0.02552 25622000 30472 23507.9 29808 29627 25781 28794 40793 30742 4041.3 TRUE FALSE 29031.64895 25903.38174 31174.72628 26648.83767 30277.19824 27796.85656 34569.27864 28050.06751 4668.004164 6.219285144 5.54913424 6.678384421 5.708829028 6.486112089 5.954762589 7.405580077 6.009006531 1 12.18859013 0.362987017 19.81673796 1 6.262185416 0.907253436 0.527658366 0 1.37E-17 0.518231782 0.122148402 2.306678231 -0.362987017 5.262185416 DKS(ph)PSSLLEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKSPSSLLEDAK 12 1 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 DKS(0.967)PS(0.033)SLLEDAK 151.04 4.16E-05 151980000 333510 335490 240100 390030 147080 342890 317150 398700 171790 TRUE FALSE 317745.6433 369676.8124 251108.8225 350823.4434 172730.7054 331015.6333 268762.9426 363787.7144 198430.3158 1.60129586 1.863005715 1.265476102 1.767993172 0.870485463 1.668170672 1.354444967 1.833327296 1 17.59827293 3.74068362 24.98425734 1.415636157 1.732150789 0.163399636 0.314973757 295.7090265 3479989.291 0.072227155 0.122660037 5504.06584 -3.74068362 0.316514632 DKS(ph)PVREPIDNLTPEER ddPTM_SK-BR-3_Trastuzumab_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 290.39 2.98E-46 40511230000 7855040 6942430 6651970 7813790 4726010 7692980 8129550 8389490 4859860 TRUE FALSE 7483747.826 7649871.51 6956969.404 7028332.984 5550224.648 7426570.174 6889237.838 7654861.78 5613502.268 1.333169111 1.3627627 1.239327798 1.252040642 0.988727604 1.322983375 1.227261967 1.363651677 1 22.42046972 -5 0.126970341 0.223397945 1.371868999 0.323093221 0.111880683 174.7973283 1.412075937 35.69972039 0.886707403 1.00E-05 5 1.148471054 DKSDS(ph)PAIQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKSDSPAIQLR 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 DKS(0.012)DS(0.988)PAIQLR 104.95 0.0015326 94984000 269160 243030 256980 300440 230350 288410 333860 322750 181170 TRUE FALSE 256437.3402 267795.0333 268762.7872 270239.2004 270522.9671 278422.2894 282923.5252 294488.299 209264.9183 1.225419637 1.279693871 1.28431841 1.291373645 1.292729662 1.330477615 1.351987364 1.40725116 1 17.67497095 4.440133578 0.885507403 1.304252765 1.203302639 0 0.108761554 4.729376892 3.929898339 0.032940086 0.422871749 27550.75968 -4.440133578 -0.100950126 DKSEEVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKSEEVQK 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 134.59 0.00079343 98871000 258960 237100 204330 239020 125130 239480 260090 264440 161750 FALSE TRUE 246719.474 261260.7596 213698.7326 214993.2555 146952.6324 231186.7476 220408.4936 241284.2317 186833.3639 1.320532205 1.398362445 1.143793208 1.150721964 0.786543845 1.237395413 1.179706285 1.291440815 1 17.51139258 3.686279147 5.539962428 1.118234556 1.35947296 0.348998237 0.140044491 0.209511856 14.79698908 0.036711024 0.058319111 4856.005241 -3.686279147 0.241238404 DKSFLAMVVDIVQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKSFLAMVVDIVQELK 16 1 O00764;F2Z2Y4;O00764-3 O00764 PDXK Pyridoxal kinase 0 105.31 0.0011794 281440000 166290 144250 163010 170540 92386 173350 188160 193420 94927 FALSE TRUE 158429.8013 158949.239 170484.1697 153396.9952 108498.0891 167346.846 159452.7362 176483.1194 109647.7943 1.444897293 1.449634623 1.554834466 1.398997546 0.989514562 1.526221727 1.454226573 1.60954555 1 16.74251727 3.007820724 24.61563877 1.35259683 1.47128938 0.109611381 0.202976563 438.5505764 1380317.308 0.056201548 0.067048399 1018.171002 -3.007820724 0.11869255 DKST(ph)TPGGTGIKPFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKSTTPGGTGIKPFLER 17 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 DKS(0.113)T(0.443)T(0.443)PGGTGIKPFLER 115.36 0.01518 327060000 835810 777340 891630 1003500 639800 988420 1052900 1100000 782920 TRUE FALSE 796302.9177 856551.8298 932512.1174 902626.2735 751380.9174 954190.7676 892260.7672 1003678.169 904331.235 0.880543419 0.947166035 1.031162124 0.998114671 0.830869142 1.055134148 0.986652603 1.109856798 1 19.78649177 2.175358026 24.99999976 1.032080923 0.940697988 0.375660065 0.064011153 75.49163648 29860.06837 0.023400937 0.017282742 149.746964 -2.175358026 -0.091382935 DKTEFAQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKTEFAQDK 9 1 Q9UJA5;Q9UJA5-2;Q9UJA5-3 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 ; 108.2 0.0024174 194480000 412781 408770 349691 567807 331200 541724 599908 647869 343545 FALSE TRUE 393269.6602 450424.1277 365724.6782 510729.9616 388961.1751 522963.962 508381.0165 591138.1558 396820.204 0.991052512 1.135083655 0.92163825 1.287056345 0.980194988 1.31788643 1.281136926 1.489687646 1 18.59812596 2.227910005 24.9956884 1.294851376 1.070051264 0.307993171 0.153940481 220.3513102 517133.9441 0.050385487 0.037588904 169.0090673 -2.227910005 -0.224800111 DKTLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKTLKR 6 2 Q8IWF6 Q8IWF6 DENND6A Protein DENND6A 0 54.525 0.091258 185680000 159880 141100 148320 156900 111900 154650 195730 152950 144560 FALSE TRUE 152322.7893 155478.2504 155120.6187 141128.1139 131415.3246 149294.4317 165867.7937 139556.8872 166977.6265 0.912234725 0.931132234 0.92899044 0.845191759 0.787023551 0.894098418 0.993353404 0.835781955 1 17.34929528 -0.448919309 5.888197791 1 0.899639514 0.245962518 0.058261485 0 7.34E-11 0.058032484 0.013678388 0.3556974 0.448919309 -0.100360485 DKVAGHSLGYGFVNYVTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKVAGHSLGYGFVNYVTAK 19 1 Q15717;Q15717-2;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 110.77 0.00013776 145860000 411340 343290 412950 475250 301120 398150 480290 492470 329870 FALSE TRUE 391896.7734 378271.6413 431884.166 427476.9671 353635.2327 384361.9657 407012.9394 449346.7161 381024.5549 1.028534168 0.992774971 1.13348119 1.121914485 0.928116648 1.008759044 1.068206587 1.179311701 1 18.53952445 1.512275 6.176723925 1.100321194 1.033464214 0.084568756 0.072706992 0.268164326 22.46195007 0.039792907 0.017896715 32.52932111 -1.512275 -0.06685698 DKVVALAEGR ddPTM_SK-BR-3_Trastuzumab_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 ; 121.04 0.0004793 312300000 462670 392840 352410 437660 373880 421520 513230 489750 453830 FALSE TRUE 440800.506 432870.8426 368568.3471 393665.5853 439084.5536 406922.6567 434927.3374 446864.8937 524207.6386 0.840889132 0.82576218 0.703096102 0.750972623 0.837615711 0.776262356 0.829685234 0.852457806 1 18.99977885 0.691586894 1.083848274 0.999955319 0.793747217 0.708621472 0.042013738 0.615184168 1.224487304 0.041996126 0.013225699 4.915717239 -0.691586894 -0.206208102 DKVVEDDEDDFPTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 120.24 0.00013594 216720000 352480 312040 324550 383310 228070 352640 374490 379160 272880 FALSE TRUE 335818.9689 343837.2308 339430.9385 344778.9506 267845.3358 340427.9884 317354.6725 345958.7403 315196.8367 1.065426203 1.090865106 1.076885612 1.093852826 0.849771649 1.080048873 1.006845994 1.097595851 1 18.26589353 DKVVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKVVGK 6 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 94.887 0.092227 0 1133740 910830 945580 1267870 680180 1194690 1157860 1449130 862820 FALSE TRUE 1080150.357 1003644.613 988935.7783 1140421.299 798803.1766 1153317.586 981207.1914 1322236.495 996621.7189 1.083811778 1.007046699 0.992288006 1.144287022 0.801510906 1.157227024 0.984533221 1.326718523 1 19.92668649 1.287403877 24.99999943 1.163365495 1.026612566 0.174911477 0.125412342 150.0856966 76819.74941 0.071389849 0.026069488 19.382236 -1.287403877 -0.136752929 DKWLAPDGLIFPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DKWLAPDGLIFPDR 14 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;; 170.91 2.83E-06 1013894000 1469360 1493870 1448840 1667390 1165200 1595650 1604230 1628130 1205310 FALSE TRUE 1399906.265 1646097.051 1515270.747 1499780.789 1368410.511 1540392.24 1359475.25 1485562.306 1392223.319 1.005518472 1.1823513 1.088381962 1.077255904 0.982895842 1.106426117 0.976477862 1.067043114 1 20.40895921 2.943120052 6.069440121 1.027629432 1.097322448 0.228460764 0.056659081 0.292360282 23.32943328 0.016233401 0.017469554 877.2432843 -2.943120052 0.069693016 DKWSPALQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKWSPALQIR 10 1 P61088;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ; 142.19 3.30E-05 2055200000 4360100 3063800 2009670 2225000 3855200 2658700 5070400 3730300 3686400 FALSE TRUE 4154006.714 3376004.703 2101815.357 2001338.773 4527545.659 2566628.552 4296817.356 3403655.156 4258068.084 0.975561365 0.792848925 0.493607738 0.470010985 1.063286347 0.602768322 1.0091002 0.799342587 1 22.02176759 1.706858229 11.64580207 0.926554651 0.752018587 0.187984403 0.19595295 0.231510854 64.15583942 0.092243866 0.050363981 50.91646322 -1.706858229 -0.174536064 DKYEESRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DKYEESRR 8 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;H0Y9C3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 53.327 0.077215 100850000 75073 55335 61744 69590 53693 70506 82782 89626 65360 FALSE TRUE 71524.44807 60973.69941 64575.02347 62594.68099 63057.0422 68064.35954 70152.0855 81777.8723 75495.69499 0.947397704 0.80764472 0.855347096 0.829115899 0.835240237 0.901566103 0.92921968 1.083212391 1 16.20410676 1.50837004 2.334450998 1.040219708 0.858840012 0.721857911 0.045004193 0.138931311 1.53494436 0.034201832 0.011644489 32.23814465 -1.50837004 -0.181379696 DKYGPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DKYGPPTR 8 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;; 90.108 0.012248 584370000 904740 742070 799330 1016560 819220 865590 1084390 953740 962040 FALSE TRUE 861974.7332 817687.7767 835980.0711 914373.4575 962091.7086 835614.4013 918946.3893 870225.4695 1111228.25 0.775695482 0.735841423 0.752302753 0.822849363 0.865791262 0.751973684 0.826964568 0.783120362 1 20.08372375 -5 0.198678975 1.962446674 0.751133506 0.747302735 0.038827538 68.11556414 0.672900551 26.00027413 0.091854593 1.00E-05 5 -1.211313168 DKYGPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKYGPPVR 8 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 107.15 0.0037006 932970000 2262960 1949380 2223240 2584730 2280040 2310420 2775570 2462300 2836610 FALSE TRUE 2155994.366 2148024.038 2325177.753 2324908.03 2677678.254 2230409.576 2352105.82 2246687.959 3276496.991 0.658018112 0.655585537 0.70965356 0.709571239 0.817238124 0.680729933 0.717872113 0.68569816 1 21.64372278 -5 0.262922516 2.95537293 0.677200861 0.803150858 0.045855585 86.09929048 0.842953316 91.13837461 0.05961295 1.00E-05 5 -2.278172069 DKYGVFPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DKYGVFPLR 9 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 143.89 9.20E-05 1230470000 3330500 3133900 3428000 4553700 3926800 4200500 5214300 4794900 4634300 FALSE TRUE 3173073.865 3453247.973 3585177.191 4095953.425 4611632.677 4055035.632 4418762.768 4375033.137 5352963.575 0.59276956 0.645109559 0.669755574 0.76517491 0.861510192 0.757530959 0.8254797 0.817310463 1 22.35190641 5.438851846 0.121313984 1.105148871 5.00E-15 0.883037759 0.040114734 14.3784931 0.230119288 0.349672808 2.625186181 274695.6906 -5.438851846 -1.105148871 DLAAFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLAAFDK 7 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 89.752 0.041043 34680000 149090 153840 140910 179300 129990 154630 165540 176810 121220 FALSE TRUE 142042.8112 169516.4709 147370.8629 161276.4234 152660.2148 149275.1243 140283.8326 161327.5791 140018.1785 1.014459784 1.210674733 1.052512356 1.151824892 1.090288536 1.066112457 1.001897283 1.152190243 1 17.09525462 2.273097041 3.268687347 1.048516451 1.111683144 0.118556845 0.066572272 0.428733386 9.494640996 0.024002005 0.018345169 187.5413515 -2.273097041 0.063166694 DLAAFDKSHDQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLAAFDKSHDQAVR 14 1 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 180.62 1.04E-06 298240000 267320 79876 292010 182660 293890 234350 418350 272030 369770 FALSE TRUE 254684.3134 88015.45521 305398.9473 164298.6698 345144.323 226234.4007 354523.024 248209.6111 427112.0431 0.596293917 0.206071116 0.715032396 0.384673466 0.808088483 0.529683966 0.830046892 0.581134658 1 18.70425505 1.531691434 0.270728193 1.050918195 0.346634087 0.411830767 0.175130222 1.426359716 0.418794457 0.378090738 0.356875416 34.01664159 -1.531691434 -0.704284109 DLADELALVDVIEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 272.92 4.55E-33 712456300 959570 1308128 866315 1204168 493443 979117 842447 1035266 428991.8 FALSE TRUE 914213.0278 1441427.73 906036.3997 1083122.745 579499.303 945209.9328 713916.2375 944612.6207 495517.6574 1.844965591 2.908933131 1.828464407 2.185840865 1.16948265 1.907520184 1.44074833 1.906314753 1 18.91857694 3.080552767 1.871134843 1.54577208 2.338415377 0.383742726 0.419568715 0.304809503 2.179860099 0.127207131 0.158452529 1203.795641 -3.080552767 0.792643297 DLADELALVDVIEDKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 247.78 7.94E-21 261770000 335890 363970 337220 370340 164910 336350 332450 399980 129750 FALSE TRUE 320013.1454 401058.9568 352681.8706 333112.7196 193670.2518 324702.1152 281728.6466 364955.6308 149870.9673 2.135257756 2.676028346 2.353236767 2.222663439 1.292246625 2.166544468 1.879808022 2.435132283 1 17.19336141 2.984632228 22.10723797 1.83927194 2.398004742 0.320891767 0.423707366 180.1083879 259095.7327 0.115323343 0.126323438 965.2331476 -2.984632228 0.558732802 DLAEDAPWKK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 138.71 9.21E-05 1429610000 4872500 4190240 3008530 4445040 2939090 3775880 5185850 4784190 3080730 FALSE TRUE 4642186.581 4617230.22 3146474.076 3998216.134 3451666.365 3645120.329 4394653.338 4365260.961 3558473.874 1.304544236 1.297531016 0.884220086 1.123576082 0.969985024 1.02434933 1.234982606 1.226722779 1 21.76282721 3.85267462 11.84928282 1.081141925 1.301820087 0.438979472 0.109349357 0.537310686 53.04508794 0.028362926 0.051153223 7123.191502 -3.85267462 0.220678162 DLAEITTLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLAEITTLDR 10 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;;; 191.45 1.84E-06 193651000 242035 188981 201416 222919 236336 193142 249277 209586 237808 FALSE TRUE 230594.4852 208238.3788 210651.1228 200510.7586 277552.9236 186453.4441 211245.2154 191233.5388 274686.0501 0.839483786 0.758095938 0.76687958 0.729963384 1.01043691 0.678787452 0.769042386 0.696189481 1 18.06742412 -2.36425507 2.316797322 2.522806588 0.781887755 0.355573002 0.092603294 5775353.733 990923.2854 45769430.99 0.021810282 0.004322599 2.36425507 -1.740918833 DLAFTLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLAFTLEER 9 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ;;; 159.37 0.00015379 351044000 839520 769380 714970 830230 814620 688660 883820 838080 848270 FALSE TRUE 799837.5534 847780.6967 747752.0817 746773.7031 956689.4701 664811.5315 748977.0265 764693.2723 979815.3792 0.816314553 0.865245346 0.763156098 0.762157564 0.976397687 0.678506937 0.764406277 0.780446285 1 19.90215041 3.751817204 24.54005401 0.801636302 0.840779944 0 0.100621425 2656.264628 4917151.388 0.023682166 0.042391297 5646.992412 -3.751817204 0.039143642 DLAGAPPGEVVGCFT(ph)PQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLAGAPPGEVVGCFTPQSR 19 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 1 DLAGAPPGEVVGCFT(0.976)PQS(0.024)R;DLAGAPPGEVVGCFT(0.986)PQS(0.014)R;DLAGAPPGEVVGCFT(0.861)PQS(0.139)R;DLAGAPPGEVVGCFT(0.5)PQS(0.5)R 221.85 2.87E-18 370474000 194947 159331 179757 204562 195587 172841 204017 217269 234265 TRUE FALSE 185732.2417 175567.01 187999.0363 183999.0391 229697.3109 166855.4728 172890.4596 198243.7745 270593.6197 0.686388104 0.648821691 0.694765222 0.679982918 0.848864475 0.616627521 0.638930289 0.732625458 1 18.0457683 0.905287586 7.767837969 0.999999654 0.683506049 0.707918408 0.062498585 1.641745224 134.695749 0.058216217 0.014583113 8.040583864 -0.905287586 -0.316493605 DLAGCIHGLSNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLAGCIHGLSNVK 13 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 156.02 4.70E-05 1773900000 5929200 4648000 4586000 4465700 4514700 3868500 5404300 5122600 4524000 FALSE TRUE 5648938.467 5121636.484 4796272.636 4016799.352 5302062.251 3734532.875 4579774.778 4674037.987 5225558.815 1.081020933 0.980112686 0.917848752 0.768683215 1.01464024 0.7146667 0.876418186 0.894457063 1 22.31715389 3.949007291 1.620907597 0.866409444 1.067408506 0.332548075 0.09129949 0.364651615 1.817283867 0.023553814 0.070210071 8892.160455 -3.949007291 0.200999062 DLAILQCHGELDPMVPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLAILQCHGELDPMVPVR 18 0 O95372;Q5QPQ1;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;;;;; 192.62 1.65E-14 672931000 734794 616667 664287 727519 735776 651977 751471 692261 731589 FALSE TRUE 700061.7438 679506.0684 694745.216 654387.4079 864095.1014 629398.873 636820.2972 631642.9569 845040.0857 0.828436137 0.804111047 0.822144686 0.774386232 1.022549245 0.744815404 0.753597738 0.747470999 1 19.68866025 -0.259390587 7.564656064 0.999999999 0.810612153 0.34961819 0.080477234 0 0 0.074189766 0.017486695 0.550312545 0.259390587 -0.189387846 DLALAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLALAIR 7 0 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 95.793 0.030721 23387000 108000 96817 120900 103950 115020 123650 152020 117400 79128 FALSE TRUE 102895.054 106682.7624 126443.3846 93500.74851 135079.4516 119367.9695 128826.557 107119.8336 91398.76611 1.125781653 1.167223223 1.38342551 1.02299793 1.477913295 1.306012921 1.409499958 1.172005249 1 16.47988707 3.920818647 8.002293682 1.280689726 1.14117849 0.054775232 0.157739031 0.556713536 51.05391448 0.036569659 0.066295896 8333.331278 -3.920818647 -0.139511237 DLANDIMTLMSHTKPYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLANDIMTLMSHTKPYIR 18 1 O14617-5;O14617-2;O14617;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 126.25 1.68E-05 75772000 306170 287790 290800 316940 251900 299230 320350 333490 207880 FALSE TRUE 291697.9509 317116.1282 304133.4676 285080.5891 295831.2802 288867.5901 271474.7239 304287.8477 240116.9687 1.214816064 1.320673545 1.266605477 1.187257155 1.23202988 1.203028639 1.130593666 1.267248414 1 17.87337783 -5 0.142241831 0.183213786 1.310506953 0.672723515 0.050344538 74.98620523 0.649030073 17.2323203 0.280682474 1.00E-05 5 1.127293167 DLAPIGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLAPIGIR 8 0 Q99714 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 81.297 0.054034 49516000 73946 57427 62756 60821 73973 60622 78929 62847 76509 FALSE TRUE 70450.71913 63278.87659 65633.42467 54707.15753 86873.86778 58522.64494 66886.93142 57343.78351 88373.62497 0.797191686 0.716038033 0.742681142 0.619043946 0.983029358 0.66221845 0.756865314 0.648878933 1 16.43132824 -1.075588543 4.863629439 1.0000082 0.743071763 0.392973678 0.101227081 7.87E-06 1.50E-06 0.08570762 0.020200835 0.084025568 1.075588543 -0.256936437 DLAQGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLAQGTK 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 101.54 0.021088 307200000 581880 495820 485940 575800 449780 563680 623910 582230 533640 FALSE TRUE 554375.6856 546344.6217 508220.8297 517919.4901 528221.4896 544159.6203 528721.0706 531246.8546 616394.1657 0.899385031 0.886355926 0.82450623 0.84024074 0.856954071 0.882811114 0.85776456 0.861862237 1 19.23349368 -1.054584003 3.940620819 1.00002463 0.866050186 0.790401745 0.022023778 2067084.874 1660091.967 381.5969161 0.005660925 0.088189321 1.054584003 -0.133974444 DLCNTHLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLCNTHLMR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 127.76 0.00043624 299841000 202092 180104 172498 214870 218749 214417 249777 193666 220663 FALSE TRUE 192539.5117 198456.8024 180407.2039 193270.8594 256898.7563 206991.6855 211668.9312 176707.5784 254882.291 0.755405607 0.778621385 0.707805957 0.758274961 1.007911359 0.812106972 0.830457582 0.693290921 1 17.95947161 2.951446992 24.99951245 0.854589582 0.752390667 0.285964295 0.09173699 545.4189022 280831.0454 0.02600873 0.027586954 894.2253804 -2.951446992 -0.102198915 DLCQADKTWNAVLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLCQADKTWNAVLLR 15 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 ; 179.14 6.23E-07 242379000 370950 244027 332800 328080 347240 349860 473970 379800 416600 FALSE TRUE 353415.9287 268893.6287 348059.2092 295100.7751 407798.5461 337744.2605 401657.1714 346542.6986 481204.2003 0.734440656 0.558793187 0.723308751 0.613254778 0.847454253 0.701873052 0.83469174 0.72015726 1 18.87628971 0.272562029 0.246908052 1.099128354 0.614463729 0.586336064 0.079804024 3.398505796 0.414462947 0.483278222 0.151087373 1.873104592 -0.272562029 -0.484664625 DLDANGDAQVDFSEFIVFVAAITSACHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLDANGDAQVDFSEFIVFVAAITSACHK 28 0 P25815 P25815 S100P Protein S100-P 0 ;;;;; 281.85 8.14E-62 4391072000 2660621 2389698 2165621 2988975 1989384 2588525 3197721 2972249 1742907 FALSE TRUE 2534858.718 2633210.943 2264916.865 2688517.554 2336331.94 2498883.73 2709849.931 2711983.121 2013188.116 1.259126605 1.307980572 1.125039854 1.335452724 1.160513477 1.241256945 1.34604904 1.347108648 1 20.94105056 DLDAPDDVDFF ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLDAPDDVDFF 11 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 93.178 0.021969 23636000 129266 109270 116920 141466 113866 104243 130448 127383 116825 FALSE TRUE 123155.8524 120404.7372 122280.8976 127245.5689 133724.1943 100633.0388 110545.7618 116228.6692 134941.6243 0.912660219 0.892272772 0.906176269 0.94296752 0.990978099 0.745752389 0.819211732 0.861325553 1 17.04197591 2.247209833 24.99998567 0.835698176 0.922111223 0.185774548 0.06865788 232.5248984 672098.1822 0.022081228 0.018207303 176.6891302 -2.247209833 0.086413048 DLDDFQSWLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLDDFQSWLSR 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 248.88 6.24E-16 471958000 769912 585561 574820 754232 670773 612621 819310 753686 693974 FALSE TRUE 733519.7856 645230.3316 601176.0656 678415.1664 787755.5988 591405.7812 694309.2118 687689.2583 801591.9436 0.91507879 0.804936148 0.749977679 0.846334811 0.982738917 0.737789078 0.866162912 0.857904404 1 19.61250848 0.588574539 2.014610634 0.999956536 0.842039345 0.31720065 0.071800027 3.210016087 14.2721169 0.064538629 0.017756412 3.877702969 -0.588574539 -0.157917191 DLDDIEDENEQLKQENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLDDIEDENEQLKQENK 17 1 Q96IZ0;H0YHP5 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 235.24 3.40E-20 171450000 414090 431030 325130 468060 154520 433850 359780 477520 127150 FALSE TRUE 394516.7863 474952.447 340037.5321 421009.7195 181468.2391 418825.6657 304888.9532 435705.8173 146867.7726 2.686203919 3.23387792 2.315263084 2.866590213 1.235589237 2.851719327 2.075941834 2.966653675 1 17.16415833 3.298389511 1.789166788 2.176123128 2.930804505 0.191889942 0.665539991 0.521498491 3.435686446 0.18890885 0.277986578 1987.87701 -3.298389511 0.754681377 DLDEEGS(ph)EK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLDEEGSEK 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EK 175.49 5.65E-05 129760000 564940 973420 429130 702390 226430 697780 408900 635100 172200 TRUE FALSE 538236.4058 1072612.605 448806.035 631784.4227 265919.3203 673615.7036 346514.795 579487.2771 198903.8965 2.706012377 5.392617357 2.256396394 3.176330046 1.336923635 3.386639052 1.742121703 2.913403343 1 17.60171201 3.704699204 24.35941419 2.322459618 4.049314999 0.358285338 0.993369587 398.1081172 286393.1441 0.236069227 0.36574345 5066.396837 -3.704699204 1.726855381 DLDEEGS(ph)EKELHENVLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLDEEGSEKELHENVLDK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EKELHENVLDK 171.75 7.54E-12 122680000 234010 340290 171350 278530 115710 301390 190710 276680 64917 TRUE FALSE 222948.8111 374965.9379 179206.567 250531.6352 135889.7874 290952.7887 161613.6869 252452.4324 74983.99681 2.973285241 5.000612848 2.389930847 3.341134721 1.812250522 3.880198457 2.155309049 3.366750816 1 16.19429511 0.241587891 0.176983265 7.83E-11 4.300014382 0.346203251 0.909843878 9.649799418 0.725156499 11.25028391 4.366283695 1.744166301 -0.241587891 4.300014382 DLDEEIFDDDDFYHQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 ;;;;; 198.07 1.77E-15 152286900 271003 239605 218901 282073 202821.4 206180.8 265503 269811 169223.9 FALSE TRUE 258193.2253 264021.0219 228937.8274 253718.4861 238193.3879 199040.7072 224995.6411 246184.9185 195466.2781 1.320909303 1.350724148 1.171239508 1.298016663 1.218590696 1.018286679 1.151071393 1.259475142 1 17.57656021 8 0.101986656 0.899272291 2.278212952 0.526537489 0.081754854 84.96246959 0.6120193 0.918133055 16.4139181 100000000 -8 1.378940661 DLDELSRYPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLDELSRYPEDK 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 201.48 1.35E-07 4338570000 8919120 7889910 7947570 9452510 5409370 9243500 9554960 10119650 6048240 FALSE TRUE 8497530.874 8693900.799 8311973.946 8502325.736 6352762.415 8923395.277 8097175.363 9233519.798 6986170.169 1.216336085 1.244444465 1.189775477 1.217022422 0.90933405 1.277294292 1.15902922 1.321685498 1 22.73607035 -1.379196407 3.569090492 0.998841487 1.191678237 0.230798488 0.110077966 0.000943851 0.000164172 0.098464392 0.023070061 0.041764145 1.379196407 0.19283675 DLDELSRYPEDKITPENLPQILLQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLDELSRYPEDKITPENLPQILLQLK 26 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 103.02 0.0020781 146930000 345950 142460 380160 227870 271420 321540 552940 377010 365180 FALSE TRUE 329597.6291 156976.836 397590.712 204964.0747 318755.5621 310404.9892 468578.8476 343997.0057 421810.2493 0.781388384 0.37215036 0.942581914 0.485915349 0.755684725 0.735887735 1.110875917 0.815525479 1 18.68623463 1.94345171 3.890197832 0.981212827 0.646254006 0.397715715 0.171770026 0.201393956 5.847294601 0.074660292 0.043565424 87.7913464 -1.94345171 -0.334958821 DLDEVLQTHSVFVNVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLDEVLQTHSVFVNVSK 17 0 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 233.63 4.10E-20 501020000 1143210 1088030 997990 1321260 868820 1135550 1279560 1193000 859650 FALSE TRUE 1089172.729 1198901.494 1043748.829 1188444.435 1020341.933 1096225.619 1084339.621 1088534.596 992960.1315 1.096894724 1.207401441 1.051148778 1.196870244 1.027575932 1.103997617 1.09202735 1.096252066 1 19.92137627 -1.11992887 0.147664743 0.871439839 1.178210996 0.312194186 0.054290509 31.03715793 0.917655835 1.880994946 0.345677369 0.075870183 1.11992887 0.306771157 DLDFTIDLDFKGQLCELSCSTDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLDFTIDLDFKGQLCELSCSTDYR 24 1 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 68.552 0.030851 9705800 9775.3 6894.5 12223 10765 9964.8 11090 18918 13126 12806 FALSE TRUE 9313.240942 7597.057388 12783.43664 9682.881748 11702.65797 10705.95052 16031.71165 11976.61785 14791.88908 0.62961809 0.513596157 0.864219342 0.654607515 0.791153713 0.723771688 1.08381773 0.809674667 1 13.85251869 2.572979065 0.517457189 1.003629298 0.559688599 0.52820272 0.116968544 0.635305751 0.354527622 0.099257471 0.108406134 374.0925548 -2.572979065 -0.443940699 DLDGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLDGFR 6 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;; 143.18 0.026596 869400000 2140300 1975620 1889410 2290220 2013250 1892320 2246790 2108490 1920570 FALSE TRUE 2039132.261 2176937.924 1976041.317 2060002.734 2364360.163 1826788.484 1904000.92 1923859.438 2218402.187 0.919189619 0.981308952 0.890749806 0.928597504 1.06579419 0.823470377 0.858275804 0.867227525 1 21.08108951 2.200255311 24.99999885 0.871739016 0.952662817 0.204307574 0.06509357 205.2060135 133926.7356 0.022177604 0.016379536 158.5825186 -2.200255311 0.080923801 DLDGFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 907300000 2893500 2059700 2330150 2694550 2133070 2525270 3115610 2775720 2509000 FALSE TRUE 2756729.989 2269585.772 2436989.682 2423688.715 2505076.733 2437819.267 2640266.472 2532663.242 2898082.906 0.951225372 0.783133487 0.840897159 0.836307585 0.864390983 0.841183412 0.911038972 0.873909865 1 21.46666744 0.54590777 0.70771301 1.00122981 0.851528131 0.501545023 0.044033621 1.253762783 1.069728114 0.046502492 0.015677608 3.514857887 -0.54590777 -0.149701679 DLDIFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLDIFDR 7 0 Q14165;F5H1S8;H0YG07 Q14165 MLEC Malectin 0 ;; 166.05 0.002647 97904000 335863 276552 270328 408070 425860 302616 399287 313764 346056 FALSE TRUE 319987.4216 304732.9632 282722.8062 367050.0283 500129.8492 292136.332 338368.4347 286289.1608 399720.5971 0.800527728 0.762364926 0.70730107 0.918266487 1.251198594 0.730851335 0.846512382 0.716223189 1 18.60863239 3.227803944 24.71724655 0.902405137 0.764195099 0.186975866 0.150263473 338.0507327 776789.2138 0.043135382 0.052057221 1689.677977 -3.227803944 -0.138210038 DLDIIDNYDYSHTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 295.03 4.97E-44 2768409000 4262814 3348768 3063553 4311914 2808984 3845180 4846781 4515614 2986085 FALSE TRUE 4061319.23 3690011.266 3204019.935 3878472.213 3298869.92 3712020.452 4107315.541 4120202.899 3449151.811 1.177483466 1.069831503 0.92892981 1.124471298 0.95642932 1.076212546 1.190819009 1.194555394 1 21.7178102 1.894688846 7.08923891 1.146944712 1.059452448 0.119902728 0.089270277 0.463176333 27.29570768 0.037256662 0.023050831 78.46732478 -1.894688846 -0.087492263 DLDKADSMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 169.52 4.20E-06 1878540000 3964430 3123690 3510300 3777600 3207980 3906870 5086110 4663980 3868460 FALSE TRUE 3777039.251 3441997.562 3671250.727 3397868.471 3767450.696 3771574.112 4310130.507 4255577.186 4468361.019 0.845285158 0.770304268 0.821610141 0.760428367 0.843139281 0.844062084 0.964588691 0.952379892 1 22.09131432 1.82520921 1.613920585 0.98428349 0.802171962 0.872874211 0.028828408 0.109981185 0.545327399 0.01890902 0.007998193 66.86659528 -1.82520921 -0.182111528 DLDLKKPIYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLDLKKPIYQR 11 2 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 93.839 0.0050341 1504370000 2384000 1632870 2249600 2103960 1805740 2503700 3302800 2945500 2446600 FALSE TRUE 2271313.045 1799261.309 2352746.385 1892465.944 2120660.484 2416996.241 2798897.2 2687576.405 2826006.232 0.803718342 0.63667988 0.83253404 0.669660924 0.750408991 0.855269254 0.990407299 0.951015739 1 21.43033322 2.015543088 2.320923699 0.980430213 0.730111576 0.784357846 0.057914144 0.123264524 1.250633112 0.02840302 0.015666688 103.6437428 -2.015543088 -0.250318637 DLDLLASVPS(ph)PSSSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLDLLASVPSPSSSGSR 17 0 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 DLDLLAS(0.003)VPS(0.971)PS(0.017)S(0.003)S(0.003)GS(0.003)R;DLDLLAS(0.004)VPS(0.994)PS(0.001)SSGSR;DLDLLASVPS(0.978)PS(0.02)S(0.002)SGSR;DLDLLASVPS(0.998)PS(0.002)SSGSR;DLDLLASVPS(0.999)PSSSGSR;DLDLLASVPS(0.997)PS(0.002)SSGSR 264.16 1.98E-27 702567000 773071 837500 744528 867140 669674 736930 820505 817166 766248 TRUE FALSE 736529.4659 922842.2022 778665.3452 779973.4397 786464.9336 711409.9293 695321.8926 745610.613 885073.8264 0.832167266 1.042672571 0.879774457 0.881252407 0.888586816 0.803785976 0.78560892 0.842427593 1 19.75543827 2.999004971 1.568100995 0.838055861 0.93456076 0.051224019 0.079005251 0.564807765 2.840555058 0.027310656 0.032393887 997.7114842 -2.999004971 0.096504898 DLDSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DLDSLHR 7 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;;;;;;;; 150.17 0.0019672 4397320000 8858250 7462060 8019540 9231180 9180610 8053880 10349130 9142610 9004660 FALSE TRUE 8439538.078 8222452.398 8387243.841 8303244.248 10781705.48 7774972.116 8770180.144 8342034.6 10401056.68 0.811411603 0.790540101 0.806383822 0.798307759 1.036597127 0.747517522 0.84320088 0.802037221 1 23.31022677 -5 0.320772043 2.632868824 0.819583931 0.317652301 0.077755905 383.6221395 3.39095748 425.7154426 0.063765855 1.00E-05 5 -1.813284893 DLDTGEEVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLDTGEEVTR 10 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 185.58 3.33E-06 288680000 343930 309190 296430 350690 312190 315830 371240 323200 286970 FALSE TRUE 327673.1105 340696.8125 310021.6087 315437.9749 366635.8372 304892.7279 314600.5197 294898.8946 331471.842 0.988539806 1.027830329 0.935287917 0.951628268 1.106084411 0.919814866 0.949101794 0.889664995 1 18.3385268 DLDVFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLDVFLR 7 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 0 ; 91.041 0.038841 26120000 102070 85678 86636 107757 98617 76306 112961 109449 102719 FALSE TRUE 97245.35338 94408.68561 90608.34629 96925.06164 115815.7736 73663.50409 95726.72478 99865.06533 118648.1379 0.81961129 0.795703053 0.763672721 0.816911781 0.976128034 0.620856807 0.80681186 0.841690962 1 16.85632993 0.833174035 3.143839614 0.999884017 0.798240661 0.350968028 0.085103791 0.857153026 14.10237464 0.075057778 0.019563556 6.810422185 -0.833174035 -0.201643356 DLEADIIGDTSGHFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLEADIIGDTSGHFQK 16 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 ;;; 315.13 8.54E-58 738772000 1427866 1028948 1077837 2178400 1490550 1394212 1630474 1243576 1059221 FALSE TRUE 1360373.604 1133798.971 1127256.893 1959423.093 1750501.448 1345930.089 1381715.246 1134681.893 1223479.583 1.111889093 0.926700361 0.921353252 1.601516789 1.430756567 1.100083816 1.129332491 0.927422009 1 20.2225586 1.347725047 3.68221098 0.96381609 1.159906793 0.147790339 0.207967602 0.547954184 11.91967757 0.176457482 0.057362449 22.27024769 -1.347725047 0.196090704 DLEAEHVEVEDTTLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DLEAEHVEVEDTTLNR 16 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;;;;;;; 268.56 1.54E-27 10244940000 9072600 7928820 7947710 9225460 7961390 8193730 9781020 8689750 6652060 FALSE TRUE 8643756.178 8736775.772 8312120.365 8298099.234 9349853.895 7909979.076 8288745.758 7928829.423 7683627.491 1.124957735 1.137063943 1.081796375 1.079971569 1.216854136 1.029458948 1.078754243 1.031912262 1 22.87335615 1.566499624 1.13255915 1.007872722 1.122554613 0.456272411 0.045896747 0.39244786 0.963914937 0.037613736 0.013631015 36.85527227 -1.566499624 0.114681891 DLEAHIDSANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DLEAHIDSANK 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 194.17 6.33E-07 7132980000 19100350 16367810 15159590 20189190 11834570 18048730 18866290 18903570 10136660 FALSE TRUE 18197514.31 18035708.45 15854672.2 18159734.26 13898515.26 17423697.95 15987890.96 17248273.2 11708601.46 1.554200505 1.540381104 1.354104694 1.550973814 1.187034618 1.488110942 1.365482548 1.473128388 1 23.48106543 -3.677487438 0.161970637 4.11E-14 1.577653904 0.610019667 0.111557427 50.77746978 0.69613746 17.54205811 0.440167669 0.000210142 3.677487438 1.577653904 DLEAHIDSANKNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLEAHIDSANKNR 13 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 143.42 2.45E-05 119650000 258670 101850 312410 206580 272960 248690 450480 320220 363060 FALSE TRUE 246443.1817 112228.6308 326734.3075 185814.1859 320564.1376 240077.8029 381751.0024 292179.8392 419361.4905 0.587662881 0.267617875 0.779123298 0.443088338 0.764410049 0.572484142 0.910314874 0.696725488 1 18.67783486 2.029117713 0.400809939 0.994265332 0.414468217 0.475326037 0.156078397 0.829269155 0.332219954 0.158535297 0.160733961 106.934468 -2.029117713 -0.579797115 DLEALMFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DLEALMFDR 9 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;;;;;;; 180.44 0.00011317 765172000 1181783 936496 915249 1022111 1094285 863729 1260505 1057996 1072975 FALSE TRUE 1125922.46 1031926.007 957214.072 919366.4604 1285127.958 833817.8482 1068191.811 965352.2615 1239366.483 0.90846612 0.832623781 0.772341422 0.741803553 1.036923279 0.672777471 0.861885347 0.778907833 1 20.24117143 -0.576847793 7.582022912 1.000000437 0.829081606 0.233418762 0.099092545 0 0 0.085064432 0.020049879 0.264942852 0.576847793 -0.170918831 DLEDSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 205.13 0.00019074 3168160000 8477100 8167270 6964800 9017610 6555480 7776180 8298180 8136240 6374140 FALSE TRUE 8076404.283 8999524.098 7284142.969 8111142.71 7698753.636 7506888.937 7032140.234 7423787.693 7362609.077 1.096948677 1.222328118 0.989342622 1.101666899 1.045655631 1.019596295 0.955115253 1.008309366 1 22.81178567 3.065241443 0.770893316 0.983623996 1.155895498 0.46768849 0.055681878 0.475320753 0.631000928 0.031310758 0.044100835 1162.094492 -3.065241443 0.172271502 DLEEAEGR ddPTM_SK-BR-3_Trastuzumab_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 ; 137.9 0.0016941 296560000 388460 315670 339430 345090 349680 312320 346260 354870 368840 FALSE TRUE 370098.2657 347837.1319 354993.2012 310400.8976 410664.0813 301504.2801 293431.6775 323795.7015 426037.8234 0.868698142 0.816446599 0.833243392 0.728575916 0.963914607 0.707693692 0.688745603 0.760016327 1 18.70062199 DLEEDHACIPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLEEDHACIPIK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 150.06 6.43E-05 1173460000 2583840 3035170 2221240 3067740 1636210 2678860 2585940 2864500 1475070 FALSE TRUE 2461707.004 3344457.274 2323086.051 2759364.947 1921564.506 2586090.406 2191407.359 2613669.194 1703816.322 1.444819475 1.962921255 1.363460381 1.619520198 1.127800269 1.517822299 1.286175822 1.534008778 1 20.70033839 -0.478695211 0.082686054 0.118147978 2.226581558 0.359094217 0.213482675 55.31117925 1.133534511 19.97274894 9.387320853 0.332127463 0.478695211 2.10843358 DLEEDHACIPIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DLEEDHACIPIKK 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 200.93 6.87E-08 18372360000 36666200 35016800 32758000 40731800 20913900 39519400 39906300 41679700 20714400 FALSE TRUE 34933061.39 38585051.73 34259986.7 36637362.08 24561277.54 38150833.27 33817861.01 38030004.51 23926683.36 1.460004334 1.612636869 1.43187362 1.53123446 1.026522447 1.594488994 1.413395267 1.589439035 1 24.51211709 -2.022030731 2.745631981 0.468317879 1.462543237 0.422240268 0.168072582 46265688.54 42816779.12 154364213.6 0.03872938 0.009505375 2.022030731 0.994225358 DLEEFFSTVGK ddPTM_SK-BR-3_Trastuzumab_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 0 127.76 0.00065101 42044000 139870 112640 119750 143890 138740 125360 181670 138590 153700 FALSE TRUE 133258.6223 124118.1441 125240.6559 129425.9038 162936.2121 121018.7518 153952.9049 126454.3249 177535.011 0.750604749 0.699119252 0.705442015 0.729016227 0.917769465 0.68166133 0.867169264 0.712278238 1 17.43774404 -5 0.161248658 1.912706451 0.692668127 0.503208832 0.075983325 99.4032695 0.91692955 28.95971651 0.280457676 1.00E-05 5 -1.220038324 DLEEWNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ; 201.49 0.00025906 2202010000 2539280 2177330 2201810 2608830 2249510 2369840 2794640 2470270 2329560 FALSE TRUE 2419253.267 2399202.402 2302765.166 2346585.452 2641823.832 2287771.847 2368266.341 2253960.063 2690816.267 0.899077836 0.891626244 0.855786846 0.872071973 0.981792724 0.850214812 0.880129338 0.837649189 1 21.35961245 -1.517477383 4.43955576 1.000828242 0.885093844 0.460345187 0.03959455 0.000303114 3.29E-05 0.03580089 0.008378558 0.030375443 1.517477383 -0.115734398 DLEFTIYDDDDVSPFLEGLEERPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DLEFTIYDDDDVSPFLEGLEERPQR 25 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;;;;;; 312.15 1.45E-74 860580000 210389.9 185780.2 173370.5 209368.6 172998 179956.8 200488.3 202849.2 175091.3 FALSE TRUE 200445.1864 204711.4136 181319.7089 188322.4706 203168.7964 173724.8509 169900.1276 185086.6487 202243.5646 0.99110786 1.012202361 0.896541303 0.93116669 1.00457484 0.858988276 0.840076805 0.915167061 1 17.62573427 3.53348705 0.798964007 0.897555975 1.012298578 0.152757793 0.05716603 0.928148964 1.173961241 0.026698 0.07025051 3415.757653 -3.53348705 0.114742603 DLEFTIYDDDDVSPFLEGLEERPQRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DLEFTIYDDDDVSPFLEGLEERPQRK 26 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;; 374.1 5.32E-127 918574400 843879.9 408011.8 714223.3 659141.1 680110.4 745526.4 1112226 847054.6 831394 FALSE TRUE 803991.3695 449588.6663 746971.1448 592882.9843 798721.4384 719708.6338 942535.4963 772882.0087 960322.3353 0.837209903 0.468164334 0.777833772 0.617379147 0.831722234 0.749444855 0.981478262 0.804815196 1 19.87315921 2.199493368 1.039268303 0.938477137 0.659622292 0.433335223 0.117673971 0.437486559 0.894833377 0.078292573 0.042708867 158.3045392 -2.199493368 -0.278854845 DLEGENIEIVFAKPPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLEGENIEIVFAKPPDQK 18 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 57.248 0.08521 85862000 637440 508900 612340 671770 502620 693820 821030 733730 554000 FALSE TRUE 607309.4745 560757.4886 640416.3947 604242.4033 590276.7689 669792.8394 695766.7942 669480.7115 639911.4906 0.949052304 0.876304765 1.000789022 0.944259342 0.92243502 1.046696065 1.087285983 1.046208298 1 19.28751285 2.21489372 7.289470437 1.056412503 0.934052646 0.661736092 0.037373585 0.090939598 18.82816768 0.013548799 0.010221886 164.018834 -2.21489372 -0.122359858 DLEGSDIDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLEGSDIDTR 10 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;;; 203.29 4.84E-07 2655350000 4256110 3986150 4132090 4998910 4061210 4454270 5078430 4753600 4516630 FALSE TRUE 4054932.115 4392343.217 4321550.414 4496410.069 4769483.738 4300017.513 4303622.232 4337349.584 5217045.913 0.777246776 0.841921519 0.828352 0.861868986 0.914211571 0.824224587 0.824915537 0.831380374 1 22.3148017 -5 0.337204832 2.72965888 0.829980324 0.683951809 0.034505805 234.6072805 1.990325255 291.9460603 0.028977138 1.00E-05 5 -1.899678556 DLEGSDIDTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLEGSDIDTRR 11 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 139.32 6.27E-05 470850000 523570 510690 573130 595330 596550 566810 686850 632460 721490 FALSE TRUE 498821.8837 562729.8916 599408.5774 535486.2973 700588.1311 547181.2276 582058.4176 577078.4495 833374.9843 0.598556344 0.675242121 0.719254344 0.642551441 0.84066374 0.656584656 0.698435193 0.692459529 1 19.66860627 -5 0.228603931 2.662069198 0.650123897 0.716757582 0.061643668 83.16319231 0.831865679 63.96753286 0.102320221 1.00E-05 5 -2.011945301 DLEIERPILGQNDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DLEIERPILGQNDNK 15 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ;;;;;; 249.13 1.55E-18 3922070000 3302961 2920723 3002322 3515434 2118305 3311548 3659030 3631842 2438930 FALSE TRUE 3146836.579 3218347.994 3139981.433 3162055.895 2487736.721 3196868.262 3100777.771 3313818.661 2817146.808 1.117029674 1.142414014 1.114596309 1.12243206 0.883069606 1.134789374 1.100680221 1.176303149 1 21.42580332 2.953734665 24.99962239 1.067195698 1.126278598 0.138597333 0.079228645 920.3762638 497327.6658 0.023353065 0.024770504 898.9481953 -2.953734665 0.0590829 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK 40 1 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;; 299.94 1.77E-93 553170000 208665 168757 192695 212199 136318 219703 243036 228952 158614 FALSE TRUE 198801.819 185953.5302 201530.2564 190868.3534 160091.816 212094.63 205956.3945 208903.7491 183211.049 1.085097324 1.014968972 1.099989643 1.041794992 0.873810924 1.15765196 1.124148329 1.140235538 1 17.48314699 DLEKPFLLPVEAVYSVPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLEKPFLLPVEAVYSVPGR 19 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 207.22 2.99E-16 2681600000 4693700 3642900 3961500 3749800 3475400 3405000 4290900 3980600 3765400 FALSE TRUE 4471838.103 4014115.652 4143138.693 3372862.98 4081508.66 3287083.996 3636244.397 3632037.562 4349319.001 1.028169721 0.922929693 0.952594807 0.775492204 0.938424765 0.75576981 0.836049137 0.835081897 1 22.0523581 3.968235283 0.973160986 0.84462892 1.02977201 0.305863278 0.076289833 0.734201178 1.127172497 0.0237259 0.110359403 9294.697999 -3.968235283 0.18514309 DLELPLS(ph)PSLLGGPGPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 DLELPLS(0.558)PS(0.442)LLGGPGPER 109.35 0.00038277 9845600 18166 17845 17612 18875 18777 19896 20702 19715 15699 TRUE FALSE 17307.32918 19663.42579 18419.52762 16977.64914 22051.70285 19206.99653 17543.52968 17988.65008 18133.52074 0.954438436 1.084368892 1.015772275 0.93625774 1.216073986 1.059198421 0.967464065 0.992010892 1 14.14637144 1.740489977 10.87283326 0.985451279 1.043396696 0.112922482 0.076365462 0.199205161 130.7837265 0.035028744 0.019086446 55.01612232 -1.740489977 0.057945416 DLEPESDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLEPESDR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 134.15 0.002068 261440000 291170 277450 257470 338540 266190 293540 310600 322850 270660 FALSE TRUE 277406.9711 305722.4704 269275.2542 304509.316 312613.4517 283374.6362 263212.2654 294579.5425 312632.5705 0.887325881 0.977897057 0.861315421 0.974016609 0.999938846 0.906414312 0.841922085 0.942254807 1 18.25410856 -0.184215271 7.617430521 1.000001429 0.921702654 0.176403952 0.051494235 0 0 0.050138636 0.01181779 0.654311765 0.184215271 -0.078298775 DLEPHSFGGLLEGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLEPHSFGGLLEGIR 15 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 ;;; 186.68 3.72E-07 224613000 243814 210373 214896 244296 237083 223217 274184 255184 229010 FALSE TRUE 232289.3954 231810.2479 224749.1942 219738.9019 278430.2001 215486.9393 232352.1951 232838.7361 264523.7012 0.878142089 0.876330729 0.849637266 0.830696459 1.052571845 0.814622426 0.878379495 0.880218805 1 18.01303747 -1.63249088 2.423476192 1.01527462 0.881051709 0.246579534 0.064457664 16023494.78 12796686.3 1533486.158 0.016017896 0.023308221 1.63249088 -0.134222911 DLESAEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 167.12 9.66E-05 289580000 168850 142850 147420 164110 191310 183580 270190 216170 230030 FALSE TRUE 160868.7951 157406.5774 154179.3528 147613.351 224674.4034 177222.5786 228967.5531 197241.0088 265701.8776 0.60544847 0.592418009 0.580271973 0.55556006 0.845588317 0.666997841 0.861746086 0.742339537 1 18.0194489 1.612148159 0.398610582 1.001226824 0.554166934 0.716331615 0.078082903 0.516020694 0.2361049 0.087764264 0.070197231 40.94003024 -1.612148159 -0.44705989 DLESCS(ph)DDDNQGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLESCSDDDNQGSK 14 0 A0A0A0MRK1;E9PAV9;Q5T3I0;Q5T3I0-3;F8W895 A0A0A0MRK1 GPATCH4 G patch domain-containing protein 4 1 DLES(0.002)CS(0.998)DDDNQGSK 159.13 5.20E-06 118120000 161360 167350 135100 184150 84428 142120 142030 155960 82179 TRUE FALSE 153732.8326 184403.1553 141294.4686 165638.8921 99152.21647 137198.3488 120360.7149 142303.3156 94922.89961 1.619554746 1.942662477 1.488518252 1.744983485 1.044555285 1.44536618 1.267983968 1.49914632 1 16.53446855 2.7573482 24.79693465 1.283842471 1.719042933 0.574719644 0.189806989 502.409149 663107.6631 0.05288118 0.05600162 571.9370089 -2.7573482 0.435200462 DLESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLESLR 6 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 149.06 0.024861 969180000 1270460 1087510 1137010 1257090 1251880 1115160 1327520 1227220 1197210 FALSE TRUE 1210407.874 1198328.505 1189143.033 1130724.925 1470207.476 1076541.73 1124982.442 1119758.111 1382867.212 0.875288576 0.86655356 0.859911221 0.817667029 1.063158821 0.778485252 0.813514438 0.809736539 1 20.3992312 -0.303607254 7.500889184 1 0.859595422 0.240148081 0.077945183 0 0 0.07078251 0.016683598 0.497041608 0.303607254 -0.140404578 DLFAFQES(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLFAFQESPPR 11 0 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 DLFAFQES(1)PPR 97.203 0.0067568 60891000 38122 40517 37432 47933 43135 44919 48232 45297 43601 TRUE FALSE 36320.04861 44645.72836 39148.29423 43114.68377 50657.73034 43363.44377 40873.32256 41330.55455 50362.4204 0.721173612 0.886488934 0.777331469 0.856088398 1.005863696 0.861027795 0.811583761 0.820662594 1 15.62006 -4.99999999 0.020625996 2.071004502 1.09E-07 0.347202287 0.07206133 3928.398714 6.129837036 418.5871384 224.7093391 1.00E-05 4.99999999 -2.071004393 DLFDFSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLFDFSTR 8 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ;;;;; 175.38 0.00061997 470293000 1389650 1163770 1188340 1423210 1294090 1206570 1517210 1362620 1375170 FALSE TRUE 1323963.999 1282359.486 1242826.564 1280146.227 1519778.886 1164786.178 1285731.749 1243301.769 1588424.34 0.83350775 0.807315434 0.782427298 0.805922067 0.956783932 0.733296607 0.809438458 0.782726465 1 20.59916494 -1.083090435 5.082397683 1.000004076 0.813663616 0.51153988 0.057142093 2.42E-06 4.36E-07 0.0506948 0.011948618 0.082586596 1.083090435 -0.186340459 DLFDLILTCEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLFDLILTCEER 12 0 Q9NP77 Q9NP77 SSU72 RNA polymerase II subunit A C-terminal domain phosphatase SSU72 0 ;; 209.85 1.17E-07 37706500 101842 84272 88465 97199 90928 82026 114348 96231 96150 FALSE TRUE 97028.13049 92859.41261 92521.20775 87428.37185 106785.8144 79185.41905 96902.11245 87804.50349 111060.4509 0.873651508 0.836115934 0.833070701 0.78721427 0.961510722 0.712993855 0.872516829 0.790600999 1 16.76098563 -1.045682639 5.967777753 1.000000331 0.835868162 0.392549374 0.065046188 2.44E-07 3.92E-08 0.053774231 0.012674682 0.090015513 1.045682639 -0.164132169 DLFDLNS(ph)S(ph)EEDDTEGFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 DLFDLNS(1)S(1)EEDDTEGFSER;DLFDLNS(0.999)S(0.999)EEDDT(0.001)EGFSER 143.4 2.13E-07 41091000 239383 211807 211325 255605 177444 236737 251691 231716 199818 TRUE FALSE 228067.84 233390.3741 221014.4603 229911.0998 208390.1774 228538.7383 213290.9153 211425.7186 230804.7549 0.988141861 1.011202625 0.95758192 0.99612809 0.902885114 0.990182106 0.924118376 0.916037101 1 17.81631342 3.188892246 1.432825612 0.944907003 0.997734238 0.218219261 0.034219041 0.457143802 1.960618441 0.010850815 0.015260616 1544.871089 -3.188892246 0.052827235 DLFDLNS(ph)SEEDDTEGFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 DLFDLNS(0.894)S(0.106)EEDDTEGFSER 180.31 3.55E-14 35187000 38586 36883 38437 43439 33735 39777 45106 42120 38158 TRUE FALSE 36762.11625 40641.41963 40199.37447 39072.42919 39618.37332 38399.51252 38224.25127 38431.74951 44075.34776 0.834074332 0.922089597 0.91206029 0.886491683 0.898878292 0.871224266 0.867247866 0.871955673 1 15.42768433 -1.544718672 3.24191174 1.00390016 0.883301938 0.68712348 0.024810439 7436949.502 10795013.38 249069.6576 0.006017103 0.028528657 1.544718672 -0.120598221 DLFDLNSS(ph)EEDDTEGFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 DLFDLNS(0.321)S(0.679)EEDDTEGFSER 201.61 6.21E-16 41055000 62750 52418 54954 62093 50889 50029 63345 61178 52685 TRUE FALSE 59783.93186 57759.45379 57473.69526 55851.29367 59764.02549 48296.48319 53680.55684 55820.93 60855.12072 0.98239772 0.949130543 0.944434824 0.917774758 0.982070609 0.793630554 0.882104188 0.917275807 1 15.89309104 2.289783965 24.99999992 0.884363278 0.9546283 0.199913103 0.053446998 119.8225726 58479.85453 0.016860136 0.014106184 194.8874912 -2.289783965 0.070265021 DLFDPIIEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLFDPIIEDR 10 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 0 ;;; 152.28 4.26E-05 228582000 139707 158664 121119 159784 104014 126559 127065 132905 97855 FALSE TRUE 133103.327 174832.042 126672.426 143722.2088 122154.0087 122176.2301 107678.9005 121267.1336 113029.8536 1.177594438 1.546777567 1.120698841 1.271542023 1.080723408 1.080920006 0.95265894 1.07287703 1 16.78634434 2.842019919 1.097571892 1.005579697 1.343702096 0.530923645 0.11427417 0.318654804 0.811223117 0.052230473 0.053742112 695.0561952 -2.842019919 0.338122399 DLFDYS(ph)PPLHK ddPTM_SK-BR-3_Trastuzumab_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(0.001)S(0.999)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK 164.93 1.43E-05 2296998000 2612450 2521090 2199370 2836470 1724680 2609920 2713290 2708280 1521210 TRUE FALSE 2488964.666 2777991.937 2300213.29 2551342.647 2025463.646 2519537.816 2299327.778 2471128.646 1757111.478 1.416509253 1.580999255 1.309087852 1.45200955 1.152723474 1.433908917 1.308583893 1.406358491 1 20.74477429 -4.098139603 0.134944563 8.61E-15 1.556665837 0.550482145 0.110013222 73.67626145 0.780040721 20.98627649 0.725874011 7.98E-05 4.098139603 1.556665837 DLFEDELVPLFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLFEDELVPLFEK 13 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 186.72 1.76E-05 154262000 844372 619768 664263 800111 590974 664044 984300 877720 681603 FALSE TRUE 804460.2089 682923.0638 694720.1156 719682.3222 694039.6785 641047.9898 834126.9571 800862.1837 787302.5121 1.021793017 0.867421421 0.882405562 0.914111553 0.881541298 0.814233385 1.059474528 1.01722295 1 19.58655856 1.682643899 9.072742333 1.027676358 0.902817305 0.554747202 0.054034405 0.092712405 12.55074905 0.026380911 0.014073097 48.15527853 -1.682643899 -0.124859053 DLFHGATFVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLFHGATFVPR 11 0 Q96DV4 Q96DV4 MRPL38 "39S ribosomal protein L38, mitochondrial" 0 184.24 0.00091462 0 157240 113010 107080 104240 141480 86985 142720 122640 127640 FALSE TRUE 149807.5768 124525.8475 111989.7239 93761.59716 166154.0672 83972.68764 120945.4428 111900.9914 147433.7593 1.016100909 0.844622345 0.759593491 0.635957447 1.126974365 0.569562141 0.820337508 0.758991645 1 17.16970738 4.363885483 2.037969752 0.795995315 1.015183153 0.131192524 0.160570352 0.632181753 4.590354586 0.037430985 0.193170389 23114.55212 -4.363885483 0.219187838 DLFPYEESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLFPYEESK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 147.51 0.00021457 563792000 2265821 2153242 1747215 2459970 1335111 2128672 2071258 2271255 1247792 FALSE TRUE 2158720.132 2372659.808 1827326.536 2212689.142 1567953.936 2054955.555 1755249.551 2072371.872 1441293.211 1.497766114 1.646202029 1.267838163 1.535210966 1.087879915 1.425772036 1.217829612 1.437855848 1 20.45893243 7.999999193 0.046444356 0.203833855 3.447582719 0.447520346 0.151244064 426.1650181 1.499151633 26.00745549 101.9412378 99999814.27 -7.999999193 3.243748863 DLFPYEESKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLFPYEESKEK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;; 148.18 3.19E-05 2722630000 1905110 1196800 1830670 1695930 1303100 2100510 2652420 2251540 1492050 FALSE TRUE 1815059.226 1318755.281 1914608.03 1525451.894 1530360.227 2027768.812 2247744.614 2054383.221 1723429.494 1.053167091 0.765192476 1.110929131 0.885125791 0.887973795 1.176589364 1.304227775 1.192032067 1 20.71685085 2.194741896 6.528472123 1.207186786 0.932063954 0.452821591 0.121041942 0.139197571 14.67625745 0.041974387 0.031241257 156.5820216 -2.194741896 -0.275122832 DLFQVAFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLFQVAFNR 9 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 106.68 0.0067373 234510000 160800 157880 164050 143530 165950 152870 197250 165520 197830 FALSE TRUE 153199.3027 173968.1515 171571.8548 129102.0917 194891.6275 147576.0736 167155.8898 151026.1913 228508.466 0.670431627 0.761320377 0.75083369 0.564977281 0.852885807 0.645823221 0.73150852 0.660921645 1 17.80188809 -1.202082142 3.587846892 1.000379093 0.708531494 0.587928347 0.077603473 99845693.92 164664394.7 450618.1308 0.01612892 0.062793958 1.202082142 -0.291847599 DLFSLDSEDPSPAS(ph)PPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DLFSLDSEDPSPASPPLR 18 0 Q9BTK6;H3BTX0 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.004)PAS(0.996)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.001)PAS(0.999)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR;DLFSLDSEDPS(0.008)PAS(0.992)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR 298.93 1.98E-49 1941284000 1705607 1432371 1527877 1719661 1603867 1570861 1883257 1780717 1770799 TRUE FALSE 1624986.337 1578331.233 1597931.672 1546797.409 1883580.897 1516461.69 1595931.556 1624787.979 2045405.465 0.794456828 0.771647119 0.781229785 0.756230212 0.920883868 0.74139906 0.780251927 0.79435985 1 20.96395543 0.909238388 18.35282063 1 0.789928925 0.643580408 0.048492833 2081.389289 420878.6101 0.042657811 0.010664218 8.114063237 -0.909238388 -0.210071075 DLGAYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLGAYLR 7 0 Q5TAQ0;V5IRT4;Q9BRT2 Q5TAQ0 UQCC2 Ubiquinol-cytochrome-c reductase complex assembly factor 2 0 ;;; 129.96 0.0083975 298875000 663780 517028 468477 483044 634970 386341 596710 531240 603460 FALSE TRUE 632404.4349 569713.741 489957.1338 434487.4994 745708.567 372961.9143 505670.9302 484721.8093 697041.4948 0.907269423 0.817331171 0.702909565 0.623330896 1.069819476 0.535064149 0.725453124 0.695398786 1 19.41088502 4.096517799 2.615233966 0.745292222 0.889934596 0.060865017 0.161594161 0.595710868 8.048703457 0.038399944 0.103448457 12488.71627 -4.096517799 0.144642374 DLGEELEALKTELEDTLDSTAAQQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLGEELEALKTELEDTLDSTAAQQELR 27 1 P35579 P35579 MYH9 Myosin-9 0 ; 241.06 3.14E-45 6750600000 2488040 1943600 2210310 2495050 1437980 2307830 2772300 2618400 1657320 FALSE TRUE 2370435.28 2141655.05 2311654.9 2244242.834 1688763.257 2227909.268 2349334.718 2389119.015 1914328.721 1.238259267 1.118749892 1.207553789 1.172339321 0.882169942 1.163807053 1.227236834 1.248019208 1 20.86840715 5.331050801 1.020752511 1.135402132 1.467514591 0.084233887 0.111250961 15.85850317 5.714004666 0.032881144 7.68867874 214314.1278 -5.331050801 0.332112459 DLGEELEALRGELEDTLDSTNAQQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLGEELEALRGELEDTLDSTNAQQELR 27 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 217.84 3.07E-34 501490000 328280 248420 267180 292490 316960 278520 372530 333390 326400 FALSE TRUE 312762.855 273734.2804 279430.4673 263088.3495 372237.7236 268874.7826 315693.7065 304196.6042 377016.445 0.829573508 0.726053954 0.741162543 0.697816642 0.987324899 0.713164601 0.837347311 0.806852349 1 18.52426793 -2.208301168 0.256403592 1.268833575 0.761177524 0.394674286 0.082893332 34.96505117 1.225228879 5.531177139 0.110505702 0.006190117 2.208301168 -0.507656051 DLGGIVLANACGPCIGQWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLGGIVLANACGPCIGQWDR 20 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 204.43 2.23E-22 0 23611 22732 20518 27183 22151 22093 27131 24261 24636 FALSE TRUE 22494.95482 25048.41664 21458.7706 24450.5132 26014.12739 21327.91387 22991.66765 22136.57822 28456.42506 0.7905053 0.880237647 0.754092285 0.859226454 0.914174122 0.74949379 0.807960508 0.777911427 1 14.79646681 -0.998862651 5.106807439 1.000001394 0.819282304 0.533163309 0.053855331 8.01E-07 1.57E-07 0.048829907 0.011509231 0.100262227 0.998862651 -0.18071909 DLGGIVLANACGPCIGQWDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLGGIVLANACGPCIGQWDRK 21 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 214.79 1.09E-24 307010000 372290 238180 380310 285060 377400 315420 449730 394280 412230 FALSE TRUE 354692.5895 262450.8128 397747.5897 256405.2272 443218.4405 304496.9263 381115.4286 359754.753 476156.523 0.744907551 0.551186007 0.835329499 0.538489372 0.930825094 0.639489142 0.80039947 0.755538852 1 18.86107637 -3.441471604 0.158139091 1.642577327 0.617602965 0.365573735 0.119126274 69.57010304 1.005001461 14.99890332 0.483054312 0.00036185 3.441471604 -1.024974362 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(0.998)GDQEDEDDES(0.002)EDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 419.17 8.29E-188 2240810000 991444 892592 899560 1058522 674307 1011562.4 1087531 998751 429985 TRUE FALSE 944580.407 983548.1396 940805.7158 952117.3575 791905.9273 976531.7404 921608.1721 911295.0677 496664.8777 1.901846596 1.9803054 1.894246519 1.917021719 1.594447207 1.966178371 1.855593607 1.834828893 1 18.9219132 -2.114498586 0.40763631 1.99E-17 1.906088322 0.870666074 0.105353527 17.25647903 1.014346951 16.05819814 0.061616383 0.00768248 2.114498586 1.906088322 DLGLPTEAYISVEEVHDDGTPTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLGLPTEAYISVEEVHDDGTPTSK 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;; 165.41 1.43E-11 124142000 230416 193135 211431 237832 186108 217132 253303 245617 185272 FALSE TRUE 219524.6923 212815.6761 221125.3205 213924.6755 218565.1763 209612.6644 214656.9751 224109.4734 214003.0355 1.025801769 0.99445167 1.033281233 0.999633837 1.021318112 0.979484538 1.003055749 1.047225675 1 17.70727174 DLGNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLGNLR 6 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 104.94 0.077699 157230000 186280 183360 159700 192380 159530 163460 177030 190840 171730 FALSE TRUE 177474.9136 202044.5925 167022.403 173041.5969 187351.9815 157799.3392 150020.8221 174129.0379 198361.0113 0.894706638 1.018570086 0.842012258 0.8723569 0.944500032 0.795515904 0.756301962 0.877839031 1 17.59776896 3.719121888 24.17115583 0.852556297 0.956638364 0.157802084 0.075663978 646.5726845 803983.1696 0.019921869 0.030917906 5237.47409 -3.719121888 0.104082067 DLGTESQIFISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLGTESQIFISR 12 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 227.81 6.34E-06 81429000 337690 310630 327381 348903 351706 312784 348917 349361 360296 FALSE TRUE 321728.0629 342283.5502 342391.7427 313830.6076 413043.415 301952.2117 295683.3033 318769.0988 416168.8635 0.77307096 0.82246314 0.822723112 0.754094395 0.992489951 0.725552145 0.710488769 0.765960952 1 18.66680951 DLGYIYFYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLGYIYFYQR 10 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 179.68 4.84E-06 267790000 824650 798640 454570 530200 792130 482700 862540 692830 648500 FALSE TRUE 785670.4288 880022.324 475412.4841 476903.2887 930277.2212 465983.978 730943.6814 632162.1323 749066.0679 1.048866665 1.174826042 0.634673635 0.636663853 1.241916115 0.622086619 0.975806691 0.843933745 1 19.51473345 3.761891193 24.98182897 0.850633393 1.111846381 0.23581381 0.195423736 974.8638075 1043857.511 0.04608246 0.083014124 5779.512315 -3.761891193 0.261212988 DLHDQFQHQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLHDQFQHQLK 11 0 B7Z879;A0A087WXL6;A0A0G2JS92 B7Z879 VPS11 0 97.911 0.0034197 57711000 55290 46112 47478 49433 50057 45164 64126 54786 18733 FALSE TRUE 52676.55127 50810.86522 49654.91326 44463.90092 58786.92495 43599.95936 54342.40095 49988.6474 21638.01797 2.434444382 2.348221788 2.294799521 2.054897126 2.716835019 2.014970106 2.511431548 2.310223029 1 14.40128073 0.927846244 21.90342968 1.000000001 2.344651202 0.8110734 0.202633846 4960.887716 1505959.542 0.167603445 0.041900861 8.469275175 -0.927846244 1.344651201 DLHILPPPLIPT(ph)PPPDDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLHILPPPLIPTPPPDDPR 19 0 Q9NRS6;E9PK26;E9PMW6;Q9NRS6-2 Q9NRS6 SNX15 Sorting nexin-15 1 DLHILPPPLIPT(1)PPPDDPR 80.293 0.027605 31284000 49120 50065 58563 64121 45498 53203 59159 40674 27480 TRUE FALSE 46798.19495 55166.68042 61248.17148 57675.43526 53432.83679 51360.56677 50133.20802 37112.36893 31741.45805 1.474355553 1.738000829 1.929595401 1.817037994 1.683376885 1.618090974 1.579423602 1.169208071 1 14.95408078 1.218080978 1.768790925 0.989760909 1.710939304 0.828550765 0.117672834 0.142318691 0.804010384 0.118062682 0.034790561 16.52269849 -1.218080978 0.721178394 DLIADLKYELTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLIADLKYELTGK 13 1 P08133;P08133-2;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 P08133 ANXA6 Annexin A6;Annexin 0 ; 126.48 0.00017146 263850000 893430 724350 798710 1167200 613550 966370 936170 792510 394030 FALSE TRUE 851199.3345 798162.0885 835331.6435 1049870.838 720552.9257 932904.3646 793340.0726 723113.623 455134.16 1.870216322 1.753685306 1.835352555 2.306728281 1.583165996 2.049734884 1.743090592 1.588792243 1 18.79593235 0.834091453 1.459267862 1.001546168 1.883266107 0.687929697 0.189703629 0.339416709 1.352327954 0.162473659 0.047803793 6.824823956 -0.834091453 0.88171994 DLIADLKYELTGKFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLIADLKYELTGKFER 16 2 P08133;P08133-2;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 P08133 ANXA6 Annexin A6;Annexin 0 ; 186.68 8.22E-10 113437000 434520 160385 409710 485500 557140 447270 761410 435130 483230 FALSE TRUE 413981.1007 176728.4138 428495.6088 436696.6176 654305.0396 431780.9277 645242.9202 397027.7104 558166.8404 0.741679854 0.316622918 0.767683742 0.782376497 1.172239181 0.773569651 1.156003678 0.711306516 1 19.09033689 3.296960422 2.251195898 0.967671807 0.533976805 0.444801347 0.183665276 0.214455616 2.222971417 0.050507754 0.071245196 1981.346456 -3.296960422 -0.433695002 DLIDFDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLIDFDDR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 190.26 0.00043587 432869000 1426710 1506830 1276080 1690080 1231190 1315540 1419530 1486150 1162340 FALSE TRUE 1359272.246 1660377.69 1334589.53 1520189.947 1445909.146 1269982.52 1202954.627 1356014.827 1342589.751 1.012425609 1.236697725 0.994041202 1.132281806 1.076955299 0.945920017 0.895995688 1.009999389 1 20.3565871 2.28557006 4.553967671 0.947035092 1.10285678 0.419270718 0.073264892 0.160080932 7.108303659 0.025208649 0.020241193 193.0056668 -2.28557006 0.155821688 DLIDFDDRQQIYAAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLIDFDDRQQIYAAEK 16 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 175.51 3.19E-09 48221000 172090 99452 174410 161430 141290 167780 224810 218060 197000 FALSE TRUE 163955.6467 109586.2719 182406.871 145202.7497 165930.9313 161969.7365 190511.1056 198965.5104 227549.7539 0.720526584 0.481592575 0.801613133 0.63811429 0.729207254 0.711799217 0.837228353 0.874382446 1 17.7958225 1.504463399 0.555719115 1.006384099 0.622856127 0.659797027 0.081413207 0.415699274 0.30841037 0.076005237 0.041885472 31.94945095 -1.504463399 -0.383527972 DLIDYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLIDYVR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 ;;; 143.23 0.0056669 197042000 844870 755050 766430 880430 799540 743160 950770 861480 862440 FALSE TRUE 804934.6695 831990.4534 801571.5736 791927.5037 938979.5229 717424.1829 805712.5744 786044.2442 996182.7905 0.808019047 0.835178505 0.804643065 0.79496204 0.942577539 0.720173235 0.808799933 0.789056237 1 19.92605096 -1.997899208 2.853635368 1.184208294 0.813229021 0.536167001 0.054681587 2311300.119 7672612.085 2804415.869 0.011570614 0.01004849 1.997899208 -0.370979274 DLIEAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DLIEAIR 7 0 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;; 148.98 0.0047622 389561000 777449 831715 598609 900610 578861 671654 696030 779018 590877 FALSE TRUE 740700.5265 916467.7041 626055.8148 810078.9718 679814.1751 648394.4536 589837.84 710803.0541 682507.1874 1.085264068 1.342795682 0.917288237 1.186916397 0.996054236 0.950018499 0.864222166 1.041458709 1 19.38048471 2.998781355 1.012700501 0.941451803 1.19211175 0.301214276 0.115843973 0.473074675 1.052789087 0.051945685 0.063544071 997.1978984 -2.998781355 0.250659948 DLIEAIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DLIEAIRR 8 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;;;; 182.73 0.00036401 3850300000 3740516 3086788 2855518 3345567 3253705 3047973 3890745 3696965 3380579 FALSE TRUE 3563709.222 3401335.207 2986446.325 3009264.249 3821150.122 2942420.931 3297140.392 3373239.146 3904821.926 0.912643211 0.871060261 0.764809864 0.770653389 0.978572184 0.753535241 0.844376633 0.863865039 1 21.89682533 -0.835128574 5.618863516 1.000000044 0.846452627 0.327773331 0.06975713 3.62E-08 7.54E-09 0.063932503 0.015069031 0.146174436 0.835128574 -0.153547417 DLIHDQDEDEEEEEGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLIHDQDEDEEEEEGQR 17 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 367.88 1.11E-104 5037970000 4155130 4162100 3904030 4891160 3556280 4007240 4688260 4460010 2788430 FALSE TRUE 3958725.24 4586222.722 4083033.637 4399491.304 4176494.106 3868468.274 3972979.831 4069467.88 3220845.483 1.22909505 1.423918889 1.267690008 1.365942988 1.296707379 1.201072294 1.23352078 1.263478146 1 21.61900802 0.064567954 0.361192133 0.94291187 1.335038833 0.695281398 0.061541018 2.334352676 0.44488638 0.262667626 0.049715195 1.160293752 -0.064567954 0.392126964 DLIHDVSFDFHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLIHDVSFDFHGR 13 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ;; 225.23 7.40E-12 191180000 218619 224325 171244 253076 196377 192783 211017 209688 43029.7 FALSE TRUE 208285.3131 247183.9725 179095.7068 227636.3197 230625.0866 186106.8764 178822.4811 191326.6071 49702.52611 4.190638373 4.973267797 3.6033522 4.579974852 4.640107952 3.74441484 3.597854979 3.849434266 1 15.60103156 -0.492671891 0.357621111 1.30E-18 4.546146058 0.860644199 0.408333635 2.733907089 0.35537548 3.677775959 0.314125921 0.321608937 0.492671891 4.546146058 DLILQCLDDKDESIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLILQCLDDKDESIR 15 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 88.427 0.0061922 189740000 150430 124460 202280 145830 373860 96654 215510 134970 430190 FALSE TRUE 143319.472 137142.6155 211554.7381 131170.8913 439061.0656 93306.84774 182629.9914 123151.3113 496901.6681 0.288426224 0.275995482 0.425747691 0.263977563 0.883597488 0.187777288 0.367537489 0.247838394 1 18.92260086 -1.486297495 3.582551571 1.009225898 0.361149004 0.509394804 0.194948791 15969822.48 11111890.77 1094194.202 0.04192069 0.032636419 1.486297495 -0.648076894 DLISHDEMFSDIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 DLISHDEMFSDIYK 14 0 Q5W0H4;A0A0B4J2C3;P13693 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;;;;;; 283.21 1.94E-33 7635430000 14603052 12564106 12232863 14524950 10338156 13563923 16047239 15485290 9313705 FALSE TRUE 13912794.67 13844402.69 12793751.87 13064874.43 12141127.13 13094200.95 13598937.96 14129315.91 10758026.8 1.293247816 1.286890518 1.18922848 1.214430366 1.128564499 1.217156379 1.264073627 1.313374299 1 23.35891015 -1.522472371 3.134798138 0.99232302 1.241283531 0.649534359 0.054990173 12704806.58 12247892.25 805366.5273 0.014120415 0.030028084 1.522472371 0.248960512 DLISLDS(ph)SPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.003)LDS(0.657)S(0.34)PAK 76.073 0.038131 16631000 96727 102440 94003 111220 63027 92288 101530 110040 129630 TRUE FALSE 92154.9064 112878.7525 98313.13053 100039.9543 74018.88884 89092.04342 86039.73377 100404.3142 149732.3583 0.615464202 0.75387013 0.656592413 0.668125149 0.494341301 0.595008617 0.574623513 0.670558558 1 17.19202651 0.957538165 21.16887767 1.000000001 0.628979507 0.755197078 0.06692552 628.3264496 313246.3331 0.069638264 0.017409566 9.06855653 -0.957538165 -0.371020494 DLISLDS(ph)SPAKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.578)S(0.422)PAKER 52.862 0.090405 48350000 98473 91453 91208 102360 67954 105250 111540 109130 78649 TRUE FALSE 93818.37644 100772.1647 95389.97702 92070.57833 79805.15608 101605.1661 94522.52443 99573.99867 90845.48524 1.0327247 1.109269926 1.05002441 1.013485459 0.87847135 1.118439357 1.04047575 1.096080872 1 16.4711272 -1.565273367 8.044992013 0.999985587 1.045305674 0.03584876 0.067550948 1.68E-05 9.06E-07 0.062796613 0.014796597 0.02720988 1.565273367 0.045320088 DLISLDSS(ph)PAKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.24)S(0.76)PAKER;DLISLDS(0.262)S(0.738)PAKER;DLISLDS(0.263)S(0.737)PAKER 103.01 0.00099586 484060000 805710 763570 758040 853090 517290 887220 938770 980830 635420 TRUE FALSE 767625.6851 841378.6511 792796.8838 767335.7724 607505.2122 856495.3489 795543.3948 894943.3255 733957.6883 1.04587185 1.146358522 1.080167013 1.045476851 0.827711491 1.166954666 1.083909069 1.219339125 1 19.48533737 -0.69476859 7.394301272 1.000001076 1.077548474 0.051308331 0.1039929 0 0 0.095197234 0.022438203 0.201944212 0.69476859 0.077547398 DLKDEIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLKDEIVR 8 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 81.338 0.021086 180970000 441320 429110 385990 476320 317190 430880 523370 483830 379600 FALSE TRUE 420459.6782 472836.7969 403688.0233 428439.4087 372507.8356 415958.5176 443520.2942 441463.2803 438466.4293 0.958932429 1.078387683 0.920681713 0.977131612 0.849569798 0.948666739 1.01152623 1.006834847 1 18.74210686 -0.336017658 6.472914305 0.999999555 0.975206107 0.016383538 0.060273669 0 0 0.059243235 0.013963764 0.461298818 0.336017658 -0.024793448 DLKDYFSK ddPTM_SK-BR-3_Trastuzumab_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 ; 104.05 0.0042457 4447300000 10837400 8102300 9281800 11464800 7722700 11030600 12694800 12177800 8315100 FALSE TRUE 10325137.58 8927933.582 9707379.711 10312336.52 9069536.435 10648607.56 10757975.1 11111447.27 9604563.24 1.075024165 0.929551231 1.010704961 1.073691355 0.94429452 1.108702946 1.120089986 1.15689251 1 23.19528858 2.214841608 24.90056834 1.107973834 1.005586235 0.343300948 0.060757125 209.3953686 219824.8409 0.020961225 0.015489221 163.9991543 -2.214841608 -0.102387599 DLKDYFTK ddPTM_SK-BR-3_Trastuzumab_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 ; 101.38 0.004957 2550100000 10656900 8465700 9212700 10585300 7002300 10920600 12416100 11655400 8017800 FALSE TRUE 10153169.46 9328364.455 9635111.408 9521245.533 8223498.903 10542416.88 10521795.91 10634791.39 9261159.475 1.096317312 1.007256649 1.040378522 1.028083531 0.887955652 1.138347408 1.1361208 1.148321807 1 23.1427614 DLKEEFTEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLKEEFTEALR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 172.09 1.26E-05 559551000 1900450 1658130 1663180 2234560 1505100 2071130 2422060 2451760 1755520 FALSE TRUE 1810619.495 1827095.332 1739438.448 2009937.783 1767588.963 1999406.249 2052530.263 2237070.897 2027757.076 0.89291736 0.901042513 0.85781402 0.991212314 0.871696607 0.986018628 1.012217039 1.103224308 1 20.9514534 1.918038073 1.845903495 1.049405341 0.902729259 0.656550078 0.044821043 0.187775902 1.189734241 0.025555199 0.012072414 82.80147494 -1.918038073 -0.146676082 DLKPENILLDEEGHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 109.42 0.00058503 109216000 302040 259050 262020 307480 179921 292850 294140 331520 118590 FALSE TRUE 287763.1678 285447.4895 274033.8762 276571.5262 211299.1654 282708.5311 249263.5407 302490.3513 136980.3315 2.100762676 2.083857488 2.000534479 2.019060132 1.542551132 2.06386222 1.81970315 2.208275801 1 17.06360923 -1.973360791 2.724163377 0.173321547 1.977114334 0.737596396 0.183658878 8862944.32 2279340.404 46034723.53 0.042565041 0.010632593 1.973360791 1.803792786 DLKPENLLLASK ddPTM_SK-BR-3_Trastuzumab_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 ; 134.24 0.00024156 245280000 1109820 855570 922300 1102660 663710 1073270 1182320 1190760 824010 FALSE TRUE 1057361.008 942753.5557 964588.3673 991818.5219 779460.8139 1036102.391 1001935.369 1086490.742 951793.2623 1.110914576 0.990502447 1.013443156 1.042052472 0.818939201 1.088579245 1.052681721 1.141519682 1 19.86028872 DLKPQNLLIDDKGTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLKPQNLLIDDKGTIK 16 2 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 105.77 0.0007072 229270000 308170 244260 274230 278120 202760 310030 393390 354960 266900 FALSE TRUE 293603.4148 269150.3717 286803.7168 250162.8492 238121.2798 299293.5834 333371.1304 323877.8206 308289.4889 0.952362716 0.87304427 0.930306504 0.811454358 0.772395065 0.970819941 1.081357433 1.050563942 1 18.23392618 2.010733117 8.388002142 1.046513143 0.876000556 0.685259414 0.054862118 0.085136098 44.29038445 0.021756784 0.015597712 102.5021835 -2.010733117 -0.170512587 DLLDDLKSELTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLLDDLKSELTGK 13 1 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 223.72 1.40E-11 999610000 3142400 3289100 2454700 3554800 1320500 3288200 2843500 3536200 1282280 FALSE TRUE 2993864.98 3624263.029 2567250.423 3197464.75 1550794.782 3174328.81 2409671.851 3226551.581 1481129.433 2.021339197 2.446959022 1.733305925 2.158801708 1.047035287 2.143181236 1.626915107 2.178439985 1 20.49826629 -1.332447555 0.126996394 2.04E-12 2.505286798 0.338623353 0.392456997 44.02913965 1.010902836 19.57395156 3.949604345 0.046510654 1.332447555 2.505286798 DLLDDLKSELTGKFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLDDLKSELTGKFEK 16 2 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 65.943 0.031468 538370000 99715 68103 90647 77703 62604 96680 121500 117400 63616 FALSE TRUE 95001.66957 75042.77313 94803.25461 69892.14681 73522.11778 93331.94736 102962.9435 107119.8336 73481.24437 1.292869635 1.021250712 1.290169422 0.951156277 1.000556243 1.270146527 1.401213934 1.457784698 1 16.16508844 2.057951413 7.012703864 1.332201624 1.11690661 0.195161515 0.164011315 0.261080221 25.54265188 0.057201443 0.041963463 114.2750481 -2.057951413 -0.215295014 DLLDQILMLDPAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLDQILMLDPAKR 14 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 96.247 0.0055272 36702000 44422 41028 43049 51559 44178 40376 59679 54327 42510 FALSE TRUE 42322.2601 45208.79984 45022.83923 46376.19136 51882.62921 38977.769 50573.87247 49569.83987 49102.23369 0.86192128 0.920707602 0.916920389 0.944482315 1.056624624 0.79380847 1.029970913 1.009523114 1 15.58350103 8 0.187596345 1.011876633 0.34189912 0.242867573 0.069800751 72.56834849 0.840096036 0.132455337 14.03779644 99999999.95 -8 -0.669977513 DLLDTVLPHLYNETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLLDTVLPHLYNETK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 238.22 9.21E-18 553420000 1940530 1768590 1700750 2105980 1374590 2059470 2301700 2130190 1486230 FALSE TRUE 1848804.993 1948811.332 1778731.07 1894282.889 1614318.061 1988150.037 1950533.391 1943659.271 1716706.958 1.076948506 1.135203258 1.036129703 1.103439862 0.940357382 1.158118471 1.136206376 1.132202128 1 20.71121236 DLLFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLLFGR 6 0 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;; 131.65 0.035445 236518000 295903 298828 390784 424821 281387 316151 388977 348938 346511 FALSE TRUE 281916.2516 329278.9129 408701.8329 382117.186 330460.8037 305202.6116 329631.4146 318383.1389 400246.1561 0.704357174 0.822691006 1.021126191 0.954705448 0.825643916 0.762537271 0.823571718 0.795468324 1 18.61052802 4.274511558 2.917146675 0.869080599 0.720031029 0.277733154 0.087873414 0.350226036 5.91254303 0.02304157 0.074946681 18815.31779 -4.274511558 -0.149049569 DLLHNEDRHDDYFQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLHNEDRHDDYFQER 16 1 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 110.04 0.00059687 192680000 65900 53368 64657 71297 102630 54551 76831 63844 53592 FALSE TRUE 62785.0376 58806.25987 67621.5874 64130.0901 120528.6395 52661.88519 65109.01985 58253.4809 61902.77365 1.014252414 0.949977786 1.092383805 1.035980883 1.947063635 0.850719315 1.051794871 0.941047993 1 15.91771643 DLLHPS(ph)PEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEK 72.175 0.030283 98750000 250940 308560 202820 317780 165630 281690 262220 270880 134130 TRUE FALSE 239078.5635 340002.6148 212119.4976 285836.1507 194515.8196 271935.0047 222213.523 247160.3112 154930.1954 1.543137301 2.19455358 1.369129479 1.844935069 1.255506192 1.755209848 1.434281565 1.595301101 1 17.24125882 -2.092042652 0.136855643 2.72E-10 2.004077075 0.378415939 0.260397059 46.38542083 0.886289625 16.63763317 1.891135396 0.008090164 2.092042652 2.004077075 DLLHPS(ph)PEEEKRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK 128.74 8.44E-05 3748060000 3498550 2988002 3176132 3521230 1692512 3801240 4043220 3999130 1306329 TRUE FALSE 3333180.475 3292482.801 3321760.794 3167269.271 1987685.557 3669602.106 3426352.53 3648944.976 1508907.83 2.209002041 2.182030431 2.201433864 2.099047542 1.317300844 2.431959086 2.270750051 2.418268966 1 20.52507325 2.999023411 24.53182556 2.002800003 2.190123568 0.060010534 0.460030913 116.336524 2922515.846 0.125709765 0.148387839 997.7538474 -2.999023411 0.187323566 DLLHPSPEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;;; 227.81 3.73E-12 4959510000 14918800 15362800 12743000 17852800 8934210 15428000 15626900 17085100 7958950 FALSE TRUE 14213617.89 16928286.79 13327279.15 16058202.63 10492333.4 14893724.49 13242729.4 15589038.07 9193183.317 1.546104042 1.841395543 1.449691439 1.746751051 1.141316673 1.620083488 1.440494434 1.695717091 1 23.13213308 -2.99867215 0.201360972 2.27E-13 1.68139116 0.427829827 0.198050227 49.85533818 1.018603965 22.17840029 0.45420934 0.001003062 2.99867215 1.68139116 DLLHPSPEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLLHPSPEEEKR 12 1 P42677 P42677 RPS27 40S ribosomal protein S27 0 ; 125.03 0.00020282 315250000 675570 671600 612310 780130 567210 701470 804430 857040 566560 FALSE TRUE 643637.145 740036.8035 640385.0192 701709.8502 666131.2444 677177.918 681699.4291 781993.0341 654419.2312 0.983524191 1.130829854 0.978554707 1.072263492 1.017896805 1.034776922 1.041686119 1.194942014 1 19.31985562 1.396613456 24.99999995 1.104419945 1.041260513 0.131794466 0.063188479 52.65964122 16349.24838 0.036637029 0.0133812 24.92375401 -1.396613456 -0.063159433 DLLHPSPEEEKRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;; 188.09 3.84E-06 3235790000 4263840 2216650 3965030 3501300 2905760 4199240 5929870 4917090 3217670 FALSE TRUE 4062296.733 2442529.155 4146830.547 3149342.672 3412523.624 4053819.266 5025159.422 4486523.532 3716649.83 1.092999588 0.657185709 1.115744215 0.847360611 0.918171951 1.090718645 1.352066956 1.207141845 1 21.82557134 2.083809054 3.710646827 1.225379003 0.91002053 0.367962619 0.153576463 0.18894743 5.084403615 0.059278592 0.040528161 121.2855477 -2.083809054 -0.315358473 DLLIAYYDVDYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLLIAYYDVDYEK 13 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 222.49 4.04E-11 508583000 1275758 1085625 1122014 1339869 917834 1165518 1423821 1301754 968860 FALSE TRUE 1215455.448 1196251.422 1173459.452 1205182.823 1077903.959 1125155.819 1206590.956 1187765.519 1119105.861 1.08609515 1.068934999 1.048568766 1.076915835 0.963183196 1.005406065 1.078174102 1.061352246 1 20.09391508 DLLIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLLIFR 6 0 H3BPB8;P34949-2;P34949;F5GX71 H3BPB8 MPI Mannose-6-phosphate isomerase 0 ;; 155.88 0.022848 154958000 210069 191810 182014 207647 218922 169296 223954 210447 209500 FALSE TRUE 200139.4547 211355.6571 190359.5219 186773.9291 257101.9275 163433.2371 189785.7041 192019.145 241988.19 0.827062902 0.873413108 0.786647984 0.771830762 1.062456509 0.675376914 0.784276721 0.793506266 1 17.88457711 DLLLTGHEDGTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLLTGHEDGTVR 13 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 154.47 4.62E-05 47493000 97513 91179 84332 106320 113040 100520 102820 111500 83391 FALSE TRUE 92903.75374 100470.2438 88198.70562 95632.51161 132754.1402 97038.9672 87132.92058 101736.4689 96322.85038 0.964503785 1.043057212 0.915657139 0.992833074 1.378220637 1.007434548 0.904592423 1.056202848 1 16.55559046 2.003408946 24.99989195 0.971251518 1.051464137 0.05835655 0.128569208 285.9133921 2096759.241 0.048580929 0.035705887 100.7880275 -2.003408946 0.080212619 DLLNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLNHK 6 0 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 0 72.021 0.086696 130220000 119710 102210 100740 127030 97744 111960 127700 130740 104080 FALSE TRUE 114051.5455 112625.3152 105359.0286 114260.7031 114790.5227 108082.7971 108217.0196 119291.7125 120220.1948 0.948688743 0.936825259 0.876383779 0.95042853 0.954835607 0.899040276 0.900156748 0.992276819 1 16.87531974 1.222941469 23.27994562 0.996138679 0.92460543 0.57917548 0.025639582 90.6810347 135148.6641 0.024644875 0.006271059 16.70865413 -1.222941469 -0.071533249 DLLPSDMAVALLEAQAGTGHIIDPATSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 107.87 0.00042865 19129000 9265.2 8983.4 9853.1 13399 12072 12504 11281 12794 12413 FALSE TRUE 8827.252358 9898.818673 10304.87438 12052.10706 14177.35298 12070.98334 9559.87626 11673.68953 14337.94464 0.615656747 0.690393143 0.7187135 0.84057425 0.988799534 0.841890776 0.666753604 0.814181518 1 13.80755061 3.460840988 2.457465878 0.834974482 0.651874215 0.445872897 0.095955943 0.301476371 3.658978183 0.029656724 0.046030635 2889.621687 -3.460840988 -0.183100267 DLLQFFKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLLQFFKPR 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 179.51 4.53E-05 146612000 504840 471650 423200 488830 422920 428650 557910 517660 448740 FALSE TRUE 480977.2137 519711.6712 442604.1386 439691.8797 496677.1141 413805.743 472790.5828 472330.9461 518328.3074 0.927939314 1.002668895 0.85390694 0.848288379 0.958228804 0.798346795 0.912145017 0.91125825 1 18.98350666 3.737816131 24.99982192 0.889650864 0.965304104 0.174012392 0.059600435 82.69039684 2776768.354 0.013946673 0.023079977 5467.844196 -3.737816131 0.07565324 DLLSDLQDIS(ph)DSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.985)DS(0.015)ER;DLLSDLQDIS(0.951)DS(0.049)ER;DLLSDLQDIS(1)DSER;DLLSDLQDIS(1)DSER;DLLSDLQDIS(0.99)DS(0.01)ER;DLLSDLQDIS(0.999)DS(0.001)ER;DLLSDLQDIS(0.807)DS(0.193)ER 309.15 1.18E-55 1581594000 2929322 3203860 2671204 3363640 2450807 2950533 2947962 3060182 2457814 TRUE FALSE 2790858.754 3530336.976 2793681.346 3025520.517 2878226.965 2848355.302 2498196.254 2792216.241 2838959.242 0.983056999 1.24353211 0.984051234 1.065714672 1.013831732 1.003309685 0.879969045 0.983535163 1 21.43693071 2.650877906 1.122209088 0.944701743 1.098070646 0.263539155 0.079021183 0.490966006 1.275621731 0.040331382 0.034172408 447.5874558 -2.650877906 0.153368903 DLLSDLQDISDS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.156)DS(0.844)ER 208.38 8.52E-09 933790000 728160 778530 719160 852610 604420 800040 740490 754520 620360 TRUE FALSE 693741.3199 857863.0921 752134.1973 766904.0229 709830.6566 772334.4142 627514.6505 688450.2288 716562.2604 0.968152187 1.197192679 1.049642493 1.070254555 0.990605696 1.077832949 0.875729417 0.960768194 1 19.45073254 2.174097098 1.351005191 0.940334361 1.07842938 0.291413335 0.072308507 0.440201601 1.541241899 0.0437777 0.02390807 149.3128199 -2.174097098 0.138095019 DLLVEGLAEILHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLLVEGLAEILHQK 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 146.96 8.16E-06 65448000 240811 221003 239341 272651 206949 240117 294707 269420 190979 FALSE TRUE 229428.3413 243523.457 250315.0216 245243.6035 243040.8401 231801.6881 249744.0345 245828.1565 220595.0479 1.040043026 1.103938911 1.134726386 1.111736668 1.101751115 1.050801866 1.132137991 1.11438656 1 17.75104088 -2.515695574 1.959188377 1.69E-05 1.097645351 0.501055801 0.030934322 818552.9674 41700.73724 3658786.636 0.008264053 0.003050032 2.515695574 1.097628465 DLLVGPGVELLLT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 150.39 3.57E-05 40429000 85565 80897 64405 98042 68087 71281 61475 62004 46454 TRUE FALSE 81520.51202 89140.49627 67358.03296 88186.63189 79961.35124 68812.5211 52095.85968 56574.60106 53657.84907 1.519265372 1.661275989 1.25532488 1.643499198 1.490207912 1.282431598 0.970889825 1.054358347 1 15.7115016 2.005504956 2.410942703 1.005003659 1.531499473 0.809363084 0.111813651 0.113932627 1.245088614 0.056138632 0.031029976 101.2756305 -2.005504956 0.526495814 DLLYFDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLLYFDGLR 9 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 137.9 0.00035264 305430000 607060 617560 488390 603110 594490 459930 630120 569770 600450 FALSE TRUE 578365.4769 680490.0661 510783.1646 542484.237 698168.8678 444002.5088 533983.6211 519877.9183 693564.7193 0.833902678 0.981148618 0.736460708 0.782168155 1.006638383 0.640174588 0.769911742 0.749573765 1 19.40367099 2.235114693 24.99994315 0.7659891 0.870492523 0.080365926 0.119610622 162.8989052 1181802.274 0.040292087 0.030963981 171.836213 -2.235114693 0.104503423 DLLYFDGLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLLYFDGLRK 10 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 103.22 0.004559 204080000 188890 160450 161890 170800 175390 152020 211470 187520 189340 FALSE TRUE 179961.544 176800.0374 169312.8166 153630.8595 205977.9605 146755.5093 179206.3676 171099.7547 218701.8802 0.822862354 0.808406573 0.774171747 0.702467027 0.941820712 0.671029939 0.81940936 0.782342404 1 17.7386061 -0.890874948 5.317156521 1.000000263 0.792000071 0.451352168 0.072633177 1.96E-07 4.10E-08 0.06085068 0.014342624 0.12856568 0.890874948 -0.208000192 DLMPHDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DLMPHDLAR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;;;;;;;;;; 154.05 5.81E-05 3329731000 3462870 2728467 2659124 2667100 2962253 2310484 2843962 2788710 2532887 FALSE TRUE 3299186.998 3006500.889 2781047.466 2398998.041 3478868.985 2230471.36 2410063.364 2544515.769 2925674.18 1.127667264 1.027626695 0.950566363 0.819981274 1.189082848 0.762378591 0.823763419 0.86971946 1 21.48033768 4.346833477 0.561006575 0.875506511 1.238719037 0.248693632 0.119718713 3.068960786 0.997460516 0.064307348 0.686697674 22224.57563 -4.346833477 0.363212526 DLMTDLKSEISGDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLMTDLKSEISGDLAR 16 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 155.2 2.57E-07 221806000 366330 186726 269580 458470 386190 330180 444030 292180 299030 FALSE TRUE 349014.3069 205753.5917 281940.5097 412383.7246 453541.4137 318745.7838 376285.0683 266595.1703 345402.0452 1.010458136 0.595693032 0.816267632 1.193923807 1.313082595 0.92282541 1.089411813 0.771840161 1 18.3979171 3.328824404 7.56281376 1.058400099 0.788159713 0.294894845 0.174763979 0.257753326 18.65986745 0.047182776 0.063901304 2132.182644 -3.328824404 -0.270240386 DLMVGDEASELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 ;;; 210.87 8.97E-08 452374000 759440 714390 729620 803610 730110 732450 820810 789650 843850 FALSE TRUE 723542.7763 787187.1532 763073.7987 722829.596 857440.9528 707085.0728 695580.3593 720504.0598 974709.9482 0.742315986 0.807611695 0.78287269 0.741584301 0.879688316 0.725431267 0.71362805 0.739198426 1 19.89461344 -0.967192586 4.783793434 1.000002681 0.766133933 0.695559736 0.048538946 1.37E-06 2.96E-07 0.04643784 0.010945378 0.107846837 0.967192586 -0.233868748 DLNES(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;DLNES(1)PVK 101.12 0.0058987 1701420000 3620020 3898790 2901080 4032070 2062340 3647530 3344940 3665350 2058640 TRUE FALSE 3448908.829 4296081.134 3034097.388 3626758.663 2422011.443 3521215.122 2834607.969 3344392.523 2377883.377 1.450411262 1.806682857 1.275965599 1.525204599 1.018557708 1.4808191 1.192071906 1.406457758 1 21.18124653 3.901737845 0.141551429 0.870883721 2.143867838 0.353763139 0.195523222 18.58311771 0.613645825 1.224085155 4.866145789 7975.131354 -3.901737845 1.272984117 DLNES(ph)PVKSFVSISEATDCLVDFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLNESPVKSFVSISEATDCLVDFKK 25 2 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 DLNES(1)PVKSFVSISEATDCLVDFKK;DLNES(0.658)PVKS(0.342)FVSISEATDCLVDFKK 187.92 6.73E-18 340120000 1251110 758420 1202560 1110970 656150 1292680 1508970 1419570 733040 TRUE FALSE 1191972.51 835703.8603 1257698.565 999293.1849 770582.3523 1247914.167 1278748.912 1295264.925 846716.0994 1.407759355 0.986994178 1.485384022 1.180198635 0.910083501 1.473828321 1.510245185 1.529751148 1 19.69151879 DLNHVCVISETGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLNHVCVISETGK 13 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 146 4.21E-05 214160000 957160 926790 947430 1092790 769430 1056690 1142990 1057920 734410 FALSE TRUE 911916.9437 1021230.955 990870.6026 982940.673 903618.3484 1020096.56 968605.883 965282.9164 848298.552 1.074995285 1.203857949 1.168068247 1.158720206 1.06521265 1.20252069 1.141821922 1.137904708 1 19.69421257 0.595744 2.796681184 1.00000296 1.147160387 0.495748998 0.045703569 4.734992269 31.76024094 0.040820831 0.010748542 3.942248534 -0.595744 0.147157427 DLNYCFSGMSDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 223.72 1.53E-11 11181420000 6326720 4371270 5193940 5720500 7528430 4940450 7717820 6126470 7385000 FALSE TRUE 6027668.484 4816707.383 5432087.287 5145464.472 8841385.808 4769360.978 6540324.812 5590003.808 8530228.083 0.706624539 0.564663375 0.63680446 0.603203622 1.03647707 0.559112949 0.766723322 0.655317039 1 23.02415289 -4.999999999 0.175672572 2.250724047 0.616350532 0.333795289 0.137500878 145.6280198 1.390395846 63.56836223 0.416414825 1.00E-05 4.999999999 -1.634373515 DLPAIQES(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPAIQESPTR 11 0 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.742)PT(0.258)R;DLPAIQES(0.5)PT(0.5)R 185.2 4.79E-06 625710000 392190 395050 312350 428160 333630 379990 363980 366320 320890 TRUE FALSE 373651.9559 435306.0441 326671.5565 385120.5433 391814.9664 366830.851 308448.166 334243.0788 370651.9823 1.008093775 1.174433336 0.881343071 1.039035434 1.057096643 0.989690784 0.8321773 0.901770649 1 18.4997057 1.957543668 5.612964453 0.89560546 1.041551908 0.304003768 0.081442807 0.200079002 15.91040341 0.034397408 0.021384902 90.68671454 -1.957543668 0.145946448 DLPAIQES(ph)PTRDLPPCQDLPPSQVSLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPAIQESPTRDLPPCQDLPPSQVSLPAK 29 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.98)PT(0.02)RDLPPCQDLPPSQVSLPAK;DLPAIQES(0.973)PT(0.027)RDLPPCQDLPPSQVSLPAK 145.85 3.59E-08 197550000 116366 81245 109949 109346 84341 108054 134417 118548 119572 TRUE FALSE 110865.6098 89523.95787 114990.2704 98354.33234 99050.0437 104312.0629 113909.2179 108167.3087 138114.6151 0.8027073 0.648185985 0.832571342 0.712121105 0.717158308 0.755257239 0.824744129 0.78317062 1 17.07550647 0.343058339 0.56321523 1.011686872 0.734705375 0.675008245 0.053710005 1.27745353 0.628454003 0.083693919 0.022193449 2.203222404 -0.343058339 -0.276981497 DLPDGHAAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR 158.93 1.88E-05 5152760000 6453630 5184780 5839780 6608070 6963040 5459120 6853300 5558770 6038030 TRUE FALSE 6148579.7 5713114.977 6107539.689 5943814.249 8177391.971 5270069.306 5807703.216 5072014.63 6974376.854 0.881595564 0.819157768 0.875711166 0.852235888 1.172490696 0.755633 0.832720017 0.727235527 1 22.73363289 -0.902591479 4.555579607 1.000001335 0.863519184 0.111954537 0.11981249 0.003386075 68348363.87 236.0874541 0.02634744 0.125143565 0.902591479 -0.136482152 DLPEHAVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 96.342 0.007433 5115780000 9947500 8340600 7405800 8197900 7114200 7819600 10641600 8985000 7328800 FALSE TRUE 9477301.389 9190516.622 7745363.255 7373831.517 8354914.228 7548805.291 9018028.474 8198225.768 8465312.874 1.119545318 1.085667684 0.914952982 0.871064263 0.986958705 0.891733762 1.06529181 0.968449234 1 23.01313196 3.831698045 5.509737952 0.959997821 1.106135986 0.538413996 0.056210566 0.163671809 7.649406549 0.014787879 0.027066365 6787.31562 -3.831698045 0.146138165 DLPLLLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPLLLFR 8 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 107.32 0.0093669 50473000 176952 146540 107959 105596 205403 96367 191236 146560 180783 FALSE TRUE 168587.8296 161472.5926 112909.0269 94981.28946 241225.2182 93029.78663 162059.4359 133726.4294 208817.9043 0.807343749 0.773269865 0.54070568 0.45485223 1.155194134 0.445506753 0.776080176 0.640397335 1 17.67188589 -1.889728406 2.372419287 1.160020819 0.707604426 0.172102533 0.206622634 15004084.09 8010961.372 13444473.66 0.044652604 0.012890554 1.889728406 -0.452416392 DLPS(ph)PDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPSPDSR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 DLPS(1)PDSR;DLPS(1)PDSR 134.25 0.0009281 197610000 717700 603850 621810 774140 625530 638950 780270 714170 543190 TRUE FALSE 683775.7433 665383.0015 650320.6036 696321.9764 734622.2339 616823.0013 661225.4809 651633.4887 627425.131 1.089812489 1.060497849 1.036491163 1.109808871 1.170852422 0.98310216 1.053871527 1.03858366 1 19.25908379 2.209707062 24.99998589 1.025207306 1.086809511 0.457107829 0.039769177 233.897315 202657.4711 0.014859303 0.010976113 162.0716533 -2.209707062 0.061602205 DLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.489)S(0.489)PS(0.011)S(0.011)DEPPMEASQSHLR;DLPTIPGVT(0.613)S(0.376)PS(0.009)S(0.001)DEPPMEASQSHLR 122.68 0.00049168 136071000 130400 126867 110513 144440 120789 125813 138701 133261 105219 TRUE FALSE 124236.2504 139794.8915 115580.1304 129920.6168 141854.5634 121456.0643 117539.615 121591.9604 121535.8251 1.022219171 1.150236084 0.950996385 1.068990289 1.167183118 0.999343725 0.967119077 1.000461882 1 16.89102211 2.028465994 24.99479154 0.984962963 1.073355666 0.301724989 0.060649003 231.8132847 203544.51 0.021700565 0.016026686 106.7741184 -2.028465994 0.088392703 DLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.171)S(0.779)PS(0.039)S(0.011)DEPPMEASQSHLR;DLPTIPGVT(0.017)S(0.746)PS(0.119)S(0.119)DEPPMEASQSHLR;DLPTIPGVT(0.1)S(0.685)PS(0.182)S(0.033)DEPPMEASQSHLR;DLPTIPGVT(0.161)S(0.67)PS(0.139)S(0.03)DEPPMEASQSHLR;DLPTIPGVT(0.151)S(0.793)PS(0.04)S(0.016)DEPPMEASQSHLR;DLPTIPGVT(0.174)S(0.818)PS(0.006)S(0.002)DEPPMEASQSHLR 142.55 1.79E-07 614833000 413084 377436 352802 482223 379699 413602 429871 411540 352285 TRUE FALSE 393558.338 415897.1575 368978.3207 433749.0279 445918.3854 399278.859 364286.2838 375503.3759 406915.5586 0.967174466 1.02207239 0.90676877 1.065943581 1.095849928 0.981232717 0.895238032 0.922804174 1 18.63436992 1.989469702 24.50882661 0.930339217 1.009324518 0.245271791 0.057048397 490.5025331 1141624.143 0.021911986 0.015177116 97.60446873 -1.989469702 0.078985301 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.497)QS(0.497)HLRNS(0.006)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.353)QS(0.353)HLRNS(0.295)PEDK 239.06 1.36E-46 280600000 262165 238262 232871 289398 155079 277125 268164 304946 177362 TRUE FALSE 249772.98 262541.1687 243548.3657 260307.1632 182124.7285 267528.0918 227250.6566 278243.3116 204866.3931 1.219199383 1.281523849 1.188815608 1.270619155 0.888992703 1.305866168 1.10926274 1.358169622 1 17.64432381 -2.347748253 2.004655951 4.67E-05 1.200852827 0.19245581 0.130502691 1878349.189 225944.3296 8497602.841 0.02907702 0.004490056 2.347748253 1.200806114 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.381)QS(0.381)HLRNS(0.238)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR 156.96 1.55E-11 1374350000 636529 571736 614802 665262 418750 648317 722318 741557 454808 TRUE FALSE 606441.5356 629996.5484 642991.2798 598388.5998 491779.8674 625865.6197 612115.1228 676622.3378 525337.3018 1.154385066 1.199222949 1.223958926 1.139055989 0.936122118 1.191359566 1.16518496 1.287976954 1 19.0028845 -2.231952891 2.504498541 0.386363453 1.161038259 0.240997228 0.090419914 9814432.674 7192266.14 32453713.36 0.021821625 0.005862017 2.231952891 0.774674807 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.112)QS(0.444)HLRNS(0.444)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.149)QS(0.799)HLRNS(0.052)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.125)QS(0.438)HLRNS(0.438)PEDK 199.31 5.14E-27 624407000 653260 589080 594170 732910 452672 682960 720070 781370 425296 TRUE FALSE 622381.6944 649107.9217 621413.2822 659236.4944 531617.8535 659308.924 610210.0965 712949.1005 491248.7316 1.266938018 1.321342693 1.264966691 1.341960705 1.082176542 1.342108145 1.242161165 1.451299626 1 18.90609416 -1.642293453 3.08022319 0.977502644 1.284567609 0.483449822 0.093815601 19736145.73 23266242.41 3560314.716 0.019897071 0.022788018 1.642293453 0.307064965 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.005)QS(0.633)HLRNS(0.362)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.116)QS(0.701)HLRNS(0.184)PEDKR 304.83 1.55E-90 1945600000 592420 553590 548920 653340 388300 642780 674140 703900 400510 TRUE FALSE 564417.4807 610001.4504 574088.525 587665.0219 456019.3971 620520.3674 571287.5616 642262.7844 462619.0453 1.220048086 1.318582658 1.240953071 1.270300105 0.985734162 1.34132041 1.234898492 1.388318944 1 18.81946514 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.028)QS(0.123)HLRNS(0.849)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.149)QS(0.149)HLRNS(0.702)PEDK 239.84 1.27E-46 314070000 517550 472850 473800 557050 320510 544660 548060 598300 365720 TRUE FALSE 493086.4372 521033.9526 495524.1987 501054.2757 376406.8425 525798.2876 464443.3812 545909.6802 422433.9898 1.167250858 1.23340916 1.17302161 1.186112595 0.891042983 1.244687455 1.099446049 1.292295822 1 18.6883664 -2.369969759 2.150438248 0.000214922 1.160065343 0.177019491 0.109021312 1873709.804 252260.3878 9158388.282 0.024244205 0.004266092 2.369969759 1.159850421 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.137)QS(0.137)HLRNS(0.725)PEDKR 76.162 0.0020546 468380000 166400 133290 135710 178100 107060 174370 176870 178520 120760 TRUE FALSE 158534.6018 146872.4025 141932.4377 160197.0496 125731.2301 168331.5232 149885.2331 162887.8424 139486.844 1.136555944 1.052948065 1.017532791 1.148474257 0.901384148 1.206791396 1.074547453 1.167764914 1 17.08976953 DLPVSEQQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLPVSEQQER 10 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 112.01 0.0039033 105330000 166330 151240 131720 159730 112220 154710 152860 178100 129630 FALSE TRUE 158467.9105 166651.5279 137759.4923 143673.6369 131791.1325 149352.3539 129538.3995 162504.6198 149732.3583 1.058341111 1.11299608 0.920038219 0.959536326 0.880178032 0.997462109 0.865132968 1.08530061 1 17.19202651 3.738465971 24.9999992 0.946987872 1.085668601 0.390601156 0.065003814 6.365821268 1681689.432 0.015128431 0.025165724 5476.031914 -3.738465971 0.138680728 DLPVTEAVFSALVTGHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLPVTEAVFSALVTGHAR 18 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 182.07 7.03E-14 49285000 67412 60673 60014 59171 66654 47308 61550 60879 60650 FALSE TRUE 64225.56836 66855.64768 62765.70126 53223.01866 78278.4365 45669.7121 52159.41706 55548.11202 70055.29224 0.916783962 0.954326869 0.895945178 0.759728737 1.117380772 0.651909522 0.74454642 0.79291814 1 16.09620642 2.218832024 24.99896288 0.768245987 0.922032766 0.205361739 0.122324289 298.0990667 377732.0514 0.041015819 0.030333163 165.5129672 -2.218832024 0.15378678 DLQANVEHLVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLQANVEHLVQK 12 0 A0A2R8Y891;P08237;P08237-3;P08237-2 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 155.98 6.66E-05 438400000 1101560 994270 978850 1231110 861380 1060820 1255690 1235490 893210 FALSE TRUE 1049491.442 1095587.243 1023731.241 1107356.484 1011604.399 1024083.537 1064111.428 1127303.946 1031724.445 1.01722068 1.061899084 0.992252578 1.073306433 0.980498625 0.992594042 1.031391117 1.092640532 1 19.97662627 -1.416044589 3.225207505 0.999615448 1.029415955 0.06173951 0.036910366 2692278.144 1188854.45 7077.918957 0.007947497 0.038366785 1.416044589 0.029800507 DLQEQDADAGS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;DLQEQDADAGS(1)ER 258.65 6.37E-24 1500030000 2811030 3148250 2726440 3228070 2461480 2828370 2823140 2921320 2443680 TRUE FALSE 2678158.183 3469060.254 2851449.971 2903578.271 2890761.333 2730422.838 2392418.142 2665513.734 2822633.414 0.948815446 1.229015513 1.010209104 1.02867707 1.024136297 0.967331721 0.847583725 0.944335783 1 21.42861034 2.412686345 1.472646119 0.913293846 1.075059121 0.29968638 0.080834421 0.385100884 1.686304674 0.040279806 0.028497525 258.6344337 -2.412686345 0.161765275 DLQGLTVEHAIDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLQGLTVEHAIDSFR 15 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;; 183.7 4.95E-07 341922000 381642 352585 344142 381301 574051 277873 381848 336814 550077 FALSE TRUE 363602.539 388513.8124 359921.2511 342971.8991 674165.3126 268250.1883 323590.0745 307320.7806 635380.1318 0.57225985 0.611466731 0.566466015 0.539790091 1.061042483 0.422188506 0.509285793 0.483680186 1 19.27726045 -1.187415472 3.928563218 1.000252516 0.593090408 0.348430002 0.173686115 14230747.92 12903881.26 27332.04942 0.038351059 0.064950803 1.187415472 -0.407162108 DLQGRDEQSEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLQGRDEQSEEK 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 209.19 5.30E-08 3347450000 2225950 1409771 2179580 2246130 1640913 2364300 2964200 2540850 2045050 FALSE TRUE 2120733.755 1553428.268 2279515.899 2020344.745 1927087.708 2282423.698 2511956.849 2318359.704 2362185.909 0.89778444 0.657623205 0.96500275 0.855286088 0.815806961 0.966233728 1.063403536 0.981446759 1 21.17169108 2.134671315 3.822614119 1.020759654 0.825228291 0.510547464 0.080316809 0.16862975 4.662423327 0.032156373 0.022827454 136.3550776 -2.134671315 -0.195531363 DLQHPNEFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLQHPNEFIR 10 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ;; 115.33 0.0012376 773901000 1472260 1348880 1201050 1527630 1282950 1292050 1467570 1337470 1177550 FALSE TRUE 1402669.188 1486332.406 1256119.331 1374069.73 1506696.074 1247305.985 1243665.243 1220354.036 1360158.44 1.031254262 1.092764168 0.923509566 1.010227698 1.107735709 0.917029919 0.914353215 0.897214619 1 20.37534328 2.214807712 24.96870313 0.923585029 1.035046025 0.440657959 0.056123609 193.0928779 202975.0909 0.020378682 0.015058949 163.9863547 -2.214807712 0.111460995 DLQSNVEHLTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLQSNVEHLTEK 12 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 173.44 3.31E-05 1585970000 2699490 2452490 2397460 3043010 2032880 2721810 3024800 3024450 2139450 FALSE TRUE 2571890.458 2702401.519 2507385.912 2737120.853 2387413.628 2627553.037 2563311.206 2759613.124 2471224.979 1.040735052 1.093547347 1.014632797 1.10759679 0.966085099 1.063259339 1.037263393 1.116698458 1 21.23679493 DLQSS(ph)PPSLPLGFLGEGDAVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.107)S(0.836)PPS(0.057)LPLGFLGEGDAVTK;DLQS(0.037)S(0.721)PPS(0.242)LPLGFLGEGDAVTK;DLQS(0.195)S(0.8)PPS(0.005)LPLGFLGEGDAVTK;DLQS(0.103)S(0.893)PPS(0.004)LPLGFLGEGDAVTK 232.02 4.58E-27 246470000 178459 155552 154010 182058 117614 161107 192210 190051 138221 TRUE FALSE 170023.5967 171402.9256 161071.5108 163757.184 138125.8444 155527.8242 162884.8343 173409.1269 159655.6067 1.064939717 1.073579119 1.00886849 1.025690155 0.865148723 0.974145709 1.020226208 1.086144924 1 17.28460369 3.58828438 2.340621556 0.990721911 1.0703415 0.227389612 0.055193753 0.406411191 4.357678818 0.016083673 0.027649788 3875.113078 -3.58828438 0.079619589 DLQSSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DLQSSDR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 254.37 2.89E-12 3749220000 4249110 3564730 3774640 4342980 3805210 3763930 4349580 3931410 4094950 FALSE TRUE 4048262.991 3927980.04 3947710.978 3906415.399 4468837.419 3633584.16 3685971.685 3587154.899 4729973.932 0.855874271 0.830444331 0.8346158 0.825885186 0.944791131 0.768203845 0.779279493 0.758387879 1 22.1734008 DLRAS(ph)PKPTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLRASPKPTSK 11 2 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 DLRAS(1)PKPTSK 71.08 0.026094 171050000 1186100 1066400 1023300 1182100 641360 1198200 1322500 1336000 734340 TRUE FALSE 1130035.404 1175067.372 1070219.317 1063273.062 753212.9809 1156706.034 1120728.336 1219012.757 848217.6967 1.332246908 1.385337015 1.261727174 1.253537938 0.887994891 1.36369005 1.321274409 1.437146103 1 19.69407506 3.589919879 3.710722922 1.23001573 1.358405279 0.112785806 0.163688937 0.552206396 13.61544985 0.043904263 0.069979727 3889.733782 -3.589919879 0.128389549 DLRNPHPSSAFLNLIGFVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLRNPHPSSAFLNLIGFVSR 20 1 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 89.483 0.0012453 22577000 23784 13384 21485 17053 31924 14874 37988 24088 35924 FALSE TRUE 22659.77746 14747.84482 22470.1085 15338.80004 37491.53549 14358.90965 32192.2329 21978.72702 41494.91045 0.546085706 0.355413342 0.541514809 0.369654974 0.903521302 0.346040261 0.775811601 0.529672839 1 15.34064677 -4.661647564 0.130480153 2.468533919 0.334139063 0.424790372 0.173605936 108.0469475 0.966124808 41.67282149 1.147499892 2.18E-05 4.661647564 -2.134394856 DLRPVDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLRPVDNR 8 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 75.378 0.035152 325290000 320950 325780 326230 362570 334870 313800 335960 358570 384840 FALSE TRUE 305779.3296 358977.3524 341187.9682 326123.7748 393271.222 302933.0273 284703.1317 327171.7099 444519.0217 0.687888065 0.807563535 0.767544135 0.733655387 0.884711796 0.681484959 0.640474575 0.736012845 1 18.76188563 -0.945219816 4.576101756 1.000003722 0.739605495 0.581597507 0.068623482 8091.685206 43246787.63 407.8831145 0.016597047 0.113443648 0.945219816 -0.260398227 DLS(ph)GMFT(ph)T(ph)ESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSGMFTTESR 11 0 Q10570 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 3 DLS(1)GMFT(1)T(1)ESR 49.418 0.053128 0 3715.3 3038.3 3419.4 2553.9 4076.9 2471.5 3046.6 2561.7 4677.9 TRUE FALSE 3539.685132 3347.906224 3576.182872 2297.17712 4787.910069 2385.911335 2581.785215 2337.383968 5403.324841 0.655093898 0.619601139 0.66184858 0.425141406 0.886104428 0.441563557 0.477814178 0.432582537 1 12.3996317 -1.71035441 6.654014501 1.004992133 0.57772821 0.46757051 0.142511031 0.009993353 0.000435005 0.13065488 0.030614113 0.019482541 1.71035441 -0.427263922 DLS(ph)LEEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 151.98 8.56E-05 73751000 118514 109511 113056 124237 74163 122957 131274 134062 141915 TRUE FALSE 112912.0781 120670.2954 118239.7294 111748.4607 87097.00372 118698.9683 111245.7403 122322.8206 163922.4534 0.688813983 0.736142566 0.72131503 0.681715399 0.531330528 0.724116592 0.67864858 0.746223705 1 17.32265396 0.708982459 2.068466676 0.999981997 0.683990544 0.754655004 0.056961513 0.650335502 3.883354218 0.053959501 0.014819512 5.116611688 -0.708982459 -0.315991453 DLS(ph)PEPAPDEGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSPEPAPDEGPR 13 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 DLS(1)PEPAPDEGPR 180.09 1.38E-05 137120000 161990 171280 145260 169530 117720 141290 158000 154940 112060 TRUE FALSE 154333.0537 188733.6267 151920.3147 152488.5223 138250.3307 136397.0919 133894.1981 141372.6322 129437.6925 1.192334712 1.458104074 1.173694554 1.178084369 1.068084019 1.053766405 1.034429737 1.092206061 1 16.98189827 3.165047517 1.581505079 1.049144812 1.320286072 0.665197929 0.075231278 0.191318878 0.992256651 0.024616762 0.033335455 1462.337162 -3.165047517 0.271141261 DLS(ph)PEPAPDEGPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSPEPAPDEGPRR 14 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 DLS(1)PEPAPDEGPRR 86.016 0.0045981 297880000 499690 433200 443630 484980 374050 492090 472170 526790 369090 TRUE FALSE 476070.644 477343.5725 463970.8743 436228.889 439284.2016 475048.7999 400131.7945 480661.4749 426326.5921 1.116680622 1.119666428 1.088299165 1.023227021 1.030393622 1.114283764 0.93855697 1.127448965 1 18.70159952 3.40616717 3.4374684 1.034109897 1.117152622 0.279417432 0.053394725 0.255020993 6.061466739 0.013971098 0.019926897 2547.810774 -3.40616717 0.083042725 DLS(ph)PQHMVVR ddPTM_SK-BR-3_Trastuzumab_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 205.8 1.04E-07 342040000 538990 410770 430200 438380 412310 372110 477160 417430 322000 TRUE FALSE 513513.0109 452627.93 449925.0955 394313.2095 484216.7335 359223.7374 404360.4784 380877.6163 371934.1155 1.380655846 1.216957281 1.20969031 1.060169512 1.301888462 0.965826265 1.087183083 1.024045928 1 18.50468756 8 0.205774558 0.97263179 3.021784417 0.639825341 0.081855329 27.40643503 0.337005308 0.126028884 18.28053071 100000000 -8 2.049152627 DLS(ph)PTLIDNSAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSPTLIDNSAAK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 DLS(0.983)PT(0.017)LIDNSAAK 69.602 0.049578 54331000 86119 78868 75606 92059 68141 86997 94222 102370 59057 TRUE FALSE 82048.32554 86904.73887 79072.60988 82805.05442 80024.76883 83984.27208 79846.70339 93405.9401 68215.25794 1.202785535 1.273978014 1.1591631 1.213878785 1.173121252 1.231165499 1.170510906 1.369282224 1 16.05780685 -1.148978978 4.341355654 0.999955507 1.220231937 0.567318684 0.06145451 2.35E-05 4.61E-06 0.052824951 0.012448448 0.070961212 1.148978978 0.22027643 DLSELGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 131.41 0.0026594 0 97644 92904 88889 100100 109370 94323 118750 102630 106020 FALSE TRUE 93028.56163 102371.0232 92964.64857 90037.75782 128444.0934 91056.57086 100632.5065 93643.17312 122461.0401 0.759658431 0.835947687 0.759136526 0.735235939 1.048856789 0.743555426 0.821751199 0.764677264 1 16.90196332 -2.151775333 2.226519522 1.414521117 0.809626611 0.302574383 0.09130947 4145272.726 974603.0857 8671023.563 0.020143287 0.007050577 2.151775333 -0.604894506 DLSGFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSGFYR 7 0 Q9H0G5;A0A024QZ33;K7ERM9 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 81.635 0.062041 50354000 142440 145060 114050 166620 135940 128840 140050 141390 141810 FALSE TRUE 135707.1435 159841.7789 119279.3053 149871.041 159647.893 124378.2385 118682.8003 129009.142 163801.1705 0.828487019 0.975828063 0.728195683 0.914957082 0.974644396 0.759324479 0.724554043 0.787595972 1 17.32158614 2.213488247 24.99531806 0.786105032 0.88608857 0.057344964 0.10286768 370.6585035 369516.9943 0.035447691 0.026190139 163.4888908 -2.213488247 0.099983538 DLSHIGDAVVISCAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLSHIGDAVVISCAK 15 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;; 201.3 6.48E-09 2623380000 8061960 7991560 8025330 9047960 6771440 8741060 9908890 9802280 7570550 FALSE TRUE 7680887.128 8805909.05 8393299.319 8138441.871 7952376.992 8438354.9 8397106.841 8943940.398 8744552.229 0.878362542 1.007016577 0.959831801 0.93068709 0.909409285 0.964984219 0.960267218 1.022801416 1 23.05995308 1.416592008 2.504701688 1.011500148 0.943418112 0.39550281 0.034633137 0.300750497 3.372301025 0.028563667 0.009087356 26.09708546 -1.416592008 -0.068082036 DLSLDDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLSLDDFK 8 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;;;; 182.68 0.00052876 1071115000 4707580 4533690 3740680 4311540 2549230 3656440 3694140 4259720 2301970 FALSE TRUE 4485062.023 4995678.165 3912193.878 3878135.808 2993814.905 3529816.566 3130531.095 3886716.335 2658947.751 1.686780803 1.878817726 1.471331611 1.458522758 1.125939727 1.327523854 1.177357131 1.461749797 1 21.342424 3.342836693 1.679903166 1.238118734 1.782585546 0.697876906 0.143538036 0.164814886 0.955693881 0.040882918 0.063292886 2202.098255 -3.342836693 0.544466812 DLSLEEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSLEEIQK 9 0 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 0 130.75 0.00082007 60329000 181120 162680 156920 194940 131990 166890 202610 181550 144600 FALSE TRUE 172558.8165 179257.277 164114.9372 175344.2608 155009.0142 161110.5575 171698.1233 165652.5195 167023.8295 1.033138906 1.073243725 0.982583969 1.049815834 0.928065263 0.964596237 1.02798579 0.991789735 1 17.34969442 3.733109705 24.73807653 0.993432707 1.053191317 0.356625027 0.034067157 378.3056573 1716881.165 0.008762033 0.014011575 5408.909377 -3.733109705 0.05975861 DLSLEEIQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLSLEEIQKK 10 1 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 0 161.62 1.13E-05 111270000 516470 412560 514750 546420 343850 566900 634120 680230 440180 FALSE TRUE 492057.4866 454600.333 538351.7967 491492.8235 403817.3311 547268.1109 537373.3476 620665.4551 508440.8663 0.967777217 0.894106598 1.05882873 0.966666639 0.794226739 1.07636531 1.056904319 1.220722991 1 18.95572047 2.039050818 24.97282677 1.090807637 0.93994902 0.441585231 0.085134271 138.2829951 88430.78226 0.029829163 0.02203027 109.4084381 -2.039050818 -0.150858617 DLSLLSHGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLSLLSHGGR 10 0 A6NP24;Q08257;Q08257-2 A6NP24 CRYZ Quinone oxidoreductase 0 ;;; 169.76 4.53E-06 1417870000 1499760 1311730 1283210 1344400 1541770 1229410 1569390 1307880 1582100 FALSE TRUE 1428869.317 1445396.778 1342046.448 1209258.358 1810654.2 1186835.223 1329950.732 1193355.094 1827443.988 0.781895 0.790939032 0.73438445 0.661721161 0.99081242 0.649450944 0.727765524 0.653018698 1 20.80139576 3.768309583 22.53507771 0.75759935 0.786417025 0 0.127559187 1509.001893 1143066.939 0.029558796 0.053269799 5865.561369 -3.768309583 0.028817674 DLSQAPFSWPAGALVAQACHAATAALHTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLSQAPFSWPAGALVAQACHAATAALHTHR 30 0 Q6GMV3 Q6GMV3 PTRHD1 Putative peptidyl-tRNA hydrolase PTRHD1 0 ; 41.209 0.054994 49391000 61375 56031 61816 54958 66336 53305 65149 49389 18346.2 FALSE TRUE 58473.92538 61740.6226 64650.32474 49433.51743 77904.9774 51459.03448 55209.32351 45064.23733 21191.235 2.759344861 2.913498086 3.050804956 2.332734144 3.67628302 2.428316919 2.605290514 2.126550781 1 14.37118005 0.859723107 1.036998282 1.002446101 2.888881406 0.735569849 0.357164767 0.319587951 0.681314514 0.296990519 0.09608227 7.23974229 -0.859723107 1.886435305 DLSSHQLNEFLAQTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLSSHQLNEFLAQTLQR 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 216.17 5.38E-15 792880000 560680 535480 502070 635690 503080 560340 596740 568560 570800 FALSE TRUE 534177.7676 590046.0208 525090.4061 571789.2335 590816.9927 540935.2853 505696.3531 518773.8723 659316.7488 0.810198996 0.894935586 0.796415997 0.867245121 0.896104936 0.820448269 0.767000617 0.786835574 1 19.33061221 2.041766565 24.98313074 0.817473429 0.853338399 0 0.071224215 428.7150359 256438.8625 0.023918859 0.01766522 110.0947387 -2.041766565 0.03586497 DLSSS(ph)PPGPYGQEMYAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 DLSSSPPGPYGQEMYAFR 18 0 O43741;O43741-2 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 DLS(0.008)S(0.057)S(0.882)PPGPY(0.053)GQEMYAFR;DLS(0.002)S(0.02)S(0.978)PPGPYGQEMYAFR;DLSS(0.028)S(0.972)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR;DLSS(0.004)S(0.995)PPGPYGQEMYAFR;DLSS(0.016)S(0.984)PPGPYGQEMYAFR;DLSS(0.002)S(0.997)PPGPYGQEMYAFR;DLS(0.009)S(0.085)S(0.906)PPGPYGQEMYAFR;DLSS(0.001)S(0.999)PPGPYGQEMYAFR;DLSS(0.03)S(0.97)PPGPYGQEMYAFR;DLS(0.005)S(0.035)S(0.961)PPGPYGQEMYAFR;DLSS(0.001)S(0.999)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR 296.46 2.54E-49 4036178000 3514085 2962190 3011342 3590026 2999767 3182333 3832448 3487407 3427861 TRUE FALSE 3347981.166 3264040.529 3149415.009 3229149.766 3522925.415 3072128.01 3247737.67 3182031.155 3959436.177 0.845570181 0.824370032 0.795420072 0.815557979 0.889754313 0.775900374 0.820252562 0.803657645 1 21.91686357 -2.251563136 2.394617862 1.712696096 0.82196984 0.772359797 0.030485253 3748058.227 1126628.935 14277226.26 0.006834835 0.00560321 2.251563136 -0.890726256 DLSTIEPLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 110.86 0.0043984 0 538460 495040 435320 546600 345190 505230 563890 570340 396890 FALSE TRUE 513008.0629 545485.1388 455279.8526 491654.7295 405391.0267 487733.7584 477858.2239 520398.006 458437.6742 1.119035568 1.189878515 0.993111776 1.07245708 0.884288202 1.063904181 1.042362465 1.13515541 1 18.80636608 3.738459901 24.99999959 1.028167116 1.154457044 0.385198768 0.066766187 8.102195307 2011176.424 0.016505028 0.027506776 5475.955389 -3.738459901 0.126289928 DLSYCLSGMYDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 DLSYCLSGMYDHR 13 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;;;;;;;;; 196.11 1.44E-07 7345210000 9217280 7272710 6974620 7581700 8769040 7090510 10043470 8455300 8892750 FALSE TRUE 8781597.441 8013807.417 7294413.226 6819573.112 10298357.8 6844963.861 8511154.191 7714909.108 10271792.25 0.854923584 0.780176158 0.710140261 0.663912679 1.002586262 0.66638457 0.828594853 0.751077214 1 23.29218459 -1.754236187 2.685342213 1.046965399 0.785318487 0.319421254 0.099809998 25330843.63 19325424.3 7869410.293 0.022957592 0.017610181 1.754236187 -0.261646911 DLTDYLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 191.63 0.00041919 7146850000 9472750 8767850 7112460 8179660 6698300 7885060 9729390 9121620 7008200 FALSE TRUE 9024991.881 9661303.883 7438573.326 7357425.036 7866481.399 7611998.395 8244992.863 8322882.596 8094995.863 1.114885299 1.193490898 0.918910084 0.908885583 0.971770898 0.940333822 1.018529596 1.028151556 1 22.94859891 3.740611479 24.99965278 0.969124068 1.154188105 0.75782097 0.043402389 78.97719526 962712.015 0.01168201 0.019814886 5503.151624 -3.740611479 0.185064037 DLTEYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLTEYLK 7 0 Q9NTI5-2;Q9NTI5;Q9NTI5-3;Q29RF7;Q29RF7-3 Q9NTI5-2;Q29RF7 PDS5B;PDS5A Sister chromatid cohesion protein PDS5 homolog B;Sister chromatid cohesion protein PDS5 homolog A 0 129.4 0.020872 0 77418 63205 66938 80950 65680 71360 80216 72071 83523 FALSE TRUE 73758.60457 69645.66136 70007.17351 72812.75221 77134.5712 68888.78531 67977.57593 65760.08117 96475.32026 0.764533399 0.721901323 0.725648522 0.754729313 0.799526459 0.714056042 0.704611042 0.681625943 1 16.55787231 -1.408000587 3.450806163 1.002413641 0.733532857 0.864909028 0.033121124 2310918.512 1439685.465 39591.30231 0.007893166 0.039084037 1.408000587 -0.268880784 DLTEYLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DLTEYLSR 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;;;; 221.33 1.29E-05 2456186000 2558910 2261359 2045764 2320618 2630690 2164659 2903000 2365402 2792320 FALSE TRUE 2437955.396 2491794.053 2139564.303 2087345.07 3089481.503 2089696.316 2460094.033 2158274.861 3225338.724 0.755875771 0.772568175 0.663361118 0.647170808 0.957878154 0.6478998 0.762739744 0.669162232 1 21.62101925 -1.192156795 4.896349912 1.000028909 0.739070351 0.447163228 0.092627239 2.61E-05 4.31E-06 0.080182758 0.018897166 0.064245573 1.192156795 -0.260958559 DLTPEHLPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLTPEHLPLLR 11 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ;;; 156.51 3.10E-05 351306000 699150 644600 627900 763870 682150 659630 771900 718430 669440 FALSE TRUE 666102.5651 710285.4728 656689.8361 687084.3363 801116.744 636786.8477 654132.4781 655520.4606 773253.3362 0.861428634 0.918567615 0.849255742 0.888563042 1.036033996 0.823516457 0.845948472 0.847743462 1 19.56058163 4.742209989 5.64070034 0.892481039 0.860366167 0.017940286 0.069645945 0.789760599 92.64453963 0.015740866 0.097177332 55234.44431 -4.742209989 -0.032114872 DLTQMADELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLTQMADELRR 11 1 P41227-2;P41227;C9JN83 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ;;; 182.41 9.30E-06 934030000 638160 535060 623990 632970 776100 567860 713250 582240 548440 FALSE TRUE 607995.4415 589583.2223 652600.5587 569342.653 911451.5943 548194.8658 604430.6128 531255.979 633489.2742 0.959756489 0.93069172 1.030168284 0.898740794 1.438779836 0.86535777 0.954129197 0.838618743 1 19.27296067 DLTRPLGPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLTRPLGPEK 10 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 81.431 0.020437 0 91444 65483 81262 102880 109450 122950 174250 148040 141630 FALSE TRUE 87121.62334 72155.79215 84987.94308 92538.30694 128538.0453 118692.2107 147664.9622 135076.8328 163593.2571 0.53255021 0.441068253 0.519507617 0.565660887 0.785717258 0.725532414 0.902634771 0.825687044 1 17.31975376 2.433911597 0.739963904 0.940986952 0.465507956 0.896320171 0.058843206 0.179058893 0.196040511 0.042295103 0.030855904 271.5886377 -2.433911597 -0.475478996 DLTTAGAVTQCYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLTTAGAVTQCYR 13 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 157.68 0.00011116 154270000 32574 25578 26327 25187 28060 29989 33347 30336 33587 FALSE TRUE 31034.29158 28184.42728 27534.11899 22655.15491 32953.65512 28950.47341 28259.30269 27679.61902 38795.50042 0.799945644 0.726487015 0.709724548 0.583963466 0.849419514 0.746232761 0.728417017 0.713474983 1 15.24360172 -1.391227164 3.110471374 1.003392108 0.734329066 0.605892925 0.067855716 9840907.786 12699514.88 299460.988 0.015509518 0.040623079 1.391227164 -0.269063043 DLTTGYDDSQPDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLTTGYDDSQPDKK 14 1 Q96G03 Q96G03 PGM2 Phosphoglucomutase-2 0 ;;; 196.37 4.00E-08 649600000 832430 746844 668788 825530 439108 791918 840310 905680 459920 FALSE TRUE 793082.6836 822948.2527 699452.5913 742546.156 515688.2962 764493.6811 712105.2761 826373.8579 531242.0447 1.492883878 1.549102261 1.316636359 1.397754872 0.970721917 1.439068479 1.340453534 1.555550556 1 19.01900981 3.730611311 20.18409963 1.305337175 1.520993094 0.21636503 0.181711334 58.11938448 147574.6438 0.044192744 0.070310042 5377.882521 -3.730611311 0.215655919 DLTVLCHLEQLLLVTHLDLSHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLTVLCHLEQLLLVTHLDLSHNR 23 0 Q92696;H0YKZ8;H0YMG5;H0YLG7 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 284.97 1.03E-52 66040000 103520 132300 90804 124250 102220 107490 120310 109410 32926 FALSE TRUE 98626.81476 145781.5204 94967.45322 111760.1539 120047.1356 103767.5943 101954.4999 99829.48038 38031.99592 2.593258975 3.833128315 2.497041003 2.938582403 3.156477401 2.728428836 2.680755963 2.624881445 1 15.21492603 -0.664040816 0.352707354 0.280874548 3.135438173 0.730139127 0.366997102 4.891938477 0.561347885 4.228908801 0.285233385 0.216750039 0.664040816 2.854563626 DLVDGINRLS(ph)FSSTGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DLVDGINRLSFSSTGSTR 18 1 A0A087WUD2;Q14511-3;Q14511 A0A087WUD2 NEDD9 Enhancer of filamentation 1;Enhancer of filamentation 1 p55 1 DLVDGINRLS(0.929)FS(0.041)S(0.012)T(0.009)GS(0.004)T(0.004)R;DLVDGINRLS(0.998)FS(0.002)STGSTR 147.26 4.71E-08 292740000 185033 152946 169157 189141 165023 156810 205573 197470 175518 TRUE FALSE 176286.8568 168531.3713 176913.0158 170128.1873 193802.959 151379.6304 174209.0632 180178.4799 202736.435 0.869537125 0.831283096 0.872625662 0.839159411 0.955935518 0.746681919 0.859288382 0.888732605 1 17.62924586 0.850560837 2.880589129 0.999852655 0.85138821 0.449502868 0.050861278 0.521507066 7.966212528 0.043663855 0.011495136 7.088605985 -0.850560837 -0.148464445 DLVEAVAHILGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 235.01 2.62E-16 2908000000 3526700 3206600 2893080 3777100 3093200 2829480 3615100 3640500 2705180 FALSE TRUE 3359999.88 3533356.186 3025730.58 3397418.732 3632653.101 2731494.398 3063550.099 3321718.52 3124685.498 1.075308181 1.130787783 0.968331239 1.087283419 1.162565994 0.874166184 0.980434703 1.063056913 1 21.57527956 2.245787554 24.99999569 0.974367372 1.085064727 0.37836104 0.067018957 165.485941 572462.8529 0.022700679 0.018630793 176.1114343 -2.245787554 0.110697355 DLVHSNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLVHSNKK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 112.84 0.0019236 819940000 1761400 1372400 1477500 1852000 1126700 1735000 2031000 1862300 1292800 FALSE TRUE 1678142.113 1512249.12 1545244.836 1665833.441 1323196.123 1674916.515 1721133.648 1699227.139 1493280.821 1.123795397 1.012702433 1.034798555 1.115552693 0.886099992 1.121635322 1.152585384 1.137915331 1 20.51005407 DLVHTEGQLQNEEIVAHDGSATYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLVHTEGQLQNEEIVAHDGSATYLR 25 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 269.28 2.91E-46 50817000 18951 18372 14515 17832 16220 17758 19709 16498 12817 FALSE TRUE 18055.22379 20244.12769 15180.52711 16039.49348 19048.76286 17143.03601 16702.03007 15053.34766 14804.5949 1.219568918 1.367421927 1.025392941 1.083413196 1.286679102 1.157953738 1.128165288 1.016802402 1 13.85375739 6.340059698 0.093974991 0.856508639 1.840191386 0.33528852 0.098389821 103.4208022 0.998931182 1.821552609 13.31266338 2188062.373 -6.340059698 0.983682747 DLVILLYETALLSSGFSLEDPQTHANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DLVILLYETALLSSGFSLEDPQTHANR 27 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;; 303.89 3.90E-71 26010010000 18947666 17243660 16283068 18783686 15713668 16996042 21886302 19486317 14604491 FALSE TRUE 18052047.38 19000808.56 17029662.77 16895514.2 18454126.72 16407464.8 18547144.66 17779991.78 16869280.87 1.070113629 1.126355575 1.009507335 1.001555094 1.093948631 0.972623844 1.099462674 1.05398635 1 24.00789514 3.738962377 24.99999889 1.038321075 1.098234602 0.278569951 0.042981005 43.52327561 2708261.413 0.010481643 0.017549193 5482.294698 -3.738962377 0.059913527 DLVLPTQALPAS(ph)PALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLVLPTQALPASPALK 16 0 Q15554;J3KSZ6;U3KQ35;H3BR06 Q15554 TERF2 Telomeric repeat-binding factor 2 1 DLVLPT(0.001)QALPAS(0.999)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK 261.31 8.31E-27 258981000 902886 881238 876162 992580 652754 1001304 1053635 1079751 825545 TRUE FALSE 860208.3681 971037.1541 916334.8943 892803.9726 766594.0909 966628.5914 892883.6294 985202.2783 953566.3023 0.902096022 1.018321591 0.960955617 0.936278862 0.803923219 1.013698354 0.936362398 1.033176483 1 19.86297373 1.242974956 24.96383335 1.016588255 0.943759802 0.220319102 0.060275043 160.2154737 906088.2802 0.041815778 0.014084466 17.49745783 -1.242974956 -0.072828453 DLVQPDKPAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 204.52 6.81E-08 2744100000 6303170 5415400 5287215 6664240 2553434 7059800 6351550 7645370 2741621 TRUE FALSE 6005231.646 5967235.417 5529639.038 5994337.934 2998752.081 6815317.356 5382504.393 6975900.872 3166777.582 1.89632252 1.884324131 1.746140641 1.892882521 0.946941174 2.1521301 1.699678696 2.202838908 1 21.59458411 3.414801462 2.134893506 1.685449289 1.886132664 0.051547534 0.413768567 1.124175324 10.36312034 0.114062174 0.176240192 2598.971168 -3.414801462 0.200683375 DLVSSLTSGLLTIGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLVSSLTSGLLTIGDR 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 201.95 7.36E-11 122320000 94907 84638 95109 96949 91362 79693 94760 78984 91457 FALSE TRUE 90420.9342 93262.70843 99469.84173 87203.50233 107295.5039 76933.21143 80302.62161 72067.74224 105639.6845 0.855937186 0.882837817 0.941595407 0.825480526 1.015674218 0.728260519 0.760155826 0.682203308 1 16.68879237 2.212742214 24.99944888 0.769741319 0.895092758 0.227018912 0.097596761 263.9672457 255592.6103 0.031999492 0.023641159 163.2082898 -2.212742214 0.125351439 DLVVLLFETALLSSGFSLEDPQTHSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLVVLLFETALLSSGFSLEDPQTHSNR 27 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;; 240.96 3.47E-45 3504020000 2983714.8 2644686.7 2453241.9 3078234.4 2452328 2721400.6 3427886.3 2976160.5 2197517 FALSE TRUE 2842680.515 2914183.281 2565725.468 2768804.43 2880013.227 2627157.815 2904899.287 2715552.109 2538296.713 1.119916557 1.148086142 1.010805969 1.090811967 1.134624338 1.035008162 1.144428574 1.069832418 1 21.27542929 -5 0.218726146 0.501598849 1.112938982 0.294272156 0.04573207 185.5092644 1.854576917 40.78158854 0.084621597 1.00E-05 5 0.611340134 DLYANTVLSGGTTMYPGIADR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;;; 367.73 6.27E-112 1271222000 1215437 1087485 1083204 1219666 1053306 1121096 1277522 1229429 1240884 FALSE TRUE 1157985.702 1198300.958 1132869.975 1097062.856 1237002.233 1082272.164 1082612.556 1121773.679 1433313.953 0.807907925 0.836035228 0.790385088 0.76540304 0.863036483 0.755083813 0.755321298 0.782643382 1 20.45092322 -1.128076774 5.108079546 1.000007199 0.795308997 0.778188526 0.034481044 2.93E-06 5.01E-07 0.03464982 0.008166754 0.074460033 1.128076774 -0.204698202 DLYCHK ddPTM_SK-BR-3_Trastuzumab_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 91.584 0.047726 112380000 156970 138080 93396 117620 149110 104390 150050 142290 135830 FALSE TRUE 149550.3392 152150.509 97678.29898 105796.6141 175114.7368 100774.9481 127157.1166 129830.3333 156893.8227 0.953194566 0.969767365 0.622575812 0.674319819 1.116135319 0.64231304 0.810466049 0.82750443 1 17.25942903 DLYDAGVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DLYDAGVKR 9 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2 Annexin A2;Annexin 0 ;; 85.862 0.023295 1846760000 2178710 1909610 1755310 2130820 2201650 1733370 1985650 1688350 1861180 FALSE TRUE 2075726.696 2104201.43 1835792.7 1916625.925 2585617.063 1673342.962 1682702.624 1540509.123 2149802.289 0.965543067 0.978788348 0.853935596 0.891535903 1.202723188 0.77837063 0.782724361 0.716581767 1 21.03577255 DLYDDKDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DLYDDKDGLR 10 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;; 149.94 2.05E-05 584693000 2079120 2146230 1812110 2405650 1312330 2072830 2035600 2250710 1326930 FALSE TRUE 1980844.118 2364933.277 1895197.036 2163829.492 1541199.937 2001047.377 1725031.834 2053625.901 1532703.527 1.292385698 1.542981558 1.236505953 1.411773023 1.005543413 1.305567151 1.125483045 1.339871582 1 20.54764723 2.766083993 24.77223276 1.172302978 1.383397844 0.3850977 0.134023351 637.1652282 573475.2686 0.036760766 0.038981122 583.5579534 -2.766083993 0.211094867 DLYDDKDGLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLYDDKDGLRK 11 2 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 71.176 0.02798 149050000 550150 528680 450720 534660 303640 525170 567260 565280 296340 FALSE TRUE 524145.4998 582553.0931 471385.9578 480914.961 356594.7199 506983.2312 480714.0686 515781.0865 342294.8937 1.531268825 1.701904129 1.377134063 1.404972642 1.041776335 1.481129986 1.404385743 1.506832547 1 18.38488025 -0.602400945 0.054022553 5.80E-14 2.37507252 0.395979942 0.166435054 148.3747377 1.837349367 51.473264 30.25259723 0.249803809 0.602400945 2.37507252 DLYEDELVPLFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DLYEDELVPLFEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 250.94 1.05E-17 357216900 1255104 1088117 1088447 1299555 881607 1097292 1332334 1272719 927574 FALSE TRUE 1195777.721 1198997.359 1138353.372 1168921.262 1035358.982 1059292.503 1129061.978 1161272.977 1071417.439 1.116070803 1.11907583 1.062474187 1.091004515 0.966345091 0.988683276 1.05380213 1.083866041 1 20.03108925 3.270566719 1.658853184 1.024104855 1.115937335 0.497997668 0.037553883 0.289302996 1.646036314 0.012390572 0.018127217 1864.518596 -3.270566719 0.09183248 DLYVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DLYVLR 6 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 100.27 0.088053 36954000 70813 57366 49969 57256 114470 38742 70105 49483 105800 FALSE TRUE 67465.80983 63211.66062 52260.12808 51500.5181 134433.5318 37400.35483 59409.19468 45150.00619 122206.9236 0.552062091 0.517251059 0.427636393 0.421420625 1.100048408 0.30604121 0.486136079 0.369455386 1 16.8989665 -1.442686771 3.410767772 1.005989309 0.52276496 0.322744731 0.217378244 57939528.12 91078121.48 3421438.685 0.048594949 0.03608388 1.442686771 -0.48322435 DMAEAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMAEAHK 7 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 64.836 0.054779 33627000 43308 47594 42371 51704 37288 45296 54007 48343 43410 FALSE TRUE 41260.91667 52443.88271 44313.75226 46506.61569 43791.01539 43727.38816 45767.24024 44109.83064 50141.80109 0.822884615 1.045911427 0.883768658 0.927501898 0.873343487 0.872074541 0.912756208 0.879701759 1 15.6137262 -1.137844405 5.022765308 1.000004268 0.908665213 0.210558129 0.058320582 2.67E-06 4.58E-07 0.054037711 0.012736216 0.072804059 1.137844405 -0.091339055 DMAIATGGAVFGEEGLTLNLEDVQPHDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMAIATGGAVFGEEGLTLNLEDVQPHDLGK 30 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 295.75 5.31E-81 105358000 231633 176175 195775 207261 162668 162913 209587 209432 171824 FALSE TRUE 220684.1671 194127.4328 204751.4774 186426.7305 191037.2477 157271.282 177610.6538 191093.0238 198469.5884 1.111929384 0.978121809 1.031651645 0.939321395 0.96255174 0.792420054 0.894901104 0.962832771 1 17.59855843 3.866248694 0.723050983 0.902933083 1.11332105 0.450333398 0.061921913 0.898655363 0.743748337 0.0280002 0.129096151 7349.345993 -3.866248694 0.210387967 DMDDAYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 112.84 0.0068939 686840000 1832410 1567990 1602530 1790950 1535890 1616270 1852320 1810840 1529220 FALSE TRUE 1745795.611 1727769.964 1676007.586 1610920.303 1803748.73 1560298.165 1569714.564 1652273.25 1766363.627 0.988355729 0.978150782 0.948846296 0.911998118 1.021165009 0.883339161 0.888670113 0.935409462 1 20.75235094 2.223855735 24.99580029 0.913257224 0.968979828 0.169538382 0.042622057 292.3141506 496881.0971 0.014837591 0.011004549 167.4386581 -2.223855735 0.055722604 DMDDEESWIKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMDDEESWIKEK 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 64.65 0.05734 74071000 64813 48291 60689 88003 56910 79852 97889 96198 56379 FALSE TRUE 61749.41794 53211.9078 63471.65068 79156.77125 66835.08598 77086.70522 82954.2352 87774.39314 65121.96738 0.9482118 0.81711149 0.974658065 1.215515661 1.026306309 1.183728139 1.273828764 1.347846152 1 15.99085666 3.361602058 3.703757534 1.188125418 0.883351174 0.571472338 0.107960917 0.144178626 3.764490666 0.030101226 0.041738676 2299.333983 -3.361602058 -0.304774244 DMDEPS(ph)PVPNVEEVTLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 234.12 9.74E-24 832891000 892721 902475 758114 986473 500663 907383 850694 950264 549158 TRUE FALSE 850523.8475 994438.2285 792874.2768 887310.8599 587978.4687 875960.0992 720905.0062 867053.8465 634318.6179 1.340846419 1.567726692 1.249962171 1.398840953 0.926944996 1.380946538 1.136502991 1.366905877 1 19.27484816 3.276989792 1.87515961 1.190810568 1.444533685 0.279977332 0.165012206 0.369992104 2.67681029 0.046565181 0.066786855 1892.299139 -3.276989792 0.253723117 DMEESIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMEESIR 7 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 128.86 0.021314 0 174600 167400 128480 186310 139490 147120 169440 153430 146200 FALSE TRUE 166347.004 184458.2503 134370.9351 167581.7648 163817.0118 142025.1975 143588.816 139994.8558 168871.9493 0.985048166 1.092296566 0.795697187 0.992359983 0.970066447 0.841023024 0.85028222 0.829000058 1 17.36557018 3.748890228 24.97670351 0.891728971 1.038672368 0.377729897 0.075412234 617.8866292 1494028.384 0.018688498 0.033242445 5609.061837 -3.748890228 0.146943397 DMES(ph)PTKLDVTLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 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(0.989)PT(0.011)KLDVTLAK;DMES(0.935)PT(0.065)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.993)PT(0.007)KLDVTLAK;DMES(0.937)PT(0.063)KLDVTLAK;DMES(0.5)PT(0.5)KLDVTLAK;DMES(0.972)PT(0.028)KLDVTLAK;DMES(0.805)PT(0.195)KLDVTLAK;DMES(0.997)PT(0.003)KLDVTLAK;DMES(0.86)PT(0.14)KLDVTLAK;DMES(0.977)PT(0.023)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.931)PT(0.069)KLDVTLAK;DMES(0.992)PT(0.008)KLDVTLAK;DMES(0.985)PT(0.015)KLDVTLAK;DMES(0.99)PT(0.01)KLDVTLAK;DMES(0.869)PT(0.131)KLDVTLAK;DMES(0.975)PT(0.025)KLDVTLAK;DMES(0.956)PT(0.044)KLDVTLAK 275.37 2.77E-33 22968610000 39629590 33609990 32730460 40218870 17855850 40501660 41473360 44540040 18634500 TRUE FALSE 37756377.82 37034886.19 34231183.97 36175992.78 20969904.59 39099077.36 35145837.22 40639877.98 21524243.09 1.754132662 1.720612708 1.59035483 1.680709172 0.974245854 1.816513463 1.632848927 1.888097891 1 24.35945917 3.593305192 1.948316073 1.535665643 1.744416299 0.087872227 0.304421765 0.904452472 6.76021625 0.084085031 0.153383429 3920.172633 -3.593305192 0.208750657 DMESPT(ph)KLDVTLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.194)PT(0.806)KLDVTLAK 176.28 3.84E-06 156990000 332580 276400 276590 338950 148150 343570 336200 338370 146470 TRUE FALSE 316859.6025 304565.4742 289271.9251 304878.102 173987.3131 331672.0848 284906.5153 308740.529 169183.8195 1.872871788 1.800204506 1.709808455 1.802052365 1.028392157 1.960424381 1.684005693 1.82488213 1 17.36823207 -1.942232741 2.476236589 0.482830011 1.719032928 0.433667787 0.254933112 6027426.467 2681747.679 17956059.82 0.057901359 0.01142266 1.942232741 1.236202918 DMFCAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DMFCAGR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 106.85 0.017705 620450000 741820 798950 715470 787900 1027680 625000 794930 658890 974310 FALSE TRUE 706755.6387 880363.9133 748275.0072 708698.7951 1206907.067 603356.0933 673648.8286 601194.0986 1125401.019 0.628003376 0.782266853 0.66489633 0.62973001 1.072424004 0.53612542 0.598585586 0.534204331 1 20.10200774 DMFDPHGWSEDSYYEALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMFDPHGWSEDSYYEALAK 19 0 X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5;J3QLM2;J3KRR6 X6R3T8 SAP30BP SAP30-binding protein 0 144.68 1.33E-07 33423000 119300 96692 98527 123680 84652 107870 122950 122110 81749 FALSE TRUE 113660.9254 106545.0247 103044.5604 111247.4514 99415.282 104134.4349 104191.7194 111417.4011 94426.2174 1.203700927 1.128341552 1.091270658 1.178141564 1.052835587 1.102812733 1.103419392 1.179941378 1 16.52689986 -4.999970565 0.018185384 0.012607804 1.92796047 0.421461473 0.046875191 3665.587445 5.04823213 348.8401953 201.5313696 1.00E-05 4.999970565 1.915352666 DMFEEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMFEEALR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 133.6 0.0021228 137991000 262690 230849 221827 251170 247060 215053 291270 270890 274280 FALSE TRUE 250273.1643 254372.7756 231997.9874 225921.9144 290147.1858 207605.6607 246831.412 247169.4355 316813.9416 0.789968911 0.802909033 0.732284653 0.713105974 0.915828339 0.655292061 0.779105271 0.780172218 1 18.2732763 0.586015375 3.251061803 0.99999876 0.771180969 0.534382803 0.06721338 8.021019053 62.04830265 0.058044251 0.015055169 3.85492005 -0.586015375 -0.22881779 DMGPPKENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMGPPKENK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 83 0.015378 137497000 439090 375030 384240 448000 278990 420760 461860 471370 327120 FALSE TRUE 418335.0859 413245.9834 401857.7841 402966.1889 327645.7677 406188.9757 391394.7744 430094.3439 377848.0989 1.107151491 1.093682844 1.063543221 1.066476687 0.867136208 1.075006006 1.035852173 1.138273145 1 18.52744684 3.396264932 2.308524666 1.027655973 1.099419158 0.156421372 0.068585061 0.517613536 5.588095703 0.019757229 0.029662229 2490.376053 -3.396264932 0.071763185 DMGSCEIYPQTIQHNPNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMGSCEIYPQTIQHNPNGR 19 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 265.22 2.14E-31 1389010000 913740 919900 910050 1051710 953670 929130 1075070 1035880 938270 FALSE TRUE 870549.3211 1013638.856 951776.6927 945990.1127 1119989.746 896953.9951 911048.3265 945172.8557 1083772.12 0.803258642 0.935287813 0.878207398 0.872868102 1.03341812 0.827622319 0.840627204 0.872114016 1 20.04763001 4.670896417 3.444100228 0.897182083 0.797952953 0.178922094 0.06686589 0.475392408 9.305805851 0.015475791 0.109661821 46870.15792 -4.670896417 -0.09922913 DMHSAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DMHSAYK 7 0 P08621;P08621-2 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;;;;; 151.29 0.0018911 2807850000 5037460 4657330 4569320 5485240 4280960 5043110 6006680 4769060 2140402 FALSE TRUE 4799349.249 5131917.222 4778827.842 4933853.254 5027558.069 4868465.836 5090250.646 4351455.824 2472324.611 1.941229412 2.075745717 1.932928961 1.995633273 2.033534774 1.969185525 2.058892519 1.76006654 1 21.23743675 0.842597856 3.059423486 1.000228035 2.003447264 0.977218482 0.04794054 0.086338398 1.414973014 0.042847399 0.011201778 6.959817575 -0.842597856 1.00321923 DMLGS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMLGSLR 7 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DMLGS(1)LR;DMLGS(1)LR 96.331 0.013437 71773000 238390 190702 156910 304860 292280 197079 270530 182655 223190 TRUE FALSE 227121.7771 210134.7506 164104.4787 274214.8936 343253.5395 190254.1048 229255.6799 166660.7599 257801.1653 0.880995929 0.81510396 0.636554449 1.06366817 1.331466206 0.737987761 0.889273249 0.646470157 1 17.97589926 -2.69068275 2.153475628 4.778662003 0.877047715 0.035480341 0.20430537 8262760.756 753118.3589 152288850.2 0.048403695 0.002038531 2.69068275 -3.901614288 DMLGSLRDS(ph)ALFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DMLGSLRDSALFVK 14 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DMLGS(0.038)LRDS(0.962)ALFVK;DMLGS(0.001)LRDS(0.999)ALFVK;DMLGS(0.043)LRDS(0.957)ALFVK;DMLGSLRDS(1)ALFVK;DMLGSLRDS(1)ALFVK 179.09 1.15E-06 488647000 1480880 1254240 1325360 1628900 1222120 1403610 1731190 1585300 1290780 TRUE FALSE 1410881.737 1382048.482 1386129.067 1465159.877 1435257.341 1355002.634 1467065.17 1446482.728 1490947.57 0.946298693 0.926959814 0.929696721 0.982703823 0.962647762 0.908819774 0.98398173 0.97017679 1 20.50779809 1.008512716 0.384746256 1.005384889 0.935917173 0.390771381 0.022571959 1.408565245 0.58000613 0.035809985 0.019426394 10.19794618 -1.008512716 -0.069467716 DMLLANKVPAAAR ddPTM_SK-BR-3_Trastuzumab_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 ; 183.89 9.09E-06 2160300000 3277600 2702900 2543000 3018400 2443900 2859700 3442800 3089800 2832200 FALSE TRUE 3122674.344 2978328.583 2659599.065 2714984.697 2870115.386 2760667.872 2917537.629 2819240.732 3271403.111 0.954536704 0.910413202 0.812984207 0.829914445 0.877334675 0.843878843 0.89183067 0.86178335 1 21.64147811 -0.681069985 7.114000686 1.000000544 0.877887972 0.484815958 0.040903085 0 0 0.043726848 0.010306517 0.2084155 0.681069985 -0.122112573 DMLLELEEQLAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMLLELEEQLAESR 14 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 110.86 0.0033536 0 13299 7210.6 7018.8 8680.8 7145.4 7644.3 8615.3 8996.7 8671.7 FALSE TRUE 12670.38263 7945.368338 7340.618923 7808.189492 8391.555498 7379.575974 7300.877754 8208.901253 10016.46295 1.264955773 0.793230942 0.732855396 0.779535604 0.837776323 0.736744699 0.728887811 0.819540919 1 13.29008553 4.528325974 2.165092547 0.783672989 1.297216981 0.755602618 0.081559625 0.166932917 1.228085833 0.018573822 0.140448537 33754.05659 -4.528325974 0.513543992 DMLLELEEQLAESRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMLLELEEQLAESRR 15 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 79.614 0.03114 13698000 13299 10760 13123 14983 14535 13950 16539 14991 15964 FALSE TRUE 12670.38263 11856.45623 13724.70253 13476.88037 17069.8994 13466.908 14015.67179 13678.30857 18439.61559 0.68712835 0.642988254 0.744305241 0.730865582 0.925718832 0.730324769 0.760084814 0.741789247 1 14.17052096 -5 0.102761877 1.805168976 0.570998328 0.592500083 0.068847134 124.7965046 0.867228425 21.64040583 1.058203391 1.00E-05 5 -1.234170648 DMLPS(ph)PEQTLSPLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DMLPSPEQTLSPLSK 15 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 DMLPS(0.985)PEQT(0.015)LSPLSK;DMLPS(0.996)PEQT(0.003)LSPLSK 150.59 1.53E-08 0 109016 107822 96774 123549 78013 103400 105566 111989 71626 TRUE FALSE 103863.0297 118809.1844 101211.1836 111129.6198 91618.4425 99819.23207 89459.96785 102182.6495 82733.39427 1.255394278 1.436048713 1.223341367 1.34322568 1.107393735 1.206516824 1.081304214 1.235083492 1 16.33618215 2.73967168 24.99999984 1.133551694 1.323128126 0.548109856 0.08471059 69.12516641 1555392.809 0.023962274 0.024148607 549.1255865 -2.73967168 0.189576432 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR 267.51 9.52E-44 1270165400 1253356.7 1166518.6 1176389.3 1329755.6 1202813.9 1245959.9 1437643.3 1334514.8 1275077 TRUE FALSE 1194113.013 1285388.172 1230327.913 1196086.041 1412584.263 1202811.996 1218304.41 1217657.609 1472809.429 0.810772249 0.872745751 0.835361241 0.812111884 0.95910865 0.816678636 0.82719759 0.826758429 1 20.49013934 -1.143595586 4.056696116 1.000049345 0.845043854 0.548072472 0.044207107 5778579.296 1629000.585 2639.928365 0.009578838 0.071846301 1.143595586 -0.155005491 DMQGLS(ph)LDAASQPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;DMQGLS(1)LDAASQPSK;DMQGLS(1)LDAASQPSK;DMQGLS(1)LDAASQPSK 294.05 5.61E-44 756769000 2179050 1516628 1500732 2827470 2497600 2556270 2694620 1550653 1943661 TRUE FALSE 2076050.625 1671174.117 1569542.047 2543247.344 2933180.649 2467745.729 2283506.229 1414869.603 2245074.021 0.924713664 0.744373727 0.69910481 1.132812246 1.306496188 1.099182346 1.017118459 0.63021067 1 21.09833158 3.236444394 24.9999954 1.047978443 0.799080358 0.288254623 0.177390333 68.79799226 812748.5144 0.050833411 0.063664195 1723.631388 -3.236444394 -0.248898086 DMS(ph)PLS(ph)ETEMALGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 2 DMS(1)PLS(0.822)ET(0.178)EMALGK;DMS(1)PLS(0.999)ET(0.001)EMALGK;DMS(1)PLS(0.831)ET(0.169)EMALGK 238.02 3.79E-17 62133000 468509 444958 346444 473766 274112 461806 427373 429428 243048 TRUE FALSE 446363.5081 490299.7261 362328.8001 426142.1416 321917.046 445813.5424 362169.3996 391825.0078 280738.6425 1.589961054 1.746463264 1.290626744 1.517931902 1.146678787 1.588002059 1.290058954 1.395693177 1 18.09886813 8 0.04361011 6.46E-15 3.890589616 0.505524928 0.157844972 454.8710174 1.506252571 34.84162795 125.8119532 100000000 -8 3.890589616 DMS(ph)PLSETEMALGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK 395.95 2.45E-114 628015000 2123466 1870138 1565588 2205655 1094393 1949631 1861768 1980579 971949 TRUE FALSE 2023093.97 2060707.188 1637371.758 1983938.369 1285254.793 1882114.79 1577721.098 1807149.003 1122673.887 1.802031733 1.835534978 1.458457151 1.76715464 1.14481579 1.676457261 1.405324481 1.60968294 1 20.09850749 2.691658646 0.06019244 1.14E-12 3.143674593 0.525668966 0.192179682 44.28852409 1.104473189 24.01172035 32.74173634 491.6529467 -2.691658646 3.143674593 DMSGHYQNALYLGDVSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DMSGHYQNALYLGDVSER 18 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;;;; 204.63 1.05E-15 1070950000 683720 595995 657360 676083 733855 627891 773973 724674 802059 FALSE TRUE 651401.9106 656727.5681 687500.6062 608121.8524 861839.0797 606146.9772 655889.2039 661217.7028 926438.2134 0.703125045 0.708873575 0.742090078 0.656408429 0.930271514 0.654276743 0.707968642 0.713720239 1 19.82133524 -1.101411496 4.343476969 1.000034395 0.723977232 0.553542619 0.076980172 0.990035341 40172632.21 2868.465566 0.016242266 0.079175079 1.101411496 -0.276057163 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMSPLSETEMALGKDVT(0.829)PPPET(0.171)EVVLIK;DMS(0.001)PLS(0.005)ET(0.005)EMALGKDVT(0.989)PPPET(0.001)EVVLIK;DMSPLSETEMALGKDVT(0.998)PPPET(0.002)EVVLIK;DMSPLSETEMALGKDVT(0.993)PPPET(0.007)EVVLIK;DMSPLSETEMALGKDVT(1)PPPETEVVLIK;DMSPLSETEMALGKDVT(0.989)PPPET(0.011)EVVLIK;DMSPLSETEMALGKDVT(0.997)PPPET(0.003)EVVLIK;DMSPLSETEMALGKDVT(1)PPPETEVVLIK;DMS(0.001)PLS(0.001)ET(0.001)EMALGKDVT(0.988)PPPET(0.008)EVVLIK 173.7 2.95E-12 667183000 1926520 1540346 1756895 1954820 1171716 1948114 2318839 2295014 1354209 TRUE FALSE 1835457.218 1697309.009 1837450.374 1758317.78 1376062.899 1880650.324 1965057.522 2094050.408 1564212.815 1.173406329 1.08508829 1.174680552 1.124091148 0.879715909 1.202298246 1.2562597 1.338724748 1 20.57700538 2.025126351 24.99984324 1.227421011 1.095575416 0.166784437 0.117744655 313.9964492 312414.0804 0.040842756 0.030163341 105.9561943 -2.025126351 -0.131845595 DMTGKEDNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DMTGKEDNYR 10 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 67.726 0.06518 214260000 226830 173280 208350 226350 177710 187070 232040 228590 176090 FALSE TRUE 216108.1954 190937.429 217903.0536 203596.868 208702.5677 180591.719 196638.0363 208573.4478 203397.1379 1.062493788 0.938741966 1.07131819 1.000981971 1.026084093 0.887877386 0.966768945 1.025449276 1 17.63393985 DMVTELFDPLVQGEVQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DMVTELFDPLVQGEVQHR 18 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ;;;;; 226.67 3.39E-19 217973500 269889.5 233138.2 231065.7 271588.1 253972 242839 295151.8 261423.2 256998 FALSE TRUE 257132.3582 256895.2476 241660.2909 244287.5482 298264.6364 234429.4245 250120.9721 238531.5987 296851.9373 0.866197339 0.865398589 0.814076853 0.822927249 1.004758935 0.789718358 0.842578204 0.803537282 1 18.179384 -1.064986302 4.306056766 1.000013889 0.852470971 0.378438962 0.059929925 51078707720 11091201543 7365543.729 0.01293413 0.086102091 1.064986302 -0.147542918 DNALLSAIEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNALLSAIEESR 12 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 103.97 0.0050903 12486000 21268 20789 23117 23502 20659 21062 23417 23481 20509 FALSE TRUE 20262.70379 22907.42274 24176.93732 21139.53431 24261.92306 20332.61766 19844.30657 21424.87916 23689.43097 0.855347847 0.966989151 1.020579065 0.892361422 1.024166561 0.858299116 0.83768608 0.904406661 1 14.53195592 2.192757035 24.99945285 0.880324267 0.94558841 0.094052336 0.06703067 211.4512347 115408.0969 0.023731931 0.017527254 155.868026 -2.192757035 0.065264143 DNDFIYHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DNDFIYHDR 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;; 122.42 0.00058627 1101410000 2658350 2729860 2380350 3075340 2111210 2648280 2577270 2690240 1831150 FALSE TRUE 2532695.064 3008035.838 2489491.402 2766200.98 2479404.356 2556569.4 2184060.127 2454668.324 2115115.39 1.197426427 1.422161577 1.177000278 1.307825093 1.172231249 1.208713913 1.032596206 1.160536364 1 21.01230494 2.074033146 0.734381155 1.030474474 1.300528865 0.547002703 0.080985648 0.437955357 0.447957989 0.063900752 0.036049488 118.5859252 -2.074033146 0.270054392 DNDFIYHDRVPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNDFIYHDRVPDLK 14 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 143.02 5.55E-06 52467000 280840 165560 250100 251340 220840 272370 350060 313600 239760 FALSE TRUE 267565.2498 182430.7522 261567.3324 226074.8257 259354.4261 262937.7586 296651.9177 286139.5215 276940.7563 0.966146166 0.658735661 0.944488402 0.816329199 0.936497862 0.949436848 1.07117465 1.033215643 1 18.07921786 2.342698061 1.341971149 1.041723491 0.829007339 0.458407277 0.086355227 0.333032036 1.1928835 0.046566257 0.029932678 220.139543 -2.342698061 -0.212716152 DNDKTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNDKTR 6 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 84.244 0.051138 48965000 113260 74764 124760 157950 123640 120910 218790 226250 161620 FALSE TRUE 107906.4243 82382.5366 130480.3694 142072.5659 145202.7769 116722.8564 185409.5671 206438.3506 186683.2042 0.578018921 0.441295921 0.698940057 0.761035609 0.77780311 0.625245624 0.993177549 1.105821766 1 17.51023261 2.298045048 0.546694065 1.073744168 0.504598057 0.722857492 0.10905826 0.436884079 0.268128273 0.100361646 0.084304571 198.6300941 -2.298045048 -0.56914611 DNEEKDSAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNEEKDSAFR 10 1 O14787-2;O14787;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 146.16 2.66E-05 596890000 1117650 1015280 949590 1285440 736900 1190950 1114110 1255120 782730 FALSE TRUE 1064820.899 1118738.186 993129.6408 1156225.129 865415.1267 1149707.103 944132.0575 1145215.039 904111.7708 1.177753607 1.23738925 1.098458922 1.278851981 0.95719927 1.271642666 1.044264756 1.266674183 1 19.78614161 -5 0.145663526 0.446801147 1.217892795 0.167059989 0.108368954 211.2131025 1.852327628 34.19212243 0.506954301 1.00E-05 5 0.771091649 DNFFEVFTPVFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 172.09 5.58E-05 167153000 337919 332011 296214 337582 247380 297416 375259 368789 288168 FALSE TRUE 321946.2386 365843.2984 309795.7049 303647.616 290522.9937 287116.4093 318006.3474 336495.8801 332855.6217 0.967224879 1.099105061 0.930720963 0.912250226 0.87281985 0.862585429 0.955388243 1.010936449 1 18.34453701 3.67104816 10.30758469 0.926895201 1.033108983 0.332536097 0.056962993 0.569705848 85.20820499 0.014840985 0.023006551 4688.653728 -3.67104816 0.106213782 DNFHGLAIFLDTYPNDETTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DNFHGLAIFLDTYPNDETTER 21 0 Q12907;D6RBV2;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;;; 189.64 2.09E-17 269219000 324623 306711 253758 333667 352737 291105 401248 282817 263028 FALSE TRUE 309278.7141 337965.1996 265393.0553 300126.1592 414254.2211 281023.9609 340030.2482 258052.0442 303817.0389 1.017976856 1.112397122 0.873529201 0.987851637 1.363498975 0.924977618 1.119194135 0.849366596 1 18.21284326 1.242303939 24.99457274 0.924683298 1.058204973 0.138410276 0.137286686 168.1865051 1123061.544 0.091858863 0.030668428 17.47044387 -1.242303939 0.133521676 DNFNFLHLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNFNFLHLNR 10 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 147.74 2.63E-05 62224000 96330 83425 63465 75513 87077 66119 104530 86839 80659 FALSE TRUE 91776.67181 91926.10235 66374.93303 67922.28977 102263.2012 63829.28245 88582.02867 79234.9168 93167.18577 0.985075067 0.986678964 0.712428228 0.729036615 1.097631107 0.68510476 0.950785708 0.850459485 1 16.5075343 3.88759371 22.25877574 0.857379462 0.985956221 0.136107286 0.130808362 15.83388448 3103.847252 0.030480916 0.054950329 7719.580675 -3.88759371 0.128576759 DNFWEMGDTGPCGPCSEIHYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DNFWEMGDTGPCGPCSEIHYDR 22 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;;; 255.94 4.27E-37 747025000 474347 378085 411102 476821 416457 407797 480658 462883 414711 FALSE TRUE 451925.5574 416612.2913 429951.4333 428890.0472 489086.9689 393674.8876 407324.7942 422350.5106 479022.2638 0.943433305 0.869713838 0.897560439 0.895344704 1.021010934 0.821830043 0.850325392 0.881692862 1 18.86973319 DNGIRPSSLEQMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNGIRPSSLEQMAK 14 1 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 184.99 1.12E-06 947260000 1201490 979630 1033230 1120260 914960 989280 1186540 1233130 1094100 FALSE TRUE 1144697.949 1079455.411 1080604.618 1007649.336 1074528.734 955020.9855 1005511.531 1125150.6 1263767.44 0.905782118 0.854156688 0.855066038 0.797337631 0.850258283 0.755693615 0.795646017 0.890314598 1 20.26929957 0.94886196 5.43119752 0.999963196 0.832989367 0.634636784 0.041082159 0.21588104 19.62362411 0.044125517 0.011125565 8.889185302 -0.94886196 -0.166973829 DNGLLAKPTHGDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DNGLLAKPTHGDIIR 15 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;; 211.78 7.26E-10 1667890000 2459700 2458430 2099510 2204080 1542990 1879220 1929440 2191020 1398480 FALSE TRUE 2343434.856 2708946.812 2195774.61 1982521.691 1812086.967 1814142.14 1635068.491 1999162.673 1615349.136 1.450729631 1.677003907 1.3593189 1.227302288 1.121792761 1.123065039 1.012207488 1.237604075 1 20.62341459 3.285088089 1.839687404 1.095577147 1.563845686 0.813246964 0.089572147 0.11630004 0.810010523 0.026663524 0.038616866 1927.915917 -3.285088089 0.468268539 DNHFAIFIIPQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNHFAIFIIPQGR 13 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 0 74.769 0.033209 37450000 151390 151580 152260 179870 160660 168400 211400 135860 75057 FALSE TRUE 144234.0947 167026.1743 159241.2716 161789.1259 188679.0531 162568.2658 179147.0474 123963.3782 86696.45622 1.663667709 1.926562879 1.836767944 1.86615616 2.176317941 1.875143147 2.066371051 1.429855193 1 16.4036854 1.018041447 4.072034164 1.002942346 1.908340638 0.83441069 0.137074022 0.068917613 2.893155501 0.133427416 0.034145764 10.42416909 -1.018041447 0.905398291 DNHVVAAGGVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DNHVVAAGGVEK 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ;;;;;; 141.85 6.09E-05 2905820000 4754470 4791970 4880640 6209340 4530060 5281300 6582090 4292750 1266517 FALSE TRUE 4529735.626 5280277.191 5104422.172 5585165.346 5320101.03 5098407.257 5577871.282 3916854.053 1462921.988 3.096361708 3.60940449 3.489196426 3.817814889 3.63662661 3.48508485 3.812828933 2.677418266 1 20.48042141 0.924569127 3.561667353 1.001759597 3.550573469 0.940519686 0.205676062 0.073862616 2.287614172 0.205704085 0.053077771 8.405607887 -0.924569127 2.548813872 DNIACVILTFKEPFGTEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNIACVILTFKEPFGTEGR 19 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 282.17 8.95E-40 2202630000 3038100 2219730 2779400 2876300 2253650 2696630 3126500 3086700 2410590 FALSE TRUE 2894495.034 2445923.011 2906838.239 2587168.859 2646685.846 2603245.027 2649495.003 2816412.184 2784411.986 1.039535474 0.878434306 1.043968441 0.929161659 0.950536724 0.93493529 0.951545611 1.011492624 1 21.40894126 1.23813478 24.99992093 1.005746332 0.957878577 0.121074608 0.04933087 21.16531134 1241870.424 0.035006811 0.010799863 17.30353277 -1.23813478 -0.047867755 DNIQGITKPAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 ; 142.39 5.59E-05 1295570000 1434070 1971250 2828100 1928920 1417390 1744690 1745720 2229700 1245690 FALSE TRUE 1366284.353 2172122.616 2957771.182 1735021.297 1664582.367 1684270.948 1479378.352 2034455.648 1438865.243 0.949556854 1.509608093 2.055627653 1.205826123 1.156871622 1.17055503 1.028156291 1.413930636 1 20.45650005 3.025742343 24.99989071 1.149872706 1.452110539 0.238786593 0.284327497 370.8158663 360118.2808 0.084566559 0.10107359 1061.065865 -3.025742343 0.302237833 DNKAQDWEKHFLDAS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNKAQDWEKHFLDASTSK 18 2 Q96L12 Q96L12 CALR3 Calreticulin-3 1 DNKAQDWEKHFLDAS(0.333)T(0.333)S(0.333)K;DNKAQDWEKHFLDAS(0.333)T(0.333)S(0.333)K 62.684 0.023512 3308200000 4950300 7009000 5558800 4279700 1083100 7383200 3058300 3433300 140988 TRUE FALSE 4716309.13 7723225.069 5813676.478 3849496.425 1271992.297 7127517.933 2591700.165 3132662.051 162851.699 28.96076098 47.42489711 35.69920679 23.63804891 7.81074011 43.766924 15.91448036 19.23628719 1 17.31319925 1.526655237 0.284110586 2.57E-22 41.92442995 0.449853548 10.9849505 1.476877476 0.458238334 23.14533973 21.45248334 33.62445373 -1.526655237 41.92442995 DNKDGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNKDGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR 36 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 ; 201.7 2.26E-30 153508000 360780 235941 328630 346070 258867 369790 451310 414980 293644 FALSE TRUE 343726.6444 259983.6561 343698.0106 311282.3861 304013.3228 356984.0796 382454.3706 378642.1513 339180.8118 1.013402387 0.766504611 1.013317967 0.91774763 0.896316396 1.052489018 1.127582568 1.116343077 1 18.37169503 2.14824141 4.305026206 1.094067443 0.912583242 0.492475567 0.076555955 0.156029548 5.289896666 0.028460127 0.020624827 140.6829318 -2.14824141 -0.181484201 DNKGTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNKGTPR 7 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 59.205 0.095701 6491200 19784 11756 20054 20502 24839 18332 29900 28541 40488 FALSE TRUE 18848.84953 12953.94977 20973.49574 18441.10001 29170.91374 17697.15824 25338.20585 26041.79873 46766.67226 0.403040213 0.276991052 0.448470989 0.394321407 0.623754318 0.378413887 0.541800488 0.556845238 1 15.51319316 -5 0.1521253 3.096446195 0.262127341 0.838346673 0.080002002 45.44192783 0.407694592 28.55175161 0.354640766 1.00E-05 5 -2.834318854 DNKPLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DNKPLVER 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 94.692 0.0092834 528305000 1138790 1097010 995650 1308750 857860 1074990 1210930 1191930 894880 FALSE TRUE 1084961.654 1208796.566 1041301.537 1177191.964 1007470.512 1037762.827 1026180.388 1087558.29 1033653.42 1.049637753 1.169440881 1.007399112 1.138865253 0.974669549 1.003975614 0.992770273 1.05214985 1 19.97932111 2.73274455 24.9954568 1.003254719 1.095057015 0.447229022 0.047758448 389.6891042 1674744.341 0.014010744 0.013542247 540.4363473 -2.73274455 0.091802296 DNLEDETEDDDLFETEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNLEDETEDDDLFETEFR 18 0 Q8IZH2-2;Q8IZH2;Q8IZH2-3 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 277.41 9.04E-39 33151000 78491 91875 67365 87925 62256 78448 76578 80726 54668 FALSE TRUE 74780.88598 101237.167 70453.75188 79086.61195 73113.42669 75731.32609 64894.61965 73657.20348 63145.63423 1.184260589 1.603233037 1.11573433 1.25244782 1.157854024 1.199312146 1.027697646 1.166465495 1 15.94639537 2.979832546 0.89845359 1.083317402 1.375825334 0.343211785 0.133528826 0.540708463 0.962070537 0.067735021 0.082578826 954.6244334 -2.979832546 0.292507932 DNLEFFLAGIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 262.23 4.89E-21 4943071200 5881954 5187674 4902551 5538049 5559712 4499671 6478559 5575187 5733801 FALSE TRUE 5603925.691 5716303.878 5127337.813 4981353.793 6529324.013 4343846.265 5490135.838 5086994.07 6622969.575 0.846134899 0.863102844 0.774175052 0.752132972 0.985860487 0.65587592 0.828953806 0.768083563 1 22.6590468 DNLEWLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DNLEWLAR 8 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 154.28 0.00099468 955298000 1378370 1386300 1252290 1515390 1157840 1277840 1433350 1413750 1140780 FALSE TRUE 1313217.182 1527565.546 1309708.735 1363060.118 1359766.929 1233588.08 1214666.132 1289954.555 1317686.336 0.996608332 1.159278581 0.993945751 1.034434433 1.031935213 0.936177333 0.921817354 0.978954187 1 20.32957556 2.343206993 3.9160287 0.94874097 1.054780535 0.394514571 0.050520721 0.190263841 5.465778435 0.018297544 0.014868184 220.3976672 -2.343206993 0.106039565 DNLGEVPLT(ph)PTEEASLPLAVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNLGEVPLTPTEEASLPLAVTK 22 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 DNLGEVPLT(0.69)PT(0.309)EEAS(0.001)LPLAVTK;DNLGEVPLT(0.839)PT(0.133)EEAS(0.028)LPLAVTK 91.583 0.0081076 50427000 170780 153956 161121 203446 134288 173247 190511 188353 136298 TRUE FALSE 162707.5679 169644.2914 168508.5572 182995.2216 157707.7847 167247.4129 161445.048 171859.8128 157434.3977 1.033494396 1.077555438 1.070341423 1.162358571 1.001736513 1.062330821 1.025475057 1.091628102 1 17.26439126 DNLSYIEHIFEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;;;; 231.13 6.55E-13 489182000 908090 921395 703167 988392 734864 756990 839818 879714 584969 FALSE TRUE 865166.3854 1015286.198 735407.9025 889036.9583 863024.0489 730775.2465 711688.3398 802681.5785 675683.0049 1.280432361 1.502607274 1.08839189 1.315760426 1.277261738 1.081535633 1.053287318 1.18795585 1 19.36598704 2.599919273 0.56823768 1.033588771 1.385002395 0.456555316 0.111408261 0.676258954 0.45562001 0.091394401 0.093224346 398.0331773 -2.599919273 0.351413624 DNLTLWTSDQQDDDGGEGNN ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DNLTLWTSDQQDDDGGEGNN 20 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;; 509.71 2.22E-276 4731317000 9519520 8266610 8692160 9852400 8690020 8892340 10439100 9582250 9434530 FALSE TRUE 9069551.155 9108986.957 9090704.134 8862018.034 10205556.74 8584396.036 8846423.568 8743177.391 10897588.73 0.832253022 0.835871786 0.834194092 0.813209074 0.936496778 0.78773353 0.811778072 0.80230385 1 23.37750561 -0.926291941 4.293033295 1.000003933 0.831349651 0.633767993 0.04019871 2231488.175 779689.3251 83.43740746 0.008794341 0.118497192 0.926291941 -0.168654281 DNLTLWTSENQGDEGDAGEGEN ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 338.91 9.61E-81 2446829000 4917719 4428251 4733699 5108240 4690640 4643974 5639330 5047870 4995230 FALSE TRUE 4685268.169 4879494.811 4950743.781 4594750.01 5508686.131 4483152.016 4778946.635 4605851.742 5769864.756 0.812023915 0.845686167 0.858034632 0.796335825 0.954734013 0.776994298 0.828259732 0.798259914 1 22.46010607 -1.387827413 3.208419813 1.00180135 0.833814918 0.530273775 0.049161955 18835514.79 24064949.21 312209.7368 0.010544324 0.040942333 1.387827413 -0.167986432 DNNLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 96.492 0.029528 301449000 704390 533620 529080 733590 560510 629410 749330 708090 622080 FALSE TRUE 671094.8807 587996.4847 553338.8413 659848.1395 658262.7665 607613.3739 635005.9461 646085.8858 718548.9893 0.933958423 0.81831092 0.770078101 0.918306405 0.916100052 0.845611619 0.883733685 0.899153566 1 19.45472699 0.05833222 0.553886365 1.009971677 0.862338423 0.412377498 0.049190919 3.949995544 1.50514474 0.133722032 0.021826876 1.143752931 -0.05833222 -0.147633254 DNNLLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 139.31 0.0062827 2183490000 2930470 2593870 2793960 3063460 3110510 2847930 3331190 2942690 3053310 FALSE TRUE 2791952.491 2858188.302 2922065.83 2755515.181 3652981.959 2749305.47 2822955.784 2685012.463 3526801.721 0.791638632 0.810419334 0.828531361 0.781307088 1.035777526 0.779546367 0.8004294 0.761316534 1 21.74992904 -1.960256717 2.786675522 1.137805949 0.822151195 0.336867405 0.077747221 25444040.35 15130379.62 22671793.19 0.017627767 0.010958302 1.960256717 -0.315654754 DNPAQDFSTLYGS(ph)SPLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNPAQDFSTLYGSSPLER 18 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 DNPAQDFSTLYGS(0.5)S(0.5)PLER;DNPAQDFSTLYGS(0.5)S(0.5)PLER 107.57 0.00043669 85454000 111968 118030 112089 135598 114193 119847 140711 135393 129254 TRUE FALSE 106675.4945 130057.3912 117228.3915 121967.4314 134108.223 115696.6683 119242.9526 123537.2712 149298.0502 0.714513648 0.871125852 0.78519707 0.816939212 0.898258369 0.774937571 0.798690622 0.827454016 1 17.1878358 -5 0.347108682 3.148171708 0.803717922 0.588124842 0.05005644 296.5494453 2.449002307 473.5762143 0.036734715 1.00E-05 5 -2.344453785 DNPAQDFSTLYGSS(ph)PLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNPAQDFSTLYGSSPLER 18 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 DNPAQDFSTLYGS(0.04)S(0.96)PLER 245.61 3.34E-24 66104000 87947 80776 86346 95386 79069 87047 104360 91794 96331 TRUE FALSE 83789.9196 89007.16623 90305.04951 85797.61806 92858.60857 84032.54056 88437.9653 83756.03073 111269.5195 0.753035692 0.799924064 0.811588384 0.771079254 0.834537697 0.755216172 0.794808549 0.752731126 1 16.76369892 -1.196266234 4.887552065 1.000025354 0.785046038 0.862121883 0.02713012 6.68E-06 1.10E-06 0.023423246 0.005520261 0.063640527 1.196266234 -0.214979317 DNPGVVTCLDEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNPGVVTCLDEAR 13 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 171.62 1.47E-06 0 61223 60449 61385 72787 53290 67022 66260 72917 49648 FALSE TRUE 58329.11012 66608.82182 64199.56297 65470.31247 62583.75913 64701.01133 56150.82005 66532.00092 57347.15827 1.017122938 1.1615017 1.119489874 1.141648766 1.091314043 1.128233958 0.979138666 1.160162124 1 15.80743438 1.771101718 25 1.045075667 1.109582243 0.197582293 0.060255743 46.26253949 35559.1743 0.025620582 0.014213123 59.03393298 -1.771101718 0.064506576 DNPKPNVSEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNPKPNVSEALR 12 1 P82909 P82909 MRPS36 "28S ribosomal protein S36, mitochondrial" 0 ; 175.15 2.60E-05 924530000 920700 736290 706480 739000 715990 742320 957770 879800 849000 FALSE TRUE 877180.3357 811318.7881 738872.8068 664714.316 840858.4293 716613.2723 811644.5958 802760.0479 980658.5839 0.894480862 0.827320335 0.75344551 0.6778244 0.857442583 0.730746953 0.827652569 0.818592792 1 19.90339142 0.472835898 1.587044227 0.999967319 0.799749438 0.507436062 0.062802573 2.879315691 7.688013959 0.061224196 0.017508558 2.970543373 -0.472835898 -0.200217881 DNPS(ph)PGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNPSPGPSR 9 0 Q9NQS1 Q9NQS1 AVEN Cell death regulator Aven 1 DNPS(0.999)PGPS(0.001)R 64.65 0.077678 0 117100 99163 99135 128740 120020 110640 135840 101810 127270 TRUE FALSE 111564.9151 109267.8224 103680.4378 115798.8106 140951.45 106808.5091 115115.1131 92894.97667 147006.3816 0.758912054 0.743286252 0.705278483 0.787712815 0.958811777 0.726556956 0.783062013 0.631911184 1 17.16551926 -1.522907302 2.859892494 1.010155939 0.764821416 0.449300709 0.082773012 13859396.37 15219204.44 1097049.654 0.018710793 0.029998027 1.522907302 -0.245334523 DNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK 123.55 6.19E-05 5289710000 5203040 5817730 4131350 6005390 1929550 5357720 4484820 5590830 1764760 TRUE FALSE 4957102.611 6410563.301 4320776.484 5401716.788 2266062.909 5172180.813 3800578.34 5101267.286 2038429.968 2.431823849 3.144853344 2.119659028 2.649939843 1.11167072 2.537335545 1.864463533 2.502547238 1 20.95902696 3.240883919 1.807851198 1.93346414 2.751640144 0.26716251 0.576136208 0.411201486 2.771995786 0.165852462 0.233079624 1741.341376 -3.240883919 0.818176004 DNSEEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 116.37 0.012727 198342000 561330 539300 518270 659230 467730 579030 601450 594230 488760 FALSE TRUE 534797.0433 594255.2831 542033.1921 592962.9479 549301.9639 558978.0459 509687.7561 542196.071 564554.4046 0.947290534 1.052609418 0.960107986 1.050320294 0.972983223 0.990122549 0.902814241 0.960396494 1 19.10675309 1.923129536 9.132879911 0.944125695 0.999016466 0.16609713 0.041453013 0.522206119 58.86783867 0.015804971 0.010000685 83.77791279 -1.923129536 0.054890772 DNSTMGYMAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNSTMGYMAAK 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 157.25 7.14E-05 185690000 87477 79684 76874 83323 82725 79900 105690 86388 97826 FALSE TRUE 83342.13557 87803.89019 80398.74894 74947.21374 97152.21381 77133.04297 89565.04937 78823.40875 112996.3565 0.737564805 0.777050632 0.711516295 0.663271065 0.859781827 0.682615311 0.792636614 0.697574782 1 16.78591673 -1.83299452 2.641890424 1.092392563 0.744788866 0.662613808 0.058169039 16065486 10739592.98 9411147.486 0.012171805 0.014689448 1.83299452 -0.347603697 DNT(ph)FFRESPVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 DNT(0.742)FFRES(0.258)PVGR 121.92 0.0023416 502240000 508360 424460 454750 498900 455780 477520 546450 489270 527100 TRUE FALSE 484330.8303 467712.9566 475600.7373 448749.6242 535267.8877 460983.3627 463079.0163 446426.925 608839.9759 0.795497749 0.768203428 0.781158853 0.737056767 0.879160221 0.757150287 0.760592331 0.733241808 1 19.21570356 -1.251642874 5.268099305 1.000025479 0.776843673 0.746888255 0.040887354 1.12E-05 1.59E-06 0.036270842 0.008548144 0.056021809 1.251642874 -0.223181807 DNTFFRES(ph)PVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;DNT(0.002)FFRES(0.998)PVGR;DNTFFRES(1)PVGR 203.06 7.84E-08 10051770000 4988300 3996460 4270250 4876300 4224630 4361980 5238790 4642340 4789330 TRUE FALSE 4752512.945 4403703.818 4466045.186 4386125.06 4961404.134 4210923.539 4439516.369 4235832.099 5532034.836 0.859089483 0.796036892 0.807306049 0.792859262 0.896849764 0.761188905 0.802510559 0.765691509 1 22.39937881 -2.067984709 2.866611781 1.296040247 0.810998937 0.68307978 0.04062767 22678110.59 19758812.25 43451868.28 0.009078356 0.008550968 2.067984709 -0.48504131 DNTIEHLLPLFLAQLKDECPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNTIEHLLPLFLAQLKDECPEVR 23 1 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 156.28 1.17E-08 617660000 968700 848070 854250 1051540 720530 973240 1151940 1106580 732800 FALSE TRUE 922911.4708 934489.2972 893418.2075 945837.2014 846190.2039 939536.4548 976190.3962 1009681.989 846438.8814 1.090346263 1.104024541 1.055502325 1.117431184 0.999706207 1.109987355 1.153291062 1.192858706 1 19.69104637 2.006218003 24.99874399 1.13222151 1.078184367 0.081710915 0.058340532 268.619195 1079944.858 0.019623252 0.014450421 101.4420467 -2.006218003 -0.054037143 DNTINLIHTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DNTINLIHTFR 11 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 162.32 2.53E-05 794114000 1511199 1796400 1550250 1646970 1264850 1527792 1503440 1662590 1152231 FALSE TRUE 1439767.618 1979455.202 1621330.496 1481413.447 1485439.44 1474884.18 1274062.615 1517004.806 1330913.099 1.081789352 1.487291097 1.218209136 1.113080522 1.116105508 1.108174667 0.957284602 1.139822583 1 20.34398494 3.227068138 2.645511015 1.060425824 1.29213206 0.406544618 0.110521956 0.234460003 3.360535206 0.032795264 0.043455317 1686.817656 -3.227068138 0.231706236 DNTRPGANS(ph)PEMWSEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 1 DNT(0.017)RPGANS(0.98)PEMWS(0.003)EAIK;DNT(0.053)RPGANS(0.947)PEMWSEAIK;DNT(0.001)RPGANS(0.998)PEMWS(0.001)EAIK 113.54 0.0003703 407409000 384783 393266 374293 425861 279688 419794 442841 423302 352467 TRUE FALSE 366595.0702 433340.2525 391454.7043 383052.6432 328465.4986 405256.4285 375277.4721 386235.4328 407125.7822 0.900446708 1.064389119 0.961508019 0.940870512 0.806791201 0.995408412 0.9217728 0.948688218 1 18.63511506 3.338650729 4.043385949 0.929279196 0.98628061 0.073782272 0.065441744 0.431942412 13.04012263 0.017542303 0.024004098 2180.975209 -3.338650729 0.057001413 DNVKNEDKDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNVKNEDKDQK 11 2 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 75.89 0.020727 177780000 508310 415480 441420 534180 243560 571710 590330 640880 249890 FALSE TRUE 484283.1937 457817.8844 461659.5436 480483.2115 286036.7869 551911.5393 500264.3163 584761.1497 288641.6649 1.677800721 1.58611157 1.599421011 1.664635671 0.990975391 1.912099348 1.733167374 2.025906931 1 18.13892004 DNVPFHSLVFPCSALGAEDNYTLVSHLIATEYLNYEDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNVPFHSLVFPCSALGAEDNYTLVSHLIATEYLNYEDGK 39 0 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 230.67 1.55E-40 21271000 19005 20682 14300 21916 11772 19212 19385 19486 7951.4 FALSE TRUE 18106.67131 22789.51931 14955.66914 19712.96204 13825.03307 18546.68362 16427.46222 17779.70254 9184.462502 1.97144594 2.48131225 1.628366292 2.146338127 1.505263163 2.019354276 1.788614436 1.935845732 1 13.16497958 -1.734740502 0.189046498 9.60E-14 2.245326646 0.554924213 0.265747447 21.04245676 0.64615472 10.84722642 0.801071035 0.018418722 1.734740502 2.245326646 DNVPFHSLVFPCSALGAEDNYTLVSHLIATEYLNYEDGKFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DNVPFHSLVFPCSALGAEDNYTLVSHLIATEYLNYEDGKFSK 42 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 78.172 0.00065318 104200000 43501 23676 31434 36505 36704 37422 57281 38982 31953 FALSE TRUE 41444.79394 26088.61132 32875.27999 32835.44805 43105.16598 36126.06676 48541.73141 35568.52942 36908.10805 1.122918408 0.70685312 0.890733276 0.889654057 1.167905056 0.978811125 1.315205086 0.963705031 1 15.17165016 2.747184392 23.79956355 1.112950462 0.893755867 0.274853509 0.143149644 352.0695049 971627.3559 0.041962487 0.043814901 558.7073591 -2.747184392 -0.219194594 DNYSPGWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DNYSPGWK 8 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 120.15 0.0036205 778890000 716130 729340 657300 791100 517140 707210 790360 777090 603450 FALSE TRUE 682279.9541 803660.5752 687437.8552 711577.125 607329.0523 682719.1404 669776.066 709043.88 697029.944 0.9788388 1.152978552 0.986238627 1.020870238 0.871309845 0.979468883 0.96089999 1.017235897 1 19.41086111 3.514959131 18.91745352 0.970800832 1.066526167 0.287669892 0.058452696 32.63693938 16316.12494 0.014661273 0.022687395 3273.098923 -3.514959131 0.095725335 DNYVPEVSALDQEIIEVDPDTKEMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DNYVPEVSALDQEIIEVDPDTKEMLK 26 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 118.14 0.00059111 64116000 146635 93986.2 150641 123112 107031 149164 201270 177470 122477 FALSE TRUE 139703.8542 103563.5006 157548.0389 110736.5479 125697.1725 143998.4133 170562.5649 161929.786 141470.1076 0.987515006 0.73205218 1.113648964 0.782755804 0.888506941 1.01787166 1.205643848 1.144621918 1 17.11013772 2.038772193 3.669899836 1.135998483 0.890825867 0.418433195 0.115435331 0.181203846 5.095203362 0.046055603 0.030017753 109.3382687 -2.038772193 -0.245172616 DPAGMPHPETGKDLYEPSHGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DPAGMPHPETGKDLYEPSHGAK 22 1 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 79.635 0.004762 29192000 97812 83442 118360 109880 75057 127430 118030 123630 53438 FALSE TRUE 93188.6206 91944.83467 123786.9231 98834.65364 88146.91704 123017.0671 100022.3557 112804.3018 61724.89212 1.509741328 1.489590852 2.005461959 1.601212254 1.428061095 1.992989585 1.62045412 1.827533397 1 15.91356479 -0.729628616 7.282025042 1.00000178 1.666353999 0.530222098 0.201816833 0 3.83E-10 0.187181685 0.044119146 0.186368017 0.729628616 0.666352219 DPDQTDGLGLSYLSSHIANVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DPDQTDGLGLSYLSSHIANVER 22 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;; 303.07 6.11E-56 305048000 299523 286043 249379 341407 262732 267271 286000 306478 253595 FALSE TRUE 285365.1414 315191.1069 260813.2738 307088.1197 308552.3776 258015.3383 242365.4472 279641.1616 292921.2174 0.974204409 1.076026891 0.890387102 1.048364207 1.053363018 0.880835265 0.827408302 0.954663387 1 18.16015317 2.229396571 24.99205771 0.892689921 1.011012623 0.28246401 0.069185187 185.0633707 504698.4067 0.024125005 0.018067825 169.5885673 -2.229396571 0.118322701 DPEKRPTAAELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DPEKRPTAAELLR 13 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ;;; 103.39 0.00090809 1242090000 1736330 1452290 1387070 1730190 1202570 1575840 1835860 1709980 1127970 FALSE TRUE 1654257.122 1600280.002 1450668.531 1556268.014 1412297.827 1521268.266 1555765.839 1560245.086 1302889.827 1.269683045 1.228254277 1.113423792 1.194473993 1.083973332 1.167610825 1.194088562 1.197526494 1 20.31328366 -5 0.082393136 0.476242738 1.34487777 0.542085712 0.052438782 196.7539275 1.142890187 19.30513122 1.684765204 1.00E-05 5 0.868635032 DPETLVGYSMVGCQR ddPTM_SK-BR-3_Trastuzumab_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 0 120.55 0.00029027 73712000 91870 82643 114660 106420 101290 74243 123820 93189 62095 FALSE TRUE 87527.48717 91064.41566 119917.2744 95722.45942 118954.9439 71671.94629 104928.9849 85028.87713 71724.37546 1.220331116 1.269643898 1.671918001 1.334587562 1.658500937 0.999269019 1.462947348 1.185494842 1 16.13017588 0.99484735 5.016197514 1.000269389 1.357467025 0.279172942 0.198959134 0.195000193 17.57057437 0.176066834 0.044525912 9.882056886 -0.99484735 0.357197637 DPGMSQS(ph)HNDLVFLEQPEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.03)QS(0.97)HNDLVFLEQPEGSR;DPGMS(0.123)QS(0.877)HNDLVFLEQPEGSR 268.83 1.30E-37 168910000 155101 135228 140387 191209 191155 154656 189319 157984 126960 TRUE FALSE 147769.6831 149007.8869 146823.8828 171988.308 224492.3715 149300.2239 160434.9095 144150.0834 146648.3084 1.007646694 1.01609005 1.001197248 1.172794354 1.530821419 1.018083506 1.09401132 0.982964516 1 17.1620009 3.243542552 24.88917773 1.144954564 1.009883225 0.123161619 0.154822962 231.9087658 1158580.725 0.043138868 0.05662335 1752.03409 -3.243542552 -0.13507134 DPGVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DPGVLDR 7 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 117.93 0.01191 6059120000 3420630 3442540 3049390 3745710 3286130 3044420 3439710 3267750 3680180 FALSE TRUE 3258943.599 3793338.74 3189207.548 3369184.114 3859230.032 2938990.972 2914919.065 2981608.487 4250883.519 0.766650882 0.892364781 0.75024581 0.792584436 0.907865392 0.691383558 0.685720757 0.701409124 1 22.0193313 2.220184722 24.99975906 0.735395291 0.821925491 0.014170973 0.103803687 450.6892708 613142.9094 0.03472324 0.025692389 166.0292944 -2.220184722 0.0865302 DPHLACVAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 102.66 0.0028385 1367120000 260929 219688 224958 220827 285178 206791 246110 241314 291652 FALSE TRUE 248595.4033 242074.457 235272.5468 198629.0504 334912.9529 199629.7758 208561.3994 220183.2669 336879.9026 0.737934799 0.718577912 0.698387007 0.589613832 0.994161273 0.592584403 0.619097185 0.653595733 1 18.36187484 -0.997245059 4.925486061 1.000003464 0.698951151 0.397645528 0.115833488 4.11E-06 8.37E-07 0.104599133 0.024653968 0.100636365 0.997245059 -0.301052313 DPLELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DPLELFR 7 0 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 107.43 0.0174 52305000 90520 94269 84000 99923 80831 75467 87440 91391 75181 FALSE TRUE 86241.29899 103875.1183 87851.48309 89878.5502 94927.90081 72853.55887 74099.42205 83388.31955 86839.68551 0.993109297 1.196171056 1.011651327 1.034993962 1.09313962 0.838943145 0.853289848 0.960255891 1 16.40606688 2.245344751 24.99985951 0.893583055 1.073116968 0.512613128 0.072690174 105.6067627 389166.7651 0.02462368 0.020171248 175.9319639 -2.245344751 0.179533913 DPLGGLADMFGQMPGS(ph)GIGTGPGVIQDRFSPTMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGS(0.404)GIGT(0.402)GPGVIQDRFS(0.158)PT(0.037)MGR 55.541 0.070239 64274000 78287 74032 84680 84138 74896 87332 81695 86967 84015 TRUE FALSE 74586.52866 81575.94497 88562.66176 75680.28839 87957.83869 84307.67094 69230.92732 79351.70844 97043.61711 0.768587681 0.840611133 0.912606768 0.779858487 0.906374281 0.868760599 0.713400112 0.817691166 1 16.5663457 4.506878034 2.833696943 0.839958856 0.769379587 0.078591902 0.079085473 0.796207188 11.69670469 0.018926199 0.100972244 32127.58147 -4.506878034 -0.070579269 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGS(0.001)GIGT(0.011)GPGVIQDRFS(0.833)PT(0.155)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR 293.34 2.69E-90 457019000 204601 177870 205360 213073 185749 209899 214330 213117 215150 TRUE FALSE 194929.9162 195995.1552 214775.9591 191654.4972 218143.5668 202630.145 181630.0221 194455.3457 248514.3632 0.784380885 0.788667314 0.864239621 0.771200887 0.877790579 0.815365931 0.730863278 0.782471255 1 17.92296971 -1.118966892 4.750855409 1.000013146 0.798420587 0.67479034 0.043166871 6083420.443 1432825.26 836.6161258 0.010077019 0.076038424 1.118966892 -0.201592558 DPNNYRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DPNNYRPR 8 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 109.71 0.0032514 116285000 52947 41321 53177 45669 53376 40287 54093 43050 55242 FALSE TRUE 50444.30024 45531.65688 55615.21805 41078.26535 62684.7575 38891.85109 45840.11936 39280.31378 63808.64722 0.790555864 0.713565619 0.871593749 0.643772704 0.982386561 0.609507532 0.718399799 0.615595464 1 15.96146433 DPPHNNFFFFDGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DPPHNNFFFFDGMK 14 0 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 190.11 6.41E-07 448620000 1189020 1039610 976700 1179360 864150 1075480 1226810 1136440 815410 FALSE TRUE 1132817.381 1145547.441 1021482.661 1060808.492 1014857.486 1038235.858 1039637.603 1036927.289 941859.6183 1.202745461 1.21626134 1.084538121 1.126291511 1.077503979 1.102325482 1.103813756 1.100936136 1 19.84515252 8 0.138584231 0.99292183 1.801406593 0.721093765 0.032496164 36.7826992 0.340346791 0.141222997 5.883837584 100000000 -8 0.808484764 DPQALSEHLKNPVIAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DPQALSEHLKNPVIAQK 17 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 233.49 2.48E-20 1819480000 2834700 2258800 2296600 2949100 1867050 2677800 2984100 2920400 1784360 FALSE TRUE 2700709.349 2488974.288 2401901.382 2652650.865 2192662.929 2585067.115 2528820.738 2664674.294 2061069.436 1.310343699 1.207613021 1.165366552 1.287026443 1.063847191 1.25423582 1.226945922 1.292860031 1 20.97496168 -2.297976636 2.168084743 1.16E-05 1.225922261 0.494544871 0.071813519 924975.4296 153252.2195 4541562.945 0.015985529 0.005035277 2.297976636 1.22591063 DPQFQK ddPTM_SK-BR-3_Trastuzumab_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 97.596 0.095131 153030000 291050 293910 259150 338090 213860 274090 320860 297140 237370 FALSE TRUE 277292.6433 323859.7631 271032.2838 304104.5509 251157.1163 264598.1946 271906.914 271120.8464 274180.1273 1.011352085 1.181193423 0.988519068 1.109141475 0.916029614 0.965052417 0.991709052 0.988842076 1 18.06476448 2.747546663 24.99412834 0.97287504 1.079190094 0.434994508 0.056532219 556.6703317 1548344.614 0.016381962 0.017145418 559.1736051 -2.747546663 0.106315054 DPS(ph)KIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;DPS(1)KIK 74.464 0.048604 4655920000 10180000 10535100 9831100 11083800 3639340 12131100 9168900 11986400 3720170 TRUE FALSE 9698811.575 11608638.67 10281865.66 9969635.366 4274039.744 11710996.97 7770015.907 10936807.27 4297074.964 2.257072929 2.701521096 2.392759202 2.320098078 0.994639326 2.725341555 1.808210462 2.545174884 1 22.03492351 2.981267646 24.82872196 1.907168736 2.461601775 0.214703443 0.562341239 1086.052388 1439505.687 0.152300121 0.164164647 957.7841512 -2.981267646 0.55443304 DPS(ph)VDITQDLVDESEEERFDDMSSPGLELPSCELSR ddPTM_SK-BR-3_Trastuzumab_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(0.517)VDIT(0.369)QDLVDES(0.113)EEERFDDMSSPGLELPSCELSR 82.058 0.0008842 26731000 24369 19158 14105 20701 20364 20838 24783 19309 21823 TRUE FALSE 23217.12566 21110.22198 14751.7282 18620.09615 23915.47515 20116.37483 21001.89818 17618.2016 25207.19938 0.921051375 0.837467965 0.585218849 0.738681671 0.948755742 0.798040851 0.83317063 0.698935305 1 14.62154822 DPSQQELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 189.72 8.81E-05 2970197000 1715412 1489477 1527630 1831238 1631875 1533950 1783124 1744435 1772957 FALSE TRUE 1634327.874 1641256.4 1597673.347 1647158.477 1916473.483 1480828.927 1511075.684 1591683.024 2047898.117 0.798051359 0.801434596 0.78015275 0.804316613 0.935824623 0.723096972 0.737866631 0.777227642 1 20.96571251 -2.192361303 2.344418285 1.586651839 0.792331279 0.5633825 0.056750724 3984906.847 830049.7964 12418944.57 0.014668765 0.006421533 2.192361303 -0.794320561 DPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.457)T(0.457)S(0.087)EGLEDAVHSR;DPTSLLGVLQAEADS(0.341)T(0.341)S(0.319)EGLEDAVHSR;DPTSLLGVLQAEADS(0.45)T(0.45)S(0.099)EGLEDAVHS(0.001)R 84.516 0.0057063 30581100 34490.9 34643.6 32245.6 41687.5 29828.4 39471.8 36948 33783 29918.4 TRUE FALSE 32860.58351 38173.82223 33724.09266 37496.9933 35030.46352 38104.88167 31310.904 30824.78143 34557.99267 0.950882299 1.104630775 0.975869547 1.085045467 1.013671826 1.102635851 0.906039431 0.891972567 1 15.0767318 1.681222151 8.191011048 0.925014302 1.03782587 0.424755183 0.057811338 0.100248304 11.93656133 0.025392319 0.013366596 47.99789054 -1.681222151 0.112811568 DPTVHDDVLELEMDELNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DPTVHDDVLELEMDELNR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 358.67 8.75E-91 398775000 453126 603400 429975 656430 421855 550556 513271 520555 345638 FALSE TRUE 431707.632 664887.146 449689.7791 590444.4093 495426.3784 531490.1077 434962.0821 474972.4446 399237.7758 1.081329619 1.665391369 1.126370815 1.478929212 1.240930615 1.33126207 1.089481278 1.189698153 1 18.60688871 1.604945187 0.920249034 1.028309783 1.354696117 0.271566224 0.172357486 0.614529026 1.00989947 0.142056561 0.056380291 40.26662096 -1.604945187 0.326386334 DPVQEAWAEDVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DPVQEAWAEDVDLR 14 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 214.23 1.62E-11 2697855000 1564315 2265289 1357058 2076090 1289694 1475845 1359497 1633929 1088281 FALSE TRUE 1490372.93 2496124.525 1419280.452 1867397.489 1514616.225 1424736.118 1152080.764 1490853.515 1257046.059 1.185615212 1.985706495 1.129060022 1.485544205 1.204901136 1.133400091 0.916498449 1.185997525 1 20.26160608 2.684764725 1.109755503 1.01776648 1.53718952 0.362623962 0.239345683 0.436150758 1.11371937 0.119025762 0.104271625 483.9101433 -2.684764725 0.51942304 DQADFSVLHYAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQADFSVLHYAGK 13 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 177.84 1.51E-05 448530000 1702560 1474450 1477900 1799560 1347610 1577040 1863510 1738970 1345200 FALSE TRUE 1622083.363 1624698.131 1545663.177 1618664.81 1582632.757 1522426.709 1579197.324 1586696.568 1553806.746 1.043941512 1.045624326 0.994758956 1.041741397 1.018551864 0.979804415 1.016340886 1.021167254 1 20.56737565 3.818962865 0.754173846 1.007299992 1.053219878 0.34060397 0.017823351 1.022045106 0.962299025 0.007732923 0.032456344 6591.175335 -3.818962865 0.045919886 DQDELNPYAAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQDELNPYAAWR 12 0 O43615;M0QXM9 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 ; 257.8 7.58E-21 153648000 286700 247390 244420 260890 208780 216570 252790 266070 221400 FALSE TRUE 273148.2592 272599.3223 255626.8988 234664.8415 245191.1659 209070.1266 214222.2427 242771.5003 255733.5812 1.068096954 1.065950435 0.999582837 0.917614497 0.958775788 0.817530985 0.837677405 0.949314123 1 17.96428209 3.332350461 1.370391786 0.887294739 1.073444599 0.550764998 0.056156163 0.244763628 0.95586668 0.01869068 0.030430955 2149.564399 -3.332350461 0.18614986 DQDEQEELDFLFDEEMEQMDGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQDEQEELDFLFDEEMEQMDGRK 23 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 0 69.72 0.038661 12642000 13038 8810.3 10902 11654 7512.2 12833 14019 14655 10296 FALSE TRUE 12421.71958 9708.079586 11401.86748 10482.51778 8822.325302 12388.58999 11880.14407 13371.73051 11892.6511 1.04448701 0.816309123 0.958732195 0.881428177 0.741829995 1.04170129 0.99894834 1.124369193 1 13.53778273 DQDGYYWITGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DQDGYYWITGR 11 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;;;;; 176.95 1.91E-05 846003000 858675 742379 811892 866453 829363 776850 924519 837472 883809 FALSE TRUE 818087.1345 818028.2641 849118.0513 779355.4983 974003.6446 749947.4897 783466.6466 764138.512 1020865.586 0.80136616 0.801308493 0.831762832 0.763426164 0.954095875 0.734619229 0.767453284 0.748520199 1 19.96136149 -2.301220187 2.358638839 2.029211601 0.79956004 0.509738485 0.061539094 3316718.212 405310.0621 18520560.54 0.013916607 0.004997811 2.301220187 -1.229651561 DQDLASCDRDRSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQDLASCDRDRSSR 14 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 DQDLASCDRDRS(0.15)S(0.849)R;DQDLASCDRDRS(0.157)S(0.842)R 93.152 0.0024394 531830000 298300 187366 260120 294050 235540 271500 322230 272680 284860 TRUE FALSE 284199.9502 206458.8084 272046.7593 264491.5353 276618.1014 262097.8869 273067.8953 248802.6936 329034.6339 0.86373871 0.627468318 0.826802808 0.803841019 0.840696002 0.796566257 0.829906238 0.756159589 1 18.32787992 -5 0.215876841 2.0506376 0.759437853 0.469908231 0.067215156 126.2985394 1.261642591 57.58874711 0.128842572 1.00E-05 5 -1.291199747 DQDS(ph)SDDERALEDWVSSETSALPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;DQDS(0.5)S(0.5)DDERALEDWVSSETSALPR 53.615 0.06873 28160000 41921 39758 31252 42270 29209 34115 36103 37484 25178 TRUE FALSE 39939.47741 43809.3854 32684.93511 38020.93929 34303.04035 32933.589 30594.82427 34201.70224 29082.47565 1.37331766 1.506384323 1.123870454 1.307348788 1.179508951 1.13242041 1.052002059 1.176024444 1 14.82786246 3.21863698 0.557796623 1.05418173 1.482740025 0.636301592 0.0917711 0.570390412 0.364078997 0.06438554 0.127796474 1654.38651 -3.21863698 0.428558295 DQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.5)S(0.5)DDERALEDWVSSETSALPRPR;DQDS(0.589)S(0.411)DDERALEDWVSSETSALPRPR;DQDS(0.573)S(0.427)DDERALEDWVSSETSALPRPR 155.58 2.30E-08 163696000 177485 148786 177968 182472 156731 171916 217165 184299 172922 TRUE FALSE 169095.6358 163947.4626 186128.0088 164129.5679 184064.8368 165962.5058 184032.4907 168160.8025 199737.8606 0.846587799 0.82081315 0.931861432 0.821724872 0.921532033 0.830901589 0.921370091 0.841907498 1 17.6077483 -4.999999998 0.170564163 1.520901516 0.834249273 0.472982482 0.043538867 101.8062552 0.961418519 17.95831694 0.135062034 1.00E-05 4.999999998 -0.686652243 DQDSS(ph)DDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.105)S(0.487)DDERALEDWVS(0.184)S(0.184)ET(0.02)S(0.02)ALPRPR;DQDS(0.416)S(0.584)DDERALEDWVSSETSALPRPR 145.29 1.19E-07 100620000 103987 77834 97748 99012 93802 93123 104389 102981 93690 TRUE FALSE 99071.74059 85765.37309 102229.8425 89059.12565 110161.0391 89898.12716 88462.54081 93963.4377 108218.9667 0.915474834 0.792517021 0.944657352 0.822953022 1.017945767 0.830705836 0.817440265 0.868271437 1 16.72359385 3.73547016 24.99067741 0.886018429 0.853995931 0.034475441 0.077063543 1088.634818 8803180.274 0.019201618 0.031224518 5438.387633 -3.73547016 -0.032022498 DQECDKFNQCGTCNEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQECDKFNQCGTCNEFK 17 1 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;; 312.21 3.42E-58 1772480000 2055820 1604490 1665240 1863540 1015300 1866060 2010910 2076650 1099720 FALSE TRUE 1958645.463 1767989.355 1741592.901 1676213.419 1192367.999 1801437.874 1704108.747 1894807.517 1270258.961 1.541926113 1.391833799 1.371053427 1.319584014 0.938681037 1.418165846 1.341544361 1.491670262 1 20.27669121 3.990327858 1.239554634 1.275364788 1.532406612 0.224814586 0.172110682 0.868922696 2.331878451 0.051105397 0.202432915 9779.752352 -3.990327858 0.257041824 DQEGQDVLLFIDNIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQEGQDVLLFIDNIFR 16 0 P06576;H0YH81;F8W0P7 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 288.77 1.25E-36 1313230000 780079 685408 616057 696731 727875 503798 759910 655833 741960 FALSE TRUE 743206.2116 755251.8544 644303.8228 626694.2762 854816.1695 486351.3489 643971.7728 598404.7857 857019.3674 0.867198852 0.881254127 0.751796106 0.731248674 0.997429232 0.567491666 0.751408658 0.698239513 1 19.70896828 2.240926019 24.9999996 0.729549093 0.84309024 0.098488615 0.12804769 108.6449487 1148284.127 0.041095939 0.032875728 174.1510188 -2.240926019 0.113541147 DQEKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQEKLR 6 1 A0A1B0GV03 A0A1B0GV03 0 95.62 0.039342 179370000 364800 303060 302330 383670 261050 322400 307180 352270 328540 FALSE TRUE 347556.627 333942.1586 316192.1295 345102.7627 306577.0373 311235.2072 260314.0493 321423.3713 379488.3053 0.915855962 0.879980105 0.833206518 0.909389717 0.807869526 0.820144397 0.685960662 0.846991506 1 18.5336959 2.685094873 7.123169799 0.801212264 0.884401601 0.021532462 0.081341328 0.408295523 46.84956545 0.024505387 0.02317414 484.2781476 -2.685094873 0.083189337 DQELYFFHELSPGSCFFLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQELYFFHELSPGSCFFLPK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 214.3 1.27E-24 457650000 947750 861720 889680 1030750 689510 881140 1031530 1084850 629000 FALSE TRUE 902951.7358 949530.2477 930472.708 927137.0517 809760.3257 850625.9009 874151.1532 989854.7828 726542.1075 1.242807163 1.306917022 1.280686554 1.276095414 1.114540117 1.170786789 1.203166539 1.362419016 1 19.47068689 2.819233799 10.99568752 1.184290302 1.278252447 0.248297678 0.090175236 1.056934525 140.8754131 0.025179932 0.026712883 659.528852 -2.819233799 0.093962145 DQFLDTLQAHGHDVNSFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQFLDTLQAHGHDVNSFVR 19 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 161.08 1.75E-11 149292000 145906 116575 126955 155804 139569 131974 152820 134769 18920.8 FALSE TRUE 139009.3125 128454.125 132776.0123 140142.2859 163909.7894 127403.7073 129504.5023 122967.9119 21854.94103 6.360543931 5.877578203 6.07533153 6.412384537 7.49989621 5.829515033 5.92563952 5.6265497 1 14.41567186 0.228705102 0.973591124 0.965685064 6.312176868 0.927512441 0.461691229 0.924271575 0.956752512 0.511627103 0.142084659 1.693187688 -0.228705102 5.346491804 DQGELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DQGELER 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 126.04 0.0092852 2062470000 2801700 2364810 2479900 2854080 2265530 2657160 2954060 2759350 2539570 FALSE TRUE 2669269.193 2605786.828 2593605.868 2567182.456 2660637.715 2565141.883 2503363.892 2517726.686 2933393.545 0.909959456 0.888318184 0.88416567 0.875157873 0.907016966 0.874462237 0.853401991 0.858298297 1 21.48413921 -1.167268735 5.325675238 1.000004339 0.881909843 0.810013484 0.018057201 1.03E-06 1.61E-07 0.019343523 0.004559145 0.068034824 1.167268735 -0.118094496 DQGFRGDGGSTTGLSAT(ph)PPASLPGSLTNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DQGFRGDGGSTTGLSATPPASLPGSLTNVK 30 1 P15056;H7C560;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DQGFRGDGGS(0.001)T(0.001)T(0.001)GLS(0.065)AT(0.924)PPAS(0.007)LPGSLTNVK;DQGFRGDGGSTTGLSAT(0.999)PPASLPGSLTNVK;DQGFRGDGGSTTGLS(0.007)AT(0.992)PPASLPGSLTNVK;DQGFRGDGGS(0.004)T(0.004)T(0.004)GLS(0.025)AT(0.961)PPAS(0.001)LPGSLTNVK 182.34 1.01E-17 486470000 564119 338809 546681 515907 472083 555810 768450 607113 620735 TRUE FALSE 537454.2128 373334.0223 571746.8646 464047.0482 554414.1257 536562.1603 651208.8389 553950.9672 716995.4135 0.749592261 0.520692344 0.797420533 0.647210623 0.773246405 0.748348107 0.908246868 0.772600433 1 19.45160436 1.672367533 0.447726329 0.993053108 0.634537992 0.55880087 0.086002791 0.60387283 0.315051394 0.086631258 0.063922159 47.02919372 -1.672367533 -0.358515116 DQGGELLSLR ddPTM_SK-BR-3_Trastuzumab_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 ; 140.78 9.00E-05 225970000 326490 307690 320780 324280 320600 318090 355020 337520 297160 FALSE TRUE 311057.4647 339043.9608 335488.0803 291682.7583 376512.5385 307074.4635 300855.1786 307964.9595 343242.0551 0.906233546 0.987769289 0.977409601 0.849787355 1.09693009 0.894629487 0.876510247 0.897223854 1 18.3888668 DQGGFGDRNEYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DQGGFGDRNEYGSR 14 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;; 271.19 5.44E-33 4914730000 2389410 1921340 2104530 2449390 2211010 2240980 2636500 2379220 2392140 FALSE TRUE 2276467.325 2117126.73 2201024.782 2203172.664 2596609.444 2163374.301 2234253.502 2170882.884 2763100.854 0.823881373 0.766214063 0.796577794 0.797355138 0.939744722 0.782951624 0.808603674 0.785669072 1 21.39785679 -1.413641343 2.991554339 1.003334726 0.810528099 0.602236406 0.047829854 13773847.76 17102146.73 393660.0123 0.011166743 0.038579683 1.413641343 -0.192806627 DQHDTFFLRDPAEALQLPMDYVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DQHDTFFLRDPAEALQLPMDYVQR 24 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;;;;; 139.62 1.86E-07 351370000 299036 254645 312191 331959 353835 301279 423211 304564 160004.1 FALSE TRUE 284901.1609 280593.615 326505.2661 298589.8506 415543.712 290845.6327 358642.3891 277894.7616 184816.7186 1.541533488 1.518226365 1.766643562 1.615599784 2.248409749 1.573697633 1.940530011 1.503623501 1 17.49573574 0.968545682 11.44269333 1.000000148 1.723499915 0.535486071 0.219551669 1.825748783 664.6085488 0.208081266 0.05203296 9.30134347 -0.968545682 0.723499768 DQHFDQNLNFMYIEVDKVTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQHFDQNLNFMYIEVDKVTER 21 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 74.662 0.0078904 43519000 27476 28361 25138 32145 22091 25980 29767 27889 19911.4 FALSE TRUE 26177.26393 31251.01814 26290.60216 28913.72353 25943.66341 25080.30609 25225.49744 25446.89131 22999.15822 1.138183567 1.35878965 1.143111496 1.257164425 1.12802665 1.090488002 1.0968009 1.106427073 1 14.48929344 2.570727371 2.670668439 1.083024835 1.233599906 0.517237576 0.068081569 0.21642824 3.030156864 0.023066568 0.02079866 372.1580105 -2.570727371 0.150575072 DQHFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQHFVK 6 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 108.24 0.030583 282530000 606550 682000 533180 778380 622870 632090 780710 624580 262740 FALSE TRUE 577879.5836 751496.5754 557626.8304 700135.7636 731498.3308 610200.5648 661598.3508 569888.4641 303484.3773 1.904149362 2.476228207 1.837415274 2.30699112 2.41033274 2.010649017 2.180007935 1.877818124 1 18.21126273 0.709672516 1.622939178 0.999800535 2.17885285 0.757934788 0.205653781 0.46280511 1.880420904 0.177244323 0.050767823 5.124748021 -0.709672516 1.179052315 DQHHLGS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQHHLGSPSR 10 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 1 DQHHLGS(0.836)PS(0.164)R 91.812 0.006373 96651000 75257 74685 66585 80316 77883 74759 85185 62628 14349 TRUE FALSE 71699.75076 82295.48641 69637.98811 72242.48309 91465.77054 72170.07708 72188.46372 57143.96031 16574.16964 4.325993539 4.965285635 4.201597404 4.358739212 5.518573331 4.354370606 4.355479961 3.44777214 1 14.01664897 0.793453762 1.409776527 1.001878536 4.646339381 0.898386956 0.383691511 0.198935489 0.709074567 0.339630039 0.100486776 6.215180727 -0.793453762 3.644460846 DQKLPHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQKLPHLER 9 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;; 104.52 0.0019506 434972000 1266120 913050 1077100 1080500 1056340 1140020 1525960 1247980 1085070 FALSE TRUE 1206273.017 1006090.833 1126486.1 971886.0872 1240565.362 1100540.822 1293146.776 1138700.255 1253337.114 0.962448972 0.802729626 0.89878939 0.775438688 0.989809803 0.878088432 1.031762932 0.908534697 1 20.25734308 2.713407125 24.99453543 0.96228487 0.863894223 0.36766628 0.066233244 806.7159545 801617.1717 0.019680008 0.018561218 516.9007061 -2.713407125 -0.098390647 DQLIYNLLK ddPTM_SK-BR-3_Trastuzumab_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 748750000 2551900 2516900 1664610 2195320 1659510 1998180 2354500 2222320 1540460 FALSE TRUE 2431276.744 2773374.971 1740934.015 1974642.263 1948928.019 1928982.526 1995277.782 2027721.88 1779346.669 1.36638733 1.558647912 0.978411934 1.109756911 1.095305402 1.084095954 1.121354156 1.139587869 1 20.76291619 3.739560232 24.99999997 1.085389547 1.462517633 0.8464485 0.068428691 27.12301471 678330.6008 0.016623777 0.027949825 5489.846883 -3.739560232 0.377128086 DQLIYNLLKEEQTPQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 213.99 1.54E-13 2999981000 2614426 1814682 2419626 2476459 1633476 2721658 3042536 2845885 1788520 FALSE TRUE 2490847.264 1999600.159 2530568.245 2227520.636 1918353.697 2627406.301 2578341.253 2596684.222 2065874.547 1.205710806 0.967919452 1.224938005 1.07824584 0.928591574 1.271813095 1.248062839 1.256941873 1 20.97832122 2.204384614 24.9998903 1.220465535 1.083389796 0.169537592 0.118159285 250.3649589 183141.541 0.040507224 0.029918057 160.0975235 -2.204384614 -0.137075739 DQLKEVWEETDGLDPNDFDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQLKEVWEETDGLDPNDFDPK 21 1 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 104.63 0.00037368 49554000 98318 73959 78396 85327 53537 92529 111150 97823 54936 FALSE TRUE 93670.70299 81495.50618 81990.53414 76749.76785 62873.83585 89324.69753 94192.02609 89257.09953 63455.19431 1.476170769 1.284300002 1.292101223 1.209511194 0.990838284 1.407681412 1.484386379 1.406616125 1 15.95345064 4.54219996 2.139664659 1.283973351 1.491429869 0.131401592 0.164277708 1.010314869 7.099658546 0.043078774 0.345311761 34849.77351 -4.54219996 0.207456517 DQMSHLFNVAHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQMSHLFNVAHTLR 14 0 F8VPD4;P27708;H7BZB3 F8VPD4;H7BZB3 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 128.06 4.39E-05 94085000 204110 133960 237850 179330 222010 232610 300850 243870 221800 FALSE TRUE 194462.1248 147610.6763 248755.6578 161303.4077 260728.4737 224554.6574 254949.807 222515.45 256195.6112 0.75903769 0.576163954 0.970959872 0.629610347 1.017692975 0.876496894 0.995137293 0.868537322 1 17.96688624 3.022397102 0.946402751 0.957306206 0.68225331 0.375318169 0.123285928 0.471109468 0.925892625 0.054940691 0.069755568 1052.924187 -3.022397102 -0.275052896 DQPAFTPSGILT(ph)PHALGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQPAFTPSGILTPHALGSR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 DQPAFTPSGILT(1)PHALGSR;DQPAFTPSGILT(1)PHALGSR 157.66 1.38E-08 130621000 147994 160987 154132 189244 162349 138505 165615 164104 167895 TRUE FALSE 140998.6169 177391.7583 161199.1047 170220.8336 190662.6142 133708.5371 140347.39 149734.1838 193931.2991 0.727054465 0.914714433 0.831217578 0.877737809 0.98314514 0.689463422 0.723696436 0.772099112 1 17.56518614 2.219042757 24.99986067 0.764982159 0.859491685 0.064199823 0.105252804 431.8069123 553085.6627 0.036484609 0.026984507 165.5932986 -2.219042757 0.094509526 DQPGRQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DQPGRQEK 8 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;;;; 134.23 0.00080768 3897486000 6798780 4402818 4898565 4628504 3554032 4338644 5522018 4880523 4634410 FALSE TRUE 6477415.143 4851470.16 5123169.051 4163237.984 4173854.056 4188395.67 4679532.735 4453158.533 5353090.634 1.21003278 0.906293297 0.957048816 0.777726041 0.779709208 0.782425697 0.874174016 0.83188551 1 22.35194065 4.669054334 0.977857174 0.836670429 1.383491704 0.695114954 0.073142729 0.841174364 0.693499323 0.02118703 0.474781309 46671.77666 -4.669054334 0.546821275 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 DQQNLPYGVT(0.001)PAS(0.969)PS(0.03)GHS(0.001)QGR 106.67 0.00023281 277200000 44458 34380 42688 44185 33748 40905 50324 42893 46005 TRUE FALSE 42356.55845 37883.36109 44645.28702 39743.43985 39633.64051 39488.44959 42646.14954 39137.06153 53139.22044 0.79708656 0.712907731 0.840156981 0.747911609 0.745845351 0.743113077 0.802536228 0.736500483 1 15.69748944 -1.798450288 2.789574751 1.064190559 0.765722069 0.792808344 0.037633154 9639860.838 6549373.129 4167131.44 0.008117153 0.015905587 1.798450288 -0.29846849 DQREEELGEYYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQREEELGEYYMK 13 1 O00267;O00267-2;M0QYL9 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 116.43 0.00053433 115667000 151333 121386 139173 149148 117142 129025 165187 163600 145106 FALSE TRUE 144179.789 133755.3714 145554.2197 134155.3597 137571.5277 124556.8319 139984.6893 149274.3167 167608.2974 0.860218684 0.798023567 0.868418939 0.800410014 0.820791869 0.743142397 0.835189495 0.890614123 1 17.35473405 0.957260642 2.395308383 0.999172598 0.81661162 0.743264194 0.034664033 0.154481504 1.994907891 0.031396087 0.008519461 9.062763398 -0.957260642 -0.182560978 DQRPS(ph)SPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.637)S(0.363)PIR;DQRPS(0.51)S(0.49)PIR;DQRPS(0.5)S(0.5)PIR 107.85 0.0016395 2484800000 239108 197975 194986 221728 239860 225325 240506 219374 223709 TRUE FALSE 227805.8387 218148.8776 203926.301 199439.4802 281691.5081 217521.9388 203812.3925 200164.4496 258400.6492 0.881599328 0.844227281 0.789186489 0.771822675 1.090134676 0.841801054 0.788745667 0.774628277 1 17.97925017 4.630548664 3.45049688 0.852940393 0.882216156 0 0.104875913 2.400415068 47.31494844 0.024311083 0.152786473 42711.87763 -4.630548664 0.029275763 DQRPS(ph)SPIRHQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DQRPSSPIRHQGR 13 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.5)S(0.5)PIRHQGR;DQRPS(0.5)S(0.5)PIRHQGR;DQRPS(0.5)S(0.5)PIRHQGR;DQRPS(0.5)S(0.5)PIRHQGR;DQRPS(0.5)S(0.5)PIRHQGR 85.493 0.0048317 422868000 6215.9 4156.6 6260.54 3228.6 7286.6 6512.28 11341.3 5634.5 20950.6 TRUE FALSE 5922.086726 4580.162266 6547.591952 2904.054994 8557.380733 6286.758111 9610.976388 5141.11331 24199.51205 0.244719262 0.18926672 0.270567106 0.120004692 0.353617904 0.259788631 0.397155793 0.212446982 1 14.56269034 -5 0.269706997 6.115473201 0.203195794 0.902932419 0.076791442 53.51188666 0.519694681 152.3201009 0.083636362 1.00E-05 5 -5.912277406 DQRPSS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.085)S(0.915)PIR 107.09 0.001714 367560000 77575 74266 60452 76473 73770 52565 81534 70379 80778 TRUE FALSE 73908.18349 81833.78983 63223.784 68785.78875 86635.46464 50744.66087 69094.49083 64216.24166 93304.63968 0.792116917 0.877060242 0.677606003 0.737217238 0.928522579 0.543859995 0.740525777 0.688242748 1 16.5096612 3.746875308 24.57595703 0.741567972 0.834588577 0.041508669 0.129696227 1122.410354 3317526.515 0.030143213 0.053170949 5583.09873 -3.746875308 0.093020606 DQS(ph)LSPS(ph)KGENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQSLSPSKGENK 12 1 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 2 DQS(0.744)LS(0.358)PS(0.899)KGENK 116.11 0.0036167 0 334980 283540 298470 350800 140250 347950 334000 326530 139480 TRUE FALSE 319146.1593 312433.0484 312155.1447 315536.9175 164709.5556 335900.4043 283042.1657 297937.3022 161109.846 1.98092275 1.939254838 1.937529905 1.958520384 1.0223432 2.084915432 1.756827237 1.849280534 1 17.29768514 -2.260821448 0.251666877 5.16E-15 1.93839018 0.43303666 0.294466804 35.30876688 1.18660886 21.08705946 0.422382246 0.005485024 2.260821448 1.93839018 DQS(ph)PFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(1)PFSK;DQS(0.997)PFS(0.003)K 196.07 0.00047549 11126374000 23237160 21393050 18788200 24965380 12054980 22836570 22415760 22794970 11952410 TRUE FALSE 22138785.5 23573026.12 19649657.55 22455812.57 14157364.7 22045733.85 18995824.12 20798921.58 13805928.7 1.603570899 1.707456748 1.423276766 1.62653401 1.025455441 1.596830922 1.375917878 1.506521005 1 23.7187846 -2.365431927 0.08388534 4.41E-11 2.037851017 0.435520877 0.182485451 104.736137 1.117608666 26.88571055 6.12478643 0.004310901 2.365431927 2.037851017 DQS(ph)TPIIEVEGPLLSDTHVTFK ddPTM_SK-BR-3_Trastuzumab_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 180.71 3.37E-17 119770000 174600 134820 144530 179460 129790 141370 187430 179260 154320 TRUE FALSE 166347.004 148558.3113 151156.8435 161420.3398 152425.3349 136474.3215 158834.1111 163563.0441 178251.1574 0.933216964 0.8334213 0.847999226 0.905578074 0.855115541 0.76562937 0.891069171 0.917598777 1 17.44355192 0.98579474 2.237780978 0.998580281 0.86033654 0.506222152 0.044576855 0.259772537 2.86068803 0.041404856 0.011381051 9.678203276 -0.98579474 -0.138243741 DQSSWQNSDASQEVGGHQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQSSWQNSDASQEVGGHQER 20 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 244.49 6.74E-30 615520000 389809 361014 388700 409818 423226 354181 469828 358685 430857 FALSE TRUE 371383.5011 397801.737 406522.2795 368622.316 497036.4804 341915.6232 398147.1096 327276.6399 497672.103 0.746241348 0.799324966 0.816847633 0.740693147 0.998722808 0.687029916 0.800018943 0.657615 1 18.92483599 4.506584207 2.02725446 0.803271768 0.742138907 0.027091154 0.113409113 2.08229244 13.24974319 0.026080964 0.19832905 32105.85253 -4.506584207 -0.06113286 DQST(ph)PIIEVEGPLLSDTHVTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.224)T(0.776)PIIEVEGPLLSDTHVTFK;DQS(0.179)T(0.821)PIIEVEGPLLSDTHVTFK;DQS(0.14)T(0.86)PIIEVEGPLLSDTHVTFK 185.02 1.36E-16 242119000 364162 267897 306489 340626 275487 323587 410010 363549 280060 TRUE FALSE 346948.784 295196.0089 320541.8238 306385.6273 323531.8456 312381.1011 347455.4441 331714.7223 323490.2745 1.072516893 0.912534417 0.990885505 0.947124694 1.000128508 0.965658401 1.074083123 1.025424096 1 18.30336281 1.750983484 25 1.039249014 0.980281499 0.226327147 0.044549127 4.606692612 9285.517021 0.019445608 0.010783567 56.36162213 -1.750983484 -0.058967516 DQTAS(ph)APATPLVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQTASAPATPLVNK 14 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 DQTAS(0.991)APAT(0.009)PLVNK;DQTAS(1)APATPLVNK 218.28 5.71E-12 190238000 525060 465440 473470 537750 384010 480390 593460 569930 449790 TRUE FALSE 500241.4544 512868.8652 495179.0678 483694.3483 450981.2224 463753.9738 502916.7774 520023.9078 519541.136 0.962852448 0.987157377 0.95310849 0.931002985 0.868037565 0.892622242 0.968001843 1.000929227 1 18.98687846 1.454487445 4.916596496 0.997452213 0.938786917 0.401579162 0.033938985 0.249422361 12.12355408 0.025968654 0.010120078 28.47655473 -1.454487445 -0.058665296 DQTDFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DQTDFEHR 8 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ;;; 131.62 0.00099742 696260000 969630 1043030 816290 1113880 844750 917550 963190 967950 818300 FALSE TRUE 923797.5115 1149315.943 853717.7039 1001910.666 992074.1325 885775.0134 816237.6753 883191.1666 945197.7847 0.977358947 1.215952853 0.903215938 1.060001073 1.049594221 0.937131919 0.863562832 0.934398261 1 19.85025672 2.204558373 4.421714286 0.913936255 1.054517776 0.265925717 0.08523061 0.21311707 9.353744057 0.031474291 0.023522997 160.1615905 -2.204558373 0.140581522 DQTDFEHRIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQTDFEHRIPK 11 1 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 237.49 8.37E-16 264060000 417840 212200 354570 355080 320840 386270 512220 405590 357710 FALSE TRUE 398089.5313 233823.4213 370827.3852 319386.6838 376794.3944 372893.373 434071.4314 370074.3894 413181.8399 0.963472962 0.565909241 0.897491974 0.772993034 0.91193358 0.902492165 1.050557865 0.895669542 1 18.65641732 2.504773143 1.395884114 0.984272959 0.777545153 0.321724593 0.110649531 0.416814086 1.644367118 0.052219169 0.039899018 319.7224583 -2.504773143 -0.206727806 DQTVGNSHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DQTVGNSHAK 10 0 Q8N392 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 0 67.726 0.069532 0 314380 264210 234280 309280 282940 259550 343610 330470 305960 FALSE TRUE 299519.8804 291133.2994 245021.9697 278190.5868 332284.6464 250561.7184 291185.9837 301532.2949 353406.7142 0.84752176 0.823791082 0.693314416 0.787168369 0.940232975 0.708989695 0.823940157 0.85321609 1 18.43096992 0.813612595 2.274253125 0.999765601 0.804972866 0.446085341 0.068897108 0.655700623 5.906237072 0.062057785 0.016848992 6.510473788 -0.813612595 -0.194792735 DQVANSAFVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DQVANSAFVER 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 236.77 3.41E-15 8828100000 2712259 2330238 2497621 2834893 2659131 2497512 2946277 2618154 2956412 FALSE TRUE 2584055.892 2567691.901 2612139.393 2549924.17 3122882.604 2411022.533 2496768.332 2388894.556 3414877.274 0.756705347 0.751913377 0.764929215 0.74671034 0.914493364 0.7060349 0.731144381 0.699555025 1 21.7034023 -0.977794478 4.642268079 1.000003217 0.758240414 0.620883607 0.059197072 2.52E-06 5.54E-07 0.054199368 0.012774684 0.105245981 0.977794478 -0.241762804 DQVLHEHIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 96.103 0.00403 90114000 73054 57115 70788 82025 64812 70801 83458 64718 26139 FALSE TRUE 69600.8822 62935.08343 74033.69982 73779.69116 76115.19228 68349.14362 70724.94929 59050.94883 30192.50262 2.305237266 2.084460643 2.452055755 2.443642784 2.520996462 2.263778676 2.342467273 1.955814977 1 14.88190272 0.826056173 2.260294645 1.000398403 2.328961414 0.924259233 0.12148306 0.179893784 1.653374082 0.126620107 0.034425555 6.699712602 -0.826056173 1.328563011 DQVNLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 113.42 0.0029919 496740000 1633990 1487850 1497040 1745650 1023740 1721640 1909540 1906750 1177220 TRUE FALSE 1556754.531 1639463.607 1565680.765 1570173.945 1202279.932 1662019.175 1618204.602 1739784.862 1359777.265 1.144859949 1.205685408 1.151424432 1.154728782 0.884174168 1.222273101 1.190051226 1.27946312 1 20.37493892 -0.478266508 7.073530986 1 1.155656161 0.178111611 0.103971002 0 0 0.096295252 0.022697009 0.332455477 0.478266508 0.155656161 DQVTYQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQVTYQQLR 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 174.92 0.00012635 297890000 221360 166174 104103 138313 211080 144992 252250 175450 217720 FALSE TRUE 210896.7515 183107.3195 108876.2255 124409.5145 247892.2852 139970.8907 213764.6296 160086.6679 251482.9056 0.838612672 0.728110402 0.432936884 0.494703662 0.985722209 0.556582128 0.850016541 0.636570774 1 17.94010081 1.653884285 11.92064362 0.806916661 0.688157768 0.132051268 0.182845071 0.308812649 64.51239391 0.083751746 0.045585753 45.06966033 -1.653884285 -0.118758892 DQWEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DQWEDR 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 211.23 0.00011265 10301800000 12450400 10827500 10528000 12667600 10422200 10592400 12147800 11279300 10466900 FALSE TRUE 11861894.27 11930834.56 11010719.21 11394228.78 12239828.38 10225582.53 10294430 10291624.7 12090053.39 0.981128361 0.986830593 0.910725441 0.942446523 1.012388282 0.845784729 0.851479283 0.851247249 1 23.52731728 2.231267555 24.99911789 0.871223159 0.967112641 0.348229271 0.052113675 144.416427 495025.5827 0.017658158 0.013305263 170.3207476 -2.231267555 0.095889482 DQYSVIFESGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 238.92 8.72E-16 492340000 410710 472690 397990 469130 305220 421960 416480 431530 325530 FALSE TRUE 391296.5522 520857.6484 416238.2352 421972.1611 358450.2714 407347.4194 352938.3268 393742.9455 376011.5298 1.040650409 1.385217226 1.106982638 1.122231973 0.953295958 1.083337576 0.93863698 1.047156574 1 18.52041738 3.11908462 2.03965609 1.002921048 1.210394196 0.406709103 0.096254055 0.262125558 2.230249084 0.029523115 0.037477564 1315.481122 -3.11908462 0.207473149 DRAEAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 200.6 0.00010806 4198956700 3970650 3272837 3422758 3969895 3747966 3590809 4508208 3705575 4093556 FALSE TRUE 3782965.244 3606342.811 3579694.84 3570833.612 4401610.084 3466458.384 3820398.071 3381095.209 4728363.757 0.800057998 0.762704182 0.757068412 0.755194354 0.93089498 0.733120073 0.807974654 0.715066645 1 22.1729096 -1.181003277 4.6543197 1.000033254 0.78436797 0.568933917 0.059412235 1.84E-05 3.23E-06 0.051528544 0.012143523 0.065916892 1.181003277 -0.215665284 DRAS(ph)PAAAEEVVPEWASCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DRASPAAAEEVVPEWASCLK 20 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK 209.18 3.00E-22 2159410000 3418770 2903820 2926420 3347920 2419960 3209250 3708610 3639690 2900980 TRUE FALSE 3257171.517 3199722.559 3060599.252 3011380.721 2842000.258 3098112.868 3142793.431 3320979.448 3350849.162 0.97204361 0.954899013 0.913380192 0.898691817 0.848143297 0.924575449 0.93790955 0.991085927 1 21.67609531 1.268953714 2.854301378 1.000710442 0.923620409 0.473023227 0.032923312 0.283610318 3.858377067 0.033709973 0.009814487 18.57606464 -1.268953714 -0.077090033 DRCTLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRCTLAEK 8 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 91.658 0.011246 44925000 128380 104050 109890 105080 86757 114420 141500 129530 114480 FALSE TRUE 122311.7318 114652.8133 114928.5652 94517.15876 101887.3933 110457.6067 119911.5762 118187.6665 132232.9737 0.924971498 0.867051614 0.869136963 0.714777533 0.770514271 0.835325741 0.906820537 0.893783624 1 17.01272245 1.051527847 1.260978013 0.994643248 0.839037695 0.440427958 0.059423728 0.503904916 1.649238102 0.061604451 0.019089806 11.25972664 -1.051527847 -0.155605553 DRDAS(ph)PSKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.743)PS(0.257)KEER;DRDAS(0.899)PS(0.101)KEER;DRDAS(0.901)PS(0.099)KEER;DRDAS(0.751)PS(0.249)KEER;DRDAS(0.925)PS(0.075)KEER;DRDAS(0.999)PS(0.001)KEER;DRDAS(0.959)PS(0.041)KEER 174.48 8.63E-06 4333411000 5080926 4368444 4390853 5071524 2903149 5218422 5393658 5365106 3116451 TRUE FALSE 4840760.697 4813593.41 4592177.953 4561724.772 3409457.266 5037706.738 4570756.411 4895308.876 3599734.304 1.344754998 1.337207972 1.275699139 1.267239298 0.947141366 1.399466269 1.269748271 1.359908388 1 21.77945899 -2.277102169 1.996888776 3.16E-05 1.279674491 0.325381303 0.12435631 1820953.45 260334.4468 8208908.871 0.029060363 0.005283209 2.277102169 1.279642897 DRDASPS(ph)KEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.329)PS(0.671)KEER 94.532 0.006642 149950000 193370 165630 161250 193760 110730 184630 190750 195440 125880 TRUE FALSE 184229.7833 182507.8853 168643.472 174282.8767 130041.2769 178236.2168 161647.5841 178326.2375 145400.8275 1.267047695 1.255205273 1.159852216 1.198637447 0.894364077 1.225826702 1.111737718 1.226445823 1 17.14967595 3.523270097 1.785431312 1.11132694 1.265137892 0.279830745 0.101254262 0.425260538 2.704363502 0.028470703 0.05041909 3336.338426 -3.523270097 0.153810952 DRDDRDFDFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDDRDFDFCR 11 2 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 160.56 1.54E-05 109740000 41022 29747 30253 34611 31512 30491 40844 39823 33571 FALSE TRUE 39082.97136 32778.25312 31640.12997 31131.83652 37007.68282 29435.08902 34612.49765 36335.887 38777.01922 1.007890037 0.845301 0.815950545 0.802842435 0.954371521 0.759085913 0.89260336 0.937046935 1 15.24291429 1.060651815 2.710812899 0.99785348 0.86938394 0.27531827 0.072108375 0.339476365 5.208482645 0.067084305 0.0180575 11.49878133 -1.060651815 -0.128469541 DRDGYSYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 176.32 2.31E-06 1001990000 564637 463916 547678 593307 562440 504929 668191 578802 640659 FALSE TRUE 537947.728 511189.5678 572789.578 533666.6532 660529.3579 487443.1821 566246.1908 528119.0285 740009.1257 0.726947424 0.690788194 0.774030425 0.72116226 0.892596233 0.65869888 0.765188119 0.713665562 1 19.49718354 -1.697726045 2.747978689 1.038354786 0.740119395 0.62432151 0.062648165 18191085.64 16241265.77 4850935.858 0.013576889 0.020057369 1.697726045 -0.29823539 DRDLEVDTTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDLEVDTTLK 11 1 P02452 P02452 COL1A1 Collagen alpha-1(I) chain 0 166.62 1.84E-05 103260000 324130 261380 329550 275100 232780 386430 352260 371320 252200 FALSE TRUE 308809.0173 288014.9192 344660.1935 247446.4253 273376.7583 373047.8322 298516.2673 338805.2523 291309.8879 1.060070496 0.988689128 1.183139357 0.849426798 0.938439681 1.280587607 1.024737847 1.163040687 1 18.15219515 DRDNQDREENDKDPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDNQDREENDKDPER 16 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 83.418 0.0034323 367040000 173900 177210 161410 200730 85223 167430 150850 161210 90454 FALSE TRUE 165680.0916 195267.9005 168810.8082 180552.239 100085.8642 161631.8571 127835.0619 147093.5978 104481.1443 1.585741549 1.868929573 1.615705965 1.728084433 0.957932313 1.546995471 1.223522797 1.407848265 1 16.67288308 2.766090116 24.65697153 1.266010928 1.710520208 0.606500221 0.187531083 394.2109885 353076.8155 0.050794893 0.053863668 583.5661812 -2.766090116 0.44450928 DRDPEAQFEMPYVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 95.347 0.0037577 32220000 20352 18155 16285 18986 15946 17306 19968 16272 18836 FALSE TRUE 19390.00129 20005.01514 17031.68336 17077.49121 18726.97735 16706.68888 16921.51486 14847.13742 21756.99068 0.891207869 0.919475282 0.782814297 0.784919728 0.860733804 0.767876823 0.777750706 0.682407675 1 14.4091914 3.738446434 24.99987711 0.796590561 0.90534158 0.18584759 0.081943358 12.18831177 2668726.073 0.018977175 0.031552062 5475.785578 -3.738446434 0.108751019 DRDS(ph)QRDLVEAVAHILGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRDSQRDLVEAVAHILGIR 19 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 1 DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR 253.98 3.58E-31 1096715000 305749 173303 300316 270806 330858 283472 414249 323086 322439 TRUE FALSE 291296.8507 190962.7727 314085.7857 243584.0664 388559.5304 273655.2936 351047.7068 294794.8771 372441.1933 0.782128443 0.512732684 0.843316452 0.654020207 1.043277536 0.73476108 0.942558753 0.791520601 1 18.50665312 2.763177374 24.92002569 0.888605145 0.6845758 0.398587085 0.123610316 696.0631188 704637.1582 0.034201244 0.036260346 579.6653947 -2.763177374 -0.204029345 DRDVTFSPATIENELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRDVTFSPATIENELIK 17 1 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ;;; 221.91 3.22E-15 139014000 293516 216802 223623 252897 176605 249386 283165 272018 203803 FALSE TRUE 279642.0804 238894.3703 233876.3357 227475.3131 207404.8561 240749.7003 239962.9786 248198.6619 235407.7284 1.187905267 1.014811077 0.993494722 0.966303505 0.88104523 1.022692424 1.01935047 1.054335232 1 17.84480216 4.492809652 1.704695716 0.989893773 1.210241503 0.64442907 0.045552366 0.358871342 1.482419911 0.012582681 0.111110376 31103.52794 -4.492809652 0.22034773 DRDYDKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDYDKER 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 96.89 0.0048485 157460000 250060 162550 184360 192290 174340 196020 259390 219580 190550 FALSE TRUE 238240.1594 179114.0298 192813.0884 172960.6439 204744.8408 189231.7782 219815.2915 200352.4111 220099.5208 1.082420164 0.813786551 0.876026843 0.785829261 0.930237558 0.859755521 0.998708633 0.910280997 1 17.74779648 1.737686366 16.05378689 0.965613127 0.893941467 0.164649985 0.082854843 0.124730812 488.2077771 0.038318015 0.021171078 54.66210677 -1.737686366 -0.07167166 DRDYSDHPSGGSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 178.85 1.16E-06 5174094000 3908520 2374661 3217570 3725080 5043090 2929930 5125650 4055260 5277616 FALSE TRUE 3723772.006 2616641.656 3365098.767 3350627.881 5922603.299 2828465.789 4343637.953 3700159.936 6096041.735 0.610850806 0.429236178 0.552013735 0.549639918 0.971549008 0.463983994 0.712534156 0.606977461 1 22.53944135 -4.999999999 0.135972839 2.365663035 0.447862261 0.42358346 0.146685994 126.1090081 1.063274736 46.66475414 0.903397051 1.00E-05 4.999999999 -1.917800773 DRDYSDHPSGGSYRDS(ph)YESYGNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRDYSDHPSGGSYRDSYESYGNSR 24 2 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" 1 DRDYSDHPS(0.081)GGS(0.081)YRDS(0.837)YESYGNSR 96.068 0.0034677 277260000 42301 35609 57279 53687 83446 28025 69454 43001 103650 TRUE FALSE 40301.51556 39237.59758 59905.29881 48290.28076 97998.95598 27054.48722 58857.51669 39235.60448 119723.5126 0.33662156 0.327735102 0.500363692 0.403348346 0.818543942 0.22597472 0.49161201 0.327718454 1 16.86934699 -1.440712603 3.001892463 1.01205384 0.423401387 0.555266757 0.160530698 40854678.28 48588672.7 4165807.047 0.035566788 0.036248279 1.440712603 -0.588652453 DREDYVPYTGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DREDYVPYTGEK 12 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;; 175.01 2.63E-05 933750000 1194680 1096080 1004510 1386240 742321 1125560 1193240 1311720 778340 FALSE TRUE 1138209.844 1207771.798 1050567.777 1246892.522 871781.5474 1086581.575 1011189.323 1196858.843 899040.992 1.266026637 1.343400144 1.168542688 1.386913981 0.96967942 1.208600703 1.124742177 1.331261704 1 19.77802737 2.757397818 24.99809451 1.140422675 1.29030259 0.334216444 0.114384041 956.421737 1269227.153 0.031232821 0.033076863 572.0023571 -2.757397818 0.149879915 DREEALHQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 229.82 8.68E-10 3873700000 3258572 2782650 2651085 3009172 2883786 2938858 3644904 3133869 2709681 FALSE TRUE 3104545.759 3066205.199 2772639.87 2706684.314 3386717.365 2837084.611 3088806.952 2859450.817 3129884.49 0.99190426 0.979654428 0.885860126 0.864787286 1.08205826 0.90645026 0.986875701 0.913596277 1 21.57767798 DREEDEEDAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 258.02 2.92E-21 1335530000 1004790 869470 877580 1043640 824920 926630 1017120 953550 799440 FALSE TRUE 957295.568 958069.9815 917817.911 938731.3244 968785.7868 894540.5708 861939.6633 870052.1069 923413.0722 1.036692675 1.037531318 0.993940782 1.016588732 1.049135881 0.968732843 0.93342805 0.942213331 1 19.81661663 2.114742699 5.258732393 0.951214564 1.026979077 0.666898722 0.02290688 0.106343296 4.484736696 0.008336001 0.006082029 130.2394937 -2.114742699 0.075764514 DREEDEEDAYERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DREEDEEDAYERR 13 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 200.97 5.94E-08 947650000 444740 340800 393210 389790 368760 452390 486270 421330 335800 FALSE TRUE 423718.0216 375527.9075 411239.0674 350607.5686 433071.6272 436723.6209 412080.5805 384436.1116 387874.149 1.092411089 0.968169465 1.060238401 0.903920949 1.116526142 1.125941551 1.062407953 0.991136204 1 18.5652291 DREGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVRSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 DREGPTDHLESACPLNLPLQNNHT(0.082)AADMY(0.073)LS(0.422)PVRS(0.422)PK 87.712 0.00046066 31037000 41837 42801 39510 48538 33346 41120 49535 50637 33966 TRUE FALSE 39859.44792 47162.47056 41321.57258 43658.86802 39161.53184 39696.00409 41977.52598 46202.95584 39233.27381 1.015960282 1.202103877 1.053227747 1.112802063 0.9981714 1.011794333 1.06994706 1.17764722 1 15.25979011 2.794603747 24.99777408 1.053624183 1.102430125 0.088755342 0.069353202 675.5183489 301310.6513 0.020407086 0.021644966 623.1659956 -2.794603747 0.048805942 DRELALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 103.83 0.007558 91646000 82440 56386 56901 67075 70594 58615 83547 69716 73144 FALSE TRUE 78543.22458 62131.79751 59509.96713 60332.49357 82905.57125 56585.14785 70800.3707 63611.29745 84486.79795 0.929650862 0.735402442 0.704370015 0.714105577 0.981284334 0.66975136 0.838005137 0.752914053 1 16.3664383 -2.132962446 2.019735597 1.384495577 0.792815541 0.301040371 0.100187361 5822370.252 1347272.108 10252831.7 0.023170831 0.007362708 2.132962446 -0.591680037 DRELDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRELDLR 7 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ;; 111.17 0.0060554 1030450000 2453140 2697400 2596630 3611470 2456580 2667460 3040020 2321170 2101220 FALSE TRUE 2337184.934 2972268.127 2715688.054 3248438.174 2885006.774 2575085.191 2576209.115 2117916.05 2427066.466 0.962967008 1.224634005 1.118917876 1.338421596 1.18868058 1.06098668 1.061449759 0.872623836 1 21.21078219 1.645485974 1.882950146 0.943867838 1.157501282 0.424996453 0.102211924 0.315730251 2.329401262 0.078087716 0.029214133 44.20648396 -1.645485974 0.213633444 DRELWVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DRELWVQR 8 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;;; 136.57 0.00071634 1210278000 1601110 1531730 1301440 1595910 1495970 1545960 1927760 1755610 1648170 FALSE TRUE 1525428.703 1687815.028 1361112.311 1435486.095 1756866.694 1492423.018 1633644.806 1601879.481 1903759.786 0.801271628 0.886569325 0.714960113 0.754026903 0.922840532 0.783934522 0.858114988 0.841429414 1 20.86042002 -0.120308943 0.533478353 1.018304886 0.813222808 0.484758013 0.059879106 4.587025519 1.436933376 0.230717825 0.026390547 0.75803814 0.120308943 -0.205082078 DRENQEEFLRAPS(ph)PMEIDPADKYVYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRENQEEFLRAPSPMEIDPADKYVYPR 27 3 Q8NEV8-2;Q8NEV8;E9PPH6;F5GXG5;A0A087WZJ0 Q8NEV8-2 EXPH5 Exophilin-5 1 DRENQEEFLRAPS(1)PMEIDPADKYVYPR 98.636 0.02046 53643000 62934 44988 60382 57020 47771 53629 68758 64106 49907 TRUE FALSE 59959.23454 49572.32835 63150.57443 51288.24127 56102.24728 51771.81428 58267.70427 58492.53879 57646.32267 1.040122453 0.859939126 1.095483138 0.889705343 0.973214677 0.898093961 1.010779206 1.014679447 1 15.81494096 1.606929099 25 1.009554249 0.957034559 0.098141961 0.069830962 0.214155142 5292.186029 0.031467911 0.01586875 40.45098477 -1.606929099 -0.05251969 DRENYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DRENYDR 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;; 166.3 0.0010294 1988047000 1974029 1862708 1785401 2062499 1741725 1944947 2118409 2008125 1910126 FALSE TRUE 1880720.561 2052520.063 1867263.402 1855172.682 2045481.289 1877592.998 1795206.8 1832282.929 2206338.585 0.85241702 0.930283356 0.846317703 0.84083771 0.927093105 0.850999484 0.813658798 0.830463167 1 21.07322277 3.700968074 24.97747101 0.861795652 0.89135026 0 0.058204644 1699.357558 1129096.89 0.014291858 0.022141243 5023.056627 -3.700968074 0.029554607 DREPYFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DREPYFDR 8 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 72.006 0.043113 131160000 55370 53670 53890 55583 91373 38709 64756 47624 88371 FALSE TRUE 52752.76983 59139.03402 56360.9098 49995.69124 107308.4223 37368.49762 54876.28287 43453.79009 102075.1233 0.516803391 0.579367745 0.552151278 0.489793101 1.051269092 0.366088195 0.537606824 0.425704017 1 16.63927179 -1.580795483 2.737860697 1.031000662 0.564289547 0.355962348 0.183947495 22969181.41 22516998.73 5163603.137 0.044171765 0.026254546 1.580795483 -0.466711115 DREREPEAAS(ph)SRGSPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DREREPEAASSRGSPVR 17 3 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 DREREPEAAS(0.963)S(0.032)RGS(0.005)PVR;DREREPEAAS(0.961)S(0.03)RGS(0.009)PVR;DREREPEAAS(0.748)S(0.045)RGS(0.206)PVR 156.22 3.94E-07 1950250000 497540 247019 537850 403931 591060 489180 755850 551720 807070 TRUE FALSE 474022.2702 272190.5169 562510.9545 363327.0885 694140.6769 472239.5739 640531.2004 503408.4719 932226.2937 0.508484124 0.291979017 0.603406017 0.389741301 0.744605341 0.506571824 0.687098406 0.540006729 1 19.83032068 -5 0.107548535 2.60290068 0.22344634 0.624362551 0.120253676 94.78193004 0.681735191 33.26417154 1.421419432 1.00E-05 5 -2.37945434 DREREPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DREREPEAASSRGSPVR 17 3 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 DREREPEAAS(0.156)S(0.004)RGS(0.84)PVR 156.05 4.28E-07 257220000 103990 54088 123170 76402 120920 100840 142900 105710 178000 TRUE FALSE 99074.59879 59599.62869 128817.4663 68721.92581 142008.4097 97347.88551 121097.9805 96453.472 205603.3309 0.481872538 0.289876766 0.626533947 0.334245197 0.690691192 0.473474263 0.588988417 0.469124073 1 17.64950411 -4.999999999 0.179527718 3.112955922 0.37582067 0.637420934 0.12058314 74.77174625 0.719196355 56.25899768 0.332137267 1.00E-05 4.999999999 -2.737135251 DRESEKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRESEKDR 8 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 140.75 0.00036249 131344000 221654 191287 185126 211019 125513 209088 240396 240031 159030 FALSE TRUE 211176.8547 210779.3628 193614.2102 189806.9692 147402.4275 201847.2301 203719.175 219012.6132 183691.5602 1.149627422 1.147463512 1.054017996 1.033291726 0.802445291 1.098837801 1.109028498 1.192284572 1 17.48692582 3.715823348 4.405383103 1.042522883 1.149625248 0.166994269 0.099763691 0.35657895 17.34926418 0.027418794 0.045959764 5197.845274 -3.715823348 0.107102366 DREVGIPPEQSLETAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DREVGIPPEQSLETAK 16 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 165.8 6.29E-09 104230000 156060 154070 145890 180680 111370 167680 182520 196190 136250 FALSE TRUE 148683.3531 169769.9082 152579.2008 162517.7031 130792.8927 161873.1996 154673.2218 179010.5635 157378.9541 0.94474737 1.078733234 0.969501937 1.032652072 0.83106978 1.028556839 0.982807534 1.137449188 1 17.2638831 1.275790134 24.99265915 1.068724714 0.986880304 0.195694077 0.073094912 233.7516652 156920.4147 0.044896033 0.016393714 18.87079229 -1.275790134 -0.08184441 DRFGIDDQDYLVSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRFGIDDQDYLVSLTR 16 1 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 225.17 6.50E-15 236160000 211650 206447 181993 207450 205390 206548 242440 226790 204820 FALSE TRUE 201645.7239 227484.184 190337.5591 186596.7319 241209.951 199395.191 205451.3253 206931.0653 236582.4395 0.85232752 0.96154298 0.804529531 0.788717591 1.019559826 0.84281484 0.86841325 0.874667899 1 17.85198347 -1.368932341 3.686578352 1.000563589 0.879862962 0.240642655 0.0686847 0.000298564 5.11E-05 0.062088705 0.014566102 0.04276295 1.368932341 -0.120700627 DRGDAYYDT(ph)DYRHSYEYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.973)DYRHS(0.027)YEYQR 139.79 8.65E-06 173140000 112820 130310 102000 123720 103420 117070 108370 118560 77067 TRUE FALSE 107487.2222 143588.7372 106676.8009 111283.4305 121456.4153 113015.8365 91836.16615 108178.2579 89018.15676 1.207475262 1.613027526 1.198371262 1.250120589 1.364400474 1.269581855 1.031656569 1.215238125 1 16.44181201 1.882263017 0.652723777 1.018638116 1.380735637 0.395442804 0.132155684 0.633527311 0.537845964 0.117871442 0.0656563 76.25406787 -1.882263017 0.362097521 DRGDAYYDTDYRHS(ph)YEYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.026)DYRHS(0.974)YEYQR;DRGDAYYDT(0.255)DYRHS(0.744)Y(0.002)EYQR 137.16 2.31E-06 243108000 167209 177801 152080 190332 134091 176180 169393 203615 116369 TRUE FALSE 159305.3619 195919.124 159053.0184 171199.4658 157476.4279 170078.8424 143548.9867 185785.3912 134414.9102 1.18517627 1.457569876 1.183298923 1.27366425 1.17156964 1.265327204 1.06795434 1.382178442 1 17.03633365 -4.99999999 0.118114347 0.182126955 1.375842301 0.286215863 0.11407964 169.8618949 1.307128495 33.17437217 1.054345963 1.00E-05 4.99999999 1.193715346 DRGEEDADGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 77.279 0.019315 0 151320 179440 146550 183020 76559 162210 129280 163520 71342 FALSE TRUE 144167.4035 197725.14 153269.4625 164622.4819 89910.86536 156592.627 109555.9616 149201.3219 82405.353 1.749490758 2.399421067 1.859945463 1.997715875 1.091080398 1.900272511 1.329476273 1.810578033 1 16.33045044 2.852756465 8.004719824 1.476654687 2.036041619 0.435033055 0.322160509 0.256828111 16.38128541 0.087940783 0.093380894 712.4534034 -2.852756465 0.559386933 DRGEQGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRGEQGLLR 9 1 P55327-2;P55327-4;E5RFR7 P55327-2 TPD52 0 97.456 0.0060909 345300000 163530 124140 194110 169410 198220 168230 208980 171250 209380 FALSE TRUE 155800.261 136790.0071 203010.1355 152380.5849 232789.5052 162404.1529 177096.2628 156254.4421 241849.581 0.644203146 0.565599521 0.839406604 0.630063465 0.962538385 0.671508928 0.732257886 0.646081095 1 17.88375051 -5 0.131433865 1.919046757 0.588201166 0.359599376 0.11692786 149.4547992 1.234200569 36.84537508 0.808656519 1.00E-05 5 -1.330845591 DRGFGAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DRGFGAPR 8 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;;; 126.24 0.0011195 1108489000 1372175 1120898 1001497 1217838 1354641 1084846 1558708 1356801 1577156 FALSE TRUE 1307315.007 1235118.781 1047416.628 1095418.61 1590889.962 1047277.511 1320898.467 1237992.312 1821733.297 0.717621514 0.677991 0.574956076 0.601305697 0.873283682 0.574879711 0.725077852 0.679568361 1 20.79688033 -4.018409072 0.400032791 3.101405685 0.672570395 0.574068353 0.087336255 216.3778601 3.33969226 386.6674328 0.0496795 9.58E-05 4.018409072 -2.42883529 DRGQYQDHAIDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRGQYQDHAIDRR 13 2 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 102.73 0.0010009 46208000 40750 26519 32409 31374 40138 31958 43479 34426 38721 FALSE TRUE 38823.82826 29221.31625 33894.98471 28220.22591 47138.05449 30851.28645 36845.48 31411.47694 44725.65492 0.868043818 0.653345743 0.75784211 0.630962832 1.053937714 0.689789484 0.823810855 0.702314522 1 15.44881499 DRGS(ph)WAQPVDTGVSEASLGDGEPHIPSLLSMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRGSWAQPVDTGVSEASLGDGEPHIPSLLSMSTR 34 1 Q9NX05;F8W881 Q9NX05 FAM120C Constitutive coactivator of PPAR-gamma-like protein 2 1 DRGS(0.987)WAQPVDT(0.009)GVS(0.003)EASLGDGEPHIPSLLSMSTR 52.246 0.037867 14888000 3348 4230.7 2323.7 2912.5 3975.8 3134.5 4348.5 3011.2 5232.5 TRUE FALSE 3189.746675 4661.81314 2430.243943 2619.729967 4669.178261 3025.951479 3685.056459 2747.523365 6043.929376 0.527760415 0.771321577 0.402096681 0.433448143 0.772540176 0.500659636 0.609712032 0.454592235 1 12.56127109 -1.853070587 2.787564091 1.165830803 0.574145355 0.531517559 0.129419675 14399744.29 12295163.93 16000622.79 0.029823414 0.014025857 1.853070587 -0.591685448 DRGVAASAGSSGENKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRGVAASAGSSGENKK 16 2 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7;C9JW34;C9JGY5;F8WE44 P35249 RFC4 Replication factor C subunit 4 0 59.421 0.057301 39866000 42384 35626 35689 45017 24842 42119 48668 41940 27843 FALSE TRUE 40380.59232 39256.3299 37325.37595 40491.80563 29174.43693 40660.40847 41242.80275 38267.51126 32160.75024 1.255586142 1.220628549 1.160587849 1.259044187 0.907144165 1.26428669 1.282395543 1.189882418 1 14.97301344 3.966936857 1.643357295 1.169976827 1.252383978 0.070391189 0.119306516 1.260621662 6.456345665 0.033389055 0.101075059 9266.950785 -3.966936857 0.082407151 DRISSLPVSRPIS(ph)PSPSAILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRISSLPVSRPISPSPSAILER 22 2 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 DRIS(0.015)S(0.015)LPVS(0.22)RPIS(0.631)PS(0.112)PS(0.007)AILER 61.112 0.026085 114100000 301440 306110 300240 334930 227460 319530 360460 359250 301550 TRUE FALSE 287191.5286 337302.957 314006.301 301262.2001 267128.952 308464.596 305465.2067 327792.1655 348312.8339 0.824521811 0.968390838 0.901506549 0.864918461 0.766922508 0.885596412 0.876985218 0.941085523 1 18.41002411 1.035135209 2.465728662 0.999638348 0.874069713 0.421214648 0.051471572 0.287260968 3.765440862 0.049915282 0.013582442 10.84264425 -1.035135209 -0.125568635 DRKNS(ph)ASAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRKNSASAER 10 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRKNS(0.933)AS(0.067)AER 57.414 0.092739 33695000 64162 51090 67656 65732 44676 62824 80301 72673 52912 TRUE FALSE 61129.18942 56296.12908 70758.09452 59124.49448 52467.48026 60648.38913 68049.60762 66309.36686 61117.32272 1.000194163 0.921115759 1.15774205 0.967393398 0.858471509 0.992327321 1.11342586 1.084952087 1 15.89929373 1.837199097 6.726714975 1.075863688 0.977773736 0.18999567 0.080119885 0.350326099 19.9487619 0.034427952 0.020898495 68.73834902 -1.837199097 -0.098089951 DRLEFWCTDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRLEFWCTDVK 11 1 Q9UNM6;J3KNQ3;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 147.18 3.23E-05 185842000 311760 298668 291375 344720 242844 326200 356530 342730 262457 FALSE TRUE 297023.7226 329102.6088 304734.832 310068.0907 285195.9167 314903.6122 302134.8004 312718.7443 303157.4911 0.979767056 1.085582967 1.005203041 1.022795411 0.940751672 1.038745937 0.996626536 1.031538898 1 18.20970795 3.543848843 24.99999381 1.004574888 1.034794697 0.089088441 0.036502214 369.3040021 138360.945 0.00901069 0.013959291 3498.233892 -3.543848843 0.030219809 DRLGS(ph)YSGPTSVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DRLGSYSGPTSVSR 14 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 DRLGS(1)YSGPTSVSR;DRLGS(1)YSGPTSVSR;DRLGS(1)YSGPTSVSR;DRLGS(0.999)YS(0.001)GPTSVSR;DRLGS(1)YSGPTSVSR 220.1 2.89E-12 1634120000 422317 364752 395642 437564 431630 412174 518570 426384 497218 TRUE FALSE 402354.9124 401920.6435 413782.577 393579.2354 506906.1353 397900.311 439452.6223 389047.5566 574324.028 0.700571268 0.699815129 0.720468859 0.685291258 0.882613491 0.692815017 0.765164961 0.677400801 1 19.1315054 -2.270787275 2.348491416 2.175712799 0.728153299 0.669142869 0.060104033 1724313.903 405442.7415 10731719.19 0.013872165 0.005360592 2.270787275 -1.4475595 DRLIEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 78.334 0.028174 136046000 173386 139608 129743 142496 181122 132607 180486 159827 194189 FALSE TRUE 165190.3874 153834.2139 135691.8449 128172.0314 212709.6195 128014.7863 152949.5458 145831.7006 224302.8383 0.736461423 0.685832667 0.604949299 0.571424028 0.948314435 0.570722989 0.681888589 0.650155396 1 17.77508835 -1.903503822 2.326868931 1.189396305 0.682365578 0.461309273 0.108253961 11010755.56 5402772.199 11400792.2 0.024356575 0.012488095 1.903503822 -0.507030727 DRLSASSLTMESFAFLWAGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 245.66 2.82E-30 914431000 917123 974705 841126 910586 838925 857138 932133 966028 790386 FALSE TRUE 873772.4134 1074028.548 879692.4591 819052.1653 985233.2544 827455.0961 789918.9911 881437.4671 912955.0241 0.957081554 1.176430951 0.963566042 0.897144047 1.079169541 0.906348149 0.865233193 0.965477426 1 19.80018426 3.505516206 23.86435562 0.941775075 1.067296682 0.256179938 0.078875782 440.0369614 369824.7097 0.020448544 0.031591182 3202.699603 -3.505516206 0.125521607 DRNVATPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRNVATPR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ; 76.1 0.033449 115730000 106941 103843 108551 100016 200811 71147 108359 122071 167407 FALSE TRUE 101886.1109 114424.7198 113528.1707 89962.20166 235832.3748 68683.16155 91826.8444 111381.8161 193367.6226 0.526903675 0.591747048 0.587110547 0.465239219 1.219606321 0.355194735 0.474882212 0.576010682 1 17.56098672 -2.295796955 2.201505581 2.840557982 0.589196819 0.226164942 0.232061202 7649128.625 1091489.828 70028716.95 0.055766294 0.005060612 2.295796955 -2.251361164 DRPFFAGLVK ddPTM_SK-BR-3_Trastuzumab_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 ; 167.12 4.87E-06 6244800000 12240800 9770400 5760400 6752600 9909500 7496700 12671700 10419900 9262000 FALSE TRUE 11662201.64 10766014.87 6024520.038 6073815.819 11637713.66 7237087.399 10738399.43 9507478.317 10698303.66 1.090098208 1.006329154 0.563128532 0.567736345 1.087809249 0.676470554 1.003747863 0.888690265 1 23.35087872 1.616508913 25 0.959666511 0.859738891 0.081283188 0.194939065 2.436943429 7029.088668 0.096797854 0.052621629 41.35318012 -1.616508913 -0.099927619 DRPFFPGLVK ddPTM_SK-BR-3_Trastuzumab_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 ; 136.48 0.00010642 16923800000 20373600 17521500 11617100 13080300 16322800 14155100 22404000 17749800 17290200 FALSE TRUE 19410580.3 19306960.77 12149755.53 11765443.39 19169491.15 13664905.34 18985858.32 16195533.41 19971475.91 0.971915165 0.966726789 0.608355416 0.589112364 0.959843491 0.684221106 0.950648736 0.810933227 1 24.25143762 -0.623973332 7.770660423 1.000003583 0.83415401 0.120405351 0.149060777 0 0 0.146294822 0.03448202 0.237698624 0.623973332 -0.165849573 DRPFMGGQKPNLADLAVYGVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRPFMGGQKPNLADLAVYGVLR 22 2 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 150.83 2.99E-08 221250000 255980 228176 242574 247230 253140 192975 279360 229376 250660 FALSE TRUE 243880.3327 251427.3938 253696.2578 222377.9707 297287.5359 186292.2274 236738.5012 209290.6214 289531.0726 0.842328702 0.8683952 0.876231541 0.768062539 1.026789744 0.643427407 0.817661811 0.722860657 1 18.14335866 2.229145225 24.99998861 0.779837052 0.86725275 0.106900472 0.109417793 373.0418765 990502.99 0.035279642 0.026402501 169.490447 -2.229145225 0.087415698 DRPGS(ph)PES(ph)PLLDAPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 DRPGS(1)PES(1)PLLDAPFSR;DRPGS(1)PES(0.999)PLLDAPFS(0.001)R;DRPGS(1)PES(1)PLLDAPFSR 143.69 6.45E-06 263454000 372310 269803 332027 354100 351821 319664 355828 323551 322157 TRUE FALSE 354711.6441 297296.2324 347250.7664 318505.1953 413178.471 308593.9555 301539.9034 295219.1592 372115.4622 0.953230059 0.798935445 0.933180159 0.855931096 1.110350182 0.829296245 0.810339623 0.793353647 1 18.50539081 -0.989699742 5.145932362 1.000000751 0.881288075 0.121308799 0.096166589 7.94E-07 1.56E-07 0.089212988 0.02102757 0.102400071 0.989699742 -0.118712676 DRPGS(ph)PESPLLDAPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(0.836)PES(0.164)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR 248.45 4.35E-21 3128370000 1853724 1479564 1506816 1716591 1460267 1630966 1899861 1722297 1669648 TRUE FALSE 1766102.14 1630333.254 1575905.004 1544036.011 1714937.102 1574485.238 1610002.311 1571483.544 1928568.484 0.915758063 0.845359274 0.817137175 0.800612487 0.889228003 0.816401 0.834817288 0.814844563 1 20.87909895 -1.399769192 7.465167341 1.000005152 0.844130275 0.658827856 0.03574847 3.11E-06 2.50E-07 0.035116471 0.008276758 0.03983188 1.399769192 -0.155874877 DRPHEGTRPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DRPHEGTRPVR 11 2 P31146;H3BRY3;H3BTU6;H3BRJ0 P31146 CORO1A Coronin-1A;Coronin 0 ;;;;; 109.16 0.0011059 218308000 100764.2 101427.8 93137.4 102065.1 133343.4 89333.8 107260.4 114889.2 100054.9 FALSE TRUE 96001.27596 111763.4081 97407.84192 91805.32224 156598.4467 86240.14811 90895.85601 104828.8926 115570.9029 0.830669949 0.967054902 0.842840538 0.794363633 1.354998904 0.746209867 0.786494297 0.90705264 1 16.81841869 -0.716354919 3.704541381 1.000001316 0.898036488 0.02898292 0.172396626 30254985.73 64879638.07 805.6699465 0.03834899 0.192152076 0.716354919 -0.101964827 DRPMEESLLLFEAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 DRPMEESLLLFEAMR 15 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;;;;;;;;;;;;;; 268.12 1.35E-25 799096000 575244 525511.4 533729.6 643436 626050.9 524077.7 652966 597206.5 676910 FALSE TRUE 548053.3561 579061.6091 558201.6301 578756.5908 735233.9787 505928.7578 553344.0442 544911.9329 781881.7456 0.70094149 0.740599985 0.713920786 0.740209877 0.940339102 0.647065571 0.707708099 0.696923718 1 19.5765909 -1.536019217 2.940574175 1.011475444 0.733920755 0.535240106 0.077301745 26038095.17 29087655.94 2384061.545 0.018423508 0.029105883 1.536019217 -0.277554689 DRPPCS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRPPCSPSR 9 1 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;X6R242;B1ALY4 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 1 DRPPCS(0.556)PS(0.444)R;DRPPCS(0.677)PS(0.323)R 60.157 0.059087 1234010000 285430 257430 261060 268420 241840 284520 293870 263300 249140 TRUE FALSE 271938.2896 283662.4097 273029.8592 241437.9116 284016.8194 274667.0011 249034.7342 240244.0562 287775.3588 0.944967251 0.985707779 0.948760382 0.83898049 0.986939329 0.954449339 0.865378937 0.834831923 1 18.13458354 3.462114824 24.90628755 0.908814229 0.965653626 0.128449432 0.057317625 374.0413103 620797.468 0.015122827 0.020484008 2898.109727 -3.462114824 0.056839397 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 263.57 3.00E-45 853620000 840420 857090 752060 928450 647930 765900 828400 861310 663630 FALSE TRUE 800695.0122 944428.4454 786542.6949 835120.4421 760928.7869 739376.691 702012.3654 785889.1303 766542.351 1.044554174 1.23206297 1.026091636 1.089464191 0.992676772 0.964560784 0.915816803 1.025239022 1 19.54800598 2.920974846 1.383507532 0.962674942 1.128811388 0.473892706 0.061252211 0.284135153 1.118932967 0.023349589 0.026026615 833.6328993 -2.920974846 0.166136446 DRPQEADGIDSVIVVDNVPQVGPDRLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRPQEADGIDSVIVVDNVPQVGPDRLEK 28 2 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 130.57 1.35E-05 138040000 149840 86235 154450 137040 117860 146170 181130 165820 145740 FALSE TRUE 142757.3602 95022.44454 161531.6853 123264.4788 138414.7467 141108.0962 153495.2918 151299.9217 168340.6149 0.848026843 0.564465353 0.959552663 0.732232557 0.822230255 0.838229659 0.911813777 0.898772538 1 17.36102377 1.863005508 0.466565543 0.999635827 0.726238217 0.347813585 0.09941761 0.899975151 0.466974456 0.09669828 0.075252175 72.94667624 -1.863005508 -0.27339761 DRPVGGS(ph)PGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR 106.35 0.0011694 4002100000 637540 537960 568310 597170 762920 461620 671840 596230 840950 TRUE FALSE 607404.7477 592778.7356 594367.5756 537141.3371 895973.0065 445633.9837 569338.4688 544020.9404 971360.231 0.625313584 0.610256336 0.611892022 0.552978514 0.922390044 0.45877314 0.586124952 0.560060957 1 19.8896469 -1.046089441 5.000483011 1.000004503 0.614041597 0.508349164 0.118675568 7.86E-06 1.50E-06 0.104122095 0.024541397 0.089931235 1.046089441 -0.385962906 DRQS(ph)PLHGNHITISHTQATGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRQSPLHGNHITISHTQATGSR 22 1 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR 218 6.09E-26 806650000 184745 142044 149165 165017 186673 154717 193731 171647 58250 TRUE FALSE 176012.47 156518.4451 156004.3628 148429.1776 219228.7121 149359.1115 164173.7778 156616.6787 67283.1125 2.615997736 2.326266418 2.318625833 2.20603911 3.258302179 2.219860318 2.44004434 2.327726422 1 16.03795683 0.229956635 1.126264025 0.995657351 2.484364169 0.703031304 0.300949242 2.445240495 3.089605762 0.285498628 0.081785521 1.698074087 -0.229956635 1.488706818 DRRPVHLDQAAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRRPVHLDQAAFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 85.845 0.0054643 119726000 162254 139166 137629 156484 172599 142422 199283 163159 187461 FALSE TRUE 154584.575 153347.1736 143939.4258 140753.931 202700.211 137489.8904 168878.7183 148871.933 216531.4945 0.713912659 0.708198011 0.66475053 0.650039069 0.936123456 0.634964862 0.779926812 0.68753016 1 17.72421735 -5 0.298719957 3.282282311 0.707932065 0.504580685 0.086335905 207.932596 1.927108272 297.0260934 0.077664162 1.00E-05 5 -2.574350246 DRS(ph)PAAET(ph)PPLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 2 DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR 112.55 0.002044 910630000 653140 554630 629160 701630 554890 652550 712010 627410 662470 TRUE FALSE 622267.3666 611147.4276 658007.6083 631100.8194 651662.6403 629952.0299 603379.7975 572470.6543 765202.4642 0.813206172 0.79867415 0.859913081 0.824750114 0.851621199 0.823248825 0.788523072 0.748129653 1 19.54548199 -1.080804051 4.296585887 1.000020154 0.813586081 0.775567322 0.031527896 4253607.655 1069992.943 833.953622 0.007348705 0.083022527 1.080804051 -0.186434073 DRS(ph)PAAETPPLQR ddPTM_SK-BR-3_Trastuzumab_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 DRS(1)PAAETPPLQR 118.52 0.00025525 471750000 129340 118310 120060 132100 108360 115720 147380 131870 105500 TRUE FALSE 123226.3545 130365.9235 125564.8698 118821.057 127257.9497 111712.5874 124894.4742 120322.7637 121860.4012 1.011209165 1.069797262 1.030399281 0.975058804 1.044292883 0.916725912 1.02489794 0.987381976 1 16.89486987 3.368263587 5.665397091 0.992279902 1.041952385 0.267064974 0.035895893 0.240091556 11.09798907 0.009046784 0.012312886 2334.874744 -3.368263587 0.049672483 DRS(ph)PHRS(ph)SPSDTRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(0.997)PHRS(0.57)S(0.365)PS(0.067)DT(0.001)RPK;DRS(0.999)PHRS(0.859)S(0.136)PS(0.005)DTRPK;DRS(0.997)PHRS(0.533)S(0.461)PS(0.008)DTRPK;DRS(0.989)PHRS(0.526)S(0.483)PS(0.001)DTRPK;DRS(0.999)PHRS(0.55)S(0.445)PS(0.006)DTRPK;DRS(0.888)PHRS(0.58)S(0.519)PS(0.013)DTRPK;DRS(0.919)PHRS(0.56)S(0.515)PS(0.006)DTRPK;DRS(0.933)PHRS(0.555)S(0.507)PS(0.006)DTRPK 144.18 6.15E-06 898658400 856504 627854.2 747988.9 883696 745878.9 758374.9 1094174 974670 864035 TRUE FALSE 816018.7533 691833.2568 782284.9309 794865.1992 875959.944 732112.1871 927237.6604 889322.7277 998025.1349 0.817633469 0.693202238 0.783832895 0.796438057 0.87769327 0.733560871 0.929072453 0.891082495 1 19.92871662 1.424654527 0.555228409 1.00300812 0.756803611 0.635020369 0.055457566 0.442884605 0.335760005 0.051936292 0.027778049 26.58609348 -1.424654527 -0.246204509 DRS(ph)PLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 78.098 0.028555 17452100000 3079750 3130850 2585470 3175130 2329190 2890740 2769480 2736100 2566510 TRUE FALSE 2934176.321 3449887.174 2704016.357 2855959.9 2735399.999 2790632.949 2346944.961 2496512.579 2964511.263 0.989767304 1.163728813 0.912128886 0.963383049 0.922715333 0.941346718 0.791680231 0.842132938 1 21.49936285 3.253038149 1.169064945 0.876872691 1.072409346 0.366689621 0.079064138 0.378420777 1.098331844 0.029368985 0.046251156 1790.763151 -3.253038149 0.195536655 DRS(ph)PPKSPEKLPQSSSSESSPPSPQPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRSPPKSPEKLPQSSSSESSPPSPQPTK 28 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DRS(0.125)PPKS(0.125)PEKLPQS(0.125)S(0.125)S(0.125)S(0.125)ES(0.125)S(0.125)PPSPQPTK;DRS(0.972)PPKS(0.024)PEKLPQS(0.001)S(0.001)S(0.001)S(0.001)ESSPPSPQPTK;DRS(0.37)PPKS(0.37)PEKLPQS(0.049)S(0.049)S(0.049)S(0.049)ES(0.049)S(0.013)PPSPQPTK 125.82 2.63E-05 525644000 584731 467142 511636 585494 272180 593841 624619 632477 248607 TRUE FALSE 557091.9245 514744.3009 535095.0167 526639.0308 319648.1058 573276.1373 529321.8996 577093.9609 287159.7039 1.940007309 1.792536676 1.863405657 1.833958678 1.113137051 1.996366933 1.843301454 2.009662056 1 18.13149379 2.96750125 24.99448945 1.671865161 1.858927693 0.10896687 0.337207514 1850.864659 1423483.341 0.096219827 0.102135673 927.9001605 -2.96750125 0.187062532 DRS(ph)SPPPGYIPDELHQVAR ddPTM_SK-BR-3_Trastuzumab_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(0.629)S(0.371)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR 193.39 3.25E-15 1672030000 1062160 947500 959180 1096810 963980 1022140 1212270 1090880 995540 TRUE FALSE 1011953.802 1044051.327 1003159.352 986556.575 1132097.807 986743.0355 1027315.947 995356.7641 1149923.259 0.880018553 0.907931307 0.872370694 0.857932534 0.984498573 0.858094684 0.893377831 0.865585383 1 20.13310615 -2.386371529 2.304095067 1.846056942 0.891073558 0.465879076 0.037006484 1623233.983 325973.0944 7221036.822 0.008220459 0.004107981 2.386371529 -0.954983384 DRS(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.333)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)APNVHINT(0.002)IEPVNIDDLIR;DRS(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR;DRS(0.357)S(0.357)S(0.283)APNVHINT(0.003)IEPVNIDDLIR;DRS(0.371)S(0.371)S(0.257)APNVHINTIEPVNIDDLIR 229.95 1.43E-33 853112000 289782 243346 286039 294354 275741.3 285255 349481 338266 307698 TRUE FALSE 276084.5792 268143.2341 299154.1711 264764.9767 323830.4954 275376.5478 296161.2548 308645.6358 355414.2343 0.776796629 0.754452715 0.841705655 0.744947588 0.911135414 0.774804499 0.833284731 0.868411014 1 18.43914194 -4.999999999 0.133114942 1.680400574 0.72605137 0.661537007 0.045802617 75.93755685 0.632053387 13.63020296 0.28555144 1.00E-05 4.999999999 -0.954349204 DRSPAAET(ph)PPLQR ddPTM_SK-BR-3_Trastuzumab_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 DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR 93.117 0.0093141 880020000 750450 707750 714620 846870 678050 737330 831970 822670 818680 TRUE FALSE 714977.7157 779870.5296 747386.0339 761741.0187 796301.7053 711796.0772 705037.6963 750632.6536 945636.7132 0.75608075 0.824704158 0.790352176 0.805532408 0.842079939 0.752716204 0.745569294 0.793785439 1 19.85092652 -2.102333729 2.255453662 1.361590476 0.787491583 0.820077078 0.031075851 2335696.335 590778.1322 4336134.845 0.008104453 0.007900713 2.102333729 -0.574098893 DRT(ph)PPHLLYSDRDR ddPTM_SK-BR-3_Trastuzumab_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 156.39 0.00026613 1410660000 312677 228596 261022 297448 241427 269641 306658 295847 211457 TRUE FALSE 297897.3779 251890.1923 272990.1169 267547.9619 283531.7924 260303.2646 259871.6899 269941.0683 244248.6716 1.219647894 1.031285823 1.117672883 1.095391677 1.160832485 1.065730523 1.063963576 1.105189504 1 17.89799119 7.554603841 0.013752525 5.04E-07 2.381264903 0.405256633 0.048360437 6505.798257 7.426513872 531.0556211 776.0865521 35859467.93 -7.554603841 2.381264398 DRT(ph)PPLLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;DRT(1)PPLLYR;DRT(1)PPLLYR 104.59 0.00523 5914150000 1145050 936110 878020 1056480 855490 962400 1147450 1022980 869325 TRUE FALSE 1090925.756 1031500.673 918278.0855 950280.6232 1004687.185 929071.8467 972385.4281 933402.448 1004135.481 1.086432833 1.02725249 0.914496204 0.946366941 1.000549432 0.925245511 0.968380708 0.929558277 1 19.9375225 3.97025131 3.5122633 0.95434559 1.06886454 0.681990218 0.029975883 0.108211668 2.810927754 0.007139839 0.015075093 9337.944967 -3.97025131 0.114518949 DRTDIQCLIPCAIDQDPYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRTDIQCLIPCAIDQDPYFR 20 1 P23381;P23381-2;H0YJP3 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 115.24 0.00010251 131175000 141423 122887 134261 145018 143205 139085 163526 148352 161849 FALSE TRUE 134738.2151 135409.325 140416.9997 130440.5151 168179.9067 134268.4516 138577.1053 135361.5124 186947.7163 0.720726724 0.724316551 0.751103049 0.697737944 0.899609313 0.718213917 0.74126129 0.724060797 1 17.51227532 -1.792978939 2.650796821 1.072031611 0.745122673 0.667023317 0.056132632 12570378.17 8826780.722 5829482.69 0.012871967 0.016107237 1.792978939 -0.326908938 DRVAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRVAQK 6 1 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 91.584 0.043527 69819000 174800 153810 136690 169990 109470 134850 176680 194910 162100 FALSE TRUE 166537.5504 169483.4139 142957.3717 152902.2822 128561.5333 130180.1107 149724.221 177842.6471 187237.6401 0.889444827 0.905178114 0.763507656 0.816621498 0.686622269 0.695266778 0.799648089 0.949823161 1 17.51451096 1.159856203 4.238637857 0.993851146 0.802009398 0.534128046 0.070687516 0.203490756 6.349800372 0.077604887 0.020273128 14.44961256 -1.159856203 -0.191841748 DRVEASSLPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRVEASSLPEVR 12 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 0 116.19 0.0007922 120360000 101710 86428 99384 120260 99564 96946 121880 104190 126170 FALSE TRUE 96902.36987 95235.11146 103940.8547 108171.2363 116927.9301 93588.73571 103284.9675 95066.57125 145735.7992 0.664918094 0.653477814 0.713214291 0.742242036 0.802328122 0.642180825 0.708713769 0.652321336 1 17.15299579 -1.616219676 2.915675634 1.023171174 0.695036072 0.790848543 0.048887538 8838111.007 9174713.365 1562723.689 0.011819452 0.024198047 1.616219676 -0.328135103 DRVGVQDFVLLENFTSEAAFIENLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRVGVQDFVLLENFTSEAAFIENLRR 26 2 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 284.59 2.37E-61 110374000 68175 50378 72584 68444 71751 59108 90283 74223 76795 FALSE TRUE 64952.50286 55511.57548 75912.0482 61563.87908 84264.35168 57061.07514 76508.67019 67723.64064 88703.97639 0.732238909 0.625807069 0.855790814 0.694037422 0.949950105 0.643275279 0.862516804 0.763479197 1 16.43671116 -5 0.097707038 1.778339609 0.584036341 0.37234468 0.099153917 175.3960508 1.171917987 27.93031408 1.575582169 1.00E-05 5 -1.194303269 DRVHHEPQLSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 71.176 0.027214 273620000 376180 383250 329100 409520 234350 362900 377810 403120 67890 FALSE TRUE 358398.7169 422303.6107 344189.5605 368354.2716 275220.5658 350332.682 320168.1455 367820.6757 78418.03447 4.570360879 5.385286862 4.38916332 4.697315791 3.509659069 4.467501441 4.082838185 4.690511286 1 16.25889786 -0.782465531 0.401265837 5.24E-14 4.746307492 0.829898885 0.490987595 4.645080849 0.599574984 7.063513696 0.313281677 0.165019197 0.782465531 4.746307492 DRVTDALNATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRVTDALNATR 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 141.34 3.48E-05 1256920000 1688990 1858030 1599040 1748990 1525210 1601240 1684910 1163420 1169970 FALSE TRUE 1609154.79 2047365.369 1672357.566 1573178.202 1791206.141 1545788.657 1427846.034 1061544.777 1351402.972 1.190729059 1.514992501 1.237497327 1.164107401 1.325441913 1.143839912 1.056565705 0.785513129 1 20.3660265 1.767474524 1.534431693 0.897261634 1.304848957 0.655781173 0.113548191 0.217303557 0.985438991 0.084626007 0.033887052 58.54293931 -1.767474524 0.407587323 DRVTNQPIGGR ddPTM_SK-BR-3_Trastuzumab_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 95.138 0.0072794 88996000 30376 30945 42351 36234 100090 28002 47620 32978 93270 FALSE TRUE 28940.18668 34098.33068 44292.83524 32591.68948 117545.6643 27032.28372 40354.6944 30090.27149 107733.8352 0.268626719 0.316505308 0.411132075 0.302520461 1.091074722 0.250917306 0.37457772 0.279301961 1 16.71711189 -2.167600317 2.2299197 2.412917571 0.402452372 0.358719195 0.246861321 15408211.38 3352179.039 109956893.6 0.059670514 0.00679829 2.167600317 -2.010465199 DRVTSAVEALLSADSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DRVTSAVEALLSADSASR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 218.05 7.37E-19 278395000 376850 326279 365692 414959 385466 346687 417609 380861 411423 FALSE TRUE 359037.0473 359527.201 382459.3399 373246.5329 452691.1484 334681.1423 353895.0771 347510.7918 475224.3776 0.755510585 0.756542 0.804797392 0.785411167 0.952584021 0.704259205 0.744690495 0.731256241 1 18.85824932 -2.218056434 2.358376804 1.731101501 0.776297447 0.512924929 0.067504613 5220713.826 907869.8175 20423384.1 0.015892581 0.006052622 2.218056434 -0.954804054 DRVVVVSHDENLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRVVVVSHDENLCR 14 1 Q7L5L3-1;Q7L5L3 Q7L5L3-1 GDPD3 Glycerophosphodiester phosphodiesterase domain-containing protein 3 0 ;;; 216.39 3.69E-12 1255610000 487204 185543 347415 519805 748130 361716 610972 410913 698911 FALSE TRUE 464174.8325 204450.0426 363344.3214 467553.2138 878603.6351 349189.6842 517757.0001 374931.2793 807294.5483 0.574975805 0.253253342 0.450076521 0.579160623 1.088330941 0.432543097 0.641348317 0.464429346 1 19.62273562 3.158025049 4.000784219 0.686414123 0.40864713 0.267874539 0.218999854 0.29215511 8.967498635 0.060678478 0.074948018 1438.881569 -3.158025049 -0.277766992 DRWQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRWQER 6 1 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 79.469 0.061166 140330000 107100 106080 147530 170560 105600 125830 120530 158740 124740 FALSE TRUE 102037.5953 116889.6726 154294.3964 153414.9848 124016.6066 121472.4755 102140.9348 144839.8841 144084.0421 0.708181099 0.811260365 1.07086388 1.064760417 0.860724094 0.843066822 0.708898316 1.005245841 1 17.13655103 3.991243957 21.61652041 0.91089761 0.746835558 0.292629732 0.113294148 119.8454749 295879.2594 0.031577894 0.060215602 9800.403496 -3.991243957 -0.164062053 DRYDSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRYDSDR 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 110.41 0.006211 536393000 742395 809929 581348 761037 887780 564095 711317 653850 851020 FALSE TRUE 707303.4596 892461.6859 608003.3808 684536.1149 1042608.551 544560.2487 602792.5274 596595.4277 982991.8352 0.719541541 0.907903458 0.618523328 0.696380265 1.060648231 0.553982474 0.613222314 0.606917989 1 19.90681991 DRYDSDRYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 143.4 5.74E-05 1655830000 1138769 796695 773249 714796 1279335 803243 1397534 1059662 1477718 FALSE TRUE 1084941.646 877879.1263 808703.2315 642943.3481 1502450.619 775426.4935 1184314.521 966872.3777 1706874.96 0.635630419 0.514319529 0.473791725 0.376678645 0.880234729 0.454296016 0.693849607 0.566457649 1 20.70292594 -1.851298343 0.308519864 1.414652677 0.537276225 0.485311473 0.139414207 24.28398519 1.227075457 7.456340472 0.126257443 0.01408321 1.851298343 -0.877376451 DRYDSFIELQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRYDSFIELQEK 12 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 228.38 9.76E-12 387450000 700950 688340 623500 732090 496650 662910 727300 764970 543920 FALSE TRUE 667817.4826 758482.6286 652088.0917 658498.9223 583265.6028 639953.2605 616337.0272 697985.1714 628268.3356 1.062949451 1.207259041 1.037913348 1.048117317 0.928370204 1.018598621 0.981009216 1.110966655 1 19.26102135 3.561859947 5.579470644 1.010240476 1.134934755 0.421087244 0.057539219 0.176475329 8.927445108 0.014503061 0.022526725 3646.363384 -3.561859947 0.124694279 DRYLPDTLLLEECGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DRYLPDTLLLEECGLLR 17 1 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 240.61 2.28E-20 361796800 435817 319090 359601 399638 405036 367221 501344 433747 457094 FALSE TRUE 415216.7941 351605.6338 376089.0615 359465.629 475674.1502 354504.0447 424854.765 395765.8132 527977.803 0.786428505 0.665947757 0.712319835 0.680834738 0.900935887 0.671437403 0.804683005 0.749587977 1 19.01011775 -5 0.227980177 2.381074009 0.713427337 0.563920746 0.070834827 108.4822244 1.085193215 68.90112855 0.112033537 1.00E-05 5 -1.667646673 DRYS(ph)AGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DRYSAGKR 8 2 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 1 DRYS(1)AGKR 58.511 0.082286 119570000 128260 110230 124360 133880 89641 150570 153060 135830 119590 TRUE FALSE 122197.404 121462.5623 130062.029 120422.128 105274.362 145355.7231 129707.8859 123936.0051 138135.4064 0.88462044 0.87930072 0.941554612 0.871768732 0.762109909 1.052269848 0.938990873 0.897206649 1 17.07572363 2.228056878 24.99996865 0.967072414 0.874478609 0.432462552 0.058946339 221.9099122 528164.3442 0.021028754 0.015694966 169.0662336 -2.228056878 -0.092593805 DRYSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DRYSAGK 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 112.41 0.0058006 1038420000 1101100 961000 935760 1139970 805560 1097560 1226480 1116980 963430 FALSE TRUE 1049053.185 1058926.993 978665.5216 1025378.05 946049.409 1059551.222 1039357.95 1019171.31 1112833.804 0.942686304 0.951558974 0.879435472 0.921411667 0.850126412 0.952119911 0.9339741 0.915834248 1 20.08580672 -0.386509268 0.794415499 1.004091659 0.921019938 0.383527746 0.03224968 15.7666124 7.398156269 0.234432305 0.010796046 0.410667876 0.386509268 -0.083071721 DS(ph)LGAYASQDANEQGQDLGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSLGAYASQDANEQGQDLGKR 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(1)LGAYASQDANEQGQDLGKR;DS(1)LGAYASQDANEQGQDLGKR 210.96 1.07E-22 556270000 334884 387819 306254 399433 185559 367340 354814 384282 206034 TRUE FALSE 319054.697 427338.197 320296.0488 359281.236 217920.4308 354618.9237 300680.6077 350632.2309 237984.7004 1.340652136 1.795654074 1.345868235 1.509682073 0.915690927 1.490091266 1.263445117 1.473339379 1 17.8605093 3.204212374 2.24687376 1.270557952 1.555600463 0.220928109 0.223612088 0.399344111 4.133150337 0.063464212 0.084321397 1600.340418 -3.204212374 0.285042512 DS(ph)LGTYSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(1)LGTYSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(0.999)LGT(0.001)YSSR;DS(0.919)LGT(0.081)YSSR;DS(0.999)LGT(0.001)YSSR 213.35 2.14E-06 1786848000 2468150 2923740 2187220 2876990 1926260 2497790 2389760 2639240 1819810 TRUE FALSE 2351485.441 3221672.43 2287506.2 2587789.499 2262199.134 2411290.906 2025158.221 2408134.154 2102016.84 1.118680591 1.532657764 1.088243518 1.231098367 1.076204096 1.147132059 0.963435774 1.145630286 1 21.0033428 3.016731952 1.177625956 1.050760764 1.308743675 0.31970231 0.129053108 0.440694636 1.296823101 0.051420575 0.063115093 1039.278521 -3.016731952 0.257982911 DS(ph)LSPVLHPSDLILTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.5)LS(0.5)PVLHPSDLILTR;DS(0.615)LS(0.385)PVLHPSDLILTR;DS(0.592)LS(0.408)PVLHPSDLILTR;DS(0.58)LS(0.42)PVLHPSDLILTR 103.41 0.00092824 173817000 218055 161854 210532 236793 234515 183002 256681 252071 211643 TRUE FALSE 207747.9723 178347.1066 220185.1004 212990.1178 275414.3417 176664.5949 217519.5992 229998.3269 244463.5155 0.849811768 0.729544882 0.900686959 0.871255235 1.126607139 0.722662416 0.889783487 0.940828845 1 17.89925964 7.999999971 0.09267987 1.061811734 0.301546115 0.156197947 0.108880479 250.0611644 1.659441643 1.714674992 24.16268151 99999993.27 -7.999999971 -0.760265619 DS(ph)MALSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSMALSK 7 0 F8VW93;F8VXS0;P20132 F8VW93 SDS L-serine dehydratase/L-threonine deaminase 1 DS(1)MALSK 71.378 0.057146 69229000 153250 190440 144580 149100 1017500 89736 202730 104280 866110 TRUE FALSE 146006.1762 209846.0525 151209.136 134112.1847 1194951.678 86628.41982 171799.8151 95148.69038 1000421.915 0.1459446 0.209757553 0.151145365 0.134055625 1.194447722 0.086591885 0.171727361 0.095108563 1 19.93217714 -2.286130005 2.174586781 4.081447472 0.264620903 0.323239361 0.330093258 13901466.25 1932073.452 210578667.4 0.085777899 0.005174519 2.286130005 -3.816826569 DS(ph)QDGSSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 DS(0.936)QDGS(0.063)S(0.001)YR 132.03 0.00033205 209290000 189080 214760 170220 253070 169500 205390 215160 217200 182120 TRUE FALSE 180142.5631 236644.2882 178024.7554 227630.9228 199060.7463 198277.2928 182333.3903 198180.8166 210362.2395 0.856344578 1.124937103 0.846277145 1.082090224 0.946276037 0.94255173 0.866759124 0.942093111 1 17.68251623 2.366973162 3.634762135 0.920632428 0.983549557 0.020623008 0.091404446 0.557377321 14.21495219 0.030791223 0.025110119 232.7947391 -2.366973162 0.06291713 DS(ph)RPLSPILHIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.601)RPLS(0.399)PILHIVK;DS(0.695)RPLS(0.305)PILHIVK 122.1 0.00014471 405550000 1143840 1149410 882070 1162480 761600 1042360 1086940 1106260 767450 TRUE FALSE 1089772.95 1266536.186 922513.782 1045625.302 894422.7989 1006262.812 921107.34 1009390.01 886462.2264 1.22935069 1.4287537 1.040669026 1.179548627 1.00898016 1.135144603 1.039082448 1.138672331 1 19.75769963 3.730120381 24.99933929 1.081355509 1.329052197 0.658566292 0.075277622 292.1533735 865336.4204 0.017792955 0.028061292 5371.80676 -3.730120381 0.247696688 DS(ph)RPLSPILHIVKDESPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSRPLSPILHIVKDESPAK 19 2 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.585)RPLS(0.415)PILHIVKDESPAK 176.48 2.92E-13 39577000 107180 78964 105850 106020 72693 112010 127670 121970 71535 TRUE FALSE 102113.8138 87010.52137 110703.3272 95362.66818 85370.63618 108131.0656 108191.5967 111289.6602 82628.28245 1.235821571 1.05303558 1.339775243 1.154116549 1.033189044 1.308644721 1.309377292 1.346871276 1 16.33434806 2.195454589 24.99962904 1.273031885 1.162383855 0.060146321 0.128307586 252.6163122 146505.0839 0.043713371 0.032284677 156.8391895 -2.195454589 -0.11064803 DS(ph)SQEYTDSTGIDLHEFLVNTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.499)S(0.499)QEYT(0.002)DSTGIDLHEFLVNTLK;DS(0.495)S(0.495)QEYT(0.01)DS(0.001)TGIDLHEFLVNTLK;DS(0.466)S(0.466)QEY(0.001)T(0.052)DS(0.008)T(0.008)GIDLHEFLVNTLK;DS(0.499)S(0.499)QEYT(0.002)DSTGIDLHEFLVNTLK 168.09 6.48E-12 185237000 241880 207388 209331 298163 197222 276713 288303 231848 145801 TRUE FALSE 230446.8118 228521.073 218929.0334 268191.0888 231617.4544 267130.3594 244317.0823 211546.16 168411.0744 1.368359014 1.356924263 1.299968153 1.592478937 1.375310116 1.586180483 1.450718625 1.256129745 1 17.36162749 -0.626487032 7.133661444 1 1.414986759 0.581863955 0.109378038 0 1.05E-10 0.100923779 0.023787963 0.236326797 0.626487032 0.414986759 DS(ph)STSPGDYVLSVSENSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.489)S(0.489)T(0.021)S(0.001)PGDYVLSVSENSR 101.42 0.00070107 30597000 61647 60647 55325 65310 53754 51263 56333 61896 43292 TRUE FALSE 58733.06848 66826.99825 57861.70597 58744.91472 63128.68058 49487.74946 47738.36622 56476.05811 50005.50226 1.174532118 1.336392902 1.157106786 1.174769017 1.262434687 0.989646083 0.954662269 1.129396878 1 15.60979923 2.235838875 24.99930562 1.007328137 1.227537524 0.684834397 0.068038171 37.27901992 342403.5539 0.024266327 0.018735258 172.1229873 -2.235838875 0.220209387 DS(ph)VQHQGVS(ph)LTMEGTVNLQLSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSVQHQGVSLTMEGTVNLQLSAK 23 0 O14972-2;O14972 O14972-2 DSCR3 Down syndrome critical region protein 3 2 DS(0.5)VQHQGVS(0.5)LT(0.5)MEGT(0.5)VNLQLSAK 41.912 0.093283 719400000 295820 291660 281030 319480 428840 194390 307660 211410 406820 TRUE FALSE 281837.1749 321380.4856 293915.5035 287365.2634 503629.5602 187658.2256 260720.8164 192897.8196 469907.5679 0.599771517 0.68392277 0.625475144 0.611535721 1.071763033 0.399351358 0.554834257 0.410501624 1 18.84201748 DSAAPS(ph)PIPGADNLSADPVVSPPTSIPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSAAPSPIPGADNLSADPVVSPPTSIPFK 29 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 DS(0.001)AAPS(0.994)PIPGADNLS(0.005)ADPVVSPPTSIPFK;DS(0.001)AAPS(0.974)PIPGADNLS(0.025)ADPVVSPPTSIPFK 104.3 0.00034823 126297000 149914 134716 132908 172501 100488 152286 165885 156410 121781 TRUE FALSE 142827.8623 148443.7136 139001.9633 155160.8717 118013.0754 147012.2976 140576.1966 142713.9112 140666.1755 1.015367495 1.055290748 0.988169066 1.103043224 0.838958442 1.04511477 0.999360337 1.014557414 1 17.10191594 DSAATTDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSAATTDEER 10 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 200.05 6.22E-07 159796000 269160 222520 218030 287450 219506 250610 252560 262370 245020 FALSE TRUE 256437.3402 245195.041 228026.8912 258554.9799 257787.7769 241931.3129 214027.3334 239395.4919 283016.4502 0.906086342 0.866363212 0.805701898 0.913568733 0.910857926 0.854831275 0.756236372 0.845871297 1 18.11052639 2.000921685 24.99201746 0.831596739 0.879331525 0 0.06889124 71.75024788 1945515.092 0.023852036 0.017466897 100.2124513 -2.000921685 0.047734786 DSAIPVES(ph)DT(ph)DDEGAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 2 DSAIPVES(1)DT(1)DDEGAPR;DSAIPVES(1)DT(1)DDEGAPR 280.38 3.42E-35 401640000 327320 291780 289380 317720 292100 319260 340870 303770 296690 TRUE FALSE 311848.2323 321512.7137 302648.3592 285782.182 343042.1475 308203.9461 288864.021 277170.2884 342699.1699 0.90997662 0.938177685 0.883131288 0.833915594 1.001000812 0.899342552 0.842908435 0.808785993 1 18.38658317 1.987150002 24.73653576 0.867614008 0.914603433 0.021523262 0.064238994 1177.111331 2265964.398 0.023352733 0.015881292 97.08452322 -1.987150002 0.046989425 DSAIPVES(ph)DTDDEGAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.561)DT(0.439)DDEGAPR 248.41 7.62E-21 127110000 40471 31799 37108 38992 36367 40424 42919 40125 40852 TRUE FALSE 38558.01604 35039.35425 38809.4385 35072.45008 42709.39329 39024.10674 36370.91829 36611.44228 47187.11952 0.817130107 0.742561839 0.822458309 0.743263213 0.905107023 0.827007606 0.770780642 0.775877881 1 15.52610549 -1.642738909 2.764073985 1.020814593 0.797577698 0.631534417 0.047837444 8003477.414 7146470.834 1183136.336 0.010894888 0.022764656 1.642738909 -0.223236895 DSAIPVESDT(ph)DDEGAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.006)DT(0.994)DDEGAPR;DSAIPVES(0.02)DT(0.98)DDEGAPR 357.93 5.79E-87 1117780000 1062870 956770 966470 1146270 968170 1055160 1132410 950090 959210 TRUE FALSE 1012630.242 1054265.951 1010783.605 1031044.762 1137018.541 1018619.545 959640.0564 866895.0829 1107959.388 0.913959711 0.951538443 0.912293011 0.930579923 1.026227634 0.919365417 0.866132881 0.782424963 1 20.07947357 1.847735361 4.382291881 0.869283462 0.944169995 0.170829543 0.061204189 0.309493995 9.126968993 0.026726436 0.01500928 70.42637917 -1.847735361 0.074886534 DSALAEAPEGLS(ph)PAPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR 261.06 9.54E-31 383250000 435780 388110 416705 455371 389346 384044 464700 445400 411562 TRUE FALSE 415181.543 427658.8502 435811.3364 409596.2419 457247.8191 370744.46 393801.4802 406398.4148 475384.933 0.873358649 0.899605395 0.916754626 0.861609642 0.961847521 0.779882647 0.828384437 0.854882826 1 18.85873665 2.240612764 24.99993513 0.846453734 0.898337502 0.039513123 0.062140458 99.13641441 1207727.664 0.019689715 0.015718204 174.0254492 -2.240612764 0.051883768 DSASFNPELLTHILDGSPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSASFNPELLTHILDGSPEK 20 0 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 165.3 1.69E-11 58339000 141839 118364 126250 156911 112551 148956 166390 157799 114273 FALSE TRUE 135134.5516 130425.4262 132038.6874 141138.0082 132179.8588 143797.6164 141004.1495 143981.283 131993.8732 1.023794122 0.988117274 1.000339517 1.069276965 1.001409047 1.089426447 1.068262838 1.090817926 1 17.01011144 2.905887875 1.194949809 1.064741057 1.003891026 0.252653965 0.034347669 0.47167866 1.413365485 0.013746489 0.015098711 805.1705371 -2.905887875 -0.060850031 DSAYISS(ph)SPLGSHQVFDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYIS(0.011)S(0.494)S(0.494)PLGSHQVFDFR;DS(0.004)AYIS(0.017)S(0.623)S(0.355)PLGSHQVFDFR 132.83 8.30E-06 130461000 192205 132486 160202 187477 181429 159726 204113 165064 167284 TRUE FALSE 183119.8506 145986.474 167547.4202 168631.4558 213070.1602 154194.6486 172971.8131 150610.1211 193225.5484 0.947699992 0.755523663 0.867108007 0.872718216 1.102701801 0.798003421 0.895180863 0.779452419 1 17.55992633 -2.477504965 2.243364849 2.474936226 0.874850599 0.132974728 0.098288828 6422799.018 882311.2034 47760264.96 0.023810776 0.00333039 2.477504965 -1.600085627 DSAYISSS(ph)PLGSHQVFDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYIS(0.003)S(0.177)S(0.819)PLGSHQVFDFR;DSAYIS(0.001)S(0.052)S(0.947)PLGSHQVFDFR;DSAYISS(0.01)S(0.989)PLGSHQVFDFR;DSAYIS(0.001)S(0.372)S(0.627)PLGSHQVFDFR 229.89 4.50E-20 2394000000 3282360 2288990 2529080 3232870 2957730 2553640 3233760 2842150 2414010 TRUE FALSE 3127209.348 2522240.683 2645040.82 2907895.766 3473557.176 2465206.806 2740390.52 2593276.279 2788362.342 1.12152187 0.904559872 0.948600108 1.042868684 1.245733786 0.884105616 0.9827957 0.930035613 1 21.41098662 DSAYQSITHYRPVS(ph)ASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSAYQSITHYRPVSASR 17 1 P50402;Q5HY57 P50402 EMD Emerin 1 DSAYQSITHYRPVS(0.934)AS(0.066)R;DSAYQSITHYRPVS(0.954)AS(0.046)R;DSAYQSITHYRPVS(0.999)AS(0.001)R;DSAYQSITHYRPVS(0.984)AS(0.016)R;DSAYQSITHYRPVS(0.947)AS(0.053)R;DSAYQSITHYRPVS(0.967)AS(0.033)R 238.87 1.76E-20 2778469000 678892 575714 666760 964567 1095670 776019 1047872 802712 1032549 TRUE FALSE 646802.1206 634379.9111 697331.6055 867606.8926 1286754.501 749145.2674 887999.8809 732422.2818 1192671.425 0.542313756 0.531898306 0.5846804 0.727448377 1.078884321 0.628123766 0.744546957 0.614102314 1 20.18576521 3.226595001 3.737153064 0.78797572 0.542121058 0.396296219 0.144826494 0.223158581 6.720035569 0.040197377 0.051876435 1684.980973 -3.226595001 -0.245854662 DSDAGSS(ph)TPTTSTR ddPTM_SK-BR-3_Trastuzumab_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(0.023)S(0.542)T(0.419)PT(0.013)T(0.003)STR 173.54 2.81E-06 406720000 744110 633730 635470 737080 586270 700180 736450 678700 632040 TRUE FALSE 708937.395 698307.8075 664606.9281 662987.318 688515.3024 675932.591 624091.0267 619269.43 730053.5352 0.971075902 0.956515891 0.910353688 0.908135207 0.943102484 0.925867157 0.854856523 0.84825208 1 19.47764274 3.854793204 0.727580189 0.898295681 0.984469262 0.148229737 0.043911247 1.498414457 1.268192292 0.019557266 0.08828055 7158.024881 -3.854793204 0.086173581 DSDAGSST(ph)PTTSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.295)S(0.107)T(0.596)PT(0.001)TSTR;DSDAGS(0.245)S(0.117)T(0.608)PT(0.023)T(0.007)STR;DSDAGS(0.078)S(0.037)T(0.884)PT(0.001)TSTR;DSDAGS(0.171)S(0.232)T(0.596)PT(0.001)TSTR 229.31 1.49E-11 489204000 1434520 1255460 1324980 1449030 1146380 1408070 1539890 1369450 1282330 TRUE FALSE 1366713.083 1383392.801 1385731.644 1303370.751 1346308.309 1359308.183 1304951.498 1249533.698 1481187.187 0.922714627 0.933975674 0.935554706 0.879950058 0.908938668 0.917715326 0.881017274 0.843602827 1 20.49832254 3.255340904 24.98836175 0.899169422 0.930292243 0.069710338 0.040126755 480.2312779 715131.7965 0.009920084 0.013394971 1800.283514 -3.255340904 0.031122822 DSDELKSWVNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSDELKSWVNEK 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 174.73 2.70E-05 67182000 300020 172010 283030 265390 179060 283410 364420 330960 238420 FALSE TRUE 285838.6492 189538.0146 296007.2055 238712.493 210288.0073 273595.4406 308821.036 301979.3879 275392.9559 1.03793014 0.688245689 1.074853946 0.866806822 0.763592542 0.993472908 1.121383207 1.096539985 1 18.07113213 2.014077179 7.945204964 1.079278247 0.880327472 0.351636115 0.116309812 0.148544655 55.88851814 0.042089072 0.030229013 103.2944954 -2.014077179 -0.198950775 DSDKTDTDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DSDKTDTDWR 10 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 105.86 0.0022734 4270730000 18171100 17521900 15861700 19965200 11318300 18737500 19108600 18897500 11555700 FALSE TRUE 17312188.11 19307401.53 16588974.63 17958260.16 13292207.94 18088615.68 16193232.12 17242734.72 13347698.94 1.297016676 1.44649663 1.242834043 1.34541993 0.995842654 1.355186071 1.213185298 1.291813278 1 23.67008772 -4.999999984 0.090159728 0.107575596 1.512477622 0.369779152 0.11559193 206.3005671 1.292008744 35.66032265 2.492631177 1.00E-05 4.999999984 1.404902026 DSDLSHVQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSDLSHVQNK 10 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;; 147.75 2.63E-05 620130000 1533280 1286270 1366530 1566000 1212580 1402360 1661420 1641670 1255800 FALSE TRUE 1460804.893 1417342.375 1429186.752 1408582.705 1424053.568 1353795.922 1407939.865 1497916.672 1450543.05 1.007074483 0.977111555 0.985277033 0.971072665 0.981738231 0.933302822 0.970629493 1.032659232 1 20.46816168 1.248540719 24.99076695 1.016329618 0.975565274 0.429988764 0.019696643 178.6350482 447320.2421 0.013942392 0.004958038 17.72314206 -1.248540719 -0.040764344 DSDPVMAGIGEEIAHFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSDPVMAGIGEEIAHFQK 18 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ; 216.93 8.69E-19 58112000 155677 138309 137355 163697 115549 152185 164861 154660 108215 FALSE TRUE 148318.4567 152402.8443 143652.8626 147241.8666 135700.709 146914.7953 139708.4266 141117.1505 124996.4295 1.186581547 1.219257581 1.149255728 1.17796858 1.085636682 1.175351935 1.117699338 1.128969452 1 16.93152736 -4.999999994 0.092666636 0.462032096 1.290489707 0.758588488 0.030359535 86.39435154 0.553301294 9.047204897 0.58884434 1.00E-05 4.999999994 0.828457611 DSDQVAQS(ph)DGEESPAAEEQLLGEHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 DS(0.001)DQVAQS(0.997)DGEES(0.002)PAAEEQLLGEHIK 80.813 5.65E-06 0 52885 64071 40620 57385 33310 57935 40247 57439 36450 TRUE FALSE 50385.23086 70599.90774 42482.46718 51616.55078 39119.25345 55928.69642 34106.58096 52409.33666 42102.47984 1.196728341 1.676858656 1.009025296 1.225974122 0.929143689 1.328394352 0.810084848 1.244804032 1 15.36161759 3.719994549 24.98758395 1.069815388 1.436793512 0.374719195 0.192339508 653.7130204 879815.2599 0.046305525 0.071876093 5248.008729 -3.719994549 0.366978125 DSDQVAQS(ph)DGEESPAAEEQLLGEHIKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSDQVAQSDGEESPAAEEQLLGEHIKEEK 29 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 DSDQVAQS(1)DGEESPAAEEQLLGEHIKEEK 169.23 1.90E-12 30608000 47306 53199 40344 56239 23637 52240 45614 57135 16783 TRUE FALSE 45069.93913 58620.03858 42193.81231 50585.74887 27759.28532 50430.9157 38654.74654 52131.95651 19385.62192 2.324915822 3.023892595 2.176551904 2.609446788 1.43195227 2.601459778 1.99399053 2.689207327 1 14.2426994 3.196255696 1.912412338 2.067792967 2.64158643 0.173155836 0.553537945 0.536632059 4.039812652 0.158502524 0.213707371 1571.287648 -3.196255696 0.573793464 DSDYVYPSLES(ph)DEDNPIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSDYVYPSLESDEDNPIFK 19 0 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 DSDYVY(0.004)PS(0.187)LES(0.809)DEDNPIFK 68.567 0.015559 11298000 59670 57773 51942 66627 43794 63707 66804 67658 48351 TRUE FALSE 56849.51735 63660.13438 54323.59208 59929.52738 51431.65973 61500.81062 56611.82286 61733.50684 55849.02614 1.017914211 1.139861136 0.97268647 1.073063069 0.920905221 1.101197548 1.013658192 1.10536407 1 15.7692445 DSEDNPQTLLFSATCPHWVFNVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSEDNPQTLLFSATCPHWVFNVAK 24 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 315.39 1.31E-73 260400000 744400 907750 699560 848590 507180 832300 748130 868620 436380 FALSE TRUE 709213.6873 1000250.757 731635.518 763288.121 595632.0314 803477.2423 633989.0281 792559.028 504051.5817 1.407026013 1.984421423 1.45150922 1.514305577 1.181688647 1.594037736 1.257786011 1.57237683 1 18.94321185 -2.197227706 0.098719683 2.41E-08 1.990053492 0.355763152 0.213688973 82.24460307 1.08608904 23.14243858 4.434403608 0.006349979 2.197227706 1.990053468 DSEGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSEGTWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 103.29 0.019566 189550000 277970 244570 264290 263410 214060 265110 315150 275120 231610 FALSE TRUE 264830.909 269491.9611 276407.9579 236931.5264 251391.9962 255929.1742 267068.0794 251029.0343 267526.8959 0.989922557 1.007345299 1.033196894 0.885636285 0.939688682 0.95664839 0.99828497 0.938331951 1 18.02932442 3.282858858 24.999997 0.95573342 1.006662511 0.386058372 0.033713925 151.5811733 85544.76964 0.009284121 0.012570703 1918.04529 -3.282858858 0.050929091 DSEHIDDETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSEHIDDETR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 134.57 0.00016728 775470000 855660 737560 734420 901540 774920 773830 923850 863450 637670 FALSE TRUE 815214.6476 812718.2025 768093.8834 810915.4864 910065.8027 747032.0731 782899.7148 787841.7406 736556.6068 1.106791576 1.10340223 1.04281718 1.100954738 1.235568039 1.014222215 1.062918597 1.069628231 1 19.49043688 DSEHIDDETRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSEHIDDETRR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 164.65 1.46E-05 3172060000 1893590 1454910 1592930 1896060 1678330 1664050 2221960 1864250 1536990 FALSE TRUE 1804083.753 1603166.983 1665967.416 1705464.447 1971030.221 1606423.531 1882959.193 1701006.387 1775338.559 1.016191387 0.903020427 0.938394205 0.96064181 1.110227799 0.904854752 1.06061978 0.958130706 1 20.75966274 2.972247382 24.98119513 1.009060015 0.950831108 0.154817598 0.060681728 1128.652492 1015944.121 0.016635748 0.017685395 938.0962118 -2.972247382 -0.058228907 DSENLAS(ph)PSEYPENGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.999)PS(0.001)EYPENGER;DSENLAS(0.999)PS(0.001)EYPENGER;DSENLAS(0.999)PS(0.001)EYPENGER;DSENLAS(0.989)PS(0.011)EYPENGER;DSENLAS(0.996)PS(0.004)EYPENGER;DSENLAS(0.557)PS(0.443)EYPENGER;DSENLAS(1)PSEYPENGER 548.18 0 5951261000 3028969 2634273 2834897 3189389 2616869 2863046 3163595 2904987 2506358 TRUE FALSE 2885795.638 2902708.414 2964879.832 2868785.558 3073250.125 2763897.999 2680930.479 2650610.938 2895031.198 0.996809858 1.002651859 1.024127075 0.990934246 1.061560279 0.954704046 0.926045454 0.915572495 1 21.46514746 2.06456352 8.772144681 0.93932408 1.011057776 0.548056001 0.029483922 0.186003394 23.14601832 0.009940123 0.007331399 116.0281907 -2.06456352 0.071733695 DSEQVAELKQELATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSEQVAELKQELATLK 16 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 202.5 2.76E-11 175795000 444340 354790 437410 500690 340490 509260 586890 577460 405570 FALSE TRUE 423336.9288 390943.5044 457465.6812 450359.69 399871.3482 491624.1985 497349.1515 526894.5411 468463.7242 0.903670673 0.83452247 0.97652317 0.961354459 0.853580176 1.049439205 1.061659902 1.124728584 1 18.83757781 2.184361647 7.363199054 1.064437189 0.901826154 0.684118734 0.051592145 0.124632782 14.03764788 0.019286424 0.014283925 152.8838627 -2.184361647 -0.162611035 DSES(ph)PSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(1)PSQK;DSES(1)PSQK;DSES(0.997)PS(0.003)QK;DSES(0.996)PS(0.004)QK;DSES(0.872)PS(0.128)QK;DSES(0.999)PS(0.001)QK 241.13 9.36E-09 1675316000 2246409 2412350 2434747 3262780 1453427 2481449 2656310 4015980 2092180 TRUE FALSE 2140225.699 2658171.208 2546382.558 2934799.156 1706904.209 2395515.799 2251041.123 3664319.501 2416624.589 0.885626054 1.099952065 1.053693888 1.214420795 0.706317488 0.991265176 0.931481511 1.516296539 1 21.20456194 1.272162704 24.99991844 1.258149551 0.986810285 0.285226775 0.180849202 189.7883058 141202.3736 0.108336042 0.039556045 18.71383103 -1.272162704 -0.271339266 DSES(ph)PSQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSESPSQKK 9 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DS(0.248)ES(0.733)PS(0.019)QKK;DS(0.022)ES(0.967)PS(0.011)QKK;DSES(0.992)PS(0.008)QKK;DSES(1)PSQKK;DSES(1)PSQKK;DS(0.001)ES(0.907)PS(0.092)QKK 146.5 5.80E-05 823626800 1883039 1869856 1834653 2264232 859989 2081721 1963403 2707595 1100066 TRUE FALSE 1794031.478 2060396.452 1918773.655 2036627.098 1009970.809 2009630.48 1663849.812 2470503.628 1270658.617 1.41189101 1.621518498 1.510062285 1.602812172 0.794840405 1.581566011 1.309438892 1.944270156 1 20.27714505 -1.931144834 2.793587474 0.704579571 1.460311025 0.20461905 0.291670836 105960289 100320991.2 206113573.6 0.063844931 0.011718045 1.931144834 0.755731455 DSESPS(ph)QKK ddPTM_SK-BR-3_Trastuzumab_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 DS(0.002)ES(0.108)PS(0.89)QKK 80.245 0.02612 59355000 119080 115470 109100 138980 52608 132320 123980 169220 67276 TRUE FALSE 113451.3244 127236.5243 114102.3429 125009.4664 61782.81854 127737.7252 105064.574 154402.1997 77708.81848 1.459954309 1.637349876 1.468331975 1.608690864 0.795055436 1.643799606 1.352028972 1.986932793 1 16.24579071 DSETGENIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSETGENIR 9 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 169.21 0.00013642 86475000 147250 144400 123600 145920 123020 113480 117740 131980 130180 FALSE TRUE 140289.7843 159114.5242 129267.1823 131251.8444 144474.6491 109550.1591 99776.60056 120423.1315 150367.6495 0.932978501 1.058169923 0.859674156 0.872872887 0.960809386 0.728548724 0.663550976 0.800857976 1 17.19813469 2.241243868 24.98873975 0.757287472 0.9466604 0.269677263 0.10341566 62.61580277 583138.6105 0.035215727 0.028224032 174.2785221 -2.241243868 0.189372928 DSFDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 210.74 1.13E-22 4405100000 4664770 3400550 4232250 4766970 5193470 4069290 6073180 5144740 5523690 FALSE TRUE 4444275.567 3747069.911 4426302.849 4287785.119 6099209.524 3928369.467 5146604.849 4694239.292 6380275.634 0.696564823 0.587289661 0.693747904 0.672037599 0.955947654 0.615705291 0.806643027 0.735742397 1 22.60518732 -5 0.106589038 1.947509048 0.531890406 0.479007945 0.097706065 135.2511728 0.966320071 27.96850361 1.227825851 1.00E-05 5 -1.415618642 DSFIENSSSNCTSGSS(ph)KPNS(ph)PSISPSILSNTEHK ddPTM_SK-BR-3_Trastuzumab_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 DSFIENSSSNCTS(0.002)GS(0.138)S(0.859)KPNS(0.965)PS(0.033)IS(0.002)PSILSNTEHK 129.9 6.74E-08 121470000 209380 159550 186920 214710 100510 219170 222560 250580 102550 TRUE FALSE 199483.0224 175808.3264 195490.4669 193126.9429 118038.9122 211580.0879 188604.3844 228637.8868 118452.9302 1.684069967 1.484204114 1.650364128 1.630410852 0.996504788 1.786195474 1.592230636 1.930200345 1 16.85395436 DSFIENSSSNCTSGSSKPNS(ph)PSIS(ph)PSILSNTEHK ddPTM_SK-BR-3_Trastuzumab_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 DSFIENS(0.004)S(0.004)S(0.005)NCT(0.004)S(0.004)GS(0.004)S(0.005)KPNS(0.968)PS(0.004)IS(0.956)PS(0.023)ILS(0.017)NT(0.001)EHK 117.65 4.31E-06 46486000 36401 32304 32836 39107 23258 42039 42449 41038 24298 TRUE FALSE 34680.39687 35595.81433 34341.56308 35175.89006 27314.18784 40583.17889 35972.62542 37444.49516 28066.00974 1.235672516 1.268289103 1.22359977 1.253327081 0.973212369 1.445990337 1.281714991 1.334158133 1 14.77653634 DSFLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSFLKR 6 1 P46778;M0R181;Q9H553-2;Q9H553 P46778;Q9H553 RPL21;ALG2 "60S ribosomal protein L21;Alpha-1,3/1,6-mannosyltransferase ALG2" 0 ;;; 105.22 0.053178 5170780000 9079940 6711200 7070170 8208970 6449240 7867650 9712420 8753650 7309040 FALSE TRUE 8650749.231 7395078.91 7394344.288 7383788.74 7573985.414 7595191.308 8230611.948 7987134 8442488.594 1.024668157 0.875935908 0.875848893 0.874598604 0.897127112 0.899638918 0.974903532 0.946063937 1 23.00923689 1.715248099 6.674288171 0.970012707 0.91033344 0.314919591 0.045387862 0.190610215 21.03950002 0.023896445 0.012366273 51.90964976 -1.715248099 -0.059679267 DSFPWEVPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSFPWEVPKK 10 1 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 103.22 0.004559 132530000 516840 429580 517380 621290 389450 659340 792610 778310 505770 FALSE TRUE 492409.9975 473354.6904 541102.3848 558836.7488 457369.9567 636506.8905 671682.7872 710157.0503 584202.2285 0.842875931 0.810258276 0.926224445 0.956580995 0.782896631 1.089531774 1.149743624 1.215601406 1 19.15610834 2.146101706 5.667993861 1.133041933 0.862108189 0.743476135 0.072886736 0.094385135 4.654876604 0.02643686 0.01942998 139.9915127 -2.146101706 -0.270933745 DSGAALYVFSEFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGAALYVFSEFNR 14 0 Q9BQ52;Q9BQ52-4;V9GZ72 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 109.24 0.0038508 0 45369 41187 40607 43860 42058 36433 45237 43512 51327 FALSE TRUE 43224.49728 45384.00213 42468.87112 39451.10947 49392.90188 35171.31607 38335.26482 39701.85861 59286.52902 0.729077887 0.765502769 0.71633256 0.665431256 0.833121836 0.593242962 0.646610039 0.669660701 1 15.85541671 -0.971931452 5.018802154 1.000002052 0.703691092 0.666140159 0.066211962 1.54E-06 3.15E-07 0.064856164 0.015286639 0.106676448 0.971931452 -0.29631096 DSGNKPPGLLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGNKPPGLLPR 12 1 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;C9JNT3 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 138.89 6.05E-05 269420000 428980 377320 470770 534010 385490 475750 588710 533860 497060 FALSE TRUE 408702.9656 415769.337 492355.2702 480330.3002 452719.3339 459274.6582 498891.4771 487112.3882 574141.5262 0.711850558 0.724158275 0.857550356 0.836606095 0.788515224 0.799932834 0.868934669 0.848418667 1 19.13104688 1.302904975 0.039110071 1.723451798 5.45E-12 0.795111607 0.036716105 29.21851693 1.038209464 23.12209722 22.08778011 20.08653266 -1.302904975 -1.723451798 DSGREDEPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSGREDEPGSPR 12 1 Q2TAM9 Q2TAM9 TUSC1 Tumor suppressor candidate gene 1 protein 1 DSGREDEPGS(1)PR;DSGREDEPGS(1)PR 122.16 0.00022013 314920000 672140 611780 632020 721730 594560 679920 679260 650220 614000 TRUE FALSE 640369.2743 674121.0775 660998.7422 649180.3292 698251.0758 656374.1999 575626.4115 593283.2898 709215.9841 0.902925609 0.950515911 0.932013317 0.915349264 0.984539395 0.925492677 0.811637674 0.836534008 1 19.43586553 1.913341634 9.104898425 0.863144759 0.936254456 0.145278456 0.05394675 0.471311685 46.47771311 0.020289744 0.012829817 81.91088791 -1.913341634 0.073109698 DSGS(ph)DGEDDVNEQHSGSDTGSVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGSDGEDDVNEQHSGSDTGSVER 24 0 Q96ST2;Q96ST2-3;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 1 DS(0.026)GS(0.974)DGEDDVNEQHSGSDTGSVER 203.19 7.89E-25 130140000 46623 38189 43725 44710 37415 45689 49410 42458 31657 TRUE FALSE 44419.22319 42080.50252 45729.8345 40215.66586 43940.16415 44106.77847 41871.59702 38740.15244 36566.20588 1.214761612 1.150803085 1.250603758 1.099804174 1.20166047 1.206216981 1.145090009 1.059452341 1 15.15822332 1.185141282 2.113399972 1.001726247 1.184819148 0.727042545 0.040219371 0.139789123 1.111183301 0.03335663 0.009527346 15.31585626 -1.185141282 0.183092901 DSGS(ph)ISLQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 DSGS(0.975)IS(0.025)LQETR;DSGS(1)ISLQETR 203.88 2.54E-06 164020000 383370 340230 340260 409220 324840 356890 417330 393200 329200 TRUE FALSE 365248.8599 374899.8238 355861.2576 368084.4281 381491.9932 344530.8098 353658.6437 358769.3235 380250.6547 0.960547616 0.985928148 0.935859684 0.968004719 1.003264527 0.906062371 0.930067153 0.943507445 1 18.53659121 2.23622653 24.99921069 0.936936433 0.970161732 0.138176299 0.029133181 84.64561496 906577.7052 0.009684742 0.007494201 172.2766943 -2.23622653 0.0332253 DSGS(ph)QEVLSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGSQEVLSELR 12 0 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 DSGS(1)QEVLSELR 175.62 2.85E-05 42010000 117080 108740 96583 115200 74754 102510 110010 98979 82423 TRUE FALSE 111545.8604 119820.7296 101011.4261 103619.8771 87791.07393 98960.053 93225.95403 90311.87404 95204.73788 1.171641905 1.258558474 1.060991589 1.088389921 0.922129254 1.039444624 0.97921549 0.948606929 1 16.53874575 3.389261236 1.631042352 0.984794864 1.215366496 0.762996708 0.049779873 0.142166255 0.773591335 0.014389124 0.023370497 2450.536843 -3.389261236 0.230571631 DSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.047)VDS(0.84)DDES(0.113)VVK 168.59 4.49E-12 66646000 268800 298660 208310 340740 148650 280120 252440 284270 157040 TRUE FALSE 256094.3567 329093.7935 217861.2195 306488.1678 174574.5129 270419.3742 213925.6416 259377.8118 181392.9612 1.411820807 1.814258897 1.201045609 1.689636499 0.962410624 1.490793096 1.179349189 1.429922143 1 17.46875895 2.453231004 0.173294717 0.889891998 1.848812852 0.256089085 0.23792519 6.772391287 0.670904549 1.1314292 2.093450892 283.9428936 -2.453231004 0.958920854 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.002)VDS(0.996)DDES(0.002)VVKDK 185.47 4.46E-18 299910000 646830 590980 545080 814350 292910 687970 606530 685730 352370 TRUE FALSE 616255.6278 651201.5339 570072.4572 732489.9908 343993.4113 664145.4264 513992.7088 625683.8459 407013.7399 1.514090477 1.599949756 1.400622144 1.799668952 0.845164125 1.631751858 1.262838716 1.53725485 1 18.63471797 -3.538823829 0.119136516 5.92E-17 1.706596575 0.243886288 0.254659939 130.8065293 1.442298608 35.42166829 2.406779071 0.000289185 3.538823829 1.706596575 DSHGVAQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DSHGVAQVR 9 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;;;;;; 213.98 1.01E-06 5685436000 2232507 2438349 2049707 2434817 2280257 2315979 2807252 1932928 743180 FALSE TRUE 2126980.819 2686819.535 2143688.093 2190064.569 2677933.099 2235776.067 2378954.149 1763670.577 858428.5588 2.477761017 3.129927945 2.497223644 2.551248496 3.119575964 2.604498701 2.771289613 2.054533903 1 19.71133855 0.931436912 2.322167268 1.001252085 2.758533515 0.851388803 0.233686049 0.119347097 1.412199901 0.205217648 0.05585434 8.539587867 -0.931436912 1.75728143 DSIEKEHVEEISELFYDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSIEKEHVEEISELFYDAK 19 1 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;;; 148.24 5.85E-08 210507000 576890 326447 551630 500654 368818 548980 709870 645340 313328 FALSE TRUE 549621.553 359712.3204 576922.7811 450327.3087 433139.7424 529968.6849 601566.2938 588830.6084 361917.306 1.518638495 0.993907488 1.594073485 1.24428233 1.196792016 1.4643364 1.662165041 1.626975551 1 18.46530057 2.089193129 6.436876953 1.517713743 1.296356851 0.024228922 0.245667002 0.374326724 22.23349848 0.084701354 0.062194988 122.798519 -2.089193129 -0.221356892 DSIKLDDDSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSIKLDDDSER 11 1 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 184.34 4.51E-06 1898620000 4979350 3981240 4496000 5107730 3273800 5215860 5899420 5396220 3841260 FALSE TRUE 4743985.994 4386932.882 4702146.047 4594291.276 3844749.683 5035233.46 4999355.129 4923698.37 4436942.982 1.069201478 0.988728703 1.059771574 1.035463222 0.866531235 1.134842949 1.126756677 1.109705126 1 22.08113458 DSIVAELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSIVAELDR 9 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;;; 137.14 0.00040287 340349000 1197470 1195960 1029770 1194260 935540 1070720 1205750 1135960 969670 FALSE TRUE 1140867.966 1317829.684 1076985.973 1074210.716 1098697.88 1033640.698 1021790.692 1036489.32 1120041.471 1.018594396 1.17659008 0.961559014 0.959081198 0.980943928 0.922859309 0.912279338 0.925402627 1 20.09512072 3.626521454 6.537896689 0.944620907 1.097004898 0.633426661 0.046018453 0.12601034 6.45007561 0.011940776 0.01858624 4231.764136 -3.626521454 0.152383991 DSIVAELDREMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DSIVAELDREMSR 13 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;;;;;;; 176.91 1.45E-05 378564000 420035 244525.4 419568 337725 483261 374357 555496 426234 536436 FALSE TRUE 400180.778 269442.8163 438805.6078 303776.2414 567541.5654 361392.9232 470744.8828 388910.6914 619623.7551 0.645844796 0.434849074 0.708180737 0.490259192 0.91594546 0.583245752 0.759726978 0.6276562 1 19.24103293 -5 0.110893109 2.203653111 0.423819362 0.437904046 0.130900722 133.7115751 0.983719291 36.29102033 1.41171418 1.00E-05 5 -1.779833749 DSKPS(ph)STPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.133)KPS(0.289)S(0.289)T(0.289)PR;DS(0.009)KPS(0.33)S(0.33)T(0.33)PR 72.2 0.02872 7705730000 4250100 5037200 4370400 5267700 3068380 4979400 5140900 4908100 3801230 TRUE FALSE 4049206.196 5550496.407 4570787.163 4738180.788 3603504.501 4806962.129 4356561.286 4478320.745 4390705.334 0.92222226 1.26414687 1.041014328 1.079138869 0.820711987 1.094804083 0.992223562 1.019954746 1 22.06602129 2.963406768 24.99865363 0.990284948 1.089949401 0.148696055 0.106212298 990.2365955 676479.7788 0.030730538 0.032604423 919.1931269 -2.963406768 0.099664453 DSKPSS(ph)TPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.003)KPS(0.107)S(0.558)T(0.332)PR;DS(0.001)KPS(0.085)S(0.457)T(0.457)PR 75.819 0.022517 5238500000 6238600 7370800 6559900 7796100 4092200 7167000 7353600 7229000 5289700 TRUE FALSE 5943713.742 8121892.9 6860677.904 7012421.216 4805878.384 6918804.993 6231673.262 6595990.437 6109999.66 0.972784627 1.329278781 1.122860603 1.147695844 0.786559517 1.132374039 1.019913848 1.07954023 1 22.54274087 2.949050147 24.99944133 1.01188817 1.154921468 0.239414243 0.122326788 482.3601 236678.189 0.035242062 0.037380358 889.3037984 -2.949050147 0.143033298 DSKPSST(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.013)KPS(0.044)S(0.228)T(0.715)PR;DSKPS(0.029)S(0.194)T(0.777)PR;DSKPSS(0.023)T(0.976)PR;DSKPS(0.027)S(0.148)T(0.825)PR;DS(0.001)KPS(0.019)S(0.125)T(0.856)PR;DS(0.001)KPS(0.006)S(0.026)T(0.967)PR 102.53 0.020943 10059656000 9425080 10526560 9416440 11459930 6298340 10439660 10778610 10584390 8224780 TRUE FALSE 8979575.147 11599228.43 9848193.088 10307956.06 7396768.502 10078131.96 9134135.082 9657564.7 9500236.876 0.945194869 1.220940971 1.036626056 1.085020952 0.778587797 1.060829544 0.96146393 1.016560411 1 23.17953205 DSKPSSTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;; 147.74 8.36E-05 36445690000 12768850 11531690 10312810 13175420 8656780 11718360 12836730 12018440 9686190 FALSE TRUE 12165291.77 12706782.32 10785662.54 11851001.75 10166519.69 11312550.25 10878251.08 10966041.68 11188274.87 1.08732507 1.135723109 0.964014798 1.059234054 0.908676253 1.011107645 0.972290295 0.980136956 1 23.41548427 3.737592412 24.99998215 0.984679902 1.111524094 0.639207054 0.039497374 42.83806957 1106127.685 0.009223898 0.015226228 5465.028254 -3.737592412 0.126844192 DSLDPSFTHAMQLLTAEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSLDPSFTHAMQLLTAEIEK 20 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;; 296.45 1.24E-54 466500000 1267006 1404554 1140854 1529869 806000 1315521 1258371 1439389 709967 FALSE TRUE 1207117.137 1547679.649 1193163.284 1376083.662 946566.1448 1269964.178 1066383.392 1313348.468 820065.0564 1.471977288 1.887264477 1.454961744 1.678017678 1.154257382 1.54861394 1.300364385 1.601517414 1 19.64537884 -2.591477432 0.111911533 2.82E-09 1.898895323 0.414626047 0.195643548 68.96884199 0.923246559 19.83589875 2.53606511 0.002561666 2.591477432 1.898895321 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.618)S(0.382)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.615)S(0.385)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR 254.23 2.62E-59 2010550000 369316.8 359648.3 345222.3 438257.5 346913.8 373796.3 428666.9 387030.7 341269.8 TRUE FALSE 351859.9268 396296.8707 361051.0839 394203.0235 407415.4569 360851.6404 363265.8914 353140.2401 394192.1776 0.89261012 1.005339256 0.915926557 1.000027514 1.03354526 0.915420602 0.921545155 0.895858062 1 18.58853962 -0.105966623 7.22169074 0.999999997 0.949126353 0.09971585 0.04933783 5956779.601 1649691.174 0.046439083 0.011263132 0.783489853 0.105966623 -0.050873644 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.788)S(0.212)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.963)S(0.037)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.967)S(0.033)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.554)S(0.446)PEQLAAGAEEGGGPRR 262.89 8.42E-60 363416000 184292 113160 181287 155191 166037 160585 219812 189648 177049 TRUE FALSE 175580.8824 124691.1327 189599.1883 139590.9058 194993.8002 155023.9012 186275.6423 173041.4157 204504.8547 0.85856584 0.609722116 0.927113386 0.682579913 0.95349228 0.758045091 0.910861713 0.846148205 1 17.64177557 1.27599604 0.325223321 1.016676651 0.736866609 0.265645592 0.105333567 1.644346204 0.587238584 0.17634434 0.127212396 18.87974133 -1.27599604 -0.279810041 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.172)S(0.828)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.205)S(0.795)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.279)S(0.721)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.21)S(0.79)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.265)S(0.735)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.214)S(0.786)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.067)S(0.933)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.057)S(0.943)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.049)S(0.951)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.386)S(0.614)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.225)S(0.775)PEQLAAGAEEGGGPR 248.46 1.74E-47 4314686000 852818 824245 801135 980398 803254 849806 959750 912422 744720 TRUE FALSE 812506.9833 908236.5026 837867.8322 881846.5304 943341.2433 820377.0051 813322.5105 832525.4926 860207.3741 0.944547801 1.05583436 0.974030051 1.025155744 1.096643986 0.953696783 0.945495859 0.967819525 1 19.71432497 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.053)S(0.947)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.251)S(0.749)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.064)S(0.936)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.114)S(0.886)PEQLAAGAEEGGGPRR 288.32 3.33E-75 555908000 362666 245722 390603 345738 384808 348885 477848 398956 426713 TRUE FALSE 345523.4969 270761.3512 408512.5339 310983.7594 451918.3934 336803.025 404943.5113 364021.2976 492885.4727 0.701021872 0.549339281 0.82881837 0.630945274 0.916883167 0.683329178 0.821577291 0.738551485 1 18.91089293 -4.999999998 0.067830861 1.995094947 0.353939684 0.448765205 0.099452489 250.1965662 1.225807268 39.20131016 5.207027592 1.00E-05 4.999999998 -1.641155263 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ;; 185.3 1.18E-19 297529000 178353 147385 159581 175298 166345 160780 187687 166663 146977 FALSE TRUE 169922.6072 162403.6991 166897.9467 157676.712 195355.5153 155212.1483 159051.901 152069.1042 169769.4425 1.000902192 0.956613255 0.983085909 0.928769687 1.150710708 0.914252565 0.93687002 0.895738962 1 17.37321728 DSLHEKFPDAGEDELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSLHEKFPDAGEDELLK 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 79.511 0.008043 84541000 199120 192460 161750 236180 107730 197060 206090 233960 100350 FALSE TRUE 189707.9922 212071.8928 169166.3975 212438.7377 126518.0779 190235.7628 174647.1854 213473.2221 115911.7655 1.636658638 1.829597642 1.459441126 1.832762505 1.091503329 1.641211848 1.506725264 1.841687263 1 16.82266749 DSLIIIDELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSLIIIDELGR 11 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ; 155.06 7.38E-05 29861000 81308 84942 75192 91299 67465 77948 80235 83664 71101 FALSE TRUE 77464.73198 93597.68637 78639.62758 82121.45106 79230.87464 75248.64121 67993.67713 76337.93663 82126.97995 0.943231226 1.139670379 0.957537068 0.999932679 0.96473625 0.916247514 0.827909138 0.929511065 1 16.32556863 2.630286601 1.447654387 0.895731526 1.029762638 0.259536495 0.06782307 0.383409579 1.625221612 0.029318974 0.025438528 426.8611211 -2.630286601 0.134031112 DSLLDGHFVLATLSDTDS(ph)HSQDLGSPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLATLS(0.009)DT(0.061)DS(0.398)HS(0.302)QDLGS(0.23)PER 102.67 0.0018508 25743000 12290 11665 12148 13185 9710.3 11560 14584 14335 5816.3 TRUE FALSE 11709.07606 12853.67676 12704.99782 11859.61875 11403.77325 11159.6743 12358.94295 13079.75141 6718.262098 1.742872768 1.913244314 1.891113748 1.765280749 1.697429049 1.661095405 1.839604166 1.946895077 1 12.71387236 -1.051438944 4.246207074 0.999927434 1.806737816 0.881113689 0.093181268 14518468.56 26860857.32 14829.56972 0.022862009 0.088830285 1.051438944 0.806810382 DSLLDGHFVLATLSDTDSHS(ph)QDLGS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLAT(0.031)LS(0.006)DT(0.043)DS(0.158)HS(0.764)QDLGS(0.998)PER;DSLLDGHFVLAT(0.001)LSDT(0.005)DS(0.188)HS(0.807)QDLGS(1)PER 81.718 0.0026626 58247000 54068 59284 53715 62318 51226 60375 60363 60650 42425 TRUE FALSE 51512.31279 65325.107 56177.88588 56053.67624 60159.79818 58284.19861 51153.51571 55339.16447 49004.05232 1.051184756 1.333055205 1.14639266 1.143857979 1.227649456 1.189375079 1.043862972 1.129277312 1 15.58061344 1.756054231 7.776019973 1.066048011 1.188331231 0.360143839 0.077411679 0.154725424 31.05741944 0.035246798 0.019048648 57.0235474 -1.756054231 0.12228322 DSLLDGHFVLATLSDTDSHSQDLGS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLATLSDTDSHS(0.001)QDLGS(0.999)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDT(0.002)DS(0.002)HS(0.002)QDLGS(0.994)PER;DSLLDGHFVLATLSDT(0.006)DS(0.155)HS(0.345)QDLGS(0.494)PER;DSLLDGHFVLATLSDTDS(0.001)HS(0.065)QDLGS(0.934)PER;DSLLDGHFVLATLSDTDS(0.002)HS(0.093)QDLGS(0.906)PER;DSLLDGHFVLATLSDTDSHS(0.002)QDLGS(0.998)PER;DSLLDGHFVLATLSDTDSHSQDLGS(0.999)PER;DSLLDGHFVLATLSDTDSHS(0.001)QDLGS(0.999)PER;DSLLDGHFVLAT(0.043)LS(0.008)DT(0.043)DS(0.216)HS(0.124)QDLGS(0.566)PER 222.99 3.42E-34 733729000 619455 597602 595174 684893 559466 600922 643221 645883 354689 TRUE FALSE 590174.5898 658498.3232 622463.3166 616046.2544 657036.6933 580111.9205 545085.8229 589326.0605 409692.3586 1.440531114 1.6072995 1.519343243 1.503680119 1.603731872 1.415969589 1.330475933 1.438459976 1 18.64418146 0.466032795 0.497738652 0.972330327 1.542252426 0.833059079 0.070795162 0.767043404 0.338098232 0.118845072 0.036337657 2.9243732 -0.466032795 0.569922099 DSLLQDGEFSMDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;;;;;;;;;; 314.48 1.82E-55 7088759000 3789680.5 2993977.1 3239340.3 3632730.6 3748199.1 3153149.6 4008752 3668161.8 4516486.4 FALSE TRUE 3610549.813 3299066.77 3387867.257 3267561.618 4401883.836 3043955.239 3397143.257 3346958.107 5216880.044 0.692089867 0.632383099 0.64940486 0.62634402 0.843777085 0.58348193 0.651182935 0.641563172 1 22.31475583 -1.660780734 2.636362484 1.042975118 0.662908779 0.699076998 0.069055365 10566177.98 9214480.779 3067081.348 0.015449046 0.021838322 1.660780734 -0.380066339 DSLPLPVRSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSLPLPVRSR 10 1 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 0 ; 61.161 0.085171 210418000 132543 124066 115961 156819 155950 135660 160033 134188 159112 FALSE TRUE 126277.9551 136708.4665 121277.9266 141055.2562 183147.6306 130962.0602 135617.0266 122437.7873 183786.2763 0.687091319 0.743844803 0.659885651 0.767496132 0.996525063 0.712578016 0.737906167 0.666196572 1 17.48766952 -2.374130649 2.331598671 2.892785486 0.746050764 0.411685221 0.095257688 5530247.545 453570.2178 56296349.13 0.02296638 0.004225415 2.374130649 -2.146734723 DSLS(ph)PVLHPSDLILTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DSLS(1)PVLHPSDLILTR;DS(0.06)LS(0.94)PVLHPSDLILTR;DS(0.026)LS(0.974)PVLHPSDLILTR 223.18 5.77E-15 480450000 776750 560640 681880 794400 819900 648420 894420 734250 699710 TRUE FALSE 740034.5669 617769.8534 713144.8725 714545.4027 962890.3004 625965.0528 757959.8018 669955.1775 808217.4532 0.915637944 0.764360941 0.882367573 0.884100436 1.191375287 0.774500786 0.937816672 0.828929362 1 19.62438398 3.232045433 3.408159796 0.935763059 0.840555442 0.109066052 0.115877333 0.486372568 11.86053725 0.032079735 0.041793752 1706.260878 -3.232045433 -0.095207617 DSLYAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSLYAQGK 8 0 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 107.29 0.014402 0 115100 100670 89569 113560 91567 102690 128070 116870 113880 FALSE TRUE 109659.4511 110928.3875 93675.82725 102144.7331 107536.2558 99133.81955 108530.5693 106636.2432 131539.9288 0.833659043 0.84330582 0.712147468 0.776530244 0.817517972 0.753640514 0.825076996 0.810675847 1 17.00514127 0.238370632 1.24810175 1.000289038 0.7978472 0.724014155 0.039611436 3.090204758 4.501982324 0.040477485 0.011704272 1.731293235 -0.238370632 -0.202441838 DSMVMHNS(ph)DPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSMVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 50 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 DS(0.01)MVMHNS(0.99)DPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 181.6 9.12E-30 67513000 32389 19760 30635 32078 25656 34919 39110 38904 14724 TRUE FALSE 30858.03616 21773.56647 32039.64505 28853.4585 30130.39828 33709.74627 33143.0512 35497.35952 17007.32272 1.814397049 1.280246563 1.883873528 1.696531486 1.77161325 1.982072477 1.948751825 2.087180922 1 14.05386843 3.704263214 24.57385059 1.823969394 1.547321605 0.052223525 0.325576696 892.1733896 639235.79 0.077352438 0.119841336 5061.313212 -3.704263214 -0.276647789 DSNAPKS(ph)PLTGYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSNAPKSPLTGYVR 14 1 Q9NP66;H0YNS8;H0YKM5 Q9NP66 HMG20A High mobility group protein 20A 1 DSNAPKS(0.984)PLT(0.016)GYVR 104.45 0.00064017 201050000 378420 277760 300180 357480 277940 390110 450470 430250 316790 TRUE FALSE 360532.8366 306064.0598 313943.5499 321545.4312 326412.648 376600.3929 381742.5281 392575.0291 365916.1753 0.985288055 0.836432168 0.857965761 0.878740687 0.89204214 1.029198539 1.043251307 1.072855084 1 18.48115367 2.225589007 5.226819865 1.041427434 0.888852687 0.750168752 0.041944475 0.08710791 6.761436412 0.015797456 0.012092773 168.108242 -2.225589007 -0.152574747 DSNELS(ph)DS(ph)AGEEDSADLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSNELSDSAGEEDSADLKR 19 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 2 DSNELS(1)DS(1)AGEEDSADLKR;DSNELS(1)DS(1)AGEEDSADLKR 171.29 3.70E-11 228370000 898170 693990 803740 914710 513570 904090 983390 752840 562850 TRUE FALSE 855715.2841 764708.37 840592.274 822761.613 603136.4454 872781.1366 833355.7943 686917.3385 650133.9034 1.316213906 1.176232105 1.292952528 1.265526392 0.92771111 1.342463656 1.281821775 1.056578245 1 19.31037736 -4.999999986 0.160465907 0.16968149 1.279221013 0.265260708 0.123395617 190.9612817 1.757634491 50.27888008 0.497404566 1.00E-05 4.999999986 1.109539523 DSNNLCLHFNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DSNNLCLHFNPR 12 0 P09382 P09382 LGALS1 Galectin-1 0 ;;;;; 243.11 2.51E-16 5623900000 3708630 2951880 2709570 3119020 3393990 2828530 3961130 3292790 3293590 FALSE TRUE 3533330.41 3252679.928 2833806.465 2805490.184 3985900.781 2730577.297 3356786.867 3004455.851 3804343.116 0.928762286 0.854991211 0.744887193 0.737444047 1.047723788 0.717752635 0.882356498 0.789743659 1 21.85921594 -1.088961899 4.682516905 1.000008513 0.842946038 0.204088231 0.10013697 0.093325006 56932888.49 1016.731972 0.02135196 0.081477576 1.088961899 -0.157062475 DSNPEEIEIDFETLKPSTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSNPEEIEIDFETLKPSTLR 20 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 0 85.974 0.0023451 21718000 24786 21520 25705 26170 20004 23670 29535 28711 20852 FALSE TRUE 23614.4149 23712.91247 26883.59968 23539.34188 23492.69127 22850.30196 25028.8933 26196.91263 24085.62166 0.98043618 0.984525656 1.11616798 0.977319258 0.975382392 0.948711322 1.039163267 1.087657732 1 14.55588454 1.568515303 8.103914119 1.049842426 0.997052756 0.155955718 0.049148234 0.19723849 24.47597195 0.025813437 0.012096712 37.0267252 -1.568515303 -0.05278967 DSNYHLLMSVQESLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSNYHLLMSVQESLER 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 109.38 0.00097677 33604000 56124 58882 46916 49647 48640 50025 50288 58571 53750 FALSE TRUE 53471.12975 64882.14274 49067.14501 44656.38924 57122.8006 48292.62171 42615.642 53442.21274 62085.27548 0.861253 1.045048802 0.790318552 0.719275044 0.920070019 0.777843399 0.686404976 0.860787237 1 15.92196353 3.717147983 24.4168102 0.799469997 0.9531509 0.195520478 0.102833898 631.0323855 719565.7621 0.025552409 0.039631414 5213.72335 -3.717147983 0.153680904 DSPAFPDS(ph)PWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 DSPAFPDS(1)PWR 188.48 3.28E-06 42668000 115880 128520 101760 134290 99972 107000 112220 113760 92341 TRUE FALSE 110402.5821 141616.3341 106425.7967 120790.9141 117407.0851 103294.5632 95098.77794 103798.5713 106660.7707 1.035081421 1.327726522 0.997796997 1.132477417 1.100752267 0.96844006 0.891600326 0.973165398 1 16.70267013 2.267747035 3.021149535 0.93918775 1.139268048 0.431830447 0.090433414 0.204311955 3.851325827 0.035228126 0.026456032 185.2452306 -2.267747035 0.200080298 DSPCQLEALKLESCGVTSDNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSPCQLEALKLESCGVTSDNCR 22 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ; 244.78 7.02E-31 966020000 622070 406910 516200 594770 423270 566940 653040 625830 498280 FALSE TRUE 592665.9839 448374.5916 539868.2806 534982.5896 497088.154 547306.7256 553406.7541 571029.0075 575550.7175 1.029737199 0.779035762 0.938002967 0.929514243 0.863673937 0.950927015 0.961525609 0.992143681 1 19.13458354 1.749947237 1.726985329 0.993839024 0.904123194 0.233139769 0.063132565 0.484195285 2.849937889 0.044703282 0.018040592 56.22730096 -1.749947237 -0.08971583 DSPFYQHYDLDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSPFYQHYDLDLK 13 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ;;; 212.11 1.65E-08 751490000 2157740 1842580 1954100 2382650 1469300 2214760 2433350 2381790 1328470 FALSE TRUE 2055747.906 2030340.997 2043697.418 2143141.495 1725545.455 2138062.306 2062097.766 2173227.841 1534482.343 1.339701246 1.32314393 1.331848116 1.396654387 1.124513073 1.393344352 1.343839358 1.416261224 1 20.54932061 -1.167751017 5.029968262 0.999978364 1.332205051 0.628971 0.080530816 1.76E-05 2.92E-06 0.070309083 0.016570931 0.067959314 1.167751017 0.332226687 DSPSVWAAVPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 ;;; 163.16 0.0001413 507261000 1458880 1235740 1164650 1568800 1027410 1359310 1508060 1547790 1044970 FALSE TRUE 1389921.634 1361663.311 1218050.354 1411101.243 1206589.979 1312236.754 1277977.75 1412257.302 1207018.611 1.151532894 1.128121223 1.009139663 1.169079939 0.999644884 1.087171931 1.05878877 1.170037719 1 20.20301649 3.975496869 23.25964737 1.073760854 1.142753546 0.182735691 0.061414619 421.8526243 400445.7096 0.013777809 0.024903604 9451.415781 -3.975496869 0.068992692 DSQDAGGFGPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 211.67 6.05E-08 648780000 589330 558480 494530 579580 523210 523383 606660 558930 585570 FALSE TRUE 561473.5388 615389.7469 517204.6897 521319.5173 614457.6583 505258.1155 514102.8749 509987.1261 676377.2049 0.830118955 0.90983218 0.764669013 0.770752641 0.90845412 0.747006422 0.760083089 0.753998098 1 19.36746851 3.73657802 24.99713246 0.80056978 0.869975567 0.048669053 0.083960043 336.8607341 4247243.664 0.019945011 0.032676877 5452.278353 -3.73657802 0.069405788 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DSQDAS(0.007)AEQS(0.993)DHDDEVASLASASGGFGTK;DSQDAS(0.006)AEQS(0.994)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.001)AEQS(0.999)DHDDEVASLASASGGFGTK 355.14 2.55E-120 2060360000 1675760 1501640 1521950 1846310 1091570 1658220 1867300 1878190 1102850 TRUE FALSE 1596550.146 1654658.823 1591732.913 1660715.411 1281939.462 1600795.426 1582409.09 1713725.727 1273874.345 1.253302692 1.298918397 1.249521131 1.30367286 1.006331172 1.256635265 1.242201867 1.345286317 1 20.28079155 -2.296474706 2.060148884 2.78E-05 1.245026465 0.419222046 0.090432726 1713984.471 228182.2488 7979858.719 0.022695782 0.005052721 2.296474706 1.244998693 DSQDGSSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;; 160.59 0.00015164 206680000 504397 464734 491313 515393 452791 477640 530979 489566 520222 FALSE TRUE 480555.1534 512090.923 513840.187 463584.7165 531757.607 461099.207 449968.4015 446697.0057 600895.3708 0.799731828 0.852213127 0.855124223 0.771489911 0.884942093 0.767353568 0.748829868 0.743385666 1 19.19675428 2.201335315 24.9981732 0.78817563 0.830601088 0 0.07980937 480.8555303 322909.5006 0.026341594 0.019455082 158.9773724 -2.201335315 0.042425459 DSQQTLINIPSLNDSDS(ph)EIEDISEIESNR ddPTM_SK-BR-3_Trastuzumab_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(0.081)LNDS(0.397)DS(0.522)EIEDISEIESNR;DSQQTLINIPS(0.3)LNDS(0.298)DS(0.401)EIEDISEIESNR 143.83 4.46E-08 97125000 199442 172923 191621 197577 186590 193478 221762 196004 198487 TRUE FALSE 190014.7719 190544.0503 200407.0124 177716.1846 219131.2369 186777.8083 187928.134 178840.8507 229267.3502 0.828791242 0.831099806 0.874119286 0.775148247 0.955789111 0.814672513 0.819689911 0.780053725 1 17.80667139 -1.095017037 4.789913516 1.000007626 0.835146212 0.508390448 0.051015658 3.71E-06 7.01E-07 0.044119197 0.010398514 0.08034946 1.095017037 -0.164861415 DSQRDLVEAVAHILGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSQRDLVEAVAHILGIR 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 0 118.15 0.00010975 28734000 64214 39617 63712 56755 67161 65568 93780 70992 85259 FALSE TRUE 61178.73148 43654.01734 66633.25822 51049.87957 78873.85714 63297.36372 79472.13861 64775.56413 98480.53028 0.621226666 0.443275612 0.67661352 0.518375352 0.800908128 0.642739875 0.806983252 0.657749953 1 16.58755091 0.758667345 0.207598103 1.136254848 0.450037184 0.621383319 0.096290496 2.583154259 0.354966434 0.598731343 0.318101988 5.736768766 -0.758667345 -0.686217664 DSRPLS(ph)PILHIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.08)RPLS(0.92)PILHIVK 125.98 0.00011744 85815000 209430 201680 161130 217060 134970 195230 209120 210460 142380 TRUE FALSE 199530.659 222231.4213 168517.9699 195240.7164 158508.7253 188469.1361 177214.9032 192031.0067 164459.5632 1.213250571 1.351283057 1.024677231 1.187165481 0.963815799 1.145990737 1.077559126 1.16764877 1 17.32737338 3.737385329 24.99996523 1.087093715 1.282266817 0.527285548 0.079069813 66.76437191 1420177.397 0.018286491 0.030180633 5462.423017 -3.737385329 0.195173102 DSRPLS(ph)PILHIVKDESPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSRPLSPILHIVKDESPAK 19 2 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.036)RPLS(0.964)PILHIVKDESPAK 186.82 1.03E-14 46473000 106960 80244 100140 96223 60473 106410 115160 123180 68496 TRUE FALSE 101904.2128 88420.95483 104731.5181 86550.48123 71019.47205 102724.995 97590.22694 112393.7062 79118.00985 1.288002731 1.117583152 1.323738024 1.093941587 0.897639769 1.298376883 1.233476766 1.420583081 1 16.27171852 DSS(ph)TSPGDYVLSVSENSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.002)S(0.995)T(0.003)SPGDYVLSVSENSR;DS(0.003)S(0.996)TSPGDYVLSVSENSR 237.89 7.64E-24 165734000 365500 376740 289210 403130 241580 360950 345780 355870 230790 TRUE FALSE 348223.5394 415130.2343 302470.5646 362606.6065 283711.4755 348450.211 293024.9103 324708.1362 266579.7345 1.306264109 1.557246034 1.134634503 1.3602182 1.064264979 1.307114405 1.099201749 1.218052591 1 18.02420758 2.94564454 0.272387878 1.004255669 1.536634456 0.393784393 0.127795714 2.742229051 0.386874772 0.181749785 0.485519748 882.3574149 -2.94564454 0.532378786 DSS(ph)VEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSVEVR 7 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 1 DS(0.009)S(0.991)VEVR;DS(0.01)S(0.99)VEVR 166.52 0.0011754 283630000 915240 748270 758040 948590 697980 843440 955060 862360 716490 TRUE FALSE 871978.419 824519.5637 792796.8838 853235.931 819707.491 814231.4613 809348.0561 786847.1867 827599.6099 1.053623526 0.996278338 0.957947387 1.03097672 0.990463844 0.983847082 0.977946396 0.950758286 1 19.65857344 7.999998224 0.59403567 0.98173162 5.563302795 0.474536362 0.02228298 129.7680162 1.022770457 0.009132093 770.3628474 99999591 -7.999998224 4.581571175 DSSDSADGRAT(ph)PSENLVPSSAR ddPTM_SK-BR-3_Trastuzumab_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 DSSDSADGRAT(0.999)PS(0.001)ENLVPSSAR;DSSDSADGRAT(0.998)PS(0.001)ENLVPSSAR;DSSDS(0.01)ADGRAT(0.934)PS(0.056)ENLVPSSAR 167.27 1.74E-11 1283310000 1209010 957600 1118150 1099730 1000330 1030180 1216820 1106610 1016460 TRUE FALSE 1151862.493 1055180.529 1169418.284 989183.051 1174787.235 994504.6083 1031171.761 1009709.362 1174087.425 0.981070462 0.898723984 0.996023174 0.842512261 1.000596046 0.847044766 0.878275108 0.85999504 1 20.16310841 2.221550584 24.99764009 0.883939648 0.938801203 0.108121222 0.062533612 417.5099581 613561.3336 0.020423709 0.015121362 166.5522806 -2.221550584 0.054861555 DSSFFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSSFFDK 7 0 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ;; 99.375 0.024601 289740000 514038 528898 427321 558365 351299 465108 472131 504711 316834 FALSE TRUE 489740.4425 582793.3075 446914.0905 502237.0894 412565.4344 449001.1933 400098.7447 460515.8292 365966.9986 1.338209304 1.592475031 1.221186862 1.372356227 1.127329612 1.226889843 1.093264546 1.258353434 1 18.48135403 3.075416494 1.097004623 1.137766954 1.45568312 0.523046253 0.113607365 0.325347743 0.842002408 0.044411681 0.058473473 1189.642562 -3.075416494 0.317916166 DSSFFDKFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSFFDKFFK 10 1 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 174.1 2.93E-06 1259690000 4658000 3287400 3962300 4368600 3708900 4543800 6590800 5218600 4652600 FALSE TRUE 4437825.571 3622389.797 4143975.374 3929460.028 4355730.986 4386447.067 5585252.412 4761631.718 5374101.446 0.825780015 0.674045668 0.77110107 0.731184565 0.81050405 0.816219625 1.039290469 0.886033092 1 22.35759212 1.935714434 3.451403311 0.975404059 0.756868824 0.74426641 0.056714319 0.110970988 2.431081613 0.02607745 0.014767093 86.24112912 -1.935714434 -0.218535234 DSSFTEVPRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DSSFTEVPRS(1)PK 83.27 0.0078085 287520000 708740 555990 609720 663300 402690 654970 669700 697910 491000 TRUE FALSE 675239.2648 612646.0131 637676.2651 596623.8238 472919.0085 632288.2247 567524.9651 636797.3005 567141.7723 1.190600477 1.080234331 1.124368361 1.051983566 0.833863827 1.11486802 1.000675656 1.122818547 1 19.1133499 3.796294883 1.128375057 1.02036302 1.169416715 0.285003661 0.083059732 0.701852877 1.649637637 0.026488249 0.08359951 6255.973248 -3.796294883 0.149053695 DSSGQHVDVSPTSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSGQHVDVSPTSQR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 117.13 0.00039408 888930000 955820 663300 807090 820460 894950 659220 866810 818150 786640 FALSE TRUE 910640.2829 730891.0241 844095.8748 737985.802 1051028.997 636391.0461 734562.2144 746508.4487 908628.1136 1.002214514 0.804389621 0.928978382 0.812197852 1.156720754 0.7003867 0.808429987 0.821577538 1 19.79333042 DSSPSSSPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSSPSSSPSPK 11 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSSPS(0.003)S(0.001)S(0.011)PS(0.984)PK;DSSPSSS(0.001)PS(0.998)PK;DSSPS(0.001)S(0.018)S(0.018)PS(0.963)PK 168.61 1.87E-05 162256000 531980 465810 424910 640840 264432 566260 474050 545520 280129 TRUE FALSE 506834.3597 513276.5686 444392.5438 576421.5457 310548.8571 546650.2742 401724.966 497751.3768 323569.9746 1.566382543 1.586292329 1.373404761 1.781443245 0.959757955 1.689434487 1.24153969 1.538311388 1 18.30371821 -3.426758414 0.130492707 8.32E-12 1.695936253 0.297671282 0.231767583 98.05776153 1.207111334 28.73385559 1.639617831 0.000374319 3.426758414 1.695936253 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 43 3 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 171.03 1.89E-20 593600000 885670 626930 865110 780590 724520 874980 1160780 983160 896390 FALSE TRUE 843806.1343 690814.8798 904776.1492 702123.6102 850876.0586 844679.2232 983681.6918 897069.2983 1035397.583 0.814958571 0.667197694 0.873844177 0.678119808 0.821786792 0.815801811 0.950052142 0.866400804 1 19.98175342 1.896278727 1.093148522 0.959634787 0.753377651 0.552580461 0.069295305 0.328642122 0.722351606 0.050168176 0.02181336 78.75510718 -1.896278727 -0.206257137 DSSSEKDGRS(ph)PNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSSEKDGRSPNKR 14 3 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 DS(0.001)S(0.001)S(0.001)EKDGRS(0.998)PNKR;DSSSEKDGRS(1)PNKR 95.197 0.021351 215850000 217393 159948 207037 222990 123026 234810 259560 248180 132696 TRUE FALSE 207117.2637 176246.883 216529.8512 200574.6215 144481.6954 226678.4708 219959.3549 226448.0435 153273.818 1.351289258 1.149882513 1.412699534 1.308603284 0.942637806 1.478911884 1.435074547 1.477408513 1 17.22575175 DSSSLSSCTSGILEERS(ph)PAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSSLSSCTSGILEERSPAFR 21 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR 286.85 8.73E-46 202627000 148681 151508 142826 166420 132845 122219 131103 143539 121780 TRUE FALSE 141653.1438 166946.8375 149374.7134 149691.1454 156013.1259 117986.5254 111100.8295 130969.9642 140665.0204 1.007024656 1.186839748 1.061917973 1.064167516 1.109111032 0.838776584 0.789825567 0.931076993 1 17.10190409 2.239295996 24.99995326 0.862356377 1.090356239 0.633167694 0.072712969 10.23380515 347923.7208 0.024695182 0.019530247 173.4986084 -2.239295996 0.227999863 DSSSLSSCTSGILEERS(ph)PAFRGPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSSSLSSCTSGILEERSPAFRGPDR 25 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR 280.17 1.63E-53 917396000 365195 264860 360504 359559 392743 318996 454214 398212 488538 TRUE FALSE 347932.9561 291849.5351 377033.465 323415.4462 461237.2549 307949.0885 384915.3121 363342.4462 564297.9779 0.616576649 0.517190468 0.66814605 0.573128841 0.817364713 0.545720702 0.682113577 0.643884012 1 19.10609765 -5 0.211580569 2.818894154 0.572343836 0.669430121 0.081840311 79.74815584 0.795253207 61.53814151 0.154265173 1.00E-05 5 -2.246550317 DSST(ph)PYQEIAAVPSAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSSTPYQEIAAVPSAGR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 DS(0.028)S(0.194)T(0.777)PY(0.001)QEIAAVPSAGR;DS(0.002)S(0.103)T(0.895)PYQEIAAVPSAGR 127.83 0.00043538 105105000 144205 130479 129699 165881 128476 129438 163319 144307 159991 TRUE FALSE 137388.7154 143774.9584 135645.8274 149206.3267 150882.1737 124955.5296 138401.687 131670.7141 184801.5872 0.743439045 0.77799634 0.734007914 0.807386609 0.816454967 0.676160479 0.748920446 0.712497745 1 17.49561762 -1.495610885 3.24400299 1.005689177 0.753218029 0.777527609 0.041668326 13788383.85 17350473.94 700317.3911 0.009664865 0.031943987 1.495610885 -0.252471148 DSTAPQRVPVASPS(ph)AHNISSSGGAPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSTAPQRVPVASPSAHNISSSGGAPDR 27 1 Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 DS(0.069)T(0.069)APQRVPVAS(0.361)PS(0.501)AHNISSSGGAPDR;DS(0.001)T(0.001)APQRVPVAS(0.168)PS(0.829)AHNISSSGGAPDR 138.15 3.89E-06 280050000 101656 49740 103002 75423 107761 89080 139584 108873 137911 TRUE FALSE 96850.92234 54808.56255 107724.7436 67841.33675 126554.4843 85995.13726 118287.8972 99339.50295 159297.5335 0.607987583 0.3440641 0.67624866 0.425878137 0.794453508 0.539839729 0.742559502 0.6236098 1 17.2813644 -0.469741761 0.195716227 1.284291087 0.418881325 0.538286698 0.12611641 9.116760973 0.513299687 1.91727135 0.384518496 0.339045698 0.469741761 -0.865409763 DSTFDLPADSIAPFHICYYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSTFDLPADSIAPFHICYYGR 21 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ; 209.45 2.58E-22 87930000 107850 92554 96284 114344 94415 100578 109383 111815 90623 FALSE TRUE 102752.1442 101985.3578 100698.7166 102849.9239 110880.9461 97094.95864 92694.61439 102023.8858 104676.352 0.98161755 0.974292243 0.962000631 0.982551664 1.059274077 0.927573008 0.885535392 0.974660311 1 16.67557603 DSTLIMQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 223.19 1.06E-08 731778000 683625 670473 395391 564483 548719 465303 622038 564067 441378 FALSE TRUE 651311.4011 738794.961 413520.0684 507740.0964 644415.4199 449189.4404 527134.6786 514674.3032 509824.646 1.27752043 1.449115822 0.811102546 0.995911242 1.263994248 0.881066547 1.033952914 1.009512402 1 18.95964159 3.749502297 24.99968202 1.005884894 1.363318144 0.602412116 0.122835863 426.4564274 974370.3581 0.029849014 0.053149199 5616.972487 -3.749502297 0.35743325 DSVLS(ph)YTSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSVLSYTSVR 10 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 DSVLS(0.998)YT(0.002)SVR;DSVLS(0.874)YT(0.126)SVR 149.49 2.44E-05 101809000 153219 175082 154444 190411 139600 180082 178442 177595 135197 TRUE FALSE 145976.6415 192923.0549 161525.4102 171270.5245 163946.1958 173845.7152 151217.3956 162043.8403 156162.6603 0.93477302 1.235398107 1.034340795 1.096744409 1.049842488 1.113234847 0.968332605 1.037660604 1 17.25269001 1.741061388 15.58594078 1.002569366 1.082678948 0.176749897 0.076126095 0.109614159 374.3178574 0.033464163 0.018479013 55.08855586 -1.741061388 0.080109583 DSWLDNIDWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSWLDNIDWVK 11 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 96.113 0.0073081 0 159930 142660 139170 169530 134540 141560 175860 139180 108180 FALSE TRUE 152370.4259 157197.2162 145551.0822 152488.5223 158003.7334 136657.7417 149029.3271 126992.6614 124956.0019 1.219392615 1.258020534 1.164818656 1.220337719 1.264474943 1.093646881 1.192654413 1.016299013 1 16.93106067 1.337875968 0.974246631 0.991032427 1.224616797 0.717653609 0.049915896 0.239108343 0.470453043 0.041641874 0.014838475 21.77087919 -1.337875968 0.23358437 DSYCSYMGHFDLLNYFAIAENESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DSYCSYMGHFDLLNYFAIAENESK 24 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ;; 282.18 2.58E-52 199339000 506077 406246 436791 553136 386422 501897 637505 582872 382580 FALSE TRUE 482155.7432 447642.9293 456818.2994 497533.7184 453813.8745 484516.181 540241.9037 531832.6377 441908.5525 1.091075836 1.012976388 1.03373944 1.125874835 1.026940692 1.096417298 1.222519683 1.203490258 1 18.75338833 1.968272155 7.685956702 1.165253153 1.05724606 0.219212459 0.067772629 0.252366538 52.24825347 0.025471266 0.016388264 92.95487163 -1.968272155 -0.108007093 DSYESYGNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 278.02 1.42E-23 6247080000 2851154 2386694 2336026 2695477 2414008 2580435 2897311 2629076 2628291 FALSE TRUE 2716385.601 2629900.832 2443135.103 2424522.531 2835010.231 2491073.889 2455272.994 2398860.168 3035872.945 0.89476261 0.866274999 0.804755386 0.798624506 0.933836917 0.820546161 0.808753541 0.790171464 1 21.53367998 3.987104578 6.015580065 0.840180566 0.884640298 0.02003506 0.067723623 0.39888076 59.80745388 0.015603763 0.030685576 9707.436946 -3.987104578 0.044459732 DSYGGPPRREPLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSYGGPPRREPLPSR 15 2 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 ;;; 105.39 0.00074169 362274000 299290 225190 277871 280806 267334 306100 383795 331250 351253 FALSE TRUE 285143.1548 248137.117 290611.6602 252578.8474 313956.965 295499.6802 325240.0239 302243.9939 405723.5213 0.702801637 0.611591648 0.71628004 0.622539326 0.773819975 0.728327703 0.801629698 0.744950633 1 18.63013742 0.132941091 0.284681872 1.08688677 0.635108323 0.810945055 0.046905933 1.897156459 0.260418106 0.249017593 0.060652638 1.358129215 -0.132941091 -0.451778447 DSYLILETLPTEYDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DSYLILETLPTEYDSR 16 0 P17980;E9PM69;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 186.17 3.59E-09 146169000 275785 249586 236703 299578 230673 249097 281519 274781 240381 FALSE TRUE 262749.1896 275019.0972 247556.0667 269463.8503 270902.2982 240470.7084 238568.1061 250719.7189 277658.0578 0.946304932 0.990495645 0.891586107 0.970488134 0.975668779 0.866067819 0.859215497 0.902980165 1 18.08294974 2.241441071 24.99893671 0.89041879 0.956809177 0.166845035 0.046873845 83.36252182 723496.2478 0.015310716 0.012281539 174.3576759 -2.241441071 0.066390387 DSYS(ph)SSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSYSSSR 7 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" 1 DS(0.004)YS(0.476)S(0.476)S(0.044)R;DSYS(0.986)S(0.013)S(0.001)R 114.89 0.0060865 367430000 331900 280030 297640 343790 313430 314370 350800 369840 387300 TRUE FALSE 316211.7448 308565.3754 311287.0884 309231.576 368092.0928 303483.2881 297279.0171 337454.849 447360.5059 0.706838759 0.689746572 0.695830509 0.691235753 0.822808647 0.678386411 0.664517795 0.754324185 1 18.77107837 0.89280114 6.500409398 0.999998486 0.705016061 0.817853785 0.043126299 0.760918624 46.00902622 0.040398553 0.010142892 7.812699856 -0.89280114 -0.294982425 DSYSECNSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSYSECNSNR 10 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 96.342 0.015833 25446000 30004 33788 33612 35028 36283 30415 38551 32477 38650 FALSE TRUE 28585.77038 37231.03561 35153.14345 31506.91889 42610.74371 29361.72092 32669.33691 29633.14171 44643.6446 0.640309962 0.833960487 0.787416524 0.705742534 0.954463823 0.657690948 0.731780239 0.663770666 1 15.44616719 -2.187743024 2.39842633 1.70739146 0.749208801 0.414131752 0.094574796 6910764.022 901140.9024 26783224.24 0.021218176 0.006490184 2.187743024 -0.958182659 DSYSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DSYSSSR 7 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" 0 150.17 0.0045767 302840000 330430 298100 297920 368820 350370 306740 357600 337720 361920 FALSE TRUE 314811.2287 328476.7289 311579.9267 331745.5129 411474.4171 296117.5169 303041.5522 308147.4464 418044.7052 0.753056371 0.785745459 0.74532681 0.79356468 0.984283288 0.708339355 0.724902262 0.737116013 1 18.6732977 -2.094872914 2.39275526 1.376782733 0.776619202 0.445641729 0.077406944 7777377.2 2511644.272 15941153.91 0.0182835 0.008037613 2.094872914 -0.600163531 DSYVGDEAQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 9160020000 10498440 10334380 8622430 11398950 6340170 10017080 10208550 10328170 6440820 FALSE TRUE 10002199.55 11387465.07 9017776.944 10253105.89 7445893.641 9670186.008 8651048.205 9423780.682 7439629.47 1.344448616 1.530649492 1.21212716 1.378174267 1.000842 1.299820918 1.162833208 1.266700273 1 22.82679934 6.026964215 0.112794467 0.879950928 2.17754536 0.416163577 0.124816642 52.36889836 0.65812548 1.17406024 10.41998381 1064055.338 -6.026964215 1.297594432 DSYVGDEAQSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 220.53 4.70E-11 1.70236E+11 74304027 51842586 67722229 66994444 51167719 69185757 82020898 75487554 62899522 FALSE TRUE 70791822.9 57125404.45 70827360.19 60260035.21 60091352.99 66789836.89 69507103.59 68877463.59 72653658.63 0.97437382 0.786270169 0.974862953 0.829415013 0.827093282 0.919290758 0.956691031 0.948024709 1 26.11453211 1.885425135 3.044308829 0.964584205 0.876589769 0.303493849 0.061431932 0.319287845 5.186841514 0.030314583 0.016037691 76.81130353 -1.885425135 -0.087994436 DSYYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DSYYDR 6 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 114.19 0.059325 888350000 1532500 1232050 1243440 1590550 1382370 1322480 1635620 1425240 1575630 FALSE TRUE 1460061.762 1357597.296 1300452.954 1430664.892 1623454.89 1276682.186 1386076.129 1300438.43 1819970.653 0.802244673 0.745944608 0.714546112 0.786092287 0.892022565 0.70148504 0.761592571 0.714538132 1 20.79548376 -2.203027611 2.379053441 1.714126484 0.765183085 0.641573919 0.05524539 4295419.593 749932.8101 16576675.18 0.01318613 0.00626574 2.203027611 -0.9489434 DT(ph)HEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.167)HEDHDT(0.167)S(0.167)T(0.167)ENT(0.167)DES(0.167)NHDPQFEPIVSLPEQEIK 121.41 7.75E-08 112910000 47940 54706 54603 66024 43393 61095 78873 59130 12629 TRUE FALSE 45673.97121 60280.6036 57106.60156 59387.14208 50960.72546 58979.26483 66839.47525 53952.26373 14587.44082 3.131047575 4.132363198 3.914778628 4.071114517 3.49346579 4.043153666 4.581987757 3.698542081 1 13.83243918 0.95427617 23.52265912 0.999999996 3.925309382 0.848442493 0.383940937 2340.553701 1204101.046 0.38631579 0.096578947 9.000697594 -0.95427617 2.925309386 DTAAVVS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DTAAVVSR 8 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DTAAVVS(1)R;DTAAVVS(1)R;DTAAVVS(1)R;DTAAVVS(1)R;DTAAVVS(1)R 116.12 0.0024477 1160803000 1466110 1266780 1327510 1628590 1535040 1275570 1543390 1376010 1680450 TRUE FALSE 1396809.886 1395866.322 1388377.647 1464881.039 1802750.49 1231396.691 1307917.509 1255519.27 1941045.603 0.719617243 0.719131132 0.715273069 0.754686565 0.928752259 0.63439864 0.673821113 0.646826261 1 20.88840258 -2.336034302 2.279271126 2.619079398 0.722472482 0.532060687 0.081313221 3151267.2 596333.8224 26090362.14 0.019310679 0.004612811 2.336034302 -1.896606916 DTAAWTVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTAAWTVGR 9 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 128 0.00099985 250490000 184610 179920 231950 234440 173940 213900 238670 129590 125860 FALSE TRUE 175883.8512 198254.0526 242585.1369 210873.6458 204275.0809 206492.5894 202256.508 118242.4126 145377.726 1.209840434 1.363716836 1.668654089 1.450522385 1.40513328 1.420386706 1.391248258 0.813346142 1 17.14944672 1.246186385 24.98641025 0.906673032 1.40565942 0.7570033 0.119781218 76.91168426 252013.0213 0.087328385 0.030543909 17.62732393 -1.246186385 0.498986388 DTASLSTTPSES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTASLSTTPSESPR 14 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 DTASLSTTPS(0.001)ES(0.999)PR 121.13 0.00012208 127710000 274400 229510 274190 265020 243690 314850 317130 311860 306090 TRUE FALSE 261429.6558 252897.3299 286761.8827 238379.6861 286189.4588 303946.6656 268745.994 284551.8851 353556.8739 0.739427445 0.71529462 0.811077096 0.674232927 0.809458053 0.859682523 0.76012097 0.804826341 1 18.43158278 -4.999999999 0.15675767 1.877727899 0.69830896 0.712181158 0.047976491 67.00499019 0.610062309 18.19921211 0.199187168 1.00E-05 4.999999999 -1.17941894 DTCVQS(ph)PISSFPCTDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTCVQSPISSFPCTDLK 17 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 DTCVQS(0.65)PIS(0.317)S(0.032)FPCTDLK;DTCVQS(0.718)PIS(0.195)S(0.087)FPCTDLK;DTCVQS(1)PISSFPCTDLK;DTCVQS(0.427)PIS(0.427)S(0.147)FPCTDLK 268.7 5.18E-28 666170000 1598360 1462390 1327260 1653280 963810 1568350 1570810 1698380 1034290 TRUE FALSE 1522808.69 1611409.204 1388116.184 1487089.153 1131898.159 1514037.646 1331154.085 1549660.844 1194682.411 1.274655655 1.348818053 1.161912297 1.244756883 0.94744691 1.267313918 1.114232597 1.297132049 1 20.18819572 3.726181904 20.94043153 1.152966839 1.311736831 0.271013585 0.111680082 92.88437239 157128.5838 0.026276873 0.04120012 5323.311793 -3.726181904 0.158769992 DTDFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DTDFEHR 7 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;;; 163.67 0.0012263 1953420000 3597070 3128760 3296210 3706770 3261980 3474820 3935840 3697570 3320340 FALSE TRUE 3427043.63 3447584.201 3447344.489 3334158.437 3830868.279 3354486.112 3335355.321 3373791.169 3835241.369 0.89356661 0.898922354 0.898859852 0.869347745 0.998859761 0.874647979 0.869659821 0.879681575 1 21.87088595 2.085021194 0.00718682 1.813186312 2.06E-06 0.177018473 0.044808702 6587.413678 32.99855408 4124.950913 4197.229818 121.6245353 -2.085021194 -1.813184257 DTDIVDEAIYYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTDIVDEAIYYFK 13 0 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 172.34 5.48E-05 30746000 92806 107514 80552 103385 59473 82114 75181 98135 51922 FALSE TRUE 88419.2443 118469.7988 84245.38888 92992.54338 69845.07237 79270.37159 63710.75766 89541.77915 59973.79858 1.474297883 1.975359268 1.404703235 1.550552834 1.164593106 1.321750055 1.062309861 1.493014971 1 15.87204473 3.061983447 1.453926089 1.202076901 1.706732937 0.486948936 0.199882079 0.280388632 1.228773409 0.067353626 0.084583495 1153.409296 -3.061983447 0.504656036 DTDSEEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 162.25 0.0021707 742390000 2134360 2858810 896990 3250890 1281570 1567770 1315540 1601750 957550 FALSE TRUE 2033473.033 3150125.989 938117.8787 2924104.361 1505075.402 1513477.732 1114830.211 1461492.279 1106041.964 1.838513456 2.848107118 0.848175666 2.643755352 1.360776039 1.368372794 1.007945673 1.321371455 1 20.07697469 2.544238641 0.860710859 1.036684531 2.193580581 0.331367253 0.556290585 0.580599056 0.880268473 0.34861351 0.266431405 350.1375119 -2.544238641 1.15689605 DTDSEEEIREAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;; 322.81 2.95E-51 11277980000 9494330 8222880 4543580 11244060 6731530 6757250 7227190 7439810 5132580 FALSE TRUE 9045551.837 9060800.821 4751907.637 10113785.73 7905506.701 6523244.738 6124549.429 6788340.795 5928514.293 1.525770436 1.528342578 0.801534314 1.705956202 1.333471813 1.100316946 1.033066486 1.145032374 1 22.49923917 4.589038789 0.218050187 0.936401375 2.04142058 0.275767342 0.239336861 13.15109141 0.597471968 0.429364845 3.979961262 38818.50353 -4.589038789 1.105019206 DTDSEEEIREAFRVFDKDGNGYISAAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTDSEEEIREAFRVFDKDGNGYISAAELR 29 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;; 197.89 1.78E-25 236127000 266653.9 239613 292360 256574.4 218887 273638.7 301937 285899 246985.3 FALSE TRUE 254049.6986 264029.8371 305764.9952 230783.0539 257060.8235 264162.5232 255870.9652 260864.1679 285286.5189 0.890507198 0.925490059 1.071782138 0.808951838 0.901061938 0.925955156 0.896891189 0.914393603 1 18.12205205 -1.557812159 7.383516661 1.00004565 0.915987238 0.141711259 0.064254258 4.43E-05 2.66E-06 0.057138886 0.013460459 0.027681387 1.557812159 -0.084058413 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK 201.6 9.13E-23 819575000 836774 590455 810935 849715 440790 949720 1024402 1057936 486778 TRUE FALSE 797221.3513 650623.0358 848117.1719 764300.0338 517663.6364 916830.9583 868110.6605 965297.5154 562265.0461 1.417874643 1.15714651 1.508393911 1.359323399 0.920675471 1.630602799 1.543952743 1.716801573 1 19.10089084 DTERVSLPEEPPTAPPQNVIASGRTNQSIMIQWQPPPESHQNGILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTERVSLPEEPPTAPPQNVIASGRTNQSIMIQWQPPPESHQNGILK 46 2 Q58EX2-2;Q58EX2-3;Q58EX2;Q58EX2-4 Q58EX2-2 SDK2 Protein sidekick-2 0 14.661 0.092374 471030000 813800 310860 1044400 546430 411050 965060 1328300 960730 105560 FALSE TRUE 775333.2868 342536.9874 1092286.773 491501.8183 482736.9899 931639.7302 1125643.439 876603.388 121929.7057 6.358854739 2.809298895 8.958331909 4.031026037 3.959141763 7.640793727 9.231904833 7.189416092 1 16.89569013 2.225794192 24.71075986 7.220464924 5.112951038 0 2.729786381 406.6031232 787017.0923 0.929035384 0.69074657 168.1876845 -2.225794192 -2.107513886 DTFFKDVDYVCISDNYWLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTFFKDVDYVCISDNYWLGK 20 1 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 127.5 1.95E-05 12312000 22216 9243.7 22532 17377 19827 20748 37346 26114 28174 FALSE TRUE 21165.89371 10185.64354 23565.11449 15630.23095 23284.82252 20029.49156 31648.18179 23827.31972 32543.08003 0.650396142 0.312989537 0.724120595 0.480293535 0.715507644 0.61547621 0.972501121 0.732177769 1 14.99006318 2.021778 0.733081999 0.959812333 0.502340558 0.535986848 0.138625197 0.439528497 0.448081863 0.109783268 0.060139209 105.1424276 -2.021778 -0.457471776 DTFNHLTTWLEDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTFNHLTTWLEDAR 14 0 P61019;P61019-2;E9PKL7;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ; 166.92 3.73E-06 162400000 241180 202053 226741 302010 269630 233456 244670 238768 223083 FALSE TRUE 229779.8994 222642.4304 237137.2991 271651.381 316653.3866 225371.3602 207341.0978 217860.2081 257677.5723 0.891734183 0.864034958 0.920286919 1.054229821 1.228874457 0.874625441 0.804653257 0.845476019 1 17.97520745 -1.067482285 4.782660736 1.000002549 0.926507803 0.021805615 0.123376446 3.55E-06 6.92E-07 0.126419693 0.029796374 0.085608663 1.067482285 -0.073494746 DTGIFLDLMHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTGIFLDLMHLK 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 182.08 1.73E-05 1128824100 4819526 4457478 3546052 4260515 3640405 3983249 5214900 4890222 3368017 FALSE TRUE 4591716.557 4911700.076 3708641.992 3832239.938 4275290.479 3845308.088 4419271.227 4462008.237 3890311.875 1.180295232 1.262546612 0.953301974 0.985072678 1.098958288 0.988431831 1.135968367 1.146953864 1 21.89145439 3.750650667 24.94958249 1.051256177 1.221420931 0.532995802 0.068752153 542.6156311 1119763.581 0.01770894 0.031618651 5631.844659 -3.750650667 0.170164754 DTGKTPVEPEVAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;;;;;;; 218.78 1.14E-12 6414675000 12969840 9145960 12272160 12402830 11031900 12438880 16450380 13558930 12498070 FALSE TRUE 12356781.37 10077943.72 12834850.67 11156073.96 12955859.87 12008118.47 13940572.4 12371638.21 14436206.86 0.855957627 0.698101919 0.889073619 0.772784296 0.897455958 0.831805652 0.965667265 0.856986764 1 23.78318839 1.881315488 0.473213683 0.989486084 0.777606617 0.446245005 0.064476356 0.715578609 0.376471242 0.059960608 0.046366941 76.08788069 -1.881315488 -0.211879467 DTGQLYAALHHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTGQLYAALHHR 12 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EIJ4 Q9H6Z4 RANBP3 Ran-binding protein 3 0 81.92 0.009454 80145000 89281 74413 73529 87885 77128 69703 92758 76881 15776 FALSE TRUE 85060.86407 81995.7693 76900.37738 79050.63283 90579.09878 67289.16763 78606.06348 70148.89207 18222.46151 4.667912951 4.49970874 4.220087245 4.338087519 4.970738928 3.692649734 4.313690741 3.84958377 1 14.15343023 -0.738138572 0.43069991 1.03E-14 4.550869466 0.923907183 0.304881437 2.62056509 0.386127119 3.819294951 0.161024261 0.182751701 0.738138572 4.550869466 DTGSEVPSGSGHGPCT(ph)PPPAPANFEDVAPTGSGEPGAT(ph)RESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTGSEVPSGSGHGPCTPPPAPANFEDVAPTGSGEPGATRESPK 43 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 2 DTGSEVPS(0.005)GS(0.006)GHGPCT(0.989)PPPAPANFEDVAPT(0.028)GS(0.026)GEPGAT(0.53)RES(0.415)PK 70.247 0.0019626 41652000 30726 24801 25017 32455 16049 25537 24768 31594 16792 TRUE FALSE 29273.64287 27328.2501 26164.0542 29192.56174 18847.94052 24652.64729 20989.1867 28827.46187 19396.0176 1.509260482 1.408961915 1.348939496 1.505080184 0.971742804 1.271015927 1.08213898 1.486256739 1 14.24347285 2.757090708 24.99301351 1.16918525 1.439504036 0.461216441 0.150698016 697.2111971 940383.2365 0.041113129 0.043532587 571.59801 -2.757090708 0.270318785 DTHDQLSEPSEVR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 180.11 1.32E-05 3045060000 1749400 1671610 1640730 1957790 1695890 1745450 1958470 1628210 919990 FALSE TRUE 1666709.329 1841948.959 1715959.093 1760989.23 1991652.679 1685004.629 1659669.432 1485635.301 1062657.351 1.568435327 1.733342322 1.614781183 1.657156212 1.874219077 1.585651883 1.561810522 1.398037947 1 20.01924505 0.910004795 1.19074676 1.002044957 1.677662998 0.864214669 0.085236084 0.190762588 0.542141299 0.076788067 0.023881527 8.128394905 -0.910004795 0.675618041 DTHEDHDTST(ph)ENT(ph)DESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 2 DT(0.008)HEDHDT(0.336)S(0.456)T(0.488)ENT(0.703)DES(0.009)NHDPQFEPIVSLPEQEIK 202.8 3.16E-27 93386000 56863 66587 68476 76108 48482 77973 87722 69134 33260 TRUE FALSE 54175.19868 73372.291 71615.69233 68457.47924 56937.24545 75272.77546 74338.39777 63080.26046 38417.79093 1.410159131 1.9098519 1.864128327 1.781921281 1.482054123 1.959320763 1.93499928 1.64195439 1 15.22948694 0.968156672 22.15739334 0.999999995 1.768344618 0.626658911 0.183753432 609.9482074 424418.6638 0.177098913 0.044274728 9.293015718 -0.968156672 0.768344623 DTHEDHDTST(ph)ENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.001)HEDHDT(0.306)S(0.306)T(0.387)ENT(0.001)DESNHDPQFEPIVSLPEQEIK;DT(0.001)HEDHDT(0.274)S(0.274)T(0.325)ENT(0.052)DES(0.073)NHDPQFEPIVSLPEQEIK 278.3 1.30E-73 328390000 416680 457270 492780 580640 374630 562520 668040 499790 112229 TRUE FALSE 396984.3622 503866.3329 515374.4504 522272.9641 439965.3534 543039.7914 566118.2286 456025.738 129632.9001 3.062373531 3.886870789 3.975645456 4.028861219 3.393932813 4.189058416 4.367087584 3.517824083 1 16.98407239 0.122971113 16.44395153 1 3.823612977 0.837332683 0.388125791 0 0 0.394367225 0.092953246 1.327306169 -0.122971113 2.823612977 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 0 64.984 0.0019838 290940000 55288 54287 67376 69275 51811 66880 84497 65971 14221 FALSE TRUE 52674.64581 59818.90702 70465.25624 62311.34539 60846.822 64563.92883 71605.43076 60194.22951 16426.32005 3.206722239 3.641649916 4.289777384 3.793384349 3.704227229 3.930516917 4.359188823 3.664498763 1 14.00372169 -0.655328296 15.70406503 0.999944938 3.824706295 0.879645418 0.328250452 0 0 0.352843134 0.083165924 0.22114224 0.655328296 2.824761357 DTHPGS(ph)PGSPGPALRPLPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.924)PGS(0.076)PGPALRPLPAR 139.26 2.02E-07 115690000 132340 131900 114760 151250 130970 123810 147270 144820 111190 TRUE FALSE 126084.5505 145340.76 120021.8595 136046.0626 153811.1265 119522.4287 124801.2567 132138.7931 128432.7773 0.981716296 1.131648501 0.934511127 1.059278367 1.197600252 0.930622472 0.971724347 1.028855685 1 16.97065391 DTHPGSPGS(ph)PGPALRPLPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.476)PGS(0.524)PGPALRPLPAR 111.53 0.0001007 112200000 142020 149340 123240 149190 136760 142720 161920 151420 128010 TRUE FALSE 135306.9961 164557.9158 128890.6759 134193.1378 160610.9007 137777.5706 137216.1301 138160.8621 147861.137 0.91509506 1.112922023 0.87170083 0.907561922 1.086227956 0.931803809 0.928006729 0.934396048 1 17.17388339 DTIEEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTIEEHR 7 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 98.458 0.023828 0 387490 362910 362520 414830 409820 358710 415920 376960 450100 FALSE TRUE 369174.1156 399890.9416 379141.9006 373130.5003 481292.4782 346287.7828 352463.7651 343951.384 519899.2092 0.710087858 0.769170129 0.729260391 0.717697765 0.925741893 0.666067147 0.677946338 0.661573201 1 18.98787244 -2.141248153 2.570155386 1.617320053 0.732416302 0.551529049 0.075893724 8721387.194 1805745.054 31640501 0.017862722 0.007223569 2.141248153 -0.884903751 DTIIDVVGAPLT(ph)PNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 DTIIDVVGAPLT(0.999)PNS(0.001)R;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.999)PNS(0.001)R 355.06 2.46E-86 620147000 928885 995858 859703 1049150 781583 916066 965470 1003699 850850 TRUE FALSE 884978.4469 1097337.062 899121.2329 943687.4487 917890.8277 884342.4047 818169.8194 915809.7946 982795.4725 0.900470618 1.116546721 0.914860984 0.960207363 0.933959154 0.899823442 0.832492459 0.931841691 1 19.90653169 3.038884342 1.400022518 0.898748541 1.001539848 0.103708145 0.070948638 0.531152434 2.162545089 0.025859101 0.031938747 1093.665072 -3.038884342 0.102791307 DTILAELLQIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTILAELLQIHK 12 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 0 87.001 0.010794 14557000 80936 64107 76166 86649 76415 76288 94491 85627 84688 FALSE TRUE 77110.31568 70639.57618 79658.28644 77938.8779 89741.75181 73646.12743 80074.6625 78129.04594 97820.98251 0.788279914 0.722131125 0.814327196 0.796750103 0.917407999 0.752866364 0.818583707 0.798694144 1 16.57785633 -5 0.19980509 1.918334342 0.762806969 0.609025676 0.050158816 92.07909592 0.910615455 33.78797913 0.115835364 1.00E-05 5 -1.155527373 DTLENTIGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTLENTIGHR 10 0 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 ;;; 218.07 6.95E-09 2561780000 3167990 2853020 2050020 2829610 2710040 2403790 2760840 2744120 2434540 FALSE TRUE 3018245.391 3143745.982 2144015.445 2545172.227 3182670.118 2320546.15 2339623.152 2503830.305 2812076.029 1.073315714 1.117944874 0.762431535 0.905086563 1.131786653 0.825207471 0.831991428 0.890384996 1 21.42320417 3.762327015 24.63652818 0.899820339 1.095630334 0.369949968 0.102198346 610.00505 632335.881 0.025852514 0.046571783 5785.315064 -3.762327015 0.195809995 DTLRT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTLRTPPR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DTLRT(1)PPR;DT(0.213)LRT(0.787)PPR;DT(0.019)LRT(0.981)PPR 122.69 0.0022304 1712070000 1013992 1259281 824628 1217201 851762 959119 822595 969600 734114 TRUE FALSE 966062.6077 1387603.166 862438.0095 1094845.643 1000309.023 925904.4685 697093.0248 884696.6838 847956.6498 1.139283014 1.636408142 1.017077948 1.291157565 1.179670002 1.091924297 0.822085687 1.043327727 1 19.69363099 2.445971164 1.050442639 0.930373116 1.33378407 0.380595153 0.169633474 0.437429539 0.965026633 0.102560666 0.070172669 279.2358429 -2.445971164 0.403410955 DTLRT(ph)PPRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTLRTPPRER 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DT(0.024)LRT(0.976)PPRER;DT(0.001)LRT(0.999)PPRER;DT(0.002)LRT(0.998)PPRER 123.28 0.020486 2331800000 269129 255642 237520 293019 230231 251992 281824 267695 269898 TRUE FALSE 256407.8055 281692.2104 248410.5269 263564.1734 270383.2135 243265.4539 238826.5727 244254.2067 311752.4034 0.822472586 0.903576708 0.796819926 0.84542788 0.867301136 0.78031621 0.766077728 0.783487806 1 18.25004116 2.246193687 24.97736943 0.806785546 0.850214446 0 0.072276744 432.7468086 1416060.793 0.02267717 0.018630505 176.2762028 -2.246193687 0.043428901 DTLYEAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DTLYEAVR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 201.49 0.00025906 1926340000 2678380 2068213 1427301 1743699 2553300 1786314 2866510 2137980 2456030 FALSE TRUE 2551778.285 2278966.256 1492744.163 1568419.064 2998594.712 1724453.498 2429171.252 1950767.137 2836898.589 0.899495772 0.803330181 0.526188764 0.552863987 1.056997498 0.607865754 0.856277084 0.687640772 1 21.43588315 -1.61888926 2.821092165 1.020153837 0.760263975 0.183528909 0.164929211 41065312.54 40306858.4 6090777.907 0.039331933 0.02404976 1.61888926 -0.259889862 DTNGENIAESLVAEGLATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTNGENIAESLVAEGLATR 19 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 86.497 0.0066703 8411600 20719 16463 17477 16935 14810 16344 16591 16201 17028 FALSE TRUE 19739.65393 18140.59842 18278.33774 15232.66163 17392.85931 15778.00318 14059.73824 14782.35455 19668.61527 1.003611777 0.922311925 0.929314925 0.774465381 0.884295059 0.802191866 0.714831118 0.75157068 1 14.26360777 3.554835888 0.955717706 0.793897199 0.994506045 0.320728368 0.083685318 0.550904262 1.003763215 0.030786464 0.076710003 3587.863301 -3.554835888 0.200608845 DTNGENIAESLVAEGLATRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTNGENIAESLVAEGLATRR 20 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 196.89 2.74E-21 403177000 222990 98198 246458 146951 279888 216528 378858 264515 438776 FALSE TRUE 212449.7046 108204.4878 257758.3431 132179.2063 328700.3786 209029.5811 321056.2539 241352.6643 506819.1411 0.41918248 0.21349724 0.508580521 0.260801528 0.648555573 0.412434267 0.633473024 0.476210634 1 18.95111149 -3.110301311 0.143338876 2.159177744 0.189480192 0.691371912 0.123313667 34.47529055 0.504487396 12.74150562 0.685846436 0.000775709 3.110301311 -1.969697551 DTNYTLNTDSLDWALYDHLMDFLADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTNYTLNTDSLDWALYDHLMDFLADR 26 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ; 103.27 0.0027645 164757000 303240 225980 193116 278710 222882 235447 378150 236130 169794 FALSE TRUE 288906.4462 249007.6189 201970.5596 250693.5413 261752.5502 227293.4114 320456.2723 215453.2054 196124.7863 1.473074625 1.269638701 1.029806397 1.278234873 1.334622488 1.158922417 1.633940708 1.098551639 1 17.58141235 DTPDEPWAFPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTPDEPWAFPAR 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 191.48 1.23E-05 826650000 909020 921870 777170 956900 696250 843480 861030 900130 969350 FALSE TRUE 866052.4261 1015809.601 812804.0132 860710.594 817675.7796 814270.0761 729664.0596 821309.8453 1119671.847 0.773487722 0.907238673 0.725930562 0.768716831 0.730281628 0.72723993 0.651676705 0.733527281 1 20.09464454 3.717564875 24.2842725 0.739660336 0.840363204 0.063228276 0.097624651 824.975677 954190.3797 0.023302046 0.036143962 5218.730557 -3.717564875 0.100702868 DTPENNPDTPFDFTPENYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTPENNPDTPFDFTPENYKR 20 1 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ;; 218.25 1.61E-24 480984000 762500 573311 654660 632927 517712 571890 742970 724850 577181 FALSE TRUE 726458.1361 631732.0427 684676.8085 569303.9755 608000.8089 552085.3059 629616.2809 661378.2913 666687.2816 1.089653509 0.947568763 1.026983456 0.853929558 0.911973013 0.828102352 0.944395218 0.992036761 1 19.34665068 4.676292816 0.876291901 0.920295764 1.170828628 0.374044174 0.061875396 1.924994474 1.226413549 0.019771911 0.456493945 47456.18428 -4.676292816 0.250532863 DTPGFIVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DTPGFIVNR 9 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;;; 160.52 0.00015176 691456000 871920 717250 724960 766170 798650 660777 752970 732841 686760 FALSE TRUE 830706.0696 790338.5904 758200.1331 689153.136 937934.3071 637894.1268 638090.5973 668669.557 793259.2333 1.047206304 0.996318173 0.955803729 0.868761569 1.182380573 0.804143337 0.804391012 0.84293952 1 19.59743288 2.190218384 24.99997529 0.84053341 1.002698352 0.357436201 0.095749463 106.9357636 55300.6581 0.032701285 0.024151549 154.9595633 -2.190218384 0.162164942 DTPLEHHLYVVSYEAAGEIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTPLEHHLYVVSYEAAGEIVR 21 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R1L4 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 135.28 3.96E-06 25859000 18899 20115 16643 20415 20316 20019 21625 19069 12062 FALSE TRUE 18005.68172 22164.74137 17406.09801 18362.84541 23859.10397 19325.73701 18325.70908 17399.21727 13932.51336 1.292349863 1.590864534 1.249315006 1.317985129 1.712476662 1.387096249 1.315319685 1.248821144 1 13.76616792 1.009756063 1.287107577 1.005600302 1.431190359 0.483484476 0.139496021 0.388992252 1.32318835 0.125203252 0.038426038 10.22718384 -1.009756063 0.425590057 DTPLYTDNTANGIALLWAPRPFNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTPLYTDNTANGIALLWAPRPFNLR 25 1 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 78.916 0.02346 44658000 123610 108800 102460 116100 95948 117140 123650 127000 103050 FALSE TRUE 117767.2003 119886.8437 107157.8923 104429.4074 112681.3008 113083.4124 104784.9215 115879.2067 119030.4677 0.989387025 1.007194595 0.900255997 0.877333421 0.946659313 0.950037538 0.88032017 0.973525594 1 16.86097138 3.745848825 24.92637469 0.92439406 0.998290815 0.305703699 0.03969594 486.5886365 1664175.487 0.009408282 0.0165502 5569.918303 -3.745848825 0.073896755 DTPRPDHPPHDGHS(ph)PASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(0.999)PAS(0.001)R 161.66 1.88E-11 1061977000 601157 584982 560421 678893 625723 601332 725614 574708 183941 TRUE FALSE 572741.5 644592.3309 586116.8572 610649.3858 734848.8931 580507.7221 614908.2575 524383.5208 212465.6308 2.695690111 3.033866364 2.75864315 2.874109019 3.458671834 2.73224295 2.89415401 2.468086338 1 17.69686996 0.692894788 1.604168873 1.000119188 2.931078004 0.886659783 0.215477575 0.328605812 1.273153577 0.19178458 0.055025166 4.930543428 -0.692894788 1.930958816 DTQRQESDKNGES(ph)ASPERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTQRQESDKNGESASPERDR 20 3 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 DTQRQESDKNGES(0.5)AS(0.5)PERDR 75.326 0.069727 48391000 23073 6712.3 27031 14133 24968 22535 38415 23434 32084 TRUE FALSE 21982.38502 7396.291001 28270.39809 12712.32399 29322.41129 21754.6073 32554.08621 21381.99473 37059.42286 0.593165876 0.199579228 0.762839675 0.343025417 0.791226874 0.587019592 0.87842939 0.57696513 1 15.17755279 1.960272667 0.353309561 0.989138613 0.367156023 0.38054481 0.188356798 1.133541559 0.394821515 0.219816682 0.243106886 91.25836159 -1.960272667 -0.621982591 DTQRQESDKNGESAS(ph)PERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTQRQESDKNGESASPERDR 20 3 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 DTQRQESDKNGES(0.067)AS(0.933)PERDR;DTQRQESDKNGES(0.149)AS(0.851)PERDR 109.25 0.0011062 169270000 61521 18724.2 74126 37821.6 59208 61996 104844 68674 89020 TRUE FALSE 58613.02425 20632.21727 77524.75042 34019.70091 69533.85645 59849.06297 88848.12221 62660.5405 102824.7669 0.570028272 0.20065416 0.753950169 0.330851233 0.676236461 0.582049099 0.864073169 0.609391515 1 16.64982828 1.745564087 0.418523551 0.990479933 0.384261891 0.459650066 0.171270947 0.773194993 0.36125316 0.176372705 0.145093305 55.66267676 -1.745564087 -0.606218042 DTQS(ph)PSTCSEGLLGWSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DTQS(0.996)PS(0.004)TCSEGLLGWSQK;DT(0.001)QS(0.801)PS(0.193)T(0.005)CSEGLLGWSQK;DTQS(0.792)PS(0.206)T(0.002)CSEGLLGWSQK;DTQS(0.956)PS(0.044)TCSEGLLGWSQK 295.53 2.75E-49 542968000 626980 719290 545180 760150 411167 639740 615830 657000 410342 TRUE FALSE 597343.898 792586.4688 570177.0423 683738.2778 482874.3946 617585.6434 521873.823 599469.597 473975.7416 1.260283693 1.672208932 1.202966718 1.442559645 1.01877449 1.302989983 1.101055976 1.26476852 1 18.8544537 3.036435011 1.593440449 1.154770116 1.444787099 0.336731603 0.16261225 0.36396459 1.895545103 0.052556458 0.064145393 1087.514386 -3.036435011 0.290016983 DTQSPS(ph)TCSEGLLGWSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DTQS(0.215)PS(0.781)T(0.004)CSEGLLGWSQK;DT(0.008)QS(0.307)PS(0.581)T(0.104)CSEGLLGWSQK;DTQS(0.167)PS(0.735)T(0.098)CSEGLLGWSQK 360.94 5.18E-91 434228000 682888 782883 602711 819860 407096 659305 641987 675656 437357 TRUE FALSE 650609.2376 862659.6678 630345.8955 737446.1152 478093.4135 636473.1025 544040.0922 616491.9788 505180.0898 1.28787585 1.707628003 1.247764724 1.459768764 0.946382138 1.259893482 1.076923068 1.220341005 1 18.94643826 2.756862241 24.56730951 1.116264835 1.447528506 0.526242993 0.152236143 479.0732722 643086.396 0.043236336 0.04577121 571.2973919 -2.756862241 0.331263671 DTS(ph)GLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTSGLER 7 0 Q9H307 Q9H307 PNN Pinin 1 DT(0.021)S(0.979)GLER 118.67 0.005197 307580000 790600 642180 660080 745530 582120 697370 849380 728080 664960 TRUE FALSE 753229.9048 707618.8721 690345.3209 670587.908 683641.5437 673219.902 719791.4811 664325.4554 768078.6007 0.980667739 0.921284451 0.89879515 0.873071984 0.890067166 0.876498709 0.937132581 0.864918584 1 19.55089443 4.354054411 1.779128277 0.901815068 0.982524655 0.254837817 0.039341003 0.508831467 2.674444319 0.009280349 0.053794951 22597.18866 -4.354054411 0.080709587 DTS(ph)PSSGSAVSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;DTS(0.993)PS(0.003)S(0.003)GSAVSSSK;DT(0.002)S(0.993)PS(0.002)S(0.004)GSAVSSSK;DTS(1)PSSGSAVSSSK;DTS(1)PSSGSAVSSSK;DTS(0.986)PS(0.014)S(0.001)GSAVSSSK;DTS(0.991)PS(0.009)SGSAVSSSK;DT(0.019)S(0.587)PS(0.386)S(0.009)GSAVSSSK;DT(0.476)S(0.505)PS(0.018)SGSAVSSSK;DT(0.33)S(0.646)PS(0.02)S(0.003)GS(0.001)AVSSSK;DT(0.018)S(0.886)PS(0.082)S(0.012)GS(0.003)AVSSSK 424.13 9.66E-153 8597968000 13851250 12452280 11993800 14113390 8081510 13638590 14187760 13658500 8906970 TRUE FALSE 13196528.86 13721181.49 12543727.59 12694685.22 9490922.785 13166282.21 12023156.64 12462489.33 10288217.42 1.282683708 1.333679192 1.219232359 1.233905225 0.922504104 1.279743776 1.168633608 1.211336116 1 23.2944897 8 0.078011337 0.861461129 2.080356092 0.334062858 0.104738218 220.9358507 1.259503878 3.053849859 29.11442362 99999999.89 -8 1.218894963 DTSEDIEELVEPVAAHGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTSEDIEELVEPVAAHGPK 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 194.4 3.20E-15 258714000 556356 500934 499439 611236 406822 552035 602517 625278 411904 FALSE TRUE 530058.1545 551979.7441 522338.7722 549793.396 477771.628 532917.8895 510591.9657 570525.3435 475779.9686 1.114082537 1.160157595 1.097857847 1.155562303 1.004186093 1.120093162 1.07316827 1.199136956 1 18.85993501 DTSFEQHVLWHTGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 266.42 1.52E-25 32915063000 39674450 35113390 37880810 45314440 33738630 39977810 46694870 42555730 1409632 FALSE TRUE 37799117.38 38691484.36 39617682.61 40759346.4 39622636.39 38593368.42 39570709.97 38829324.68 1628230.531 23.21484375 23.76290312 24.33174041 25.0329088 24.33478284 23.70264387 24.30289152 23.84755963 1 20.63487355 0.887649616 18.31050989 1.000000002 24.04778649 0.995595106 0.482196002 675.5763082 110103.9374 0.509194402 0.127298601 7.720574459 -0.887649616 23.04778649 DTSFLGSDDIGNIDVREPELEDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTSFLGSDDIGNIDVREPELEDLTR 25 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 ;; 152.88 1.05E-07 132889000 106914 59991 96745 90653 111049 95354 131699 103242 124157 FALSE TRUE 101860.3871 66104.1511 101180.8539 81540.38821 130415.9104 92051.86707 111605.8987 94201.58316 143410.6335 0.710270812 0.460943164 0.705532439 0.568579792 0.909388009 0.641876163 0.778226105 0.656866098 1 17.12979247 -5 0.114629116 2.103286132 0.487982924 0.446115514 0.115783748 129.6514675 0.976906806 33.12903428 1.160633767 1.00E-05 5 -1.615303208 DTSLYRPALEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;;; 238.65 1.39E-17 1909895000 1429382 1157373 1316359 1463563 1443305 1405966 1630195 1475847 1581669 FALSE TRUE 1361817.946 1275310.625 1376715.362 1316442.867 1695016.935 1357277.045 1381478.812 1346614.013 1826946.15 0.745406724 0.698055947 0.753560997 0.720570153 0.927787026 0.74292121 0.756168326 0.737084677 1 20.80100268 -5 0.269876595 2.658140933 0.738636356 0.587732087 0.062672625 147.1985902 1.429248827 136.1525031 0.074433342 1.00E-05 5 -1.919504577 DTSPDKGELVS(ph)DEEEDT ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(1)DEEEDT;DTSPDKGELVS(0.996)DEEEDT(0.004);DTSPDKGELVS(1)DEEEDT 265.43 3.95E-27 474080000 1841980 1584180 1659760 1863540 1143790 1838530 1959700 1974270 1308830 TRUE FALSE 1754913.256 1745609.743 1735861.638 1676213.419 1343266.614 1774861.245 1660711.773 1801392.453 1511796.672 1.160813017 1.154659073 1.148211046 1.10875586 0.88852333 1.174007906 1.098502069 1.191557361 1 20.52783269 3.15381943 4.620920738 1.079386622 1.155576875 0.162463845 0.08497991 0.399048217 15.28947884 0.023893797 0.029188756 1425.01498 -3.15381943 0.076190253 DTSQSDKDLDDALDKLSDSLGQR ddPTM_SK-BR-3_Trastuzumab_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 0 118.51 0.00015501 24255000 85055 75857 76099 101020 33502 85871 84313 101030 39697 FALSE TRUE 81034.61871 83586.91454 79588.21442 90865.27767 39344.73819 82897.26574 71449.50334 92183.27761 45853.00802 1.767269416 1.822931977 1.735725045 1.981664488 0.858062315 1.80789155 1.55822936 2.010408512 1 15.48472876 DTSSS(ph)PTTGSTVQSVDLIFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.013)S(0.013)S(0.114)S(0.803)PT(0.051)T(0.006)GSTVQSVDLIFTR 105.77 0.00040139 20874000 29123 32264 30025 30830 19697 33210 26503 28375 30144 TRUE FALSE 27746.41351 35551.73828 31401.67595 27730.90983 23132.15056 32059.92937 22459.48059 25890.33457 34818.57757 0.796885325 1.021056596 0.90186556 0.796440055 0.664362308 0.920770796 0.645043025 0.743578181 1 15.08756965 3.215715586 4.415759399 0.769660481 0.9168664 0.142967761 0.119554453 0.264259838 11.95882997 0.031693045 0.040133534 1643.295198 -3.215715586 0.147205919 DTTALSFFHMLNGAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTTALSFFHMLNGAALR 17 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 242.19 2.15E-20 126123000 164197 166744 133154 136808 165328 127629 165457 148107 128284 FALSE TRUE 156435.7332 183735.4032 139259.2426 123055.7999 194161.1509 123209.1757 140213.4958 135137.9659 148177.6275 1.055731124 1.239967235 0.939812878 0.830461399 1.310327032 0.83149648 0.946252806 0.911999795 1 17.17696811 3.724853932 24.5696648 0.964027543 1.147849181 0.222456913 0.140318057 760.127458 1362552.91 0.034862646 0.054353757 5307.059195 -3.724853932 0.183821638 DTTDKGQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTTDKGQQLR 10 1 Q13144;A0A3B3IUB1 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 ; 80.24 0.022437 215330000 657280 608770 570070 771840 765500 626400 739010 714440 555380 FALSE TRUE 626211.677 670804.3551 596208.2734 694253.1768 899002.9576 604707.6109 626260.4517 651879.8461 641505.4939 0.976159492 1.045672035 0.929389193 1.082224834 1.401395571 0.942638242 0.976235523 1.016171884 1 19.2911021 DTTINEIEDTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DTTINEIEDTFR 12 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ;;; 247.3 2.95E-16 159491000 259704 254793 227165 282889 235537 235005 266670 278265 259237 FALSE TRUE 247428.3066 280756.6964 237580.7399 254452.4603 276614.5782 226866.7179 225984.5938 253898.6414 299438.15 0.82630856 0.937611645 0.793421747 0.849766338 0.923778678 0.757641329 0.754695398 0.847916812 1 18.19189851 2.23691957 24.99996985 0.810451422 0.868240953 0 0.080845707 97.05202024 1478465.972 0.026942351 0.020955333 172.5518301 -2.23691957 0.057789531 DTTS(ph)PMELAALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTTSPMELAALEK 13 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 DT(0.023)T(0.023)S(0.954)PMELAALEK;DT(0.001)T(0.043)S(0.956)PMELAALEK 130.72 0.00014561 55378000 233270 221630 194049 269320 170712 218900 244670 251090 171951 TRUE FALSE 222243.7894 244214.349 202946.3386 242247.4419 200484.1188 211319.4381 207341.0978 229103.2285 198616.2829 1.118960572 1.22957869 1.021801111 1.21967564 1.009404243 1.063958277 1.043927994 1.153496708 1 17.59962438 2.730515225 24.99666031 1.056562171 1.151028132 0.306453543 0.06963748 697.6112465 2167443.217 0.020379079 0.019520013 537.6692824 -2.730515225 0.094465961 DTVTISGPQAPVFEFVEQLRK ddPTM_SK-BR-3_Trastuzumab_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 ; 254.54 3.46E-36 4651700000 1165280 927590 1127090 1156350 913640 1140390 1448910 1301960 1132880 FALSE TRUE 1110199.524 1022112.476 1178768.191 1040111.501 1072978.527 1100898.008 1227852.168 1187953.48 1308561.244 0.848412352 0.781096399 0.900812397 0.79485122 0.819968138 0.841304152 0.938322278 0.907831777 1 20.31955002 1.494537493 1.078629642 0.985259999 0.823231759 0.689716628 0.037730217 0.240066648 0.544029629 0.031598674 0.011311689 31.22751983 -1.494537493 -0.16202824 DTYGVRPLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTYGVRPLFK 10 1 P08243-2;P08243;P08243-3;F8WEJ5;C9J057;C9JT45 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 77.379 0.030257 330510000 421570 442130 396970 463780 334040 388110 489350 495920 440210 FALSE TRUE 401643.2216 487183.5497 415171.4672 417159.9533 392296.4702 374669.6534 414690.67 452494.6158 508475.5185 0.789896872 0.958125872 0.816502372 0.820413054 0.771514962 0.736848953 0.815556806 0.889904429 1 18.95581879 -1.997104053 6.172135669 1.16519649 0.827862699 0.444032642 0.061512088 0.044362066 2.08E-05 0.018895562 0.014701942 0.010066904 1.997104053 -0.337333791 DTYS(ph)DRSGSSSPDS(ph)EITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DTYSDRSGSSSPDSEITELKFPSINHD 27 2 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 DT(0.065)Y(0.042)S(0.307)DRS(0.176)GS(0.342)S(0.29)S(0.237)PDS(0.538)EIT(0.003)ELKFPSINHD 89.742 0.034188 388810000 388710 233360 345040 344020 289080 336420 442680 386810 295260 TRUE FALSE 370336.4486 257139.6493 360860.4253 309438.456 339495.4605 324769.691 375141.0356 352938.8658 341047.4128 1.08587966 0.753970385 1.058094598 0.907317999 0.995449453 0.952271382 1.099967399 1.034867448 1 18.37961279 1.757015472 25 1.053061213 0.948210826 0.151739527 0.093108894 11.33697323 15373.10271 0.040452906 0.022433719 57.14989961 -1.757015472 -0.104850388 DTYSDRS(ph)GSS(ph)SPDSEITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTYSDRSGSSSPDSEITELKFPSINHD 27 2 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 DT(0.03)Y(0.018)S(0.133)DRS(0.789)GS(0.063)S(0.53)S(0.437)PDSEITELKFPSINHD;DT(0.001)YS(0.003)DRS(0.912)GS(0.091)S(0.533)S(0.429)PDS(0.031)EIT(0.001)ELKFPSINHD 146.78 7.64E-08 516120000 222514 152321 209180 202411 181851 210135 279159 251396 197561 TRUE FALSE 211996.2042 167842.6831 218771.1099 182064.2617 213565.7568 202857.9723 236568.1674 229382.4335 228197.7509 0.929002163 0.735514186 0.958690912 0.797835478 0.9358802 0.888956931 1.036680539 1.005191474 1 17.79992505 2.036607245 1.389560901 1.02107539 0.850627795 0.469372639 0.068255471 0.31922016 1.151810209 0.042514376 0.020676851 108.7945762 -2.036607245 -0.170447596 DTYYDTPELSLMQADHWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DTYYDTPELSLMQADHWLR 19 0 G3V5B9;G3V5Q5;Q9BU02-2;Q9BU02 G3V5B9 THTPA Thiamine-triphosphatase 0 ; 155.2 2.82E-08 31672000 57581 48824 49106 55993 49159 49992 61117 53934 44270 FALSE TRUE 54859.26024 53799.22111 51357.55867 50364.47726 57732.31404 48260.7645 51792.47916 49211.25304 51135.1655 1.072828448 1.052098308 1.004349124 0.98492841 1.129013928 0.943788175 1.012854435 0.962375941 1 15.64202815 2.209445602 24.99993993 0.98293472 1.046403919 0.392159201 0.042484636 229.1228219 196737.5913 0.015053044 0.011119068 161.9741098 -2.209445602 0.063469199 DVACGANHTLVLDSQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVACGANHTLVLDSQKR 17 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 154.48 8.84E-08 621010000 279740 244560 292370 306270 267260 268770 376860 307210 195620 FALSE TRUE 266517.2446 269480.942 305775.4537 275483.1577 313870.0594 259462.4275 319363.0855 280309.0638 225955.7505 1.179510785 1.192627058 1.353253692 1.219190736 1.389077546 1.148288667 1.413387731 1.240548484 1 17.78568075 3.901424043 10.18080797 1.275186214 1.184424882 0.022130667 0.122181995 0.9381142 91.14514398 0.027115301 0.048942696 7969.370959 -3.901424043 -0.090761331 DVAEAKPELSLLGDGDH ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVAEAKPELSLLGDGDH 17 1 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 ;; 205.52 7.12E-12 327317000 790290 710312 565915 716292 605567 638175 898067 810812 577680 FALSE TRUE 752934.5579 782693.6004 591862.7625 644288.9673 711177.6931 616074.8397 761050.385 739813.0029 667263.664 1.128391367 1.172989993 0.886999839 0.965568788 1.065812109 0.923285461 1.140554216 1.108726644 1 19.34789742 3.783276374 24.99324155 1.020789753 1.150690743 0.341765412 0.078871467 491.3863001 274651.9018 0.020390202 0.036758807 6071.225637 -3.783276374 0.12990099 DVAEVDTVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVAEVDTVRR 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 ;; 192.38 1.10E-06 881880000 1213640 952420 1116910 1150960 1226970 1090580 1409160 1258650 1490050 FALSE TRUE 1156273.642 1049472.681 1168121.428 1035263.314 1440953.18 1052812.941 1194166.761 1148435.933 1721119.344 0.671814913 0.609761714 0.678698681 0.601505827 0.83721863 0.611702463 0.693831468 0.667261069 1 20.71491571 -5 0.309466766 3.937642818 0.65193716 0.704442535 0.066892214 147.9124908 1.341144081 283.1445336 0.056390766 1.00E-05 5 -3.285705658 DVAFTVGEGEDHDIPIGIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVAFTVGEGEDHDIPIGIDK 20 0 Q13451;Q13451-2 Q13451 FKBP5 "Peptidyl-prolyl cis-trans isomerase FKBP5;Peptidyl-prolyl cis-trans isomerase FKBP5, N-terminally processed" 0 148.06 1.15E-07 57622000 160150 139760 145760 167440 117960 158850 196090 173850 121230 FALSE TRUE 152580.0269 154001.7029 152443.2402 150608.6131 138532.1867 153348.9847 166172.8691 158626.7724 140029.7292 1.089625951 1.099778624 1.08864911 1.075547413 0.989305538 1.09511734 1.186697068 1.13280782 1 17.09537363 1.991576856 24.8429857 1.130661117 1.073163631 0.033106544 0.056247461 601.1127868 1772905.428 0.020396025 0.014371857 98.07918671 -1.991576856 -0.057497485 DVCISLEIDDLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVCISLEIDDLKK 13 1 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 103.83 0.0025323 99596000 181990 144300 165720 169210 141720 188780 190760 189580 181580 FALSE TRUE 173387.6934 159004.3341 173318.4259 152200.6893 166435.9231 182242.5013 161656.0585 172979.3702 209738.499 0.826685106 0.758107523 0.82635485 0.725668821 0.793540165 0.86890343 0.770750526 0.824738286 1 17.67823218 -1.261811305 0.449048159 1.098219554 0.789167047 0.717541076 0.039901301 11.84859015 1.334026841 1.433992763 0.019906532 0.054725368 1.261811305 -0.309052507 DVCLYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVCLYPR 7 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 118.69 0.011517 777200000 630950 548590 391040 442590 656900 436200 666250 554840 651980 FALSE TRUE 601126.2439 604491.9447 408969.5708 398100.0123 771463.152 421094.2846 564601.326 506255.2682 753085.7285 0.798217548 0.802686762 0.543058453 0.528625092 1.024402831 0.559158498 0.749717203 0.672241219 1 19.52245458 -1.97453849 2.490326708 1.243669421 0.717998202 0.268724256 0.149921103 14246352.18 5979177.216 19991042.52 0.035299391 0.0106038 1.97453849 -0.525671219 DVCTELLPLIKPQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVCTELLPLIKPQGR 15 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ; 188.4 2.74E-07 1667500000 1493540 1143880 1187590 1481190 1236710 1250730 1648950 1309660 1376210 FALSE TRUE 1422943.324 1260442.672 1242042.176 1332297.967 1452391.832 1207416.906 1397372.392 1194979.227 1589625.618 0.895143679 0.792917941 0.781342577 0.838120594 0.913669115 0.759560549 0.879057544 0.751736267 1 20.6002556 -1.511509 2.95823951 1.006094991 0.829827859 0.483217567 0.056309464 22186825.27 25087990.56 1094965.503 0.01252423 0.030795765 1.511509 -0.176267131 DVDDFFEHER ddPTM_SK-BR-3_Trastuzumab_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 ;; 150.94 2.07E-05 270770000 656284 688780 540288 730689 513733 591465 613233 645904 359677 FALSE TRUE 625262.7559 758967.4651 565060.7392 657238.7535 603327.8725 570982.4187 519673.0431 589345.2216 415453.8722 1.505011261 1.82683931 1.36010464 1.581977682 1.452213863 1.374358159 1.250856179 1.418557537 1 18.66432878 1.516220737 0.286537988 0.946390411 1.723018164 0.641491476 0.127904528 0.88390443 0.277141058 0.257192525 0.235755279 32.82620953 -1.516220737 0.776627753 DVDDGS(ph)GSPHS(ph)PHQLSSK ddPTM_SK-BR-3_Trastuzumab_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 2 DVDDGS(0.827)GS(0.173)PHS(0.999)PHQLS(0.001)SK 136.64 3.09E-06 217940000 533880 427960 465310 559770 392670 528040 581880 489050 188040 TRUE FALSE 508644.5504 471569.6106 486644.9238 503500.8561 461151.5237 509753.8424 493103.519 446226.1894 217200.2828 2.341822689 2.171127977 2.240535406 2.318140886 2.12316263 2.34692992 2.270271073 2.054445711 1 17.72866646 0.733336306 2.619548292 1.000122221 2.257097791 0.968279625 0.071075581 0.225703108 2.012667531 0.063207391 0.016794796 5.411732303 -0.733336306 1.25697557 DVDDGSGS(ph)PHS(ph)PHQLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 2 DVDDGS(0.04)GS(0.96)PHS(1)PHQLSSK;DVDDGS(0.466)GS(0.545)PHS(0.979)PHQLS(0.005)S(0.006)K;DVDDGS(0.441)GS(0.559)PHS(1)PHQLSSK 192.1 1.01E-14 1509010000 2156110 1736240 1968460 2326420 1596610 2187360 2391530 2102560 789820 TRUE FALSE 2054194.953 1913164.83 2058715.838 2092563.842 1875058.278 2111611.175 2026658.175 1918448.7 912301.2518 2.251662978 2.097075748 2.256618452 2.293720235 2.055306046 2.314598572 2.221479112 2.102867552 1 19.79915077 0.664822602 3.006132344 1.000017499 2.207791956 0.956236045 0.080945106 0.681896391 5.913527787 0.072199182 0.018872208 4.621921893 -0.664822602 1.207774456 DVDDGSGSPHS(ph)PHQLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 DVDDGSGS(0.002)PHS(0.997)PHQLSSK;DVDDGSGS(0.004)PHS(0.996)PHQLSSK;DVDDGSGSPHS(1)PHQLSSK;DVDDGSGS(0.001)PHS(0.999)PHQLSSK 256.06 9.01E-31 1527390000 1677490 1325280 1512970 1747270 1222020 1444760 1826330 1524520 298619 TRUE FALSE 1598198.372 1460327.539 1582341.171 1571631.1 1435139.901 1394727.599 1547689.816 1391024.947 344927.3094 4.633435303 4.233725481 4.587462715 4.556412488 4.16070245 4.043540656 4.487002837 4.032806069 1 18.39593283 -1.00572255 0.534361278 2.22E-15 4.439502133 0.968871321 0.189374814 3.280641219 0.557790623 5.377939017 0.081446527 0.098690977 1.00572255 4.439502133 DVDEAHYAYSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVDEAHYAYSFK 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 135.6 0.00012484 328090000 353210 298097 325820 386390 293529 325340 411440 387540 320820 FALSE TRUE 336514.4633 328473.4232 340759.1693 347549.3431 344720.3647 314073.3942 348667.2714 353604.9431 370571.1271 0.908096823 0.886397777 0.919551321 0.937874858 0.930240754 0.847538762 0.940891629 0.95421612 1 18.49939095 1.134800047 1.9881625 0.996938983 0.905917132 0.573588586 0.026417787 0.211123913 1.56938667 0.023738396 0.006770598 13.63955016 -1.134800047 -0.09102185 DVDEIEAWISEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDEIEAWISEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 233.54 1.24E-15 102996000 313627 269831 263736 317690 209745 285123 325490 320411 224933 FALSE TRUE 298802.4733 297327.0857 275828.5565 285755.1976 246324.4616 275249.119 275830.5225 292354.1142 259814.4608 1.150060979 1.144382359 1.06163666 1.099843314 0.948078336 1.059406463 1.061644227 1.125241887 1 17.98712221 3.664772796 1.877389154 1.048213212 1.152048869 0.405244562 0.048677503 0.30998876 2.138906191 0.013586417 0.026805524 4621.39187 -3.664772796 0.103835658 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.008)VGS(0.934)PS(0.058)RPSSSR;DVDELPSLQPS(0.122)VGS(0.852)PS(0.026)RPSSSR;DVDELPSLQPS(0.357)VGS(0.613)PS(0.029)RPSSSR;DVDELPSLQPS(0.024)VGS(0.877)PS(0.097)RPS(0.001)S(0.001)S(0.001)R 163.16 9.33E-12 1088070000 678390 578260 642220 736520 665030 662840 777130 720830 700470 TRUE FALSE 646323.8491 637185.3514 671666.4222 662483.6103 781011.0214 639885.6846 658564.5455 657710.3038 809095.3101 0.798822884 0.787528173 0.830144995 0.818795514 0.96528927 0.790865645 0.813951752 0.812895954 1 19.62595013 -2.849641711 1.990878129 9.669443917 0.823625556 0.530895277 0.050918843 1343569.718 42347.81159 53020803.51 0.013577503 0.001413703 2.849641711 -8.845818361 DVDFELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDFELIK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 141.39 0.0014757 204632000 835400 816430 630419 865100 537398 695110 808050 813360 544410 FALSE TRUE 795912.2976 899625.1452 659324.3347 778138.5044 631120.0411 671038.1664 684767.1316 742137.8865 628834.3223 1.265694746 1.430623478 1.048486559 1.237430078 1.00363485 1.067114409 1.088946814 1.180180312 1 19.26232044 3.733456513 24.97391371 1.093903174 1.348159116 0.628748831 0.082607188 216.9692097 1061610.958 0.020023817 0.032097145 5413.230414 -3.733456513 0.254255942 DVDFELIKVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DVDFELIKVEGK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 171.29 3.54E-05 1365291000 4948920 3147141 4751590 4459740 3327990 5047090 6688090 5715500 4027192 FALSE TRUE 4714994.359 3467838.246 4969455.101 4011438.462 3908390.402 4872308.008 5667699.035 5215020.52 4651708.367 1.013604892 0.745497777 1.068307535 0.862358116 0.840205381 1.04742336 1.218412374 1.121097908 1 22.14932922 2.054558655 4.977415017 1.137022176 0.9004083 0.460221697 0.10330908 0.142696009 7.488539253 0.037739285 0.026834986 113.3857964 -2.054558655 -0.236613876 DVDFMYVELIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDFMYVELIQR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 160.36 0.00015885 86604000 118836 119860 113265 143993 122161 134124 139055 132026 125554 FALSE TRUE 113218.8578 132073.8703 118458.3123 129518.5501 143465.8397 129479.2522 117839.6058 120465.1035 145024.2731 0.780689021 0.910701826 0.816817142 0.893081877 0.989253983 0.892810903 0.812550915 0.830654765 1 17.14593486 DVDIIDHHDNTYTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 128.96 3.98E-05 548490000 2320550 1898270 1969820 2346620 1572090 2135890 2584210 2352010 343730 FALSE TRUE 2210862.2 2091705.871 2060138.195 2110733.299 1846261.998 2061923.594 2189941.302 2146055.536 397033.8929 5.568447027 5.268330761 5.188821993 5.316254701 4.650137007 5.193318834 5.515754049 5.405219993 1 18.59890264 -0.599264925 6.527442041 0.999999997 5.277647681 0.966040491 0.251193132 1.48E-08 2.26E-09 0.24753878 0.05834545 0.251614158 0.599264925 4.277647684 DVDKFGNEITQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVDKFGNEITQLAR 14 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 183.23 1.31E-06 144740000 404840 452020 363990 509150 324873 383340 361640 441400 315674 FALSE TRUE 385704.0155 498081.3519 380679.3015 457969.2747 381530.7483 370064.8397 306465.176 402748.676 364627.1117 1.057803995 1.366001967 1.044023577 1.255993479 1.046358694 1.01491312 0.840489273 1.104549451 1 18.47606231 2.481251339 2.615915134 0.962206135 1.190760119 0.378786076 0.11278241 0.236138171 3.275030871 0.03968961 0.033744566 302.8665696 -2.481251339 0.228553984 DVDLEFLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 167.33 0.00013974 347910000 983220 889230 854000 1038250 738360 928720 1103040 1090390 802090 FALSE TRUE 936745.1392 979843.548 893156.7447 933883.1375 867129.7502 896558.1935 934750.9893 994909.6711 926474.0207 1.011086246 1.057604991 0.964038629 1.007997112 0.935946104 0.96771002 1.008933838 1.073866778 1 19.821391 -0.685132206 6.126424131 1 1.004400558 0.000144286 0.041359863 0 8.93E-18 0.040176155 0.00946961 0.206475152 0.685132206 0.004400558 DVDREDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVDREDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 140.5 0.0023895 879619000 1269101 1142095 1122261 1311885 1071919 1145887 1288605 1226005 1169266 FALSE TRUE 1209113.111 1258475.779 1173717.777 1180011.827 1258861.334 1106204.646 1092004.64 1118649.503 1350589.799 0.895248218 0.931797189 0.869040902 0.873701125 0.932082661 0.819053014 0.808539085 0.828267401 1 20.36515814 2.234505744 24.99998021 0.842746621 0.901556378 0.036095298 0.058108278 158.9136741 979756.9482 0.019113275 0.014635467 171.5954405 -2.234505744 0.058809757 DVDVSEDS(ph)PPPLPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVDVSEDSPPPLPER 15 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVS(0.001)EDS(0.999)PPPLPER 182.37 5.76E-07 234610000 472590 508130 355850 555390 334670 430330 388640 418670 294060 TRUE FALSE 450251.6073 559909.0247 372166.0745 499561.142 393036.342 415427.5642 329345.8301 382009.0353 339661.3229 1.325589865 1.648433268 1.095697536 1.470762516 1.157141881 1.223064082 0.969630063 1.124676286 1 18.37373742 2.547119644 0.729721934 1.006083143 1.460432026 0.491504436 0.1497738 0.480959094 0.526879859 0.104094883 0.084631864 352.4679596 -2.547119644 0.454348883 DVDVSEDS(ph)PPPLPERTPESFVLASEHNTPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVDVSEDSPPPLPERTPESFVLASEHNTPVR 31 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVS(0.009)EDS(0.991)PPPLPERTPESFVLASEHNTPVR 168.65 6.13E-13 41795000 40187 20200 32638 27404 44734 33238 48065 38675 49407 TRUE FALSE 38287.44015 22258.40297 34134.48458 24649.29786 52535.59544 32086.95973 40731.80148 35288.41197 57068.78522 0.670899862 0.390027629 0.59812881 0.431922596 0.920566212 0.562250617 0.713731707 0.618348749 1 15.80041423 -2.334734053 0.171238118 1.594948784 0.469831449 0.441752727 0.1422862 37.62899742 0.834791748 9.130528157 0.529772233 0.004626643 2.334734053 -1.125117335 DVDYVCISDNYWLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVDYVCISDNYWLGK 15 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 291.22 1.50E-43 309708000 703020 654605 595144 723000 514652 628278 697180 714702 528882 FALSE TRUE 669789.6379 721309.9937 622431.9411 650322.6664 604407.1459 606520.5753 590812.3864 652118.904 610898.3194 1.096401179 1.180736582 1.018879773 1.064535039 0.98937438 0.992833924 0.967120661 1.067475361 1 19.22057275 3.690960094 8.128356462 1.009855068 1.138471068 0.655002189 0.037382931 0.161618868 25.7223933 0.009838972 0.015341864 4908.627706 -3.690960094 0.128615999 DVEDEETWIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVEDEETWIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 175.91 6.18E-06 955050000 1285240 1090910 1136130 1290040 1000450 1132250 1402950 1246180 1012320 FALSE TRUE 1224489.252 1202074.969 1188222.684 1160362.728 1174928.163 1093039.899 1188904.211 1137057.873 1169305.415 1.04719369 1.028024803 1.01617821 0.992352137 1.004808622 0.934777077 1.016761057 0.972421626 1 20.15722037 3.532687582 1.137003577 0.984705731 1.044021271 0.49851513 0.021933919 0.375945524 0.980740826 0.007174478 0.015815592 3409.475561 -3.532687582 0.05931554 DVEDEILWVGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVEDEILWVGER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 215.87 9.40E-11 222825000 265750 223193 241126 251891 200642 225092 271936 285042 221849 FALSE TRUE 253188.5242 245936.6204 252181.8656 226570.4381 235633.9013 217297.0076 230447.1688 260082.2114 256252.2099 0.988044256 0.959744388 0.984115867 0.884169695 0.919539002 0.847981009 0.899298269 1.014946218 1 17.96720492 3.252078195 24.99812771 0.915343579 0.975073957 0.146370836 0.050943281 322.7615371 596880.8873 0.013279977 0.017883367 1786.809263 -3.252078195 0.059730378 DVEDEILWVTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 127.42 0.00062811 28597000 67082 54947 59711 78631 59674 60459 73434 61625 50816 FALSE TRUE 63911.1668 60546.16177 62448.80841 70726.86249 70081.12671 58365.28967 62230.29459 56228.78831 58696.28575 1.088845163 1.031516066 1.063931178 1.204963169 1.193961863 0.994360868 1.06020839 0.957961608 1 15.84098159 2.202174726 24.99643385 1.013235222 1.104126714 0.468325068 0.058833998 208.951089 143544.419 0.023965449 0.01770019 159.2849436 -2.202174726 0.090891491 DVEDMELS(ph)DVEDDGSK ddPTM_SK-BR-3_Trastuzumab_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 411.66 4.82E-140 563315000 1489951 2041580 1218021 1883500 767582 1654330 1254350 1669640 670792 TRUE FALSE 1419523.969 2249619.323 1273868.468 1694167.002 901448.0578 1597040.137 1062975.87 1523437.47 774814.9974 1.832081173 2.903427696 1.644093715 2.186543894 1.163436512 2.061188984 1.37190926 1.966195124 1 19.56349235 3.252090653 1.66400525 1.582209864 2.330713216 0.27859141 0.466593756 0.39106704 2.240242037 0.137739137 0.198375093 1786.86052 -3.252090653 0.748503352 DVEDMFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVEDMFSR 8 0 Q15717;Q15717-2;M0QZR9;M0R055 Q15717 ELAVL1 ELAV-like protein 1 0 ;; 255.13 1.20E-12 550706000 1508590 1269390 1332980 1515500 1359380 1337680 1660440 1474250 1369460 FALSE TRUE 1437281.94 1398742.284 1394098.451 1363159.061 1596455.442 1291355.806 1407109.382 1345156.855 1581828.863 0.908620379 0.884256393 0.881320656 0.861761404 1.009246625 0.816368848 0.889545902 0.850380775 1 20.59316209 4.69658943 3.822334262 0.892543944 0.909547321 0 0.061371861 2.051332654 53.21607945 0.013038356 0.089040388 49726.676 -4.69658943 0.017003376 DVEPEDPMFLMDPFAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DVEPEDPMFLMDPFAIHR 18 0 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;;;; 156.49 1.12E-08 85273800 163963.6 154368.6 161884.8 182310.2 172558.5 154742.8 188629.8 180356.6 148553.9 FALSE TRUE 156213.3656 170098.9358 169307.3782 163984.0323 202652.6478 149384.018 159850.8596 164563.62 171590.8801 0.910382682 0.991305224 0.986692172 0.955668694 1.181022253 0.870582504 0.931581326 0.959046424 1 17.38861335 -0.041189228 6.705939971 0.999999997 0.969770418 0.008772379 0.081999218 1442679.485 215134.5609 0.074747714 0.018128984 0.909516898 0.041189228 -0.030229579 DVES(ph)PSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DVESPSWR 8 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 DVES(0.999)PS(0.001)WR;DVES(0.998)PS(0.002)WR;DVES(0.871)PS(0.129)WR;DVES(0.992)PS(0.008)WR;DVES(0.998)PS(0.002)WR;DVES(1)PSWR;DVES(0.994)PS(0.006)WR;DVES(0.999)PS(0.001)WR 233.09 1.65E-08 2014120000 2488725 2314275 2183560 2610650 2122473 2201986 2460860 2411859 2164380 TRUE FALSE 2371087.901 2550102.254 2283678.386 2348222.502 2492631.619 2125730.673 2085410.61 2200663.84 2500020.996 0.948427195 1.020032335 0.913463683 0.939281112 0.997044274 0.850285128 0.834157238 0.880258143 1 21.25350878 2.235250683 24.99811976 0.87175979 0.966565548 0.279646295 0.053824608 78.17612862 590413.6172 0.018256402 0.014038602 171.8900284 -2.235250683 0.094805758 DVESYIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 190.51 0.00018605 871666000 1041130 1236940 814360 1104140 1048970 873980 951010 976930 875650 FALSE TRUE 991917.8482 1362985.592 851699.2115 993149.7495 1231910.036 843713.8535 805915.958 891384.8302 1011441.33 0.980697366 1.347567627 0.84206487 0.981915332 1.217974785 0.834169841 0.796799512 0.881301568 1 19.94798121 2.220760194 24.98624973 0.853278235 1.088124444 0.297484343 0.14659307 256.7053101 360332.0895 0.053950799 0.039930565 166.249441 -2.220760194 0.234846209 DVFERPSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVFERPSAK 9 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 105.98 0.0027459 216800000 479880 397010 381650 471070 391670 455550 486150 453880 463270 FALSE TRUE 457197.0234 437465.7704 399149.03 423717.1486 459977.124 439774.1893 411978.8887 414135.861 535111.5455 0.854395737 0.817522578 0.745917432 0.791829577 0.859591104 0.821836481 0.769893478 0.773924361 1 19.02948013 -1.647840152 6.856383153 1.000746368 0.806136611 0.743231876 0.036124302 0.000431472 2.22E-05 0.03661748 0.008598915 0.022498826 1.647840152 -0.194609757 DVFFYQADDEHYIPR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 271.2 2.17E-33 556306000 1102020 995750 1006240 1196920 1023800 1012800 1139540 1144800 895320 FALSE TRUE 1049929.699 1097218.057 1052377.099 1076603.328 1202350.396 977726.482 965682.2439 1044555.243 1034161.653 1.015247177 1.06097345 1.017613732 1.041039691 1.162632933 0.945429063 0.933782684 1.010050257 1 19.98003028 2.142747418 21.01286361 0.962488929 1.053096778 0.452934076 0.046767241 4.092435934 891.6562512 0.016677332 0.01231703 138.9144483 -2.142747418 0.090607849 DVFHMVVEVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVFHMVVEVPR 11 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 153.34 3.25E-05 92173000 185140 228710 152660 223090 147780 157500 161750 170320 119210 FALSE TRUE 176388.7991 252015.809 159659.612 200664.5694 173552.7852 152045.7355 137072.0668 155405.8779 137696.478 1.280997174 1.83022698 1.159503964 1.457296311 1.260401049 1.104209329 0.995465307 1.128611858 1 17.07113213 2.603615621 0.98187624 1.018544594 1.514167397 0.501974546 0.174780552 0.380886055 0.758246422 0.100114864 0.080139931 401.4353572 -2.603615621 0.495622803 DVFISAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVFISAAER 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 151.48 0.00019253 91291000 191710 157410 119340 133180 181830 119920 197080 136310 156590 FALSE TRUE 182648.2482 173450.258 124811.857 119792.4934 213541.0944 115767.1403 167011.8264 124373.9738 180873.1774 1.009813897 0.95896064 0.690051774 0.662301039 1.18061228 0.640045926 0.923364253 0.687630834 1 17.46461895 3.949846259 12.41098956 0.825416167 0.990760134 0.130649838 0.171554241 2.53754373 626.6555693 0.039679894 0.07162878 8909.354889 -3.949846259 0.165343967 DVFLAWVASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVFLAWVASR 10 0 O94842-3;O94842-2;O94842;A0A669KB71 O94842-3 TOX4 TOX high mobility group box family member 4 0 117.31 0.0022669 15340000 57951 43201 46998 43415 64614 41645 70488 51022 64623 FALSE TRUE 55211.77108 47603.23102 49152.90479 39050.84172 75882.66114 40202.82321 59733.761 46554.2432 74644.40479 0.739663894 0.637733413 0.658494162 0.523158324 1.016588736 0.538591249 0.800244321 0.623680279 1 16.1877465 -5 0.330204261 4.08882146 0.68269537 0.313161735 0.142021374 405.1267808 3.499599485 878.5518475 0.103871262 1.00E-05 5 -3.406126089 DVFLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVFLYR 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;; 142.53 0.026789 1710790000 1676210 1685170 1475060 1703630 1963400 1324650 1794730 1550380 1955810 FALSE TRUE 1596978.875 1856890.739 1542692.96 1532377.876 2305816.338 1278777.038 1520910.976 1414620.508 2259107.026 0.706907135 0.821957843 0.682877324 0.678311323 1.020676007 0.566054208 0.673235468 0.626185697 1 21.10732119 DVFQHSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVFQHSQSR 9 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ; 133.23 0.00028289 247490000 746590 639010 636860 663750 576650 568570 682090 624980 603760 FALSE TRUE 711300.1703 704125.8455 666060.6609 597028.589 677217.5774 548880.2783 578024.6431 570253.438 697388.0172 1.019948942 1.00966152 0.955079016 0.856092411 0.971077163 0.78705149 0.828842235 0.817698934 1 19.41160205 3.371560784 1.069059735 0.85234181 1.027275795 0.398093058 0.067768604 0.395147701 0.950156871 0.02424452 0.045147556 2352.66875 -3.371560784 0.174933985 DVFRDPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DVFRDPALK 9 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;; 139.43 0.00010168 5906020000 9380300 8970700 7973040 10395900 6449640 9668200 10012200 9963800 6704260 FALSE TRUE 8936911.809 9884824.529 8338611.77 9350884.381 7574455.174 9333387.81 8484655.003 9091316.851 7743922.4 1.154054928 1.276462239 1.076794335 1.207512666 0.9781161 1.205253272 1.095653412 1.173993795 1 22.88463307 -4.99999998 0.049227447 0.397678167 1.458608651 0.236590698 0.082178023 693.940751 2.527718394 55.82700558 12.77954275 1.00E-05 4.99999998 1.060930484 DVFRDPALKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVFRDPALKR 10 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 133.89 0.00010411 3756760000 4098340 3837390 3518030 4269980 3018330 4215540 4554480 4495260 3306950 FALSE TRUE 3904619.59 4228424.404 3679335.155 3840753.498 3544725.796 4069554.793 3859610.427 4101631.204 3819774.916 1.022211956 1.106982609 0.963233498 1.005492099 0.92799337 1.065391255 1.010428759 1.073788716 1 21.8650562 3.739745158 24.99990784 1.00756259 1.064597281 0.209652671 0.046772633 146.6261012 3094540.789 0.011612608 0.019540421 5492.185 -3.739745158 0.05703469 DVGAQILLHSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVGAQILLHSHK 12 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 119.25 0.00031082 1155310000 5291800 6141100 3814700 5436300 3770700 4590000 4791100 4798100 150391 FALSE TRUE 5041667.101 6766885.072 3989607.768 4889832.796 4428308.886 4431047.149 4060129.7 4377952.928 173712.8682 29.02299153 38.95442602 22.9666795 28.14893823 25.49211772 25.50788088 23.37264788 25.20223731 1 17.4063451 0.299063443 0.347086418 3.41E-19 32.5427301 0.797740582 4.242744987 1.553971825 0.328580117 14.98536803 3.935999108 1.990964164 -0.299063443 32.5427301 DVGAQILLHSHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVGAQILLHSHKK 13 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 124.3 8.68E-05 837500000 3338000 2835300 2829500 3250900 2356300 3094500 3929200 3599700 97380 FALSE TRUE 3180219.355 3124220.293 2959235.374 2924113.356 2767237.974 2987336.689 3329728.375 3284491.185 112481.1931 28.27334303 27.77549036 26.30871254 25.99646462 24.60178363 26.55854377 29.6025343 29.20035871 1 16.77932428 -0.233344928 8.862807033 1 27.37711006 0.967463822 1.515066252 0 0 1.588350351 0.374377768 0.584325813 0.233344928 26.37711006 DVGAYSK ddPTM_SK-BR-3_Trastuzumab_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 85.212 0.048802 22387000 72712 50437 66859 81992 82026 62736 79899 74885 96550 FALSE TRUE 69275.04786 55576.58764 69924.55128 73750.00839 96331.30843 60563.43659 67708.9401 68327.67241 111522.4809 0.621175635 0.498344255 0.626999603 0.66130172 0.863783765 0.543060342 0.607132657 0.612680707 1 16.76697503 -2.475770422 1.955945391 4.237493063 0.620147936 0.596691099 0.095512567 3568256.764 246318.0386 51158066.73 0.023613853 0.003343717 2.475770422 -3.617345127 DVGRPNFEEGGPTSVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVGRPNFEEGGPTSVGR 17 1 Q6Y7W6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 223.11 2.87E-15 122170000 60949 54233 59928 67867 63613 55966 63621 67091 69463 FALSE TRUE 58068.06156 59759.40436 62675.75808 61044.88022 74707.08706 54027.88339 53914.44797 61216.15637 80234.96727 0.723725123 0.744804994 0.78115266 0.760826387 0.931103852 0.673370791 0.671957001 0.762961069 1 16.2919435 -1.507357101 2.600861774 1.013065477 0.749850063 0.528928879 0.072072139 5704733.79 5536443.52 529298.3659 0.018149916 0.031091588 1.507357101 -0.263215414 DVGRPQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DVGRPQPGR 9 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;;;; 162.88 5.79E-05 10137420000 4922480 3191040 3371560 4805560 3792400 3840090 4961280 4786990 4549650 FALSE TRUE 4689804.126 3516210.604 3526149.361 4322495.979 4453793.359 3707106.72 4204345.616 4367815.778 5255186.486 0.892414406 0.669093402 0.67098463 0.822519998 0.847504341 0.705418681 0.800037378 0.831143821 1 22.32531053 0.765388455 1.532411534 0.999748056 0.76698369 0.489063648 0.073373287 0.695710174 2.790732255 0.068491632 0.019882458 5.826241138 -0.765388455 -0.232764366 DVGRPQPGRENFQNWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVGRPQPGRENFQNWLK 17 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 273.88 6.35E-36 527860000 364860 192860 337710 316230 349610 319960 555010 409530 514400 FALSE TRUE 347613.7909 212512.6533 353194.3375 284441.9596 410581.8733 308879.705 470333.031 373669.3821 594170.5248 0.585040449 0.357662732 0.594432613 0.478721087 0.691016899 0.519850265 0.791579204 0.628892492 1 19.18051751 0.887422977 0.343387773 1.048512695 0.451753891 0.6812703 0.099427424 0.917780556 0.293440058 0.1923599 0.096953089 7.716546494 -0.887422977 -0.596758804 DVGSLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVGSLDEK 8 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 125.31 0.0029482 194952000 563260 517280 450900 598900 382410 515000 608040 555690 395750 FALSE TRUE 536635.8161 569991.4201 471574.211 538697.4342 449102.1829 497165.4209 515272.3306 507030.8377 457120.8888 1.173947263 1.246916153 1.031618162 1.178457269 0.982458238 1.087601624 1.127212392 1.10918326 1 18.80221622 3.742664049 24.99998282 1.083074682 1.210431711 0.45487307 0.061538793 279.2280884 1701177.512 0.014602243 0.025186025 5529.22228 -3.742664049 0.127357029 DVHEDSLTVVFENNWQPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVHEDSLTVVFENNWQPER 19 0 B4DXZ6;P51114;C9JAJ4;P51114-2 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;; 167.82 1.72E-11 192304000 208398 183676 181647 239226 181621 190639 223810 204064 151481 FALSE TRUE 198547.4395 202392.7932 189975.6946 215178.548 213295.6449 184037.1236 189663.6739 186195.0743 174971.8998 1.134739005 1.156715984 1.085749739 1.229789173 1.219027999 1.051809598 1.083966478 1.064142725 1 17.41676372 2.219432432 24.99942584 1.05968406 1.16060139 0.607872211 0.045608316 187.0509141 244463.1897 0.016854338 0.012466727 165.7419454 -2.219432432 0.10091733 DVHGEQETEGRS(ph)SPGPDTLVVLEFNPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVHGEQETEGRSSPGPDTLVVLEFNPASK 29 1 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 DVHGEQET(0.171)EGRS(0.276)S(0.276)PGPDT(0.276)LVVLEFNPASK 66.36 0.005857 26160000 26914 18376 23939 22992 21385 23463 28187 25422 16778 TRUE FALSE 25641.82856 20248.53529 25036.62683 20680.80048 25114.53723 22650.47043 23886.55546 23195.91491 19379.84655 1.323118245 1.044824335 1.291889838 1.067129217 1.295910015 1.168764178 1.232546161 1.196909111 1 14.24226953 -1.444687253 2.798022205 0.994490836 1.198150655 0.321511876 0.092306591 13704882.3 14898642.19 594176.6116 0.020078614 0.03591805 1.444687253 0.203659819 DVHMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVHMPK 6 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 64.866 0.080065 44459000 156660 171880 162800 172150 130180 164880 158630 167060 125500 FALSE TRUE 149254.9923 189394.7674 170264.541 154845.1549 152883.3508 159170.1643 134428.0801 152431.3408 144961.899 1.029615321 1.306514116 1.174546844 1.0681783 1.054645061 1.098013791 0.927333878 1.051526931 1 17.14531423 2.828757229 1.377679882 1.006346865 1.177285709 0.395608182 0.079620701 0.376473783 1.459998419 0.03305006 0.033975852 674.1510708 -2.828757229 0.170938843 DVHNIYGLYVHMATADGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVHNIYGLYVHMATADGLR 19 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 221.92 1.48E-19 669973000 355256 314955 346428 368515 367854 340074 399492 318636 175404.8 FALSE TRUE 338463.7529 347049.2726 362312.0665 331471.1721 432007.6211 328297.1521 338542.1582 290734.5426 202605.6805 1.670554113 1.712929626 1.788262133 1.636040861 2.132258187 1.620374864 1.670941098 1.434977252 1 17.6283151 0.92520639 1.400576641 1.001609973 1.757351684 0.74680623 0.142575587 0.241004493 0.947991156 0.125396354 0.037438158 8.417950933 -0.92520639 0.755741711 DVHTLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 ;; 133.57 0.0009136 284347000 153361 132346 122051 144765 141103 129236 147753 132427 116415 FALSE TRUE 146111.9295 145832.2079 127647.1591 130212.9472 165711.3185 124760.5249 125210.5662 120830.9898 134468.0436 1.086592216 1.084512007 0.949275052 0.968356077 1.232347211 0.927807987 0.931154814 0.89858517 1 17.03690383 DVIATDKEDVAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVIATDKEDVAFK 13 1 A0A5K1VW95;P40925;P40925-3;C9JF79;C9JRL4;C9JLV6 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;; 206.2 5.82E-08 1811130000 3697660 4281420 2967790 4580460 1732550 4030220 3329750 4340810 1810250 FALSE TRUE 3522878.94 4717701.566 3103866.107 4120023.458 2034706.171 3890652.471 2821735.482 3960705.664 2090974.325 1.684802582 2.256221662 1.484411392 1.970384528 0.973089984 1.860688783 1.349483563 1.894191439 1 20.99574392 3.247594145 1.69765032 1.48070654 1.941621378 0.19301015 0.373769063 0.495153138 2.95016911 0.108680643 0.155335848 1768.455536 -3.247594145 0.460914838 DVIEEYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;; 143.89 0.0013825 2450993000 4859180 4477160 3789410 4944370 3111290 4311840 4807300 4851100 3164530 FALSE TRUE 4629496.191 4933387.694 3963158.197 4447352.534 3653897.991 4162519.9 4073858.093 4426311.967 3655269.15 1.266526759 1.349664687 1.084231567 1.216696323 0.999624881 1.138772476 1.114516586 1.210940094 1 21.80154621 3.736714623 24.99998255 1.115581426 1.308095729 0.545061109 0.075351194 100.5141005 1361248.878 0.017659921 0.028988372 5453.993582 -3.736714623 0.192514303 DVIKEIEDFDSLEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVIKEIEDFDSLEALR 16 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 188.6 1.05E-09 145156000 327423 334727 280283 389366 217685 320117 336661 366913 213995 FALSE TRUE 311946.3637 368836.0619 293134.2528 350226.1899 255649.1951 309031.268 285297.1812 334784.1526 247180.2517 1.262019767 1.492174473 1.185912915 1.416885805 1.034262217 1.250226367 1.154207018 1.354413026 1 17.91520396 2.753684707 24.99283868 1.174454603 1.347636376 0.324401785 0.128147537 918.6280773 1518048.529 0.035278884 0.037294885 567.132724 -2.753684707 0.173181773 DVIRPGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVIRPGMR 8 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;;; 133.58 0.00083289 1504410000 1443980 1148807 1287943 1474850 1435560 1234858 1514570 1363701 1410860 FALSE TRUE 1375725.927 1265871.739 1346996.46 1326595.276 1685921.209 1192094.558 1283494.53 1244288.111 1629648.963 0.84418544 0.776775716 0.826556204 0.814037444 1.034530287 0.731503891 0.787589572 0.763531373 1 20.6361298 2.947611356 24.9999634 0.843313063 0.812614004 0.034709553 0.097503198 1728.125841 824664.5662 0.028664832 0.030403949 886.3624647 -2.947611356 -0.030699059 DVITLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 97.071 0.096521 95697000 178520 183250 146660 211470 172300 173150 209640 185930 203520 FALSE TRUE 170081.7134 201923.3833 153384.5061 190212.6338 202349.0654 167153.7721 177655.5677 169648.9835 235080.8422 0.72350308 0.858952952 0.652475568 0.809137113 0.860763742 0.71104804 0.755721164 0.72166231 1 17.84279745 -2.266571906 2.339016301 1.982823228 0.766164119 0.561682281 0.066062123 3804942.372 737186.109 19735455.5 0.015716545 0.005412876 2.266571906 -1.216659109 DVKPHNVMIDHEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 71.692 0.013687 98752000 109735 114836 100451 121892 85587 105701 106386 83920 14333.7 FALSE TRUE 104548.044 126537.919 105056.7777 109639.1846 100513.3457 102040.5479 90154.86179 76571.51991 16556.49699 6.314623443 7.642795395 6.345350576 6.622124514 6.070930691 6.163172556 5.445286031 4.62486237 1 14.01510984 0.472050686 0.485682424 0.623017295 6.94833168 0.955664654 0.377669499 0.36171088 0.153610231 0.631386355 0.194251826 2.965177429 -0.472050686 6.325314385 DVKPSNILVNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 91.845 0.0036821 521260000 913660 849930 871780 1027700 828850 902640 1082130 1000690 895580 FALSE TRUE 870473.1025 936538.8333 911751.9753 924393.6435 973401.1776 871381.3505 917031.1938 913064.2786 1034461.972 0.84147424 0.905339063 0.881377953 0.893598477 0.940973379 0.842352231 0.8864813 0.882646538 1 19.98044918 -2.208580524 1.980474596 1.300798886 0.883816002 0.618133019 0.028582026 2071768.076 373156.013 2787951.906 0.006703015 0.006186136 2.208580524 -0.416982884 DVLDGHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVLDGHLR 8 0 P15924 P15924 DSP Desmoplakin 0 ;; 157.68 0.00037306 334020000 688240 645930 594670 643570 682610 575300 804220 740890 635180 FALSE TRUE 655708.2592 711751.0014 621936.2077 578877.1209 801656.9679 555377.2167 681521.4685 676013.7439 733680.4704 0.893724565 0.970110327 0.847693557 0.789004402 1.092651366 0.75697424 0.928907741 0.921400761 1 19.48479236 -1.57706436 4.685548094 1.00101808 0.90239614 0.100676958 0.093641804 0.000886261 8.00E-05 0.080687044 0.018824027 0.026481077 1.57706436 -0.09862194 DVLDIEQFS(ph)TVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVLDIEQFSTVK 12 0 P43250-2;F8W9W2;P43250-3;P43250;P34947 P43250-2 GRK6;GRK5 G protein-coupled receptor kinase 6;G protein-coupled receptor kinase 5 1 DVLDIEQFS(0.853)T(0.147)VK;DVLDIEQFS(0.746)T(0.254)VK 130.2 0.00023152 46479000 184275 169747 216560 263580 140396 305920 277090 261190 149321 TRUE FALSE 175564.6859 187044.4123 226489.4902 237084.4376 164881.0179 295325.9137 234814.8314 238318.8189 172476.9381 1.017902381 1.084460418 1.313158111 1.374586309 0.955959793 1.712263199 1.361427412 1.381743099 1 17.39604395 3.771783869 3.332827788 1.33302433 1.040327506 0.183609186 0.211458608 0.312167321 7.184861985 0.052719314 0.097238752 5912.673113 -3.771783869 -0.292696824 DVLFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVLFLK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;; 119.7 0.04836 1083771000 2941170 2536740 2374230 2748560 2186550 2437710 3003030 2771360 2208800 FALSE TRUE 2802146.723 2795236.69 2483090.794 2472269.527 2567883.628 2353291.491 2544862.619 2528685.026 2551329.423 1.098308473 1.095600068 0.973253697 0.969012274 1.006488462 0.922378533 0.99746532 0.991124472 1 21.28281776 3.740423896 24.54459195 0.978150002 1.096954281 0.808321611 0.023672548 41.80842324 550730.3467 0.005630033 0.009534248 5500.775187 -3.740423896 0.11880428 DVLKDVLLPWYNAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVLKDVLLPWYNAYR 15 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 174.39 8.35E-07 231820000 1136260 888060 873100 935620 927870 932160 1278340 1126420 946510 FALSE TRUE 1082551.242 978554.3236 913132.4986 841569.7 1089690.234 899879.0655 1083305.755 1027784.693 1093289.937 0.990177633 0.895054725 0.835215315 0.769758937 0.996707459 0.823092791 0.990867764 0.940084289 1 20.06024462 1.654947847 9.704048942 0.973807073 0.892396932 0.265180333 0.07128554 0.176192462 27.29180531 0.033902521 0.018087537 45.18016861 -1.654947847 -0.081410141 DVLLPWYNAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVLLPWYNAYR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 195.7 1.47E-07 486880000 974820 966120 724380 909250 885600 757220 990310 903340 825670 FALSE TRUE 928742.1905 1064568.726 757593.5395 817850.4625 1040048.36 730997.2815 839220.0212 824238.7607 953710.6867 0.973819633 1.116238647 0.794364109 0.857545662 1.090528159 0.766476974 0.879952414 0.864244023 1 19.86319216 3.743252378 24.99631077 0.886807859 1.04502914 0.285473738 0.099383541 418.9948144 2232272.056 0.024023059 0.041603017 5536.717669 -3.743252378 0.15822128 DVLLQVDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVLLQVDDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 95.573 0.017053 23048000 34807 36298 27188 36120 31774 27754 37109 31698 32312 FALSE TRUE 33161.74209 39996.80747 28434.59669 32489.14898 37315.37554 26792.87202 31447.3405 28922.35508 37322.77993 0.888512114 1.07164599 0.761856345 0.870491133 0.999801612 0.717869142 0.842577658 0.774924996 1 15.18776883 3.736262297 24.99939797 0.844465511 0.98007905 0.210149975 0.101902458 249.2834309 2711524.909 0.024764284 0.040510268 5448.316109 -3.736262297 0.135613539 DVLLQVDDERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DVLLQVDDERR 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 249.2 3.80E-16 5641700000 4633480 4180258 3973270 5159805 3677760 4324892 4782110 4847667 3888750 FALSE TRUE 4414464.583 4606231.043 4155448.36 4641131.598 4319160.18 4175119.906 4052511.29 4423179.578 4491797.489 0.982783528 1.025476116 0.925119258 1.033245958 0.961566097 0.929498695 0.902202581 0.98472373 1 22.09886146 2.487402319 18.6236788 0.941287003 0.993090132 0.136178996 0.03998351 21.34384235 38666.44743 0.012396993 0.0110104 307.1866364 -2.487402319 0.051803129 DVLSVAFSSDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 255.19 6.29E-11 620785000 938632 986130 814084 933132 857833 835587 968106 976376 853035 FALSE TRUE 894264.7255 1086617.768 851410.5566 839331.7985 1007438.804 806650.4127 820403.6492 890879.3413 985319.3111 0.907588754 1.102807746 0.864096082 0.851837358 1.02244906 0.818669038 0.83262719 0.904152929 1 19.91023181 3.712659776 24.9541552 0.887128952 1.005198271 0.216148325 0.08153368 818.9952169 789060.6963 0.020621341 0.031958681 5160.119696 -3.712659776 0.118069319 DVMQNHLLQMLCLVAMEKPASTNSDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVMQNHLLQMLCLVAMEKPASTNSDDVR 28 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 191.42 2.41E-18 652159000 974470 1034700 824770 1169150 687630 928110 917650 1044900 594080 FALSE TRUE 928408.7343 1140137.106 862586.5203 1051624.821 807552.4543 895969.318 777645.6387 953403.0166 686206.8923 1.35295746 1.661506346 1.25703564 1.532518593 1.176835242 1.305683939 1.133252445 1.389381289 1 19.38828409 2.739543791 1.125842906 1.190348942 1.486102824 0.367981395 0.152016299 0.450907514 1.190515419 0.068381061 0.063426691 548.963906 -2.739543791 0.295753882 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK 31 2 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 297.45 1.25E-81 551830000 886442 703936 810156 878652 577355 945138 1079494 950906 581474 FALSE TRUE 844541.6434 775667.8787 847302.454 790328.2316 678045.5292 912407.6341 914797.364 867639.6296 671646.0182 1.257420755 1.154876018 1.26153127 1.176703517 1.009528101 1.358465039 1.362023059 1.291810874 1 19.35734156 DVNFEFPEFQL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVNFEFPEFQL 11 0 P62081 P62081 RPS7 40S ribosomal protein S7 0 ; 97.813 0.013927 53411000 220900 194003 198471 228168 203532 180653 230722 224795 230056 FALSE TRUE 210458.4948 213772.1263 207571.0917 205232.1191 239027.9164 174396.9413 195521.1214 205110.7581 265731.9095 0.791995569 0.804465398 0.781129718 0.772327718 0.899507766 0.656289046 0.735783376 0.771871013 1 18.01961195 -1.607103929 8.647641447 1.000089906 0.775398704 0.578183779 0.059939407 0.000101514 4.61E-06 0.056705167 0.013360231 0.024711327 1.607103929 -0.224691202 DVNLRPEQLGDICVGNVLQPGAGAIMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVNLRPEQLGDICVGNVLQPGAGAIMAR 28 1 P09110;C9JDE9;P09110-2;B4DVF4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 282.9 6.34E-62 716720000 646900 528230 539370 612710 598870 568550 694420 613530 656920 FALSE TRUE 616322.319 582057.2375 564100.648 551119.2267 703312.7384 548860.9709 588473.4751 559806.0607 758791.7985 0.812241672 0.76708425 0.743419538 0.726311523 0.926885003 0.723335402 0.77554011 0.737759767 1 19.53334456 -1.15081876 4.416221894 1.000039581 0.777331593 0.581530468 0.059561123 2.11E-05 4.05E-06 0.052332527 0.012332705 0.070661238 1.15081876 -0.222707988 DVNQQEFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DVNQQEFVR 9 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;; 234.03 8.50E-10 6921373000 2219674 1898400 1804944 2143842 2009704 1933299 2378238 2094453 2164223 FALSE TRUE 2114754.409 2091849.118 1887702.468 1928338.929 2360195.741 1866348.371 2015394.114 1911051.592 2499839.65 0.845956023 0.836793319 0.755129421 0.771385048 0.944138854 0.746587235 0.806209356 0.76446967 1 21.25340413 -2.160523583 2.466885761 1.468738328 0.811676565 0.513879409 0.058374442 4790319.412 1370159.309 12553848.61 0.013660671 0.006909974 2.160523583 -0.657061763 DVPLVHLDEITLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVPLVHLDEITLFK 14 0 Q96ME1-4 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 67.964 0.056247 0 15208 12404 15843 20167 29978 14671 22900 16925 32868 FALSE TRUE 14489.14798 13667.9817 16569.41722 18139.77485 35206.15371 14162.93959 19406.18441 15442.95727 37965.00157 0.381644867 0.360015307 0.436439261 0.477802557 0.927331812 0.373052522 0.511159847 0.406768251 1 15.21238245 -5 0.203477871 3.359252115 0.395301141 0.481752459 0.166273479 124.2478815 1.232650701 119.8912586 0.372712724 1.00E-05 5 -2.963950974 DVPNETLQVEEDDRPELPWWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 ;;; 270.68 1.11E-44 841200000 579690 602430 527193 670160 436776 629930 632960 644770 463418 FALSE TRUE 552289.2025 663818.3019 551365.3205 602794.2436 512949.5961 608115.3661 536390.3269 588310.5207 535282.4966 1.031771459 1.240127047 1.030045488 1.126123584 0.958278291 1.136064358 1.002069618 1.099065492 1 19.02994095 3.660424078 24.99996024 1.051869648 1.135959533 0.182989064 0.075234526 152.4806547 48785.50825 0.017909428 0.027745168 4575.347426 -3.660424078 0.084089884 DVPPDILLDS(ph)PERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 243.09 9.95E-18 176660000 280441 264332 254407 297605 180515 315006 321797 326948 218801 TRUE FALSE 267185.1097 291267.7313 266071.8126 267689.18 211996.7588 304097.2632 272700.9574 298318.6999 252731.5416 1.057189411 1.152478751 1.052784353 1.0591839 0.838821927 1.203242228 1.07901434 1.180377795 1 17.9472462 -0.853066578 7.81693536 1.000000003 1.080396737 0.055797876 0.100218845 0 0 0.090258553 0.021274145 0.140259867 0.853066578 0.080396734 DVQALWTNDHALAWHLSDDFREDPVAWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVQALWTNDHALAWHLSDDFREDPVAWAR 29 1 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 114.06 0.00015161 82725000 29590 18356 24378 30043 47649 33104 63718 41408 21670 FALSE TRUE 28191.33934 20226.49727 25495.75541 27023.02056 55958.97051 31957.60018 53996.64884 37782.096 25030.47292 1.126280731 0.808074915 1.018588642 1.079604874 2.235633769 1.276747758 2.157236461 1.509443953 1 14.61139793 2.895318433 7.549650665 1.712653908 0.976838052 0.40277883 0.374675565 0.212240125 13.58520652 0.100337205 0.10665005 785.8115953 -2.895318433 -0.735815856 DVQEIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 157.21 0.0034697 1926100000 3671560 3008250 3151350 3604580 3290260 3169340 3831220 3390100 3578680 FALSE TRUE 3498012.635 3314794.095 3295842.515 3242240.77 3864080.302 3059584.961 3246697.024 3093244.872 4133643.417 0.846229895 0.801906154 0.797321438 0.784354247 0.93478801 0.740166641 0.785432292 0.748309556 1 21.97898251 -1.207923739 5.19462426 1.000014928 0.805666593 0.557769037 0.054615037 8.82E-06 1.35E-06 0.049412919 0.011645842 0.061954986 1.207923739 -0.194348335 DVQGTDASLDEELDRVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVQGTDASLDEELDRVK 17 1 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 ;;; 267.39 8.19E-28 479769000 651910 426243 559920 494348 425340 481714 601590 600540 522980 FALSE TRUE 621095.5063 469677.6463 585592.8858 444655.1998 499519.1613 465032.1234 509806.3965 547953.5339 604081.0674 1.02816582 0.777507642 0.969394536 0.73608531 0.826907494 0.769817411 0.843937054 0.907086091 1 19.20438265 -0.967141141 5.373956412 1.00000041 0.854514298 0.195572919 0.090749435 4.17E-07 8.00E-08 0.082212071 0.019377516 0.107859613 0.967141141 -0.145486111 DVQIGDIVTVGECRPLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVQIGDIVTVGECRPLSK 18 1 P62280;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;; 278.93 3.08E-39 2726822000 4043208 3701218 3739692 4340224 3224837 4126763 4519505 4376141 3553950 FALSE TRUE 3852093.571 4078376.322 3911160.577 3903936.438 3787247.552 3983852.163 3829971.506 3992942.895 4105078.415 0.938372713 0.993495351 0.952761478 0.951001672 0.922576177 0.970469199 0.932983763 0.972683708 1 21.96897835 0.99300322 22.93420022 1.000000002 0.953805841 0.386595822 0.019745354 98.53973121 322999.069 0.018594041 0.00464851 9.840184024 -0.99300322 -0.046194161 DVQIILESCHNQNILGTILHPNGNITELLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVQIILESCHNQNILGTILHPNGNITELLLK 31 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 362 1.43E-121 640071000 392921 346603 352407 434740 355710 389939 495490 460694 199422 FALSE TRUE 374348.403 381922.2398 368565.2095 391039.1092 417745.7114 376435.3147 419893.9002 420353.1911 230347.3453 1.62514746 1.658027529 1.600041056 1.697606321 1.813546889 1.634207307 1.822872757 1.824866662 1 17.81345145 -0.955067588 5.180889973 0.999997281 1.704805905 0.873598364 0.084803251 2.76E-06 5.56E-07 0.085022781 0.020039984 0.110900221 0.955067588 0.704808623 DVQNFPAATDEKDKFVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVQNFPAATDEKDKFVEK 18 2 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 168.27 1.19E-11 460950000 387180 338810 346740 429260 216508 412440 429010 482140 211225 FALSE TRUE 368878.7687 373335.1242 362638.372 386109.9693 254266.9267 398157.0994 363556.6452 439921.2656 243980.6942 1.511917859 1.530183056 1.486340438 1.582543121 1.042160026 1.631920512 1.490104151 1.803098672 1 17.89640747 DVQSMDELKDVYNHFLLYYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVQSMDELKDVYNHFLLYYGR 21 1 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 114.88 0.0001002 22290000 125950 136670 113650 154000 86855 127800 147630 149900 84128 FALSE TRUE 119996.5931 150596.8284 118860.9649 138519.6274 102002.4845 123374.254 125106.3321 136773.9613 97174.14057 1.234861378 1.54976239 1.223174851 1.425478287 1.049687539 1.269620222 1.287444698 1.40751398 1 16.56828482 2.791733402 24.99975143 1.231434801 1.369000875 0.199481507 0.148067703 551.677878 259376.0864 0.041911546 0.044453856 619.0609384 -2.791733402 0.137566074 DVRPYIVGAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVRPYIVGAVVR 12 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 140.01 5.41E-05 633570000 716630 470560 433370 443750 735790 410430 762500 564010 787160 FALSE TRUE 682756.3201 518510.599 453240.4432 399143.4069 864111.543 396216.7062 646166.6207 514622.2944 909228.7525 0.750918092 0.570275189 0.498488903 0.438991184 0.950378594 0.435772302 0.710675525 0.565998703 1 19.79428378 -1.530696955 2.673120101 1.021167333 0.619315639 0.372694982 0.156815656 13377239.3 13203814.82 2046576.348 0.034853729 0.029464769 1.530696955 -0.401851694 DVSELTGFPEMLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVSELTGFPEMLGGR 15 0 P31939-2;P31939;F8WEF0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 75.695 0.07227 32338000 45727 31199 41828 45677 48431 37950 62889 40981 60500 FALSE TRUE 43565.57533 34378.21357 43745.85517 41085.46118 56877.35107 36635.78198 53294.12801 37392.48639 69882.03101 0.623415987 0.4919464 0.625995761 0.587925974 0.813905238 0.524251821 0.762629924 0.535080132 1 16.09263392 -5 0.195573196 2.679478125 0.554078052 0.564667863 0.103090184 91.92330331 0.905146326 60.26068549 0.23129829 1.00E-05 5 -2.125400073 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 1 DVSGFSDPYCLLGIEQGVGVPGGS(0.855)PGS(0.145)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.854)PGS(0.146)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.815)PGS(0.185)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.821)PGS(0.179)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.989)PGS(0.011)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.961)PGS(0.039)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.787)PGS(0.213)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.981)PGS(0.019)R 197.7 3.43E-25 3606601000 1115978 932110 1073632 1141121 1062494 1072645 1281707 1154737 1305850 TRUE FALSE 1063227.932 1027093.069 1122859.089 1026413.349 1247792.617 1035499.035 1086159.057 1053622.107 1508354.549 0.704892581 0.680936103 0.744426495 0.680485467 0.827254188 0.686509041 0.720095324 0.698524168 1 20.52454415 -1.73110597 2.630218015 1.055786149 0.715670321 0.806142799 0.043464454 14047194.75 11120560.31 5130401.239 0.00948901 0.018573512 1.73110597 -0.340115829 DVSLGDWEFGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVSLGDWEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 142.1 9.79E-05 76371000 121830 112880 122990 152640 121320 133080 170500 166240 134920 FALSE TRUE 116071.3373 124382.6003 128629.2132 137296.3372 142478.1696 128471.4062 144487.0936 151683.1443 155842.7045 0.744798017 0.798129118 0.825378471 0.880993035 0.914243436 0.824365867 0.927134151 0.97330924 1 17.24973109 7.910901579 0.127310572 1.05852512 1.01E-09 0.841886848 0.03176976 28.71604644 0.253756427 0.174567143 5.421783612 81451967.42 -7.910901579 -1.058525119 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGK 32 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVSLGDWEFGKRDS(1)LGAYASQDANEQGQDLGK;DVSLGDWEFGKRDS(1)LGAYASQDANEQGQDLGK 218.16 4.05E-36 332540000 454920 385490 433610 489580 285830 472770 523650 563290 310700 TRUE FALSE 433416.8332 424771.8693 453491.4474 440366.4883 335678.6615 456397.8564 443757.575 513965.3414 358881.7692 1.207686961 1.183598348 1.263623528 1.227051709 0.935346095 1.271722042 1.236500745 1.432129981 1 18.45314911 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGKR 33 3 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVSLGDWEFGKRDS(0.998)LGAYAS(0.002)QDANEQGQDLGKR;DVSLGDWEFGKRDS(0.936)LGAYAS(0.064)QDANEQGQDLGKR;DVSLGDWEFGKRDS(1)LGAYASQDANEQGQDLGKR 295.23 9.10E-90 976110000 677260 453196 706870 609828 496390 711300 888160 817800 654634 TRUE FALSE 645247.262 499377.1876 739280.6887 548526.9308 582960.2588 686667.5026 752654.8798 746189.0966 756151.2973 0.853330893 0.660419667 0.977688845 0.725419546 0.770957163 0.908108609 0.995376035 0.986825122 1 19.5283154 2.034919696 2.987867981 0.990542109 0.788845897 0.542267122 0.082545764 0.187259481 3.296006043 0.036718249 0.022370286 108.3726508 -2.034919696 -0.201696213 DVSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVSSLR 6 0 Q69YN2;A0A286YF56 Q69YN2 CWF19L1 CWF19-like protein 1 0 101.72 0.084216 115230000 84592 96453 78761 82872 87321 86411 84898 95901 95171 FALSE TRUE 80593.50381 106281.6704 82372.26976 74541.54911 102549.7548 83418.5654 71945.25084 87503.40004 109929.6326 0.733137207 0.966815479 0.749318157 0.678084219 0.932867256 0.758836025 0.654466399 0.795994655 1 16.74622081 DVT(ph)PPPETEVVLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.999)PPPET(0.001)EVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK 172.43 3.20E-05 1391252000 963499 1101645 786223 1145201 550209 949062 866033 998642 555689 TRUE FALSE 917956.3117 1213903.878 822272.1022 1030083.22 646165.2754 916195.745 733903.7601 911195.6123 641862.4121 1.430144988 1.89122132 1.281072215 1.604834931 1.006703716 1.427402085 1.143397317 1.419612046 1 19.29190455 3.158937075 1.509370101 1.22687783 1.636890593 0.346539989 0.219334878 0.359556143 1.703454286 0.068651796 0.093186117 1441.906418 -3.158937075 0.410012762 DVTGS(ph)PPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DVTGSPPAK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 DVT(0.012)GS(0.988)PPAK;DVT(0.001)GS(0.999)PPAK 140.78 0.00011358 397910000 1229140 1094110 1134550 1354350 855750 1243140 1373990 1289900 1030140 TRUE FALSE 1171040.988 1205601.053 1186570.24 1218208.165 1004992.529 1200089.75 1164362.59 1176949.518 1189888.85 0.984159981 1.013204765 0.997210991 1.023799967 0.844610426 1.008572986 0.978547358 0.989125596 1 20.18239538 DVTNFTVGGFAPMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 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;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR 319.43 5.56E-58 5312607000 4395820 3803537 3843784 4309537 4335090 3734178 4456020 4314650 4570230 TRUE FALSE 4188038.3 4191121.745 4020025.298 3876334.153 5091128.323 3604862.48 3776172.309 3936836.373 5278957.927 0.793345649 0.79392975 0.761518723 0.734299119 0.964419189 0.68287388 0.715325328 0.745760134 1 22.33182174 -1.762590901 2.547661641 1.056462024 0.772659916 0.469475425 0.075513051 13642909.51 9922603.889 4825502.915 0.017852205 0.017274644 1.762590901 -0.283802108 DVTNNVHYENYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DVTNNVHYENYR 12 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;;; 264.61 1.48E-21 4225520000 5070100 4285530 3851110 4922900 4713410 4155750 5331920 4855620 4314750 FALSE TRUE 4830446.421 4722230.379 4027687.203 4428040.739 5535427.212 4011835.335 4518437.677 4430436.172 4983859.393 0.969218038 0.947504736 0.808146235 0.888476257 1.110670823 0.804965594 0.906614196 0.888956895 1 22.24883194 DVVICPDASLEDAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVVICPDASLEDAKK 15 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 217.48 3.31E-12 3194890000 3576080 3122040 2946210 3546290 1809200 3581240 3606260 3939080 2043700 FALSE TRUE 3407045.786 3440179.425 3081296.643 3189810.192 2124723.907 3457220.761 3056058.803 3594153.273 2360626.558 1.443280291 1.457316242 1.305287629 1.351255742 0.900067781 1.464535231 1.294596468 1.522542081 1 21.1707384 3.626368401 2.516027441 1.270986459 1.45328822 0.147298851 0.188325141 0.532403042 6.560278551 0.049612413 0.086156186 4230.273054 -3.626368401 0.182301761 DVVLS(ph)TSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DVVLSTSPK 9 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 DVVLS(0.381)T(0.381)S(0.239)PK 72.006 0.050323 41922000 160690 161720 151340 184950 104250 181350 200980 193210 130970 TRUE FALSE 153094.5022 178199.4519 158279.0887 166358.4746 122431.167 175069.804 170316.8097 176291.5081 151280.1587 1.011993268 1.177943317 1.046264692 1.099671471 0.809300889 1.157255555 1.125837064 1.165331327 1 17.20686326 -0.647773096 7.648800229 1.000001421 1.079008952 0.043201686 0.107645318 0 0 0.098532436 0.023224318 0.225022997 0.647773096 0.079007531 DVVLSTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DVVLSTSPK 9 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 DVVLS(0.001)T(0.048)S(0.95)PK;DVVLS(0.002)T(0.143)S(0.855)PK;DVVLST(0.16)S(0.84)PK;DVVLST(0.005)S(0.995)PK 148.28 9.48E-05 339854000 1661440 1583960 1581350 1907380 958910 1769820 1787060 1888040 1149320 TRUE FALSE 1582907.024 1745367.325 1653856.462 1715646.539 1126143.6 1708530.69 1514411.175 1722713.208 1327550.676 1.192351488 1.314727458 1.245795352 1.292339773 0.848286714 1.286979639 1.140755832 1.297662861 1 20.3403355 -5 0.122123395 0.379680815 1.296366012 0.160186355 0.138144637 264.1455703 2.079630329 41.15557504 1.169676966 1.00E-05 5 0.916685197 DVYDYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DVYDYFR 7 0 P49354;E9PQP6;H0YCW1 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 ;; 114.72 0.01359 219569000 804090 651620 444730 521920 779200 485040 832380 668290 735210 FALSE TRUE 766082.2593 718020.8188 465121.3104 469455.61 915092.2333 468242.9432 705385.1433 609770.9848 849222.6119 0.902098282 0.845503651 0.547702456 0.5528063 1.077564611 0.551378327 0.830624542 0.718034325 1 19.69578326 -0.731653465 6.660677943 1.000000001 0.763876312 0.166131594 0.172292573 1.16E-09 5.23E-10 0.155904919 0.036747142 0.18550112 0.731653465 -0.236123689 DVYKEHFQDDVFNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DVYKEHFQDDVFNEK 15 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 240.24 4.70E-18 1252886000 2622630 1990980 2519300 2565410 1690737 2678460 3022750 3058690 1587170 FALSE TRUE 2498663.477 2193863.126 2634812.397 2307530.113 1985600.997 2585704.259 2561573.971 2790854.888 1833300.217 1.36293197 1.19667423 1.437196359 1.258675525 1.083074653 1.410409618 1.397247405 1.522311982 1 20.80601163 DVYLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 137.28 0.0030404 43014400000 11137600 11150330 9602740 11548870 9010260 10241710 10437570 10492550 8745910 TRUE FALSE 10611147.72 12286561.3 10043035.13 10387955.65 10581646.49 9887037.015 8845126.997 9573766.697 10102181.05 1.050381859 1.216228578 0.994145232 1.028288405 1.047461576 0.978703209 0.875566073 0.947693042 1 23.26816347 2.854785898 0.878037946 0.930959569 1.124132808 0.454704517 0.064621575 0.419441085 0.705118947 0.036930888 0.039123019 715.7904463 -2.854785898 0.193173239 DVYLS(ph)PRDDGYSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 DVYLSPRDDGYSTK 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" 1 DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK 189.77 4.12E-07 14919370000 13557750 5926642 13406240 10927510 12538610 13086170 20421540 14948330 16588610 TRUE FALSE 12916902.03 6530573.558 14020929.36 9829055.934 14725339.61 12632992.65 17305859.01 13639374.98 19161086.92 0.674121572 0.340824797 0.731739772 0.512969644 0.768502313 0.659304595 0.903177314 0.711826789 1 24.19167606 1.954308997 0.48891199 0.973429766 0.505807795 0.513455597 0.128077112 0.626592466 0.338150587 0.116753458 0.090426944 90.01377948 -1.954308997 -0.467621971 DVYVQLYLQHLTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 228.19 1.75E-12 202100000 328710 294450 319100 384790 415310 331770 438870 347430 355860 FALSE TRUE 313172.5297 324454.7898 333731.0506 346110.1781 487739.9325 320280.7217 371912.3211 317007.1874 411044.9513 0.761893629 0.789341382 0.811908891 0.842025129 1.186585387 0.779186609 0.9047972 0.771222676 1 18.64893665 2.993122922 24.56293836 0.919237939 0.789698525 0.237389678 0.115947851 375.4289033 1340932.776 0.032257071 0.037183822 984.2896577 -2.993122922 -0.129539414 DWALNHLDDNEVWITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DWALNHLDDNEVWITR 16 0 Q9H9F9 Q9H9F9 ACTR5 Actin-related protein 5 0 ; 206.8 1.91E-11 81167000 75199 71633 71775 80242 78107 63282 88201 83370 73070 FALSE TRUE 71644.4923 78932.48414 75065.95475 72175.92171 91728.83607 61090.52847 74744.31753 76069.68083 84401.32241 0.848855092 0.935204353 0.889393111 0.85515155 1.086817522 0.723810086 0.885582304 0.901285414 1 16.36497798 2.183199556 0.007006323 1.79699538 2.90E-06 0.056472541 0.092749725 15736.40776 69.58184243 8830.510064 9009.844501 152.475321 -2.183199556 -1.796992482 DWDAWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DWDAWK 6 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;;;; 129.96 0.037149 2249820000 6147720 5827260 5183730 5077500 4023810 4441590 5004810 5313210 3730000 FALSE TRUE 5857129.459 6421064.419 5421409.148 4567100.053 4725561.19 4287776.625 4241234.315 4847957.165 4308429.35 1.359458165 1.490349243 1.258326111 1.060038284 1.096817612 0.995206438 0.984403821 1.125226103 1 22.0387306 3.391964497 2.55886692 1.034115393 1.424626543 0.892206008 0.055461304 0.072128201 0.95592459 0.015881817 0.023363591 2465.837749 -3.391964497 0.39051115 DWDDDQND ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 153.04 0.0010411 407150000 1736720 1522740 1564550 1786770 1339070 1661570 1827970 1732410 1334340 FALSE TRUE 1654628.687 1677908.937 1636286.165 1607160.485 1572603.384 1604029.414 1549079.604 1580710.996 1541262.632 1.073554015 1.088658676 1.061653044 1.042755758 1.020334465 1.040724261 1.005071797 1.025594836 1 20.55568129 3.116054407 1.164896189 1.016356895 1.082805958 0.836911312 0.011567756 0.151847176 0.43974188 0.004322099 0.005884512 1306.33453 -3.116054407 0.066449063 DWEDDS(ph)DEDMSNFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 30 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(0.995)DEDMS(0.005)NFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR 439.03 5.77E-175 1.10029E+11 17533215 21951418 14510719 20456532 11477744 18461845 15226462 16818883 7846922 TRUE FALSE 16704454.67 24188292.45 15176049.82 18400202.54 13479458.92 17822506.68 12903385.57 15346132.44 9063782.587 1.842989338 2.668675271 1.674361634 2.030079866 1.487178095 1.966343136 1.423620375 1.693126716 1 23.11168183 1.693842198 0.279130036 0.908258631 2.371733781 0.513111757 0.305463092 1.174923894 0.345105954 0.594988437 0.632055311 49.4131111 -1.693842198 1.46347515 DWEDDSDEDMS(ph)NFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 DWEDDS(0.379)DEDMS(0.621)NFDR 58.752 0.0885 0 10123 12177 8991.8 10673 8258.4 11172 8853.3 8528.5 7096.5 TRUE FALSE 9644.505852 13417.85014 9404.082924 9600.129763 9698.662345 10785.11084 7502.566483 7781.699328 8196.988976 1.176591292 1.636924264 1.147260653 1.171177586 1.183198169 1.315740557 0.915283222 0.949336317 1 13.00087834 2.277583912 0.66967386 0.93461545 1.374426998 0.421106265 0.156819675 0.62316046 0.547996164 0.132055879 0.090905438 189.48896 -2.277583912 0.439811547 DWEDDSDEDMSNFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;; 280.57 2.39E-33 217906000 323782 408286 280555 386936 213225 326058 281745 322187 197479 FALSE TRUE 308477.4665 449890.8076 293418.7243 348040.4581 250411.3725 314766.5297 238759.6256 293974.5983 228103.0347 1.352360204 1.972313994 1.286342922 1.525803717 1.09779939 1.379931355 1.046718321 1.288779865 1 17.79932612 3.047819238 1.322638141 1.162535253 1.639183888 0.418249457 0.212793938 0.345100955 1.263337305 0.07608141 0.095211426 1116.398484 -3.047819238 0.476648635 DWEQFEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DWEQFEYK 8 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7;F5H3L6;F5H2F3;F5GZW1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 155.07 0.00096527 830540000 805990 854530 682230 803510 489720 735030 715590 768110 442159 FALSE TRUE 767892.45 941607.5785 713510.9203 722739.6482 575127.0129 709575.7268 606413.6028 700850.2164 510726.7595 1.503528914 1.843662117 1.397050198 1.415119993 1.126095319 1.389345112 1.187354278 1.372260614 1 18.96219213 3.3666299 2.058125114 1.244913685 1.669034952 0.566527757 0.15110506 0.192297228 1.658926741 0.041161014 0.0618915 2326.108132 -3.3666299 0.424121267 DWEQFHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 236.16 3.21E-10 1430980000 993140 1016320 873160 1167500 861300 954100 948050 966560 682460 FALSE TRUE 946196.2404 1119884.163 913195.2497 1050140.682 1011510.447 921059.2778 803407.5604 881922.8823 788292.4113 1.200311238 1.420645623 1.158447343 1.332171497 1.283166542 1.168423373 1.019174546 1.118776319 1 19.58837136 2.023737791 2.819338296 1.050548239 1.288562184 0.657025256 0.076608041 0.151175102 2.330121768 0.034675778 0.020491084 105.6179639 -2.023737791 0.238013945 DWILPSDYDHAEAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 301.48 5.90E-46 1358880000 1975220 2316130 1615250 2397340 1612780 1804780 1760880 1882420 1144450 FALSE TRUE 1881855.265 2552146.28 1689310.81 2156354.829 1894048.321 1742280.016 1492225.415 1717585.325 1321925.461 1.423571389 1.930627978 1.277916842 1.631222707 1.432795099 1.317986579 1.128827199 1.29930573 1 20.3342094 2.144541009 0.651867513 1.053153312 1.647119148 0.526471988 0.177556984 0.50682612 0.420365288 0.146305673 0.094183329 139.4893368 -2.144541009 0.593965836 DWNEELQTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DWNEELQTTR 10 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;; 199.17 6.59E-07 564940000 365070 355780 338573 402370 362340 371290 442180 383350 411080 FALSE TRUE 347813.8646 392034.3865 354096.9069 361923.0031 425531.9813 358432.1342 374717.3198 349781.8417 474828.1869 0.732504671 0.825634192 0.745736914 0.762218868 0.896180962 0.754867011 0.789164018 0.736649279 1 18.85704605 -1.572047735 2.799693683 1.013757234 0.782781304 0.660996162 0.049404009 7185876.23 7431467.63 738191.4709 0.010903287 0.026788739 1.572047735 -0.230975931 DWPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DWPDAR 6 0 P12532;P12532-2;F8WCN3;P17540;H0YJJ7;P12277;H0YJG0;G3V4N7;P06732 P12532;P12277 CKMT1A;CKMT1B;CKMT2;CKB;CKM "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial;Creatine kinase B-type;Creatine kinase M-type;Creatine kinase M-type, N-terminally processed" 0 ; 120.9 0.046264 1270720000 1787010 1445430 1520900 1800370 1583670 1426140 1738890 1564370 1458980 FALSE TRUE 1702541.579 1592720.96 1590634.769 1619393.387 1859861.547 1376752.414 1473590.394 1427385.47 1685231.167 1.010271832 0.945105331 0.943867406 0.960932493 1.103623991 0.816951669 0.874414396 0.846996838 1 20.68451507 2.215881776 24.99997045 0.872114331 0.984184728 0.39273298 0.065551953 217.4302916 239682.3308 0.022402202 0.016556721 164.3924153 -2.215881776 0.112070398 DWQSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DWQSGR 6 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 122.54 0.04461 824970000 646930 634210 669180 700770 545900 675890 752100 595830 512620 FALSE TRUE 616350.901 698836.72 699862.5649 630327.2682 641104.7872 652483.7598 637353.3317 543655.9665 592114.4915 1.040931965 1.180239177 1.181971688 1.064536128 1.082737876 1.101955397 1.076402184 0.918160211 1 19.17551664 1.381025691 4.179184978 0.960641557 1.110317183 0.606744964 0.048894622 0.145667715 3.995331979 0.036140282 0.012430447 24.04505037 -1.381025691 0.149675626 DWQSYYYHHPQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 196.18 8.32E-08 6190250000 2221851 2104987 1863564 2355912 2204567 1948655 2145061 2121287 280870 FALSE TRUE 2116828.507 2319487.568 1949010.253 2119091.25 2589042.787 1881172.589 1817792.548 1935535.865 324425.8851 6.524844668 7.149514496 6.007567035 6.531819275 7.980382903 5.798466383 5.603105767 5.966034011 1 18.30752941 -0.185246258 0.501283168 0.291091113 6.819869319 0.885915721 0.62454417 1.687018866 0.456398165 2.870518767 0.296018019 0.652760313 0.185246258 6.528778206 DWQSYYYHHPQDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DWQSYYYHHPQDRDR 15 1 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 130.72 3.74E-05 3067751000 654080 261892 487860 445135 988669 475976 905824 622530 138084 FALSE TRUE 623162.9347 288579.0925 510228.8636 400389.1841 1161092.561 459492.8318 767623.9122 568017.973 159497.3615 3.907042279 1.809303238 3.198979963 2.510318543 7.279697606 2.880880458 4.81276872 3.561300122 1 17.28317303 DWTISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DWTISR 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 172.39 0.01195 1365170000 1449870 1269710 1216800 1346110 1324300 1206520 1571250 1335280 1468770 FALSE TRUE 1381337.518 1399094.893 1272591.484 1210796.465 1555257.501 1164737.91 1331526.955 1218355.804 1696539.35 0.814208947 0.824675769 0.750110207 0.713686049 0.916723506 0.686537515 0.784848848 0.718141789 1 20.69416346 -1.427573937 6.016825567 1.000078893 0.780602535 0.527429933 0.066479706 6.42E-05 6.10E-06 0.058701194 0.013831047 0.037361651 1.427573937 -0.219476359 DWVLNEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DWVLNEFK 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 130.96 0.0023855 538868000 1382650 1125110 874320 978200 1054440 1043710 1504130 1271680 1072800 FALSE TRUE 1317294.875 1239759.988 914408.4368 879869.4775 1238334.002 1007566.061 1274647.343 1160324.958 1239164.345 1.063050983 1.000480681 0.737923457 0.710050673 0.999329917 0.813101236 1.028634619 0.936376972 1 20.24093611 1.683266459 12.24294578 0.986295041 0.905700033 0.130717566 0.116431248 0.3391411 65.05890945 0.059594917 0.032598377 48.2243585 -1.683266459 -0.080595008 DWVLNEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DWVLNEFR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;; 196.77 0.00034763 1337857000 2313990 2102760 1432130 1735543 2185057 1519673 2264010 1943223 1987244 FALSE TRUE 2204612.279 2317033.635 1497794.577 1561082.92 2566130.249 1467046.343 1918593.693 1773064.092 2295415.65 0.960441425 1.009417895 0.652515625 0.680087251 1.117937071 0.639120128 0.835837158 0.77243705 1 21.13032399 3.76993152 24.84904355 0.805388454 0.984929709 0.179438131 0.151102698 867.6596389 687274.3153 0.035390095 0.063792778 5887.508126 -3.76993152 0.179541255 DWYDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DWYDVK 6 0 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;; 153.61 0.023518 2244406000 7321100 7090760 6618350 8046340 4898650 6978400 7846280 7827060 5232370 FALSE TRUE 6975046.112 7813316.506 6921807.894 7237506.616 5752973.009 6736736.258 6649185.879 7141681.133 6043779.216 1.154086849 1.292786554 1.145278086 1.197513403 0.951883383 1.114656247 1.100170215 1.181658177 1 22.52701953 2.955466164 24.87967157 1.080845493 1.206611255 0.420342497 0.073631048 394.4890443 220388.6184 0.021183806 0.022469864 902.5393872 -2.955466164 0.125765763 DWYPHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;; 157.58 0.0014664 26969330000 8181630 7003330 5323540 7355950 6050760 5717690 6372560 6087090 4519660 FALSE TRUE 7794900.564 7716977.289 5567629.575 6616515.931 7106010.628 5519684.962 5400308.932 5554072.13 5220545.79 1.493119853 1.478193584 1.066484195 1.267399272 1.361162398 1.057300364 1.034433783 1.063887255 1 22.31576921 4.176415674 0.313031228 0.971340795 1.834827407 0.653916255 0.11056452 2.807968323 0.293408392 0.124367196 0.902028305 15011.20909 -4.176415674 0.863486612 DYAAYNVLDDPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYAAYNVLDDPELR 14 0 Q86SX6 Q86SX6 GLRX5 "Glutaredoxin-related protein 5, mitochondrial" 0 ;;; 245.15 2.86E-17 178004000 426433 333114 373705 371762 386817 308264 388110 375259 409707 FALSE TRUE 406276.3572 367058.6953 390839.7439 334391.7775 454277.7623 297588.7404 328896.6914 342399.3326 473242.2691 0.858495497 0.775625339 0.825876659 0.706597443 0.959926431 0.628829587 0.694985873 0.723518069 1 18.85221941 2.21925404 24.99956216 0.728134356 0.816177581 0.031924208 0.115994955 487.735563 631551.6382 0.038290545 0.02832215 165.6738789 -2.21925404 0.088043224 DYAFIHFDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DYAFIHFDER 10 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 156.51 1.08E-05 1213490000 2040202 2143952 1662757 2348529 1637651 1721996 1889805 1911532 1242537 FALSE TRUE 1943765.695 2362423.146 1738996.053 2112450.403 1923256.816 1662362.847 1601480.539 1744148.124 1435223.292 1.354329814 1.646031777 1.211655401 1.471861845 1.340040136 1.158260778 1.115840683 1.215245136 1 20.45284378 2.283598558 0.713399408 1.054969872 1.479251103 0.586339712 0.119163495 0.434143943 0.429736612 0.092828772 0.061392036 192.1314934 -2.283598558 0.424281231 DYAFVHFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DYAFVHFEDR 10 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 176.48 2.48E-06 2206630000 2980520 2776520 2437460 3107920 2679290 2457890 2855920 2789020 2180370 FALSE TRUE 2839636.726 3059450.545 2549219.952 2795505.977 3146557.328 2372772.653 2420196.951 2544798.623 2518490.644 1.127515297 1.214795279 1.012201478 1.1099926 1.249382179 0.942140746 0.96097119 1.010445931 1 21.26412794 2.222176988 24.9992306 0.972440812 1.143785054 0.61082375 0.065121822 155.5094439 237285.1182 0.023831098 0.017650665 166.7926804 -2.222176988 0.171344242 DYAFVHMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DYAFVHMEK 9 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 ;; 142.43 0.00010435 210430000 1308150 1281570 1023870 1428320 898840 1200640 1237990 1250960 759870 FALSE TRUE 1246316.342 1412163.44 1070815.452 1284742.56 1055597.411 1159061.536 1049111.888 1141419.311 877706.7587 1.419968947 1.608923967 1.220015047 1.463749193 1.202676635 1.320556694 1.195287467 1.30045633 1 19.74337949 2.83066763 0.119456971 0.769925228 1.922538781 0.580287462 0.108789914 9.978142339 0.476160603 1.492849309 2.887860774 677.1230996 -2.83066763 1.152613554 DYAFVHMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 112.75 0.0019122 150140000 168650 159090 134580 193820 131790 135010 159260 163490 129580 FALSE TRUE 160678.2487 175301.4519 140750.6261 174336.8454 154774.1343 130334.5698 134961.962 149173.9489 149674.6046 1.073517108 1.17121707 0.940377471 1.16477238 1.034070774 0.870786131 0.901702479 0.996655039 1 17.19146993 2.426240401 5.667269389 0.929492666 1.092591749 0.460745816 0.073577033 0.143606942 10.23591701 0.024031556 0.020151678 266.8335294 -2.426240401 0.163099082 DYALHWLVLGTHTSDEQNHLVVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYALHWLVLGTHTSDEQNHLVVAR 24 0 Q16576;E9PC52;Q16576-2;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 249.34 1.07E-38 255683000 166000 115829 145242 189324 213134 128403 259283 182455 109168 FALSE TRUE 158153.509 127632.1068 151901.4894 170292.7918 250304.5021 123956.3719 219724.6163 166478.2729 126097.2159 1.254218881 1.012172282 1.204637932 1.350488118 1.985012122 0.983022274 1.742501726 1.320237499 1 16.9441769 3.210595363 3.791081696 1.458012876 1.134233298 0.106596866 0.307079409 0.334467206 10.25461987 0.080078519 0.102142039 1624.03492 -3.210595363 -0.323779578 DYAPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 128.38 0.0087545 159240000 239780 258150 234330 299460 256810 241960 268020 245980 298680 FALSE TRUE 228446.0746 284455.7785 245074.2623 269357.7119 301597.5827 233580.8645 227128.6265 224440.6872 344997.769 0.662166817 0.824514835 0.710364774 0.78075204 0.874201545 0.677050362 0.658348102 0.650556923 1 18.39622751 DYAPPPRDYTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYAPPPRDYTYR 12 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 ;;; 166.48 4.72E-05 688060000 315565 116673 347061 224991 452672 292841 579450 361598 700506 FALSE TRUE 300648.8678 128562.1113 362974.0901 202374.4772 531617.8535 282699.8427 491044.2602 329934.5622 809136.8928 0.371567371 0.158887961 0.448594167 0.250111544 0.657018433 0.349384443 0.606874145 0.407761116 1 19.62602428 -4.999999997 0.124634473 3.072459106 0.109886465 0.677734612 0.134907239 74.20182627 0.592185384 38.25400668 1.013848336 1.00E-05 4.999999997 -2.962572641 DYAVSTVPVADGLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYAVSTVPVADGLHLK 16 0 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ; 214.53 1.69E-14 581210000 717340 654070 578720 751920 463030 634120 684760 732680 486720 FALSE TRUE 683432.7598 720720.4766 605254.8844 676335.573 543782.2854 612160.2654 580287.2855 668522.655 562198.0518 1.215644127 1.281969004 1.076586592 1.203020129 0.967243276 1.088869418 1.03217591 1.189123038 1 19.10071893 3.46664015 1.420808006 1.064556662 1.250067327 0.426385745 0.077928156 0.318160846 1.305926722 0.022963859 0.04217134 2928.465753 -3.46664015 0.185510665 DYDDMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 176.48 0.00027278 88061682000 56462650 48758480 50808970 56251380 45182690 54344610 60335510 57010410 45353180 TRUE FALSE 53793772.43 53727024.55 53138611.53 50596884.41 53062536.83 52462642.53 51130219.81 52018276.27 52386319.52 1.026866803 1.025592655 1.014360467 0.965841557 1.012908281 1.001456926 0.976022371 0.99297444 1 25.64268677 3.462967834 23.65227481 0.990956751 1.025187539 0.563283635 0.013058703 76.698051 128171.9377 0.003438923 0.004659341 2903.807575 -3.462967834 0.034230787 DYDDMSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;;;;; 203.07 0.00022944 18349260000 20777950 18098890 19000760 20700220 18176700 19867820 22328030 20660470 18160380 FALSE TRUE 19795817.48 19943187.47 19871963.64 18619394.56 21346710.73 19179792.41 18921478.94 18851329.72 20976598.98 0.943709583 0.95073503 0.947339636 0.887626949 1.01764403 0.914342331 0.902027967 0.898683802 1 24.32227745 DYDEEEQGYDS(ph)EK ddPTM_SK-BR-3_Trastuzumab_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 228.76 7.24E-12 253061000 554260 694890 428000 625300 315530 704160 526660 606400 233950 TRUE FALSE 528061.2282 765700.081 447624.2233 562443.656 370558.3321 679774.7626 446308.3442 553300.4013 270229.7711 1.954119363 2.833514893 1.656457841 2.081353411 1.371271309 2.515543568 1.651588359 2.047518299 1 18.0438271 -1.419515957 0.177245919 5.34E-13 2.425035453 0.361075519 0.422837151 27.4303152 0.886892308 14.53330794 1.583266183 0.038061337 1.419515957 2.425035453 DYDEEEQGYDS(ph)EKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYDEEEQGYDSEKEK 15 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEK 231.06 1.48E-13 1468800000 1517800 1569600 1149300 1668400 604430 1636500 1465800 1629500 406730 TRUE FALSE 1446056.602 1729544.024 1201996.542 1500689.262 709842.4006 1579827.595 1242165.289 1486812.341 469803.6111 3.078002314 3.681419179 2.55850852 3.194290607 1.510934322 3.362740424 2.644009666 3.164752902 1 18.84169828 3.726151025 24.12006512 2.602502603 3.379710739 0.18034861 0.75935282 697.6912131 1356077.353 0.177600767 0.277513 5322.933311 -3.726151025 0.777208136 DYDEEEQGYDS(ph)EKEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;DYDEEEQGY(0.004)DS(0.996)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK 257.75 5.78E-27 5227270000 4379214 4678711 3326451 4512274 1194282 4894492 3872651 4666334 916440 TRUE FALSE 4172217.233 5155476.97 3478972.069 4058691.645 1402564.403 4724994.515 3281806.964 4257725.057 1058556.835 3.941420145 4.870288303 3.286523647 3.834174521 1.324977891 4.463619109 3.100265244 4.022197881 1 20.0136673 3.629159516 5.113653475 3.12686249 4.400874405 0.207522652 1.120812957 0.317941724 12.33181106 0.268467909 0.42195311 4257.547642 -3.629159516 1.274011916 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DYDEEEQGYDSEKEKKEEK 19 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKKEEK;DYDEEEQGYDS(1)EKEKKEEK;DYDEEEQGYDS(1)EKEKKEEK;DYDEEEQGY(0.033)DS(0.967)EKEKKEEK;DYDEEEQGYDS(1)EKEKKEEK 234.39 2.16E-23 2459140000 2826260 2021880 2302220 2578930 704080 3129930 2758960 3306020 574816 TRUE FALSE 2692668.291 2227911.871 2407779.064 2319691.057 826871.3291 3021539.739 2338029.98 3016527.362 663955.5295 4.055494941 3.355513693 3.626416164 3.493744616 1.245371553 4.55081644 3.521365327 4.543267174 1 19.34072709 4.700143319 1.038916917 3.269766271 4.42564878 0.048171733 1.189477223 6.355514648 5.810513607 0.332249142 8.061001863 50135.26552 -4.700143319 1.15588251 DYDS(ph)PERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;DYDS(1)PERER 105.13 0.0082794 258586000 616960 642970 548440 684360 520150 620780 571220 624580 521210 TRUE FALSE 587797.5235 708489.374 573586.5165 615566.8326 610863.9953 599282.2329 484069.8978 569888.4641 602036.5848 0.976348512 1.17682113 0.952743622 1.022474129 1.014662581 0.995424943 0.804053956 0.946601051 1 19.19949163 1.953076011 7.432719947 0.895683407 1.037599203 0.290705798 0.076717328 0.255248812 35.23707927 0.031382512 0.019802593 89.75858771 -1.953076011 0.141915796 DYDTLSKCS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYDTLSKCSPK 11 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 DYDT(0.121)LS(0.301)KCS(0.578)PK;DYDT(0.005)LS(0.027)KCS(0.968)PK 64.244 0.042108 600260000 1132460 654950 1130440 927540 606130 1201560 1418910 1385880 802580 TRUE FALSE 1078930.86 721690.1496 1182271.792 834301.917 711838.8801 1159949.676 1202429.219 1264525 927040.0074 1.163844981 0.778488678 1.275319061 0.899963227 0.767862093 1.251240148 1.297062921 1.364045769 1 19.82227208 2.162835796 11.83641112 1.258005333 0.977099591 0.318166851 0.180233396 0.612635654 93.21056947 0.062601716 0.046236608 145.4908883 -2.162835796 -0.280905742 DYDVDHPGEADSVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYDVDHPGEADSVLR 15 0 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 0 125.28 9.14E-05 49385000 76488 72185 66267 80746 92658 70909 92050 82358 86457 FALSE TRUE 72872.56382 79540.73357 69305.4075 72629.25867 108817.5259 68453.40355 78006.08189 75146.29691 99864.31 0.72971579 0.79648809 0.693995758 0.727279432 1.08965381 0.685464142 0.781120722 0.752484015 1 16.60768155 -2.20814763 2.144154034 1.612631914 0.780817443 0.262643205 0.114763674 7467574.476 1327416.582 22197572.81 0.025872362 0.006192305 2.20814763 -0.831814472 DYDVYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 114.02 0.013954 698607000 2159520 1865500 1852230 2335560 2121870 1987140 2432990 2220710 2110820 FALSE TRUE 2057443.769 2055596.571 1937156.578 2100785.072 2491923.456 1918324.844 2061792.691 2026252.86 2438155.185 0.843852673 0.843095051 0.794517342 0.861628942 1.02205285 0.786793579 0.845636366 0.831059841 1 21.21735852 -2.392457347 2.236685779 2.116398998 0.852093911 0.338604504 0.064281658 2436707.086 338753.432 13789210.76 0.01475199 0.004050817 2.392457347 -1.264305087 DYDWINAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYDWINAER 9 0 O95347-2;O95347;A0A0C4DGE5 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ; 161.27 0.00015044 186662000 313820 340450 272770 388100 262850 313420 318830 332040 263690 FALSE TRUE 298986.3505 375142.2421 285276.7743 349087.4507 308690.9568 302566.1868 270186.6278 302964.8173 304581.6985 0.981629402 1.231663767 0.93661824 1.146120901 1.013491481 0.99338269 0.887074401 0.99469147 1 18.21646973 2.35061504 2.454242979 0.94909658 1.082484977 0.230431291 0.087035667 0.322504821 3.982003116 0.033044803 0.025333069 224.1893821 -2.35061504 0.133388397 DYEEIGPSICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYEEIGPSICR 11 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 192.64 3.03E-06 133250000 130450 116360 124990 133600 135220 136690 154290 152390 140960 FALSE TRUE 124283.887 128217.2163 130720.9151 120170.2742 158802.3252 131956.391 130750.2268 139045.9237 162819.3569 0.76332378 0.787481407 0.802858564 0.738058892 0.975328292 0.810446581 0.80303859 0.853988902 1 17.3129127 -5 0.129239661 1.63063956 0.730518456 0.523762876 0.059402818 114.2377846 0.933418245 18.6715214 0.435469217 1.00E-05 5 -0.900121104 DYEEVGADS(ph)ADGEDEGEEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 1 DYEEVGADS(1)ADGEDEGEEY;DYEEVGADS(1)ADGEDEGEEY 316.6 6.55E-49 157930000 573820 546340 497590 583470 407880 530150 522050 531980 416500 TRUE FALSE 546696.6658 602012.6671 520404.9937 524818.4871 479014.1429 511790.7726 442401.6844 485397.011 481088.6928 1.136373966 1.251354846 1.081723602 1.090897572 0.995687801 1.06381792 0.919584457 1.008955351 1 18.87594337 3.122470056 1.162297129 0.984022255 1.193202787 0.692810478 0.050237145 0.215976336 0.622903489 0.019270442 0.026424311 1325.775705 -3.122470056 0.209180532 DYEEVGADSADGEDEGEEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ;; 445.43 9.95E-191 3135200000 6090300 6408987.5 5817403.9 6772991.4 4925379.9 6207427.6 6246084.7 6436707 4829328.5 FALSE TRUE 5802423.589 7062070.613 6084137.623 6092157.437 5784364.595 5992462.826 5293129.762 5873074.812 5578236.099 1.040189674 1.266004251 1.090692024 1.092129721 1.036952272 1.074257654 0.948889518 1.052855187 1 22.41137757 2.826423654 1.233086168 1.006453653 1.150416899 0.3919423 0.064254466 0.386570217 1.219199949 0.027873662 0.028373037 670.5384 -2.826423654 0.143963246 DYEEVGVDSVEGEGEEEGEEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 DYEEVGVDSVEGEGEEEGEEY 21 0 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;;;;;;;;;;;;;; 317.99 1.99E-66 1909673000 4798944 5019944 4763892 5352256 4049248 4996857 5108508 5236342 4088329 FALSE TRUE 4572107.428 5531482.001 4982321.16 4814237.058 4755435.569 4823814.589 4329111.28 4777820.135 4722326.181 0.96818967 1.171346872 1.055056548 1.019463051 1.007011245 1.02149119 0.916732795 1.011751402 1 22.17106626 2.800905242 1.410520307 0.975463896 1.072626821 0.25054243 0.056336816 0.457625971 1.851698924 0.02325146 0.023372625 632.2738818 -2.800905242 0.097162925 DYEHQFHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYEHQFHLR 9 0 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 150.08 4.98E-05 204174000 186688 176738 146781 189986 168331 150374 190183 156015 30816.4 FALSE TRUE 177863.6282 194747.8031 153511.054 170888.2463 197687.8731 145166.5107 161167.0904 142353.4995 35595.24992 4.996836055 5.471173922 4.312683697 4.800872215 5.553771178 4.078255132 4.527769597 3.99922742 1 15.11939711 -0.411593316 0.386540692 8.77E-12 5.159644927 0.893071069 0.418785975 2.096932392 0.322959397 3.180757586 0.277993413 0.387620452 0.411593316 5.159644927 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.941)PT(0.022)NT(0.037)LLGSAK;DYEIESQNPLAS(0.989)PT(0.01)NT(0.001)LLGSAK;DYEIESQNPLAS(0.985)PT(0.014)NT(0.001)LLGSAK;DYEIESQNPLAS(0.983)PT(0.015)NT(0.001)LLGSAK;DYEIESQNPLAS(0.998)PT(0.002)NTLLGSAK;DYEIESQNPLAS(0.987)PT(0.013)NTLLGSAK;DYEIESQNPLAS(0.947)PT(0.02)NT(0.033)LLGSAK 346.04 4.38E-96 1706757000 1170179 1010515 1046928 1191193 786555 1038634 1202749 1105966 738942 TRUE FALSE 1114866.958 1113487.627 1094930.684 1071452.017 923729.943 1002665.844 1019247.55 1009121.754 853533.3514 1.306178553 1.304562529 1.282821207 1.255313591 1.082242353 1.174723685 1.194150818 1.182287432 1 19.703088 7.999997867 0.032819464 0.202297669 2.733748096 0.756452002 0.048505753 537.5375045 1.350645162 31.81037389 83.86529398 99999508.81 -7.999997867 2.531450426 DYEYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYEYNR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 164.78 0.017396 4020890000 3694320 2995510 3046740 3667710 3368640 3157960 3956770 3398850 3557720 FALSE TRUE 3519696.815 3300755.875 3186436.043 3299024.823 3956129.749 3048599.053 3353092.065 3101228.676 4109433.047 0.856492069 0.803214418 0.775395537 0.80279318 0.962694781 0.741853929 0.815950041 0.754660957 1 21.97050794 -1.435960157 3.101427634 1.003268428 0.815425878 0.471605633 0.061816195 22658051.08 29627111.25 658149.4627 0.013545539 0.036647119 1.435960157 -0.18784255 DYFEEYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DYFEEYGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 170.66 0.0006837 15165200000 11291680 12724110 8771010 12933150 5822840 10679500 9475600 10899660 5369790 FALSE TRUE 10757944.66 14020711.28 9173169.484 11633085.19 6838341.452 10309666.24 8029923.189 9945227.988 6202509.608 1.734450302 2.260490053 1.478944825 1.875544888 1.102512029 1.662176585 1.294624869 1.603420005 1 22.56442063 3.20234096 1.413341479 1.378201173 1.972714505 0.402866257 0.285998476 0.342056184 1.42893754 0.090267609 0.128865371 1593.459245 -3.20234096 0.594513331 DYFEEYGKIDTIEIITDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;;;;;;;; 309.45 3.74E-61 15952209500 15355548.4 10182181.7 13483834 14147907.9 10583980 13683557.8 17376679.7 15948298.8 11303419.4 FALSE TRUE 14629722.06 11219757.59 14102081.13 12725733.32 12429822.76 13209692.76 14725548.07 14551781.21 13056295.95 1.12051091 0.859336954 1.080098152 0.974681745 0.952017541 1.011748877 1.127850358 1.114541311 1 23.63824233 1.873172554 5.723594961 1.091901734 0.991742606 0.190502289 0.077530156 0.301935644 12.52676133 0.032335848 0.019361194 74.67453958 -1.873172554 -0.100159128 DYFEQYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 170.22 0.00068978 13415852000 8141480 7858810 6521400 8679000 5069910 7798810 7727570 8061800 5458250 FALSE TRUE 7756648.375 8659631.674 6820412.641 7806570.431 5954100.699 7528735.254 6548587.27 7355866.054 6304687.533 1.230298621 1.373522737 1.081800264 1.238216865 0.944392671 1.194148832 1.03868546 1.166729678 1 22.58799344 3.728932213 24.95236433 1.098556445 1.301910679 0.451530161 0.094805213 467.5561873 1211689.181 0.022153321 0.034796881 5357.130337 -3.728932213 0.203354235 DYFEQYGKIEVIEIMTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 DYFEQYGKIEVIEIMTDR 18 1 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 ;;;;;;;;;;;;;;; 277.11 3.64E-39 1607969300 2223036 822472.6 2656891 1598579 2524510 2035545 3723174 2430657 3034186 FALSE TRUE 2117957.494 906283.493 2778712.08 1437886.802 2964783.745 1965053.566 3155135.426 2217815.787 3504712.068 0.604317117 0.25859 0.792850319 0.410272449 0.845942174 0.560689017 0.900255246 0.632809699 1 21.74086449 2.064631444 0.318465409 1.003960565 0.385761978 0.374725027 0.179208536 1.363245009 0.39538178 0.233155805 0.301472795 116.046339 -2.064631444 -0.618198587 DYFFALAHTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYFFALAHTVR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 268.91 1.73E-21 885410000 1885930 1433820 776260 861160 1853240 1004630 1846290 1420550 1433230 FALSE TRUE 1796785.826 1579927.888 811852.2888 774594.5607 2176444.469 969839.4112 1564604.551 1296159.111 1655487.988 1.085351171 0.954357808 0.490400592 0.467895005 1.314684543 0.58583295 0.945101723 0.782946853 1 20.65882511 3.987940334 24.22415829 0.793908096 1.036228753 0.124411023 0.254027833 790.3491748 1587576.806 0.060905298 0.113182063 9726.135921 -3.987940334 0.242320657 DYFGAHTYELLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 152.14 4.51E-05 476570000 1363960 1322390 1004210 1490460 1105350 1137080 1327060 1234150 1008520 FALSE TRUE 1299488.314 1457143.044 1050254.022 1340636.129 1298122.69 1097702.634 1124592.624 1126081.283 1164916.131 1.11552092 1.250856612 0.901570503 1.150843476 1.114348626 0.942301858 0.965385056 0.966662967 1 20.15179466 2.96611998 0.619894202 0.957414716 1.1764675 0.298842044 0.09214281 0.847055961 0.711643863 0.065673729 0.09063382 924.9536698 -2.96611998 0.219052784 DYGALKDIVINANPASPPLSLLVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYGALKDIVINANPASPPLSLLVLHR 26 1 Q13155;A8MU58 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 115.01 0.00076881 69592000 330030 238700 350340 332870 286300 342570 417220 364680 330220 FALSE TRUE 314430.136 263023.8014 366403.4355 299409.2752 336230.6294 330706.715 353565.4262 332746.6859 381428.8311 0.82434811 0.68957504 0.960607604 0.784967603 0.881502923 0.86702076 0.926949925 0.872368995 1 18.54105437 2.636763268 0.197693736 1.032062822 0.67722055 0.40825247 0.067991911 4.291573472 0.442888463 0.216632288 0.474123148 433.2746376 -2.636763268 -0.354842272 DYGHSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 107.69 0.0039539 131420000 100900.2 82296 83889.6 105474 135518.7 81477.7 120097.6 98512.3 162344.5 FALSE TRUE 96130.84751 90682.05596 87736.02114 94871.55313 159153.1184 78656.10682 101774.5054 89886.04077 187520.0559 0.512643019 0.483585905 0.4678754 0.5059275 0.848725847 0.419454369 0.542739308 0.479340945 1 17.51668538 -2.207066577 2.208744476 2.348447207 0.529596635 0.611336494 0.117116895 6435687.226 1183580.997 43377374.02 0.027235673 0.006207739 2.207066577 -1.818850572 DYGHSSSRDDYPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 187.16 5.89E-07 2253858000 522074 274190 487961 442326 924301 423735 788358 557622 1158868 FALSE TRUE 497396.5967 302130.2727 510334.4945 397862.5501 1085498.802 409060.9507 668079.5079 508793.6615 1338579.331 0.371585445 0.22570965 0.38125084 0.297227472 0.810933485 0.305593357 0.499095939 0.380099744 1 20.35227121 -5 0.179480302 3.444174032 0.272140892 0.587069621 0.157402276 88.3999984 0.850206726 77.05405169 0.455486996 1.00E-05 5 -3.17203314 DYGNSPLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 DYGNSPLHR 9 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;A0A087WUW5;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;; 154.01 7.67E-05 8719650000 5663130 4077770 4762200 5384150 5961140 4539030 6575020 5522720 6364010 FALSE TRUE 5395445.068 4493299.399 4980551.58 4842925.013 7000760.929 4381842.253 5571879.94 5039121.359 7350908.168 0.733983468 0.611257724 0.677542348 0.658819958 0.952366805 0.59609536 0.757985247 0.685510041 1 22.80949107 -5 0.259973745 2.898867402 0.681145041 0.455079924 0.099581501 168.1561608 1.651510114 170.5680211 0.120406388 1.00E-05 5 -2.217722361 DYGVLLEGSGLALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DYGVLLEGSGLALR 14 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;;; 211.63 8.29E-09 578866000 1102213 842911 883805 887772 978907 712543 963874 954000 1020843 FALSE TRUE 1050113.576 928804.5892 924328.3335 798531.4719 1149628.071 687867.4572 816817.3185 870462.7025 1179150.119 0.890568181 0.787689858 0.783893686 0.677209339 0.974963283 0.58335868 0.692716988 0.738211945 1 20.16931597 2.229967837 24.99998517 0.71902396 0.815831007 0.03620786 0.129249765 391.0143447 1137615.222 0.043188634 0.032402818 169.8117889 -2.229967837 0.096807047 DYGVYLEDSGHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYGVYLEDSGHTLR 14 0 Q13162;H7C3T4 Q13162 PRDX4 Peroxiredoxin-4 0 ; 199.31 2.08E-08 521780000 1427510 1347110 533760 519790 1823510 499610 1355010 582720 584130 FALSE TRUE 1360034.431 1484382.041 558233.424 467539.7217 2141529.567 482308.3804 1148278.338 531693.9476 674713.8971 2.0157202 2.200016995 0.827363163 0.692945149 3.173981707 0.714833921 1.701874443 0.788028748 1 19.36391635 8 0.17697699 0.984084351 5.881027894 0.11306374 0.772766394 112.9379984 1.255516625 1.688831434 148.1891083 100000000 -8 4.896943543 DYIHVVDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYIHVVDLAK 10 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 129.7 0.0002961 249560000 877130 898340 717880 1028680 583060 850180 872250 935810 527710 FALSE TRUE 835669.8032 989881.8673 750795.5081 925275.132 684745.4794 820738.0534 739172.2425 853865.5154 609544.5716 1.370974072 1.623969622 1.231731924 1.517977807 1.123372287 1.346477504 1.212663154 1.400825395 1 19.21737219 -2.817427851 0.069046764 2.44E-17 1.912187897 0.409562336 0.140640015 158.4867509 1.238277157 32.7083726 8.326027457 0.001522552 2.817427851 1.912187897 DYIPVDQEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYIPVDQEELR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 167.12 4.57E-05 233600000 284470 293490 253070 346890 245620 292070 287900 310670 262010 FALSE TRUE 271023.6669 323396.9647 264673.5098 312019.9582 288456.0502 281955.5427 243975.5674 283466.0878 302641.1726 0.895528075 1.068582182 0.874545613 1.030989787 0.953128907 0.93164965 0.80615458 0.936640859 1 18.20724875 2.094964827 3.953255654 0.888080119 0.971234219 0.043879295 0.074815821 0.333393576 9.844148601 0.027776597 0.019419471 124.4413824 -2.094964827 0.0831541 DYIPVDQEELRDYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYIPVDQEELRDYVK 15 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 148.03 3.29E-06 217160000 305320 119399 296810 239280 324910 283290 439150 354790 460070 FALSE TRUE 290888.1287 131565.8938 310419.0321 215227.1198 381574.2011 273479.5963 372149.602 323722.7067 531415.3059 0.547383798 0.24757641 0.584136416 0.405007378 0.718033893 0.51462499 0.70029899 0.609170837 1 19.01948026 0.554869739 0.246260784 1.144849914 0.34580174 0.642704902 0.118883136 2.314176677 0.345527735 0.586463776 0.240709397 3.588142972 -0.554869739 -0.799048174 DYKVDQEIINIMQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYKVDQEIINIMQDR 15 1 H3BV16;O96000-2;O96000 H3BV16 NDUFB10 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 0 176.21 7.40E-07 38388000 79026 48495 62545 109850 85600 55778 104720 73210 81387 FALSE TRUE 75290.59759 53436.69563 65412.75012 98807.6693 100528.6129 53846.39387 88743.04069 66799.34429 94008.08029 0.800894959 0.568426623 0.695820507 1.051055069 1.069361406 0.57278474 0.943993755 0.710570241 1 16.52049715 7.991749142 0.106018179 1.033129755 1.22E-10 0.09886227 0.177703503 233.7219593 1.742672626 1.789647017 35.23738432 98118102.7 -7.991749142 -1.033129755 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR 29 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;;; 182.66 9.44E-18 279357000 150870 129560 114640.2 146876 116969 121140 142215 131264 112960 FALSE TRUE 143738.6741 142762.3113 119896.5666 132111.7454 137368.3566 116944.8914 120517.4898 119769.8283 130477.2599 1.101637743 1.094154732 0.91890776 1.012526976 1.052814542 0.896285617 0.923666621 0.917936416 1 16.99343886 3.917287751 0.631570723 0.937180353 1.153064306 0.460292156 0.055457745 1.107439407 0.648627703 0.029272687 0.152037404 8265.854395 -3.917287751 0.215883953 DYLHLPPEIVPATLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYLHLPPEIVPATLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;; 98.694 0.0028295 876200000 920846 1029820 710790 1003590 760427 819688 899300 947880 661153 FALSE TRUE 877319.4345 1134759.829 743380.4246 902707.2265 893045.228 791301.999 762095.2682 864878.6022 763681.2305 1.148803191 1.48590771 0.973417173 1.182047156 1.169395282 1.036167929 0.997923267 1.132512582 1 19.54261104 3.72838031 24.99480959 1.072111256 1.317355456 0.477950451 0.107369821 501.7684538 1231948.045 0.027498382 0.043138387 5350.326809 -3.72838031 0.245244201 DYLHYHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYLHYHIK 8 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 125.96 0.0007168 431620000 1134260 1178880 666030 784700 926110 838460 1154380 937770 53037 FALSE TRUE 1080645.778 1299009.212 696568.1343 705820.4652 1087623.291 809423.92 978258.1294 855653.8874 61261.70708 17.63982476 21.20426077 11.37036768 11.52139728 17.75372157 13.21255901 15.96850914 13.96718975 1 15.90269795 -0.206977509 0.438890875 6.00E-31 16.92463815 0.684715091 3.047869852 3.69076841 0.795523387 17.37913374 1.883714722 0.620901189 0.206977509 16.92463815 DYLHYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 DYLHYIR 7 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;;;;; 157.99 0.0014387 4751410000 5693910 5670190 2874270 3399900 5087240 3480420 5210370 4614810 3684610 FALSE TRUE 5424770.159 6247988.807 3006058.123 3058135.593 5974453.045 3359892.183 4415432.361 4210712.772 4256000.5 1.274616899 1.46804231 0.706310566 0.718546812 1.403771697 0.789448258 1.037460489 0.989359088 1 22.02106689 3.751892135 24.97901499 0.955185875 1.371329629 0.424528612 0.204202286 651.1601987 1220063.137 0.049492772 0.088589968 5647.966804 -3.751892135 0.416143754 DYLIDGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DYLIDGSR 8 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ;;;; 145.63 0.0013173 2575950000 4612830 3939930 4027910 4701270 4231600 4104940 4908350 4604560 4574650 FALSE TRUE 4394790.668 4341413.346 4212593.658 4228689.408 4969589.7 3962784.899 4159491.059 4201360.316 5284063.358 0.831706656 0.821605089 0.797226182 0.800272276 0.940486395 0.7499503 0.787176606 0.795100291 1 22.33321633 -0.966429373 4.542843236 1.000003531 0.81471255 0.57906096 0.049448828 5969238.157 1313987.169 221.6298675 0.010990636 0.10803653 0.966429373 -0.185290981 DYLLCDYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 DYLLCDYNR 9 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;;;; 190.93 8.49E-05 5067890000 5533350 4233540 3183720 3542270 5110270 3493180 5579120 4568970 4939120 FALSE TRUE 5271799.512 4664942.539 3329696.711 3186194.29 6001499.47 3372210.301 4727922.776 4168886.765 5705053.504 0.924057856 0.817686028 0.583639874 0.558486312 1.051961996 0.591091792 0.828725405 0.730735788 1 22.44380899 -0.469197858 7.27444377 1 0.769801903 0.184492789 0.157037904 0 0 0.14280558 0.033659598 0.33947058 0.469197858 -0.230198097 DYLLS(ph)ES(ph)EDEGDNDGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYLLSESEDEGDNDGER 17 0 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 2 DYLLS(1)ES(1)EDEGDNDGER;DYLLS(1)ES(1)EDEGDNDGER 315.96 4.04E-58 428220000 964000 944680 885410 1018750 802840 934030 925770 884270 740640 TRUE FALSE 918433.6305 1040943.966 926006.9243 916343.3145 942855.0418 901684.3069 784526.7836 806838.631 855494.6685 1.073570256 1.216774346 1.082422788 1.071126856 1.102116795 1.053991731 0.91704462 0.943125259 1 19.70639934 1.971712527 2.805503317 0.946155611 1.117990824 0.693733946 0.046735932 0.142595363 2.101513686 0.024425982 0.013644713 93.69416116 -1.971712527 0.171835213 DYNHWLATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYNHWLATK 9 0 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 116.77 0.0012606 862680000 3151400 2234100 2346000 2560600 2489400 2210000 2835000 2637200 2195300 FALSE TRUE 3002439.567 2461757.33 2453566.421 2303203.623 2923550.572 2133467.146 2402468.682 2406272.787 2535735.912 1.184050576 0.970825597 0.967595406 0.908297908 1.152939688 0.841360149 0.947444357 0.948944555 1 21.27397307 4.543928 1.859712607 0.960608863 1.211616277 0.4251056 0.078887695 0.467976331 2.280667711 0.019021797 0.179535382 34988.71558 -4.543928 0.251007414 DYNPYNYSDSIS(ph)PFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYNPYNYSDSISPFNK 16 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 DYNPYNYSDSIS(1)PFNK 165.58 7.32E-09 45053000 83759 83635 74055 82251 84202 72715 96210 83922 84393 TRUE FALSE 79799.87806 92157.50159 77450.495 73982.97321 98886.80214 70196.86132 81531.39748 76573.34478 97480.23542 0.818626235 0.945396789 0.794525112 0.758953576 1.01442925 0.720113785 0.836389009 0.785526876 1 16.57282211 3.719332066 24.92540335 0.83362842 0.882011528 0.015425309 0.100397093 2487.490273 3224461.223 0.024049467 0.037313353 5240.009398 -3.719332066 0.048383108 DYNVTANSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 DYNVTANSK 9 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;; 236.16 7.47E-10 2259400000 2321520 2048010 1958940 2300330 1643020 2205090 2424850 2333980 1807320 FALSE TRUE 2211786.35 2256704.547 2048759.337 2069096.458 1929562.168 2128727.18 2054894.597 2129604.338 2087589.955 1.059492716 1.081009487 0.981399308 0.991141221 0.924301328 1.019705606 0.984338228 1.020125783 1 20.99340693 3.736508906 24.99000211 0.98726465 1.070251104 0.611948805 0.026973895 97.43217707 1186731.084 0.006653917 0.0108968 5451.410752 -3.736508906 0.082986454 DYPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 124.89 0.042251 1167910000 660530 623550 624980 704760 621600 641910 693820 680000 741390 FALSE TRUE 629308.0559 687090.4539 653635.9512 633916.1858 730006.8432 619680.4957 587965.0161 620455.5951 856360.9747 0.734863071 0.802337419 0.76327153 0.740244131 0.852452254 0.723620662 0.686585486 0.724525771 1 19.70785953 -1.730711531 6.96688502 1.003281646 0.753286167 0.739729108 0.045953278 0.002461375 9.51E-05 0.046755382 0.01090582 0.018590389 1.730711531 -0.249995479 DYPVVSIEDPFDQDDWGAWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DYPVVSIEDPFDQDDWGAWQK 21 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;; 312.29 1.43E-66 2387379000 5077522 4676670 3738226 4875011 3634195 4676592 4984774 5129782 3375423 FALSE TRUE 4837517.598 5153227.99 3909627.36 4384965.632 4267997.457 4514640.446 4224255.175 4680591.093 3898866.36 1.240749785 1.321724705 1.002760033 1.12467708 1.09467652 1.1579367 1.083457289 1.20050052 1 21.89462327 3.750440993 24.99871819 1.102189472 1.281237255 0.589970238 0.064371518 438.918595 923571.1868 0.014746984 0.0263166 5629.126297 -3.750440993 0.179047784 DYQDNKADVILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 DYQDNKADVILK 12 1 P47813;O14602;X6RAC9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;; 131.66 0.00017758 1539980000 910330 625174 780410 808470 589490 859490 1044220 938170 663330 FALSE TRUE 867300.505 688879.9414 816192.5704 727201.0596 692296.8694 829725.6458 884905.0606 856018.8612 766195.8286 1.131956704 0.899091219 1.065253216 0.949106002 0.90355082 1.082915901 1.154933279 1.117232474 1 19.54735365 2.042497152 12.13300595 1.110684718 0.991995185 0.263727455 0.079931241 0.943050981 267.3295596 0.028297737 0.020889323 110.2801001 -2.042497152 -0.118689533 DYQGPLKEHEVTIFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;; 307.92 8.40E-58 3319050000 4124400 2954350 3764570 3856110 3219360 3844950 4784820 4399500 3332130 FALSE TRUE 3929447.786 3255401.624 3937179.258 3468486.497 3780815.365 3711798.417 4054807.83 4014256.457 3848859.702 1.020938171 0.845809376 1.022946941 0.901172494 0.98232091 0.964389119 1.053508868 1.042972924 1 21.87599965 1.895747926 3.01948525 1.036932532 0.947136121 0.292307501 0.054473821 0.276094636 4.437615068 0.026490385 0.014095848 78.65891035 -1.895747926 -0.089796411 DYQTSPLLETQAEDHPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYQTSPLLETQAEDHPPR 18 0 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ;;; 245.03 3.49E-24 1693640000 1009920 792950 844570 1006290 958700 866580 1039170 961340 935350 FALSE TRUE 962183.0831 873752.5065 883294.3699 905135.8174 1125896.976 836570.1173 880625.5308 877159.9732 1080399.301 0.890580994 0.808731092 0.817562885 0.837778974 1.042111908 0.774315678 0.815092651 0.811884988 1 20.04313318 2.15234361 0.009656053 1.720064482 4.22E-06 0.089697144 0.084096704 5763.146047 36.23178757 3182.440409 3267.381112 142.0180712 -2.15234361 -1.72006026 DYS(ph)YER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYSYER 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 DYS(1)YER;DYS(1)YER;DYS(1)YER;DYS(1)YER 134.81 0.014551 2724700000 3269680 2712440 2873130 3205120 4343520 2829650 3277440 3023930 4049730 TRUE FALSE 3115128.706 2988840.72 3004865.852 2882935.248 5101028.513 2731658.511 2777406.334 2759138.658 4677741.445 0.665947176 0.638949535 0.642375362 0.616309234 1.090489625 0.583969538 0.593749434 0.5898442 1 22.15738069 DYSDHPSGGSYR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 126.34 0.00028916 1192380000 1514290 1136776 1316440 1661140 2263170 1244813 2177820 1646200 2240040 FALSE TRUE 1442712.513 1252614.767 1376800.076 1494159.051 2657866.131 1201704.814 1845553.561 1502050.001 2587413.963 0.557588594 0.484118423 0.532114341 0.577471975 1.027228797 0.464442424 0.713281132 0.580521719 1 21.30307946 -4.999999993 0.11706666 2.234709736 0.411963478 0.379755551 0.15804459 158.102486 1.209104682 46.67629324 1.52751051 1.00E-05 4.999999993 -1.822746258 DYSEADGLS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYSEADGLSER 11 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1;Q4VXN5;Q4VXN6;Q4VXN7;Q4VXN2 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DYSEADGLS(1)ER;DYSEADGLS(1)ER 234.49 1.77E-15 347240000 815840 1139120 803580 1057230 779310 927610 892000 1009830 813700 TRUE FALSE 777276.86 1255197.623 840424.9378 950955.2318 915221.4173 895486.6331 755909.0173 921403.9318 939884.4402 0.826991944 1.335480799 0.89417901 1.011778886 0.973759516 0.952762483 0.804257401 0.980337467 1 19.84212386 2.929309659 1.291876846 0.912107923 1.063888032 0.049823212 0.141644896 0.775468365 2.689878238 0.056899588 0.06389868 849.7861702 -2.929309659 0.151780109 DYSNFDQEFLNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYSNFDQEFLNEK 13 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 ; 264.3 7.28E-24 152431000 342780 328260 341180 398190 269810 373930 397880 432980 315090 FALSE TRUE 326577.4687 361710.0672 356823.4405 358163.1847 316864.7786 360980.7103 337176.0984 395065.9758 363952.5479 0.897307824 0.993838535 0.980411986 0.984093082 0.87062113 0.991834547 0.926428735 1.085487595 1 18.47339084 1.245630706 24.99998248 1.042743806 0.950695617 0.416282813 0.046016078 133.697784 472770.7352 0.029388416 0.010228937 17.6047842 -1.245630706 -0.092048189 DYTQINVGNLELSANHNILQIVDVCMESEKDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYTQINVGNLELSANHNILQIVDVCMESEKDHK 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 141.78 2.89E-10 306096000 86001 53033 76748 83155 59826 89196 107465 90185 52083 FALSE TRUE 81935.90317 58437.12299 80266.97171 74796.10142 70259.63546 86107.12015 91069.24052 82287.9233 60159.76564 1.361971781 0.971365536 1.334230126 1.243291104 1.167884128 1.43130744 1.513789815 1.367823203 1 15.87651133 2.24011953 24.99752125 1.38849213 1.202354052 0.045223103 0.172554295 61.03137731 978670.6546 0.057142779 0.045456373 173.8279186 -2.24011953 -0.186138078 DYTYEELLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYTYEELLNR 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 256.36 8.47E-17 2505730000 2576550 2192040 2262990 2698100 2365260 2223500 2850390 2514200 2607060 FALSE TRUE 2454761.588 2415411.368 2366750.33 2426881.862 2777760.595 2146499.637 2415510.654 2294043.319 3011349.55 0.815169925 0.802102622 0.785943409 0.805911709 0.922430475 0.712803214 0.802135592 0.761799081 1 21.52197875 -1.082226293 4.733912321 1.000008821 0.801399033 0.589366631 0.052191848 4.50E-06 8.73E-07 0.046013588 0.010845016 0.082751087 1.082226293 -0.198609788 DYVAPTANLDQKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYVAPTANLDQKDK 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 135.23 3.11E-05 1037780000 653666 336536 714353 535944 433724 685764 940706 815225 540418 FALSE TRUE 622768.5036 370829.401 747106.7916 482069.8909 509365.3283 662015.8207 797184.0224 743839.5772 624223.2634 0.997669488 0.594065333 1.196858297 0.772271588 0.815998631 1.060543334 1.277081566 1.191624249 1 19.2517026 2.070168392 4.208186199 1.184196431 0.859137763 0.367339659 0.168821013 0.188856531 6.585795928 0.064067443 0.044656114 117.5353194 -2.070168392 -0.325058668 DYVAVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYVAVAR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 84.359 0.050259 98604000 197280 163790 176870 197850 213930 207630 221530 194240 184440 FALSE TRUE 187954.9654 180480.3872 184979.6644 177961.7421 251239.3243 200439.721 187731.5298 177231.3159 213042.0132 0.88224366 0.847158664 0.868277865 0.835336371 1.179294734 0.940845977 0.881194873 0.831907816 1 17.70077844 DYVDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYVDLFR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 129.4 0.008525 224321000 880620 1411260 797890 1386990 782180 1002130 866620 979670 710240 FALSE TRUE 838994.8378 1555068.998 834474.0457 1247567.13 918591.9444 967425.9868 734401.2024 893884.9012 820380.3918 1.022690018 1.895546278 1.017179413 1.52071788 1.119714651 1.179240748 0.895195948 1.089598082 1 19.64593348 2.426826949 1.361620239 0.990424992 1.405834985 0.251352982 0.258461355 0.491911999 1.836356885 0.128670513 0.090381946 267.194152 -2.426826949 0.415409994 DYVFIEFCVEDSKDVNVNFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 DYVFIEFCVEDSKDVNVNFEK 21 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;;;; 256 1.79E-36 398742200 1006315 706070 878213 995834 583450.9 992646 1239954 1092481 695519.9 FALSE TRUE 958748.4843 778019.3357 918479.9347 895730.8744 685204.5522 958270.4201 1050776.244 996817.572 803377.5739 1.193397122 0.968435467 1.143273057 1.114956284 0.852904754 1.192802054 1.30794819 1.240783418 1 19.61571866 2.024517749 24.99723499 1.225439145 1.058955671 0.192238117 0.123304897 260.8551827 265955.5082 0.042476713 0.031369913 105.8078157 -2.024517749 -0.166483474 DYVFYLAVGNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 DYVFYLAVGNYR 12 0 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 134.59 0.00033201 93101000 255560 227480 215190 269130 217877 241360 289690 262320 227781 FALSE TRUE 243480.1853 250660.4706 225056.6744 242076.5411 255874.6798 233001.6427 245492.47 239349.8702 263104.1141 0.925413827 0.952704489 0.855390175 0.920078889 0.972522534 0.885587226 0.933062072 0.909715422 1 18.00527428 -1.412487835 2.84929801 1.001656555 0.921705351 0.375851087 0.032548572 8695434.066 10390795.25 117908.9914 0.007879685 0.038682289 1.412487835 -0.079951204 DYYFDSYAHFGIHEEMLKDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 DYYFDSYAHFGIHEEMLKDEVR 22 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9;E9PMW9;E9PMZ2;Q9NR22-2;Q9NR22 E9PKG1 PRMT1;PRMT8 Protein arginine N-methyltransferase 1;Protein arginine N-methyltransferase 8 0 67.76 0.013178 65775000 43464 40393 54790 54637 55153 54654 68889 57340 30058 FALSE TRUE 41409.54286 44509.09262 57302.17569 49144.78496 64771.66574 52761.31828 58378.71782 52319.00562 34719.24113 1.192697234 1.281971932 1.65044436 1.415491335 1.865584144 1.519656437 1.681451435 1.506916739 1 15.08344779 3.83936337 4.812564943 1.564347436 1.226141533 0.196045261 0.226087297 0.242627972 9.015904147 0.050938869 0.094178408 6908.175622 -3.83936337 -0.338205903 DYYINIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 DYYINIR 7 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;; 168.74 0.0024144 1635340000 2051250 2212240 1863090 2179620 1952440 1962760 1972490 2059290 1808210 FALSE TRUE 1954291.478 2437669.771 1948514.519 1960520.457 2292944.918 1894789.129 1671550.423 1878967.651 2088617.972 0.935686422 1.16712094 0.932920498 0.938668767 1.097828779 0.907197561 0.800314105 0.899622466 1 20.9941172 2.080490286 6.808054945 0.871935435 1.020465513 0.264341603 0.089060272 0.216581218 15.03907004 0.032258683 0.023710568 120.3622467 -2.080490286 0.148530078 DYYSSR ddPTM_SK-BR-3_Trastuzumab_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 1310010000 1295800 1192540 1082760 1381240 1524980 1141340 1418940 1255930 1486180 FALSE TRUE 1234550.102 1314061.182 1132405.617 1242395.131 1790936.029 1101815.11 1202454.642 1145954.111 1716649.204 0.719162715 0.76548032 0.659660468 0.723732681 1.043274319 0.641840573 0.70046614 0.667552875 1 20.71116383 -2.211108495 2.367563558 1.822096674 0.739968621 0.340553176 0.113639141 7314522.922 1496580.184 32224245.71 0.025934548 0.006150232 2.211108495 -1.082128053 EAAAALVEEETRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 109.95 0.0017584 202563000 203456 189401 237604 213199 296180 190261 229794 223703 344560 FALSE TRUE 193839.0381 208701.1772 248498.3784 191767.8315 347833.6982 183672.2139 194734.7048 204114.3794 397992.605 0.487041808 0.52438456 0.624379386 0.481837675 0.873970254 0.461496549 0.489292269 0.512859729 1 18.6023821 -2.054123088 2.464687692 1.611477207 0.550241298 0.567692144 0.121393069 10246839.31 3080729.659 35327238.11 0.027971184 0.008828297 2.054123088 -1.061235909 EAAANTNRPS(ph)PGGHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAAANTNRPSPGGHER 16 1 O60356;O60356-2 O60356 NUPR1 Nuclear protein 1 1 EAAANT(0.002)NRPS(0.998)PGGHER 87.963 0.0037993 108570000 168930 106790 135060 148200 155440 123010 154360 160000 152740 TRUE FALSE 160945.0137 117672.0224 141252.6346 133302.6544 182548.6868 118750.1329 130809.547 145989.5518 176426.1391 0.912251521 0.666976124 0.800633258 0.755572021 1.034703178 0.673086956 0.741440852 0.827482552 1 17.4287048 0.967625143 20.48704363 1.000000004 0.790030758 0.247918742 0.109179567 492.2222888 311483.9857 0.098124715 0.024531179 9.281649045 -0.967625143 -0.209969246 EAADGYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAADGYQR 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 134.81 0.0020022 1648460000 1996580 1807940 1688330 2100480 2016970 1767620 2144750 1902390 1992460 FALSE TRUE 1902205.62 1992171.141 1765741.6 1889335.76 2368728.929 1706406.876 1817528.996 1735806.646 2301440.521 0.826528256 0.865619217 0.767233211 0.820936167 1.029237518 0.741451652 0.789735377 0.75422616 1 21.13410573 -0.297461217 7.519354116 0.999999999 0.826076102 0.313563602 0.081630392 0 0 0.07515451 0.017714088 0.504125636 0.297461217 -0.173923898 EAAEMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 114.78 0.013557 1304746000 2065900 1841780 1685080 2040330 1296500 1884700 2086990 2047290 1588190 FALSE TRUE 1968249.001 2029459.476 1762342.585 1835232.152 1522609.19 1819432.366 1768581.345 1868018.434 1834478.394 1.072920241 1.106286933 0.960677755 1.000410884 0.829995706 0.991798199 0.964078591 1.018283148 1 20.80693848 3.734400139 24.57579445 0.962462811 1.089603591 0.484921235 0.052636671 191.8646147 1133341.33 0.013085528 0.021107168 5425.004952 -3.734400139 0.12714078 EAAEPLSEPKEDQEAAELLS(ph)EPEEESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAAEPLSEPKEDQEAAELLSEPEEESER 28 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 EAAEPLSEPKEDQEAAELLS(1)EPEEESER;EAAEPLSEPKEDQEAAELLS(1)EPEEESER 216.16 2.10E-34 493160000 450070 398350 426380 498480 304090 498300 517030 522880 350770 TRUE FALSE 428796.0831 438942.3179 445929.9447 448371.8433 357123.1997 481043.7461 438147.5776 477093.8552 405165.6201 1.058322972 1.083365163 1.100611509 1.106638424 0.88142523 1.187276813 1.081403643 1.177527983 1 18.62815224 EAAEVLQNNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAAEVLQNNRR 11 1 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;; 151.79 5.33E-05 907760000 632770 500840 512930 609260 578470 527880 629890 583660 611460 FALSE TRUE 602860.2161 551876.1654 536448.3479 548016.0273 679354.9848 509599.3832 533788.7118 532551.6362 706282.0939 0.853568597 0.781382071 0.759538366 0.775916637 0.961874852 0.721523861 0.755772681 0.754021149 1 19.429885 -1.210643715 3.552246097 1.000310149 0.794753484 0.471379971 0.068071612 18458469.41 30826562.55 66582.56158 0.015801129 0.061568176 1.210643715 -0.205556665 EAAFS(ph)PGQQDWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR 200 1.19E-07 840250000 1154330 1112680 1102850 1253150 1077350 1179560 1347680 1288060 1288250 TRUE FALSE 1099767.109 1226063.357 1153416.763 1127180.981 1265239.499 1138711.541 1142066.664 1175270.638 1488025.231 0.739078267 0.823953339 0.775132531 0.757501256 0.850280945 0.765250157 0.767504906 0.789819026 1 20.50496756 0.927577135 20.64076134 1 0.783102706 0.815971413 0.032319248 2295.094019 654111.4093 0.028823526 0.007205882 8.464028849 -0.927577135 -0.216897294 EAAGPAPS(ph)PMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAAGPAPSPMR 11 0 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 EAAGPAPS(1)PMR 90.412 0.044981 31554000 125000 106500 114080 124780 116890 116410 138690 121920 125660 TRUE FALSE 119091.4977 117352.4711 119310.6808 112236.8773 137275.579 112378.6925 117530.2933 111244.0385 145146.711 0.820490502 0.808509337 0.822000581 0.77326504 0.9457712 0.774242087 0.809734457 0.766424797 1 17.14715236 -1.587280258 3.505136334 1.006600289 0.81540442 0.56916921 0.050567484 0.002410544 0.000283835 0.045249381 0.010326471 0.025865432 1.587280258 -0.191195869 EAAIWELEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAAIWELEER 10 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 98.044 0.013134 36031000 62635 55863 52711 71353 69903 54056 71335 62873 71797 FALSE TRUE 59674.36768 61555.50321 55127.85149 64180.46088 82094.06107 52184.02717 60451.53559 57367.50681 82930.91207 0.719567242 0.742250407 0.664744305 0.77390275 0.989909058 0.629246994 0.728938511 0.691750583 1 16.33962234 -2.299288508 2.294162902 2.258135059 0.741155226 0.411135142 0.096821866 4051674.876 374567.1137 26753952.79 0.023154506 0.00502009 2.299288508 -1.516979834 EAALILGVS(ph)PTANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAALILGVSPTANK 14 0 Q96DA6-2;Q96DA6 Q96DA6-2 DNAJC19 Mitochondrial import inner membrane translocase subunit TIM14 1 EAALILGVS(0.986)PT(0.014)ANK;EAALILGVS(0.962)PT(0.038)ANK 154.46 6.41E-06 43508000 240303 189966 210162 241865 174052 191798 230063 234536 204888 TRUE FALSE 228944.3534 209323.7514 219798.1356 217552.2707 204406.6137 185155.9872 194962.664 213998.7845 236660.9846 0.967393733 0.88448779 0.928746814 0.919257017 0.863710654 0.782368025 0.823805682 0.904241926 1 17.85246236 2.716501695 4.627618708 0.852394182 0.923537801 0.085852297 0.06120642 0.280757782 15.88225353 0.018367652 0.017952654 520.5970403 -2.716501695 0.071143619 EAALPPVS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_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 177.81 8.20E-06 8615590000 14042450 14486320 11602650 16365630 7879710 12896780 11853980 12585540 6710950 TRUE FALSE 13378691.22 15962492.48 12134642.98 14720525.78 9253928.929 12450161.27 10045437.64 11483483.4 7751649.851 1.725915318 2.05923807 1.56542713 1.899018411 1.193801204 1.606130503 1.295909623 1.481424422 1 22.88607197 2.188233777 0.319000338 0.998356612 2.020008491 0.584788151 0.205169724 1.004886755 0.274296691 0.261442672 0.367201883 154.2530559 -2.188233777 1.021651878 EAALPPVS(ph)PLKAALSEEELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(1)PLKAALSEEELEK 173.05 2.91E-12 459869000 1806230 1159950 1710130 1764580 976270 1720310 1905180 1722850 949860 TRUE FALSE 1720853.088 1278150.224 1788541.152 1587201.066 1146531.179 1660735.233 1614509.8 1571988.121 1097159.438 1.568462184 1.164963067 1.630156102 1.446645776 1.044999605 1.513668093 1.471536173 1.43278002 1 20.06534176 -1.849776937 2.403044222 0.824357461 1.403405302 0.343809926 0.177482819 11441631.71 6498052.632 11516352.65 0.039944324 0.014132632 1.849776937 0.579047841 EAALSTALSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 270.02 1.23E-22 3611600000 4174420 2968590 3297990 3694310 3128050 3616450 4489170 4069880 3674490 FALSE TRUE 3977103.44 3271092.696 3449206.104 3322950.94 3673580.93 3491211.43 3804264.667 3713499.731 4244311.143 0.937043328 0.770700494 0.812665704 0.782918789 0.865530543 0.822562558 0.896320873 0.874935792 1 22.01709899 0.794955059 0.792362474 0.999183537 0.83014281 0.537357375 0.04788669 0.709984527 0.89818486 0.045638315 0.016245819 6.236702951 -0.794955059 -0.169040727 EAALYPHLPPEADPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAALYPHLPPEADPR 15 0 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 0 62.378 0.081586 79556000 116580 85202 94983 103780 105350 88399 117580 106560 106320 FALSE TRUE 111069.4944 93884.18067 99338.0645 93347.83723 123723.0066 85337.72046 99641.0115 97229.04149 122807.5626 0.904419012 0.764482078 0.808892078 0.76011473 1.007454297 0.694889783 0.811358921 0.791718681 1 16.90603988 -1.836850863 2.390869314 1.074903427 0.816096277 0.309871645 0.08535962 18827209.08 11132473.27 8076967.29 0.020387183 0.01455959 1.836850863 -0.25880715 EAARS(ph)PDKPGGSPSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.958)PDKPGGS(0.018)PS(0.014)AS(0.01)R;EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR;EAARS(1)PDKPGGSPSASR 124.4 2.63E-05 921350000 837343 801719 815773 962072 591298 953744 984989 986663 751907 TRUE FALSE 797763.4558 883415.0776 853176.999 865362.6947 694420.184 920715.6061 834710.8375 900265.5571 868508.8974 0.918543792 1.017162956 0.982346872 0.996377466 0.799554485 1.060110736 0.961084958 1.036564576 1 19.7281811 EAARSPDKPGGS(ph)PSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.014)PDKPGGS(0.438)PS(0.11)AS(0.438)R 55.575 0.092745 146100000 38388 37746 35872 43949 24735 49094 47461 51355 33348 TRUE FALSE 36573.47532 41592.36031 37516.76668 39531.16302 29048.77617 47393.86247 40219.95277 46858.08395 38519.43752 0.949481033 1.0797759 0.973969743 1.026265324 0.754132927 1.230388228 1.044146939 1.216478925 1 15.23329902 2.201720543 24.99999888 1.121328727 0.976790168 0.360652197 0.108017159 200.6388577 136154.1429 0.03700536 0.027331001 159.1184512 -2.201720543 -0.144538559 EAARSPDKPGGSPSAS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.057)PDKPGGS(0.204)PS(0.148)AS(0.591)R 71.853 0.023338 265300000 129060 131400 129660 140010 91075 161700 136140 159940 101710 TRUE FALSE 122959.5896 144789.8094 135605.0393 125935.9288 106958.4512 156100.2885 115369.3426 145934.8057 117482.6673 1.046618981 1.232435496 1.154255707 1.071953265 0.910418989 1.328709094 0.982011604 1.242181583 1 16.8420884 -1.416781272 4.925563742 0.999840572 1.1189172 0.083296567 0.126046398 0.00019521 2.31E-05 0.107960815 0.025412622 0.03830176 1.416781272 0.119076628 EAASGT(ph)TPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.003)GT(0.555)T(0.441)PQK;EAAS(0.001)GT(0.578)T(0.421)PQK 162.93 7.40E-05 1682592000 1683810 1662490 1606290 1842630 1109970 1798590 2014250 1984400 1518700 TRUE FALSE 1604219.638 1831899.621 1679939.985 1657405.332 1303548.417 1736304.377 1706939.168 1810635.416 1754212.24 0.91449575 1.044286193 0.957660623 0.944814598 0.743096181 0.989791508 0.973051681 1.032164396 1 20.74239188 -0.638273214 5.860842212 1 0.953411687 0.033236563 0.08300496 5.83E-10 9.94E-11 0.078197303 0.018431281 0.229999444 0.638273214 -0.046588313 EAASGTT(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.074)T(0.926)PQK;EAAS(0.001)GT(0.099)T(0.9)PQK;EAASGT(0.158)T(0.842)PQK;EAAS(0.001)GT(0.024)T(0.975)PQK;EAAS(0.001)GT(0.149)T(0.85)PQK;EAASGT(0.069)T(0.931)PQK;EAAS(0.001)GT(0.105)T(0.894)PQK;EAAS(0.007)GT(0.065)T(0.929)PQK;EAAS(0.006)GT(0.371)T(0.623)PQK;EAASGT(0.133)T(0.867)PQK 208.63 1.23E-06 5218986000 7730850 7273370 7006530 8027490 4882820 7951200 8616650 8529790 6734090 TRUE FALSE 7365428.042 8014534.672 7327786.331 7220551.454 5734382.262 7675847.95 7302021.787 7782876.368 7778378.284 0.946910496 1.03036062 0.942071221 0.928284945 0.7372208 0.986818546 0.938758893 1.00057828 1 22.89103797 -0.227041616 16.06221284 1 0.94312823 0.054160236 0.078507996 0 0 0.075004552 0.017678742 0.592868511 0.227041616 -0.05687177 EAASS(ph)PAGEPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.081)S(0.919)PAGEPLR;EAAS(0.116)S(0.884)PAGEPLR;EAAS(0.004)S(0.996)PAGEPLR;EAAS(0.047)S(0.953)PAGEPLR 237.53 4.36E-16 862520000 1729350 1850070 1474880 1927220 1666690 1629240 1676750 1673990 1674190 TRUE FALSE 1647607.053 2038594.236 1542504.707 1733492.184 1957360.208 1572819.01 1420930.992 1527406.561 1933814.835 0.851998352 1.054182748 0.797648606 0.896410635 1.012175609 0.813324514 0.734781307 0.789841165 1 20.88301823 2.128193832 8.685686618 0.802795785 0.927026909 0.127169019 0.100238628 0.33787088 24.7048709 0.034963152 0.025809862 134.3364391 -2.128193832 0.124231124 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EAASSSSGTQPAPPAPAS(0.989)PWDS(0.011)KK;EAASSSSGTQPAPPAPAS(0.987)PWDS(0.013)KK;EAASSSSGTQPAPPAPAS(0.956)PWDS(0.044)KK 186.17 1.34E-17 1395100000 1458220 1367590 1330760 1606510 832235 1602870 1684110 1725510 946350 TRUE FALSE 1389292.831 1506948.976 1391776.662 1445020.563 977376.5205 1547362.21 1427168.089 1574415.197 1093105.125 1.270959946 1.378594741 1.273232218 1.321941074 0.894128569 1.415565781 1.305609183 1.440314533 1 20.06000072 EAATLEVERPLPMEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAATLEVERPLPMEVEK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 133.86 1.72E-05 89399000 38560 42568 34171 41681 32472 35373 35765 42248 30189 FALSE TRUE 36737.34522 46905.7276 35737.77415 37491.14669 38135.10652 34148.02414 30308.39238 38548.54115 34870.55594 1.05353483 1.345138508 1.024869641 1.075151964 1.093619115 0.979279602 0.869168603 1.105475382 1 15.08972174 2.984253401 1.09271332 0.972789247 1.186266966 0.276679476 0.103207388 0.475620332 1.216509326 0.045737285 0.054631217 964.3915604 -2.984253401 0.213477718 EAATQEDPEQLPELEAHGVS(ph)ES(ph)EGEERPVAEEEILLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 2 EAATQEDPEQLPELEAHGVS(1)ES(1)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(1)ES(1)EGEERPVAEEEILLR 206.4 2.37E-30 192084000 67958 63212 61061 74836 76985 68214 80451 68296 77254 TRUE FALSE 64745.76002 69653.37467 63860.70725 67313.3431 90411.15963 65851.73208 68176.72237 62315.64018 89234.15576 0.725571497 0.78056854 0.715653179 0.754345043 1.01319006 0.737965541 0.764020478 0.698338429 1 16.44530841 -2.407833347 2.336876271 3.02908296 0.773944297 0.39229197 0.088514614 5471716.042 493459.3209 59875361.4 0.022442883 0.003909909 2.407833347 -2.255138662 EAATQEDPEQLPELEAHGVS(ph)ESEGEERPVAEEEILLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 EAATQEDPEQLPELEAHGVS(0.998)ES(0.002)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.982)ES(0.018)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.81)ES(0.19)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.975)ES(0.025)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.998)ES(0.002)EGEERPVAEEEILLR 353.73 2.27E-145 765372000 297908 265761 256268 317377 294796 280633 320199 316495 285789 TRUE FALSE 283826.4792 292842.348 268018.1413 285473.661 346208.3291 270914.6088 271346.7617 288781.02 330107.6985 0.859799637 0.887111538 0.811911211 0.864789468 1.048773872 0.820685522 0.821994649 0.874808498 1 18.33257726 -2.454751865 2.054541247 2.107713692 0.871167954 0.258692055 0.06704815 2031264.546 181206.258 10462384.56 0.015984193 0.003509523 2.454751865 -1.236545738 EAAVGVPPPAQPAPGEPTPPAPPS(ph)PDWTSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAAVGVPPPAQPAPGEPTPPAPPSPDWTSSSR 32 0 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 EAAVGVPPPAQPAPGEPT(0.067)PPAPPS(0.857)PDWT(0.047)S(0.008)S(0.011)S(0.011)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.616)PDWT(0.215)S(0.056)S(0.056)S(0.056)R 125.02 8.94E-08 387150000 257920 221280 246120 290070 251090 246790 287710 248440 255510 TRUE FALSE 245728.6327 243828.6836 257404.8454 260911.6125 294880.0165 238243.6004 243814.5553 226685.2765 295133.1858 0.832602515 0.826164916 0.872165035 0.884047017 0.999142186 0.807240974 0.826117045 0.768077896 1 18.17100663 3.737206457 22.3039956 0.870373609 0.82938371 0.062350864 0.074538601 83.72794398 1379127.404 0.01898132 0.031289152 5460.173683 -3.737206457 -0.040989898 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EAAVSASDILQESAIHS(0.989)PGT(0.011)VEK;EAAVSASDILQESAIHS(0.999)PGT(0.001)VEK;EAAVSASDILQESAIHS(1)PGTVEK 259.45 7.10E-44 400340000 377211 333412 355688 409262 268526 373287 426672 417771 298625 TRUE FALSE 359380.9836 367387.0619 371996.6466 368122.2062 315356.8494 360359.9776 361575.35 381188.7565 344934.2398 1.041882603 1.065093051 1.078456713 1.06722431 0.914252089 1.044720808 1.048244298 1.10510559 1 18.39596182 5.188234505 16.32198399 1.042717829 0.054782803 0 0.05231691 17375.78529 1219925.478 0.011663496 122679.663 154253.3145 -5.188234505 -0.987935025 EAAVSHAGSMHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAAVSHAGSMHR 12 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 118.61 0.00042513 54096000 32762.2 24905.6 30019.8 35380 43557 33372.7 41642 33594.4 10323.8 FALSE TRUE 31213.59573 27443.50896 31396.23752 31823.53518 51153.32701 32216.99503 35288.74809 30652.69624 11924.76218 2.617544507 2.301388367 2.632860686 2.668693489 4.28967272 2.701688684 2.959283176 2.570507972 1 13.54167287 3.224605776 3.692223313 2.884376896 2.474190962 0 0.799702855 0.710862274 20.77548186 0.212123554 0.273598136 1677.280801 -3.224605776 -0.410185935 EAAYHPEVAPDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAAYHPEVAPDVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 79.633 0.019979 275580000 321730 252400 255690 302340 317420 266630 303740 296960 318580 FALSE TRUE 306522.4605 278119.847 267413.6394 271948.2088 372777.9475 257396.5362 257398.8844 270956.6081 367983.7593 0.83297823 0.755793809 0.726699569 0.739022313 1.01302826 0.699477979 0.69948436 0.736327627 1 18.48928257 -1.86655859 2.586499722 1.102612753 0.772734787 0.367929218 0.092478624 17628461.04 11215695.49 11128683.02 0.021751263 0.013596947 1.86655859 -0.329877966 EAAYTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAAYTKR 7 1 P04183;K7ERV3;K7ES52;K7ERJ1 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 79.116 0.05371 111410000 175230 147170 146200 150530 197810 140980 220060 163440 200660 FALSE TRUE 166947.2252 162166.7903 152903.4146 135398.4384 232308.0014 136097.8273 186485.8053 149128.3272 231777.328 0.720291439 0.699666321 0.659699618 0.584174646 1.002289583 0.587192149 0.804590367 0.643412056 1 17.82237993 -5 0.349035254 4.247849929 0.706847399 0.35057939 0.121861654 455.4039997 3.740552118 1106.639849 0.081829504 1.00E-05 5 -3.54100253 EACPELDYFVVFSSVSCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 387.96 1.51E-126 430700000 321460 261780 285440 317320 295870 262680 361710 311420 325220 FALSE TRUE 306265.2229 288455.6796 298527.7063 285422.3907 347469.6343 253583.3257 306524.4962 284150.4139 375653.4566 0.815286583 0.767877081 0.794689097 0.759802381 0.924973877 0.6750459 0.815976776 0.756416343 1 18.51904285 -0.969584384 4.594883615 1.000003201 0.788788463 0.529215437 0.062614733 2.15E-06 4.81E-07 0.05210506 0.012281054 0.107254523 0.969584384 -0.211214738 EADDIVNWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 210.6 1.73E-07 1703784800 3774505 3234729 3273883 3868444 2788716 3613721 4078196 3766757 2928287 FALSE TRUE 3596091.629 3564351.563 3423993.774 3479580.66 3275067.187 3488576.936 3455992.299 3436919.788 3382390.792 1.06318041 1.053796495 1.012299874 1.028734074 0.968269898 1.031393813 1.021760202 1.016121436 1 21.68961192 3.780969137 3.484209082 1.012556038 1.060151208 0.549420887 0.017815107 0.16202691 4.078017175 0.004534382 0.008377473 6039.05712 -3.780969137 0.04759517 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER 32 0 P23258;K7EIS0;Q9NRH3 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 226.57 3.33E-36 53982000 29069 27557 29036 33071 26271 29409 28663 32040 26604 FALSE TRUE 27694.96598 30365.08963 30367.32932 29746.64025 30852.65408 28390.55896 24289.93292 29234.40775 30729.61245 0.901246836 0.988137735 0.988210618 0.968012216 1.004004009 0.923882753 0.790440588 0.951343197 1 14.90734195 2.000480987 24.99859447 0.88227308 0.966660456 0.09116644 0.061159635 19.58343993 1017773.842 0.021540954 0.015759852 100.1108126 -2.000480987 0.084387376 EADIDGDGQVNYEEFVQMMTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EADIDGDGQVNYEEFVQMMTAK 22 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;M0QZ52 P0DP25 CALM2;CALM3 0 76.027 0.001991 0 10647 10848 7342 12141 5899.5 8100.2 8205.2 11551 6005.4 FALSE TRUE 10143.73741 11953.42353 7678.637962 10920.56361 6928.370932 7819.688043 6953.346041 10539.5332 6936.686761 1.462331767 1.723218007 1.106960459 1.574319843 0.998801181 1.127294386 1.002401619 1.519390102 1 12.76003102 3.285310895 1.152531589 1.128722787 1.580038502 0.314125728 0.224510541 0.451446263 1.271212029 0.078756529 0.129083003 1928.905247 -3.285310895 0.451315715 EADKSHPEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EADKSHPEQR 10 1 O14745 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 152.7 1.06E-05 3202137000 5682159 4650316 5124125 5798825 4267914 5454376 6242564 5993305 4474108 FALSE TRUE 5413574.605 5124188.487 5359071.2 5215916.094 5012236.85 5265489.591 5290146.209 5468499.442 5167929.818 1.047532532 0.991536005 1.036986064 1.009285396 0.969873243 1.018877921 1.023649004 1.058160547 1 22.30115505 1.663277837 3.642093827 1.031822001 1.011781614 0.069112099 0.025507688 0.437034532 13.64364537 0.014151731 0.006413436 46.0551114 -1.663277837 -0.020040387 EADNVKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EADNVKDK 8 1 Q9Y2B0;F8VXJ7;F8W031;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 61.691 0.07694 97946000 304060 248530 224760 210750 197580 215910 238780 219780 223670 FALSE TRUE 289687.6864 273855.4896 235065.4683 189565.0096 232037.8894 208432.9826 202349.7255 200534.8981 258355.6013 1.121275037 1.059994396 0.909852417 0.73373679 0.898133767 0.80676781 0.783221748 0.776197215 1 17.97899864 3.673218533 2.642006232 0.820548345 1.099986912 0.658678508 0.075410435 0.128822419 1.763159477 0.018683333 0.033211615 4712.143773 -3.673218533 0.279438567 EAEAAIYHLQLFEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 EAEAAIYHLQLFEELR 16 0 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;; 270.51 3.96E-35 2618020100 2432622.4 3111103.5 2312784.9 3015085.1 2259139.4 2349734.7 2424044.5 2576825.4 1998418.7 FALSE TRUE 2317637.16 3428128.484 2418828.375 2712003.017 2653132.596 2268362.798 2054211.991 2351184.907 2308323.265 1.004034918 1.48511629 1.047872459 1.174880078 1.149376535 0.982688531 0.889915213 1.018568301 1 21.13841385 2.287575226 2.828675485 0.950965907 1.200931198 0.357889275 0.130962611 0.247880397 4.072071362 0.051580295 0.038819011 193.8988467 -2.287575226 0.249965292 EAEAAIYHLQLFEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 EAEAAIYHLQLFEELRR 17 1 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;; 254.59 3.13E-27 11767127000 7700227.2 7548672.7 7140178.2 7938780.5 8101506.7 7253763.6 8798542.6 7883955.4 7590074.8 FALSE TRUE 7336252.721 8317891.03 7467562.433 7140759.201 9514406.903 7002563.948 7456163.33 7193594.47 8767104.835 0.836793087 0.948761443 0.851770633 0.814494561 1.085239322 0.798731631 0.85047042 0.820521096 1 23.06366907 -0.540229533 7.286364703 1 0.878222086 0.174220778 0.084805311 0 0 0.07527905 0.017743442 0.288250764 0.540229533 -0.121777914 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.738)PS(0.131)S(0.131)K;EAEALLQSMGLTPESPIVPPPMS(0.701)PS(0.142)S(0.156)K;EAEALLQSMGLTPESPIVPPPMS(0.741)PS(0.13)S(0.13)K;EAEALLQSMGLTPESPIVPPPMS(0.945)PS(0.045)S(0.01)K;EAEALLQSMGLTPESPIVPPPMS(0.709)PS(0.237)S(0.053)K;EAEALLQSMGLTPESPIVPPPMS(0.782)PS(0.182)S(0.036)K;EAEALLQSMGLTPESPIVPPPMS(0.683)PS(0.136)S(0.181)K;EAEALLQSMGLTPESPIVPPPMS(0.773)PS(0.19)S(0.037)K;EAEALLQSMGLTPESPIVPPPMS(0.7)PS(0.241)S(0.059)K 153.82 1.50E-07 1354482000 1912365 1447889 1596986 1869996 1294048 1594891 1849133 1651805 1257913 TRUE FALSE 1821971.296 1595430.535 1670209.388 1682020.449 1519729.561 1539659.525 1567013.799 1507164.197 1452983.724 1.253951622 1.098037445 1.149503164 1.157631997 1.045937086 1.059653663 1.07847994 1.037289113 1 20.47058711 8 0.189494913 0.998058844 2.055460836 0.796905798 0.033041907 23.51460217 0.274084207 0.066379497 7.272871077 100000000 -8 1.057401993 EAEAMALLAEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEAMALLAEAER 13 0 P54920;M0R0Y2;M0R2M1;M0QZM9;M0QZN5;M0R031 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 142.08 9.34E-05 37378000 85718 86464 77398 99040 116681 77577 96417 81616 121310 FALSE TRUE 81666.28002 95274.7799 80946.77486 89084.31104 137030.1295 74890.48904 81706.81583 74469.27037 140122.1352 0.582822121 0.679940965 0.577687278 0.635761872 0.977933495 0.5344658 0.58311141 0.531459717 1 17.09632535 -1.271930517 4.165508495 1.000335737 0.637940972 0.438760277 0.128704618 0.000382478 6.69E-05 0.118774279 0.027969728 0.053464989 1.271930517 -0.362394766 EAEDELSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAEDELSAR 9 0 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 100.98 0.010072 0 122770 126740 119040 132590 115720 111590 119960 120410 117910 FALSE TRUE 116966.9054 139654.9501 124498.1017 119261.8013 135901.5314 107725.6103 101657.8988 109866.2621 136194.8806 0.858820133 1.025405283 0.914117338 0.875670222 0.997846107 0.790966664 0.746414978 0.806684228 1 17.05531295 2.225734969 24.99818658 0.806694139 0.936328225 0.222191412 0.083763886 234.1937403 456458.8236 0.028630007 0.021277838 168.1647513 -2.225734969 0.129634086 EAEDGFR ddPTM_SK-BR-3_Trastuzumab_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 ; 129.39 0.0085261 137394000 539020 499370 468250 592870 497640 496210 610590 564850 527050 FALSE TRUE 513541.5928 550256.3707 489719.7257 533273.5812 584428.2584 479026.1233 517433.2812 515388.7395 608782.2222 0.843555502 0.90386406 0.804425142 0.87596773 0.959995606 0.786859579 0.849948081 0.846589668 1 19.2155667 -0.890625537 4.087556374 1.000003955 0.859940759 0.45524019 0.048495724 8894313.098 19203490.91 540.0508902 0.011291959 0.128639535 0.890625537 -0.140063195 EAEDS(ph)DS(ph)DDNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEDSDSDDNIK 12 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIK;EAEDS(1)DS(1)DDNIK 275.66 1.14E-27 167864000 968270 1377360 2144200 1211220 610110 1770830 886220 1055940 534440 TRUE FALSE 922501.796 1517714.55 2242513.691 1089465.864 716512.9908 1709505.713 751010.8625 963476.2957 617318.2257 1.494369934 2.458561058 3.632670473 1.764836707 1.160686597 2.769245491 1.216570046 1.560744938 1 19.23565486 1.522915426 0.771371868 1.019246824 2.262319016 0.260413323 0.713274501 0.845268357 1.04684421 0.652010832 0.277560548 33.33614879 -1.522915426 1.243072193 EAEDS(ph)DS(ph)DDNIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAEDSDSDDNIKR 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIKR;EAEDS(1)DS(1)DDNIKR;EAEDS(1)DS(1)DDNIKR 220.25 1.41E-11 923680000 3056600 2084590 1790430 2880030 1405160 2521120 2949360 2689530 1458720 TRUE FALSE 2912120.576 2297012.091 1872522.986 2590523.913 1650219.459 2433812.982 2499380.963 2454020.495 1684930.847 1.7283324 1.363267872 1.111335215 1.537466013 0.979398924 1.444458677 1.483373022 1.456451758 1 20.68425795 4.449109874 2.367951601 1.319434646 1.728408575 0.303891143 0.203052924 0.403765615 3.968764747 0.048063091 0.26185503 28126.12316 -4.449109874 0.408973929 EAEDSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EAEDSLRR 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 182.53 0.00036567 1664060000 2143513 1682679 1885041 2049870 2050530 1946487 2391120 2080002 2240800 FALSE TRUE 2042193.389 1854145.903 1971471.994 1843813.173 2408141.783 1879079.667 2026310.728 1897865.998 2588291.82 0.789012032 0.716358909 0.761688454 0.712366805 0.930398097 0.725992198 0.782875684 0.733250395 1 21.30356885 -1.542356794 3.029363364 1.009542111 0.767598871 0.569692242 0.063085016 52319186.13 62497415.02 4112542.912 0.013597294 0.028684231 1.542356794 -0.24194324 EAEDTQVFGDLPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEDTQVFGDLPRPR 15 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 138.39 9.92E-06 102510000 108945 84129 100119 107997 111541 100734 126849 110360 109872 FALSE TRUE 103795.3858 92701.84075 104709.5552 97140.93638 130993.7151 97245.55632 107495.8553 100696.2933 126910.3886 0.817863588 0.730451161 0.825066855 0.765429351 1.03217488 0.766253712 0.847021717 0.793444055 1 16.95345064 -5 0.151000458 1.63399197 0.762389833 0.311574458 0.08224285 154.5741668 1.38158556 29.58797474 0.378996338 1.00E-05 5 -0.871602136 EAEEEFWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEEEFWYR 9 0 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 132.9 0.00067957 101058000 228816 203155 203659 214390 219301 170951 240230 200072 219986 FALSE TRUE 218000.3211 223856.7255 212996.9666 192839.1099 257547.025 165030.924 203578.5014 182552.635 254100.3053 0.857930182 0.88097779 0.838239711 0.758909398 1.013564406 0.649471569 0.801173777 0.718427452 1 17.95503858 2.228532948 24.99978376 0.773920673 0.86385489 0.101713543 0.10792624 373.6502207 931533.1167 0.035106932 0.026229234 169.2516642 -2.228532948 0.089934217 EAEEES(ph)DHN ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN 187.85 4.20E-05 4507110000 6357639 6366963 6497463 7956062 5239771 6404430 7030470 8760586 6754380 TRUE FALSE 6057126.004 7015763.768 6795378.105 7156303.532 6153585.403 6182642.983 5957842.678 7993462.647 7801814.754 0.776373984 0.899247674 0.870999674 0.917261401 0.788737697 0.792462161 0.763648313 1.024564528 1 22.89537831 1.227697472 24.99865039 1.012282427 0.830870256 0.676249604 0.05248277 149.7458512 344589.0992 0.051299652 0.013329602 16.89263787 -1.227697472 -0.181412171 EAEEGEDDRDS(ph)ANGEDDS ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.99)ANGEDDS(0.01);EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(1)ANGEDDS 252.33 4.65E-30 14871922000 3510797 4178386 3161703 4352727 2606538 3735249 2910102 3350419 2339939 TRUE FALSE 3344848.584 4604168.284 3306670.21 3915182.612 3061117.402 3605896.391 2466112.492 3057038.551 2702804.789 1.237547231 1.703477921 1.223421766 1.448562851 1.132570659 1.334131272 0.912427158 1.131061541 1 21.36602589 2.344696374 0.909126431 1.003059816 1.447135887 0.46780016 0.164140072 0.431661511 0.694735053 0.109533867 0.068767253 221.1548021 -2.344696374 0.44407607 EAEEGPTGASESQDS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEEGPTGASESQDSPR 17 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 EAEEGPTGASESQDS(1)PR;EAEEGPTGASES(0.009)QDS(0.991)PR 211.89 2.17E-12 99831000 97778 89500 93782 102984 99377 89904 99845 93194 102492 TRUE FALSE 93156.22772 98620.15175 98081.99746 92631.85266 116708.3173 86790.60194 84611.81147 85033.43931 118385.9359 0.786885934 0.833039423 0.828493661 0.782456564 0.985829241 0.733115815 0.714711683 0.718273152 1 16.85313818 -1.508360799 8.602178146 1.000011956 0.797348304 0.396398909 0.078391951 1.80E-05 1.03E-06 0.076007428 0.017914067 0.031019815 1.508360799 -0.202663652 EAEEVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEEVYR 7 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 139.54 0.0087129 447290000 593580 502890 535550 616890 562190 542100 620460 552660 631570 FALSE TRUE 565522.6498 554135.0627 560105.4972 554879.0452 660235.758 523326.9411 525797.4315 504266.1606 729510.65 0.775208216 0.759598318 0.767782482 0.760618156 0.905039231 0.717367102 0.720753606 0.691238929 1 19.47656951 -2.269212638 2.458525565 2.092512132 0.762039002 0.63114388 0.057131595 2537299.422 910343.2155 15242942.21 0.013826441 0.005380063 2.269212638 -1.33047313 EAEGSSAEYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEGSSAEYKK 11 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 160.52 4.39E-05 960830000 1499580 1225380 1289630 1508180 908750 1493300 1659510 1603050 1099730 FALSE TRUE 1428697.825 1350247.615 1348760.811 1356574.881 1067235.712 1441586.647 1406321.271 1462678.444 1270270.512 1.124719351 1.062960686 1.061790224 1.067941725 0.840164124 1.134865868 1.107103768 1.151470045 1 20.27670433 -1.460722907 7.293116679 0.999991797 1.070314512 0.058041773 0.087030012 1.12E-05 8.27E-07 0.081138115 0.019122207 0.034616017 1.460722907 0.070322715 EAEKLESEHPDQAQAILSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAEKLESEHPDQAQAILSR 19 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 174.2 2.97E-12 205720000 531550 411820 452920 562870 377230 506790 606430 588830 409600 FALSE TRUE 506424.6849 453784.9262 473686.83 506289.2382 443018.7926 489239.7352 513907.9656 537268.9236 473118.6761 1.070396732 0.959135518 1.00120087 1.070110448 0.936379845 1.034074028 1.086213653 1.135590182 1 18.85184259 1.867684867 4.281548174 1.082016782 1.007629906 0.240470063 0.052791111 0.276276113 7.774532286 0.023272629 0.01314743 73.73689854 -1.867684867 -0.074386877 EAELDKYLECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAELDKYLECR 11 1 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 112.51 0.0013833 149800000 300560 213210 280190 294340 227200 288860 350660 305850 262670 FALSE TRUE 286353.1245 234936.3414 293036.9886 264752.384 266823.6081 278856.7058 297160.3767 279068.1526 303403.5221 0.943802901 0.774336236 0.965832521 0.872608143 0.879434775 0.91909515 0.979422963 0.919792067 1 18.21087831 1.870270344 0.797430755 0.985345728 0.873269007 0.290249908 0.054479048 0.673440672 0.806964476 0.045392767 0.021765343 74.17718428 -1.870270344 -0.112076721 EAELDVNEELDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAELDVNEELDKK 13 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 134.9 0.00014458 159056000 181498 156964 164543 214727 104901 205096 217239 243630 120420 FALSE TRUE 172918.9492 172958.8101 172087.4593 193142.234 123195.7012 197993.4741 184095.2007 222296.4656 139094.1186 1.243179446 1.24346602 1.237201551 1.388572256 0.88570029 1.423449648 1.323529726 1.598173006 1 17.08570189 EAELSKGESVCLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAELSKGESVCLDR 14 1 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 115.58 0.00037487 222510000 286290 175370 256640 215270 212720 220410 309490 255540 250660 FALSE TRUE 272757.6391 193240.4024 268407.1979 193630.6506 249818.3007 212777.1464 262271.6163 233163.5629 289531.0726 0.942066897 0.667425436 0.927041079 0.668773299 0.862837617 0.734902629 0.905849635 0.805314472 1 18.14335866 0.3671837 0.705703667 1.003020241 0.801274404 0.253680203 0.099574498 2.771393422 2.01145575 0.10952078 0.031939498 2.329076213 -0.3671837 -0.201745838 EAEMEEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 59.597 0.074045 30085000 35726 30929 40154 40651 39881 34436 37377 36549 38754 FALSE TRUE 34037.30278 34080.70026 41995.10062 36564.68425 46836.23377 33243.47269 31674.45217 33348.5758 44763.77239 0.760376102 0.76134558 0.938149275 0.816836524 1.046297737 0.74264234 0.707591217 0.744990291 1 15.450044 -0.362994074 7.374833012 0.999995928 0.806769479 0.236639459 0.103664386 0 0 0.101480168 0.023919105 0.433516794 0.362994074 -0.19322645 EAEMEEHREHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAEMEEHREHIK 12 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 0 126.19 0.00018827 528790000 299890 260840 300200 307710 232510 305530 361220 281080 2043.6 FALSE TRUE 285714.794 287419.8926 313964.4669 276778.4062 273059.6704 294949.4195 306109.2547 256467.1451 2360.511051 121.03938 121.7617229 133.0069888 117.2535948 115.6782004 124.9515097 129.6792297 108.6489915 1 11.20488352 0.782754647 3.977134438 1.002007676 123.1855544 0.981797458 5.193467684 0.286259057 5.124306953 5.019945763 1.283060153 6.063936528 -0.782754647 122.1835467 EAENPEGEEKEAATLEVERPLPMEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EAENPEGEEKEAATLEVERPLPMEVEK 27 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;;;;; 233.87 3.26E-45 1209317000 1114822 836150 1003945 1120533 665126 1199135 1243464 1275098 721310 FALSE TRUE 1062126.573 921354.6356 1049976.871 1007894.894 781123.7638 1157608.654 1053750.729 1163443.659 833167.0709 1.274806231 1.105846196 1.260223679 1.209715229 0.937535569 1.389407593 1.264753212 1.396410996 1 19.6682463 EAEQEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAEQEAAR 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 ;; 137.06 0.0033321 67934000 179816 169992 150441 205501 196568 157976 197772 171710 203599 FALSE TRUE 171316.454 187314.3781 157338.8687 184843.6491 230849.397 152505.2515 167598.2491 156674.1621 235172.0931 0.728472719 0.796499175 0.669037157 0.785993128 0.981619009 0.648483625 0.712662148 0.666210689 1 17.84335735 4.737939357 5.157634086 0.766514867 0.726844703 0.003884523 0.124033264 1.244149582 99.09861415 0.027251331 0.172370081 54693.95849 -4.737939357 -0.039670164 EAEREEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAEREEER 8 1 P49756 P49756 RBM25 RNA-binding protein 25 0 83.998 0.016201 47714000 32631 32639 30551 38338 40432 33825 41435 35750 36602 FALSE TRUE 31088.5973 35964.95121 31951.79357 34484.1914 47483.328 32653.63177 35113.32974 32619.54048 42278.05122 0.735336573 0.850676655 0.755753698 0.81565234 1.123120074 0.772354232 0.830533308 0.771547873 1 15.36762126 -3.601320117 0.021295911 1.980975449 2.90E-06 0.181071288 0.109952863 4235.975461 8.684853727 518.1489951 312.6216143 0.000250426 3.601320117 -1.980972546 EAESSPFVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAESSPFVER 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 204.34 4.39E-07 447950000 201640 146560 169920 191310 192960 168200 217970 172280 191570 FALSE TRUE 192108.8768 161494.6306 177711.0001 172079.1553 226612.1629 162375.1918 184714.6732 157194.2499 221277.6972 0.868180026 0.729827871 0.803113022 0.777661543 1.024107562 0.73380731 0.834764079 0.710393555 1 17.75549852 -1.15237981 4.207238575 1.00005081 0.810108663 0.304577708 0.090115642 3.94E-05 7.94E-06 0.078845818 0.018579097 0.070407705 1.15237981 -0.189942148 EAFAGDDVIRDFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAFAGDDVIRDFLK 14 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;Q5TAP6 Q9BVJ6-3 UTP14A;UTP14C U3 small nucleolar RNA-associated protein 14 homolog A;U3 small nucleolar RNA-associated protein 14 homolog C 0 ; 116.08 0.00034855 84314000 204378 151706 184453 202070 189897 188083 255620 226940 210396 FALSE TRUE 194717.457 167165.0139 192910.3525 181757.5397 223014.9767 181569.6385 216620.4742 207067.9305 243023.1371 0.801230119 0.687856374 0.793794183 0.747902203 0.91766973 0.747129021 0.891357411 0.852050274 1 17.89073415 1.055043953 0.31543591 1.026340366 0.728250664 0.590130211 0.059094338 1.093995046 0.340487648 0.12095206 0.072984017 11.3512569 -1.055043953 -0.298089701 EAFEETHLTSLDPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAFEETHLTSLDPVK 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 157.75 1.90E-06 193849000 415680 369500 339640 444330 287220 365950 430400 429320 306230 FALSE TRUE 396031.6302 407152.4701 355212.8299 399665.1042 337311.0771 353277.0597 364734.5752 391726.4648 353718.5844 1.119623474 1.151063269 1.004224391 1.129895691 0.953614234 0.998751763 1.031143376 1.107452314 1 18.43224249 3.742672778 24.99778779 1.032105434 1.135343377 0.400275115 0.052511049 300.4171173 1826226.741 0.012804494 0.022042654 5529.333413 -3.742672778 0.103237942 EAFGFIER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 102.46 0.011539 237656000 404165 356876 274304 327089 490410 289273 497186 321752 504674 FALSE TRUE 385060.9214 393242.0701 286881.1097 294209.3923 575937.3487 279255.4035 421331.1443 293577.6892 582936.2664 0.660554067 0.674588446 0.492131175 0.504702502 0.987993683 0.479049631 0.722773944 0.503618845 1 19.15297863 -1.845150189 2.746403397 1.136279438 0.636984639 0.363880785 0.154109526 27137365.71 19766413.54 24348412.76 0.034807235 0.014283999 1.845150189 -0.499294799 EAFLQEVWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAFLQEVWK 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 136.33 0.00045578 92553000 357770 305770 302470 342350 299510 296560 419840 324870 370390 FALSE TRUE 340858.9211 336928.3106 316338.5487 307936.3276 351744.4492 286290.0528 355785.6971 296422.6606 427828.1895 0.796719173 0.787531815 0.739405576 0.719766334 0.822162863 0.669170615 0.831608823 0.69285444 1 18.70667202 -1.504695448 2.993251581 1.007767723 0.763827929 0.665096829 0.053930039 13439953.85 15587944.71 858068.224 0.011871345 0.031282723 1.504695448 -0.243939794 EAFNMIDQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 214.71 1.99E-08 896990000 712460 639440 524310 794940 600820 617260 631070 673950 594640 FALSE TRUE 678783.4278 704599.663 548350.1321 715031.1209 705602.8178 595884.1314 534788.6811 614935.3652 686853.7342 0.988250327 1.025836547 0.79835066 1.041023853 1.027297054 0.867556077 0.778606353 0.895293036 1 19.38964338 2.174958758 7.937684146 0.856703287 0.978783147 0.178240141 0.087745498 0.300294628 32.78287628 0.031269739 0.023115308 149.6093576 -2.174958758 0.122079861 EAFQLFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 EAFQLFDR 8 0 P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2 P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;; 236.82 2.93E-08 9842171000 6472780 5401170 4942700 5701640 6233130 4990560 6552220 5784350 6309510 FALSE TRUE 6166824.517 5951555.364 5169327.684 5128500.315 7320185.899 4817735.656 5552558.499 5277841.649 7287956.586 0.846166473 0.816628817 0.709297266 0.703695234 1.00442227 0.661054385 0.761881391 0.724186758 1 22.79708293 3.986848161 23.1246761 0.779426449 0.835089896 0.005451487 0.11898787 903.6071728 1588812.133 0.027543893 0.050974705 9701.707138 -3.986848161 0.055663446 EAFSLFDKDGDGTITTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479 P0DP25 CALM2;CALM3;CALM1 0 ;;;; 255.24 4.22E-27 8742352000 9807730 9171560 6515810 10980360 5480840 9576970 9502820 9651210 5343440 FALSE TRUE 9344138.04 10106152.39 6814566.334 9876593.351 6436696.761 9245317.128 8052990.278 8806098.888 6172073.385 1.51393826 1.637399908 1.104096777 1.600206727 1.042874308 1.497927285 1.304746359 1.426765098 1 22.55732378 -1.431846861 0.055686452 9.44E-13 2.206928748 0.294331322 0.193825607 214.3324146 1.991830037 56.24381377 26.35915104 0.036995861 1.431846861 2.206928748 EAFVHVVTLEDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAFVHVVTLEDMR 13 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 171.29 2.53E-05 82666000 165700 137100 121830 151350 155010 129410 169920 158660 144920 FALSE TRUE 157867.6894 151070.6459 127416.026 136136.0105 182043.6949 124928.4993 143995.5832 144766.8893 167393.4535 0.943093569 0.902488375 0.761176876 0.813269621 1.087519799 0.746316518 0.86022231 0.864830053 1 17.35288358 3.993247034 24.16672157 0.865517533 0.927866657 0.032172107 0.102986844 775.2228137 2774310.548 0.024257074 0.046994696 9845.709864 -3.993247034 0.062349124 EAFVVEEWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAFVVEEWVK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 163.77 1.48E-05 29952000 91612 70771 72915 90870 75421 80493 98545 87810 88264 FALSE TRUE 87281.68232 77982.64536 76258.22487 81735.57496 88574.39852 77705.50723 83510.15035 80120.89089 101951.5303 0.856109585 0.764899213 0.747985093 0.801710133 0.868789299 0.762180881 0.819116202 0.785872371 1 16.63752391 -1.583631477 2.978806418 1.011441461 0.801012541 0.718552283 0.039173131 30910896.96 32253868.43 2779646.77 0.008967154 0.02608366 1.583631477 -0.210428919 EAGDVCYADVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EAGDVCYADVYR 12 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 251.64 1.13E-20 3846910000 2200120 1745800 1751870 1895130 1992970 1814950 2285700 1960320 2209310 FALSE TRUE 2096124.688 1923699.005 1832194.972 1704627.932 2340543.337 1752097.826 1936974.485 1788663.988 2551918.511 0.821391701 0.753824621 0.717967664 0.667978983 0.917170093 0.686580633 0.759026778 0.700909524 1 21.28315083 -2.194444922 2.423797046 1.722902922 0.755815608 0.533615018 0.072499557 4930787.124 1269089.317 19518806.16 0.015946071 0.006390798 2.194444922 -0.967087314 EAGELPT(ph)SPLHLLSPGTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.5)S(0.5)PLHLLSPGTPR;EAGELPT(0.57)S(0.43)PLHLLSPGTPR 87.772 0.0097984 51438000 42310 52570 35975 55658 43126 38140 36559 44228 34120 TRUE FALSE 40310.09015 57926.94277 37624.48933 50063.1521 50647.16075 36819.20224 30981.2531 40355.16185 39411.15534 1.022809146 1.469810826 0.954665983 1.270278724 1.285097083 0.934233009 0.786103651 1.023952774 1 15.26631642 2.190213526 7.119304888 0.902449409 1.21294584 0.410552699 0.154885802 0.174592324 20.4406687 0.054590067 0.040511279 154.95783 -2.190213526 0.310496431 EAGELPTS(ph)PLHLLSPGTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.035)S(0.965)PLHLLSPGTPR;EAGELPT(0.045)S(0.955)PLHLLSPGTPR 204.5 2.93E-16 141414000 159604 211640 148803 211820 133135 165637 151870 178636 115290 TRUE FALSE 152059.8352 233206.3566 155625.7647 190527.4512 156353.7018 159900.9492 128699.4422 162993.6848 133168.5844 1.141859666 1.751211502 1.168637224 1.430723711 1.174103506 1.200740775 0.966439966 1.223964988 1 17.02289425 2.53726455 1.226882837 1.061783809 1.416619587 0.335373938 0.182264068 0.44330012 1.354663147 0.091051706 0.06977011 344.5597548 -2.53726455 0.354835778 EAGENAPVLS(ph)DDELVSMSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAGENAPVLSDDELVSMSVR 20 0 O60675 O60675 MAFK Transcription factor MafK 1 EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR 300.06 8.83E-55 302780000 352488 270054 297848 344497 318163 313605 364973 331018 488094 TRUE FALSE 335826.5908 297572.8096 311504.6254 309867.5071 373650.5265 302744.7802 309289.6657 302032.3091 563785.1247 0.595664157 0.527812453 0.552523669 0.54961987 0.662753432 0.536986109 0.548594938 0.53572238 1 19.10478589 -1.260974819 3.586264815 1.000975051 0.562379449 0.922652582 0.039697555 11428724.04 18015539.78 122257.5962 0.00907759 0.054830876 1.260974819 -0.438595601 EAGEQGDIEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 208.84 4.23E-08 1449090000 1932380 1616220 1733440 1930950 1823770 1764690 2104930 1856960 1966870 FALSE TRUE 1841040.227 1780914.655 1812919.939 1736847.237 2141834.911 1703578.343 1783784.269 1694354.738 2271882.154 0.810359034 0.783893941 0.797981504 0.764497064 0.942757927 0.749853305 0.785157041 0.74579341 1 21.11545657 -2.243232489 2.391506595 1.773361085 0.797394128 0.568676599 0.055413649 8664281.044 1616577.381 36220414.12 0.013473828 0.005711728 2.243232489 -0.975966957 EAGICYASIAMATDYDCWKEHEEAVSVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAGICYASIAMATDYDCWKEHEEAVSVDR 29 1 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ; 104.51 0.00032082 59798000 83171 45864 66469 66777 67692 72449 107159 75983 69584 FALSE TRUE 79239.67166 50537.59374 69516.6694 60064.44909 79497.46337 69940.07296 90809.92644 69329.52571 80374.73133 0.985877904 0.628774652 0.86490702 0.747305131 0.989085277 0.87017489 1.129831788 0.862578631 1 16.29445439 2.729387324 24.58725169 0.982491877 0.800198939 0.328220504 0.115422514 537.7666121 1441377.21 0.035011479 0.033450286 536.2747189 -2.729387324 -0.182292938 EAGLAHLCEFIEDCEHTVLATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAGLAHLCEFIEDCEHTVLATK 22 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ;;; 300.51 5.47E-56 116363400 181853.4 170838.3 175585.1 195219.8 145697.4 204423.8 213727.1 216109.3 103258.4 FALSE TRUE 173257.5502 188246.917 183635.8505 175595.9348 171106.9804 197344.5525 181119.1055 197185.624 119271.1853 1.452635435 1.578310105 1.539649749 1.472241048 1.434604511 1.654586999 1.518548718 1.653254502 1 16.86388602 -1.206297943 4.583550833 0.99987676 1.535456722 0.833894001 0.075450477 6.247321906 21325686.77 4803.169063 0.016341235 0.062187351 1.206297943 0.535579961 EAGS(ph)PAQEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAGSPAQEFK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EAGS(1)PAQEFK;EAGS(1)PAQEFK 174.89 3.11E-06 417570000 868610 840170 742730 949240 507140 875080 847460 949670 564740 TRUE FALSE 827552.5267 925784.2782 776784.9052 853820.5918 595585.0554 844775.7602 718164.4123 866511.8603 652316.9949 1.268635546 1.419224526 1.190808934 1.308904411 0.913030107 1.295038711 1.100943894 1.328360087 1 19.31521369 3.29916167 1.917648851 1.148518491 1.336843056 0.232099578 0.137726889 0.411632007 3.10832323 0.038602435 0.056042793 1991.414522 -3.29916167 0.188324565 EAGSQKDENLALYVENQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAGSQKDENLALYVENQFR 19 1 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;; 198.49 6.74E-16 240331000 456657 450688 406471 551614 438552 428871 561756 527601 448781 FALSE TRUE 435071.7286 496613.6196 425108.0974 496164.7127 515035.3299 414019.0897 476049.8048 481401.4595 518375.6654 0.839298134 0.958018774 0.820077264 0.957152787 0.993556149 0.798685427 0.91834906 0.928672952 1 18.98363847 -4.999999999 0.26832225 1.671337483 0.894134418 0.202117422 0.063471234 344.12138 3.347851896 127.8440319 0.072746224 1.00E-05 4.999999999 -0.777203066 EAGVFVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAGVFVPR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 158.36 0.0008502 710295000 1064770 900920 872050 992150 1076050 920500 1106290 968660 1165240 FALSE TRUE 1014440.432 992724.7723 912034.3551 892417.197 1263712.779 888622.8542 937505.1421 883838.9952 1345939.468 0.75370435 0.737570148 0.677619148 0.663044081 0.938907588 0.660224977 0.696543317 0.656670687 1 20.3601821 -2.269656389 2.366707974 2.197492127 0.724562183 0.521749697 0.083322762 3153332.806 781997.4585 20080356.47 0.01876982 0.005374569 2.269656389 -1.472929944 EAHLEKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAHLEKEEK 9 1 A0A1W2PRI9;E9PNW5 A0A1W2PRI9 C4orf50 0 ;; 82.287 0.011344 620750000 1354790 1356820 1156000 1446230 644590 1390090 1163370 1281820 485960 FALSE TRUE 1290751.762 1495081.501 1209003.743 1300852.213 757006.2919 1341950.835 985876.5397 1169577.045 561320.1949 2.299492827 2.663509195 2.153857557 2.317486926 1.348617596 2.390704712 1.756353234 2.083618327 1 19.09846444 -0.432421735 0.143085281 4.00E-11 2.888424819 0.572446195 0.330384987 14.32986729 0.556924777 8.830233679 2.617596438 0.369469221 0.432421735 2.888424819 EAHLPPGAMAAVGLSWEECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 240.07 1.09E-29 3155130000 6401240 5904760 6198000 7286760 4865580 6819670 7447430 7335130 5148060 FALSE TRUE 6098666.071 6506461.757 6482184.431 6554281.041 5714135.612 6583503.118 6311187.772 6692827.131 5946394.852 1.025607317 1.09418596 1.090103263 1.102227686 0.960941167 1.107141938 1.061346905 1.125526861 1 22.50358383 EAHQLFLEPEVLDPESVELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EAHQLFLEPEVLDPESVELK 20 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;;;;;; 220.62 8.40E-25 665451100 1377245 1254229 1238564 1493842 941842 1440535 1516423 1527670 976882 FALSE TRUE 1312145.358 1382036.361 1295353.385 1343678.164 1106098.947 1390648.912 1285064.82 1393899.116 1128371.871 1.162866065 1.224805754 1.14798447 1.190811468 0.980261007 1.232438478 1.138866408 1.235318915 1 20.10581118 -1.448095155 3.288931695 0.997474279 1.165419105 0.328939885 0.07367208 8904270.325 14740274.18 206150.3048 0.01619744 0.035637304 1.448095155 0.167944826 EAIAELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 102.51 0.011517 50140000 142490 125510 136140 151820 148500 132430 147810 135330 143080 FALSE TRUE 135754.7801 138299.6117 142382.1537 136558.7652 174398.353 127843.9159 125258.8698 123479.7878 165268.1156 0.82142148 0.83681968 0.861522219 0.826286211 1.055245002 0.773554629 0.7579131 0.747148277 1 17.33444889 -0.553204266 7.307701367 0.999981698 0.833088942 0.265320288 0.086242315 0 0 0.082341946 0.019408183 0.279766515 0.553204266 -0.166892756 EAIEGTYIDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAIEGTYIDKK 11 1 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 ;; 169.23 2.75E-05 1731230000 2517480 2294880 2315340 2734600 1498680 2808700 2894450 3030820 1828990 FALSE TRUE 2398483.71 2528730.881 2421500.629 2459712.813 1760049.318 2711434.015 2452848.492 2765425.333 2112620.428 1.135312183 1.196964134 1.146207145 1.164294721 0.833111947 1.283445894 1.161045524 1.309002458 1 21.01060215 -0.332058539 7.26611245 0.999964891 1.153362924 0.125577508 0.127437375 0 0 0.113520166 0.02675696 0.465523341 0.332058539 0.153398033 EAIESAIGGNAYQHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAIESAIGGNAYQHSK 16 0 P63172 P63172 DYNLT1 Dynein light chain Tctex-type 1 0 293.77 1.32E-45 330710000 311300 274230 301780 349080 268040 283430 342700 371310 254390 FALSE TRUE 296585.4659 302174.3488 315616.9115 313989.8152 314786.0911 273614.748 290414.8209 338796.128 293839.502 1.009345115 1.028365304 1.074113281 1.068575917 1.071285818 0.931170745 0.988345062 1.152997217 1 18.16466883 EAIHSQLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAIHSQLLEK 10 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;; 141.1 3.81E-05 1456250000 2685590 2241470 2284090 2536420 2081280 2523020 2921750 2707280 2100920 FALSE TRUE 2558647.483 2469878.341 2388817.786 2281454.243 2444254.573 2435647.185 2475983.376 2470216.211 2426719.944 1.054364551 1.017784664 0.984381322 0.940139075 1.00722565 1.003678727 1.020300419 1.017923893 1 21.21057619 -0.521666103 7.543261728 1.00000334 1.007985922 0 0.029205982 0 0 0.030264531 0.007133418 0.300838834 0.521666103 0.007982582 EAILAIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAILAIHK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 98.392 0.0075549 702240000 1107230 575370 435123 736046 1116450 622430 1313060 889682 1152560 FALSE TRUE 1054893.432 634000.8571 455073.8199 662057.2577 1311158.527 600875.093 1112728.581 811776.7276 1331293.118 0.792382547 0.476229351 0.341828418 0.497303898 0.984875914 0.451346953 0.835825383 0.609765585 1 20.34439682 0.529641284 0.433936715 1.026086069 0.566985691 0.286140923 0.194479521 2.700538867 0.988482139 0.36674447 0.121274891 3.385643953 -0.529641284 -0.459100378 EAILEYILHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAILEYILHQK 11 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 162.38 2.52E-05 62621000 304270 239020 245400 292780 248370 267850 324390 299480 230810 FALSE TRUE 289887.7601 263376.4097 256651.8327 263349.1982 291685.6494 258574.2873 274898.3477 273255.9436 266602.836 1.087339371 0.987898005 0.962674803 0.987795937 1.09408307 0.969885734 1.031115617 1.024955127 1 18.0243326 2.811728367 0.003239009 7.96E-09 2.03553648 0.029779506 0.044423169 119078.9098 143.4939294 44666.49273 45507.79799 648.2288671 -2.811728367 2.035536472 EAKPEAPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAKPEAPAAK 10 1 O75363;G3XAF7;O75363-2 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 82.362 0.016636 250900000 449810 352710 362920 437340 295420 405990 447510 445830 320670 FALSE TRUE 428548.3727 388651.55 379560.241 393377.7523 346941.1545 391930.4645 379234.1304 406790.7617 370397.8658 1.156994714 1.049281289 1.024736576 1.062041088 0.936671581 1.058133701 1.023856143 1.098253525 1 18.49871626 4.505036518 1.486718181 1.028429199 1.178575087 0.469268222 0.042392378 0.574688864 1.639321817 0.010647263 0.112362775 31991.64101 -4.505036518 0.150145887 EALAEAALES(ph)PRPALVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;EALAEAALES(1)PRPALVR 272.84 7.31E-36 14562760000 3733360 3409690 3495820 3979660 3801170 3600690 4239340 3960030 4475590 TRUE FALSE 3556891.472 3757141.287 3656106.805 3579617.016 4464092.845 3475997.202 3592550.822 3613268.78 5169641.639 0.688034436 0.726770161 0.707226353 0.692430398 0.863520754 0.672386491 0.694932274 0.698939894 1 22.30163285 -1.180088455 3.751770804 1.000236641 0.716616377 0.731665953 0.053658382 16116447.54 25164675.13 44151.3492 0.012120504 0.066055889 1.180088455 -0.283620265 EALAEAALESPRPALVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 233.31 3.80E-20 2060843000 1266221 1035097 1109682 1286151 1363907 1121120 1478969 1327321 1427932 FALSE TRUE 1206369.243 1140574.561 1160562.017 1156864.658 1601771.949 1082295.333 1253325.116 1211093.737 1649368.402 0.73141285 0.691522015 0.703640264 0.701398582 0.971142619 0.656187746 0.759881852 0.734277276 1 20.65348224 -5 0.270389279 2.783379064 0.721007777 0.469190213 0.085658018 181.1537007 1.757782028 180.5079218 0.097387946 1.00E-05 5 -2.062371287 EALAPNSLS(ph)PS(ph)PQGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALAPNSLSPSPQGHR 16 0 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 2 EALAPNS(0.029)LS(0.974)PS(0.998)PQGHR 63.125 0.03761 108520000 65142 55376 54821 73439 55895 74087 77647 64632 68578 TRUE FALSE 62062.86676 61018.87736 57334.59708 66056.7722 65643.0703 71521.34861 65800.52407 58972.47944 79212.72599 0.783496162 0.770316595 0.723805378 0.833916159 0.828693489 0.902902251 0.830681223 0.744482388 1 16.27344461 3.099237318 6.033053864 0.850805053 0.765353901 0.325526138 0.066071016 0.257445346 13.27147952 0.0174274 0.020931408 1256.716502 -3.099237318 -0.085451152 EALAPNSLS(ph)PSPQGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALAPNSLSPSPQGHR 16 0 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 EALAPNSLS(0.997)PS(0.003)PQGHR;EALAPNSLS(0.993)PS(0.006)PQGHR 145.55 7.79E-07 564900000 311970 262130 270910 322300 390510 276500 372810 296460 357900 TRUE FALSE 297223.7964 288841.345 283331.4915 289901.7917 458614.8204 266924.7357 315930.9874 270500.3908 413401.3041 0.718971598 0.698694809 0.685366709 0.701259983 1.109369554 0.645679472 0.76422349 0.654328828 1 18.65718341 EALAPNSLSPS(ph)PQGHR ddPTM_SK-BR-3_Trastuzumab_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 EALAPNSLS(0.02)PS(0.98)PQGHR 56.514 0.081134 181710000 107630 82333 93384 102150 70644 85853 112370 71067 71297 TRUE FALSE 102542.5432 90722.8263 97665.74877 91881.68793 82964.29123 82879.88908 95225.89268 64843.99673 82353.37463 1.2451529 1.101628521 1.185934993 1.115700338 1.007418234 1.006393356 1.156308325 0.787387245 1 16.32954015 3.202988473 0.383218191 0.958863895 1.260960074 0.468376763 0.093286633 1.860875125 0.475260197 0.090071798 0.230848276 1595.836791 -3.202988473 0.302096179 EALASLPS(ph)SPGLLQSLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALASLPSSPGLLQSLLER 19 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EALASLPS(0.698)S(0.301)PGLLQSLLER;EALASLPS(0.705)S(0.295)PGLLQSLLER 175.51 6.41E-15 0 193401 178783 193539 206471 194785 179932 234830 200590 224120 TRUE FALSE 184259.318 197001.191 202412.9546 185716.1428 228755.4423 173700.9097 199002.3706 183025.2762 258875.385 0.711768398 0.7609885 0.781893399 0.717395912 0.883650805 0.670982719 0.768718782 0.707001464 1 17.98189827 -1.15990283 4.284007652 1.000062428 0.750692038 0.64903671 0.057704865 2.169046265 28850781.94 3503.076415 0.011826636 0.069198578 1.15990283 -0.24937039 EALASLPSS(ph)PGLLQSLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALASLPSSPGLLQSLLER 19 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EALASLPS(0.044)S(0.955)PGLLQSLLER 176.1 1.34E-12 21129000 66019 65963 65113 73860 71506 68793 75288 72504 78613 TRUE FALSE 62898.41271 72684.70469 68098.49546 66435.45248 83976.62376 66410.68116 63801.43284 66155.16539 90803.90254 0.692684025 0.800457939 0.749951198 0.731636533 0.924812937 0.731363733 0.702628753 0.728549804 1 16.47046668 -2.433394218 2.203840891 3.196425362 0.75647263 0.570173765 0.066089856 2474669.96 274148.1268 27058485.29 0.015494006 0.003686428 2.433394218 -2.439952732 EALEALVPVTIEVEVPFDLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EALEALVPVTIEVEVPFDLHR 21 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;; 197.72 8.95E-22 274912000 537150 478221 510578 562290 543493 500025 630966 576519 545708 FALSE TRUE 511759.984 526952.2636 533988.5063 505767.5409 638278.0071 482709.0089 534700.5482 526035.94 630333.6095 0.811887509 0.835989475 0.847152204 0.802380729 1.012603481 0.765799255 0.848281831 0.834535763 1 19.26575606 -2.767421502 1.829640984 4.988132219 0.842754796 0.362881698 0.064564182 1755454.211 40649.54174 29227954.27 0.014963367 0.001708356 2.767421502 -4.145377423 EALEAYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALEAYRR 8 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 ; 135.79 0.0013127 166825000 146987 118352 106936 117850 191281 107499 170875 136897 193383 FALSE TRUE 140039.2158 130412.2034 111839.1214 106003.4941 224640.3458 103776.2827 144804.8804 124909.5729 223371.848 0.626933148 0.583834555 0.50068584 0.474560671 1.005678862 0.464589802 0.648268265 0.559200159 1 17.76908785 -1.651259482 2.573917121 1.049551924 0.608197346 0.390771071 0.15383366 22120933.58 18748523.54 7247922.656 0.035892174 0.022322381 1.651259482 -0.441354578 EALEEFYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALEEFYGR 9 0 Q9H2P9-6;Q9H2P9-4;Q9H2P9;Q9H2P9-5;Q9H2P9-3;Q9H2P9-2 Q9H2P9-6 DPH5 Diphthine synthase 0 101.43 0.0092776 92228000 206130 217500 218340 253990 218700 225390 240190 240950 227890 FALSE TRUE 196386.6434 239663.4973 228351.105 228458.4427 256841.2108 217584.6878 203544.6041 219851.1406 263230.0173 0.746064774 0.910471761 0.867496448 0.867904219 0.975729187 0.826595272 0.773257572 0.835205433 1 18.00596449 4.652142722 3.288246222 0.868579936 0.739867074 0.259373351 0.068762994 0.412692085 7.282978986 0.016683526 0.117831362 44889.28853 -4.652142722 -0.128712861 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALGLGPPAAQLTPPPAPVGLR 22 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR 133.93 9.31E-05 141450000 244000 251070 209220 268980 206516 202687 220430 244600 213400 TRUE FALSE 232466.6036 276654.3184 218812.9439 241941.6194 242532.325 195667.8984 186799.355 223181.5273 246492.9821 0.943096236 1.122361846 0.887704559 0.981535528 0.983931968 0.793807177 0.75782829 0.905427511 1 17.91118705 2.252089464 20.46574463 0.833047465 0.994473558 0.277305691 0.088808738 23.68050265 35822.24349 0.029588416 0.024538215 178.6855628 -2.252089464 0.161426092 EALIEIDYGDLCEDLKDAQAEEEIKQEMNTLQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALIEIDYGDLCEDLKDAQAEEEIKQEMNTLQQK 34 2 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 56.164 0.025017 32843000 27666 19863 19248 29812 15460 28833 28201 31418 13797 FALSE TRUE 26358.28301 21887.06228 20130.53984 26815.24112 18156.21911 27834.50598 23898.4195 28666.87336 15936.56829 1.653949741 1.373386157 1.26316654 1.682623299 1.13928035 1.746580912 1.499596341 1.798810938 1 13.96005338 4.688564652 3.727623035 1.464535966 1.664437927 0.055248731 0.260476138 0.762462994 18.29308709 0.055369005 0.377899177 48816.27675 -4.688564652 0.199901961 EALLDESRPLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALLDESRPLFER 13 1 A0A5F9ZGM7;Q9BU89 A0A5F9ZGM7 DOHH Deoxyhypusine hydroxylase 0 ; 127.36 0.00016223 123235000 211100 203917 189544 203359 206891 200205 248507 227894 249972 FALSE TRUE 201121.7214 224696.3741 198234.7799 182916.967 242972.7249 193271.8506 210592.693 207938.3932 288736.3811 0.696558295 0.778205965 0.686559758 0.633508553 0.841503672 0.669371313 0.729359744 0.72016693 1 18.13939337 -1.217924289 5.067047676 1.000030314 0.721735153 0.699888835 0.057726493 1.77E-05 2.73E-06 0.049957272 0.011773761 0.060544641 1.217924289 -0.278295161 EALLSSAVDHGSDEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EALLSSAVDHGSDEVK 16 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 283.05 1.28E-35 1715350000 3101150 2411030 2809610 3222750 2532620 2894940 3805770 3557780 2621180 FALSE TRUE 2954564.785 2656716.698 2938433.398 2898793.047 2974308.126 2794687.502 3225129.889 3246241.922 3027659.207 0.975857778 0.87748208 0.970529771 0.957437033 0.982378769 0.923052203 1.065222229 1.072195284 1 21.52977139 1.724111196 7.46927279 1.050385574 0.944440974 0.622153189 0.035804594 0.071709728 10.97323317 0.017094335 0.008997178 52.97990756 -1.724111196 -0.105944601 EALLSSAVDHGSDEVKFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALLSSAVDHGSDEVKFR 18 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 163.41 1.99E-11 31693000 32293 13307 38289 23351 55253 29662 71378 41302 87061 FALSE TRUE 30766.57389 14662.99843 40044.58852 21003.71312 64889.10571 28634.7975 60487.97515 37685.37792 100561.9752 0.305946396 0.145810565 0.398208055 0.208863371 0.645264829 0.284747763 0.601499473 0.374747789 1 16.61772537 -4.99999999 0.1216943 3.179539353 0.044277277 0.68736296 0.140696724 73.4747676 0.577097142 38.99585078 1.121618454 1.00E-05 4.99999999 -3.135262076 EALNIIGDISTSTVSTPVPPPVDDT(ph)WLQSASSHSPTPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.25)WLQS(0.179)AS(0.179)S(0.179)HS(0.179)PT(0.035)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.192)WLQS(0.192)AS(0.192)S(0.192)HS(0.192)PT(0.042)PQR 166.27 7.03E-18 299300000 92395 77814 86804 95058 109093 81006 106264 101244 110597 TRUE FALSE 88027.67146 85743.33507 90784.04926 85502.58924 128118.7847 78200.74191 90051.47513 92378.53863 127747.8179 0.689073778 0.67119217 0.710650489 0.66930763 1.002903899 0.612149336 0.704915956 0.723132028 1 16.96293912 -2.053489046 2.028218813 1.36364528 0.716807634 0.409128345 0.104418995 2791652.305 817884.7072 4703878.947 0.026075836 0.008841195 2.053489046 -0.646837645 EALNSCNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EALNSCNKR 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;;;; 187.55 6.48E-05 9687120000 6255300 5160780 4729060 5719060 5105550 5771130 7520650 6570160 5760030 FALSE TRUE 5959624.366 5686669.349 4945892.079 5144169.223 5995956.304 5571274.321 6373236.716 5994841.96 6653266.034 0.895744186 0.854718468 0.743378072 0.773179548 0.901204953 0.83737435 0.957910999 0.901037465 1 22.66563129 1.689079037 1.158189619 0.972658354 0.831732688 0.52290505 0.053404229 0.407005991 1.027830121 0.047365185 0.018097414 48.87412968 -1.689079037 -0.140925666 EALNVFGNDYDTEDGTGVRDYIHVVDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALNVFGNDYDTEDGTGVRDYIHVVDLAK 29 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 42.659 0.087831 94255000 29956 26384 27910 31091 31329 30792 42636 34527 29421 FALSE TRUE 28540.03925 29072.5596 29189.70111 27965.67361 36792.76768 29725.66532 36131.09514 31503.63284 33983.45842 0.839821507 0.855491493 0.858938509 0.822920177 1.082666962 0.874709835 1.063196532 0.927028452 1 15.05254506 2.756990603 24.99403723 0.989603415 0.846476161 0.593136157 0.059755784 506.7350573 687213.7898 0.015789615 0.016717922 571.4662721 -2.756990603 -0.143127254 EALPWGLEPQDVQS(ph)S(ph)DEMRSPEGYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 2 EALPWGLEPQDVQS(0.752)S(0.699)DEMRS(0.517)PEGY(0.032)LR 45.685 0.086921 16509000 14629 11513 11167 14837 13450 12476 11647 14270 15095 TRUE FALSE 13937.51616 12686.18779 11679.018 13345.55657 15795.67574 12043.95299 9870.036238 13020.44315 17435.85551 0.799359467 0.727591932 0.669827643 0.765408762 0.90593064 0.690757789 0.566076969 0.746762506 1 14.08976953 4.550629094 2.957545284 0.733838949 0.799554662 0 0.122833068 1.376583326 21.5502857 0.029513565 0.172667148 35532.77235 -4.550629094 0.065715713 EALPWGLEPQDVQSSDEMRS(ph)PEGYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 1 EALPWGLEPQDVQS(0.014)S(0.014)DEMRS(0.971)PEGYLR;EALPWGLEPQDVQSSDEMRS(1)PEGYLR;EALPWGLEPQDVQS(0.019)S(0.019)DEMRS(0.962)PEGYLR 129.48 0.00012016 201076000 125845 108058 121398 116326 126764 116995 133987 125608 148098 TRUE FALSE 119896.5563 119069.2331 126964.2184 104632.6895 148871.6015 112943.4338 113544.8223 114609.0976 171064.2815 0.700885978 0.696049649 0.742201804 0.611657142 0.870267014 0.660239723 0.663755293 0.669976787 1 17.38417903 -1.636398733 3.876998696 1.011670294 0.700247079 0.65078072 0.068622729 0.006373545 0.000597738 0.061176961 0.01403061 0.02309943 1.636398733 -0.311423214 EALS(ph)PCPSTVSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EALSPCPSTVSTK 13 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 EALS(0.993)PCPS(0.007)TVSTK;EALS(0.993)PCPS(0.006)TVSTK 199.87 1.20E-07 193174000 294640 256100 279620 311450 243960 295670 338150 313170 264710 TRUE FALSE 280712.9511 282196.8812 292440.8536 280142.4543 286506.5468 285430.8738 286559.0069 285747.1746 305759.8748 0.918083026 0.922936279 0.956439604 0.916217193 0.937031214 0.933513182 0.937202787 0.934547657 1 18.22203957 -5 0.238714639 1.391754163 0.9239879 0.789065302 0.011139012 70.68280274 0.705106889 13.42499208 0.016474502 1.00E-05 5 -0.467766263 EALSVALEEAQAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EALSVALEEAQAWR 14 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 224.24 7.50E-12 248398000 242306 215139 201459 250509 249095 213410 260909 239037 248772 FALSE TRUE 230852.6756 237061.9087 210696.0944 225327.3594 292537.0891 206019.5582 221102.5401 218105.6531 287350.2912 0.803384171 0.824992756 0.733237797 0.784155667 1.018050436 0.716963109 0.769452988 0.759023602 1 18.13245099 -1.121863726 4.30222645 1.000033145 0.801223589 0.360344352 0.083257928 2.49E-05 5.09E-06 0.07589209 0.017884957 0.07553292 1.121863726 -0.198809556 EALTYDGALLGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 110.66 0.0024215 129970000 73926 84727 65563 80828 65982 68612 68869 71859 73417 FALSE TRUE 70431.66449 93360.77763 68569.1284 72703.01588 77489.23991 66235.94924 58361.76918 65566.64501 84802.1334 0.830541186 1.100924869 0.80857787 0.857325317 0.913765218 0.781064657 0.688211096 0.773172117 1 16.37181294 2.950105714 1.100659436 0.784183945 0.950941384 0.079150967 0.114133624 0.655110062 1.693678896 0.050180519 0.057784686 891.4679098 -2.950105714 0.166757439 EAMEDGEIDGNKVTLDWAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EAMEDGEIDGNKVTLDWAKPK 21 2 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 188.26 1.45E-17 3459980000 5675790 4677710 4887120 5811120 2799910 5954570 6150710 6238230 2811850 FALSE TRUE 5407506.655 5154373.967 5111199.286 5226975.177 3288213.418 5748361.748 5212306.224 5691977.51 3247897.337 1.664925364 1.586987959 1.573694842 1.609341255 1.012412979 1.769871751 1.604824809 1.752511523 1 21.6310746 2.916263213 23.51955482 1.485375862 1.60955263 0.081741323 0.264724878 172.7341508 48512.3282 0.075854332 0.080455719 824.6377512 -2.916263213 0.124176769 EAMEHPYFYTVVK ddPTM_SK-BR-3_Trastuzumab_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 ; 129.71 0.00015056 200483000 340590 282220 293100 342620 290530 293050 355430 358820 264460 FALSE TRUE 324490.9857 310978.5389 306538.9249 308179.1867 341198.34 282901.605 301202.6256 327399.8186 305471.1061 1.062264087 1.018029308 1.003495646 1.008865259 1.116957818 0.926115758 0.986026565 1.071786536 1 18.2206764 2.227276422 24.99957666 0.991422237 1.037264254 0.182730546 0.047280399 372.5132831 825278.6996 0.016837836 0.012546293 168.7626832 -2.227276422 0.045842016 EAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK 40 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 202.8 1.84E-31 89931000 72007 55851 39286 51639 57434 47263 71571 54595 14200 FALSE TRUE 68603.37181 61542.2804 41087.30196 46448.14961 67450.47142 45626.27046 60651.52946 49814.37237 16402.06348 4.182606165 3.752105977 2.505008106 2.831847937 4.112316204 2.781739659 3.697798728 3.037079599 1 14.00158971 -1.055102842 0.392683495 2.74E-17 3.575224551 0.6346902 0.567006864 10.73514949 1.139277571 13.16618759 0.381484252 0.088084026 1.055102842 3.575224551 EANFTVSSMHGDMPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EANFTVSSMHGDMPQK 16 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 166.48 6.66E-09 463490000 448980 374450 425200 495640 400430 440070 566290 472170 442850 FALSE TRUE 427757.6052 412606.8807 444695.8406 445817.3255 470264.8652 424830.2656 479892.0599 430824.2917 511524.9162 0.836240018 0.806621276 0.869353235 0.871545669 0.919339118 0.830517248 0.938159696 0.842235203 1 18.96444499 -5 0.074811802 1.466316296 0.707860365 0.579910703 0.037845393 169.8411251 0.907684351 13.34828475 1.448717305 1.00E-05 5 -0.758455931 EANLQQNEEKNHSDSSTSESEVSSVS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EANLQQNEEKNHSDSSTSESEVSSVSPLK 29 1 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 EANLQQNEEKNHSDSSTSESEVS(0.004)S(0.021)VS(0.975)PLK 175.02 4.37E-13 112740000 78585 52166 83942 91408 51280 99406 111340 121440 65232 TRUE FALSE 74870.44279 57481.77471 87790.82373 82219.49418 60223.21576 95963.54529 94353.0381 110806.0698 75347.8454 0.993664018 0.762885447 1.165140466 1.091199008 0.799269248 1.273607026 1.252232729 1.47059374 1 16.20127864 2.220574601 24.71875821 1.268334858 0.953127214 0.430857984 0.162863357 180.7102853 248354.1342 0.057837389 0.042806219 166.1784106 -2.220574601 -0.315207644 EANNFLWPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EANNFLWPFK 10 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 166.07 1.32E-05 278500000 1234860 1184820 914440 1179780 950470 1073960 1231350 1132740 984770 FALSE TRUE 1176490.615 1305554.505 956367.9785 1061186.273 1116231.667 1036768.496 1043484.942 1033551.281 1137483.102 1.034292829 1.147757274 0.840775548 0.932924868 0.981317142 0.911458372 0.917363027 0.908630008 1 20.11741368 3.74438898 24.99987126 0.925086308 1.091025055 0.644759121 0.050439181 243.2015343 1043172.984 0.012056793 0.021001915 5551.226916 -3.74438898 0.165938746 EANSSPGLGTPLKS(ph)PSLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EANSSPGLGTPLKSPSLAK 19 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 EANSSPGLGTPLKS(1)PSLAK 253.39 4.30E-31 164790000 277000 231330 245050 317380 169580 283220 312220 318300 202000 TRUE FALSE 263906.759 254902.79 256285.7849 285476.3594 199154.6983 273412.0204 264585.1047 290427.9646 233325.1283 1.13106874 1.092478945 1.098406274 1.223513136 0.85355015 1.171807007 1.133976038 1.244735047 1 17.83198216 EAPAPPKAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAPAPPKAEAK 11 1 P62750 P62750 RPL23A 60S ribosomal protein L23a 0 ;;; 96.745 0.0061867 640493000 1133370 880694 1087384 1161807 826975 1266074 1403006 1346453 972419 FALSE TRUE 1079797.846 970437.7199 1137241.632 1045019.953 971199.1782 1222229.54 1188951.667 1228550.437 1123216.772 0.961344126 0.863980795 1.012486334 0.930381365 0.864658722 1.088151077 1.058523783 1.093778572 1 20.09920495 2.228986781 24.99999793 1.065124688 0.925275105 0.642399878 0.04944162 114.151529 298079.714 0.017165842 0.012839759 169.4286228 -2.228986781 -0.139849583 EAPCVLIYIPDGHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAPCVLIYIPDGHTK 15 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 164.65 1.47E-06 356220000 1162380 1009840 1072420 1244650 926770 1166830 1318950 1291140 1046240 FALSE TRUE 1107436.601 1112743.844 1121591.518 1119535.417 1088398.395 1126422.385 1117719.953 1178080.937 1208485.556 0.916383813 0.92077546 0.928096751 0.926395365 0.90063004 0.932094206 0.924893101 0.974840726 1 20.2047688 1.134124371 2.439016515 1.000172383 0.920254269 0.915284249 0.008549619 0.064173665 0.709799302 0.007399694 0.002050879 13.61834623 -1.134124371 -0.079918114 EAPGS(ph)PPLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 83.087 0.025091 102830000 144640 122130 129790 143080 139470 120900 157680 135800 144480 TRUE FALSE 137803.1538 134575.1859 135740.9999 128697.3266 163793.5238 116713.2027 133623.02 123908.6321 166885.2205 0.825736116 0.806393673 0.813379396 0.771172703 0.981474113 0.699362126 0.800688159 0.742478164 1 17.34849667 -2.163819224 2.479020015 1.494713265 0.805819344 0.413562484 0.072938882 11003022.99 2129847.631 30713818.31 0.016105655 0.006857736 2.163819224 -0.688893921 EAPGS(ph)PPLSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 EAPGS(0.999)PPLS(0.001)PR;EAPGS(0.999)PPLS(0.001)PR 161.23 2.79E-05 1059150000 1398040 1171010 1261200 1400880 1240120 1235960 1475570 1315240 1450400 TRUE FALSE 1331957.42 1290337.25 1319027.267 1260060.881 1456396.535 1193158.395 1250444.696 1200070.613 1675320.624 0.795046274 0.770203167 0.787328257 0.752131182 0.869324065 0.712197043 0.746391274 0.716322951 1 20.6760058 -0.7806687 6.253765316 1.000000005 0.769183109 0.726891339 0.044571098 3.33E-09 5.81E-10 0.040649918 0.009581277 0.165703354 0.7806687 -0.230816896 EAPIDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAPIDKK 7 1 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 ; 79.474 0.052153 1239640000 3297900 2763500 3073700 4017400 2397310 4228300 4833200 4516200 2913100 FALSE TRUE 3142014.803 3045103.792 3214632.185 3613563.319 2815400.105 4081872.911 4095806.572 4120737.586 3364848.67 0.933775962 0.90497496 0.955357135 1.073915553 0.836709279 1.213092567 1.217233514 1.224642767 1 21.68211019 2.226919725 24.99997519 1.186752674 0.942088551 0.613892924 0.086948817 122.9287031 263999.8526 0.029318741 0.021831572 168.6241311 -2.226919725 -0.244664122 EAPPMEKPEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAPPMEKPEVVK 12 1 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 ;; 117.92 0.00062198 657500000 820032 692629 775734 979370 617724 929750 1068930 1076800 784210 FALSE TRUE 781270.7125 763208.6826 811302.1712 880921.8669 725454.87 897552.5244 905845.0963 982509.6835 905821.2816 0.862499842 0.842559893 0.895653688 0.97251178 0.800880797 0.990871536 1.000026291 1.084661736 1 19.78886691 2.095022202 6.192368101 1.020316809 0.87499401 0.683690728 0.049096298 0.120511491 6.546858613 0.018039399 0.013234883 124.4578236 -2.095022202 -0.145322799 EAPPPVLLT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAPPPVLLTPK 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 EAPPPVLLT(1)PK 108.56 0.022872 22639000 51819 48789 47715 52545 36970 52427 61505 54135 43169 TRUE FALSE 49369.61857 53760.65457 49902.77995 47263.07677 43417.55629 50611.43984 52121.28263 49394.65241 49863.42804 0.99009676 1.078158014 1.000789194 0.947850531 0.87072947 1.015001211 1.045280773 0.990598809 1 15.60569445 -0.003034999 8.442676361 1 0.999590411 0 0.055730047 0 0 0.057052417 0.013447384 0.993036019 0.003034999 -0.000409589 EAPS(ph)PTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAPSPTLR 8 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 EAPS(0.995)PT(0.005)LR;EAPS(0.996)PT(0.004)LR 97.857 0.0087685 82401000 682320 577440 561090 635690 533540 532430 623560 568830 542940 TRUE FALSE 650068.0858 636281.7925 586816.5315 571789.2335 626589.2071 513991.8156 528424.4695 519020.2296 627136.3622 1.036565769 1.014582842 0.935708032 0.911746261 0.999127534 0.819585415 0.842598997 0.82760347 1 19.25841965 3.375599989 0.760934627 0.866079386 1.046171137 0.388979591 0.063201713 0.598373088 0.729675354 0.031173514 0.066653373 2374.652084 -3.375599989 0.180091751 EAPS(ph)PTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAPSPTLRR 9 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 EAPS(1)PTLRR;EAPS(0.999)PT(0.001)LRR;EAPS(0.997)PT(0.003)LRR;EAPS(1)PTLRR 119.03 0.00083149 467550000 316720 229756 267160 276731 310806 277977 316551 276358 308986 TRUE FALSE 301749.2733 253168.3976 279409.5503 248913.4741 365010.468 268350.5868 268255.3311 252158.6285 356901.9708 0.845468218 0.709349957 0.782874775 0.69742813 1.022719116 0.751888778 0.751621882 0.706520695 1 18.44516834 -1.296753452 3.549551653 1.000693431 0.781458635 0.336915852 0.095421255 30965198.56 45327004.27 226565.3453 0.021327247 0.050494787 1.296753452 -0.219234796 EAPSPLMIHS(ph)PQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPS(0.001)PLMIHS(0.994)PQMS(0.071)QFQS(0.238)LT(0.194)HQS(0.502)PPQQNVQPK;EAPSPLMIHS(1)PQMSQFQS(0.012)LT(0.032)HQS(0.956)PPQQNVQPK;EAPS(0.018)PLMIHS(0.944)PQMS(0.258)QFQS(0.19)LT(0.058)HQS(0.532)PPQQNVQPK 204.91 2.51E-27 242647000 116432 90349 102013 118774 98938 111578 134273 121823 82300 TRUE FALSE 110928.4901 99555.66582 106690.397 106834.6119 116192.7559 107714.0259 113787.1878 111155.5323 95062.66367 1.16689861 1.047263584 1.12231651 1.123833561 1.222275406 1.133084449 1.196970328 1.169286952 1 16.53659121 2.983757758 22.53192162 1.160150647 1.108198344 0.017696669 0.065859737 382.0354609 529977.2068 0.017656662 0.019246056 963.2915653 -2.983757758 -0.051952303 EAPSPLMIHSPQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMSQFQS(0.001)LT(0.017)HQS(0.982)PPQQNVQPK;EAPSPLMIHSPQMSQFQS(0.001)LT(0.006)HQS(0.992)PPQQNVQPK;EAPSPLMIHSPQMS(0.002)QFQS(0.199)LT(0.153)HQS(0.645)PPQQNVQPK 272.58 3.78E-73 948740000 527873 418233 513983 562964 454957 514347 628469 582401 303726 TRUE FALSE 502921.4894 460851.4182 537549.6289 506373.7892 534301.3568 496535.0344 532584.5114 531402.8809 350826.2769 1.433534266 1.313617162 1.532238787 1.443374749 1.522979868 1.415330228 1.518086148 1.514718013 1 18.42039728 -0.992399984 5.150509231 0.999997073 1.452954494 0.823283118 0.067119968 2.38E-06 4.65E-07 0.068464024 0.016137021 0.10176537 0.992399984 0.452957421 EAQLYAAQAHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAQLYAAQAHLK 12 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;E9PI86 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 174.05 3.14E-05 1203460000 2449570 1916720 1808110 2036240 2179240 1986030 2709770 2370900 2147650 FALSE TRUE 2333783.681 2112035.947 1891013.632 1831553.287 2559298.766 1917253.283 2296344.818 2163291.427 2480696.593 0.940777557 0.851388256 0.762291381 0.738322168 1.031685525 0.772868914 0.925685481 0.872049985 1 21.24231386 0.439667206 0.672213558 1.002463813 0.854720506 0.202893052 0.0889864 3.155966084 2.255778521 0.10304622 0.031979222 2.752118986 -0.439667206 -0.147743307 EAQQKVPDEEENEES(ph)DNEKETEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EAQQKVPDEEENEESDNEKETEK 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK 269.83 2.56E-45 7339860000 7047530 7254650 8259010 8603360 2123488 9287200 6724190 9259230 2100180 TRUE FALSE 6714407.224 7993907.083 8637693.778 7738533.907 2493823.635 8965581.935 5698291.317 8448442.735 2425865.188 2.767840215 3.295280843 3.560665209 3.190009876 1.028014107 3.695828597 2.348972789 3.482651376 1 21.21006795 EAQTSFLHLGYLPNQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAQTSFLHLGYLPNQLFR 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 147.92 7.31E-08 669420000 1319180 1107340 1170570 1279820 1397860 1087790 1477240 1313610 1323890 FALSE TRUE 1256824.976 1220179.205 1224241.792 1151170.062 1641646.341 1050119.56 1251859.907 1198583.345 1529192.1 0.821888222 0.797924084 0.800580772 0.752796239 1.073538336 0.686715266 0.818641364 0.783801685 1 20.54433822 -0.999995153 4.495801436 1.000005582 0.815244396 0.251162014 0.099272133 5.21E-06 1.16E-06 0.085395623 0.020127299 0.100001116 0.999995153 -0.184761186 EARNS(ph)WDSPAFSNDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EARNSWDSPAFSNDVIR 17 1 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 EARNS(1)WDSPAFSNDVIR;EARNS(0.998)WDS(0.002)PAFSNDVIR 224.1 1.71E-15 88293000 86927 45587 81657 63995 107871 80637 111614 76091 129067 TRUE FALSE 82818.13298 50232.36713 85401.05422 57562.10102 126683.6682 77844.52047 94585.23437 69428.06866 149082.0512 0.555520482 0.336944432 0.572845983 0.386110203 0.849758017 0.522158904 0.634450852 0.465703739 1 17.18574705 -4.999999998 0.167778743 2.789667199 0.419174541 0.509772056 0.140938503 99.16880637 0.930410695 59.10267784 0.479346968 1.00E-05 4.999999998 -2.370492658 EARS(ph)PQPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EARSPQPNK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK;EARS(1)PQPNK 98.407 0.0036547 21998440000 17296510 10243720 16391560 15144450 13848760 16131040 21238730 17456840 17311210 TRUE FALSE 16478938.25 11287566.71 17143129.24 13622101.11 16263979.36 15572418.04 17998371.66 15928226.55 19995744.03 0.824122284 0.56449846 0.857338902 0.681250025 0.813372052 0.778786626 0.900110125 0.796580838 1 24.25318963 1.338356196 0.416886616 1.002667823 0.699869152 0.436346295 0.088147788 0.842632566 0.426260647 0.102006852 0.06692905 21.79496602 -1.338356196 -0.302798671 EAS(ph)HVLEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EASHVLEVK 9 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK 68.915 0.059497 61303400 70615 88563 77759 81006 720450 47677.4 68543 53571.3 541009 TRUE FALSE 67277.1689 97587.67039 81324.32706 72863.12298 846096.2519 46026.31968 58085.50647 48880.31297 624905.9126 0.107659677 0.156163781 0.130138514 0.116598549 1.353957828 0.073653199 0.092950803 0.078220276 1 19.25327946 -2.20755893 2.329605609 3.287545307 0.248760839 0.260157235 0.389516202 6796842.087 1385433.165 81991624.37 0.093631855 0.006200705 2.20755893 -3.038784468 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;EAS(1)PAPLAQGEPGREDLPTR 152.28 4.01E-08 1698070000 862380 822010 714460 950020 569740 817640 862630 926730 544330 TRUE FALSE 821617.0065 905773.7535 747218.6977 854522.1847 669102.4756 789324.9218 731019.9502 845580.6083 628741.9163 1.306763531 1.440612961 1.188434679 1.359098483 1.06419257 1.25540369 1.162670933 1.344877105 1 19.26210842 -1.560443328 0.040647144 3.18E-14 2.103020908 0.389172059 0.106497783 322.2112879 2.085330028 71.15663143 39.83121656 0.027514186 1.560443328 2.103020908 EASDGEVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EASDGEVRR 9 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 150.27 0.00013733 97870000 176531 152233 170459 179796 185907 169686 216973 183116 215825 FALSE TRUE 168186.7295 167745.7158 178274.7138 161722.5645 218329.1219 163809.7313 183869.7839 167081.3923 249294.0387 0.674652031 0.67288298 0.715118238 0.648722149 0.875789582 0.657094458 0.737561896 0.670218161 1 17.92748886 -5 0.321859629 3.816062844 0.692693713 0.655447016 0.066498168 188.5258971 1.662158346 362.0376398 0.052765822 1.00E-05 5 -3.123369131 EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EASRPPEEPSAPSPTLPAQFK 21 1 A0A0C4DFX9;Q9H3P2;H0Y3X6;Q9H3P2-7 A0A0C4DFX9 NELFA Negative elongation factor A 1 EASRPPEEPS(0.001)APS(0.963)PT(0.036)LPAQFK;EASRPPEEPSAPS(0.797)PT(0.203)LPAQFK;EASRPPEEPSAPS(0.926)PT(0.074)LPAQFK;EASRPPEEPSAPS(0.981)PT(0.019)LPAQFK;EASRPPEEPSAPS(0.954)PT(0.046)LPAQFK 246.27 1.68E-30 1867270000 2045998 1752741 1919663 2155232 1601089 2088615 2383271 2182607 2018005 TRUE FALSE 1949287.729 1931347.301 2007681.447 1938583.985 1880318.415 2016285.739 2019659.237 1991486.36 2330946.909 0.836264319 0.828567692 0.86131582 0.831672303 0.806675779 0.865007148 0.866454414 0.854367962 1 21.15248471 -0.713102554 0.413017977 1.049077363 0.832528872 0.896401576 0.01692504 3.180008239 0.447214801 0.217651072 0.010346856 0.193596475 0.713102554 -0.216548492 EATAQKPTGSVGSTVTT(ph)PPPLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGS(0.023)T(0.065)VT(0.066)T(0.846)PPPLVR 112.8 0.0013388 240250000 411060 400920 437570 492610 373190 458230 553560 499310 458410 TRUE FALSE 391630.0084 441774.2038 457633.0173 443091.9069 438274.2178 442361.3802 469104.2552 455587.7694 529497.8816 0.73962526 0.834326669 0.864277334 0.836815259 0.82771666 0.8354356 0.885941703 0.860414716 1 19.01426539 -5 0.065237921 1.592512354 0.602110005 0.820914481 0.027237029 141.53572 0.669484697 12.97361268 1.858107689 1.00E-05 5 -0.990402348 EATDAIGHLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 203.03 3.80E-08 4905580000 5522820 5325120 5163570 6208100 5233410 5197840 5668560 5558660 4706240 FALSE TRUE 5261767.244 5867755.782 5400324.792 5584049.993 6146115.047 5017837.497 4803717.062 5071914.262 5436059.663 0.967937729 1.079413426 0.993426328 1.027223824 1.130619498 0.9230652 0.883676295 0.933012987 1 22.37412986 2.147706648 11.95457432 0.920431499 1.03591227 0.482372306 0.052921611 0.378402926 47.5788265 0.018526784 0.01368304 140.5098104 -2.147706648 0.115480771 EATGLS(ph)PQAAQEKDGIVIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EATGLSPQAAQEKDGIVIVK 20 1 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 EATGLS(1)PQAAQEKDGIVIVK;EATGLS(1)PQAAQEKDGIVIVK;EATGLS(1)PQAAQEKDGIVIVK 230.93 8.10E-26 799880000 1173460 885700 1054300 1134520 746790 956420 1160090 1110600 819300 TRUE FALSE 1117992.871 975953.837 1102640.698 1020475.894 877029.9396 923298.9356 983096.964 1013349.976 946352.8596 1.181369993 1.031279007 1.165147531 1.078324944 0.926747281 0.975639188 1.038827065 1.07079507 1 19.85201869 2.987502195 24.42691016 1.005081215 1.11458995 0.522799532 0.054203635 376.6046785 736074.6503 0.015896297 0.017668956 971.6328615 -2.987502195 0.109508735 EATNPPVIQEEKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 180.62 1.58E-06 404720000 311950 261176 286510 341800 183335 335300 357730 360410 225394 FALSE TRUE 297204.7417 287790.1313 299646.7669 307441.6146 215308.566 323688.4769 303151.7183 328850.5897 260346.9504 1.141571819 1.105410034 1.150951707 1.180891937 0.827006292 1.243296595 1.164414324 1.263124416 1 17.99007598 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.003)PS(0.997)PR 104.24 0.001988 75948000 148980 135370 147870 149660 139050 147500 199230 156200 129680 TRUE FALSE 141938.0106 149164.3569 154649.9858 134615.8925 163300.276 142392.038 168833.8044 142522.2999 149790.1121 0.947579307 0.995822453 1.032444556 0.898696787 1.090193963 0.950610398 1.127135844 0.951480027 1 17.19258287 2.727008586 24.96918294 1.033445323 0.97437221 0.143492404 0.064095407 1213.62998 2623200.98 0.018559436 0.017632647 533.3454396 -2.727008586 -0.059073113 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.008)S(0.064)DPS(0.464)RT(0.464)PEEEPLNLEGLVAHR;EAT(0.088)S(0.071)DPS(0.42)RT(0.42)PEEEPLNLEGLVAHR;EAT(0.001)S(0.003)DPS(0.498)RT(0.498)PEEEPLNLEGLVAHR;EAT(0.003)S(0.019)DPS(0.494)RT(0.484)PEEEPLNLEGLVAHR 242.48 7.52E-38 727090000 439648 403042 413482 475265 474628 490472 513305 480566 462874 TRUE FALSE 418866.7103 444112.438 432440.5587 427490.4593 557402.9729 473486.8317 434990.8948 438485.0934 534654.1359 0.783434902 0.830653703 0.808822994 0.799564486 1.042548697 0.88559463 0.813593061 0.820128498 1 19.0282464 EATSDPSRT(ph)PEEEPLNLEGLVAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.008)S(0.043)DPS(0.2)RT(0.749)PEEEPLNLEGLVAHR;EAT(0.007)S(0.037)DPS(0.17)RT(0.786)PEEEPLNLEGLVAHR 177.73 6.12E-17 505790000 216835 189781 208974 229867 225587 220489 255542 222818 235401 TRUE FALSE 206585.6393 209119.8997 218555.6646 206760.3324 264929.3014 212853.4106 216554.3745 203306.8747 271905.7848 0.759769195 0.769089557 0.80379189 0.760411672 0.974342277 0.782820457 0.796431656 0.747710737 1 18.05274732 -2.518470827 2.278701981 4.07396505 0.797604585 0.4875446 0.064645853 1767936.446 329677.4299 27837815.93 0.015309226 0.003030604 2.518470827 -3.276360466 EATTDFTVDSRPLTQVGGDHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EATTDFTVDSRPLTQVGGDHIK 22 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 ;;;; 263.71 1.18E-37 3493100000 2741650 2179740 2555340 2914630 2188700 2656950 3116140 3102450 2392130 FALSE TRUE 2612057.638 2401857.984 2672504.867 2621645.855 2570408.587 2564939.155 2640715.611 2830783.031 2763089.303 0.945339564 0.86926542 0.967216247 0.948809672 0.9302662 0.928286738 0.955711279 1.024499291 1 21.39785076 1.418078981 3.08142999 1.012117982 0.92769502 0.606744813 0.026224727 0.165115139 2.759037204 0.021130129 0.007009574 26.18659198 -1.418078981 -0.084422962 EATVKPFAIDIFPVTNKDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EATVKPFAIDIFPVTNKDFR 20 2 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;F8WA42;E9PBT8;J3QT17;Q8NBJ7-5;F8WES7;E9PG02;F8WEX5;Q8NBJ7-4;F8WEV7 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 130.87 8.65E-06 99224000 591820 295270 685210 511290 705820 571370 992300 672900 968000 FALSE TRUE 563845.8415 325358.3487 716627.5563 459894.1578 828914.7845 551583.3136 840906.4102 613977.3087 1118112.496 0.504283642 0.290988921 0.640926167 0.411312958 0.741351865 0.493316474 0.752076748 0.549119441 1 20.09263392 -5 0.083350609 2.617463154 0.077801692 0.589370428 0.127978083 136.568969 0.801103284 39.59902164 3.362292399 1.00E-05 5 -2.539661462 EAVAHENNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVAHENNR 9 0 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 88.496 0.012745 49441000 36584 38291 30767 37584 40519 34370 40437 37560 53138 FALSE TRUE 34854.74682 42192.89643 32177.69738 33805.98492 47585.50077 33179.75828 34267.59297 34271.04728 61378.36965 0.567866938 0.687422893 0.524251419 0.550780106 0.775281277 0.54057738 0.558300802 0.55835708 1 15.9054427 -1.21143355 4.735007823 1.000074113 0.598429086 0.727580652 0.077793356 5.76E-05 9.60E-06 0.071327521 0.016808967 0.061456306 1.21143355 -0.401645026 EAVCFIPGEGHTLQEHQIVLVEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVCFIPGEGHTLQEHQIVLVEGGR 25 0 O15235 O15235 MRPS12 "28S ribosomal protein S12, mitochondrial" 0 81.888 0.01221 76621000 51946 39582 45667 48352 51481 46275 49329 45185 12518 FALSE TRUE 49490.61553 43615.4508 47760.87712 43491.5651 60459.2701 44672.48515 41802.95506 41228.36186 14459.22751 3.422770373 3.016444051 3.303141686 3.007876118 4.181362391 3.089548534 2.891091868 2.851353009 1 13.81970286 0.516077552 0.932442113 0.994576562 3.312529216 0.813422617 0.343823049 0.654333465 0.848220547 0.322162071 0.103429335 3.281538864 -0.516077552 2.317952654 EAVCIVLSDDTCSDEKIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVCIVLSDDTCSDEKIR 18 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 163.56 2.99E-11 122100000 109920 62263 88427 107890 92096 88050 125490 105070 113450 FALSE TRUE 104724.2994 68607.67049 92481.46542 97044.69222 108157.5132 85000.80642 106344.1957 95869.51379 131043.2466 0.79915831 0.523549838 0.705732404 0.740554701 0.8253574 0.648646982 0.811519849 0.731586833 1 16.99968348 -1.881746846 0.21364543 1.326578101 0.65038994 0.509996834 0.086734742 23.22710417 0.770155607 4.008930215 0.193047564 0.01312965 1.881746846 -0.676188161 EAVEKEFEPLLNWMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVEKEFEPLLNWMK 15 1 P14625 P14625 HSP90B1 Endoplasmin 0 198.95 6.99E-09 357890000 1076600 684850 991770 859850 830570 1071800 1422500 1137700 946160 FALSE TRUE 1025711.252 754636.9936 1037243.635 773416.2444 975421.145 1034683.297 1205471.499 1038076.957 1092885.66 0.938534825 0.690499492 0.949087057 0.707682672 0.892518934 0.946744325 1.103017033 0.949849554 1 20.05971104 2.219962112 2.613627527 1.026879285 0.819462421 0.457440826 0.091880878 0.206562812 2.886388435 0.036002021 0.025153025 165.9442132 -2.219962112 -0.207416863 EAVELPLTHFELYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EAVELPLTHFELYK 14 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 196.33 2.50E-08 192818000 794309 692298 718993 851829 644231 769591 915463 871786 647567 FALSE TRUE 756763.5877 762843.9533 751959.5402 766201.5306 756584.6824 742939.8707 775792.3057 795447.7962 747988.383 1.011731739 1.019860696 1.005309116 1.024349506 1.011492557 0.993250547 1.037171597 1.063449399 1 19.51265634 1.617519012 8.988775312 1.038029697 1.012441995 0.258199274 0.017353906 0.111501523 23.24895481 0.007783358 0.003930319 41.44947286 -1.617519012 -0.025587703 EAVFFQSHSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVFFQSHSAR 11 0 P36954 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 121.02 0.00042029 90449000 49922 50300 41396 36224 65293 38641 58768 52545 78941 FALSE TRUE 47562.286 55425.62719 43294.04755 32582.6947 76680.07853 37302.85248 49801.86225 47943.88124 91182.76711 0.521614857 0.607851998 0.474805151 0.35733391 0.840949238 0.409099808 0.546176255 0.525799806 1 16.47647357 -1.242928915 3.86067646 1.000550516 0.538051595 0.56046528 0.12926842 29575408.52 40578962.32 180489.3716 0.02768743 0.057157218 1.242928915 -0.462498921 EAVLDVIPTDIHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EAVLDVIPTDIHQR 14 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;; 170.56 3.15E-06 4740116000 5328480 4213570 4357750 5181180 5240330 4670300 5720520 5091380 5090450 FALSE TRUE 5076613.31 4642937.573 4557557.148 4660357.943 6154241.893 4508566.34 4847749.609 4645551.776 5879850.988 0.863391491 0.789635245 0.775114396 0.792597968 1.046666303 0.766782415 0.824468106 0.790079848 1 22.48734816 -1.042929279 4.46852049 1.000009008 0.829656072 0.297909203 0.081464083 1.04601E+11 22405433538 10139526.28 0.017807761 0.09058801 1.042929279 -0.170352936 EAVTEILGIEPDREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EAVTEILGIEPDREK 15 1 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;;; 238.22 8.40E-18 764726000 1030398 965351 907579 1129987 727839 1030023 1136100 1159480 797943 FALSE TRUE 981693.1286 1063721.364 949192.3949 1016398.56 854773.8912 994353.0452 962767.0791 1057949.784 921683.9251 1.065108224 1.154106452 1.029845882 1.102762598 0.927404578 1.078843862 1.044574016 1.147844457 1 19.81391256 3.722644519 24.80289254 1.048219006 1.109607342 0.146683004 0.062423746 1161.455405 1809958.095 0.015266068 0.023744471 5280.128833 -3.722644519 0.061388336 EAVTHIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EAVTHIGR 8 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;;;; 133.86 0.00090124 1594033000 1976050 1722330 1762120 1985600 2060730 1786400 2117180 1953070 2085970 FALSE TRUE 1882646.033 1897837.385 1842914.945 1786003.716 2420120.66 1724536.52 1794165.306 1782048.837 2409451.574 0.781358734 0.787663635 0.764869054 0.741249061 1.004428014 0.715738195 0.744636384 0.739607659 1 21.20027337 -2.121600284 2.431466486 1.427518007 0.783614026 0.4106105 0.080959122 5997825.491 1649828.295 14173374.59 0.018290845 0.007557875 2.121600284 -0.64390398 EAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.499)RIS(0.499)EDET(0.002)ERNGDDGTHDK 146.59 2.65E-08 462260000 54430 39446 44792 58742 38849 37722 68629 51206 39243 TRUE FALSE 51857.20177 43465.59225 46845.75751 52837.14256 45624.2533 36415.67768 58158.38559 46722.13118 45328.60401 1.144028211 0.958899864 1.033470113 1.165646807 1.006522356 0.803370818 1.283039415 1.030742777 1 15.46813411 1.710811256 25 1.126769207 1.027124976 0.085415462 0.123716483 1.671778939 1498.724369 0.053348271 0.02958426 51.38202971 -1.710811256 -0.099644231 EAVVDLHADDSRIS(ph)EDETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.021)RIS(0.979)EDETER;EAVVDLHADDSRIS(1)EDETER;EAVVDLHADDSRIS(1)EDETER 289.14 1.24E-54 929694000 983750 1046050 896410 1117030 898410 1003360 954830 954050 736010 TRUE FALSE 937250.0871 1152643.684 937511.2852 1004744.022 1055092.42 968613.3916 809153.1468 870508.3243 850146.6718 1.102456927 1.35581744 1.102764166 1.181847857 1.241071046 1.139348566 0.951780644 1.023950752 1 19.69735224 1.898809847 4.047475554 0.99129602 1.204345105 0.61687449 0.073514804 0.143127462 3.875315028 0.033980028 0.019301584 79.21544153 -1.898809847 0.213049086 EAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.211)RIS(0.789)EDETERNGDDGTHDK;EAVVDLHADDS(0.068)RIS(0.932)EDET(0.001)ERNGDDGTHDK 210.21 4.70E-26 999400000 208851 138039 167097 181263 141276 177240 222713 187199 118977 TRUE FALSE 198979.0271 152105.331 174758.5627 163042.0989 165914.4897 171102.1344 188734.0414 170806.8632 137427.3455 1.447885255 1.106805421 1.271643297 1.186387602 1.207288761 1.245037032 1.373336877 1.24288847 1 17.06830958 4.703477922 3.889777396 1.227172025 1.461276433 0.34458325 0.101197792 0.25884275 7.141648684 0.023031993 0.158632859 50521.69612 -4.703477922 0.234104408 EAWPHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAWPHIK 7 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 105.39 0.0079373 763490000 2034400 1668630 1735250 2044900 1572170 1822340 2140360 1977880 1514130 FALSE TRUE 1938237.944 1838665.294 1814812.929 1839342.767 1846355.95 1759231.909 1813808.772 1804686.342 1748933.547 1.108239902 1.05130655 1.037668316 1.051693914 1.055703891 1.005888366 1.037094162 1.031878166 1 20.73804404 8 0.30548418 1.018436277 1.796288109 0.750184782 0.014872893 25.07028635 0.358505344 0.013900129 10.72217813 100000000 -8 0.777851832 EAYHAVVLSYGAEDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAYHAVVLSYGAEDHR 16 0 P22570-4;P22570-5;P22570;P22570-2;P22570-7;P22570-3 P22570-4 FDXR "NADPH:adrenodoxin oxidoreductase, mitochondrial" 0 176.33 1.85E-09 88279000 94126 83729 100680 103780 121990 82675 103920 106710 66767 FALSE TRUE 89676.85052 92261.08029 105296.2776 93347.83723 143265.0174 79811.94402 88065.09538 97365.90669 77120.88536 1.162808882 1.196317701 1.365340622 1.210409305 1.857668214 1.034894032 1.141909808 1.26251023 1 16.23483399 EAYPEEAYIADLDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EAYPEEAYIADLDAK 15 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 273.15 4.49E-33 196075000 325983 279158 278534 342427 220850 317069 340873 357457 234824 FALSE TRUE 310574.4296 307604.5176 291305.0594 308005.5874 259366.1701 306088.821 288866.5633 326156.1701 271239.3066 1.145019995 1.134070579 1.073978042 1.135549236 0.956226342 1.128482538 1.06498784 1.202466465 1 18.04920674 4.096167646 0.010936289 7.12E-07 2.237135536 0.135512246 0.067863337 7806.416066 16.53477196 1585.06832 1800.954597 12478.65122 -4.096167646 2.237134824 EAYPGDVFYLHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EAYPGDVFYLHSR 13 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;;;;; 216.34 2.76E-11 8359007000 9412548 7433489 7499394 7518144 8682051 6215397 8104241 7563827 7998696 FALSE TRUE 8967635.51 8190969.98 7843248.633 6762405.882 10196197.95 6000156.243 6867790.191 6901498.21 9239092.924 0.970618608 0.886555644 0.848919769 0.731933961 1.103592964 0.649431312 0.743340309 0.746988721 1 23.13931979 2.21056786 24.99999204 0.757310605 0.900301184 0.170384391 0.128359986 300.9810508 268800.7011 0.043490549 0.032126486 162.3932074 -2.21056786 0.142990579 EAYSGCSGPVDSECPPPPS(ph)SPVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.55)S(0.45)PVHK 112.99 0.0009711 143650000 91002 77629 73694 97157 55406 74110 78378 72506 47391 TRUE FALSE 86700.51581 85539.48336 77072.94279 87390.59377 65068.78886 71543.55212 66419.99659 66156.99026 54740.15424 1.583855892 1.562646005 1.407978181 1.596462323 1.188684792 1.306966579 1.213368824 1.208564192 1 15.74031188 2.355063952 0.353666748 0.995568338 1.673153368 0.812518307 0.085669756 0.550563069 0.162354269 0.093379125 0.133426519 226.4977812 -2.355063952 0.67758503 EAYSGCSGPVDSECPPPPSS(ph)PVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.152)S(0.848)PVHK 147.18 1.17E-07 138480000 90910 91836 80314 102960 69316 86286 89585 87640 53158 TRUE FALSE 86612.86447 101194.1928 83996.47634 92610.26519 81404.68845 83297.89418 75917.16291 79965.77699 61401.47115 1.410599174 1.648074401 1.36798801 1.50827437 1.325777493 1.356610723 1.236406254 1.302343014 1 15.9059856 1.333705763 0.359170619 0.975596236 1.551578126 0.747849578 0.084721723 0.54158211 0.223243849 0.120131744 0.08649673 21.56283021 -1.333705763 0.57598189 EAYVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 218510000 567110 497850 484400 571430 469230 542810 631300 573280 469650 FALSE TRUE 540303.8342 548581.481 506610.2191 513988.7708 551063.5634 524012.3536 534983.5904 523080.5641 542480.9234 0.995986791 1.011245663 0.933876561 0.947478056 1.015821091 0.965955356 0.986179545 0.964237711 1 19.04921288 ECADLWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ECADLWPR 8 0 J3KTJ3;P62829 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;;; 135.84 0.0018994 1118240000 2534170 2318090 2037580 2360400 2561480 2151700 2668180 2288910 2446060 FALSE TRUE 2414384.806 2554306.006 2131005.058 2123128.108 3008201.301 2077186.089 2261100.137 2088480.906 2825382.492 0.854533789 0.904056712 0.754235954 0.75144803 1.064705862 0.73518757 0.800281074 0.739185194 1 21.43001476 ECFGACLFTCYDLLRPDVVLETAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ECFGACLFTCYDLLRPDVVLETAWR 25 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 175.48 1.56E-12 362430000 348280 362130 301640 389110 297700 346590 359020 366420 278540 FALSE TRUE 331817.4946 399031.4587 315470.4924 349995.9235 349618.7857 334587.5014 304244.9051 334334.3223 321734.5606 1.031339294 1.240250528 0.980530322 1.087840619 1.086668417 1.039948897 0.945639488 1.039161978 1 18.29551139 2.451711349 0.888006474 0.986014523 1.114011483 0.215201926 0.070966601 0.691707416 1.09019775 0.048186359 0.033487369 282.9510755 -2.451711349 0.12799696 ECHGLVDALVTSINHALDAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ECHGLVDALVTSINHALDAGK 21 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 285.55 1.33E-45 153331000 555670 520260 487040 628420 475310 526340 649270 632570 282180 FALSE TRUE 529404.5803 573275.0855 509371.2657 565250.0277 558203.9135 508112.7138 550211.9368 577178.8173 325939.0332 1.624244188 1.758841461 1.562780808 1.734220115 1.712602225 1.558919497 1.688082374 1.770818339 1 18.31424261 -1.264645367 3.760189027 0.99884165 1.675686892 0.890613818 0.074487854 12453289.6 16963167.83 155528.8504 0.016303953 0.054369412 1.264645367 0.676845242 ECINAAPDS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ECINAAPDSPSK 12 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.949)PS(0.051)K;ECINAAPDS(0.997)PS(0.003)K 205.52 1.06E-07 468380000 1199000 1232080 1028410 1437860 703330 1230890 1106060 1245030 729150 TRUE FALSE 1142325.646 1357630.353 1075563.616 1293323.581 825990.5293 1188263.971 937310.2328 1136008.573 842222.858 1.356322303 1.611960943 1.277053461 1.535607314 0.980726801 1.410866446 1.112900492 1.348821826 1 19.68384251 2.757448022 24.97488296 1.19213874 1.453800727 0.414756754 0.160807359 747.9432291 989006.553 0.043273153 0.045830456 572.0684835 -2.757448022 0.261661987 ECINAAPDS(ph)PSKQLPDQISFFSGNPSVEIVHGIMHLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ECINAAPDSPSKQLPDQISFFSGNPSVEIVHGIMHLYK 38 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.8)PS(0.194)KQLPDQIS(0.006)FFSGNPSVEIVHGIMHLYK;ECINAAPDS(0.5)PS(0.5)KQLPDQISFFSGNPSVEIVHGIMHLYK 190.22 6.00E-24 308030000 245456 144149 240448 209681 165991 226698 306450 249056 40863 TRUE FALSE 233853.7813 158837.947 251472.7786 188603.4675 194939.7778 218847.3914 259695.4242 227247.3363 47199.82534 4.954547599 3.365223194 5.327832822 3.995850962 4.130095322 4.636614433 5.502042058 4.814580026 1 15.5264939 3.746672141 24.90723282 4.463731543 4.159885585 0 1.315226252 4047.222085 12427360.96 0.302652496 0.532661491 5580.48752 -3.746672141 -0.303845958 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 493.8 7.65E-297 699248000 603526 522545 526616 680646 497517 579629 694231 664267 278692 FALSE TRUE 574998.5221 575792.9296 550761.8645 612226.1709 584283.8073 559556.3024 588313.3105 606100.26 321910.132 1.786208214 1.788676007 1.710918079 1.901854307 1.815052554 1.738237622 1.827570033 1.882824427 1 18.29629846 -1.718192822 7.761877934 0.994785761 1.802682629 0.950541158 0.057803893 0.004833196 0.000175477 0.051863385 0.012251022 0.019134062 1.718192822 0.807896868 ECPGIEPVCVDLGDWEATER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ECPGIEPVCVDLGDWEATER 20 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 246.63 1.10E-29 48690000 42616 33665 38351 40837 40251 37958 43199 45153 49220 FALSE TRUE 40601.62614 37095.50177 40109.43128 36731.98717 47270.76166 36643.50494 36608.19915 41199.16395 56852.78622 0.714153674 0.652483444 0.705496317 0.646089482 0.831459015 0.644533142 0.643912138 0.724663938 1 15.79494343 0.957521507 20.55110204 1.000000001 0.687777271 0.74576659 0.056205826 373.7358278 180814.3561 0.050418315 0.012604579 9.068208712 -0.957521507 -0.31222273 ECPPHAEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ECPPHAEQR 9 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 106.4 0.002942 119970000 89460 79753 67407 85136 93372 81811 97703 85613 105040 FALSE TRUE 85231.40309 87879.92137 70497.67762 76577.96753 109656.0472 78977.86456 82796.61291 78116.27186 121329.0667 0.702481321 0.724310536 0.581045248 0.631159289 0.903790412 0.650939356 0.682413663 0.643838068 1 16.88856569 -1.438497791 5.4146131 1.00028008 0.692674058 0.563435091 0.085728407 0.000272573 2.83E-05 0.07805801 0.018381923 0.03643361 1.438497791 -0.307606022 ECPSDECGAGVFMASHFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 ECPSDECGAGVFMASHFDR 19 0 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;;;;;;;;;;;;;; 340.42 9.60E-76 17015801000 5826213 4944771 5398395 5922870 5803765 5478786 6360813 6115003 6187177 FALSE TRUE 5550819.458 5448648.787 5645916.75 5327491.855 6815939.778 5289054.267 5390354.153 5579540.92 7146652.809 0.77670199 0.762405693 0.79000854 0.745452731 0.953724766 0.740074327 0.754248779 0.780720859 1 22.76883627 -1.342387301 3.337587216 1.00137603 0.784320933 0.542320549 0.061150205 1181076007 1455914927 15535392.33 0.013790923 0.045458249 1.342387301 -0.217055097 ECREPELGLEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ECREPELGLEELLR 14 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;; 195.2 5.15E-08 106169000 105960 95509 106409 105782 121590 92857 129576 124651 153203 FALSE TRUE 100951.4808 105241.4757 111287.9579 95148.59239 142795.2575 89641.33881 109806.8014 113735.8976 176960.9388 0.570473244 0.594715853 0.62888431 0.537681327 0.806930945 0.506560032 0.620514347 0.642717531 1 17.43307142 -5 0.357689459 5.756248879 0.597396561 0.701150314 0.079572997 238.4984259 1.910547278 872.5132163 0.052067974 1.00E-05 5 -5.158852318 ECS(ph)PTSSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.807)PT(0.096)S(0.096)SLER;ECS(0.931)PT(0.068)SSLER;ECS(0.989)PT(0.01)SSLER 221.95 5.39E-09 762760000 1939170 1642640 1718720 1914010 1656930 1850900 1948990 1867970 1694300 TRUE FALSE 1847509.277 1810026.884 1797525.012 1721610.078 1945898.067 1786802.869 1651635.78 1704400.644 1957043.391 0.94403082 0.924878259 0.918490117 0.879699493 0.99430502 0.913011371 0.843944385 0.870905904 1 20.90024431 1.992840857 24.9817057 0.885327403 0.931350562 0.014002102 0.049519363 559.935462 1953885.655 0.017208203 0.012214361 98.36505913 -1.992840857 0.046023159 ECS(ph)VEKGTGDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ECSVEKGTGDSLR 13 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ECS(0.999)VEKGT(0.001)GDSLR;ECS(0.966)VEKGT(0.033)GDSLR;ECS(1)VEKGTGDSLR;ECS(0.999)VEKGT(0.001)GDSLR;ECS(0.993)VEKGT(0.007)GDSLR;ECS(0.997)VEKGT(0.002)GDS(0.001)LR 126.63 0.00011281 1256060000 2539090 1520380 2246470 2099590 1594870 2272000 2821870 2555760 1844990 TRUE FALSE 2419072.248 1675308.451 2349472.872 1888535.224 1873014.823 2193320.07 2391341.904 2331964.105 2131101.626 1.135127587 0.78612321 1.102468715 0.886177928 0.878895122 1.029195437 1.122115377 1.094252886 1 21.02316796 2.015683166 9.126568901 1.083263006 0.953726795 0.195773968 0.106378955 0.275803078 140.0854981 0.037813434 0.027439752 103.6771777 -2.015683166 -0.129536211 ECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ECSEAMEVETSVISIDSPQKLAILDQELEHK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETS(0.011)VIS(0.008)IDS(0.981)PQKLAILDQELEHK 133.85 1.57E-06 25110000 19614 15288 19025 23806 13806 24956 21411 21186 13129 TRUE FALSE 18686.88509 16845.86458 19897.31507 21412.97565 16213.76203 24091.76746 18144.35871 19330.84153 15164.97827 1.23223949 1.110840008 1.312056946 1.412001737 1.069158277 1.588645037 1.196464538 1.274702884 1 13.88845581 -1.211877733 3.135435143 0.999103565 1.265351991 0.252319416 0.147761512 14288455.1 20113171.9 125227.7925 0.035034378 0.061393482 1.211877733 0.266248427 ECSPT(ph)SSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.2)PT(0.561)S(0.2)S(0.039)LER 155.33 0.00014417 238240000 720750 632540 587400 713560 466160 729040 752690 734800 533760 TRUE FALSE 686681.5759 696996.5451 614332.871 641831.5931 547458.1564 703793.162 637853.3164 670457.0166 616532.7747 1.113779517 1.130510126 0.996431814 1.04103402 0.88796278 1.141534061 1.03458136 1.087463707 1 19.23381806 3.748775624 24.59168398 1.030568251 1.122144832 0.267824063 0.065193843 684.7050775 1648357.446 0.015787792 0.028077219 5607.581889 -3.748775624 0.091576581 ECSPTS(ph)SLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.093)PT(0.093)S(0.809)S(0.006)LER 165.39 6.15E-06 165840000 280420 246790 259010 296790 253920 263960 290650 268730 259460 TRUE FALSE 267165.1023 271938.1816 270885.8647 266956.1053 298203.5676 254818.999 246306.0043 245198.5766 299695.7317 0.891454479 0.907380896 0.903869612 0.890757115 0.99502107 0.85025902 0.821853561 0.818158388 1 18.19313901 ECSPWMSDFKVEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ECSPWMSDFKVEFLR 15 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 151.8 2.68E-06 228770000 320640 275700 331390 371680 337720 367080 461860 385910 394850 FALSE TRUE 305483.9826 303794.1434 346584.5593 334318.0203 396618.2611 354367.9276 391394.7744 352117.6746 456081.3214 0.669801565 0.666096438 0.759918337 0.733022829 0.869621803 0.776984084 0.858168831 0.772050198 1 18.79893156 4.772121303 0.06711347 1.331707248 2.47E-15 0.78499246 0.04624695 50.27054105 0.526979047 3.102433524 8.229703697 59172.68872 -4.772121303 -1.331707248 ECYQSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ECYQSHR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 151.04 0.0019084 1069035000 1276040 1087410 977950 1160540 1320990 1035120 1410130 1205620 1306670 FALSE TRUE 1215724.118 1198218.315 1022789.975 1043880.314 1551370.238 999273.5348 1194988.77 1100049.521 1509301.71 0.805487803 0.793889192 0.677657733 0.691631307 1.027872842 0.662076726 0.791749431 0.728846667 1 20.5254498 -1.143587554 4.506327834 1.000020288 0.774998023 0.322045338 0.103719223 2.93E-05 5.56E-06 0.09064761 0.021362895 0.07184763 1.143587554 -0.225022265 EDAANNYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 219.56 1.14E-06 21059125000 8908815 8882367 7442620 9680011 7531561 8497240 8460951 8916464 7537414 FALSE TRUE 8487712.971 9787490.296 7783871.489 8706957.903 8845062.854 8202978.448 7170077.529 8135691.143 8706277.667 0.974895736 1.124187703 0.89405275 1.000078132 1.015940818 0.942191228 0.823552591 0.934462632 1 23.0536246 2.084609386 4.398045788 0.896018226 1.010643988 0.197935855 0.071220258 0.23030738 8.250304105 0.02735828 0.01940206 121.5092629 -2.084609386 0.114625762 EDAEHHPDEDVDESES ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDAEHHPDEDVDESES 16 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 132.97 3.63E-05 382290000 206340 242800 185610 263470 163130 195890 197260 209490 33633 FALSE TRUE 196586.7171 267541.596 194120.4021 236985.495 191579.8204 189106.2802 167164.3641 191145.945 38848.63387 5.060325102 6.886769737 4.996839857 6.100227253 4.931442918 4.867771691 4.302966345 4.920274563 1 15.24557625 -0.07458762 0.335231056 1.42E-10 6.028955062 0.830872036 0.626296663 1.947774963 0.299703787 3.373923341 0.559492841 0.842194459 0.07458762 6.028955062 EDAKEDHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDAKEDHER 9 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 ; 128.17 0.00025536 131443000 292020 261430 257750 307600 181248 308240 311860 315390 193320 FALSE TRUE 278216.7933 288070.0142 269568.0924 276679.4636 212857.5938 297565.5715 264280.0293 287772.7796 223299.0783 1.245937939 1.290063606 1.207206472 1.239053317 0.953239912 1.33258755 1.183524945 1.288732501 1 17.76861777 -2.049678159 2.39774811 0.709825416 1.220563857 0.304262069 0.10329278 4768000.294 1905304.222 7577920.049 0.023820233 0.008919117 2.049678159 0.510738441 EDAPIGPHLQSMPSEQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDAPIGPHLQSMPSEQIR 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 115.34 0.00014571 153220000 79902 73060 71147 65445 82551 63439 80320 73507 98157 FALSE TRUE 76125.19081 80504.89706 74409.16032 58866.34426 96947.86826 61242.09152 68065.70882 67070.33739 113378.6862 0.671424174 0.710053183 0.656288786 0.51920115 0.855080187 0.54015524 0.600339544 0.591560368 1 16.79078993 -1.23947298 5.76444419 1.000014632 0.645749101 0.583284328 0.094802547 1.65E-05 2.18E-06 0.084915324 0.020013908 0.057613866 1.23947298 -0.354265531 EDAQEIADTPSGDKTSLETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDAQEIADTPSGDKTSLETR 20 1 E5RK69 E5RK69 ANXA6 Annexin 0 148.01 1.05E-07 245470000 347640 272280 268320 430270 285130 327610 327650 317100 225450 FALSE TRUE 331207.7462 300025.6416 280622.7374 387018.4421 334856.5817 316264.7836 277660.9748 289333.0429 260411.6346 1.271862322 1.152120726 1.077612135 1.486179536 1.285874121 1.214480237 1.066238746 1.111060354 1 17.99043438 1.777142897 3.594646119 1.063300124 1.245181881 0.410081737 0.107317574 0.24661702 6.186698384 0.057728865 0.029238855 59.86085244 -1.777142897 0.181881757 EDAQVAAEILEIADTPSGDKTSLETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EDAQVAAEILEIADTPSGDKTSLETR 26 1 P08133;P08133-2;E7EMC6 P08133 ANXA6 Annexin A6;Annexin 0 ;; 162.45 1.46E-11 128142000 91318 63770 64784 129651 90161 91821 105141 81034 66229 FALSE TRUE 87001.57911 70268.2355 67754.41048 116618.2352 105885.0499 88641.21575 89099.8094 73938.23337 76499.45507 1.137283645 0.918545569 0.885684877 1.524432234 1.384128158 1.158716956 1.164711687 0.966519739 1 16.22316185 6.30496117 9.62319824 1.128799277 1.103599335 0 0.202816327 0 0 0.045747758 0 2018185.911 -6.30496117 -0.025199942 EDCCPGKPLNVFR ddPTM_SK-BR-3_Trastuzumab_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 ; 170.66 2.41E-05 358780000 609710 562210 460590 678810 425670 501650 618100 651720 509260 FALSE TRUE 580890.2166 619499.8382 481708.5071 610574.7291 499906.7132 484277.7347 523797.4928 594651.9418 588233.4399 0.987516481 1.053153045 0.818907043 1.037980312 0.849844091 0.823274744 0.890458545 1.010911488 1 19.16602928 3.758582416 24.95300692 0.909346593 1.020334769 0.213812869 0.079385957 960.5227987 1197087.83 0.018935635 0.034080751 5735.647016 -3.758582416 0.110988177 EDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK 289.21 2.04E-71 3959618000 3835316 4469620 3120616 4477079 2003359 4241696 3744369 4080339 922135 TRUE FALSE 3654028.214 4925079.36 3263699.33 4027034.513 2352744.175 4094805.004 3173096.739 3723042.886 1065134.986 3.43057759 4.623901593 3.064118044 3.78077386 2.208869491 3.844400059 2.97905597 3.495371886 1 20.02260485 3.288895153 1.650353475 2.952763666 3.985074283 0.206741965 0.880429516 0.537329194 3.023508014 0.256088286 0.380779408 1944.890491 -3.288895153 1.032310617 EDDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EDDKYR 6 1 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ;;;;;; 117.7 0.035661 1339111000 3731546 4032980 2886605 4257520 2425387 3518279 3825590 3727785 2579005 FALSE TRUE 3555163.216 4443945.247 3018958.694 3829546.001 2848373.725 3396440.116 3241925.984 3401360.383 2978943.924 1.193430728 1.491785465 1.013432536 1.28553813 0.956168964 1.140149061 1.088280299 1.141800742 1 21.50636954 3.729161207 24.99260564 1.098028484 1.342608101 0.451980435 0.11563498 481.6608071 1280714.128 0.027559611 0.043335222 5359.955786 -3.729161207 0.244579617 EDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIK 38 2 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ;;; 250.59 2.94E-51 621925000 505595 359731 518228 506142 397253 616184 904331 526212 355807.8 FALSE TRUE 481696.5263 396387.9979 541989.2664 455263.6446 466533.7974 594845.3936 766358.6968 480134.0877 410984.6564 1.172054769 0.96448369 1.31875791 1.107738786 1.135161107 1.447366427 1.864689313 1.168253073 1 18.64872501 2.221626664 5.533581877 1.490983172 1.124213368 0.097851452 0.247511409 0.192128799 17.66028817 0.086378645 0.065880539 166.5814598 -2.221626664 -0.366769804 EDDLNSFNATDLKDLSSHQLNEFLAQTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDDLNSFNATDLKDLSSHQLNEFLAQTLQR 30 1 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 142.32 2.95E-08 264640000 121821 92213 116079 117081 111496 123302 152741 135142 105053 FALSE TRUE 116062.7628 101609.6095 121401.337 105311.7954 130940.8671 119032.0208 129437.5552 123308.25 121344.0827 0.956476494 0.837367651 1.000471834 0.86787747 1.07908737 0.980946233 1.066698534 1.016186758 1 16.88874423 2.739630654 24.99757185 1.031495688 0.911783784 0.534776175 0.052296524 66.28337637 1548486.723 0.014778824 0.014885315 549.0737155 -2.739630654 -0.119711905 EDDRETLVSQCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EDDRETLVSQCR 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ;; 152.32 6.36E-05 437990000 602190 503960 531900 637390 598640 585440 689070 611900 694780 FALSE TRUE 573725.6721 555314.097 556288.1411 573318.3462 703042.6265 565166.066 583939.7159 558318.7921 802522.934 0.714902525 0.691960408 0.693174136 0.714394969 0.876040543 0.704236654 0.727629942 0.69570447 1 19.6141831 -1.175664464 3.477801673 1.000361722 0.725523797 0.714504289 0.054172283 10053291.47 16428764.36 41622.36286 0.012515063 0.066732214 1.175664464 -0.274837925 EDEIS(ph)PPPPNPVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 186.69 1.08E-06 148899000 534780 637450 453720 646160 298620 539030 521110 587690 316160 TRUE FALSE 509502.0092 702406.8797 474523.5108 581206.7692 350699.2335 520363.2559 441605.0987 536228.7481 365188.4781 1.395175477 1.923409203 1.299393435 1.591525484 0.960323927 1.42491696 1.209252551 1.468361628 1 18.47828172 3.22714159 1.772905128 1.250842274 1.638801593 0.296890566 0.23449326 0.362231672 2.350465734 0.068924955 0.09618656 1687.102969 -3.22714159 0.387959319 EDENDAS(ph)DDEDDDEKRR ddPTM_SK-BR-3_Trastuzumab_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 207.64 4.64E-12 312360000 350250 355250 281120 397560 157240 388540 315730 380530 151997 TRUE FALSE 333694.3766 391450.3789 294009.6301 357596.5135 184662.6062 375084.7624 267559.5897 347208.7759 175567.9185 1.900656906 2.229623625 1.67462047 2.036798731 1.051801535 2.136408324 1.523966292 1.97763224 1 17.42166972 -1.942665188 0.150465045 4.28E-12 2.185541453 0.354268943 0.34277112 43.35739369 0.962446763 18.27285885 1.887728914 0.011411292 1.942665188 2.185541453 EDENSWFNLFVIHQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EDENSWFNLFVIHQNR 16 0 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ;; 310.04 1.24E-57 155587000 290148 241603 252469 286030 253189 254693 313990 293269 240657 FALSE TRUE 276433.2791 266222.6204 264044.9534 257277.721 297345.0814 245872.9175 266085.0587 267588.8116 277976.8585 0.994447094 0.957715048 0.949881061 0.925536472 1.069675667 0.884508584 0.957220181 0.962629814 1 18.08460526 EDERPEGPGAAWPGLEGQAYSQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDERPEGPGAAWPGLEGQAYSQLER 25 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 185.72 1.52E-17 193203000 70256 75502 75737 68024 62355 68323 75849 83340 72817 FALSE TRUE 66935.13811 83195.73964 79209.61636 61186.09828 73229.69226 65956.95738 64276.84199 76042.30779 84109.08846 0.795813382 0.989140902 0.941748601 0.727461198 0.87065136 0.784183476 0.764208044 0.90409145 1 16.35997408 4.771454872 22.64491063 0.859931874 0.795812954 0.048500018 0.092809456 3284.206028 3466015.769 0.02216486 0.859072921 59081.95692 -4.771454872 -0.06411892 EDFEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EDFEEAR 7 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;; 187.93 0.0013425 1911540000 3553380 4514700 2901970 4210000 2427710 3344310 2996730 3269580 2106820 FALSE TRUE 3385418.77 4974753.063 3035028.195 3786802.802 2851101.855 3228495.706 2539523.8 2983278.242 2433534.885 1.391152759 2.044249742 1.247168558 1.556091439 1.171588652 1.32666917 1.043553481 1.225903216 1 21.21462203 2.924635219 0.977945913 1.116210928 1.689364446 0.466237751 0.217631557 0.398144385 0.825882435 0.103214098 0.116656998 840.6887184 -2.924635219 0.573153518 EDFLQLFNLRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDFLQLFNLRPK 12 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 145.14 5.80E-05 50019000 127530 94427 101820 112500 97848 106890 141960 111800 96031 FALSE TRUE 121501.9096 104049.2187 106488.5477 101191.2863 114912.6602 103188.3725 120301.3947 102010.1993 110922.997 1.09537168 0.93803108 0.960022273 0.912266067 1.035967863 0.930270325 1.084548723 0.919648784 1 16.75919898 EDFPQKWPDLLTEMVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDFPQKWPDLLTEMVNR 17 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 159.26 2.95E-09 494320000 555440 561090 510500 624540 397570 616570 588510 615710 412490 FALSE TRUE 529185.452 618265.7089 533906.93 561760.0527 466906.0821 595218.0263 498721.9908 561795.1683 476456.8425 1.110668176 1.297632133 1.120577736 1.179036594 0.979954616 1.249259058 1.046730672 1.179110295 1 18.86198602 -4.999999982 0.085131908 0.48914315 1.291472355 0.196921849 0.091557164 306.9712399 1.833055087 28.68117258 2.31421223 1.00E-05 4.999999982 0.802329204 EDGKVFDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDGKVFDEK 9 1 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 113.47 0.0016368 612200000 1748500 1400100 1530600 1785200 929810 1941600 2101900 2167500 1083700 FALSE TRUE 1665851.87 1542771.782 1600779.524 1605748.304 1091968.57 1874361.905 1781216.551 1977702.209 1251754.661 1.330813395 1.232487347 1.278828491 1.282797943 0.872350312 1.497387598 1.422975768 1.579943954 1 20.2555204 EDGLAQQQTQLNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 385.3 1.63E-113 2539480000 1054530 962443 952755 1109014 928666 977808 1154294 1150266 1030972 FALSE TRUE 1004684.457 1060517.036 996439.7592 997533.8057 1090625.056 943946.2638 978185.2502 1049542.611 1190849.872 0.843670122 0.890554772 0.836746749 0.83766546 0.915837573 0.792666049 0.821417773 0.881339147 1 20.18356012 0.923669756 7.505323377 0.999999367 0.849631289 0.660082155 0.034065897 0.961626178 94.4136408 0.032467534 0.008135846 8.388218911 -0.923669756 -0.150368078 EDGNEEDKENQGDETQGQQPPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDGNEEDKENQGDETQGQQPPQR 23 1 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;; 264.49 5.38E-44 2253030000 1079000 1200640 944060 1335810 545876 1211080 1066530 1214840 551682 FALSE TRUE 1027997.808 1322986.581 987346.0848 1201531.841 641076.6016 1169139.996 903811.2603 1108462.169 637234.027 1.613218637 2.07613926 1.549424612 1.885542501 1.006030084 1.834710556 1.418334901 1.739489924 1 19.28146378 -2.296856116 0.134723026 2.23E-11 1.996131342 0.329086193 0.289308943 59.08756178 1.040428074 20.7815913 2.153913348 0.005048285 2.296856116 1.996131342 EDGNEEDKENQGDETQGQQPPQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EDGNEEDKENQGDETQGQQPPQRR 24 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;; 278.19 2.30E-52 2554632000 1359322 944775.7 1331107 1223217 777596 1464676 1662438 1562865 914387.9 FALSE TRUE 1295069.543 1041049.418 1392139.573 1100256.903 913208.4962 1413953.903 1408802.55 1426012.255 1056186.505 1.226175052 0.985668168 1.318081196 1.041725962 0.864628067 1.338735058 1.333857745 1.350151936 1 20.01043318 2.181944476 24.99982294 1.29087512 1.094451224 0.20299276 0.15883416 107.958933 47670.20787 0.054961479 0.040591765 152.0353143 -2.181944476 -0.196423895 EDGSGDRGDGPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EDGSGDRGDGPFR 13 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 157.56 3.55E-05 3102910000 3373670 3221620 2627050 3580540 2803880 3000630 3484570 3479050 2995840 FALSE TRUE 3214203.305 3549906.741 2747502.841 3220617.317 3292875.784 2896717.431 2952934.848 3174405.938 3460419.567 0.928847859 1.025860209 0.793979686 0.930701395 0.951582813 0.837100061 0.8533459 0.917347124 1 21.72251554 3.759232053 24.95904734 0.889364221 0.977354029 0.204646003 0.063627399 968.6504194 1169561.562 0.015133383 0.027241209 5744.23307 -3.759232053 0.087989809 EDGTFYEFGEDIPEAPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDGTFYEFGEDIPEAPER 18 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 230.96 2.45E-19 77394000 86203 111716 116234 104123 71936 105468 86483 95950 70086 FALSE TRUE 82128.35503 123099.9874 121563.4439 93656.35822 84481.61562 101815.6167 73288.42998 87548.10934 80954.57893 1.014499193 1.520605617 1.5016253 1.156900072 1.043568094 1.257688176 0.905303084 1.081447282 1 16.30482506 3.035325322 7.221547902 1.060379989 1.336051603 0.400509299 0.160653508 0.203154602 31.92726643 0.0471092 0.056030847 1084.739168 -3.035325322 0.275671614 EDGWIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDGWIR 6 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 123.34 0.043811 774018000 1223510 1131950 1069580 1269880 1156100 1035780 1299690 1165960 1207210 FALSE TRUE 1165677.107 1247296.992 1118621.301 1142229.25 1357723.474 999910.6789 1101398.42 1063862.361 1394417.961 0.835959619 0.894492919 0.802213778 0.819144103 0.973684728 0.717081038 0.789862474 0.762943673 1 20.41123163 2.219093388 24.99914542 0.795918502 0.861511026 0.043464307 0.087320226 495.1739228 635881.5167 0.029004345 0.021451503 165.6126048 -2.219093388 0.065592524 EDHLVYADEESSNITDGRIT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEESS(0.001)NIT(0.275)DGRIT(0.724)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESS(0.001)NIT(0.015)DGRIT(0.926)PEPAVS(0.045)NT(0.012)EEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.001)DGRIT(0.999)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.006)DGRIT(0.994)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVY(0.002)ADEES(0.017)S(0.017)NIT(0.126)DGRIT(0.362)PEPAVS(0.362)NT(0.112)EEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.004)DGRIT(0.982)PEPAVS(0.009)NT(0.002)EEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 286.8 2.04E-88 2052440000 144494.5 134006 134150.6 169425.1 169378 121150.5 159483.9 141280.6 119778.4 TRUE FALSE 137664.5313 147661.3638 140301.5377 152394.1671 198917.4696 116955.0278 135151.7019 128909.3217 138353.0225 0.995023664 1.067279638 1.014083647 1.101487805 1.437752974 0.845337714 0.976861217 0.931741998 1 17.07799464 EDHLVYADEESSNITDGRITPEPAVS(ph)NTEEPSTTSTASNYPDVLTRPSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEESSNIT(0.003)DGRIT(0.065)PEPAVS(0.438)NT(0.438)EEPS(0.014)T(0.014)T(0.014)S(0.003)T(0.003)AS(0.003)NY(0.003)PDVLT(0.003)RPS(0.003)LHR 58.325 0.0011957 196710000 6240.2 5764.5 7599.1 7097.3 8331.6 6716.7 7201.7 6069.1 6493.8 TRUE FALSE 5945.238113 6351.909104 7947.526252 6383.86592 9784.628402 6484.098995 6102.948397 5537.65743 7500.825338 0.792611192 0.846828025 1.059553568 0.851088465 1.304473569 0.864451404 0.813636916 0.738273081 1 12.87283363 -1.409717303 7.928400153 1.00000204 0.902342781 0.028461646 0.163434551 5.74E-06 4.27E-07 0.154133073 0.036328755 0.038929847 1.409717303 -0.097659259 EDINAIEMEEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDINAIEMEEDKR 13 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 120.54 0.00041947 106440000 180130 300400 247350 238360 1447800 162830 277190 183610 1532100 FALSE TRUE 171615.6119 331011.1015 258691.2422 214399.5999 1700295.862 157191.1563 234899.5746 167532.135 1769690.243 0.096974944 0.187044655 0.146178826 0.121150919 0.960787272 0.088824107 0.132734853 0.094667491 1 20.75506543 -2.210108427 2.225048594 3.287792975 0.220371194 0.459880603 0.262612659 9396804.354 1802829.082 108152324.3 0.065593191 0.006164411 2.210108427 -3.067421781 EDIQGALHNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDIQGALHNYR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ;;; 132.32 0.0001849 656890000 772760 579950 660660 729510 747850 745820 919890 805980 622850 FALSE TRUE 736233.1663 639047.5643 690951.9145 656178.2688 878274.8032 719992.0664 779543.8856 735404.1184 719438.3969 1.023344277 0.888258907 0.960404556 0.912070125 1.220778328 1.000769586 1.083545011 1.022191923 1 19.45651163 2.834488038 24.43385326 1.066289726 0.945782993 0.41074148 0.071080675 37.20816531 9473.361318 0.019504833 0.020688003 683.105902 -2.834488038 -0.120506733 EDITQSAQHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 273.15 9.27E-28 4527710000 5699790 4684340 4791200 5750860 5338690 4829170 6131540 5265160 5159470 FALSE TRUE 5430372.223 5161679.572 5010881.259 5172772.627 6269755.846 4661934.632 5196060.96 4804114.678 5959574.257 0.911201369 0.866115489 0.840811951 0.867976873 1.052047609 0.782259677 0.87188459 0.806117093 1 22.50677784 -0.405916273 7.277867224 0.999999994 0.875831409 0.227370198 0.072508215 0 0 0.064418889 0.015183678 0.39272064 0.405916273 -0.124168586 EDITYRLPELDPRGS(ph)DEENLDSETSASTESLLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDITYRLPELDPRGSDEENLDSETSASTESLLEER 35 2 M0R300;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 1 EDIT(0.001)YRLPELDPRGS(0.987)DEENLDS(0.005)ET(0.005)S(0.002)ASTESLLEER 73.238 0.0019749 19390000 18837 12114 19397 17491 16104 20573 26771 23246 19151 TRUE FALSE 17946.61234 13348.43037 20286.37164 15732.77145 18912.5325 19860.55185 22686.59227 21210.45701 22120.83927 0.81129889 0.603432366 0.917070613 0.711219464 0.85496451 0.897820901 1.025575567 0.95884504 1 14.4331185 2.303174876 1.152936827 1.006543746 0.738583687 0.59862038 0.082239783 0.289080887 0.749218428 0.049595614 0.029792802 200.9901972 -2.303174876 -0.267960058 EDKNGHDGDTHQEDDGEKS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDKNGHDGDTHQEDDGEKSD 20 2 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D 238.42 6.52E-30 1320320000 932300 753880 903000 985850 414330 1088980 1068230 1045300 75730 TRUE FALSE 888232.0266 830701.2291 944403.4432 886750.485 486589.0208 1051268.35 905251.8941 953767.9905 87473.82162 10.15426113 9.49656953 10.79641229 10.13732416 5.562681632 12.01809101 10.34883211 10.90346772 1 16.4165637 2.895342017 23.28117137 8.90494418 10.07532905 0.063605658 3.167456007 79.27456738 17591.85253 0.875339716 0.928438637 785.8542689 -2.895342017 1.170384867 EDKS(ph)PSEESAPTTSPESVSGSVPSSGSSGR ddPTM_SK-BR-3_Trastuzumab_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(0.983)PS(0.017)EESAPTTSPESVSGSVPSSGSSGR;EDKS(0.968)PS(0.032)EES(0.001)APTTSPESVSGSVPSSGSSGR;EDKS(0.894)PS(0.104)EES(0.002)APTTSPESVSGSVPSSGSSGR 300.93 1.83E-81 2778210000 1010770 910530 762010 981630 393410 965880 756420 903520 417970 TRUE FALSE 962992.9053 1003314.042 796948.9122 882954.6874 462020.5794 932431.3334 641014.2364 824402.9989 482786.6529 1.994655195 2.0781727 1.650726894 1.82887137 0.95698706 1.931352758 1.327738107 1.707592772 1 18.88102627 8 0.100938056 0.726186683 4.799246154 0.440713271 0.295765476 99.39456478 0.709725678 3.222522522 56.11042732 99999999.97 -8 4.073059471 EDKSPIAPEELALVHNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDKSPIAPEELALVHNLR 18 1 V9GZ61;V9GYC9;V9GYW1;V9GYA7;V9GZ03;V9GYJ9;V9GYL9;P51398-2;P51398-3;P51398 V9GZ61 DAP3 "28S ribosomal protein S29, mitochondrial" 0 60.764 0.039069 32783000 46339 42477 42624 48821 56771 41557 46520 38840 47053 FALSE TRUE 44148.64731 46805.45459 44578.35256 43913.42033 66671.84443 40117.87067 39422.5196 35438.9637 54349.73893 0.81230652 0.861190054 0.820212819 0.807978496 1.226718762 0.73814284 0.725348831 0.652053982 1 15.72998548 EDKSPSEESAPTTS(ph)PESVSGSVPSSGSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKSPSEESAPT(0.025)T(0.098)S(0.818)PES(0.042)VS(0.014)GS(0.004)VPSSGSSGR;EDKSPSEESAPTT(0.035)S(0.965)PESVSGSVPSSGSSGR 150.82 1.37E-08 195154000 198725 245237 209715 253652 143368 222349 203960 251717 151593 TRUE FALSE 189331.6631 270226.9291 219330.6402 228154.4191 168371.3338 214648.9984 172842.156 229675.325 175101.2682 1.081269513 1.543260833 1.252593099 1.302985532 0.961565473 1.225856332 0.987098253 1.311671397 1 17.41783001 2.813996249 9.741319735 1.098150156 1.310669967 0.287850682 0.153719713 0.580455871 72.29082792 0.043360869 0.046003453 651.6227656 -2.813996249 0.212519811 EDKYEEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 89.548 0.010974 298060000 1024260 1210590 809420 1320100 475140 1163850 914460 1230650 461430 FALSE TRUE 975845.2597 1333950.497 846532.7076 1187401.04 558004.2656 1123545.583 774942.3318 1122887.762 532986.2077 1.830901523 2.502786147 1.588282577 2.227826954 1.046939409 2.108019994 1.453963199 2.106785777 1 19.02373867 3.191990178 1.625056956 1.623504109 2.126211656 0.165029685 0.454453285 0.567180493 3.103498878 0.135677549 0.18696831 1555.930442 -3.191990178 0.502707547 EDLAAFVEELDKVESQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDLAAFVEELDKVESQER 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 164.68 2.74E-11 19039000 43176 54427 31070 53229 18592.2 41939 33204 50181 20208.7 FALSE TRUE 41135.15605 59973.17318 32494.59023 47878.31979 21834.67379 40486.64191 28138.11997 45786.88561 23342.56198 1.76223827 2.569262672 1.392074711 2.051116746 0.93540177 1.734455795 1.205442658 1.96151929 1 14.51067529 3.367146133 1.65514004 1.424137096 2.135497063 0.264259193 0.434905354 0.389884101 2.189730996 0.123993959 0.196732742 2328.874755 -3.367146133 0.711359967 EDLAAFVEELDKVESQEREDVLAGMSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDLAAFVEELDKVESQEREDVLAGMSGK 28 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 111.79 0.00032087 50714000 54542 49097 49341 60692 33487 55313 57075 69097 35937 FALSE TRUE 51963.90775 54100.04012 51603.33365 54591.12485 39327.1222 53397.49694 48367.1605 63046.50037 41509.92642 1.251842926 1.303303686 1.243156471 1.315134224 0.947414886 1.286378983 1.165195043 1.51882949 1 15.34116875 -1.539227382 2.913105505 0.988820458 1.245989603 0.240024186 0.14136466 14110558.95 16093596.34 1248093.848 0.03053299 0.028891668 1.539227382 0.257169145 EDLPAENGETKTEESPASDEAGEKEAKS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDLPAENGETKTEESPASDEAGEKEAKSD 29 3 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 EDLPAENGETKTEESPASDEAGEKEAKS(1)D;EDLPAENGETKTEESPASDEAGEKEAKS(1)D 359.45 1.11E-119 384810000 807240 728330 700890 865080 258980 954470 798530 987080 212878 TRUE FALSE 769083.365 802547.655 733026.4998 778120.5149 304146.03 921416.4646 676699.5825 900646.0424 245890.033 3.127753311 3.263847848 2.981115138 3.164506122 1.236918903 3.74727049 2.752041529 3.66280012 1 17.90765373 2.900470917 21.44882447 2.654990459 3.147021246 0.102167245 0.882552081 36.0324635 7750.466772 0.243996456 0.258797764 795.190013 -2.900470917 0.492030786 EDLQELNDR ddPTM_SK-BR-3_Trastuzumab_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 ; 218.58 8.91E-05 453940000 871640 907830 651990 983180 642090 741320 783690 789340 543030 FALSE TRUE 830439.3046 1000338.909 681884.3864 884348.8785 754070.2927 715647.9025 664123.697 720221.205 627240.319 1.323957149 1.594825586 1.087118232 1.409904389 1.202203159 1.140946908 1.058802626 1.148238057 1 19.25865877 2.705183732 0.603475318 1.032204256 1.452848186 0.502855906 0.126806619 0.578794004 0.447438898 0.095493332 0.101961291 507.2052405 -2.705183732 0.42064393 EDLRLPEGDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 EDLRLPEGDLGK 12 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;;;;;; 187.74 9.21E-06 21266410000 32225520 34689630 26519670 37186400 18792870 32713320 30531720 33530190 18222680 FALSE TRUE 30702283.53 38224542.74 27735623.1 33448352.42 22070340.58 31580449.53 25873545.36 30594108.81 21048560.15 1.458640559 1.816016985 1.317696931 1.589104062 1.048543959 1.500361512 1.229231129 1.453501265 1 24.32721821 3.442092734 0.065010012 0.280362732 2.694146312 0.369157737 0.194692551 74.27221723 1.271980912 17.31869393 30.16795221 2767.53253 -3.442092734 2.41378358 EDLSKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDLSKSPK 8 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 EDLS(0.004)KS(0.996)PK;EDLS(0.005)KS(0.995)PK 76.943 0.02089 1352410000 3604700 2430500 3047600 3632500 1523180 3890400 4015200 3989900 1564900 TRUE FALSE 3434312.975 2678170.713 3187335.474 3267354.199 1788822.11 3755674.473 3402607.496 3640523.204 1807576.7 1.899954218 1.481636001 1.763319629 1.807588137 0.989624457 2.077740034 1.882413895 2.014035258 1 20.78562543 EDLTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 1285800000 3810660 4374230 3081760 4279760 3070520 3406690 3379110 3643740 2730830 FALSE TRUE 3630537.654 4819969.01 3223061.744 3849550.394 3606017.716 3288715.471 2863564.708 3324674.809 3154313.169 1.150975651 1.528056585 1.021795101 1.220408434 1.143202188 1.042609055 0.907825113 1.054009108 1 21.58889447 2.789863893 0.870785483 0.971331931 1.313226793 0.410026367 0.129917916 0.468574687 0.767254751 0.075227381 0.074207944 616.4017923 -2.789863893 0.341894862 EDLTEIRDMLLANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDLTEIRDMLLANK 14 1 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 0 212.17 2.57E-09 51679000 237580 159940 235800 238250 207410 232580 295790 277010 225120 FALSE TRUE 226350.0642 176238.0678 246611.6632 214300.6574 243582.2383 224525.6963 250661.8029 252753.5359 260030.4598 0.870475191 0.677759321 0.948395289 0.824136747 0.93674502 0.863459213 0.963970925 0.972015109 1 17.9883211 2.527461464 0.517735736 0.997249892 0.77755153 0.441584104 0.070505446 0.765394504 0.427100694 0.06014255 0.063298772 336.8693231 -2.527461464 -0.219698362 EDLTEIRDMLLANKVPAAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDLTEIRDMLLANKVPAAAR 20 2 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 0 207.13 3.92E-22 241100000 280080 135600 299110 227420 287570 274740 411030 333890 384750 FALSE TRUE 266841.1735 149417.7942 312824.4894 204559.3095 337722.117 265225.6849 348319.8244 304652.8215 444415.065 0.600432331 0.336212262 0.703901632 0.460288873 0.759924997 0.596797242 0.783771415 0.685514164 1 18.7615482 1.252429797 0.285871495 1.057103317 0.430615195 0.58901602 0.116208644 1.058756985 0.316494046 0.256817829 0.189608775 17.88256439 -1.252429797 -0.626488121 EDLVGPEVGAS(ph)PQSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDLVGPEVGASPQSGR 16 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.999)PQS(0.001)GR 141.18 1.90E-05 0 112510 117220 86616 127410 88191 108230 114720 108100 91751 TRUE FALSE 107191.8753 129164.8513 90587.42927 114602.5047 103571.4825 104481.968 97217.35702 98634.19093 105979.2765 1.011441848 1.218774609 0.8547655 1.081367118 0.97728052 0.985871686 0.917324219 0.93069319 1 16.69342266 3.739921265 24.9999092 0.964333556 1.115108225 0.404119349 0.076333065 102.5698838 1884556.73 0.01860677 0.031377689 5494.412542 -3.739921265 0.150774669 EDLVGPEVGAS(ph)PQSGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDLVGPEVGASPQSGRK 17 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.998)PQS(0.002)GRK 163.78 1.64E-09 133180000 199380 181790 172690 223250 128700 186720 200320 222270 157980 TRUE FALSE 189955.7025 200314.6077 180608.0073 200808.4859 151145.2393 180253.8396 169757.5049 202806.8605 182478.7315 1.040974479 1.097742219 0.989748262 1.100448716 0.82828962 0.98780739 0.930286524 1.11139999 1 17.4773688 EDLYLKPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 118.4 0.0007566 6675580000 9898020 10256480 9263680 11142900 7107430 10261380 10336900 10031570 6849630 FALSE TRUE 9430160.211 11301626.97 9688428.891 10022794.52 8346963.542 9906025.838 8759816.055 9153152.55 7911835.637 1.191905475 1.428445621 1.224548807 1.266810255 1.054997086 1.25205152 1.10717872 1.156893668 1 22.91558102 1.940284741 0.367704482 1.005219113 1.329813575 0.466099274 0.087818412 0.988740187 0.365444104 0.103502638 0.108837236 87.15348161 -1.940284741 0.324594462 EDMAALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 135.83 0.0019006 565830000 1773090 1986190 1484770 2043350 1088660 1775540 1614370 1944790 1022380 FALSE TRUE 1689279.55 2188585.019 1552848.173 1837948.576 1278521.959 1714052.605 1368068.207 1774493.878 1180925.469 1.430470927 1.853279548 1.314941725 1.55636289 1.082644073 1.451448588 1.158471252 1.502629865 1 20.17148648 3.224623669 1.576560628 1.264444152 1.624811701 0.310782687 0.207709189 0.374948574 1.93444977 0.06256682 0.089063396 1677.349906 -3.224623669 0.360367548 EDMAALEKDYEEVGADSADGEDEGEEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDMAALEKDYEEVGADSADGEDEGEEY 27 1 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ; 364.53 1.01E-126 232020000 766650 524800 743410 756030 627790 785300 1030010 861610 767110 FALSE TRUE 730411.9739 578277.7166 777496.0838 680032.428 737276.3772 758104.8641 872863.0571 786162.8607 886069.5009 0.824328084 0.652632458 0.877466252 0.767470754 0.83207511 0.855581716 0.985095476 0.8872474 1 19.75706034 2.162749734 0.772407151 0.981825795 0.753080494 0.58320541 0.064400198 0.400288154 0.452308338 0.050192993 0.029066475 145.4620601 -2.162749734 -0.228745302 EDMAALEKDYEEVGVDSVEGEGEEEGEEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDMAALEKDYEEVGVDSVEGEGEEEGEEY 29 1 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;; 293.88 8.75E-81 265065000 991822 648059 975865 966571 805359 925337 1274767 1091103 951963 FALSE TRUE 944940.5397 714096.9489 1020609.376 869409.4467 945813.3546 893292.3477 1080277.881 995560.237 1099588.56 0.859358285 0.649421952 0.928173876 0.790667963 0.86015205 0.812387815 0.982438269 0.905393411 1 20.06853237 1.931815537 0.587448062 0.998648759 0.772859883 0.417430843 0.077362661 0.644370758 0.45872063 0.067950704 0.042737714 85.47036075 -1.931815537 -0.225788876 EDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 154.33 3.02E-08 122509000 77358.2 53065.9 42394.5 73563.1 51862.2 60846.3 83108.2 74030.5 23862 TRUE FALSE 73701.6312 58473.37554 44338.32976 66168.39743 60906.95126 58739.17737 70428.5177 67547.99696 27562.39709 2.673992068 2.121490934 1.608652891 2.400676444 2.20978426 2.131134574 2.555239208 2.450730128 1 14.75041374 -1.141225578 4.333308126 0.999757427 2.276985331 0.648023746 0.293855879 0.000684767 0.000135705 0.282913852 0.066671176 0.072239449 1.141225578 1.277227904 EDPDGEHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDPDGEHAR 9 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 152.97 7.92E-05 381090000 814180 854470 654188 954300 592274 740472 746390 803540 500899 FALSE TRUE 775695.3249 941541.4645 684183.1669 858371.9509 695566.3981 714829.269 632514.4971 733177.7778 578575.8587 1.340697703 1.627343157 1.182529752 1.483594481 1.202204322 1.235497918 1.093226562 1.267211147 1 19.1421466 2.41214746 0.517490397 1.051928303 1.487108694 0.480566712 0.130684009 0.682220697 0.379935824 0.110044663 0.106187531 258.3137119 -2.41214746 0.435180391 EDPVAWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDPVAWAR 8 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 103.91 0.010893 83527000 180840 207500 151420 252260 200360 177350 219540 190930 146370 FALSE TRUE 172292.0516 228644.4859 158362.7568 226902.3455 235302.7206 171208.325 186045.1409 174211.157 169068.312 1.019067675 1.352379302 0.936679114 1.342074945 1.391761222 1.012657682 1.10041402 1.03041874 1 17.36724676 2.167088855 24.99999297 1.049130309 1.204555013 0.25727226 0.144797906 68.67979392 24021.77801 0.051536729 0.038062406 146.9226844 -2.167088855 0.155424704 EDQEAAELLS(ph)EPEEESER ddPTM_SK-BR-3_Trastuzumab_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 296.53 1.89E-39 268950000 721180 861580 684750 927400 603190 885590 704070 821450 523760 TRUE FALSE 687091.2506 949375.9815 716146.4648 834175.9901 708386.145 854921.7962 596651.1904 749519.4832 604982.0258 1.135721759 1.56926312 1.183748333 1.378844254 1.170920977 1.413135862 0.986229615 1.238911986 1 19.20653275 1.702517518 0.880654552 1.03343433 1.333230082 0.272371706 0.155142067 0.623636638 0.922507179 0.125726248 0.052964505 50.41009519 -1.702517518 0.299795752 EDQIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EDQIYR 6 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 196.36 0.00056877 8315800000 8504870 7167960 6790860 8109210 7089110 7118810 8012340 7266870 7045160 FALSE TRUE 8102861.65 7898383.273 7102227.648 7294056.804 8325448.54 6872283.825 6789910.376 6630544.339 8137687.431 0.995720433 0.9705931 0.872757489 0.896330421 1.02307303 0.844500834 0.83437837 0.814794669 1 22.95618744 2.2135832 24.99877239 0.856372666 0.952169626 0.238910364 0.066391046 258.0799169 258298.8642 0.023532872 0.01738718 163.5246393 -2.2135832 0.09579696 EDQKMS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDQKMSPK 8 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 EDQKMS(1)PK;EDQKMS(1)PK;EDQKMS(1)PK;EDQKMS(1)PK 69.423 0.081844 1048580000 2914430 3250250 2361130 3373530 1089280 3331790 2803690 3376800 1059070 TRUE FALSE 2776670.67 3581454.17 2469390.146 3034416.355 1279250.087 3216409.277 2375935.597 3081109.49 1223305.167 2.269810302 2.927686621 2.018621529 2.480506449 1.045732596 2.629277931 1.942226406 2.518676104 1 20.22235291 3.438427717 2.173878663 1.973259655 2.584148031 0.162882804 0.5839876 0.504748532 4.806354928 0.156020694 0.244295757 2744.275553 -3.438427717 0.610888376 EDQSILCTGESGAGKTENTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDQSILCTGESGAGKTENTKK 21 2 P35579;P35579-2;Q5BKV1;A0A494C024;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 ; 134.15 4.90E-06 184357000 148168 125200 152677 162739 97850 175821 197744 187187 107250 FALSE TRUE 141164.3923 137958.0223 159677.3915 146380.1665 114915.009 169732.2747 167574.521 170795.9139 123881.7822 1.139508891 1.113626393 1.288949744 1.181611726 0.927618306 1.370114892 1.352697047 1.378700813 1 16.91860452 2.190887782 24.99999826 1.312238582 1.138380621 0.188649158 0.140028508 149.096576 78186.43931 0.047681936 0.035215522 155.1985939 -2.190887782 -0.173857961 EDQTEYLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 294.75 7.40E-32 26200510000 6331360 7279770 4938210 7532700 4569680 5791710 5448570 5893860 4232530 FALSE TRUE 6032089.16 8021586.839 5164631.813 6775498.685 5366630.745 5591141.63 4617290.577 5377762.373 4888889.136 1.233836357 1.640779043 1.056401908 1.385897388 1.09771987 1.143642549 0.944445752 1.099996794 1 22.22107526 2.777018257 0.88455379 1.00674386 1.408303613 0.431785147 0.153916206 0.447204015 0.752819451 0.085272351 0.082723183 598.4367521 -2.777018257 0.401559753 EDQTEYLEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 238.87 2.02E-15 3818390000 2609950 1831490 2621230 2361890 2662380 2452780 3213370 2819030 3082650 FALSE TRUE 2486582.836 2018120.913 2741415.988 2124468.33 3126698.229 2367839.614 2723111.389 2572180.789 3560691.618 0.698342654 0.566777786 0.769911097 0.596644854 0.878115424 0.664994295 0.764770354 0.722382353 1 21.76372606 -5 0.143858877 2.071665588 0.59460231 0.554925678 0.085090917 89.3209017 0.777999748 27.27327593 0.424916754 1.00E-05 5 -1.477063278 EDRPIS(ph)FYQLGSNQLQSNAVSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDRPISFYQLGSNQLQSNAVSLAR 24 1 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 EDRPIS(1)FYQLGSNQLQSNAVSLAR 229.28 1.77E-33 56276000 35743 33483 35945 35877 32127 41449 42873 44165 46266 TRUE FALSE 34053.49923 36894.95577 37593.1138 32270.5758 37729.93863 40013.61074 36331.93643 40297.67847 53440.69499 0.637220366 0.690390643 0.703454808 0.603857712 0.706015119 0.748747948 0.679855238 0.754063518 1 15.70565115 -4.999999999 0.219534937 2.614896806 0.645519093 0.88424561 0.036480806 45.40314333 0.453982506 32.31827288 0.065643327 1.00E-05 4.999999999 -1.969377713 EDRS(ph)KDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDRSKDRDR 9 3 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 1 EDRS(1)KDRDR 84.718 0.084563 33896000 27509 20891 25061 31202 17225 30741 30269 32638 24322 TRUE FALSE 26208.70409 23019.81665 26210.07164 28065.51568 20229.03455 29676.43146 25650.90812 29780.0437 28093.73154 0.932902205 0.819393345 0.932950883 0.998995653 0.720055095 1.056336408 0.913047385 1.060024499 1 14.77796064 EDS(ph)GTFSLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.998)GT(0.002)FSLGK;EDS(0.978)GT(0.022)FSLGK;EDS(0.659)GT(0.341)FSLGK;EDS(0.638)GT(0.362)FSLGK 232.19 3.47E-10 747820000 2233780 2251300 1843340 2834760 1263380 2476290 2263530 2258110 1192050 TRUE FALSE 2128193.646 2480710.03 1927858.962 2549804.539 1483713.072 2390535.456 1918186.926 2060377.917 1376907.026 1.545633515 1.801653985 1.400137356 1.85183494 1.077569541 1.736163308 1.39311289 1.496381294 1 20.39299972 -2.888207622 0.168651623 1.61E-09 1.727842527 0.388278438 0.220936163 52.13242279 0.946948228 19.64479079 0.780014184 0.001293577 2.888207622 1.727842525 EDS(ph)LPEESSAPDFANLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDSLPEESSAPDFANLK 17 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 EDS(1)LPEESSAPDFANLK;EDS(1)LPEESSAPDFANLK 250.52 2.59E-21 93935000 183463 105758 111869 211250 145464 150585 165792 120527 92458 TRUE FALSE 174791.0676 116534.8604 116998.3043 190014.7487 170832.8755 145370.2037 140497.3854 109973.0169 106795.9144 1.636683093 1.091192122 1.09553165 1.779232377 1.599619952 1.361196301 1.315568916 1.029749289 1 16.70449693 1.309051857 2.407186325 0.989006657 1.410766876 0.372189784 0.217855462 0.341179667 3.289175641 0.19977982 0.059179539 20.37285325 -1.309051857 0.421760219 EDSARPGAHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EDSARPGAHAK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;; 127.87 0.00016685 1358180000 2928820 2427770 2637470 3040880 2247570 2775490 3506330 3125870 2499780 FALSE TRUE 2790380.483 2675162.523 2758400.608 2735204.965 2639545.496 2679374.085 2971374.96 2852152.252 2887433.115 0.96638792 0.926484672 0.955312382 0.947279073 0.914149485 0.927943256 1.029071442 0.987781236 1 21.4613561 1.748957404 13.88547985 1.005968181 0.940062928 0.751533 0.017893402 0.067802264 83.25306356 0.008002501 0.004407844 56.09929508 -1.748957404 -0.065905253 EDSEKDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDSEKDEK 8 1 P29374;P29374-3;P29374-2;H7C485 P29374 ARID4A AT-rich interactive domain-containing protein 4A 0 51.193 0.090602 470040000 400510 473160 471980 510940 1789000 209030 459760 237450 1423600 FALSE TRUE 381578.686 521375.5419 493620.7499 459579.3405 2101001.034 201791.2387 389615.1679 216657.6192 1644364.617 0.232052358 0.317068086 0.300189353 0.279487491 1.277697788 0.122716846 0.236939645 0.131757651 1 20.6490988 -2.309727229 2.331406918 4.407246856 0.353967656 0.266323488 0.332413981 31628310.38 3676177.563 569677356 0.076520297 0.004900865 2.309727229 -4.0532792 EDSGT(ph)FSLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.332)GT(0.668)FSLGK 199.19 3.17E-06 164010000 453510 526410 409350 584270 270570 534150 456130 479320 239670 TRUE FALSE 432073.4811 580051.7775 428119.1024 525538.0696 317757.3223 515652.2516 386538.9911 437348.1998 276836.7995 1.560751612 2.09528422 1.546467461 1.898367813 1.147814607 1.8626579 1.396270264 1.579805143 1 18.07867621 -0.594568118 0.195340838 0.529122294 1.908704948 0.404364975 0.257676214 13.09378148 0.689758054 4.332512798 0.784644375 0.254350082 0.594568118 1.379582654 EDSHPFDLGLYNEAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDSHPFDLGLYNEAVK 16 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 226.25 6.12E-15 146400000 332800 284130 294020 362460 238190 326470 352870 372510 222490 FALSE TRUE 317069.2035 313083.17 307501.1078 326024.8322 279730.2606 315164.262 299033.2006 339891.0496 256992.6129 1.233767773 1.218257469 1.196536758 1.268615578 1.088475881 1.226355336 1.163586755 1.322571282 1 17.97136736 -1.104013981 4.004589317 0.999946455 1.210526015 0.54526075 0.061530742 0.816965403 14535200.19 1629.970964 0.012748143 0.078702045 1.104013981 0.21057956 EDSQRPGAHLTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 115.37 0.00040216 23643890000 26027430 21706840 21729640 28661090 21426040 24459620 29995320 28400970 22720550 FALSE TRUE 24797164.97 23918791.67 22725965.49 25780022.78 25162734.59 23612577.23 25418983.03 25914030.5 26243936.85 0.944872147 0.911402577 0.865951081 0.982323 0.958801827 0.899734569 0.968565927 0.987429236 1 24.64548082 1.532992619 4.12087279 0.990432908 0.92772399 0.43500574 0.032055749 0.175741284 6.576499956 0.019719545 0.008190448 34.1187113 -1.532992619 -0.062708917 EDSVKPGAHLTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EDSVKPGAHLTVK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 111.39 0.00059097 3152600000 6444440 5270080 5533660 7215700 4544510 6284650 7619300 7744520 5094110 FALSE TRUE 6139824.093 5807107.144 5787383.785 6490364.127 5337071.105 6067010.995 6456835.847 7066368.773 5884078.562 1.04346399 0.986918696 0.983566709 1.103038319 0.907036004 1.031089393 1.097340183 1.200930392 1 22.48838508 1.740771941 3.847616687 1.113673321 1.00701524 0.276518655 0.068592486 0.217123851 6.948537419 0.033180756 0.016410351 55.05185292 -1.740771941 -0.106658081 EDTEEHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 3458226500 4099043 4509024 3186800.6 4716655 3048259 3794525.3 3667404.5 3762637 455084.2 FALSE TRUE 3905289.361 4968498.672 3332918.56 4242527.878 3579874.404 3663119.937 3107874.587 3433160.557 525656.3335 7.429358522 9.451990503 6.340489684 8.070915555 6.810294438 6.968659377 5.912369716 6.531188418 1 19.00376037 0.067057819 0.350185441 1.30E-11 8.305745539 0.852475627 0.839384197 1.503043961 0.273024433 3.597487572 0.69697481 1.166964968 -0.067057819 8.305745539 EDTEEHHLRDYFEEYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDTEEHHLRDYFEEYGK 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 52.887 0.0901 28136000 73811 16180 79698 39195 92641 61282 148760 82009 22721 FALSE TRUE 70322.10031 17828.7604 83352.23213 35255.04413 108797.5611 59159.78897 126063.9298 74827.8572 26244.45664 2.679503001 0.679334331 3.175993822 1.34333298 4.145544431 2.254182275 4.803449794 2.851187138 1 14.67972511 3.712314224 24.56253224 3.023071151 1.679418518 0.101491151 1.246706301 885.0529072 828271.5072 0.310790948 0.481655166 5156.01562 -3.712314224 -1.343652633 EDTEEHHLRDYFEEYGKIDTIEIITDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EDTEEHHLRDYFEEYGKIDTIEIITDR 27 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 227.99 6.57E-35 262245300 243557.9 42437.69 291347.8 113759.1 411787 197819.2 670364 235536.3 94310.3 FALSE TRUE 232045.4008 46762.13886 304706.3848 102323.8191 483602.5224 190968.6715 568087.6597 214911.4929 108935.4597 2.130118159 0.429264622 2.797127637 0.93930681 4.439348987 1.753044161 5.214901204 1.972833213 1 16.73311412 2.752686565 24.9704796 3.211511264 1.51292272 0.1533836 1.398684017 990.760941 1751369.602 0.383834402 0.405319038 565.8307752 -2.752686565 -1.698588544 EDTEEHHLRDYFEQYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDTEEHHLRDYFEQYGK 17 1 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 53.169 0.088616 42773000 160050 67908 168200 109380 165300 155900 260500 170870 115370 FALSE TRUE 152484.7537 74827.9024 175912.1364 98384.91459 194128.2677 150501.1439 220755.9406 155907.717 133260.9904 1.144256494 0.56151393 1.320057249 0.738287434 1.456752401 1.129371345 1.656568362 1.169942656 1 17.023895 2.733176455 24.93190065 1.33741013 0.921414295 0.264953939 0.273437843 445.2852077 2061932.531 0.079981517 0.077436441 540.974078 -2.733176455 -0.415995835 EDTEEHHLRDYFEQYGKIEVIEIMTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDTEEHHLRDYFEQYGKIEVIEIMTDR 27 2 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" 0 104.87 0.001278 24289000 8438.1 4609.8 13567 6449.1 12652 9673 23245 6859.2 3964.4 FALSE TRUE 8039.247736 5079.543861 14189.06037 5800.824216 14858.50479 9338.021585 19698.54833 6258.572085 4579.178905 1.755609008 1.10926958 3.098603629 1.266782612 3.244796743 2.039234933 4.301764298 1.366745483 1 12.16087322 3.557006036 1.225477434 2.625653686 1.429479457 0.008467744 1.085350193 0.858959504 2.585166546 0.342215952 0.746037211 3605.836548 -3.557006036 -1.196174229 EDTEEYNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EDTEEYNLR 9 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 243.85 3.75E-10 849750000 1275050 1385040 1026150 1463760 898990 1205870 1101770 1180150 905060 FALSE TRUE 1214780.913 1526177.151 1073199.993 1316620.064 1055773.571 1164110.42 933674.7511 1076809.81 1045412.082 1.162011549 1.459880918 1.02658082 1.259426867 1.009911392 1.113542152 0.893116472 1.030033829 1 19.99564031 2.864337159 0.925543757 0.97364545 1.292165121 0.43905968 0.119685804 0.414053646 0.769824813 0.060731957 0.064537579 731.7069147 -2.864337159 0.318519671 EDTEEYNLRDYFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDTEEYNLRDYFEK 14 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 136.6 2.38E-05 35829000 36621 10999 35908 22319 23662 34047 45974 30222 35149 FALSE TRUE 34889.99791 12119.8106 37554.41732 20075.45172 27788.64531 32867.94385 38959.82193 27575.60146 40599.7274 0.859365324 0.298519507 0.924991859 0.494472574 0.684453987 0.809560703 0.959607968 0.679206567 1 15.30918242 2.227177094 3.121078354 0.876182386 0.62385841 0.23058067 0.19191616 0.319265315 6.459201105 0.071735233 0.052502772 168.7240896 -2.227177094 -0.252323976 EDTLLLIGHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDTLLLIGHLER 12 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ; 99.531 0.0037439 45725000 81539 102877 77064 97665 67969 92330 75545 91389 59862 FALSE TRUE 77684.81306 113360.2833 80597.46063 87847.52865 79822.77208 89132.58895 64019.22277 83386.49468 69145.09323 1.123504351 1.639455209 1.165628056 1.270481021 1.154424246 1.289066003 0.925867907 1.205964021 1 16.07733926 2.463065867 0.813158067 1.038787834 1.359531229 0.273296644 0.163295341 0.683111124 0.906604668 0.113891745 0.081858178 290.4463123 -2.463065867 0.320743395 EDVETGLDPLSLLATECTGGKT(ph)PDSEDKLFSPVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDVETGLDPLSLLATECTGGKTPDSEDKLFSPVIAR 36 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 EDVETGLDPLS(0.001)LLAT(0.012)ECT(0.046)GGKT(0.938)PDS(0.003)EDKLFSPVIAR 104.36 0.0012958 91639000 44795 37612 35351 50392 19222 48413 44664 56393 16818 TRUE FALSE 42677.62913 41444.70556 36971.87832 45326.50042 22574.31071 46736.44567 37849.68649 51454.92996 19426.04955 2.196927843 2.133460304 1.903211367 2.333284506 1.162063891 2.405864639 1.948398536 2.648759329 1 14.24570493 3.879791425 1.448759916 1.960570486 2.198578099 0.033189867 0.514008378 1.912304804 7.557441827 0.137971328 0.405714512 7582.133476 -3.879791425 0.238007613 EDVEVAES(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLR;EDVEVAES(1)PLR 283.73 1.54E-27 733900000 687950 706750 631250 796390 623260 690110 749140 740060 642120 TRUE FALSE 655431.9669 778768.6285 660193.4369 716335.3642 731956.3467 666211.3177 634844.9341 675256.4231 741696.6901 0.883692722 1.049982613 0.890112422 0.965806338 0.986867484 0.89822609 0.855936048 0.910421244 1 19.50046981 2.221542433 24.64836532 0.898764493 0.959210759 0.062608342 0.059390006 324.4473666 469911.2917 0.020655194 0.015295076 166.549155 -2.221542433 0.060446266 EDVEVAES(ph)PLRVLAETPDSFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EDVEVAESPLRVLAETPDSFEK 22 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLRVLAETPDSFEK;EDVEVAES(1)PLRVLAETPDSFEK 132.93 5.96E-06 13491000 44505 28448 43857 35156 38747 42910 65949 45856 50424 TRUE FALSE 42401.33685 31346.88354 45867.88683 31622.05209 45504.46453 41424.01594 55887.26881 41840.60554 58243.49639 0.728001227 0.538204014 0.78751946 0.542928465 0.781279754 0.711221312 0.959545224 0.718373864 1 15.82980934 2.090160162 1.323364057 0.895314876 0.647481387 0.439500997 0.111461151 0.360974293 1.189015929 0.06674044 0.033681487 123.0722562 -2.090160162 -0.247833489 EDVFVHQTAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 199.43 5.03E-08 511400000 917070 1059750 714080 1139240 663750 845310 896230 961070 658000 FALSE TRUE 873721.9186 1167739.73 746821.2743 1024721.431 779507.7898 816036.7027 759493.6531 876913.6158 760039.2794 1.149574689 1.536420237 0.982608787 1.34824799 1.025615137 1.073677012 0.999282108 1.153774074 1 19.53571445 3.014011262 1.103974475 1.042238659 1.313671787 0.262805474 0.152102469 0.513238457 1.340320858 0.061950075 0.0763002 1032.788188 -3.014011262 0.271433128 EDVSLHGYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EDVSLHGYKK 10 1 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 98.04 0.0036664 146850000 470700 348260 377750 477540 391250 431290 629250 504920 407010 FALSE TRUE 448450.9438 383748.0899 395070.2111 429536.7719 459483.8761 416354.3192 533246.3555 460706.5281 470127.0321 0.953893125 0.816264677 0.840347787 0.91366108 0.977361106 0.885620887 1.134260145 0.97996179 1 18.84269111 2.242535258 1.313410844 1.042342079 0.876166562 0.437911144 0.067625323 0.347888405 1.167130382 0.039822537 0.02306794 174.7975165 -2.242535258 -0.166175517 EEADEYIDIGALNGIFVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 194.85 5.16E-18 31851000 32481 29856 28647 34813 25353 23878 33597 30574 28826 FALSE TRUE 30945.6875 32898.36034 29960.49329 31313.5311 29774.55517 23051.09887 28471.1606 27896.77848 33296.18886 0.929406294 0.98805183 0.899817496 0.940453913 0.89423313 0.692304425 0.855087671 0.837836985 1 15.02306943 2.470916687 24.99700642 0.826631008 0.941533073 0.229132795 0.076802923 169.4029001 682484.3458 0.023855147 0.020009081 295.7445073 -2.470916687 0.114902065 EEADKLVR ddPTM_SK-BR-3_Trastuzumab_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 ;; 102.61 0.0044983 623240000 2234120 1502530 1805920 2112950 1598950 1954770 2386130 2312360 1804290 FALSE TRUE 2128517.575 1655639.515 1888723.218 1900552.252 1877806.374 1887075.825 2022082.044 2109877.5 2084090.078 1.021317455 0.794418405 0.906257958 0.911933832 0.901019775 0.905467496 0.970246951 1.012373468 1 20.9909862 1.605402103 2.622191672 1.005371563 0.90186457 0.379494528 0.0538409 0.247584099 3.888039022 0.036671453 0.014280786 40.30900731 -1.605402103 -0.103506992 EEAEKPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEAEKPER 8 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 95.502 0.0087598 869764000 1194840 1260970 951640 1347170 735310 1159270 1085940 1123730 732780 FALSE TRUE 1138362.281 1389464.277 995273.6353 1211749.912 863547.8312 1119124.189 920259.9083 1025330.244 846415.7799 1.34492091 1.641585979 1.175868479 1.431624907 1.020240704 1.322192019 1.087243327 1.211378933 1 19.691007 3.191723043 1.2128041 1.143977918 1.479871837 0.412910553 0.150946854 0.370309331 1.15614056 0.051941733 0.07590292 1554.973681 -3.191723043 0.33589392 EEAERELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEAERELER 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 0 115.78 0.0012953 172380000 146820 106290 141940 133830 149530 126030 162870 151470 171600 FALSE TRUE 139880.1096 117121.0718 148448.0894 120377.1541 175607.9847 121665.5495 138021.1902 138206.4838 198210.8516 0.70571368 0.590891321 0.748940273 0.607318687 0.885965542 0.613818812 0.696335186 0.697270017 1 17.59667642 -4.999999998 0.327976299 4.126747719 0.674094094 0.561532977 0.084975622 237.5246934 2.063276937 517.3397765 0.064674531 1.00E-05 4.999999998 -3.452653625 EEAIEHNYGGHDDDLSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EEAIEHNYGGHDDDLSVR 18 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 190.71 1.52E-14 843090000 666710 745090 635530 778430 635660 681590 680290 730260 273475 FALSE TRUE 635195.9396 821015.5181 664669.6791 700180.7375 746518.9027 657986.3674 576499.2661 666314.563 315884.1063 2.010851217 2.599103601 2.104156765 2.216574761 2.363268325 2.082999285 1.825034102 2.109364003 1 18.26903582 -0.034940983 0.404668905 0.796061507 2.311512693 0.79416453 0.190541272 1.920619586 0.410014319 0.814518142 0.124199701 0.922696806 0.034940983 1.515451186 EEALGLYQWIYHTHEDAQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEALGLYQWIYHTHEDAQEAR 21 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 243.48 2.44E-30 97107000 148524 196293 155986 189627 150582 167178 173496 153528 12144.2 FALSE TRUE 141503.5649 216295.4799 163138.1124 170565.3337 176843.4531 161388.5839 147025.9987 140084.2744 14027.46051 10.08761099 15.41943245 11.62991065 12.15938791 12.60694714 11.50518897 10.48129835 9.986431564 1 13.77596623 0.133106392 0.551665558 0.232744354 12.69783651 0.871603649 1.331914979 1.050617075 0.421761942 3.008459622 0.565063948 1.358646241 -0.133106392 12.46509216 EEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 157.68 2.04E-09 545860000 1497520 1840630 1211710 1821670 845020 1722570 1452430 1706840 835270 TRUE FALSE 1426735.197 2028192.29 1267268.102 1638552.271 992391.2205 1662916.969 1230835.128 1557380.041 964799.4056 1.478789466 2.10219065 1.313504232 1.69833466 1.028598499 1.723588302 1.275742005 1.614200871 1 19.87986949 -0.78052735 0.080430657 1.15E-08 2.334872766 0.253450107 0.290153795 83.88337372 1.45842718 30.68415468 13.18174949 0.165757295 0.78052735 2.334872754 EEAPAS(ph)PLRPLYPQISPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPAS(1)PLRPLYPQISPLK 135.01 5.21E-06 146540000 217160 202470 151840 231600 133930 192980 194310 198050 141870 TRUE FALSE 206895.2772 223101.9232 158802.0142 208319.128 157287.3496 186297.0542 164664.4408 180707.6921 163870.475 1.262553716 1.361452837 0.969070323 1.271242595 0.959827263 1.136855521 1.004845081 1.102747106 1 17.32219642 3.745804811 24.9941434 1.068547288 1.312003289 0.538141457 0.095617281 350.7510544 1210168.37 0.021633412 0.038037123 5569.353841 -3.745804811 0.243456001 EEAPASPLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPASPLRPLYPQIS(1)PLK;EEAPASPLRPLYPQIS(1)PLK 121.84 2.08E-05 239190000 279618 368750 232005 359860 170263 317070 270100 342530 176663 TRUE FALSE 266401.0113 406326.0442 242642.6587 323686.1891 199956.8133 306089.7864 228891.2843 312536.2573 204058.9958 1.305509763 1.991218484 1.189080922 1.586238273 0.979897076 1.500006335 1.121691712 1.531597547 1 17.63862679 3.709555766 24.92563146 1.28253497 1.648364262 0.254072838 0.267224401 749.1604995 643799.25 0.06330673 0.098092886 5123.37053 -3.709555766 0.365829292 EEAQAEIEQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEAQAEIEQYR 11 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 160.81 7.42E-05 281880000 449970 385490 421990 500960 418580 432260 532440 489370 427310 FALSE TRUE 428700.8099 424771.8693 441338.6589 450602.549 491580.2195 417290.7278 451206.4991 446518.1685 493575.0524 0.868562558 0.860602389 0.894167274 0.912936233 0.9959584 0.84544534 0.914159856 0.904661138 1 18.91290995 -5 0.094211995 1.31308944 0.820238913 0.405540323 0.039909141 199.9879404 1.298008565 12.665996 0.788958421 1.00E-05 5 -0.492850527 EEAS(ph)DDDMEGDEAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 426.94 4.05E-160 3098220000 3425930 2054600 1153920 3203230 2008760 1911180 3536530 3419010 2723200 TRUE FALSE 3263993.078 2263966.076 1206828.373 2881235.235 2359087.108 1844995.357 2996967.396 3119623.359 3145499.948 1.037670683 0.719747612 0.383668222 0.915986419 0.749987966 0.586550751 0.95277935 0.991773458 1 21.58485791 1.597462076 7.143874267 0.987112677 0.748713831 0.312250725 0.173906741 0.1645931 18.27432425 0.093780139 0.044912146 39.57875022 -1.597462076 -0.238398846 EEASDYLELDTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEASDYLELDTIK 13 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ; 224.82 3.14E-11 58877000 123765 146848 106840 149330 82258 131691 117295 137410 84411 FALSE TRUE 117914.8737 161811.9782 111738.7197 134319.0647 96603.76916 127130.5076 99399.49348 125377.6519 97501.02677 1.209370584 1.659592555 1.146026082 1.377616925 0.990797455 1.303888911 1.019471248 1.285911093 1 16.57312979 3.204341863 1.594885655 1.132707661 1.417397174 0.259749308 0.175899879 0.402818163 2.125564785 0.053828504 0.075177144 1600.817646 -3.204341863 0.284689513 EEASLLSHS(ph)PGTSNQSQPCS(ph)PKPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEASLLS(0.001)HS(0.998)PGT(0.003)S(0.073)NQS(0.237)QPCS(0.688)PKPIR 102.39 0.0065567 147660000 101200 75636 89514 89832 54854 102510 110190 110780 63693 TRUE FALSE 96416.47656 83343.39439 93618.30544 80801.91669 64420.52023 98960.053 93378.49172 101079.5159 73570.18514 1.310537365 1.132841983 1.272503328 1.098297042 0.875633521 1.345110833 1.269243669 1.373919553 1 16.1668336 EEASLLSHS(ph)PGTSNQSQPCSPKPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.656)PGT(0.339)S(0.005)NQSQPCSPKPIR;EEASLLSHS(0.903)PGT(0.083)S(0.014)NQSQPCSPKPIR;EEASLLSHS(0.876)PGT(0.097)S(0.021)NQS(0.006)QPCSPKPIR 203.94 3.00E-25 1727440000 951630 707230 835060 937590 730540 883300 1099730 1008190 739010 TRUE FALSE 906648.3358 779297.5411 873348.327 843341.6719 857945.9447 852711.0995 931945.9906 919907.5388 853611.8965 1.062131795 0.912941284 1.023121082 0.987968508 1.005077305 0.998944723 1.09176781 1.077664853 1 19.70322076 1.755592596 25 1.064544288 0.994223373 0.271634977 0.043858188 6.73236818 9892.877176 0.018948387 0.010508036 56.96296618 -1.755592596 -0.070320915 EEASLLSHSPGTSNQSQPCS(ph)PKPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHSPGT(0.009)S(0.008)NQS(0.032)QPCS(0.951)PKPIR;EEASLLSHSPGTSNQS(0.012)QPCS(0.988)PKPIR 225.8 4.24E-34 1650840000 1000940 770390 951940 1085790 639710 956410 1065760 1092430 700370 TRUE FALSE 953627.5499 848893.6169 995587.3906 976644.3263 751275.2215 923289.2819 903158.738 996771.0379 808979.8026 1.178802668 1.049338456 1.230670268 1.207254277 0.928669936 1.141300783 1.116416918 1.232133404 1 19.62574416 EEASNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EEASNFR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 192.56 0.0011853 2036148000 1967161 1721238 1647678 1930935 1906976 1724049 2172350 1985576 2016317 FALSE TRUE 1874177.198 1896634.109 1723225.666 1736833.745 2239552.011 1664344.751 1840918.11 1811708.439 2328997.142 0.804714254 0.814356563 0.739900292 0.745743184 0.961595001 0.714618632 0.790433821 0.777892083 1 21.15127744 -1.029522485 4.508044725 1.000008674 0.794319741 0.483358887 0.067039728 5.30E-06 1.14E-06 0.058832092 0.013866272 0.0934281 1.029522485 -0.205688933 EEAT(ph)SPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.642)S(0.358)PGAK;EEAT(0.678)S(0.322)PGAK 113.27 0.02043 173283000 1181210 1045960 992680 1250560 749050 1109220 1138240 1223020 854940 TRUE FALSE 1125376.544 1152544.513 1038195.36 1124851.333 879684.0828 1070807.433 964580.5828 1115925.885 987519.7288 1.139599049 1.167110367 1.05131607 1.139067201 0.890801528 1.084340294 0.976770949 1.130028953 1 19.91345005 3.333207539 1.522256836 1.021330005 1.151573395 0.303373419 0.072878267 0.381443326 1.826387304 0.021547391 0.033996173 2153.810746 -3.333207539 0.13024339 EEATS(ph)PGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.127)S(0.873)PGAK;EEAT(0.125)S(0.875)PGAK;EEAT(0.395)S(0.605)PGAK 175.33 5.66E-05 851411000 3767450 3396370 3113720 3889410 1939932 3463680 3528720 3946180 2477870 TRUE FALSE 3589370.105 3742463.964 3256487.142 3498439.117 2278255.527 3343731.893 2990348.955 3600631.559 2862125.424 1.254092527 1.307582097 1.137786316 1.222322085 0.796001289 1.16826882 1.044800109 1.258027174 1 21.44865546 3.355032818 1.892612466 1.067728614 1.277031426 0.293789156 0.128076462 0.361639774 2.647289451 0.036636395 0.055619628 2264.815444 -3.355032818 0.209302813 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK 224.91 9.73E-33 2297080000 2132023 2041667 1895702 2289630 1376962 2224205 2095000 2165288 1493828 TRUE FALSE 2031246.498 2249715.188 1982621.812 2059472.042 1617103.737 2147180.223 1775369.273 1975683.904 1725483.217 1.177204437 1.303817485 1.149024107 1.193562489 0.937188911 1.244393572 1.028911354 1.145003257 1 20.71856901 3.187265844 2.137188697 1.084313032 1.234666088 0.314975972 0.093329724 0.318258077 2.982110504 0.026121458 0.034521421 1539.096475 -3.187265844 0.150353056 EEATYGVWAERDS(ph)DDERPSFGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEATYGVWAERDSDDERPSFGGKR 24 3 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(0.966)DDERPS(0.034)FGGKR;EEATYGVWAERDS(1)DDERPSFGGKR 148.19 9.13E-07 381380000 292780 166075 311970 224300 277200 300560 435170 328050 421330 TRUE FALSE 278940.8696 182998.2313 326274.1331 201752.9379 325543.5922 290151.5318 368776.8241 299324.2029 486667.7045 0.573164948 0.376022961 0.670424871 0.414559947 0.668923763 0.596200506 0.757758981 0.61504842 1 18.89257751 0.546078601 0.286121191 1.0963081 0.447824937 0.663539037 0.100818337 1.760390429 0.327993514 0.363056692 0.137510486 3.516240738 -0.546078601 -0.648483164 EEATYGVWAERDSDDERPS(ph)FGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(0.02)DDERPS(0.98)FGGK 239.47 2.53E-37 195430000 219250 221950 185440 250030 153580 228120 238030 245250 170650 TRUE FALSE 208886.487 244566.9573 193942.6074 224896.5094 180364.3034 220220.1472 201714.1518 223774.6098 197113.5304 1.059726781 1.240741601 0.983913215 1.140949121 0.915027512 1.117224915 1.023339957 1.13525748 1 17.58866728 3.729259546 24.99123299 1.047588483 1.150234194 0.216365279 0.083075663 809.0511132 2173856.007 0.019550805 0.030773599 5361.169592 -3.729259546 0.102645711 EEAYHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EEAYHSR 7 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 173.68 0.00085451 1062854000 2286967 1748186 1870952 2351414 2218370 2001147 2439196 2124497 2123632 FALSE TRUE 2178866.602 1926328.141 1956737 2115045.397 2605253.026 1931846.778 2067051.851 1938464.78 2452954.005 0.888262315 0.785309524 0.797706356 0.862244214 1.062088005 0.787559316 0.842678602 0.790257288 1 21.22608875 -2.444011792 2.204321474 2.431013673 0.849745671 0.241399819 0.082357675 3051646.056 396464.0681 21743863.54 0.019827232 0.003597396 2.444011792 -1.581268002 EEDCHS(ph)PTSKPPKPDQPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEDCHSPTSKPPKPDQPLK 19 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 EEDCHS(0.993)PT(0.005)S(0.001)KPPKPDQPLK 105.16 0.00016094 129870000 319720 361560 232300 404380 142820 317940 283200 341420 120750 TRUE FALSE 304607.4692 398403.3751 242951.1848 363730.9541 167727.7628 306929.6581 239992.6387 311523.4548 139475.2933 2.183952885 2.856444074 1.741894059 2.607852226 1.202562539 2.200602349 1.720682086 2.233538625 1 17.08965006 0.032800682 0.122496285 7.36E-13 3.074498982 0.380107739 0.45494992 19.64259763 0.820623077 13.75634082 6.121476264 1.078451656 -0.032800682 3.074498982 EEDEENDNDNES(ph)DHDEADS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEDEENDNDNES(0.998)DHDEADS(0.002) 224.9 4.28E-26 0 132950 135150 131340 162190 111250 139800 128710 121130 97963 TRUE FALSE 126665.717 148921.9387 137362.0689 145886.3531 130651.9648 134958.6909 109072.9256 110523.215 113154.6017 1.119404028 1.316092641 1.21393268 1.289265755 1.15463236 1.192692908 0.963928324 0.976745209 1 16.78793573 1.792556226 3.657950509 0.975114199 1.222796062 0.785705952 0.057591602 0.094580747 2.353139218 0.029314311 0.015123697 62.02349373 -1.792556226 0.247681863 EEDEEPES(ph)PPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEK 119.25 0.00020556 0 288090 431360 286090 346010 166830 352410 236250 314020 132900 TRUE FALSE 274472.5566 475316.0744 299207.5095 311228.4174 195925.0992 340205.9533 200205.7235 286522.7441 153509.4532 1.787984719 3.096330971 1.949114554 2.027421835 1.27630641 2.216188946 1.304191496 1.866482735 1 17.22796798 3.221365117 2.118274413 1.594843011 2.431675476 0.341682782 0.474696053 0.302156129 2.7839188 0.136101981 0.18416477 1664.811691 -3.221365117 0.836832464 EEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 166.62 2.04E-05 13402690000 10278200 11909090 7998550 11852660 4887740 11747790 9750280 11395960 4262500 TRUE FALSE 9792369.855 13122639.81 8365291.429 10661208.1 5740160.308 11340961.09 8262695.71 10398069.33 4923506.73 1.988901487 2.665303518 1.699051487 2.165368848 1.165868277 2.303431621 1.67821355 2.111923452 1 22.2312548 -1.398169198 0.15146389 2.03E-11 2.463400734 0.356034855 0.405554915 33.44710711 0.911697104 16.22485297 2.383344745 0.039978896 1.398169198 2.463400734 EEDEPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEDEPEER 8 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 195.81 0.00036559 1769060000 1345530 1224120 1215240 1407460 1066620 1274940 1345530 1308940 1115030 FALSE TRUE 1281929.463 1348859.22 1270959.956 1265979.447 1252638.19 1230788.508 1140244.686 1194322.274 1287943.158 0.995330777 1.047297167 0.986813703 0.982946677 0.972588101 0.955623314 0.885322213 0.927309771 1 20.29663749 2.694942867 1.168948767 0.926876242 1.017431514 0.425691379 0.033045683 0.330323012 0.932131961 0.015802577 0.014067726 495.3850167 -2.694942867 0.090555272 EEDEPEERS(ph)GDET(ph)PGSEVPGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 2 EEDEPEERS(1)GDET(0.986)PGS(0.014)EVPGDK;EEDEPEERS(1)GDET(0.998)PGS(0.002)EVPGDK 139.19 7.93E-07 434950000 527160 511030 424320 581440 262420 510940 518200 471900 273680 TRUE FALSE 502242.1915 563104.538 443775.4917 522992.5465 308185.9649 493246.0197 439139.0726 430577.9343 316120.8966 1.588766187 1.781294891 1.403815744 1.654406754 0.97489906 1.560308176 1.389149143 1.362067294 1 18.27011688 6.129357041 0.048533677 4.26E-08 3.606939985 0.440123187 0.195160953 302.1156571 1.590695818 34.99044125 96.27852576 1346967.265 -6.129357041 3.606939942 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;EEDEPEERS(0.884)GDET(0.115)PGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK 316.7 1.30E-67 15165910000 6008518 5770235 4916551 6587320 3101345 6211700 5578387 6129590 3086803 TRUE FALSE 5724507.262 6358228.507 5141979.726 5925150.079 3642218.586 5996587.271 4727301.609 5592850.605 3565488.644 1.605532322 1.78326988 1.442152883 1.661805904 1.021520176 1.681841641 1.325849577 1.568607045 1 21.76566838 -2.090379336 0.087181264 1.24E-12 2.083462196 0.390579628 0.209685599 94.59795652 1.134943076 26.04473629 6.25486481 0.008121209 2.090379336 2.083462196 EEDEPEERS(ph)GDETPGSEVPGDKAAEEQGDDQDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEDEPEERSGDETPGSEVPGDKAAEEQGDDQDSEK 35 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 EEDEPEERS(0.961)GDET(0.039)PGSEVPGDKAAEEQGDDQDSEK;EEDEPEERS(1)GDETPGSEVPGDKAAEEQGDDQDSEK;EEDEPEERS(1)GDETPGSEVPGDKAAEEQGDDQDSEK;EEDEPEERS(0.917)GDET(0.074)PGS(0.01)EVPGDKAAEEQGDDQDSEK;EEDEPEERS(0.998)GDET(0.002)PGSEVPGDKAAEEQGDDQDSEK 423.18 1.44E-208 2943480000 1186467 606177 1062636 936402 596156 1128802 1459780 1233678 640771 TRUE FALSE 1130385.056 667947.1255 1111358.912 842273.0919 700125.4177 1089711.304 1237063.75 1125650.614 740138.4941 1.52726154 0.902462351 1.501555345 1.137993901 0.945938393 1.472307294 1.671394962 1.520864842 1 19.49743573 2.090281677 11.58324728 1.496937542 1.202257086 0.106457158 0.265177754 0.661032599 80.48757498 0.091482439 0.067560695 123.1066965 -2.090281677 -0.294680456 EEDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEDFTR 6 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 155.73 0.022892 1354940000 2248830 2751980 1984010 2553450 1692670 2181270 1994930 2238590 1616340 FALSE TRUE 2142532.263 3032409.891 2074978.821 2296772.355 1987871.112 2105732.073 1690566.789 2042567.192 1866993.752 1.147584056 1.624220696 1.111401052 1.230198201 1.064744384 1.127873123 0.905502114 1.094040722 1 20.83228567 3.036131291 1.199672881 1.01365941 1.36932811 0.423942332 0.144398279 0.355525712 1.084088789 0.056963565 0.071171033 1086.75411 -3.036131291 0.3556687 EEDGADAS(ph)EEDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEDGADASEEDLTR 14 0 E5RHA3;Q86X53 E5RHA3 ERICH1 Glutamate-rich protein 1 1 EEDGADAS(1)EEDLTR;EEDGADAS(1)EEDLTR 298.75 1.01E-43 674960000 1002670 807980 669610 1035170 825590 845460 1075040 981360 905500 TRUE FALSE 955275.7762 890314.0806 700312.2808 931112.7449 969572.6346 816181.5082 911022.9035 895426.9159 1045920.315 0.913335139 0.851225536 0.669565617 0.890232966 0.927004305 0.780347696 0.871025154 0.856113896 1 19.99634151 0.174645703 1.100758355 1.000608835 0.844619755 0.306284309 0.073785451 6.951914688 8.061552194 0.077842309 0.021179697 1.495015525 -0.174645703 -0.155989081 EEDRPPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEDRPPLR 8 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 103.42 0.004356 284950000 364070 349630 357470 402020 370340 364770 424000 383720 390060 FALSE TRUE 346861.1326 385257.6945 373860.3531 361608.1858 434927.1787 352137.9234 359311.0127 350119.4426 450548.5126 0.769864116 0.855085931 0.82978934 0.802595449 0.965328187 0.781576042 0.797496835 0.77709599 1 18.78132293 -2.390460207 2.333565689 2.44790763 0.822369468 0.491319339 0.056806574 5839277.673 626254.7003 44774399.99 0.013961448 0.004069488 2.390460207 -1.625538162 EEEADMSS(ph)PTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EEEADMSSPTQR 12 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 EEEADMS(0.19)S(0.81)PTQR;EEEADMS(0.028)S(0.972)PTQR;EEEADMS(0.003)S(0.995)PT(0.003)QR;EEEADMS(0.001)S(0.989)PT(0.01)QR 185.2 3.88E-05 642744000 1268100 1428760 1016270 1504260 999880 1236200 1114860 1173810 801002 TRUE FALSE 1208159.426 1574352.268 1062866.985 1353048.927 1174258.755 1193390.084 944767.6312 1071024.974 925217.2992 1.30581154 1.701602715 1.148775521 1.46241205 1.269170774 1.289848433 1.02113053 1.157592897 1 19.81943272 2.180252184 0.700761002 1.010283597 1.467703491 0.491082517 0.147843455 0.505700252 0.478027102 0.117883093 0.073426816 151.444039 -2.180252184 0.457419894 EEEEEEEEDQEGDRETTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEEEEEEEDQEGDRETTIR 19 1 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 271.68 2.26E-39 440570000 283470 295200 283670 347200 227490 329410 326000 312330 237010 FALSE TRUE 270070.9349 325281.2156 296676.5501 312298.7964 267164.184 318002.4491 276262.7126 284980.7294 273764.3003 0.986508959 1.188179815 1.083693344 1.140757929 0.975891245 1.161592102 1.009126143 1.040971117 1 18.0625748 1.617275445 19.16461091 1.018775904 1.089974891 0.200773909 0.068356103 0.284269523 561.3032764 0.029944295 0.016140231 41.42623312 -1.617275445 0.071198987 EEEEGISQES(ph)S(ph)EEEQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEEEGISQESSEEEQ 15 0 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 EEEEGISQES(1)S(1)EEEQ;EEEEGISQES(1)S(1)EEEQ 313.04 4.70E-56 701730000 652180 598870 491860 631320 460660 580300 525940 507990 412870 TRUE FALSE 621352.7439 659895.5339 514412.2675 567858.5142 540998.9581 560204.0655 445698.1934 463507.7026 476895.771 1.302910996 1.383731151 1.078668126 1.190739253 1.134417605 1.174688684 0.934581979 0.971926636 1 18.86331446 2.976155976 0.491300879 0.954400318 1.384461547 0.680061959 0.080588553 0.590161777 0.290301319 0.068989787 0.114432104 946.5770611 -2.976155976 0.430061229 EEEEIS(ph)ELQEDDRDQFSDQLASVGMLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEEEISELQEDDRDQFSDQLASVGMLGR 28 1 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 EEEEIS(1)ELQEDDRDQFSDQLASVGMLGR 63.25 0.028953 43035000 37133 42568 46394 48094 50145 41175 47489 38386 57841 TRUE FALSE 35377.79668 46905.7276 48521.21079 43259.49975 58890.27212 39749.09943 40243.68085 35024.71834 66810.68687 0.52952302 0.702069232 0.726249243 0.647493714 0.881449883 0.594951216 0.602353946 0.524238262 1 16.02779127 -2.114308618 2.432637608 1.661663803 0.651215105 0.525534751 0.104202417 8900947.076 2308004.75 32597796.27 0.024510459 0.007685841 2.114308618 -1.010448698 EEEITLYPDKHGCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEEITLYPDKHGCVR 15 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 92.935 0.0030348 115611000 217199 191657 208872 211703 188991 200832 238730 240710 189543 FALSE TRUE 206932.4337 211187.0662 218448.9878 190422.2122 221950.9706 193877.1375 202307.3539 219632.1563 218936.3604 0.945171617 0.964604809 0.997773908 0.869760564 1.013769345 0.885541064 0.924046392 1.003178074 1 17.74015205 1.227775288 24.96545213 1.001589096 0.94318268 0.233964672 0.044108648 327.2816566 757553.3389 0.036850499 0.009583718 16.89566493 -1.227775288 -0.058406416 EEEKLELQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEEKLELQK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 78.655 0.026591 136090000 203660 197700 178870 230050 127150 227090 220330 241390 143880 FALSE TRUE 194033.3954 217845.8548 187071.3664 206924.9369 149324.9197 219225.8164 186714.6119 220252.6119 166192.1756 1.167524252 1.310806926 1.125632815 1.245094339 0.898507521 1.319110335 1.123486176 1.325288698 1 17.34249294 -1.852764049 2.697245577 0.923581071 1.190845502 0.178568656 0.12765225 29026270.96 22329737.52 14356637.02 0.027408984 0.014035761 1.852764049 0.267264431 EEEMGEEEEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 198.62 6.44E-07 240820000 84217 87649 71734 101440 62505 82752 70248 75631 63768 FALSE TRUE 80236.22931 96580.53275 75023.07485 91243.05848 73405.85221 79886.27749 59530.37741 69008.34869 73656.81576 1.089325251 1.311223296 1.018548984 1.238759204 0.996592799 1.084574138 0.808212747 0.936890198 1 16.16853141 2.317912245 1.42074304 0.905326763 1.174546682 0.470948496 0.104022403 0.290443254 1.166695742 0.052908262 0.033671553 207.9276499 -2.317912245 0.269219919 EEEMMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEEMMIR 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 105.12 0.042161 0 287020 258290 230330 300390 249610 263880 313040 276400 214690 FALSE TRUE 273453.1334 284610.0447 240890.8583 270194.2265 293141.905 254741.7694 265279.9986 252196.9507 247983.0287 1.102709064 1.147699688 0.971400582 1.089567411 1.182104705 1.027254852 1.06975062 1.016992784 1 17.91988186 1.462709798 1.249088858 1.00204948 1.097207236 0.244229497 0.057418063 0.582678326 1.747184564 0.050447813 0.017094405 29.02082791 -1.462709798 0.095157757 EEEPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 89.298 0.028822 2681380000 5993020 6220320 4391440 7272270 3159610 6138640 5897930 6351450 3388960 FALSE TRUE 5709741.822 6854177.68 4592791.868 6541247.603 3710644.984 5926057.358 4998092.456 5795283.367 3914502.608 1.458612343 1.750970268 1.173275976 1.671029057 0.947922471 1.513872374 1.276814184 1.480464812 1 21.90039757 -0.298092037 0.056302472 2.18E-10 2.359838661 0.243027685 0.231754026 139.979544 2.090355861 54.1778279 33.68117866 0.503393916 0.298092037 2.359838661 EEERKDDNDEEEEDIDFFEDIDS(ph)DEDEGGLFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEERKDDNDEEEEDIDFFEDIDSDEDEGGLFGSK 34 2 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 1 EEERKDDNDEEEEDIDFFEDIDS(0.999)DEDEGGLFGS(0.001)K 40.535 0.080163 17187000 16240 15370 12317 14893 12994 16309 17012 16129 13939 TRUE FALSE 15472.36738 16936.22047 12881.74663 13395.92735 15260.14949 15744.21524 14416.50695 14716.65925 16100.58893 0.960981456 1.051900682 0.80007922 0.832014742 0.947800702 0.977865798 0.895402461 0.914044779 1 13.97482584 3.763812699 24.99555271 0.907182422 1.006441068 0.283852905 0.063858688 876.3512053 867445.5853 0.016077016 0.028969138 5805.140021 -3.763812699 0.099258646 EEFEHQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEFEHQQK 8 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 83.005 0.023797 0 262480 239170 191110 311590 235290 219540 281020 258480 242920 FALSE TRUE 250073.0906 263541.6949 199872.5825 280268.3812 276324.5015 211937.2748 238145.2377 235846.1209 280590.7929 0.891237692 0.939238569 0.712327659 0.998850954 0.984795326 0.755325121 0.848727912 0.840534069 1 18.09810814 2.244054052 24.99908299 0.845231693 0.904123633 0.037174736 0.09760278 355.1775708 1616318.118 0.032148474 0.026183161 175.4098801 -2.244054052 0.058891939 EEFKQEVEATAGLLYVDDPNWSGIGVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEFKQEVEATAGLLYVDDPNWSGIGVVR 28 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 80.984 0.0049902 59479000 87498 76896 81644 94655 62067 82812 103860 96235 71168 FALSE TRUE 83362.14294 84731.78982 85387.45816 85140.09957 72891.46515 79944.19968 88014.24948 87808.15323 82204.36996 1.014084081 1.030745566 1.038721642 1.035712573 0.886710344 0.972505473 1.070676042 1.068168922 1 16.32692747 -0.817216224 4.441976913 0.999999913 1.015804768 0.007056541 0.053167192 63.42563635 15970379.75 3.85780186 0.012627672 0.152329416 0.817216224 0.015804856 EEFTAFLHPEEYDYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EEFTAFLHPEEYDYMK 16 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;;; 254.53 1.39E-26 1688643000 4135175 5009600 3286386 5075700 2338019 4042549 3508063 4308650 1845185 FALSE TRUE 3939713.473 5520083.935 3437070.049 4565480.993 2745768.773 3902554.514 2972843.559 3931361.764 2131326.866 1.848479244 2.589975298 1.612643327 2.142083913 1.288290791 1.831044584 1.394832302 1.844560695 1 21.02332043 2.063020273 0.21805884 0.866426237 2.501817131 0.426496428 0.338752336 2.357115299 0.422956888 1.00074783 1.46697648 115.6166211 -2.063020273 1.635390894 EEFTAFLHPEEYDYMKDIVVQETMEDIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEFTAFLHPEEYDYMKDIVVQETMEDIDK 29 1 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 262.95 1.83E-58 45069000 86456 80529 77378 100504 41262 83160 80222 96670 30537 FALSE TRUE 82369.39622 88734.99665 80925.85784 90401.14697 48458.07974 80280.14835 67982.66052 88205.06232 35272.522 2.335228431 2.515697535 2.294303136 2.562934031 1.373819534 2.275996833 1.927354685 2.500673536 1 15.10625711 2.775745012 24.99993981 1.914772791 2.424241282 0.320686413 0.428922161 719.512248 483743.7295 0.115559122 0.122566226 596.6848515 -2.775745012 0.509468491 EEGAQTLEEDRAQT(ph)PHEDGGPQPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEGAQTLEEDRAQTPHEDGGPQPHR 25 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EEGAQT(0.003)LEEDRAQT(0.997)PHEDGGPQPHR;EEGAQTLEEDRAQT(1)PHEDGGPQPHR 227.74 2.82E-34 382520000 166936 134059 193694 167705 236436 140767 236777 159561 91133 TRUE FALSE 159045.2661 147719.7645 202575.0615 150846.9748 277670.3635 135892.2035 200652.3199 145588.993 105265.4402 1.510897269 1.403307337 1.924421359 1.43301519 2.637811261 1.290947943 1.90615571 1.383065446 1 16.68367234 0.984975182 5.417795799 1.0003504 1.696906153 0.278315463 0.385389033 0.192471989 23.54004665 0.337794973 0.085187622 9.659956761 -0.984975182 0.696555753 EEGFPIRPHYFWPLLVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEGFPIRPHYFWPLLVGR 18 1 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 148.13 4.30E-08 174113000 488330 529170 407700 477850 410180 355730 409000 441380 326750 FALSE TRUE 465247.6087 583093.0246 426393.4483 429815.6101 481715.2621 343410.9809 346599.5382 402730.4273 377420.7212 1.232702877 1.544941737 1.129756328 1.138823562 1.276334963 0.909889049 0.918337332 1.067059662 1 18.52581411 2.873196916 0.903304563 0.960286657 1.374229357 0.525322393 0.12952148 0.377229402 0.670799485 0.07109011 0.076552211 746.7872861 -2.873196916 0.413942699 EEGGENLDQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEGGENLDQAR 11 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 178.84 1.71E-05 228110000 211543 189832 132915 324330 207128 195154 210372 149317 167262 FALSE TRUE 201543.7816 209176.0966 139009.2842 291727.7322 243251.0576 188395.768 178275.8877 136242.0119 193200.1367 1.043186537 1.082691245 0.719509244 1.509976842 1.259062554 0.975132685 0.922752389 0.705185898 1 17.55973659 1.834533478 2.761580462 0.856335366 1.108125472 0.220690298 0.208658871 0.408551938 5.688369989 0.114530402 0.056859781 68.31773788 -1.834533478 0.251790106 EEGINKSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEGINKSEK 9 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 82.171 0.017518 164720000 192030 131300 167740 190360 118820 195650 206850 207290 138950 FALSE TRUE 182953.1225 144679.6193 175431.0449 171224.6511 139542.1704 188874.5914 175291.2334 189138.5887 160497.6563 1.139911489 0.901443813 1.093044278 1.066835835 0.869434318 1.176805916 1.092173166 1.178450782 1 17.29219271 2.193038938 24.99998383 1.11865178 1.016182736 0.207595884 0.094410288 186.0530055 102177.0479 0.032434074 0.023954246 155.9692336 -2.193038938 -0.102469045 EEGLGFPSFLDPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEGLGFPSFLDPDR 14 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 73.067 0.085779 9777900 25558 34201 17528 28241 19028 23149 20842 22134 15795 FALSE TRUE 24349.92399 37686.12078 18331.67614 25402.16103 22346.47718 22347.34433 17662.17011 20195.82962 18244.40793 1.334651367 2.065625858 1.004783285 1.392325863 1.224839812 1.224887341 0.968086779 1.10695999 1 14.15516671 3.72337289 24.98695556 1.140013942 1.700138633 0.548252 0.214415222 500.8268331 823963.9902 0.054900969 0.085404765 5288.991757 -3.72337289 0.560124691 EEGS(ph)DIEDEDMEELLNDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEGSDIEDEDMEELLNDTR 19 0 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR 261.15 4.03E-31 181983000 231692 224372 221129 255772 201233 236722 257772 244132 204136 TRUE FALSE 220740.3783 247235.7619 231267.9834 230061.3126 236327.9715 228524.2578 218444.1471 222754.5079 235792.3683 0.936164219 1.048531654 0.980811996 0.975694482 1.002271503 0.969175803 0.926425858 0.944706181 1 17.8471575 2.007199764 6.506794263 0.94850808 0.990818356 0.145195627 0.033222095 0.191231889 38.06675257 0.012467057 0.008685041 101.6716249 -2.007199764 0.042310276 EEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.055)LS(0.625)DT(0.32)EADAVSGQLPDPTTNPSAGK 200.8 2.79E-25 152200000 233120 301690 169020 287320 107050 235650 179970 234420 99196 TRUE FALSE 222100.8796 332432.554 176769.7342 258438.0477 125719.4861 227489.3814 152512.2711 213892.9421 114578.8091 1.938411487 2.901344121 1.542778596 2.255548385 1.097231566 1.985440268 1.331068741 1.866775749 1 16.80598072 3.265480594 1.44966861 1.523466376 2.377837511 0.32709395 0.464811922 0.382585317 1.675160323 0.142680376 0.214529096 1842.810143 -3.265480594 0.854371135 EEGWWVVIGDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEGWWVVIGDAK 12 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 133.81 0.00036443 53438000 180364 203315 194974 221420 133156 231490 222030 220860 157621 FALSE TRUE 171838.5512 224033.0296 203913.7508 199162.4409 156378.3642 223473.4433 188155.2456 201520.3275 182064.0597 0.943835656 1.230517599 1.120011007 1.093914094 0.858919462 1.227444031 1.033456279 1.106864957 1 17.47408663 2.976868767 24.96940648 1.05288474 1.104765171 0.045560147 0.113590892 2644.158832 2854286.079 0.032726318 0.034948899 948.1319182 -2.976868767 0.051880431 EEHDKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEHDKEER 8 1 Q9Y6I3 Q9Y6I3 EPN1 Epsin-1 0 ;; 133.13 0.00056025 215072000 458681 457005 391586 498321 286851 464388 464803 498862 300296 FALSE TRUE 437000.0581 503574.3291 409540.6054 448228.8263 336877.7236 448306.1271 393888.7657 455178.9986 346864.37 1.259858596 1.451790304 1.180693784 1.292230812 0.971208786 1.292453668 1.13556998 1.312267958 1 18.40401213 7.99999975 0.041782262 0.457412304 2.520810799 0.271611321 0.124812218 772.6831388 2.455185744 32.32008467 110.6774036 99999942.4 -7.99999975 2.063398494 EEHETDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEHETDEKR 9 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 131.44 0.00021622 65645000 98816 87323 79633 108121 70124 91400 86850 114632 74471 FALSE TRUE 94145.16351 96221.31298 83284.25182 97252.47166 82353.6034 88234.79508 73599.43739 104594.2144 86019.58233 1.094461993 1.11859777 0.968201072 1.130585258 0.957382042 1.025752424 0.855612587 1.215934925 1 16.39237751 3.749132271 24.5784949 1.008693551 1.106529891 0.103138439 0.0978495 955.5258423 2221534.706 0.023519878 0.041827161 5612.188779 -3.749132271 0.097836341 EEHGGLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEHGGLIR 8 0 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 128.69 0.0011229 333460000 269832 294734 235947 337370 295897 245052 264824 257168 270259 FALSE TRUE 257077.5761 324767.7297 246765.4033 303456.9266 347501.3431 236565.7878 224420.235 234649.0066 312169.3854 0.8235195 1.040357398 0.790485598 0.972090605 1.113182007 0.757812261 0.71890533 0.751672065 1 18.25196953 2.185836193 24.99999073 0.775809466 0.943164058 0.233812907 0.120748156 112.26976 53233.38619 0.041798392 0.030870187 153.4038266 -2.185836193 0.167354592 EEHGGLIRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;EEHGGLIRS(1)PR;EEHGGLIRS(1)PR 145.1 2.20E-05 26665580000 11130610 10064920 9497770 12215880 10278230 10259850 11380640 10718310 9239180 TRUE FALSE 10604488.12 11090546.79 9933252.149 10987916.53 12070750.06 9904548.822 9644314.348 9779757.955 10671944.85 0.99367906 1.039224523 0.930781811 1.029607695 1.13107313 0.928092205 0.903707289 0.916398847 1 23.34731978 2.065476822 24.99999356 0.925974068 1.020737184 0.376088315 0.05526294 53.88322508 20572.76477 0.019711323 0.014557776 116.2724496 -2.065476822 0.094763116 EEHLCTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EEHLCTQR 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 182.53 0.00022805 3674142000 3799536 3842517 2885643 3910677 3153631 3285871 3419652 3301013 2857547 FALSE TRUE 3619939.463 4234073.851 3017952.586 3517568.318 3703623.248 3172080.463 2897921.281 3011958.802 3300680.794 1.096725097 1.282788041 0.914342457 1.065709936 1.122078589 0.961038241 0.877976836 0.912526533 1 21.65433219 2.92511608 0.673790228 0.916182389 1.17954329 0.35338762 0.098082595 0.668698407 0.67073884 0.068138937 0.085627436 841.6200635 -2.92511608 0.2633609 EEHSKT(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.003)KT(0.997)PEER;EEHS(0.002)KT(0.998)PEER;EEHS(0.005)KT(0.995)PEER;EEHS(0.008)KT(0.992)PEER 141.46 5.49E-05 528005000 415894 377002 328790 437229 255038 352091 341112 383525 227946 TRUE FALSE 396235.5148 415418.9324 343865.3467 393277.9102 299516.5465 339898.0004 289069.0994 349941.5178 263294.7015 1.504912604 1.577771714 1.306009368 1.493679546 1.137571492 1.290941285 1.097891822 1.329086821 1 18.00631896 2.99972508 0.336879313 1.033643686 1.679083549 0.635084249 0.112958544 1.18071726 0.24470026 0.117728686 0.282969074 999.3671738 -2.99972508 0.645439863 EEHSKTPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 145.91 1.78E-05 186507000 192177 158524 216779 198344 167002 179408 235954 232209 208885 FALSE TRUE 183093.1741 174677.7758 226718.5316 178406.0843 196127.0959 173195.056 199954.8837 211875.5489 241277.819 0.758847932 0.723969475 0.93965758 0.739421821 0.812868322 0.717824194 0.828732971 0.878139358 1 17.88033577 1.004892295 1.720984044 0.998292261 0.779307165 0.541330688 0.06388272 0.269844401 1.649122277 0.056685004 0.016316514 10.11328614 -1.004892295 -0.218985096 EEHYFCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEHYFCK 7 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 88.254 0.018743 363660000 864990 658100 623980 715270 741890 666900 904610 791290 615450 FALSE TRUE 824103.6369 725161.1382 652590.1002 643369.7007 871275.3811 643805.0858 766595.1302 722000.4527 710890.8427 1.159254821 1.020073821 0.917989178 0.905018973 1.225610641 0.905631423 1.078358426 1.01562773 1 19.43926853 4.466720349 2.590348509 1.010134716 1.157513052 0.197465224 0.095345511 0.472448825 5.698748034 0.022286014 0.116019067 29290.0659 -4.466720349 0.147378336 EEIDHAEYYLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEIDHAEYYLYK 12 0 Q92552;Q92552-2;G5EA06;D6RH20;E5RJ73;D6RJC7 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 ;; 114.82 0.0010168 405640000 843710 767470 754800 730000 662710 668170 777430 840950 626200 FALSE TRUE 803829.5004 845676.0655 789408.3266 656619.0131 778286.4142 645031.1054 658818.775 767311.9598 723307.8978 1.111324103 1.169178531 1.091386295 0.907800143 1.076009838 0.891779431 0.910841395 1.060837248 1 19.46425038 3.388869135 5.120666915 0.965626586 1.13891689 0.557673791 0.06335494 0.127425449 5.611486352 0.016874921 0.02311148 2448.32538 -3.388869135 0.173290304 EEIDSILNKVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEIDSILNKVEER 13 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 161.21 1.03E-06 0 83236 79011 62868 85554 46266 81353 67075 81120 51814 FALSE TRUE 79301.59924 87062.31073 65750.55998 76953.94938 54334.77575 78535.72521 56841.47683 74016.70276 59849.05049 1.325026857 1.454698279 1.098606568 1.285800673 0.907863622 1.312230095 0.949747345 1.236723092 1 15.86904074 3.731989822 24.79999642 1.111895836 1.389862571 0.40525437 0.139437147 356.9933243 1347392.376 0.032252272 0.05128435 5394.979793 -3.731989822 0.277966735 EEIIPVAAEYDKTGEYPVPLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEIIPVAAEYDKTGEYPVPLIR 22 1 B7Z9I1;Q5T4U5;P11310;P11310-2;E9PJM9 B7Z9I1 ACADM "Medium-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 115.63 0.00017273 33901000 55155 30035 45161 34890 43216 43819 61249 51047 62040 FALSE TRUE 52547.93246 33095.60065 47231.67652 31382.79091 50752.85672 42301.53704 51904.34013 46577.05406 71660.84634 0.733286518 0.461836586 0.659100177 0.437934974 0.708236915 0.590301946 0.72430543 0.649965168 1 16.12889746 0.240489276 0.524210053 1.025839204 0.583013174 0.608518091 0.098025023 1.750243331 0.703492383 0.188600143 0.042267181 1.739759738 -0.240489276 -0.44282603 EEIKDDNPHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEIKDDNPHLK 11 1 Q9HAV7 Q9HAV7 GRPEL1 "GrpE protein homolog 1, mitochondrial" 0 ;; 114.82 0.00072477 543216000 1245935 1084653 1062682 1204699 603696 1035730 1025951 1236493 531404 FALSE TRUE 1187042.122 1195180.374 1111407.021 1083600.368 708980.3913 999862.4104 869423.3321 1128219.118 613811.4183 1.933887325 1.947145879 1.810665276 1.765363653 1.155045948 1.628940715 1.416433951 1.838054953 1 19.22743596 8 0.054967265 1.28E-12 4.888173661 0.55298723 0.217436341 272.6114403 1.125571122 21.86111123 109.4655113 100000000 -8 4.888173661 EEIQPGDIVIIDQFIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 170.56 3.30E-13 0 17808 12675 13205 17281 17959 13084 13926 14827 14800 FALSE TRUE 16966.25113 13966.59691 13810.46231 15543.88105 21091.04391 12630.8978 11801.33293 13528.66928 17095.10841 0.99246233 0.816993761 0.80786047 0.909258992 1.233747304 0.738860351 0.690333904 0.79137663 1 14.06129595 EEIVDKYDLFVGSQATDFGEALVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 267.71 1.24E-44 1859483000 4743635 4607013 4012883 5267305 3065633 4345875 4757070 4752912 3200478 FALSE TRUE 4519412.775 5076472.862 4196877.655 4737825.494 3600278.425 4195376.259 4031291.602 4336721.829 3696791.782 1.222522944 1.373210384 1.135275639 1.281604638 0.973892671 1.134869505 1.090483814 1.173104163 1 21.81784236 3.092292222 1.658562286 1.088853522 1.284259492 0.445448942 0.089603487 0.288092012 1.63046429 0.027987487 0.035553201 1236.77934 -3.092292222 0.19540597 EEIVDKYDLFVGSQATDFGEALVRHDEF ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEIVDKYDLFVGSQATDFGEALVRHDEF 28 2 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ;;;; 231.74 1.33E-35 355533000 458161 146970.6 485702 317551 528266 383773 763053 500093 601755 FALSE TRUE 436504.6375 161947.0712 507971.9171 285630.1702 620395.4231 370482.8448 646635.2504 456302.2058 695072.0921 0.627999085 0.2329932 0.730819037 0.410936036 0.8925627 0.533013552 0.930313931 0.65648184 1 19.40680309 2.192213358 0.445083942 0.96168142 0.416610609 0.376632346 0.187702577 0.92569268 0.411431676 0.171911028 0.170382155 155.6730228 -2.192213358 -0.545070811 EEIVYLPCIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EEIVYLPCIYR 11 0 Q13228;Q13228-4;Q13228-3;H0Y532;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;; 205.12 7.19E-08 2809100000 2927190 2092910 2139070 2513170 2613840 2075820 2947460 2450640 2595940 FALSE TRUE 2788827.53 2306179.908 2237148.475 2260541.377 3069692.868 2003933.833 2497770.843 2236048.97 2998505.117 0.930072627 0.769109879 0.74608793 0.753889451 1.023741081 0.66831096 0.833005363 0.745721245 1 21.515812 -1.84674766 4.284564852 1.04173311 0.810721911 0.257303074 0.102069322 0.038427774 0.001374503 0.093334462 0.02106521 0.014231555 1.84674766 -0.231011199 EEKDKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEKDKDDQEWESPSPPKPTVFISGVIAR 28 3 P51397 P51397 DAP Death-associated protein 1 1 EEKDKDDQEWES(0.003)PS(0.996)PPKPTVFISGVIAR;EEKDKDDQEWES(0.01)PS(0.99)PPKPTVFISGVIAR 178.8 1.18E-17 947520000 860830 840360 749900 983360 360055 1046440 838990 1056860 266095 TRUE FALSE 820140.2719 925993.6394 784283.6568 884510.7845 422848.478 1010201.52 710986.6664 964315.7356 307359.6536 2.668340696 3.012736475 2.551680572 2.877771283 1.375744907 3.286708287 2.313207534 3.137418085 1 18.22956827 EEKDQLQVLVS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEKDQLQVLVSK 12 1 E7EVQ3;O15123-2;O15123-3;O15123 E7EVQ3 ANGPT2 Angiopoietin-2 1 EEKDQLQVLVS(1)K 56.087 0.074361 849500000 575800 548990 652710 592590 2061400 296960 633060 317060 1565300 TRUE FALSE 548583.0751 604932.7051 682637.3991 533021.7274 2420907.507 286676.2007 536475.0701 289296.5456 1808038.73 0.303413343 0.334579506 0.377556845 0.294806587 1.338968833 0.158556449 0.296716581 0.160005724 1 20.78599415 EEKREEDEENDNDNES(ph)DHDEADS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEKREEDEENDNDNESDHDEADS 23 2 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEKREEDEENDNDNES(0.997)DHDEADS(0.003) 121.3 3.65E-05 184310000 157830 115380 152680 159490 99006 156710 186110 156440 93550 TRUE FALSE 150369.6887 127137.3532 159680.529 143457.7622 116272.6151 151283.0934 157715.5014 142741.2843 108057.2562 1.391574189 1.176573954 1.477739993 1.327608781 1.076027831 1.400027159 1.459554933 1.320978241 1 16.72143643 -2.195879859 2.269709424 0.085038813 1.328706398 0.415012429 0.122666227 1927409.668 362941.2958 9105354.113 0.029199873 0.006369717 2.195879859 1.243667585 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 36 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 191.99 8.91E-24 53066000 60168 99658 52986 93430 39128.5 73877 57711 76945 33880.4 FALSE TRUE 57323.97788 109813.2635 55415.46051 84038.23889 45952.49801 71318.62097 48906.12701 70207.28789 39134.39939 1.464797691 2.806054653 1.416029411 2.14742631 1.174222646 1.822402338 1.249696629 1.794004481 1 15.25614968 2.969765477 1.490847579 1.439261757 2.072501323 0.206992369 0.472374811 0.516710813 2.353102021 0.162652466 0.188789069 932.7504699 -2.969765477 0.633239566 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 37 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;; 398.23 3.82E-180 8955358800 1522689.5 1505094.6 1323884.3 1771010.5 981364.8 1535514.7 1573624.1 1628132.8 1027710.5 FALSE TRUE 1450714.985 1658465.451 1384585.705 1592985.16 1152514.51 1482339.441 1333538.842 1485564.861 1187082.596 1.222084285 1.397093561 1.166376889 1.341932875 0.970879798 1.24872477 1.123374942 1.251441868 1 20.17898889 2.771754855 24.99872067 1.136932627 1.288016061 0.350561797 0.108559145 699.5082877 526801.5942 0.029626722 0.031422319 591.2278114 -2.771754855 0.151083434 EELEEVIKDI ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 166.33 4.55E-05 188729000 896830 833260 761020 979930 571920 863610 881500 965080 574840 FALSE TRUE 854438.6232 918170.1413 795913.5198 881425.5747 671662.6669 833702.9692 747010.9851 880572.479 663983.2513 1.286837615 1.382821238 1.198695175 1.327481639 1.011565677 1.255608432 1.125044922 1.326196824 1 19.34078733 7.999999957 0.02694737 3.17E-09 2.939426541 0.346873033 0.106369197 1587.655734 3.287205105 119.6673109 265.5375737 99999990.16 -7.999999957 2.939426538 EELEFEVPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EELEFEVPFR 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;; 203.35 4.81E-07 282809000 503369 564716 412094 596637 394869 458088 468705 512757 359022 FALSE TRUE 479575.745 622261.2024 430988.9175 536661.9152 463734.0286 442224.2977 397195.4439 467857.2788 414697.2981 1.15644772 1.500519066 1.039285569 1.294105165 1.118247046 1.066378536 0.957796074 1.128189841 1 18.66169912 2.709222505 1.011418221 1.014210952 1.298633678 0.37428452 0.124505278 0.449556873 0.965358917 0.06502918 0.058124802 511.9440562 -2.709222505 0.284422726 EELFQGDAFHQSDTHIFIIMGASGDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EELFQGDAFHQSDTHIFIIMGASGDLAK 28 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 144.26 6.03E-08 61316000 113344 79811 103331 124494 108311 94349 154288 137767 40759 FALSE TRUE 107986.4537 87943.83164 108068.8286 111979.6266 127200.4041 91081.67047 130748.5319 125703.3911 47079.69755 2.293694721 1.867977838 2.29544441 2.378512022 2.701810137 1.934627349 2.777174423 2.670012716 1 15.52281743 3.53157789 9.705541425 2.358680905 2.080541527 0 0.527746954 1.657439964 287.8973554 0.123630308 0.191081658 3400.774927 -3.53157789 -0.278139378 EELGLIEQAYDNPHEALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 252.77 7.36E-31 220422000 304567 281867 271784 325370 285092 306823 333577 324428 285216 FALSE TRUE 290170.7215 310589.5678 284245.5652 292663.1894 334811.9545 296197.6426 282683.7021 296019.3644 329445.8406 0.880784292 0.942763664 0.862799071 0.88834993 1.016288304 0.89907841 0.858058191 0.898537265 1 18.32968179 4.747633866 7.072152978 0.912885177 0.88026252 0.034787262 0.053423899 0.455155194 158.4503641 0.012156799 0.072025068 55928.58939 -4.747633866 -0.032622657 EELIFHCGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EELIFHCGFR 10 0 Q2NL82 Q2NL82 TSR1 Pre-rRNA-processing protein TSR1 homolog 0 134.59 0.00016656 60091000 34224 32195 30868 32835 34867 29101 36679 34632 33939 FALSE TRUE 32606.29935 35475.7071 32283.32833 29534.36342 40947.79376 28093.22507 31082.94489 31599.43848 39202.08678 0.831749073 0.904944354 0.823510455 0.753387532 1.044530971 0.716625756 0.792890059 0.806065214 1 15.25864283 EELLAEFGSGTLDLPALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EELLAEFGSGTLDLPALTR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 193.16 1.37E-14 108405000 114134 105828 104073 121303 121479 105956 124941 115000 112364 FALSE TRUE 108739.112 116611.9935 108844.85 109109.392 142664.8991 102286.7172 105878.9558 104929.9903 129788.8352 0.837815609 0.898474767 0.838630301 0.84066855 1.099207793 0.788101049 0.815778611 0.808467001 1 16.98580676 -0.914289354 7.514993692 0.999999999 0.865349759 0.186920669 0.087894114 1.20E-09 2.40E-10 0.080745688 0.019031941 0.12181777 0.914289354 -0.13465024 EELMSS(ph)DLEETAGSTSIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.001)S(0.999)DLEETAGSTSIPK;EELMS(0.01)S(0.959)DLEET(0.031)AGSTSIPK;EELMS(0.032)S(0.968)DLEETAGSTSIPK;EELMS(0.034)S(0.966)DLEETAGSTSIPK;EELMS(0.171)S(0.829)DLEETAGSTSIPK;EELMS(0.023)S(0.977)DLEETAGSTSIPK;EELMS(0.034)S(0.966)DLEETAGSTSIPK;EELMS(0.193)S(0.807)DLEETAGSTSIPK;EELMS(0.198)S(0.802)DLEETAGSTSIPK;EELMS(0.002)S(0.998)DLEETAGSTSIPK;EELMS(0.029)S(0.971)DLEETAGSTSIPK 427.75 5.36E-134 1897206000 3613859 4144783 3041998 4174477 2100509 3463781 3244966 3697632 2065343 TRUE FALSE 3443039.047 4567141.1 3181476.617 3754850.641 2466837.105 3343829.395 2749886.839 3373847.74 2385625.844 1.443243523 1.914441492 1.333602512 1.573947839 1.03404191 1.401657097 1.15268991 1.414240103 1 21.18593636 3.156728537 1.604393611 1.225833317 1.65841935 0.410857725 0.205355717 0.305048758 1.626241947 0.063229082 0.084859213 1434.592437 -3.156728537 0.432586032 EELMSS(ph)DLEETAGSTSIPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.065)S(0.935)DLEETAGSTSIPKR;EELMS(0.187)S(0.813)DLEETAGSTSIPKR;EELMS(0.202)S(0.798)DLEETAGSTSIPKR;EELMS(0.288)S(0.712)DLEETAGSTSIPKR;EELMS(0.148)S(0.852)DLEETAGSTSIPKR;EELMS(0.135)S(0.865)DLEETAGSTSIPKR 194.62 1.32E-18 592792000 1348865 1069738 1275128 1282294 1005246 1256412 1482935 1425224 1138583 TRUE FALSE 1285106.825 1178745.518 1333593.88 1153395.371 1180560.584 1212902.137 1256686.03 1300423.831 1315148.637 0.977157098 0.896283116 1.014025216 0.877007616 0.897663238 0.922254796 0.955546769 0.988803695 1 20.32679443 1.355141293 2.444571635 0.998179956 0.93041326 0.299922036 0.039976855 0.34870529 3.520637597 0.032772502 0.009969274 22.65381205 -1.355141293 -0.067766696 EELRQEWEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EELRQEWEAK 10 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ; 150.09 2.02E-05 223480000 478870 423020 421090 483880 369950 442030 485600 480820 296223 FALSE TRUE 456234.7641 466126.2189 440397.393 435239.4631 434469.1629 426722.3903 411512.8013 438716.8518 342159.7499 1.333396942 1.362305821 1.28711046 1.272035835 1.269784546 1.24714374 1.202692022 1.282198891 1 18.38431053 -5 0.118467858 0.043577133 1.43329582 0.895562689 0.031882937 41.77336567 0.322123229 9.530242993 0.299915604 1.00E-05 5 1.389718688 EELSHS(ph)PEPCTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EELSHSPEPCTK 12 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EELS(0.007)HS(0.993)PEPCTK;EELS(0.001)HS(0.999)PEPCTK 105.14 0.0013285 309370000 481430 489130 429330 559450 350420 530010 525580 548840 318760 TRUE FALSE 458673.758 538972.9031 449015.2052 503213.0231 411533.1371 511655.6208 445393.1181 500780.66 368191.6728 1.245747234 1.46383784 1.21951483 1.36671484 1.117714407 1.389644738 1.209677326 1.360108598 1 18.49009747 -3.924426493 0.255679955 2.61E-10 1.329431626 0.435064756 0.103866057 88.36708079 1.443449935 46.30158773 0.12834134 0.000119007 3.924426493 1.329431626 EELSNVLAAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EELSNVLAAMR 11 0 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 140.78 8.94E-05 50466000 66267 52902 45685 54288 63321 52259 69872 59494 71869 FALSE TRUE 63134.69024 58292.77394 47779.70244 48830.8671 74364.16235 50449.25773 59211.74311 54284.38996 83014.07746 0.760529927 0.702203478 0.575561446 0.588223933 0.895801828 0.607719308 0.713273518 0.653917885 1 16.34106839 -1.194727374 4.29086135 1.000108326 0.690936506 0.521887961 0.09404236 9.04E-05 1.70E-05 0.084421493 0.019891388 0.063866428 1.194727374 -0.30917182 EEMQSNVEVVHTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EEMQSNVEVVHTYR 14 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;;;; 224.67 3.06E-12 2522260000 1904112 2059610 1680577 2218920 1665330 1769038 1888880 2054110 1664030 FALSE TRUE 1814108.399 2269486.601 1757633.118 1995869.946 1955763.025 1707775.77 1600696.664 1874241.239 1922079.274 0.943826004 1.180745577 0.914443614 1.038391066 1.017524642 0.888504337 0.832794301 0.97511131 1 20.87423641 2.27306766 6.21788953 0.900967923 1.031059451 0.21211912 0.084257644 0.194197533 21.04703185 0.028621361 0.023350633 187.528664 -2.27306766 0.130091528 EENEGVYNGSWGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 206.69 2.62E-07 0 126470 109010 106270 144340 100370 93025 121950 115570 124210 FALSE TRUE 120492.0137 120118.2429 111142.5846 129830.669 117874.4962 89803.52092 103344.2877 105450.0781 143471.8524 0.839830334 0.837225148 0.774664736 0.904920838 0.821586215 0.625931285 0.720310542 0.734987918 1 17.1304082 2.448900322 24.97040956 0.737809248 0.838121594 0.057600525 0.100037476 316.6174431 280147.3014 0.030536606 0.025549159 281.1255525 -2.448900322 0.100312346 EENKGGEDKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EENKGGEDKLK 11 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 91.937 0.0058318 961510000 2272570 2952380 2013020 2599990 842260 2611460 1947450 2768400 753770 FALSE TRUE 2165150.12 3253230.879 2105318.958 2338634.066 989149.8773 2521024.485 1650330.735 2525984.22 870660.8019 2.486789477 3.736507801 2.418070222 2.686044968 1.136090973 2.895530016 1.895492173 2.901226533 1 19.73175125 3.318840726 2.278884694 2.097030516 3.092400904 0.251094581 0.716111218 0.359198984 3.807918393 0.19403514 0.277160465 2083.726551 -3.318840726 0.995370388 EENSGLLQELEELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EENSGLLQELEELRK 15 1 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ; 119.45 0.00033953 46317000 56025 48601.7 46200 55882 57893 46359 49334.2 51023 85786 FALSE TRUE 53376.80928 53554.26849 48318.3157 50264.63519 67989.52087 44753.57621 41807.36171 46555.15563 99089.25475 0.538674041 0.540464944 0.487624171 0.507266255 0.686144235 0.451649135 0.421916199 0.469830515 1 16.596441 -1.539593168 2.888254705 1.022845313 0.511743061 0.820893879 0.071495583 10677893.62 11203925.48 1893738.033 0.017627075 0.028867344 1.539593168 -0.511102252 EEPCLLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEPCLLKR 8 1 Q60FE5;P21333-2;P21333;H0Y5F3;H7C2E7 Q60FE5 FLNA Filamin-A 0 102.51 0.0079378 80006000 87312 60704 65184 79602 83844 82758 120580 90461 95910 FALSE TRUE 83184.9348 66889.80661 68172.75088 71600.25573 98466.36705 79892.06971 102183.3064 82539.75528 110783.233 0.750880188 0.603789985 0.615370657 0.646309498 0.888820126 0.721156691 0.922371587 0.745056387 1 16.75738002 2.745171811 24.51174134 0.8455488 0.654308432 0.559197573 0.088606371 290.7701021 1078062.822 0.024705891 0.025645674 556.1242221 -2.745171811 -0.191240369 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_SK-BR-3_Trastuzumab_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 202.61 8.31E-25 117007000 193716 262064 177435 243766 161752 225698 202387 218632 147693 TRUE FALSE 184559.4286 288768.6195 185570.5703 219262.1786 189961.4976 217882.0217 171509.1461 199487.423 170596.4761 1.081847836 1.692699791 1.087774932 1.285267923 1.113513608 1.277177739 1.005349876 1.169352542 1 17.38022832 2.665509502 0.783490681 1.066968085 1.358405964 0.193253771 0.181623373 0.862096498 1.119468339 0.119411213 0.105829496 462.9237921 -2.665509502 0.291437878 EEPFFPPPEEFVFIHAVPVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 EEPFFPPPEEFVFIHAVPVEER 22 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;;;;;;;; 208.44 6.88E-23 535130900 833979.4 871088 691511.5 944990 674960.7 742683 773216 814674.7 605809.8 FALSE TRUE 794558.8465 959852.8575 723217.9863 849997.8098 792673.6324 716963.7015 655247.6981 743337.4644 699755.6897 1.135480366 1.37169711 1.033529269 1.214706536 1.132786262 1.024591457 0.936394956 1.062281415 1 19.41649179 2.354468231 2.079983406 0.987905048 1.206685973 0.484557728 0.088769243 0.236763062 2.098000381 0.037777591 0.027930072 226.1873077 -2.354468231 0.218780925 EEPGPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEPGPRPR 8 1 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;; 94.302 0.0095355 241463000 885800 684580 782400 866670 941140 759580 981110 864530 1066750 FALSE TRUE 843929.9895 754339.4803 818273.8139 779550.685 1105274.518 733275.5541 831423.6502 788827.17 1232176.142 0.684910185 0.612201011 0.664088344 0.632661726 0.89701016 0.595106113 0.674760387 0.640190264 1 20.23277708 -2.140434412 2.233450869 1.67589847 0.671736892 0.598310679 0.083618236 3874835.599 987778.3585 13254141.23 0.019554793 0.007237117 2.140434412 -1.004161578 EEPLDPEEAEGPLSLVT(ph)TANHSPDFDHDRDYEDEPVNEDME ddPTM_SK-BR-3_Trastuzumab_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(0.008)LVT(0.33)T(0.33)ANHS(0.33)PDFDHDRDY(0.001)EDEPVNEDME 89.677 0.00036708 27915000 17179 16987 16295 17256 13820 19549 19089 15344 11316 TRUE FALSE 16366.98272 18717.99461 17042.14187 15521.3941 16230.20362 18872.01323 16176.62246 14000.39802 13070.82749 1.252176477 1.432043582 1.303830372 1.187483663 1.241712022 1.443826969 1.237612728 1.071117956 1 13.67406286 1.246886956 2.939429914 1.008698984 1.313691624 0.666437903 0.079731849 0.14767519 2.166632384 0.071293607 0.020458726 17.65578193 -1.246886956 0.304992639 EEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 EEPLS(1)EEEPCT(0.007)S(0.039)T(0.035)AIAS(0.919)PEKK;EEPLS(0.999)EEEPCT(0.001)S(0.001)T(0.001)AIAS(0.997)PEKK 90.907 0.0073261 271680000 599160 656590 502940 724130 262080 744690 609700 711080 254680 TRUE FALSE 570838.8942 723497.2675 526000.2965 651339.0766 307786.669 718901.1986 516679.0671 648814.0655 294174.4737 1.94047732 2.459415525 1.788055537 2.214125068 1.046272524 2.443791909 1.756369479 2.205541689 1 18.16631254 3.435299798 2.161794902 1.813572694 2.187028974 0.095752551 0.487728237 0.689370219 6.495095018 0.130021729 0.203371053 2724.581468 -3.435299798 0.37345628 EEPLS(ph)EEEPCTSTAIASPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK 215.68 3.96E-25 548090000 1418060 1302960 1137520 1568320 713940 1474080 1402330 1517820 708640 TRUE FALSE 1351031.114 1435733.105 1189676.417 1410669.494 838450.91 1423032.24 1188378.803 1384911.634 818532.272 1.650553265 1.754033597 1.453426405 1.72341341 1.024334579 1.738516963 1.451841111 1.69194506 1 19.64267977 -3.031352994 0.210867237 5.86E-14 1.667987309 0.372383112 0.222759786 57.93287185 1.21487006 26.98794999 0.454325253 0.000930351 3.031352994 1.667987309 EEPPEPVPS(ph)PIIPILPSTAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEPPEPVPSPIIPILPSTAGK 21 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 EEPPEPVPS(0.997)PIIPILPS(0.001)T(0.001)AGK 51.819 0.080415 14649000 31128 32736 30162 39785 19388 31700 31500 30728 26312 TRUE FALSE 29656.64113 36071.83562 31544.95753 35785.73621 22769.26106 30602.22105 26694.09646 28037.29342 30392.33058 0.975793582 1.186872969 1.037924928 1.177459429 0.749177856 1.006906034 0.878316863 0.922512124 1 14.89141969 2.754021788 24.99805883 0.909827204 1.093571317 0.491044487 0.092633095 623.4450022 1008002.67 0.025279304 0.026725666 567.5730788 -2.754021788 0.183744113 EEPSQNDIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEPSQNDISPK 11 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 EEPSQNDIS(1)PK;EEPSQNDIS(1)PK;EEPSQNDIS(1)PK 159.12 3.04E-05 476600000 955550 970840 852350 1167290 544360 1086670 1142380 1182610 656310 TRUE FALSE 910383.0452 1069769.7 891431.0906 1049951.791 639296.2116 1049038.345 968088.9498 1079054.399 758087.2028 1.200894886 1.41114333 1.175895184 1.38500134 0.84330168 1.383796404 1.277015291 1.423390864 1 19.53200429 3.709989401 24.87610681 1.229297626 1.306019192 0.035628089 0.186960183 2568.27708 2236122.381 0.04593052 0.071168524 5128.488674 -3.709989401 0.076721566 EEPVLT(ph)LVDEAIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEPVLTLVDEAIVK 14 0 Q02156 Q02156 PRKCE Protein kinase C epsilon type 1 EEPVLT(1)LVDEAIVK 167.55 4.72E-07 0 12281 7742 10884 13496 8848.2 14587 15315 12516 10223 TRUE FALSE 11700.50147 8530.918602 11383.04217 12139.35644 10391.32328 14081.84853 12978.41547 11420.03269 11808.33063 0.990868382 0.722449165 0.963984032 1.028033244 0.87999935 1.192535082 1.099089776 0.96711661 1 13.5275174 3.068904632 1.289418572 1.062818564 0.861658219 0.261578772 0.106741738 0.444418967 1.553310407 0.040604504 0.051969267 1171.937988 -3.068904632 -0.201160345 EEPVS(ph)S(ph)GPEEAVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 2 EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK 181.58 2.37E-06 900650000 1724620 1838030 1624650 2009950 1122610 1904510 1901640 1862460 1206530 TRUE FALSE 1643100.63 2025327.347 1699141.809 1807906.007 1318392.829 1838556.341 1611509.892 1699373.129 1393632.51 1.179005669 1.453272173 1.219217977 1.297261648 0.946011821 1.319254773 1.156337758 1.21938396 1 20.41041875 -3.428030214 0.090639745 0.39631611 1.460516456 0.253457243 0.127317858 174.3683281 1.535741558 23.26741758 3.061880888 0.000373224 3.428030214 1.064200345 EEPVSS(ph)GPEEAVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.001)S(0.999)GPEEAVGK;EEPVS(0.02)S(0.98)GPEEAVGK;EEPVS(0.014)S(0.986)GPEEAVGK;EEPVS(0.045)S(0.955)GPEEAVGK;EEPVSS(1)GPEEAVGK;EEPVS(0.134)S(0.866)GPEEAVGK 290.64 1.92E-43 2039360000 5642810 5824720 4910360 6366110 3618980 5855580 5983420 6213600 3775320 TRUE FALSE 5376085.554 6418265.59 5135504.863 5726176.528 4250128.966 5652799.796 5070539.386 5669504.244 4360777.344 1.232827345 1.471816854 1.177658123 1.313109126 0.974626456 1.296282601 1.162760441 1.300113213 1 22.0561539 -4.86951005 0.049567178 1.94E-11 1.763707927 0.259829501 0.127566971 636.4589957 2.384915684 86.0952419 20.0975792 1.35E-05 4.86951005 1.763707927 EEQNGEDEDGGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 207.34 1.27E-07 149390000 146890 157290 125480 168530 117790 137040 151240 135920 116610 FALSE TRUE 139946.8008 173318.0298 131233.3821 151589.0442 138332.5387 132294.2704 128165.5603 124018.1242 134693.2832 1.03900356 1.286760748 0.974312742 1.125438779 1.027018834 0.982189069 0.951536388 0.920744682 1 17.03931838 2.699722841 0.974815247 0.948541007 1.143762019 0.397025856 0.081586414 0.447820453 0.894938901 0.04425989 0.039172841 500.8674875 -2.699722841 0.195221013 EEQRS(ph)PFNDRFPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEQRSPFNDRFPLK 14 2 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK 185.71 5.98E-07 271780000 850260 843410 706550 1019730 584680 827210 852630 927030 617950 TRUE FALSE 810069.8949 929354.4379 738946.0164 917224.803 686648.0069 798563.5103 722545.6339 845854.3387 713778.5299 1.1349037 1.302020723 1.035259517 1.285027168 0.961990279 1.118783316 1.012282667 1.18503752 1 19.44511698 2.739694818 24.99983349 1.057953501 1.193486799 0.322750214 0.096108218 110.4817911 2435225.817 0.0268929 0.027101598 549.1548431 -2.739694818 0.135533298 EEQT(ph)DTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 EEQT(0.997)DT(0.385)S(0.617)DGESVTHHIR;EEQT(0.996)DT(0.004)S(1)DGESVTHHIR;EEQT(0.997)DT(0.071)S(0.932)DGESVTHHIR 156.41 1.14E-07 995780000 803400 699790 744220 837570 771370 745990 842320 822940 559740 TRUE FALSE 765424.8742 771099.3966 778343.2231 753375.8723 905896.6838 720156.1792 713808.6137 750879.0109 646541.6204 1.183875639 1.192652371 1.203856331 1.165239558 1.4011421 1.113858964 1.104041242 1.161377686 1 19.30238372 1.162012165 0.907545816 1.013235884 1.2112436 0.408331095 0.077675349 0.538756922 0.9744183 0.070131307 0.024904212 14.52152293 -1.162012165 0.198007716 EEQTDTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 EEQTDT(0.015)S(0.985)DGESVTHHIR;EEQT(0.004)DT(0.32)S(0.676)DGESVTHHIR;EEQTDT(0.003)S(0.996)DGESVTHHIR;EEQTDT(0.003)S(0.992)DGES(0.003)VT(0.001)HHIR;EEQTDT(0.009)S(0.991)DGESVTHHIR 149.41 2.10E-07 1656170000 1019030 877295 917701 1144300 822249 1014180 1069950 991272 461240 TRUE FALSE 970862.4714 966692.3579 959778.4986 1029272.79 965648.9653 979058.6923 906709.4765 904470.9686 532766.7435 1.822303068 1.81447579 1.801498517 1.931938888 1.812517348 1.837687326 1.70188828 1.697686614 1 19.0231445 0.198164753 0.735015063 0.980263351 1.838272053 0.97198752 0.04365125 0.455352997 0.303794366 0.063064604 0.014778712 1.578209861 -0.198164753 0.858008702 EEQTPQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 116.73 0.0051555 544359000 474278 485418 418073 548156 348871 464203 474498 514246 391352 FALSE TRUE 451859.8189 534882.6461 437242.0606 493054.3175 409713.9919 448127.5337 402104.6153 469215.8941 452040.8694 0.999599482 1.183261697 0.967262233 1.090729513 0.906364932 0.99134296 0.88953155 1.037994407 1 18.78609369 2.74680785 24.96974032 0.954808047 1.068822507 0.297495261 0.071170691 604.4917585 1830189.701 0.020326515 0.02122673 558.2231593 -2.74680785 0.114014459 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 40 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 480.9 1.75E-296 927280000 994660 1039980 836010 1216560 734090 971110 1071210 1067570 217886 FALSE TRUE 947644.393 1145955.144 874341.8854 1094269.077 862115.0636 937480.2172 907777.2404 974087.9113 251674.6481 3.765354994 4.553319745 3.474095989 4.347951158 3.425514132 3.724968821 3.606947491 3.870425244 1 17.94120037 -0.95126414 0.428845361 1.59E-12 4.022461835 0.862156928 0.357536528 4.837679016 0.619718885 6.677308418 0.190551513 0.111875724 0.95126414 4.022461835 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICR 45 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 132.59 4.41E-10 79092000 38846 16420.1 40616 35503 54819 33912 66801 44139 27365.6 FALSE TRUE 37009.82657 18093.32686 42478.28377 31934.17099 64379.41624 32737.61894 56609.28057 40273.95516 31609.31748 1.170851809 0.572404857 1.343853242 1.010277144 2.036722757 1.035695217 1.790904868 1.27411657 1 14.94806226 3.304232258 1.940021597 1.456926038 0.891937886 0.186752676 0.374506612 0.367939027 2.841622824 0.103971316 0.151170073 2014.801464 -3.304232258 -0.564988152 EERLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EERLSPR 7 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EERLS(1)PR;EERLS(1)PR 114.4 0.0035811 449940000 489720 419020 445880 495870 482200 454100 503990 458820 532800 TRUE FALSE 466571.9061 461718.6144 466324.039 446024.2055 566295.5273 438374.4031 427097.0691 418643.2884 615423.9028 0.758130947 0.750244851 0.757728188 0.724743065 0.920171486 0.71231293 0.693988432 0.680251915 1 19.23122095 -1.693295138 2.630701693 1.039122544 0.749049863 0.587204819 0.06595214 11923848.72 10077377.74 3105860.595 0.015635809 0.020263052 1.693295138 -0.290072681 EES(ph)DGEYDEFGR ddPTM_SK-BR-3_Trastuzumab_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 338.52 1.81E-58 3777900000 2874300 2896800 2335500 2849500 1538180 3057000 2689000 2729800 1279680 TRUE FALSE 2738437.535 3191987.213 2442584.985 2563062.846 1806438.105 2951135.323 2278743.663 2490764.24 1478126.239 1.852641177 2.15948214 1.6524874 1.733994553 1.22211355 1.996538081 1.54164347 1.685082218 1 20.49533806 -1.407521289 0.116026531 5.23E-11 2.31858238 0.50754287 0.239276141 38.44388374 0.777788642 14.89569402 3.281751231 0.039127195 1.407521289 2.31858238 EES(ph)DGEYDEFGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESDGEYDEFGRK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGRK 137.19 3.89E-05 114320000 143500 157030 117930 144350 70471 149940 128830 144440 66877 TRUE FALSE 136717.0394 173031.5355 123337.2071 129839.6638 82761.12009 144747.5402 109174.6174 131792.0679 77247.9436 1.769846976 2.239950055 1.596640653 1.68081709 1.07136988 1.873804447 1.413301278 1.706091602 1 16.23720891 7.191229222 0.056452839 5.28E-09 4.627723697 0.395173067 0.284592699 293.9133602 1.440973641 27.98266842 118.786247 15532065.8 -7.191229222 4.627723692 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_SK-BR-3_Trastuzumab_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 334.73 1.92E-80 4731530000 3536190 3587990 2775330 3812060 1087560 4023990 3146530 4497520 848070 TRUE FALSE 3369041.307 3953610.26 2902581.626 3428864.486 1277230.12 3884638.217 2666469.059 4103693.306 979584.3643 3.439255902 4.036007928 2.963074679 3.500325864 1.303849026 3.96559843 2.722041261 4.189218872 1 19.90181022 3.672009591 6.752552168 2.900096338 3.736040403 0.119069603 1.028978921 0.469628998 39.97900046 0.242706586 0.378998235 4699.044858 -3.672009591 0.835944065 EES(ph)EES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 306 3.65E-46 641007000 1402702 1408458 1356994 1573026 991973 1468839 1405649 1463667 1086204 TRUE FALSE 1336399.056 1551981.471 1419213.517 1414902.438 1164972.777 1417972.737 1191191.429 1335500.558 1254646.969 1.065159435 1.236986587 1.131165621 1.127729531 0.928526355 1.130176673 0.949423589 1.064443299 1 20.25885005 2.899430775 6.804292208 1.016119131 1.150163941 0.450850072 0.069025699 0.204446519 11.92489065 0.019207968 0.02044405 793.2877989 -2.899430775 0.13404481 EES(ph)EES(ph)EAEPVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 EES(1)EES(1)EAEPVQR;EES(1)EES(1)EAEPVQR 310.33 2.09E-50 986620000 2188200 2056200 1980610 2329100 1575410 2198800 2299400 2241100 1789040 TRUE FALSE 2084768.123 2265729.118 2071422.928 2094974.443 1850161.005 2122655.005 1948584.299 2044857.403 2066475.186 1.008852241 1.096422126 1.00239429 1.013791241 0.895322149 1.027186302 0.942950736 0.989538813 1 20.97874061 3.309931231 2.334494471 0.970578184 1.051284154 0.325348488 0.042916654 0.26189816 2.913907397 0.01165463 0.016491529 2041.414671 -3.309931231 0.08070597 EES(ph)EESDEDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 EES(0.556)EES(0.444)DEDMGFGLFD 69.979 0.046893 13193000 40191 33863 34380 35885 31187 36763 42371 38947 34247 TRUE FALSE 38291.25108 37313.6782 35956.35701 32277.77162 36626.00293 35489.88809 35906.52575 35536.59421 39557.84985 0.967981102 0.943268614 0.908956304 0.815963753 0.925884573 0.897164235 0.907696598 0.898344939 1 15.27167639 3.827802931 3.225683039 0.900579965 0.959273063 0.162278346 0.04456973 0.332752744 6.679370247 0.010722573 0.020750817 6726.713499 -3.827802931 0.058693097 EES(ph)EESEAEPVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EES(1)EESEAEPVQR;EES(1)EESEAEPVQR 233.59 1.28E-16 299030000 266910 262680 249280 268400 188182 240000 275290 261500 215850 TRUE FALSE 254293.6933 289447.3906 260709.7346 241419.9221 221000.8812 231688.7398 233289.4545 238601.6737 249322.9156 1.019937107 1.160933763 1.045670968 0.968302178 0.886404207 0.929271741 0.935691988 0.95699857 1 17.92765596 3.272994212 3.073148426 0.936288783 1.091666751 0.663653209 0.044184054 0.122062716 2.363226754 0.012242366 0.016459828 1874.969517 -3.272994212 0.155377969 EES(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;EES(1)PLR 142.08 0.012138 10851276000 8151027 8710164 6404960 8854008 5944934 7712123 7298371 7704261 5360547 TRUE FALSE 7765744.107 9597739.614 6698633.751 7963986.294 6981728.607 7445050.247 6184870.46 7029635.064 6191833.251 1.254191415 1.55006429 1.08184983 1.286208134 1.127570515 1.202398376 0.998875488 1.135307554 1 22.56193519 2.934118261 0.655068178 1.041148127 1.398062373 0.442033843 0.120391316 0.598850106 0.56627596 0.080618417 0.103897624 859.2474687 -2.934118261 0.356914247 EES(ph)S(ph)EDENEVSNILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESSEDENEVSNILR 15 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 2 EES(1)S(1)EDENEVSNILR 135.09 4.55E-05 48980000 71840 72814 61954 79024 51591 68316 66987 75083 53669 TRUE FALSE 68444.26557 80233.82938 64794.65218 71080.35738 60588.45407 65950.19979 56766.90285 68508.33448 61991.71442 1.104087316 1.294266986 1.045214716 1.146610608 0.977363743 1.063855072 0.915717582 1.105120823 1 15.91978778 3.10991392 1.339690997 1.002155445 1.190237518 0.393165226 0.080639341 0.327826466 1.234102283 0.027883307 0.03690469 1287.994236 -3.10991392 0.188082073 EES(ph)WESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 EES(0.998)WES(0.002)GR 107.56 0.0041737 114950000 212230 198470 173880 207520 179590 203610 206950 196910 170860 TRUE FALSE 202198.3085 218694.3186 181852.57 186659.6953 210910.4391 196558.9346 175375.9766 179667.5165 197356.0962 1.024535408 1.108120412 0.921443895 0.945801518 1.068679626 0.995960796 0.888627106 0.910372266 1 17.59044156 3.465938674 0.604176495 0.94117117 1.07585161 0.180738722 0.063647118 1.43023334 1.005576447 0.042267117 0.111963284 2923.739493 -3.465938674 0.134680441 EES(ph)WGPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESWGPPR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 EES(1)WGPPR 94.692 0.0095904 0 109580 105980 97015 128920 104380 100200 123740 127900 115160 TRUE FALSE 104400.3706 116779.4825 101463.2337 115960.7167 122583.839 96730.04888 104861.1904 116700.398 133018.4246 0.784856465 0.877919603 0.762775788 0.871764321 0.921555336 0.727192862 0.788320796 0.877325064 1 17.02126656 0.934137446 4.955569704 0.999952281 0.820262962 0.493286623 0.058215593 0.298282754 19.43959182 0.054170204 0.013700769 8.592854268 -0.934137446 -0.179689319 EESEES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;EES(0.007)EES(0.993)DEDMGFGLFD;EES(0.022)EES(0.978)DEDMGFGLFD 239.61 3.06E-19 240451000 370084 326546 337056 383504 326883 359309 379724 358270 322980 TRUE FALSE 352590.8628 359821.4087 352510.351 344953.4493 383891.2917 346866.0392 321790.1297 326897.9795 373066.0888 0.945116357 0.964497764 0.944900546 0.924644345 1.02901685 0.929771023 0.862555293 0.876246835 1 18.5090717 1.998667665 24.98545307 0.89728759 0.959857765 0.171266648 0.045563638 57.36547255 1075791.385 0.015509755 0.011297786 99.69368856 -1.998667665 0.062570175 EESGKPGAHVTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EESGKPGAHVTVK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 186.13 4.85E-06 26283700000 50158500 42899600 41350000 53550100 34693700 48948200 57802400 55682500 37942600 FALSE TRUE 47787607.11 47271118.01 43245938.4 48167142.21 40744270.3 47253111.56 48983582.27 50806645.11 43826544.62 1.090380442 1.078595596 0.986752179 1.099040379 0.929671062 1.078184739 1.117669273 1.159266503 1 25.3853016 2.005043154 24.99972023 1.103521484 1.044313132 0.129716651 0.063920948 244.7349452 1213180.827 0.022554041 0.016602415 101.1679976 -2.005043154 -0.059208352 EESGKPGAHVTVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESGKPGAHVTVKK 14 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 104.55 0.00063139 1224300000 1830200 1237500 1821200 1596000 1453600 1923000 2828900 2343900 1838900 FALSE TRUE 1743690.073 1363602.657 1904703.821 1435567.048 1707107.38 1856406.028 2397299.349 2138655.69 2124067.22 0.820920382 0.641977167 0.896724832 0.675857635 0.803697436 0.873986478 1.128636291 1.006868177 1 21.01839799 2.002031401 2.944750195 1.054839084 0.756986391 0.710509906 0.080148023 0.121360347 2.036019526 0.035810383 0.020931946 100.468843 -2.002031401 -0.297852694 EESKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EESKPR 6 1 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 74.717 0.072587 69461000 202430 191870 185640 220200 148590 190830 187750 278340 216500 FALSE TRUE 192861.5351 211421.7711 194151.7776 198065.0776 174504.049 184221.5093 159105.2892 253967.074 250073.7143 0.771218741 0.845437801 0.77637819 0.792026776 0.697810441 0.736668825 0.636233559 1.015568848 1 17.9319939 1.222101706 24.99406528 1.007784762 0.755363844 0.784794443 0.055902318 143.3079786 217617.7587 0.060639086 0.015336571 16.67637705 -1.222101706 -0.252420918 EESLADDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EESLADDLFR 10 0 O60934;A0A0C4DG07;A0A087X1V5 O60934 NBN Nibrin 0 ; 177.36 5.43E-06 66831000 127658 130566 120671 144292 127500 132860 142521 142920 138642 FALSE TRUE 121623.8593 143870.8238 126203.8847 129787.494 149735.9596 128259.0249 120776.8039 130405.1671 160141.8933 0.759475593 0.898395922 0.788075388 0.810453101 0.935020541 0.800908633 0.754186187 0.814310138 1 17.28899124 -0.936491993 4.424367472 1.000003208 0.81991647 0.499037465 0.05664478 5269.310049 32939161.45 286.4724286 0.013074705 0.115746537 0.936491993 -0.180086738 EESQIPVDEVFFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EESQIPVDEVFFHR 14 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ; 159.22 4.95E-06 94194000 237110 209292 215948 259930 230590 227920 255940 226380 209454 FALSE TRUE 225902.2802 230619.0927 225849.4294 233801.3426 270804.823 220027.0733 216891.6523 206556.9671 241935.0566 0.933731074 0.953227267 0.933512624 0.966380589 1.119328579 0.909446842 0.89648708 0.853770305 1 17.88426031 -0.925315986 4.684174336 1.000000501 0.945816855 0.057238726 0.069210092 3.59E-07 8.25E-08 0.066470039 0.015666994 0.118763781 0.925315986 -0.054183646 EETEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EETEELKR 8 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 118.32 0.00306 1466560000 1641840 1670840 1371430 1831900 1229830 1566590 1463420 1723200 1440540 FALSE TRUE 1564233.477 1841100.496 1434311.422 1647753.932 1444311.963 1512338.595 1240148.401 1572307.473 1663931.586 0.940082808 1.106476078 0.862001439 0.990277452 0.868011627 0.908894698 0.745312134 0.944935168 1 20.66616469 3.722345929 24.64009246 0.886277264 1.023279447 0.249126184 0.08322572 679.6113267 1032748.239 0.021640888 0.033644775 5276.499832 -3.722345929 0.137002183 EETKEDAEEKQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EETKEDAEEKQ 11 2 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 100.55 0.012327 3039980000 3860430 4180610 3146430 4588480 1538190 4240640 3509490 4349560 1484330 FALSE TRUE 3677955.125 4606618.912 3290696.928 4127237.273 1806449.849 4093785.573 2974052.844 3968689.468 1714512.315 2.145190263 2.686839208 1.919319504 2.407236878 1.05362314 2.387725965 1.734634868 2.314762882 1 20.70936684 EETNGPSNQKPVKS(ph)PDNSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EETNGPSNQKPVKSPDNSIK 20 2 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EETNGPS(0.001)NQKPVKS(0.999)PDNSIK 94.73 0.00069224 145100000 283700 373200 247950 368980 105260 333960 238320 386230 93896 TRUE FALSE 270290.0632 411229.5043 259318.7528 331889.4294 123617.3107 322394.8815 201959.907 352409.6537 108456.9121 2.492142344 3.791639428 2.390984103 3.060103989 1.139782687 2.972561869 1.862121123 3.249305616 1 16.72676248 EETPGQRPAVTETHQLAELNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EETPGQRPAVTETHQLAELNEK 22 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 268.3 3.59E-38 147020000 186980 171040 160930 190500 119190 191360 165990 186180 116350 FALSE TRUE 178141.826 188469.1705 168308.7997 171350.5781 139976.6983 184733.1552 140665.1769 169877.0922 134392.9638 1.32552941 1.402373794 1.252363182 1.274996646 1.041547819 1.374574606 1.046670696 1.264032636 1 17.03609808 7.994432821 0.074311708 0.755910286 2.42060726 0.424565306 0.108637357 172.4737045 0.942113805 3.459806421 29.75484065 98726290.93 -7.994432821 1.664696975 EETVNDPEEAGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EETVNDPEEAGHR 13 0 O00567 O00567 NOP56 Nucleolar protein 56 0 ; 155.08 4.65E-05 415650000 464160 482810 406470 517320 408350 392700 437590 437870 346070 FALSE TRUE 442220.0767 532008.8879 425107.0516 465318.0108 479566.1107 379100.7005 370827.6086 399527.7815 399736.7681 1.106278211 1.330898057 1.063467475 1.164061072 1.199704778 0.948375858 0.927679509 0.999477189 1 18.60869075 2.237552541 25 0.958570278 1.183000377 0.660113869 0.072367764 14.68279584 364113.4811 0.02565078 0.020035437 172.8035027 -2.237552541 0.224430099 EEVFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EEVFWR 6 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;; 132.01 0.035093 113893000 299098 330347 255419 326860 254757 257711 279623 266242 214261 FALSE TRUE 284960.2303 364009.7349 267130.2138 294003.4118 299186.5401 248786.4035 236961.3757 242928.439 247487.5016 1.151412611 1.470820678 1.079368502 1.187952563 1.208895553 1.005248353 0.957468051 0.981578615 1 17.91699614 2.476240962 0.945439114 0.955469052 1.280522228 0.535719893 0.104385465 0.375413731 0.674596361 0.067498324 0.04762021 299.3925315 -2.476240962 0.325053176 EEVSSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEVSSWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 92.47 0.036399 154590000 470700 412590 432000 525380 405160 460160 551490 511520 504500 FALSE TRUE 448450.9438 454633.3901 451807.6273 472567.8042 475819.7757 444224.5438 467350.0717 466728.5971 582735.2834 0.769562024 0.78017138 0.775322244 0.810947642 0.816528172 0.762309331 0.801993778 0.8009273 1 19.15248114 -5 0.325876487 3.089426728 0.779594107 0.939142642 0.01689365 74.49028747 0.650421703 107.595239 0.01417762 1.00E-05 5 -2.309832621 EEVVGGDDS(ph)DGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 1 EEVVGGDDS(1)DGLR;EEVVGGDDS(1)DGLR 205.26 7.48E-08 171552000 300810 388150 270120 384270 269130 334090 291190 313680 231960 TRUE FALSE 286591.3074 427702.9263 282505.2692 345642.4495 316066.1868 322520.3795 246763.6174 286212.5163 267931.1721 1.069645257 1.596316408 1.054394929 1.290041942 1.179654403 1.203743398 0.920996297 1.068231494 1 18.03150291 1.89660557 3.829335255 0.993342332 1.261977067 0.338797719 0.15325175 0.242689057 5.953727204 0.072356797 0.040596365 78.81439929 -1.89660557 0.268634735 EEVVLLTHGDSVDKVADGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEVVLLTHGDSVDKVADGFK 20 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 206.28 4.69E-22 89440000 173480 121660 159050 174930 106680 179490 209810 183660 122430 FALSE TRUE 165279.9442 134057.2923 166342.5998 157345.7041 125284.9582 173274.2163 177799.6311 167577.7568 141415.8191 1.168751454 0.947965321 1.176265858 1.112645707 0.885933123 1.225281707 1.257282475 1.185000079 1 17.10958399 EEWYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEWYAR 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 166.22 0.016361 646240000 578900 566500 455870 555840 520600 483280 546870 532810 501400 FALSE TRUE 551536.5443 624226.9941 476772.0904 499965.9072 611392.4752 466543.8924 463434.9375 486154.3318 579154.5512 0.952313235 1.077824551 0.82322083 0.863268546 1.055663767 0.805560263 0.800192171 0.839420722 1 19.14358887 3.735307091 24.99921341 0.872682 1.015068894 0.267222339 0.08880077 305.2950387 2345806.154 0.023005724 0.037315364 5436.346008 -3.735307091 0.142386894 EEYEERLARLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EEYEERLARLK 11 2 A0A0A0MRS8;Q9P2E2-3;Q9P2E2 A0A0A0MRS8 KIF17 Kinesin-like protein;Kinesin-like protein KIF17 0 88.948 0.033042 170140000 223990 191170 217200 226400 186380 209400 261880 231990 228900 FALSE TRUE 213402.4366 210650.4403 227158.8348 203641.8419 218884.613 202148.4255 221925.3962 211675.7257 264396.6429 0.807129902 0.796721312 0.859159301 0.770213417 0.82786457 0.764565023 0.839365409 0.800599143 1 18.01234433 -1.234630452 0.726631587 1.053524273 0.807370807 0.81265768 0.028924361 25.50250254 5.723570915 2.822843483 0.008745379 0.058259875 1.234630452 -0.246153466 EEYEGPNKKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EEYEGPNKKPR 11 2 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 194.17 3.56E-07 4044620000 6247050 5165750 5465100 6159030 3818940 6160470 6973270 6457830 4356570 FALSE TRUE 5951764.327 5692145.798 5715680.241 5539912.603 4484961.927 5947131.379 5909369.589 5892348.17 5032164.625 1.18274436 1.13115254 1.135829343 1.10090051 0.891258983 1.181823693 1.174319608 1.170937084 1 22.26274769 -0.897147936 0.010323861 1.47E-05 2.14638489 0.10065082 0.089072538 13743.31742 28.33510609 3119.89855 2776.09266 0.126722013 0.897147936 2.146370196 EEYLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EEYLLLR 7 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 97.602 0.02763 129659000 429900 389350 362780 460960 599900 358510 536120 435460 654980 FALSE TRUE 409579.479 429025.2077 379413.8218 414623.425 704522.3701 346094.7088 454325.0475 397328.8139 756550.9532 0.541377256 0.567080387 0.501504651 0.548044283 0.931229241 0.457463846 0.600521413 0.525184473 1 19.52907772 -1.892458136 2.384416049 1.231324632 0.582485823 0.505320111 0.129328443 14405431.39 7483703.931 18724768.84 0.029916864 0.012809786 1.892458136 -0.648838809 EFADFEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFADFEYR 8 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A0G2JQ95;A0A096LP11;A0A140TA66 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 134.15 0.002068 220482000 865920 804040 758830 894420 829750 712120 871610 819770 858690 FALSE TRUE 824989.6777 885972.5901 793623.1061 804511.2023 974458.1373 687459.1058 738629.8863 747986.5929 991851.2596 0.831767535 0.893251464 0.800143266 0.811120815 0.982463981 0.693107055 0.744698239 0.754131817 1 19.91976426 2.218926719 24.99967065 0.770293646 0.859581635 0.072565369 0.09575889 400.4441821 509878.8904 0.031953682 0.023632656 165.5490599 -2.218926719 0.089287989 EFAEILHFTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFAEILHFTLR 11 0 Q9H0Q0 Q9H0Q0 FAM49A Protein FAM49A 0 60.49 0.09332 15349000 80066 64143 50368 58229 83067 53619 89344 71286 68905 FALSE TRUE 76281.43886 70679.24462 52677.42262 52375.71029 97553.8585 51762.16059 75712.93188 65043.81993 79590.43548 0.958424695 0.888036913 0.661856193 0.658065382 1.225698263 0.650356544 0.951281789 0.817231613 1 16.28030745 EFAGEDTSDLFLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 ; 127.02 0.00066907 25648000 35130 37789 37620 40281 46470 34175 50168 42040 59921 FALSE TRUE 33469.47452 41639.74206 39344.91421 36231.87735 54574.35329 32991.51118 42513.9502 38358.75473 69213.24265 0.483570387 0.601615247 0.56845934 0.523481865 0.788495831 0.476664724 0.614245895 0.554211207 1 16.07876048 -5 0.382076759 7.059867137 0.565831113 0.696795865 0.087741281 318.0451621 2.360773054 1598.31511 0.052349593 1.00E-05 5 -6.494036024 EFALHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFALHK 6 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;F8WCE3 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 74.743 0.079523 210510000 247990 265590 174570 250020 206370 228600 265990 273360 185660 FALSE TRUE 236268.0042 292653.923 182574.2072 224887.5146 242360.8627 220683.5247 225408.3403 249423.1492 214451.2046 1.101733164 1.364664393 0.851355475 1.048665197 1.130144562 1.029061716 1.051093841 1.163076466 1 17.71028989 3.750491292 24.99786695 1.045012638 1.233198765 0.379181521 0.103057134 701.5516139 1469929.013 0.024913178 0.044449265 5629.778288 -3.750491292 0.188186127 EFDEDSEDRLVNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFDEDSEDRLVNEK 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 116.96 0.00030197 81452000 246940 254460 185954 282940 148986 256420 248640 252490 145095 FALSE TRUE 235267.6356 280389.7633 194480.1748 254498.3336 174969.1112 247540.1111 210705.4014 230380.6371 167595.5916 1.403781767 1.673013954 1.160413428 1.51852642 1.043995905 1.477008487 1.257225202 1.374622297 1 17.35462468 -2.752690183 0.066892433 1.29E-09 1.956183068 0.312150836 0.176278585 207.4162603 1.595378291 43.26146724 11.70646995 0.001767298 2.752690183 1.956183067 EFDKHFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFDKHFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 71.223 0.029621 1069546000 2515503 1946998 2503798 2886038 2424054 3219930 3845120 3111397 2538819 FALSE TRUE 2396600.158 2145399.31 2618599.615 2595927.977 2846808.25 3108423.017 3258476.324 2838946.584 2932526.084 0.817247687 0.73158746 0.892950153 0.885219058 0.970769967 1.05998137 1.111149988 0.968089116 1 21.48371251 2.956013102 1.184456583 1.052518885 0.778816706 0.783470519 0.052067558 0.172318989 0.510207758 0.022006236 0.02540438 903.6767364 -2.956013102 -0.273702179 EFDLTKEEDLAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 74.296 0.030497 70920000 70420 58947 62440 89955 53372 56657 70922 63330 47186 FALSE TRUE 67091.38616 64953.76632 65302.93576 80912.5525 62680.0599 54694.95388 60101.54633 57784.48947 54503.36389 1.23095863 1.191738669 1.198145052 1.484542361 1.15002186 1.003515196 1.102712604 1.060200423 1 15.73405765 2.479972194 24.46230652 1.056960004 1.25929983 0.613849664 0.086952368 64.70415454 555200.5466 0.029126161 0.024814974 301.9758374 -2.479972194 0.202339826 EFEDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFEDRDR 7 1 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 73.248 0.04506 135446000 374720 342620 360360 413990 349040 354360 420220 370910 432020 FALSE TRUE 357007.7282 377533.3675 376882.8624 372374.9387 409912.4655 342088.4243 356107.7211 338431.1541 499015.4551 0.715424191 0.756556463 0.755252886 0.74621925 0.821442425 0.685526712 0.713620625 0.67819774 1 18.92872497 -1.02527975 4.75216474 1.000006188 0.734791524 0.807544987 0.040803772 2.61E-06 5.34E-07 0.038473103 0.009067986 0.094345296 1.02527975 -0.265214664 EFEFLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EFEFLMR 7 0 P85037 P85037 FOXK1 Forkhead box protein K1 0 ;;;; 146.94 0.0050827 164810000 405322 342162 312834 359157 391851 312282 448934 390237 405079 FALSE TRUE 386163.2323 377028.6968 327177.7483 323053.856 460189.6903 301467.596 380440.8731 356065.7795 467896.5825 0.825317489 0.805794936 0.699252272 0.690438589 0.983528642 0.644303907 0.813087523 0.760992478 1 18.83583017 -1.245473701 5.377668586 1.000019198 0.780793374 0.357891249 0.093444199 1.92E-05 2.69E-06 0.080650843 0.019007922 0.05682328 1.245473701 -0.219225824 EFEKDKDDDEVFEK ddPTM_SK-BR-3_Trastuzumab_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 0 153.23 3.63E-06 101230000 363030 334780 318140 409360 150920 432210 409150 493530 153380 FALSE TRUE 345870.2914 368894.4626 332727.0337 368210.3551 177240.4002 417242.4593 346726.6529 450313.8968 177165.387 1.952245284 2.082203916 1.87805891 2.078342509 1.000423408 2.355101447 1.957078969 2.541771304 1 17.43473725 3.607619874 3.675261559 1.879497743 2.016615321 0.015537382 0.501853482 1.495190321 36.06265986 0.126150751 0.202696556 4051.537604 -3.607619874 0.137117577 EFEPLLNWMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFEPLLNWMK 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 101.65 0.0074206 79817000 289380 251200 225960 261510 226800 245280 302260 270640 219400 FALSE TRUE 275701.5809 276797.5656 236320.4895 235222.518 266353.8482 236785.8921 256144.6856 246941.3268 253423.4315 1.087908799 1.092233516 0.932512389 0.928179832 1.051022972 0.934348851 1.010737974 0.974421842 1 17.9511904 3.75232882 24.79498131 0.97697087 1.090071174 0.603053254 0.03850524 409.8182724 738034.2838 0.009190698 0.016454807 5653.648704 -3.75232882 0.113100304 EFESVLVDAFSHVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EFESVLVDAFSHVAR 15 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;;; 237.48 9.72E-18 988037500 1515757.1 1303877.9 1387681.6 1546723.6 1496053.2 1333858.1 1690456.3 1579445.5 1444838.8 FALSE TRUE 1444110.266 1436744.54 1451308.174 1391244.005 1756964.404 1287666.26 1432546.144 1441140.879 1668897.022 0.865308193 0.860894664 0.869621166 0.833630827 1.052769812 0.771567234 0.858378992 0.863528942 1 20.67046351 -2.548668079 1.986750105 2.606756878 0.869436657 0.245123275 0.070489358 3011829.908 171988.8042 21808266.72 0.016048195 0.00282704 2.548668079 -1.737320221 EFETAETLLNSEVHMLLEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EFETAETLLNSEVHMLLEHR 20 0 O15514;E9PHV4 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ;;;;; 161.32 1.32E-11 64013200 37603.8 32418.3 33483.2 43670.6 39196 34072.9 44219.5 40727.7 9383 FALSE TRUE 35826.3429 35721.76163 35018.43784 39280.74832 46031.76999 32892.94693 37473.00313 37161.36668 10838.06772 3.305602422 3.295952983 3.231059147 3.624331324 4.247230335 3.034945692 3.45753543 3.428781554 1 13.40381995 -0.853482086 1.005355259 0.828288167 3.440445214 0.851518513 0.321895779 34.20358647 15.93489008 20.79911201 0.095314725 0.140125738 0.853482086 2.612157048 EFFNGKEPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EFFNGKEPSR 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;;; 150.06 2.03E-05 5288550000 11652290 9121150 9884350 11217300 10288000 10662420 13370740 11809240 11890220 FALSE TRUE 11101509.34 10050605.55 10337557.22 10089715.69 12082223.94 10293177.72 11330788.04 10775160.34 13734094.59 0.808317525 0.731799646 0.752693027 0.734647313 0.879724824 0.749461688 0.82501165 0.784555565 1 23.71125847 -5 0.236836075 2.237117686 0.758522731 0.704319609 0.044588942 85.66169455 0.855168975 50.86583072 0.06556414 1.00E-05 5 -1.478594955 EFFVTS(ph)APWSVIDQQAIHPELNGATYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFFVTSAPWSVIDQQAIHPELNGATYR 27 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 EFFVT(0.148)S(0.851)APWS(0.001)VIDQQAIHPELNGATYR;EFFVT(0.124)S(0.875)APWS(0.001)VIDQQAIHPELNGATYR 215.05 2.57E-34 81345000 75078 60027 66341 81936 73483 59243 78797 61783 51802 TRUE FALSE 71529.21173 66143.81955 69382.80047 73699.63761 86298.41193 57191.40006 66775.07044 56372.95299 59835.18959 1.195437204 1.105433441 1.159565148 1.231710606 1.442268547 0.955815473 1.115983268 0.942137117 1 15.86870657 EFGFQNNGFSVYINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFGFQNNGFSVYINR 15 0 Q8TAT6;Q8TAT6-2;A0A0D9SFI9;I3L4U9 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 179.8 4.16E-11 48659000 36518 31282 42462 36525 41426 38757 48509 49714 54027 FALSE TRUE 34791.86651 34469.67136 44408.9247 32853.43761 48650.68128 37414.83537 41108.06112 45360.77861 62405.23123 0.557515225 0.552352274 0.711621828 0.526453263 0.779592998 0.599546458 0.658727807 0.726874618 1 15.92937935 -5 0.15397686 2.383945526 0.515124991 0.739822698 0.071594229 60.48450831 0.545938413 25.44441834 0.300447821 1.00E-05 5 -1.868820534 EFGIADPDEIMWFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFGIADPDEIMWFK 14 0 Q15067-2;Q15067;Q15067-3;I3L0T4;I3L4S5;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 125.74 0.00025197 9742500 133340 151133 149526 161243 120501 119209 150362 145123 114514 FALSE TRUE 127037.2825 166533.6245 156381.915 145034.5473 141516.3362 115080.7624 127421.5153 132415.2608 132272.2463 0.96042281 1.259021671 1.182273073 1.096485101 1.069886845 0.870029547 0.963327674 1.001081213 1 17.01315086 2.434931171 4.813523563 0.953358864 1.128285242 0.475658871 0.082318158 0.165272432 8.792449882 0.029101532 0.024545384 272.2269839 -2.434931171 0.174926379 EFGYDS(ph)PHDLDS(ph)D ddPTM_SK-BR-3_Trastuzumab_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 146.59 6.19E-05 165500000 411390 362940 358590 419330 366830 370260 401740 370280 336910 TRUE FALSE 391944.41 399923.9986 375031.7062 377178.1517 430805.0359 357437.8034 340447.1845 337856.3202 389156.2821 1.007164546 1.027669389 0.963704618 0.969220257 1.107023208 0.918494239 0.874834097 0.868176452 1 18.56999012 2.029013406 23.7963036 0.899488176 1.011671996 0.458830881 0.052875095 88.49360225 72580.35968 0.018041461 0.013324194 106.908788 -2.029013406 0.11218382 EFHGNIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFHGNIIK 8 0 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 109.71 0.0035651 103810000 407380 416080 286010 410860 333150 335520 419760 409060 313730 FALSE TRUE 388123.9547 458479.025 299123.8414 369559.5722 391251.2545 323900.8583 355717.9026 373240.5378 362381.6461 1.071036458 1.265182798 0.825438718 1.019807643 1.07966631 0.893811433 0.981611255 1.029965347 1 18.46715036 3.748586456 24.99507868 0.976350819 1.168109625 0.471701013 0.084628405 516.5286287 1287736.618 0.020365181 0.03617987 5605.139893 -3.748586456 0.191758806 EFHLNESGDPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EFHLNESGDPSSK 13 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;;;;; 211.51 2.13E-08 23608650000 30737600 25810600 26715600 31047400 23625610 30022400 34505900 31487300 22412070 FALSE TRUE 29284694.56 28440729.48 27940536.69 27926456.37 27745908.9 28982716.76 29241391.21 28730105.09 25887619.35 1.131223932 1.098622824 1.079301125 1.078757223 1.071782945 1.119558982 1.129551189 1.109800971 1 24.62575896 4.417028354 2.285616113 1.092912094 1.130948822 0.109314884 0.036236803 0.792639648 7.302076888 0.008791329 0.045819295 26123.319 -4.417028354 0.038036729 EFIDFSDTDEVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFIDFSDTDEVFR 13 0 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 0 77.64 0.059087 15242000 20932 20584 18389 25351 25849 23716 25438 23683 26089 FALSE TRUE 19942.58584 22681.533 19232.15384 22802.66932 30357.05742 22894.70897 21556.9659 21609.19097 30134.74888 0.661780389 0.752670384 0.638205213 0.756690205 1.007377149 0.759744475 0.715352432 0.717085484 1 14.87914042 -5 0.177450135 1.964664329 0.69563648 0.384550367 0.09923524 151.1764857 1.448437828 51.92716501 0.324224571 1.00E-05 5 -1.269027849 EFIEKYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFIEKYDK 8 1 E5RK69;H0YC77;P08133;P08133-2;E7EMC6;E5RFF0 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 77.732 0.029596 390320000 322950 159350 238460 389930 372640 283370 473730 281670 370390 FALSE TRUE 307684.7935 175587.9462 249393.6269 350733.4956 437628.298 273556.8258 401453.7879 257005.4816 427828.1895 0.719178402 0.410416963 0.582929393 0.819799873 1.022906645 0.639408138 0.938352819 0.600721242 1 18.70667202 3.246989855 5.250701213 0.837218117 0.554995655 0.398046394 0.154304977 0.153334119 12.25957928 0.039930246 0.05174386 1765.996569 -3.246989855 -0.282222461 EFIEMWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFIEMWR 7 0 Q7L0Y3;C9JVB6 Q7L0Y3 TRMT10C Mitochondrial ribonuclease P protein 1 0 110.61 0.015737 29278000 106310 90622 77655 73429 112660 62497 95069 84560 107540 FALSE TRUE 101284.937 99856.48483 81215.55856 66047.77741 132307.8683 60332.71322 80564.47799 77155.47812 124216.754 0.815388696 0.803889022 0.653821292 0.531713922 1.065137062 0.485705119 0.648579804 0.621135842 1 16.92250025 3.754641025 20.43265918 0.69096685 0.809639121 0.030508899 0.185926407 192.773572 244939.4858 0.043350415 0.077565022 5683.829275 -3.754641025 0.118672271 EFITGDVEPT(ph)DAESEWHSENEEEEKLAGDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFIT(0.001)GDVEPT(0.347)DAES(0.347)EWHS(0.305)ENEEEEKLAGDMK 46.034 0.07696 48873000 79901 81051 75459 77232 58122 62914 60739 61033 42201 TRUE FALSE 76124.23808 89310.18905 78918.86979 69468.49263 68258.4584 60735.2724 51472.15 55688.62696 48745.31555 1.561672896 1.832179935 1.619004183 1.425131663 1.400308063 1.245971469 1.055940441 1.142440588 1 15.57297596 2.52000247 0.846410705 1.036335394 1.707794089 0.891833146 0.086235715 0.17080903 0.249005443 0.059618981 0.044674367 331.1330047 -2.52000247 0.671458695 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAES(0.006)EWHS(0.994)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK 401.18 1.54E-140 3704480000 3034720 3522920 2455488 3364330 2190869 3802110 3025620 3453580 1424667 TRUE FALSE 2891274.8 3881909.553 2568074.554 3026141.157 2572955.86 3670441.977 2564006.1 3151166.227 1645597.082 1.756976134 2.358967207 1.560573108 1.838932014 1.563539391 2.230462133 1.558100781 1.914907519 1 20.65017971 -2.11333136 0.271729085 4.72E-13 1.967002831 0.475636262 0.275919403 27.92479084 1.084044786 17.86383156 0.328783462 0.007703155 2.11333136 1.967002831 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.014)EWHS(0.986)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.077)EWHS(0.923)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.001)EWHS(0.999)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.006)EWHS(0.994)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.001)EWHS(0.999)ENEEEEKLAGDMK 456.91 4.31E-222 9528264000 2960863 2307400 2651809 2830961 1966829 2861911 3344853 3315519 2345309 TRUE FALSE 2820908.874 2542526.683 2773397.066 2546387.422 2309843.355 2762802.304 2834534.242 3025194.58 2709007.542 1.041307132 0.938545443 1.023768677 0.939970592 0.852652981 1.019857738 1.046336785 1.116716928 1 21.36933298 2.009287421 24.99460367 1.052899162 0.963468125 0.366820925 0.05779507 220.1378185 592439.4455 0.02130322 0.015713143 102.1615376 -2.009287421 -0.089431037 EFKEEISRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFKEEISRR 9 2 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 107.24 0.0015777 121634000 228387 190406 214781 239977 194073 227194 276200 286405 258190 FALSE TRUE 217591.5991 209808.5879 224628.9213 215854.056 227919.2698 219326.2148 234060.6172 261325.8599 298228.7865 0.729612998 0.703515547 0.753210057 0.72378679 0.764243024 0.735429391 0.784835763 0.876259676 1 18.18605999 1.042443018 1.224176796 1.000801583 0.729124642 0.967220212 0.016182826 0.072122288 0.223467701 0.014851649 0.004636514 11.02663549 -1.042443018 -0.271676941 EFLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFLEFR 6 0 O75323;C9K068;H7C333;C9J7B1 O75323 GBAS Protein NipSnap homolog 2 0 107.22 0.07317 72897000 254970 231650 220840 220000 235430 179550 225960 216430 206430 FALSE TRUE 242918.0734 255255.3984 230965.7324 197885.182 276488.9175 173332.1385 191485.652 197478.2418 238442.1101 1.018771698 1.070513083 0.968644894 0.829908702 1.159564128 0.726935936 0.803069776 0.828202039 1 17.86327952 2.227205642 24.99999823 0.817554695 1.008629274 0.378743283 0.106497225 194.7147439 428696.1813 0.036698001 0.027340445 168.735181 -2.227205642 0.191074579 EFLHAQEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 144.47 2.38E-05 992480000 1730720 1415620 1528510 1769130 1483300 1632400 2011950 1825950 1465680 FALSE TRUE 1648912.296 1559873.287 1598593.695 1591293.691 1741987.05 1575869.579 1704990.076 1666060.138 1692970.169 0.97397599 0.921382619 0.944253906 0.939941956 1.028953187 0.930831274 1.007099893 0.984104841 1 20.69112512 2.786123094 24.99982183 0.987053599 0.944167603 0.394596072 0.027729335 398.2467504 209325.8952 0.007644224 0.008107905 611.115212 -2.786123094 -0.042885997 EFLHNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFLHNQGK 8 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 128.69 0.0011229 692960000 1555140 1315370 1270050 1618280 1202260 1455960 1613270 1549320 1223780 FALSE TRUE 1481631.614 1449407.698 1328283.049 1455607.42 1411933.763 1405539.74 1367136.032 1413653.327 1413557.552 1.04815797 1.025361646 0.939673837 1.029747546 0.998851275 0.99432792 0.967159795 1.000067755 1 20.43089919 3.983489551 24.63159118 0.989018214 1.039609358 0.417003985 0.023598939 482.2610882 719477.9881 0.005619195 0.010251833 9626.968495 -3.983489551 0.050591145 EFLLIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFLLIFR 7 0 Q96C19;H0Y4Y4 Q96C19 EFHD2 EF-hand domain-containing protein D2 0 95.62 0.031016 10581000 71219 47215 47413 60079 115260 35893 76423 53487 103520 FALSE TRUE 67852.61901 52026.26218 49586.93295 54039.74478 135361.3075 34650.01641 64763.26775 48803.39473 119573.3529 0.567456021 0.435099133 0.414698858 0.451938024 1.132035727 0.28978042 0.541619568 0.408146076 1 16.86753639 -1.238987044 4.617444232 1.000145037 0.526386752 0.296676275 0.227313549 0.000311034 5.13E-05 0.201697786 0.047526186 0.057678367 1.238987044 -0.473758285 EFLLSLDDSVDETEAVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFLLSLDDSVDETEAVKR 18 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A286YEP7;H7C0U8 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 166.37 4.14E-11 132036200 172302 175245 152151 184686 140213 176608 189121 200485 140538 FALSE TRUE 164157.6259 193102.6647 159127.2738 166121.0124 164666.1028 170492.0207 160267.118 182929.4706 162331.9153 1.011246776 1.189554527 0.98025871 1.023341665 1.014379104 1.050268029 0.987280399 1.126885433 1 17.30858714 3.714831038 24.99984987 1.024175534 1.100400684 0.216086554 0.058782119 936.9753719 987132.3624 0.014379239 0.022288439 5185.982391 -3.714831038 0.07622515 EFMKDTDSINLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFMKDTDSINLYK 13 1 O14980 O14980 XPO1 Exportin-1 0 70.332 0.041293 151010000 282320 193610 291800 283060 213920 315060 391430 320730 283000 FALSE TRUE 268975.2931 213339.0791 305179.3186 254606.271 251227.5803 304149.3932 331710.1644 292645.1809 326886.1946 0.822840785 0.652640223 0.933595005 0.778883523 0.768547539 0.93044429 1.014757337 0.895250964 1 18.31842892 2.160502717 4.359895708 0.971491347 0.780916052 0.557284539 0.074928415 0.146963848 5.262608109 0.028352779 0.020665371 144.7113907 -2.160502717 -0.190575295 EFNAEVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EFNAEVHR 8 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;; 243.29 7.08E-09 6813710000 7562460 7744850 5988490 7440720 7290220 6397720 7219170 6884710 6101530 FALSE TRUE 7204997.503 8534059.02 6263068.19 6692764.689 8561632.06 6176165.352 6117753.027 6281848.294 7047724.11 1.022315487 1.210895728 0.888665347 0.949634887 1.214808061 0.876334722 0.868046611 0.891330052 1 22.74872602 2.20045773 24.99955924 0.893958249 1.062480894 0.319334046 0.106470487 174.806549 114690.7687 0.039100249 0.02887804 158.656449 -2.20045773 0.168522645 EFNAEVHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EFNAEVHRK 9 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;; 163.91 4.07E-05 4963840000 6069490 4310960 5518000 5406910 5376310 5739100 7314810 6350600 5713080 FALSE TRUE 5782597.236 4750251.725 5771005.758 4863397.134 6313936.762 5540353.528 6198801.389 5794507.797 6599035.268 0.876279183 0.71984033 0.874522642 0.73698608 0.956796942 0.839570225 0.939349638 0.878084078 1 22.6538237 1.772233176 0.499423208 0.988163656 0.793878631 0.401097522 0.068506811 0.755911814 0.442554316 0.062190362 0.042899133 59.18793336 -1.772233176 -0.194285025 EFNKYDTDGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFNKYDTDGSK 11 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 133.32 0.00014967 4051800000 7603600 6987100 7353200 9154500 5409200 9179800 9765300 10280100 6362030 FALSE TRUE 7244192.897 7699093.434 7690351.493 8234272.268 6352562.767 8861901.224 8275424.133 9379919.946 7348621.12 0.985789413 1.047692255 1.046502652 1.120519365 0.864456428 1.205927082 1.126119308 1.276419044 1 22.80904214 2.199934082 24.99999885 1.160261355 1.021661357 0.347685029 0.093983019 166.5107895 107768.7319 0.031142078 0.023000391 158.4652652 -2.199934082 -0.138599998 EFPDVLECTVSHAVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFPDVLECTVSHAVEK 16 0 P48507 P48507 GCLM Glutamate--cysteine ligase regulatory subunit 0 ;; 233.78 1.17E-19 141159000 531570 446170 441360 549260 395560 492380 581290 542740 431740 FALSE TRUE 506443.7396 491635.2303 461596.7926 494047.3413 464545.5388 475328.7571 492603.5344 495214.8084 498692.0342 1.015544073 0.985849375 0.925614931 0.99068625 0.931527891 0.953150892 0.987791063 0.993027308 1 18.92778963 1.546907965 6.12041255 0.994592473 0.970828457 0.172465116 0.026985445 0.306334024 23.26665407 0.016006987 0.007331588 35.22962052 -1.546907965 -0.023764016 EFPGFLENQKDPLAVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFPGFLENQKDPLAVDK 17 1 P60903 P60903 S100A10 Protein S100-A10 0 ;; 123.55 4.85E-05 309060000 466055 404996 364107 513827 351167 411793 458987 443035 307071 FALSE TRUE 444025.5038 446265.5528 380801.6661 462176.1338 412410.4136 397532.5052 388960.1033 404240.5067 354690.0024 1.25186924 1.258184752 1.073618268 1.303042461 1.162734813 1.120788583 1.096619867 1.139700877 1 18.43619914 2.35155773 0.137028683 0.894906282 1.41921731 0.551283768 0.062141792 6.024259782 0.486627721 0.647677001 1.030143991 224.6765416 -2.35155773 0.524311028 EFQQNNWHAVGCGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFQQNNWHAVGCGFR 15 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;E5RJR3;Q9NZL9-5 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 136.81 2.06E-05 343570000 345190 313660 274310 374610 339140 305410 347070 343890 302290 FALSE TRUE 328873.5528 345622.3106 286887.3848 336953.4911 398285.9086 294833.5751 294118.0971 313777.1685 349167.5893 0.941878808 0.989846484 0.821632344 0.965019382 1.140672619 0.844389869 0.842340773 0.898643454 1 18.41356012 EFRPEDQPWLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 ;; 203.7 1.11E-07 675490000 360811 309627 295834 358891 342024 303707 365729 328405 378200 FALSE TRUE 343756.1791 341178.3433 309398.2815 322814.5948 401672.8773 293189.5504 309930.324 299648.1172 436849.3244 0.786898731 0.780997759 0.708249422 0.738960957 0.919476934 0.671145711 0.70946733 0.685930138 1 18.73677623 -1.08326152 5.706233002 1.000001457 0.751867941 0.552654877 0.070631537 1.27E-06 2.04E-07 0.06640271 0.015651177 0.082554068 1.08326152 -0.248133516 EFSDFIQAVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFSDFIQAVER 11 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 0 82.171 0.045758 4542700 13267 14086 12793 13225 11624 13437 15162 10351 14032 FALSE TRUE 12639.8952 15521.37941 13379.5717 11895.59787 13651.22192 12971.67332 12848.75843 9444.611566 16208.01089 0.779854807 0.95763629 0.825491283 0.733933235 0.842251527 0.800324815 0.792741226 0.582712563 1 13.98441943 3.479783948 24.48203462 0.784996094 0.872548589 0.073782276 0.110130184 160.9339795 1479710.39 0.027322547 0.037692723 3018.449731 -3.479783948 0.087552495 EFSDIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFSDIFR 7 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 119.57 0.011058 114651000 347660 423540 261530 385680 302510 281980 306950 324970 268200 FALSE TRUE 331226.8008 466699.2075 273521.4092 346910.7137 355267.6482 272214.9619 260119.14 296513.904 309791.0862 1.069194097 1.506496566 0.882922141 1.119821483 1.146797516 0.878704953 0.83965986 0.957141497 1 18.24093611 2.974447874 0.879201318 0.902890668 1.257765184 0.280538828 0.163732562 0.572789253 0.978042193 0.086744448 0.105531673 942.8614388 -2.974447874 0.354874516 EFSFEAWNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFSFEAWNAK 10 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 142.43 0.011247 159440000 292131 232124 230440 265763 269707 274933 367609 307653 260537 FALSE TRUE 278322.5466 255777.6995 241005.9019 239047.9983 316743.8154 265412.0013 311523.4954 280713.2723 300939.7473 0.924844754 0.849929934 0.800844369 0.794338403 1.052515722 0.881943989 1.035168994 0.932788955 1 18.19911514 2.74333381 24.99997312 0.978782859 0.850566447 0.570033016 0.059358482 307.1156752 1608544.876 0.017659937 0.018182665 553.7755919 -2.74333381 -0.128216411 EFSHIAFLTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFSHIAFLTIK 11 0 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 ; 141.1 3.83E-05 376340000 902280 851080 661260 663560 812950 708070 1001450 891030 719130 FALSE TRUE 859631.0125 937806.0196 691579.4251 596857.6881 954728.2226 683549.3584 848660.4096 813006.6896 830649.0076 1.034890796 1.129003961 0.8325772 0.718543792 1.149376227 0.82290998 1.021683529 0.978760803 1 19.66387947 3.751195793 24.95431758 0.931848014 1.081947383 0.207173428 0.121967201 1042.584928 2059086.201 0.029490275 0.052714848 5638.918183 -3.751195793 0.150099369 EFSITDVVPYPISLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFSITDVVPYPISLR 15 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 163.78 3.53E-06 19765000 131220 122180 130170 149670 132320 123660 147900 138300 146470 FALSE TRUE 125017.4907 134630.2809 136138.4233 134624.8872 155396.5661 119377.6232 125335.1386 126189.7188 169183.8195 0.738944723 0.795763338 0.804677561 0.795731457 0.918507258 0.705608985 0.740822255 0.745873448 1 17.36823207 4.511814672 2.104410156 0.798646997 0.735134346 0.043668226 0.088035167 1.53384723 10.67911815 0.020949789 0.15526478 32494.86011 -4.511814672 -0.063512651 EFTELLSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFTELLSQDR 10 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ;;; 196.79 7.61E-07 232534000 407803 353822 348799 396235 435442 338976 421294 383680 435193 FALSE TRUE 388526.9604 389876.8641 364791.7792 356404.705 511382.9469 327237.1761 357017.8627 350082.9452 502680.5078 0.772910336 0.775595747 0.725693106 0.709008405 1.017312068 0.650984415 0.710228181 0.696432306 1 18.93928222 -1.834877701 2.451198857 1.095687619 0.756976727 0.371130819 0.099297584 10392600.75 6195250.746 5838187.762 0.022351569 0.01462589 1.834877701 -0.338710891 EFTGS(ph)PPSSATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFTGSPPSSATK 12 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFTGS(0.953)PPS(0.041)S(0.006)ATK;EFT(0.006)GS(0.965)PPS(0.018)S(0.012)ATK 132.97 0.00017999 253760000 972280 936100 773780 1119360 710110 924340 1002460 980150 691600 TRUE FALSE 926322.2513 1031489.654 809258.5784 1006839.806 833952.9592 892329.874 849516.3156 894322.8699 798849.7958 1.159569992 1.291218524 1.013029712 1.26036185 1.043942132 1.117018342 1.063424338 1.119513173 1 19.60756474 2.776504101 0.271449326 0.999329131 1.270016958 0.290620086 0.082046265 3.092307401 0.474948597 0.119119385 0.281714671 597.7286883 -2.776504101 0.270687827 EFTGS(ph)PPSSATKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFTGSPPSSATKK 13 1 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFT(0.011)GS(0.876)PPS(0.109)S(0.004)ATKK;EFT(0.078)GS(0.921)PPSSATKK;EFT(0.01)GS(0.985)PPS(0.004)S(0.001)ATKK;EFT(0.157)GS(0.826)PPS(0.008)S(0.003)AT(0.005)KK 98.408 0.0020415 1916160000 2476400 1930520 2344470 2553640 1612720 2549570 3030990 2695820 1799210 TRUE FALSE 2359345.48 2127242.183 2451966.268 2296943.256 1893977.857 2461277.752 2568556.808 2459759.709 2078222.298 1.135270987 1.023587412 1.179838303 1.105244255 0.911345172 1.184318807 1.235939394 1.183588354 1 20.98691855 EFTKLEEVLTNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFTKLEEVLTNKK 13 2 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 72.315 0.022431 82845000 638030 337750 479670 557900 470770 561680 788890 683750 548270 FALSE TRUE 607871.5864 372167.109 501663.344 501818.8321 552872.1389 542228.8808 668530.3415 623877.2252 633292.9114 0.959858504 0.587669785 0.792150575 0.792396098 0.873011728 0.856205511 1.055641599 0.985132178 1 19.27251341 2.135305083 1.328752395 1.022369526 0.77017078 0.506467439 0.094864114 0.330676049 1.108588461 0.060907572 0.032001715 136.5542064 -2.135305083 -0.252198746 EFTMAEIEHFVDPSEKDHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFTMAEIEHFVDPSEKDHPK 20 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 196.62 1.12E-21 255175000 830155 934636 690994 977990 439389 869222 797205 930278 109690.4 FALSE TRUE 790915.2184 1029876.471 722676.7584 879680.5871 516018.3025 839120.6242 675576.7356 848817.9266 126700.627 6.242393878 8.128424423 5.703813591 6.942985271 4.072736771 6.622860865 5.332070973 6.699397995 1 16.95106414 -0.490970341 0.379297941 3.71E-21 6.766177666 0.683150355 1.100902349 4.74516778 0.674964215 9.55916314 0.754310351 0.322871461 0.490970341 6.766177666 EFTYKHDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFTYKHDEL 9 1 Q9NWM8 Q9NWM8 FKBP14 Peptidyl-prolyl cis-trans isomerase FKBP14 0 ; 108.98 0.0023018 402920000 369840 243440 276640 324950 272950 301780 365160 338790 273590 FALSE TRUE 352358.3962 268246.8128 289324.2176 292285.4086 320552.3936 291329.2829 309448.1354 309123.7516 316016.9399 1.114998444 0.848836815 0.915533888 0.924904243 1.014351932 0.921878691 0.979213758 0.978187282 1 18.26964237 1.20401637 1.662094322 0.998215056 0.955790324 0.036659241 0.070112515 1.375538523 7.019947358 0.063946837 0.018988034 15.99618322 -1.20401637 -0.042424732 EFVEAVLELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EFVEAVLELR 10 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ;;; 147.4 6.27E-05 164134000 357550 307334 279473 336934 360813 239270 336943 311672 339181 FALSE TRUE 340649.3201 338651.684 292287.1135 303064.7542 423738.673 230984.0199 285536.157 284380.3474 391779.4572 0.869492552 0.864393673 0.746050126 0.773559585 1.081574506 0.58957665 0.728818604 0.72586845 1 18.57968223 2.211320907 24.99998136 0.732116279 0.857136076 0.115236841 0.134177505 365.9857633 335891.0726 0.045484119 0.033600362 162.6750343 -2.211320907 0.125019797 EFVISDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFVISDR 7 0 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ;; 150.84 0.0044711 280547000 682670 678210 603460 769010 688810 605910 670330 659450 668540 FALSE TRUE 650401.542 747320.3701 631129.2379 691707.6538 808938.2459 584927.1848 568058.847 601705.062 772213.7688 0.842255821 0.967763591 0.817298607 0.895746336 1.047557397 0.757467956 0.735623826 0.779194941 1 19.55864075 2.190448378 24.999997 0.788189407 0.909669513 0.166412976 0.096787593 145.435144 75569.80917 0.033032823 0.024396408 155.0416489 -2.190448378 0.121480106 EFVISDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EFVISDRK 8 1 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ;; 129.72 0.0017294 851000000 961810 696870 858720 1035410 888630 984030 1290000 1190100 1031070 FALSE TRUE 916347.1474 767881.8453 898093.1614 931328.6196 1043606.791 949952.7944 1093186.808 1085888.535 1190963.07 0.769416929 0.644757058 0.754089849 0.781996221 0.876271328 0.797634132 0.917901516 0.911773474 1 20.18369725 2.132874707 0.495016105 0.993562807 0.692805754 0.797369017 0.045641667 0.372699081 0.197251762 0.043042514 0.036342122 135.7921634 -2.132874707 -0.300757053 EFVTAFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFVTAFKK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 75.378 0.050466 161610000 742100 455952 612490 526580 672580 598460 995860 770440 879110 FALSE TRUE 707022.4037 502414.0272 640573.2723 473647.178 789877.7391 577735.1801 843923.2668 702976.1892 1015437.889 0.696273412 0.494775734 0.630834519 0.466446233 0.777869083 0.568951766 0.831092946 0.692288713 1 19.95367057 0.996557148 0.536274579 1.001927291 0.577326382 0.587388943 0.102624026 0.602273864 0.427846047 0.101505221 0.046817055 9.921038792 -0.996557148 -0.424600909 EFWEIVHSFTDEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFWEIVHSFTDEQKR 15 1 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG63;S4R306 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ; 150.57 2.05E-06 63012000 389075 387598 391313 445080 319506 416927 444005 460730 290112 FALSE TRUE 370684.1958 427094.6769 409255.0881 400339.7128 375227.7452 402488.7134 376263.8825 420386.0387 335101.0873 1.106186192 1.274524891 1.221288452 1.194683419 1.119744935 1.201096412 1.122836949 1.254505147 1 18.35423684 -3.874021114 0.386661566 1.00E-11 1.189805892 0.503261055 0.057478454 201.6646438 3.507671281 164.8340327 0.035663296 0.000133653 3.874021114 1.189805892 EFWGDIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EFWGDIAK 8 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 95.099 0.02301 35211000 122730 98441 91013 103810 112300 94214 140550 114710 114080 FALSE TRUE 116928.7961 108472.2498 95186.03607 93374.82157 131885.0844 90951.34556 119106.5161 104665.3843 131770.9438 0.887364033 0.823187925 0.722359827 0.708614653 1.000866205 0.690223072 0.90389059 0.794297903 1 17.00767276 -0.953359962 0.557927553 1.047552449 0.817109398 0.261744479 0.096538092 29.25497988 5.487546681 2.426408788 0.037534956 0.111337134 0.953359962 -0.230443051 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA 33 2 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 65.301 0.0016661 71789000 27991.7 19890.4 26270.7 29411.6 30406.6 28549.4 33074.4 23169.6 2471.31 FALSE TRUE 26668.58782 21917.25437 27475.23758 26455.09009 35709.50141 27560.72712 28028.29283 21140.74699 2854.548133 9.34249015 7.678011843 9.625074197 9.267698023 12.50968621 9.655022734 9.818819484 7.405987221 1 11.47904667 0.834742839 2.755115609 1.002851837 9.561193415 0.842746405 1.181063475 0.275875174 3.691097936 1.193492406 0.315779762 6.835067998 -0.834742839 8.558341578 EFYILWTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EFYILWTK 8 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 128.1 0.0026707 113435000 604930 741560 567710 679190 515400 573990 633310 626190 480020 FALSE TRUE 576336.1578 817125.8071 593740.065 610916.5308 605285.5968 554112.5824 536686.928 571357.484 554459.05 1.03945667 1.473735179 1.070845656 1.101824437 1.091668712 0.999375125 0.967946917 1.030477335 1 19.08072139 3.506089252 23.4935615 1.031547716 1.259211783 0.410917951 0.110021458 279.1165878 226367.3558 0.028564624 0.044138444 3206.92831 -3.506089252 0.227664066 EGAAHAFAQYNLDQFTPVKIEGYEDQVLITEHGDLGNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGAAHAFAQYNLDQFTPVKIEGYEDQVLITEHGDLGNGK 39 1 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 145.43 2.09E-13 59333000 122000 107940 118920 126690 93068 136590 160390 139790 86143 FALSE TRUE 116233.3018 118939.2087 124372.5996 113954.8805 109299.0297 131859.8541 135919.5597 127549.2465 99501.61648 1.168154909 1.195349512 1.249955569 1.145256575 1.098464865 1.325203135 1.366003534 1.28188115 1 16.60243234 2.225657911 24.99050486 1.285490995 1.176777938 0.039325603 0.106707414 350.9317087 679695.236 0.036111473 0.026837905 168.134916 -2.225657911 -0.108713058 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR 39 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 138.69 4.30E-10 108150000 57681 34947 53600 52516 43593 49742 70077 61507 36999 FALSE TRUE 54954.53344 38508.13903 56057.61302 47236.99191 51195.6054 48019.42207 59385.4666 56121.12101 42736.61596 1.285888745 0.901057282 1.311699857 1.105304921 1.197933066 1.123613112 1.389568764 1.313185889 1 15.38318505 1.770102786 25 1.275437938 1.141014478 0.031793801 0.150124405 50.42645303 39987.97413 0.063568411 0.035261824 58.89830355 -1.770102786 -0.134423461 EGALCEENMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 EGALCEENMR 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 231.81 1.18E-09 4511021000 2161690 1890576 1810502 2188694 2141497 1988508 2391673 2158764 2411009 FALSE TRUE 2059511.198 2083227.844 1893515.308 1968682.321 2514973.399 1919645.469 2026779.358 1969731.18 2784895.962 0.739528954 0.748045123 0.679923176 0.706914135 0.903076249 0.68930599 0.72777561 0.707290759 1 21.409192 -1.304197919 5.357138186 1.000049046 0.738113468 0.63520938 0.062460609 3.40E-05 4.42E-06 0.056188738 0.013241338 0.049636606 1.304197919 -0.261935578 EGAPIEPDPPVSHWKPEAVQYYEDGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGAPIEPDPPVSHWKPEAVQYYEDGAR 27 1 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 90.097 0.0040984 78693000 221850 183870 187780 224960 183910 182040 213860 190960 175270 FALSE TRUE 211363.5902 202606.562 196389.8987 202346.5934 215983.8458 175735.9092 181231.7292 174238.5301 202449.9764 1.044028722 1.000773453 0.970066296 0.99948934 1.066850437 0.868046083 0.895192642 0.860649792 1 17.62720595 2.231036405 24.99740082 0.895976429 1.013798101 0.584987085 0.045783193 105.0239901 348914.3003 0.015434008 0.011619992 170.2301198 -2.231036405 0.117821673 EGASGRPGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 EGASGRPGS(1)PK;EGAS(0.001)GRPGS(0.999)PK 63.037 0.046739 403200000 602710 588310 551440 734790 480450 672100 717900 760660 536210 TRUE FALSE 574221.0928 648259.4579 576724.0694 660927.5132 564240.3279 648825.0085 608371.1699 694052.5779 619362.7082 0.927116026 1.046655618 0.931157239 1.067108989 0.911001454 1.047568735 0.982253471 1.120591487 1 19.240425 1.272109915 24.99929104 1.060295913 0.99021199 0.196454811 0.060979233 235.8577888 175749.7829 0.034726089 0.012679387 18.7115565 -1.272109915 -0.070083923 EGATVYATGTHAQVEDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 268.55 1.73E-31 3800580000 1925660 1467780 1760060 1616810 1857540 1336780 1730070 1609460 1803520 FALSE TRUE 1834637.868 1617348.451 1840760.492 1454285.187 2181494.388 1290486.973 1466116.047 1468527.15 2083200.67 0.880682257 0.776376695 0.883621304 0.698101344 1.047183989 0.619473194 0.703780518 0.704937921 1 20.99037039 2.195329139 24.99997924 0.725268964 0.842279405 0.097923991 0.132432633 236.3307324 136664.3744 0.043434168 0.032078463 156.7938913 -2.195329139 0.117010441 EGDELEDNGKNFYES(ph)DDDQKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGDELEDNGKNFYESDDDQKEK 22 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 EGDELEDNGKNFY(0.002)ES(0.998)DDDQKEK 71.974 0.0082428 260900000 272680 243360 251760 298640 197150 272610 293800 299790 198340 TRUE FALSE 259790.9568 268158.6607 263303.445 268620.1398 231532.8976 263169.4473 248975.414 273538.7983 229097.5542 1.133975252 1.170499884 1.149307097 1.172514219 1.010630159 1.148722204 1.086765919 1.193983931 1 17.80560253 EGDIIPPLTGAT(ph)PPLIGHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGDIIPPLTGATPPLIGHLK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EGDIIPPLTGAT(1)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK 215.48 4.39E-24 125306000 372880 414450 386060 455870 287189 447610 478070 471330 351070 TRUE FALSE 355254.7014 456682.9262 403761.2329 410045.0815 337274.6707 432109.1535 405131.6411 430057.8465 405512.1426 0.876064275 1.126188043 0.995682226 1.011178306 0.831725207 1.065588692 0.999061677 1.060530133 1 18.62938559 EGDIVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGDIVKR 7 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 113.7 0.0097355 4399220000 8348170 5708150 7210560 6423800 6057160 6407640 7701610 7280580 6317370 FALSE TRUE 7953568.549 6289816.975 7541171.308 5778067.42 7113526.786 6185741.82 6526587.945 6643053.818 7297035.475 1.089972575 0.861968809 1.033456852 0.79183765 0.974851611 0.847706146 0.894416365 0.910377076 1 22.79887904 4.63641231 2.83858551 0.908316106 1.103471558 0.357138963 0.073297028 0.310832357 3.960165459 0.015550977 0.124879518 43292.46454 -4.63641231 0.195155452 EGDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGDKFK 6 1 P26447 P26447 S100A4 Protein S100-A4 0 64.803 0.096415 7519300000 2239900 1303300 1803100 1954100 1165000 2195800 2403400 2221900 1254900 FALSE TRUE 2134024.366 1436107.752 1885773.919 1757670.155 1368175.631 2119758.895 2036717.189 2027338.657 1449503.483 1.472245077 0.9907584 1.300979226 1.21260154 0.943892614 1.462403451 1.405113691 1.398643522 1 20.46712737 2.194785315 24.99998068 1.360176198 1.190533769 0.084753303 0.193352125 245.4606803 140180.6219 0.066677925 0.049245181 156.597677 -2.194785315 -0.169642429 EGDKHTLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 EGDKHTLSK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;; 132.91 0.00017527 91137460000 141305710 105630050 112291670 141948220 82561870 136629310 151279100 143158850 79002380 FALSE TRUE 134626469.1 116393872.2 117440354.1 127679315.2 96960633.99 131897802.7 128198694.9 130623102.2 91253665.6 1.475299302 1.275498046 1.286965881 1.399169167 1.062539607 1.445397309 1.404860769 1.431428549 1 26.44337918 4.612912277 2.988577206 1.311745424 1.482160995 0.111998591 0.152724647 0.687594308 10.15430293 0.034208426 0.239314382 41012.12547 -4.612912277 0.170415571 EGDKHTLSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGDKHTLSKK 10 2 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;; 125.74 0.00024087 13336480000 11050790 5701060 9690410 8010400 6856880 10602580 14601500 11626730 7420810 FALSE TRUE 10528441.06 6282004.496 10134724.88 7205179.373 8052717.701 10235410 12373773 10608631.88 8571591.315 1.228294802 0.732886609 1.182362121 0.8405883 0.939465894 1.194108494 1.443579441 1.237650221 1 23.03113163 2.120235006 4.642583514 1.285418756 0.97566207 0.272972663 0.181054145 0.205236862 7.433877275 0.064875319 0.046935443 131.8970269 -2.120235006 -0.309756686 EGDLIAAQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 181.41 4.40E-06 724700000 1538450 1222710 1168060 1430580 1393600 1209710 1564860 1314130 1421850 FALSE TRUE 1465730.517 1347305.539 1221616.706 1286775.38 1636643.399 1167817.439 1326111.866 1199057.811 1642343.236 0.892462967 0.820355642 0.743825456 0.783499668 0.996529448 0.711067829 0.807451108 0.730089657 1 20.64732424 EGDNVNYDWIHWDPEHSYEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGDNVNYDWIHWDPEHSYEFK 21 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 256.11 1.12E-36 124441000 195071 163211 172356 209377 142837 204799 222047 203432 18830.7 FALSE TRUE 185850.3804 179842.3865 180258.6931 188330.0262 167747.7276 197706.7593 188169.652 185618.4156 21750.86878 8.544503775 8.268285201 8.287424971 8.658505923 7.712231142 9.089602869 8.651132691 8.533839153 1 14.40878541 -1.607779734 10.22739469 0.999272014 8.4736344 0.978094432 0.351239792 0.00544588 0.000208849 0.317647878 0.074885068 0.024672904 1.607779734 7.474362385 EGDPAIYAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGDPAIYAER 10 0 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ; 110.79 0.0042782 351125000 553690 498210 436820 553150 447800 494240 572860 547590 508950 FALSE TRUE 527518.171 548978.1654 456848.6291 497546.3111 525896.1782 477124.3449 485459.6857 499640.1166 587875.3666 0.897329946 0.933834273 0.77711817 0.846346589 0.89457087 0.81160799 0.825786745 0.849908237 1 19.1651508 3.774004275 24.97350506 0.847646597 0.915582123 0.119058965 0.060403674 842.0598728 593310.267 0.013667167 0.024637677 5942.980089 -3.774004275 0.067935526 EGDPVSLSTPLETEFGSPSELS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGDPVSLSTPLETEFGSPSELSPR 24 0 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 EGDPVSLSTPLETEFGSPS(0.001)ELS(0.999)PR;EGDPVSLSTPLETEFGSPS(0.001)ELS(0.999)PR 152.13 6.38E-08 57140000 96698 89358 98492 101165 92870 94145 116203 99062 89889 TRUE FALSE 92127.27718 98463.68179 103007.9556 90995.702 109066.4986 90884.73504 98474.09814 90387.60612 103828.527 0.887302168 0.948329757 0.99209686 0.876403669 1.050448289 0.875334917 0.948430079 0.870546936 1 16.66384336 EGDVLTLLESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;;;;;; 329.18 9.64E-58 3062679000 2512424 2185304 2264203 2582947 2298471 2250790 2706459 2479133 2448154 FALSE TRUE 2393666.697 2407988.962 2368018.947 2323304.26 2699323.615 2172844.578 2293538.972 2262046.972 2827801.219 0.846476294 0.851541101 0.837406438 0.82159391 0.954566253 0.768386605 0.811067962 0.799931394 1 21.43124928 -0.962668885 4.112886847 1.000008644 0.836508394 0.529918706 0.048433137 9518025.495 25205565.46 1313.891022 0.011074277 0.108976063 0.962668885 -0.16350025 EGDYVLFHHEGGVDVGDVDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EGDYVLFHHEGGVDVGDVDAK 21 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;;;;;; 179.46 3.32E-17 2021140000 3148536 3044831 2962493 3412115 2014098 3347980 3238409 3432870 171929.9 FALSE TRUE 2999710.943 3355102.741 3098326.234 3069122.718 2365356.054 3232038.613 2744330.23 3132269.704 198591.9108 15.10489995 16.89445822 15.6014725 15.45441959 11.91063646 16.27477474 13.81894267 15.7723932 1 17.59944733 -0.655917228 0.813146031 8.65E-23 15.25941468 0.908281034 1.406304436 7.372931597 2.946605348 26.13427708 0.445471497 0.22084256 0.655917228 15.25941468 EGEELVMDEEAYVLYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGEELVMDEEAYVLYHR 17 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 148.7 3.52E-07 17144000 31409 32101 23910 33906 27231 26931 30973 31949 21642 FALSE TRUE 29924.35882 35372.1284 25006.29715 30497.70446 31980.07778 25998.37272 26247.49999 29151.37619 24998.13083 1.197063853 1.41499093 1.000326677 1.219999394 1.27929876 1.040012667 1.049978503 1.166142236 1 14.6095326 2.641121031 0.412613202 1.01624184 1.311117488 0.264616489 0.114796575 1.492400964 0.528392013 0.113657069 0.167903366 437.6440528 -2.641121031 0.294875648 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGEEPTVYSDEEEPKDESAR 20 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPT(0.001)VYS(0.999)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR 269.44 1.31E-37 15078700000 10262770 8773830 7701140 13383500 6319210 11982790 10878220 10131180 4563810 TRUE FALSE 9777669.201 9667893.252 8054244.886 12038165.15 7421278.223 11567822.98 9218547.747 9244040.17 5271542.346 1.854802363 1.833978107 1.527872558 2.283613478 1.407800172 2.194390601 1.748738252 1.753574109 1 22.3297937 0.563461304 1.930904191 1.000157595 1.840460403 0.499519397 0.261199544 2.112915752 8.473165525 0.210877163 0.058386967 3.659833299 -0.563461304 0.840302808 EGERPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGERPSLR 8 1 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ; 137.13 0.00069432 440670000 339190 312190 284490 361020 266730 300220 324220 344000 306340 FALSE TRUE 323157.1609 344002.5159 297534.1479 324729.5837 313247.6276 289823.3061 274754.2843 313877.5363 353845.6426 0.913271557 0.972182428 0.840858589 0.917715367 0.885266313 0.819067048 0.776480621 0.887046493 1 18.43276063 3.305154692 1.100616926 0.849363753 0.939972378 0.021292411 0.066386476 0.732609762 1.884475402 0.024779337 0.042182304 2019.085416 -3.305154692 0.090608624 EGES(ph)LEDLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGESLEDLMK 10 0 P13796 P13796 LCP1 Plastin-2 1 EGES(1)LEDLMK;EGES(1)LEDLMK 165.35 6.17E-06 85991000 375330 335370 128179 286070 146588 272120 289810 342500 116907 TRUE FALSE 357588.8947 369544.5843 134056.1339 257313.7001 172152.9008 262696.4162 245594.1618 312508.8843 135036.3405 2.648093791 2.736630621 0.992741165 1.905514465 1.274863494 1.945375706 1.818726432 2.314257652 1 17.04298819 3.764107633 24.53458181 1.669219012 2.692362509 0.524570006 0.426280773 415.0868824 398635.1835 0.099514902 0.179310643 5809.083685 -3.764107633 1.023143497 EGEVLYIIEEDKGDGWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGEVLYIIEEDKGDGWTR 18 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;;;; 200.48 1.38E-15 168677000 407709 349161 344458.8 420118 239260.9 394178.9 432260 426417 256509.9 FALSE TRUE 388437.4036 384740.9029 360252.5767 377886.9405 280987.9252 380528.3859 366310.798 389077.6669 296288.1452 1.311012303 1.29853627 1.215885895 1.27540351 0.948360337 1.284318634 1.236332955 1.313173251 1 18.17664138 -5 0.194814185 0.007095331 1.279189029 0.30013215 0.108635964 175.7281392 1.728873342 68.58602257 0.268648673 1.00E-05 5 1.272093699 EGFDKIDISAVVAYTIAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGFDKIDISAVVAYTIAVK 19 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 153.14 4.44E-08 6572500 41970 44968 36299 46920 26171 46133 40000 47659 21307 FALSE TRUE 39986.16128 49550.29032 37963.34505 42203.51246 30735.21411 44535.40264 33897.26535 43485.7253 24611.18074 1.624715275 2.013324385 1.542524329 1.714810553 1.248831352 1.809559773 1.377311626 1.766909348 1 14.58702625 -2.563145035 0.157112163 4.99E-11 1.887226537 0.449375001 0.218798228 43.60978915 0.822975777 16.55456957 1.011950541 0.002734355 2.563145035 1.887226537 EGFHFEETLTGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGFHFEETLTGFK 13 0 Q96G03-2;H0Y921;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 ; 192.15 2.96E-06 136562000 629940 644460 572460 688510 494550 635070 662580 709640 451730 FALSE TRUE 600163.9846 710131.2067 598707.8572 619299.6667 580799.3634 613077.3667 561491.2519 647500.1596 521781.9813 1.150219835 1.360973035 1.147429154 1.186893547 1.113107359 1.174968452 1.076103185 1.240940053 1 18.9930876 -1.203459409 0.097794147 0.697143542 1.379628543 0.343935429 0.077768904 57.98180952 1.051097882 6.19969255 1.865373805 0.062595137 1.203459409 0.682485 EGGDGEEQDVGDAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;; 318.47 4.45E-56 659770000 876500 731340 733330 862130 719780 798180 971280 858080 813720 FALSE TRUE 835069.5821 805864.3775 766953.9059 775467.0545 845309.4041 770538.8265 823093.3972 782941.9662 939907.5417 0.888459285 0.857386862 0.815988671 0.825046103 0.899353784 0.819802792 0.875717409 0.832998919 1 19.84215932 -1.821666595 2.536769302 1.051425988 0.854242413 0.71839942 0.029116701 12707537.17 8625028.972 3999592.445 0.006701283 0.015077641 1.821666595 -0.197183575 EGGFLLLHTLLR ddPTM_SK-BR-3_Trastuzumab_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 ; 237.53 4.16E-16 2200500000 2855290 5217600 2375740 3344370 2374840 2672820 2500940 3233080 1732150 FALSE TRUE 2720326.1 5749279.372 2484670.029 3008187.574 2789011.344 2580259.573 2119375.67 2949974.376 2000762.975 1.359644363 2.873543464 1.24186126 1.503520212 1.393973888 1.289637806 1.059283731 1.474424713 1 20.93211883 3.693794001 24.99273204 1.283394586 2.11659429 0.44158222 0.390928138 329.4874955 183949.3523 0.098333408 0.152338209 4940.762766 -3.693794001 0.833199704 EGHALGGGMEADGPASLQELPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGHALGGGMEADGPASLQELPPSPR 25 0 Q6ZVX7 Q6ZVX7 NCCRP1 F-box only protein 50 1 EGHALGGGMEADGPASLQELPPS(1)PR;EGHALGGGMEADGPASLQELPPS(1)PR 162.02 1.29E-11 273850000 283610 261620 250370 261700 268750 263880 287230 264070 230520 TRUE FALSE 270204.3174 288279.3754 261849.7121 235393.4188 315619.9149 254741.7694 243407.7882 240946.6309 266267.8643 1.014783808 1.082666796 0.983407115 0.884047421 1.185347379 0.956712407 0.91414632 0.904903157 1 18.0225188 2.018696345 24.98790648 0.93146517 1.030743329 0.226493461 0.079103362 303.1937599 405220.6884 0.027783663 0.020516667 104.3990016 -2.018696345 0.099278159 EGHGSSS(ph)FDRELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGHGSSSFDRELER 14 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGS(0.08)S(0.084)S(0.836)FDRELER 92.671 0.0029471 300780000 73319 66664 74126 85864 95308 74833 78859 84973 93273 TRUE FALSE 69853.35617 73457.13739 77524.75042 77232.78759 111929.685 72241.51445 66827.61121 77532.31365 107737.3005 0.648367426 0.681817134 0.719572052 0.716862101 1.038913028 0.67053392 0.620282956 0.719642253 1 16.7171583 -2.396222984 2.142253467 2.996441853 0.71727817 0.351069147 0.115978581 5802327.765 549679.5426 56168084.58 0.028231388 0.004015846 2.396222984 -2.279163683 EGHILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EGHILK 6 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 0 ;;;;; 106.84 0.03178 2317800000 10718360 9588120 9545420 11106970 8740200 10227580 12029150 11255190 8737370 FALSE TRUE 10211724.36 10565160.33 9983086.949 9990476.274 10264488.11 9873396.34 10193882.24 10269625.9 10092316.72 1.01183154 1.046851841 0.989176938 0.989909112 1.017059651 0.978308214 1.010063648 1.017568729 1 23.26675405 3.730708988 24.96722543 1.000224964 1.029341691 0.395788389 0.014918646 460.8359035 1465403.838 0.003718088 0.00587705 5379.092196 -3.730708988 0.029116726 EGHLSPDIVAEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 77.22 0.026541 183060000 1024000 869990 827800 1176000 832400 883340 1101800 1203300 873670 FALSE TRUE 975597.5494 958642.9701 865755.4488 1057786.246 977570.2965 852749.7143 933700.1741 1097932.673 1009154.282 0.966747669 0.949946889 0.857901973 1.048190812 0.968702521 0.845014216 0.925230355 1.087973061 1 19.94471532 1.249243673 24.99741518 1.043986535 0.937459411 0.347792403 0.060686814 201.7458991 472075.0564 0.039850188 0.014218645 17.75185219 -1.249243673 -0.106527124 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK 390.85 4.09E-146 3727060000 1113557 1184441 969177 1289183 798852 1168020 1087146 1182957 958462 TRUE FALSE 1060921.367 1305136.884 1013614.724 1159591.876 938171.5359 1127571.175 921281.9109 1079371.014 1107095.392 0.958292642 1.178883856 0.915562229 1.047418212 0.847417072 1.018495048 0.832161273 0.974957553 1 20.07834811 2.762456314 24.21627453 0.923735474 1.037181678 0.189185879 0.089956014 658.513964 667346.9136 0.025479258 0.027010448 578.7037729 -2.762456314 0.113446204 EGHSLEMENENLVENGADS(ph)DEDDNSFLKQQS(ph)PQEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGHSLEMENENLVENGADSDEDDNSFLKQQSPQEPK 36 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 2 EGHSLEMENENLVENGADS(0.959)DEDDNS(0.267)FLKQQS(0.774)PQEPK 59.158 0.03891 197210000 28883 18757 30457 26991 27916 31409 41522 26026 29616 TRUE FALSE 27517.75783 20668.35962 31853.48358 24277.8134 32784.54156 30321.29845 35187.0563 23747.02547 34208.69802 0.804408218 0.60418434 0.931151591 0.709697089 0.958368586 0.886362247 1.028599693 0.69418092 1 15.06207558 3.089971114 1.191313726 0.922913456 0.719742797 0.225019318 0.124634485 0.519886431 1.568851284 0.046218922 0.061031016 1230.186944 -3.089971114 -0.203170659 EGHYIHWDHVMVPHWDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGHYIHWDHVMVPHWDPK 18 0 H0YCZ3;Q5VSG8-3;Q5VSG8 H0YCZ3 MANEAL "Glycoprotein endo-alpha-1,2-mannosidase-like protein" 0 34.498 0.091036 122490000 177650 120270 153600 238700 308050 166700 270670 175250 296060 FALSE TRUE 169252.8366 132525.6497 160642.7119 214705.4225 361773.8225 160927.1372 229374.3203 159904.1809 341971.4727 0.494932619 0.387534225 0.469754716 0.627846004 1.057906438 0.470586438 0.670741096 0.467595088 1 18.38351645 3.191595208 4.190938029 0.70067334 0.441165156 0.300751524 0.192330203 0.260061515 9.588074759 0.052493558 0.065650757 1554.51604 -3.191595208 -0.259508184 EGIDPTPYYWYTDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 226.04 2.14E-12 1295678000 432425 380173 382499 446371 372298 371674 438145 397950 376311 FALSE TRUE 411985.1272 418913.0609 400036.9575 401500.939 437226.6533 358802.8362 371297.9332 363103.3883 434667.3879 0.947816971 0.963755443 0.920328896 0.923696947 1.005887871 0.825465278 0.854211619 0.83535917 1 18.72955233 2.231739853 24.99979494 0.863812134 0.950699297 0.301059986 0.053536501 151.0087967 553479.5416 0.017479747 0.013194262 170.5060734 -2.231739853 0.086887162 EGIDPTPYYWYTDQRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGIDPTPYYWYTDQRK 16 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 166.9 1.04E-08 361570000 652880 409160 667790 572760 640250 648310 950330 738090 817560 FALSE TRUE 622019.6563 450853.8692 698408.832 515185.0766 751909.3973 625858.8621 805339.7045 673458.9267 944343.0293 0.658679777 0.477425951 0.73957112 0.545548663 0.796224861 0.662745255 0.852804203 0.713150736 1 19.84895148 1.316377528 0.303285373 1.035874565 0.536691165 0.59726964 0.094238049 0.916428911 0.30181654 0.176147365 0.134759654 20.71941685 -1.316377528 -0.499183401 EGILPERAEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 122.46 0.00032662 170964000 688050 550710 632370 685020 595550 728110 820390 676550 786350 FALSE TRUE 655527.2401 606827.9751 661364.79 616160.4881 699413.7314 702895.3681 695224.438 617307.6954 908293.1419 0.721713299 0.668097057 0.728140244 0.678371838 0.77003084 0.773864005 0.76541857 0.679634874 1 19.79279846 -5 0.236769248 2.548913558 0.693979199 0.822661939 0.040107567 64.33849069 0.64231328 47.90920033 0.061861276 1.00E-05 5 -1.85493436 EGIPALDNFLDKL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGIPALDNFLDKL 13 1 P13639 P13639 EEF2 Elongation factor 2 0 115.33 0.00029896 0 244200 243110 263560 225450 228290 230110 286380 217180 199710 FALSE TRUE 232657.15 267883.1854 275644.4867 202787.3377 268103.7037 222141.233 242687.4713 198162.5679 230680.0068 1.008570934 1.161276129 1.194921443 0.879085017 1.162232078 0.962984335 1.052052471 0.859036596 1 17.81553344 1.996364264 0.897986274 0.950870354 1.09044536 0.199784775 0.10339961 0.893671552 1.329824656 0.078957886 0.038352033 99.16633525 -1.996364264 0.139575006 EGIQWEAKEDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGIQWEAKEDNSEGEEILEEVGGDLEEEDDHHMEFCR 37 1 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 EGIQWEAKEDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EGIQWEAKEDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR 166.6 4.42E-18 144823000 205959 83404 55494.9 142489 82099 119402 237622 242285 53982 TRUE FALSE 196223.7262 91902.96242 58039.39606 128165.735 96417.03961 115267.0788 201368.3997 221069.241 62353.25286 3.146968558 1.473908067 0.93081585 2.055477928 1.546303283 1.848613721 3.229477059 3.545432369 1 15.9281772 1.75467295 25 2.809351226 1.855942558 0.128691606 0.868995307 8.950900737 13904.70301 0.380730838 0.211136012 56.84247115 -1.75467295 -0.953408667 EGIREETVSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;;; 195.77 5.72E-08 3602113000 2953390 2670220 2562640 2996000 2719420 2647420 3200330 2867380 2829150 FALSE TRUE 2813789.108 2942318.454 2680139.579 2694836.388 3193685.987 2555739.182 2712060.88 2616297.006 3267880.133 0.861044161 0.900375269 0.820146232 0.824643585 0.97729594 0.782078619 0.829914431 0.800609845 1 21.63992364 EGIREETVSLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGIREETVSLRK 12 2 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 60.157 0.052833 34841000 46429 42895 41085 45167 50578 41052 52619 43789 41138 FALSE TRUE 44234.39318 47266.04927 42968.78789 40626.72735 59398.78719 39630.35895 44591.00514 39954.60302 47517.47094 0.930907986 0.994708858 0.904273461 0.854985052 1.250041006 0.834016587 0.938412846 0.840840268 1 15.53617043 EGIVALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGIVALR 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 98.133 0.026723 98616000 144040 144730 113750 140630 180040 114050 141730 124320 131930 FALSE TRUE 137231.5147 159478.1515 118965.55 126493.6052 211438.919 110100.4199 120106.4854 113433.8817 152389.0306 0.900534075 1.04651989 0.780670036 0.83007028 1.38749435 0.722495704 0.788157028 0.744370387 1 17.21739953 EGIVALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGIVALRR 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 152.63 0.00072797 1869090000 1932950 1517890 1666300 1503440 2664120 1584890 2618180 1886180 3100620 FALSE TRUE 1841583.284 1672564.717 1742701.503 1352311.355 3128741.685 1530004.862 2218728.555 1721016.08 3581448.314 0.514200715 0.467007917 0.486591276 0.377587846 0.873596772 0.427202832 0.619505954 0.480536344 1 21.77211169 -5 0.246392209 3.78814272 0.485106103 0.536734596 0.136903181 128.7087408 1.278636171 180.4128451 0.181195333 1.00E-05 5 -3.303036616 EGKDQELAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGKDQELAK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 111.06 0.0019942 163660000 305330 233040 279690 312530 193840 319340 327490 343680 247260 FALSE TRUE 290897.656 256787.0409 292514.0632 281113.8906 227645.6346 308281.1757 277525.3857 313585.5572 285603.818 1.0185356 0.89910227 1.024195213 0.984279176 0.797067897 1.079401452 0.971714551 1.097973968 1 18.12365574 EGKPTIVEEDDPELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGKPTIVEEDDPELFK 16 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ; 202.5 2.76E-11 313710000 1452500 1250610 1209880 1454100 775480 1420490 1535660 1624770 868860 FALSE TRUE 1383843.204 1378048.581 1265354.195 1307931.105 910723.4665 1371298.075 1301366.863 1482496.525 1003598.371 1.378881476 1.37310763 1.260817306 1.303241558 0.907458095 1.366381328 1.296700852 1.477181079 1 19.9367506 3.675886741 2.525689835 1.240094829 1.379876945 0.11680112 0.165896288 0.627568281 7.847113002 0.04431091 0.07986007 4741.18325 -3.675886741 0.139782116 EGKTDYYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGKTDYYAR 9 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ; 99.283 0.0049633 684610000 578640 192939 556180 313030 725120 517790 1050820 607830 1098930 FALSE TRUE 551288.834 212599.7035 581681.4031 281563.6297 851580.6984 499858.8025 890498.1094 554605.1829 1269346.452 0.434309194 0.167487531 0.458252672 0.221817794 0.670881222 0.393792256 0.70154063 0.436921836 1 20.27565446 0.348478549 0.250246442 1.185632571 0.233451242 0.615463377 0.150348972 2.883740433 0.378558477 0.822003979 0.274281054 2.230892016 -0.348478549 -0.952181329 EGLDWDLIYVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGLDWDLIYVGR 12 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 ; 108.67 0.0039111 15963000 72267 73188 68129 81087 73053 65116 73588 75768 76375 FALSE TRUE 68851.08213 80645.94041 71252.78204 72935.9807 85793.42007 62861.01659 62360.79906 69133.35225 88218.84493 0.78045776 0.914157746 0.807682101 0.82676191 0.972506726 0.712557693 0.706887504 0.783657418 1 16.42879925 2.209132184 24.99984996 0.766628984 0.856478849 0.034800608 0.098363022 355.4531325 301960.2309 0.033344253 0.024630166 161.8572601 -2.209132184 0.089849865 EGLEDKYNLQLNPEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGLEDKYNLQLNPEWR 16 1 M0R2P8;M0QYF4;M0R3A4;M0QXD5;M0QYA2;Q9NWS0 M0R2P8 PIH1D1 PIH1 domain-containing protein 1 0 ; 198.07 3.80E-11 197396000 398730 358390 350710 417210 328620 374020 455130 433810 363610 FALSE TRUE 379882.8231 394910.3485 366790.4004 375271.2582 385931.224 361067.5936 385691.5595 395823.2966 419996.7817 0.904489843 0.940269939 0.873317169 0.893509842 0.918890908 0.859691334 0.918320273 0.942443642 1 18.68001875 0.96635787 2.15924901 0.999395055 0.902753283 0.669741764 0.022652345 0.208485369 2.121227435 0.021345778 0.005891543 9.254604634 -0.96635787 -0.096641772 EGLELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EGLELLK 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 119.21 0.011243 1242703000 2889580 2645642 2077206 2702055 1879278 2606922 2663091 2830850 1975735 FALSE TRUE 2752995.28 2915235.928 2172447.95 2430439.298 2207023.488 2516643.637 2256787.557 2582965.767 2282121.893 1.206331392 1.277423409 0.951942119 1.064991009 0.967092728 1.102764776 0.98889878 1.131826382 1 21.12194442 3.745635983 24.99887656 1.030039431 1.241877413 0.686107369 0.059679347 247.1093244 873090.659 0.01343996 0.023610673 5567.189231 -3.745635983 0.211837981 EGLELPEDEEEKK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 198.33 2.03E-07 2760520000 3745540 4022350 2981140 4326510 1433280 4002180 3285940 4319150 1320700 FALSE TRUE 3568495.747 4432232.038 3117828.218 3891600.995 1683243.578 3863583.503 2784609.503 3940942.329 1525507.411 2.339218887 2.90541495 2.04379749 2.551020708 1.103399149 2.532654693 1.825366093 2.583364919 1 20.54085776 3.279195712 1.82219135 1.931666314 2.592815309 0.196516212 0.567855029 0.499470784 3.415074029 0.161215442 0.232885532 1901.935181 -3.279195712 0.661148995 EGLELPEDEEEKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 200 1.12E-08 11687800000 12368180 13311220 10229020 14467730 4253350 14219470 11692980 15193680 3665570 FALSE TRUE 11783560.64 14667648.45 10698030.68 13013406.29 4995132.893 13727046.19 9909001.145 13863240.83 4234007.874 2.783074806 3.464246852 2.526691259 3.073543243 1.179764668 3.242092739 2.340336022 3.274259577 1 22.01359252 3.255260015 2.080482865 2.387205254 3.086109971 0.135655308 0.789600377 0.599331189 5.326754379 0.221073028 0.306825821 1799.948232 -3.255260015 0.698904716 EGLELPEDEEEKKKMEESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGLELPEDEEEKKKMEESK 19 3 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 83.776 0.0021668 348260000 513560 277690 516220 433570 196531 579890 607090 655800 181831 FALSE TRUE 489285.0366 305986.9267 539889.1976 389986.7199 230805.9442 559808.2639 514467.2705 598374.6754 210028.4228 2.32961344 1.456883419 2.570553025 1.856828303 1.098927188 2.665392885 2.449512612 2.849017611 1 17.68022505 EGLELPEDEEEKKKQEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 181.14 3.29E-14 3790310000 6633230 5841050 5469180 6893940 1672850 7821700 5827650 7919480 1279280 FALSE TRUE 6319690.364 6436259.636 5719947.313 6200948.054 1964594.51 7550832.568 4938534.96 7226008.347 1477664.209 4.276810879 4.355698404 3.870938525 4.196452764 1.329527032 5.109978656 3.342122609 4.890155899 1 20.49488703 2.916224606 24.99999717 3.378081808 4.200244102 0.121193031 1.302879543 211.2119541 63026.27672 0.356796094 0.3784395 824.5644478 -2.916224606 0.822162294 EGLEQALPSGKPS(ph)SPVELDLFGDPSPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.153)GKPS(0.547)S(0.3)PVELDLFGDPSPSSK 134.78 4.42E-06 151910000 302590 292860 259350 357620 153210 330630 307170 342460 170100 TRUE FALSE 288287.1704 322702.767 271241.454 321671.3582 179929.7755 319180.2002 260305.5749 312472.3869 196478.2392 1.46727277 1.642435153 1.380516515 1.637185672 0.915774572 1.624506619 1.324857022 1.590366384 1 17.58401001 -3.548433558 0.197642068 1.58E-14 1.538588241 0.273067626 0.221361087 91.1143194 1.507016747 38.22774034 0.511553586 0.000282857 3.548433558 1.538588241 EGLHNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGLHNAK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 91.626 0.016266 371650000 1809300 1452060 1295580 1931790 1155330 1357860 1545050 1492180 1283210 FALSE TRUE 1723777.975 1600026.565 1354983.625 1737602.799 1356819.186 1310836.968 1309324.246 1361516.809 1482203.653 1.162983218 1.079491716 0.914168321 1.172310428 0.915406721 0.884383846 0.883363256 0.918576071 1 20.49931226 2.686231963 10.82274907 0.90767194 1.081384316 0.521383391 0.076540592 0.617351966 126.3853112 0.023850672 0.022496381 485.5477694 -2.686231963 0.173712376 EGLISQDGS(ph)SLEALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGLISQDGSSLEALLR 16 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 EGLIS(0.003)QDGS(0.579)S(0.418)LEALLR 77.562 0.024733 12574000 29555 22031 24073 26448 28436 24659 28900 26140 28881 TRUE FALSE 28157.99372 24275.98395 25176.77086 23789.39679 33395.2294 23805.05265 24490.77422 23851.04302 33359.71798 0.844071696 0.727703512 0.754705747 0.713117443 1.0010645 0.713586747 0.734142124 0.714965368 1 15.02581947 -1.208918997 4.989778223 1.00002554 0.773776346 0.385533608 0.089081503 2.36E-05 3.74E-06 0.080442477 0.018958335 0.061813168 1.208918997 -0.226249194 EGLLFEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGLLFEGR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 101.6 0.012282 790273000 1444000 1160270 1166290 1469950 1254260 1100320 1375160 1122800 1237740 FALSE TRUE 1375744.982 1278502.832 1219765.55 1322187.833 1473002.547 1062215.643 1165354.085 1024481.68 1429682.398 0.962273148 0.894256538 0.853172391 0.924812277 1.03030054 0.742973156 0.815113963 0.716579907 1 20.44726326 2.225494248 24.99999933 0.802376616 0.92635207 0.288042608 0.087299296 252.5897396 483278.9632 0.029311685 0.021778441 168.0715665 -2.225494248 0.123975454 EGLLLWCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 176.4 0.00012373 1011170000 1314900 790555 415618 543446 1533210 522899 1336730 714141 1016742 FALSE TRUE 1252747.283 871113.4533 434674.4964 488817.7756 1800601.339 504790.8765 1132787.288 651607.0281 1174413.157 1.066700655 0.741743609 0.370120595 0.416223007 1.533192411 0.429823928 0.964556027 0.554836281 1 20.1635086 EGLMLDSHEELYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGLMLDSHEELYK 13 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 170.18 2.72E-05 111960000 237470 220360 216070 263290 152890 242960 243550 250370 137010 FALSE TRUE 226245.2637 242814.9345 225977.0232 236823.589 179553.9676 234546.2343 206391.9744 228446.2755 158256.811 1.429608383 1.534309537 1.427913413 1.496451163 1.134573396 1.482060916 1.304158557 1.443516232 1 17.27190807 -3.75402806 0.174686819 8.99E-18 1.516045452 0.569506015 0.11234207 54.41681341 0.770246903 19.79954717 0.357886595 0.000176186 3.75402806 1.516045452 EGLQNMEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGLQNMEAR 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 78.655 0.067831 173280000 185760 143410 141670 169430 186010 136550 196340 161670 190480 FALSE TRUE 176979.4929 158023.642 148165.7096 152398.5745 218450.0851 131821.2393 166384.727 147513.3177 220018.6656 0.804383994 0.718228345 0.673423363 0.692662025 0.992870694 0.599136618 0.756230052 0.670458197 1 17.7472664 -0.992085778 4.492156356 1.000007155 0.739829695 0.377714664 0.105500991 0.081481235 56970573.32 1020.522267 0.022271507 0.101839023 0.992085778 -0.26017746 EGLRPGDTTS(ph)TFCGTPNYIAPEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGLRPGDTTSTFCGTPNYIAPEILR 25 1 P41743 P41743 PRKCI Protein kinase C iota type 1 EGLRPGDT(0.005)T(0.028)S(0.583)T(0.384)FCGTPNYIAPEILR 142.55 2.09E-07 186900000 61734 41755 71133 87442 78270 112510 112260 74550 84905 TRUE FALSE 58815.95617 46009.88197 74394.51841 78652.16403 91920.26322 108613.7505 95132.6752 68022.00679 98071.63377 0.599724445 0.469145666 0.758573255 0.801986885 0.937276761 1.107494046 0.970032532 0.693595122 1 16.58154829 3.327546847 1.639045816 0.952342705 0.533722106 0.660816325 0.113664804 0.190367017 1.053556633 0.036061785 0.055474273 2125.919656 -3.327546847 -0.4186206 EGLRPGDTTST(ph)FCGTPNYIAPEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGLRPGDTTSTFCGTPNYIAPEILR 25 1 P41743 P41743 PRKCI Protein kinase C iota type 1 EGLRPGDT(0.038)T(0.038)S(0.168)T(0.756)FCGTPNYIAPEILR;EGLRPGDT(0.034)T(0.034)S(0.13)T(0.803)FCGTPNYIAPEILR;EGLRPGDT(0.033)T(0.182)S(0.121)T(0.665)FCGTPNYIAPEILR 171.93 1.05E-11 574230000 163579 104657 196522 208999 183309 261247 263213 179283 209128 TRUE FALSE 155846.9449 115321.6673 205532.7281 187990.0234 215278.0316 252199.9509 223055.0226 163584.0301 241558.5022 0.645172674 0.477406782 0.85086108 0.778238074 0.891204531 1.044053298 0.923399593 0.677202535 1 17.88201311 3.658825778 5.268286875 0.888996573 0.562036378 0.59150833 0.110379639 0.130054376 6.286655385 0.029029325 0.045806715 4558.540087 -3.658825778 -0.326960195 EGLSGDALSSPSAPEPVVGT(ph)PDDKLDADYIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGLSGDALSSPSAPEPVVGTPDDKLDADYIKR 32 2 K7EJ08;Q92503-3;Q92503;Q92503-2 K7EJ08 SEC14L1 SEC14-like protein 1 1 EGLSGDALSSPSAPEPVVGT(1)PDDKLDADYIKR;EGLSGDALSSPSAPEPVVGT(1)PDDKLDADYIKR;EGLSGDALSSPS(0.001)APEPVVGT(0.999)PDDKLDADYIKR 137.69 7.86E-07 750045000 192549 167549 202428 215334 114672 234525 243127 261100 133440 TRUE FALSE 183447.5904 184622.4336 211709.524 193688.2172 134670.7605 226403.3404 206033.5108 238236.6998 154133.1937 1.190188732 1.197810992 1.373549194 1.256628845 0.873729774 1.468881135 1.336723816 1.54565473 1 17.23381806 EGMAALQSDPWQQELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGMAALQSDPWQQELYR 17 0 P49748;P49748-3;P49748-2;G3V1M7 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ; 173.44 3.44E-09 102695000 226890 181870 174587 191029 196886 163814 193496 200804 192366 FALSE TRUE 216165.3594 200402.7598 182591.9866 171826.402 231222.8561 158141.0801 163974.6314 183220.5372 222197.1368 0.972853937 0.901914231 0.821756703 0.773306103 1.040620322 0.711715202 0.737969146 0.8245855 1 17.7614807 2.214966485 24.99693272 0.787399322 0.898994062 0.101829544 0.106478087 359.331003 380692.7726 0.037391102 0.027631071 164.0463171 -2.214966485 0.11159474 EGMNIVEAMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 213.13 8.28E-09 10465260000 8185398 5687895 5897845 7519302 8261819 6632537 8470100 7315514 7816555 FALSE TRUE 7798490.458 6267497.967 6168267.027 6763447.477 9702677.618 6402850.581 7177830.681 6674928.812 9028706.428 0.863743939 0.694174522 0.683183917 0.749104817 1.074647592 0.709165885 0.795001005 0.739300681 1 23.10608787 2.926769682 24.99999469 0.841467367 0.74783877 0.174417658 0.120231521 292.9817313 100019.4717 0.035143376 0.037275189 844.8306908 -2.926769682 -0.093628597 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEY(0.002)ADS(0.998)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 318.55 6.05E-74 1.03999E+11 23505212 22378715 22473891 24670289 22155820 22790795 24491858 23421380 20713345 TRUE FALSE 22394167.21 24659131.5 23504341.13 22190384.68 26019787.99 22001544.05 20755175.24 21370479.8 23925464.75 0.935997166 1.030664681 0.982398519 0.927479776 1.087535321 0.919586904 0.867493085 0.893210645 1 24.51204361 2.024755114 24.998241 0.902518646 0.990550659 0.272223467 0.056619274 222.5501094 224734.8303 0.01919682 0.014177232 105.8656612 -2.024755114 0.088032012 EGNASGVSLLEALDTILPPTRPTDKPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGNASGVSLLEALDTILPPTRPTDKPLR 28 2 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 165.46 3.81E-12 153350000 213410 241940 177140 261410 147230 246510 210960 210140 143260 FALSE TRUE 203322.5322 266593.9611 185262.0442 235132.5702 172906.8654 237973.2969 178774.1775 191739.0276 165476.0291 1.228712904 1.61107299 1.11957028 1.420946414 1.044905817 1.438113412 1.080362989 1.1587118 1 17.33626272 1.805284934 0.396848323 0.992047654 1.409533222 0.281112225 0.167608572 1.201297055 0.514280814 0.179198504 0.161016167 63.86823787 -1.805284934 0.417485567 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK 36 3 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 256.9 2.25E-62 987320000 1286030 843460 1139000 1115510 881970 1233380 1504350 1302200 1040320 FALSE TRUE 1225241.911 929409.5329 1191224.277 1003376.815 1035785.289 1190667.741 1274833.778 1188172.465 1201647.512 1.019635041 0.773446059 0.991325879 0.835000951 0.861970984 0.990862736 1.060904937 0.988786189 1 20.19658233 2.115212149 5.001893323 1.023772597 0.892646568 0.377619515 0.072776082 0.194036768 7.714487731 0.026243458 0.019084413 130.3803519 -2.115212149 -0.13112603 EGNDLYHEMIESGVINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGNDLYHEMIESGVINLK 18 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;; 288.82 6.72E-41 1959870000 5691700 5207350 4816970 5090450 3918590 4440530 5055340 5213760 3351610 FALSE TRUE 5422664.621 5737984.885 5037832.839 4578748.295 4601990.855 4286753.333 4284055.035 4757215.535 3871360.561 1.400712885 1.482162355 1.301308096 1.182723289 1.188727008 1.107298911 1.106601921 1.228822648 1 21.88440925 3.359370035 1.805550812 1.129604035 1.444401061 0.803662289 0.063419215 0.122608876 0.817605688 0.018169795 0.02798974 2287.547049 -3.359370035 0.314797025 EGNPEEDLTADKANAQAAALYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGNPEEDLTADKANAQAAALYK 22 1 P40121-2;P40121;E7ENU9 P40121-2 CAPG Macrophage-capping protein 0 112.58 0.00026272 59922000 48667 34366 36580 48911 34140 39152 53183 46073 36933 FALSE TRUE 46366.60736 37867.93447 38257.22918 43994.37336 40094.00519 37796.15642 45068.95658 42038.60387 42660.38101 1.086877479 0.887660484 0.896785923 1.031270052 0.939841704 0.885977938 1.056459307 0.985424951 1 15.38060923 1.708793416 16.9664213 1.015558979 0.957304794 0.151610681 0.065818704 0.382583154 204.4238001 0.030015365 0.01659838 51.14384977 -1.708793416 -0.058254185 EGNTTEDDFPSS(ph)PGNGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPS(0.002)S(0.998)PGNGNK;EGNTTEDDFPS(0.009)S(0.991)PGNGNK 397.32 4.77E-127 1104920000 3468680 3111150 3354400 3738710 2262930 3705910 3953640 3861350 2532760 TRUE FALSE 3304722.371 3428179.722 3508202.558 3362887.768 2657584.276 3577573.407 3350439.604 3523229.724 2925527.485 1.129615903 1.171815934 1.199169236 1.149497923 0.908412001 1.222881489 1.145242908 1.204305802 1 21.48026534 -2.457857608 1.84959814 6.31E-05 1.14227813 0.203815789 0.087792739 2083758.056 155003.3081 8712567.408 0.021048534 0.003484515 2.457857608 1.142215016 EGPDLDRPGS(ph)DRQER ddPTM_SK-BR-3_Trastuzumab_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 129.46 5.18E-05 1996650000 2258690 1708940 2019890 2222830 1940070 2163200 2651450 2304250 2273640 TRUE FALSE 2151926.2 1883082.929 2112503.954 1999386.905 2278417.594 2088287.842 2246922.605 2102477.654 2626224.479 0.819399186 0.717030453 0.80438819 0.761316072 0.867563916 0.795167305 0.855571419 0.800570428 1 21.32455881 -5 0.164253989 1.782863982 0.746472219 0.710111768 0.040540407 64.15685505 0.596614203 16.26145073 0.145126467 1.00E-05 5 -1.036391764 EGPDLDRPGSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ;;; 99.5 0.0034303 1538790000 2188640 1904380 1808800 2235640 1858080 1889640 2131490 2122750 1911590 FALSE TRUE 2085187.325 2098438.487 1891735.269 2010909.22 2182128.564 1824201.293 1806292.053 1936870.757 2208029.614 0.944365651 0.950367003 0.856752671 0.910725656 0.988269609 0.826167041 0.818056081 0.877194193 1 21.07432809 2.225400962 24.99785207 0.858748264 0.929943298 0.099766845 0.060335162 314.8266721 598034.9672 0.020970954 0.015578316 168.0354687 -2.225400962 0.071195035 EGPLGWSSDGSLGSVLLDSPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDSPS(0.134)S(0.866)PR;EGPLGWSSDGSLGSVLLDS(0.001)PS(0.138)S(0.861)PR;EGPLGWSSDGSLGSVLLDSPS(0.157)S(0.843)PR 191.65 5.79E-18 60985000 58375 51770 60241 63017 55493 49550 60120 51212 54650 TRUE FALSE 55615.72944 57045.42186 63003.10944 56682.41144 65170.96163 47834.07108 50947.58982 46727.60579 63124.84289 0.881043451 0.9036921 0.998071545 0.897941426 1.032413843 0.757769349 0.807092541 0.740241142 1 15.94592027 2.223743253 24.99659419 0.807994648 0.932211981 0.309382928 0.083642094 249.0239164 420095.6291 0.028114207 0.020849341 167.3952974 -2.223743253 0.124217333 EGPLPAARPAGAT(ph)LERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 127.92 0.0011637 1185680000 748430 513400 584560 836340 755560 671880 1092570 1098180 866660 TRUE FALSE 713053.1971 565716.0437 611362.6542 752269.5143 887329.4248 648612.6271 925878.3801 1002017.537 1001057.207 0.712300149 0.565118597 0.610717 0.75147505 0.886392325 0.647927634 0.924900569 1.000959317 1 19.93309299 1.93291156 0.633520392 1.025118129 0.628744254 0.68806407 0.088602791 0.404113949 0.32408257 0.07954539 0.046627028 85.68633346 -1.93291156 -0.396373875 EGPPAPPPVKPPPS(ph)PVNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR;EGPPAPPPVKPPPS(1)PVNIR 177.41 2.44E-14 15606780000 6186140 5495910 5805010 6340480 4642600 5780220 6840280 6497570 5380020 TRUE FALSE 5893733.422 6055949.477 6071175.45 5703122.904 5452267.97 5580049.532 5796669.656 5928608.325 6214326.024 0.94841072 0.974514284 0.976964425 0.917737963 0.877370764 0.897933181 0.932791365 0.954022737 1 22.5671665 3.233332213 24.99741253 0.922537131 0.965716615 0.18639017 0.033778336 163.2386947 780456.4377 0.009159125 0.011258089 1711.32389 -3.233332213 0.043179484 EGPSCPS(ph)PGPFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGPSCPSPGPFCR 13 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 EGPS(0.002)CPS(0.998)PGPFCR 88.075 0.005657 0 130770 126710 114840 135970 106780 124330 130900 134630 101170 TRUE FALSE 124588.7613 139621.8931 120105.5276 122302.0373 125402.3982 120024.4209 110928.8009 122841.0835 116858.9269 1.066146717 1.194790135 1.027782222 1.046578473 1.073109274 1.027088166 0.949253975 1.051191267 1 16.83440842 3.011200035 0.86542146 0.997828214 1.125758564 0.377772209 0.049484386 0.498485803 0.82779481 0.026475006 0.033769117 1026.124449 -3.011200035 0.12793035 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 EGPTDHLESACPLNLPLQNNHT(0.002)AADMYLS(0.081)PVRS(0.917)PK 271.35 2.69E-74 138740000 87340 77462 84686 91292 51278 103290 98683 100190 36804 TRUE FALSE 83211.61129 85355.46587 88568.93687 82115.15472 60220.86696 99713.0414 83627.09591 91416.83246 42511.37635 1.957396312 2.00782645 2.083417298 1.931604238 1.416582386 2.345561352 1.967169805 2.150408674 1 15.37556135 3.003692955 24.77480959 1.871181009 2.006200886 0.049099605 0.378033186 437.0279694 2931822.1 0.09959002 0.118503836 1008.539599 -3.003692955 0.135019877 EGPYSISVLYGDEEVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;; 200.21 2.02E-17 49498000 66747 56818 54231 67782 56457 53598 61718 61855 61493 FALSE TRUE 63592.00159 62607.8188 56717.54499 60968.42458 66303.08293 51741.88782 52301.78557 56438.64829 71029.02038 0.895296053 0.881439987 0.79851228 0.858359362 0.933464696 0.728461234 0.736343896 0.794585762 1 16.11612097 2.236582779 24.99998238 0.784518793 0.872409127 0.059732339 0.08299135 78.04554775 986478.702 0.027441565 0.021291887 172.41807 -2.236582779 0.087890334 EGQEKEESKKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGQEKEESKKDR 12 3 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 76.073 0.014062 88325000 250800 136584 228226 212519 126026 261200 296990 283830 138374 FALSE TRUE 238945.181 150502.0649 238690.3878 191156.1864 148004.8945 252154.5785 251678.7209 258976.3405 159832.3332 1.494973991 0.94162465 1.493379863 1.195979453 0.926000963 1.577619331 1.574642101 1.620300069 1 17.28619976 2.206634903 24.99997241 1.503078657 1.21182056 0.151883793 0.256451875 270.6984903 211973.5405 0.08756895 0.064679395 160.9292186 -2.206634903 -0.291258097 EGQGGAGRTS(ph)PGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGQGGAGRTSPGGR 14 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 EGQGGAGRT(0.266)S(0.734)PGGR;EGQGGAGRT(0.167)S(0.833)PGGR 105.94 0.00058791 245089000 236120 125207 230070 187942 264020 210160 294910 230210 309770 TRUE FALSE 224959.0755 137965.7356 240618.9371 169049.7131 310065.0044 202882.1065 249916.0631 210051.592 357807.5495 0.628715285 0.38558643 0.672481443 0.472459883 0.866569207 0.567014605 0.698465036 0.587051873 1 18.4488243 -5 0.140468642 2.399608463 0.453812609 0.48987839 0.12707647 103.8572997 0.892530562 40.56650314 0.693793391 1.00E-05 5 -1.945795854 EGQGGAGRTS(ph)PGGRT(ph)SPEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGQGGAGRTSPGGRTSPEAR 20 2 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 EGQGGAGRT(0.471)S(0.529)PGGRT(0.586)S(0.414)PEAR 87.489 0.0044533 149210000 42277 25083 42069 29833 54429 34738 62176 46650 72423 TRUE FALSE 40278.64999 27638.98622 43997.90526 26834.13016 63921.40037 33535.01435 52689.90926 42565.07869 83653.98895 0.481491086 0.330396513 0.525951073 0.320775261 0.764116585 0.400877648 0.629855311 0.508823061 1 16.35214671 -5 0.163452102 2.986662352 0.350572906 0.626267966 0.126388921 74.83049333 0.694404452 47.93758692 0.437246397 1.00E-05 5 -2.636089446 EGQHYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EGQHYPER 8 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;;;; 76.465 0.035731 949702000 697068 615741 600364 674354 748377 554106 667293 575929 709081 FALSE TRUE 664118.9771 678485.7079 627891.2832 606566.6547 878893.7119 534917.1703 565485.1972 525497.6036 819041.66 0.810848837 0.82838974 0.766617028 0.740580955 1.073075711 0.653101297 0.690422997 0.641600579 1 19.64357731 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEK 181.93 1.40E-17 195770000 313370 380360 234730 387480 128600 377180 294060 372260 114680 TRUE FALSE 298557.6211 419119.1164 245492.6027 348529.7742 151027.7993 364118.162 249195.7462 339662.9409 132463.9887 2.253877632 3.164023072 1.85327805 2.631128488 1.140142319 2.748808681 1.881233901 2.564190798 1 17.01524068 3.723750379 24.89284808 2.040535191 2.708950382 0.188082793 0.622960008 1050.216239 1765189.772 0.144795731 0.225344063 5293.590947 -3.723750379 0.668415191 EGQPSPADEKGNDS(ph)DGEGESDDPEKK ddPTM_SK-BR-3_Trastuzumab_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 184.44 8.24E-18 353552000 355599 361013 318707 374934 117308 427582 335673 425725 98144 TRUE FALSE 338790.54 397800.6351 333320.0312 337244.922 137766.4781 412774.7281 284459.9188 388446.2621 113363.6703 2.988528328 3.509066301 2.94027205 2.974894172 1.215261271 3.641155294 2.509268782 3.426549804 1 16.79059885 2.985052671 24.78528563 2.515088331 3.170814078 0.152394979 0.835640673 1224.384516 2030248.03 0.227283561 0.248954523 966.1680491 -2.985052671 0.655725746 EGQT(ph)IKLCIGNITNK ddPTM_SK-BR-3_Trastuzumab_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 70.802 0.073728 175190000 296710 281510 331590 331790 483750 282090 446100 331520 712490 TRUE FALSE 282685.1063 310196.1891 346793.7295 298437.8388 568115.8468 272321.1526 378039.2518 302490.3513 822979.3103 0.343489931 0.376918575 0.421388151 0.362631035 0.690316074 0.330896718 0.459354503 0.367555232 1 19.65049664 -5 0.372850486 8.831860163 0.401294243 0.751971324 0.104504615 256.5393618 1.961809046 1620.667513 0.066558887 1.00E-05 5 -8.43056592 EGRGES(ph)ENAGTNQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(0.945)ENAGT(0.047)NQET(0.007)R;EGRGES(1)ENAGTNQETR;EGRGES(0.529)ENAGT(0.036)NQET(0.434)R;EGRGES(1)ENAGTNQETR;EGRGES(0.893)ENAGT(0.107)NQETR 249.88 6.80E-21 1243630000 745729 549621 731223 755999 724056 676855 857559 754270 751142 TRUE FALSE 710479.8681 605628.0048 764750.2978 680004.5442 850331.1372 653415.3416 726722.6244 688222.1202 867625.2651 0.818878722 0.698029471 0.881429263 0.783753737 0.980067284 0.753107785 0.837599657 0.79322508 1 19.72671254 -5 0.189379951 1.787408062 0.777461547 0.34604805 0.07644373 144.4833299 1.411786808 43.08924022 0.19520749 1.00E-05 5 -1.009946515 EGRPPEPT(ph)PAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EGRPPEPT(1)PAKR 151.9 0.0033051 1024200000 414620 445640 396510 440170 354010 426090 467670 472210 371520 TRUE FALSE 395021.7343 491051.2227 414690.3757 395923.2753 415749.2319 411334.3965 396318.3522 430860.7891 429133.4241 0.920510294 1.144285658 0.966343688 0.922611135 0.968811117 0.958523325 0.923531773 1.00402524 1 18.71106675 3.510039113 24.83004858 0.955703649 1.036217439 0.182539943 0.059323901 725.4632325 547217.3166 0.014810608 0.022925284 3236.22801 -3.510039113 0.080513789 EGRPPEPTPAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 77.593 0.015751 86886000 184090 138310 173910 171490 132310 181920 199670 194230 155610 FALSE TRUE 175388.4305 152403.9462 181883.9455 154251.4994 155384.8221 175620.0648 169206.6743 177222.1915 179741.2041 0.975783107 0.847907674 1.011921259 0.858186637 0.86449194 0.977071817 0.941390569 0.985985336 1 17.45556165 1.575507183 1.344630503 0.994434343 0.913605242 0.232316064 0.054183802 0.570499244 1.982509422 0.043647819 0.015338828 37.62765756 -1.575507183 -0.080829101 EGRPSGEAFVELESEDEVK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 194.92 1.88E-15 501153000 876200 762550 746370 917890 533460 861390 898940 934280 578058 FALSE TRUE 834783.7625 840254.7119 780591.8028 825621.9533 626495.2551 831559.8483 761790.1928 852469.4903 667700.2823 1.250237246 1.258430967 1.169075143 1.236515807 0.938288139 1.245408861 1.140916386 1.276724771 1 19.34884112 -4.999882784 0.027680981 9.68E-06 1.907213839 0.23725531 0.100498021 2323.546607 4.847539747 251.8172602 109.3913907 1.00E-05 4.999882784 1.907204163 EGS(ph)GGPQESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGSGGPQESSR 11 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 EGS(1)GGPQESSR;EGS(1)GGPQESSR;EGS(1)GGPQESSR;EGS(0.989)GGPQES(0.011)SR;EGS(1)GGPQESSR 152.32 3.46E-05 402406000 501270 412311 438780 509097 331400 469184 510074 469111 351969 TRUE FALSE 477575.9605 454325.9597 458898.497 457921.6023 389196.0551 452936.0404 432252.8431 428033.1539 406550.5549 1.174702518 1.117514056 1.128761212 1.126358326 0.957312812 1.114095246 1.063220399 1.05284115 1 18.63307524 8 0.165187059 0.997565212 1.717682378 0.513211127 0.045640187 47.00915334 0.497187454 0.117643323 8.311985988 100000000 -8 0.720117165 EGS(ph)LKGHTLAGEEFMGLGLGNLVSGGVDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSLKGHTLAGEEFMGLGLGNLVSGGVDKR 30 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 EGS(0.964)LKGHT(0.036)LAGEEFMGLGLGNLVSGGVDKR 83.854 0.00075282 25595000 55229 59984 46341 61341 86590 58921 74186 70288 69375 TRUE FALSE 52618.43462 66096.4378 48465.78069 55174.88614 101691.2686 56880.551 62867.56318 64133.2101 80133.32068 0.656636143 0.824830885 0.60481433 0.688538621 1.269026015 0.70982396 0.784537102 0.800331367 1 16.29011464 EGS(ph)PANWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK 106.62 0.0043645 3161169000 5094990 5020970 4422990 5876360 2932570 5210650 5061470 5408230 2877720 TRUE FALSE 4854159.92 5532612.551 4625788.466 5285657.128 3444009.28 5030203.884 4289249.791 4934656.71 3323982.12 1.460344775 1.664453162 1.391640598 1.590158111 1.036109448 1.513306541 1.290394965 1.484561749 1 21.66448119 -3.467492485 0.104653927 1.48E-13 1.752118049 0.403463429 0.169029154 104.3660867 1.041528774 25.80130512 2.473732206 0.000340806 3.467492485 1.752118049 EGS(ph)PANWKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSPANWKR 9 1 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWKR 68.676 0.035156 350500000 218220 185310 186880 212450 135820 210860 219060 222840 143210 TRUE FALSE 207905.1731 204193.2997 195448.6328 191094.1224 159506.965 203557.8653 185638.3737 203326.9483 165418.2754 1.256845246 1.234405928 1.181541957 1.155217717 0.964264466 1.230564548 1.122236181 1.22916859 1 17.33575911 8 0.108327957 0.990919667 1.798608563 0.31075562 0.083031768 131.0098055 0.992881156 0.755562071 15.80584229 100000000 -8 0.807688896 EGS(ph)PAPLEPEPGAAQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGSPAPLEPEPGAAQPK 17 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK 185.26 6.18E-10 239680000 337010 373840 276590 375550 146138 354240 314370 360240 163437 TRUE FALSE 321080.2052 411934.721 289271.9251 337799.0005 171624.4209 341972.58 266407.0827 328695.4758 188781.9752 1.700799056 2.182065955 1.53230691 1.789360452 0.909114447 1.811468386 1.41118919 1.741138027 1 17.5263615 5.660011712 0.056384785 1.21E-10 4.007571842 0.302406559 0.319313592 256.7534928 1.756154728 36.00064723 103.0483656 457100.516 -5.660011712 4.007571842 EGS(ph)PEPWLPLTDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSPEPWLPLTDGR 14 0 J3KSM5;Q494U1-3;Q494U1;Q494U1-2 J3KSM5 PLEKHN1 Pleckstrin homology domain-containing family N member 1 1 EGS(1)PEPWLPLTDGR 131.03 6.15E-05 40910000 89757 90469 89361 103970 82588 93206 99406 95608 82357 TRUE FALSE 85514.36449 99687.89395 93458.29024 93518.73807 96991.32105 89978.25285 84239.78898 87236.05667 95128.50294 0.898935249 1.047928758 0.982442563 0.983077996 1.019582124 0.945860074 0.885536788 0.917033843 1 16.53759005 2.023282225 8.601654996 0.920007738 0.986273772 0.195397042 0.047328918 0.257827677 83.27318359 0.016950997 0.012360875 105.507231 -2.023282225 0.066266034 EGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 EGSPIPHDPEFGSK 14 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 EGS(1)PIPHDPEFGSK;EGS(0.999)PIPHDPEFGS(0.001)K;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK 239.37 2.45E-17 11496530000 25784430 26009170 20421950 26860500 11671310 26527930 24094030 27136890 9715290 TRUE FALSE 24565651.09 28659533.99 21358316.61 24160431.51 13706782.77 25609261.13 20418043.21 24760640.05 11221887.55 2.189083697 2.553896023 1.903273091 2.152973944 1.22143291 2.282081424 1.819483853 2.206459469 1 23.41981203 -1.488284885 0.15885547 9.90E-16 2.495034388 0.44946906 0.357228431 28.85198822 0.801607097 14.574679 1.851121625 0.032487412 1.488284885 2.495034388 EGS(ph)PYKAPIYIPDDIPIPAEFELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSPYKAPIYIPDDIPIPAEFELR 24 1 C9JU02;Q03112-9;Q03112-8;Q03112;Q03112-3 C9JU02 MECOM MDS1 and EVI1 complex locus protein EVI1 1 EGS(0.916)PY(0.07)KAPIY(0.014)IPDDIPIPAEFELR 48.088 0.091553 140820000 73915 67402 77689 78780 185540 39054 85789 52801 103350 TRUE FALSE 70421.18444 74270.34043 81251.11749 70860.88473 217898.1173 37701.55019 72700.31243 48177.46452 119376.9902 0.589905847 0.622149548 0.680626286 0.593589138 1.825294112 0.315819239 0.6089977 0.403574126 1 16.86516526 EGS(ph)RSPGDS(ph)PGGKEEAPEPPDGGDPGNLQGEDSQAFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSRSPGDSPGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 39 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 EGS(0.843)RS(0.158)PGDS(1)PGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 182.42 9.29E-24 114620000 42137 21431 41279 34348 25563 38859 54989 47834 34125 TRUE FALSE 40145.26752 23614.84327 43171.68298 30895.27378 30021.17911 37513.30309 46599.41811 43645.40138 39416.93071 1.018477766 0.599104061 1.095257348 0.783807192 0.761631577 0.951705331 1.182218333 1.107275493 1 15.26652782 1.963613136 4.881607889 1.109006003 0.840803567 0.379277719 0.14213039 0.18332652 10.51597208 0.058744477 0.03628776 91.9630012 -1.963613136 -0.268202436 EGS(ph)RSPGDSPGGKEEAPEPPDGGDPGNLQGEDSQAFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSRSPGDSPGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 39 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EGS(0.498)RS(0.498)PGDS(0.003)PGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 56.111 0.014306 89094000 20410 9077.4 22987 17994 16000 19621 31322 21554 22429 TRUE FALSE 19445.25975 10002.39738 24040.97669 16185.20893 18790.39493 18941.51985 26543.25363 19666.6175 25907.17477 0.750574307 0.386085996 0.927965975 0.624738478 0.725296954 0.731130276 1.024552228 0.759118571 1 14.66106407 2.182822982 0.61139322 0.97672247 0.602677397 0.322030125 0.154077697 0.759229734 0.564077572 0.129948436 0.090639324 152.3431678 -2.182822982 -0.374045073 EGS(ph)YDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSYDR 6 0 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 EGS(1)YDR 69.716 0.097313 142450000 247410 205480 207000 260670 149960 231290 230180 267610 180540 TRUE FALSE 235715.4196 226418.6456 216491.1548 234466.9564 176112.9765 223280.3693 195061.8135 244176.6497 208537.2211 1.130327806 1.08574692 1.038141554 1.124341041 0.844515792 1.070697922 0.935381283 1.170902002 1 17.66994538 3.448764053 1.285449847 1.005903264 1.114112912 0.135466423 0.090905035 0.70723494 2.395704713 0.028298976 0.053261073 2810.373572 -3.448764053 0.108209648 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR 30 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 206 1.00E-25 59648000 27634 25373 19745 30910 25253 24477 33710 26636 22565 FALSE TRUE 26327.79559 27958.53755 20650.32778 27802.86807 29657.1152 23629.35535 28566.92037 24303.61063 26064.26495 1.010110802 1.072677 0.792285062 1.066704475 1.137845831 0.906580538 1.096018646 0.932449493 1 14.66978555 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR 34 0 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;; 346.86 4.46E-132 683295000 310244 363191 299160 296120 302627 245560 332604 287504 130391 FALSE TRUE 295579.381 400200.5758 312876.7819 266353.455 355405.053 237056.1956 281859.1511 262328.6256 150611.3703 1.962530321 2.657173724 2.07737823 1.768481718 2.359749149 1.57395949 1.871433415 1.741758441 1 17.20047116 0.675393274 0.287061593 0.780038616 2.374112332 0.626622743 0.271643311 1.754816223 0.362496336 0.92534627 0.399306919 4.735799137 -0.675393274 1.594073716 EGSGSSGTGEQKEDQKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EGSGSSGTGEQKEDQKEEK 19 2 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;;;; 163.53 1.43E-11 1642119000 3604850 3795950 2911250 3728110 1141984 3202810 2641340 3533940 931494 FALSE TRUE 3434455.885 4182761.621 3044733.692 3353353.3 1341145.648 3091895.887 2238355.071 3224489.479 1075945.332 3.192035675 3.887522438 2.829821926 3.116657696 1.246481218 2.873655189 2.080361339 2.996889696 1 20.03717335 3.145522527 2.054066051 2.181078173 3.484947558 0.415597224 0.684655429 0.277388563 2.398115492 0.195695525 0.252663468 1398.049429 -3.145522527 1.303869386 EGSGSSGTGEQKEDQKEEKQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EGSGSSGTGEQKEDQKEEKQ 20 3 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;;;; 183.65 5.25E-17 4526890000 5927650 4302650 5471220 4767260 2307869 5469540 5760170 6348960 2330268 FALSE TRUE 5647461.732 4741094.927 5722080.849 4288045.968 2710360.623 5280128.458 4881350.274 5793011.404 2691634.06 2.098153614 1.761418834 2.125876223 1.593101392 1.006957321 1.961681395 1.813526715 2.152228451 1 21.36005085 3.224863691 24.92546816 1.639353681 1.959779274 0.194273401 0.379208553 431.4683608 785178.4502 0.105478433 0.126700094 1678.277185 -3.224863691 0.320425592 EGSQGELT(ph)PANSQSR ddPTM_SK-BR-3_Trastuzumab_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 EGSQGELT(1)PANSQSR 156.13 2.44E-05 79584000 252700 274660 258490 302830 226250 265890 287480 267630 279340 TRUE FALSE 240755.3718 302648.1663 270342.0222 272388.9531 265707.9284 256682.1626 243619.6461 244194.8984 322658.6205 0.746161288 0.937982583 0.837857739 0.844201691 0.82349552 0.795522408 0.755038392 0.756821243 1 18.29964905 2.526004416 2.939969157 0.800881077 0.846850477 0 0.083182748 0.796975131 13.75994821 0.027549104 0.0243662 335.7410282 -2.526004416 0.045969401 EGSRS(ph)PGDSPGGKEEAPEPPDGGDPGNLQGEDSQAFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGSRSPGDSPGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 39 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EGS(0.22)RS(0.772)PGDS(0.008)PGGKEEAPEPPDGGDPGNLQGEDSQAFSSK 193.58 1.31E-24 119130000 65448 30503 70576 53750 46857 68580 100590 75839 69360 TRUE FALSE 62354.40275 33611.29038 73811.97941 48346.94788 55028.84596 66205.0574 85243.14804 69198.13511 80115.99456 0.77830155 0.419532836 0.9213139 0.60346187 0.686864668 0.826365044 1.063996628 0.863724347 1 16.28980267 2.062317986 3.070813475 0.979185815 0.661343044 0.490867269 0.135732814 0.191199532 3.580086343 0.058351481 0.03695899 115.4298114 -2.062317986 -0.317842771 EGSTHNWQHITDQIGMFCFTGLKPEQVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGSTHNWQHITDQIGMFCFTGLKPEQVER 29 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 187.45 3.81E-18 544650000 620900 517950 589230 633780 586340 482720 713290 628110 67449 FALSE TRUE 591551.2875 570729.6939 616246.7783 570071.2303 688597.5104 466003.2854 604464.51 573109.3586 77908.64644 7.592883647 7.325627128 7.909863751 7.317175389 8.838524886 5.981406515 7.758631906 7.356171424 1 16.24949583 -0.873486005 0.717650316 4.23E-13 7.557469518 0.896036065 0.697338484 8.433654968 2.416321374 20.53689764 0.216104094 0.133817834 0.873486005 7.557469518 EGTAPS(ph)ENGETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGTAPSENGETK 12 0 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGTAPS(1)ENGETK;EGTAPS(0.994)ENGET(0.006)K 150.81 0.00032016 0 376270 507660 331928 482630 261961 418680 361960 429150 246985 TRUE FALSE 358484.4628 559391.1312 347147.2271 434115.1155 307646.9155 404181.0066 306736.3541 391571.3509 285286.1724 1.256578473 1.960807026 1.216838602 1.521682989 1.078380045 1.416756386 1.075188298 1.372556362 1 18.1220503 3.151559897 1.522374445 1.204393616 1.583407286 0.249524713 0.241387444 0.436342872 2.101106387 0.077532146 0.10444263 1417.620214 -3.151559897 0.37901367 EGTAPS(ph)ENGETKAEEAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTAPSENGETKAEEAQK 18 1 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGT(0.001)APS(0.994)ENGET(0.005)KAEEAQK 77.045 0.0061202 0 95518 123150 75202 113070 47104 109260 86462 105130 48487 TRUE FALSE 91003.05344 135699.125 78650.08608 101703.9888 55318.92269 105476.2988 73270.63392 95924.25987 56006.11632 1.624877057 2.422934028 1.404312444 1.815944319 0.987730025 1.883299642 1.308261289 1.712746146 1 15.77329677 3.772573498 0.094116892 0.442700927 3.149069945 0.257113942 0.371202195 50.65789492 1.103793071 9.368212681 23.62965804 5923.433243 -3.772573498 2.706369017 EGTAPS(ph)ENGETKAEEAQKTESVDNEGE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTAPSENGETKAEEAQKTESVDNEGE 27 2 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGT(0.026)APS(0.973)ENGET(0.002)KAEEAQKTESVDNEGE 84.516 0.0069769 245590000 158860 141150 154050 167780 73499 178260 172970 165970 85497 TRUE FALSE 151351.0026 155533.3455 161113.3449 150914.4356 86317.20233 172086.8115 146580.2497 151436.7869 98755.4381 1.532583983 1.574934489 1.631437701 1.528163294 0.874050118 1.742555294 1.484275221 1.533452637 1 16.59157257 -1.92134257 2.33025199 0.674845317 1.495902835 0.306959827 0.229996469 9845912.004 4762015.285 17458126.33 0.052235281 0.011985535 1.92134257 0.821057518 EGTETFADHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 152.97 1.71E-05 737680000 1104059 988112 927981 1187180 1020400 1042391 1205060 1087639 958603 FALSE TRUE 1051872.319 1088801.736 970529.8467 1067842.411 1198357.437 1006292.738 1021205.965 992399.5632 1107258.257 0.949979205 0.983331331 0.876516242 0.964402301 1.082274554 0.908814842 0.922283449 0.896267476 1 20.07856033 -0.990470684 4.506217245 1.000001417 0.949824572 0.074453041 0.057311062 7053786.638 1565345.594 98.53784856 0.012997318 0.102218456 0.990470684 -0.050176845 EGTGQQERES(ph)PRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 2 EGT(0.003)GQQERES(0.997)PRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 347.48 1.51E-159 309050000 101900 91163 108410 113720 109370 105130 124950 109310 120310 TRUE FALSE 97083.38895 100452.6133 113380.7057 102288.6495 128444.0934 101489.3217 105886.5826 99738.23691 138967.0603 0.6986072 0.72285197 0.815881875 0.736063995 0.924277257 0.730312072 0.761954541 0.717711353 1 17.08438343 -2.545686936 2.245216843 5.02882275 0.760148018 0.563250745 0.065402429 1922119.809 250576.0168 39201557.09 0.015649268 0.002846512 2.545686936 -4.268674732 EGTGQQERES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 EGT(0.165)GQQERES(0.835)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 278.07 5.67E-87 202420000 39900 35762 33882 45527 40745 42885 47280 42661 46108 TRUE FALSE 38014.00607 39406.18846 35435.52321 40950.53946 47850.9151 41399.8817 40066.56764 38925.37668 53258.19315 0.713768227 0.739908475 0.665353462 0.76890591 0.898470494 0.777342964 0.752308054 0.730880535 1 15.70071586 -5 0.214939565 2.193175318 0.721175671 0.627407724 0.059251463 102.3596739 1.022179727 52.89004616 0.121300876 1.00E-05 5 -1.471999648 EGTQASEGYFSQS(ph)QEEEFAQSEELCAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTQASEGYFSQSQEEEFAQSEELCAK 27 0 Q16643;Q16643-3;Q16643-2 Q16643 DBN1 Drebrin 1 EGT(0.003)QAS(0.006)EGY(0.014)FS(0.23)QS(0.746)QEEEFAQS(0.002)EELCAK 64.779 0.016852 15052000 26933 23919 27538 29502 23757 27424 30374 28155 30749 TRUE FALSE 25659.93047 26356.37329 28800.64454 26536.40291 27900.21328 26474.3 25739.88844 25689.59894 35517.39788 0.722460878 0.742069376 0.810888361 0.747138149 0.785536524 0.745389628 0.724712112 0.723296201 1 15.11623827 -1.959904319 2.501011322 1.199558392 0.748584203 0.885167306 0.028272111 2984029.374 1467586.878 3456193.255 0.007158418 0.010967198 1.959904319 -0.450974189 EGTSDPPS(ph)PLLLPSPGGWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGTSDPPSPLLLPSPGGWK 19 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 EGTSDPPS(1)PLLLPSPGGWK 92.977 0.0019199 36095000 92455 95139 73566 100160 63785 77288 89144 93379 70194 TRUE FALSE 88084.83538 104833.7723 76939.07387 90091.72651 74909.0838 74611.49718 75543.44556 85202.23973 81079.32702 1.086403139 1.292977829 0.948935773 1.111155332 0.923898687 0.920228373 0.931722652 1.050850357 1 16.30704649 3.725620793 24.78429407 0.977118328 1.189690486 0.547675227 0.077593162 414.9963614 794863.3824 0.019985775 0.03117545 5316.438479 -3.725620793 0.212572158 EGTTPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGTTPKPK 8 1 P61927 P61927 RPL37 60S ribosomal protein L37 0 ; 66.692 0.055656 737450000 1164290 983830 991190 1200790 739650 1130720 1305530 1297780 860860 FALSE TRUE 1109256.319 1084083.396 1036637.042 1080084.308 868644.7258 1091562.883 1106347.421 1184139.503 994357.7721 1.115550509 1.090234748 1.042519173 1.086212969 0.873573627 1.097756676 1.112625105 1.190858599 1 19.9234055 -0.43045952 7.185339682 0.999994942 1.076675084 0.080375409 0.080951066 0 0 0.075944753 0.01790035 0.371142321 0.43045952 0.076680142 EGVHGGLINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;; 147.2 2.73E-05 8471910000 13568750 12728330 11232110 15356430 9325860 12694050 13172360 13052870 9197270 FALSE TRUE 12927382.08 14025361.3 11747113.35 13812772.48 10952287.03 12254451.87 11162674.56 11909891.51 10623535.66 1.216862492 1.320215957 1.105763065 1.30020484 1.030945571 1.153519154 1.050749479 1.121085474 1 23.34076066 2.677152221 0.560326482 1.035486626 1.27719746 0.480037028 0.077904738 0.656328967 0.433368059 0.058543199 0.064767261 475.5018607 -2.677152221 0.241710834 EGVHGGLINKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ; 172.8 8.39E-06 1196930000 5021200 4095800 4264700 5102400 3519400 4925100 6043200 5441800 4029500 FALSE TRUE 4783857.827 4513166.677 4460240.713 4589497.058 4133182.246 4754542.552 5121198.849 4965287.143 4654374.28 1.027819754 0.969661313 0.958290083 0.986061022 0.888021031 1.021521319 1.100298029 1.066800142 1 22.1501558 2.002406671 24.99332591 1.065360139 0.97116985 0.485534716 0.042173618 56.34886207 585177.8093 0.01525789 0.011202962 100.5556949 -2.002406671 -0.094190289 EGVKFDESEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 140.39 3.59E-05 3301520000 6632470 6112630 5699400 7549200 3413670 7309400 7055150 7397680 3511220 FALSE TRUE 6318966.287 6735513.946 5960723.127 6790340.073 4009012.967 7056273.645 5978757.291 6749899.922 4055722.065 1.558037308 1.660743473 1.469707005 1.674261689 0.988483161 1.739831658 1.474153602 1.664290554 1 21.95152736 -1.286499098 3.741626604 0.998883759 1.533733715 0.382401208 0.211065835 35404284.81 64720112.36 464567.1535 0.04556422 0.051701233 1.286499098 0.534849955 EGVKFDESEKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGVKFDESEKTK 12 2 P14625 P14625 HSP90B1 Endoplasmin 0 100.45 0.0018136 450090000 664010 359840 603960 482220 321560 658470 711050 684980 343920 FALSE TRUE 632623.5632 396508.1051 631652.1634 433746.3294 377639.9622 635667.0188 602566.2632 624999.5199 397253.3571 1.592493939 0.998123988 1.590048648 1.09186322 0.950627491 1.600155184 1.516831142 1.573302047 1 18.59969989 2.201686556 24.99997735 1.47592999 1.251396611 0.08125832 0.271659218 327.0328874 221720.8001 0.09382778 0.069298244 159.1059994 -2.201686556 -0.224533379 EGVKTENDHINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EGVKTENDHINLK 13 1 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ; 122.46 0.00014107 488730000 2254980 1421060 1954910 2114460 1569010 2186630 2923430 2470410 1783330 FALSE TRUE 2148391.564 1565867.63 2044544.557 1901910.464 1842644.847 2110906.455 2477407.061 2254087.804 2059879.708 1.04296943 0.760174307 0.992555317 0.923311422 0.894540026 1.024771712 1.202695017 1.09428128 1 20.97412866 2.0340052 4.440079307 1.120816504 0.915870668 0.453726975 0.08764035 0.146870435 6.672511938 0.033947056 0.023131264 108.1446899 -2.0340052 -0.204945836 EGVKTENNDHINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGVKTENNDHINLK 14 1 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;; 133.47 2.67E-05 1777240000 3731950 2220180 3307640 3419780 2669130 3681500 4967730 4244140 3214690 FALSE TRUE 3555548.12 2446418.866 3459298.566 3076017.217 3134625.427 3554008.732 4209811.55 3872500.602 3713207.707 0.957540865 0.658842451 0.931620001 0.82839891 0.844182624 0.957126294 1.13373985 1.042898999 1 21.82423459 2.058825042 3.179913755 1.070648869 0.832018552 0.563819002 0.085783695 0.15878096 3.203912975 0.036840329 0.023508335 114.5051557 -2.058825042 -0.238630317 EGVVECSFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGVVECSFVK 10 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 163.94 0.0072732 0 221230 132960 144930 156690 148500 138050 201960 163780 174730 FALSE TRUE 210772.8963 146508.7752 151575.1839 140939.2235 174398.353 133269.2939 171147.2928 149438.5549 201826.236 1.04432853 0.725915412 0.751018237 0.698319635 0.864101499 0.660316996 0.847993284 0.740431759 1 17.6227542 4.6023405 2.889476183 0.776628082 1.055673836 0.398899471 0.098560785 0.261962189 3.626071051 0.020766315 0.145816738 40025.84417 -4.6023405 0.279045754 EGWPLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGWPLDIR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 80.18 0.06076 47891000 153620 130380 120280 130810 133800 99942 123720 119820 136610 FALSE TRUE 146358.687 143665.8702 125794.957 117660.7303 157134.6776 96480.98348 104844.2417 109327.9256 157794.7811 0.927525524 0.910460214 0.797206068 0.745656665 0.995816697 0.611433298 0.664434153 0.692848805 1 17.26768996 2.233082705 24.99998596 0.70521078 0.87542227 0.196329776 0.124233044 156.0762352 712290.2578 0.041989126 0.031897342 171.0340993 -2.233082705 0.17021149 EGYAWAEDKEHCEEYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGYAWAEDKEHCEEYGR 17 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;; 256.45 2.56E-27 1619130000 1362250 1122730 1210820 1372740 1028620 1318920 1474600 1402470 908720 FALSE TRUE 1297859.142 1237137.463 1266337.295 1234749.567 1208011.002 1273245.47 1249622.687 1279662.292 1049639.657 1.236480667 1.178630643 1.206449553 1.176355676 1.150881633 1.213031026 1.190525414 1.219144383 1 20.0014627 -1.128491058 4.604460729 0.999980979 1.195913811 0.865553724 0.024329887 4.52E-06 8.56E-07 0.022416414 0.005283087 0.074389038 1.128491058 0.195932832 EGYGGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EGYGGFR 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 123.1 0.0099498 1318820000 2464630 2728110 2170110 2677970 2057880 2445700 2298920 2308580 1897860 FALSE TRUE 2348131.824 3006107.511 2269611.69 2408775.368 2416773.62 2361004.796 1948177.531 2106428.497 2192170.436 1.071144737 1.371292789 1.035326293 1.098808436 1.10245699 1.077016986 0.888698023 0.960887193 1 21.06392854 2.518418418 0.836958131 0.940144461 1.199265395 0.413873157 0.096679895 0.49913176 0.71136474 0.066924792 0.050217923 329.9274253 -2.518418418 0.259120934 EGYKFYPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EGYKFYPPK 9 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 70.1 0.04867 417400000 688260 513180 688890 700430 605870 734760 846130 810140 738810 FALSE TRUE 655727.3138 565473.6254 720476.2879 630021.4457 711533.5362 709315.077 717037.3283 739199.8468 853380.8815 0.768387631 0.662627483 0.844261107 0.738265245 0.833781904 0.831182292 0.840231301 0.866201555 1 19.70283026 1.084892529 0.2208018 1.065402067 0.672796391 0.730704729 0.045751292 1.375726143 0.266469802 0.208682834 0.142189166 12.15885079 -1.084892529 -0.392605676 EHAALEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHAALEPR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 99.802 0.0065549 78652000 40922 32618 36500 29616 45385 30944 46682 36569 39630 FALSE TRUE 38987.69816 35941.81128 38173.5611 26638.94341 53300.12963 29872.40152 39559.80353 33366.8245 45775.618 0.851713202 0.785173698 0.833927815 0.581946123 1.164378155 0.652583249 0.864211239 0.728921333 1 15.48229174 EHALLAYTLGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 168.94 4.52E-05 6491392000 13167525 14162523 11740557 13435090 11094429 13132855 14820460 13889776 8787024 FALSE TRUE 12545122.19 15605700.2 12278873.15 12084569.23 13029293.9 12678060.94 12559326.63 12673513.58 10149670.8 1.236012717 1.537557276 1.209780434 1.19063657 1.283715911 1.249110556 1.237412215 1.248662525 1 23.2749296 -4.999999923 0.11107924 0.040790821 1.45680724 0.463105961 0.095054931 136.3068492 1.004040036 29.48738522 1.141080067 1.00E-05 4.999999923 1.416016419 EHALTSGTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHALTSGTIK 10 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;; 157.24 9.51E-06 907070000 769090 691880 598730 726300 670770 650530 923700 726010 659280 FALSE TRUE 732736.6399 762383.3586 626182.3627 653290.9441 787752.0756 628001.983 782772.6001 662436.7156 761517.7753 0.962205563 1.001136655 0.822282005 0.857880099 1.034450017 0.82467147 1.027911134 0.869890024 1 19.53851819 EHAMLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 78.496 0.035177 334120000 1231990 1116990 1042680 1160980 1212390 1077060 1465060 1245530 1019200 FALSE TRUE 1173756.274 1230812.551 1090487.909 1044276.085 1423830.432 1039761.142 1241538.189 1136464.79 1177252.331 0.997030325 1.045495956 0.926299215 0.887045247 1.209452209 0.883210094 1.054606695 0.965353613 1 20.16699215 EHAPSIIFMDEIDSIGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHAPSIIFMDEIDSIGSSR 19 0 P62195-2;P62195;J3QSA9;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;;;; 370.51 5.54E-108 378478600 233478.1 196124.6 209940.3 243769.8 253278.7 207703.8 276270.2 219632.8 206713.3 FALSE TRUE 222442.0529 216109.9197 219566.2704 219265.5966 297450.4251 200510.9653 234120.1069 200400.5877 238769.3428 0.931618985 0.90509911 0.919574799 0.918315534 1.245764727 0.839768468 0.980528338 0.839306191 1 17.86525809 2.923449475 24.99999998 0.979557475 0.917803332 0.072341665 0.110981475 346.7289961 113233.3499 0.031775687 0.033703215 838.3965363 -2.923449475 -0.061754142 EHASGSGAQSEAAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHASGSGAQSEAAGR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 106.35 0.0026553 9507100 29143.9 26652 33332.5 41896.8 57367.8 25134.8 41947.7 37612.3 46880.7 FALSE TRUE 27766.3256 29367.8691 34860.8281 37685.25407 67372.72616 24264.37557 35547.80794 34318.76762 54150.71952 0.512760049 0.542335713 0.643774051 0.695932656 1.24417047 0.448089624 0.656460491 0.633763834 1 15.72469289 3.483866907 2.492124598 0.753241392 0.527310334 0.186775613 0.216407423 0.505414151 6.281203432 0.0612465 0.096365875 3046.961085 -3.483866907 -0.225931057 EHDPVGQMVNNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHDPVGQMVNNPK 13 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 172.76 2.28E-05 613530000 1369870 1252150 1336320 1601860 1160830 1515710 1627660 1516300 972040 FALSE TRUE 1305118.96 1379745.509 1397591.594 1440837.989 1363278.384 1463220.583 1379330.573 1383524.734 1122778.999 1.162400581 1.228866509 1.244761075 1.283278358 1.214200111 1.303213352 1.228496948 1.232232465 1 20.09864255 -0.506860088 8.08096684 1 1.235334716 0.795353483 0.037799522 0 0 0.03722666 0.008774408 0.311271897 0.506860088 0.235334716 EHDQLIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHDQLIEK 8 0 O14980 O14980 XPO1 Exportin-1 0 ;; 123.21 0.0013574 423740000 2574050 2961030 2376530 3249520 1764560 2955710 2782900 2723850 983140 FALSE TRUE 2452379.758 3262762.323 2485496.251 2922872.076 2072298.705 2853353.022 2358317.494 2485335.254 1135600.33 2.159544774 2.873160774 2.188706876 2.573856311 1.824848629 2.512638422 2.076714343 2.188565104 1 20.11502374 -1.401319383 0.280977513 8.87E-12 2.507299831 0.687702773 0.280690087 10.43733621 0.59024286 7.896256501 0.315487043 0.039689956 1.401319383 2.507299831 EHDYRDEHFDFIQSHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHDYRDEHFDFIQSHIR 17 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 223.07 1.06E-15 1467360000 414588 584680 434961 556057 358551 486212 415216 398592 17830.39 FALSE TRUE 394991.2469 644259.5567 454904.3921 500161.0939 421082.1809 469374.3565 351867.1732 363689.1714 20595.43582 19.17858162 31.2816666 22.08763127 24.2850454 20.4454125 22.79021239 17.08471607 17.65872665 1 14.33003703 0.50501958 0.477811352 3.56E-14 25.11825119 0.818961928 3.27032754 0.755457364 0.32011003 5.355423001 1.713490944 3.199039337 -0.50501958 25.11825119 EHDYRDEHLDFIQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHDYRDEHLDFIQSHLR 17 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;; 186.94 1.66E-10 788760000 128284.4 169215.8 129037 174227 163223 151934.9 139878 119775.1 31252.3 FALSE TRUE 122220.6506 186459.0824 134953.4741 156713.371 191689.0395 146673.3563 118537.0421 109286.9573 36098.74707 3.385731101 5.165250806 3.738453133 4.34124128 5.310129993 4.063114879 3.28368854 3.027444611 1 15.13966114 0.995799345 1.038851315 1.041062895 4.379215345 0.756139027 0.60027376 0.260345731 0.592742037 0.542171263 0.17766719 9.903742609 -0.995799345 3.33815245 EHDYRDEHLDFIQSHLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHDYRDEHLDFIQSHLRR 18 2 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ; 151.57 1.50E-08 675640000 201833 168327 249437 202755 239652 227331 279702 224150 60659 FALSE TRUE 192292.7541 185479.7127 260873.9332 182373.6822 281447.2329 219458.4705 237028.3228 204522.2377 70065.68792 2.744463942 2.647226027 3.723276556 2.602895763 4.016905297 3.132181771 3.382944346 2.91900706 1 16.09642049 EHEEAVSVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHEEAVSVDR 10 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ; 188.28 1.14E-06 164643000 343500 379950 289080 402730 288220 325030 374430 318440 234960 FALSE TRUE 327263.4358 418667.337 302334.6039 362246.8153 338485.4767 313774.1296 317303.8266 290555.7054 271396.3968 1.205850334 1.542641472 1.113996381 1.334751749 1.247199597 1.156146999 1.169152687 1.070595295 1 18.05004204 1.853177409 0.526635056 0.998673716 1.352242857 0.467272672 0.110064432 0.661133876 0.407326484 0.101456418 0.068726562 71.31442892 -1.853177409 0.353569141 EHEVFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;;;; 176.65 0.00074396 1901280000 2083370 2008940 1841020 2400480 1753320 1998740 2198090 2026890 1120156 FALSE TRUE 1984893.229 2213653.27 1925432.588 2159179.19 2059098.453 1929523.133 1862731 1849404.766 1293864.072 1.534081727 1.710885493 1.488125863 1.668783636 1.591433365 1.491287358 1.43966514 1.429365578 1 20.30325463 0.488615357 0.50369766 0.967589592 1.620641059 0.879709274 0.067307187 0.571311237 0.261631625 0.10195648 0.032050571 3.080458464 -0.488615357 0.653051467 EHEVTIFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHEVTIFVR 9 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;; 170.5 5.77E-05 1347540000 490957 552321 386200 571759 365907 425715 431845 398627 224843 FALSE TRUE 467750.4356 608603.1378 403907.652 514284.699 429721.0649 410972.3828 365959.1139 363721.1066 259710.5041 1.801045503 2.343390538 1.555222625 1.980222944 1.654615652 1.582424955 1.409104014 1.400486699 1 17.98654484 1.843590668 0.440977106 0.999619847 2.080757029 0.697399995 0.198110491 0.483556306 0.234080523 0.197936504 0.16236978 69.75746146 -1.843590668 1.081137182 EHFGTFFECLQESLLDLHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHFGTFFECLQESLLDLHTK 20 0 O75691 O75691 UTP20 Small subunit processome component 20 homolog 0 129.11 1.07E-05 17961000 55667 56381 62282 70733 76282 64982 95918 61880 70844 FALSE TRUE 53035.73123 62126.288 65137.69131 63622.78446 89585.55665 62731.65705 81283.94745 56461.45915 81830.1257 0.64811988 0.759210468 0.796011136 0.77749831 1.094774765 0.766608343 0.993325462 0.689983776 1 16.32034445 3.655290126 1.039630884 0.901007413 0.664874833 0.314812229 0.120575717 0.616043514 1.284874966 0.039208716 0.107054642 4521.579033 -3.655290126 -0.236132579 EHFGTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHFGTVK 7 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ; 140.98 0.0025874 264090000 800670 758860 600700 837280 669870 711800 908730 850690 519290 FALSE TRUE 762823.9159 836188.6968 628242.6892 753115.0237 786695.1159 687150.1875 770086.5485 776199.0738 599818.841 1.271757177 1.394068741 1.047387388 1.255570803 1.311554526 1.145596204 1.28386522 1.294055839 1 19.19416731 -1.696813594 2.652510498 0.959543965 1.257773844 0.407373734 0.094582402 10778580.04 8865716.888 2913346.658 0.021981732 0.020099553 1.696813594 0.298229879 EHFQDDVFNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHFQDDVFNEK 11 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 210.79 1.16E-08 502400000 914150 1088080 813570 1148570 563890 948840 791540 991880 398060 FALSE TRUE 870939.9412 1198956.589 850872.9892 1033113.561 662232.2375 915981.4329 670776.0354 905025.7289 459789.1118 1.894216107 2.607622839 1.850572289 2.246929157 1.440295606 1.992177303 1.458877599 1.968349632 1 18.81061278 0.945844591 0.225207022 0.729343611 2.426311029 0.502908456 0.315919562 2.372650453 0.424050046 1.473281011 0.888668522 8.827639535 -0.945844591 1.696967418 EHFQSYDLDHMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHFQSYDLDHMEK 13 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 155.43 2.70E-05 162895000 287460 230850 224030 301980 207857 274960 315460 274690 101040 FALSE TRUE 273872.3355 254373.8775 234301.9971 271624.3967 244107.195 265438.0663 267330.7832 250636.6874 116708.7672 2.346630353 2.179561002 2.007578375 2.327369257 2.091592611 2.274362695 2.290580131 2.147539499 1 16.83255341 0.869858671 9.193631859 1.000000012 2.220530875 0.929464103 0.104760628 5.093460412 360.0218979 0.095343898 0.023856715 7.410690415 -0.869858671 1.220530863 EHGAVAVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EHGAVAVER 9 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;; 132.88 0.0013403 455334000 581543 535114 549828 602132 666493 569095 647996 596069 617769 FALSE TRUE 554054.6149 589642.725 575038.1577 541604.5474 782729.1682 549387.0975 549132.3089 543874.0384 713569.4614 0.776455054 0.826328419 0.805861502 0.759007464 1.096920777 0.769913971 0.769556909 0.762187941 1 19.44469435 -2.388404044 2.280981394 2.394842054 0.818642901 0.238650974 0.100536515 6180105.742 688918.1581 44628574.03 0.023072094 0.004088801 2.388404044 -1.576199153 EHGVPILISEIHPGQPADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHGVPILISEIHPGQPADR 19 0 Q9HD26-2;Q9HD26;A0A0J9YVX5 Q9HD26-2 GOPC Golgi-associated PDZ and coiled-coil motif-containing protein 0 71.073 0.011911 40414000 62765 56648 59627 70923 59170 53592 69101 59615 38409 FALSE TRUE 59798.22284 62420.4956 62360.95693 63793.6853 69489.22927 51736.0956 58558.37332 54394.79456 44365.27155 1.34786108 1.406967509 1.405625498 1.437919414 1.566297846 1.1661395 1.319914683 1.226066981 1 15.43714318 1.040997484 0.756182959 1.005251753 1.411339544 0.667389909 0.091215207 0.399452167 0.521891899 0.08345348 0.03187255 10.98999473 -1.040997484 0.40608779 EHHFGSSGMTLHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHHFGSSGMTLHER 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 113.53 0.00018435 139160000 22443 18032 19461 25803 26350 25167 28919 17456 7762.1 FALSE TRUE 21382.16387 19869.4813 20353.3061 23209.23342 30945.43166 24295.46048 24506.87542 15927.4601 8965.806825 2.384856632 2.216139795 2.270103126 2.588638577 3.451494357 2.709790759 2.733370894 1.776467016 1 13.1302177 3.241185901 24.47224015 2.551313305 2.287959337 0 0.657588602 207.4663694 1933917.104 0.169032525 0.218697814 1742.55262 -3.241185901 -0.263353968 EHHQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHHQLQR 7 0 Q13268;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 125.25 0.0040673 49638000 69694 76259 63300 74512 73183 60592 70519 55841 11940 FALSE TRUE 66399.70274 84029.8788 66202.36761 67021.9122 85946.09203 58493.68385 59760.03138 50951.26601 13791.59422 4.814505248 6.092832885 4.800196885 4.85962037 6.231773547 4.241256153 4.333076396 3.69437102 1 13.75150161 0.776180353 0.686982968 0.959097999 5.388769803 0.844481463 0.570383864 0.349827735 0.34074763 0.541994875 0.203318506 5.972832732 -0.776180353 4.429671805 EHIEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EHIEELLR 8 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;;;; 172.21 0.00028488 527831000 805901 819289 709441 868207 789641 763031 821972 820297 485439 FALSE TRUE 767807.6569 902775.4806 741969.5716 780933.1829 927354.1404 736607.0451 696565.0748 748467.446 560718.4008 1.369328447 1.610033627 1.323248123 1.392736856 1.653867858 1.313684452 1.242272545 1.334836604 1 19.09691689 1.023179982 0.635881367 1.004304431 1.47449081 0.576557777 0.118333798 0.54617313 0.525025192 0.114791769 0.048354974 10.54823951 -1.023179982 0.470186379 EHIKNPDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHIKNPDWR 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 135.86 0.00012558 859630000 1394200 1307080 1249010 1407200 1271310 1349860 1716270 1411300 816460 FALSE TRUE 1328298.929 1440272.938 1306278.344 1265745.582 1493026.061 1303114.01 1454421.49 1287719.09 943072.4469 1.408480264 1.527213464 1.38513043 1.342150952 1.583150973 1.381775084 1.542216078 1.365450867 1 19.84700908 0.93048335 8.693397794 1.000000399 1.456323124 0.768002816 0.077774435 1.059987709 132.6294891 0.067352003 0.016857571 8.520858428 -0.93048335 0.456322725 EHIYDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 124.59 0.0041312 780540000 1802850 1491700 1472140 1777490 1703510 1461940 1944400 1771670 1350850 FALSE TRUE 1717632.853 1643705.926 1539639.075 1598813.328 2000601.605 1411312.651 1647746.069 1616533.183 1560332.919 1.100811777 1.053432832 0.986737546 1.024661666 1.2821633 0.904494569 1.056022115 1.036018124 1 20.57342245 EHKLDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHKLDGK 7 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;; 116.37 0.0032871 1652560000 5677000 4301130 5483160 5370090 3832160 6097120 7266580 6583590 3396500 FALSE TRUE 5408659.461 4739420.037 5734568.31 4830278.351 4500487.491 5885975.206 6157929.761 6007095.958 3923211.873 1.378630478 1.208045905 1.461702425 1.23120507 1.147143625 1.500295012 1.569614377 1.531167868 1 21.90360382 2.214546958 24.99796998 1.462672572 1.288840352 0.043781831 0.182416092 376.0821636 391495.1438 0.06140018 0.045369951 163.8879256 -2.214546958 -0.17383222 EHLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHLASK 6 0 Q96TA1;Q96TA1-2;Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q96TA1;Q9P0K7-3 FAM129B;RAI14 Niban-like protein 1;Ankycorbin 0 75.269 0.078136 169530000 260200 235330 221470 272280 214000 230890 297980 269420 171040 FALSE TRUE 247900.8617 259310.3945 231624.6186 244909.8971 251321.5322 222894.2214 252517.6782 245828.1565 197564.0096 1.25478756 1.31253863 1.172402904 1.239648343 1.2721018 1.128212683 1.278156273 1.244296251 1 17.59196063 -4.068559426 0.287430635 3.27E-12 1.258637 0.659121227 0.053391383 78.60480823 1.229815334 46.56073699 0.055295011 8.54E-05 4.068559426 1.258637 EHLELFWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 223.84 3.32E-07 805260000 981330 951710 678025 815753 1039630 702931 1073860 867770 576848 FALSE TRUE 934944.4757 1048690.331 709113.1169 733751.9586 1220941.143 678588.3232 910022.9342 791783.4585 666302.6417 1.403182904 1.573894902 1.064250796 1.10122925 1.83241228 1.01843859 1.365780168 1.188324057 1 19.34581809 -4.047037182 0.081403889 1.91E-10 1.703443573 0.168205309 0.24466745 320.9311161 2.229953819 61.88770468 7.905186897 8.97E-05 4.047037182 1.703443573 EHLLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHLLLAR 7 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;;; 116.11 0.0055283 2436640000 3973800 3105730 2430060 2465640 4477960 2176880 4257200 2847870 2627360 FALSE TRUE 3785966.349 3422207.418 2541480.655 2217789.183 5258914.806 2101494.1 3607685.951 2598495.405 3034797.57 1.247518578 1.127655911 0.837446517 0.730786529 1.732871694 0.692465989 1.188773178 0.85623352 1 21.53316886 3.991933149 19.57537719 1.019825911 1.202571178 0.065409017 0.296296361 72.83938704 176777.0307 0.068615776 0.131790291 9815.968349 -3.991933149 0.182745266 EHLLVSIPLLINHLQAESIVVHTYAAHALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHLLVSIPLLINHLQAESIVVHTYAAHALER 31 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 202.14 2.85E-26 2111260000 206835.1 264992.7 245912.3 325568.4 268528 273462.7 311615.8 253346.2 54994.2 FALSE TRUE 197058.4147 291995.7574 257187.6222 292841.6459 315359.1982 263992.6181 264073.0865 231161.8637 63522.41966 3.102186846 4.596735435 4.048769294 4.610051812 4.96453378 4.155896761 4.157163532 3.639059483 1 15.95497825 0.648605239 1.784565417 1.000454079 4.229673244 0.811624987 0.486660837 0.662232537 2.798477354 0.46859632 0.13168357 4.452513441 -0.648605239 3.229219166 EHMDAINHDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHMDAINHDTK 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 116.24 0.00071104 41776000 85056 87480 90138 113100 77675 96627 106770 91590 36285 FALSE TRUE 81035.57144 96394.31146 94270.91646 101730.9731 91221.49541 93280.78276 90480.27553 83569.89405 41911.89248 1.933474407 2.299927437 2.249264132 2.427257924 2.176506237 2.225639961 2.158821045 1.99394227 1 15.35507205 0.553828606 1.415242258 0.999855378 2.214586582 0.905247358 0.12237226 0.535991135 1.37587676 0.117759116 0.03450801 3.579551426 -0.553828606 1.214731204 EHMGDILYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHMGDILYK 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 114.5 0.0016287 264855000 1083760 1058450 1033750 1208760 1045850 1087460 1288830 1160810 766720 FALSE TRUE 1032532.813 1166307.258 1081148.46 1087253.148 1228245.909 1049800.988 1092195.313 1059163.323 885619.0217 1.165888251 1.316940162 1.22078279 1.227675921 1.386878419 1.185386675 1.233256384 1.19595819 1 19.75632668 0.532065426 0.992672703 0.999569044 1.254314305 0.605963694 0.062889848 1.02496967 1.49059951 0.056282485 0.017877832 3.404594756 -0.532065426 0.254745261 EHMQPTHPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 EHMQPTHPIR 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;;;;;;;;;;; 115.18 0.00088039 3992588000 1811115 1974409 1785262 2072019 2165476 1815160 2056093 1779804 954908.9 FALSE TRUE 1725507.183 2175603.522 1867118.029 1863735.714 2543134.329 1752300.554 1742398.25 1623954.926 1102991.295 1.564388759 1.972457563 1.692776758 1.689710265 2.305670353 1.588680311 1.57970263 1.472318896 1 20.07298997 1.032218837 1.063202523 1.013406172 1.81522105 0.591524226 0.21382329 0.355758431 0.850670181 0.19006877 0.062023255 10.77007772 -1.032218837 0.801814878 EHNFFHLDPANVVMFEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHNFFHLDPANVVMFEQR 18 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 97.284 0.00083026 166849000 173649 186591 195191 234521 193383 200713 248760 157265 9214.9 FALSE TRUE 165440.9559 205604.835 204140.7004 210946.5035 227108.934 193762.2585 210807.0932 143494.0429 10643.89963 15.54326531 19.316683 19.17912678 19.81853558 21.33700447 18.20406667 19.80543791 13.48134123 1 13.37773919 0.88029929 2.865018527 1.00898073 18.93437513 0.935340784 1.50089535 0.11299397 1.896375 1.497183444 0.394744294 7.591005222 -0.88029929 17.9253944 EHNGQVTGIDWAPESNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHNGQVTGIDWAPESNR 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 159.7 3.18E-09 1506310000 1857140 1787860 1596000 1913020 1273780 1691010 1747350 1686170 1011340 FALSE TRUE 1769356.673 1970044.967 1669178.179 1720719.595 1495926.829 1632449.9 1480759.665 1538520.016 1168173.442 1.514635249 1.686431908 1.428878725 1.473000098 1.280569113 1.39743795 1.267585456 1.317030469 1 20.15582306 1.792580955 0.197785074 0.873951552 1.782185598 0.803196649 0.080170784 1.120310218 0.2157503 0.354221036 0.423114348 62.02702541 -1.792580955 0.908234046 EHNSMWASLS(ph)SPDAEAVEPDFSSIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNS(0.021)MWAS(0.073)LS(0.501)S(0.405)PDAEAVEPDFSSIER;EHNSMWAS(0.012)LS(0.494)S(0.494)PDAEAVEPDFSSIER 164.14 9.09E-12 98726000 40216 29015 43973 49401 67160 35222 55737 42001 59311 TRUE FALSE 38315.06938 31971.66149 45989.20555 44435.11762 78872.68274 34002.25331 47233.29697 38323.16978 68508.64696 0.55927348 0.466680673 0.671290524 0.648605973 1.151280696 0.496320608 0.689450151 0.559391719 1 16.06399847 3.514207666 2.672816739 0.738209495 0.513747134 0.20139554 0.195869519 0.428093158 6.078245266 0.052868693 0.083929844 3267.440337 -3.514207666 -0.224462361 EHNSMWASLSS(ph)PDAEAVEPDFSSIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWASLS(0.156)S(0.844)PDAEAVEPDFSSIER;EHNSMWAS(0.001)LS(0.288)S(0.711)PDAEAVEPDFSSIER;EHNSMWASLS(0.207)S(0.793)PDAEAVEPDFSSIER;EHNS(0.012)MWAS(0.008)LS(0.176)S(0.804)PDAEAVEPDFSSIER 254.15 9.33E-53 406599000 132382 107112 140554 160884 252335 119813 192435 143803 208176 TRUE FALSE 126124.5652 118026.8346 146998.5399 144711.6347 296342.1441 115663.8458 163075.5064 131210.847 240458.8709 0.524516167 0.49084001 0.611325086 0.601814498 1.232402627 0.481013012 0.678184614 0.545668565 1 17.87543062 2.984798041 24.85696109 0.753150213 0.53842091 0.213961146 0.216311793 1069.684908 1749061.973 0.061972597 0.067782523 965.6017419 -2.984798041 -0.214729303 EHPDAWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHPDAWTR 8 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;H7BZC5 O14980 XPO1 Exportin-1 0 ;; 97.431 0.0082369 1030320000 1483240 1458360 1319190 1652350 1766300 1409800 1613840 1438770 1591420 FALSE TRUE 1413130.185 1606968.542 1379676.166 1486252.639 2074342.161 1360978.273 1367619.068 1312783.671 1838209.286 0.768753697 0.874203256 0.750554454 0.808532875 1.128458102 0.740382656 0.743995299 0.714164422 1 20.8098696 -0.90505174 5.459477477 1.000000193 0.816815531 0.189082757 0.119659487 2.71E-07 5.43E-08 0.111734657 0.026336084 0.124436635 0.90505174 -0.183184662 EHPDRFIECYIAEQNMVSIAVGCATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHPDRFIECYIAEQNMVSIAVGCATR 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 90.974 0.0061384 42601000 20754 6241.3 20335 14990 36891 18702 37322 19924 37965 FALSE TRUE 19772.99955 6877.295566 21267.37986 13483.17672 43324.77872 18054.34505 31627.84343 18179.34894 43852.4183 0.450898726 0.156828194 0.484976215 0.307467119 0.987967834 0.411706942 0.721233735 0.414557501 1 15.42036878 2.785852807 24.99832198 0.668169252 0.33654259 0.399390469 0.214357712 394.2054688 208373.4851 0.057949882 0.061464996 610.7349969 -2.785852807 -0.331626662 EHPVKQELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHPVKQELER 10 1 J3KPZ4;Q13901 J3KPZ4 C1D Nuclear nucleic acid-binding protein C1D 0 110.08 0.001162 31186000 87073 71721 80577 92262 76855 84581 103260 90787 79556 FALSE TRUE 82957.23185 79029.45144 84271.53515 82987.64847 90258.48767 81651.93876 87505.7905 82837.20899 91893.13816 0.902757632 0.860014719 0.917060151 0.903088632 0.982211398 0.888553165 0.952255982 0.901451519 1 16.48766952 -5 0.057820794 1.337420056 0.76289378 0.439941152 0.032285596 341.840077 1.447688618 16.60058607 2.952126962 1.00E-05 5 -0.574526276 EHPWEVMPDLYFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHPWEVMPDLYFYR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 128.76 7.18E-05 179777000 408640 633360 331410 472570 312600 344320 347320 410090 211257 FALSE TRUE 389324.397 697900.1041 346605.4763 425066.3658 367117.341 332396.1121 294329.955 374180.3456 244017.6566 1.595476337 2.860039367 1.420411462 1.741949217 1.504470398 1.362180576 1.206183024 1.533415044 1 17.89662602 3.663254822 12.33154342 1.407788697 2.22760098 0.48444246 0.356762306 0.81056117 131.5639938 0.090252984 0.139834926 4605.267083 -3.663254822 0.819812283 EHPWEVMPDLYFYRDPEEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHPWEVMPDLYFYRDPEEIEK 21 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 84.493 0.0018255 14676000 16563 23418 16953 23993 12221 17297 17915 19460 12998 FALSE TRUE 15780.09981 25804.32082 17730.31182 21581.17806 14352.33853 16698.00055 15181.73772 17755.97924 15013.66346 1.051049257 1.718722476 1.180945069 1.437435848 0.955951795 1.112186949 1.011194754 1.182654672 1 13.87398843 2.741690698 24.99231602 1.054568431 1.366870504 0.391472154 0.181781568 258.9151705 2067329.3 0.053190434 0.054277784 551.684393 -2.741690698 0.312302073 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK 29 2 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;;;;; 186.56 8.27E-18 2455802000 2140589 2159157 1949538 2347383 1155376 2426005 2369715 2541392 943791 FALSE TRUE 2039407.6 2379177.553 2038926.246 2111419.601 1356873.209 2341991.839 2008171.454 2318854.244 1090149.288 1.870759925 2.182432791 1.870318376 1.936816933 1.244667335 2.148322128 1.842106834 2.127097884 1 20.05609428 3.269809948 2.687173639 1.765233464 2.020020995 0.100207423 0.367837705 0.654612099 9.663528533 0.100346695 0.136201175 1861.272447 -3.269809948 0.254787531 EHPYLFSQCQAIHCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHPYLFSQCQAIHCR 15 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;; 223.96 6.93E-13 991120000 96856 100445 95399 108942 138751 115168 108932 114531 123802 FALSE TRUE 92277.80883 110680.4597 99773.13851 97990.94318 162949.1305 111179.7033 92312.42273 104502.0585 143000.5819 0.645296737 0.773986079 0.697711416 0.685248563 1.139499772 0.777477279 0.645538791 0.730780652 1 17.12566149 4.240087474 0.808877631 0.804526718 0.628889488 0.121297576 0.150322407 3.632049677 2.915791653 0.057985542 0.502706457 17381.50884 -4.240087474 -0.17563723 EHQFDSK ddPTM_SK-BR-3_Trastuzumab_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 60.436 0.097517 56418000 202070 214470 170310 226070 213320 209830 191200 182430 165870 FALSE TRUE 192518.5516 236324.7368 178118.882 203345.0141 250522.9405 202563.5345 162028.9284 166455.4621 191592.2725 1.004834637 1.233477393 0.929676754 1.061342462 1.307583742 1.057263594 0.845696574 0.8688005 1 17.54767985 1.858231666 5.17285406 0.893766618 1.110476916 0.399062438 0.113097497 0.205660435 7.530389947 0.049681898 0.029055617 72.14922433 -1.858231666 0.216710299 EHQISPGDFPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EHQISPGDFPSLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;; 128.85 0.00016057 1195260000 988100 937000 921730 1138620 1023790 941090 1141920 1031480 889528 FALSE TRUE 941394.4712 1032481.365 963992.2322 1024163.754 1202338.652 908499.8173 967699.1312 941158.143 1027471.459 0.916224449 1.004875956 0.938218014 0.996780733 1.170191776 0.884209298 0.941825802 0.915994439 1 19.97066689 -0.310954307 6.294882016 1 0.970502976 0.012875797 0.07956568 0 0 0.073546502 0.017335077 0.488703774 0.310954307 -0.029497023 EHQMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 71.029 0.067745 48711000 96182 89674 68596 95194 68530 83914 97298 96024 56595 FALSE TRUE 91635.66747 98811.88255 71741.19445 85624.91826 80481.6103 81008.03714 82453.4031 87615.6295 65371.46355 1.401768639 1.511544597 1.097439013 1.309821038 1.231142855 1.239195709 1.261305754 1.340273336 1 15.99637338 8 0.030791683 3.29E-11 3.181156427 0.44319757 0.107642098 1096.134463 2.587424304 84.16852967 209.0962331 100000000 -8 3.181156427 EHQTSAYS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTS(0.013)AY(0.042)S(0.945)PPR;EHQTSAY(0.003)S(0.996)PPR;EHQTSAY(0.002)S(0.998)PPR;EHQT(0.005)S(0.073)AYS(0.922)PPR;EHQTSAY(0.008)S(0.992)PPR;EHQT(0.003)S(0.003)AYS(0.995)PPR 118.19 0.00048539 759342000 469748 554488 458187 611999 441715 485407 495050 505305 339790 TRUE FALSE 447543.943 610990.9576 479195.3272 550479.6978 518749.9561 468597.2339 419521.0303 461057.8154 392482.8978 1.14028903 1.556732691 1.220933014 1.402557158 1.32171353 1.193930325 1.068889963 1.174720779 1 18.58227027 2.079423544 2.495082427 1.09001124 1.343062868 0.486099398 0.116152017 0.234716928 2.849435649 0.053387393 0.03214238 120.0669681 -2.079423544 0.253051628 EHQTSAYS(ph)PPRAGQEH ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHQTSAYSPPRAGQEH 16 1 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTS(0.002)AYS(0.998)PPRAGQEH;EHQT(0.001)S(0.002)AYS(0.997)PPRAGQEH;EHQT(0.005)S(0.061)AY(0.008)S(0.926)PPRAGQEH 122.34 5.68E-05 345317000 121672 74268 111592 116825 203035 97077 166272 110979 163657 TRUE FALSE 115920.8057 81835.99364 116708.6036 105081.529 238444.2397 93715.19915 140904.1526 101261.0904 189036.0917 0.613220495 0.432912006 0.617387942 0.555880774 1.261368861 0.495752945 0.745382278 0.535670673 1 17.52830218 2.950551488 24.99942317 0.77694293 0.543061489 0.235149312 0.222430698 555.9967459 281092.0084 0.062793837 0.066603987 892.3834094 -2.950551488 -0.233881442 EHSLQVS(ph)PSLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 EHSLQVS(0.999)PS(0.001)LEK;EHSLQVS(0.998)PS(0.002)LEK;EHSLQVS(1)PSLEK 238.12 2.56E-16 732240000 1139700 1242570 1318160 1489250 1010720 1431810 1589750 1529830 898610 TRUE FALSE 1085828.64 1369189.296 1378598.94 1339547.761 1186989.248 1382226.061 1347204.44 1395869.975 1037961.849 1.046116137 1.319113315 1.328178816 1.290555873 1.143576952 1.33167328 1.297932521 1.34481819 1 19.98532199 4.606568902 2.986563689 1.27207595 1.037680225 0.260036688 0.108601627 0.338510548 5.030847646 0.023430638 0.160859028 40417.44924 -4.606568902 -0.234395725 EHSNPNYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHSNPNYDK 9 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 111.06 0.0026203 14153000 372345 374930 318109 446685 260001 381145 412019 391315 230134 FALSE TRUE 354744.9898 413135.7933 332694.6123 401783.3752 305345.0921 367945.8531 349157.9343 357049.3841 265822.0054 1.334520779 1.554182065 1.251569116 1.511475224 1.148682524 1.384181316 1.313502747 1.343189717 1 18.02010101 -4.001245769 0.176161803 4.36E-13 1.455919713 0.497302665 0.1140018 66.69686344 0.877259673 23.99863101 0.345143263 9.97E-05 4.001245769 1.455919713 EHTAKYLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHTAKYLLR 9 1 Q9NYQ8 Q9NYQ8 FAT2 Protocadherin Fat 2 0 65.224 0.061254 2001500000 845480 417670 983880 566340 4295500 451220 1306900 554350 4107800 FALSE TRUE 805515.836 460231.0479 1028991.871 509410.4272 5044633.84 435594.1383 1107508.402 505808.1752 4744816.644 0.169767537 0.096996593 0.216866519 0.107361457 1.063188363 0.091804209 0.233414373 0.10660226 1 22.17792091 -1.886429231 2.584586321 1.3815567 0.249921869 0.389963001 0.290295556 67199568.6 38908437.87 156476493.7 0.067127506 0.012988852 1.886429231 -1.13163483 EHTALLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EHTALLK 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 122.79 0.0043066 3785120000 5897810 5937670 5123200 6413670 5209510 5897650 7253080 6028240 4321400 FALSE TRUE 5619032.21 6542725.324 5358103.788 5768955.706 6118046.895 5693412.902 6146489.434 5500375.348 4991540.641 1.125711001 1.310762707 1.073436875 1.155746516 1.225683077 1.14061235 1.231381226 1.10193941 1 22.25105374 0.985160602 4.713581806 1.000186411 1.186655794 0.444800634 0.065502713 0.139400101 10.59558284 0.058715027 0.014887233 9.664081901 -0.985160602 0.186469383 EHTLAWK ddPTM_SK-BR-3_Trastuzumab_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 ; 117.93 0.0051196 432710000 1593220 1427610 1138220 1293430 1822700 1237900 1909600 1339820 1467370 FALSE TRUE 1517911.648 1573085.082 1190408.513 1163411.959 2140578.303 1195031.213 1618255.448 1222498.258 1694922.245 0.895564178 0.92811637 0.702338126 0.686410225 1.262935989 0.705065507 0.954766776 0.721270997 1 20.69278766 EHVEEISELFYDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;; 162.93 4.36E-06 431932000 532580 545483 519150 632027 601946 497386 572869 539355 540726 FALSE TRUE 507405.9989 601068.3379 542953.541 568494.4452 706925.1918 480161.3981 485467.3126 492126.2169 624579.0264 0.812396794 0.962357544 0.869311197 0.910204187 1.131842668 0.768776052 0.777271237 0.787932665 1 19.2525246 EHVIEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EHVIEALR 8 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;; 112.84 0.0029633 3689110000 4400180 4569190 3194850 4753940 3863820 3637890 4333390 4374550 3001623 FALSE TRUE 4192192.212 5034795.656 3341337.033 4276064.919 4537668.985 3511908.957 3672251.767 3991491.211 3467099.365 1.209135295 1.452163646 0.963726932 1.233326325 1.308779619 1.012924231 1.059171192 1.151248 1 21.72529775 2.787997216 0.420394154 1.015328248 1.337176926 0.236701055 0.133776104 1.631101424 0.581206373 0.128522617 0.209110577 613.7580703 -2.787997216 0.321848679 EHVVAASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 99.802 0.0065549 374021000 876050 793940 802420 936380 849180 879800 1084120 918190 822020 FALSE TRUE 834640.8527 874843.3886 839211.7507 842253.3034 997276.7231 849332.3054 918717.5828 837788.416 949494.6633 0.879036908 0.921377889 0.88385094 0.887054278 1.050323674 0.894509825 0.967585831 0.882351896 1 19.85680037 EHYPNGVCTVYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EHYPNGVCTVYGK 13 0 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 120.14 0.00029364 326740000 478390 487210 433990 527860 396920 457580 508560 499710 325040 FALSE TRUE 455777.4528 536857.2529 453888.8708 474798.5099 466142.7223 441733.8899 430969.8317 455952.7433 375445.5431 1.213964212 1.429920431 1.208933969 1.264626838 1.241572129 1.176559152 1.14788906 1.214431098 1 18.51824414 1.171539847 0.309845889 0.973636301 1.336091193 0.605127068 0.066717025 1.014901868 0.326798475 0.139941254 0.094084771 14.84362064 -1.171539847 0.362454892 EHYVDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 125.25 0.0040673 21890350000 15497060 17724520 12928390 18297420 9890720 15422900 14052130 15762960 7240760 FALSE TRUE 14764544.69 19530668.74 13521169.47 16458128.58 11615658.44 14888801.11 11908219.48 14382671.66 8363620.08 1.765329432 2.3351932 1.616664715 1.967823553 1.38883143 1.780186207 1.423811623 1.719670612 1 22.9956961 0.971314202 0.179646621 0.651032801 2.293631957 0.535822723 0.243133574 3.214769982 0.43659628 1.958290284 1.291718402 9.360826632 -0.971314202 1.642599157 EHYVDLKDRPFFAGLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EHYVDLKDRPFFAGLVK 17 2 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 56.215 0.067595 270240000 156140 50176 154900 109850 179770 145310 255760 167050 160260 FALSE TRUE 148759.5716 55288.99145 162002.3182 98807.6693 211121.8311 140277.8783 216739.1146 152422.2164 185112.3023 0.803617965 0.298678104 0.875156952 0.533771489 1.140506754 0.757798788 1.170852028 0.823404034 1 17.49804125 2.746231153 24.99401284 0.985639617 0.606227806 0.438096823 0.196595484 478.9107077 1560503.78 0.055439777 0.057796304 557.4823902 -2.746231153 -0.37941181 EIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIAATCSGTEWGQSSGAASPGLFQAGHR 28 0 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR 240.4 1.84E-45 495810000 187012 204185 164493 199304 180571 181076 187322 179526 151658 TRUE FALSE 178172.3134 224991.6836 172035.1668 179269.5833 212062.5252 174805.2927 158742.5885 163805.7517 175176.3481 1.017102567 1.284372497 0.982068462 1.023366369 1.210565967 0.997881818 0.906187338 0.935090573 1 17.41844847 2.038510454 7.548872327 0.940305334 1.110999191 0.378349583 0.09301319 0.195585256 31.59879547 0.034442152 0.025198874 109.2723931 -2.038510454 0.170693856 EIAAVISPELEHLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIAAVISPELEHLDK 15 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-6 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 210.34 1.93E-09 43524000 85423 71602 76182 103050 76554 93074 101190 96107 73803 FALSE TRUE 81385.22408 78898.3252 79675.02005 92691.21822 89904.99336 89850.82404 85751.60702 87691.36158 85247.99231 0.954687869 0.925515347 0.934626352 1.087312624 1.054628865 1.053993433 1.005907643 1.028661898 1 16.37937824 3.255667852 24.99966801 1.038268248 0.937886424 0.770605783 0.025755728 107.8904338 157664.7523 0.007143198 0.009648519 1801.63932 -3.255667852 -0.100381824 EIADYLAAGKDER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 137.46 5.52E-05 568755000 934240 769690 766650 841120 760020 850630 1035670 944700 853330 FALSE TRUE 890080.3267 848122.2861 801801.6608 756569.0196 892567.2474 821172.4698 877659.5201 861977.0598 985660.0582 0.90302972 0.86046125 0.813466726 0.767576015 0.905552822 0.833119353 0.890428209 0.874517591 1 19.91073064 0.420546935 0.806089536 1.001235376 0.850867582 0.559274002 0.041277637 1.572665236 1.478410212 0.044534759 0.013928213 2.633582542 -0.420546935 -0.150367794 EIAIVHS(ph)DAEKEQEEEEQKQEMEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIAIVHSDAEKEQEEEEQKQEMEVK 25 2 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEKEQEEEEQKQEMEVK 301.78 1.31E-63 60760000 89635 101970 62661 109470 29516 99840 79496 102530 17003 TRUE FALSE 85398.13119 112360.8589 65534.06883 98465.86762 34663.58105 96382.51577 67367.42516 93551.92965 19639.7384 4.348231603 5.721097534 3.336809661 5.013603828 1.764971628 4.907525436 3.430158986 4.763399988 1 14.26148809 3.728509922 24.88574644 3.629410339 5.034664584 0.183326721 1.34549166 929.3318234 2301047.718 0.310900392 0.488069625 5351.923808 -3.728509922 1.405254245 EIAVHIGDRDNAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIAVHIGDRDNAVR 14 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ;;; 144.8 5.26E-06 410736000 160752 135547 151078 155355 191286 143997 179579 161662 189108 FALSE TRUE 153153.5715 149359.3934 158005.0757 139738.4202 224646.2178 139010.3478 152180.9254 147506.0183 218433.9028 0.701143777 0.683773862 0.723354176 0.639728625 1.028440251 0.636395477 0.69669096 0.67528903 1 17.73683727 -2.317834652 2.204982431 2.40950632 0.719330588 0.376186526 0.111965738 4847062.274 575985.4981 34120632.21 0.025784489 0.004810225 2.317834652 -1.690175731 EIDCLS(ph)PEAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 213.18 3.56E-09 260084000 516220 526740 548280 628420 417250 608990 637150 665450 571970 TRUE FALSE 491819.3036 580415.4049 573419.1803 565250.0277 490018.2679 587900.5236 539941.0654 607179.6702 660668.1864 0.744427102 0.878527855 0.867938236 0.85557325 0.74170102 0.889857474 0.817265121 0.919038759 1 19.33356635 1.019235661 2.677945781 1.000042034 0.828474699 0.559938957 0.051149743 0.182976856 2.943392687 0.045711773 0.012264393 10.45287268 -1.019235661 -0.171567335 EIDSWFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIDSWFSER 9 0 H0Y6F5;Q9H4I2;Q9H4I2-2;Q9Y6X8 H0Y6F5;Q9Y6X8 ZHX3;ZHX2 Zinc fingers and homeoboxes protein 3;Zinc fingers and homeoboxes protein 2 0 114.5 0.0037886 16085000 34991 34309 32374 34390 48713 31749 41679 33253 51585 FALSE TRUE 33337.04478 37805.12611 33858.37992 30933.05186 57208.53178 30649.52417 35320.10306 30341.19103 59584.53834 0.559491534 0.634478795 0.568241038 0.519145616 0.960123773 0.514387206 0.592772958 0.509212488 1 15.86265039 -1.352759427 5.101781244 1.0001954 0.608250092 0.468944426 0.131351518 0.000266495 3.38E-05 0.116097281 0.027350896 0.044385444 1.352759427 -0.391945308 EIDVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EIDVDR 6 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;; 139.92 0.027558 2368130000 5036080 4934920 4821010 5717990 5076390 4950050 5598550 5408110 5285990 FALSE TRUE 4798034.479 5437793.959 5042058.077 5143206.782 5961710.809 4778628.527 4744388.373 4934547.218 6105714.332 0.785826886 0.890607333 0.825793315 0.842359551 0.976414959 0.78264856 0.777040673 0.808185079 1 22.54172866 -2.432600319 2.285954835 2.605619757 0.835312422 0.423746991 0.060056937 3904288.406 493823.2445 32411629.07 0.015499864 0.003693173 2.432600319 -1.770307334 EIEDFDSLEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 210.08 1.11E-07 221240000 344730 439460 280860 432870 272260 317780 302240 350250 243130 FALSE TRUE 328435.2961 484241.4736 293737.7088 389357.0852 319742.0578 306775.1989 256127.737 319580.2532 280833.3587 1.169502433 1.724301828 1.045950204 1.3864346 1.138547284 1.092374497 0.912027468 1.137971125 1 18.09935479 2.709291047 1.045168891 0.999586234 1.404863707 0.356911928 0.183708374 0.451424131 1.031786285 0.093745815 0.083876035 512.024859 -2.709291047 0.405277473 EIEDPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIEDPEDR 8 0 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 128.61 0.0026201 633460000 1973760 2037700 1770540 2811000 2414800 2043130 2229800 1899280 1804690 FALSE TRUE 1880464.276 2245343.947 1851721.01 2528432.939 2835940.355 1972375.896 1889603.057 1732968.974 2084552.108 0.902095116 1.077134958 0.888306415 1.212938228 1.360455488 0.946186899 0.906479166 0.831338765 1 20.99130601 2.021043888 24.99740106 0.90824417 1.073594692 0.255909807 0.141342299 353.9593791 420455.8499 0.054499195 0.040246876 104.9648496 -2.021043888 0.165350522 EIEELKELLPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EIEELKELLPEIR 13 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;;;; 171.87 2.22E-05 718899000 1909931 1546500 1862418 2031009 1543116 2057492 2423271 2314967 1873727 FALSE TRUE 1819652.347 1704090.108 1947811.707 1826848.117 1812234.942 1986240.536 2053556.503 2112256.217 2164295.013 0.840759848 0.787364984 0.89997514 0.844084612 0.837332679 0.917730958 0.948833911 0.975955775 1 21.04546573 1.879216525 0.894572462 1.001184306 0.828603189 0.822162695 0.028623213 0.214071392 0.317132517 0.02409581 0.01096079 75.7210321 -1.879216525 -0.172581117 EIEELKQELIQAEIQNGVK ddPTM_SK-BR-3_Trastuzumab_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 ; 208.28 2.53E-16 272150000 374204 316515 336917 413250 226736 403609 424348 441963 269168 FALSE TRUE 356516.1185 348768.2383 352364.9777 371709.3249 266278.6866 389631.9191 359605.9189 403262.3767 310909.1987 1.146688872 1.121768799 1.133337255 1.195555894 0.856451619 1.253201645 1.156626824 1.297042282 1 18.24613378 EIEENSR ddPTM_SK-BR-3_Trastuzumab_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 ; 110.81 0.015635 286150000 631060 556560 593520 667160 640090 551830 683710 608860 699820 FALSE TRUE 601231.0444 613274.0968 620733.4791 600095.8093 751721.4933 532719.9887 579397.4823 555544.9906 808344.5114 0.743780697 0.758679113 0.767907087 0.742376302 0.929951874 0.659025924 0.716770479 0.68726265 1 19.62461077 -2.178655133 2.482051485 1.693938142 0.750043373 0.544571448 0.07164065 3155702.652 1140258.19 12275186.87 0.016313264 0.006627426 2.178655133 -0.943894768 EIEGEEIEIVLAKPPDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIEGEEIEIVLAKPPDKK 18 2 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 156.11 7.85E-09 401290000 768850 812860 700370 899940 419093 890950 821940 904190 413460 FALSE TRUE 732507.9842 895691.3581 732482.6573 809476.3214 492182.6865 860096.1781 696537.957 825014.3302 477577.2651 1.533799948 1.875489944 1.533746915 1.694964104 1.030582321 1.800957124 1.458482235 1.727499172 1 18.86537463 -2.759707266 0.284441374 8.73E-17 1.640981995 0.359569017 0.237548862 58.25059957 1.742149833 36.24007376 0.249411034 0.001738973 2.759707266 1.640981995 EIEHVMYHDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIEHVMYHDWR 11 0 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 ;;; 170.4 9.11E-06 493926000 437055 367279 317235 327415 520099 295669 466209 345944 84365.4 FALSE TRUE 416396.2763 404705.1477 331780.5385 294502.6222 610804.1009 285429.9084 395080.2545 315651.3094 97448.35535 4.272994396 4.153021836 3.404680739 3.022140508 6.267977522 2.929037718 4.054252666 3.239165076 1 16.57235022 0.602846626 1.126111787 0.997223203 4.069910517 0.511885414 0.925558162 1.028299568 1.976248686 0.798885646 0.247499006 4.007251739 -0.602846626 3.072687314 EIEIDIEPTDKVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EIEIDIEPTDKVER 14 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 ;;;;;; 222.75 3.44E-12 4035180000 6473440 5674210 5844360 6766270 4538440 6579070 6950860 7033070 5204680 FALSE TRUE 6167453.32 6252418.45 6112329.687 6086111.685 5329942.499 6351235.156 5890378.646 6417217.106 6011795.193 1.025892121 1.040025192 1.016722874 1.01236178 0.886580851 1.05646233 0.979803612 1.067437745 1 22.51936443 3.313793728 3.162704745 0.996527788 1.03195312 0.068743631 0.04868242 0.576764572 11.59579023 0.013186049 0.018095066 2059.651429 -3.313793728 0.035425332 EIENMILNDPDFQHEDLNFLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIENMILNDPDFQHEDLNFLTR 22 0 Q15067-2;Q15067;I3L0T4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 71.651 0.016153 65107000 26338 23607 29384 26135 29259 24248 31835 26387 29169 FALSE TRUE 25093.05494 26012.58014 30731.28546 23507.86015 34361.76034 23408.28568 26977.98606 24076.41439 33692.37955 0.744769449 0.772061234 0.912113833 0.697720389 1.019867424 0.694764988 0.800714774 0.71459525 1 15.0401347 -2.336647335 2.263336247 2.196478084 0.793032797 0.286526901 0.101847317 3977156.707 404090.8092 24572056.31 0.023485976 0.004606305 2.336647335 -1.403445286 EIENYPHFFLDFENAQPTEGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIENYPHFFLDFENAQPTEGER 22 0 Q9H0Q0;C9JPE5;C9IYV6 Q9H0Q0 FAM49A Protein FAM49A 0 ; 174.71 2.32E-12 38386000 57324 54196 52384 60959 52154.2 57043 56351 57461 50655 FALSE TRUE 54614.40813 59718.63402 54785.85821 54831.28551 61249.87597 55067.58661 47753.61999 52429.41022 58510.31869 0.933414983 1.02065132 0.936345237 0.937121635 1.04682178 0.941160258 0.816157236 0.896071178 1 15.83640346 1.990689062 24.98059231 0.882401552 0.975554072 0.209481083 0.058030163 444.0048424 1191233.89 0.020583352 0.014386263 97.87889603 -1.990689062 0.093152521 EIEQEAAVELSQLRDPQHDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIEQEAAVELSQLRDPQHDLDR 22 1 P47985 P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial;Cytochrome b-c1 complex subunit 11" 0 ;;; 222.57 5.06E-26 248088000 109275 76068 90747 126389 144081 79245 133854 92956 115908 FALSE TRUE 104109.7873 83819.41568 94907.83971 113684.1376 169208.6808 76500.72578 113432.1139 84816.27985 133882.4207 0.777621041 0.626067375 0.708889481 0.849134166 1.263860333 0.57140232 0.84725174 0.633513193 1 17.03060702 3.247707704 6.803650822 0.851819027 0.697255469 0.128354363 0.19137838 0.29798711 64.09694476 0.051596376 0.066871473 1768.918013 -3.247707704 -0.154563558 EIES(ph)SPQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.696)S(0.304)PQYR;EIES(0.75)S(0.25)PQYR 150.04 9.04E-05 313480000 546950 530680 569040 629120 659950 580170 707770 618340 768360 TRUE FALSE 521096.7575 584756.8953 595131.0469 565879.6624 775045.0711 560078.5674 599786.6874 564194.8716 887513.3446 0.587142448 0.658871102 0.670560111 0.6376013 0.87327709 0.631064953 0.675805824 0.635702973 1 19.75940929 -5 0.32123564 4.143106837 0.654595521 0.641582888 0.076808585 204.9510528 1.80964525 438.4273565 0.064909026 1.00E-05 5 -3.488511316 EIESEIDS(ph)EEELINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 EIESEIDS(1)EEELINK 197.14 8.99E-09 27009000 48247 41490 43519 57044 38240 56511 51364 51782 42478 TRUE FALSE 45966.45993 45717.87817 45514.3892 51309.82874 44909.04389 54554.0099 43527.47844 47247.69357 49065.27129 0.936843081 0.931776733 0.927629421 1.045746358 0.91529187 1.111866061 0.887134164 0.962955922 1 15.58241462 EIESS(ph)PQYR ddPTM_SK-BR-3_Trastuzumab_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(0.207)S(0.793)PQYR 112.94 0.0020293 0 447340 452660 451770 535590 539660 444010 552160 516410 688260 TRUE FALSE 426195.1247 498786.5686 472484.1014 481751.4756 633776.5331 428633.8224 467917.8509 471190.4027 794991.8457 0.536099995 0.627410924 0.59432572 0.605982915 0.797211363 0.539167571 0.58858195 0.59269841 1 19.60058054 -1.08147717 4.3727233 1.000033224 0.60768321 0.742199493 0.07218754 23018896678 4835228403 9140918.026 0.016052248 0.082893949 1.08147717 -0.392350014 EIEVGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIEVGGGR 8 0 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ; 125.5 0.0029293 109020000 194200 192002 179128 211896 208327 173914 213933 199972 222449 FALSE TRUE 185020.5509 211567.2221 187341.196 190595.8115 244659.1628 167891.3146 181293.5917 182461.3916 256945.2548 0.720077711 0.823394159 0.729109382 0.741775954 0.952184009 0.653412785 0.705572834 0.710117771 1 17.97110148 -2.195592013 2.248098398 1.67401121 0.755122006 0.470115099 0.081923182 4007362.537 929475.6955 13704784.54 0.020143551 0.00637394 2.195592013 -0.918889204 EIEVGGGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EIEVGGGRK 9 1 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 102.07 0.005844 8000590000 3777410 3041710 3440770 3736260 2938540 3706640 4474960 4002210 3607040 FALSE TRUE 3598859.315 3351663.707 3598532.708 3360684.046 3451020.446 3578278.127 3792222.664 3651755.275 4166401.341 0.86378124 0.804450516 0.863702849 0.806615535 0.828297651 0.85884144 0.910191399 0.876477079 1 21.99037039 0.906135919 0.630681839 0.999666588 0.830091975 0.794571193 0.025629907 0.374561691 0.33925797 0.02520895 0.01026791 8.056305354 -0.906135919 -0.169574613 EIEYEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIEYEVVR 8 0 F8VPD4;P27708;P31327;P31327-3;P31327-2;A0A669KBF2 F8VPD4;P31327 CAD;CPS1 "CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase;Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 148.38 0.0012147 165315000 350900 280520 264410 277890 351960 242760 316860 291690 344230 FALSE TRUE 334313.6524 309105.3069 276533.46 249955.9692 413341.7126 234353.1603 268517.1875 266148.0773 397611.4303 0.840804934 0.777405485 0.695486696 0.628643822 1.039561947 0.589402473 0.675325624 0.669367269 1 18.60099971 4.155716594 2.681846199 0.736088957 0.829925889 0.01325519 0.150957834 0.869588361 12.28848232 0.036075877 0.103177388 14312.53607 -4.155716594 0.093836932 EIFDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EIFDSR 6 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;;; 172.39 0.01195 66436300000 111514300 84545600 85388900 94574000 107590500 94791700 116754600 102314100 113916200 FALSE TRUE 106243240 93160892.76 89304065.53 85067241.84 126354249.1 91509039.66 98941541.42 93354935 131581742.5 0.807431472 0.708007745 0.67869648 0.646497304 0.960271894 0.695453928 0.751939741 0.709482435 1 26.97138408 -1.563501456 2.920530916 1.013511708 0.745020141 0.454682877 0.087858223 20986848.57 23122161.85 2225189.223 0.020646319 0.027321123 1.563501456 -0.268491566 EIFITFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIFITFR 7 0 Q96EY1-2;Q96EY1;Q96EY1-3 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 113.89 0.014024 33067000 145620 135240 146980 135260 119450 128450 143410 134320 110930 FALSE TRUE 138736.8312 149021.1098 153719.1784 121663.4078 140282.0422 124001.7443 121530.1706 122558.2287 128132.4578 1.082761023 1.163023892 1.19968961 0.949512792 1.094820505 0.967762161 0.948472952 0.956496354 1 16.96727645 3.233659394 24.99990951 0.984947281 1.142215527 0.693233204 0.050838087 67.89159508 346298.1418 0.014680287 0.018076541 1712.613623 -3.233659394 0.157268246 EIGDYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIGDYIR 7 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 148.33 0.0048655 268090000 805440 706450 733840 920120 857470 708630 883290 771770 914140 FALSE TRUE 767368.4474 778438.0582 767487.2899 827627.7895 1007012.497 684089.9654 748527.8878 704189.7274 1055900.162 0.726743375 0.737226952 0.726855926 0.783812541 0.953700485 0.647873719 0.708900249 0.666909384 1 20.010042 -2.365599361 2.306274285 2.794784043 0.742490713 0.481815279 0.083420242 2708394.315 538078.2798 25153969.76 0.019635852 0.00430924 2.365599361 -2.052293331 EIGFSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIGFSDK 7 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 91.9 0.059326 0 231890 201280 195020 197170 192130 203690 225150 216160 195920 FALSE TRUE 220929.0193 221790.6608 203961.8599 177350.097 225637.4112 196636.1642 190799.2323 197231.8845 226302.273 0.976256298 0.980063779 0.901280651 0.783686768 0.997062063 0.868909365 0.84311673 0.871541774 1 17.78789155 3.691499009 4.847819174 0.883416756 0.978547959 0.205557622 0.065455775 0.232147788 12.61859535 0.016030507 0.025911076 4914.722589 -3.691499009 0.095131203 EIGNLLHPSVPISNDEDVDNKVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIGNLLHPSVPISNDEDVDNKVER 24 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 170.65 4.61E-12 596631000 806530 740030 812280 892690 664060 837990 1004020 1002900 718420 FALSE TRUE 768406.9253 815439.8983 849523.8415 802955.1052 779871.8538 808970.1962 850838.3089 915080.7593 829828.9044 0.925982358 0.982660274 1.023733732 0.967615253 0.939798372 0.974863845 1.025317755 1.102734256 1 19.66245438 1.628805479 3.510568855 1.054465807 0.968089801 0.495780533 0.03548683 0.146406998 4.258865046 0.02073166 0.009020535 42.540783 -1.628805479 -0.086376006 EIGTHKPLPGITVGDIGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIGTHKPLPGITVGDIGPK 19 1 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 106.67 0.00018599 162860000 564530 637470 550100 675750 382060 645450 690540 737020 434930 FALSE TRUE 537845.7857 702428.9177 575322.6291 607822.3262 448691.143 623097.9047 585185.4404 672482.6216 502376.7231 1.07060252 1.398211512 1.145201604 1.209893489 0.893136808 1.24030011 1.164833905 1.338602269 1 18.93841009 -1.966351724 2.77302651 0.849019782 1.18719314 0.145462935 0.138690246 18133912.51 7937899.54 17513999.27 0.032051873 0.010805585 1.966351724 0.338173358 EIHQDWANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EIHQDWANR 9 0 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;;;; 172.59 5.61E-05 1033570000 723159 645859 583875 713828 753259 630737 767111 682924 729918 FALSE TRUE 688976.7072 711672.7664 610646.2463 642072.6533 884627.1311 608894.4195 650074.128 623123.5542 843109.9555 0.817184879 0.844104333 0.724278301 0.761552688 1.049242896 0.722200486 0.771043117 0.739077448 1 19.68536127 -2.088470509 2.491949856 1.323160104 0.805519934 0.294433204 0.095512895 7877494.305 2158591.077 14490354.32 0.022155498 0.008156982 2.088470509 -0.51764017 EIHQFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIHQFNR 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 91.041 0.016695 168060000 265140 176080 220100 225330 239850 193830 229100 204850 225980 FALSE TRUE 252607.3577 194022.7522 230191.8027 202679.4003 281679.7641 187117.6185 194146.5873 186912.248 261023.8243 0.967755945 0.743314342 0.881880431 0.776478549 1.079134308 0.716860306 0.743788763 0.716073518 1 17.99382197 EIIDAS(ph)DKEGMS(ph)PAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR 71.428 0.028466 629960000 523320 521750 411740 535220 246331 587470 532680 702490 277321 TRUE FALSE 498583.7007 574916.9182 430618.6863 481418.6687 289291.0484 567125.7666 451409.8827 640976.2515 320326.5243 1.556485844 1.794783992 1.344311674 1.502899798 0.903113 1.770461462 1.409217934 2.001008979 1 18.28918374 -1.454226813 3.254030277 0.991041617 1.535367589 0.24308773 0.296844518 82893070.68 121397268 6934439.144 0.066326068 0.035137688 1.454226813 0.544325972 EIIDASDKEGMS(ph)PAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EIIDAS(0.001)DKEGMS(0.999)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDAS(0.001)DKEGMS(0.999)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR 140.32 8.93E-07 3589840000 6036436 5322169 4593572 6277950 2912225 6017540 6290550 6652130 3070112 TRUE FALSE 5751105.633 5864504.072 4804191.82 5646878.539 3420116.118 5809151.081 5330811.064 6069634.232 3546209.289 1.621761482 1.65373885 1.35474007 1.592370353 0.964442829 1.638129791 1.50324209 1.711583761 1 21.75784625 3.748178296 23.89776238 1.42560153 1.6377502 0.131935127 0.249472921 722.4344315 1795076.287 0.058746168 0.104076041 5599.874525 -3.748178296 0.212148669 EIIDLVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 180.44 0.00011317 4037189900 2802486 3193120 2299440 3041342 2743841 2543809 2932810 2917981 2709945 FALSE TRUE 2670018.041 3518502.558 2404871.598 2735620.524 3222366.002 2455716.256 2485355.97 2662467.114 3130189.43 0.852989284 1.124054194 0.768283087 0.873947275 1.029447602 0.784526404 0.793995388 0.850576993 1 21.57781854 2.224255946 24.99321892 0.833182004 0.939388006 0.071555289 0.113171589 417.9895519 730309.3551 0.040668381 0.030173367 167.5930273 -2.224255946 0.106206002 EIIDPVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIIDPVLDR 9 0 P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8 P68366-2 TUBA4A Tubulin alpha-4A chain 0 84.213 0.036585 0 125180 104230 105880 119450 128620 107580 134720 117370 127470 FALSE TRUE 119262.9895 114851.1555 110734.7027 107442.6591 151051.2873 103854.4776 114165.9897 107092.4606 147237.3966 0.810004742 0.780040657 0.752082727 0.72972398 1.025903003 0.705353939 0.77538718 0.727345519 1 17.16778462 -1.129661325 4.779456114 1.000014649 0.788385146 0.354772437 0.089752581 1.28E-05 2.32E-06 0.079196126 0.018665414 0.074188856 1.129661325 -0.211629503 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 230.36 1.17E-35 77794000 153810 170670 143930 170500 110160 145940 159320 151160 117710 FALSE TRUE 146539.7061 188061.467 150529.3329 153361.0161 129371.8691 140886.0612 135012.8079 137923.6291 135963.8656 1.0777842 1.383172405 1.107127487 1.127954221 0.951516556 1.036202233 0.99300507 1.014413855 1 17.05286376 3.159330989 1.970513816 1.002857447 1.226194794 0.530745556 0.082821057 0.214589842 1.710867414 0.025312881 0.033134943 1443.214849 -3.159330989 0.223337348 EIIKQEES(ph)VDPDYWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 1 EIIKQEES(1)VDPDYWEK;EIIKQEES(1)VDPDYWEK;EIIKQEES(1)VDPDYWEK;EIIKQEES(1)VDPDYWEK 174.7 2.29E-09 423008000 1233490 1036048 1128340 1368250 720273 1492470 1431920 1619450 897168 TRUE FALSE 1175185.372 1141622.469 1180075.505 1230710.91 845888.3832 1440785.39 1213454.305 1477642.373 1036296.231 1.134024555 1.101637191 1.138743411 1.187605313 0.816261179 1.390321943 1.17095312 1.425888012 1 19.98300503 2.192653432 24.9999999 1.256002106 1.092457609 0.232583059 0.152376044 178.4399522 97173.16604 0.050366551 0.037198296 155.8308474 -2.192653432 -0.163544498 EIIKQEESVDPDYWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 220.8 1.02E-14 379304000 1400090 1313170 1249290 1482710 835300 1467850 1434660 1560260 873550 FALSE TRUE 1333910.52 1446983.516 1306571.182 1333665.174 980976.0555 1417017.986 1215776.268 1423635.363 1009015.673 1.321991875 1.43405455 1.294896817 1.32174872 0.97221092 1.404356766 1.204913165 1.410915015 1 19.94451715 -5 0.145409378 0.014846956 1.394526159 0.298605547 0.135666411 160.7601571 1.408519545 46.46364178 0.69372282 1.00E-05 5 1.379679203 EIILDDDECPLQIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 147.72 8.51E-06 24471000 30395 32275 26385 36924 36805 31649 37899 38186 34626 FALSE TRUE 28958.28859 35563.85919 27594.77835 33212.32937 43223.78035 30552.98719 32116.81149 34842.2314 39995.62323 0.724036438 0.889193775 0.689944952 0.830399096 1.080712759 0.763908266 0.803008152 0.871151106 1 15.28755451 -5 0.104008883 1.509133566 0.724188154 0.24502233 0.104106285 286.5094049 2.009438726 32.00379206 1.51088112 1.00E-05 5 -0.784945413 EIKDILIQYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIKDILIQYDR 11 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;; 156.81 2.82E-05 1307147000 1903450 1607020 1726740 1794390 1743630 1987040 2451890 2119190 1957460 FALSE TRUE 1813477.691 1770777.165 1805912.737 1614014.508 2047718.52 1918228.307 2077809.148 1933622.489 2261012.899 0.802064283 0.78317871 0.798718458 0.713845776 0.905664236 0.848393349 0.918972709 0.855201883 1 21.10853779 1.54715215 0.488317023 0.992273276 0.7745046 0.652699301 0.047411974 0.495627359 0.301652529 0.046697422 0.029694343 35.24943414 -1.54715215 -0.217768676 EIKDSLAEVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIKDSLAEVEEK 12 1 Q32MZ4-2;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;; 167.55 4.46E-05 239939000 638389 521702 584881 649067 453193 664182 739550 760723 472627 FALSE TRUE 608213.6171 574864.0269 611698.3724 583821.552 532229.7157 641181.2108 626718.0647 694110.0613 545919.5813 1.114108447 1.053019614 1.120491723 1.069427755 0.974923293 1.17449755 1.148004369 1.271451117 1 19.05832892 2.181645371 24.9999187 1.159937299 1.071503895 0.215103231 0.076200385 110.2652993 48432.92125 0.025579154 0.018891466 151.9306414 -2.181645371 -0.088433404 EIKEEEEGS(ph)EDDSNVKPDFMVTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIKEEEEGSEDDSNVKPDFMVTLK 24 2 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 EIKEEEEGS(0.862)EDDS(0.138)NVKPDFMVTLK;EIKEEEEGS(0.999)EDDS(0.001)NVKPDFMVTLK;EIKEEEEGS(1)EDDSNVKPDFMVTLK 146.89 9.77E-08 344909000 403694 344700 315626 373180 172886 405959 373717 444011 187043 TRUE FALSE 384612.1847 379825.3219 330097.7643 335667.2374 203037.2637 391900.538 316699.6079 405131.043 216048.6732 1.780210816 1.758054407 1.527886098 1.553664887 0.939775564 1.813945591 1.465871571 1.875184129 1 17.72099685 3.671987707 2.545060963 1.469033422 1.777935014 0.165433567 0.296491044 0.486330669 6.170780018 0.076309842 0.136823087 4698.80808 -3.671987707 0.308901592 EILDAFDK ddPTM_SK-BR-3_Trastuzumab_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 ; 126.41 0.0028389 134713000 393400 282760 218790 323000 314460 270900 416790 398600 356800 FALSE TRUE 374804.7616 311573.5655 228821.7379 290531.4263 369301.7244 261518.6651 353201.0306 363696.4709 412130.7217 0.909431746 0.756006648 0.555216406 0.704949694 0.896079096 0.634552707 0.857012137 0.882478427 1 18.65274249 1.163179999 1.66395635 0.99304098 0.754479166 0.377257591 0.108303524 0.392014657 2.049323488 0.101328177 0.029881155 14.56062439 -1.163179999 -0.238561814 EILDESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EILDESLR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 141.39 0.0014757 231389000 851930 717680 752810 793360 727550 800260 1010370 889910 874190 FALSE TRUE 811660.9573 790812.4079 787327.0831 713609.9455 854434.4896 772546.7955 856219.4998 811984.7627 1009754.92 0.803819759 0.783172621 0.779720967 0.706715987 0.84618007 0.765083467 0.847947836 0.804140437 1 19.94557375 -0.045355706 0.521099187 1.020609107 0.779139535 0.753812654 0.038075849 2.058829384 0.656899363 0.122115241 0.016368831 0.900833015 0.045355706 -0.241469572 EILDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILDKK 6 1 P08238;Q58FF7;Q58FF6 P08238 HSP90AB1;HSP90AB3P;HSP90AB4P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4 0 86.086 0.086548 361740000 746060 673000 706800 941430 540060 895540 924710 973850 639180 FALSE TRUE 710795.2223 741579.4651 739207.4791 846795.6678 634246.293 864527.2252 783628.506 888574.5313 738300.7699 0.962744794 1.004440867 1.001228103 1.146952167 0.859062213 1.170968879 1.061394675 1.203540031 1 19.49384914 2.205885258 24.99999531 1.110477257 1.00046689 0.291728722 0.088082593 235.4587544 180148.6392 0.029308764 0.021647638 160.651675 -2.205885258 -0.110010367 EILFYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EILFYDR 7 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;;;;; 165.11 0.0027282 649514000 1003644 868460 726175 850701 1135125 739085 1129175 926089 1170469 FALSE TRUE 956203.7372 956957.0614 759470.842 765186.9193 1333090.441 713490.3011 956898.615 844995.7377 1351979.355 0.707262085 0.707819286 0.561747367 0.565975299 0.986028696 0.527737571 0.707776056 0.625006391 1 20.36664169 -1.200190966 5.298596907 1.000018664 0.677245504 0.388365609 0.128632703 2.54E-05 3.83E-06 0.111448846 0.026267227 0.063067996 1.200190966 -0.32277316 EILFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILFYR 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 99.511 0.090068 32409000 105710 101750 80143 88001 163470 63073 107120 87767 134090 FALSE TRUE 100713.2978 112118.4407 83817.63582 79154.97229 191979.1162 60888.76619 90776.87661 80081.6562 154883.9924 0.650249882 0.723886562 0.541163968 0.511059736 1.239502632 0.393124979 0.586095924 0.51704282 1 17.24082852 EILGTAQSVGCNVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EILGTAQSVGCNVDGR 16 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ; 300.07 1.68E-45 382470000 86593 68237 82927 86578 86806 77053 97018 88547 108695 FALSE TRUE 82499.9205 75190.42788 86729.28498 77875.01495 101944.9389 74384.63529 82216.12224 80793.35526 125550.8655 0.657103559 0.598884186 0.690790021 0.620266652 0.811981172 0.592466129 0.654843134 0.643510938 1 16.93791245 -1.908745079 2.557912818 1.201728432 0.654701163 0.750652727 0.061774581 4729123.49 2542063.237 5725305.189 0.013682006 0.012338289 1.908745079 -0.547027269 EILHNTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EILHNTEK 8 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 125.82 0.0012457 706340000 1071310 1017670 955290 1156420 855620 987350 1186450 1209020 948110 FALSE TRUE 1020671.299 1121371.73 999090.9914 1040174.465 1004839.857 953157.8219 1005435.262 1103151.799 1095138.057 0.932002402 1.023954672 0.912296843 0.949811267 0.917546287 0.870354031 0.918089967 1.007317564 1 20.06268132 1.230750316 24.9882079 1.003658835 0.936573613 0.366760784 0.038782063 250.1419591 800269.1982 0.038586304 0.010348687 17.01180188 -1.230750316 -0.067085223 EILKEQENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EILKEQENR 9 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 123.51 0.00050672 2550890000 4554100 3383600 4322400 4543100 3976000 4868600 5794300 4969000 4967100 FALSE TRUE 4338836.718 3728392.687 4520586.315 4086418.957 4669413.141 4699999.161 4910273.115 4533888.018 5737372.5 0.75624107 0.649843232 0.787919264 0.712245711 0.813859156 0.819190171 0.855840041 0.790237695 1 22.45195876 0.798860416 0.230266678 1.070381626 0.661618416 0.746683104 0.046268469 1.629434748 0.267126472 0.229825632 0.121219776 6.293038892 -0.798860416 -0.40876321 EILKEQENRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EILKEQENRK 10 2 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 124.1 0.00024996 830250000 2759400 1791730 3038100 2614600 2565500 3484400 4275000 3908800 3242500 FALSE TRUE 2628968.631 1974309.324 3177399.89 2351775.441 3012922.388 3363734.354 3622770.234 3566524.75 3745330.34 0.701932378 0.527138902 0.848363055 0.627922033 0.804447703 0.898114198 0.967276557 0.95225906 1 21.83666154 2.392845601 0.915971548 0.996387428 0.638890421 0.725061068 0.081047963 0.264376321 0.436987977 0.053274739 0.034873744 247.0845563 -2.392845601 -0.357497008 EILLSADHIIIATGGRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILLSADHIIIATGGRPR 18 1 A0A096LPK7;A0A182DWF2;D3YTF8;A0A182DWF3;Q9NNW7-3;Q9NNW7-2;Q9NNW7;A0A096LNY7;A0A096LPD9;E7EWK1 A0A096LPK7 TXNRD2 "Thioredoxin reductase 2, mitochondrial" 0 161.2 2.32E-11 95324000 78172 70895 77192 78571 89161 67943 86105 73594 88447 FALSE TRUE 74476.96448 78119.2811 80731.32955 70672.8938 104710.6502 65590.11687 72968.10082 67149.71921 102162.909 0.729001995 0.76465404 0.790221523 0.691766655 1.024938025 0.642014969 0.714232802 0.657280806 1 16.64051199 -2.179827186 2.412689293 1.675257941 0.751384146 0.347674097 0.106858497 12392390.88 2519078.272 45808922.05 0.025439913 0.006609564 2.179827186 -0.923873795 EILNLIHLEELSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILNLIHLEELSLR 14 0 Q96CX6 Q96CX6 LRRC58 Leucine-rich repeat-containing protein 58 0 117.37 0.00030709 20742000 74889 84238 74626 85843 83859 75138 95593 86140 92928 FALSE TRUE 71349.14539 92821.94797 78047.67592 77213.89855 98483.98305 72535.95222 81008.53216 78597.12494 107338.7996 0.664709738 0.864756717 0.727115229 0.719347513 0.91750591 0.675766381 0.754699442 0.732234059 1 16.71181213 -1.47516386 5.890208952 1.000194534 0.759901706 0.485764869 0.078518278 0.000181491 1.62E-05 0.068788231 0.016200529 0.033483908 1.47516386 -0.240292827 EILS(ph)PLFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EILSPLFPR 9 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 EILS(1)PLFPR;EILS(1)PLFPR 70.1 0.055979 14558000 14056.5 13401.5 11654.4 13117.7 14293 13305.7 17885.1 14136.3 19443.8 TRUE FALSE 13392.0771 14767.12809 12188.76577 11799.08387 16785.69467 12844.92027 15156.39951 12898.45063 22459.0452 0.5962888 0.657513619 0.542710772 0.525359995 0.747391286 0.571926373 0.67484612 0.574309839 1 14.45500898 -4.999999934 0.414974261 7.848933844 0.609807952 0.767826546 0.067042595 392.0376069 2.594692147 2444.246753 0.035970495 1.00E-05 4.999999934 -7.239125891 EILSDDKHDWEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILSDDKHDWEQR 13 1 Q7Z460;C9J151;C9JP76;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 104.95 0.00089584 32827000 53702 55104 48749 65301 46681 57956 56097 59298 40236 FALSE TRUE 51163.61289 60719.16025 50984.18987 58736.81942 54822.15162 55948.96919 47538.37236 54105.55276 46475.59338 1.100870568 1.306474126 1.097009982 1.263820753 1.179590138 1.2038355 1.022867464 1.164171317 1 15.50418566 1.749826018 24.99999953 1.069726728 1.196784162 0.39023891 0.076013773 2.923837032 6500.22477 0.031350183 0.017385158 56.21160915 -1.749826018 0.127057434 EILSEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EILSEVER 8 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 151.5 0.0010986 1664540000 2688340 2289280 2395990 2615050 2854970 2384350 3076270 2687410 2891460 FALSE TRUE 2561267.496 2522560.235 2505848.511 2352180.206 3352875.864 2301779.362 2606928.512 2452086.134 3339852.849 0.766880342 0.755290831 0.750287101 0.704276599 1.003899278 0.689185861 0.780551907 0.734189871 1 21.67135311 -1.429137291 3.200103997 1.003370365 0.772137225 0.404072015 0.086602101 163304136.3 199064182.7 4973077.206 0.018745668 0.0372274 1.429137291 -0.23123314 EILSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 0 ;; 111.28 0.036031 0 653730 565700 559070 659350 690640 573170 693260 632170 713200 FALSE TRUE 622829.4785 623345.4731 584703.9125 593070.8853 811087.3973 553320.9792 587490.4544 576813.8435 823799.4135 0.756045062 0.756671421 0.709764905 0.719921471 0.98456904 0.671669547 0.713147454 0.700187247 1 19.65193357 -1.491134965 3.124884708 1.006400586 0.750629478 0.448136003 0.086660538 35203564.12 45804286.56 1966270.69 0.019502503 0.03227491 1.491134965 -0.255771109 EILWRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EILWRPK 7 1 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 73.616 0.04415 178060000 812150 702030 721280 680850 635320 819010 920850 787600 754720 FALSE TRUE 773761.279 773567.6551 754351.4014 612409.6645 746119.6069 790647.4783 780357.4199 718633.5687 871758.123 0.887587117 0.88736501 0.865321907 0.702499522 0.855879156 0.906957397 0.895153597 0.824349725 1 19.73356838 2.310929835 6.078138307 0.897802772 0.844983733 0.19168912 0.066923806 0.45266829 28.79462578 0.0235248 0.019469173 204.6114036 -2.310929835 -0.052819039 EIPS(ph)ATQS(ph)PISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 2 EIPS(0.999)AT(0.366)QS(0.636)PISK;EIPS(1)AT(0.057)QS(0.943)PISK 130.72 0.00030922 259720000 606750 655210 646110 773920 561830 707470 745820 741110 708810 TRUE FALSE 578070.13 721976.6439 675734.7826 696124.0912 659812.9741 682970.1365 632031.4611 676214.4795 818728.6347 0.706058278 0.881826546 0.825346463 0.850250085 0.805899472 0.834183767 0.771966967 0.825932367 1 19.64302583 0.950864951 21.6858788 1.000000001 0.81096507 0.61245322 0.046978176 1694.973536 748082.6597 0.043406324 0.010851581 8.930277425 -0.950864951 -0.189034931 EIPSATQS(ph)PISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 EIPSAT(0.024)QS(0.975)PIS(0.001)K;EIPSAT(0.081)QS(0.919)PISK;EIPSAT(0.001)QS(0.999)PISK;EIPSAT(0.007)QS(0.992)PIS(0.001)K;EIPSAT(0.299)QS(0.698)PIS(0.002)K 198.87 1.87E-07 2566700000 6334980 6319670 6011240 7400270 4489460 6972250 7210140 7059110 5822210 TRUE FALSE 6035538.05 6963651.558 6286861.3 6656380.8 5272420.403 6730799.234 6110100.72 6440976.906 6725088.591 0.897465954 1.03547358 0.934836949 0.989783363 0.783992706 1.000849155 0.908553194 0.957753466 1 22.68112184 0.982339459 22.69844271 1.000000007 0.940977663 0.077814601 0.068736752 979.8890009 1259420.521 0.060486992 0.015121748 9.601508232 -0.982339459 -0.059022344 EIPSHVLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIPSHVLSK 9 0 E5RHG8;Q15369-2;Q15369 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 160.36 6.54E-05 1240250000 2428940 2341870 2041180 2563100 2087850 2255120 2742430 2612310 2212430 FALSE TRUE 2314128.82 2580509.215 2134770.122 2305452.318 2451970.379 2177024.629 2324021.935 2383562.288 2555522.345 0.905540437 1.009777598 0.835355686 0.90214524 0.959479139 0.851890273 0.909411706 0.932710408 1 21.28518678 0.865670246 4.40300434 0.999990534 0.915810023 0.242260923 0.049024998 1.514875017 47.4943127 0.046556853 0.011834534 7.339563735 -0.865670246 -0.084180511 EIPYTFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EIPYTFEDR 9 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ;;;;; 212.58 7.64E-06 1049120000 1264800 1114030 1098300 1127760 1171030 872796 1061700 1128550 1058760 FALSE TRUE 1205015.411 1227550.924 1148658.141 1014395.422 1375257.261 842570.8557 899718.1655 1029728.179 1222947.093 0.985337319 1.003764537 0.939254157 0.829467953 1.124543546 0.688967544 0.73569672 0.8420055 1 20.22193056 2.227825408 24.9999906 0.7845525 0.972626961 0.329246427 0.109066721 194.7431851 453511.6293 0.037084852 0.027665773 168.9761489 -2.227825408 0.188074462 EIQGHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIQGHQPR 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 64.711 0.066151 66802000 63115 49255 54398 56156 62998 52414 56040 54187 69054 FALSE TRUE 60131.67903 54274.1405 56892.20211 50511.09219 73984.83125 50598.89004 47490.06875 49442.09902 79762.54164 0.753883688 0.680446478 0.713269674 0.633268338 0.927563612 0.634369078 0.595393123 0.619866143 1 16.28342376 EIQNGNLHES(ph)DSESVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(0.983)DS(0.017)ESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(0.999)DS(0.001)ESVPR;EIQNGNLHES(0.991)DS(0.009)ESVPR 242.71 1.31E-20 1366360000 776910 612695 751460 1088890 1107280 782450 948960 776840 863110 TRUE FALSE 740187.004 675129.3171 785915.1843 979432.7084 1300389.281 755353.5603 804178.7232 708815.7713 996956.6906 0.742446498 0.677190216 0.788314268 0.982422524 1.304358849 0.757659352 0.806633559 0.710979502 1 19.92717131 3.432838696 4.999543863 0.914906843 0.712476142 0.237564916 0.164608354 0.289986425 16.57777241 0.047654427 0.066367023 2709.185211 -3.432838696 -0.202430701 EIQSTLEGDRGS(ph)GNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EIQSTLEGDRGSGNWR 16 1 J3QRV5;Q6P1M3 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR;EIQSTLEGDRGS(1)GNWR 249.06 1.00E-20 7241330000 1975451 1888680 1857617 2107832 2071237 1907983 2256221 1988818 2154031 TRUE FALSE 1882075.346 2081138.639 1942790.577 1895948.723 2432460.077 1841909.07 1911993.048 1814666.553 2488067.126 0.756440743 0.836447947 0.780843313 0.762016709 0.977650503 0.740297177 0.768465219 0.729347908 1 21.24659398 -2.121133145 2.604777568 1.423431605 0.795246478 0.451337182 0.071387539 4308492.616 2224839.361 10872957.36 0.01600921 0.007566009 2.121133145 -0.628185127 EIQTAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 195.6 0.0010794 11736580000 8114770 7086390 6808990 7449910 8686490 7037350 8881600 7575940 9063060 FALSE TRUE 7731200.904 7808501.198 7121188.927 6701030.893 10201411.11 6793644.805 7526548.798 6912550.531 10468513.06 0.738519488 0.745903564 0.680248368 0.640112961 0.974485206 0.648959864 0.718970188 0.66031828 1 23.3195532 -1.291635617 3.306513674 1.001234846 0.727861534 0.448391531 0.095507876 15932528.74 23788864.07 197978.2661 0.02158092 0.05109335 1.291635617 -0.273373312 EIQVQHPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EIQVQHPAAK 10 0 P49368;B4DUR8;Q5SZX6;E9PRC8;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 99.522 0.0046376 2014150000 3449720 2963660 2952980 3497690 2666150 3282380 3591640 3500290 2977350 FALSE TRUE 3286658.572 3265660.323 3088377.054 3146095.556 3131125.716 3168710.358 3043669.353 3193786.051 3439062.232 0.95568453 0.949578723 0.898028836 0.914812046 0.910459161 0.921387909 0.885028868 0.928679342 1 21.71358379 3.82683144 6.767775117 0.915239888 0.953157805 0.105823586 0.030998326 0.330306353 21.50126309 0.006968464 0.012649139 6711.683063 -3.82683144 0.037917917 EIRPALELLEPIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIRPALELLEPIEQK 15 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 224.55 1.02E-12 476360000 925670 1079900 729922 1113760 547173 911560 810449 977350 568420 FALSE TRUE 881915.4136 1189943.038 763389.6457 1001802.729 642599.798 879992.4486 686800.1201 891768.0527 656567.6705 1.343220894 1.812369221 1.162697586 1.525817937 0.978725921 1.34029208 1.046046205 1.358227176 1 19.32458419 3.210249922 1.403685872 1.161257286 1.554162697 0.310872634 0.2134465 0.391933162 1.61575212 0.067897743 0.097778914 1622.743664 -3.210249922 0.392905411 EIRPVCR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 178.6 0.00065049 2084350000 998793 904968 897912 1088580 993720 912609 1064880 958058 1133940 FALSE TRUE 951582.0343 997185.2681 939082.1534 979153.8702 1167024.453 881005.1215 902412.9981 874165.3625 1309785.624 0.726517391 0.761334718 0.716973935 0.747568039 0.891004171 0.672633067 0.688977632 0.667411023 1 20.32089927 -1.268378397 3.574761332 1.00064274 0.734478852 0.634876813 0.063382352 17833782.89 29822568.53 126364.9126 0.01507522 0.053904076 1.268378397 -0.266163887 EIS(ph)DDEAEEEK ddPTM_SK-BR-3_Trastuzumab_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 271.32 5.14E-27 453390000 572590 818630 416450 689370 303530 680510 460650 583710 193233 TRUE FALSE 545524.8055 902049.3277 435544.6444 620073.2179 356465.5359 656943.7681 390369.3821 532597.258 223198.5867 2.444123027 4.04146523 1.95137725 2.778123405 1.597077926 2.943315088 1.74897784 2.386203541 1 17.76796837 1.251593883 0.144076551 0.036495772 4.025438753 0.377399651 0.660616401 4.983141765 0.657840971 8.56861358 7.154874735 17.84817778 -1.251593883 3.988942981 EIS(ph)DDEAEEEKGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 193.8 1.32E-07 920480000 1061460 1448360 792890 1289750 464740 1367200 919860 1238190 319429 TRUE FALSE 1011286.889 1595949.531 829244.7908 1160101.88 545790.5089 1319853.521 779518.4626 1129767.52 368964.4179 2.740879175 4.325483578 2.247492578 3.144210724 1.479249712 3.577183753 2.112719885 3.061995858 1 18.49312217 -0.281134522 0.182942082 2.95E-13 3.688400198 0.338547075 0.796410088 13.89411764 0.793044092 12.42853978 3.14303193 0.523438277 0.281134522 3.688400198 EIS(ph)SS(ph)PTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 EIS(0.999)S(0.001)S(0.998)PT(0.001)SK;EIS(0.942)S(0.059)S(0.999)PTSK;EIS(0.973)S(0.027)S(1)PTSK;EIS(0.997)S(0.003)S(0.999)PT(0.001)SK;EIS(0.995)S(0.008)S(0.927)PT(0.062)S(0.008)K;EIS(0.997)S(0.005)S(0.987)PT(0.01)SK;EIS(0.939)S(0.062)S(0.998)PT(0.001)SK;EIS(0.979)S(0.022)S(0.999)PTSK 215.71 9.20E-07 6211550000 13420310 10659780 11237020 12833710 7499120 12597560 13961570 12647780 8763830 TRUE FALSE 12785958.54 11746023.7 11752248.48 11543641.09 8806964.154 12161303.34 11831476.07 11540273.33 10122880 1.263075187 1.160344063 1.160958985 1.14035147 0.870005785 1.201367925 1.168785571 1.140018783 1 23.27111646 4.156716612 1.101647678 1.102034221 1.270172366 0.247005238 0.0961165 1.158427004 2.116887389 0.030257807 0.180661177 14345.53046 -4.156716612 0.168138145 EIS(ph)TPTHWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.429)T(0.429)PT(0.143)HWSK;EIS(0.5)T(0.5)PTHWSK 80.17 0.015981 227171000 1300470 1216630 1183250 1492140 1110780 1293410 1543030 1472810 1014600 TRUE FALSE 1238999.36 1340605.98 1237503.183 1342147.252 1304499.68 1248618.887 1307612.434 1343842.949 1171938.986 1.057221728 1.14392131 1.05594506 1.145236457 1.113112283 1.065429943 1.115768354 1.146683372 1 20.16046603 -1.304300531 5.393198557 0.999981426 1.10494507 0.466186686 0.035447049 7.07E-06 9.12E-07 0.030645074 0.007221835 0.04962488 1.304300531 0.104963644 EISEVFPDQFIHLGGDEVEFK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 269.85 6.38E-38 401195000 848214 700860 721095 831831 596880 835821 892527 890603 565204 FALSE TRUE 808120.6052 772278.4308 754157.919 748213.7675 700975.683 806876.3092 756355.6138 812617.0799 652852.9497 1.237829446 1.182928608 1.155172722 1.146067836 1.073711444 1.23592351 1.158539016 1.24471687 1 19.31639855 -1.661733742 2.739406994 0.978783827 1.179286053 0.541724065 0.051844781 29698237.81 27907431.76 4437490.718 0.012315597 0.021790453 1.661733742 0.200502226 EISLWFKPEELVDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;; 190.19 2.07E-07 5761197000 6364430 6255020 5179054 6209450 2899965 5404706 5146510 5551530 2857355 FALSE TRUE 6063596.007 6892413.649 5416518.749 5585264.289 3405717.978 5217539.676 4361315.377 5065408.603 3300459.02 1.837197787 2.088319718 1.64114104 1.69226894 1.031892218 1.580852737 1.321426914 1.534758824 1 21.65423525 3.234022514 1.811409332 1.341975302 1.951470713 0.59149121 0.215137308 0.205754024 1.392540071 0.06203244 0.08669857 1714.046161 -3.234022514 0.609495411 EISS(ph)SPTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EIS(0.317)S(0.547)S(0.12)PT(0.011)S(0.004)K 65.842 0.068619 983000000 288900 198590 245750 281200 226920 285590 316830 277640 258540 TRUE FALSE 275244.2695 218826.5468 257017.8806 252933.2418 266494.7762 275699.9467 268491.7645 253328.3697 298633.0628 0.921680496 0.732760615 0.860647774 0.846969989 0.892382021 0.923206373 0.899069119 0.848293111 1 18.18801437 2.811582566 1.899530219 0.909229667 0.827756009 0.271156939 0.058782665 0.435858849 3.113865749 0.020258417 0.020962037 648.0112801 -2.811582566 -0.081473658 EISSS(ph)PTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EISS(0.075)S(0.922)PT(0.002)SK;EISSS(0.998)PT(0.001)SK;EISS(0.003)S(0.997)PTSK;EISS(0.001)S(0.999)PTSK;EISS(0.004)S(0.995)PT(0.001)SK;EISS(0.008)S(0.975)PT(0.014)S(0.003)K;EISS(0.243)S(0.756)PT(0.001)SK;EISS(0.092)S(0.889)PT(0.015)S(0.004)K;EISS(0.045)S(0.955)PTSK 218.55 5.51E-07 3639889000 9815400 8541010 8702080 10130670 6941160 9841480 10829510 10056850 7518440 TRUE FALSE 9351445.494 9411348.629 9101078.976 9112315.805 8151696.106 9500667.08 9177269.352 9176218.899 8684361.276 1.076814425 1.083712242 1.047984841 1.049278757 0.938663863 1.093997218 1.056758126 1.056637167 1 23.04998831 3.599605234 2.896605374 1.037105763 1.080526878 0.177012708 0.04117983 0.467322531 7.516225365 0.011258825 0.018639212 3977.454627 -3.599605234 0.043421115 EIST(ph)PTHWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.194)T(0.8)PT(0.006)HWSK;EIS(0.228)T(0.737)PT(0.035)HWSK 102.97 0.010583 223277000 1190250 1159800 1066570 1318980 1007060 1221800 1376530 1339020 946920 TRUE FALSE 1133989.241 1277984.939 1115473.289 1186393.625 1182690.945 1179488.76 1166515.067 1221768.31 1093763.517 1.03677735 1.168428932 1.019848689 1.084689337 1.081304072 1.078376396 1.06651488 1.117031507 1 20.06086942 -1.050492365 4.211151497 0.999993525 1.083540247 0.283472908 0.040680306 0.015675221 10523391.86 192.8699149 0.008776851 0.089024109 1.050492365 0.083546721 EITALAPS(ph)TMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.952)T(0.048)MK;EITALAPS(0.91)T(0.09)MK;EITALAPS(0.98)T(0.02)MK 182.03 6.26E-06 296460000 1886560 1449550 1371190 1883690 1367980 1550360 1909430 1750280 1350220 TRUE FALSE 1797386.048 1597260.793 1434060.418 1694337.902 1606555.279 1496670.644 1618111.384 1597016.204 1559605.222 1.152462189 1.024144297 0.919502191 1.086388965 1.030103809 0.95964711 1.037513444 1.02398747 1 20.57274946 4.449452439 2.48610562 1.010081926 1.150980116 0.497997349 0.044945614 0.2443843 2.696162818 0.010712375 0.055568685 28148.31738 -4.449452439 0.140898189 EITLENKDNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EITLENKDNIR 11 1 Q9NT62;Q9NT62-2;C9JNW8 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 105.25 0.0022715 104280000 196410 141560 185010 179890 140050 193780 216500 191480 200490 FALSE TRUE 187126.0885 155985.1249 193492.8915 161807.1154 164474.6757 187069.35 183468.9487 174712.9961 231580.9652 0.808037432 0.673566261 0.835530206 0.698706456 0.710225365 0.807792427 0.792245375 0.754435909 1 17.82115715 -1.395888804 0.390927959 1.147374335 0.745488494 0.669730798 0.052895 13.15331635 1.134873509 1.997923438 0.03246533 0.04018937 1.395888804 -0.401885841 EIVHLQAGQCGNQIGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 268.12 6.73E-28 9602780000 9899350 9406220 8982220 10738270 7577690 9815900 10442970 10487990 7888830 FALSE TRUE 9431427.344 10364724.51 9394063.672 9658838.698 8899236.737 9475972.922 8849703.128 9569605.995 9112189.466 1.035034157 1.13745709 1.030933752 1.059990986 0.976629905 1.039922727 0.971193933 1.050198312 1 23.11936631 3.16645025 1.788924511 1.006377075 1.083345489 0.35180587 0.038025413 0.296719041 1.957041257 0.011482021 0.015288415 1467.068021 -3.16645025 0.076968413 EIVLADVIDNDSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 332.53 4.16E-68 709400000 862670 1003790 875390 1004420 820760 827540 886870 956690 822120 FALSE TRUE 821893.2987 1106077.342 915527.4974 903453.7933 963900.2841 798882.0823 751561.693 872917.1519 949610.1708 0.865505998 1.164769898 0.964108774 0.951394394 1.0150484 0.841273721 0.791442337 0.919237366 1 19.85697586 2.240006121 24.98115463 0.86107877 1.001059433 0.212609008 0.092572207 41.79056627 722238.9261 0.031948221 0.025396976 173.7825322 -2.240006121 0.139980663 EIVVIHQDPEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIVVIHQDPEALK 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 96.464 0.0017612 0 217620 246280 190700 278090 150940 222010 212050 237200 124740 FALSE TRUE 207333.5339 271376.212 199443.7836 250135.8649 177263.8882 214321.738 179697.8779 216429.5105 144084.0421 1.438976384 1.883457793 1.38421841 1.736041419 1.2302812 1.487477273 1.247174047 1.502106044 1 17.13655103 1.147690601 0.273626509 0.924734195 1.712955317 0.43886446 0.188186158 1.626879876 0.436378945 0.491980829 0.335585702 14.05046188 -1.147690601 0.788221121 EIVWLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EIVWLER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 101.33 0.021265 182036000 276090 242620 239160 282260 264670 218930 282200 252420 290890 FALSE TRUE 263039.7729 267343.2538 250125.7226 253886.6885 310828.3642 211348.3992 239145.207 230316.7666 335999.7355 0.782857083 0.795665072 0.744422379 0.755615739 0.925085145 0.629013588 0.711742248 0.685467107 1 18.35810057 2.219416916 24.99998734 0.726609447 0.793803875 0.004717442 0.109258132 603.084618 787570.8215 0.036080934 0.026688433 165.7360242 -2.219416916 0.067194428 EIYDDSFIRPVTFWIVGDFDSPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIYDDSFIRPVTFWIVGDFDSPSGR 25 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 83.312 0.017337 187240000 310930 265370 286090 289190 303040 295700 378010 313040 302820 FALSE TRUE 296232.9551 292411.5047 299207.5095 260120.0718 355890.0801 285459.8349 320337.6319 285628.5581 349779.779 0.846912752 0.835987448 0.855416829 0.743668123 1.017468995 0.816113029 0.915826617 0.816595399 1 18.41608736 2.755291201 24.99914423 0.900652691 0.827953351 0.281183285 0.071679089 1220.227811 1823285.084 0.019400411 0.020523093 569.2344835 -2.755291201 -0.07269934 EIYENMAPGENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIYENMAPGENKR 13 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 134.21 0.00015756 136300000 106520 115850 87860 120520 80763 104580 103390 115590 91686 FALSE TRUE 101485.0107 127655.2467 91888.46791 108405.1006 94848.04163 100958.3684 87615.95661 105468.3268 105904.1966 0.958271853 1.205384213 0.867656532 1.023614777 0.895602296 0.953299034 0.827313359 0.995884301 1 16.69240023 3.723260531 24.9980322 0.927213842 1.081828044 0.326888209 0.085013581 705.8003858 1153171.573 0.021108801 0.032836256 5287.62358 -3.723260531 0.154614202 EIYHFTLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EIYHFTLEK 9 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 170.18 5.79E-05 124210000 297050 256090 245630 287130 256510 273780 353270 324940 268810 FALSE TRUE 283009.0352 282185.8622 256892.3785 258267.1469 301245.2628 264298.93 299372.1733 296486.531 310495.6819 0.911474947 0.908823789 0.827362161 0.831789818 0.970207576 0.851216121 0.964174997 0.954881334 1 18.24421368 1.451253596 1.223709607 0.995703759 0.885448146 0.462539311 0.044378739 0.391295746 1.129663688 0.038677201 0.013121794 28.26529978 -1.451253596 -0.110255613 EKAEELAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKAEELAAR 9 1 A0A087WTZ5;Q04323;E9PJ81;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ;; 117.02 0.0011117 571920000 1038780 892980 943640 1064000 918100 1031040 1171490 1067940 1000520 FALSE TRUE 989678.9281 983975.6772 986906.8274 957044.6985 1078216.349 995334.8263 992757.6846 974425.5121 1155675.532 0.856364006 0.851429013 0.853965322 0.828125778 0.932974974 0.861258025 0.859028038 0.843165305 1 20.14030497 -2.282108006 2.366177125 1.648516071 0.860568601 0.718596336 0.02737752 1864825.654 318767.0202 6517227.086 0.006222041 0.005222663 2.282108006 -0.78794747 EKAEGDVAALNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKAEGDVAALNR 12 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;; 160.84 6.11E-05 1603210000 2598300 2265250 2294780 2862910 2369720 2448370 2813190 2748190 2660250 FALSE TRUE 2475483.508 2496081.55 2399997.933 2575124.848 2782998.418 2363582.333 2383986.198 2507543.915 3072787.983 0.80561481 0.812318183 0.781048984 0.838041824 0.90569165 0.769197988 0.775838167 0.816048464 1 21.5511168 0.932613118 22.18720813 1 0.810166542 0.695000081 0.038918886 6925.715901 2280303.135 0.03767415 0.009418537 8.562747117 -0.932613118 -0.189833458 EKAEGDVAALNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKAEGDVAALNRR 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 167.98 1.74E-05 1198540000 2042860 1218120 1816590 1635310 1812230 1795000 2589650 2312750 2407520 FALSE TRUE 1946298.056 1342247.813 1899882.448 1470925.532 2128282.338 1732838.7 2194551.33 2110233.349 2780865.906 0.699889215 0.482672613 0.683198152 0.528945149 0.765330804 0.623129183 0.789161148 0.758840383 1 21.40710275 1.006838508 0.498098084 1.009085401 0.588948922 0.675797801 0.082349199 0.531109988 0.334066068 0.086387622 0.041705599 10.15870871 -1.006838508 -0.420136479 EKCEGFELHFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKCEGFELHFWR 12 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;; 110.29 0.00090456 275620000 1047850 906210 1001740 1138810 1055780 1091990 1511850 1071120 757020 FALSE TRUE 998320.2071 998553.8293 1047670.77 1024334.655 1239907.698 1054174.112 1281189.515 977327.0544 874414.7953 1.141700955 1.141968131 1.198139345 1.171451651 1.417985725 1.20557671 1.46519652 1.117692724 1 19.73795829 2.962648593 24.50170541 1.284007472 1.157770113 0.025906899 0.136377524 728.2369007 477707.4763 0.037127601 0.039391053 917.5898337 -2.962648593 -0.126237358 EKDAESVECPDADS(ph)LNIPDVDEEGYSIKPETNQNDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDAESVECPDADSLNIPDVDEEGYSIKPETNQNDTK 37 2 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 EKDAESVECPDADS(1)LNIPDVDEEGYSIKPETNQNDTK 148.87 1.47E-13 58754000 108850 86576 93666 112160 46068 117640 118780 125140 49981 TRUE FALSE 103704.8762 95398.19283 97960.67875 100885.4637 54102.24461 113566.0973 100657.9295 114182.0782 57731.79821 1.796321601 1.652437578 1.696823619 1.747485213 0.937130772 1.967132513 1.743543984 1.977802212 1 15.81707854 EKDDANFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 75.294 0.035351 335630000 1165670 975900 910510 1220010 708310 1150370 1224180 1257300 791590 FALSE TRUE 1110571.089 1075345.32 952257.7841 1097372.277 831839.0397 1110532.398 1037408.857 1147204.147 914345.7343 1.214607394 1.176081737 1.041463583 1.20017214 0.909764227 1.214565078 1.134591455 1.25467217 1 19.80238026 3.982239502 22.27993958 1.116124771 1.200160346 0.108593511 0.104426211 374.3319396 469590.6313 0.024358243 0.044433865 9599.29862 -3.982239502 0.084035575 EKDDLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKDDLQR 7 1 A0A087X0P0;Q02224-3;Q02224 A0A087X0P0 CENPE Kinesin-like protein;Centromere-associated protein E 0 ;; 83.005 0.020932 310620000 838750 499160 397360 587025 725590 572692 986640 774640 797050 FALSE TRUE 799103.9497 550024.9715 415579.349 528016.1317 852132.6663 552859.5324 836109.9471 706808.415 920652.4432 0.867975701 0.597429546 0.451396563 0.573523848 0.925574762 0.600508407 0.908171105 0.767725563 1 19.8122971 1.396386284 0.733100872 0.978861982 0.655914109 0.3410558 0.147745266 0.716895231 0.852469851 0.137593182 0.058329017 24.91072019 -1.396386284 -0.322947873 EKDECT(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKDECTPTR 9 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.994)PT(0.006)R;EKDECT(0.997)PT(0.003)R;EKDECT(0.98)PT(0.02)R 107.99 0.0043381 2849160000 4632500 3965400 3996400 4749100 2852190 4560000 4888300 4953700 3231680 TRUE FALSE 4413530.906 4369478.768 4179638.893 4271711.445 3349611.033 4402086.057 4142500.055 4519927.767 3732832.429 1.182354416 1.170553153 1.119696363 1.144361963 0.897337637 1.17928842 1.109747125 1.210857399 1 21.83183932 3.569763452 1.996839481 1.094188203 1.178760282 0.138705239 0.088806471 0.644122765 5.068512032 0.024865223 0.04409993 3713.32919 -3.569763452 0.08457208 EKDECT(ph)PTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKDECTPTRK 10 2 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.808)PT(0.192)RK;EKDECT(0.99)PT(0.01)RK 127.79 0.0122 1263465000 1877160 1730080 1758210 2108790 1066845 2266270 2168070 2375290 1288173 TRUE FALSE 1788430.367 1906377.119 1838825.668 1896810.423 1252902.43 2187788.502 1837291.102 2167297.015 1487936.29 1.201953591 1.281222275 1.235822851 1.274792769 0.842040374 1.470350926 1.234791513 1.456579176 1 20.50488132 EKDFS(ph)PEALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKDFSPEALKK 11 2 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 EKDFS(1)PEALKK;EKDFS(1)PEALKK;EKDFS(1)PEALKK;EKDFS(1)PEALKK 102.73 0.0014765 902360000 2399120 2370050 2065120 2541480 1183590 2512830 2528320 2683110 1134690 TRUE FALSE 2285718.352 2611560.79 2159807.795 2286005.602 1390007.721 2425810.067 2142578.348 2448162.664 1310651.93 1.743955279 1.992566241 1.647888158 1.744174444 1.060546808 1.850842326 1.634742451 1.86789689 1 20.32185317 -2.545893285 0.274525803 9.63E-25 1.773906424 0.407070559 0.254424812 46.94490364 1.507185866 29.28701485 0.305495749 0.00284516 2.545893285 1.773906424 EKDIEMFLESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDIEMFLESSR 12 1 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 114.74 0.00093464 47693000 123690 109780 108580 120720 107760 118710 135890 137480 117920 FALSE TRUE 117843.4188 120966.7068 113558.5004 108584.9962 126553.3099 114599.0429 115157.4847 125441.5224 136206.4313 0.865182486 0.888113033 0.833723483 0.797209024 0.92912874 0.841362936 0.845462902 0.920966221 1 17.0554353 0.977099964 3.541493934 0.999700686 0.859175456 0.6442866 0.034696349 0.134453953 4.502492295 0.031629351 0.008177322 9.486367921 -0.977099964 -0.140525231 EKDIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EKDIQR 6 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;; 91.041 0.04409 1353110000 3087130 2669770 2522350 3631400 2812370 3278800 3910360 3772160 3259770 FALSE TRUE 2941207.483 2941822.598 2638002.242 3266364.773 3302846.438 3165254.334 3313762.763 3441849.673 3765278.483 0.781139429 0.781302794 0.700612785 0.867496199 0.877185168 0.840642823 0.880084376 0.914102287 1 21.84432514 1.654440254 0.359574148 1.008803161 0.747657763 0.760587481 0.040090055 0.580598715 0.231381881 0.054748873 0.049038362 45.12739388 -1.654440254 -0.261145398 EKDKEPFTFS(ph)SPASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDKEPFTFSSPASGR 16 2 Q6P1X5;H0YEX2 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 1 EKDKEPFT(0.002)FS(0.597)S(0.402)PASGR 114.88 0.00028625 95934000 245850 251160 232260 298050 183660 281970 305830 315690 191020 TRUE FALSE 234229.1577 276753.4895 242909.3507 268089.4477 215690.2459 272205.3082 259170.0165 288046.51 220642.406 1.061578152 1.254307794 1.1009187 1.215040448 0.977555719 1.233694434 1.17461562 1.305490251 1 17.75135057 EKDKEPFTFSS(ph)PASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDKEPFTFSSPASGR 16 2 Q6P1X5;H0YEX2 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 1 EKDKEPFT(0.001)FS(0.438)S(0.561)PASGR 123.6 4.54E-05 99766000 287550 233830 223580 314390 195050 312430 337460 317720 225120 TRUE FALSE 273958.0814 257657.5428 233831.3642 282786.9199 229066.6582 301610.4708 285974.2791 289898.7525 260030.4598 1.0535615 0.990874465 0.899246051 1.087514594 0.880922406 1.159904386 1.099772232 1.114864592 1 17.9883211 2.220438787 24.99996023 1.103786165 0.991039247 0.358264212 0.072898694 244.5634764 337385.1988 0.024515628 0.018140892 166.1264507 -2.220438787 -0.112746918 EKDLAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKDLAEKR 8 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 59.8 0.054181 72487000 148729 130584 149919 164761 119841 160530 185333 176389 136334 FALSE TRUE 141698.8749 143890.6581 156792.9344 148198.9113 140741.2325 154970.8058 157057.047 160943.4441 157475.9804 0.899812622 0.913730829 0.995662539 0.941088989 0.893731425 0.984091704 0.997339699 1.022019 1 17.26477227 2.082558337 5.648812839 1.002570876 0.927877537 0.616367989 0.028607306 0.145531945 7.62867375 0.011529838 0.00840551 120.9367622 -2.082558337 -0.074693339 EKDLDLEPLS(ph)DLEEGLEETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDLDLEPLSDLEEGLEETR 20 1 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 EKDLDLEPLS(1)DLEEGLEETR 70.533 0.011207 12356000 29173 31889 27556 32737 18759 31173 29621 31813 17391 TRUE FALSE 27794.05011 35138.52535 28819.46986 29446.21456 22030.56366 30093.47119 25101.77242 29027.28507 20087.90746 1.383620975 1.749237716 1.434667594 1.465867693 1.096707743 1.4980889 1.24959618 1.445012883 1 14.29403967 -2.905161462 0.091214119 6.23E-10 1.853173785 0.421212935 0.161484118 104.5123304 1.051709517 24.88891955 4.014109821 0.001244052 2.905161462 1.853173784 EKDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKDLFR 6 1 O60524-4;O60524-3;O60524;O60524-5;O60524-2 O60524-4 NEMF Nuclear export mediator factor NEMF 0 ;; 88.029 0.047213 565720000 1001390 909600 832430 1037140 854500 841230 1102480 977290 861890 FALSE TRUE 954056.2793 1002289.274 870597.7389 932884.7168 1003524.529 812097.9942 934276.4276 891713.3067 995547.4993 0.958323214 1.006771927 0.874491413 0.937056964 1.008012707 0.815730033 0.938454899 0.895701418 1 19.92513063 3.75105129 24.85025163 0.920120932 0.982547571 0.14940379 0.057230587 1078.442547 2145560.373 0.013396892 0.023925025 5637.042253 -3.75105129 0.062426639 EKDNIDITLQWLIQHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKDNIDITLQWLIQHSK 17 1 Q96BM9;Q9NVJ2 Q96BM9;Q9NVJ2 ARL8A;ARL8B ADP-ribosylation factor-like protein 8A;ADP-ribosylation factor-like protein 8B 0 ; 253.71 3.06E-27 196896000 713610 609390 662120 811790 484640 763950 799250 789220 455330 FALSE TRUE 679879.0695 671487.5338 692478.8569 730187.3269 569161.0626 737494.2199 677309.7333 720111.7129 525940.2509 1.292692598 1.276737296 1.316649288 1.388346539 1.082178178 1.402239548 1.287807374 1.369189203 1 19.00453939 -1.009562757 4.180313186 0.999979327 1.299254692 0.531008489 0.089156538 4271229.699 2063039.027 788.6347185 0.018326145 0.097822159 1.009562757 0.299275365 EKDQADFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKDQADFR 8 1 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 73.985 0.038441 743280000 3035810 2637080 2652530 3088830 2288090 2846490 3334430 3060760 2547040 FALSE TRUE 2892313.278 2905801.45 2774151.124 2778334.94 2687132.172 2747915.338 2825701.462 2792743.628 2942021.955 0.983103907 0.987688568 0.94294032 0.944362409 0.913362379 0.934022716 0.960462398 0.949259955 1 21.48837658 3.739140316 24.93945554 0.945890207 0.985396239 0.309660603 0.022040408 45.57002022 1960470.862 0.005327743 0.00890996 5484.54136 -3.739140316 0.039506033 EKDRES(ph)EKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDRESEKDR 10 3 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 EKDRES(1)EKDR 83.53 0.085874 221020000 526420 461210 414300 587830 222050 597710 538140 610160 269830 TRUE FALSE 501537.1699 508207.8234 433296.0648 528740.2116 260775.4497 577011.1528 456036.8594 556731.1557 311673.8583 1.609173039 1.630575712 1.390222674 1.696453512 0.836693366 1.851329964 1.463186107 1.786261956 1 18.24967763 3.754585139 22.72835543 1.463098075 1.619874438 0.049615339 0.320068782 821.5777704 1165271.516 0.073659182 0.132051371 5683.097922 -3.754585139 0.156776363 EKDS(ph)PHMQDPNQADEEAMTQIIR ddPTM_SK-BR-3_Trastuzumab_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 366.34 1.55E-118 895850000 980800 840753 888120 997000 689858 982740 1073690 1048880 600400 TRUE FALSE 934439.5278 926426.6866 928841.1805 896779.6658 810169.0168 948707.4674 909878.8708 957034.5067 693506.9656 1.347411885 1.335857796 1.339339367 1.293108376 1.168220446 1.367985492 1.31199673 1.379992638 1 19.40355085 -1.676886682 2.856318963 0.961965868 1.318521489 0.743098987 0.058758243 13402062.37 14234622.06 3754460.858 0.01407658 0.021043274 1.676886682 0.356555621 EKDTAVQGNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKDTAVQGNIR 11 1 Q9UBV8 Q9UBV8 PEF1 Peflin 0 81.431 0.019783 172640000 107000 82512 84765 99740 82875 88895 95315 114470 102640 FALSE TRUE 101942.3221 90920.06661 88651.55909 89713.94571 97328.37376 85816.54386 80772.94617 104446.4 118556.887 0.859859976 0.766889794 0.747755456 0.756716442 0.820942387 0.723842756 0.681301173 0.880981296 1 16.85521995 0.997677466 6.224714855 0.999899507 0.766828381 0.720369264 0.048595223 0.069527404 13.93845974 0.051281648 0.012887171 9.946664427 -0.997677466 -0.233071126 EKDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKDVER 6 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 73.637 0.075182 870980000 2194800 1680860 1950560 2025000 1810920 1981920 2484700 2253400 2397100 FALSE TRUE 2091056.154 1852141.545 2039995.105 1821443.153 2126743.875 1913285.613 2105613.38 2056080.35 2768830.025 0.7552129 0.668925694 0.73677152 0.657838559 0.768101998 0.691008692 0.760470437 0.742580921 1 21.40084506 -0.430661064 0.536301164 1.041797718 0.708827413 0.853394222 0.03646639 2.694169037 0.680734587 0.246328707 0.014232727 0.370970125 0.430661064 -0.332970305 EKEAAYQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKEAAYQER 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 95.618 0.0071694 517874000 930350 835790 806205 936940 787650 835116 1027920 904150 846430 FALSE TRUE 886374.1993 920957.9512 843170.2967 842757.0111 925015.9106 806195.7235 871091.925 824977.8328 977690.0414 0.906600417 0.941973337 0.862410642 0.861987926 0.946123896 0.824592345 0.890969416 0.843803044 1 19.89901763 3.741153789 24.96511764 0.883157142 0.924286877 0.058608176 0.05181254 451.0089411 4341961.332 0.011768113 0.020065823 5510.027792 -3.741153789 0.041129735 EKEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEALR 6 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1;Q9UDT6;Q9UDT6-2 P55196-5;P55196-1;Q9UDT6 MLLT4;CLIP2 Afadin;CAP-Gly domain-containing linker protein 2 0 68.422 0.087718 115020000 318950 290730 265720 312250 262070 298530 369130 322580 314570 FALSE TRUE 303873.8656 320355.7175 277903.5248 280862.0368 307774.925 288191.8312 312812.439 294333.1851 363351.909 0.836307332 0.881667908 0.764832984 0.772975261 0.847043644 0.793147976 0.860907652 0.810049921 1 18.47100796 -1.41779824 2.895332002 1.003569386 0.826257205 0.688916597 0.037675337 7471020.828 8574947.815 219593.764 0.009243608 0.038212175 1.41779824 -0.177312181 EKEDDEEEEDEDASGGDQDQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEDDEEEEDEDASGGDQDQEER 23 1 O60216;E5RI01;E5RFZ5 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 56.488 0.017718 0 21810 25472 19815 22186 22931 24554 22869 20392 21066 FALSE TRUE 20779.08452 28067.62576 20723.53735 19955.82113 26930.15914 23703.68882 19379.91403 18606.36838 24332.80769 0.853953427 1.15348899 0.851670617 0.820119954 1.106742776 0.974145241 0.796452028 0.764661794 1 14.57061518 1.757967592 12.13127367 0.836078967 0.970289563 0.134042777 0.122881171 0.341076524 203.2067955 0.054979345 0.030226612 57.27532895 -1.757967592 0.134210596 EKEDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKEDFEK 7 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 73.931 0.043371 451140000 1414430 1563540 1126120 1794930 624750 1472420 1287560 1520730 660850 FALSE TRUE 1347572.697 1722866.504 1177753.716 1614500.226 733706.2022 1421429.726 1091119.074 1387566.819 763331.2428 1.765383914 2.257036535 1.542913024 2.115071591 0.961189797 1.862140112 1.429417549 1.817778104 1 19.54194972 0.046389254 0.092230563 1.35E-08 2.686803039 0.316506136 0.35153815 37.28678816 1.13929568 21.1688724 11.3879573 1.112728608 -0.046389254 2.686803025 EKEEDKDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEEDKDKK 9 3 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 65.347 0.029271 43076000 118040 137790 117320 170630 41516 144490 123940 186590 48144 FALSE TRUE 112460.4831 151830.9577 122699.238 153477.9482 48756.37726 139486.2751 105030.6767 170251.1904 55609.92563 2.02230954 2.730285213 2.20642694 2.759902058 0.876756743 2.508298177 1.888703779 3.061525231 1 15.76305479 EKEEEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKEEEEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 91.584 0.011294 640420000 1874870 1729510 1662930 2077030 1133320 1875460 1920290 2066370 1271770 FALSE TRUE 1786248.611 1905749.035 1739176.985 1868242.998 1330970.649 1810512.35 1627314.492 1885427.688 1468989.596 1.215970906 1.297319627 1.183927367 1.271787767 0.90604498 1.232488204 1.107778092 1.283486073 1 20.48639275 7.99999974 0.02111781 1.07E-06 2.707058018 0.201492185 0.114589829 3867.852864 6.293994253 294.0558956 549.5204874 99999940.24 -7.99999974 2.70705695 EKEEEEQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEEEEQRR 9 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 58.978 0.059221 14388000 29079 22015 23678 26888 19831 24338 30592 27976 21339 FALSE TRUE 27704.4933 24258.35353 24763.65972 24185.16716 23289.52012 23495.16896 25924.62854 25526.27313 24648.14314 1.123999205 0.984185843 1.004686624 0.981216598 0.944879296 0.953222676 1.051788299 1.035626619 1 14.58919135 4.578077273 2.390195081 0.995126571 1.13361048 0.603114708 0.032852316 0.28560957 2.554636138 0.008893295 0.071021815 37850.99257 -4.578077273 0.138483909 EKEEEERQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEEEERQR 9 2 A0A0A0MRP0;Q8IWC1-2;Q8IWC1-4;Q8IWC1;Q8IWC1-3 A0A0A0MRP0 MAP7D3 MAP7 domain-containing protein 3 0 52.79 0.082028 18121000 11582 10831 10327 12367 11420 9960 13047 13033 13241 FALSE TRUE 11034.54181 11934.69121 10800.50316 11123.84566 13411.64438 9615.082703 11056.44053 11891.76143 15294.34665 0.721478469 0.78033351 0.706176171 0.72731748 0.876902079 0.628669071 0.722910287 0.777526605 1 13.90071086 0.825581171 4.28002236 0.99998913 0.738308216 0.634604917 0.06207777 1.000413193 23.92478255 0.055291678 0.014073784 6.692388917 -0.825581171 -0.261680914 EKEEETKT(ph)SNGDLSDSTVSADPVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEEETKTSNGDLSDSTVSADPVVK 25 2 Q2M389;A0A087X256 Q2M389 KIAA1033 WASH complex subunit 7 1 EKEEET(0.099)KT(0.451)S(0.451)NGDLSDSTVSADPVVK 173.03 2.40E-10 88198000 186570 194730 180700 216620 87081 263380 218830 280460 92646 TRUE FALSE 177751.2058 214573.2084 188985.2737 194844.946 102267.8988 254259.0846 185443.4644 255901.4356 107013.0685 1.661023353 2.005112192 1.76600182 1.820758425 0.955658036 2.375962937 1.73290484 2.391310138 1 16.70742746 EKEELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKEELDR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 99.802 0.0093578 2934700000 3953500 3455800 3492500 4211200 2800640 4032400 4525200 4123400 3144530 FALSE TRUE 3766625.89 3807949.949 3652634.58 3787882.175 3289070.729 3892756.977 3834797.629 3762333.236 3632167.652 1.037018731 1.048395975 1.005634907 1.042870962 0.905539348 1.07174485 1.055787617 1.035836888 1 21.79239936 -0.677548217 7.358169704 0.999998936 1.028579021 0.02506241 0.045934333 0 0 0.042178782 0.009941634 0.210112448 0.677548217 0.028580085 EKEELEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEELEEIR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 106.29 0.0026992 160250000 427360 357660 376870 464490 301650 409630 439990 460280 319350 FALSE TRUE 407159.5397 394105.9606 394149.8623 417798.5827 354257.6645 395444.4104 372861.4445 419975.4431 368873.167 1.103792783 1.068405067 1.068524082 1.132634792 0.960377973 1.072033549 1.010812057 1.138536171 1 18.49276532 2.766082298 24.99852511 1.037797731 1.088966383 0.241130805 0.049931567 1102.167717 1001120 0.013650325 0.014476052 583.555676 -2.766082298 0.051168652 EKEELEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKEELEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 132.01 0.00089427 1152800000 2766800 2435700 2475570 2975400 1900950 2791080 3152510 3101770 2174580 FALSE TRUE 2636018.847 2683900.599 2589077.333 2676307.139 2232475.078 2694424.2 2671536.7 2830162.575 2511802.76 1.049452962 1.068515666 1.030764586 1.065492554 0.888793943 1.072705326 1.063593345 1.126745547 1 21.26029175 -0.563262878 7.28022937 0.999999994 1.045992699 0.052789187 0.06090723 0 0 0.055532684 0.013089179 0.273361357 0.563262878 0.045992704 EKEELETGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKEELETGKK 10 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 106.49 0.0013551 159739000 631070 620860 576080 794700 350474 810760 758740 843180 333477 FALSE TRUE 601240.5718 684126.3399 602493.8378 714815.2462 411596.5546 782683.1779 642980.2778 769346.6892 385190.91 1.560889824 1.776070832 1.564143447 1.85574277 1.068552097 2.031935743 1.669250912 1.997312681 1 18.55521413 4.754542027 20.15117005 1.65823549 1.560888891 0 0.349204593 160.211913 710032.2522 0.071665048 0.533794535 56825.33786 -4.754542027 -0.097346599 EKEELMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EKEELMLR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;;; 141.48 0.00057715 7315500000 8799240 7007600 6415580 7212860 6320340 6803090 8507450 7804260 6597180 FALSE TRUE 8383317.364 7721682.407 6709740.689 6487809.609 7422605.295 6567497.287 7209482.252 7120877.621 7620236.981 1.100138668 1.013312634 0.880516014 0.851392106 0.97406489 0.861849481 0.946096856 0.934469314 1 22.86140443 3.998705035 2.857812065 0.916810682 1.07838094 0.595215319 0.048449952 0.146187535 2.416650897 0.011715425 0.02720078 9970.22675 -3.998705035 0.161570258 EKEES(ph)PQPR ddPTM_SK-BR-3_Trastuzumab_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 92.99 0.0058756 1209280000 1054350 932500 894070 1057060 604230 1035280 1042270 1092560 709830 TRUE FALSE 1004512.965 1027522.81 935063.9939 950802.3205 709607.5207 999427.994 883252.5689 996889.6544 819906.8111 1.225155044 1.25321902 1.14045155 1.159646813 0.865473382 1.218953155 1.077259704 1.215857267 1 19.64510042 3.484481201 2.202041956 1.090021322 1.239327555 0.261010496 0.103373617 0.376826468 3.651449973 0.028145084 0.045458588 3051.273944 -3.484481201 0.149306232 EKEESPQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEESPQPR 9 1 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 0 60.436 0.087311 441720000 652850 650260 704000 705890 1922400 432260 820650 510740 1801300 FALSE TRUE 621991.0743 716522.2333 736279.0964 634932.5961 2257665.951 417290.7278 695444.7702 466016.898 2080636.404 0.298942705 0.344376476 0.353872063 0.305162687 1.085084326 0.200559178 0.33424618 0.223978056 1 20.98859344 -1.53052564 2.824914071 1.028832714 0.38750703 0.365014458 0.251386783 40897392.69 42876266.22 9025909.36 0.059374348 0.029476394 1.53052564 -0.641325684 EKEHASGSGAQSEAAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKEHASGSGAQSEAAGR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 149.09 2.03E-07 131290700 150517 106786.3 138991.2 144109 188324 125386.5 217889 178140 234710 FALSE TRUE 143402.3597 117667.9454 145364.084 129622.8895 221167.646 121044.3341 184646.0312 162541.1172 271107.6281 0.528949926 0.434026686 0.536185887 0.478123358 0.815792781 0.446480739 0.681080177 0.59954461 1 18.04850618 -5 0.149003464 2.622775965 0.412041321 0.644376782 0.106421929 75.16693428 0.667230667 35.88849999 0.485536426 1.00E-05 5 -2.210734643 EKEHQVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKEHQVVR 8 1 Q9H307 Q9H307 PNN Pinin 0 ; 118.5 0.0011269 107671000 225701 190938 181277 238975 190547 203816 261473 240540 218413 FALSE TRUE 215032.561 210394.7993 189588.7298 214952.779 223778.3365 196757.8008 221580.4916 219477.0424 252283.3725 0.852345356 0.833962211 0.751491182 0.852029116 0.887011832 0.779907922 0.878300022 0.869962377 1 17.9446856 0.554516685 0.834180231 1.001080724 0.828452442 0.641269695 0.039737649 0.906170051 1.020599484 0.037632413 0.012469528 3.585227217 -0.554516685 -0.172628282 EKEIAETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKEIAETR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 96.948 0.0093452 0 1009730 848360 820510 1025990 716970 949630 1005730 1028080 812200 FALSE TRUE 962002.064 934808.8485 858131.1951 922855.5359 842009.341 916744.075 852287.417 938055.865 938151.8279 1.025422576 0.996436633 0.914703963 0.983695292 0.897519267 0.977180929 0.908474931 0.999897711 1 19.8394619 3.930281694 5.251716543 0.94863126 1.015175583 0.281015105 0.037731525 0.19150231 10.00018988 0.008445663 0.01581484 8516.902852 -3.930281694 0.066544323 EKEIS(ph)DDEAEEEKGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 214.49 8.86E-15 5625290000 7184920 8738470 5237090 8308680 2344659 8746340 6296900 8335400 1608729 TRUE FALSE 6845303.071 9628930.028 5477215.757 7473475.701 2753566.787 8443452.053 5336192.254 7605508.187 1858202.477 3.683830559 5.181851895 2.947588233 4.021884479 1.481844321 4.543881604 2.871695803 4.092938354 1 20.82547628 3.722034681 24.48861784 3.129934129 4.432841253 0.202152962 1.164139703 828.5119703 1227713.291 0.271039226 0.421270536 5272.719652 -3.722034681 1.302907124 EKELQK ddPTM_SK-BR-3_Trastuzumab_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 79.597 0.060858 78303000 234890 230120 215940 238950 270300 215570 264080 212080 313110 FALSE TRUE 223787.2152 253569.4896 225841.0626 214930.292 317440.2344 208104.7568 223789.7458 193509.1509 361665.4997 0.61876849 0.701116059 0.624447349 0.594279223 0.877717766 0.575406714 0.618775487 0.53505007 1 18.46429646 -0.986846758 4.244359853 1.000017116 0.646779493 0.589636188 0.093503612 23518175.19 49104028.63 6052.551428 0.020905985 0.103074976 0.986846758 -0.353237623 EKELS(ph)PPPGLPSK ddPTM_SK-BR-3_Trastuzumab_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 83.849 0.0060649 456810000 1474330 1515950 1458990 1694020 831630 1685640 1779930 1890810 1034220 TRUE FALSE 1404641.343 1670427.028 1525886.135 1523733.891 976666.0087 1627265.864 1508368.988 1725240.653 1194601.556 1.175824137 1.39831312 1.277318054 1.275516413 0.817566329 1.362182944 1.262654465 1.444197561 1 20.18809807 -1.952558464 2.660384511 0.809820355 1.25437828 0.174356179 0.172042446 66440917.21 31487428.47 78064065.05 0.039145285 0.01115428 1.952558464 0.444557925 EKEPIAASTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKEPIAASTNR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 73.927 0.038506 310290000 323500 272790 242510 318390 216624 306440 315600 311660 263840 FALSE TRUE 308208.7961 300587.6111 253629.3234 286384.8323 254403.157 295827.906 267449.4236 284369.3982 304754.9597 1.011333159 0.986325576 0.832240183 0.939721646 0.834779382 0.970707437 0.87758842 0.933108352 1 18.21729017 3.923824466 9.185241929 0.907280204 1.001999799 0.306819716 0.053951348 0.35846259 41.09897562 0.011883825 0.021483597 8391.207612 -3.923824466 0.094719595 EKEPS(ph)RER ddPTM_SK-BR-3_Trastuzumab_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 92.611 0.0091789 797411000 1394105 1157501 1226070 1463327 915267 1518183 1593591 1499179 1080657 TRUE FALSE 1328208.419 1275451.668 1282286.522 1316230.59 1074889.275 1465607.942 1350459.425 1367902.939 1248239.768 1.064065137 1.021800218 1.027275813 1.05446936 0.861124042 1.17413976 1.081891043 1.095865533 1 20.25146365 EKEQEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EKEQEDR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;;;; 121.05 0.004082 1244457000 3321490 3326740 2893480 3662520 2015390 3033630 3317480 4251480 2991440 FALSE TRUE 3164489.75 3665738.588 3026148.92 3294356.531 2366873.378 2928574.632 2811337.496 3879197.873 3455337.237 0.915826599 1.060891698 0.875789746 0.953411 0.684990557 0.847551029 0.81362174 1.122668384 1 21.72039509 3.709469568 22.43222763 0.878379944 0.988359139 0.063532801 0.121641596 349.6138577 269588.2443 0.030428901 0.04715643 5122.353759 -3.709469568 0.109979195 EKEQEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EKEQEDRR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;;;;; 145.72 0.00031766 753625500 1667430 1427288 1516320 1691068 1106331 1703967 1917039 1847276 1438569 FALSE TRUE 1588613.888 1572730.27 1585844.772 1521078.632 1299274.776 1644958.196 1624559.492 1685518.72 1661654.933 0.956043193 0.946484278 0.954376712 0.915399823 0.781916119 0.989951742 0.977675605 1.014361458 1 20.66418939 2.060360319 24.99999912 0.992108557 0.918993482 0.403925972 0.050496748 84.69887334 35079.89232 0.019315848 0.014265698 114.91066 -2.060360319 -0.073115074 EKEQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 EKEQFR 6 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;; 138.07 0.011364 43748000000 30414920 26977600 24468750 30717680 21748500 27913150 30105820 28306260 22502560 FALSE TRUE 28977267.01 29726648.11 25590666.39 27629880.45 25541431.51 26946510.62 25512624.23 25827613.81 25992142.08 1.114847207 1.143678271 0.984553959 1.06300898 0.982659738 1.036717579 0.98155143 0.993670077 1 24.6315722 3.740835546 24.99993216 1.006965727 1.129262746 0.786651432 0.026678929 72.57625122 797560.712 0.006336158 0.010751991 5505.991624 -3.740835546 0.122297018 EKEQFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EKEQFRK 7 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 94.662 0.0078942 14799253000 21927900 15417390 19521830 20157360 16395550 20401590 25366620 22449130 19626960 FALSE TRUE 20891411.62 16988439.57 20416925.22 18131103.88 19254928.73 19695077.82 21496476.23 20483365.17 22670608.72 0.921519659 0.749359657 0.900590075 0.799762552 0.849334439 0.868749405 0.948209045 0.90352074 1 24.43431979 1.572039636 0.932351447 0.983451646 0.835665145 0.477858904 0.051814537 0.407394485 0.691916495 0.043287719 0.016872892 37.32842245 -1.572039636 -0.147786501 EKEQMMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKEQMMR 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 145.34 0.0020913 2065460000 3094380 2560060 2569760 3056790 2561140 2566030 3232630 2993250 2690550 FALSE TRUE 2948114.79 2820933.025 2687586.038 2749515.662 3007802.005 2477167.738 2739432.922 2731145.162 3107786.753 0.948621969 0.907698388 0.864791008 0.884718251 0.967827668 0.797084207 0.881473904 0.878807132 1 21.56745608 4.247844135 2.241099262 0.887521822 0.945103944 0.058058975 0.055822714 0.657640574 6.281523673 0.01324756 0.049462092 17694.73793 -4.247844135 0.057582122 EKESFNLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKESFNLKR 9 2 H3BP71;O75150-4;O75150;A0A087WTK2 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 59.067 0.058891 264300000 135020 100160 114850 129060 126360 147040 196710 175970 167910 FALSE TRUE 128637.8722 110366.4179 120115.9861 116086.6436 148397.144 141947.9679 166698.2767 160561.1339 193948.6252 0.663257458 0.569049756 0.619318574 0.598543266 0.765136354 0.731884373 0.859497078 0.827853942 1 17.56531502 1.741125779 0.612080012 0.984492733 0.598049577 0.885082542 0.045186726 0.206914145 0.164332441 0.040045164 0.022166068 55.09672433 -1.741125779 -0.386443156 EKETLAVNYEKEEEFLTNELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKETLAVNYEKEEEFLTNELSR 22 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 228.48 2.02E-26 143560000 220410 177430 167880 236550 153320 256800 280470 267660 177370 FALSE TRUE 209991.6561 195510.3187 175577.4641 212771.5446 180058.9595 247906.9516 237679.1503 244222.2714 204875.6337 1.024971356 0.954287805 0.856995343 1.038540019 0.878869567 1.210036289 1.16011429 1.192051329 1 17.64438889 2.234106514 24.99998503 1.156564988 0.957696985 0.584260186 0.078931301 69.66765992 391026.1342 0.026140944 0.019965828 171.4377718 -2.234106514 -0.198868004 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 EKEVDGLLTS(0.002)EPMGS(0.998)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.918)PVS(0.061)S(0.021)K;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTS(0.001)EPMGS(0.999)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.991)PVS(0.004)S(0.005)K;EKEVDGLLTSEPMGS(1)PVSSK 216.51 6.79E-25 4404960000 8243627 7208750 6802448 8407386 4323602 8020283 8049901 8480730 4572598 TRUE FALSE 7853967.089 7943329.821 7114346.969 7562259.586 5077636.82 7742538.589 6821740.756 7738112.322 5281693.144 1.487016923 1.503936258 1.34698226 1.431787001 0.961365358 1.465919806 1.291582182 1.465081767 1 22.33256906 -3.825192161 0.065427011 2.30E-13 1.872849297 0.345135937 0.159245003 294.802119 1.74616055 53.6970783 10.85605583 0.000149557 3.825192161 1.872849297 EKEWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKEWQR 6 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-4;C9JMV9;A0A1B0GV31 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 66.258 0.092919 291610000 277400 285950 254470 282340 260320 234790 295100 301310 266460 FALSE TRUE 264287.8518 315088.6301 266137.7012 253958.6468 305719.7256 226659.1634 250077.0751 274925.6991 307781.2559 0.858687287 1.023742103 0.864697561 0.825127073 0.993301963 0.736429393 0.812515611 0.8932503 1 18.23154585 3.522820699 23.75131505 0.858372178 0.941715648 0.06445515 0.088932635 429.6728245 223311.5681 0.022196659 0.034384617 3332.887842 -3.522820699 0.08334347 EKFEPTVFR ddPTM_SK-BR-3_Trastuzumab_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 ; 110.84 0.0024891 624000000 1426940 1227380 1217900 1316520 1368990 1340940 1842960 1546250 1317440 FALSE TRUE 1359491.374 1352451.417 1273741.92 1184180.908 1607741.423 1294502.912 1561782.604 1410852.153 1521741.867 0.893378439 0.888752191 0.837028899 0.778174626 1.056513892 0.850671812 1.026312437 0.927129748 1 20.53729222 2.740687105 24.99709794 0.967981803 0.860113604 0.471972921 0.064004958 180.6941039 2124090.701 0.018445821 0.018717356 550.4109998 -2.740687105 -0.107868199 EKFGDQDVWILPQAEWQPGETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKFGDQDVWILPQAEWQPGETLR 23 1 Q9H2W6;A0A087WT51 Q9H2W6 MRPL46 "39S ribosomal protein L46, mitochondrial" 0 86.551 0.0061583 35893000 50682 30910 40807 41379 44678 37838 47733 46081 51441 FALSE TRUE 48286.3623 34059.76414 42678.04131 37219.50431 52469.82905 36527.66057 40450.45417 42045.90335 59418.20756 0.812652624 0.573220996 0.718265378 0.626398975 0.883059776 0.614755343 0.680775403 0.707626586 1 15.85861746 0.907124861 14.71176347 1.000000001 0.695052014 0.508815209 0.091847153 233.1989029 36941.35316 0.079873267 0.019969009 8.074671461 -0.907124861 -0.304947986 EKFPEFCSS(ph)PSPPVEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.013)S(0.534)PS(0.453)PPVEVK 186.13 3.27E-10 414450000 477070 436570 418130 493060 272800 475610 496010 546790 313070 TRUE FALSE 454519.8466 481056.9793 437301.6741 443496.672 320376.2336 459139.5064 420334.5647 498910.1689 361619.2967 1.256901528 1.3302857 1.209287442 1.226418712 0.885948943 1.269676454 1.16236763 1.379655824 1 18.46411214 3.404794551 2.543548228 1.156767683 1.291621662 0.149582338 0.136598393 0.498452475 6.524212792 0.037608377 0.055844184 2539.770945 -3.404794551 0.134853979 EKFPEFCSSPS(ph)PPVEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.011)S(0.25)PS(0.739)PPVEVK;EKFPEFCS(0.002)S(0.288)PS(0.71)PPVEVK 169.05 1.22E-09 965660000 1025350 909860 898610 1098420 549610 1081990 1090840 1166540 627730 TRUE FALSE 976883.7375 1002575.768 939812.1573 988004.7347 645461.81 1044520.415 924412.3233 1064391.573 725075.1624 1.347286169 1.382719779 1.296158255 1.362623885 0.890199863 1.440568467 1.274919307 1.46797412 1 19.46777103 -1.212561201 3.827917803 0.999715972 1.309089283 0.268778617 0.159541259 10766761.58 3410600.211 26534.43315 0.034315738 0.061296941 1.212561201 0.309373311 EKGKFEDMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 99.215 0.0027261 3246916000 11265480 7689360 10563540 11733810 7402830 13102630 15379780 14507340 8162130 FALSE TRUE 10732983.09 8472914.526 11047888.76 10554305.13 8693881.208 12648882.64 13033312.09 13237000.4 9427871.434 1.13843121 0.898709172 1.171832776 1.11947911 0.922146772 1.341647765 1.382423613 1.404028523 1 23.16850065 2.224682703 24.96564843 1.322227414 1.046186317 0.383862594 0.141941312 186.876345 336178.6341 0.048226604 0.035799164 167.7577926 -2.224682703 -0.276041096 EKGPTTGEGALDLSDVHS(ph)PPKSPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKGPTTGEGALDLSDVHSPPKSPEGK 26 2 O95684;O95684-2 O95684 FGFR1OP FGFR1 oncogene partner 1 EKGPTTGEGALDLS(0.001)DVHS(0.956)PPKS(0.043)PEGK 121.83 6.67E-05 245380000 177180 152000 173540 198370 82681 203010 201940 224000 88013 TRUE FALSE 168805.0525 167488.9728 181496.9807 178429.4707 97100.54022 195979.7128 171130.3441 204385.3725 101661.6065 1.66046021 1.647514519 1.785305061 1.75513133 0.95513482 1.927765255 1.683333069 2.01044799 1 16.63341541 EKGTWVQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKGTWVQLK 9 1 P46778 P46778 RPL21 60S ribosomal protein L21 0 ; 137.98 0.0001364 1268940000 2809280 2120200 1319500 1618110 2219190 1714230 3044590 2315590 2247370 FALSE TRUE 2676490.902 2336250.79 1380000.38 1455454.509 2606216.033 1654865.785 2580081.878 2112824.664 2595880.662 1.031053138 0.899983896 0.531611642 0.560678513 1.003981451 0.637496866 0.993913902 0.813914405 1 21.30779263 -1.204243709 15.56911959 1 0.825479474 0.091596059 0.182572243 0 0 0.176154619 0.041520042 0.062482197 1.204243709 -0.174520526 EKHLAEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EKHLAEIK 8 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;;;; 101.11 0.0033832 1246030000 6398060 4576010 3867470 5048780 3888060 5031750 6633390 6203960 3943580 FALSE TRUE 6095636.384 5042310.621 4044797.325 4541267.042 4566136.433 4857499.236 5621344.525 5660708.373 4555130.245 1.338191458 1.106952019 0.887965241 0.996956574 1.002416218 1.066379878 1.23406889 1.242710541 1 22.11906088 -0.198220927 7.398855753 0.999999809 1.116562264 0.059812549 0.133767112 0 0 0.138572892 0.032661944 0.633547341 0.198220927 0.116562455 EKHLDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKHLDLEK 8 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ; 114.5 0.0015892 545900000 1156120 997490 1016200 1038060 846200 1137060 1308950 1285980 768330 FALSE TRUE 1101472.499 1099135.365 1062793.775 933712.2366 993777.0121 1097683.327 1109245.637 1173372.774 887478.6923 1.241125571 1.238492118 1.197542864 1.052095385 1.11977563 1.236855979 1.249884247 1.322141911 1 19.75935296 EKHPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EKHPDGK 7 1 P53396;P53396-2;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;;; 91.318 0.0099092 2095881000 9722890 9746480 8557950 10477870 5091040 9537480 9529240 11809860 5611940 FALSE TRUE 9263308.259 10739657.39 8950340.472 9424614.601 5978915.764 9207194.676 8075379.422 10775726.05 6482210.993 1.429035289 1.656789235 1.380754264 1.453919752 0.922357475 1.420378739 1.245775466 1.662353487 1 22.62805455 3.261112747 2.354931202 1.27715075 1.53445562 0.195749844 0.217794903 0.420229127 4.772056957 0.060812871 0.083311565 1824.369265 -3.261112747 0.257304869 EKHPNS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.6)S(0.4)PR;EKHPNS(0.852)S(0.148)PR;EKHPNS(0.865)S(0.135)PR;EKHPNS(0.851)S(0.149)PR 82.362 0.011305 271635000 448304 369202 393714 461311 337159 415748 477226 458840 396453 TRUE FALSE 427113.5584 406824.1035 411766.1763 414939.1418 395959.4229 401350.5425 404416.4088 418661.5371 457932.9064 0.932698988 0.888392378 0.899184511 0.906113398 0.864666892 0.87643962 0.883134632 0.914242089 1 18.80477671 -0.999769975 4.999972626 1.000001048 0.894934818 0.741129609 0.019385537 2.32E-07 4.64E-08 0.019201138 0.004525707 0.100052979 0.999769975 -0.10506623 EKHPNSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.22)S(0.78)PR;EKHPNS(0.377)S(0.623)PR;EKHPNS(0.403)S(0.597)PR;EKHPNS(0.408)S(0.592)PR 84.718 0.0092675 272706900 614495 534357 550388 630768 492936 610614 685678 630435 531772 TRUE FALSE 585449.0392 588808.5858 575623.8342 567362.0023 578903.8823 589468.2841 581065.2278 575230.7693 614236.4858 0.953132959 0.958602427 0.937137157 0.923686585 0.942477198 0.95967644 0.94599595 0.936497233 1 19.22843469 -1.714977472 2.93822909 1.007827848 0.946152681 0.714787946 0.010951302 5294728.805 5418464.689 306343.3629 0.002807331 0.019276249 1.714977472 -0.061675167 EKIDLENTLEQEQEALVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKIDLENTLEQEQEALVNR 19 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 301.77 4.99E-50 602886000 683970 600356 612274 707240 507977 677920 771590 713510 615409 FALSE TRUE 651640.0936 661532.9589 640347.3685 636146.8915 596568.028 654443.4604 653869.7743 651031.2818 710843.4846 0.916713887 0.930630966 0.900827513 0.894918368 0.839239637 0.920657605 0.919850556 0.915857423 1 19.43917241 0.423956838 1.054662988 1.00009454 0.904316257 0.595983085 0.024953358 1.751269912 2.48404929 0.025504687 0.00786286 2.654341751 -0.423956838 -0.095778283 EKIETELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKIETELR 8 1 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 134.68 0.00079016 13323890000 25721400 27857100 22572600 27903700 16646100 25681800 24676000 26925700 17211000 FALSE TRUE 24505600.4 30695770.16 23607576.04 25098767.06 19549174.57 24792432.83 20911222.99 24567942.97 19879993.98 1.23267645 1.544053293 1.187504185 1.262513816 0.98335918 1.247104645 1.051872703 1.235812395 1 24.24481398 3.359322819 2.120038764 1.120440493 1.383425448 0.400016955 0.125309437 0.252850507 2.314954221 0.034206112 0.050863131 2287.298361 -3.359322819 0.262984955 EKINIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKINIR 6 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;;; 126.24 0.016029 5522010000 11058670 7656540 7686260 9069790 9750970 7748900 11819000 8531330 10042540 FALSE TRUE 10535948.59 8436750.131 8038682.624 8158077.478 11451536.08 7480553.65 10015794.48 7784281.518 11599885.81 0.908280371 0.727313205 0.692996703 0.703289464 0.987211104 0.644881663 0.863439058 0.671065357 1 23.46760727 -1.756524563 3.511262432 1.030636159 0.780648571 0.284342184 0.111935149 0.025687238 0.001781186 0.103706045 0.022760864 0.017517634 1.756524563 -0.249987588 EKKDELCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKKDELCR 8 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;;;;; 113.62 0.0015823 1260289000 1670559 1265644 1437550 1951835 1272153 2106825 2423768 2277339 1528424 FALSE TRUE 1591594.987 1394614.563 1503463.089 1755632.838 1494016.08 2033865.122 2053977.676 2077923.124 1765444.188 0.901526651 0.789951091 0.851606128 0.99444256 0.846255062 1.152041586 1.163433934 1.176997346 1 20.75159978 2.236849609 24.9999945 1.140144631 0.871377242 0.746374949 0.071015561 19.85707961 290129.7512 0.02465613 0.019163953 172.524036 -2.236849609 -0.268767388 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 43 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 174.02 9.03E-21 1545170000 384337 194211 334022 349435 291953 340921 552620 409198 115797 FALSE TRUE 366170.1517 214001.3217 349337.2391 314309.1299 342869.5108 329114.8203 468307.6694 373366.4538 133754.2074 2.737634643 1.599959552 2.61178505 2.349900883 2.563429723 2.460594151 3.501255614 2.791437079 1 17.02922475 2.88062344 1.464321145 2.711213746 2.211926329 0 0.699489725 1.004862169 4.385863414 0.256441225 0.276494143 759.6673132 -2.88062344 -0.499287417 EKKEEWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKKEEWDR 8 2 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 94.692 0.0057251 808960000 1009000 756690 873300 963790 530020 1019800 1121400 1031800 605540 FALSE TRUE 961306.5696 833797.5713 913341.6688 866907.9981 622455.3202 984484.0703 950309.8341 941450.1221 699444.0505 1.374386656 1.192086159 1.305810905 1.239424365 0.889928679 1.407523689 1.358664547 1.345997755 1 19.41584913 4.654719606 3.223107803 1.238553469 1.382222964 0.070631438 0.163217422 0.882245794 14.87670541 0.038407998 0.280451314 45156.43065 -4.654719606 0.143669495 EKKPGDGEVS(ph)PSTEDAPFQHSPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKKPGDGEVSPSTEDAPFQHSPLGK 25 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 EKKPGDGEVS(0.923)PS(0.039)T(0.039)EDAPFQHSPLGK;EKKPGDGEVS(0.984)PS(0.014)T(0.001)EDAPFQHSPLGK 116.34 0.00067975 396140000 431580 340630 351020 435440 220772 431120 446620 494120 174520 TRUE FALSE 411180.0687 375340.5843 367114.6142 391668.7439 259274.5669 416190.2063 378479.9163 450852.2333 201583.6703 2.039748895 1.861959274 1.821152545 1.94295869 1.286188343 2.064602781 1.877532618 2.236551367 1 17.62101925 4.436739544 1.083786539 1.79157206 2.094247246 0.054233418 0.362760973 3.698820266 5.062619109 0.100369957 1.144328032 27336.28819 -4.436739544 0.302675186 EKLCYVALDFEQEMATAASSSSLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 228.63 3.84E-34 1594233000 1840060 1687960 1688250 1915480 1291457 1840950 2214870 2095760 1542080 FALSE TRUE 1753084.01 1859965.043 1765657.932 1722932.311 1516686.692 1777197.44 1876950.903 1912244.144 1781217.891 0.984205256 1.044209725 0.991264427 0.967277681 0.85148858 0.997742864 1.053745818 1.073559924 1 20.76443258 1.836577822 4.955978447 1.046946731 0.976748637 0.293321925 0.051336038 0.315230106 11.51218523 0.02554308 0.014639513 68.64008647 -1.836577822 -0.070198094 EKLDQLKQEFEFWYPVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKLDQLKQEFEFWYPVDLR 19 2 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 196.89 4.58E-16 450410000 1346910 1052920 1275460 1400870 979610 1422860 1729100 1542150 1123220 FALSE TRUE 1283244.234 1160213.745 1333941.103 1260051.886 1150453.674 1373586.001 1465294.038 1407111.171 1297403.221 0.989086672 0.894258413 1.028162318 0.971210697 0.886735639 1.058719432 1.129405272 1.08455964 1 20.30719549 2.092885416 6.495328888 1.087676826 0.953521825 0.534521206 0.052305556 0.135370271 7.908328902 0.01845868 0.013561728 123.8469787 -2.092885416 -0.134155001 EKLDSVIEFSIPDSLLIR ddPTM_SK-BR-3_Trastuzumab_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 ; 183.56 5.71E-14 346640000 1956400 1488480 1679260 1928290 1551100 1608740 2026370 1932030 1620550 FALSE TRUE 1863924.849 1640157.804 1756255.732 1734454.626 1821611.349 1553028.93 1717210.04 1762851.211 1871856.617 0.99576262 0.876219786 0.93824266 0.926595878 0.973157523 0.829673019 0.917383321 0.941766156 1 20.8360385 0.892909372 3.913069951 0.999955605 0.920581561 0.218620859 0.045960162 0.76276863 24.02598491 0.041585654 0.010647356 7.814647134 -0.892909372 -0.079374044 EKLEAEMEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKLEAEMEAAR 11 1 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 117.93 0.00071892 248800000 883200 790300 707209 901430 694070 811680 956250 943610 732750 FALSE TRUE 841452.8863 870832.4685 739635.2322 810816.5438 815115.5882 783571.3181 810356.4998 860982.506 846381.1276 0.994177279 1.028889279 0.873879637 0.957980415 0.963059739 0.925790158 0.957436872 1.017251541 1 19.69094793 -0.471816896 5.774984228 1 0.966878177 0.056992117 0.044281845 0 0 0.043603835 0.010277522 0.337429543 0.471816896 -0.033121823 EKLEAYQHLFYLLQTNPTYLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKLEAYQHLFYLLQTNPTYLAK 22 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 184.26 2.38E-17 111800000 278670 241670 232480 266910 207200 258170 308780 305520 211070 FALSE TRUE 265497.8214 266296.4478 243139.438 240079.6997 243335.6144 249229.5082 261669.9399 278767.0491 243801.6576 1.088991043 1.092266765 0.997283777 0.984733665 0.998088433 1.022263387 1.073290241 1.143417366 1 17.89534841 -0.803943022 7.411371301 0.999995023 1.051458693 0.087330653 0.050656678 0 5.19E-11 0.051666215 0.012177844 0.157056884 0.803943022 0.05146367 EKLEMEMEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;; 158.11 2.76E-05 1626130000 3067440 2649610 2646820 3151800 2453280 2946270 3468560 3268580 2705060 FALSE TRUE 2922448.19 2919608.271 2768179.315 2834975.076 2881131.255 2844239.931 2939367.468 2982365.807 3124546.889 0.935319038 0.934410132 0.885945839 0.907323582 0.922095701 0.910288766 0.940733992 0.954495456 1 21.57521556 1.007414383 1.303929103 0.999337054 0.918257993 0.772506042 0.014676713 0.242022221 0.8438724 0.014948521 0.004571249 10.17218811 -1.007414383 -0.08107906 EKLIFPYVELDLHSYDLGIENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKLIFPYVELDLHSYDLGIENR 22 1 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 209.97 3.03E-23 166685000 400750 293300 383870 393750 393040 394650 472440 424640 364400 FALSE TRUE 381807.3417 323187.6035 401470.8192 354169.5019 461586.0516 380983.1715 400360.601 387456.2704 420909.2909 0.907101245 0.767831954 0.953817908 0.841439022 1.096640206 0.905143174 0.951180242 0.920522019 1 18.68314983 3.26290885 1.815634895 0.960485226 0.844199039 0.269638685 0.074819312 0.384565689 2.612797045 0.02192129 0.031299369 1831.929897 -3.26290885 -0.116286187 EKLILPHVDIQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKLILPHVDIQLK 13 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 146.47 2.54E-05 92969000 669610 481500 519650 522710 445740 476920 590390 606990 397930 FALSE TRUE 637958.8623 530565.3974 543476.4665 470166.1977 523476.9149 460404.1408 500315.1622 553838.7377 459638.9521 1.387956481 1.15430904 1.182398628 1.022903293 1.138887191 1.00166476 1.088496003 1.204943 1 18.81014154 4.812162055 0.783279054 1.078505898 1.60737671 0.663567256 0.067565171 1.495025998 0.648365738 0.022179096 0.711166169 64887.65144 -4.812162055 0.528870812 EKLQEEGGGS(ph)DEEETGSPSEDGMQSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKLQEEGGGSDEEETGSPSEDGMQSAR 27 1 Q13610;Q13610-2 Q13610 PWP1 Periodic tryptophan protein 1 homolog 1 EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR 288.18 2.67E-62 397190000 290630 260630 271050 296510 210078 289090 333210 337840 235910 TRUE FALSE 276892.4959 287188.4933 283477.9106 266704.2515 246715.5367 279078.7408 282372.6947 308256.9386 272493.7179 1.016142676 1.053927024 1.040309893 0.978753762 0.905398989 1.024165779 1.036253961 1.131244202 1 18.05586344 -0.616326109 5.8459086 0.999999941 1.022333375 0.01610109 0.056755989 4.04E-10 6.20E-19 0.054245006 0.01278567 0.241921179 0.616326109 0.022333434 EKLQQEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKLQQEAK 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 91.584 0.011294 78874000 138760 123730 127670 129290 80033 128970 148600 149250 106710 FALSE TRUE 132201.0898 136338.2277 133523.7958 116293.5236 93990.72986 124503.7366 125928.3408 136180.8788 123258.0418 1.072555493 1.106120345 1.083286687 0.943496439 0.762552516 1.010106397 1.021664298 1.104843763 1 16.91132225 3.249487044 23.02817889 0.970902877 1.089240086 0.275461659 0.086705243 107.8582662 227314.6197 0.024946803 0.033390972 1776.180279 -3.249487044 0.118337209 EKLQSFDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKLQSFDSPER 11 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 EKLQSFDS(1)PER;EKLQS(0.001)FDS(0.999)PER 164.63 1.37E-05 370970000 880970 771680 823840 936650 741000 884800 1035700 961090 899520 TRUE FALSE 839328.294 850315.0693 861613.8789 842496.1625 870230.1654 854159.1541 877684.9431 876931.8645 1039012.967 0.807813108 0.81838735 0.829261911 0.810862029 0.837554672 0.822087097 0.844729537 0.844004735 1 19.98678223 -5 0.247562961 2.053838893 0.809181143 0.981129968 0.007675735 18.74109705 0.186034407 9.96469877 0.009707408 1.00E-05 5 -1.24465775 EKMDLTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKMDLTAK 8 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 65.224 0.068027 73935000 335360 251250 256620 304480 201060 315040 364710 336730 260210 FALSE TRUE 319508.1974 276852.6606 268386.2808 273873.0919 236124.8003 304130.0858 309066.7911 307244.1361 300562.0378 1.06303577 0.921116528 0.892948034 0.911203204 0.785610858 1.011871253 1.028296166 1.02223201 1 18.19730328 2.041013377 24.99999404 1.020011531 0.925533199 0.353409672 0.066871265 186.8189578 113876.1002 0.026593949 0.019640914 109.9039692 -2.041013377 -0.094478332 EKMLRAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EKMLRAAR 8 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 0 ;;;;;;; 83.206 0.029476 69151860000 41957440 31331740 33034850 25125930 41935490 40567800 56519460 44710830 48391480 FALSE TRUE 39974194.96 34524479.93 34549530.55 22600223.78 49249026.18 39162926.91 47896378.33 40795712.7 55895783.57 0.715155821 0.617658036 0.618106203 0.404327882 0.881086605 0.700641881 0.856887144 0.729853132 1 25.73623612 2.709906367 24.99482834 0.816588175 0.609285271 0.533554032 0.112425049 612.9558888 534675.0362 0.033792872 0.031865331 512.7508236 -2.709906367 -0.207302904 EKNEIQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKNEIQNR 8 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 113.66 0.0025593 336700000 202133 140983 151641 171010 160268 158322 225029 178719 169986 FALSE TRUE 192578.5737 155349.328 158593.8898 153819.7499 188218.6885 152839.2694 190696.6931 163069.4169 196346.5607 0.980809508 0.791199639 0.807724308 0.783409444 0.958604458 0.778415822 0.971225024 0.830518326 1 17.5830428 1.715163737 15.93771405 0.925411317 0.853289014 0.185792064 0.081949593 0.312775194 194.6745227 0.035628338 0.019680481 51.89956733 -1.715163737 -0.072122303 EKNGNEEGEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 83.769 0.015012 58299000 197958 165944 171505 193757 134733 166214 204570 187078 161330 FALSE TRUE 188600.9177 182853.8823 179368.6739 174280.1782 158230.3925 160457.9675 173359.0893 170696.4586 186348.2324 1.012088578 0.981248278 0.962545614 0.935239234 0.849111314 0.861065143 0.930296397 0.916007929 1 17.50764161 3.363933745 1.937785179 0.904713009 0.997307723 0.402241976 0.04169374 0.270008132 2.068522085 0.012216897 0.018573195 2311.712091 -3.363933745 0.092594715 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_SK-BR-3_Trastuzumab_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(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.602)S(0.398)DPEAAFLSR 213.38 2.33E-26 1904020000 1226600 1202200 1053820 1399770 944230 1229650 1337060 1338930 948960 TRUE FALSE 1168621.049 1324705.547 1102138.689 1259062.46 1108903.413 1187066.912 1133066.94 1221686.191 1096119.87 1.066143476 1.208540765 1.005491023 1.148653988 1.011662541 1.082971803 1.033707144 1.114555282 1 20.06397415 3.730945918 24.9997281 1.060006441 1.137342122 0.243950901 0.05878526 682.9350104 2242135.191 0.0138528 0.02191808 5382.027564 -3.730945918 0.07733568 EKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.205)S(0.795)DPEAAFLSR;EKPELSEPSHLNGPS(0.097)S(0.903)DPEAAFLSR 250.02 1.22E-39 506636000 282743 299175 286624 359310 257680 306131 329828 346073 249984 TRUE FALSE 269378.2987 329661.2726 299765.9939 323191.4762 302619.3104 295529.6067 279506.6809 315769.0135 288750.242 0.932911075 1.141683104 1.038149758 1.119276902 1.048031366 1.0234783 0.967987694 1.093571425 1 18.13946263 2.239182661 4.174949289 1.01255894 1.059062078 0.065081849 0.062899651 0.482850489 19.42592715 0.022949976 0.017603586 173.4533377 -2.239182661 0.046503138 EKPEVTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKPEVTDR 8 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 81.338 0.02403 0 246740 245590 231330 254230 218160 233550 257670 261340 217310 FALSE TRUE 235077.0892 270615.9002 241936.7093 228674.3174 256207.0349 225462.1049 218357.7091 238455.6841 251009.3249 0.936527315 1.078110944 0.963855464 0.911019212 1.020707239 0.898222028 0.869918714 0.949987353 1 17.93738144 3.484029747 22.68056555 0.931969783 1.009596485 0.173255367 0.056064037 117.1239705 384518.0468 0.015118825 0.021338463 3048.103764 -3.484029747 0.077626702 EKPKEEEWEKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKPKEEEWEKPK 12 3 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 108.17 0.00075999 853730000 1627390 1456060 1399830 1789370 662140 1800830 1643520 1938050 613580 FALSE TRUE 1550466.5 1604434.169 1464013.59 1609499.128 777617.0064 1738466.806 1392770.839 1768344.068 708730.8527 2.187666156 2.263813073 2.065683446 2.270959592 1.097196493 2.452929485 1.965161857 2.495085491 1 19.43487833 EKPLWFDVYDAFPPLREPVFQRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKPLWFDVYDAFPPLREPVFQRPR 24 3 J3QLR8;Q9Y3D9 J3QLR8 MRPS23 "28S ribosomal protein S23, mitochondrial" 0 105.92 0.0012188 56871000 164030 129130 138050 136790 146590 129910 174740 150580 171250 FALSE TRUE 156276.627 142288.4938 144379.7291 123039.6093 172155.2496 125411.1841 148080.2037 137394.4169 197806.5754 0.790047685 0.719331466 0.729903588 0.622019814 0.870321167 0.634009177 0.748611129 0.694589736 1 17.59373086 -1.995843266 2.607484125 1.265237132 0.728038256 0.592761235 0.071330458 13856547.83 4903651.033 22079208.57 0.014825202 0.010096172 1.995843266 -0.537198877 EKPSYDTETDPSEGLMNVLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKPSYDTETDPSEGLMNVLKK 21 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 139.83 9.61E-08 202430000 226120 176950 216720 214550 149470 235550 288850 284760 187880 FALSE TRUE 215431.7557 194981.4062 226656.8264 192983.0264 175537.5207 227392.8444 244780.6274 259824.9048 217015.4708 0.992702294 0.89846777 1.044427042 0.889259303 0.808870999 1.047818589 1.127940909 1.197264434 1 17.72743837 2.022853055 10.51290814 1.113990465 0.932107568 0.540276821 0.077864597 0.29033893 130.1903754 0.027830435 0.020424415 105.4030201 -2.022853055 -0.181882896 EKPYFPIPEEYTFIQNVPLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 255.2 4.10E-37 5115554000 4818926 4401015 4384592 5243465 4333992 4578201 5203714 4976623 5014926 FALSE TRUE 4591144.918 4849483.432 4585629.88 4716381.936 5089838.833 4419656.751 4409791.857 4540843.507 5792615.111 0.792585875 0.837183783 0.791633794 0.814205993 0.878677201 0.762981256 0.761278243 0.783902162 1 22.46578338 -1.602906766 5.387511994 1.001431662 0.802673681 0.759158913 0.034905524 0.000624156 4.60E-05 0.035143787 0.0082264 0.024951303 1.602906766 -0.198757981 EKQDTFALASQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKQDTFALASQQK 13 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 134.21 8.96E-05 1155900000 1298370 1133420 995910 1219620 875540 1214690 1383330 1333940 1024240 FALSE TRUE 1236998.623 1248916.787 1041573.459 1097021.48 1028233.899 1172624.981 1172277.602 1217133.142 1183073.908 1.045580174 1.05565407 0.880395934 0.927263692 0.869120595 0.991167984 0.99087436 1.028788763 1 20.17410877 1.606480797 2.874012056 1.012687622 0.970778625 0.102145944 0.061518817 0.758007345 14.5601914 0.047695668 0.019118809 40.40925068 -1.606480797 -0.041908998 EKQEEEVDYES(ph)EEEEEREGEENDDEDMQEER ddPTM_SK-BR-3_Trastuzumab_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 133.66 2.38E-06 178330000 26308 33770 26739 33860 19065 33785 30420 37876 19777 TRUE FALSE 25064.47298 37211.20139 27965.0096 30456.32847 22389.92996 32615.01698 25778.8703 34559.37665 22843.91615 1.097205611 1.628932673 1.224177563 1.333235872 0.980126604 1.427733177 1.12847859 1.512848166 1 14.47952237 EKQFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKQFQK 6 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 83.614 0.05179 291520000 271973 216691 250895 298960 235079 251305 333450 315890 295830 FALSE TRUE 259117.3753 238772.0593 262398.7839 268907.9728 276076.7032 242602.2448 282576.0783 288228.997 341705.8055 0.758305452 0.698765006 0.767908475 0.786957577 0.807936824 0.709974021 0.826957206 0.843500439 1 18.38239523 0.218387726 0.386272636 1.038095486 0.732788215 0.823967423 0.035373298 1.327479179 0.315413891 0.115997766 0.026226635 1.653437281 -0.218387726 -0.305307271 EKQLAAENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EKQLAAENR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 152.69 7.28E-05 3224880000 5998750 4121810 4306200 4506480 5361570 4824120 6943330 5638380 6213500 FALSE TRUE 5715200.976 4541827.125 4503643.529 4053480.069 6296626.11 4657059.515 5883997.485 5144653.556 7177057.846 0.796315301 0.632825765 0.627505536 0.564782973 0.877326928 0.648881424 0.819834201 0.716819297 1 22.77496112 0.192155588 0.46359358 1.028178238 0.680437243 0.493881178 0.094743419 2.623230663 0.827654745 0.240638068 0.04993983 1.556523164 -0.192155588 -0.347740995 EKQPPIDNIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKQPPIDNIIR 11 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 71.888 0.043593 252830000 558210 491890 832830 866300 534930 690420 510860 811620 424090 FALSE TRUE 531824.5196 542014.1502 871016.0793 779217.8781 628221.6226 666510.5823 432918.9244 740550.2501 489855.7112 1.085675858 1.106477148 1.778107429 1.590708979 1.282462587 1.360626337 0.883768249 1.511772208 1 18.90199734 EKQPVAGSEGAQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKQPVAGSEGAQYR 14 1 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;;;;; 208.39 7.40E-09 3228820000 2824750 2142140 2484890 2740400 2305380 2565250 3037640 2801380 2657350 FALSE TRUE 2691229.666 2360426.501 2598824.664 2464929.786 2707437.542 2476414.749 2574192.228 2556076.316 3069438.266 0.87678247 0.769009277 0.846677613 0.803055664 0.882062875 0.806797379 0.83865255 0.832750521 1 21.54954322 -4.99999791 0.422424353 4.203959904 0.826809796 0.708753494 0.033802583 478.6419263 3.081461998 1424.114359 0.017508559 1.00E-05 4.99999791 -3.377150109 EKQSDDEVYAPGLDIESSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKQSDDEVYAPGLDIESSLK 20 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 124.86 2.38E-05 49548000 49539 42644 39274 44818 29300 49662 49881 55253 39832 FALSE TRUE 47197.38965 46989.47208 41074.75175 40312.80949 34409.91072 47942.19249 42270.73732 50414.75441 46008.94313 1.025830772 1.021311704 0.89275582 0.876195078 0.747896135 1.042018991 0.918750453 1.095759889 1 15.4896267 1.246763934 24.9918669 1.047879954 0.942121079 0.216538216 0.089997368 283.7133551 864367.2898 0.064708288 0.022752011 17.65078131 -1.246763934 -0.105758875 EKS(ph)PSLGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKSPSLGKK 9 2 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.992)PS(0.008)LGKK 67.08 0.032305 772230000 726850 612290 570570 638550 346600 682910 651380 713210 371140 TRUE FALSE 692493.241 674683.0471 596731.1989 574361.7408 407046.9303 659260.6555 552000.0176 650757.5514 428694.4957 1.615353703 1.573808514 1.391973083 1.339792665 0.949503514 1.537833264 1.28763029 1.517998383 1 18.70959037 8 0.214578302 1.18558871 3.670866552 0.317924576 0.189173949 57.32727357 0.722977946 0.290897512 48.98707793 100000000 -8 2.485277842 EKS(ph)PVREPVDNLSPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKSPVREPVDNLSPEER 17 2 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06 Q86U06-3 RBM23 Probable RNA-binding protein 23 1 EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER;EKS(1)PVREPVDNLSPEER 187.18 2.51E-10 590560000 348704 321975 323713 355048 259178 361204 362907 378380 312248 TRUE FALSE 332221.453 354784.6186 338555.5612 319357.9005 304378.5611 348695.4149 307538.8719 345247.0413 360669.8251 0.921123504 0.983682565 0.938685572 0.885457774 0.843925774 0.966799523 0.852688111 0.957238497 1 18.4603192 3.423508357 6.684849338 0.906767105 0.953842892 0.048099189 0.051786173 0.349764239 33.49564288 0.012877876 0.017564018 2651.602114 -3.423508357 0.047075787 EKS(ph)TFREESPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 EKS(0.759)T(0.225)FREES(0.015)PLR 79.036 0.018992 360850000 333950 231820 344030 319320 311210 325590 427580 350810 413140 TRUE FALSE 318164.8453 255442.7216 359804.1158 287221.3469 365484.9255 314314.7367 362344.818 320091.2166 477207.6412 0.666722026 0.535286319 0.753978111 0.601879187 0.765882383 0.658654031 0.759302213 0.670758783 1 18.86425762 -4.999999998 0.157002335 2.234891215 0.574781883 0.689790101 0.06941505 65.58428067 0.597569867 25.12343748 0.273142712 1.00E-05 4.999999998 -1.660109333 EKSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EKSELR 6 1 A0A6E1W127;A7E2Y1 A0A6E1W127 MYH7B Myosin-7B 0 81.958 0.055182 274010000 192950 164800 183490 232770 186840 201130 237160 209560 220070 FALSE TRUE 183829.6359 181593.3074 191903.198 209371.5174 219424.8368 194164.8177 200976.8863 191209.8155 254197.3316 0.723176891 0.714379282 0.754937893 0.823657416 0.863206688 0.763834995 0.790633344 0.75221016 1 17.95558936 -5 0.167904176 1.866547735 0.713636671 0.72073764 0.044380212 74.07604469 0.695198597 21.4926976 0.173722634 1.00E-05 5 -1.152911064 EKSTFREES(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 EKS(0.15)T(0.089)FREES(0.761)PLR;EKSTFREES(1)PLR;EKSTFREES(0.999)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKS(0.008)T(0.003)FREES(0.99)PLR;EKS(0.031)T(0.031)FREES(0.937)PLR;EKS(0.013)T(0.013)FREES(0.973)PLR 174.59 1.56E-05 13550370000 10430320 7129280 9968630 9314100 9256230 9540790 12969730 11233050 12124640 TRUE FALSE 9937299.445 7855761.737 10425701.55 8377828.972 10870513.58 9210390.05 10990959.48 10249424.59 14004867.25 0.709560417 0.560930825 0.744434157 0.598208382 0.776195403 0.657656362 0.784795692 0.731847322 1 23.73942497 -0.315393888 0.294123214 1.116812818 0.629510348 0.698137153 0.065993666 3.737788924 0.404214465 0.514644366 0.072028713 0.483733441 0.315393888 -0.48730247 EKT(ph)PELPEPSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(0.991)PELPEPS(0.009)VK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(0.996)PELPEPS(0.004)VK;EKT(0.989)PELPEPS(0.011)VK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK 199.84 1.06E-06 7006926000 13415670 11100260 11162970 13476860 5452630 13874500 13135360 14228550 5706190 TRUE FALSE 12781537.87 12231389.11 11674803.22 12122140.43 6403566.946 13394022.59 11131319.58 12982622.73 6591076.802 1.939218469 1.855749748 1.771304381 1.839174507 0.971550953 2.032144821 1.688846894 1.969727121 1 22.65208275 2.957588797 24.99980822 1.603393518 1.859687398 0.154156885 0.350046233 1022.569193 602765.7787 0.098468071 0.104449154 906.9613857 -2.957588797 0.25629388 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 146.17 2.31E-07 2848780000 4744600 3972100 3444750 4706600 1065510 5328400 4261700 7611700 802070 TRUE FALSE 4520332.161 4376861.506 3602695.195 4233483.626 1251334.607 5143876.172 3611499.394 6945179.196 926450.9192 4.879192267 4.724331765 3.888705942 4.569571402 1.350675552 5.552238187 3.898209089 7.496543046 1 19.82135502 2.907304624 23.79284228 4.044372025 4.556189544 0.024257161 1.865330513 215.179457 55214.3921 0.519708173 0.551234037 807.8014418 -2.907304624 0.51181752 EKTGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKTGVR 6 1 P35227 P35227 PCGF2 Polycomb group RING finger protein 2 0 ; 70.268 0.083281 75418000 275470 210942 234770 274200 232040 247670 306440 297070 293880 FALSE TRUE 262449.079 232437.2296 245534.4367 246636.8951 272507.7025 239093.1258 259686.9498 271056.9759 339453.4095 0.77315199 0.684739711 0.723322936 0.726570681 0.802783813 0.704347398 0.765014999 0.7985101 1 18.37285405 0.408655935 0.841840384 1.002658284 0.731240432 0.857232868 0.033371848 0.688610071 0.684821377 0.033265259 0.010353606 2.562453156 -0.408655935 -0.271417851 EKTPSPKEEDEEPES(ph)PPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK 188.3 8.60E-15 1216515000 2068680 1832600 1789410 2229810 901371 2405540 2280660 2471200 876384 TRUE FALSE 1970897.596 2019344.023 1871456.218 2005665.262 1058569.817 2322235.547 1932703.43 2254808.627 1012289.155 1.946970969 1.994829258 1.848736806 1.981316557 1.045718817 2.294043689 1.909240478 2.22743533 1 19.94919002 EKTPSPKEEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK;EKTPSPKEEDEEPES(1)PPEKK 184.29 2.90E-17 19317040000 11967270 10397470 10633580 12379620 4175160 14194740 12805280 14776190 3706524 TRUE FALSE 11401600.86 11456984.01 11121140.16 11135197.08 4903306.582 13703172.59 10851599.35 13482308.47 4281312.812 2.663108576 2.676044596 2.597600468 2.600883787 1.145281085 3.200694086 2.534642954 3.149106142 1 22.02962182 2.970719283 24.9786558 2.348649433 2.647694052 0.061778564 0.720478701 2614.514267 2230378.448 0.202988939 0.215633652 934.8012461 -2.970719283 0.299044619 EKVESELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 EKVESELR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;;;;; 142.92 0.00055605 10121470000 22111050 22468970 19113480 23313810 16038640 22401740 22928460 23765910 16775820 FALSE TRUE 21065904.49 24758583.59 19989851.96 20970261.53 18835773.74 21625962.13 19430302.32 21684840.93 19377328.49 1.087141837 1.277708824 1.031610316 1.082206019 0.972052146 1.116044564 1.002733805 1.119083105 1 24.20786635 3.714831661 24.90469323 1.046398044 1.182425337 0.422812735 0.066147307 549.4762368 576702.3155 0.01581264 0.02451228 5185.989837 -3.714831661 0.136027294 EKVFDVIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKVFDVIIR 9 1 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 140.07 0.00010029 675910000 1445270 1339870 1283210 1473900 1236860 1329480 1591140 1496650 1342500 FALSE TRUE 1376954.951 1476404.276 1342046.448 1325740.772 1452567.992 1283439.774 1348382.37 1365595.392 1550688.043 0.887963867 0.952096253 0.865452245 0.854937121 0.936724829 0.827658264 0.869538122 0.880638371 1 20.56447705 -0.933015887 5.455586106 1.000000171 0.88693585 0.495052365 0.03661741 7.75E-08 1.51E-08 0.03609964 0.008508754 0.116676693 0.933015887 -0.113064321 EKVGEVTYVELLMDAEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKVGEVTYVELLMDAEGK 18 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 149.94 5.33E-08 153599000 469273 414406 421544 483933 297800 489215 532992 536880 321058 FALSE TRUE 447091.3953 456634.4425 440872.2094 435287.1354 349736.2257 472273.3619 451674.2813 489867.941 370846.0349 1.205598424 1.231331603 1.18882816 1.173767802 0.943076622 1.273502525 1.217956345 1.320946956 1 18.50046082 -2.303807796 2.33462132 2.19E-05 1.195306503 0.276309802 0.098850444 1815849.372 665050.4036 9513852.658 0.022993789 0.004968121 2.303807796 1.195284617 EKVIET(ph)PENDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EKVIETPENDFK 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 EKVIET(1)PENDFK;EKVIET(1)PENDFK;EKVIET(1)PENDFK 143.28 9.80E-05 1089240000 1358960 1381190 1179910 1528220 719230 1497170 1418810 1713250 768750 TRUE FALSE 1294724.654 1521934.831 1234010.041 1374600.422 844663.4843 1445322.627 1202344.476 1563228.747 887963.8238 1.45808266 1.713960401 1.389707562 1.548036514 0.95123637 1.627681882 1.35404669 1.760464453 1 19.76014138 3.709376939 22.85214992 1.393055039 1.586021514 0.100243289 0.257773431 494.1382318 386932.1471 0.061488679 0.095286497 5121.261346 -3.709376939 0.192966475 EKVLATVTKPVGGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 172.97 5.60E-07 1895220000 3575600 3299000 3119300 3938100 2095920 3808100 3909700 4285300 2572400 FALSE TRUE 3406588.474 3635171.851 3262322.99 3542234.706 2461447.784 3676224.542 3313203.458 3910056.414 2971314.654 1.146491998 1.223422045 1.097939253 1.192143922 0.82840361 1.237238384 1.115063144 1.31593482 1 21.50266996 3.727677575 24.05949845 1.116316628 1.184957023 0.048110415 0.133308813 1327.71135 2935216.558 0.032733821 0.051337023 5341.676396 -3.727677575 0.068640396 EKVPAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKVPAGR 7 1 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 ;;; 100.15 0.0091254 311391000 474390 418413 402241 477720 490540 442251 536410 454000 581480 FALSE TRUE 451966.5249 461049.7604 420684.1477 429698.678 576090.0207 426935.737 454570.8027 414245.3532 671652.9486 0.672916758 0.686440462 0.626341548 0.639762959 0.857719782 0.635649315 0.676794174 0.616755058 1 19.35735644 -1.403275962 5.211088139 1.000250115 0.67809941 0.688453198 0.068374227 0.00018334 2.10E-05 0.061090358 0.014388087 0.039511547 1.403275962 -0.322150705 EKVS(ph)SIDLEIDSLSSLLDDMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 1 EKVS(0.677)S(0.323)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK 281.59 1.62E-45 1487123000 859524 744221 720653 963150 427548 892111 891830 937409 399140 TRUE FALSE 818896.0039 820057.966 753695.6529 866332.3321 502112.2358 861216.9724 755764.9539 855324.4984 461036.5927 1.776206091 1.778726416 1.634784884 1.879096683 1.089094106 1.868001339 1.639273251 1.855220414 1 18.81452174 -1.878639834 2.640706784 0.668616562 1.693137829 0.470198185 0.230176197 12225943.73 6863364.966 25261711.48 0.049980822 0.013223919 1.878639834 1.024521266 EKYEITEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EKYEITEQR 9 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 147.72 8.37E-05 4964530000 10880180 11558400 9197500 12880190 7356810 10706860 10542730 11358910 7949090 FALSE TRUE 10365895.45 12736214.1 9619214.473 11585448.83 8639835.335 10336078.75 8934242.908 10364263.62 9181794.279 1.12896185 1.387116038 1.047639947 1.261784841 0.940974615 1.125714478 0.973038889 1.128784125 1 23.13034468 3.023087451 1.479856193 1.035789022 1.239595934 0.312491897 0.111964446 0.376475561 1.700020071 0.037306993 0.045272101 1054.599232 -3.023087451 0.203806912 EKYIDQEELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 207.47 2.09E-08 8188790000 15003510 13447720 12742750 15775880 8615700 15056060 16361250 16669470 9607020 FALSE TRUE 14294323.82 14818057.96 13327017.69 14190058.57 10118275.35 14534664.87 13865040.82 15209802.84 11096827.6 1.288145075 1.33534182 1.200975466 1.278749124 0.911816937 1.309803612 1.249459875 1.370644241 1 23.40364396 -2.136717907 2.396736152 0.474428272 1.247139464 0.266540351 0.126586911 4939824.294 1509749.801 14109211.64 0.029954197 0.007299315 2.136717907 0.772711192 ELAAQLNEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELAAQLNEEAKR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 130.78 0.00033733 270810000 521540 422700 468650 539470 525870 501650 631390 540320 720110 FALSE TRUE 496887.8378 465773.6106 490138.0661 485241.4507 617581.5615 484277.7347 535059.8592 493006.7164 831780.981 0.597378215 0.55997146 0.589263373 0.583376468 0.742480984 0.58221785 0.643270129 0.592712177 1 19.66584417 -5 0.300417425 4.258450461 0.588455568 0.849524619 0.051363484 93.20952483 0.861010304 191.3070666 0.047911946 1.00E-05 5 -3.669994893 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(ph)SPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(0.5)S(0.5)PVR;ELAEAAKEPLPVEQDDDIEVIVDET(0.006)S(0.006)DHT(0.025)EET(0.481)S(0.481)PVR 265.07 2.94E-62 56125000 50970 39246.2 47197.9 50043.5 35871.3 43515.8 61636.4 57390.1 47203.9 TRUE FALSE 48560.74911 43245.4324 49361.9704 45013.0323 42127.24336 42008.83693 52232.63515 52364.7186 54524.03973 0.890630066 0.79314432 0.905324892 0.825563046 0.772636136 0.770464499 0.957974417 0.960396898 1 15.73460484 1.634285724 5.883222475 0.973272299 0.828675251 0.69905405 0.045354348 0.079613484 5.824595571 0.024127316 0.011691185 43.08099489 -1.634285724 -0.144597049 ELAEDGYSGVEVR ddPTM_SK-BR-3_Trastuzumab_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 ; 149.49 9.71E-05 231176000 171757 138607 153547 174921 144069 157448 181718 180607 173018 FALSE TRUE 163638.387 152731.2109 160587.2818 157337.6088 169194.588 151995.5363 153993.5816 164792.0936 199848.7478 0.81881117 0.764234015 0.803544098 0.787283436 0.846613201 0.760552858 0.770550646 0.824584069 1 17.60854901 0.857878762 5.072752641 0.999996159 0.791434663 0.860096892 0.026021526 0.533806003 18.79038376 0.023902801 0.006039076 7.209062022 -0.857878762 -0.208561496 ELAGHTGYLSCCR ddPTM_SK-BR-3_Trastuzumab_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 ; 182.1 1.15E-05 1040660000 961090 757120 588330 685790 1158660 554790 1067520 795770 1067160 FALSE TRUE 915661.1804 834271.3888 615305.5124 616853.0863 1360729.937 535577.4832 904650.2177 726088.1602 1232649.723 0.742839725 0.676811404 0.499173043 0.500428528 1.103906416 0.434492844 0.733906966 0.589046626 1 20.23333146 -1.24598109 4.712164671 1.000093691 0.665220694 0.244283644 0.187701931 0.000164614 2.63E-05 0.161932407 0.038157196 0.056756932 1.24598109 -0.334872997 ELAILLGMLDPAEKDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELAILLGMLDPAEKDEK 17 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 156 8.33E-08 414868000 654084 599616 571889 691303 349568 673607 682473 745767 363912 FALSE TRUE 623166.7456 660717.5521 598110.6763 621811.9091 410532.5485 650279.8207 578349.2094 680463.6879 420345.6144 1.482510402 1.571843572 1.422902145 1.479287253 0.976654768 1.547012264 1.375889719 1.618819525 1 18.6812165 -1.934841947 2.529763242 0.700792374 1.437344371 0.371944301 0.177347638 8650498.834 4024797.669 15253661.78 0.042971139 0.011618714 1.934841947 0.736551997 ELALGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELALGQDR 8 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ;;;; 149.19 0.0011847 1602250000 2136160 1640010 1506690 1677730 2426740 1542200 2273340 1803370 2493310 FALSE TRUE 2035187.95 1807128.884 1575773.227 1509081.393 2849962.688 1488793.227 1926500.23 1645457.363 2879959.781 0.706672351 0.62748407 0.547151123 0.523993912 0.989584197 0.516949312 0.668933033 0.571347341 1 21.45761723 -1.917875778 2.64799939 1.214398599 0.646128575 0.399186238 0.137229696 13225943.35 7656224.6 17596814.84 0.030717161 0.012081594 1.917875778 -0.568270024 ELAMPGEDLKFNLILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELAMPGEDLKFNLILR 16 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 190.82 7.25E-10 320140000 849060 554890 669580 655200 720520 615160 844790 782990 723010 FALSE TRUE 808926.6165 611433.9219 700280.9053 589338.0512 846178.4599 593856.855 715901.7699 714427.2447 835130.6982 0.968622778 0.732141596 0.838528516 0.705683616 1.013228782 0.71109451 0.857233211 0.855467589 1 19.67164247 0.685218746 2.002360484 0.999877925 0.828893608 0.209866084 0.10149138 2.136239964 11.52560079 0.085905675 0.023701562 4.844162971 -0.685218746 -0.170984316 ELAPLFEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELAPLFEELR 10 0 Q9UHA4;Q9UHA4-2 Q9UHA4 LAMTOR3 Ragulator complex protein LAMTOR3 0 74.464 0.097506 9527500 27881 29643 21114 29810 24413 19756 27732 26427 26541 FALSE TRUE 26563.12038 32663.6554 22082.09778 26813.44216 28670.61947 19071.84477 23500.97407 24112.91178 30656.84273 0.866466277 1.065460514 0.720299151 0.87463156 0.935211095 0.622107271 0.766581682 0.786542567 1 14.9039215 3.734221399 24.99713277 0.799060683 0.965963395 0.214530677 0.116976422 426.4365543 2456593.323 0.029153826 0.046957112 5422.772671 -3.734221399 0.166902712 ELAPYDENWFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ELAPYDENWFYTR 13 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;;; 322.07 9.05E-51 3647044000 500181 484388 395861 503683 390606 450096 498604 470351 395123 FALSE TRUE 476538.4354 533747.6879 414011.6184 453051.8279 458727.5627 434509.0627 422532.8023 429164.573 456396.6568 1.044132178 1.169482028 0.907131137 0.992671224 1.005107193 0.952042606 0.925801703 0.94033242 1 18.7999287 3.73581169 24.999879 0.958061746 1.106807105 0.661777832 0.043475927 120.099117 1092231.397 0.011112543 0.018103269 5442.666077 -3.73581169 0.148745358 ELAQIAGRPTEDEDEKEKVADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELAQIAGRPTEDEDEKEKVADEDDVDNEEAALLHEEATMTIEELLTR 47 3 O15355 O15355 PPM1G Protein phosphatase 1G 0 111 5.65E-08 33306000 60034 45215 53435 64121 30025 63667 76955 73449 23436 FALSE TRUE 57196.3118 49822.45991 55885.0476 57675.43526 35261.35049 61462.19583 65214.10137 67017.41618 27070.33519 2.112877857 1.840481825 2.064438701 2.130577064 1.302582707 2.270463051 2.409061466 2.475677369 1 14.72442513 4.761724127 20.04841419 2.005185755 2.112879468 0 0.472024095 715.5818251 1222990.168 0.104027539 1.333218304 57772.8945 -4.761724127 0.107693713 ELAQPSGGHLPQAS(ph)PISVYLFPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELAQPSGGHLPQASPISVYLFPGER 25 0 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 ELAQPSGGHLPQAS(0.998)PIS(0.002)VYLFPGER;ELAQPSGGHLPQAS(1)PISVYLFPGER;ELAQPSGGHLPQAS(0.999)PIS(0.001)VYLFPGER 215.3 1.12E-33 137379000 114137 111557 117018 133845 145488 119685 139606 129908 156113 TRUE FALSE 108741.9702 122924.7851 122383.391 120390.6463 170861.0611 115540.2784 118306.5407 118532.5668 180322.2067 0.603042588 0.681695213 0.678692842 0.66764182 0.947532 0.640743481 0.656084144 0.657337601 1 17.46021755 -2.438912953 2.189805145 3.859063183 0.687351999 0.5154279 0.093895973 2647166.318 235905.6114 37604539.72 0.022076435 0.00363988 2.438912953 -3.171711184 ELAQQVQQVAAEYCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELAQQVQQVAAEYCR 15 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 130.61 0.00013646 27103000 44266 38153 37053 43614 49650 34925 50700 37855 54784 FALSE TRUE 42173.63391 42040.83408 38751.9167 39229.83786 58308.94428 33715.53849 42964.78383 34540.21552 63279.62292 0.666464684 0.664366065 0.612391713 0.619944242 0.921448984 0.532802456 0.678967128 0.545834724 1 15.94945338 -1.239100779 5.133527652 1.000042403 0.658419278 0.5091414 0.106333159 4.60E-05 6.82E-06 0.091864509 0.021649991 0.057663264 1.239100779 -0.341623125 ELAVEGMHR ddPTM_SK-BR-3_Trastuzumab_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" 0 121.73 0.0006056 72646000 88955 97587 76865 88670 86090 76112 84288 90500 73151 FALSE TRUE 84750.27344 107531.2262 80389.33628 79756.72314 101104.0687 73476.22236 71428.31754 82575.34023 84494.88348 1.003022549 1.272635949 0.951410701 0.943923701 1.196570308 0.869593747 0.84535672 0.977282136 1 16.36657636 2.737530019 0.87162323 0.910952031 1.114499371 0.153466589 0.12249372 0.761585862 1.237029542 0.074623845 0.069501725 546.424318 -2.737530019 0.20354734 ELCGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELCGER 6 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 97.473 0.095458 179530000 192410 187810 163290 223730 181990 188710 200040 194200 234150 FALSE TRUE 183315.1606 206948.0525 170777.008 201240.2353 213728.9984 182174.9254 169520.224 177194.8185 270460.7861 0.677788315 0.76516842 0.631429829 0.744064373 0.790240247 0.673572417 0.626783004 0.655159001 1 18.04505991 -1.139268167 4.249974579 1.000065934 0.696854147 0.750084514 0.055227756 2.772616206 32216543.56 4253.307658 0.013312096 0.072565774 1.139268167 -0.303211787 ELCQQIHAECKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELCQQIHAECKR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 180.28 1.27E-05 343650000 380280 323720 368770 384300 342960 379730 468850 411970 364990 FALSE TRUE 362304.918 356707.436 385678.4693 345669.4339 402772.1154 366579.8549 397318.3215 375895.7228 421590.7851 0.8593758 0.846098749 0.914817123 0.819916958 0.955362711 0.869515815 0.942426484 0.891612758 1 18.68548381 -4.999999704 0.071576062 1.422652032 0.739125773 0.52071265 0.037956416 196.6941654 1.01102069 13.4164348 1.598800419 1.00E-05 4.999999704 -0.683526258 ELCTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELCTSPR 7 0 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 ELCT(0.014)S(0.986)PR;ELCT(0.006)S(0.994)PR 71.708 0.056207 353610000 946980 824360 824200 1026180 1020810 871820 1036290 876300 1033130 TRUE FALSE 902218.1321 908363.2212 861990.3852 923026.4368 1198838.941 841628.6548 878184.9277 799566.5264 1193342.524 0.756042891 0.761192368 0.722332749 0.773479884 1.0046059 0.705269977 0.73590349 0.670022655 1 20.18657677 -2.067142685 2.322044132 1.334812733 0.7661193 0.400389911 0.089952653 7512299.366 2204873.053 13336199.24 0.021143715 0.008567563 2.067142685 -0.568693433 ELDALDANDELTPLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 257.91 2.54E-26 91177000 535755 447552 489532 561458 466475 561128 616130 560235 549960 FALSE TRUE 510430.9229 493158.0576 511977.5264 505019.1751 547828.0923 541695.9967 522128.0525 511177.8534 635244.988 0.803518221 0.776327349 0.805952878 0.794999071 0.862388689 0.85273557 0.821931794 0.804694036 1 19.27695356 -5 0.210096091 1.893448739 0.786555004 0.844400756 0.025034354 54.72428084 0.545300932 20.60560265 0.053728313 1.00E-05 5 -1.106893735 ELDALGHELPVLAPQWEGYDELQTDGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 136.53 7.75E-06 54242000 28335 29901 27819 30882 30473 27097 31819 33734 32399 FALSE TRUE 26995.6607 32947.94589 29094.52867 27777.68269 35787.48155 26158.6241 26964.42715 30780.07212 37423.27145 0.721360257 0.8804133 0.777444824 0.742256933 0.9562895 0.698993516 0.720525654 0.822484805 1 15.19164806 0.970204018 23.06195907 1.000000002 0.786002726 0.419467545 0.078834829 1270.367673 983260.9908 0.072603534 0.018150883 9.33692817 -0.970204018 -0.213997276 ELDDLEQWIQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELDDLEQWIQER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 186.81 2.62E-05 25033000 53074 42461 45189 69613 59495 50513 62510 51479 58375 FALSE TRUE 50565.2972 46787.82417 47260.96035 62615.36898 69870.90916 48763.72214 52972.95143 46971.22585 67427.49686 0.74992102 0.693898281 0.700915243 0.928632559 1.036237624 0.72320232 0.785628325 0.696618265 1 16.04104942 -2.736552068 2.195612034 9.927862055 0.784482155 0.259416352 0.11156468 4077232.892 346486.9878 187041073.7 0.028350948 0.001834205 2.736552068 -9.1433799 ELDDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELDDTR 6 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 129.16 0.037954 1468240000 4460900 3836040 3919720 4445300 4136770 3983250 4919700 4341100 4486200 FALSE TRUE 4250042.098 4226936.837 4099443.039 3998449.998 4858221.378 3845309.054 4169109.409 3960970.27 5181896.984 0.82017109 0.815712248 0.791108556 0.771618967 0.937537237 0.742065901 0.804552738 0.764386147 1 22.3050489 -0.985195261 4.34332688 1.000007131 0.807046751 0.574144696 0.052528213 8652978.246 27392872.04 1045.476518 0.01139674 0.103467687 0.985195261 -0.19296038 ELDEEGS(ph)DPPLPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR 139.3 1.09E-05 193758000 606040 627120 575730 673850 574430 608810 689800 690540 600860 TRUE FALSE 577393.6903 691024.241 602127.79 606113.3178 674610.4101 587726.757 584558.341 630072.6568 694038.3 0.831933469 0.995657215 0.867571415 0.873313933 0.972007467 0.846821792 0.842256603 0.907835572 1 19.40465575 ELDEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELDEGR 6 0 O15541 O15541 RNF113A RING finger protein 113A 0 101.33 0.085259 638030000 1101400 848450 884830 1040700 908460 895020 1070600 940980 972950 FALSE TRUE 1049339.005 934908.0196 925400.3307 936086.8588 1066895.136 864025.233 907260.3071 858582.8028 1123830.117 0.93371675 0.831894435 0.823434358 0.832943382 0.949338446 0.768821924 0.807293107 0.763979173 1 20.09999254 2.214209922 24.99831094 0.815923343 0.869703552 0.03313491 0.077629136 517.6604964 531424.4541 0.026244762 0.019392017 163.7607889 -2.214209922 0.053780209 ELDGERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELDGERER 8 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A590UJB9;A0A590UK79;A0A5F9UKJ4 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;; 139.78 0.000602 1478850000 2280260 1569810 2172230 2035680 2552910 1954620 2836580 2330950 3020150 FALSE TRUE 2172476.629 1729775.424 2271828.894 1831049.579 2998136.696 1886931.019 2403807.624 2126839.661 3488499.437 0.6227539 0.495850854 0.651233843 0.524881718 0.859434479 0.54090048 0.689066364 0.60967178 1 21.73417517 -5 0.204329689 2.779154597 0.558664575 0.577935658 0.101407167 92.88261437 0.922086814 67.52960041 0.205228302 1.00E-05 5 -2.220490021 ELDGHVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 72.485 0.046033 75065000 208710 181520 168630 199180 177610 191930 240640 213140 177920 FALSE TRUE 198844.6919 200017.0944 176361.8523 179158.048 208585.1278 185283.416 203925.9483 194476.3317 205510.9249 0.967562634 0.973267453 0.858162905 0.871768973 1.014958829 0.901574532 0.992287629 0.946306537 1 17.64885556 1.32820228 0.90845155 0.993781771 0.936029613 0.148313603 0.04979875 1.136278927 1.986817863 0.046128609 0.016943455 21.29130492 -1.32820228 -0.057752158 ELDGLWSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELDGLWSFR 9 0 F8WBK6;F2Z3L6;P08236-3;P08236-2;P08236 F8WBK6 GUSB Beta-glucuronidase 0 81.642 0.048166 18807000 24894 18770 17875 19490 24947 14299 24778 21073 24815 FALSE TRUE 23717.30996 20682.68434 18694.58643 17530.82817 29297.7489 13803.82204 20997.66102 19227.73641 28663.18346 0.827448563 0.721576665 0.652215985 0.611614833 1.022138694 0.481587192 0.732565559 0.6708165 1 14.80691123 -1.655110498 7.365161865 1.000815284 0.717202314 0.287965638 0.140804697 0.001692754 7.93E-05 0.122429676 0.028779504 0.022125317 1.655110498 -0.28361297 ELDLFLAYYVQEQDSGQS(ph)GSPSHNDPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.154)GQS(0.362)GS(0.362)PS(0.122)HNDPAK;ELDLFLAYYVQEQDS(0.087)GQS(0.413)GS(0.413)PS(0.087)HNDPAK 122.08 3.03E-05 68587000 27968 31287 24282 33458 19087.2 26009 23517 33521 18379.1 TRUE FALSE 26646.00807 34475.18087 25395.35372 30094.73827 22416.00164 25108.30181 19929.04973 30585.72353 21229.23696 1.255156185 1.623948187 1.196244301 1.4176081 1.055902371 1.182722764 0.938754877 1.440735887 1 14.3737649 2.74206431 24.93321962 1.109739942 1.392070651 0.334633152 0.173389393 287.8359914 2048322.172 0.049852848 0.050965412 552.1591966 -2.74206431 0.282330709 ELDLFLAYYVQEQDSGQSGSPS(ph)HNDPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ELDLFLAY(0.001)Y(0.001)VQEQDS(0.228)GQS(0.228)GS(0.228)PS(0.316)HNDPAK;ELDLFLAYYVQEQDS(0.235)GQS(0.235)GS(0.235)PS(0.295)HNDPAK 77.19 0.0049587 14394300 11268.2 11802.3 11541.5 14218.4 10382.5 12504 13444.3 14390.2 11244 TRUE FALSE 10735.57452 13004.96779 12070.68919 12789.13942 12193.20471 12070.98334 11393.12511 13130.1178 12987.66209 0.826597923 1.001332472 0.929396615 0.984714518 0.938829839 0.929419264 0.877226789 1.010968541 1 13.66485413 7.999997201 0.010592612 1.758890622 4.10E-06 0.202259916 0.052637946 23314.14515 19.09689624 1353.918342 1853.380307 99999355.5 -7.999997201 -1.758886523 ELDRNELFEK ddPTM_SK-BR-3_Trastuzumab_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 90.689 0.0097219 182130000 150250 118600 129670 168670 129800 121190 137780 139160 144160 FALSE TRUE 143147.9803 130685.4748 135615.4978 151714.9711 152437.0789 116993.1599 116759.1305 126974.4127 166515.5965 0.859667102 0.78482423 0.814431204 0.911115681 0.915452258 0.702595807 0.701190357 0.762537656 1 17.34529779 2.23366643 24.99995393 0.757374668 0.847992054 0.053359675 0.093594525 203.3811007 1038877.348 0.03192554 0.024323545 171.2641366 -2.23366643 0.090617387 ELDRYS(ph)LDSEDLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.998)LDS(0.002)EDLYSR;ELDRYS(0.968)LDS(0.032)EDLYSR 276.14 9.48E-34 177090000 234150 210520 213520 267080 297350 219680 271100 221570 304440 TRUE FALSE 223082.1935 231972.2273 223310.1032 240232.611 349207.7459 212072.4265 229738.7159 202168.1562 351651.0003 0.63438521 0.659666053 0.635033323 0.683156342 0.993052047 0.60307642 0.653314552 0.574911364 1 18.4237848 -2.174822631 2.452203533 1.864268945 0.677963812 0.431486436 0.115575856 4705980.074 1485777.322 22528771.84 0.028311131 0.006686169 2.174822631 -1.186305133 ELDTVTLEDIKEHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELDTVTLEDIKEHVK 15 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 269.23 4.38E-26 403001000 1327150 1127960 1241520 1339080 832830 1394990 1526370 1483770 773910 FALSE TRUE 1264418.25 1242900.406 1298444.92 1204473.134 978075.2883 1346681.147 1293494.223 1353843.233 893924.0102 1.414458315 1.390387094 1.452522703 1.347399914 1.094136948 1.506482801 1.44698454 1.514494764 1 19.76979267 3.212259041 23.08893707 1.349991729 1.412298729 0.053417217 0.16700754 402.6634141 353476.8875 0.045913866 0.054902176 1630.26814 -3.212259041 0.062306999 ELEAIFGRPVVDGEEGEPHSIS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR;ELEAIFGRPVVDGEEGEPHS(0.027)IS(0.973)PR;ELEAIFGRPVVDGEEGEPHS(0.003)IS(0.997)PR;ELEAIFGRPVVDGEEGEPHS(0.002)IS(0.998)PR;ELEAIFGRPVVDGEEGEPHS(0.214)IS(0.786)PR;ELEAIFGRPVVDGEEGEPHS(0.027)IS(0.973)PR 249.97 1.34E-38 801848000 833221 880918 750213 926181 765765 771182 711764 736534 538059 TRUE FALSE 793836.2946 970684.5457 784611.0081 833079.5263 899314.1735 744475.774 603171.3294 672039.1783 621498.4417 1.277294103 1.561845502 1.262450483 1.340437031 1.447009539 1.19787231 0.970511411 1.081320778 1 19.24539125 2.003882785 3.585464476 1.021636056 1.386045787 0.772262176 0.089357049 0.102051168 2.745543571 0.03938539 0.024359174 100.8980529 -2.003882785 0.364409731 ELEAIFGRPVVDGEEGEPHSISPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;; 214.16 1.11E-27 267311000 268039 250613 244648 289650 287657 251857 280864 286923 248718 FALSE TRUE 255369.3277 276150.7496 255865.3528 260533.8317 337824.2897 243135.1289 238013.0384 261798.501 287287.9172 0.888896861 0.961233429 0.890623439 0.906873614 1.175908451 0.846311712 0.828482592 0.911275711 1 18.13213779 -0.954140504 5.847825945 1.000000059 0.922344194 0.053902031 0.095965807 7.25E-08 1.31E-08 0.090974079 0.02144278 0.111137212 0.954140504 -0.077655865 ELEAMGLGT(ph)PSEAIEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ELEAMGLGTPSEAIEIR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ELEAMGLGT(0.999)PS(0.001)EAIEIR;ELEAMGLGT(0.997)PS(0.003)EAIEIR;ELEAMGLGT(0.931)PS(0.069)EAIEIR;ELEAMGLGT(0.969)PS(0.031)EAIEIR;ELEAMGLGT(0.828)PS(0.172)EAIEIR;ELEAMGLGT(0.963)PS(0.037)EAIEIR;ELEAMGLGT(0.787)PS(0.213)EAIEIR;ELEAMGLGT(0.995)PS(0.005)EAIEIR;ELEAMGLGT(0.5)PS(0.5)EAIEIR 346.18 1.04E-62 533246800 1319851 1180409 1143853 1340449 1303993 1238957 1379254 1382434 1351061 TRUE FALSE 1257464.259 1300694.019 1196299.791 1205704.52 1531408.966 1196051.608 1168823.471 1261380.75 1560576.64 0.805768988 0.833470133 0.766575483 0.772601928 0.981309682 0.76641645 0.748968965 0.808278631 1 20.57364778 -0.896272458 4.330337932 1.00000264 0.808462599 0.450958326 0.065706984 3780214.508 1309476.99 109.3642119 0.014869949 0.126977725 0.896272458 -0.191540041 ELEAMGLGTPS(ph)EAIEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEAMGLGTPSEAIEIR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ELEAMGLGT(0.402)PS(0.598)EAIEIR 216.17 5.64E-15 101760000 265160 257670 254410 304080 280900 269580 312570 307340 302070 TRUE FALSE 252626.4123 283926.8659 266074.9501 273513.3007 329888.8711 260244.377 264881.7058 280427.6803 348913.4728 0.724037425 0.81374578 0.762581473 0.783900084 0.945474729 0.745870817 0.759161587 0.803716973 1 18.41250978 0.946531426 20.72266662 1.000000001 0.788412092 0.539621776 0.060376133 1439.478976 557896.8767 0.055786309 0.013946577 8.841611464 -0.946531426 -0.211587908 ELEDAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEDAKK 7 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 91.041 0.02677 193090000 588330 547400 660080 906940 543470 847820 993440 1020500 688000 FALSE TRUE 560520.8069 603180.6823 690345.3209 815772.6681 638250.9959 818459.7808 841872.4822 931139.61 794691.5262 0.705331299 0.759012349 0.868695963 1.026527453 0.803143075 1.029908781 1.059370151 1.171699432 1 19.60003544 3.367744055 0.515499746 1.088727071 0.644243978 0.684062987 0.083496138 0.668074748 0.334438182 0.061828929 0.154181816 2332.083278 -3.367744055 -0.444483093 ELEDAYWKDDDKHVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEDAYWKDDDKHVMR 16 2 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 137.73 6.28E-06 129300000 404150 323030 355620 435450 254660 439570 457270 447700 210790 FALSE TRUE 385046.6304 355947.1243 371925.5288 391677.7387 299072.6234 424347.5807 387505.0632 408497.0146 243478.2366 1.581441675 1.461925834 1.527551431 1.608676587 1.228334111 1.742856308 1.591538811 1.677755763 1 17.8934333 ELEDYIDNLLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 141.08 0.0001401 64556000 185820 142230 154682 194379 183059 162436 187625 174176 191788 FALSE TRUE 177036.6569 156723.3987 161774.3227 174839.6536 214984.4316 156810.8006 158999.3603 158924.2261 221529.5035 0.799156113 0.707460615 0.730260846 0.789238683 0.970455078 0.707855153 0.717734468 0.717395306 1 17.75713933 -2.299682535 2.327489612 2.178814873 0.763484344 0.459819935 0.07911101 5807913.178 854178.0914 36065196.88 0.019402843 0.005015537 2.299682535 -1.415330529 ELEEEEENS(ph)DEDELDSHTMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK 314.05 8.09E-67 1734440000 1435720 1135000 1152020 1393930 917846 1309840 1464480 1444960 882326 TRUE FALSE 1367856.361 1250657.79 1204841.257 1253809.508 1077918.052 1264479.912 1241046.679 1318431.642 1019152.61 1.342150673 1.227154578 1.182199059 1.230247066 1.057661082 1.240716945 1.217724085 1.293654777 1 19.95893867 -4.984423767 0.209320142 8.03E-32 1.256488019 0.448315331 0.075572852 140.2112188 1.404918581 59.53716174 0.160847003 1.04E-05 4.984423767 1.256488019 ELEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELEEER 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q14980;Q9ULV0 NUMA1;MYO5B Nuclear mitotic apparatus protein 1;Unconventional myosin-Vb 0 ; 116.11 0.05549 544020000 972610 871290 884410 1036870 947950 909850 1084100 986610 996940 FALSE TRUE 926636.6528 960075.4416 924961.0733 932641.8577 1113272.18 878341.6664 918700.6341 900217.1981 1151540.364 0.804693159 0.833731471 0.803238082 0.809908091 0.966767831 0.762753694 0.797801504 0.781750451 1 20.13513355 -1.805185433 2.437116475 1.060404 0.819751717 0.510586305 0.055357639 23191729.77 14916324.25 8265644.058 0.012834342 0.015660822 1.805185433 -0.240652283 ELEEEWVKLPTSAPRPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEEEWVKLPTSAPRPTR 18 2 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 77.468 0.0076078 44699000 55001 37932 53443 52300 57873 53475 67631 60812 81779 FALSE TRUE 52401.21173 41797.31393 55893.41441 47042.70464 67966.03288 51623.14734 57312.64882 55486.9789 94460.86965 0.554739883 0.442482841 0.591709717 0.498012614 0.719515214 0.546502986 0.606734291 0.58740703 1 16.5274292 -4.999999999 0.206120084 3.078300031 0.493443065 0.802865065 0.068188416 56.12607871 0.557909546 48.07332014 0.139306407 1.00E-05 4.999999999 -2.584856966 ELEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELEELKR 7 1 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 0 ;;;; 138.48 0.0044601 3708460000 4597050 3644780 3883110 4694000 3549560 4294410 5096400 4720520 4037830 FALSE TRUE 4379756.557 4016187.226 4061154.434 4222150.202 4168602.14 4145693.505 4318850.578 4307166.244 4663996.054 0.93905666 0.861104336 0.870745684 0.905264531 0.893783376 0.888871572 0.925997906 0.923492686 1 22.15313514 0.736332277 0.807262558 1.000113656 0.891665256 0.700233834 0.021600601 0.556911714 0.696471855 0.020837273 0.007279857 5.449194092 -0.736332277 -0.108448399 ELEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 100.07 0.088599 264930000 598850 582850 536410 642370 522600 534580 577240 550340 537350 FALSE TRUE 570543.5473 642243.0776 561004.9291 577797.7472 613741.2745 516067.3606 489171.4363 502149.3121 620679.4936 0.919224097 1.034741899 0.903856072 0.930911611 0.988821575 0.831455471 0.788122439 0.809031581 1 19.24348896 2.230945129 24.87786127 0.833704418 0.959550335 0.311865411 0.068641225 140.8274186 460043.2847 0.023275678 0.0175205 170.1943464 -2.230945129 0.125845918 ELEELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELEELRK 7 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 0 ; 91.906 0.025751 574597000 642570 559270 589580 849110 601370 788760 881580 810300 757510 FALSE TRUE 612196.9896 616260.2488 616612.8262 763755.8496 706248.7376 761445.0434 747078.7797 739345.8363 874980.782 0.699669069 0.704312896 0.704715851 0.872883 0.807159142 0.87024202 0.853823073 0.844985229 1 19.7388918 6.688485684 0.093926723 1.143478914 5.12E-07 0.817401628 0.040476755 39.49655113 0.351272011 0.693805478 5.85406722 4880740.127 -6.688485684 -1.143478403 ELEEQLENETLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEEQLENETLHK 13 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 93.348 0.0056552 37440000 32693 33554 29173 41479 28899 31899 35267 34610 24519 FALSE TRUE 31147.66668 36973.19075 30510.61091 37309.45212 33938.97645 30794.32963 29886.37143 31579.36492 28321.28129 1.099797229 1.305491456 1.077303339 1.317364554 1.198355968 1.087321202 1.055261982 1.115040121 1 14.78959892 2.205764376 4.403210954 1.065447077 1.20544471 0.418035121 0.079594776 0.188950556 8.243869043 0.027755618 0.020758701 160.6069651 -2.205764376 0.139997633 ELEEWYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELEEWYAR 8 0 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;;;;; 163.67 0.00077834 2319350000 3571020 3025290 2960900 3563480 3246050 2948460 3577930 3312050 3211180 FALSE TRUE 3402224.962 3333570.49 3096660.194 3205272.22 3812160.092 2846354.091 3032051.065 3022029.344 3709153.394 0.917251081 0.898741609 0.834869811 0.864151972 1.027770946 0.76738646 0.817450977 0.814749088 1 21.8226585 2.19370882 24.99999537 0.830434424 0.902642213 0.097554417 0.078246543 221.3606946 123383.0821 0.026565611 0.019620091 156.2099955 -2.19370882 0.07220779 ELEFYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ELEFYLR 7 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;;;;;;; 187.14 0.0013693 5513593000 4212020 3427454 2829448 3307371 4192010 2828293 4299040 3630554 4129430 FALSE TRUE 4012926.162 3776715.459 2959180.99 2974907.783 4923095.217 2730348.504 3643142.491 3312643.445 4769800.914 0.841319425 0.791797295 0.620399267 0.623696426 1.032138512 0.572423997 0.763793407 0.694503503 1 22.18549762 -1.816466504 7.271171193 1.011672275 0.747849998 0.272134181 0.132085822 0.023089743 0.000582814 0.118152645 0.027632373 0.015259261 1.816466504 -0.263822276 ELEFYLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELEFYLRK 8 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 109.86 0.0056706 158690000 324140 173320 245460 217410 322690 243090 435340 329280 427430 FALSE TRUE 308818.5446 190981.505 256714.5838 195555.5337 378967.0338 234671.7323 368920.8874 300446.4976 493713.6614 0.625501315 0.386826454 0.519966539 0.396090992 0.767584662 0.475319503 0.747236539 0.608544023 1 18.91331504 0.549036396 0.404988434 1.042345958 0.482192977 0.600130224 0.118801693 1.349759221 0.445602929 0.229916549 0.078430311 3.540270093 -0.549036396 -0.560152981 ELEIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELEIEER 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 86.833 0.046031 352470000 758610 727490 741110 830520 1243900 669820 832750 767850 1133070 FALSE TRUE 722752.0087 801622.0581 775090.6266 747034.5517 1460835.766 646623.9654 705698.693 700612.9834 1308780.709 0.552233085 0.612495319 0.59222345 0.570786647 1.116180699 0.494065936 0.539203159 0.535317321 1 20.31979196 ELELAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELELAHR 7 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 132.09 0.0094701 0 71901 76331 60871 73614 82274 68775 73797 82831 75742 FALSE TRUE 68502.38222 84109.21568 63661.99556 66214.18086 96622.55955 66393.30451 62537.91228 75577.87853 87487.68252 0.782994591 0.961383514 0.727668098 0.756840037 1.104413293 0.758887452 0.714819623 0.863868791 1 16.41679229 -0.399365388 7.48852194 0.999998532 0.832696322 0.158752479 0.120166671 0 0 0.112191312 0.026443746 0.398689329 0.399365388 -0.16730221 ELELVEDVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELELVEDVWR 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4 A0A1B0GVV3 RILPL1 RILP-like protein 1 0 99.653 0.010582 3311200 9921.3 9300.6 8383.7 10406 8590.7 9882 11818 11542 10518 FALSE TRUE 9452.339811 10248.34171 8768.100938 9359.96911 10088.91536 9539.783862 10014.94705 10531.32129 12149.07772 0.778029413 0.843548947 0.721709181 0.770426309 0.83042644 0.785227001 0.824338051 0.866841215 1 13.56855918 0.785506965 1.061553439 1.000193039 0.790295275 0.805716493 0.03291352 0.345153353 0.725157631 0.030550733 0.009748137 6.102488429 -0.785506965 -0.209897763 ELELVQNAFFTDPNDQSAWFYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELELVQNAFFTDPNDQSAWFYHR 23 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 181.83 4.13E-17 89609000 119340 118110 124520 124340 126900 122840 144210 131990 116590 FALSE TRUE 113699.0347 130145.5433 130229.3652 111841.107 149031.3198 118586.02 122208.1159 120432.2559 134670.1817 0.844277725 0.966402077 0.9670245 0.830481592 1.106639331 0.880566273 0.907462323 0.894275587 1 17.03907092 4.636926671 3.213918094 0.938383716 0.840209455 0.141887868 0.075758869 0.549493996 9.303860288 0.016771272 0.116199561 43343.76874 -4.636926671 -0.098174261 ELELVYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELELVYAR 8 0 Q14764 Q14764 MVP Major vault protein 0 ;; 121.62 0.0033163 72009000 151426 115935 107971 138609 158219 114826 159163 132551 163989 FALSE TRUE 144268.3931 127748.9083 112921.5771 124675.76 185812.3435 110849.5468 134879.7611 120944.1317 189419.5766 0.761634017 0.674422943 0.596145231 0.658198916 0.980956387 0.585206391 0.71206875 0.638498586 1 17.53122592 -1.515979815 5.760605442 1.00048574 0.701700348 0.412990026 0.112065012 0.000643664 5.41E-05 0.099901374 0.02350968 0.030480367 1.515979815 -0.298785392 ELESQISELQEDLESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 271.53 3.03E-35 161783000 267242 238218 187381.9 276666 228910.3 245289 288587 250374 253481 FALSE TRUE 254610.0003 262492.685 195973.5455 248855.008 268832.1838 236794.5804 244557.7529 228449.9252 292789.5389 0.869600742 0.896523442 0.669332471 0.849945012 0.918175509 0.808753555 0.835268069 0.780253031 1 18.15950448 -1.966088519 2.765834834 1.133147424 0.834752244 0.374068233 0.069306424 18731857.89 10161828.1 15976933.51 0.016711178 0.010812136 1.966088519 -0.29839518 ELEVQHPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELEVQHPAAK 10 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 113.69 0.0014551 3065150000 7828680 7073430 6960490 8268530 6025460 7736970 8824470 8218870 6629750 FALSE TRUE 7458633.811 7794220.559 7279635.351 7437361.655 7076298.316 7469036.789 7478135.029 7499182.172 7657857.77 0.973984375 1.017806911 0.950609892 0.971206554 0.924057162 0.975342846 0.976530938 0.979279375 1 22.86850943 -0.459274211 6.51520287 0.999999998 0.973834968 0.1201795 0.023562872 0 0 0.023476939 0.005533568 0.347316798 0.459274211 -0.02616503 ELFDDPS(ph)YVNVQNLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.614)Y(0.386)VNVQNLDK;ELFDDPS(0.983)Y(0.017)VNVQNLDK;ELFDDPS(0.612)Y(0.388)VNVQNLDK 263.07 6.69E-27 362014000 807740 787470 743260 1013080 620220 659840 622850 531200 380039 TRUE FALSE 769559.731 867714.0883 777339.2062 911243.2737 728386.1716 636989.5753 527822.7931 484685.3119 438973.5071 1.753089238 1.976688967 1.770811207 2.075850271 1.659294148 1.451088881 1.202402388 1.104133402 1 18.74377435 2.007961673 1.328446621 1.053505668 1.888820936 0.91844308 0.103941358 0.105049148 0.344700188 0.068347322 0.032240374 101.85015 -2.007961673 0.835315269 ELFDDPSY(ph)VNVQNLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.025)Y(0.975)VNVQNLDK;ELFDDPS(0.357)Y(0.643)VNVQNLDK;ELFDDPS(0.015)Y(0.985)VNVQNLDK 302.58 5.01E-45 222129000 608547 591074 583925 760910 491506 488331 467248 408266 327804 TRUE FALSE 579782.1893 651305.1126 610698.5388 684421.8812 577224.4908 471419.975 395960.736 372516.0647 378638.1701 1.531230169 1.720125344 1.612881603 1.807588181 1.524475175 1.245040813 1.045749656 0.983831251 1 18.53046033 2.11847529 1.91255851 1.007198701 1.6609528 0.940131869 0.074192297 0.073505279 0.520840629 0.039450379 0.022573583 131.363675 -2.11847529 0.653754099 ELFDELVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELFDELVK 8 0 P55263-3;P55263-2;P55263;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 123.92 0.0030874 15118000 18142 21919 15611 20963 13295 12451 11705 16682 13040 FALSE TRUE 17284.46361 24152.57102 16326.77979 18855.75941 15613.64379 12019.81875 9919.187273 15221.23564 15062.1766 1.147540895 1.603524621 1.083958861 1.251861528 1.036612716 0.798013399 0.658549394 1.010560163 1 13.87864265 2.672714283 1.572888881 0.815373847 1.332087509 0.540001959 0.171665901 0.236152237 1.173311297 0.069499629 0.063515378 470.6675786 -2.672714283 0.516713662 ELFDELVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFDELVKK 9 1 P55263-3;P55263-2;P55263;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 ; 113.62 0.0028389 642420000 646300 530970 571800 663160 424730 590050 686080 688470 461290 FALSE TRUE 615750.6798 585076.4467 598017.5956 596497.8969 498802.7775 569616.4205 581405.8953 628183.917 532824.4973 1.155635079 1.098065967 1.122353793 1.119501637 0.936148357 1.069050735 1.09117711 1.178969661 1 19.02330089 2.953160205 24.9996782 1.060660325 1.123468265 0.224526862 0.063125008 680.152351 363015.2859 0.01875414 0.01989232 897.7599037 -2.953160205 0.062807939 ELFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELFEER 6 0 Q9H307 Q9H307 PNN Pinin 0 103.29 0.080996 57441000 151400 142750 154710 175500 139550 141510 162520 154930 131520 FALSE TRUE 144243.622 157296.3873 161803.6065 157858.4066 163887.4758 136609.4732 137724.5891 141363.5079 151915.4499 0.949499357 1.035420607 1.065089868 1.03912016 1.078807165 0.899246741 0.906587113 0.930540692 1 17.21290907 2.229407688 24.99983514 0.923229614 1.027876458 0.555349004 0.043594585 142.3725064 388865.9127 0.016405556 0.012284119 169.5929085 -2.229407688 0.104646844 ELFEMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFEMAR 7 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 143 0.005702 91420000 176288 187424 148988 161627 173495 152266 174266 175092 168960 FALSE TRUE 167955.2156 206522.7187 155819.2472 145379.9469 203752.4731 146992.9902 147678.5211 159760.0163 195161.4539 0.860596251 1.058214697 0.798412002 0.744921418 1.044020061 0.753186592 0.756699226 0.818604356 1 17.57430861 3.718230062 24.77306707 0.829153857 0.959405488 0.13977695 0.112573227 998.2774415 1216414.967 0.028269402 0.043852483 5226.729955 -3.718230062 0.130251631 ELFGKDEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ELFGKDEQQR 10 1 G3XA94;Q9NPL8 G3XA94 TIMMDC1 "Complex I assembly factor TIMMDC1, mitochondrial" 0 ;;;;;; 54.608 0.081718 38707170000 11168050 9133280 12955490 9477430 27280400 8568780 16140490 8641730 29105900 FALSE TRUE 10640158.41 10063971.62 13549512.03 8524740.73 32038093.12 8272041 13677961.81 7885014.309 33619494.32 0.316487759 0.299349286 0.403025456 0.253565406 0.952961779 0.246048942 0.406846149 0.234536969 1 25.00279469 -1.657173486 2.921246428 1.06126203 0.385145278 0.456610856 0.209397266 58764371.74 58187200.16 27032282.67 0.049220948 0.022020466 1.657173486 -0.676116752 ELFGPELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELFGPELFR 9 0 P35249;C9J8M3;C9JZI1;P35249-2;C9JXZ7;C9JTT7 P35249 RFC4 Replication factor C subunit 4 0 114.28 0.0038702 26723000 49529 43549 43161 51587 51279 39665 53396 49274 56953 FALSE TRUE 47187.86233 47986.69261 45139.97454 46401.37675 60222.04136 38291.3911 45249.45952 44959.30734 65784.98036 0.717304498 0.729447548 0.686174478 0.705349101 0.915437552 0.582068899 0.687838763 0.683428149 1 16.00547061 -1.135235525 4.631796371 1.000028411 0.712326666 0.546018661 0.082128914 2.24E-05 4.17E-06 0.073773964 0.017386975 0.073242722 1.135235525 -0.287701745 ELFLAEHS(ph)DLEEGGLDLTVSLKPVSFYISDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFLAEHSDLEEGGLDLTVSLKPVSFYISDKK 32 2 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 ELFLAEHS(1)DLEEGGLDLTVSLKPVSFYISDKK;ELFLAEHS(1)DLEEGGLDLTVSLKPVSFYISDKK 278.72 7.39E-74 282367000 633990 528673 594660 633930 411657 688810 755780 739380 378459 TRUE FALSE 604022.5491 582545.3798 621925.7492 570206.152 483449.8505 664956.337 640471.8801 674635.9675 437148.4888 1.381733129 1.332602982 1.422687634 1.304376354 1.105916783 1.521122351 1.465112877 1.543265011 1 18.73776389 ELFLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELFLAGR 7 0 Q7Z4W1;J3KS22;J3KRZ4 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 132.72 0.0077741 172558000 247739 250898 356673 330685 241553 245397 320600 272196 290372 FALSE TRUE 236028.8684 276464.7914 373026.8098 297443.9155 283679.7667 236898.8404 271686.5818 248361.0752 335401.4067 0.703720568 0.824280357 1.112180219 0.88682966 0.845791821 0.706314391 0.810034115 0.740489068 1 18.35552921 2.459548833 24.21581054 0.793803825 0.86530584 0.042864841 0.125821864 519.4849999 715874.1535 0.044257173 0.037036465 288.1036982 -2.459548833 0.071502015 ELFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFLSR 6 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;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 ; 122.79 0.04436 121973000 174950 131177 112156 126894 190900 115168 192854 146729 194480 FALSE TRUE 166680.4602 144544.0854 117298.4635 114138.374 224192.8996 111179.7033 163430.5803 133880.6309 224638.9651 0.741992646 0.643450638 0.522164369 0.508096954 0.9980143 0.494926173 0.727525522 0.595981338 1 17.77724867 -1.735169636 2.398250136 1.07914135 0.658340873 0.347974516 0.148733264 9477666.849 6597382.94 4460833.779 0.034705211 0.018400531 1.735169636 -0.420800477 ELFQETLESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELFQETLESLR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;; 185.77 1.01E-05 52049000 103199 91157 82468 91199 107808 80911 109026 93340 108514 FALSE TRUE 98320.98779 100446.0019 86249.23937 82031.50325 126609.6811 78109.03178 92392.0813 85166.65477 125341.7969 0.784422995 0.801376751 0.688112358 0.65446248 1.010115414 0.623168278 0.737121085 0.679475298 1 16.93550806 -1.089275732 4.491931072 1.00001914 0.751055156 0.348913889 0.108383435 60696149650 12305814918 13197710.38 0.023176514 0.08141872 1.089275732 -0.248963985 ELFQT(ph)PDHTEESTTDDKTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELFQTPDHTEESTTDDKTTK 20 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PDHTEESTTDDKTTK 128.98 2.75E-05 98332000 80649 88252 80238 103660 43915 105770 97133 122940 58439 TRUE FALSE 76836.8816 97244.97913 83916.99167 93239.89986 51573.7621 102107.1584 82313.57688 112174.7219 67501.42165 1.138300197 1.440636016 1.243188508 1.381302757 0.764039643 1.512666784 1.219434715 1.661812731 1 16.04263027 ELFQT(ph)PGHTEEAVAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELFQTPGHTEEAVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PGHTEEAVAAGK 106.73 0.0027174 43861000 40564 39999 41754 49930 35358 43601 48129 49878 42656 TRUE FALSE 38646.62011 44074.94358 43668.4622 44910.94154 41524.42401 42091.08644 40786.0371 45510.4179 49270.87462 0.784370491 0.89454356 0.886293628 0.911510946 0.842778301 0.854279263 0.827792025 0.923677898 1 15.58844746 0.98986662 4.435740337 0.999780896 0.857261931 0.630211351 0.035956667 0.111608649 6.899727361 0.034902651 0.008877656 9.769371392 -0.98986662 -0.142518965 ELFQT(ph)PGHTEELVAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFQTPGHTEELVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PGHTEELVAAGK;ELFQT(0.993)PGHT(0.007)EELVAAGK 161.68 1.08E-08 120012000 225592 252336 242687 271051 202701 254937 274210 270935 234546 TRUE FALSE 214928.7132 278049.3253 253814.439 243804.4385 238051.9902 246108.4678 232374.2283 247210.4951 270918.1958 0.793334359 1.026322077 0.936867449 0.899919025 0.878685869 0.908423545 0.857728391 0.912491294 1 18.04749777 0.956839994 22.42619535 1.000000001 0.903070504 0.21799606 0.058750234 4312.318072 2240710.73 0.055652051 0.013913013 9.053989653 -0.956839994 -0.096929497 ELFQT(ph)PVCTDKPTTHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFQTPVCTDKPTTHEK 17 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PVCTDKPTTHEK;ELFQT(1)PVCTDKPTTHEK 184.2 9.51E-10 301590000 366360 452950 361490 496560 262440 453810 440820 461260 284010 TRUE FALSE 349042.8889 499106.12 378064.6741 446644.8454 308209.4529 438094.4459 373564.8128 420869.6291 328052.8203 1.063983808 1.521419994 1.152450614 1.361502837 0.93951167 1.335438743 1.138733733 1.282932513 1 18.3235686 ELFSPLHALNFGIGGDGTQHVLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELFSPLHALNFGIGGDGTQHVLWR 24 0 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;; 316.71 6.69E-74 573361000 637333 559972 566004 685067 749895 550218 789143 710155 423052 FALSE TRUE 607207.5322 617033.7834 591955.8433 616202.7636 880676.4506 531163.8127 668744.7417 647970.0634 488656.7435 1.242605449 1.262714148 1.211393992 1.261013527 1.802239429 1.086987583 1.368536812 1.326022964 1 18.89846188 -1.065246412 4.967873128 0.99999577 1.313454594 0.224161804 0.186830453 1.35E-05 2.54E-06 0.165456083 0.038997487 0.086050538 1.065246412 0.313458824 ELFSPLHALNFGIGGDTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 252.77 7.36E-31 947340000 1313950 1036670 1123200 1321800 1450580 1125820 1484830 1354750 1575300 FALSE TRUE 1251842.187 1142307.852 1174699.831 1188930.153 1703560.693 1086832.571 1258291.913 1236120.908 1819589.478 0.68798056 0.62778328 0.645585087 0.653405709 0.936233537 0.59729548 0.691525164 0.679340545 1 20.79518157 -5 0.377392322 5.352920182 0.677608653 0.525055422 0.092463269 449.5347944 3.38810884 1600.264465 0.058787843 1.00E-05 5 -4.675311529 ELGDVLFQMAEVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 196.33 2.50E-08 66296000 180556 240510 180698 224790 194423 177010 192425 203976 157613 FALSE TRUE 172021.4757 265018.2424 188983.182 202193.6821 228330.3096 170880.0993 163067.0321 186114.7801 182054.8191 0.94488834 1.455705725 1.038056466 1.110619775 1.254184376 0.938618929 0.895702915 1.022300761 1 17.4740134 2.227226556 24.99725687 0.948459549 1.173451551 0.328611213 0.138120352 223.5924538 493129.3994 0.049699728 0.037029978 168.7433071 -2.227226556 0.224992002 ELGENLDQILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELGENLDQILR 11 0 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 121.61 0.00094935 70331000 110548 129756 101861 140376 107005 116547 111889 116671 119564 FALSE TRUE 105322.6151 142978.2839 106531.4276 126265.1378 125666.6381 112510.9482 94818.27807 106454.6687 138105.3745 0.762625028 1.035283996 0.771377856 0.914266648 0.909933003 0.814674654 0.686564722 0.770822056 1 17.07540994 2.073834011 5.504568942 0.776388159 0.885519324 0.021189836 0.110646626 0.331093824 17.86114344 0.03894601 0.028278161 118.531563 -2.073834011 0.109131165 ELGITALHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 157.66 8.77E-06 1057520000 3684600 3567200 2377600 3272100 2995300 2856200 3673300 3332800 2766800 FALSE TRUE 3510436.26 3930701.736 2486615.312 2943182.291 3517679.372 2757289.078 3112870.62 3040962.364 3195861.213 1.098432011 1.229935055 0.778073623 0.920935577 1.100698415 0.862768717 0.974031853 0.951531422 1 21.60777333 3.75530139 24.99403046 0.942884053 1.164183544 0.518212609 0.089394135 562.3448046 839580.3385 0.021496095 0.038626525 5692.478385 -3.75530139 0.221299491 ELGLPEELVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELGLPEELVSR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 152.97 7.61E-05 113712000 177522 163349 172621 182916 240528 155359 201935 169585 246400 FALSE TRUE 169130.8869 179994.4488 180535.8436 164528.9362 282476.007 149978.8789 171126.107 154735.2384 284610.4536 0.594253952 0.632423885 0.634326116 0.578084656 0.992500463 0.526961947 0.601264306 0.54367377 1 18.11862913 -2.162566052 2.332574003 1.871696143 0.635965603 0.430947354 0.1307356 12995656.81 2664074.586 59979858.22 0.029787451 0.006877553 2.162566052 -1.23573054 ELGNDAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELGNDAYK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 84.213 0.040972 68200000 163330 141020 150920 170090 106010 148290 165420 168900 143960 FALSE TRUE 155609.7146 155390.0983 157839.8313 152992.2301 124498.1104 143154.6801 140182.1409 154110.2206 166284.5816 0.935803627 0.934482902 0.949215073 0.920062634 0.748705077 0.860901707 0.84302549 0.92678599 1 17.34329488 2.97855248 24.73779536 0.860296938 0.937677422 0.155873273 0.063975677 857.9388187 989556.5876 0.017459608 0.018692188 951.814859 -2.97855248 0.077380485 ELGTVMR ddPTM_SK-BR-3_Trastuzumab_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 ;; 151.17 0.019389 105940000 948979 789229 660537 891766 880262 718848 853792 781698 854365 FALSE TRUE 904122.6434 869652.3324 690823.2748 802123.9874 1033779.414 693954.1135 723530.3494 713248.3791 986855.5607 0.91616512 0.881235681 0.700024707 0.812807891 1.047548856 0.703197247 0.733167424 0.722748503 1 19.91247942 ELHDLFNLPHDRPYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELHDLFNLPHDRPYFK 16 1 H0YA18;D6RGX2;Q9NUQ7 H0YA18 UFSP2 Ufm1-specific protease 2 0 ; 142.01 1.00E-06 194663000 282780 250660 258830 293690 241370 226180 273550 280660 79997 FALSE TRUE 269413.5498 276202.539 270697.6115 264167.7232 283464.8516 218347.3299 231814.9234 256083.9225 92402.52619 2.915651345 2.989123245 2.929547737 2.858879883 3.067717553 2.363001737 2.508750929 2.771395254 1 16.49564467 -1.071929078 0.309941613 2.70E-16 3.016052168 0.905404492 0.186219448 4.119263644 0.313049396 3.806312857 0.184511292 0.084736578 1.071929078 3.016052168 ELHGQNPVVTPCNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELHGQNPVVTPCNK 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 94.532 0.0041277 98272000 178200 145910 158670 175470 137980 156630 196940 162840 145450 FALSE TRUE 169776.8392 160778.3949 165945.1764 157831.4222 162043.6683 151205.8638 166893.1859 148580.8663 168005.6431 1.010542479 0.95698211 0.987735729 0.939441195 0.964513247 0.900004672 0.993378453 0.884380212 1 17.35815017 5.487605717 0.583843535 0.947928012 1.126933403 0.20184523 0.03744079 11.70027383 1.583746872 0.015081961 1.714147261 307330.5386 -5.487605717 0.17900539 ELHINLIPNK ddPTM_SK-BR-3_Trastuzumab_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 ; 113.63 0.0014628 859200000 6145800 6801300 3897200 5937100 4301900 4968200 5459200 5644100 3648300 FALSE TRUE 5855300.214 7494360.202 4075890.475 5340291.428 5052149.998 4796149.988 4626298.775 5149872.683 4214059.731 1.389467779 1.778418124 0.967212317 1.267255751 1.198879541 1.138130519 1.09782468 1.222069219 1 22.00677933 3.736724802 24.99999971 1.138154184 1.583942955 0.678945066 0.130372103 78.03114992 1062625.915 0.031523867 0.051749821 5454.121423 -3.736724802 0.445788771 ELHINLIPNKQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELHINLIPNKQDR 13 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 171.21 1.53E-05 26540790000 10976770 9858870 9783390 10899060 9073500 10428540 11842090 11158520 9258110 FALSE TRUE 10457919.84 10863500.06 10231968.11 9803465.782 10655915.53 10067397.04 10035361.68 10181420.83 10693810.41 0.977941391 1.015868025 0.956812185 0.916742059 0.996456372 0.941422809 0.938427117 0.952085406 1 23.35027267 3.66439514 7.41095786 0.952820665 0.996812756 0.259896472 0.026872339 0.270538579 23.87917925 0.006524683 0.010150179 4617.374925 -3.66439514 0.043992091 ELHIQGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELHIQGNR 8 0 Q15404;Q15404-2 Q15404 RSU1 Ras suppressor protein 1 0 ; 111.17 0.0032855 545500000 393700 341770 330290 390870 486840 363280 418830 361270 458250 FALSE TRUE 375090.5812 376596.7516 345434.1232 351579.005 571744.7419 350699.5225 354929.7912 329635.2836 529313.0696 0.708636538 0.711482057 0.652608339 0.664217502 1.080163659 0.662555948 0.670547945 0.622760522 1 19.01376175 -2.053275038 2.747097704 1.391522079 0.72049528 0.3107513 0.130282949 42349807.92 13338245.32 104322565.7 0.029948249 0.008845552 2.053275038 -0.671026799 ELHSEFSEVMNEIWASDQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 362.49 4.43E-96 1031537100 599665.6 481286.7 514319.8 509485.3 725419.4 440617.4 617282.7 493176.4 625463.1 FALSE TRUE 571320.5955 530330.3619 537901.8716 458270.8697 851932.3137 425358.709 523104.8869 449991.2599 722456.7231 0.790802518 0.734065232 0.744545458 0.634322936 1.179215704 0.588767044 0.724063975 0.622862582 1 19.46255164 -2.035001618 2.298804616 1.297697328 0.752531435 0.183663778 0.164095287 21910524.84 7723792.24 34348254.93 0.036386976 0.00922568 2.035001618 -0.545165893 ELHWHPQCPGLLVSTALSGFTIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELHWHPQCPGLLVSTALSGFTIFR 24 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ;; 187.79 1.04E-17 232188000 150505.6 140939.4 125137.1 153898.8 193351.4 135391.8 216853.7 155588.7 52644 FALSE TRUE 143391.4986 155301.2851 130874.7598 138428.6002 227071.8229 130703.148 183768.6853 141964.5286 60807.76265 2.358111733 2.553971373 2.1522706 2.276495536 3.734257158 2.149448398 3.022125421 2.334644828 1 15.89196789 ELHYLPFPS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELHYLPFPSP 10 0 Q8N565 Q8N565 MREG Melanoregulin 1 ELHYLPFPS(1)P;ELHYLPFPS(1)P 105.86 0.0026148 27160000 87321 63873 71986 90858 105206 70376 102731 80064 92185 TRUE FALSE 83193.50938 70381.73132 75286.6293 81724.78122 123553.8931 67938.86147 87057.49917 73053.17171 106480.579 0.781302188 0.660981862 0.707045642 0.767508798 1.160342048 0.638039933 0.8175904 0.686070384 1 16.7002308 2.993347041 24.82802849 0.84175074 0.716755811 0.161150071 0.149157893 552.8934793 2063342.899 0.041284616 0.047673869 984.7977357 -2.993347041 -0.12499493 ELIIGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ELIIGDR 7 0 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;;;; 138.9 0.0063773 3620920000 4652360 3624000 3967810 3837240 4564960 3319890 3997100 3790780 4418570 FALSE TRUE 4432452.163 3993289.72 4149738.013 3451513.345 5361087.579 3204921.377 3387268.983 3458839.207 5103779.269 0.868464706 0.782418187 0.813071607 0.676266187 1.05041525 0.627950624 0.663678581 0.677701567 1 22.28313451 ELILGSETPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 ELILGSETPS(0.052)S(0.948)PR;ELILGSETPS(0.014)S(0.986)PR;ELILGSET(0.006)PS(0.419)S(0.574)PR;ELILGSETPS(0.01)S(0.99)PR 225.21 1.57E-08 155158000 869610 812658 802874 957600 863820 847780 949870 914460 1002000 TRUE FALSE 828505.2587 895468.7741 839686.5671 861340.2287 1014469.935 818421.166 804949.8859 834385.0345 1157385.042 0.715842376 0.773699971 0.725503213 0.744212338 0.876518961 0.707129552 0.695490141 0.7209226 1 20.14243747 -1.059833284 5.061675959 1.000004465 0.743788787 0.708200342 0.051453369 2.56E-06 4.75E-07 0.049148609 0.011584236 0.0871298 1.059833284 -0.256215678 ELIPQES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELIPQESPR 9 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 ELIPQES(1)PR;ELIPQES(1)PR 75.088 0.025828 124370000 348140 292580 311820 354110 417400 336320 376040 357930 466560 TRUE FALSE 331684.1121 322394.2346 326117.2554 318514.19 490194.4278 324673.1541 318668.1916 326587.7517 538911.7419 0.61547019 0.598231973 0.605140378 0.591032196 0.90960057 0.602460716 0.591317959 0.606013427 1 19.0396895 -1.479804201 3.135818318 1.0085239 0.635311045 0.578814716 0.096463599 39959177.56 43789047.85 2906084.815 0.02245802 0.033128044 1.479804201 -0.373212855 ELIPTEEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELIPTEEALR 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 ; 115.71 0.0027597 92152000 164257 138375 137866 158371 182091 146155 177366 159396 209791 FALSE TRUE 156492.8971 152475.5698 144187.2925 142451.2462 213847.6127 141093.6157 150305.5591 145438.4412 242324.3168 0.645799395 0.629221086 0.595017844 0.5878537 0.882485157 0.582251165 0.620266101 0.600180961 1 17.88657966 -1.56215288 2.995147598 1.017491538 0.641607971 0.621781027 0.087526432 34107688.52 35577005.43 4742429.555 0.019604737 0.027406093 1.56215288 -0.375883568 ELISNASDALDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELISNASDALDK 12 0 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;; 197.07 4.63E-07 205773000 661910 756760 528840 781800 399640 655280 588570 676260 415690 FALSE TRUE 630622.8261 833874.7044 553087.8371 703211.9787 469337.0895 632587.4893 498772.8367 617043.0893 480153.0821 1.31337869 1.736685102 1.151898962 1.464557877 0.977473866 1.317470434 1.038778788 1.285096592 1 18.87313491 3.213814102 1.401744411 1.139550803 1.504687954 0.336061987 0.188873671 0.373925483 1.537338216 0.060063516 0.086808122 1636.116038 -3.213814102 0.365137151 ELISNASDALDKIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELISNASDALDKIR 14 1 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;;; 254.18 2.75E-24 7206320000 6269900 4384370 5827440 5899480 5727680 6658530 8031510 7489740 6817660 FALSE TRUE 5973534.253 4831142.288 6094633.888 5306453.062 6726585.579 6427943.437 6806155.641 6833898.66 7874907.893 0.758552904 0.613485561 0.773930816 0.673843191 0.854179588 0.816256333 0.864283841 0.867806805 1 22.90883162 1.820898982 0.461916785 0.993164173 0.674280865 0.734040319 0.055696733 0.428435402 0.222192334 0.053880772 0.041485027 66.20624889 -1.820898982 -0.318883307 ELISNSSDALDKIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELISNSSDALDKIR 14 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;; 215.48 5.92E-12 3810250000 4213540 2750170 3964990 3486100 3611170 3956320 5011410 4405220 4338590 FALSE TRUE 4014374.315 3030415.45 4146788.713 3135670.605 4240956.905 3819311.646 4246827.364 4019475.583 5011396.379 0.801049051 0.604704801 0.827471706 0.62570796 0.846262515 0.762125236 0.847433937 0.802066985 1 22.25678122 0.842468007 0.394476265 1.018061387 0.702367316 0.513178068 0.078641438 1.129474577 0.439884152 0.122392559 0.05694652 6.957736977 -0.842468007 -0.315694071 ELKAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELKAPR 6 1 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3;K7EMM4;K7EJN4;K7EK65;A0A494C1R3;A0A0A0MTS0;K7EPS2;K7EKB9;K7ERZ7 K7ENH8 TCF3 Transcription factor E2-alpha 0 ; 76.592 0.068081 463940000 1094160 971900 935670 989020 867800 847350 1049020 1031080 964270 FALSE TRUE 1042441.225 1070937.715 978571.395 889601.8306 1019144.045 818006.057 888972.7324 940793.1691 1113804.067 0.93592873 0.961513561 0.878584864 0.798705856 0.915011963 0.734425454 0.798141037 0.844666667 1 20.08706403 3.54473526 3.676756304 0.831186627 0.948008344 0.215668748 0.072814166 0.247331546 6.499883278 0.018301735 0.028589797 3505.381259 -3.54473526 0.116821717 ELKENGELLPILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELKENGELLPILR 13 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 101.3 0.0018279 90066000 347430 263110 298890 313070 285120 317390 377830 334170 351570 FALSE TRUE 331007.6724 289921.2081 312594.4021 281599.6088 334844.8377 306398.7047 320185.0942 304908.3033 406089.68 0.815109787 0.713933947 0.76976692 0.693441923 0.824558845 0.754509951 0.788459077 0.750839822 1 18.63143884 -5 0.401896722 4.867795849 0.759010874 0.769790417 0.040535931 327.3452421 2.27099367 1111.669581 0.022457815 1.00E-05 5 -4.108784975 ELKEQLGEEIDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELKEQLGEEIDSK 13 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 137.52 5.45E-05 343410000 700630 670770 704910 752420 474900 815300 809830 832980 500470 FALSE TRUE 667512.6084 739122.2256 737230.8208 676785.3121 557722.4096 787065.9566 686275.56 760039.8553 578080.3316 1.154705621 1.278580476 1.275308604 1.170746132 0.964783576 1.361516581 1.187162964 1.314765118 1 19.14091046 3.214124393 24.6529064 1.180540394 1.233638364 0.057310234 0.124740116 727.8284755 734280.2895 0.034052789 0.04072136 1637.285413 -3.214124393 0.05309797 ELKIDIIPNPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELKIDIIPNPQER 13 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;; 127.36 0.00016223 2703964000 2719090 1625560 2665650 2283530 2491750 2640650 3771720 3115850 3211980 FALSE TRUE 2590564.004 1791206.412 2787872.689 2053985.226 2926310.411 2549203.628 3196274.842 2843009.656 3710077.454 0.698250653 0.482794883 0.751432477 0.553623274 0.788746447 0.687102536 0.861511621 0.766293882 1 21.82301788 1.508261884 0.440552709 1.000466613 0.586243213 0.607651981 0.091117451 0.550321922 0.294009861 0.092919221 0.064012013 32.23011717 -1.508261884 -0.414223399 ELKPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELKPAR 6 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 98.133 0.036737 434630000 1631420 1428530 1400150 1414610 1259590 1256800 1495290 1501840 1379880 FALSE TRUE 1554306.01 1574098.831 1464348.262 1272410.715 1479262.097 1213276.701 1267156.048 1370330.928 1593864.743 0.975180621 0.987598752 0.918740608 0.798317875 0.928097634 0.761216851 0.795021066 0.859753586 1 20.60409778 3.467957496 3.821380389 0.840354103 0.979525847 0.334313871 0.069902866 0.185595048 6.019526961 0.017987386 0.02645357 2937.362164 -3.467957496 0.139171744 ELKTDS(ph)SPNQAR ddPTM_SK-BR-3_Trastuzumab_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(0.849)S(0.15)PNQAR;ELKTDS(0.5)S(0.5)PNQAR;ELKT(0.002)DS(0.499)S(0.499)PNQAR 108.66 0.0010188 2235100000 1430420 853740 1390150 1299670 1255330 1378300 1955290 1725750 1752390 TRUE FALSE 1362806.881 940737.0766 1453889.753 1169024.702 1474259.155 1330569.125 1656974.599 1574634.181 2024141.691 0.673276425 0.46475851 0.718274693 0.577540944 0.728337923 0.657349795 0.818606033 0.777926856 1 20.94887885 1.292702404 0.44385741 1.010177529 0.570439107 0.718626957 0.075566179 0.456371923 0.252598076 0.082015858 0.050017351 19.62015364 -1.292702404 -0.439738422 ELKTDSS(ph)PNQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.003)DS(0.164)S(0.832)PNQAR;ELKTDS(0.382)S(0.618)PNQAR;ELKT(0.003)DS(0.253)S(0.744)PNQAR 117.4 0.00044675 1298391000 1202550 798190 1256500 1138130 992610 1178800 1568050 1372010 1433130 TRUE FALSE 1145707.845 879526.4685 1314111.768 1023723.01 1165720.87 1137977.86 1328815.173 1251869.531 1655372.481 0.692114831 0.531316352 0.793846571 0.618424567 0.704204572 0.687445196 0.802728805 0.756246431 1 20.65872445 0.502402653 0.327969468 1.056826548 0.614425868 0.688618242 0.069288159 1.491725273 0.334415426 0.205947558 0.070366224 3.179820855 -0.502402653 -0.442400679 ELKTDSSPNQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;; 160.18 6.27E-05 509194000 800420 415755 839920 705695 821430 825430 1202770 955690 1108150 FALSE TRUE 762585.7329 458120.9072 878431.1628 634757.1979 964687.1319 796845.1521 1019265.346 872004.7172 1279996.242 0.595771853 0.357908009 0.686276361 0.495905517 0.753664034 0.622537103 0.796303389 0.681255685 1 20.28770814 1.387552421 0.273005783 1.056723008 0.42368543 0.634151893 0.104284527 0.969269914 0.284778665 0.238770379 0.199959269 24.40913676 -1.387552421 -0.633037579 ELLAKPIGPDDAIDALSSDFTCGS(ph)PTAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLAKPIGPDDAIDALSSDFTCGSPTAAGK 30 1 P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0 P20810-5 CAST Calpastatin 1 ELLAKPIGPDDAIDALSSDFT(0.011)CGS(0.939)PT(0.051)AAGK 160.86 2.60E-12 191730000 86564 77240 82540 88345 64208 88317 104930 97485 63578 TRUE FALSE 82472.29127 85110.84381 86324.54064 79464.39276 75405.85487 85258.56014 88921.00133 88948.6966 73437.35153 1.123029215 1.158958514 1.175485483 1.082070515 1.026805206 1.160969975 1.210841615 1.211218743 1 16.16422641 2.027363442 24.99275765 1.169561783 1.119471335 0 0.072177127 493.1401531 450414.0927 0.025496336 0.018829995 106.5033925 -2.027363442 -0.050090449 ELLAKPIGPDDAIDALSSDFTCGS(ph)PTAAGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLAKPIGPDDAIDALSSDFTCGSPTAAGKK 31 2 P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0 P20810-5 CAST Calpastatin 1 ELLAKPIGPDDAIDALS(0.009)S(0.009)DFT(0.179)CGS(0.751)PT(0.053)AAGKK 76.853 0.0014177 69877000 60251 45834 59902 58338 36265 61262 65658 65115 61330 TRUE FALSE 57403.05464 50504.53671 62648.56595 52473.75341 42589.60452 59140.48158 55640.66621 59413.1854 70840.74317 0.810311299 0.712930645 0.884357831 0.740728443 0.601202114 0.834837114 0.785433124 0.838686648 1 16.11229173 0.777390544 1.153248195 0.999404426 0.760123738 0.493357087 0.075310616 0.665022073 1.609594274 0.067580973 0.021019824 5.989499651 -0.777390544 -0.239280689 ELLDLAMQNAWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLDLAMQNAWFR 13 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 217.14 6.12E-11 214470000 318600 288010 255890 293680 350210 247755 371660 324520 329900 FALSE TRUE 303540.4094 317358.5464 267622.8096 264158.7284 411286.5131 239175.1822 314956.441 296103.3084 381059.2071 0.796570202 0.832832643 0.702312934 0.69322227 1.079324434 0.627658846 0.826528884 0.777053284 1 18.53965565 -0.96949419 4.682581599 1.000002518 0.793911637 0.227577255 0.120415543 3.42E-06 7.52E-07 0.102892139 0.024251547 0.1072768 0.96949419 -0.206090881 ELLDMMIAEEESLKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLDMMIAEEESLKER 16 1 O43663-2;O43663-4;O43663;H0YLA0 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ; 82.55 0.0088295 20230300 124398 109656 107283 126463 97234 109551 129274 119904 89065 FALSE TRUE 118517.9531 120830.0711 112202.0317 113750.699 114191.5788 105757.2214 109550.877 109404.5701 102876.7453 1.152038322 1.174512964 1.090645231 1.10569885 1.109984365 1.027999292 1.064875028 1.06345287 1 16.65055738 3.099463241 0.302536899 1.002014039 1.215058655 0.781587034 0.024566965 1.158952123 0.184578206 0.030630059 0.086485517 1257.370426 -3.099463241 0.213044616 ELLDTELDLHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLDTELDLHKR 12 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 0 130.44 0.00014055 42614000 98001 91891 86787 110300 91383 94874 108280 103420 89875 FALSE TRUE 93368.68695 101254.7974 90766.26979 99212.43444 107320.1663 91588.48959 91759.8973 94363.99654 103812.356 0.899398593 0.97536364 0.874330121 0.955690038 1.033789911 0.882250371 0.883901501 0.908986176 1 16.66361864 -0.27999524 7.509703212 1 0.926748849 0.176425258 0.049761722 0 0 0.04745931 0.011186267 0.524813212 0.27999524 -0.073251151 ELLDTS(ph)FEDLSKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.204)S(0.796)FEDLSKPK;ELLDT(0.019)S(0.981)FEDLSKPK 211.78 2.04E-09 181917000 249721 368670 239150 357080 130055 324566 267286 336198 133297 TRUE FALSE 237917.1832 406237.8921 250115.2641 321185.64 152736.5508 313326.198 226506.6117 306758.7208 153968.018 1.545237682 2.638456333 1.624462452 2.086054261 0.992001799 2.035008323 1.471127671 1.992353509 1 17.23227118 ELLEIVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLEIVKK 8 1 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 101.64 0.013311 0 1114000 623780 1183200 926120 950980 1256800 1700900 1378600 1369000 FALSE TRUE 1061343.428 687343.8912 1237450.89 833024.6581 1116830.611 1213276.701 1441396.466 1257882.476 1581297.528 0.671185156 0.434670819 0.782554117 0.526798179 0.70627481 0.767266551 0.911527679 0.795474889 1 20.59267741 2.042569742 0.746843661 0.959125445 0.571267643 0.622607377 0.101719184 0.377220389 0.397567202 0.080602014 0.044144431 110.2985344 -2.042569742 -0.387857802 ELLELASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLELASR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 102.51 0.011517 24669000 58850 49021 51891 58812 74716 48817 63766 57766 73371 FALSE TRUE 56068.27713 54016.29563 54270.25368 52900.10602 87746.44674 47126.45505 54037.32556 52707.7028 84748.99995 0.661580398 0.637367941 0.640364532 0.624197407 1.035368521 0.556070928 0.637616085 0.621927136 1 16.37090872 -1.590176836 2.805579776 1.023163205 0.672411681 0.376148056 0.130694419 20219640.89 19881950.33 3465145.916 0.029457001 0.025693494 1.590176836 -0.350751525 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 S(0.81)QGDS(0.19)NPAAIPHAAEDIQGDDRWMSQHNR;S(1)QGDSNPAAIPHAAEDIQGDDRWMSQHNR;S(1)QGDSNPAAIPHAAEDIQGDDRWMSQHNR 125.74 2.85E-25 488810000 11809.6 12241.4 2463 4872.2 11121 13468.5 16521.1 16878.9 24554 TRUE FALSE 11251.38361 13488.81258 2575.930986 4382.437199 13060.49888 13002.08247 14000.50276 15400.89404 28361.70892 0.396710355 0.475599429 0.090824252 0.154519504 0.4604976 0.458437907 0.493641015 0.543017139 1 14.79165684 0.694708862 0.673789192 1.005696736 0.328674103 0.744636579 0.122975123 0.666434957 0.591444538 0.139897094 0.051205823 4.95118167 -0.694708862 -0.677022634 ELLHSVHPES(ph)PNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLHSVHPESPNLK 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 ELLHSVHPES(1)PNLK 77.324 0.041765 310210000 131730 132440 118180 131950 92696 144860 137430 135180 42290 TRUE FALSE 125503.384 145935.7866 123598.6699 118686.1353 108862.1531 139843.4619 116462.5294 123342.9226 48848.11721 2.569257346 2.987541688 2.530264767 2.429697235 2.228584422 2.862821944 2.384176424 2.525029205 1 15.57601534 -1.446909312 0.381222773 7.81E-17 2.676163712 0.836336839 0.217875826 9.127915538 0.740122513 9.21349833 0.147901085 0.035734745 1.446909312 2.676163712 ELLLPNWQGSGSHGLTIAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLLPNWQGSGSHGLTIAQR 20 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 224.03 6.07E-25 445620000 400530 266350 394610 367320 489990 338300 494900 393370 528100 FALSE TRUE 381597.7407 293491.3678 412703.2588 330396.2957 575444.1009 326584.5862 419393.9155 358924.4374 609995.0508 0.625575142 0.481137294 0.676568209 0.541637666 0.943358639 0.535388911 0.687536587 0.588405491 1 19.21843801 -5 0.201103305 2.678372373 0.568088421 0.441775676 0.127623346 122.9551032 1.217401923 83.12785791 0.275293982 1.00E-05 5 -2.110283952 ELLLTGPGLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELLLTGPGLEER 12 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;;; 154.05 0.00016557 103832000 179792 145622 158490 178041 181688 153875 198169 179983 210434 FALSE TRUE 171293.5885 160461.0474 165756.9233 160143.9804 213374.3297 148546.2702 167934.6794 164222.7344 243067.03 0.704717495 0.66015143 0.681939148 0.658846987 0.877841514 0.611132946 0.690898636 0.675627354 1 17.89099469 -1.414561887 5.570153239 1.000168509 0.692664707 0.65393237 0.069675699 0.000132041 1.39E-05 0.06109338 0.014392024 0.038497995 1.414561887 -0.307503802 ELLPLIYHHLLR ddPTM_SK-BR-3_Trastuzumab_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 ; 122.42 0.00020749 207808000 410490 315410 237228 268841 451590 242850 432130 328030 93002 FALSE TRUE 391086.9512 347550.6376 248105.1385 241816.5919 530347.153 234440.0436 366200.6319 299305.9542 107424.2752 3.640582639 3.235308193 2.309581685 2.251042341 4.936939553 2.182374917 3.408918806 2.786204084 1 16.71296052 3.985600349 11.34281797 2.862607118 3.48895782 0.07238086 1.013355903 1.654073461 1300.931652 0.232965311 0.439833811 9673.872265 -3.985600349 0.626350703 ELLSPLS(ph)EPDDRYPLIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLSPLS(1)EPDDRYPLIVK;ELLS(0.005)PLS(0.995)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK 281.96 1.43E-39 805940000 864970 787640 756170 921330 658100 838220 900700 916550 743180 TRUE FALSE 824084.5823 867901.4115 790841.1425 828716.158 772872.4316 809192.2312 763281.6725 836292.0231 858428.5588 0.959992039 1.011035109 0.921266114 0.965387451 0.900334016 0.942643652 0.889161555 0.974212722 1 19.71133855 3.729687705 24.95843092 0.933907975 0.985513574 0.177943999 0.03598127 683.1087265 1921502.917 0.00863864 0.013598115 5366.457636 -3.729687705 0.0516056 ELLTEFGYKGEETPVIVGSALCALEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLTEFGYKGEETPVIVGSALCALEGR 27 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 202.17 3.89E-25 127220000 216400 202730 186170 200480 147150 174360 175120 198570 153570 FALSE TRUE 206171.2009 223388.4175 194706.0786 180327.3695 172812.9134 168321.8695 148402.2277 181182.1581 177384.8513 1.162281894 1.259343263 1.097647726 1.016588329 0.974225883 0.948907803 0.83661162 1.021407165 1 17.43652328 3.249827476 1.565017748 0.934381306 1.212535546 0.757857896 0.057448362 0.149601278 0.760436472 0.019001362 0.027673006 1777.573125 -3.249827476 0.27815424 ELLTEFGYKGEETPVIVGSALCALEGRDPELGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLTEFGYKGEETPVIVGSALCALEGRDPELGLK 34 2 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 253.93 1.10E-59 194920000 311020 186380 234370 227570 238970 223990 391610 310650 277700 FALSE TRUE 296318.701 205372.3339 245116.0963 204694.2312 280646.2923 216233.1701 331862.7021 283447.8391 320764.2977 0.923789534 0.640259329 0.764162652 0.638145307 0.874929954 0.674118571 1.034599874 0.883663928 1 18.29115405 1.732350589 10.43790578 0.966762168 0.753569694 0.52076555 0.099453576 0.070459946 32.51801503 0.04328682 0.023505049 53.99463239 -1.732350589 -0.213192474 ELLTLDEKDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;;; 91.937 0.0094564 7705740000 16956300 16732200 15615600 18016600 12274000 18659300 19738300 19040400 13376800 FALSE TRUE 16154809.3 18437230.2 16331590.71 16205537.14 14414581.71 18013123.76 16726859.82 17373121.64 15451205.82 1.045537124 1.193255103 1.056978393 1.048820223 0.932909824 1.165806991 1.082560158 1.124386137 1 23.8812161 -2.617852155 1.720102771 9.50E-05 1.086539499 0.107952603 0.072033698 1680844.1 59540.84757 6574572.423 0.017964311 0.002410726 2.617852155 1.086444499 ELLTSDS(ph)PPHNDIMTPVDPGVAQPNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLTSDSPPHNDIMTPVDPGVAQPNSR 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 ELLT(0.001)S(0.004)DS(0.995)PPHNDIMTPVDPGVAQPNSR;ELLT(0.189)S(0.166)DS(0.645)PPHNDIMTPVDPGVAQPNSR 218.01 2.14E-34 107343000 78535 62970 65366 69704 70137 66419 76257 67037 68846 TRUE FALSE 74822.80619 69386.71459 68363.09576 62697.22149 82368.87059 64118.89338 64622.59409 61166.88489 79522.28606 0.940903612 0.872544264 0.859672164 0.788423278 1.03579606 0.806300932 0.812635015 0.769179156 1 16.27907161 ELLTTMGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 203.64 0.0013884 0 372700 377050 306750 422870 343750 350510 332650 330520 314970 FALSE TRUE 355083.2096 415471.8237 320814.7909 380362.3042 403699.8912 338371.7508 281898.133 301577.9166 363813.939 0.976002213 1.141989845 0.881810059 1.045485792 1.109632831 0.930068133 0.774841486 0.828934475 1 18.47284129 2.014818577 6.414436921 0.844731582 1.03436165 0.403207582 0.090267922 0.120020397 20.38938577 0.032849842 0.023173376 103.4709835 -2.014818577 0.189630068 ELLTTMGDRFT(ph)DEEVDELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 1 ELLTTMGDRFT(1)DEEVDELYR 119.32 8.51E-05 32421000 23939 22605 25525 29941 26998 28392 32975 28125 21501 TRUE FALSE 22807.45091 24908.4752 26695.3465 26931.2738 31706.44265 27408.77792 27944.05812 25662.2259 24835.26527 0.918349398 1.002947822 1.074896773 1.084396462 1.276670183 1.103623321 1.125176551 1.033297838 1 14.60010254 3.874785567 1.490847119 1.1180512 0.929837307 0.407611185 0.072948189 0.349409384 1.47038644 0.020581634 0.058842619 7495.240408 -3.874785567 -0.188213893 ELLTTMGDRFTDEEVDELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;;;;; 253.95 3.72E-36 1461463000 1067513 565307 929147 886351 1258349 838114 1360049 1084171 1527151 FALSE TRUE 1017053.776 622912.426 971749.309 797253.3135 1477804.667 809089.902 1152548.546 989235.2397 1763973.777 0.576569668 0.353130207 0.550886482 0.451964379 0.837770202 0.458674563 0.653381904 0.560799289 1 20.75039768 -5 0.162299062 2.740546761 0.422913261 0.563543541 0.12583328 88.49736129 0.818689241 49.38955944 0.464834954 1.00E-05 5 -2.3176335 ELLVSQHTVQLVGGLS(ph)PLSSPSDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(0.996)PLS(0.004)SPSDTK;ELLVSQHTVQLVGGLS(1)PLSSPSDTK 288.07 2.16E-54 853270000 1298710 1154980 1052590 1528260 984060 1220230 1429750 1474360 1055930 TRUE FALSE 1237322.552 1272673.775 1100852.293 1374636.401 1155679.752 1177973.129 1211615.378 1345257.222 1219678.231 1.014466373 1.04345043 0.902575994 1.127048402 0.947528391 0.965806472 0.99338936 1.102960754 1 20.21806916 -0.950846661 4.300732021 0.999999692 1.010008291 0.002290683 0.067620037 1.77E-07 4.30E-08 0.057881052 0.013642275 0.11198332 0.950846661 0.010008598 ELLVSQHTVQLVGGLS(ph)PLSSPSDTKAESPAEKVPEESVLPLVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTKAESPAEKVPEESVLPLVQK 44 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(0.526)PLS(0.149)S(0.149)PS(0.149)DT(0.013)KAES(0.013)PAEKVPEESVLPLVQK 92.667 3.75E-05 212820000 51704 35001 50547 58848 37965 57705 77127 69867 44689 TRUE FALSE 49260.05439 38567.64169 52864.62995 52932.48724 44586.08398 55706.66138 65359.85962 63749.07509 51619.14188 0.954298204 0.747157746 1.024128415 1.025442991 0.863750972 1.079186119 1.26619423 1.234989052 1 15.65561854 2.052652985 4.226858683 1.192945789 0.912019277 0.524333372 0.106332339 0.142170052 5.328982702 0.042798613 0.029424789 112.8893532 -2.052652985 -0.280926512 ELMWLNEKEEEEVGFDWSDR ddPTM_SK-BR-3_Trastuzumab_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 82.482 0.0034929 19699000 21487 22773 19999 24295 16679 20654 23470 24514 15162 FALSE TRUE 20471.35209 25093.59459 20915.97393 21852.82044 19587.81232 19938.7468 19889.22044 22367.4242 17513.24552 1.168906818 1.432835197 1.194294564 1.247788162 1.118457015 1.138495248 1.135667311 1.277171851 1 14.09615885 3.099631678 1.80849793 1.142952279 1.295060096 0.290416421 0.09612366 0.382358813 2.563247285 0.029989407 0.037979978 1257.858179 -3.099631678 0.152107817 ELNDIRFEFTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELNDIRFEFTPGR 13 1 O95747;C9JIG9;Q9UEW8-2;Q9UEW8 O95747;Q9UEW8-2 OXSR1;STK39 Serine/threonine-protein kinase OSR1;STE20/SPS1-related proline-alanine-rich protein kinase 0 ;;; 126.71 0.00016912 954490000 2026890 1377050 1950320 1942670 2309530 1867490 2435230 2091680 2471880 FALSE TRUE 1931082.927 1517372.961 2039744.101 1747389.121 2712311.301 1802818.353 2063690.937 1908521.411 2855206.526 0.676337389 0.531440702 0.714394592 0.612000955 0.949952753 0.631414343 0.722781669 0.668435503 1 21.44516367 -4.999999999 0.151131096 2.134093947 0.581297731 0.457662297 0.107246064 113.7744496 1.017366821 38.84119606 0.495746848 1.00E-05 4.999999999 -1.552796216 ELNEDKLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELNEDKLEK 9 1 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ; 106.29 0.0026992 351000000 1386060 1504850 1181650 1591110 739180 1486930 1441020 1560120 761050 FALSE TRUE 1320543.691 1658195.926 1235829.821 1431168.6 868092.758 1435437.241 1221165.933 1423507.622 879069.7471 1.50220582 1.886307578 1.405838189 1.628048974 0.987512949 1.632904836 1.389157046 1.619334105 1 19.74561811 -3.137395451 0.11454835 6.60E-13 1.836534886 0.306268706 0.23376903 105.9062452 1.250022482 29.73926564 2.7422809 0.000728794 3.137395451 1.836534886 ELNHMLSDTGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 ELNHMLSDTGNR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;;;;; 197.38 1.96E-07 4762220000 4186100 3698690 3860700 4148300 4493170 3470653 4326450 4143460 4326980 FALSE TRUE 3988231.349 4075590.716 4037716.914 3731305.003 5276777.425 3350463.416 3666370.592 3780636.677 4997985.959 0.797967698 0.815446612 0.807868799 0.746561722 1.055780762 0.670362711 0.733569606 0.756432032 1 22.25291542 -0.04981967 7.877796487 0.999999999 0.795664567 0.283157465 0.100946979 4149127.851 526686.3268 0.091579575 0.02221131 0.891621085 0.04981967 -0.204335432 ELNHMLSDTGNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ELNHMLSDTGNRK 13 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;;; 155.08 2.52E-05 6518550000 7667790 6854420 6696530 7735690 6113150 6591370 7934120 7939840 6712240 FALSE TRUE 7305348.763 7552893.191 7003572.524 6958083.744 7179281.425 6363109.204 6723624.274 7244585.518 7753139.898 0.942243898 0.974172179 0.903320799 0.897453656 0.925983733 0.820713838 0.867213073 0.934406655 1 22.88634927 3.652190813 5.191869425 0.894367689 0.958033153 0.127828832 0.047701303 0.279044173 12.52286415 0.012023403 0.018960798 4489.425955 -3.652190813 0.063665464 ELNLQDFSHLDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELNLQDFSHLDHR 13 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91;Q5VZK9-4 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ; 124.51 0.00012196 107255000 66091 63636 64500 78715 71136 60219 75555 68276 6243.6 FALSE TRUE 62967.00941 70120.58075 67457.3888 70802.41865 83542.09588 58133.60093 64027.69709 62297.39149 7211.8256 8.731077663 9.723000061 9.353718814 9.817544486 11.58404273 8.060871706 8.878153832 8.638227675 1 12.81614879 -0.088901575 0.717547435 0.638745513 9.586965357 0.8992065 0.885874564 1.67168611 0.848690125 2.529708253 0.303369289 0.814888944 0.088901575 8.948219844 ELNNYEIRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELNNYEIRPGR 11 1 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;;; 167.71 1.73E-05 893121000 559271 600889 571500 646593 596395 549021 636196 605144 585270 FALSE TRUE 532835.3682 662120.2723 597703.8403 581596.2432 700406.0992 530008.2651 539132.6157 552154.3833 676030.6825 0.788182226 0.979423404 0.884137149 0.860310424 1.036056672 0.784000311 0.797497258 0.816759354 1 19.3667292 ELNQHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELNQHLR 7 0 O60675;I3L2F8;O15525 O60675 MAFK;MAFG Transcription factor MafK;Transcription factor MafG 0 133.9 0.0032266 61078000 51031 42382 41381 48428 70723 37726 59227 44335 67245 FALSE TRUE 48618.86576 46700.77398 43278.35978 43559.92543 83057.06881 36419.53916 50190.83337 40452.79237 77673.01116 0.625942847 0.601248404 0.557186584 0.560811597 1.069316968 0.468882803 0.64618112 0.52080886 1 16.24512578 -2.137602291 2.448053815 1.801751748 0.630912794 0.332974409 0.163999441 8875631.435 2441564.08 39529973.54 0.036134086 0.007284466 2.137602291 -1.170838954 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.354)NHDGADET(0.323)S(0.323)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 46.446 0.019011 630850000 59050 47218 43887 60208 24540 59722 58736 65080 28073 TRUE FALSE 56258.82353 52029.56788 45899.26236 54155.77745 28819.76823 57653.81217 49774.74444 59381.25019 32426.41746 1.734968829 1.604542591 1.415489775 1.67011288 0.888774354 1.777988957 1.535005971 1.831261509 1 14.98488202 4.079398341 2.010139163 1.476687059 1.718998166 0.08455533 0.30488391 0.868291928 6.788073247 0.075775335 0.233634815 12006.00007 -4.079398341 0.242311107 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNS(0.005)NHDGADET(0.497)S(0.497)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR 330.01 6.38E-117 626867000 144949 140455 115127 178812 94863 150044 142745 150471 73099 TRUE FALSE 138097.548 154767.5242 120405.6868 160837.478 111407.0772 144847.9387 120966.6286 137294.9615 84434.81958 1.635552118 1.832982234 1.426019353 1.90487146 1.319444723 1.715500067 1.432662842 1.626046721 1 16.36555045 -2.664481961 0.203273325 3.55E-10 1.753531513 0.544537878 0.178689476 31.2805419 0.728522809 14.22604031 0.382459458 0.0021653 2.664481961 1.753531513 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.007)NHDGADET(0.496)S(0.496)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.015)NHDGADET(0.492)S(0.492)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.092)NHDGADET(0.454)S(0.454)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.002)NHDGADET(0.499)S(0.499)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 165.17 4.07E-20 192445000 141297 136052.7 122820 156582 86632.8 151202 154051 177931 77146.8 TRUE FALSE 134618.1708 149916.6248 128451.4185 140842.0799 101741.5329 145965.8368 130547.6906 162350.4184 89110.33173 1.51069094 1.682370853 1.441487378 1.580535917 1.141747886 1.638034939 1.465011835 1.821903423 1 16.44330509 3.719478584 23.27806268 1.465693447 1.596530912 0.061687767 0.237325482 919.7147278 1121954.369 0.056247254 0.087342266 5241.777523 -3.719478584 0.130837465 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.164)S(0.836)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.25)S(0.75)EKEQQEAIEHIDEVQNEIDR 257.84 1.16E-59 811870000 329128 356110 281103 404980 218072 390570 364730 396270 174154 TRUE FALSE 313570.7717 392398.0139 293991.8506 364270.641 256103.6878 377044.463 309083.7398 361570.498 201160.9129 1.558805671 1.950667296 1.461476021 1.810842056 1.273128483 1.874342573 1.536499986 1.797419255 1 17.61799048 -1.806365505 2.696609812 0.800027312 1.665482435 0.498191856 0.207382191 15141777.8 10546707.53 19736076.11 0.043223816 0.015618326 1.806365505 0.865455123 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 0 50.665 0.0076679 24772000 55322 51032 49218 62601 39502 55298 67143 67934 35057 FALSE TRUE 52707.0387 56232.21882 51474.69398 56308.22855 46391.13629 53383.01639 56899.10218 61985.33882 40493.46051 1.301618534 1.388674075 1.271185355 1.390551161 1.145645141 1.318312036 1.40514299 1.530749361 1 15.30540132 1.975848351 24.02018969 1.358166898 1.307832339 0 0.14956941 2194.017958 2182072.832 0.054837074 0.035637551 94.5906808 -1.975848351 -0.050334558 ELNVS(ph)FINEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELNVSFINEK 10 0 P49585;C9JEJ2;C9J050;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 1 ELNVS(1)FINEK;ELNVS(1)FINEK 107.65 0.0026709 15180000 83475 81041 75410 108473 82037 106459 113724 95949 89719 TRUE FALSE 79529.30218 89299.17004 78867.62309 97569.08795 96344.22683 102772.2981 96373.31512 87547.1969 103632.1643 0.767419099 0.861693574 0.761034218 0.941494261 0.929674947 0.99170271 0.929955635 0.844787885 1 16.66111232 3.226915234 24.99869811 0.938862044 0.806454259 0.646306337 0.049652909 130.510016 280160.403 0.01342509 0.016171143 1686.223876 -3.226915234 -0.132407785 ELNYFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELNYFAK 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 126.67 0.0091423 2045788000 4482960 3565590 3463790 4145980 3919570 3752400 4881370 4303220 4204420 FALSE TRUE 4271059.365 3928927.675 3622608.198 3729218.214 4603141.767 3622453.447 4136627.354 3926407.244 4856419.98 0.879466641 0.809017278 0.745942116 0.767894504 0.947846724 0.745910251 0.851785342 0.808498289 1 22.21146176 -1.447349526 3.122068797 1.003358104 0.821252239 0.453491528 0.062231455 18024729.84 22774848.66 532911.107 0.014165301 0.035698542 1.447349526 -0.182105865 ELPDVLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELPDVLER 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 115.49 0.0057067 66111000 179661 180223 180240 185905 221748 181805 203420 186224 229762 FALSE TRUE 171168.7806 198587.9286 188504.1823 167217.4762 260420.781 175509.0473 172384.5429 169917.2393 265392.3175 0.644965092 0.748280623 0.710285 0.630076551 0.981267218 0.661319246 0.649546093 0.640249277 1 18.01776708 -2.286634075 2.39757328 2.423528471 0.707505894 0.439366912 0.103568668 4928709.897 629217.1781 38576145.28 0.023367284 0.005168517 2.286634075 -1.716022577 ELPDVQGESDSIS(ph)PLLLHLEDDDFSENEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGES(0.003)DS(0.094)IS(0.903)PLLLHLEDDDFSENEK 126.04 1.36E-05 16880000 104530 84129 84856 101730 63402 93985 98897 106480 64336 TRUE FALSE 99589.07406 92701.84075 88746.73153 91503.90713 74459.28873 90730.27588 83808.44628 97156.04671 74312.8983 1.340131745 1.247452903 1.194230525 1.231332773 1.00196992 1.220922316 1.127777926 1.307391435 1 16.18132502 8 0.274338808 1.116289381 2.836025003 0.33869814 0.092903003 53.14387975 0.74701926 0.095042843 43.51034175 100000000 -8 1.719735621 ELPESGIQLGT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELPESGIQLGTPR 13 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR 223.26 1.80E-10 407118000 381364 372742 407358 427310 420477 367081 462120 422862 526726 TRUE FALSE 363337.6795 410724.8336 426035.7672 384355.987 493808.0557 354368.8929 391615.1066 385833.9615 608407.9779 0.597194141 0.675081275 0.700246845 0.631740544 0.811639679 0.582452739 0.643671879 0.634169793 1 19.21467955 -0.991895052 4.272862705 1.000016056 0.657630796 0.738064633 0.063734944 24445821.99 33622647.82 5319.871358 0.014219316 0.101883756 0.991895052 -0.342385259 ELPEVTNSVFHEINMWVSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPEVTNSVFHEINMWVSQR 20 0 A0A0C4DFN3;Q99685-2;Q99685;H7C5K5;H7C599;H7C4E0;E7EWX8 A0A0C4DFN3 MGLL Monoglyceride lipase 0 82.36 0.0039193 0 80488 60271 85321 72403 68437 91736 104440 97073 76471 FALSE TRUE 76683.49175 66412.68342 89233.05224 65124.91288 80372.39113 88559.15932 88505.75983 88572.7735 88329.73212 0.868150394 0.751872352 1.010226682 0.737293223 0.909913222 1.002597395 1.001992848 1.002751524 1 16.43061152 2.405459436 3.908965635 1.001450486 0.83765785 0.511131494 0.073468735 0.164099914 4.993256196 0.024231578 0.020144702 254.3662197 -2.405459436 -0.163792636 ELPGFLQSGKDKDAVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPGFLQSGKDKDAVDK 17 2 P25815 P25815 S100P Protein S100-P 0 92.474 0.001856 223020000 368780 256010 304830 349610 242610 397920 513500 449820 226450 FALSE TRUE 351348.5003 282097.7101 318806.757 314466.5386 284921.1072 384139.9306 435156.1439 410431.3762 261566.7095 1.343246245 1.078492407 1.21883537 1.202242209 1.089286583 1.468611703 1.663652629 1.569126962 1 17.99681941 2.17549628 7.098442592 1.502595152 1.188462145 0.238148023 0.191692262 0.213079247 19.62100524 0.064824489 0.04793598 149.7946422 -2.17549628 -0.314133006 ELPGHTGYLSCCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 262.43 4.11E-24 1772960000 1134524 832047 731781 861610 1319876 674208 1148410 917762 1359260 FALSE TRUE 1080897.299 916833.5353 765333.8827 774999.3258 1550061.957 650860.0079 973198.9625 837397.8939 1570047.099 0.688448964 0.583952887 0.487459187 0.493615336 0.987270992 0.414548079 0.619853356 0.533358454 1 20.58237641 -1.171082912 4.761526786 1.000044906 0.602613317 0.389955231 0.156801545 6.74E-05 1.17E-05 0.136851156 0.03225249 0.067439926 1.171082912 -0.397431589 ELPPAAAIGATSLVAAPHS(ph)SSSSPSKDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.187)S(0.187)S(0.187)S(0.187)S(0.187)PS(0.044)KDS(0.011)S(0.011)R;ELPPAAAIGATSLVAAPHS(0.19)S(0.19)S(0.19)S(0.19)S(0.19)PS(0.043)KDS(0.003)S(0.003)R;ELPPAAAIGATSLVAAPHS(0.194)S(0.194)S(0.194)S(0.194)S(0.194)PS(0.028)KDS(0.001)S(0.001)R 138.71 4.13E-07 331871000 285981 218931 301862 315955 344874 280526 458608 418144 498125 TRUE FALSE 272463.2449 241240.3178 315702.6713 284194.6031 405019.9164 270811.3143 388638.9267 381529.0946 575371.6809 0.473543023 0.419277357 0.548693448 0.493932205 0.703927443 0.470671956 0.675457169 0.663100231 1 19.13413469 -5 0.115196293 2.571709447 0.288662042 0.825465498 0.070935991 54.12597594 0.409264599 19.65592701 0.677779754 1.00E-05 5 -2.283047404 ELPPLS(ph)PSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELPPLSPSLSR 11 0 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 ELPPLS(0.932)PS(0.068)LSR;ELPPLS(0.849)PS(0.15)LSR 146.36 3.76E-05 134463000 141217 134798 135309 152714 140116 128606 151102 135448 166529 TRUE FALSE 134541.9523 148534.0695 141513.0515 137362.8986 164552.186 124152.342 128048.6147 123587.4551 192353.4668 0.699451663 0.772193358 0.735692753 0.714117093 0.855467743 0.645438546 0.665694343 0.642501833 1 17.55340031 -1.13387899 4.537859975 1.000033117 0.717911852 0.663888759 0.063425515 2.11E-05 4.03E-06 0.061079997 0.014395005 0.073471856 1.13387899 -0.282121265 ELPPPSEEIKTGEDEDEEDNDALLKENES(ph)PDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPPPSEEIKTGEDEDEEDNDALLKENESPDVR 33 2 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 ELPPPSEEIKTGEDEDEEDNDALLKENES(1)PDVR 91.761 0.0001355 24363000 43846 55119 68454 60048 21909 66226 56428 52730 21687 TRUE FALSE 41773.48647 60735.68877 71592.68361 54011.86096 25729.92266 63932.57701 47818.87223 48112.68166 25050.1092 1.667596981 2.424567825 2.857978903 2.156152715 1.027138144 2.552187558 1.908928694 1.920657562 1 14.61252927 2.981532362 24.88211678 1.800531492 2.279591299 0.222072768 0.53335859 1310.069984 1765107.473 0.155077562 0.167265799 958.3681285 -2.981532362 0.479059807 ELPPPSEEIKTGEDEDEEDNDALLKENES(ph)PDVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPPPSEEIKTGEDEDEEDNDALLKENESPDVRR 34 3 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 ELPPPSEEIKTGEDEDEEDNDALLKENES(1)PDVRR 110.51 7.72E-06 74249000 48935 31640 43699 40573 26986 43999 57149 48224 22595 TRUE FALSE 46621.93953 34864.15197 45702.64237 36494.52496 31692.34986 42475.3036 48429.87044 44001.25091 26098.9172 1.786355318 1.335846683 1.751131743 1.398315672 1.214316656 1.627473786 1.855627575 1.685941626 1 14.67170233 2.037455623 24.99781815 1.642083385 1.501224476 0 0.283589122 516.2623249 344550.5458 0.097895416 0.072300372 109.0073101 -2.037455623 -0.14085891 ELPPS(ph)PEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 52.928 0.088774 99198000 454000 519180 338100 539780 217630 483510 418490 488580 221270 TRUE FALSE 432540.3197 572085.0323 353602.2194 485520.2889 255584.6031 466765.9275 354641.6644 445797.3451 255583.4215 1.692364541 2.238349533 1.38351 1.89965486 1.000004623 1.82627623 1.38757695 1.744234201 1 17.96343473 2.035962163 0.069610788 1.26E-13 3.114749232 0.290298337 0.330361157 28.27515068 1.467481356 29.3190135 34.098439 108.6330974 -2.035962163 3.114749232 ELPSFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELPSFLGK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 174.27 0.00063491 1564320000 5867600 4858300 3706000 5730700 4286000 4519800 5528400 4999800 4448900 FALSE TRUE 5590250.176 5353366.293 3875923.766 5154639.148 5033477.043 4363278.193 4684941.044 4561991.006 5138812.69 1.087848597 1.041751591 0.754244998 1.003079789 0.979501949 0.849082941 0.911677721 0.887751954 1 22.29300364 3.973304376 24.69786489 0.91026481 1.070562253 0.423338018 0.07479888 458.4203823 424115.2727 0.017487313 0.031562469 9403.821481 -3.973304376 0.160297443 ELPSFLGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELPSFLGKR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 141.02 0.00017271 6753100000 6607700 3100200 6422800 4186300 7461700 5534300 8681000 6571300 10114700 FALSE TRUE 6295367.116 3416113.905 6717291.733 3765485.171 8763018.118 5342645.803 7356554.012 5995882.135 11683236.02 0.538837622 0.292394496 0.5749513 0.322298134 0.750050594 0.45729161 0.6296675 0.513203887 1 23.47793659 -5 0.165400472 2.954163031 0.370582829 0.594932134 0.130075962 79.94663532 0.745649532 50.97265205 0.440963887 1.00E-05 5 -2.583580202 ELPSLSPAPDTGLS(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.044)GLS(0.772)PS(0.184)KR 94.18 0.0012322 166320000 140200 117750 122750 149290 128380 127700 157970 141090 129190 TRUE FALSE 133573.0238 129748.8589 128378.2089 134283.0856 150769.4314 123277.717 133868.7752 128735.4116 149224.1254 0.895116815 0.869489826 0.86030465 0.899875172 1.010355604 0.826124574 0.897098742 0.862698383 1 17.18712127 -2.480832861 2.13264916 2.174072447 0.889287875 0.34025697 0.048066006 1636808.047 155222.6796 9323804.565 0.010866871 0.003304967 2.480832861 -1.284784572 ELPSLSPAPDTGLSPS(ph)KR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.011)GLS(0.426)PS(0.563)KR 86.684 0.0020839 197480000 127980 126960 118480 157280 115850 135440 152470 145240 133170 TRUE FALSE 121930.639 139897.3683 123912.4252 141469.9156 136054.2033 130749.6788 129207.9012 132522.0156 153821.3235 0.79267709 0.909479682 0.805560779 0.919702889 0.884495077 0.850010102 0.83998693 0.861532151 1 17.23089599 -1.484690142 2.442295081 1.007827837 0.858024116 0.551722599 0.040245309 1778615.717 1626763.76 93406.47298 0.009638768 0.032757433 1.484690142 -0.14980372 ELPTAFDYVEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELPTAFDYVEFTR 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 199.03 2.82E-07 85835000 62973 57493 54184 61483 56613 57271 72030 63522 69536 FALSE TRUE 59996.39109 63351.60206 56668.39 55302.61203 66486.28928 55287.69091 61040.50058 57959.67693 80319.28774 0.746973645 0.78874706 0.705539001 0.688534642 0.827774886 0.688348869 0.759973131 0.721615923 1 16.29345886 -2.001201009 2.433228592 1.257343194 0.744361515 0.773341976 0.044041672 3774648.175 1602595.183 5441460.63 0.009723114 0.009972384 2.001201009 -0.512981679 ELQAHGADELLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELQAHGADELLKR 13 1 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 88.768 0.0050355 328120000 246310 245390 230650 264480 191090 276820 261280 273490 194940 FALSE TRUE 234667.4144 270395.52 241225.5306 237893.9679 224416.0355 267233.654 221416.9373 249541.7657 225170.2996 1.042177476 1.20084896 1.071302614 1.056506868 0.996650251 1.18680685 0.983331006 1.108235705 1 17.78065702 3.500129893 24.02837612 1.056566219 1.123940323 0.128822229 0.070226237 785.1092145 819902.3546 0.016935643 0.026011802 3163.223607 -3.500129893 0.067374104 ELQELVQYPVEHPDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 224.86 1.08E-12 4196180000 4149684 4777385 3501271 4994426 2613475 4011445 3895703 4253608 2329045 FALSE TRUE 3953536.661 5264205.963 3661807.739 4492376.81 3069264.213 3872527.654 3301341.958 3881139.534 2690221.403 1.469595274 1.956792834 1.361154786 1.669891112 1.140896511 1.43948288 1.227163665 1.442684059 1 21.35929348 3.011242925 1.418530518 1.272727146 1.686394053 0.390311169 0.209567946 0.360272017 1.499845174 0.071692711 0.086360905 1026.225792 -3.011242925 0.413666907 ELQELVQYPVEHPDKFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELQELVQYPVEHPDKFLK 18 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 181.88 4.28E-14 761346000 1607800 1039723 1443720 1466850 1229690 1603390 2017210 1767050 1393170 FALSE TRUE 1531802.48 1145671.956 1509915.99 1319399.451 1444147.547 1547864.202 1709447.566 1612317.734 1609215.688 0.951893827 0.711944312 0.938293108 0.81990218 0.897423234 0.961874914 1.062286167 1.001927676 1 20.61792628 2.208338021 2.181503685 1.027059775 0.847172677 0.533707164 0.068210466 0.210537373 2.021645019 0.030458089 0.019925531 161.5615537 -2.208338021 -0.179887098 ELQEMDKDDESLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELQEMDKDDESLIK 14 1 P52566;F5H3P3;H0YGX7;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 174.62 2.29E-06 124660000 249060 233930 203390 274860 131950 263010 239700 280700 114410 FALSE TRUE 237287.4274 257767.733 212715.6327 247230.5506 154962.0382 253901.8978 203129.3626 256120.4199 132152.1185 1.795562796 1.950538031 1.609627111 1.87080278 1.172603512 1.921285112 1.537087449 1.938072752 1 17.01184003 -2.467151049 0.280429095 1.43E-20 1.796411434 0.447863619 0.245360044 38.99373306 1.323954069 24.89082503 0.263638401 0.003410743 2.467151049 1.796411434 ELQNAGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 121.64 0.0033144 164844000 203142 188949 200098 213502 205334 187990 230530 199508 237425 FALSE TRUE 193539.8802 208203.1179 209272.6912 192040.3733 241144.1846 181479.8592 195358.4145 182038.0219 274243.6564 0.705722359 0.759190279 0.763090363 0.700254569 0.879306336 0.661746789 0.712353449 0.66378207 1 18.06509872 -1.193924072 4.198264552 1.000107318 0.731708591 0.647642249 0.062426028 7.078501707 32144029.36 6609.6048 0.013445732 0.063984669 1.193924072 -0.268398727 ELQNTVSQLLESEGWNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELQNTVSQLLESEGWNRR 18 1 Q7L0Y3;C9JVB6 Q7L0Y3 TRMT10C Mitochondrial ribonuclease P protein 1 0 ; 165.9 4.33E-11 100867000 94821 69797 98579 78379 99403 84618 112440 88199 106991 FALSE TRUE 90338.99925 76909.39365 103098.9447 70500.19401 116738.8517 81687.65744 95285.2129 80475.82799 123582.6178 0.731000855 0.622331805 0.834251179 0.570470146 0.944621936 0.660996335 0.771024393 0.65119051 1 16.91511631 -2.320868095 2.289445083 2.514560883 0.720973813 0.390284623 0.108681216 6656195.58 1064542.496 51998660.77 0.023186676 0.004776743 2.320868095 -1.793587069 ELQQAELPNRS(ph)PGFGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 181.83 4.73E-10 820360000 1194680 1175990 973640 1288510 820130 1190780 1067600 1212140 839990 TRUE FALSE 1138209.844 1295824.718 1018282.357 1158986.527 963160.4123 1149542.99 904718.0122 1105998.596 970251.3591 1.173108219 1.335555684 1.049503665 1.194521931 0.992691639 1.184788848 0.932457351 1.13990935 1 19.88799902 3.319550943 1.199500211 1.047278452 1.249344722 0.323891667 0.098638567 0.421587984 1.276044824 0.03286285 0.055202528 2087.136933 -3.319550943 0.20206627 ELQREPLTPEEVQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELQREPLTPEEVQSVR 16 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 ;; 164.53 6.70E-09 521760000 284676 255187 264815 287381 316345 266540 310136 313581 355320 FALSE TRUE 271219.9297 281190.8454 276957.0297 258492.9159 371515.4678 257309.653 262819.0572 286122.1852 410421.2109 0.660833121 0.685127469 0.674811687 0.629823481 0.905205331 0.626940436 0.640364217 0.697142783 1 18.64674577 0.933531222 21.07649318 1 0.68513737 0.597173819 0.079984977 3633.82731 1152248.051 0.072005306 0.018001327 8.580868023 -0.933531222 -0.314862631 ELQTLHNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 140.16 0.00010975 232110000 440730 346022 281157 341120 344695 319684 446959 398813 428328 FALSE TRUE 419897.5663 381282.0352 294048.3266 306829.9695 404809.6989 308613.2629 378767.1956 363890.8195 494750.9186 0.848704976 0.770654527 0.59433609 0.620170591 0.81820909 0.623775017 0.765571485 0.73550307 1 18.91634286 0.232800636 1.502728814 1.000101075 0.7264761 0.509619338 0.085674386 7.759478485 14.12458591 0.08468291 0.024150585 1.709230508 -0.232800636 -0.273624975 ELRAPS(ph)PPVEHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELRAPSPPVEHPR 13 1 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR 137.73 3.46E-05 414487000 525563 273488 496628 396124 570251 435493 664694 473393 638514 TRUE FALSE 500720.6786 301356.7381 519398.885 356304.8629 669702.5939 420411.7682 563282.7224 431940.1993 737531.49 0.678914304 0.408601859 0.704239605 0.48310461 0.908032542 0.570025516 0.763740572 0.58565662 1 19.49234512 -5 0.137704452 2.28641486 0.48931139 0.397384689 0.140634907 123.222099 1.046777853 43.38725708 0.800760346 1.00E-05 5 -1.79710347 ELS(ph)GTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSGTIK 7 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 1 ELS(0.962)GT(0.038)IK 94.309 0.014995 67411000 233750 223580 187940 254780 138440 220390 227050 232340 141250 TRUE FALSE 222701.1007 246363.0562 196557.2349 229169.0303 162583.8922 212757.839 192409.3524 211995.0779 163154.3286 1.364972065 1.510000123 1.204731965 1.40461508 0.9965037 1.304028161 1.179308904 1.299353071 1 17.31587774 7.999999964 0.084336959 0.810014686 2.568001475 0.398848102 0.127628085 147.1045366 0.898870262 2.654444477 30.01617959 99999991.74 -7.999999964 1.757986789 ELS(ph)NSPLRENS(ph)FGSPLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.5)NS(0.5)PLRENS(0.541)FGS(0.459)PLEFR 94.594 0.00089421 23314000 35452 34523 32991 40289 35727 32944 40475 39328 41375 TRUE FALSE 33776.25422 38040.93295 34503.66998 36239.07318 41957.77749 31803.14102 34299.79538 35884.23183 47791.22369 0.706745959 0.795981563 0.721966657 0.75827883 0.877938966 0.66545986 0.717700714 0.750854008 1 15.54445809 0.903730029 20.29913982 1 0.748092198 0.655052055 0.057155872 11511.79374 2427340.893 0.052499327 0.013124832 8.011798706 -0.903730029 -0.251907802 ELS(ph)NSPLRENSFGS(ph)PLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.544)NS(0.456)PLRENS(0.002)FGS(0.998)PLEFR 134.2 5.80E-06 50322000 94856 85926 86078 103180 89653 84100 110520 93100 116480 TRUE FALSE 90372.34487 94681.95709 90024.76144 92808.15037 105288.4548 81187.59591 93658.14416 84947.67045 134543.1235 0.671697984 0.703729441 0.669114549 0.689802258 0.782562884 0.603431776 0.696119889 0.63137876 1 17.03770913 -1.144775952 4.494191845 1.000043112 0.682917333 0.819829632 0.046992503 1.91E-05 3.63E-06 0.040502815 0.009545239 0.071651296 1.144775952 -0.317125779 ELS(ph)PAALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 149.49 9.18E-05 1259480000 3273150 3113220 2992280 3576810 2224840 3211220 3351350 3324460 2449530 TRUE FALSE 3118434.686 3430460.657 3129478.998 3217262.263 2612851.392 3100014.646 2840040.006 3033352.658 2829390.602 1.102157717 1.212437991 1.106061141 1.137086644 0.923467898 1.095647467 1.003763851 1.072086921 1 21.43205993 2.884367226 9.196695487 1.024379835 1.146696452 0.546587382 0.054282132 0.239080343 17.59437503 0.014973467 0.015894073 766.2442447 -2.884367226 0.122316617 ELS(ph)PAALEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSPAALEKR 10 1 O75683 O75683 SURF6 Surfeit locus protein 6 1 ELS(1)PAALEKR 84.297 0.0091982 59592000 126190 99124 116130 113250 95621 125800 144760 152860 133890 TRUE FALSE 120225.2488 109224.8483 121454.6754 101865.8948 112297.2721 121443.5145 122674.2033 139474.768 154652.9774 0.777387224 0.706257649 0.785336806 0.658673997 0.726124217 0.785264639 0.793222383 0.901856339 1 17.23867508 1.157256959 1.214747838 1.000574794 0.732907717 0.85300408 0.03728179 0.145127046 0.43661471 0.032442621 0.010295414 14.36339019 -1.157256959 -0.267667077 ELS(ph)PAGSISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ELSPAGSISK 10 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 ELS(0.997)PAGS(0.003)ISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(0.994)PAGS(0.006)ISK;ELS(1)PAGSISK 208.33 1.21E-07 5297950000 10807770 9146380 8854910 10511830 7373970 9936610 11512880 11062640 8304940 TRUE FALSE 10296908.13 10078406.52 9260916.382 9455160.877 8659988.033 9592502.704 9756378.707 10093936.59 9592827.679 1.073396549 1.050618948 0.965400056 0.985648986 0.902756551 0.999966123 1.017049303 1.052237873 1 23.19352471 3.860056325 4.838754716 0.988611201 1.065013469 0.39041609 0.038233243 0.216173407 7.61370359 0.010217084 0.018957351 7245.299203 -3.860056325 0.076402268 ELS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELSPEAR 7 0 Q9P0B6 Q9P0B6 CCDC167 Coiled-coil domain-containing protein 167 1 ELS(1)PEAR;ELS(1)PEAR 82.426 0.025723 243329000 289510 218329 282030 344910 343740 308150 366220 321340 356880 TRUE FALSE 275825.4361 240576.9733 294961.3545 310238.9915 403688.1472 297478.6882 310346.4129 293201.7661 412223.1277 0.669116839 0.583608626 0.715538102 0.752599674 0.979295241 0.721644828 0.752860264 0.711269568 1 18.65306592 -4.999997764 0.040079283 2.237737708 1.18E-10 0.460544807 0.095059744 736.1421389 2.202996848 110.8211676 33.25685635 1.00E-05 4.999997764 -2.237737708 ELS(ph)PQHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ELSPQHKR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR 83.397 0.011142 3413520000 2459208 1844185 2224057 2315814 1814273 2275192 2800773 2471912 1982258 TRUE FALSE 2342966.112 2032109.548 2326032.213 2083023.977 2130681.637 2196401.531 2373463.639 2255458.281 2289656.447 1.023282823 0.88751723 1.015886998 0.909753941 0.930568269 0.959271219 1.036602519 0.985064062 1 21.12669971 1.857894541 6.721731097 1.009577768 0.951203264 0.246230841 0.043481913 0.303538293 15.34039748 0.017581172 0.010746046 72.09323948 -1.857894541 -0.058374504 ELSDFISYLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 280.2 5.68E-27 3104357000 1098150 844180 723960 819740 1187120 788684 1183310 968580 1078880 FALSE TRUE 1046242.626 930202.9018 757154.2821 737338.1778 1394153.352 761371.6753 1002774.327 883766.0004 1246187.2 0.839554945 0.74643914 0.60757668 0.591675294 1.118735092 0.610960918 0.80467391 0.709175957 1 20.24908937 ELSDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELSDFLR 7 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;;;; 173.93 0.0019657 682177000 2173655 1799905 1413960 1670298 2294910 1488952 2308065 1958384 2274811 FALSE TRUE 2070910.636 1983317.366 1478791.465 1502396.472 2695141.577 1437389.219 1955927.294 1786897.515 2627577.072 0.788144583 0.754808446 0.562796609 0.571780173 1.025713615 0.547039794 0.744384366 0.680055224 1 21.32530165 -1.657538467 2.536852631 1.038635513 0.714074828 0.2969461 0.140385924 16446174.84 13447424.38 4125289.071 0.031585172 0.022001968 1.657538467 -0.324560685 ELSDIAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 ELSDIAHR 8 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;;;;; 217.81 7.24E-06 91073626000 47962449.9 41379146.7 42241976.8 48489309.2 49960922.3 43687308 54632143.3 47449311.9 47907150.7 FALSE TRUE 45695359.95 45595728.79 44178813.22 43615071.72 58674091.33 42174405.57 46297006.45 43294398.61 55336346.95 0.825774784 0.823974319 0.798368806 0.788181261 1.060317396 0.762146544 0.836647321 0.782386279 1 25.72172407 -2.30879917 2.252297485 1.821523394 0.834404673 0.279507382 0.083391445 4083387.499 696744.6123 17029906.32 0.018514894 0.004911349 2.30879917 -0.987118721 ELSDIALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSDIALR 8 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 89.369 0.032464 48940000 245760 207480 212060 264630 276180 210310 274100 246810 253800 FALSE TRUE 234143.4118 228622.4479 221783.1608 238028.8896 324345.7046 203026.912 232281.0108 225198.008 293158.0078 0.798693557 0.779860832 0.756531136 0.811947425 1.10638528 0.692551138 0.792340665 0.768179623 1 18.16131894 -1.737301853 2.653424389 1.038193193 0.809749466 0.222965901 0.109347539 28214157.68 22346999.09 7103233.388 0.025129194 0.018310413 1.737301853 -0.228443727 ELSDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELSDLAR 7 0 P61077-3;P61077-2;P61077;A0A087WY85;D6RA11;D6RGD0;D6R933;D6RIZ3;D6R980;D6R9F6 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ;;; 145.88 0.0052498 441988000 1117840 997000 875000 1050660 1265820 910120 1217640 1027870 1222540 FALSE TRUE 1065001.919 1098595.433 915119.6155 945045.6607 1486578.607 878602.3162 1031866.655 937864.2537 1412125.259 0.754183746 0.777973077 0.648044222 0.669236425 1.052724323 0.622184406 0.730718927 0.664150894 1 20.42943663 -1.106598513 4.23955385 1.000041182 0.74250038 0.311688972 0.121416024 20071668649 76901447204 14870292.4 0.026869574 0.078235072 1.106598513 -0.257540802 ELSDSVTLSSSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSDSVTLSSSDR 13 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 62.14 0.0789 33547000 14083 10008 15837 11898 47623 9720.2 20953 10961 49838 FALSE TRUE 13417.3245 11027.82658 16563.14211 10701.99044 55928.43612 9383.587037 17756.23502 10001.19673 57566.6225 0.233074721 0.19156633 0.287721277 0.185906172 0.971542774 0.163003953 0.308446705 0.173732561 1 15.81294495 -2.221831856 2.335825716 3.285899826 0.306850688 0.448162104 0.238969397 14043253.06 2557069.305 169692401 0.055218827 0.006000233 2.221831856 -2.979049137 ELSEALGQIFDSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELSEALGQIFDSQR 14 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EJY8 Q08380 LGALS3BP Galectin-3-binding protein 0 ;; 340.88 1.41E-68 143621000 214631 131335 114806 105344 206471 116958 234251 131235 170902 FALSE TRUE 204485.818 144718.1858 120069.9687 94754.62098 242479.477 112907.7151 198511.7076 119743.3677 197404.6093 1.035871547 0.733104391 0.608242984 0.480002069 1.228337463 0.571960885 1.00560827 0.606588509 1 17.59079615 2.775121857 24.99971542 0.867192094 0.747275799 0.103529781 0.234888274 1836.00058 1255410.489 0.06796058 0.072081102 595.8293019 -2.775121857 -0.119916296 ELSEPMEFQYLPDTDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELSEPMEFQYLPDTDDR 17 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ; 252.14 1.30E-26 71102000 66809 66299 52688 75227 61321 59607 64427 65398 60943 FALSE TRUE 63651.07097 73054.94348 55103.79692 67665.03904 72015.36299 57542.79464 54597.47787 59671.40442 70393.72919 0.904215073 1.037804707 0.782794115 0.961236744 1.023036623 0.817442055 0.775601442 0.847680683 1 16.1031593 2.216894026 24.99858664 0.833564042 0.945142597 0.137995886 0.090960716 314.0637883 362359.7698 0.031883216 0.023567778 164.7760266 -2.216894026 0.111578555 ELSEQIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELSEQIQR 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 176.09 0.00061035 1153690000 1803680 1419420 1486000 1737230 1599580 1575680 1882190 1747700 1688280 FALSE TRUE 1718423.621 1564060.512 1554134.57 1562600.34 1878546.246 1521113.807 1595027.347 1594662.123 1950089.84 0.881202284 0.802045362 0.79695537 0.801296591 0.963312668 0.780022425 0.817925059 0.817737773 1 20.89510916 -1.561736376 6.017793026 1.000388831 0.831290116 0.490757595 0.053588543 0.000260753 1.90E-05 0.048396728 0.011381319 0.027432389 1.561736376 -0.169098715 ELSESVQQQSTPVPLIS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELSESVQQQSTPVPLISPKR 20 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 1 ELSESVQQQSTPVPLIS(1)PKR;ELSESVQQQSTPVPLIS(1)PKR;ELSESVQQQST(0.001)PVPLIS(0.999)PKR;ELSESVQQQS(0.001)T(0.021)PVPLIS(0.978)PKR;ELSESVQQQST(0.002)PVPLIS(0.998)PKR 211.98 1.34E-22 929439000 934573 599491 945912 882616 769838 946237 1188491 1066716 940516 TRUE FALSE 890397.5864 660579.8145 989283.0008 793893.7628 904097.5035 913468.5754 1007164.87 973308.692 1086366.418 0.819610743 0.608063544 0.91063474 0.730778999 0.832221513 0.840847582 0.927094996 0.895930393 1 20.05107936 1.968527276 0.516470172 0.995141061 0.725976845 0.496688251 0.077535924 0.62782691 0.365473024 0.070281416 0.051575261 93.00949282 -1.968527276 -0.269164215 ELSFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ELSFGR 6 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;; 185.89 0.0048112 3197412000 2293310 1845664 1892219 2198584 2202880 1877068 2282300 1991939 2284690 FALSE TRUE 2184909.781 2033739.26 1978979.113 1977578.159 2587061.575 1812064.664 1934093.218 1817514.261 2638988.057 0.827934699 0.77065118 0.749900746 0.749369878 0.980323336 0.686651332 0.732891994 0.688716365 1 21.33155339 ELSLKAS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELSLKASPLR 10 1 Q86W50 Q86W50 METTL16 Methyltransferase-like protein 16 1 ELS(0.015)LKAS(0.985)PLR 53.377 0.087211 154290000 360960 365080 376250 380020 263620 434560 492730 429970 158670 TRUE FALSE 343898.1362 402282.0671 393501.4347 341819.6676 309595.2445 419511.0782 417554.9889 392319.5474 183275.7332 1.876397546 2.194955437 2.147046026 1.865056882 1.689232061 2.288961396 2.278288465 2.140597342 1 17.48365625 3.25594742 24.81293269 1.982036484 2.0709184 0.007817835 0.384410518 1563.392298 2231123.322 0.09949831 0.13441438 1802.799462 -3.25594742 0.088881916 ELSNS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.001)NS(0.999)PLR;ELS(0.028)NS(0.972)PLR;ELS(0.002)NS(0.998)PLR;ELS(0.002)NS(0.998)PLR;ELS(0.002)NS(0.998)PLR 164.48 0.00034602 5425750000 5893720 7005620 4766770 6835730 4903170 5754210 5003480 5605040 4366460 TRUE FALSE 5615135.536 7719500.643 4985331.119 6148589.433 5758281.296 5554940.265 4240107.231 5114232.983 5043588.316 1.113321545 1.530557246 0.988449256 1.219090268 1.141703274 1.101386536 0.840692571 1.014006827 1 22.26601909 2.502288665 0.885311318 0.933469107 1.280029694 0.348015263 0.14699989 0.52489801 0.832720522 0.097049869 0.070811456 317.8986365 -2.502288665 0.346560587 ELSNS(ph)PLRENS(ph)FGSPLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.004)NS(0.996)PLRENS(1)FGSPLEFR;ELS(0.018)NS(0.982)PLRENS(1)FGSPLEFR;ELS(0.002)NS(0.998)PLRENS(1)FGSPLEFR;ELS(0.023)NS(0.977)PLRENS(0.992)FGS(0.008)PLEFR 291.64 8.40E-50 1046960000 1383730 1193810 1221520 1454190 1359210 1231700 1482350 1372160 1460120 TRUE FALSE 1318323.825 1315460.596 1277527.9 1308012.058 1596255.794 1189045.92 1256190.282 1252006.396 1686547.952 0.781669933 0.779972247 0.757480923 0.775555807 0.946463331 0.705017559 0.744829271 0.742348532 1 20.68564191 -1.472358306 3.093411735 1.005164162 0.777843583 0.542633543 0.063705169 18628496.63 23482287.86 834858.3696 0.015093508 0.033700915 1.472358306 -0.227320579 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELSNS(1)PLRENSFGS(1)PLEFR;ELSNS(1)PLRENSFGS(1)PLEFR;ELS(0.016)NS(0.984)PLRENSFGS(1)PLEFR;ELSNS(1)PLRENSFGS(1)PLEFR;ELS(0.15)NS(0.85)PLRENS(0.058)FGS(0.942)PLEFR 317.65 5.16E-62 2614966000 1674438 1420269 1505854 1607357 1554702 1483099 1795391 1635931 1861083 TRUE FALSE 1595290.634 1564996.026 1574898.895 1445782.421 1825841.537 1431738.91 1521471.128 1492680.209 2149690.247 0.74210256 0.728010014 0.732616663 0.672553836 0.849350989 0.666021029 0.707762958 0.694369903 1 21.03569736 -0.988832206 4.195032991 1.000015159 0.724154429 0.744011595 0.050860048 18981712.7 55955644.06 4943.785489 0.011046292 0.102604827 0.988832206 -0.27586073 ELSNS(ph)PLRENSFGSPLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.031)NS(0.969)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.002)NS(0.998)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR 298.32 5.23E-50 29859860000 7298760 5729940 6307700 6956620 7048500 6539220 7935420 7084340 8074220 TRUE FALSE 6953762.08 6313827.4 6596914.284 6257327.341 8277756.168 6312765.172 6724725.935 6463997.633 9326328.8 0.745605503 0.676989578 0.707343096 0.670931454 0.887568554 0.676875682 0.721047486 0.69309133 1 23.15287786 -1.507220183 3.095103337 1.008317806 0.720675365 0.657160824 0.062994649 16616746.75 22112230.54 1195424.626 0.014288612 0.031101391 1.507220183 -0.287642441 ELSNSVSTYRPFGLGSES(ph)PYKQPSDGMERPSSLMDSSQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.037)ES(0.962)PY(0.001)KQPSDGMERPSSLMDSSQEK;ELSNSVSTYRPFGLGS(0.027)ES(0.973)PYKQPSDGMERPSSLMDSSQEK;ELSNSVSTYRPFGLGS(0.178)ES(0.821)PYKQPSDGMERPSSLMDSSQEK;ELSNSVS(0.001)T(0.001)YRPFGLGS(0.09)ES(0.904)PY(0.004)KQPSDGMERPSSLMDSSQEK 186.95 2.41E-24 936740000 1160350 1120370 1042560 1211230 556905 1234720 1138330 1327170 583915 TRUE FALSE 1105502.555 1234536.977 1090362.407 1089474.859 654029.0557 1191961.337 964656.8516 1210955.959 674465.556 1.639079335 1.830392917 1.616631713 1.615315785 0.969699712 1.767267915 1.430253692 1.795430394 1 19.36338524 -3.108956515 0.169135601 5.23E-18 1.751585302 0.323284793 0.252392428 73.37695585 1.244222677 28.46853378 0.947678416 0.000778114 3.108956515 1.751585302 ELSPLISLPS(ph)PVPPLS(ph)PIHSNQQTLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELSPLISLPSPVPPLSPIHSNQQTLPR 27 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2;E7ETI4;E7EMC5 A0A669KBI3 AFF1 AF4/FMR2 family member 1 2 ELSPLIS(0.003)LPS(0.997)PVPPLS(0.997)PIHS(0.003)NQQTLPR;ELSPLIS(0.093)LPS(0.907)PVPPLS(0.999)PIHS(0.001)NQQTLPR 181.18 9.11E-18 125121000 60800 59464 55520 68999 71814 57752 72686 71235 70496 TRUE FALSE 57926.10449 65523.4492 58065.64692 62063.08943 84338.33886 55752.03376 61596.41573 64997.28576 81428.15964 0.711376811 0.804678007 0.713090498 0.762182146 1.035739224 0.684677561 0.756451036 0.798216318 1 16.31324018 ELSSTEAQLHDAQELLQEETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELSSTEAQLHDAQELLQEETR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 348.2 2.75E-95 316876000 152103 122882 131873 152428 157418 134261 166112 146638 157922 FALSE TRUE 144913.3926 135403.8155 137919.5075 137105.6478 184871.6494 129611.5079 140768.5635 133797.5993 182411.7372 0.794430199 0.742297714 0.756088997 0.751627335 1.013485493 0.710543685 0.771707817 0.733492271 1 17.47683904 -2.262629535 2.257415884 1.853717587 0.78202947 0.390764038 0.084639167 6399830.483 910026.3224 27945372.17 0.019071416 0.005462236 2.262629535 -1.071688117 ELSVEEQIKR ddPTM_SK-BR-3_Trastuzumab_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 ; 77.64 0.05194 168524000 322230 220450 241550 268600 274690 246650 308480 277030 273490 FALSE TRUE 306998.8265 242914.1056 252625.3064 241599.8177 322595.849 238108.4487 261415.7104 252771.7846 315901.4324 0.971818406 0.768955379 0.799696616 0.764794942 1.021191473 0.753742858 0.82752303 0.800160299 1 18.26911495 -1.692432486 2.37445108 1.030182914 0.83775713 0.244334079 0.08925806 7253317.959 5288708.191 1310207.172 0.021659642 0.020303341 1.692432486 -0.192425784 ELSVQDQPSLS(ph)PTSLQNSSSHTTTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.944)PT(0.042)S(0.014)LQNSSSHTTTAK;ELSVQDQPSLS(0.834)PT(0.121)S(0.044)LQNS(0.001)S(0.001)SHTTTAK 193.18 2.11E-18 259630000 239390 160995 212470 251660 266540 178710 284090 224820 261170 TRUE FALSE 228074.5091 177400.5735 222211.9597 226362.6587 313024.4916 172521.2279 240746.8528 205133.569 301670.9097 0.756037463 0.588059928 0.73660387 0.7503629 1.037635654 0.571885529 0.798044641 0.679991217 1 18.20261606 -5 0.235515984 2.454279629 0.705197209 0.27399525 0.129361528 213.8594075 2.135960819 149.0554077 0.198882781 1.00E-05 5 -1.74908242 ELT(ph)NRHSLPFSLPSQMEPRPDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.674)NRHS(0.326)LPFSLPSQMEPRPDVPR;ELT(0.61)NRHS(0.389)LPFS(0.001)LPSQMEPRPDVPR;ELT(0.565)NRHS(0.435)LPFSLPSQMEPRPDVPR 194.66 8.99E-17 392599000 211990 191474 208977 235940 208316 214502 253132 235147 230369 TRUE FALSE 201969.6528 210985.4183 218558.8022 212222.8629 244646.2444 207073.742 214512.0643 214556.2821 266093.448 0.75901776 0.792899712 0.821361081 0.797550126 0.919399731 0.778199326 0.806153124 0.806319298 1 18.02157346 -5 0.276057024 2.366813817 0.793930298 0.663318198 0.04247829 133.395189 1.284425587 104.3456694 0.048663698 1.00E-05 5 -1.572883519 ELTDEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 135 0.00054241 535750000 822030 846020 756990 955640 777960 831730 921330 869300 746250 FALSE TRUE 783174.271 932230.3998 791698.7403 859577.2516 913635.9777 802926.9815 780764.1871 793179.4836 861974.6387 0.908581571 1.081505601 0.918471037 0.997218727 1.059933711 0.931497222 0.905785567 0.920188887 1 19.7172859 2.051821992 24.97498436 0.928302663 0.994413972 0.161930338 0.058436619 137.7943536 66407.59963 0.020438657 0.015094945 112.6735537 -2.051821992 0.066111308 ELTDEEAERLQLEIDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELTDEEAERLQLEIDQK 17 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 108.25 0.00060605 36734000 145720 134990 162450 155100 209280 140510 186960 184800 260470 FALSE TRUE 138832.1044 148745.6345 169898.4932 139509.0533 245778.3657 135644.1035 158435.8182 168617.9323 300862.3573 0.46144724 0.494397624 0.564705052 0.463697269 0.816912983 0.450851029 0.526605653 0.560448751 1 18.19874409 -5 0.303058614 4.939195385 0.510699522 0.654042414 0.10485262 163.8538091 1.505638107 410.7396753 0.096203844 1.00E-05 5 -4.428495863 ELTDEEAERLQLEIDQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELTDEEAERLQLEIDQKK 18 2 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;;; 176.46 4.52E-13 180541000 278702 177024 278120 254041 189962 289482 347481 340489 233261 FALSE TRUE 265528.3088 195062.9469 290872.0771 228504.316 223091.3127 279457.1658 294466.3915 310673.9781 269433.9245 0.985504365 0.723973223 1.079567384 0.848090367 0.828000086 1.037201111 1.092907629 1.153061845 1 18.03957199 2.105452134 4.888115706 1.086142398 0.88533092 0.438933667 0.100431819 0.17651575 6.916281539 0.036663229 0.026554129 127.4829586 -2.105452134 -0.200811478 ELTHIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELTHIYR 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 177.71 0.00072635 1214080000 997282 826830 824202 963727 1059768 882541 1079715 958174 1075911 FALSE TRUE 950142.4563 911084.917 861992.4769 866851.331 1244591.204 851978.3839 914984.6464 874271.205 1242757.783 0.764543557 0.733115439 0.693612616 0.697522351 1.001475284 0.685554656 0.736253403 0.703492842 1 20.24511371 -1.089527843 4.509615058 1.000019511 0.751019989 0.417973495 0.09198521 1.67E-05 3.38E-06 0.082617271 0.019471552 0.081371469 1.089527843 -0.248999522 ELTIGS(ph)KLQDAEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELTIGSKLQDAEIAR 15 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 1 ELT(0.008)IGS(0.992)KLQDAEIAR 77.681 0.015241 41565000 66947 59040 59956 78433 45957 60919 71794 71966 44820 TRUE FALSE 63782.54799 65056.24312 62705.0419 70548.76583 53971.88625 58809.35975 60840.50671 65664.27552 51770.45669 1.232025987 1.256628728 1.211212841 1.362722493 1.042522892 1.135963704 1.175197412 1.268373503 1 15.65984142 2.736048224 24.99993661 1.139339538 1.257384506 0.414692807 0.082061949 245.6699205 2444560.329 0.024135549 0.023759149 544.5631179 -2.736048224 0.118044968 ELTIGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELTIGSK 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 138.9 0.0063773 3626400000 8293430 7414130 6492310 8957000 5886750 7771370 8254480 8234870 6416490 FALSE TRUE 7901416 8169638.276 6789988.835 8056625.343 6913397.336 7502245.508 6995107.472 7513781.127 7411526.498 1.066098327 1.10228821 0.916139049 1.087039943 0.932789937 1.01224026 0.943814675 1.013796703 1 22.82133928 3.758354607 24.98107205 0.985199562 1.084193279 0.402238288 0.049467388 641.0666555 809058.02 0.011078331 0.019938839 5732.639176 -3.758354607 0.098993718 ELTNRHS(ph)LPFSLPSQMEPRPDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.079)NRHS(0.92)LPFSLPSQMEPRPDVPR;ELT(0.006)NRHS(0.992)LPFS(0.002)LPSQMEPRPDVPR;ELT(0.003)NRHS(0.997)LPFSLPSQMEPRPDVPR 141.84 1.42E-07 375980000 225211 179905 214560 239941 252502 201286 258328 238046 225977 TRUE FALSE 214565.7224 198237.524 224397.7882 215821.6748 296538.2689 194315.4153 218915.3191 217201.4303 261020.359 0.822026769 0.759471502 0.859694581 0.826838472 1.136073331 0.744445437 0.838690591 0.832124479 1 17.99380281 -5 0.104901902 1.422816849 0.758268738 0.146639223 0.107707045 343.1127312 2.422106585 32.74402964 1.507406418 1.00E-05 5 -0.664548111 ELTPAS(ph)PTCTNSVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ELTPASPTCTNSVSK 15 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 ELTPAS(0.985)PT(0.015)CTNSVSK;ELTPAS(0.999)PT(0.001)CTNSVSK;ELTPAS(0.697)PT(0.302)CT(0.001)NSVSK;ELTPAS(0.984)PT(0.016)CTNSVSK;ELTPAS(0.982)PT(0.017)CT(0.001)NSVSK;ELTPAS(0.999)PT(0.001)CTNSVSK;ELTPAS(0.61)PT(0.243)CT(0.146)NS(0.001)VSK 371.87 1.36E-97 1263886000 2300695 2304484 2126246 2667761 1732678 2499904 2555299 2622013 1997628 TRUE FALSE 2191945.707 2539313.54 2223736.482 2399592.596 2034856.495 2413331.698 2165441.206 2392415.642 2307409.948 0.949959373 1.100503854 0.963737061 1.039950702 0.881879051 1.045905042 0.938472684 1.036840308 1 21.13784291 ELTVDPTAAGDVRPIMHHPPNQIDDLET(ph)QWGVGSSPQRDDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 42 2 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.333)QWGVGS(0.333)S(0.333)PQRDDLK 55.044 0.020267 47494000 37194 28563 26779 42704 25567 38481 40375 39545 5590 TRUE FALSE 35435.91333 31473.60217 28006.84364 38411.31279 30025.87671 37148.39332 34215.05221 36082.23016 6456.86865 5.48809574 4.874437421 4.337527237 5.94890726 4.650222628 5.75331408 5.299016298 5.588193304 1 12.65661896 -0.324998244 7.299065675 1.000000053 5.228689296 0.876706837 0.499968187 0 0 0.437633842 0.10315128 0.473153172 0.324998244 4.228689242 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQRDDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 42 2 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.008)QWGVGS(0.496)S(0.496)PQRDDLK 100.35 1.55E-05 266480000 140800 143240 122940 163530 97483 153320 157160 153110 9486.5 TRUE FALSE 134144.663 157836.3189 128576.9206 147091.6537 114484.0043 148010.49 133182.3556 139702.8767 10957.61797 12.24213724 14.40425458 11.73402111 13.42368881 10.44789156 13.50754246 12.15431638 12.74938377 1 13.41964659 -0.797662428 0.878909529 1.08E-13 12.71694738 0.918041998 1.086963739 11.77741616 4.749478439 37.90833411 0.317959657 0.159344682 0.797662428 12.71694738 ELVALCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELVALCR 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 104.11 0.019134 112017000 187867 145046 155613 175256 187920 147996 187790 191046 216346 FALSE TRUE 178986.8992 159826.3523 162748.01 157638.9339 220693.1885 142870.8614 159139.1865 174316.9994 249895.8327 0.716246034 0.639571899 0.651263401 0.630818578 0.883140731 0.571721664 0.63682209 0.697558649 1 17.93096732 0.945687913 19.79799322 1.000000001 0.672128801 0.602004249 0.082328862 725.2566088 264374.0443 0.073514202 0.018378551 8.824455419 -0.945687913 -0.3278712 ELVALMSAIRDGETPDPEDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELVALMSAIRDGETPDPEDPSR 22 1 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 84.762 0.0029566 29798000 69994 28182 73338 48159 111910 56496 116670 83792 144820 FALSE TRUE 66685.52233 31053.77784 76700.61984 43317.96582 131427.0686 54539.52935 98869.84871 76454.72827 167277.946 0.398651011 0.185641793 0.458522009 0.258958021 0.785680789 0.326041362 0.591051308 0.457052051 1 17.35188773 -4.999999996 0.125285623 2.981411183 0.148905063 0.586375363 0.157646532 91.34012858 0.731469952 45.29604019 1.178952542 1.00E-05 4.999999996 -2.83250612 ELVEFAQDDDRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 253.69 7.90E-24 688850000 909500 758510 780430 951010 884340 804880 992420 982030 1028390 FALSE TRUE 866509.7375 835803.0314 816213.4875 855412.668 1038568.616 777006.8038 841008.102 896038.2471 1187867.469 0.729466679 0.703616399 0.687125045 0.720124669 0.874313544 0.654119103 0.707998261 0.7543251 1 20.17994245 0.801246899 4.471179062 0.999996497 0.722933492 0.690554841 0.057337752 1.462907567 32.47467909 0.052116851 0.013235387 6.327714832 -0.801246899 -0.277063004 ELVGPPLAETVFT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 ELVGPPLAET(0.001)VFT(0.999)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK 179.81 7.32E-06 67497000 106898 122537 85799 118295 67640 112923 84048 111760 62836 TRUE FALSE 101845.1434 135023.6596 89732.96902 106403.7619 79436.39458 109012.4482 71224.93395 101973.7019 72580.28596 1.403206698 1.860335184 1.236327025 1.466014641 1.094462409 1.501956719 0.981326169 1.404977958 1 16.14729012 3.715179548 24.086818 1.243150805 1.631770923 0.374548856 0.210065952 408.1491482 420468.9985 0.050498224 0.078293468 5190.14568 -3.715179548 0.388620119 ELVGPPLAETVFT(ph)PKT(ph)SPENVQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 ELVGPPLAETVFT(0.999)PKT(0.544)S(0.457)PENVQDR;ELVGPPLAETVFT(1)PKT(0.942)S(0.058)PENVQDR 192.42 3.53E-17 151713000 167095 151244 152612 166538 98296 174162 181418 179408 117056 TRUE FALSE 159196.7505 166655.9356 159609.4112 149797.2838 115438.7913 168130.7263 153739.3521 163698.0844 135208.4466 1.177417199 1.232585239 1.180469232 1.10789886 0.853783873 1.243492773 1.137054348 1.210709009 1 17.04482576 3.296529237 4.391766372 1.100739995 1.204401266 0.169872332 0.108813052 0.384695197 15.01142641 0.030236122 0.040662022 1979.380269 -3.296529237 0.10366127 ELVLDNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELVLDNSR 8 0 P39687;H0YN26;H7BZ09 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 105.57 0.01015 143990000 379210 310100 301260 328260 442250 302180 391530 342080 414020 FALSE TRUE 361285.4948 341699.5426 315073.069 295262.6811 519378.26 291715.4308 331794.9076 312125.6617 478224.1071 0.755473197 0.714517603 0.658839787 0.617414883 1.086056207 0.609997335 0.693806319 0.652676553 1 18.86732733 -2.138571554 2.407754349 1.597010369 0.723129653 0.289369473 0.136123791 6326343.228 1732451.683 20638204.58 0.030206392 0.007268226 2.138571554 -0.873880716 ELVLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELVLQR 6 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 103.71 0.080148 425540000 442470 405490 380820 404030 500510 380520 494980 394630 438820 FALSE TRUE 421555.32 446809.892 398280.9737 363416.1368 587798.7855 367342.497 419461.7101 360074.1051 506869.9644 0.83168337 0.881507928 0.785765584 0.716981006 1.159663872 0.724727293 0.827552902 0.710387536 1 18.95125615 -0.992575023 4.10639202 1.000011708 0.834474518 0.144335881 0.129801248 34112549.21 88036322.71 6274.945014 0.02824496 0.101724363 0.992575023 -0.16553719 ELVSDLSSQFVIS(ph)PPALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELVSDLSSQFVISPPALR 18 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 ELVSDLSSQFVIS(1)PPALR 186.56 4.97E-14 10365000 14989 17454 15291 17811 19851 18431 24049 18732 20742 TRUE FALSE 14280.49968 19232.58244 15992.10747 16020.60444 23313.00811 17792.72985 20379.88336 17091.72678 23958.56342 0.596049914 0.802743558 0.667490249 0.668679677 0.973055342 0.74264594 0.850630441 0.713386962 1 14.54825379 -0.506687248 0.042890601 1.81650973 1.63E-10 0.456499573 0.097027196 194.5128116 1.985081906 50.72338508 33.82969868 0.311395801 0.506687248 -1.81650973 ELVVNCCTEFIHLISSEANEICNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELVVNCCTEFIHLISSEANEICNK 24 0 Q01658 Q01658 DR1 Protein Dr1 0 ; 233.5 1.47E-45 70207000 150615 120825 134600 143921 107232 135714 168696 154035 120721 FALSE TRUE 143495.7274 133137.2049 140771.5431 129453.7876 125933.2268 131014.1902 142958.3269 140546.8788 139441.7961 1.02907257 0.954786933 1.009536215 0.928371487 0.903123958 0.939561837 1.025218628 1.007925046 1 17.08930353 -0.652307334 5.740376689 1 0.975797693 0.032339986 0.043122953 3.18E-10 5.54E-11 0.04270508 0.010065684 0.222685873 0.652307334 -0.024202307 ELWAVLNGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELWAVLNGWR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ; 186.76 3.03E-06 266870000 520720 441580 321830 340690 477910 297070 557170 399040 413820 FALSE TRUE 496106.5976 486577.504 336586.2238 306443.1939 561257.3527 286782.3914 472163.4834 364097.9422 477993.0921 1.037894911 1.01795928 0.704165456 0.641103813 1.174195531 0.599971833 0.98780399 0.761722184 1 18.86663024 3.848814223 8.345364315 0.838280486 1.029982373 0.166069911 0.176690136 0.457475707 31.45672524 0.040666663 0.073541021 7060.154799 -3.848814223 0.191701887 ELYHEEFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ELYHEEFAR 9 0 Q9Y6U3;Q9Y6U3-2;F8WBX5;C9JGB6 Q9Y6U3 SCIN Adseverin 0 ;;;;; 192.91 3.42E-05 5062930000 3574410 2908210 3094900 3680810 4451940 2913430 3678480 3182600 3955180 FALSE TRUE 3405454.723 3204559.905 3236804.226 3310807.986 5228356.926 2812537.189 3117260.316 2903914.672 4568529.114 0.745416005 0.701442374 0.708500295 0.724698892 1.144428939 0.615632979 0.682333468 0.63563449 1 22.12329832 -2.330237827 2.276698426 2.462947566 0.741009245 0.227796398 0.147543279 6649032.122 1062786.904 49912033.23 0.034096295 0.004674791 2.330237827 -1.721938321 ELYIQHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ELYIQHAK 8 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ; 124.98 0.0012814 300260000 930420 870310 706550 874180 780720 644730 699620 747820 650020 FALSE TRUE 886440.8905 958995.5785 738946.0164 786305.7656 916877.3208 622402.8384 592880.1196 682336.9164 750821.7818 1.180627563 1.277261265 0.984182977 1.047260195 1.221165053 0.82896215 0.789641609 0.908786789 1 19.51811098 2.233559423 24.99990131 0.855054 1.152544248 0.622143653 0.099631682 74.29039485 371357.7713 0.037713254 0.028719953 171.2219438 -2.233559423 0.297490248 ELYQQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 139.14 0.0015711 282050000 332447 303379 239499 268107 301486 279803 344614 296867 341776 FALSE TRUE 316732.8892 334293.665 250480.266 241156.375 354065.0629 270113.352 292036.805 270871.7517 394776.8765 0.802308615 0.846791403 0.634485657 0.610867529 0.896873865 0.684217765 0.739751547 0.686138849 1 18.59067796 -1.799707889 8.598907294 1.004808468 0.746311936 0.449198048 0.090842033 0.008341588 0.000194298 0.087615904 0.020450728 0.015859596 1.799707889 -0.258496532 ELYVAADEASIAPILAEAQAHFGR ddPTM_SK-BR-3_Trastuzumab_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 0 104.18 0.0030963 17869000 21847 17617 18545 24031 22526 15937 22324 21035 15916 FALSE TRUE 20814.33561 19412.19233 19395.30659 21615.35822 26454.52727 15385.09769 18918.06379 19193.06389 18384.17199 1.13218782 1.055918773 1.05500028 1.175759139 1.438983887 0.836866501 1.02904084 1.043999365 1 14.16617658 2.189261636 24.99999996 0.9800543 1.147115052 0.382237233 0.120380295 137.0606512 69503.89178 0.044733026 0.033037588 154.6185642 -2.189261636 0.167060751 EMAEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMAEMR 6 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 108.98 0.069669 171590000 494320 379870 319140 397800 516160 349830 515340 428870 517510 FALSE TRUE 470954.4732 418579.1849 333772.8847 357812.3882 606178.1406 337715.2994 436715.4181 391315.8692 597762.8077 0.787861786 0.700242938 0.55837011 0.5985859 1.014078047 0.564965393 0.730583122 0.654634019 1 19.18921361 -1.681677757 2.62510885 1.043190898 0.704148784 0.334204804 0.132496004 28745583.69 24084542.82 8267645.366 0.030594472 0.020812404 1.681677757 -0.339042114 EMDDFLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMDDFLQK 8 0 O15305;H3BRM0;H3BPH4;H3BR08;H3BM92;H3BV34;H3BT06;H3BNY9;O15305-2 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 78.334 0.060086 0 78298 80427 70611 79275 60316 76940 91812 83344 68536 FALSE TRUE 74597.00871 88622.60274 73848.58419 71306.12639 70835.0913 74275.54851 77804.39316 76045.95753 79164.21285 0.942307212 1.119478102 0.932853136 0.900736884 0.894786783 0.938246536 0.982822798 0.960610291 1 16.27256077 3.688526681 24.99929285 0.941927655 1.030892822 0.316539629 0.052813572 358.8455283 179295.7162 0.013819041 0.021408375 4881.200883 -3.688526681 0.088965167 EMDEAATAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 137.05 0.00030754 319160000 176689 179478 174197 195587 175646 177202 218140 199386 188650 FALSE TRUE 168337.2611 197767.0122 182184.1048 175926.2232 206278.6068 171065.4503 184858.7366 181926.7048 217904.8785 0.772526353 0.907584142 0.836071712 0.807353302 0.946645198 0.785046445 0.848346021 0.834890463 1 17.73333897 -1.903600129 2.171804095 1.096520793 0.843658351 0.472480452 0.052347535 5635176.617 2546681.152 2774887.825 0.012000081 0.012485326 1.903600129 -0.252862442 EMDEEDKAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 90.685 0.011189 227200000 512520 435370 457120 526670 289900 530230 540900 580260 275460 FALSE TRUE 488294.1953 479734.698 478079.4042 473728.131 340458.4682 511868.0021 458375.7707 529449.3582 318176.9299 1.534662477 1.507760786 1.502558354 1.488882714 1.070028768 1.608752722 1.440631697 1.664009262 1 18.27946971 -1.978650303 2.783645721 0.585260327 1.475573495 0.474221613 0.157890626 48572047.3 42102841.31 129972820.4 0.035198611 0.010503879 1.978650303 0.890313168 EMDRETLIDVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 EMDRETLIDVAR 12 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;;;;;;;;; 252.42 4.25E-21 6489310000 5919670 4731640 5386530 5807520 6431400 5488500 7114490 5861910 7287750 FALSE TRUE 5639858.931 5213799.495 5633507.729 5223737.056 7553034.124 5298431.869 6029043.884 5348610.084 8417897.049 0.669984308 0.619370784 0.66922982 0.620551312 0.897259028 0.629424646 0.716217346 0.635385543 1 23.00502843 -5 0.294099195 3.547217788 0.662075758 0.588117299 0.082919094 171.785725 1.606005003 269.1472783 0.079146908 1.00E-05 5 -2.88514203 EMDTART(ph)PLSEAEFEEIMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.182)ART(0.818)PLSEAEFEEIMNR;EMDT(0.362)ART(0.638)PLSEAEFEEIMNR 238.72 1.97E-29 273680000 135662 110491 113627 138796 114684 122122 129168 132229 118019 TRUE FALSE 129249.5261 121750.1585 118836.9103 124843.9624 134684.8533 117892.8845 109461.0493 120650.3278 136320.7838 0.94812781 0.893115159 0.871744624 0.915810186 0.987999405 0.864819591 0.802966696 0.885047199 1 17.05664601 2.07327004 24.99999997 0.864051505 0.91943219 0.010637851 0.058839592 68.75106093 23456.23236 0.020565508 0.015188634 118.3777389 -2.07327004 0.055380685 EMEADERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EMEADERDR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 126.55 0.00049369 514189000 703910 551370 641150 676340 746160 652260 809790 689880 823610 FALSE TRUE 670637.5693 607555.2299 670547.3617 608353.0182 876290.0678 629672.0726 686241.6627 629470.4499 951331.2324 0.704946444 0.638636901 0.704851621 0.639475503 0.921119835 0.66188521 0.721348821 0.661673273 1 19.85958822 -5 0.389986225 5.449036679 0.6976249 0.555746492 0.081882371 479.9349047 3.469607778 1812.603863 0.048934277 1.00E-05 5 -4.751411778 EMEAELEDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EMEAELEDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 218.58 1.56E-08 3162760000 3233980 2677500 2835110 3316440 2968580 2963300 3589280 3236920 3301650 FALSE TRUE 3081116.175 2950340.294 2965102.598 2983065.15 3486299.412 2860680.178 3041669.414 2953478.125 3813653.02 0.80791728 0.773625781 0.77749669 0.782206754 0.914162719 0.750115483 0.797573717 0.774448569 1 21.86274216 -1.895047419 2.370919664 1.1149148 0.796175735 0.673660105 0.044355765 4823751.01 2428919.994 3093727.92 0.010408915 0.01273364 1.895047419 -0.318739065 EMEAELEDERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EMEAELEDERK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 184.55 7.79E-06 2403750000 2637880 2269940 2238190 2751210 1613770 2589850 2768590 2707830 1721370 FALSE TRUE 2513192.64 2501249.467 2340813.225 2474653.144 1895210.977 2500162.845 2346190.747 2470718.05 1988311.268 1.263983502 1.25797681 1.177287109 1.244600473 0.953176199 1.257430305 1.179991677 1.242621359 1 20.9231122 -5 0.103491674 0.431932507 1.31979406 0.301021796 0.092795731 220.0981567 1.53780259 27.66257009 1.325119115 1.00E-05 5 0.887861553 EMEEQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMEEQMR 7 0 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 98.523 0.026056 41630000 83635 75181 70388 85011 96526 73078 83494 78976 87252 FALSE TRUE 79681.7393 82842.02937 73615.35942 76465.53277 113360.1038 70547.29054 70755.45683 72060.44276 100782.5945 0.790629966 0.821987465 0.730437232 0.758717645 1.124798427 0.699994784 0.702060283 0.715008808 1 16.62088698 -0.722427429 7.925257406 1 0.79158951 0.215035776 0.124294891 0 0 0.116222545 0.027393916 0.189484012 0.722427429 -0.208410491 EMEHNTVCAAGTS(ph)PVGEIGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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(0.02)S(0.98)PVGEIGEEK;EMEHNTVCAAGT(0.026)S(0.974)PVGEIGEEK;EMEHNTVCAAGT(0.007)S(0.993)PVGEIGEEK;EMEHNTVCAAGT(0.059)S(0.941)PVGEIGEEK;EMEHNTVCAAGT(0.043)S(0.957)PVGEIGEEK;EMEHNTVCAAGT(0.037)S(0.963)PVGEIGEEK;EMEHNTVCAAGT(0.004)S(0.996)PVGEIGEEK;EMEHNTVCAAGT(0.009)S(0.991)PVGEIGEEK;EMEHNTVCAAGT(0.008)S(0.992)PVGEIGEEK;EMEHNTVCAAGT(0.01)S(0.99)PVGEIGEEK;EMEHNTVCAAGT(0.008)S(0.992)PVGEIGEEK;EMEHNTVCAAGT(0.007)S(0.993)PVGEIGEEK;EMEHNTVCAAGT(0.056)S(0.944)PVGEIGEEK 256.97 2.55E-37 11006630000 11743622 9291693 10704594 11681860 8560177 11556657 13684572 13035196 8843178 TRUE FALSE 11188524.26 10238527.08 11195410.22 10507577.24 10053069.16 11156447.07 11596739.21 11893765.13 10214532.88 1.095353492 1.002349026 1.096027626 1.028688963 0.984192745 1.092213144 1.135317625 1.164396383 1 23.28411989 2.014005263 24.70782925 1.114646323 1.042446323 0.195054948 0.054677654 240.4156905 424135.2249 0.018627097 0.013750391 103.2773921 -2.014005263 -0.0722 EMFEDTVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EMFEDTVEER 10 0 Q16576;E9PC52 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;; 276.03 1.67E-23 1084180000 1505800 1269090 1311520 1565900 1499720 1364570 1647630 1448520 1606900 FALSE TRUE 1434623.818 1398411.714 1371654.489 1408492.757 1761270.693 1317314.599 1396253.783 1321679.91 1856089.845 0.772928003 0.753418116 0.739002206 0.758849449 0.948914568 0.709725665 0.752255494 0.71207755 1 20.82383512 -1.342751827 3.810523742 1.000725237 0.767767138 0.539689209 0.067218236 225.7898134 32185072.34 35403.2475 0.014832819 0.045420109 1.342751827 -0.2329581 EMFEVTGLHDVDQGWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EMFEVTGLHDVDQGWMR 17 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 226.25 2.13E-15 255240000 245560 232930 214505 243760 268740 236060 260260 256840 229310 FALSE TRUE 233952.8655 256665.8318 224340.2664 219256.7817 315608.1709 227885.183 220552.557 234349.728 264870.2236 0.88327356 0.969024862 0.846981829 0.827789469 1.191557762 0.860365427 0.832681583 0.884771889 1 18.01492614 -0.883252681 3.832231292 1.000004543 0.911153945 0.062370075 0.107110407 22779402.74 50916783.14 1547.659241 0.025158876 0.130842044 0.883252681 -0.088850598 EMFNPMYALFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMFNPMYALFR 11 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 94.309 0.0079242 0 48942 49053 44259 41274 56778 43255 69130 51450 56300 FALSE TRUE 46628.60865 54051.55647 46288.31893 37125.0591 66680.06522 41757.0685 58582.94884 46944.76525 65030.71646 0.717024372 0.831169629 0.711791619 0.570884978 1.025362611 0.642113001 0.900850429 0.721886023 1 15.9888337 -5 0.199481696 2.047397541 0.733881435 0.252011846 0.128741723 189.8122951 1.876574511 78.99896462 0.273177874 1.00E-05 5 -1.313516106 EMFPYEAST(ph)PTGISASCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.033)T(0.965)PT(0.002)GISASCR;EMFPYEAS(0.038)T(0.959)PT(0.003)GISASCR 143.28 1.19E-06 118262000 181269 190870 211033 290130 294510 239690 301890 221650 322270 TRUE FALSE 172700.7736 210319.87 220709.0718 260965.5812 345872.4508 231389.4752 255831.1359 202241.151 372245.9857 0.463942609 0.565002386 0.592911892 0.701056804 0.92915025 0.621603682 0.687263653 0.54329975 1 18.50589677 3.489901651 1.925645495 0.728773903 0.506705436 0.346629757 0.13593422 0.374318115 2.777925313 0.038408801 0.064537468 3089.59569 -3.489901651 -0.222068467 EMKPVIFLDVFLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EMKPVIFLDVFLPR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 158.17 4.66E-06 210310000 418010 402500 422510 515570 488220 468930 570260 486830 533730 FALSE TRUE 398251.4957 443515.2076 441882.5014 463743.9241 573365.4134 452690.8365 483256.3635 444200.5844 616498.1225 0.645989795 0.719410476 0.71676212 0.752222768 0.930035944 0.734293942 0.783873212 0.720522201 1 19.23373698 -5 0.083187829 1.755282344 0.524788292 0.57902691 0.069383831 171.4730298 1.004184379 24.04604514 2.051254958 1.00E-05 5 -1.230494051 EMLFEFIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMLFEFIDR 9 0 O60942-2;O60942 O60942-2 RNGTT mRNA-capping enzyme;Polynucleotide 5-triphosphatase;mRNA guanylyltransferase 0 92.062 0.017682 0 10476 10192 10374 11273 13587 11226 14377 11711 12999 FALSE TRUE 9980.820241 11230.57639 10849.65816 10139.81662 15956.5685 10837.24081 12183.5246 10685.52276 15014.81853 0.664731327 0.747966175 0.722596689 0.675320624 1.062721369 0.721769683 0.811433357 0.711665128 1 13.87409942 -5 0.058960839 1.784765663 0.415690427 0.321577222 0.111482153 485.1997755 2.092242646 56.94717665 9.794836958 1.00E-05 5 -1.369075236 EMLQQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 126.52 0.0091752 614279000 1172840 1011350 876120 1046960 877540 1017960 1181880 1142990 976570 FALSE TRUE 1117402.178 1114407.715 916290.9686 941717.5917 1030582.698 982707.79 1001562.499 1042903.736 1128011.488 0.990594679 0.98794004 0.812306416 0.834847519 0.913627839 0.871185977 0.887900974 0.924550634 1 20.10535033 3.773196044 22.18865546 0.88493328 0.989267559 0.37784292 0.051226976 129.3779085 82882.64395 0.01199141 0.021614731 5931.930362 -3.773196044 0.104334279 EMLWGSSTQLASDGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMLWGSSTQLASDGSPK 17 0 A0A0J9YW64;A6NIW2;Q5JSL3 A0A0J9YW64 DOCK11 Dedicator of cytokinesis protein 11 1 EMLWGSSTQLAS(0.002)DGS(0.998)PK 236.95 3.50E-20 41023000 43638 45311 44083 58888 30966 51047 57223 52019 37477 TRUE FALSE 41575.31822 49928.24241 46104.24915 52968.46636 36366.4606 49279.22959 48492.58038 47463.94059 43288.74175 0.960418726 1.153377077 1.065040176 1.223608361 0.840090497 1.13838443 1.120212286 1.096449993 1 15.40170425 EMNDAAMFYTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 227.72 2.85E-11 470810000 476330 401720 366000 428370 475820 392090 488270 468490 538210 FALSE TRUE 453814.8249 442655.7247 382781.462 385309.4338 558802.8573 378511.825 413775.4438 427466.532 621672.858 0.729989767 0.712039651 0.615728123 0.619794525 0.898869639 0.608860143 0.665583898 0.687606876 1 19.24579607 -1.441956553 6.563336556 1.000066909 0.692309961 0.570716807 0.083864619 7.63E-05 6.49E-06 0.075476326 0.017786091 0.036144602 1.441956553 -0.307756948 EMNPALGIDCLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EMNPALGIDCLHK 13 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;; 175.45 1.82E-05 1576930000 2505310 2207130 2213990 2547690 1983050 2311340 2782620 2633750 2097120 FALSE TRUE 2386888.961 2432039.056 2315503.631 2291591.361 2328893.292 2231297.716 2358080.213 2403124.888 2422330.659 0.985368761 1.004007875 0.955899073 0.946027477 0.961426667 0.921136719 0.973475774 0.992071367 1 21.20796438 1.23871229 4.368792468 0.997684104 0.966344174 0.2676368 0.022127031 0.336821904 14.04281145 0.021528408 0.006294751 17.32655772 -1.23871229 -0.03133993 EMPQDLRS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EMPQDLRSPAR 11 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 EMPQDLRS(1)PAR;EMPQDLRS(1)PAR 63.631 0.04446 394430000 543930 527360 478200 570350 506390 487960 515070 501950 462830 TRUE FALSE 518219.5069 581098.5836 500125.943 513017.3344 594704.2557 471061.8228 436486.6116 457996.597 534603.3126 0.96935334 1.086971535 0.9355085 0.959622438 1.112421569 0.881142731 0.816468214 0.856703627 1 19.02810925 2.117348518 8.289358395 0.865394395 1.012806403 0.408989038 0.072061997 0.193722179 13.23089719 0.025053137 0.018488349 131.0232953 -2.117348518 0.147412008 EMPQDLRS(ph)PART(ph)PPSEEDSAEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMPQDLRSPARTPPSEEDSAEAER 24 2 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 EMPQDLRS(1)PART(0.996)PPS(0.004)EEDSAEAER 72.37 0.053956 147060000 243900 208550 222840 254970 265240 214060 239490 232480 305370 TRUE FALSE 232371.3304 229801.4821 233057.4344 229339.9312 311497.772 206647.0485 202951.402 212122.8187 352725.22 0.658788533 0.651502839 0.660733685 0.65019431 0.88311738 0.585858444 0.575381034 0.601382625 1 18.42818521 -1.104294894 4.813198726 1.000016845 0.655117993 0.610593467 0.085705179 1.53E-05 2.85E-06 0.08198256 0.019322532 0.078651155 1.104294894 -0.344898851 EMQDVDLAEVKPLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EMQDVDLAEVKPLVEK 16 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1;E5RJ98 Q92597 NDRG1 Protein NDRG1 0 ;;;; 204.78 2.22E-11 893084000 2090940 2124730 1755050 2296170 1218473 2284900 2234150 2438260 1431841 FALSE TRUE 1992105.41 2341242.403 1835520.778 2065354.629 1430974.305 2205773.34 1893289.385 2224753.028 1653883.589 1.204501588 1.415602898 1.109824652 1.248790811 0.865220693 1.333693226 1.144753716 1.345169057 1 20.65742626 3.72470378 24.75706301 1.158415079 1.31005225 0.158502552 0.152627031 1084.569507 1937725.967 0.03681172 0.057350972 5305.224658 -3.72470378 0.151637171 EMQPTHPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 25 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 ;;;;;;;;;;;;;;;;;;;;;;;; 158.79 5.05E-05 15377038000 7798941 9041504 7151571 8315781 7617028 7436072 7809276 7777567 6920208 FALSE TRUE 7430300.515 9962843.537 7479477.604 7479862.895 8945435.272 7178558.962 6617827.519 7096522.002 7993358.513 0.929559271 1.246390178 0.935711515 0.935759716 1.119108477 0.898065431 0.827915764 0.887802291 1 22.93037037 2.152783865 7.332208658 0.881083985 1.04381462 0.259168589 0.105550759 0.255338155 18.57979093 0.038925829 0.028727094 142.1621114 -2.152783865 0.162730635 EMTLDEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMTLDEWK 8 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 143.89 0.0013825 111710000 377590 359510 308650 378660 262200 354050 399640 392390 251130 FALSE TRUE 359742.069 396144.4777 322801.9078 340596.3774 307927.597 341789.1597 338667.5781 358030.2514 290073.9578 1.240173615 1.365667159 1.112826226 1.174170822 1.061548576 1.178282816 1.167521485 1.234272301 1 18.14606125 8 0.07381561 0.866618063 1.978551105 0.371713791 0.079861754 219.4524411 1.190262313 2.957992577 25.1412505 99999999.99 -8 1.111933042 EMTNHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EMTNHQK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 65.252 0.053923 28039000 31144 26129 24716 37993 25257 27982 31204 32924 34865 FALSE TRUE 29671.88484 28791.57481 25849.25305 34173.87146 29661.8128 27012.97632 26443.2567 30041.00002 40271.68613 0.736792712 0.714933433 0.641871636 0.84858308 0.73654261 0.670768446 0.656621543 0.745958337 1 15.29747826 0.960366579 22.52997915 1.000000001 0.713452592 0.70633468 0.057267297 1159.862881 659335.9426 0.054218246 0.013554561 9.12780974 -0.960366579 -0.286547409 EMVANWDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EMVANWDSLR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;; 172.98 8.26E-06 269975000 447528 405401 276344 308061 466787 343475 491506 408396 453252 FALSE TRUE 426374.2384 446711.8228 289014.6457 277094.123 548194.505 331580.3746 416517.7326 372634.6812 523540.0053 0.814406223 0.853252509 0.552039277 0.529270199 1.047091912 0.633342956 0.795579571 0.711759708 1 18.99794026 -1.38064516 5.915971146 1.000053784 0.751837827 0.218797436 0.152166267 0.000101242 1.06E-05 0.138186312 0.032563786 0.041625057 1.38064516 -0.248215956 EMVELPLRHPALFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EMVELPLRHPALFK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 160.27 2.87E-06 1612040000 3888600 2666380 3616420 3474300 3653810 3500360 5023040 4152210 4264690 FALSE TRUE 3704793.584 2938087.153 3782236.434 3125056.763 4291033.307 3379141.656 4256682.994 3788620.48 4926036.344 0.752084095 0.596440413 0.767805223 0.634395799 0.871092499 0.685975786 0.864119283 0.769101203 1 22.23199584 0.702933483 0.307233076 1.04584341 0.658921328 0.550256458 0.079934312 1.685925692 0.395592905 0.217078042 0.0940488 5.045840088 -0.702933483 -0.386922081 ENAEVDGDDDAEEMEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 455.31 6.51E-183 220790000 683480 748060 549050 755230 401500 700370 652610 746010 386920 FALSE TRUE 651173.2549 824288.1645 574224.4856 679312.8456 471521.4729 676116.0113 553042.3585 680685.4096 446921.5775 1.457019056 1.84436869 1.284843951 1.519982207 1.05504298 1.512829197 1.237448327 1.523053358 1 18.76966217 7.999999787 0.041993148 5.30E-08 3.793696499 0.315698241 0.206092248 680.3631691 2.172375283 52.14693083 179.6696906 99999950.95 -7.999999787 3.793696446 ENALSSGTLQEEQRT(ph)PPPGQDTQQFHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENALSSGTLQEEQRTPPPGQDTQQFHEK 28 1 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ENALS(0.009)S(0.048)GT(0.048)LQEEQRT(0.894)PPPGQDTQQFHEK 94.188 0.0035186 116380000 93362 85232 84670 102240 72822 87516 101140 98881 72890 TRUE FALSE 88948.96329 93917.2377 88552.20325 91962.64096 85522.13374 84485.29898 85709.23544 90222.45544 84193.40893 1.056483689 1.115493943 1.051771206 1.092278388 1.015781815 1.003466899 1.018004099 1.071609483 1 16.36141968 2.735048642 24.98439408 1.020933192 1.081072339 0.542561174 0.026076924 209.7283134 1492009.736 0.007801731 0.007625706 543.3111808 -2.735048642 0.060139148 ENALVQMADGNQAQLAMSHLNGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENALVQMADGNQAQLAMSHLNGHK 24 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 269.57 2.25E-45 519500000 644940 654440 619400 760450 579910 662310 808900 674880 49070 FALSE TRUE 614454.9643 721128.18 647800.1027 684008.1212 681046.1204 639374.0386 685487.4485 615783.9294 56679.52499 10.84086298 12.72290444 11.42917311 12.06799318 12.01573444 11.28051159 12.09409304 10.86430999 1 15.79054005 0.663515634 3.016778775 1.00006713 11.80223463 0.976898913 0.517179968 0.486976147 4.22502566 0.450861294 0.117807789 4.608033571 -0.663515634 10.80216751 ENAS(ph)PAPGTTAEEAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.998)PAPGT(0.001)T(0.001)AEEAMSR 316.75 2.68E-58 523720000 403790 450610 337910 493300 339970 415390 380920 396780 322420 TRUE FALSE 384703.6469 496527.6713 353403.5077 443712.5468 399260.6604 401004.9401 322803.6579 362035.8397 372419.2469 1.032985406 1.333249222 0.948939967 1.191432909 1.07207311 1.076756756 0.866774907 0.972119037 1 18.50656811 1.966578341 3.256921355 0.93524434 1.132733936 0.334237553 0.106683678 0.237964826 4.848042685 0.049073622 0.028309286 92.59303958 -1.966578341 0.197489596 ENDFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENDFDR 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 101.28 0.085378 792850000 1196300 1082900 1050300 1219500 1058600 1171200 1300600 1219700 1125800 FALSE TRUE 1139753.27 1193248.741 1098457.294 1096913.543 1243219.505 1130641.05 1102169.583 1112896.602 1300383.314 0.87647485 0.917613082 0.844718078 0.843530927 0.956040801 0.869467516 0.847572843 0.855821964 1 20.31050552 -1.856898905 2.660344402 1.050775308 0.877970342 0.542217341 0.03566421 11409551.62 7862900.108 3679695.443 0.008371648 0.013902762 1.856898905 -0.172804966 ENDLYVLPPLQEEEKHS(ph)S(ph)EEEDEKEWQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENDLYVLPPLQEEEKHSSEEEDEKEWQER 29 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;P28715-3 R4GMW8 BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 2 ENDLY(0.001)VLPPLQEEEKHS(0.999)S(1)EEEDEKEWQER 45.07 0.064581 43047000 29256 24939 23332 28021 15737 31129 27569 41486 14170 TRUE FALSE 27873.12686 27480.31245 24401.79528 25204.27584 18481.52782 30050.99492 23362.84271 37853.26591 16367.41123 1.702964902 1.678965114 1.490876898 1.539906066 1.129166217 1.836026144 1.427399995 2.312721626 1 13.99853853 ENDPMDSHQSQES(ph)PNLENIANPLEENVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDS(0.253)HQS(0.145)QES(0.602)PNLENIANPLEENVTK 83.998 0.0013814 33131000 28946 22765 25046 30323 26210 28147 36284 26720 39220 TRUE FALSE 27577.77995 25084.77938 26194.38387 27274.87443 30781.0157 27172.26233 30748.2094 24380.25515 45302.03729 0.608753637 0.553722986 0.578216465 0.602067281 0.679462063 0.599802215 0.678737894 0.538171275 1 15.46728831 -5 0.322065601 4.770146495 0.590043299 0.867202747 0.048226771 105.6617466 0.931121292 271.7965298 0.039409003 1.00E-05 5 -4.180103196 ENDWYLAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENDWYLAYK 9 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 91.584 0.018834 0 151540 159970 134120 161070 130730 147870 161510 155940 105530 FALSE TRUE 144377.0045 176271.1249 140269.5347 144878.9376 153529.2706 142749.2248 136868.6832 142285.0669 121895.0534 1.184436944 1.446089238 1.150740171 1.188554691 1.259520106 1.171083 1.122840339 1.167275151 1 16.89528006 1.519060248 0.325443899 0.984275147 1.318658393 0.461154561 0.08240966 1.085184432 0.394861102 0.134802167 0.117300208 33.04153753 -1.519060248 0.334383247 ENEFSFEDNAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 112.15 0.00054203 183690000 134550 118046 127634 137133 135172 107624 162136 143833 154091 FALSE TRUE 128190.0882 130075.0216 133486.1451 123348.1303 158745.954 103896.9539 137399.1754 131238.22 177986.6453 0.72022307 0.730813379 0.749978432 0.693019019 0.891898118 0.583734548 0.771963397 0.737348692 1 17.44140947 0.265936923 1.822686498 1.000012343 0.732527392 0.550242301 0.075337177 9.027273379 21.40376883 0.062520837 0.017403787 1.84474747 -0.265936923 -0.26748495 ENFQNWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ENFQNWLK 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;; 194.2 0.0003877 1933663000 1561620 1009548 907820 1264190 1101231 1002642 1584840 1353920 1200440 FALSE TRUE 1487805.317 1112422.089 949444.445 1137111.219 1293285.338 967920.2561 1343043.55 1235363.587 1386598.104 1.07298958 0.802267135 0.684729369 0.820072677 0.932703812 0.69805393 0.968588913 0.890931254 1 20.40311826 1.610781203 25 0.947326285 0.846045696 0.189159738 0.11349881 0.566389527 4806.822568 0.056078801 0.02937986 40.81137276 -1.610781203 -0.101280589 ENFS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ENFSPER 7 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 ENFS(1)PER;ENFS(1)PER;ENFS(1)PER;ENFS(1)PER 123.96 0.0043985 2228880000 2847480 2631590 2402980 2913680 2464690 2554390 2642340 2697890 2290850 TRUE FALSE 2712885.264 2899752.013 2513159.01 2620791.351 2894531.156 2465930.834 2239202.503 2461648.449 2646103.318 1.025237845 1.095857442 0.949758459 0.990434248 1.093884406 0.931910261 0.846226407 0.930291887 1 21.33543796 2.097323884 6.389565992 0.903816742 1.033385142 0.430417934 0.057548356 0.158746205 8.830993329 0.020970435 0.015404382 125.1191783 -2.097323884 0.129568401 ENFSCLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENFSCLTR 8 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;C9JF79;C9JRL4 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ; 214.23 2.08E-05 526160000 462210 373140 360180 401050 452960 381290 428240 381460 479010 FALSE TRUE 440362.2493 411163.3902 376694.6093 360735.6921 531956.0806 368085.8317 362904.1228 348057.3402 553292.4244 0.795894232 0.743121308 0.680823725 0.651980176 0.961437492 0.665264543 0.655899316 0.629065797 1 19.07768265 4.3514628 2.662275484 0.729390818 0.791815986 0 0.131282082 1.298708368 17.32188996 0.030720876 0.121122583 22462.74362 -4.3514628 0.062425168 ENFTAGS(ph)DCVTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ENFTAGSDCVTLK 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK 313.16 1.24E-50 337314000 986480 800350 918350 1067450 778140 996390 1179160 1064750 869610 TRUE FALSE 939851.0454 881906.5749 960457.2559 960147.898 913847.3696 961884.7645 999257.4852 971514.8454 1004464.677 0.935673565 0.877986648 0.956188184 0.955880201 0.909785471 0.957609348 0.994815953 0.967196624 1 19.9379954 2.133093379 0.597287139 1.000331098 0.911772269 0.521149378 0.025205101 0.567179695 0.405329442 0.022786093 0.015755365 135.8605532 -2.133093379 -0.088558829 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR 34 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 49.623 0.045002 49249000 11782 9686.9 12245 13309 9006.7 12895 12809 11601 8648.1 FALSE TRUE 11225.08821 10674.00612 12806.44536 11971.15403 10577.46563 12448.44292 10854.7518 10585.15494 9989.20318 1.123722084 1.068554311 1.28202872 1.198409304 1.058889827 1.24618978 1.086648414 1.059659589 1 13.28615389 1.255069256 2.22168778 1.009522803 1.151157128 0.369823477 0.071815445 0.340751296 2.845910015 0.064640739 0.018747405 17.99157799 -1.255069256 0.141634325 ENGDKSEAQKPSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENGDKSEAQKPSEK 14 2 A0A494C039;Q9Y4L1 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 61.641 0.046893 56316000 77201 92943 63533 98499 32187 89137 68234 86554 29384 FALSE TRUE 73551.86173 102413.9974 66446.05089 88597.69338 37800.40261 86050.16334 57823.6501 78974.87291 33940.72065 2.167068357 3.017437326 1.9577089 2.610365711 1.113718327 2.535307492 1.70366595 2.326847262 1 15.05072958 -0.519779766 0.148366724 3.75E-12 2.913780081 0.350633082 0.51552118 21.207498 0.824189859 13.18192136 3.553419295 0.302148355 0.519779766 2.913780081 ENGEEGCHQNGLALPVVEEGEVLS(ph)HSLEAEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENGEEGCHQNGLALPVVEEGEVLSHSLEAEHR 32 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 ENGEEGCHQNGLALPVVEEGEVLS(0.5)HS(0.5)LEAEHR 80.011 0.00046079 28509000 41168 32724 35420 37614 35832 34203 42707 38643 10090 TRUE FALSE 39222.07023 36058.6128 37044.04204 33832.96926 42081.08946 33018.54153 36191.26278 35259.21406 11654.70567 3.365341978 3.093910205 3.178462253 2.902944975 3.610652268 2.833065242 3.105291872 3.025319992 1 13.50862495 -1.295515135 0.482461769 1.33E-09 3.202185959 0.90946332 0.212976849 6.764429007 0.821982429 8.919381622 0.0931609 0.05063897 1.295515135 3.202185958 ENGSGHEASLQLRPPPEPST(ph)PVSGQDDLIQHQDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.03)T(0.97)PVSGQDDLIQHQDMR 181.61 1.95E-20 99236000 29562 24939 26277 30316 35250 23844 30082 30780 28775 TRUE FALSE 28164.66285 27480.31245 27481.82644 27268.57808 41397.58884 23018.2763 25492.43841 28084.74002 33237.28004 0.8473817 0.826791856 0.826837407 0.820421468 1.245516745 0.692543923 0.76698329 0.844977086 1 15.0205147 -1.657102526 7.661183513 1.000351544 0.851070809 0.083006143 0.14527978 0.000828103 3.71E-05 0.133534414 0.031401449 0.022024065 1.657102526 -0.149280735 ENIFGESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENIFGESR 8 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 ; 113.62 0.0065447 149004000 432910 393030 426570 490650 451200 422690 523300 466870 512900 FALSE TRUE 412447.2022 433080.2038 446128.6564 441328.9298 529889.1371 408052.1393 443460.9739 425988.3878 592437.9125 0.696186374 0.731013655 0.753038668 0.744937015 0.894421383 0.688767769 0.748535778 0.719043091 1 19.17630444 -1.83518845 2.397871875 1.102752549 0.744725915 0.663570369 0.056595477 8974465.324 5396361.681 5301973.143 0.013142254 0.014615428 1.83518845 -0.358026634 ENISEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ENISEWR 7 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ;; 134.08 0.0074653 749665000 1982980 2116670 1820220 2201260 1884620 1857840 2037880 2051260 1753710 FALSE TRUE 1889248.465 2332361.079 1903678.887 1979985.163 2213297.131 1793502.535 1726963.978 1871640.8 2025666.39 0.932655285 1.151404343 0.939779076 0.97744879 1.092626674 0.885388899 0.852541162 0.923963003 1 20.94996516 2.221519069 24.9193637 0.897123281 1.023567909 0.299909858 0.075977468 230.9677875 337735.3521 0.02703758 0.020018654 166.5401952 -2.221519069 0.126444628 ENIVEAIIHSPELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ENIVEAIIHSPELIR 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ;;;;; 165.45 1.42E-06 351723000 521843 594117 526048 637826 487831 555316 589775 589774 417580 FALSE TRUE 497176.5156 654658.1978 550167.8211 573710.5187 572908.5719 536085.2677 499793.9918 538130.262 482336.1737 1.030767632 1.357265396 1.140631475 1.189441203 1.187778573 1.111434922 1.036194296 1.115674692 1 18.87967949 2.076024927 2.823366413 1.055879234 1.190761333 0.334138392 0.083717421 0.298534323 4.690372392 0.037439044 0.023405366 119.1310383 -2.076024927 0.134882099 ENLATVEGNFASIDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENLATVEGNFASIDER 16 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 244.86 1.03E-19 27259000 19590 20133 22660 18720 20406 17470 24918 31344 24440 FALSE TRUE 18664.01952 22184.57559 23698.98341 16838.23003 23964.79994 16865.00952 21116.30145 28599.3532 28230.03038 0.661140611 0.78585022 0.839495498 0.596465176 0.848911589 0.597413793 0.748008456 1.013082622 1 14.78494306 1.253731527 6.419188647 1.009228846 0.724649357 0.63980733 0.087812746 0.079520467 12.81312628 0.059446912 0.019311652 17.93624497 -1.253731527 -0.284579489 ENLELNGSILS(ph)GGYPGSAPLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENLELNGSILSGGYPGSAPLQR 22 0 O43663-2;O43663-4;O43663;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 ENLELNGS(0.379)ILS(0.618)GGYPGS(0.002)APLQR 58.373 0.020005 0 8218.9 8483 9596.5 8150.4 13543 11112 9464 10609 10431 TRUE FALSE 7830.408885 9347.427344 10036.50902 7331.106307 15904.89491 10727.18865 8020.092982 9680.019718 12048.58621 0.649902715 0.775811135 0.833003047 0.608461954 1.320063171 0.890327585 0.665645981 0.803415401 1 13.55657625 3.985998985 0.990526398 0.870911977 0.649217429 0.139610212 0.191655174 1.724819759 2.730153659 0.066528477 0.314968311 9682.755937 -3.985998985 -0.221694548 ENLLDFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENLLDFIK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 81.338 0.053787 5960700 27559 27063 20160 29504 20080 22793 24283 24792 22808 FALSE TRUE 26256.34069 29820.75047 21084.35594 26538.20187 23581.94564 22003.67269 20578.18236 22621.08105 26344.94815 0.996636643 1.131934301 0.800318749 1.007335513 0.895122112 0.83521412 0.781105442 0.85864967 1 14.68523872 3.739072637 24.99977189 0.870818431 1.064285475 0.458706214 0.081310499 34.24774574 1672143.939 0.020897443 0.034979683 5483.68673 -3.739072637 0.193467044 ENLSAAFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENLSAAFSR 9 0 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 98.254 0.011347 74270000 301570 275310 262340 296960 318040 283510 331900 289160 358150 FALSE TRUE 287315.3838 303364.402 274368.5485 267109.0166 373506.0753 273691.9776 281262.5592 263839.6175 413690.0728 0.694518439 0.733313226 0.663222462 0.645674224 0.902864487 0.661587008 0.679887137 0.637771208 1 18.65819081 -1.030490612 4.67268485 1.000008727 0.704148629 0.600689558 0.076253661 96553304567 20030910920 9456612.915 0.016609426 0.093220062 1.030490612 -0.295860098 ENLWLNLTDGSILCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENLWLNLTDGSILCGR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 154.47 3.86E-08 0 79764 73590 72428 73812 73395 74838 92598 80014 70091 FALSE TRUE 75993.7138 81088.90466 75748.89544 66392.27753 86195.06476 72246.34129 78470.47442 73007.54998 80960.3543 0.938653424 1.001587819 0.935629495 0.820059128 1.064657702 0.892366911 0.969245689 0.901769151 1 16.30492798 ENPEDVLS(ph)PTSVATYLSSK ddPTM_SK-BR-3_Trastuzumab_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(0.859)PT(0.059)S(0.078)VAT(0.004)YLSSK 62.617 0.047194 11137000 36677 34368 33488 40705 25649 36446 37402 40062 28196 TRUE FALSE 34943.3509 37870.13827 35023.45792 36613.25607 30122.17748 35183.86588 31695.63797 36553.9589 32568.49167 1.072918919 1.16278453 1.075378568 1.124192561 0.92488709 1.080303817 0.973199443 1.12237187 1 14.99118929 2.789058147 24.99927689 1.019763258 1.111966358 0.357324139 0.059019109 345.3568923 170971.4645 0.015912288 0.016877505 615.259244 -2.789058147 0.0922031 ENPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 152.63 0.016408 972227000 1901500 1516152 1544051 1885042 1243543 1611900 1929502 2077505 1826896 FALSE TRUE 1811619.863 1670649.613 1614847.266 1695553.997 1460416.505 1556079.499 1635121.032 1895587.649 2110201.701 0.858505546 0.791701386 0.765257304 0.803503284 0.692074366 0.737407944 0.774864806 0.898296901 1 21.00894947 1.041327673 3.095587548 0.998612411 0.777589592 0.757654296 0.043081714 0.11879426 2.491549049 0.04464922 0.011768477 10.99835347 -1.041327673 -0.221022819 ENPSATLEDLEKPGVDEEPQHVLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENPSATLEDLEKPGVDEEPQHVLLR 25 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 255.83 4.25E-45 229650000 193198 137987 123070 171273 138695 154759 212275 195814 128824 FALSE TRUE 184065.9134 152048.0322 128712.8812 154056.3126 162883.3641 149399.657 179888.5501 178667.4881 148801.368 1.236990734 1.021818779 0.86499797 1.035315164 1.094636201 1.004020723 1.208917314 1.200711328 1 17.18302826 1.741307879 25 1.154435849 1.050297048 0.135797399 0.107130915 0.852445524 7804.158768 0.050358259 0.027926042 55.1198312 -1.741307879 -0.104138801 ENPVYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENPVYEK 7 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ; 93.374 0.034855 328170000 609910 492500 536660 582940 477570 578600 672830 611000 543810 FALSE TRUE 581080.763 542686.3099 561266.3918 524341.7637 560858.0568 558562.9369 570177.4261 557497.6009 628141.2774 0.92507973 0.863955816 0.893535279 0.834751325 0.892885211 0.889231383 0.907721633 0.88753537 1 19.26072955 -0.251434254 0.626950472 1.009188322 0.883580664 0.689993768 0.023916297 4.049854925 1.481110585 0.112971113 0.008950364 0.560487261 0.251434254 -0.125607658 ENPYYDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 186.16 0.00048615 1160990000 1564310 1362680 1425200 1600730 1550120 1510080 1790620 1552720 1762530 FALSE TRUE 1490368.166 1501538.641 1490546.83 1439821.579 1820460.437 1457785.551 1517428.032 1416755.605 2035854.151 0.732060382 0.737547255 0.73214814 0.707232185 0.894199831 0.716055986 0.745352034 0.69590231 1 20.95720278 -1.134645523 4.299860633 1.000046877 0.745258364 0.678902742 0.055099793 13549615247 2726867964 6761390.323 0.011873454 0.073342292 1.134645523 -0.254788512 ENQPENSQT(ph)PTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENS(0.043)QT(0.956)PT(0.001)KK;ENQPENSQT(0.989)PT(0.011)KK;ENQPENSQT(0.998)PT(0.001)KK;ENQPENS(0.002)QT(0.995)PT(0.003)KK;ENQPENS(0.001)QT(0.99)PT(0.009)KK;ENQPENS(0.006)QT(0.991)PT(0.002)KK;ENQPENSQT(1)PTKK 195.92 8.55E-08 4222832000 2321002 2071036 2052556 2478770 1175154 2475580 2560140 2681340 1462232 TRUE FALSE 2211292.835 2282076.923 2146667.723 2229599.33 1380100.486 2389850.044 2169543.623 2446547.655 1688987.471 1.309241705 1.351150889 1.270979069 1.320080444 0.817117065 1.414960197 1.284523219 1.448529191 1 20.6877272 -2.066945794 2.650615726 0.579366925 1.279544621 0.202541845 0.172717847 5354470.567 4239801.635 13821504.23 0.039217181 0.008571448 2.066945794 0.700177696 ENQRS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 115.15 0.0015254 2824350000 1988150 1965350 1550720 2030290 1641620 1731230 1796010 1833090 1482620 TRUE FALSE 1894174.09 2165621.399 1621822.046 1826201.392 1927918.008 1671277.071 1521995.689 1672574.922 1712537.137 1.106063073 1.264569014 0.947028833 1.066371848 1.125767124 0.975907053 0.888737333 0.976664906 1 20.70770384 2.987447253 0.678970672 0.941550613 1.179817659 0.364625738 0.085719652 0.653196829 0.668178548 0.058322419 0.078555426 971.5099493 -2.987447253 0.238267046 ENREDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ENREDYR 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 115.49 0.005169 1706418000 2467450 1722007 2460028 2094792 2564038 2252063 3019400 2552797 3225870 FALSE TRUE 2350818.529 1897481.471 2572822.717 1884219.528 3011205.415 2174073.494 2558735.075 2329260.561 3726121.444 0.630902284 0.509237688 0.690482786 0.505678507 0.808133997 0.583468233 0.686702007 0.625116652 1 21.82924327 -5 0.211461833 2.829068636 0.570390846 0.640984628 0.087640023 82.02269874 0.817888015 63.5858156 0.159900751 1.00E-05 5 -2.258677789 ENRKRIIS(ph)PS(ph)FDNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENRKRIISPSFDNIK 15 3 Q6P9A2 Q6P9A2 GALNT18 Polypeptide N-acetylgalactosaminyltransferase 18 2 ENRKRIIS(1)PS(1)FDNIK 70.802 0.065468 1751500000 1259600 557810 1086400 1376300 1579800 1322100 2223900 883360 1574900 TRUE FALSE 1200061.204 614651.4732 1136212.515 1237951.709 1855316.62 1276315.345 1884603.21 806008.3154 1819127.449 0.659690559 0.337882579 0.624592035 0.680519504 1.019893698 0.701608536 1.035992949 0.443074132 1 20.79481519 3.171510748 2.463496891 0.846265939 0.502242695 0.33053267 0.193905222 0.266495576 3.303507945 0.054007988 0.069685663 1484.262612 -3.171510748 -0.344023244 ENS(ph)FGSPLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.999)FGS(0.001)PLEFR;ENS(0.974)FGS(0.026)PLEFR 150.26 3.56E-05 115908000 192498 182441 144309 199329 123961 177876 170270 171416 120061 TRUE FALSE 183399.001 201031.9453 150925.7104 179292.0702 145579.7592 171716.1095 144292.1843 156405.9063 138679.4467 1.322467066 1.449616004 1.088306263 1.292852506 1.049757283 1.238223209 1.040472743 1.127823265 1 17.08139446 3.404443589 0.433373186 1.038182177 1.46372696 0.51135225 0.101316787 1.197840994 0.382528314 0.081883951 0.235473325 2537.719337 -3.404443589 0.425544784 ENSFGS(ph)PLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENSFGS(1)PLEFR;ENS(0.001)FGS(0.999)PLEFR;ENSFGS(1)PLEFR;ENSFGS(1)PLEFR;ENSFGS(1)PLEFR;ENS(0.001)FGS(0.999)PLEFR 198.98 5.44E-08 1416494000 2200750 2469110 1739660 2428720 1861720 2118150 1988110 2117770 1688600 TRUE FALSE 2096724.909 2720715.116 1819425.132 2184580.451 2186403.379 2044797.934 1684787.305 1932326.832 1950459.464 1.074990251 1.394909849 0.932818736 1.120033762 1.120968376 1.048367306 0.863789962 0.990703405 1 20.89538258 2.710785815 0.750400493 0.939606139 1.206702913 0.271048166 0.121717939 0.683309446 0.8234594 0.083374638 0.078716437 513.790199 -2.710785815 0.267096773 ENSIWDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENSIWDEK 8 0 H3BPZ3;A0A0A0MRF9;P16885 H3BPZ3 PLCG2 "Phosphoinositide phospholipase C;1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2" 0 49.813 0.092247 888790000 50035 69601 57188 38108 1001400 34342 48471 24050 413680 FALSE TRUE 47669.94471 76693.42103 59810.12637 34277.31144 1176043.843 33152.72793 41075.85872 21944.0545 477831.3816 0.09976311 0.160503106 0.125169942 0.071735162 2.46121098 0.069381646 0.085963083 0.045924264 1 18.86614208 ENTEGEYSGIEHVIVDGVVQSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ENTEGEYSGIEHVIVDGVVQSIK 23 0 H0YL72;P50213;P50213-2;H0YLI6;H0YMU3 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 ;;;;;; 282.05 5.12E-52 284237400 490872 443524 444403 447952 382989 397034 484258 456632 388552 FALSE TRUE 467669.4534 488719.5998 464779.3171 402923.0139 449782.1603 383284.613 410375.5481 416646.8813 448806.6597 1.042028774 1.088931256 1.035589172 0.89776523 1.002173543 0.854008301 0.914370452 0.928343803 1 18.77573456 3.339690069 4.814689278 0.925572423 1.064815385 0.617102737 0.045634405 0.113161287 4.368399293 0.011791848 0.016051078 2186.2009 -3.339690069 0.139242962 ENVEYIEREES(ph)DGEYDEFGR ddPTM_SK-BR-3_Trastuzumab_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(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR 231.23 6.89E-26 21122206000 4341828 3944900 4025334 4512528 4026557 3914202 4654043 4354603 4525218 TRUE FALSE 4136598.395 4346889.795 4209899.545 4058920.112 4728787.266 3778652.203 3943983.263 3973290.876 5226965.696 0.791395742 0.831627764 0.805419394 0.776534676 0.904690702 0.722915057 0.754545465 0.760152468 1 22.31754226 ENVEYIEREES(ph)DGEYDEFGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ENVEYIEREESDGEYDEFGRK 21 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 ENVEYIEREES(1)DGEYDEFGRK;ENVEYIEREES(1)DGEYDEFGRK;ENVEYIEREES(1)DGEYDEFGRK;ENVEYIEREES(1)DGEYDEFGRK;ENVEYIEREES(1)DGEYDEFGRK;ENVEYIEREES(1)DGEYDEFGRK 243.35 2.24E-30 2662970000 1181158 967832 1077426 1149277 761636 1148406 1212123 1262290 901432 TRUE FALSE 1125327.002 1066455.181 1126827.048 1033749.492 894465.0773 1108636.412 1027191.374 1151757.196 1041221.471 1.080775833 1.02423472 1.082216492 0.992823834 0.859053624 1.064746016 0.986525348 1.106159667 1 19.98984554 3.225962761 24.86779071 0.997745966 1.056852639 0.160116871 0.064904108 375.369727 740966.9212 0.017854965 0.021474728 1682.529786 -3.225962761 0.059106673 ENVFQEHQTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENVFQEHQTLK 11 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 103.88 0.0026748 358200000 95698 95149 92558 103970 99222 96620 121450 108420 101170 FALSE TRUE 91174.5452 104844.7913 96801.87585 93518.73807 116526.2854 93274.02517 102920.5719 98926.17003 116858.9269 0.780210358 0.897191118 0.828365264 0.800270382 0.997153478 0.798176294 0.880724945 0.846543543 1 16.83440842 -5 0.196598627 1.639598543 0.829694311 0.366351719 0.061824174 148.2815476 1.461724003 37.30564476 0.139320587 1.00E-05 5 -0.809904233 ENVSDLTLGPGNS(ph)PITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENVSDLTLGPGNSPITR 17 0 Q6DCA0 Q6DCA0 AMMECR1L AMMECR1-like protein 1 ENVSDLT(0.155)LGPGNS(0.838)PIT(0.007)R 70.96 0.033071 21240000 38210 36416 38746 44731 43353 34929 45825 40004 42758 TRUE FALSE 36403.88902 40126.8318 40522.54243 40234.5549 50913.74947 33719.39997 38833.55462 36501.03769 49388.69226 0.737089551 0.81247002 0.820482191 0.814651149 1.030878672 0.682735226 0.786284326 0.739056574 1 15.59189315 4.478829565 1.637602057 0.825334922 0.726987428 0.072186702 0.106560781 1.776190931 6.716673408 0.026892766 0.237743153 30118.23828 -4.478829565 -0.098347493 ENVVVIHPDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ENVVVIHPDFR 11 0 A3KMH1-2;A3KMH1-3;A3KMH1 A3KMH1-2 VWA8 von Willebrand factor A domain-containing protein 8 0 87.001 0.01405 53015000 53692 53630 52580 46797 67755 45747 55416 46788 68981 FALSE TRUE 51154.08557 59094.95797 54990.84501 42092.87665 79571.45055 44162.76992 46961.27142 42690.99468 79678.22117 0.642008378 0.741670147 0.690161555 0.528285848 0.998659977 0.554264004 0.589386544 0.535792517 1 16.28189782 ENYSHHTQDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ENYSHHTQDDRR 12 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ; 139.3 3.84E-05 224730000 93440 81735 89936 103505 148490 85019 133157 104703 25597 FALSE TRUE 89023.27638 90063.88942 94059.65456 93100.48075 174386.609 82074.77071 112841.4541 95534.65025 29566.45203 3.01095567 3.046151406 3.181296642 3.148855353 5.898124294 2.775942498 3.816536862 3.231184119 1 14.85167351 2.96863415 24.99348261 3.595879659 3.075356693 0 1.197642808 2320.342098 1848936.22 0.32682193 0.346996849 930.3238406 -2.96863415 -0.520522966 EPAAAISRPR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 166.69 4.99E-06 497790000 486960 470261 392726 477150 487431 432999 424440 435167 472770 FALSE TRUE 463942.3659 518181.1305 410732.8756 429185.9755 572438.8121 418004.1361 359683.8826 397061.4705 546084.757 0.84957941 0.948902389 0.752141257 0.785932898 1.048260009 0.765456517 0.658659444 0.72710594 1 19.05876536 2.030406003 24.97002896 0.746010611 0.877171057 0.077478879 0.120937627 284.469587 233611.0161 0.041748232 0.030832805 107.252149 -2.030406003 0.131160447 EPAHLMSLFGGKPMIIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPAHLMSLFGGKPMIIYK 18 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 136.01 4.32E-06 55996000 179470 149820 134410 174540 151660 150770 202360 181170 152790 FALSE TRUE 170986.8088 165086.8283 140572.8314 156994.9076 178109.456 145548.7971 171486.2654 165305.7944 176483.8929 0.968852205 0.935421503 0.796519326 0.889570742 1.00921083 0.824714339 0.971682246 0.936662217 1 17.42917699 1.024201378 1.286330314 0.997521192 0.912938517 0.164260664 0.064554133 0.897084172 3.049910451 0.058550682 0.017996784 10.5730766 -1.024201378 -0.084582676 EPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;EPAITS(0.002)QNS(0.997)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR 290.82 1.64E-40 3886930000 1534963 1471896 1244902 1633137 1437470 1419210 1544664 1616148 1526064 TRUE FALSE 1462408.341 1621883.876 1301981.988 1468970.966 1688164.313 1370062.402 1308997.137 1474629.513 1762718.211 0.829632514 0.920103886 0.738621738 0.833355528 0.957705152 0.777244141 0.742601471 0.836565654 1 20.74937043 EPDCFKDIVNMLMHHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EPDCFKDIVNMLMHHDR 17 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 183.74 4.35E-10 364289000 690154 535787 629916 703124 564674 629018 803830 723707 118016 FALSE TRUE 657531.7882 590384.3044 658798.2717 632444.6397 663152.9668 607234.9489 681190.9701 660335.3785 136317.3185 4.823538162 4.330955969 4.832828864 4.63950323 4.864774146 4.454569349 4.997097782 4.84410481 1 17.05660934 -0.891127087 6.591396643 0.99999982 4.708715719 0.971113375 0.20180301 5.25E-07 8.74E-08 0.189446815 0.04465304 0.12849106 0.891127087 3.7087159 EPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.001)S(0.01)RGS(0.989)PVR;EPEAAS(0.042)S(0.274)RGS(0.684)PVR 126.63 0.00015113 660326000 508320 346609 530310 500310 610170 502440 643920 526200 706180 TRUE FALSE 484292.721 381928.8512 554625.238 450017.8883 716583.4548 485040.3768 545678.1776 480123.1384 815690.7877 0.593720964 0.468227491 0.679945448 0.55170157 0.878498894 0.594637556 0.668976757 0.588609245 1 19.63766283 -5 0.161048408 2.396506867 0.518274418 0.543415955 0.106909691 95.71518292 0.882417271 42.86024502 0.417343839 1.00E-05 5 -1.878232449 EPEKEIRPALELLEPIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPEKEIRPALELLEPIEQK 19 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 145.61 6.95E-08 128936000 367550 358100 324330 409880 218080 396090 390050 432460 222280 FALSE TRUE 350176.6399 394590.7971 339200.8513 368678.0837 256113.083 382373.304 330540.7087 394591.5098 256750.0472 1.363881502 1.536867477 1.321132576 1.43594164 0.997519127 1.489282313 1.287402719 1.536870252 1 17.97000502 -2.005743835 2.575489077 0.61342906 1.373668941 0.355034725 0.157162048 21854976.55 10801974.72 50050146.18 0.035014128 0.009868614 2.005743835 0.760239881 EPFELEAFYTNLHEVPYPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPFELEAFYTNLHEVPYPDAR 21 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 207.43 3.67E-22 271030000 239648 213120 208874 245782 225595 202536 255320 240942 225348 FALSE TRUE 228320.314 234837.1703 218451.0795 221075.5264 264938.6966 195522.1275 216366.2447 219843.8412 260293.8169 0.877163802 0.902200341 0.839248055 0.849330687 1.017844756 0.751159324 0.831238511 0.844598784 1 17.98978152 2.205044017 24.99998242 0.838190557 0.891221769 0.036570745 0.07792722 427.733934 319043.8432 0.026265504 0.019399393 160.3407894 -2.205044017 0.053031213 EPFFHGHDNYDQLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPFFHGHDNYDQLVR 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ; 189.1 1.57E-07 149854000 95652 97207 85803 101225 105411 73693 86617 87132 20475.7 FALSE TRUE 91130.71952 107112.5038 89737.15242 91049.67069 123794.645 71140.99293 73401.98582 79502.26016 23650.96698 3.853149835 4.528884756 3.794227631 3.849722963 5.234231866 3.007952825 3.103551152 3.361480325 1 14.52961155 0.69764238 0.55484623 0.928503043 4.230555401 0.737977808 0.567503031 0.648402694 0.411995773 0.662461718 0.253404548 4.984738499 -0.69764238 3.302052358 EPFHSILSVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPFHSILSVLK 11 0 Q8NCW5-2;Q8NCW5;Q5T3I4 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ; 137.89 6.89E-05 171114000 1489380 1418700 904960 1113800 1080010 1046800 1356020 1351110 975840 FALSE TRUE 1418979.959 1563267.143 946453.3111 1001838.708 1268363.402 1010549.054 1149134.244 1232799.646 1127168.283 1.258889183 1.386897738 0.839673477 0.888810236 1.12526534 0.896537871 1.019487738 1.093713924 1 20.10427149 3.746516772 24.99884408 0.980694902 1.32289348 0.697321421 0.09378276 285.7081103 897714.2672 0.023099422 0.040724757 5578.491448 -3.746516772 0.342198578 EPGEYAVHIMCDDEDIKDSPYMAFIHPATGGYNPDLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPGEYAVHIMCDDEDIKDSPYMAFIHPATGGYNPDLVR 38 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 100.33 5.68E-05 100760000 47619 29230 29755 45119 34168 35890 46479 45907 14190 FALSE TRUE 45368.14424 32208.57023 31119.29618 40583.5524 40126.88838 34647.1203 39387.7749 41887.13971 16390.51273 2.767951497 1.965073989 1.898616395 2.476039223 2.448177738 2.113852134 2.403083757 2.555572264 1 14.00057337 -1.258869342 8.494707842 0.999999338 2.314376303 0.706568459 0.268926061 3.29E-06 2.86E-07 0.252406559 0.059492766 0.055097343 1.258869342 1.314376964 EPHLNYS(ph)PTCLEPPVLSIHPGAID ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPHLNYSPTCLEPPVLSIHPGAID 24 0 O75054;O75054-2 O75054 IGSF3 Immunoglobulin superfamily member 3 1 EPHLNY(0.022)S(0.822)PT(0.156)CLEPPVLSIHPGAID 71.528 0.019137 14269000 14876 11450 14238 17117 21959 12959 18950 16789 15256 TRUE FALSE 14172.84096 12616.76802 14890.82638 15396.36664 25788.64265 12510.22658 16058.82946 15318.86616 17621.82256 0.804277816 0.71597407 0.845021923 0.87371023 1.463449229 0.709928076 0.91130355 0.869312246 1 14.10507552 3.253766383 3.224996972 0.970853039 0.767045778 0.17864336 0.193542589 0.406030025 8.754390822 0.055202288 0.073146925 1793.768456 -3.253766383 -0.203807261 EPLGPALAHELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EPLGPALAHELR 12 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;; 196.38 2.07E-07 1084680000 794441 872419 589855 857456 657979 619943 683797 763294 582056 FALSE TRUE 756889.3484 961319.488 616900.4352 771262.8938 772730.3293 598474.2185 579471.2089 696455.9309 672318.2717 1.12579024 1.429857745 0.917572021 1.147169319 1.149351969 0.890165036 0.861900135 1.035902132 1 19.35878483 3.02007325 0.853207399 0.932554052 1.25722074 0.315543777 0.137672404 0.551802701 0.892175583 0.073598827 0.09520709 1047.305177 -3.02007325 0.324666688 EPLIPAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 EPLIPAS(1)PK 84.718 0.016052 42229000 240510 200510 211670 242770 125550 239420 222640 221330 135260 TRUE FALSE 229141.5689 220942.197 221375.2789 218366.2984 147445.8802 231128.8254 188672.1789 201949.1719 156235.43 1.466642803 1.414161928 1.416933911 1.39767464 0.943741636 1.47936243 1.207614553 1.292595232 1 17.25336213 7.999993005 0.035104378 8.10E-07 3.340334314 0.417595455 0.144118246 895.1769373 2.402098836 67.41737049 190.0311894 99998389.44 -7.999993005 3.340333505 EPNEDCKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 79.16 0.025288 142750000 198510 208630 188220 201850 157340 196940 194000 204050 159560 FALSE TRUE 189126.8257 229889.6342 196850.0732 181559.6545 184780.0462 190119.9184 164401.7369 186182.3003 184303.7499 1.026169168 1.247341057 1.068074162 0.985111017 1.002584301 1.031557516 0.892015149 1.010192687 1 17.4917259 3.395267805 3.784278459 0.979429171 1.139763621 0.480822657 0.064356238 0.161163966 4.509701157 0.017894125 0.025115289 2484.664784 -3.395267805 0.16033445 EPPTVPS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPPTVPSER 9 0 P27815 P27815 PDE4A "cAMP-specific 3,5-cyclic phosphodiesterase 4A" 1 EPPTVPS(1)ER 54.784 0.085524 320720000 11767 5673.2 4840 0 6173.4 12302 8847.9 0 7219 TRUE FALSE 11210.79723 6251.30553 5061.918787 0 7250.039005 11875.97866 7497.990352 0 8338.48565 1.344464415 0.749693145 0.607054926 0 0.869467108 1.424236864 0.899202885 0 1 13.02556968 EPPYRVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EPPYRVPR 8 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 167.33 0.00028571 1108960000 445681 389674 356080 416322 483370 364829 486765 410730 476664 FALSE TRUE 424614.5424 429382.2236 372406.6202 374472.5216 567669.575 352194.8803 412500.0592 374764.3038 550582.6187 0.771209493 0.779868832 0.676386445 0.680138655 1.031034318 0.639676714 0.749206468 0.680668606 1 19.07059954 -1.829637339 2.689900786 1.085795793 0.75351902 0.338376401 0.109362786 22594936.07 14430028.59 12489933.4 0.024256336 0.01480344 1.829637339 -0.332276773 EPQGALERPPVDHGLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPQGALERPPVDHGLAR 17 1 Q96HY7;C9JWN1 Q96HY7 DHTKD1 "Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial" 0 ; 143.71 3.24E-07 213345000 78718 70063 76892 63192 105705 60491 95013 70916 110145 FALSE TRUE 74997.15614 77202.49936 80417.57426 56839.8201 124139.9185 58396.1815 80517.02182 64706.21909 127225.7241 0.589481072 0.60681517 0.632085805 0.446763581 0.975745428 0.458996653 0.632867468 0.508593836 1 16.95703088 -1.371035079 5.198562065 1.000210794 0.607742032 0.414033263 0.147141029 0.000311408 3.77E-05 0.12341661 0.029074138 0.042556404 1.371035079 -0.392468762 EPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPSPALGPNLDGSGLLPR 18 0 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR 167.14 2.51E-11 148468000 31615.1 40286 25730.1 42286 21780.3 34343.4 25897.8 38073 20715.9 TRUE FALSE 30120.71688 44391.1892 26909.85054 38035.33094 25578.77742 33154.07945 21946.61496 34739.12628 23928.41597 1.258784406 1.855166228 1.124598075 1.589546545 1.068970778 1.38555262 0.917177927 1.451793814 1 14.54643728 2.826497395 1.159421528 1.138059968 1.516264433 0.199569297 0.257326358 0.584289165 1.643844471 0.109213156 0.110797278 670.6522643 -2.826497395 0.378204466 EPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPSPALGPNLDGSGLLPRPIFYCSFPTR 28 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR;EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR 183.59 7.12E-18 196294000 31890 29220 25716 20980.1 24931 29398 26527 30973 21861.9 TRUE FALSE 30382.6229 32197.55122 26895.10404 18871.14049 29278.95851 28379.93989 22479.81895 28260.83992 25252.1318 1.203170613 1.275042895 1.065062714 0.747308807 1.159464822 1.12386313 0.890214701 1.119146698 1 14.62411757 3.626790015 4.908214358 1.001631345 1.237812911 0.372529725 0.122212951 0.199422347 7.294607502 0.031141911 0.049049372 4234.381809 -3.626790015 0.236181566 EPS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 91.069 0.050678 2693900000 6404370 8042300 4701790 7931000 2857980 6345340 5254420 6620290 2815400 TRUE FALSE 6101648.122 8861819.513 4917371.722 7133760.812 3356410.807 6125599.285 4452761.725 6040582.311 3251997.853 1.876276799 2.72503855 1.512107924 2.193654835 1.032107326 1.88364186 1.369238827 1.857498862 1 21.63289487 3.268331697 1.501455088 1.500432683 2.261548039 0.311368728 0.434053219 0.388572191 1.820796887 0.131211594 0.196072581 1854.947817 -3.268331697 0.761115356 EPS(ph)PEKNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK 126.83 0.00028006 7705010000 7894450 6700650 6627290 7829280 3317580 8438420 7832830 8488600 3726840 TRUE FALSE 7521294.994 7383453.853 6931157.802 7042265.9 3896164.902 8146195.4 6637787.924 7745293.183 4304779.313 1.747196417 1.715175928 1.61010758 1.635917985 0.905078894 1.892360748 1.541957773 1.799231185 1 22.03750785 -2.099338169 2.147916033 4.50E-05 1.611820576 0.334789404 0.268283191 3179089.909 839585.9022 15531768.99 0.061155239 0.007955397 2.099338169 1.611775595 EPS(ph)PKQDVVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPSPKQDVVGK 11 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;Q9ULU4-4;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 EPS(1)PKQDVVGK 86.944 0.0085346 357790000 289170 196440 262600 293610 166180 316940 349720 352140 177140 TRUE FALSE 275501.5072 216457.4593 274640.4697 264095.765 195161.7394 305964.2883 296363.791 321304.7548 204609.9665 1.346471591 1.057902814 1.342263402 1.290727766 0.953823231 1.495353787 1.448432821 1.570327977 1 17.64251689 2.199836824 24.99969838 1.422221714 1.203327091 0.160547906 0.193527265 218.885231 141308.8774 0.064839158 0.047887771 158.4297819 -2.199836824 -0.218894623 EPSAPSIPTPAYQSS(ph)PAGGHAPTPPTPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 EPSAPSIPTPAYQS(0.065)S(0.935)PAGGHAPTPPTPAPR;EPSAPSIPTPAYQS(0.002)S(0.998)PAGGHAPTPPTPAPR 248.49 2.47E-46 647440000 170082 187869 185612 212554 208601 192586 212799 205688 239860 TRUE FALSE 162042.5609 207013.0647 194122.4938 191187.6681 244980.9484 185916.6985 180332.6042 187676.8683 277056.2638 0.584872396 0.747187816 0.70066091 0.690068023 0.884228153 0.671043116 0.650888025 0.677396229 1 18.07981946 -2.187071807 2.249970608 1.795273036 0.698307886 0.598612749 0.076974706 3085293.437 687369.4182 12480952.07 0.018210058 0.006500222 2.187071807 -1.09696515 EPSVPASCAVSATYERS(ph)PS(ph)PAHLPDDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 2 EPSVPAS(0.001)CAVS(0.008)AT(0.039)Y(0.021)ERS(0.933)PS(0.998)PAHLPDDPK;EPSVPASCAVS(0.003)AT(0.017)Y(0.048)ERS(0.935)PS(0.997)PAHLPDDPK 142.37 1.57E-07 246710000 109382 120205 105000 136700 112455 107525 118271 125543 114796 TRUE FALSE 104211.7296 132454.0262 109814.3539 122958.6563 132067.1164 103801.3823 100226.5868 114549.7894 132597.9774 0.785922468 0.998914378 0.828175181 0.927304162 0.995996462 0.782827795 0.755868142 0.863887909 1 17.01669924 2.213902273 24.9996588 0.820631127 0.906045752 0.043445719 0.092693505 398.6609939 404176.4545 0.032243687 0.023824189 163.6448237 -2.213902273 0.085414625 EPTEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EPTEEER 7 0 Q15056;Q15056-2 Q15056;Q15056-2;REV__B4E135 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 163.84 0.0028378 1494120000 1449770 1688150 1248830 1687700 1271910 1386770 1371860 1432040 1240020 FALSE TRUE 1381242.245 1860174.404 1306090.091 1518049.19 1493730.701 1338745.807 1162557.561 1306642.986 1432315.968 0.96434186 1.298717912 0.911872882 1.059856361 1.042877922 0.934672123 0.81166278 0.912258897 1 20.44991836 2.228487836 2.84418529 0.883992962 1.078130092 0.273595628 0.110278768 0.268516721 4.472331805 0.044831937 0.032223333 169.2340844 -2.228487836 0.19413713 EPTGVEENKTDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPT(0.001)GVEENKT(0.001)DS(0.006)LFVLPS(0.031)RDDAT(0.961)PVRDEPMDAESITFK 73.141 0.0015769 84967000 44362 34620 41281 45927 26918 44410 46533 51433 30695 TRUE FALSE 42265.09618 38147.81736 43173.77468 41310.3307 31612.49068 42872.07056 39433.53621 46929.25386 35455.02383 1.192076372 1.075949562 1.21770542 1.165147453 0.891622322 1.209195931 1.112212938 1.323627762 1 15.11370245 -0.432285837 6.293589821 1.000000939 1.140094893 0.14257131 0.112764756 0 0 0.098636488 0.023248843 0.369584853 0.432285837 0.140093954 EPTPSIAS(ph)DIS(ph)LPIATQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 2 EPTPSIAS(1)DIS(1)LPIATQELR;EPTPS(0.002)IAS(0.998)DIS(1)LPIATQELR 175.16 3.42E-12 67800000 167812 131380 146836 213476 214387 176555 194891 158921 192817 TRUE FALSE 159879.8593 144767.7714 153568.5758 192016.9869 251776.0249 170440.8561 165156.7985 145005.0347 222718.0756 0.717857583 0.65000459 0.689520038 0.862152685 1.13046965 0.765276261 0.741550941 0.651069898 1 17.76485913 3.244264916 22.95513205 0.844719091 0.682705275 0.264071914 0.134526238 73.16761453 294432.7975 0.038358965 0.050430145 1754.950681 -3.244264916 -0.162013816 EPTPSIAS(ph)DISLPIATQELR ddPTM_SK-BR-3_Trastuzumab_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;EPTPS(0.001)IAS(0.999)DISLPIATQELR;EPTPS(0.004)IAS(0.996)DISLPIATQELR 178.12 6.61E-17 114888000 109056 102467 95749.3 143720 133540 106194 123118 104832 133709 TRUE FALSE 103901.139 112908.5038 100139.5001 129272.9925 156829.3337 102516.4752 104334.0879 95652.35433 154443.9088 0.672743521 0.73106479 0.648387501 0.837022279 1.015445251 0.66377804 0.675546797 0.619333938 1 17.23672345 -1.982375955 2.847988949 1.239637721 0.730945468 0.341085039 0.116634913 35804845.08 13668590.95 56353670.87 0.028232976 0.010414155 1.982375955 -0.508692253 EPTPSIASDIS(ph)LPIATQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPSIAS(0.002)DIS(0.998)LPIATQELR;EPTPSIAS(0.001)DIS(0.999)LPIATQELR;EPTPSIAS(0.039)DIS(0.96)LPIAT(0.001)QELR 126.84 2.37E-05 43338000 47983.6 40284 42776.4 64141 58331.2 46042.3 54658 46898.7 57247 TRUE FALSE 45715.51032 44388.9854 44737.74025 57693.42482 68504.14281 44447.84361 46318.91824 42792.0012 66124.57238 0.691354343 0.671293345 0.676567555 0.872495999 1.035986175 0.672183456 0.700479664 0.647142199 1 16.01289887 3.26249598 24.52407535 0.799105586 0.679588087 0.197437821 0.129530213 354.0210003 362725.3255 0.036338201 0.049173733 1830.189165 -3.26249598 -0.119517499 EPWLLPSQHNDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EPWLLPSQHNDIIR 14 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 192.54 3.62E-07 898860000 1362430 1189060 1156240 1390190 1594590 1167630 1593800 1439710 1565320 FALSE TRUE 1298030.634 1310226.566 1209254.748 1250445.46 1872685.991 1127194.68 1350636.538 1313641.36 1808061.831 0.717912746 0.724658053 0.668812718 0.691594413 1.035742229 0.623427065 0.747007937 0.726546702 1 20.78601258 -1.927794858 2.517116307 1.171527185 0.739325416 0.350768723 0.110273194 12013571.75 5916567.778 12110833.98 0.024250701 0.011808783 1.927794858 -0.432201769 EPYGHLGPAELLEAS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EPYGHLGPAELLEASPAAR 19 0 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 EPYGHLGPAELLEAS(1)PAAR;EPYGHLGPAELLEAS(1)PAAR 159.73 2.12E-11 53260000 61048 61603 64351 64947 68426 62544 70597 72823 78944 TRUE FALSE 58162.38203 67880.41574 67301.557 58418.40417 80359.47274 60378.0856 59826.13105 66446.23206 91186.23233 0.637841706 0.744415182 0.738067088 0.640649391 0.881267607 0.66214037 0.656087323 0.728687109 1 16.4765284 0.947559162 20.64094372 1.000000001 0.706248084 0.615403799 0.071914473 1058.949035 416808.5337 0.064404247 0.016101062 8.862559454 -0.947559162 -0.293751917 EQAAEHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQAAEHYK 8 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 71.614 0.048287 626900000 1258970 1120230 1039810 1305590 1132360 1167110 1432250 1321060 1161110 FALSE TRUE 1199460.983 1234382.711 1087486.317 1174349.613 1329843.225 1126692.688 1213733.957 1205380.983 1341169.009 0.894339919 0.920378194 0.810849572 0.875616425 0.99155529 0.840082555 0.904982109 0.898753979 1 20.35505962 0.407649607 1.808495679 0.999997834 0.892542872 0.337375387 0.047650755 6.947103473 19.81878756 0.04246236 0.011859363 2.556522429 -0.407649607 -0.107454962 EQAEAEVASLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 242.07 1.04E-16 4051409000 3524359 2534574 3354976 3253331 3693428 3290930 4207381 3586182 4456361 FALSE TRUE 3357769.535 2792849.972 3508804.968 2926299.987 4337560.674 3176964.269 3565467.755 3272156.893 5147430.704 0.652319522 0.54257165 0.681661429 0.568497209 0.84266519 0.617194179 0.692669403 0.63568741 1 22.29542107 -5 0.219991834 2.781455148 0.60365247 0.642714369 0.081078489 88.6531249 0.886512503 69.98344165 0.140443066 1.00E-05 5 -2.177802678 EQAEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQAEEER 7 0 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 217.09 8.35E-05 1134450000 2092020 1666780 1818890 1843010 1841930 1503260 1889440 1902390 2037760 FALSE TRUE 1993134.361 1836626.777 1902287.906 1657747.133 2163162.009 1451201.729 1601171.226 1735806.646 2353765.413 0.846785474 0.780293043 0.808189251 0.704295816 0.91902192 0.616544759 0.680259476 0.737459492 1 21.16653911 4.119361553 0.743640596 0.747598823 0.857107725 0 0.114741251 4.023789721 2.931428248 0.045123383 0.320223678 13163.20222 -4.119361553 0.109508902 EQAIGEYEDLRAENQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQAIGEYEDLRAENQK 16 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 140.02 2.23E-05 0 157320 142870 120870 170920 113390 148890 164050 171810 127570 FALSE TRUE 149883.7954 157428.6154 126412.0091 153738.7969 133165.1801 143733.902 139021.1595 156765.4056 147352.9041 1.017175714 1.068378098 0.857886106 1.043337407 0.903716021 0.9754399 0.943457208 1.063877272 1 17.16891597 EQAQPPENGKET(ph)SPSHPGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQAQPPENGKETSPSHPGFK 20 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EQAQPPENGKET(0.593)S(0.401)PS(0.006)HPGFK;EQAQPPENGKET(0.498)S(0.498)PS(0.005)HPGFK 182.53 6.89E-17 854740000 773726 965959 785558 1050269 478105 1005626 881940 1010529 483297 TRUE FALSE 737153.5054 1064391.32 821576.6113 944693.9647 561486.3606 970800.9195 747383.8551 922041.7236 558244.2304 1.320485668 1.906676795 1.471715365 1.692259254 1.005807727 1.739025442 1.338811607 1.6516816 1 19.09053691 EQAQPPENGKETS(ph)PSHPGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQAQPPENGKETSPSHPGFK 20 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EQAQPPENGKET(0.086)S(0.912)PS(0.002)HPGFK;EQAQPPENGKET(0.392)S(0.596)PS(0.012)HPGFK 155.97 1.44E-08 976380000 819960 994790 815540 1081810 437840 1001540 930950 1033990 470960 TRUE FALSE 781202.1158 1096160.232 852933.3157 973064.4035 514199.1574 966856.4187 788916.4794 943448.3541 543994.0715 1.436048951 2.015022386 1.567909212 1.788740824 0.94522934 1.777328963 1.450229921 1.734298963 1 19.0532314 EQDFFFELDAMDHLQSFIADCDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 EQDFFFELDAMDHLQSFIADCDRR 24 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;;;;;;;;;;;; 274.3 3.61E-52 2121718800 1130210 898448.6 1023992.3 1155183 1153610 961569.4 1359172 1108193 1086546 FALSE TRUE 1076787.213 990001.5338 1070943.36 1039061.81 1354799.219 928270.0106 1151805.348 1011153.746 1255042.004 0.857969064 0.788819442 0.853312763 0.827909987 1.07948516 0.739632624 0.91774247 0.80567323 1 20.25930422 -5 0.187550916 1.584078115 0.830579461 0.175203384 0.092219909 223.0547974 2.173890661 48.98561522 0.233077802 1.00E-05 5 -0.753498655 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_SK-BR-3_Trastuzumab_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 138.4 2.05E-05 4771430000 5863040 4556300 5158120 5758140 3317530 5992680 6738830 6643260 4174040 TRUE FALSE 5585905.719 5020592.15 5394624.904 5179320.827 3896106.182 5785151.989 5710697.716 6061540.936 4821328.805 1.158582197 1.041329549 1.118908318 1.074251734 0.808098003 1.199908204 1.184465517 1.257234506 1 22.20099939 EQDVVTGVS(ph)PLLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 EQDVVT(0.015)GVS(0.985)PLLFR;EQDVVT(0.23)GVS(0.77)PLLFR 113.88 0.00053469 25334000 42746 42304 42992 46437 43907 43629 51097 51797 53166 TRUE FALSE 40725.48129 46614.8257 44963.22572 41769.06454 51564.3669 42118.11679 43301.21419 47261.38009 61410.71175 0.663165759 0.75906669 0.73217236 0.680159265 0.839664049 0.685843163 0.705108489 0.769595055 1 15.9062027 -5 0.373291148 4.696593113 0.719247614 0.740490747 0.050679409 266.4384968 2.034663328 795.3367471 0.032311791 1.00E-05 5 -3.977345499 EQEEEEQKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 98.105 0.0051108 315880000 618100 510200 566100 628830 520790 595110 679870 599100 581590 FALSE TRUE 588883.638 562189.96 592056.2449 565618.8137 611615.6111 574501.1915 576143.3448 546639.628 671780.0068 0.876601911 0.836866168 0.881324599 0.8419703 0.91044033 0.855192452 0.857636933 0.813718215 1 19.35762933 -1.057578629 4.821057424 1.000004017 0.85960198 0.736521852 0.026461347 1.03E-06 2.00E-07 0.022996397 0.005420148 0.087583313 1.057578629 -0.140402037 EQEEELRR ddPTM_SK-BR-3_Trastuzumab_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 ; 147.4 0.00086235 375780000 317110 271870 275860 320780 316630 262890 335860 318420 300640 FALSE TRUE 302120.8388 299573.8621 288508.4539 288534.585 371850.1718 253786.0534 284618.3885 290537.4567 347261.7157 0.87000906 0.862674601 0.83080985 0.830885099 1.0708067 0.730820709 0.819607736 0.836652713 1 18.40566384 4.327041191 3.726200043 0.860812213 0.868917994 0 0.096867334 5.50056739 145.3264287 0.022543473 0.070419266 21234.45853 -4.327041191 0.008105781 EQEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQEELRR 7 1 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;; 112.84 0.010043 495370000 711708 606994 665280 732583 696546 627170 813450 731487 904448 FALSE TRUE 678066.9733 668847.3787 695783.7461 658942.365 818023.4019 605450.9456 689343.2625 667434.1204 1044705.177 0.649051032 0.640225964 0.666009666 0.630744807 0.783018425 0.5795424 0.659844785 0.638873182 1 19.99466443 -1.801221619 2.583852072 1.105900972 0.654428032 0.81845244 0.050925089 6353404.819 4497461.681 4220883.244 0.010920131 0.015804413 1.801221619 -0.45147294 EQEKGEGS(ph)DSKESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQEKGEGSDSKESPK 15 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 EQEKGEGS(0.995)DS(0.005)KESPK 99.86 0.0012416 179770000 295810 301470 294780 342000 123450 383530 341070 382090 108160 TRUE FALSE 281827.6475 332190.1357 308295.9546 307621.5102 144979.6409 370248.2599 289033.5073 348632.174 124932.9004 2.255832104 2.658948401 2.467692286 2.462293833 1.160460059 2.963576918 2.313509943 2.790555353 1 16.93079393 EQELQQTLQQEQSVLDQLRGEAEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 334.73 3.84E-95 254863500 81706.2 56346.8 81733.2 73518.2 88160.2 81294.9 102002.3 83760.4 113840.5 FALSE TRUE 77844.10985 62088.60298 85480.74807 66128.01086 103535.311 78479.63723 86439.97573 76425.89533 131494.3033 0.591996063 0.472177132 0.650071873 0.502896393 0.787374877 0.59682918 0.657366696 0.581210694 1 17.00464077 -4.999999997 0.192525064 2.749913673 0.52688473 0.680363905 0.08545097 72.74342259 0.713725865 48.82664176 0.203328202 1.00E-05 4.999999997 -2.223028944 EQEPMPTVDSHEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQEPMPTVDSHEPR 14 0 A6NGP5;Q9H910;Q9H910-3;Q9H910-2;H3BU16 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ; 153.2 6.46E-06 938900000 380420 362652 356800 393420 397450 366270 404900 397420 392560 FALSE TRUE 362438.3005 399606.6511 373159.6329 353872.6742 466765.1542 353585.9781 343125.0685 362619.7979 453436.1999 0.799314877 0.881285286 0.82295951 0.7804244 1.029395435 0.779792125 0.756721825 0.799715149 1 18.79054005 0.001726295 7.743141553 0.999999999 0.830155098 0.316634937 0.077919126 1234797.069 159469.78 0.072718964 0.017636939 1.003982852 -0.001726295 -0.169844901 EQEVAEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQEVAEERR 9 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;; 136.48 0.0022141 243590000 320140 233802 291507 305685 364940 300167 375160 327433 437100 FALSE TRUE 305007.6167 257626.6896 304872.8843 274956.963 428585.4205 289772.1415 317922.4517 298761.2307 504883.2356 0.60411516 0.510269843 0.603848302 0.544595153 0.848880276 0.573938925 0.629695005 0.591743218 1 18.94559025 -5 0.248176916 3.344940948 0.571210936 0.642112451 0.090541287 109.5985367 1.087471185 130.3135479 0.124936257 1.00E-05 5 -2.773730012 EQFAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 143.18 0.026596 6058121000 2873390 3937550 2459390 2990950 2677250 2757600 2683920 2936750 2332840 FALSE TRUE 2737570.549 4338790.822 2572155.464 2690294.024 3144161.552 2662103.621 2274438.71 2679592.601 2694604.913 1.01594506 1.610176988 0.95455755 0.998400178 1.166835827 0.987938383 0.844071314 0.994428752 1 21.36164233 3.699072178 24.99486656 0.984462169 1.313061173 0.40863132 0.160196751 424.0315512 268397.7725 0.041718672 0.064631231 5001.176457 -3.699072178 0.328599004 EQFLDGDGWTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 282.16 9.33E-28 11224590000 17082200 15078500 15331700 17394000 17190900 15834800 18342100 16629500 17828200 FALSE TRUE 16274758.26 16615016.29 16034673.61 15645522.07 20188987.52 15286436.91 15543675.77 15173332.82 20592906.2 0.790308959 0.806832029 0.778650349 0.759752991 0.980385542 0.742315667 0.754807292 0.736823286 1 24.29564411 -1.977917484 2.642072763 1.180417967 0.793611749 0.463340436 0.069763408 22783510.22 12842287.11 25125562.27 0.015944323 0.010521618 1.977917484 -0.386806218 EQFVEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EQFVEFR 7 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;; 195.81 0.0010681 4325620000 10781600 9215120 9121060 10758980 10911120 9157250 11517720 10095990 11402400 FALSE TRUE 10271975.14 10154151.2 9539269.623 9677466.89 12814015.87 8840132.136 9760480.277 9211931.593 13170625.96 0.779915485 0.770969522 0.724283694 0.734776534 0.972923832 0.671200607 0.741079453 0.699430052 1 23.65082058 -1.042799302 4.474296788 1.000012052 0.762443352 0.458067091 0.081413858 9.31E-06 1.99E-06 0.07296101 0.017196179 0.090615126 1.042799302 -0.237568699 EQGDGAEDEEWDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQGDGAEDEEWDD 13 0 Q7Z6K5;H0YMP5 Q7Z6K5 ARPIN Arpin 0 ; 197.31 3.14E-07 209270000 805440 752050 767520 830830 732590 777190 922730 850970 762890 FALSE TRUE 767368.4474 828684.75 802711.5512 747313.3899 860353.4641 750275.7154 781950.5914 776454.5555 881195.0849 0.870826972 0.940410091 0.910935121 0.848068042 0.97634846 0.851429755 0.887375117 0.881138092 1 19.74910192 -1.433354423 2.917523865 1.002279422 0.897039255 0.409842283 0.039265206 11430842.9 13860388.68 217014.0616 0.008725022 0.03686766 1.433354423 -0.105240166 EQGVLSFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQGVLSFWR 9 0 P05141;P12236 P05141;P12236 SLC25A5;SLC25A6 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed;ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ;; 144.65 0.00023043 516110000 462970 253279 211070 320882 692674 193065 547241 277974 499577 FALSE TRUE 441086.3256 279088.4181 220747.7683 288626.3317 813476.1263 186379.1106 463749.3347 253633.1229 577048.8497 0.764382991 0.48364782 0.382546068 0.5001766 1.409717958 0.322986712 0.803656978 0.439534925 1 19.13833393 EQGVTFPS(ph)GDIQEQLIR ddPTM_SK-BR-3_Trastuzumab_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 1 EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR 212.74 1.36E-12 115434000 228888 235715 190793 281771 222351 221286 247538 245572 227102 TRUE FALSE 218068.9179 259734.6265 199541.0478 253446.8438 261128.944 213622.8103 209771.5318 224068.4138 262319.8183 0.831309351 0.990144886 0.760678507 0.966174975 0.99546022 0.814360164 0.799678549 0.854180272 1 18.00096728 2.190225394 24.99943168 0.843645234 0.908692148 0.02247628 0.089884005 254.2823466 131515.5235 0.031177155 0.023025896 154.9620645 -2.190225394 0.065046914 EQGVTFPSGDIQEQLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 206.49 1.61E-11 118750000 105610 102060 80817 113510 101710 91274 92580 100470 92313 FALSE TRUE 100618.0246 112460.03 84522.53939 102099.7591 119448.1918 88113.15849 78455.22065 91672.31418 106628.4286 0.943632256 1.054690869 0.792682969 0.957528499 1.12022838 0.826357095 0.735781458 0.859736145 1 16.70223261 2.064681302 23.81316745 0.822128423 0.973101863 0.206457976 0.106704878 43.82067742 16132.33442 0.037824449 0.0279352 116.0596621 -2.064681302 0.15097344 EQGYDVIAYLANIGQKEDFEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQGYDVIAYLANIGQKEDFEEAR 23 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;; 263.57 6.23E-44 685360000 998260 761570 886770 998860 764850 964260 1081900 1067990 833560 FALSE TRUE 951074.2282 839174.8488 927429.2816 898452.6951 898239.5978 930867.4344 916836.2845 974471.1338 962824.2276 0.987796319 0.871576374 0.963238414 0.933143007 0.932921682 0.966809318 0.952236409 1.012096607 1 19.87691292 1.474987973 1.238275718 1.007148656 0.934734008 0.390726556 0.03125688 0.404713098 1.192943246 0.026474054 0.009032081 29.85299947 -1.474987973 -0.072414648 EQHDAQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQHDAQVR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;;; 169.09 0.00030306 291777000 257499 220513 207406 233530 266742 201936 275059 227557 250312 FALSE TRUE 245327.5326 242983.5254 216915.7703 210055.1207 313261.7203 194942.9057 233093.6977 207630.9027 289129.1065 0.848505138 0.840398009 0.750238441 0.72650977 1.083466567 0.674241719 0.806192433 0.718125218 1 18.14135433 -0.386436148 7.355694661 0.999999991 0.809674857 0.225456936 0.112841246 0 0 0.098592539 0.023238484 0.410737024 0.386436148 -0.190325134 EQHGVAASCLEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQHGVAASCLEDLR 14 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 0 ;; 222.42 3.90E-12 960210000 647712 534112 599784 642280 688540 587440 703600 604250 671320 FALSE TRUE 617095.9374 588538.62 627284.6897 577716.7941 808621.158 567096.8055 596252.8975 551338.6667 775424.877 0.795816533 0.758988572 0.808956107 0.745032577 1.042810441 0.731336874 0.768937024 0.711014933 1 19.56462749 -2.362480194 2.297498962 2.403955751 0.79370625 0.325170212 0.092619692 3477753.558 539117.6885 25403221.77 0.021755322 0.004340301 2.362480194 -1.610249501 EQIDIFEGIKDSQAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQIDIFEGIKDSQAQR 16 1 E9PDQ8;Q96I99;Q96I99-2;H0Y852 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 ;;; 250.95 3.88E-21 623410000 1283280 707680 1161370 937690 1002650 932970 1336070 1195270 1207110 FALSE TRUE 1222621.898 779793.3966 1214619.963 843431.6197 1177511.843 900661.015 1132227.983 1090605.822 1394302.454 0.876869932 0.559271336 0.871130909 0.604912957 0.844516797 0.645958137 0.812039009 0.782187408 1 20.41111212 0.511488055 0.856439856 1.001401285 0.728973863 0.342320185 0.110986978 1.639812925 1.849473375 0.097259885 0.031652021 3.247043112 -0.511488055 -0.272427422 EQIEWLIEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQIEWLIEHK 10 0 Q93034 Q93034 CUL5 Cullin-5 0 95.401 0.0074474 33970000 86433 100230 76392 96947 61020 84635 83112 89396 56803 FALSE TRUE 82347.48338 110443.551 79894.64876 87201.70337 71661.86868 81704.06873 70431.73794 81568.01232 65611.71913 1.25507279 1.683290004 1.217688697 1.329056829 1.092211416 1.245266392 1.073462773 1.243192731 1 16.0016659 3.235424499 1.662589151 1.142637814 1.45845881 0.420906097 0.141761698 0.289407417 1.655802058 0.043268888 0.061494712 1719.58837 -3.235424499 0.315820996 EQIKFFEEVLLFEDELHDHGVSSLSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQIKFFEEVLLFEDELHDHGVSSLSVK 27 1 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 92.275 0.0038873 44497000 61630 42502 63340 58776 54746 68754 88647 66046 15289 FALSE TRUE 58716.87204 46833.00212 66244.20165 52867.72481 64293.68507 66373.03174 75122.27204 60262.66211 17659.94003 3.324862481 2.65193438 3.751100033 2.993652567 3.640651381 3.75839508 4.253823733 3.41239336 1 14.10819282 3.734228558 24.80152914 3.474480926 2.988398442 0 0.905332115 958.9119351 5489890.488 0.213511879 0.343730052 5422.862063 -3.734228558 -0.486082483 EQIKGGTGDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQIKGGTGDEK 11 1 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 119.69 0.00050383 280610000 454810 334800 455540 475940 312850 502710 604960 574760 414130 FALSE TRUE 433312.0326 368916.5006 476426.9596 428097.607 367410.9409 485301.0266 512662.2411 524430.9674 478351.1653 0.905845045 0.771225257 0.99597742 0.894944213 0.768077863 1.014528785 1.071727798 1.09633049 1 18.86771059 2.085953891 6.253329605 1.058981842 0.865238169 0.625223737 0.069181916 0.126416078 7.421287498 0.02535083 0.018589412 121.8860186 -2.085953891 -0.193743673 EQISDIDDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;; 261.35 2.56E-20 1032090000 1630420 1489020 1471910 1677560 1521880 1559000 1701110 1561660 1563840 FALSE TRUE 1553353.278 1640752.831 1539398.529 1508928.482 1787295.39 1505011.439 1441574.426 1424912.772 1806352.32 0.85993926 0.908323815 0.852213886 0.83534561 0.989450048 0.833177128 0.79805828 0.788834357 1 20.78464788 EQIVPKPEEEVAQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQIVPKPEEEVAQKK 15 2 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 137.44 9.40E-06 131680000 368240 301980 359670 480490 238700 494940 501280 499170 256540 FALSE TRUE 350834.025 332752.1053 376161.2253 432190.2323 280329.2044 477800.1037 424800.5294 455460.0285 296322.913 1.183958478 1.122937481 1.269430101 1.458511014 0.946026082 1.612430503 1.433573007 1.537039522 1 18.17681066 2.226356005 24.99999809 1.438519724 1.200329967 0.177995804 0.204024984 297.8132175 610038.1381 0.067972089 0.050567113 168.4053967 -2.226356005 -0.238189757 EQIVVDLSHPGVSEDDQVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQIVVDLSHPGVSEDDQVSR 20 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 207.17 6.93E-22 253200000 208829 183108 206938 246808 229371 193281 245217 236148 223260 FALSE TRUE 198958.067 201766.9134 216426.312 221998.3909 269373.2298 186587.6305 207804.6429 215469.6292 257882.0205 0.771508097 0.782400079 0.839245448 0.860852534 1.044559947 0.723538733 0.805812838 0.835535679 1 17.97635167 -2.98023118 1.670701279 8.568538444 0.82569636 0.272680176 0.085022918 2381801.606 29202.90703 68861480.49 0.022557325 0.001046571 2.98023118 -7.742842084 EQIYDVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EQIYDVYR 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;;; 167.04 0.00073276 2690930000 5230000 4492270 2714700 3388670 5093090 3269950 5111790 4220320 4772940 FALSE TRUE 4982788.265 4950037.42 2839171.68 3048034.454 5981323.283 3156710.812 4331892.551 3850766.407 5513103.158 0.903808277 0.89786773 0.514986134 0.552870927 1.084928599 0.572583302 0.785744875 0.698475305 1 22.39443317 3.934113852 24.99997119 0.732237676 0.901584278 0.108617214 0.184075949 323.8457053 122880.2577 0.043246159 0.077963153 8592.387451 -3.934113852 0.169346602 EQLAIAEFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQLAIAEFAR 10 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 110.84 0.0042643 59018000 85558 79883 90048 77326 206830 67659 95047 79901 153050 FALSE TRUE 81513.8429 88023.16852 94176.78987 69553.04357 242901.0865 65315.95186 80545.83449 72904.44486 176784.2123 0.461092322 0.497913062 0.532721721 0.3934347 1.373997617 0.369467109 0.455616672 0.412392283 1 17.43162992 EQLDPDELETITMHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQLDPDELETITMHK 15 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 161.14 1.27E-06 95674000 159914 170780 161325 170586 120855 188510 174026 184529 116984 FALSE TRUE 152355.1821 188182.6762 168721.9108 153438.3712 141932.0737 181981.8514 147475.1375 168370.6625 135125.2812 1.127510565 1.392653354 1.248633189 1.135526748 1.050373938 1.346763905 1.091395601 1.246033762 1 17.0439381 -5 0.152480784 0.229042643 1.274912364 0.246030152 0.109776686 175.4568637 1.576009774 40.79967239 0.50186972 1.00E-05 5 1.045869721 EQLEEEEEAKHNLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;; 298.69 2.12E-44 7645180000 11795540 9701560 10104660 12211640 6300480 11968140 12707160 12702900 6050020 FALSE TRUE 11237988.2 10690159.99 10567968.66 10984102.75 7399281.717 11553680.31 10768449.36 11590566.73 6988226.202 1.608131717 1.52973869 1.512253374 1.57180126 1.058821152 1.653306573 1.540941728 1.65858494 1 22.73649488 -2.024214183 2.744341989 0.395259443 1.518927994 0.476516355 0.170182544 26816625.8 25589956.49 101624271.6 0.039549731 0.009457706 2.024214183 1.123668551 EQLEHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQLEHIK 7 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 66.351 0.068109 151930000 377830 300260 306160 356010 308180 341400 417640 382490 324300 FALSE TRUE 359970.7247 330856.8354 320197.7388 320223.1984 361926.4944 329577.2324 353921.3475 348997.1479 374590.7877 0.960970575 0.883248724 0.854793415 0.854861382 0.966191658 0.879832722 0.94482128 0.931675736 1 18.51495589 0.90712631 0.776311435 0.99924919 0.89978911 0.391745958 0.038927877 0.835434209 1.090885594 0.037188698 0.013647829 8.07469841 -0.90712631 -0.09946008 EQLEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQLEWER 7 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;; 99.136 0.02501 669680000 888160 810950 830920 910410 832430 828610 1016440 890770 901870 FALSE TRUE 846178.437 893586.727 869018.5039 818893.8571 977605.5284 799915.0279 861363.4098 812769.4565 1041727.393 0.812283945 0.85779325 0.834209131 0.786092275 0.938446598 0.767873662 0.826860669 0.780213194 1 19.99054636 -1.449532527 3.950032202 1.001155144 0.827416 0.562831337 0.048312697 0.000437478 6.10E-05 0.041639356 0.009750321 0.035519551 1.449532527 -0.173739145 EQLMFPFHFVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQLMFPFHFVDR 12 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 100.45 0.0032246 147323000 433160 392790 382720 428230 374670 389040 443680 462860 361470 FALSE TRUE 412685.3852 432815.7476 400268.0906 385183.5068 440012.3294 375567.4473 375988.4673 422329.5246 417524.9215 0.988408988 1.036622547 0.95866874 0.922540158 1.05385884 0.899509054 0.900517425 1.011507345 1 18.67150279 3.678036553 8.133171394 0.954375493 1.012445337 0.116311179 0.05093023 0.49220234 61.43883417 0.0132184 0.020554223 4764.710876 -3.678036553 0.058069845 EQLNRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQLNRPR 7 1 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 ;;; 125.81 0.0036596 280209000 282259 235755 224116 224756 340072 212132 288487 256320 360814 FALSE TRUE 268917.1765 259778.7025 234391.9403 202163.0999 399380.4491 204785.8156 244473.0097 233875.262 416767.1923 0.645245551 0.623318503 0.56240497 0.48507441 0.958281881 0.491367409 0.586593701 0.561165241 1 18.66888219 -1.472405003 5.703578774 1.000377761 0.614169395 0.45661851 0.132269966 0.000574958 5.32E-05 0.115892693 0.027290128 0.033697292 1.472405003 -0.386208365 EQLQLLEEQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EQLQLLEEQHR 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 ;;;; 210.79 1.16E-08 845250000 1579130 1422980 1374810 1614920 1542340 1440830 1684880 1553280 1541250 FALSE TRUE 1504487.654 1567983.28 1437846.398 1452585.173 1811323.608 1390933.696 1427820.611 1417266.569 1780259.178 0.845094733 0.880761239 0.807661275 0.815940281 1.017449386 0.781309661 0.802029631 0.796101256 1 20.76365586 EQLSAQELMESGLQIQKS(ph)PEPEVLSTQEDLFDQSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNK 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EQLS(0.021)AQELMES(0.049)GLQIQKS(0.93)PEPEVLSTQEDLFDQSNK;EQLS(0.052)AQELMES(0.027)GLQIQKS(0.921)PEPEVLSTQEDLFDQSNK;EQLS(0.002)AQELMES(0.004)GLQIQKS(0.995)PEPEVLSTQEDLFDQSNK 123.43 1.43E-08 122092000 97646 78499 82610 88494 55150 99784 112457 104713 62384 TRUE FALSE 93030.4671 86498.13735 86397.75021 79598.41499 64768.14254 96328.45506 95299.61924 95543.7746 72058.19211 1.291046366 1.200392833 1.198999693 1.104640745 0.898831079 1.336814764 1.322536917 1.325925225 1 16.13687484 EQMDNAVYTFETLLHQELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQMDNAVYTFETLLHQELGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 155.76 1.99E-08 16577000 30696 33909 25985 37684 23712 32412 32719 33347 23101 FALSE TRUE 29245.06091 37364.36565 27176.43795 33895.93273 27847.36529 31289.56431 27727.11562 30426.9599 26683.3851 1.096002655 1.400285815 1.018477898 1.270301073 1.043621909 1.172623496 1.039115372 1.140296098 1 14.70365408 2.301028119 0.49152408 1.026829866 1.234499981 0.182755027 0.113097586 1.312421126 0.671948052 0.09905114 0.093710692 199.9991358 -2.301028119 0.207670115 EQMMNSSISSGSGS(ph)LR ddPTM_SK-BR-3_Trastuzumab_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;EQMMNSSISSGSGS(1)LR 310.08 1.30E-57 693070000 913610 794280 849780 972240 1001920 770480 1045560 938210 1011650 TRUE FALSE 870425.4659 875218.035 888743.2535 874508.5881 1176654.531 743798.0844 886040.619 856055.3586 1168531.515 0.74488831 0.748989671 0.760564214 0.748382544 1.006951473 0.636523769 0.758251367 0.732590732 1 20.15626521 -2.457211307 2.167234125 3.308467828 0.764291225 0.384261758 0.092572802 2872393.807 257194.5692 32571017.13 0.021142361 0.003489705 2.457211307 -2.544176603 EQMQPTHPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQMQPTHPIR 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 ; 100.92 0.0027947 230130000 118914 121785 122866 117491 105230 99428 122801 133400 123233 FALSE TRUE 113293.1709 134195.03 128499.5276 105680.5815 123582.0787 95984.78343 104065.4521 121718.7888 142343.3443 0.795914775 0.942755916 0.902743492 0.742434302 0.8681971 0.674318732 0.731087587 0.855106991 1 17.11901551 3.247539091 24.99767785 0.787310376 0.881738573 0.063240289 0.097666072 319.3039448 888993.9282 0.025182464 0.033612174 1768.231369 -3.247539091 0.094428198 EQNSALPT(ph)SSQDEELMEVVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQNSALPTSSQDEELMEVVEK 21 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EQNS(0.004)ALPT(0.452)S(0.318)S(0.225)QDEELMEVVEK;EQNS(0.002)ALPT(0.333)S(0.333)S(0.333)QDEELMEVVEK 97.488 0.0041353 29304000 74692 66210 58173 81339 47881.3 65755 75368 72143 48154 TRUE FALSE 71161.45719 72956.87427 60840.28959 73162.64919 56231.78356 63477.88786 63869.22737 65825.77647 55621.47638 1.279388139 1.311667345 1.093827305 1.315366904 1.010972509 1.141247806 1.148283568 1.183459713 1 15.76335442 8 0.120168365 0.965556323 2.081766967 0.415767814 0.0861777 78.24745743 0.646016596 0.527745406 14.63293081 100000000 -8 1.116210644 EQNSALPTS(ph)SQDEELMEVVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQNSALPTSSQDEELMEVVEK 21 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EQNSALPT(0.09)S(0.556)S(0.353)QDEELMEVVEK 146.89 6.74E-08 20101000 57156 61959 46823 61531 39807 56209 62485 57178 41652 TRUE FALSE 54454.34915 68272.69254 48969.88086 55345.78698 46749.3282 54262.46824 52951.76563 52171.1912 48111.17943 1.131843987 1.419060878 1.017848272 1.150372692 0.971693663 1.127855706 1.100612503 1.084388116 1 15.55408455 3.722377031 24.95777109 1.073988227 1.275452444 0.494970714 0.088122533 545.9585264 841958.5481 0.021603733 0.033577404 5276.877731 -3.722377031 0.201464216 EQPFGEGVPLDGDDPEHIQWIFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQPFGEGVPLDGDDPEHIQWIFQK 24 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 204.31 1.10E-24 302758000 258649 222226 229125 270969 223746 257532 282798 270154 207007 FALSE TRUE 246423.1744 244871.082 239630.6079 243730.6813 262767.2316 248613.6023 239651.9712 246497.8836 239108.5883 1.030591064 1.024099903 1.00218319 1.019330519 1.098945184 1.039751872 1.002272536 1.030903513 1 17.86730642 1.746197544 24.99999948 1.012279899 1.034563316 0.164065434 0.026194785 3.619769919 11882.0765 0.012382878 0.006867091 55.74392491 -1.746197544 0.022283417 EQQAQVEKEDFSDMVAEHAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 202.47 3.83E-22 526470000 674750 572930 604090 697940 440470 703460 713520 753980 414030 FALSE TRUE 642855.9047 631312.2184 631788.124 627781.7452 517287.8285 679099.0038 604659.4193 687957.5141 478235.6578 1.344224117 1.320086046 1.321081173 1.312703758 1.081658843 1.420009137 1.264354528 1.438532453 1 18.86736218 -2.065943099 2.664258817 0.535350814 1.310083343 0.507840179 0.096750078 2471712.457 2567598.261 6949524.197 0.020914599 0.008591261 2.065943099 0.774732529 EQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDR 18 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 312.46 3.37E-61 419120000 779640 903620 620670 996580 637420 732220 707640 803050 477900 FALSE TRUE 742787.9623 995699.9053 649128.3334 896401.885 748585.8462 706863.0378 599676.5213 732730.6848 552010.2912 1.34560528 1.803770548 1.175935202 1.623886183 1.356108497 1.280525108 1.086350256 1.327385914 1 19.07433564 2.196856788 0.863884029 1.095376125 1.53143411 0.400920467 0.183545633 0.525020475 0.739857208 0.133467579 0.075328277 157.3463918 -2.196856788 0.436057985 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK 78.618 0.0025639 15104000 12939 10116 9797.5 12185 8104.9 12001 13279 14264 7782.2 TRUE FALSE 12327.39911 11146.8319 10246.72507 10960.14065 9518.391994 11585.40236 11253.04466 13014.96854 8989.02383 1.371383517 1.24004921 1.139915219 1.219280409 1.058890506 1.288838764 1.251865039 1.447873405 1 13.13394874 4.396973911 2.328545142 1.212876018 1.368344986 0.150642192 0.123496932 0.614798771 5.981249309 0.029416578 0.143517586 24944.44878 -4.396973911 0.155468968 EQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 248.51 3.49E-46 143745000 63103 64039 52126.9 71581 41620.1 61365 63175 65218 36616.9 FALSE TRUE 60120.24625 70564.64691 54516.96993 64385.54188 48878.63226 59239.91466 53536.49346 59507.16618 42295.26184 1.421441638 1.668381843 1.288961637 1.522287346 1.15565267 1.400627685 1.265779927 1.406946395 1 15.36820843 -2.890340021 0.080144445 1.92E-15 1.886760976 0.493746475 0.132690148 108.6378448 0.966262764 24.11975903 4.838157549 0.001287241 2.890340021 1.886760976 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;;; 400.36 1.13E-167 954622000 686649 488329 651598 625472 395959.5 716285 844162 808988 394808.1 FALSE TRUE 654192.4626 538090.2803 681474.4128 562598.3662 465014.7114 691479.8708 715369.5828 738148.722 456032.9237 1.434529019 1.179937352 1.494353537 1.233679274 1.019695481 1.516293747 1.568679684 1.61863033 1 18.79877846 EQQHVMEELFQSSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQQHVMEELFQSSFR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 277 1.46E-33 443879000 390999 443020 396872 520861 449014 485332 450227 441995 378051 FALSE TRUE 372517.2522 488164.2417 415068.9738 468503.0627 527321.8994 468524.8311 381536.6022 403291.5746 436677.2183 0.85307233 1.117906365 0.950516666 1.072881852 1.207578223 1.072931702 0.873726831 0.923546175 1 18.73620774 1.744492209 24.9996052 0.923878489 1.04290393 0.225435433 0.098558817 1.769753457 7485.065627 0.045968404 0.025491807 55.52546555 -1.744492209 0.119025441 EQQIEEHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQQIEEHRR 9 1 Q16643;Q16643-3;Q16643-2;D6R9W4 Q16643 DBN1 Drebrin 0 54.608 0.086941 28555000 17377 15562 15146 17943 19692 14327 21504 18218 22877 FALSE TRUE 16555.62365 17147.78549 15840.45908 16139.33555 23126.27857 13830.8524 18223.16985 16622.73534 26424.64832 0.626522005 0.648931455 0.599457707 0.610768225 0.875178291 0.523407246 0.689627715 0.629061743 1 14.68959665 -1.548709075 2.558733463 1.024493922 0.650091268 0.596881305 0.090299071 5051696.094 4677327.606 848330.2194 0.020840028 0.028267729 1.548709075 -0.374402654 EQQILTLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQQILTLFR 9 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 156.83 0.00016285 148598000 214682 178100 152765 174971 217536 157779 229695 188301 218774 FALSE TRUE 204534.4073 196248.5925 159769.4264 157382.5827 255474.2095 152315.0737 194650.8091 171812.3662 252700.3546 0.809395015 0.776605924 0.632248525 0.622803173 1.010976854 0.602749743 0.770283087 0.679905521 1 17.94706816 -2.090238762 2.490927512 1.430811243 0.743315895 0.321013111 0.119481888 23243218.32 6511949.837 56852953.74 0.030030858 0.008123838 2.090238762 -0.687495348 EQS(ph)PLLHLDLFNFDCPEAEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EQSPLLHLDLFNFDCPEAEGSR 22 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 EQS(1)PLLHLDLFNFDCPEAEGSR;EQS(1)PLLHLDLFNFDCPEAEGSR;EQS(1)PLLHLDLFNFDCPEAEGSR;EQS(1)PLLHLDLFNFDCPEAEGSR 139.93 8.59E-08 44254100 40013.4 28833.1 29345.3 37922.4 34874.4 32892.8 36862.5 36130.4 33442 TRUE FALSE 38122.04588 31771.22567 30690.81103 34110.3683 40956.48432 31753.71409 31238.4486 32966.63064 38628.01456 0.98690151 0.822491811 0.794522094 0.883047412 1.060279302 0.822038473 0.808699307 0.853438392 1 15.23735991 -0.569560185 4.852748596 1.000000009 0.875783005 0.168803491 0.084175903 15742252.09 54468559.75 5.04328816 0.020282607 0.269426193 0.569560185 -0.124217004 EQS(ph)PSQHGKDPASLLASELVQLHMQLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQSPSQHGKDPASLLASELVQLHMQLEEK 29 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 EQS(0.831)PS(0.169)QHGKDPASLLASELVQLHMQLEEK 79.422 0.0019494 25200000 17815 15732 19659 21325 16268 21277 25342 27404 12633 TRUE FALSE 16972.92026 17335.10869 20560.3846 19181.37049 19105.13405 20540.17215 21475.61246 25004.36048 14592.06112 1.163161264 1.187982187 1.409011683 1.314507274 1.309282759 1.407626516 1.471732628 1.713559193 1 13.83289606 3.734717368 0.799434231 1.42275188 1.122848049 0.140165884 0.179443844 1.22462277 1.388560634 0.071628054 0.255870231 5428.969081 -3.734717368 -0.299903831 EQSDDET(ph)EESVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQSDDETEESVK 12 0 O94885;A0A1B0GWB9;A0A1B0GVI0 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EQS(0.278)DDET(0.722)EESVK 289.72 3.91E-21 0 312400 312450 276100 334840 165190 338120 306370 320230 139350 TRUE FALSE 297633.4711 344289.0102 288759.4581 301181.247 193999.0837 326410.8196 259627.6296 292188.9636 160959.6863 1.849118111 2.138976648 1.793986213 1.871159506 1.205265046 2.027904174 1.612997861 1.815292824 1 17.29633987 -2.112358953 0.178443781 8.81E-14 2.054253887 0.512350516 0.245924145 29.94741878 0.749786224 13.6407766 0.848700046 0.007720422 2.112358953 2.054253887 EQSEVSVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;EQSEVSVS(1)PR;EQSEVSVS(1)PR 176.51 2.60E-06 10268570000 6663740 5348730 5890220 6580050 6195260 6005730 6912070 6048290 6887240 TRUE FALSE 6348758.216 5893771.668 6160292.413 5918610.873 7275711.383 5797750.064 5857506.773 5518669.664 7955278.004 0.79805611 0.740863068 0.774365448 0.743985423 0.914576634 0.728792892 0.736304472 0.69371173 1 22.92348092 -1.203896645 5.054697411 1.000022135 0.766042966 0.604294749 0.059423781 1.40E-05 2.20E-06 0.054266142 0.012789443 0.062532149 1.203896645 -0.233979169 EQSGLQAS(ph)LEAEQEALEKDQERLEYEIQQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQSGLQASLEAEQEALEKDQERLEYEIQQLK 31 2 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 EQS(0.001)GLQAS(0.999)LEAEQEALEKDQERLEYEIQQLK 160.4 1.07E-12 15438000 22614 13186 21140 20459 13497 22318 30312 22985 17958 TRUE FALSE 21545.08104 14529.66839 22109.28991 18402.42245 15850.87253 21545.12206 25687.34768 20972.31155 20742.83492 1.038675818 0.700466857 1.065876 0.887170077 0.76416134 1.038677796 1.238372083 1.011062935 1 14.34032546 2.036426478 8.166599473 1.116883019 0.887191085 0.32812116 0.126716893 0.211171649 41.57802947 0.044749689 0.032812366 108.7493019 -2.036426478 -0.229691934 EQSISLMSVGFLLEKPDEAVVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQSISLMSVGFLLEKPDEAVVWR 23 1 H3BQR2;Q9Y5Y2;H3BRE1;H3BNF0;H3BNS4 H3BQR2 NUBP2 Cytosolic Fe-S cluster assembly factor NUBP2 0 245.41 1.50E-37 140270000 109640 94163 77151 105580 98030 99393 126700 111970 92227 FALSE TRUE 104457.5345 103758.3168 80688.44966 94966.89781 115126.401 95950.99549 107369.588 102165.3132 106529.0921 0.980554066 0.973990435 0.757431121 0.891464443 1.080703859 0.900702274 1.007889825 0.95903674 1 16.70088795 EQST(ph)PPKS(ph)PQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 2 EQST(1)PPKS(1)PQ;EQST(1)PPKS(1)PQ;EQST(1)PPKS(1)PQ 130.1 0.0071625 1214970000 3111500 2516300 2697930 3131300 1744700 3080450 3254350 2965240 1902490 TRUE FALSE 2964425.561 2772713.831 2821632.759 2816535.775 2048975.128 2973773.244 2757839.137 2705587.866 2197518.433 1.348987803 1.261747701 1.284008688 1.281689261 0.932404069 1.353241547 1.254978842 1.231201443 1 21.06744384 -5 0.145024512 0.169708184 1.331171774 0.319527618 0.115482199 168.2535742 1.472041831 40.80351124 0.615685815 1.00E-05 5 1.16146359 EQSTCNFQAIVISLKEEFYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQSTCNFQAIVISLKEEFYTK 21 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 209.01 2.56E-22 159240000 114410 121399 115050 127083 81603 119440 125662 126269 94962 FALSE TRUE 109002.066 133769.6961 120325.1563 114308.3754 95834.53736 115303.7629 106489.954 115212.217 109688.222 0.993744489 1.219544758 1.096974262 1.04212078 0.873699433 1.051195477 0.970842193 1.050360877 1 16.7430491 3.116369124 3.814462243 0.988776264 1.112764283 0.33406699 0.072724071 0.226779075 6.219483141 0.020529653 0.025052105 1307.281527 -3.116369124 0.123988019 EQSTPPKS(ph)PQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EQST(0.01)PPKS(0.99)PQ;EQSTPPKS(1)PQ;EQSTPPKS(1)PQ;EQST(0.015)PPKS(0.985)PQ;EQST(0.056)PPKS(0.944)PQ;EQS(0.002)T(0.245)PPKS(0.753)PQ 148.13 6.75E-05 1719746000 4705602 3935406 4436471 4996172 3101985 4422597 4986200 4414853 3227307 TRUE FALSE 4483177.519 4336428.346 4639887.584 4493947.298 3642970.202 4269441.357 4225463.612 4028265.067 3727781.287 1.202639633 1.163273275 1.244678061 1.205528692 0.977248911 1.145303608 1.13350631 1.080606601 1 21.82988579 1.674020162 0.178567328 0.944247536 1.274026836 0.471996346 0.063219617 3.147244803 0.574327036 0.410181951 0.447765182 47.20849575 -1.674020162 0.3297793 EQTLS(ph)PTITSGLHNIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.005)LS(0.667)PT(0.315)IT(0.013)SGLHNIAR;EQTLS(0.941)PT(0.007)IT(0.001)S(0.051)GLHNIAR;EQTLS(0.823)PT(0.175)IT(0.002)SGLHNIAR;EQT(0.002)LS(0.83)PT(0.167)IT(0.001)SGLHNIAR;EQT(0.004)LS(0.985)PT(0.004)IT(0.007)SGLHNIAR 241.71 1.45E-20 3155820000 1565830 1204705 1406822 1691961 1652050 1375016 1747260 1528810 1848200 TRUE FALSE 1491816.319 1327465.809 1471326.18 1521881.866 1940166.997 1327398.851 1480683.396 1394939.292 2134809.417 0.698805386 0.621819352 0.689207275 0.712888867 0.908824451 0.621787988 0.693590437 0.653425679 1 21.02567585 -1.732429173 2.686096693 1.058136976 0.69560266 0.577110123 0.080615021 17849835.37 14711100.44 6948295.726 0.020831996 0.018517009 1.732429173 -0.362534315 EQTLSPT(ph)ITSGLHNIAR ddPTM_SK-BR-3_Trastuzumab_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 EQTLS(0.019)PT(0.618)IT(0.182)S(0.182)GLHNIAR 278.32 8.92E-35 259620000 212730 163270 208430 215650 227960 183150 231040 203600 224070 TRUE FALSE 202674.6745 179907.3986 217986.7217 193972.4523 267716.1518 176807.4696 195790.6047 185771.7046 258817.6312 0.783079088 0.695112608 0.842240618 0.749456099 1.034381431 0.683135336 0.756480939 0.71777067 1 17.98157637 -2.356879592 2.248259943 2.413755737 0.777179163 0.315023903 0.100402706 4155089.236 339018.7791 30193551.6 0.022843637 0.004396635 2.356879592 -1.636576574 EQTPEHGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQTPEHGKK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 82.749 0.011406 80017000 51634 49922 48346 59582 39166 55660 58423 56063 40348 FALSE TRUE 49193.36315 55009.10856 50562.71192 53592.70416 45996.538 53732.48024 49509.49834 51153.82651 46604.96177 1.05553918 1.180327297 1.084921219 1.149935589 0.986945086 1.152934756 1.062322475 1.097604731 1 15.50819594 -2.027486005 0.221973387 0.880045835 1.119654388 0.229402287 0.055747461 43.25270757 1.408536256 2.765942584 0.104294243 0.009386723 2.027486005 0.239608553 EQVANSAFVER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 256.48 3.95E-20 3608630000 1718444 1560002 1531165 1770736 1484810 1623082 1850746 1692187 1666513 FALSE TRUE 1637216.558 1718967.977 1601370.43 1592738.253 1743760.394 1566874.263 1568380.706 1544010.135 1924947.325 0.850525382 0.892994814 0.831903507 0.827419136 0.905874343 0.81398293 0.814765519 0.802105136 1 20.87638754 2.198421334 24.99978962 0.838319045 0.86206885 0 0.061208519 605.1564279 376903.8815 0.020365246 0.015040883 157.9142544 -2.198421334 0.023749805 EQWDTIEELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 EQWDTIEELIR 11 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;;;;;;;;;; 242.97 1.98E-15 1879316000 1221471 988799 985608 1052472 1061597 829474 1017709 954628 965844 FALSE TRUE 1163734.487 1089558.742 1030799.102 946675.515 1246739.181 800749.1074 862438.8005 871035.7115 1115622.155 1.04312601 0.976637778 0.923967938 0.84856285 1.117528166 0.717760134 0.773056359 0.780762293 1 20.08941706 2.226032639 24.99839759 0.79330409 0.978098394 0.382928782 0.101312714 197.3120684 393714.9862 0.034647631 0.025764401 168.2800527 -2.226032639 0.184794303 EQWDTIEELIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQWDTIEELIRK 12 1 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ; 182.1 2.78E-05 110695000 234380 93788 226770 146679 215381 167187 284610 229490 286780 FALSE TRUE 223301.3219 103345.1038 237167.6288 131934.5482 252943.3782 161397.2723 241187.5173 209394.639 331252.3777 0.674112359 0.31198298 0.715972608 0.398290117 0.76359717 0.487233551 0.728108033 0.632130222 1 18.33757128 0.061143903 0.33996454 1.096248392 0.502960371 0.465075879 0.14396937 3.611306645 0.623073024 0.618877417 0.121383197 1.151181768 -0.061143903 -0.593288021 EQWEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQWEER 6 0 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4 A0A2R8Y5S7 RDX Radixin 0 106.43 0.074747 149810000 317130 244910 245550 313270 297350 256470 308730 289470 321620 FALSE TRUE 302139.8934 269866.6074 256808.7104 281779.5044 349207.7459 247588.3796 261627.5683 264122.4722 371495.187 0.813307693 0.726433658 0.691284085 0.75850109 0.940006111 0.666464569 0.704255607 0.710971451 1 18.50298399 -1.745413923 2.478089443 1.058546957 0.749714339 0.500567547 0.07802165 11800621.82 8504451.749 4234352.819 0.01940199 0.017971572 1.745413923 -0.308832618 EQWIQDAEECDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EQWIQDAEECDR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 196.02 4.92E-07 241966000 285556 282505 270265 327859 284269 287633 330377 320567 318921 FALSE TRUE 272058.3338 311292.5807 282656.9176 294901.9904 333845.4236 277672.1971 279971.9209 292496.454 368377.6399 0.738531073 0.845036579 0.767302048 0.800542591 0.906258653 0.753770498 0.760013341 0.794012509 1 18.49082597 -1.538023392 2.575388835 1.013250952 0.794815722 0.629929644 0.049211543 5212387.303 4848210.695 478034.5043 0.011611013 0.028971875 1.538023392 -0.21843523 EQYAQEHGLNFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EQYAQEHGLNFQR 13 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 158.93 4.64E-05 283210000 231850 255120 170170 232790 201500 205630 253520 247520 205280 FALSE TRUE 220890.91 281117.018 177972.4628 209389.5069 236641.5362 198508.9815 214840.8678 225845.8366 237113.774 0.931581942 1.185578608 0.75057834 0.883076101 0.998008392 0.837188739 0.906066586 0.952478773 1 17.85521995 3.743352358 24.9999922 0.899393265 1.058580265 0.313299347 0.095013436 403.0055619 2102597.749 0.022892564 0.039685045 5537.992434 -3.743352358 0.159187 EQYPGIEIESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EQYPGIEIESR 11 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;;; 234.67 3.89E-15 1799605000 1295861 1123128 1148782 1318963 1200717 1154201 1374168 1284667 1349580 FALSE TRUE 1234608.219 1237576.02 1201454.791 1186378.333 1410121.665 1114230.73 1164513.433 1172174.747 1558865.974 0.791991255 0.793895076 0.770723597 0.761052171 0.904581721 0.714770063 0.747026013 0.751940684 1 20.57206546 -1.995983967 2.900626614 1.214989377 0.779157975 0.658319421 0.049923271 13881868.39 18483945.97 19966041.7 0.011515119 0.010092901 1.995983967 -0.435831402 EQYVPPRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 106.13 0.0014882 1481610000 2098240 2039810 1947740 2441300 1404060 2217030 2309580 2256880 1414620 TRUE FALSE 1999060.354 2247668.958 2037045.806 2195895.886 1648927.619 2140253.695 1957211.153 2059255.623 1633992.045 1.223421105 1.375569095 1.246668129 1.343884074 1.009140543 1.30983116 1.197809475 1.260260495 1 20.63996953 -4.999999993 0.159880951 0.057280483 1.321300818 0.38330506 0.09909046 127.4502653 1.171124019 38.04974537 0.382465625 1.00E-05 4.999999993 1.264020335 ERALS(ph)PGLEESGLGLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERALSPGLEESGLGLLAR 18 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ERALS(1)PGLEESGLGLLAR;ERALS(0.996)PGLEES(0.004)GLGLLAR 88.222 0.0018876 44810000 24614 18073.4 26442 24140 48127 23269 39047 31444 71508 TRUE FALSE 23450.545 19915.10001 27654.39185 21713.40134 56520.33356 22463.1887 33089.663 28690.59666 82597.09543 0.283914887 0.241111384 0.334810706 0.262883352 0.684289602 0.271961 0.400615334 0.347356 1 16.33380343 -4.999999999 0.23185771 4.558275633 0.271765865 0.729130433 0.124623158 80.29013118 0.802707064 134.1874302 0.197064319 1.00E-05 4.999999999 -4.286509767 ERAS(ph)LDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERASLDK 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 ERAS(1)LDK;ERAS(1)LDK 94.363 0.0086334 551640000 854940 829260 702410 914630 537040 829490 798480 903620 550120 TRUE FALSE 814528.6805 913762.5368 734616.1933 822689.6547 630699.606 800764.5533 676657.2109 824494.2424 635429.8 1.281854708 1.438022795 1.156093393 1.294697943 0.992555914 1.260193578 1.064881142 1.297537891 1 19.27737322 3.447483663 1.76974539 1.141095088 1.356338539 0.318449534 0.119525968 0.336630232 2.130816466 0.032465369 0.054042792 2802.100214 -3.447483663 0.215243451 ERASS(ph)PPDRIDIFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERASSPPDRIDIFGR 15 2 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 ERAS(0.06)S(0.94)PPDRIDIFGR;ERAS(0.182)S(0.818)PPDRIDIFGR 161.08 8.73E-07 139717000 20111.7 14406.8 19637.2 17871.9 35323 19845.2 26688.8 17629.9 35240 TRUE FALSE 19161.0598 15874.8693 20537.58504 16075.38266 41483.32002 19157.95575 22616.93339 16086.13249 40704.83922 0.47073174 0.389999558 0.504548978 0.39492559 1.019125018 0.470655483 0.555632544 0.395189683 1 15.3129127 ERAVELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ERAVELLR 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ;;; 153.24 0.00040507 766720000 493967 537490 447484 425462 414964 470050 507085 591380 575460 FALSE TRUE 470618.1589 592260.8421 468001.584 382693.7514 487333.5902 453772.0506 429719.87 539595.6321 664699.3978 0.708016527 0.891020579 0.704080048 0.575739579 0.733163881 0.682672577 0.646487527 0.811788959 1 19.34234252 0.950191941 5.902460394 0.999967167 0.716632902 0.581742188 0.079492651 0.269790065 29.01188907 0.083483041 0.021002027 8.916449226 -0.950191941 -0.283334265 ERDAEQSGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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(0.029)GS(0.971)PR;ERDAEQS(0.011)GS(0.989)PR;ERDAEQS(0.021)GS(0.979)PR;ERDAEQS(0.001)GS(0.999)PR;ERDAEQS(0.003)GS(0.997)PR 116.06 0.00062975 1184722000 1566674 1375217 1384231 1576358 1452740 1551931 1660430 1469759 1507930 TRUE FALSE 1492620.425 1515353.176 1447699.361 1417899.499 1706097.396 1498187.24 1407100.908 1341059.11 1741772.083 0.856955074 0.870006582 0.831164637 0.814055704 0.979518166 0.860151139 0.807855931 0.769939491 1 20.73212442 -1.303855397 3.502965363 1.000534077 0.850763197 0.427704911 0.054954195 3564339.07 1997826.791 13887.36456 0.012581673 0.049675769 1.303855397 -0.14977088 ERDEDSLHQTDLFDSHMLWFLMHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERDEDSLHQTDLFDSHMLWFLMHHLR 26 1 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 281.75 2.33E-61 39243000 39660 39666 43237 46859 53739 46943 66491 43249 20844 FALSE TRUE 37785.3504 43708.0105 45219.45922 42148.64429 63111.06459 45317.35214 56346.57676 39461.88828 24076.38106 1.569394931 1.815389546 1.878166785 1.75062208 2.621285334 1.882232717 2.340325841 1.639029062 1 14.55533094 0.987212555 23.13634905 0.999999977 1.962367051 0.520258923 0.300259657 207.2971773 375065.1177 0.294272048 0.073568012 9.709850767 -0.987212555 0.962367074 ERDEIRHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERDEIRHDR 9 2 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ;; 138.76 7.17E-05 133829000 48006.7 28091.2 43404.9 34910 61886.4 43463.4 66996 48872.3 88225 FALSE TRUE 45737.51843 30953.72522 45395.0576 31400.78048 72679.36857 41958.25156 56774.52973 44592.78232 101906.4824 0.448818538 0.303746381 0.445457998 0.308133298 0.713196716 0.4117329 0.55712383 0.437585336 1 16.6368863 -4.999999998 0.19102704 3.415571716 0.345315543 0.701304154 0.11370628 68.50601966 0.670870839 62.83957151 0.272391209 1.00E-05 4.999999998 -3.070256173 ERDFYFGK ddPTM_SK-BR-3_Trastuzumab_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 ; 123.35 0.0012323 470720000 751010 615690 585930 698200 582990 642580 782600 668800 637500 FALSE TRUE 715511.2457 678429.511 612795.4701 628015.6095 684663.2714 620327.2935 663199.9966 610236.3265 736360.2441 0.971686415 0.921328272 0.832195213 0.852864633 0.929793911 0.842423662 0.90064612 0.828719817 1 19.49005221 4.077780716 3.17146404 0.878984057 0.959723134 0.215071556 0.05253976 0.285808427 5.690018509 0.011823026 0.028833022 11961.36426 -4.077780716 0.080739077 ERDHS(ph)PTPSVFNS(ph)DEERYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(1)PT(0.003)PS(0.317)VFNS(0.68)DEERYR 115.79 7.03E-05 563840000 154020 131330 161700 160500 134220 161050 182730 160430 128520 TRUE FALSE 146739.7798 144712.6763 169114.1049 144366.2351 157627.9255 155472.7981 154851.1824 146381.8987 148450.2252 0.988477987 0.974822882 1.139197362 0.972489162 1.061823418 1.047305909 1.043118542 0.986067205 1 17.17961976 ERDHS(ph)PTPSVFNSDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.999)PT(0.001)PSVFNSDEER;ERDHS(0.87)PT(0.115)PS(0.015)VFNSDEER;ERDHS(0.845)PT(0.149)PS(0.006)VFNSDEER;ERDHS(0.958)PT(0.023)PS(0.02)VFNSDEER 218.66 2.76E-15 1575570000 1736850 1852780 1435720 1881860 1227030 1796660 1559470 1726810 1110680 TRUE FALSE 1654752.543 2041580.388 1501549.182 1692691.857 1441023.644 1734441.214 1321544.21 1575601.362 1282918.582 1.289834418 1.59135616 1.170416582 1.319407078 1.123238578 1.351949561 1.030107622 1.228138234 1 20.29099818 2.559630974 0.387357243 1.022227644 1.470403011 0.395741187 0.133311506 1.199403594 0.384529732 0.133418039 0.199115586 362.7696731 -2.559630974 0.448175367 ERDHS(ph)PTPSVFNSDEERYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.991)PT(0.009)PSVFNSDEERYR;ERDHS(1)PTPSVFNSDEERYR;ERDHS(0.999)PT(0.001)PSVFNSDEERYR;ERDHS(0.999)PT(0.001)PSVFNSDEERYR;ERDHS(0.998)PT(0.002)PSVFNSDEERYR;ERDHS(0.981)PT(0.018)PSVFNSDEERYR 232.02 1.06E-20 3917000000 640099 453816 608636 572058 641204 514883 756624 604504 761870 TRUE FALSE 609842.7888 500060.3663 636542.5626 514553.643 753029.7746 497052.4726 641187.1124 551570.4251 880016.9085 0.692989854 0.568239498 0.723329923 0.584708814 0.855699211 0.564821503 0.728607719 0.626772531 1 19.74717172 -5 0.357182983 5.048122595 0.655334286 0.569689766 0.090080474 306.226679 2.4567687 952.1265036 0.057535196 1.00E-05 5 -4.392788309 ERDHSPTPS(ph)VFNSDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.181)PT(0.303)PS(0.516)VFNSDEER 160.48 1.86E-09 211020000 153010 138210 131930 176490 166810 157640 160200 150110 126120 TRUE FALSE 145777.5205 152293.7561 137979.121 158748.8899 195901.6112 152180.8873 135758.5477 136965.5726 145678.0455 1.000682842 1.045413231 0.9471511 1.089724189 1.344757273 1.044638448 0.931908081 0.940193645 1 17.15242395 1.831513864 5.540119833 0.952862126 1.075709014 0.232160899 0.104820743 0.360646559 16.02383644 0.050027928 0.029246613 67.84437774 -1.831513864 0.122846888 ERDLFFELDAMDHLESFIAECDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERDLFFELDAMDHLESFIAECDRR 24 2 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 139.26 4.73E-07 14178000 7973.7 8093.7 9656.7 7972.7 12770 7364.7 11837 9310.7 10581 FALSE TRUE 7596.799003 8918.457232 10099.46925 7171.269049 14997.08396 7109.658592 10031.04825 8495.405749 12221.84744 0.621575342 0.729714331 0.82634555 0.586758187 1.227071769 0.581717177 0.820747297 0.695099967 1 13.57717476 -4.999999564 0.032785328 2.140075524 1.56E-09 0.145215541 0.185689595 2308.39424 5.684368824 301.1959043 112.3172151 1.00E-05 4.999999564 -2.140075522 ERDLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 68.016 0.058895 79983000 47706 54954 55572 62014 46855 55811 47122 47978 38172 TRUE FALSE 45451.03192 60553.87508 58120.03117 55780.2349 55026.49717 53878.25108 39932.67345 43776.79197 44091.5188 1.030833892 1.373367866 1.318168046 1.265101235 1.248006389 1.221964054 0.905676977 0.992861964 1 15.42821355 1.78233429 6.504258497 0.962567337 1.246541947 0.673610803 0.090789497 0.116002319 11.07323245 0.042905431 0.024175921 60.58070035 -1.78233429 0.28397461 ERDLS(ph)RDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;ERDLS(1)RDR;ERDLS(1)RDR;ERDLS(1)RDR 97.734 0.0063176 1484350000 1126050 914630 882810 1046180 1042540 861120 1200930 1090580 1088590 TRUE FALSE 1072823.848 1007831.837 923287.7117 941015.9988 1224358.646 831299.1985 1017706.072 995083.0337 1257402.977 0.853206066 0.80151857 0.734281474 0.748380603 0.973720174 0.66112393 0.809371451 0.791379575 1 20.26201565 -0.920537388 6.184312287 1.000000043 0.797261393 0.382474974 0.081210352 4.33E-08 7.51E-09 0.070876438 0.016705733 0.120077769 0.920537388 -0.20273865 ERDQRPS(ph)SPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.707)S(0.293)PIR;ERDQRPS(0.709)S(0.291)PIR 117.08 0.00071087 350000000 307540 289530 287520 337410 297540 297000 304780 296710 308660 TRUE FALSE 293003.1937 319033.4362 300703.0764 303492.9058 349430.8818 286714.8155 258280.2133 270728.4994 356525.4164 0.82182975 0.894840652 0.843426759 0.851251809 0.980100901 0.804191798 0.724437029 0.759352593 1 18.4436454 2.026622828 24.99678543 0.789062358 0.874229283 0.041759687 0.085251192 332.2919392 311995.1949 0.028763158 0.021242479 106.3219242 -2.026622828 0.085166925 ERDQRPS(ph)SPIRHQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERDQRPSSPIRHQGR 15 3 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.566)S(0.434)PIRHQGR 70.235 0.033747 27044000 3303.7 2400.4 3561.6 3669.8 6603.9 3074.5 4287.3 4282.2 5774 TRUE FALSE 3147.540648 2645.003489 3724.902883 3300.904732 7755.618069 2968.029294 3633.193643 3907.227867 6669.40243 0.471937431 0.396587778 0.558506241 0.494932607 1.162865512 0.445021773 0.544755498 0.58584377 1 12.70334179 2.965935766 24.99983508 0.695133947 0.466760451 0.255497916 0.216589356 963.4257103 707060.9459 0.063652364 0.067549659 924.5614163 -2.965935766 -0.228373496 ERDTSPDKGELVS(ph)DEEEDT ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERDTSPDKGELVSDEEEDT 19 2 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 ERDTSPDKGELVS(0.994)DEEEDT(0.006);ERDTSPDKGELVS(0.666)DEEEDT(0.334) 154.87 2.48E-08 174960000 357340 281630 320020 372840 234452 348650 368910 389450 284420 TRUE FALSE 340449.2464 310328.4172 334693.2335 335361.4149 275340.3546 336576.1631 312626.004 355347.6934 328526.401 1.036291894 0.944607241 1.018771193 1.020805067 0.838107238 1.024502634 0.951600855 1.081641209 1 18.32564979 1.247289754 24.98577628 1.040820613 0.976634456 0.160615793 0.061238864 288.1037481 824667.9481 0.038540116 0.013588014 17.67216485 -1.247289754 -0.064186158 ERECETKTLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERECETKTLEK 11 2 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 65.5 0.036712 153290000 172960 170130 167760 199350 115490 171970 186440 171350 22670 FALSE TRUE 164784.5236 187466.4404 175451.9619 179310.9593 135631.4194 166014.6358 157995.1538 156345.6856 26185.54782 6.292956891 7.159156712 6.700335741 6.847707006 5.179628869 6.339933651 6.033677618 5.970686071 1 14.67648317 -0.554995091 0.479191701 5.70E-14 6.638643995 0.919966294 0.496741951 2.437426299 0.475515733 4.855239957 0.246561228 0.278615266 0.554995091 6.638643995 EREDES(ph)EDESDILEESPCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EREDESEDESDILEESPCGR 20 1 Q9NSY0 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 EREDES(1)EDESDILEESPCGR 259.8 1.59E-36 192800000 142160 124210 132190 134560 151220 129200 162140 145990 146340 TRUE FALSE 135440.3785 136867.1402 138251.0423 121033.7732 177592.7201 124725.7716 137402.5651 133206.3417 169033.6598 0.80126277 0.809703466 0.817890605 0.71603356 1.050635242 0.737875354 0.81287103 0.78804625 1 17.36695103 -1.287079231 3.268163052 1.000860827 0.81550391 0.292288343 0.089573244 33643701.82 45695002.11 283182.7711 0.019145978 0.051632216 1.287079231 -0.185356917 EREDLYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EREDLYAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 119.75 0.0014909 294780000 527910 427610 473950 556120 387440 492430 578240 580660 461340 FALSE TRUE 502956.7405 471183.9452 495681.0763 500217.761 455009.4133 475377.0256 490018.8679 529814.3321 532882.251 0.943842171 0.88421775 0.930188753 0.938702237 0.853864831 0.892086431 0.919563125 0.994242783 1 19.02345726 1.256475964 4.007332471 1.00086967 0.907370381 0.654115952 0.026817929 0.125067189 3.931815293 0.022093954 0.006597999 18.04994838 -1.256475964 -0.093499289 EREDSGDAEAHAFKS(ph)PSKENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EREDSGDAEAHAFKSPSKENK 21 3 Q9NPI1-2;Q9NPI1 Q9NPI1-2 BRD7 Bromodomain-containing protein 7 1 EREDSGDAEAHAFKS(0.999)PS(0.001)KENK 124 1.82E-05 122070000 154300 141620 148780 162480 61981 177980 173740 201140 58630 TRUE FALSE 147006.5448 156051.239 155601.7102 146147.2017 72790.46678 171816.508 147232.772 183527.1153 67722.04096 2.170734117 2.304290255 2.297652403 2.15804485 1.074841599 2.537084021 2.174074643 2.710005675 1 16.04733783 2.990678213 24.90959076 1.998085892 2.251754239 0.071034593 0.546535269 1511.45226 4038904.51 0.151205219 0.171726804 978.76451 -2.990678213 0.253668347 EREEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EREEIEK 7 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;;;;; 133.86 0.0029461 5755440000 4384020 3777430 3867880 4589090 3126700 4394420 4986240 4610680 3606760 FALSE TRUE 4176796.063 4162354.412 4045226.124 4127785.954 3671995.49 4242240.134 4225497.509 4206944.416 4166077.92 1.002572718 0.999106232 0.97099147 0.99080863 0.881403459 1.018281514 1.014262717 1.009809345 1 21.99025839 EREEQETTSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EREEQETTSSK 11 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 121.56 0.0003731 584890000 753050 798520 777470 846220 573270 838810 826130 800280 539490 FALSE TRUE 717454.8189 879890.0958 813117.7685 761156.3579 673248.1065 809761.7994 700088.6956 730203.2406 623151.3539 1.151333162 1.412000617 1.304847953 1.221463057 1.080392592 1.299462473 1.123464936 1.171791149 1 19.24922309 1.116293029 0.380976364 0.98710778 1.294884554 0.42859378 0.090667881 1.187851148 0.505271816 0.138090329 0.082016511 13.07052489 -1.116293029 0.307776774 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 236.49 3.67E-45 2156750000 587456 631232 539775 679202 373908 638837 589301 651513 382163 TRUE FALSE 559688.1191 695555.2585 564524.2177 610927.3246 439117.4368 616713.9145 499392.3092 594463.0678 441426.8862 1.267906728 1.575697539 1.278862333 1.383983041 0.994768218 1.397091871 1.131313757 1.34668523 1 18.75181498 0.808042238 0.128952855 0.760097527 1.600818402 0.293598895 0.152455132 11.23792403 0.88443426 3.126445956 2.070704905 6.427502266 -0.808042238 0.840720875 ERELEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERELEEAR 8 1 Q9Y490;Q9Y4G6;H0YMT1;A0A1B0GVU7 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 ; 131.52 0.00091355 196791000 289340 211960 224577 252250 310770 224780 267870 287630 502820 FALSE TRUE 275663.4716 233558.965 234874.0776 226893.3508 364968.1896 216995.8122 227001.5117 262443.5924 580794.7576 0.474631474 0.402136834 0.404401167 0.390660122 0.628394428 0.373618752 0.390846351 0.451869768 1 19.14766891 0.928542042 20.87189038 1 0.434194419 0.851488315 0.073566166 2241.228983 654633.8839 0.06682951 0.016707377 8.482854963 -0.928542042 -0.565805581 ERELEECQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERELEECQR 9 1 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 179.57 4.53E-05 396270000 164670 156800 157540 193770 217830 159290 205500 159880 189330 FALSE TRUE 156886.3754 172778.0983 164763.3648 174291.8715 255819.483 153773.7474 174147.2007 145880.0596 218690.3294 0.717390549 0.790058247 0.753409468 0.796980241 1.169779586 0.703157509 0.796318709 0.667062234 1 17.7385299 2.993973747 24.75085725 0.851062333 0.758619991 0.112634503 0.143452367 631.2783956 2592790.044 0.040732871 0.047190309 986.2198663 -2.993973747 -0.092442341 EREMAEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EREMAEMR 8 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 ; 147.75 0.00048539 777130000 771210 696150 688300 758430 1080630 642000 899470 765800 1110800 FALSE TRUE 734756.4317 767088.4765 719859.2358 682191.1755 1269091.53 619767.379 762239.3316 698742.4922 1283057.191 0.572660702 0.597859925 0.561049999 0.531691947 0.989115325 0.483039559 0.594080558 0.544591852 1 20.29115405 -1.505510478 2.907053051 1.014308516 0.60702191 0.437431613 0.139237866 31695375.34 34174688.66 3602380.028 0.031071489 0.031224071 1.505510478 -0.407286606 ERENMDT(ph)DDERQYQDFLEDLEEDEAIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERENMDTDDERQYQDFLEDLEEDEAIRK 28 3 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 ERENMDT(0.997)DDERQY(0.003)QDFLEDLEEDEAIRK 43.438 0.07117 7530200 7948.8 4928.4 6983.9 7529.7 6373.6 5896.7 8419.2 7400.8 8540.4 TRUE FALSE 7573.075977 5430.609563 7304.118723 6772.800251 7485.153822 5692.4958 7134.696411 6752.746718 9864.801614 0.767686597 0.550503677 0.740422262 0.686562236 0.758773883 0.577051219 0.723247835 0.684529399 1 13.26807432 -0.10250571 1.142471673 1.002172407 0.678692718 0.650688182 0.072153633 8.483480204 8.016985271 0.140280891 0.019303263 0.789758465 0.10250571 -0.323479688 ERENMDTDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 79.82 0.027389 158540000 267950 262050 241090 301450 225660 262400 267450 260630 214320 FALSE TRUE 255284.5345 288753.1929 252144.215 271147.6733 265015.0326 253313.0222 226645.5904 237807.8555 247555.651 1.031220792 1.166417295 1.018535485 1.095299874 1.070527098 1.023256876 0.915533899 0.960623822 1 17.91739336 2.027254807 3.139882923 0.951346896 1.082837764 0.584556122 0.044808239 0.150937374 2.965910734 0.01969933 0.012081017 106.4767549 -2.027254807 0.131490868 EREPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.02)S(0.02)RGS(0.959)PVR;EREPEAAS(0.026)S(0.121)RGS(0.853)PVR;EREPEAAS(0.001)S(0.035)RGS(0.964)PVR 114.9 0.00029717 518176000 131173 88905 129164 111495 143531 125324 162659 127710 173549 TRUE FALSE 124972.7122 97964.52058 135086.2972 100287.3108 168562.761 120983.9985 137842.3821 116527.0354 200462.0926 0.623423165 0.488693495 0.673874524 0.500280674 0.840871004 0.603525569 0.687623183 0.581292123 1 17.61296992 -5 0.194414719 2.669515923 0.553435133 0.579484762 0.100100539 89.73040821 0.882392239 58.09485939 0.229998189 1.00E-05 5 -2.11608079 EREQPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EREQPPR 7 1 Q15233;Q15233-2;H7C367;Q8WXF1;Q8WXF1-2 Q15233;Q8WXF1 NONO;PSPC1 Non-POU domain-containing octamer-binding protein;Paraspeckle component 1 0 143.12 0.0022281 53647000 46735 41806 41012 48374 45287 43905 42233 49869 55278 FALSE TRUE 44525.92917 46066.07893 42892.44077 43511.35362 53185.03846 42384.55884 35789.58019 45502.20599 63850.22992 0.697349551 0.721470839 0.671766426 0.681459623 0.832965496 0.663812157 0.560523905 0.712639658 1 15.96240419 0.95647722 23.94407065 1.000000001 0.686559263 0.681361683 0.066179227 4175.436667 2297120.165 0.067402201 0.01685055 9.046429862 -0.95647722 -0.313440738 ERESLNASIVDAINQAADCWGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERESLNASIVDAINQAADCWGIR 23 1 A0A087WYB4;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 118.67 0.00023764 69698000 79264 63524 77477 71666 105820 69231 84864 67017 90165 FALSE TRUE 75517.34781 69997.16782 81029.39709 64461.99752 124274.9745 66833.51311 71916.43817 61148.6362 104147.3277 0.725101157 0.672097589 0.778026656 0.618950087 1.193261289 0.641720864 0.690526005 0.587135912 1 16.6682663 ERESSANNSVS(ph)PSESLR ddPTM_SK-BR-3_Trastuzumab_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 ERESSANNSVS(0.618)PS(0.381)ESLR 141.78 3.70E-07 423950000 70571 59068 65598 72926 64686 67629 76129 63680 74162 TRUE FALSE 67235.24869 65087.09635 68605.73319 65595.33993 75967.21792 65286.99077 64514.12284 58103.84161 85662.66419 0.784883932 0.759807052 0.800882553 0.765740134 0.886818296 0.762140559 0.753118333 0.678286651 1 16.38637893 -1.139210456 4.018558503 1.000077243 0.775101922 0.658128667 0.051193451 5589828.755 3169293.379 3550.620151 0.011386823 0.072575418 1.139210456 -0.224975321 EREVDEDS(ph)EPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 200.13 9.91E-08 1666980000 559270 582400 465430 598100 514420 585910 507840 527860 435980 TRUE FALSE 532834.4155 641747.2221 486770.4259 537977.8517 604134.6851 565619.7898 430359.6809 481637.78 503589.5517 1.058072817 1.274345784 0.966601519 1.068286365 1.199656909 1.123176182 0.854584213 0.956409398 1 18.94188883 1.752408981 25 0.927636166 1.124774926 0.464750636 0.089468355 3.440978934 6220.695889 0.040120887 0.022249166 56.54692337 -1.752408981 0.197138761 EREVDEDS(ph)EPEREVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EREVDEDSEPEREVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPEREVR;EREVDEDS(1)EPEREVR;EREVDEDS(1)EPEREVR 207.76 1.69E-09 2583280000 1022130 827610 1089230 1054140 1146340 904230 1248940 1076270 1382650 TRUE FALSE 973815.9406 911944.3999 1139172.273 948175.8445 1346261.333 872916.2884 1058391.265 982026.0931 1597064.3 0.609753746 0.571012952 0.713291426 0.593699229 0.842960007 0.546575544 0.66271049 0.614894524 1 20.60699097 -2.286134849 2.186105358 2.521955457 0.639550834 0.63581467 0.084517821 3301978.935 403250.7747 24901385.06 0.019588613 0.005174461 2.286134849 -1.882404623 EREVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EREVEER 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 182.53 0.00059817 1704979000 1917591 1774545 1773225 1986400 1951132 1876265 2141866 1995422 2060227 FALSE TRUE 1826950.274 1955373.153 1854529.12 1786723.298 2291408.803 1811289.473 1815085.004 1820692.271 2379716.481 0.76771762 0.821683242 0.779306751 0.750813516 0.962891513 0.761136668 0.762731619 0.765087894 1 21.18235827 -2.057709042 2.14833476 1.271384281 0.796003804 0.513432144 0.062281227 2642290.503 803146.0937 3518359.725 0.014514878 0.008755702 2.057709042 -0.475380476 EREWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EREWQK 6 1 O75937;S4R3J5 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;; 105.2 0.03026 1085960000 636300 550940 592600 760570 628140 689590 817760 759780 685500 FALSE TRUE 606223.36 607081.4124 619771.2962 684116.0586 737687.4171 665709.3254 692995.6928 693249.6354 791803.839 0.765623163 0.766706831 0.782733381 0.863996895 0.931654257 0.840750313 0.875211332 0.875532046 1 19.59478354 8 0.071493491 1.16586104 0.070368075 0.773762874 0.03510165 108.8478309 0.573484512 1.500044283 11.95831842 99999999.9 -8 -1.095492966 ERFESDRDRDHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERFESDRDRDHER 13 3 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 0 ; 206.66 2.63E-08 294750000 105135 67439 109601 80535 117563 104814 120765 108857 106124 FALSE TRUE 100165.4769 74311.11077 114626.3143 72439.46879 138065.95 101184.2649 102340.0812 99324.90399 122581.1679 0.817135932 0.606219634 0.935105418 0.590951041 1.126322683 0.825447062 0.83487605 0.810278656 1 16.90337783 2.759613358 24.99425186 0.895340825 0.735348478 0.301062608 0.135071921 1071.131681 1271667.912 0.03787071 0.040131839 574.9278646 -2.759613358 -0.159992347 ERFS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 79.489 0.019673 2517030000 1033113 1071710 799790 1031240 989010 913342 1015160 950214 944027 TRUE FALSE 984279.7959 1180918.467 836461.1626 927577.796 1161493.031 881712.7375 860278.6973 867008.2248 1090421.886 0.902659612 1.082992265 0.767098656 0.850659555 1.065177658 0.8085978 0.788941151 0.79511264 1 20.05645499 2.175984941 24.99995203 0.825328581 0.939903009 0.114289536 0.10975139 104.6796722 41819.94133 0.039636307 0.029273361 149.9632835 -2.175984941 0.114574428 ERFS(ph)PPRHELS(ph)PPQK ddPTM_SK-BR-3_Trastuzumab_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 83.395 0.0046823 637950000 451605 444320 435946 479181 354521 460702 479484 456883 405133 TRUE FALSE 430258.5266 489596.7131 455934.5553 431012.8155 416349.3502 444747.7742 406329.9095 416875.9024 467958.9565 0.919436461 1.046238578 0.974304582 0.92104833 0.889713391 0.950399107 0.868302452 0.890838602 1 18.83602247 3.242468069 4.121899169 0.910475981 0.98675936 0.248462911 0.047517662 0.21675198 8.387132504 0.012840106 0.01667791 1747.70476 -3.242468069 0.076283379 ERFS(ph)PPRHELS(ph)PPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;ERFS(1)PPRHELS(1)PPQKR 103.02 0.0021124 14027020000 1244516 994095 1125865 1181269 1000080 1225631 1404566 1222368 1089029 TRUE FALSE 1185690.195 1095394.411 1177487.024 1062525.596 1174493.635 1183187.091 1190273.66 1115330.978 1257910.055 0.942587421 0.870805036 0.936066151 0.844675334 0.933686499 0.94059753 0.946231136 0.886653996 1 20.26259734 2.50804992 24.99724342 0.939413054 0.899720985 0.232451782 0.03876832 991.8986981 801673.476 0.011227246 0.010573941 322.1439057 -2.50804992 -0.039692069 ERFS(ph)PPRHELSPPQK ddPTM_SK-BR-3_Trastuzumab_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(0.999)PPRHELS(0.001)PPQK;ERFS(1)PPRHELSPPQK;ERFS(0.999)PPRHELS(0.001)PPQK 104.89 0.00070852 840851000 1216460 1421700 1212680 1595420 1074340 1428390 1358000 1435750 951520 TRUE FALSE 1158960.347 1566572.846 1268282.578 1435045.351 1261704.556 1378924.496 1150812.159 1310028.119 1099076.862 1.054485256 1.425353313 1.153952577 1.305682432 1.147967535 1.254620622 1.047071591 1.191934945 1 20.06786085 1.376630168 0.68969219 1.015510985 1.242611191 0.265672675 0.110283746 0.754875481 0.816824091 0.096653103 0.042545992 23.80291622 -1.376630168 0.227100206 ERFS(ph)PPRHELSPPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR 159.77 6.43E-09 3643810000 1535670 1282821 1535116 1590951 1467992 1495322 1872100 1654579 1621412 TRUE FALSE 1463081.923 1413541.918 1605502.587 1431025.583 1724009.34 1443538.624 1586476.762 1509695.291 1872852.292 0.781205186 0.754753551 0.857249979 0.764088865 0.920526059 0.770770141 0.847091235 0.806094158 1 20.83680569 -5 0.172780231 1.74941662 0.765190965 0.583184413 0.050232701 84.74681651 0.804256879 21.79432041 0.154372504 1.00E-05 5 -0.984225655 ERFSPLTTNLINLLAENGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERFSPLTTNLINLLAENGR 19 1 A0A494C0K9;H7C0C1;P48047 A0A494C0K9 ATP5O "ATP synthase subunit O, mitochondrial" 0 61.276 0.050934 83316000 207730 219720 219620 259070 169590 249350 267880 231800 166400 FALSE TRUE 197911.0146 242109.7178 229689.7942 233027.7914 199166.4423 240714.947 227009.986 211502.3632 192204.4621 1.02969001 1.259646707 1.195028417 1.212395325 1.036221741 1.252390003 1.181085931 1.100402981 1 17.5522823 0.962470898 3.57655201 1.000362002 1.169299915 0.321029285 0.078173624 0.268976809 9.260302644 0.070234878 0.01813318 9.172144711 -0.962470898 0.168937913 ERFTEHEVQIYVGEIVLALEHLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERFTEHEVQIYVGEIVLALEHLHK 24 1 O75582-3;O75582;O75582-2;A0A3B3ISL8;G3V2D1 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 157.83 1.18E-09 104227000 256487 371554 320496 343243 204371 320679 331717 271490 65176.8 FALSE TRUE 244363.3678 409415.775 335191.0586 308739.5615 240013.2377 309573.8058 281107.4792 247716.8963 75284.08527 3.245883469 5.438277872 4.45234949 4.100993728 3.188100604 4.112075012 3.733956231 3.290428455 1 16.2000573 -0.191003092 0.381599466 0.313267172 4.392509455 0.71393308 0.612033975 3.079042494 0.537382805 3.593556478 0.450188144 0.64416468 0.191003092 4.079242283 ERGDYVLAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERGDYVLAVK 10 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 ; 106.29 0.0022219 804860000 1853180 1548470 1420600 1720510 1611750 1500510 2032000 1887550 1703160 FALSE TRUE 1765583.854 1706260.853 1485735.915 1547561.066 1892838.69 1448546.962 1721981.08 1722266.115 1967277.354 0.897475819 0.867320945 0.755224428 0.786651187 0.962161581 0.736320661 0.875311799 0.875456687 1 20.90776894 0.757054262 1.853888864 0.999697834 0.842072369 0.358117154 0.06734685 0.997793016 5.539973752 0.060373044 0.016907266 5.715500439 -0.757054262 -0.157625465 ERHPGSFDVVHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ERHPGSFDVVHVK 13 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;;; 223.72 9.88E-12 3295650000 4937320 4118140 4366790 4853120 4628070 4582300 5899710 5062450 2146071 FALSE TRUE 4703942.668 4537783.148 4567011.641 4365275.157 5435203.943 4423613.802 4999600.884 4619155.04 2478872.73 1.897613625 1.830583351 1.842374393 1.760992045 2.192611132 1.784526389 2.016884862 1.863409518 1 21.24125277 0.938957728 22.25287908 0.999999999 1.901238925 0.837021109 0.124736672 2879.66831 1049780.858 0.108628206 0.027157051 8.688758531 -0.938957728 0.901238926 ERHPS(ph)WR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;ERHPS(1)WR;ERHPS(1)WR 115.78 0.0033933 1.08135E+11 17853377.8 15470568.6 15942906.3 18165281.7 18223719.9 16151006.8 18608700.6 16849911.2 15275513.9 TRUE FALSE 17009484.01 17047037.13 16673904.32 16339273.07 21401930.88 15591693.38 15769601.55 15374443.65 17644362.58 0.96401805 0.966146385 0.944998962 0.926033627 1.212961408 0.883664304 0.893747308 0.871351605 1 24.07270398 ERHPS(ph)WRS(ph)EETQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.973)EET(0.027)QER;ERHPS(1)WRS(0.956)EET(0.044)QER 112.14 0.0003275 2296380000 388530 351730 398510 438750 443290 359350 428490 385930 404590 TRUE FALSE 370164.9569 387571.6869 416782.0777 394646.0164 520599.6356 346905.6194 363115.9807 352135.9233 467331.7508 0.792081763 0.829328814 0.891833429 0.844466518 1.113983021 0.742311257 0.77699831 0.753503101 1 18.83408753 -0.638400998 7.17527911 0.999990336 0.83921984 0.177034897 0.106050567 0 0 0.099821091 0.023528057 0.22993178 0.638400998 -0.160770497 ERHPS(ph)WRSEET(ph)QER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.352)EET(0.648)QER;ERHPS(1)WRS(0.087)EET(0.913)QER;ERHPS(1)WRS(0.133)EET(0.867)QER 149.44 1.42E-05 2317530000 767090 663080 748880 840000 811050 748360 898690 725880 768500 TRUE FALSE 730831.1759 730648.6059 783216.8887 755561.6041 952496.8632 722444.1056 761578.3349 662318.0991 887675.055 0.823309354 0.823103682 0.882323869 0.85116913 1.073024253 0.813860997 0.857947208 0.746126745 1 19.75967213 -2.441363791 2.311937081 2.484958075 0.858352843 0.217351069 0.084165822 4033522.807 989001.5902 30701252.86 0.019833966 0.003619397 2.441363791 -1.626605232 ERLDQPMTEIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERLDQPMTEIVSR 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 115.83 0.00066486 148940000 38135 40087 40394 40129 44839 36929 47944 39486 56472 FALSE TRUE 36332.43413 44171.91088 42246.10486 36095.15668 52658.9074 35650.13947 40629.26225 36028.39651 65229.38934 0.556994853 0.677178053 0.647654459 0.553357268 0.807288063 0.546534926 0.622867432 0.5523338 1 15.9932345 -1.251925313 4.935544095 1.000076618 0.622872811 0.689776494 0.079963683 5.98E-05 9.07E-06 0.068718035 0.016193719 0.055985387 1.251925313 -0.377203807 ERLEHPVLHVSWNDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERLEHPVLHVSWNDAR 16 1 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ; 119.47 0.00012355 199955000 117327 100245 92406 110574 168182 91554 154045 108155 66975 FALSE TRUE 111781.1852 110460.0795 96642.9065 99458.89144 197512.8876 88383.46202 130542.606 98684.37483 77361.14094 1.444926792 1.427849669 1.249243552 1.285644062 2.553127903 1.142478781 1.687444167 1.275632361 1 16.23932145 0.993452196 5.276570359 1.000364344 1.526440277 0.17347318 0.391450129 0.247963224 26.90508007 0.344183796 0.086877944 9.850362118 -0.993452196 0.526075933 ERLEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERLEIAR 7 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 90.657 0.028749 0 39911 29784 23280 31832 44729 29251 43161 37358 43164 FALSE TRUE 38024.48613 32819.02346 24347.41103 28632.18688 52529.72344 28238.03054 36575.99674 34086.73547 49857.65267 0.762660978 0.658254485 0.488338494 0.574278678 1.053593995 0.566373045 0.733608479 0.683681113 1 15.60552734 ERLELCDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERLELCDER 9 1 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 78.342 0.0274 301440000 487290 374350 422870 577760 603480 377190 579940 477430 594050 FALSE TRUE 464256.7674 412496.6906 442259.0078 519682.4671 708726.7209 364127.8157 491459.5017 435623.6982 686172.24 0.676589259 0.601156192 0.644530603 0.757364459 1.032869999 0.530665326 0.716233437 0.634860568 1 19.38821124 -2.567024556 2.148787919 6.07139391 0.693355644 0.33230524 0.133726954 4722413.291 211286.6488 117532562.3 0.031359269 0.002710038 2.567024556 -5.378038266 ERLEQEQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 231.05 7.90E-10 876100000 481070 362310 430490 511150 489600 467330 526750 514230 557220 FALSE TRUE 458330.7745 399229.8009 450228.3923 459768.2309 574986.085 451146.2449 446384.6131 469201.2951 643630.8317 0.712101956 0.620277621 0.699513401 0.714335312 0.893347641 0.700939456 0.693541377 0.728991329 1 19.29587391 -5 0.233476983 2.568355611 0.681109556 0.627763513 0.067802231 110.486838 1.104174312 82.09007883 0.115542902 1.00E-05 5 -1.887246055 ERLEQQVPVNQVFGQDEMIDVIGVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERLEQQVPVNQVFGQDEMIDVIGVTK 26 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 163.16 1.39E-11 101920000 47747 36970 42382 49969 35238 42815 55526 49177 46170 FALSE TRUE 45490.09394 40737.28503 44325.25662 44946.02119 41383.49604 41332.30581 47054.4889 44870.80118 53329.8078 0.852995648 0.763874589 0.831153504 0.842793609 0.775991847 0.775031967 0.882329992 0.841383141 1 15.70265451 0.60281761 0.858510926 1.000113181 0.808568614 0.720201785 0.036030664 0.667998603 0.82515272 0.033958959 0.011321016 4.006984015 -0.60281761 -0.191544567 ERLNS(ph)SENGEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.5)S(0.5)ENGEDR;ERLNS(0.896)S(0.104)ENGEDR;ERLNS(0.907)S(0.093)ENGEDR 187.56 6.25E-06 842540000 739826 675962 668814 748635 704035 609035 710322 593428 619625 TRUE FALSE 704855.8912 744843.2963 699479.7834 673380.7875 826818.4811 587943.9652 601949.3329 541464.2984 715713.2804 0.984829974 1.040700678 0.977318435 0.940852721 1.155237025 0.821479748 0.841048154 0.756538006 1 19.44902222 2.208116457 24.99991955 0.840754023 1.013943213 0.493884593 0.082350425 147.8629884 121420.2245 0.027383685 0.020226559 161.4791509 -2.208116457 0.17318919 ERMSPQEAWLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERMSPQEAWLLNR 13 1 I3L2X7 I3L2X7 CEP131 0 89.029 0.062286 490950000 113720 122170 123360 136000 121360 108250 129660 140310 137870 FALSE TRUE 108344.681 134619.2619 129016.178 122329.0216 142525.1456 104501.2754 109877.9856 128023.7126 159250.1755 0.680342616 0.845331953 0.810147792 0.768156275 0.89497638 0.656208227 0.689970892 0.803915677 1 17.28093544 0.970374977 22.72665043 1.000000003 0.762309382 0.494799419 0.074554113 923.5490657 708496.5185 0.072168586 0.018042147 9.340604348 -0.970374977 -0.237690621 ERNEEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERNEEEAKR 9 2 Q96IZ7-2;Q96IZ7;C9J713;H7C5Q0 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 0 68.893 0.031936 28917000 52385 41640 42357 54754 54512 52155 64654 53688 41017 FALSE TRUE 49908.86487 45883.16334 44299.11035 49250.02389 64018.87554 50348.85927 54789.84485 48986.7941 47377.70687 1.053425084 0.968454709 0.935020145 1.039518946 1.351244705 1.062712035 1.156447799 1.033962961 1 15.53192075 2.988285645 24.9539928 1.134452684 0.991090807 0.278586661 0.099077337 605.4852909 1289812.474 0.027040587 0.030199063 973.3872314 -2.988285645 -0.143361877 ERNHKPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERNHKPSR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERNHKPS(1)R 80.763 0.012839 38019000 20210 30452 18161 29381 16274 24504 22862 20132 15070 TRUE FALSE 19254.71335 33555.09342 18993.69981 26427.56606 19112.18045 23655.42034 19373.98201 18369.13535 17406.97863 1.106149077 1.927680508 1.091154313 1.518216723 1.097960815 1.358961876 1.11300085 1.055274194 1 14.08737819 2.147560009 0.648123866 1.00738321 1.473820487 0.24584613 0.24753856 0.905411186 0.743513652 0.20418161 0.132323216 140.4623757 -2.147560009 0.466437277 ERNS(ph)YLGLVSLPAASVAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERNSYLGLVSLPAASVAGR 19 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4;F8WA47;F6R503 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 ERNS(1)YLGLVSLPAASVAGR 96.679 0.00074963 58112000 68159 51976 56478 64318 67992 57649 71502 65921 73735 TRUE FALSE 64937.25915 57272.41349 59067.57216 57852.63244 79849.78327 55652.60067 60593.05668 60148.60777 85169.44721 0.762447818 0.672452568 0.693530064 0.679265093 0.937540232 0.65343386 0.711441235 0.706222827 1 16.37804837 -1.30762657 5.545852936 1.000039927 0.723898436 0.532291908 0.080362227 3.66E-05 4.57E-06 0.071787011 0.016917919 0.04924628 1.30762657 -0.276141491 ERPAYAVHGNMLHYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPAYAVHGNMLHYVK 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 145.55 7.80E-07 551200000 1018400 833560 818940 963020 874550 875240 1027760 971990 146236 FALSE TRUE 970262.2503 918500.7117 856489.209 866215.4 1027071.243 844930.2193 870956.3359 886877.4028 168913.532 5.744135705 5.437697624 5.070577821 5.128158707 6.080455668 5.002146419 5.156225943 5.250481665 1 17.36592538 -0.893660648 0.578948897 5.98E-14 5.456122883 0.947395545 0.323270362 4.086347791 0.842912398 7.732120015 0.127556762 0.127743659 0.893660648 5.456122883 ERPDLEAPAPGS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_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 220.28 1.02E-12 2789220000 1901980 1584100 1610090 1849770 1699180 1588110 1815230 1834860 1912370 TRUE FALSE 1812077.175 1745521.591 1683914.219 1663827.605 1995516.454 1533113.352 1538283.325 1674189.931 2208930.573 0.820341389 0.79021116 0.762321025 0.75322766 0.903385774 0.694052304 0.69639279 0.757918765 1 21.07491664 4.238489475 2.151868631 0.774718283 0.817919796 0 0.094818137 1.58950113 13.91347545 0.023193125 0.088009312 17317.67061 -4.238489475 0.043201514 ERPDLPPVQYEPVLCSRPTCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPDLPPVQYEPVLCSRPTCK 21 2 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 175.86 6.49E-13 332210000 108156 84239 97899 112959 92428 105135 133618 108799 115646 FALSE TRUE 103043.6802 92823.04987 102387.766 101604.1467 108547.4139 101494.1486 113232.12 99271.98278 133579.791 0.771401717 0.694888419 0.766491437 0.760625136 0.812603561 0.759801672 0.847674032 0.743166178 1 17.02734224 -5 0.17407418 1.933413331 0.715220951 0.774593687 0.039280922 55.05995043 0.523965631 17.69904045 0.121055775 1.00E-05 5 -1.21819238 ERPEDLELLPGDVLVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPEDLELLPGDVLVVSR 18 1 O00459;E9PFP1 O00459 PIK3R2 Phosphatidylinositol 3-kinase regulatory subunit beta 0 92.993 0.0020355 10323000 16701 13411 13700 16346 14099 12230 14745 14640 16280 FALSE TRUE 15911.57683 14777.59615 14328.15855 14702.86902 16557.86114 11806.47203 12495.37944 13358.04399 18804.61925 0.846152566 0.785849261 0.761948879 0.781875391 0.880520946 0.627849566 0.664484575 0.710359716 1 14.19879948 2.243047695 24.99972864 0.713086989 0.807396278 0.02330721 0.106450031 195.0920379 1086960.512 0.033640532 0.027263432 175.003887 -2.243047695 0.094309289 ERPEIS(ph)PPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.96)PPS(0.033)DFEHT(0.007)IHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.25)PPS(0.25)DFEHT(0.25)IHVGFDAVT(0.25)GEFTGMPEQWAR 118.58 1.76E-06 25062400 7144.8 8202.5 8965.5 7918 6138.8 6015.7 8872.7 6439.6 4577 TRUE FALSE 6807.079464 9038.344075 9376.577043 7122.067597 7209.404776 5807.374801 7519.006657 5875.714486 5286.777784 1.287566783 1.709613009 1.773590158 1.347147145 1.363667071 1.098471515 1.422228617 1.111398044 1 12.36817297 2.869222969 2.418621396 1.225088544 1.568954997 0.486792233 0.178795305 0.274643141 3.150317315 0.058292707 0.062857164 739.98509 -2.869222969 0.343866453 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 123.19 3.44E-08 35723000 12766 11382 11716 14848 15337 14167 14499 11728 4747.8 FALSE TRUE 12162.57648 12541.83874 12253.19019 13355.45083 18011.76794 13676.39324 12286.91126 10701.03415 5484.064576 2.217803294 2.286960441 2.234326387 2.435319761 3.284382905 2.493842487 2.240475306 1.95129616 1 12.42102984 0.878240539 1.606176376 1.00561738 2.455819367 0.701750944 0.305534152 0.320095377 1.615237012 0.303941917 0.087880117 7.555105599 -0.878240539 1.450201987 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHR 33 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.997)PMVPS(0.003)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.998)PMVPS(0.002)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.998)PMVPS(0.002)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR 200.81 3.39E-27 1302734000 628547 552534 612276 669526 673029 565094 727140 651867 733463 TRUE FALSE 598836.829 608837.8428 640349.4602 602223.9745 790405.0445 545524.6531 616201.4382 594786.0697 847204.696 0.70683842 0.71864314 0.755837949 0.710836445 0.932956401 0.643911272 0.727334776 0.702057097 1 19.69235106 -1.360527237 3.129493502 1.002633245 0.734685761 0.547179065 0.075069573 30733529.47 41929045.88 749174.252 0.016822484 0.043598622 1.360527237 -0.267947484 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHRR 34 2 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR 160.8 3.09E-14 170413000 45768 29390 48115 37895 54190 38890 62584 51156 66856 TRUE FALSE 43604.63734 32384.87441 50321.12034 34085.7226 63640.71884 37543.22955 53035.66137 46676.50944 77223.68703 0.564653658 0.41936452 0.651628047 0.441389474 0.824108784 0.486162096 0.68677971 0.604432542 1 16.23675582 -5 0.155249029 2.583543567 0.449065062 0.575563899 0.115692061 83.2522966 0.75447398 40.42132347 0.460997561 1.00E-05 5 -2.134478505 ERPETVLIDLIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPETVLIDLIQR 13 1 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 0 94.717 0.0045848 24293000 27964 25798 28071 30713 32024 27912 36548 31177 28359 FALSE TRUE 26642.19714 28426.84553 29358.08312 27625.67089 37608.97546 26945.40044 30971.93135 28446.9766 32756.76888 0.8133341 0.86781592 0.89624478 0.843357627 1.148128364 0.822590303 0.945512406 0.868430482 1 14.99950544 3.573264993 1.329765397 0.938847385 0.830111499 0.185328533 0.090840223 0.725747643 2.559728977 0.02755292 0.058547536 3743.38929 -3.573264993 -0.108735886 ERPIS(ph)LGIFPLPAGDGLLT(ph)PDAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 ERPIS(1)LGIFPLPAGDGLLT(1)PDAQK;ERPIS(1)LGIFPLPAGDGLLT(1)PDAQK 253.76 1.98E-43 142619000 295083 266324 258137 348784 199682 310123 324134 350612 210211 TRUE FALSE 281135.0114 293462.7184 269972.8368 313723.5697 234506.4776 299383.3627 274681.4052 319910.5546 242809.4483 1.157842141 1.208613258 1.111871217 1.29205668 0.965804582 1.232997171 1.131263248 1.317537505 1 17.88946504 ERPIS(ph)LGIFPLPAGDGLLTPDAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;ERPIS(1)LGIFPLPAGDGLLTPDAQK;ERPIS(1)LGIFPLPAGDGLLTPDAQK 196.06 1.22E-24 357448000 789166 737144 801846 892106 645526 820229 966309 895693 706083 TRUE FALSE 751863.6872 812259.8117 838611.4322 802429.81 758105.53 791824.2641 818880.8146 817261.3726 815578.7455 0.92187749 0.995930578 1.028240911 0.983877785 0.929530759 0.97087408 1.004048743 1.002063108 1 19.63746465 4.565284577 2.87598503 0.988243256 0.920669604 0.398192799 0.025910073 0.325683699 4.678678096 0.006713739 0.04219136 36752.30462 -4.565284577 -0.067573652 ERPISLGIFPLPAGDGLLT(ph)PDAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ERPISLGIFPLPAGDGLLT(1)PDAQK 263.07 6.10E-44 3167207000 7114033 6716256 6038660 7662616 4412789 7201645 6950653 7535537 4376415 TRUE FALSE 6777766.759 7400650.122 6315538.534 6892355.282 5182378.004 6952250.228 5890203.227 6875685.432 5055087.087 1.340781403 1.46400052 1.249343172 1.363449366 1.025180757 1.375297816 1.165203116 1.360151727 1 22.26930452 -4.185321442 0.058327655 5.24E-10 1.798514213 0.37479179 0.121928278 327.6224646 1.619779844 52.07976965 11.33492929 6.53E-05 4.185321442 1.798514212 ERPISLGIFPLPAGDGLLT(ph)PDAQKGGETPGSEQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPISLGIFPLPAGDGLLTPDAQKGGETPGSEQWK 35 2 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)PDAQKGGETPGSEQWK;ERPISLGIFPLPAGDGLLT(1)PDAQKGGETPGSEQWK 159.74 8.25E-13 137426000 395990 169613 410490 290200 286080 404960 608150 463600 408630 TRUE FALSE 377272.3375 186896.7575 429311.3725 261028.5447 335972.2614 390936.1337 515365.5481 423004.7263 471998.2534 0.799308758 0.395969172 0.909561358 0.553028624 0.711808273 0.828257585 1.091880202 0.89619977 1 18.848422 2.085431561 2.652185897 1.002092973 0.649329299 0.505480004 0.144354198 0.19869457 2.746773845 0.063736292 0.039405525 121.7395133 -2.085431561 -0.352763674 ERPLCPLQPQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPLCPLQPQNR 12 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 188.91 7.85E-06 590100000 307730 252000 264370 292470 298940 269490 332730 289020 319110 FALSE TRUE 293184.2128 277679.0865 276491.626 263070.3599 351075.0414 260157.4937 281965.9275 263711.8766 368595.949 0.795408125 0.753342752 0.750121174 0.713709309 0.952465816 0.705806709 0.764972942 0.715449742 1 18.49168069 -0.987041744 4.417739705 1.000006561 0.769225359 0.513937864 0.070627101 13053.19136 37578032.72 678.5373576 0.014939034 0.103028708 0.987041744 -0.230781201 ERPMYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPMYGR 7 1 P50402;Q5HY57 P50402 EMD Emerin 0 89.142 0.016498 30521000 28594 21537 21442 29830 34774 26727 27588 24574 35734 FALSE TRUE 27242.41829 23731.64479 22425.13691 26831.43173 40838.57459 25801.43729 23378.94391 22422.17029 41275.44622 0.660015113 0.574957922 0.54330453 0.650057945 0.989415702 0.625103776 0.566412869 0.543232656 1 15.33299619 2.997946615 24.97206077 0.708282815 0.598318679 0.143581686 0.158394983 197.9520477 2407429.398 0.045324371 0.053384632 995.2830658 -2.997946615 -0.109964137 ERPQDRPEDLDVPPALADFIHQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPQDRPEDLDVPPALADFIHQQR 24 2 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 ; 187.29 1.16E-17 75208000 66397 57926 57346 78463 76866 64664 74963 71687 75333 FALSE TRUE 63258.5454 63828.72526 59975.37082 70575.75017 90271.40606 62424.66947 63526.01756 65409.70624 87015.25689 0.726982229 0.733534871 0.689251207 0.811073284 1.03742044 0.717399129 0.730056082 0.75170388 1 16.40898076 -2.46263649 2.142321109 3.263196319 0.769050449 0.338550656 0.098700844 3221659.575 203200.7582 35622400.98 0.024179416 0.003446383 2.46263649 -2.49414587 ERPS(ph)SREDTPSR ddPTM_SK-BR-3_Trastuzumab_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(0.8)S(0.177)REDT(0.013)PS(0.01)R;ERPS(0.495)S(0.495)REDT(0.001)PS(0.01)R;ERPS(0.77)S(0.23)REDTPSR;ERPS(0.5)S(0.5)REDTPSR 105.53 0.0015911 2078810000 925750 802010 839310 906780 920860 866770 1034940 905380 997330 TRUE FALSE 881991.6322 883735.7308 877793.1937 815628.7516 1081457.692 836753.5376 877040.895 826100.1275 1151990.843 0.765623822 0.767137809 0.761979315 0.708016697 0.93877282 0.726354331 0.761326273 0.717106505 1 20.13569782 -1.009989248 4.25614475 1.000013377 0.768700828 0.562129016 0.064268292 7405194.56 1757750.485 969.6730589 0.01359934 0.097726141 1.009989248 -0.231312549 ERPSQPEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPSQPEGLR 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 0 116.74 0.00095818 375720000 163830 180770 165070 174120 175620 147990 165440 162490 187270 FALSE TRUE 156086.0806 199190.6685 172638.6228 156617.1268 206248.0724 142865.0692 140199.0895 148261.5142 216310.8752 0.721582216 0.920853694 0.798104222 0.72403723 0.953479904 0.660461796 0.648137036 0.685409433 1 17.72274667 2.205978086 24.99960438 0.709471299 0.821911045 0.044367051 0.124034825 328.8113101 252285.2571 0.041776003 0.03085579 160.6860171 -2.205978086 0.112439746 ERPSQPEGLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 107.39 0.0012397 446730000 272260 304920 316630 338100 303280 326890 334790 336200 312820 FALSE TRUE 259390.8094 335991.6947 331147.7987 304113.5457 356171.936 315569.7173 283711.6367 306760.5457 361330.5279 0.717876817 0.929873533 0.916467813 0.841649189 0.985723343 0.873354707 0.785185902 0.848974891 1 18.46295962 4.627329475 3.121286631 0.885231622 0.710764047 0.406892435 0.066496395 0.306508525 4.909745036 0.01618707 0.11271263 42396.44819 -4.627329475 -0.174467574 ERPSS(ph)AIYPSDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ERPSSAIYPSDSFR 14 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ERPS(0.039)S(0.957)AIYPS(0.004)DSFR;ERPS(0.166)S(0.702)AIYPS(0.003)DS(0.129)FR;ERPS(0.028)S(0.972)AIYPSDSFR;ERPS(0.002)S(0.998)AIYPSDSFR;ERPS(0.033)S(0.967)AIYPSDSFR;ERPS(0.066)S(0.925)AIYPS(0.009)DSFR 275.31 1.21E-32 2086660000 1637380 1410990 1439770 1708460 1532290 1345700 1667220 1499640 1516570 TRUE FALSE 1559984.292 1554771.485 1505784.879 1536722.355 1799520.891 1299098.072 1412854.968 1368323.572 1751751.93 0.890528085 0.887552317 0.859587966 0.877248844 1.02726925 0.741599338 0.806538268 0.781117205 1 20.74036706 2.212328354 24.99999985 0.812493603 0.900323278 0.155153685 0.081493541 318.8455552 303865.7163 0.027259676 0.020138741 163.052835 -2.212328354 0.087829675 ERPSS(ph)REDTPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.387)S(0.608)REDT(0.005)PS(0.001)R;ERPS(0.196)S(0.803)REDTPSR 85.469 0.0091801 1401080000 444380 370000 405800 440690 442590 432220 524720 418710 485000 TRUE FALSE 423375.0381 407703.4207 424406.3314 396391.0039 519777.5559 417252.113 444664.3269 382045.5327 560211.323 0.755741665 0.727767191 0.757582566 0.707574067 0.927824081 0.744811995 0.793743912 0.681966817 1 19.09561162 -1.890280638 2.635590846 1.121588586 0.763343896 0.560618096 0.066173607 22161428.01 12178712.82 16726532.17 0.014908219 0.012874174 1.890280638 -0.358244691 ERPT(ph)SPAPHRPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPTSPAPHRPPK 13 2 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.895)S(0.105)PAPHRPPK 108.63 0.057223 312560000 261730 224130 222040 271230 202660 244250 270500 267140 195680 TRUE FALSE 249358.5416 246969.1018 232220.7536 243965.4451 238003.8398 235791.5613 229230.2569 243747.8054 226025.055 1.103234071 1.092662501 1.027411557 1.079373457 1.052997597 1.043209839 1.014180737 1.078410557 1 17.78612318 8 0.156621122 1.000587699 1.413617166 0.511741927 0.023845508 43.28998533 0.440061225 0.068452542 4.107512035 99999999.96 -8 0.413029466 ERPT(ph)SPAPHRPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.856)S(0.144)PAPHRPPKR;ERPT(0.991)S(0.009)PAPHRPPKR 125.89 4.69E-05 232894000 68471 48368 62826 61392 48118 59259 69694 61471 61271 TRUE FALSE 65234.51153 53296.75419 65706.63424 55220.75952 56509.76397 57206.84597 59060.90028 56088.27336 70772.59375 0.921748209 0.753070523 0.928419191 0.780256263 0.798469591 0.808319194 0.834516543 0.792514028 1 16.11090317 -1.960764691 5.176014707 1.108582619 0.826682328 0.475187788 0.057080839 0.038884455 0.000294753 0.030047233 0.011599187 0.010945493 1.960764691 -0.281900291 ERPTPSLNNNCTT(ph)SEDSLVLYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCTT(0.636)S(0.364)EDSLVLYNR 228.47 1.11E-32 225690000 72313 49368 74532 82923 82613 87227 94548 69479 71982 TRUE FALSE 68894.9078 54398.65533 77949.36592 74587.4225 97020.68104 84206.30712 80122.96611 63395.05043 83144.60093 0.828615533 0.654265637 0.937515666 0.897080769 1.166890934 1.012769394 0.963658075 0.762467433 1 16.34333496 3.616727453 5.105304292 0.97292377 0.742493559 0.419598737 0.108374387 0.187287121 7.021957682 0.028430945 0.044609254 4137.399454 -3.616727453 -0.230430211 ERPTPSLNNNCTTS(ph)EDSLVLYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCTT(0.138)S(0.862)EDSLVLYNR;ERPTPSLNNNCTT(0.039)S(0.961)EDSLVLYNR 223.75 8.58E-33 329420000 99404 64744 95671 115223 91882 106000 124072 79532 98844 TRUE FALSE 94705.36992 71341.48721 100057.61 103640.5651 107906.1917 102329.1934 105142.5377 72567.75645 114172.2227 0.829495719 0.62485853 0.876374372 0.907756394 0.945117728 0.896270485 0.920911717 0.635599052 1 16.80085217 3.636596795 8.050813453 0.887008098 0.727514428 0.27040247 0.106458659 0.319511463 22.55777802 0.026195953 0.040651812 4331.085876 -3.636596795 -0.15949367 ERPTPSLNNNCTTSEDSLVLYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 320.34 1.29E-73 1271760000 208080 168074 197881 213884 229032 185889 236490 237810 235470 FALSE TRUE 198244.4708 185200.9317 206954.0396 192383.974 268975.1083 179451.6173 200409.1071 216986.0957 271985.485 0.728878862 0.680922115 0.760901044 0.707331768 0.988931848 0.659783802 0.736837508 0.797785572 1 18.05317014 -5 0.221292024 2.280748946 0.717053324 0.426209531 0.089829461 144.5358598 1.44562651 82.5950124 0.160162292 1.00E-05 5 -1.563695622 ERPTS(ph)PAPHRPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.073)S(0.927)PAPHRPPKR;ERPT(0.189)S(0.811)PAPHRPPKR;ERPT(0.167)S(0.833)PAPHRPPKR 165.02 2.88E-06 717630000 65336 49805 61793 60209 51235 57956 73116 63389 58160 TRUE FALSE 62247.69676 54880.18612 64626.27017 54156.67693 60170.36778 55948.96919 61960.81133 57838.32311 67179.15576 0.926592424 0.816922831 0.961998844 0.806152985 0.895670199 0.832832276 0.922321971 0.860956385 1 16.03572604 -1.497535203 2.933610936 1.004094009 0.877588123 0.366249016 0.050461897 19699594.8 22847542.13 655249.9139 0.010773451 0.031802759 1.497535203 -0.126505886 ERPVQSLKTS(ph)RDTSPS(ph)SGSAVSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERPVQSLKTSRDTSPSSGSAVSSSK 25 3 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 2 ERPVQS(0.039)LKT(0.337)S(0.602)RDT(0.138)S(0.432)PS(0.433)S(0.019)GS(0.001)AVSSSK 147.25 3.45E-07 349250000 295920 160650 291840 272450 207900 307760 462690 326050 294070 TRUE FALSE 281932.4481 177020.4176 305221.1527 245062.8084 244157.6942 297102.194 392098.1426 297499.3335 339672.8737 0.830011667 0.521149704 0.898573823 0.721467115 0.718802451 0.874671536 1.154340464 0.875840718 1 18.37378648 2.030675605 4.156018378 1.026220456 0.725074095 0.526483304 0.117115432 0.140973965 5.458922313 0.046742199 0.031203838 107.3187498 -2.030675605 -0.30114636 ERPVS(ph)EMFSLEDSIIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ERPVSEMFSLEDSIIER 17 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER 269.57 1.39E-28 305682000 221205.6 193544.6 217137.9 230599.2 220750.2 215569.3 244165.1 218299.9 238146.9 TRUE FALSE 210749.6497 213267.0148 227093.8875 207418.9303 259248.965 208104.0811 206913.2296 199184.4035 275077.505 0.766146435 0.77529791 0.825563281 0.75403814 0.94245789 0.756528896 0.752199747 0.724102843 1 18.06947864 -2.230549737 2.460095879 1.791146613 0.785681779 0.546624715 0.060939826 10073341.82 1115770.43 44784592.11 0.013951811 0.005880988 2.230549737 -1.005464834 ERQELGS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERQELGSPEER 11 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ERQELGS(1)PEER;ERQELGS(1)PEER;ERQELGS(1)PEER 187 2.29E-06 1177360000 962720 916310 886920 950230 952150 874540 1029040 923760 1017210 TRUE FALSE 917214.1335 1009683.031 927586.1593 854711.0751 1118204.659 844254.4605 872041.0484 842870.6772 1174953.732 0.780638513 0.859338546 0.789466116 0.727442326 0.951701015 0.718542729 0.74219182 0.717364995 1 20.16417252 ERQEQEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERQEQEEAR 9 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 159.09 6.05E-05 276420000 84145 76222 72353 91500 87166 79170 93112 77580 92920 FALSE TRUE 80167.63261 83989.10846 75670.45662 82302.24616 102367.7228 76428.32305 78906.05428 70786.68392 107329.559 0.746929675 0.782534739 0.705029046 0.766818078 0.953770087 0.712090162 0.735175426 0.659526458 1 16.71168793 -2.158855652 2.431439414 1.584236218 0.759965989 0.489816546 0.077673899 13592144.77 3981631.673 43615439.18 0.019694103 0.006936563 2.158855652 -0.824270229 ERQEQEEARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERQEQEEARR 10 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 93.345 0.0049769 76217000 56704 50168 57172 58084 65809 53502 67545 62379 70786 FALSE TRUE 54023.7143 55280.17624 59793.39275 52245.28597 77286.06876 51649.21232 57239.7697 56916.76407 81763.13136 0.660734409 0.676101506 0.731300181 0.638983428 0.945243504 0.631693178 0.700068218 0.696117714 1 16.31916283 -2.060357288 2.290293928 1.404705612 0.705659362 0.512358485 0.088812482 8513638.708 2633835.956 18021498.4 0.020111845 0.008702474 2.060357288 -0.69904625 ERQEQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERQEQLER 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 121.73 0.0012956 158471000 125031 116886 106692 141785 140723 122013 154262 154128 160994 FALSE TRUE 119121.0324 128796.8163 111583.9337 127532.5024 165265.0466 117787.6592 130726.4987 140631.7352 185960.1273 0.640572977 0.692604475 0.600042253 0.685805631 0.888712269 0.633402767 0.702981336 0.756246714 1 17.50463379 -5 0.197829275 2.381545651 0.643041304 0.634577328 0.074575616 89.45347853 0.882943429 48.72068968 0.176069588 1.00E-05 5 -1.738504348 ERRT(ph)PPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERRTPPGR 8 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ERRT(1)PPGR;ERRT(1)PPGR;ERRT(1)PPGR 77.541 0.052975 1291270000 321679 221794 275205 291300 323355 280021 314396 292813 373662 TRUE FALSE 306473.8712 244395.0608 287823.4215 262017.9706 379748.0096 270323.8026 266429.1159 267172.7414 431607.5946 0.710075251 0.566243652 0.666863663 0.607074514 0.879845523 0.626318457 0.617294782 0.619017702 1 18.71936073 -1.221465411 4.112976244 1.000213004 0.656488345 0.601495776 0.086476632 12259179.18 3640735.791 23634.75735 0.019179687 0.060052984 1.221465411 -0.343724659 ERRT(ph)PS(ph)DDEEDNLFAPPK ddPTM_SK-BR-3_Trastuzumab_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 124 3.62E-05 73732000 182700 163820 164130 188320 129890 178180 198360 189920 142200 TRUE FALSE 174064.1331 180513.4442 171655.5228 169389.7158 152542.7749 172009.5819 168096.5389 173289.598 164251.6497 1.059740547 1.099005365 1.0450764 1.031281671 0.928713807 1.047231989 1.023408527 1.055025007 1 17.32554834 3.406985079 2.871358067 1.01412055 1.078893331 0.362752575 0.035658926 0.258904284 4.31793335 0.01002539 0.014638691 2552.613599 -3.406985079 0.064772781 ERS(ph)AEKTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSAEKTEK 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(0.933)AEKT(0.067)EK;ERS(1)AEKTEK 158.11 3.50E-05 489500000 796390 675690 675010 793850 285875 826290 818320 935920 386260 TRUE FALSE 758746.223 744543.5792 705959.8762 714050.6898 335731.5095 797675.3701 693470.2545 853965.8832 446159.2281 1.700617572 1.668784444 1.582304773 1.600439137 0.752492582 1.787871504 1.554311131 1.914038373 1 18.76719915 2.981339119 24.95208199 1.44733292 1.652840912 0.10037703 0.33922245 1998.08901 2671714.691 0.097781878 0.105360079 957.9417887 -2.981339119 0.205507992 ERS(ph)DS(ph)GGSSSEPFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.937)DS(0.614)GGS(0.44)S(0.009)SEPFDR 118.5 0.0034205 254080000 408400 339640 367180 448440 398630 403780 459350 385340 400220 TRUE FALSE 389095.7414 374249.7021 384015.5662 403361.9592 468150.9458 389796.9974 389267.721 351597.5868 462284.0736 0.841681043 0.809566506 0.83069175 0.872541327 1.012691054 0.843197981 0.842053065 0.760566082 1 18.81842013 -2.45730426 2.281856257 2.646915769 0.851024496 0.345030419 0.064241736 2002733.576 472514.2605 16844216.54 0.015754092 0.003488958 2.45730426 -1.795891273 ERS(ph)HERPDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK;ERS(1)HERPDRK 78.401 0.021489 2692080000 605423 516217 616778 655282 426865 623906 737035 697561 434835 TRUE FALSE 576805.8546 568820.0992 645057.8814 589411.8084 501310.1208 602299.9788 624586.7742 636478.8608 502266.991 1.148404862 1.132505439 1.284292802 1.173502976 0.998094897 1.199162974 1.243535381 1.267212204 1 18.93809494 2.04345341 24.99982728 1.203320152 1.14832433 0 0.099431193 387.7266867 223067.0414 0.03489021 0.025768121 110.5231897 -2.04345341 -0.054995822 ERS(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSKDASPINRWSPTR 16 3 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 ERS(1)KDAS(1)PINRWS(0.987)PT(0.013)R 72.399 0.074026 210590000 207960 158680 172950 191220 115360 210720 220010 216460 132530 TRUE FALSE 198130.1429 174849.6724 180879.9286 171998.2023 135478.7475 203422.7136 186443.4337 197505.6149 153082.0755 1.294273952 1.142195595 1.181587903 1.123568528 0.885007255 1.328847371 1.217931186 1.290194258 1 17.22394584 4.590116939 2.455234382 1.157813559 1.304670743 0.107184076 0.129906492 0.944347523 8.907542535 0.031573892 0.255078746 38914.99139 -4.590116939 0.146857184 ERS(ph)PALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK;ERS(1)PALK 96.957 0.0074797 23712959500 28591676.7 29525235 22943735.4 31297553.5 16334238.1 28020364.3 26751276.3 27703890 16257941.5 TRUE FALSE 27240204.81 32533890.01 23995728.36 28151463.96 19182924.05 27050012.06 22669877.78 25277990.52 18779140.03 1.450556562 1.732448342 1.277786327 1.499081636 1.021501731 1.440428689 1.207184021 1.346067524 1 24.16262766 4.455172288 0.128293506 0.849854777 2.222844268 0.411053504 0.169572601 25.46765102 0.599499011 1.314455479 6.369787149 28521.49511 -4.455172288 1.372989491 ERS(ph)PALKS(ph)PLQSVVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.783)PLQS(0.217)VVVR;ERS(1)PALKS(0.829)PLQS(0.171)VVVR 98.002 0.014175 570560000 925880 896520 882470 1033160 645620 1028870 1156680 1082030 784800 TRUE FALSE 882115.4873 987876.4073 922932.1224 929304.7939 758215.9236 993239.9739 980207.2221 987281.717 906502.7758 0.973097392 1.089766555 1.018123879 1.025153832 0.836418755 1.095683323 1.081306366 1.089110528 1 19.78995191 ERS(ph)PALKSPLQSVVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(0.995)PALKS(0.005)PLQSVVVR;ERS(0.998)PALKS(0.002)PLQSVVVR;ERS(1)PALKSPLQSVVVR 198.98 2.05E-11 29373990000 19136600 11762640 17588050 16983260 15418310 17512160 22950420 19930750 19050050 TRUE FALSE 18232050.84 12961266.39 18394479.49 15276070.44 18107258.38 16905709.51 19448911.92 18185507.87 22004234.46 0.828570104 0.589035097 0.835951804 0.694233215 0.822898811 0.768293464 0.883871327 0.826454922 1 24.39127784 1.235053725 0.463040174 1.00302437 0.714890614 0.510976735 0.076176268 0.686061807 0.403649451 0.081532661 0.04669322 17.18120915 -1.235053725 -0.288133756 ERS(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_SK-BR-3_Trastuzumab_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 164.94 9.70E-19 944000000 95882 109794 81241 108025 76246 87360 85167 96535 79130 TRUE FALSE 91349.84788 120982.1334 84965.98021 97166.12177 89543.27826 84334.70129 72173.20995 88081.88364 91401.07626 0.999439521 1.323640141 0.929594964 1.063074153 0.979674222 0.922688274 0.789631949 0.96368541 1 16.47992353 2.992345369 1.117407311 0.893458438 1.14377122 0.302609834 0.113261728 0.427814583 1.14084219 0.048320949 0.058102514 982.5289812 -2.992345369 0.250312782 ERS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSPQR 6 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 ERS(1)PQR 88.948 0.030719 39914000 8091.5 9505.9 7647.8 8760.8 8186.1 6586.9 8597.4 11001 10486 TRUE FALSE 7709.030831 10474.56202 7998.459195 7880.14774 9613.753248 6358.794001 7285.708728 10037.69412 12112.11532 0.636472707 0.864800387 0.660368481 0.650600455 0.793730326 0.524994506 0.601522404 0.828731716 1 13.56416323 0.987663744 5.135394684 0.999695989 0.683930316 0.558644355 0.094811596 0.121243429 12.225434 0.094868942 0.023968759 9.719943583 -0.987663744 -0.315765672 ERS(ph)PS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ERSPSPLR 8 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLR;ERS(1)PS(1)PLR;ERS(1)PS(1)PLR;ERS(1)PS(1)PLR 96.604 0.0050203 4462350000 513366 553264 504027 533901 400888 525771 577381 424091 324455 TRUE FALSE 489100.2066 609642.2306 527137.1365 480232.2571 470802.7403 507563.4184 489290.9241 386955.3438 374769.8243 1.305068271 1.626711093 1.406562381 1.281405882 1.25624506 1.354333742 1.305577163 1.032514676 1 18.51564527 1.44360236 0.47676024 0.977044307 1.4602615 0.629335876 0.107957841 0.578443452 0.349355431 0.119815292 0.074302112 27.77169325 -1.44360236 0.483217193 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(0.999)PS(0.998)PLRGNVVPS(0.632)PLPT(0.37)R;ERS(1)PS(1)PLRGNVVPS(0.998)PLPT(0.002)R;ERS(1)PS(1)PLRGNVVPS(0.5)PLPT(0.5)R;ERS(1)PS(1)PLRGNVVPS(0.93)PLPT(0.07)R;ERS(1)PS(1)PLRGNVVPS(0.848)PLPT(0.153)R;ERS(1)PS(1)PLRGNVVPS(1)PLPTR;ERS(1)PS(1)PLRGNVVPS(0.982)PLPT(0.018)R 134.4 6.48E-06 9654190000 2914220 2467174 2578051 2969300 2751991 2584044 3096360 2567813 2830233 TRUE FALSE 2776470.596 2718581.836 2696257.188 2670820.323 3231937.359 2494557.908 2623953.413 2342961.681 3269131.079 0.849299257 0.831591567 0.824762643 0.816981717 0.988622751 0.763064511 0.80264552 0.716692486 1 21.64047579 -0.255432111 9.813215744 1 0.826553673 0.386265102 0.069582814 0 0 0.063244556 0.014906885 0.555351422 0.255432111 -0.173446327 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSPSPLRGNVVPSPLPTRR 20 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(1)PLPTRR 74.13 0.027468 807170000 240000 176260 257080 215860 246020 243530 296190 241970 343560 TRUE FALSE 228655.6756 194221.0944 268867.3723 194161.3427 288925.8101 235096.495 251000.7756 220781.824 396837.5301 0.576194685 0.489422193 0.677525062 0.489271624 0.72807078 0.592425054 0.632502615 0.556353186 1 18.59818895 -5 0.260540932 3.659009526 0.555324078 0.738774127 0.075714495 90.10088753 0.884387672 128.2938135 0.089245136 1.00E-05 5 -3.103685448 ERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;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 154.92 1.53E-07 6269470000 3716600 3358940 3154586 4026100 3211630 3369335 3677212 3299004 3123714 TRUE FALSE 3540923.684 3701219.805 3299226.888 3621388.779 3771737.255 3252654.084 3116185.773 3010125.721 3608123.613 0.98137538 1.02580183 0.914388542 1.003676472 1.045345908 0.901480779 0.863658263 0.834263469 1 21.78281734 2.122117909 6.527910551 0.883979585 0.993823406 0.41606467 0.054410995 0.170545989 9.094986099 0.018816346 0.013848682 132.4701138 -2.122117909 0.109843821 ERS(ph)PS(ph)PLRGNVVPSPLPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ERSPSPLRGNVVPSPLPTRR 20 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(0.989)PLRGNVVPS(0.011)PLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR 111.81 0.00023354 4035580000 920886 567523 867207 828135 875433 823348 1166891 874942 1113557 TRUE FALSE 877357.5438 625354.2389 906969.2987 744889.2964 1028108.238 794835.2523 988860.3465 798327.4401 1286241.732 0.682109375 0.486187179 0.705131295 0.579120765 0.799311834 0.61795169 0.768798214 0.620666722 1 20.29473037 -5 0.161064561 2.322365663 0.557056875 0.590468935 0.090026062 81.29720408 0.749528779 34.21975637 0.333062098 1.00E-05 5 -1.765308788 ERS(ph)PS(ph)PPTIQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(0.732)PS(0.649)PPT(0.617)IQS(0.001)K;ERS(1)PS(0.868)PPT(0.132)IQSK;ERS(1)PS(0.997)PPT(0.003)IQSK 116.19 0.0010133 609740000 1392620 1246540 1267800 1446040 986920 1421110 1564620 1448490 1247700 TRUE FALSE 1326793.613 1373563.843 1325929.884 1300681.312 1159038.536 1371896.604 1325908.483 1321652.537 1441186.944 0.920625612 0.95307819 0.920026295 0.902507005 0.804224976 0.951921338 0.920011445 0.917058361 1 20.45882606 0.158828555 1.071594442 1.000371946 0.913167286 0.315136396 0.04112193 7.188873934 7.923637152 0.046378565 0.012274168 1.441546163 -0.158828555 -0.08720466 ERS(ph)PS(ph)PSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 ERS(0.999)PS(0.614)PS(0.387)FR 59.116 0.059397 418620000 366490 356940 316410 411580 562720 317520 407240 314930 520810 TRUE FALSE 349166.744 393312.5918 330917.7115 370207.1964 660858.1898 306524.2028 345108.0585 287353.0597 601574.5549 0.580421398 0.653805233 0.550085952 0.615397033 1.098547444 0.509536516 0.573674627 0.477668241 1 19.19838402 2.968416075 24.98796081 0.694535766 0.602542218 0.081661784 0.199517858 2345.959889 1856032.251 0.058917859 0.062550436 929.856807 -2.968416075 -0.091993548 ERS(ph)PSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSPSPLR 8 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 ERS(0.973)PS(0.027)PLR 61.577 0.051527 113900000 113880 73154 83358 94537 137240 75949 100240 93408 165430 TRUE FALSE 108497.1181 80608.47577 87180.04675 85033.96115 161174.6125 73318.86709 84946.54697 85228.70033 191084.0395 0.567797909 0.421848292 0.456239291 0.445008183 0.843475012 0.383699587 0.444550718 0.446027311 1 17.54384776 -1.320924256 4.054592913 1.000888561 0.496075785 0.590467294 0.13052158 1532.333121 132772845.1 184587.1961 0.028753171 0.047761257 1.320924256 -0.504812775 ERS(ph)PSPSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 ERS(0.988)PS(0.012)PSFR;ERS(0.999)PS(0.001)PSFR 80.69 0.01417 270800000 106607 68259 107533 107604 130297 103238 146672 115849 108418 TRUE FALSE 101567.8984 75214.6697 112463.4944 96787.44149 153020.7555 99662.84217 124294.4926 105704.6474 125230.9097 0.811044962 0.600607868 0.898049009 0.772871823 1.221908839 0.795832614 0.992522476 0.844077933 1 16.93423117 3.337189587 1.982570179 0.953037959 0.712844569 0.314562057 0.137133422 0.317514978 2.552146947 0.038127948 0.05654711 2173.649855 -3.337189587 -0.24019339 ERS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSPVK 6 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 ERS(1)PVK;ERS(1)PVK 57.598 0.087846 2171300000 3049400 2980100 2400800 3313100 1717750 3041900 3120700 3565700 2370100 TRUE FALSE 2905260.905 3283775.578 2510879.055 2980060.894 2017325.056 2936558.24 2644579.899 3253468.405 2737643.003 1.061227085 1.199490063 0.917168181 1.088549855 0.736883901 1.072659305 0.966006121 1.188419528 1 21.3845029 3.739658632 24.9999652 0.990711488 1.130358574 0.171527521 0.122686724 139.9238804 3185807.511 0.029181614 0.049111784 5491.090882 -3.739658632 0.139647086 ERS(ph)PVKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ERSPVKAK 8 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 ERS(1)PVKAK;ERS(1)PVKAK;ERS(1)PVKAK 105.78 0.0022547 388471000 1122580 476590 1314490 836150 818360 1195940 1768470 1320870 1284800 TRUE FALSE 1069517.868 525155.0628 1374760.667 752098.6134 961081.7249 1154524.298 1498657.421 1205207.62 1484040.222 0.720679839 0.353868483 0.926363481 0.50679126 0.647611642 0.777960247 1.009849598 0.812112504 1 20.50109876 2.066651373 2.765200776 0.937997471 0.607261988 0.450073451 0.154997522 0.223451513 3.352921447 0.068772295 0.042287315 116.5873345 -2.066651373 -0.330735483 ERS(ph)RTGSES(ph)S(ph)QTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSRTGSESSQTGTSTTSSR 20 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 3 ERS(0.497)RT(0.588)GS(0.526)ES(0.68)S(0.698)QT(0.007)GT(0.001)S(0.001)TTSSR 56.452 0.059879 117660000 147120 82575 172310 150690 178900 144680 252710 138090 221230 TRUE FALSE 140165.9292 90989.48638 180210.5839 135542.3549 210100.1034 139669.6953 214154.4482 125998.1075 255537.2185 0.548514733 0.356071366 0.705222452 0.530421188 0.822189834 0.546572809 0.8380558 0.493071453 1 17.96317391 -3.068897582 0.068017048 2.129934563 1.24E-12 0.435859588 0.145312497 164.4110427 1.192128688 36.69325851 8.814390473 0.000853301 3.068897582 -2.129934563 ERSDS(ph)GGS(ph)SSEPFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.03)DS(0.986)GGS(0.954)S(0.03)S(0.001)EPFDR;ERS(0.04)DS(0.934)GGS(0.682)S(0.305)S(0.04)EPFDR 142.4 0.00023149 387780000 518390 418900 486270 530170 483880 456440 592430 490800 489780 TRUE FALSE 493886.732 461586.3862 508565.9605 476876.3043 568268.5188 440633.3684 502043.9228 447822.9501 565732.581 0.873003869 0.815909145 0.898951161 0.842935904 1.004482573 0.77887218 0.887422679 0.791580625 1 19.10976073 -2.356509492 2.289271834 1.908449351 0.861290117 0.316219189 0.0639366 4165068.969 369946.5211 19947741.22 0.01358978 0.004400383 2.356509492 -1.047159234 ERSDS(ph)GGSSSEPFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERS(0.007)DS(0.756)GGS(0.076)S(0.153)S(0.008)EPFDR;ERSDS(0.846)GGS(0.107)S(0.017)S(0.029)EPFDR 108.66 0.0027925 380830000 449940 427240 426100 553970 382320 450350 463020 392150 337750 TRUE FALSE 428672.2279 470776.2417 445637.1065 498283.8831 448996.487 434754.2666 392377.7951 357811.2671 390126.545 1.098803025 1.206727017 1.142288604 1.277236552 1.150899606 1.114392938 1.005770564 0.91716719 1 18.57358264 1.78089721 2.049641856 0.957029582 1.175214498 0.772472541 0.050199166 0.135339628 1.121457244 0.03196292 0.013877646 60.38057016 -1.78089721 0.218184916 ERSDTFINLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ERSDTFINLR 10 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;; 221.32 4.95E-09 3254370000 1127540 853836 755638 846787 1195290 857940 1239360 982194 1252733 FALSE TRUE 1074243.419 940842.8591 790284.7497 761666.362 1403748.198 828229.3227 1050272.87 896187.8864 1447000.436 0.742393293 0.650202195 0.546153775 0.526376042 0.970109036 0.572376692 0.725827611 0.619341822 1 20.46463393 -1.825455972 2.580591407 1.116036547 0.672486318 0.398189815 0.127785648 34738491.72 22813362.62 25024121.69 0.028570657 0.014946656 1.825455972 -0.443550229 ERSDYDR ddPTM_SK-BR-3_Trastuzumab_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 ; 119.86 0.0042738 361440000 375740 339310 331390 392100 346920 335480 366600 373220 452860 FALSE TRUE 357979.5148 373886.0748 346584.5593 352685.3631 407422.7382 323862.2435 310668.4369 340538.8782 523087.2159 0.684359135 0.714768137 0.66257509 0.674238162 0.778881085 0.619136224 0.593913266 0.651017398 1 18.99669199 -2.1221701 2.496065174 1.662735695 0.671635278 0.806894323 0.050370654 3114549.304 1166504.791 11664132.17 0.013513444 0.007547965 2.1221701 -0.991100418 ERSDYDRS(ph)R ddPTM_SK-BR-3_Trastuzumab_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;ERSDYDRS(0.999)R 160.62 5.13E-05 2063598000 739603 558381 662499 703129 788884 723951 861952 779963 883393 TRUE FALSE 704643.4319 615280.6587 692875.2345 632449.1371 926465.1198 698880.3953 730445.3916 711665.3049 1020385.075 0.690566189 0.602988689 0.679033094 0.619814179 0.907956362 0.684918285 0.715852681 0.69744778 1 19.96068227 -5 0.182961415 2.269661271 0.631869868 0.588618613 0.080051196 90.90014327 0.879587853 41.97214659 0.22591283 1.00E-05 5 -1.637791403 ERSRT(ph)GS(ph)ES(ph)SQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERSRTGSESSQTGTSTTSSR 20 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 3 ERS(0.575)RT(0.708)GS(0.708)ES(0.886)S(0.123)QTGTSTTSSR 65.155 0.04019 130320000 150760 78162 168910 126250 183590 144050 219860 128560 206140 TRUE FALSE 143633.8736 86126.79666 176654.6906 113559.1101 215608.0379 139061.5124 186316.319 117302.6049 238107.1384 0.603232119 0.361714467 0.741912619 0.476924425 0.905508501 0.584029162 0.78248943 0.492646317 1 17.86125135 -4.999999968 0.083521631 2.235749666 0.255543194 0.348255396 0.160803486 223.9282191 1.315825715 50.72283255 4.285752553 1.00E-05 4.999999968 -1.980206472 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 ERVDDS(0.001)T(0.001)GT(0.001)VIS(0.996)DVEEDAGELSR;ERVDDSTGTVIS(1)DVEEDAGELSR 184.44 2.02E-17 60023000 39322 41712 42314 43671 41816 42274 46736 42993 50541 TRUE FALSE 37463.32699 45962.50022 44254.13875 39281.10811 49108.69716 40810.04078 39605.56483 39228.305 58378.64015 0.641730038 0.787317075 0.758053607 0.672867816 0.841210022 0.699057749 0.678425615 0.671963322 1 15.83315299 -1.667950452 2.878505979 1.030997758 0.719835254 0.677215971 0.061001661 27308619.82 24872113.73 6202753.093 0.014271277 0.021480755 1.667950452 -0.311162504 ERVEAVNMAEGIIHDTETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ERVEAVNMAEGIIHDTETK 19 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 241.38 1.39E-24 556102400 1289919 1076863 962560 1171125 805202 939665 1100926 1186823 831253 FALSE TRUE 1228947.085 1186596.564 1006694.328 1053401.29 945628.9739 907124.1654 932959.5188 1082898.486 960159.4698 1.279940597 1.235832798 1.04846576 1.097110765 0.984866581 0.944764067 0.971671424 1.127831908 1 19.87291451 3.694714708 1.290649459 1.001402222 1.287184335 0.748493833 0.056247137 0.195946161 0.63241507 0.0175559 0.04388888 4951.248317 -3.694714708 0.285782113 ERVYFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERVYFFK 7 1 P04004 P04004 VTN Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B 0 94.302 0.013042 301700000 563120 588380 532780 508720 562480 658360 705200 727750 635750 FALSE TRUE 536502.4336 648336.5909 557208.49 457582.4991 660576.3339 635560.8281 597608.7881 664024.352 734338.863 0.730592456 0.88288476 0.758789325 0.623121725 0.899552464 0.865487121 0.813805204 0.904247869 1 19.48608643 0.993783057 0.601314799 1.002356168 0.778186811 0.462670587 0.077773171 0.846836751 0.732079153 0.079892858 0.034461705 9.857869334 -0.993783057 -0.224169357 ERYENNDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ERYENNDKYR 10 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 80.706 0.013051 40952000 45111 36569 34534 37952 42859 36543 52902 37871 50923 FALSE TRUE 42978.69243 40295.42268 36117.41806 34136.99286 50333.59603 35277.50675 44830.82829 34554.81447 58819.87876 0.730683118 0.685064701 0.614034215 0.580364897 0.85572424 0.599754836 0.762171382 0.587468305 1 15.84401619 -1.367937748 3.430809378 1.00214003 0.683820597 0.56964659 0.088072817 28356010.13 36343209.77 592741.1692 0.01883028 0.042860995 1.367937748 -0.318319434 ES(ph)ASPTIPNLDLLEAHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.488)AS(0.488)PT(0.024)IPNLDLLEAHTK 62.611 0.032269 66813000 69935 54025 61818 68570 59137 68510 83311 67559 64934 TRUE FALSE 66629.31115 59530.20892 64652.41645 61677.21333 69450.47408 66137.48152 70600.37684 61643.17581 75003.63308 0.888347783 0.793697671 0.861990464 0.82232301 0.925961466 0.881790372 0.941292761 0.821869199 1 16.19467286 2.737508976 24.97835808 0.910481049 0.839936434 0.334349466 0.050723826 102.6050204 2437033.937 0.014236693 0.014132322 546.3978424 -2.737508976 -0.070544615 ES(ph)EELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ES(1)EELLK;ES(1)EELLK 149.94 0.0020797 1598220000 2781890 2244050 2180080 3219450 1670010 3125830 3046610 2540770 1451690 TRUE FALSE 2650395.573 2472721.246 2280038.824 2895824.769 1961259.215 3017581.723 2581793.69 2318286.709 1676810.671 1.580617072 1.474657389 1.359747325 1.726983743 1.16963665 1.799595968 1.53970495 1.382557226 1 20.67728837 0.879727566 3.407187849 1.000322517 1.523806275 0.467931252 0.175066773 0.420785826 9.73211968 0.14733881 0.038135718 7.581018674 -0.879727566 0.523483759 ES(ph)GGSGFRSPHLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.419)GGS(0.38)GFRS(0.201)PHLWK 52.026 0.096532 65931000 275280 216280 245920 266170 216800 232290 275780 273220 217480 TRUE FALSE 262268.06 238319.1779 257195.6752 239414.0859 254609.8514 224245.7391 233704.696 249295.4084 251205.6877 1.044037109 0.948701361 1.023844952 0.953059973 1.0135513 0.892677794 0.930332024 0.992395557 1 17.9385096 2.264818301 24.99978699 0.944170309 0.993666699 0.187635279 0.041898962 292.7262637 278702.078 0.013472295 0.011268278 184.0002025 -2.264818301 0.049496389 ES(ph)HTPVSIQEEIVGDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.5)HT(0.5)PVSIQEEIVGDFK;ES(0.499)HT(0.499)PVS(0.001)IQEEIVGDFK;ES(0.546)HT(0.453)PVS(0.001)IQEEIVGDFK;ES(0.566)HT(0.426)PVS(0.008)IQEEIVGDFK 186.75 3.26E-10 192521000 349964 358234 303162 405407 230019 356417 321379 382813 177437 TRUE FALSE 333421.8953 394738.4519 317062.2776 364654.7181 270134.2408 344074.1899 272346.731 349291.8643 204953.0237 1.62682106 1.92599477 1.546999755 1.779211214 1.318030034 1.678795383 1.328825143 1.704253287 1 17.64493375 -2.342797117 0.137176661 2.39E-12 1.939585616 0.546019694 0.180409379 36.96320749 0.653425991 12.80975445 1.242827201 0.004541537 2.342797117 1.939585616 ES(ph)KGSPVFLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.6)KGS(0.4)PVFLPR 85.457 0.0092061 262220000 380570 294570 345830 354930 271760 365710 400230 404840 301650 TRUE FALSE 362581.2103 324587.0179 361686.6476 319251.7621 319154.858 353045.371 339167.5628 369390.0634 348428.3414 1.040619167 0.931574672 1.038051744 0.916262325 0.915984207 1.013251016 0.973421282 1.060160784 1 18.41050245 1.258450829 24.79042447 1.030080384 0.97543006 0.184776798 0.047578172 303.3569209 378094.9448 0.02969586 0.010811737 18.1322137 -1.258450829 -0.054650323 ES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESPEGSYTDDANQEVR 16 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 ES(0.787)PEGS(0.209)YT(0.004)DDANQEVR;ES(1)PEGSYTDDANQEVR;ES(1)PEGSYTDDANQEVR 428.3 3.58E-160 897280000 699470 850290 602850 807890 524670 728710 611630 684990 466070 TRUE FALSE 666407.4393 936935.5177 630491.2688 726679.3623 616172.2819 703474.59 518314.6101 625008.6442 538345.7552 1.237879992 1.740397335 1.171164187 1.349837637 1.144566064 1.306733792 0.962791301 1.16097998 1 19.03817352 2.677227105 0.749570294 1.040486852 1.468847134 0.399868634 0.167477665 0.566280691 0.675636733 0.112207877 0.102357507 475.5838573 -2.677227105 0.428360282 ES(ph)PHFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESPHFYR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 ES(1)PHFYR;ES(1)PHFYR;ES(0.925)PHFY(0.075)R 93.649 0.0095202 788102000 1363330 1343970 1317390 1771980 1552120 1430680 1500670 1422890 1301580 TRUE FALSE 1298888.093 1480922.071 1377793.635 1593857.204 1822809.237 1381135.193 1271715.23 1298294.208 1503422.379 0.863954209 0.985033941 0.916438157 1.06015264 1.212439872 0.918660792 0.845880205 0.863559188 1 20.51981895 -0.764198818 4.26694636 1.000000221 0.954530268 0.012935976 0.110366132 6271367.843 2939533.745 12.92520751 0.026865659 0.172108049 0.764198818 -0.045469954 ES(ph)PSLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 104.42 0.0070637 0 345040 296020 276500 352970 357510 300230 440420 349160 438010 TRUE FALSE 328730.643 326184.7745 289177.7985 317488.785 419859.6308 289832.9598 373225.8401 318585.6994 505934.3538 0.649749598 0.644717585 0.571571779 0.627529605 0.82986978 0.572866732 0.73769618 0.629697701 1 18.94859068 -4.999999999 0.274579668 3.412597287 0.635712083 0.665411435 0.076294421 122.4850799 1.181836249 167.8929673 0.081328023 1.00E-05 4.999999999 -2.776885205 ES(ph)PSPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESPSPAPKPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 ES(0.972)PS(0.028)PAPKPR 171.32 2.46E-06 167200000 335760 326930 335570 380690 225660 360050 389280 379940 251090 TRUE FALSE 319889.2902 360244.5387 350956.2164 342422.3179 265015.0326 347581.3782 329888.1864 346670.4394 290027.7548 1.102960958 1.24210367 1.210078038 1.180653618 0.913757488 1.198441778 1.137436611 1.195300911 1 18.14583144 -5 0.245051706 0.132874532 1.164881164 0.191632492 0.092338185 295.6501362 2.939576892 128.4992597 0.133642825 1.00E-05 5 1.032006632 ES(ph)SPEKEAEEGCPEKESEEGCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.5)S(0.5)PEKEAEEGCPEKESEEGCPK;ES(0.541)S(0.459)PEKEAEEGCPEKESEEGCPK 153.77 2.46E-08 549267000 483032 407884 398775 465512 168940 521180 439237 517340 144798 TRUE FALSE 460200.0346 449447.8433 417059.2282 418717.8493 198403.0825 503131.4059 372223.3285 472038.967 167252.5343 2.75152802 2.687240855 2.493589887 2.503506754 1.186248587 3.008213944 2.225516821 2.822312792 1 17.35166855 -1.911239966 2.678876505 0.15107043 2.468297496 0.457049936 0.499940402 35630385.98 31451963.54 192072166.9 0.114125114 0.012267612 1.911239966 2.317227066 ES(ph)SPKKEETVASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESSPKKEETVASK 13 2 J3QQY0 J3QQY0 MSL1 1 ES(0.629)S(0.371)PKKEETVASK;ES(0.5)S(0.5)PKKEETVASK 112.16 0.00048147 318449000 278160 331510 228570 380890 112267 318450 250720 350450 77771 TRUE FALSE 265011.9281 365291.2459 239050.1606 342602.2136 131846.3293 307421.9967 212468.0592 319762.7401 89831.32948 2.950105822 4.066412553 2.661100108 3.813838841 1.467709874 3.422213591 2.365188854 3.559590423 1 16.45493107 2.771614355 24.99982466 2.527243926 3.401940075 0.240733339 0.863599834 949.9357094 718471.6128 0.232088056 0.246151997 591.0365726 -2.771614355 0.874696149 ES(ph)SPSHGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.492)S(0.492)PS(0.016)HGLLK 172.92 2.30E-06 86278000 167570 140800 139190 162330 135810 162000 195590 168220 131310 TRUE FALSE 159649.2982 155147.6801 145571.9992 146012.28 159495.221 156389.8994 165749.1532 153489.765 151672.8842 1.052589585 1.022909803 0.959776034 0.962678865 1.051573733 1.031099924 1.092806761 1.011978943 1 17.21060366 ESADPLGAWLQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 147.24 1.88E-05 228508000 227423 210725 213740 245412 220738 218276 257064 232837 234322 FALSE TRUE 216673.1655 232198.1171 223540.1904 220742.7195 259234.6373 210717.0474 217844.1655 212448.5579 270659.459 0.800537939 0.857897662 0.825909396 0.815573637 0.957788944 0.778531991 0.804864409 0.784929367 1 18.04611928 -1.658173547 2.820910038 1.018588193 0.828669441 0.527435905 0.051088455 14455208.49 14329866.35 1955561.212 0.011552475 0.021969818 1.658173547 -0.189918752 ESAGADTRPTVRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESAGADTRPTVRPR 14 2 O75489;E9PS48;O75489-2;G3V194 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;; 125.61 5.07E-05 1328790000 1367450 1101080 1155950 1126750 1218660 998020 1257300 1219040 1355280 FALSE TRUE 1302813.349 1213281.304 1208951.451 1013486.949 1431193.918 963458.3172 1065475.793 1112294.395 1565449.901 0.832229347 0.775036814 0.77227093 0.64740938 0.914238084 0.61545139 0.680619541 0.710526983 1 20.57814591 4.172444559 1.248244203 0.737619575 0.835811303 0 0.11926665 1.825439349 4.506601708 0.032419533 0.178650122 14874.57478 -4.172444559 0.098191728 ESAIRPFINGDVIMEDFNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESAIRPFINGDVIMEDFNER 20 1 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 0 123.19 2.66E-05 34884000 30617 20665 24699 26719 29009 25254 31718 25841 32275 FALSE TRUE 29169.79509 22770.78699 25831.47358 24033.15536 34068.16042 24379.44765 26878.83656 23578.22505 37280.04216 0.7824507 0.610803681 0.692903551 0.644665455 0.913844471 0.653954401 0.720998019 0.632462403 1 15.18611587 -1.862317506 2.785875714 1.121829287 0.70523335 0.520960968 0.088438455 14605466.18 13701096.43 11936901.48 0.019694306 0.013730378 1.862317506 -0.416595936 ESAS(ph)PTIPNLDLLEAHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.102)AS(0.729)PT(0.169)IPNLDLLEAHTK;ESAS(0.996)PT(0.003)IPNLDLLEAHTK;ES(0.003)AS(0.982)PT(0.015)IPNLDLLEAHTK;ES(0.007)AS(0.89)PT(0.102)IPNLDLLEAHTK;ESAS(0.974)PT(0.026)IPNLDLLEAHTK 333.1 3.68E-75 1449906000 2361560 2195470 2156340 2515110 1713253 2325490 2505980 2488820 1736770 TRUE FALSE 2249933.739 2419190.889 2255210.322 2262286.364 2012043.781 2244957.698 2123646.726 2270885.727 2006099.421 1.121546477 1.205917744 1.124176747 1.127704011 1.002963143 1.119066021 1.058594954 1.131990619 1 20.93596168 3.683666455 0.112801936 0.936083138 1.329849935 0.388039794 0.049162079 26.94605738 0.748882776 0.709941357 2.016406497 4826.879482 -3.683666455 0.393766797 ESCFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESCFYR 6 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 96.666 0.097591 70925000 133480 113180 99367 110240 137040 111960 145510 124640 145780 FALSE TRUE 127170.6649 124713.1707 103923.0752 99158.46576 160939.7326 108082.7971 123309.777 113725.8608 168386.8179 0.755229338 0.740634999 0.61716871 0.58887309 0.955773942 0.641872081 0.732300655 0.675384583 1 17.36141968 -1.834771183 2.674186072 1.102333173 0.716929204 0.439400831 0.101665031 30846673.48 20807448.4 20246351.52 0.023834251 0.014629478 1.834771183 -0.385403969 ESDFYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESDFYLR 7 0 P61326;P61326-2 P61326 MAGOH Protein mago nashi homolog 0 170.72 0.0022433 171940000 194630 200880 260750 278100 202260 212430 267890 228900 231960 FALSE TRUE 185430.2256 221349.9004 272705.6454 250144.8596 237534.08 205073.4958 227018.4604 208856.3025 267931.1721 0.692081568 0.826144635 1.017819775 0.933616114 0.886548878 0.765396181 0.847301412 0.779514757 1 18.03150291 4.282777077 2.733554559 0.877876549 0.707600771 0.34817336 0.083190147 0.303170634 4.423880426 0.021348006 0.073264189 19176.84141 -4.282777077 -0.170275778 ESDGFREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESDGFREEK 9 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 128.91 0.00036865 937940000 1803240 1455450 1717580 1983770 1437840 2021380 2238600 2235300 1687260 FALSE TRUE 1718004.419 1603762.01 1796332.742 1784357.671 1688598.841 1951379.104 1897060.455 2039565.282 1948911.663 0.881519902 0.822901335 0.921710704 0.915566213 0.866431697 1.001266061 0.973394788 1.046514996 1 20.89423727 2.218987983 0.912464731 1.023111841 0.864087575 0.719088939 0.036713963 0.278188998 0.438794592 0.026416003 0.014922852 165.5724148 -2.218987983 -0.159024266 ESDKEDGRES(ph)PSYDTPSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESDKEDGRESPSYDTPSQR 19 2 C9JRP1;A0A0A0MST8;E9PFN4;Q9Y6M7-11;Q9Y6M7-14;Q9Y6M7-10;Q9Y6M7-2;Q9Y6M7-9;Q9Y6M7-6;Q9Y6M7-13;Q9Y6M7-12;Q9Y6M7;Q9Y6M7-8;Q9Y6M7-7 C9JRP1 SLC4A7 Anion exchange protein;Sodium bicarbonate cotransporter 3 1 ESDKEDGRES(0.999)PS(0.001)YDTPSQR;ESDKEDGRES(0.999)PS(0.001)YDTPSQR;ESDKEDGRES(1)PSYDTPSQR 128.07 1.16E-05 248663000 372630 295261 283223 454550 251587 352420 388520 382370 247133 TRUE FALSE 355016.5184 325348.4316 296209.0547 408857.7704 295463.6931 340215.607 329244.1383 348887.6557 285457.1235 1.243677208 1.139745359 1.037665661 1.432291356 1.035054545 1.19182735 1.153392616 1.222206864 1 18.12291454 -1.56081367 2.64605213 0.987689224 1.179177988 0.205952266 0.112178005 10205361.66 9622930.183 886818.9908 0.023883187 0.027490734 1.56081367 0.191488764 ESDLSHVQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESDLSHVQNK 10 0 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 163.38 6.48E-06 716010000 2632600 2094050 2136800 2638200 2116050 2399300 2932400 2740900 2273700 FALSE TRUE 2508162.215 2307436.076 2234774.394 2373003.124 2485088.45 2316211.639 2485008.523 2500892.266 2626293.784 0.955019667 0.878590236 0.850923232 0.903555854 0.946233992 0.881931661 0.946203558 0.952251527 1 21.32459688 1.147757186 0.993459024 0.999415679 0.901842889 0.511189556 0.031365353 0.427880228 0.907353192 0.029309809 0.009974929 14.05261624 -1.147757186 -0.09757279 ESDQTLAALLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK 234.77 1.20E-16 3851527000 4712500 5027160 3885260 5535660 2334011 5017780 4375580 5197240 2460000 TRUE FALSE 4489749.464 5539433.319 4063403.014 4979204.94 2741061.779 4844013.02 3708004.908 4742142.113 2841484.236 1.580071924 1.949485853 1.43002835 1.752325379 0.96465845 1.704747455 1.304953538 1.668896154 1 21.43821328 -0.832369477 0.077713942 3.01E-12 2.354551043 0.299798911 0.267502742 85.48879809 1.402461605 30.75965842 13.33400209 0.147106046 0.832369477 2.354551043 ESDTKNEVNGTSEDIKSEGDT(ph)QSN ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.5)QS(0.5)N;ESDTKNEVNGTSEDIKS(0.001)EGDT(0.5)QS(0.5)N;ESDTKNEVNGTSEDIKSEGDT(0.5)QS(0.5)N 161.04 1.55E-14 918350000 1334580 1158070 1191540 1406290 622960 1472760 1354420 1433030 606830 TRUE FALSE 1271497.048 1276078.65 1246173.288 1264927.057 731604.0268 1421757.952 1147778.353 1307546.296 700934.0971 1.814003704 1.820540126 1.777875114 1.80463051 1.043755796 2.028376074 1.637498244 1.865434 1 19.41891928 -1.84517068 2.449496805 0.695774807 1.728570552 0.433031827 0.26031043 6986107.639 4199124.244 12441994.89 0.061403845 0.014283325 1.84517068 1.032795745 ESDTKNEVNGTSEDIKSEGDTQS(ph)N ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.012)QS(0.988)N 276.19 3.81E-52 504860000 1081200 987790 1044000 1246700 528810 1229600 1158800 1276300 532410 TRUE FALSE 1030093.819 1088446.924 1091868.433 1121379.347 621034.2966 1187018.644 982003.7772 1164540.406 614973.4236 1.675021682 1.769908881 1.77547255 1.823459851 1.009855504 1.930195026 1.596823114 1.893643467 1 19.23016454 -1.076485248 4.694321638 0.999978463 1.682751346 0.408797764 0.258613531 7.66E-05 1.51E-05 0.224507986 0.0529146 0.083852256 1.076485248 0.682772883 ESDVPLKTEEFEVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESDVPLKTEEFEVTK 15 1 Q969H8;M0QXF7;M0QYN0 Q969H8 MYDGF Myeloid-derived growth factor 0 ; 182.15 5.09E-07 348010000 801520 747170 699590 847540 515690 859110 911970 915540 601420 FALSE TRUE 763633.7381 823307.4725 731666.8935 762343.669 605626.1727 829358.8053 772832.227 835370.464 694685.142 1.099251577 1.185151981 1.053235271 1.097394522 0.871799519 1.193862881 1.112492812 1.202516671 1 19.40599972 3.730228401 24.86422161 1.082120209 1.14220178 0.072801815 0.096401842 1517.746877 4529123.503 0.024600595 0.038788043 5373.14303 -3.730228401 0.060081571 ESDWDGIIACHQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESDWDGIIACHQGK 14 0 A0A0A0MTB8;Q8NI36 A0A0A0MTB8 WDR36 WD repeat-containing protein 36 0 117.93 0.00027474 82550000 151000 134500 170080 151540 247420 150990 180610 158120 357870 FALSE TRUE 143862.5293 148205.7029 177878.3362 136306.9113 290569.9697 145761.1784 153054.6274 144274.1746 413366.6519 0.348026452 0.358533283 0.430316126 0.329748205 0.702935199 0.352619588 0.370263607 0.349022288 1 18.65706248 -1.829130301 2.435901754 1.229951996 0.400378741 0.744718148 0.109413837 9176182.84 5568815.811 12339212.96 0.026973444 0.014820734 1.829130301 -0.829573256 ESEDAELLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESEDAELLWR 10 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YB83;E5RGC8 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;; 197.66 7.24E-07 721400000 1148090 999000 946720 1239020 991200 850710 1062630 1029600 913590 FALSE TRUE 1093822.061 1100799.236 990128.0484 1114471.356 1164064.966 821249.6994 900506.277 939442.7657 1055264.871 1.036537926 1.043149702 0.938274433 1.056105804 1.103102167 0.778240347 0.853346209 0.89024357 1 20.00917373 2.241680047 24.99999996 0.86342686 1.033109788 0.558436083 0.067711663 51.49171568 412672.5167 0.022345277 0.017964366 174.4536444 -2.241680047 0.169682928 ESEDDPES(ph)EPDDHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESEDDPESEPDDHEK 15 0 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 ESEDDPES(1)EPDDHEK;ESEDDPES(1)EPDDHEK 170.89 7.18E-07 747980000 2037810 1767360 1720790 2091260 1143890 1956740 2067390 2014850 1065320 TRUE FALSE 1941486.76 1947455.993 1799689.924 1881042.572 1343384.054 1888977.603 1751971.685 1838419.053 1230524.385 1.57777187 1.582622837 1.462539017 1.528651195 1.091716727 1.535099691 1.423760233 1.494012695 1 20.23084182 -3.609311349 0.15292358 1.38E-15 1.62740906 0.529255799 0.138564739 64.12517912 0.857604625 21.36801195 0.680934832 0.00024586 3.609311349 1.62740906 ESEDDPES(ph)EPDDHEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESEDDPESEPDDHEKR 16 1 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 ESEDDPES(1)EPDDHEKR 183.56 1.20E-09 90338000 301510 282800 295320 312030 182280 307960 333560 334120 180610 TRUE FALSE 287258.2198 311617.6415 308860.7141 280664.1516 214069.5743 297295.268 282669.2958 304862.6815 208618.0764 1.376957476 1.493723108 1.480507919 1.345349149 1.026131474 1.425069549 1.354960705 1.461343556 1 17.67050464 -3.543231537 0.266338893 6.71E-19 1.408069928 0.416214191 0.134777651 88.2786537 1.747996742 49.08045331 0.172948137 0.000286265 3.543231537 1.408069928 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESEDKPEIEDVGSDEEEEK 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK 206.33 2.24E-16 2336020000 2574000 3997090 1843240 3221530 1206430 3618840 2171290 2814560 583547 TRUE FALSE 2452332.121 4404398.015 1927754.377 2897695.684 1416831.01 3493518.663 1840019.832 2568102.205 674040.4884 3.638256401 6.534322628 2.859997894 4.298993508 2.101996889 5.182950763 2.729835765 3.810011787 1 19.36247573 3.716394902 24.96356678 3.305821697 5.086289751 0.259562642 1.343889044 883.8205783 995380.3121 0.315528882 0.489247695 5204.690415 -3.716394902 1.780468054 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK 281.4 4.79E-45 11160100000 12827782 19382410 8696253 15722390 3865381 17267360 10198154 14594900 1799210 TRUE FALSE 12221438.17 21357499.61 9094984.802 14141945.49 4539502.223 16669386.99 8642238.305 13316893.18 2078222.298 5.880717467 10.27681189 4.37632914 6.804828099 2.184319852 8.020983613 4.158476365 6.407829037 1 20.98691855 3.718686318 24.93452595 4.972119587 8.078764875 0.259912978 2.332024032 877.7040984 1101177.802 0.5442631 0.844417566 5232.223875 -3.718686318 3.106645288 ESEDKPEIEDVGS(ph)DEEEEKKDGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ESEDKPEIEDVGSDEEEEKKDGDK 24 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ES(0.001)EDKPEIEDVGS(0.999)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK 215.86 9.84E-33 34773500000 8140050 11228560 5820840 10043640 1889687 9614090 6495540 9297320 1210587 TRUE FALSE 7755285.969 12372763.03 6087731.272 9034034.226 2219247.815 9281151.653 5504526.074 8483197.373 1398318.649 5.54615071 8.848314393 4.35360801 6.460640592 1.587083041 6.63736528 3.936531975 6.066712604 1 20.41526173 3.715768758 24.0072745 4.498881433 7.197232539 0.255501108 2.038243647 536.6087112 565224.2353 0.476223242 0.73843824 5197.191963 -3.715768758 2.698351106 ESEDSETQPFDTHLEAYGPCLS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR 313.4 9.35E-75 3614694000 2505755 2260986 2366823 2647455 2384015 2436146 2859430 2540411 2360908 TRUE FALSE 2387312.927 2491383.044 2475344.176 2381327.794 2799786.461 2351781.653 2423171.436 2317959.145 2727025.555 0.875427413 0.913589915 0.907708463 0.873232665 1.026681417 0.862398099 0.888576725 0.849995388 1 21.37889679 4.591341373 2.455054135 0.909652604 0.872776531 0.037489598 0.057204965 1.57258225 14.80752339 0.013159488 0.106780094 39024.8617 -4.591341373 -0.036876073 ESEEGNPVRGSEEDS(ph)PKKESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESEEGNPVRGSEEDSPKKESK 21 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ESEEGNPVRGS(0.001)EEDS(0.998)PKKES(0.001)K;ESEEGNPVRGS(0.217)EEDS(0.778)PKKES(0.004)K;ESEEGNPVRGS(0.003)EEDS(0.989)PKKES(0.008)K;ESEEGNPVRGS(0.001)EEDS(0.999)PKKESK 99.219 0.00062018 749544000 711702 406473 674696 671424 291637 784080 848700 840910 335078 TRUE FALSE 678061.2569 447893.0608 705631.479 603931.1839 342498.4005 756927.113 719215.2276 767275.4625 387040.1849 1.751914358 1.157226248 1.823147845 1.560383669 0.8849169 1.955680941 1.858244326 1.982418086 1 18.56212384 ESEEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESEEQKR 7 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 113.89 0.0096659 377240000 597060 469060 450530 442760 342950 391760 435400 529730 455960 FALSE TRUE 568838.1571 516857.7473 471187.2461 398252.9236 402760.3714 378193.253 368971.7333 483344.0329 526667.9481 1.080069822 0.981373082 0.894657151 0.756174597 0.764733022 0.718086708 0.700577536 0.917739602 1 19.00653414 3.681217839 1.66767528 0.77965146 1.05501553 0.464327669 0.095149265 0.24728192 1.344712686 0.026295903 0.055696727 4799.741403 -3.681217839 0.275364069 ESEIIDFFLGASLKDEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESEIIDFFLGASLKDEVLK 19 1 P15880;E9PQD7;E9PPT0;E9PMM9;I3L404 P15880 RPS2 40S ribosomal protein S2 0 173.27 6.15E-12 202690000 117410 114140 106650 123480 75865 96481 113000 118240 71740 FALSE TRUE 111860.262 125770.9958 111540.008 111067.5558 89095.83198 93139.83878 95759.77461 107886.2788 82865.0728 1.34990845 1.51778055 1.346043685 1.340342222 1.075191621 1.123993929 1.155610819 1.301951173 1 16.33847652 2.954394065 2.714662421 1.141702253 1.421361659 0.667697234 0.090014188 0.151451086 2.221579408 0.027146385 0.030658383 900.3141277 -2.954394065 0.279659407 ESEITDEDIDGILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESEITDEDIDGILER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;; 250.48 1.79E-18 271187000 588780 519140 513550 629600 579420 499750 610010 554250 639980 FALSE TRUE 560949.5362 572040.9562 537096.7755 566311.4118 680470.6645 482443.5322 516941.7709 505716.9317 739224.8298 0.758834814 0.773838937 0.726567553 0.76608819 0.920519221 0.652634371 0.699302499 0.684117891 1 19.49565369 ESEKQQDS(ph)QPEEVMDVLEMVENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ESEKQQDSQPEEVMDVLEMVENVK 24 1 Q9H307 Q9H307 PNN Pinin 1 ES(0.239)EKQQDS(0.761)QPEEVMDVLEMVENVK;ES(0.019)EKQQDS(0.981)QPEEVMDVLEMVENVK;ES(0.031)EKQQDS(0.969)QPEEVMDVLEMVENVK;ES(0.048)EKQQDS(0.952)QPEEVMDVLEMVENVK;ES(0.025)EKQQDS(0.975)QPEEVMDVLEMVENVK 219.24 6.69E-33 153076000 227052 162778 209444 221208 125683 225806 261368 252499 155920 TRUE FALSE 216319.7019 179365.2633 219047.2146 198971.7516 147602.0754 217986.2816 221491.5112 230388.849 180099.2773 1.201113659 0.995924392 1.216258154 1.104789284 0.81955951 1.210367331 1.229830095 1.279232501 1 17.45843287 ESESVDKVMDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 186.13 1.11E-05 1949060000 3387600 2420050 3053500 3160400 1896870 3504500 3989700 3775800 2090680 FALSE TRUE 3227474.862 2666655.846 3193505.995 2842710.588 2227683.527 3383138.286 3380997.989 3445170.935 2414891.977 1.336488295 1.104254713 1.322421883 1.177158488 0.922477506 1.400948083 1.400061792 1.426635629 1 21.20352722 ESFDGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESFDGSVR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 137.9 0.0016941 379324000 1012260 1098150 880820 1154090 897270 968870 952790 999370 850390 FALSE TRUE 964412.4759 1210052.733 921206.4682 1038078.681 1053753.604 935317.789 807424.3863 911859.8648 982264.138 0.981826006 1.23190157 0.937839867 1.056822336 1.072780287 0.952205983 0.822003324 0.9283245 1 19.9057515 2.122017981 3.986069457 0.894931077 1.068147288 0.344046738 0.087718677 0.197183055 5.785228427 0.033778344 0.023989707 132.4396367 -2.122017981 0.173216212 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR 34 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 90.376 0.00015499 181161000 125178 125206 131539 139092 143440 120842 168089 110796 26914 FALSE TRUE 119261.084 137964.6337 137570.1933 125110.2079 168455.8906 116657.2112 142443.9359 101094.1149 31087.68566 3.836280555 4.437919093 4.425231095 4.024429778 5.41873372 3.752521577 4.582005152 3.251902247 1 14.9240556 0.897127791 2.960502782 1.001419436 4.336970137 0.838318934 0.468017984 0.141418961 2.677093481 0.401034643 0.105378552 7.890922739 -0.897127791 3.335550701 ESGCVLGLRPGAQES(ph)PVSWPEGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESGCVLGLRPGAQESPVSWPEGSK 24 1 Q6ZUT6;Q6ZUT6-4;Q6ZUT6-2 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 ESGCVLGLRPGAQES(0.968)PVS(0.032)WPEGSK 140.74 1.76E-07 119930000 136800 108040 122150 135340 132330 122630 140960 124780 161950 TRUE FALSE 130333.7351 119049.3988 127750.6983 121735.3661 155408.3101 118383.2924 119453.9631 113853.6017 187064.3789 0.69673198 0.636408704 0.682923703 0.650767221 0.830774469 0.632847863 0.638571404 0.608633254 1 17.51317534 -1.084672065 4.860719413 1.000011706 0.670717543 0.735497782 0.061771099 7.43E-06 1.40E-06 0.056686706 0.01336071 0.082286376 1.084672065 -0.329294163 ESGHSNWLGDPEEPLTGFSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESGHSNWLGDPEEPLTGFSWR 21 0 Q6DD88;F5H6I7;F5GWF8 Q6DD88 ATL3 Atlastin-3 0 54.368 0.070592 0 12971 10455 13669 14170 19920 12304 13772 12935 18588 FALSE TRUE 12357.88654 11520.37639 14295.73717 12745.60468 23394.04169 11877.90939 11670.82846 11802.34283 21470.53211 0.575574302 0.536566878 0.665830595 0.593632455 1.089588352 0.553219144 0.543574253 0.549699596 1 14.39007033 3.536985951 2.348705646 0.693471975 0.556159617 0.100180925 0.189967019 0.771517407 8.404108766 0.053791995 0.088980223 3443.387918 -3.536985951 -0.137312359 ESGLQAAHPNSIFLIDHAWTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESGLQAAHPNSIFLIDHAWTCR 22 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 217.94 7.06E-26 363740000 546230 499760 509810 568570 618080 529050 607650 537770 358780 FALSE TRUE 520410.7904 550686.1122 533185.2928 511416.2634 725872.9563 510728.8658 514941.8322 490680.0079 414417.77 1.255763696 1.328818772 1.286588876 1.234059687 1.751548821 1.23240098 1.242566969 1.184022606 1 18.66072634 1.12267813 1.339118267 1.010720973 1.343818096 0.361630874 0.150364814 0.45747718 1.649614305 0.134874869 0.041464399 13.26411048 -1.12267813 0.333097124 ESGS(ph)PYSVLVDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESGSPYSVLVDTK 13 0 Q9Y2D9;D6RF85 Q9Y2D9 ZNF652 Zinc finger protein 652 1 ES(0.1)GS(0.898)PYS(0.001)VLVDTK;ESGS(1)PYSVLVDTK 227.34 9.73E-12 66009000 176062 161654 165185 188763 132887 163663 169181 183904 159105 TRUE FALSE 167739.8982 178126.7264 172758.8956 169788.1846 156062.4507 157995.3093 143369.3312 167800.3908 183778.1908 0.912730164 0.969248449 0.940040246 0.923875591 0.849189178 0.859706522 0.780121573 0.913059325 1 17.48760604 2.842662985 3.736793661 0.858020048 0.941871235 0.129423831 0.058700155 0.27803209 7.070960266 0.017166462 0.018254465 696.0861372 -2.842662985 0.083851186 ESGVAGDPWKEETDT(ph)DLEVVLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESGVAGDPWKEETDTDLEVVLEK 23 1 Q1ED39 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 ESGVAGDPWKEET(0.167)DT(0.833)DLEVVLEK 130.87 5.32E-05 23841000 48241 51759 47912 56202 32518 56107 51834 62290 30001 TRUE FALSE 45960.74353 57033.30095 50108.81259 50552.46818 38189.1289 54164.00052 43925.7713 56835.55738 34653.40186 1.326298172 1.645821128 1.445999813 1.458802469 1.102031167 1.563021164 1.26757458 1.640114804 1 15.08070937 -2.099779623 2.448830908 0.246129365 1.429426424 0.393955953 0.168067635 2469627.753 933832.8077 10395201.75 0.037052279 0.007947314 2.099779623 1.183297059 ESHATLVFHNLLGEIDQQYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESHATLVFHNLLGEIDQQYSR 21 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 310.17 9.54E-67 420690000 440940 396440 467450 517900 523140 442500 515480 526960 242910 FALSE TRUE 420097.6401 436837.6867 488883.0449 465839.7081 614375.4504 427176.114 436834.0586 480816.5888 280579.2422 1.497251318 1.556913773 1.74240632 1.660278588 2.189668222 1.522479392 1.556900843 1.713657023 1 18.09804875 -1.170464279 10.12210235 0.999999997 1.659784298 0.533192308 0.199148979 9.74E-09 1.13E-09 0.191198741 0.045065975 0.06753606 1.170464279 0.6597843 ESHT(ph)PVSIQEEIVGDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.124)HT(0.875)PVSIQEEIVGDFK;ES(0.136)HT(0.86)PVS(0.004)IQEEIVGDFK 189.11 1.37E-09 167367000 411910 434150 379680 464530 255481 423430 376360 428070 191151 TRUE FALSE 392439.8306 478390.3786 397088.7036 417834.5619 300036.8055 408766.5129 318939.3697 390585.9215 220793.7208 1.777404852 2.166684708 1.798460129 1.892420492 1.358900989 1.851350262 1.444512862 1.769008285 1 17.75233962 -1.41732889 0.136381569 1.63E-08 2.240977868 0.605715973 0.205433338 23.08657754 0.555648763 9.519275338 1.64057819 0.038253494 1.41732889 2.240977852 ESIESEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 185.81 6.80E-05 8972400000 8042763 5958011 6823488 7677405 7981658 7151712 8952283 8017830 8543404 FALSE TRUE 7662597.532 6565139.095 7136351.674 6905657.663 9373656.628 6904046.42 7586447.808 7315746.3 9868271.459 0.776488321 0.665277513 0.723161265 0.699783918 0.949878271 0.699620643 0.768771698 0.741340196 1 23.23436597 -5 0.249355275 2.515791126 0.725651458 0.499610423 0.077553271 146.4628659 1.452016808 113.1375093 0.10519394 1.00E-05 5 -1.790139668 ESIWLPFMETELHCDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESIWLPFMETELHCDEK 17 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ;; 263.71 2.03E-27 124018000 385964 397894 376010 450612 262318 428169 426008 458253 221762 FALSE TRUE 367720.2466 438439.851 393250.4304 405315.6257 308066.1761 413341.4002 361012.6554 418125.938 256151.7184 1.435556431 1.711641264 1.535224643 1.582326397 1.202670738 1.61365851 1.409370422 1.632337041 1 17.96663904 -2.789455106 0.349400031 1.75E-17 1.540939754 0.547970344 0.144929176 54.9294266 1.883562352 41.26091571 0.103776004 0.001623846 2.789455106 1.540939754 ESKEETPGTEWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESKEETPGTEWEK 13 1 P09497-2;P09497;D6RJD1 P09497-2 CLTB Clathrin light chain B 0 ;; 172.09 2.19E-05 763960000 745340 581700 639780 718190 396885 724110 850710 836710 463634 FALSE TRUE 710109.2553 640975.8913 669114.5458 645996.1767 466101.6183 699033.8891 720918.5651 763443.2367 535531.9928 1.325988484 1.19689561 1.249438978 1.20627 0.870352518 1.30530743 1.346172731 1.425579138 1 19.03061324 ESKGS(ph)PVFLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.053)KGS(0.947)PVFLPR;ES(0.048)KGS(0.952)PVFLPR;ES(0.129)KGS(0.871)PVFLPR;ES(0.005)KGS(0.995)PVFLPR;ES(0.007)KGS(0.993)PVFLPR;ES(0.033)KGS(0.967)PVFLPR;ES(0.332)KGS(0.668)PVFLPR;ES(0.037)KGS(0.963)PVFLPR 134.88 7.97E-05 6849549000 7568320 6166280 6830910 7697700 5952880 7701960 9161490 8462870 7108060 TRUE FALSE 7210580.513 6794630.942 7144113.98 6923912.571 6991060.387 7435239.194 7763736.438 7721816.238 8210341.642 0.878231483 0.827569819 0.870136018 0.843316012 0.851494456 0.905594373 0.945604553 0.940498773 1 22.96901082 1.718292626 1.052267631 0.985361612 0.850442583 0.879612063 0.018567195 0.14695452 0.304487826 0.015163157 0.006011618 52.27482963 -1.718292626 -0.134919028 ESKKEDLVFIFWAPESAPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESKKEDLVFIFWAPESAPLK 20 2 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 84.249 0.0015841 689870000 1697500 822770 2065700 1280200 1170800 1976000 2761300 1967100 1421200 FALSE TRUE 1617262.539 906611.1984 2160414.388 1151511.864 1374987.149 1907570.625 2340012.97 1794850.296 1641592.438 0.985179087 0.552275448 1.316047966 0.701460263 0.837593496 1.162024496 1.425453064 1.093359262 1 20.64666456 2.179592192 4.893007089 1.235446161 0.855117644 0.274280427 0.225647671 0.200579731 9.688651658 0.080882281 0.059740784 151.2140663 -2.179592192 -0.380328517 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLASPK 38 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLS(0.073)LAS(0.927)PK 189.5 2.28E-23 78868000 26247 19632 21666 26959 18174 21489 26647 21490 7684.7 TRUE FALSE 25006.35633 21632.52312 22659.40753 24249.0301 21343.53985 20744.83054 22581.51074 19608.22167 8876.404028 2.817171937 2.437081847 2.552768831 2.731852902 2.404525501 2.337075969 2.543993116 2.209027621 1 13.11575962 -1.362108538 0.333305382 2.71E-19 2.652364339 0.93243164 0.131245624 4.597092696 0.329027487 4.111598732 0.110836154 0.043440165 1.362108538 2.652364339 ESLCDS(ph)PHQNLSRPLLENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 285.6 2.96E-40 576080000 592811 539014 657449 670146 464279 655456 757557 766673 529038 TRUE FALSE 564789.9989 593940.1394 687593.687 602781.6509 545249.1106 632757.3944 641977.7662 699539.0477 611078.5111 0.924251121 0.971953896 1.125213331 0.986422595 0.892273416 1.035476429 1.050565115 1.144761328 1 19.22099822 1.891664522 3.194624234 1.071546923 0.980159993 0.231109476 0.069696502 0.361828289 6.424935964 0.035827013 0.019260579 77.92279509 -1.891664522 -0.09138693 ESLIDGIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESLIDGIKR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 132.01 0.00050837 861770000 1847730 1563740 1705120 1884740 1428540 1802980 2131800 2008850 1605340 FALSE TRUE 1760391.465 1723086.884 1783301.439 1695282.354 1677676.924 1740542.351 1806554.757 1832944.444 1854287.928 0.949362522 0.929244514 0.961717655 0.914249793 0.90475535 0.938658082 0.974257951 0.98848966 1 20.82243385 1.621983496 2.614438942 0.992736394 0.932764162 0.727814492 0.01610792 0.132918937 2.082318413 0.011293612 0.004478287 41.87776505 -1.621983496 -0.059972232 ESLKEEDES(ph)DDDNM ddPTM_SK-BR-3_Trastuzumab_2h_R1 26 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;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM;ESLKEEDES(1)DDDNM 207.21 3.46E-08 60325557000 60081970 51149600 51755220 58699660 33323840 60189270 62280280 63505270 36620610 TRUE FALSE 57242014.35 56361802.39 54128248.03 52799058.65 39135507.15 58104900.49 52778279.43 57944411.9 42299547.17 1.353253597 1.332444581 1.279641312 1.248218059 0.925199199 1.373653015 1.247726819 1.369858918 1 25.33413888 -2.271058201 2.096722382 2.22E-05 1.270185636 0.29332612 0.129747097 3135019.518 351370.6734 14924779.29 0.032786129 0.005357249 2.271058201 1.270163435 ESLKELSLAGNELGDEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESLKELSLAGNELGDEGAR 19 1 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 253.11 6.59E-31 468970000 771240 470550 774630 668550 733140 725780 1005330 807430 877650 FALSE TRUE 734785.0137 518499.58 810147.5517 601346.0838 860999.3839 700646.0566 851948.4443 736727.1487 1013751.48 0.724817698 0.511466163 0.799157948 0.593188859 0.849319978 0.691141834 0.840391813 0.726733488 1 19.95127259 0.325934751 0.199899851 1.140206806 0.569258831 0.489168295 0.097957135 5.234924266 0.490762331 0.855932507 0.325430853 2.118042892 -0.325934751 -0.570947975 ESLLGDMEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESLLGDMEWR 10 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 104.89 0.0060998 74916000 208560 206390 190376 233960 263120 179696 234930 210840 266130 FALSE TRUE 198701.7821 227421.3756 199104.9279 210441.8963 309008.0447 173473.0825 199087.1137 192377.7319 307400.0812 0.646394696 0.739822107 0.647706166 0.684586339 1.005230849 0.564323476 0.647648214 0.625821994 1 18.22975802 -1.468658381 3.201697872 1.006053507 0.694444065 0.393899475 0.118822065 44060674.96 56836889.81 2396252.537 0.02680843 0.033989253 1.468658381 -0.311609442 ESLLVSVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESLLVSVQR 9 0 J3QRZ1;A6NIZ0;Q9GZM8-3;Q9GZM8;Q9GZM8-2 J3QRZ1 NDEL1 Nuclear distribution protein nudE-like 1 0 ;;; 98.033 0.0062881 987140000 473747 438251 526943 441491 1708740 228505 534041 247288 1578390 FALSE TRUE 451353.9182 482909.2752 551103.8578 397111.4859 2006743.715 220591.8146 452563.2371 225634.1518 1823158.66 0.247566999 0.264875069 0.302279703 0.2178151 1.100696148 0.120994305 0.248230309 0.12376002 1 20.79800869 -1.387776711 3.46695127 1.005096832 0.321979732 0.360291469 0.281180249 358119694.3 516057887.6 18336370.92 0.063756821 0.040947113 1.387776711 -0.6831171 ESLWPFLIDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESLWPFLIDKR 11 1 Q9NZL9;Q9NZL9-2;Q9NZL9-4 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 209.19 2.73E-08 262630000 479360 380710 395020 429510 444640 419280 600140 514660 509350 FALSE TRUE 456701.6028 419504.7818 413132.0577 386334.8388 522185.0752 404760.2285 508577.6207 469593.642 588337.3966 0.776257986 0.713034365 0.702202614 0.656655248 0.88756057 0.687972974 0.864431912 0.79817065 1 19.16628422 0.702242425 0.50659623 1.009213401 0.724561018 0.589434365 0.067936615 0.9326098 0.507478352 0.0830298 0.032341148 5.037817433 -0.702242425 -0.284652382 ESNCYDPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ESNCYDPER 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 129.63 0.0008934 2347070000 4080890 3507610 3638590 4302630 4009970 3839760 4556140 4184820 4665010 FALSE TRUE 3887994.417 3865039.447 3805422.951 3870121.458 4709307.498 3706788.148 3861017.164 3818374.976 5388435.925 0.72154415 0.717284106 0.706220321 0.718227239 0.873965574 0.687915417 0.71653764 0.708623992 1 22.36143514 -1.322050956 4.5349729 1.00022774 0.729653508 0.727104695 0.051726573 0.000112515 1.68E-05 0.047312841 0.011142421 0.047637509 1.322050956 -0.270574232 ESNEEEQVWHFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESNEEEQVWHFLGK 14 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4;H0YAK2 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;;; 208.39 8.11E-09 444338000 728460 772750 571839 716780 475464 541056 579451 659310 392819 FALSE TRUE 694027.1395 851494.1035 598058.3838 644727.9126 558384.7711 522319.0951 491045.1076 601577.3212 453735.3643 1.529585732 1.876631558 1.31807752 1.420933794 1.230639741 1.151153593 1.082227982 1.325833004 1 18.79149158 3.217450917 1.197312032 1.144281561 1.697397472 0.665874889 0.144069299 0.228648103 0.696014894 0.05178589 0.077985895 1649.874524 -3.217450917 0.553115911 KRCPS(ph)QSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRCPSQSSSR 10 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 KRCPS(0.953)QS(0.041)S(0.002)S(0.003)R 70.622 0.042079 9180600 14851 10977 13169 9775.4 10977 12988 18058 19603 25471 TRUE FALSE 14149.02266 12095.56878 13772.81168 8792.75822 12891.38532 12538.2223 15302.92044 17886.4574 29420.91259 0.480917192 0.411121468 0.468129995 0.298860825 0.438170818 0.426167008 0.520137518 0.607950462 1 14.84455438 0.750434614 1.05895001 0.999702889 0.419603514 0.930009929 0.049769768 0.201492777 0.408393415 0.045132673 0.014373899 5.629043616 -0.750434614 -0.580099374 ESNRLS(ph)APSYLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESNRLSAPSYLAR 13 1 H0YJH0;Q9H4B6 H0YJH0 SAV1 Protein salvador homolog 1 1 ESNRLS(1)APSYLAR;ES(0.034)NRLS(0.927)APS(0.039)YLAR;ESNRLS(1)APSYLAR;ES(0.003)NRLS(0.937)APS(0.061)YLAR 142.94 2.46E-05 598851000 599650 507320 526100 619670 601270 512950 632280 623870 626970 TRUE FALSE 571305.7329 559016.4848 550222.2054 557379.5943 706131.2976 495186.4129 535814.0734 569240.6355 724197.3055 0.788881329 0.771911854 0.759768369 0.769651572 0.975053749 0.683772791 0.739873056 0.786029762 1 19.46602328 -0.702619026 3.447908505 1.00000665 0.780503903 0.453914866 0.074221657 1323422.957 2671438.071 136.4675153 0.017253456 0.198326603 0.702619026 -0.219502747 ESNYFGLS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESNYFGLSPEER 12 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 ESNYFGLS(1)PEER;ESNYFGLS(1)PEER;ESNYFGLS(1)PEER 212.35 2.24E-08 221241000 724510 699516 734502 765392 722972 718476 847251 755258 875419 TRUE FALSE 690263.8481 770797.4757 768179.6432 688453.342 849058.0879 693594.996 717987.2991 689123.6056 1011174.507 0.68263573 0.762279379 0.759690476 0.680845232 0.839675132 0.685930065 0.710052809 0.681508088 1 19.94760057 -1.322886163 4.966778876 1.000118662 0.72622773 0.743488554 0.050700646 6.06E-05 8.27E-06 0.044686533 0.010528173 0.047545984 1.322886163 -0.273890931 ESPEIEPLPFTLAHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESPEIEPLPFTLAHER 16 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ; 108.63 0.0010348 32796000 57076 52077 49534 55708 52744 54350 61814 63355 57017 FALSE TRUE 54378.13059 57383.70551 51805.1829 50108.126 61942.5369 52467.84587 52383.13901 57807.30033 65858.90516 0.825676201 0.871312776 0.786608626 0.760840556 0.94053396 0.796670484 0.795384297 0.87774463 1 16.00709091 0.926806669 5.232184594 0.999977677 0.827546505 0.546494711 0.05034687 0.338986525 22.39382313 0.045859645 0.011575829 8.449026438 -0.926806669 -0.172431172 ESPFSTSAS(ph)PLLSGSQHFDVPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESPFSTSASPLLSGSQHFDVPPRR 24 1 O14980 O14980 XPO1 Exportin-1 1 ES(0.008)PFS(0.036)T(0.031)S(0.12)AS(0.795)PLLS(0.008)GS(0.003)QHFDVPPRR 58.349 0.03819 40635000 12899 10952 11683 13346 15180 15144 16564 16812 17912 TRUE FALSE 12289.28983 12068.02125 12218.67711 12004.43472 17827.38719 14619.55948 14036.85758 15339.85215 20689.70148 0.593981013 0.583286388 0.590568072 0.580213046 0.861655119 0.70661046 0.678446598 0.741424528 1 14.33662521 -5 0.10153118 2.14470022 0.41934827 0.732880267 0.070906363 92.77116972 0.638726242 22.20681096 1.124290277 1.00E-05 5 -1.72535195 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 360.47 9.28E-147 7264004000 2018723 2173812 2039103 2351181 1939273 2049509 2175919 2248795 2098375 TRUE FALSE 1923301.965 2395325.914 2132597.889 2114835.819 2277481.597 1978533.989 1843942.593 2051878.588 2423780.278 0.793513332 0.988260337 0.879864363 0.872536112 0.939640287 0.816300886 0.76077135 0.846561302 1 21.20882749 2.221114178 24.92278295 0.827212797 0.896620523 0.000774907 0.079235094 428.5593404 612206.5209 0.027463188 0.020329623 166.3850025 -2.221114178 0.069407726 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGRR 41 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR 230.11 5.61E-45 1948780000 326240 130517 386373 242393 412305 288056 550989 383777 633768 TRUE FALSE 310819.2817 143816.8307 404088.5842 218027.1951 484210.8615 278080.5485 466925.5084 350171.4514 732049.5046 0.424587791 0.196457794 0.551996254 0.297831217 0.661445515 0.37986577 0.637833241 0.47834395 1 19.48158169 -5 0.124421606 2.925478833 0.174898764 0.653345286 0.131585638 77.40113897 0.617020137 36.97448795 0.985753449 1.00E-05 5 -2.750580069 ESQAKDVIEEYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ESQAKDVIEEYFK 13 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;; 161.04 3.78E-05 650120000 1805080 829270 1962830 1323630 1524120 1779040 2800050 2195420 2034590 FALSE TRUE 1719757.446 913773.5558 2052827.697 1190576.198 1789926.045 1717431.399 2372850.946 2003177.386 2350103.826 0.731779348 0.388822632 0.873505108 0.506605787 0.761637008 0.730789585 1.009679198 0.85237825 1 21.16429306 2.091080182 1.303431843 0.966894117 0.608316256 0.48506073 0.140489587 0.330253014 1.054574443 0.087789869 0.044234599 123.3332517 -2.091080182 -0.35857786 ESQFLKEELVAAVEDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESQFLKEELVAAVEDVR 17 1 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6 P35221-2 CTNNA1 Catenin alpha-1 0 72.184 0.026386 15956000 43547 46310 48673 50491 35540 50554 48622 49632 38837 FALSE TRUE 41488.61961 51029.04165 50904.70519 45415.54875 41738.16475 48803.3023 41203.8209 45285.95896 44859.64361 0.924853973 1.137526684 1.134755007 1.012392099 0.930416771 1.087911057 0.918505311 1.009503316 1 15.45313054 3.010909574 24.8107626 0.985497399 1.062552644 0.182989045 0.073478791 324.0711163 737003.2015 0.02080512 0.024845271 1025.438395 -3.010909574 0.077055245 ESQLAHIKDEPPPLS(ph)PAPLT(ph)PATPSSLDPFFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 ES(0.001)QLAHIKDEPPPLS(0.999)PAPLT(1)PATPSSLDPFFSR;ES(0.001)QLAHIKDEPPPLS(0.999)PAPLT(1)PATPSSLDPFFSR 143.98 5.91E-09 110366000 118599 79763 127540 129387 104939 118203 145351 121363 113986 TRUE FALSE 112993.0603 87890.94038 133387.8352 116380.7729 123240.3284 114109.6005 123175.0354 110735.8123 131662.3667 0.858203169 0.66754793 1.013105252 0.883933472 0.936033063 0.866683497 0.935537151 0.841058953 1 17.00648351 3.738340577 24.99999998 0.918764954 0.762875551 0.479258249 0.070093096 14.35478532 1630966.129 0.016583643 0.027567619 5474.451055 -3.738340577 -0.155889402 ESQLAHIKDEPPPLS(ph)PAPLTPAT(ph)PSSLDPFFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 ES(0.074)QLAHIKDEPPPLS(0.926)PAPLT(0.003)PAT(0.927)PS(0.034)S(0.037)LDPFFSR 95.657 0.0025178 35545000 37041 28081 36112 34323 32662 38871 51261 43958 34680 TRUE FALSE 35290.14534 30942.48583 37767.77092 30872.78683 38358.24246 37524.88752 43440.19298 40108.80448 40057.99728 0.880976278 0.772442157 0.942827238 0.770702205 0.957567654 0.936763944 1.084432471 1.001268341 1 15.28980267 2.319310496 1.722314767 1.031801586 0.840287534 0.612749602 0.061304177 0.199706886 1.198630783 0.027135323 0.018335686 208.5981707 -2.319310496 -0.191514052 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ES(0.001)QLAHIKDEPPPLS(0.999)PAPLTPATPSSLDPFFSR;ESQLAHIKDEPPPLS(1)PAPLTPATPSSLDPFFSR;ESQLAHIKDEPPPLS(1)PAPLTPATPSSLDPFFSR;ESQLAHIKDEPPPLS(1)PAPLTPATPSSLDPFFSR;ES(0.037)QLAHIKDEPPPLS(0.94)PAPLT(0.023)PATPSSLDPFFSR 259.74 1.18E-59 4277513000 1871160 1207929 1686000 1787820 1486040 1698030 2005050 1759710 1422244 TRUE FALSE 1782713.975 1331018.338 1763304.768 1608104.937 1745204.906 1639226.795 1699142.797 1605620.464 1642798.336 1.08516909 0.810214078 1.073354367 0.978881523 1.062336665 0.997825941 1.034297856 0.977369181 1 20.64772396 ESQSHPGDFVLSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESQSHPGDFVLSVR 14 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;;; 161.08 4.65E-06 1045960000 713401 552722 621700 725969 788080 611109 816015 732183 826909 FALSE TRUE 679679.9486 609045.0002 650205.5599 652993.2169 925520.9025 589946.1421 691516.9246 668069.175 955141.8245 0.711601074 0.63764876 0.680742423 0.683661002 0.968987933 0.617652925 0.723993973 0.699445002 1 19.86535544 -4.999999965 0.304151299 3.463191393 0.695570784 0.46166381 0.096108028 245.8790683 2.254355563 387.1134528 0.088194052 1.00E-05 4.999999965 -2.767620609 ESQSVEEALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESQSVEEALKK 11 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 116.24 0.0016288 291000000 190470 157510 143290 161230 111410 174890 178710 183320 123850 FALSE TRUE 181466.8606 173560.4481 149859.9882 145022.8541 130839.8687 168833.5154 151444.5073 167267.529 143056.0255 1.268502043 1.213234098 1.047561525 1.01374866 0.914605787 1.180191571 1.058637738 1.169244905 1 17.12622074 3.815862582 3.837629096 1.057242095 1.248650535 0.503102619 0.077426342 0.173245078 4.899398758 0.019821163 0.037106385 6544.290684 -3.815862582 0.19140844 ESRPGLVTVTSSQST(ph)PAKAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESRPGLVTVTSSQSTPAKAPR 21 2 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ESRPGLVTVTSSQS(0.053)T(0.947)PAKAPR 114.74 0.0081149 220920000 123000 143190 138130 152900 98850 140370 157210 167410 134430 TRUE FALSE 117186.0338 157781.2238 144463.3971 137530.2015 116089.4087 135508.9517 133224.7271 152750.6929 155276.7178 0.754691594 1.016129308 0.930360966 0.885710385 0.747629202 0.872693303 0.857982633 0.983732108 1 17.244482 1.214779695 7.975525344 0.993236579 0.872258819 0.310010871 0.077416932 0.28060688 71.53086939 0.069424052 0.018678846 16.39757761 -1.214779695 -0.12097776 ESRPSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESRPSEER 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 143.7 0.00054464 318223000 309197 295160 275417 330460 298687 267860 298942 305979 300005 FALSE TRUE 294581.8706 325237.1396 288045.1419 297241.533 350777.9182 258583.941 253332.9075 279185.8567 346528.2432 0.850094837 0.938558822 0.831231357 0.857770005 1.012263575 0.746213176 0.731059913 0.805665518 1 18.40261342 2.207513179 24.999942 0.789255146 0.894301197 0.112152592 0.090100221 268.3110596 216047.192 0.03058971 0.022594313 161.2549961 -2.207513179 0.105046051 ESRPSEEREWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESRPSEEREWDR 12 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 112.42 0.00071734 92836000 38930 29910 36045 37379 36634 32082 42362 33555 40306 FALSE TRUE 37089.85605 32957.863 37697.6989 33621.5919 43022.958 30970.9923 35898.89887 30616.74631 46556.44863 0.796664203 0.707911879 0.809720243 0.722168312 0.924103089 0.665235283 0.771083275 0.657626327 1 15.50669339 -1.065391813 4.767385995 1.000005877 0.757282073 0.491454328 0.077742245 6.13E-06 1.20E-06 0.065728844 0.015491895 0.086021733 1.065391813 -0.242723804 ESRPSEEREWDREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESRPSEEREWDREK 14 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 56.514 0.054387 108210000 34105 18818 26765 27625 33354 27722 40594 28520 38784 FALSE TRUE 32492.92424 20735.57559 27992.20172 24848.08252 39170.92704 26761.98019 34400.63974 26022.63761 44798.42464 0.725313993 0.462863946 0.624847904 0.554664203 0.874381797 0.597386636 0.767898425 0.580882873 1 15.45116038 -5 0.179877902 2.464817001 0.569890321 0.464756087 0.117460916 109.5760899 1.054635606 57.22598789 0.334673437 1.00E-05 5 -1.894926679 ESRQES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESRQESDPEDDDVKKPALQSSVVATSK 27 3 Q9H307 Q9H307 PNN Pinin 1 ES(0.208)RQES(0.792)DPEDDDVKKPALQSSVVATSK 210.9 6.43E-25 232790000 270410 89402 304400 160740 173320 278080 433710 319600 231640 TRUE FALSE 257628.2552 98512.16544 318357.0411 144582.1098 203546.9531 268450.0199 367539.5739 291614.1297 267561.5481 0.962874737 0.368185063 1.189846012 0.540369537 0.760748151 1.003320626 1.373663654 1.089895509 1 18.02951127 2.092406874 3.617250829 1.195326506 0.737525593 0.353501266 0.23921848 0.205309644 5.227353125 0.092258367 0.063084665 123.7105888 -2.092406874 -0.457800913 ESRS(ph)PQQSAALPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESRSPQQSAALPR 13 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 ES(0.112)RS(0.888)PQQSAALPR;ES(0.078)RS(0.922)PQQSAALPR 184.22 5.87E-06 1012940000 873890 778070 751580 916700 637380 880810 905620 890490 711470 TRUE FALSE 832582.9516 857356.2176 786040.6864 824551.5744 748538.8702 850307.3288 767451.0361 812513.9748 821801.1339 1.013119741 1.043264827 0.956485278 1.003346844 0.910851591 1.034687461 0.93386466 0.988699019 1 19.6484298 3.739141039 24.99995639 0.972488301 1.028192285 0.265114519 0.036273646 52.40440494 2257121.551 0.008235175 0.01379296 5484.550498 -3.739141039 0.055703984 ESS(ph)PEKEAEEGCPEKESEEGCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.028)S(0.972)PEKEAEEGCPEKESEEGCPK;ES(0.139)S(0.811)PEKEAEEGCPEKES(0.05)EEGCPK;ES(0.017)S(0.983)PEKEAEEGCPEKESEEGCPK;ES(0.138)S(0.862)PEKEAEEGCPEKESEEGCPK 339.02 3.48E-87 1514230000 2602752 2164907 1984146 2507488 772251 2767297 2383476 2765218 609473 TRUE FALSE 2479725.071 2385513.485 2075121.057 2255430.542 906931.3299 2671464.811 2019832.961 2523080.853 703986.9601 3.522401993 3.388576238 2.947669736 3.203795908 1.288278592 3.794764623 2.869134054 3.58398805 1 19.42518918 3.59403779 1.763301982 2.742985362 3.489092946 0.122119881 0.892690944 0.784951259 4.818797864 0.244903504 0.464306841 3926.791032 -3.59403779 0.746107584 ESS(ph)PKKEETVASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESSPKKEETVASK 13 2 J3QQY0 J3QQY0 MSL1 1 ES(0.441)S(0.559)PKKEETVASK 116.6 0.00029853 268060000 265380 314890 208370 344350 79635 301210 232160 310690 76945 TRUE FALSE 252836.0133 346977.649 217923.9706 309735.2838 93523.31879 290779.0222 196739.7281 283484.3365 88877.23762 2.844778034 3.904010276 2.451966065 3.484978742 1.052275265 3.271692842 2.213612094 3.189616871 1 16.43952636 ESS(ph)PKKEETVASKA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESSPKKEETVASKA 14 3 J3QQY0 J3QQY0 MSL1 1 ES(0.121)S(0.879)PKKEETVASKA;ES(0.448)S(0.552)PKKEETVASKA 113.47 0.0029478 732810000 780050 652940 706670 766830 263132 900360 808870 957910 296815 TRUE FALSE 743178.5824 719475.3283 739071.5185 689746.7915 309022.1375 869180.3074 685462.0256 874030.3222 342843.5543 2.167690112 2.09855288 2.1557107 2.011841211 0.901350291 2.535209709 1.999343482 2.549356146 1 18.38719087 -1.741163343 2.855153698 0.80871669 2.048841054 0.349061532 0.451619478 35803792.47 37292995.75 49259554.64 0.103411952 0.01814833 1.741163343 1.240124364 ESS(ph)PLS(ph)SRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESSPLSSRK 9 1 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 2 ESS(0.981)PLS(0.615)S(0.404)RK;ESS(0.998)PLS(0.613)S(0.389)RK 72.365 0.031384 2316844000 625418 545291 555998 630759 748530 500118 641776 518843 721710 TRUE FALSE 595855.7306 600856.7728 581491.0583 567353.907 879073.395 482798.7883 543861.2842 473410.3564 833629.1008 0.714773189 0.72077231 0.697541698 0.680583135 1.054513805 0.579152992 0.65240199 0.567890871 1 19.66904612 ESSANNS(ph)VSPSESLR ddPTM_SK-BR-3_Trastuzumab_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(0.791)VS(0.209)PSESLR 409.35 4.90E-133 1147600000 494350 419160 466650 520830 472990 463500 568340 494990 558340 TRUE FALSE 470983.0552 461872.8805 488046.3641 468475.1789 555479.3062 447448.8788 481629.2947 451646.0515 644924.5156 0.730291753 0.716165798 0.756749592 0.726403118 0.861309026 0.693800387 0.746799483 0.700308394 1 19.29877079 -2.051697216 2.52938508 1.350722314 0.740464571 0.751987513 0.046655263 6405317.187 2711973.176 12972611.79 0.010270688 0.008877747 2.051697216 -0.610257743 ESSANNSVS(ph)PSESLR ddPTM_SK-BR-3_Trastuzumab_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 ESSANNS(0.001)VS(0.999)PSESLR;ESSANNS(0.007)VS(0.993)PSESLR;ESSANNS(0.001)VS(0.999)PSESLR;ESSANNS(0.005)VS(0.943)PS(0.051)ESLR;ESSANNS(0.011)VS(0.969)PS(0.02)ESLR;ESSANNS(0.057)VS(0.943)PSESLR;ESSANNSVS(1)PSESLR 458.49 1.61E-198 2747151000 2626008 2331719 2441023 2772896 2591450 2420934 3009908 2578598 2906068 TRUE FALSE 2501881.806 2569323.817 2552946.319 2494159.226 3043398.06 2337096.449 2550691.254 2352802.289 3356726.183 0.745333897 0.7654255 0.760546491 0.743033268 0.906656633 0.696242804 0.759874686 0.70092172 1 21.67862343 -2.14717065 2.511429389 1.561148418 0.760426016 0.634127822 0.057348093 3577009.956 977493.8525 11488784.39 0.012593183 0.00712573 2.14717065 -0.800722402 ESSPSHPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESSPSHPTR 9 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 90.15 0.011625 21065000 20868 16141 19840 21361 23008 19428 25429 22210 24371 FALSE TRUE 19881.611 17785.78625 20749.68362 19213.7517 27020.58792 18755.20349 21549.33901 20265.17466 28150.33021 0.706265641 0.63181448 0.737102672 0.682540899 0.95986753 0.666251634 0.76550928 0.719891188 1 14.78086423 -5 0.162598756 2.012031588 0.655941715 0.479722768 0.087922316 109.0043113 1.00921833 35.6802458 0.333082816 1.00E-05 5 -1.356089872 ESSSASLKSS(ph)PIAQPASSFQVETASQGHSISHHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESSSASLKSSPIAQPASSFQVETASQGHSISHHK 34 1 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 ES(0.004)S(0.004)S(0.004)AS(0.053)LKS(0.23)S(0.703)PIAQPASSFQVETASQGHSISHHK 142.26 1.41E-10 61596000 71705 38742 68601 79311 80596 63634 120930 78089 8132.7 TRUE FALSE 68315.64676 42689.85385 71746.42371 71338.5076 94651.91688 61430.33862 102479.9075 71251.11318 9393.87758 7.272358637 4.5444337 7.63757278 7.594149167 10.07591552 6.539401658 10.90922323 7.584845829 1 13.19750508 3.571448126 6.634957069 8.023372385 5.913100282 0 2.752305742 0.511612343 30.49868119 0.650097719 1.009149343 3727.761561 -3.571448126 -2.110272103 ESSSCGKDT(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESSSCGKDTPSK 12 1 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 1 ESS(0.003)S(0.003)CGKDT(0.99)PS(0.003)K 81.651 0.0276 232350000 694340 806640 610850 828980 324650 754320 662970 863680 331680 TRUE FALSE 661519.9242 888837.5331 638858.0767 745649.3554 381268.8572 728197.7093 561821.7502 788051.6005 383115.2404 1.726686528 2.320026559 1.667535011 1.946279544 0.995180606 1.900727594 1.46645628 2.056957065 1 18.54741889 2.911291675 24.99999454 1.535831517 1.948195537 0.239590939 0.373429739 96.64552166 27234.03323 0.1027184 0.108949342 815.2516291 -2.911291675 0.412364021 ESSTSEGADQKMS(ph)S(ph)PEDDSDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 2 ES(0.004)S(0.004)T(0.004)S(0.005)EGADQKMS(0.984)S(0.999)PEDDSDTKR;ES(0.001)S(0.002)T(0.002)S(0.002)EGADQKMS(0.995)S(0.999)PEDDSDTKR;ESSTSEGADQKMS(1)S(0.998)PEDDS(0.002)DTKR;ESSTSEGADQKMS(0.996)S(0.997)PEDDS(0.006)DTKR;ES(0.006)S(0.006)T(0.006)S(0.005)EGADQKMS(0.983)S(0.983)PEDDS(0.008)DT(0.003)KR;ESSTSEGADQKMS(1)S(0.999)PEDDS(0.001)DTKR 139.16 4.46E-07 1801020000 1701730 1395780 1484260 1748140 671588 1807820 1870120 2043080 847570 TRUE FALSE 1621292.595 1538011.569 1552314.789 1572413.646 788712.7346 1745214.74 1584798.847 1864177.084 979006.8268 1.656058519 1.570991669 1.585601598 1.606131441 0.805625367 1.782637968 1.618782222 1.904151261 1 19.90095939 2.908387626 24.66127399 1.473315547 1.603800149 0.058732587 0.329384258 222.1483831 59789.06261 0.09628189 0.102122396 809.8183734 -2.908387626 0.130484602 ESSTVFELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;;;; 185.77 2.27E-06 2479170000 2298770 1673460 1903720 2060300 1939980 2072820 2732970 2426100 2178570 FALSE TRUE 2190111.698 1843987.477 1991007.445 1853194.73 2278311.898 2001037.724 2316005.232 2213657.822 2516411.509 0.870331299 0.732784551 0.791209005 0.736443433 0.90538129 0.79519495 0.920360292 0.879688324 1 21.26293643 1.368730991 0.654352206 0.993925577 0.787735914 0.576632812 0.055240067 0.441220279 0.439285637 0.049072641 0.02242415 23.37388975 -1.368730991 -0.206189663 ESSYACYYDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESSYACYYDEKR 12 1 Q99538-3;Q99538-2;Q99538 Q99538-3 LGMN Legumain 0 ; 131.69 0.00031141 252760000 142105 119901 124688 146652 111442 137935 153559 168877 120353 FALSE TRUE 135387.9783 132119.0482 130405.0681 131910.2623 130877.4495 133158.2764 130130.7542 154089.2346 139016.7286 0.973897024 0.950382372 0.938053064 0.948880496 0.941451082 0.957857934 0.93607982 1.108422247 1 17.08489897 1.252669539 24.9999998 1.054211132 0.95025117 0.711163887 0.027736162 93.03310626 164849.6088 0.01609082 0.005812895 17.89243872 -1.252669539 -0.103959962 ESTAEKDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESTAEKDEL 9 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 106.6 0.023729 242290000 468460 464840 410800 520430 273050 506350 435060 467910 259030 FALSE TRUE 446316.8242 512207.7245 429635.5863 468115.3876 320669.8335 488814.9725 368683.6066 426937.3199 299199.0495 1.491705355 1.711929652 1.435952377 1.564561747 1.07176087 1.633745072 1.23223522 1.426934078 1 18.19074607 -2.35725191 0.089666292 9.15E-10 1.953656563 0.441974022 0.173450985 85.4387169 0.977437222 21.92729995 4.547789505 0.004392867 2.35725191 1.953656562 ESTLHLVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 148.52 8.98E-05 734120000 1198860 904270 826600 1206780 1061380 942980 1197830 1165500 1069610 FALSE TRUE 1142192.264 996416.1411 864500.4276 1085472.182 1246484.336 910324.3662 1015079.034 1063442.641 1235479.656 0.924492976 0.806501456 0.699728582 0.878583614 1.008907213 0.73681858 0.821607243 0.860752855 1 20.23663982 0.869922481 6.090240655 0.999999102 0.838341914 0.246243692 0.087527469 3.61153405 168.5929944 0.081578478 0.020507101 7.411779334 -0.869922481 -0.161657188 ESTQLS(ph)PADLTEGKPTDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.004)T(0.03)QLS(0.967)PADLTEGKPTDPSK;ES(0.004)T(0.029)QLS(0.967)PADLTEGKPTDPSK 165.87 9.71E-12 188103000 663460 784870 524270 781710 316970 711450 620420 709100 321450 TRUE FALSE 632099.5607 864849.1453 548308.2981 703131.0256 372249.4676 686812.3081 525763.5342 647007.4448 371298.8243 1.702401191 2.32925366 1.476730499 1.893706577 1.002560319 1.849756216 1.416011848 1.742551828 1 18.50222122 2.316769235 0.072509653 2.06E-14 3.240164979 0.312167468 0.336002884 32.51321224 1.343526716 25.45052844 32.64374817 207.3811291 -2.316769235 3.240164979 ESTSSKS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 ESTSSKSPPR 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ESTSS(0.005)KS(0.994)PPR;EST(0.001)S(0.004)S(0.059)KS(0.936)PPR;EST(0.003)S(0.004)S(0.043)KS(0.95)PPR;ESTSS(0.001)KS(0.999)PPR;ESTSS(0.002)KS(0.998)PPR;ES(0.047)T(0.027)S(0.027)S(0.037)KS(0.862)PPR;ESTSS(0.003)KS(0.997)PPR;ESTSS(0.001)KS(0.999)PPR;EST(0.002)S(0.002)S(0.015)KS(0.981)PPR;ES(0.001)T(0.001)S(0.001)S(0.033)KS(0.964)PPR;ESTSS(0.001)KS(0.999)PPR 126.51 0.0002306 26316940000 5030220 4165330 4333420 4885730 3226220 4977070 5351990 5026470 3895090 TRUE FALSE 4792451.47 4589781.863 4532111.593 4394607.138 3788871.747 4804712.818 4535445.629 4586325.64 4499120.664 1.065197364 1.020150871 1.007332751 0.976770233 0.842136059 1.06792264 1.008073792 1.019382671 1 22.10121163 4.075566237 1.598286241 0.98810796 1.0609236 0.159608811 0.057347568 0.786905916 3.696624151 0.016249737 0.059586294 11900.52819 -4.075566237 0.07281564 ESTSSKS(ph)PPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ES(0.003)T(0.003)S(0.008)S(0.198)KS(0.788)PPRK;ES(0.002)T(0.001)S(0.025)S(0.156)KS(0.816)PPRK;EST(0.001)S(0.064)S(0.064)KS(0.87)PPRK;ES(0.008)T(0.029)S(0.025)S(0.058)KS(0.879)PPRK;ES(0.001)T(0.001)S(0.001)S(0.009)KS(0.988)PPRK;ESTSS(0.001)KS(0.999)PPRK;ES(0.03)T(0.03)S(0.026)S(0.168)KS(0.746)PPRK;ES(0.032)T(0.032)S(0.019)S(0.016)KS(0.9)PPRK 104.9 0.0013239 14720470000 3374480 3016190 3071180 3651630 1954872 3614850 3724250 3839560 2270666 TRUE FALSE 3214975.018 3323543.19 3211996.641 3284561.215 2295801.058 3489666.838 3156047.262 3503347.772 2622789.286 1.225784715 1.26717888 1.224649139 1.252316086 0.87532806 1.330517421 1.203317124 1.335733599 1 21.32267048 ESVDHLTIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESVDHLTIPSR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 178.81 7.38E-06 1006400000 1138491 761764 982119 1096160 1143440 929682 1250660 1090613 1195820 FALSE TRUE 1084676.787 839388.6177 1027150.128 985971.9142 1342855.574 897486.8792 1059848.847 995113.144 1381261.658 0.785279733 0.607697037 0.743631825 0.713819795 0.972194925 0.649758772 0.767304906 0.720437824 1 20.39755521 -5 0.267358444 2.756638771 0.718931226 0.399834029 0.096977595 201.3363812 1.96106014 195.1274942 0.113824826 1.00E-05 5 -2.037707545 ESVFTNERFPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESVFTNERFPLR 12 1 O43709 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ; 111.63 0.0002979 0 129838 98426 111035 112629 147201 112956 157986 126070 173142 FALSE TRUE 123700.8151 108455.7213 116126.0646 101307.3189 172872.8078 109044.3054 133882.3341 115030.6425 199991.9771 0.618528887 0.542300361 0.580653616 0.506556915 0.864398714 0.545243399 0.669438525 0.575176285 1 17.6095826 -5 0.26805513 3.636752608 0.581968982 0.594538303 0.10025166 134.6425301 1.310328665 196.3331621 0.112489817 1.00E-05 5 -3.054783627 ESVFTVEGGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ESVFTVEGGHR 11 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 183.33 5.39E-06 1546060000 1462850 1370120 1288210 1329450 1405010 1071920 1267070 1400490 1197850 FALSE TRUE 1393703.98 1509736.786 1347275.703 1195811.16 1650043.299 1034799.142 1073755.2 1277855.671 1383606.46 1.007297971 1.09116055 0.973741986 0.86427116 1.192566923 0.747899906 0.776055353 0.923568737 1 20.40000222 2.222016228 24.99992237 0.832618596 1.023327602 0.342663989 0.109505519 223.9757405 338443.4997 0.03810878 0.028224321 166.7309511 -2.222016228 0.190709007 ESVPEFPLS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 243.3 2.57E-16 1374173000 1309785 1477122 1044507 1654669 687283 1372590 1213813 1441105 714901 TRUE FALSE 1247874.059 1627642.411 1092398.679 1488338.528 807144.9376 1325056.864 1028623.534 1314914.206 825764.1959 1.511174818 1.97107409 1.322894217 1.802377163 0.977452088 1.604643154 1.24566255 1.592360401 1 19.65537034 2.763042601 24.9978965 1.321193036 1.671168174 0.315239763 0.265613645 897.8061279 916724.3889 0.07253372 0.076900135 579.4855367 -2.763042601 0.349975138 ESVPEFPLS(ph)PPKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESVPEFPLSPPKKK 14 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 ESVPEFPLS(1)PPKKK;ESVPEFPLS(1)PPKKK 84.14 0.0043055 1442850000 2398110 1659530 2213630 2347330 1467080 2556680 2990150 2729680 1603670 TRUE FALSE 2284756.093 1828637.994 2315127.125 2111371.929 1722938.288 2468141.531 2533947.7 2490654.748 1852358.953 1.233430534 0.987194189 1.249826402 1.139828717 0.930131973 1.33243156 1.367957164 1.34458537 1 20.82093226 2.201708974 24.99890132 1.301502374 1.110878633 0.201027712 0.141916858 198.5667522 134699.7677 0.04834927 0.035709224 159.1142125 -2.201708974 -0.190623741 ESVQVPDDQDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ESVQVPDDQDFR 12 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5H1Z6;F5GWK5;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ;;;;; 311.77 6.05E-46 2451772000 2273622 2078072 1988750 2280620 2253845 2093707 2550980 2331420 2455570 FALSE TRUE 2166152.394 2289829.899 2079936.155 2051367.745 2646914.854 2021201.402 2161781.149 2127268.505 2836367.254 0.763706601 0.807310794 0.733309888 0.723237705 0.93320597 0.712602149 0.762165459 0.749997555 1 21.43561291 -1.6954111 2.45961774 1.04023182 0.77416734 0.564416376 0.062612441 7697156.042 5804152.492 1917707.801 0.015615668 0.020164567 1.6954111 -0.266064481 ESVS(ph)PEDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESVSPEDSEK 10 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 ESVS(1)PEDSEK 157.47 9.56E-06 80548000 254630 259580 217250 275970 155880 276810 260900 266820 168020 TRUE FALSE 242594.1445 286031.4971 227211.1274 248228.9713 183065.4226 267224.0003 221094.9132 243455.8263 194075.6835 1.249997631 1.473814195 1.17073465 1.279031803 0.94326821 1.37690614 1.139220068 1.254437557 1 17.56625984 7.999999805 0.027896074 1.28E-07 2.971474767 0.241821546 0.138465988 1895.007855 4.059557834 142.2581446 324.5948045 99999955.1 -7.999999805 2.971474639 ESVSTEDLSPPS(ph)PPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 ESVSTEDLSPPS(1)PPLPK 168.69 2.17E-09 31018000 68336 62788 61108 70575 47167 67500 71850 69163 62397 TRUE FALSE 65105.89271 69186.16858 63909.86224 63480.66692 55392.90987 65162.45807 60887.96288 63106.72106 72073.20808 0.903330023 0.959942958 0.886735362 0.880780371 0.76856451 0.904114855 0.844807169 0.875591954 1 16.13717544 3.528785589 4.027977053 0.867062104 0.931510997 0.095086016 0.058845417 0.333945027 11.13175944 0.014421714 0.022213203 3378.97975 -3.528785589 0.064448893 ESWHGKPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESWHGKPLPK 10 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 113.93 0.00085522 3570100000 9076200 6931900 5425300 8780800 7581500 6319400 9967000 8786900 7675600 FALSE TRUE 8647186.013 7638268.491 5674055.371 7898137.302 8903711.2 6100557.593 8446351.093 8017472.454 8865892.846 0.975331663 0.861534041 0.63998691 0.890845112 1.0042656 0.688092863 0.952679131 0.904305138 1 23.0798345 1.115696252 1.653505034 0.992345558 0.857024712 0.142644403 0.115358654 0.730920497 3.891422597 0.104087931 0.030531498 13.05257665 -1.115696252 -0.135320846 ESYDDVSSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESYDDVSSFR 10 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 ; 95.608 0.013001 111250000 604150 522360 578290 717540 688860 630860 741950 655400 700670 FALSE TRUE 575593.0268 575589.0779 604805.1685 645411.516 808996.9659 609013.16 628751.9007 598009.7015 809326.3251 0.711200178 0.711195299 0.747294571 0.797467592 0.999593045 0.752493946 0.776883046 0.738898122 1 19.626362 -5 0.103416043 1.641028446 0.640527376 0.407141304 0.083080105 187.9375336 1.312366418 26.59661435 1.276777596 1.00E-05 5 -1.000501071 ESYDYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESYDYLK 7 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 89.142 0.042085 553630000 952520 916360 756290 790360 692490 909120 961570 993700 655910 FALSE TRUE 907496.2673 1009738.126 790966.6446 710911.5112 813260.0367 877636.9464 814864.8361 906686.3601 757625.1729 1.197816941 1.332767392 1.044007872 0.938341988 1.07343323 1.158405209 1.075551427 1.196747934 1 19.53112474 3.731505513 24.98120253 1.072989402 1.265292169 0.515252236 0.078896504 382.8298425 1355551.101 0.020667596 0.032819271 5388.966856 -3.731505513 0.192302766 ESYELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESYELR 6 0 P35268;K7ERI7;K7EMH1 P35268 RPL22 60S ribosomal protein L22 0 ; 108.98 0.069669 4939800000 10518100 9867700 9494100 10543900 11835500 9443500 12266200 10315200 11610100 FALSE TRUE 10020930.26 10873229.85 9929413.876 9484007.14 13899607.45 9116469.227 10394765.91 9411946.404 13410535.01 0.747243138 0.810797618 0.740418922 0.707205725 1.036469271 0.67979907 0.775119404 0.701832283 1 23.67686346 -1.591341942 2.806504249 1.015885331 0.776809068 0.331844011 0.10036432 27921081.49 27581043.69 3283661.837 0.021935554 0.025624657 1.591341942 -0.239076263 ESYPVFYLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESYPVFYLFR 10 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 128.69 0.00075148 65401000 202360 155750 99532 88372 211980 111770 214320 130000 195460 FALSE TRUE 192794.8438 171621.1021 104095.6407 79488.67866 248949.2449 107899.3769 181621.5477 118616.5108 225770.9385 0.853940038 0.760155861 0.461067493 0.352076663 1.102662931 0.47791526 0.804450515 0.525384319 1 17.78450027 -0.477603154 11.1658077 1.000000047 0.684586477 0.175185411 0.224135004 0 0 0.199619371 0.047050737 0.332963667 0.477603154 -0.31541357 ESYS(ph)VYVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 ESYS(1)VYVYK 113.69 0.0019939 0 103460 71582 82706 94061 88988 85137 117010 89325 87094 TRUE FALSE 98569.65084 78876.28718 86498.15191 84605.80958 104507.479 82188.68434 99157.97546 81503.22946 100600.0927 0.9798167 0.784057798 0.859821791 0.841011249 1.038840782 0.816984181 0.985664852 0.81017052 1 16.61827211 ESYSIYVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 190.51 8.60E-05 1433220000 1502290 1319980 1185140 1460590 1245390 1273650 1647610 1473440 1360010 FALSE TRUE 1431279.729 1454487.463 1239479.841 1313768.718 1462585.622 1229543.181 1396236.834 1344417.782 1570913.405 0.911113066 0.925886467 0.789018566 0.836308809 0.931041531 0.782693163 0.888805729 0.855819155 1 20.58317222 -1.350154764 5.656245385 1.000027465 0.869843555 0.396035416 0.052066058 1.77E-05 2.03E-06 0.049363524 0.011632641 0.044652444 1.350154764 -0.130183911 ESYSVYVYK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 219.7 1.12E-06 12017470000 7254710 5880200 5533110 6600890 5482560 6132720 7473940 6363530 6110490 FALSE TRUE 6911794.236 6479399.065 5786808.566 5937355.996 6438716.728 5920342.369 6333653.185 5806305.578 7058073.581 0.979274891 0.9180124 0.819884987 0.841214806 0.912248456 0.838804286 0.897362873 0.822647357 1 22.75084304 4.111442134 2.905265312 0.871125645 0.966650796 0.260840916 0.054235342 0.268481226 4.44443901 0.012249863 0.031943458 12925.3447 -4.111442134 0.095525151 ESYTEEIVS(ph)EAESHVS(ph)GISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 2 ESYTEEIVS(0.999)EAES(0.121)HVS(0.521)GIS(0.358)R;ESYTEEIVS(1)EAESHVS(0.999)GIS(0.001)R 137.62 1.73E-06 80592000 156634 167006 169236 176700 166552 163307 178253 181472 176956 TRUE FALSE 149230.2212 184024.1013 176995.638 158937.7803 195598.6161 157651.6376 151057.231 165581.3496 204397.4327 0.730098315 0.900324915 0.865938655 0.777591862 0.956952411 0.7712995 0.739036831 0.810095056 1 17.64101755 -2.332421954 2.258568161 2.029762795 0.817228006 0.386463037 0.071676362 6010135.073 806300.7056 31587789.2 0.017197915 0.00465134 2.332421954 -1.212534789 ESYTEEIVS(ph)EAESHVSGISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR 370.13 2.65E-112 567974000 853072 725873 834437 890023 1050550 819848 1126075 985212 1125750 TRUE FALSE 812748.9772 799840.2839 872696.7618 800556.1971 1233765.587 791456.4582 954271.577 898941.6143 1300325.56 0.625034993 0.615107715 0.671137128 0.615658279 0.94881284 0.608660233 0.733871275 0.691320421 1 20.31044144 -5 0.146971161 2.112260162 0.578775483 0.518222384 0.097439701 102.953736 0.907262521 33.51614262 0.479418445 1.00E-05 5 -1.533484679 ESYTEEIVSEAESHVS(ph)GISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 ESYTEEIVSEAESHVS(0.998)GIS(0.002)R;ESYTEEIVSEAESHVS(0.999)GIS(0.001)R 213.14 6.67E-23 56696000 82972 85953 83088 92193 84073 73494 91555 82761 75933 TRUE FALSE 79050.07799 94711.70842 86897.66699 82925.58448 98735.30458 70948.88435 77586.60323 75514.0081 87708.30183 0.901283873 1.079848845 0.990757604 0.945470186 1.125723592 0.808918687 0.884598169 0.860967622 1 16.42042578 2.223342094 24.99976156 0.877100597 1.004890676 0.364444791 0.077998441 230.2894506 378298.578 0.026533109 0.019670682 167.2407451 -2.223342094 0.127790079 ET(ph)ERASPIKMDLAPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.634)ERAS(0.366)PIKMDLAPSK 91.319 0.0069145 360470000 718160 701910 642490 794870 502800 813310 850410 945160 532670 TRUE FALSE 684214.0001 773435.427 671948.802 714968.1574 590488.1608 785144.8708 720664.3356 862396.7798 615273.7431 1.112048105 1.25705905 1.092113567 1.162032616 0.959716171 1.276090325 1.171290574 1.401647298 1 19.2308689 ET(ph)REGILS(ph)LKKPLNY(ph)EK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETREGILSLKKPLNYEK 17 3 H0YAK3;D6RER2;D6RIH8;Q13634-2;Q13634 H0YAK3 CDH18 Cadherin-18 3 ET(1)REGILS(1)LKKPLNY(1)EK 59.862 0.043662 93897000 164540 135690 159120 168860 199500 120300 205390 141400 293420 TRUE FALSE 156762.5203 149516.9653 166415.8094 151885.872 234292.7368 116133.9808 174053.9833 129018.2664 338922.075 0.462532635 0.441154402 0.491014961 0.448143934 0.691287922 0.34265688 0.513551628 0.380672361 1 18.37059408 -1.369906142 3.298565237 1.004379535 0.471941218 0.763700998 0.092409305 31478401.29 44413647.57 1337775.044 0.021492877 0.042667172 1.369906142 -0.532438318 ET(ph)SPSHPGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETSPSHPGFK 10 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ET(0.496)S(0.496)PS(0.009)HPGFK;ET(0.497)S(0.497)PS(0.005)HPGFK 109.24 0.0075259 268570000 551380 844740 495890 834870 384640 634100 545490 667140 352560 TRUE FALSE 525317.3601 930819.9664 518627.047 750947.2815 451721.0942 612140.958 462265.4819 608721.6849 407233.2042 1.289966915 2.285717267 1.273538213 1.844022722 1.10924426 1.503170546 1.13513701 1.494774195 1 18.63549567 2.740530764 24.97803502 1.26775424 1.710575515 0.295656418 0.322812887 202.535704 2567809.555 0.09306208 0.094333127 550.2128944 -2.740530764 0.442821275 ET(ph)SSDVALASHILTALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETSSDVALASHILTALR 17 0 O00273;O00273-2 O00273 DFFA DNA fragmentation factor subunit alpha 1 ET(0.333)S(0.333)S(0.333)DVALASHILTALR;ET(0.698)S(0.295)S(0.007)DVALASHILTALR;ET(0.333)S(0.333)S(0.333)DVALASHILTALR;ET(0.49)S(0.49)S(0.02)DVALASHILTALR 138.04 1.83E-05 75403500 47130.9 35446.9 39550.8 52457.4 44973.3 50717.6 58162.5 46131.8 41404 TRUE FALSE 44903.11576 39058.97941 41364.2433 47184.28249 52816.62928 48961.23679 49288.7424 42092.25503 47824.72086 0.938910148 0.81671108 0.864913429 0.986608633 1.104379249 1.023764194 1.030612234 0.880135927 1 15.54546893 3.178821887 4.774994783 1.015285804 0.870357408 0.496086376 0.061974212 0.148149431 6.773820713 0.017485022 0.021502669 1509.460968 -3.178821887 -0.144928396 ETAAGGLTLKEERS(ph)PQTLAPVGEDAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETAAGGLTLKEERSPQTLAPVGEDAMK 27 2 Q92797 Q92797 SYMPK Symplekin 1 ET(0.062)AAGGLT(0.062)LKEERS(0.625)PQT(0.252)LAPVGEDAMK 56.648 0.03776 86245000 174070 106330 142980 154090 95439 156920 159730 290010 1372400 TRUE FALSE 165842.0561 117165.1479 149535.7744 138600.5804 112083.5314 151485.8211 135360.2549 264615.187 1585224.783 0.104617375 0.073910747 0.094330959 0.087432762 0.070705134 0.095561098 0.085388682 0.166925972 1 20.596256 0.484613175 1.946741303 1.000006473 0.086363974 0.998624028 0.010569021 0.142474628 0.501789573 0.009501341 0.002624652 3.052201311 -0.484613175 -0.9136425 ETAAVIFLHGLGDTGHSWADALSTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETAAVIFLHGLGDTGHSWADALSTIR 26 0 O95372;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 268.75 8.09E-54 478840000 189181 173949 156522 194597 211798 162995 210536 184719 64376 FALSE TRUE 180238.7891 191674.6009 163698.6885 175035.7398 248735.5041 157350.4423 178414.8664 168544.0251 74359.10129 2.423896819 2.577688508 2.201461364 2.353924897 3.345057966 2.116088543 2.399368246 2.266622675 1 16.18222171 0.327522324 0.91876668 0.99026895 2.513340048 0.666249246 0.329740658 1.544307069 1.619819662 0.324889539 0.096838833 2.125799614 -0.327522324 1.523071098 ETAENYLGHTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ETAENYLGHTAK 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 181.98 1.75E-05 3019530000 3368030 3202150 2603630 3143730 2485890 2495820 2991170 3021750 2554570 FALSE TRUE 3208829.897 3528452.726 2723009.011 2827716.288 2919428.429 2409389.128 2534812.08 2757149.551 2950719.669 1.087473653 1.195793949 0.922828773 0.958314108 0.989395387 0.816542877 0.859048763 0.934399015 1 21.49263543 3.728153188 23.73684253 0.913912766 1.141633798 0.67808099 0.061406569 167.5578182 382159.478 0.016648463 0.026134865 5347.529481 -3.728153188 0.227721032 ETAIELGYLTAEQFDEWVKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 253.95 2.04E-36 744920000 1700120 1479970 1488150 1620190 971500 1431020 1685270 1688950 1018700 FALSE TRUE 1619758.697 1630780.626 1556383.149 1457325.423 1140929.292 1381463.419 1428151.109 1541056.584 1176674.793 1.376555958 1.385922971 1.322696091 1.238511636 0.969621597 1.174040123 1.213717773 1.309670772 1 20.16628422 3.197075273 2.943558109 1.152324005 1.375338669 0.519719902 0.099144612 0.201919322 3.576460181 0.028949336 0.037348306 1574.255696 -3.197075273 0.223014664 ETAIQTEDSAISES(ph)PEEPLPNLKPKPNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETAIQTEDSAISESPEEPLPNLKPKPNLR 29 2 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 ETAIQTEDSAIS(0.006)ES(0.994)PEEPLPNLKPKPNLR;ETAIQTEDSAIS(0.015)ES(0.985)PEEPLPNLKPKPNLR 120.43 1.85E-05 459010000 91502 72165 75698 88138 69358 80688 90490 99477 76342 TRUE FALSE 87176.8818 79518.69554 79168.82818 79278.20079 81454.01324 77893.75433 76684.08854 90766.26652 88180.72746 0.988616042 0.901769557 0.89780194 0.899042263 0.92371673 0.883342161 0.869624132 1.029320909 1 16.42817576 1.22978652 24.99971849 1.014660522 0.910134049 0.646277925 0.032451183 144.277785 411070.088 0.031853589 0.008448187 16.97409077 -1.22978652 -0.104526473 ETAVPGPLGIEDISPNLS(ph)PDDKSFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ETAVPGPLGIEDISPNLS(0.983)PDDKS(0.009)FS(0.009)R 129.71 4.68E-05 124270000 98105 85960 97455 94701 74670 118750 115740 125120 87975 TRUE FALSE 93467.77108 94719.42173 101923.4081 85181.47556 87692.42436 114637.6577 98081.73729 114163.8295 101617.7137 0.919798012 0.932115261 1.003008279 0.838254203 0.862963958 1.128126717 0.965203149 1.123463866 1 16.63279238 2.246944057 24.99999981 1.044818036 0.915710154 0.54095828 0.065116233 147.806302 440768.9388 0.021361498 0.017595975 176.5810346 -2.246944057 -0.129107882 ETCAWFTDNYEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETCAWFTDNYEQAR 14 0 Q13630 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 209.64 1.48E-08 230110000 153958 135465 128495 160569 151181 139315 166580 147657 154332 FALSE TRUE 146680.7105 149269.0375 134386.6228 144428.2991 177546.9185 134490.4866 141165.1615 134727.3703 178265.0183 0.82282386 0.837343405 0.753858632 0.810188675 0.995971729 0.754441269 0.791883696 0.755770098 1 17.4436641 -1.020511296 4.433847492 1.000007486 0.816553117 0.403614555 0.070549225 8660408.964 1993312.894 699.0059057 0.015692519 0.095386893 1.020511296 -0.183454369 ETCSLWPGQALSLQVEQLLHHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETCSLWPGQALSLQVEQLLHHR 22 0 P19623;K7EKM4 P19623 SRM Spermidine synthase 0 90.972 0.001328 71773000 112270 129830 124060 135400 111230 116480 127370 126340 16327 FALSE TRUE 106963.2196 143059.8246 129748.2737 121789.3348 130628.4768 112446.2684 107937.3672 115276.9998 18858.90777 5.671761105 7.585795865 6.879946351 6.457920905 6.926619418 5.962501633 5.723415613 6.11260213 1 14.2029585 -0.44729167 0.477849257 2.17E-12 6.752502724 0.909544463 0.542128351 2.192921952 0.458051653 4.276823473 0.271300837 0.357032976 0.44729167 6.752502724 ETCSTLAES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;ETCSTLAES(1)PR;ETCSTLAES(1)PR 203.88 3.68E-08 988760000 1240630 1125020 1121910 1356460 1153710 1147020 1316460 1218800 1257640 TRUE FALSE 1181987.879 1239660.817 1173350.683 1220106.064 1354916.659 1107298.41 1115609.849 1112075.411 1452668.388 0.81366669 0.853368069 0.807720945 0.839906804 0.932708848 0.762251329 0.767972827 0.765539761 1 20.47027397 ETDFYHTLHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETDFYHTLHSR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;R4GMQ2 Q8TDM6-4 DLG5 Disks large homolog 5 0 156.01 1.81E-05 25076000 69505 47861 54909 60813 72045 54716 70939 57323 10108 FALSE TRUE 66219.6364 52738.09031 57426.63196 54699.9617 84609.62519 52821.1712 60115.95267 52303.49423 11675.49702 5.671676016 4.516988891 4.918559945 4.685022113 7.246768602 4.524104724 5.148898808 4.479765972 1 13.51119635 0.524261867 1.36189384 0.99918382 5.23235192 0.736708805 0.792733866 0.998284976 2.323702947 0.705028417 0.208090781 3.343966105 -0.524261867 4.233168101 ETDKQILQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 104.82 0.0023991 276090000 316330 216309 266733 276019 227029 271589 360540 299956 286667 FALSE TRUE 301377.7078 238351.133 278962.9719 248273.0457 266622.7857 262183.8048 305533.0012 273690.2625 331121.8543 0.9101716 0.71982906 0.842478285 0.749793596 0.805210475 0.791804592 0.922720736 0.826554511 1 18.33700271 0.878073911 0.713634879 0.996622342 0.80078485 0.475457958 0.06091043 0.705754147 0.782694566 0.056603256 0.021503343 7.552207453 -0.878073911 -0.195837492 ETDLLLDDSLVSIFGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETDLLLDDSLVSIFGNR 17 0 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;; 229.75 2.35E-15 251678000 289650 292758 242641 314031 270318 270188 285710 275115 248094 FALSE TRUE 275958.8185 322590.373 253766.3299 282464.0073 317461.3736 260831.3218 242119.6921 251024.4721 286567.1504 0.96298134 1.125706043 0.885538798 0.985681739 1.107807971 0.910192677 0.844896883 0.875970856 1 18.12851372 2.079114653 8.458403057 0.88670855 1.016958634 0.296429389 0.078846936 0.264664078 25.21804325 0.028087692 0.02071924 119.981601 -2.079114653 0.130250084 ETDLLLDDSLVSIFGNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ETDLLLDDSLVSIFGNRR 18 1 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;;;;;;; 264.16 9.68E-31 3193801500 4782812.1 3531463.5 4312242.6 4576661 4674281.3 3985316.2 5024643.3 4523812.6 4971495.3 FALSE TRUE 4556738.051 3891323.646 4509963.189 4116606.341 5489474.479 3847303.701 4258041.681 4127683.587 5742449.4 0.793518189 0.677641782 0.785372735 0.716872898 0.955946513 0.669976073 0.741502691 0.718801908 1 22.45323481 -0.920220339 4.233140338 1.000006302 0.753215919 0.469006047 0.080994299 20054308.98 45576675.43 2034.722561 0.017827774 0.120165462 0.920220339 -0.246790383 ETDLQELFRPFGS(ph)ISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 ETDLQELFRPFGS(0.994)IS(0.006)R 69.922 0.027169 14312000 12833 16363 7963.6 13749 13724 12002 13337 14578 13768 TRUE FALSE 12226.40952 18030.4083 8328.738937 12366.9244 16117.46125 11586.36773 11302.1957 13301.47304 15903.07112 0.768808077 1.133768953 0.523718901 0.777643784 1.013481052 0.72856165 0.710692646 0.836409077 1 13.95701778 3.756827658 24.95945524 0.785854599 0.95128847 0.125518413 0.164836766 1372.668309 1875560.773 0.039789086 0.071559869 5712.51901 -3.756827658 0.165433871 ETDLQELFRPFGSISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;;; 231.06 1.53E-15 1162905000 1073077 976170 952973 1140808 902062 926859 1096387 1027073 969834 FALSE TRUE 1022354.777 1075642.833 996667.7547 1026131.812 1059381.327 894761.6404 929113.0266 937137.0433 1120230.903 0.912628614 0.960197428 0.8896985 0.916000272 0.94568122 0.798729653 0.829394211 0.836557035 1 20.0953647 2.25235344 24.99624577 0.847635212 0.926553026 0.176435135 0.056983032 252.7852073 458112.9124 0.017618944 0.01467077 178.7942055 -2.25235344 0.078917813 ETDPS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETDPSPEER 9 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H0Y482 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 ETDPS(1)PEER;ET(0.001)DPS(0.999)PEER 130.01 0.0003916 1130150000 2726950 2295360 2400750 2822100 2667800 2405940 3030100 2631840 2773600 TRUE FALSE 2598052.478 2529259.794 2510826.762 2538417.146 3133063.475 2322621.695 2567802.593 2401382.137 3203715.722 0.810949754 0.789476974 0.783723332 0.792335328 0.97794678 0.724977462 0.801507629 0.749561555 1 21.61131471 -1.017834995 4.235667027 1.00001296 0.803527988 0.45928837 0.066898407 7878764.323 1893776.799 985.9838678 0.014377037 0.095976521 1.017834995 -0.196484972 ETDPVKS(ph)PPLPEHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETDPVKSPPLPEHQK 15 1 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 ET(0.001)DPVKS(0.999)PPLPEHQK;ET(0.002)DPVKS(0.998)PPLPEHQK;ET(0.008)DPVKS(0.992)PPLPEHQK 149.36 2.04E-06 606370000 639200 646140 546930 737840 362871 699480 637800 747770 546004 TRUE FALSE 608986.2828 711982.4006 572007.2815 663670.9214 426155.5875 675256.8322 540491.896 682291.2946 630675.5117 0.965609527 1.12892032 0.90697557 1.052317569 0.675712914 1.070688206 0.857004729 1.08184206 1 19.26653839 3.720928286 24.44311196 0.938853758 1.047264935 0.089351534 0.126812495 1080.322545 1497614.854 0.029980442 0.046579611 5259.304131 -3.720928286 0.108411178 ETDVVNFDDIASSENLLHLTANRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETDVVNFDDIASSENLLHLTANRPK 25 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 228.71 2.49E-34 189136000 159107 128842 128920 161748 123712 143424 176493 170260 157854 FALSE TRUE 151586.3274 141971.1463 134831.1095 145488.7837 145287.3336 138457.1909 149565.7513 155351.1318 182333.1921 0.831369899 0.778635775 0.739476493 0.797928134 0.796823288 0.75936361 0.82028812 0.852017836 1 17.47621769 0.788667959 1.362776737 0.999656308 0.786384776 0.877349409 0.025159422 0.243758072 0.810944082 0.023811143 0.007098113 6.147067174 -0.788667959 -0.213271533 ETEDGHESPLFDFIESCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETEDGHESPLFDFIESCLR 19 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ;; 116.96 0.00010824 25322400 35364.2 30213.1 28714.3 42288 37310.7 33439.6 36196 36417.4 29229.3 FALSE TRUE 33692.60435 33291.84924 30030.87906 38037.1299 43817.67427 32281.57827 30673.63541 33228.4994 33762.03056 0.99794366 0.986073666 0.889486757 1.126624473 1.297838831 0.956150378 0.908524603 0.984197302 1 15.04311405 2.043190065 24.9997951 0.948639785 1.046587878 0.155982634 0.108399122 267.8195589 155021.4351 0.042557364 0.031430673 110.4561914 -2.043190065 0.097948093 ETEEILADVLKVEVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETEEILADVLKVEVFR 16 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ; 209.67 1.06E-11 51707000 130069 136364 132770 132578 101967 130842 151136 158462 112144 FALSE TRUE 123920.8961 150259.6466 138857.6358 119251.0076 119750.0125 126310.9087 128077.4274 144586.2272 129534.7188 0.956661637 1.159995159 1.071972342 0.920610387 0.924462674 0.975112386 0.988749801 1.116196712 1 16.98297931 3.268551273 24.93226597 0.983381889 1.068514081 0.194143095 0.071737636 286.5066885 238180.8905 0.01964322 0.026593664 1855.885902 -3.268551273 0.085132193 ETEELMAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETEELMAWMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;; 208.72 2.53E-07 101350000 179641 211763 126138 157217 134617 126990 128703 145315 121282 FALSE TRUE 171149.7259 233341.8905 131921.5521 141413.2485 158094.1622 122592.3045 109066.9936 132590.4482 140089.7931 1.22171446 1.665659469 0.941692818 1.009447193 1.128520206 0.875098048 0.778550608 0.946467585 1 17.09599232 3.721817161 24.76922447 0.939858441 1.44368695 0.682265866 0.138587176 346.0867903 511979.2511 0.03774824 0.058657481 5270.079429 -3.721817161 0.50382851 ETEEQDS(ph)DSAEQGDPAGEGKEVLCDFCLDDTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETEEQDSDSAEQGDPAGEGKEVLCDFCLDDTRR 33 2 H0Y626;O95361 H0Y626 TRIM16 Tripartite motif-containing protein 16 1 ETEEQDS(0.99)DS(0.009)AEQGDPAGEGKEVLCDFCLDDTRR;ETEEQDS(0.972)DS(0.027)AEQGDPAGEGKEVLCDFCLDDTRR 197.79 3.59E-27 279630000 223700 132906 199386 196129 183423 208187 302780 240630 241350 TRUE FALSE 213126.1443 146449.2725 208528.0453 176413.7403 215411.9131 200977.432 256585.3501 219559.1615 278777.3254 0.764503153 0.525327059 0.748009348 0.632812371 0.772702417 0.720924601 0.920395336 0.78757898 1 18.0887537 1.687254792 0.613937462 0.980519357 0.645653135 0.599183366 0.083637506 0.42820988 0.347349531 0.072610815 0.039192242 48.6692655 -1.687254792 -0.334866223 ETERAS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETERASPIK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.007)ERAS(0.993)PIK;ET(0.015)ERAS(0.985)PIK 61.375 0.054252 995830000 1704480 2127540 1425730 2125660 998910 1800590 1613340 1887840 1018660 TRUE FALSE 1623912.608 2344338.745 1491101.131 1911984.618 1173119.588 1738235.117 1367195.352 1722530.722 1176628.59 1.380140362 1.992420348 1.267265765 1.62496869 0.997017748 1.477301445 1.161959996 1.463954502 1 20.16622757 3.223739731 1.639895955 1.254997655 1.661705844 0.268543959 0.255396834 0.398914554 2.222223586 0.076622474 0.10815927 1673.939397 -3.223739731 0.406708189 ETERAS(ph)PIKMDLAPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.003)ERAS(0.997)PIKMDLAPSK;ET(0.139)ERAS(0.857)PIKMDLAPS(0.005)K;ET(0.015)ERAS(0.985)PIKMDLAPSK;ET(0.004)ERAS(0.996)PIKMDLAPSK;ET(0.139)ERAS(0.861)PIKMDLAPSK;ET(0.007)ERAS(0.993)PIKMDLAPSK;ET(0.022)ERAS(0.978)PIKMDLAPSK;ET(0.04)ERAS(0.96)PIKMDLAPSK;ET(0.38)ERAS(0.62)PIKMDLAPSK;ET(0.037)ERAS(0.963)PIKMDLAPSK 171.5 2.56E-09 6527490000 10766590 10332860 10095610 12005530 6146380 12282890 12183700 13565390 7260670 TRUE FALSE 10257674.63 11385790.18 10558503.7 10798711.32 7218306.726 11857530.44 10324852.8 12377532.54 8386617.621 1.223100312 1.357614082 1.258970443 1.287612218 0.860693435 1.413863249 1.231110474 1.475867042 1 22.99965765 -2.071511349 2.73885332 0.58783525 1.262538439 0.203236293 0.164016119 27205957.93 24613022.86 69151202.64 0.036445959 0.008481812 2.071511349 0.674703189 ETES(ph)APGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 2 ETES(1)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR 208 1.78E-07 7354450000 8813450 7996350 8562970 9381250 8288510 9107940 10229140 8763270 8841960 TRUE FALSE 8396855.685 8811187.156 8955590.644 8438228.927 9734023.52 8792529.754 8668496.822 7995911.622 10213126 0.822163135 0.862731661 0.876870671 0.826214122 0.953089536 0.860904855 0.848760392 0.782905412 1 23.28392117 -2.373767799 2.362685736 2.103036595 0.855635367 0.521099122 0.04390557 6521014.264 726939.6233 38584013.59 0.010210953 0.004228947 2.373767799 -1.247401228 ETESAPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 ETESAPGS(1)PR;ETESAPGS(1)PR 198.97 3.01E-07 3224700000 3093600 2893300 2864000 3135100 2816500 2857800 3342700 3018300 3008000 TRUE FALSE 2947371.659 3188130.559 2995317.233 2819953.792 3307696.708 2758833.669 2832709.722 2754001.651 3474465.277 0.848295039 0.917588839 0.86209445 0.811622384 0.952001659 0.794031153 0.81529372 0.79264043 1 21.72835953 ETFAS(ph)DTNEALASLDESQEGHAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 ET(0.176)FAS(0.814)DT(0.009)NEALASLDESQEGHAEAK 77.276 0.018207 23392000 17919 16261 14506 19539 16029 16531 19652 17189 16223 TRUE FALSE 17072.00438 17918.01439 15171.11445 17574.9026 18824.45253 15958.52732 16653.72647 15683.84004 18738.77998 0.911052075 0.956199625 0.809610576 0.937889372 1.004571938 0.851631074 0.888730562 0.836972313 1 14.19373941 ETFASDTNEALASLDES(ph)QEGHAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 ETFASDTNEALASLDES(1)QEGHAEAK 176.15 5.22E-13 62925000 77540 92228 73688 102430 56196 80540 78629 88710 55085 TRUE FALSE 73874.83787 101626.1381 77066.66769 92133.5418 65996.56461 77750.87961 66632.70193 80942.08212 63627.30046 1.161055668 1.597209646 1.211220139 1.448019028 1.037236597 1.221973572 1.047234464 1.272128183 1 15.95735829 2.738795149 24.99966291 1.121486941 1.365415216 0.403371659 0.143856407 19.81035365 2111760.885 0.04121317 0.041251455 548.0184112 -2.738795149 0.243928276 ETFGVNNAVYGIDAMNPSSRDDFTEFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETFGVNNAVYGIDAMNPSSRDDFTEFGK 28 1 O75822;O75822-3;H0YGJ7 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 244.74 1.60E-45 81007000 58488 48125 57153 53921 51407 54481 70168 64333 64100 FALSE TRUE 55723.38815 53028.99221 59773.52158 48500.75864 60372.36452 52594.30931 59462.58288 58699.66147 74040.30062 0.752608886 0.716217948 0.807310628 0.65505891 0.815398695 0.710347052 0.803111041 0.792806903 1 16.17602313 0.215418036 0.613660394 1.011236868 0.738364943 0.730828452 0.047756679 1.298675809 0.662021369 0.073447367 0.016390586 1.642169704 -0.215418036 -0.272871924 ETFLTS(ph)PEELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETFLTSPEELYR 12 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 1 ETFLT(0.495)S(0.505)PEELYR 134.06 0.00015965 11667000 51423 43030 50982 55694 57805 49256 55272 48481 63257 TRUE FALSE 48992.3367 47414.80592 53319.57513 50095.53331 67886.1737 47550.25237 46839.24126 44235.74663 73066.57249 0.670516421 0.6489261 0.729739651 0.685614934 0.92910029 0.65077984 0.641048836 0.605417021 1 16.15692391 -2.158814625 2.444716648 1.754279579 0.691513531 0.534633449 0.08932873 9867292.622 1634474.579 41477087.08 0.022749136 0.006937219 2.158814625 -1.062766047 ETFLTSPEELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 576281000 514860 452943 439663 526035 489725 458729 549267 509553 558361 FALSE TRUE 490523.5882 499098.4067 459821.9834 473156.9624 575132.8849 442843.0997 465466.2312 464933.838 644948.7722 0.760562093 0.773857441 0.712958925 0.733634953 0.891749717 0.686632984 0.721710392 0.720884911 1 19.29882505 -0.977876771 4.847238394 1.00000277 0.750589995 0.663830231 0.055854352 1.59E-06 3.34E-07 0.051317574 0.012095534 0.105226041 0.977876771 -0.249412775 ETFS(ph)SAEGTVDKDTTIMELR ddPTM_SK-BR-3_Trastuzumab_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 ET(0.063)FS(0.883)S(0.053)AEGT(0.001)VDKDTTIMELR;ET(0.035)FS(0.937)S(0.027)AEGT(0.001)VDKDTTIMELR 86.617 0.0015018 76986000 57864 48932 50990 59903 51555 62485 64737 66744 54325 TRUE FALSE 55128.8834 53918.22643 53327.94194 53881.43663 60546.17568 60321.12878 54860.18167 60899.54153 62749.44355 0.878555733 0.859262224 0.849855217 0.858675927 0.96488785 0.961301414 0.874273596 0.970519228 1 15.93731505 2.747626684 24.87242554 0.941143465 0.862433366 0.640646449 0.033683265 443.0583858 1215513.789 0.010224006 0.010708725 559.2766455 -2.747626684 -0.0787101 ETGANLAICQWGFDDEANHLLLQNNLPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETGANLAICQWGFDDEANHLLLQNNLPAVR 30 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 344.56 1.05E-106 521650000 283742 251408 286607 321843 303931 268709 327078 294711 289344 FALSE TRUE 270330.078 277026.761 299748.2144 289490.7302 356936.4702 259403.54 277176.2439 268904.5425 334213.9898 0.808853268 0.82889038 0.896875127 0.86618376 1.06798782 0.776160029 0.829337647 0.804587931 1 18.3504126 3.858777587 4.483574968 0.880490288 0.816075134 0.097343329 0.087729204 0.561853497 18.04680137 0.022155333 0.041423984 7223.997499 -3.858777587 -0.064415153 ETGDDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETGDDYR 7 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 77.748 0.086555 345840000 469250 406300 405870 479320 457300 440350 498520 469670 486870 FALSE TRUE 447069.4825 447702.4319 424479.541 431137.843 537052.9752 425100.5691 422461.6181 428543.2049 562371.313 0.794972062 0.796097563 0.754802977 0.766642666 0.954979322 0.755907279 0.751214737 0.762028921 1 19.10116348 -1.02334868 4.813240957 1.000004162 0.791013781 0.541816083 0.060081368 2.58E-06 5.23E-07 0.055863724 0.013166944 0.094765732 1.02334868 -0.20899038 ETGEHLVHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 ;; 155.06 7.74E-06 564783000 835650 835370 684000 950770 625210 804860 867850 798860 36338.3 FALSE TRUE 796150.4806 920495.1527 715362.0766 855196.7933 734246.4261 776987.4964 735443.5433 728907.5834 41973.45797 18.96795068 21.93041024 17.0432009 20.37470427 17.49311259 18.51140063 17.5216334 17.3659169 1 15.3571897 -0.195638159 0.588701894 2.27E-15 19.58852842 0.94294257 1.373663525 1.256619691 0.434681144 5.678761396 0.530231026 0.637326301 0.195638159 19.58852842 ETGEHLVHVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETGEHLVHVKK 11 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 98.898 0.0021058 95605000 148940 83646 145400 126960 118280 134910 187700 161610 42134 FALSE TRUE 141899.9014 92169.6225 152066.7338 114197.7396 138907.9946 130238.0329 159062.9177 147458.5717 48667.92553 2.915675978 1.893847364 3.124578091 2.3464682 2.854200031 2.676054742 3.268331574 3.029892276 1 15.57068366 2.724351274 23.5048817 2.759463702 2.52662115 0 0.698052583 1666.101002 2756030.402 0.20224459 0.191643467 530.0920296 -2.724351274 -0.232842551 ETGLSHLCEFIEDCEFTVLATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ETGLSHLCEFIEDCEFTVLATR 22 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;;;;; 244.92 7.54E-31 651762000 581967 603111.9 481313 649310.3 525937 529677.1 579190.4 615713.9 492144 FALSE TRUE 554458.5733 664569.6883 503381.6771 584040.395 617660.2463 511334.2492 490824.2669 561798.7268 568463.178 0.975364095 1.169063739 0.885513252 1.027402333 1.086543984 0.899502851 0.863423148 0.988276371 1 19.11670738 2.229238273 24.99902555 0.918708294 1.036477147 0.212753601 0.082708671 231.292246 620234.1841 0.029682639 0.022220564 169.5267643 -2.229238273 0.117768853 ETGVDLTKDNMALQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETGVDLTKDNMALQR 15 1 P38646;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 203.04 5.11E-09 1080750000 747840 383703 772880 587470 693165 628489 913610 775660 883640 FALSE TRUE 712491.0853 422802.7719 808317.3125 528416.3995 814052.7565 606724.2683 774222.0149 707739.0984 1020670.378 0.698061882 0.414240269 0.791947459 0.517715034 0.79756675 0.59443703 0.758542651 0.693406131 1 19.9610856 -1.559461084 0.193370329 1.376536191 0.537567072 0.472976932 0.117892791 20.48354235 0.691835148 3.995866285 0.325532551 0.027576485 1.559461084 -0.838969119 ETHADLWPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ETHADLWPAK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;;; 120.09 0.00060585 1989378000 2254504 1916799 1640937 1943047 1838582 1832312 2420633 1980348 1760025 FALSE TRUE 2147938.064 2112122.997 1716175.585 1747728.224 2159230.119 1768858.576 2051320.978 1806938.231 2032960.688 1.056556615 1.03893942 0.84417549 0.859696026 1.062111103 0.870089907 1.009031306 0.888821039 1 20.95515089 3.893571953 9.131501861 0.936640777 1.049950358 0.30584053 0.071671009 0.362494105 28.40595354 0.017031888 0.030773131 7826.578634 -3.893571953 0.11330958 ETHKPLGDWSYAYMQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETHKPLGDWSYAYMQ 15 1 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 86.548 0.0068533 318280000 1480150 1134360 1082000 1064320 1152850 904610 1206410 1125520 998790 FALSE TRUE 1410186.243 1249952.574 1131610.77 957332.5315 1353906.675 873283.1289 1022349.997 1026963.502 1153677.252 1.222340339 1.083450828 0.980872916 0.829809663 1.173557572 0.756956183 0.886166383 0.890165339 1 20.13780825 4.13907489 0.840932872 0.902854493 1.281785025 0.434236808 0.111134907 0.909361744 0.870376485 0.038868904 0.271682925 13774.46975 -4.13907489 0.378930532 ETHPDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETHPDSLR 8 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 ; 73.248 0.044057 168566000 239480 188868 178080 211956 429860 187946 292350 228240 356230 FALSE TRUE 228160.255 208113.8639 186245.1441 190649.7802 504827.4479 181437.3829 247746.6381 208254.0956 411472.329 0.554497202 0.505778516 0.45263103 0.463335604 1.226880673 0.440946742 0.602097931 0.506119321 1 18.65043589 ETHQQVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ETHQQVVSR 9 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;; 143.89 0.00010086 777276000 611020 640290 532575 671143 534967 554385 600277 560911 475884 FALSE TRUE 582138.2955 705536.2789 556994.0905 603678.4306 628265.0754 535186.5084 508693.7188 511794.6593 549681.6602 1.05904624 1.283536145 1.013303028 1.098232803 1.142961683 0.973629916 0.925433311 0.93107465 1 19.06823682 2.186346658 4.791572903 0.945786086 1.130872387 0.548557959 0.072528198 0.139778306 6.747671239 0.027528778 0.020388824 153.5842419 -2.186346658 0.1850863 ETHSLFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETHSLFFR 8 0 A0A0C4DGS1;P39656-2;P39656-3;P39656;U3KQ84 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 ; 149.65 0.00050176 234052000 40156.7 34767 29337 43747 44227 27936 42896 32212.8 38824 FALSE TRUE 38258.57237 38309.79683 30682.13047 39349.46845 51940.1748 26968.56932 36351.42736 29392.07646 44844.62763 0.853136137 0.854278402 0.684187429 0.877462263 1.158225133 0.601377929 0.8106083 0.655420237 1 15.45264754 -0.953614732 5.017360614 1.00000103 0.816712706 0.128031251 0.1538555 1.65E-06 3.44E-07 0.138517193 0.032648632 0.11127184 0.953614732 -0.183288324 ETHVMDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ETHVMDYR 8 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;;;;;; 128.38 0.0010521 5145920000 5371682 4766817 4501402 5286578 5491877 4598275 5599753 5189274 4708227 FALSE TRUE 5117773.238 5252561.072 4707795.734 4755161.136 6449658.61 4439035.584 4745407.833 4734873.658 5438354.797 0.941051739 0.96583641 0.865665428 0.874374937 1.185957675 0.816246043 0.872581509 0.870644494 1 22.37473884 ETIEDVEEMLNNLPGVTSVHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETIEDVEEMLNNLPGVTSVHSR 22 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 131.82 1.15E-05 96484000 68825 58393 63189 66182 77928 61664 86931 76745 82940 FALSE TRUE 65571.77865 64343.31309 66086.27815 59529.25962 91518.61853 59528.56022 73668.07935 70024.80095 95801.9116 0.684451673 0.671628697 0.689822124 0.62137862 0.955290108 0.621371319 0.76896252 0.730933233 1 16.54776682 -5 0.185402558 2.211198275 0.657476467 0.490158525 0.092949696 106.4527094 1.034137199 47.465766 0.239255879 1.00E-05 5 -1.553721808 ETIELVHTEPTDVAQLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETIELVHTEPTDVAQLPSR 19 0 Q6IBS0;H0Y858;D6RG15 Q6IBS0 TWF2 Twinfilin-2 0 ; 218.79 3.28E-19 303230000 735190 808340 628460 818790 466190 782750 750140 820510 437350 FALSE TRUE 700439.0257 890710.765 657275.5126 736483.6736 547493.3884 755643.1712 635692.3657 748661.7946 505172.0043 1.386535714 1.763183148 1.301092513 1.457886952 1.083776187 1.495813633 1.25836816 1.481993832 1 18.94641516 -3.247749353 0.084506419 6.46E-10 1.847094254 0.337469318 0.177056781 152.3027504 1.30879719 33.67422408 5.41725332 0.000565263 3.247749353 1.847094253 ETIFELEDEVEQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETIFELEDEVEQHR 14 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 101.32 0.0030668 0 19601 18609 18096 23912 16908 16416 18799 20320 18148 FALSE TRUE 18674.49958 20505.27826 18925.7195 21508.32033 19856.74985 15847.5098 15930.86728 18540.67308 20962.29915 0.890861228 0.978197959 0.902845597 1.026047771 0.947260112 0.756000555 0.759977098 0.884477077 1 14.35550934 2.258431072 24.57014105 0.819950532 0.949129494 0.242494652 0.079281625 188.1634218 232666.4353 0.025365836 0.021193852 181.3138885 -2.258431072 0.129178962 ETIFELEDQVEQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETIFELEDQVEQHR 14 0 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;J3KRN9;J3QQM0 Q5M775-4 SPECC1 Cytospin-B 0 96.464 0.003361 19156000 19720 17582 17068 21001 17202 19529 18564 21196 22100 FALSE TRUE 18787.87468 19373.62579 17850.58468 18889.93958 20202.02335 18852.70583 15731.72085 19339.96587 25527.15513 0.735995632 0.758941828 0.699278262 0.73999392 0.79139345 0.738535326 0.616273955 0.757623236 1 14.63974515 -2.239288596 2.035174336 1.840424614 0.726168784 0.768193389 0.046617006 2040901.718 333959.9267 7883477.941 0.012851856 0.005763833 2.239288596 -1.11425583 ETIPLQETSLYTQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETIPLQETSLYTQDR 15 0 A0A2C9F2P4;A0A286YFF7;P50897;P50897-2;E9PIA8;E9PSE5 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 162.32 3.73E-06 90095000 10537 8945.5 10529 12166 12983 9807.4 9763.4 14259 10301 FALSE TRUE 10038.93689 9857.05662 11011.76506 10943.05057 15247.23109 9467.767279 8273.814013 13010.40637 11898.42647 0.843719707 0.828433629 0.925480785 0.919705693 1.281449369 0.795715913 0.695370437 1.093456047 1 13.53848317 3.708285051 5.640122947 0.933758803 0.835827902 0.077435092 0.158825159 0.559114135 55.04327539 0.044100287 0.071220657 5108.401816 -3.708285051 -0.097930901 ETKPEPMEEDLPENKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETKPEPMEEDLPENKK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 118.72 0.00014076 663430000 834110 820080 727680 851050 315550 801830 657860 884420 336730 FALSE TRUE 794683.2733 903647.0844 761044.8478 765500.8371 370581.8201 774062.426 557491.3746 806975.4962 388948.3686 2.043158778 2.323308586 1.956673197 1.968129703 0.952778955 1.99014185 1.433330024 2.074762517 1 18.56921913 2.980469056 22.65643966 1.542124213 2.121904594 0.383870798 0.366901731 219.8873879 255076.1952 0.099148661 0.106840428 956.0245757 -2.980469056 0.579780381 ETLAVNYEKEEEFLTNELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETLAVNYEKEEEFLTNELSR 20 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 190.63 1.60E-17 29847000 30330 33938 28869 36501 25187 33248 35455 35049 27910 FALSE TRUE 28896.36101 37396.32078 30192.67221 32831.85013 29579.60483 32096.61342 30045.68857 31979.92375 32238.14026 0.896340818 1.160002422 0.936551301 1.018416381 0.917534467 0.995609957 0.931991993 0.991990341 1 14.9764809 ETLEQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETLEQQKR 8 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 134.48 0.0014028 1418140000 1128900 864900 934620 1041430 906650 1093310 1240770 1189080 1065340 FALSE TRUE 1075539.134 953034.2933 977473.2515 936743.4778 1064769.473 1055448.401 1051467.748 1084957.851 1230547.486 0.874033019 0.774479899 0.794340131 0.761241227 0.865281092 0.857706356 0.854471493 0.881687106 1 20.2308689 0.746633154 0.580867966 1.003381134 0.808292359 0.729998601 0.035094749 0.636832944 0.453767853 0.040397558 0.015798998 5.579986569 -0.746633154 -0.195088774 ETLQQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ETLQQHK 7 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 130.77 0.0035314 3154560000 6569970 5598740 4561630 5415270 5029720 5396420 7059810 6221350 5120010 FALSE TRUE 6259420.539 6169257.971 4770785.248 4870916.771 5906901.576 5209540.622 5982706.322 5676575.613 5913995.001 1.058408155 1.043162527 0.806694163 0.823625446 0.99880057 0.880883501 1.011618427 0.959854652 1 22.49570159 3.955002248 24.10149492 0.927395816 1.052691098 0.345596383 0.071531104 279.6780137 149799.9285 0.018330981 0.033047529 9015.758038 -3.955002248 0.125295282 ETLVYLTHLDYVDTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 ;;;;; 224.59 7.66E-15 1358053000 1270463 1219749 1275130 1475133 1410061 1408702 1566885 1454020 1305521 FALSE TRUE 1210410.732 1344042.81 1333595.972 1326849.828 1655975.192 1359918.297 1327827.915 1326698.301 1507974.529 0.802673194 0.891290127 0.884362399 0.879888753 1.098145333 0.901817816 0.880537363 0.879788269 1 20.52418063 4.305546397 0.926210561 0.932300938 0.781277468 0.283123715 0.068372271 1.627721976 1.709756454 0.02326322 0.215914403 20209.07319 -4.305546397 -0.15102347 ETMQSLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 267.53 6.39E-14 22533440000 12552192 13661389 10687923 13928570 11230717 11434530 12209514 12078541 10721086 FALSE TRUE 11958874.76 15053500.07 11177974.84 12528443.68 13189350.49 11038549.36 10346728.4 11020879.92 12383657.26 0.965698138 1.215594049 0.902639229 1.011691733 1.065061008 0.8913804 0.835514758 0.889953564 1 23.56193411 2.23228444 24.07708222 0.88464445 1.044298274 0.318730963 0.089985171 89.98708129 345209.3144 0.032360801 0.024514851 170.7200147 -2.23228444 0.159653823 ETNPWAHAPDAANKEIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETNPWAHAPDAANKEIAATCSGTEWGQSSGAASPGLFQAGHR 42 1 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 ETNPWAHAPDAANKEIAATCSGTEWGQS(0.004)S(0.086)GAAS(0.91)PGLFQAGHR 153.54 3.47E-14 135580000 72085 43753 74837 60256 72939 67722 105000 88336 60211 TRUE FALSE 68677.68491 48211.48044 78268.35047 54198.9524 85659.53851 65376.77016 88980.32154 80600.83154 69548.21436 0.98748308 0.693209465 1.125382602 0.779300416 1.231656906 0.94002083 1.279404832 1.158920215 1 16.08572585 2.76033013 1.423088122 1.14570465 0.872702095 0.261581083 0.160775488 0.421354245 1.730538637 0.061381698 0.059616917 575.8775255 -2.76033013 -0.273002554 ETPEHPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETPEHPLK 8 0 Q8N163-2;Q8N163;H0YB24;G3V119;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 75.38 0.038541 184200000 561040 432290 433480 603290 442330 496760 549320 490650 418810 FALSE TRUE 534520.7511 476340.8425 453355.4868 542646.143 519472.212 479557.0766 465511.145 447686.0849 483756.9158 1.104936661 0.984669835 0.937155567 1.121733096 1.073829014 0.991318286 0.962283184 0.925436041 1 18.88392276 2.031586425 4.723083945 0.961951385 1.04037636 0.311373844 0.056269877 0.251901455 13.64152515 0.023019503 0.015851833 107.5440592 -2.031586425 0.078424974 ETPGTLSSDTNDSGVELGEES(ph)RSSPLKLEFDFTEDTGNIEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETPGTLSSDTNDSGVELGEESRSSPLKLEFDFTEDTGNIEAR 42 2 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 ETPGTLSSDTNDSGVELGEES(0.333)RS(0.333)S(0.333)PLKLEFDFTEDTGNIEAR 160.15 6.56E-20 57696000 55670 38414 46307 55346 37433 50202 55282 50114 41601 TRUE FALSE 53038.58943 42328.43027 48430.22175 49782.51493 43961.30335 48463.49215 46847.71558 45725.75249 48052.27061 1.103768641 0.880883041 1.007865417 1.036007545 0.914864226 1.008557796 0.974932401 0.951583597 1 15.55231698 4.728059177 4.563273239 0.972461269 1.110813211 0.442024913 0.046560786 0.158524845 7.711590386 0.010293187 0.067524515 53463.72046 -4.728059177 0.138351942 ETPHS(ph)PGVEDAPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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(0.001)PHS(0.999)PGVEDAPIAK;ET(0.276)PHS(0.724)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.001)PHS(0.999)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.017)PHS(0.983)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.368)PHS(0.632)PGVEDAPIAK;ET(0.007)PHS(0.993)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.004)PHS(0.996)PGVEDAPIAK;ET(0.088)PHS(0.912)PGVEDAPIAK;ET(0.037)PHS(0.963)PGVEDAPIAK;ET(0.001)PHS(0.999)PGVEDAPIAK 294.26 5.53E-44 77611462600 53321461.5 40598697.1 42542687.5 50157264.5 37737268.7 45893602.6 54014420 48873697.8 35001011 TRUE FALSE 50801061.69 44735750.49 44493311.8 45115360.98 44318636.41 44304295.63 45773528.19 44594057.72 40428789.03 1.2565566 1.106532042 1.100535358 1.115921651 1.096214789 1.095860072 1.132201317 1.103027293 1 25.26887966 4.552257736 1.835193414 1.099998352 1.277605306 0.670268956 0.035611779 0.296158672 1.379490975 0.008147611 0.080233583 35666.27354 -4.552257736 0.177606955 ETQS(ph)PEQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK 234.9 3.64E-10 11039100000 20099080 20668940 17118850 24058960 12528780 20365030 19874960 20640140 13370960 TRUE FALSE 19149036.32 22775128.48 17903766.21 21640507.63 14713795.27 19659783.9 16842669.82 18832779.92 15444460.19 1.239864397 1.474647104 1.159235479 1.401182519 0.952690809 1.272934351 1.090531467 1.219387385 1 23.88058611 2.756884398 24.96953053 1.124575667 1.327094119 0.410598023 0.12484151 759.5058675 1034965.268 0.034096368 0.036100534 571.326539 -2.756884398 0.202518452 ETQS(ph)PEQVKSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ET(0.001)QS(0.999)PEQVKSEK;ET(0.003)QS(0.997)PEQVKSEK 225.7 1.03E-11 14293290000 7755800 5462550 7648620 7208430 4964300 8235280 9765410 8749920 6449540 TRUE FALSE 7389198.705 6019190.055 7999316.793 6483824.921 5830072.348 7950090.189 8275517.35 7983730.619 7449701.724 0.991878464 0.807977323 1.073776789 0.870346916 0.782591379 1.067168926 1.110852173 1.071684601 1 22.82875123 2.138246029 9.508266665 1.076859198 0.90610622 0.44028818 0.087402247 0.249414615 21.60410974 0.030931064 0.022840218 137.4820594 -2.138246029 -0.170752978 ETSFGS(ph)SENITMTSLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.994)S(0.006)ENITMTSLSK;ETSFGS(0.993)S(0.007)ENITMTSLSK 357.28 6.03E-88 400120000 476850 444320 477370 532430 371930 500660 578230 563980 470210 TRUE FALSE 454310.2455 489596.7131 499257.8867 478909.1248 436794.4742 483322.0187 490010.3936 514594.9214 543127.7653 0.836470301 0.901439301 0.919227332 0.881761448 0.804220484 0.889886413 0.902200964 0.947465687 1 19.05093209 1.144986926 1.53723379 0.998653653 0.872549101 0.643058325 0.032260178 0.239129002 1.095255576 0.030387229 0.00907596 13.96326325 -1.144986926 -0.126104551 ETSSALTHAGAHLDLSAFSSWEELASLGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ETSSALTHAGAHLDLSAFSSWEELASLGLDR 31 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 203.04 4.96E-26 134855000 183371 130543 162105 173137 183186 149848 219745 175329 47355.3 FALSE TRUE 174703.4162 143845.4801 169537.6746 155732.9398 215133.5804 144658.7262 186218.8644 159976.2633 54698.91807 3.193909906 2.629768288 3.099470348 2.847093605 3.933050013 2.644635969 3.404434145 2.924669608 1 15.73922468 0.951387834 22.32406248 0.999999996 3.082839266 0.750604197 0.378852994 1670.175009 766992.3658 0.330971352 0.082742838 8.941035802 -0.951387834 2.082839271 ETSSDVALASHILTALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETSSDVALASHILTALR 17 0 O00273;O00273-2 O00273 DFFA DNA fragmentation factor subunit alpha 0 ; 177.04 1.05E-09 92148000 212983 162169 190615 214368 209527 166079 228730 201632 219458 FALSE TRUE 202915.7157 178694.2055 199354.8863 192819.3214 246068.4425 160327.6426 193833.0376 183976.0332 253490.4258 0.800486705 0.704934732 0.78643951 0.760657215 0.970720853 0.632480071 0.764656247 0.725771132 1 17.95157173 -1.726263419 2.778620245 1.040783923 0.764788758 0.416345662 0.086138573 16021734.12 14447688.02 4552930.643 0.018896339 0.018781773 1.726263419 -0.275995165 ETVFTKS(ph)PYQEFTDHLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ETVFTKSPYQEFTDHLVK 18 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 ET(0.01)VFT(0.077)KS(0.913)PYQEFTDHLVK;ET(0.027)VFT(0.147)KS(0.826)PYQEFTDHLVK 162.86 2.09E-11 192052000 403784 355023 363462 442959 282574 447550 509220 525088 310508 TRUE FALSE 384697.9305 391200.2473 380127.0922 398431.9198 331854.8161 432051.2313 431529.1365 479108.5111 358659.9948 1.072597826 1.090727299 1.059853616 1.110890329 0.925262982 1.204626213 1.203170531 1.335829248 1 18.45225731 2.171178867 24.9998186 1.202937989 1.062095877 0.321019178 0.094801583 55.21390579 20484.45154 0.031475041 0.023245863 148.3128794 -2.171178867 -0.140842112 ETVQTTEDQILKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETVQTTEDQILKR 13 1 P18206;P18206-2 P18206 VCL Vinculin 0 ;;; 226.23 1.78E-11 915920000 730800 614560 615430 769750 590540 716060 759280 732010 676400 FALSE TRUE 696256.5323 677184.3627 643648.0742 692373.2676 693529.989 691262.6627 643437.8909 667911.3238 781292.6574 0.891159703 0.866748658 0.823824553 0.886189395 0.887669918 0.884767899 0.823555533 0.854879817 1 19.57550353 -2.197851133 2.452133751 1.41405002 0.864518787 0.744993034 0.02484898 3744776.083 1599343.662 8463892.786 0.00639653 0.00634087 2.197851133 -0.549531233 ETVRDYEHQFHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETVRDYEHQFHLR 13 1 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 117.92 0.00030241 26741000 16362 7024.5 19697 13240 19952 14167 26170 15379 1409.6 FALSE TRUE 15588.60069 7740.304536 20600.12693 11909.09005 23431.62248 13676.39324 22177.28585 14032.33323 1628.193569 9.574169181 4.753921576 12.65213629 7.314296208 14.3911774 8.399734221 13.62079195 8.618344588 1 10.66905651 0.966686383 23.67560484 0.999999899 9.857538764 0.482992899 2.929660819 2260.931219 1606820.089 2.775881666 0.693970416 9.261607729 -0.966686383 8.857538865 ETVVEVPQVTWEDIGGLEDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 262.8 3.58E-37 1112140000 1386448 1180102 1204106 1436196 1010165 1338254 1513520 1424932 1112554 FALSE TRUE 1320913.351 1300355.735 1259315.451 1291826.849 1186337.456 1291909.928 1282604.726 1300157.4 1285083.192 1.027881587 1.011884478 0.979948581 1.005247643 0.923160044 1.005312291 0.998071358 1.011730142 1 20.29343033 3.943573113 3.074733459 0.988532246 1.023419803 0.213901651 0.02520246 0.348143387 6.546608942 0.006408666 0.013695382 8781.589116 -3.943573113 0.034887557 ETVYCLNDDDETEVLKEDIIQGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ETVYCLNDDDETEVLKEDIIQGFR 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;;;; 382.07 3.84E-120 3806205000 1438372 1201866 1244603 1489304 1029262 1376375 1597537 1532428 1157543 FALSE TRUE 1370383.006 1324337.512 1301669.279 1339596.332 1208764.967 1328710.789 1353803.39 1398240.48 1337048.857 1.024931138 0.990492984 0.973539054 1.001905298 0.904054449 0.993763827 1.012530981 1.045766184 1 20.35062075 1.689349246 3.644491536 1.023743253 0.983160392 0.233862027 0.032749771 0.298651855 9.205801368 0.018870519 0.008765491 48.90454759 -1.689349246 -0.040582861 ETWYLSWALDTNQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 167.14 1.50E-08 129157000 106829 99909 98943 122075 101274 91972 111097 112674 107375 FALSE TRUE 101779.4049 110089.8407 103479.6344 109803.7891 118936.1535 88786.98658 94147.11221 102807.6672 124026.1666 0.820628482 0.887633986 0.834337118 0.885327605 0.958960168 0.715873021 0.759090721 0.828919171 1 16.920285 2.236152379 24.99991788 0.797665165 0.872022072 0.039040453 0.083089394 111.9860923 1162503.885 0.027604244 0.021357769 172.2472826 -2.236152379 0.074356907 ETYLAILMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETYLAILMDR 10 0 E9PDQ8;Q96I99;Q96I99-2;H0Y852 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 138.66 0.00013688 42362000 49747 39034 35798 40907 51303 27593 53757 39580 47092 FALSE TRUE 47395.5579 43011.60898 37439.37371 36794.95064 60250.22696 26637.44749 45555.38233 36114.16537 54394.78685 0.871325372 0.790730352 0.68828974 0.676442593 1.107647083 0.48970589 0.837495374 0.663926958 1 15.73118077 4.339252333 2.688577938 0.76804736 0.864456504 0.020611431 0.175536615 1.058662959 14.49863809 0.03950416 0.151203283 21839.98489 -4.339252333 0.096409144 ETYYLSDS(ph)PLLGPPVGEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ETYYLSDSPLLGPPVGEPR 19 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 ETYYLSDS(1)PLLGPPVGEPR 221.91 2.68E-19 27358000 34608 35293 35213 38057 32042 33652 40003 37287 40621 TRUE FALSE 32972.14843 38889.39682 36827.55088 34231.43806 37630.11466 32486.6228 33899.80764 34021.95261 46920.29722 0.70272676 0.828839524 0.784895942 0.72956567 0.802000773 0.692378879 0.722497718 0.725100961 1 15.51792453 -1.07040256 6.603180294 1.000000181 0.750479605 0.762530235 0.044095446 1.18E-07 1.67E-08 0.042806581 0.010089601 0.085034946 1.07040256 -0.249520577 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_SK-BR-3_Trastuzumab_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 EVAATEEDVT(0.013)RLPS(0.951)PT(0.029)S(0.006)PFSSLSQDQAATSK 118.81 1.55E-05 126650000 72227 54779 59251 72141 50334 59764 75045 80221 64977 TRUE FALSE 68812.97285 60361.04238 61967.71696 64889.24962 59112.23366 57694.35769 63595.50695 73196.42396 75053.3013 0.916854711 0.804242336 0.82564945 0.864575555 0.787603378 0.768711791 0.847337903 0.975259218 1 16.19562791 1.22873126 4.202049175 0.99654212 0.829876223 0.721001707 0.040869582 0.109414676 4.043963117 0.036377482 0.010391723 16.93289674 -1.22873126 -0.166665897 EVADEVTRPRPSGEEVLQDIQVMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVADEVTRPRPSGEEVLQDIQVMLK 25 2 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 107.75 0.0019929 38411000 54962 47900 42858 55331 44214 52199 63999 59754 52026 FALSE TRUE 52364.05518 52781.06446 44823.08169 49769.02276 51924.9076 50391.33554 54234.77713 54521.62298 60093.92637 0.871370176 0.878309467 0.745883726 0.828187236 0.864062489 0.838542904 0.902500143 0.907273435 1 15.87493157 1.049112485 0.946819168 0.997893277 0.840092718 0.657205697 0.037838448 0.3801909 0.73999563 0.037114877 0.01270088 11.19727863 -1.049112485 -0.157800558 EVAEMDSVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVAEMDSVKR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 147.37 4.33E-05 569100000 719000 557980 608510 693360 562800 679160 770200 716760 614960 FALSE TRUE 685014.2949 614838.7964 636410.7854 623662.1355 660952.1418 655640.5189 652691.8443 653996.6946 710324.856 0.964367626 0.865574098 0.895943286 0.877995653 0.930492768 0.923015031 0.918863867 0.920700844 1 19.43811944 -0.028171723 0.54725079 1.007616256 0.905534827 0.5153655 0.0272232 3.63549908 1.271201902 0.08714863 0.011979614 0.937191361 0.028171723 -0.102081429 EVAWVIFDEIHYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVAWVIFDEIHYMR 14 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 169.04 3.39E-06 42813000 151910 155960 142670 159120 155680 131170 175510 148340 114040 FALSE TRUE 144729.5154 171852.5013 149211.5606 143124.9553 182830.5427 126627.55 148732.726 135350.5632 131724.7408 1.098726895 1.304633437 1.132752737 1.086545735 1.387974208 0.961304226 1.129117622 1.027525751 1 17.00716681 2.209277129 24.99999998 1.046949241 1.198298024 0.417370234 0.10036147 220.3361593 188104.8578 0.034699177 0.02563106 161.9112886 -2.209277129 0.151348783 EVCGFAPYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EVCGFAPYER 10 0 Q9Y3U8;J3QSB5 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;;;; 192.91 1.47E-06 4358530000 2461720 1946850 1731390 2046020 2608370 1854170 2708660 2251310 2651330 FALSE TRUE 2345359.374 2145236.228 1810775.944 1840350.182 3063268.902 1789959.628 2295404.169 2054173.361 3062484.715 0.765835455 0.700488795 0.591276729 0.600933671 1.000256062 0.58447953 0.749523469 0.670753833 1 21.54627121 -1.84348491 2.40407106 1.121818104 0.710188173 0.364164391 0.121248852 14714628.67 8663586.184 10304928.66 0.026913492 0.014338875 1.84348491 -0.411629931 EVDDFFEQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVDDFFEQEK 10 0 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 134.68 0.0091761 0 63193 77535 52560 77913 38235 62312 59852 65032 41317 FALSE TRUE 60205.99213 85435.90465 54969.92799 70081.03721 44903.17189 60154.11982 50720.47814 59337.45332 47724.22934 1.261539326 1.790199775 1.15182432 1.468458227 0.94088836 1.260452408 1.06278255 1.24334021 1 15.54243428 3.159526046 1.546984215 1.120609575 1.501373436 0.341731201 0.19910639 0.349909717 1.738483478 0.062720948 0.08484332 1443.863196 -3.159526046 0.380763861 EVDDFFEQEKNFLINYYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVDDFFEQEKNFLINYYNR 19 1 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 248.46 6.50E-25 241130000 392530 278020 413650 396680 354350 405770 511180 451390 396590 FALSE TRUE 373975.8848 306350.5541 432616.2617 356804.9728 416148.5278 391718.0832 433190.1025 411863.8986 458091.1517 0.816378757 0.668754576 0.944389037 0.778895142 0.908440441 0.855109473 0.945641715 0.899087217 1 18.80527517 2.660977993 0.353206915 0.994612216 0.715973138 0.458187503 0.070412786 1.296763556 0.338050401 0.07505036 0.133084928 458.1186718 -2.660977993 -0.278639078 EVDDLEQWIAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVDDLEQWIAER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 282.95 8.26E-28 238846000 304808 261850 277776 316401 292711 269947 333672 301899 320334 FALSE TRUE 290400.3299 288532.8127 290512.3044 284595.7704 343759.7057 260598.6677 282764.2081 275463.1231 370009.7607 0.784845052 0.779797841 0.785147678 0.769157467 0.929055777 0.704302144 0.764207429 0.744475288 1 18.4972038 -1.279486458 3.552291807 1.000601193 0.781732844 0.586748218 0.057327574 18373201.96 27293881.3 117161.6404 0.012816832 0.05254284 1.279486458 -0.21886835 EVDEDS(ph)EPER ddPTM_SK-BR-3_Trastuzumab_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 251.75 5.08E-17 1173040000 1018880 1145260 892050 1164120 918570 1103350 999750 989940 778750 TRUE FALSE 970719.5616 1261963.296 932951.3749 1047100.446 1078768.317 1065140.713 847219.7758 903255.6056 899514.5727 1.07915935 1.402938134 1.037172052 1.164072798 1.199278311 1.184128357 0.941863313 1.004158946 1 19.77878713 1.764265486 7.452078783 0.981187454 1.191362491 0.471793878 0.09689523 0.133676735 22.11729251 0.044987486 0.024597285 58.11195495 -1.764265486 0.210175037 EVDEDS(ph)EPEREVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;EVDEDS(1)EPEREVR 243.92 1.37E-16 3753260000 2881680 2120620 2730180 2590920 2651430 2567200 3601940 2810570 3333690 TRUE FALSE 2745468.697 2336713.589 2855361.454 2330475.799 3113838.553 2478297.22 3052397.899 2564461.591 3850661.619 0.712986227 0.606834311 0.741524895 0.605214384 0.808650269 0.643602961 0.792694399 0.665979472 1 21.87667492 -5 0.218956557 2.548844061 0.65603001 0.646951586 0.070230721 82.32515016 0.823064122 56.11624973 0.115734625 1.00E-05 5 -1.892814051 EVDEQMLNVQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 250.72 9.20E-17 1133404000 1413624 1350362 1226725 1454799 1014900 1387293 1476593 1458719 1125218 FALSE TRUE 1346804.795 1487965.423 1282971.555 1308559.841 1191898.239 1339250.696 1251311.618 1330985.831 1299711.061 1.036234003 1.144843241 0.987120594 1.006808267 0.917048623 1.030421865 0.962761383 1.024062864 1 20.3097595 3.71755977 24.1679566 0.986963985 1.090538616 0.508857772 0.041096878 321.2078576 369648.6395 0.009931364 0.015404898 5218.669218 -3.71755977 0.103574631 EVDGEGKPYYEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVDGEGKPYYEVR 13 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;E9PQ14 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 145.1 3.80E-05 468100000 754380 663730 712210 866450 601040 771160 851140 839730 682340 FALSE TRUE 718721.9524 731364.8416 744865.533 779352.7999 705861.1857 744454.5358 721282.9607 766198.7895 788153.8023 0.91190571 0.927946854 0.945076368 0.988833395 0.895588125 0.9445549 0.915155086 0.972143746 1 19.58811766 1.041425699 4.558594124 0.999717818 0.931849855 0.460139532 0.02497682 0.145316762 6.69350761 0.022633977 0.005754315 11.00083621 -1.041425699 -0.067867963 EVDGLLTSEPMGS(ph)PVSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(0.999)PVS(0.001)SK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.996)PVS(0.004)SK;EVDGLLTSEPMGS(0.963)PVS(0.036)S(0.001)K;EVDGLLTSEPMGS(0.997)PVS(0.002)SK;EVDGLLTSEPMGS(0.991)PVS(0.007)S(0.001)K;EVDGLLTSEPMGS(0.999)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTS(0.001)EPMGS(0.999)PVSSK 417.21 7.05E-148 1754760000 3319410 2828484 2752891 3324402 2215714 3157794 3284057 3262868 2375851 TRUE FALSE 3162508.068 3116709.735 2879113.775 2990226.795 2602133.82 3048438.802 2783013.789 2977153.98 2744285.839 1.152397474 1.135708858 1.049130427 1.089619293 0.948200724 1.110831371 1.014112214 1.084855644 1 21.38799933 3.732302106 1.821881528 1.039883829 1.151808584 0.442449562 0.047517563 0.271639771 1.757458616 0.012200577 0.02607339 5398.8605 -3.732302106 0.111924756 EVDIGIPDATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVDIGIPDATGR 12 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 165.18 0.00012867 281176000 685730 624390 577210 748540 654210 656370 747950 666950 666790 FALSE TRUE 653316.9019 688016.0509 603675.6494 673295.3371 768304.0169 633639.7423 633836.4905 608548.3223 770192.3877 0.84825157 0.893304143 0.783798515 0.874191108 0.997548183 0.8227032 0.822958654 0.79012508 1 19.55485934 2.306454331 0.007684301 1.732835922 5.03E-06 0.10600206 0.07218862 11436.02631 49.24448236 5476.941153 5623.549934 202.513664 -2.306454331 -1.732830893 EVDRPGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 EVDRPGSK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;;; 112.84 0.0027025 10488740000 12819010 11327400 11161300 13145020 9256070 12347700 13957680 13099310 10843910 FALSE TRUE 12213080.8 12481674.94 11673056.65 11823657.62 10870325.68 11920096.05 11828179.57 11952264.97 12525528.18 0.975055154 0.996498891 0.93194127 0.943964793 0.867853676 0.951664144 0.944325812 0.954232412 1 23.5783681 3.734992777 24.89022057 0.937772135 0.985777023 0.229869904 0.032608865 323.2697764 2255226.634 0.007985712 0.012944294 5432.412967 -3.734992777 0.048004888 EVDWSQNTATFSPAIS(ph)PTHPGEGLVLRPLCTADLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 1 EVDWSQNTATFSPAIS(0.805)PT(0.188)HPGEGLVLRPLCT(0.007)ADLNR 111.68 9.03E-06 51571000 2992 2903.5 1349.1 2419.4 2913.8 2064.9 1973.8 1644.3 2558.3 TRUE FALSE 2850.57409 3199.369951 1410.957569 2176.197315 3421.965797 1993.391995 1672.660559 1500.316375 2955.028098 0.96465211 1.082686812 0.477476871 0.73643879 1.158014639 0.674576325 0.5660388 0.50771645 1 11.52895613 2.030937095 24.97176547 0.637352129 0.895070071 0.142671873 0.226601459 285.5129651 230458.7971 0.083349127 0.061556805 107.3833864 -2.030937095 0.257717942 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 131.84 6.72E-09 215500000 6903.9 7497.9 9029.5 10886 7954.8 6690.3 6405.7 6414.9 9465.6 FALSE TRUE 6577.566329 8261.944534 9443.511506 9791.718598 9342.114601 6458.613233 5428.392816 5853.177348 10933.4769 0.601598777 0.755655736 0.863724467 0.895572258 0.854450481 0.590719063 0.496492823 0.535344557 1 13.41646464 2.225132749 24.90231898 0.600304295 0.779203026 0.111555219 0.161000601 332.7271901 617046.6479 0.057885312 0.042993212 167.9317248 -2.225132749 0.178898731 EVDYEAGDIPTEWEAWIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVDYEAGDIPTEWEAWIR 18 0 Q8N183 Q8N183 NDUFAF2 "Mimitin, mitochondrial" 0 ; 113.65 0.00056042 21135500 44266 28503 33860 34408 36103 27759 39074 40400 45852 FALSE TRUE 42173.63391 31407.48811 35412.51449 30949.24247 42399.35177 26797.69887 33112.54366 36862.36183 52962.49398 0.796292447 0.593013768 0.668633817 0.584361501 0.80055429 0.505975018 0.625207409 0.696008799 1 15.69268344 0.837753964 5.138365973 0.999996295 0.651714881 0.58912004 0.090232365 1.612889067 50.66578064 0.080555192 0.020342801 6.882622716 -0.837753964 -0.348281415 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 280.11 6.50E-45 10095200000 7434610 7344530 6307480 7977750 2669530 8452480 6949870 10463800 2508580 TRUE FALSE 7083190.719 8092945.957 6596684.197 7175811.413 3135095.187 8159768.498 5889539.688 9547534.2 2897597.774 2.444504473 2.792984599 2.276604522 2.476469121 1.081963554 2.816045957 2.032559433 3.294982583 1 21.46642591 2.9690205 24.99733622 2.1270278 2.535207814 0.087890591 0.695356922 1754.352344 1415585.893 0.191450461 0.203273322 931.1518285 -2.9690205 0.408180013 EVEEDEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVEEDEYK 8 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 193.28 0.00039898 1905400000 3472000 3251750 2844251 3774570 1998330 3411942 3198530 3486170 1984839 FALSE TRUE 3307885.441 3583107.022 2974662.722 3395143.052 2346838.119 3293785.593 2710535.503 3180902.473 2292637.695 1.442829562 1.562875386 1.29748487 1.480889484 1.023641077 1.436679507 1.182278172 1.387442281 1 21.12857695 7.999999084 0.037453853 3.66E-07 3.460039595 0.420432243 0.145188811 698.910247 1.997529199 52.52472115 158.5696207 99999789.19 -7.999999084 3.460039228 EVEEDEYKAFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVEEDEYKAFYK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 141.32 5.51E-05 437720000 621650 290310 668550 535770 647490 680160 1152460 777790 820260 FALSE TRUE 592265.8365 319892.9191 699203.6788 481913.3817 760412.051 656605.8887 976631.0606 709682.5843 947461.7315 0.625107924 0.337631493 0.737975641 0.50863625 0.802578116 0.693015735 1.030786815 0.749035619 1 19.85370815 2.46423564 0.832685746 0.945012396 0.499005781 0.560133491 0.136920842 0.382369374 0.532018298 0.089683251 0.064043605 291.2296848 -2.46423564 -0.446006615 EVEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVEEEER 7 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;Q8NFC6 Q9UPQ0-4;Q8NFC6 LIMCH1;BOD1L1 LIM and calponin homology domains-containing protein 1;Biorientation of chromosomes in cell division protein 1-like 1 0 86.953 0.045825 126140000 214970 179460 220540 246150 220360 205110 234560 208190 233780 FALSE TRUE 204808.7941 197747.178 230651.9771 221406.5343 258790.7142 198006.9893 198773.564 189959.7799 270033.4084 0.758457242 0.732306344 0.854160893 0.819922748 0.958365544 0.733268489 0.736107303 0.703467697 1 18.04277838 -2.362481415 2.331435942 2.521821417 0.782628403 0.438813048 0.075553438 3880890.5 563888.3728 31237699.32 0.018486378 0.004340288 2.362481415 -1.739193014 EVEEEPGIHSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVEEEPGIHSLK 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 177.83 2.28E-05 1419080000 2808980 2397990 2445540 2826190 2188140 2735930 2951370 2824750 2113630 FALSE TRUE 2676205.082 2642347.907 2557670.428 2542096.012 2569750.923 2641184.058 2501084.301 2577399.915 2441400.945 1.096175983 1.082308054 1.047624084 1.041244789 1.052572265 1.081831341 1.024446355 1.055705299 1 21.21927781 7.999999999 0.075002832 0.949626044 1.326672016 0.625319571 0.017493249 132.7552749 0.730496598 0.595403297 5.228374665 99999999.76 -7.999999999 0.377045972 EVEELEQLTQQLMQDMEHPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;;;;; 139.11 4.03E-07 894811900 219829.1 247416.8 227186.2 261923 216311 228526.1 240785 232238.8 238287.5 FALSE TRUE 209438.2141 272628.8532 237602.912 235594.0024 254035.5699 220612.1839 204048.8259 211902.7395 275239.9085 0.760929675 0.990513529 0.863257488 0.85595873 0.922960523 0.801526875 0.741348982 0.769883774 1 18.07033014 2.215312464 22.05634661 0.799457975 0.881521599 0.030733206 0.090430178 107.7234072 102198.1625 0.03115094 0.023032625 164.1770561 -2.215312464 0.082063624 EVEERPAPTPWGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVEERPAPTPWGSK 14 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 161.49 4.18E-06 577170000 694850 738750 643580 729770 494920 725950 740780 784470 574050 FALSE TRUE 662005.8176 814029.4649 673088.7796 656412.1331 581233.8913 700810.1695 627760.4056 715777.6481 663070.7422 0.99839395 1.227666089 1.01510855 0.989957921 0.876579005 1.05691614 0.946747256 1.079489114 1 19.33880327 3.500708902 23.10233509 0.986789816 1.114422961 0.290598473 0.077267194 289.3523122 283397.5196 0.019050849 0.029268314 3167.443681 -3.500708902 0.127633145 EVEERPEKDFTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVEERPEKDFTEK 13 2 Q32MZ4-3 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 57.414 0.064541 144850000 100260 88574 90564 84053 58925 80364 86419 102950 71157 FALSE TRUE 95520.9085 97599.7913 94716.44898 75603.83275 69201.50134 77580.97453 73234.19436 93935.15223 82191.66414 1.162172703 1.187465813 1.152385099 0.919847938 0.841952795 0.943903197 0.891017296 1.142879308 1 16.32670446 3.264881361 6.859464057 0.940951078 1.172237949 0.602490413 0.080032403 0.099382241 16.26611564 0.021115253 0.028009494 1840.269215 -3.264881361 0.231286872 EVEERS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVEERSR 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5 Q04637-9;Q9UKE5-6 EIF4G1;TNIK Eukaryotic translation initiation factor 4 gamma 1;TRAF2 and NCK-interacting protein kinase 1 EVEERS(1)R;EVEERS(1)R;EVEERS(1)R 72.928 0.030447 535263000 939532 499981 962645 843808 1038675 788647 1191220 1013595 1287430 TRUE FALSE 895122.1843 550929.6323 1006783.225 758986.8167 1219819.591 761335.9566 1009477.511 924839.2484 1487078.069 0.601933552 0.370477949 0.677021097 0.51038801 0.820279457 0.511967712 0.678832895 0.621917079 1 20.50404896 -4.999999996 0.144206514 2.475190406 0.442335297 0.554489386 0.116135916 91.08198918 0.794398599 38.39028763 0.592433955 1.00E-05 4.999999996 -2.032855109 EVEEYKNFRPDDPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVEEYKNFRPDDPTR 15 2 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 68.944 0.028756 89977000 99216 66939 100570 108010 94554 90501 123470 111710 103370 FALSE TRUE 94526.25631 73760.1602 105181.234 97152.62959 111044.1877 87366.92768 104632.3838 101928.0802 119400.0917 0.791676581 0.617756311 0.880914181 0.81367299 0.930017608 0.73171575 0.87631745 0.853668358 1 16.86544442 2.380806881 0.041406727 1.644697966 1.45E-09 0.402421022 0.081716702 90.9171209 1.988111159 36.03345078 42.10826909 240.3293885 -2.380806881 -1.644697965 EVEGERR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 133.79 0.0051908 1698440000 2409050 1830540 2118370 2243170 2623770 2218240 2900260 2460300 3212370 FALSE TRUE 2295178.981 2017074.107 2215499.36 2017682.29 3081354.657 2141421.793 2457772.07 2244863.089 3710527.933 0.618558605 0.543608388 0.597084674 0.543772295 0.830435645 0.577120515 0.662378 0.604998299 1 21.82319304 -5 0.244795242 3.242573621 0.581801122 0.680989557 0.081440597 96.01154498 0.954771126 107.4327296 0.112483534 1.00E-05 5 -2.660772499 EVEHFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVEHFLK 7 0 O15427 O15427 SLC16A3 Monocarboxylate transporter 4 0 80.18 0.030613 86192000 217900 156210 175950 282180 214740 196880 242440 220450 208550 FALSE TRUE 207600.2988 172127.9766 184017.4815 253814.7303 252190.588 190061.9962 205451.3253 201146.2293 240890.8689 0.861802275 0.714547535 0.76390393 1.053650275 1.046908043 0.788996267 0.852881333 0.835009771 1 17.87802018 8 0.061282016 1.124853366 0.312360948 0.118790438 0.110469502 697.263605 3.187667826 8.39565668 50.30063767 100000000 -8 -0.812492418 EVELVS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVELVSE 7 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 EVELVS(1)E;EVELVS(1)E 85.38 0.021874 226220000 1229570 1038840 967230 1123970 1385760 1053530 1316750 1158200 1281140 TRUE FALSE 1171450.663 1144698.977 1011578.452 1010986.4 1627436.105 1017045.992 1115855.604 1056781.868 1479812.648 0.791620929 0.773543177 0.683585489 0.683185403 1.099758208 0.68728024 0.754051944 0.714132204 1 20.4969831 EVEMDAVGKDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVEMDAVGKDGR 12 1 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;; 112.44 0.0011617 641240000 1959220 988920 1866010 1359980 1818250 1534020 2133100 1787950 2064100 FALSE TRUE 1866611.553 1089692.072 1951568.404 1223272.227 2135352.224 1480896.503 1807656.418 1631387.619 2384190.086 0.78291222 0.457049158 0.818545642 0.513076635 0.895630024 0.621131894 0.758184689 0.684252329 1 21.18506783 -4.999999994 0.194589706 2.427492839 0.625326586 0.340482579 0.134563762 138.2938398 1.360231218 76.34727168 0.300848872 1.00E-05 4.999999994 -1.802166253 EVEPEPTEDKDLEADEEDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;; 247.36 3.66E-30 2791940000 5545350 6133430 4625680 6810830 3208500 5832510 5333530 6337710 3182060 FALSE TRUE 5283232.295 6758433.49 4837772.003 6126192.429 3768061.384 5630528.716 4519802.042 5782746.514 3675517.613 1.437411775 1.838770536 1.31621516 1.666756379 1.025178432 1.531900894 1.229704906 1.57331487 1 21.809516 2.768189656 24.96972975 1.302911644 1.582489566 0.284212478 0.227189336 853.8096949 719542.4637 0.061986394 0.065737909 586.3941869 -2.768189656 0.279577922 EVESPYEVHDYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVESPYEVHDYIR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 190.1 4.70E-06 106810000 155240 136740 149240 150260 174110 138940 164240 160080 169010 FALSE TRUE 147902.1129 150673.9615 156082.8016 135155.5793 204474.7289 134128.473 139182.1715 146062.5466 195219.2076 0.757620701 0.771819348 0.799525843 0.692327261 1.047410915 0.687065963 0.712953265 0.74819762 1 17.57473548 -2.222329342 2.200501331 1.699920864 0.773158561 0.318203875 0.102386073 4955794.355 952758.1335 17238703.09 0.023264848 0.005993364 2.222329342 -0.926762303 EVETYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVETYHR 7 0 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ; 110.63 0.0067597 483550000 573680 543170 494570 619290 511810 493160 555550 560840 526480 FALSE TRUE 546563.2833 598519.6405 517246.5237 557037.7926 601069.502 476081.7455 470790.6441 511729.8764 608123.8295 0.898769719 0.984206853 0.850561183 0.915994022 0.98839985 0.782869742 0.774169045 0.841489597 1 19.2140056 2.232045501 24.99976467 0.823031613 0.928659551 0.177402099 0.074136987 171.6289674 658567.6282 0.025034502 0.018929832 170.6261146 -2.232045501 0.105627938 EVEVEVESMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVEVEVESMDK 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 107.83 0.0033067 0 68038 63554 68468 81011 51281 68402 74651 73493 58845 FALSE TRUE 64821.97858 70030.22485 71607.32552 72867.62037 60224.39016 66033.22159 63261.61889 67057.56331 67970.38206 0.953679774 1.030305005 1.053507768 1.072049592 0.886038718 0.971499933 0.930723309 0.986570345 1 16.05261861 2.745291948 24.99974791 0.950475282 1.021133817 0.401147393 0.043479818 554.9109008 2060904.261 0.01322012 0.013737034 556.2780817 -2.745291948 0.070658535 EVEVIGGADKYHSVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVEVIGGADKYHSVCR 16 1 P04183 P04183 TK1 "Thymidine kinase, cytosolic" 0 ;; 179.14 1.61E-09 1766490000 1755590 1667940 1701690 1863600 1432600 1689060 2046690 1913640 1618980 FALSE TRUE 1672606.74 1837904.982 1779714.17 1676267.387 1682444.986 1630567.429 1734429.85 1746071.537 1870043.15 0.894421468 0.982814211 0.951696847 0.896378989 0.899682441 0.871941072 0.927481192 0.933706549 1 20.83464013 0.750695136 2.609582519 0.999965962 0.920713157 0.39660498 0.031553902 1.554400731 14.52796856 0.031991141 0.008506952 5.632421355 -0.750695136 -0.079252806 EVFEDAAEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVFEDAAEIR 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 224.86 8.77E-09 3595520000 4647290 3946940 4040320 4692310 4352960 4180300 4832740 4365530 4392840 FALSE TRUE 4427621.812 4349137.673 4225572.668 4220630.084 5112114.846 4035535.163 4095416.754 3983261.05 5074059.192 0.872599559 0.857131836 0.832779538 0.831805449 1.007500041 0.795326781 0.807128297 0.785024553 1 22.27470892 -0.055719168 7.521784808 0.999999998 0.849093854 0.367529495 0.062389079 1958055.064 325397.3572 0.058276646 0.014134163 0.879591111 0.055719168 -0.150906144 EVFEFRPELVNDDDEEADDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ;; 266.14 5.21E-37 401133000 321050 374340 316484 395010 353707 329209 337983 330241 289542 FALSE TRUE 305874.6028 412485.6716 330995.1044 355302.8443 415393.3888 317808.4098 286417.4859 301323.3473 334442.6946 0.914580009 1.233352315 0.989691537 1.062372867 1.242046532 0.950262676 0.856402279 0.900971533 1 18.35139951 2.019096523 24.34171445 0.903210071 1.08748841 0.374316186 0.103720295 158.9625643 202623.2733 0.03649406 0.02694833 104.4952437 -2.019096523 0.184278339 EVFGSGTACQVCPVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVFGSGTACQVCPVHR 16 0 M0QZP4;B3KSI3;M0QZ10;M0QXF9;O15382-2;O15382 M0QZP4 BCAT2 "Branched-chain-amino-acid aminotransferase;Branched-chain-amino-acid aminotransferase, mitochondrial" 0 157.68 1.46E-08 0 75040 58035 57631 64800 72043 44342 63448 68889 62240 FALSE TRUE 71493.00791 63948.83248 60273.43835 58286.18089 84607.27639 42806.42542 53767.8423 62856.71396 71891.86132 0.994452037 0.889514213 0.838390289 0.810747974 1.176868631 0.595427975 0.747898876 0.874323085 1 16.13354084 2.221649444 24.9997044 0.772886604 0.928932105 0.168709917 0.142778172 355.2586618 525173.7662 0.049408741 0.036583878 166.5901978 -2.221649444 0.1560455 EVGKDVSDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVGKDVSDEK 10 1 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 74.76 0.037416 329510000 478060 397260 362040 483410 234240 408220 389590 423750 189310 FALSE TRUE 455463.0512 437741.2456 378639.8921 434816.7084 275091.3818 394083.239 330150.8902 386644.2036 218667.2279 2.082904949 2.001860314 1.731580428 1.98848594 1.258036627 1.802205309 1.509832513 1.768185417 1 17.73837749 3.287627069 0.070617307 7.20E-14 3.659052229 0.642528282 0.20478254 36.66509756 0.742462318 14.05001115 24.39775356 1939.219946 -3.287627069 3.659052229 EVGKDVSDEKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVGKDVSDEKLR 12 2 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 130.07 0.00012544 1218830000 2559900 1988710 2000660 2184680 1345490 2202230 2276340 2665000 1408150 FALSE TRUE 2438898.6 2191361.81 2092392.24 1965071.816 1580143.03 2125966.223 1929042.525 2431638.472 1626518.71 1.499459296 1.347271197 1.286423714 1.208145841 0.971487767 1.307065335 1.185994673 1.494995696 1 20.63335599 3.973799175 1.358886038 1.202867278 1.487318384 0.311843105 0.146822137 0.556589967 1.860127645 0.041180701 0.146715013 9414.541529 -3.973799175 0.284451105 EVGKGNEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVGKGNEGK 9 1 Q9NZW4 Q9NZW4 DSPP Dentin sialophosphoprotein;Dentin phosphoprotein;Dentin sialoprotein 0 59.245 0.094431 455700000 985980 640710 671440 814270 1919200 341060 718250 345140 1789200 FALSE TRUE 939374.6794 705999.0774 702226.1881 732418.0326 2253907.872 329249.0067 608667.7709 314917.7119 2066659.998 0.454537602 0.341613559 0.339787962 0.354396966 1.090604103 0.15931455 0.294517614 0.15238003 1 20.97886963 -0.969034614 4.230554353 1.000025489 0.395984109 0.341804977 0.262344129 132366335.5 280424271 51334.69849 0.059936268 0.107390382 0.969034614 -0.604041379 EVGSIIGK ddPTM_SK-BR-3_Trastuzumab_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 0 130.27 0.0044022 0 127420 128310 132560 157750 116560 146180 164150 153380 149700 FALSE TRUE 121397.1091 141384.9349 138638.0071 141892.6703 136888.0271 141117.7499 139105.9027 139949.2341 172914.7114 0.702063509 0.817657062 0.801771035 0.820593396 0.791650554 0.816111878 0.804476967 0.80935412 1 17.39970109 -5 0.186593213 1.86675429 0.754163165 0.823478338 0.030616058 55.20433276 0.53725963 17.77841829 0.086793807 1.00E-05 5 -1.112591125 EVGVYEALKDDSWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVGVYEALKDDSWLK 15 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;; 203.99 4.68E-09 1457800000 2837397 2792719 2323753 3207931 1547732 2636978 2810626 2940300 1586561 FALSE TRUE 2703278.867 3077300.241 2430299.374 2885463.681 1817655.971 2545658.791 2381813.383 2682831.744 1832596.777 1.475108382 1.679202037 1.326150632 1.574521858 0.991847194 1.38909924 1.299693098 1.463950924 1 20.80545796 8 0.039351338 4.23E-12 3.639056811 0.372819235 0.175612781 730.3920087 2.190070134 56.01227317 178.714925 99999999.95 -8 3.639056811 EVGVYEALKDDSWLKGEFVTTVQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVGVYEALKDDSWLKGEFVTTVQQR 25 2 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ; 242.94 6.22E-39 509860000 412930 269480 447050 365250 350910 425990 630600 487870 451870 FALSE TRUE 393411.6172 296940.3184 467547.6847 328534.3761 412108.5929 411237.8595 534390.3882 445149.5164 521943.6918 0.753743408 0.568912553 0.895781848 0.629444098 0.789565234 0.787896982 1.023846818 0.852868851 1 18.99353465 2.034828865 2.072231077 0.959996551 0.70651231 0.523135079 0.099221372 0.226599255 1.836008194 0.050718459 0.0274873 108.3499875 -2.034828865 -0.253484241 EVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 EVHDELEDLPS(0.999)PPPPLS(0.93)PPPT(0.026)T(0.024)S(0.021)PHK 59.954 0.031058 158450000 106420 99852 119130 131900 77095 96516 115140 100810 75728 TRUE FALSE 101389.7375 110027.0323 124592.2283 118641.1614 90540.34359 93173.62672 97573.27831 91982.54197 87471.51147 1.159117246 1.257861336 1.424374933 1.356340589 1.03508379 1.065188256 1.115486364 1.051571425 1 16.4165256 2.731847286 24.98508955 1.066027092 1.283848654 0.72944772 0.073943633 344.6224533 1282582.623 0.026288569 0.025309374 539.3209437 -2.731847286 0.217821562 EVIEIEDAS(ph)PTKCPITTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVIEIEDASPTKCPITTK 18 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 EVIEIEDAS(0.989)PT(0.011)KCPITTK;EVIEIEDAS(0.979)PT(0.021)KCPITTK 197.92 1.08E-15 263910000 418060 435260 446330 477550 274540 524940 556270 549710 344080 TRUE FALSE 398299.1323 479613.4888 466794.672 429545.7667 322419.6891 506761.1962 471400.7949 501574.4782 397438.1691 1.002166282 1.206762526 1.174508913 1.080786397 0.811244903 1.27506927 1.186098446 1.262018893 1 18.60037091 EVIGGLCSLANIPLT(ph)PETQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVIGGLCSLANIPLTPETQR 20 0 Q01664 Q01664 TFAP4 Transcription factor AP-4 1 EVIGGLCSLANIPLT(0.992)PET(0.008)QR;EVIGGLCSLANIPLT(0.992)PET(0.008)QR 128.79 0.00021345 26517000 79119 85002 77402 86917 95563 78279 109662 85890 105486 TRUE FALSE 75379.20167 93663.80044 80950.95826 78179.93803 112229.1569 75568.1786 92931.04782 78369.01627 121844.2301 0.618652205 0.768717569 0.664380728 0.641638409 0.921087169 0.620203177 0.762703722 0.643190212 1 16.89467841 -2.181932372 2.372290954 1.785819377 0.709148529 0.496262071 0.093302229 4111451.484 888647.849 17383052.43 0.019894956 0.006577603 2.181932372 -1.076670848 EVIKPYDWTYTTDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVIKPYDWTYTTDYK 15 1 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 205.42 4.02E-09 412200000 517200 506070 434790 589300 319820 534180 479130 563090 299560 FALSE TRUE 492752.981 557639.1084 454725.5516 530062.4444 375596.5067 515681.2127 406029.9187 513782.8545 346014.2349 1.424082975 1.61160742 1.314181631 1.531909358 1.085494378 1.490346814 1.173448598 1.484860456 1 18.40047187 -3.484201507 0.086281666 1.22E-14 1.787910977 0.380986993 0.159458415 137.8501495 1.143824449 29.68976523 4.197186507 0.000327943 3.484201507 1.787910977 EVIKS(ph)PTASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.951)PT(0.049)ASR;EVIKS(0.882)PT(0.118)ASR;EVIKS(0.974)PT(0.026)ASR;EVIKS(0.95)PT(0.05)ASR;EVIKS(0.962)PT(0.038)ASR 125.84 0.00024129 1504320000 1837310 1617340 1572410 1909700 1796410 1624570 1869070 1816930 2034110 TRUE FALSE 1750463.997 1782148.785 1644506.554 1717733.328 2109703.335 1568310.734 1583909.044 1657829.977 2349549.39 0.745021154 0.758506628 0.699924233 0.731090538 0.897918275 0.667494261 0.674133113 0.705594862 1 21.16395266 -1.459196883 3.050338806 1.005951699 0.733892183 0.624265879 0.06461555 17126686.07 20857719.75 871818.8733 0.015496262 0.034737865 1.459196883 -0.272059516 EVIQSDSLWLVEFYAPWCGHCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVIQSDSLWLVEFYAPWCGHCQR 23 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 196.32 3.16E-24 54004000 87962 78936 93577 78004 90403 79791 108410 84050 73393 FALSE TRUE 83804.21058 86979.66814 97867.59801 70162.88972 106169.2546 77027.81766 91870.06341 76690.13642 84774.4116 0.988555497 1.026013233 1.154447388 0.827642309 1.25237383 0.908621083 1.083700396 0.904637791 1 16.37134125 1.236490265 24.99914795 0.95231891 1.031317425 0.074427362 0.120052096 145.1490537 1752432.717 0.082665906 0.024629432 17.2381345 -1.236490265 0.078998515 EVIRNDGVLLLQALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVIRNDGVLLLQALTR 16 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 219.68 1.11E-14 151741000 187539 169546 244829 208181 381950 168240 281170 189534 333670 FALSE TRUE 178674.4031 186822.9302 256054.6518 187254.2504 448561.9591 162413.8066 238272.3525 172937.3982 385413.8394 0.463591041 0.48473332 0.664362889 0.48585243 1.163844972 0.421401076 0.618224693 0.44870573 1 18.55604885 3.703147038 1.827168591 0.670470463 0.462321535 0.119147166 0.23587002 0.755596259 4.925666765 0.06409007 0.132804473 5048.321885 -3.703147038 -0.208148928 EVKPEETTCSEHCLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVKPEETTCSEHCLQK 16 1 Q9Y5J7 Q9Y5J7 TIMM9 Mitochondrial import inner membrane translocase subunit Tim9 0 227.4 3.04E-15 308950000 387570 306790 352250 414090 264350 323800 416910 395890 254980 FALSE TRUE 369250.3342 338052.2498 368401.0109 372464.8865 310452.5563 312586.7248 353302.7224 361223.7729 294520.9961 1.253731785 1.147803567 1.250848041 1.264646295 1.054093122 1.061339357 1.199584162 1.226478851 1 18.16801096 2.747372127 24.97202811 1.123080883 1.219600631 0.385029375 0.074228922 833.5778691 2362380.329 0.02262476 0.023665531 558.9489276 -2.747372127 0.096519747 EVLAGRPLFPHVLCHNCAVEFNFGQK ddPTM_SK-BR-3_Trastuzumab_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 0 127.4 6.18E-05 764430000 789000 591470 769000 686800 646890 715870 881650 750440 92483 FALSE TRUE 751705.5336 651741.4654 804259.4106 617761.5592 759707.4112 691079.2424 747138.0999 684727.4953 106824.7913 7.036807884 6.101031956 7.528771185 5.782941877 7.111714443 6.469277721 6.994051575 6.409818235 1 16.70488697 0.929559472 18.24354921 0.999999998 6.690376993 0.92555497 0.506876452 229.1875598 59358.36277 0.415002937 0.103750734 8.502751204 -0.929559472 5.690376995 EVLAS(ph)PDRLWGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 216.71 1.64E-11 401837000 331482 322852 326448 367219 345343 316460 379797 343709 352105 TRUE FALSE 315813.5028 355750.9859 341415.9637 330305.4484 405570.7099 305500.9108 321851.9922 313612.0178 406707.6451 0.776512334 0.874709365 0.839462862 0.812144675 0.997204539 0.751156057 0.791359582 0.771099392 1 18.63363258 -2.333458649 2.23618901 1.963229106 0.82700123 0.375901227 0.070172968 4308172.871 613799.2144 20946783.14 0.016481054 0.00464025 2.333458649 -1.136227876 EVLDEDT(ph)DEEKETLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 EVLDEDT(1)DEEKETLK 222.3 2.30E-12 242380000 312490 281000 281230 322580 139290 317870 308070 363870 141740 TRUE FALSE 297719.217 309634.2195 294124.6737 290153.6455 163582.1319 306862.0822 261068.2634 332007.6138 163720.3153 1.818462275 1.891238842 1.796506885 1.772251935 0.999155979 1.87430669 1.594599076 2.027895031 1 17.32087382 2.978706905 24.77133421 1.552861811 1.837376602 0.186096911 0.324534012 1223.260765 1423082.758 0.090159192 0.09653334 952.1533625 -2.978706905 0.284514791 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR 30 1 P53582 P53582 METAP1 Methionine aminopeptidase 1 0 ; 168.09 1.51E-12 237645000 305650 264060 275190 305460 273670 274410 327740 282250 16975.4 FALSE TRUE 291202.5302 290968.0142 287807.7337 274754.5805 321397.9614 264907.1129 277737.2436 257534.6937 19607.85833 14.85131753 14.83935722 14.67818304 14.01247274 16.39128333 13.51025229 14.16458845 13.1342592 1 14.25914435 -0.239896924 0.696078307 0.17607579 14.84970117 0.973122707 0.707825328 1.012261346 0.437274715 2.874828581 0.225752918 0.575576529 0.239896924 14.67362538 EVLEGLEYLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVLEGLEYLHK 11 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ;;;; 211.64 8.64E-09 1410710000 3042290 2768860 2654350 3199340 2380420 2804680 3098930 3035770 2246220 FALSE TRUE 2898486.981 3051009.982 2776054.573 2877736.265 2795564.494 2707553.228 2626131.313 2769941.885 2594552.325 1.11714339 1.175929255 1.069955131 1.109145588 1.077474702 1.043553141 1.012171266 1.067599161 1 21.3070542 2.753948898 0.707369303 1.018028787 1.146622497 0.678455336 0.029145284 0.354286067 0.382913892 0.019771152 0.020060611 567.4778286 -2.753948898 0.128593711 EVLHGNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 EVLHGNQR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;;;;;; 205.7 7.74E-05 6075860000 6591580 5825550 5429710 6294250 7290890 5959410 7606100 6247900 6967430 FALSE TRUE 6280009.077 6419180.168 5678667.574 5661540.032 8562418.908 5753034.137 6445649.749 5700800.754 8047903.46 0.78032858 0.797621418 0.705608312 0.703480113 1.063931613 0.714848801 0.800910421 0.708358491 1 22.94018157 EVLLLHNNDQDNALEDLMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVLLLHNNDQDNALEDLMAR 20 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 0 93.269 0.0015343 18203000 17759 16629 13069 16306 19216 18027 18439 19723 17870 FALSE TRUE 16919.56726 18323.51401 13668.22658 14666.8899 22567.26432 17402.72047 15625.79189 17995.94956 20641.18833 0.819699282 0.887716042 0.662182155 0.710564221 1.093312262 0.84310652 0.757019976 0.871846585 1 14.33323841 EVLPSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVLPSTR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 110.81 0.015635 168204000 350290 333420 412560 370480 536810 372760 503590 379640 300110 FALSE TRUE 333732.4859 367395.8771 431476.2841 333238.6465 630429.494 359851.2277 426758.0964 346396.709 346649.5261 0.962737465 1.059848202 1.24470467 0.961312858 1.818636538 1.038083715 1.231093841 0.999270684 1 18.40311826 3.973425356 1.666002399 1.207615778 0.970691759 0.076333065 0.247948321 0.850235367 4.48231164 0.065310844 0.19754455 9406.441437 -3.973425356 -0.23692402 EVLS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVLSPLK 7 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 EVLS(1)PLK;EVLS(1)PLK;EVLS(1)PLK;EVLS(1)PLK 116.52 0.005704 238982000 719820 633818 538359 685690 466611 622867 704340 684307 483637 TRUE FALSE 685795.5351 698404.7748 563043.2927 616763.1385 547987.8107 601296.9596 596879.9969 624385.4513 558636.9559 1.227622927 1.250194366 1.007887657 1.104050013 0.98093727 1.07636445 1.068457771 1.117694497 1 19.09155149 3.745480853 24.9914417 1.05526359 1.238908661 0.753412316 0.044689983 215.4081042 777913.2803 0.010423488 0.018298716 5565.200981 -3.745480853 0.183645071 EVLYDS(ph)EGLS(ph)GEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 EVLYDS(1)EGLS(1)GEER;EVLYDS(1)EGLS(1)GEER 180.78 2.50E-06 772650000 1028840 1083600 980260 1127430 947710 1033890 1016580 1010950 888860 TRUE FALSE 980208.7722 1194020.072 1025205.891 1014098.594 1112990.324 998086.1301 861482.0502 922425.8586 1026699.869 0.954717928 1.162968953 0.998544873 0.987726428 1.084046426 0.972130376 0.839078757 0.89843769 1 19.96958308 1.997076983 5.833930041 0.896548289 1.042413091 0.401007676 0.069055014 0.128562255 16.77284781 0.026842861 0.018054447 99.32921039 -1.997076983 0.145864802 EVMNADDPDLQRPDEEAIKEITEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVMNADDPDLQRPDEEAIKEITEK 24 2 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 121.35 7.19E-05 48985000 111430 97058 100400 115730 66982 131890 133510 135810 71561 FALSE TRUE 106162.9247 106948.3205 105003.4393 104096.6005 78663.63959 127322.6162 113140.5974 123917.7564 82658.3144 1.284358694 1.29386041 1.270331243 1.259360311 0.951672438 1.540348568 1.368774554 1.499156586 1 16.33487232 EVMSLHEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVMSLHEASR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 210.87 6.93E-08 1767410000 1089290 882930 964040 1051770 1225290 947610 1339190 1161840 1309890 FALSE TRUE 1037801.42 972901.5708 1008242.188 946044.0814 1438980.188 914794.0281 1134871.97 1060103.13 1513021.051 0.685913405 0.64301919 0.66637684 0.625268287 0.951064221 0.60461421 0.750070178 0.700653259 1 20.52900063 -5 0.211479514 2.454839285 0.656686678 0.491463336 0.095946109 117.1184854 1.167855163 72.28928058 0.181702386 1.00E-05 5 -1.798152607 EVNKFQMAYSNLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVNKFQMAYSNLLR 14 1 P37108 P37108 SRP14 Signal recognition particle 14 kDa protein 0 100.43 0.0016314 174810000 105020 64736 74031 76762 116410 92734 133640 104560 113050 FALSE TRUE 100055.9127 71332.672 77425.39458 69045.73792 136711.8671 89522.59833 113250.7635 95404.17209 130581.2166 0.766235109 0.546270542 0.592929034 0.528757043 1.046948946 0.685570258 0.86728219 0.730611757 1 16.99458786 2.7582136 24.96332842 0.843766703 0.614821444 0.509061298 0.124537692 683.1080377 867686.537 0.034800565 0.036864008 573.0778197 -2.7582136 -0.228945259 EVPAHSTEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVPAHSTEVGR 11 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 165.66 9.79E-05 1279980000 491545 396503 435875 486260 673020 407042 586000 456666 674230 FALSE TRUE 468310.642 436907.1065 455860.2999 437380.221 790394.4749 392946.0335 496594.9374 416677.9041 778786.1449 0.60133407 0.561010374 0.585347214 0.561617877 1.014905671 0.504562178 0.637652507 0.535035076 1 19.57086769 -1.969896947 2.358984579 1.320696817 0.62230387 0.402738236 0.143409253 8106514.302 3385390.418 14196767.07 0.033209216 0.010717736 1.969896947 -0.698392947 EVPIPEHIDIYHLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVPIPEHIDIYHLTR 15 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;;; 159.13 1.03E-06 622870000 566503 478610 510823 565237 620946 494053 613471 559334 64863 FALSE TRUE 539725.5259 527380.9031 534244.7398 508418.3029 729238.7858 476943.8207 519874.7318 510355.7497 74921.62277 7.203868603 7.039101446 7.130715007 6.78600228 9.733355457 6.365903502 6.938914463 6.811861929 1 16.19309453 -0.015162549 0.88152612 0.888551224 7.346030849 0.830420258 0.892226891 2.395387336 1.735833559 1.65924159 0.265339476 0.96568937 0.015162549 6.457479626 EVPVY(ph)IGEDS(ph)T(ph)IARESY(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVPVYIGEDSTIARESYR 18 1 H0YL34;A0A075B7B1;O15061-2;O15061 H0YL34 SYNM Synemin 4 EVPVY(0.816)IGEDS(0.816)T(0.834)IARES(0.718)Y(0.816)R;EVPVY(0.812)IGEDS(0.812)T(0.826)IARES(0.738)Y(0.812)R 56.529 0.040428 585830000 98263 88943 93376 85115 49449 111046 118594 125718 70304 TRUE FALSE 93618.30273 98006.39282 97657.38196 76559.07849 58072.88994 107200.4492 100500.3072 114709.4654 81206.38526 1.152844107 1.206880377 1.202582551 0.942771658 0.715127139 1.320098769 1.237591193 1.412567067 1 16.30930555 EVQAEQPSSSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSS(0.001)S(0.999)PR;EVQAEQPSSS(0.041)S(0.959)PR;EVQAEQPS(0.013)S(0.06)S(0.273)S(0.653)PR;EVQAEQPSSS(0.001)S(0.999)PR;EVQAEQPSSSS(1)PR 303.44 4.17E-41 5356851500 5468138 5122938 5117615 5798758 5441272 5203547 5938351 5378788 5789973 TRUE FALSE 5209669.954 5644971.206 5352262.71 5215855.829 6390228.114 5023346.863 5032346.49 4907792.808 6687852.442 0.778975015 0.84406336 0.800296172 0.779899957 0.955497773 0.751115086 0.752460754 0.733836886 1 22.67311159 -2.211993993 2.471432708 1.666346541 0.80061371 0.498014387 0.063247579 6517500.739 901287.6051 24660410.2 0.015678457 0.006137705 2.211993993 -0.865732831 EVQDKDYPLT(ph)PPPS(ph)PTVDEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVQDKDYPLTPPPSPTVDEPK 21 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 2 EVQDKDYPLT(1)PPPS(0.574)PT(0.426)VDEPK 128.92 2.86E-05 0 166910 148990 144380 174650 78448 169800 176860 178730 87045 TRUE FALSE 159020.4951 164172.2504 150999.9658 157093.8502 92129.30636 163919.7834 149876.7587 163079.4537 100543.494 1.581609 1.632848072 1.501837262 1.562446697 0.916312957 1.63033705 1.490665907 1.621979177 1 16.61746021 -2.156938047 1.913799203 6.03E-05 1.500795582 0.348844372 0.211071328 1992570.78 415266.1945 8630459.191 0.055660476 0.006967259 2.156938047 1.500735285 EVQQGEEFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVQQGEEFER 10 0 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 183.78 3.79E-06 243520000 293060 248640 282990 307990 244130 301510 357490 297380 249250 FALSE TRUE 279207.6346 273976.6987 295965.3714 277030.2601 286706.1947 291068.6331 302948.3347 271339.8307 287902.417 0.96979955 0.951630422 1.028005859 0.96223666 0.995845043 1.010997532 1.052260477 0.942471527 1 18.13522038 3.594677144 0.881541976 1.007367185 0.957848724 0.086807563 0.033110605 1.07535387 1.627380812 0.013382119 0.036800645 3932.576174 -3.594677144 -0.049518461 EVQQGEEFERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVQQGEEFERR 11 1 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;; 162.38 5.43E-05 292330000 1141650 1114019 1032130 1183490 1053950 1208790 1334470 1286690 1234370 FALSE TRUE 1087686.467 1227538.803 1079454.181 1064523.337 1237758.546 1166929.299 1130872.092 1174020.602 1425789.795 0.762865936 0.860953562 0.757092094 0.746620112 0.868121339 0.818444137 0.793154851 0.823417734 1 20.44332987 -4.999999995 0.342000515 3.141131512 0.798131248 0.704678101 0.040281335 221.9530719 1.85895055 347.2217432 0.030581269 1.00E-05 4.999999995 -2.343000264 EVQTNDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVQTNDLK 8 0 P61247;E9PFI5;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 89.247 0.032665 69754000 197180 190980 193030 227840 162040 210970 238330 233010 157120 FALSE TRUE 187859.6922 210441.0791 201880.6164 204937.0903 190299.7247 203664.056 201968.3813 212606.4091 181485.3671 1.03512308 1.159548466 1.11237958 1.129221014 1.048567869 1.122206485 1.112863172 1.171479621 1 17.46949371 EVRPDTQYTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EVRPDTQYTGR 11 1 O43709;O43709-3;H7C0G4 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ;;;; 176.32 2.61E-05 967990000 528440 550991 487581 562059 578760 489280 616282 528726 638310 FALSE TRUE 503461.6885 607137.6093 509937.0711 505559.7615 679695.5608 472336.1109 522256.8621 482427.9485 737295.8548 0.682848934 0.823465377 0.691631545 0.685694566 0.921876281 0.640633075 0.708340972 0.654320712 1 19.49188412 -1.675323348 2.86527194 1.031645649 0.730375911 0.504245859 0.085256549 18927332.8 18971101.75 4399826.145 0.019009106 0.021119161 1.675323348 -0.301269737 EVS(ph)DSEAGGGPQGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.971)DS(0.029)EAGGGPQGER;EVS(0.981)DS(0.019)EAGGGPQGER 162.61 1.66E-06 270300000 246290 362340 246850 302620 230010 272530 251350 272330 214880 TRUE FALSE 234648.3598 399262.8579 258168.3167 272200.0627 270123.6712 263092.2178 213001.9411 248483.3415 248202.4929 0.945390826 1.608617437 1.040151989 1.09668545 1.088319734 1.059990231 0.858178089 1.00113153 1 17.92115808 2.887326503 1.125228439 0.959111267 1.257038987 0.219029284 0.177153486 0.567631836 1.519855644 0.080591755 0.086895802 771.4832528 -2.887326503 0.29792772 EVS(ph)PAPAVAGQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVSPAPAVAGQSK 13 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK 245.56 4.30E-17 303210000 744520 666840 692750 824820 586150 742360 866460 805650 707190 TRUE FALSE 709328.0151 734791.7541 724513.2727 741907.5265 688374.3744 716651.8871 734265.6134 735103.015 816857.4134 0.868362095 0.899534903 0.886951946 0.908246059 0.842710568 0.877328008 0.898890799 0.89991595 1 19.63972475 0.468161403 1.183462484 1.000049058 0.88259555 0.803335012 0.01810487 0.903630987 1.595575031 0.016622843 0.005042675 2.938741615 -0.468161403 -0.117453508 EVS(ph)PEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;EVS(1)PEVVR 173.14 0.00029318 3026640000 5078240 4086880 4523470 5018940 4622890 4699490 5892720 4990950 4962820 TRUE FALSE 4838201.659 4503337.718 4730875.574 4514426.616 5429120.552 4536745.483 4993677.337 4553915.959 5732428.779 0.844005542 0.785589824 0.825282922 0.78752424 0.947089055 0.79141768 0.871127672 0.794413003 1 22.45071509 -5 0.286315173 2.284663674 0.820285095 0.521729376 0.050290016 178.0517172 1.687408359 136.4197887 0.048923838 1.00E-05 5 -1.46437858 EVS(ph)S(ph)RPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Trastuzumab_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 2 EVS(0.495)S(0.495)RPS(0.495)T(0.495)PGLS(0.018)VVS(0.001)GIS(0.001)AT(0.001)SEDIPNKIEDLR 43.068 0.069698 299690000 29170 22593 25529 31437 23774 32576 30282 26984 24676 TRUE FALSE 27791.19191 24895.25239 26699.5299 28276.89303 27920.17807 31447.88495 25661.92473 24621.13791 28502.62805 0.97503963 0.873437086 0.936739232 0.992080203 0.979565043 1.103332819 0.90033539 0.863819921 1 14.79880733 7.13432975 7.013009945 0.954148975 0.971103356 0 0.070515607 0 0 0.0153715 0 13624787.88 -7.13432975 0.016954382 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Trastuzumab_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 2 EVS(0.5)S(0.5)RPS(0.579)T(0.42)PGLS(0.001)VVSGISATSEDIPNKIEDLR 85.939 9.97E-05 121430000 55532 58756 50195 65852 48408 64578 65026 68165 47687 TRUE FALSE 52907.11241 64743.3032 52496.4904 59232.43185 56850.33987 62341.64767 55105.08942 62196.11123 55082.05641 0.960514474 1.175397351 0.953059741 1.075348956 1.032102713 1.131795937 1.000418158 1.129153762 1 15.7492948 4.751855396 24.28047081 1.062657228 0.960514385 0.176572757 0.068975183 100.9147386 1320307.928 0.014435508 0.093445037 56474.89024 -4.751855396 -0.102142843 EVS(ph)SRPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Trastuzumab_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(0.497)S(0.497)RPS(0.003)T(0.003)PGLSVVSGISATSEDIPNKIEDLR 91.269 6.58E-05 42779000 49249 38979 57300 55040 46869 54909 73720 74162 36290 TRUE FALSE 46921.09737 42951.00442 59927.26168 49507.27463 55042.93876 53007.48756 62472.66004 67667.98212 41917.66786 1.119363261 1.024651576 1.429642076 1.181059853 1.313120256 1.264561944 1.490365835 1.61430694 1 15.35527083 3.563870708 0.845412564 1.377944095 1.046271759 0.173074919 0.181409254 0.886377149 1.245745391 0.074131005 0.198887095 3663.284999 -3.563870708 -0.331672335 EVSEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVSEDR 6 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 129.16 0.037954 1965810000 2375120 1925830 2017880 2381000 2262240 2005340 2369120 2276690 2635720 FALSE TRUE 2262852.785 2122074.266 2110401.794 2141657.356 2656773.94 1935894.573 2007667.232 2077330.954 3044453.996 0.743270481 0.697029506 0.693195495 0.703461888 0.872660235 0.635875784 0.659450671 0.682332844 1 21.53775208 -1.484488574 3.73301572 1.003467451 0.708644949 0.66795609 0.064038326 10662080.33 4244728.394 300310.0552 0.014609849 0.03277264 1.484488574 -0.294822502 EVSEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EVSEDRR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;; 190.54 0.00086419 6224434000 6413309 5359576 5400040 6844474 6398320 5555256 6841687 5951777 6454452 FALSE TRUE 6110164.594 5905722.888 5647637.175 6156454.47 7514184.982 5362876.092 5797861.992 5430607.854 7455375.451 0.819564975 0.792142921 0.757525521 0.825773901 1.007888205 0.719330116 0.777675387 0.728415073 1 22.82984958 3.048362746 24.49609951 0.827838694 0.794159823 0.045900542 0.099008658 454.5009776 230204.6322 0.027615025 0.033006259 1117.7965 -3.048362746 -0.033678871 EVSEDRRQDLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVSEDRRQDLLSR 13 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 264.29 1.76E-24 1506610000 675173 214919 860690 389666 1323480 624071 1460220 816880 2198650 FALSE TRUE 643258.9104 236819.4904 900153.4878 350496.0334 1554294.493 602459.2648 1237436.62 745349.6566 2539605.413 0.253290888 0.093250506 0.3544462 0.138012004 0.612022043 0.23722554 0.487255467 0.29349034 1 21.27617293 -5 0.156054874 3.60898445 0.093501299 0.704186756 0.144449735 63.74975773 0.579178311 51.31573741 0.572514318 1.00E-05 5 -3.515483151 EVSFQSTGESEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVSFQSTGESEWK 13 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ; 214.81 7.03E-11 139743000 328120 302290 265420 306770 198126 243544 271330 304280 206444 FALSE TRUE 312610.4179 333093.6947 277589.7695 275932.8968 232679.1117 235110.0102 229933.6252 277635.6301 238458.2812 1.310964821 1.396863607 1.164102032 1.157153761 0.975764442 0.985958672 0.964250954 1.164294353 1 17.86337736 3.323684018 1.54371746 1.01118447 1.355348713 0.773751473 0.070133946 0.144622299 0.712288567 0.021847354 0.034041688 2107.094522 -3.323684018 0.344164243 EVSGHSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVSGHSVR 8 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 114.39 0.0026662 40752000 80945 58792 75323 87042 101310 67832 89734 75535 104970 FALSE TRUE 77118.89027 64782.97164 78776.63405 78292.37279 118978.4319 65482.96083 76043.43022 68920.75496 121248.2115 0.636041467 0.534300431 0.649713782 0.645719816 0.981279892 0.540073623 0.627171562 0.568426982 1 16.88760394 -2.115687681 2.429907473 1.685850548 0.641053326 0.434596577 0.126023098 8904874.875 2396643.268 33745315.12 0.029438232 0.007661474 2.115687681 -1.044797223 EVSMDDHK ddPTM_SK-BR-3_Trastuzumab_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 ; 171.53 0.00028884 241267000 386800 293570 288230 504150 358910 365170 457940 420860 307790 FALSE TRUE 368516.7306 323485.1168 301445.6306 453471.8842 421503.7904 352524.0713 388072.8424 384007.2673 355520.5012 1.036555499 0.909891597 0.847899431 1.275515428 1.185596299 0.99157171 1.091562487 1.080126929 1 18.43957323 3.256901602 24.99995551 1.103408173 0.941844693 0.428393783 0.093734698 242.9880819 331206.5698 0.025824468 0.034902865 1806.764721 -3.256901602 -0.16156348 EVSQVDTICECLLEHEEQVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EVSQVDTICECLLEHEEQVLR 21 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ;;; 227.19 2.14E-25 64453300 78909.9 74344.7 69462.5 82749.2 83754 76912.9 91904.6 81381.8 79436.9 FALSE TRUE 75179.98541 81920.50945 72647.42433 74431.0932 98360.67108 74249.38699 77882.86533 74255.57816 91755.56874 0.819350656 0.892812399 0.791749485 0.811188838 1.071985847 0.809208509 0.848808049 0.809275984 1 16.4855081 -2.540541645 2.227725944 3.271457767 0.858084303 0.233133149 0.08159306 3142395.417 352816.6932 36347775.39 0.018407656 0.002880437 2.540541645 -2.413373463 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.461)S(0.539)RPS(0.538)T(0.461)PGLS(0.001)VVSGISATSEDIPNK;EVS(0.461)S(0.539)RPS(0.535)T(0.457)PGLS(0.008)VVSGISATSEDIPNK;EVS(0.116)S(0.883)RPS(0.537)T(0.464)PGLSVVSGISATSEDIPNK;EVS(0.154)S(0.844)RPS(0.56)T(0.442)PGLSVVSGISATSEDIPNK 175.28 7.11E-13 280658000 399347 479154 321020 480900 268376 396219 340286 432452 262247 TRUE FALSE 380470.6587 527980.3374 335739.0845 432559.0183 315180.6894 382497.8367 288369.1209 394584.2103 302914.9254 1.256031403 1.742998753 1.108360983 1.427988462 1.040492439 1.262723638 0.951980562 1.302623863 1 18.20855314 3.109791833 1.21737466 1.102667532 1.474154733 0.299572334 0.195326925 0.436555485 1.372553065 0.070784403 0.095051268 1287.632214 -3.109791833 0.371487201 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.176)S(0.824)RPS(0.534)T(0.465)PGLS(0.001)VVSGISATSEDIPNKIEDLR;EVS(0.478)S(0.522)RPS(0.522)T(0.478)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.481)S(0.519)RPS(0.519)T(0.481)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.155)S(0.844)RPS(0.55)T(0.45)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.096)S(0.904)RPS(0.614)T(0.386)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.145)S(0.855)RPS(0.53)T(0.47)PGLSVVSGISATSEDIPNKIEDLR 205.79 2.58E-27 1930259000 569002 519694 532582 593404 386209 560073 583259 614891 439872 TRUE FALSE 542106.4031 572651.4094 557001.4115 533753.9025 453563.7273 540677.5316 494272.1273 561047.8843 508085.1032 1.066959845 1.127077739 1.096275817 1.050520669 0.892692434 1.064147577 0.972813657 1.10423998 1 18.95471064 3.000882875 9.099234082 1.00367518 1.095956871 0.345276018 0.056631727 0.101140799 121.7864091 0.015159748 0.017487006 1002.034963 -3.000882875 0.092281691 EVSSRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Trastuzumab_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(0.014)S(0.079)RPS(0.454)T(0.454)PGLSVVSGISATSEDIPNKIEDLR 164.8 2.89E-14 172240000 112050 91905 105670 114920 79413 111870 121840 109650 75476 TRUE FALSE 106753.6186 101270.224 110515.074 103368.0233 93262.60206 107995.9138 103251.0703 100048.4647 87180.4326 1.224513522 1.161616443 1.267659161 1.185679173 1.069765305 1.238763225 1.184337668 1.147602297 1 16.41171674 -4.849376126 0.24183132 8.12E-17 1.205961003 0.569158261 0.052204202 116.5513265 1.242580323 57.21535766 0.076456009 1.41E-05 4.849376126 1.205961003 KRLNLEEWILEQLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRLNLEEWILEQLTR 15 2 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ; 173.03 5.59E-07 144721000 528580 376560 555930 367190 580970 536230 1011480 826340 1147950 FALSE TRUE 503595.0709 414931.8921 581419.9404 330279.3636 682290.9841 517660.2206 857160.1489 753981.2889 1325968.223 0.379794223 0.312927478 0.438487085 0.249085429 0.514560585 0.390401679 0.646440943 0.568626967 1 20.33861477 0.849838991 0.506887784 1.019204703 0.33431133 0.859015827 0.079608341 0.358117944 0.214918685 0.085712697 0.037298598 7.076833712 -0.849838991 -0.684893373 EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPT(ph)LPSPTSVITQAPPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPTLPSPTSVITQAPPSNR 50 2 P17544;K7ELQ4;P17544-1 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 EVTPKPVLISTPT(0.001)PT(0.001)IVRPGS(0.001)LPLHLGY(0.109)DPLHPT(0.351)LPS(0.305)PT(0.102)S(0.117)VIT(0.014)QAPPSNR 55.965 0.014074 98139000 100240 94845 102450 121920 101510 105020 146820 132530 41887 TRUE FALSE 95501.85386 104509.8133 107147.4338 109664.37 119213.3119 101383.1311 124419.9125 120924.9706 48382.62203 1.973887521 2.160069234 2.2145851 2.266606591 2.463969642 2.095445158 2.571582673 2.499347194 1 15.56220134 4.258694922 1.348112895 2.257690239 1.959237749 0 0.448303624 2.155785159 6.073692712 0.11320894 0.696307952 18142.40769 -4.258694922 -0.29845249 EVTSLFNKDDEQHLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVTSLFNKDDEQHLLER 17 1 Q86YL5;Q86YL5-2 Q86YL5 TDRP Testis development-related protein 0 163.45 1.63E-09 72479000 161030 148690 140030 157040 136090 156200 194390 173020 143520 FALSE TRUE 153418.431 163841.68 146450.514 141254.0408 159824.0529 150790.7548 164732.2353 157869.4516 165776.3486 0.925454278 0.988329647 0.883422245 0.852075957 0.964094422 0.909603548 0.993701675 0.952303829 1 17.33887867 1.732590105 9.704534352 0.97907015 0.926335051 0.339005839 0.039838478 0.134881649 49.10990048 0.019506003 0.010538787 54.02441899 -1.732590105 -0.052735099 EVTYELDHPGFQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVTYELDHPGFQIR 14 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 211.38 3.92E-09 165857000 178005 181116 179219 197301 202304 183178 214128 203604 207912 FALSE TRUE 169591.0564 199571.9263 187436.3684 177467.9286 237585.7535 176834.4999 181458.8409 185775.3544 240153.9311 0.706176475 0.831016696 0.780484282 0.738975739 0.989306119 0.736338144 0.755593881 0.773567826 1 17.8735999 -2.526095161 2.084523057 3.65775085 0.787278842 0.416390192 0.078508215 4351036.327 213702.9992 54865311.15 0.019735759 0.002977864 2.526095161 -2.870472008 EVVDGLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVVDGLEK 8 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 79.906 0.056261 0 219540 227600 220660 258180 220910 261580 276590 274600 233210 FALSE TRUE 209162.7793 250792.6988 230777.4793 232227.2559 259436.6341 252521.419 234391.1156 250554.5683 269375.0157 0.776474309 0.931016925 0.85671449 0.862096491 0.963105778 0.937434447 0.870129381 0.930132914 1 18.03925652 8 0.262079087 0.944551734 3.06E-13 0.532123616 0.043639728 45.89556947 0.636327271 0.052059689 19.416777 100000000 -8 -0.944551734 EVVEAHVDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVVEAHVDQK 10 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A096LNH5;A0A096LPI6;H7C1F6;H7C2G3 P0DPI2-2 C21orf33 0 98.04 0.005648 289500000 1261400 1007000 1133800 1144400 1233100 959270 1220200 1092000 1264900 FALSE TRUE 1201776.122 1109614.445 1185785.851 1029362.738 1448152.25 926050.2394 1034036.079 996378.6909 1461054.232 0.822540393 0.759461504 0.811596056 0.704534243 0.991169402 0.633823317 0.707732853 0.681958732 1 20.4785783 EVVEEAENGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;; 264.64 3.44E-17 11259370000 6596230 6705450 5842620 7316330 5710450 6440080 6563790 6505830 5918640 FALSE TRUE 6284439.28 7388742.978 6110509.906 6580878.608 6706350.672 6217058.415 5562363.283 5936145.036 6836472.463 0.919251751 1.080782965 0.893810359 0.962613196 0.98096653 0.909395664 0.813630613 0.868305265 1 22.70482067 2.096643551 4.304467535 0.870712132 0.974712514 0.177947204 0.067654223 0.2384501 8.008812908 0.025295753 0.017979065 124.9233295 -2.096643551 0.104000381 EVVETPLLHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVVETPLLHPER 12 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 208.95 6.09E-08 221660000 263840 258720 231030 269950 284490 234960 279250 259710 243430 FALSE TRUE 251368.8061 285083.8621 241622.954 242814.1131 334104.9659 226823.2763 236645.2837 236968.4156 281179.8811 0.893978634 1.013884283 0.859318074 0.863554363 1.188225006 0.806683876 0.841615278 0.842764477 1 18.10113385 EVVKPVPIT(ph)SPAVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 EVVKPVPIT(0.5)S(0.5)PAVSK 148.06 5.82E-06 669740000 1070700 1041200 1031900 1245200 794630 1151000 1333700 1253800 1006700 TRUE FALSE 1020090.133 1147299.464 1079213.636 1120030.13 933213.2204 1111140.581 1130219.57 1144010.625 1162813.894 0.877260014 0.986657856 0.928105212 0.963206697 0.802547359 0.955561837 0.97196944 0.983829511 1 20.14918878 2.00919718 24.99767686 0.977555291 0.918218595 0.308821375 0.049930373 283.7493352 771219.4252 0.01822928 0.013445885 102.140312 -2.00919718 -0.059336697 EVVKPVPITS(ph)PAVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 EVVKPVPIT(0.053)S(0.947)PAVSK;EVVKPVPIT(0.164)S(0.835)PAVSK;EVVKPVPIT(0.286)S(0.714)PAVSK 132.79 2.74E-05 2070530000 1721010 1582040 1716390 1859340 1199260 1731010 2019570 1956560 1524970 TRUE FALSE 1639661.268 1743251.675 1795088.179 1672435.611 1408410.564 1671064.69 1711447.505 1785233.234 1761454.559 0.93085641 0.989665993 1.019094231 0.949462819 0.799572465 0.948684529 0.971610364 1.013499454 1 20.74833583 1.494474693 3.098800745 1.005409649 0.943107725 0.191463685 0.056679956 0.449120592 8.776163587 0.043206047 0.01557742 31.22300461 -1.494474693 -0.062301924 EVWALVQAGIR ddPTM_SK-BR-3_Trastuzumab_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 0 106.2 0.0054987 31191000 68464 96337 67673 73564 68855 68267 82483 77477 67743 FALSE TRUE 65227.8424 106153.8498 70775.87399 66169.20696 80863.2902 65902.89667 69898.70345 70692.70315 78248.23846 0.833601416 1.35662926 0.904504375 0.845631905 1.033419944 0.842228502 0.893294275 0.903441465 1 16.25577065 EVWDYVFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EVWDYVFFK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 152.63 0.00018614 391210000 1843280 1383770 1335370 1579340 1493280 1253910 1967720 1692640 1576640 FALSE TRUE 1756151.807 1524777.736 1396598.035 1420581.743 1753707.559 1210486.782 1667508.174 1544423.468 1821137.279 0.964315995 0.837266775 0.76688235 0.780051981 0.96297384 0.664687279 0.915641118 0.848054392 1 20.79640825 0.480903175 1.462192868 0.999832558 0.843393782 0.226066104 0.091823873 4.131432825 10.00121479 0.081717359 0.023740765 3.026238657 -0.480903175 -0.156438776 EVWYFGLHYVDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EVWYFGLHYVDNK 13 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 212.17 1.61E-08 1419192800 2314691 2821009 2051917 2619702 1453628 2348771 2053083 2369103 1007244 FALSE TRUE 2205280.144 3108473.024 2145999.424 2356364.578 1707140.263 2267432.471 1739847.481 2161651.782 1163442.255 1.895478812 2.671789692 1.844525944 2.02533866 1.46731843 1.94889988 1.495430885 1.857979433 1 20.14996818 1.416375115 0.204378889 0.734205541 2.547786343 0.537460624 0.294786103 1.864253785 0.395523792 1.410511156 1.268482661 26.08405544 -1.416375115 1.813580803 EVYELLDS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_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 253.72 2.14E-20 445832000 910290 1288360 868120 1225570 538320 1118770 942910 1160390 615500 TRUE FALSE 867262.3957 1419645.349 907924.1607 1102373.375 632202.8376 1080026.714 799051.7618 1058780.1 710948.5965 1.219866528 1.99683262 1.277060205 1.55056692 0.889238464 1.519134744 1.123923397 1.489249863 1 19.43938573 3.208961616 2.071650067 1.237854434 1.591806666 0.176406641 0.289206165 0.439130726 3.871441448 0.08300813 0.111711887 1617.937034 -3.208961616 0.353952232 EVYELLDS(ph)PGKVLLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;EVYELLDS(1)PGKVLLQSK 240.71 1.50E-20 932320000 2306330 2242180 2445940 2624160 1381180 2878490 3014330 3138900 1918430 TRUE FALSE 2197314.352 2470660.691 2558088.768 2360374.451 1622057.355 2778807.17 2554438.597 2864041.276 2215930.326 0.991599025 1.11495414 1.154408484 1.065184416 0.731998355 1.254013782 1.152761243 1.292478036 1 21.07948109 EVYELLDSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVYELLDSPGK 11 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 158.79 6.84E-05 24140000 154870 127470 136300 173060 142860 153310 199500 167870 155370 FALSE TRUE 147549.602 140459.3379 142549.4898 155663.68 167774.7388 148000.8363 169062.6109 153170.4129 179463.9861 0.822168309 0.782660304 0.794306941 0.867381158 0.934865777 0.824682654 0.942041992 0.853488303 1 17.45333483 1.816627811 0.178588188 1.05088279 0.721186138 0.601294943 0.044284507 2.213744171 0.376186724 0.256225947 0.309068664 65.55831929 -1.816627811 -0.329696652 EVYQQQQYGSGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 144.57 6.55E-06 0 13900 9885 11701 15043 15078 14777 19038 16857 13048 FALSE TRUE 13242.97455 10892.29274 12237.50242 13530.84906 17707.59843 14265.26878 16133.40344 15380.91172 15071.4172 0.878681439 0.722711912 0.811967598 0.897782132 1.17491263 0.946511439 1.070463595 1.020535197 1 13.87952746 2.987901808 4.440028222 1.041525951 0.801140933 0.717437872 0.068860682 0.094180829 4.63006471 0.019229355 0.021780714 972.527316 -2.987901808 -0.240385018 EWAMNVGDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EWAMNVGDKK 10 1 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 102.62 0.0046865 1483770000 1065550 982680 886130 1371880 763230 1210320 1292190 1420790 830030 FALSE TRUE 1015183.563 1082816.209 926759.937 1233976.016 896337.0704 1168406.315 1095042.683 1296378.096 958746.8132 1.058865124 1.129407884 0.966636785 1.287071831 0.934904876 1.218680781 1.142160441 1.352158962 1 19.87079035 EWCISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EWCISR 6 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 120.86 0.046304 532020000 503650 425940 427410 478980 499320 429890 544780 491120 470250 FALSE TRUE 479843.4626 469343.7703 447007.1713 430832.0204 586401.2499 415002.8015 461663.8054 448114.9292 543173.9683 0.883406589 0.864076332 0.822953966 0.793175015 1.079582756 0.764032936 0.84993728 0.824993382 1 19.05105481 -1.406425026 5.674545087 1.000059815 0.860336702 0.210339374 0.085084867 5.81E-05 6.07E-06 0.074284785 0.017501607 0.039226086 1.406425026 -0.139723113 EWDFDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EWDFDLK 7 0 Q96EY4;H0Y9X1 Q96EY4 TMA16 Translation machinery-associated protein 16 0 ;;; 117.16 0.012315 221252000 796710 776850 674970 866340 540620 777180 839890 909540 559480 FALSE TRUE 759051.0972 856011.8982 705918.0421 779253.8573 634903.9568 750266.0617 711749.3549 829895.8558 646241.301 1.174562963 1.324601038 1.092344363 1.205824908 0.982456485 1.160968915 1.101367792 1.284188823 1 19.30171343 3.725378085 24.60484607 1.121715693 1.249582004 0.246724766 0.095308251 718.8548608 1341723.971 0.022782357 0.035549535 5313.468187 -3.725378085 0.127866311 EWDRDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 99.919 0.042612 570580000 789200 568690 490933 609240 567780 587480 811500 687980 551540 FALSE TRUE 751896.08 626640.1575 513442.7636 547998.0377 666800.6522 567135.4203 687690.7708 627736.824 637070.0063 1.180240904 0.98362841 0.805944023 0.86018496 1.046667785 0.890224645 1.079458716 0.985349832 1 19.28109239 4.425896738 2.567187857 0.956069078 1.174041022 0.415827759 0.083559442 0.296355469 3.556188809 0.021673442 0.102821493 26662.24641 -4.425896738 0.217971944 EWEEAER ddPTM_SK-BR-3_Trastuzumab_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 ; 113.14 0.014418 263270000 563460 551400 480520 606290 544480 537440 579240 536650 488210 FALSE TRUE 536826.3625 607588.2869 502552.3173 545344.5773 639437.1396 518828.318 490866.2995 489658.081 563919.1134 0.951956317 1.077438719 0.891178017 0.967061702 1.133916415 0.920040314 0.870455156 0.868312617 1 19.10512872 2.02315853 24.99279912 0.897708413 1.004711634 0.251518946 0.0753835 258.3885033 278852.9093 0.026492564 0.019565018 105.4771848 -2.02315853 0.107003221 EWFLQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EWFLQAAK 8 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6 P06744 GPI Glucose-6-phosphate isomerase 0 ; 157.54 0.0008731 349800000 919110 954470 564140 698440 703890 716700 906730 842070 674860 FALSE TRUE 875665.4918 1051731.578 590006.377 628231.4843 826648.1931 691880.4993 768391.6853 768333.8867 779513.8421 1.123348226 1.349214756 0.756890186 0.805927298 1.060466343 0.887579491 0.985731932 0.985657785 1 19.57221512 3.745094695 24.99996497 0.92726353 1.236281496 0.597881154 0.105774552 313.7965712 1200610.153 0.026556577 0.046492113 5560.254821 -3.745094695 0.309017966 EWHHFLVVNMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EWHHFLVVNMK 11 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 91.855 0.0060318 319220000 586750 278140 349730 494240 483120 396450 601620 430970 194719 FALSE TRUE 559015.4903 306482.7822 365765.4664 444558.0562 567375.975 382720.8371 509831.8195 393231.9821 224915.028 2.485451929 1.362660312 1.626238449 1.976560037 2.522623677 1.701624122 2.266775253 1.748357971 1 17.77902053 0.975689302 21.7416688 0.999999977 1.969936572 0.416581488 0.367919167 384.7902552 344129.3521 0.342628194 0.085657048 9.455604567 -0.975689302 0.969936595 EWLEVLEDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EWLEVLEDTKR 11 1 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 72.34 0.07466 19652000 36812 35218 32837 36362 30521 33690 37574 40863 33412 FALSE TRUE 35071.96971 38806.75424 34342.60893 32706.82268 35843.85274 32523.30685 31841.39621 37284.81909 38593.36232 0.908756522 1.005529239 0.889857915 0.847472744 0.928756931 0.842717631 0.825048513 0.966094086 1 15.23606512 3.627765555 8.071546558 0.884387319 0.956971238 0.092516631 0.060848048 0.396620133 26.00646731 0.015021494 0.023307199 4243.904034 -3.627765555 0.072583919 EWLTNFMEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 81.865 0.0459 80700000 30349 29587 20440 26502 36238 24089 32019 29859 23870 FALSE TRUE 28914.46292 32601.94894 21377.19422 23837.96861 42557.89573 23254.79189 27133.91348 27244.38767 27571.63769 1.048703136 1.182445138 0.77533277 0.864582978 1.543538915 0.843431651 0.984124113 0.988130918 1 14.75089734 7.999999997 0.191964568 0.983860987 1.467438977 0.000688373 0.215672466 326.3290168 3.836876792 0.410333735 46.93652945 99999999.38 -7.999999997 0.48357799 EWNGVVSESDS(ph)PVKRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EWNGVVSESDSPVKRPGR 18 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSESDS(1)PVKRPGR 210.16 2.31E-16 700450000 713400 800000 652510 868120 464510 781500 756680 786280 555460 TRUE FALSE 679678.9958 881520.9095 682428.2289 780854.9283 545520.3969 754436.459 641234.5686 717429.1549 641597.8999 1.059353523 1.373946064 1.063638502 1.217047201 0.850252778 1.175871148 0.999433709 1.118191246 1 19.29130989 EWPSNLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 EWPSNLDLR 9 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;;; 158.37 0.00015556 743235000 1754964 1479378 1240925 1345012 1605918 1152196 1347846 1291134 1285640 FALSE TRUE 1672010.33 1630128.3 1297822.639 1209808.838 1885989.591 1112295.164 1142207.338 1178075.462 1485010.485 1.125924932 1.097721744 0.873948468 0.814680334 1.270017693 0.749015024 0.76915776 0.793311208 1 20.50204169 3.953326197 0.531788778 0.838479943 1.228824593 0.20600488 0.156909633 2.539590083 0.97955361 0.101086015 0.563546079 8981.031025 -3.953326197 0.39034465 EWPSNLDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EWPSNLDLRK 10 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 80.596 0.037735 485990000 430720 251790 362970 264220 426600 301560 475660 368760 445960 FALSE TRUE 410360.7192 277447.6873 379612.5335 237660.1036 500998.9049 291116.9016 403089.3309 336469.4195 515117.1992 0.796635639 0.538610801 0.736944008 0.461370935 0.972592074 0.565146926 0.782519651 0.653190031 1 18.97454119 -4.999982297 0.269711032 3.170207988 0.66252502 0.304633827 0.147195178 235.811146 2.290151408 284.7064702 0.156314874 1.00E-05 4.999982297 -2.507682968 EWPVSSFNRPFPNS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EWPVSSFNRPFPNSP 15 1 Q96H12 Q96H12 MSANTD3 Myb/SANT-like DNA-binding domain-containing protein 3 1 EWPVS(0.001)S(0.001)FNRPFPNS(0.999)P;EWPVSSFNRPFPNS(1)P 93.226 0.012992 44487000 125384 99103 106967 126864 146607 105833 138398 108161 141777 TRUE FALSE 119457.3468 109201.7084 111871.5428 114111.3897 172175.2144 102167.9767 117282.8432 98689.84944 163763.0531 0.729452368 0.666827507 0.683130539 0.696807904 1.051367883 0.623876844 0.716174015 0.602638065 1 17.32125038 -2.01859742 2.703834961 1.314127907 0.720215813 0.334044771 0.123667398 35082624.3 18295831.93 68370240.15 0.027911261 0.009580818 2.01859742 -0.593912095 EWQHEEFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EWQHEEFYR 9 0 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 208.6 9.78E-06 2014990000 2528630 2061500 1881410 2092940 2273530 1780000 2303910 2193150 2025220 FALSE TRUE 2409106.671 2271569.194 1967674.509 1882553.695 2670032.912 1718358.154 1952406.215 2001106.159 2339280.774 1.029849301 0.97105453 0.841145078 0.804757477 1.141390526 0.734566869 0.83461816 0.855436501 1 21.1576336 3.915249086 3.878508946 0.876079351 1.010514634 0.149128642 0.112943881 0.346213161 9.698233586 0.027818416 0.054513108 8227.143748 -3.915249086 0.134435283 EWSGLLEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EWSGLLEELAR 11 0 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 145.89 8.38E-05 249231000 259870 236186 236779 271586 265025 219518 277000 263301 263990 FALSE TRUE 247586.4601 260253.6219 247635.5514 244285.6593 311245.2761 211916.0366 234738.5625 240244.9686 304928.2209 0.811949971 0.853491425 0.812110964 0.801125126 1.020716532 0.694970233 0.769815801 0.787873841 1 18.21811015 EWSLESSPAQNWT(ph)PPQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;EWSLESSPAQNWT(1)PPQPR;EWSLESSPAQNWT(1)PPQPR;EWSLES(0.005)S(0.165)PAQNWT(0.83)PPQPR 186.98 5.06E-13 183199000 228204 240830 240822 286536 260533 242725 292898 284249 344201 TRUE FALSE 217417.2492 265370.8508 251863.9269 257732.8569 305969.8727 234319.3724 248211.0307 259358.6507 397577.9331 0.546854418 0.667468762 0.63349574 0.648257449 0.769584645 0.589367148 0.624307865 0.652346695 1 18.60087816 -2.523605308 1.112106227 2.381707664 0.638509042 0.795573384 0.057100886 7337.639189 532.7258122 25075.89317 0.016376923 0.002994985 2.523605308 -1.743198622 EWTDGLFTHVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 190.66 6.36E-06 1270207000 1869180 1521909 1536769 1842100 1879480 1589557 1943960 1798030 1644485 FALSE TRUE 1780827.566 1676993.257 1607231.379 1656928.608 2207260.717 1534510.243 1647373.199 1640584.961 1899503.335 0.937522737 0.882858812 0.846132433 0.872295709 1.162019922 0.807848143 0.867265231 0.86369154 1 20.85719081 -0.962420382 4.720802039 1.000001228 0.902858579 0.08620582 0.097037259 1.18E-06 2.59E-07 0.088192083 0.02078681 0.109038437 0.962420382 -0.097142649 EYAENIGDGRS(ph)PEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYAENIGDGRSPEFR 15 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 1 EYAENIGDGRS(1)PEFR 231.4 1.21E-13 204620000 209480 257860 186590 249310 195450 214110 190090 219970 157480 TRUE FALSE 199578.2955 284136.2272 195145.3361 224248.8851 229536.4181 206695.317 161088.2793 200708.2607 181901.1941 1.097179689 1.562036074 1.072809538 1.232806009 1.261874169 1.136305443 0.885581208 1.103391661 1 17.47279549 2.017962755 3.830592892 0.98671091 1.265352251 0.387108267 0.141175986 0.200453223 6.401479388 0.060166857 0.038623757 104.2228044 -2.017962755 0.278641341 EYCIQAFESFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYCIQAFESFVR 12 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 147.71 0.0001531 61302000 100927 111612 84617 110759 100146 90842 107286 99816 95764 FALSE TRUE 96156.38073 122985.3897 88496.77315 99625.29489 117611.4307 87696.11876 90917.55026 91075.58188 110614.592 0.869292007 1.111836942 0.800046102 0.900652374 1.06325421 0.792807867 0.821930892 0.823359561 1 16.75518219 2.218086575 24.99623522 0.84039472 0.955001774 0.140287968 0.104879111 359.3455248 438713.0198 0.037077191 0.027414834 165.2291142 -2.218086575 0.114607054 EYCLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYCLSPR 7 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 EYCLS(1)PR 61.161 0.097709 85256000 110000 79350 95210 106150 112860 89593 110750 106830 139960 TRUE FALSE 104800.518 87435.85521 99575.47268 95479.60033 132542.7483 86490.37195 93853.05344 97475.39886 161664.282 0.648260189 0.540848319 0.615939844 0.590604178 0.819864145 0.534999883 0.580542915 0.602949505 1 17.30264144 -0.930038353 5.019085274 1.000001658 0.611148821 0.695210097 0.079672348 0.003930909 50231043.07 205.1304863 0.017575252 0.11747938 0.930038353 -0.388852837 EYEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYEEEER 7 0 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 172.03 0.0021301 696540000 1186700 1534110 1252410 1481170 940720 1272130 1099050 1203050 779260 FALSE TRUE 1130607.043 1690437.553 1309834.237 1332279.978 1104781.27 1228075.819 931369.7371 1097704.564 900103.6609 1.256085373 1.878047637 1.455203766 1.480140605 1.227393375 1.364371541 1.034736084 1.219531274 1 19.77973163 2.426797877 0.955064753 1.082525242 1.569370102 0.518690216 0.17362637 0.407811334 0.739206285 0.112440739 0.075588605 267.1762669 -2.426797877 0.48684486 EYELFEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYELFEFR 8 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A087WU65;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;; 183.26 0.00052167 136845000 286914 267428 211576 264504 255313 212804 282392 271448 248062 FALSE TRUE 273352.1438 294679.2172 221276.9689 237915.5554 299839.5064 205434.5441 239307.9139 247678.5741 286530.188 0.954008182 1.028440386 0.772264069 0.830333296 1.046449969 0.716973473 0.835192674 0.86440656 1 18.12832762 3.750757605 24.96083653 0.85527251 0.99122429 0.210544442 0.098539655 908.2005586 1858605.103 0.023530538 0.042017484 5633.23157 -3.750757605 0.135951781 EYELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYELRK 6 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;; 85.061 0.088417 1751780000 2790440 2024290 2375720 2508780 2391210 2586860 3392900 2741130 2704780 FALSE TRUE 2658541.431 2230567.452 2484649.112 2256592.668 2808236.267 2497276.39 2875250.79 2501102.126 3124223.468 0.850944709 0.713958997 0.795285336 0.722289136 0.898858963 0.79932707 0.920308941 0.800551609 1 21.57506622 0.904037418 0.392592597 1.009643745 0.767671192 0.493503561 0.062856973 1.144466039 0.459522326 0.097511708 0.048039921 8.017471366 -0.904037418 -0.241972553 EYESCHEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYESCHEGR 9 0 Q12933-4;Q12933-3;Q12933;B1AMX7;B1AMX8 Q12933-4 TRAF2 TNF receptor-associated factor 2 0 62.005 0.085458 128470000 100450 128670 170610 164340 81219 173730 132220 152790 101130 FALSE TRUE 95701.92757 141781.6193 178432.6373 147820.231 95383.56789 167713.6865 112047.4106 139410.8976 116812.7239 0.819276568 1.213751504 1.527510286 1.265446315 0.816551183 1.435748444 0.959205529 1.19345644 1 16.8338379 0.54197302 0.79873604 1.001356497 1.151405554 0.037807239 0.236086161 6.607837899 6.854532062 0.235312587 0.078203635 3.483156753 -0.54197302 0.150049058 EYFSWEGAFQHVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 237.32 2.73E-17 4724546000 4432660 3903247 3676526 4539477 3543825 4310068 4709712 4798299 3700965 FALSE TRUE 4223136.946 4300992.307 3845098.354 4083160.148 4161866.958 4160809.264 3991158.935 4378134.502 4274891.75 0.987893307 1.006105548 0.899460987 0.955149367 0.973560783 0.973313363 0.93362807 1.024150963 1 22.02745646 1.223814929 24.99844603 1.012075506 0.964688148 0.329170173 0.029830887 365.6640454 619894.8129 0.029413926 0.007478705 16.74229266 -1.223814929 -0.047387358 EYGEQIDPSTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYGEQIDPSTHR 12 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 109.6 0.0015804 1048170000 1352600 1295790 1102460 1497690 1242010 1224430 1348210 1273720 1025170 FALSE TRUE 1288665.279 1427832.474 1153008.881 1347139.356 1458616.151 1182027.682 1142515.803 1162186.324 1184148.128 1.088263578 1.205788736 0.973703251 1.13764429 1.23178521 0.998209307 0.964841962 0.9814535 1 20.17541813 2.10259257 8.289939312 0.979090067 1.127835402 0.508830078 0.069098811 0.192869134 13.97993184 0.024970485 0.01842426 126.6463185 -2.10259257 0.148745335 EYGS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;EYGS(1)PLK;EYGS(1)PLK 138.08 0.0029586 7136991000 9817340 11075050 8016060 11278540 5216910 10278550 8879730 10438860 5102233 TRUE FALSE 9353293.794 12203610.19 8383604.28 10144799.73 6126737.452 9922601.236 7524964.101 9524778.079 5893461.235 1.58706292 2.070703395 1.422526415 1.721365311 1.039582209 1.683662765 1.276832714 1.6161603 1 22.49068375 4.646269654 0.057894056 5.23E-15 3.541651418 0.342242896 0.263016889 159.1466158 1.492000743 29.62550423 66.76383981 44286.3261 -4.646269654 3.541651418 EYGS(ph)PLKAYT(ph)PVVVTLWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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)PLKAYT(0.973)PVVVT(0.027)LWYR;EYGS(1)PLKAYT(0.992)PVVVT(0.008)LWYR;EYGS(1)PLKAY(0.002)T(0.994)PVVVT(0.004)LWYR;EY(0.001)GS(0.999)PLKAYT(1)PVVVTLWYR 166.29 4.63E-11 2126040000 2816330 1960300 2393040 2547680 1887850 2725960 3342510 2938030 2223080 TRUE FALSE 2683207.662 2160056.799 2502763.251 2291582.366 2217090.442 2631559.322 2832548.71 2680760.518 2567823.892 1.044934456 0.841201301 0.974663122 0.892421935 0.863412187 1.024820795 1.103093058 1.043981453 1 21.29211483 2.077696555 6.102205895 1.061360961 0.924587008 0.47828835 0.062002135 0.156108826 9.526493581 0.02248795 0.016453965 119.5904652 -2.077696555 -0.136773953 EYGS(ph)PLKAYT(ph)PVVVTQWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYGSPLKAYTPVVVTQWYR 19 1 Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 Q5QPR3 CDK11A Cyclin-dependent kinase 11A 2 EY(0.001)GS(0.999)PLKAY(0.001)T(0.998)PVVVT(0.001)QWYR;EYGS(1)PLKAY(0.001)T(1)PVVVTQWYR 153.82 9.61E-08 369940000 760950 530170 702930 716450 525570 755890 922780 822440 659240 TRUE FALSE 724981.4016 584194.9258 735160.0358 644431.0848 617229.2416 729713.3398 781992.963 750422.7936 761471.5723 0.952079405 0.767192036 0.965446463 0.846296971 0.810574241 0.958293607 1.026949648 0.985490228 1 19.53843065 2.056665372 5.46480768 1.00404455 0.86597112 0.532291525 0.059151462 0.138903949 8.652954749 0.021533679 0.015521386 113.9371553 -2.056665372 -0.13807343 EYGS(ph)TSSIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYGSTSSIDK 10 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 EYGS(0.93)T(0.031)S(0.031)S(0.007)IDK 88.338 0.012863 169630000 238720 246550 236010 231440 189600 270360 274030 241050 164220 TRUE FALSE 227436.1787 271673.7253 246831.2919 208175.2115 222666.18 260997.3654 232221.6906 219942.3841 189686.3989 1.199011527 1.432225647 1.301259834 1.097470418 1.173864765 1.37594138 1.224240072 1.159505296 1 17.53325671 -4.887344254 0.169708576 3.74E-09 1.323817881 0.40057766 0.098471759 128.3449389 1.252540359 42.98244723 0.360928862 1.30E-05 4.887344254 1.323817878 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.001)QS(0.984)S(0.015)DS(0.551)S(0.401)PT(0.048)R 159.95 4.74E-11 374840000 120920 123390 108890 141970 109360 117380 118660 125900 114140 TRUE FALSE 115204.3512 135963.5813 113882.7142 127698.9059 128432.3494 113315.1012 100556.2377 114875.5286 131840.2483 0.873817766 1.031275222 0.863793232 0.968588178 0.974151301 0.859487923 0.762712745 0.871323667 1 17.00843134 2.154902374 6.098939546 0.842339719 0.945664955 0.114888468 0.076505346 0.250675247 14.47461649 0.026592673 0.01959472 142.8572791 -2.154902374 0.103325236 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.001)QS(0.999)SDS(0.009)S(0.985)PT(0.006)R;EYIPGQPPLS(0.003)QS(0.996)S(0.001)DS(0.075)S(0.925)PTR;EYIPGQPPLSQS(0.999)S(0.001)DS(0.265)S(0.735)PTR 262.46 4.82E-31 1099150000 2095080 2200460 1938060 2343670 2011700 2066800 2172440 2203580 2090380 TRUE FALSE 1996049.72 2424689.376 2026921.968 2108079.839 2362539.843 1995226.198 1840994.378 2010622.853 2414545.454 0.826677219 1.004201172 0.839463165 0.873075235 0.978461532 0.826336151 0.762460021 0.832712778 1 21.20332019 2.187849592 24.7793265 0.827417256 0.906551455 0.03471538 0.082152553 159.6219823 77996.124 0.028368347 0.020951443 154.1166614 -2.187849592 0.0791342 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.694)S(0.304)PT(0.003)R;EYIPGQPPLSQSS(0.001)DS(0.421)S(0.421)PT(0.158)R;EYIPGQPPLS(0.059)QS(0.035)S(0.022)DS(0.548)S(0.335)PT(0.001)R 202.94 5.55E-16 6578510000 1066720 1046670 989840 1209670 988240 1089480 1105610 1072070 978530 TRUE FALSE 1016298.26 1153326.863 1035225.143 1088071.673 1160588.743 1051751.034 936928.8886 978193.8674 1130275.435 0.899159823 1.020394523 0.915905196 0.96266064 1.026819399 0.930526314 0.828938558 0.865447339 1 20.10824295 1.993276474 24.81846882 0.879274455 0.965426398 0.192845396 0.058633894 306.4165228 1131071.992 0.020600739 0.014655963 98.4637732 -1.993276474 0.086151944 EYIPGQPPLSQSSDSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.112)S(0.873)PT(0.014)R;EYIPGQPPLSQSSDS(0.126)S(0.828)PT(0.047)R;EYIPGQPPLSQSSDS(0.231)S(0.759)PT(0.01)R;EYIPGQPPLSQSSDS(0.042)S(0.942)PT(0.016)R;EYIPGQPPLSQSS(0.002)DS(0.231)S(0.756)PT(0.01)R;EYIPGQPPLSQSSDS(0.033)S(0.965)PT(0.001)R;EYIPGQPPLSQSSDS(0.059)S(0.94)PT(0.001)R;EYIPGQPPLSQSSDS(0.192)S(0.802)PT(0.005)R;EYIPGQPPLSQSSDS(0.033)S(0.725)PT(0.241)R 340.75 9.35E-76 15648370000 2256060 2158839 2045974 2491640 2221085 2074148 2271697 2158590 2281870 TRUE FALSE 2149420.515 2378827.148 2139783.932 2241175.613 2608441.521 2002319.735 1925107.9 1969572.416 2635730.745 0.815493206 0.902530409 0.811837072 0.850305221 0.989646429 0.75968296 0.73038868 0.747258581 1 21.32977157 EYLSEEVQAVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYLSEEVQAVHK 12 0 Q53GS9;B9A018;A0A087X1B2;Q53GS9-2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 89.189 0.0095634 138360000 83814 84520 85581 91622 68817 90144 98997 89776 78149 FALSE TRUE 79852.27832 93132.68409 89504.9735 82411.98249 80818.66301 87022.29068 83893.18945 81914.73751 90267.94779 0.884613867 1.031735919 0.991547672 0.9129706 0.895319601 0.964044191 0.929379603 0.907462056 1 16.46192619 3.236366352 24.99905008 0.931471048 0.970580562 0.105138638 0.046615567 114.490574 1304386.542 0.012846857 0.016084408 1723.321683 -3.236366352 0.039109514 EYPS(ph)PPPSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYPSPPPSPLR 11 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 EYPS(0.999)PPPS(0.001)PLR;EYPS(0.999)PPPS(0.001)PLR;EYPS(1)PPPSPLR;EYPS(0.997)PPPS(0.003)PLR 134.18 0.00015333 315097000 988790 926830 814290 976060 833320 919660 1038890 1105060 1032880 TRUE FALSE 942051.8563 1021275.031 851626.0019 877944.5944 978650.7442 887811.9436 880388.25 1008295.088 1193053.755 0.789613923 0.856017616 0.71382031 0.735880165 0.820290569 0.744150831 0.737928401 0.84513802 1 20.18622762 0.927664332 4.804537117 0.999949019 0.776477292 0.741193003 0.042900408 0.211913295 12.28769997 0.043992533 0.011140301 8.465728411 -0.927664332 -0.223471727 EYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(0.995)PPYAPS(0.005)HQQYPPSHATPLPK;EYS(0.998)PPYAPS(0.002)HQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK 187.13 4.22E-17 2304830000 1441070 1254410 1264110 1546370 1050390 1436280 1735500 1642750 827490 TRUE FALSE 1372953.477 1382235.805 1322070.694 1390925.95 1233577.683 1386541.263 1470717.6 1498902.101 955812.923 1.436424894 1.446136343 1.383189808 1.455228232 1.29060578 1.450640842 1.538708637 1.568196103 1 19.86636875 -1.025650706 4.718298763 0.999988716 1.446400206 0.773466919 0.075878586 9.15E-06 1.89E-06 0.074624701 0.017588767 0.094264744 1.025650706 0.44641149 EYSSELNAPSQESDSHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYSSELNAPSQESDSHPR 18 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 88.264 0.0032983 518950000 182735 138388 167612 175200 185761 175650 213810 194381 197513 FALSE TRUE 174097.4787 152489.8945 175297.176 157588.5631 218157.6596 169567.1965 181189.3576 177359.9692 228142.3073 0.763109135 0.668398143 0.768367683 0.690746776 0.956235002 0.74325187 0.794194465 0.777409378 1 17.79957448 -5 0.142941388 1.829042912 0.68098873 0.504248485 0.074079989 105.3912479 0.914711523 24.81526924 0.396494269 1.00E-05 5 -1.148054183 EYTAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 EYTAGR 6 0 P07237;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 206.5 2.46E-09 6722387000 3688163 3163597 3051590 3506466 3609347 3149022 3657189 3364717 3769167 FALSE TRUE 3513830.844 3485971.131 3191508.42 3153989.376 4238815.974 3039970.579 3099217.649 3070084.542 4353670.168 0.807096245 0.800697112 0.7330616 0.724443804 0.973618995 0.698254682 0.711863216 0.705171596 1 22.05380068 EYTINIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;; 163.9 0.00033324 3777310000 6227000 6106290 5114910 6889540 4571890 5654240 5891420 5967780 4497930 FALSE TRUE 5932662.051 6728527.893 5349433.683 6196990.35 5369226.168 5458432.251 4992575.676 5445209.546 5195446.012 1.141896583 1.295081862 1.02963897 1.192773505 1.033448554 1.050618607 0.960952277 1.04807355 1 22.30881617 2.879533118 0.907456176 0.996471612 1.207406613 0.509000148 0.070013045 0.373381112 0.670258872 0.035782937 0.038784339 757.7625155 -2.879533118 0.210935001 EYTINIHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 170.47 3.74E-05 3337500000 4437800 3195000 4245800 4247100 4452700 4373000 5733400 5063400 5097300 FALSE TRUE 4228033.989 3520574.132 4440474.13 3820173.439 5229249.47 4221561.913 4858664.529 4620021.853 5887763.251 0.718105299 0.597947639 0.754186937 0.648832719 0.888155527 0.717006057 0.825213977 0.784682002 1 22.48928823 0.180388154 0.174169413 1.168735941 0.58186537 0.627507795 0.070520217 5.82181266 0.411308568 0.905385887 0.33987978 1.51491461 -0.180388154 -0.586870571 EYTLDVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYTLDVYR 8 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 ;; 147.16 0.0012605 287854000 708040 537313 281368 329335 752330 373827 738310 549420 725620 FALSE TRUE 674572.3524 592065.8056 294269.0011 296229.6201 883536.1138 360881.2773 625667.2495 501309.8721 838145.4436 0.804839253 0.706399838 0.35109539 0.353434624 1.054156078 0.430571185 0.746490068 0.598117995 1 19.67684109 -3.288845164 0.636599274 3.370427491 0.64159375 0.219928642 0.217584347 1913.36832 48.30663535 6310.285361 0.07815343 0.000514227 3.288845164 -2.728833741 EYVAYSHTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYVAYSHTGR 10 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ;; 142 3.65E-05 610050000 628810 486500 299917 416880 668580 308100 625430 384100 483730 FALSE TRUE 599087.3975 536074.9031 313668.4911 374974.4304 785180.1403 297430.4197 530009.1667 350466.1678 558744.3778 1.072202999 0.959427825 0.561381024 0.67110193 1.405258239 0.532319307 0.948571812 0.627238826 1 19.09182888 3.987883442 24.03024264 0.821596105 1.0299124 0.095660915 0.258675465 829.9774365 1646067.862 0.060731162 0.112850818 9724.861877 -3.987883442 0.208316295 EYVEHTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYVEHTVK 8 0 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;;; 109.71 0.0035651 864040000 1831470 1466860 1487940 1699060 1328220 1628990 1841760 1761010 1337140 FALSE TRUE 1744900.043 1616334.702 1556163.521 1528267.261 1559861.147 1572577.668 1560765.686 1606806.629 1544496.842 1.129753066 1.046512144 1.007553708 0.989491995 1.009947774 1.018181213 1.010533426 1.040343097 1 20.55870549 4.313095415 1.618285409 1.010764853 1.133557799 0.882324546 0.013655164 0.142699398 0.611310021 0.003689435 0.021404412 20563.42327 -4.313095415 0.122792945 EYVEPELHINDLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 157.09 5.39E-06 113072000 189370 210511 188309 230140 212860 188480 222740 218062 183367 FALSE TRUE 180418.8554 231962.3102 196943.1539 207005.89 249982.7166 181952.8903 188756.9221 198967.3353 211802.6179 0.851825427 1.095181507 0.929842869 0.977352839 1.180262639 0.859068184 0.891192583 0.939399793 1 17.6923609 EYVESQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 EYVESQLQR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 215.42 1.49E-06 724430000 892570 742190 722000 803980 945700 731990 954450 823790 1041190 FALSE TRUE 850379.985 817820.0048 755104.4142 723162.4029 1110629.781 706641.0028 808831.1228 751654.5804 1202652.428 0.707087073 0.680013598 0.627865871 0.601306235 0.923483589 0.587568766 0.672539384 0.62499735 1 20.19778833 -1.124836109 5.173427711 1.000009526 0.679004385 0.533495885 0.094593232 9.40E-06 1.59E-06 0.082836782 0.019524237 0.075017725 1.124836109 -0.321005141 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYVSNDAAQSDDEEKLQSQPTDTDGGR 27 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 EYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;EYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;EYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 285.09 1.25E-61 1296690000 1171590 1069540 965500 1201110 690067 1138860 1119050 1214390 796490 TRUE FALSE 1116211.263 1178527.342 1009769.13 1080372.141 810414.4663 1099420.993 948318.3697 1108051.574 920005.6013 1.213265725 1.281000181 1.097568459 1.174310395 0.880879926 1.195015542 1.030774561 1.204396552 1 19.81128312 3.679486376 5.493081287 1.082531749 1.247020684 0.320517699 0.099206919 0.202212692 12.94049377 0.023652767 0.037471552 4780.643691 -3.679486376 0.164488935 EYVTCHTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 EYVTCHTCR 9 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;;; 193.82 3.31E-05 1191731000 1234659 1061105 803420 971046 1209101 884178 1266759 1070329 1090968 FALSE TRUE 1176299.116 1169232.806 840257.6017 873434.6112 1419967.832 853558.6942 1073491.649 976605.3186 1260149.746 0.933459789 0.927852273 0.666791867 0.693119698 1.126824678 0.677347035 0.851876257 0.774991482 1 20.26516375 3.94034673 24.99397536 0.819041127 0.931358535 0.078534567 0.14514859 498.5780909 208897.695 0.03417229 0.061605028 8716.592236 -3.94034673 0.112317408 EYWDYEAHVPSWGNQDDYQLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYWDYEAHVPSWGNQDDYQLVR 22 0 P19784;H3BNI9 P19784 CSNK2A2 Casein kinase II subunit alpha 0 139.44 1.37E-07 66535000 82406 89505 76434 92719 89575 82641 101440 87684 75909 FALSE TRUE 78510.83169 98625.66126 79938.5745 83398.70997 105196.8516 79779.12145 85963.46493 80005.92412 87680.58003 0.895418708 1.124829024 0.911702163 0.951165126 1.199773674 0.909883596 0.980416244 0.912470288 1 16.41996972 EYWDYESHVVEWGNQDDYQLVR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 234.47 1.94E-30 386316000 345894 395456 350921 391267 315153 357491 358096 377496 239069 FALSE TRUE 329544.2761 435753.416 367011.075 351936.0978 370115.5834 345110.997 303461.8783 344440.449 276142.5995 1.193384421 1.578001427 1.329063591 1.274472314 1.340306002 1.249756458 1.09893178 1.247328191 1 18.07505394 1.715799212 0.603493869 1.027448736 1.386914831 0.491493636 0.109110579 0.563579068 0.441420561 0.100729354 0.055890544 51.97556418 -1.715799212 0.359466095 EYWMDPEGEMKPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 EYWMDPEGEMKPGR 14 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 70.26 0.040773 359580000 1180430 1191770 1050790 1347210 1127950 1135850 1213840 1181670 1032650 FALSE TRUE 1124633.413 1313212.718 1098969.761 1211785.891 1324664.123 1096515.23 1028646.414 1078196.71 1192788.088 0.942861037 1.100960624 0.921345352 1.015927224 1.11056116 0.919287542 0.862388235 0.903929811 1 20.18590632 2.075554983 10.3586688 0.902831992 1.018141186 0.322536816 0.067923134 0.3771416 49.11162576 0.023695019 0.01749551 119.0021979 -2.075554983 0.115309194 EYYDHLPELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 EYYDHLPELK 10 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 102.52 0.0029357 1183761000 3864120 3199670 3370850 3906260 2669710 3615510 4077440 3984960 2608630 FALSE TRUE 3681470.706 3525720.011 3525406.807 3513595.323 3135306.579 3490303.982 3455351.641 3636015.777 3013163.017 1.221796061 1.170105962 1.170002017 1.166082055 1.040536659 1.158352191 1.146752307 1.206710608 1 21.5228473 -5 0.162419579 0.433646356 1.201001136 0.501728489 0.04905033 112.7532991 1.043421423 20.854618 0.195632886 1.00E-05 5 0.767354779 EYYS(ph)TESEPLTNGGQKPSSSDTFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 EYYSTESEPLTNGGQKPSSSDTFFR 25 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 EY(0.013)Y(0.065)S(0.836)T(0.073)ES(0.014)EPLTNGGQKPSSSDTFFR 79.67 0.01487 54779000 43460 31385 28777 50622 50209 35595 45115 29760 48699 TRUE FALSE 41405.73193 34583.16718 30096.45391 45533.38038 58965.4337 34362.33622 38231.87816 27154.05663 56250.9922 0.736088917 0.614801016 0.535038632 0.80946804 1.048255887 0.610875202 0.679665845 0.48273027 1 15.77959092 3.222141008 24.9880357 0.752578131 0.641026146 0.123870058 0.173541943 618.8571661 941800.5297 0.049403743 0.059211606 1667.788627 -3.222141008 -0.111551985 FAAGHDAEGSHSHVHFDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAAGHDAEGSHSHVHFDEK 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 37.687 0.073194 202660000 73298 78687 80174 90367 73375 85065 94482 71485 38558 FALSE TRUE 69833.3488 86705.29476 83850.0572 81283.13747 86171.57677 82119.17772 80067.03562 65225.39443 44537.37771 1.567971721 1.94679838 1.882689586 1.825054407 1.934814782 1.843826061 1.79774921 1.464509088 1 15.442729 0.967066494 2.185974613 1.001455995 1.833223865 0.871855288 0.103890409 0.110613837 1.157701803 0.098644631 0.027174123 9.269717402 -0.967066494 0.83176787 FACHSASLTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FACHSASLTVR 11 0 Q15233;Q15233-2;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 93.561 0.0091579 450550000 459320 447830 397310 521330 395380 488190 528790 530330 412380 FALSE TRUE 437608.8539 493464.3861 415527.0565 468924.9179 464334.1468 471283.8579 448113.3736 483891.4937 476329.7843 0.918709827 1.03597214 0.872351615 0.984454329 0.974816529 0.989406654 0.940762867 1.015874946 1 18.86160124 1.226842741 24.86424715 1.007937504 0.963176084 0.169420321 0.044007912 422.513203 896503.9991 0.037042287 0.009561064 16.85942431 -1.226842741 -0.04476142 FACNGTVIEHPEYGEVIQLQGDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FACNGTVIEHPEYGEVIQLQGDQR 24 0 K7EM18;P41567;O60739;K7EQP2 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;; 359.37 2.23E-102 2651407000 1654204 1675208 1538758 1816806 1512887 1532579 1641868 1657803 1343826 FALSE TRUE 1576013.055 1845913.6 1609311.576 1634177.209 1776734.014 1479505.405 1391370.882 1512636.981 1552219.673 1.015328618 1.189208997 1.036780814 1.052800218 1.144640829 0.953154654 0.896374982 0.974499298 1 20.56590131 2.187458052 8.500534294 0.941505016 1.091017761 0.562529927 0.057070464 0.178001943 26.85176243 0.020414458 0.015112205 153.9777795 -2.187458052 0.149512744 FADDQLIIDFDNFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FADDQLIIDFDNFVR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 114.56 0.0013874 119680000 44815 54015 48575 49411 39525 36680 41447 40221 45468 FALSE TRUE 42696.68376 59519.18991 50802.2118 44444.11241 46418.14749 35409.7624 35123.49892 36699.03602 52518.94522 0.812976795 1.133289895 0.967312112 0.846249143 0.883836248 0.674228362 0.668777691 0.698777096 1 15.68055032 2.727819644 1.603311988 0.729116777 0.977936096 0.286575228 0.12763515 0.34909374 1.797399417 0.048486406 0.046491571 534.3424094 -2.727819644 0.248819319 FAEAFEAIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FAEAFEAIPR 10 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 169.44 1.08E-05 467428000 646946 570321 570940 644526 681659 549682 731420 599931 718123 FALSE TRUE 616366.1447 628437.3583 597118.1637 579737.022 800540.1138 530646.3745 619828.4456 547397.8612 829485.8472 0.743070116 0.757622762 0.719865403 0.698911288 0.965104006 0.639729269 0.747244148 0.659924293 1 19.66185784 -1.360864852 4.950149315 1.000175922 0.743472426 0.460367602 0.0879527 0.000152735 1.97E-05 0.07617017 0.01794125 0.043564742 1.360864852 -0.256703496 FAELPEFRPEEVLPS(ph)PTLQS(ph)LATSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.853)PT(0.207)LQS(0.36)LAT(0.299)S(0.281)PR 51.566 0.066434 14310000 14706 11171 13917 14245 16197 12015 12878 13241 14948 TRUE FALSE 14010.87652 12309.3376 14555.10822 12813.06554 19021.75167 11598.91754 10913.22458 12081.54785 17266.0595 0.81146926 0.712921069 0.842989578 0.742095528 1.10168459 0.671775603 0.63206226 0.699728149 1 14.07565124 -0.441991874 7.998202344 0.999999997 0.768901905 0.220350765 0.131166277 0 0 0.125039145 0.029472009 0.361416625 0.441991874 -0.231098092 FAELPEFRPEEVLPS(ph)PTLQSLATS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.999)PT(0.001)LQSLAT(0.225)S(0.775)PR;FAELPEFRPEEVLPS(1)PTLQS(0.003)LAT(0.253)S(0.744)PR 134.96 2.01E-05 221078000 303110 253137 281370 313430 324200 263200 294530 234790 287400 TRUE FALSE 288782.591 278931.9481 294271.0928 281923.4209 380740.3774 254085.318 249594.0391 214230.5429 331968.5242 0.869909555 0.84023613 0.886442754 0.849247445 1.146917101 0.765389787 0.751860556 0.645333902 1 18.34068693 FAELPEFRPEEVLPSPTLQSLAT(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.5)S(0.5)PR 249 1.68E-45 186630000 136150 122950 107990 127140 124460 108990 149990 129220 131860 TRUE FALSE 129714.4593 135478.7448 112941.4483 114359.6456 146165.7846 105215.649 127106.2707 117904.8118 152308.1754 0.85165789 0.889504089 0.74153241 0.750843777 0.9596713 0.690807626 0.834533474 0.774120046 1 17.21663386 -1.052145359 3.987069401 1.000029814 0.817345347 0.362674909 0.07816409 26758487066 33787996114 9700759.602 0.017530132 0.088685913 1.052145359 -0.182684466 FAELPEFRPEEVLPSPTLQSLATS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.353)S(0.647)PR;FAELPEFRPEEVLPSPTLQSLAT(0.175)S(0.825)PR 213.72 1.06E-26 452000000 254260 199820 213307 251140 217731 216988 252950 240860 240400 TRUE FALSE 242241.6337 220181.8852 223087.3369 225894.9301 255703.2175 209473.6512 214357.8318 219769.0215 277680.0042 0.872376945 0.792933887 0.803397197 0.813508091 0.92085571 0.754370671 0.771959913 0.791447055 1 18.08306377 FAELVYTGFWHSPECEFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAELVYTGFWHSPECEFVR 19 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ; 263.15 3.01E-31 1440920000 1667120 1754240 1495210 1882020 1624900 1637090 1897690 1826280 1278500 FALSE TRUE 1588318.542 1932999.05 1563766.857 1692835.774 1908282.046 1580397.163 1608162.537 1666361.241 1476763.25 1.075540403 1.308943089 1.058915068 1.146314938 1.292205806 1.070176389 1.088977896 1.128387533 1 20.49400713 1.198618088 0.666678806 1.006576019 1.177370341 0.238668361 0.086661249 0.90099155 0.955540044 0.080148422 0.034396116 15.79858123 -1.198618088 0.170794322 FAEMEER ddPTM_SK-BR-3_Trastuzumab_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 ; 87.323 0.045195 626600000 1246650 1078600 1121680 1285160 1303760 1236260 1462000 1334880 1347870 FALSE TRUE 1187723.325 1188510.566 1173110.137 1155973.275 1531135.331 1193448.006 1238945.049 1217990.831 1556890.796 0.76288159 0.763387239 0.753495454 0.742488348 0.983457116 0.766558586 0.7957816 0.782322584 1 20.57023632 -5 0.206554948 1.970434364 0.759688954 0.474491205 0.068679 125.9059303 1.251911603 50.65908082 0.145112692 1.00E-05 5 -1.21074541 FAEQTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAEQTLR 7 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 ; 110.31 0.015895 116370000 337300 229503 273292 275774 318460 298972 404770 317882 311820 FALSE TRUE 321356.4975 252889.6166 285822.7085 248052.6736 373999.3232 288618.5247 343014.9024 290046.5669 360175.453 0.892222096 0.702128961 0.793565209 0.688699553 1.038380934 0.801327581 0.952355024 0.805292433 1 18.45834034 2.750271267 24.96276251 0.909719274 0.773013545 0.395454239 0.091858892 757.7206922 1615178.171 0.025343545 0.026678914 562.6926818 -2.750271267 -0.136705729 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR 39 1 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 248.06 5.99E-51 29359000 22549 19281 19123 22654 15396 23238 23842 18989 14205 FALSE TRUE 21483.15346 21245.75582 19999.80847 20376.77688 18081.05753 22433.26223 20204.46501 17326.22249 16407.83885 1.309322553 1.294854003 1.218917899 1.241892797 1.101976786 1.367228337 1.231390995 1.055972249 1 14.00209761 -5 0.113882202 0.156592298 1.382179987 0.529756141 0.07994237 125.9690236 0.944742387 24.2449782 0.8673357 1.00E-05 5 1.225587689 FAEVEHVVNAILFLLSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAEVEHVVNAILFLLSDR 18 0 Q7Z4W1 Q7Z4W1 DCXR L-xylulose reductase 0 148.24 7.08E-08 132650000 91827 113530 110930 101860 85624 94761 108400 99735 62684 FALSE TRUE 87486.51969 125098.8361 116016.2502 91620.83928 100556.7985 91479.40281 91861.5891 91001.67467 72404.71457 1.208298661 1.727771966 1.602330054 1.265398805 1.388815619 1.26344539 1.268723862 1.256847364 1 16.14379602 1.47376066 0.499077926 1.013781816 1.498266467 0.466633786 0.149522463 0.740168879 0.473770528 0.158263144 0.095340189 29.76875421 -1.47376066 0.484484652 FAEWCLEYGEHGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FAEWCLEYGEHGCR 14 0 O43813;H7C2E3 O43813 LANCL1 LanC-like protein 1 0 ;;; 231.22 6.20E-13 932720000 956060 920540 914730 1020780 905200 848400 978860 977110 836920 FALSE TRUE 910868.9385 1014344.073 956671.2753 918169.255 1063066.593 819019.6953 829516.929 891549.0684 966705.2792 0.942240575 1.049279542 0.989620411 0.949792325 1.099680137 0.847227912 0.858086686 0.922255301 1 19.88271659 2.220332715 24.99999685 0.889395732 1.002889635 0.375514475 0.061703236 209.2721757 287019.8855 0.021113395 0.015623331 166.0858811 -2.220332715 0.113493902 FAFQAEVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAFQAEVNR 9 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 148.27 0.003632 0 143050 123990 92418 114670 113080 108170 169310 129260 119680 FALSE TRUE 136288.31 136624.722 96655.45671 103143.1537 132801.1162 104424.0458 143478.6499 117941.3091 138239.3632 0.985886414 0.988319961 0.699189106 0.746120001 0.960660648 0.755385755 1.037900108 0.853167336 1 17.07680895 -0.463145904 8.526035358 0.999999969 0.893067204 0.084988586 0.11688756 0 0 0.113148782 0.026669424 0.344234263 0.463145904 -0.106932765 FAGDKGYLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAGDKGYLTK 10 1 P60903 P60903 S100A10 Protein S100-A10 0 ; 100.72 0.0034837 862620000 1467510 794780 1159120 1250590 1296690 1208130 1576320 1267370 1439050 FALSE TRUE 1398143.711 875768.9856 1212266.799 1124878.317 1522832.325 1166292.155 1335823.433 1156392.364 1662210.524 0.841135157 0.526870076 0.729310025 0.67673637 0.916148889 0.701651288 0.803642748 0.695695489 1 20.66467169 2.795362747 24.97834659 0.80072234 0.684130217 0.21618046 0.118023687 439.2812911 193169.9113 0.032965017 0.034964671 624.2560314 -2.795362747 -0.116592124 FAGHSEAGGGSGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 132.86 4.80E-05 747000000 342160 434570 431630 397810 296640 417400 323930 329820 261240 FALSE TRUE 325986.7749 478853.1771 451420.6624 357821.383 348373.9221 402945.3333 274508.5291 300939.2123 301751.765 1.080314393 1.58691094 1.496000073 1.18581372 1.154505002 1.335353692 0.909716399 0.997307215 1 18.20300268 2.053833204 1.033517248 0.949045265 1.360588928 0.458958375 0.162129552 0.451062506 0.890950799 0.125501007 0.061154549 113.1965535 -2.053833204 0.411543663 FAGLHFFNPVPVMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FAGLHFFNPVPVMK 14 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;; 164.13 4.17E-06 603370000 2726130 2053810 1978700 2063330 2038050 1785230 2531960 2337290 1979760 FALSE TRUE 2597271.238 2263095.574 2069425.352 1855920.148 2393485.275 1723407.037 2145662.999 2132624.497 2286771.07 1.135781046 0.989646757 0.904955192 0.811589832 1.046665889 0.753642138 0.938293749 0.93259204 1 21.12488051 4.213565477 1.693878314 0.903807113 1.132450779 0.410709866 0.084077659 0.346552654 1.765977468 0.020619895 0.092358903 16351.79663 -4.213565477 0.228643666 FAGVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FAGVDIR 7 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 107.49 0.017367 1793633000 6329270 6682210 5902750 6696890 6058190 6296800 6755440 6819090 6158690 FALSE TRUE 6030097.951 7363134.796 6173396.926 6023705.894 7114736.418 6078740.237 5724773.556 6221974.329 7113748.191 0.847668176 1.035056991 0.867812124 0.846769626 1.000138918 0.854505961 0.804747849 0.874640789 1 22.76217848 FAHEHEEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAHEHEEMK 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 105.52 0.0021591 102400000 122750 116520 113260 141280 98211 116480 133080 126270 40482 FALSE TRUE 116947.8508 128393.5205 118453.083 127078.266 115338.9673 112446.2684 112776.2018 115213.1294 46759.74181 2.501037137 2.74581329 2.53322791 2.717685365 2.466629687 2.404766666 2.411822595 2.463938528 1 15.51297934 -1.446691509 0.373569365 6.32E-10 2.631085989 0.960162431 0.098752298 3.976504966 0.31422255 3.890993726 0.06642086 0.035752671 1.446691509 2.631085988 FAHIDGDHLTLLNVYHAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAHIDGDHLTLLNVYHAFK 19 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 294.38 4.26E-50 895150000 1246330 1191420 1151680 1318420 1128800 1255090 1496900 1348520 195591 FALSE TRUE 1187418.451 1312827.053 1204485.667 1185889.917 1325662.363 1211625.919 1268520.413 1230436.44 225922.2533 5.255872024 5.8109683 5.331416668 5.249106271 5.867781252 5.363021573 5.614853755 5.446282611 1 17.78546686 0.906876583 19.67046385 0.999999999 5.511763643 0.977336939 0.21499824 1230.756309 259973.6072 0.186894226 0.046723557 8.070056639 -0.906876583 4.511763644 FAHTNVESLVNEYDDNGEGIILFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FAHTNVESLVNEYDDNGEGIILFR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 312.41 1.67E-73 640316000 647808 762908 550697 800039 556410 597437 578686 628979 427711 FALSE TRUE 617187.3997 840649.1926 575947.0022 719617.5597 653447.7278 576747.6069 490396.8224 573902.2643 494038.2374 1.249270508 1.701587304 1.165794383 1.456602962 1.322666301 1.167414915 0.992629285 1.161655558 1 18.91426318 2.220995272 2.048668131 1.049660134 1.417356898 0.51736053 0.146869098 0.233871653 1.977369309 0.0675533 0.043821883 166.3394543 -2.220995272 0.367696765 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 170.36 5.17E-13 466330000 106180 96717 89833 114630 90954 94755 104860 99483 64082 FALSE TRUE 101161.0818 106572.5723 93951.93191 103107.1746 106816.3488 91473.61059 88861.68111 90771.74113 74019.50927 1.366681336 1.439790311 1.269286068 1.392972956 1.44308372 1.235804067 1.200517026 1.226321844 1 16.17561795 1.241312593 0.600106459 1.003558694 1.395619071 0.779092419 0.063008206 0.319726178 0.283629095 0.061203498 0.028746613 17.43061028 -1.241312593 0.392060377 FAIGS(ph)AR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;FAIGS(1)AR;FAIGS(1)AR 91.318 0.017299 215811000 487160 476350 426020 496590 475700 447870 516010 500230 487450 TRUE FALSE 464132.9123 524890.6066 445553.4384 446671.8297 558661.9294 432360.1496 437283.1973 456427.2093 563041.2565 0.824331977 0.932241822 0.791333554 0.793319894 0.992222014 0.767901365 0.776645037 0.810646119 1 19.10288111 FAIQDIS(ph)VEETSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FAIQDISVEETSAK 14 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;G3V2N5;A0A494C1A0;G3V2W4;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V5M4;G3V2X9;G3V2E8 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 1 FAIQDIS(1)VEETSAK 140.22 1.05E-05 28147000 123740 111010 85558 103580 77269 86107 127540 90320 83963 TRUE FALSE 117891.0554 122322.0452 89480.91893 93167.94161 90744.68914 83125.093 108081.4306 82411.10198 96983.55322 1.215577812 1.261265866 0.922640138 0.960657127 0.935670906 0.857105048 1.114430509 0.849743067 1 16.56545249 3.740017435 24.98967881 0.957261621 1.238421854 0.719070228 0.075159276 58.91703118 1010633.381 0.018624228 0.031433549 5495.629353 -3.740017435 0.281160233 FALNHPELVEGLVLINVDPCAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FALNHPELVEGLVLINVDPCAK 22 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3;Q5TH29 Q5TH30 NDRG3 Protein NDRG3 0 159.78 1.92E-11 60161000 294240 290340 279810 360130 209800 330890 319200 354210 183570 FALSE TRUE 280331.8583 319925.9761 292639.5653 323929.0482 246389.0536 319431.1963 270500.1775 323193.4946 212037.0981 1.322088733 1.508820763 1.380133797 1.527699875 1.162009176 1.506487305 1.275720994 1.52423089 1 17.69395718 -1.882377319 2.640520845 0.805607442 1.397530296 0.516674537 0.121817775 15053480.87 8165719.865 18221179.83 0.02554101 0.013110603 1.882377319 0.591922854 FALVT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FALVTPK 7 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FALVT(1)PK 111.46 0.073498 93889000 558830 564630 556330 657510 380650 624040 658890 671760 419920 TRUE FALSE 532415.2134 622166.4389 581838.2808 591415.8456 447035.2395 602429.3383 558364.2292 612937.1332 485039.0489 1.097674949 1.282714124 1.199569977 1.219315944 0.921647938 1.242022348 1.151173767 1.26368616 1 18.88774137 FAMEPEEFDSDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FAMEPEEFDSDTLR 14 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 264.17 2.67E-24 421425000 428439 388502 382867 446836 412073 386753 451763 408035 406637 FALSE TRUE 408187.5376 428090.7955 400421.8307 401919.1963 483938.4007 373359.6466 382838.2572 372305.2923 469696.1891 0.869045879 0.911420628 0.852512411 0.855700356 1.030322178 0.794896053 0.815076354 0.792651294 1 18.84136836 FAPPLVIKEDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FAPPLVIKEDELR 13 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;;; 158.11 4.36E-05 1196063000 3839642 2973595 3316599 3146871 2555600 2845405 3382091 3431300 2591955 FALSE TRUE 3658149.732 3276607.711 3468668.345 2830541.548 3001295.831 2746867.911 2866090.902 3130837.182 2993902.144 1.221866834 1.094427124 1.158577728 0.94543556 1.002469582 0.91748754 0.957309479 1.045737981 1 21.51359564 3.242661593 24.98539187 0.97169522 1.1536879 0.770560013 0.046247729 43.87919993 267334.2584 0.01245799 0.016274763 1748.483719 -3.242661593 0.18199268 FAQHGTFEYEYSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FAQHGTFEYEYSQR 14 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 234.66 3.23E-17 2670020000 2258240 1805530 2129430 2331210 2444250 2071620 2725400 2373210 2620950 FALSE TRUE 2151497.471 1989515.56 2227066.472 2096872.342 2870526.426 1999879.28 2309590.175 2165399.151 3027393.54 0.710676508 0.657171106 0.735638245 0.692632892 0.948184102 0.66059442 0.76289724 0.715268472 1 21.5296448 -4.999999999 0.214789966 2.313460329 0.694037054 0.503979096 0.082279617 118.1008754 1.179310225 67.07081082 0.154434073 1.00E-05 4.999999999 -1.619423275 FAQPGSFEYEYAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FAQPGSFEYEYAMR 14 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 205.49 2.83E-08 829070000 387170 288607 322610 409317 382576 326672 445610 399991 418118 FALSE TRUE 368869.2414 318016.3814 337401.9876 368171.6775 449297.1333 315359.2667 377624.0103 364965.6676 482957.604 0.763771475 0.658476808 0.698616162 0.762327116 0.930303467 0.652975052 0.781898881 0.755688832 1 18.88153702 -5 0.222320843 2.313585203 0.713093761 0.511106993 0.077180812 123.6078294 1.236458318 72.76390473 0.137322023 1.00E-05 5 -1.600491442 FAQPGTFEFEYASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAQPGTFEFEYASR 14 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 156.52 1.29E-05 202994000 225570 204420 216643 244820 208687 201565 278980 238530 206470 FALSE TRUE 214907.7531 225250.6304 226576.2958 220210.2285 245081.9467 194584.7535 236416.4772 217643.0487 238488.3131 0.901124883 0.944493369 0.950051987 0.923358573 1.027647617 0.815908968 0.991312631 0.912594189 1 17.86355904 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(0.989)PLS(0.01)S(0.001)QPVLITVQR;FAQSAPGS(0.944)PLS(0.056)SQPVLITVQR;FAQSAPGS(0.938)PLS(0.055)S(0.007)QPVLITVQR;FAQSAPGS(0.953)PLS(0.039)S(0.008)QPVLITVQR;FAQSAPGS(1)PLSSQPVLITVQR 325.9 5.82E-68 883142000 800028 761002 793210 880531 886970 828813 965434 889448 978181 TRUE FALSE 762212.2619 838548.969 829579.4631 792018.351 1041657.287 800110.998 818139.3119 811563.2179 1129872.314 0.674600353 0.742162596 0.734224083 0.700980404 0.921924783 0.708142848 0.724098911 0.718278701 1 20.10772831 -2.352053638 2.260476788 2.635475786 0.738292145 0.594925582 0.067257592 2775971.312 363701.5335 23208395.93 0.015934494 0.004445764 2.352053638 -1.897183641 FAS(ph)AENIPDLPYDYSSSLESVADETSPER ddPTM_SK-BR-3_Trastuzumab_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(0.999)AENIPDLPYDYSSSLESVADETSPER 70.647 0.0050186 9396200 28267 24701 25270 30027 20928 24311 26752 25877 23857 TRUE FALSE 26930.87493 27218.05998 26428.6545 27008.62891 24577.83657 23469.10397 22670.49107 23611.0727 27556.62172 0.977292326 0.987713961 0.959067289 0.980113934 0.891903109 0.851668402 0.822687603 0.856820293 1 14.75011141 2.641779711 3.261352873 0.863094593 0.977855117 0.445585311 0.048432919 0.174041704 3.537463257 0.014907732 0.01404915 438.3083164 -2.641779711 0.114760524 FAS(ph)DDEHDEHDENGATGPVK ddPTM_SK-BR-3_Trastuzumab_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 258.87 1.84E-36 7638140000 7985830 9840980 6999920 10031880 5593350 8935490 7384510 7616840 2612070 TRUE FALSE 7608355.642 10843787.05 7320873.256 9023456.363 6568828.469 8626051.741 6257867.374 6949869.11 3017136.475 2.521714117 3.59406581 2.426430928 2.990735235 2.177173132 2.859019409 2.074108157 2.303465278 1 21.52474853 0.453368771 0.311428126 0.652480931 3.094405604 0.670740861 0.38789669 1.737664556 0.345416422 1.313191893 0.433769463 2.840329802 -0.453368771 2.441924674 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FASDDEHDEHDENGATGPVKR 21 1 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR 178.11 2.93E-17 8114790000 3980400 3408120 3642790 3976120 2201130 4013700 4234100 3715180 555586 TRUE FALSE 3792254.38 3755411.303 3809815.525 3576432.863 2585006.375 3874704.563 3588110.28 3389859.144 641743.4393 5.909299804 5.85188889 5.936664547 5.57299482 4.028099419 6.037778223 5.591191215 5.282265366 1 19.29163712 2.980868377 19.19295543 4.872685435 5.873595631 0.1625096 1.404682216 81.3372394 81599.1801 0.378687842 0.410110524 956.9040159 -2.980868377 1.000910196 FASEAEDKIR ddPTM_SK-BR-3_Trastuzumab_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 84.31 0.013688 257270000 394980 309470 304710 362920 275550 333770 382350 388280 307270 FALSE TRUE 376310.0782 341005.3448 318681.2549 326438.5921 323605.8328 322211.4612 324015.4852 354280.1448 354919.8623 1.060267734 0.960795326 0.897896367 0.919752955 0.911771549 0.907842855 0.91292576 0.998197572 1 18.43713379 4.343577724 1.976414612 0.927760426 1.05974876 0.512989969 0.037000016 0.252224734 1.724652135 0.008889456 0.045157564 22058.58876 -4.343577724 0.131988334 FASENDLPEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FASENDLPEWK 11 0 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 155.26 7.36E-05 234210000 616440 622570 589060 663380 485570 630700 666210 692000 539500 FALSE TRUE 587302.1029 686010.5908 616068.9837 596695.7821 570253.2543 608858.7009 564567.4287 631404.8115 623162.9046 0.942453568 1.10085274 0.988616266 0.957527763 0.915094994 0.977045804 0.905970854 1.013225927 1 19.24924983 3.430811476 4.651768385 0.953031955 1.02507241 0.180373063 0.050279259 0.233890852 11.15316575 0.013185907 0.018461506 2696.568619 -3.430811476 0.072040455 FATHAAALSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FATHAAALSVR 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 108.35 0.002075 836820000 669460 500720 377940 434800 537630 480170 716740 624750 568850 FALSE TRUE 637815.9525 551743.9373 395268.9228 391093.0779 631392.5018 463541.5925 607388.1492 570043.578 657064.3527 0.970705457 0.839710654 0.601568052 0.595212746 0.960929472 0.705473658 0.924396745 0.86756126 1 19.32567515 1.203704772 1.133019171 0.989564269 0.793506076 0.219281035 0.131409281 0.796993375 2.103267001 0.12637349 0.041309324 15.98471039 -1.203704772 -0.196058193 FATLAELVQYYMEHHGQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FATLAELVQYYMEHHGQLK 19 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 218.37 1.96E-19 290030000 433910 485350 375880 486830 291340 450870 488040 477200 133200 FALSE TRUE 413399.9342 534807.7168 393114.4698 437892.9235 342149.6038 435256.2588 413580.5345 435413.8382 153855.9757 2.686928033 3.476028242 2.555080932 2.8461223 2.22383045 2.828985074 2.68810186 2.830009275 1 17.23122095 -1.337574946 0.377280897 8.44E-19 2.909266355 0.750625504 0.317772795 10.49069007 0.893899892 11.08943362 0.220628441 0.045964766 1.337574946 2.909266355 FATVEVTDKPVDEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FATVEVTDKPVDEALR 16 1 Q9NRV9;A0A3B3IRV5;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 276.22 2.50E-35 304740000 523380 438460 470880 577820 390120 481780 561010 591890 430970 FALSE TRUE 498640.8646 483139.5725 492470.3138 519736.4358 458156.8045 465095.8378 475417.6208 540060.9738 497802.6265 1.001683876 0.970544442 0.989288299 1.044061257 0.920358351 0.934297677 0.955032367 1.084889764 1 18.92521432 1.251210738 24.99869177 1.042444897 0.973390711 0.339540281 0.039911755 222.9834681 440656.5221 0.026463754 0.009522562 17.83243865 -1.251210738 -0.069054187 FAVLHGEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FAVLHGEAPR 10 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 148.32 2.53E-05 779980000 1647640 1554230 1345410 1514310 1604630 1433570 1758280 1524920 1499070 FALSE TRUE 1569759.323 1712607.804 1407098.379 1362088.682 1884476.964 1383925.111 1490022.093 1391389.921 1731538.119 0.906569313 0.989067341 0.812629167 0.786635112 1.088325427 0.799246113 0.860519371 0.803557199 1 20.72362272 FAVQDVNDVLDLEWDQHLEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAVQDVNDVLDLEWDQHLEQK 21 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ; 203.06 6.05E-22 71166000 181355 160004 142638 182975 128243 174849 193010 194287 142326 FALSE TRUE 172782.7086 176308.5895 149178.0934 164582.0054 150608.5386 168793.9353 163562.7796 177274.2003 164397.1892 1.051007681 1.072455012 0.907424842 1.001124205 0.916125996 1.026744655 0.994924429 1.078328657 1 17.32682611 -0.122147596 6.918821768 1.000000002 1.00877472 0 0.057836375 0 0 0.055752479 0.013140985 0.754835652 0.122147596 0.008774718 FAYLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FAYLGR 6 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 141.66 0.027043 1831970000 2509400 2050850 1781900 2333200 2766000 1977560 2794000 2256500 2688800 FALSE TRUE 2390785.635 2259833.947 1863601.878 2098662.303 3248389.524 1909076.601 2367723.985 2058908.898 3105765.372 0.76978952 0.727625457 0.600045932 0.675731117 1.045922385 0.614687967 0.762364088 0.662931243 1 21.56651741 FCACPEEAAHALELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FCACPEEAAHALELR 15 0 M0QWZ7;Q9NP81;Q9NP81-2;M0R1C0;M0R2H5;B4DJM9 M0QWZ7 SARS2 "Serine--tRNA ligase, mitochondrial" 0 ; 179.39 6.72E-07 148415000 228212 157256 178106 186380 225196 162326 222106 200603 214435 FALSE TRUE 217424.871 173280.5652 186272.3363 167644.7283 264470.1111 156704.6099 188219.6504 183037.1379 247688.4846 0.877815823 0.69959072 0.752042779 0.67683699 1.067752954 0.632668128 0.759904728 0.738981217 1 17.91816727 -1.562380995 2.71485141 1.014709841 0.772682792 0.249953131 0.122009753 54987216.6 53519145.54 5861592.17 0.027868284 0.027391701 1.562380995 -0.24202705 FCFTPHTEEGCLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 302.35 2.10E-44 33768430000 7431380 6450730 7127290 7773190 7701020 6938300 8561080 7645170 7826440 FALSE TRUE 7080113.395 7108066.721 7454083.296 6991814.173 9044075.45 6698024.931 7254930.011 6975718.385 9040124.343 0.783187612 0.786279751 0.824555395 0.773420133 1.000437063 0.74092177 0.802525467 0.77163965 1 23.10791119 -1.849033288 2.480553601 1.081013774 0.808061774 0.412632496 0.071054376 7853874.668 4824321.813 3770328.93 0.0157349 0.014156853 1.849033288 -0.272952 FCIWTESAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FCIWTESAFR 10 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 280.54 1.09E-23 5787420000 2420646 1736663 906718.6 1043901.2 2580744 1081036.8 2512642 1864941 2318891 FALSE TRUE 2306226.861 1913630.934 948292.5447 938966.2681 3030824.937 1043600.225 2129292.315 1701636.879 2678492.773 0.861016645 0.714443195 0.354039613 0.350557701 1.131541204 0.389622192 0.794959141 0.635296424 1 21.35298997 -0.615661444 0.720648618 1.033988312 0.661201911 0.161863184 0.246633401 36.14266203 12.49951267 3.405621174 0.081693053 0.24229171 0.615661444 -0.372786401 FCLDNGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FCLDNGAK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 131.06 0.0023756 152650000 922830 722600 752720 894320 735250 841200 1038150 933930 854960 FALSE TRUE 879209.6548 796233.7615 787232.9565 804421.2545 863477.3672 812069.0331 879761.1506 852150.1381 987542.8303 0.890300276 0.8062777 0.797163356 0.814568472 0.874369537 0.822312722 0.890858729 0.862899423 1 19.91348379 0.419028252 0.608988652 1.004826592 0.831912327 0.719081539 0.031586883 1.072410984 0.639864633 0.043168708 0.012853278 2.624389261 -0.419028252 -0.172914265 FCNVDDDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FCNVDDDELR 10 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 202.44 5.20E-07 957651000 902370 1241720 766750 1151090 729030 922260 814170 920980 739300 FALSE TRUE 859716.7584 1368252.68 801906.2459 1035380.246 856172.6012 890321.9049 689953.4132 840334.1088 853946.8682 1.006756732 1.6022691 0.939058712 1.212464481 1.002606407 1.04259637 0.807958245 0.984059009 1 19.70378678 2.865120661 1.072407574 0.922828433 1.270632306 0.259295621 0.183890478 0.513068904 1.254372986 0.085077132 0.089674748 733.0281644 -2.865120661 0.347803873 FCNVDDDELREYCIQAFESFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FCNVDDDELREYCIQAFESFVR 22 1 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 275.2 1.81E-45 394800000 209176 135181 202683 198313 259680 204505 264750 227850 297880 FALSE TRUE 199288.665 148956.0976 211976.216 178378.2005 304968.1098 197422.9406 224357.525 207898.2461 344073.709 0.579203408 0.43291915 0.616077923 0.518430196 0.886345285 0.573780953 0.65206239 0.604225899 1 18.39235813 -5 0.137074631 2.370958749 0.444753902 0.561154329 0.111910693 97.22887155 0.823728441 36.49060719 0.685276611 1.00E-05 5 -1.926204848 FCQLLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FCQLLWR 7 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 107.49 0.017367 225070000 447640 422600 264150 319040 417780 299530 450960 372440 360210 FALSE TRUE 426480.9443 465663.4205 276261.5388 286969.4931 490640.6997 289157.201 382157.7696 339827.1792 416069.5271 1.025023263 1.119196168 0.663979265 0.689715238 1.179227672 0.694973273 0.918494974 0.816755751 1 18.6664651 3.764096435 24.92142185 0.84988763 1.072109747 0.250669892 0.158273024 873.1992773 852186.8355 0.037462847 0.067507058 5808.933899 -3.764096435 0.222222117 FCSNSGRLS(ph)GPAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.999)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR 156.15 1.32E-06 1459410000 2110360 1736800 1920920 2456160 2110950 2072790 2296080 2080890 1733290 TRUE FALSE 2010607.465 1913781.895 2008996.082 2209262.13 2479099.012 2001008.763 1945770.826 1898676.24 2002079.761 1.004259423 0.955896929 1.003454568 1.103483574 1.238261862 0.999465057 0.971874779 0.948351947 1 20.93306802 2.011068451 24.99622337 0.974130342 1.047372637 0.211087064 0.076797958 438.1915863 989577.5664 0.032043242 0.023644551 102.5813597 -2.011068451 0.073242295 FCYHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FCYHER 6 0 P28331-4;P28331;P28331-2;F8WDL5;C9JPQ5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 ; 132.01 0.019546 275380000 383490 319120 325880 313080 407310 281670 417020 339360 399280 FALSE TRUE 365363.1877 351638.6908 340821.9203 281608.6036 478344.735 271915.6973 353395.9399 309643.8393 461198.3032 0.792204102 0.76244576 0.738992139 0.610601994 1.037178003 0.589585208 0.766255941 0.671389806 1 18.81502768 -1.99904518 2.902296432 1.249340204 0.749013727 0.296091901 0.122964737 17037330.53 22575865.59 28385223.08 0.025864198 0.01002201 1.99904518 -0.500326477 FDADYAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDADYAEK 8 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;P50225;P50225-2 A0A0A6YYL2;P50225 SULT1A4;SULT1A3;SULT1A1 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A1 0 ;; 133.86 0.0020967 288069000 697230 650887 628527 770030 567020 655416 759720 735688 619500 FALSE TRUE 664273.3197 717213.1253 657345.5846 692625.1214 665908.1085 632718.7796 643810.7608 671267.2586 715568.896 0.928314972 1.002297793 0.918633535 0.967936317 0.930599572 0.884217834 0.899718761 0.938088928 1 19.44873115 2.559963129 5.283643273 0.91715561 0.957123522 0.036293907 0.03825926 0.344108028 16.2537661 0.011609334 0.010813594 363.0472316 -2.559963129 0.039967912 FDAGELITQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FDAGELITQR 10 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ;;; 173.37 7.98E-06 272950000 502703 393485 406971 456805 490793 353873 467848 416587 494552 FALSE TRUE 478941.2255 433581.5689 425631.0229 410886.0935 576387.1438 341618.2893 396469.195 380108.4338 571244.5983 0.838417075 0.759012112 0.745094175 0.719282239 1.009002353 0.598024542 0.694044541 0.665403988 1 19.12374909 FDASFFGVHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 139.15 4.27E-05 23286070000 20924940 16813960 16187360 19611340 16184150 17843010 23344390 19652080 16804080 FALSE TRUE 19935859.56 18527321.64 16929566.47 17639970.84 19006660.64 17225102.09 19782774.56 17931239.69 19409970.9 1.027093737 0.954525987 0.872209781 0.908809752 0.97922149 0.88743575 1.019206812 0.923815898 1 24.21029462 1.718697824 24.99999969 0.980166731 0.94483964 0.12866977 0.050555838 2.372529773 2974.222411 0.023877366 0.013241214 52.32362498 -1.718697824 -0.035327091 FDDDKVSIVTPEDILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDDDKVSIVTPEDILR 16 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 278.72 2.01E-35 225532000 625805 761121 520664 800910 353073 681030 601032 711076 366546 FALSE TRUE 596224.4379 838680.0952 544536.9594 720401.0052 414648.8194 657445.7603 509333.5297 648810.4158 423388.0816 1.408222063 1.980877903 1.286141446 1.701514607 0.979358743 1.55282066 1.202994491 1.532424846 1 18.69162113 3.153193888 1.639618808 1.294329174 1.66459855 0.219323625 0.272774118 0.462895063 2.573616079 0.08305586 0.110802826 1422.963919 -3.153193888 0.370269376 FDDGAGGDNEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDDGAGGDNEVQR 13 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 149.49 0.00010186 262298000 305090 260850 277660 326900 253870 266440 331860 311080 285080 FALSE TRUE 290669.0003 287430.9116 290390.9856 294039.3909 298144.8476 257213.116 281228.662 283840.1861 329288.7504 0.882717675 0.872884091 0.881873387 0.892953041 0.90542069 0.781117228 0.854048799 0.861979602 1 18.3289937 -0.751604195 10.60583394 1 0.865836559 0.607217314 0.033706608 0 0 0.032840918 0.007740679 0.177172292 0.751604195 -0.134163441 FDDKPDYSYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 78.653 0.026716 268820000 123060 117960 124550 137970 122740 125700 143190 144120 124740 FALSE TRUE 117243.1977 129980.2581 130260.7407 124100.9935 144145.8171 121346.9775 121343.7356 131500.0888 144084.0421 0.813713968 0.902114184 0.904060844 0.861309772 1.000428743 0.842195816 0.842173317 0.912662408 1 17.13655103 -3.442723598 0.987828935 4.176732706 0.88065461 0.325167882 0.051842434 56757.20614 647.7604927 403289.697 0.015246051 0.000360808 3.442723598 -3.296078097 FDDPLLGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDDPLLGPR 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 86.833 0.032269 37771000 50017 36561 34036 42786 40151 38236 54010 48282 46710 FALSE TRUE 47652.79553 40286.60747 35596.58427 38485.06999 47153.32169 36911.87773 45769.78254 44054.17212 53953.54824 0.883218937 0.746690603 0.659763545 0.713300075 0.873961458 0.684141802 0.848318304 0.816520388 1 15.71943022 0.643176018 0.949260076 0.999830729 0.767347697 0.481738568 0.075266123 1.049174121 1.590642967 0.070819522 0.023102839 4.39719796 -0.643176018 -0.232483033 FDDTNPEKEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDDTNPEKEEAK 12 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 101.6 0.0012894 0 91828 102920 80297 105330 45840 99838 83885 101400 53794 FALSE TRUE 87487.47243 113407.665 83978.69687 94742.02829 53834.48149 96380.58503 71086.8026 92520.87844 62136.09878 1.407997511 1.825149426 1.351528315 1.524750188 0.866396226 1.551120636 1.144049981 1.489003659 1 15.92314404 3.230620745 2.074498509 1.245319933 1.60231784 0.263392225 0.242451776 0.358164175 3.166573861 0.067897707 0.092706685 1700.672718 -3.230620745 0.356997907 FDEDDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FDEDDDK 7 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;;; 100.37 0.022898 4253340000 8475120 8816480 7135820 8820350 4199880 9867080 8323650 9265960 3936730 FALSE TRUE 8074517.874 9714889.336 7463004.405 7933711.66 4932337.742 9525380.545 7053724.318 8454583.42 4547217.982 1.775705037 2.136446806 1.641224246 1.744739683 1.08469349 2.094771041 1.551217546 1.859287031 1 22.11655273 -2.448285502 0.198434393 8.79E-17 1.921429777 0.363831038 0.297815978 44.96923 1.109041692 21.49870723 0.756505184 0.003562169 2.448285502 1.921429777 FDEILEASDGIMVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FDEILEASDGIMVAR 15 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 197.43 1.96E-08 97374000 287031 301087 248991 333442 232429 260079 266178 275917 227198 FALSE TRUE 273463.6135 331768.1076 260407.4836 299923.7767 272964.544 251072.399 225567.6574 251756.2448 262430.7055 1.042041224 1.264212231 0.992290453 1.142868462 1.040139505 0.956718836 0.85953226 0.95932465 1 18.00157701 2.379212571 2.272265458 0.920801482 1.122514576 0.488591323 0.078905904 0.209268011 2.213913266 0.031159208 0.02403737 239.4487482 -2.379212571 0.201713094 FDEISFVNFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDEISFVNFAR 11 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;; 148.5 8.10E-05 125965000 176799 153172 156717 189068 156398 159791 174521 179124 178881 FALSE TRUE 168442.0617 168780.4009 163902.6295 170062.5254 183673.7617 154257.3976 147894.6162 163438.953 206620.9519 0.815222561 0.816860049 0.793252707 0.82306525 0.888940642 0.746571905 0.715777441 0.791008615 1 17.65662703 2.204867303 24.99983822 0.780200277 0.823153193 0 0.08099003 545.9679106 405095.3396 0.027315743 0.020175104 160.2755599 -2.204867303 0.042952916 FDESEKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDESEKTK 8 1 P14625 P14625 HSP90B1 Endoplasmin 0 102.61 0.0044983 339690000 510190 379030 467360 473040 297240 538360 613670 598860 322700 FALSE TRUE 486074.3298 417653.5879 488788.9183 425489.1205 349078.5619 519716.4582 520043.3707 546420.6436 372742.6679 1.304047998 1.120487736 1.311330739 1.141509028 0.936513557 1.394303639 1.395180685 1.465946055 1 18.50782045 FDEVLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDEVLIR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 79.597 0.074894 25329000 35284 35880 28672 34830 31747 31364 32402 32698 36251 FALSE TRUE 33616.19525 39536.21279 29986.63956 31328.82223 37283.66675 30277.85682 27458.4798 29834.78978 41872.61994 0.802820442 0.944202031 0.716139559 0.748193504 0.890406829 0.723094396 0.655762162 0.712513089 1 15.35371957 3.72962825 24.97546262 0.757729843 0.873511238 0.099992564 0.106330024 944.5943563 2641145.03 0.026608098 0.041896824 5365.723017 -3.72962825 0.115781395 FDFDSDEDFNAFFNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDFDSDEDFNAFFNSSR 17 0 Q9HAV4 Q9HAV4 XPO5 Exportin-5 0 ; 147.68 9.08E-07 33368000 91119 82491 78839 100784 82792 88614 91616 90715 88130 FALSE TRUE 86811.98545 90896.92668 82453.84613 90653.00084 97230.89859 85545.27496 77638.29656 82771.51369 101796.7503 0.852797218 0.892925623 0.809985053 0.890529418 0.955147373 0.840353692 0.762679519 0.813105659 1 16.63533198 -1.582746918 8.594468355 1.000038475 0.851662032 0.435270824 0.052907879 4.19E-05 2.03E-06 0.055002238 0.012960798 0.02613684 1.582746918 -0.148376443 FDFLCQYHKPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDFLCQYHKPASK 13 1 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 171.76 1.47E-05 714600000 2256730 2295650 1883090 2668330 1482190 2174920 2235180 2453700 1402030 FALSE TRUE 2150058.845 2529579.345 1969431.539 2400104.399 1740683.467 2099601.975 1894162.239 2238841.02 1619449.652 1.327647848 1.561999376 1.21611162 1.482049409 1.07486112 1.296491047 1.169633299 1.382470284 1 20.62707219 2.747600013 24.96630538 1.202177058 1.40671279 0.363577099 0.138208542 670.706016 1852452.838 0.038123051 0.039896725 559.2422998 -2.747600013 0.204535732 FDGGEEVLISGEFNDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDGGEEVLISGEFNDLR 17 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ; 155.42 2.36E-07 22044000 46324 42936 39443 40975 32325 33886 39736 39470 30985.6 FALSE TRUE 44134.35633 47311.22721 41251.50056 36856.11515 37962.46977 32712.51932 33673.5434 36013.79756 35790.6886 1.233123979 1.321886476 1.152576332 1.029768261 1.060680061 0.913995249 0.94084648 1.006233715 1 15.12729668 3.296562872 1.573361493 0.969282691 1.281563775 0.869249052 0.046443126 0.108758219 0.55716988 0.015242833 0.023077366 1979.533576 -3.296562872 0.312281084 FDGGEEVLISGEFNDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FDGGEEVLISGEFNDLRK 18 1 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;; 284.57 2.39E-39 1260026000 1566773 1284826 1312398 1371170 1024209 1204550 1349044 1422731 1113907 FALSE TRUE 1492714.745 1415751.23 1372572.746 1233337.387 1202830.725 1162836.131 1143222.561 1298149.131 1286646.009 1.160159621 1.100342457 1.066783511 0.958567763 0.934857542 0.903773162 0.88852921 1.008940394 1 20.29518375 3.403742483 1.550394422 0.930815296 1.13923666 0.782849151 0.040461286 0.141830918 0.697480572 0.012519775 0.020937188 2533.625861 -3.403742483 0.208421364 FDGILGMAYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDGILGMAYPR 11 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96;F8W787 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 188.66 7.10E-06 343320000 450880 349280 264030 278430 470280 280020 516820 329470 408510 FALSE TRUE 429567.796 384872.0291 276136.0367 250441.6874 552296.6831 270322.8372 437969.6169 300619.8602 471859.6444 0.910371974 0.815649386 0.585207995 0.530754622 1.170468146 0.572888231 0.928177737 0.637095932 1 18.84799827 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK 259.45 7.10E-44 7390799000 7718950 6780450 7015490 8257580 5090781 7791190 8612700 8287770 4771930 TRUE FALSE 7354090.531 7471385.564 7337157.156 7427512.37 5978611.595 7521379.137 7298674.432 7562048.923 5511936.533 1.334211758 1.355491944 1.33113963 1.347532274 1.084666262 1.364562 1.324157923 1.371940493 1 22.39412785 -1.49269538 2.745756439 0.987194119 1.31657173 0.585086254 0.083135231 5953338.73 6207220.187 574934.3256 0.018815851 0.032159154 1.49269538 0.329377611 FDKDHDVMLFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDKDHDVMLFLK 12 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 131.06 0.00012343 286640000 2104130 1717280 1531450 1863550 1422560 1776130 2374110 2160420 1291460 FALSE TRUE 2004671.945 1892272.784 1601668.497 1676222.413 1670654.014 1714622.173 2011895.916 1971242.172 1491733.021 1.343854374 1.268506333 1.073696482 1.123674538 1.119941699 1.149416249 1.348697044 1.32144435 1 20.50855793 3.978045546 11.95566217 1.181858075 1.315639946 0.237728718 0.106018025 1.669281014 909.1598781 0.02823822 0.052072999 9507.044932 -3.978045546 0.133781871 FDKVVMEFLHECMVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDKVVMEFLHECMVNK 16 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 154.82 1.91E-07 23569000 162790 118010 147430 152220 118470 156120 199840 181450 115010 FALSE TRUE 155095.2393 130035.3532 154189.8113 136918.5564 139131.1305 150713.5253 169350.7377 165561.2761 132845.1634 1.167488792 0.978848983 1.160673128 1.030662712 1.047317997 1.134505174 1.274797918 1.246272516 1 17.01938618 1.993202616 6.701939603 1.204692602 1.074652301 0.164112897 0.092156228 0.16460188 38.38121975 0.033557973 0.022694732 98.44702933 -1.993202616 -0.130040301 FDLLWLIQDRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDLLWLIQDRPDR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 180.48 1.17E-05 231080000 313920 431810 303080 401830 282460 321820 348870 362430 271950 FALSE TRUE 299081.6237 475811.9299 316976.5178 361437.285 331720.9346 310675.2927 295643.4741 330693.7078 314122.6171 0.952117445 1.514733114 1.009085308 1.150624837 1.05602372 0.989025546 0.941172198 1.052753574 1 18.2609683 2.923809038 1.330277007 0.987261435 1.214042285 0.195733309 0.149558069 0.531253725 1.944935198 0.058856838 0.065761154 839.0909525 -2.923809038 0.22678085 FDLLWLIQDRPDRDNDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDLLWLIQDRPDRDNDLR 18 2 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 149.34 3.54E-08 339380000 674030 485410 684820 659810 751260 680560 953480 825060 961750 FALSE TRUE 642169.9377 534873.8309 716219.6744 593484.6452 882279.5061 656992.0366 808009.1141 752813.3725 1110893.278 0.578066274 0.481480842 0.644724105 0.534240919 0.79420726 0.591408778 0.7273508 0.677664891 1 20.0832888 -5 0.109215851 2.288827164 0.385516895 0.735184124 0.076118003 73.5027069 0.534747451 20.98117292 0.855510317 1.00E-05 5 -1.903310269 FDLMYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDLMYAK 7 0 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 0 123.96 0.009755 64621000 465660 576020 267910 327460 307250 334050 388200 400560 268530 FALSE TRUE 443649.1746 634717.0929 280193.9385 294543.0987 360834.3027 322481.7647 328972.9602 365484.8429 310172.2609 1.430331563 2.046337383 0.903349441 0.949611347 1.163335179 1.039686024 1.060613735 1.17832859 1 18.24271014 3.730119158 24.99973792 1.046491634 1.73833448 0.748683474 0.16767954 246.9906527 731473.4683 0.042209044 0.066566627 5371.791634 -3.730119158 0.691842846 FDLSQNHPLGMAIFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 212.7 3.82E-12 2089280000 3907580 5128390 2995780 4397490 2499220 3523630 3456880 4093140 2034910 FALSE TRUE 3722876.437 5650978.771 3133139.476 3955445.951 2935083.177 3401605.81 2929469.466 3734722.962 2350473.45 1.583883637 2.404187451 1.332982288 1.682829453 1.248719987 1.447200269 1.246331655 1.588923696 1 21.16451995 3.714744198 24.82228499 1.379197682 1.99403556 0.483614091 0.270360962 484.3106432 504765.1416 0.065665021 0.101790014 5184.945522 -3.714744198 0.614837878 FDMIWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDMIWDR 7 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 77.058 0.090912 31402000 81346 78183 56696 68390 89076 51747 93966 76814 66738 FALSE TRUE 77500.93579 86149.93659 59295.56768 61515.30727 104610.8262 49954.98841 79629.7609 70087.75894 77087.38819 1.00536466 1.117562011 0.769199334 0.797994441 1.357042036 0.648030626 1.032980398 0.909198775 1 16.23420723 3.780536788 24.95845332 0.93280254 1.06146334 0.075116987 0.190734206 1170.056795 695696.0003 0.044552458 0.08031725 6033.048097 -3.780536788 0.1286608 FDNSYSLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDNSYSLWR 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 98.943 0.013196 30596000 54926 48841 29109 35125 58888 34628 54902 40267 47120 FALSE TRUE 52329.75683 53817.95343 30443.67644 31594.16827 69158.04856 33428.82368 46525.69156 36741.00801 54427.12894 0.961464583 0.988807502 0.559347462 0.580485667 1.27065399 0.61419414 0.854825387 0.675049534 1 15.73203831 FDPFGPIGT(ph)SPPGPNPDHLPPPGYDDMYL ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.52)S(0.48)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.541)S(0.459)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.534)S(0.466)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.545)S(0.455)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.546)S(0.454)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.548)S(0.452)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.5)S(0.5)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.529)S(0.471)PPGPNPDHLPPPGYDDMYL 168.57 9.71E-12 522977000 274140.7 254281.8 266425 304825.8 311875 284247.2 338586.7 296482.2 280824.5 TRUE FALSE 261182.6124 280193.4045 278640.8498 274184.1315 366265.9013 274403.6482 286929.0803 270520.6468 324373.3292 0.805191392 0.863799145 0.859012825 0.845273353 1.12914925 0.845950094 0.884564341 0.833979315 1 18.30729568 2.93703736 24.99999399 0.926784337 0.843126686 0.229970051 0.085218916 362.983126 144125.7853 0.025063911 0.026584321 865.0423305 -2.93703736 -0.083657652 FDPFGPIGT(ph)SPPGPRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.675)S(0.325)PPGPRPDR 78.975 0.017828 134490000 200460 193060 187760 258330 222490 221610 250620 221170 243410 TRUE FALSE 190984.6531 212733.0335 196368.9817 232362.1776 261292.1856 213935.5901 212383.316 201803.1823 281156.7796 0.679281692 0.756634906 0.698432319 0.826450559 0.929346914 0.76091208 0.755391054 0.717760328 1 18.10101531 -5 0.219442122 2.155050815 0.733656938 0.505700484 0.071791652 135.4539593 1.354368724 69.5480941 0.141609339 1.00E-05 5 -1.421393877 FDPFGPIGTS(ph)PPGPNPDHLPPPGYDDMYL ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.021)S(0.979)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.2)S(0.8)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.168)S(0.832)PPGPNPDHLPPPGYDDMYL 241.23 6.53E-45 410909000 193096 187085 201002 231365 203755 213399 247563 207607 200655 TRUE FALSE 183968.7348 206149.1742 210218.1405 208107.7506 239289.8075 206008.9391 209792.7175 189427.8305 231771.5526 0.79375028 0.889449857 0.907005792 0.897900317 1.032438213 0.888844799 0.905170264 0.817304058 1 17.82234398 4.458873665 1.254950336 0.919279823 0.770128225 0.316831093 0.059007916 1.022511361 1.984751059 0.016107283 0.173821754 28765.61507 -4.458873665 -0.149151598 FDPFGPIGTS(ph)PPGPRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.222)S(0.778)PPGPRPDR;FDPFGPIGT(0.417)S(0.583)PPGPRPDR 83.395 0.0024299 56547000 57831 58434 60527 63219 61839 62197 70003 55928 72373 TRUE FALSE 55097.44324 64388.49103 63302.22282 56864.10601 72623.70202 60043.10229 59322.75666 51030.64783 83596.23521 0.659090007 0.770231947 0.757237723 0.680223288 0.868743692 0.718251272 0.70963431 0.610441938 1 16.35115035 -1.284502886 3.393204118 1.001022457 0.72522516 0.61233372 0.069533293 23910697.13 36719813.57 253638.2831 0.015515302 0.051939422 1.284502886 -0.275797296 FDPYEHEALFHTPVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FDPYEHEALFHTPVEGK 17 0 Q9HAV7 Q9HAV7 GRPEL1 "GrpE protein homolog 1, mitochondrial" 0 ; 157.91 4.75E-09 255320000 1089640 941720 840490 1004870 694620 838550 885340 929380 65830 FALSE TRUE 1038134.877 1037682.339 879027.2979 903858.5585 815761.5081 809510.8032 750265.1226 847998.5602 76038.58019 13.65273883 13.64678741 11.56028026 11.8868416 10.72825802 10.64605364 9.866900733 11.15221455 1 16.21444397 0.092125225 0.340087248 3.92E-18 13.46868557 0.921638092 0.996393523 1.179180527 0.208000632 4.59798119 0.938704534 1.23630386 -0.092125225 13.46868557 FDQLFDDES(ph)DPFEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK 158.64 9.87E-09 398571000 642355 680820 557491 727570 380310 615526 608445 686826 387756 TRUE FALSE 611992.1522 750196.332 583052.5138 654433.2813 446635.9436 594210.1803 515615.5404 626683.8743 447887.2201 1.366397889 1.674967042 1.301784216 1.461156407 0.997206269 1.326695993 1.151217354 1.39920017 1 18.77277598 3.097234755 1.941990961 1.197379812 1.502260639 0.377356504 0.1632682 0.296802701 2.287629595 0.048257328 0.060621489 1250.935033 -3.097234755 0.304880827 FDQLFDDESDPFEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 225.55 1.57E-14 175020000 709120 755100 590910 819650 429147 704210 680420 769320 434490 FALSE TRUE 675601.3029 832045.5485 618003.808 737257.2248 503990.1009 679823.0311 576609.4322 701954.2624 501868.4901 1.346171988 1.657895574 1.231405877 1.469024733 1.004227424 1.354584009 1.148925353 1.398681679 1 18.93694984 3.230074232 1.602746283 1.207999185 1.486781205 0.284077141 0.172860449 0.397469212 2.117294223 0.051614101 0.073564199 1698.53395 -3.230074232 0.27878202 FDREVDIGIPDATGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 185.14 3.97E-07 314124000 403103 290669 344674 378088 332903 372065 431035 368331 374454 FALSE TRUE 384049.1201 320288.5016 360477.6438 340081.8759 390961.1778 359180.2958 365272.6942 336077.985 432522.4139 0.887928828 0.740513072 0.833431129 0.786275728 0.903909636 0.830431636 0.844517377 0.777018657 1 18.72241537 -1.806138012 2.753288231 1.051261086 0.824723123 0.555987715 0.049002206 12485513.47 11014816.66 4308280.519 0.010906605 0.01562651 1.806138012 -0.226537963 FDRPPAR ddPTM_SK-BR-3_Trastuzumab_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 942180000 1222750 918130 807410 1083340 1068270 930460 1418710 1152640 1238350 FALSE TRUE 1164953.031 1011688.491 844430.5471 974440.605 1254575.95 898237.9369 1202259.733 1051708.731 1430386.993 0.814432064 0.707283061 0.590351109 0.681242635 0.877088477 0.627968474 0.840513608 0.735261671 1 20.44797409 -0.032350128 0.536359872 1.023700311 0.720579685 0.473001759 0.089380339 3.917146986 1.322052777 0.284094983 0.0388424 0.928217756 0.032350128 -0.303120626 FDSEYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FDSEYER 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 130.77 0.0082156 1132050000 2912660 3068330 2357060 3129810 2273770 2527380 2828020 2786150 2304190 FALSE TRUE 2774984.334 3380996.315 2465133.532 2815195.553 2670314.768 2439856.197 2396553.609 2542179.936 2661512.017 1.042634531 1.270329156 0.926215443 1.057742943 1.003307425 0.916718084 0.900448164 0.955163801 1 21.34381465 3.723495128 24.8920034 0.960232127 1.156481848 0.553553597 0.071116632 469.4329205 775622.0239 0.018950478 0.029482687 5290.480621 -3.723495128 0.196249721 FDSLTDLVEHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDSLTDLVEHYK 12 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4;H0YF12 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 172.11 3.66E-05 86691000 477950 475920 407100 550310 316420 443400 482420 492710 276950 FALSE TRUE 455358.2507 524416.7891 425765.9377 494991.7933 371603.5478 428044.9468 408817.9687 449565.7004 319897.9915 1.423448295 1.639325044 1.330942828 1.54734261 1.161631388 1.338067003 1.277963537 1.405340803 1 18.28725241 -2.780904489 0.079608255 5.15E-16 1.896841831 0.53990482 0.122744585 99.08231873 0.899627154 22.18504257 4.677373975 0.001656134 2.780904489 1.896841831 FDSPDLLLEAGDPAT(ph)SPCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDSPDLLLEAGDPATSPCR 19 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 FDSPDLLLEAGDPAT(0.5)S(0.5)PCR;FDSPDLLLEAGDPAT(0.5)S(0.5)PCR;FDSPDLLLEAGDPAT(0.5)S(0.5)PCR 104.44 0.0017925 30047000 95161 86070 83579 98011 86378 88333 104992 105241 102421 TRUE FALSE 90662.92812 94840.63085 87411.17982 88158.74807 101442.2959 85274.00606 88973.54209 96025.54012 118303.9256 0.766356042 0.801669348 0.738869648 0.745188696 0.857471934 0.720804535 0.752075991 0.811685155 1 16.85213842 0.845828399 4.218704108 0.999985369 0.770215958 0.782629303 0.038029541 0.503964276 13.2560158 0.034383488 0.008759472 7.011781893 -0.845828399 -0.22976941 FDSSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 160.03 0.0031676 552300000 875880 882820 613930 899910 635160 720350 745850 853210 622520 FALSE TRUE 834478.8882 972780.3617 642079.2978 809449.3371 745931.7029 695404.0989 632056.884 778498.4092 719057.2222 1.160518054 1.352855283 0.892946038 1.125709209 1.037374606 0.967105367 0.879007768 1.082665447 1 19.45574706 3.738805589 24.99999992 0.990987944 1.256686673 0.59745956 0.088195812 12.86375355 1312735.066 0.022677671 0.037874847 5480.315848 -3.738805589 0.265698728 FDSSLDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 148.52 0.0008336 3779830000 4353900 4164300 3054020 4089300 2228470 3742960 3648510 4075700 2317990 FALSE TRUE 4148099.776 4588646.904 3194049.838 3678235.795 2617114.462 3613340.357 3091862.79 3718810.101 2677452.051 1.549271358 1.713811048 1.192943805 1.373782135 0.97746455 1.349544376 1.154778025 1.388936209 1 21.35242931 3.733421364 24.8097038 1.21441751 1.631541212 0.592677032 0.146738381 206.7986519 998319.7127 0.033945633 0.054416862 5412.792313 -3.733421364 0.417123702 FDSSLLS(ph)SDDETK ddPTM_SK-BR-3_Trastuzumab_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(0.7)S(0.3)DDETK 185.27 9.23E-06 60444000 297380 247380 250050 319890 165620 293140 290130 321970 183540 TRUE FALSE 283323.4368 272588.3032 261515.0398 287734.0494 194504.0756 282988.4883 245865.3399 293776.5999 212002.4458 1.336415887 1.285779049 1.233547277 1.357220424 0.91746147 1.33483596 1.15972879 1.385722692 1 17.69372138 -5 0.126672581 0.264100703 1.350438461 0.225181039 0.137935542 210.4218874 1.697274139 40.53877597 1.015257186 1.00E-05 5 1.086337758 FDSSLLSS(ph)DDETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FDSSLLSSDDETK 13 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 FDSSLLS(0.044)S(0.956)DDETK;FDSSLLS(0.144)S(0.856)DDETK;FDSSLLS(0.021)S(0.979)DDETK 232.53 6.18E-13 260126000 2009280 1933450 1776490 2216680 1213910 2147310 2001030 2302250 1283820 TRUE FALSE 1914305.316 2130470.753 1857943.824 1993855.115 1425615.52 2072948.116 1695736.122 2100652.785 1482908.249 1.290912852 1.436684134 1.252905448 1.344557303 0.961364616 1.397893712 1.143520594 1.416576371 1 20.49999791 -5 0.115113492 0.148172943 1.424801795 0.244424018 0.145520526 203.0199807 1.534320004 41.19333155 1.423732201 1.00E-05 5 1.276628853 FDTQYPYGEKQDEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDTQYPYGEKQDEFKR 16 2 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 63.827 0.036776 264930000 243170 218640 311890 252020 386830 236200 301850 197290 131740 FALSE TRUE 231675.836 240919.6646 326190.465 226686.4708 454293.0295 228020.3348 255797.2386 180014.2417 152169.5664 1.522484696 1.58323159 2.143598571 1.489696502 2.98543947 1.498462145 1.681001298 1.182984522 1 17.21532033 1.270980813 1.844441837 1.001229087 1.845828511 0.340037231 0.447567589 0.392938543 2.346338412 0.394285761 0.116943599 18.66297236 -1.270980813 0.844599423 FDVHDVTLHADAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDVHDVTLHADAIHR 15 0 P13639 P13639 EEF2 Elongation factor 2 0 94.487 0.0015476 22955000 69611 55355 57211 61299 66346 61998 79347 57508 1066.8 FALSE TRUE 66320.62599 60995.73743 59834.18094 55137.10806 77916.72139 59850.99371 67241.15784 52472.29465 1232.233896 53.82145892 49.50012952 48.55748666 44.74565118 63.23208741 48.5711308 54.56850204 42.58306385 1 10.26706041 0.801671495 3.272785629 1.003713361 51.71840899 0.911451594 4.94866294 0.295837365 4.519431842 4.337713331 1.125707202 6.33390427 -0.801671495 50.71469563 FDVNTSAVQVLIEHIGNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FDVNTSAVQVLIEHIGNLDR 20 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 156.87 1.34E-08 32635000 55703 68048 60194 69928 56378 55174 65535 54392 56126 FALSE TRUE 53070.02958 74982.16856 62953.95444 62898.70459 66210.30535 53263.31055 55536.43212 49629.14813 64829.73343 0.818606321 1.156601525 0.97106607 0.97021384 1.021295351 0.821587684 0.856650632 0.765530652 1 15.98436802 2.238480486 25 0.848837652 0.993711211 0.279995964 0.099785616 2.402059088 748944.5416 0.033809934 0.026588974 173.1731218 -2.238480486 0.144873559 FDWFLK ddPTM_SK-BR-3_Trastuzumab_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 49533000 381810 338200 294460 331960 280020 253900 359620 338300 265310 FALSE TRUE 363762.598 372662.9645 307961.2823 298590.7501 328855.3993 245107.3793 304753.3641 308676.6586 306452.9198 1.187009731 1.216052909 1.004922004 0.974344608 1.073102516 0.799820669 0.994454105 1.00725638 1 18.22530592 3.679006817 4.137791817 0.97009685 1.202770881 0.640447678 0.069382008 0.114505644 4.001405948 0.017739868 0.029029446 4775.367695 -3.679006817 0.232674032 FEAELKAEQDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEAELKAEQDER 12 1 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ; 74.46 0.033238 127237000 264430 167307 263700 238690 197610 252360 334600 293880 246440 FALSE TRUE 251930.9179 184355.7735 275790.9058 214696.4277 232073.1214 243620.7099 283550.6246 268146.3092 284656.6566 0.885034346 0.647642587 0.968854581 0.75422943 0.815273826 0.855840551 0.996114505 0.941999082 1 18.11886331 1.902057987 2.895813809 0.978655311 0.802681764 0.443084135 0.083949915 0.226121125 3.374639671 0.041943012 0.022200472 79.81012425 -1.902057987 -0.175973547 FEAFEHENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEAFEHENK 9 0 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 166.19 6.09E-05 164450000 294800 456680 243180 445960 170600 336920 220970 333910 119680 FALSE TRUE 280865.3882 503216.2112 254330.0435 401131.2535 200352.586 325252.3759 187256.9681 304671.0702 138239.3632 2.031732365 3.640180334 1.839780202 2.901715144 1.449316471 2.352820271 1.354585003 2.203938612 1 17.07680895 2.086246999 0.434454646 1.137651642 2.858978344 0.338616715 0.626978404 1.00964064 0.444748149 0.600658652 0.574483832 121.968308 -2.086246999 1.721326703 FEAHPNDLYVEGLPENIPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FEAHPNDLYVEGLPENIPFR 20 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;; 178.41 6.20E-17 793360000 1154230 969960 975030 1149750 1039400 1066860 1217670 1165380 983150 FALSE TRUE 1099671.835 1068800.027 1019736.09 1034174.946 1220671.031 1029914.371 1031892.077 1063333.149 1135611.881 0.968351823 0.941166648 0.897961801 0.910676405 1.074901603 0.906924618 0.908666152 0.936352611 1 20.11503842 4.502439713 3.078482578 0.941614114 0.967551365 0.005955077 0.054118273 1.32444528 23.94287482 0.012956345 0.063304276 31800.92211 -4.502439713 0.025937251 FEAHPNDLYVEGLPENIPFRS(ph)PSWYGIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEAHPNDLYVEGLPENIPFRSPSWYGIPR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 FEAHPNDLYVEGLPENIPFRS(0.803)PS(0.197)WYGIPR;FEAHPNDLYVEGLPENIPFRS(0.995)PS(0.005)WYGIPR 268.23 5.21E-59 149070000 148548 144517 145241 156341 155692 151425 181249 156334 157382 TRUE FALSE 141526.4304 159243.4466 151900.4435 140625.3057 182844.6355 146181.1143 153596.1362 142644.5662 181787.9968 0.778524616 0.875984385 0.835591162 0.773567607 1.005812478 0.804129628 0.844919021 0.784675384 1 17.47189742 -2.544541372 2.316093887 3.925867994 0.839668846 0.360647949 0.067792188 6801611.976 789420.8899 103748664 0.014913041 0.002854031 2.544541372 -3.086199147 FEALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEALEK 6 0 P21266 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 97.071 0.096521 444770000 1362120 1238740 1195510 1393170 916930 1280590 1384240 1359650 971000 FALSE TRUE 1297735.287 1364969.014 1250325.316 1253125.905 1076842.302 1236242.847 1173048.765 1240591.838 1121577.721 1.157062291 1.21700796 1.114791506 1.117288514 0.960113848 1.10223556 1.045891643 1.106113125 1 20.09709817 3.30480824 2.050645824 1.051435421 1.184994788 0.560812437 0.049049014 0.199766913 1.721157418 0.013745193 0.01978967 2017.475364 -3.30480824 0.133559368 FEDEDS(ph)DDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 1 FEDEDS(1)DDVPR 158.4 3.13E-05 58730000 109640 140250 108450 147640 100860 130550 110200 127980 93331 TRUE FALSE 104457.5345 154541.6345 113422.5398 132798.9467 118449.9521 126029.0208 93386.96604 116773.3927 107804.2948 0.968955223 1.433538754 1.052115224 1.231852098 1.098749844 1.169053802 0.866263874 1.083197965 1 16.71805513 1.760259449 25 0.973229981 1.17246315 0.277795378 0.132196501 11.92385125 13749.14656 0.057044595 0.031635103 57.57838098 -1.760259449 0.199233169 FEDENFILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 7229576000 8614060 7009449 6385614 9308770 5111743 7732798 7806264 7931616 4990577 FALSE TRUE 8206890.455 7723719.822 6678400.718 8373034.754 6003229.361 7465009.266 6615275.055 7237081.655 5764490.193 1.423697531 1.339879081 1.158541431 1.452519559 1.041415487 1.29499904 1.147590651 1.255459097 1 22.45876159 8 0.077188032 0.788803717 2.436502682 0.45514204 0.11116532 160.707885 0.907476796 3.042283 28.36068253 99999999.97 -8 1.647698965 FEDHEGLPTVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEDHEGLPTVVK 12 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 146.07 6.44E-05 107990000 306000 259600 265930 310440 240360 292590 349720 320300 244530 FALSE TRUE 291535.9864 286053.5351 278123.1535 279233.9814 282278.7079 282457.5349 296363.791 292252.834 282450.4635 1.032166784 1.012756473 0.984679402 0.988612226 0.999391909 1.000025036 1.049259354 1.034704742 1 18.10763834 1.754376786 25 1.032579732 1.004930047 0.28863755 0.017883411 6.757544559 10694.28904 0.008637791 0.004790313 56.80372105 -1.754376786 -0.027649685 FEDKTVAYTEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEDKTVAYTEQK 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 196.11 1.92E-07 292110000 561670 388420 509940 547620 375840 534030 717240 630980 395410 FALSE TRUE 535120.9722 428000.4396 533321.2534 492572.1972 441386.377 515536.4072 607811.865 575728.0462 456728.1633 1.171639971 0.937101046 1.167699512 1.078480017 0.966409371 1.128759837 1.330795676 1.260548598 1 18.80097623 1.992233244 23.86230085 1.232846843 1.060830052 0.206693939 0.111959609 208.773141 641427.1813 0.039470301 0.027856686 98.2275347 -1.992233244 -0.172016791 FEDPKFEVIEKPQA ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FEDPKFEVIEKPQA 14 2 P18859;P18859-2 P18859 ATP5J "ATP synthase-coupling factor 6, mitochondrial" 0 ;; 101.36 0.0056391 481620000 1699450 1294420 1373530 1504300 1042570 1354310 1577660 1695300 1132380 FALSE TRUE 1619120.366 1426322.87 1436507.709 1353084.906 1224393.878 1307409.905 1336958.991 1546850.545 1307983.707 1.237875027 1.090474493 1.098261164 1.034481469 0.936092607 0.999561308 1.022152634 1.182622181 1 20.31891314 4.400354479 0.952226403 1.026347137 1.286053913 0.50012909 0.063821958 0.977777705 1.006408834 0.020698378 0.234103751 25139.37513 -4.400354479 0.259706777 FEDYLNAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEDYLNAESR 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 194.06 1.17E-06 204760000 211380 235060 161480 220020 169740 172530 205590 194020 162850 FALSE TRUE 201388.4863 259012.8812 168884.0177 197903.1716 199342.6023 166555.2428 174223.4696 177030.5802 188103.9463 1.070623399 1.376966759 0.897822832 1.052094735 1.059747051 0.885442576 0.926208477 0.941131665 1 17.52117059 3.726366304 24.97479319 0.963187258 1.223795084 0.570719572 0.092902155 442.4102279 906086.9791 0.024063303 0.037576737 5325.572536 -3.726366304 0.260607825 FEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEEAKR 6 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 127.1 0.027589 288630000 528270 479830 414170 502870 336210 462080 521080 505070 354990 FALSE TRUE 503299.724 528725.2225 433160.1042 452320.5522 394844.9176 446078.0537 441579.6757 460843.3933 410040.0362 1.227440444 1.2894478 1.056384904 1.103113141 0.962942354 1.087889022 1.076918439 1.123898528 1 18.64540526 3.734106692 24.95147405 1.062447082 1.258444127 0.737512165 0.049493838 152.0183177 851626.8233 0.012181722 0.019591139 5421.340585 -3.734106692 0.195997044 FEEEIKAEQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEEEIKAEQEER 12 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 0 86.803 0.0099461 74369000 157380 130170 140700 163630 162960 136700 169320 168720 165090 FALSE TRUE 149940.9593 143434.471 147151.2342 147181.6015 191380.1724 131966.0447 143487.1242 153945.9824 190691.314 0.786301988 0.75218146 0.771672454 0.771831702 1.003612427 0.692040146 0.752457578 0.807304639 1 17.54087961 0.952076387 19.57688997 1.000000002 0.785090183 0.395115108 0.080908345 638.2875757 260743.6094 0.073599385 0.018399846 8.955222624 -0.952076387 -0.214909818 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FEEESKEPVADEEEEDSDDDVEPITEFR 28 1 P54105;E9PJF4 P54105 CLNS1A Methylosome subunit pICln 1 FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR 403.29 4.50E-166 14101190000 7330682 5739493 5012603 7096439 4488208 6429347 8397270 7825829 5474614 TRUE FALSE 6984175.19 6324353.862 5242435.806 6383091.469 5270950.054 6206697.101 7116112.235 7140557.925 6323589.179 1.104463777 1.000120926 0.829028524 1.009409576 0.833537712 0.981514916 1.125328043 1.129193837 1 22.59231221 1.789149052 6.93676965 1.095423231 0.967121372 0.305109652 0.088160664 0.277691297 28.46834041 0.041603401 0.02394275 61.53880402 -1.789149052 -0.128301859 FEEFLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FEEFLQR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q02218-3 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ;;; 143.02 0.0056997 198511000 534070 541640 396473 436730 442186 373389 419048 450398 374048 FALSE TRUE 508825.5695 596833.7318 414651.6792 392829.0707 519303.0984 360458.4453 355114.5313 410958.7634 432053.4535 1.177691245 1.381388638 0.959723099 0.909214051 1.201941783 0.834291318 0.821922677 0.95117574 1 18.72085029 3.723977159 22.25056296 0.940469343 1.279539889 0.577882142 0.115203863 109.2267983 166651.9156 0.030934632 0.048253829 5296.355876 -3.723977159 0.339070546 FEEGKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEEGKGR 7 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 72.492 0.062265 0 69232 53704 70236 66425 84061 75675 93503 78665 97978 FALSE TRUE 65959.54056 59176.49866 73456.39007 59747.8328 98721.21179 73054.35577 79237.40005 71776.67557 113171.9278 0.582825987 0.522890259 0.649069 0.527938632 0.872311833 0.64551658 0.700150661 0.634226852 1 16.78815662 -5 0.118768243 2.192637277 0.450635994 0.619220682 0.092276013 94.04908655 0.726504224 26.97300619 0.841750916 1.00E-05 5 -1.742001282 FEELCSDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 247.07 2.66E-12 1426742000 1874217 1715516 1320550 1641046 1814911 1291274 1897342 1584020 1736305 FALSE TRUE 1785626.477 1890329.031 1381098.524 1476084.938 2131430.904 1246556.858 1607867.631 1445314.811 2005562.312 0.890337072 0.942543156 0.688634063 0.735995551 1.062759751 0.621549802 0.801704151 0.720653157 1 20.93557536 3.76519144 24.71253167 0.793431903 0.916440132 0.101128642 0.13571243 1175.590998 1090905.818 0.031655962 0.057045989 5823.598688 -3.76519144 0.123008229 FEELNADLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 341.36 2.65E-53 5455220000 4198406 3972673 2947292 3832216 3563956 3174971 4267872 3827174 3807800 FALSE TRUE 3999955.669 4377492.895 3082428.253 3446994.367 4185508.798 3065020.958 3616729.742 3492046.355 4398294.176 0.909433409 0.995270603 0.700823576 0.783711646 0.951620931 0.696865838 0.822302828 0.793954705 1 22.06851267 3.756614812 24.85569805 0.810931802 0.952352014 0.232798981 0.097477955 854.3373622 1176185.694 0.022387977 0.040258651 5709.720003 -3.756614812 0.141420212 FEELNMDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FEELNMDLFR 10 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 323.61 2.90E-42 204735000 360465 291835 215244 292247 345974 241529 371112 307284 331087 FALSE TRUE 343426.5338 321573.3183 225113.1503 262869.7763 406311.7561 233164.7902 314492.0485 280376.5839 382430.281 0.898010829 0.840867824 0.588638404 0.687366533 1.062446611 0.609692281 0.822351325 0.733144309 1 18.54483724 -1.225958619 5.76218948 1.00000736 0.787640216 0.194370294 0.139853126 1.23E-05 1.66E-06 0.126427982 0.029798329 0.059434879 1.225958619 -0.212367145 FEELTNLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEELTNLIR 9 0 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 0 73.233 0.079873 0 169800 161250 150780 188160 160750 172270 190500 175620 83903 FALSE TRUE 161773.8905 177681.5583 157693.4121 169245.7993 188784.7491 166304.2467 161435.7262 160241.7818 96914.24872 1.669247739 1.833389421 1.62714373 1.746345884 1.947956586 1.715993767 1.665758424 1.653438828 1 16.56442117 0.288765759 0.943424333 0.995216575 1.757095058 0.871059975 0.089546121 0.984819253 1.03356212 0.092230568 0.026835999 1.944311113 -0.288765759 0.761878483 FEFTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEFTPGR 7 0 O95747;C9JIG9;Q9UEW8-2;Q9UEW8 O95747;Q9UEW8-2 OXSR1;STK39 Serine/threonine-protein kinase OSR1;STE20/SPS1-related proline-alanine-rich protein kinase 0 105.39 0.018466 118820000 267790 264670 230890 292580 239440 255550 270130 249110 237640 FALSE TRUE 255132.0974 291640.1739 241476.5349 263169.3025 281198.2602 246700.2394 228916.7072 227296.6078 274491.9975 0.929470075 1.062472409 0.879721584 0.958750364 1.024431542 0.898752028 0.833964958 0.828062785 1 18.06640456 2.067037438 6.295933184 0.868213642 0.974606967 0.243311279 0.068051034 0.212512463 15.25934228 0.024029103 0.017575812 116.6910205 -2.067037438 0.106393325 FEGGDRDLEHLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FEGGDRDLEHLSK 13 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 163.27 2.34E-05 1224781000 2480910 2092890 1985400 2805300 1877680 2205520 2759090 2788590 2034460 FALSE TRUE 2363642.301 2306157.87 2076432.554 2523305.914 2205146.798 2129142.289 2338140.146 2544406.276 2349953.666 1.005825066 0.981363124 0.883605742 1.073768369 0.938378841 0.906035859 0.994972871 1.082747423 1 21.16420088 1.452071845 9.553664795 1.040758704 0.96866589 0.238698772 0.055865195 0.240945139 69.31777655 0.029497809 0.013006716 28.31860429 -1.452071845 -0.072092814 FEGKPLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEGKPLLQR 9 1 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 147.75 8.36E-05 5568100000 6761400 6138000 5186500 6312200 5443200 5902700 7520000 6764400 6180700 FALSE TRUE 6441802.022 6763469.178 5424306.155 5677685.664 6392492.357 5698288.019 6372685.886 6172073.276 7139171.389 0.902317884 0.947374535 0.75979492 0.795286365 0.895410967 0.798172184 0.892636629 0.864536364 1 22.76732521 -0.326228703 4.654531819 0.999999614 0.863685861 0.371931257 0.057836398 3816330.552 13391986.96 0.221616679 0.014389883 0.471814514 0.326228703 -0.136313752 FEGLS(ph)PLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FEGLSPLQR 9 0 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR;FEGLS(1)PLQR 126.03 0.00050883 191083000 314723 308620 320652 352594 333822 345813 399823 368462 400216 TRUE FALSE 299846.6675 340068.7289 335354.2114 317150.5812 392040.4511 333837.4091 338822.6581 336197.5139 462279.4533 0.648626422 0.735634531 0.725436117 0.686058139 0.848059433 0.72215498 0.732939039 0.727260343 1 18.81840572 -5 0.235905127 2.517569237 0.69705053 0.757270646 0.048780547 79.05374572 0.78946153 57.48112512 0.075918844 1.00E-05 5 -1.820518707 FEHCNFNDVTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEHCNFNDVTTR 12 0 E9PNW4;A0A2U3TZL5;P13987;P13987-2 E9PNW4 CD59 CD59 glycoprotein 0 ; 157.56 7.10E-05 638910000 710820 518590 479660 749400 752630 581280 709680 634230 649590 FALSE TRUE 677220.9473 571434.9106 501652.8854 674068.8882 883888.4337 561150.1278 601405.2818 578693.4589 750325.0996 0.90257003 0.761583094 0.668580707 0.898369105 1.178007285 0.747875992 0.801526275 0.771256965 1 19.51715629 4.756001921 22.31035879 0.841470531 0.902570126 0.005203955 0.146509138 554.4250925 2060398.178 0.034058456 0.294286172 57016.67941 -4.756001921 0.061099595 FEHLLED ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 141.55 0.0059305 374020000 1231290 1146460 1192450 1315680 1227700 1181390 1546520 1313760 1108510 FALSE TRUE 1173089.362 1263285.577 1247125.012 1183425.347 1441810.491 1140478.168 1310569.97 1198720.21 1280412.069 0.916181119 0.986624234 0.974002856 0.924253508 1.126051937 0.890711823 1.023553278 0.936198774 1 20.28817675 5.222917497 0.953100838 0.985284778 0.799960276 0.094764291 0.063886975 9.907512293 3.781716874 0.017344041 2.355712891 167077.3187 -5.222917497 -0.185324502 FEIGEGENLDLPYGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 312.25 8.70E-58 341767000 443353 358070 361577 424497 406501 378372 456950 409141 440397 FALSE TRUE 422396.5823 394557.7401 378155.6631 381825.7551 477394.6457 365268.8828 387233.885 373314.445 508691.5175 0.830359005 0.775632631 0.74338897 0.750603739 0.938475735 0.718055777 0.761235192 0.733871968 1 18.95643151 -1.150861005 4.080414034 1.000066518 0.782086807 0.539902948 0.063401277 3.324577232 32416332.19 4735.771007 0.013951265 0.070654365 1.150861005 -0.21797971 FEIWDTAGQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 164.97 5.15E-05 303675000 751853 920022 604512 1008540 699799 740694 670276 780598 635871 FALSE TRUE 716314.3987 1013773.288 632229.4731 907159.6431 821843.724 715043.5811 568013.0857 712244.7009 734478.6271 0.975269221 1.380262475 0.860786754 1.235106931 1.118948454 0.97353899 0.7733555 0.969728287 1 19.48636098 2.129600036 3.769341247 0.886239403 1.132212844 0.265704503 0.150562816 0.236551823 6.376042194 0.056609634 0.039984543 134.7721125 -2.129600036 0.24597344 FEKEAAEMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 121.08 0.00047845 662160000 1846040 1042040 1741030 1557750 1253570 1858770 2397160 2060780 1596670 FALSE TRUE 1758781.348 1148225.061 1820857.948 1401162.01 1472192.211 1794400.329 2031429.215 1880327.178 1844273.429 0.953644574 0.622589385 0.987303682 0.759736592 0.798250513 0.97295786 1.101479414 1.019549026 1 20.81462113 2.109134206 3.853819257 1.049103778 0.81307877 0.484184519 0.103306266 0.168660813 4.713542307 0.039276106 0.027544211 128.5683901 -2.109134206 -0.236025008 FELAVDAVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 156.48 1.09E-05 126755000 238450 214370 191189 246470 221120 197246 230100 221220 177190 FALSE TRUE 227178.9411 236214.5467 199955.2048 221694.3673 259683.258 190415.3216 194994.0189 201848.804 204667.7202 1.109989112 1.154136795 0.976974799 1.083191659 1.268804175 0.930363231 0.952734602 0.986226865 1 17.64292406 2.200001844 24.99999379 0.961070745 1.114629544 0.510980324 0.073371356 128.5649379 83355.70621 0.026577467 0.0196291 158.4899922 -2.200001844 0.153558799 FELSENCSERPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FELSENCSERPGLR 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 190.27 5.68E-07 124110000 77275 78201 75179 90466 85174 84203 82805 85443 79143 FALSE TRUE 73622.36389 86169.77081 78626.03151 81372.18581 100028.3186 81287.029 70171.57643 77961.15796 91416.09223 0.805354529 0.942610526 0.860089614 0.890129777 1.094209085 0.889198247 0.767606389 0.852816567 1 16.48016053 -0.956145155 6.818448325 1.000000009 0.884495185 0.138846271 0.087519256 1.22E-08 1.79E-09 0.086111465 0.020296665 0.110625398 0.956145155 -0.115504824 FENAFLSHVVSQHQALLGTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FENAFLSHVVSQHQALLGTIR 21 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 256.58 1.09E-36 827315000 443606 417161.7 414137.8 416703.4 490264.8 336347.7 478869.2 449810.2 206885.2 FALSE TRUE 422637.6235 459670.9515 433126.4278 374815.5825 575766.8259 324699.8948 405808.9085 410422.4343 238967.9002 1.768595795 1.923567773 1.812487901 1.568476696 2.409389819 1.358759459 1.698173304 1.717479352 1 17.86645731 -0.102515998 0.435501476 0.875158028 1.8589783 0.47676282 0.263515928 4.044336801 0.926576829 1.092797038 0.142688299 0.789739757 0.102515998 0.983820273 FENLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 616960000 531240 474120 458750 545380 402920 515150 551710 551430 445640 FALSE TRUE 506129.338 522433.367 479784.1413 490557.3662 473189.1204 497310.2263 467536.5067 503143.8659 514747.5752 0.983257353 1.014931186 0.932076545 0.953005686 0.919264399 0.966124466 0.908283068 0.977457477 1 18.9735056 3.736473065 24.99801183 0.944646129 0.99909427 0.314117798 0.028476018 149.7132231 1792785.448 0.006592974 0.010802119 5450.960873 -3.736473065 0.054448141 FEPES(ph)PGFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;FEPES(1)PGFESR;FEPES(1)PGFESR 279.38 2.80E-27 2973380000 3486460 3143610 3093710 3309120 3106410 3087910 3466040 3134200 3193110 TRUE FALSE 3321661.945 3463947.433 3235559.664 2976480.971 3648166.92 2980974.902 2937231.94 2859752.833 3688281.191 0.90059889 0.939176612 0.877254064 0.807010316 0.989123858 0.808228752 0.796368766 0.775361933 1 21.81451722 2.184173794 24.99999868 0.823922311 0.901931859 0.095690907 0.076722803 139.8088423 64264.87024 0.025880423 0.019113971 152.8177474 -2.184173794 0.078009547 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 34 2 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ; 178.76 5.48E-20 811820000 320850 280709 249575 343210 187522 296390 313420 359700 181718 FALSE TRUE 305684.0564 309313.5662 261018.2606 308709.8787 220225.7774 286125.94 265602.0226 328202.7611 209897.8994 1.45634643 1.473638217 1.243548704 1.470762117 1.049204295 1.363167239 1.265386759 1.563630518 1 17.6793282 -4.750312537 0.138472163 9.36E-21 1.482996269 0.314765299 0.153803917 148.4283665 1.349722908 42.82598128 0.905447462 1.78E-05 4.750312537 1.482996269 FEPYANPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FEPYANPTKR 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 103.63 0.0044715 398750000 394620 353630 302080 417570 368660 332360 442200 387580 355880 FALSE TRUE 375967.0947 389665.299 315930.6668 375595.0703 432954.1873 320850.2899 374734.2684 353641.4405 411068.0528 0.914610348 0.947933794 0.768560497 0.913705329 1.05324212 0.780528401 0.911611267 0.860299014 1 18.64901773 FERPDGSHFDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FERPDGSHFDVR 12 1 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 ; 125.53 0.00018246 610610000 601210 519920 538570 521030 606710 441320 524540 512120 519310 FALSE TRUE 572791.9948 572900.4391 563263.9672 468655.0745 712520.0319 426036.9777 444511.7892 467276.0579 599841.9425 0.954904874 0.955085663 0.939020644 0.781297607 1.1878463 0.71024873 0.741048196 0.778998641 1 19.19422288 FESPATGILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FESPATGILSPR 12 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR 181.77 1.86E-05 207182000 303926 297515 307591 333850 332300 293559 340427 294806 336050 TRUE FALSE 289560.0203 327832.1167 321694.3516 300290.7637 390253.0148 283392.9782 288488.6088 268991.2238 388162.9177 0.745975484 0.844573507 0.828761164 0.773620431 1.005384587 0.730087717 0.743215273 0.692985372 1 18.56630277 -0.224019299 10.65750371 0.999999028 0.796678279 0.353124302 0.08694113 0 0 0.080636091 0.019006109 0.597008756 0.224019299 -0.203320749 FESPEVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;; 163.2 0.00014702 1764197000 2898890 2351360 2580540 2676220 2372470 2845120 3156570 2951000 2607790 FALSE TRUE 2761865.215 2590966.257 2698860.312 2407201.281 2786228.017 2746592.781 2674977.272 2692594.796 3012192.754 0.916895245 0.860159515 0.895978621 0.79915247 0.924983308 0.911825041 0.888049833 0.89389857 1 21.52238266 -0.700635031 0.449794364 1.031140988 0.879503331 0.511311714 0.035334765 9.059420505 1.458902459 0.43614013 0.018291522 0.199234695 0.700635031 -0.151637656 FEVGDIMLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEVGDIMLIR 10 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 108.98 0.0048383 167574000 416002 377736 375659 437659 387312 341433 449150 421855 385969 FALSE TRUE 396338.4099 416227.7279 392883.3367 393664.6858 454859.0902 329609.0896 380623.9183 384915.1398 445823.1013 0.889003752 0.93361633 0.881253878 0.883006477 1.020268104 0.739327075 0.853755486 0.863380876 1 18.76611185 2.241142498 24.99993105 0.848103056 0.916571003 0.110911756 0.074047846 112.9976071 1094147.786 0.023630398 0.018929974 174.2378479 -2.241142498 0.068467948 FEWELPLDEAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FEWELPLDEAQR 12 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ; 155.15 0.00016772 27995000 71860 68275 67556 93321 79019 76239 77550 70139 75682 FALSE TRUE 68463.32021 75232.30012 70653.50942 83940.19578 92799.88858 73598.82431 65718.3232 63997.25733 87418.37803 0.783168503 0.860600503 0.808222607 0.960212231 1.061560403 0.841914778 0.751767817 0.732080127 1 16.41564899 -3.065352595 9.296739101 0.997771572 0.855763326 0 0.109506031 0 0 0 0.024403293 0.000860295 3.065352595 -0.142008247 FFALPYVDHFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFALPYVDHFLR 12 0 Q9HD33-3;Q9HD33-2;Q9HD33 Q9HD33-3 MRPL47 "39S ribosomal protein L47, mitochondrial" 0 144.65 0.00032974 0 205630 142310 70405 76842 225390 69107 190950 128840 149880 FALSE TRUE 195910.2774 156811.5508 73633.13889 69117.69617 264697.9446 66713.80726 161817.0705 117558.0866 173122.6249 1.131627235 0.905783117 0.425323605 0.399241267 1.528962172 0.385355798 0.934696262 0.679045195 1 17.40143475 4.155418383 3.35390598 0.760954049 1.083953322 0.098299972 0.345902978 0.482760146 10.43752853 0.08114278 0.207919167 14302.71164 -4.155418383 0.322999274 FFAPECGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFAPECGR 8 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 138.55 0.0016298 126630000 178950 159650 161060 170350 171600 161700 201640 183450 161770 FALSE TRUE 170491.3881 175918.5165 168444.7603 153226.0944 201526.9857 156100.2885 170876.1146 167386.1455 186856.4654 0.912418994 0.941463364 0.901466053 0.820020298 1.078512243 0.835402126 0.914477935 0.895800662 1 17.51157096 -1.188625632 4.28799632 1.000028686 0.913533603 0.135782203 0.069369787 1.67E-05 3.15E-06 0.058830333 0.013861845 0.06477007 1.188625632 -0.086495083 FFCFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFCFLR 6 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 142.14 0.026902 55119000 295860 245310 78197 80462 270450 98275 253600 167423 178966 FALSE TRUE 281875.2841 270307.3679 81782.4098 72373.80689 317616.3944 94871.71211 214908.6623 152762.5546 206719.1332 1.363566496 1.307606914 0.395620901 0.350106958 1.536463458 0.45894016 1.039616696 0.738986044 1 17.6573124 3.856401995 8.582486915 0.79779556 1.341750124 0.29257215 0.353738908 0.339196461 22.81916844 0.084465087 0.152693024 7184.590099 -3.856401995 0.543954565 FFDANYDGKDYDPVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFDANYDGKDYDPVAAR 17 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 149.47 2.95E-07 502900000 1988700 1667000 1521500 2102800 1349400 1823300 2257200 2204500 1622600 FALSE TRUE 1894698.092 1836869.195 1591262.28 1891422.549 1584734.933 1760158.664 1912822.684 2011462.293 1874224.521 1.010923756 0.980068916 0.849024363 1.009176077 0.845541671 0.939139705 1.020594204 1.073223763 1 20.83786236 1.653874303 4.426858275 1.039034076 0.94496399 0.348508425 0.059253705 0.193023367 8.681237808 0.032675611 0.015282026 45.06862449 -1.653874303 -0.094070086 FFDDDLLVSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFDDDLLVSTSR 12 0 O43924 O43924 PDE6D "Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit delta" 0 76.465 0.072221 9097300 34200 30706 30726 36501 33575 34273 33185 32104 29677 FALSE TRUE 32583.43378 33834.97631 32134.81749 32831.85013 39430.46937 33086.11742 28122.01877 29292.80357 34279.15759 0.950531929 0.987042235 0.937444784 0.957778792 1.150275332 0.965196339 0.820382435 0.854536856 1 15.06504404 1.915771248 7.29174151 0.875734326 0.992348575 0.28441601 0.074470201 0.304884628 23.05783525 0.030630387 0.019049805 82.37041385 -1.915771248 0.11661425 FFDEESYSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ;;;; 190.02 5.71E-06 323082000 420435 344769 335809 384787 480511 292409 453242 386709 456131 FALSE TRUE 400561.8708 379901.3531 351206.1748 346107.4797 564311.9663 282282.803 384091.6085 352846.7099 526865.4659 0.760273536 0.721059507 0.66659555 0.656918136 1.071074122 0.535777767 0.729012686 0.669709314 1 19.00707509 -1.023786683 4.018027947 1.000031743 0.725993712 0.283919418 0.136601071 28198735.99 65851711.7 13333.35091 0.02961555 0.094670205 1.023786683 -0.274038031 FFDHSGTLVMDAYEPEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFDHSGTLVMDAYEPEISR 19 0 E9PL01;A0A087WUC6;E9PI68;Q15005;E9PRB9 E9PL01 SPCS2 Signal peptidase complex subunit 2 0 ; 119.38 6.09E-05 97229000 57999 46860 54985 80886 91856 58406 78157 58888 76201 FALSE TRUE 55257.50221 51635.08728 57506.11664 72755.18561 107875.6573 56383.38558 66232.7142 53731.45454 88017.8619 0.627798733 0.586643281 0.653345985 0.826595694 1.225610972 0.640590266 0.752491742 0.610460802 1 16.42550871 3.29521063 4.555016555 0.829202314 0.610559165 0.259210653 0.175367815 0.292495709 12.36257495 0.049255174 0.066192131 1973.37958 -3.29521063 -0.218643149 FFDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FFDQYR 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 114.59 0.058529 192566000 628170 523720 474220 550350 674360 500430 731430 588910 681600 FALSE TRUE 598477.649 577087.6634 495963.4561 495027.7724 791968.1705 483099.9836 619836.9199 537341.9184 787299.0469 0.760165596 0.732996776 0.629955616 0.628767143 1.005930559 0.613616879 0.787295402 0.682513107 1 19.58655221 -1.969047661 2.648286997 1.220880396 0.733232275 0.356941148 0.113759954 13589734.38 7520700.569 18417441.37 0.024620479 0.010738716 1.969047661 -0.487648121 FFDS(ph)EDEDFEILSL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFDSEDEDFEILSL 14 0 Q9Y4P1;Q9Y4P1-4 Q9Y4P1 ATG4B Cysteine protease ATG4B 1 FFDS(1)EDEDFEILSL 116.3 0.00099831 0 147370 122290 139810 144890 142730 113980 160420 150430 143530 TRUE FALSE 140404.1122 134751.49 146220.4268 130325.3819 167622.0668 110032.844 135944.9827 137257.5517 165787.8994 0.846889988 0.812794484 0.881972854 0.78609707 1.011063337 0.663696473 0.819993396 0.827910555 1 17.33897918 -0.825210789 4.816831469 1.000000326 0.828002205 0.276912512 0.085523743 0.000209126 48922231.14 49.94365038 0.017836051 0.149550962 0.825210789 -0.171998122 FFDTELENLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFDTELENLER 11 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 0 76.228 0.083582 9196500 19069 14879 21815 24416 22017 14781 22232 21186 21732 FALSE TRUE 18167.64616 16395.18702 22815.23933 21961.65729 25856.75783 14269.13026 18840.10008 19330.84153 25102.08757 0.72375041 0.65314038 0.908898085 0.874893661 1.030064044 0.568443968 0.750539174 0.770089 1 14.61551973 -2.345131779 1.930464568 2.057929414 0.77192352 0.204784005 0.130935135 5654379.785 644253.0758 26048276.41 0.034661207 0.004517189 2.345131779 -1.286005894 FFEDLEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFEDLEQR 8 0 Q5VV41;Q5VV41-2;B0QZD3 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;;; 148.04 0.0012274 235195000 714050 688480 660230 775690 737130 658600 777210 727930 711150 FALSE TRUE 680298.2716 758636.8947 690502.1986 697716.1675 865685.2386 635792.5169 658632.3401 664188.5902 821431.5099 0.828186238 0.923554655 0.840608365 0.849390557 1.053873912 0.774005513 0.801810415 0.808574522 1 19.64778076 -0.189898194 8.340881383 1 0.860457114 0.235491492 0.079270512 0 0 0.074343537 0.01752294 0.645805599 0.189898194 -0.139542886 FFEDYGLFMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFEDYGLFMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 256.36 8.47E-17 425621000 621681.6 534424.7 477881 488632.4 656370 358259.7 592401 512105.9 607545 FALSE TRUE 592295.9428 588883.1845 499792.3165 439514.1428 770840.7202 345853.0768 502019.3473 467263.1926 701759.9757 0.844014996 0.839151854 0.712198378 0.626302665 1.098439277 0.492836709 0.715371872 0.665844746 1 19.42061814 2.207981276 24.99993008 0.689786561 0.813832811 0.073338566 0.171366966 433.6166957 354497.8328 0.057690055 0.04261192 161.4288959 -2.207981276 0.12404625 FFEEVLLFEDELHDHGVSSLSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFEEVLLFEDELHDHGVSSLSVK 23 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 94.463 0.0024529 46639000 115300 124910 112030 132430 94282 119060 137800 120370 29546 FALSE TRUE 109849.9975 137638.471 117166.6863 119117.8848 110724.7509 114936.9223 116776.0791 109829.7647 34127.84278 3.218779406 4.033025817 3.433170009 3.490343224 3.244411071 3.367834383 3.421724598 3.218186552 1 15.0586616 -1.096051589 0.444906524 1.25E-20 3.568066224 0.925062291 0.21856351 4.573020015 0.564030043 5.971408207 0.118149716 0.080158284 1.096051589 3.568066224 FFEEVNDPAKNDALEMVEETTWQGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FFEEVNDPAKNDALEMVEETTWQGLK 26 1 P49748;P49748-3;P49748-2;K7EQP4;J3KS89 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;;; 218.86 3.08E-34 163587000 648342 519020 546897 568999 379447 506275 619025 642869 379834 FALSE TRUE 617696.1586 571908.7281 571972.7684 511802.1395 445622.4367 488742.5698 524581.3671 586575.9823 438736.7168 1.407897117 1.303535141 1.303681106 1.16653592 1.015694424 1.113976905 1.195663246 1.336965793 1 18.74299592 3.314663433 2.799680663 1.14181808 1.351503386 0.497352072 0.096211699 0.22048018 3.503240787 0.028026667 0.03889358 2063.780161 -3.314663433 0.209685306 FFEHFIEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FFEHFIEGGR 10 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;;; 215.06 8.37E-09 2547573000 2999538 2796386 2459090 2777682 2926039 2522838 3070104 2897653 2507521 FALSE TRUE 2857755.783 3081340.913 2571841.709 2498464.128 3436339.275 2435471.487 2601703.248 2643919.142 2896374.55 0.986666515 1.063861341 0.887952046 0.862617761 1.186427796 0.840868971 0.898262018 0.912837444 1 21.46581675 FFEHHPIPQEEASLAETALT(ph)SGSSPSAPASDSIGPQILTSPSPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEAS(0.03)LAET(0.172)ALT(0.187)S(0.187)GS(0.187)S(0.187)PS(0.037)APAS(0.009)DS(0.002)IGPQILTSPSPSK 69.477 0.0020484 48501000 42497 41399 40378 52020 33129 40924 50526 46385 10881 TRUE FALSE 40488.25103 45617.60517 42229.37124 46790.85077 38906.68711 39506.79162 42817.33073 42323.2835 12568.36991 3.221440117 3.629556219 3.359972021 3.722905286 3.09560328 3.143350483 3.406752908 3.367444132 1 13.61750993 -1.36201755 0.59196687 2.61E-13 3.406213822 0.935484724 0.195431332 10.46944657 1.60738894 16.74120945 0.075297941 0.043449267 1.36201755 3.406213822 FFEVILIDPFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFEVILIDPFHK 12 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 141.73 6.08E-05 832130000 1923660 2051530 1504300 2072900 1375700 1655190 1966900 2002480 950580 FALSE TRUE 1832732.404 2260583.239 1573273.643 1864528.154 1615621.644 1597870.355 1666813.28 1827132.235 1097991.092 1.669168738 2.058835684 1.432865581 1.69812685 1.471434201 1.45526714 1.518057199 1.66406836 1 20.06643492 -1.759412999 0.106985298 5.36E-11 2.165742597 0.569679005 0.174987743 43.24522531 0.710838691 14.4231361 2.99479819 0.017401513 1.759412999 2.165742597 FFFDPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFFDPSAR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 113.89 0.0064252 443400000 1758510 1606330 1470910 1781080 1727890 1435070 1766320 1650780 1592100 FALSE TRUE 1675388.717 1770016.853 1538352.678 1602042.455 2029233.469 1385373.166 1496835.443 1506228.952 1838994.737 0.91103508 0.962491528 0.836518261 0.871151191 1.103447133 0.753331773 0.813942212 0.81905017 1 20.81048592 FFGNS(ph)WAETYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 1 FFGNS(1)WAETYR;FFGNS(1)WAETYR;FFGNS(1)WAETYR 150.22 3.57E-05 68888000 112574 116125 107515 117649 198332 101771 132065 111347 230027 TRUE FALSE 107252.8501 127958.2695 112444.6691 105822.699 232921.038 98246.64475 111916.0587 101596.8664 265698.4123 0.403663873 0.48159215 0.423204144 0.398281262 0.876636921 0.369767527 0.421214631 0.382376641 1 18.01943008 -1.046466974 4.29953415 1.000040794 0.46744794 0.558867915 0.148084713 97835129.54 247668487.6 63892.05631 0.033513322 0.089853092 1.046466974 -0.532592854 FFGNSWAETYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 164.85 5.19E-05 191230000 349100 300290 293420 325640 357340 269760 382430 333800 259310 FALSE TRUE 332598.7348 330889.8924 306873.5972 292906.0485 419659.9829 260418.1436 324083.2797 304570.7024 299522.4704 1.110429993 1.10472477 1.024542822 0.977910098 1.401096827 0.86944443 1.081999889 1.016854268 1 18.19230471 FFHLAFEEEFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;; 166.14 5.27E-05 359499000 574762 422308 454312 575153 633783 448672 681739 557671 569368 FALSE TRUE 547594.1393 465341.6653 475142.6546 517337.5277 744314.5545 433134.3761 577727.1946 508838.3708 657662.6815 0.832636783 0.707568908 0.722471668 0.786630506 1.131757321 0.658596555 0.878455188 0.773707229 1 19.32698828 2.982669275 24.98678207 0.871498467 0.755319629 0.189461506 0.128462326 1295.20683 1867383.446 0.035789511 0.038767802 960.8802673 -2.982669275 -0.116178839 FFIEEMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFIEEMIR 8 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 103.92 0.010888 21948000 55010 51837 42786 44437 58264 37440 63569 47654 51840 FALSE TRUE 52409.78632 57119.24923 44747.78042 39970.10834 68425.22315 36143.44341 53870.38153 43481.16313 59879.08244 0.875260344 0.953909895 0.747302373 0.667513708 1.142723308 0.603607169 0.899652756 0.726149456 1 15.86976449 3.751642347 24.71394119 0.820216381 0.914585119 0.04845014 0.159909205 1831.07298 3459243.947 0.036486754 0.065274255 5644.71926 -3.751642347 0.094368738 FFIGQFSDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FFIGQFSDDR 10 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ;; 112.75 0.0036748 90551000 201819 235009 168044 229706 185017 188932 197451 205682 175365 FALSE TRUE 192279.4158 258956.6843 175748.9836 206615.5165 217283.9062 182389.2375 167326.2235 187671.3937 202559.7086 0.949248087 1.278421489 0.867640385 1.020022777 1.072690654 0.900422097 0.826058769 0.92649913 1 17.62798771 2.228190522 14.69100096 0.891008727 1.053886924 0.212675635 0.113038322 1.741849667 2461.884676 0.040884725 0.030967251 169.118268 -2.228190522 0.162878197 FFMPAWNLEIIGTYAQTEMGHGTHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFMPAWNLEIIGTYAQTEMGHGTHLR 26 0 Q15067-2;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 142.32 1.63E-07 75023500 49857 47023.7 45532.3 52318.8 64382.3 44276.7 67699.8 45571.7 19468.9 FALSE TRUE 47500.35842 51815.46849 47620.00099 47059.61482 75610.55274 42743.38678 57370.95212 41581.20036 22488.03758 2.112250046 2.304134734 2.117570323 2.092651022 3.362256598 1.90071662 2.551176461 1.849036414 1 14.45687015 0.942240184 4.075185182 1.000683293 2.33237821 0.536944593 0.401609177 0.196958559 8.984328275 0.349478311 0.089286884 8.754678137 -0.942240184 1.331694918 FFPASADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FFPASADR 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 158.03 0.0008548 1389453000 2343670 1604000 1131431 1135927 2574500 1260211 2632900 1731853 2398460 FALSE TRUE 2232889.364 1767449.424 1183308.23 1021741.46 3023491.985 1216569.577 2231202.748 1580202.77 2770400.927 0.805980586 0.637976044 0.427125265 0.368806352 1.09135539 0.439131234 0.805371788 0.570387757 1 21.40166334 -3.427538156 0.397354171 2.310426632 0.644823793 0.208514589 0.217053109 287.538823 6.901748347 315.6213016 0.125504269 0.000373647 3.427538156 -1.665602839 FFPLESWQIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFPLESWQIGK 11 0 P30046;J3KQ18;H7C342 P30046 DDT D-dopachrome decarboxylase 0 ; 214.58 3.13E-11 262450000 927140 753410 758760 931830 771920 794610 1014040 908860 929830 FALSE TRUE 883315.9296 830183.3356 793549.8965 838160.678 906542.6036 767092.4565 859329.5739 829275.4002 1074023.287 0.822436478 0.772965861 0.738857254 0.780393394 0.844062335 0.7142233 0.800103297 0.772120502 1 20.03459384 -1.016465636 5.084966966 1.000002179 0.781504555 0.7746191 0.037182097 8.39E-07 1.62E-07 0.032904891 0.00775568 0.096279619 1.016465636 -0.218497624 FFQGS(ph)QEFLASASASAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFQGSQEFLASASASAER 18 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FFQGS(1)QEFLASASASAER;FFQGS(0.996)QEFLAS(0.001)AS(0.001)AS(0.001)AER;FFQGS(0.984)QEFLAS(0.016)ASASAER;FFQGS(1)QEFLASASASAER 219.06 7.90E-19 120801900 105217 94779 96140 101358 108754 97010 116199 113499 109053 TRUE FALSE 100243.6009 104437.0879 100548.1141 91169.30127 127720.6632 93650.51938 98470.70841 103560.4259 125964.3823 0.795809094 0.829100147 0.798226548 0.723770479 1.013942679 0.743468254 0.78173454 0.822140545 1 16.94265633 0.942302591 20.6692448 1 0.810726259 0.360552791 0.078130051 2497.25661 894608.2279 0.06804313 0.017010782 8.755936246 -0.942302591 -0.189273742 FFQTSGLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFQTSGLSK 9 0 P0CE72;P0CE71 P0CE72 OCM;OCM2 Oncomodulin-1;Putative oncomodulin-2 0 ;;; 64.711 0.039679 2243400000 2989500 2574230 2972020 3226990 8164700 1630670 3565430 1828360 7909700 FALSE TRUE 2848192.26 2836546.964 3108290.057 2902606.834 9588621.095 1574199.489 3021458.17 1668259.106 9136295.879 0.311744748 0.310470129 0.340213375 0.317700617 1.0495086 0.172301719 0.330709317 0.182596878 1 23.12317794 -1.780478983 2.555814871 1.172498169 0.372035678 0.386347599 0.246722615 28073111.2 19764852 30226274.48 0.061950508 0.016577576 1.780478983 -0.800462491 FFSDCK ddPTM_SK-BR-3_Trastuzumab_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 ; 100.82 0.086601 975870000 2729300 2110500 2172010 2673000 2062870 2479700 2938900 2764300 2321150 FALSE TRUE 2600291.398 2325562.349 2271598.807 2404304.962 2422633.875 2393827.367 2490516.828 2522243.238 2681102.087 0.969859152 0.867390451 0.847263078 0.896759946 0.903596281 0.892852002 0.928915329 0.940748676 1 21.35439472 0.998948915 1.08190995 0.999131486 0.896424196 0.525979275 0.031535917 0.459920726 1.128622559 0.030558294 0.009874347 9.975827143 -0.998948915 -0.10270729 FFSGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFSGYGR 7 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 117.6 0.012086 923420000 444590 371020 386840 429260 443490 384820 439670 386340 390420 FALSE TRUE 423575.1118 408827.3598 404576.9966 386109.9693 520834.5156 371493.5869 372590.2664 352510.0215 450964.3396 0.939265203 0.906562502 0.897137448 0.856187364 1.154935036 0.823775971 0.826207825 0.78168048 1 18.78265383 FFT(ph)TPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.881)T(0.119)PSK;FFT(0.898)T(0.102)PSK;FFT(0.716)T(0.284)PSK 136.39 0.033362 663800000 3468250 4045020 3874190 4665280 2731580 4450090 4483730 4241440 3217380 TRUE FALSE 3304312.696 4457212.137 4051825.444 4196317.191 3207966.687 4295982.267 3799654.639 3870037.028 3716314.858 0.889136906 1.19936343 1.090280452 1.129160836 0.863211759 1.15597909 1.022425382 1.041364141 1 21.82544131 FFTDDLFQYAGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFTDDLFQYAGEKR 14 1 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 71.879 0.051803 0 47060 40248 45587 41700 56407 48977 63358 51319 51380 FALSE TRUE 44835.56706 44349.31696 47677.20904 37508.23678 66244.36294 47280.91421 53691.57345 46825.2363 59347.74799 0.755472088 0.747278852 0.803353297 0.632007752 1.116206852 0.796675793 0.90469437 0.788997694 1 15.85690567 2.764124654 24.99994571 0.9042486 0.7428039 0.443611918 0.102779205 741.0616914 724708.3609 0.028102532 0.02979829 580.931136 -2.764124654 -0.1614447 FFTDYGCDMEQGSVCTYHPGAVHCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FFTDYGCDMEQGSVCTYHPGAVHCVR 26 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 161.66 9.76E-12 87894000 94981 69640 75870 116300 105610 98595 109560 103800 30702 FALSE TRUE 90491.43636 76736.39517 79348.71455 104609.303 124028.3506 95180.63043 92844.60979 94710.72172 35463.10936 2.55170621 2.163837198 2.237500208 2.94980629 3.497390748 2.683933591 2.61806174 2.670682956 1 15.11403141 3.255906878 24.61377596 2.696730555 2.318146679 0.008339307 0.639087484 531.8337135 754648.8282 0.158841545 0.214546916 1802.631178 -3.255906878 -0.378583876 FFTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 FFTESR 6 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;;;; 153.61 0.023518 4327776000 10713050 9813230 9568030 10959980 10465690 9513220 11323840 10489060 10708870 FALSE TRUE 10206665.36 10813209.29 10006733.64 9858261.988 12290903.02 9183774.806 9596180.231 9570582.3 12369546.87 0.825144645 0.874179904 0.808981424 0.796978426 0.99364214 0.742450383 0.775790765 0.773721334 1 23.56028932 FFTNFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FFTNFESR 8 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;J3QQV6;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;; 126.62 0.002818 380697000 796660 587875 487655 568277 799350 579461 848740 676646 785640 FALSE TRUE 759003.4606 647780.1309 510014.4641 511152.7163 938756.3869 559394.1203 719249.1248 617395.2891 907473.0387 0.836392298 0.713828514 0.562016107 0.563270416 1.034473033 0.616430568 0.792584566 0.6803456 1 19.79149526 FFVADTANEALEAAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFVADTANEALEAAKR 16 1 E9PDQ8;Q96I99;Q96I99-2 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 ; 270.99 6.18E-35 317650000 342240 254450 294370 261000 259290 244950 357380 315480 333450 FALSE TRUE 326062.9935 280378.7443 307867.1557 234763.7841 304510.0939 236467.3201 302855.1173 287854.8987 385159.723 0.846565656 0.727954476 0.799323339 0.609523193 0.790607314 0.613946127 0.786310456 0.747365006 1 18.55509732 0.292109423 1.655414632 1.000020198 0.740811296 0.533264437 0.07644664 6.520752829 14.2988938 0.067456432 0.019070843 1.959338276 -0.292109423 -0.259208902 FFVGGNWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FFVGGNWK 8 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 141.98 0.0014534 1617590000 3131100 1928150 1495540 1927120 3008100 1849110 3712400 2545300 3143600 FALSE TRUE 2983099.108 2124630.677 1564111.988 1733402.236 3532711.688 1785074.857 3146005.197 2322420.039 3631093.433 0.821542922 0.585121456 0.430755093 0.477377481 0.972905752 0.491608076 0.866407118 0.639592476 1 21.79197262 0.457722946 0.513500712 1.014682891 0.629162643 0.275830115 0.176974313 2.710959399 1.25201765 0.278331484 0.084440186 2.868949781 -0.457722946 -0.385520248 FGAPPHAGGGIGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGAPPHAGGGIGLER 15 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 155.98 2.21E-06 194540000 197830 204280 207310 229650 188160 193850 201360 205730 189300 FALSE TRUE 188478.968 225096.3642 216815.3686 206565.1457 220975.0444 187136.9259 170638.8338 187715.1906 218655.6772 0.861989821 1.029455842 0.991583531 0.944705156 1.010607395 0.855852125 0.780399741 0.858496761 1 17.73830128 2.189695992 8.936635392 0.846981863 0.966477464 0.267288552 0.071481872 0.304406575 51.68595947 0.025116699 0.018593402 154.7732819 -2.189695992 0.119495601 FGAVWTGDNTAEWDHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGAVWTGDNTAEWDHLK 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 290.5 5.67E-46 1228060000 2143700 2343000 1897220 2141000 1442730 2096900 2040230 2150600 1250940 FALSE TRUE 2042371.549 2581754.364 1984209.414 1925782.612 1694341.655 2024283.827 1728955.442 1962282.063 1444929.386 1.41347499 1.786768536 1.37322241 1.332786661 1.172612081 1.400956923 1.19656743 1.358047031 1 20.46256756 2.815830809 0.221761707 0.97262758 1.797357406 0.488293513 0.145884425 3.47799095 0.377253172 0.35023641 0.887706574 654.3811922 -2.815830809 0.824729826 FGCRDPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGCRDPVR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;; 89.698 0.012514 769777000 1819130 1014890 690820 727030 1716540 961460 2009170 1361230 1666650 FALSE TRUE 1733143.33 1118308.445 722494.7803 653947.5631 2015904.033 928164.3991 1702634.216 1242033.485 1925105.57 0.900284824 0.580907594 0.375301382 0.33969439 1.047165446 0.482136883 0.884436803 0.645176817 1 20.87650613 0.791986033 0.615605569 0.996267786 0.62528295 0.193423545 0.228839901 1.864681993 1.515930628 0.239070061 0.094008667 6.194211545 -0.791986033 -0.370984836 FGDFLQHS(ph)PSILQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGDFLQHSPSILQSK 15 0 Q96Q89-3;Q96Q89;Q96Q89-2;Q96Q89-5 Q96Q89-3 KIF20B Kinesin-like protein KIF20B 1 FGDFLQHS(0.998)PS(0.002)ILQSK 126.4 0.00023817 0 145510 135280 127990 156870 108880 135880 166880 157270 114440 TRUE FALSE 138632.0307 149065.1858 133858.4681 141101.1296 127868.6375 131174.4415 141419.391 143498.6051 132186.7707 1.048758737 1.127686114 1.01264648 1.067437602 0.967333091 0.992341675 1.069845267 1.085574633 1 17.01221827 3.724639148 24.83965815 1.030132023 1.088222428 0.263353759 0.041823701 887.1639377 1582939.834 0.011037625 0.017199981 5304.435191 -3.724639148 0.058090405 FGDILHVINASDDEWWQAR ddPTM_SK-BR-3_Trastuzumab_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 ; 212.83 6.35E-17 181413000 492310 459840 449220 541930 488890 434790 580970 527540 436250 FALSE TRUE 469039.482 506698.2188 469817.1813 487454.1668 574152.2612 419733.1133 492332.3563 481345.8009 503901.4219 0.930815952 1.005550286 0.932359309 0.967360173 1.139413854 0.832966717 0.977041014 0.955238029 1 18.942782 -0.146651389 7.326727443 0.999999998 0.967547354 0.017660852 0.075955647 0 0 0.065965035 0.015548108 0.713425471 0.146651389 -0.032452644 FGDRFPAMSDAYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FGDRFPAMSDAYDR 14 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;;;; 260.49 1.67E-24 2495200000 3197890 1773536 2441110 2317210 3300610 2358230 4058100 2912010 3725640 FALSE TRUE 3046732.077 1954261.335 2553037.308 2084279.648 3876235.339 2276563.904 3438962.313 2657018.967 4303393.223 0.707983658 0.454121023 0.593261451 0.484333999 0.900739286 0.529016008 0.799128068 0.617424165 1 22.03704324 -0.417302281 0.267693159 1.163317341 0.550779533 0.431546175 0.135226288 7.932230737 0.704379827 1.337024133 0.187293902 0.38255838 0.417302281 -0.612537807 FGDYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGDYNK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 107.74 0.072131 329330000 1329300 1147000 1068700 1356200 917250 1134000 1330500 1240500 993470 FALSE TRUE 1266466.623 1263880.604 1117700.952 1219872.199 1077218.11 1094729.296 1127507.789 1131875.244 1147532.254 1.103643596 1.101390048 0.974003954 1.063039575 0.93872578 0.953985644 0.982549976 0.98635593 1 20.13010327 3.68061873 1.218481847 0.975818629 1.114848973 0.633832676 0.035421932 0.257381953 0.740553918 0.010800771 0.027538401 4793.124721 -3.68061873 0.139030344 FGEEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGEEIAR 7 0 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 138.37 0.0064966 100330000 218500 194860 181210 238140 183290 204130 240710 223120 175260 FALSE TRUE 208171.938 214716.4555 189518.6577 214201.7148 215255.718 197060.9269 203985.2686 203582.43 202438.4257 1.028322253 1.060650688 0.936179271 1.058107985 1.063314523 0.973436373 1.007641054 1.005651122 1 17.62712363 4.040057112 0.264024112 0.995144044 1.062547259 0.046506482 0.039544738 16.11770921 1.278897626 0.054446137 0.346861179 10966.22399 -4.040057112 0.067403216 FGEENIEVYHSYFWPLEWTIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 269.57 7.57E-45 576220000 625040 465200 520640 583870 505890 452220 676810 595870 442440 FALSE TRUE 595495.5979 512604.4089 544511.859 525178.2783 594117.0558 436559.508 573550.204 543692.4639 511051.3355 1.16523636 1.003038977 1.065473899 1.027642904 1.162538897 0.854238073 1.122294698 1.063870547 1 18.96310869 4.643370001 3.167467982 1.041296156 1.17169322 0.190522563 0.082190913 0.45360822 7.403901414 0.017795568 0.127974567 43991.62459 -4.643370001 0.130397065 FGEILKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGEILKR 7 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ; 132.29 0.0054255 990800000 1560570 1234820 1367780 1714940 1514770 1513050 1877210 1665650 1702770 FALSE TRUE 1486804.949 1360649.562 1430494.066 1542550.973 1778945.408 1460652.699 1590807.137 1519796.856 1966826.875 0.755940936 0.691799354 0.727310616 0.784284063 0.904474833 0.742644265 0.808819097 0.772715115 1 20.90743854 -5 0.145096078 1.812846387 0.690432071 0.650739395 0.053657053 82.72703215 0.723969949 19.39966199 0.292147613 1.00E-05 5 -1.122414316 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK 321.49 6.62E-68 2333630000 4089100 3981570 3221310 4305700 1514115 4294260 3549460 4905400 1355112 TRUE FALSE 3895816.347 4387296.51 3369010.25 3872882.856 1778176.177 4145548.699 3007924.687 4475857.171 1565255.848 2.488932625 2.802926126 2.152370332 2.474281032 1.13602909 2.64847993 1.921682446 2.859505158 1 20.57796706 3.448187349 2.012004523 2.035491975 2.638452305 0.156217954 0.596799306 0.552027347 4.500106412 0.16054825 0.257910032 2806.644129 -3.448187349 0.602960331 FGESTTGFNFS(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGESTTGFNFSFK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FGESTTGFNFS(1)FK;FGESTTGFNFS(1)FK 138.19 5.46E-05 72638000 205742 170325 214320 223500 166621 221220 245100 221020 179130 TRUE FALSE 196016.9834 187681.3111 224146.784 201033.3554 195679.6496 213559.0959 207705.4934 201666.3171 206908.5655 0.94736041 0.907073666 1.083313218 0.9716048 0.945730058 1.032142364 1.003851595 0.974663937 1 17.65863385 3.783356764 24.99999014 1.000349896 0.927217014 0.394701113 0.038278158 393.5879211 219653.6778 0.009209463 0.016602495 6072.34956 -3.783356764 -0.073132882 FGEVVDCTIKTDPVTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGEVVDCTIKTDPVTGR 17 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 98.062 0.0017516 84480000 266980 115540 283370 206010 257480 256730 405570 297450 351980 FALSE TRUE 254360.3845 127313.6574 296362.7948 185301.4834 302384.4305 247839.3757 343692.8477 271403.7011 406563.2607 0.62563544 0.313145996 0.728946325 0.455775279 0.743757392 0.609596094 0.845361303 0.667555894 1 18.63312033 1.58068951 0.361774068 1.01083008 0.453836622 0.520625632 0.132024222 0.802060403 0.328069528 0.165539964 0.140653768 38.07934854 -1.58068951 -0.556993458 FGEVVDCTLKLDPITGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGEVVDCTLKLDPITGR 17 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RD83;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 154.12 1.37E-07 625336000 1900120 816248 2098570 1409932 1860820 1866990 3086900 2098860 2393950 FALSE TRUE 1810305.093 899424.5992 2194791.51 1268202.957 2185346.419 1802335.668 2615936.71 1915072.692 2765191.539 0.654676201 0.325266654 0.793721331 0.458631143 0.790305622 0.65179415 0.946023692 0.692564209 1 21.39894799 2.132191049 0.524769291 0.960943658 0.495903611 0.430549273 0.153122517 0.695647668 0.403206336 0.131066796 0.103581288 135.5785699 -2.132191049 -0.465040047 FGEYHKDDPSSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGEYHKDDPSSFR 13 1 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 93.494 0.0033578 481690000 953360 740470 773580 961940 661300 925260 1030130 948870 658660 FALSE TRUE 908296.5622 815924.7348 809049.4082 865243.9636 776630.5106 893218.0142 872964.7489 865781.9125 760801.6288 1.193867794 1.07245398 1.06341703 1.137279326 1.020805531 1.174048504 1.14742755 1.137986408 1 19.53716081 4.651433111 3.349610788 1.103645497 1.197982522 0.215311651 0.057177445 0.429703406 7.895952214 0.013111113 0.090325814 44816.00198 -4.651433111 0.094337025 FGFNPLEFENFSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGFNPLEFENFSWR 14 0 O15230 O15230 LAMA5 Laminin subunit alpha-5 0 98.105 0.0072651 0 34254 32946 39229 36793 41562 34272 51137 32658 45825 FALSE TRUE 32634.8813 36303.23486 41027.68845 33094.49774 48810.39964 33085.15205 43335.11145 29798.29239 52931.30696 0.616551587 0.68585563 0.775111948 0.625234849 0.922146126 0.625058287 0.818704732 0.562961584 1 15.69183366 -5 0.290467078 3.245067875 0.691147647 0.398066365 0.110936743 236.6236823 2.226634286 322.5679537 0.104051327 1.00E-05 5 -2.553920228 FGGEHVPNS(ph)PFQVTALAGDQPSVQPPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGGEHVPNSPFQVTALAGDQPSVQPPLR 28 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 1 FGGEHVPNS(1)PFQVTALAGDQPSVQPPLR 133.25 1.07E-05 49639000 50208 33961 45694 45752 45301 40411 49012 44235 40602 TRUE FALSE 47834.76734 37421.66451 47789.1151 41152.92204 53201.48006 39011.55694 41534.31923 40361.5489 46898.35079 1.01996694 0.797931353 1.01899351 0.877491881 1.134399806 0.831832171 0.885624303 0.86061766 1 15.51724957 -0.502886061 5.813172205 0.999999999 0.922416529 0.043253343 0.102563359 12093070.75 2080287.716 0.090192392 0.021865308 0.314133273 0.502886061 -0.07758347 FGGPVHHQAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGGPVHHQAQR 11 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ;; 179.8 4.01E-06 193097000 530160 341195 173433 222091 497890 262740 543340 390230 148352 FALSE TRUE 505100.3875 375963.1584 181385.0746 199765.9907 584721.8584 253641.2479 460443.5039 356059.3925 171357.6705 2.947638037 2.194025849 1.058517393 1.165783768 3.412288792 1.480186135 2.687031766 2.077872508 1 17.38665125 0.952992749 22.18946753 0.999999991 2.175473184 0.179256023 0.755606808 5121.778736 2417707.398 0.697241922 0.17431048 8.974138117 -0.952992749 1.175473193 FGGS(ph)GSQVDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGGSGSQVDSAR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 FGGS(0.969)GS(0.031)QVDSAR;FGGS(0.857)GS(0.143)QVDSAR 104.3 0.000985 0 140819 129490 134514 154223 130387 134845 165715 137300 160385 TRUE FALSE 134162.7649 142685.1782 140681.6 138720.211 153126.4515 130175.2838 140432.1332 125277.2841 185256.6867 0.724199312 0.770202581 0.759387434 0.748800022 0.826563695 0.702675224 0.758040834 0.676236234 1 17.49916609 -1.354129029 5.394027511 1.000082588 0.748366346 0.796323195 0.040388904 3.59E-05 4.30E-06 0.035015642 0.008250567 0.04424569 1.354129029 -0.251716243 FGHEFLEFEFRPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGHEFLEFEFRPDGK 15 1 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 223.06 7.92E-13 373380000 1685840 1788800 1513560 1939610 1232510 1721840 1806540 1906000 1080160 FALSE TRUE 1606153.684 1971080.754 1582958.223 1744636.718 1447459.354 1662212.249 1530919.144 1739100.536 1247665.696 1.287326957 1.579814817 1.268735871 1.398320659 1.160133967 1.332257715 1.227026717 1.393883427 1 20.25079999 -4.563695 0.124451942 6.69E-13 1.501196045 0.447877276 0.114454661 107.1607362 0.949122668 27.44507188 0.935384731 2.73E-05 4.563695 1.501196045 FGINIPS(ph)PEHSNTIDVCNTVDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGINIPSPEHSNTIDVCNTVDIK 23 0 C9IZ03;Q9HCI7-2;Q9HCI7 C9IZ03 MSL2 E3 ubiquitin-protein ligase MSL2 1 FGINIPS(1)PEHSNTIDVCNTVDIK 287.53 7.04E-53 85035000 157900 146760 151620 159670 91692 158690 153030 164890 100640 TRUE FALSE 150436.3799 161715.0109 158571.927 143619.6682 107683.0558 153194.5255 129682.4629 150451.3575 116246.7372 1.294112708 1.391135913 1.364097873 1.235472683 0.926331856 1.317839358 1.115579379 1.294241551 1 16.8268307 3.048968677 5.219631285 1.145063514 1.347735087 0.411045357 0.118952043 0.182187891 11.07340027 0.03166379 0.037689749 1119.357149 -3.048968677 0.202671573 FGKPNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGKPNKR 7 2 P51858;P51858-2;P51858-3;Q5TGJ6 P51858 HDGF;HDGFL1 Hepatoma-derived growth factor;Hepatoma-derived growth factor-like protein 1 0 ; 71.378 0.030641 2484800000 3105000 2194000 2165900 2979100 2374100 2587600 3335700 3073200 2534100 FALSE TRUE 2958232.804 2417571.094 2265208.657 2679635.208 2788142.288 2497990.763 2826777.701 2804094.316 2927075.286 1.010644591 0.825934033 0.773881242 0.915465079 0.952535216 0.853408443 0.965734539 0.957985034 1 21.48102842 1.450465736 1.20764641 0.997071267 0.887580468 0.25821339 0.066588432 0.627963704 1.768868643 0.06103411 0.020776086 28.2140698 -1.450465736 -0.109490799 FGLGT(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGLGTPEK 8 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 FGLGT(1)PEK 97.456 0.091872 48476000 222200 267220 190740 284590 143000 236460 234190 271980 161400 TRUE FALSE 211697.0464 294450.0218 199485.6177 255982.4725 167939.1547 228271.3309 198460.0143 248163.9893 186429.0877 1.135536568 1.579421031 1.070034833 1.373082257 0.900820558 1.22444053 1.064533527 1.331144149 1 17.50826745 3.708584693 24.99027876 1.140925569 1.357478919 0.209057999 0.177621014 858.7125992 715890.1123 0.042542441 0.065916357 5111.92758 -3.708584693 0.21655335 FGLSVGHHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGLSVGHHLGK 11 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 119.22 0.00035561 1242800000 1240300 839180 995690 1217900 1283200 979610 1546400 1292200 285480 FALSE TRUE 1181673.477 924693.3961 1041343.371 1095474.378 1506989.674 945685.8601 1310468.278 1179048.118 329750.7804 3.583535043 2.804218977 3.157970908 3.322128235 4.570086755 2.867880582 3.974117292 3.575573396 1 18.33101655 3.00266205 24.04241492 3.454614999 3.168562358 0 0.954710164 263.6788364 2381344.005 0.242848849 0.288482166 1006.148422 -3.00266205 -0.286052641 FGNDVQHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGNDVQHFK 9 0 P62993;J3KT38 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 136.99 0.00017727 347970000 1570730 1296040 1245560 1553890 1116990 1388830 1641250 1636570 1184240 FALSE TRUE 1496484.706 1428107.949 1302670.158 1397690.025 1311792.702 1340734.469 1390847.169 1493263.255 1367885.891 1.094012824 1.044025645 0.952323704 1.021788465 0.958992787 0.980150814 1.01678596 1.091657765 1 20.38351645 4.081454378 3.150432603 1.001982229 1.082312784 0.353546479 0.039249916 0.23818737 4.667282176 0.009746765 0.023904851 12062.97363 -4.081454378 0.080330555 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;FGQAATMEGIGAIGGT(1)PPAFNR 231.51 1.26E-25 1366985000 1262136 1335313 1434668 1525042 1400429 1394333 1663543 1578754 1884354 TRUE FALSE 1202477.333 1471382.913 1500448.947 1371741.881 1644663.374 1346046.899 1409738.962 1440509.93 2176569.994 0.552464352 0.676009922 0.689363977 0.630230998 0.755621633 0.618425735 0.64768832 0.661825686 1 21.05362498 -5 0.372861408 5.68590804 0.642260844 0.815829342 0.051725253 222.5160589 1.701568337 841.0194486 0.034530454 1.00E-05 5 -5.043647196 FGQGDLPKPINSDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGQGDLPKPINSDFR 15 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 117.4 0.00034009 196760000 644590 494220 553400 640810 473250 612220 660180 707520 556820 FALSE TRUE 614121.5082 544581.5799 578773.9374 576394.5613 555784.6502 591018.6679 559457.416 645565.798 643168.8018 0.954837216 0.846716412 0.89987875 0.896179292 0.864134965 0.918916879 0.869845388 1.003726854 1 19.2948379 1.232060192 24.99767581 1.001863516 0.89202146 0.695551549 0.029957634 85.00817994 326887.743 0.024305819 0.006648237 17.06318862 -1.232060192 -0.109842056 FGQYNKEDPTSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGQYNKEDPTSFR 13 1 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 132.06 0.00011238 1047170000 2361180 1748410 2135610 2336670 1985710 2292010 2903360 2572340 2529040 FALSE TRUE 2249571.701 1926574.967 2233529.831 2101783.492 2332017.195 2212637.119 2460399.108 2347092.273 2921230.607 0.770076726 0.659508004 0.764585249 0.719485647 0.79829959 0.757433225 0.842247477 0.803460113 1 21.47814482 0.499070158 0.348967518 1.037168187 0.706939825 0.815152747 0.038235504 0.996170696 0.246641295 0.101754649 0.033905796 3.15551434 -0.499070158 -0.330228362 FGS(ph)LAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGSLAK 6 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 FGS(1)LAK 69.598 0.097638 155040000 729220 503140 476070 779150 401200 645550 738450 591740 279480 TRUE FALSE 694751.2158 554410.538 497898.2804 700828.3617 471169.153 623194.4416 625785.8899 539924.1086 322820.331 2.15212968 1.717396597 1.542338671 2.170954845 1.459539898 1.930468381 1.938495906 1.672522009 1 18.30037192 0.870557144 4.472886263 1.000060676 1.847727074 0.56996928 0.229362302 0.623195637 20.59318584 0.201293633 0.051128448 7.422618572 -0.870557144 0.847666398 FGTVLTEHVAAAELGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGTVLTEHVAAAELGAR 17 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;; 169.64 1.95E-09 887310000 978440 963420 901190 1088390 890630 993790 1082130 1048460 912010 FALSE TRUE 932191.0803 1061593.593 942510.4529 978982.9694 1045955.59 959374.8031 917031.1938 956651.2842 1053439.853 0.884902045 1.00774011 0.894697927 0.929320233 0.992895406 0.910706767 0.870511203 0.90812141 1 20.00667651 2.035869643 24.99887399 0.906519575 0.943721344 0 0.050138305 364.456914 254001.9428 0.017379308 0.012835435 108.6099574 -2.035869643 0.037201769 FGVEQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FGVEQDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 143.11 0.0056859 1749460000 2364670 2338190 2167350 2567610 2260020 2223900 2563640 2411010 2296400 FALSE TRUE 2252896.735 2576454.219 2266725.141 2309508.965 2654166.772 2146885.785 2172509.634 2199889.183 2652513.984 0.849343962 0.971325405 0.854557282 0.87068682 1.000623103 0.809377745 0.819037957 0.82936007 1 21.33892893 2.186924276 24.99999311 0.844686533 0.908070321 0.058725692 0.071909672 180.1190881 87204.28302 0.024358596 0.017990036 153.788647 -2.186924276 0.063383787 FGVEQDVDMVFASFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGVEQDVDMVFASFIR 16 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 260.19 2.07E-26 168420000 603100 437270 493570 595850 635020 427500 676710 602450 540040 FALSE TRUE 574592.6582 481828.3101 516200.6727 535954.026 745767.2869 412695.5678 573465.4609 549696.2842 623786.6451 0.921136518 0.772424857 0.827527612 0.859194454 1.195548659 0.661597312 0.919329494 0.881224836 1 19.25069314 -4.999999998 0.205987918 1.587485615 0.854196509 0.070403459 0.135639504 394.5938763 3.922019917 95.79580303 0.278572946 1.00E-05 4.999999998 -0.733289106 FGVLFRDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGVLFRDDK 9 1 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 95.608 0.0072323 319950000 495620 310060 539400 445620 387650 496200 634620 537640 554650 FALSE TRUE 472193.0248 341655.4665 564132.0235 400825.431 455256.0373 479016.4696 537797.0634 490561.3914 640662.2892 0.737038894 0.533284809 0.880545075 0.625642304 0.710602208 0.747689504 0.839439237 0.765709797 1 19.28920455 0.705316009 0.317950763 1.046524526 0.642296495 0.499729705 0.091629275 1.819189819 0.451650518 0.244351168 0.104962626 5.073597479 -0.705316009 -0.404228031 FGVQMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FGVQMDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 127.12 0.0090405 744460000 975750 836790 813790 956310 923920 881920 1103130 989320 936970 FALSE TRUE 929628.2313 922059.8524 851103.0764 860179.9019 1085051.355 851378.8893 934827.2581 902689.8961 1082270.522 0.858961057 0.851968 0.786405117 0.794791953 1.002569444 0.786659963 0.863764871 0.834070482 1 20.04562973 -1.880541345 2.483928324 1.076664095 0.848182427 0.372512033 0.062235942 12817698.28 7279873.5 5773430.396 0.013582342 0.013166146 1.880541345 -0.228481668 FGVQSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGVQSER 7 0 Q14247 Q14247 CTTN Src substrate cortactin 0 85.265 0.048711 162220000 81003 81485 73192 86665 83342 82052 101560 91379 92069 FALSE TRUE 77174.14872 89788.41414 76547.9256 77953.26955 97876.81841 79210.51867 86065.15672 83377.37033 106346.5903 0.725685219 0.844299887 0.719796708 0.733011461 0.920356902 0.744833647 0.809289292 0.784015455 1 16.69841425 -5 0.284835901 2.607378197 0.773735522 0.552715246 0.06127238 174.236478 1.655280076 165.9611766 0.061811028 1.00E-05 5 -1.833642675 FGVQTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGVQTDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 83.753 0.051295 217900000 202300 181950 190120 226540 242330 182760 227430 204400 269750 FALSE TRUE 192737.6799 200490.9119 198837.1901 203767.7688 284592.2753 176430.9754 192731.3765 186501.6524 311581.4523 0.618578797 0.64346228 0.63815477 0.653979135 0.913380027 0.566243511 0.618558566 0.59856468 1 18.24924983 -1.369828805 3.025339809 1.004294707 0.65337737 0.564411537 0.094840107 24567081.93 30819855.57 927935.1894 0.022956464 0.042674771 1.369828805 -0.350917338 FGVYDIDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FGVYDIDNK 9 0 O75131;A0A087WYQ3;E5RHZ0;A0A087WXR6;A0A087WUS8 O75131 CPNE3 Copine-3 0 112.84 0.0044133 60957000 93516 83400 53886 90746 75521 73678 77396 85301 63202 FALSE TRUE 89095.68401 91898.55482 56356.7264 81624.03967 88691.83849 71126.51239 65587.81872 77831.59223 73003.04337 1.220437942 1.258831832 0.771977767 1.118090917 1.214906042 0.974295168 0.898425815 1.066141748 1 16.15566899 3.794822939 24.9999384 1.006615749 1.239635175 0.398378084 0.119229214 263.7566378 117198.1274 0.030273062 0.05457552 6234.805921 -3.794822939 0.233019426 FGWDCHGLPVEYEIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FGWDCHGLPVEYEIDK 16 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 140.22 1.72E-06 849480000 1835380 1677870 1456260 1803980 1195040 1622890 1803640 1793830 1089020 FALSE TRUE 1748625.225 1848846.861 1523030.961 1622640.503 1403454.598 1566688.912 1528461.592 1636752.736 1257899.66 1.390115031 1.469788823 1.210773013 1.289960205 1.115712678 1.245480035 1.215090234 1.301179091 1 20.26258541 8 0.089899238 0.865317964 2.476874776 0.58019381 0.08515291 99.8030798 0.645002236 1.51405939 19.84004074 99999999.99 -8 1.611556812 FGYDEIDNGYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FGYDEIDNGYLK 12 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 158.79 0.00013811 56901000 295290 231672 228584 274800 226229 261600 321910 287900 281620 FALSE TRUE 281332.2269 255279.6402 239064.8025 247176.5819 265683.266 252540.7264 272796.7172 262689.9497 325292.1913 0.864860069 0.784770268 0.734923275 0.759860177 0.816752671 0.776350411 0.838620553 0.80755074 1 18.31137666 0.00427821 0.738874939 1.006612043 0.793760427 0.752905281 0.036649951 2.600711563 1.486048341 0.086035879 0.013310088 1.009899622 -0.00427821 -0.212851616 FGYVDFESAEDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 ;;; 240.12 5.10E-17 327371000 574688 514585 511408 592354 381418 543850 574707 617174 378715 FALSE TRUE 547523.6372 567021.7965 534856.5627 532809.4505 447937.1784 525016.3381 487024.8919 563130.9727 437444.188 1.251642272 1.296215179 1.222685264 1.218005554 1.023987038 1.200190453 1.113341782 1.287320733 1 18.73873943 7.999999988 0.023177218 4.44E-08 2.775486881 0.399182937 0.079640156 2037.179695 3.634890402 153.7883471 305.3905775 99999997.27 -7.999999988 2.775486837 FHCVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHCVCR 6 0 H0YC42;U3KQQ8;E5RGC7;E5RK86;E5RFH3;H0YAT2;Q9Y2Q9;H7C5V3 H0YC42;E5RGC7 MRPS28 "28S ribosomal protein S28, mitochondrial" 0 ; 141.66 0.011624 172078000 216689 178520 171892 175720 225620 158386 222972 187362 154918 FALSE TRUE 206446.5404 196711.391 179773.4182 158056.2918 264968.0566 152901.0531 188953.5262 170955.59 178941.8922 1.153707149 1.099303179 1.004646905 0.883282778 1.48074916 0.85447321 1.055949079 0.955369298 1 17.44913165 FHDFLGDSWGILFSHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FHDFLGDSWGILFSHPR 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 284.44 1.97E-36 5076163000 496671 545584 399040 512816 576029 440318 741279 409916 69082.1 FALSE TRUE 473194.3461 601179.6299 417336.3787 461266.7614 676488.2752 425069.6773 628183.274 374021.5819 79794.99925 5.930125329 7.534051451 5.230106932 5.780647481 8.477827954 5.327021509 7.872464189 4.687280976 1 16.28401072 3.737136521 24.98636553 6.002162171 6.732088307 0.013677864 2.075377684 561.959808 9859842.851 0.483665859 0.795612371 5459.294475 -3.737136521 0.729926136 FHDIDDVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FHDIDDVKK 9 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;; 214.13 4.96E-07 452338000 1980770 2095970 1831070 2215370 1115980 2020700 1970980 1992090 508842 FALSE TRUE 1887142.928 2309551.726 1915026.371 1992676.799 1310606.559 1950722.652 1670270.801 1817652.039 587750.6186 3.210788501 3.929475619 3.258229443 3.390344026 2.229868446 3.318963164 2.841801861 3.092556573 1 19.16484463 2.878434122 6.279435701 2.697852066 3.504624399 0.311056402 0.666147917 0.30573591 14.49864577 0.181704998 0.193414242 755.8473975 -2.878434122 0.806772333 FHDIISDAEIEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FHDIISDAEIEIVK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 206.18 1.12E-08 420978000 1328250 1191400 1292800 1517920 1022578 1326440 1603470 1321580 529640 FALSE TRUE 1265466.255 1312805.015 1352076.159 1365335.798 1200915.279 1280505.05 1358831.202 1205855.449 611773.8662 2.068519636 2.145899142 2.210091397 2.231765483 1.963005198 2.093101914 2.221133129 1.971080355 1 19.22263895 0.826079631 4.470289019 1.000020084 2.131814137 0.950493536 0.080654391 0.359965339 9.073733267 0.076374789 0.019397047 6.700074487 -0.826079631 1.131794053 FHDLLSQLDDQYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 153.14 6.47E-06 138303000 91134 102776 100010 125577 96424 98414 118439 103281 56043 FALSE TRUE 86826.27643 113248.9912 104595.5574 112953.7614 113240.3151 95005.8985 100368.9553 94237.16811 64733.86221 1.341280645 1.74945519 1.615778108 1.744894519 1.749321162 1.467638347 1.550486126 1.455763103 1 15.98223296 0.57770139 0.900225478 0.998401631 1.619908389 0.691862015 0.127542448 0.798984383 1.041252076 0.123740771 0.040548511 3.781824661 -0.57770139 0.621506758 FHDPDSAVVAQHLTNTVFVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHDPDSAVVAQHLTNTVFVDR 21 0 Q05519-2;Q05519;B4DWT1;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 0 192.94 5.24E-18 222650000 115940 112710 134730 122530 111190 120630 137760 124610 104270 FALSE TRUE 110459.746 124195.2771 140907.5038 110213.0516 130581.5008 116452.5529 116742.1819 113698.4878 120439.6591 0.917137651 1.03118257 1.169942732 0.915089369 1.084206829 0.966895404 0.969300169 0.944028642 1 16.877951 2.099472751 23.30710446 0.967636731 1.017361374 0.109219606 0.074575255 19.09703813 4441.7541 0.026943624 0.019899187 125.739796 -2.099472751 0.049724642 FHDT(ph)SSPLLISGTSAAELPWAVKPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHDTSSPLLISGTSAAELPWAVKPEDK 27 1 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 FHDT(0.333)S(0.333)S(0.333)PLLISGTSAAELPWAVKPEDK 78.837 0.019522 55916000 39016 29671 38964 46134 25941 42422 46130 42491 17125 TRUE FALSE 37171.791 32694.50863 40750.53794 41496.52267 30465.10219 40952.9155 39092.02126 38770.26278 19780.65754 1.879198956 1.652852468 2.060120492 2.09783333 1.540146081 2.070351576 1.976275116 1.960008797 1 14.27180276 -1.061924052 6.801683806 0.999999628 1.893656412 0.711176671 0.181050418 9.89E-07 1.37E-07 0.169907247 0.040047505 0.08671135 1.061924052 0.893656784 FHDTS(ph)SPLMVTPPSAEAHWAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDT(0.002)S(0.499)S(0.499)PLMVTPPSAEAHWAVR 169.41 1.39E-11 87923000 41396 41396 41338 52001 37802 43481 53107 38325 23977 TRUE FALSE 39439.29312 45614.29946 43233.38819 46773.76068 44394.65683 41975.24207 45004.55177 34969.05983 27695.2307 1.424046383 1.647009189 1.561040912 1.688874203 1.602971187 1.515612653 1.624992846 1.262638329 1 14.75734994 1.035523816 3.27524113 1.002243768 1.579911776 0.873885743 0.07451741 0.067056637 1.606129319 0.068906579 0.018024449 10.85235062 -1.035523816 0.577668007 FHDTSS(ph)PLLISGTSAAELPWAVKPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHDTSSPLLISGTSAAELPWAVKPEDK 27 1 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 FHDT(0.024)S(0.119)S(0.857)PLLISGTSAAELPWAVKPEDK;FHDT(0.021)S(0.127)S(0.852)PLLISGTSAAELPWAVKPEDK 247.82 7.49E-46 189964000 764520 626330 625710 980370 383950 820970 889190 801640 169808 TRUE FALSE 728382.6547 690153.7391 654399.4224 881821.345 450910.7584 792539.603 753527.7344 731444.1518 196140.9574 3.713567347 3.518662029 3.336373143 4.495855209 2.298911785 4.040663478 3.841766373 3.729176005 1 17.5815313 2.757960779 24.98062315 3.299831136 3.695159134 0.093863631 0.94981042 3012.294725 3878777.881 0.262321648 0.277885677 572.7443041 -2.757960779 0.395327997 FHDTSS(ph)PLMVTPPSAEAHWAVR ddPTM_SK-BR-3_Trastuzumab_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 FHDT(0.001)S(0.121)S(0.878)PLMVTPPSAEAHWAVR;FHDT(0.001)S(0.128)S(0.871)PLMVTPPSAEAHWAVR;FHDTS(0.104)S(0.896)PLMVTPPSAEAHWAVR;FHDT(0.064)S(0.411)S(0.525)PLMVTPPSAEAHWAVR;FHDT(0.004)S(0.235)S(0.762)PLMVTPPSAEAHWAVR;FHDTS(0.008)S(0.992)PLMVTPPSAEAHWAVR;FHDT(0.001)S(0.01)S(0.989)PLMVTPPSAEAHWAVR 226.24 9.07E-26 3138230000 549276 503626 505580 695200 513886 509701 645429 527244 197355 TRUE FALSE 523312.812 554946.062 528761.3431 625317.1752 603507.5557 492049.9266 546956.9519 481075.7203 227959.8055 2.295636334 2.434403122 2.319537613 2.743102776 2.647429684 2.158494238 2.399356987 2.110353267 1 17.79841994 0.465312483 0.998928253 0.995260422 2.445408387 0.881548741 0.164356735 0.609293693 0.83336155 0.158090197 0.049580674 2.919526912 -0.465312483 1.450147965 FHFPPLDTHS(ph)PTNDVQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.032)HS(0.965)PT(0.003)NDVQPGR;FHFPPLDT(0.158)HS(0.839)PT(0.003)NDVQPGR 210.38 2.99E-16 118540000 128232 107580 123594 151387 145503 114308 148489 95075 24330 TRUE FALSE 122170.7275 118542.5243 129260.9072 136169.2911 170878.6771 110349.4853 125834.2759 86749.72898 28102.97214 4.347252913 4.218149017 4.599545789 4.845369752 6.080448583 3.926612628 4.477614511 3.08685247 1 14.7784351 0.918971154 1.609478435 0.99932241 4.650718725 0.814938528 0.566373326 0.195875835 1.023051527 0.532287922 0.154215594 8.297956504 -0.918971154 3.651396315 FHGTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FHGTVK 6 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;; 130.84 0.015589 26285830000 22495630 17309170 18054800 23698060 20469800 20679040 30773780 19524380 13526310 FALSE TRUE 21432306.15 19072994.1 18882630.44 21315885.99 24039726.64 19962919.66 26078674.66 17814721.78 15623901.07 1.371764072 1.22075748 1.208573349 1.364312657 1.53865072 1.277716722 1.669152572 1.140222387 1 23.89725138 3.07526762 7.396230309 1.393311226 1.272886717 0 0.196066336 0.593509723 49.42262351 0.051539664 0.061707807 1189.234828 -3.07526762 -0.120424509 FHHTIGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHHTIGGSR 9 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 97.431 0.006696 357220000 280260 267802 256200 328780 343920 267388 353300 249733 222104 FALSE TRUE 267012.6652 295091.3283 267947.0234 295730.4098 403899.5391 258128.2865 299397.5962 227865.0546 256546.754 1.040795337 1.150243859 1.044437395 1.152734951 1.574370102 1.006164695 1.167029368 0.888200888 1 17.96886225 1.245952169 24.96405439 0.944100426 1.155343237 0.242920975 0.159749108 215.4746861 727757.4785 0.107018209 0.037347881 17.61782003 -1.245952169 0.211242811 FHINWEDNTEKLEDAES(ph)SNPNLQSLLSTDALPSASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASK 36 1 Q9Y294 Q9Y294 ASF1A Histone chaperone ASF1A 1 FHINWEDNT(0.003)EKLEDAES(0.431)S(0.431)NPNLQS(0.118)LLS(0.01)T(0.007)DALPSASK 63.426 0.0066805 92877000 241990 233960 255970 294390 155020 294230 327280 280120 71085 TRUE FALSE 230551.6123 257800.79 267706.4777 264797.3579 182055.4389 284040.7413 277347.4251 255591.2078 82108.49875 2.807889753 3.139757686 3.260399128 3.224968937 2.217254507 3.459334243 3.377816296 3.112847168 1 16.32524394 2.871076474 17.82866849 2.878923026 3.088547134 0.04008032 0.72560102 11.45458581 1563.61941 0.202757606 0.215058829 743.1499865 -2.871076474 0.209624107 FHKPGENYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHKPGENYK 9 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 ; 161.76 3.86E-05 1315930000 1193210 1109200 1205720 1466710 787010 1278130 1548010 1289420 439520 FALSE TRUE 1136809.328 1222228.741 1261003.455 1319273.524 924264.2948 1233868.038 1311832.643 1176511.549 507678.5168 2.239230715 2.407485644 2.483862154 2.598639652 1.820570034 2.430412154 2.583982973 2.317434183 1 18.95355569 2.787902768 24.98812666 2.197929997 2.409579613 0.104025637 0.455227422 1253.212146 634656.2112 0.127518501 0.135253635 613.6246089 -2.787902768 0.211649615 FHLGLFTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHLGLFTDR 9 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 94.692 0.0085502 141720000 74071 85657 78574 88128 97959 80334 118550 91093 62481 FALSE TRUE 70569.81062 94385.54568 82176.69562 79269.20601 115043.0186 77552.01344 100463.0202 83116.41401 72170.23437 0.977824324 1.307818195 1.138650807 1.098364259 1.594050783 1.074570619 1.39202846 1.151671665 1 16.13911632 4.632329561 2.952678743 1.239788673 0.961966473 0.148411353 0.175315996 0.497263676 6.986329155 0.038075274 0.287462691 42887.38447 -4.632329561 -0.2778222 FHMVDGNVSGEFTDLVPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHMVDGNVSGEFTDLVPEK 19 0 O95433;O95433-2;G3V438;H0YJ63 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 56.529 0.09429 72624000 179570 179640 188820 225760 152240 219960 221650 217640 86489 FALSE TRUE 171082.082 197945.5202 197477.5838 203066.1759 178790.6078 212342.73 187833.2216 198582.2878 99901.2724 1.712511541 1.981411402 1.976727413 2.032668564 1.789672979 2.125525781 1.880188481 1.987785371 1 16.60821543 -1.373641265 5.629135608 0.999722605 1.931015576 0.860349625 0.118474004 0.00038364 4.27E-05 0.106700499 0.025142387 0.042301789 1.373641265 0.931292971 FHMYEGYPLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHMYEGYPLWK 11 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 157.38 3.06E-05 1211280000 4190900 4837600 3481200 4174900 3629700 3765400 4628500 3985000 1417650 FALSE TRUE 3992804.463 5330556.94 3640816.463 3755231.12 4262718.531 3635003.254 3922337.317 3636052.274 1637491.922 2.4383659 3.255318008 2.223410336 2.293282227 2.603199732 2.219860267 2.395332316 2.220500893 1 20.64305636 -1.047438251 0.24284812 9.18E-14 2.823500486 0.73544596 0.283859492 8.132816578 0.454194474 6.113320796 0.506108273 0.089652365 1.047438251 2.823500486 FHPEPYGLEDDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 162.32 4.06E-05 1386900000 1749110 1535620 1619470 1726450 1810140 1566830 1870680 1741780 1481100 FALSE TRUE 1666433.037 1692101.424 1693724.301 1552903.966 2125827.843 1512570.284 1585273.409 1589260.509 1710781.424 0.974077117 0.989081013 0.990029631 0.907716173 1.24260634 0.884139998 0.926637025 0.928967598 1 20.70622402 FHPLQEHVVKEELLNALYCEFINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHPLQEHVVKEELLNALYCEFINR 24 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 176.48 2.19E-13 285710000 681340 510250 691820 668520 625990 663630 870930 720820 67583 FALSE TRUE 649134.4085 562245.0551 723540.6313 601319.0995 735162.4578 640648.3267 738053.6328 657701.1795 78063.42647 8.315474196 7.202413223 9.268625065 7.70295549 9.41750178 8.206766672 9.45453801 8.425215356 1 16.25235917 0.892140087 21.38344013 1.000000036 8.461876362 0.912406344 0.730157015 23512.82245 4661467.819 0.704622428 0.176155602 7.800816957 -0.892140087 7.461876325 FHQLDIDDLQSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 12844012000 9188945 8716228 9106544 10512642 10076184 9225715 11583120 8731716 4525525 FALSE TRUE 8754601.781 9604421.543 9524088.05 9455891.253 11833467.3 8906226.176 9815902.305 7967120.657 5227320.304 1.674778141 1.837350877 1.82198287 1.808936645 2.26377314 1.703784283 1.877807698 1.524130949 1 22.31764013 0.919804315 2.433438645 1.000388411 1.849383916 0.748110696 0.159732268 0.180610003 2.34500426 0.145353588 0.039253624 8.31389078 -0.919804315 0.848995505 FHS(ph)PSTTWS(ph)PNKDTPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.887)PS(0.048)T(0.072)T(0.039)WS(0.95)PNKDT(0.005)PQEK;FHS(0.986)PS(0.012)T(0.003)T(0.014)WS(0.985)PNKDTPQEK;FHS(0.994)PS(0.006)TTWS(1)PNKDTPQEK 190.24 3.80E-14 794110000 606300 638340 607330 748180 336669 768910 694070 609350 163158 TRUE FALSE 577641.4006 703387.5717 635176.6812 672971.525 395383.967 742282.4539 588176.874 555992.0836 188459.7093 3.065065751 3.732296809 3.370357958 3.570903974 2.097976105 3.938679819 3.120968806 2.95019071 1 17.5238966 FHS(ph)PSTTWSPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHSPSTTWSPNK 12 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.84)PS(0.142)T(0.012)T(0.007)WSPNK;FHS(0.526)PS(0.385)T(0.074)T(0.015)WSPNK 86.996 0.0069546 533510000 1336460 1494520 1064970 1561630 998350 1346460 1417400 1174740 548390 TRUE FALSE 1273288.184 1646813.287 1113799.928 1404651.985 1172461.924 1299831.753 1201149.598 1071873.538 633431.5204 2.010143391 2.599828449 1.758358863 2.217527768 1.85096871 2.052047792 1.896258015 1.692169561 1 19.27282913 -0.499486063 0.241300719 0.421037938 2.332884311 0.709652986 0.220086254 5.337873913 0.391383603 2.699781759 0.398856797 0.316602207 0.499486063 1.911846373 FHS(ph)PSTTWSPNKDTPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.943)PS(0.055)T(0.002)TWSPNKDTPQEK;FHS(0.997)PS(0.003)TTWSPNKDTPQEK;FHS(0.883)PS(0.115)T(0.002)TWSPNKDTPQEK 235.61 5.13E-24 961540000 1591980 1413100 1591860 1867100 1002190 1841450 2096080 1561870 545300 TRUE FALSE 1516730.26 1557096.497 1664848.356 1679415.561 1176971.619 1777680.125 1776284.499 1425104.383 629862.339 2.408034528 2.472121923 2.643194 2.666321602 1.868617229 2.82233119 2.820115427 2.262564841 1 19.26467703 FHSEDYIDFLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHSEDYIDFLQR 12 0 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 0 ; 232.17 1.71E-12 95505000 105691 105510 94658 116264 110018 101833 129805 103200 87123 FALSE TRUE 100695.1959 116261.589 98998.16293 104576.9218 129205.1044 98306.49768 110000.8632 94163.2609 100633.5899 1.000612181 1.155296051 0.983748697 1.039185047 1.28391628 0.976875592 1.093082969 0.935704083 1 16.61875241 1.243831682 24.96560037 0.967852027 1.077407846 0.190789098 0.092653677 179.9266197 852227.6949 0.060497026 0.020631771 17.53200888 -1.243831682 0.109555819 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(ph)PVSRQSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVSRQSIR 39 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 FHSGWEPPVDVLQEAPWEVEGLAS(0.093)APIEEVS(0.341)PVS(0.283)RQS(0.283)IR 45.021 0.038842 25906000 12400 6977.8 11519 13596 20037 11975 23925 10747 12419 TRUE FALSE 11813.87657 7688.845753 12047.15754 12229.30425 23531.44646 11560.30275 20274.80184 9805.935707 14344.87509 0.823560784 0.535999491 0.839823105 0.85252079 1.640407902 0.805883821 1.413382947 0.6835846 1 13.80824779 2.985290639 23.55353737 1.143249495 0.721600696 0.271355776 0.283742176 327.5836768 524549.0788 0.07578149 0.083183841 966.6975979 -2.985290639 -0.421648799 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVS(ph)RQSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVSRQSIR 39 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 FHSGWEPPVDVLQEAPWEVEGLAS(0.005)APIEEVS(0.079)PVS(0.458)RQS(0.458)IR 147.58 1.63E-13 58423000 27738 12147 26869 30908 47979 31433 64766 26277 26441 TRUE FALSE 26426.87971 13384.79311 28100.97023 27801.06912 56346.52241 30344.46733 54884.75719 23976.04658 30541.33524 0.865282395 0.438251733 0.920096322 0.910276807 1.844926621 0.99355405 1.797064757 0.785035965 1 14.89847552 3.067560988 2.844835803 1.348467278 0.685060628 0.304472944 0.363465838 0.234832355 3.859606488 0.100564719 0.121231063 1168.317785 -3.067560988 -0.663406649 FHSMNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FHSMNQR 7 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 91.041 0.012664 23041000 36600 25597 24824.8 24360.1 26936 26750 34584 28651 25943 FALSE TRUE 34869.99053 28205.3634 25963.04164 21911.37647 31633.62987 25823.64079 29307.57562 26142.16655 29966.10794 1.163647632 0.941242134 0.866413539 0.731205284 1.055646931 0.861761589 0.978024096 0.872391123 1 14.8710441 4.443152134 2.126372701 0.908367342 1.169154897 0.438293341 0.089425138 0.326787148 2.485195478 0.021446788 0.128910701 27742.91776 -4.443152134 0.260787554 FHSPPDKDEAEAPSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHSPPDKDEAEAPSQK 16 1 F5H8D7;P18887;M0QYS5;M0QZ96;M0R0D2;M0R1U8 F5H8D7 XRCC1 DNA repair protein XRCC1 0 134.81 1.58E-05 158020000 86081 88611 95965 121750 73359 97014 105890 118140 46346 FALSE TRUE 82012.12173 97640.56164 100365.0902 109511.4587 86152.78637 93654.38085 89734.5357 107795.0353 53533.10098 1.531988998 1.823928744 1.874823022 2.045677472 1.609336743 1.749466763 1.676243932 2.01361463 1 15.7081436 -0.801078455 6.5164939 0.999999988 1.773768121 0.697682244 0.163226349 2.94E-08 5.20E-09 0.15172613 0.035762191 0.158096241 0.801078455 0.773768133 FHSS(ph)DS(ph)EEEEHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHSSDSEEEEHKK 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 FHS(0.096)S(0.904)DS(1)EEEEHKK 101.39 0.0020054 112530000 190590 201720 199260 246490 125670 260650 222750 173200 82703 TRUE FALSE 181581.1884 222275.4973 208396.2681 221712.3569 147586.8082 251623.6251 188765.3964 158033.6898 95528.15885 1.900813232 2.326806043 2.18151664 2.320911023 1.544956063 2.634025696 1.976018367 1.654315248 1 16.54363844 0.979337935 2.175300801 1.006734283 2.145273083 0.622431945 0.286613283 0.192075769 1.985807914 0.241983228 0.066779167 9.535378461 -0.979337935 1.1385388 FHTVSGSK ddPTM_SK-BR-3_Trastuzumab_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 ; 132.76 0.00094853 1077350000 4396400 4176800 4610200 5798700 3989900 5218800 6182500 5420900 2862600 FALSE TRUE 4188590.885 4602420.669 4821582.23 5215803.659 4685737.297 5038071.647 5239246.076 4946217.258 3306517.388 1.266768141 1.391923927 1.458205618 1.57743119 1.417121626 1.523679163 1.584520951 1.495899364 1 21.65688106 4.148719854 1.68860771 1.477598321 1.27403847 0.050327246 0.168801758 0.719464511 3.74393255 0.041036687 0.163007115 14083.80016 -4.148719854 -0.20355985 FHVDISLTDFIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FHVDISLTDFIQK 13 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 122.45 0.00023492 46248000 139860 166590 146780 176130 112200 145900 160360 151940 77264 FALSE TRUE 133249.095 183565.7104 153510.0082 158425.0778 131767.6445 140847.4464 135894.1368 138635.3281 89245.70651 1.493058884 2.056857608 1.720082839 1.775156296 1.4764592 1.57819857 1.522696633 1.553411739 1 16.44549514 0.282423704 0.328595573 0.866374872 1.805385656 0.654369103 0.15720975 2.208175481 0.422044187 0.616709937 0.162971015 1.916124412 -0.282423704 0.939010783 FHVEEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;; 178.3 0.00025035 7666670000 22159530 24534550 18618750 26797620 12648410 22477150 21054970 21132260 7550710 FALSE TRUE 21112092.93 27034648.54 19472438.1 24103872.33 14854288.7 21698760.66 17842647.63 19281807.29 8721635.543 2.420657551 3.09972234 2.232659002 2.763687178 1.703154027 2.487923343 2.045791473 2.210801769 1 23.05616727 -0.640575122 0.19136326 1.17E-14 2.951997441 0.644195508 0.342523817 8.878370469 0.44522313 6.200158547 1.111754091 0.228783594 0.640575122 2.951997441 FHVEEEGKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;;;;;; 183.64 9.89E-07 12428788000 44143340 31062265 42239560 42195020 27321490 46776980 57167320 48706940 18242182 FALSE TRUE 42056771.8 34227545.12 44176285.61 37953496.42 32086349.21 45157081.45 48445395.38 44441902.12 21071086.42 1.995947004 1.62438445 2.096535733 1.801212129 1.522766723 2.143082732 2.299140843 2.109141467 1 24.32876137 3.732674293 24.79503903 1.930849754 1.810165732 0 0.388554197 2277.25673 9592519.838 0.097208745 0.155167748 5403.489267 -3.732674293 -0.120684022 FHVLVASQDFVESVLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FHVLVASQDFVESVLVR 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 ;; 217.37 4.99E-15 101068000 168429 177282 186098 184437 168147 175494 214599 181746 93110 FALSE TRUE 160467.695 195347.2374 194630.7774 165897.0424 197471.7836 169416.5988 181857.9812 165831.3567 107549.0233 1.492042327 1.81635529 1.809693584 1.542524863 1.836109502 1.575249999 1.690931035 1.541914112 1 16.7146349 0.53688901 1.289647798 0.999506431 1.687868841 0.76348332 0.118321973 0.812837386 1.776318693 0.103627058 0.030965553 3.442619389 -0.53688901 0.688362411 FICDASSLHQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FICDASSLHQVR 12 0 Q9BSH4 Q9BSH4 TACO1 Translational activator of cytochrome c oxidase 1 0 130.36 0.00021785 204960000 294220 196060 223090 239710 382420 202840 320940 263000 352950 FALSE TRUE 280312.8037 216038.7369 233318.8972 215613.8954 449113.9269 195815.5999 271974.7085 239970.3257 407683.6834 0.687574252 0.529917546 0.572303741 0.52887546 1.101623502 0.480312575 0.667121888 0.588618911 1 18.63709069 FICEQDHQNFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FICEQDHQNFLR 12 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 318.64 1.38E-46 3273460000 1777130 1512460 1517550 1719540 1854420 1539930 1922060 1748470 1863560 FALSE TRUE 1693128.587 1666581.394 1587131.169 1546688.572 2177830.261 1486601.838 1628814.446 1595364.698 2152551.367 0.786568262 0.774235365 0.737325572 0.718537358 1.011743689 0.690623165 0.756690164 0.741150582 1 21.03761623 -1.295646195 3.516762229 1.000743847 0.776159218 0.388963704 0.087788564 21030182.38 27601487.4 158985.0755 0.02005719 0.050623691 1.295646195 -0.224584628 FICVTPTTCSNTIDLPMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FICVTPTTCSNTIDLPMSPR 20 0 P40763;P40763-2;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 1 FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR 208.97 3.32E-22 783230000 685612 546859 626271 701592 721352 566689 652100 589329 702332 TRUE FALSE 653204.4795 602584.5538 654986.1448 631066.6392 847155.5604 547064.4178 552610.1684 537724.2285 811246.0595 0.805186628 0.742788882 0.807382837 0.777897941 1.044264623 0.674350786 0.681186875 0.6628374 1 19.62978004 -0.821367956 8.552137203 1.000003761 0.77140185 0.296465904 0.109084538 0 0 0.104051135 0.024525088 0.150880128 0.821367956 -0.228601911 FIDFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIDFFK 6 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 101.52 0.084748 37722000 266810 248860 213262 266800 247330 207516 302030 274210 256320 FALSE TRUE 254198.4201 274219.1169 223040.2736 239980.7571 290464.2737 200329.6689 255949.7763 250198.7187 296068.7965 0.858578895 0.926200667 0.753339346 0.810557411 0.981070201 0.676632159 0.864494264 0.84506953 1 18.17557292 0.431923588 2.815904606 0.999999163 0.843188558 0.264253102 0.08397756 32.74384771 159.7318632 0.074876954 0.019691017 2.703482661 -0.431923588 -0.156810605 FIEEHATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FIEEHATK 8 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;; 130.27 0.001055 2741630000 6748980 5524300 6001580 6680540 6098180 6334520 8340340 7236590 6928110 FALSE TRUE 6429969.091 6087232.451 6276758.379 6008999.427 7161700.661 6115153.984 7067867.952 6602915.816 8002485.915 0.803496458 0.760667687 0.784351069 0.750891597 0.894934491 0.764156794 0.883209046 0.825108083 1 22.9320168 -0.093104621 0.300006442 1.060897782 0.767085645 0.679471202 0.043917777 3.164277525 0.405124903 0.26528127 0.047555518 0.807040592 0.093104621 -0.293812137 FIGEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FIGEGAR 7 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 92.692 0.036019 411200000 73039 63604 51797 67244 72037 59079 80099 65605 83029 FALSE TRUE 69586.59122 70085.31991 54171.94368 60484.50536 84600.22999 57033.07942 67878.42643 59860.27841 95904.71327 0.725580515 0.730780767 0.564851735 0.630672918 0.88212797 0.594684844 0.707769453 0.624164093 1 16.5493141 -1.279537274 3.287497594 1.001323211 0.687902881 0.55185626 0.089780766 27078295.93 38975135.36 360131.087 0.019784126 0.052536692 1.279537274 -0.31342033 FIGPDQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIGPDQHR 8 0 Q96EY7-2;Q96EY7 Q96EY7-2 PTCD3 "Pentatricopeptide repeat domain-containing protein 3, mitochondrial" 0 ; 167.24 0.00031378 190374000 260700 208609 206976 210410 258400 187890 225420 228040 236210 FALSE TRUE 248377.2277 229866.4943 216466.0543 189259.187 303464.8782 181383.3222 191028.0389 208071.6087 272840.2404 0.910339425 0.842494838 0.793380236 0.693663027 1.112243845 0.664796813 0.700146132 0.762613346 1 18.05769691 FIHQQPQSS(ph)SPVYGSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.171)S(0.699)S(0.13)PVYGSSAK;FIHQQPQS(0.047)S(0.888)S(0.066)PVYGSSAK 174.01 4.45E-12 2141400000 1781470 1645030 1808980 1883250 1474960 1877530 2095740 1981030 1217360 TRUE FALSE 1697263.444 1812660.427 1891923.522 1693942.132 1732192.557 1812510.665 1775996.372 1807560.511 1406141.971 1.207035618 1.289102 1.345471198 1.204673615 1.231876007 1.288995494 1.26302778 1.285475114 1 20.42331083 -1.13524097 4.366052872 0.99995962 1.263928645 0.793763533 0.042363036 1.75E-05 3.46E-06 0.039249109 0.009249555 0.073241804 1.13524097 0.263969026 FIHQQPQSSS(ph)PVYGSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.007)S(0.329)S(0.663)PVYGSSAK;FIHQQPQSS(0.007)S(0.993)PVYGSSAK 219.69 4.63E-19 1838210000 2228740 1955530 2149220 2360100 1704280 2250280 2551600 2387900 1993610 TRUE FALSE 2123391.877 2154800.73 2247763.863 2122858.264 2001505.892 2172352.239 2162306.557 2178802.817 2302768.857 0.922103784 0.935743387 0.976113541 0.921872058 0.869173598 0.943365303 0.939002866 0.946166529 1 21.13493818 0.701518605 1.228949946 0.999798775 0.928759821 0.418980606 0.026200402 1.020948831 2.549045011 0.024729338 0.007528878 5.029428107 -0.701518605 -0.071038954 FIHQQPQSSSPVY(ph)GSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQSSS(0.001)PVY(0.999)GSSAK;FIHQQPQSSSPVY(0.948)GS(0.024)S(0.028)AK 167.28 2.22E-10 0 181462 163622 154162 188985 124342 166057 196541 208224 141328 TRUE FALSE 172884.6509 180295.2678 161230.4802 169987.8688 146027.2054 160306.4045 166555.0607 189990.8027 163244.4244 1.05905394 1.104449775 0.987663014 1.04130888 0.894531044 0.982002326 1.020280241 1.163842522 1 17.31667419 3.737810343 24.99631116 1.008785695 1.081751859 0.152212707 0.067129828 107.2741175 3574024.765 0.017102665 0.028392427 5467.771324 -3.737810343 0.072966164 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGSVS(0.019)EDNS(0.981)EDEISNLVK 154.6 2.54E-08 33650000 49861 40503 51566 54134 37373 52083 55985 60279 49722 TRUE FALSE 47504.16934 44630.30175 53930.35211 48692.34747 43890.83937 50279.35265 47443.46001 55000.6512 57432.63382 0.827128519 0.777089588 0.939019309 0.847816724 0.764214288 0.875449188 0.826071466 0.957655039 1 15.8095831 1.147686657 3.560971106 0.998799937 0.832380951 0.598089316 0.048847995 0.145460782 3.257069934 0.044384716 0.011762216 14.05033427 -1.147686657 -0.166418986 FIIHAPPGEFNEVFNDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FIIHAPPGEFNEVFNDVR 18 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ;;;;; 201.12 1.44E-15 1456697000 1457223 1270597 1345730 1544436 1595994 1294247 1663750 1471179 1468426 FALSE TRUE 1388342.957 1400072.279 1407433.052 1389186.359 1874334.848 1249426.902 1409914.381 1342354.768 1696142.004 0.818529907 0.825445202 0.829784917 0.819027154 1.105057739 0.736628713 0.831247842 0.791416499 1 20.69382553 -2.534272771 2.049520463 2.963031978 0.842270606 0.202208512 0.096877819 3090304.065 159069.0704 28335160.01 0.022019785 0.002922316 2.534272771 -2.120761372 FIILFS(ph)LDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIILFSLDLK 10 0 Q5T6F7;F1DAM0;Q13285 Q5T6F7 NR5A1 Steroidogenic factor 1 1 FIILFS(1)LDLK;FIILFS(1)LDLK 63.816 0.049034 1055160000 1579640 1469960 1734610 1366300 1279160 1867480 2083430 1899370 948040 TRUE FALSE 1504973.548 1619750.595 1814143.584 1228956.928 1502245.099 1802808.699 1765564.489 1733051.094 1095057.201 1.374333273 1.479147019 1.65666559 1.122276468 1.371841669 1.646314637 1.612303436 1.582612389 1 20.0625748 2.268643285 24.98224543 1.526972117 1.408083694 0 0.22442541 588.1922771 488464.0745 0.071171554 0.059539218 185.6279143 -2.268643285 -0.118888423 FIKDNWEELYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIKDNWEELYNR 12 1 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 176.25 2.33E-05 642880000 982770 996500 903440 1004980 853170 987670 1109640 1088670 952290 FALSE TRUE 936316.4098 1098044.483 944863.6176 903957.5011 1001962.578 953466.7402 940344.0381 993340.2834 1099966.27 0.851222838 0.998252868 0.858993265 0.821804746 0.910903003 0.866814526 0.854884431 0.903064313 1 20.06902785 0.965866104 21.97003766 1.000000001 0.885824394 0.374989185 0.047846336 1188.780378 765152.2602 0.047317536 0.011829384 9.244131278 -0.965866104 -0.114175608 FIKIDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIKIDGK 7 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ; 60.973 0.085988 427550000 1761700 882120 2048650 1399670 1520570 1760070 2536100 2136900 2136900 FALSE TRUE 1678427.932 972009.0309 2142582.629 1258972.512 1785756.927 1699118.335 2149171.366 1949781.708 2468279.538 0.679999127 0.393800222 0.868046992 0.51006075 0.72348245 0.688381647 0.870716356 0.789935531 1 21.23507436 1.671635183 0.473004109 1.000748198 0.557390819 0.476734662 0.127772248 0.6688444 0.37539405 0.123158535 0.085780455 46.94995531 -1.671635183 -0.443357379 FILAPAKQEDEWDKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FILAPAKQEDEWDKPR 16 2 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 173.03 2.45E-09 544000000 1676980 1102980 1422900 1527310 1032640 1689740 1981710 1846690 1282580 FALSE TRUE 1597712.479 1215374.916 1488141.372 1373781.897 1212732.089 1631223.88 1679363.743 1684984.034 1481475.956 1.078459946 0.820381128 1.004499173 0.927306239 0.818597213 1.101080226 1.133574754 1.137368465 1 20.49860378 2.170177676 10.77966017 1.107563982 0.931766908 0.472002079 0.085122722 0.379175725 57.74113941 0.029952554 0.022124954 147.9713636 -2.170177676 -0.175797074 FILTADRDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FILTADRDEK 10 1 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 0 80.688 0.02121 126210000 85687 97510 77035 99099 61310 90466 84466 98532 62906 FALSE TRUE 81636.74533 107446.3799 80567.13095 89137.38024 72002.44459 87333.13974 71579.16038 89904.01573 72661.1412 1.123526881 1.478732347 1.108806298 1.226754477 0.990934678 1.201923591 0.985109223 1.237305308 1 16.1488964 3.619480168 11.98099538 1.104932526 1.301084686 0.289792652 0.126148841 0.59243673 56.40987901 0.030512412 0.047273446 4163.707067 -3.619480168 0.196152161 FINDQYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FINDQYEK 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9 Q9UHD8 9-Sep Septin-9 0 110.87 0.012285 0 82029 66506 76483 80246 62206 75718 83823 82367 73845 FALSE TRUE 78151.65174 73283.03701 79989.8212 72179.51962 73054.7067 73095.86667 71034.26183 75154.50883 85296.50545 0.916235095 0.859156382 0.937785444 0.846218954 0.856479481 0.856962032 0.83279217 0.881097161 1 16.38019902 0.952195932 22.45176007 1 0.871053899 0.610704846 0.031846366 2529.56837 1188044.586 0.030629435 0.007657359 8.957688005 -0.952195932 -0.128946101 FINYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FINYVK 6 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 113.82 0.060051 979070000 1854990 1587920 1579860 1689780 1562360 1708970 2087570 1965140 1760800 FALSE TRUE 1767308.299 1749730.853 1652298.144 1519920.104 1834835.089 1649787.94 1769072.856 1793061.924 2033855.871 0.868944709 0.860302285 0.81239687 0.747309643 0.902146074 0.811162661 0.869812301 0.881607172 1 20.95578602 0.68315079 1.082674788 0.999929543 0.837505682 0.6046885 0.04157338 0.72864852 1.434868839 0.038259801 0.01204582 4.821151617 -0.68315079 -0.162423861 FIPHENGVHTIDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FIPHENGVHTIDVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 220.85 2.59E-12 2423760000 2877020 2519870 2630310 2969520 2432300 2711090 3116540 2739450 473733.2 FALSE TRUE 2741028.966 2776647.618 2750912.315 2671018.208 2856492.35 2617204.274 2641054.584 2499569.235 547197.3252 5.009214849 5.074307732 5.027276613 4.881270586 5.220223526 4.782925927 4.826512233 4.567948563 1 19.06170165 -0.470934182 0.625763219 0.553437546 5.043802407 0.993004813 0.104206462 0.699128884 0.217379376 0.798664053 0.035394638 0.338116074 0.470934182 4.490364861 FIQELSGSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIQELSGSSPK 11 0 Q01664;I3L254 Q01664 TFAP4 Transcription factor AP-4 1 FIQELSGS(0.029)S(0.971)PK;FIQELSGS(0.003)S(0.997)PK 197.25 6.05E-08 111094000 770680 711970 654000 782120 448110 784010 839620 846300 516070 TRUE FALSE 734251.4837 784520.5524 683986.5469 703499.8117 526260.2421 756859.5371 711520.5483 772193.4855 596099.4999 1.231759939 1.316089936 1.147436874 1.180171786 0.882839597 1.269686583 1.193627152 1.29541039 1 19.18519364 3.725829399 23.24127428 1.148427918 1.273924932 0.170520828 0.122693348 478.6794402 873847.0212 0.031183144 0.048741351 5318.992759 -3.725829399 0.125497015 FIQELSGSS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIQELSGSSPKR 12 1 Q01664;I3L254 Q01664 TFAP4 Transcription factor AP-4 1 FIQELSGS(0.009)S(0.991)PKR;FIQELSGS(0.042)S(0.958)PKR 150.76 4.19E-05 232560000 247629 226559 238123 264578 174581 237133 282470 285848 200015 TRUE FALSE 235924.0679 249645.6197 249041.1751 237982.1168 205027.8711 228921.0248 239374.0136 260817.6337 231032.3047 1.021173503 1.080565854 1.077949577 1.03008156 0.887442435 0.990861538 1.036106245 1.128922789 1 17.81773507 -1.543163924 5.762549443 0.999927802 1.03098296 0.023647693 0.063764701 5.96E-05 4.72E-06 0.062182463 0.01462248 0.028630971 1.543163924 0.031055158 FIQENIFGICPHMTEDNKDLIQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIQENIFGICPHMTEDNKDLIQGK 24 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 320.06 4.56E-74 975240000 2045400 1437680 1818300 1982150 1309680 1996360 2465400 2327200 1368070 FALSE TRUE 1948717.996 1584181.227 1901670.854 1782900.516 1538087.777 1927225.553 2089257.95 2123418.031 1580223.308 1.233191528 1.002504657 1.203419063 1.128258586 0.973335711 1.219590638 1.322128296 1.343745545 1 20.59169702 2.017232962 24.69376371 1.261027375 1.109192869 0.152204717 0.121640726 257.9368784 369605.7588 0.041290087 0.030487965 104.0478145 -2.017232962 -0.151834506 FIQENVFVAANHNGS(ph)PLSIK ddPTM_SK-BR-3_Trastuzumab_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 195.3 3.85E-19 515430000 694130 774950 764790 897230 613390 780990 876350 893750 674750 TRUE FALSE 661319.8505 853918.286 799856.378 807038.7358 720365.0218 753944.1205 742646.7122 815488.5119 779386.7839 0.848513042 1.095628389 1.026263717 1.035479113 0.924271538 0.967355537 0.952860284 1.046320683 1 19.57197994 4.717755004 4.216962653 1.000517549 0.839641106 0.494743485 0.0497141 0.180530101 6.545030305 0.012279045 0.082426448 52210.15763 -4.717755004 -0.160876444 FISADVHGIWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FISADVHGIWSR 12 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 91.858 0.0080615 91055000 294300 192270 186810 201920 343010 208420 308110 266480 327860 FALSE TRUE 280389.0222 211862.5316 195375.4233 181622.618 402830.8354 201202.3631 261102.1607 243145.5985 378702.8543 0.740393211 0.559442658 0.51590692 0.479591363 1.063712171 0.531293495 0.689464465 0.642048497 1 18.53070677 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 369.1 9.04E-127 2174661000 1699981 1367973 1488655 1795372 1211478 1661777 2055482 1917529 1117857 FALSE TRUE 1619626.267 1507371.004 1556911.304 1614897.796 1422759.38 1604229.246 1741880.469 1749619.995 1291208.554 1.254349084 1.167410949 1.205778338 1.250687033 1.101881934 1.24242458 1.349031079 1.355025096 1 20.30029061 2.003363348 24.98687819 1.279031933 1.198001038 0 0.107868077 204.7817524 1521345.475 0.035999152 0.026457253 100.777446 -2.003363348 -0.081030895 FITHAPPGEFNEVFNDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;;; 247.4 2.23E-24 2064902000 1217961 1127860 1103959 1306216 1301986 1133425 1382179 1220264 1259700 FALSE TRUE 1160390.397 1242790.216 1154576.612 1174912.686 1529051.946 1094174.208 1171302.208 1113411.215 1455047.842 0.797492951 0.854123267 0.793497353 0.807473577 1.050860255 0.751985039 0.80499223 0.765205915 1 20.47263516 -2.33193994 2.232347377 1.944719065 0.828514911 0.293520138 0.083760732 3002148.64 528963.5925 14248149.1 0.020038031 0.004656505 2.33193994 -1.116204154 FITIFGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FITIFGTR 8 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 129.68 0.002513 143421000 337522 355297 309304 367621 302023 323818 342999 319107 220462 FALSE TRUE 321568.004 391502.1682 323485.8943 330667.0386 354695.7156 312604.1015 290668.2029 291164.2994 254650.121 1.262783629 1.537412064 1.270315102 1.298515144 1.392874718 1.227582772 1.141441448 1.143389598 1 17.95815688 1.658257674 0.738002301 1.009677429 1.38182809 0.677411699 0.082964963 0.335828073 0.369028217 0.073718968 0.033905266 45.52580924 -1.658257674 0.37215066 FITLLLPGGAQTAVRPGS(ph)PSTSTMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQTAVRPGS(0.906)PS(0.067)T(0.019)S(0.004)T(0.005)MR;FITLLLPGGAQT(0.004)AVRPGS(0.765)PS(0.185)T(0.033)S(0.006)T(0.008)MR 140.38 2.38E-07 242670000 384550 410090 352860 422970 354560 401080 389870 386830 329470 TRUE FALSE 366373.0836 451878.6372 369038.98 380452.252 416395.1517 387190.499 330388.171 352957.1145 380562.5249 0.96271456 1.187396571 0.969719707 0.999710237 1.094157003 1.017416255 0.868157397 0.927461564 1 18.53777398 1.91235314 5.890138823 0.921178797 1.050389377 0.326711311 0.071928652 0.22634108 12.02142892 0.030567585 0.018560381 81.72466336 -1.91235314 0.12921058 FIVDGWHEMDAENPLHQPSPSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FIVDGWHEMDAENPLHQPSPSLNK 24 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 270.58 4.02E-52 534720000 998640 682180 932730 821660 856130 795590 1145600 926450 434910 FALSE TRUE 951436.2663 751694.9176 975496.5931 739065.1757 1005438.801 768038.5188 970817.6796 845325.1266 502353.6216 1.893957215 1.49634617 1.941852415 1.471205032 2.001456261 1.528880227 1.932538431 1.682729237 1 18.93834375 0.954070541 22.78849052 0.999999998 1.744046161 0.589087577 0.195926256 2483.369069 1232157.339 0.160591497 0.040147874 8.996436965 -0.954070541 0.744046163 FIVLNSLNQNAKPEGPEQAELGRLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FIVLNSLNQNAKPEGPEQAELGRLSPR 27 2 P41182-2;P41182 P41182-2 BCL6 B-cell lymphoma 6 protein 1 FIVLNSLNQNAKPEGPEQAELGRLS(1)PR;FIVLNSLNQNAKPEGPEQAELGRLS(1)PR 138.28 3.01E-06 279730000 509400 427190 462580 517410 460590 486080 537050 464980 390380 TRUE FALSE 485321.6715 470721.1467 483789.7506 465398.9638 540916.7502 469246.9277 455113.1589 424263.8862 450918.1366 1.076296632 1.043917085 1.072899294 1.032114093 1.199589695 1.040647713 1.00930329 0.940888937 1 18.78250601 1.685492089 2.859764834 0.973374121 1.077487556 0.475885478 0.048244367 0.19650849 3.636367399 0.028541161 0.012462602 48.47212831 -1.685492089 0.104113435 FIVS(ph)PVPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;FIVS(1)PVPESR;FIVS(1)PVPESR 178.65 2.30E-06 254392000 517780 449392 468168 511801 495930 477071 536370 498501 567950 TRUE FALSE 493305.5655 495185.5557 489633.9659 460353.7911 582420.035 460549.9116 454536.9054 454849.6097 656024.7853 0.75196178 0.754827511 0.746365041 0.701732315 0.887801876 0.702031268 0.692865446 0.693342111 1 19.3233908 -1.506456248 3.393084174 1.005473979 0.741174941 0.668094193 0.057289594 6158251.551 5914738.407 226613.1229 0.012905495 0.031156148 1.506456248 -0.264299037 FIYVDVLS(ph)EDEEKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FIYVDVLSEDEEKPK 15 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 FIYVDVLS(1)EDEEKPK 204.23 3.03E-09 43094000 157450 165150 120810 164090 65616 162270 142490 189570 66653 TRUE FALSE 150007.6505 181978.9728 126349.258 147595.3614 77059.40963 156650.5492 120750.5335 172970.2458 76989.20682 1.948424418 2.363694604 1.641129493 1.917091597 1.000911853 2.034707924 1.568408592 2.246681749 1 16.23236859 3.724099954 24.20868802 1.658379979 2.156059503 0.219085695 0.41028433 653.0989197 1093357.469 0.09688833 0.15089161 5297.853615 -3.724099954 0.497679524 FKAEAPLPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 98.507 0.0033121 7059650000 15639660 12370600 13555150 16273690 7833560 13421610 13159980 12512600 5996850 TRUE FALSE 14900404.27 13631178.2 14176667.04 14637827.76 9199730.384 12956816.28 11152183.35 11416930.41 6926810.87 2.151120414 1.967886587 2.046636945 2.113213142 1.328133618 1.870531262 1.610002577 1.648223205 1 22.72375985 -0.234546784 0.116716647 1.57E-12 2.664442202 0.73522101 0.188925658 13.20380733 0.448065045 7.265720607 2.914868749 0.582710999 0.234546784 2.664442202 FKDIFQEIFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDIFQEIFDK 11 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 231.66 8.24E-13 1634360000 6976200 6177600 4816500 5067600 3637200 4615500 5299900 5457200 3091700 FALSE TRUE 6646448.851 6807104.463 5037341.289 4558195.22 4271526.528 4455664.078 4491302.916 4979338.638 3571145.046 1.86115343 1.906140573 1.410567542 1.276395991 1.196122385 1.247684992 1.257664659 1.39432551 1 21.7679553 3.622571987 2.861782755 1.244164655 1.891443742 0.875996971 0.100221719 0.070815378 1.115312052 0.025140737 0.042322736 4193.454998 -3.622571987 0.647279087 FKDIFQEIFDKHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDIFQEIFDKHYK 14 2 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 215.48 3.90E-12 481950000 1770790 680470 1640230 1046610 1291950 1262000 2218460 1554600 1235830 FALSE TRUE 1687088.266 749810.6666 1715436.168 941402.7744 1517265.671 1218296.624 1879993.182 1418470.983 1427476.205 1.181867873 0.525270169 1.201726629 0.659487543 1.06290085 0.853461949 1.317004918 0.993691508 1 20.44503527 1.762269347 25 1.133428271 0.896838509 0.125490238 0.228299298 20.50655962 21639.28617 0.094974773 0.052670175 57.84546905 -1.762269347 -0.236589762 FKDIFQEIYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 227.93 3.32E-12 1098120000 3979300 3599600 2850900 3658300 2759600 3283700 4425300 3714700 2925200 FALSE TRUE 3791206.375 3966403.332 2981616.585 3290560.734 3240873.366 3169984.646 3750139.209 3389421.175 3378825.076 1.122048727 1.17390017 0.88244183 0.973877209 0.959171692 0.938191405 1.109894453 1.003136031 1 21.68809023 3.758004206 24.99642457 0.989046536 1.147974467 0.578040211 0.059010762 579.0042934 744357.923 0.015919533 0.028649743 5728.015778 -3.758004206 0.158927931 FKDIFQEIYDKQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDIFQEIYDKQYK 14 2 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 170.45 1.78E-06 133496000 1068580 478660 1086540 737780 884820 987430 1744780 1210370 1232010 FALSE TRUE 1018070.341 527435.9982 1136358.934 663616.9527 1039132.328 953235.0515 1478581.766 1104383.586 1423063.819 0.715407368 0.370634114 0.798529847 0.46632972 0.730207819 0.669847015 1.039012971 0.776060477 1 20.44056893 2.02452892 1.919699177 0.940413646 0.584298931 0.49606108 0.14542617 0.246237623 1.703004262 0.076413078 0.040042494 105.8105373 -2.02452892 -0.356114715 FKDLEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKDLEDK 7 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 90.71 0.015448 187380000 375940 332120 324760 395250 191800 398170 394310 415210 210160 FALSE TRUE 358170.0612 365963.4056 339650.5672 355518.7191 225249.8593 384381.2731 334150.7675 378852.0112 242750.5395 1.475465563 1.507569896 1.399175334 1.464543477 0.92790673 1.583441478 1.376519155 1.560663931 1 17.88911498 -1.707647598 2.780141339 0.936087436 1.415766199 0.331934287 0.183576797 26178237.83 22714144.86 11695787.72 0.040696924 0.019604348 1.707647598 0.479678763 FKDPLKDGEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDPLKDGEAK 11 2 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 70.412 0.029155 1988620000 3613500 3114300 3052500 3716600 1979520 3924600 3811500 4105900 1919560 FALSE TRUE 3442697.016 3431650.711 3192460.144 3343000.307 2324747.661 3788690.118 3229985.672 3746365.629 2217235.561 1.552697908 1.54771589 1.439838058 1.507733488 1.048489255 1.708744973 1.456762524 1.689656117 1 21.08033062 -2.102503161 2.59395091 0.087559169 1.494570629 0.424753778 0.18065288 11101671.33 1814822.742 60509405.63 0.039888741 0.007897631 2.102503161 1.40701146 FKDPNAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 59.35 0.090452 1784900000 4640400 3978300 3660100 4908500 3090600 4470300 5006400 5182600 3348400 FALSE TRUE 4421057.488 4383693.293 3827919.205 4415088.254 3629599.661 4315492.39 4242581.731 4728784.069 3867652.771 1.143085419 1.133424729 0.989726698 1.141542045 0.938450238 1.115791061 1.096939664 1.222649589 1 21.88302685 -0.967546116 7.179596306 0.999999999 1.097695225 0.127205975 0.080427471 4.29E-09 7.47E-10 0.071997139 0.016969888 0.107759082 0.967546116 0.097695225 FKDPNCVGTVLASRPHTLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKDPNCVGTVLASRPHTLDGR 21 2 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 147.35 6.03E-08 2911300000 2286700 2015080 2081590 2482900 1895530 2256600 2625100 2487100 2118900 FALSE TRUE 2178612.223 2220418.943 2177032.96 2233314.175 2226109.832 2178453.376 2224592.782 2269316.339 2447488.19 0.890142078 0.907223558 0.889496819 0.912492319 0.909548753 0.890077176 0.908928914 0.927202161 1 21.22287047 0.74626405 1.561060494 0.999946637 0.900247383 0.932768189 0.008378261 0.190414973 0.767577545 0.007386314 0.00213456 5.57524619 -0.74626405 -0.099699253 FKDSIQTLGHVDSSGQVHCVSPLLYESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKDSIQTLGHVDSSGQVHCVSPLLYESGR 29 1 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 166.88 2.67E-12 181400000 85979 63529 75615 102030 110040 88667 117140 97281 71622 FALSE TRUE 81914.94306 70002.67733 79082.02254 91773.75056 129230.9412 85596.43956 99268.14158 88762.55992 82728.77397 0.990162662 0.846170854 0.955919189 1.109332898 1.562103909 1.034663461 1.199922794 1.072934551 1 16.33610158 3.196162634 4.048545688 1.188509852 0.918083527 0.32632665 0.158121721 0.209135112 7.239617206 0.043280457 0.054426383 1570.95098 -3.196162634 -0.270426325 FKEANNFLWPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKEANNFLWPFK 12 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 166.04 4.83E-05 1580810000 7742700 5685000 6572300 6800900 6380900 6997900 10049900 8030400 7757100 FALSE TRUE 7376717.916 6264307.963 6873646.456 6117260.611 7493726.94 6755560.968 8516603.176 7327215.604 8960031.45 0.82329152 0.69913906 0.767145349 0.682727582 0.836350517 0.753966212 0.950510411 0.817766728 1 23.09507237 1.547827565 0.781671626 0.976501772 0.745429924 0.576216969 0.065117926 0.375994663 0.472081651 0.054397612 0.023148249 35.30429678 -1.547827565 -0.231071848 FKEEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKEEGVR 7 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 76.679 0.036576 1063540000 1214120 1177680 979530 1366720 1024090 1270370 1182080 1226230 1030480 FALSE TRUE 1156730.954 1297686.931 1024442.419 1229334.709 1202690.972 1226376.768 1001731.986 1118854.801 1190281.575 0.97181287 1.09023525 0.860672332 1.032809996 1.010425597 1.030324919 0.841592449 0.939991699 1 20.18287147 1.756914408 24.9999574 0.912231199 1.00411867 0.179166964 0.069960437 9.458568612 12896.64844 0.029916319 0.016590117 57.13660185 -1.756914408 0.091887472 FKEIAEAYDVLSDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKEIAEAYDVLSDPR 15 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 72.433 0.037173 175533000 707800 613700 546160 780980 513254 612600 705650 736250 626950 FALSE TRUE 674343.6967 676236.7277 571201.9762 702474.4066 602765.3351 591385.5084 597990.1323 671780.0469 724174.204 0.931189889 0.933803944 0.788763219 0.970035114 0.832348531 0.81663432 0.825754534 0.927649788 1 19.46597726 FKFPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKFPGR 6 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 124.12 0.016864 7605100000 13923700 12299500 11283500 14852600 11666100 12549800 15512900 13883900 12687100 FALSE TRUE 13265554.3 13552833.03 11800859.64 13359588.43 13700664.15 12115197.28 13146122.19 12668152.11 14654550.67 0.905217403 0.924820783 0.805269291 0.911634122 0.934908511 0.826719123 0.897067572 0.86445176 1 23.8048454 -1.258456971 6.639685612 1.000001348 0.886936733 0.433578758 0.041612733 7.78E-07 8.69E-08 0.0377432 0.008896052 0.055149684 1.258456971 -0.113064615 FKFTIGDHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKFTIGDHSR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 153.95 9.23E-06 285760000 600570 395560 464850 501870 570840 505180 770400 593400 650800 FALSE TRUE 572182.2463 435868.0137 486163.8323 451421.0741 670394.3153 487685.4899 652861.3306 541438.7502 751722.7402 0.761161284 0.5798255 0.646732906 0.600515389 0.89181061 0.648757133 0.868486871 0.720263897 1 19.51984112 0.832466432 0.380051581 1.02153757 0.644462164 0.493785537 0.097715683 1.301241597 0.473220427 0.168026136 0.078192073 6.799334891 -0.832466432 -0.377075405 FKGDSR ddPTM_SK-BR-3_Trastuzumab_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 ; 88.591 0.046631 1037430000 5391700 4502200 4611800 5643600 4342900 4985000 6165400 5548000 5192900 FALSE TRUE 5136845.026 4960979.299 4823255.592 5076294.606 5100300.385 4812368.2 5224754.995 5062187.708 5998188.41 0.856399412 0.827079605 0.804118721 0.846304627 0.850306799 0.802303607 0.871055498 0.843952767 1 22.51609541 -0.194182775 0.681568714 1.00971459 0.833499832 0.856453862 0.020998255 2.341349478 1.014573634 0.079942223 0.007180797 0.639465657 0.194182775 -0.176214758 FKGPEFVR ddPTM_SK-BR-3_Trastuzumab_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 598100000 1059250 925610 841790 1109730 931230 978490 1178440 1090430 966710 FALSE TRUE 1009181.352 1019930.711 880386.9041 998177.8321 1093636.217 944604.6459 998647.3345 994946.1685 1116622.45 0.903780281 0.913406955 0.788437403 0.893925993 0.979414499 0.845948106 0.89434646 0.891031851 1 20.09071004 0.377569375 3.073326413 0.999999967 0.890053521 0.343137549 0.048331681 65.78255229 321.719913 0.044071668 0.011487028 2.385444821 -0.377569375 -0.109946446 FKGPGDTSNFDDYEEEEIRVS(ph)INEK ddPTM_SK-BR-3_Trastuzumab_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 228.79 2.12E-34 977223000 733095 633644 677690 816689 471488 814608 874958 881473 613301 TRUE FALSE 698443.0522 698213.044 708762.7568 734593.8701 553715.3579 786397.9207 741467.0874 804286.5511 708408.5868 0.985932505 0.985607822 1.000499952 1.036963532 0.781632759 1.110090893 1.046665867 1.135342747 1 19.43422217 FKGQILMPNIGYGSNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKGQILMPNIGYGSNKK 17 2 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 136.2 6.24E-06 867680000 1778840 1460750 1640310 1872520 1233820 1821090 2167950 2004170 1533750 FALSE TRUE 1694757.759 1609602.086 1715519.836 1684290.732 1448997.817 1758025.197 1837189.41 1828674.25 1771596.117 0.95662761 0.908560405 0.968347029 0.950719363 0.81790528 0.992339721 1.03702497 1.03221848 1 20.75661831 2.01334609 24.9941755 1.024066882 0.923946943 0.563059529 0.042231257 158.080527 296047.5215 0.014975161 0.011054536 103.1207564 -2.01334609 -0.100119939 FKGTESISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKGTESISK 9 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 114.89 0.0020101 0 685120 581700 590520 775960 571480 714140 894900 821980 682390 FALSE TRUE 652735.7354 640975.8913 617595.9261 697959.0266 671145.9311 689409.1527 758366.569 750003.0736 788211.556 0.828122514 0.81320286 0.783540816 0.885497074 0.851479436 0.874649892 0.962135816 0.951525092 1 19.58822338 1.884897642 0.780673301 0.998773281 0.814987267 0.869064868 0.025153934 0.193111849 0.222350194 0.02093991 0.0102421 76.71806528 -1.884897642 -0.183786014 FKIDSNIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKIDSNISPK 10 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 FKIDS(0.003)NIS(0.997)PK;FKIDS(0.253)NIS(0.747)PK 101.43 0.0020218 4765100000 9882000 9013000 9147000 10957100 5541600 11289300 11218500 12422800 6193700 TRUE FALSE 9414897.444 9931434.947 9566398.998 9855671.491 6508053.285 10898348.71 9506911.783 11334993.77 7154187.363 1.315998165 1.388198889 1.337174792 1.377608803 0.90968449 1.523352431 1.328859771 1.584385927 1 22.77035647 FKIPEMHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKIPEMHLK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 102.53 0.0021447 300010000 1178240 874480 709770 811610 820470 807010 1187340 1003030 753970 FALSE TRUE 1122546.93 963590.5062 742313.6566 730025.4208 963559.7082 779063.0413 1006189.476 915199.3758 870891.8169 1.288962542 1.106441107 0.852360353 0.838250408 1.106405744 0.89455777 1.1553553 1.050876077 1 19.73213399 4.17533026 2.710954492 0.99470173 1.259003974 0.450057195 0.105572557 0.237018593 3.427796001 0.027680552 0.080757925 14973.73904 -4.17533026 0.264302244 FKIPGS(ph)PPESMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 1 FKIPGS(0.988)PPES(0.012)MGR;FKIPGS(0.962)PPES(0.038)MGR;FKIPGS(0.982)PPES(0.018)MGR;FKIPGS(0.987)PPES(0.013)MGR 84.94 0.0057615 875760000 1765670 1535610 1684400 1879980 1357210 1854600 2140190 1954070 1604820 TRUE FALSE 1682210.278 1692090.405 1761631.406 1691000.839 1593906.994 1790374.737 1813664.708 1782961.272 1853687.289 0.9074941 0.912824086 0.950339044 0.912236302 0.859857541 0.965845074 0.978409206 0.961845766 1 20.82196646 2.071952007 9.990651459 0.976301894 0.91113366 0.675916497 0.023473961 0.224439563 29.4870924 0.008492161 0.006269446 118.0190207 -2.071952007 -0.065168234 FKIPGSPPESMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 164.88 3.31E-05 4934680000 4299770 3364450 3855360 4273830 3569520 4118120 4623390 4323230 4347990 FALSE TRUE 4096528.393 3707291.28 4032132.069 3844216.489 4192043.158 3975508.472 3918006.941 3944665.062 5022254.083 0.815675258 0.738172784 0.802853062 0.76543648 0.834693564 0.791578524 0.780129176 0.785437176 1 22.25990359 -1.442191077 2.637308153 1.007192521 0.78690196 0.862794252 0.026397735 1833377.584 1894773.115 97702.77295 0.006017725 0.036125089 1.442191077 -0.220290561 FKKYEEIDNAPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKKYEEIDNAPEER 14 2 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 53.828 0.08184 290250000 416260 450640 443210 408620 256140 564090 452010 452990 228210 FALSE TRUE 396584.2147 496560.7283 463531.6169 367544.7413 300810.7349 544555.4219 383047.5728 413323.7941 263599.6413 1.504494516 1.883768604 1.758468315 1.394329444 1.141165191 2.065842803 1.45314148 1.567998318 1 18.00798888 -2.626175071 0.301470698 1.98E-13 1.657799562 0.342753286 0.259620302 60.24103632 2.016542545 39.54567282 0.252691225 0.002364966 2.626175071 1.657799562 FKLDLDFPNLPYLLDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKLDLDFPNLPYLLDGK 17 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 154.19 1.34E-07 1875830000 4645800 4386000 3898800 4996600 2962100 4637100 5159200 5124600 3059600 FALSE TRUE 4426202.241 4832938.386 4077563.836 4494332.275 3478689.302 4476516.064 4372069.285 4675862.857 3534067.142 1.252438639 1.36752874 1.15378788 1.27171672 0.984330281 1.266675444 1.237121172 1.323082632 1 21.75289802 -2.310297716 2.007108947 3.22E-05 1.238337765 0.327534835 0.104167614 2476706.673 327770.7971 11214387.39 0.024598737 0.004894432 2.310297716 1.238305581 FKLLEQALVIEEQLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKLLEQALVIEEQLRR 16 2 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 ; 132.59 2.15E-05 58078000 83159 40233 85305 69174 89759 77468 128782 86888 111429 FALSE TRUE 79228.23888 44332.78844 89216.31863 62220.4981 105412.9412 74785.26374 109133.9407 79279.6261 128708.8402 0.61556175 0.344442451 0.693163877 0.483420548 0.819003116 0.581042169 0.847913325 0.615961001 1 16.97375162 1.385998826 0.239684854 1.074809158 0.405726905 0.485720477 0.134756504 1.548537031 0.390181183 0.415372298 0.357013816 24.32197435 -1.385998826 -0.669082253 FKLPPGEYILVPSTFEPNKDGDFCIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKLPPGEYILVPSTFEPNKDGDFCIR 26 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 150.18 7.93E-08 408780000 1064130 794950 945820 1079150 736520 1088940 1240960 1162660 873750 FALSE TRUE 1013830.684 875956.3088 989186.7825 970671.7917 864968.8548 1051229.735 1051628.76 1060851.327 1009246.688 1.004541998 0.867930824 0.980123883 0.961778526 0.857044036 1.0415984 1.041993769 1.051131839 1 19.94484742 2.206966493 24.99815774 1.037854066 0.934956207 0.524927173 0.046909891 145.1224326 114824.1047 0.016436865 0.012140523 161.0521375 -2.206966493 -0.102897859 FKMPDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKMPDLHLK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 101.32 0.0024408 732310000 5530300 4420700 4216200 4867800 3999300 4608200 6022700 5435400 3820300 FALSE TRUE 5268893.679 4871174.356 4409516.94 4378479.496 4696776.654 4448616.879 5103826.501 4959447.561 4412732.613 1.194020608 1.103890669 0.999271274 0.992237663 1.064369194 1.008131983 1.156613588 1.123894873 1 22.0732409 4.223459633 2.499334281 1.057461156 1.182753991 0.3919202 0.056188515 0.30772118 3.750392487 0.015379597 0.050775268 16728.60141 -4.223459633 0.125292835 FKMPDMHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKMPDMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 101.32 0.0024408 441510000 3242600 2238000 2161130 2550200 2352500 2279400 3389600 2946700 2172000 FALSE TRUE 3089328.724 2466054.744 2260219.948 2293849.051 2762775.255 2200463.806 2872454.266 2688671.327 2508822.667 1.231385847 0.982952991 0.900908613 0.914312949 1.10122381 0.877090213 1.144941133 1.071686477 1 21.25857907 4.555349459 2.759330759 1.002860723 1.236363411 0.405565499 0.087866167 0.315136372 4.143505706 0.021667199 0.137536986 35921.08611 -4.555349459 0.233502688 FKMPEMHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKMPEMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 111.06 0.0013138 1592160000 6084600 4433400 3822300 4365400 4588400 4272800 6765600 5443600 4134200 FALSE TRUE 5796993.017 4885168.5 3997556.236 3926581.698 5388615.507 4124831.865 5733383.461 4966929.526 4775310.621 1.213950982 1.023005389 0.837130095 0.822267285 1.128432459 0.863782943 1.200630475 1.040127003 1 22.18716315 -0.03969457 7.790503202 1.000000005 1.026943844 0 0.141488592 0 0 0.136267206 0.032118489 0.912652462 0.03969457 0.02694384 FKMPEMNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKMPEMNIK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 96.143 0.0069018 2571100000 6086500 5092200 4162900 4984200 4655500 4706000 7084000 5887400 5079600 FALSE TRUE 5798803.207 5611100.969 4353773.083 4483178.747 5467417.726 4543030.04 6003205.693 5371868.045 5867318.425 0.988322567 0.956331421 0.742037975 0.764093308 0.93184268 0.7742941 1.02316003 0.915557612 1 22.48426986 1.689399253 11.34580723 0.97614698 0.875242738 0.28227062 0.08777985 0.197272522 37.21117162 0.044532307 0.024255969 48.91017904 -1.689399253 -0.100904242 FKMPFLSISS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKMPFLSISSPK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKMPFLSIS(0.013)S(0.987)PK;FKMPFLSIS(0.075)S(0.925)PK 197.88 1.15E-07 426080000 2447500 2206000 2382500 2639300 1638330 2641600 3181800 3186400 2036650 TRUE FALSE 2331811.525 2430793.908 2491739.982 2373992.55 1924054.233 2550120.73 2696357.972 2907381.924 2352483.28 0.991212794 1.033288495 1.059195618 1.009143219 0.817882214 1.084012265 1.146175191 1.235877827 1 21.16575304 2.009944807 24.99863303 1.136467982 0.991028803 0.384909715 0.085205999 199.8648122 502405.835 0.030374591 0.022408227 102.3162953 -2.009944807 -0.14543918 FKNELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 117.04 0.0048531 1062190000 3045070 3090890 2651480 3312290 2270390 2991610 3290630 3224700 2554200 FALSE TRUE 2901135.576 3405855.205 2773052.981 2979332.316 2666345.297 2888009.796 2788583.957 2942328.173 2950292.291 0.983338358 1.154412807 0.93992483 1.009843101 0.903756318 0.978889381 0.945189046 0.997300566 1 21.49242646 3.715203253 24.92709135 0.964215989 1.068875598 0.397646827 0.051546014 576.3103961 615041.4059 0.012565384 0.019481752 5190.428979 -3.715203253 0.104659609 FKNWDDVLTVDYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKNWDDVLTVDYTR 14 1 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 140.49 9.06E-06 154870000 256400 180040 213770 237420 205430 240180 267980 267180 287660 FALSE TRUE 244280.4801 198386.2807 223571.5659 213554.0905 241256.927 231862.5064 227094.7292 243784.3028 332268.8436 0.735189245 0.597065552 0.672863467 0.642714761 0.726089525 0.697815973 0.683466818 0.733695944 1 18.34199149 -0.676535977 0.454834421 1.084134928 0.663344807 0.869599743 0.038814608 3.528524506 0.586916681 0.467582577 0.020168837 0.210602743 0.676535977 -0.420790121 FKPES(ph)SSPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKPESSSPVKK 11 2 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 FKPES(0.454)S(0.092)S(0.454)PVKK 69.03 0.02902 311880000 1294000 1140100 1222200 1463100 604840 1369300 1344100 1510100 621830 TRUE FALSE 1232835.184 1256277.486 1278239.079 1316026.408 710323.9045 1321880.798 1139032.859 1377867.638 718260.2205 1.716418575 1.749056192 1.779632287 1.832241812 0.98895064 1.840392604 1.585821999 1.918340455 1 19.45414709 -1.614567429 2.974812253 0.951968288 1.673292724 0.400675377 0.259939916 21969789.22 23847202.99 8237831.789 0.057132087 0.024290283 1.614567429 0.721324437 FKPESSS(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKPESSSPVKK 11 2 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 FKPES(0.096)S(0.096)S(0.807)PVKK 63.76 0.037879 238940000 1294700 1186200 1155300 1370500 587450 1414400 1367000 1481200 604380 TRUE FALSE 1233502.097 1307075.129 1208271.648 1232734.736 689901.094 1365418.973 1158439.043 1351498.276 698104.1637 1.766931299 1.872321061 1.730789917 1.765832093 0.988249505 1.955895759 1.659407154 1.935955042 1 19.41308279 2.96849645 24.98576006 1.572748316 1.797348716 0.133226262 0.327767954 1507.303585 1195456.864 0.092349132 0.098045987 930.0289115 -2.96849645 0.2246004 FKPGYLEATLNWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FKPGYLEATLNWFR 14 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 165.86 3.55E-06 84577000 922410 735530 768450 720280 367340 936280 977760 690320 232910 FALSE TRUE 878809.5073 810481.3432 803684.1926 647876.086 431403.9797 903856.3888 828584.7542 629871.9212 269028.4933 3.266603833 3.012622691 2.987357149 2.408206202 1.603562413 3.359705055 3.079914488 2.34128331 1 18.03739945 3.335132178 4.456701301 2.488026805 3.117908043 0.200239681 0.680801945 0.401673551 14.08806403 0.186287016 0.253798966 2163.37685 -3.335132178 0.629881238 FKPNQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKPNQTR 7 1 Q9NZJ9;A0A024RBG1;Q9NZJ9-2 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ; 92.925 0.013965 615840000 620750 503910 508480 638270 568770 532970 649540 646510 587200 FALSE TRUE 591408.3777 555259.0019 531794.311 574109.887 667963.3079 514513.1153 550440.7434 589898.157 678259.977 0.871949397 0.81865217 0.784056747 0.846445178 0.984818994 0.758578027 0.811548318 0.869722786 1 19.37147884 0.907010779 6.526683252 0.999998347 0.837571008 0.406137457 0.060629087 1.370525394 95.70338064 0.055969285 0.014051363 8.072550654 -0.907010779 -0.162427339 FKRPQFS(ph)PTGDCQAEAAAAANGTGGEEDDGPAAELLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FKRPQFSPTGDCQAEAAAAANGTGGEEDDGPAAELLEK 38 2 Q7Z4Q2 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 1 FKRPQFS(0.487)PT(0.487)GDCQAEAAAAANGT(0.027)GGEEDDGPAAELLEK;FKRPQFS(0.966)PT(0.034)GDCQAEAAAAANGTGGEEDDGPAAELLEK;FKRPQFS(0.499)PT(0.499)GDCQAEAAAAANGT(0.003)GGEEDDGPAAELLEK;FKRPQFS(0.5)PT(0.5)GDCQAEAAAAANGT(0.001)GGEEDDGPAAELLEK 263.46 7.31E-63 620730000 191147 156945 188245 191614 136093 204275 221311 220821 150256 TRUE FALSE 182111.8601 172937.8739 196876.2194 172352.5967 159827.5761 197200.9055 187545.9423 201484.7426 173556.9331 1.049291762 0.996433106 1.134361019 0.993060857 0.920894218 1.136231795 1.080601846 1.160914399 1 17.40504947 2.195364459 24.99996275 1.100204621 1.022609842 0.235861745 0.067093323 191.9973046 111118.1492 0.023383934 0.017270269 156.8066436 -2.195364459 -0.077594779 FKTIEEVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FKTIEEVVGR 10 1 P05091;P05091-2 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 164.9 5.49E-06 542900000 1031490 569670 1091320 813260 1243230 955100 1547330 1210020 1712200 FALSE TRUE 982733.5119 627720.0207 1141358.101 731509.5597 1460048.918 922024.6475 1311256.39 1104064.234 1977719.231 0.49690244 0.317395923 0.577108259 0.369875333 0.738248835 0.466206038 0.663014431 0.558251251 1 20.9154062 -5 0.127102753 2.691499067 0.289489454 0.662092186 0.113259912 75.35376985 0.609146454 32.22705876 0.797517116 1.00E-05 5 -2.402009613 FKYDDAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 164.46 0.00030095 3837509000 9439490 7872970 7516570 9495900 6889330 8424580 10024100 9310000 7222310 FALSE TRUE 8993304.015 8675234.594 7861212.169 8541354.091 8090826.971 8132834.682 8494739.44 8494767.045 8342308.948 1.078035358 1.039908093 0.942330501 1.023859718 0.969854631 0.974890133 1.018271979 1.018275288 1 22.99201531 3.965387118 7.52502332 0.993722382 1.064000182 0.555342333 0.025642462 0.146722137 27.82770017 0.006215054 0.011512693 9233.941477 -3.965387118 0.0702778 FKYDDAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 143.89 5.67E-05 3960270000 7573080 5417340 6587810 6662490 6108450 7022840 9334250 8010790 7552800 FALSE TRUE 7215115.517 5969373.105 6889867.605 5992763.847 7173761.746 6779637.29 7910138.727 7309322.76 8724049.65 0.82703742 0.684243367 0.789755662 0.686924546 0.822297217 0.777120439 0.906704919 0.837835988 1 23.05656655 1.327238179 0.672705256 0.990964903 0.746054147 0.656480068 0.054886446 0.357139322 0.376139339 0.047915498 0.021178161 21.24409225 -1.327238179 -0.244910756 FLAAGTHLGGTNLDFQMEQYIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLAAGTHLGGTNLDFQMEQYIYK 23 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 312.15 3.30E-73 1348940000 1184620 1236980 1084500 1417820 954810 1140050 1368860 1259430 975790 FALSE TRUE 1128625.36 1363029.668 1134225.398 1275298.04 1121328.562 1100569.783 1160015.266 1149147.633 1127110.53 1.001343995 1.209313224 1.006312485 1.13147558 0.994870097 0.976452401 1.029193886 1.019551856 1 20.10419757 2.727254318 24.78032459 1.005437109 1.093459778 0.317003282 0.060269893 724.6044945 1588132.401 0.018230256 0.017332566 533.647302 -2.727254318 0.088022669 FLASSGHDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLASSGHDQR 10 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 136.02 0.0046577 0 201640 147330 170070 181320 226280 149300 249120 195070 227510 FALSE TRUE 192108.8768 162343.0945 177867.8777 163093.3691 265743.1604 144129.7036 211112.1686 177988.6367 262791.0888 0.731032691 0.617764838 0.676841359 0.620619861 1.01123353 0.548457348 0.803345994 0.677300884 1 18.00355683 -5 0.219502814 2.478327357 0.670353535 0.338111012 0.126904642 162.5632944 1.625447685 106.2086509 0.215909057 1.00E-05 5 -1.807973823 FLCADYAEQDELDYHR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 215 1.65E-14 457359000 779960 651780 696920 778300 781940 691460 861620 782850 748640 FALSE TRUE 743092.8365 718197.123 728874.4713 700063.8053 918310.0884 667514.5668 730164.0443 714299.5039 864735.2677 0.85932986 0.830539877 0.842887411 0.809570086 1.06195517 0.771929389 0.844378704 0.82603258 1 19.721899 -2.261560906 2.275628733 1.57608304 0.853705613 0.256178272 0.077129963 3984523.589 709642.8495 11815459.75 0.017027049 0.005475693 2.261560906 -0.722377427 FLDAGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FLDAGHK 7 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 134.44 0.0031745 3021950000 9046350 8545810 7005400 9403030 6159330 8052130 8558440 8677690 5721030 FALSE TRUE 8618746.964 9416637.755 7326604.519 8457819.56 7233515.202 7773282.719 7252692.791 7917825.46 6608218.113 1.304246745 1.424988945 1.108711062 1.279894128 1.09462416 1.17630541 1.097526242 1.19817859 1 22.65582988 4.349090696 0.220888818 1.004538803 1.636424079 0.522128285 0.085255378 6.560814298 0.334946052 0.147242013 1.143861471 22340.38719 -4.349090696 0.631885276 FLDAGHKLNFAVASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLDAGHKLNFAVASR 15 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 163.7 9.15E-07 194680000 405180 210420 318630 268300 467040 315080 616620 403760 584490 FALSE TRUE 386027.9444 231862.0372 333239.5007 241329.9743 548491.6281 304168.7006 522543.294 368404.6339 675129.724 0.571783363 0.343433312 0.493593289 0.35745719 0.812424055 0.450533712 0.773989465 0.545679772 1 19.36480521 0.518280453 0.302561554 1.091206204 0.41337186 0.533466002 0.14348552 2.237115064 0.445759033 0.477926319 0.171582675 3.298226319 -0.518280453 -0.677834344 FLDFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLDFWR 6 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 127.54 0.039587 323690000 646330 490510 452330 514100 724560 391700 762900 544550 703330 FALSE TRUE 615779.2618 540493.5267 473069.7779 462421.6913 850923.0346 378135.3308 646505.5934 496866.3152 812398.8243 0.757976555 0.665305649 0.582312238 0.569205269 1.047420318 0.465455291 0.795798288 0.611603932 1 19.63182863 -1.853995662 2.507310843 1.132897372 0.691214419 0.277065056 0.158814991 24852551.42 15582542.87 19765864.89 0.035405581 0.013996013 1.853995662 -0.441682953 FLDGIYVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLDGIYVSEK 10 0 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 131.44 0.00058181 94245000 363820 325240 302371 341610 327620 304700 408790 363480 361380 FALSE TRUE 346622.9496 358382.3258 316235.0094 307270.7138 384756.8243 294148.1626 346421.5776 331651.7643 417420.9647 0.830391808 0.858563312 0.757592541 0.736117109 0.921747724 0.704679897 0.829909388 0.794525892 1 18.67114354 -1.440902336 4.018157853 1.001088906 0.807897424 0.492290906 0.062392216 0.000555498 7.73E-05 0.055137774 0.012924172 0.036232447 1.440902336 -0.193191483 FLDNFSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLDNFSSGR 9 0 Q9HAB8;Q5VVM3 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 72.243 0.091083 0 57716 53717 54555 57405 55268 48662 70413 54529 64988 FALSE TRUE 54987.87906 59190.82337 57056.40071 51634.54034 64906.7217 46976.82274 59670.20363 49754.15168 75066.00713 0.732527027 0.788517008 0.760083064 0.68785516 0.864661971 0.625806867 0.794903125 0.662805357 1 16.19587213 -1.044038934 5.077212435 1.000003572 0.745018115 0.580831513 0.069375118 2.37E-06 4.46E-07 0.056702568 0.013364736 0.090356847 1.044038934 -0.254985457 FLDSTGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLDSTGSR 8 0 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 146.27 0.0012937 156120000 124030 101810 129370 133410 139290 113450 137140 136890 158630 FALSE TRUE 118167.3477 112184.5547 135301.7425 119999.3733 163582.1319 109521.1981 116216.7743 124903.1859 183229.5302 0.644914319 0.612262415 0.738427601 0.654912847 0.89277166 0.597726785 0.6342688 0.681676069 1 17.48329251 -1.10136186 2.912617906 1.000784489 0.674051973 0.580689949 0.084644446 1925927.971 2648679.544 14470.15302 0.020177757 0.079184128 1.10136186 -0.326732516 FLEEHPGGEEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLEEHPGGEEVLR 13 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ; 156.81 4.74E-05 185983000 480650 330500 392290 540170 594440 453780 516910 439290 496480 FALSE TRUE 457930.6271 364178.3257 410276.8845 485871.0853 698110.1478 438065.4848 438045.8858 400823.4388 573471.5827 0.79852366 0.635041625 0.715426704 0.847245269 1.217340438 0.763883509 0.763849333 0.698942111 1 19.12936247 3.217037784 5.689985132 0.871255627 0.709985037 0.211455646 0.150110775 0.283140186 27.53201954 0.043925794 0.054772361 1648.305789 -3.217037784 -0.16127059 FLEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 98.133 0.093712 29611000 60270 59735 58248 72300 68671 56627 66294 69959 70237 FALSE TRUE 57421.15654 65822.06441 60918.72842 65032.26664 80647.20066 54665.99279 56179.63273 63833.01908 81128.99524 0.70777601 0.811326015 0.750887254 0.801590929 0.994061376 0.673815726 0.692472926 0.786808944 1 16.30793 4.623524712 2.627296076 0.794075915 0.70048756 0.058450738 0.110316744 1.20903426 12.94790301 0.026379062 0.222000223 42026.6441 -4.623524712 -0.093588354 FLEESVSMS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FLEESVSMSPEER 13 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 1 FLEESVSMS(1)PEER;FLEESVS(0.001)MS(0.999)PEER;FLEESVSMS(1)PEER;FLEESVSMS(1)PEER;FLEES(0.296)VS(0.016)MS(0.688)PEER 264.09 3.40E-24 276186000 790290 660508 657153 764316 779965 705841 827738 723107 818931 TRUE FALSE 752934.5579 727814.5161 687284.1151 687485.5036 915990.6491 681397.5492 701451.3656 659787.9176 945926.637 0.795975638 0.769419623 0.726572324 0.726785225 0.968352738 0.720349256 0.741549438 0.697504322 1 19.85136877 -1.707816122 2.880816343 1.033182902 0.769328989 0.477088425 0.076221979 18706912.61 19762241.05 4558387.19 0.018047403 0.019596742 1.707816122 -0.263853914 FLEFQYLTGGLVDPEVHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLEFQYLTGGLVDPEVHGR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 167.16 1.85E-11 366150000 637230 559210 585550 609220 567730 646140 759940 633230 633820 FALSE TRUE 607109.4008 616194.1348 612398.0467 547980.0482 666741.9323 623764.0098 643997.1957 577781.0242 732109.5685 0.8292603 0.841669282 0.836484145 0.748494586 0.910713315 0.852009093 0.879645921 0.789200209 1 19.48170005 -5 0.296667584 2.304063226 0.830444296 0.559849431 0.045102509 189.2530576 1.760873361 153.2820872 0.042224711 1.00E-05 5 -1.47361893 FLEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FLEGVR 6 0 F8VWS0;P05388;F8VU65;F8VW21;Q8NHW5;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;; 136.44 0.030638 1975260000 2468720 2304860 1851760 2365740 2444130 2113410 2671890 2461700 2480030 FALSE TRUE 2352028.498 2539727.854 1936665.028 2127931.321 2870385.498 2040222.082 2264244.108 2246140.498 2864620.386 0.821061146 0.886584438 0.67606341 0.742831871 1.002012522 0.712213769 0.79041681 0.784097086 1 21.44991254 -2.1544328 2.390996182 1.454224981 0.805916367 0.315119438 0.091608068 10934479.18 1987188.935 27040560.19 0.021215537 0.007007566 2.1544328 -0.648308614 FLEIGKFDLSQNHPLGMAIFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 224.57 4.08E-26 2165103000 6327182 4927836 5737600 6118986 4988600 6369700 7758176 7824976 5034114 FALSE TRUE 6028108.646 5429988.091 6000674.635 5503893.902 5858610.261 6149115.692 6574523.763 7139779.619 5814778.688 1.036687545 0.93382541 1.031969565 0.946535405 1.007537961 1.057497804 1.130657608 1.227867818 1 22.47129285 2.018135467 2.311945867 1.133022129 0.986367381 0.459240105 0.063229707 0.224558995 2.262740395 0.030232326 0.016697149 104.2642604 -2.018135467 -0.146654748 FLENHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLENHEK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 108.46 0.0072477 194130000 200470 177940 187770 211140 149510 172450 202010 195650 157080 FALSE TRUE 190994.1804 196072.2883 196379.4402 189915.8061 175584.4967 166478.0133 171189.6643 178517.8488 181439.1641 1.052662369 1.080650306 1.082343171 1.046718921 0.967732063 0.917541778 0.943509992 0.983899202 1 17.46912637 2.772122479 3.190264461 0.952513166 1.070390951 0.820558729 0.024006706 0.088613388 1.843175383 0.007518001 0.007685375 591.7284888 -2.772122479 0.117877785 FLEPTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLEPTLR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 139.92 0.0061873 54907000 127306 116403 114875 135075 131263 119096 146280 126937 137178 FALSE TRUE 121288.4977 128264.598 120142.1324 121497.0044 154155.2256 114971.6757 123962.2994 115821.7233 158450.8636 0.765464415 0.809491315 0.758229584 0.766780323 0.972889779 0.72559829 0.782339058 0.73096303 1 17.273676 -1.220257984 3.788131361 1.000232098 0.789911526 0.475430285 0.069657358 4726529.799 1522550.79 8995.408202 0.015015912 0.060220175 1.220257984 -0.210320572 FLESAAADFS(ph)DEDEDDDVDGREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FLESAAADFSDEDEDDDVDGREK 23 1 O43815-2;O43815 O43815-2 STRN Striatin 1 FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK 397.48 9.76E-138 2747429000 2276790 1490337 2137730 2136204 1568562 2214690 2662920 2613580 2235198 TRUE FALSE 2169170.649 1642204.035 2235747.035 1921468.715 1842118.716 2137994.73 2256642.646 2384721.08 2581821.09 0.840170784 0.636064227 0.865957383 0.744230002 0.713495882 0.828095618 0.874050745 0.923658533 1 21.2999576 1.480490267 1.114850498 0.991757128 0.753347755 0.616643412 0.065047728 0.278118356 0.672067529 0.055307217 0.01948637 30.23362811 -1.480490267 -0.238409373 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL 40 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;; 99.53 4.16E-05 203000000 263087 161268 248730 249496 147668 276026 327655 298707 162949 FALSE TRUE 250651.3989 177701.3925 260134.5165 224416.1881 173421.2524 266467.1504 277665.212 272550.6315 188218.2987 1.331705794 0.944123891 1.382089405 1.192318651 0.921383594 1.415734561 1.475229634 1.448055972 1 17.52204737 2.191710317 24.99998026 1.386643388 1.153865542 0.15137556 0.195842909 161.6766978 86271.94401 0.067208318 0.049636779 155.4928119 -2.191710317 -0.232777846 FLEVQYLTGGLIEPDTPGRVPLDEALQR ddPTM_SK-BR-3_Trastuzumab_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 0 148.85 6.33E-08 83969000 10367 11355 8642.1 13762 11119 11350 13321 10954 15098 FALSE TRUE 9876.972455 12512.08741 9038.348833 12378.61761 13058.15008 10956.94665 11288.63679 9994.809689 17439.32073 0.566362223 0.717464149 0.518274133 0.709810766 0.748776302 0.628289761 0.647309432 0.573119208 1 14.09005623 -1.258177101 3.647784618 1.000701073 0.643080673 0.708203359 0.072840027 15191280.46 26897959.44 121200.7537 0.016089765 0.055185235 1.258177101 -0.3576204 FLFEGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FLFEGQR 7 0 B8ZZN6;P63165;B8ZZ67;P63165-2;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 ;;; 124.34 0.0096679 444618000 1139730 944610 810300 943680 1188660 897380 1290770 1085100 1242690 FALSE TRUE 1085857.222 1040866.833 847453.0565 848819.4935 1395961.928 866303.5056 1093839.33 990082.8915 1435400.018 0.756484052 0.725140602 0.590395044 0.591346999 0.972524669 0.603527584 0.762044946 0.689760958 1 20.45302141 -4.999992442 0.471733891 8.496318889 0.711626317 0.392780245 0.112673605 1737.338927 9.190645701 13674.5312 0.051739823 1.00E-05 4.999992442 -7.784692572 FLGDIEVWDQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 132.32 0.00027954 40003000 89195 80605 75621 90302 68934 89504 101470 97571 75554 FALSE TRUE 84978.92912 88818.74114 79088.29765 81224.6714 80956.06777 86404.45404 85988.88788 89027.16598 87270.52844 0.973741429 1.017740384 0.90624291 0.930722809 0.927644982 0.990075981 0.985314165 1.020128646 1 16.41320691 1.758155834 2.133991357 1.006286082 0.960046943 0.329355728 0.031943248 0.454079873 4.165307636 0.023632053 0.01017473 57.30015989 -1.758155834 -0.046239139 FLGEVHCGTNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLGEVHCGTNVR 12 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 66.023 0.070003 0 162930 142980 144080 155870 147590 133840 169790 155510 156780 FALSE TRUE 155228.6218 157549.8246 150686.2105 140201.6515 173329.6493 129205.0872 143885.4171 141892.72 181092.6417 0.857177963 0.869995728 0.832094607 0.7741985 0.95713248 0.713475081 0.794540384 0.78353664 1 17.4663684 2.228752885 24.99990474 0.801267529 0.854656101 0.012532655 0.08517126 492.9242591 1256454.626 0.027970847 0.020913892 169.3373991 -2.228752885 0.053388572 FLGMHPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLGMHPCER 9 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 98.033 0.0062881 210410000 374900 317280 309970 337870 442960 303190 412000 354700 402550 FALSE TRUE 357179.22 349611.1927 324182.4311 303906.6657 520212.0838 292690.4543 349141.8331 323640.5876 464975.3981 0.768167997 0.751891808 0.697203406 0.653597302 1.118794857 0.629475141 0.750882379 0.696038089 1 18.82679486 -1.622512691 2.778627732 1.021630209 0.757810515 0.23908675 0.135531636 27563452.7 26905927.37 4321515.25 0.029452746 0.023849941 1.622512691 -0.263819693 FLGQNLS(ph)VRT(ph)GRYRS(ph)ILQLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLGQNLSVRTGRYRSILQLVK 21 3 O43692 O43692 PI15 Peptidase inhibitor 15 3 FLGQNLS(0.758)VRT(0.758)GRY(0.726)RS(0.758)ILQLVK;FLGQNLS(0.759)VRT(0.759)GRY(0.723)RS(0.759)ILQLVK 70.335 0.014346 109323000 65611 60379 69218 79513 97109 60098 91220 69520 113857 TRUE FALSE 62509.69806 66531.68875 72391.71377 71520.20218 114044.7789 58016.79119 77302.71363 63432.46025 131513.3621 0.475310623 0.505892996 0.550451396 0.543824605 0.86717256 0.441147502 0.587793608 0.482327113 1 17.00484986 -2.265549642 2.294015653 2.816027579 0.553408754 0.581279118 0.118200823 6784701.188 1090069.947 63894523.83 0.028658472 0.005425632 2.265549642 -2.262618825 FLGTEPEPDAVGLDSGHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLGTEPEPDAVGLDSGHIR 19 0 Q16762 Q16762 TST Thiosulfate sulfurtransferase 0 136.43 5.85E-06 45556000 46854 39419 45459 44855 58883 39122 52885 49720 54720 FALSE TRUE 44639.30428 43435.84092 47543.34012 40346.09018 69152.17656 37767.19533 44816.42195 45366.25322 63205.69813 0.70625443 0.687214004 0.752200221 0.638329951 1.094081366 0.597528331 0.709056672 0.717755749 1 15.94776701 -2.097994081 2.316658192 1.452818743 0.731526629 0.273101423 0.13408593 11168020.35 3118393.872 26659420.89 0.029398253 0.007980056 2.097994081 -0.721292114 FLGVAEQLHNEGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLGVAEQLHNEGFK 14 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 257.8 2.33E-24 839260000 3555800 2734400 3016800 2930500 2613800 2721000 3287400 3140500 2436900 FALSE TRUE 3387724.381 3013038.469 3155123.264 2635920.572 3069645.892 2626771.088 2785846.753 2865501.171 2814802.006 1.203539138 1.070426432 1.120904155 0.936449728 1.090537056 0.933199238 0.989713218 1.018011627 1 21.42460202 4.537246586 0.567464834 0.985742616 1.310415806 0.599627639 0.053153809 1.839905046 0.52806572 0.025317685 0.382121393 34454.55027 -4.537246586 0.32467319 FLHKHDLDLICR ddPTM_SK-BR-3_Trastuzumab_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 87.618 0.00674 169890000 597740 438860 495340 497510 628400 539380 773040 572990 26042 FALSE TRUE 569486.0148 483580.3329 518051.829 447499.3496 737992.761 520701.1354 655098.5501 522815.958 30080.46036 18.93209107 16.0762278 17.22220414 14.87674538 24.53395833 17.31027814 21.77820892 17.38058367 1 14.87653903 0.950458807 22.70739071 0.999999912 18.60901291 0.79840143 2.773043516 2061.19995 944760.2021 2.54115296 0.63528824 8.921929917 -0.950458807 17.609013 FLHNPDAAQGFVGCALSSTIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLHNPDAAQGFVGCALSSTIQR 22 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 256.4 4.14E-37 2690100000 1202960 1011100 1039520 1214480 1091520 1040600 1103160 1053480 1035610 FALSE TRUE 1146098.465 1114132.24 1087183.02 1092398.163 1281880.742 1004563.761 934852.6811 961231.7064 1196207.11 0.958110394 0.931387408 0.908858517 0.91321825 1.07162107 0.83979083 0.781514065 0.803566288 1 20.19003577 2.043360638 24.9930404 0.830725876 0.949727558 0.281836644 0.074595981 129.8163457 74825.51079 0.025284509 0.018673838 110.4995828 -2.043360638 0.119001683 FLIATGERPR ddPTM_SK-BR-3_Trastuzumab_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 ; 246.86 1.09E-12 2228900000 1951390 1513170 1467510 1772010 1998240 1636240 1976390 1574090 1986410 FALSE TRUE 1859151.662 1667363.743 1534796.785 1593884.188 2346732.423 1579576.599 1674855.407 1436254.335 2294452.318 0.810281237 0.726693569 0.6689164 0.694668691 1.02278544 0.688432959 0.729958689 0.625968264 1 21.12971839 4.706066157 3.997533965 0.75676414 0.813366019 0.000762522 0.135363308 1.322699207 39.57616422 0.029665116 0.199817743 50823.68577 -4.706066157 0.056601879 FLIDGFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FLIDGFPR 8 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;;; 116.88 0.0050846 397102000 2053943 1688060 1554179 1841736 2118242 1532154 2270839 1844473 2120365 FALSE TRUE 1956857.185 1860075.233 1625439.644 1656601.198 2487662.734 1479095.123 1924380.804 1682961.166 2449180.375 0.798984511 0.759468454 0.663666776 0.676390034 1.015712342 0.603914329 0.785724409 0.687152806 1 21.2238676 -0.985575516 4.476454456 1.000006689 0.752093529 0.33203327 0.111854941 18285777.33 59661898.95 2151.5592 0.024083998 0.103377133 0.985575516 -0.24791316 FLISYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLISYDR 7 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 81.635 0.062041 27362000 69127 66768 64853 70263 82060 62065 78687 71558 87717 FALSE TRUE 65859.50371 73571.73511 67826.5742 63200.02975 96371.23802 59915.67349 66681.85296 65292.00217 101319.7044 0.650016738 0.726134522 0.669431229 0.623768399 0.951159882 0.591352628 0.658133118 0.64441564 1 16.62855525 -1.354463927 5.282280319 1.000121079 0.688844299 0.49159215 0.099298122 0.000129344 1.58E-05 0.087828053 0.020693264 0.044211584 1.354463927 -0.31127678 FLKNEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLKNEVER 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 93.111 0.010306 381240000 478080 351050 447010 438930 464410 453770 574090 502820 511320 FALSE TRUE 455482.1059 386822.3941 467505.8507 394807.9225 545402.957 438055.8311 486502.0266 458790.4152 590612.8941 0.771202441 0.654950811 0.791560522 0.66847156 0.923452506 0.741697033 0.823724019 0.776803926 1 19.17185333 -4.999999977 0.132573513 1.824662269 0.664385728 0.524689698 0.07220643 99.35175487 0.824861537 21.57531611 0.458820016 1.00E-05 4.999999977 -1.160276541 FLKS(ph)PPLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLKSPPLHK 9 1 Q9NYF8-4;E9PJA7 Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 FLKS(1)PPLHK;FLKS(1)PPLHK 96.103 0.0045867 364770000 615220 522870 544650 725630 439170 659020 732690 741450 449690 TRUE FALSE 586139.7698 576151.0475 569622.7412 652688.2938 515761.109 636197.9722 620904.6837 676524.7073 519425.6285 1.128438294 1.109207971 1.096639653 1.25655774 0.992945054 1.224810516 1.195367825 1.302447685 1 18.98655767 FLLESFNNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLLESFNNDR 10 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 168.83 1.12E-05 429730000 166478 150092 162819 171897 158358 150320 188082 160378 170250 FALSE TRUE 158608.9149 165386.5454 170284.4122 154617.587 185975.5851 145114.3807 159386.6365 146334.4521 196651.5005 0.806548206 0.841013392 0.86591972 0.786251753 0.945711498 0.737926639 0.810503028 0.74413087 1 17.58528167 FLLSLPEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLLSLPEHR 9 0 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 156.92 6.98E-05 1019890000 1683690 1371740 1443500 1584800 1728960 1488450 1899440 1665700 1779620 FALSE TRUE 1604105.31 1511521.866 1509685.903 1425492.893 2030490.077 1436904.603 1609645.542 1519842.478 2055594.381 0.780360817 0.735321073 0.734427919 0.693469931 0.987787326 0.699021469 0.783056014 0.739368862 1 20.97112418 -1.414037609 3.290513246 1.002718954 0.767971736 0.433113716 0.083008671 23518551.81 30945755.51 601085.1862 0.01806984 0.038544498 1.414037609 -0.234747218 FLMECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLMECR 6 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 100.82 0.086601 99015000 204190 113290 70826 90927 215180 101290 211020 149570 197250 FALSE TRUE 194538.3434 124834.3798 74073.44216 81786.84521 252707.3239 97782.3019 178825.0234 136472.8579 227838.5226 0.853843069 0.547907256 0.325113775 0.358968467 1.109150994 0.429173701 0.784876154 0.598989391 1 17.79765217 2.791027827 24.99995793 0.742920482 0.551890102 0.220077491 0.235929911 680.8934255 324435.6855 0.069950638 0.074193793 618.0560005 -2.791027827 -0.19103038 FLMECRNS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 FLMECRNSPVTK 12 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 FLMECRNS(0.939)PVT(0.061)K;FLMECRNS(1)PVTK;FLMECRNS(0.999)PVT(0.001)K;FLMECRNS(0.998)PVT(0.002)K;FLMECRNS(0.999)PVT(0.001)K;FLMECRNS(0.937)PVT(0.063)K;FLMECRNS(0.99)PVT(0.01)K;FLMECRNS(0.991)PVT(0.009)K;FLMECRNS(1)PVTK;FLMECRNS(1)PVTK;FLMECRNS(1)PVTK;FLMECRNS(1)PVTK;FLMECRNS(1)PVTK 173.19 2.04E-05 19452730000 14757856 7727618 12207253 12030934 11781476 14165080 18448230 15494940 15772062 TRUE FALSE 14060281.39 8515071.06 12766967.62 10821561.66 13836161.68 13674539.73 15633613.69 14138120.91 18217912.82 0.771783328 0.467401021 0.700792003 0.594006666 0.759481167 0.750609571 0.858145159 0.77605602 1 24.11885435 1.632698628 0.560154232 0.979820971 0.611780839 0.60171379 0.089618307 0.473627102 0.341065373 0.082673075 0.047596585 42.92384602 -1.632698628 -0.368040132 FLMECRNS(ph)PVTKT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLMECRNSPVTKTPPR 16 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 FLMECRNS(1)PVT(0.382)KT(0.618)PPR;FLMECRNS(1)PVT(0.008)KT(0.992)PPR 169.19 1.08E-08 326830000 834620 383530 830010 702300 659690 854330 1212870 975010 988410 TRUE FALSE 795169.1667 422612.143 868066.7795 631703.4697 774739.7271 824744.3379 1027824.406 889632.9555 1141687.575 0.696485785 0.370164441 0.760336539 0.553306775 0.678591713 0.72239057 0.900267664 0.779226275 1 20.12273648 1.90382571 0.64293232 0.973262147 0.550421006 0.583667611 0.11143417 0.444684458 0.366975387 0.095044722 0.054201855 80.13564007 -1.90382571 -0.422841141 FLMECRNS(ph)PVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLMECRNSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 42 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 FLMECRNS(0.906)PVT(0.416)KT(0.505)PPRDLPT(0.173)IPGVTSPSSDEPPMEASQSHLR 89.331 8.00E-05 53363000 47010 15734 43655 32948 51133 35469 93617 51585 76283 TRUE FALSE 44787.93046 17337.31249 45656.62493 29636.00444 60050.57901 34240.69964 79334.00726 47067.94393 88112.57804 0.508303485 0.196763196 0.5181624 0.336342496 0.681521076 0.388601723 0.900370969 0.534179625 1 16.42706036 1.575724262 0.460223322 0.987753213 0.335943427 0.535466957 0.167039461 0.601761359 0.335088499 0.162629173 0.111169294 37.64647022 -1.575724262 -0.651809786 FLMMT(ph)LK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLMMTLK 7 0 A0A5F9ZHW2 A0A5F9ZHW2 1 FLMMT(1)LK;FLMMT(1)LK 59.205 0.040121 39004000 56889 50932 115956 94054 58802 96830 77092 86747 84850 TRUE FALSE 54199.96971 56122.0287 121272.6973 84599.51323 69057.05018 93476.75282 65330.19951 79150.97281 98008.10465 0.553015181 0.572626406 1.237374172 0.863188953 0.704605506 0.95376554 0.666579562 0.807596199 1 16.58061344 3.945008603 24.99998953 0.863365181 0.560367683 0.409241004 0.161182267 261.8149707 119025.3183 0.040027934 0.072161534 8810.663268 -3.945008603 -0.302997497 FLMPEAYPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_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 111.79 0.0014092 99622000 320980 284720 278400 330450 328320 287800 313800 319230 337860 TRUE FALSE 305807.9115 313733.2917 291164.9154 297232.5382 385578.9041 277833.4138 265924.0467 291276.5289 390253.6033 0.783613294 0.803921576 0.746091549 0.761639446 0.988021381 0.711930426 0.681413431 0.746377551 1 18.57405243 -0.108769695 9.826073201 1 0.775422191 0.41862491 0.082219501 0 0 0.079689099 0.018782901 0.778449251 0.108769695 -0.224577809 FLNDTTKPVGLLLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLNDTTKPVGLLLSER 16 1 Q9P287-4;Q9P287-3;Q9P287;Q9P287-2 Q9P287-4 BCCIP BRCA2 and CDKN1A-interacting protein 0 77.221 0.022369 69841000 143960 121820 141290 142890 109330 127630 145880 131800 110650 FALSE TRUE 137155.2961 134233.5965 147768.2863 128526.4257 128397.1174 123210.1411 123623.3267 120258.8933 127809.0369 1.073126748 1.050266865 1.156164618 1.005612974 1.004601244 0.964017444 0.96725028 0.940926371 1 16.96363032 3.046135952 8.246114499 0.975150583 1.08140596 0.731270987 0.0324456 0.135372501 21.57799658 0.009250159 0.011047697 1112.079798 -3.046135952 0.106255378 FLNRHDLDLICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FLNRHDLDLICR 12 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ;;; 154.28 3.71E-05 543223000 719131 413747 598737 491879 803618 562801 908079 715042 857528 FALSE TRUE 685139.1028 455908.2897 626189.6837 442434.3884 943768.7248 543311.0603 769534.8705 652429.1318 990509.0626 0.691704022 0.460276747 0.632189757 0.446673741 0.952811802 0.548517001 0.77690846 0.658680628 1 19.91781065 -0.292788699 0.245082708 1.169110316 0.539708249 0.401942339 0.14325939 8.234084123 0.693109594 1.395087084 0.249470866 0.50957874 0.292788699 -0.629402067 FLPIS(ph)STPQPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLPISSTPQPER 12 0 Q08AE8;J3KNG6;Q08AE8-4;Q08AE8-3;Q08AE8-5;Q08AE8-2 Q08AE8 SPIRE1 Protein spire homolog 1 1 FLPIS(0.333)S(0.333)T(0.333)PQPER 68.44 0.05524 25208000 39942 30662 35140 43271 44469 38009 50154 41159 51050 TRUE FALSE 38054.02082 33786.49266 36751.20376 38921.31687 52224.37952 36692.7388 42502.08616 37554.89976 58966.57327 0.645349029 0.572977041 0.623254867 0.660057295 0.88566075 0.622263373 0.720782704 0.636884555 1 15.84760974 -5 0.179094809 2.343475976 0.595876898 0.600822381 0.084512167 89.29633117 0.858218587 42.76006189 0.255405589 1.00E-05 5 -1.747599078 FLPISST(ph)PQPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FLPISSTPQPER 12 0 Q08AE8;J3KNG6;Q08AE8-4;Q08AE8-3;Q08AE8-5;Q08AE8-2 Q08AE8 SPIRE1 Protein spire homolog 1 1 FLPIS(0.213)S(0.213)T(0.573)PQPER;FLPIS(0.243)S(0.243)T(0.513)PQPER;FLPIS(0.059)S(0.059)T(0.882)PQPER;FLPIS(0.008)S(0.05)T(0.941)PQPER 196.11 2.35E-06 212608000 391048 331155 351026 409851 391918 342572 399868 378593 453405 TRUE FALSE 372563.936 364900.071 367120.8893 368651.9988 460268.3751 330708.6457 338860.7925 345441.3899 523716.7317 0.711384444 0.696750837 0.700991332 0.703914877 0.878849858 0.631464732 0.647030679 0.659595863 1 18.99842717 -1.807724642 2.535235446 1.097172137 0.701430529 0.654224345 0.06766721 12050956.83 7680525.947 7166561.369 0.015995519 0.015569525 1.807724642 -0.395741607 FLPLFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FLPLFDR 7 0 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ;;;;; 170.17 0.0022912 2742816000 2049315 1429043 1444702 1436610 1905356 1073872 1802413 1525880 1817523 FALSE TRUE 1952447.941 1574664.106 1510943.016 1292199.233 2237649.483 1036683.543 1527421.793 1392265.858 2099375.184 0.930013823 0.750063218 0.719710811 0.615516104 1.065864501 0.493805753 0.727560183 0.663181059 1 21.00152859 4.491504463 2.043508638 0.734259985 0.941587941 0.085932215 0.169291385 0.87780722 5.789742257 0.039073181 0.2813138 31010.19259 -4.491504463 0.207327956 FLPLNIRNS(ph)PFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLPLNIRNSPFTR 13 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 FLPLNIRNS(1)PFTR;FLPLNIRNS(1)PFTR 118.7 0.00024631 1075800000 1027600 690160 857970 865560 974540 817480 1049870 859740 991440 TRUE FALSE 979027.3845 760488.0886 897308.7731 778552.2643 1144499.467 789170.4626 889693.0493 784456.6078 1145187.452 0.854905791 0.664073019 0.783547507 0.67984701 0.999399239 0.689119027 0.776897309 0.685002797 1 20.12715234 -1.115488934 4.354293506 1.000029197 0.764975592 0.342042161 0.101711466 1.175664497 52584286.58 3543.767392 0.021207631 0.076649807 1.115488934 -0.235053605 FLPSELRDEH ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FLPSELRDEH 10 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 162.38 6.19E-06 705608000 986792 639697 967965 851672 1551600 839374 1272620 948146 1574320 FALSE TRUE 940148.2978 704882.8516 1012347.153 766060.3125 1822198.549 810306.2679 1078458.446 865121.3098 1818457.505 0.517003172 0.387626793 0.556706522 0.421269296 1.002057262 0.445600882 0.59306222 0.475744584 1 20.79428378 -5 0.196661192 2.997860489 0.46494654 0.393188194 0.173562436 137.1273257 1.351858778 107.9409103 0.402440174 1.00E-05 5 -2.532913949 FLQDYFDGNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLQDYFDGNLK 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 119.45 0.0013604 52518000 288160 311440 271170 330560 198620 273660 295910 286110 213180 FALSE TRUE 274539.2479 343176.0901 283603.4127 297331.4808 233259.2651 264183.0856 250763.4947 261056.6916 246238.8656 1.114930607 1.393671503 1.151741062 1.207492083 0.947288579 1.072873224 1.018374959 1.060176634 1 17.90969897 2.846868812 5.295125109 1.025540638 1.234898587 0.599121141 0.079672604 0.146181044 5.977683243 0.023591747 0.025099888 702.8599734 -2.846868812 0.209357949 FLQDYFDGNLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 180.28 3.15E-05 5671300000 3422700 2734100 2951000 3373100 2978300 3300500 4204500 3582100 3234200 FALSE TRUE 3260915.754 3012707.898 3086306.269 3034029.58 3497714.577 3186202.857 3563026.304 3268432.334 3735743.218 0.872896118 0.806454759 0.826155892 0.81216224 0.936283458 0.852896645 0.953766385 0.874908189 1 21.83296386 1.499767385 0.469721979 0.994503153 0.825832461 0.571921571 0.041782512 0.589455184 0.344300426 0.042115841 0.027200641 31.60584349 -1.499767385 -0.168670691 FLQEHGSDS(ph)FLAEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.014)DS(0.986)FLAEHK;FLQEHGS(0.008)DS(0.992)FLAEHK;FLQEHGS(0.005)DS(0.995)FLAEHK 152.81 4.62E-06 256028000 245414 215979 212467 262024 204475 232826 274846 257681 125024 TRUE FALSE 233813.7666 237987.5056 222208.8221 235684.8497 240135.3753 224763.1772 232913.1948 235117.0856 144412.0834 1.619073426 1.647975018 1.538713499 1.632029981 1.662848216 1.556401459 1.612837301 1.628098426 1 17.13983194 -1.688254473 2.80442528 0.918104428 1.613230307 0.962280975 0.03809373 4262737.816 4035353.775 2491457.421 0.008635276 0.020499607 1.688254473 0.69512588 FLQEHGSDSFLAEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 234.57 6.78E-18 299170000 230230 155650 202700 216170 240010 179300 312000 259520 72162 FALSE TRUE 219347.4842 171510.912 211993.9955 194440.1809 281867.668 173090.796 264398.6697 236795.053 83352.51441 2.631564095 2.057657327 2.543342537 2.332745236 3.381633656 2.076611573 3.172053916 2.840886741 1 16.3469381 FLQEHLAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLQEHLAPK 9 0 A0A0A0MT83;P26440;A0A087WVD3;H0YN10 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 78.816 0.028702 352440000 1097200 809100 849190 937280 798820 755970 1060900 959520 848370 FALSE TRUE 1045337.53 891548.2099 888126.2015 843062.8337 938133.9551 729790.5693 899040.2202 875499.3421 979930.8867 1.06674618 0.909807234 0.906315143 0.860328871 0.957347062 0.744736776 0.917452682 0.893429684 1 19.90232048 4.59106106 1.31804628 0.886014231 1.118163814 0.379386872 0.066715885 0.879698293 1.650907562 0.01669196 0.256011206 38999.68145 -4.59106106 0.232149583 FLQFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLQFFK 6 0 O14787-2;O14787;A0A075B780;Q92973-2;Q92973;Q92973-3 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 123.34 0.043811 21599000 98190 81802 74286 82830 100040 77077 121910 98697 98504 FALSE TRUE 93548.75329 90137.7168 77692.08658 74503.77103 117486.9443 74407.80416 103310.3905 90054.56745 113779.4972 0.822193414 0.792214054 0.682830286 0.654808404 1.032584492 0.653964958 0.907987757 0.791483261 1 16.79588109 0.175239093 0.448090067 1.022369505 0.772379542 0.256656321 0.115100163 4.532106507 1.333986869 0.304234994 0.061834603 1.497059607 -0.175239093 -0.249989962 FLQPVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLQPVHK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 66.993 0.066368 742280000 1423780 1291050 1344290 1538250 1260730 1416340 1736680 1489860 1347950 FALSE TRUE 1356480.741 1422609.463 1405927.026 1383622.188 1480600.913 1367291.791 1471717.57 1359399.96 1556983.202 0.871223748 0.91369609 0.9029815 0.888655822 0.950942124 0.878167336 0.94523664 0.873098668 1 20.57032195 -5 0.213885329 1.460051037 0.891803842 0.528000651 0.028314182 107.5676369 1.073758692 21.31132259 0.050259547 1.00E-05 5 -0.568247195 FLRPEDPTRPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLRPEDPTRPSR 12 2 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 ; 129.54 0.00013074 216340000 571110 460360 518870 551080 534800 499130 617190 566650 613200 FALSE TRUE 544114.7621 507271.2074 542660.7027 495684.3914 628068.9507 481845.0029 523026.33 517031.122 708291.9242 0.768206926 0.716189455 0.766154017 0.699830641 0.886737416 0.680291539 0.738433282 0.729968964 1 19.43398457 -1.066419533 4.653567918 1.000011484 0.746157265 0.665116056 0.056127907 5.91E-06 1.18E-06 0.04799195 0.011311299 0.085818411 1.066419533 -0.253854219 FLRT(ph)AEADGGLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLRTAEADGGLAR 13 1 Q8NC60 Q8NC60 NOA1 Nitric oxide-associated protein 1 1 FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR 76.522 0.045977 177458000 8313.5 8677.6 9239.2 8051.3 15027.6 5155.5 9549 9031.7 12209.3 TRUE FALSE 7920.537331 9561.857306 9662.826459 7241.968028 17648.40868 4976.963742 8092.124671 8240.836468 14102.65589 0.561634446 0.678018196 0.68517778 0.513518027 1.251424471 0.352909678 0.573801469 0.584346419 1 13.78367926 -2.001716336 2.843614875 1.360310625 0.643716761 0.181625077 0.233065376 170980135 163917180.1 403142065.5 0.051241365 0.009960558 2.001716336 -0.716593863 FLSAIVSSVDKIPYGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLSAIVSSVDKIPYGMR 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 183.31 6.37E-10 87337000 216524 215800 183147 223850 155325 195704 202065 201253 162663 FALSE TRUE 206289.3396 237790.2653 191544.4711 201348.1727 182413.6308 188926.7214 171236.2731 183630.2204 187887.9473 1.09793812 1.265596164 1.019461194 1.071639643 0.97086393 1.00552869 0.911374442 0.97733901 1 17.519513 3.284652614 1.403439594 0.965502644 1.177867268 0.609598576 0.060195165 0.2182692 0.896574292 0.019726038 0.030453216 1925.983729 -3.284652614 0.212364624 FLSAQSHSTS(ph)PQGLDSPLPLEGSGAHQVLHNESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLS(0.004)AQS(0.003)HS(0.028)T(0.176)S(0.79)PQGLDSPLPLEGSGAHQVLHNESK 264.49 3.15E-60 249310000 211420 180240 205890 237460 193840 227360 267150 229510 19577 TRUE FALSE 201426.5956 198606.6609 215330.2602 213590.0697 227645.6346 219486.4662 226391.361 209412.8877 22612.90117 8.907596334 8.78289165 9.522451741 9.445496091 10.06706892 9.706249742 10.01160175 9.260770481 1 14.46485848 0.925023066 21.80352285 0.999999993 9.45229713 0.976918637 0.408932013 2493.551532 725133.639 0.477269223 0.119317305 8.414398308 -0.925023066 8.452297137 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(ph)KGSPTSAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGSPTSAYPER 44 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.485)KGS(0.485)PT(0.025)S(0.006)AYPER;FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.498)KGS(0.498)PT(0.003)SAYPER 350.3 1.13E-154 792210000 168803 106642 156571 183131 165073 167715 265030 203825 24903.4 TRUE FALSE 160824.0167 117508.941 163749.9352 164722.324 193861.6789 161906.9875 224594.8059 185977.0025 28765.29208 5.590905048 4.085094659 5.692622023 5.72642626 6.739430226 5.628553572 7.80784027 6.465326405 1 14.8120415 3.523635673 4.702004901 6.061152434 4.832106008 0 1.848100284 0.508590954 25.0099262 0.448550137 0.685881685 3339.14803 -3.523635673 -1.229046426 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGS(ph)PTSAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGSPTSAYPER 44 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.127)KGS(0.833)PT(0.032)S(0.008)AYPER 342.24 1.75E-134 645830000 97758 61540 87925 83235 92865 80223 126930 112550 14468 TRUE FALSE 93137.17308 67810.99597 91956.44822 74868.05966 109060.6266 77444.85739 107564.4973 102694.5253 16711.62355 5.573197171 4.057714427 5.50254426 4.479999172 6.526034187 4.634191117 6.436507917 6.14509566 1 14.02856428 3.629466382 19.53334667 5.2777594 4.809073284 0 1.63985649 26.44191071 4683.1616 0.382310125 0.59227176 4260.557018 -3.629466382 -0.468686115 FLSDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLSDLR 6 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;A0A087WYX8;A0A5F9ZHT2;A0A5F9ZH12;A0A1W2PQW0;Q14CM0;P53992;G5EA31;A0A590UJL7 A0A0A0MTR7;P53992;A0A590UJL7 RNF213;FRMPD4;SEC24C E3 ubiquitin-protein ligase RNF213;FERM and PDZ domain-containing protein 4;Protein transport protein Sec24C 0 98.03 0.093984 37558000 237100 245900 164300 232140 236720 188920 244890 224780 221030 FALSE TRUE 225892.7529 270957.4896 171833.3175 208804.8462 278003.8931 182377.653 207527.5328 205097.0716 255306.2035 0.884791477 1.061303979 0.673047952 0.817860449 1.088903792 0.714348694 0.812857384 0.803337595 1 17.96186907 3.759949047 24.96204231 0.836211455 0.973047712 0.144615656 0.128967777 1274.076907 1486946.827 0.031077205 0.055958804 5753.724288 -3.759949047 0.136836258 FLSDLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLSDLRR 7 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;P53992;G5EA31 A0A0A0MTR7;P53992 RNF213;SEC24C E3 ubiquitin-protein ligase RNF213;Protein transport protein Sec24C 0 ; 114.78 0.0093439 672440000 1175990 805090 617500 658310 1356400 731490 1408110 1046050 1328380 FALSE TRUE 1120403.283 887129.5863 645812.9858 592135.4281 1592955.731 706158.3179 1193276.958 954452.3165 1534378.386 0.730200121 0.578168719 0.420895518 0.385912258 1.038176597 0.460224365 0.777694061 0.622044944 1 20.54922287 -0.218180289 0.400444973 1.076172134 0.591116445 0.285425116 0.190514673 7.628455971 1.410658893 1.05445823 0.121181077 0.605089631 0.218180289 -0.485055689 FLSDPQVHTVLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLSDPQVHTVLVER 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 116.58 0.00035347 178177000 696380 607005 598089 728640 724610 647680 799960 741230 718540 FALSE TRUE 663463.4975 668859.4996 625511.9722 655395.7229 850981.7546 625250.6792 677911.4097 676323.9717 829967.5134 0.7993849 0.805886362 0.753658381 0.789664309 1.025319354 0.753343558 0.816792704 0.814880053 1 19.66269534 -5 0.297345855 2.482864558 0.80755168 0.354908002 0.076395126 293.3805535 2.726204025 270.9958622 0.073375448 1.00E-05 5 -1.675312878 FLSHS(ph)TDSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLSHSTDSLNK 11 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 FLS(0.013)HS(0.983)T(0.004)DSLNK;FLS(0.006)HS(0.992)T(0.002)DSLNK;FLSHS(0.879)T(0.121)DSLNK 188.13 2.11E-06 1558300000 2455240 1965700 2091500 2417280 1848630 2257850 2765230 2556560 1923990 TRUE FALSE 2339185.671 2166007.065 2187397.344 2174290.422 2171030.487 2179660.088 2343343.377 2332694.053 2222352.543 1.052571825 0.974646022 0.984271083 0.978373314 0.976906429 0.980789522 1.054442682 1.049650768 1 21.08365627 1.744064785 12.28713103 1.038647571 0.992743553 0.3654849 0.026759591 0.090852084 99.60445362 0.012682739 0.006953873 55.47084541 -1.744064785 -0.045904018 FLSNGHVTIPGQQDKDMFQETMEAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLSNGHVTIPGQQDKDMFQETMEAMR 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 87.339 0.0073967 791310000 932580 653219 808100 955230 803220 817490 1063830 941880 811270 FALSE TRUE 888498.7916 719782.7587 845152.1843 859208.4656 943301.3137 789180.1163 901523.1949 859403.994 937077.6082 0.948159239 0.768114351 0.901902016 0.916902141 1.006641612 0.842171566 0.962058198 0.917110799 1 19.83780901 3.417864904 3.906447413 0.936399603 0.855109446 0.220554197 0.063054963 0.286513886 8.933845967 0.016476716 0.023313143 2617.368695 -3.417864904 -0.081290156 FLSQIESDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FLSQIESDR 9 0 P19367-4;P19367-2;P19367;P19367-3;Q2TB90 P19367-4;Q2TB90 HK1;HKDC1 Hexokinase-1;Putative hexokinase HKDC1 0 ;; 147.24 0.00021605 328309000 537969 604396 452972 635640 474141 475077 464261 464992 421790 FALSE TRUE 512540.2715 665984.6395 473741.2143 571744.2596 556831.0403 458624.9644 393429.4577 424274.8354 487199.039 1.052014127 1.366966242 0.972377153 1.173533225 1.142923109 0.941350306 0.807533321 0.870844976 1 18.89415176 2.177958355 3.548031701 0.871897784 1.159972623 0.526255437 0.11096398 0.156008368 3.979993881 0.042631654 0.030697392 150.6462604 -2.177958355 0.288074838 FLSQPFQVAEVFTGHMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FLSQPFQVAEVFTGHMGK 18 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ;;; 224.86 3.32E-19 1857560000 1809060 1360290 1552590 1594660 1501490 1327220 1804970 1689080 1615980 FALSE TRUE 1723549.319 1498905.098 1623777.787 1434361.747 1763349.381 1281258.039 1529588.676 1541175.201 1866577.925 0.92337389 0.803023049 0.869922314 0.768444611 0.944696365 0.686420867 0.819461462 0.825668824 1 20.83196431 4.630032801 2.918320798 0.827156103 0.929303613 0.065746968 0.087869634 0.678687342 9.301143637 0.018851514 0.143220154 42661.17387 -4.630032801 0.10214751 FLTAVNLEHPEMLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLTAVNLEHPEMLEK 15 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4;C9JNT3 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 161.08 1.67E-06 441010000 1537360 1357550 1265290 1559080 1154350 1393060 1565600 1566990 932260 FALSE TRUE 1464692.04 1495885.888 1323304.798 1402358.316 1355668.275 1344817.983 1326738.966 1429776.048 1076830.119 1.360188588 1.389156805 1.228889102 1.302302277 1.258943495 1.248867355 1.232078247 1.327763797 1 20.03835924 -5 0.127281696 0.027560074 1.426975299 0.76455389 0.051799517 65.34181147 0.528692795 16.30781634 0.401567062 1.00E-05 5 1.399415225 FLTWILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLTWILNR 8 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 200.12 0.00028468 191329000 243630 209954 121026 144216 267790 125097 288710 195103 231740 FALSE TRUE 232114.0927 231348.5513 126575.1618 129719.1337 314492.4912 120764.8595 244661.987 178018.747 267677.0556 0.867142281 0.864282337 0.47286519 0.484610582 1.174895213 0.451158801 0.91401927 0.665050453 1 18.03013396 -1.411179359 3.326876237 1.00270685 0.752871148 0.110597568 0.230615904 54321654.69 65148671.72 1364619.095 0.050207938 0.03879901 1.411179359 -0.249835702 FLVEAPHDWDLEEVMNSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLVEAPHDWDLEEVMNSIR 19 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 212.92 5.94E-17 58489000 200190 181430 187100 198020 222770 168940 215100 194410 183070 FALSE TRUE 190727.4154 199917.9233 195678.7201 178114.6534 261621.0175 163089.5654 182282.5444 177386.4298 211459.5606 0.901956927 0.945419175 0.925371828 0.842310714 1.237215365 0.771256523 0.862020823 0.838866917 1 17.69002226 -0.876768212 4.75801691 1.000000301 0.914729471 0.043407331 0.124533663 4.69E-07 1.11E-07 0.110911914 0.02614207 0.132810309 0.876768212 -0.08527083 FLVHNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLVHNVK 7 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 103.29 0.0084102 4077100000 3854400 3386100 3154700 3812600 3021200 3251600 4109000 3655300 3093300 FALSE TRUE 3672210.151 3731147.44 3299346.115 3429350.205 3548096.323 3138996.277 3482096.583 3335222.554 3572993.166 1.027768591 1.044263805 0.923412378 0.959797583 0.993031937 0.878534084 0.974560102 0.933453382 1 21.76870172 3.745993802 24.99839984 0.949823049 1.036016204 0.493660925 0.035402136 380.0153077 1278018.769 0.008173869 0.014379547 5571.777972 -3.745993802 0.086193155 FLVYVANFDEKDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLVYVANFDEKDPR 14 1 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 124.12 9.02E-05 7420000000 27893000 29989000 26541000 30823000 20386400 28979000 30736000 31379000 21087600 FALSE TRUE 26574553.17 33044913.19 27757931.1 27724613.48 23941781.71 27975449.96 26046658.69 28631288.41 24357757.31 1.091009851 1.356648429 1.139593057 1.138225212 0.982922254 1.148523224 1.069337311 1.175448464 1 24.53787797 3.374527792 3.039204659 1.086210449 1.225737467 0.284905506 0.087858889 0.271859588 5.028864589 0.023579044 0.0335302 2368.796713 -3.374527792 0.139527018 FLWESYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLWESYR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 120.65 0.010504 78744000 233910 162290 127310 146490 270670 146530 275380 166020 209880 FALSE TRUE 222853.5379 178827.5355 133147.2894 131764.5469 317874.7623 141455.6294 233365.7233 151482.4087 242427.1185 0.919259938 0.737654833 0.549226053 0.543522308 1.311217839 0.583497549 0.962622188 0.624857523 1 17.88719157 FLYDDNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 176.65 0.00060272 1334180000 2189710 2094280 1994560 2440140 2296390 2052010 2316010 2297350 2318340 FALSE TRUE 2086206.748 2307689.513 2086012.549 2194852.491 2696879.689 1980948.379 1962660.138 2096181.855 2677856.327 0.779058506 0.861767485 0.778985985 0.819630415 1.007103952 0.739751554 0.732922121 0.78278354 1 21.35264713 -0.217557349 8.719649149 0.999999996 0.811030105 0.36101653 0.078259942 0 0 0.075310844 0.017750936 0.605958177 0.217557349 -0.188969891 FLYIWPNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLYIWPNAR 9 0 Q9HCC0-2;Q9HCC0;D6RD67 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 146.94 0.0002177 135637000 253670 185933 161283 156792 273860 146864 263650 180541 247690 FALSE TRUE 241679.5218 204879.7841 168677.9851 141030.9703 321621.0973 141778.0629 223425.3502 164731.8729 286100.5002 0.844736453 0.716111241 0.589575988 0.492942061 1.124154264 0.495553355 0.780933099 0.57578324 1 18.12616249 FLYQLHETEKEDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FLYQLHETEKEDLIR 15 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 153.24 1.62E-06 90352000 112840 108260 92647 124950 90514 111600 117800 117260 92738 FALSE TRUE 107506.2768 119291.8171 96894.95659 112389.7886 106299.6129 107735.264 99827.44645 106992.0928 107119.3354 1.003612246 1.113634776 0.90455151 1.049201698 0.992347577 1.005749929 0.931927425 0.998812141 1 16.70885939 3.748937427 24.99866187 0.981837059 1.058623506 0.302534823 0.047556807 728.6043021 1755266.551 0.011397712 0.020273224 5609.671457 -3.748937427 0.076786446 FLYTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FLYTGR 6 0 U3KQ56;Q9UBQ7;Q9UBQ7-2 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 ; 114.67 0.058367 601740000 839080 677480 769420 814880 951580 761490 1063160 835790 1232390 FALSE TRUE 799418.3513 746515.9822 804698.6681 732966.7142 1117535.251 735119.4104 900955.4157 762603.7968 1423502.747 0.561585394 0.524421877 0.565294777 0.514903618 0.785060129 0.516415871 0.63291442 0.535723446 1 20.44101385 -5 0.310126663 4.738405316 0.558029874 0.721867589 0.081678451 144.6631533 1.309822328 353.3623781 0.069211836 1.00E-05 5 -4.180375442 FMAGEVSYGSWYQHVQEWWELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FMAGEVSYGSWYQHVQEWWELSR 23 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;H3BPL6;P50226;E9PKR8 A0A0A6YYL2;P50226 SULT1A4;SULT1A3;SULT1A2 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A2 0 130.87 3.29E-05 17428000 16618 13781 15573 15644 19400 14808 17597 16286 12698 FALSE TRUE 15832.50007 15185.29957 16287.03745 14071.4354 22783.35386 14295.19525 14912.25446 14859.9115 14667.14099 1.079453732 1.035327852 1.110443915 0.959385023 1.553360255 0.974640883 1.016711742 1.013143019 1 13.84030006 FMDQHPEMDFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FMDQHPEMDFSK 12 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 125.53 0.00030366 476760000 1280420 1122120 1031380 1212100 981280 1130920 1386130 1279880 798710 FALSE TRUE 1219897.084 1236465.304 1078669.793 1090257.405 1152414.921 1091755.957 1174650.41 1167806.922 922569.8676 1.322281517 1.340240287 1.169201197 1.181761342 1.249135661 1.183385666 1.273237347 1.265819493 1 19.81529865 -5 0.170845982 0.039695712 1.313989521 0.631526215 0.058811837 91.15620146 0.861393924 29.90551054 0.223206187 1.00E-05 5 1.274293809 FMEQSRS(ph)PSVSPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FMEQSRSPSVSPSK 14 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 FMEQS(0.058)RS(0.838)PS(0.105)VSPSK;FMEQS(0.006)RS(0.992)PS(0.002)VSPSK 165.3 2.41E-06 493780000 492390 501760 468200 599710 365650 496530 495370 539470 421970 TRUE FALSE 469115.7005 552889.9145 489667.4331 539426.0114 429419.2442 479335.0416 419792.2084 492231.1469 487406.9525 0.96247232 1.134349667 1.004637769 1.106726132 0.881028147 0.983439073 0.861276611 1.009897673 1 18.8947673 2.738771632 24.99999935 0.935293036 1.053177171 0.369516991 0.067110116 17.04000497 2018898.508 0.019148971 0.019167 547.9887369 -2.738771632 0.117884135 FMERDPDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FMERDPDELR 10 1 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ;; 199.68 2.50E-07 783220000 1357210 1115430 1216000 1439870 1530820 1218080 1637730 1385610 1626080 FALSE TRUE 1293057.373 1229093.585 1271754.803 1295131.532 1797794.523 1175897.584 1387864.21 1264278.643 1878244.182 0.68843944 0.654384343 0.677097693 0.689543748 0.957167625 0.626062147 0.738915751 0.673117295 1 20.8409532 -5 0.292132418 3.27490215 0.693293349 0.48440494 0.092231046 212.0207219 1.989234598 294.4875061 0.091045851 1.00E-05 5 -2.581608801 FMFNIADGGFTELHSLWQNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 340.02 3.40E-81 255288000 234874 247378 267480 263888 249985 232282 277906 244167 214640 FALSE TRUE 223771.9715 272586.0994 279744.2226 237361.4769 293582.3049 224238.0161 235506.3356 222786.4431 247925.275 0.902578293 1.099468779 1.128340879 0.957391201 1.184156415 0.904458072 0.949908539 0.89860319 1 17.91954583 FMKPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FMKPGK 6 1 P61353;K7EQQ9;K7ERY7 P61353 RPL27 60S ribosomal protein L27 0 ; 65.619 0.094454 1417370000 1356010 1344040 1036560 1610170 1004050 1400920 1477670 1570800 1103600 FALSE TRUE 1291914.095 1480999.204 1084087.301 1448312.652 1179156.002 1352405.789 1252224.302 1433252.425 1274740.652 1.013472107 1.161804326 0.850437538 1.1361626 0.925016395 1.060926226 0.982336525 1.124348253 1 20.28177233 FMLQDVLDLR ddPTM_SK-BR-3_Trastuzumab_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 ; 179.8 4.81E-06 201685000 525810 470770 431170 521580 547620 400680 574940 512220 530610 FALSE TRUE 500956.0034 518741.9982 450939.571 469149.7875 643124.7546 386804.3511 487222.3435 467367.3014 612894.2888 0.817361187 0.846380865 0.735754239 0.765466078 1.049324111 0.631111039 0.79495331 0.762557769 1 19.22527874 -2.332378222 2.271836272 2.127461919 0.801866249 0.261680288 0.105358171 4708528.256 561531.056 27412560.97 0.023454844 0.004651808 2.332378222 -1.32559567 FMQASEDLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FMQASEDLLK 10 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 78.655 0.068283 39369000 105820 109170 78538 94603 91766 97689 119920 96515 97869 FALSE TRUE 100818.0983 120294.5471 82139.04498 85093.32671 107769.9613 94306.00544 101624.0015 88063.63494 113046.0247 0.891832319 1.0641201 0.726598261 0.752731703 0.953328183 0.834226641 0.898961302 0.779006915 1 16.78655073 3.748127593 24.94289515 0.847667772 0.977976202 0.242581823 0.094520706 804.5238934 2097538.298 0.022705957 0.040284416 5599.220792 -3.748127593 0.13030843 FMQASEDLLKEHYVDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FMQASEDLLKEHYVDLK 17 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 ; 220.34 2.43E-15 1198560000 2022900 1026990 2059960 1743520 1473210 2040290 2832700 2317700 1582550 FALSE TRUE 1927281.526 1131641.449 2154411.204 1568258.057 1730137.358 1969634.246 2400519.589 2114749.901 1827963.771 1.054332452 0.619072143 1.178585286 0.857926225 0.946483396 1.077501795 1.31322055 1.156888301 1 20.80180605 2.137806842 3.186568548 1.192060677 0.905539837 0.277829152 0.162009652 0.244741683 4.934371523 0.064962654 0.044532021 137.3430987 -2.137806842 -0.28652084 FMQDPMEVFVDDETKLTLHGLQQYYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FMQDPMEVFVDDETKLTLHGLQQYYVK 27 1 O00148;O00148-2 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 265.1 1.55E-53 178093000 353170 269260 294840 341710 227740 339610 380510 366390 239450 FALSE TRUE 336476.354 296697.9001 308358.7056 307360.6616 267457.7839 327849.2205 322456.211 334306.9492 276582.6831 1.216548883 1.072727681 1.114887968 1.111279485 0.967008422 1.185357004 1.165858279 1.20870528 1 18.07735131 FMRDPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FMRDPIR 7 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;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 ;;; 100.19 0.0090994 909549000 811216 537146 228861 299032 867181 352931 913504 597440 847814 FALSE TRUE 772871.4274 591881.7881 239354.5032 268972.7352 1018417.092 340708.911 774132.1871 545124.9864 979288.6651 0.789217168 0.604399713 0.244416699 0.274661338 1.039955968 0.347914689 0.790504593 0.556654035 1 19.90137466 -0.024222255 0.569488548 1.030251797 0.570669472 0.220992565 0.249045203 7.134080284 2.666304927 0.740146498 0.102195887 0.945753037 0.024222255 -0.459582326 FMS(ph)SPSLSDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FMSSPSLSDLGK 12 0 B1AHC3;B1AHC4;F8WEZ7;E9PH80;P85299;P85299-5 B1AHC3;P85299 PRR5-ARHGAP8;PRR5 Proline-rich protein 5 1 FMS(0.5)S(0.5)PSLSDLGK 182.1 1.82E-05 29274000 83056 74036 65792 81428 52084 79894 81708 87664 52894 TRUE FALSE 79130.10748 81580.35257 68808.62828 73242.70274 61167.43311 77127.25075 69241.94393 79987.67542 61096.53137 1.295165302 1.335269789 1.126228064 1.198802961 1.001160487 1.262383461 1.133320376 1.30920158 1 15.89880286 3.74036781 24.98228267 1.154620397 1.315217553 0.33330834 0.098308887 155.0963038 2144007.971 0.022716061 0.038497669 5500.064845 -3.74036781 0.160597156 FMSS(ph)PSLSDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FMSSPSLSDLGK 12 0 B1AHC3;B1AHC4;F8WEZ7;E9PH80;P85299;P85299-5 B1AHC3;P85299 PRR5-ARHGAP8;PRR5 Proline-rich protein 5 1 FMS(0.065)S(0.785)PS(0.124)LS(0.026)DLGK 65.179 0.064456 64326000 287260 217340 241010 280410 186470 265920 313790 310490 231010 TRUE FALSE 273681.7891 239487.1931 252060.5469 252222.6541 218990.309 256711.1237 265915.5724 283301.8496 266833.851 1.025663678 0.897514285 0.94463482 0.945242341 0.820699129 0.962063557 0.996558613 1.061716302 1 18.02558218 1.681092479 2.970797683 1.028931569 0.931480321 0.387454086 0.05304346 0.231312165 4.667643522 0.032206 0.014142773 47.98356145 -1.681092479 -0.097451248 FMSVQRPGPYDRPGTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FMSVQRPGPYDRPGTAR 17 2 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;; 218.57 2.59E-15 5774770000 2908170 2623120 2632950 2895170 2847030 2733920 3412550 2920890 3128270 FALSE TRUE 2770706.568 2890418.91 2753673.362 2604142.011 3343551.131 2639243.665 2891902.822 2665121.387 3613386.135 0.766789506 0.799919744 0.762075588 0.720692977 0.925323507 0.730407315 0.800330414 0.737568942 1 21.78492 -1.784367026 2.821770717 1.053594306 0.78242198 0.586240944 0.057959632 23024838.54 19200064.62 8526320.555 0.012505518 0.016429826 1.784367026 -0.271172326 FMVGEVSYGSWYQHVQEWWELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FMVGEVSYGSWYQHVQEWWELSR 23 0 P50225;H3BRY5;P50225-2;H3BQX5 P50225 SULT1A1 Sulfotransferase 1A1;Sulfotransferase 0 202.95 1.99E-24 25377000 9239.1 10180 8891.1 10710 8391.5 8460.8 10502 8579 5269 FALSE TRUE 8802.386053 11217.35357 9298.765729 9633.410452 9854.974943 8167.800374 8899.727018 7827.77728 6086.08961 1.446312266 1.843113443 1.527871971 1.58285715 1.619262215 1.342044054 1.462306274 1.28617516 1 12.57129986 1.09617719 0.535992715 0.990212048 1.642810881 0.728908912 0.116121167 0.429188588 0.313514753 0.11840276 0.057188161 12.47892543 -1.09617719 0.652598833 FNADEFEDMVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FNADEFEDMVAEK 13 0 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 205.02 1.70E-07 333520000 959011 996700 808504 1096743 658173 958658 954349 1020394 694832 FALSE TRUE 913680.4506 1098264.863 845574.7081 986496.31 772958.1628 925459.4331 808745.5322 931042.8919 802582.9978 1.138424877 1.36841282 1.053566685 1.229151767 0.963088135 1.153101219 1.007678376 1.16005808 1 19.61429107 3.304268696 1.542980605 1.066728935 1.243550883 0.269983563 0.103751707 0.394493126 1.944493906 0.030882085 0.047307389 2014.970518 -3.304268696 0.176821948 FNADEFEDMVAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 FNADEFEDMVAEKR 14 1 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;;;;;;; 237.89 4.20E-17 6169100000 7042320 5328410 6479410 7317180 5640697 6976210 8429900 8010680 6807380 FALSE TRUE 6709443.49 5871381.037 6776497.358 6581643.165 6624432.771 6734622.098 7143763.929 7309222.392 7863033.723 0.853289421 0.746706837 0.861817156 0.837036111 0.84247798 0.85649157 0.908525155 0.929567728 1 22.90665461 1.426246415 0.572065355 1.002418473 0.806866382 0.783710705 0.030811227 0.310526423 0.246236427 0.029591153 0.015419078 26.68372249 -1.426246415 -0.195552091 FNAHGDANTIVCNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNAHGDANTIVCNSK 15 0 P09382 P09382 LGALS1 Galectin-1 0 ; 216.01 2.26E-12 663460000 1982080 1719050 1851670 2116500 1583050 1854820 2235800 2067300 1740650 FALSE TRUE 1888391.007 1894223.149 1936570.901 1903745.399 1859133.419 1790587.118 1894687.647 1886276.253 2010581.112 0.939226473 0.942127198 0.963189642 0.946863266 0.924674666 0.890581886 0.942358224 0.938174661 1 20.93918111 0.522051394 2.645439947 0.99999849 0.935667075 0.538633535 0.018661882 7.466605339 40.19115639 0.018412137 0.004877331 3.326989222 -0.522051394 -0.064331415 FNDEHIPESPYLVPVIAPSDDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;;;;; 153.24 5.30E-08 2803148000 3064429 2856901 2806526 3256016 2676401 2811514 3194739 3089208 2330604 FALSE TRUE 2919579.514 3148022.46 2935207.993 2928715.086 3143164.487 2714150.565 2707322.89 2818700.571 2692022.165 1.084530266 1.169389502 1.090335745 1.087923838 1.167584921 1.008219992 1.005683729 1.04705697 1 21.36025886 2.224519284 24.99775698 1.014371495 1.120671882 0.724543021 0.032078685 116.3821745 207193.665 0.011356515 0.008427914 167.6946795 -2.224519284 0.106300388 FNDEHIPESPYLVPVIAPSDDARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNDEHIPESPYLVPVIAPSDDARR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 115.5 0.00068421 166740000 176390 97561 173650 147450 180040 159110 219950 167250 182260 FALSE TRUE 168052.3943 107502.5768 181612.0243 132628.0459 211438.919 153599.9808 186392.5878 152604.7034 210523.9499 0.798257843 0.510642978 0.86266681 0.629990298 1.004346152 0.729608108 0.885374742 0.724880487 1 17.68362484 3.053985869 1.73195861 0.848437968 0.674394882 0.204021319 0.138176429 0.478704199 2.93468546 0.042705941 0.052505443 1132.363517 -3.053985869 -0.174043085 FNDFDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FNDFDHR 7 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;; 143.89 0.0023914 302568000 849360 736400 756350 916360 807520 790030 910480 849610 683190 FALSE TRUE 809212.4361 811439.9972 791029.3956 824245.7518 948351.2323 762671.063 771569.5539 775213.6443 789135.6159 1.025441533 1.02826432 1.002399815 1.044491891 1.201759511 0.966463872 0.977740123 0.982357948 1 19.58991373 FNDILGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 163.67 0.0028529 198438000 736630 680590 683840 758070 673090 736060 830590 754750 732940 FALSE TRUE 701810.9598 749942.8948 715194.7404 681867.3634 790476.6829 710570.0576 703868.2407 688660.0888 846600.5919 0.828975277 0.885828456 0.844784125 0.805418009 0.933706745 0.839321475 0.831405326 0.81344154 1 19.69132197 -1.308277741 3.317336116 1.000761477 0.849596755 0.62120716 0.037314138 16501552.56 26190909.27 127953.4146 0.008398925 0.049172497 1.308277741 -0.151164722 FNDS(ph)EGDDT(ph)EETEDYR ddPTM_SK-BR-3_Trastuzumab_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 264.1 2.90E-26 718110000 1117850 1106710 998690 1197500 946490 1126750 1114090 1184070 818700 TRUE FALSE 1065011.446 1219485.007 1044480.924 1077125.025 1111557.556 1087730.365 944115.1088 1080386.554 945659.8147 1.126209901 1.289559933 1.104499639 1.139019559 1.175430677 1.150234311 0.998366531 1.142468504 1 19.85096177 1.914044536 0.573502313 1.012285745 1.198004756 0.389317826 0.065300967 0.696077078 0.479288888 0.059410108 0.037932959 82.04356741 -1.914044536 0.185719012 FNDS(ph)EGDDTEETEDYR ddPTM_SK-BR-3_Trastuzumab_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(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(0.999)EGDDT(0.001)EETEDYR;FNDS(1)EGDDTEETEDYR 526.22 1.48E-286 11520348000 4679437 4723388 3868920 4948083 3925587 4782704 4641906 4951361 3483116 TRUE FALSE 4458249.287 5204706.607 4046313.809 4450692.296 4610208.13 4617077.761 3933697.985 4517793.582 4023259.84 1.108118656 1.293654105 1.005730172 1.106240331 1.145888735 1.147596214 0.977738983 1.122918668 1 21.93993349 2.42859538 0.354164178 1.001346725 1.202466883 0.197319642 0.082508772 1.985331317 0.569539548 0.095870593 0.143796812 268.2843749 -2.42859538 0.201120158 FNDS(ph)EGDDTEETEDYRQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FNDSEGDDTEETEDYRQFR 19 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 FNDS(1)EGDDTEETEDYRQFR;FNDS(1)EGDDTEETEDYRQFR;FNDS(1)EGDDTEETEDYRQFR;FNDS(1)EGDDTEETEDYRQFR;FNDS(1)EGDDTEETEDYRQFR 340.75 5.40E-76 2130230000 827260 286115 882360 533659 1039980 688140 1485590 904070 1527280 TRUE FALSE 788157.0593 315270.4438 922817.0788 480014.5834 1221352.183 664309.5393 1258935.961 824904.838 1764122.782 0.446769957 0.178712302 0.523102523 0.272098172 0.692328332 0.376566499 0.713632845 0.467600581 1 20.75051954 -0.184254068 0.200307563 1.325778212 0.22318878 0.591779349 0.151227177 6.447814542 0.437880139 1.811580659 0.449576766 0.654253316 0.184254068 -1.102589432 FNDYFEFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNDYFEFPR 9 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 83.862 0.036949 41106000 117100 95993 104480 118870 130260 101550 146550 109330 148820 FALSE TRUE 111564.9151 105774.7958 109270.5113 106920.9618 152977.3028 98033.29804 124191.1059 99756.48561 171898.2455 0.649017183 0.615333772 0.63566973 0.622001472 0.889929401 0.570298421 0.722468723 0.580322884 1 17.39119529 -2.146058613 2.386443736 1.755742932 0.661343901 0.57612716 0.091479892 7774177.049 1459829.278 31922537.44 0.020053559 0.007143999 2.146058613 -1.094399031 FNEEHIPDSPFVVPVAS(ph)PSGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDSPFVVPVAS(0.861)PS(0.139)GDAR;FNEEHIPDSPFVVPVAS(0.958)PS(0.042)GDAR;FNEEHIPDSPFVVPVAS(0.885)PS(0.115)GDAR 119.75 0.00010015 266262000 329536 304764 329268 355712 295906 327390 378209 356553 296532 TRUE FALSE 313959.4864 335819.7981 344365.2635 319955.154 347511.9127 316052.4022 320506.2708 325331.3291 342516.6681 0.916625425 0.980448046 1.005397096 0.934130172 1.014583946 0.922735831 0.935739194 0.94982627 1 18.38581467 3.642427623 0.002218111 1.912584767 2.42E-08 0.04711149 0.035116971 510348.0874 262.8597134 112114.9943 114542.1383 4389.627048 -3.642427623 -1.912584743 FNEEHIPDSPFVVPVASPSGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;; 152.88 5.70E-08 821536000 970570 794510 861620 988290 840760 877100 986580 927190 775940 FALSE TRUE 924693.0796 875471.4723 901126.1293 888945.2116 987388.2778 846725.8071 836059.1012 846000.3283 896268.8122 1.031713998 0.976795645 1.005419487 0.99182879 1.101665331 0.944723051 0.932821816 0.943913608 1 19.77357197 FNEGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FNEGER 6 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 131.3 0.035801 5742780000 5264070 4361390 4520220 5130590 4712380 4702160 5479700 5011740 4956520 FALSE TRUE 5015247.843 4805820.599 4727476.558 4614853.346 5534217.58 4539323.02 4643671.123 4572885.477 5725151.807 0.876002596 0.839422388 0.825738202 0.806066547 0.966649928 0.792873826 0.811100086 0.798736109 1 22.44888252 -1.253225321 5.329919042 1.000016757 0.839876584 0.493810872 0.051044287 9.61E-06 1.35E-06 0.046709266 0.011008328 0.055818052 1.253225321 -0.160140173 FNEYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNEYWR 6 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 128.48 0.038633 1058030000 1471150 1642210 1003320 1520530 1496140 1002870 1246220 1047240 1422280 FALSE TRUE 1401611.655 1809553.066 1049323.214 1367683.436 1757066.342 968140.3604 1056086.251 955538.1138 1642839.918 0.853163865 1.101478632 0.638725175 0.832511689 1.069529857 0.589309007 0.642841849 0.581637994 1 20.64776048 2.225908523 24.99946722 0.6673661 0.907646747 0.22780819 0.173012044 265.766739 525129.0932 0.060468333 0.044955826 168.231967 -2.225908523 0.240280648 FNFLAPELPAVSEFSTSETMGHSADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FNFLAPELPAVSEFSTSETMGHSADR 26 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;;;; 180.83 2.10E-17 635940000 1364900 1084990 1165500 1184240 1433630 972971 1381100 1124460 1321950 FALSE TRUE 1300383.882 1195551.715 1218939.328 1065197.945 1683654.618 939276.7703 1170387.829 1025996.321 1526951.254 0.851621084 0.782966523 0.798283065 0.697597872 1.102624994 0.615132125 0.766486701 0.671924738 1 20.54222258 FNFLNPNDPYHAYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNFLNPNDPYHAYYR 15 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 188.25 3.07E-07 511600000 599380 515050 449200 608400 546710 504240 612460 541180 466580 FALSE TRUE 571048.4953 567534.1806 469796.2643 547242.4761 642056.0509 486778.0424 519017.9784 493791.4102 538934.8434 1.059587262 1.05306641 0.871712546 1.015414911 1.191342625 0.903222436 0.96304402 0.916235824 1 19.03975134 FNGGHS(ph)PTHSPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.87)PT(0.13)HSPEK 123.92 0.00014028 269680000 349720 277950 258760 329040 274810 312980 391960 320060 27480 TRUE FALSE 333189.4287 306273.421 270624.4019 295964.2741 322736.777 302141.4241 332159.3032 292033.8497 31741.45805 10.49697932 9.649002907 8.525896999 9.324217986 10.16767335 9.51882625 10.46452569 9.200391777 1 14.95408078 0.945703363 21.38649298 1.000000003 9.765884606 0.957283177 0.576519337 563.3626641 221899.2182 0.566091995 0.141522999 8.824769349 -0.945703363 8.765884603 FNGGHSPT(ph)HSPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.414)PT(0.584)HS(0.002)PEK;FNGGHS(0.25)PT(0.75)HSPEK;FNGGHS(0.369)PT(0.631)HSPEK;FNGGHS(0.245)PT(0.755)HSPEK;FNGGHS(0.115)PT(0.885)HSPEK;FNGGHS(0.149)PT(0.849)HS(0.001)PEK 158.74 0.00014931 4330210000 5291580 4277690 4378290 5175560 4156130 4830430 5906210 5250990 446491 TRUE FALSE 5041457.5 4713591.474 4579038.927 4655302.876 4880957.756 4663150.998 5005109.19 4791185.478 515730.5439 9.775371189 9.139639934 8.878742943 9.026618514 9.464162659 9.041835999 9.704891922 9.290094478 1 18.97625797 0.879903364 21.75542099 0.999999996 9.310236793 0.987654844 0.291273907 21896.29281 3966504.093 0.282435239 0.07060881 7.584088002 -0.879903364 8.310236797 FNGS(ph)TEALDKLDADAVSPTVSQLSAVFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.801)T(0.199)EALDKLDADAVSPTVSQLSAVFEK 139.75 5.39E-08 170310000 66404 60752 61121 66105 40831 71712 68230 78438 44959 TRUE FALSE 63265.21452 66942.69787 63923.45831 59459.99981 47951.91347 69228.59546 57820.26037 71569.55289 51931.0121 1.218254988 1.289069771 1.230930339 1.144980569 0.923377218 1.333087738 1.113405228 1.378165955 1 15.66430872 -2.340009518 2.04161259 4.01E-05 1.202221322 0.202321659 0.127202974 2987678.827 386546.8618 13750146.52 0.028742238 0.004570782 2.340009518 1.202181211 FNGST(ph)EALDKLDADAVSPTVSQLSAVFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.351)T(0.649)EALDKLDADAVSPTVSQLSAVFEK 361.06 2.07E-120 174250000 312480 317030 280020 352570 183480 347310 352690 357700 190650 TRUE FALSE 297709.6897 349335.7174 292859.194 317128.9938 215478.8539 335282.5676 298880.6629 326377.8917 220215.0283 1.351904509 1.586339135 1.32987833 1.440087882 0.978492956 1.522523554 1.357221917 1.482087277 1 17.7485534 -1.977711192 2.927339145 0.664560014 1.3898259 0.346246541 0.16416594 18246035.63 29964299.71 40794521.29 0.036993613 0.010526617 1.977711192 0.725265886 FNHDGEEEEEDDDYGSR ddPTM_SK-BR-3_Trastuzumab_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 ; 227.1 1.86E-15 637830000 236298 213382 220660 270910 249320 248700 264550 235640 133070 FALSE TRUE 225128.6618 235125.8684 230777.4793 243677.6121 292801.3291 240087.4566 224188.0387 215006.1124 153705.816 1.46467237 1.529713543 1.501423208 1.585350629 1.904946324 1.561993312 1.458552738 1.398815725 1 17.22981223 0.8346589 1.328354978 1.003170688 1.576888232 0.69332267 0.122196437 0.400517171 1.330759298 0.12063801 0.036269285 6.833747065 -0.8346589 0.573717544 FNHPEIVQLVSELEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNHPEIVQLVSELEAER 17 0 Q7Z4H3-2;Q7Z4H3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 101.67 0.0010304 22105000 17790 16541 17101 20858 13210 17619 17543 22426 15153 FALSE TRUE 16949.10196 18226.54671 17885.09777 18761.31421 15513.81982 17008.84961 14866.49315 20462.26055 17502.84985 0.968362415 1.041347373 1.021839182 1.07190054 0.886359647 0.971776011 0.849375575 1.169081648 1 14.09530222 2.749357062 24.94077629 0.956160087 1.021830811 0.051525254 0.087890821 1505.044044 3476788.642 0.024945791 0.026219542 561.5094404 -2.749357062 0.065670725 FNHWELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 126.67 0.0039297 1553119000 4540280 3924780 4000310 4733220 3181010 4431440 5019730 4474210 2746530 FALSE TRUE 4325669.962 4324719.544 4183728.17 4257427.733 3735777.137 4277978.122 4253877.995 4082424.453 3172447.845 1.363511766 1.36321218 1.318769724 1.342000859 1.177569284 1.348478629 1.340881932 1.286837374 1 21.59716502 -3.615344272 0.28849841 2.07E-14 1.346794824 0.782131205 0.053112345 45.72819023 0.904629572 27.28761468 0.057545471 0.000242469 3.615344272 1.346794824 FNLILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNLILR 6 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 142.53 0.026789 77671000 350080 303680 229850 270160 258710 201870 263730 258880 255440 FALSE TRUE 333532.4122 334625.3373 240388.8499 243003.0035 303828.9421 194879.1913 223493.1448 236211.0948 295052.3306 1.13041782 1.134121993 0.81473293 0.823592896 1.029745949 0.660490262 0.757469512 0.80057356 1 18.17061133 3.739292412 24.53955219 0.822983199 1.132269929 0.551896891 0.108196978 30.77852755 1032087.321 0.02730238 0.045787824 5486.462455 -3.739292412 0.30928673 FNLLAHLADDLGHVVPNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNLLAHLADDLGHVVPNSR 19 0 Q8N5N7;Q8N5N7-2 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 ; 189.51 8.01E-15 144255000 271290 216320 236110 226260 274920 191146 257270 240980 76992 FALSE TRUE 258466.6593 238363.2539 246935.877 203515.9149 322865.961 184526.5661 218018.7364 219878.5137 88931.52614 2.906355829 2.680300949 2.776696721 2.288456341 3.630500622 2.074928589 2.451534859 2.472447322 1 16.44040732 -0.471374589 0.379302294 0.52155681 2.828722441 0.645685777 0.398089193 4.710746609 0.678429094 3.225080033 0.262539418 0.337773373 0.471374589 2.307165631 FNLTYVSHDGDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FNLTYVSHDGDDK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;; 185.12 8.92E-06 958960000 2107680 2561070 1838720 2501830 1149080 2241100 1852920 2375030 906080 FALSE TRUE 2008054.143 2822045.945 1923027.131 2250341.295 1349479.188 2163490.145 1570223.023 2167059.782 1046590.259 1.918663132 2.696419082 1.837421201 2.150164571 1.289405454 2.067179708 1.500322604 2.070590438 1 19.99726531 -0.016004729 0.118694752 6.40E-13 2.858099608 0.420732606 0.364538587 19.54022324 0.764368845 12.39507333 5.498237651 0.963818528 0.016004729 2.858099608 FNNWGGSLSLGHPFGATGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNNWGGSLSLGHPFGATGCR 20 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 213.48 6.98E-23 1133800000 934900 641310 750720 762240 938260 681370 991180 867850 836930 FALSE TRUE 890709.1298 706660.2181 785141.2546 685618.187 1101892.247 657773.9861 839957.2867 791856.4532 966716.83 0.921375425 0.730989879 0.812172945 0.70922339 1.139829382 0.680420539 0.868876242 0.819119342 1 19.88273383 FNPFVTSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 156.62 0.00016402 1751282000 1867740 1824200 1588565 1969950 1691890 1632336 1853330 1789790 1695630 FALSE TRUE 1779455.632 2010088.054 1661402.277 1771926.883 1986955.08 1575807.795 1570570.47 1633066.499 1958579.64 0.908543924 1.026298861 0.848268941 0.90469994 1.014487764 0.804566617 0.801892574 0.833801427 1 20.90137636 2.225527496 24.99961373 0.837699747 0.943447806 0.190248984 0.076322574 267.0422031 512226.3149 0.026462692 0.019664576 168.0844341 -2.225527496 0.105748059 FNQTYQLAHGTAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNQTYQLAHGTAEEK 15 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 174.39 9.15E-07 239750000 350060 377480 373920 441480 229090 397210 387530 435150 237900 FALSE TRUE 333513.3576 415945.6412 391064.6019 397101.5916 269043.2235 383454.5181 328405.181 397045.9591 274792.317 1.21369244 1.513672747 1.423127859 1.445097141 0.979078405 1.395433913 1.195103213 1.444894688 1 18.06798214 FNQVLDQFGEKFQADGTYTLIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNQVLDQFGEKFQADGTYTLIIR 23 1 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 94.837 0.0037604 21912000 44498 27767 51690 40616 49915 45754 65228 47260 66871 FALSE TRUE 42394.66773 30596.48887 54060.03763 36533.20251 58620.1602 44169.52751 55276.27061 43121.66386 77241.01315 0.548862139 0.396117135 0.699887734 0.472976739 0.758925314 0.571840344 0.715633682 0.558274188 1 16.23707947 -5 0.120227676 2.381258321 0.375000481 0.602652529 0.107119292 89.9898929 0.701009283 30.14052813 0.903080666 1.00E-05 5 -2.00625784 FNSLNELVDYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNSLNELVDYHR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 165.51 5.44E-05 456870000 584940 526610 462580 561910 528090 505570 627970 571930 440650 FALSE TRUE 557291.0454 580272.1577 483789.7506 505425.7392 620188.7288 488061.9841 532161.643 521848.7772 508983.7515 1.094909305 1.140060279 0.950501365 0.993009576 1.218484337 0.958895019 1.045537586 1.025275907 1 18.95726008 8 0.212459798 1.007350642 1.581327079 0.084721459 0.080064646 104.6566418 1.312163484 0.125479035 20.38747506 100000000 -8 0.573976437 FNT(ph)AS(ph)GRNKAFS(ph)LHVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FNTASGRNKAFSLHVLK 17 2 Q5T764 Q5T764 IFIT1B Interferon-induced protein with tetratricopeptide repeats 1B 3 FNT(1)AS(1)GRNKAFS(1)LHVLK 74.816 0.014148 94708000 157070 206290 149130 224390 142230 225620 166290 228790 108050 TRUE FALSE 149645.6124 227311.1855 155967.758 201833.8909 167034.867 217806.7228 140919.4064 208755.9347 124805.8422 1.199027304 1.82131847 1.24968315 1.617183037 1.338357757 1.745164482 1.129109054 1.672645536 1 16.92932594 -2.823788359 0.386870648 1.19E-11 1.48208816 0.264296012 0.241761548 122.6483833 4.39789 101.351965 0.140190827 0.001500416 2.823788359 1.48208816 FNVLHWHIVDDQSFPYQSITFPELSNK ddPTM_SK-BR-3_Trastuzumab_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 0 131.17 2.52E-05 76225000 59569 59072 58736 61268 58761 59370 69500 60921 39964 FALSE TRUE 56753.29142 65091.50396 61429.1037 55109.22424 69008.8998 57314.00201 58896.49854 55586.43428 46161.41301 1.22945308 1.410084738 1.33074574 1.193837464 1.494947734 1.241599818 1.275881623 1.20417532 1 15.49439977 0.818791946 1.025089252 1.00053672 1.324628312 0.56958321 0.087246138 0.516042667 1.046276031 0.075049763 0.024288855 6.588581863 -0.818791946 0.324091592 FNWYVDGVEVHNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FNWYVDGVEVHNAK 14 0 A0A0A0MS08;P01857 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 259 2.11E-24 3739100000 25529000 1796980 1055690 946220 471650 218700 150654 56682 63696 FALSE TRUE 24322294.76 1980094.305 1104094.431 851104.1679 553905.6107 211126.3642 127668.9653 51718.62359 73573.65037 330.5843144 26.91309042 15.00665558 11.56805682 7.528586769 2.869592077 1.735253922 0.702950354 1 16.16690155 4.247789576 4.305723957 6.929481362 200 0.813597132 43.8518127 0.082491274 3.74934497 9.977657279 26.43371406 17692.51513 -4.247789576 193.0705186 FPAMSDAYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FPAMSDAYDR 10 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 99.802 0.010345 188370000 154000 142630 105430 141750 135860 110660 131690 128710 118880 FALSE TRUE 146720.7252 157164.1592 110264.0698 127501.0207 159553.941 106827.8165 111598.2718 117439.4701 137315.3032 1.068495075 1.144549482 0.802999135 0.928527394 1.161953091 0.777974588 0.812715475 0.855254056 1 17.06713289 3.744996698 0.696256347 0.873076316 1.146058262 0.190196234 0.126839208 1.36523738 1.127539799 0.063685603 0.244420972 5559.000301 -3.744996698 0.272981946 FPDSVEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FPDSVEELR 9 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 81.548 0.048788 55532000 125189 106390 123387 119885 122391 116516 129861 122721 117542 FALSE TRUE 119271.5641 117231.262 129044.416 107833.932 143735.9516 112481.0217 110048.3194 111974.8987 135769.813 0.878483673 0.863456017 0.95046471 0.794240852 1.058673857 0.828468562 0.810550718 0.824740759 1 17.05080322 -0.426237428 7.474171566 0.999999216 0.873528664 0.198094303 0.078164612 0 0 0.069916486 0.016479474 0.374768061 0.426237428 -0.126470552 FPEFCSSPS(ph)PPVEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FPEFCSSPSPPVEVK 15 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 FPEFCSS(0.002)PS(0.998)PPVEVK;FPEFCSS(0.001)PS(0.999)PPVEVK 209.66 2.38E-09 160405000 324830 293280 314890 368740 231220 353860 388660 391360 277330 TRUE FALSE 309475.9297 323165.5654 329328.018 331673.5546 271544.6948 341605.7395 329362.7788 357090.4437 320336.92 0.966095103 1.00883022 1.028067629 1.035389722 0.847684665 1.066395155 1.028176143 1.114733961 1 18.28923056 FPEHELTFDPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FPEHELTFDPQR 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;;; 181.66 1.79E-05 1631370000 1790970 1535540 1388710 1606300 1846740 1441100 1979140 1715860 1663420 FALSE TRUE 1706314.397 1692013.272 1452383.727 1444831.672 2168810.871 1391194.346 1677185.844 1565610.202 1921374.678 0.888069577 0.880626403 0.755908644 0.751978096 1.128780813 0.724061976 0.87290931 0.814838574 1 20.87370745 FPGLALRPSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.083)S(0.917)R;FPGLALRPS(0.407)S(0.593)R;FPGLALRPS(0.378)S(0.622)R;FPGLALRPS(0.107)S(0.893)R;FPGLALRPS(0.025)S(0.975)R 113.52 0.00083593 4406220000 2645120 2134352 1978279 2399560 2466590 2288840 2550290 2356250 2450480 TRUE FALSE 2520090.42 2351844.895 2068985.049 2158351.67 2896762.515 2209576.897 2161196.421 2149924.259 2830487.923 0.89033781 0.830897343 0.730964097 0.762536965 1.023414547 0.780634632 0.763542004 0.759559594 1 21.43261934 -0.99903824 4.629532048 1.000003666 0.819326422 0.308827251 0.085662412 0.022455789 51897916.7 501.9812671 0.019686418 0.100221699 0.99903824 -0.180677244 FPGQLNADLR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 152.06 4.35E-05 1587440000 971870 848750 544140 619220 1054210 642220 1042270 812390 1039200 FALSE TRUE 925931.6312 935238.5899 569089.3572 556974.8292 1238063.89 619979.7604 883252.5689 741252.8248 1200353.829 0.771382245 0.779135758 0.474101339 0.464008875 1.031415788 0.516497507 0.735826844 0.617528605 1 20.1950283 -1.50739774 3.121264448 1.009151105 0.6842695 0.261255912 0.171608123 251937257.7 293648948 19630373.91 0.038462287 0.031088678 1.50739774 -0.324881604 FPGQLNADLRK ddPTM_SK-BR-3_Trastuzumab_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 ; 130.56 0.00035527 5400900000 999790 712830 769440 874700 989110 945400 1375470 1074550 1218590 FALSE TRUE 952531.9081 785468.1874 804719.5851 786773.4942 1161610.471 912660.5609 1165616.789 980456.7055 1407562.714 0.676724311 0.558034239 0.571711354 0.558961591 0.825263741 0.648397796 0.828110022 0.696563426 1 20.42476777 0.965650401 0.375145799 1.022404563 0.580889206 0.656018522 0.083259 0.857701312 0.331508257 0.136378451 0.071948133 9.239541084 -0.965650401 -0.441515357 FPHHDNELAQSEAYFENDCWVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FPHHDNELAQSEAYFENDCWVR 22 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 145.75 5.23E-08 33469000 27238 26100 24651 22714 78629 24693 17551 22913 140610 FALSE TRUE 25950.51372 28759.61967 25781.27273 20430.74557 92341.87271 23837.87522 14873.2726 20906.61625 162415.0807 0.159778966 0.177074811 0.158736939 0.125793402 0.568554794 0.146771317 0.091575687 0.128723368 1 17.30932607 -1.413642098 3.16220302 1.011334737 0.18955532 0.777612542 0.135330607 37282141.2 47890503.5 3810749.677 0.031427945 0.038579616 1.413642098 -0.821779417 FPLDYYSIPFPTPTT(ph)PLTGR ddPTM_SK-BR-3_Trastuzumab_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(0.004)PT(0.2)T(0.786)PLT(0.01)GR;FPLDYYSIPFPTPT(0.004)T(0.995)PLT(0.001)GR 276.67 1.66E-43 418510000 502410 433784 475060 583670 605890 430400 504000 438890 477720 TRUE FALSE 478662.075 477987.0828 496841.9709 524998.3827 711557.0242 415495.1401 427105.5434 400458.4649 551802.3777 0.867451998 0.866228748 0.900398387 0.951424647 1.289514241 0.752978162 0.774019034 0.725728052 1 19.07379215 FPPEDFRHS(ph)PEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR 86.367 0.0044621 93122000 88227 73804 75854 87069 84908 79018 84679 81033 61692 TRUE FALSE 84056.68456 81324.71151 79331.98093 78316.6587 99715.92832 76281.58685 71759.66331 73937.32094 71258.88028 1.179595922 1.141257219 1.113292555 1.099044195 1.399347393 1.070485342 1.007027658 1.037587465 1 16.12078219 2.01356798 24.9999759 1.021428489 1.177614371 0.480445919 0.082818105 201.9945478 372187.9025 0.02966527 0.021898714 103.1734564 -2.01356798 0.156185882 FPQLDS(ph)TSFANSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FPQLDSTSFANSR 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 FPQLDS(0.732)T(0.24)S(0.028)FANSR;FPQLDS(0.946)T(0.052)S(0.002)FANSR;FPQLDS(0.885)T(0.114)S(0.001)FANSR;FPQLDS(0.959)T(0.039)S(0.002)FANSR 191.44 3.73E-06 231246000 241668 211367 227247 249921 236054 225526 272535 231571 284918 TRUE FALSE 230244.8326 232905.5376 237666.4997 224798.4663 277221.7429 217715.9781 230954.7803 211293.4156 329101.6283 0.699616206 0.707700958 0.722167499 0.683067013 0.842359074 0.661546341 0.701773435 0.642030903 1 18.32817364 -1.538865071 5.603957768 1.000759995 0.708262952 0.748867152 0.053225165 0.000459879 3.78E-05 0.046894551 0.011025498 0.028915781 1.538865071 -0.292497044 FPQLDSTSFANSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FPQLDSTSFANSR 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 ;;; 148.13 9.63E-05 1398100000 101070 101366 103149 111002 141705 110478 139411 123539 168644 FALSE TRUE 96292.6214 111695.3106 107878.4837 99843.86807 166418.3071 106652.1192 118141.2915 112721.2702 194796.4502 0.494324313 0.573395 0.553801076 0.512554864 0.854318993 0.547505455 0.606485854 0.578661829 1 17.57160786 -5 0.222546049 3.114650968 0.534967355 0.637699912 0.097909443 96.2241378 0.962558415 91.42742302 0.171523012 1.00E-05 5 -2.579683613 FPSLLTHNENMVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FPSLLTHNENMVAK 14 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 204.13 1.41E-08 396880000 360870 399740 321120 435820 270740 365510 374870 375040 272060 FALSE TRUE 343812.3903 440473.9605 335843.6696 392010.5456 317956.9703 352852.2971 317676.6965 342199.5094 314249.6753 1.094073971 1.401668785 1.068716043 1.247449326 1.011797291 1.12284061 1.010905409 1.088941489 1 18.26155173 2.864939375 1.396475854 1.045304422 1.231172065 0.330227472 0.101244552 0.402598258 1.605599052 0.037977403 0.040327567 732.7222428 -2.864939375 0.185867643 KNAT(ph)QEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNATQEALR 9 1 Q9NPF2-2;Q9NPF2 Q9NPF2-2 CHST11 Carbohydrate sulfotransferase 11 1 KNAT(1)QEALR 55.567 0.074799 730890000 1716000 1016200 1295500 1152400 2117900 1612800 2869500 2426500 3228700 TRUE FALSE 1634888.081 1119751.935 1354899.956 1036558.563 2487261.089 1556948.332 2431705.073 2214022.796 3729390.306 0.438379453 0.300250669 0.363303341 0.27794317 0.666935044 0.417480661 0.652038235 0.593668834 1 21.83050836 0.888236758 0.412736539 1.0359695 0.331881645 0.777835413 0.102228086 0.595944093 0.257563585 0.146912292 0.070323385 7.731019314 -0.888236758 -0.704087855 FPTTATKIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FPTTATKISPK 11 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 FPTTATKIS(1)PK;FPTTAT(0.001)KIS(0.999)PK 107.61 0.0013168 895820000 2592000 2412000 2125930 2930600 1102870 2727800 2517100 3072300 1233540 TRUE FALSE 2469481.297 2657785.542 2223405.993 2636010.52 1295210.179 2633335.602 2133070.165 2803273.125 1424831.083 1.733174778 1.865333774 1.560469883 1.850051246 0.909027178 1.848173888 1.497068804 1.967442427 1 20.44235946 FQDLGAAYEVLSDSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQDLGAAYEVLSDSEKR 17 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ; 151.28 4.10E-07 206797000 409030 306760 364140 411330 345580 392210 492740 464510 450810 FALSE TRUE 389695.9625 338019.1928 380836.1792 369982.3269 405849.0426 378627.6694 417563.4632 423835.0419 520719.3124 0.748380084 0.64913896 0.731365575 0.710521615 0.779400788 0.727124307 0.801897401 0.813941469 1 18.99014639 0.512373265 0.424138241 1.025587438 0.696256572 0.883810635 0.031685625 0.624530385 0.21695533 0.060915455 0.019780157 3.253668217 -0.512373265 -0.329330866 FQDNFEFVQWFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQDNFEFVQWFK 12 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 207.88 1.71E-07 193450000 506490 465250 374150 521050 388740 391610 503570 480860 433020 FALSE TRUE 482549.2215 512659.5039 391305.1476 468673.0641 456536.1329 378048.4475 426741.1478 438753.3492 500170.53 0.964769399 1.024969432 0.782343469 0.937026546 0.91276096 0.755839108 0.853191306 0.877207518 1 18.93206053 3.753163759 24.99244786 0.864293504 0.994869424 0.320921319 0.071984309 737.0659032 1261442.952 0.01705067 0.030572861 5664.528408 -3.753163759 0.130575919 FQEAEERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FQEAEERPK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 110.53 0.0020716 295720000 427350 394110 378530 428100 305660 433210 483670 470040 357060 FALSE TRUE 407150.0124 434270.2571 395885.9749 385066.5747 358967.0072 418207.8291 409877.2583 428880.8058 412431.0412 0.987195365 1.052952406 0.959884042 0.933650808 0.87036855 1.014006676 0.993807976 1.039884885 1 18.65379339 -0.773237806 6.702277195 1 0.984942595 0.008293058 0.052660728 0 6.87E-19 0.052533824 0.012382341 0.168562977 0.773237806 -0.015057405 FQEHIIQAPKPVEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQEHIIQAPKPVEAIK 16 1 Q9UHD1-2;Q9UHD1;E9PPQ5;E9PIZ4;E9PSD5 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 ; 191.99 3.65E-10 771710000 2256570 2006350 1780150 2298620 1375270 2155860 2239290 2417290 1347690 FALSE TRUE 2149906.408 2210799.346 1861771.638 2067558.351 1615116.653 2081202.028 1897645.183 2205619.273 1556682.882 1.381081807 1.420198919 1.195986453 1.328182107 1.037537363 1.336946691 1.219031316 1.416871283 1 20.57004365 -5 0.059955783 0.09580376 1.696508492 0.331628417 0.121372965 435.6628829 1.907831119 60.52232508 10.11133932 1.00E-05 5 1.600704732 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR 33 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 308.39 2.63E-104 1382886000 1473758 1232044 1356014 1517834 1143121 1477863 1773462 1567734 1212602 FALSE TRUE 1404096.38 1357590.684 1418188.583 1365258.443 1342480.94 1426684.234 1502887.8 1430454.9 1400646.125 1.002463331 0.969260301 1.012524547 0.974734744 0.958472605 1.018590069 1.072996079 1.02128216 1 20.41766107 2.023704079 8.07770173 1.041119645 0.984459328 0.450892873 0.024069448 0.133195921 37.09942185 0.008427488 0.006128814 105.6097657 -2.023704079 -0.056660317 FQEKPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQEKPDR 7 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ; 80.438 0.02728 560370000 937670 779180 791760 943280 664410 846230 976250 887650 804150 FALSE TRUE 893348.1974 858579.3279 828062.9792 848459.7023 780282.8936 816924.8429 827305.1324 809922.6603 928853.475 0.961775158 0.924343129 0.891489348 0.91344838 0.840049496 0.879498075 0.890673454 0.871959552 1 19.82509151 4.098387927 1.355006034 0.889547676 0.962566193 0.174058896 0.041706207 0.65920385 2.079235685 0.010823383 0.047883951 12542.61024 -4.098387927 0.073018518 FQEKPDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FQEKPDRR 8 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 48.794 0.093347 126870000 209210 222170 195970 214650 135910 201190 168740 192590 91851 FALSE TRUE 199321.0579 244809.3756 204955.4183 193072.9742 159612.661 194222.7399 142995.6139 175725.7986 106094.784 1.87870742 2.307459108 1.931814277 1.819815894 1.504434573 1.83065305 1.347810029 1.6563095 1 16.6949942 1.797309749 0.312574939 0.958990095 2.228002776 0.71357879 0.190493242 0.707215252 0.227394535 0.292889553 0.318732381 62.70609401 -1.797309749 1.269012681 FQELIFEDFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FQELIFEDFAR 11 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;;; 172.8 3.01E-05 258042500 382781 409112 364027 395280 371971 339594 390690 396627 335787 FALSE TRUE 364687.7007 450800.9779 380717.998 355545.7034 436842.6246 327833.7746 331083.065 361896.2372 387859.133 0.940258124 1.162280167 0.981588328 0.916687718 1.126291964 0.845239281 0.853616782 0.933061017 1 18.56517325 2.224810082 24.99965439 0.889458046 1.029406905 0.302447957 0.086501404 238.6303232 433847.5809 0.030870639 0.022921012 167.8070032 -2.224810082 0.139948859 FQELLAS(ph)PAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQELLASPAYR 11 0 Q9NSI2-2;Q9NSI2 Q9NSI2-2 FAM207A Protein FAM207A 1 FQELLAS(1)PAYR;FQELLAS(1)PAYR 114.56 0.0013014 47920000 72029 74125 75594 78394 83289 77727 81211 77955 98621 TRUE FALSE 68624.33192 81678.42177 79060.05967 70513.68618 97814.57523 75035.2945 68820.77041 71128.84693 113914.641 0.602418893 0.717014258 0.694028959 0.619004595 0.858665527 0.658697546 0.604143329 0.624404785 1 16.79759366 -0.980154341 4.337285246 1.000012048 0.671142165 0.647055515 0.07605727 8074615.602 3723349.907 891.9746928 0.01719507 0.104675648 0.980154341 -0.328869882 FQESEERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FQESEERPK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 152.97 7.22E-05 1504690000 2215150 1900860 1935990 2306660 1576020 2249630 2469070 2396480 1833370 FALSE TRUE 2110444.25 2094559.795 2024757.056 2074790.154 1850877.389 2171724.749 2092368.024 2186631.507 2117679.656 0.996583333 0.989082456 0.956120559 0.979746936 0.87401198 1.025520901 0.988047469 1.032560095 1 21.01405294 FQETEFLS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 FQETEFLS(1)PPR;FQETEFLS(1)PPR 137.81 7.42E-05 245760000 244890 298230 284800 301150 296150 296280 330350 307580 358910 TRUE FALSE 233314.535 328619.9761 297858.3617 270877.8299 347798.4662 286019.7493 279949.0402 280646.6646 414567.9297 0.562789638 0.79268065 0.718479024 0.653397937 0.838942044 0.689922516 0.675279056 0.676961831 1 18.66124899 -1.472387084 3.11847206 1.006725471 0.701746659 0.611468051 0.074887191 41128543.96 48553629.32 2390766.889 0.017005262 0.033698682 1.472387084 -0.304978812 FQEYHIQQNEALAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQEYHIQQNEALAAK 15 0 Q9Y5J7 Q9Y5J7 TIMM9 Mitochondrial import inner membrane translocase subunit Tim9 0 ; 193.69 8.26E-08 323510000 351240 270640 284090 329390 249380 265360 363280 328980 243540 FALSE TRUE 334637.5813 298218.5237 297115.8075 296279.0914 292871.793 256170.5167 307854.9639 300172.7672 281306.9394 1.189581679 1.060117907 1.056197932 1.053223543 1.041111157 0.910644143 1.09437387 1.067064921 1 18.10178562 4.982884861 0.796457437 1.028215732 1.348680591 0.512372153 0.048735947 2.737224199 1.022539586 0.016583842 0.849100848 96135.7373 -4.982884861 0.320464859 FQGIKHECQANGPEDLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FQGIKHECQANGPEDLNR 18 1 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;; 293.83 1.79E-49 10969580000 7189960 3916140 7322020 6271000 7274560 7037230 10457880 7779200 8718070 FALSE TRUE 6850104.84 4315199.118 7657741.859 5640627.166 8543240.961 6793528.961 8862338.334 7098012.008 10070023.77 0.680247137 0.428519258 0.760449234 0.560140402 0.848383396 0.67462889 0.880071243 0.704865467 1 23.26356375 1.84354054 0.304902749 1.013074112 0.512090993 0.484795538 0.116271173 1.105630199 0.338425914 0.174900368 0.199568355 69.74941034 -1.84354054 -0.500983118 FQNVADLHLYLYSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FQNVADLHLYLYSAK 15 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 176.33 8.05E-07 441303000 1671792 1761930 1477052 1774880 1277886 1771422 1800930 1895690 1210906 FALSE TRUE 1592769.705 1941472.67 1544776.295 1596465.69 1500748.914 1710077.212 1526165.052 1729693.334 1398687.118 1.138760545 1.388067885 1.10444736 1.141403013 1.072969712 1.222630272 1.091141137 1.23665494 1 20.41564184 -4.999998821 0.066974275 0.379942231 1.418250593 0.223101659 0.094474995 416.7587387 2.018655597 40.89230787 5.568425343 1.00E-05 4.999998821 1.038308363 FQPGETLTEILETPATSEQEAEHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FQPGETLTEILETPATSEQEAEHQR 25 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 250.99 7.84E-40 186631000 109473 101290 103182 115657 106691 100103 119864 112836 107061 FALSE TRUE 104298.4282 111611.5662 107912.9968 104030.9386 125297.8766 96636.40801 101576.5453 102955.4817 123663.4731 0.843405297 0.90254271 0.872634369 0.841242252 1.013216542 0.78144666 0.821394894 0.83254561 1 16.9160599 FQPLDQVVVDNVFPNCILLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQPLDQVVVDNVFPNCILLLK 21 0 Q5TBB1;A0A2R8YEC1;A0A2R8YEH2;A0A2R8Y6Y1;A0A2R8YGP2;A0A2R8Y6Q6;A0A2R8YCJ4;A0A087WZJ6;A0A2R8Y761;A0A087WXR7;A0A2R8YCX2;A0A2R8Y7Q3;A0A2R8Y883;A0A2R8Y6M7;A0A2R8YCP1;A0A2R8YE60;A0A2R8Y687;A0A2R8Y4S2;A0A2R8Y7R8;Q5TBB1-2 Q5TBB1 RNASEH2B Ribonuclease H2 subunit B 0 ; 79.97 0.0040282 166408000 73530 91891 95978 64239 417330 35930 63121 28922 236393 FALSE TRUE 70054.38262 101254.7974 100378.6862 57781.57367 490112.2199 34685.73509 53490.73215 26389.43635 273051.6191 0.256560949 0.370826577 0.367617986 0.211614104 1.794943467 0.127029956 0.195899707 0.096646328 1 18.05881419 FQQAVDAVEEFLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQQAVDAVEEFLRR 14 1 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EQB2;Q49A26-5 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 0 ; 223.7 5.49E-12 89636000 130914 97469 128077 124352 144079 113249 153236 130620 146002 FALSE TRUE 124725.9547 107401.2019 133949.4571 111851.9007 169206.332 109327.1587 129857.0338 119182.2203 168643.2445 0.739584648 0.636854457 0.794277041 0.663245664 1.003338927 0.648274759 0.770010291 0.706712093 1 17.363615 -5 0.261572469 2.677470315 0.71896516 0.356632838 0.105835637 205.4588141 2.014493272 185.6282031 0.125729769 1.00E-05 5 -1.958505155 FQQDDAHIFCAMEQIEDEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQQDDAHIFCAMEQIEDEIK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 247.31 4.06E-30 83683000 96328 158169 92337 132067 61665 119942 96051 108568 45439 FALSE TRUE 91774.76634 174286.6009 96570.74278 118791.3742 72419.35648 115788.3785 81396.65585 99061.21036 52485.44805 1.748575458 3.320665201 1.839952718 2.26332019 1.379798766 2.206104411 1.550842355 1.887403348 1 15.67962986 1.675893813 0.317152409 0.962423518 2.590917567 0.342892353 0.503497491 1.387591867 0.473995601 0.788718277 0.780366599 47.41260455 -1.675893813 1.628494049 FQS(ph)LGVAFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FQSLGVAFYR 10 0 P51149;C9J592;C9J8S3;C9IZZ0 P51149 RAB7A Ras-related protein Rab-7a 1 FQS(1)LGVAFYR 109.02 0.002175 11541000 26111 28199 25056 24365 47531 23742 37821 25432 43051 TRUE FALSE 24876.78478 31072.51016 26204.84238 21915.78391 55820.39135 22919.80859 32050.71182 23205.03926 49727.12921 0.500265854 0.624860326 0.526972757 0.440720875 1.122533962 0.460911558 0.644531714 0.466647474 1 15.60174552 -2.204666913 2.252112938 2.153688026 0.600843621 0.288467458 0.198171632 5561874.515 1196800.065 32639988.84 0.043412145 0.006242134 2.204666913 -1.552844405 FQSDSSSYPTVDSNS(ph)LLGQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FQSDSSSYPTVDSNSLLGQSR 21 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 FQSDSSSYPT(0.002)VDS(0.049)NS(0.949)LLGQS(0.001)R 108.08 0.00029158 0 32655 28634 32394 32573 31642 37596 46761 37437 48772 TRUE FALSE 31111.46287 31551.83715 33879.29694 29298.70016 37160.35478 36294.04109 39626.75063 34158.81781 56335.31267 0.552255085 0.560072105 0.601386508 0.520076996 0.659628092 0.644250282 0.703408728 0.606348242 1 15.78175191 -5 0.168025173 2.56279533 0.505603168 0.896278527 0.043509962 35.39487226 0.332275361 18.34176826 0.147768584 1.00E-05 5 -2.057192162 FQSGDFHVINGVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQSGDFHVINGVLR 14 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 168.67 3.45E-06 1782850000 2755800 2510500 2011530 2309800 2963500 2289520 3284800 2733400 2897700 FALSE TRUE 2625538.795 2766322.804 2103760.64 2077614.516 3480333.462 2210233.348 2783643.431 2494049.005 3347060.517 0.784431229 0.826493214 0.628539768 0.6207281 1.039817907 0.660350578 0.831668091 0.745146075 1 21.67446321 FQSSHHPTDITSLDQYVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FQSSHHPTDITSLDQYVER 19 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 217.97 2.01E-19 1310530000 937044 771282 885654 1044991 1391890 846123 1345800 1106550 427660 FALSE TRUE 892751.7872 849876.5127 926262.1119 939946.5193 1634635.175 816821.5483 1140473.493 1009654.616 493979.3286 1.807265477 1.720469792 1.875102982 1.90280537 3.309116557 1.653554109 2.308747404 2.043920782 1 18.91409115 0.901159055 19.7204116 1 2.055596002 0.336612075 0.47456851 17505.66088 3492682.18 0.438914579 0.109728645 7.964509879 -0.901159055 1.055596002 FQVWDLGGQTSIRPYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQVWDLGGQTSIRPYWR 17 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 158.15 3.08E-09 337190000 691410 686770 547480 634810 587230 612580 683660 681860 555120 FALSE TRUE 658728.4195 756752.6438 572582.4995 570997.6927 689642.7261 591366.201 579355.1107 622152.7236 641205.1744 1.027328608 1.180203582 0.892978601 0.890506994 1.075541424 0.922272971 0.903540916 0.970286499 1 19.29042654 3.733199711 24.99033362 0.945142013 1.103766097 0.47333741 0.066908471 311.5439169 1452289.481 0.017004076 0.027204111 5410.030467 -3.733199711 0.158624083 FQVWDYEEGEVEALLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FQVWDYEEGEVEALLDR 17 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 172.1 3.82E-09 113341000 60382 55873 51790 63921 58781 50809 71053 63704 65087 FALSE TRUE 57527.86253 61566.52222 54164.62273 57495.53964 69032.38779 49049.47159 60212.55987 58125.74004 75180.35954 0.765198023 0.818917635 0.720462406 0.764768086 0.918223698 0.652424009 0.800908113 0.773150599 1 16.19806819 -1.792816357 2.233222628 1.07642003 0.778157408 0.51739048 0.067747445 2894992.22 1687768.443 1199445.849 0.015376585 0.016113268 1.792816357 -0.298262622 FQWDLNAWTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FQWDLNAWTK 10 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 97.163 0.014532 96986000 222910 226910 177130 202720 193580 182750 234350 220830 211690 FALSE TRUE 212373.4861 250032.387 185251.5857 182342.2005 227340.2907 176421.3217 198595.6034 201492.9545 244517.804 0.86853997 1.022552889 0.757620029 0.745721569 0.929749437 0.721507059 0.812192814 0.824042058 1 17.89957999 3.733036813 24.991294 0.813873559 0.94554643 0.211684693 0.092121428 490.69703 2220056.98 0.021786404 0.034829398 5408.001614 -3.733036813 0.131672871 FRADNLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRADNLNK 8 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 119.86 0.0014704 517830000 862860 710330 617710 635610 729400 651440 926090 830780 826680 FALSE TRUE 822074.3178 782713.4346 646032.6145 571717.2752 856607.1291 628880.4695 784797.9617 758032.499 954877.3123 0.860921406 0.819700525 0.676560859 0.598733751 0.897086063 0.65859819 0.821883557 0.793853293 1 19.86495585 0.494139457 1.285679661 0.999915217 0.766215203 0.386831454 0.093819178 2.37812224 4.891511768 0.087734555 0.026186442 3.119891258 -0.494139457 -0.233700014 ASSHSSQTQGGGS(ph)VTKK ddPTM_SK-BR-3_Trastuzumab_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 ASSHSSQTQGGGS(0.943)VT(0.057)KK;ASSHSSQTQGGGS(0.998)VT(0.002)KK 232.29 1.18E-16 123221000 98615 69542 94143 111829 119121 101053 186890 151357 188233 TRUE FALSE 93953.66439 76628.40886 98459.54967 100587.7365 139895.6647 97553.50927 158376.498 138103.3787 217423.2123 0.432123431 0.352438951 0.452847461 0.462635684 0.643425618 0.448680287 0.728424975 0.635182312 1 17.73014645 0.909374877 0.294053324 1.088806609 0.335253159 0.847978337 0.074192312 0.711706557 0.181525495 0.191428715 0.103007468 8.116613697 -0.909374877 -0.753553449 FRDASLVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRDASLVFK 9 1 P61221;D6R9I9 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 113.44 0.0020812 377350000 973120 758270 827510 849510 791030 906280 1170950 1041740 918230 FALSE TRUE 927122.5461 835538.5751 865452.152 764115.6408 928985.3816 874895.2964 992300.0715 950519.723 1060624.419 0.874128985 0.787779878 0.815983619 0.72043942 0.875885342 0.824887001 0.935581016 0.896188798 1 20.01648244 1.52444512 0.963869887 0.983575212 0.8087148 0.627168432 0.047701539 0.314553304 0.575208645 0.040818317 0.015419493 33.45377408 -1.52444512 -0.174860412 FRDGPPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FRDGPPLR 8 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 123.86 0.0012125 5169860000 4626400 3725560 4181360 4458630 4518800 4175930 5058510 4622120 4831410 FALSE TRUE 4407719.241 4105198.8 4373079.492 4010440.042 5306877.289 4031316.497 4286741.394 4217382.669 5580640.387 0.789823199 0.735614287 0.783616071 0.718634379 0.950944143 0.72237525 0.768145069 0.755716616 1 22.41199925 -1.817428832 2.536198148 1.077274055 0.775506011 0.527561766 0.065949229 8761377.228 5803547.349 4142749.19 0.014773492 0.015225486 1.817428832 -0.301768044 FRDQDLASCDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRDQDLASCDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 157.03 2.81E-05 355160000 486160 452470 409910 483630 442290 439610 509930 440290 450240 FALSE TRUE 463180.1803 498577.2074 428704.779 435014.5936 519425.236 424386.1955 432130.813 401735.8735 520060.9197 0.890626776 0.958690008 0.824335694 0.836468531 0.998777674 0.816031698 0.830923449 0.772478489 1 18.9883211 FRDQDLASCDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FRDQDLASCDRDR 13 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;; 224.16 8.20E-12 1939710000 551053 478599 452386 443984 538103 485914 606626 521922 576516 FALSE TRUE 525005.8168 527368.7822 473128.3456 399353.8848 631947.9928 469086.6763 514074.0622 476219.7428 665919.1568 0.788392722 0.791941149 0.710489165 0.599703253 0.948986054 0.704419856 0.771976684 0.715131466 1 19.34498752 -1.448257206 2.807110308 1.006811371 0.758096662 0.431415633 0.088679744 20737658.45 22947245.64 1115542.911 0.01941389 0.035624009 1.448257206 -0.248714709 FRDQDLASCDRDRSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FRDQDLASCDRDRSSR 16 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 FRDQDLASCDRDRS(0.001)S(0.999)R;FRDQDLASCDRDRS(0.117)S(0.883)R;FRDQDLASCDRDRS(0.095)S(0.905)R;FRDQDLASCDRDRS(0.099)S(0.901)R 184.88 9.68E-09 12835400000 2751500 1358040 2908610 2153910 3130150 2481710 3866630 2945090 3908570 TRUE FALSE 2621442.048 1496425.82 3041972.646 1937394.875 3676047.169 2395767.76 3276704.578 2687202.307 4514691.073 0.580647049 0.331456969 0.673794197 0.429131217 0.814241132 0.530660398 0.725787108 0.595212887 1 22.10619584 -4.999999118 0.105545922 2.438365195 0.295023814 0.526734406 0.130712199 116.5797716 0.826779862 36.11765278 1.632826304 1.00E-05 4.999999118 -2.143341381 FRDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 163.72 0.0011166 8200298000 3624220 2920321 3455564 3607888 3808362 3400738 4477850 3932036 4407942 FALSE TRUE 3452910.303 3217905.03 3614005.027 3245216.244 4472539.127 3282969.59 3794671.741 3587726.083 5091503.133 0.678171105 0.63201474 0.709811019 0.637378817 0.87843197 0.644793788 0.745294983 0.704649686 1 22.27966021 -5 0.200562002 2.372579708 0.650255908 0.645377337 0.069880987 80.77427721 0.799373884 44.40676157 0.149198435 1.00E-05 5 -1.7223238 FRDYEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FRDYEEK 7 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 113.26 0.0056276 394480000 290740 168020 208620 330590 299170 282630 330000 189320 279950 FALSE TRUE 276997.2964 185141.429 218185.4334 297358.4651 351345.1533 272842.4522 279652.4391 172742.1372 323363.2162 0.8566135 0.572549442 0.674737949 0.919580367 1.086534076 0.843764654 0.864824523 0.534204661 1 18.30279605 3.243020234 24.99324793 0.875498515 0.695898401 0.213820368 0.156728499 165.0174291 924808.4101 0.042744241 0.05596668 1749.928215 -3.243020234 -0.179600115 FREDHPDLIQNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FREDHPDLIQNAK 13 1 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 122.45 0.00014115 431220000 435690 381160 387630 415710 340420 386490 483350 450570 356330 FALSE TRUE 415095.7972 420000.6373 405403.2189 373922.041 399789.1402 373105.7544 409606.0802 411115.7022 411587.8365 1.008522994 1.020439867 0.98497376 0.908486617 0.97133371 0.906503354 0.995185095 0.998852895 1 18.65084082 3.479225427 24.96363588 0.960566536 1.012519001 0.281044769 0.033415023 86.83301038 1030180.011 0.008776708 0.012088019 3014.570373 -3.479225427 0.051952465 FREFLESQEDYDPCWSLQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FREFLESQEDYDPCWSLQEK 20 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3;F8VWB3;E5RGL6 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ; 125.88 2.22E-05 106275000 205836 153886 198670 203915 156263 199060 230328 226738 197773 FALSE TRUE 196106.5402 169567.1584 207779.216 183417.0768 183515.2177 192166.5023 195187.2333 206883.6187 228442.6268 0.858449857 0.742274595 0.909546607 0.802902153 0.803331761 0.841202472 0.854425621 0.905626159 1 17.80147235 0.967715415 1.061059857 1.000063419 0.818288428 0.633357045 0.042720423 0.338509056 0.794611471 0.0374408 0.012140497 9.283578511 -0.967715415 -0.181774991 FREGERPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FREGERPSLR 10 2 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ; 138.76 3.16E-05 193061000 146380 129494 160863 150202 249847 125462 184022 130194 294020 FALSE TRUE 139460.9075 142689.5858 168238.7277 135103.4096 293420.2377 121117.2195 155946.0641 118793.5232 339615.12 0.410643989 0.420150863 0.495380558 0.397813294 0.863978723 0.356630822 0.459184692 0.349788676 1 18.37354116 -1.188295478 3.966142307 1.000299483 0.466181554 0.562708559 0.147033729 10580757.61 6350183.997 27303.91847 0.031866297 0.064819328 1.188295478 -0.534117928 FRELAEEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 211.37 5.48E-08 1388500000 1082880 793480 828900 945790 1111790 896010 1252050 1049560 1212340 FALSE TRUE 1031694.408 874336.5141 866905.8849 850717.3923 1305685.824 864980.949 1061026.777 957654.9623 1400343.495 0.736743815 0.624372889 0.619066599 0.607506226 0.932403962 0.617691982 0.757690367 0.683871468 1 20.41734932 -5 0.235668506 2.705530297 0.662766124 0.491287226 0.097412136 135.0141066 1.348410913 110.0013549 0.146188472 1.00E-05 5 -2.042764173 FRFS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRFSGR 6 1 Q9H329-2;Q9H329;H7C3Q2 Q9H329-2;H7C3Q2 EPB41L4B;HECW1 Band 4.1-like protein 4B 1 FRFS(1)GR;FRFS(1)GR 95.815 0.025991 625150000 182093 159496 142282 216439 227850 153611 196728 168647 221690 TRUE FALSE 173485.8248 175748.8237 148805.7704 194682.1405 267586.9679 148291.4126 166713.5304 153879.3746 256068.553 0.677497579 0.686335052 0.581116926 0.760273522 1.044981763 0.579108254 0.651050387 0.600930387 1 17.96617057 -1.699405539 2.727594292 1.046044326 0.695570624 0.330815257 0.135108394 46671149.39 40400788.51 14795525.76 0.033144783 0.019979953 1.699405539 -0.350473703 FRGPFTDVVTTNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FRGPFTDVVTTNLK 14 1 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 114.43 0.00043578 174620000 157740 133960 128790 151280 176770 149680 208950 154960 153840 FALSE TRUE 150283.9428 147610.6763 134695.1489 136073.047 207598.632 144496.5441 177070.8399 141390.8809 177696.7215 0.845732783 0.8306888 0.758005819 0.765760031 1.16827497 0.813163816 0.99647781 0.795686492 1 17.43905754 FRGQKPTLWALLNSEYVTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FRGQKPTLWALLNSEYVTEEK 21 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 179.95 3.13E-17 104980000 320360 258990 266070 293830 199240 293570 337720 354900 214260 FALSE TRUE 305217.2177 285381.3754 278269.5727 264293.6502 233987.3929 283403.5973 286194.6113 323823.0746 247486.3465 1.233268914 1.153119675 1.124383533 1.067912044 0.945455764 1.145128211 1.156405658 1.30844824 1 17.91698941 4.213616002 1.698480791 1.110393046 1.230522135 0.148261101 0.096632255 0.842930012 4.323166936 0.026442878 0.118150459 16353.69909 -4.213616002 0.120129089 FRGTEPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRGTEPEPR 9 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 81.338 0.019668 250920000 482450 349310 438650 435550 451860 451740 513150 492820 521000 FALSE TRUE 459645.5446 384905.0861 458762.5364 391767.6865 530664.2409 436096.1305 434859.5429 449666.0682 601794.0191 0.763792145 0.639596064 0.762324852 0.650999635 0.88180378 0.724660127 0.722605292 0.747209267 1 19.19891024 -5 0.279347944 2.965552288 0.712763312 0.610099906 0.066256862 142.8506961 1.368843882 162.7068947 0.069738664 1.00E-05 5 -2.252788977 FRIDELEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FRIDELEPR 9 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;;; 160.53 5.95E-05 1911934000 1796768 1521019 1540050 1769214 1743452 1523544 1943770 1694986 1790064 FALSE TRUE 1711838.337 1676012.565 1610662.816 1591369.247 2047509.477 1470783.289 1647212.187 1546564.04 2067657.983 0.827911749 0.810585009 0.778979323 0.769648201 0.990255397 0.711328131 0.796656024 0.747978657 1 20.97956613 -1.150151181 4.704905045 1.000019555 0.805142255 0.410711816 0.073711192 0.340989427 42062851.91 1609.586848 0.015700076 0.070769939 1.150151181 -0.1948773 FRKVQHELDEAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRKVQHELDEAEER 14 2 P13533;P12883 P13533 MYH6;MYH7 Myosin-6;Myosin-7 0 ; 59.898 0.054689 762400000 179781 135390 201216 162670 731400 91979 207808 99706 618900 FALSE TRUE 171283.1084 149186.3949 210441.9526 146318.1025 858955.9284 88793.74417 176103.0729 90975.21407 714875.8511 0.239598398 0.208688536 0.294375523 0.204676242 1.201545593 0.124208622 0.246340777 0.127260158 1 19.44733319 -2.223515615 2.336410725 3.260676127 0.320780725 0.308415485 0.31459173 33628904.42 5745093.045 402331437.8 0.072900082 0.005977016 2.223515615 -2.939895402 FRLEAPDADELPKGEFDPGQDTYQHPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FRLEAPDADELPKGEFDPGQDTYQHPPK 28 2 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 128.08 1.85E-05 107430000 256080 179510 193220 188250 130340 199000 204360 223750 117170 FALSE TRUE 243975.6059 197802.2731 202079.3281 169326.7523 153071.2547 192108.5801 173181.1287 204157.2638 135340.1252 1.802684943 1.461519803 1.493122072 1.25112011 1.131011624 1.419450291 1.279599294 1.508475506 1 17.0462301 4.444264027 0.810101926 1.28412514 1.969042173 0.56416792 0.147399856 1.164499203 0.782017118 0.049736279 0.66212326 27814.03695 -4.444264027 0.684917034 FRLS(ph)LFSDLPEDTELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 FRLSLFSDLPEDTELQR 17 1 Q9BST9 Q9BST9 RTKN Rhotekin 1 FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(0.994)LFS(0.006)DLPEDTELQR;FRLS(0.999)LFS(0.001)DLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(0.964)LFS(0.036)DLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR 273.41 7.05E-36 3221609700 1256290 1216753.2 1142844.2 1385219 1368623 1177453.8 1436967 1258466 1421803 TRUE FALSE 1196907.661 1340741.734 1195244.737 1245974.154 1607310.418 1136678.28 1217731.292 1148268.045 1642288.948 0.728804552 0.816386018 0.727791987 0.758681446 0.978701355 0.692130506 0.741484191 0.699187586 1 20.64727655 -2.370990675 2.288709846 2.630261365 0.769259753 0.438959866 0.082452199 5199525.316 478483.6846 44156269.36 0.018722289 0.004256076 2.370990675 -1.861001612 FRNS(ph)VEGLNQEIEIIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FRNSVEGLNQEIEIIIK 17 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK 228.48 8.59E-16 290067000 397715 354324 372427 447820 316839 407804 454482 441003 377697 TRUE FALSE 378915.8001 390430.0184 389503.1463 402804.2828 372095.6213 393681.6452 385142.4238 402386.4394 436268.3218 0.868538423 0.894930938 0.892806392 0.923294823 0.852905432 0.902384211 0.882810886 0.922337056 1 18.7348562 0.87039533 2.644044501 0.999962327 0.88807878 0.778930649 0.01883987 0.209435327 2.914445267 0.016281266 0.004335516 7.419853494 -0.87039533 -0.111883546 FRPAGAAPRPPPKPM ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FRPAGAAPRPPPKPM 15 3 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ;; 119.17 0.00028572 2234730000 1594790 1325160 1363480 1661120 1184820 1465850 1649960 1568200 1311070 FALSE TRUE 1519407.437 1460195.311 1425996.907 1494141.062 1391452.233 1415087.247 1398228.298 1430880.094 1514384.04 1.003317123 0.964217314 0.941634928 0.986632864 0.918823889 0.934430904 0.923298359 0.944859466 1 20.53029968 4.631930909 0.721001512 0.941277986 1.036249862 0.263915102 0.026224271 2.551135783 1.109400336 0.009532759 0.192671416 42848.03487 -4.631930909 0.094971876 FRPDMEEEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FRPDMEEEEAK 11 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;; 210.79 1.05E-08 887650000 1626550 1693400 1183480 1909000 821470 1525250 1268850 1619810 865830 FALSE TRUE 1549666.205 1865959.385 1237743.729 1717103.693 964734.1079 1472430.21 1075263.628 1477970.849 1000098.494 1.549513587 1.865775617 1.23762183 1.716934585 0.964639096 1.472285198 1.075157732 1.477825292 1 19.93171066 3.167732055 1.16609124 1.216804515 1.6877001 0.329061724 0.248154464 0.443272682 1.286007697 0.086957219 0.125003239 1471.404415 -3.167732055 0.470895585 FRPFTFSQS(ph)TPIGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRPFTFSQSTPIGLDR 16 1 A0A0A0MRY4;Q96N96-6;J3KQJ8;Q96N96-5;Q96N96-4;Q96N96 A0A0A0MRY4 SPATA13 Spermatogenesis-associated protein 13 1 FRPFTFSQS(0.882)T(0.118)PIGLDR;FRPFTFS(0.024)QS(0.897)T(0.079)PIGLDR 171.13 3.05E-09 661180000 417120 271310 397310 394650 435050 378940 515990 431390 499890 TRUE FALSE 397403.5643 298956.7975 415527.0565 354979.0322 510922.5823 365817.2128 437266.2487 393615.2047 577410.3881 0.688251497 0.517754449 0.719639038 0.614777703 0.884851732 0.633548028 0.757288503 0.681690549 1 19.13923754 -4.999999994 0.136967717 2.110318693 0.555360098 0.539633121 0.092937072 96.76268875 0.819399411 29.28863769 0.551651612 1.00E-05 4.999999994 -1.554958595 FRPFTFSQST(ph)PIGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FRPFTFSQSTPIGLDR 16 1 A0A0A0MRY4;Q96N96-6;J3KQJ8;Q96N96-5;Q96N96-4;Q96N96 A0A0A0MRY4 SPATA13 Spermatogenesis-associated protein 13 1 FRPFT(0.001)FS(0.019)QS(0.387)T(0.594)PIGLDR 93.5 0.0071309 37640000 25350 17150 18478 27946 27764 19741 26070 21765 34566 TRUE FALSE 24151.75574 18897.6045 19325.23458 25136.81499 32606.03281 19057.36422 22092.54269 19859.14122 39926.31874 0.604908153 0.473311968 0.484022449 0.629580081 0.816655125 0.477313332 0.553332824 0.497394747 1 15.28505244 -1.343418257 5.463063779 1.000113112 0.56302411 0.632927338 0.103574806 0.000139825 1.68E-05 0.09827023 0.023156569 0.045350465 1.343418257 -0.437089002 FRPPETTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRPPETTER 9 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 94.409 0.0079723 376040000 274340 331810 439940 378690 336220 363050 340050 364920 370230 FALSE TRUE 261372.4919 365621.8162 460111.6842 340623.3617 394856.6615 350477.4875 288169.1271 332965.6702 427643.3775 0.611192656 0.854968966 1.075923792 0.796512654 0.923331641 0.819555513 0.673853828 0.778605931 1 18.70604867 -0.071902138 8.02148102 1 0.808301752 0.167909969 0.126976363 17107216.42 2132675.461 0.125792664 0.030509203 0.847418346 0.071902138 -0.191698248 FRPSLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 137.14 0.00069414 490900000 676240 510540 442428 502983 810040 492583 778290 634340 831350 FALSE TRUE 644275.4754 562564.6064 462713.7614 452422.1932 951310.7195 475524.7272 659547.5662 578793.8268 960271.5121 0.670930531 0.585839108 0.48185722 0.471139868 0.99066848 0.495198203 0.686834461 0.602739766 1 19.87308285 -4.999999992 0.291181911 3.965606862 0.60138864 0.386338899 0.149751747 254.4641213 2.391496548 458.5077783 0.145230927 1.00E-05 4.999999992 -3.364218222 FRQDLMNIAGTTLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRQDLMNIAGTTLSSK 16 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 192.85 4.27E-10 379260000 999210 792930 832410 993650 868360 901080 1126740 961270 978460 FALSE TRUE 951979.3235 873730.4685 870576.8219 893766.4142 1019801.709 869875.3737 954835.119 877096.1028 1130194.58 0.842314537 0.773079684 0.770289327 0.790807557 0.902324014 0.769668683 0.844841354 0.776057609 1 20.10813974 -2.103484177 2.411755174 1.338463453 0.809501214 0.658652844 0.043282497 5234709.345 1411005.559 9727958.606 0.009576692 0.007879811 2.103484177 -0.528962239 FRREEDAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FRREEDAEK 9 2 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;;; 114.4 0.00092473 889582000 1167150 689078 1022630 937960 971660 1110440 1446580 1220760 1183920 FALSE TRUE 1111981.133 759295.8316 1069518.597 843674.4788 1141117.196 1071985.184 1225877.653 1113863.783 1367516.267 0.813139236 0.555237148 0.782088391 0.616939264 0.834445062 0.78389209 0.896426377 0.814515929 1 20.38312656 1.727770161 0.602214448 0.976630798 0.679918701 0.522705826 0.087291771 0.516739074 0.401963986 0.075955382 0.042441657 53.42815306 -1.727770161 -0.296712097 FRRS(ph)ET(ph)PPHWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 79.022 0.053463 2305590000 1071220 788040 1002300 1085380 1196080 958090 1292270 954100 1286650 TRUE FALSE 1020585.554 868342.1719 1048256.446 976275.5403 1404675.973 924911.1031 1095110.477 870553.946 1486177.111 0.68671866 0.584279065 0.705337499 0.6569039 0.945160549 0.622342449 0.736864045 0.585767295 1 20.50317462 -2.067291949 2.604118326 1.466689924 0.688318629 0.471896176 0.102900914 10695029.35 4201732.95 29647461.99 0.02358216 0.008564619 2.067291949 -0.778371295 FRS(ph)FSELPSCDGNESWAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRSFSELPSCDGNESWAYR 19 1 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 FRS(0.986)FS(0.014)ELPSCDGNESWAYR;FRS(0.901)FS(0.099)ELPSCDGNESWAYR 212.99 3.39E-17 529120000 171948 125708 165107 152433 156491 156106 188732 181117 202846 TRUE FALSE 163820.3588 138517.7881 172677.3193 137110.1452 183782.9809 150700.0101 159937.4671 165257.4353 234302.3217 0.699183677 0.591192555 0.736985097 0.585184749 0.784383951 0.643186158 0.682611533 0.705317105 1 17.83801172 -4.999999992 0.302204926 3.773413507 0.655682881 0.740381032 0.0601079 122.0741125 1.12365414 214.5977965 0.051362856 1.00E-05 4.999999992 -3.117730626 FRSETITEEELVGLMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FRSETITEEELVGLMNK 17 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ;;; 192.96 1.43E-10 443331000 799070 534050 699880 718620 692200 733680 1000640 830790 863010 FALSE TRUE 761299.5447 588470.3022 731970.1903 646382.9523 812919.4608 708272.4776 847973.99 758041.6233 996841.1832 0.763711971 0.590335063 0.734289677 0.648431228 0.815495462 0.71051687 0.850661073 0.760443726 1 19.92700415 0.763225007 0.373277272 1.025964053 0.66635441 0.650374284 0.066292946 1.019712518 0.343254557 0.122435844 0.053466381 5.797289744 -0.763225007 -0.359609643 FRTPS(ph)FLKK ddPTM_SK-BR-3_Trastuzumab_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 FRTPS(1)FLKK 116.24 0.00070244 715130000 1649100 1434200 1392500 1629700 1066600 1714200 1793400 1847200 1249900 TRUE FALSE 1571150.311 1580346.611 1456347.502 1465879.46 1252614.702 1654836.824 1519783.892 1685449.375 1443728.108 1.088259141 1.094628969 1.008740838 1.01534316 0.867625071 1.146224704 1.052680129 1.167428525 1 20.46136764 -0.379342071 7.649272437 1.000000007 1.0562762 0.041271552 0.083317812 0 0 0.07699808 0.018148622 0.417501393 0.379342071 0.056276193 FRYS(ph)GK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FRYSGK 6 1 Q9HCM4-2;Q9HCM4-4;Q9HCM4-3;Q9HCM4;Q5JV61;A2A2Y4-3;A2A2Y4-5;A2A2Y4-2;A2A2Y4 Q9HCM4-2 EPB41L5;FRMD3 Band 4.1-like protein 5;FERM domain-containing protein 3 1 FRYS(1)GK;FRYS(1)GK 69.825 0.056009 255430000 328320 329870 212832 464130 337750 301230 331090 272606 234333 TRUE FALSE 312800.9643 363484.128 222590.5577 417474.7706 396653.4931 290798.3296 280576.1396 248735.1735 270672.1648 1.155645112 1.342894377 0.822362203 1.542363142 1.465438802 1.074356241 1.036590297 0.918953649 1 18.04618701 2.018130403 23.81242586 1.005803449 1.259608634 0.310104849 0.194299293 174.3418685 228978.5501 0.070440647 0.052011374 104.2630447 -2.018130403 0.253805185 FRYS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FRYSGR 6 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;A0A1B0GWG0;E9PK52;A0A2R8Y5B3;E9PII3;E9PHY5;A0A2R8Y6D0;H0Y5B0;J3KT37;H0YKW6;O43491;O43491-4;O43491-3;O43491-2;A0A087WVP2;H0Y5N1;B5MC67;Q7Z6J6-2;Q7Z6J6;Q9Y2J2;A0A1B0GTF8;A8K968;A0A0A0MRA8;A0A0A0MSA4;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2-4;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 Q9H4G0-2;A0A087WVP2;Q9Y2J2;A0A2R8Y4N6 EPB41L1;EPB41L2;EPB41L3;FRMD5;EPB41 "Band 4.1-like protein 1;Band 4.1-like protein 2;FERM domain-containing protein 5;Band 4.1-like protein 3;Band 4.1-like protein 3, N-terminally processed;Protein 4.1" 1 FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR 98.299 0.02428 2522630000 1447235 1139190 1163904 1572650 1607676 1272246 1633868 1272311 1463655 TRUE FALSE 1378827.07 1255274.756 1217270.15 1414564.234 1888054.185 1228187.802 1384591.429 1160900.704 1690631.142 0.815569426 0.74248884 0.720009303 0.836707783 1.116774758 0.72646704 0.818979016 0.686667053 1 20.6891305 3.09840372 7.334315864 0.856473887 0.764468983 0.134863672 0.124993435 0.518902056 33.79475186 0.035060163 0.042010729 1254.306635 -3.09840372 -0.092004904 FS(ph)GGFGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;FS(1)GGFGAR 157.34 0.00039692 1535610000 1394420 1490620 1228270 1611480 1111410 1362530 1466000 1393150 1118880 TRUE FALSE 1328508.53 1642515.873 1284587.394 1449490.969 1305239.552 1315345.244 1242334.775 1271158.4 1292390.196 1.027946927 1.270913288 0.993962503 1.121558314 1.009942319 1.017761701 0.961269111 0.983571683 1 20.30161028 2.821247518 1.082553016 0.979473246 1.134979053 0.339440778 0.073964325 0.454137722 1.124458189 0.034490146 0.034723463 662.5940287 -2.821247518 0.155505807 FS(ph)PGAPGGSGSQPNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK 270.99 4.04E-35 163377000 344230 434670 291420 437490 207093 363800 332600 344950 203315 TRUE FALSE 327958.9301 478963.3672 304781.8953 393512.674 243209.9536 351201.5148 281855.7614 314744.3493 234844.0518 1.396496643 2.039495416 1.297805471 1.675633983 1.035623222 1.495466937 1.200182671 1.340227044 1 17.84134353 3.079462075 1.507862003 1.249279805 1.687200407 0.326548907 0.250589457 0.38973899 1.833697508 0.081877705 0.103967696 1200.776211 -3.079462075 0.437920602 FS(ph)PPRHELS(ph)PPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 62.739 0.04003 282000000 449620 387520 420870 452100 273270 433680 433750 424970 273780 TRUE FALSE 428367.3537 427008.7286 440167.3058 406654.0491 320928.2015 418661.5529 367573.4711 387757.3739 316236.4041 1.354579511 1.350283279 1.391893217 1.285917889 1.014836361 1.323887912 1.162337626 1.226162987 1 18.27064393 7.999999981 0.033966298 0.088259487 3.022838009 0.542496443 0.093438372 750.2669519 1.94952672 50.54400409 137.805026 99999995.62 -7.999999981 2.934578522 FS(ph)PTMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSPTMGR 7 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.963)PT(0.037)MGR;FS(0.993)PT(0.007)MGR 134.48 0.0033258 206846000 507280 600150 435030 564060 415790 503680 476880 511610 384830 TRUE FALSE 483301.8797 661305.9673 454976.5558 507359.6172 488303.6444 486237.4353 404123.1975 466810.7162 444507.471 1.087275043 1.487727452 1.023552101 1.141397277 1.098527418 1.093879107 0.909148268 1.050175186 1 18.76184814 2.967579446 0.926214346 0.992843363 1.268470357 0.318206812 0.125222158 0.527968101 0.993620845 0.063333908 0.075711306 928.067247 -2.967579446 0.275626994 FS(ph)PVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;FS(1)PVLGR 162.49 0.0013321 2557596000 4277460 3734500 3186920 4212290 3288850 3610040 4196860 3867790 3330980 TRUE FALSE 4075272.943 4115049.796 3333043.434 3788862.606 3862424.399 3485023.41 3556551.926 3529105.803 3847531.366 1.05919161 1.069529889 0.86628103 0.984751584 1.003870802 0.905781676 0.924372432 0.917238995 1 21.87550166 3.760840811 24.86230167 0.940965983 1.064360775 0.571975386 0.043546587 451.3770175 503686.5512 0.010596894 0.019084711 5765.550903 -3.760840811 0.123394793 FS(ph)PVTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK 91.867 0.016877 810500000 3060380 3153760 2540680 3596570 1698740 2996070 2812870 2939700 1565140 TRUE FALSE 2915721.902 3475131.73 2657172.691 3235035.951 1994999.718 2892315.345 2383715.02 2682284.284 1807853.918 1.612808355 1.922241446 1.469793917 1.789434378 1.10351821 1.599861204 1.318532983 1.483684195 1 20.78584668 1.662726201 0.157166586 0.73766715 2.082742599 0.484743093 0.203255995 3.090504456 0.495548456 1.72001764 1.852107553 45.99664979 -1.662726201 1.345075448 FS(ph)QIQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSQIQPK 7 0 Q86V21;Q86V21-2 Q86V21 AACS Acetoacetyl-CoA synthetase 1 FS(1)QIQPK 56.729 0.077199 402670000 317340 274080 289080 322360 579410 191740 362040 199120 729990 TRUE FALSE 302339.9671 302009.0636 302334.6039 289955.7604 680458.9206 185099.9957 306804.1487 181683.9972 843193.1209 0.358565505 0.358173064 0.358559144 0.343878233 0.807002457 0.219522659 0.363859881 0.215471394 1 19.68550357 -1.47017587 3.426140751 1.009502327 0.378197798 0.590804523 0.162647069 127450777.5 185243986.3 11712833.26 0.03586273 0.033870697 1.47017587 -0.631304529 FSALQQAVPTESTDNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 158.64 5.31E-09 2593250000 1590650 1416060 1464930 1573890 1541470 1539410 1634570 1625160 1697550 FALSE TRUE 1515463.127 1560358.124 1532098.49 1415679.587 1810301.88 1486099.846 1385186.326 1482852.375 1960797.384 0.772881043 0.795777339 0.781365021 0.721991777 0.923247804 0.757905869 0.706440317 0.75624967 1 20.90300903 -0.939346877 4.871655414 1.000001529 0.775284301 0.590841985 0.058309355 9.40E-07 2.05E-07 0.054815859 0.012920134 0.11498816 0.939346877 -0.224717229 FSCMAWTHDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSCMAWTHDGK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 87.001 0.01405 359380000 371720 322810 276840 342920 289690 324230 376730 395370 290800 FALSE TRUE 354149.5323 355704.706 289533.3878 308449.0301 340211.8443 313001.8338 319252.9194 360749.3068 335895.7788 1.054343504 1.058973433 0.86197388 0.918287902 1.012849419 0.931842118 0.950452311 1.073991784 1 18.35765414 3.822961492 24.99969542 0.959738503 1.05665916 0.307404197 0.057394173 86.80691321 25710.83808 0.013956362 0.025160187 6652.141706 -3.822961492 0.096920657 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_SK-BR-3_Trastuzumab_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 ; 301.85 4.08E-81 226160000 195846 179125 160110 199112 148075 182664 224438 215640 131472 FALSE TRUE 186588.7477 197378.0411 167451.2019 179096.8835 173899.2331 176338.2999 190195.861 196757.4184 151860.0063 1.228689187 1.299736817 1.102668214 1.17935517 1.145128578 1.161189863 1.252442073 1.295650008 1 17.21238245 -1.475079949 3.080594916 0.994878422 1.212533625 0.510809503 0.063872493 13321360.03 13563423.18 568152.7261 0.015912206 0.033490378 1.475079949 0.217655203 FSDFLGLHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSDFLGLHSK 10 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 100.88 0.0037132 2655800000 688670 683130 625210 572420 4804200 308470 591030 344130 2676200 FALSE TRUE 656117.9339 752741.7237 653876.4969 514879.2541 5642050.959 297787.6066 500857.5185 313996.1529 3091211.428 0.212252688 0.243510268 0.211527588 0.16656229 1.825190897 0.096333626 0.16202629 0.101577055 1 21.5597409 FSDHVALLSVFQAWDDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FSDHVALLSVFQAWDDAR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;; 271.82 5.76E-39 689024000 1090937.4 881228.8 978017.1 1140579.5 1209826.6 978185.8 1362017 1158110.3 1174379 FALSE TRUE 1039370.951 971027.0166 1022860.151 1025926.282 1420819.976 944310.9805 1154216.291 1056700.023 1356495.697 0.766217654 0.71583494 0.754045998 0.756306329 1.047419449 0.696140048 0.850880909 0.778992535 1 20.37145304 -5 0.107994957 1.653612387 0.6681386 0.319811448 0.096893669 192.5140687 1.388967271 28.10772989 1.186097298 1.00E-05 5 -0.985473787 FSDIQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 113.89 0.014024 155376000 481840 396680 437570 470340 438300 438250 537900 463200 457590 FALSE TRUE 459064.3781 437102.143 457633.0173 423060.5296 514739.3812 423073.2926 455833.4758 422639.7524 528550.7202 0.868534202 0.8269824 0.865826116 0.800416145 0.973869416 0.800440292 0.862421445 0.799620048 1 19.01168239 -1.488599908 5.700327266 1.000182056 0.850254765 0.454517445 0.051721543 0.000103508 9.29E-06 0.043316405 0.010197435 0.032463855 1.488599908 -0.149927292 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK 29 0 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 125.47 2.21E-05 42710000 36317 29503 32893 37493 27240 32880 36936 39315 26614 FALSE TRUE 34600.36738 32509.38924 34401.17659 33724.13241 31990.64738 31741.35736 31300.73482 35872.37018 30741.16319 1.125538652 1.057519816 1.11905904 1.097035014 1.040645312 1.032535989 1.018202682 1.166916488 1 14.90788413 2.74409878 23.79219844 1.04828956 1.096675191 0.197835753 0.047706823 364.0089088 1563795.466 0.013700852 0.014161128 554.7518769 -2.74409878 0.048385631 FSDSLQEMINFHTILFDQTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSDSLQEMINFHTILFDQTQR 21 0 Q15057;A0A0U1RQT1 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 0 103.31 0.00044102 11821000 15023 14000 15353 14132 14863 13534 15767 13669 15489 FALSE TRUE 14312.89256 15426.61592 16056.95024 12711.42451 17455.10249 13065.31419 13361.45457 12472.0699 17890.95501 0.800007185 0.862257823 0.897489834 0.710494465 0.975638387 0.730274833 0.746827353 0.697115939 1 14.12694278 FSEAEHWLDYFPPLAIQDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSEAEHWLDYFPPLAIQDLK 20 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 179.78 5.70E-17 90408000 306690 362600 276260 381960 195500 311870 282360 335840 152330 FALSE TRUE 292193.3715 399549.3522 288926.7943 343564.6551 229595.1381 301069.8637 239280.7961 306432.0692 175952.5584 1.660637243 2.270778873 1.642072141 1.952598236 1.304869564 1.711085456 1.359916549 1.741560748 1 17.42482697 1.211467329 0.23182325 0.838460086 2.104216257 0.472178026 0.255171817 1.910763839 0.428500405 0.963503566 0.721291905 16.27298893 -1.211467329 1.26575617 FSEAEHWLDYFPPLAIQDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSEAEHWLDYFPPLAIQDLKR 21 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 132.45 7.48E-06 276820000 708440 596590 714850 730480 571540 758970 840260 843280 550550 FALSE TRUE 674953.4452 657383.1993 747626.5796 657050.7626 671216.395 732686.6786 712062.9046 769437.9327 635926.4822 1.061370243 1.033740877 1.175649388 1.033218117 1.055493699 1.152156262 1.119725195 1.209947933 1 19.27850046 2.243631965 24.99776918 1.130062809 1.068693068 0.112467503 0.065013322 205.3059058 1011999.008 0.020826445 0.016929267 175.2394838 -2.243631965 -0.06136974 FSEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FSEEQR 6 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 137.59 0.029481 1686760000 2857410 2862260 2658910 3276230 2716530 2767380 3063000 2889000 2810410 FALSE TRUE 2722345.892 3153927.548 2780823.654 2946897.136 3190291.972 2671544.937 2595683.094 2636023.844 3246234.029 0.838616646 0.971565057 0.856630677 0.907789491 0.98276709 0.822967449 0.799598264 0.812025202 1 21.63033558 2.200783061 24.99601379 0.836732234 0.91038444 0.085247914 0.07138655 249.871641 165329.4278 0.024213057 0.017882941 158.7753437 -2.200783061 0.073652206 FSEGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.974)PS(0.026)QDQEK;FSEGVLQS(0.984)PS(0.016)QDQEK;FSEGVLQS(0.98)PS(0.02)QDQEK;FSEGVLQS(0.984)PS(0.016)QDQEK;FSEGVLQS(0.999)PS(0.001)QDQEK 343.43 9.21E-70 575388000 1784640 1673850 1658880 1929730 1241082 1846720 1946730 1983660 1273734 TRUE FALSE 1700283.604 1844417.218 1734941.289 1735749.874 1457526.308 1782767.623 1649720.584 1809960.214 1471258.163 1.155666386 1.253632615 1.17922288 1.179772468 0.99066659 1.211729979 1.121299188 1.230212521 1 20.48861899 -5 0.179379136 0.345235699 1.201452285 0.309865388 0.073984301 156.7931429 1.507713393 36.86296849 0.218501691 1.00E-05 5 0.856216586 FSEGVLQSPS(ph)QDQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.187)PS(0.813)QDQEK 361.77 3.96E-83 253400000 607970 551390 535600 600340 382140 596240 623780 572350 393480 TRUE FALSE 579232.463 607577.2679 560157.7898 539992.6826 448785.095 575592.0593 528610.9045 522231.9998 454498.8688 1.274442034 1.336806997 1.232473452 1.188105669 0.987428409 1.266432325 1.163063191 1.149028162 1 18.79391718 7.999999991 0.079986921 0.845933769 2.125194252 0.482409475 0.081137667 158.2596708 0.922611901 2.225216404 22.38331181 99999998.04 -7.999999991 1.279260483 FSELSEELLWEYVHSGEPMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSELSEELLWEYVHSGEPMDK 21 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 86.727 0.0020551 11685000 37783 38615 33587 41090 25408 35163 37940 37678 28752 FALSE TRUE 35997.07247 42549.9124 35126.99717 36959.55513 29839.14716 33945.29649 32151.55618 34378.71458 33210.71332 1.083899407 1.281210433 1.057700774 1.112880497 0.898479562 1.022118862 0.968107968 1.035169412 1 15.01936109 3.198714485 1.889679934 0.98723107 1.176322471 0.51453419 0.070358169 0.215292448 1.583139901 0.020814507 0.028160332 1580.208831 -3.198714485 0.189091401 FSEVLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSEVLKR 7 1 P12277;H0YJG0;H0YJK0 P12277 CKB Creatine kinase B-type 0 ; 81.784 0.042111 615240000 827230 657600 631660 632330 470700 537570 632020 609880 465960 FALSE TRUE 788128.4773 724610.1876 660622.2358 568766.9871 552789.931 518953.8161 535593.7412 556475.674 538218.697 1.464327571 1.346311809 1.227423424 1.056758136 1.027073073 0.964206221 0.995122882 1.033921113 1 19.03783298 3.525319357 1.195604483 0.993464383 1.448334212 0.981867315 0.022688099 0.050725546 0.146522845 0.007729475 0.016441788 3352.118456 -3.525319357 0.45486983 FSFSGNTLVSSSADPEGHFETPIWIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FSFSGNTLVSSSADPEGHFETPIWIER 27 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 180.34 1.83E-17 293760000 219779 220249 208525 245062 228280 198396 241764 239128 180313 FALSE TRUE 209390.4822 242692.6235 218086.0775 220427.9022 268091.9597 191525.4968 204878.4615 218188.6846 208275.0191 1.005355722 1.165250756 1.047106266 1.058350171 1.287201705 0.919579782 0.983691959 1.047598918 1 17.66813028 FSFSPEPTLEDIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;;;; 293.96 2.36E-43 1991508000 1884654 1458892 1579346 1797482 1996180 1621578 2010300 1795279 2358860 FALSE TRUE 1795570.14 1607554.753 1651760.576 1616795.694 2344313.16 1565422.347 1703591.813 1638074.853 2724659.961 0.659007056 0.590001973 0.606226318 0.593393567 0.860405773 0.57453861 0.625249329 0.601203408 1 21.37764476 -1.782356617 2.672359541 1.095325626 0.636195972 0.656003834 0.082192479 25160692.9 19294074.67 15680734.83 0.018409697 0.016506059 1.782356617 -0.459129654 FSFWDKDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSFWDKDAR 9 1 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 147.73 8.36E-05 733820000 6413000 3973400 2693900 2923100 5891600 3281000 7894200 4910900 5779500 FALSE TRUE 6109870.199 4378293.977 2817417.98 2629264.434 6919093.175 3167378.147 6689794.803 4480875.562 6675755.342 0.915232792 0.655849975 0.422037333 0.393852725 1.036450981 0.47445989 1.002103052 0.671216264 1 22.67049965 1.720220932 15.83916929 0.876741848 0.667083563 0.20484647 0.221886438 0.28029722 218.2126487 0.099501142 0.054956656 52.50745058 -1.720220932 -0.209658285 FSGDLDDQTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FSGDLDDQTCR 11 0 P05455 P05455 SSB Lupus La protein 0 ;;;;; 275.28 8.84E-27 1849765000 3602470 3406270 3167260 3870450 3001910 3369200 3601670 3626910 3179000 FALSE TRUE 3432188.383 3753372.786 3312482.004 3481385.013 3525442.154 3252523.759 3052169.092 3309318.533 3671983.084 0.934696131 1.022165054 0.902096205 0.948093968 0.960092155 0.885767632 0.831204562 0.901234689 1 21.80812798 2.234658061 10.394223 0.88392369 0.958541482 0.124388927 0.052143066 0.141070424 248.9007926 0.01779377 0.013834849 171.6556335 -2.234658061 0.074617793 FSGEEGEIEDDES(ph)GTENREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.996)GT(0.004)ENREEK;FSGEEGEIEDDES(0.965)GT(0.035)ENREEK 213.05 3.74E-23 330720000 280170 348430 199498 320280 187191 360810 243410 306420 110665 TRUE FALSE 266926.9193 383935.4131 208645.1806 288084.8459 219837.0511 348315.0592 206273.334 279588.2404 127826.363 2.088199281 3.003569875 1.632254691 2.253720118 1.719809951 2.724907844 1.613699468 2.187250218 1 16.96382588 -1.267810777 0.204141455 8.50E-14 2.524405718 0.395741337 0.448594761 20.01545055 0.814234768 12.14097828 1.141061652 0.053974574 1.267810777 2.524405718 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.991)GT(0.009)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.993)GT(0.007)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.987)GT(0.013)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.996)GT(0.004)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.872)GT(0.128)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.997)GT(0.003)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.993)GT(0.007)ENREEKDNIQPTTE 275.54 2.98E-71 3069540000 3248227 3174721 2788686 3603006 1947879 3291613 3109294 3541236 1871863 TRUE FALSE 3094689.747 3498228.679 2916550.011 3240824.992 2287588.481 3177623.616 2634914.094 3231146.603 2162141.954 1.431307385 1.617945886 1.348916988 1.498895568 1.058019561 1.469664659 1.218659159 1.494419271 1 21.04402981 -3.473153197 0.082128722 6.20E-13 1.817843981 0.388821994 0.156516374 151.6641984 1.203841775 32.01062921 4.97507615 0.000336393 3.473153197 1.817843981 FSGWYDADLSPAGHEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 262.5 7.67E-31 235120000 536410 555570 492800 652820 401450 568300 568810 640290 390600 FALSE TRUE 511054.9624 612183.2146 515395.3674 587197.2933 471462.7529 548619.6285 482027.5876 584222.8132 451172.2531 1.132726933 1.356872481 1.142347216 1.301492477 1.044972845 1.215987075 1.068389256 1.294899696 1 18.78331882 2.746144497 24.96316384 1.131538909 1.237707545 0.203907748 0.105927447 868.8871312 2860037.235 0.028950028 0.030183352 557.3711651 -2.746144497 0.106168636 FSGWYDADLSPAGHEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSGWYDADLSPAGHEEAKR 19 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 201.12 3.99E-16 1833000000 1743270 1697240 1601690 1705840 1455020 1678470 2132790 1899760 1586960 FALSE TRUE 1660869.082 1870190.686 1675129.071 1534365.722 1708775.027 1620344.163 1807393.714 1733406.943 1833057.652 0.906064837 1.020257428 0.913844182 0.837052627 0.932199282 0.883957011 0.985999383 0.945636893 1 20.80582073 1.665700524 9.469387528 0.974073783 0.924565298 0.255090628 0.04787185 0.212659822 29.64873545 0.024337845 0.012996038 46.31274512 -1.665700524 -0.049508484 FSHDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSHDLK 6 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 85.306 0.054863 132550000 246430 246880 216480 284030 207050 247400 291500 285880 197320 FALSE TRUE 234781.7423 272037.3527 226405.8221 255478.7648 243159.4544 238832.476 247026.3212 260846.8317 227919.3778 1.030108736 1.193568337 0.99335925 1.120917261 1.066866086 1.047881397 1.083832027 1.144469742 1 17.79816406 3.734926608 24.99773477 1.070813957 1.111838533 0.087191621 0.060571213 730.2475578 5023262.568 0.014600918 0.023606774 5431.585348 -3.734926608 0.041024575 FSHEEIAMATVTALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FSHEEIAMATVTALR 15 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;; 235.22 1.13E-17 7334960000 4368800 3650420 3286938 4376170 4045580 3493760 4390690 3727390 3202340 FALSE TRUE 4162295.482 4022401.948 3437647.359 3936269.077 4751127.871 3372770.215 3720809.6 3400999.971 3698942.532 1.125266328 1.087446456 0.929359494 1.064160647 1.284455714 0.911820118 1.005911708 0.919451963 1 21.81868146 FSHEEIAMATVTALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FSHEEIAMATVTALRR 16 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 254.18 9.23E-27 14089397000 4162676 2726506 3449742 3461086 4543950 3351313 5535390 4095421 4396020 FALSE TRUE 3965914.555 3004340.061 3607916.083 3113171.06 5336413.441 3235256.19 4690864.591 3736804.226 5077732.33 0.781040492 0.59166964 0.710536879 0.613102633 1.05094422 0.637145871 0.923810923 0.735919892 1 22.27575292 2.775830723 24.99909172 0.850483965 0.67425975 0.356735098 0.129027905 620.4965941 416199.7653 0.034514661 0.036607492 596.8026221 -2.775830723 -0.176224215 FSHQGVQLIDFSPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FSHQGVQLIDFSPCER 16 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 121.41 9.89E-05 811430000 813420 765220 757990 848900 821610 788530 926820 871680 803520 FALSE TRUE 774971.2486 843196.788 792744.5913 763566.9592 964898.5239 761223.0084 785416.5868 795351.0781 928125.7778 0.834985157 0.908494094 0.854134871 0.822697718 1.039620434 0.820172251 0.846239384 0.856943204 1 19.8239608 2.573969713 0.010714763 1.760086655 1.62E-06 0.155452361 0.069500816 4922.527022 23.43865097 1875.823839 1972.051702 374.9468535 -2.573969713 -1.760085035 FSKEEPVSS(ph)GPEEAVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FSKEEPVSSGPEEAVGK 17 1 O00567 O00567 NOP56 Nucleolar protein 56 1 FSKEEPVS(0.035)S(0.965)GPEEAVGK;FSKEEPVS(0.052)S(0.948)GPEEAVGK;FSKEEPVS(0.063)S(0.937)GPEEAVGK 186.63 3.10E-10 778220000 1344050 1122690 1302070 1404390 836100 1423940 1562030 1549590 983520 TRUE FALSE 1280519.42 1237093.387 1361771.197 1263218.049 981915.5753 1374628.601 1323713.635 1413899.685 1136039.258 1.127178846 1.088953025 1.198700826 1.111949292 0.864332432 1.210018572 1.165200608 1.244586993 1 20.11558126 FSLCS(ph)DNLEGISEGPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)DNLEGISEGPSNR;FSLCS(1)DNLEGISEGPSNR;FSLCS(1)DNLEGISEGPSNR;FSLCS(1)DNLEGISEGPSNR 320.25 1.57E-61 189249000 232758 197507 209992 245395 200185 220075 251195 219248 220286 TRUE FALSE 221755.9906 217633.1878 219620.3409 220727.4284 235097.2006 212453.7476 212870.5892 200049.4828 254446.8278 0.871521931 0.855318927 0.863128626 0.867479584 0.923954143 0.834963239 0.836601466 0.78621331 1 17.95700468 FSLHEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSLHEQQR 8 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 0 67.993 0.057659 30133000 97824 64059 58263 88852 102990 78454 116160 100020 114150 FALSE TRUE 93200.05339 70586.68493 60934.41618 79920.42815 120951.4234 75737.11831 98437.65858 91261.71856 131851.799 0.706854621 0.535348668 0.462143229 0.606138322 0.917328579 0.574410959 0.746578047 0.692153761 1 17.00855773 -0.353934013 0.275681292 1.144823658 0.575194385 0.483755586 0.119123743 7.316113938 0.70319451 1.158266992 0.167820334 0.442655625 0.353934013 -0.569629273 FSLYFLAYEDKNDIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSLYFLAYEDKNDIPK 16 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 233.14 1.10E-19 538150000 2142600 1331060 1491170 2247900 1021980 1875400 2183900 2208200 1133980 FALSE TRUE 2041323.544 1466696.527 1559541.619 2021936.821 1200212.988 1810454.428 1850705.945 2014838.302 1309831.827 1.558462317 1.11975942 1.190642636 1.543661392 0.916310754 1.382203723 1.412934017 1.538241979 1 20.32095016 FSPDDKYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSPDDKYSR 9 1 Q9NPE3 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 109.42 0.0022365 326810000 520790 346970 446820 554480 452250 491160 571520 495170 519440 FALSE TRUE 496173.2888 382326.6375 467307.139 498742.617 531122.2568 474151.006 484324.1273 451810.2897 599992.1023 0.826966367 0.63721945 0.778855484 0.831248637 0.885215413 0.790262079 0.807217504 0.753027062 1 19.19458399 -5 0.179405866 1.872395271 0.737185411 0.489779818 0.066034843 113.8423968 1.09475538 35.49326061 0.21023134 1.00E-05 5 -1.135209859 FSPFLQTAEDNTQDEVAGAPADHHGPS(ph)DEEQGSPPEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSPFLQTAEDNTQDEVAGAPADHHGPSDEEQGSPPEDK 38 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 FSPFLQTAEDNTQDEVAGAPADHHGPS(1)DEEQGSPPEDK 205.8 2.25E-30 66424000 61315 69776 59747 67530 39908 67020 61757 64336 24734 TRUE FALSE 58416.76146 76886.25373 62486.45905 60741.7561 46867.94256 64699.0806 52334.8354 58702.39877 28569.6224 2.04471591 2.691189007 2.187164331 2.126095867 1.640481695 2.264610981 1.831835041 2.054713848 1 14.80219435 -1.318629168 0.20257704 1.11E-11 2.458308657 0.662184877 0.256907851 12.93477538 0.51003224 7.606496137 0.693779067 0.048014326 1.318629168 2.458308657 FSPPS(ph)PLPQAVFSTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR 221.46 3.86E-15 318724000 266474 214735 236733 302610 284231 237458 303493 285762 307622 TRUE FALSE 253878.3021 236616.7406 247587.4422 272191.0679 333800.7964 229234.7699 257189.5688 260739.1644 355326.4486 0.714493118 0.665913673 0.696788666 0.766030981 0.939420068 0.645138494 0.72381206 0.733801735 1 18.43878555 -5 0.338003852 3.87382162 0.71962987 0.514478825 0.080360427 318.9237779 2.69992741 661.0701308 0.06432042 1.00E-05 5 -3.15419175 FSPSS(ph)PESANECSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSPSSPESANECSK 14 0 Q8NEV8-2;Q8NEV8;E9PPH6;F5GXG5 Q8NEV8-2 EXPH5 Exophilin-5 1 FSPS(0.003)S(0.997)PESANECSK;FSPS(0.003)S(0.997)PESANECSK 327.31 2.65E-68 260110000 451960 361060 392750 469240 343420 438130 497360 461350 359070 TRUE FALSE 430596.7465 397852.4245 410757.976 422071.1037 403312.3393 422957.4482 421478.5974 420951.7482 414752.7417 1.038201085 0.959252066 0.99036832 1.01764512 0.972416331 1.019782163 1.016216543 1.01494627 1 18.66189199 2.184880067 24.99997092 1.014519127 0.995264322 0.126455149 0.022183385 180.1016241 83874.93069 0.007999165 0.005907779 153.06647 -2.184880067 -0.019254804 FSQMLHPIFEEASDVIKEEFPNENQVVFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSQMLHPIFEEASDVIKEEFPNENQVVFAR 30 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 169.57 1.16E-12 71467000 88965 70052 68712 84168 74051 80055 105210 89091 52017 FALSE TRUE 84759.80076 77190.37844 71862.51317 75707.27273 86965.47095 77282.67528 89158.28219 81289.71974 60083.53069 1.410699401 1.284717751 1.196043447 1.260033687 1.447409464 1.286253893 1.483905509 1.352945122 1 15.87468197 -1.031918372 6.081351537 0.999999554 1.34400578 0.592881538 0.088560539 5.41E-07 8.63E-08 0.086728411 0.020442056 0.092914101 1.031918372 0.344006226 FSS(ph)PTEELDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 FSS(1)PTEELDYR;FSS(0.997)PT(0.002)EELDYR;FSS(1)PTEELDYR;FS(0.001)S(0.999)PTEELDYR;FSS(0.994)PT(0.005)EELDYR;FS(0.014)S(0.983)PT(0.003)EELDYR;FSS(1)PTEELDYR;FSS(0.998)PT(0.001)EELDYR 360.54 2.02E-71 10199260000 12548800 10793460 10454740 12336670 10229010 11120040 12261020 11756060 10466880 TRUE FALSE 11955643.09 11893325.85 10934100.17 11096564.49 12012946.11 10734950.23 10390376.21 10726637.06 12090030.29 0.988884461 0.983730029 0.904389808 0.917827683 0.993624153 0.887917562 0.859416888 0.887229958 1 23.52731452 3.836877392 0.746974468 0.904982087 1.007805659 0.169948126 0.047414855 1.297875344 1.181018976 0.021243876 0.092176556 6868.744972 -3.836877392 0.102823571 FSSETWQNLGTLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSSETWQNLGTLHR 14 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 162.41 4.44E-06 833790000 619360 612530 506140 594220 652850 543020 716310 599850 631370 FALSE TRUE 590084.0803 674947.5034 529347.0196 534487.8767 766706.8333 524215.0812 607023.7536 547323.954 729279.635 0.80913281 0.925498905 0.725849173 0.732898399 1.051320778 0.718812176 0.832360763 0.750499435 1 19.47611258 3.781961427 24.99607622 0.82225217 0.8673158 0.013436189 0.117409718 1996.301616 1149735.183 0.02742569 0.049442264 6052.871121 -3.781961427 0.045063631 FSSPTEELDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 81.338 0.051061 38452000 30937 27320 35456 34959 33873 32234 41148 36091 43097 FALSE TRUE 29474.66932 30103.93906 37081.69267 31444.8549 39780.44048 31117.7285 34870.11687 32930.68071 49780.26265 0.592095496 0.604736445 0.744907534 0.631673142 0.799120743 0.625101734 0.700480773 0.661520831 1 15.60328622 -5 0.211344668 2.609138175 0.616889453 0.727228545 0.063710008 73.31751615 0.731042474 50.09470609 0.126366138 1.00E-05 5 -1.992248723 FSSVSS(ph)PQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.001)S(0.038)VS(0.478)S(0.484)PQPR;FSS(0.042)VS(0.033)S(0.925)PQPR 107.03 0.002453 144433000 276290 268470 283710 310690 287500 249580 320360 311000 330740 TRUE FALSE 263230.3193 295827.3982 296718.3841 279458.8509 337639.909 240936.982 271483.1982 283767.1913 382029.47 0.689031449 0.774357534 0.776689778 0.731511239 0.883805925 0.630676429 0.710634177 0.742788747 1 18.54332441 0.903599428 19.86513076 1 0.739666217 0.603533567 0.065576506 9400.592799 1937172.653 0.059756506 0.014939127 8.009389756 -0.903599428 -0.260333783 FSTLTDDPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 67.153 0.063727 100710000 379010 360110 358910 438860 351410 375380 422810 382920 370590 TRUE FALSE 361094.9484 396805.6184 375366.3785 394744.959 412695.7927 362380.4965 358302.5691 349389.4948 428059.2045 0.843563097 0.926987702 0.876902948 0.922173743 0.964109143 0.846566299 0.837039749 0.816217689 1 18.70745082 -0.031477228 7.835381284 0.999999999 0.880400141 0.400061144 0.046471102 3129850.491 399450.9428 0.046062648 0.011171833 0.930085283 0.031477228 -0.119599858 FSVCVLGDQQHCDEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;;;;; 262.36 7.01E-27 5606443000 6908823 6353240 6585064 7570139 4939932 7490670 8061328 7624677 4683689 FALSE TRUE 6582256.629 7000642.379 6886995.698 6809174.245 5801454.577 7231266.22 6831424.357 6957019.861 5410011.569 1.216680694 1.294016157 1.273009421 1.258624711 1.0723553 1.336645241 1.262737477 1.285952862 1 22.36720025 -1.021383348 4.583708406 0.999992545 1.252257679 0.556674648 0.07008882 5.48E-06 1.17E-06 0.06300189 0.014849203 0.095195551 1.021383348 0.252265134 FSVS(ph)PVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSVSPVVR 8 0 P13639 P13639 EEF2 Elongation factor 2 1 FS(0.054)VS(0.946)PVVR 77.662 0.03423 38280000 119930 87761 105830 100230 141180 81446 112990 81896 160480 TRUE FALSE 114261.1466 96703.94568 110682.4102 90154.68998 165801.7473 78625.5046 95751.3003 74724.75208 185366.4188 0.616406938 0.521690748 0.597100656 0.486359345 0.894454068 0.424162613 0.516551493 0.403119144 1 17.50002038 -1.069047615 4.638830775 1.000016348 0.55785994 0.508552034 0.136711299 16949722.62 3906170.02 3666.416437 0.029321973 0.085300659 1.069047615 -0.442156408 FSWFAGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSWFAGEK 8 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 131.06 0.0023756 1185830000 1496540 1625270 975300 1179310 1052120 1237410 1385040 1388550 898710 FALSE TRUE 1425801.52 1790886.861 1020018.47 1060763.518 1235609.395 1194558.181 1173726.71 1266961.201 1038077.357 1.373502187 1.725195959 0.982603525 1.021854018 1.190286434 1.150741006 1.130673646 1.220488235 1 19.98548253 3.734699489 24.99982247 1.109802944 1.549349078 0.725761899 0.11482163 146.029543 945505.478 0.029078644 0.046981206 5428.745581 -3.734699489 0.439546134 FSWNVWPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FSWNVWPSSR 10 0 F5H365;Q15436;G3V4V1;G3V1W4;G3V3G5;G3V2R6;G3V5X8;G3V4Q2;A0A2R8YF30;G3V5K1;A0A2R8Y633;A0A2R8Y7S7;A0A2R8YFH5;Q15437;Q5QPE2 F5H365;A0A2R8YFH5 SEC23A;SEC23B Protein transport protein Sec23A;Protein transport protein Sec23B 0 ; 128.91 0.00073798 509650000 451870 376550 348540 370640 444900 342380 509590 386590 400540 FALSE TRUE 430511.0006 414920.8731 364520.9038 333382.563 522490.4191 330523.2948 431842.6862 352738.1302 462653.6975 0.930525365 0.896828179 0.787891474 0.720587698 1.129333715 0.71440755 0.933403728 0.76242367 1 18.8195732 FSYDTFVDYDVDEEDMMNQVLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FSYDTFVDYDVDEEDMMNQVLQR 23 0 Q9Y508 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 93.269 6.61E-05 0 8278.1 6887.2 6084.1 7276.7 6887.2 6327.9 5936.4 8091.1 7357 FALSE TRUE 7886.810619 7589.01351 6363.062003 6545.232291 8088.325499 6108.763236 5030.693151 7382.60039 8497.885986 0.928090896 0.893047226 0.748781757 0.770218888 0.951804427 0.718856813 0.591993486 0.868757289 1 13.05288827 2.21546882 24.81563859 0.741302448 0.860461555 0 0.12497171 374.211667 402144.477 0.044868574 0.033159411 164.2361742 -2.21546882 0.119159107 FT(ph)DTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTDTRK 6 1 P13639 P13639 EEF2 Elongation factor 2 1 FT(1)DTRK;FT(1)DTRK 75.738 0.045063 293890000 430660 263720 176413 588720 377630 433770 294130 178895 257290 TRUE FALSE 410303.5553 290593.3678 184501.7105 529540.7471 443488.5524 418748.4361 249255.0664 163230.0054 297189.2191 1.380613861 0.977805886 0.620822354 1.781830272 1.492276718 1.409029699 0.838708306 0.549246052 1 18.18102226 1.624864414 5.392635429 0.751479065 1.251718384 0.323830686 0.326240619 0.177152718 11.07447141 0.179392749 0.085134522 42.15648706 -1.624864414 0.500239318 FT(ph)DTRKDEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTDTRKDEQER 11 2 P13639 P13639 EEF2 Elongation factor 2 1 FT(0.912)DT(0.088)RKDEQER 69.92 0.085511 180240000 801500 446850 511950 913700 707640 821760 714260 516560 549830 TRUE FALSE 763614.6834 492384.523 535423.4139 821853.1401 831052.192 793302.2451 605286.5187 471327.2679 635094.8283 1.202363253 0.775292919 0.843060579 1.294063663 1.308548196 1.249108338 0.953064789 0.742136838 1 19.2766125 3.262569318 24.99568909 1.100256413 0.942339721 0.108928103 0.202331778 530.3162558 552113.6152 0.058111399 0.078642653 1830.498248 -3.262569318 -0.157916692 FTASAGIQVVGDDLTVTNPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FTASAGIQVVGDDLTVTNPKR 21 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 329.56 7.62E-80 749340000 1109330 530835 954685 763043 1016856 981177 1472821 1163283 1368463 FALSE TRUE 1056894.169 584927.69 998458.2516 686340.468 1194195.364 947198.5945 1248115.106 1061419.774 1580677.253 0.668633756 0.370048781 0.631664845 0.434206582 0.755496014 0.599235924 0.789607811 0.671496836 1 20.59211139 1.122629031 0.426150291 1.011132542 0.505927091 0.586519874 0.113667894 0.699813013 0.354732876 0.136803308 0.077231926 13.26261097 -1.122629031 -0.505205452 FTCEMFHPNIYPDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTCEMFHPNIYPDGR 15 0 P60604-2;P60604 P60604-2 UBE2G2 Ubiquitin-conjugating enzyme E2 G2 0 ; 91.207 0.0057173 181874000 147324 122960 132800 158247 165668 128040 176301 156010 145342 FALSE TRUE 140360.2865 135489.7638 138889.0114 142339.7109 194560.4467 123605.9427 149403.0445 142348.9373 167880.8951 0.836070635 0.80705886 0.827306831 0.847861282 1.158919523 0.736271645 0.889934762 0.84791624 1 17.35707853 -5 0.035850842 1.589798959 0.488468551 0.123707091 0.110291281 2182.007304 5.861828534 152.7512728 51.98435131 1.00E-05 5 -1.101330408 FTDCGHFQNTEFHELITVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTDCGHFQNTEFHELITVVK 20 0 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 130.85 8.91E-06 7775800 20642 13624 20892 24026 15266 23101 22667 22461 4888.9 FALSE TRUE 19666.29357 15012.30109 21849.91887 21610.86083 17928.38557 22301.00658 19208.73284 20494.19577 5647.045643 3.482580948 2.658434523 3.869265497 3.826932205 3.174825688 3.949145799 3.40155438 3.629188971 1 12.46328058 6.778986439 7.241153679 3.321444146 3.776438572 0 0.877300596 0 0 0.165236732 0 6011549.654 -6.778986439 0.454994426 FTDDDKTDHLSWEWNLTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FTDDDKTDHLSWEWNLTIK 19 1 P52565;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;; 282.49 5.62E-40 1334830000 2502322 1956857 2215036 2686570 1719314 2470331 3159629 2979124 1703519 FALSE TRUE 2384042.198 2156262.953 2316597.592 2416510.879 2019161.817 2384782.818 2677569.565 2718256.109 1967692.026 1.211593159 1.095833557 1.177317162 1.228094055 1.026157443 1.211969549 1.360766588 1.381443881 1 20.908073 1.996950356 24.89849208 1.28720853 1.14880047 0.103336537 0.118166658 156.611552 1278645.485 0.040011955 0.028979017 99.30025331 -1.996950356 -0.13840806 FTDDYQLFEELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTDDYQLFEELGK 13 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q5SWX3;Q13555-6;Q13555-11;Q13555-5 Q13555-8 CAMK2G Calcium/calmodulin-dependent protein kinase type II subunit gamma 0 211.77 4.48E-08 21227000 46723 42527 48953 48880 37196 46563 49425 53470 42169 FALSE TRUE 44514.49639 46860.54965 51197.54347 43966.48953 43682.97062 44950.51163 41884.3085 48787.88334 48708.35315 0.913898613 0.96206393 1.051103972 0.902647835 0.89682709 0.922850163 0.85989991 1.001632783 1 15.57188159 FTDEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FTDEESR 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 179.16 0.0016406 569790000 1437620 1237690 1318940 1487010 1420740 1377220 1554140 1451640 1570210 FALSE TRUE 1369666.552 1363812.018 1379414.704 1337532.93 1668516.606 1329526.526 1317027.399 1324526.706 1813710.147 0.755173892 0.75194596 0.760548595 0.737456827 0.919946668 0.733042448 0.726150979 0.730285767 1 20.79051248 -1.084064174 4.255596026 1.000023832 0.762298119 0.631287395 0.056586648 7369190.924 1877216.978 2052.405421 0.0127123 0.082401634 1.084064174 -0.237725713 FTDEEVDELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;; 359.43 5.97E-71 7120680000 9239860 9247690 7528030 10422660 7439810 7928530 8412110 8661610 7102480 FALSE TRUE 8803110.129 10190040.12 7873197.622 9374954.415 8737310.508 7653963.018 7128688.121 7903153.51 8203896.324 1.073040148 1.242097623 0.959690044 1.142744136 1.065019615 0.932966814 0.868939323 0.963341466 1 22.96787783 2.31687169 3.398211235 0.922031391 1.115111415 0.496441773 0.077143685 0.166205129 3.840959093 0.02811378 0.022231686 207.4300588 -2.31687169 0.193080024 FTDFDEVRQEIEAETDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FTDFDEVRQEIEAETDR 17 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ;; 138.08 4.40E-06 37002000 61165 44250 62432 54527 60256 59994 67406 65707 67056 FALSE TRUE 58273.85167 48759.12531 65294.56895 49045.84237 70764.62732 57916.39274 57121.9767 59953.34675 77454.70201 0.752360414 0.629517951 0.843003294 0.63321969 0.913625971 0.747745343 0.737488819 0.774043992 1 16.2410652 -5 0.193810517 2.120285495 0.699854911 0.465625348 0.083720393 112.2371129 1.102937821 48.57237128 0.19543102 1.00E-05 5 -1.420430584 FTDFDEVRQEIEAETDRVTGTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTDFDEVRQEIEAETDRVTGTNK 23 2 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 61.703 0.028517 20725000 22324 11085 24016 17650 22809 21006 31944 26140 26477 FALSE TRUE 21268.78876 12214.5741 25117.15736 15875.78847 26786.88238 20278.55695 27070.35611 23851.04302 30582.91793 0.695446681 0.399392044 0.821280605 0.519106401 0.875877261 0.663068089 0.885146282 0.779881209 1 14.90043844 1.982987238 0.395409849 0.994284411 0.536876649 0.433359833 0.134654655 0.909709724 0.363730033 0.138374285 0.138532247 96.15840206 -1.982987238 -0.457407762 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FT(0.001)DKDQQPS(0.999)GS(0.999)EGEDDDAEAALKK;FT(0.008)DKDQQPS(0.992)GS(1)EGEDDDAEAALKK;FTDKDQQPS(1)GS(1)EGEDDDAEAALKK;FTDKDQQPS(1)GS(1)EGEDDDAEAALKK;FTDKDQQPS(1)GS(1)EGEDDDAEAALKK 134.21 1.96E-05 2116040000 2564600 2244780 2176850 2762590 1050340 2812000 2685000 2927350 1127700 TRUE FALSE 2443376.441 2473525.634 2276660.726 2484889.205 1233518.963 2714619.735 2275353.937 2671015.715 1302577.957 1.875800545 1.898946333 1.747811495 1.907670241 0.946982833 2.084036292 1.746808262 2.050561121 1 20.31293829 FTDLFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTDLFEK 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 114.93 0.013479 76212000 414690 336180 358250 411250 304970 349460 441700 403110 331300 FALSE TRUE 395088.4255 370437.1242 374676.1169 369910.3687 358156.6714 337358.1126 374310.5526 367811.5514 382676.312 1.032435019 0.968016866 0.979094094 0.966640362 0.935925899 0.881575635 0.978138811 0.961155786 1 18.54576507 4.734799949 0.788989757 0.949719849 1.080953515 0.355783412 0.031587519 2.524074697 1.203202383 0.011071919 0.292587716 54300.01495 -4.734799949 0.131233666 FTDLLQLVEFHQLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTDLLQLVEFHQLNR 15 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 287.42 1.95E-34 1114750000 2010820 1608270 1566970 1886300 1835330 1519160 2003030 1821890 1591380 FALSE TRUE 1915772.524 1772154.541 1638817.124 1696685.54 2155410.971 1466551.108 1697430.985 1662355.653 1838163.083 1.042221194 0.964089943 0.891551538 0.923033193 1.172589631 0.797835144 0.923438731 0.904357001 1 20.80983334 FTEDLVGSVVHVLSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTEDLVGSVVHVLSHR 16 0 Q6P9B6;H3BUB0;H3BM75 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 126.77 4.04E-05 20353000 88947 74850 77236 86136 89590 75420 96964 80824 11224 FALSE TRUE 84742.65159 82477.3001 80777.347 77477.44563 105214.4676 72808.18649 82170.36093 73746.62209 12964.5606 6.53648467 6.361750519 6.23062744 5.976094991 8.115544438 5.615939387 6.338075273 5.688324069 1 13.66228569 0.248483948 0.99620692 0.969065926 6.498507988 0.875337259 0.642467163 1.087452736 1.184948272 0.62207673 0.177064468 1.772082546 -0.248483948 5.529442062 FTENDSEKVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTENDSEKVDR 11 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 70.438 0.047211 249140000 349070 298870 318710 369690 268590 396180 405650 395020 353740 FALSE TRUE 332570.1529 329325.1928 333323.1687 332528.0588 315432.011 382460.1873 343760.6422 360429.9547 408596.1925 0.813933558 0.80599183 0.815776492 0.813830537 0.771989599 0.936034633 0.841321208 0.882117752 1 18.64031623 0.658223525 0.405731133 1.01500292 0.799933061 0.706786434 0.037299977 0.975321656 0.350427028 0.066433469 0.025583338 4.552222965 -0.658223525 -0.21506986 FTFPDPPPLS(ph)PPVLGLHGVTFGYQGQKPLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTFPDPPPLSPPVLGLHGVTFGYQGQKPLFK 31 1 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 FTFPDPPPLS(1)PPVLGLHGVTFGYQGQKPLFK 237.16 5.32E-46 266030000 952040 814530 792800 908070 657500 852030 1000900 947890 693790 TRUE FALSE 907038.956 897531.533 829150.6642 816789.0784 772167.7918 822523.9875 848194.3222 864887.7265 801379.4098 1.131847094 1.119983271 1.034654315 1.01922893 0.96354833 1.026385227 1.058417913 1.07924875 1 19.61212592 3.738696573 4.08547557 1.026734103 1.127700263 0.647025585 0.030811378 0.126808811 5.127630662 0.008677464 0.015088759 5478.940362 -3.738696573 0.100966159 FTFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTFSGR 6 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 102.81 0.08195 437194000 427689 381502 381044 429285 384065 426286 480797 437437 401519 FALSE TRUE 407472.9886 420377.4875 398515.2443 386132.4562 451045.8144 411523.6089 407442.5872 399132.6973 463784.5158 0.878582563 0.906406905 0.85926811 0.832568667 0.972533146 0.887316404 0.878517012 0.860599446 1 18.82309513 2.770064974 24.99617897 0.906898116 0.875896273 0.194224311 0.046428335 1623.286173 1287944.26 0.013460169 0.014274873 588.9317574 -2.770064974 -0.031001843 FTGS(ph)FDDDPDPHRDPYGEEVDRR ddPTM_SK-BR-3_Trastuzumab_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(0.029)GS(0.971)FDDDPDPHRDPYGEEVDRR;FT(0.144)GS(0.856)FDDDPDPHRDPYGEEVDRR;FT(0.144)GS(0.856)FDDDPDPHRDPYGEEVDRR;FT(0.229)GS(0.771)FDDDPDPHRDPYGEEVDRR;FT(0.119)GS(0.881)FDDDPDPHRDPYGEEVDRR 185.35 1.60E-17 3544270000 711825 580320 633251 817695 816911 825762 849135 635525 787370 TRUE FALSE 678178.443 639455.2678 662286.1847 735498.7451 959380.0198 797165.6549 719583.8603 579875.0619 909471.3183 0.745684256 0.70310658 0.728210084 0.808710215 1.054876609 0.876515442 0.791211164 0.637595766 1 19.79466862 3.125830289 4.433080626 0.860503067 0.723945463 0.25588342 0.112277806 0.312270654 10.65522101 0.032771336 0.039837225 1336.073311 -3.125830289 -0.136557604 FTHESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTHESQR 7 0 A0A0A0MTI1;Q15392-2;Q15392 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 111.82 0.006494 35413000 17561 19324 15441 20222 35475 13714 27794 19347 35175 FALSE TRUE 16730.92633 21293.13757 16148.98512 18189.24614 41661.82877 13239.08074 23553.51483 17652.87412 40629.75935 0.411789944 0.524077374 0.397466915 0.447682842 1.02540181 0.32584689 0.579710912 0.434481385 1 15.3102492 -2.2254464 2.185078153 2.499164647 0.517882919 0.380386817 0.19320512 8351071.332 1462792.773 61854329.11 0.044598956 0.005950502 2.2254464 -1.981281728 FTIGDHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FTIGDHSR 8 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 188.98 0.00019411 2638910000 2622600 2243560 2143750 2615170 2529720 2285190 2917290 2502110 2632230 FALSE TRUE 2498634.895 2472181.315 2242043.058 2352288.143 2970902.367 2206053.297 2472203.831 2283011.984 3040422.785 0.821805082 0.813104456 0.737411609 0.773671397 0.977134622 0.725574518 0.813111862 0.750886355 1 21.53584052 -1.000667459 4.583004588 1.000005166 0.803621731 0.438478707 0.070530161 3.38E-06 7.37E-07 0.062021741 0.01461828 0.09984643 1.000667459 -0.196383435 FTLDCTHPVEDGIMDAANFEQFLQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 FTLDCTHPVEDGIMDAANFEQFLQER 26 0 P35268 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;;;;;;;;;; 350.06 6.57E-110 5612647500 2201547.3 2002714.4 2041197.9 2266269.1 2296506.7 2087515.7 2446376.9 2186301.4 2092356.4 FALSE TRUE 2097484.522 2206793.274 2134788.843 2038459.424 2697016.741 2015224.508 2073137.173 1994857.259 2416828.344 0.867866569 0.913094751 0.883301807 0.843444024 1.11593227 0.833830219 0.857792478 0.825402956 1 21.20468358 -0.416291443 8.937974332 1 0.892636589 0.140788571 0.083395151 0 0 0.075080799 0.017696714 0.383449837 0.416291443 -0.107363411 FTLRDEGK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 138.1 0.00065654 1840050000 2553360 1870910 2285870 2385690 1943530 2508070 3059160 2727400 2256340 FALSE TRUE 2432667.733 2061557.856 2390679.401 2145875.909 2282481.017 2421214.907 2592428.957 2488574.397 2606241.683 0.93340067 0.791007937 0.917289987 0.82336029 0.875774887 0.929006286 0.994700136 0.954851736 1 21.31353944 2.070757774 2.571012543 0.981536053 0.862929794 0.608394353 0.042231375 0.176278582 2.271467354 0.019042285 0.011478055 117.6949352 -2.070757774 -0.118606259 FTLTQSEADADILFNFSHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTLTQSEADADILFNFSHFK 20 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 99.86 0.00059744 29856000 31806 26657 32097 33781 22475 33207 38096 39896 30523 FALSE TRUE 30302.59341 29373.37861 33568.6792 30385.2697 26394.63288 32057.03326 32283.75552 36402.49474 35256.35095 0.859493186 0.833137231 0.952131412 0.86183819 0.748649028 0.909255564 0.915686242 1.03250886 1 15.10559554 1.493907176 2.10308378 1.016263759 0.85549959 0.590937767 0.052682875 0.204258125 1.777303231 0.042089139 0.013933772 31.18223038 -1.493907176 -0.160764169 FTPGTFTNQIQAAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTPGTFTNQIQAAFR 15 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 128.21 0.00017076 70308000 64123 53022 71005 60744 74738 62909 76748 71661 74432 FALSE TRUE 61092.03287 58425.00208 74260.64948 54637.89771 87772.28354 60730.44556 65038.68303 65385.98294 85974.53441 0.710582887 0.679561715 0.863751691 0.635512575 1.020910251 0.706377138 0.756487761 0.760527328 1 16.39162178 -5 0.178955698 1.951625144 0.708653877 0.313206603 0.108458822 152.9308923 1.469426003 52.03197307 0.311954283 1.00E-05 5 -1.242971267 FTPGTFTNQIQAAFREPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTPGTFTNQIQAAFREPR 18 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 319.99 1.42E-61 1736920000 1348190 639300 1372160 1002510 1721310 1199800 1926660 1415930 2212900 FALSE TRUE 1284463.731 704445.3968 1435074.893 901735.7902 2021505.919 1158250.625 1632712.631 1291943.663 2556065.23 0.502516022 0.275597582 0.561439073 0.352782777 0.790866327 0.453138133 0.638760158 0.505442368 1 21.28549322 -5 0.133630216 2.734436379 0.294901107 0.578780534 0.135870986 88.76380948 0.740564346 40.9159708 0.845059766 1.00E-05 5 -2.439535272 FTPVASKFS(ph)PGAPGGSGSQPNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FTPVAS(0.099)KFS(0.901)PGAPGGSGSQPNQK;FTPVASKFS(1)PGAPGGSGSQPNQK 295.95 6.87E-62 1508210000 1883760 1523450 1820340 1902160 1181980 1900260 2182270 2054910 1513780 TRUE FALSE 1794718.398 1678691.287 1903804.39 1710951.263 1388116.938 1834453.52 1849324.631 1874971.187 1748529.271 1.026415987 0.960059013 1.088803271 0.978508791 0.793876866 1.049140869 1.057645795 1.072313296 1 20.73771052 2.066267948 25 1.050661624 0.974430568 0.192526293 0.075785223 91.75389254 34613.5961 0.027915128 0.020616688 116.4844484 -2.066267948 -0.076231056 FTQDTQPHYIYSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FTQDTQPHYIYSPR 14 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 172.57 2.84E-06 1202950000 1556700 1410880 1319710 1544810 1446990 1476650 1896710 1743480 1551530 FALSE TRUE 1483117.876 1554650.276 1380220.009 1389522.764 1699344.598 1425513.24 1607332.054 1590811.648 1792133.348 0.827571161 0.867485825 0.770154749 0.775345632 0.948224416 0.795428109 0.896881951 0.887663661 1 20.77324656 0.723915237 0.581976803 1.003832489 0.827212194 0.518113653 0.051706447 0.998825606 0.702778854 0.056023118 0.021601301 5.295600772 -0.723915237 -0.176620295 FTRNEFNLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTRNEFNLESK 11 1 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 78.324 0.027536 86784000 94662 78202 96196 101450 89835 107600 128930 112670 107410 FALSE TRUE 90187.51486 86170.87271 100606.6818 91252.05326 105502.1956 103873.785 109259.3605 102804.0175 124066.5942 0.726928271 0.694553383 0.810908709 0.73550865 0.850367468 0.837242174 0.880650922 0.828619647 1 16.92075519 2.204857765 0.159988686 1.086935244 0.561107725 0.819337092 0.037207849 2.010320785 0.221164005 0.247656664 0.379326982 160.2720401 -2.204857765 -0.525827518 FTRPLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTRPLFK 7 1 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 100.45 0.0089232 177660000 525560 475940 382810 527270 587030 422120 694460 467580 721350 FALSE TRUE 500717.8204 524438.8271 400362.2172 474267.8179 689407.8461 407501.8786 588507.3724 426636.2164 833213.2739 0.600947964 0.629417274 0.480503887 0.569203387 0.827408621 0.489072716 0.706310606 0.51203723 1 19.6683263 -1.907196222 2.438930091 1.23234603 0.608648727 0.585488028 0.105142029 9339667.337 4923493.577 12432283.31 0.022503414 0.01238237 1.907196222 -0.623697303 FTSGAFLS(ph)PSVSVQECR ddPTM_SK-BR-3_Trastuzumab_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(0.978)PS(0.022)VSVQECR;FTSGAFLS(1)PSVSVQECR 308.12 5.06E-58 167716000 290240 279190 274010 331220 296110 310070 345700 317890 363700 TRUE FALSE 276520.9304 307639.7784 286573.6295 297925.1363 347751.4902 299332.1982 292957.1158 290053.8664 420100.7385 0.65822529 0.732300018 0.682154548 0.709175464 0.827781192 0.712524808 0.697349681 0.69043884 1 18.6803758 -2.163331467 2.452731953 1.721494922 0.713179798 0.799499519 0.045050385 2267546.967 593332.8086 9110474.648 0.010596694 0.006865442 2.163331467 -1.008315123 FTVDTISAGQGDVMVFVEDPEGNKEEAQVTPDSDKNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTVDTISAGQGDVMVFVEDPEGNKEEAQVTPDSDKNK 37 2 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 74.605 0.0018231 109450000 46212 43393 42508 45562 17429 50260 41356 51588 19226 FALSE TRUE 44027.65034 47814.79603 44457.03385 40982.0212 20468.61208 48519.4836 35046.38264 47070.68123 22207.46989 1.982560398 2.153095165 2.001895492 1.845416043 0.921699419 2.18482717 1.578134872 2.119587755 1 14.43875741 -2.069081946 0.147824674 2.32E-18 2.208260709 0.315543914 0.379401834 55.05790472 1.148956347 23.1000323 2.276221889 0.008529392 2.069081946 2.208260709 FTVHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FTVHTK 6 0 G3V5X9;Q9UNH7;A0A0A0MRI2;G3V2U1;H0YJF8;G3V4Z5;G3V5U2;Q9Y5X3;Q5QPE5 G3V5X9;Q9Y5X3 SNX6;SNX5 "Sorting nexin-6;Sorting nexin-6, N-terminally processed;Sorting nexin-5" 0 ; 93.885 0.045111 1023310000 1835920 1627240 1525970 1925790 1449190 1810440 2045790 1964330 1584880 FALSE TRUE 1749139.7 1793057.606 1595937.234 1732205.93 1701928.277 1747744.009 1733667.162 1792322.852 1830655.096 0.955472008 0.979462276 0.871784771 0.946221893 0.929682648 0.954709608 0.947020095 0.979060914 1 20.80392858 1.103251003 1.850335 1.000341767 0.942544131 0.363812998 0.027627914 0.393136394 2.621125662 0.026075361 0.007487353 12.68384725 -1.103251003 -0.057797636 FTVWLHGVLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FTVWLHGVLDK 11 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V3Y4;A0A3B3IT62;G3V473;G3V240;G3V572;G3V3R9;Q6PJT7-9;Q6PJT7-2;Q6PJT7-3;Q6PJT7-11 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 96.64 0.0068613 19643000 158690 118650 70898 92245 129420 99381 174100 136540 101590 FALSE TRUE 151189.0382 130740.5699 74148.74343 82972.35735 151990.807 95939.41105 147537.8474 124583.8338 117344.0584 1.288425169 1.114164379 0.631891759 0.707086141 1.295257801 0.817590702 1.25730991 1.061696992 1 16.84038527 1.721668541 24.99999984 1.125197322 1.004486869 0.055653683 0.230111751 3.236932748 4771.54993 0.110366401 0.061203694 52.68276262 -1.721668541 -0.120710454 FVAFSGEGQS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FVAFSGEGQSLR 12 0 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 FVAFSGEGQS(1)LR;FVAFSGEGQS(1)LR;FVAFSGEGQS(1)LR 188.19 9.98E-06 227002000 296689 214689 220804 392319 327538 302253 410100 247727 345602 TRUE FALSE 282665.099 236566.0532 230928.0818 352882.3488 384660.5235 291785.9028 347531.713 226034.7106 399196.1931 0.708085658 0.592605985 0.578482675 0.88398225 0.963587655 0.730933581 0.870578726 0.566224615 1 18.60673844 3.238669353 24.99999999 0.83101616 0.630822287 0.383462763 0.125078652 2.904291065 667579.3948 0.032724209 0.041626465 1732.48448 -3.238669353 -0.200193873 FVDGEWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 FVDGEWYR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;;;;; 197.84 0.00032761 11667990000 10157010 8661430 7950380 9179480 10388300 7932480 10955470 9078370 10545120 FALSE TRUE 9676908.267 9544039.564 8314912.787 8256741.231 12200016.23 7657776.229 9284011.84 8283419.795 12180403.35 0.794465338 0.783556939 0.682646752 0.67787092 1.001610199 0.62869644 0.7622089 0.680061206 1 23.53805857 -1.258637143 5.318300538 1.000027938 0.755101289 0.363520058 0.10327945 3.08E-05 4.30E-06 0.090092278 0.021232534 0.055126809 1.258637143 -0.244926649 FVDGLMIHSGDPVNYYVDTAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 FVDGLMIHSGDPVNYYVDTAVR 22 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;;;; 292.53 1.99E-55 3633299000 3841117 4241033 3625053 4386941 3978029 3778896 3881650 4109494 3359007 FALSE TRUE 3659555.012 4673199.084 3791265.266 3945957.356 4671795.998 3648031.884 3289433.001 3749644.92 3879904.65 0.94320746 1.204462353 0.977154236 1.017024312 1.204100724 0.940237509 0.847812845 0.966427079 1 21.88758977 2.029096276 24.06058334 0.914383994 1.069840364 0.316906056 0.093116039 129.8905711 107409.6368 0.032722801 0.024166896 106.9291897 -2.029096276 0.155456371 FVDILGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVDILGLR 8 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ; 137.18 0.0017663 32967000 265760 232250 251700 268830 258910 240870 296350 263980 234390 FALSE TRUE 253198.0515 255916.539 263240.694 241806.6977 304063.822 232528.6115 251136.3647 240864.5118 270738.0041 0.935214294 0.945255321 0.972307877 0.893139101 1.123092501 0.85886949 0.927599232 0.889659036 1 18.04653789 -0.286210288 6.866812448 1.000000004 0.942706859 0.058760737 0.071496552 0 58796263.91 0.061997313 0.015036556 0.517356265 0.286210288 -0.057293145 FVDKLFEAVEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVDKLFEAVEEGR 13 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 83.54 0.0092626 64257000 142560 108650 127970 143830 136030 148640 169830 160010 143710 FALSE TRUE 135821.4713 119721.5585 133837.5511 129371.9351 159753.5889 143492.5595 143919.3144 145998.6761 165995.8128 0.818222273 0.7212324 0.806270645 0.779368666 0.962395293 0.864434814 0.867005691 0.879532282 1 17.34078733 2.761121796 23.17000788 0.899126139 0.776760755 0.629894978 0.049975266 204.0595682 209565.4838 0.014225276 0.01507405 576.9282384 -2.761121796 -0.122365384 FVDKYSISLS(ph)PPEQQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVDKYSISLSPPEQQKK 17 2 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 FVDKYS(0.12)IS(0.12)LS(0.761)PPEQQKK;FVDKYSIS(0.016)LS(0.984)PPEQQKK 141.47 3.25E-07 237797000 1004450 654920 936670 962210 571460 1021320 1202540 1158270 752790 TRUE FALSE 956971.6391 721657.0926 979617.246 865486.8227 671122.4431 985951.4323 1019070.437 1056845.738 869528.8285 1.100563441 0.829940387 1.126606978 0.995351499 0.771823108 1.133891597 1.171980047 1.215423461 1 19.72987433 2.04132529 24.99977695 1.149416789 0.96631141 0.317454491 0.119338788 149.0955709 90194.88198 0.041580842 0.030709456 109.9829312 -2.04132529 -0.183105379 FVEDTKNEVHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVEDTKNEVHER 12 1 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 ; 139.89 3.56E-05 97690000 161122 127832 141002 156305 104623 151486 163782 160666 129745 FALSE TRUE 153506.0824 140858.2261 147467.0812 140592.9244 122869.2181 146240.0018 138794.0478 146597.2333 149865.192 1.024294437 0.939899548 0.983998214 0.938129279 0.81986495 0.975810326 0.92612598 0.978194011 1 17.19330581 4.909116265 0.991500949 0.937240038 1.095059456 0.184264269 0.050590767 3.775850899 2.385715591 0.014628133 0.687371867 81117.81887 -4.909116265 0.157819418 FVEGLPINDFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FVEGLPINDFSR 12 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;; 251.43 1.15E-17 976653000 1042009 864807 845720 933766 1115684 799331 1086604 914342 1175625 FALSE TRUE 992755.2996 952931.8165 884497.0985 839902.0676 1310258.936 771649.967 920822.6029 834277.3672 1357934.921 0.731077229 0.701750726 0.651354557 0.618514227 0.964890818 0.568252539 0.678105106 0.614372128 1 20.37298291 -1.445150104 5.34201942 1.000333918 0.692632217 0.447606097 0.107852377 0.000388774 4.04E-05 0.094653499 0.022286212 0.03587979 1.445150104 -0.307701701 FVEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FVEVGR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;;;; 159.65 0.021057 1135100000 1590520 1446490 1374320 1597810 1681630 1525260 1804490 1590380 1731870 FALSE TRUE 1515339.272 1593888.976 1437333.931 1437195.103 1974905.74 1472439.864 1529181.909 1451117.896 2000439.554 0.757503154 0.796769376 0.718509054 0.718439655 0.987235898 0.736058163 0.764422952 0.725399522 1 20.93188561 -1.579176269 2.987912744 1.012345084 0.776601583 0.442942489 0.07909881 27917100.55 32070511.23 2754819.33 0.017486769 0.026352616 1.579176269 -0.235743501 FVEWLQNA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVEWLQNA 8 0 E7ETZ4 E7ETZ4 BZW2 0 ; 91.626 0.02874 52559000 113189 105386 116008 122442 119384 115468 131858 120318 134616 FALSE TRUE 107838.7803 116124.9532 121327.0815 110133.8975 140204.5318 111469.3142 111740.6404 109782.3181 155491.5618 0.693534614 0.746824792 0.780280809 0.708295012 0.901685791 0.716883366 0.718628324 0.706033928 1 17.24647676 -1.726186825 2.574036841 1.05038012 0.744616692 0.635017809 0.060377806 8898453.46 7046709.961 2881431.514 0.015435168 0.018785085 1.726186825 -0.305763428 FVFDRPLPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVFDRPLPVSR 11 1 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 222.25 7.12E-12 4407000000 4136100 3305600 2946500 3758100 4517100 3182600 4664600 3759500 4769400 FALSE TRUE 3940594.75 3642444.398 3081599.939 3380328.648 5304880.81 3072385.764 3952929.599 3430298.25 5509014.193 0.715299437 0.661178982 0.559374115 0.613599553 0.96294557 0.557701552 0.717538467 0.622670069 1 22.39336275 -1.820048383 2.347088038 1.121674131 0.678093793 0.43655395 0.115559869 10501063.84 6210937.354 7220292.326 0.026762836 0.015133926 1.820048383 -0.443580338 FVFDVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVFDVFR 7 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 134.44 0.0073853 92146000 582140 268080 101008 111303 729140 136689 615770 297420 570560 FALSE TRUE 554623.3959 295397.6568 105639.3167 100114.611 856301.7851 131955.4257 521822.9771 271376.3281 659039.5308 0.841563169 0.448224489 0.160292838 0.151909872 1.299317788 0.20022384 0.791793136 0.411775494 1 19.33000548 FVFLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVFLLDR 7 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 110.63 0.015726 72858000 284690 245430 190577 201177 322180 175684 322110 250850 273940 FALSE TRUE 271233.2679 270439.596 199315.144 180954.3057 378368.09 169600.019 272966.2035 228884.2442 316421.2161 0.857190524 0.854682247 0.629904487 0.571877916 1.195773452 0.535994461 0.862667197 0.723353026 1 18.27148681 FVFSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVFSFK 6 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 118.03 0.051687 55216000 400860 337930 339110 386610 370010 329360 451640 392990 392690 FALSE TRUE 381912.1422 372365.4512 354658.5289 347747.2283 434539.6269 317954.1806 382734.0231 358577.7122 453586.3596 0.841983305 0.820936175 0.781898577 0.766661565 0.958008586 0.700978268 0.843795266 0.790539011 1 18.79101773 -2.222149254 2.293263186 1.599014152 0.814686157 0.44267476 0.065884422 4790018.727 824050.475 14909885.22 0.014255148 0.00599585 2.222149254 -0.784327995 FVFSLVDAMNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVFSLVDAMNGK 12 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 211.64 6.87E-08 87801000 373490 296600 297350 334320 271920 287870 378060 348470 281260 FALSE TRUE 355835.8679 326823.8772 310983.7916 300713.5184 319342.7619 277900.9897 320380.0035 317956.1194 324876.3643 1.095296263 1.005994628 0.957237355 0.925624488 0.982967051 0.85540538 0.986159778 0.978698835 1 18.30953126 4.213536183 1.46850565 0.949763323 1.098228167 0.534389195 0.041504798 0.342786606 1.234820896 0.010900107 0.055987886 16350.6937 -4.213536183 0.148464845 FVFSLVDAMNGKEGVVECSFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVFSLVDAMNGKEGVVECSFVK 22 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 110.67 0.00031919 12634000 4045.4 5163.1 5379.3 4226 11045 2687.3 6316.3 4684.4 6670.8 FALSE TRUE 3854.181959 5689.22576 5625.946226 3801.194451 12971.2445 2594.238127 5352.632428 4274.209102 7705.273594 0.500200533 0.738354802 0.730142305 0.493323748 1.683424261 0.336683454 0.6946713 0.554712179 1 12.91163047 4.671380483 1.143231668 0.769500257 0.388205305 0.055230139 0.365785148 4.84312427 5.756518411 0.100222414 2.159732762 46922.42868 -4.671380483 -0.381294951 FVGHTK ddPTM_SK-BR-3_Trastuzumab_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 71.359 0.088439 559960000 1828600 1810100 1629800 1897300 1162600 1698200 1796400 1855200 1341300 FALSE TRUE 1742165.702 1994551.248 1704527.942 1706579.799 1365357.072 1639390.908 1522326.187 1692748.853 1549301.954 1.124484287 1.287387035 1.10019092 1.101515296 0.881272414 1.058148093 0.982588438 1.092588084 1 20.56318692 3.277555731 2.235760365 1.006215361 1.202736648 0.533523091 0.072331012 0.18940163 1.939058942 0.020264012 0.028249954 1894.766643 -3.277555731 0.196521287 FVGQDVEGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVGQDVEGER 10 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 88.948 0.02756 292159000 523740 442570 479080 557350 439290 452390 502660 509820 448980 FALSE TRUE 498983.8482 487668.3862 501046.2919 501324.1191 515902.0369 436723.6209 425969.985 465177.4581 518605.5253 0.962164543 0.940345527 0.966141445 0.966677165 0.994787004 0.842111392 0.821375717 0.896977443 1 18.98427805 2.236184172 24.99990388 0.868277753 0.962205972 0.323504651 0.050148444 53.01933625 557746.4169 0.016738446 0.012946934 172.2598926 -2.236184172 0.093928219 FVHDNYVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FVHDNYVIR 9 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;; 229.48 1.25E-07 2005060000 2017710 1275910 1053600 1066250 2135830 1029810 1723670 1267970 1676160 FALSE TRUE 1922336.847 1405926.68 1101908.602 959068.5243 2508318.076 994147.4215 1460692.484 1156939.825 1936090.332 0.992896259 0.726167915 0.569141111 0.495363521 1.295558391 0.513481941 0.754454717 0.597565003 1 20.88471484 FVHLLDQSDQDFQEELDLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FVHLLDQSDQDFQEELDLMK 20 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 195.39 2.45E-19 123437000 115443 104110 103433 122838 81330 114719 114584 136554 70640 FALSE TRUE 109986.2382 114718.9274 108175.5054 110490.0909 95513.92625 110746.2523 97102.10632 124596.6078 81594.49042 1.347961579 1.405964138 1.325769728 1.354136662 1.17059284 1.357276106 1.190057145 1.527022317 1 16.31618412 -2.205780871 2.35170221 0.00011052 1.32810315 0.520644426 0.100789102 1340883.365 388533.735 7177414.104 0.023291807 0.006226144 2.205780871 1.327992631 FVHSENQHLVSPEALDFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 105.38 0.00014857 33121000 50466 42479 47111 52291 44987 47963 55896 48627 23473 FALSE TRUE 48080.57219 46807.65839 49271.08595 47034.60933 52832.71856 46302.02928 47368.0386 44368.96209 27113.07296 1.773335404 1.726387063 1.81724462 1.734757599 1.948606808 1.707738159 1.747055329 1.636441659 1 14.72670101 0.478594933 1.190772357 0.999262354 1.782391334 0.931268677 0.066226732 0.462930986 0.835269643 0.058516555 0.017742151 3.010197097 -0.478594933 0.78312898 FVIHCNSPVWGADKCEELLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVIHCNSPVWGADKCEELLEK 21 1 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 114.72 0.00010253 357240000 145560 120830 127800 137990 93965 137450 141100 161390 99299 FALSE TRUE 138679.6673 133142.7144 133659.7564 124118.983 110352.4662 132690.072 119572.6035 147257.836 114697.7818 1.209087614 1.160813333 1.165321198 1.08213935 0.962115087 1.156866942 1.042501447 1.283876931 1 16.80747796 3.297807156 4.5445338 1.085608276 1.181223482 0.190722199 0.088246862 0.31290387 12.99904977 0.022937856 0.030861414 1985.213209 -3.297807156 0.095615207 FVIKPIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVIKPIDK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 104.17 0.0073999 0 7851200 6392800 6494600 8166400 5120900 6998700 8196300 7941500 5965500 FALSE TRUE 7480089.336 7044233.588 6792383.834 7345497.957 6013983.339 6756333.264 6945803.9 7246100.159 6890599.272 1.085549898 1.02229622 0.985746459 1.066017289 0.872780886 0.980514611 1.008011586 1.051592158 1 22.71619803 4.409135604 1.083055806 0.991102206 1.105504606 0.236673703 0.051345075 1.400883384 1.968873964 0.015226076 0.162050444 25652.84898 -4.409135604 0.1144024 FVIKPIDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVIKPIDKK 9 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 99.653 0.0029199 1437480000 5630000 4479900 5371700 6384500 4063000 5987600 7273200 7369700 4912800 FALSE TRUE 5363881.058 4936406.903 5617997.758 5742717.93 4771585.914 5780247.911 6163539.759 6724369.999 5674651.933 0.945235253 0.869904791 0.990016273 1.011994744 0.840859663 1.018608362 1.086152919 1.184983692 1 22.43610047 1.934378927 3.3423938 1.097949344 0.930392032 0.536190129 0.067027151 0.174444479 3.564870345 0.031199032 0.017528764 85.97633481 -1.934378927 -0.167557312 FVINYDYPNSSEDYIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FVINYDYPNSSEDYIHR 17 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 280.15 6.61E-36 4763400000 2567100 2392140 2197810 2710400 2814500 2348820 2987470 2649260 2606550 FALSE TRUE 2445758.271 2635901.786 2298581.762 2437945.443 3305347.909 2267479.774 2531676.583 2417276.75 3010760.462 0.812339042 0.87549369 0.763455543 0.809744074 1.097844864 0.753125266 0.840876123 0.802879133 1 21.5216965 -2.318455739 2.247102567 1.805158954 0.845037639 0.203685969 0.096639123 4910288.324 767515.6762 20059170.31 0.021552631 0.00480335 2.318455739 -0.960121315 FVINYDYPNSSEDYVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FVINYDYPNSSEDYVHR 17 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 265.27 1.55E-27 2727460000 2630700 2092580 2282850 2735790 2578060 2283210 2785030 2422680 2464210 FALSE TRUE 2506352.025 2305816.281 2387520.931 2460783.192 3027672.848 2204141.865 2360122.523 2210537.296 2846347.101 0.880550381 0.81009666 0.83880175 0.864540797 1.06370472 0.774375642 0.829175936 0.776622533 1 21.44068017 2.647897157 0.008870789 1.721546621 1.61E-06 0.063864279 0.090446241 12380.20321 46.0609848 4368.56357 4567.026512 444.5259894 -2.647897157 -1.721545006 FVKDFQDYMEPEEGCQGS(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVKDFQDYMEPEEGCQGSPQRR 22 2 O43237;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 FVKDFQDYMEPEEGCQGS(1)PQRR 84.524 0.0017105 60954000 37050 26090 46978 37611 51252 42520 55175 48136 66313 TRUE FALSE 35298.71993 28748.60066 49131.98777 33830.27082 60190.33257 41047.52174 46757.04039 43920.95666 76596.48136 0.460839967 0.375325343 0.641439227 0.441668732 0.785810673 0.535893046 0.610433267 0.573406975 1 16.2249905 -5 0.115773935 2.486018429 0.298094024 0.658376466 0.106000552 87.86244686 0.666712698 30.74979678 1.043329355 1.00E-05 5 -2.187924405 FVKEPAFEDITLESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FVKEPAFEDITLESER 16 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 236.16 9.21E-20 590499000 534970 418478 500250 518000 479370 486578 624960 562150 587250 FALSE TRUE 509683.0283 461121.384 523186.9573 465929.6559 562971.9762 469727.6819 529610.8738 512925.1659 678317.7307 0.751392755 0.67980146 0.771300725 0.686889985 0.829953207 0.692489169 0.78077109 0.756172429 1 19.37160168 -4.999999995 0.255508217 2.644247595 0.717829264 0.759782606 0.045674838 78.94189179 0.778667427 67.89381576 0.053804121 1.00E-05 4.999999995 -1.926418331 FVKWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVKWPR 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 113.82 0.023541 998960000 1260780 585360 900220 747740 1564860 1018320 2046200 1341120 2150400 FALSE TRUE 1201185.428 645008.8495 941495.9774 672575.7546 1837771.089 983055.3231 1734014.609 1223684.423 2483873.049 0.483593728 0.25967867 0.379043517 0.270777025 0.739881247 0.395775188 0.698109193 0.492651757 1 21.24416001 0.485653477 0.308674193 1.105957644 0.318317979 0.61992977 0.142010436 1.934070559 0.388265143 0.47553817 0.16339676 3.059521274 -0.485653477 -0.787639665 FVLCPECENPETDLHVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVLCPECENPETDLHVNPK 19 0 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 188.41 1.62E-14 108650000 116130 99553 97738 125310 95965 129770 118810 124140 97742 FALSE TRUE 110640.765 109697.5639 102219.384 112713.6007 112701.2656 125276.0324 100683.3524 113269.6435 112899.3302 0.979994876 0.97164052 0.905402927 0.998354911 0.998245653 1.109626002 0.891797606 1.003280031 1 16.7846774 FVLDHEDGLNLNEDLENFLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVLDHEDGLNLNEDLENFLQK 21 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7;F5H3L6;F5H2F3 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 309.41 1.73E-66 308980000 240610 271440 235520 272940 188753 246660 238160 248660 163366 FALSE TRUE 229236.8421 299100.0446 246318.825 245503.5526 221671.4634 238118.1024 201824.3179 226886.0122 188699.9649 1.214821859 1.585056175 1.305346427 1.301025958 1.174729754 1.261887369 1.069551433 1.202363828 1 17.52573463 2.382772588 0.698711772 1.066350715 1.401462754 0.50949846 0.109567025 0.526970474 0.510671923 0.085588118 0.061904634 241.4196346 -2.382772588 0.335112039 FVLINWTGEGVNDVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVLINWTGEGVNDVRK 16 1 Q9UJU6-2;Q9UJU6-3;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 156.67 2.25E-07 357520000 206470 162534 192745 206480 192029 197630 267690 206737 214443 FALSE TRUE 196710.5723 179096.3994 201582.5489 185724.2381 225518.7968 190786.0235 226848.974 188634.0123 247697.7252 0.794155748 0.723044183 0.813824789 0.749801953 0.910459701 0.770237286 0.915829864 0.761549232 1 17.91822109 -5 0.107754139 1.648495714 0.683265988 0.501772164 0.062387097 119.7080458 0.862246809 17.07748089 0.725535732 1.00E-05 5 -0.965229726 FVLMAT(ph)PNLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FVLMATPNLSR 11 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 FVLMAT(1)PNLSR;FVLMAT(0.997)PNLS(0.003)R;FVLMAT(1)PNLSR;FVLMAT(1)PNLSR;FVLMAT(0.996)PNLS(0.004)R 145 0.00040745 623615000 880127 838855 828563 835691 882345 781166 922317 956734 958579 TRUE FALSE 838525.141 924335.2782 866553.4331 751685.753 1036225.689 754114.0255 781600.6021 872957.299 1107230.536 0.757317572 0.834817365 0.782631444 0.678888207 0.935871668 0.681081312 0.705905931 0.788415123 1 20.07852421 0.953808448 22.1050865 1.000000001 0.768259442 0.473894322 0.076249079 2312.249151 1106535.18 0.069437223 0.017359306 8.991009323 -0.953808448 -0.231740559 FVMEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FVMEEGR 7 0 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;; 190.71 0.0012481 546790000 1345020 1058210 1046220 1187440 1931480 1074590 1500010 1218960 2035840 FALSE TRUE 1281443.57 1166042.802 1094190.222 1068076.275 2268329.5 1037376.679 1271155.925 1112221.4 2351547.67 0.544936251 0.49586186 0.465306418 0.454201413 0.96461132 0.441146353 0.54056141 0.47297421 1 21.16517915 -1.487835447 2.853624474 1.015685622 0.544819387 0.465360154 0.152419018 38001975.26 41324930.72 4693124.475 0.037330477 0.03252105 1.487835447 -0.470866235 FVMEEGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVMEEGRK 8 1 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 95.909 0.014937 317000000 599030 486770 436830 505890 453780 537090 639660 506040 467060 FALSE TRUE 570715.0391 536372.4164 456859.0876 455036.9761 532919.0883 518490.4386 542068.1188 461728.4549 539489.2794 1.057880223 0.994222567 0.846836267 0.843458792 0.987821461 0.961076445 1.00478015 0.855862151 1 19.04123477 3.982699494 10.42618845 0.933038468 1.034097033 0.312752545 0.062712192 0.533543473 318.657137 0.016250492 0.030501072 9609.471308 -3.982699494 0.101058565 FVMQEEFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 FVMQEEFSR 9 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;; 265.55 4.41E-15 1730350000 2112357 2046912 2046323 2274424 1734008 1957473 2450428 2289487 2188359 FALSE TRUE 2012510.071 2255494.66 2140148.934 2045794.578 2036418.446 1889685.219 2076570.203 2089007.381 2527718.537 0.796176489 0.892304514 0.846672168 0.809344295 0.805634969 0.747585299 0.821519553 0.826439871 1 21.2694044 0.633651783 3.900362857 0.999999734 0.820233051 0.708594362 0.036640925 8.463200106 89.46124202 0.03750405 0.009594842 4.301815526 -0.633651783 -0.179766683 FVPDKEFSGSDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVPDKEFSGSDRR 13 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ; 105.19 0.00082807 142559000 529850 430950 476700 513470 422710 482300 614910 572140 576180 FALSE TRUE 504805.0406 474864.2949 498557.1665 461855.0201 496430.4902 465597.8301 521094.1859 522040.3885 665531.0517 0.758499606 0.713511855 0.749111804 0.693964645 0.745916346 0.69958844 0.782975016 0.784396742 1 19.34414645 0.520908679 0.959930572 1.000660404 0.728283024 0.921866808 0.024360037 0.365046827 0.497792546 0.021112004 0.006744004 3.318246761 -0.520908679 -0.272377381 FVPYLIAGIQHGCQDIGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVPYLIAGIQHGCQDIGAR 19 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ; 228.46 1.03E-19 511680000 775140 748690 732870 900140 821690 736940 991830 735840 708770 FALSE TRUE 738500.6684 824982.3622 766472.8144 809656.217 964992.4758 711419.583 840508.1173 671405.9487 818682.4317 0.902059993 1.007695207 0.936227266 0.988974706 1.178714039 0.868981128 1.026659526 0.82010548 1 19.64294441 -0.843104857 4.07451047 1.000000497 0.971930394 0.008557771 0.098392822 9438298.502 4632999.171 41.32878214 0.020568138 0.143514289 0.843104857 -0.028070102 FVPYLIAGIQHSCQDIGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FVPYLIAGIQHSCQDIGAK 19 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 229.54 7.79E-20 133486000 206653 141992 182817 173703 181417 189308 253130 195271 203836 FALSE TRUE 196884.9222 156461.1462 191199.3403 156242.0444 213056.0674 182752.2165 214510.3694 178172.036 235445.8458 0.836221686 0.664531352 0.812073535 0.663600769 0.904904763 0.776196394 0.911081564 0.756743171 1 17.84503574 0.531184493 0.314860062 1.03511502 0.73594642 0.396408788 0.082890867 2.697283693 0.578398485 0.254663684 0.091226556 3.3976958 -0.531184493 -0.2991686 FVS(ph)EGDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;FVS(1)EGDGGR 176.45 5.57E-05 1232270000 2943740 2293850 2485790 3049480 3131680 2730970 3237340 2908550 3525010 TRUE FALSE 2804595.244 2527595.923 2599765.93 2742940.477 3677844 2636395.824 2743424.325 2653861.943 4071650.548 0.6888104 0.620779189 0.638504189 0.67366795 0.903280858 0.647500514 0.673786783 0.651790204 1 21.95718232 -1.490388864 2.719176058 1.013018343 0.683485812 0.604585736 0.079431101 8170441.408 8471666.612 795543.0228 0.019590318 0.032330404 1.490388864 -0.329532532 FVSEDDRNSFTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 132.97 0.00010277 1236790000 2324280 1828230 1970180 2177490 1916330 2083090 2566580 2431620 2179260 FALSE TRUE 2214415.891 2014528.716 2060514.702 1958604.568 2250537.345 2010952.071 2175001.083 2218694.462 2517208.511 0.87971095 0.800302679 0.818571323 0.778085947 0.894060756 0.798881802 0.864052808 0.881410679 1 21.2633933 0.720310689 1.03199736 1.000097949 0.828054892 0.687244326 0.035993071 0.513147482 0.966312751 0.031377216 0.010050395 5.251830361 -0.720310689 -0.172043058 FVSRPPT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVSRPPTPK 9 1 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 FVSRPPT(1)PK 71.176 0.081356 172710000 277000 228490 237510 281240 202500 262420 274870 282830 225510 TRUE FALSE 263906.759 251773.3908 248400.0684 252969.2209 237815.9359 253332.3296 232933.5332 258063.9058 260480.9391 1.013151902 0.966571265 0.953620903 0.97116212 0.912987863 0.972556113 0.894244063 0.990720883 1 17.99081828 4.559749166 0.904799377 0.946652595 1.039006279 0.187359549 0.033098481 1.968781941 1.526960022 0.009979425 0.169870948 36286.84134 -4.559749166 0.092353684 FVVDVDKNIDINDVTPNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVVDVDKNIDINDVTPNCR 19 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 109.72 0.00022788 61783000 114730 101500 126570 129480 105360 112780 136380 134670 121930 FALSE TRUE 109306.9403 111842.9654 132373.3597 116464.4244 123734.7506 108874.4003 115572.7262 122877.5809 140838.2817 0.776116685 0.794123331 0.939896157 0.826937272 0.878559076 0.773045503 0.820605909 0.872472878 1 17.10368 -4.999999999 0.279631379 2.252219076 0.817264883 0.511628967 0.050869995 189.1898918 1.812107009 137.4522783 0.058487858 1.00E-05 4.999999999 -1.434954193 FVYVWDTTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FVYVWDTTSR 10 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 120.87 0.0012333 84002000 89352 77121 72578 88143 95377 66371 97209 85833 111320 FALSE TRUE 85128.50804 84979.71758 75905.77309 79282.69818 112010.7186 64072.55563 82377.98168 78317.00749 128582.9371 0.662051358 0.660894202 0.590325395 0.616588017 0.871116504 0.498297497 0.64066029 0.609077762 1 16.97233968 -1.121897678 5.513980085 1.000005125 0.643915147 0.590506263 0.093264879 5.32E-06 8.47E-07 0.081751152 0.019268654 0.075527015 1.121897678 -0.356089979 FWAELAPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FWAELAPEPR 10 0 Q3KQV9;A0A087X226 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ;; 145.17 7.19E-05 83789400 216535 171178 124878 128907 231735 132997 229204 175074 221552 FALSE TRUE 206299.8197 188621.2328 130603.7798 115949.0235 272149.5106 128391.2805 194234.7202 159743.5924 255909.1526 0.806144749 0.737063254 0.510352125 0.453086661 1.063461419 0.501706481 0.758998724 0.624219926 1 17.96527222 -1.224742137 4.015491912 1.000237994 0.690709334 0.236610983 0.178953053 24412105.75 7445851.901 50643.89947 0.038260077 0.059601592 1.224742137 -0.30952866 FWAWDPEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 114.84 0.0030291 17899000 77460 66345 69450 80722 76432 64238 83731 69239 71303 FALSE TRUE 73798.61931 73105.63093 72634.3512 72607.6712 89761.7166 62013.42195 70956.29812 63176.0661 82360.30507 0.896045968 0.887631862 0.881909691 0.881585749 1.089866247 0.752952796 0.861535154 0.767069355 1 16.32966155 FWEGDFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FWEGDFHR 8 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;;; 140.5 0.00064854 804860000 806020 661430 603190 693280 831500 599780 866820 712750 671610 FALSE TRUE 767921.032 728830.469 630846.8581 623590.1773 976513.3367 579009.4682 734570.6888 650337.8315 775759.8487 0.989895305 0.939505274 0.813198645 0.803844358 1.258783035 0.746377206 0.946904754 0.838323655 1 19.56525058 1.017681651 0.002236511 0.203774898 1.641282051 0 0.144966625 914455.7283 1356.4499 437194.038 434627.3156 10.41553664 -1.017681651 1.437507154 FWETLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FWETLDR 7 0 A0A1B0GUB2;Q6P1J9 A0A1B0GUB2 CDC73 Parafibromin 0 ;;; 173.59 0.0019951 209149000 499554 510721 450968 520429 493984 448057 513137 520193 495275 FALSE TRUE 475941.0724 562764.0505 471645.3289 468114.4882 580134.6532 432540.6737 434848.5262 474642.1432 572079.7175 0.831948866 0.983716138 0.824439872 0.818267933 1.014080093 0.756084616 0.760118761 0.829678328 1 19.12585667 2.201785756 24.9997916 0.808284627 0.894323647 0.051560102 0.093777989 294.3329012 200087.799 0.032246489 0.023816263 159.1423459 -2.201785756 0.08603902 FWEVISDEHGIDPAGGYVGDSALQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FWEVISDEHGIDPAGGYVGDSALQLER 27 0 K7ESM5;Q9BUF5;K7EL29;K7ESQ3;K7EQT3;K7EJ64;K7ERA8;K7EJZ4;K7EN98;K7EPE5 K7ESM5 TUBB6 Tubulin beta-6 chain 0 ; 148.1 1.26E-07 104458000 73200 64103 72265 82748 82787 70751 92114 81874 74408 FALSE TRUE 69739.98107 70635.16858 75578.42173 74430.01383 97225.02659 68300.87513 78060.31751 74704.67852 85946.81262 0.811431849 0.821847448 0.879362706 0.866000862 1.131223179 0.794687703 0.908239819 0.869196614 1 16.39115652 3.469829279 2.062488165 0.923283687 0.815916197 0.214656918 0.089144588 0.484362041 4.131832707 0.025214713 0.040925323 2950.049335 -3.469829279 -0.10736749 FWEVISDEHGIDPTGSYHGDSDLQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;; 261.78 2.44E-53 11181408000 89395 68787 84500 90189 104141 81001 107260 87304 45720 FALSE TRUE 85169.47551 75796.4735 88374.40858 81123.03037 122303.1574 78195.91506 90895.51703 79659.19893 52810.02409 1.612752067 1.435266785 1.673440035 1.536129395 2.315908003 1.480702128 1.721179238 1.508410577 1 15.68852418 0.847510833 3.373770992 1.000065697 1.661594437 0.4344761 0.243693191 0.723515068 14.12539324 0.222075604 0.057503172 7.038997862 -0.847510833 0.66152874 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;;;;;;;;;;;;;;;;;;; 348.5 2.33E-110 22952192900 4346503.9 3522308.7 4126190.1 4427372.7 4622719.4 3926088.8 5151075.4 4409163.8 1406484.9 FALSE TRUE 4141053.275 3881235.961 4315379.997 3982324.785 5428920.2 3790127.36 4365184.242 4023074.043 1624595.395 2.54897514 2.389047743 2.656279841 2.451271743 3.341706013 2.332966948 2.68693624 2.476354455 1 20.63164903 0.753312995 4.25057395 1.000003332 2.60769232 0.76869035 0.278651979 1.9783945 33.7329836 0.247083694 0.062904839 5.666475239 -0.753312995 1.607688988 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 344.13 1.32E-96 14187700000 3041942 2498786 2843165 3159301 3295217 2722288 3638411 3076376 1190459 FALSE TRUE 2898155.43 2753415.134 2973526.928 2841722.061 3869901.801 2628014.484 3083304.578 2806992.209 1375069.302 2.107643176 2.002382811 2.162456048 2.066602794 2.814332192 1.911186935 2.242290315 2.041345993 1 20.3910729 0.778707803 4.112136705 1.000006381 2.16869707 0.698560005 0.24281918 1.508167258 27.54189234 0.216234256 0.055155744 6.007693987 -0.778707803 1.168690689 FWSFFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FWSFFLR 7 0 Q6PKG0;Q6PKG0-3;Q659C4-7;A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;Q659C4-6;Q659C4-5 Q6PKG0;A0A3B3ISF0 LARP1;LARP1B La-related protein 1;La-related protein 1B 0 97.068 0.028543 6964300 37475 30198 18547 16699 43096 17767 45502 27928 29125 FALSE TRUE 35703.63102 33275.21053 19397.3983 15020.38479 50611.92876 17151.72434 38559.8342 25482.47626 33641.55625 1.061295463 0.989110322 0.576590398 0.446483055 1.504446714 0.509837423 1.146196505 0.757470198 1 15.03795683 FWTHWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FWTHWNR 7 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 193.98 0.00048877 714070000 1053670 708160 440720 495820 1179030 473300 1250000 688690 892430 FALSE TRUE 1003865.107 780322.3091 460927.4479 445979.2316 1384652.459 456909.5023 1059289.542 628384.6526 1030823.486 0.973847725 0.756989261 0.447144884 0.432643646 1.343248846 0.443247082 1.027614869 0.609594815 1 19.97536588 FWVLAAHPNLNLFAAGHDGGMIVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FWVLAAHPNLNLFAAGHDGGMIVFK 25 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 59.678 0.045412 3825400 20142 16884 15269 18756 11322 15717 21666 15586 7549.5 FALSE TRUE 19189.92758 18604.4988 15969.09875 16870.61125 13296.55322 15172.71635 18360.45378 14221.20721 8720.237902 2.20061973 2.133485233 1.831268703 1.934650343 1.524792484 1.739942937 2.105499183 1.630827894 1 13.09015178 -1.691865222 0.158157997 4.97E-18 2.302967286 0.718521488 0.188077763 21.47071027 0.550016926 9.929875736 1.102536086 0.020329878 1.691865222 2.302967286 FYAFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FYAFGR 6 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 164.54 0.017566 8277061000 5336071 5127703 4457555 5109169 5023251 4596534 5156567 4969289 4925705 FALSE TRUE 5083845.499 5650221.765 4661938.306 4595585.625 5899304.384 4437354.875 4369837.997 4534151.711 5689558.174 0.893539594 0.99308621 0.819384944 0.807722759 1.036865114 0.779912032 0.768045227 0.796925099 1 22.43988519 2.176827127 24.99999922 0.810336656 0.911150992 0.104697368 0.094758464 102.8107999 41633.80706 0.033077673 0.024429488 150.2543752 -2.176827127 0.100814336 FYALSASFEPFSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYALSASFEPFSNK 14 0 P27797 P27797 CALR Calreticulin 0 184.03 3.12E-06 45608000 255000 197780 175040 224800 186800 192090 252290 229240 177340 FALSE TRUE 242946.6554 217934.0069 183065.7571 202202.6769 219377.8609 185437.8751 213798.5269 209166.5303 204840.9815 1.186025636 1.063917998 0.893696934 0.987120231 1.070966656 0.905277224 1.043729264 1.021116618 1 17.64414485 4.190078057 2.60902708 0.991616219 1.167890516 0.545397449 0.056519707 0.183606419 2.455926034 0.013732026 0.041862392 15490.95017 -4.190078057 0.176274297 FYCDYCDTYLTHDS(ph)PSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 1 FYCDYCDTYLTHDS(0.999)PSVR;FYCDYCDTYLTHDS(1)PSVR 295.23 1.73E-49 404060000 517130 539280 505070 616290 524500 525560 587710 601350 511170 TRUE FALSE 492686.2898 594233.2451 528227.9591 554339.3583 615972.6339 507359.7254 498044.0455 548692.606 590439.6329 0.834439733 1.006425064 0.894634997 0.938858653 1.04324405 0.859291445 0.843513914 0.929295013 1 19.17143004 0.967800233 22.81371968 1.000000004 0.916268621 0.129041953 0.067052947 3035.619086 2150757.414 0.064311767 0.016077942 9.285391788 -0.967800233 -0.083731384 FYCDYCDTYLTHDSPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 ;;; 302.34 1.16E-49 1263840000 623390 457083 587106 670540 1127990 519810 973080 767660 1180280 FALSE TRUE 593923.5901 503660.2774 614025.3908 603136.0453 1324711.099 501808.8494 824618.7742 700439.6208 1363311.794 0.435647658 0.369438803 0.450392488 0.442405067 0.971686084 0.368080766 0.604864403 0.51377801 1 20.37868412 -4.999999998 0.12840896 2.613190779 0.298499354 0.459799809 0.169769696 125.24051 1.019113952 52.23973317 1.246754902 1.00E-05 4.999999998 -2.314691425 FYEAFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FYEAFSK 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 155.51 0.0037367 2050420000 6236100 5335260 4963060 6125550 4774650 5462440 6455510 6160570 5165690 FALSE TRUE 5941331.912 5878929.06 5190621.21 5509798.076 5607347.448 5273274.333 5470603.386 5621117.832 5966758.823 0.995738572 0.985280155 0.86992308 0.923415583 0.939764387 0.883775344 0.916846742 0.942072237 1 22.50851603 3.864476533 7.7592283 0.919623108 0.991721386 0.366854115 0.035230748 0.214055491 12.51898877 0.008023648 0.014531812 7319.417719 -3.864476533 0.072098278 FYEDDENGWQAFGDFSPTDVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FYEDDENGWQAFGDFSPTDVHK 22 0 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 ;; 234.23 1.96E-30 141995000 249267 211378 224173 253779 181139 220516 271117 246062 208206 FALSE TRUE 237484.6429 232917.6585 234451.5538 228268.6528 212729.5842 212879.4756 229753.1222 224515.5068 240493.5231 0.987488727 0.968498675 0.97487679 0.949167569 0.884554318 0.885177583 0.955340166 0.933561553 1 17.87563851 3.07728863 4.098276061 0.926469292 0.97640068 0.267110665 0.033323653 0.247393617 8.063921773 0.009408598 0.011308146 1194.781887 -3.07728863 0.049931387 FYEEEENGGVWEGFGDFSPTDVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 110.9 0.0018842 34004000 20542 16794 18223 23150 21211 20665 25855 22101 22997 FALSE TRUE 19571.02037 18505.32769 19058.54258 20822.91802 24910.19168 19949.36587 21910.34489 20165.71928 26563.25731 0.736770349 0.696651298 0.717477618 0.78389927 0.937768715 0.751013539 0.824836527 0.759158376 1 14.69714445 -5 0.097217343 1.719157921 0.608376694 0.572800144 0.063670729 135.0878754 0.899019533 19.90472339 1.138534416 1.00E-05 5 -1.110781227 FYEEVHDLER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 248.88 6.86E-13 3898020000 5147100 4138090 4114490 5033590 5390400 4186410 5745430 4890880 4806050 FALSE TRUE 4903806.784 4559766.076 4303143.436 4527603.97 6330484.053 4041433.572 4868859.131 4462608.619 5551347.688 0.883354288 0.82138002 0.775152932 0.815586453 1.14035085 0.728009449 0.877058942 0.803878422 1 22.40440662 FYEQFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FYEQFSK 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 123.69 0.0098156 3007957000 3895620 3185620 3049950 3635840 2960250 3498710 3882660 3794130 3410640 FALSE TRUE 3711481.763 3510238.3 3189793.224 3270358.456 3476516.663 3377548.795 3290288.907 3461895.863 3939544.632 0.942109332 0.891026407 0.809685769 0.830136161 0.882466627 0.857344975 0.835195236 0.878755335 1 21.90959745 0.954061083 22.01804968 1.000000001 0.86694826 0.569252299 0.036824456 2154.604612 1032682.18 0.039783648 0.009945912 8.99624104 -0.954061083 -0.13305174 FYFHDGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;;;;; 178.3 0.00025035 1715050000 1725700 1642990 1527550 1774970 1828440 1574590 2022110 1810220 1838640 FALSE TRUE 1644129.581 1810412.549 1597589.678 1596546.643 2147319.357 1520061.553 1713599.981 1651707.54 2123766.901 0.774157268 0.85245351 0.752243421 0.751752296 1.011089944 0.715738414 0.806868202 0.777725437 1 21.018194 -1.841854181 2.576064004 1.075665318 0.806600675 0.359551095 0.081665835 17893729.85 11457323.62 8348130.299 0.017572434 0.014392818 1.841854181 -0.269064643 FYGAEIVSALEYLHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYGAEIVSALEYLHSR 16 0 P31751;P31751-2;M0R0P9;J3QKW1 P31751 AKT2 RAC-beta serine/threonine-protein kinase 0 103.39 0.001443 23196000 60384 61096 60938 61727 65663 50281 66319 59587 54552 FALSE TRUE 57529.76799 67321.75186 63732.06758 55522.08469 77114.60641 48539.75636 56200.81852 54369.24639 63011.64555 0.913002152 1.068401742 1.011433157 0.881140053 1.223815149 0.770329928 0.891911615 0.862844414 1 15.94333087 2.198804506 24.99983152 0.870728816 1.009871829 0.28868498 0.106696711 183.7406022 115540.525 0.035751613 0.026404658 158.0536413 -2.198804506 0.139143013 FYGDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYGDEEK 7 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 121.52 0.010307 51299000 184050 191360 155520 211690 108000 186920 180540 175880 112750 FALSE TRUE 175350.3213 210859.8016 162650.7458 190410.519 126835.1658 180446.9135 152995.3072 160479.0148 130234.6942 1.346417883 1.619075492 1.248904886 1.462056791 0.973896907 1.385551789 1.174766126 1.232229367 1 16.9907543 2.531576894 0.257884533 0.987688241 1.592866644 0.383332613 0.154733734 2.609245088 0.425814319 0.266798995 0.539860039 340.0767124 -2.531576894 0.605178403 FYGDEEKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;;; 161.76 5.86E-05 10876770000 13203270 12849800 10513240 15823950 7062320 15210950 14214030 16251080 6775760 FALSE TRUE 12579177.59 14159209.23 10995282.45 14233296.48 8293986.372 14684190.99 12045418.66 14828049.28 7826510.255 1.607252426 1.809134438 1.404876771 1.81860063 1.059729829 1.876211812 1.539053585 1.894592711 1 22.89993774 3.748996792 24.42828685 1.550749156 1.708193416 0.052898235 0.313070298 1651.160256 3864907.072 0.070724062 0.125783285 5610.438324 -3.748996792 0.157444259 FYGDEEKDKGLQTSQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYGDEEKDKGLQTSQDAR 18 2 P27797 P27797 CALR Calreticulin 0 ; 117.84 6.75E-05 1042630000 1434540 839570 1445630 1163600 962740 1497400 1976710 1702410 1112580 FALSE TRUE 1366732.137 925123.1375 1511913.565 1046632.717 1130641.551 1445544.663 1675126.585 1553337.955 1285113.224 1.063511068 0.719876755 1.17648277 0.814428408 0.879799173 1.124838369 1.303485602 1.208716809 1 20.29346404 2.115866787 4.556352509 1.206403004 0.920620854 0.369021935 0.14607789 0.180346325 6.383080565 0.052514797 0.037874436 130.5770303 -2.115866787 -0.285782149 FYGPEGPYGVFAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYGPEGPYGVFAGR 14 0 O00264 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 100.55 0.0040437 56569000 97540 70373 71804 105720 93542 96348 118910 104170 99719 FALSE TRUE 92929.47751 77544.08871 75096.28442 95092.82475 109855.6952 93011.4446 100768.0956 95048.32256 115182.9132 0.806799159 0.673225625 0.651974172 0.825581001 0.953749928 0.807510784 0.874852812 0.82519464 1 16.81356719 3.058228576 6.006723636 0.878108998 0.71743229 0.586814282 0.068863348 0.140481572 10.31620899 0.018858172 0.022540813 1143.480008 -3.058228576 -0.160676708 FYHDAK ddPTM_SK-BR-3_Trastuzumab_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 69645000 415030 344030 329130 425550 322200 369190 445590 439240 315510 FALSE TRUE 395412.3544 379087.0481 344220.9361 382772.9055 378391.578 356404.8577 377607.0617 400777.817 364437.6794 1.084993064 1.040197185 0.944526199 1.050311006 1.038288847 0.977958312 1.036136171 1.099715643 1 18.4753126 -0.351184489 6.309720215 1.000000186 1.033260025 0.052723437 0.045211908 0 0 0.042399302 0.009993611 0.445466974 0.351184489 0.033259839 FYHDWNDKEIEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 288.53 3.64E-35 1086610000 3894200 3654900 3312100 4266800 2417800 3859800 4186000 4257600 2146100 FALSE TRUE 3710128.884 4027338.465 3463963.061 3837893.158 2839463.554 3726134.158 3547348.819 3884781.973 2478906.227 1.496679803 1.624643329 1.397375594 1.548220387 1.145450168 1.50313639 1.431013719 1.567135509 1 21.24127227 -3.067500884 0.296372087 2.55E-24 1.503374107 0.532706561 0.13377732 55.36914306 1.465727312 34.94304479 0.132822527 0.00085605 3.067500884 1.503374107 FYHEELNAPIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYHEELNAPIRR 12 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 0 115.14 0.00063764 61003000 44242 42568 45443 51339 46447 46306 49196 47489 47661 FALSE TRUE 42150.76834 46905.7276 47526.6065 46178.30618 54547.34209 44702.41161 41690.24665 43330.6114 55052.02446 0.765653375 0.852025481 0.86330352 0.838812135 0.990832628 0.812003047 0.757288166 0.787084795 1 15.748508 4.539381732 2.355264471 0.850387618 0.761296241 0.111600573 0.079308619 0.920846708 8.295542542 0.019800043 0.141234864 34624.35817 -4.539381732 -0.089091377 FYKNEGGTWSVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYKNEGGTWSVEK 13 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 175.66 1.63E-05 850440000 1231540 512570 1062530 735040 1129250 1008400 1786310 1214030 1454500 FALSE TRUE 1173327.545 564801.4657 1111248.051 661152.3827 1326190.842 973478.8551 1513775.602 1107723.097 1680056.431 0.698385794 0.336180056 0.661434956 0.393529866 0.789372796 0.579432236 0.90102664 0.659336839 1 20.68007826 1.668344235 0.5808417 0.965731889 0.508760527 0.449811582 0.151120659 0.589044912 0.442244486 0.130739914 0.073748196 46.59552776 -1.668344235 -0.456971362 FYNELTEILVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYNELTEILVR 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 190.86 4.85E-06 152641000 220938 190267 205902 212390 227232 199462 255580 221917 241430 FALSE TRUE 210494.6986 209655.4236 215342.8104 191040.1537 266861.1889 192554.5809 216586.577 202484.771 278869.7313 0.754813717 0.751804158 0.772198579 0.685051593 0.956938523 0.690482183 0.776658607 0.726090889 1 18.08923183 -1.349731398 3.353062724 1.00155785 0.763853143 0.493200828 0.075101006 18491474.99 28460124.18 288544.7985 0.01585583 0.044695994 1.349731398 -0.237704707 FYPDRPHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYPDRPHQK 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1;H3BQD1;H3BUV0;H3BTM1;H3BRA2 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 92.538 0.0060132 398480000 1163330 1117540 1028690 1229420 954800 1213930 1329920 1318750 1184830 FALSE TRUE 1108341.696 1231418.597 1075856.454 1105836.366 1121316.818 1171891.3 1127016.278 1203273.259 1368567.385 0.809855407 0.899786602 0.786118729 0.808024784 0.819336212 0.856290536 0.823500758 0.879221054 1 20.38423504 0.853583114 2.783237413 0.999962789 0.833116613 0.750198568 0.031103113 0.29771595 4.325482473 0.029438299 0.007783085 7.138107994 -0.853583114 -0.166846176 FYPPKVELFFKDDANNDPQWSEEQLIAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYPPKVELFFKDDANNDPQWSEEQLIAAK 29 2 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 212.21 2.75E-26 41052000 162870 127530 162510 162380 95681 184290 176710 193370 104950 FALSE TRUE 155171.4579 140525.452 169961.2442 146057.2539 112367.7361 177907.9911 149749.644 176437.4977 121225.11 1.280027363 1.159210761 1.402030027 1.204843237 0.926934495 1.467583664 1.235302191 1.455453393 1 16.88732904 FYQHKFPEVEDVVMVNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYQHKFPEVEDVVMVNVR 18 1 P05198;G3V4T5 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 77.39 0.0082047 156840000 89104 74835 85587 81806 99375 89502 109280 94703 105620 FALSE TRUE 84892.23051 82460.77158 89511.24861 73582.70546 116705.9685 86402.5233 92607.32894 86410.30327 121999.0102 0.695843601 0.675913448 0.733704712 0.603141824 0.956614061 0.70822315 0.759082625 0.708286921 1 16.89650992 -5 0.182830917 2.123538168 0.671918979 0.47844961 0.089457465 109.9162594 1.063363897 44.94053224 0.242740456 1.00E-05 5 -1.451619189 FYS(ph)TSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FYS(0.333)T(0.333)S(0.333)LK;FYS(0.333)T(0.333)S(0.333)LK;FYS(0.333)T(0.333)S(0.333)LK 77.674 0.039238 178076000 351728 359449 403957 410379 1470880 266547 501210 323161 1673950 TRUE FALSE 335102.5145 396077.2618 422478.828 369126.9233 1727401.006 257316.4106 424741.2091 294863.3097 1933537.617 0.173310574 0.204845904 0.218500444 0.190907547 0.89338888 0.133080633 0.219670518 0.152499391 1 20.8828114 -2.20928577 2.210781431 3.13041965 0.265871228 0.512262581 0.222749134 11751786.98 2217965.777 125173435.6 0.052096933 0.006176099 2.20928577 -2.864548422 FYTLIPHDFGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 FYTLIPHDFGMK 12 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 153.95 5.96E-05 1181290000 3731970 3170090 2872050 3446210 2948720 3085320 4204660 3838290 2933710 FALSE TRUE 3555567.174 3493125.775 3003736.333 3099790.423 3462975.834 2978474.595 3563161.893 3502188.98 3388654.763 1.049256245 1.030829642 0.886409665 0.914755453 1.021932323 0.878954866 1.051497465 1.033504214 1 21.69228123 -0.803209978 7.393409775 1.000000032 0.987852623 0.002124393 0.067004295 0 0 0.064699191 0.015249745 0.157322204 0.803209978 -0.012147409 FYTQQWEDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 FYTQQWEDYR 10 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 ;; 142.83 8.16E-05 279784000 364600 395034 285112 413276 342853 331107 345786 390178 349353 FALSE TRUE 347366.0806 435288.4137 298184.6672 371732.7113 402646.4546 319640.6816 293029.9949 356011.9459 403528.879 0.86082087 1.07870449 0.738942571 0.921204728 0.997813231 0.792113522 0.726168585 0.882246512 1 18.6223124 2.223094552 24.9628384 0.81521884 0.92774365 0.045469021 0.113022513 389.8530245 629234.0688 0.040141015 0.02975341 167.1454472 -2.223094552 0.11252481 FYVEDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYVEDLK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 102.72 0.019862 58847000 293890 272230 257480 325610 218640 278840 323170 308390 247270 FALSE TRUE 279998.4021 299970.5465 269285.7127 292879.0642 256770.7468 269183.7009 273864.4811 281385.7367 285615.3687 0.980333808 1.050260523 0.94282641 1.025431739 0.899008859 0.942469245 0.958857649 0.985191161 1 18.12371409 3.727648088 24.9841826 0.961409376 1.015297167 0.227159873 0.038301346 801.6731454 1835426.717 0.009479453 0.014844072 5341.313733 -3.727648088 0.053887791 FYVHNDIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 FYVHNDIFR 9 0 Q13283;E5RIZ6 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;;; 193.82 3.31E-05 1563251000 5587420 2287467 1775240 2664654 5690830 2605610 6592650 4062620 5429320 FALSE TRUE 5323313.73 2520562.488 1856636.51 2396797.917 6683308.95 2515377.072 5586820.16 3706875.455 6271271.216 0.848841255 0.401922099 0.296054252 0.382186934 1.065702426 0.401095246 0.89085928 0.591088366 1 22.58032648 2.770481665 24.99720617 0.759723862 0.499250925 0.28526088 0.238579989 979.7938588 767269.8022 0.069245211 0.073439787 589.497089 -2.770481665 -0.260472937 FYWGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 FYWGHK 6 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 123.07 0.018947 4902800000 7432100 6319200 6033400 7305500 5835900 6294600 7652800 7281300 5235000 FALSE TRUE 7080799.362 6963133.664 6310037.358 6571137.26 6853679.112 6076616.424 6485224.807 6643710.771 6046817.063 1.170996127 1.151537014 1.043530388 1.086710114 1.133435829 1.004928107 1.072502234 1.09871205 1 22.5277445 8 0.207112966 1.022792271 1.822089816 0.497188069 0.040851442 37.52468556 0.463277794 0.066351477 9.846017924 100000000 -8 0.799297545 FYYDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FYYDGK 6 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 102.98 0.081604 107290000 452200 435600 377540 464660 394530 367620 426180 385420 369820 FALSE TRUE 430825.4022 479988.1352 394850.5824 417951.494 463335.9071 354889.2272 361158.4137 351670.5816 427169.7968 1.008557734 1.123647175 0.924341059 0.97842005 1.084664484 0.830791947 0.845468047 0.823257131 1 18.70445012 2.233049264 24.99999109 0.859115509 1.029532259 0.500404129 0.073134219 95.6495918 433870.7298 0.025667391 0.01949451 171.0209301 -2.233049264 0.17041675 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTKVDAAEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTKVDAAEGR 40 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.084)S(0.297)S(0.297)PES(0.107)QHGGT(0.107)QS(0.107)PGGGQPLLQPT(0.001)KVDAAEGR;GAAAADLLS(0.088)S(0.456)S(0.456)PESQHGGTQSPGGGQPLLQPTKVDAAEGR;GAAAADLLS(0.082)S(0.457)S(0.457)PES(0.003)QHGGTQSPGGGQPLLQPTKVDAAEGR 151 9.92E-14 502185000 104167 66359 105574 93078 113166 100876 147906 125415 129713 TRUE FALSE 99243.23235 73121.05754 110414.6723 83721.6226 132902.1146 97382.63883 125340.2232 114432.9977 149828.2296 0.662380064 0.488032581 0.736941714 0.558784035 0.887029867 0.649961887 0.836559463 0.763761262 1 17.19294995 1.532905805 0.268524645 1.04438395 0.521283027 0.557378116 0.101365043 1.117456204 0.325059389 0.220279486 0.208564596 34.11189176 -1.532905805 -0.523100923 GAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.021)S(0.155)S(0.82)PES(0.004)QHGGTQSPGGGQPLLQPTK;GAAAADLLSS(0.026)S(0.974)PESQHGGTQSPGGGQPLLQPTK 354.77 4.12E-132 592170000 480890 490200 429920 596750 455370 492890 541630 537800 465700 TRUE FALSE 458159.2827 540151.9373 449632.2572 536763.5562 534786.3838 475821.0957 458994.3958 490707.3809 537918.3775 0.851726399 1.004152228 0.835874504 0.997853166 0.994177567 0.884560029 0.853278889 0.912233903 1 19.03702775 -0.279731845 10.90814155 1 0.916817279 0.145944107 0.063303539 0 0 0.059268498 0.013969719 0.525131602 0.279731845 -0.083182721 GAAAHPDSEEQQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GAAAHPDSEEQQQR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;;; 232.6 1.06E-13 985211200 1349431.9 1226329.9 1241156.9 1411415.7 1563989.1 1204901.6 1507928 1336859.6 1509259.4 FALSE TRUE 1285646.928 1351294.311 1298065.172 1269537.512 1836748.304 1163175.555 1277865.889 1219797.086 1743307.64 0.737475646 0.775132444 0.744599027 0.728234927 1.053599641 0.667223345 0.733012269 0.699702714 1 20.73339575 -1.470407253 2.867818512 1.007067643 0.76603022 0.323124553 0.105795658 37211280.13 41418689.45 2098770.158 0.023632683 0.033852656 1.470407253 -0.241037423 GAADVEKVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 121.04 0.00094029 0 287990 273900 267540 309200 188570 344140 352670 353040 203410 FALSE TRUE 274377.2834 301810.7214 279806.9736 278118.6286 221456.5483 332222.3455 298863.7143 322125.946 234953.7839 1.167792571 1.284553568 1.190902181 1.18371632 0.942553657 1.41399019 1.272010645 1.371018337 1 17.84201748 GAAEEAELEDS(ph)DDEEKPVKQDDFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GAAEEAELEDSDDEEKPVKQDDFPK 25 2 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK 325.65 4.66E-76 947153000 1924810 1957800 1584450 2008060 618580 2216950 1765840 2321350 629759 TRUE FALSE 1833828.046 2157302.046 1657098.6 1806205.994 726460.1562 2140176.466 1496428.676 2118080.288 727418.8094 2.521007186 2.965694615 2.278052998 2.483034492 0.998682117 2.942151671 2.057176219 2.911775528 1 19.47242671 3.457188282 2.468729411 2.12050075 2.736243396 0.138828318 0.672203274 0.533527085 6.539859281 0.177211217 0.274118054 2865.419959 -3.457188282 0.615742646 GAAS(ph)PVLQEDHCDSLPSVLQVEEK ddPTM_SK-BR-3_Trastuzumab_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 336.9 2.97E-87 281822000 395474 425081 318042 478930 275403 389396 376184 404652 233023 TRUE FALSE 376780.7278 468397.2372 332624.5403 430787.0465 323433.196 375911.1189 318790.2217 369218.5257 269159.0167 1.399844346 1.740224953 1.235791928 1.600492719 1.201643549 1.396613509 1.184393618 1.371748679 1 18.03809923 1.642270651 0.262287028 0.949386531 1.631793985 0.435619403 0.159382434 1.428238333 0.397480276 0.350797712 0.364441273 43.88040739 -1.642270651 0.682407453 GAASTLVPGVSETSASPGS(ph)PSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 GAASTLVPGVSETSAS(0.008)PGS(0.992)PSVR;GAASTLVPGVSETSASPGS(1)PSVR 378.51 6.78E-119 224690000 243830 207131 227120 246730 262070 236890 258400 243340 292390 TRUE FALSE 232304.6391 228237.8844 237533.6767 221928.2316 307774.925 228686.4399 218976.3342 222031.8596 337732.3479 0.687836509 0.675795155 0.703319295 0.657112749 0.911298331 0.677123294 0.648372404 0.657419584 1 18.36552084 -1.076279262 4.461334531 1.000022774 0.699062133 0.60089057 0.076211918 9950843.959 2400601.884 2211.789614 0.017181316 0.083892037 1.076279262 -0.300960641 GACHGQTGMFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GACHGQTGMFPR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 77.387 0.021664 27595000 69213 56814 56542 70737 56425 71673 82978 79990 63274 FALSE TRUE 65941.43866 62603.41119 59134.50663 63626.38237 66265.50214 69190.94604 70318.1821 72985.65155 73086.20876 0.902241884 0.856569416 0.809106227 0.870566191 0.906675873 0.946703177 0.962126553 0.998624129 1 16.15731158 2.148450974 1.239018396 0.99211307 0.860622888 0.848129356 0.024038381 0.188494682 0.548326774 0.017522318 0.009214053 140.750833 -2.148450974 -0.131490182 GADDDRPSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GADDDRPSWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 113.93 0.0012981 1391570000 1628490 1784890 1436930 1858030 1793220 1670020 1761070 1695460 1656640 FALSE TRUE 1551514.505 1966772.32 1502814.662 1671257.294 2105957 1612186.789 1492386.427 1546996.534 1913543.27 0.810807118 1.027817009 0.785357031 0.873383592 1.100553634 0.842513892 0.779907332 0.808446069 1 20.86781509 2.034156616 24.99839688 0.831549472 0.92085951 0.051607977 0.109561021 351.9087171 257551.9769 0.038376094 0.02834251 108.1824011 -2.034156616 0.089310038 GADNDGS(ph)GS(ph)ESGYTTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(1)GS(0.988)ES(0.012)GYTTPK;GADNDGS(1)GS(1)ESGYTTPK;GADNDGS(1)GS(0.999)ES(0.001)GYTTPK;GADNDGS(1)GS(1)ESGYTTPK;GADNDGS(1)GS(0.999)ES(0.001)GYTTPK 229.08 1.79E-15 1435720000 4234100 3535440 4033780 4374290 3232000 4359000 4974550 4565110 3904250 TRUE FALSE 4033962.484 3895705.355 4218732.803 3934578.059 3795659.777 4208046.737 4215591.034 4165364.767 4509701.15 0.894507718 0.863850004 0.935479461 0.8724698 0.841665479 0.933109888 0.934782792 0.92364541 1 22.1046004 1.120791642 0.698136377 0.997534786 0.882652489 0.596943737 0.028800522 0.456702788 0.524486724 0.027096103 0.011050896 13.20661879 -1.120791642 -0.114882297 GADNDGS(ph)GSES(ph)GYTTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(1)GS(0.263)ES(0.737)GYTTPK 278.57 1.14E-35 289430000 570590 449750 524070 571310 433180 545660 641580 594270 496370 TRUE FALSE 543619.3415 495580.0363 548099.1279 513880.8334 508726.4549 526763.6574 543695.1876 542232.5684 573344.5245 0.948154763 0.864366912 0.955968191 0.896286284 0.887296264 0.918755887 0.94828705 0.945736019 1 19.12904279 1.117351287 0.98043238 0.997709365 0.908682488 0.503551223 0.027667498 0.400906317 0.832538241 0.024225742 0.008250667 13.10241307 -1.117351287 -0.089026876 GADNDGS(ph)GSESGYTT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(0.933)GS(0.062)ES(0.073)GY(0.018)T(0.193)T(0.722)PK 75.97 0.014508 0 88533 78323 87031 100600 62443 94084 98396 98295 76304 TRUE FALSE 84348.22055 86304.20275 91021.45744 90487.49687 73333.03943 90825.84749 83383.88303 89687.76871 88136.83461 0.957014407 0.97920697 1.032728913 1.0266706 0.832036228 1.030509524 0.94607304 1.017596889 1 16.42745746 1.219964077 24.82380769 1.008798471 0.972521195 0.063862724 0.058495292 773.7032506 1032756.409 0.05074169 0.012782692 16.59449638 -1.219964077 -0.036277276 GADNDGS(ph)GSESGYTTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(0.912)GS(0.087)ES(0.001)GYTTPK;GADNDGS(1)GSESGYTTPK;GADNDGS(0.959)GS(0.041)ESGYTTPK;GADNDGS(0.913)GS(0.087)ESGYTTPK;GADNDGS(0.991)GS(0.009)ESGYTTPK;GADNDGS(0.817)GS(0.183)ESGYTTPK;GADNDGS(0.929)GS(0.071)ES(0.001)GYTTPK;GADNDGS(0.971)GS(0.027)ES(0.002)GYTTPK;GADNDGS(0.934)GS(0.036)ES(0.008)GY(0.002)T(0.018)T(0.002)PK 322.38 1.12E-58 2824112000 3879193 3317692 3501907 3973818 2878328 3747335 4284594 4012199 3236097 TRUE FALSE 3695831.235 3655768.587 3662472.9 3574362.265 3380307.492 3617563.849 3630900.493 3660869.586 3737934.395 0.98873625 0.978018392 0.97981198 0.956239968 0.904324992 0.967797577 0.971365495 0.979383049 1 21.83380982 0.980630057 1.796469535 0.999625568 0.965048746 0.211411452 0.02294178 0.706518217 4.755628047 0.023141079 0.006596253 9.563790574 -0.980630057 -0.034576823 GADNDGSGSESGYTT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGSGSESGYT(0.109)T(0.891)PK 195.48 3.69E-17 0 183700 176300 181620 213320 128590 187810 204320 198290 162410 TRUE FALSE 175016.8651 194265.1704 189947.4566 191876.6683 151016.0553 181306.0926 173147.2314 180926.6764 187595.7133 0.932947038 1.03555229 1.012536232 1.022820111 0.805008028 0.966472471 0.922980746 0.96444995 1 17.51726734 GADPES(ph)PRREEMGCNADQESQSGPGVPQTQGGEVKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GADPESPRREEMGCNADQESQSGPGVPQTQGGEVKPK 37 3 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 GADPES(0.999)PRREEMGCNADQES(0.001)QSGPGVPQTQGGEVKPK 86.075 0.00058649 66306000 44589 41177 45879 52066 32317 50834 60003 57042 39720 TRUE FALSE 42481.36634 45372.98311 47982.59753 46832.22676 37953.07457 49073.60583 50848.44032 52047.10008 45879.57474 0.925931999 0.988958232 1.045837888 1.020764186 0.827232484 1.069617714 1.108302346 1.134428564 1 15.4855644 2.026490204 24.99975745 1.091948003 0.967015187 0.417847579 0.067771676 190.4584465 179741.6246 0.024073286 0.017778941 106.2894609 -2.026490204 -0.124932816 GADPFKGDPFQNDPFAEQQTTSTDPFGGDPFKESDPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GADPFKGDPFQNDPFAEQQTTSTDPFGGDPFKESDPFR 38 2 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 46.898 0.034867 26497000 18407 11988 18012 17594 13524 16659 23057 18946 16527 FALSE TRUE 17536.93759 13209.59083 18837.86802 15825.41769 15882.58132 16082.09465 19539.23118 17286.9878 19089.92275 0.918648955 0.691966699 0.986796451 0.828993281 0.831987721 0.842438959 1.023536419 0.905555671 1 14.22052364 1.752451712 24.99999984 0.974385707 0.840902716 0.352607727 0.079961469 4.428563913 7981.408767 0.034768636 0.019281083 56.55248741 -1.752451712 -0.133482991 GADS(ph)GEEKEEGINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 223.97 2.01E-12 3886880000 4761130 5459730 3987700 5850150 2922600 5247370 4461670 5039810 2559870 TRUE FALSE 4536080.821 6016082.694 4170539.989 5262081.807 3432300.515 5065652.261 3780960.297 4598497.519 2956841.566 1.534096677 2.0346314 1.41047124 1.779629274 1.160799603 1.713197055 1.278715891 1.555205924 1 21.49562551 0.511371949 0.165424266 0.652320238 1.959843749 0.387616124 0.238446262 7.499011373 0.626799735 2.890595727 1.422262494 3.246175155 -0.511371949 1.307523511 GADS(ph)GEEKEEGINREDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK 174.55 6.99E-10 1063600000 1079560 1231860 909070 1265250 462196 1245030 1028610 1233820 437801 TRUE FALSE 1028531.338 1357387.935 950751.7587 1138064.666 542802.8361 1201914.299 871676.6528 1125780.18 505692.9431 2.033904867 2.684213717 1.880096947 2.250505335 1.073384241 2.376766999 1.723727144 2.226212952 1 18.94790212 3.322594061 2.024591685 1.792465694 2.33915568 0.185169171 0.486275417 0.482972822 4.051700747 0.134237368 0.196182983 2101.812939 -3.322594061 0.546689987 GADS(ph)GEEKEEGINREDKTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GADSGEEKEEGINREDKTDK 20 3 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK 156.89 7.29E-08 1131370000 1283980 1204400 1157390 1370470 395677 1418890 1217970 1535070 380471 TRUE FALSE 1223288.81 1327129.729 1210457.476 1232707.752 464682.9435 1369753.484 1032146.307 1400651.133 439472.4995 2.783538928 3.019824291 2.754341802 2.804971308 1.057365237 3.116812736 2.348602718 3.187118954 1 18.74541336 2.962568606 24.99827663 2.276938108 2.866187157 0.17470381 0.722636206 1060.045054 707943.1095 0.199838221 0.212014023 917.4208503 -2.962568606 0.589249049 GADSLEDFLYHEGYACTSIHGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 275.5 5.74E-52 271732000 269046 246262 257031 312715 350342 249513 303586 296113 144728 FALSE TRUE 256328.7288 271356.3778 268816.1256 281280.2941 411441.5339 240872.3022 257268.38 270183.7759 167171.6791 1.53332628 1.62321979 1.60802432 1.682583412 2.46119161 1.440867877 1.538947155 1.616205433 1 17.35097093 0.534778266 0.95158155 1.00136333 1.703576943 0.381475039 0.280103591 1.73038693 2.360936489 0.268349804 0.086101658 3.425928274 -0.534778266 0.702213613 GAEADQIIEYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAEADQIIEYLK 12 0 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 176.8 5.60E-05 22822000 55799 49349 45992 56643 50173 55176 60365 55728 53727 FALSE TRUE 53161.49185 54377.71921 48100.77869 50949.13803 58923.15531 53265.24128 51155.21057 50848.16089 62058.70876 0.856632259 0.876230271 0.775085071 0.820982889 0.949474401 0.858304054 0.824303496 0.819355767 1 15.92134606 GAEDDELEEEADWIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 318.57 1.38E-57 130054000 201478 210614 184772 241520 193917 202304 215413 217713 184384 FALSE TRUE 191954.5342 232075.806 193243.979 217241.9507 227736.0634 195298.1618 182547.7905 198648.8956 212977.329 0.901290927 1.089673756 0.907345302 1.02002383 1.069297209 0.916990379 0.85712311 0.932723199 1 17.70034034 2.098867273 9.561749179 0.907366223 0.998180319 0.183574606 0.069358961 0.367624132 32.36343349 0.024280511 0.01792648 125.5646161 -2.098867273 0.090814095 GAEEEPPPPLQAVLVADSFDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 184.6 6.17E-17 311469000 384945 338853 371161 424482 452275 378810 457526 424534 516664 FALSE TRUE 366749.4127 373382.5059 388179.099 381812.2629 531151.6168 365691.7147 387722.0057 387359.5524 596785.6144 0.614541309 0.625656009 0.650449826 0.639781278 0.890020812 0.612768984 0.6496839 0.649076558 1 19.18685323 -2.250315579 2.094749222 2.131158491 0.661822256 0.626052005 0.080931539 5851513.522 947086.9531 31308424.07 0.019563897 0.005619329 2.250315579 -1.469336235 GAEEMETVIPVDVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAEEMETVIPVDVMR 15 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;; 238.98 2.02E-17 163774000 275989 248309 244543 290746 316547 250178 315984 280834 325284 FALSE TRUE 262943.5469 273611.9694 255755.5384 261519.6597 371752.6966 241514.2731 267774.8374 256242.6862 375727.3814 0.699825352 0.728219403 0.680694437 0.69603567 0.98942136 0.64279125 0.712683852 0.681990983 1 18.51932673 -1.760463374 2.7722832 1.059048141 0.727537327 0.443210643 0.095461027 23591347.66 20745731.02 9566287.68 0.021562721 0.017359477 1.760463374 -0.331510813 GAEETSWS(ph)GEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GAEETSWSGEER 12 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GAEETS(0.003)WS(0.997)GEER;GAEETSWS(1)GEER;GAEETSWS(1)GEER 263.89 1.75E-21 2389300000 1291850 1118460 1136950 1286560 1260160 1271600 1379500 1216010 1330340 TRUE FALSE 1230786.811 1232432.346 1189080.282 1157232.544 1479931.505 1227564.173 1169031.939 1109529.718 1536642.333 0.800958547 0.802029411 0.77381721 0.753091673 0.963094322 0.798861353 0.760770359 0.722048127 1 20.55134997 -1.034676706 4.023193383 1.000025587 0.797839985 0.497603804 0.064148598 26478427.49 33137494.38 8348.266398 0.014883819 0.092325846 1.034676706 -0.202185602 GAEFLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAEFLLR 7 0 Q9BXT2 Q9BXT2 CACNG6 Voltage-dependent calcium channel gamma-6 subunit 0 ;;;;; 143.97 0.0055495 950909000 1056453 1047160 936341 1112755 1020020 989478 1098700 1099857 996219 FALSE TRUE 1006516.56 1153866.795 979273.161 1000898.753 1197911.165 955212.1288 931073.136 1003547.69 1150707.555 0.874693623 1.002745476 0.851018278 0.869811578 1.041021379 0.830108506 0.809130984 0.872113585 1 20.1340898 GAEILADTFKDYAVSTVPVADGLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAEILADTFKDYAVSTVPVADGLHLK 26 1 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 113.5 0.00095144 68555000 246520 143130 273710 192820 233400 238350 345310 297060 261610 FALSE TRUE 234867.4882 157715.1097 286259.8742 173437.3673 274104.8861 230095.8797 292626.6174 271047.8516 302179.1427 0.777245862 0.521925863 0.947318441 0.573955455 0.907093996 0.761455201 0.968387874 0.896977366 1 18.20504456 2.155761888 0.638784788 0.99268421 0.672963432 0.373285865 0.128928001 0.668162051 0.53512831 0.101913454 0.06720973 143.1402886 -2.155761888 -0.319720778 GAEILEVLHSLPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAEILEVLHSLPAVR 15 0 Q15008;Q15008-4;Q15008-3;Q15008-2;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 209.21 2.50E-09 94799000 94184 110470 85409 112510 98408 89505 100560 99426 79640 FALSE TRUE 89732.10897 121727.0186 89325.08713 101200.281 115570.324 86405.41941 85217.72509 90719.73235 91990.16446 0.975453294 1.323261235 0.971028671 1.100120667 1.256333487 0.939289759 0.926378658 0.986189479 1 16.489192 2.212681474 24.99804924 0.95294027 1.13047418 0.350170187 0.10933898 226.2962553 218590.2664 0.038909517 0.028746385 163.1854653 -2.212681474 0.17753391 GAEQDNPNQYSWGENYAGSSGLMSAS(ph)PELGPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAEQDNPNQYSWGENYAGSSGLMSASPELGPAQR 34 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 GAEQDNPNQYSWGENY(0.023)AGS(0.054)S(0.05)GLMS(0.168)AS(0.705)PELGPAQR;GAEQDNPNQYSWGENYAGSS(0.002)GLMS(0.03)AS(0.968)PELGPAQR 95.361 3.18E-12 45380000 53520 48648 50308 63501 58660 52918 61659 63870 78556 TRUE FALSE 50990.21567 53605.28651 52614.67156 57117.75884 68890.28543 51085.43639 52251.7871 58277.2042 90738.06327 0.56194957 0.590769569 0.579852266 0.62947959 0.759221466 0.562998973 0.575853013 0.642257528 1 16.46942025 -4.999999999 0.414764313 8.006788951 0.600171167 0.815064245 0.05802539 366.4342917 2.427103773 2335.964357 0.034551733 1.00E-05 4.999999999 -7.406617784 GAEVHLVPWNHDFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GAEVHLVPWNHDFTK 15 0 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;; 224.33 6.64E-13 2469477000 6902650 5058870 5625440 5630630 5940420 5090670 6582170 5631030 1269104 FALSE TRUE 6576375.414 5574374.604 5883371.988 5064628.375 6976427.367 4914378.821 5577939.077 5137947.161 1465910.167 4.486206293 3.802671358 4.013460117 3.454937751 4.75910975 3.352442007 3.805102934 3.504953631 1 20.48336526 -0.809246928 0.404351627 3.01E-18 4.112266879 0.842118386 0.402364753 4.162838472 0.534517476 5.534655035 0.23088912 0.155150461 0.809246928 4.112266879 GAFGKPQGTVAR ddPTM_SK-BR-3_Trastuzumab_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 ; 173.76 2.94E-05 2780200000 5207800 4973300 4554500 5533800 5138000 4765900 5962800 5690500 5893200 FALSE TRUE 4961637.615 5480084.924 4763328.33 4977531.91 6034065.573 4600855.688 5053065.346 5192209.653 6807087.358 0.728892896 0.805055766 0.699760129 0.731227858 0.886438686 0.675891971 0.742324151 0.762765245 1 22.69860619 0.917276044 17.23196281 1 0.753869605 0.638623923 0.058188118 647.6692362 134915.7847 0.051479362 0.01286984 8.265631579 -0.917276044 -0.246130395 GAGAELKDTQS(ph)PSTCSEGLLGWSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAGAELKDTQSPSTCSEGLLGWSQK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GAGAELKDT(0.111)QS(0.874)PS(0.014)TCSEGLLGWSQK 106.6 0.0023275 216960000 99120 86523 106430 106980 74900 112210 135400 117520 87015 TRUE FALSE 94434.79404 95339.79207 111309.9208 96226.16715 87962.53629 108324.1396 114742.2432 107229.3258 100508.8418 0.939567031 0.948571194 1.107463968 0.957390071 0.875172121 1.077757316 1.141613426 1.066864605 1 16.6169629 2.105377911 8.929646584 1.091251858 0.967152975 0.365780336 0.067345441 0.246122136 19.00893507 0.024696738 0.018230152 127.461173 -2.105377911 -0.124098883 GAGATS(ph)GSPPAGRN ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.005)S(0.711)GS(0.283)PPAGRN;GAGAT(0.055)S(0.619)GS(0.326)PPAGRN;GAGAT(0.011)S(0.495)GS(0.495)PPAGRN;GAGAT(0.089)S(0.455)GS(0.455)PPAGRN 153.32 6.80E-06 523237000 638196 529932 629906 637267 755143 639732 748682 661989 805083 TRUE FALSE 608029.7399 583932.6733 658787.8132 573207.7104 886839.7001 617577.9204 634456.8104 604021.7337 929931.1598 0.653843818 0.627931075 0.708426432 0.616398004 0.953661667 0.664111439 0.682262126 0.649533815 1 19.8267644 -5 0.325045776 4.011000443 0.677223849 0.491338877 0.09674 284.4837479 2.489046263 591.0101552 0.079516095 1.00E-05 5 -3.333776594 GAGATSGS(ph)PPAGRN ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.015)S(0.086)GS(0.899)PPAGRN 105.83 0.001035 81228000 158720 159400 180410 162190 183990 174860 177170 163620 193760 TRUE FALSE 151217.6202 175643.0412 188681.9769 145886.3531 216077.7977 168804.5544 150139.4625 149292.5654 223807.3112 0.675659876 0.784795815 0.843055466 0.651839085 0.965463535 0.754240572 0.670842529 0.667058483 1 17.77189764 4.554159357 2.820209943 0.775807919 0.674054002 0.070594766 0.119996967 0.891249114 12.37774551 0.027585908 0.170715374 35822.7859 -4.554159357 -0.101753918 GAGDGS(ph)DEEVDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK 196.37 1.49E-07 1130480000 2775470 3348650 2392210 3358640 1616950 3092830 2545740 2949440 1350220 TRUE FALSE 2644279.034 3689881.242 2501895.195 3021023.126 1898945.568 2985724.522 2157340.607 2691171.398 1559605.222 1.695479726 2.365907212 1.604184931 1.93704348 1.217580925 1.914410442 1.383260698 1.725546542 1 20.57274946 0.562152332 0.155849977 0.510526041 2.305750962 0.411562611 0.297681852 7.729497326 0.623135639 4.137884878 2.175351338 3.648819099 -0.562152332 1.795224921 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_SK-BR-3_Trastuzumab_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 216.4 2.01E-32 6556170000 15881580 13337700 14871370 15915600 7281920 17738100 17090400 17707200 6487580 TRUE FALSE 15130889.19 14696826.79 15553237.02 14315733.65 8551884.542 17123825.15 14482945.59 16156663.7 7493640.772 2.019163935 1.961239835 2.075524768 1.910384296 1.141218908 2.285114228 1.932698141 2.156049934 1 22.83723539 2.996164447 24.90812248 1.792813206 2.004733927 0.095163826 0.4019547 479.867573 3116300.217 0.109042141 0.127565944 991.2071965 -2.996164447 0.211920722 GAGGEENKENERPSAGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GAGGEENKENERPSAGSK 18 2 Q9UHB9;Q9UHB9-4;Q9UHB9-2;K7EN53;K7EQC2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 160.45 2.28E-11 212883000 443255 375545 344197 342143 206431 347160 353656 368343 221898 FALSE TRUE 422303.2146 413813.4625 359978.7729 307750.1356 242432.501 335137.7622 299699.2819 336088.9342 256308.8085 1.647634418 1.61451128 1.404472889 1.200700582 0.945860981 1.307554602 1.169289825 1.311265641 1 17.96752353 3.478851988 2.271911166 1.163248271 1.635848019 0.750186707 0.114478326 0.131490108 1.357661434 0.031712785 0.050651691 3011.979339 -3.478851988 0.472599748 GAGHMVPTDKPLAAFTMFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAGHMVPTDKPLAAFTMFSR 20 1 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 57.989 0.047028 184750000 618340 491090 460860 525580 994270 425850 682250 501760 1035500 FALSE TRUE 589112.2936 541132.6293 481990.8869 472747.6999 1167670.373 411102.7077 578160.2321 457823.2344 1196080.051 0.492535841 0.452421749 0.402975442 0.395247542 0.976247678 0.343708356 0.483379211 0.382769727 1 20.18988252 -2.034981272 3.030432039 1.651398658 0.489685411 0.444708602 0.178685542 363712078.8 413781114.5 1631555354 0.039719599 0.009226112 2.034981272 -1.161713248 GAGHPCYLDKPEEWHTGLLDFLQGLQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAGHPCYLDKPEEWHTGLLDFLQGLQ 26 1 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 116.2 0.00062399 428600000 508080 392130 456360 558060 416600 499550 567480 515970 193475 FALSE TRUE 484064.0653 432088.4928 477284.5574 501962.7486 489254.9081 482250.4582 480900.5035 470788.9315 223478.1149 2.166046844 1.933471173 2.135710504 2.24613828 2.189274365 2.157931476 2.151890818 2.106644455 1 17.76977403 0.883002025 14.57113353 1 2.128479521 0.951511073 0.080586013 171.7121736 21386.20793 0.084786584 0.021197076 7.638393452 -0.883002025 1.128479521 GAGSIAGASAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAGSIAGASASPK 13 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GAGSIAGAS(0.001)AS(0.999)PK 99.991 0.0027344 40626000 113810 111570 103750 136770 83151 114610 129600 129700 101560 TRUE FALSE 108430.4268 122939.1098 108507.0401 123021.6198 97652.50807 110641.027 109827.1397 118342.7804 117309.4061 0.924311447 1.047990216 0.924964534 1.048693569 0.832435448 0.943155631 0.936217678 1.008808964 1 16.83995917 1.227121495 24.91954663 1.004404525 0.955970394 0.108670199 0.062256601 583.2401988 1270517.024 0.05421613 0.014032423 16.87024908 -1.227121495 -0.048434131 GAGTDDHTLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 215.87 1.25E-11 3976540000 5649030 5534630 4560180 5763550 5285520 4929550 5042240 5302440 4666520 FALSE TRUE 5382011.547 6098615.089 4769268.764 5184187.004 6207313.015 4758838.447 4272953.681 4838130.244 5390180.088 0.998484551 1.131430674 0.884806943 0.961783636 1.151596591 0.882871884 0.792729299 0.8975823 1 22.36190204 2.101753561 9.132257267 0.864855596 1.028101646 0.320317101 0.092068537 0.259667569 21.12843313 0.03311701 0.024447241 126.4018881 -2.101753561 0.16324605 GAGTDEGCLIEILASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAGTDEGCLIEILASR 16 0 P09525;P09525-2 P09525 ANXA4 Annexin A4 0 179.93 5.93E-09 21002000 20012 15677 15701 26194 25620 17756 20826 18637 21001 FALSE TRUE 19066.07242 17274.50412 16420.90638 23560.92935 30088.11989 17141.10527 17648.6112 17005.04548 24257.72782 0.78597932 0.712123751 0.676935058 0.971275196 1.240351945 0.70662452 0.727545932 0.701015594 1 14.5661568 3.250525542 24.99323784 0.870890605 0.730960301 0.176270439 0.165306862 480.2499988 1003176.376 0.048450063 0.065101712 1780.432618 -3.250525542 -0.139930303 GAGWTGHVAGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAGWTGHVAGTR 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ;;;;; 154.94 7.19E-05 2185430000 1955750 1535520 1385988 1658190 1945100 1430760 1862330 1642360 1598980 FALSE TRUE 1863305.573 1691991.234 1449536.921 1491505.591 2284324.824 1381212.422 1578197.354 1498546.252 1846941.652 1.00886001 0.916104324 0.784830923 0.807554256 1.236814829 0.747837605 0.854492264 0.81136632 1 20.81670686 GAHLTALEMLTAFASHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAHLTALEMLTAFASHIR 18 0 Q96EL3 Q96EL3 MRPL53 "39S ribosomal protein L53, mitochondrial" 0 262.36 4.52E-31 29992000 80981 78479 60413 65709 98878 56489 92513 68366 48230 FALSE TRUE 77153.18862 86476.09932 63182.99581 59103.80648 116122.2919 54532.77177 78398.44273 62379.51061 55709.26208 1.384925697 1.552275081 1.134156035 1.060933214 2.084434214 0.978881603 1.407278428 1.119733206 1 15.76562959 1.170661919 1.179249133 1.00020401 1.401465398 0.151341684 0.308288249 0.797828944 2.272661795 0.262979999 0.084391074 14.81364451 -1.170661919 0.401261388 GAHNGQGLGNAFLSHISACDGIFHLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAHNGQGLGNAFLSHISACDGIFHLTR 27 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 365.13 3.73E-127 292420000 56462 69055 70190 78597 103385 63801 97349 75768 46925 FALSE TRUE 53793.15316 76091.78301 73408.28093 70696.28024 121415.3113 61591.55537 82496.62211 69133.35225 54201.88934 0.992459005 1.403858499 1.354349116 1.304313947 2.240056809 1.136335949 1.522024843 1.275478643 1 15.72605552 4.643598896 1.254981126 1.448269373 0.831431684 0.123600767 0.331372919 2.11655993 3.276118337 0.086119377 1.619232181 44014.81654 -4.643598896 -0.616837689 GAHVTINAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAHVTINAR 9 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 147.51 9.22E-05 301580000 361740 268300 236610 273930 396350 256000 391210 330100 390670 FALSE TRUE 344641.2671 295640.075 247458.8025 246394.036 465473.3145 247134.6558 331523.7294 301194.694 451253.1083 0.763742699 0.655153548 0.548381381 0.546021803 1.031512705 0.547663055 0.734673564 0.667462868 1 18.78357734 -5 0.411678101 6.453973889 0.682121649 0.318149063 0.14406042 1004.619258 6.729620287 4943.260988 0.0787816 1.00E-05 5 -5.771852241 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 GAILSEEELAAMS(0.999)PT(0.001)AAAVAK;GAILSEEELAAMS(0.999)PT(0.001)AAAVAK 300.24 4.73E-55 117600000 305030 298750 297290 344110 252052 287310 337000 324680 297593 TRUE FALSE 290611.8364 329192.9647 310921.0406 309519.409 296009.789 277360.3827 285584.4606 296249.298 343742.2025 0.845435429 0.957673984 0.90451809 0.900440524 0.86113892 0.806884871 0.830810004 0.861835689 1 18.39096746 2.729855004 4.270038018 0.853341023 0.905605975 0.007575886 0.05831004 0.377094547 17.28958844 0.017285557 0.017139781 536.8525295 -2.729855004 0.052264951 GAKEEHGGLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GAKEEHGGLIR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 153.95 1.94E-05 1300050000 2185600 1558350 1906840 2114090 1840140 1990170 2350610 2226490 2066650 FALSE TRUE 2082291.019 1717147.637 1994270.5 1901577.657 2161059.833 1921249.914 1991981.273 2031526.732 2387135.527 0.872296942 0.719333954 0.835424079 0.796593924 0.905294152 0.804834871 0.834465094 0.851031167 1 21.18684905 -4.999984566 0.208254404 1.864171499 0.794568508 0.564183325 0.048397164 100.0817234 0.99622233 35.9765898 0.098507732 1.00E-05 4.999984566 -1.069602992 GAKEEHGGLIRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR;GAKEEHGGLIRS(1)PR 130.06 3.35E-05 48122920000 23284650 14424780 22442840 20382640 21623570 21279400 29093050 24143230 24659410 TRUE FALSE 22184030.74 15894681.48 23471866.41 18333738.3 25394713.76 20542489.04 24654370.89 22029120.79 28483465.36 0.778838897 0.558031871 0.824052345 0.643662492 0.891559838 0.721207507 0.865567816 0.773400305 1 24.76362134 0.81057787 0.248187618 1.064300008 0.644155677 0.439559801 0.093809384 2.573050574 0.473977169 0.375066422 0.194416723 6.46513905 -0.81057787 -0.420144331 GALALEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GALALEEKR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 180.8 7.73E-05 1233310000 990580 664860 912510 938870 1108400 1072240 1564450 1329990 1457350 FALSE TRUE 943757.2465 732609.9899 954349.4861 844493.0039 1301704.609 1035108.06 1325764.419 1213529.025 1683348.395 0.560642853 0.435209961 0.566935216 0.501674523 0.773282948 0.614910177 0.787575777 0.720901881 1 20.68290236 1.487186143 0.350008179 1.021680473 0.453384823 0.786491619 0.076164683 0.486096097 0.193854767 0.104140657 0.084938802 30.70337682 -1.487186143 -0.56829565 GALHTVS(ph)HEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GALHTVSHEDIR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHT(0.001)VS(0.999)HEDIR;GALHT(0.001)VS(0.999)HEDIR;GALHT(0.01)VS(0.99)HEDIR;GALHT(0.001)VS(0.999)HEDIR;GALHT(0.007)VS(0.993)HEDIR;GALHT(0.01)VS(0.99)HEDIR 214.48 2.82E-11 6142360000 5792730 5563470 5293380 6270260 6272680 5529440 6168120 5800390 952696 TRUE FALSE 5518919.133 6130393.918 5536086.709 5639961.552 7366633.406 5337954.106 5227060.009 5292477.102 1100435.23 5.015214874 5.570881185 5.030815588 5.125209916 6.694290773 4.850766279 4.749993336 4.809439899 1 20.0696428 0.172243344 0.775692766 0.913507445 5.388442665 0.866782973 0.527788189 1.14646811 0.81137598 0.747574137 0.17209577 1.486768475 -0.172243344 4.47493522 GALPPS(ph)PALPRPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GALPPSPALPRPSR 14 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 GALPPS(1)PALPRPSR 155.2 3.58E-06 253670000 208410 162080 162470 185560 244370 165130 200530 184960 213070 TRUE FALSE 198558.8723 178596.1363 169919.4102 166907.1563 286988.0506 159411.5067 169935.4655 168763.9219 246111.8074 0.806783203 0.725670735 0.690415515 0.678176143 1.166088103 0.647719865 0.690480751 0.685720542 1 17.90895435 4.751949073 19.46142201 0.76793023 0.806783537 0 0.168471445 55.24861737 549739.2824 0.03727776 0.235947839 56487.07325 -4.751949073 0.038853307 GALQNIIPAS(ph)TGAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.5)T(0.5)GAAK;GALQNIIPAS(0.91)T(0.09)GAAK;GALQNIIPAS(0.972)T(0.028)GAAK;GALQNIIPAS(0.928)T(0.072)GAAK;GALQNIIPAS(0.5)T(0.5)GAAK 287.03 2.54E-34 1422400000 5215250 3983490 3759440 5313590 3858710 4512000 5513290 4686330 3980960 TRUE FALSE 4968735.468 4389412.16 3931814.043 4779457.838 4531667.802 4355748.309 4672136.352 4275970.101 4598306.945 1.080557589 0.95457137 0.855056892 1.039395129 0.985507896 0.947250447 1.016055781 0.929900973 1 22.13267134 4.560557486 2.998082096 0.967798583 1.081207795 0.327992134 0.051262982 0.326423626 5.212075151 0.012040445 0.071684101 36354.44226 -4.560557486 0.113409212 GALQNIIPAST(ph)GAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.162)T(0.838)GAAK 245.96 4.34E-17 539590000 2163200 1680300 1539900 2278400 1629500 1911600 2360200 2127400 1760700 TRUE FALSE 2060949.823 1851524.48 1610505.938 2049370.903 1913684.284 1845400.813 2000108.142 1941113.578 2033740.364 1.013379023 0.910403566 0.79189358 1.007685612 0.940967843 0.907392529 0.983462874 0.95445496 1 20.95570408 1.683892839 7.963579419 0.976432819 0.931367934 0.128521322 0.061661414 0.297155609 34.59325251 0.029886502 0.015682532 48.2939623 -1.683892839 -0.045064885 GALQNIIPASTGAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 233.37 2.92E-17 290120000 1002580 895020 885400 1033600 846990 985310 1124140 1058340 925680 FALSE TRUE 955190.0303 986223.5556 925996.4658 929700.5643 994704.7878 951188.4676 952631.7968 965666.139 1069229.727 0.893344065 0.922368253 0.866040705 0.869504973 0.930300349 0.889601593 0.89095147 0.903141874 1 20.02814042 0.803508864 5.815453378 0.999999943 0.89618316 0.732622894 0.01985731 3.862429616 114.2237177 0.018517712 0.004659662 6.360757866 -0.803508864 -0.103816783 GALSIS(ph)APLGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GALSISAPLGDFR 13 0 Q6NZY7 Q6NZY7 CDC42EP5 Cdc42 effector protein 5 1 GALS(0.017)IS(0.983)APLGDFR;GALS(0.001)IS(0.999)APLGDFR 115.57 0.00068538 32800000 79024 69766 75003 81614 86072 68631 86771 82846 82850 TRUE FALSE 75288.69213 76875.23472 78441.96174 73410.00566 101082.9295 66254.29126 73532.49029 75591.56505 95697.95486 0.786732509 0.803311156 0.819682739 0.767101092 1.05627053 0.692327139 0.768381 0.789897393 1 16.54620047 -2.186284825 2.121556687 1.480529744 0.806583513 0.28638185 0.093850479 4686762.14 969952.1063 10802902.29 0.022501351 0.006512012 2.186284825 -0.673946231 GANDFMCDEMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GANDFMCDEMER 12 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;; 240.41 7.69E-16 1530230000 1098754 1177305 1121260 1185001 1167522 1081084 1109000 1140746 1173472 FALSE TRUE 1046818.076 1297273.718 1172670.88 1065882.448 1371137.467 1043645.79 939801.6818 1040856.233 1355448.044 0.772304095 0.957081109 0.865153692 0.786369092 1.011575082 0.769963699 0.693351313 0.767905666 1 20.37033838 2.102646157 21.17633115 0.772194034 0.876106625 0.055561014 0.106455515 6.179224656 1255.238002 0.036223062 0.02675252 126.6619462 -2.102646157 0.103912591 GANFLTQILLRPGASDLTGSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GANFLTQILLRPGASDLTGSFR 22 1 Q5QPJ9;Q5QPK2;O60762;H0Y368 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 0 160.77 1.65E-11 36064000 52095 52729 41766 44490 57437 44416 59433 48920 54365 FALSE TRUE 49632.57259 58102.14505 43681.01241 40017.78067 67453.99461 42877.86278 50365.40429 44636.30546 62795.64654 0.79038238 0.925257534 0.695605744 0.637269984 1.07418266 0.68281585 0.802052484 0.710818471 1 15.93837692 3.753530162 24.9033252 0.79034781 0.857819941 0.0234728 0.143001881 2695.936793 4484945.055 0.033442755 0.060007401 5669.30944 -3.753530162 0.067472131 GANLKDYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GANLKDYYSR 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 186.87 1.18E-06 1657770000 1302820 735340 1213960 1056700 1427110 1187040 1762590 1419420 1972710 FALSE TRUE 1241238.281 810271.982 1269621.267 950478.5084 1675997.532 1145932.507 1493674.523 1295128.06 2278627.792 0.544730598 0.355596462 0.557186773 0.417127585 0.735529312 0.502904648 0.655514924 0.5683807 1 21.11973385 -5 0.1484442 2.719700491 0.378112051 0.699209629 0.098363573 65.57684161 0.580954383 33.00703671 0.453448665 1.00E-05 5 -2.341588441 GAPANVS(ph)SSDLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAPANVSSSDLTGR 14 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 GAPANVS(0.935)S(0.053)S(0.013)DLTGR 170.78 3.27E-06 133580000 139510 129320 129540 162060 136630 166730 162200 141250 137950 TRUE FALSE 132915.6388 142497.855 135479.5371 145769.4209 160458.2287 160956.0983 137453.411 128881.4012 159342.5814 0.834150154 0.894286096 0.850240632 0.914817744 1.007001564 1.010126087 0.862628243 0.80883214 1 17.28177233 3.128285535 5.251164759 0.932603557 0.863655967 0.226706719 0.065282467 0.356788015 15.08513678 0.019539993 0.023607084 1343.648077 -3.128285535 -0.06894759 GAPHSS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GAPHSSPAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 GAPHS(0.008)S(0.992)PAR;GAPHSS(1)PAR;GAPHS(0.159)S(0.841)PAR 155.26 4.75E-05 168620000 113829 103131 82347 98641 134614 102403 141620 119761 136047 TRUE FALSE 108448.5288 113640.1662 86122.6914 88725.41927 158090.639 98856.75843 120013.268 109274.0919 157144.4739 0.690119901 0.723157253 0.548047852 0.564610495 1.006020988 0.62908199 0.763712939 0.695373431 1 17.26173201 GAPKPSS(ph)LAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAPKPSSLAQK 11 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 GAPKPS(0.045)S(0.955)LAQK;GAPKPS(0.089)S(0.911)LAQK 68.171 0.035105 233250000 501010 443370 414090 495930 330020 477490 513900 613460 508260 TRUE FALSE 477328.2502 488549.9071 433076.4361 446078.1742 387575.3835 460954.4016 435495.1166 559742.1902 587078.365 0.813057129 0.83217154 0.737680797 0.759827309 0.660176574 0.785166733 0.741800657 0.953436924 1 19.16319357 1.166546019 4.854845571 0.993635712 0.767393294 0.781735707 0.047397071 0.102565468 4.229296441 0.04823588 0.012477432 14.67391567 -1.166546019 -0.226242418 GAPPSTFKGT(ph)PTAENPEYLGLDVPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.077)T(0.077)FKGT(0.787)PT(0.058)AENPEYLGLDVPV;GAPPS(0.052)T(0.052)FKGT(0.783)PT(0.113)AENPEYLGLDVPV;GAPPS(0.016)T(0.014)FKGT(0.962)PT(0.008)AENPEYLGLDVPV 151.73 2.27E-07 262129000 617820 448776 504630 723640 616320 583390 751120 700210 640980 TRUE FALSE 588616.873 494506.7846 527767.7846 650898.3324 723806.0129 563187.058 636522.8487 638895.9004 740379.9047 0.795020056 0.667909517 0.712833751 0.879141003 0.977614341 0.760673074 0.859724642 0.862929823 1 19.49790621 2.237801746 0.131350236 1.11202834 0.554985935 0.44670054 0.078748177 8.13219845 0.690617326 1.068763967 1.570821924 172.9026885 -2.237801746 -0.557042406 GAPPSTFKGTPT(ph)AENPEYLGLDVPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.006)T(0.005)FKGT(0.392)PT(0.598)AENPEYLGLDVPV 114.57 0.002853 140730000 322540 251570 271080 376840 318570 309640 402780 369360 354990 TRUE FALSE 307294.1734 277205.269 283509.2861 338959.3273 374128.5071 298917.0892 341328.5134 337016.8803 410040.0362 0.749424803 0.676044397 0.691418547 0.826649345 0.912419457 0.728994885 0.832427284 0.821912132 1 18.64540526 -4.999999999 0.078889967 1.797939135 0.527066478 0.611935702 0.06210867 166.6617683 0.932748617 22.99811272 2.219419581 1.00E-05 4.999999999 -1.270872658 GAPQHYPK ddPTM_SK-BR-3_Trastuzumab_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 ; 63.486 0.073008 130039000 273710 209499 208797 256452 284940 248953 331580 281690 289770 FALSE TRUE 260772.2707 230847.1863 218370.549 230672.9577 334633.4458 240331.6952 280991.3811 257023.7303 334706.0517 0.779108323 0.689701262 0.65242486 0.68918072 0.999783076 0.718038093 0.839516883 0.767908823 1 18.35253511 GAPS(ph)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 36 0 O96013;O96013-4;O96013-3;M0R0L9 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 GAPS(1)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 193.51 5.36E-24 106190000 30714 25434 28536 26445 41537 20747 34558 26043 37503 TRUE FALSE 29262.21009 28025.75352 29844.40383 23786.69836 48781.03965 20028.52619 29285.5424 23762.53686 43318.7737 0.675508736 0.646965533 0.688948492 0.549108304 1.126094658 0.462352105 0.676047355 0.548550543 1 15.40270478 -1.478620129 2.863077031 1.010561227 0.671123311 0.253957765 0.176836682 36239496.95 40020028.66 3034286.954 0.039316823 0.033218489 1.478620129 -0.339437916 GAPSS(ph)PATGVLPSPQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.04)S(0.952)PAT(0.008)GVLPSPQGK;GAPS(0.016)S(0.984)PATGVLPSPQGK;GAPSS(1)PATGVLPSPQGK;GAPS(0.082)S(0.918)PATGVLPSPQGK 289.65 6.24E-46 534710000 1168520 1075980 1114760 1328610 986010 1221830 1324640 1210480 1165640 TRUE FALSE 1113286.375 1185623.585 1165872.849 1195055.599 1157969.832 1179517.721 1122541.839 1104483.954 1346401.498 0.826860619 0.880586948 0.86591767 0.887592297 0.860047938 0.876051997 0.833734841 0.82032288 1 20.36067726 -1.165018519 4.977202767 1.000009971 0.857244463 0.794447674 0.022953464 2.51E-06 4.22E-07 0.021992261 0.005183264 0.068388248 1.165018519 -0.142765508 GAPVGGHILSYLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAPVGGHILSYLLEK 15 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 180.28 6.36E-07 208884000 732950 640830 648570 760320 651220 663370 829660 780260 707830 FALSE TRUE 698304.9061 706131.3056 678307.576 683891.1891 764792.5618 640397.3306 703080.1292 711936.298 817596.6613 0.854094615 0.863667061 0.829635942 0.836465242 0.935415466 0.783268035 0.859935177 0.87076713 1 19.64102978 0.696625846 2.60558988 0.999976799 0.851895029 0.603830858 0.037442835 1.313466316 10.46754675 0.032154322 0.008544919 4.973084582 -0.696625846 -0.148081769 GAPVNIS(ph)SSDLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.979)S(0.021)SDLTGR;GAPVNIS(0.904)S(0.087)S(0.009)DLTGR;GAPVNIS(0.479)S(0.479)S(0.041)DLTGR;GAPVNIS(0.372)S(0.372)S(0.255)DLTGR;GAPVNIS(0.493)S(0.493)S(0.014)DLTGR;GAPVNIS(0.828)S(0.072)S(0.1)DLTGR 243.47 1.63E-17 1461400000 1153454 1043426 1147008 1253000 1336620 1180637 1366540 1277890 1533870 TRUE FALSE 1098932.515 1149752.296 1199599.451 1127046.059 1569726.105 1139751.245 1158049.225 1165991.177 1771734.726 0.620257931 0.648941559 0.67707622 0.636125738 0.885982581 0.64329678 0.6536245 0.658107086 1 20.75673118 -1.625227752 2.836426087 1.028213376 0.673771352 0.641185907 0.075661446 29550966.16 29140318.4 6155041.297 0.017874085 0.023701304 1.625227752 -0.354442025 GAPVNISS(ph)SDLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.068)S(0.865)S(0.068)DLTGR;GAPVNIS(0.168)S(0.765)S(0.067)DLTGR 301.9 6.56E-44 795840000 605790 563560 551920 647180 688220 539330 659160 611030 746340 TRUE FALSE 577155.5073 620987.4047 577226.0779 582124.2368 808245.3501 520652.8669 558593.0357 557524.9739 862078.5954 0.66949291 0.720337343 0.669574771 0.675256572 0.937554133 0.603950579 0.647960683 0.646721745 1 19.71745988 -1.359559926 3.318933221 1.002274607 0.69502103 0.52548038 0.090673025 196052027.8 258070650.4 4290999.282 0.020755013 0.043695838 1.359559926 -0.307253577 GAPVNISSS(ph)DLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.001)S(0.041)S(0.958)DLTGR 184.59 1.34E-06 106970000 262200 264710 253290 312390 268260 295820 321520 363840 328960 TRUE FALSE 249806.3256 291684.25 264903.597 280987.9637 315044.4591 285575.6792 272466.2189 331980.2408 379973.4367 0.657431024 0.767643792 0.697163463 0.739493703 0.829122324 0.751567482 0.717066491 0.873693287 1 18.53553904 -5 0.150225724 1.940995751 0.663990063 0.762628697 0.04818176 65.08650685 0.580208788 18.13557507 0.237279779 1.00E-05 5 -1.277005688 GAQAS(ph)SGSPALPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAQASSGSPALPR 13 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 GAQAS(0.423)S(0.423)GS(0.155)PALPR 100.11 0.0012999 0 209700 169830 189550 204830 230850 188740 244770 209760 235870 TRUE FALSE 199787.8966 187135.8701 198241.055 184240.0992 271110.1669 182203.8865 207425.841 191392.3024 272447.5149 0.733307832 0.686869433 0.727630256 0.676240704 0.995091355 0.668766924 0.761342386 0.702492377 1 18.05561881 -2.076779529 2.383807694 1.394293626 0.74133101 0.424181053 0.093703818 7097717.653 1997470.136 15224079.06 0.020665877 0.008379546 2.076779529 -0.652962616 GAQASS(ph)GSPALPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAQASSGSPALPR 13 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 GAQAS(0.173)S(0.645)GS(0.182)PALPR 94.487 0.0017346 0 193350 155660 167300 208670 211980 181900 210100 187110 203790 TRUE FALSE 184210.7287 171521.931 174970.8705 187694.0952 248949.2449 175600.7574 178045.3862 170725.6565 235392.7124 0.782567679 0.728662877 0.74331473 0.797365786 1.057591131 0.745990628 0.756375949 0.725280128 1 17.84471013 -2.448659114 2.24022734 3.144466814 0.788076893 0.310445214 0.097187036 2752556.659 327878.8739 30169240.98 0.023221483 0.003559106 2.448659114 -2.356389921 GAQPGRHS(ph)VTGYGDCAVGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GAQPGRHSVTGYGDCAVGAR 20 1 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 GAQPGRHS(0.997)VT(0.003)GYGDCAVGAR;GAQPGRHS(0.994)VT(0.006)GYGDCAVGAR;GAQPGRHS(0.906)VT(0.094)GYGDCAVGAR;GAQPGRHS(0.999)VT(0.001)GYGDCAVGAR 222.89 4.14E-25 775581000 398070 357193 338751 417624 404381 381546 407979 372776 375378 TRUE FALSE 379254.02 393591.3728 354283.0684 375643.6421 474904.9184 368332.9663 345734.3105 340133.7572 433589.7031 0.874684102 0.907750738 0.817092901 0.866357387 1.095286431 0.849496572 0.797376663 0.784459951 1 18.72597097 -1.147530702 4.990547553 1.000006966 0.874904386 0.171875264 0.086857928 6.69E-06 1.14E-06 0.083541152 0.019689742 0.071198247 1.147530702 -0.12510258 GAS(ph)PLGPGSAAGSGAAASGGLGLGLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GASPLGPGSAAGSGAAASGGLGLGLGGR 28 0 A0A6I8PS01;Q6P1R3-3;Q6P1R3;B4E1M0;E9PPE2 A0A6I8PS01 MSANTD2 Myb/SANT-like DNA-binding domain-containing protein 2 1 GAS(0.999)PLGPGS(0.001)AAGSGAAASGGLGLGLGGR;GAS(0.999)PLGPGS(0.001)AAGSGAAASGGLGLGLGGR 273.45 1.85E-61 154449000 70489 63194 71026 72539 78298 74606 91432 69560 85175 TRUE FALSE 67157.12467 69633.54045 74282.61235 65247.2419 91953.14641 72022.37551 77482.36914 63468.95764 98383.50399 0.682605538 0.707776585 0.755031172 0.663192906 0.934639881 0.732057434 0.787554478 0.645117881 1 16.58612882 -5 0.233036389 2.391791572 0.711438119 0.477740817 0.083599164 137.3786732 1.373079622 90.64208385 0.129062354 1.00E-05 5 -1.680353453 GAS(ph)PPISAIEEFSIIPEAPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GASPPISAIEEFSIIPEAPMR 21 0 A0A2R8YF49;C9J591;A0A2R8YFR7;Q12774;A0A5F9ZH52 A0A2R8YF49;A0A2R8YFR7;A0A5F9ZH52 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR 205.65 4.87E-22 457399000 115827.1 105944.7 111420.2 120505.6 127534.4 113509.8 133508.5 121542.1 140498.6 TRUE FALSE 110352.1825 116740.5854 116528.9264 108392.1481 149776.359 109578.9272 113139.3263 110899.2294 162286.4053 0.679984145 0.719349136 0.718044904 0.66790652 0.922913775 0.675219387 0.697158373 0.683355018 1 17.30818263 -1.344823652 3.09419003 1.002640095 0.718733323 0.584313394 0.074076492 13350053.04 17312030.98 320192.6553 0.017754885 0.045203946 1.344823652 -0.283906771 GAS(ph)QAGMTGYGMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GASQAGMTGYGMPR 14 0 P37802;P37802-2;C9J5W6;Q9UI15 P37802 TAGLN2;TAGLN3 Transgelin-2;Transgelin-3 1 GAS(1)QAGMTGYGMPR;GAS(1)QAGMTGYGMPR 112.03 0.00041093 245490000 506060 428120 435080 628560 538410 548290 638030 479670 497510 TRUE FALSE 482139.5467 471745.9147 455028.8484 565375.9546 632308.5335 529302.5798 540686.8053 437667.5519 574661.3099 0.838997751 0.820911216 0.791820922 0.983842039 1.100315129 0.92106876 0.940879081 0.761609568 1 19.13235239 3.239068923 24.99998653 0.95260272 0.821137047 0.359835927 0.084215385 14.84746724 730213.0774 0.023476161 0.029944705 1734.079177 -3.239068923 -0.131465673 GAS(ph)TVSSSSSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GASTVSSSSSTK 12 0 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 1 GAS(0.976)T(0.024)VSSSSSTK;GAS(0.978)T(0.022)VSSSSSTK 115.12 0.00020189 0 133623 93659 104539 131068 117775 94122 103480 89752 86476 TRUE FALSE 127306.9056 103202.9586 109332.2166 117892.7956 138314.9227 90862.53154 87692.22546 81892.83907 99886.25642 1.274518739 1.03320479 1.094567165 1.180270438 1.384724262 0.909659995 0.877920833 0.81986093 1 16.60799857 2.123241982 9.143922009 0.887966907 1.173621662 0.65539428 0.104413433 0.17025262 12.91975937 0.038556188 0.028466056 132.8134267 -2.123241982 0.285654755 GASDEEIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GASDEEIKR 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 104.42 0.0052312 1266950000 4082950 3516280 3246910 4413000 3113650 3741670 3944330 4358930 3500930 FALSE TRUE 3889957.045 3874592.93 3395784.035 3969396.856 3656669.574 3612095.03 3342550.016 3977238.981 4043836.344 0.961947199 0.958147808 0.839743191 0.981591864 0.904257557 0.893234721 0.826578954 0.983531143 1 21.94729318 3.946418161 24.98461184 0.906316132 0.960522695 0.050693499 0.059041064 542.1483807 252797.7746 0.014138411 0.02548849 8839.305845 -3.946418161 0.054206563 GASFEELCHNYTQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GASFEELCHNYTQDR 15 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 201.3 6.48E-09 510530000 415960 360980 361760 426720 475630 370580 436730 424940 439400 FALSE TRUE 396298.3952 397764.2724 378347.0538 383825.2949 558579.7214 357746.7217 370098.8174 387730.0009 507539.9079 0.780822136 0.783710337 0.745452817 0.756246531 1.100563153 0.704864221 0.729201412 0.763939928 1 18.95316174 -2.201698928 2.271576147 1.599219862 0.791381644 0.249615864 0.111161638 10608531.18 1768259.574 32765757.6 0.027607416 0.006284939 2.201698928 -0.807838217 GASIVEDKLVEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GASIVEDKLVEDLR 14 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;; 138.87 1.18E-05 365281000 1912390 1106630 1767490 1393380 1629390 1444740 1987080 1767370 1822760 FALSE TRUE 1821995.115 1219396.855 1848531.165 1253314.795 1913555.1 1394708.292 1683914.451 1612609.713 2105424.311 0.865381436 0.579169172 0.877985095 0.59527896 0.908869101 0.66243573 0.799798141 0.765930983 1 21.00567958 -0.789993536 0.464938056 1.071560613 0.738196145 0.306571902 0.114658578 14.39473835 2.299045237 1.577842997 0.052169978 0.162183424 0.789993536 -0.333364468 GASQEEEKGAEYVASVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GASQEEEKGAEYVASVLK 18 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ; 220.04 6.38E-19 157476000 456820 352870 375010 440940 294065 446510 502610 495730 333130 FALSE TRUE 435227.0239 388827.8542 392204.5794 396615.8735 345349.8429 431047.2467 425927.6134 452321.2532 384790.099 1.131076462 1.010493397 1.019268896 1.030733053 0.897501895 1.120213976 1.106908973 1.175501278 1 18.55371215 GASWIDTADGSANHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GASWIDTADGSANHR 15 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-2;E9PBT8;J3QT17;Q8NBJ7-5 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ;;;; 266.35 2.67E-25 1469300000 1499300 1288550 1415170 1559330 1807120 1351420 1685390 1514850 1677250 FALSE TRUE 1428431.06 1419854.71 1480056.944 1402583.186 2122281.156 1304619.987 1428252.801 1382201.703 1937349.364 0.737312065 0.732885218 0.763959754 0.723970189 1.095456088 0.673404607 0.737220053 0.713449897 1 20.88565271 -2.24050558 2.254729185 1.809282279 0.767855457 0.270091291 0.117491629 7250093.105 1255274.735 29914311.86 0.026628898 0.005747704 2.24050558 -1.041426822 GATKES(ph)SEKDR ddPTM_SK-BR-3_Trastuzumab_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(0.14)KES(0.844)S(0.016)EKDR;GAT(0.005)KES(0.848)S(0.147)EKDR 137.8 3.70E-05 413160000 1098460 1017540 964270 1222130 570930 1255890 1215550 1303530 608420 TRUE FALSE 1046537.973 1121228.483 1008482.733 1099279.171 670500.0112 1212398.214 1030095.522 1189386.003 702770.6662 1.489160011 1.595440073 1.435009715 1.564207534 0.954080817 1.725169067 1.465763402 1.692424086 1 19.42269445 -1.934552329 2.827662985 0.678313163 1.492607348 0.345887253 0.211810616 62229044.57 56042870.39 133033396.5 0.046123361 0.011626465 1.934552329 0.814294185 GATQQILDEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GATQQILDEAER 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;; 257.01 8.05E-21 843717000 951459 799737 783192 970652 1069612 817754 1060836 861823 1173178 FALSE TRUE 906485.4187 881231.1095 819102.1279 873080.2168 1256151.994 789434.9739 898985.9846 786357.2093 1355108.452 0.668939388 0.650303013 0.604455036 0.644288075 0.926975248 0.582562209 0.663405193 0.580290978 1 20.36997689 -1.697376426 2.714576046 1.050409074 0.665569996 0.534113341 0.098281112 22868220.78 19598874.67 7898100.796 0.022578812 0.020073522 1.697376426 -0.384839078 GATYGKPVHHGVNQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GATYGKPVHHGVNQLK 16 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 165.34 4.56E-09 2124080000 2800400 2445800 2501300 3186400 2236900 2959300 3460700 3115900 747040 FALSE TRUE 2668030.642 2695029.801 2615987.079 2866097.018 2627014.652 2856818.699 2932706.655 2843055.278 862887.1478 3.091980972 3.123270299 3.031667682 3.321520115 3.044447537 3.31076747 3.398714029 3.294817039 1 19.71881236 -0.35013732 8.225328435 1 3.201830552 0.967334024 0.127176995 0 0 0.132748683 0.031289165 0.446542377 0.35013732 2.201830552 GAVAAEGAS(ph)DTEREEPTESQGLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.973)DT(0.027)EREEPTESQGLAAR;GAVAAEGAS(0.563)DT(0.437)EREEPTESQGLAAR;GAVAAEGAS(0.944)DT(0.056)EREEPTESQGLAAR;GAVAAEGAS(0.998)DT(0.002)EREEPTESQGLAAR;GAVAAEGAS(0.73)DT(0.27)EREEPTESQGLAAR;GAVAAEGAS(0.808)DT(0.192)EREEPTESQGLAAR 302.2 1.55E-63 5741490000 2826240 2786740 2726340 3054140 3038240 2758150 3091520 2853420 3201760 TRUE FALSE 2692649.236 3070711.974 2851345.386 2747132.045 3568108.094 2662634.574 2619851.844 2603559.418 3698272.588 0.728082955 0.8303098 0.77099384 0.742814917 0.964803975 0.719967096 0.708398795 0.703993379 1 21.81842013 -2.218940388 2.39724491 1.76422758 0.77179861 0.459572352 0.077981469 10479320.61 2816899.434 43140679.91 0.018647181 0.006040315 2.218940388 -0.992428971 GAVAEDGDELRTEPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAVAEDGDELRTEPEAK 17 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 163.35 2.49E-09 171070000 250630 199100 211860 260940 209760 253010 252900 254780 224880 FALSE TRUE 238783.2166 219388.5164 221573.9906 234709.8154 246342.0776 244248.2003 214315.4602 232470.1125 259753.2419 0.919269438 0.844603574 0.853017229 0.903587627 0.948369598 0.940308573 0.825073284 0.894965202 1 17.98678223 0.952646337 23.32602877 1 0.886709512 0.414886411 0.040451548 6238.715133 3073144.297 0.039722856 0.009930714 8.966982807 -0.952646337 -0.113290488 GAVDGGLSIPHSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GAVDGGLSIPHSTK 14 0 P46777;A0A2R8Y6J3;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 202.13 1.69E-08 2939660000 6270300 5370440 5674620 6650660 6172260 6320560 8356900 7470520 7247410 FALSE TRUE 5973915.346 5917693.942 5934806.94 5982123.021 7248700.19 6101677.422 7081901.42 6816361.665 8371301.328 0.713618482 0.706902512 0.708946758 0.714598936 0.86589885 0.728880395 0.845973779 0.814253531 1 22.99702048 0.267003923 0.223302522 1.103436979 0.661315703 0.794596227 0.043339016 2.506155475 0.263177024 0.319188854 0.106663666 1.849285322 -0.267003923 -0.442121277 GAVEALAAALAHISGATSVDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAVEALAAALAHISGATSVDQR 22 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 136.04 1.23E-08 0 20257 19989 21169 21145 29116 20243 27727 23411 24817 FALSE TRUE 19299.49176 22025.90183 22139.61959 19019.46443 34193.82118 19541.97983 23496.73691 21361.00873 28665.49361 0.673265635 0.768376855 0.772343916 0.66349684 1.192856528 0.681724867 0.819687155 0.745181961 1 14.8070275 GAVEKGEELSCEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAVEKGEELSCEER 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 107.82 0.00078545 275500000 195550 137450 175990 174930 169190 187700 218250 206630 187580 FALSE TRUE 186306.739 151456.3113 184059.3156 157345.7041 198696.6824 181199.9019 184951.9541 188536.3818 216668.9484 0.859868202 0.699021768 0.849495587 0.726203294 0.917051954 0.836298433 0.853615414 0.870158752 1 17.72513288 0.675677395 0.343226545 1.024246727 0.774505755 0.497643936 0.060538026 1.736666161 0.477524797 0.14174851 0.057716475 4.738898374 -0.675677395 -0.249740972 GAVIVVSHDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 150.1 3.40E-05 290790000 609510 568370 442870 513680 637220 523410 764030 644440 657880 FALSE TRUE 580699.6702 626287.5492 463176.0276 462043.9105 748350.9662 505284.1805 647463.1911 588009.4172 759900.6704 0.764178389 0.824170281 0.609521804 0.608031982 0.984801034 0.664934511 0.85203661 0.773797734 1 19.53545133 0.049511765 0.484992084 1.02462825 0.745149347 0.32425182 0.112721824 4.760745245 1.451934704 0.340415248 0.055331118 1.120757787 -0.049511765 -0.279478903 GAVRS(ph)PPVDCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAVRSPPVDCPR 12 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 GAVRS(1)PPVDCPR 62.69 0.046015 360320000 252420 239760 226650 271830 295260 233990 272190 249230 313750 TRUE FALSE 240488.6068 264191.8166 237042.1267 244505.132 346753.2505 225886.8676 230662.4164 227406.0999 362404.7476 0.663591215 0.728996566 0.654081185 0.674674197 0.956812108 0.623299968 0.636477358 0.627492055 1 18.46724233 -1.9474497 2.485116737 1.225710056 0.695059913 0.489361086 0.097694447 7649564.051 3582097.978 9977523.244 0.024519063 0.011286266 1.9474497 -0.530650143 GAYQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GAYQDR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 116.35 0.055015 249730000 296110 233360 223390 290620 277120 244040 274100 283560 286040 FALSE TRUE 282113.4671 257139.6493 233632.6525 261406.3255 325449.6403 235588.8336 232281.0108 258729.9832 330397.6223 0.853860464 0.778273304 0.707125708 0.791187066 0.98502416 0.713046395 0.703034753 0.783086698 1 18.33384378 -2.394771073 2.156577245 2.519697394 0.786026382 0.385539463 0.083490499 4209320.222 411736.543 31229844.57 0.021762583 0.004029294 2.394771073 -1.733671012 GCDVVVIPAGVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GCDVVVIPAGVPR 13 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ; 199.11 2.80E-07 268380000 487350 340560 356060 377110 466570 312350 445620 379430 486010 FALSE TRUE 464313.9313 375263.4512 372385.7032 339202.1863 547939.6603 301533.2412 377632.4846 346205.0977 561377.9486 0.827096847 0.668468457 0.663342235 0.604231404 0.976061959 0.537130541 0.67268849 0.616705908 1 19.09861287 -1.000717704 4.607631946 1.000006941 0.696884145 0.373642484 0.123804431 14483076.26 3145535.165 1103.775288 0.026614626 0.099834879 1.000717704 -0.303122796 GCFQAEIVPVTTTVHDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GCFQAEIVPVTTTVHDDK 18 0 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 229.96 1.60E-19 823880000 1886650 2217400 1477240 2309500 1163630 1857400 1709680 1937710 995650 FALSE TRUE 1797471.793 2443355.581 1544972.915 2077344.672 1366566.704 1793077.772 1448836.916 1768033.84 1150050.317 1.562950566 2.124564069 1.34339593 1.806307639 1.188266881 1.559129845 1.259803066 1.537353465 1 20.13326555 2.214320352 0.253517701 0.962588863 1.987101041 0.389396358 0.249916311 2.110296138 0.412909917 0.485304488 0.783885823 163.8024345 -2.214320352 1.024512178 GCFQAEIVPVTTTVHDDKGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GCFQAEIVPVTTTVHDDKGTK 21 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 142.99 8.49E-08 488900000 1162390 1017820 940480 1243680 687990 1172870 1179940 1250120 658840 FALSE TRUE 1107446.128 1121537.015 983601.9383 1118662.924 807975.2382 1132253.218 999918.4819 1140652.865 761009.5423 1.455232907 1.473748952 1.292496196 1.469972269 1.061714989 1.487830513 1.313936851 1.498868019 1 19.53755502 -2.184897023 2.246120872 0.000116535 1.38427462 0.44472497 0.134021437 2947161.302 565632.2122 15011558.26 0.032239495 0.006532854 2.184897023 1.384158084 GCHLLVATPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 110.38 0.001802 798120000 1794830 1485450 1796580 2288520 1853830 2205510 2569750 2415440 2020110 FALSE TRUE 1709991.943 1636819.044 1878954.97 2058473.622 2177137.365 2129132.636 2177687.441 2203931.269 2333378.342 0.732839554 0.701480345 0.805250883 0.882185964 0.933040873 0.912467815 0.933276615 0.944523753 1 21.15398882 3.311074338 1.611750344 0.938722349 0.713910271 0.931244963 0.025296303 0.074294631 0.398488124 0.007544144 0.011494055 2046.794957 -3.311074338 -0.224812078 GCLTTPNS(ph)PSMHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.014)MHS(0.001)R 93.768 0.014842 189170000 99940 76627 85472 93529 122330 80589 112510 103930 134910 TRUE FALSE 95216.03426 84435.37842 89390.97574 84127.28723 143664.3133 77798.18272 95344.53311 94829.33823 155831.1538 0.611020531 0.541838884 0.573639953 0.5398618 0.921922926 0.499246658 0.611845134 0.608539024 1 17.24962416 -4.999999999 0.379908907 6.521450222 0.598347125 0.522979372 0.115834127 457.5332574 3.420354973 2081.547531 0.071893996 1.00E-05 4.999999999 -5.923103098 GCNES(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GCNESFR 7 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;R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 Q8TEW0-4;R4GN62 PARD3;PARD3B Partitioning defective 3 homolog;Partitioning defective 3 homolog B 1 GCNES(1)FR;GCNES(1)FR 94.309 0.014995 88273000 258223 236158 288075 288384 493980 232359 273240 246302 450990 TRUE FALSE 246017.3105 260222.7687 301283.5237 259395.0924 580129.9556 224312.3496 231552.2196 224734.4912 520927.2259 0.472268099 0.499537662 0.578360102 0.49794881 1.113648753 0.430602085 0.44450013 0.431412451 1 18.99072231 3.540483375 2.023585819 0.618157151 0.48345022 0.068108665 0.236877152 1.091333814 8.854474789 0.068455566 0.118056134 3471.229873 -3.540483375 -0.134706931 GCNPSGHTQSVT(ph)TPEPAKEGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQS(0.001)VT(0.772)T(0.219)PEPAKEGT(0.008)K;GCNPSGHTQS(0.001)VT(0.5)T(0.5)PEPAKEGTK;GCNPSGHTQS(0.001)VT(0.61)T(0.389)PEPAKEGTK;GCNPSGHTQSVT(0.5)T(0.5)PEPAKEGTK 195.09 1.90E-18 1244850000 1271460 920228 1371490 1391043 1045513 1471380 1879360 1788190 1396220 TRUE FALSE 1211360.606 1014000.279 1434374.173 1251212.715 1227850.136 1420425.742 1592629.115 1631606.604 1612738.667 0.75112021 0.628744322 0.88940273 0.775831039 0.761344762 0.88075382 0.987530806 1.011699315 1 20.62108125 2.043978194 1.005561673 1.028373106 0.730397544 0.735581072 0.064591581 0.257655648 0.481048485 0.051299203 0.024929556 110.6568221 -2.043978194 -0.297975562 GCNPSGHTQSVTT(ph)PEPAKEGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQSVT(0.184)T(0.815)PEPAKEGTK 137.03 5.31E-06 318140000 311510 245570 375120 378770 280460 380690 489880 466410 391230 TRUE FALSE 296785.5397 270593.8622 392319.623 340695.32 329372.1352 367506.6098 415139.8087 425568.6678 451899.9503 0.656750547 0.598791529 0.868155933 0.753917587 0.728860747 0.813247732 0.918654247 0.941732053 1 18.78564387 2.544131084 0.335135253 1.026219959 0.569861607 0.739651799 0.065091103 0.847752209 0.210893507 0.081260675 0.139533752 350.050808 -2.544131084 -0.456358352 GCNPSGHTQSVTTPEPAKEGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 139.69 8.12E-08 155660000 163840 87326 175810 146330 139970 162300 220170 208410 177700 FALSE TRUE 156095.6079 96224.61868 183871.0624 131620.6304 164380.7237 156679.5103 186579.0228 190160.5155 205256.8084 0.760489306 0.468801105 0.895809809 0.641248548 0.80085394 0.763334047 0.909002845 0.926451683 1 17.64707055 1.974820958 0.56665341 1.006755391 0.639389933 0.504074172 0.108774477 0.577154391 0.385635346 0.095233807 0.063498561 94.36717583 -1.974820958 -0.367365459 GCQLLVYPGAFNLTTGPAHWELLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GCQLLVYPGAFNLTTGPAHWELLQR 25 0 Q9NQR4 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 232.81 7.13E-36 181587000 663600 567900 569610 658120 796280 595620 749970 670960 700370 FALSE TRUE 632232.9431 625769.6556 595727.1819 591964.5273 935150.9799 574993.5301 635548.3024 612207.1854 808979.8026 0.781518823 0.773529393 0.736393146 0.731742035 1.155963322 0.710763765 0.785617021 0.756764487 1 19.62574416 GCRLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR 64.841 0.043728 18581320000 4455826 3608573 3498563 3859450 7250000 3296700 5337029 4017651 6714580 TRUE FALSE 4245207.936 3976290.691 3658975.574 3471490.754 8514397.705 3182534.452 4522767.205 3665844.18 7755842.773 0.547356111 0.512683252 0.47177021 0.447596845 1.09780432 0.410340249 0.58314323 0.472655814 1 22.88685213 -1.419554362 3.039119317 1.007461137 0.565370885 0.326531544 0.194982659 89598897.33 110847918.6 5800050.05 0.045339677 0.038057972 1.419554362 -0.442090252 GCWDSIHVVEVQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GCWDSIHVVEVQEK 14 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 183.58 1.39E-06 583330000 1288350 1316340 1224600 1360510 1073230 1255230 1454270 1430500 1077200 FALSE TRUE 1227452.249 1450476.543 1280749.121 1223748.95 1260400.972 1211761.07 1232394.402 1305237.836 1244246.674 0.986502334 1.165746771 1.029336986 0.983525996 1.012983195 0.973891347 0.990474339 1.049018545 1 20.2468411 3.486654612 24.13292324 0.999689543 1.07969411 0.297421944 0.04679941 284.3707453 719860.5335 0.012105332 0.017374655 3066.582211 -3.486654612 0.080004567 GDAASS(ph)PAPAASVGSSQGGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GDAAS(0.006)S(0.994)PAPAASVGSSQGGAR;GDAAS(0.137)S(0.863)PAPAASVGSSQGGAR 141.07 1.67E-07 176083000 113615 105056 116011 129581 123259 122166 126969 123261 156275 TRUE FALSE 108244.6441 115761.3258 121330.2191 116555.2717 144755.3306 117935.3608 107597.5471 112467.6134 180509.3289 0.599662327 0.64130384 0.67215484 0.645702205 0.801927144 0.653347733 0.596077487 0.623057069 1 17.46171387 -1.303561591 3.726480916 1.000883971 0.650359267 0.780759537 0.057564061 31725591 29199781.36 281386.6973 0.014159449 0.049709387 1.303561591 -0.350524704 GDADQASNILASFGLSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDADQASNILASFGLSAR 18 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 102.5 0.0020628 0 72289 54144 55135 50779 50280 50988 55491 51630 69432 FALSE TRUE 68872.04223 59661.33516 57662.99429 45674.59845 59048.81608 49222.27278 47024.82879 47109.00349 80199.15995 0.858762639 0.743914714 0.718997485 0.569514674 0.736277239 0.613750478 0.58635064 0.587400211 1 16.2912995 4.089118606 1.2761317 0.655075408 0.85957163 0.125053262 0.127570647 0.791278971 2.169058535 0.034004784 0.156227388 12277.74491 -4.089118606 0.204496222 GDARPAEIDSLWEISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDARPAEIDSLWEISK 16 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 113.14 0.0006241 175860000 425060 303510 327110 369820 338210 374460 445240 419780 334960 FALSE TRUE 404968.2562 334438.0141 342108.3171 332644.991 397193.7169 361492.3563 377310.4606 383021.8378 386903.8861 1.046689555 0.864395593 0.884220421 0.859761308 1.026595315 0.934320821 0.975204629 0.989966376 1 18.56161569 2.732077235 24.9689479 0.978764121 0.918665941 0.276816581 0.056611466 859.9927837 3312015.19 0.018517213 0.017841877 539.6065775 -2.732077235 -0.06009818 GDASKEDIDTAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GDASKEDIDTAMK 13 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0D9SFP2;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;; 94.673 0.0052965 953963000 1476350 1087410 1400780 1306430 999356 1370850 1584060 1611440 1065503 FALSE TRUE 1406565.861 1198218.315 1465007.149 1175105.174 1173643.37 1323377.121 1342382.554 1470333.771 1230735.763 1.142865839 0.973578855 1.190350676 0.954798917 0.953611169 1.07527315 1.090715484 1.194678675 1 20.23108962 1.798096898 3.440814399 1.10717893 1.043968146 0.057799837 0.08948233 0.578116968 12.63090428 0.044743609 0.022858783 62.8198504 -1.798096898 -0.063210783 GDCFIIDLGTEIYQWCGSSCNKYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDCFIIDLGTEIYQWCGSSCNKYER 25 1 Q9Y6U3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ; 281.91 2.29E-53 153504000 240964 215633 251173 246327 200916 254449 257854 246846 212300 FALSE TRUE 229574.1093 237606.2479 262689.5305 221565.742 235955.6868 245637.3673 218513.6365 225230.8556 245222.3997 0.936187353 0.968941859 1.071229752 0.903529784 0.962210985 1.001692209 0.891083509 0.918475865 1 17.90373124 1.742426269 25 0.926613328 0.971059695 0.094568885 0.051148734 1.321270647 8587.601543 0.022176492 0.012298029 55.26195812 -1.742426269 0.044446367 GDDDEES(ph)DEEAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDDDEESDEEAVK 13 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVK 225.09 1.58E-08 0 132420 196070 124690 194140 78915 165760 113040 146060 67852 TRUE FALSE 126160.769 216049.7559 130407.1598 174624.6784 92677.75101 160019.6896 95793.67188 133270.2121 78374.14162 1.609724412 2.756645897 1.66390543 2.228090474 1.182504192 2.04174089 1.222261194 1.700436003 1 16.25809012 1.982643896 0.469595216 1.079159257 2.190267651 0.330314238 0.43185855 0.944694089 0.47799512 0.401147034 0.330377636 96.08241181 -1.982643896 1.111108394 GDDDEES(ph)DEEAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDDDEESDEEAVKK 14 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVKK 182.31 9.41E-07 203860000 231740 362050 225220 338050 133280 275530 202990 265920 95295 TRUE FALSE 220786.1095 398943.3066 235546.5598 304068.5717 156523.9898 265988.327 172020.1473 242634.6351 110072.8619 2.005817834 3.624356628 2.139914923 2.762429962 1.422003454 2.416475073 1.562784363 2.204309317 1 16.7480993 2.751325462 24.6522069 1.797132788 2.701232205 0.372405305 0.580710463 646.2005234 1247978.715 0.16283783 0.171655822 564.060207 -2.751325462 0.904099417 GDDEEWNEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDDEEWNEVLNK 12 0 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 112.15 0.0030364 22991000 32522 42389 37950 41271 36918 33691 43435 40347 42302 FALSE TRUE 30984.74951 46708.48729 39690.04504 37122.36067 43356.48751 32524.27222 36808.19301 36814.00279 48861.97811 0.634128022 0.955927064 0.812288953 0.75973921 0.887325671 0.665635602 0.753309515 0.753428416 1 15.57642465 2.260718213 24.99497207 0.766657879 0.811649596 0 0.118208448 960.8460955 1083883.889 0.037847761 0.031643564 182.2712674 -2.260718213 0.044991717 GDDGIFDDNFIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;;;;; 295.37 3.08E-43 1155000000 1601865 1645792 1318168 1798144 1568469 1450169 1606808 1609101 1556096 FALSE TRUE 1526148.016 1813500.076 1378607.307 1617391.149 1842009.497 1399949.284 1361659.929 1468199.586 1797407.42 0.849082962 1.00895326 0.766997672 0.899846707 1.024814673 0.778871428 0.757568881 0.816842954 1 20.77748603 2.198470878 24.99997467 0.810229067 0.910952842 0.086432454 0.098350923 239.8520714 149570.4798 0.034147155 0.025219656 157.93227 -2.198470878 0.100723775 GDDILTILTEVNYEVSNKDDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDDILTILTEVNYEVSNKDDKK 22 2 Q14790-3;Q14790-2;Q14790;Q14790-4;Q14790-9;H7C0E2 Q14790-3 CASP8 Caspase-8;Caspase-8 subunit p18;Caspase-8 subunit p10 0 167.99 5.59E-12 35009000 69062 60591 70402 75620 56517 73898 88791 79883 64516 FALSE TRUE 65797.57613 66765.29179 73630.00134 68018.53393 66373.54691 71338.89373 75244.30219 72888.02103 74520.81178 0.882942289 0.895928133 0.988046152 0.912745478 0.890671281 0.957301619 1.009708569 0.978089466 1 16.18535577 2.015061969 4.309629721 0.994895866 0.912301476 0.614987893 0.029650159 0.138448761 6.136162998 0.013090546 0.008621154 103.5289881 -2.015061969 -0.08259439 GDDLLPAGTEDYIHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GDDLLPAGTEDYIHIR 16 0 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;;; 248.23 2.20E-20 1091767000 2220521 2789960 1898853 2757870 2146464 2151281 2047472 2249469 1753596 FALSE TRUE 2115561.373 3074260.096 1985917.288 2480643.668 2520806.642 2076781.6 1735092.542 2052493.569 2025534.712 1.044445874 1.517752364 0.980441005 1.224685834 1.244514166 1.025300424 0.856609631 1.013309502 1 20.94987138 2.119849201 4.109119773 0.940658241 1.221830987 0.373696785 0.14703196 0.200637878 6.156761905 0.056229582 0.040082298 131.7799083 -2.119849201 0.281172746 GDDWNDREWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDDWNDREWDR 11 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 100.19 0.0038453 573360000 426970 359520 410350 393560 495560 389040 433770 464320 466590 FALSE TRUE 406787.9743 396155.4967 429164.9534 353998.6011 581985.5071 375567.4473 367590.4198 423661.6793 538946.3942 0.754783739 0.735055473 0.796303599 0.656834529 1.079857873 0.696854922 0.68205377 0.786092427 1 19.03978226 0.954846638 22.00971313 1.000000002 0.764396206 0.267465095 0.117567493 3016.798953 1470522.421 0.105169813 0.026292453 9.012528218 -0.954846638 -0.235603796 GDEELDSLIK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 218.55 1.57E-08 1152193000 3321330 3425160 2736200 3673620 2220780 3238330 3141600 3235600 2233190 FALSE TRUE 3164337.313 3774187.698 2861657.476 3304340.738 2608083.329 3126185.82 2662291.221 2952273.711 2579501.7 1.22672426 1.46314604 1.109383831 1.280999636 1.011080291 1.211934003 1.03209516 1.144513187 1 21.29866097 3.241026744 1.301611617 1.089230709 1.335164499 0.413770507 0.108415287 0.343500549 1.224192921 0.035441498 0.053517082 1741.914137 -3.241026744 0.245933789 GDEGIFEESFIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;;;; 259.47 4.70E-24 162873000 339208 351538 302665 380273 267425 338281 342074 354359 257268 FALSE TRUE 323174.3101 387360.1219 316542.4896 342047.2356 314063.8353 326566.2441 289884.3287 323329.4474 297163.8075 1.087529174 1.303523888 1.065212121 1.151039349 1.056871084 1.098943532 0.975503481 1.088051234 1 18.18089889 2.792230854 0.966824839 1.024085456 1.185245231 0.370189226 0.071129366 0.472100588 0.942955873 0.03675495 0.035932343 619.7704336 -2.792230854 0.161159775 GDFCIQVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 190.93 8.49E-05 11932020000 5864500 4959050 5307190 5654580 6262360 5632050 6672250 5626670 5602820 FALSE TRUE 5587296.707 5464382.833 5550529.911 5086170.875 7354513.601 5437010.696 5654275.718 5133968.946 6471676.71 0.863346078 0.844353493 0.857664893 0.785912385 1.136415481 0.840123965 0.873695639 0.793298117 1 22.62570811 GDFDENLNYPEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDFDENLNYPEQK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 191.33 8.51E-06 97431000 174904 155317 167566 191760 133315 155052 185578 181325 145933 FALSE TRUE 166636.6345 171143.9789 175249.0668 172483.9205 156565.0938 149682.5104 157264.6677 165447.2217 168563.5443 0.988568645 1.015308379 1.039661734 1.023257557 0.928819422 0.887988627 0.932969631 0.981512476 1 17.36293303 2.738164859 24.9885164 0.936570969 1.014617396 0.516738537 0.033094424 24.94653982 1575106.507 0.01012856 0.010101486 547.2236508 -2.738164859 0.078046427 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK 37 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 240.94 4.76E-50 326870000 182150 175050 178960 193700 166490 186820 212410 210060 106950 FALSE TRUE 173540.1305 192887.794 187165.493 174228.908 195525.8033 180350.3766 180002.9533 191666.0328 123535.2598 1.404782172 1.5613987 1.515077504 1.410357725 1.582753002 1.459910125 1.457097784 1.55150872 1 16.91456335 -1.18634428 4.891140434 0.999948588 1.490644876 0.865044249 0.061173555 3.11E-05 5.17E-06 0.053694282 0.012654542 0.065111203 1.18634428 0.490696287 GDFIALDLGGSSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDFIALDLGGSSFR 14 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 75.819 0.067903 26568000 75003 78901 62406 68235 79848 71573 70327 70640 81038 FALSE TRUE 71457.75683 86941.1016 65267.37683 61375.88816 93773.46592 69094.40906 59597.32451 64454.38711 93604.95916 0.763397126 0.928808713 0.697264092 0.655690561 1.001800191 0.738149022 0.636689819 0.688578764 1 16.51429734 2.027966783 24.99907723 0.722895898 0.814458581 0 0.139490252 508.4837146 454523.5519 0.048587399 0.035883523 106.6514547 -2.027966783 0.091562683 GDFVTSFYWPWQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDFVTSFYWPWQTK 14 0 G3V3Y1;Q8N8N7;Q8N8N7-2 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 98.353 0.0071889 0 18347 17377 23062 19319 28575 19647 29805 25545 39855 FALSE TRUE 17479.77367 19147.73606 24119.41551 17377.01742 33558.47095 18966.61946 25257.69984 23308.14438 46035.50985 0.379701968 0.41593405 0.52393067 0.377469859 0.728969247 0.41199977 0.548656894 0.506307945 1 15.4904595 -4.999999999 0.19152543 3.263394582 0.384483538 0.734623466 0.099022779 64.00867067 0.627233106 55.24926558 0.236314113 1.00E-05 4.999999999 -2.878911044 GDFYTAHGEDALLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDFYTAHGEDALLAAR 16 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 72.315 0.038195 442750000 275840 246900 250210 297760 203330 275190 318580 305190 213560 FALSE TRUE 262801.5899 272059.3907 261682.376 267828.5991 238790.6876 265660.1013 269974.7699 278465.9457 246677.7941 1.065363791 1.102893723 1.060826642 1.085742639 0.968026686 1.076951828 1.094442939 1.128865072 1 17.91226832 -1.081890065 6.932524227 0.999999968 1.07374666 0.228955579 0.042010601 2.00E-08 2.62E-09 0.039259067 0.009253447 0.082815177 1.081890065 0.073746692 GDGDVAWQHTQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDGDVAWQHTQLFR 14 0 Q96IV0-5;Q96IV0;A0A0C4DFP4;Q96IV0-2;Q96IV0-4 Q96IV0-5 NGLY1 Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase 0 97.45 0.0036467 0 186330 156040 212180 161690 493600 145160 264970 171870 623410 FALSE TRUE 177522.5502 171940.6534 221908.6629 145436.614 579683.6837 140133.0728 224543.96 156820.1517 720085.2389 0.246529911 0.238778195 0.308169993 0.201971386 0.805020923 0.194606229 0.311829694 0.217779984 1 19.45780817 -2.057332771 2.528790606 1.963069662 0.310280533 0.591316226 0.1787672 23234626.12 7893547.826 129294111.3 0.039880222 0.008763291 2.057332771 -1.652789129 GDGGITHSEEINGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDGGITHSEEINGK 14 0 O75363;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 209.25 6.91E-09 246010000 656650 644600 613140 707840 541030 619640 701340 706560 527410 FALSE TRUE 625611.4559 710285.4728 641253.0755 636686.5784 635385.4607 598181.7114 594337.702 644689.8607 609198.0492 1.026942645 1.165935239 1.052618399 1.045122484 1.042986696 0.981916656 0.975606706 1.05825989 1 19.2165518 2.951268379 1.434282185 1.000996182 1.09418632 0.376161624 0.042178477 0.346950526 1.466049702 0.015977625 0.018276399 893.8576861 -2.951268379 0.093190137 GDGPVQGIINFEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDGPVQGIINFEQK 14 0 P00441 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 176.25 5.25E-06 66695000 108710 92196 82582 102280 74050 99660 112890 107160 89179 FALSE TRUE 103571.4937 101590.8772 86368.46638 91998.62008 86964.29655 96208.74921 95666.55713 97776.50231 103008.4239 1.005466251 0.986238537 0.838460226 0.893117443 0.844244512 0.93398914 0.92872557 0.949208799 1 16.6524028 0.850200306 1.954187863 0.999895637 0.925484079 0.187101937 0.053109412 1.233822814 8.994427335 0.056926538 0.015859636 7.082723802 -0.850200306 -0.074411558 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR 31 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;;;; 157.43 5.63E-10 454076500 206378.9 187827.3 209770.5 213454 248570.3 200061.3 256349.6 218020.9 152836.2 FALSE TRUE 196623.7784 206967.1154 219388.6849 191997.1984 291920.8816 193133.127 217238.7603 198929.8342 176537.2573 1.113780634 1.172370742 1.242733054 1.087573248 1.653593616 1.094007746 1.230554749 1.126843349 1 17.42961316 0.92315812 1.859024052 0.999922649 1.221307656 0.173127037 0.161885097 0.78106207 5.578810325 0.142966472 0.040339296 8.3783427 -0.92315812 0.221385007 GDIDHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDIDHVK 7 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 104.21 0.0082028 245826000 477090 493170 427050 499650 373460 396690 413330 483850 332260 FALSE TRUE 454538.9012 543424.5837 446630.6649 449424.2327 438591.3058 382952.5258 350268.9172 441481.5289 383785.1839 1.184357605 1.415960299 1.163751712 1.171030701 1.142804163 0.997830406 0.912669201 1.150334999 1 18.54993949 2.811326075 1.171209484 0.99700746 1.289243124 0.569967957 0.090026234 0.282165598 0.807738735 0.041142898 0.041135373 647.6286824 -2.811326075 0.292235663 GDIFLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GDIFLVR 7 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 134.44 0.0073853 239217000 577590 457128 445480 526501 649340 428025 615820 527918 649610 FALSE TRUE 550288.4654 503709.8629 465905.6986 473576.1192 762584.6904 413202.3869 521865.3487 481690.7013 750348.2011 0.73337747 0.671301487 0.620919325 0.631141807 1.016307748 0.550680852 0.695497568 0.641956229 1 19.51720071 -0.95004064 4.086002879 1.000015068 0.694370582 0.37362225 0.124045466 30140501.09 61545359.45 6763.083123 0.027218384 0.112191346 0.95004064 -0.305644487 GDKEEVAYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDKEEVAYEER 11 1 Q9NRV9;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 121.04 0.00038293 782710000 1291540 984780 1068210 1287790 973460 1143840 1330540 1259780 1063950 FALSE TRUE 1230491.464 1085130.202 1117188.485 1158338.903 1143231.116 1104228.534 1127541.686 1149466.985 1228941.932 1.001260866 0.882979231 0.909065315 0.942549743 0.930256415 0.898519698 0.917489799 0.935330592 1 20.22898532 0.866961427 6.031961877 0.999999629 0.925164591 0.348921449 0.031493735 2.892446867 130.7442964 0.029529084 0.007424492 7.361417125 -0.866961427 -0.074835038 GDKHDDLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDKHDDLQR 9 1 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 118.4 0.00059784 52554000 25627 29726 20655 28356 21915 24671 27373 31020 22977 FALSE TRUE 24415.6625 32755.1132 21602.05218 25505.60101 25736.96906 23816.63708 23196.74611 28303.72435 26540.15581 0.919951739 1.23417185 0.813938408 0.961019264 0.969736924 0.897381208 0.874024489 1.066449065 1 14.69588922 3.728799361 24.97340373 0.931136055 1.077061801 0.234506108 0.101619366 746.4117628 1909636.114 0.025147681 0.039502775 5355.49183 -3.728799361 0.145925746 GDKSELNEIKENQRS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GDKSELNEIKENQRSPVR 18 3 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR;GDKSELNEIKENQRS(1)PVR 186.62 2.60E-13 4246150000 2666340 2020908 2227670 2605170 1551935 2716450 2837800 2960780 1764651 TRUE FALSE 2540307.392 2226840.823 2329810.873 2343293.362 1822591.973 2622378.655 2404841.49 2701518.407 2038304.064 1.246284809 1.092496876 1.143014388 1.14962895 0.894170798 1.286549294 1.179824704 1.325375568 1 20.95893785 GDKVDILYNNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDKVDILYNNIK 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 162.32 5.39E-05 550260000 1736280 1738120 1466520 1817350 1217500 1666160 1794730 1925940 1333680 FALSE TRUE 1654209.485 1915236.404 1533761.393 1634666.525 1429831.615 1608460.461 1520910.976 1757294.484 1540500.283 1.073813166 1.24325612 0.995625518 1.061127053 0.928160566 1.044115655 0.987283802 1.140729738 1 20.55496752 3.722160188 24.97912856 1.019030672 1.158534646 0.407698951 0.068103432 610.5118782 929857.277 0.016560413 0.025735327 5274.24364 -3.722160188 0.139503974 GDLEEYGQDLLHTVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDLEEYGQDLLHTVFK 16 0 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 96.993 0.0032246 18481800 37290 37848 29204 46589 28990 29388 27797 36514 24151.6 FALSE TRUE 35527.3756 41704.75423 30543.03229 41905.78521 34045.84682 28370.28619 23556.05712 33316.64059 27896.90678 1.273523831 1.494959802 1.094853724 1.502166012 1.220416553 1.016968885 0.844396739 1.194277231 1 14.76781754 2.338369514 3.403813943 0.981857863 1.346947309 0.537884589 0.141941136 0.154353249 3.530156597 0.048844754 0.039079051 217.9563439 -2.338369514 0.365089446 GDLGIEIPAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 806563000 3111491 2644278 2766131 3287012 2542444 3074099 3517430 3258137 2840950 FALSE TRUE 2964416.987 2913732.934 2892960.842 2956595.309 2985845.429 2967642.181 2980781.451 2972837.252 3281510.016 0.903369782 0.887924437 0.881594396 0.900986221 0.909899837 0.90435262 0.908356652 0.905935754 1 21.64592841 -4.999999996 0.258164728 1.645521583 0.89133201 0.946525652 0.007534083 40.56032555 0.399077806 13.8556161 0.010249786 1.00E-05 4.999999996 -0.754189573 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK 245.2 5.01E-39 378814000 299654 231174 262624 302013 182230 319561 344009 338368 195985 TRUE FALSE 285489.9493 254730.8934 274665.5702 271654.0795 214010.8543 308494.5224 291524.1089 308738.7041 226377.3528 1.261124161 1.125249016 1.213308517 1.200005548 0.945372192 1.362744632 1.287779476 1.363823281 1 17.78837011 GDLSSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 185.22 0.0014344 4145950000 5729490 5102760 3976580 4457420 6725380 4229420 6159380 4978860 6269870 FALSE TRUE 5458668.362 5622737.045 4158910.126 4009351.673 7898284.143 4082954.125 5219653.456 4542884.624 7242169.418 0.753733867 0.776388499 0.574263026 0.553611969 1.090596434 0.563775008 0.720730648 0.627282291 1 22.7879905 GDLSYLDQGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDLSYLDQGHR 11 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 95.362 0.0036949 0 82938 68580 67272 83299 89970 66468 90354 79568 79347 FALSE TRUE 79017.68511 75568.37997 70356.48774 74925.62626 105660.7395 64166.19649 76568.83783 72600.6041 91651.72751 0.862151617 0.824516701 0.767650427 0.817503699 1.152850496 0.700108969 0.835432565 0.792135687 1 16.48387445 -2.286237509 2.142308398 1.646404607 0.842545925 0.146238644 0.118375532 6542275.679 901316.9591 20485829.22 0.026443367 0.005173238 2.286237509 -0.803858682 GDMEQNDSDNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GDMEQNDSDNRR 12 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;;;;; 174.9 4.67E-05 1856935000 988272 915165 916294.2 1068997 1157800 886218 1072584 960347 1194997 FALSE TRUE 941558.3411 1008421.354 958307.1954 961539.3906 1359719.953 855528.0484 908941.6114 876253.9256 1380311.032 0.68213491 0.730575451 0.694269026 0.696610669 0.985082291 0.619808166 0.658504924 0.634823533 1 20.39656196 -1.939837156 2.597287951 1.201277354 0.711482211 0.43910371 0.102028076 16919196.95 10273824.18 20653954.96 0.025042725 0.011485842 1.939837156 -0.489795143 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 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 324.03 1.14E-83 2439775300 2695070 3087465 2431696 3271890 1926263.8 2842607 2631170 2934794 1723570 TRUE FALSE 2567679.382 3402081.194 2543191.667 2942993.401 2262203.597 2744166.807 2229736.692 2677807.879 1990852.433 1.289738677 1.708856537 1.277438561 1.478257932 1.136298984 1.378387851 1.119990942 1.345055934 1 20.92495486 1.901120314 0.362659056 1.014132106 1.520945364 0.374777176 0.15743791 1.117295547 0.41218685 0.184578264 0.191925213 79.63799427 -1.901120314 0.506813258 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 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;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(1)DEDDENEFFDAPEIITMPENLGHKR 271.58 2.30E-71 1195101700 1172610.6 748588 1141539.3 1047015.7 986843.9 1125809.1 1516314.8 1290930.5 1180672 TRUE FALSE 1117183.621 824869.9683 1193880.006 941767.6926 1158949.164 1086822.049 1284973.128 1177889.782 1363764.584 0.819190962 0.604847771 0.875429689 0.690564709 0.849816147 0.796927902 0.942225032 0.863704627 1 20.37916319 1.857065803 0.595480642 0.987629723 0.723108327 0.491965562 0.081041888 0.544227262 0.401904505 0.069021238 0.041303976 71.95579947 -1.857065803 -0.264521396 GDNIYEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 113.71 0.0065069 474270000 1031980 960460 946400 1097750 1140480 957250 1211900 1043270 1152500 FALSE TRUE 983200.3506 1058331.966 989793.3761 987402.0844 1339379.351 924100.1925 1027002.397 951915.7481 1331223.814 0.738568782 0.795006786 0.743521387 0.741725076 1.006126346 0.694173424 0.771472375 0.715068149 1 20.34432172 -2.287296029 2.364230906 2.069850858 0.776123856 0.398909168 0.086525272 2552991.535 554355.9782 14721894.46 0.020005804 0.005160645 2.287296029 -1.293727002 GDNPFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDNPFPK 7 0 P14550;Q5T621;V9GYP9 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 87.323 0.045195 55676000 260770 214370 216580 253250 239570 229300 276980 268020 247250 FALSE TRUE 248443.9189 236214.5467 226510.4072 227792.8289 281350.9321 221359.2835 234721.6139 244550.7479 285592.2672 0.869925231 0.827104141 0.793125141 0.797615534 0.985148985 0.775088505 0.821876643 0.85629331 1 18.12359739 0.871129072 6.87518303 0.999999809 0.837626578 0.426565012 0.058364246 3.819478529 203.7594961 0.05213234 0.013077416 7.432399948 -0.871129072 -0.162373231 GDNRLDLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDNRLDLLK 9 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 123.79 0.00049957 488180000 1721600 1571800 1173100 1405240 1316990 1413940 1738350 1676320 1328000 FALSE TRUE 1640223.38 1731968.207 1226887.795 1263982.605 1546672.639 1364974.903 1473132.781 1529532.534 1533939.458 1.069288212 1.129098152 0.799828044 0.824010752 1.008300967 0.889849268 0.960359141 0.997127055 1 20.54881011 3.759170704 24.99759725 0.923323425 1.099193203 0.494063293 0.072985816 597.9008026 725180.5447 0.018260171 0.032872906 5743.421693 -3.759170704 0.175869778 GDPESPWWEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDPESPWWEGR 11 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 ; 128.27 0.00062657 129916000 111993 83122 105388 107118 131362 89898 126629 113657 147122 FALSE TRUE 106699.3128 91592.2263 110220.144 96350.29513 154271.4912 86784.80972 107309.4203 103704.5905 169936.9284 0.627875965 0.538977768 0.648594423 0.566976796 0.907816169 0.510688351 0.631466164 0.610253413 1 17.37463987 -2.198263356 2.20148681 2.027022457 0.624131039 0.536391204 0.10786981 4244934.169 868285.7183 21694596.1 0.023797883 0.006334854 2.198263356 -1.402891417 GDPIVQHRPMLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDPIVQHRPMLEER 14 1 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 102.64 0.0015631 194764000 204048 187230 169194 218180 212400 191497 203905 205813 197234 FALSE TRUE 194403.0554 206308.9499 176951.7123 196248.1319 249442.4928 184865.4109 172795.5473 187790.9226 227820.0414 0.853318498 0.905578581 0.776717058 0.86141733 1.094910225 0.81145368 0.758473865 0.824295007 1 17.79753514 -0.531729353 5.070015826 1.000000001 0.859118758 0.180373698 0.093213701 2868524.475 848673.2702 0.162145818 0.021913624 0.293948093 0.531729353 -0.140881244 GDQCCYSHS(ph)PPTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GDQCCYSHSPPTPR 14 0 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 1 GDQCCYS(0.001)HS(0.999)PPTPR;GDQCCYSHS(0.994)PPT(0.006)PR;GDQCCYSHS(0.997)PPT(0.003)PR;GDQCCYSHS(0.92)PPT(0.08)PR 149.74 4.77E-06 1333350000 511213 428407 476604 527143 522781 457075 588675 504926 511953 TRUE FALSE 487048.9746 472062.1604 498456.7648 474153.5841 613953.8409 441246.3781 498861.817 460712.0027 591344.0565 0.823630455 0.79828681 0.842921746 0.801823539 1.038234568 0.746175383 0.843606715 0.779092979 1 19.17363824 -2.145917485 2.408178644 1.375985021 0.832630491 0.307187744 0.078208933 11158385.88 2755851.607 22925372.94 0.019482947 0.007146321 2.145917485 -0.54335453 GDQENVHPDVMLVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDQENVHPDVMLVQPR 16 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 139.67 1.77E-06 279130000 191972 232249 169574 234713 191172 189793 191444 215142 180447 FALSE TRUE 182897.864 255915.4371 177349.1356 211119.2033 224512.3363 183220.4208 162235.7017 196303.0259 208429.7992 0.877503432 1.227825571 0.850881862 1.012903165 1.07716045 0.879050988 0.778370954 0.941818429 1 17.66920203 2.207267405 13.19171498 0.870180949 1.020042956 0.151746102 0.118280532 1.732167299 727.4468313 0.042030527 0.031130554 161.1637652 -2.207267405 0.149862007 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDQPAASGDSDDDEPPPLPR 20 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 GDQPAASGDS(1)DDDEPPPLPR;GDQPAAS(0.011)GDS(0.989)DDDEPPPLPR 215.11 1.28E-24 77429000 54550 50109 38541 69930 64872 61420 48031 46196 47001 TRUE FALSE 51971.52961 55215.16407 40308.14297 62900.50354 76185.65626 59293.01 40702.9888 42150.83334 54289.67503 0.957300437 1.017047238 0.742464252 1.158608953 1.403317596 1.092159973 0.749737197 0.776406072 1 15.72839023 1.749131717 12.39106281 0.824021304 1.053187932 0.252913528 0.176715479 0.170119162 159.35418 0.08548778 0.046917462 56.12181615 -1.749131717 0.229166628 GDQVLNFS(ph)DAEDLIDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 179.95 8.50E-14 68702000 249349 267129 232092 293935 183095 257526 245539 279842 204846 TRUE FALSE 237562.7669 294349.7488 242733.6478 264388.0954 215026.71 248607.81 208077.5159 255337.5509 236612.4715 1.004016253 1.244016205 1.025870049 1.117388672 0.908771667 1.050696138 0.879402149 1.079138176 1 17.85216659 2.7542724 24.3263196 0.973809666 1.107768052 0.295722998 0.086256799 581.2971081 900012.2234 0.024355786 0.025747343 567.9006946 -2.7542724 0.133958387 GDQVLNFS(ph)DAEDLIDDSKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDQVLNFSDAEDLIDDSKLK 20 1 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSKLK 100.93 0.00026995 30955000 68601 50051 66786 67442 46501 74418 83506 79047 53736 TRUE FALSE 65358.36668 55151.2538 69848.20416 60662.60203 54610.75968 71840.886 70765.62601 72125.22563 62069.10443 1.052993551 0.888545989 1.12532966 0.977339734 0.879838048 1.157433906 1.140110312 1.162014923 1 15.92158771 2.218445466 24.99968828 1.129119338 0.983928866 0.367129258 0.083942309 223.8138258 278160.5345 0.029143902 0.021550897 165.3657122 -2.218445466 -0.145190472 GDREEEVERPVS(ph)SPGDPEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDREEEVERPVSSPGDPEQK 20 2 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 GDREEEVERPVS(0.5)S(0.5)PGDPEQK 59.324 0.035218 104300000 374660 219530 255910 328420 233290 344860 393970 391630 303700 TRUE FALSE 356950.5643 241900.3566 267643.7266 295406.5976 273975.7021 332917.4117 333862.6407 357336.801 350796.2449 1.017543858 0.689575103 0.762960637 0.842103078 0.781010932 0.949033567 0.951728092 1.018644886 1 18.42027378 2.142511637 4.924955569 0.97654931 0.817847035 0.474342994 0.084652647 0.201425529 8.143764419 0.032885692 0.024021495 138.8390513 -2.142511637 -0.158702275 GDRS(ph)PEPGQTWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDRSPEPGQTWTR 13 1 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GDRS(1)PEPGQTWTR 85.176 0.0056961 146300000 77553 94865 91309 89303 96379 76238 94830 74833 76746 TRUE FALSE 73887.22339 104531.8514 95495.60797 80326.09278 113187.4671 73597.85894 80361.94183 68280.22581 88647.37772 0.833495872 1.17918718 1.077252485 0.906130501 1.276828148 0.830231653 0.906534902 0.770245297 1 16.43579033 GDRWEDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GDRWEDLSR 9 1 Q9NR50-3;Q9NR50-2;Q9NR50;H0Y580 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ;;; 208.6 8.92E-06 659250000 969830 968660 788620 913300 1026280 825680 1022480 963460 969950 FALSE TRUE 923988.0579 1067367.555 824779.0071 821493.3488 1205262.907 797086.4946 866481.8969 879094.3348 1120364.892 0.824720646 0.952696361 0.736169986 0.733237318 1.075777111 0.711452581 0.773392582 0.78465002 1 20.09553725 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_SK-BR-3_Trastuzumab_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 363.78 2.27E-92 500590000 670450 692630 536090 731070 509870 675730 619040 579400 479740 TRUE FALSE 638759.1572 763209.7845 560670.2568 657581.4547 598791.1666 652329.3007 524594.0786 528664.6644 554135.629 1.152712664 1.377297803 1.01179247 1.186679615 1.080585935 1.177201513 0.946688953 0.954034783 1 19.0798796 2.451949337 0.610882622 0.955217307 1.246450755 0.429103608 0.099506577 0.646956887 0.491721195 0.080847636 0.068385561 283.1061719 -2.451949337 0.291233448 GDS(ph)ETDLEALFNAVMNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(1)ETDLEALFNAVMNPK;GDS(1)ETDLEALFNAVMNPK 341.97 1.58E-75 474710000 335810 326480 279930 366910 262310 354490 354920 375550 272810 TRUE FALSE 319936.9268 359748.6832 292765.0674 330027.5097 308056.7809 342213.9224 300770.4354 342664.8511 315115.9815 1.015298955 1.141638966 0.929070833 1.047320762 0.977598088 1.085993547 0.954475346 1.08742454 1 18.2655234 3.748475819 24.99760662 1.010990263 1.078468952 0.178466846 0.059543685 967.6117956 2439477.903 0.013573927 0.024089318 5603.712154 -3.748475819 0.067478689 GDS(ph)LILEHQWELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;GDS(1)LILEHQWELEK 278.4 2.29E-33 394185000 892310 1007730 707940 1004720 703680 972980 883180 914160 508360 TRUE FALSE 850132.2747 1110418.833 740399.7492 903723.6368 826401.5692 939285.4586 748434.6703 834111.3041 587193.8725 1.447788055 1.89105998 1.260911913 1.539054951 1.407374307 1.599617269 1.274595505 1.420504101 1 19.16347739 -0.740222109 0.172748293 0.561969893 1.731092389 0.466496344 0.170726054 15.12784492 0.636298487 3.940498204 0.752914218 0.181877046 0.740222109 1.169122496 GDS(ph)LILEHQWELEKLELLHEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDSLILEHQWELEKLELLHEVEK 23 1 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 GDS(1)LILEHQWELEKLELLHEVEK 227.57 4.97E-33 221540000 186090 129710 157270 163270 112870 167680 206130 199020 102850 TRUE FALSE 177293.8945 142927.5965 164480.9851 146857.7894 132554.4923 161873.1996 174681.0827 181592.7537 118799.4527 1.492379724 1.203099789 1.384526454 1.236182373 1.115783695 1.362575297 1.470386257 1.528565575 1 16.85816866 2.014844499 24.88576149 1.393057067 1.291210122 0 0.173070082 600.8047527 1007202.89 0.059682455 0.044060499 103.4771595 -2.014844499 -0.101846945 GDS(ph)PELKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 93.839 0.0055276 1146500000 2979490 2712320 2527890 2802040 3365880 2719760 3240680 2780780 3501840 TRUE FALSE 2838655.412 2988708.492 2643796.257 2520373.616 3952888.406 2625574.029 2746254.747 2537280.161 4044887.462 0.701788477 0.73888545 0.653614293 0.623101048 0.977255472 0.64910929 0.678944661 0.62728078 1 21.94766813 -1.026667249 4.49966879 1.000011034 0.708199114 0.447949513 0.102464336 12349457.11 2817714.916 1480.799074 0.022223489 0.094044359 1.026667249 -0.29181192 GDS(ph)PENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;GDS(1)PENR;GDS(1)PENR 143.21 0.0025562 833520000 2037575 2030468.1 2056319 2478509 2088304 1890014.6 2261569 2708456 2863259 TRUE FALSE 1941262.868 2237375.108 2150603.26 2229364.566 2452503.556 1824562.92 1916525.112 2471289.234 3307278.582 0.586966843 0.676500347 0.650263716 0.674078252 0.741547316 0.55168105 0.579487051 0.747227418 1 21.65721314 0.923921065 4.626774762 0.999902216 0.636616195 0.813359038 0.055026205 0.163796927 8.598209796 0.05432266 0.013778998 8.393074239 -0.923921065 -0.363286021 GDS(ph)RS(ph)PSHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(0.666)RS(0.863)PS(0.471)HKR 52.891 0.078927 978900000 106410 127510 107040 117190 83432 127260 142070 133680 112910 TRUE FALSE 101380.2102 140503.414 111947.8899 105409.8386 97982.51438 122852.9543 120394.6122 121974.2705 130419.5061 0.77733932 1.077319016 0.858367687 0.808236756 0.751287267 0.941982974 0.923133477 0.93524561 1 16.99280014 1.301890994 1.323925281 0.988977682 0.879271784 0.180506997 0.091633226 0.843811578 2.844648315 0.087231541 0.027741572 20.03968979 -1.301890994 -0.109705898 GDS(ph)RSPS(ph)HKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(0.999)RS(0.203)PS(0.798)HKR 82.55 0.086951 1150400000 1496200 1218500 1347500 1483500 1136300 1416500 1733700 1391200 1239400 TRUE FALSE 1425477.591 1342666.535 1409284.208 1334375.762 1334470.36 1367446.25 1469192.223 1269379.153 1431599.822 0.995723504 0.937878389 0.984412114 0.932087124 0.932153204 0.955187496 1.026259015 0.886685744 1 20.44919684 GDS(ph)RSPSHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GDS(0.872)RS(0.123)PS(0.005)HKR;GDS(0.999)RS(0.001)PSHKR 68.676 0.030923 64776000 48014.8 23195.8 36958.6 44649 41811.3 38905.1 53807.1 41660.5 46106.2 TRUE FALSE 45745.23556 25559.47839 38653.18837 40160.79769 49103.17748 37557.80663 45597.83866 38012.48576 53256.11402 0.858966832 0.4799351 0.725798138 0.754106799 0.922019535 0.70522995 0.856199133 0.713767545 1 15.70065954 3.199460233 2.929831641 0.821801897 0.663682795 0.22085276 0.126291429 0.346743784 6.087667617 0.03514583 0.045421577 1582.924618 -3.199460233 -0.158119102 GDSFFIR ddPTM_SK-BR-3_Trastuzumab_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 ; 115.78 0.032104 45161000 372000 295680 357310 324660 402370 355770 486700 345820 282130 FALSE TRUE 354416.2972 325810.1282 373693.0169 292024.56 472543.2006 343449.5957 412444.9761 315538.1675 325881.2795 1.087562617 0.999781665 1.146715201 0.896107197 1.450047089 1.053910173 1.265629547 0.968261104 1 18.31398695 3.726011206 23.76692322 1.132042479 1.043672141 0.018066696 0.159537578 1103.979257 2090791.164 0.038354504 0.059917736 5321.219889 -3.726011206 -0.088370338 GDSIEEILADS(ph)EDEEDNEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDSIEEILADSEDEEDNEEEER 22 0 Q5JTH9-2;Q5JTH9-3;Q5JTH9 Q5JTH9-2 RRP12 RRP12-like protein 1 GDSIEEILADS(1)EDEEDNEEEER 167.51 6.75E-12 104170000 140690 162190 132120 176750 152040 147000 135680 153880 138860 TRUE FALSE 134039.8625 178717.3454 138177.8327 158982.7542 178555.7279 141909.3531 114979.5241 140405.4514 160393.6996 0.835692816 1.114241681 0.861491649 0.991203237 1.11323405 0.884756406 0.716858108 0.875380091 1 17.29125795 2.008717301 24.91887299 0.824666196 0.983849448 0.174804824 0.113360209 213.9489393 611581.7793 0.039416021 0.029067682 102.0275131 -2.008717301 0.159183252 GDTGGEDTAAPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDTGGEDTAAPGR 13 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 107.03 0.0030885 46122000 172160 143000 158650 187330 150780 182540 205120 119080 108450 FALSE TRUE 164022.338 157571.8626 165924.2594 168499.2325 177075.9843 176218.594 173825.1767 108652.7239 125267.8721 1.309372748 1.257879294 1.324555583 1.345111317 1.413578608 1.406734153 1.387627759 0.867363052 1 16.93465692 1.240468237 24.99999656 0.933681398 1.343804717 0.904066343 0.056259637 14.83289518 194412.6652 0.047288032 0.015282486 17.3967546 -1.240468237 0.41012332 GDTHPLTLDEILDETQHLDIGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDTHPLTLDEILDETQHLDIGLK 23 0 P29084;E5RH41;E5RIW4 P29084 GTF2E2 Transcription initiation factor IIE subunit beta 0 252.47 1.05E-43 22501000 49402 47013 50834 52794 42388 47645 62199 57455 24742 FALSE TRUE 47066.86537 51803.67815 53164.78918 47487.04682 49780.45378 45995.0417 52709.40019 52423.93561 28578.863 1.646911753 1.812657073 1.860283567 1.661614279 1.741862641 1.609407684 1.844349098 1.834360437 1 14.8026609 -1.194835261 5.623364613 0.999977705 1.751524419 0.877047656 0.088419543 2.36E-05 3.38E-06 0.081750033 0.019268098 0.063850564 1.194835261 0.751546714 GDTNIKPILQVINIRPITTGNS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_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(0.019)T(0.019)GNS(0.962)PPR;GDTNIKPILQVINIRPIT(0.122)T(0.35)GNS(0.528)PPR 128.35 5.86E-05 162836000 378120 367440 359390 456570 352190 381540 438490 434570 387940 TRUE FALSE 360247.017 404882.5537 375868.387 410674.7162 413611.8245 368327.1741 371590.2971 396516.747 448099.7539 0.803943796 0.90355451 0.838805163 0.916480566 0.923035152 0.821975846 0.829257981 0.884884992 1 18.77346041 -2.628625073 1.420202736 2.070131258 0.863021141 0.509832827 0.041474964 274275.7902 14199.01882 937847.5905 0.011544539 0.002351662 2.628625073 -1.207110117 GDTSGDYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GDTSGDYKK 9 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 125.75 0.00079034 4240310000 11854300 9659900 9589300 11637300 6983200 11061500 12272100 12127600 8465600 FALSE TRUE 11293970.73 10644254.79 10028978.89 10467496.49 8201067.869 10678437.48 10399765.75 11065643.05 9778402.012 1.154991451 1.088547472 1.025625545 1.070471073 0.838692034 1.092043206 1.063544508 1.131641248 1 23.22116729 4.108146731 1.742347625 1.032960668 1.149902818 0.209172118 0.078013519 0.594951182 3.371401565 0.02109233 0.075970348 12827.63904 -4.108146731 0.116942149 GDTSGDYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDTSGDYRK 9 1 P09525;Q6P452;P09525-2 P09525 ANXA4 Annexin A4;Annexin 0 114.5 0.0026115 340130000 861450 663170 545140 933930 790140 687740 723510 636920 629780 FALSE TRUE 820730.9657 730747.777 570135.2082 840049.582 927940.1658 663923.3914 613125.2613 581147.9083 727443.0659 1.128240826 1.004542914 0.783752344 1.154797704 1.275618958 0.912680899 0.842849826 0.798891261 1 19.47247481 2.020248705 24.99756159 0.866780697 1.059909139 0.308213085 0.134354764 281.6441836 347695.7309 0.050308707 0.03715136 104.7728373 -2.020248705 0.193128442 GDTSHS(ph)PTPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GDTSHSPTPGK 11 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 GDT(0.051)S(0.051)HS(0.892)PT(0.007)PGK;GDT(0.024)S(0.024)HS(0.951)PT(0.001)PGK;GDT(0.002)S(0.002)HS(0.996)PT(0.001)PGK 83.087 0.011055 576480000 399717 328439 346797 397754 327582 365763 402767 392399 364393 TRUE FALSE 380823.1696 361907.3075 362697.9855 357771.0122 384712.1971 353096.5356 341317.4968 358038.4633 420901.2054 0.90478042 0.859839085 0.861717621 0.85001185 0.914020184 0.838905974 0.810920692 0.850647275 1 18.68312212 GDVEEDETIPDSEQDIRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GDVEEDETIPDSEQDIRPR 19 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;;;; 310.9 1.46E-61 2152000000 1394970 1261340 1281930 1527260 1459270 1346630 1507370 1449270 1521510 FALSE TRUE 1329032.533 1389871.98 1340707.759 1373736.923 1713766.226 1299995.865 1277393.022 1322364.236 1757458 0.756224349 0.790842216 0.762867595 0.78166131 0.975139222 0.73970238 0.72684128 0.752430064 1 20.74505878 -1.698580268 2.704004338 1.033211646 0.783011819 0.48050482 0.069972628 19140385.41 16069674.41 4328757.138 0.016845566 0.020017956 1.698580268 -0.250199828 GDVEGSQS(ph)QDEGEGSGESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDVEGSQSQDEGEGSGESER 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GDVEGSQS(1)QDEGEGSGESER;GDVEGSQS(1)QDEGEGSGESER 406.27 2.74E-151 360030000 210048 203063 218874 220678 212047 218720 221150 211356 223898 TRUE FALSE 200119.4473 223755.3506 228909.5894 198495.0282 249027.9297 211145.6716 187409.5058 192848.5482 258618.9583 0.773800376 0.865193148 0.885123004 0.767519247 0.962914441 0.816435396 0.72465494 0.745686045 1 17.98046851 -1.585267865 8.668202627 1.000046452 0.817194642 0.390198254 0.071632347 6.42E-05 3.07E-06 0.069295166 0.016328892 0.025985563 1.585267865 -0.182851809 GDVPTKRPPVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDVPTKRPPVLR 12 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 106.49 0.0010777 2153390000 1171550 838010 1114960 1169690 1301980 1171910 1611970 1310670 1447310 FALSE TRUE 1116173.153 923404.1717 1166082.019 1052110.539 1529044.9 1131326.463 1366034.371 1195900.787 1671751.443 0.66766693 0.552357335 0.697521168 0.629346272 0.914636507 0.676731261 0.817127676 0.715358011 1 20.67292893 -4.999998783 0.061415097 2.16429739 0.222731106 0.571805396 0.088099247 239.0575493 1.070243879 41.00963655 6.565531462 1.00E-05 4.999998783 -1.941566284 GDVTAEEAAGAS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK 266.44 2.74E-25 78343000 189962 222840 180277 246340 126362 208360 206190 218700 148071 TRUE FALSE 180982.8727 245547.6493 188542.8788 221577.4352 148399.4928 201144.441 174731.9286 199549.4686 171033.0944 1.058174579 1.435673313 1.102376586 1.295523746 0.867665368 1.176055673 1.021626423 1.166730154 1 17.38391598 2.769728456 24.99843396 1.056354513 1.233388361 0.30033888 0.132974776 784.7751768 629434.4141 0.036959933 0.03919893 588.4755935 -2.769728456 0.177033849 GDVTAEEAAGAS(ph)PAKANGQENGHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GDVTAEEAAGASPAKANGQENGHVK 25 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAKANGQENGHVK 163.01 1.12E-11 68433000 102750 87578 102260 111000 98825 97671 129170 118390 108660 TRUE FALSE 97893.21113 96502.29777 106948.7221 99842.06911 116060.0487 94288.62878 109462.7441 108023.144 125510.4378 0.779960717 0.768878664 0.852110183 0.795488175 0.924704357 0.751241334 0.872140565 0.860670601 1 16.93744782 -5 0.116062926 1.599143627 0.723666315 0.601808032 0.048276556 97.02508258 0.737536156 13.62545053 0.458586511 1.00E-05 5 -0.875477312 GDYPLEAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GDYPLEAVR 9 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 219.56 1.14E-06 4545020000 4885180 4906110 3574140 4322940 4477840 4355970 4448740 4387160 3726110 FALSE TRUE 4654267.223 5406048.187 3738017.854 3888389.858 5258773.878 4205121.667 3770003.006 4002997.013 4303936.108 1.081397843 1.256070734 0.868511465 0.903449717 1.221852218 0.977040913 0.87594307 0.930078168 1 22.03722523 3.740269643 24.9999757 0.965821062 1.16873429 0.373786043 0.107917828 146.1470378 2137858.449 0.028410453 0.048083062 5498.821766 -3.740269643 0.202913227 GEAAAERPGEAAVAS(ph)SPSKANGQENGHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.498)S(0.498)PS(0.005)KANGQENGHVK 65.377 0.0048132 140040000 137710 167620 136080 166970 82055 164320 147510 168260 81558 TRUE FALSE 131200.7212 184700.6686 142319.4026 150185.8584 96365.36602 158629.5572 125004.6403 153526.2624 94205.5981 1.392706207 1.960612451 1.510731904 1.594234965 1.02292611 1.683865507 1.32693431 1.629693622 1 16.52352517 -3.063679082 0.141811759 6.23E-11 1.756122456 0.291305808 0.247027117 82.18883771 1.207324326 26.76927898 1.527925634 0.000863616 3.063679082 1.756122456 GEADRDTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GEADRDTYR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;;; 218.94 4.66E-07 7930750000 5997010 5643045 4467776 5964035 5909159 5043950 5921421 5423706 5488449 FALSE TRUE 5713543.222 6218077.701 4672627.949 5364518.871 6939714.459 4869276.747 5017999.472 4948777.55 6339569.64 0.90125096 0.980835933 0.737057594 0.846196063 1.094666492 0.768076861 0.791536296 0.780617271 1 22.59595348 GEADRDTYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GEADRDTYRR 10 2 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;;;;; 181.44 1.06E-06 11121761000 1574317.6 1200687.5 1628492.8 1604229.4 2136980 1545154.3 2110161 1801115 2373392 FALSE TRUE 1499902.727 1323038.921 1703160.806 1442969.213 2509668.635 1491645.219 1788217.184 1643399.822 2741445.51 0.547121116 0.482606317 0.621263782 0.526353417 0.915454503 0.544109016 0.652289888 0.599464704 1 21.38650537 -5 0.148341024 2.390864044 0.475365299 0.53488209 0.116204363 99.88486326 0.884569804 41.09121196 0.566107168 1.00E-05 5 -1.915498745 GEAGVPAEFSIWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GEAGVPAEFSIWTR 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 213.38 2.61E-09 503770000 695150 568280 595680 649100 753540 619490 730330 676170 794850 FALSE TRUE 662291.6372 626188.3781 622992.5172 583851.2348 884957.1374 598036.906 618904.7451 616960.9702 918111.2785 0.721363143 0.68203974 0.678558832 0.635926438 0.963888755 0.651377366 0.674106461 0.671989316 1 19.8083095 -1.67111548 2.739753923 1.036714032 0.707425052 0.489169733 0.09313359 16580384.41 15161092.33 4264101.435 0.021151638 0.021324778 1.67111548 -0.32928898 GEAHLAVNDFELAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 209.39 6.70E-09 1102801000 1460310 1748370 1230870 1754870 1460720 1324380 1365040 1393370 1276260 FALSE TRUE 1391284.04 1926530.891 1287306.607 1578467.134 1715469.106 1278516.389 1156778.077 1271359.136 1474175.883 0.943770724 1.306852807 0.873238141 1.07074546 1.163680078 0.867275339 0.784694751 0.862420252 1 20.49147723 2.205141216 11.59328747 0.852592467 1.083021289 0.351227836 0.127717953 0.657119873 225.3672954 0.045379746 0.033636988 160.376679 -2.205141216 0.230428822 GEASEDLCEMALDPELLLLRDDGEEEFAGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEASEDLCEMALDPELLLLRDDGEEEFAGAK 31 1 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 90.37 0.00049863 6066800 15794 13842 13965 18145 12638 17889 19567 20830 14221 FALSE TRUE 15047.44892 15252.51554 14605.30906 16321.03013 14842.0632 17269.49944 16581.69478 19006.01477 16426.32005 0.91605721 0.928541237 0.889140661 0.99359017 0.903553757 1.051330998 1.009458888 1.157046418 1 14.00372169 2.106075808 1.553459717 1.066283174 0.923722305 0.576583522 0.052519987 0.255056431 1.172126682 0.028401463 0.015064185 127.6661636 -2.106075808 -0.142560868 GECEESWIHFI ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GECEESWIHFI 11 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 141.39 8.88E-05 43034000 132210 107340 115600 131280 146840 103420 144550 130340 139230 FALSE TRUE 125960.6953 118278.068 120900.3743 118083.485 172448.8495 99838.53947 122496.2427 118926.7386 160821.0773 0.783234993 0.735463722 0.751769459 0.734253787 1.072302539 0.620805066 0.761692713 0.739497214 1 17.29509697 -2.353871779 2.155451917 2.32510921 0.771213463 0.276594247 0.114280619 6031129.669 697702.4304 38930029.39 0.025285373 0.004427191 2.353871779 -1.553895747 GEDEEENNLEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEDEEENNLEVR 12 0 P04843;F8WF32 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 140.09 0.00013814 282670000 371110 324330 328720 403600 366540 355380 403540 369570 358510 FALSE TRUE 353568.3658 357379.5957 343792.1371 363029.3612 430464.4599 343073.1015 341972.5615 337208.4916 414105.8998 0.853811467 0.863014982 0.830203427 0.876658269 1.039503326 0.82846707 0.825809441 0.814304968 1 18.65964023 -2.250823853 2.349747078 1.523948776 0.865154888 0.297652282 0.064432858 12406211.23 3192007.654 34218227.69 0.016409871 0.005612756 2.250823853 -0.658793888 GEDS(ph)AEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_SK-BR-3_Trastuzumab_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 139.18 6.53E-11 40992000 128060 145910 103110 160910 69215 142630 127430 142070 64768 TRUE FALSE 122006.8576 160778.3949 107837.6955 144735.0211 81286.07409 137690.6873 107988.2131 129629.5976 74811.89065 1.630848472 2.149102148 1.441451279 1.934652631 1.086539498 1.840492015 1.443463227 1.732740565 1 16.19097997 -2.20399313 0.137002058 5.74E-14 2.022750386 0.33478252 0.292938258 54.12274376 0.998491846 19.57057405 2.072869492 0.006251826 2.20399313 2.022750386 GEDSVPDTVHHVVVPVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEDSVPDTVHHVVVPVNPK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 79.013 0.0053899 227270000 207810 233810 185120 249140 143700 196500 182600 217100 26800 FALSE TRUE 197987.2331 257635.5048 193607.9351 224095.9739 168761.2345 189695.1557 154741.0163 198089.5731 30956.00712 6.395761325 8.322633594 6.254292885 7.239175678 5.45164736 6.127894821 4.998739524 6.399067305 1 14.91793178 -0.011217348 0.325419189 1.00E-14 7.395458871 0.812234151 0.833080861 2.027330918 0.310676482 4.318342524 0.797298361 0.974501815 0.011217348 7.395458871 GEDVPS(ph)EEEEEEENGFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 GEDVPS(1)EEEEEEENGFEDR 242.09 2.27E-24 623020000 173190 193360 156310 181280 127860 166470 150430 162320 120540 TRUE FALSE 165003.6519 213063.6038 163476.9681 163057.39 150158.7435 160705.1022 127479.1407 148106.4003 139232.7276 1.185092433 1.530269553 1.174127455 1.171113953 1.078473044 1.154219306 0.91558316 1.063732665 1 17.08713884 3.036228985 1.156523272 1.016847277 1.351716063 0.554015174 0.108193892 0.297636576 0.848033566 0.044402733 0.055698354 1086.998601 -3.036228985 0.334868787 GEEDADGSKTQDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEEDADGSKTQDLFR 15 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 84.842 0.0074532 35884000 76125 60989 69667 69123 60657 76450 84356 82067 70536 FALSE TRUE 72526.72212 67203.84844 72861.30086 62174.62471 71235.5616 73802.51733 71485.9429 74880.77842 81474.36263 0.890178453 0.824846569 0.894285006 0.763118884 0.874331008 0.905837308 0.877404138 0.919071669 1 16.31405854 0.920778832 0.722054655 1.000077299 0.849459485 0.581663254 0.03949001 0.549514743 0.635644506 0.036062416 0.013760633 8.332567329 -0.920778832 -0.150617814 GEEDWLYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;;; 175.51 0.00012529 889895000 572761 509970 487440 597272 594819 474079 577820 543072 569636 FALSE TRUE 545687.7226 561936.5228 509789.6061 537233.0838 698555.2453 457661.5254 489662.9466 495517.7367 657972.2416 0.829347635 0.854042902 0.774788926 0.816498098 1.061678899 0.695563576 0.744200007 0.753098239 1 19.3276672 -1.342747831 7.685705952 1.000001637 0.815702504 0.25602517 0.098488792 2.69E-06 2.30E-07 0.092976594 0.021914599 0.045420527 1.342747831 -0.184299133 GEEGHDPKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEEGHDPKEPEQLR 14 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 130.98 3.54E-05 305800000 495040 437710 405140 506510 357130 471460 500340 517610 347600 FALSE TRUE 471640.4403 482313.1466 423716.0697 455594.6525 419413.3589 455133.222 424003.9436 472285.3244 401504.0327 1.174684192 1.201266008 1.055322077 1.134719991 1.044605595 1.133570736 1.056039066 1.176290363 1 18.61505495 8 0.126110026 1.002339468 1.625124638 0.335888909 0.054553827 82.64954526 0.709549321 0.287039058 9.113572559 100000000 -8 0.62278517 GEEGRPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 69.825 0.048261 41963000 116520 116290 100150 132350 79252 118050 109280 102130 95473 FALSE TRUE 111012.3305 128140.0832 104741.9766 119045.9266 93073.52371 113961.8989 92607.32894 93186.95577 110278.4652 1.006654656 1.161968322 0.949795378 1.079502932 0.843986389 1.033401205 0.839758957 0.845014986 1 16.75079157 2.921950154 1.244959973 0.901609195 1.074593675 0.325381783 0.088240441 0.410048542 1.327245046 0.034066657 0.038000584 835.5071177 -2.921950154 0.17298448 GEEGRPGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 67.563 0.034054 274823000 492735 426921 449071 522448 359657 507731 552454 528674 435671 FALSE TRUE 469444.3931 470424.7353 469661.3495 469930.5345 422381.0669 490148.1482 468166.9958 482380.5019 503232.6336 0.932857612 0.934805702 0.933288738 0.93382365 0.839335605 0.973999132 0.930319229 0.958563634 1 18.94086596 0.966535504 1.128362615 0.999356472 0.92386176 0.357322693 0.033193848 0.606189559 1.593853592 0.029122013 0.009250308 9.258390709 -0.966535504 -0.075494713 GEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 318.97 1.19E-58 3742870000 2503130 2626290 2112570 2789270 1144544 2795780 2455370 2873370 1208710 TRUE FALSE 2384812.006 2893911.937 2209433.424 2508887.28 1344152.111 2698961.438 2080758.211 2621762.49 1396150.574 1.708133815 2.072779249 1.582518008 1.797003366 0.962755835 1.933144955 1.490353727 1.877850813 1 20.41302311 -2.640129809 0.158199267 1.26E-17 1.927239154 0.301367348 0.310320552 64.28842552 1.191441429 25.13895236 1.429759634 0.002290183 2.640129809 1.927239154 GEEHCGHLIEAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEEHCGHLIEAHK 13 0 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ; 152.4 1.57E-05 126161000 178585 228100 145004 244850 128183 167289 147884 142262 18375.6 FALSE TRUE 170143.641 251343.6493 151652.5768 220237.2128 150538.0746 161495.74 125321.5797 129804.7851 21225.1942 8.016117044 11.8417597 7.144932358 10.37621662 7.0924239 7.608681385 5.904378474 6.115599409 1 14.37349013 0.946398408 0.397036809 0.470458122 10.01111527 0.764101244 1.390500629 0.592187716 0.248220253 2.024386221 1.030990472 8.838903825 -0.946398408 9.540657152 GEEIYS(ph)MDEGIRT(ph)RSKSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEEIYSMDEGIRTRSKSAK 19 3 Q96P70 Q96P70 IPO9 Importin-9 2 GEEIY(0.023)S(0.857)MDEGIRT(0.374)RS(0.374)KS(0.374)AK 48.547 0.065155 371300000 133310 139480 148120 131820 592970 91743 162500 219310 481830 TRUE FALSE 127008.7005 153693.1706 154911.4485 118569.2032 696383.7803 88565.91691 137707.6405 200106.0538 556549.7356 0.228207278 0.276153524 0.278342507 0.21304332 1.25125166 0.159133877 0.247430969 0.359547478 1 19.08615109 -2.160112929 2.173786432 2.428602533 0.359003388 0.275832722 0.316277963 19551273.63 4288910.192 137545836.7 0.076515347 0.006916511 2.160112929 -2.069599145 GEEKPAGHRTS(ph)PVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.233)S(0.767)PVAK;GEEKPAGHRT(0.083)S(0.917)PVAK;GEEKPAGHRT(0.073)S(0.927)PVAK 136.68 1.11E-05 1072600000 1948350 2195950 1756640 2338920 1107260 2191090 1990120 2214670 1066600 TRUE FALSE 1856255.357 2419719.802 1837183.682 2103807.318 1300365.793 2115212.004 1686490.643 2020741.754 1232002.881 1.506697254 1.964053688 1.491217034 1.707631817 1.055489248 1.716888846 1.368901542 1.640208628 1 20.2325742 -2.756101183 0.134572024 1.01E-12 1.852263833 0.349331884 0.238953831 67.56964991 1.033794816 22.00844917 1.733413661 0.001753472 2.756101183 1.852263833 GEEVEGAGWMPGREPT(ph)T(ph)HAEAQGDEGDGEEGLQRTRITEEQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEEVEGAGWMPGREPTTHAEAQGDEGDGEEGLQRTRITEEQDK 43 3 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 2 GEEVEGAGWMPGREPT(0.662)T(0.662)HAEAQGDEGDGEEGLQRT(0.338)RIT(0.338)EEQDK 49.193 0.01919 125400000 65757 51894 59257 61468 24740 69669 68619 72214 21564 TRUE FALSE 62648.79693 57182.0576 61973.99206 55289.11986 29054.64817 67256.34506 58149.91128 65890.55933 24908.03499 2.515204309 2.295727368 2.488112454 2.219730295 1.166476929 2.700186711 2.334584455 2.645353572 1 14.60432359 3.007148578 22.78544303 2.090637892 2.407660743 0.105805278 0.55905683 171.2313252 545767.3599 0.152059271 0.181220681 1016.596424 -3.007148578 0.317022851 GEFKDEEETVTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEFKDEEETVTTK 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 150.57 1.45E-06 0 371290 341570 319270 403140 215190 388830 418270 421540 253050 FALSE TRUE 353739.8575 376376.3713 333908.8453 362615.6013 252719.0679 375364.7196 354455.2294 384627.7229 292291.7016 1.210228876 1.287673818 1.142382228 1.240594924 0.864612531 1.284212715 1.212676335 1.31590367 1 18.15704934 -2.326836165 2.144957862 0.000205916 1.198998172 0.187160523 0.12730298 1587405.703 273615.7752 7689109.289 0.029302375 0.00471155 2.326836165 1.198792256 GEFSAS(ph)PMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK 204 2.05E-07 5375430000 7967520 7225430 6867460 8026950 5987164 7718210 8843850 8726700 7304130 TRUE FALSE 7590911.12 7961709.532 7182339.834 7220065.736 7031323.506 7450926.452 7494558.254 7962543.885 8436817.176 0.899736353 0.943686389 0.851309171 0.855780751 0.833409491 0.883144235 0.88831583 0.943785283 1 23.00826741 1.028300882 2.41251323 0.999603293 0.883384619 0.642832722 0.030216342 0.209647734 2.64352531 0.032754512 0.008935588 10.67335322 -1.028300882 -0.116218674 GEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GEGDAPFS(0.001)EPGT(0.007)T(0.008)S(0.029)T(0.03)QRPS(0.948)S(0.972)PET(0.005)ATK 82.126 0.0091216 76520000 107660 133420 94744 140670 86019 116980 110000 113760 79827 TRUE FALSE 102571.1252 147015.6497 99088.10611 126529.5843 101020.6864 112928.9533 93217.47971 103798.5713 92206.16346 1.112410725 1.594423238 1.074636471 1.372246492 1.09559581 1.224744085 1.01096799 1.1257227 1 16.49257557 2.378265949 0.825633197 1.034760731 1.326112001 0.278255935 0.154435739 0.684818098 0.91701204 0.107381064 0.071218788 238.9273954 -2.378265949 0.29135127 GEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGT(0.001)T(0.001)S(0.008)T(0.007)QRPS(0.563)S(0.417)PET(0.002)ATK;GEGDAPFSEPGT(0.008)T(0.008)S(0.008)T(0.008)QRPS(0.546)S(0.413)PET(0.009)ATK 99.7 0.0031417 703900000 452530 457040 367160 503570 285204 453320 429450 442590 272638 TRUE FALSE 431139.8037 503612.8956 383994.6492 452950.1869 334943.4873 437621.4147 363929.5151 403834.4733 314917.3086 1.369057184 1.599190905 1.219350727 1.438314677 1.063591864 1.38963913 1.155635163 1.282350834 1 18.26461353 2.819333268 0.148042292 0.868958649 1.770143311 0.429400979 0.13589386 8.462136047 0.526856234 0.942499649 2.047785845 659.6799242 -2.819333268 0.901184662 GEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGTTSTQRPS(0.289)S(0.711)PETATK;GEGDAPFSEPGTTSTQRPS(0.289)S(0.711)PETATK;GEGDAPFSEPGTTS(0.001)T(0.002)QRPS(0.217)S(0.78)PETATK;GEGDAPFSEPGTTS(0.002)T(0.003)QRPS(0.069)S(0.924)PET(0.003)ATK;GEGDAPFSEPGTTSTQRPS(0.007)S(0.993)PETATK;GEGDAPFSEPGTT(0.001)S(0.003)T(0.003)QRPS(0.218)S(0.775)PET(0.001)ATK 237.5 3.42E-45 8339970000 6602310 6823540 5593390 7324620 4316120 6602990 6064460 6558360 4289730 TRUE FALSE 6290231.891 7518866.484 5849852.464 6588335.282 5068849.961 6374326.801 5139215.246 5984075.23 4954959.419 1.26948202 1.517442596 1.180605524 1.32964465 1.022985161 1.286453886 1.037186142 1.207694095 1 22.24044181 3.14370398 1.345514838 1.119557507 1.382996545 0.40584423 0.122649477 0.345476632 1.312948208 0.040609091 0.055430416 1392.207535 -3.14370398 0.263439038 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_SK-BR-3_Trastuzumab_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(0.996)PVAPAPVPS(0.004)R;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR 284.51 1.91E-81 789361000 263628 408936 244696 394519 207618 291346 257369 325505 151590 TRUE FALSE 251166.8269 450607.0433 255915.5536 354861.2006 243826.5135 281256.615 218102.6321 297002.0566 175097.803 1.434437341 2.57345915 1.461557765 2.026645649 1.392516121 1.606282947 1.245604619 1.696206643 1 17.41780146 2.647673808 1.140059565 1.34919537 1.956105168 0.27805407 0.370799139 0.549584973 1.471383896 0.179538411 0.15191772 444.2974373 -2.647673808 0.606909798 GEGERPAQNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GEGERPAQNEK 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;;;; 186.76 3.54E-06 7958493000 4873910 4096303 4300776 5277665 4109414 5007978 5889649 5351620 4916070 FALSE TRUE 4643529.933 4513720.933 4497970.834 4747144.087 4826094.501 4834550.466 4991074.874 4883003.782 5678429.028 0.817749048 0.794889028 0.792115356 0.835996024 0.84989959 0.851388728 0.878953466 0.859921601 1 22.43706042 -0.229400248 0.237659156 1.080796517 0.782752625 0.9305139 0.015459813 2.074059105 0.173485997 0.165742288 0.03273397 0.589657399 0.229400248 -0.298043892 GEGPAIPGDT(ph)PPPTPR ddPTM_SK-BR-3_Trastuzumab_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 184.99 1.94E-08 519079000 1146050 1054210 1081270 1221960 1292780 1120310 1273710 1233600 1330490 TRUE FALSE 1091878.488 1161635.198 1130847.299 1099126.259 1518240.423 1081513.384 1079382.146 1125579.444 1536815.594 0.710481135 0.755871558 0.735837991 0.715197232 0.987913207 0.703736602 0.702349814 0.732410218 1 20.55151263 -1.370697518 2.98602482 1.003264346 0.751955501 0.452489235 0.084452648 11904713.37 14406779.78 336512.3679 0.02048279 0.042589494 1.370697518 -0.251308845 GEGPGEAGGPLT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEGPGEAGGPLTPR 14 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR 118.16 0.0029218 167774000 490830 378500 432050 496920 477750 457770 513330 449860 498980 TRUE FALSE 467629.4386 417069.5803 451859.9199 446968.6575 561069.4487 441917.3101 435012.0805 410467.8735 576359.27 0.811350598 0.723627782 0.783990027 0.775503546 0.973471718 0.766739312 0.754758539 0.71217363 1 19.13660886 -2.067272792 2.214752898 1.302639995 0.785233346 0.461896162 0.071968924 10853955.35 3311865.255 16596927.82 0.01791128 0.008564997 2.067272792 -0.517406648 GEGQLGPAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEGQLGPAER 10 0 P13639 P13639 EEF2 Elongation factor 2 0 142.83 8.16E-05 59919000 86802 86179 76273 89776 89434 82913 88601 91790 98856 FALSE TRUE 82699.04148 94960.73808 79770.19249 80751.54592 105031.2613 80041.70202 75083.29018 83752.38099 114186.0836 0.72424799 0.831631448 0.6985982 0.707192535 0.919825411 0.700975981 0.657552022 0.733472752 1 16.80102731 -1.047205811 4.999313482 1.000004367 0.746801098 0.524169633 0.075848962 3.68E-06 7.01E-07 0.073132673 0.017237239 0.089700361 1.047205811 -0.253203269 GEGS(ph)DSKESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEGSDSKESPK 11 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 GEGS(0.999)DS(0.001)KESPK 88.282 0.0079304 140520000 428770 432720 397070 505930 221750 496430 489110 532300 265920 TRUE FALSE 408502.8918 476814.66 415276.0523 455072.9552 260423.1298 479238.5046 414487.2864 485688.9901 307157.5155 1.329945944 1.552345738 1.351997042 1.48156217 0.847848796 1.560236948 1.349429089 1.581237527 1 18.22861916 -1.958476634 2.697551667 0.702185706 1.385446529 0.244326703 0.210946842 51005480.53 52050828.25 95829439.86 0.046301537 0.01100331 1.958476634 0.683260822 GEGYAKPNEGAIVEVALEGYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEGYAKPNEGAIVEVALEGYYK 22 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 207.17 7.66E-23 339460000 984700 1015090 860000 1136110 648655 975640 980030 1059180 703684 FALSE TRUE 938155.1825 1118528.825 899431.8507 1021906.064 761780.2266 941853.3422 830508.424 966432.5841 812807.7208 1.154215392 1.376129675 1.106573951 1.257254377 0.937220707 1.15876525 1.021777233 1.189005172 1 19.63255458 2.76533081 24.78130993 1.067383101 1.234773017 0.390638134 0.100064931 619.5980457 573564.1681 0.027806649 0.029486084 582.5467849 -2.76533081 0.167389916 GEGYAKPNEGAIVEVALEGYYKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEGYAKPNEGAIVEVALEGYYKDK 24 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 240.41 8.58E-38 502370000 1345740 854200 1276510 1178260 817950 1330570 1732550 1547580 1058340 FALSE TRUE 1282129.537 941243.9511 1335039.246 1059819.066 960600.221 1284492.027 1468217.677 1412065.691 1222461.962 1.048809351 0.76995766 1.092090623 0.866954637 0.785791502 1.050741919 1.201033425 1.155099901 1 20.22135814 2.025671658 7.909901032 1.137501887 0.911859996 0.420774005 0.111830014 0.157062001 39.17380874 0.039586583 0.028804956 106.0893181 -2.025671658 -0.225641891 GEHPEGDPGEVPAPS(ph)PQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEHPEGDPGEVPAPSPQER 19 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 GEHPEGDPGEVPAPS(1)PQER 83.039 0.0023213 138850000 80340 77545 70247 86183 81161 69364 74786 74863 65408 TRUE FALSE 76542.48742 85446.92366 73467.89443 77519.7211 95315.4527 66961.90729 63376.02216 68307.59885 75551.13858 1.013121561 1.130981283 0.972426039 1.026056292 1.261601804 0.886312351 0.838849332 0.904124016 1 16.20516588 2.133910907 24.99950648 0.887712286 1.074126729 0.481949075 0.088205843 7.603356747 1798.154849 0.030732631 0.022697558 136.116542 -2.133910907 0.186414443 GEHSIVYLKPSYAFGSVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEHSIVYLKPSYAFGSVGK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 300.12 4.20E-50 1674780000 4130600 4115600 3201400 4660600 2948700 3824700 4075000 4103600 2773100 FALSE TRUE 3935354.724 4534984.319 3348187.357 4192107.633 3462952.346 3692249.68 3453283.907 3744267.029 3203138.185 1.228593491 1.415794155 1.045283457 1.308750167 1.08111238 1.152697594 1.078093953 1.16893709 1 21.61105461 2.995167764 0.338025901 1.023199702 1.372396793 0.356104153 0.101470798 1.97956521 0.413961188 0.107659266 0.257073522 988.9350374 -2.995167764 0.349197091 GEIKDSSPSSSPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEIKDSSPSSSPSPK 15 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 GEIKDSSPS(0.003)S(0.008)S(0.008)PS(0.981)PK 83.776 0.0051983 235760000 295320 168940 243130 247320 152700 295790 332670 289760 184490 TRUE FALSE 281360.8089 186155.1781 254277.751 222458.9237 179330.8317 285546.7181 281915.0816 264387.0783 213099.767 1.320324339 0.873558806 1.19323336 1.043919132 0.841534621 1.339967294 1.32292534 1.240672771 1 17.70116949 2.20868546 24.99999478 1.263428119 1.059826534 0.193741698 0.16585372 270.4271749 226296.081 0.058070266 0.042893393 161.6908558 -2.20868546 -0.203601585 GEKPNPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GEKPNPLR 8 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;;;;; 92.062 0.010984 4429960000 7141790 5672300 5804870 7118100 6263180 6304640 7541230 7003920 6950020 FALSE TRUE 6804211.74 6250313.819 6071029.031 6402575.064 7355476.609 6086308.736 6390676.859 6390619.635 8027793.606 0.847581798 0.778584269 0.75625126 0.797551031 0.916251335 0.758154611 0.796068904 0.796061776 1 22.93657209 -0.985104053 4.564610231 1.000004552 0.804663588 0.630001946 0.046760876 0.01376006 27037905.64 287.6188251 0.010402153 0.103489419 0.985104053 -0.195340964 GELS(ph)EEELPYYVELPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR 140.81 6.79E-07 31083000 26123 35196 26345 31853 29558 34000 29083 28716 27160 TRUE FALSE 24888.21756 38782.51241 27552.94431 28651.07592 34712.90584 32822.57147 24645.8542 26201.47481 31371.83409 0.793330014 1.236220755 0.878270114 0.913273857 1.106499089 1.046243308 0.785604506 0.835191042 1 14.93718226 1.745448604 24.99999332 0.856382198 1.004418445 0.150296291 0.133652028 2.235623293 8138.882594 0.058831225 0.032624936 55.64787751 -1.745448604 0.148036248 GEMMDLQHGSLFLQTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEMMDLQHGSLFLQTPK 17 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 193.9 1.05E-10 339636000 408630 421110 359510 461140 627310 328204 431750 380903 452660 FALSE TRUE 389314.8697 464021.5878 375993.8891 414785.3311 736712.6654 316838.2132 365878.6079 347549.114 522856.2009 0.744592622 0.887474581 0.719115291 0.793306707 1.409015833 0.605975816 0.69976909 0.664712618 1 18.9960547 -0.978615805 3.988722718 1.00001511 0.813981138 0.062670566 0.224177757 57401277.66 118025450.9 12587.59095 0.051659924 0.105047131 0.978615805 -0.186033972 GEMMDLQHGSLFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 242.07 1.82E-17 7228506000 5953570 5594028 4714047 7186771 9257557 4875879 7597481 6899887 8408692 FALSE TRUE 5672156.545 6164065.813 4930190.718 6464343.125 10872072.01 4707026.088 6438345.736 6295696.316 9712669.01 0.58399566 0.634641807 0.507604111 0.665557852 1.119370175 0.484627457 0.662881205 0.648194261 1 23.21143637 -5 0.230106396 2.808392437 0.618659258 0.272310172 0.173486574 220.714844 2.207329205 186.4615343 0.286714457 1.00E-05 5 -2.189733179 GENLEHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GENLEHLR 8 0 C9JXZ5;Q9BV40;B8ZZT4 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ; 164.71 0.0003285 505260000 822430 650150 631630 778200 1013640 701460 969190 765310 938530 FALSE TRUE 783555.3638 716401.0242 660590.8603 699973.8575 1190418.495 677168.2643 821322.2651 698295.3992 1084072.439 0.722788751 0.660842392 0.609360442 0.645689192 1.098098662 0.624652228 0.757626737 0.644140902 1 20.04802973 GEPGRPALYFCGSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GEPGRPALYFCGSIR 15 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 124.2 8.95E-05 647730000 721150 708630 549350 731220 537330 707080 846520 830710 647380 FALSE TRUE 687062.6687 780840.2026 574538.2409 657716.3764 631040.1819 682593.6423 717367.8266 757968.6285 747772.384 0.918812574 1.04422177 0.768333056 0.87956762 0.843893403 0.912836121 0.959339823 1.013635492 1 19.51223967 1.535369398 2.725742758 1.005446055 0.906302069 0.308068655 0.069163385 0.376500751 6.019697749 0.054938146 0.019974911 34.30594589 -1.535369398 -0.099143986 GEPNVS(ph)YICSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.963)Y(0.037)ICSR;GEPNVS(0.676)Y(0.324)ICSR;GEPNVS(0.546)Y(0.454)ICSR;GEPNVS(0.505)Y(0.495)ICSR 207.42 2.42E-08 5181410000 644630 583100 656260 676210 586470 697450 742260 668870 616609 TRUE FALSE 614159.6174 642518.5529 686350.1701 608236.0861 688750.1823 673297.1316 629014.6045 610300.1969 712229.5745 0.862305694 0.902122821 0.963664238 0.853988809 0.967033955 0.945337228 0.883162715 0.856886907 1 19.44198282 4.279867124 2.660064555 0.918253149 0.86669802 0.130445069 0.048430831 0.548286807 7.54859754 0.011424264 0.039726075 19048.77814 -4.279867124 -0.051555129 GEPNVSY(ph)ICSR ddPTM_SK-BR-3_Trastuzumab_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(0.176)Y(0.824)ICSR;GEPNVS(0.243)Y(0.757)ICSR;GEPNVS(0.079)Y(0.921)ICSR;GEPNVS(0.337)Y(0.663)ICSR;GEPNVS(0.429)Y(0.57)ICS(0.001)R;GEPNVS(0.297)Y(0.703)ICSR 238.86 1.30E-14 8623020000 1626850 1365830 1317310 1553210 1472610 1554950 1779740 1556240 1549800 TRUE FALSE 1549952.025 1505009.63 1377709.966 1397078.38 1729432.718 1501101.692 1508207.976 1419967.375 1790135.069 0.865829653 0.840724064 0.769612299 0.780431826 0.966090631 0.838541023 0.842510715 0.793218009 1 20.77163701 GEQGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GEQGLLR 7 0 P55327-2;P55327-4;P55327-3;E5RFR7 P55327-2 TPD52 0 ;;; 143.02 0.0056997 1089010000 1911490 1709300 1070410 1398740 1923450 1257040 1741380 1502970 1648160 FALSE TRUE 1821137.656 1883479.613 1119489.357 1258135.998 2258899.071 1213508.39 1475700.498 1371361.979 1903748.235 0.956606353 0.989353308 0.588044856 0.6608731 1.186553468 0.63743113 0.775155281 0.720348392 1 20.86041127 3.814547055 24.99995401 0.786408465 0.97298054 0.143921884 0.178905858 202.6260332 66663.41205 0.042910236 0.077357523 6524.497296 -3.814547055 0.186572075 GES(ph)ENAGTNQETR ddPTM_SK-BR-3_Trastuzumab_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 321.25 4.85E-51 818818000 754047 719165 622146 829717 617992 706143 717263 666233 576346 TRUE FALSE 718404.6927 792448.7311 650672.0095 746312.2708 725769.6091 681689.0908 607831.3559 607894.1066 665722.7941 1.079134888 1.190358417 0.977391814 1.121055607 1.090197926 1.023983401 0.913039724 0.913133983 1 19.34456204 2.008504138 2.7697253 0.93446728 1.100472154 0.581510553 0.057426473 0.171396568 2.520369774 0.027571918 0.015941635 101.9774477 -2.008504138 0.166004874 GESAADS(ph)DGWDSAPSDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GESAADSDGWDSAPSDLR 18 0 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;A0A087WVQ2;Q9BUL5-2 I3L4Q4 PHF23 PHD finger protein 23 1 GES(0.001)AADS(0.999)DGWDSAPSDLR 143.28 1.12E-07 39733000 48789 48437 45063 62261 59446 49159 51081 57037 62560 TRUE FALSE 46482.84066 53372.78537 47129.18312 56002.40599 69813.36358 47456.6115 43287.65528 52042.53791 72261.48529 0.64325886 0.73860626 0.652203355 0.774996608 0.966121348 0.656734515 0.59904187 0.720197457 1 16.14093929 -2.345618413 2.064823876 2.48974364 0.711995683 0.427807663 0.101891336 4697956.444 532980.2064 32647114.32 0.025291028 0.00451213 2.345618413 -1.777747957 GESAEDKEHEEGRDS(ph)EEGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 227.25 2.01E-25 3247350000 2025932 2374099 1699193 2315929 1468795 2275095 1874529 2088360 1035955 TRUE FALSE 1930170.209 2616022.387 1777102.68 2083127.417 1724952.383 2196307.89 1588535.173 1905492.127 1196605.61 1.613037907 2.186202676 1.485119796 1.740863822 1.441537937 1.835448431 1.327534452 1.592414502 1 20.1905163 0.386244099 0.211411526 0.704505197 1.980905786 0.496216178 0.222971357 4.585716545 0.484944735 1.726345814 0.66504795 2.433571433 -0.386244099 1.276400589 GESDDFHMDFDS(ph)AVAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GESDDFHMDFDSAVAPR 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GESDDFHMDFDS(1)AVAPR;GESDDFHMDFDS(1)AVAPR 224.97 1.64E-15 105316000 120840 113876 134195 142976 158036 134032 155696 150048 161275 TRUE FALSE 115128.1327 125480.0939 140347.9735 128603.7808 185597.4284 129390.4382 131941.7156 136909.0017 186284.7033 0.618022471 0.673593116 0.753405787 0.690361466 0.996310621 0.694584343 0.708279925 0.734944948 1 17.50714969 -5 0.097537882 1.789882931 0.543030782 0.438403045 0.097851406 188.0953474 1.255050507 31.21508762 1.769337321 1.00E-05 5 -1.246852149 GESDPAYQQYQDAANNLREDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GESDPAYQQYQDAANNLREDYK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 150.94 4.77E-08 91965000 232760 222440 214380 226410 149240 239750 229980 249810 163300 FALSE TRUE 221757.8961 245106.8889 224209.5351 203650.8366 175267.4087 231447.3974 194892.3271 227935.3121 188623.73 1.175662766 1.299448849 1.188660277 1.079667106 0.929190663 1.227032237 1.033233343 1.208412707 1 17.52515166 3.352093488 3.97982105 1.081196449 1.238309221 0.348879208 0.092720967 0.216603226 6.323741046 0.024024623 0.033043304 2249.538797 -3.352093488 0.157112772 GESEDDFWWCIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 270.61 1.06E-31 559795000 777900 852491 762794 881958 792089 786744 843333 861775 777259 FALSE TRUE 741130.2086 939360.8021 797768.8594 793301.9062 930229.0708 759498.858 714667.062 786313.4124 897792.356 0.825502917 1.046300735 0.888589499 0.883614013 1.036129417 0.845962714 0.796027118 0.875829926 1 19.77602229 GESEFDSFRQSLPVFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GESEFDSFRQSLPVFEK 17 1 Q9H6S0;D6RA70 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 0 ; 78.069 0.0098809 164627000 182346 142160 160118 186712 154421 163347 227463 191177 197335 FALSE TRUE 173726.866 156646.2656 167459.5687 167943.355 181351.9735 157690.2524 192759.3417 174436.5284 227936.704 0.762171528 0.687235811 0.734675749 0.736798208 0.795624269 0.691815972 0.845670479 0.765284947 1 17.79827373 -0.358382405 0.34922245 1.074391856 0.718389667 0.781928972 0.042285003 2.944273427 0.401484109 0.304671036 0.032700973 0.438144732 0.358382405 -0.356002189 GESENAGTNQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 177.16 3.65E-05 11508000 21865 22216 19521 20910 23413 24314 21657 21492 26204 FALSE TRUE 20831.48478 24479.83566 20416.05716 18808.08707 27496.21979 23472.00008 18352.82689 19610.04654 30267.58249 0.688244091 0.80878067 0.674518924 0.621393766 0.908437924 0.775483146 0.606352585 0.647889423 1 14.88548583 -0.953570555 4.137325166 1.000012763 0.71887746 0.480235219 0.092694398 3320064.804 1605035.222 365.5347647 0.021578257 0.111283159 0.953570555 -0.281135302 GESFYQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GESFYQDR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 180.87 0.00055093 2134490000 2038130 1714900 1728020 2033980 2250570 1799150 2257560 1941620 2277050 FALSE TRUE 1941791.634 1889650.26 1807251.426 1829520.466 2643068.695 1736844.984 1913127.759 1771601.46 2630163.284 0.738277979 0.718453592 0.687125182 0.695591972 1.004906696 0.660356334 0.727379844 0.673570903 1 21.32672094 -1.246078803 3.763601575 1.000380449 0.737375339 0.413765057 0.097926075 10515812.67 7000917.572 30156.06025 0.021300504 0.056744163 1.246078803 -0.26300511 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK 34 0 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;;;;;;; 400.68 4.65E-168 300705900 244420.7 187483.7 233947.5 264025.1 309024.7 229366.8 371609 308696.5 84929.9 FALSE TRUE 232867.4179 206588.5022 244674.2243 237484.7953 362918.5098 221423.7702 314913.222 281665.398 98100.39513 2.37376636 2.105888584 2.494120681 2.420834238 3.699460225 2.257113949 3.210111657 2.871195346 1 16.58197133 2.979642481 24.52164357 2.782244373 2.306342298 0.000522065 0.712149562 1346.029333 1621361.547 0.188238267 0.202012601 954.2067434 -2.979642481 -0.475902076 GEVPGGSAHYGGPS(ph)PEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEVPGGSAHYGGPSPEKK 18 1 O94762-4;O94762;J3KS37 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 GEVPGGSAHYGGPS(1)PEKK 136.14 3.25E-06 184190000 299870 284660 300080 358790 179650 365570 398860 405270 206340 TRUE FALSE 285695.7394 313667.1776 313838.9648 322723.7475 210980.9031 352910.2192 338006.5814 369782.4103 238338.1534 1.19869914 1.316059444 1.316780215 1.35405827 0.885216656 1.480712233 1.418180751 1.551503211 1 17.86265039 GEVPPKET(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK 95.631 0.011786 907000000 2252730 2293960 2083570 2558330 1100430 2501050 2274160 2700270 1190250 TRUE FALSE 2146247.917 2527717.132 2179103.745 2301161.808 1292344.644 2414438.011 1927195.124 2463820.044 1374827.891 1.56110298 1.838569866 1.585001119 1.673781731 0.940004674 1.756174738 1.401771914 1.792093439 1 20.39081959 -3.063016974 0.201659737 8.97E-16 1.682599346 0.295375859 0.262439024 70.57633733 1.41038957 31.65787233 0.608359804 0.000864934 3.063016974 1.682599346 GEVQVSDKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GEVQVSDKER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;;;; 207.88 1.13E-07 2891660000 3413980 2787570 2798090 3149260 3010710 2983780 3998410 3292990 3311250 FALSE TRUE 3252607.931 3071626.552 2926385.194 2832690.402 3535776.871 2880450.95 3388379.119 3004638.338 3824741.738 0.850412434 0.803093846 0.765119685 0.74062266 0.924448528 0.753109922 0.885910566 0.785579405 1 21.8669309 -3.11018952 0.336465682 1.453060426 0.808054751 0.494536335 0.059012603 73.56005729 2.047807759 23.56529068 0.043815283 0.000775908 3.11018952 -0.645005676 GEVTAADLFNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GEVTAADLFNSR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 121.02 0.00089257 71534000 119490 119940 117640 134830 133180 116220 141200 128340 129010 FALSE TRUE 113841.9445 132162.0224 123033.9104 121276.6322 156406.5498 112195.2723 119657.3467 117101.8692 149016.2119 0.763956774 0.88689694 0.825641108 0.813848579 1.049594187 0.752906485 0.802982073 0.785833083 1 17.18510977 4.66528575 3.368652332 0.852819088 0.758931256 0.088594524 0.094747138 0.713144744 13.25789506 0.021387038 0.152956985 46268.53512 -4.66528575 -0.093887833 GEWIKPGAIVIDCGINYVPDDKKPNGR ddPTM_SK-BR-3_Trastuzumab_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" 0 236.03 2.23E-45 497920000 395690 387060 340480 431670 217070 439350 409060 476670 250840 FALSE TRUE 376986.5179 426501.8541 356091.3448 388277.7115 254926.9393 424135.1993 346650.3841 434930.2478 289738.9861 1.301124584 1.472020938 1.229007354 1.34009481 0.879850319 1.463852708 1.19642299 1.501110547 1 18.1443943 -2.095543139 2.680577123 0.458735087 1.300126493 0.213345334 0.179750271 3564488.657 6300071.821 11642516.85 0.040009086 0.008025218 2.095543139 0.841391406 GEWKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GEWKPR 6 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 130.84 0.014218 10537820000 20420630 17256360 15511100 20620340 18282380 19115810 23895750 21380790 19308060 FALSE TRUE 19455387.29 19014802.7 16222299.28 18547544.25 21470821.28 18453824.71 20250014.46 19508574.68 22302255.33 0.872350666 0.852595507 0.727383802 0.831644332 0.962719732 0.827442087 0.907980568 0.874735509 1 24.41068628 0.492714381 0.409320291 1.01357991 0.834024607 0.421302673 0.05715936 2.371983555 0.763993086 0.126749247 0.040380534 3.109670552 -0.492714381 -0.179555303 GEYVLLEAALTDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEYVLLEAALTDLR 14 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ;; 197.56 5.41E-08 41439000 86738 61347 63651 96771 115293 65641 99648 81768 107448 FALSE TRUE 82638.06664 67598.32905 66569.46131 87043.39523 135400.0627 63367.83571 84444.86744 74607.96044 124110.4871 0.665842739 0.544662507 0.536372573 0.701337955 1.090963914 0.510575997 0.680400742 0.601141468 1 16.9212655 3.097116528 6.36067002 0.744530331 0.587609394 0.191696254 0.174964804 0.396167542 21.99622998 0.048691224 0.05843182 1250.594539 -3.097116528 -0.156920937 GEYWECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GEYWECK 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;; 117.17 0.01231 512010000 796080 646361 621248 782730 708667 728930 777410 744280 725560 FALSE TRUE 758450.8761 712225.9208 649732.8353 704048.4933 832258.3004 703686.9713 658801.8264 679106.8975 838076.1392 0.904990419 0.849834386 0.775267073 0.840077005 0.993058102 0.839645634 0.786088275 0.810316469 1 19.67672179 -0.798621711 6.678134073 0.999999999 0.849733539 0.364309697 0.062307443 9.12E-10 2.73E-10 0.061218393 0.014429313 0.158993104 0.798621711 -0.15026646 GFAFISFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFAFISFHR 9 0 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 160.88 6.50E-05 81828000 204960 113150 68829 84088 291030 82060 254480 153890 228630 FALSE TRUE 195271.947 124680.1136 71984.87773 75635.31448 341785.5399 79218.24162 215654.4022 140414.5758 264084.7727 0.739429029 0.472121555 0.272582463 0.286405436 1.294226609 0.299972773 0.816610515 0.531702659 1 18.01064159 GFAFVQYVNER ddPTM_SK-BR-3_Trastuzumab_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 ; 244.61 1.60E-15 2049610000 1830570 1165330 856520 1006130 2156470 994980 1821850 1232420 2046940 FALSE TRUE 1744042.584 1284078.452 895792.2892 904991.9009 2532557.685 960523.5931 1543893.322 1124502.771 2364369.001 0.737635531 0.543095621 0.37887161 0.382762547 1.071134702 0.406249444 0.652983236 0.475603753 1 21.17302378 -1.938868205 2.743743325 1.280818858 0.586782455 0.283607068 0.209084977 66206932.97 46129087.02 119277799.2 0.045511743 0.011511497 1.938868205 -0.694036404 GFAFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 112.88 0.061925 792590000 554230 375710 283830 348090 638750 312370 596920 443250 605280 FALSE TRUE 528032.6463 413995.2761 296843.8862 313099.3319 750147.7978 301552.5486 505848.8908 404436.6802 699143.7311 0.755256212 0.592146161 0.424582061 0.447832567 1.072952191 0.43131696 0.72352632 0.5784743 1 19.41522955 -1.594870774 2.396452432 1.039253019 0.632399131 0.265352309 0.194279304 5379443.425 4397432.814 1327897.415 0.046036255 0.025417289 1.594870774 -0.406853888 GFAFVTFDDHDSVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 257.04 8.96E-25 1321449000 3071076 3421975 2498863 3813662 3001552 2675534 2978878 2988547 2109315 FALSE TRUE 2925912.324 3770678.143 2613438.34 3430305.45 3525021.718 2582879.587 2524395.45 2726853.981 2436416.797 1.200907959 1.547632633 1.072656511 1.407930472 1.446805704 1.060114012 1.036109853 1.119206691 1 21.21632953 2.224675547 24.81946645 1.05475869 1.343322745 0.526781817 0.132369909 160.3172171 286563.8326 0.04641971 0.034459131 167.7550284 -2.224675547 0.288564055 GFAFVTFDDHDSVDKIVIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 267.55 4.14E-37 1283661000 1424558 923606 1472291 1291989 1404962 1498975 2127168 1761177 1409864 FALSE TRUE 1357221.967 1017722.501 1539796.999 1162115.811 1649986.928 1447065.12 1802629.453 1606959.005 1628498.509 0.833419226 0.624945308 0.945531722 0.713611836 1.013195234 0.888588545 1.106927298 0.986773397 1 20.63511097 2.654256524 1.096335729 1.033095457 0.749790143 0.502318767 0.102548899 0.329934592 0.819991733 0.049731095 0.042177211 451.0830667 -2.654256524 -0.283305315 GFAFVTFDDHDTVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 291.51 6.34E-44 1640180000 2508920 2725910 2069280 2974190 1668220 2412900 2295430 2524750 1287540 FALSE TRUE 2390328.324 3003683.328 2164158.535 2675218.771 1959157.04 2329340.668 1945219.995 2303669.505 1487205.127 1.607262024 2.019683279 1.455184961 1.798822988 1.317341504 1.566253791 1.307970205 1.548992444 1 20.50417222 1.399108646 0.222788151 0.858243062 1.951999412 0.543472981 0.188201525 1.563972898 0.363707174 0.698182478 0.613229575 25.06736274 -1.399108646 1.09375635 GFAFVTFDDHDTVDKIVVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFAFVTFDDHDTVDKIVVQK 20 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 348.64 2.93E-95 555000000 1122220 742920 1108200 1056260 905760 1092050 1522690 1205380 940680 FALSE TRUE 1069174.885 818624.3926 1159012.066 950082.738 1063724.257 1054232.035 1290375.674 1099830.537 1086555.85 0.984003615 0.753412162 1.0666843 0.874398438 0.978987189 0.970251124 1.187583385 1.012217216 1 20.0513309 2.119745766 2.476343526 1.084507631 0.911811328 0.25845598 0.097189654 0.288501968 3.500627534 0.043593269 0.027262764 131.7485264 -2.119745766 -0.172696302 GFAFVTFES(ph)PADAK ddPTM_SK-BR-3_Trastuzumab_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 251.87 3.61E-24 73516000 278260 313340 254590 362530 187797 289400 291340 314600 199409 TRUE FALSE 265107.2013 345269.7022 266263.2033 326087.7956 220548.7373 279378.0054 246890.7322 287051.9562 230332.3293 1.150976947 1.499006689 1.155995792 1.415727426 0.957524018 1.212934399 1.071889183 1.246251263 1 17.8133574 2.746956553 24.99989731 1.109162284 1.312227238 0.369913936 0.134110525 634.9080682 1890514.686 0.037065543 0.038735408 558.4143282 -2.746956553 0.203064954 GFAFVYFENVDDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFAFVYFENVDDAK 14 0 P62995;P62995-3;H7BXF3 P62995 TRA2B Transformer-2 protein homolog beta 0 174.24 5.98E-06 37635000 118480 100730 90996 127640 79939 107760 110280 115500 84321 FALSE TRUE 112879.6852 110994.5015 95168.25661 114809.3847 93880.33629 104028.2442 93454.76057 105386.2077 97397.07003 1.15896387 1.139608219 0.977116217 1.178776576 0.963892818 1.068083918 0.959523326 1.082026468 1 16.57159075 4.078930833 0.515538721 1.00823614 1.221343676 0.310000026 0.068147824 2.266428949 0.746808349 0.040179504 0.271172734 11993.08282 -4.078930833 0.213107536 GFAFVYFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFAFVYFER 9 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 0 117.04 0.0028307 269430000 217470 195710 142040 174900 222740 161100 245590 200070 219210 FALSE TRUE 207190.6241 215653.0715 148552.6745 157318.7197 261585.7855 155521.0666 208120.7349 182550.8102 253203.9672 0.818275584 0.851697048 0.586691734 0.621312223 1.033103029 0.614212598 0.82194895 0.720963467 1 17.94994048 -1.390034043 3.278852123 1.002298692 0.76704318 0.239389517 0.134510721 99767676.92 144145167 2225697.09 0.029926932 0.040734835 1.390034043 -0.235255512 GFAYVQFEDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 171.85 3.27E-05 181665000 309030 294350 199173 238763 308470 225396 299460 271443 290080 FALSE TRUE 294422.7643 324344.5996 208305.2791 214762.0896 362267.0703 217590.48 253771.877 247674.0119 335064.1249 0.878705724 0.968007541 0.621687801 0.640958174 1.081187282 0.649399514 0.757383015 0.739183916 1 18.3540777 3.768224857 24.97116623 0.771503872 0.92335665 0.122345626 0.151929155 1154.078382 971491.7621 0.035956267 0.064808649 5864.417181 -3.768224857 0.151852778 GFAYVQFEDVRDAEDALHNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 268.36 3.48E-38 477632200 476304.7 347315.2 415633.1 468514.6 554043.6 414237.1 545008.1 460539.5 530940.5 FALSE TRUE 453790.7208 382707.0137 434690.2888 421418.6223 650668.6284 399891.9654 461857.1046 420212.2199 613276.0411 0.739945294 0.624037119 0.708800376 0.687159768 1.06097187 0.652058679 0.753098236 0.685192624 1 19.22617706 -5 0.224445287 2.356907019 0.701282397 0.303024855 0.121851962 191.9385136 1.920241542 118.4314181 0.211339732 1.00E-05 5 -1.655624622 GFAYVQFEDVRDAEDALHNLDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFAYVQFEDVRDAEDALHNLDRK 23 2 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 ;; 197.31 1.79E-24 283119000 409748 194064 414074 313921 400915 386099 579571 461234 465234 FALSE TRUE 390380.0241 213839.3422 433059.7025 282365.0647 470834.4491 372728.2948 491146.7994 420845.9058 537380.1126 0.726450449 0.397929393 0.805872217 0.525447552 0.876166494 0.693602696 0.913965344 0.783143804 1 19.03558341 2.133059019 0.521580618 0.968609734 0.564937762 0.432095716 0.134702154 0.70989405 0.407496357 0.115435964 0.091892809 135.8498048 -2.133059019 -0.403671972 GFCFITFKEEEPVKK ddPTM_SK-BR-3_Trastuzumab_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 ; 210.1 1.16E-09 1860550000 3599700 2882200 3377500 3671500 2163200 4075100 4355000 4317700 2579600 FALSE TRUE 3429549.315 3175899.457 3532361.716 3302433.845 2540461.395 3933978.265 3690564.765 3939619.298 2979631.193 1.150997923 1.065869986 1.185502999 1.108336445 0.852609343 1.320290335 1.238597842 1.322183533 1 21.50670234 GFCFLEYEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 238.86 1.26E-15 8731340000 10243190 9270230 9104070 10796800 8122900 10236200 11296460 10938830 7178820 FALSE TRUE 9759014.709 10214876.98 9521500.615 9711485.151 9539531.188 9881717.827 9572977.553 9980968.055 8292074.741 1.176908676 1.231884335 1.14826517 1.171176751 1.150439605 1.191706314 1.154473139 1.203675602 1 22.98330169 -4.114433062 0.346463067 2.89E-15 1.186521788 0.810954198 0.026855764 86.38060072 1.304197261 62.76957521 0.02023202 7.68E-05 4.114433062 1.186521788 GFCYVEFDEVDSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFCYVEFDEVDSLK 14 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 246.78 2.14E-17 104284000 213961 254346 193057 265022 155890 214913 199471 236519 147419 FALSE TRUE 203847.4876 280264.1466 201908.8544 238381.4851 183077.1666 207470.5089 169038.0354 215808.1425 170279.9856 1.197131224 1.645901869 1.18574625 1.399938367 1.075153759 1.218408072 0.992706423 1.267372332 1 17.37754935 2.834151203 1.478612495 1.098874489 1.399529248 0.353437634 0.156000882 0.366196054 1.622201787 0.057485641 0.059660217 682.5762978 -2.834151203 0.300654759 GFCYVEFDEVDSLKEALTYDGALLGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GFCYVEFDEVDSLKEALTYDGALLGDR 27 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;; 308.18 5.64E-82 1728355300 3395384 2432568 3283392 3286184 3037217 2990486 4351075 3809570 3492594 FALSE TRUE 3234890.927 2680449.445 3433938.771 2955850.541 3566906.683 2886924.72 3687238.596 3475983.855 4034207.64 0.801865252 0.664430214 0.851205262 0.732696679 0.884165368 0.715611336 0.913993261 0.861627404 1 21.94385391 1.17946681 0.42151612 1.011485657 0.739168348 0.517061657 0.069831626 0.767640838 0.388201036 0.081944605 0.048332458 15.11704168 -1.17946681 -0.272317309 GFDILGIKPVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFDILGIKPVQR 12 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 196.24 1.91E-07 607930000 2362800 2346100 2082480 2655700 2308700 2330200 2766800 2613000 2354800 FALSE TRUE 2251115.127 2585170.257 2177963.768 2388743.99 2711336.549 2249504.59 2344673.844 2384191.868 2719970.357 0.827624875 0.9504406 0.8007307 0.878224273 0.996825771 0.827032759 0.862021837 0.87655068 1 21.3751595 -0.870710801 5.345277744 1.000000111 0.878786403 0.302599969 0.058445241 7.16E-08 1.52E-08 0.052257069 0.012317098 0.134675687 0.870710801 -0.121213708 GFDNPEENS(ph)SEFPVTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFDNPEENSSEFPVTFK 17 0 Q8IWI9-3;Q8IWI9;H3BU53 Q8IWI9-3 MGA MAX gene-associated protein 1 GFDNPEENS(0.5)S(0.5)EFPVTFK 104.45 0.0016434 0 18994 16885 13676 21272 12962 17125 19930 19344 17886 TRUE FALSE 18096.19126 18605.6007 14303.05813 19133.69815 15222.5687 16531.95696 16889.31246 17650.13681 20659.66953 0.875918719 0.90057591 0.692317857 0.926137667 0.736825372 0.800204327 0.817501579 0.854328129 1 14.33452956 0.816312502 3.99009746 0.999992321 0.82784807 0.382283545 0.070549012 1.66126294 34.87090525 0.063918186 0.016335735 6.551073946 -0.816312502 -0.172144251 GFDQTINLILDESHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 ;;;;;;; 254.72 1.37E-26 998967700 1063163.8 982125.6 943468.1 1081258.8 1172872.4 939880.8 1186555.8 1094800.3 1077109.9 FALSE TRUE 1012910.154 1082205.315 986727.0456 972568.6112 1377420.975 907332.4922 1005524.92 998933.7818 1244142.602 0.814143131 0.869840253 0.793098029 0.781717955 1.107124676 0.729283356 0.808207129 0.802909393 1 20.24672042 -2.359198489 2.099305073 1.922044839 0.83758784 0.199699888 0.101727553 8811232.5 903047.4386 38589918.11 0.022912488 0.004373222 2.359198489 -1.084457 GFEGSFEELCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFEGSFEELCR 11 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;; 232.83 9.43E-14 147742000 216648 170213 184281 226684 244759 180656 237856 204770 282171 FALSE TRUE 206407.4784 187557.8982 192730.4661 203897.2936 287444.8921 174399.8374 201566.6987 186839.2532 325928.6376 0.633290404 0.575456946 0.591327192 0.625588764 0.881925854 0.535085958 0.618438135 0.57325203 1 18.31419659 -0.995583465 4.399415683 1.000012765 0.626211489 0.602910199 0.094517644 20275903.01 62386059.87 4900.17823 0.022273652 0.101022133 0.995583465 -0.373801277 GFESPSDNSSAMLLQWHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ;;; 295.17 1.15E-49 912860000 1910830 1592650 1503780 1581270 1367370 1413110 1631220 1600780 1280360 FALSE TRUE 1820508.853 1754942.846 1572729.8 1422317.735 1605838.895 1364173.646 1382347.43 1460607.217 1478911.69 1.230978743 1.186644786 1.063437264 0.961732702 1.085824736 0.922417245 0.934705865 0.987623012 1 20.49610448 3.637726327 1.382670829 0.970420487 1.231824484 0.805575833 0.045536929 0.158490148 0.59601441 0.01427851 0.031947387 4342.365017 -3.637726327 0.261403997 GFFDPNTEENLTYLQLMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 166.38 4.66E-11 35868000 8804.4 8132 8462.1 11723 8561.9 9315.8 9222.7 8785.4 8991.3 FALSE TRUE 8388.233461 8960.660045 8850.095655 10544.58177 10055.09265 8993.19151 7815.607728 8016.103802 10385.62488 0.8076773 0.862794502 0.852148595 1.015305471 0.968174064 0.865926857 0.752540922 0.771846075 1 13.3423004 -2.085924473 9.193900397 1.87195571 0.858579172 0.22465903 0.08030845 0.032980032 0.000308225 0.001786657 0.019684523 0.008204942 2.085924473 -1.013376538 GFFDPNTHENLTYLQLLER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 258.95 4.77E-31 4004890000 3019000 2941910 2809730 3327290 3479810 2857980 3324060 3186200 3046980 FALSE TRUE 2876297.853 3241693.974 2938558.9 2992824.488 4086687.762 2759007.436 2816913.596 2907199.437 3519490.097 0.817248458 0.921069213 0.834938818 0.850357411 1.161159046 0.783922489 0.800375486 0.826028589 1 21.746935 -0.463557135 6.704544955 1 0.872396689 0.116768168 0.108447428 0 0 0.100564111 0.023703188 0.343908465 0.463557135 -0.127603311 GFFDPNTHENLTYLQLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFFDPNTHENLTYLQLLQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 358.91 3.58E-91 1239430000 2375700 2044180 2027750 2426500 2611900 1964240 2526000 2276900 2213300 FALSE TRUE 2263405.369 2252484.266 2120724.343 2182583.61 3067414.533 1896217.876 2140612.307 2077522.565 2556527.26 0.885343726 0.881071875 0.829533241 0.853729841 1.199836427 0.741716275 0.837312529 0.812634623 1 21.28575398 -3.498662206 9.051156479 0.998320487 0.884907529 0 0.126698304 0 0 0 0.025991755 0.000317203 3.498662206 -0.113412958 GFFDPNTHENLTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 165.86 3.90E-06 2982980000 4951900 4460310 4141230 5041230 5504150 4432030 5305440 4897520 4891460 FALSE TRUE 4717833.501 4914820.66 4331109.492 4534475.983 6464072.017 4278547.69 4495997.687 4468667.185 5650002.635 0.83501439 0.869879357 0.766567694 0.802561747 1.144083009 0.757264725 0.795751432 0.790914177 1 22.42982011 -2.326236258 2.241337402 1.837334339 0.844562907 0.160670548 0.111142283 6663229.848 1174223.368 28101660.57 0.025753236 0.004718063 2.326236258 -0.992771431 GFFDPNTHENLTYVQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 296.17 2.48E-49 9761390000 17647599 14837952 14387894 18050130 19383859 14811602 17571691 16332643 16049236 FALSE TRUE 16813431.97 16349956.18 15047593.17 16235696.64 22764397.87 14298672.51 14890806.81 14902470.19 18538069.55 0.90696779 0.881966492 0.811713061 0.875802984 1.227981037 0.771313996 0.803255526 0.803884685 1 24.14398768 -0.895656642 4.227354022 1.000002399 0.883030519 0.072087014 0.129018559 25927624.77 70575671.79 1069.604776 0.030168384 0.127157903 0.895656642 -0.11697188 GFFNIYHPLDPVAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFFNIYHPLDPVAYR 15 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 107.61 0.0011441 273420000 417680 359460 353010 411490 503730 339620 446960 418310 460680 FALSE TRUE 397937.0942 396089.3827 369195.8577 370126.2434 591580.3525 327858.8742 378768.043 381680.5588 532119.9016 0.747833511 0.744361152 0.693820804 0.695569255 1.111742581 0.616137215 0.711809579 0.717282999 1 19.02139184 -2.105637995 2.254942347 1.430384632 0.751369002 0.253139471 0.132233203 8356273.037 2315609.21 18430866.8 0.030126137 0.007840829 2.105637995 -0.67901563 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 272.21 1.23E-61 1627800000 907350 1050610 1044120 1114370 1170820 1003310 1188400 1093630 1407220 TRUE FALSE 864461.3637 1157668.353 1091993.935 1002351.41 1375010.637 968565.1231 1007087.754 997865.9595 1625444.491 0.531830751 0.71221648 0.671812505 0.61666296 0.845929003 0.595877084 0.619576835 0.613903437 1 20.63240286 -1.959010988 2.541649235 1.275330368 0.650025007 0.632290306 0.083644497 15974046.28 6826699.764 25916320 0.020805572 0.01098978 1.959010988 -0.625305361 GFGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGDLK 6 0 P24534;C9JZW3;F2Z2G2;F8WF65;F8WFC9 P24534 EEF1B2 Elongation factor 1-beta 0 ; 106.76 0.074087 517540000 2093800 1919630 1833620 2225100 1625530 2013100 2250300 2182800 1796520 FALSE TRUE 1994830.224 2115242.479 1917693.291 2001428.721 1909021.917 1943385.842 1906975.405 1991662.46 2075115.146 0.961310618 1.019337401 0.924138255 0.96449044 0.919959512 0.936519521 0.918973296 0.95978407 1 20.98475996 3.729645268 24.97556297 0.940702221 0.99032401 0.276763331 0.028526876 573.9787294 1607949.83 0.006799393 0.010705048 5365.933273 -3.729645268 0.049621789 GFGEYSRS(ph)PTF ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFGEYSRSPTF 11 1 D6REL5;Q6UWZ7-2;Q6UWZ7 D6REL5 FAM175A BRCA1-A complex subunit Abraxas 1 GFGEYS(0.004)RS(0.996)PTF;GFGEYS(0.002)RS(0.998)PTF;GFGEYS(0.002)RS(0.998)PTF;GFGEYS(0.046)RS(0.953)PT(0.001)F 152.96 8.60E-05 575680000 1220680 865480 1175750 1205380 1540070 1085080 1476140 1244160 1648620 TRUE FALSE 1162980.876 953673.396 1229659.3 1084212.912 1808657.72 1047503.408 1250927.732 1135214.755 1904279.57 0.61071961 0.50080535 0.64573465 0.569355955 0.949785814 0.550078583 0.656903404 0.596138704 1 20.86081387 -5 0.213595576 2.796791857 0.576005906 0.465927654 0.121745549 127.9747333 1.277316507 98.90325448 0.235044793 1.00E-05 5 -2.220785952 GFGFGQGAGALVHS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E 227.47 7.61E-13 13621480000 12917090 10679080 11392020 13269530 13993030 12182050 14179100 11988430 11450160 TRUE FALSE 12306524.75 11767290.39 11914355.39 11935651.63 16433410 11760182.55 12015817.88 10938659.51 13225792.33 0.930494328 0.889722906 0.900842466 0.902452672 1.242527448 0.889185484 0.908514029 0.827070261 1 23.65685082 -1.440680969 3.268390759 1.00095726 0.934818668 0.030642339 0.112211607 44488050.57 63000712.27 398956.071 0.025892897 0.03625092 1.440680969 -0.066138592 GFGFGQGAGALVHSE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGFGQGAGALVHSE 15 0 P21291;E9PP21 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 98.943 0.0063592 64952000 436440 559090 405210 619720 384310 530970 463610 551760 398820 FALSE TRUE 415810.3461 616061.9066 423789.2793 557424.5682 451333.5423 512582.3758 392877.7797 503444.9693 460666.9687 0.902626788 1.337325983 0.919947181 1.210038067 0.979739319 1.112696179 0.852845562 1.092861011 1 18.81336463 2.243365045 1.775251993 0.976593338 1.099650541 0.047752691 0.144987568 0.745608659 4.701751001 0.068623716 0.043389331 175.1318137 -2.243365045 0.123057203 GFGFILFK ddPTM_SK-BR-3_Trastuzumab_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 ; 149.92 0.0011573 147371000 631870 504590 400390 478850 551310 409420 720290 583530 625990 FALSE TRUE 602002.7573 556008.2947 418748.2775 430715.0882 647458.2894 395241.6827 610396.5315 532433.0197 723065.3321 0.832570351 0.768959968 0.579129242 0.595679352 0.895435393 0.5466196 0.844178948 0.736355342 1 19.46376648 0.364628592 0.961794332 1.000853734 0.723749448 0.35272475 0.118118331 2.882380727 3.355277272 0.113720699 0.03469957 2.315413663 -0.364628592 -0.277104287 GFGFITFEDEQSVDQAVNMHFHDIMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFITFEDEQSVDQAVNMHFHDIMGK 27 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 347.08 2.55E-110 282070000 380800 354300 344960 455500 326400 361230 447940 366690 22163.6 FALSE TRUE 362800.3387 390403.5728 360776.7572 409712.2746 383324.0567 348720.5145 379598.526 334580.6797 25600.61789 14.17154618 15.24977149 14.09250194 16.00399945 14.97323456 13.62156632 14.82770953 13.06924235 1 14.64389101 0.174054076 1.06920681 0.933965937 14.80307626 0.976159544 0.667649053 0.634888057 0.708087529 0.675057494 0.181877986 1.492980295 -0.174054076 13.86911032 GFGFVDFNS(ph)EEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 1 GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK 186.85 1.07E-06 91574000 233615 217217 202120 245046 159319 244721 241936 253241 172883 TRUE FALSE 222572.4819 239351.6593 211387.4019 220413.5105 187104.1832 236246.2504 205024.2197 231065.8755 199692.8127 1.114574325 1.198599269 1.058562895 1.103762862 0.936960027 1.183048339 1.026698042 1.15710662 1 17.60742288 3.72479643 24.09347395 1.068479105 1.156586797 0.202279805 0.074226854 620.5706229 1086276.992 0.01743749 0.027187298 5306.356576 -3.72479643 0.088107693 GFGFVDFNSEEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 297.32 2.59E-43 954446000 1791882 1530447 1618680 1809323 1260707 1788279 1865625 1846368 1338549 FALSE TRUE 1707183.289 1686401.289 1692898.079 1627446.415 1480573.902 1726350.45 1580989.642 1684690.23 1546124.343 1.104169466 1.090728115 1.094930099 1.052597369 0.957603383 1.116566373 1.022550126 1.089621438 1 20.56022492 8 0.187710763 1.018688171 1.442409068 0.223685446 0.045233709 75.02818796 0.868933528 0.086503928 9.186219914 100000000 -8 0.423720897 GFGFVEFEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFVEFEDPR 11 0 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 130.75 0.00050649 134899000 325530 442130 289140 399530 320840 305530 298020 349260 291860 FALSE TRUE 310142.842 487183.5497 302397.355 359368.4853 376794.3944 294949.4195 252551.5755 318676.9429 337120.1582 0.919977149 1.445133249 0.8970017 1.065995244 1.117685743 0.874908878 0.749144094 0.945291864 1 18.36290337 2.2246734 6.487481847 0.857060958 1.112974362 0.249023839 0.162099527 0.167295655 28.03895691 0.058402442 0.044716535 167.7541991 -2.2246734 0.255913403 GFGFVEFEDPRDADDAVYELDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFVEFEDPRDADDAVYELDGK 23 1 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 148.89 9.22E-08 261660000 622470 535380 601810 657950 503980 658820 734140 731250 560220 FALSE TRUE 593047.0767 589935.8307 629403.5838 591811.616 591873.9524 636004.8982 622133.4596 667217.8734 647096.0564 0.916474565 0.911666552 0.972658661 0.914565326 0.914661659 0.982860105 0.961423661 1.031095564 1 19.30362036 1.778179866 1.225608408 1.011257356 0.92449729 0.655352089 0.024407787 0.260854449 0.732281256 0.018824921 0.007516938 60.00395359 -1.778179866 -0.086760066 GFGFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFVR 6 0 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;K7EJM5;A0A087WX29;Q5JQF3;Q96DU9-2;Q96DU9 Q13148 TARDBP;TDP43;PABPC5 TAR DNA-binding protein 43;Polyadenylate-binding protein 5 0 ; 112.58 0.062524 419180000 978960 888250 738430 906820 1170730 762740 1044950 860660 1068400 FALSE TRUE 932686.5009 978763.6849 772287.7459 815664.7308 1374904.941 736326.1225 885523.6857 785296.0478 1234082.015 0.755773514 0.793110727 0.625799369 0.66094856 1.114111481 0.596658985 0.717556592 0.636340242 1 20.23500685 GFGFVSFER ddPTM_SK-BR-3_Trastuzumab_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 0 ;; 160.75 0.00015136 929600000 1354600 1105710 978410 1183820 1550770 964660 1486060 1245400 1476710 FALSE TRUE 1290570.743 1218383.106 1023271.066 1064820.164 1821223.797 931253.5823 1259334.254 1136346.174 1705710.645 0.756617628 0.714296478 0.599908941 0.624267761 1.067721423 0.545962227 0.73830474 0.666201021 1 20.7019415 -1.622230766 2.494969599 1.032490234 0.715349124 0.28844965 0.141078036 9796602.295 8242436.093 2061585.249 0.031624138 0.023865428 1.622230766 -0.31714111 GFGFVTFDDHDPVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;; 267.93 1.61E-25 28861372800 42298455.2 44677351 34274628.4 47300982 29050928.6 40384942 40021295.2 44094674 21683306.7 FALSE TRUE 40299091.05 49230023.86 35846154.01 42546197.42 34117401.35 38986401.33 33915311.58 40233510.58 25045843.16 1.609013152 1.965596588 1.431221692 1.698732886 1.362198155 1.556601672 1.35412936 1.606394735 1 24.57806784 -1.670556299 0.102209899 4.52E-13 2.133657583 0.567439726 0.166514393 42.55115008 0.686314663 13.72239043 3.169305711 0.021352253 1.670556299 2.133657583 GFGFVTFDDHDPVDKIVLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 340.58 1.53E-80 2549670000 3204440 1725220 3034840 2627600 2409840 3005420 4178600 3143130 2514970 FALSE TRUE 3052972.472 1901021.879 3173990.416 2363468.656 2830115.333 2901341.552 3541077.825 2867900.874 2904978.703 1.050944872 0.654401314 1.092603678 0.813592421 0.974229288 0.998747959 1.218968601 0.987236454 1 21.47009616 2.250311386 2.446587666 1.092739851 0.889706725 0.189820871 0.137252196 0.338843039 4.153171704 0.055749999 0.03929614 177.9554882 -2.250311386 -0.203033126 GFGFVTFSSMAEVDAAMAARPHS(ph)IDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR 199.59 3.13E-25 130645900 36176.6 31281.4 39519.4 37537.1 37744.2 33923.68 39926.6 40305.4 38845.3 TRUE FALSE 34466.60381 34469.01022 41331.40358 33763.79939 44326.77653 32748.89446 33835.06387 36776.0455 44869.23073 0.76815678 0.768210412 0.921152489 0.752493387 0.98791033 0.729874213 0.754081657 0.819627279 1 15.45343883 -2.299400505 1.989797897 1.767978003 0.805195426 0.335641035 0.082220713 3028714.169 407469.0055 10442232.26 0.018959282 0.005018795 2.299400505 -0.962782577 GFGFVTFSSMAEVDAAMAARPHSIDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;;; 273.88 4.77E-61 2836811000 440053.7 341762.5 451973.1 429769.7 528038.4 397178.99 537558.1 430311.4 506595.5 FALSE TRUE 419253.2337 376588.4873 472696.5137 386568.4332 620128.1298 383424.582 455543.7389 392631.0526 585155.7428 0.716481448 0.643569668 0.807813167 0.660624864 1.059765947 0.65525219 0.778499988 0.670985558 1 19.15846113 -5 0.238850841 2.408641414 0.718567666 0.273233971 0.124421775 216.1148266 2.155759906 148.4249401 0.181492468 1.00E-05 5 -1.690073748 GFGFVTYATVEEVDAAMNARPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 316.02 1.45E-73 3338787600 4575139 3907338 4093439 4746485 4047374 4506711 5061319 4791747 3769950 FALSE TRUE 4358881.247 4305500.184 4281127.227 4269359.31 4753234.744 4350642.468 4289121.829 4372156.23 4354574.592 1.000988996 0.988730379 0.983133286 0.98043086 1.091549736 0.999097013 0.984969195 1.00403751 1 22.05410035 6.18342819 9.806959458 1.002188485 1.000114904 0 0.032177903 0 0 0.006890648 0 1525556.124 -6.18342819 -0.002073581 GFGFVTYATVEEVDAAMNARPHKVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFGFVTYATVEEVDAAMNARPHKVDGR 27 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;; 256.52 4.09E-53 734663000 750407 325077.8 1001395 514982 1004000 796348 1354152 915171 1274558 FALSE TRUE 714936.7483 358203.5974 1047309.951 463215.031 1179097.282 768770.2691 1147551.242 835033.7756 1472209.945 0.485621464 0.243310133 0.711386277 0.314639249 0.800902946 0.522187934 0.779475268 0.567197483 1 20.48955199 1.292076593 0.147087861 1.27534089 0.11101822 0.482654485 0.165028619 3.716908267 0.516597191 1.892316982 1.615465498 19.59190171 -1.292076593 -1.164322669 GFGFVTYSCVEEVDAAMCARPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFGFVTYSCVEEVDAAMCARPHK 23 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 288.57 1.99E-53 763012000 1100713 738768 1092056 1043430 1035090 1068410 1353884 1175052 1056936 FALSE TRUE 1048684.478 814049.2991 1142127.848 938542.434 1215609.368 1031410.694 1147324.13 1072158.218 1220840.237 0.858985841 0.66679429 0.935526053 0.768767612 0.995715354 0.844836747 0.939782369 0.878213369 1 20.21944299 3.19226222 1.318464237 0.919875593 0.773474418 0.287018346 0.086224577 0.450095567 1.6464155 0.028494671 0.040893281 1556.905382 -3.19226222 -0.146401174 GFGFVYFQNHDAADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 222.16 1.44E-12 1032430000 2082930 2137530 1764240 2450000 1457490 2108100 2133700 2144110 1293560 FALSE TRUE 1984474.027 2355346.737 1845132.149 2203721.345 1711675.795 2035095.968 1808164.877 1956360.362 1494158.678 1.328154804 1.576369881 1.234897053 1.474891106 1.145578324 1.362034701 1.210155858 1.309339088 1 20.51090194 -0.588350365 0.143017731 0.655377461 1.564438491 0.47852316 0.117300847 17.44694094 0.627870395 3.289618421 0.885030931 0.25801778 0.588350365 0.90906103 GFGGITHGPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGGITHGPPEK 12 0 P49748;P49748-3;P49748-2 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 68.44 0.052662 102980000 345910 298240 256190 315740 287300 266770 350970 330490 292590 FALSE TRUE 329559.5198 328630.9951 267936.5649 284001.2153 337405.029 257531.688 297423.0805 301550.5436 337963.3629 0.975133864 0.972386451 0.792797665 0.840331369 0.998347946 0.762010668 0.880045334 0.892258087 1 18.36650733 3.814330154 12.56326914 0.872282878 0.973856301 0.198553667 0.076132674 1.537443069 252.6668446 0.017665252 0.031854165 6521.239557 -3.814330154 0.101573424 GFGHIGIAVPDVYSACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGHIGIAVPDVYSACK 17 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 182.1 7.67E-10 1130940000 2778100 1381150 1884790 2460100 2600000 2008770 3230600 2637800 2842800 FALSE TRUE 2646784.719 1521890.755 1971209.486 2212806.074 3053439.177 1939205.791 2737712.636 2406820.248 3283646.905 0.806050344 0.463475763 0.600311039 0.67388673 0.929892667 0.590564652 0.833741482 0.732971698 1 21.64686757 0.711237446 0.330093737 1.041388888 0.613544143 0.377340954 0.12870841 2.322935531 0.615317133 0.329880369 0.140974151 5.143247768 -0.711237446 -0.427844745 GFGS(ph)EEGSR ddPTM_SK-BR-3_Trastuzumab_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 201.33 2.27E-05 2345300000 3373960 3217400 3221350 3703090 3825690 3299420 3827120 3373910 3872760 TRUE FALSE 3214479.597 3545256.718 3369052.084 3330848.358 4492889.125 3185160.258 3243222.554 3078472.554 4473327.841 0.718587975 0.792532281 0.753142225 0.744601888 1.00437287 0.712033719 0.725013384 0.688183979 1 22.09291706 -2.307847699 2.343125179 2.226595858 0.767024411 0.403899103 0.088838954 6926086.681 1220337.114 44849811.45 0.021785323 0.004922121 2.307847699 -1.459571446 GFGS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 GFGS(1)FR;GFGS(1)FR 79.597 0.069997 216968000 402220 417230 347980 477580 401060 393390 385260 381650 335380 TRUE FALSE 383207.8577 459746.2114 363935.2272 429572.7511 471004.737 379766.8057 326481.5112 348230.7027 387389.0175 0.989206819 1.186781738 0.93945675 1.108892435 1.215844321 0.980324141 0.842774308 0.898917334 1 18.56342353 2.00518034 24.51952044 0.90020806 1.087659303 0.446999841 0.089208323 85.72659963 405757.1915 0.031409427 0.023115423 101.1999599 -2.00518034 0.187451243 GFGS(ph)VEELCTNSSLGMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGSVEELCTNSSLGMEK 18 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 GFGS(1)VEELCTNSSLGMEK 237.86 7.66E-24 61543000 67216 62132 66827 79009 49037 75120 86964 70598 62917 TRUE FALSE 64038.83289 68463.32144 69891.08405 71066.86521 57589.03727 72518.57556 73696.0446 64416.06486 72673.84702 0.881181271 0.942062712 0.96170888 0.977887756 0.792431385 0.997863448 1.014065549 0.886372024 1 16.14914866 7.999999969 0.073509077 1.057340429 0.654139665 0.102382506 0.065069213 482.3849281 2.606510479 2.369277042 19.96830642 99999992.85 -7.999999969 -0.403200764 GFGSDKEAILDIITSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGSDKEAILDIITSR 16 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 237.01 8.70E-20 944550000 2030600 1190220 1452060 2616200 2484300 1822610 2382200 1582100 1749340 FALSE TRUE 1934617.562 1311504.771 1518638.387 2353214.606 2917561.133 1759492.559 2018751.638 1443562.937 2020618.713 0.957438209 0.649060985 0.751570981 1.164601016 1.443894939 0.870769209 0.999075989 0.714416296 1 20.94636568 3.252468443 24.99583943 1.03754596 0.781162068 0.248396742 0.201598903 320.6228543 576235.9635 0.056218172 0.075739849 1788.415573 -3.252468443 -0.256383892 GFGSEEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 151.5 0.00019244 383940000 637600 543080 553570 693840 731520 657920 785600 735130 790360 FALSE TRUE 607461.9116 598420.4694 578951.7321 624093.885 859096.8564 635136.0654 665742.2915 670758.12 912924.9922 0.665401776 0.655497959 0.634172289 0.683620112 0.941037724 0.695715498 0.729240953 0.734735193 1 19.8001368 -5 0.135401799 1.976554467 0.599143338 0.576309076 0.080163256 102.3676319 0.860922057 27.06812942 0.532347355 1.00E-05 5 -1.377411129 GFGSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 124.32 0.042818 1650520000 1726190 1293360 1295730 1493580 1884220 1307370 1796540 1444150 1812980 FALSE TRUE 1644596.42 1425154.854 1355140.502 1343442.501 2212827.371 1262095.449 1522444.827 1317692.57 2094127.679 0.785337225 0.680548215 0.647114556 0.641528458 1.056682166 0.602683142 0.727006688 0.629232202 1 20.99791798 GFGSSAPEGLEPDS(ph)MASAASALHLLSPRPR ddPTM_SK-BR-3_Trastuzumab_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 75.529 0.0054831 54635000 32945 29706 28965 32892 33880 31045 25586 22095 24221 TRUE FALSE 31387.75514 32733.07517 30293.0739 29585.63367 39788.66127 29969.90387 21682.38578 20160.24467 27977.06898 1.12191006 1.169996585 1.082782257 1.057495826 1.42218834 1.07123101 0.775005623 0.720598883 1 14.77195721 1.839784391 4.490074398 0.81308379 1.162840373 0.614000192 0.121854807 0.133941182 4.165042415 0.054494191 0.030621465 69.14875912 -1.839784391 0.349756583 GFGSSAPEGLEPDSMAS(ph)AASALHLLSPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.008)MAS(0.331)AAS(0.331)ALHLLS(0.331)PRPR;GFGSSAPEGLEPDS(0.056)MAS(0.315)AAS(0.315)ALHLLS(0.315)PRPR;GFGSSAPEGLEPDS(0.003)MAS(0.423)AAS(0.287)ALHLLS(0.287)PRPR;GFGSSAPEGLEPDS(0.054)MAS(0.315)AAS(0.315)ALHLLS(0.315)PRPR;GFGSSAPEGLEPDS(0.055)MAS(0.327)AAS(0.327)ALHLLS(0.29)PRPR 143.05 2.83E-08 639715000 291934 267022 266141 318956 294338 239274 260322 261318 215173 TRUE FALSE 278134.8584 294231.8454 278343.8281 286893.9369 345670.454 230987.8814 220605.0978 238435.6106 248540.9299 1.119070644 1.183836584 1.11991143 1.15431264 1.390798909 0.929375622 0.887600678 0.959341428 1 17.92312393 2.195538953 24.55094126 0.929473911 1.180348414 0.694807335 0.081654028 61.64972952 35180.87105 0.028998354 0.021416877 156.869659 -2.195538953 0.250874503 GFGSSAPEGLEPDSMASAAS(ph)ALHLLSPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.114)MAS(0.114)AAS(0.386)ALHLLS(0.386)PRPR 59.046 0.047062 70563000 16940 13475 14241 16054 13530 14837 19941 13412 14806 TRUE FALSE 16139.27977 14848.11782 14893.96394 14440.22142 15889.62772 14323.19097 16898.63421 12237.57418 17102.03886 0.943705011 0.868207466 0.870888206 0.844356719 0.929107216 0.837513649 0.988106409 0.715562295 1 14.06188071 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.001)MASAAS(0.001)ALHLLS(0.998)PR;GFGSSAPEGLEPDS(0.003)MAS(0.003)AAS(0.002)ALHLLS(0.992)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR 254.29 1.10E-53 491044000 682637 676013 600326 765838 690552 604014 611876 622650 525204 TRUE FALSE 650370.1019 744899.4933 627851.5409 688854.5092 810984.0502 583096.8437 518523.0783 568127.4651 606649.9539 1.072068163 1.227890134 1.034948634 1.135505747 1.336823723 0.961175122 0.854731917 0.936499643 1 19.21050477 2.061282847 9.857113566 0.912680488 1.155276204 0.606696641 0.089183102 0.227277445 34.88249341 0.031317389 0.023114671 115.1550126 -2.061282847 0.242595715 GFGSSAPEGLEPDSMASAASALHLLS(ph)PRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.005)MAS(0.004)AAS(0.004)ALHLLS(0.987)PRPR 121.2 1.12E-05 22598000 28833 25303 26921 27281 25589 21040 25973 26686 23550 TRUE FALSE 27470.12123 27881.40447 28155.35448 24538.66205 30051.7135 20311.37952 22010.34182 24349.23237 27202.01372 1.009856164 1.024975752 1.035046698 0.902089908 1.104760618 0.746686614 0.809143839 0.895126097 1 14.73142584 2.238496181 25 0.83921947 1.011907436 0.4526424 0.081537237 1.27163124 492971.1103 0.026514569 0.020849569 173.1793801 -2.238496181 0.172687965 GFGTDEQAIIDCLGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFGTDEQAIIDCLGSR 16 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 148.96 2.05E-06 17243000 33498 26689 24516 40902 39852 29132 32516 25466 31388 FALSE TRUE 31914.61593 29408.63944 25640.08285 36790.45325 46802.17618 28123.15154 27555.087 23236.06204 36255.49073 0.880269865 0.811149949 0.707205511 1.014755352 1.290898985 0.775693584 0.760025211 0.640897739 1 15.14591188 GFGTDEQAIVDVVANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFGTDEQAIVDVVANR 16 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 204.13 6.05E-11 126203000 157928 137629 128718 157492 177567 137631 167279 151949 178308 FALSE TRUE 150463.0564 151653.5516 134619.8476 141660.6049 208534.6286 132864.804 141757.5163 138643.54 205959.094 0.730548254 0.736328504 0.653624198 0.68780942 1.012505078 0.645102876 0.688279957 0.673160565 1 17.6519983 -1.25867764 3.642922423 1.000539186 0.727623652 0.396868296 0.105212314 34042937.7 48291332.06 198654.5965 0.023954383 0.055121669 1.25867764 -0.272915534 GFGYKGS(ph)CFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFGYKGSCFHR 11 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" 1 GFGYKGS(1)CFHR;GFGYKGS(1)CFHR;GFGYKGS(1)CFHR 92.457 0.0060278 565965000 776515 403699 468851 627545 696914 529203 733127 621332 576012 TRUE FALSE 739810.6749 444836.3871 490348.2821 564462.9843 818455.5809 510876.5674 621275.0113 566924.8762 665336.9991 1.111933766 0.66858808 0.736992355 0.848386585 1.230136881 0.767846322 0.933774932 0.852086803 1 19.34372574 2.964895384 24.99716774 0.945813234 0.835471889 0.10834135 0.162739574 1469.996134 1046749.532 0.048496601 0.051459094 922.3492185 -2.964895384 -0.110341345 GFHLDVEDYLSGVLILASELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFHLDVEDYLSGVLILASELSR 22 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;; 131.71 1.17E-05 926398000 163802 241184 254468 246008 200987 189171 253872 180416 112952.5 FALSE TRUE 156059.4041 265760.9238 266135.6095 221278.8085 236039.0692 182619.9608 215139.1637 164617.8186 130468.5968 1.19614534 2.036972346 2.039844192 1.696031182 1.809163852 1.399723499 1.648972772 1.261742845 1 16.99334307 1.11797336 0.917162202 0.996872172 1.742697272 0.481857922 0.252408748 0.494119478 0.912667846 0.236837106 0.083061982 13.12119411 -1.11797336 0.745825101 GFHQVPFAPIVFIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFHQVPFAPIVFIER 15 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ; 132.44 4.74E-05 455470000 904250 833120 793520 908280 1124520 808450 1050040 961040 1000170 FALSE TRUE 861507.8946 918015.8752 829903.6769 816977.9688 1320635.932 780453.1738 889837.1127 876886.2428 1155271.255 0.745719146 0.794632318 0.718362612 0.707174151 1.143139263 0.675558377 0.770240849 0.759030607 1 20.1398002 -2.527255265 2.046794872 3.559009064 0.786792298 0.204763218 0.130456872 5912018.998 273609.5245 70508496.98 0.029224381 0.00296992 2.527255265 -2.772216766 GFIYVHKPPVHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 129.84 9.62E-05 802500000 838870 756920 767380 927350 773370 791020 895500 868400 488410 FALSE TRUE 799218.2776 834051.0085 802565.132 834131.0162 908245.4831 763626.7791 758875.028 792358.2923 564150.1283 1.416676586 1.478420312 1.422609146 1.478562131 1.609935791 1.353587885 1.345165037 1.404516728 1 19.10571961 0.232761494 0.602465289 0.980724145 1.466431253 0.804456651 0.069365399 1.200732051 0.60270277 0.124016663 0.028322154 1.709076467 -0.232761494 0.485707109 GFKDQIYDIFQK ddPTM_SK-BR-3_Trastuzumab_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 ; 192.14 4.07E-06 3366400000 6174000 5480700 5180800 5823200 5158000 6116900 7366000 6881900 5733500 FALSE TRUE 5882167.256 6039189.561 5418344.805 5237840.873 6057553.567 5905070.219 6242181.414 6279284.353 6622621.897 0.888193128 0.911903119 0.818157051 0.790901391 0.914676039 0.89165142 0.942554401 0.948156855 1 22.65897106 1.553613199 1.090114298 0.990120685 0.866960589 0.608143225 0.038072953 0.363578227 0.831032697 0.036428983 0.013282393 35.77776433 -1.553613199 -0.123160096 GFKDQIYEIFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFKDQIYEIFQK 12 1 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 139.86 5.40E-05 266310000 553790 519510 453860 510860 407800 508180 561340 571030 447870 FALSE TRUE 527613.4442 572448.6596 474669.9299 459507.3822 478920.1909 490581.5992 475697.2733 521027.586 517323.3922 1.019890947 1.106558621 0.917549713 0.888240101 0.925765581 0.948307396 0.919535595 1.007160306 1 18.9807069 3.731844065 24.99988705 0.936730068 1.063224785 0.577331732 0.042148174 285.0018268 1060814.7 0.010417662 0.016550155 5393.169441 -3.731844065 0.126494718 GFKEQIYDVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFKEQIYDVYR 11 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 109.15 0.0017948 296240000 671950 277150 387580 290710 828220 368210 989390 594730 896590 FALSE TRUE 640188.2552 305391.9001 405350.9264 261487.2785 972661.3058 355458.7954 838440.3841 542652.2883 1035628.598 0.618163941 0.294885542 0.39140569 0.252491365 0.939198963 0.343229992 0.809595627 0.523983491 1 19.98207528 0.922688846 0.401400321 1.023500522 0.406395906 0.368692919 0.212320485 1.419105873 0.597539787 0.310922465 0.154627632 8.369294418 -0.922688846 -0.617104616 GFLIDGYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFLIDGYPR 9 0 P00568;Q5T9B7;H0YID2;Q9Y6K8-2;Q9Y6K8-3;Q9Y6K8 P00568;Q9Y6K8-2 AK1;AK5 Adenylate kinase isoenzyme 1;Adenylate kinase isoenzyme 5 0 98.629 0.01369 58266000 169950 143080 136100 154290 217560 128220 190800 152860 201550 FALSE TRUE 161916.8003 157660.0147 142340.3196 138780.4761 255502.3951 123779.7092 161689.9557 139474.768 232805.3446 0.695502934 0.677218192 0.611413453 0.59612238 1.097493683 0.531687576 0.694528538 0.599104665 1 17.82876465 -1.473926129 2.926210295 1.008961126 0.688076581 0.287551942 0.154396094 32425129.18 37852210.53 2380594.768 0.033980076 0.033579473 1.473926129 -0.320884545 GFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GFNGCDSPEPDGEDSLEQSPLLEDKYR 27 1 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;GFNGCDS(1)PEPDGEDSLEQSPLLEDKYR 197.28 3.64E-25 424745000 542750 489201 507552 580488 419087 520610 583802 576858 471092 TRUE FALSE 517095.2831 539051.1381 530823.7612 522136.2434 492175.6401 502581.1452 494732.2826 526345.2554 544146.5414 0.950286814 0.990635972 0.975516191 0.95955079 0.904490983 0.923613598 0.909189428 0.96728586 1 19.0536357 2.956162758 7.368718426 0.931716446 0.972371641 0.152002671 0.029952103 0.298309005 43.47136562 0.008321133 0.008948074 903.9881919 -2.956162758 0.040655196 GFPGYMYTDLATIYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFPGYMYTDLATIYER 16 0 P21281;P15313;C9JL73 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 127.42 0.00089018 0 40892 37460 40349 40980 48123 37235 44709 40415 52259 FALSE TRUE 38959.1162 41277.21659 42199.04156 36860.61254 56515.63596 35945.54261 37887.82091 36876.04835 60363.05882 0.645413221 0.683815854 0.699087196 0.61064852 0.936261963 0.595489084 0.627665689 0.610904236 1 15.88137829 -1.434927185 2.939070349 1.007107988 0.674403522 0.518290831 0.098102516 14084569.3 16503035.64 830297.0325 0.023175883 0.036734389 1.434927185 -0.332704467 GFPTDATLDDIKEWLEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFPTDATLDDIKEWLEDK 18 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ; 170.5 1.42E-11 195191000 448820 647360 383760 623550 229290 521370 398420 494400 201631 FALSE TRUE 427605.1681 713326.72 401355.7756 560869.5693 269278.1034 503314.8262 337633.7115 451107.715 232898.9057 1.836011925 3.062816967 1.723304686 2.408210411 1.156201669 2.161087124 1.449700721 1.936925009 1 17.82934434 3.040345954 1.659442944 1.614049488 2.390081252 0.279352669 0.511417319 0.413212433 2.328018574 0.162105572 0.19788662 1097.351986 -3.040345954 0.776031765 GFPTIYFSPANKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 151.74 6.95E-05 561280000 976720 846160 868840 914380 1003040 805050 1058530 971760 1042050 FALSE TRUE 930552.3813 932384.666 908677.1734 822464.7852 1177969.858 777170.9166 897031.8073 886667.5428 1203645.792 0.773111481 0.77463376 0.754937357 0.683311312 0.978668198 0.645680749 0.74526228 0.736651554 1 20.19897947 -0.982843884 5.254355643 1.000001081 0.760985779 0.42665847 0.086873775 9.79E-07 1.90E-07 0.074857002 0.017643885 0.104029405 0.982843884 -0.239015303 GFQFVS(ph)SSLPDICYR ddPTM_SK-BR-3_Trastuzumab_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(0.541)S(0.289)S(0.17)LPDICYR 97.797 0.0034592 0 39808 38735 37632 45908 43472 40542 45199 42785 48079 TRUE FALSE 37926.35473 42682.14054 39357.46442 41293.24062 51053.50304 39138.02037 38303.06241 39038.51858 55534.84577 0.682928965 0.768565032 0.708698546 0.743555511 0.91930575 0.70474708 0.689712232 0.70295538 1 15.76110567 -1.864632484 2.370320551 1.124909138 0.73849776 0.586226263 0.068620888 8220089.472 4525754.742 5780192.969 0.016294891 0.013657384 1.864632484 -0.386411377 GFQFVSSS(ph)LPDICYR ddPTM_SK-BR-3_Trastuzumab_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(0.129)S(0.152)S(0.719)LPDICYR 79.652 0.020254 22121000 49741 52080 46880 58202 57936 55647 56823 58209 58673 TRUE FALSE 47389.84151 57387.01121 49029.49437 52351.42438 68040.02006 53719.93044 48153.60772 53111.91137 67771.70918 0.699256992 0.846769425 0.723450758 0.772467229 1.00395904 0.79266011 0.710526683 0.783688533 1 16.04839554 -2.49372947 2.069607525 3.219501524 0.78895395 0.360549586 0.08715895 3258324.803 175843.3697 34071713.46 0.020760008 0.003208267 2.49372947 -2.430547574 GFQFVSSSLPDICYR ddPTM_SK-BR-3_Trastuzumab_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 0 127.79 0.00073865 0 40916 31081 35380 34471 40032 33955 42245 43871 41058 FALSE TRUE 38981.98177 34248.18924 37002.208 31005.90959 47013.56813 32779.12984 35799.74937 40029.42267 47425.06494 0.821970024 0.722153766 0.78022472 0.653787393 0.991323221 0.691177332 0.754869802 0.844056254 1 15.53336213 0.913215546 3.561744218 0.999817919 0.770880832 0.384488614 0.090720627 0.351309787 10.36213081 0.077375949 0.019960751 8.188711045 -0.913215546 -0.228937086 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK 30 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 270.01 8.22E-60 151597000 767500 603060 620740 656730 593640 560840 696240 699660 555440 FALSE TRUE 731221.796 664512.4996 649201.543 590714.2527 697170.628 541417.9702 590015.8007 638394.0613 641574.7984 1.139729612 1.035752186 1.011887538 0.920725462 1.086655258 0.843889086 0.91963681 0.995042297 1 19.29125795 4.356897901 0.674353701 0.943595955 1.207640915 0.427895367 0.06445183 1.639396061 0.785937259 0.027216293 0.307251107 22745.62636 -4.356897901 0.26404496 GFRDDFLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFRDDFLGGR 10 1 Q15056-2 Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 178.46 2.02E-06 499280000 199823 137930 174697 189217 207411 170996 231483 212855 234771 FALSE TRUE 190377.7628 151985.2238 182707.0302 170196.5477 243583.4127 165074.3656 196166.0169 194216.2878 271178.0876 0.702039624 0.560462776 0.673752927 0.627619101 0.898241502 0.608730473 0.723384469 0.716194621 1 18.04888108 -5 0.186230882 2.364926157 0.617834081 0.567309851 0.087409555 92.69712917 0.901654239 46.75543578 0.230490328 1.00E-05 5 -1.747092076 GFS(ph)FVATGLMEDDGKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFSFVATGLMEDDGKPR 17 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 GFS(1)FVATGLMEDDGKPR;GFS(1)FVATGLMEDDGKPR;GFS(0.988)FVAT(0.012)GLMEDDGKPR;GFS(1)FVATGLMEDDGKPR;GFS(1)FVATGLMEDDGKPR 274.95 6.35E-36 343214000 342370 243834 344270 446496 312449 531761 526328 370653 346683 TRUE FALSE 326186.8486 268680.9618 360055.12 401613.3738 366940.0067 513345.9832 446026.9969 338196.6584 400444.829 0.81456127 0.670956252 0.899137893 1.002918117 0.91633099 1.281939348 1.113828834 0.844552442 1 18.61124396 3.326910638 1.693377943 1.063301721 0.74125388 0.458788166 0.12343524 0.263609843 1.555206947 0.039110277 0.059633507 2122.807622 -3.326910638 -0.322047842 GFS(ph)FVATSIAEEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFSFVATSIAEEYK 14 0 Q9UK32-2;Q9UK32 Q9UK32-2 RPS6KA6 Ribosomal protein S6 kinase alpha-6 1 GFS(1)FVATSIAEEYK 101.62 0.0013778 12447000 17256 17784 20468 22440 16617 18366 24231 22318 18747 TRUE FALSE 16440.34308 19596.20982 21406.47805 20184.28857 19514.99954 17729.98081 20534.11592 20363.7176 21654.18901 0.759222295 0.904961613 0.988560598 0.932119349 0.901211286 0.818778334 0.94827453 0.940405461 1 14.40235852 4.441917216 2.284274175 0.92501454 0.758445376 0.532971143 0.050067476 0.268895598 2.435744419 0.012539679 0.069618259 27664.14268 -4.441917216 -0.166569164 GFSDKLDFLEGDQKPLAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFSDKLDFLEGDQKPLAQR 19 2 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 155.87 1.21E-08 422990000 1095000 958470 1039800 1202300 740920 1074700 1218300 1183000 873550 FALSE TRUE 1043241.52 1056139.183 1087475.859 1081442.52 870136.2134 1037482.87 1032425.959 1079410.249 1009015.673 1.033920036 1.046702456 1.077759135 1.071779705 0.862361445 1.028212839 1.023201113 1.069765592 1 19.94451715 GFSLEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 ;;;;;;; 194.27 0.00038676 3276568000 5823830 4225260 2887350 3665600 6987320 3732330 6489650 5021730 6711470 FALSE TRUE 5548549.098 4655818.798 3019737.853 3297126.924 8205906.396 3603078.476 5499534.702 4582000.699 7752250.49 0.71573398 0.600576414 0.38953048 0.425312227 1.058519253 0.464778387 0.709411378 0.591054263 1 22.88618376 -5 0.301567865 4.180541067 0.603135788 0.285360797 0.189986186 357.6229484 3.295992112 719.2690017 0.174956603 1.00E-05 5 -3.57740528 GFSLLATEDKEALKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFSLLATEDKEALKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 143.93 2.43E-06 700190000 137620 121030 127020 154460 82728 142180 162610 167520 96240 FALSE TRUE 131114.9753 133363.0946 132843.9926 138933.3873 97155.73701 137256.2709 137800.858 152851.0607 111164.4077 1.179469023 1.199692396 1.195022718 1.249800995 0.873982411 1.234714184 1.239613118 1.375000002 1 16.76233542 GFSNLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFSNLKK 7 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 71.501 0.086817 384200000 238400 190770 209900 247500 197590 222380 263840 242140 213900 FALSE TRUE 227131.3045 210209.6799 219524.1226 222620.8298 232049.6334 214678.9248 223586.3622 220936.9379 247070.5196 0.919297474 0.850808426 0.888507957 0.901041655 0.939204053 0.868897371 0.904949577 0.894226225 1 17.91456335 -4.999999994 0.329032 2.066883788 0.889778566 0.638709446 0.024530374 218.2695229 1.891033836 162.7880937 0.019819649 1.00E-05 4.999999994 -1.177105223 GFSQYGVSGS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.007)GS(0.988)PT(0.006)K;GFSQYGVS(0.002)GS(0.997)PT(0.002)K;GFSQYGVSGS(1)PTK;GFSQYGVS(0.001)GS(0.965)PT(0.035)K;GFSQYGVSGS(1)PTK;GFSQYGVSGS(1)PTK 243.1 6.04E-17 2386130000 2429300 2379670 2340200 2786780 1897430 2643300 2881480 2816660 2278970 TRUE FALSE 2314471.803 2622161.078 2447500.485 2506647.58 2228341.191 2551761.858 2441857.304 2570018.318 2632381.028 0.879231304 0.996117602 0.9297668 0.952235848 0.846511644 0.96937405 0.927623045 0.976309391 1 21.3279369 1.091288018 2.359366075 1.000597042 0.931134971 0.260115211 0.042273894 0.383710255 4.221106115 0.037150007 0.010257886 12.33922881 -1.091288018 -0.069462071 GFSVLHTYQDHLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFSVLHTYQDHLWR 14 0 Q5SY38;P41214 Q5SY38 EIF2D Eukaryotic translation initiation factor 2D 0 ; 107.11 0.00052218 206648000 322200 263050 262470 294710 371690 297750 398420 340090 265999 FALSE TRUE 306970.2445 289855.0941 274504.5091 265085.1909 436512.6183 287438.8428 337633.7115 310309.9167 307248.7664 0.999093497 0.94338896 0.893427539 0.862770562 1.420713982 0.935524807 1.098893628 1.0099631 1 18.22904769 GFSVVADT(ph)PELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 281.54 2.07E-31 772370000 1350081 1444101 1419138 1641313 1810068 1406694 1677988 1690836 2126897 TRUE FALSE 1286265.347 1591256.534 1484206.881 1476325.099 2125743.286 1357979.834 1421980.112 1542777.436 2456725.324 0.523569051 0.647714467 0.604140343 0.600932096 0.865275115 0.55276014 0.578811192 0.627981248 1 21.22830513 -1.592069689 2.344710241 1.041919452 0.620565202 0.618064709 0.092543942 1935588.682 1542348.392 499022.8054 0.022508979 0.025581754 1.592069689 -0.42135425 GFTDADNTWEPEENLDCPELIEAFLNSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GFTDADNTWEPEENLDCPELIEAFLNSQK 29 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ;; 220.66 1.97E-34 76963000 196858 194048 155470 216511 146793 192659 206972 209239 160340 FALSE TRUE 187552.9125 213821.7118 162598.4533 194746.9029 172393.6527 185987.1705 175394.6201 190916.9239 185204.7083 1.012678966 1.154515529 0.877939091 1.051522419 0.930827592 1.004224851 0.947031108 1.030842713 1 17.49876125 3.747642262 24.99982117 0.976285706 1.083597242 0.349142396 0.060215482 579.952831 1596481.524 0.013650439 0.024177435 5592.967064 -3.747642262 0.107311536 GFTECEMTKSS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMTKS(0.078)S(0.922)PLK;GFTECEMT(0.001)KS(0.087)S(0.912)PLK;GFTECEMTKS(0.008)S(0.992)PLK;GFTECEMTKS(0.005)S(0.995)PLK;GFTECEMT(0.002)KS(0.044)S(0.954)PLK 297.7 6.50E-44 2025690000 3516600 3134240 3335700 3878370 1946550 3971600 4002020 4519160 2222160 TRUE FALSE 3350377.287 3453622.619 3488645.144 3488508.879 2286027.704 3834062.496 3391438.347 4123438.393 2566761.224 1.305293713 1.345517685 1.359162322 1.359109234 0.890627333 1.493735553 1.321290939 1.606475256 1 21.29151766 GFTIPEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFTIPEAFR 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;;; 199.75 5.64E-05 1139146000 2610380 2488450 2381644 2786740 2623620 2498711 2995090 2886500 2649610 FALSE TRUE 2486992.511 2742025.884 2490844.733 2506611.601 3081178.497 2412180.012 2538134.012 2633742.758 3060497.986 0.812610406 0.895941084 0.813869097 0.81902083 1.006757237 0.788165855 0.829320595 0.860560199 1 21.54533499 0.936952113 19.17004736 1.000000001 0.85193697 0.357057848 0.061970554 1390.136003 422680.9856 0.055076364 0.013769091 8.648725488 -0.936952113 -0.148063031 GFTSLGMEEERIETAQQFFSWFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFTSLGMEEERIETAQQFFSWFAK 24 1 Q96JB2;Q96JB2-2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 197.92 1.65E-24 31702000 79437 54172 77473 71877 85641 65750 102460 82317 103550 FALSE TRUE 75682.17044 59692.18839 81025.21368 64651.7874 100576.7633 63473.06101 86827.84519 75108.88709 119608.0051 0.632751715 0.499065161 0.677423 0.540530605 0.840886554 0.530675693 0.725936739 0.627958697 1 16.86795442 -5 0.187293542 2.593288819 0.556341306 0.579422053 0.098970101 85.55776622 0.833531412 50.70039768 0.242908657 1.00E-05 5 -2.036947513 GFVEFAAKPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GFVEFAAKPPAR 12 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 138.94 5.98E-05 1366940000 2052190 1818030 1775630 2287500 2146220 2039740 2564500 2401100 2384600 FALSE TRUE 1955187.046 2003289.324 1857044.392 2057556.154 2520520.088 1969103.292 2173238.425 2190846.955 2754391.589 0.709843529 0.727307378 0.674212192 0.747009308 0.915091412 0.714895914 0.789008518 0.79540141 1 21.39330225 -5 0.140140855 1.863195478 0.66396679 0.652296192 0.059252388 83.94642031 0.72045235 20.15091943 0.347758071 1.00E-05 5 -1.199228688 GFVEPDHYVVVGAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GFVEPDHYVVVGAQR 15 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 169.04 1.22E-06 318000000 252560 262780 219230 288960 301490 238080 285920 273650 275430 FALSE TRUE 240621.9893 289557.5808 229281.9123 259913.1918 354069.7605 229835.2299 242297.6527 249687.7553 318142.2777 0.756334528 0.910151216 0.720689856 0.816971557 1.11292898 0.72242907 0.761601553 0.784830476 1 18.27931258 -2.335025278 2.295072044 2.037921739 0.823310341 0.185498223 0.116401081 8905811.179 1166534.06 48034095.28 0.026803553 0.004623541 2.335025278 -1.214611398 GFVLHK ddPTM_SK-BR-3_Trastuzumab_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 ; 93.595 0.04544 2803700000 5480700 4884200 4511700 5245600 4874900 4844800 6004000 5459100 4858600 FALSE TRUE 5221638.173 5381905.533 4718565.908 4718302.322 5725081.017 4677023.361 5087979.529 4981072.263 5612046.874 0.930433813 0.95899155 0.840792319 0.840745352 1.02014134 0.833389932 0.906617433 0.88756783 1 22.42009563 -1.258161232 4.93551017 1.000020524 0.905894124 0.215204655 0.058261671 1.24E-05 1.86E-06 0.053029023 0.012496336 0.055187252 1.258161232 -0.0941264 GFVQVDDGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GFVQVDDGRK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;; 149.23 3.80E-05 1336257000 1868800 1518470 1657040 1903670 1429760 1900560 2005530 1927690 1614910 FALSE TRUE 1780465.528 1673203.819 1733016.923 1712309.475 1679109.691 1834743.131 1699549.564 1758891.244 1865341.995 0.954498174 0.896995738 0.929061227 0.917960074 0.900161845 0.98359611 0.911119553 0.942932314 1 20.83100873 -0.503364384 0.442451551 1.01660107 0.923056507 0.436087555 0.02568989 7.663112309 1.36875686 0.213756048 0.013395122 0.313787483 0.503364384 -0.093544563 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 373.26 1.78E-176 218260000 63701 62839 63492 75391 83675 67400 85787 70120 12747 FALSE TRUE 60689.97997 69242.36554 66403.171 67812.55345 98267.89351 65065.9211 72698.61756 63979.92107 14723.73966 4.121913412 4.702770298 4.509939224 4.605660995 6.674112406 4.419116516 4.937510392 4.345358079 1 13.84585653 0.684608897 2.680150094 1.000058711 4.815433742 0.752598882 0.688377762 1.192855851 9.529148016 0.63975731 0.169401766 4.837365439 -0.684608897 3.815375031 GGAAVDPDSGLEHSAHVLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GGAAVDPDSGLEHSAHVLEK 20 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;; 218.05 5.88E-25 2943218000 6941050 6289650 6544510 7657560 6687860 6968040 8363800 7161580 136550.1 FALSE TRUE 6612960.322 6930572.486 6844582.257 6887807.52 7854220.667 6726735.028 7087748.698 6534474.089 157725.5921 41.92699634 43.94069721 43.3955084 43.66956198 49.79674231 42.64834221 44.93721408 41.42938379 1 17.26705724 0.582261655 2.765988955 1.000106818 44.20881863 0.975935052 2.125005181 0.837930239 5.382751724 1.958663898 0.51633746 3.821744549 -0.582261655 43.20871181 GGAEPRPLPLSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGAEPRPLPLSYR 13 1 Q8NFV4;Q8NFV4-6;H0YC52;C9J7Q4;H7BZ58;Q8NFV4-3;Q8NFV4-2 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 145.41 3.81E-05 290340000 321800 248180 257170 253130 347210 235363 270780 251650 331800 FALSE TRUE 306589.1517 273469.8242 268961.4989 227684.8915 407763.3141 227212.3203 229467.5378 229614.1919 383253.8494 0.799963659 0.713547495 0.701784207 0.594083769 1.063950994 0.592850719 0.598735115 0.599117771 1 18.54794076 4.510050345 2.291555894 0.711025027 0.803502256 0.000350485 0.170279116 1.774469898 15.35832625 0.04052553 0.271729928 32363.1171 -4.510050345 0.092477229 GGAEQFMEETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGAEQFMEETER 12 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 244.06 5.18E-16 1899150000 1660040 1556340 1550280 1701500 1631940 1637500 1808960 1755060 1609180 FALSE TRUE 1581573.199 1714932.815 1621361.871 1530461.987 1916549.819 1580792.964 1532969.928 1601377.642 1858723.416 0.850892169 0.922640131 0.87229862 0.82339415 1.031110817 0.8504724 0.824743431 0.861547032 1 20.82588068 4.746587673 6.619527666 0.888463972 0.850113135 0.026696835 0.070458843 0.540730455 134.5832242 0.015703922 0.093901469 55794.02248 -4.746587673 -0.038350837 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK 33 0 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 131.84 5.65E-08 46323000 33237 26423 27893 33241 25825 31189 39106 30499 27219 FALSE TRUE 31665.95288 29115.53374 29171.92164 29899.55153 30328.87182 30108.91711 33139.66147 27828.34587 31439.9835 1.007187325 0.926067081 0.92786059 0.951004046 0.964659279 0.95766326 1.054061032 0.885125969 1 14.94031284 1.955048793 24.98365281 0.990767375 0.955170682 0.038619142 0.046734975 943.3031768 524281.2859 0.017952461 0.011588588 90.16724359 -1.955048793 -0.035596693 GGAGGS(ph)PGSSSGSGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(0.99)PGS(0.009)S(0.001)SGSGSSR;GGAGGS(0.999)PGS(0.001)SSGSGSSR;GGAGGS(0.976)PGS(0.012)S(0.012)SGSGSSR;GGAGGS(0.998)PGS(0.001)SSGSGSSR 324.78 4.62E-59 532250000 554200 540410 486530 601500 533780 490350 532770 519350 526440 TRUE FALSE 528004.0643 595478.3934 508837.8817 541036.0772 626871.063 473369.0565 451486.1515 473872.9608 608077.6265 0.868316875 0.979280223 0.836797572 0.88974837 1.030906311 0.778468136 0.742481111 0.77929682 1 19.21389598 2.203267538 24.99980433 0.79615526 0.918916836 0.193227057 0.089051036 202.3179049 143310.4713 0.030261817 0.022350689 159.6862558 -2.203267538 0.122761576 GGAPDPSPGATATPGAPAQPS(ph)SPDARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDARR 27 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.59)S(0.41)PDARR 121.9 5.69E-05 296950000 45264 23982 54729 36008 63245 36170 58088 44022 74286 TRUE FALSE 43124.46042 26425.79307 57238.37878 32388.40743 74274.90798 34917.42383 49225.60874 40167.2003 85805.89348 0.502581567 0.307971772 0.667068152 0.377461339 0.86561546 0.40693503 0.573685638 0.468117033 1 16.38878912 -5 0.223023851 3.504238915 0.44988201 0.463050897 0.159945188 127.9759154 1.280233016 144.3992689 0.267511003 1.00E-05 5 -3.054356904 GGAPDPSPGATATPGAPAQPSS(ph)PDARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDARR 27 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.273)S(0.727)PDARR 160.3 8.61E-12 237630000 89583 60920 103040 76024 118430 78703 109970 91100 140280 TRUE FALSE 85348.58913 67127.81726 107764.4859 68381.92308 139084.1545 75977.49538 93192.05676 83122.80105 162033.9059 0.5267329 0.414282535 0.665073679 0.422022309 0.858364511 0.468898746 0.575139235 0.512996342 1 17.30593621 -5 0.290635173 4.52495097 0.520804846 0.526693008 0.131274289 183.4288527 1.725559359 392.3572829 0.126021924 1.00E-05 5 -4.004146124 GGAVERPLT(ph)PAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGAVERPLTPAPR 13 1 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR 101.15 0.0033554 737080000 1201920 982030 1064250 1194610 1165370 1132710 1290580 1211410 1217600 TRUE FALSE 1145107.624 1082099.973 1113046.915 1074525.533 1368610.159 1093483.969 1093678.318 1105332.518 1406419.189 0.814200796 0.769400746 0.791404813 0.764015125 0.973116813 0.777495058 0.777633245 0.785919679 1 20.42359523 -1.601226368 2.719584553 1.016148957 0.803750696 0.49826524 0.060914117 9833665.974 9264621.945 1132020.527 0.01397551 0.025048033 1.601226368 -0.212398261 GGCWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGCWPR 6 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ;;; 122.76 0.044387 2948390000 1972090 1672720 1545470 1805470 1711280 1684970 2289050 1921460 1842130 FALSE TRUE 1878873.214 1843172.07 1616331.328 1623980.725 2009726.69 1626619.066 1939813.381 1753206.776 2127798.112 0.883012915 0.86623447 0.759626263 0.763221246 0.944510045 0.764461185 0.911652929 0.823953535 1 21.02092984 -0.575931698 0.583565198 1.023412984 0.840107204 0.379705565 0.064191487 12.96304111 3.367938523 0.675412938 0.02480346 0.265502309 0.575931698 -0.18330578 GGDAKS(ph)PVLQEK ddPTM_SK-BR-3_Trastuzumab_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 107.63 0.0010857 4245350000 7501320 6607650 6643700 7533800 4057590 7453170 7865020 8003000 4526870 TRUE FALSE 7146747.47 7280977.047 6948320.217 6776488.111 4765232.411 7195064.854 6665066.748 7302214.893 5228873.88 1.366785207 1.392456046 1.328836835 1.295974672 0.911330531 1.376025703 1.274665808 1.396517694 1 22.31806884 -5 0.140182154 0.078314615 1.397083169 0.27095694 0.144134741 188.9909806 1.62224994 49.90648584 0.860291037 1.00E-05 5 1.318768554 GGDEYDNHCGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGDEYDNHCGK 11 0 P20645;F5GX30;F5H4U1;H0YGE9 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;; 119.74 0.00054516 514470000 1414010 1139880 1053990 1387630 1255500 1150280 1582820 1299360 1158620 FALSE TRUE 1347172.55 1256035.068 1102316.484 1248142.796 1474458.802 1110445.515 1341331.739 1185581.15 1338292.872 1.006635078 0.938535274 0.823673582 0.932638006 1.101745988 0.829747762 1.002270704 0.885890656 1 20.35196244 4.493880366 3.070203769 0.938632043 1.004376649 0.06019462 0.083228486 0.758650507 13.66805762 0.019029767 0.090917861 31180.30553 -4.493880366 0.065744606 GGDISVCEWYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GGDISVCEWYQR 12 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;;;;; 300.43 4.10E-36 4384200000 1333434 1093055 1167733 1274727 1416222 1061244 1377225 1176141 1303061 FALSE TRUE 1270405.217 1204438.547 1221274.713 1146589.02 1663210.668 1024492.854 1167104.032 1073151.859 1505133.045 0.844048453 0.800220653 0.811406485 0.761785826 1.105025681 0.680665977 0.775415858 0.712994684 1 20.52145959 -0.601728794 7.292380845 1.000007188 0.81114462 0.211325412 0.114474191 0 0 0.101886479 0.024014873 0.250190725 0.601728794 -0.188862569 GGDLMAYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGDLMAYDR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 172.94 0.00012984 1579030000 1870750 1675520 1147170 1432600 2093310 1277290 1841630 1514360 1757940 FALSE TRUE 1782323.355 1846257.393 1199768.879 1288592.326 2458382.601 1233057.127 1560655.52 1381754.61 2030552.357 0.877752967 0.909238999 0.590858382 0.634601872 1.210696485 0.607252072 0.768586692 0.680482139 1 20.9534408 GGDLMAYDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GGDLMAYDRR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;; 163.86 1.02E-05 19150440000 9360170 6481640 5906660 6273310 11197720 6183376 10681680 8116820 10633140 FALSE TRUE 8917733.314 7142126.485 6177486.203 5642704.96 13150598.82 5969244.139 9051993.533 7406068.211 12282073.04 0.726077209 0.581508224 0.502967714 0.459426103 1.070714917 0.486012753 0.737008606 0.602998222 1 23.55005075 GGDS(ph)PEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GGDSPEAK 8 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;H0YD62;H0YF37 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK 117.28 0.0022122 1532858000 3275900 3625970 3810810 5008730 2510360 3688720 4467050 6340160 3851330 TRUE FALSE 3121054.699 3995460.465 3985539.408 4505242.944 2948165.989 3560978.701 3785519.479 5784981.979 4448574.587 0.701585337 0.898143976 0.89591381 1.012738543 0.662721492 0.80047634 0.850951109 1.300412495 1 22.08491171 1.299742005 8.987797679 1.149152403 0.831100448 0.542187705 0.121662167 0.194069717 26.32273467 0.076233781 0.027742276 19.94077372 -1.299742005 -0.318051954 GGDSIGET(ph)PTPGASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GGDSIGET(0.999)PT(0.001)PGASK 198.89 8.60E-08 64893000 195240 213020 192830 231770 155260 217650 221220 212340 173330 TRUE FALSE 186011.3921 234726.9802 201671.4462 208472.0393 182337.2948 210112.7259 187468.826 193746.3839 200209.1312 0.929085457 1.172408965 1.007303938 1.041271385 0.91073416 1.049466249 0.936365015 0.967720018 1 17.61114825 2.885030952 9.302571206 0.972688997 1.046924467 0.172468859 0.06914303 0.536392478 40.1655314 0.019976456 0.021203829 767.4161803 -2.885030952 0.07423547 GGDVS(ph)PSPYSSSSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(0.924)PS(0.073)PY(0.003)SSSSWR;GGDVS(0.712)PS(0.288)PYSSSSWR;GGDVS(0.982)PS(0.018)PYSSSSWR;GGDVS(0.893)PS(0.106)PYS(0.001)SSSWR;GGDVS(0.998)PS(0.002)PYSSSSWR;GGDVS(1)PSPYSSSSWR;GGDVS(0.982)PS(0.018)PYSSSSWR;GGDVS(0.957)PS(0.043)PYSSSSWR;GGDVS(0.974)PS(0.026)PYSSSSWR;GGDVS(0.963)PS(0.037)PYSSSSWR 384.66 2.73E-114 4700212000 2325849 2043735 2203847 2567128 2537693 2191469 2617350 2301883 2586564 TRUE FALSE 2215910.727 2251993.92 2304895.565 2309075.416 2980265.856 2115577.879 2218025.187 2100317.921 2987675.135 0.741683961 0.753761309 0.771467934 0.772866966 0.997520052 0.708101712 0.742391688 0.702994076 1 21.51059185 -1.636592923 3.124004958 1.016706271 0.77158338 0.423432571 0.082896999 4029339.57 4789457.948 417768.1645 0.018694961 0.023089104 1.636592923 -0.245122891 GGEFDEFVNDDT(ph)DDDLPISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGEFDEFVNDDTDDDLPISK 20 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GGEFDEFVNDDT(1)DDDLPISK;GGEFDEFVNDDT(1)DDDLPISK 161.84 8.09E-11 151318000 585700 567660 567180 633860 458770 629710 652910 662450 541500 TRUE FALSE 558015.1217 625505.1994 593185.764 570143.1885 538779.3427 607902.9848 553296.588 604442.3661 625473.0544 0.892148939 1.000051393 0.948379406 0.911539169 0.86139497 0.97190915 0.884604995 0.966376348 1 19.25458821 1.002343192 24.55075934 1.000000006 0.927988295 0.275705707 0.041378663 60.39376741 632764.4716 0.038569081 0.00964227 10.05409979 -1.002343192 -0.072011711 GGET(ph)PGSEQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.998)PGS(0.002)EQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(0.99)PGS(0.01)EQWK;GGET(1)PGSEQWK 238.01 1.50E-14 3028400000 8484610 8364460 7295840 8950860 6083170 8298210 8201440 9071880 6067570 TRUE FALSE 8083559.3 9216807.984 7630361.481 8051102.547 7144072.922 8010840.907 6950159.698 8277498.094 7008497.767 1.153394004 1.315090379 1.088729958 1.148762947 1.019344396 1.143018258 0.991676095 1.181065953 1 22.74067381 3.661312854 7.974461635 1.079561096 1.233983948 0.419792915 0.074489565 0.236260529 22.16738585 0.017903015 0.027807138 4584.720385 -3.661312854 0.154422852 GGFCNFMHLKPISR ddPTM_SK-BR-3_Trastuzumab_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 ; 223.06 2.20E-12 1103330000 2268400 1834730 1792270 2074100 2406700 1902350 2748900 2212200 2294700 FALSE TRUE 2161177.228 2021691.073 1874447.352 1865607.527 2826427.718 1836471.142 2329504.818 2018488.04 2650550.356 0.815369239 0.762743884 0.707191753 0.703856662 1.066355035 0.692864083 0.878875896 0.761535443 1 21.33786052 GGFDS(ph)PFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGFDSPFYR 9 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1;A0A2R8YEH9 A0A2R8YFV7 TSC1 Hamartin 1 GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR 106.37 0.0030919 761320000 2210420 2068430 1986860 2308110 1826850 2211210 2335080 2404940 1999060 TRUE FALSE 2105937.827 2279205.369 2077959.496 2076094.398 2145452.062 2134635.243 1978820.659 2194350.704 2309064.015 0.912030941 0.98706894 0.8999142 0.899106471 0.929143604 0.924459101 0.856979558 0.950320429 1 21.13887674 3.710399667 24.93780022 0.912967603 0.949549958 0.026464816 0.041734777 1243.814266 1101454.175 0.010237123 0.015862936 5133.335702 -3.710399667 0.036582355 GGFGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GGFGFR 6 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;; 135.03 0.032054 4473505000 3702570 3457300 3177940 3757570 4004440 3336850 3887990 3591940 3953840 FALSE TRUE 3527556.854 3809602.801 3323651.692 3379851.925 4702813.068 3221294.048 3294805.718 3277410.692 4566981.314 0.772404486 0.834162117 0.727756797 0.740062569 1.029742131 0.705344258 0.721440595 0.717631728 1 22.12280946 -0.323813515 7.525841202 1 0.782003021 0.340310058 0.095787415 0 0 0.088473254 0.020853346 0.474445668 0.323813515 -0.217996979 GGGAPWPGGAQTYS(ph)PSSTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGAPWPGGAQTYSPSSTCR 20 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GGGAPWPGGAQTYS(0.988)PS(0.009)S(0.002)T(0.001)CR 143.99 1.70E-07 100750000 105740 83632 99280 121410 134840 91249 99972 97722 147790 TRUE FALSE 100741.8798 92154.19588 103832.0862 109205.6361 158356.0533 88089.02425 84719.43529 89164.94362 170708.5184 0.590139735 0.539833611 0.608241974 0.639719899 0.927640019 0.516020085 0.496281241 0.522322755 1 17.38117553 -1.387830866 2.914088173 1.006614294 0.597519814 0.502576845 0.123289805 15189120.02 18333683.32 845659.9818 0.03029642 0.040942008 1.387830866 -0.40909448 GGGDRYEDRYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGGDRYEDRYDR 12 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 208.95 3.42E-08 2507820000 1495680 986120 1331670 1418350 1741700 1309350 1660000 1486320 1794250 FALSE TRUE 1424982.171 1086606.749 1392728.387 1275774.763 2045451.929 1264006.881 1406736.512 1356169.941 2072493.126 0.68756907 0.524299326 0.672006275 0.615574907 0.986952334 0.609896779 0.678765345 0.654366436 1 20.98293589 -5 0.208248719 2.545972678 0.621252964 0.4101906 0.120091905 141.0967431 1.404476144 91.26651238 0.249931334 1.00E-05 5 -1.924719714 GGGEYGETWHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGEYGETWHK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 140.3 3.87E-05 875090000 965960 858710 862890 1027570 831340 983230 996380 978710 817040 FALSE TRUE 920300.9851 946213.5253 902454.36 924276.7113 976325.4328 949180.4986 844363.9312 893008.9639 943742.3903 0.975161225 1.002618442 0.956250741 0.979373949 1.034525356 1.00576228 0.894697472 0.946242294 1 19.84803358 1.758221885 25 0.936775283 0.99190021 0.281236589 0.032811684 8.625737966 10978.09582 0.014170584 0.00785829 57.3088752 -1.758221885 0.055124926 GGGFGDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GGGFGDRDR 9 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 109.29 0.0022555 3352680000 3516730 2444950 2609400 2812280 4120180 2891260 3871050 3154210 3941050 FALSE TRUE 3350501.142 2694093.185 2729043.571 2529584.271 4838738.088 2791134.941 3280450.226 2878010.651 4552207.906 0.736016722 0.591821209 0.599498887 0.55568294 1.062943123 0.613138723 0.720628384 0.632223025 1 22.11813502 GGGGEGGGEAS(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGGGEGGGEASPDR 14 0 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR 231.51 5.38E-13 432760000 704552 758044 578775 773482 658092 632437 631724 658564 628405 TRUE FALSE 671249.2232 835289.5454 605312.4062 695730.1198 772863.0364 610535.5481 535342.9014 600896.6449 725854.838 0.924770613 1.150766657 0.833930387 0.9584976 1.064762534 0.841126237 0.737534385 0.827846855 1 19.46932153 2.149278273 6.692318559 0.817727182 0.99478367 0.261414051 0.106086545 0.216832502 13.54154892 0.038048999 0.028054433 141.0192085 -2.149278273 0.177056488 GGGGEGGGEAS(ph)PDRQGSLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GGGGEGGGEASPDRQGSLPSR 21 1 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(0.993)PDRQGS(0.006)LPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(0.983)PDRQGS(0.017)LPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR 266.83 1.20E-36 4654310000 1181826 881316.6 1117201.2 1069993 1377120 1085751 1348781 1142294 1558248 TRUE FALSE 1125963.427 971123.7635 1168425.98 962435.2708 1617289.292 1048151.171 1142999.686 1042268.682 1799893.141 0.625572375 0.539545233 0.649164083 0.534718006 0.898547394 0.582340777 0.635037525 0.579072534 1 20.77947983 -2.142804415 2.371852276 1.815296142 0.626258572 0.561150887 0.102630721 5911841.218 1304169.841 25983747.11 0.023241838 0.007197731 2.142804415 -1.18903757 GGGGGQDNGLEGLGNDS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GGGGGQDNGLEGLGNDSR 18 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R;GGGGGQDNGLEGLGNDS(1)R 335.82 4.64E-75 1274490000 2290160 2509240 2054840 2591800 2235320 2273800 2150520 2317750 2274080 TRUE FALSE 2181908.675 2764934.409 2149056.447 2331267.34 2625159.1 2195057.736 1822418.677 2114795.523 2626732.712 0.830655006 1.052613536 0.818148126 0.887516012 0.999400924 0.835660867 0.693796772 0.805104955 1 21.32483797 2.020851637 13.44592067 0.790391259 0.921883981 0.095015535 0.103734133 1.656898458 1066.057794 0.035931893 0.026459794 104.9183948 -2.020851637 0.131492722 GGGGNFGPGPGSNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 304.89 2.59E-44 1607690000 781105 627011 683967 776067 792319 692269 802176 710471 781435 FALSE TRUE 744183.7147 690904.1338 715327.5635 698055.2707 930499.1827 668295.5509 679789.3182 648258.3928 902615.9488 0.824474369 0.765446406 0.792504901 0.773369085 1.030891581 0.740398562 0.753132403 0.718199577 1 19.78375274 -2.182463393 2.510521611 1.579824028 0.798075917 0.342541756 0.087135264 5653727.279 1520816.891 18937325.45 0.020825361 0.006569565 2.182463393 -0.781748111 GGGHILPYDQPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGHILPYDQPLR 13 0 Q9H3G5;H7C0X5;H7C218 Q9H3G5 CPVL Probable serine carboxypeptidase CPVL 0 ; 73.881 0.035623 850370000 365840 286720 342220 375330 385730 318190 415940 354370 398360 FALSE TRUE 348547.4682 315937.094 357911.1255 337601.1153 453001.1899 307171.0005 352480.7137 323339.4842 460135.6343 0.757488537 0.686617316 0.777838313 0.733699132 0.98449491 0.667566208 0.76603655 0.702704725 1 18.81169966 -2.27117702 2.339191804 2.051404543 0.756017754 0.427233212 0.087407722 4795684.074 840131.9875 26668023.76 0.019681376 0.005355783 2.27117702 -1.29538679 GGGHVAQIYAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGHVAQIYAIR 12 0 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ; 129.89 0.00022622 796200000 1321180 1511540 1002880 1376770 1286760 1143770 1178590 1334200 1081500 FALSE TRUE 1258730.44 1665567.644 1048863.04 1238374.464 1511170.537 1104160.958 998774.4492 1217370.375 1249213.496 1.007618348 1.333293027 0.839618722 0.991323315 1.209697574 0.883884909 0.799522621 0.974509464 1 20.25258863 2.86405945 0.753086586 0.897699675 1.139224044 0.109237866 0.152528887 0.967800822 1.209646987 0.099800523 0.111320913 731.2391744 -2.86405945 0.241524369 GGGPGKS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.703)PT(0.297)R;GGGPGKS(0.792)PT(0.208)R;GGGPGKS(0.979)PT(0.021)R;GGGPGKS(0.5)PT(0.5)R;GGGPGKS(0.98)PT(0.02)R;GGGPGKS(0.788)PT(0.212)R;GGGPGKS(0.937)PT(0.063)R 85.271 0.0086925 6552680000 3920880 3735400 3531730 4098430 2983200 3990020 4286460 4130950 3459440 TRUE FALSE 3735547.773 4116041.507 3693663.314 3686448.03 3503469.135 3851844.607 3632481.801 3769222.118 3995912.287 0.934842285 1.030063027 0.924360459 0.922554792 0.876763273 0.963946236 0.909049434 0.943269483 1 21.93009348 3.699618741 24.89155914 0.92837276 0.982452676 0.191208853 0.03977467 570.9641332 364959.0175 0.009541329 0.014781617 5007.474435 -3.699618741 0.054079915 GGGPGKS(ph)PTRGST ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGPGKSPTRGST 13 2 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.434)PT(0.434)RGS(0.072)T(0.06) 58.824 0.081949 268560000 358450 132860 404540 226260 423490 344920 631290 416810 684620 TRUE FALSE 341506.7789 146398.585 423088.5591 203515.9149 497346.5219 332975.3339 534975.1161 380311.9068 790787.373 0.431856641 0.18513015 0.535021895 0.257358579 0.628925725 0.421068097 0.676509431 0.480928148 1 19.59293031 -0.164282415 0.212701068 1.303145678 0.233660415 0.659137462 0.132955881 5.093679581 0.379549306 1.421207566 0.336819796 0.685042609 0.164282415 -1.069485263 GGGPGKSPT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.058)PT(0.942)R 102.97 0.0046503 291860000 284160 289440 264440 317550 206650 289630 313740 337110 238270 TRUE FALSE 270728.32 318934.2651 276564.8356 285629.2707 242689.6946 279600.0405 265873.2008 307590.8613 275219.6947 0.983680766 1.158835182 1.004887517 1.037822787 0.881803516 1.015915815 0.96603988 1.117619368 1 18.07022419 3.514734582 24.48208669 0.996712113 1.073025235 0.129959088 0.071630841 679.624514 442357.7713 0.017759489 0.02750447 3271.407025 -3.514734582 0.076313121 GGGPLILLDLNDENS(ph)NQSFHSEGSLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGPLILLDLNDENSNQSFHSEGSLQK 27 0 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GGGPLILLDLNDENS(0.978)NQS(0.021)FHS(0.001)EGSLQK 87.659 0.004967 33196000 34909 24886 34519 32353 29642 34447 38378 37682 41886 TRUE FALSE 33258.92075 27421.91169 36101.73029 29100.81497 34811.55541 33254.09175 32522.73124 34382.36432 48381.46696 0.687431011 0.566785454 0.746189245 0.601486826 0.719522528 0.6873312 0.672214658 0.710651547 1 15.56216689 -5 0.250351359 3.044999174 0.636299806 0.8023843 0.051381698 69.35465197 0.687059932 72.48820587 0.065675396 1.00E-05 5 -2.408699368 GGGPQAQSHGEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGGPQAQSHGEAR 13 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 ;;; 119.69 0.00032888 376279000 193174 178854 165635 199133 211864 188874 217236 171331 216900 FALSE TRUE 184043.0479 197079.4259 173229.5286 179115.7725 248813.0145 182333.246 184092.6584 156328.3494 250535.7442 0.734597965 0.78663197 0.691436382 0.714931009 0.993123817 0.727773383 0.734795983 0.623976231 1 17.93465692 -2.221854194 2.377490805 1.825543651 0.754973148 0.401312846 0.095499045 4233018.79 744770.4233 18915273.59 0.021704573 0.005999925 2.221854194 -1.070570503 GGGPVTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GGGPVTLQDYRLPDS(1)DDDEDEETAIQR;GGGPVTLQDYRLPDS(1)DDDEDEETAIQR;GGGPVTLQDYRLPDS(1)DDDEDEETAIQR 248.06 7.00E-46 611710000 315482 227436 348152 308182 377885 275750 397142 338950 443779 TRUE FALSE 300569.7911 250611.987 364115.1136 277202.9599 443788.0244 266200.7084 336550.6939 309269.7411 512597.9808 0.586365539 0.488905529 0.710332711 0.540780437 0.865762334 0.519316732 0.656558758 0.603337806 1 18.96746827 -5 0.231765391 3.090151662 0.569894144 0.543066945 0.108596478 116.2190545 1.161932112 114.1372759 0.168025712 1.00E-05 5 -2.520257518 GGGQEERPFVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGQEERPFVAR 12 1 Q9HA64;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 114.02 0.001006 144630000 259190 234070 262230 266530 358010 234430 291280 270800 366170 FALSE TRUE 246938.6024 257921.9991 274253.5049 239737.898 420446.8306 226311.6303 246839.8863 247087.3164 422953.7735 0.583843006 0.609811321 0.648424301 0.566818203 0.994072774 0.535074149 0.583609609 0.584194614 1 18.69014047 -2.146432535 2.404359893 1.82577848 0.632933732 0.432485459 0.130111937 5260375.688 1269910.381 23726536.32 0.029469879 0.007137851 2.146432535 -1.192844748 GGGQLDLLGVSLAS(ph)LKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGGQLDLLGVSLASLKK 17 1 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1;H0Y7D3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GGGQLDLLGVS(0.047)LAS(0.953)LKK 144.77 3.06E-07 52514000 279500 260690 320060 342960 195540 335220 371860 372010 255300 TRUE FALSE 266288.5889 287254.6074 334735.0676 308485.0092 229642.1141 323611.2473 315125.9273 339434.8323 294890.6201 0.903007999 0.97410561 1.135116022 1.046099768 0.778736584 1.09739417 1.068619705 1.151053337 1 18.16982041 GGGQSVQFTDIETLKQES(ph)PNGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGGQSVQFTDIETLKQESPNGSR 23 1 Q02241;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23 1 GGGQSVQFTDIETLKQES(0.999)PNGS(0.001)R;GGGQSVQFTDIETLKQES(1)PNGSR;GGGQSVQFTDIETLKQES(1)PNGSR 273 7.12E-52 1048030000 1293340 1273270 1359070 1517530 1017870 1381490 1553870 1554810 1227300 TRUE FALSE 1232206.381 1403017.661 1421384.704 1364985.001 1195386.206 1333648.655 1316798.593 1418662.594 1417623.416 0.86920572 0.989697013 1.002653235 0.962868549 0.843232548 0.940763704 0.928877569 1.000733042 1 20.43504291 1.235155016 24.21298028 1.000366589 0.935394176 0.244612704 0.048503912 92.63856093 658558.5456 0.040428739 0.0117205 17.18521683 -1.235155016 -0.064972414 GGGSGGGEES(ph)EGEEVDED ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGSGGGEESEGEEVDED 18 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 GGGSGGGEES(1)EGEEVDED;GGGSGGGEES(1)EGEEVDED 185.67 5.45E-14 462190000 1588690 1588340 1503900 1610280 1298860 1692330 1535590 1620150 1463650 TRUE FALSE 1513595.772 1750193.652 1572855.303 1448411.595 1525380.773 1633724.188 1301307.542 1478281.077 1690625.367 0.895287508 1.035234468 0.930339349 0.856731257 0.902258302 0.966343118 0.769719636 0.874398969 1 20.68912557 3.454981186 6.69484219 0.881818397 0.968185006 0.129784625 0.070395449 0.225091585 38.62962501 0.018728384 0.02595611 2850.894761 -3.454981186 0.08636661 GGGSLPESLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGSLPESLRR 11 1 Q14376;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 ; 97.452 0.010031 907420000 816580 843480 710420 774780 739680 830350 928510 889400 708040 FALSE TRUE 777981.8817 929431.571 742993.4597 696897.6424 868679.9578 801594.7713 786848.7462 811519.421 817839.227 0.95126506 1.136447776 0.90848352 0.852120587 1.062164701 0.980137348 0.962106879 0.992272557 1 19.64145774 3.72106251 24.9937539 0.963908283 1.043856436 0.176337064 0.070508326 1179.709392 1685060.651 0.018182957 0.028235303 5260.929838 -3.72106251 0.079948152 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 GGGTSSGGSSTNS(0.999)LT(0.001)GSRPPK;GGGTSSGGSSTNS(0.999)LT(0.001)GSRPPK 188.39 1.54E-17 459090000 182252 142801 156895 173667 145709 170298 204506 199422 171631 TRUE FALSE 173637.3091 157352.5843 164088.7909 156209.6632 171120.6035 164400.5376 173304.8537 181959.5525 198246.6589 0.875864996 0.793721242 0.827700158 0.787956095 0.863170176 0.829272677 0.874188017 0.917844232 1 17.59693703 1.062341048 1.052010557 0.999924162 0.825743277 0.819781146 0.026428747 0.195632116 0.460217088 0.023294348 0.007658589 11.54359412 -1.062341048 -0.174180885 GGHDILVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGHDILVR 8 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 136.11 0.00080486 194260000 119530 114100 136510 156600 124720 137520 122900 133950 115700 FALSE TRUE 113880.0538 125726.9197 142769.1185 140858.2705 146471.1285 132757.6479 104149.3478 122220.6279 133642.1651 0.852126675 0.940772844 1.068293966 1.053995723 1.095994879 0.993381451 0.779315029 0.914536425 1 17.02801573 -1.007646027 6.641795957 1.000000012 0.952179644 0.005033427 0.098696707 1.94E-08 2.95E-09 0.105160552 0.024786573 0.098254845 1.007646027 -0.047820368 GGHFAAFEEPELLAQDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGHFAAFEEPELLAQDIR 18 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 ; 218.43 7.88E-19 94805000 143858 123536 85678 131821 197157 94728 151121 105489 114833 FALSE TRUE 137058.1174 136124.4588 89606.42105 118570.1026 231541.1184 91447.54561 128064.7159 96251.82393 132640.7152 1.033303517 1.026264512 0.675557433 0.893919356 1.745626282 0.689437972 0.965500795 0.72565821 1 17.01716416 GGHMDDGGYSMNFNMSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 285.5 1.89E-40 945600000 269655 211584 213233 241357 335152 236147 303944 245955 269331 FALSE TRUE 256908.9426 233144.6502 223009.944 217095.3358 393602.4027 227969.1702 257571.7605 224417.8763 311097.4759 0.825814937 0.749426364 0.716849095 0.697837021 1.265206031 0.732790163 0.827945517 0.72137479 1 18.24700716 GGIDNPAITS(ph)DQELDDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGIDNPAITSDQELDDKK 18 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GGIDNPAIT(0.027)S(0.973)DQELDDKK;GGIDNPAIT(0.05)S(0.95)DQELDDKK;GGIDNPAIT(0.061)S(0.939)DQELDDKK;GGIDNPAIT(0.049)S(0.951)DQELDDKK 190.24 1.75E-14 983750000 1555250 1449290 1395460 1734120 847980 1806870 1608400 1908580 997250 TRUE FALSE 1481736.415 1596974.299 1459443.221 1559802.963 995867.4435 1744297.639 1363009.04 1741454.617 1151898.437 1.286342934 1.386384639 1.266989497 1.35411501 0.864544487 1.514280759 1.183271889 1.51181264 1 20.13558209 -1.301210494 3.487649472 0.998932314 1.293064311 0.202896899 0.184280013 42966086.17 80417915.18 507020.3586 0.039011158 0.049979224 1.301210494 0.294131997 GGIHTADTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGIHTADTK 9 0 O00442;O00442-2 O00442 RTCA RNA 3-terminal phosphate cyclase 0 72.928 0.045363 65184000 98343 91227 90661 114710 83119 77363 108370 108340 95905 FALSE TRUE 93694.52129 100523.135 94817.89653 103179.1329 97614.92728 74683.89991 91836.16615 98853.17525 110777.4576 0.8457905 0.90743313 0.855931329 0.931409107 0.881180426 0.674179581 0.829014929 0.892358223 1 16.75730481 GGISFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGISFGR 7 0 H0Y3A8;O75129-2;O75129-3;O75129 H0Y3A8 ASTN2 Astrotactin-2 0 82.263 0.058079 73264000 35393 29474 28860 31515 36584 31949 36690 30580 44482 FALSE TRUE 33720.04303 32477.43411 30183.25955 28347.05233 42964.23802 30842.59812 31092.26664 27902.25309 51380.04138 0.656286802 0.63210214 0.587451056 0.551713303 0.836204815 0.600283637 0.605142888 0.54305626 1 15.64892043 -1.234825626 4.204478853 1.000225181 0.628729294 0.673235798 0.081756809 36.98559212 42762880.3 16965.75072 0.017861114 0.058233699 1.234825626 -0.371495887 GGKNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGKNIR 6 1 Q9NYT6 Q9NYT6 ZNF226 Zinc finger protein 226 0 86.344 0.04896 761320000 1045800 958440 807760 1144000 746610 879940 1043100 1135700 1153600 FALSE TRUE 996367.1066 1056106.126 844796.595 1029002.947 876818.5476 849467.4572 883955.9372 1036252.087 1332494.396 0.747745814 0.792578287 0.633996359 0.772238104 0.658027944 0.637501711 0.663384356 0.777678383 1 20.34569804 0.902718013 5.069688289 0.999976686 0.706857278 0.741317804 0.055497077 0.386530434 19.27617635 0.057363762 0.014494614 7.993150915 -0.902718013 -0.293119408 GGLLTSEEDSGFSTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFSTS(1)PK;GGLLTSEEDSGFS(0.007)T(0.15)S(0.843)PK;GGLLTSEEDSGFS(0.001)T(0.454)S(0.545)PK 310.93 4.29E-58 139598000 458227 553150 420456 547970 264455 474197 429724 510510 275451 TRUE FALSE 436567.5178 609516.6139 439734.3235 492887.0145 310575.8683 457775.439 364161.7114 465807.038 318166.5343 1.372135252 1.915715665 1.382088548 1.549147888 0.976142475 1.438791921 1.144563215 1.464035302 1 18.27942257 3.085005085 2.12387438 1.230388359 1.623920445 0.348706921 0.222745767 0.297135763 2.729349021 0.065248696 0.080738705 1216.20024 -3.085005085 0.393532087 GGLLTSEEDSGFSTS(ph)PKDNSLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGLLTSEEDSGFSTSPKDNSLPK 23 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFS(0.108)T(0.108)S(0.785)PKDNSLPK 162.77 9.83E-12 203270000 309150 229880 270610 273190 175210 311320 337250 341820 182990 TRUE FALSE 294537.0922 253305.0334 283017.7362 245728.4222 205766.5685 300538.9103 285796.3185 311888.4287 211367.1546 1.393485628 1.198412468 1.338986356 1.162566732 0.973503044 1.421880854 1.352132118 1.475576606 1 17.68939168 GGLRAT(ph)AGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGLRATAGPR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30 E9PP16 PPFIBP2 Liprin-beta-2 1 GGLRAT(1)AGPR 93.623 0.014 92650000 37240 24318 42115 41671 60460 43944 50902 38569 66878 TRUE FALSE 35479.739 26796.03185 44046.01441 37482.15191 71004.20486 42422.20826 43135.96502 35191.69389 77249.09867 0.459290006 0.346878246 0.570181596 0.485211511 0.919159007 0.549161207 0.558400884 0.455561223 1 16.23723048 -5 0.124021957 2.440133339 0.326644914 0.471524302 0.150283086 131.0995844 1.042861782 47.94129056 1.292415118 1.00E-05 5 -2.113488426 GGLRPGS(ph)LDAEIDLLSSTLAELNGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGLRPGSLDAEIDLLSSTLAELNGGR 26 1 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 1 GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(0.999)LDAEIDLLSSTLAELNGGR 308.06 6.83E-82 8928947400 3432475.8 2949547.4 3037656.8 3549879.6 4241563.7 3372718.2 3915848.5 3654381 4123709.2 TRUE FALSE 3270229.471 3250109.633 3176936.369 3193038.958 4981291.066 3255920.123 3318413.892 3334384.027 4763192.962 0.686562459 0.682338435 0.666976206 0.670356835 1.045788215 0.683558308 0.69667845 0.700031272 1 22.18349756 -5 0.282268255 3.020001311 0.706483668 0.355596738 0.113787435 263.0621337 2.509443458 312.1887945 0.124165687 1.00E-05 5 -2.313517643 GGLS(ph)PANDTGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGLSPANDTGAK 12 0 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK 208.05 7.48E-08 1165310000 2955960 3111650 2692800 3502280 2124350 3145790 3177880 3319450 2404880 TRUE FALSE 2816237.629 3428730.673 2816267.544 3150224.161 2494835.967 3036850.504 2693036.04 3028781.36 2777816.508 1.013831411 1.234325832 1.01384218 1.134064886 0.898128426 1.093250938 0.969479457 1.090346087 1 21.40551987 2.792738933 24.99981034 1.012065657 1.107370886 0.217379725 0.082990727 420.077517 193837.861 0.022996395 0.024391355 620.4959246 -2.792738933 0.095305229 GGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 35 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 446.98 8.25E-232 567190000 476610 291443 514790 426720 519200 476720 696210 593670 647500 FALSE TRUE 454081.5899 321141.373 538393.6307 383825.2949 609748.3156 460211.0669 589990.3777 541685.1076 747910.993 0.607133194 0.42938448 0.71986324 0.513196488 0.815268556 0.615328657 0.788851057 0.724264134 1 19.51250706 1.042645741 0.213258229 1.119568888 0.436525647 0.617506917 0.09998994 1.877086746 0.336583777 0.488832245 0.324605264 11.03178377 -1.042645741 -0.683043241 GGNFGFGDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 GGNFGFGDSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 237.44 8.31E-12 25331340000 43079570 36710190 38113880 42876280 47347230 38812280 46246910 42171100 47422500 FALSE TRUE 41043284.1 40451000.1 39861439.1 38566274.87 55604571.92 37468201.01 39191094.5 38478374.92 54776539.1 0.749285822 0.73847309 0.72771007 0.704065564 1.01511656 0.684019137 0.715472265 0.702460863 1 25.70705478 -1.760804665 2.563172937 1.060320224 0.752372293 0.398655096 0.094694802 19291804.01 13977660.42 7335282.114 0.021795091 0.01734584 1.760804665 -0.307947931 GGNFGGR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 151.7 0.0043358 2181550000 2160090 1777000 1765820 2099880 2338190 1798410 2199580 1916740 2426810 FALSE TRUE 2057986.827 1958078.32 1846784.594 1888796.073 2745969.596 1736130.611 1863993.673 1748900.084 2803147.3 0.734170062 0.698528515 0.658825383 0.673812636 0.979602319 0.619350475 0.664964582 0.62390588 1 21.41861613 -2.265789998 2.257519829 2.169449519 0.706307852 0.446310893 0.102685149 5497537.412 882216.2135 32806586.84 0.023536735 0.00542263 2.265789998 -1.463141667 GGNFPSFPHDEVTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGNFPSFPHDEVTDR 15 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 133.71 3.96E-05 323290000 369080 370640 350760 424220 411050 340450 413860 387640 384340 FALSE TRUE 351634.3198 408408.6374 366842.6929 381576.5996 482736.9899 328660.1311 350718.0559 353696.1866 443941.4843 0.792073578 0.919960517 0.826331185 0.859520034 1.087388782 0.740323089 0.790009649 0.796718034 1 18.76001 -0.365675073 7.452040962 0.999992719 0.851104224 0.18965168 0.096438577 0 0 0.089964568 0.021204852 0.430848839 0.365675073 -0.148888494 GGNIGDGGGAADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GGNIGDGGGAADR 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 161.25 9.11E-05 1068606000 1493947 1275570 1365690 1605761 1720395 1394543 1595118 1513190 1649221 FALSE TRUE 1423331.086 1405552.033 1428308.237 1444346.854 2020431.343 1346249.626 1351753.453 1380687.062 1904973.77 0.747165714 0.737832749 0.749778427 0.758197764 1.060608485 0.706702448 0.709591635 0.724780091 1 20.8613397 -2.118025696 2.401432436 1.443184179 0.769289418 0.318754362 0.103446991 8966942.11 2530130.453 21678032.82 0.024753296 0.007620339 2.118025696 -0.673894761 GGNLPPVS(ph)PNDSGAK ddPTM_SK-BR-3_Trastuzumab_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 244.54 5.71E-16 106690000 356780 294520 325620 356070 259300 339090 366890 360020 274780 TRUE FALSE 339915.7165 324531.9228 340549.9991 320277.1671 304521.8379 327347.2283 310914.1921 328494.7402 317391.479 1.070966736 1.022497276 1.07296516 1.009091889 0.959451838 1.031367412 0.979592121 1.034982858 1 18.27590387 3.112945553 6.406499155 0.999152512 1.050376494 0.481300662 0.025834653 0.168492383 8.858773638 0.006741978 0.008096104 1297.016656 -3.112945553 0.051223982 GGNRFEPYANPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGNRFEPYANPTK 13 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 175.29 1.69E-05 494950000 477790 409290 419860 569010 396410 490540 595970 520860 473950 FALSE TRUE 455205.8136 450997.1163 439110.9963 511812.0338 465543.7785 473552.4768 505043.8308 475250.7371 547447.7454 0.831505504 0.823817652 0.802105772 0.934905729 0.850389434 0.86501859 0.922542535 0.868120731 1 19.06236174 -5 0.078729994 1.492023424 0.709489436 0.647392637 0.035402706 143.2866164 0.800523255 12.15271515 1.178197854 1.00E-05 5 -0.782533988 GGNRFEPYANPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGNRFEPYANPTKR 14 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 147.35 4.53E-06 1127760000 1887890 1221450 1683280 1801090 1717440 1853050 2381630 2012010 2299990 FALSE TRUE 1798653.181 1345917.144 1760460.053 1620041.011 2016960.992 1788878.414 2018268.602 1835827.738 2656660.702 0.67703534 0.506619887 0.662658973 0.609803506 0.759209104 0.673355996 0.759701305 0.691028303 1 21.34118255 -1.41009361 0.185665251 1.349724701 0.543130895 0.758009724 0.06247013 11.27839913 0.386245386 2.051917383 0.205841737 0.03889613 1.41009361 -0.806593806 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR ddPTM_SK-BR-3_Trastuzumab_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 ; 331.31 2.05E-129 1487220000 544220 446100 546180 602810 792740 521430 772540 642000 687500 FALSE TRUE 518495.7991 491558.0972 571222.8932 542214.3935 930993.605 503372.7484 654674.8343 585783.0765 794113.9887 0.652923644 0.619001937 0.719321031 0.682791641 1.172367718 0.633879714 0.824409145 0.737656161 1 19.59898658 2.966501412 24.99035807 0.848597004 0.658668952 0.320513713 0.146071495 756.4235572 564301.4689 0.041160519 0.043684522 925.766396 -2.966501412 -0.189928053 GGPAS(ph)PGGLQGLETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 265.73 3.25E-25 781906000 732057 645209 652863 761240 687472 658820 726143 690560 728228 TRUE FALSE 697454.1164 710956.5306 682797.4143 684718.7089 807366.8991 636004.8982 615356.5488 630090.9055 841157.879 0.829159583 0.845211759 0.811735147 0.814019254 0.959828017 0.756106451 0.731558919 0.749075674 1 19.68201708 GGPEVQQVPAGERPLWFICSGMGTQWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 299.97 7.19E-71 7173062000 1321562 1168851 1178062 1352569 1382017 1257715 1447573 1352085 1464118 FALSE TRUE 1259094.383 1287958.246 1232077.308 1216606.194 1623040.327 1214160.014 1226719.152 1233689.27 1691165.942 0.744512618 0.761580052 0.728537205 0.719389011 0.959716777 0.717942565 0.725368884 0.729490371 1 20.6895868 -2.038095396 2.741742739 1.306266912 0.759204358 0.521270637 0.07202064 17373372.53 5319780.071 33483670.01 0.016965914 0.009160193 2.038095396 -0.547062553 GGPGGGFRPFVPHIPFDFYLCEMAFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGPGGGFRPFVPHIPFDFYLCEMAFPR 27 1 Q12905;A0A0A0MRL0 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 167.07 4.97E-12 443780000 368300 331390 272210 331030 418910 303750 399030 351020 344800 FALSE TRUE 350891.1889 365159.0178 284691.0978 297754.2355 491967.7714 293231.0613 338150.6448 320282.8279 398269.823 0.881038855 0.916863384 0.714819656 0.747619373 1.235262485 0.736262314 0.849049125 0.804185528 1 18.60338664 5.933962579 12.50636281 0.870860209 0.888318123 0 0.154294376 0 0 0.031211304 0 858939.5072 -5.933962579 0.017457915 GGPGKLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR 81.625 0.012568 12286310000 11899400 9773230 9923660 11682730 9317150 11172130 12864680 11958820 10501260 TRUE FALSE 11336938.94 10769133.25 10378669.63 10508359.78 10942058.01 10785236.34 10901936.79 10911642.32 12129741.77 0.934639761 0.887828732 0.855638135 0.866330049 0.902084992 0.889156302 0.898777319 0.899577463 1 23.5320455 0.015999017 0.971443786 1.001185046 0.891094197 0.728023747 0.020892822 4.042630058 3.433497954 0.036964348 0.006867899 1.037526068 -0.015999017 -0.110090849 GGPPFAFVEFEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGPPFAFVEFEDPR 14 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 125.74 0.00020814 98670000 158279 184731 128695 173454 138159 136701 137299 144810 127434 FALSE TRUE 150797.4653 203555.2989 134595.793 156018.0744 162253.8859 131967.0101 116351.5159 132129.6687 147195.8139 1.024468437 1.382887825 0.914399598 1.059935539 1.102299594 0.89654051 0.790453973 0.89764556 1 17.16737712 2.70758621 0.940194737 0.865498094 1.170643011 0.314867524 0.133225294 0.504040558 0.941289196 0.076829029 0.068680411 510.0188297 -2.70758621 0.305144917 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;;;;;; 170.91 6.18E-12 1891743000 452569 352387.4 415117 445018 558039 409900 507680 443609 556071 FALSE TRUE 431176.9603 388296.0767 434150.5251 400283.9452 655360.8249 395705.0602 430224.0918 404764.2442 642303.6507 0.671297695 0.604536618 0.675927226 0.623200483 1.020328663 0.616071635 0.669814178 0.630175843 1 19.29289597 -1.954267847 2.396696636 1.245840612 0.683565595 0.395540314 0.120693709 24547662.11 11215171.25 33594940.89 0.028690703 0.011110463 1.954267847 -0.562275017 GGPPS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.987)PT(0.013)K;GGPPS(0.99)PT(0.01)K;GGPPS(0.981)PT(0.019)K 76.619 0.028191 0 908510 791600 842990 934060 688220 891700 1009240 966710 847030 TRUE FALSE 865566.5328 872264.94 881641.9253 840166.5142 808245.3501 860820.2054 855261.902 882059.7475 978383.0864 0.884690818 0.891537223 0.901121389 0.858729598 0.826103151 0.879839623 0.874158511 0.901548442 1 19.90003994 0.756489367 2.276170531 0.999977651 0.875138402 0.789510107 0.020401076 0.505291588 3.923714204 0.020506518 0.005557266 5.708071006 -0.756489367 -0.124839248 GGPRPVS(ph)SSIDPSLLSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGPRPVSSSIDPSLLSTK 18 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 GGPRPVS(0.339)S(0.33)S(0.33)IDPS(0.001)LLSTK;GGPRPVS(0.914)S(0.042)S(0.044)IDPSLLSTK;GGPRPVS(0.917)S(0.031)S(0.052)IDPSLLSTK 164.31 1.88E-11 497720000 880660 733410 784470 947030 847160 869340 1073710 996580 946180 TRUE FALSE 839032.9471 808145.3128 820438.7254 851832.7452 994904.4358 839234.5378 909895.8195 909314.172 1092908.762 0.767706305 0.739444445 0.750692788 0.779417985 0.910327074 0.767890758 0.832545086 0.832012885 1 20.05974154 -5 0.122141642 1.707002373 0.690398263 0.725881694 0.04248082 75.09672821 0.591299403 12.97814873 0.36866268 1.00E-05 5 -1.016604109 GGPTVDPEELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGPTVDPEELFR 12 0 Q96EY1-2;Q96EY1 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 ;; 112.75 0.0028854 91115000 54722 47404 49354 48450 59117 51746 61396 50605 59581 FALSE TRUE 52135.39951 52234.52149 51616.92972 43579.71395 69426.98608 49954.02304 52028.91259 46173.75793 68820.51718 0.757556055 0.758996352 0.750022404 0.633237234 1.008812327 0.725859454 0.756008742 0.670930121 1 16.07055111 GGQGDPAVPAQQPADPST(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 GGQGDPAVPAQQPADPS(0.002)T(0.998)PER;GGQGDPAVPAQQPADPS(0.001)T(0.999)PER 206.6 6.48E-24 273970000 257860 272890 240310 279350 277350 253370 273550 251110 257500 TRUE FALSE 245671.4688 300697.8013 251328.4512 251269.2073 325719.7522 244595.7334 231814.9234 229121.4772 297431.7849 0.825975842 1.010980724 0.844995269 0.844796085 1.095107412 0.822359095 0.779388536 0.770332859 1 18.1821993 2.060248762 24.99999449 0.819257897 0.92323833 0.115209215 0.103076993 109.6485929 45497.42842 0.035391464 0.026138326 114.8811468 -2.060248762 0.103980433 GGQGDPAVPAQQPADPST(ph)PERQS(ph)SPSGSEQLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGQGDPAVPAQQPADPSTPERQSSPSGSEQLVR 33 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 2 GGQGDPAVPAQQPADPS(0.163)T(0.813)PERQS(0.539)S(0.482)PS(0.002)GSEQLVR 141.77 1.03E-09 147910000 59771 42296 60830 57519 69825 53313 72544 56478 78041 TRUE FALSE 56945.74328 46606.01049 63619.11567 51737.08084 82002.45789 51466.75744 61476.08044 51532.48691 90143.1997 0.631725338 0.517021923 0.705756129 0.573943248 0.909691005 0.570944426 0.681982453 0.571673594 1 16.45993104 -5 0.294395889 3.859191363 0.620042887 0.493296841 0.11113845 206.7483228 1.931813352 364.1791373 0.106287028 1.00E-05 5 -3.239148476 GGQS(ph)DDDEDEGVPASYHTVSLQLLDLMHTLHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR 192.88 3.66E-20 693734000 193181 155433.5 194095.7 220177.5 253286 189257.8 260593 195835.7 63581.6 TRUE FALSE 184049.717 171272.3504 202995.1798 198044.8394 297458.9982 182703.7549 220834.7517 178687.2879 73441.5098 2.506072077 2.332091903 2.764038762 2.696633551 4.050284356 2.487745084 3.006947329 2.433055753 1 16.1643081 3.725516399 19.68887564 2.781231881 2.41908226 0 0.750124204 145.4391607 219527.895 0.177019646 0.277611385 5315.160695 -3.725516399 -0.362149621 GGRT(ph)PPQQGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGRTPPQQGGR 11 1 A0A2R8Y4Z8;M0QYB4;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 GGRT(1)PPQQGGR 76.588 0.056489 44192000 27960 27147 28481 31193 29499 31273 30100 26345 36969 TRUE FALSE 26638.38621 29913.31016 29786.88202 28057.42038 34643.61626 30190.00817 25507.69218 24038.09214 42701.96371 0.623821106 0.70051369 0.69755298 0.657052228 0.811288598 0.706993439 0.597342369 0.562927089 1 15.3820148 -1.881512731 2.548924473 1.164325291 0.670594378 0.697436774 0.068370658 10662101.29 6160862.024 10558682.79 0.01711283 0.01313673 1.881512731 -0.493730913 GGS(ph)DDSSKDPIDVNYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 1 GGS(0.999)DDSSKDPIDVNYEK 137.45 4.20E-06 90854000 485220 397370 407780 457840 248020 444980 468080 495630 305590 TRUE FALSE 462284.6122 437862.4548 426477.1163 411817.0534 291274.6095 429570.231 396665.7991 452230.0097 352979.3365 1.3096648 1.240476168 1.208221197 1.166688842 0.825188841 1.216984074 1.123764929 1.28117984 1 18.4292242 3.366729083 2.354512979 1.103311176 1.272778133 0.266349716 0.123688682 0.386216692 4.348440052 0.035568366 0.052164075 2326.639427 -3.366729083 0.169466957 GGS(ph)GGTRGPPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSGGTRGPPSR 12 1 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" 1 GGS(0.932)GGT(0.068)RGPPSR 60.549 0.055206 50461000 22995 13945 17879 21916 23778 19492 25471 20730 30145 TRUE FALSE 21908.07192 15366.01135 18698.76983 19712.96204 27924.87567 18816.98715 21584.93114 18914.7713 34819.73264 0.62918553 0.441301819 0.537016468 0.566143406 0.801984207 0.540411592 0.619905137 0.543219889 1 15.08761751 -5 0.274344492 3.95910465 0.550412537 0.655618361 0.093906539 131.7413675 1.271564772 221.4026614 0.107898514 1.00E-05 5 -3.408692113 GGS(ph)LESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGSLESR 7 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 GGS(0.718)LES(0.282)R;GGS(0.999)LES(0.001)R;GGS(0.872)LES(0.128)R;GGS(1)LESR 94.85 0.014579 594160000 1730300 1460920 1458280 1894090 1896650 1590690 1884930 1598660 2076500 TRUE FALSE 1648512.148 1609789.409 1525143.58 1703692.475 2227425.159 1535604.006 1597349.309 1458672.855 2398513.015 0.687305901 0.671161423 0.635870463 0.710311958 0.928669199 0.640231676 0.665974835 0.608157157 1 21.19370884 -1.243064545 3.628544829 1.000549927 0.692535559 0.542859518 0.088400048 35793197.64 64219557.66 226115.4555 0.020724542 0.057139371 1.243064545 -0.308014368 GGS(ph)PAPLPAKVDEATSGLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGSPAPLPAKVDEATSGLIR 20 1 A0A087WWH3;Q9NZM4-2;Q9NZM4 A0A087WWH3 GLTSCR1 Glioma tumor suppressor candidate region gene 1 protein 1 GGS(1)PAPLPAKVDEATSGLIR;GGS(1)PAPLPAKVDEATSGLIR 140.8 1.20E-07 156297000 258200 153313 257720 217251 221490 230240 363330 268210 305010 TRUE FALSE 245995.3977 168935.769 269536.7169 195412.5167 260117.7859 222266.7311 307897.3355 244724.1105 352309.393 0.698236841 0.479509693 0.765056857 0.554661671 0.738322029 0.630885056 0.873940183 0.694628402 1 18.42648341 1.01679034 0.393266293 1.01936722 0.58934651 0.540626104 0.100649471 0.895051264 0.383229136 0.141523322 0.076665892 10.39418256 -1.01679034 -0.43002071 GGS(ph)PDLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GGS(1)PDLWK 160.53 0.00037008 6830230000 12099840 10363580 10207650 12363240 8365530 11822460 12881040 11801390 9157920 TRUE FALSE 11527904.54 11419640.58 10675680.85 11120463.63 9824475.783 11413045.25 10915800.77 10767997.73 10578083.46 1.089791415 1.079556673 1.009226377 1.051273954 0.928757635 1.078933182 1.031926134 1.017953561 1 23.33457493 3.778820355 6.525723728 1.020477216 1.08520901 0.343371701 0.038743969 0.221053885 27.01847023 0.009311433 0.016684299 6009.251149 -3.778820355 0.064731794 GGS(ph)PQMDDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 203.8 2.08E-07 3189356000 5137300 7097810 4847830 6756770 2732469 5924310 4445280 5889260 2773350 TRUE FALSE 4894470.01 7821084.909 5070107.801 6077566.643 3209010.728 5719149.659 3767070.893 5373565.173 3203426.954 1.52788563 2.441474403 1.582713723 1.897207812 1.001743063 1.785322326 1.175950302 1.677442705 1 21.61118466 2.772637597 21.24978 1.363291034 1.906153862 0.358727372 0.351021382 103.4898306 64533.5326 0.097781011 0.103696938 592.4307563 -2.772637597 0.542862828 GGS(ph)PQMDDIKVFQNEVLGTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGSPQMDDIKVFQNEVLGTLQR 22 1 Q13144;A0A3B3IUB1;A0A3B3ITG6 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 GGS(1)PQMDDIKVFQNEVLGTLQR;GGS(1)PQMDDIKVFQNEVLGTLQR;GGS(1)PQMDDIKVFQNEVLGTLQR;GGS(1)PQMDDIKVFQNEVLGTLQR 253.49 3.03E-37 1135760000 1633950 956160 1504600 1407690 1393200 1560780 1992690 1958960 1911280 TRUE FALSE 1556716.422 1053593.791 1573587.398 1266186.327 1636173.639 1506729.797 1688668.542 1787423.077 2207671.541 0.705139507 0.477242095 0.712781485 0.573539271 0.741130919 0.682497269 0.764909322 0.809641762 1 21.07409411 1.110966932 0.48341228 1.010692282 0.595509269 0.724012232 0.07240146 0.46106589 0.284996407 0.077269249 0.040202224 12.91120962 -1.110966932 -0.415183014 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAK 31 0 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK;GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK 267.87 2.20E-59 452640000 344590 291080 323810 351270 300280 332550 420230 368630 338200 TRUE FALSE 328301.9136 320741.3829 338657.0088 315959.6722 352648.7369 321033.7101 356116.1954 336350.803 390646.3287 0.840407011 0.82105311 0.866914608 0.808812599 0.902731476 0.821801426 0.911607685 0.861011043 1 18.57550353 -2.901721213 0.182311699 1.271551686 0.813386959 0.706513505 0.03082038 25.62255082 0.497007059 2.773024773 0.085933742 0.001253946 2.901721213 -0.458164727 GGS(ph)REYDTGGGSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGSREYDTGGGSSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 GGS(0.621)REYDT(0.165)GGGS(0.165)S(0.017)S(0.017)S(0.017)R;GGS(0.97)REYDT(0.009)GGGS(0.001)S(0.001)S(0.002)S(0.018)R 229.44 8.36E-15 204136000 337790 214170 310220 305170 399140 298030 405510 314870 417420 TRUE FALSE 321823.3361 235994.1665 324443.8938 274493.7318 468749.8896 287709.1464 343642.0018 287298.3136 482151.3617 0.667473664 0.489460749 0.672908799 0.569310291 0.972204844 0.596719556 0.712726395 0.595867473 1 18.8791266 -5 0.172194417 2.339670988 0.573115722 0.401178467 0.128690066 126.1619015 1.195766532 57.9747317 0.417202267 1.00E-05 5 -1.766555266 GGS(ph)TEDASQYYCDKNDNGDSYLVLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSTEDASQYYCDKNDNGDSYLVLIR 26 1 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 GGS(0.972)T(0.028)EDASQYYCDKNDNGDSYLVLIR 276.1 7.45E-61 52734000 58815 54564 55417 66349 52369 53295 60096 53914 47414 TRUE FALSE 56034.93151 60124.13363 57957.92426 59679.47247 61502.13702 51449.38079 50927.25146 49193.00434 54766.72096 1.023156591 1.097822411 1.058269023 1.089703225 1.122983738 0.939427811 0.929894114 0.898228038 1 15.74101188 2.225218411 24.99006241 0.935507025 1.075616251 0.780552125 0.035876525 96.36556317 180492.2056 0.01260287 0.009361008 167.9648516 -2.225218411 0.140109226 GGS(ph)TVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGSTVPK 7 0 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 1 GGS(0.998)T(0.002)VPK;GGS(0.969)T(0.031)VPK 70.525 0.059572 200922000 897770 1297410 868060 1521960 513628 994510 960340 1803110 665460 TRUE FALSE 855334.1913 1429617.554 907861.4096 1368969.689 603204.5606 960069.8693 813822.4951 1645220.13 768656.1381 1.112765707 1.859892198 1.18110214 1.780991033 0.784752155 1.249023877 1.058760159 2.14038508 1 19.55197882 -2.198776614 2.130748895 0.00010484 1.377097376 0.080671947 0.415762884 4432362.528 955024.1138 21322692.51 0.101975736 0.006327372 2.198776614 1.376992535 GGS(ph)WIQEINVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSWIQEINVAEK 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 GGS(1)WIQEINVAEK 198.95 1.28E-07 19672000 35796 32466 36251 44084 29741 39092 44790 38191 40471 TRUE FALSE 34103.99402 35774.32231 37913.14421 39652.59257 34927.82098 37738.23424 37956.46288 34846.79358 46747.03598 0.729543452 0.765274665 0.811027767 0.848237578 0.747166537 0.80728614 0.811954428 0.74543322 1 15.51258727 -5 0.292611085 2.708948959 0.77077402 0.754605565 0.038407109 124.8768409 1.170620749 130.5143994 0.039861709 1.00E-05 5 -1.938174939 GGSDDSSKDPIDVNYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 160.67 2.79E-09 2379560000 4589110 4114230 4038680 4828020 3038000 4817600 5103180 5153540 3317930 FALSE TRUE 4372191.865 4533474.714 4223857.473 4342698.257 3567826.238 4650765.304 4324596.165 4702268.717 3832457.639 1.140832405 1.182915805 1.102127635 1.133136662 0.930949948 1.213520342 1.128413298 1.226959085 1 21.86983841 -2.417535265 2.092628067 2.34E-05 1.133736273 0.206782872 0.081428278 1524179.467 143365.5846 7288654.513 0.019006022 0.003823532 2.417535265 1.133712907 GGSDGYGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 265.95 2.65E-17 6738799000 3300263 2922926 3072078 3492916 3781558 3160667 3513207 3274658 3714536 FALSE TRUE 3144266.108 3220775.482 3212935.815 3141801.448 4441060.518 3051212.309 2977202.748 2987911.585 4290567.272 0.73283226 0.750664255 0.748837068 0.732257822 1.035075373 0.711144265 0.6938949 0.696390802 1 22.03273697 -2.300083164 2.220570946 2.116028846 0.759404761 0.361738658 0.099004376 4947443.957 747504.0415 27677886.91 0.024335792 0.005010913 2.300083164 -1.356624086 GGSFENNWNIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSFENNWNIYK 12 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 132.25 0.00050633 0 100100 87303 94881 104290 87883 96292 112560 110910 111430 FALSE TRUE 95368.47138 96199.27496 99231.3877 93806.57106 103209.7674 92957.3839 95386.90469 101198.1324 128709.9953 0.740956218 0.747411067 0.770968777 0.728821183 0.801878418 0.722223505 0.741099434 0.786249212 1 16.97376457 0.772577036 3.319521998 0.999985901 0.749682945 0.922993476 0.022470814 0.38281146 5.303719325 0.019490226 0.005050092 5.923481495 -0.772577036 -0.250302955 GGSGSHNWGTVKDELTES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGSGSHNWGTVKDELTES(1)PK;GGSGSHNWGTVKDELT(0.014)ES(0.986)PK;GGSGSHNWGTVKDELTES(1)PK 294.38 8.85E-55 583460000 945320 780750 782550 1079510 537210 838840 941060 1000570 477110 TRUE FALSE 900636.597 860309.3126 818430.6915 970995.6039 630899.2539 809790.7605 797484.0132 912954.7864 551097.7821 1.634259158 1.56108288 1.485091608 1.761929798 1.14480456 1.469413935 1.447082604 1.656611252 1 19.0719488 -3.166446616 0.218777514 3.39E-16 1.599983951 0.48140125 0.166687562 51.57420326 1.057492961 24.37964079 0.313042716 0.000681637 3.166446616 1.599983951 GGSGSHNWGTVKDELTESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 125.28 1.53E-05 54603000 121250 87154 105640 123440 105070 99462 153040 145040 123590 FALSE TRUE 115518.7528 96035.09169 110483.6985 111031.5767 123394.1747 96017.606 129690.9372 132339.5287 142755.706 0.809205853 0.672723314 0.773935429 0.777773301 0.864372978 0.672600828 0.908481635 0.92703495 1 17.12318889 1.590289228 5.186101196 0.949424732 0.760404763 0.67948436 0.059979212 0.084048932 4.847004171 0.032043252 0.014750849 38.93043246 -1.590289228 -0.18901997 GGSGYHS(ph)RS(ph)PARQESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGSGYHSRSPARQESSR 17 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GGS(0.028)GY(0.02)HS(0.958)RS(0.994)PARQESSR;GGS(0.01)GY(0.006)HS(0.984)RS(0.984)PARQES(0.008)S(0.008)R;GGS(0.002)GY(0.001)HS(0.998)RS(1)PARQESSR;GGS(0.002)GYHS(0.998)RS(1)PARQESSR 82.593 0.0036717 676060000 140284 63596 161854 104704 199226 111819 221108 142156 238771 TRUE FALSE 133653.0533 70076.5047 169275.166 94178.955 233970.9513 107946.68 187373.9137 129708.067 275798.3872 0.484604187 0.254085984 0.613764162 0.341477541 0.848340535 0.391397068 0.679387271 0.47030031 1 18.07325449 -4.999999999 0.121024992 2.657236212 0.254461515 0.467258777 0.168063217 116.5199218 0.911773685 47.09444802 1.380047897 1.00E-05 4.999999999 -2.402774698 GGSISVQVNSIKFDS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.031)IKFDS(0.969)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E 278.22 6.08E-35 3636602000 9883380 8426140 9745810 10425000 6975240 10966460 11792160 11380900 8050000 TRUE FALSE 9416212.214 9284773.246 10192665.03 9377059.194 8191719.648 10586688.74 9993049.414 10384328.06 9298352.886 1.012675291 0.998539565 1.09617963 1.008464543 0.8809861 1.138555276 1.074711784 1.116792209 1 23.14854375 2.188776804 24.99999946 1.089016729 1.005277997 0.299210313 0.06251771 131.5550023 66062.24668 0.021911571 0.016182786 154.4460494 -2.188776804 -0.083738733 GGSLES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSLESR 7 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 GGS(0.039)LES(0.961)R 103.35 0.019266 0 802430 679610 643050 806340 877130 696200 861280 724340 850600 TRUE FALSE 764500.7242 748863.0317 672534.4786 725285.1713 1030101.194 672090.4194 729875.9175 660912.9496 982506.7037 0.778112476 0.762196358 0.684508794 0.7381987 1.048441899 0.684056828 0.742871183 0.672680346 1 19.90610773 -2.365469093 2.209301466 2.510084841 0.764734066 0.324227095 0.107122193 5463558.41 648214.8121 41194912.95 0.024749619 0.004310532 2.365469093 -1.745350775 GGSREYDT(ph)GGGSSSSR ddPTM_SK-BR-3_Trastuzumab_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(0.002)REYDT(0.998)GGGSSSSR 232.56 1.91E-15 350880000 391050 248700 367240 360790 456400 335130 482830 374000 448400 TRUE FALSE 372565.8415 274042.8127 384078.3172 324522.7037 535996.0155 323524.3641 409165.4157 341250.5773 517935.5819 0.719328531 0.529105978 0.741556152 0.626569626 1.034870038 0.624642089 0.789992868 0.658866834 1 18.98241315 -5 0.114615409 1.916828093 0.554323538 0.301543428 0.134828135 180.8343043 1.362446931 38.97068964 1.365812789 1.00E-05 5 -1.362504555 GGSREYDTGGGSSSS(ph)R ddPTM_SK-BR-3_Trastuzumab_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(0.001)REYDT(0.022)GGGS(0.155)S(0.068)S(0.068)S(0.686)R 171.26 1.31E-08 430800000 465780 323070 430570 433920 527660 410550 565730 454400 552550 TRUE FALSE 443763.5025 355991.2003 450312.0604 390301.5372 619683.7369 396332.5506 479417.4982 414610.3271 638236.632 0.695296196 0.557773062 0.705556588 0.611531081 0.970931009 0.620980575 0.751159482 0.649618506 1 19.28373189 -5 0.173561285 2.212633933 0.619307615 0.415865216 0.112567798 121.4177634 1.15419647 50.85036438 0.352655065 1.00E-05 5 -1.593326318 GGSSVEAPCPSDVT(ph)PEDDRSFQTVWATVFEHHVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGSSVEAPCPSDVTPEDDRSFQTVWATVFEHHVER 35 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGSSVEAPCPS(0.109)DVT(0.855)PEDDRS(0.017)FQT(0.017)VWAT(0.003)VFEHHVER 86.867 0.00042509 40453000 1402 818.28 0 1881.3 1975 765.62 1152.4 1280.2 1949.5 TRUE FALSE 1335.730238 901.6636623 0 1692.18815 2319.439375 739.1063874 976.5802147 1168.098901 2251.818503 0.593178463 0.40041578 0 0.751476261 1.03002945 0.328226447 0.433685136 0.518735813 1 11.13687484 GGTLGGGTLGPPS(ph)PPGAPS(ph)PPEPGGEIELVFRPHPLLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 2 GGTLGGGTLGPPS(1)PPGAPS(1)PPEPGGEIELVFRPHPLLVEK 92.851 0.00032252 57487000 67873 73264 57109 82478 56593 71234 65600 71863 53425 TRUE FALSE 64664.7778 80729.68489 59727.50414 74187.15474 66462.80128 68767.14872 55591.51517 65570.29475 61709.87614 1.047883772 1.308213368 0.967875936 1.202192572 1.077020494 1.114362125 0.900852807 1.062557549 1 15.91321378 1.867376633 6.875307058 0.980991841 1.132909144 0.280846965 0.0980988 0.268635665 13.7078257 0.039640755 0.024349959 73.68458351 -1.867376633 0.151917303 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK 104.31 7.39E-06 98074000 145450 161480 129870 170350 111420 140340 134320 162040 100700 TRUE FALSE 138574.8668 177934.9956 135824.668 153226.0944 130851.6127 135479.9906 113827.017 147850.9186 116316.0417 1.191365049 1.529754563 1.167720858 1.317325556 1.124966177 1.164757575 0.978601192 1.271113738 1 16.82769055 2.779390573 1.234646562 1.082577455 1.342734537 0.358147876 0.126459264 0.404074915 1.272652504 0.05385979 0.052410193 601.7146332 -2.779390573 0.260157083 GGTLKDDDWGNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGTLKDDDWGNIK 13 1 P54578-2;P54578 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14 0 137.81 5.15E-05 135470000 447400 372390 374790 513290 234230 431120 491580 526570 303510 FALSE TRUE 426252.2887 410336.9644 391974.4922 461693.114 275079.6378 416190.2063 416580.4425 480460.7393 350576.7807 1.215860012 1.170462469 1.118084579 1.316952917 0.784648765 1.187158503 1.18827163 1.370486483 1 18.41937092 -0.384601325 6.464582187 1.000000003 1.165832961 0.10496117 0.15484186 0 0 0.136842475 0.032254081 0.412475991 0.384601325 0.165832958 GGTPAFLPSS(ph)LSPQSSLPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGTPAFLPSSLSPQSSLPASR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 GGTPAFLPS(0.036)S(0.601)LS(0.362)PQSSLPASR 199.31 8.48E-22 366970000 265660 229320 253070 296710 305870 244270 316310 273640 331590 TRUE FALSE 253102.7783 252687.9687 264673.5098 266884.1471 359213.6312 235810.8687 268051.1001 249678.6309 383011.2837 0.660823294 0.659740273 0.691033192 0.696804921 0.937866968 0.615676035 0.699851705 0.651883225 1 18.54702737 -1.494899509 3.130440206 1.00788316 0.698354296 0.532635872 0.087761949 49546532.71 63783159.18 3411875.811 0.020109751 0.031996354 1.494899509 -0.309528865 GGTPAFLPSSLS(ph)PQSSLPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGTPAFLPSSLSPQSSLPASR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 GGTPAFLPS(0.23)S(0.186)LS(0.576)PQS(0.006)S(0.002)LPASR;GGTPAFLPSSLS(0.989)PQS(0.008)S(0.002)LPASR;GGTPAFLPSS(0.014)LS(0.961)PQS(0.024)S(0.001)LPASR;GGTPAFLPS(0.007)S(0.042)LS(0.939)PQS(0.007)S(0.004)LPASR 325.79 6.99E-68 848280000 1033362 968691 1016359 1115213 1231700 1033906 1217956 1074414 1323390 TRUE FALSE 984517.0262 1067401.714 1062960.065 1003109.67 1446508.09 998101.576 1032134.443 980332.6143 1528614.562 0.644058385 0.698280483 0.695374813 0.656221454 0.946287001 0.652945223 0.675209087 0.641320996 1 20.54379325 -1.988653228 3.005142547 1.277913542 0.69937151 0.524159501 0.089452022 48931635.71 46475950.64 94418648.41 0.020369404 0.010264712 1.988653228 -0.578542032 GGVDHAAAFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGVDHAAAFGR 11 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;;; 177.06 8.15E-06 1425540000 1021930 711632 729060 932590 1130230 794090 1048410 883040 1058530 FALSE TRUE 973625.3942 784148.1099 762488.1221 838844.2814 1327341.754 766590.4642 888455.7991 805716.3363 1222681.426 0.796303414 0.641334769 0.623619617 0.686069375 1.085599017 0.626974818 0.726645371 0.658974872 1 20.22161712 GGVTGS(ph)PEASISGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(0.997)PEAS(0.003)ISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK 336.16 4.79E-69 10097470000 9908290 10365840 8746730 11593790 7343540 9792410 10441150 10886970 8156260 TRUE FALSE 9439944.768 11422130.88 9147776.222 10428360.2 8624251.051 9453296.386 8848160.803 9933649.191 9421091.144 1.002001214 1.212399998 0.970989037 1.10691639 0.915419554 1.00341842 0.939186413 1.05440538 1 23.16746273 2.751591115 24.87694946 0.977243497 1.082728414 0.266343911 0.073658246 808.0103882 1542598.184 0.021033889 0.022185505 564.4053406 -2.751591115 0.105484917 GGVTGSPEASISGS(ph)KGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGSPEASIS(0.233)GS(0.767)KGDLK;GGVTGSPEASIS(0.042)GS(0.958)KGDLK 194.97 1.18E-15 512170000 673130 572370 555450 644680 319180 635170 604050 661900 336410 TRUE FALSE 641312.4789 630695.1537 580917.9319 579875.5416 374844.8909 613173.9036 511891.0784 603940.527 388578.7447 1.650405453 1.623081968 1.494981236 1.492298664 0.964656189 1.577991365 1.317341943 1.554229446 1 18.56784746 8 0.040951846 5.44E-14 3.822158346 0.402370043 0.189573308 681.2810844 2.123179573 53.49135414 178.8086084 99999999.94 -8 3.822158346 GGVVGIKVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GGVVGIKVDK 10 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 141.95 0.0050632 0 2740600 1799140 2685300 2340200 2127950 2828800 3676900 3268600 2865500 FALSE TRUE 2611057.269 1982474.411 2808423.661 2104958.65 2499063.806 2730837.947 3115921.374 2982384.056 3309867.105 0.788870727 0.598958915 0.84850043 0.635964703 0.755034485 0.825059696 0.941403771 0.901058551 1 21.65834186 1.990668418 1.669797878 0.952994623 0.711283401 0.657137578 0.073461757 0.207017602 1.076274858 0.042809528 0.020900316 97.87424348 -1.990668418 -0.241711222 GGYDKDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGYDKDGR 8 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 69.423 0.060526 0 143550 129160 133540 160210 127070 153790 163360 156960 156950 FALSE TRUE 136764.676 142321.5508 139662.9411 144105.3864 149230.9678 148464.2137 138436.4317 143215.7503 181289.0044 0.754401385 0.785053409 0.770388373 0.794893143 0.823166128 0.818936671 0.76362288 0.789985861 1 17.4679319 -1.665503763 2.338183129 1.035352229 0.785867111 0.902971304 0.021879458 1057443.014 778429.4031 222518.3058 0.005727286 0.021602113 1.665503763 -0.249485118 GGYFDEFGIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GGYFDEFGIIR 11 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 268 6.60E-21 2661370000 3328720 2831700 2448570 2747160 3807970 2298630 3604660 2959110 3547100 FALSE TRUE 3171378.002 3120253.449 2560839.356 2471010.258 4472078.762 2219027.867 3054702.913 2699994.641 4097166.152 0.774041834 0.761563806 0.625026973 0.603102282 1.091505347 0.541600654 0.745564812 0.658990761 1 21.96619497 -1.167733187 4.072949658 1.000108443 0.728692003 0.249699934 0.149605418 16.00172894 72812789.73 15429.88057 0.031394427 0.067962104 1.167733187 -0.27141644 GGYIGSTYFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GGYIGSTYFER 11 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 206.43 6.14E-08 865060000 753690 632150 692100 743680 946800 682320 828290 753630 1005140 FALSE TRUE 718064.5674 696566.8037 723833.4696 668923.8735 1111921.62 658691.0873 701919.1479 687638.162 1161011.978 0.618481619 0.599965218 0.623450476 0.576155876 0.957717613 0.567342198 0.604575286 0.592274822 1 20.14695143 -1.363908235 2.970290074 1.004623828 0.638236768 0.493897406 0.113659971 23389795.03 28978032.51 944546.0014 0.026571029 0.043260523 1.363908235 -0.36638706 GGYLS(ph)DGDSPELTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GGYLSDGDSPELTTK 15 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 GGYLS(0.999)DGDS(0.001)PELTTK 174.62 9.47E-07 76191000 193900 163960 183180 208100 166610 194110 205740 216960 176920 TRUE FALSE 184734.7313 180667.7104 191578.9842 187181.3926 195666.7312 187387.922 174350.5843 197961.8322 204355.85 0.903985529 0.884083868 0.937477367 0.915958083 0.95748045 0.916968719 0.853171486 0.968711354 1 17.64072402 1.036382462 8.086444953 0.999968391 0.907390425 0.561802598 0.028040865 0.138944578 25.72799369 0.028001896 0.007012302 10.87382808 -1.036382462 -0.092577966 GHAAPILYAVWAEAGFLAEAELLNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHAAPILYAVWAEAGFLAEAELLNLR 26 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 146.06 2.15E-07 709390000 91276 104850 78464 129090 108730 93359 133100 92089 75081 FALSE TRUE 86961.56437 115534.3342 82061.65201 116113.6279 127692.4776 90125.95442 112793.1505 84025.19897 86724.17802 1.002737257 1.332204431 0.9462373 1.338884157 1.472397669 1.039225237 1.300596362 0.968878586 1 16.40414664 1.225248344 24.71669111 0.984439035 1.205193329 0.231312359 0.166860342 324.9754246 603356.2647 0.143321028 0.036707186 16.79764287 -1.225248344 0.220754294 GHALLIDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHALLIDCR 9 0 P51570;P51570-2 P51570 GALK1 Galactokinase 0 ; 114.84 0.0015728 376880000 346510 193156 82075 104578 488300 139453 410570 218410 375460 FALSE TRUE 330131.159 212838.816 85838.21993 94065.62075 573459.3654 134623.7076 347930.0059 199284.8625 433684.4192 0.761224394 0.490768878 0.197927839 0.216898778 1.322296444 0.310418594 0.802265404 0.459515845 1 18.72628609 GHALLILRPEELGFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHALLILRPEELGFLR 16 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 105.39 0.00077337 97234000 79784 77546 68436 81305 103840 66589 85493 80140 77617 FALSE TRUE 76012.76844 85448.02556 71573.85829 73132.06693 121949.6631 64283.00623 72449.47266 73122.51675 89653.44795 0.847851033 0.953092463 0.79833916 0.815719513 1.360233944 0.717016553 0.808105815 0.81561299 1 16.45207145 GHAVGDIPGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 128.01 0.00027463 1257830000 538038 609870 459352 607802 795660 490142 562961 556363 754260 FALSE TRUE 512606.01 672016.4464 480413.7436 546704.5882 934422.8521 473168.2596 477070.96 507644.9063 871226.7886 0.588372645 0.771345022 0.551422144 0.627511224 1.072536869 0.543105728 0.547585274 0.582678257 1 19.73268879 4.743877081 5.920086583 0.686534678 0.585447699 0.025034145 0.190571012 0.640315654 93.48680748 0.042726519 0.260810632 55446.87588 -4.743877081 -0.101086979 GHDDLGDHYLDCGDLSNALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 120.9 1.92E-05 456700000 682510 655260 706990 794750 573090 770480 864280 783340 306880 FALSE TRUE 650249.1049 722031.739 739406.1908 714860.2201 673036.7146 743798.0844 732418.2124 714746.5969 354469.3831 1.834429533 2.036936823 2.085952204 2.016705121 1.898716072 2.098342254 2.066238291 2.016384576 1 18.4353015 -1.163527666 4.80737662 0.999904097 2.007090741 0.936901852 0.082104922 8.66E-05 1.51E-05 0.081598348 0.019231106 0.068623416 1.163527666 1.007186643 GHDGGHSHGGDMSNRPVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GHDGGHSHGGDMSNRPVCR 19 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 ;;;;; 113.47 0.00011378 81964600 18455.8 20652.1 22581.28 23790.8 37501.4 17586.1 28722.1 17642.54 22440.1 FALSE TRUE 17583.43091 22756.57247 23616.65402 21399.30358 44041.63229 16977.08895 24340.01613 16097.66567 25919.9961 0.678373208 0.877954317 0.911136481 0.82559054 1.699137304 0.654980382 0.939043973 0.62105201 1 14.66177788 4.331892271 1.326935548 0.956623596 0.654966559 0.079408667 0.293469254 1.77045494 4.507560867 0.080342644 0.594327951 21472.97761 -4.331892271 -0.301657037 GHDWGAPPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GHDWGAPPFR 10 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ;; 144.77 3.16E-05 601870000 392600 354510 286376 462960 627340 300302 384310 398900 331917 FALSE TRUE 374042.5761 390634.972 299506.6229 416422.3812 736747.8974 289902.4664 325676.4512 363970.2013 383388.9932 0.975621582 1.018899809 0.781208194 1.086161545 1.921672011 0.75615751 0.8494674 0.949349637 1 18.54844939 GHEDDSYEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHEDDSYEAR 10 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 138.22 7.05E-05 104790000 38266 71199 59118 55302 72780 46994 56475 48663 81427 FALSE TRUE 36457.24202 78454.25905 61828.61878 49742.93789 85472.80896 45366.586 47858.70152 44401.80974 94054.28329 0.387619157 0.834138078 0.657371643 0.528874775 0.908760409 0.48234471 0.508841276 0.472087056 1 16.52120603 -1.672195807 2.951396537 1.04277678 0.603010859 0.372360743 0.164085578 63310265.58 63692293.68 20460651.52 0.038984896 0.021271798 1.672195807 -0.439765921 GHEGPVWQVAWAHPMYGNILASCSYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHEGPVWQVAWAHPMYGNILASCSYDR 27 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 181.62 9.67E-18 163330000 63329 62137 61296 63899 69455 57342 69562 60831 39495 FALSE TRUE 60335.56368 68468.83094 64106.48223 57475.75112 81567.93001 55356.23216 58949.03931 55504.31515 45619.68289 1.322577446 1.500861615 1.405237349 1.259889317 1.787998619 1.213428693 1.292184329 1.216674726 1 15.4773688 1.209558658 1.032446931 1.014690967 1.430709666 0.443456947 0.154548981 0.421473591 0.946302381 0.131742592 0.044606436 16.20162805 -1.209558658 0.416018699 GHESEVFICAWNPVSDLLASGSGDSTAR ddPTM_SK-BR-3_Trastuzumab_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 0 138.92 1.24E-06 18705000 23420 21442 23578 23254 26830 23468 27861 26581 33460 FALSE TRUE 22312.98301 23626.96418 24659.07462 20916.46374 31509.14351 22655.29728 23610.29275 24253.42673 38648.80591 0.577326582 0.611324558 0.638029405 0.541193014 0.815268228 0.586183628 0.610893201 0.627533663 1 15.23813622 -5 0.413508681 7.669865173 0.615849911 0.723104199 0.0727266 429.2308375 2.856152443 2595.927906 0.039580695 1.00E-05 5 -7.054015262 GHEYTNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHEYTNIK 8 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 88.819 0.016888 0 140820 133540 100620 132660 101490 108160 126800 130920 109460 FALSE TRUE 134163.7177 147147.8778 105233.5265 119324.7648 119189.8239 104414.3921 107454.3312 119455.9507 126434.4978 1.061132207 1.163826965 0.832316562 0.94376746 0.942700181 0.825837836 0.849881425 0.94480504 1 16.94803063 3.74035936 24.99999768 0.894917439 1.112479594 0.657928453 0.061637702 77.19934606 1072956.066 0.015265084 0.025857095 5499.957831 -3.74035936 0.217562154 GHFEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHFEEEK 7 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 117.16 0.0052935 350520000 610610 600360 487180 695020 432850 553670 560450 593900 368410 FALSE TRUE 581747.6754 661537.3666 509517.6849 625155.2691 508338.903 534496.2691 474943.0591 541894.9675 425541.1412 1.367077396 1.554579105 1.197340599 1.46908303 1.194570521 1.256038999 1.11609199 1.273425563 1 18.69893909 2.229150538 0.334417997 1.003668779 1.509889154 0.543201117 0.109863375 1.004050176 0.287431783 0.130472651 0.180926903 169.4925204 -2.229150538 0.506220375 GHFGPINSVAFHPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHFGPINSVAFHPDGK 16 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 207.79 9.56E-12 1300430000 1596270 1474980 1293890 1648040 1424100 1538210 1905450 1676180 471780 FALSE TRUE 1520817.481 1625282.139 1353216.136 1482375.888 1672462.589 1484941.402 1614738.607 1529404.793 544941.2329 2.79079172 2.982490663 2.483233154 2.720249081 3.069069632 2.724956954 2.963142646 2.806549956 1 19.05574113 0.914988207 21.66391071 1 2.83250736 0.923422161 0.164460045 6154.518612 1568384.327 0.149653227 0.037413307 8.222203229 -0.914988207 1.832507361 GHFWVGDELYCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHFWVGDELYCEK 13 0 Q96JY6;Q96JY6-5;A0A087WVI1;B3KPU0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 0 182.07 1.15E-05 163790000 233990 203020 211410 248110 206470 221550 268760 240160 222010 FALSE TRUE 222929.7564 223707.9688 221103.3576 223169.5114 242478.3026 213877.6679 227755.7259 219130.3172 256438.1769 0.869331389 0.872366086 0.862209209 0.870266331 0.945562418 0.834032087 0.88815062 0.854515189 1 17.96825153 -1.361097796 4.908710588 1.000091464 0.87484788 0.651742387 0.028817768 2.56E-05 3.33E-06 0.024747409 0.005828767 0.043541381 1.361097796 -0.125243584 GHHVT(ph)DSENDEPLNLNAS(ph)DS(ph)ESEELHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHHVTDSENDEPLNLNASDSESEELHR 27 0 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 3 GHHVT(0.918)DS(0.082)ENDEPLNLNAS(0.992)DS(0.813)ES(0.195)EELHR 93.903 0.0073125 65257000 25293 19268 25899 25955 27129 29513 24040 28233 22797 TRUE FALSE 24097.45002 21231.43111 27086.49477 23345.95409 31860.28901 28490.95741 20372.25648 25760.76885 26332.24233 0.915130953 0.806290282 1.028643684 0.886591951 1.209934521 1.081979919 0.773662046 0.978297576 1 14.68454276 3.736340036 24.99484203 0.981960791 0.860710617 0.178257402 0.116857324 344.1488857 3873748.734 0.031858111 0.052122711 5449.291446 -3.736340036 -0.121250174 GHKGS(ph)FKDDPQLYQEIQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHKGSFKDDPQLYQEIQER 19 2 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER 113.54 9.14E-05 1514310000 1482090 1489110 1275780 1850490 929790 1540560 1690210 1476960 573714 TRUE FALSE 1412034.543 1640852.002 1334275.775 1664475.229 1091945.082 1487210.021 1432337.422 1347629.553 662682.637 2.130785483 2.476075138 2.013446106 2.511723013 1.647764738 2.24422663 2.161422892 2.033597196 1 19.33795859 -1.731550207 0.338308373 7.43E-18 2.259741943 0.703890563 0.237288232 14.46877724 0.864823491 12.09010714 0.179622934 0.018554523 1.731550207 2.259741943 GHKHEDGTQS(ph)DSEDPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHKHEDGTQSDSEDPLAK 18 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 GHKHEDGT(0.346)QS(0.654)DSEDPLAK 195.03 2.58E-15 221560000 336160 317110 268800 352670 182510 334380 325670 365860 161770 TRUE FALSE 320270.383 349423.8695 281124.7459 317218.9416 214339.6862 322800.3368 275983.0602 333823.3589 186856.4654 1.713991444 1.870012198 1.504495685 1.697661041 1.14708199 1.727531001 1.476978918 1.786522924 1 17.51157096 -2.921844029 0.167264479 2.14E-17 1.806889245 0.440794452 0.21014498 52.54555005 0.93704024 20.57328743 0.816026823 0.00119717 2.921844029 1.806889245 GHLENNPALEK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 209.85 3.43E-08 1304853000 2211162 2081974 2039539 2328488 2067914 2051505 2544330 2394480 1817074 FALSE TRUE 2106644.754 2294129.518 2133053.881 2094423.962 2428557.547 1980460.867 2156145.729 2184806.637 2098856.556 1.003710687 1.093037784 1.016293312 0.997888091 1.157086005 0.943590386 1.027295421 1.040950908 1 21.00117214 GHLSRPEAQSLS(ph)PYTTSANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHLSRPEAQSLSPYTTSANR 20 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR 210.19 2.39E-22 780380000 457649 400803 483203 525621 894605 431280 707417 568504 796390 TRUE FALSE 436016.8387 441645.2814 505358.3355 472784.5785 1050623.829 416344.6655 599487.544 518722.7759 919890.0938 0.473987971 0.480106574 0.549368168 0.51395768 1.142118864 0.452602619 0.651694749 0.563896469 1 19.81110198 2.955991209 24.99996801 0.719757771 0.497624968 0.277728847 0.200212319 645.0003008 366403.6148 0.056812375 0.06026195 903.6311831 -2.955991209 -0.222132803 GHMLADVVAIIGTQDIVFGEVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GHMLADVVAIIGTQDIVFGEVDR 23 0 O75306 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;; 163.72 1.51E-11 328755000 273431 258006 271510 249302 307560 222751 281750 242079 223334 FALSE TRUE 260506.4585 284297.1047 283959.0021 224241.6893 361198.3666 215037.077 238763.8628 220881.2794 257967.4961 1.00984218 1.102065605 1.100754965 0.869263348 1.400170068 0.833582061 0.925557934 0.856236862 1 17.97682977 GHNCPKPVLNFYEANFPANVMDVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHNCPKPVLNFYEANFPANVMDVIAR 26 1 P17844;J3KTA4;J3QRQ7;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 166.79 6.70E-12 141549000 247800 212276 231120 259560 273810 255070 322480 296810 265320 FALSE TRUE 236086.9851 233907.1657 241717.0806 233468.5357 321562.3773 246236.8619 273279.7532 270819.7429 306464.4705 0.770356788 0.763243991 0.788727908 0.761812732 1.049264787 0.803476049 0.891717571 0.883690506 1 18.2253603 2.821905563 24.99999875 0.906612787 0.770643854 0.556311922 0.067425017 68.24930203 20470.973 0.018581611 0.019708773 663.5987556 -2.821905563 -0.135968933 GHNGWVTQIATTPQFPDMILSASR ddPTM_SK-BR-3_Trastuzumab_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 ; 253.44 8.80E-44 1188950000 888880 1019700 918570 983850 916960 926360 970460 1010210 740810 FALSE TRUE 846864.404 1123608.589 960687.3431 884951.5288 1076877.534 894279.9209 822398.5033 921750.6569 855691.0313 0.989684796 1.313100814 1.122703532 1.034195167 1.258488747 1.045096756 0.961092816 1.077200325 1 19.70673044 2.017929253 23.9533613 1.007104701 1.14723653 0.286062197 0.097280665 166.5253004 222475.2805 0.034780216 0.025680562 104.2147649 -2.017929253 0.140131829 GHPEFSTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHPEFSTNR 9 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 122.33 0.00058886 759280000 331730 269230 268915 322200 562160 231557 347270 239190 613930 FALSE TRUE 316049.7803 296664.8431 281245.0187 289811.8439 660200.526 223538.123 294287.5834 218245.2556 709135.1289 0.445683435 0.418347408 0.396602858 0.408683525 0.930993966 0.315226413 0.414995071 0.307762578 1 19.43570104 -1.175957872 4.872364141 1.000052839 0.452997292 0.488721821 0.175244932 9.42E-05 1.59E-05 0.158856423 0.037439215 0.066687145 1.175957872 -0.547055547 GHPHSASSPS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHS(0.001)AS(0.021)S(0.214)PS(0.764)ER;GHPHS(0.001)AS(0.298)S(0.298)PS(0.403)ER 118.16 0.00042211 1455010000 92150 101999 85864 91159 126627 103656 130483 94180 41883 TRUE FALSE 87794.25212 112392.8141 89800.94933 81995.52413 148710.7087 100066.3667 110575.4219 85933.09992 48378.00173 1.814755653 2.323221506 1.856235192 1.694892745 3.073932436 2.068427036 2.285655007 1.77628461 1 15.56206356 GHQFSCVCLHGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GHQFSCVCLHGDR 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;;; 202.13 5.57E-08 1719670000 292505 243855 295895 281833 401433 270487 368597 307960 254832 FALSE TRUE 278678.8683 268704.1017 309462.0784 253502.6114 471442.7881 261119.9674 312360.7579 280993.3898 294350.0451 0.946760067 0.912872637 1.051340347 0.861228376 1.601639939 0.887106939 1.061188076 0.954623227 1 18.16717332 GHQQLYWSHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;;; 202.16 2.37E-08 9266320000 4115990 3094000 2345860 3041230 5097170 2884350 4670910 3415670 2148760 FALSE TRUE 3921435.31 3409282.118 2453420.001 2735519.782 5986114.834 2784464.236 3958276.892 3116575.827 2481978.726 1.579963304 1.373614561 0.988493566 1.102152792 2.411831645 1.121872725 1.594806938 1.255681926 1 21.24305932 0.980180633 6.040399809 1.000104774 1.44861857 0.122604377 0.395906102 0.323906857 56.71154822 0.351951221 0.088499388 9.553898727 -0.980180633 0.448513797 GHS(ph)CYRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHSCYRPR 8 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 GHS(1)CYRPR;GHS(1)CYRPR 84.817 0.010406 78788000 64919 58031 53891 63960 66621 59410 74636 59981 69649 TRUE FALSE 61850.40753 63944.42488 56361.95566 57530.61928 78239.68131 57352.6168 63248.90742 54728.74566 80449.8112 0.768807367 0.794836233 0.700585307 0.715111924 0.972527842 0.712899334 0.786190874 0.680284327 1 16.29580141 -1.11603509 4.645612073 1.000017955 0.77052512 0.441962381 0.082375042 1.39E-05 2.64E-06 0.072305067 0.017041135 0.076553475 1.11603509 -0.229492835 GHSERS(ph)DTNEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHSERSDTNEKR 12 2 P30414 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 GHS(0.381)ERS(0.606)DT(0.012)NEKR 69.431 0.026086 123990000 38712 23509 31969 32204 39293 35926 48758 35849 36097 TRUE FALSE 36882.16048 25904.59383 33434.81027 28966.79274 46145.68676 34681.87361 41319.0716 32709.87151 41694.7384 0.884575894 0.621291674 0.801895192 0.694734968 1.10675084 0.831804562 0.990990067 0.784508376 1 15.34757772 2.763653002 24.99026974 0.937074666 0.746800833 0.425554381 0.110802892 682.5195193 679740.9235 0.030415845 0.032249181 580.300576 -2.763653002 -0.190273832 GHSVEEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GHSVEEALR 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 207.29 1.19E-05 1208640000 666270 558140 369754 444661 734830 461156 669820 598790 609810 FALSE TRUE 634776.7375 615015.1006 386707.5866 399962.8315 862984.1193 445186.0521 567626.6569 546356.7732 704376.2203 0.901189903 0.873134389 0.549007158 0.567825574 1.225174977 0.632028793 0.805857212 0.775660446 1 19.42598668 GHTAS(ph)ESDEQQWPEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHT(0.196)AS(0.753)ES(0.051)DEQQWPEEK;GHT(0.159)AS(0.573)ES(0.268)DEQQWPEEK;GHTAS(0.997)ES(0.003)DEQQWPEEK 406.55 7.77E-140 1136500000 1672179 1595897 1470650 1860595 1315297 1759248 1688271 1514753 987181 TRUE FALSE 1593138.413 1758520.719 1538080.757 1673564.456 1544684.38 1698324.801 1430694.252 1382113.197 1140267.988 1.397161395 1.542199498 1.348876557 1.467693975 1.354667847 1.489408472 1.254700007 1.212095062 1 20.1209415 1.153321204 1.004494828 1.002460629 1.445567093 0.822643158 0.066187746 0.176799707 0.38198406 0.055717102 0.018893241 14.23381131 -1.153321204 0.443106464 GHTAS(ph)ESDEQQWPEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHTASESDEQQWPEEKR 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHTAS(0.999)ES(0.001)DEQQWPEEKR;GHTAS(1)ESDEQQWPEEKR 249.5 2.25E-21 131263000 159493 105541 142085 143912 160316 156545 198689 159439 150161 TRUE FALSE 151954.082 116295.7479 148599.7378 129445.6923 188275.0596 151123.8074 168375.3439 145477.6759 173447.201 0.876082641 0.670496539 0.85674336 0.746311798 1.085489178 0.87129574 0.970758496 0.83874329 1 17.40413703 2.764416252 24.97203909 0.946261127 0.781627836 0.471044411 0.087059233 610.0062833 589158.7877 0.024013123 0.025461486 581.3213211 -2.764416252 -0.164633291 GHTDSVQDISFDHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHTDSVQDISFDHSGK 16 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 300.89 3.73E-46 1242000000 1447000 1428520 1483600 1684100 1295970 1478180 1633990 1658160 473388 FALSE TRUE 1378603.178 1574087.812 1551624.527 1514811.068 1521986.758 1426990.256 1384694.815 1512962.72 546798.5933 2.521226635 2.878734202 2.837652742 2.770327296 2.78345039 2.609718228 2.532367186 2.766946986 1 19.06065001 -1.515200022 0.493473802 2.82E-12 2.744504356 0.949894788 0.123535236 7.858423256 0.85098187 9.937073556 0.059431175 0.030535144 1.515200022 2.744504356 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 GHTDTEGRPPS(1)PPPTSTPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHT(0.001)DT(0.003)EGRPPS(0.996)PPPTSTPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHTDT(0.004)EGRPPS(0.996)PPPTSTPEK;GHT(0.001)DT(0.007)EGRPPS(0.992)PPPTSTPEK;GHT(0.001)DT(0.055)EGRPPS(0.939)PPPT(0.004)STPEK 174.53 1.98E-12 3484930000 2911700 2503770 2597750 2984550 2229900 2814020 3139910 3013280 2179620 TRUE FALSE 2774069.711 2758907.01 2716859.407 2684537.364 2618793.854 2716569.782 2660859.061 2749421.229 2517624.338 1.101860063 1.09583744 1.079136139 1.066297828 1.040184516 1.0790211 1.05689281 1.09206969 1 21.2636316 -5 0.084553767 0.76706853 1.143984152 0.643917253 0.018088868 140.1133047 0.831897038 6.110678994 0.501280076 1.00E-05 5 0.376915623 GHTESCSCPLQQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHTESCSCPLQQSPR 15 0 O76074-2;G5E9C5;O76074;C9JGT3 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 1 GHTESCSCPLQQS(1)PR;GHTESCSCPLQQS(1)PR 167.64 8.37E-07 512230000 166859 154239 169698 197606 204690 160976 214170 206015 205260 TRUE FALSE 158971.9058 169956.1295 177478.8212 177742.2695 240387.8712 155401.3608 181494.433 187975.2344 237090.6725 0.670511008 0.716840218 0.748569395 0.749680566 1.01390691 0.655451179 0.765506425 0.792841121 1 17.85507938 -5 0.120746481 1.757221629 0.6419439 0.40291407 0.094958408 157.0214756 1.226775646 29.38001208 0.867654974 1.00E-05 5 -1.115277729 GHTGGHHS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GHTGGHHSPVK 11 0 H7C280;A0A0A0MQU4;Q96I15-2;Q96I15 H7C280 SCLY Selenocysteine lyase 1 GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK 122.97 0.00063479 266138000 220413 379760 307999 456430 247112 367872 381478 200505 61493.6 TRUE FALSE 209994.5143 418457.9758 322121.0588 410548.7892 290208.2546 355132.5004 323276.5248 182947.7193 71029.71342 2.956431952 5.8913088 4.535018421 5.779958407 4.085730331 4.999773803 4.551285782 2.575650533 1 16.11613504 1.070350948 2.580181066 1.018026234 4.736658628 0.69905913 0.826814072 0.132426563 1.805787302 0.731029646 0.198509071 11.75847358 -1.070350948 3.718632394 GHVDILAPTVQELAALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHVDILAPTVQELAALEK 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 74.618 0.01825 76213000 179920 175520 181180 207800 173080 215260 235340 203880 143180 FALSE TRUE 171415.5382 193405.6875 189487.2822 186911.5492 203265.0972 207805.4922 199434.5607 186027.1864 165383.6231 1.036472263 1.169436755 1.145743929 1.130169636 1.229052148 1.256505864 1.205890625 1.124822294 1 17.33545686 5.083341458 0.905566026 1.17792912 0.86449074 0.176977486 0.072342202 4.65818357 1.964935874 0.021299228 1.66743428 121155.0324 -5.083341458 -0.313438381 GHWDDVFLDSTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHWDDVFLDSTQR 13 0 Q9H6T3;Q9H6T3-3 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ;;; 220.53 2.06E-11 245656000 375257 353442 358577 390008 425897 350943 432209 384621 405781 FALSE TRUE 357519.3453 389458.1416 375018.1101 350803.6549 500173.302 338789.7559 366267.579 350941.5462 468707.445 0.762777185 0.83091947 0.800111272 0.748449078 1.067133256 0.722817099 0.781441778 0.748743272 1 18.83832819 -2.290341062 2.284656365 1.88823219 0.807194826 0.279107657 0.097070663 4799300.389 679445.493 22090797.62 0.021957062 0.005124588 2.290341062 -1.081037364 GHYAYDCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHYAYDCHR 9 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 66.568 0.063362 20688000 13802 10196 9693.5 10036 14903 8922 15209 15206 9726.1 FALSE TRUE 13149.60681 11234.98399 10137.95656 9027.162213 17502.07848 8613.028903 12888.58772 13874.48203 11234.37391 1.170479718 1.000054305 0.902405122 0.803530511 1.557904216 0.766667459 1.147245749 1.235002692 1 13.45563211 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHY(0.305)EVT(0.342)GS(0.342)DDET(0.01)GKLQGS(0.001)GVSLASK;GHYEVT(0.565)GS(0.435)DDETGKLQGSGVSLASK 242.9 1.63E-38 801960000 1050330 1120780 948250 1183780 547940 1082700 989710 1114740 526850 TRUE FALSE 1000682.982 1234988.756 991728.2004 1064784.185 643500.5625 1045205.828 838711.5622 1017127.456 608551.2072 1.644369398 2.029391679 1.629654479 1.749703513 1.057430426 1.717531434 1.378210333 1.671391732 1 19.21501914 -0.69898822 0.089366273 1.46E-13 2.401705008 0.419350819 0.241208338 49.84861145 1.004791493 19.88958453 8.080036514 0.199991611 0.69898822 2.401705008 GHYEVTGS(ph)DDETGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK 241.64 1.22E-17 399710000 1061700 1219580 844490 1215490 609470 1086810 954810 1003380 576190 TRUE FALSE 1011515.545 1343856.589 883210.7018 1093306.636 715761.375 1049173.497 809136.1982 915518.7279 665542.6024 1.519835907 2.019189431 1.327053593 1.642729755 1.075455384 1.576418239 1.215754176 1.375597482 1 19.34417149 2.627425345 0.294447325 1.012783796 1.898929198 0.400035094 0.229546688 2.018502558 0.385999782 0.308715939 0.625547741 424.0580822 -2.627425345 0.886145403 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.135)GS(0.865)DDETGKLQGSGVSLASK;GHYEVT(0.134)GS(0.866)DDETGKLQGSGVSLASK;GHYEVT(0.159)GS(0.841)DDETGKLQGSGVSLASK;GHYEVT(0.034)GS(0.966)DDETGKLQGSGVSLASK 199.04 4.45E-25 2700360000 1614480 1713610 1426180 1816330 842773 1620330 1501770 1619920 792434 TRUE FALSE 1538166.73 1888228.807 1491571.764 1633749.058 989752.3444 1564217.566 1272647.405 1478071.217 915320.6175 1.680467697 2.062915192 1.629562074 1.784892666 1.081317656 1.708928583 1.390384287 1.614812546 1 19.80391765 0.618853799 0.081122292 9.39E-09 2.707019243 0.466661932 0.233328856 23.80110824 0.947588461 17.80748563 12.66472939 4.157706219 -0.618853799 2.707019234 GHYEVTGS(ph)DDETGKLQGSGVSLASKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHYEVTGSDDETGKLQGSGVSLASKK 26 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.029)GS(0.971)DDETGKLQGSGVSLASKK 219.82 1.64E-34 136930000 121200 63718 138240 112970 80947 130270 182800 162100 112190 TRUE FALSE 115471.1162 70210.93664 144578.4407 101614.041 95064.13117 125758.7172 154910.5026 147905.6647 129587.8522 0.891064357 0.541801839 1.115678964 0.784132457 0.733588292 0.970451436 1.195409138 1.141354395 1 16.98357096 2.014080511 4.12937383 1.126545518 0.796909745 0.45270036 0.149633595 0.168790639 6.630795742 0.062349937 0.04057828 103.2952881 -2.014080511 -0.329635773 GHYNNVSCAVFHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GHYNNVSCAVFHPR 14 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 165.64 2.27E-06 329370000 150490 139320 107420 121700 203730 120390 167400 117150 130110 FALSE TRUE 143376.6359 153516.8664 112345.3133 109466.4848 239260.4475 116220.8641 141860.0555 106891.7249 150286.7943 0.954020189 1.021492721 0.747539488 0.728383923 1.592025757 0.773327189 0.943928947 0.711251614 1 17.19735872 GHYTEGAELVDAVLDVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GHYTEGAELVDAVLDVVR 18 0 P04350;M0R278;M0R1I1;K7ES63;K7ESM5;Q9BUF5;K7EL29 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ;;; 249.19 1.28E-24 79394800 100841 92404.2 87141.7 113871.7 128054 96071.8 113998.5 115014.9 113870.3 FALSE TRUE 96074.44578 101820.293 91137.23314 102425.1004 150386.5771 92744.80948 96605.9351 104943.5856 131528.7246 0.730444594 0.774129707 0.69290745 0.778727998 1.143374404 0.705129695 0.734485455 0.797875795 1 17.00501838 -5 0.276247632 2.485463298 0.773571557 0.200927175 0.128469529 373.5149053 3.59549208 318.3020462 0.147722162 1.00E-05 5 -1.711891741 GHYTEGAELVDSVLDVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 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 ;;;;;;;;;;;;;;;;;;;;;;; 409.84 5.68E-147 27550888600 4594363.1 4243950.7 4100077.4 4984800.7 5431427.2 4025901.4 5127223.8 4630083.1 4583717.7 FALSE TRUE 4377196.661 4676414.101 4288070.004 4483719.063 6378666.384 3886483.425 4344971.641 4224648.478 5294537.231 0.826738291 0.883252662 0.80990459 0.846857595 1.204763723 0.734055359 0.820651825 0.797925918 1 22.33607316 -0.629281565 6.001601591 0.999999994 0.863608971 0.10011148 0.126596636 1.71E-09 2.86E-10 0.115024926 0.027111635 0.234810998 0.629281565 -0.136391023 GHYTEGAELVDSVLDVVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 366.99 4.64E-108 2715361400 7645448.2 3707147.1 7923431.4 5805650.2 8374694.5 7529921.1 11734857 8991747.7 10458695 FALSE TRUE 7284063.015 4084909.604 8286728.567 5222055.212 9835238.569 7269158.044 9944489.039 8204382.603 12080576 0.602956598 0.338138645 0.685954756 0.432268727 0.814136558 0.601722802 0.82318004 0.679138362 1 23.52618591 1.637124729 0.336379956 1.015933909 0.435384893 0.544853802 0.128984131 0.841324067 0.311192129 0.17473795 0.162280446 43.36354001 -1.637124729 -0.580549017 GHYTIGK ddPTM_SK-BR-3_Trastuzumab_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 13540600000 48215900 52542400 41937600 54449000 41862800 48195100 51830100 51872800 38669900 FALSE TRUE 45936829.96 57896530.3 43860480.44 48975683.07 49163659.07 46526091.6 43922466.32 47330542.64 44666630.59 1.028437322 1.296192024 0.981951848 1.096471402 1.100679823 1.041629758 0.983339592 1.05963987 1 25.41269409 2.743668199 0.790714984 1.009292797 1.143114949 0.164251652 0.0836841 0.86938619 1.170185652 0.053779282 0.051608529 554.2021404 -2.743668199 0.133822153 GHYTIGKEIIDLVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 292.81 8.46E-46 237200000 433800 276840 440760 393260 470900 408330 603440 499980 528460 FALSE TRUE 413295.1337 305050.3107 460969.282 353728.7577 553024.8109 394189.4297 511374.1451 456199.1006 610410.8778 0.677076947 0.499745863 0.755178682 0.57949288 0.905987804 0.645777204 0.837753985 0.747363976 1 19.21942115 1.180486186 0.193124622 1.113644458 0.495047062 0.506026363 0.105111853 2.456659028 0.431441076 0.616373322 0.466677857 15.15256605 -1.180486186 -0.618597396 GHYTIGKEIIDLVLDRIR ddPTM_SK-BR-3_Trastuzumab_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 ; 266.7 2.13E-31 165635000 454920 286247 448220 364210 488650 386430 669590 510980 543660 FALSE TRUE 433416.8332 315415.8947 468771.3304 327598.9188 573870.4053 373047.8322 567431.7476 466235.8823 627968.0162 0.690189344 0.50228019 0.746489181 0.521680898 0.91385292 0.594055466 0.903599758 0.742451638 1 19.26033156 1.499803541 0.374610991 1.009648199 0.578780885 0.433645301 0.12601911 0.911428368 0.39503314 0.149796097 0.11766734 31.60847481 -1.499803541 -0.430867313 GIAYIEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 146.35 0.0012904 630551000 1411034 1199875 969677 1202089 1201949 1148171 1475886 1373773 1192732 FALSE TRUE 1344337.219 1322143.627 1014137.65 1081252.73 1411568.525 1108409.55 1250712.484 1253478.153 1377694.787 0.975787404 0.959678181 0.736111989 0.784827481 1.024587259 0.804539264 0.907829874 0.909837335 1 20.39382488 -0.573156175 9.782823172 1 0.893392112 0.129764164 0.090241671 0 0 0.086398738 0.020364378 0.267204535 0.573156175 -0.106607888 GICEYHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GICEYHEK 8 0 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 71.501 0.048579 160640000 344300 340110 280790 358940 251640 313050 384150 296310 265500 FALSE TRUE 328025.6213 374767.5957 293664.4992 322858.6693 295525.9363 302209 325540.8621 270363.5256 306672.384 1.069628824 1.222045464 0.957583775 1.052780381 0.963653566 0.985445758 1.061526499 0.881603756 1 18.22633873 3.729322215 24.99742704 0.994469229 1.145837145 0.530684013 0.062069014 426.8181951 1154891.616 0.015212228 0.023921656 5361.943275 -3.729322215 0.151367916 GICFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GICFIR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 115.97 0.05577 2067240000 4039220 3006270 2464940 2894840 4965270 2452470 4298400 2883000 4187200 FALSE TRUE 3848294.076 3312612.331 2577959.937 2603845.183 5831211.516 2367540.349 3642600.134 2630549.236 4836529.591 0.7956726 0.684915138 0.533018539 0.538370568 1.205660258 0.489512222 0.753143357 0.543891893 1 22.20554079 GIDFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIDFHK 6 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 90.939 0.04846 569050000 1897600 1685900 1665400 2036900 1684400 1841600 2191600 2011400 1696600 FALSE TRUE 1807904.209 1857695.127 1741760.237 1832146.942 1978158.827 1777824.93 1857231.169 1835271.153 1959700.063 0.922541282 0.9479487 0.888789193 0.934911917 1.009419178 0.907192363 0.94771195 0.936506146 1 20.90220143 -5 0.204142253 1.291069091 0.92724814 0.300051658 0.031113402 182.8015876 1.81449375 21.74867781 0.066426605 1.00E-05 5 -0.363820951 GIDIHGVPYVINVTLPDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIDIHGVPYVINVTLPDEK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 184.03 2.58E-14 172898000 694460 660180 599540 739620 538380 652100 744350 707470 523820 FALSE TRUE 661634.2521 727453.0926 627029.502 665271.9924 632273.3015 629517.6135 630785.7366 645520.1763 605051.3303 1.093517556 1.202299799 1.036324475 1.09952984 1.044991177 1.040436707 1.0425326 1.06688498 1 19.20669801 3.723211223 24.99284987 1.050138724 1.147908679 0.576856514 0.035776956 468.9974806 763651.329 0.00881838 0.013711952 5287.023289 -3.723211223 0.097769955 GIDVEQVSVVINFDLPVDKDGNPDNETYLHR ddPTM_SK-BR-3_Trastuzumab_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 ; 86.304 0.0004055 34473000 42786 39108 37380 39699 25375 45671 43653 39746 30155 FALSE TRUE 40763.59057 43093.14966 39093.90997 35708.3811 29800.39197 44089.40182 36992.93311 36265.62953 34831.28339 1.170315492 1.237196723 1.122379257 1.02518132 0.855563995 1.265798946 1.062060582 1.041179825 1 15.08809601 3.494461458 4.156506227 1.053284339 1.202368132 0.305872732 0.100283216 0.252334214 10.11445901 0.027034169 0.040455038 3122.205313 -3.494461458 0.149083793 GIEEEEILPGFILCDPNNLCHSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GIEEEEILPGFILCDPNNLCHSGR 24 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;; 231.37 1.23E-33 383831100 525902 616524 502511 637996 542360 520686 542918 533352 454435 FALSE TRUE 501043.6547 679348.4965 525551.6264 573863.43 636947.4123 502654.5133 460085.8877 486648.8714 524906.4589 0.95453894 1.294227733 1.00122911 1.093267991 1.213449371 0.957607789 0.876510243 0.927115419 1 19.00170082 2.102807035 6.514715572 0.920062922 1.115671041 0.418973991 0.099717508 0.180469549 9.971350667 0.03567983 0.026233119 126.708875 -2.102807035 0.195608119 GIEESLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GIEESLRK 8 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;;; 157.91 0.00059218 2125550000 2670770 1737440 2002160 1804300 2152890 1707320 2519420 2178500 2420800 FALSE TRUE 2544527.995 1914487.111 2093961.016 1622928.336 2528353.334 1648195.08 2135036.207 1987738.991 2796205.3 0.909993267 0.6846733 0.74885811 0.580403855 0.904208763 0.589439939 0.763547729 0.710870189 1 21.41503886 -1.411831174 5.707958749 1.000114992 0.738235885 0.362554781 0.109782679 0.000143657 1.48E-05 0.095052985 0.022394417 0.038740822 1.411831174 -0.261879107 GIEFEDES(ph)SDRDARPALETQPQQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.546)S(0.454)DRDARPALETQPQQEK 202.04 3.07E-25 59945000 118590 96246 103310 119430 96683 121590 124700 119910 96953 TRUE FALSE 112984.4857 106053.5768 108046.8657 107424.6695 113544.4846 117379.3078 105674.7247 109410.0447 111987.9761 1.008898363 0.947008603 0.964807736 0.959251817 1.01389889 1.048142059 0.943625632 0.976980284 1 16.77298432 2.754107645 24.90999359 0.993289877 0.970196102 0.152644437 0.030542132 1782.525255 2856020.968 0.009603897 0.010144823 567.6852949 -2.754107645 -0.023093775 GIEFEDESS(ph)DRDARPALETQPQQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.031)S(0.969)DRDARPALETQPQQEK 215.98 8.73E-34 73363000 139250 107940 108250 157520 130390 157270 168780 133680 135560 TRUE FALSE 132667.9285 118939.2087 113213.3696 141685.7903 153129.9747 151823.7005 143029.5111 121974.2705 156581.9525 0.847274711 0.759597175 0.723029492 0.904866673 0.977954179 0.969611747 0.913448254 0.778980391 1 17.25655841 3.133116111 6.447720231 0.92674721 0.783594305 0.5203867 0.066884936 0.169328411 9.147867623 0.018956221 0.02278343 1358.676647 -3.133116111 -0.143152905 GIEGHS(ph)PGNLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIEGHSPGNLPK 12 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 GIEGHS(1)PGNLPK;GIEGHS(1)PGNLPK 153 4.53E-05 644180000 1333660 1435790 1392880 1617240 1221180 1496110 1656500 1626020 1167680 TRUE FALSE 1270620.535 1582098.633 1456744.926 1454671.963 1434153.405 1444299.336 1403770.501 1483637.069 1348757.851 0.942067202 1.173004207 1.080064094 1.078527151 1.063314222 1.070836648 1.040787641 1.100002545 1 20.36319993 -0.211875893 7.691590439 1 1.068863547 0.126215252 0.0567 0 0 0.051654727 0.012175136 0.613937423 0.211875893 0.068863546 GIEHQDSQHSFLAFLNTPTDALDQFETVDS(ph)TPLSVHTPTLR ddPTM_SK-BR-3_Trastuzumab_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(0.043)VDS(0.228)T(0.228)PLS(0.228)VHT(0.228)PT(0.043)LR;GIEHQDSQHSFLAFLNTPT(0.002)DALDQFET(0.161)VDS(0.22)T(0.22)PLS(0.174)VHT(0.174)PT(0.049)LR 47.457 0.016619 323161000 123597 91747.4 119160 116655 125571 106215 155892 126793 66358.9 TRUE FALSE 117754.8148 101096.5644 124623.6039 104928.6178 147470.5426 102536.7479 132107.8122 115690.3327 76649.4993 1.536276373 1.318946181 1.625889341 1.368940681 1.923959634 1.337735391 1.723531314 1.509342315 1 16.22598875 0.944132853 22.47628348 0.999999999 1.537611495 0.460462294 0.18494463 5839.804408 2349453.971 0.161393268 0.040348317 8.79291456 -0.944132853 0.537611496 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLS(ph)VHTPTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFET(0.001)VDS(0.081)T(0.081)PLS(0.377)VHT(0.377)PT(0.081)LR 74.767 0.00080241 32924000 15205 11147 16014 17202 22552 16062 20606 18604 6502.5 TRUE FALSE 14486.28978 12282.89197 16748.25774 15472.82228 26485.06166 15505.76891 17462.17624 16974.93513 7510.87449 1.928708808 1.635347787 2.229867875 2.060056029 3.526228763 2.064442554 2.324919191 2.260047769 1 12.87476517 -1.38744689 6.82198748 0.999919808 2.210484216 0.385715559 0.494553384 0.000611568 5.49E-05 0.485499159 0.114425851 0.040978222 1.38744689 1.210564408 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(ph)PTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDS(0.006)T(0.006)PLS(0.162)VHT(0.694)PT(0.131)LR 135.89 4.89E-09 96533000 29903 20024 28772 27888 41261 21457 36033 29388 5751.1 TRUE FALSE 28489.54445 22064.46837 30091.22466 25084.64526 48456.90534 20713.93871 30535.50406 26814.63092 6642.951215 4.288687893 3.321485835 4.529797628 3.776129681 7.294484599 3.118183175 4.596677451 4.036553943 1 12.6976086 3.719057551 24.03414792 4.280579274 3.805086659 0 1.568466212 2475.440957 3050551.49 0.371681072 0.576894989 5236.698263 -3.719057551 -0.475492615 GIEHSLIEENCGVVVESIQVTLECGLGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIEHSLIEENCGVVVESIQVTLECGLGHR 29 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ; 224.21 8.08E-35 28556000 17382.8 14711.9 16326.3 16451.2 16300.2 15487 15941.8 17218.9 18035 FALSE TRUE 16561.14949 16211.05934 17074.877 14797.49412 19142.94972 14950.68131 13509.58562 15711.12183 20831.77569 0.794994615 0.778189031 0.819655379 0.710332827 0.918930292 0.717686362 0.648508597 0.754190236 1 14.3464982 GIEILTDMSRPVELSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GIEILTDMSRPVELSDR 17 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;;;; 273.88 1.03E-35 3316010000 3530778 4040270 3077601 4217810 3373410 3254459 3159425 3534823 3103120 FALSE TRUE 3363885.121 4451978.106 3218712.05 3793827.725 3961731.636 3141756.269 2677396.689 3225295.159 3584336.001 0.938496034 1.242064947 0.897993952 1.058446453 1.10529025 0.876523927 0.746971458 0.899830584 1 21.77327445 2.169473706 5.978704739 0.845119312 1.058263478 0.336625807 0.112098915 0.179022188 11.46327188 0.040011591 0.029544006 147.7317036 -2.169473706 0.213144166 GIEILTDMSRPVELSDRETLLNSATTSLNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIEILTDMSRPVELSDRETLLNSATTSLNSK 31 2 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 302.86 5.53E-82 404080000 465010 420290 475440 481090 473320 506930 622040 525550 506680 FALSE TRUE 443029.8989 463118.0288 497239.3943 432729.9192 555866.8581 489374.887 527136.3735 479530.0559 585253.3466 0.756988237 0.791312056 0.849613927 0.739389055 0.949788432 0.836176145 0.900697752 0.819354658 1 19.15870175 1.383563538 0.032006779 1.759257584 1.68E-12 0.555338343 0.054665413 62.18951693 1.917880025 52.95770682 51.61144033 24.18597155 -1.383563538 -1.759257584 GIELAVRPHSAPEYEDETMTVYQIPIHSEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIELAVRPHSAPEYEDETMTVYQIPIHSEQR 31 1 Q9BQ52;G5E9D5;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 197.36 8.35E-26 88831000 68923 69244 69755 82917 93724 61056 84681 68201 77142 FALSE TRUE 65665.14638 76300.04232 72953.33575 74582.02563 110069.4359 58941.61541 71761.35818 62228.95888 89104.78737 0.736942967 0.856295656 0.818736433 0.837014798 1.235280832 0.661486517 0.805359176 0.698379523 1 16.44321533 -1.762132716 7.270346159 1.003165986 0.830220011 0.103182817 0.15638408 0.007625344 0.000249482 0.143873083 0.033383729 0.017292878 1.762132716 -0.172945975 GIFEALRPLETLPVEGLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIFEALRPLETLPVEGLIR 19 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 176.73 7.74E-14 408480000 377890 369010 380040 408520 413470 354450 423630 399560 428370 FALSE TRUE 360027.8886 406612.5385 397465.2099 367454.7935 485579.0371 342175.3076 358997.463 364572.4082 494799.4318 0.727623893 0.821772444 0.803285502 0.742633823 0.981365389 0.691543453 0.725541381 0.736808462 1 18.91648432 -2.238999898 2.310139542 1.793261861 0.777520596 0.4216216 0.081399504 5680122.777 1008679.718 23550080.77 0.019767829 0.005767666 2.238999898 -1.015741265 GIFEPFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GIFEPFGR 8 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ;; 130 0.0024813 384582000 602900 538910 526470 641550 703580 507730 625170 593500 744080 FALSE TRUE 574402.1118 593825.5417 550609.1702 577060.1751 826284.1292 490147.1828 529788.8345 541529.9937 859468.1262 0.668322762 0.690922122 0.64063943 0.671415446 0.961390078 0.570291286 0.616414755 0.630075714 1 19.71308461 -1.053129794 4.385472827 1.000018718 0.678548485 0.475310526 0.105237745 13416566.4 3221861.785 2906.654434 0.023662602 0.088485112 1.053129794 -0.321470233 GIFGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIFGFR 6 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 161.85 0.014064 89587000 280150 242840 215216 273450 320130 208727 288000 257450 303880 FALSE TRUE 266907.8647 267585.6721 225083.8665 245962.2865 375960.5706 201498.7317 244060.3105 234906.3132 351004.1584 0.760412258 0.76234331 0.64125698 0.700738953 1.071100047 0.574063659 0.695320282 0.669240827 1 18.4211286 GIFPVLCKDPVQEAWAEDVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GIFPVLCKDPVQEAWAEDVDLR 22 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 240.71 1.12E-30 19168500000 5766043 5245266 5198731 6113324 5029859 5646363 6317403 5950335 5411890 FALSE TRUE 5493493.575 5779764.569 5437097.959 5498801.057 5907064.817 5450828.034 5353567.145 5429292.123 6251138.261 0.878798924 0.924593942 0.869777268 0.879647966 0.944958273 0.87197368 0.856414771 0.868528562 1 22.57568748 -1.378612032 5.91134926 1.000023821 0.887745577 0.629378603 0.02728295 8.70E-06 9.14E-07 0.026817489 0.006319602 0.041820379 1.378612032 -0.112278244 GIFPVLCKDPVQEAWAEDVDLRVNFAMNVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIFPVLCKDPVQEAWAEDVDLRVNFAMNVGK 31 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 65.155 0.0035481 3604900 4896.4 1144.2 6047.2 4276 7059.1 3928.6 10150 8082 10806 FALSE TRUE 4664.956876 1260.795281 6324.470101 3846.168356 8290.204805 3792.551597 8601.431082 7374.297235 12481.73929 0.373742534 0.101011185 0.506697821 0.308143622 0.664186666 0.303848006 0.689121194 0.590806863 1 13.60753136 1.03441924 0.252687056 1.138642876 0.158046854 0.660667977 0.14676213 1.324517092 0.296364137 0.487560194 0.307226357 10.82478402 -1.03441924 -0.980596022 GIGIENIHYLNDGLWHMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIGIENIHYLNDGLWHMK 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 236.16 4.74E-24 309090000 1078650 908720 960040 1109150 1080410 965060 1218900 1071580 276496 FALSE TRUE 1027664.352 1001319.601 1004058.784 997656.1348 1268833.162 931639.7302 1032934.418 977746.7744 319373.5875 3.217749971 3.135261149 3.143837884 3.123790362 3.9728807 2.917084463 3.23425123 3.061451581 1 18.28488548 0.090034199 1.121110193 0.989889228 3.247773723 0.868225057 0.273519094 2.327634771 2.54797117 0.306289151 0.074345789 1.230365653 -0.090034199 2.257884495 GIGLDESELDS(ph)EAELMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIGLDESELDSEAELMR 17 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 GIGLDESELDS(1)EAELMR 268.21 1.74E-26 0 51960 53183 44020 50658 54638 45776 55550 56664 59039 TRUE FALSE 49503.95377 58602.40816 46038.36054 45565.7616 64166.8499 44190.76564 47074.82725 51702.19977 68194.46659 0.725923323 0.85934257 0.675104049 0.668173884 0.940939245 0.648011017 0.690302742 0.758158284 1 16.05736706 0.936261317 20.87366157 1.000000001 0.746865119 0.434083738 0.091328406 3885.128239 1272336.825 0.084183754 0.021045938 8.634979625 -0.936261317 -0.253134882 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 33 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 257.04 1.92E-59 285680000 285200 271660 265600 319250 280680 277880 381610 331440 304210 FALSE TRUE 271719.1612 299342.4629 277778.0227 287158.3835 329630.5031 268256.9459 323388.3858 302417.3565 351385.3331 0.773279746 0.851892309 0.790522531 0.817217898 0.938088395 0.763426702 0.920324087 0.860643083 1 18.42269445 -4.999999999 0.100040352 1.543634995 0.723254808 0.548594458 0.051480552 128.7677639 0.876442748 14.43195868 0.762103635 1.00E-05 4.999999999 -0.820380187 GIHNFRAS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIHNFRASGDYDNDCTNPITPLCTQPDQVIK 31 1 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 GIHNFRAS(0.99)GDY(0.001)DNDCT(0.009)NPITPLCTQPDQVIK;GIHNFRAS(0.981)GDY(0.008)DNDCT(0.012)NPITPLCTQPDQVIK 227.37 1.69E-35 326800000 229449 156069 218354 216804 249920 227211 337080 267752 302960 TRUE FALSE 218603.4005 171972.6085 228365.7469 195010.45 293505.9689 219342.6261 285652.2551 244306.2154 349941.4895 0.624685575 0.491432464 0.652582657 0.557265874 0.838728695 0.626798001 0.816285761 0.698134468 1 18.4167542 0.910205732 0.218968987 1.111190171 0.478669213 0.65213511 0.087904774 1.925886907 0.321992586 0.439500022 0.259575526 8.132156573 -0.910205732 -0.632520958 GIIRPGTAFELLEAQAATGYVIDPIK ddPTM_SK-BR-3_Trastuzumab_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 0 110.68 0.0019617 47961000 115290 106990 100100 117320 85868 90298 119050 107960 95930 FALSE TRUE 109840.4702 117892.4026 104689.684 105526.7707 100843.352 87170.95762 100886.736 98506.45007 110806.3345 0.991283312 1.063950028 0.944798729 0.952353232 0.910086526 0.786696519 0.910478056 0.888996559 1 16.75768083 3.250943597 1.555659671 0.887428022 1.025667086 0.408726043 0.057098071 0.283516502 1.424370104 0.01783475 0.026033251 1782.147299 -3.250943597 0.138239063 GIITDS(ph)FGR ddPTM_SK-BR-3_Trastuzumab_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 232.21 2.63E-08 462480000 726440 708820 691990 732650 830770 666270 780460 741650 861460 TRUE FALSE 692102.6209 781049.5639 723718.426 659002.6301 975656.025 643196.9028 661386.4929 676707.1943 995050.8171 0.695545 0.784934348 0.727318056 0.662280377 0.980508742 0.646396035 0.664676096 0.680073 1 19.92441068 -1.40293185 3.046154623 1.004094187 0.729791096 0.431303685 0.09735577 134298052.4 162436749.7 4779229.389 0.022050131 0.039542867 1.40293185 -0.274303091 GIKQDLIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIKQDLIHR 9 1 F8VZQ9;H0YHG0;P82979;F8VS12 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 119.68 0.00047338 344230000 753560 460150 626110 524880 814030 666810 1013900 771380 860320 FALSE TRUE 717940.7122 507039.8081 654817.7628 472118.0652 955996.5743 643718.2025 859210.9334 703833.8779 993734.0317 0.722467672 0.510236937 0.658946702 0.475094995 0.96202459 0.647777154 0.864628669 0.708271887 1 19.92250025 2.742557325 24.99903671 0.815630239 0.596379545 0.484260423 0.124484816 298.0145044 1864055.273 0.034126005 0.035002833 552.7863687 -2.742557325 -0.219250694 GILAADES(ph)TGSIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.982)T(0.018)GSIAK;GILAADES(0.92)T(0.08)GSIAK;GILAADES(0.5)T(0.5)GSIAK;GILAADES(0.986)T(0.013)GSIAK;GILAADES(0.854)T(0.146)GSIAK 300.71 7.89E-44 950561000 1755307 1464885 1282463 1687415 1282587 1495728 1773128 1685885 1405668 TRUE FALSE 1672337.117 1614158.447 1341265.197 1517792.838 1506269.767 1443930.564 1502604.758 1538259.972 1623651.814 1.029985063 0.994153077 0.826079326 0.934801923 0.927704914 0.889310474 0.925447651 0.94740754 1 20.63081085 3.977811352 24.15042735 0.917234975 1.016548091 0.427540457 0.044115732 345.6651714 376227.6956 0.010090151 0.018259311 9501.91961 -3.977811352 0.099313116 GILAADES(ph)TGSIAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.994)T(0.006)GSIAKR 185.25 2.64E-07 461610000 414100 277020 425390 398510 388130 423850 577020 482950 508070 TRUE FALSE 394526.3137 305248.6529 444894.5523 358451.0177 455819.7491 409171.9682 488985.0013 440660.3377 586858.9007 0.672267752 0.520139769 0.758094581 0.610795912 0.776710975 0.697223758 0.833224137 0.750879534 1 19.16265415 1.060902053 0.255410821 1.067762714 0.555210442 0.688467497 0.071900728 1.183647534 0.273765656 0.229400762 0.147549502 11.50540876 -1.060902053 -0.512552272 GILAADEST(ph)GSIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.316)T(0.684)GSIAK 317.91 6.23E-55 204580000 718800 695020 585400 758360 548890 607840 765190 713990 576260 TRUE FALSE 684823.7485 765843.3282 612241.169 682128.212 644616.2422 586790.3484 648446.2118 651469.2505 665623.4577 1.028845574 1.150565413 0.919801071 1.024795933 0.968439791 0.881565007 0.974193749 0.978735414 1 19.34434675 3.73327944 24.99491717 0.961294634 1.089705494 0.532753185 0.048920046 274.8621885 1300877.559 0.012265447 0.019659614 5411.023747 -3.73327944 0.128410861 GILAADEST(ph)GSIAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.092)T(0.908)GSIAKR 190.74 1.20E-07 354160000 375750 221400 284060 283170 320160 316460 415370 358870 407980 TRUE FALSE 357989.0422 243960.9117 297084.432 254705.2136 375995.8026 305500.9108 351997.6777 327445.4403 471247.4547 0.759662548 0.517691733 0.630421298 0.540491436 0.797873387 0.648281296 0.746948709 0.694848189 1 18.8461253 0.016873898 0.399927573 1.056765973 0.620485729 0.614685834 0.085667448 2.756897703 0.599060136 0.337239986 0.056072123 1.039618258 -0.016873898 -0.436280244 GILAADESTGS(ph)IAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.034)T(0.247)GS(0.72)IAK;GILAADES(0.005)T(0.122)GS(0.873)IAK;GILAADEST(0.005)GS(0.995)IAK;GILAADEST(0.001)GS(0.999)IAK;GILAADES(0.001)T(0.029)GS(0.97)IAK 293.8 1.56E-43 496760000 1662490 1463270 1429770 1736640 1228500 1657870 1879410 1679650 1255020 TRUE FALSE 1583907.392 1612378.877 1495326.369 1562069.648 1442750.011 1600457.546 1592671.487 1532570.942 1449642.092 1.092619621 1.112259975 1.031514177 1.077555389 0.995245667 1.104036338 1.098665316 1.057206431 1 20.46726532 1.945093195 0.007929247 2.90E-06 2.130187217 0.229394446 0.037077533 3130.648648 19.93756634 2657.997857 2695.650545 88.12379577 -1.945093195 2.130184321 GILAADESTGS(ph)IAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADEST(0.003)GS(0.996)IAKR;GILAADESTGS(1)IAKR 225.13 6.37E-13 1363520000 1585980 1123040 1350460 1479450 1270210 1493730 1948460 1631150 1485490 TRUE FALSE 1511013.869 1237479.053 1412379.927 1330732.875 1491734.222 1442001.756 1651186.641 1488317.859 1715852.202 0.880620059 0.721203756 0.823136121 0.775552156 0.869383866 0.840399746 0.962312861 0.867392807 1 20.71049386 1.872986657 0.828374425 0.969873424 0.794709719 0.560129362 0.053596533 0.399515426 0.512894274 0.043260147 0.020338042 74.64258259 -1.872986657 -0.175163705 GILAADESTGSIAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 289.72 1.13E-43 1454910000 1568340 904690 1813930 1290140 1802630 1686350 2315500 2022630 2591700 FALSE TRUE 1494207.676 996878.9395 1897100.485 1160452.676 2117008.101 1627951.277 1962227.948 1845517.795 2993607.599 0.499132778 0.333002542 0.633717153 0.38764355 0.707176218 0.543809174 0.655472664 0.616486207 1 21.5134537 -5 0.108760154 2.590615776 0.24342329 0.705376929 0.100024611 78.08468585 0.566330044 27.36257559 1.130087007 1.00E-05 5 -2.347192486 GILADEDSSRPVWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 245.4 3.90E-18 38973503000 13481000 11971440 12088510 14636790 11591220 12945110 14952830 14070480 13411070 FALSE TRUE 12843779.85 13191343.35 12642780.14 13165472.06 13612725.1 12496817.59 12671501.16 12838394.18 15490790.24 0.829123605 0.851560388 0.816148172 0.84989028 0.87876247 0.806725635 0.818002243 0.828775936 1 23.88490741 -1.080013491 5.436081281 1.000001649 0.834716376 0.860528996 0.020891828 4.14E-07 7.01E-08 0.020067408 0.004729886 0.083173793 1.080013491 -0.165285272 GILEYLTVAEVVETMEDLVTYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GILEYLTVAEVVETMEDLVTYTK 23 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 80.98 0.00019653 0 142370 165240 197570 186880 133250 170380 209220 185470 132890 FALSE TRUE 135640.4523 182078.1439 206628.7799 168094.4674 156488.7578 164479.6979 177299.6464 169229.2636 153497.9025 0.88366323 1.186193042 1.346134224 1.095092927 1.019484666 1.071543619 1.15506234 1.102485837 1 17.22785942 0.93288151 19.49915017 0.999999999 1.10751752 0.076225205 0.117708349 6249.474557 1815595.136 0.114736942 0.028684236 8.568040496 -0.93288151 0.107517521 GILFVGSGVSGGEEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GILFVGSGVSGGEEGAR 17 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 138.02 3.38E-05 0 57696 54163 50820 61352 54751 58707 68364 59496 64532 FALSE TRUE 54968.82442 59682.27128 53150.14727 55184.7804 64299.55707 56673.96187 57933.81621 54286.21483 74539.29298 0.737447623 0.800682015 0.713048718 0.740344833 0.862626334 0.760323309 0.777225191 0.728289908 1 16.18571351 -1.461004481 3.003696615 1.005576247 0.767679802 0.748825644 0.042748005 18213906.37 21556025.06 853033.3567 0.009773874 0.034593581 1.461004481 -0.237896445 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK 38 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;; 414.11 6.91E-200 5451957200 2275156.5 1539487.2 2258783.2 2451557.4 4022412 1855195.2 3488834 2532752.2 1204790.7 FALSE TRUE 2167614.361 1696362.696 2362350.644 2205122.192 4723919.379 1790949.325 2956548.296 2310970.99 1391623.489 1.557615533 1.218981075 1.697550137 1.584568104 3.394538407 1.286949624 2.124531758 1.66062948 1 20.4083375 3.25713633 2.871266865 1.956421407 1.412437836 0.060772293 0.643922733 0.513254652 8.676358662 0.174671838 0.233905136 1807.741508 -3.25713633 -0.54398357 GILHLS(ph)PDVYQEMEASR ddPTM_SK-BR-3_Trastuzumab_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(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR;GILHLS(1)PDVYQEMEASR 229.15 7.75E-16 340566000 332883 350543 343037 385618 429902 343453 390977 386225 404017 TRUE FALSE 317148.2803 386263.7302 358765.5858 346854.946 504876.7727 331559.1365 331326.2779 352405.0915 466669.8929 0.679598759 0.827702271 0.768778083 0.74325546 1.081871319 0.710478952 0.709979973 0.755148547 1 18.83204287 -2.382845804 2.153223112 2.463294241 0.780758821 0.262962954 0.113166848 6649935.429 692156.8988 47379512.64 0.028143611 0.004141467 2.382845804 -1.68253542 GILHTDSQSQS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GILHTDSQSQSLR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 GILHTDS(0.002)QS(0.303)QS(0.695)LR;GILHTDSQS(0.025)QS(0.975)LR 169.15 3.77E-07 0 857100 811660 796350 906000 1067880 811050 957360 866540 1104690 TRUE FALSE 816586.5816 894369.0768 832863.4352 814927.1587 1254117.934 782963.1351 811297.1489 790661.1638 1275999.683 0.639958295 0.700916378 0.652714453 0.638657806 0.982851289 0.613607625 0.63581297 0.619640564 1 20.28319654 -1.849118792 2.418857146 1.13638284 0.683869755 0.453301951 0.10852299 8255861.082 4749654.388 6497410.398 0.025993668 0.014154066 1.849118792 -0.452513086 GILLEDGSES(ph)PAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GILLEDGSESPAKR 14 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 GILLEDGS(0.038)ES(0.962)PAKR;GILLEDGS(0.008)ES(0.992)PAKR 114.96 0.0002738 159597000 232660 209162 223891 250565 165984 246031 249551 273878 220647 TRUE FALSE 221662.6229 230475.8456 234156.6238 225377.7302 194931.557 237510.8848 211477.4116 249895.7904 254863.8099 0.869729692 0.904309818 0.918751956 0.884306525 0.764845967 0.93191295 0.829766344 0.98050716 1 17.959367 1.151792401 6.468119988 0.996530163 0.874324843 0.516655422 0.047608456 0.171070516 10.0565763 0.042118921 0.010619201 14.18379352 -1.151792401 -0.122205319 GILRT(ph)PDTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GILRTPDTIR 10 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 GILRT(1)PDTIR;GILRT(0.996)PDT(0.004)IR 94.122 0.007179 161330000 121166 89600 113072 126799 143346 113177 142490 116479 157717 TRUE FALSE 115438.7233 98730.34187 118256.463 114052.9236 168345.497 109257.6521 120750.5335 106279.4813 182174.9469 0.633669587 0.541953455 0.649136806 0.626062615 0.924086983 0.599740272 0.662827329 0.58339241 1 17.47496504 -4.999999999 0.316730728 4.238461185 0.631758478 0.516510563 0.104166781 254.5903586 2.271591069 552.2852119 0.091577326 1.00E-05 4.999999999 -3.606702707 GILSLPHQAS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_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(0.997)PVS(0.003)R;GILSLPHQAS(0.933)PVS(0.067)R 164.58 2.64E-06 507896000 450969 426001 451932 454059 538059 435885 544132 488280 536172 TRUE FALSE 429652.5891 469410.9862 472653.5292 408416.1267 631896.3192 420790.1932 461114.6697 445523.6147 619318.8154 0.69375026 0.757947239 0.763182899 0.659460227 1.020308609 0.679440351 0.744551366 0.719376844 1 19.24032275 -2.256423891 2.363625836 1.998289968 0.75274684 0.37132399 0.100256787 6595837.788 684078.8407 35569671.73 0.0222589 0.005540846 2.256423891 -1.245543128 GILTLK ddPTM_SK-BR-3_Trastuzumab_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 ; 149.11 0.024845 1110550000 3831700 3464500 3408800 4046800 3471100 3597600 4184500 3915400 3722800 FALSE TRUE 3650583.135 3817536.489 3565096.852 3640007.976 4076458.741 3473014.21 3546077.671 3572546.819 4300112.811 0.84895055 0.887775893 0.82907054 0.846491275 0.94798879 0.807656534 0.824647591 0.830803046 1 22.03594308 -0.996643012 4.866257939 1.000001919 0.853556551 0.574834008 0.039748334 8.05E-07 1.66E-07 0.037417841 0.008819354 0.10077597 0.996643012 -0.146445368 GIMVLAGDTLPIEVYCHLPVMCEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GIMVLAGDTLPIEVYCHLPVMCEDR 25 0 D6RC52;D6RCB9;Q9NX24;H0YC83 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 ;; 265.05 2.57E-45 281976000 284229 221673 253487 296092 291971 253175 311150 250271 280092 FALSE TRUE 270794.0585 244261.7307 265109.6297 266328.2696 342890.65 244407.4863 263678.3528 228355.9445 323527.2368 0.837005444 0.754995879 0.819435273 0.823202004 1.059850952 0.7554464 0.815011297 0.70583221 1 18.30352765 -2.332575326 2.309807159 2.054940551 0.820125639 0.26346651 0.093854222 5505092.117 543781.2658 30720294.29 0.021479069 0.004649697 2.332575326 -1.234814912 VRYSLDPENPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRYSLDPENPTK 12 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81;J3KSJ0 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 63.76 0.062377 173470000 390800 276040 387450 297570 351530 400840 573790 575090 669280 FALSE TRUE 372327.6585 304168.7898 405214.9657 267657.6983 412836.7207 386958.8103 486247.7971 524732.0709 773068.5242 0.481623099 0.393456441 0.524164357 0.34622765 0.53402345 0.500549173 0.628984083 0.678765277 1 19.56023677 0.923434854 0.668401435 1.004050333 0.435226275 0.908685954 0.054920156 0.202744118 0.205004317 0.048144102 0.01913621 8.383683105 -0.923434854 -0.568824058 GINGGPSRMS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GINGGPSRMSPK 12 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GINGGPS(0.005)RMS(0.995)PK 62.861 0.045281 288000000 377500 185700 416360 364210 355670 379380 602850 524960 518530 TRUE FALSE 359656.3231 204623.0411 435450.5178 327598.9188 417698.7354 366241.9755 510874.1604 478991.7194 598940.9841 0.600487081 0.341641408 0.727034097 0.546963603 0.69739548 0.611482575 0.852962435 0.799731079 1 19.19205433 1.782526812 0.443935535 1.008035475 0.473123468 0.671350711 0.103260801 0.500857752 0.249484057 0.103712849 0.081758125 60.60756172 -1.782526812 -0.534912008 GIPAPEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIPAPEEER 9 0 O95433;G3V438;H0YJU2 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 111.95 0.004751 250210000 285030 242910 246400 300250 281150 256050 311320 282850 343390 FALSE TRUE 271557.1968 267662.8052 257697.6837 270068.2996 330182.471 247182.9243 263822.4162 258082.1545 396641.1674 0.684641986 0.674823561 0.649699791 0.680888223 0.832446297 0.62319029 0.665141286 0.650669108 1 18.5974749 -1.064135905 4.501223409 1.000018334 0.681636924 0.758670797 0.056240141 1.04E-05 2.16E-06 0.051377365 0.012109019 0.086270853 1.064135905 -0.318381411 GIPDDRDGLFDTIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 92.935 0.0046065 111900000 62743 45014 58000 66845 72863 52192 67110 65731 78376 FALSE TRUE 59777.26273 49600.97778 60659.35737 60125.6136 85570.28413 50384.57795 56871.13694 59975.24518 90530.14979 0.660302263 0.547894573 0.670045919 0.664150161 0.945213107 0.556550255 0.62820107 0.662489185 1 16.46611072 -2.09341209 2.135598095 1.543004917 0.657043459 0.479751104 0.108600101 5529194.078 1523885.104 14585118.75 0.026400693 0.008064694 2.09341209 -0.885961459 GIPHLVTHDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 177.57 4.58E-06 8692118000 6186124 5684661 5057997 5885511 7210217 5450225 6634508 5841158 1173210 FALSE TRUE 5893718.178 6263934.419 5289911.165 5293888.253 8467676.562 5261482.342 5622291.954 5329675.24 1355145.415 4.349140774 4.622333773 3.903574559 3.906509364 6.248537219 3.882596129 4.148847712 3.93291759 1 20.37001624 0.371452928 0.975931261 0.985980805 4.492392352 0.712849613 0.683062569 1.287308813 1.541619493 0.643232221 0.196797721 2.352084546 -0.371452928 3.506411547 GIPLATGDT(ph)SPEPELLPGAPLPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.07)GDT(0.465)S(0.465)PEPELLPGAPLPPPK 111.49 0.0094494 42312000 97667 91640 78995 114240 68396 94576 95047 102010 72148 TRUE FALSE 93050.47447 100978.2202 82616.99889 102756.3782 80324.24075 91300.80941 80545.83449 93077.46361 83336.34336 1.116565363 1.211694875 0.991368178 1.233032 0.963856074 1.095570141 0.966515103 1.116889221 1 16.34665818 2.729118227 24.99633166 1.02711859 1.139864712 0.316535194 0.079992037 727.4331349 1925691.517 0.022918619 0.021871192 535.9425366 -2.729118227 0.112746122 GIPNERPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIPNERPTR 9 1 Q96F86;H3BPW9;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 91.584 0.0097167 58915000 23553 21643 21027 26330 37140 25282 25758 21262 32879 FALSE TRUE 22439.69637 23848.44631 21991.10875 23683.25838 43617.20424 24406.478 21828.14402 19400.18656 37977.7074 0.590864955 0.627959083 0.579053088 0.62360948 1.148494926 0.642652747 0.574762025 0.510830903 1 15.2128652 2.969120532 24.97105282 0.740160487 0.603868622 0.152278735 0.190051254 1564.967523 1265530.182 0.05764736 0.061212437 931.366326 -2.969120532 -0.136291864 GIPVLVGLLDHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIPVLVGLLDHPK 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 0 147.37 2.36E-06 0 70820 66976 59694 71729 53407 58917 73475 67494 49158 FALSE TRUE 67472.47895 73800.93055 62431.02895 64518.66464 62721.16389 56876.68952 62265.03929 61583.86755 56781.17158 1.188289658 1.299743005 1.099502304 1.136268641 1.104612007 1.001682212 1.096578981 1.084582545 1 15.793125 3.404039344 1.503536408 1.064418138 1.243078699 0.626568069 0.052949309 0.217977225 1.009594906 0.016203129 0.027391258 2535.358308 -3.404039344 0.178660561 GIPVVEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 96.253 0.0090721 500290000 801570 885400 721640 953520 682290 822350 870830 855760 660300 FALSE TRUE 763681.3747 975623.2666 754727.9078 857670.358 801281.16 793871.8133 737968.8896 780825.1177 762695.9517 1.001292026 1.279177193 0.989552791 1.124524597 1.050590551 1.040875871 0.967579398 1.023769847 1 19.54074852 2.50831592 1.058442377 0.992335745 1.121356867 0.211622898 0.080557878 0.631463698 1.431817736 0.046119799 0.03359641 322.3412755 -2.50831592 0.129021122 GIQLS(ph)PGVGSSAGPPGDLEDDEGLKHLQQEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIQLSPGVGSSAGPPGDLEDDEGLKHLQQEAEK 33 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 GIQLS(0.983)PGVGS(0.015)S(0.002)AGPPGDLEDDEGLKHLQQEAEK 82.635 0.00036995 40793000 35680 37117 37068 43438 23259 42552 36313 38010 23524 TRUE FALSE 33993.47711 40899.2645 38767.60447 39071.52971 27315.36224 41078.41357 30772.78492 34681.6429 27171.98178 1.251048871 1.505199909 1.426749244 1.437934488 1.005276776 1.511793063 1.132518974 1.276375171 1 14.72983217 0.95165002 0.395823292 0.979871127 1.404558328 0.339587088 0.154978055 1.503591671 0.628926084 0.229238749 0.117389027 8.946435181 -0.95165002 0.424687201 GIRDDIEEEDDQEAYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GIRDDIEEEDDQEAYFR 17 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 293.59 4.24E-46 124690000 55828 43627 64263 56769 57535 57027 55728 57810 77350 FALSE TRUE 53189.12108 48072.6409 67209.52211 51062.47227 67569.08578 55052.14069 47225.67009 52747.84993 89345.04295 0.595322576 0.53805605 0.752246794 0.571519925 0.756271233 0.616174539 0.528576276 0.59038362 1 16.44710007 -0.990771187 4.973884747 1.000003722 0.610450189 0.698877636 0.078523987 3.15E-06 6.38E-07 0.073820829 0.01739957 0.102147752 0.990771187 -0.389553533 GIRPAINVGLSVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIRPAINVGLSVSR 14 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 181.26 1.51E-06 916900000 686550 574440 612900 540720 644440 513050 693800 626650 644720 FALSE TRUE 654098.1421 632976.0891 641002.0712 486365.7983 756830.132 495282.9499 587948.0675 571777.2039 744699.8848 0.878337912 0.849974737 0.860752209 0.653103093 1.016288773 0.665077248 0.789510082 0.767795478 1 19.50629961 3.417495781 24.99999904 0.799035861 0.862698156 0.022645042 0.119396579 205.0290867 85964.08725 0.02917591 0.039504372 2615.145046 -3.417495781 0.063662296 GIS(ph)FMDYLSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GISFMDYLSDK 11 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 GIS(1)FMDYLSDK 90.614 0.0064788 0 16342 15076 13784 23237 19744 22087 21349 17719 18780 TRUE FALSE 15569.54605 16612.26154 14416.01003 20901.17261 23187.34735 21322.12165 18091.81795 16167.43043 21692.30649 0.71774507 0.765813518 0.664567875 0.963529288 1.068920327 0.982934741 0.834020023 0.745307118 1 14.40489584 3.233916347 24.99994543 0.927841243 0.726950712 0.547455886 0.092512446 96.02510987 516899.9827 0.027759168 0.034231895 1713.627201 -3.233916347 -0.200890532 GIS(ph)HASSSIVSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GISHASSSIVSLAR 14 0 Q6GQQ9;Q6GQQ9-2;Q5SZ59 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 GIS(0.999)HASSSIVSLAR 106.55 0.00098101 44225000 30211 19028 27135 28743 50489 25157 34835 23465 41442 TRUE FALSE 28782.9859 20966.97483 28379.16659 25853.69903 59294.26561 24285.80678 29520.28096 21410.2802 47868.6137 0.601291403 0.438010905 0.59285541 0.540097091 1.238687754 0.507343015 0.616693877 0.447271783 1 15.54679241 2.940466417 24.99999232 0.72557604 0.534121917 0.168150804 0.23398126 497.9236634 209092.9152 0.068282702 0.072424862 871.8994758 -2.940466417 -0.191454124 GIS(ph)PIVFDR ddPTM_SK-BR-3_Trastuzumab_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 208.15 1.10E-05 4394978000 5048300 5668460 4454980 5692080 5060390 4784210 4800750 5014890 4827560 TRUE FALSE 4809676.864 6246082.519 4659245.24 5119901.304 5942920.414 4618531.608 4068307.416 4575759.646 5576193.349 0.862537678 1.120133777 0.835560202 0.918171409 1.065766562 0.828258871 0.72958507 0.820588412 1 22.41084916 2.117234044 8.014098472 0.810016491 0.965453672 0.191397795 0.108734519 0.272830995 17.99650552 0.038247087 0.028218887 130.9887639 -2.117234044 0.155437182 GISDLAQHYLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GISDLAQHYLMR 12 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 138.2 7.86E-05 1471020000 1548780 1404660 827850 918070 1991010 919950 1521680 1276500 1548100 FALSE TRUE 1475572.239 1547796.451 865807.7414 825783.8594 2338241.514 888091.9008 1289519.768 1164722.893 1788171.441 0.825184993 0.865574975 0.484186092 0.461803516 1.307615959 0.496648073 0.721138778 0.65134856 1 20.77005363 GISEETTTGVHNLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GISEETTTGVHNLYK 15 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 261.35 6.05E-25 6623860000 6622820 5752330 5555000 6519860 5945440 6201660 7675700 7033710 6407920 FALSE TRUE 6309772.424 6338498.967 5809702.245 5864471.286 6982322.854 5986894.959 6504630.991 6417801.064 7401627.506 0.852484459 0.856365571 0.784922267 0.792321862 0.943349668 0.808861964 0.878810908 0.867079714 1 22.8194111 -0.264099935 0.456531197 1.026035463 0.837067686 0.552333339 0.044401786 4.651283062 1.025733301 0.244177951 0.023117094 0.544377373 0.264099935 -0.188967777 GISHVIVDEIHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;;; 255.16 4.57E-24 3736760000 1430356 1486995 1447614 1668441 1677693 1429713 1461457 1528361 624372 FALSE TRUE 1362745.907 1638521.481 1513988.534 1500726.141 1970282.128 1380201.68 1238484.893 1394529.608 721196.4209 1.88956277 2.271948991 2.099273499 2.080884066 2.731963264 1.91376668 1.717264336 1.933633568 1 19.46003271 0.761118466 0.782133088 1.008402661 2.16852997 0.659455379 0.254782274 0.59347448 0.716257256 0.245780659 0.087339919 5.769238144 -0.761118466 1.16012731 GISLNPEQWSQLKEQISDIDDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GISLNPEQWSQLKEQISDIDDAVR 24 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 290.59 7.74E-62 496910000 694290 365450 669330 604200 761590 588970 910680 752820 987710 FALSE TRUE 661472.2877 402689.7705 700019.4426 543464.6681 894411.0549 568573.8212 771739.0402 686899.0899 1140879.022 0.579791788 0.35296448 0.613579029 0.476356088 0.783966606 0.498364691 0.676442484 0.602078815 1 20.12171439 -5 0.140504444 2.565196766 0.398549292 0.619827724 0.109371518 80.03514189 0.687907896 34.82072871 0.594938991 1.00E-05 5 -2.166647474 GISQEQMQEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GISQEQMQEFR 11 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 320.73 1.12E-45 974300000 446512 310514 287375 389481 498820 309554 482904 397573 588920 FALSE TRUE 425406.2627 342155.7296 300551.428 350329.6299 585814.0501 298834.0674 409228.1257 362759.4005 680246.7058 0.625370559 0.502987705 0.441827098 0.515003787 0.861178812 0.439302484 0.601587809 0.533276233 1 19.37569854 -1.572765668 2.49702769 1.037380768 0.563951116 0.562004051 0.120663935 3816039.489 3367301.943 944082.0362 0.029066703 0.026744491 1.572765668 -0.473429652 GITGVEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GITGVEDK 8 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 130.22 0.0024594 180968000 584030 545200 413890 560430 455980 512960 556340 543720 445540 FALSE TRUE 556424.0593 600756.4998 432867.2659 504094.5117 535502.7676 495196.0666 471460.1151 496108.9944 514632.0677 1.081207516 1.167351468 0.841119886 0.979524097 1.040554604 0.96223321 0.916111033 0.964007153 1 18.97318183 3.754518922 24.99474864 0.956321384 1.124279502 0.604632659 0.056010025 474.2080273 742727.5716 0.013897892 0.024954354 5682.23148 -3.754518922 0.167958119 GITGVEDKESWHGKPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GITGVEDKESWHGKPLPK 18 2 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;; 221.91 3.59E-19 4426900000 6265070 3654820 5465540 5293100 4673970 5407270 8127630 6649560 5185090 FALSE TRUE 5968932.557 4027250.313 5716140.415 4761027.532 5489108.888 5220014.884 6887610.769 6067289.275 5989167.275 0.996621447 0.672422413 0.954413218 0.794939816 0.916506191 0.871576071 1.150011421 1.013043883 1 22.513924 1.756622093 25 1.065002168 0.857530936 0.447641839 0.097034944 5.630684746 7801.794493 0.041555719 0.023044757 57.0981573 -1.756622093 -0.207471231 GITINAAHVEYSTAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GITINAAHVEYSTAAR 16 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;; 202.35 3.06E-11 1763290000 1240380 888310 1142690 1045110 1361190 906160 1240760 1083240 1350240 FALSE TRUE 1181749.696 978829.7989 1195083.467 940053.5572 1598581.105 874779.452 1051459.274 988385.763 1559628.323 0.757712384 0.627604529 0.766261711 0.60274204 1.024975683 0.560889693 0.67417298 0.633731607 1 20.57277083 -1.346925239 4.499813636 1.000343444 0.701757129 0.334885062 0.130084012 0.000399224 5.79E-05 0.112189031 0.026413133 0.044985729 1.346925239 -0.298586314 GIVDQSQQAYQEAFEISKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIVDQSQQAYQEAFEISKK 19 1 B7Z2E6;H0YB80;P63104-2;P63104;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 264.71 3.77E-31 958380000 1284650 978980 1202290 1206230 915740 1301480 1646830 1481860 1221760 FALSE TRUE 1223927.14 1078739.175 1257416.186 1084977.469 1075444.766 1256409.421 1395575.837 1352100.483 1411224.301 0.867280375 0.764399518 0.891010865 0.768820001 0.762065084 0.890297468 0.988911427 0.958104592 1 20.42851588 1.955512581 3.537149124 0.977880992 0.811468762 0.759977152 0.043908062 0.111190245 2.685360887 0.019910367 0.011555047 90.26358551 -1.955512581 -0.16641223 GIVEFASKPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 178.1 2.05E-05 3340000000 4118100 3375100 3664800 4138500 4208600 3963900 5053400 4414000 5055600 FALSE TRUE 3923445.574 3719026.527 3832834.705 3722490.117 4942578.508 3826629.149 4282411.018 4027486.76 5839596.628 0.671869279 0.636863599 0.656352647 0.637456721 0.846390397 0.655289979 0.73334021 0.689685781 1 22.47743729 -5 0.209767044 2.502244396 0.64237031 0.730015925 0.059873953 70.66515646 0.704018255 44.61202796 0.117343981 1.00E-05 5 -1.859874086 GIVEFSGKPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 184.31 1.32E-05 3063600000 4744700 3697500 3939700 4712800 4003000 4102500 5130200 4451100 4649900 FALSE TRUE 4520427.434 4074279.454 4120339.142 4239060.39 4701121.933 3960429.396 4347493.767 4061338.087 5370982.744 0.841638793 0.758572434 0.767148088 0.789252283 0.875281519 0.737375185 0.809441023 0.756162937 1 22.35675466 -1.115235963 4.515032778 1.000021017 0.79235997 0.710152251 0.041788614 7.99E-06 1.57E-06 0.036581377 0.008621441 0.076694468 1.115235963 -0.207661047 GIWHNDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GIWHNDNK 8 0 P12277;H0YJG0;P06732 P12277 CKB;CKM "Creatine kinase B-type;Creatine kinase M-type;Creatine kinase M-type, N-terminally processed" 0 ; 106.36 0.0073058 250940000 1290660 1268150 1104780 1297970 1041520 1157400 1447850 1263130 1047950 FALSE TRUE 1229653.06 1397375.927 1155435.256 1167495.59 1223160.758 1117318.948 1226953.891 1152523.641 1210460.734 1.015855389 1.154416569 0.954541708 0.964505132 1.010491893 0.923052617 1.01362552 0.95213633 1 20.20712485 3.721996089 24.9930357 0.974949971 1.085135982 0.534307715 0.043109067 495.0442388 746936.8975 0.010519677 0.016352443 5272.251131 -3.721996089 0.110186011 GIWHNNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GIWHNNEK 8 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;;;;;; 164.77 0.00032814 5993690000 12949220 10356780 10404370 12672240 10724830 9687560 12477050 11362410 8920150 FALSE TRUE 12337136.03 11412147.66 10881420.66 11398402.36 12595236.96 9352077.368 10573446.87 10367457.14 10303441.3 1.197380144 1.107605442 1.056095758 1.106271393 1.222430117 0.907665419 1.026205377 1.006213054 1 23.29662294 2.236769765 24.99999934 0.988542697 1.13405874 0.651201116 0.055550195 30.79271756 429849.864 0.019806439 0.015392869 172.4923207 -2.236769765 0.145516043 GIYAYGFEKPSAIQQR ddPTM_SK-BR-3_Trastuzumab_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 ; 179.14 2.44E-09 4389600000 1513780 1280060 1230980 1417950 1422540 1343310 1672490 1408940 1473540 FALSE TRUE 1442226.619 1410499.569 1287421.651 1275414.972 1670630.526 1296790.838 1417320.933 1285565.744 1702049.057 0.847347268 0.828706766 0.756395149 0.7493409 0.98154076 0.761899801 0.832714502 0.755304754 1 20.69884119 -1.068407622 4.928916649 1.00000467 0.817568814 0.413011787 0.069522274 3.23E-06 6.11E-07 0.06099745 0.014376869 0.085426454 1.068407622 -0.182435857 GIYETPAGTILYHAHLDIEAFTMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GIYETPAGTILYHAHLDIEAFTMDR 25 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;;;;; 313.65 8.24E-75 914852500 850354.1 978546.8 940295.2 998411 896358.1 913032.3 973688.2 894627.5 335252.8 FALSE TRUE 810159.5469 1078261.831 983408.665 898048.8294 1052682.669 881413.7625 825134.1821 816289.1734 387242.092 2.09212677 2.784464431 2.539519038 2.31908888 2.718409725 2.276131084 2.130796727 2.107955696 1 18.56287625 0.543094972 0.696229531 0.97988002 2.492532262 0.826549584 0.206253458 0.582134963 0.482192032 0.218433181 0.073579584 3.492166742 -0.543094972 1.512652242 GIYLWDVEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GIYLWDVEGR 10 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;;;;;; 220.88 1.31E-08 1628581000 2331760 1782916 1323371 1342483 2550909 1155818 1942112 1565790 2074686 FALSE TRUE 2221542.326 1964597.167 1384048.869 1207534.058 2995786.722 1115791.733 1645807.145 1428681.127 2396417.709 0.927026335 0.819805813 0.577549091 0.50389131 1.250110409 0.465608199 0.686778077 0.596173664 1 21.19244797 3.97427647 6.145729963 0.707091111 0.888609896 0.065256193 0.238354312 0.384767752 52.34435592 0.056248574 0.107619759 9424.893902 -3.97427647 0.181518784 GKADDMSDDQGTSVQS(ph)KSPDLEASLDTLENNCHVGSDIDFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKADDMSDDQGTSVQSKSPDLEASLDTLENNCHVGSDIDFRPK 43 3 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 GKADDMS(0.004)DDQGT(0.085)S(0.085)VQS(0.401)KS(0.401)PDLEAS(0.019)LDT(0.004)LENNCHVGSDIDFRPK 80.048 0.00024427 110020000 32591 21630 32579 33274 23438 38081 48010 48020 21318 TRUE FALSE 31050.48802 23834.12159 34072.77938 29929.2343 27525.57978 36762.24542 40685.19274 43815.11423 24623.88656 1.26099054 0.967926876 1.383728734 1.215455336 1.117840586 1.492950568 1.652265276 1.779374435 1 14.58777087 2.17130442 5.362112089 1.553337895 1.175691384 0.266645123 0.227831481 0.195848321 10.57307342 0.078498559 0.057913417 148.3557625 -2.17130442 -0.377646511 GKAEEQAVR ddPTM_SK-BR-3_Trastuzumab_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 1442564000 2666270 2186060 2045604 2228630 2304680 2115292 2799790 2448080 2534310 FALSE TRUE 2540240.701 2408821.999 2139396.967 2004603.878 2706615.462 2042038.908 2372630.614 2233713.137 2927317.851 0.867770714 0.822876818 0.73083863 0.684792011 0.924605936 0.697580178 0.810513492 0.763057943 1 21.48114797 -1.608641211 5.550442485 1.001397013 0.792310267 0.445514228 0.074259695 0.001207995 8.52E-05 0.067658291 0.015845716 0.024624011 1.608641211 -0.209086746 GKAS(ph)AMGLQQTHEHSRLTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKASAMGLQQTHEHSRLTSK 20 2 Q9NQ86-3 Q9NQ86-3 TRIM36 E3 ubiquitin-protein ligase TRIM36 1 GKAS(0.85)AMGLQQT(0.15)HEHSRLTSK 52.784 0.094725 123980000 89738 92591 86066 98777 69794 97411 106980 98737 69691 TRUE FALSE 85496.26258 102026.1282 90012.21123 88847.7483 81966.0515 94037.63264 90658.23618 90091.06484 80498.32435 1.062087482 1.267431701 1.11818739 1.103721711 1.018233015 1.168193666 1.126212712 1.119166959 1 16.29667113 -4.999999998 0.196575079 0.419834978 1.152668613 0.247191926 0.065592724 190.0647548 1.873565548 43.26035603 0.161660626 1.00E-05 4.999999998 0.732833635 GKAS(ph)PFEEDQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 195.38 1.92E-07 2049350000 2643880 2337760 2423260 2923480 2065330 2644270 2850690 2813370 2354130 TRUE FALSE 2518909.032 2575980.402 2534368.868 2629606.236 2425522.898 2552698.267 2415764.884 2567016.408 2719196.457 0.926343158 0.947331479 0.9320286 0.967052685 0.891999874 0.938769341 0.888411309 0.944034919 1 21.37474896 2.74968445 24.96266001 0.923268255 0.941387615 0 0.032930853 1948.158116 4371803.94 0.008920174 0.009382699 561.9328869 -2.74968445 0.01811936 GKATRPASTSQPDPS(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKATRPASTSQPDPSPDR 18 2 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 GKATRPASTSQPDPS(1)PDR 82.975 0.0022944 27289000 49704 38213 52291 48284 46860 49112 58800 52822 64668 TRUE FALSE 47354.59042 42106.94814 54688.59407 43430.40059 55032.36916 47411.23913 49828.98006 48196.62565 74696.38316 0.633960955 0.563707992 0.732145142 0.58142575 0.736747441 0.634719341 0.667086918 0.645233726 1 16.18875077 -5 0.285850745 3.702359554 0.622464091 0.798867186 0.055231466 93.10960305 0.883085731 149.7025001 0.054327971 1.00E-05 5 -3.079895463 GKDANPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GKDANPQER 9 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ;;;; 95.822 0.0070997 738577000 604670 419558 390748 575528 540934 453111 614450 498798 621535 FALSE TRUE 576088.4474 462311.4372 408664.1823 517674.832 635272.7183 437419.6525 520704.3674 455120.6028 717919.4734 0.802441595 0.643960018 0.569234012 0.721076459 0.884880188 0.609287906 0.725296341 0.633943805 1 19.45346251 -1.436276842 2.959147993 1.006431249 0.700263543 0.506420699 0.093450629 30598699.67 36519247.36 1646775.542 0.021074045 0.036620406 1.436276842 -0.306167706 GKDETDSPTVHLGLDS(ph)DS(ph)ESELVIDLGEDHSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.997)DS(0.839)ES(0.164)ELVIDLGEDHSGR 109.52 4.04E-06 27638000 34249 36481 36203 37223 35642 37001 41987 38888 27384 TRUE FALSE 32630.11764 40198.45538 37862.94336 33481.27332 41857.95352 35719.64609 35581.11201 35482.76056 31630.57086 1.031600656 1.270873534 1.197036358 1.058509929 1.323338542 1.129276049 1.124896296 1.121786917 1 14.94903197 0.830385614 1.030155467 1.001605197 1.17070288 0.26174709 0.087181726 0.987670049 2.038053859 0.077054601 0.024921006 6.766835424 -0.830385614 0.169097683 GKDGVGAVMDSMELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKDGVGAVMDSMELER 16 1 F8WAU4;C9IZ01;Q96RP9;Q96RP9-2;C9JA25 F8WAU4 GFM1 "Elongation factor G, mitochondrial" 0 ; 76.713 0.0073806 0 137119 128964 138326 143157 124829 120674 142900 148790 131752 FALSE TRUE 130637.6566 142105.5782 144668.3839 128766.5864 146599.1381 116495.0291 121097.9805 135761.1588 152183.4273 0.858422359 0.933778275 0.950618517 0.846127523 0.963305537 0.765490903 0.795736978 0.892088983 1 17.21545173 2.247201115 24.99968439 0.838002744 0.907803727 0.046320298 0.073062776 304.4805423 880958.5324 0.02336504 0.019265834 176.6855834 -2.247201115 0.069800983 GKDIEDGDKFICNDDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKDIEDGDKFICNDDFK 17 2 A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 A0A669KAX4 CUL4B Cullin-4B 0 113.53 0.00022928 58697000 84661 81761 92586 103780 50064 111260 117060 122340 50660 FALSE TRUE 80659.24231 90092.53885 96831.15968 93347.83723 58795.14575 107407.0383 99200.34705 111627.261 58516.09406 1.378411249 1.539619831 1.654778249 1.595250652 1.004768802 1.835512777 1.69526604 1.907633495 1 15.83654585 GKDILYIGDHIFGDILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKDILYIGDHIFGDILK 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 163.7 1.61E-09 59049000 398160 310190 354780 394610 314590 388430 456880 432710 308740 FALSE TRUE 379339.7659 341798.7137 371047.0139 354943.0531 369454.3964 374978.5717 387174.5648 394819.6185 356617.8224 1.063715109 0.958445406 1.040461218 0.995303742 1.035995324 1.051485787 1.085684844 1.10712251 1 18.44401928 2.270759356 2.26046368 1.072468403 1.012240354 0.229596505 0.038703304 0.334776167 3.498800683 0.015790756 0.011083545 186.534581 -2.270759356 -0.060228049 GKDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKDLLR 6 1 Q9HBL6-2;Q9HBL6 Q9HBL6-2 LRTM1 Leucine-rich repeat and transmembrane domain-containing protein 1 0 67.035 0.091051 222740000 986950 924460 912400 1128100 1034900 1153300 1318400 1193400 1137700 FALSE TRUE 940298.8294 1018663.525 954234.4425 1014701.245 1215386.232 1113360.932 1117253.866 1088899.569 1314128.705 0.715530241 0.775162677 0.726134692 0.772147538 0.924860881 0.84722366 0.850186029 0.82860953 1 20.32567515 5.038707133 0.04927688 1.435176709 5.82E-12 0.7436276 0.044253511 131.8285375 0.930145317 8.989010924 19.65460998 109321.8905 -5.038707133 -1.435176709 GKDS(ph)TEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GKDSTEMR 8 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 GKDS(0.981)T(0.019)EMR;GKDS(0.967)T(0.033)EMR;GKDS(0.997)T(0.003)EMR;GKDS(0.994)T(0.006)EMR;GKDS(0.957)T(0.043)EMR;GKDS(0.921)T(0.079)EMR 110.66 0.0020487 2169294000 3520330 3598390 3188910 4274120 2868530 3640880 3942140 3803780 3419940 TRUE FALSE 3353930.978 3965070.032 3335124.678 3844477.337 3368800.724 3514795.413 3340694.141 3470700.858 3950286.829 0.849034797 1.003742311 0.844274055 0.973214732 0.852799017 0.889757014 0.845683943 0.878594646 1 21.91352598 2.712462253 24.9904222 0.880519405 0.920242698 0.011958836 0.064089005 1846.565746 1768172.821 0.018565211 0.01750901 515.7773336 -2.712462253 0.039723293 GKDSLYAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKDSLYAQGK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 ; 116.74 0.00095818 1424630000 2063500 1706530 1868520 2423200 2694100 2664000 3835400 3251400 3300800 FALSE TRUE 1965962.444 1880427.347 1954193.49 2179615.332 3163950.187 2571745.012 3250239.288 2966690.179 3812671.206 0.515639125 0.493204697 0.512552325 0.57167671 0.829851308 0.674525778 0.852483498 0.778113301 1 21.86237069 2.253870788 0.430139455 0.98016434 0.441208329 0.835844877 0.069476439 0.39081502 0.162379201 0.067809826 0.072743654 179.4199736 -2.253870788 -0.538956011 GKDSLYAQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKDSLYAQGR 10 1 Q969Q0 Q969Q0 RPL36AL 60S ribosomal protein L36a-like 0 ; 181.68 1.70E-06 684650000 797810 582200 538110 594960 829020 607550 906280 734420 855310 FALSE TRUE 760099.1024 641526.8419 562782.8758 535153.4904 973600.8255 586510.3912 768010.341 670110.2914 987947.1065 0.769372264 0.64935343 0.569648792 0.54168233 0.985478695 0.593665782 0.77738002 0.678285595 1 19.91407428 -2.968828491 0.290451603 1.622901181 0.673267354 0.361808814 0.127958384 70.59814512 1.937165917 26.99510086 0.128836528 0.001074414 2.968828491 -0.949633827 GKEALESEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKEALESEFR 10 1 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4;C9JKC2;C9JME6 A0A0A0MRE1 EXOC7 Exocyst complex component 7 0 91.937 0.0089456 232470000 151650 129310 145400 163770 163360 159120 179840 175970 175460 FALSE TRUE 144481.805 142486.836 152066.7338 147307.5285 191849.9323 153609.6345 152402.105 160561.1339 202669.4407 0.712893886 0.703050423 0.750319009 0.726836409 0.946614998 0.757931901 0.751973778 0.792231593 1 17.62876904 -5 0.135429392 1.7994101 0.668447974 0.585357519 0.064415869 101.1281803 0.850602536 21.96135005 0.43158366 1.00E-05 5 -1.130962126 GKEDALVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKEDALVTK 9 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 79.82 0.023585 541070000 1155860 1005410 1031260 1264430 891750 1120040 1352510 1256980 1103540 FALSE TRUE 1101224.788 1107862.422 1078544.291 1137327.094 1047270.918 1081252.734 1146159.759 1146912.168 1274671.347 0.863928409 0.869135738 0.846135197 0.892251243 0.821600737 0.848260013 0.89918061 0.899770886 1 20.28169389 0.798920942 1.100690433 0.999275413 0.859382499 0.8247223 0.020321425 0.294291824 0.667574933 0.018193856 0.005745746 6.293915992 -0.798920942 -0.139892914 GKEDKENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKEDKENR 8 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 51.995 0.081955 15956000 58535 54038 48138 72152 31904 54897 57446 75916 45838 FALSE TRUE 55768.16656 59544.53364 50345.17491 64899.14388 37468.0475 52995.90312 48681.55763 69268.39258 52946.32293 1.05329631 1.124620754 0.95087198 1.225753561 0.707660994 1.000936424 0.919451152 1.308275792 1 15.69224287 GKEKCSEKSR ddPTM_SK-BR-3_Trastuzumab_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 442340000 598330 450640 544650 595700 1102700 328130 692920 434570 1323700 FALSE TRUE 570048.1267 496560.7283 569622.7412 535819.1042 1295010.531 316766.7758 587202.3277 396516.747 1528972.635 0.372830823 0.324767571 0.372552607 0.350443881 0.846980842 0.207176223 0.384050253 0.259335411 1 20.54413116 -1.256500189 4.238366063 1.000432762 0.386534569 0.554506051 0.171874299 409.5496885 130698849.4 96900.66354 0.038292337 0.05539873 1.256500189 -0.613898193 GKEKDS(ph)PFKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKEKDSPFKPK 11 3 Q15291 Q15291 RBBP5 Retinoblastoma-binding protein 5 1 GKEKDS(1)PFKPK 57.328 0.080895 292380000 1349000 1202400 1225800 1361000 539200 1661800 1458900 1783900 572340 TRUE FALSE 1285235.443 1324925.927 1282004.142 1224189.694 633236.3093 1604251.449 1236318.01 1627692.259 661095.5641 1.94409933 2.004136768 1.939211533 1.851759051 0.95785896 2.426655897 1.870104834 2.462113418 1 19.33449931 3.243898143 5.096995941 1.816468383 1.970717624 0.028047542 0.494297424 0.943712142 68.71467222 0.131854361 0.170364413 1753.469206 -3.243898143 0.154249241 GKELNEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GKELNEFR 8 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ;;; 113.71 0.0025508 1564110000 4805290 3700970 3982660 4293000 4966650 4102250 5876380 4899560 5608410 FALSE TRUE 4578153.465 4078103.051 4165268.9 3861459.484 5832832.188 3960188.054 4979830.304 4470528.552 6478133.579 0.706708716 0.629518209 0.642973605 0.596075928 0.900387761 0.611316208 0.768713742 0.690095148 1 22.62714679 -4.99999943 0.209057379 2.492506685 0.6455131 0.556384242 0.087461545 100.4206335 1.00006449 62.66543309 0.167963472 1.00E-05 4.99999943 -1.846993585 GKELSDQAT(ph)ASPIVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 GKELSDQAT(0.5)AS(0.5)PIVAR;GKELSDQAT(0.625)AS(0.375)PIVAR 130.89 7.68E-05 282050000 494920 320880 460680 465980 456060 441680 574930 501680 487410 TRUE FALSE 471526.1124 353578.0368 481802.6337 419138.8051 535596.7196 426384.5109 487213.8692 457750.2396 562995.0535 0.837531537 0.62803045 0.855784843 0.74448044 0.951334681 0.757350368 0.865396359 0.813062631 1 19.10276272 -5 0.101997628 1.680413169 0.657859081 0.362265688 0.083855199 169.3048487 1.169788239 24.1343852 1.205890659 1.00E-05 5 -1.022554088 GKELSDQATAS(ph)PIVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 GKELSDQAT(0.336)AS(0.664)PIVAR;GKELSDQAT(0.201)AS(0.799)PIVAR 207.43 1.06E-11 279020000 454170 300020 426650 408110 369430 434210 515970 448210 443270 TRUE FALSE 432702.2842 330592.3791 446212.3245 367086.0074 433858.475 419173.1988 437249.3001 408962.3563 512010.0477 0.845105064 0.645675569 0.871491344 0.716950789 0.847363205 0.818681588 0.85398578 0.798738927 1 18.9658126 -0.91991412 0.2257579 1.144905448 0.740081163 0.468149708 0.068331065 12.36574598 0.668734876 1.274854082 0.137443594 0.12025022 0.91991412 -0.404824285 GKEVDNFVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GKEVDNFVDK 10 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 140.63 3.55E-05 769170000 2045510 1977590 1631740 2111040 1256110 1914700 2045970 2214680 1382480 FALSE TRUE 1948822.796 2179108.669 1706556.893 1898834.248 1475175.186 1848393.459 1733819.7 2020750.878 1596867.938 1.220403234 1.364614204 1.068690061 1.189099113 0.923792852 1.157511786 1.085762735 1.26544646 1 20.60681357 3.731261823 24.92588137 1.101325977 1.292508721 0.390266947 0.10071257 444.4793884 1517927.242 0.024166804 0.038300687 5385.943873 -3.731261823 0.191182744 GKEVDNFVDKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKEVDNFVDKLK 12 2 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 123.02 0.00019584 345060000 2426600 1558770 2040710 1937010 1600120 2246400 3027600 2691500 1915060 FALSE TRUE 2311899.427 1717610.435 2134278.572 1742298.075 1879180.421 2168606.605 2565684.014 2455817.991 2212037.724 1.045144665 0.776483338 0.964847276 0.787643925 0.849524581 0.980366013 1.159873535 1.110206198 1 21.07694456 1.97847651 4.355620928 1.10256266 0.884832104 0.533682323 0.087349803 0.14459923 6.422515899 0.036708981 0.022813344 95.16483743 -1.97847651 -0.217730557 GKFDGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKFDGAK 7 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 60.436 0.088936 601410000 870630 893760 685460 959540 584610 874340 808650 934880 537800 FALSE TRUE 829477.0453 984835.1601 716889.019 863085.2162 686565.7989 844061.3866 685275.5906 853016.9511 621199.2773 1.335283339 1.585377183 1.15404033 1.389385416 1.105226332 1.358761057 1.103149369 1.37317763 1 19.24469663 7.999999997 0.052899248 0.487213797 2.824177704 0.32684445 0.144136923 397.7553095 1.583839311 15.76526768 74.40783195 99999999.41 -7.999999997 2.336963907 GKFEDMAK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 121.73 0.0012956 7273340000 18834770 15044790 12195820 14535280 12796400 15777490 20836200 19105900 14017490 FALSE TRUE 17944487.75 16577871.21 12755010.41 13074166.04 15028088.11 15231111.57 17657255.01 17432886.11 16191250.76 1.108282987 1.023878356 0.787771779 0.807483389 0.928161038 0.940700122 1.09054299 1.076685574 1 23.9487111 1.755887989 9.833836761 1.061686636 0.946145454 0.262003743 0.095378587 0.240979788 97.69392125 0.052118918 0.028427161 57.00172375 -1.755887989 -0.115541182 GKFGHEFLEFEFRPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKFGHEFLEFEFRPDGK 17 2 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 128.69 2.17E-05 685180000 1773570 1586700 1611510 1844820 1654520 1647680 1962560 1763320 1641300 FALSE TRUE 1689736.861 1748386.534 1685399.328 1659375.189 1943067.764 1590620.428 1663135.427 1608914.353 1895824.421 0.891293963 0.922230199 0.889006022 0.875278939 1.024919683 0.839012522 0.877262371 0.84866211 1 20.85439393 GKFNTSDVSAIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKFNTSDVSAIEK 13 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 120.66 0.00023316 528580000 996280 729280 747220 1041600 707870 787800 974650 834640 767600 FALSE TRUE 949187.8188 803594.4611 781480.7761 936896.3891 831322.3039 760518.2885 825949.2418 761554.4969 886635.4876 1.070550223 0.906341413 0.88140029 1.056687221 0.937614516 0.857757555 0.931554459 0.858926253 1 19.75798158 2.479657786 24.87203285 0.906115731 0.974038208 0.167474461 0.069391652 161.9450216 1587989.134 0.022617419 0.019244142 301.7573007 -2.479657786 0.067922477 GKFQDNFEFVQWFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKFQDNFEFVQWFK 14 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 177.84 1.87E-06 186240000 1048800 835230 888480 956290 935710 936480 1265000 1111600 1083200 FALSE TRUE 999225.3025 920340.8866 929217.6868 860161.9124 1098897.528 904049.4628 1072001.017 1014262.411 1251177.124 0.798628175 0.735580014 0.742674773 0.687482129 0.878290936 0.722559137 0.856793971 0.810646544 1 20.25485461 0.470383816 0.509045662 1.012339211 0.751984917 0.643933565 0.054633647 1.154734671 0.53073787 0.080957487 0.024921605 2.953818564 -0.470383816 -0.260354294 GKGAYQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GKGAYQDR 8 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 86.136 0.014818 2190440000 1913020 1365380 1751770 1681070 1850990 1740410 2382180 1965130 2250340 FALSE TRUE 1822595.336 1504513.774 1832090.387 1512085.65 2173802.07 1680139.165 2018734.689 1793052.799 2599311.234 0.701183957 0.578812477 0.704836867 0.581725509 0.836299263 0.646378603 0.776642159 0.689818432 1 21.30969796 -4.999999967 0.170667226 2.262531581 0.608916726 0.638751319 0.075219665 73.30163073 0.69239401 31.16352883 0.233723605 1.00E-05 4.999999967 -1.653614855 GKGDPNKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKGDPNKPR 9 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 61.65 0.049373 137160000 427380 359180 309480 418800 273380 376700 453930 427490 373790 FALSE TRUE 407178.5944 395780.8504 323669.9641 376701.4283 321057.3854 363654.7845 384674.6415 390056.7093 431755.4441 0.94307692 0.916678309 0.749660412 0.872487964 0.743609351 0.842270293 0.89095493 0.903420477 1 18.71985484 0.901313046 1.52720904 0.998736523 0.856026311 0.36319584 0.063557628 0.658175322 3.047690261 0.064301225 0.018807857 7.967334401 -0.901313046 -0.142710212 GKGEKEPPS(ph)PGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKGEKEPPSPGMER 14 2 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 GKGEKEPPS(1)PGMER 70.453 0.023046 236050000 227320 179260 217530 223750 151170 242980 277610 273640 192820 TRUE FALSE 216575.0341 197526.7978 227503.9657 201258.2249 177534.0001 234565.5417 235255.4958 249678.6309 222721.5408 0.972402729 0.886877834 1.021472664 0.903631612 0.797111943 1.053178515 1.056276348 1.121034948 1 17.76488157 2.097806726 11.69103024 1.06269298 0.921627364 0.544759934 0.064082717 0.327108506 36.73921156 0.022778873 0.016822657 125.2583613 -2.097806726 -0.141065616 GKGEQIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKGEQIAR 8 1 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 63.283 0.067753 270840000 325160 236214 234945 330280 368520 260706 389560 300823 387730 FALSE TRUE 309790.3312 260284.4752 245717.4606 297079.6269 432789.7713 251677.6858 330125.4672 274481.3434 447857.1881 0.691716778 0.581177398 0.548651372 0.663335623 0.966356648 0.561959688 0.737122181 0.612876941 1 18.77267924 -5 0.23957992 2.874197643 0.634690445 0.417900069 0.121159045 164.5792644 1.64116054 150.4143494 0.180452555 1.00E-05 5 -2.239507198 GKGGVTGS(ph)PEASISGS(ph)KGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKGGVTGSPEASISGSKGDLK 21 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 GKGGVT(0.167)GS(0.833)PEAS(0.01)IS(0.165)GS(0.825)KGDLK;GKGGVT(0.148)GS(0.852)PEAS(0.01)IS(0.037)GS(0.953)KGDLK 115.76 7.83E-05 587780000 760120 673310 680660 801290 290660 803060 840120 876800 355440 TRUE FALSE 724190.634 741921.0545 711868.9343 720742.8068 341351.012 775249.8308 711944.2641 800022.7438 410559.8199 1.763910151 1.807096113 1.733898204 1.755512283 0.8314282 1.888274968 1.734081685 1.948614319 1 18.64723292 2.956109468 24.99964406 1.548087847 1.772078506 0.122397985 0.353945141 1166.112122 664206.3517 0.103094934 0.109354687 903.8772752 -2.956109468 0.22399066 GKGGVTGS(ph)PEASISGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.001)GS(0.998)PEAS(0.001)ISGSK;GKGGVT(0.037)GS(0.959)PEAS(0.004)ISGSK;GKGGVT(0.035)GS(0.923)PEAS(0.014)IS(0.028)GSK;GKGGVT(0.006)GS(0.993)PEAS(0.001)ISGSK;GKGGVT(0.044)GS(0.956)PEASISGSK 188.04 2.78E-10 2831130000 4855918 4619187 4475909 5519741 3407001 4953403 5341565 5684591 4109391 TRUE FALSE 4626388.38 5089887.407 4681133.855 4964886.148 4001180.896 4781865.412 4526611.155 5186818.076 4746654.368 0.974662999 1.072310518 0.986196485 1.045975915 0.842947597 1.007418076 0.953642461 1.092731358 1 22.17847957 GKGGVTGS(ph)PEASISGSKGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GKGGVTGSPEASISGSKGDLK 21 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.004)GS(0.996)PEASISGSKGDLK;GKGGVT(0.004)GS(0.973)PEAS(0.023)ISGSKGDLK;GKGGVT(0.001)GS(0.998)PEAS(0.001)ISGSKGDLK 121.94 1.51E-05 1635750000 1735520 780160 1804960 1175890 1227460 1623870 2587350 2050530 1939490 TRUE FALSE 1653485.409 859659.191 1887719.201 1057687.303 1441528.635 1567634.975 2192602.238 1870974.723 2240256.204 0.73807871 0.383732535 0.842635409 0.472127831 0.643465972 0.699757006 0.978728341 0.83516105 1 21.0952323 1.916150459 2.856072489 0.934190715 0.599915635 0.545087681 0.133636293 0.186129112 2.726494119 0.064697258 0.034517331 82.4423683 -1.916150459 -0.334275081 GKGGVTGSPEAS(ph)ISGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.001)GS(0.033)PEAS(0.966)IS(0.001)GSK 334.07 1.08E-71 193200000 191420 171840 170560 206780 115190 190220 202200 197390 137080 TRUE FALSE 182371.956 189350.6914 178380.3447 185994.0815 135279.0995 183632.6337 171350.6763 180105.4852 158337.6663 1.15179136 1.195866377 1.126581873 1.174667316 0.854370932 1.159753317 1.082185183 1.137477199 1 17.27264497 GKGIYLWDVEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKGIYLWDVEGR 12 1 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 101.15 0.0025854 179530000 423200 200050 348380 238200 521090 279990 552500 361020 616380 FALSE TRUE 403196.1747 220435.3224 364353.5676 214255.6834 611967.931 270293.8761 468205.9776 329407.1749 711965.0624 0.566314551 0.309615365 0.511757651 0.300935671 0.859547699 0.37964486 0.657624935 0.46267323 1 19.44144692 -5 0.190759603 3.186017278 0.408263385 0.469903347 0.165854434 108.2615921 1.05982067 89.67595138 0.391513729 1.00E-05 5 -2.777753893 GKGS(ph)PRPQAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GKGS(1)PRPQAPK;GKGS(1)PRPQAPK 79.466 0.015127 10774310000 8868210 7709800 7896210 9120990 5998710 9252600 10120800 9379460 7218890 TRUE FALSE 8449027.288 8495437.385 8258259.039 8204130.756 7044883.125 8932180.142 8576686.079 8558144.759 8338358.592 1.01327224 1.018838095 0.990393846 0.983902367 0.844876488 1.071215641 1.028582063 1.026358445 1 22.99133199 GKHQPWQS(ph)PERPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKHQPWQSPERPLSR 15 2 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 GKHQPWQS(1)PERPLSR 163.11 8.12E-07 819330000 779610 694490 711680 777960 685440 764980 805850 789660 590530 TRUE FALSE 742759.3803 765259.3206 744311.2319 699757.9828 804980.519 738488.5508 682902.782 720513.1841 682106.3764 1.088920154 1.121906124 1.091195241 1.025878084 1.180139267 1.082658917 1.001167568 1.056306185 1 19.37963722 1.861044699 5.383713339 1.021632681 1.101598904 0.464056055 0.04048783 0.193707831 7.443410254 0.017045931 0.010057057 72.61806937 -1.861044699 0.079966224 GKLDDYQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GKLDDYQER 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;; 129.88 0.00034377 1493980000 1364060 1276900 1207870 1419590 1172480 1359790 1563850 1423040 1453470 FALSE TRUE 1299583.587 1407017.562 1263252.034 1276890.116 1376960.141 1312700.131 1325255.96 1298431.074 1678866.704 0.774083841 0.838075803 0.752443318 0.760566704 0.820172404 0.781896578 0.789375331 0.773397358 1 20.67905626 -2.022892269 2.812943863 1.24447217 0.789219298 0.870118855 0.025930589 2621681.874 2389548.313 4156187.273 0.006034976 0.009486538 2.022892269 -0.455252872 GKLDGNQDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GKLDGNQDLIR 11 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;; 184.03 4.64E-06 5187610000 12291830 8641200 8141510 7894160 10716030 7172560 11147230 9587990 10936260 FALSE TRUE 11710819.56 9521748.104 8514806.287 7100624.039 12584902.24 6924172.449 9446515.331 8748414.766 12632199.35 0.927061016 0.753768037 0.674055725 0.562105129 0.99625583 0.548136731 0.747812402 0.692548821 1 23.59060251 -1.140213053 3.661556231 1.000179725 0.742911389 0.257018595 0.139897558 35671960.42 63601186.51 77883.29267 0.031528395 0.072408066 1.140213053 -0.257268336 GKLEAIIT(ph)PPPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKLEAIITPPPAK 13 1 O75367-2;O75367-3;O75367;D6RCF2 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 1 GKLEAIIT(1)PPPAK 70.783 0.071215 312280000 861360 952800 897850 1017100 672250 878510 990110 1009800 840010 TRUE FALSE 820645.2199 1049891.403 939017.3106 914859.1756 789490.1872 848086.9784 839050.5349 921376.5587 970274.4606 0.845786685 1.082056105 0.967785249 0.942887 0.81367718 0.874069156 0.86475587 0.949604051 1 19.88803337 4.764789998 23.87631643 0.931049026 0.845786472 0.122639871 0.075136165 2108.928806 3404362.881 0.019212465 0.411492259 58182.18108 -4.764789998 -0.085262555 GKLEEQRPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GKLEEQRPER 10 2 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;; 163.12 3.69E-06 7815580000 11451120 9410550 9816370 11954750 9744330 10974790 13006500 11969690 11371040 FALSE TRUE 10909848.25 10369495.74 10266460.27 10753035.82 11443738.07 10594730.27 11022119.54 10921560.49 13134402.81 0.830631465 0.789491224 0.781646522 0.818692405 0.871279664 0.806639664 0.839179345 0.831523187 1 23.64684727 -4.999999997 0.248175501 2.09307156 0.802608458 0.851437995 0.023778271 63.72631067 0.632313198 35.25181904 0.033798447 1.00E-05 4.999999997 -1.290463102 GKLELVDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKLELVDNK 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 68.069 0.062992 0 257600 220430 211140 254910 344680 212080 295960 251010 366320 FALSE TRUE 245423.7585 242892.0676 220820.9778 229285.9625 404792.0829 204735.6164 250805.8663 229030.2337 423127.0347 0.580023819 0.574040531 0.521878679 0.541884455 0.956667974 0.483863236 0.592743658 0.541280077 1 18.69073134 -1.509964435 2.687095075 1.019393348 0.596872263 0.47997269 0.13114216 13718476 13929076.01 1955225.604 0.030942472 0.030905485 1.509964435 -0.422521085 GKLPES(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 105.2 0.0026846 1414320000 3209900 3754450 2652490 3900190 1274190 3576620 3017510 3772140 1399100 TRUE FALSE 3058174.388 4137032.723 2774109.29 3508135.491 1496408.333 3452760.753 2557133.429 3441831.424 1616065.282 1.8923582 2.559941587 1.716582443 2.170788228 0.925957849 2.136523066 1.582320626 2.129760141 1 20.62405405 3.280927823 1.936180102 1.651055746 2.199462068 0.192359882 0.464369463 0.473881368 3.650941167 0.13092717 0.187223627 1909.53588 -3.280927823 0.548406322 GKLPES(ph)PKRAEEIWQQSVIGDYLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKLPESPKRAEEIWQQSVIGDYLAR 25 3 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 1 GKLPES(1)PKRAEEIWQQSVIGDYLAR;GKLPES(1)PKRAEEIWQQSVIGDYLAR 179.01 1.55E-16 569980000 649970 452440 686030 610410 466380 691060 851920 787370 608690 TRUE FALSE 619247.2062 498544.1504 717485.1541 549050.4271 547716.5243 667128.4189 721943.9574 718423.7087 703082.5364 0.880760329 0.709083393 1.02048496 0.78091888 0.77902166 0.948862167 1.026826752 1.021819874 1 19.42333453 2.058814795 4.258318221 1.013542007 0.82779716 0.517228296 0.081212212 0.159678665 5.937667862 0.031557433 0.021856098 114.5024541 -2.058814795 -0.185744847 GKLPIVNEDDELVAIIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 250.04 7.56E-25 173728000 353820 302770 320630 379460 318780 343850 388970 370190 375530 FALSE TRUE 337095.6298 333622.6072 335331.2026 341315.9599 374375.1311 331942.3883 329625.4826 337774.2011 433765.2745 0.77713835 0.769131664 0.77307065 0.786867875 0.863082301 0.765258097 0.759916715 0.778702725 1 18.72655504 -0.978602308 5.000306042 1.000001703 0.781996572 0.844039512 0.029147044 5.51E-07 1.13E-07 0.028122178 0.006628409 0.105050396 0.978602308 -0.218005131 GKNEELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKNEELIR 8 1 Q7L5L3-1;Q7L5L3 Q7L5L3-1 GDPD3 Glycerophosphodiester phosphodiesterase domain-containing protein 3 0 82.287 0.018845 127030000 263780 148080 166690 276070 318740 203030 336890 235970 301360 FALSE TRUE 251311.6422 163169.5204 174332.9014 248318.9191 374328.1551 195999.0202 285491.2431 215307.2158 348093.3697 0.721966185 0.468752164 0.500822241 0.713368713 1.075367093 0.563064503 0.820157084 0.618532941 1 18.40911481 3.050905064 6.524316311 0.795309029 0.569105173 0.322684783 0.164793276 0.236598856 22.54887271 0.044407381 0.053016122 1124.359163 -3.050905064 -0.226203856 GKNENESEKR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 147.91 1.47E-05 1963199000 1114561 941335 914967 1107836 625065 1065825 1168820 1107807 801284 FALSE TRUE 1061877.91 1037258.107 956919.142 996474.2205 734076.1381 1028915.213 990495.0421 1010801.546 925543.0303 1.147302584 1.120702196 1.033900219 1.076637377 0.79313021 1.111688143 1.070177193 1.09211729 1 19.81994054 3.775975849 2.328847376 1.026636298 1.141201556 0.207512543 0.08897316 0.456845156 4.864714745 0.024313915 0.049016731 5970.020872 -3.775975849 0.114565258 GKNNTVGLIQLNRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKNNTVGLIQLNRPK 15 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 159.22 1.00E-06 506930000 795410 601880 686200 629840 623610 603220 787260 843740 822220 FALSE TRUE 757812.5457 663212.2563 717662.9487 566527.2866 732367.3866 582330.3401 667149.028 769857.6527 949725.6783 0.797927826 0.698319811 0.755652885 0.596516762 0.771135711 0.61315636 0.702464978 0.810610548 1 19.85715134 0.924461091 3.001372478 0.99952044 0.706380185 0.690189385 0.063234966 0.181678964 3.822646418 0.056689527 0.014886474 8.403517158 -0.924461091 -0.293140255 GKPDAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GKPDAAK 7 1 P09429 P09429 HMGB1 High mobility group protein B1 0 ;;;; 96.711 0.011429 1241480000 3053050 2995680 2588430 3822090 2108120 3118010 3543880 4819360 3056920 FALSE TRUE 2908738.377 3300943.198 2707112.076 3437886.252 2475775.461 3010032.532 3003196.018 4397351.289 3530971.541 0.823778482 0.934854093 0.766676266 0.973637485 0.701159846 0.852465815 0.850529658 1.245365826 1 21.75163376 1.255626159 24.95903482 1.122682841 0.848668416 0.595708991 0.095607033 123.6447645 180836.7558 0.055782684 0.02025891 18.0146637 -1.255626159 -0.274014425 GKPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GKPELR 6 1 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32;B9ZVP7 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;;; 100.82 0.033949 4007830000 9669900 9058230 8516550 10181560 9166590 9550330 10982960 9784190 9609820 FALSE TRUE 9212822.991 9981273.935 8907042.242 9158090.245 10765240.39 9219599.677 9307307.736 8927434.454 11100061.81 0.829979432 0.899208861 0.80243177 0.825048581 0.969836077 0.830589941 0.838491524 0.804268896 1 23.40406437 -1.6664756 2.707793018 1.018396504 0.852682801 0.467418475 0.05025183 11881220.97 10539715.07 1512598.491 0.011283007 0.021553827 1.6664756 -0.165713704 GKPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKPQER 6 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 64.866 0.096264 100333000 168714 177523 155144 197450 139759 167836 190223 249714 199285 FALSE TRUE 160739.2236 195612.7955 162257.5059 177601.9509 164132.9254 162023.7972 161200.9877 227847.7183 230189.1 0.698292072 0.849791739 0.704887876 0.771548048 0.713035176 0.703872587 0.700298093 0.989828443 1 17.81245999 1.232457812 24.9911382 0.994914441 0.739589472 0.842706002 0.046728467 60.06999962 245976.1636 0.04196837 0.011552402 17.07881808 -1.232457812 -0.255324969 GKPVDSQTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKPVDSQTSR 10 1 Q9Y450;Q9Y450-4;E9PN23 Q9Y450 HBS1L HBS1-like protein 0 87.667 0.0116 56203000 37505 35190 39775 40832 48113 40535 52193 45314 54493 FALSE TRUE 35732.21298 38775.90101 41598.72309 36727.48978 56503.89197 39131.26279 44229.99926 41346.06594 62943.49613 0.567687135 0.616043013 0.660889935 0.583499361 0.897692303 0.62168874 0.702693717 0.656875904 1 15.94176969 -5 0.149288765 2.198839248 0.550942408 0.603776521 0.088208127 87.3333289 0.776002772 31.15616498 0.418230994 1.00E-05 5 -1.647896839 GKPYLTLEQLMDFINQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKPYLTLEQLMDFINQK 17 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 158.17 3.07E-09 53894000 362840 334950 326390 362080 280290 342250 423980 427760 302270 FALSE TRUE 345689.2723 369081.7858 341355.3043 325683.0305 329172.4873 330397.7967 359294.0641 390303.0667 349144.4878 0.990103766 1.057103287 0.977690659 0.932803014 0.94279732 0.946306782 1.029069845 1.117884086 1 18.41346467 1.522906945 5.630442431 1.063565914 0.982712067 0.3825464 0.044807467 0.160054809 10.97327377 0.027265586 0.012160092 33.33549783 -1.522906945 -0.080853847 GKQS(ph)PPGPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKQSPPGPGK 10 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(1)PPGPGK 57.532 0.070851 210910000 545240 553290 460370 629310 291390 571110 513240 586520 320540 TRUE FALSE 519467.5858 609670.88 481478.4199 566050.5632 342208.3237 551332.3175 434935.8117 535161.1995 370247.7061 1.403027155 1.646656738 1.300422425 1.528842863 0.924268586 1.489090434 1.17471575 1.44541395 1 18.49813127 4.752710369 0.041651783 5.29E-07 3.004483017 0.27685677 0.196776985 378.0422882 2.451113741 64.32953415 118.2237122 56586.17896 -4.752710369 3.004482489 GKQS(ph)PPGPGKAPLTSGIDSSTLAPSNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKQSPPGPGKAPLTSGIDSSTLAPSNLK 28 2 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(0.994)PPGPGKAPLT(0.003)S(0.003)GIDSSTLAPSNLK 163.48 4.15E-12 273770000 599080 332270 621380 498270 417880 627370 848930 741710 580840 TRUE FALSE 570762.6757 366128.6908 649870.8876 448182.9529 490758.1397 605644.0196 719410.1368 676761.9403 670913.7007 0.85072443 0.545716521 0.968635589 0.668018782 0.731477296 0.902715236 1.072284164 1.008716829 1 19.35576768 2.048518591 3.202600037 1.030055744 0.739484525 0.558503677 0.111324047 0.165976875 3.409103329 0.04737352 0.029957759 111.8197692 -2.048518591 -0.29057122 HS(ph)HSHS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.639)HS(0.362)HS(0.99)PMS(0.007)T(0.002)R 52.527 0.075941 34820000 36651 38203 48415 48352 44171 39331 49539 22864 13434 TRUE FALSE 34918.57987 42095.92913 50634.87564 43491.5651 51874.40841 37968.95761 41980.9157 20861.90695 15517.27611 2.250303444 2.712842695 3.263129127 2.802783478 3.343009949 2.446882903 2.705430735 1.344430994 1 13.92158771 1.190128785 3.188392406 0.994996705 2.779114974 0.811223584 0.326376207 0.101702699 1.833175016 0.308304999 0.084767607 15.49275972 -1.190128785 1.784118269 GKTPEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 84.213 0.016062 140880000 221170 224840 187190 254020 269590 210070 230280 236280 291990 FALSE TRUE 210715.7324 247751.4516 195772.8467 228485.427 316606.4106 202795.2232 195146.5566 215590.0706 337270.3179 0.62476809 0.734578285 0.580462722 0.677454893 0.938731913 0.601283933 0.578605784 0.639220409 1 18.36354583 -1.12563902 4.272562346 1.000058657 0.670102195 0.487627271 0.105685488 4.30512127 59148604.86 7218.759254 0.024311395 0.074879163 1.12563902 -0.329956462 GKTPPVAVTS(ph)PITHTAQSALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKTPPVAVTSPITHTAQSALK 21 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 GKTPPVAVT(0.212)S(0.769)PIT(0.014)HT(0.005)AQSALK 73.676 0.0086466 75618000 103360 67507 123650 110210 80763 104530 150220 99190 64206 TRUE FALSE 98474.37764 74386.04005 129319.4748 99131.48141 94848.04163 100910.0999 127301.18 90504.39776 74162.73856 1.327814743 1.003010966 1.743725722 1.336675038 1.278917735 1.360657681 1.716511317 1.220348648 1 16.1784069 3.764598173 24.9584826 1.419937221 1.165412884 0.108537051 0.233823313 1142.343367 1094997.217 0.055562135 0.100124341 5815.648809 -3.764598173 -0.254524337 GKTPQVGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GKTPQVGDR 9 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 80.916 0.020756 362840000 550110 439620 474110 570390 549760 517480 619420 567660 571640 FALSE TRUE 524107.3905 484417.7778 495848.4125 513053.3135 645637.9699 499559.5378 524916.1026 517952.681 660287.0117 0.793756929 0.733647292 0.750958907 0.777015608 0.97781413 0.75657938 0.794981717 0.784435665 1 19.33273374 -5 0.233973557 2.134085289 0.76952333 0.471814091 0.067642885 146.4782125 1.463664108 78.92275382 0.109648218 1.00E-05 5 -1.36456196 GKYS(ph)PTVQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKY(0.004)S(0.797)PT(0.199)VQT(0.001)R 58.098 0.068619 157590000 281500 215820 234200 284410 236120 253770 285970 262390 238130 TRUE FALSE 268194.0529 237812.3034 244938.3017 255820.5665 277299.2532 244981.8813 242340.0243 239413.7406 275057.9842 0.975045511 0.864589712 0.890496971 0.930060501 1.008148351 0.890655408 0.881050681 0.870411893 1 18.06937626 -0.899579593 7.121509961 1.000000001 0.912293136 0.253515841 0.046416918 1.33E-09 9.32E-11 0.044549254 0.01050036 0.126014467 0.899579593 -0.087706865 GLAGAVS(ph)ELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLAGAVSELLR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 GLAGAVS(1)ELLR;GLAGAVS(1)ELLR 79.82 0.027377 5607300 32375 24136 28942 33905 37629 27886 35235 30587 38057 TRUE FALSE 30844.69791 26595.48584 30269.01933 30496.80498 44191.48569 26920.30083 29859.25361 27908.64013 43958.68519 0.701674715 0.605010949 0.688578814 0.693760627 1.005295893 0.612400046 0.679257204 0.634883414 1 15.42386062 -1.46927616 2.77592454 1.010153076 0.696815156 0.405300091 0.113018632 12812168.74 13711841.46 1005684.881 0.028476285 0.033940938 1.46927616 -0.313337921 GLAGPPAS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 180.24 7.08E-06 724968000 2171760 2346340 1929070 2498470 1404160 2254490 2186940 2552260 1486130 TRUE FALSE 2069105.209 2585434.714 2017519.768 2247319.049 1649045.059 2176416.446 1853282.137 2328770.584 1716591.45 1.205356818 1.506144466 1.17530573 1.309175254 0.960650864 1.267870958 1.079629132 1.35662483 1 20.71111529 3.300333668 2.005803095 1.149355018 1.348038772 0.205627884 0.147588271 0.406657349 3.355122488 0.041197241 0.059360141 1996.795863 -3.300333668 0.198683754 GLAPDLPEDLYHLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GLAPDLPEDLYHLIK 15 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 192.65 1.25E-07 2101294100 3403489 3613761 3082169 3840354 2757787 3407741 3491591 3621607 2482813 FALSE TRUE 3242612.82 3982007.354 3223489.497 3454314.32 3238744.18 3289730.075 2958884.665 3304479.892 2867834.96 1.130683204 1.388506455 1.124014995 1.20450248 1.129334228 1.14711276 1.031748586 1.152255949 1 21.45153057 2.460535323 0.686380895 1.045531273 1.250807195 0.384614112 0.081705657 0.644331069 0.613390988 0.062033177 0.048388374 288.7588627 -2.460535323 0.205275922 GLAPDLPEDLYHLIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLAPDLPEDLYHLIKK 16 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 223.77 5.46E-15 131170000 336740 162130 377990 268940 354720 334770 517530 403220 466560 FALSE TRUE 320822.9676 178651.2313 395321.2154 241905.6402 416583.0557 323176.831 438571.2934 367911.9192 538911.7419 0.595316343 0.331503691 0.733554652 0.448878028 0.77300794 0.599684152 0.813809125 0.682694198 1 19.0396895 1.502342714 0.290872735 1.043310756 0.421219465 0.545797906 0.126701173 1.011565633 0.32294914 0.236321336 0.213158497 31.79382024 -1.502342714 -0.622091291 GLAPNT(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GLAPNTPGK 9 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 GLAPNT(1)PGK;GLAPNT(1)PGK;GLAPNT(1)PGK;GLAPNT(1)PGK;GLAPNT(1)PGK 147.83 0.0010225 1669430000 5258720 4907020 4999580 5964830 3890690 5716110 5728500 5719000 4270490 TRUE FALSE 5010150.727 5407050.917 5228815.688 5365233.956 4569225.104 5518159.677 4854512.114 5218214.042 4932735.779 1.01569412 1.096156608 1.060023468 1.08767917 0.926306478 1.118681382 0.984141931 1.057874226 1 22.23395658 GLATRLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLATRLSR 8 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 GLATRLS(1)R 73.841 0.025752 85590000 74748 62417 72332 81298 100160 65513 91168 74610 97226 TRUE FALSE 71214.81018 68777.36326 75648.49375 73125.77058 117627.8723 63244.26838 77258.64718 68076.75287 112303.3115 0.63412921 0.612425069 0.673608754 0.651145274 1.047412322 0.563155864 0.687946296 0.606186514 1 16.77704094 -2.403653408 2.24365007 3.577569355 0.679731315 0.353165652 0.134048011 7262340.517 715932.4415 95110989.84 0.0304884 0.003947722 2.403653408 -2.89783804 GLAVFISDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLAVFISDIR 10 0 O95782-2;O95782;M0R2D9;E9PR62;O94973-3;O94973;O94973-2 O95782-2;O94973-3 AP2A1;AP2A2 AP-2 complex subunit alpha-1;AP-2 complex subunit alpha-2 0 109.86 0.0045653 19039000 90589 74047 68077 60711 102710 60987 103030 82722 97783 FALSE TRUE 86307.0375 81592.47348 71198.39779 54608.21494 120622.5915 58875.0049 87310.88122 75478.42314 112946.6882 0.764139603 0.722398104 0.630371717 0.483486641 1.06796041 0.521263667 0.773027369 0.668265925 1 16.78528244 -1.529192553 2.849729985 1.013257606 0.70790268 0.252786517 0.159872973 21091007.39 22130155.92 2158992.547 0.034698411 0.029567013 1.529192553 -0.305354926 GLCT(ph)NPGHWGS(ph)HPES(ph)PPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLCTNPGHWGSHPESPPKK 19 1 Q17RG1 Q17RG1 KCTD19 BTB/POZ domain-containing protein KCTD19 3 GLCT(1)NPGHWGS(1)HPES(1)PPKK 43.523 0.086704 483710000 93510 57863 102710 87474 157640 82676 137070 85347 199170 TRUE FALSE 89089.96762 63759.30548 107419.3551 78680.94733 185132.3661 79812.90939 116157.454 77873.56423 230056.2664 0.387252949 0.277146572 0.466926447 0.342007408 0.804726465 0.346927778 0.50490889 0.338497905 1 17.81162723 -5 0.238845411 4.211255596 0.368671086 0.578565843 0.150033449 115.8007989 1.155123278 180.8164266 0.221131584 1.00E-05 5 -3.84258451 GLCTDYRPSLEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLCTDYRPSLEGR 13 1 B7Z879;A0A087WXL6;A0A0G2JS92;Q9H270 B7Z879 VPS11 Vacuolar protein sorting-associated protein 11 homolog 0 69.03 0.047881 0 159930 139940 143740 155120 179050 141620 177630 158150 187630 FALSE TRUE 152370.4259 154200.0451 150330.6212 139527.0429 210276.2633 136715.6639 150529.2811 144301.5476 216726.7021 0.703053313 0.71149537 0.693641437 0.643792581 0.970236991 0.63082058 0.694558075 0.665822652 1 17.72551739 -1.207596323 4.981313168 1.000032399 0.713087578 0.473440605 0.094724258 3.10E-05 4.93E-06 0.083364909 0.019647082 0.062001711 1.207596323 -0.286944822 GLDDDRGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 76.943 0.03101 427840000 401550 371440 362270 464450 433500 401780 407490 451000 505170 FALSE TRUE 382569.5273 409290.1583 378880.4378 417762.6036 509102.2627 387866.2579 345319.9164 411508.0491 583509.1835 0.655635829 0.70142882 0.649313582 0.715948635 0.872483719 0.664713202 0.591798597 0.705229773 1 19.15439584 0.945933545 22.76823674 1.000000001 0.68791375 0.636414326 0.072528087 4695.919243 1977528.388 0.071666922 0.017916731 8.829447825 -0.945933545 -0.312086251 GLDDDRGPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLDDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 107.83 0.0020354 1408140000 983860 987050 786560 1007330 1002050 882640 929320 914200 923170 FALSE TRUE 937354.8876 1087631.517 822624.554 906071.2746 1176807.203 852073.9555 787535.1659 834147.8015 1066330.489 0.879047254 1.01997601 0.771453656 0.84970962 1.103604572 0.799071174 0.738546984 0.782260106 1 20.02422321 GLDFSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GLDFSDR 7 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;;; 157.9 0.0033611 1159030000 2036410 1796840 1843170 2107810 2317490 1809620 2300070 1959010 2421470 FALSE TRUE 1940152.935 1979940.039 1927681.168 1895928.934 2721659.522 1746952.406 1949152.078 1787468.699 2796979.2 0.693660123 0.707885149 0.689201109 0.677848778 0.973071062 0.624585412 0.696877573 0.639071145 1 21.41543809 -1.362167152 3.877082982 1.000968862 0.712132493 0.467915287 0.096254634 0.000746027 0.000122732 0.086252545 0.020263277 0.043434302 1.362167152 -0.288836369 GLDGIPFTVDATSQIHCIEDFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLDGIPFTVDATSQIHCIEDFHR 23 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;;; 201.31 1.32E-24 448197000 411503 343188 381195 421687 469485 388228 450982 405909 126927 FALSE TRUE 392052.0687 378159.2474 398673.1678 379298.2216 551363.0354 374783.567 382176.413 370365.4561 146610.1909 2.674111986 2.579351715 2.719273233 2.58712044 3.760741542 2.556326847 2.606752032 2.526191759 1 17.16162586 0.425010142 1.138493377 0.998246699 2.782056393 0.715178838 0.352130628 1.304803301 2.070527396 0.328267767 0.099912947 2.660787195 -0.425010142 1.783809695 GLDHDFGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 148.32 2.53E-05 586910000 468502 382791 260804 288172 571400 286404 518950 369220 463980 FALSE TRUE 446356.8389 421797.8381 272762.1214 259204.4031 671051.9791 276485.7577 439774.6463 336889.1394 535931.6487 0.832861504 0.787036629 0.508949457 0.48365198 1.25212232 0.515897425 0.820579728 0.628604674 1 19.03168949 GLDHLLDENRVPDLAQMYQLFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLDHLLDENRVPDLAQMYQLFSR 23 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 268.36 1.19E-44 311590000 203319 194068 184992 219468 261229 213687 232489 229795 224555 FALSE TRUE 193708.5138 213843.7498 193474.0662 197406.6597 306787.2549 206286.9656 197018.5331 209672.9316 259377.8425 0.746819821 0.824448795 0.745915936 0.761077576 1.182781273 0.795314525 0.759581201 0.808368708 1 17.98469572 GLDIESYDS(ph)LERPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLDIESYDSLERPLRK 16 2 Q9H792 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 GLDIESYDS(1)LERPLRK;GLDIESYDS(1)LERPLRK 122.83 4.76E-05 191181000 311030 258760 258460 313610 276680 278870 332980 340220 301290 TRUE FALSE 296328.2283 285127.9382 270310.6467 282085.327 324932.9044 269212.662 282177.7854 310428.5332 348012.5144 0.851487277 0.819303693 0.7767268 0.810560871 0.933681666 0.773571785 0.810826547 0.892003938 1 18.40877966 0.948271886 3.548572859 0.999741772 0.82498035 0.612515545 0.044731725 0.169730114 5.612644649 0.040847571 0.010549224 8.877115818 -0.948271886 -0.174761422 GLDIPEVDLVIQSSPPKDVESYIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLDIPEVDLVIQSSPPKDVESYIHR 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 252.02 5.37E-45 519460000 990172 815057 988705 1074200 1010927 1020012 1282019 1091784 998210 FALSE TRUE 943368.5319 898112.2349 1034038.102 966219.3752 1187232.349 984688.7287 1086423.456 996181.605 1153007.309 0.818180878 0.778930219 0.896818341 0.83799935 1.029683281 0.854017768 0.942252011 0.863985508 1 20.13697023 3.415260486 1.599663057 0.925314995 0.798656621 0.403301373 0.061227143 0.31948818 1.66730645 0.017353149 0.029018743 2601.719581 -3.415260486 -0.126658374 GLDIPEVDWIVQYDPPDDPKEYIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLDIPEVDWIVQYDPPDDPKEYIHR 25 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 73.389 0.020604 35173000 100090 95854 105680 117360 100370 110060 133090 118320 95481 FALSE TRUE 95358.94406 105621.6316 110525.5325 105562.7498 117874.4962 106248.5946 112784.6761 107959.2735 110287.7058 0.864638024 0.957691801 1.002156421 0.957157908 1.068790899 0.963376596 1.022640514 0.978887653 1 16.75091245 4.45159712 1.041879539 1.003102501 0.828801174 0.646462894 0.031460184 0.599413248 0.732005433 0.008596382 0.104449623 28287.66628 -4.45159712 -0.174301327 GLDISHISQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLDISHISQR 10 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 123.79 0.0034141 0 168970 133890 133090 156870 270650 138840 249740 183870 290860 FALSE TRUE 160983.123 147533.5432 139192.3081 141101.1296 317851.2743 134031.936 211637.5762 167769.368 335965.0833 0.479166232 0.43913356 0.414305876 0.419987483 0.946084251 0.398946029 0.629939201 0.499365489 1 18.35795178 -5 0.168486981 2.839889398 0.407419246 0.473043291 0.159639235 110.6812794 1.040188969 68.06212925 0.54151444 1.00E-05 5 -2.432470152 GLDLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLDLGGR 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 131.3 0.0080945 76165000 468300 401580 409180 456630 540060 369540 493880 445060 535610 FALSE TRUE 446164.3871 442501.4586 427941.3077 410728.6849 634246.293 356742.7371 418529.5353 406088.187 618669.6633 0.721167391 0.715246738 0.691712125 0.663890133 1.02517762 0.576628786 0.676499205 0.656389364 1 19.23880977 -2.238921656 2.204085106 1.961455349 0.714032778 0.367499599 0.117135907 3923403.454 682048.8377 18794145.13 0.027067432 0.005768705 2.238921656 -1.247422571 GLDQDHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLDQDHAR 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 0 98.033 0.0078096 55275000 270910 241180 229150 288830 295940 233250 301240 321710 324600 FALSE TRUE 258104.6212 265756.5162 239656.7542 259796.2597 347551.8423 225172.494 255280.3053 293539.3669 374937.3102 0.688394071 0.708802536 0.639191533 0.692905861 0.926959875 0.600560381 0.680861302 0.782902525 1 18.51628987 0.887900987 3.781913041 0.999890185 0.703705661 0.540855833 0.085395846 0.38987412 11.25938907 0.077051753 0.019774851 7.72504445 -0.887900987 -0.296184524 GLDVDSLVIEHIQVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 300.61 6.72E-46 939319000 2207000 2067444 2103468 2499661 1920397 2288665 2493049 2466940 1924643 FALSE TRUE 2102679.484 2278118.894 2199914.088 2248390.327 2255313.629 2209407.957 2112688.587 2250921.656 2223106.807 0.945829268 1.024745589 0.98956743 1.011373057 1.014487303 0.993837971 0.950331572 1.012511702 1 21.08414583 4.707641907 3.972086399 0.996188924 0.942787272 0.392979593 0.02059926 0.252550136 7.4570318 0.005267876 0.036047595 51008.42424 -4.707641907 -0.053401652 GLDVDSLVIEHIQVNKAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLDVDSLVIEHIQVNKAPK 19 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 227.29 7.83E-20 62998000 146400 63773 150030 107310 155810 136030 239070 162110 231630 FALSE TRUE 139479.9621 70271.5412 156909.0239 96522.99492 182983.2147 131319.247 202595.4807 147914.789 267549.9974 0.521322981 0.26264826 0.586466176 0.360766196 0.683921571 0.490821335 0.757224753 0.552849151 1 18.02944899 0.731974688 0.274094855 1.105945457 0.347991657 0.624814333 0.125788325 1.665716 0.334632466 0.425846653 0.197686987 5.394791797 -0.731974688 -0.7579538 GLDVEDVK ddPTM_SK-BR-3_Trastuzumab_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 ; 119.27 0.0040145 187982000 508110 457790 457110 569350 385000 511230 555490 545700 439280 FALSE TRUE 484092.6473 504439.3215 478068.9456 512117.8563 452143.8781 493525.9769 470739.7982 497915.6151 507401.2989 0.954062688 0.994162456 0.942191017 1.009295517 0.891097203 0.972654146 0.927746538 0.981305362 1 18.95276769 1.003973093 24.85465846 1.000000007 0.957837588 0.171390263 0.033008013 138.6796078 867536.9863 0.028736105 0.007184026 10.0919036 -1.003973093 -0.042162418 GLDWVKEEAPDILCLQETK ddPTM_SK-BR-3_Trastuzumab_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" 0 234.47 3.55E-24 140940000 368760 258430 326330 345430 271290 360000 465200 402900 316920 FALSE TRUE 351329.4456 284764.3108 341292.5533 310706.7201 318602.8901 347533.1097 394225.196 367619.9401 366066.335 0.959742571 0.777903575 0.932324338 0.848771631 0.870341956 0.949371948 1.076922837 1.004244053 1 18.48174558 2.01443174 3.665007629 1.032970115 0.873394875 0.62639121 0.052454246 0.129666119 3.698071009 0.021938564 0.013847263 103.3788603 -2.01443174 -0.15957524 GLEDHESVVEVQAAWPVGGDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GLEDHESVVEVQAAWPVGGDSR 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;;; 206.34 9.40E-23 560101000 495638 374005 480529 511531 649964 423503 601493 490593 646148 FALSE TRUE 472210.174 412116.5347 502561.73 460110.932 763317.5158 408836.9849 509724.1957 447634.0761 746349.3318 0.632693236 0.552176464 0.673359925 0.616482004 1.022734909 0.547782342 0.682956591 0.599764825 1 19.50949152 -5 0.295216387 3.71028989 0.640694914 0.366718179 0.135685706 275.4185773 2.569554866 461.5196166 0.131913416 1.00E-05 5 -3.069594976 GLEFPMTDLDMLS(ph)PIHTPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(1)PIHTPQR 146.45 8.59E-08 9813000 18939 18720 17800 21886 19047 15477 17973 18852 16645 TRUE FALSE 18043.791 20627.58928 18616.14761 19685.9777 22368.79077 14941.02761 15230.88875 17201.21894 19226.22159 0.938499066 1.072888357 0.968268649 1.023912973 1.16345225 0.777117206 0.792193551 0.894674955 1 14.23078765 2.224051535 24.99992308 0.840071385 1.026768593 0.470385121 0.086181767 176.8536499 304726.3551 0.030040696 0.022284382 167.5141644 -2.224051535 0.186697208 GLEGERPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GLEGERPAR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;; 178.94 4.60E-05 15294120000 3818800 3314880 3440220 3683130 3731090 3417060 4076290 3737920 4094970 FALSE TRUE 3638292.892 3652670.041 3597957.49 3312894.775 4381790.915 3298726.355 3454377.094 3410607.909 4729997.033 0.769195597 0.772235165 0.760668023 0.700401026 0.926383438 0.697405587 0.73031274 0.721059207 1 22.17340785 -1.047095494 4.602275189 1.000009893 0.759650604 0.575970585 0.064794815 6.01E-06 1.24E-06 0.057347454 0.013516368 0.089723149 1.047095494 -0.240359288 GLEGKS(ph)PDTGPDWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLEGKSPDTGPDWLK 15 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 GLEGKS(0.978)PDT(0.022)GPDWLK 145.88 2.41E-06 164980000 238930 195930 194360 241160 125020 217240 230790 284700 135980 TRUE FALSE 227636.2524 215895.4898 203271.5982 216918.1386 146823.4484 209716.9243 195578.7468 259770.1587 157067.0839 1.449293173 1.374543185 1.294170575 1.38105409 0.934781781 1.335206073 1.245192448 1.653880318 1 17.26102135 3.810962495 1.421875757 1.260288312 1.437820979 0.101030927 0.196659963 1.000395973 3.85047128 0.055705372 0.151296369 6470.867327 -3.810962495 0.177532666 GLEHVTVDDLVAEITPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLEHVTVDDLVAEITPK 17 0 E5RHX8;Q9NPA8-2;Q9NPA8 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 68.257 0.037263 23911000 36871 30508 35488 40154 27436 34144 37975 38935 33969 FALSE TRUE 35128.1809 33616.79988 37115.1599 36117.64363 32220.82971 32961.58472 32181.21629 35525.64499 39236.73903 0.895287982 0.856768445 0.94592876 0.920505743 0.821190306 0.840069423 0.820180705 0.905417878 1 15.25991752 0.981963806 23.3391587 1.000000003 0.869537464 0.497062533 0.040690479 444.9756505 575808.2292 0.041121454 0.010280364 9.593206785 -0.981963806 -0.130462539 GLESTTLADKDGEIYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLESTTLADKDGEIYCK 17 1 P21291;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;; 249.69 3.97E-21 5455280000 8615760 6419990 6867080 8508810 5171210 7854360 9040890 8823150 5947370 FALSE TRUE 8208510.1 7074194.28 7181942.41 7653488.253 6073067.387 7582361.544 7661536.183 8050548.212 6869657.765 1.1948936 1.029773902 1.045458545 1.114100369 0.884042203 1.103746621 1.115271888 1.171899458 1 22.7118068 -0.869109369 7.332940184 1.000033278 1.081779778 0.082947397 0.086080821 0 1.62E-10 0.079558255 0.01875206 0.135173211 0.869109369 0.0817465 DHS(ph)PTPSVFNSDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.803)PT(0.197)PSVFNSDEER;DHS(0.996)PT(0.004)PSVFNSDEER;DHS(0.99)PT(0.01)PSVFNSDEER;DHS(0.998)PT(0.002)PSVFNSDEER;DHS(0.978)PT(0.022)PSVFNSDEER;DHS(0.973)PT(0.027)PSVFNSDEER 228.3 3.96E-13 5212490000 2263800 2530670 2404600 3080270 1946480 2625240 2814940 1474240 924570 TRUE FALSE 2156794.66 2788548.15 2514853.288 2770635.407 2285945.496 2534327.281 2385469.203 1345147.73 1067947.594 2.019569756 2.611128268 2.354847095 2.594355214 2.140503438 2.373082065 2.233695003 1.259563426 1 20.02640942 1.204479743 3.199239793 1.004154477 2.354516368 0.889986112 0.177469547 0.066969158 1.212826733 0.153212317 0.042545898 16.01325956 -1.204479743 1.350361891 GLEYLYLNVHDEDRDDQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;;; 261.58 2.20E-31 1299876000 1119331 995248 976127 1147060 1169902 1032509 1192505 1085845 1022326 FALSE TRUE 1066422.442 1096664.903 1020883.388 1031755.35 1373932.538 996752.9544 1010566.46 990762.6554 1180863.095 0.903087281 0.928697753 0.86452307 0.873729863 1.163498584 0.844088497 0.855786301 0.839015682 1 20.17141028 -0.954751503 4.111642003 1.00000441 0.908802748 0.083818958 0.094491714 9726290.774 4731411.219 370.7532355 0.021121525 0.110980965 0.954751503 -0.091201662 GLEYLYLSVHDEDRDDHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLEYLYLSVHDEDRDDHTR 19 1 O43237 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ; 176.46 3.80E-13 234040000 146108 118485 132832 140802 178418 125023 177695 144157 45929 FALSE TRUE 139201.7644 130558.7562 138922.4786 126648.3155 209534.0427 120693.4222 150584.3642 131533.8489 53051.43475 2.623901975 2.460984455 2.61863754 2.387274087 3.949639509 2.275026542 2.838459787 2.479364592 1 15.69510415 5.051588768 11.37526031 2.604085235 2.699625255 0 0.717253151 2256240.615 20227978.92 0.147901561 4302516.036 112613.0622 -5.051588768 0.09554002 GLFDDEDEESDLFTEAPQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLFDDEDEESDLFTEAPQDR 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 ; 245.5 1.34E-29 64070000 85865 72714 79863 88646 91330 78483 87902 82209 97551 FALSE TRUE 81806.33162 80123.63927 83524.79755 79735.13566 107257.9231 75765.11403 74490.93547 75010.34414 112678.7109 0.726014089 0.711080546 0.741265115 0.707632658 0.951891642 0.672399546 0.661091478 0.665701121 1 16.78185544 -2.326013303 2.37580883 2.626756921 0.726628217 0.509396785 0.083339143 11025149.34 2051915.21 95677031.19 0.02086195 0.004720486 2.326013303 -1.900128705 GLFDEYGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;; 161.92 0.00014929 342219000 1129300 1134510 966450 1175450 863890 1019400 1124120 1166470 1012070 FALSE TRUE 1075920.227 1250117.859 1010762.688 1057291.533 1014552.142 984097.9224 952614.8481 1064327.703 1169016.647 0.920363478 1.069375584 0.864626429 0.904428124 0.867868003 0.84181686 0.814885614 0.910447003 1 20.15686404 3.716999474 24.59987951 0.872478896 0.994869531 0.332260447 0.061613796 521.8226568 595366.0903 0.01531044 0.023744588 5211.940802 -3.716999474 0.122390636 GLFIIDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GLFIIDDK 8 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;;;; 192.31 0.00041081 5752844600 7688283 7050813 6331040 8407074 4970144 7175151 7357140 7334789 4883087 FALSE TRUE 7324873.099 7769298.861 6621324.446 7561978.949 5836935.54 6926673.722 6234673.17 6692515.991 5640331.193 1.298660105 1.377454372 1.173924761 1.340697681 1.03485688 1.228061524 1.105373595 1.186546634 1 22.42734845 3.185099588 0.204419278 0.971352639 1.51024655 0.52354533 0.085647931 4.462558729 0.34533497 0.207291606 0.672541011 1531.438597 -3.185099588 0.538893911 GLFIIDDKGILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLFIIDDKGILR 12 1 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ; 174.84 2.67E-05 5263600000 5566000 2546600 5164500 3620200 5920900 4545600 8341300 5703100 7581400 FALSE TRUE 5302906.211 2806101.435 5401297.433 3256290.618 6953503.085 4388184.732 7068681.487 5203706.33 8757084.792 0.605556111 0.320437851 0.616791725 0.371846419 0.794043138 0.50110109 0.807195734 0.594228154 1 23.06201925 0.964696475 0.334786516 1.045083552 0.437771962 0.506081833 0.143641093 1.243783466 0.401478571 0.272347711 0.148678536 9.219268737 -0.964696475 -0.60731159 GLFIIDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLFIIDGK 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 114.6 0.0061059 641570000 1918480 1715410 1719530 2020200 1696040 1875700 2178200 2028230 1853910 FALSE TRUE 1827797.252 1890212.229 1798372.151 1817125.658 1991828.839 1810744.039 1845875.585 1850627.429 2141404.894 0.853550516 0.882697258 0.83980949 0.848567061 0.930150503 0.845586953 0.861992792 0.864211824 1 21.03012617 -0.869030328 4.641235561 1.000000654 0.866021707 0.728142756 0.02576591 3.91981E+11 14679788.01 3162907.236 0.005715842 0.135197815 0.869030328 -0.133978947 GLFITIHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLFITIHDR 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 ; 188.66 3.91E-05 436020000 1064620 841950 755550 896830 1085520 751630 1020020 887110 907420 FALSE TRUE 1014297.522 927745.6622 790192.7148 806678.9445 1274834.344 725600.8646 864397.215 809429.9455 1048138.059 0.967713665 0.88513689 0.753901366 0.769630429 1.216284757 0.69227604 0.824697861 0.772255085 1 19.99939733 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLFSDEEDSEDLFSSQSASK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 GLFS(0.983)DEEDS(0.017)EDLFSSQSASK;GLFS(0.982)DEEDS(0.018)EDLFSSQSASK;GLFS(0.998)DEEDS(0.002)EDLFSSQSASK 198.9 9.72E-22 111864000 220508 203419 197401 221640 154144 199304 234980 228849 166930 TRUE FALSE 210085.0238 224147.6274 206452.0311 199360.3261 181026.6648 192402.0525 199129.4853 208809.7684 192816.6518 1.08955851 1.162491026 1.070716814 1.033937288 0.938853896 0.997849774 1.032740084 1.082944685 1 17.55687012 3.390619267 2.86324959 1.011915592 1.125505741 0.572562964 0.039992609 0.171269404 2.833009402 0.011667558 0.016872735 2458.21162 -3.390619267 0.113590149 GLGAFVIDSDHLGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLGAFVIDSDHLGHR 15 0 Q13057;Q13057-2;K7EQ60 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 0 68.809 0.029797 82764000 20117 20172 18766 19860 24497 16108 22701 17216 2101.8 FALSE TRUE 19166.10928 22227.54973 19626.43966 17863.63507 28769.26904 15550.17592 19237.54552 15708.47577 2427.736409 7.894641775 9.155668485 8.084254776 7.358144401 11.85024409 6.405215929 7.924066815 6.47042064 1 11.24539607 0.566153323 0.882914995 0.968243714 8.611206815 0.73837801 1.392100662 0.660578609 0.824869209 1.229720914 0.40385679 3.682589609 -0.566153323 7.6429631 GLGHPPSS(ph)PLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLGHPPSSPLLK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.123)S(0.877)PLLK;GLGHPPS(0.018)S(0.982)PLLK;GLGHPPS(0.256)S(0.744)PLLK;GLGHPPS(0.02)S(0.98)PLLK 123.02 0.00022428 438811000 1814120 1791990 1762450 2111200 1557520 1932180 2091490 2026460 1520210 TRUE FALSE 1728370.143 1974595.818 1843260.076 1898978.165 1829150.995 1865268.122 1772394.788 1849012.419 1755956.403 0.984289895 1.124513009 1.049718588 1.081449495 1.041683605 1.062251955 1.0093615 1.052994492 1 20.7438256 1.749545443 24.99773935 1.023221685 1.059488092 0.174571321 0.037123167 5.095352858 11616.79215 0.016264635 0.009019545 56.17530557 -1.749545443 0.036266406 GLGKPGGQGDAIQLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLGKPGGQGDAIQLS(1)PK;GLGKPGGQGDAIQLS(1)PK;GLGKPGGQGDAIQLS(1)PK 183.27 4.25E-10 1299660000 2341380 2072660 2206400 2567000 1418010 2565790 2544070 2839710 1634640 TRUE FALSE 2230707.608 2283866.41 2307565.622 2308960.283 1665310.495 2476936.049 2155925.396 2591049.938 1888131.623 1.181436496 1.209590678 1.222142352 1.222880998 0.881988562 1.311845011 1.141830035 1.372282476 1 20.84852791 -2.36019623 2.014219122 5.85E-05 1.188138594 0.182010503 0.12821555 1637464.75 208237.4013 7433835.153 0.028300772 0.004363186 2.36019623 1.188080078 GLGLDDALEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLGLDDALEPR 11 0 Q9Y230;X6R2L4;M0R0Z0;A0A1W2PS48 Q9Y230 RUVBL2 RuvB-like 2 0 ; 132.01 0.00044531 53490000 228590 183743 192636 218230 245320 200449 236730 211040 253070 FALSE TRUE 217785.0037 202466.6206 201468.5511 196293.1058 288103.7303 193507.4009 200612.4907 192560.2188 292314.8031 0.745035836 0.692632116 0.689217751 0.671512711 0.985594049 0.661982899 0.686289194 0.658742618 1 18.15716336 -0.968871764 4.097920341 1.000015838 0.722111428 0.448299595 0.096248609 24292968.6 49565467.2 5717.962845 0.02185654 0.107430658 0.968871764 -0.27790441 GLGPPS(ph)PPAPPR ddPTM_SK-BR-3_Trastuzumab_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 155.88 7.63E-05 1122352000 578396 538413 542617 626265 610343 526806 632579 584371 675539 TRUE FALSE 551056.3674 593277.8968 567496.5262 563311.6524 716786.626 508562.5761 536067.4554 533200.3773 780298.1379 0.706212588 0.760322072 0.727281661 0.721918489 0.918606096 0.651754184 0.687003376 0.68332904 1 19.57366593 -1.097837729 4.701934427 1.000014551 0.731267219 0.57456256 0.072457449 1.12E-05 2.14E-06 0.067050873 0.015803137 0.079829291 1.097837729 -0.268747332 GLGS(ph)SPDLELLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.986)S(0.014)PDLELLLR;GLGS(0.883)S(0.117)PDLELLLR;GLGS(0.984)S(0.016)PDLELLLR;GLGS(0.986)S(0.014)PDLELLLR 134.08 0.00010467 57583000 88220 71165 78863 101679 111197 80651 109746 87853 109399 TRUE FALSE 84050.01544 78416.79441 82478.94656 91458.03374 130589.7216 77858.03565 93002.23208 80160.12558 126364.0382 0.665141892 0.620562587 0.652709012 0.723766311 1.033440554 0.616140769 0.735986547 0.634358689 1 16.94722642 -5 0.204866427 2.319304757 0.661794449 0.340661694 0.123419503 166.1198019 1.649805771 90.47925445 0.271076366 1.00E-05 5 -1.657510308 GLGTDEDAIISVLAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLGTDEDAIISVLAYR 16 0 P09525;Q6P452;B4E1S2 P09525 ANXA4 Annexin A4;Annexin 0 ;;; 210.93 1.96E-11 68960000 107001 81721.3 69183.4 114366 123789 80887 98169 73239 92009 FALSE TRUE 101943.2748 90048.79338 72355.52732 102869.7124 145377.7624 78085.86291 83191.51605 66825.8049 106277.2858 0.959219781 0.847300462 0.680818359 0.967936955 1.367910004 0.734737083 0.782777951 0.628787275 1 16.69747376 GLGTDEDS(ph)LIEIICSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 194.58 2.00E-10 26274000 46541 28296 32589 29304 31636 26314 31127 27668 37167 TRUE FALSE 44341.09917 31179.39457 34083.23788 26358.30625 37153.30838 25402.73958 26378.00446 25245.24324 42930.66854 1.032853684 0.726273213 0.793913513 0.613973813 0.865425805 0.591715444 0.614432651 0.588046823 1 15.38972102 5.445812305 0.732431027 0.685334089 1.785438824 0.315975231 0.13668926 6.605827078 1.275079011 0.044675435 7.604758753 279133.7213 -5.445812305 1.100104735 GLGTDEDSLIEIICSR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 270.2 2.20E-28 147104000 217011 168713 143853 227297 253994 176140 195220 159302 199402 FALSE TRUE 206753.3201 185905.0465 150448.8023 204448.6737 298290.4732 170040.2276 165435.6035 145352.6724 230324.2438 0.897661995 0.807144934 0.653204369 0.887655899 1.295089342 0.738264565 0.718272644 0.631078474 1 17.81330675 GLGTDEDTIIDIITHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;;;;;;;;;;;;;;; 308.83 1.33E-57 3465015900 3705739.9 2738575.9 2422731.5 4593621 5023767.9 2946827.2 3871669.9 2855169.8 3332646.4 FALSE TRUE 3530576.919 3017639.898 2533816.136 4131861.49 5899911.431 2844777.835 3280975.549 2605155.996 3849456.183 0.917162516 0.7839133 0.658227037 1.07336239 1.532661018 0.73900772 0.852321833 0.676759488 1 21.87622322 -2.093558137 2.478629844 1.171127931 0.899718821 0.013596628 0.253987488 74815947.29 14914517.97 72560817.87 0.060588324 0.008061983 2.093558137 -0.27140911 GLGTDEESILTLLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLGTDEESILTLLTSR 16 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 240.59 1.67E-19 171669000 289687 245837 289622 264580 308623 266561 329654 276745 291508 FALSE TRUE 275994.0696 270888.0698 302901.4552 237983.9157 362446.7535 257329.9257 279359.2278 252511.7407 336713.5718 0.819670167 0.804505944 0.899581961 0.706784447 1.076424545 0.764239838 0.829664294 0.749930391 1 18.36116235 -2.35744363 2.238800095 2.068400888 0.830793733 0.215132256 0.101230751 3672101.869 636916.6676 19741995 0.022533591 0.004390929 2.35744363 -1.237607155 GLHQSIEEFR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 205.13 1.74E-07 2066830000 1299080 894531 1164991 1356770 2006170 1020050 1730410 1420340 2132040 FALSE TRUE 1237675.063 985684.7259 1218406.99 1220384.902 2356045.413 984725.4127 1466404.173 1295967.5 2462665.874 0.502575309 0.4002511 0.494751238 0.495554397 0.956705267 0.399861558 0.595453971 0.52624577 1 21.23178947 -5 0.182305927 2.891292027 0.442971755 0.458735714 0.155882042 117.7773599 1.138407496 80.90660539 0.443222519 1.00E-05 5 -2.448320272 GLHSENREDEGWQVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLHSENREDEGWQVYR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 111.07 0.00050782 69495000 54454 46785 43791 54696 54361 45596 52818 59385 53403 FALSE TRUE 51880.06734 51552.44469 45798.86067 49197.85416 63841.54119 44016.99909 44759.64403 54184.93458 61684.4645 0.841055649 0.835744383 0.74246994 0.79757285 1.034969529 0.713583225 0.725622641 0.878421091 1 15.91261957 0.988815275 23.34119365 1.000000008 0.811772456 0.304886977 0.090256718 275.1754238 574261.5166 0.085272278 0.02131807 9.745750183 -0.988815275 -0.188227552 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_SK-BR-3_Trastuzumab_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 123.36 1.86E-05 182280000 277160 259950 261324 331820 190313 302690 288010 328540 195778 TRUE FALSE 264059.1961 286439.2005 273305.9639 298464.8232 223503.5269 292207.7694 244068.7848 299771.2959 226138.2523 1.167689205 1.266655232 1.208579093 1.319833421 0.98834905 1.292164268 1.079290135 1.325610739 1 17.78684553 2.788754217 24.9999025 1.149594356 1.23512184 0.162747927 0.114528653 721.9235705 359566.7851 0.030498695 0.032348693 614.8288206 -2.788754217 0.085527483 GLIAAICAGPTALLAHEIGFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLIAAICAGPTALLAHEIGFGSK 23 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 320.62 1.35E-73 248920000 613400 621170 596630 692940 540350 622360 704690 674950 576240 FALSE TRUE 584405.7976 684467.9292 623986.0756 623284.3547 634586.8689 600807.5171 597176.598 615847.7999 665600.3562 0.878013048 1.028346699 0.937478578 0.936424311 0.953405242 0.902655042 0.897199938 0.925251608 1 19.34429668 2.255396338 24.52902308 0.919260509 0.950726041 0 0.04596681 453.9094498 661328.2652 0.015139952 0.012633555 180.0513317 -2.255396338 0.031465532 GLKAELMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLKAELMER 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 69.346 0.056409 0 300820 214850 241540 251870 345000 240570 384840 275680 428580 FALSE TRUE 286600.8348 236743.4593 252614.8479 226551.5491 405167.8908 232239.0006 326125.5899 251539.9977 495041.9975 0.578942466 0.47822904 0.510289731 0.457641069 0.818451551 0.469129896 0.658783682 0.508118501 1 18.9171914 -5 0.257157052 3.795758792 0.522450339 0.612030623 0.109791191 118.639618 1.16844582 174.940017 0.132835488 1.00E-05 5 -3.273308453 GLKEGIPALDNFLDKL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLKEGIPALDNFLDKL 16 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 205.78 8.63E-11 522160000 962840 563460 1061480 901500 859330 1023100 1442530 1192610 1153720 FALSE TRUE 917328.4614 620877.2146 1110149.908 810879.5073 1009196.88 987669.7905 1222445.555 1088178.746 1332633.005 0.688357903 0.465902624 0.833049987 0.608479232 0.757295426 0.741141625 0.917315983 0.816562956 1 20.3458481 2.017663632 0.475070202 0.993840333 0.581261027 0.581612446 0.097815412 0.577204106 0.294280944 0.091008919 0.075407034 104.1510451 -2.017663632 -0.412579306 GLKEGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 GLKEGMNPSYDEYADSDEDQHDAYLER 27 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPS(0.003)Y(0.004)DEY(0.027)ADS(0.966)DEDQHDAYLER 416.34 4.56E-166 7760322000 5694313 2547719 4012041 2792458 6569381 3420991 9095553 4758287 8232266 TRUE FALSE 5425154.11 2807334.463 4195997.048 2511754.817 7715078.966 3302521.224 7707859.339 4341626.165 9508883.767 0.570535327 0.295232809 0.441271252 0.26414823 0.81135485 0.347309033 0.8105956 0.456586311 1 23.18084456 0.525508973 0.350504084 1.067486918 0.391082763 0.439996233 0.184511771 2.20377263 0.560647029 0.464090669 0.159195151 3.353582331 -0.525508973 -0.676404155 GLKPSCTIIPLMK ddPTM_SK-BR-3_Trastuzumab_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 ; 142.85 3.70E-05 954180000 3749800 3500000 3710300 4176000 3148900 3816600 4470800 4188000 3707500 FALSE TRUE 3572554.385 3856653.979 3880420.925 3756220.546 3698067.163 3684430.185 3788697.348 3821276.518 4282440.165 0.834233345 0.900573932 0.906123793 0.877121548 0.863542051 0.860357657 0.884705262 0.89231288 1 22.03000166 0.532498927 1.554582619 0.999983045 0.874980358 0.787114118 0.020258654 1.071235229 3.045918453 0.019559277 0.005622083 3.407994828 -0.532498927 -0.125002687 GLKYELISETGGSHDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 174.78 7.87E-10 1738040000 4766300 3497800 4163200 4212800 3628000 4465900 5628800 5163300 4053700 FALSE TRUE 4541006.445 3854229.797 4354086.838 3789321.34 4260722.051 4311244.763 4770023.18 4711174.08 4682327.093 0.969818288 0.823144074 0.929898051 0.809281638 0.909958225 0.920748311 1.018729167 1.006160823 1 22.15879429 1.89957075 2.571669278 1.011136156 0.88536307 0.576175888 0.046846275 0.188142454 2.248606864 0.024337262 0.01246624 79.35435213 -1.89957075 -0.125773086 GLLALGDYMNVQCHACIGGTNVGEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLLALGDYMNVQCHACIGGTNVGEDIR 27 0 P38919 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 165.47 9.64E-12 27419000 16365 15536 15840 18955 20095 15679 16342 17151 19096 FALSE TRUE 15591.45888 17119.13606 16566.27967 17049.60739 23599.56164 15136.0323 13848.72776 15649.16752 22057.31015 0.706861298 0.776120748 0.751056206 0.772968566 1.069920198 0.686213876 0.627852066 0.709477602 1 14.42896925 -2.355706011 2.225423146 2.506791396 0.756566458 0.284880804 0.117887508 4325106.01 644448.3879 32675997.63 0.02888947 0.004408532 2.355706011 -1.750224938 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 160.38 1.17E-12 380838000 467130 461980 466140 526170 381448 509200 564220 534000 409080 TRUE FALSE 445049.6907 509056.2872 487512.9801 473278.3919 447972.4104 491566.2763 478137.8764 487240.1291 472518.0371 0.941868153 1.077326678 1.031734118 1.001609155 0.948053567 1.040312195 1.011893386 1.031156677 1 18.85000988 GLLAQGLRPES(ph)PPPAGPLLNGAPAGESPQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 309.8 9.09E-93 7179740000 6959630 6153870 6644140 7504970 5716720 7283060 8126550 7555440 6462330 TRUE FALSE 6630662.083 6780956.349 6948780.391 6750556.157 6713714.158 7030845.806 6886695.543 6893845.62 7464475.131 0.888295823 0.908430429 0.930913463 0.90435778 0.899422135 0.941907593 0.922596086 0.923553967 1 22.83160939 -5 0.152861856 1.316996526 0.887474463 0.819197877 0.013184043 52.10967058 0.468651602 4.992109183 0.060770599 1.00E-05 5 -0.429522063 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_SK-BR-3_Trastuzumab_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 215.96 4.41E-34 588120000 462637 428937 467098 507355 544126 456000 550039 492983 579967 TRUE FALSE 440769.0659 472646.168 488514.9053 456354.7115 639021.4021 440208.6057 466120.4484 449814.7951 669905.3203 0.657957255 0.705541744 0.729229774 0.681222701 0.953898085 0.657120629 0.695800487 0.671460252 1 19.35359768 -2.112564008 2.430520789 1.53308103 0.716076811 0.510152258 0.08648265 7358883.614 1733559.16 21725723.48 0.01981942 0.007716778 2.112564008 -0.817004219 GLLDDLRNDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ; 101.39 0.0024604 42851000 97498 53614 80025 97894 150234 79077 120405 88254 125751 FALSE TRUE 92889.46276 59077.32755 83694.22541 88053.50913 176434.762 76338.54366 102035.0059 80526.0119 145251.8228 0.639506348 0.406723485 0.576200861 0.606212765 1.214681913 0.52555997 0.70246971 0.554388994 1 17.14819674 2.985794501 24.75852947 0.76783552 0.534305486 0.247278405 0.208486932 858.21682 1495775.553 0.059287094 0.065223176 967.8197969 -2.985794501 -0.233530035 GLLEDVQEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLLEDVQEGR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 154.85 3.20E-05 638788000 1165730 959610 1009810 1162500 1191470 1067830 1218960 1130170 1264180 FALSE TRUE 1110628.253 1057395.35 1056110.787 1045643.291 1399261.991 1030850.779 1032985.264 1031206.323 1460222.578 0.760588331 0.724132996 0.723253293 0.716084868 0.958252538 0.705954554 0.707416308 0.706198041 1 20.47775686 -1.006436048 4.551651075 1.000007326 0.747896715 0.51715591 0.075815011 9275509.231 2050950.112 700.5226346 0.016976027 0.098528972 1.006436048 -0.252110611 GLLEFEHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GLLEFEHQR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;;; 241.96 2.01E-10 5020640000 6390720 5104560 4295250 4867550 7360000 4690140 6680180 5412830 6112370 FALSE TRUE 6088643.331 5624720.467 4492191.461 4378254.626 8643581.67 4527719.276 5660995.851 4938853.91 7060245.122 0.862384128 0.796674955 0.636265651 0.62012785 1.224260847 0.641297745 0.801812933 0.699530091 1 22.75128684 4.435091279 3.193195198 0.790437639 0.857843669 0.00630013 0.187258723 1.490357757 28.89238814 0.043028353 0.171518199 27232.7362 -4.435091279 0.067406031 GLLEPLGLECTFIDDISAYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLLEPLGLECTFIDDISAYHK 21 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 105.5 0.00049113 0 57731 71169 38436 52793 58721 42764 66891 55059 50376 FALSE TRUE 55002.17004 78421.20201 40198.32862 47486.14734 68961.92381 41283.07196 56685.54941 50237.74207 58188.0528 0.945248507 1.347719991 0.690834745 0.816080708 1.185156067 0.709476774 0.97417849 0.863368676 1 15.82843535 3.738689006 25 0.893007101 1.14648424 0.275950797 0.171830714 12.94579014 2520623.665 0.041617315 0.069437767 5478.844892 -3.738689006 0.253477139 GLLGLPEEETELDNLTEFNTAHNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLLGLPEEETELDNLTEFNTAHNKR 25 1 Q12972;A0A0A0MT09;Q12972-2 Q12972 PPP1R8 Nuclear inhibitor of protein phosphatase 1;Activator of RNA decay 0 95.195 0.0065534 20001000 31092 28067 25844 34604 23564 31179 30949 30595 23961 FALSE TRUE 29622.34278 30927.05921 27028.97296 31125.54018 27673.55414 30099.26341 26227.16163 27915.93961 27676.7495 1.070297029 1.117438274 0.97659492 1.124609672 0.999884547 1.087528845 0.947624345 1.008642276 1 14.7563869 1.744708879 24.99999349 0.983394019 1.066271475 0.359563226 0.048455342 1.181864522 4821.989351 0.02036218 0.011291869 55.5531742 -1.744708879 0.082877456 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK 308.71 1.89E-66 471936000 774520 760860 758410 858700 653970 866690 918370 947020 784710 TRUE FALSE 737909.9746 838392.499 793183.8487 772381.8446 768022.1609 836676.308 778255.7895 864093.9083 906398.8191 0.8141118 0.924970864 0.875093648 0.852143481 0.847333585 0.923077447 0.858624011 0.953326384 1 19.78978646 1.077113001 3.499366194 0.999452603 0.872848559 0.644150315 0.033557075 0.12677112 3.014931916 0.030020449 0.007827009 11.94298815 -1.077113001 -0.126604044 GLLQDDAHPTLVTYADHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLLQDDAHPTLVTYADHSK 19 0 Q86U44;F5H6D8;B4DTN4;H0YFV6 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 138.03 1.57E-06 81266000 186440 167460 166070 211030 173270 174980 236740 218380 122530 FALSE TRUE 177627.3507 184524.3644 173684.4738 189816.8635 203488.2331 168920.3987 200620.965 199257.4895 141531.3266 1.255039114 1.303770471 1.227180427 1.341165013 1.437761081 1.193519504 1.417502187 1.407868451 1 17.11076189 -1.113666307 4.843473027 0.999983709 1.319804156 0.604355494 0.082089995 1.37E-05 2.51E-06 0.075503634 0.017795471 0.076972163 1.113666307 0.319820447 GLLS(ph)PPMGQSGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLLSPPMGQSGLR 13 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GLLS(0.967)PPMGQS(0.033)GLR;GLLS(0.999)PPMGQS(0.001)GLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR 131.96 0.00013049 709022000 938800 827870 823052 970250 980580 835132 1015640 950400 1061300 TRUE FALSE 894424.7845 912230.8942 860789.7483 872718.6266 1151592.842 806211.1694 860685.4645 867177.9376 1225880.984 0.729617962 0.744143115 0.702180521 0.711911383 0.9394002 0.657658598 0.702095453 0.707391622 1 20.22538749 -1.745390839 2.80052358 1.05125554 0.735280013 0.545345882 0.075514086 31887444.12 24777884.34 11282432.01 0.017492513 0.017972528 1.745390839 -0.315975527 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.841)MT(0.158)DVPVDTGVAAR;GLLSDS(1)MTDVPVDTGVAAR;GLLS(0.001)DS(0.993)MT(0.006)DVPVDTGVAAR;GLLSDS(0.987)MT(0.013)DVPVDTGVAAR;GLLSDS(0.97)MT(0.03)DVPVDTGVAAR;GLLSDS(1)MTDVPVDTGVAAR;GLLS(0.001)DS(0.993)MT(0.006)DVPVDTGVAAR;GLLSDS(0.999)MT(0.001)DVPVDTGVAAR;GLLS(0.005)DS(0.986)MT(0.009)DVPVDTGVAAR;GLLS(0.02)DS(0.876)MT(0.104)DVPVDTGVAAR 243.09 3.38E-24 586050000 900693 813384 791851 1017723 932429 909123 999337 941732 1004344 TRUE FALSE 858119.0269 896268.7543 828158.1516 915419.5505 1095044.322 877639.8426 846869.7866 859268.9536 1160092.538 0.739698773 0.772583846 0.713872492 0.789091836 0.943928425 0.75652572 0.730001926 0.74069001 1 20.14580846 -1.436993934 3.413238037 1.002731541 0.771194842 0.550453586 0.064359719 25968513.13 37989338.86 687231.9368 0.015526349 0.03655999 1.436993934 -0.231536699 GLLYDS(ph)DEEDEERPAR ddPTM_SK-BR-3_Trastuzumab_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 355.02 1.34E-87 44224170000 12634630 13322210 12577910 14604070 12639170 13219640 14587390 14203140 13980350 TRUE FALSE 12037416.08 14679758.35 13154619.61 13136041.14 14843437.25 12761840.55 12361815.74 12959437.77 16148351.28 0.74542694 0.909056169 0.814610692 0.813460205 0.91919212 0.790287524 0.765515657 0.802523895 1 23.94488354 -2.196818762 2.39392217 1.530712323 0.820686818 0.510911712 0.055340859 3482511.608 671691.9852 10077481.54 0.013329908 0.006355961 2.196818762 -0.710025505 GLLYDS(ph)DEEDEERPARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;GLLYDS(1)DEEDEERPARK;GLLY(0.001)DS(0.999)DEEDEERPARK;GLLYDS(1)DEEDEERPARK 297.67 1.73E-46 3232984000 3126490 2506286 3163651 3108490 2580910 3127470 4088410 3751610 3665270 TRUE FALSE 2978707.014 2761679.393 3308707.528 2796018.679 3031019.887 3019164.93 3464647.966 3423099.14 4233661.352 0.703577062 0.652314666 0.781523899 0.660425681 0.715933476 0.713133309 0.818357369 0.808543446 1 22.01347444 0.907844938 0.630498894 1.003043522 0.688454242 0.852832522 0.038920409 0.294273327 0.266624254 0.03680441 0.015002101 8.088070681 -0.907844938 -0.31458928 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLMAGGRPEGQYSEDEDTDTDEYK 24 1 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQYS(1)EDEDT(0.93)DT(0.07)DEYK;GLMAGGRPEGQYS(1)EDEDT(0.926)DT(0.074)DEYK 230.88 3.71E-33 222480000 456190 509870 375110 524740 307480 546530 434290 503740 250800 TRUE FALSE 434626.8028 561826.3327 392309.1645 471992.1383 361104.4146 527603.5291 368031.0842 459629.8551 289692.7831 1.500302486 1.939386707 1.354224846 1.629285111 1.246508148 1.821251891 1.270418546 1.586611341 1 18.14416422 -2.853411958 0.156073965 5.97E-10 1.765135497 0.374013732 0.221616956 55.79817474 0.954187425 19.88178631 1.008817326 0.001401484 2.853411958 1.765135496 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYKEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQYS(1)EDEDT(0.996)DT(0.004)DEYKEAK;GLMAGGRPEGQY(0.005)S(0.995)EDEDT(0.952)DT(0.048)DEYKEAK;GLMAGGRPEGQY(0.004)S(0.994)EDEDT(0.503)DT(0.498)DEY(0.001)KEAK;GLMAGGRPEGQYS(1)EDEDT(0.999)DT(0.001)DEYKEAK;GLMAGGRPEGQY(0.001)S(0.999)EDEDT(0.995)DT(0.005)DEYKEAK;GLMAGGRPEGQYS(1)EDEDT(0.996)DT(0.004)DEYKEAK 204.75 1.35E-24 2212510000 2075836 1682928 1814969 2098401 1026321 2219180 2149899 2492060 1265187 TRUE FALSE 1977715.346 1854420.277 1898187.124 1887465.745 1205311.057 2142329.24 1821892.422 2273842.015 1461385.738 1.353315072 1.268946472 1.298895339 1.291558892 0.824772698 1.465957402 1.246688245 1.555949231 1 20.4789056 2.974117903 24.94053712 1.235604602 1.304212304 0.036628448 0.206500297 3470.451437 3344200.181 0.058999384 0.062802154 942.1453363 -2.974117903 0.068607702 GLMAGGRPEGQYS(ph)EDEDTDTDEYKEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 1 GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK;GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK;GLMAGGRPEGQY(0.003)S(0.997)EDEDTDTDEYKEAK 318.19 1.46E-82 367360000 312918 247229 271624 343493 152967 335554 369402 335531 178438 TRUE FALSE 298126.9863 272421.9162 284078.2291 308964.431 179644.3964 323933.6808 313042.9404 306150.1269 206109.2537 1.446451243 1.321735494 1.378289543 1.499032312 0.871597918 1.571660054 1.518820406 1.485377883 1 17.65304975 GLNNDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLNNDSPER 9 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 GLNNDS(1)PER 116.41 0.0013829 118070000 153060 138990 142260 167500 178090 134800 163710 151530 197410 TRUE FALSE 145825.1571 153153.239 148782.7617 150662.5818 209148.8396 130131.8422 138733.0328 138261.2299 228023.3346 0.639518571 0.671655992 0.652489194 0.660733175 0.917225599 0.570695286 0.608415946 0.606346847 1 17.79882194 -1.260758502 3.794145935 1.000526677 0.663410492 0.553323928 0.094318687 1893846252 3800496322 12142481.05 0.021930266 0.054858193 1.260758502 -0.337116185 GLNNDS(ph)PERR ddPTM_SK-BR-3_Trastuzumab_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 186.16 8.39E-07 475060000 450180 370700 388000 433040 492730 427610 513840 439840 517570 TRUE FALSE 428900.8836 408474.7515 405790.1838 389509.9965 578661.956 412801.7585 435444.2707 401325.2779 597832.1122 0.717426975 0.683259971 0.678769466 0.651537428 0.96793388 0.6904978 0.728372166 0.671300972 1 19.18938087 -1.820061821 2.361858092 1.104280716 0.722412432 0.483768466 0.089711253 8025824.605 4803437.466 4760685.884 0.021342955 0.015133458 1.820061821 -0.381868284 GLNPDGTPALSTLGGFS(ph)PASKPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGTPALSTLGGFS(0.985)PAS(0.017)KPS(0.53)S(0.467)PR 96.134 0.0041212 366410000 123350 112090 110110 122510 84831 127920 149760 136590 98240 TRUE FALSE 117519.49 123512.0984 115158.6524 110195.062 99625.49954 123490.0983 126911.3615 124629.4555 113474.5575 1.035646162 1.088456313 1.014841168 0.971099289 0.87795451 1.088262436 1.118412482 1.098303076 1 16.79200934 GLNPDGTPALSTLGGFS(ph)PASKPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGTPALSTLGGFS(0.999)PAS(0.003)KPS(0.074)S(0.924)PR 202.68 2.54E-25 330720000 421240 328860 338720 397820 269230 402360 424790 410200 313640 TRUE FALSE 401328.82 362371.2079 354250.647 357830.3778 316183.6268 388426.1723 359980.4837 374280.7134 362277.6893 1.107793364 1.00025814 0.977842847 0.987724026 0.872765936 1.072178011 0.993658992 1.033132109 1 18.46673644 4.492955931 2.022761009 0.990621744 1.115176038 0.344387004 0.050181535 0.471193043 3.023747726 0.012356066 0.090370098 31114.00597 -4.492955931 0.124554294 GLNSESMTEETLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLNSESMTEETLKR 14 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 150.37 1.16E-05 554380000 427910 347350 418700 413120 394560 360810 473790 422750 437810 FALSE TRUE 407683.5423 382745.3599 437897.8092 371592.3927 463371.1391 348315.0592 401504.6337 385731.7689 505703.3388 0.806171348 0.75685749 0.865918367 0.734803123 0.916290448 0.688773501 0.793952903 0.762762947 1 18.94793178 -1.200039606 4.865606908 1.000027073 0.788737778 0.511578143 0.064248218 1.62E-05 2.66E-06 0.053298955 0.012561076 0.063089981 1.200039606 -0.211289295 GLPGDVTNQEVHDLLSDYELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLPGDVTNQEVHDLLSDYELK 21 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 144.77 1.25E-07 34024000 107180 134500 99688 139450 97238 107860 127500 120680 87880 FALSE TRUE 102113.8138 148205.7029 104258.7934 125432.2211 114196.2764 104124.7812 108047.5333 110112.6194 101507.9816 1.005968321 1.460039897 1.027099463 1.235688259 1.124998002 1.02577925 1.064424015 1.084768091 1 16.63123365 2.475865184 3.754324835 1.050501728 1.199931191 0.206738988 0.12525039 0.321742531 10.03293159 0.042178374 0.036602487 299.1335908 -2.475865184 0.149429463 GLPPS(ph)MER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER 130.66 0.0010894 2920252000 3217300 2697290 2864803 3345042 4092320 2996294 3626250 3241361 4092190 TRUE FALSE 3065224.605 2972146.918 2996157.051 3008792.023 4806019.312 2892531.587 3072998.962 2957530.247 4726785.925 0.648479676 0.628788137 0.633867727 0.636540785 1.016762635 0.611944698 0.650124421 0.625695831 1 22.1724281 -1.688336205 2.746004892 1.044984292 0.676953742 0.409688214 0.120029514 17113323.78 14961102.17 5353229.217 0.027929786 0.020495749 1.688336205 -0.36803055 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK 30 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 428.63 8.99E-197 260880000 471040 392030 393830 503810 380900 432960 495780 483260 367350 FALSE TRUE 448774.8727 431978.3027 411887.4951 453166.0616 447328.8394 417966.4866 420139.6554 440943.1925 424316.7618 1.057641161 1.018056182 0.970707575 1.067990007 1.054233251 0.985034117 0.990155688 1.039184006 1 18.69478215 2.231865486 24.98044398 1.000787695 1.032456045 0.193825091 0.030235269 257.0074045 958919.865 0.011140686 0.008408516 170.5554046 -2.231865486 0.03166835 GLPSPYNMSS(ph)APGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPSPYNMS(0.075)S(0.925)APGS(1)R;GLPSPYNMS(0.011)S(0.989)APGS(1)R;GLPSPYNMS(0.083)S(0.917)APGS(1)R;GLPSPYNMS(0.001)S(0.999)APGS(1)R;GLPSPYNMS(0.004)S(0.996)APGS(1)R;GLPSPYNMS(0.021)S(0.979)APGS(1)R;GLPSPYNMS(0.016)S(0.984)APGS(1)R;GLPSPYNMS(0.066)S(0.934)APGS(1)R;GLPSPYNMS(0.001)S(0.999)APGS(1)R;GLPSPYNMS(0.004)S(0.996)APGS(1)R;GLPSPYNMS(0.008)S(0.992)APGS(1)R;GLPSPYNMS(0.013)S(0.987)APGS(1)R 224.9 1.57E-12 5179110000 5414720 4857700 5290410 5467120 5955940 5054020 5759730 5237810 6001590 TRUE FALSE 5158776.917 5352705.153 5532980.531 4917554.711 6994654.05 4878998.02 4880977.404 4779159.589 6932285.925 0.744166783 0.772141428 0.798146613 0.709369862 1.008996762 0.703807961 0.704093492 0.689406011 1 22.72489973 4.33394436 1.656420275 0.784034707 0.742578756 0.008683007 0.11777401 3.456216342 15.44511434 0.030138693 0.179287221 21574.67988 -4.33394436 -0.041455951 GLPSPYNMSS(ph)APGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMS(0.081)S(0.919)APGSR;GLPSPYNMS(0.003)S(0.997)APGSR;GLPSPYNMS(0.014)S(0.536)APGS(0.45)R 189.04 2.88E-07 1997610000 772420 652780 766730 786740 824880 733630 857980 750300 799690 TRUE FALSE 735909.2374 719299.0241 801885.3289 707655.4005 968738.8108 708224.2091 727079.3931 684599.7544 923701.8409 0.796695649 0.778713425 0.868121393 0.766108033 1.048757042 0.766723826 0.787136456 0.741147981 1 19.81706772 -2.288192489 2.359026925 1.878618682 0.816407122 0.292983218 0.088185002 5514216.11 1237371.891 25688658.77 0.019881947 0.005150003 2.288192489 -1.06221156 GLPSPYNMSSAPGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMSS(0.005)APGS(0.995)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMS(0.001)S(0.201)APGS(0.799)R 185.14 4.56E-07 1968310000 1973260 1751240 1810160 2057840 2097140 1822670 2154370 1977510 2212950 TRUE FALSE 1879987.91 1929693.347 1893157.626 1850982.014 2462880.552 1759550.481 1825681.289 1804348.741 2556122.984 0.735484138 0.754929774 0.740636362 0.724136524 0.963521931 0.68836691 0.714238439 0.705892773 1 21.28552582 -1.588227932 3.016218547 1.014212886 0.751772762 0.502316022 0.077125352 33459995.42 35960386.49 3787483.851 0.01759415 0.025809053 1.588227932 -0.262440124 GLPSTAS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLPSTASGR 9 0 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GLPSTAS(1)GR 106.35 0.0030939 217900000 245430 231780 240630 261120 235380 234770 289300 287120 302390 TRUE FALSE 233829.0103 255398.6455 251663.1235 234871.7215 276430.1975 226639.856 245161.9716 261978.2507 349283.0968 0.669454126 0.731208146 0.720513319 0.672439416 0.791421629 0.648871526 0.701900475 0.750045602 1 18.4140373 0.755183986 2.96439287 0.999970791 0.705038174 0.845522073 0.039309134 0.532114585 5.993875631 0.033877945 0.008875124 5.690939723 -0.755183986 -0.294932617 GLPVTCEVAPHHLFLSHDDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLPVTCEVAPHHLFLSHDDLER 22 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 192.98 3.05E-18 246320000 257220 226620 244100 271000 291510 240890 302390 235170 19210.1 FALSE TRUE 245061.7204 249712.8356 255292.2264 243758.5651 342349.2517 232547.9189 256254.8517 214577.2681 22189.1042 11.04423677 11.25384934 11.50529666 10.98550726 15.42870991 10.48027522 11.54867945 9.670388952 1 14.4375638 0.592414075 1.495392904 0.99980974 11.74321574 0.860056117 1.35549 0.55855616 1.648071998 1.211851399 0.35150744 3.912137176 -0.592414075 10.743406 GLPWSCS(ph)VEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 GLPWS(0.015)CS(0.985)VEDVQNFLSDCTIHDGAAGVHFIYTR;GLPWS(0.132)CS(0.868)VEDVQNFLSDCTIHDGAAGVHFIYTR 240.91 1.12E-46 203507000 110854 91333 109848 107002 89469 115406 129619 119550 56205 TRUE FALSE 105614.1511 100639.9365 114884.6395 96245.95567 105072.3653 111409.4613 109843.2409 109081.5682 64920.98434 1.626810687 1.550191168 1.769607171 1.482509186 1.618465375 1.71607782 1.691952795 1.680220492 1 15.98639725 -1.616733893 7.320724934 0.999001431 1.638507761 0.858281662 0.081971803 0.001290854 6.76E-05 0.07668791 0.018052416 0.024169413 1.616733893 0.63950633 GLPWSCSADEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 219.5 5.20E-11 703434000 326594 271024 284678 331441 334538 289544 360940 325491 342182 FALSE TRUE 311156.5489 298641.6537 297730.7679 298123.921 392881.3213 279517.0187 305871.9739 296989.2825 395245.8369 0.787248137 0.755584565 0.753279959 0.754274664 0.994017608 0.707197882 0.773877788 0.751403949 1 18.59239074 -2.113092342 2.152099325 1.380934087 0.782471302 0.433464166 0.077351911 4255691.506 1094613.921 7925458.072 0.017386552 0.007707396 2.113092342 -0.598462785 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 291.12 9.79E-90 46380000 6098 5564.3 5286 7147 6748.2 6491.5 7520.5 6169.4 4009.4 FALSE TRUE 5809.759625 6131.308496 5528.368329 6428.569982 7925.083943 6266.697727 6373.109602 5629.17463 4631.157275 1.254494132 1.323925778 1.193733661 1.388113078 1.711253467 1.353160205 1.376137588 1.21550064 1 12.17715704 0.952720505 2.783927322 1.000613147 1.365081667 0.442999485 0.135139695 0.297034515 5.453950502 0.132030904 0.035048922 8.968514302 -0.952720505 0.36446852 GLQDVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLQDVLR 7 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 87.323 0.07338 0 192550 148860 89871 98075 264780 102420 218170 153240 230910 FALSE TRUE 183448.5431 164029.0032 93991.67424 88216.31467 310957.5482 98873.16972 184884.1595 139821.4932 266718.3435 0.687798749 0.614989585 0.352400487 0.330747085 1.165864875 0.370702549 0.693181268 0.52422901 1 18.02495752 GLQEFLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLQEFLDR 8 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;;; 176.6 0.00060335 211163000 492858 440471 461427 495221 750660 428661 538415 489234 630750 FALSE TRUE 469561.5791 485355.4957 482583.8844 445440.4442 881574.8663 413816.3621 456269.9031 446394.0774 728563.4886 0.644503309 0.66618147 0.662377256 0.611395508 1.210017905 0.567989432 0.626259633 0.612704431 1 19.47469517 GLQEVGLPLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLQEVGLPLHR 11 0 P11172-2;P11172-3;P11172 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 107.18 0.0017245 0 72670 74312 64560 75356 75659 65007 76998 73613 75355 FALSE TRUE 69235.03312 81884.47729 67520.13986 67781.07171 88853.90565 62755.79129 65250.54093 67167.05547 87040.66854 0.79543315 0.940761125 0.775730943 0.778728758 1.020832068 0.720993903 0.749655788 0.771674398 1 16.40940202 GLQLT(ph)PGIGGMQQHFFDDEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDR 172.83 1.87E-11 30686000 36320 40466 28022 45845 43074 32697 32592 30235 27441 TRUE FALSE 34603.22558 44589.53141 29306.83642 41236.5735 50586.09196 31564.69469 27619.49181 27587.46311 31696.41013 1.091708034 1.406769133 0.924610588 1.300985611 1.595956506 0.995844468 0.871376023 0.87036554 1 14.95203183 2.019014197 24.96474078 0.908119216 1.257550499 0.460620204 0.178960462 196.9346301 258564.7682 0.064145124 0.047367528 104.4754372 -2.019014197 0.349431283 GLQPGEEELPDIS(ph)PPIVIPDDSKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLQPGEEELPDISPPIVIPDDSKDR 25 1 Q92995-2;Q92995 Q92995-2 USP13 Ubiquitin carboxyl-terminal hydrolase 13 1 GLQPGEEELPDIS(1)PPIVIPDDSKDR;GLQPGEEELPDIS(1)PPIVIPDDSKDR;GLQPGEEELPDIS(1)PPIVIPDDSKDR 131.1 5.10E-05 91600000 89140 75492 76500 88942 59724 83912 95864 90403 64704 TRUE FALSE 84926.52886 83184.72063 80007.60067 80001.38118 70139.84669 81006.1064 81238.18614 82486.83406 74737.96586 1.136323793 1.113018259 1.070508138 1.070424921 0.938476795 1.083868225 1.086973471 1.10368048 1 16.18955368 3.72866711 1.960969886 1.051918793 1.130427388 0.305022479 0.048117864 0.418824217 3.14449053 0.013906237 0.02863428 5353.86123 -3.72866711 0.078508595 GLQSIFQEQGMAESVHTWQDHGYLATYTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLQSIFQEQGMAESVHTWQDHGYLATYTNK 30 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 182.51 3.56E-18 175180000 87253 69023 74325 89425 89183 88106 109580 92455 17673 FALSE TRUE 83128.72361 76056.52217 77732.87477 80435.8291 104736.487 85054.86713 92861.55843 84359.15007 20413.63858 4.072214921 3.725769998 3.807889244 3.940298482 5.130711341 4.166570639 4.548995911 4.132489646 1 14.31724573 2.982458313 24.06200124 4.131482791 3.867971642 0 1.107837637 2873.105922 3941057.027 0.291898629 0.316092457 960.4136263 -2.982458313 -0.263511149 GLQTSQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLQTSQDAR 9 0 P27797 P27797 CALR Calreticulin 0 ; 107.9 0.0062771 330753000 397557 314271 302914 363226 427471 304546 346900 424115 358740 FALSE TRUE 378765.2685 346295.5722 316802.9065 326713.8324 502021.8071 293999.4957 293974.0337 386977.2422 414371.567 0.914071569 0.835712679 0.764538235 0.788456203 1.21152571 0.709506923 0.709445476 0.933889468 1 18.66056549 -0.804134885 7.104629201 0.999999766 0.848308728 0.081044975 0.146394754 0 2.86E-10 0.136164089 0.032094184 0.156987515 0.804134885 -0.151691039 GLQVDLQS(ph)DGAAAEDIVASEQSLGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLQVDLQSDGAAAEDIVASEQSLGQK 26 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 GLQVDLQS(1)DGAAAEDIVASEQSLGQK 98.766 0.0036883 33013000 18659 16173 19651 17780 16147 16434 18440 16669 19282 TRUE FALSE 17777.02605 17821.04709 20552.01779 15992.72062 18963.03169 15864.88646 15626.63933 15209.37399 22272.15408 0.798172731 0.800149237 0.922767403 0.718058997 0.851423334 0.712319356 0.701622271 0.682887427 1 14.44295348 2.23524094 24.98715946 0.742907323 0.814060667 0.002965021 0.102856168 189.3976542 1425571.887 0.033240735 0.02556355 171.8861722 -2.23524094 0.071153345 GLS(ph)ASLPDLDSENWIEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLS(0.548)AS(0.452)LPDLDSENWIEVK 97.836 0.0013987 8001600 27836 27517 27839 29226 24255 29495 32764 33334 24648 TRUE FALSE 26520.24745 30321.01358 29115.44569 26288.14695 28485.06432 28473.58075 27765.25005 30415.09825 28470.28596 0.931506185 1.065005586 1.02266081 0.923353808 1.00051908 1.000115728 0.975236079 1.068310248 1 14.79716936 1.254184593 24.99963483 1.034155153 0.991336948 0.155699112 0.043923477 407.1802776 651526.8221 0.028404559 0.010298354 17.95496625 -1.254184593 -0.042818205 GLS(ph)GEEEDDEPDCCNDER ddPTM_SK-BR-3_Trastuzumab_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 436.76 1.39E-169 619510000 704200 790720 686370 772650 589690 722300 643110 690450 574370 TRUE FALSE 670913.8616 871295.267 717840.7434 694981.7541 692531.7493 697286.5699 544991.758 629990.5377 663440.3661 1.011264758 1.313298544 1.081997388 1.04754216 1.043849281 1.051016196 0.821463067 0.949581258 1 19.33960727 2.525756474 1.0584585 0.914934102 1.152783745 0.405030398 0.094410628 0.414518291 0.942923707 0.055356749 0.041041372 335.5494059 -2.525756474 0.237849644 GLS(ph)GPCRPPPPPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLSGPCRPPPPPQAR 15 1 Q9UEE5 Q9UEE5 STK17A Serine/threonine-protein kinase 17A 1 GLS(1)GPCRPPPPPQAR 74.543 0.020887 119600000 69482 52886 53732 63969 64918 57717 75048 62020 75352 TRUE FALSE 66197.72356 58275.14353 56195.66535 57538.71459 76239.67865 55718.24582 63598.04925 56589.20001 87037.20332 0.760568137 0.669542923 0.645651092 0.661081841 0.875943571 0.640165857 0.730699595 0.650172545 1 16.40934458 -1.574806779 3.171720167 1.013172822 0.705581 0.623746641 0.072186244 24682157.07 27887714.9 2732238.203 0.01588853 0.026619091 1.574806779 -0.307591822 GLS(ph)GSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLSGSTSR 8 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 GLS(0.603)GS(0.379)T(0.017)S(0.001)R;GLS(0.578)GS(0.41)T(0.012)SR 78.113 0.033007 501854000 310086 283680 311512 338399 301462 261783 349886 299471 335186 TRUE FALSE 295428.8493 312587.3145 325795.1333 304382.4896 354036.8774 252717.3891 296504.4646 273247.7316 387164.933 0.763056837 0.807375069 0.841489261 0.786183003 0.914434256 0.652738323 0.765835021 0.705765704 1 18.56258876 2.24180181 24.99999851 0.758141004 0.814251181 0.015526613 0.098116949 221.0431232 1704967.052 0.030704642 0.024695351 174.5025629 -2.24180181 0.056110177 GLS(ph)LDSFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GLSLDSFLR 9 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GLS(0.998)LDS(0.002)FLR;GLS(1)LDSFLR;GLS(1)LDSFLR;GLS(1)LDSFLR;GLS(0.999)LDS(0.001)FLR;GLS(0.999)LDS(0.001)FLR 169.76 0.00039616 112181000 387674 312494 333595 433660 462756 387971 487297 413602 565186 TRUE FALSE 369349.4183 344337.4939 348890.6607 390067.6729 543460.4999 374535.467 412950.8928 377384.8162 652832.1583 0.565764743 0.527451795 0.534426278 0.597500702 0.832465884 0.573708666 0.632552927 0.578073263 1 19.3163526 -5 0.213782971 2.941128645 0.545625601 0.677979914 0.085709172 87.12784996 0.869689499 72.72078286 0.171966423 1.00E-05 5 -2.395503043 GLS(ph)SAGGGSPHREDAQPEHSASAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLS(0.493)S(0.39)AGGGS(0.118)PHREDAQPEHSASAR;GLS(0.382)S(0.382)AGGGS(0.236)PHREDAQPEHSASAR 184.66 1.54E-17 346260000 235590 218155 242221 297599 293429 250540 305804 271666 200674 TRUE FALSE 224454.1276 240385.2425 253327.0724 267683.7831 344602.9247 241863.737 259147.9833 247877.4848 231793.499 0.968336595 1.03706637 1.092899816 1.15483732 1.486680714 1.043444868 1.118012302 1.069389288 1 17.82248058 3.710245431 2.074379536 1.155354788 0.990847966 0.165478792 0.13195403 0.50950541 4.286943398 0.037064929 0.073303977 5131.512972 -3.710245431 -0.164506822 GLSAS(ph)LPDLDSENWIEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.014)AS(0.986)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK;GLS(0.01)AS(0.99)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK 444.62 1.12E-190 9031380000 11175050 10051995 9887872 11574052 7855166 11135192 12605164 12752391 9509473 TRUE FALSE 10646827.53 11076304.72 10341240.71 10410606.3 9225104.463 10749577.51 10682014.72 11635724.04 10984153.51 0.969289762 1.008389469 0.941469063 0.947784124 0.839855748 0.978644144 0.972493212 1.05931914 1 23.38892036 1.446338474 3.282374222 1.028772348 0.952579054 0.337530424 0.045930444 0.301330021 6.002986667 0.035684231 0.012377547 27.94721098 -1.446338474 -0.076193293 GLSAS(ph)LPDLDSENWIEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLSASLPDLDSENWIEVKK 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLS(0.016)AS(0.984)LPDLDSENWIEVKK;GLS(0.006)AS(0.994)LPDLDSENWIEVKK;GLSAS(1)LPDLDSENWIEVKK 250.84 1.05E-25 833040000 1514270 970750 1566060 1301130 1264280 1541170 2131610 1928810 1741450 TRUE FALSE 1442693.458 1069670.529 1637865.4 1170337.94 1484770.032 1487798.896 1806393.745 1759913.171 2011505.172 0.717220854 0.531776176 0.814248665 0.581821989 0.738138809 0.739644579 0.898030873 0.874923513 1 20.93984402 1.726599642 0.836805652 0.987709641 0.645773745 0.67779073 0.080055214 0.294361126 0.394696651 0.064767166 0.028298465 53.28434624 -1.726599642 -0.341935897 GLSDHVS(ph)LDGQELGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLSDHVSLDGQELGTR 16 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR 231.39 8.91E-16 281440000 500042 408207 474674 529189 557215 468969 573470 524095 514047 TRUE FALSE 476406.0056 449803.7574 496438.2724 475993.9163 654393.1196 452728.4859 485976.619 478202.4634 593762.7834 0.802350735 0.757547913 0.836088563 0.801656705 1.102112052 0.762473666 0.818469316 0.805376283 1 19.17952714 -5 0.165996169 1.60323409 0.789078308 0.205037649 0.098530777 213.5404001 1.994662827 43.10558542 0.366924641 1.00E-05 5 -0.814155782 GLSEDTTEETLKESFDGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 253.31 3.86E-36 1465610000 3397850 2521990 3256760 3591390 2761960 3405830 3997330 3748150 3179380 FALSE TRUE 3237240.364 2778983.648 3406085.667 3230376.654 3243644.95 3287885.253 3387463.892 3419942.116 3672422.012 0.881500098 0.756716858 0.927476651 0.879631111 0.883244066 0.895290694 0.922405944 0.931249759 1 21.80830042 1.770807579 0.288397617 1.01328548 0.807696021 0.534889315 0.041774029 1.137673987 0.336899356 0.077026873 0.085663655 58.99396396 -1.770807579 -0.205589459 GLSHS(ph)PWAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLSHSPWAVKK 11 1 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 1 GLS(0.357)HS(0.643)PWAVKK 77.204 0.020369 278770000 423560 422120 464390 472100 387060 492280 636420 555950 450150 TRUE FALSE 403539.1582 465134.5079 485682.7408 424643.6111 454563.1415 475232.2202 539322.4403 507268.0707 519956.963 0.776101076 0.894563476 0.934082579 0.816689921 0.874232242 0.91398376 1.037244385 0.975596264 1 18.98803269 1.974232041 3.055433429 1.006215218 0.858164875 0.684694287 0.044775532 0.147219659 2.620381974 0.022226381 0.012728598 94.23929761 -1.974232041 -0.148050343 GLSSAGGGS(ph)PHREDAQPEHSASAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLSS(0.002)AGGGS(0.998)PHREDAQPEHSASAR;GLS(0.005)S(0.027)AGGGS(0.967)PHREDAQPEHSASAR;GLSSAGGGS(0.999)PHREDAQPEHSASAR 240.33 9.28E-38 1462760000 862750 854170 944690 998680 1026910 900010 1100380 941180 646940 TRUE FALSE 821969.5173 941210.8941 988004.9709 898290.789 1206002.779 868842.428 932496.8211 858765.2897 747264.1511 1.099971832 1.259542416 1.322162945 1.202106093 1.613890854 1.162697858 1.247881114 1.149212482 1 19.51125879 0.964623015 1.524589218 1.001208692 1.27047579 0.30535401 0.135728514 0.574309481 2.722622695 0.123915568 0.036412231 9.217709451 -0.964623015 0.269267098 GLSTS(ph)LPDLDSEPWIEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLSTSLPDLDSEPWIEVK 18 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 GLS(0.014)T(0.109)S(0.877)LPDLDSEPWIEVK;GLS(0.007)T(0.081)S(0.913)LPDLDSEPWIEVK;GLST(0.01)S(0.99)LPDLDSEPWIEVK;GLS(0.001)T(0.01)S(0.989)LPDLDSEPWIEVK 262.23 8.33E-31 192822000 430527 399228 394478 456412 325927 425922 475592 476587 366030 TRUE FALSE 410176.8419 439909.7871 412565.2065 410532.5986 382768.5656 411172.2143 403031.7056 434854.5157 422792.063 0.970162115 1.040487336 0.975811144 0.971003561 0.905335268 0.972516398 0.953262232 1.028530462 1 18.68958877 5.101593064 19.7778864 0.979635213 0.000733448 0.006926227 0.037806927 3016.545662 611433.0411 0.008979908 5483.192732 126355.184 -5.101593064 -0.978901766 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR 33 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 181.56 3.63E-20 3772220000 1860370 1801260 1978940 2177560 2694080 2013520 2660050 1466340 70155 FALSE TRUE 1772433.997 1984810.442 2069676.356 1958667.532 3163926.699 1943791.298 2254210.517 1337939.496 81034.2791 21.87264472 24.49346701 25.54075114 24.17085156 39.04429995 23.98727204 27.81798694 16.51078421 1 16.30624471 0.939384781 2.893691065 1.027571534 26.40068567 0.755651415 4.713506077 0.149738133 2.974373664 4.408976134 1.163712385 8.697306616 -0.939384781 25.37311414 GLTLAPGLS(ph)PARPLFGSDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLTLAPGLSPARPLFGSDFEK 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 GLTLAPGLS(1)PARPLFGSDFEK 103.63 0.00026247 69784000 136680 170300 146060 174640 106010 137900 156110 158690 119740 TRUE FALSE 130219.4073 187653.7636 152756.9955 157084.8554 124498.1104 133124.4884 132292.5523 144794.2623 138308.6677 0.94151299 1.356775152 1.10446437 1.135755684 0.900146842 0.962517322 0.956502254 1.046892178 1 17.07753205 2.799530363 7.515751125 0.968655442 1.149210912 0.362093103 0.105600539 0.28356384 31.24333543 0.031414575 0.033283973 630.2754086 -2.799530363 0.180555469 GLTLNSNAWMNDTVIIDSTVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLTLNSNAWMNDTVIIDSTVGK 22 0 Q14CN2 Q14CN2 CLCA4 "Calcium-activated chloride channel regulator 4;Calcium-activated chloride channel regulator 4, 110 kDa form;Calcium-activated chloride channel regulator 4, 30 kDa form" 0 43.116 0.065694 122180000 262970 267680 291320 233490 134090 335410 235410 239090 40423 FALSE TRUE 250539.9293 294956.8963 304677.3102 210019.1416 157475.2535 323794.6676 199493.8809 218154.0121 46691.59239 5.36584675 6.317130799 6.525314186 4.49800769 3.3726683 6.934753154 4.272586791 4.672233285 1 15.51087517 3.225069408 23.84275304 4.441227149 6.02199702 0.257465069 1.492854378 191.1904033 337886.1001 0.38896622 0.467689832 1679.072342 -3.225069408 1.580769871 GLTMLDHEQVTPEDPGAQFLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 185.71 3.45E-17 168953000 219605 198715 209612 223897 258230 203935 244134 243581 221161 FALSE TRUE 209224.7069 218964.2844 219222.9175 201390.4482 303265.2302 196872.6798 206886.8745 222251.7563 255457.5183 0.81901957 0.857145587 0.858158018 0.78835201 1.187145449 0.770667002 0.80986802 0.870014544 1 17.96272387 -2.675277689 1.868028883 3.483191958 0.864025328 0.106180186 0.117343277 4189851.18 129164.9901 44279355.64 0.026768784 0.002112138 2.675277689 -2.61916663 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_SK-BR-3_Trastuzumab_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 269.16 1.66E-31 285920000 402050 394950 394540 428410 418610 370580 417740 409840 414510 TRUE FALSE 383045.8933 435195.854 412630.0493 385345.4129 491615.4515 357746.7217 354006.0907 373952.2369 478790.0938 0.800028861 0.908949161 0.861818268 0.804831633 1.026787016 0.747189063 0.739376389 0.781035869 1 18.86903378 GLVDRPLALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GLVDRPLALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 163.64 5.84E-06 1726880000 1362740 1011170 843970 967580 1582870 914420 1446850 1115000 1405070 FALSE TRUE 1298325.981 1114209.373 882666.8593 870317.0201 1858922.027 882753.4061 1226106.459 1017364.689 1622961.079 0.799973577 0.686528708 0.543862 0.536252552 1.14538916 0.543915327 0.755474962 0.626857108 1 20.63019697 GLVETAAHLGYSVVAINHIVDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLVETAAHLGYSVVAINHIVDFK 23 0 P78346;P78346-2 P78346 RPP30 Ribonuclease P protein subunit p30 0 ; 208.39 5.93E-25 61509700 117267 105781 102859 121893 96928 108064 126559 113810 64896 FALSE TRUE 111724.0213 116560.2042 107575.1869 109640.0841 113832.2125 104321.7166 107250.1001 103844.1931 74959.74024 1.490453688 1.554970759 1.435106186 1.462652935 1.518578001 1.391703283 1.430769368 1.385332883 1 16.19382833 -3.196142742 0.226601904 1.70E-08 1.536977001 0.939143203 0.037871561 12.6867646 0.263941746 6.022729808 0.06522351 0.000636586 3.196142742 1.536976984 GLVGEIIKR ddPTM_SK-BR-3_Trastuzumab_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 8145300000 9404500 8360600 8303900 9420600 8104300 8560700 10123600 8687900 8875800 FALSE TRUE 8959967.923 9212554.645 8684642.029 8473623.39 9517687.354 8264240.812 8579058.887 7927141.419 10252213.73 0.873954461 0.898591747 0.847099198 0.826516459 0.928354363 0.806093301 0.836800628 0.773212657 1 23.28943212 2.215097866 24.99922815 0.838812021 0.874584064 0.001108644 0.064887368 642.840094 684932.6395 0.021429132 0.015835196 164.0959512 -2.215097866 0.035772043 GLVGPELHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 171.85 3.89E-06 1960640000 2158490 1928320 1890640 2104770 2438860 1935680 2169030 2105610 2215820 FALSE TRUE 2056462.455 2124818 1977327.714 1893194.521 2864196.412 1868646.916 1838104.637 1921231.626 2559438.049 0.803482021 0.830189268 0.772563225 0.739691481 1.119072373 0.730100468 0.71816727 0.75064588 1 21.28739566 -0.549077276 7.514685674 1 0.80586566 0.213400657 0.115789289 0 0 0.107058455 0.02523392 0.282437738 0.549077276 -0.19413434 GLVLDHGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;; 193.41 3.36E-05 6652630000 5545650 5735410 5048750 5819180 6633390 5266750 6567260 5729670 6713560 FALSE TRUE 5283518.115 6319854.8 5280240.181 5234224.971 7790251.116 5084361.127 5565303.871 5227949.72 7754664.597 0.681334189 0.814974616 0.680911484 0.674977609 1.004589047 0.655651971 0.717671771 0.674168387 1 22.88663295 -1.606390478 3.050970296 1.016304363 0.740515693 0.381646871 0.104750965 806907118.1 785128810.4 104231486.1 0.023217757 0.024751956 1.606390478 -0.27578867 GLVMVKPGSIKPHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLVMVKPGSIKPHQK 15 2 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 189.09 1.63E-07 2016270000 3735500 2581300 2770900 3088500 2707200 2568300 3691900 3464800 3126800 FALSE TRUE 3558930.318 2844337.405 2897948.506 2778038.112 3179334.823 2479359.127 3128632.849 3161403.744 3611688.175 0.985392466 0.787536816 0.802380595 0.769179945 0.880290509 0.686482057 0.866252206 0.875325773 1 21.78424191 0.868106006 2.114869891 0.99921926 0.826090799 0.337405343 0.077741786 0.605808862 5.348461444 0.07205091 0.019830688 7.380843652 -0.868106006 -0.173128461 GLVQALGLSNFNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLVQALGLSNFNSR 14 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 142.91 2.16E-05 62075000 93056 73141 87073 92481 92257 79548 97399 95047 106250 FALSE TRUE 88657.4273 80594.15105 91065.38318 83184.63418 108346.5916 76793.23281 82538.99369 86724.1808 122726.7074 0.72239718 0.656696108 0.742017652 0.677803845 0.882828147 0.62572552 0.672543047 0.706644729 1 16.90508971 -1.785987566 2.342988057 1.092805838 0.705484628 0.629209137 0.069654684 4144816.045 2605039.68 2194708.436 0.016291203 0.016368634 1.785987566 -0.38732121 GLVQALQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLVQALQTK 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 0 148.52 0.00020894 123330000 267540 225880 195820 225560 256280 226810 319600 281660 292390 FALSE TRUE 254893.9144 248897.4288 204798.5407 202886.2803 300975.1509 218955.5128 270839.1501 256996.3572 337732.3479 0.754721649 0.736966507 0.606393027 0.600730968 0.891164713 0.648310753 0.801934289 0.760946823 1 18.36552084 0.254038266 0.570096808 1.014362652 0.706141885 0.524949523 0.085467693 2.173762978 1.014598361 0.151736386 0.035308596 1.794891767 -0.254038266 -0.308220766 GLVVDMDGFEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLVVDMDGFEEER 13 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 163.78 8.88E-05 44420000 90057 74714 77529 88181 98206 75832 90669 81431 100400 FALSE TRUE 85800.18409 82327.44154 81083.78134 79316.87835 115333.0953 73205.91883 76835.7788 74300.46995 115969.5192 0.739851167 0.709905862 0.699181836 0.68394591 0.994512145 0.631251378 0.662551499 0.640689644 1 16.82338614 -2.082810961 2.405054009 1.444860525 0.718777331 0.422504578 0.102777828 5509455.765 1585398.021 13444984.93 0.025162452 0.008263976 2.082810961 -0.726083195 GLVYETSVLDPDEGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 241.17 1.59E-19 260493000 641780 551482 588966 574900 697820 486128 615590 591470 673010 FALSE TRUE 611444.3313 607678.6428 615970.6737 517109.9598 819519.5871 469293.2655 521670.4394 539677.7512 777376.9535 0.786548056 0.78170396 0.792370639 0.66519847 1.054211324 0.603688164 0.671064967 0.694229162 1 19.56825481 GLWHEEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLWHEEMK 8 0 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 83.265 0.018284 155090000 185660 200830 174170 197890 152140 178450 206320 228490 154130 FALSE TRUE 176884.2197 221294.8053 182155.8668 177997.7212 178673.1678 172270.2318 174842.0947 208482.2043 178031.6932 0.993554667 1.243007924 1.02316539 0.99980918 1.003603148 0.967638001 0.982084097 1.171039833 1 17.44177457 3.516158651 24.8804972 1.012740292 1.120748895 0.193796455 0.081357525 638.973168 407248.2439 0.020422227 0.031631588 3282.151708 -3.516158651 0.108008603 GLWPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLWPLR 6 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 102.29 0.082972 135090000 234690 163340 191540 235070 281900 184650 283490 260800 282510 FALSE TRUE 223596.6688 179984.5317 200322.2985 211440.317 331063.2707 178255.5242 240238.3938 237962.9694 326320.2079 0.68520632 0.551558032 0.613882602 0.647953488 1.014534996 0.546259532 0.736204464 0.729231484 1 18.31592881 -4.999999998 0.14148857 2.123717367 0.56505338 0.388975261 0.128045145 136.7163148 1.179776207 43.15802639 0.717683278 1.00E-05 4.999999998 -1.558663987 GLWSTDS(ph)AEEDKETKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLWSTDSAEEDKETKR 16 2 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GLWS(0.002)T(0.009)DS(0.989)AEEDKETKR 61.959 0.042191 439340000 78863 70789 69127 88946 53512 84549 81200 90594 61401 TRUE FALSE 75135.30228 78002.47958 72296.54133 80004.97909 62844.47586 81621.04693 68811.44866 82661.10909 70922.75349 1.059396295 1.099823057 1.019370199 1.128057995 0.886097518 1.150844305 0.970230924 1.165509023 1 16.11396093 GLYGIKDDVFLSVPCILGQNGISDLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GLYGIKDDVFLSVPCILGQNGISDLVK 27 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 285.36 1.75E-61 523910000 1865720 1607480 1720450 1959730 1368840 1973010 2213780 2092760 1518140 FALSE TRUE 1777531.113 1771284.04 1799334.334 1762734.217 1607565.263 1904684.169 1876027.202 1909506.84 1753565.398 1.01366685 1.010104352 1.026100502 1.005228673 0.916740981 1.086178007 1.069835892 1.088928216 1 20.7418598 2.170359129 24.99999734 1.068036323 1.000199957 0.418018311 0.038498035 47.05262861 17246.83368 0.013379251 0.009881234 148.0332006 -2.170359129 -0.067836366 GLYNEHTVDRAPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GLYNEHTVDRAPLR 14 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 55.335 0.080228 68867000 273960 235540 285210 295970 460030 209900 335700 223640 527840 FALSE TRUE 261010.4537 259541.7938 298287.1606 266218.5333 540259.0863 202631.1104 284482.7994 204056.896 609694.7314 0.428100228 0.425691384 0.489240181 0.436642339 0.886114081 0.332348469 0.46659875 0.334686993 1 19.21772755 -1.282622273 4.970942494 1.000129548 0.472459946 0.532076787 0.154731405 0.000227492 3.28E-05 0.138711036 0.032685716 0.052164822 1.282622273 -0.527669602 GMAFLHTLEPLIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GMAFLHTLEPLIPR 14 0 A0A0A0MTH3;Q13418;Q13418-3;Q13418-2 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 156.69 2.96E-07 0 100200 90367 88731 104020 117260 91555 114780 105180 102370 FALSE TRUE 95463.74458 99575.50004 92799.40412 93563.71197 137710.1069 88384.42739 97268.20292 95969.88161 118245.0168 0.807338416 0.842111598 0.784806046 0.79126981 1.164616579 0.747468518 0.822598749 0.811618825 1 16.85141986 -2.364608651 2.20072021 1.991695914 0.843746928 0.146957123 0.116075866 5259747.085 506721.7626 26113516.28 0.026737545 0.004319081 2.364608651 -1.147948986 GMDDDRGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GMDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 98.582 0.0053959 2011840000 3258200 3234220 2789190 3555700 3408580 3013300 3406000 3110730 3547550 FALSE TRUE 3104191.343 3563790.695 2917077.12 3198274.281 4003035.273 2908948.665 2886352.145 2838337.99 4097685.936 0.757547404 0.869708111 0.711884016 0.780507421 0.976901436 0.709900346 0.704385888 0.692668505 1 21.96637798 -1.685402438 9.051404962 1.000314496 0.778606573 0.38949529 0.088276052 0.000555984 1.93E-05 0.084823448 0.019965576 0.020634672 1.685402438 -0.221707923 GMFTAEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GMFTAEDLR 9 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ; 96.492 0.017057 83322000 293470 246490 198441 225060 342930 209425 319750 270700 345100 FALSE TRUE 279598.2547 271607.6112 207539.7161 202436.5412 402736.8834 202172.5597 270966.2649 246996.0729 398616.3455 0.701421951 0.681376001 0.520650291 0.507848069 1.010337102 0.507185824 0.679767069 0.619633579 1 18.60464134 -1.151383002 4.532437446 1.000048948 0.656407318 0.356389462 0.146280137 19090593.03 4849618.867 9288.395543 0.030996471 0.070569493 1.151383002 -0.343641631 GMGEAVQEFVDKEEKDAIEELVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GMGEAVQEFVDKEEKDAIEELVK 23 2 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 157.07 5.98E-09 36039000 97115 74542 80460 96565 42600 102731 96461 109431 40998 FALSE TRUE 92524.56641 82137.91455 84149.17059 86858.10274 50029.42651 99173.39971 81744.10282 99848.64151 47355.76045 1.953818617 1.734486233 1.776957434 1.834161291 1.056459152 2.094220402 1.726170207 2.108479318 1 15.53125231 4.693314321 0.959111724 1.691781177 2.082517413 0.055247461 0.371762293 6.428404985 4.928913024 0.106985865 2.575842321 49353.08679 -4.693314321 0.390736236 GMGS(ph)LDAMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GMGSLDAMDK 10 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 GMGS(1)LDAMDK 131.12 0.00017224 116230000 435920 440780 378990 513550 318830 455790 474210 478150 310460 TRUE FALSE 415314.9255 485695.9831 396367.0664 461926.9783 374433.8511 440005.878 401860.555 436280.6512 358604.5512 1.158141814 1.354405519 1.10530406 1.28812358 1.04414138 1.226994684 1.120623131 1.216606565 1 18.45203427 -5 0.117724947 0.350123831 1.297263536 0.301058562 0.090239548 163.8538817 1.258003644 25.29607302 0.812747655 1.00E-05 5 0.947139705 GMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.618)GS(0.382)PQLNNR;GMKDDKEEEEDGT(0.531)GS(0.469)PQLNNR 80.293 0.0088449 161957000 196044 183032 162543 213583 92272 214408 186483 217928 96400 TRUE FALSE 186777.3886 201683.1689 169995.7573 192113.2311 108364.2076 206982.9972 158031.5934 198845.069 111349.2197 1.677401864 1.811267017 1.526690154 1.725321755 0.97319234 1.858863473 1.419242935 1.785778738 1 16.76473192 -2.937417959 0.209783866 2.87E-17 1.709791798 0.320532827 0.262939594 61.60506462 1.332545564 28.97579111 0.543244491 0.001155 2.937417959 1.709791798 GMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.169)GS(0.831)PQLNNR;GMKDDKEEEEDGT(0.035)GS(0.965)PQLNNR;GMKDDKEEEEDGT(0.05)GS(0.95)PQLNNR;GMKDDKEEEEDGT(0.005)GS(0.995)PQLNNR;GMKDDKEEEEDGT(0.398)GS(0.602)PQLNNR;GMKDDKEEEEDGT(0.003)GS(0.997)PQLNNR;GMKDDKEEEEDGT(0.021)GS(0.979)PQLNNR 256.73 9.70E-37 6519985000 4199612 4111158 3554869 4729609 1923562 4684843 4168431 4722317 1985096 TRUE FALSE 4001104.664 4530089.674 3717863.26 4254179.718 2259030.604 4522605.712 3532460.292 4308805.889 2292934.549 1.744971162 1.975673347 1.621443255 1.855342848 0.985213732 1.972409423 1.540584878 1.879166542 1 21.12876374 -2.563705046 0.248897156 1.80E-16 1.794958983 0.342804558 0.293853927 49.04144385 1.430553132 27.91560122 0.41367754 0.002730832 2.563705046 1.794958983 GMLPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GMLPHK 6 0 P40429;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 91.321 0.048025 1999320000 4971800 3943600 3992600 4727300 4699300 4325200 5890400 5259800 4660300 FALSE TRUE 4736792.867 4345457.324 4175664.659 4252102.823 5518856.432 4175417.239 4991711.295 4799224.028 5382995.522 0.879954822 0.807256351 0.775713939 0.78991387 1.025238904 0.775667976 0.927311062 0.89155267 1 22.35997779 0.969956096 0.429792755 1.006463391 0.82436916 0.318703952 0.074227725 1.478274301 0.714813421 0.098220246 0.04953776 9.331599599 -0.969956096 -0.182094231 GMQLMHANAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GMQLMHANAQR 11 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 ;;;;;;; 126.67 0.00030261 436812000 562410.2 433087 353396.9 412928.2 643374 393522.4 641431 478262 570174 FALSE TRUE 535826.1844 477219.0577 369600.4974 371419.8728 755578.2219 379894.6206 543568.9203 436382.8439 658593.6719 0.813591456 0.724603163 0.561196551 0.563959067 1.14726007 0.576827013 0.825347925 0.662597991 1 19.32902912 GMWSEGNGSHTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GMWSEGNGSHTIR 13 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 257.76 6.54E-24 3497350000 3435470 3082485 3054722 3204560 2898377 3396887 3719069 3447785 3094308 FALSE TRUE 3273082.142 3396593.726 3194784.025 2882431.541 3403853.031 3279251.951 3151656.719 3145878.668 3574157.481 0.91576327 0.950320109 0.893856536 0.806464616 0.952351162 0.917489498 0.88179011 0.880173491 1 21.76917177 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 201.21 7.29E-22 2910220000 7175360 8832790 5527110 8991380 3034291 8097070 6048540 8106630 2581102 TRUE FALSE 6836194.953 9732861.343 5780533.461 8087549.4 3563470.39 7816666.436 5125724.134 7396770.501 2981366.116 2.292973988 3.264564285 1.938887489 2.712699174 1.195247498 2.621840503 1.719253502 2.481000392 1 21.50754212 0.08073044 0.13616074 1.52E-10 3.279351788 0.345669509 0.563918206 16.77470337 0.817904337 13.14749521 5.565851372 1.204288224 -0.08073044 3.279351788 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK 160.41 9.94E-12 3526540000 6166070 5750240 5113970 6577980 2181435 6895590 6125370 7352750 2260571 TRUE FALSE 5874612.091 6336195.993 5348450.583 5916748.953 2561876.573 6656793.989 5190832.306 6708904.231 2611128.805 2.249836193 2.426611809 2.048328896 2.265973605 0.981137571 2.549393188 1.987964859 2.569350167 1 21.3162422 3.390721279 2.208551122 1.941285422 2.328684159 0.096229386 0.547130169 0.746230209 7.382241044 0.150341413 0.226740787 2458.789099 -3.390721279 0.387398737 GNAEGS(ph)SDEEGKLVIDEPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.875)S(0.125)DEEGKLVIDEPAK 135.62 4.15E-06 341920000 638400 761570 446810 750300 223680 640320 482280 587060 181110 TRUE FALSE 608224.0972 839174.8488 467296.6805 674878.4185 262689.7212 618145.5578 408699.3283 535653.9142 209195.6138 2.90744192 4.011436155 2.233778577 3.226063904 1.255713332 2.954868635 1.953670638 2.560540847 1 17.67449308 2.930292805 0.117849439 8.93E-14 5.3984837 0.430053871 0.681701054 14.92620099 0.656605356 9.592290565 19.36886049 851.7120769 -2.930292805 5.3984837 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK;GNAEGS(0.853)S(0.147)DEEGKLVIDEPAKEK;GNAEGS(0.586)S(0.414)DEEGKLVIDEPAKEK;GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK 183.47 2.22E-17 990850000 1198850 1077880 944550 1279220 420856 1239730 1069020 1307350 409506 TRUE FALSE 1142182.736 1187717.197 987858.5518 1150630.375 494253.1532 1196797.839 905921.3651 1192871.503 473010.099 2.4147111 2.510976404 2.088451291 2.43257042 1.044910361 2.530173968 1.915226265 2.521873224 1 18.85151146 GNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.406)S(0.594)DEEGKLVIDEPAKEK;GNAEGS(0.096)S(0.904)DEEGKLVIDEPAKEK;GNAEGS(0.113)S(0.887)DEEGKLVIDEPAKEK;GNAEGS(0.137)S(0.863)DEEGKLVIDEPAKEK;GNAEGS(0.492)S(0.508)DEEGKLVIDEPAKEK 224.79 3.45E-26 1094261000 1998100 1935870 1634170 2150570 741876 2177640 1837030 2273290 669800 TRUE FALSE 1903653.773 2133137.354 1709098.311 1934390.618 871258.9395 2102227.781 1556757.334 2074228.676 773669.1631 2.460552732 2.757169932 2.209081598 2.500281399 1.126138899 2.717218006 2.012174465 2.681027983 1 19.56135725 2.934681193 24.99999794 2.017117974 2.511413151 0.186881353 0.568985573 346.7192818 132702.0497 0.156061729 0.165528562 860.3619448 -2.934681193 0.494295177 GNAGQSNYGFANSAMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 354.93 1.81E-87 2022600000 418760.1 402169.5 406886.7 428778 496858 376611.7 486295 461439 522242 FALSE TRUE 398966.14 443151.0293 425542.8577 385676.4208 583509.8779 363569.5424 412101.7663 421032.9549 603228.6221 0.661384632 0.734631967 0.705442086 0.639353649 0.967311325 0.602706054 0.683160167 0.697965812 1 19.20234536 -1.228750765 3.276042925 1.000863004 0.709072188 0.460578881 0.098091368 18913521.14 27434251.37 165570.4624 0.022867656 0.059053988 1.228750765 -0.291790816 GNDPLTSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 GNDPLTSS(1)PGR;GNDPLTS(0.002)S(0.998)PGR;GNDPLT(0.001)S(0.114)S(0.885)PGR;GNDPLTS(0.007)S(0.993)PGR;GNDPLT(0.004)S(0.058)S(0.937)PGR;GNDPLTS(0.002)S(0.998)PGR;GNDPLTS(0.004)S(0.995)PGR 204.07 3.61E-08 9583710000 8079990 8209710 7642430 9210080 8630080 8146440 9184300 8483820 8912950 TRUE FALSE 7698064.886 9046288.783 7992842.975 8284265.26 10135163.22 7864326.74 7783066.354 7740931.745 10295124.76 0.747738863 0.878696372 0.776371647 0.804678472 0.984462399 0.763888435 0.755995341 0.751902665 1 23.29545798 -2.297249765 2.245915839 1.888574207 0.809002859 0.402805274 0.073473771 6507477.61 882972.8042 29384474.41 0.017779892 0.005043711 2.297249765 -1.079571348 GNDVLVIECNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNDVLVIECNLR 12 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 93.959 0.016003 57626000 63289 55185 62599 63569 73394 46888 60413 64309 109810 FALSE TRUE 60297.4544 60808.41424 65469.22607 57178.92335 86193.89036 45264.2568 51195.88729 58677.76304 126838.774 0.475386607 0.479415027 0.516160982 0.450800032 0.679554742 0.356864509 0.403629629 0.462616921 1 16.95263631 -1.390262048 3.296805095 1.005116796 0.473699728 0.792350157 0.083945927 38291659.5 52800482.69 1875157.679 0.020167712 0.040713454 1.390262048 -0.531417067 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 306.4 3.56E-82 302429000 230269 216182 226401 250433 226058 216596 284089 246340 232935 FALSE TRUE 219384.6407 238211.1916 236781.7098 225258.999 265482.4436 209095.2262 240746.0054 224769.1637 269057.3701 0.815382387 0.885354642 0.880041716 0.837215494 0.986713144 0.777139932 0.894775732 0.835394933 1 18.0375543 -1.4914302 2.843278368 1.004842464 0.864708394 0.368500329 0.055943436 11365194.23 12411962.53 430785.7949 0.012187274 0.032252977 1.4914302 -0.140134069 GNEFLFSHLWPLIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNEFLFSHLWPLIEK 15 0 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 63.134 0.075384 37772000 250620 251130 179810 237020 242500 184600 289690 247470 216960 FALSE TRUE 238773.6893 276720.4325 188054.4664 213194.2993 284791.9232 178207.2557 245492.47 225800.2149 250605.0487 0.952788822 1.104209328 0.750401747 0.850718293 1.136417341 0.711108003 0.979599059 0.901020215 1 17.93505595 3.763690015 24.99756915 0.903484176 1.028499065 0.142995562 0.12651916 1287.734507 1280974.425 0.029605147 0.053347597 5803.500353 -3.763690015 0.125014889 GNEPGSDRS(ph)PSPS(ph)KNDSFFTPDSNHNSLSQSTTGHLSLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNEPGSDRSPSPSKNDSFFTPDSNHNSLSQSTTGHLSLPQK 41 2 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 2 GNEPGS(0.019)DRS(0.952)PS(0.227)PS(0.702)KNDS(0.077)FFT(0.024)PDSNHNSLSQSTTGHLSLPQK 174.33 4.13E-20 132740000 49597 22923 44988 51843 85243 34776 104340 78409 78281 TRUE FALSE 47252.6481 25258.87976 47050.7443 46631.64314 100109.3522 33571.6984 88421.01666 71543.09229 90420.41768 0.522588253 0.279349293 0.520355308 0.51572028 1.107154278 0.371284487 0.977887726 0.791227182 1 16.46436096 2.930661879 7.55657411 0.819629442 0.429767803 0.469186794 0.205915414 0.238033761 23.19590425 0.056646522 0.060348053 852.4361893 -2.930661879 -0.389861639 GNFGGSFAGSFGGAGGHAPGVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNFGGSFAGSFGGAGGHAPGVAR 23 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 258.34 1.21E-43 1227260000 606740 475910 539100 564740 649250 498740 666290 593920 700020 FALSE TRUE 578060.6026 524405.7701 563818.2682 507971.2623 762478.9944 481468.5087 564635.2232 541913.2162 808575.5264 0.714912317 0.648555086 0.697298211 0.628229826 0.942990444 0.595452735 0.698308575 0.670207295 1 19.62502301 -1.228301815 4.96300039 1.00004491 0.696411733 0.503857032 0.093669715 4.15E-05 6.46E-06 0.080953301 0.019078059 0.059115067 1.228301815 -0.303633178 GNFHAVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNFHAVYR 8 0 P05109 P05109 S100A8 "Protein S100-A8;Protein S100-A8, N-terminally processed" 0 ; 119.17 0.0017451 239470000 252397 162702 152005 220131 329450 193350 280033 263040 287970 FALSE TRUE 240466.694 179281.5188 158974.5796 198003.0137 386905.9757 186654.241 237308.8227 240006.8231 332626.9169 0.722932156 0.538986804 0.477936606 0.595270568 1.163183002 0.561151944 0.713438422 0.721549613 1 18.34354539 2.949091021 24.99996373 0.793087341 0.584723815 0.317834821 0.175637316 480.8240498 236118.8812 0.051094907 0.054194948 889.3874994 -2.949091021 -0.208363526 GNFNYIEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;;;; 207.83 2.90E-07 4145224000 2895030 2284318 2256956 2691321 3048540 2305558 3057490 2693800 3134400 FALSE TRUE 2758187.669 2517092.601 2360439.665 2420784.3 3580204.411 2225715.948 2591013.746 2457916.591 3620466.744 0.761832069 0.695239807 0.651971094 0.668638734 0.988879242 0.614759396 0.71565738 0.678894951 1 21.78774427 -0.949321354 4.085477221 1.000013772 0.721049256 0.420472552 0.102569497 25177396.89 52248210.88 5157.693953 0.022738884 0.112377314 0.949321354 -0.278964517 GNFTLPEVAECFDEITYVELQKEEAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNFTLPEVAECFDEITYVELQKEEAQK 27 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;; 189.12 6.98E-18 291291000 258768 196773 234142 250995 170851 260318 297040 278733 180343 FALSE TRUE 246536.5495 216824.3924 244877.6423 225764.5057 200647.3603 251303.1224 251721.0925 254325.6609 208309.6714 1.183509857 1.040875303 1.175546199 1.083792722 0.963216729 1.206392006 1.208398491 1.220901839 1 17.6683703 GNHDAFNIPS(ph)LDSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNHDAFNIPSLDSIK 15 0 H3BTT1;H3BPV2;H3BVF7;Q0P6H9 H3BTT1 TMEM62 Transmembrane protein 62 1 GNHDAFNIPS(0.998)LDS(0.002)IK 60.49 0.080257 0 92959 108880 84219 104420 57839 87851 86788 100550 60074 TRUE FALSE 88565.0123 119974.9958 88080.52445 93923.50321 67926.10329 84808.69784 73546.89663 91745.30895 69389.9691 1.276337393 1.728996242 1.269355291 1.35356024 0.978903783 1.222204001 1.05990675 1.322169618 1 16.0824395 3.198353109 1.94818009 1.128303343 1.492568619 0.437988977 0.161788912 0.251106404 1.960703172 0.047495362 0.063970362 1578.89449 -3.198353109 0.364265276 GNHECASINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 180.15 7.28E-06 785313000 1227469 1024262 959571 1030941 1267150 969709 1251047 1089254 1126765 FALSE TRUE 1169448.973 1128635.462 1003568.279 927308.852 1488140.559 936127.7342 1060176.803 993873.1453 1301497.961 0.898540764 0.86718189 0.771087093 0.712493511 1.143405985 0.719269459 0.814581993 0.763637881 1 20.31174162 -0.95650285 4.759747845 1.000000856 0.839210241 0.146660012 0.123935015 14506285.38 3047699.62 263.3307858 0.026599214 0.110534322 0.95650285 -0.160790615 GNHVIRDEEVSSADISSSSEVISQHLVSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNHVIRDEEVSSADISSSSEVISQHLVSYR 30 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 122.7 1.10E-05 464640000 161810 119959 169086 166572 264302 149843 237957 176943 201252 FALSE TRUE 154161.562 132182.9585 176838.7603 149827.8661 310396.1851 144653.8993 201652.2893 161448.9329 232461.1323 0.663171346 0.568623912 0.760723991 0.644528677 1.335260575 0.622271336 0.867466691 0.694520117 1 17.82662999 2.896298999 22.49744449 0.882021381 0.650114405 0.276243177 0.19472869 20.32339961 4397.785743 0.054748915 0.058069995 787.5878343 -2.896298999 -0.231906976 GNIETNHNLPPSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNIETNHNLPPSHK 14 0 E9PF84;G5E9Q7;E7EQB8;P51553-2;P51553 E9PF84 IDH3G "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial" 0 ; 177.88 1.18E-06 82480000 112743 89005 99466 106886 101294 99236 127911 108099 89670 FALSE TRUE 107413.8618 98074.71069 104026.6145 96141.61621 118959.6415 95799.43244 108395.8277 98633.27849 103575.5656 1.037057931 0.946890419 1.004354781 0.928226804 1.148529972 0.924923092 1.046538602 0.952283272 1 16.66032417 4.753749923 22.57186048 0.995967541 1.037058046 0.039007127 0.066560194 214.1858742 1288837.386 0.013824852 0.100399474 56721.78939 -4.753749923 0.041090505 GNIETT(ph)SEDGQVFSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIET(0.019)T(0.699)S(0.283)EDGQVFSPK 117.65 0.0037238 90679000 220680 194860 197410 234980 166060 230610 266840 251120 186740 TRUE FALSE 210248.8937 214716.4555 206461.4438 211359.364 195020.8114 222623.9179 226128.6571 229130.6015 215698.6855 0.974734238 0.995446287 0.957175253 0.979882485 0.904135373 1.032106048 1.048354359 1.062271664 1 17.71865786 2.035101447 23.35287124 1.041743596 0.968467702 0.614082169 0.028618584 54.52347105 36273.85057 0.010115167 0.007470483 108.4180138 -2.035101447 -0.073275894 GNIETTSEDGQVFS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK 326.94 2.03E-71 221710000 225619 222148 210652 248818 153452 243362 262963 258401 181332 TRUE FALSE 214954.437 244785.1338 220310.6026 223806.3419 180213.9802 234934.3129 222843.1647 235774.0386 209452.0404 1.026270437 1.168693001 1.051842713 1.068532641 0.860406897 1.12166161 1.063934084 1.125670765 1 17.67626041 2.142890262 0.006375441 1.86E-05 2.11531371 0.015411141 0.083901569 16058.55855 67.2768702 11062.1773 11253.04413 138.9601462 -2.142890262 2.115295129 GNIIISTPEKWDILSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNIIISTPEKWDILSR 16 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 237.89 8.17E-20 291710000 482760 418050 489450 503180 556320 503040 645210 540800 656830 FALSE TRUE 459940.8915 460649.7703 511891.7666 452599.3904 653342.0319 485619.5987 546771.3644 493444.685 758687.8418 0.606232058 0.607166406 0.674706695 0.596555481 0.86114736 0.640078267 0.720680278 0.65039224 1 19.53314689 -5 0.168381935 2.283614787 0.584245022 0.663279919 0.075122317 74.03600939 0.695620391 31.78049252 0.253572264 1.00E-05 5 -1.699369765 GNILIPGINEAVAAVTEEEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNILIPGINEAVAAVTEEEHK 21 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 168.78 1.04E-11 207032000 501780 629900 463810 658160 331330 549430 464890 602740 270003 FALSE TRUE 478061.8538 694087.5261 485076.1473 592000.5064 389113.8471 530403.1013 393962.4922 549960.8903 311873.6863 1.532870117 2.225540521 1.555360932 1.898206012 1.247664886 1.700698471 1.263211709 1.76340908 1 18.25060231 2.748088292 24.8514666 1.424112744 1.829647542 0.325094098 0.289301426 686.0620918 1789486.338 0.079917131 0.083749668 559.8714111 -2.748088292 0.405534798 GNIWS(ph)AEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNIWSAEK 8 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 GNIWS(1)AEK;GNIWS(1)AEK 86.911 0.016467 311841000 542160 584310 520090 703710 415940 602380 590870 646790 473910 TRUE FALSE 516533.1713 643851.8533 543936.6409 632971.7338 488479.8043 581519.4296 500721.9294 590153.6388 547401.5424 0.943609273 1.176196637 0.993670275 1.156320698 0.89236103 1.062326984 0.914725098 1.078100066 1 19.06223997 2.740081401 24.99964619 0.984602378 1.067714962 0.162596549 0.08750582 221.1638048 3635630.44 0.024558579 0.024836755 549.6438857 -2.740081401 0.083112584 GNIWS(ph)AEKGGNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNIWSAEKGGNSK 13 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 GNIWS(1)AEKGGNSK 114.29 0.00045696 240530000 197110 119890 225720 193880 158670 214130 297440 272840 210850 TRUE FALSE 187793.0009 132106.9273 236069.4853 174390.8141 186341.9978 206714.6244 252060.0651 248948.6832 243547.5411 0.771073278 0.542427678 0.969295293 0.71604424 0.765115496 0.848764982 1.034952207 1.022176952 1 17.89384389 1.967387384 2.06090231 1.028151832 0.730672824 0.573694181 0.103584227 0.21905135 1.722605427 0.060162062 0.030618218 92.76569096 -1.967387384 -0.297479008 GNIYYQSYEHRS(ph)PS(ph)PNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNIYYQSYEHRSPSPNIR 18 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 2 GNIYYQSY(0.013)EHRS(0.99)PS(0.996)PNIR 95.835 0.0022626 80661000 194960 118680 214880 172750 173250 217180 316050 242350 213640 TRUE FALSE 185744.6272 130773.6269 224732.4605 155384.8418 203464.7451 209659.0021 267830.7678 221128.5492 246770.2001 0.752702827 0.52994092 0.910695297 0.629674255 0.824511003 0.84961232 1.085344858 0.896090975 1 17.91280866 2.249111454 1.610622489 1.001551417 0.69056756 0.54707726 0.110248986 0.247193447 1.273212589 0.055905666 0.034448961 177.4644852 -2.249111454 -0.310983857 GNKHDDGT(ph)QSDSENAGAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.462)QS(0.462)DS(0.076)ENAGAHR 71.535 0.029232 9696700 19923 21046 17356 21240 14669 18370 17352 20490 7598.5 TRUE FALSE 18981.27927 23190.61133 18151.78977 19104.91485 17227.26896 17733.84229 14704.63371 18695.78698 8776.836572 2.162656114 2.642251697 2.068147176 2.17674269 1.962810725 2.0205278 1.675391081 2.130128187 1 13.09948533 -0.831231741 0.167697644 4.21E-15 2.647251301 0.759476032 0.206528579 9.176929623 0.356965053 5.284211604 0.984046698 0.14749193 0.831231741 2.647251301 GNKHDDGTQS(ph)DSENAGAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.028)QS(0.972)DSENAGAHR;GNKHDDGT(0.001)QS(0.999)DSENAGAHR;GNKHDDGT(0.025)QS(0.975)DSENAGAHR 299.34 4.65E-50 115385000 163248 166078 126161.6 169225 109830.8 144983.3 137890.6 140588 68127.8 TRUE FALSE 155531.5906 183001.537 131946.2342 152214.1815 128985.2567 139962.492 116852.8564 128277.3694 78692.71128 1.976442139 2.325520802 1.676727514 1.934285641 1.639100428 1.778595371 1.484926044 1.630104839 1 16.2639424 1.464459166 0.170044879 0.621544341 2.536013993 0.763228755 0.167918883 1.512344989 0.266176734 1.262936667 1.192031384 29.13796154 -1.464459166 1.914469653 GNKPWISLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNKPWISLPR 10 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 122.51 0.00044385 5799600000 8048400 5969100 3887400 5390600 8422700 5394200 9496900 7401800 9126000 FALSE TRUE 7667968.082 6577358.076 4065641.135 4848726.647 9891616.213 5207397.501 8047973.482 6753659.153 10541213.47 0.727427454 0.623965931 0.385690049 0.459978034 0.938375476 0.494003609 0.763476947 0.640690863 1 23.32953762 -0.031232871 0.482432727 1.042508555 0.604534715 0.365701991 0.15747322 4.927534545 1.402764425 0.558361054 0.078650684 0.930608743 0.031232871 -0.43797384 GNKS(ph)PSPPDGSPAATPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNKSPSPPDGSPAATPEIR 19 1 O00499-6;O00499-11;O00499-2;O00499;O00499-9;O00499-10;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5 O00499-6 BIN1 Myc box-dependent-interacting protein 1 1 GNKS(0.978)PS(0.022)PPDGSPAATPEIR;GNKS(0.942)PS(0.058)PPDGSPAATPEIR 112.23 8.16E-05 163140000 193248 152059 171216 187928 135792 180119 198005 190228 148090 TRUE FALSE 184113.55 167553.985 179066.423 169037.1204 159474.0818 173881.4339 167795.7006 173570.6279 171055.0409 1.076340978 0.979532577 1.046835113 0.988203093 0.932296885 1.016523296 0.980945664 1.014706301 1 17.38410109 7.999982315 0.769854305 0.991023492 18.71708461 0.412421609 0.030098986 384.1444879 1.513742315 0.009674478 11838.4854 99995928.02 -7.999982315 17.72606112 GNLELRPGGAHPGTCS(ph)PSRPGS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.033)CS(0.845)PS(0.122)RPGS;GNLELRPGGAHPGT(0.236)CS(0.628)PS(0.136)RPGS 95.823 0.00081297 280580000 349240 317530 327280 375090 382460 353900 390360 364990 401910 TRUE FALSE 332732.1173 349886.668 342286.1117 337385.2406 449160.9029 341644.3543 330803.4125 333029.5407 464236.1501 0.716730305 0.753682512 0.737310336 0.726753486 0.96752677 0.735927941 0.712575728 0.717370977 1 18.82449934 -1.362451057 3.340578224 1.001807327 0.755974004 0.502525337 0.075481795 20631160.42 31452039.1 370237.7559 0.017678042 0.043405918 1.362451057 -0.245833324 GNLLHFPSS(ph)QGEEEKEKLEGDHTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNLLHFPSSQGEEEKEKLEGDHTIR 25 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GNLLHFPS(0.178)S(0.822)QGEEEKEKLEGDHTIR;GNLLHFPS(0.085)S(0.915)QGEEEKEKLEGDHTIR;GNLLHFPS(0.01)S(0.99)QGEEEKEKLEGDHTIR 177.06 1.49E-17 860170000 1213620 904147 1027967 1144977 601990 1173483 1257180 1350300 421073 TRUE FALSE 1156254.588 996280.6072 1075100.304 1029881.737 706976.8654 1132844.989 1065374.101 1232060.574 486370.8503 2.37731062 2.048397034 2.21045382 2.117482444 1.453575733 2.32917945 2.190456317 2.533171083 1 18.89169724 -1.882585267 2.81085343 0.461746594 2.150869828 0.619207704 0.285224239 15334378.84 2827572.268 53284062.03 0.065209565 0.013104327 1.882585267 1.689123235 GNNVYCLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNNVYCLDR 9 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 155.42 0.00017067 248660000 355400 280940 190449 220810 349880 232230 331330 306700 316930 FALSE TRUE 338600.9463 309568.1054 199181.275 198613.7593 410898.9612 224187.8169 280779.5232 279843.7221 366077.8857 0.924942368 0.845634542 0.544095349 0.54254509 1.1224359 0.612404697 0.766993949 0.764437659 1 18.4817911 -1.532800308 12.52830035 1.000000319 0.772289591 0.14691966 0.176947203 1.50E-06 5.62E-08 0.163457901 0.038527343 0.029322412 1.532800308 -0.227710728 GNPS(ph)PPAAGEGQRPPPPLCVPGGGGGAPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNPSPPAAGEGQRPPPPLCVPGGGGGAPAR 30 1 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 1 GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR 210.59 3.52E-26 555940000 85654 61259.1 73732.3 83389 80405 70945 78086 73151 88521 TRUE FALSE 81605.30517 67501.47194 77112.99889 75006.57929 94427.60654 68488.15686 66172.54655 66745.51064 102248.3846 0.798108503 0.660171525 0.754173273 0.733572267 0.923511965 0.669821407 0.647174494 0.652778143 1 16.64171852 4.753871192 22.61783093 0.735444899 0.798108658 0 0.120328653 282.7555131 1651526.884 0.026248003 0.192966734 56737.63012 -4.753871192 0.062663759 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GNRGS(0.999)GGGGGGGGQGS(0.001)TNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK 180.21 3.31E-17 723849000 367350 347177 405878 433723 342664 409039 480706 426007 433140 TRUE FALSE 349986.0935 382554.731 424487.9078 390124.34 402424.4931 394873.8769 407365.4709 388703.5687 500309.139 0.699539677 0.764636704 0.848451237 0.779766567 0.804351673 0.789259772 0.814227523 0.776926781 1 18.93246028 -5 0.168722452 1.830852219 0.729659574 0.77835517 0.036570992 61.69372059 0.580125575 17.2060547 0.136023589 1.00E-05 5 -1.101192645 GNRPVILTYHDIGLNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNRPVILTYHDIGLNHK 17 1 Q5TH30;Q9UGV2;Q9UGV2-2;Q5TH29 Q5TH30 NDRG3 Protein NDRG3 0 ; 242.48 1.34E-20 1505180000 850390 813320 856180 960980 684870 840050 839600 917010 158221 FALSE TRUE 810193.75 896198.2327 895436.6999 864380.4647 804311.1112 810958.8579 711503.5997 836711.743 182757.1046 4.433172389 4.903766858 4.899599946 4.729668193 4.400984098 4.437358863 3.8931652 4.578272045 1 17.47956797 -0.74220863 0.433005284 6.44E-19 4.734649808 0.944117351 0.271404136 2.41806781 0.358207108 3.673670318 0.152236251 0.181047015 0.74220863 4.734649808 GNRPVILTYHDIGMNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GNRPVILTYHDIGMNHK 17 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;;; 272.16 8.11E-36 6375250000 2356620 2182940 2218860 2577830 1985540 2259820 2681580 2456840 303534 FALSE TRUE 2245227.243 2405384.068 2320596.926 2318701.631 2331817.547 2181561.867 2272455.72 2241706.065 350604.5025 6.403874528 6.860676491 6.618845193 6.613439401 6.650848836 6.222287082 6.481536045 6.393831366 1 18.419485 -0.895544594 0.672868807 2.96E-18 6.609718168 0.991741182 0.158740208 2.193149475 0.563301541 4.886420935 0.056209997 0.127190714 0.895544594 6.609718168 GNRTDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNRTDGSISGDRQPVTVADYISR 23 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 GNRT(0.002)DGS(0.998)IS(1)GDRQPVTVADYISR;GNRT(0.009)DGS(0.991)IS(1)GDRQPVTVADYISR 124.82 3.02E-05 194817000 57425 47783 64269 58342 63755 53752 81778 66043 85963 TRUE FALSE 54710.63406 52652.14202 67215.79722 52477.35132 74873.85181 51890.55476 69301.26414 60259.9248 99293.703 0.550998023 0.530266678 0.676939173 0.528506338 0.754064453 0.522596632 0.697942186 0.606885663 1 16.59941461 -5 0.199503305 2.80347555 0.538537608 0.72227245 0.077234304 64.62665505 0.638942802 46.38673398 0.160312503 1.00E-05 5 -2.264937942 GNS(ph)PPSSGEACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GNSPPSSGEACR 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(0.998)PPS(0.001)S(0.001)GEACR;GNS(0.999)PPSS(0.001)GEACR;GNS(1)PPSSGEACR;GNS(0.998)PPS(0.001)S(0.001)GEACR;GNS(0.996)PPS(0.004)S(0.001)GEACR;GNS(0.874)PPS(0.046)S(0.079)GEACR 133.48 0.00017048 1869733000 594789 640233 566082 691640 586634 579203 616361 540941 569908 TRUE FALSE 566674.5027 705473.4706 592037.4196 622115.0332 688942.7839 559145.0549 522323.8092 493573.3383 658286.422 0.860832738 1.071681637 0.899361433 0.945052203 1.046569944 0.849394787 0.793459795 0.749785081 1 19.32835591 2.09858838 7.045255675 0.824055275 0.965652662 0.285856399 0.088854833 0.220603118 13.65127445 0.030562528 0.022504807 125.4840076 -2.09858838 0.141597387 GNS(ph)PPSSGEACREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GNSPPSSGEACREEK 15 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(0.995)PPS(0.001)S(0.004)GEACREEK;GNS(0.993)PPS(0.006)S(0.001)GEACREEK;GNS(0.989)PPS(0.009)S(0.002)GEACREEK;GNS(0.999)PPS(0.001)SGEACREEK;GNS(0.966)PPS(0.014)S(0.019)GEACREEK;GNS(0.995)PPS(0.004)S(0.002)GEACREEK 105.92 0.00077341 4029650000 1777970 1173220 1776680 1669670 1418230 1841080 2258610 1938580 1841710 TRUE FALSE 1693928.882 1292772.452 1858142.535 1501831.599 1665568.863 1777322.938 1914017.562 1768827.658 2127312.981 0.796276287 0.607702046 0.873469279 0.705975855 0.782944907 0.835477879 0.89973482 0.831484447 1 21.02060087 1.610259771 0.434802932 0.99836206 0.706377829 0.535165317 0.072493257 0.657267111 0.336229728 0.076415755 0.05623652 40.76240227 -1.610259771 -0.291984231 GNS(ph)RPGTPS(ph)AEGGSTSSTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.828)RPGT(0.2)PS(0.899)AEGGS(0.064)T(0.008)S(0.001)STLR;GNS(0.576)RPGT(0.449)PS(0.965)AEGGS(0.005)T(0.004)S(0.001)STLR;GNS(0.989)RPGT(0.08)PS(0.402)AEGGS(0.244)T(0.204)S(0.032)S(0.027)T(0.022)LR 123.61 0.00033262 105410000 591260 704540 526130 672290 549560 575780 538240 538890 476630 TRUE FALSE 563312.3116 776333.427 550253.5809 604710.1319 645403.09 555840.5942 456121.6025 491701.9348 550543.3461 1.023193388 1.410122259 0.999473674 1.098387868 1.172302044 1.009621855 0.828493534 0.893121202 1 19.07049663 2.052757657 3.532868941 0.891969343 1.158172182 0.442562649 0.118845177 0.189563821 4.814654703 0.050922477 0.033350041 112.9165648 -2.052757657 0.266202839 GNSIIMLEALERV ddPTM_SK-BR-3_Trastuzumab_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 0 107.85 0.025891 10269000 32244 27071 24567 28640 37826 22401 37962 31045 39827 FALSE TRUE 30719.89002 29829.56568 25693.42125 25761.05279 44422.84242 21625.24775 32170.19968 28326.53522 46003.16775 0.66777771 0.648424166 0.558514174 0.559984324 0.965647467 0.47008171 0.69930401 0.615751841 1 15.48944559 -1.576274627 3.701503518 1.00947349 0.649300352 0.419259392 0.130120607 0.009142898 0.001046623 0.113233708 0.026158576 0.026529274 1.576274627 -0.360173138 GNSLQEILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNSLQEILER 10 0 Q00341;A0A024R4E5;H7C0A4 Q00341 HDLBP Vigilin 0 77.358 0.077326 40908000 34127 31968 34904 36052 41449 31615 41788 34099 47416 FALSE TRUE 32513.88434 35225.57554 36504.38292 32427.98447 48677.69248 30520.16462 35412.47311 31113.11079 54769.03111 0.593654547 0.643165943 0.666515039 0.592086144 0.888781333 0.557252228 0.646578411 0.568078532 1 15.74107274 -1.231961296 4.416717193 1.000144281 0.644023621 0.587245388 0.0936607 0.000120217 2.09E-05 0.081929232 0.019303124 0.05861904 1.231961296 -0.35612066 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 49 1 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 339.32 1.67E-139 1213130000 1447440 960100 1362060 1397540 1096900 1499980 1864610 1548910 78915 FALSE TRUE 1379022.38 1057935.282 1424511.798 1257056.624 1288199.013 1448035.316 1580129.499 1413279.229 91152.73516 15.12869995 11.60618252 15.62774607 13.79066269 14.13231331 15.88581312 17.33496527 15.50451807 1 16.47599833 -0.493982617 8.028942431 1.000000001 14.80070849 0.89273962 1.51139258 0 0 1.654157106 0.389888569 0.320639766 0.493982617 13.80070849 GNVGFVFTKEDLTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GNVGFVFTKEDLTEIR 16 1 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0 60S acidic ribosomal protein P0 0 ;; 239.86 7.00E-20 451682000 1201686 818143 1301204 1174689 1349095 1314562 1778889 1548921 1668240 FALSE TRUE 1144884.684 901512.7019 1360865.49 1056607.03 1584376.741 1269038.388 1507486.812 1413289.266 1926942.139 0.594145855 0.467846275 0.706230593 0.548333553 0.822223309 0.658576281 0.782320746 0.733436276 1 20.87788182 1.136087573 0.150627695 1.212243868 0.345525783 0.691367039 0.083367505 2.745613315 0.347424172 0.965467314 0.744652068 13.68004649 -1.136087573 -0.866718086 GNVGFVFTKEDLTEIRDMLLANKVPAAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GNVGFVFTKEDLTEIRDMLLANKVPAAAR 29 3 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;F8VWV4;F8VPE8 F8VWS0 RPLP0 60S acidic ribosomal protein P0 0 ; 284.26 5.86E-72 315040000 482930 150114 471540 280575 564760 442450 925880 522160 892230 FALSE TRUE 460102.856 165410.7873 493160.5754 252371.0679 663253.9652 427127.8456 784620.001 476436.9023 1030592.472 0.446445 0.160500675 0.478521422 0.244879596 0.6435657 0.414448831 0.761329063 0.462294181 1 19.97504253 1.055872418 0.322032646 1.059870985 0.257810244 0.611533976 0.151238824 0.988535026 0.317382248 0.293816848 0.176312565 11.37293137 -1.055872418 -0.802060741 GNVS(ph)S(ph)YIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GNVSSYIR 8 0 Q5HYW3 Q5HYW3 RGAG4 Retrotransposon gag domain-containing protein 4 2 GNVS(0.667)S(0.667)Y(0.667)IR 67.563 0.085921 41132000 125680 118130 83012 142390 134990 103090 103910 102230 101950 TRUE FALSE 119739.3555 130167.5813 86818.18231 128076.6867 158532.2133 99519.96745 88056.62106 93278.19924 117759.8853 1.016809376 1.105364369 0.737247511 1.087608793 1.346232742 0.845109242 0.747764154 0.792105045 1 16.84548865 2.032387323 24.99843518 0.813056486 1.051904189 0.29530156 0.160087652 208.4489279 160892.2576 0.05786547 0.042736215 107.7425681 -2.032387323 0.238847702 GNVVPS(ph)PLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GNVVPSPLPTR 11 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.994)PLPT(0.006)R;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(0.997)PLPT(0.003)R;GNVVPS(1)PLPTR;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(0.996)PLPT(0.004)R;GNVVPS(0.986)PLPT(0.014)R 164.56 2.37E-05 11835400000 5667510 7515300 4359700 7042620 4779690 5050420 4638040 5286760 3929230 TRUE FALSE 5399618.034 8281117.614 4559596.557 6334682.457 5613266.423 4875522.689 3930421.815 4823823.268 4538554.921 1.189721867 1.824615491 1.004636197 1.395748772 1.236795967 1.074245608 0.866007327 1.062854444 1 22.11380158 2.559212384 0.950677961 0.944909253 1.446420259 0.37078079 0.213488808 0.481595941 0.891607795 0.129328866 0.099032247 362.4201902 -2.559212384 0.501511005 GNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GNVVPSPLPTRR 12 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR 126.07 0.00018013 23898950000 8335930 7485920 6910230 8427250 8255090 7377330 8239060 8233290 7999650 TRUE FALSE 7941907.109 8248743.759 7227070.881 7580126.819 9694775.082 7121851.212 6982040.076 7512339.48 9240194.865 0.85949563 0.89270236 0.782134034 0.820342745 1.049195956 0.770746864 0.755616107 0.813006607 1 23.13949185 GNWEQPQNQNQTQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 162.46 1.59E-06 400740000 270540 250359 245014 300530 233237 283790 317260 290600 245958 FALSE TRUE 257752.1104 275870.8667 256248.1343 270320.1534 273913.459 273962.2811 268856.1601 265153.5234 284099.9105 0.907258682 0.971034684 0.901964854 0.951496792 0.964144827 0.964316675 0.946343699 0.933310831 1 18.11603885 GNYAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 121.29 0.045867 3778580000 5367570 4784610 4291020 5026920 5855450 4801620 5399550 4906720 5915870 FALSE TRUE 5113855.604 5272167.199 4487767.511 4521604.451 6876638.626 4635338.695 4575749.478 4477061.585 6833272.906 0.748375731 0.771543486 0.656752273 0.661704064 1.006346259 0.678348247 0.669627796 0.655185538 1 22.70414532 -1.029181011 4.604422667 1.000007291 0.732539627 0.390481503 0.105610297 13209100.25 2952499.528 1209.28022 0.023665114 0.093501588 1.029181011 -0.267467664 GNYSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 111.04 0.065588 1898220000 946130 906600 782410 977180 988130 844420 1037430 944540 1050550 FALSE TRUE 901408.3099 998983.5707 818284.2724 878952.0099 1160459.559 815177.5237 879150.9998 861831.0703 1213463.929 0.742838982 0.823249499 0.674337533 0.724333035 0.956319782 0.671777302 0.72449702 0.710223889 1 20.21069979 -1.355363732 3.045132481 1.002655136 0.755890456 0.462771894 0.08344809 21316724.34 26703810.84 502619.1251 0.018655834 0.044120078 1.355363732 -0.24676468 GPAAEEALNVFYYCTYEGAVDLDHVTDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPAAEEALNVFYYCTYEGAVDLDHVTDER 29 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 136.16 5.11E-06 29250000 59114 61797 53975 67544 58336 60927 64450 59936 54189 FALSE TRUE 56319.79837 68094.18456 56449.80714 60754.34879 68509.77993 58817.08271 54616.96879 54687.6861 62592.35336 0.8997872 1.087899414 0.901864271 0.970635318 1.094539129 0.939684795 0.872582126 0.873711934 1 15.9336988 2.006283966 24.99811152 0.902488712 0.99309051 0.18123048 0.073062742 209.6627565 834050.3346 0.025625278 0.018877205 101.4574556 -2.006283966 0.090601798 GPAFNMAS(ph)PESDFGINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GPAFNMASPESDFGINLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPAFNMAS(0.955)PES(0.045)DFGINLK;GPAFNMAS(0.956)PES(0.044)DFGINLK;GPAFNMAS(0.917)PES(0.083)DFGINLK;GPAFNMAS(0.968)PES(0.032)DFGINLK;GPAFNMAS(0.6)PES(0.4)DFGINLK 212.76 1.64E-16 309115000 628277 723136 688921 847275 596538 761886 782159 839375 728384 TRUE FALSE 598579.5913 796824.3805 720508.7093 762105.3073 700574.0383 735501.6968 662826.2792 765874.8752 841338.0707 0.711461435 0.947091791 0.856384294 0.905825296 0.832690286 0.874204701 0.787823947 0.91030574 1 19.6823261 -4.99999996 0.398971801 3.398943992 0.8474112 0.33115159 0.066346722 865.5335488 6.066716141 1808.165978 0.039219493 1.00E-05 4.99999996 -2.551532792 GPAFNMASPES(ph)DFGINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPAFNMASPESDFGINLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPAFNMAS(0.182)PES(0.818)DFGINLK;GPAFNMAS(0.086)PES(0.914)DFGINLK 175.16 4.23E-12 34254000 390480 446800 428540 514310 345120 461980 455330 483720 392460 TRUE FALSE 372022.7843 492329.428 448188.9829 462610.5817 405308.8187 445981.5168 385861.0458 441362.9124 453320.6924 0.820661378 1.086051081 0.988679737 1.020492974 0.894088502 0.983810191 0.851187806 0.973621809 1 18.79017249 2.734214282 24.96562985 0.928433875 0.979767291 0.043697285 0.078687643 924.8395243 5312314.444 0.024278429 0.023652178 542.2683811 -2.734214282 0.051333416 GPAGEAGAS(ph)PPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR 141.86 5.85E-06 3566122000 1525476 1301570 1443071 1600230 1918140 1455399 1839430 1685171 1982000 TRUE FALSE 1453369.773 1434201.463 1509237.233 1439371.84 2252663.009 1404998.168 1558791.17 1537608.494 2289358.437 0.634837144 0.626464358 0.659240252 0.628722797 0.983971305 0.613708253 0.68088559 0.671632921 1 21.12651193 -5 0.234874411 2.740505899 0.647296745 0.453300827 0.107778467 150.295237 1.501408233 124.8870059 0.169459267 1.00E-05 5 -2.093209154 GPAGNNDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPAGNNDCR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 130.28 0.0027568 0 224790 175010 183210 219900 229900 189280 225640 212230 254700 FALSE TRUE 214164.6222 192843.718 191610.3597 197795.2342 269994.4872 182725.1861 191214.4738 193646.0161 294197.5752 0.727961888 0.655490508 0.651298229 0.672321089 0.917731858 0.621096846 0.649952583 0.65821758 1 18.16642583 -1.425910854 5.761368903 1.00015211 0.691180137 0.566225746 0.084061134 0.000156619 1.56E-05 0.07761326 0.01828469 0.037504998 1.425910854 -0.308971973 GPAHCLLLGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GPAHCLLLGER 11 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ;;;;;; 150.94 3.37E-05 2370754000 2965177 2118068 1858199 2089680 3544143 1975852 3264714 2291337 3646291 FALSE TRUE 2825018.96 2333901.537 1943399.262 1879621.396 4162240.417 1907427.75 2766621.919 2090695.385 4211739.186 0.670748789 0.554141991 0.461424408 0.446281527 0.988247428 0.452883634 0.656883486 0.496397164 1 22.00598467 -1.384091011 3.94932444 1.001497829 0.594512121 0.386773017 0.161839865 0.001929152 0.000300857 0.141603749 0.033259773 0.041296095 1.384091011 -0.406985708 GPALTPIRDEEWGGHS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 107.88 0.00024608 50023000 82339 74750 67933 96059 83791 76578 102470 98571 70504 TRUE FALSE 78446.99865 82367.10998 71047.79524 86402.96682 98404.12387 73926.08466 86836.31951 89939.60068 81437.40024 0.963279751 1.01141625 0.872422192 1.060974031 1.208340684 0.907765774 1.066295329 1.104401668 1 16.31340389 3.174308801 24.99962969 1.058139447 0.964439493 0.272519357 0.082625637 85.19932216 33149.24054 0.022576793 0.026984439 1493.856226 -3.174308801 -0.093699955 GPASQFYITPSTSLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYIT(0.004)PS(0.105)T(0.105)S(0.105)LS(0.68)PR;GPASQFYITPSTS(0.003)LS(0.997)PR;GPASQFYITPSTSLS(1)PR 299.46 2.86E-46 268933000 299427 275136 280536 317160 335411 286281 338152 304138 368537 TRUE FALSE 285273.6791 303172.6712 293398.8531 285278.4742 393906.5722 276367.0172 286560.7018 277506.0644 425687.8357 0.670147594 0.712194819 0.68923476 0.670158859 0.925341387 0.649224605 0.67317099 0.651900386 1 18.69943634 -1.072417103 4.164016167 1.000038763 0.703958312 0.570188632 0.080439295 8558113.677 4408181.404 2951.592533 0.01773238 0.084641412 1.072417103 -0.296080451 GPAST(ph)PTYSPAPTQPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAS(0.02)T(0.979)PT(0.001)YSPAPTQPAPR;GPAS(0.014)T(0.986)PTYSPAPTQPAPR 274.02 5.62E-38 70781000 75914 67329 74113 80415 87683 67267 91333 74852 94824 TRUE FALSE 72325.69567 74189.90165 77511.15436 72331.53142 102974.8874 64937.52692 77398.4734 68297.56206 109528.8216 0.660334829 0.677355061 0.707678155 0.660388109 0.94016247 0.592880723 0.706649376 0.623557901 1 16.74095103 -1.126515721 3.946592528 1.00010455 0.69510911 0.5106673 0.093477586 5376683.731 2304031.31 4814.238812 0.019830588 0.074728158 1.126515721 -0.30499544 GPAVGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPAVGIDLGTTYSCVGVFQHGK 22 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 330.09 9.97E-81 1527783000 2929130 2694170 2804700 3353070 2587040 2888630 3250800 3218090 2592450 FALSE TRUE 2790675.83 2968708.986 2933298.269 3016013.033 3038218.957 2788596.019 2754830.755 2936296.979 2994473.906 0.931941943 0.991395844 0.979570489 1.007192959 1.014608593 0.931247393 0.919971535 0.980571904 1 21.51387113 0.994974877 24.96263981 1.000000011 0.966017694 0.090674136 0.032274149 448.4186083 2227560.852 0.033478807 0.008369702 9.884959114 -0.994974877 -0.033982316 GPAYGLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPAYGLSR 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 114.43 0.0061828 589270000 811470 582130 245130 286930 987600 359370 798120 507990 727510 FALSE TRUE 773113.4213 641449.7088 256369.453 258087.2513 1159837.127 346924.9268 676352.1355 463507.7026 840328.5352 0.920013291 0.763332056 0.305082408 0.307126606 1.380218663 0.412844396 0.80486632 0.551579154 1 19.68059395 4.172198612 3.75274122 0.669548848 0.885645144 0.046190491 0.330161475 0.642424322 17.36819752 0.077774552 0.193680748 14866.15348 -4.172198612 0.216096296 GPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPDWHLK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 81.958 0.02579 485990000 661460 557690 529380 688780 554700 559430 622520 617700 540500 FALSE TRUE 630194.0967 614519.245 553652.5966 619542.5258 651439.5044 540056.7988 527543.1406 563610.9134 624317.9795 1.009412058 0.984304898 0.886811873 0.992350927 1.043441845 0.865034832 0.844991107 0.902762586 1 19.25192149 2.222447388 24.99882492 0.884525747 0.981812115 0.304629023 0.057069248 233.7023508 362574.5709 0.020368044 0.015088663 166.8965612 -2.222447388 0.097286368 GPEEEHPSVTLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 116.51 0.00057955 216230000 407130 385650 373990 463190 387420 396000 454020 439950 381180 FALSE TRUE 387885.7718 424948.1734 391137.8114 416629.2612 454985.9253 382286.4207 384750.9104 401425.6457 440291.4476 0.880975031 0.965152005 0.888361138 0.946257901 1.033374434 0.868257657 0.873855062 0.911727102 1 18.7480993 -0.246366301 8.665650642 1 0.919897352 0.194192109 0.05053348 0 0 0.048420203 0.011412751 0.567066118 0.246366301 -0.080102648 GPEENYSRPEAPNEFYDGDHDNDKES(ph)DVEI ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPEENYSRPEAPNEFYDGDHDNDKESDVEI 30 2 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 1 GPEENYSRPEAPNEFYDGDHDNDKES(1)DVEI 112.23 9.80E-05 216130000 132200 157970 113230 142840 85065 164590 111160 130950 60132 TRUE FALSE 125951.168 174067.3226 118421.7075 128481.4518 99900.30907 158890.207 94200.50041 119483.3238 69456.96345 1.813369916 2.506117658 1.704965228 1.849799436 1.438305162 2.287606586 1.356242711 1.720249747 1 16.08383172 0.368367328 0.194052132 0.55690957 2.309893019 0.439311127 0.324641863 6.06089578 0.562368671 3.064716396 1.230305147 2.335432547 -0.368367328 1.752983449 GPELLTMWFGESEANVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPELLTMWFGESEANVR 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 94.688 0.0097847 8710000 18492 17949 18491 20926 24476 18295 24815 17845 24245 FALSE TRUE 17617.91981 19778.02351 19338.83064 18822.47872 28744.60665 17661.43956 21029.01599 16282.3972 28004.79077 0.629103783 0.706237146 0.69055437 0.672116384 1.026417476 0.630657794 0.750907806 0.581414706 1 14.77338603 -2.433305686 2.353825422 4.009777534 0.71254144 0.358272846 0.121567771 2753948.133 590558.9722 45216634 0.028530769 0.00368718 2.433305686 -3.297236094 GPESESEDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GPESESEDHR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 211.78 5.26E-08 1492897000 1845157 1618110 1831999 2266171 2363596 2095381 2317371 1961185 2157196 FALSE TRUE 1757940.085 1782997.249 1915997.966 2038371.186 2775806.394 2022817.431 1963813.493 1789453.245 2491722.938 0.70551186 0.71556802 0.768945029 0.818056917 1.114010852 0.811814749 0.788134773 0.718158996 1 21.24871223 3.318072568 2.834494169 0.867467083 0.714427624 0.286489498 0.111393684 0.352662068 5.735756932 0.032893853 0.045679395 2080.044223 -3.318072568 -0.153039459 GPEVDIRDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPEVDIRDPK 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 77.744 0.029259 306770000 746080 885730 627980 960540 519750 735660 661910 817450 485250 FALSE TRUE 710814.277 975986.894 656773.5042 863984.6943 610394.2354 710183.9097 560923.4727 745869.7444 560500.0917 1.268178699 1.741278741 1.17176342 1.541453261 1.089017191 1.267054047 1.000755363 1.330721895 1 19.09635508 2.733677695 24.89082991 1.136950822 1.449998859 0.388893813 0.181890649 354.9422996 1809322.432 0.053341609 0.05174416 541.5988013 -2.733677695 0.313048037 GPGAGSALDDGRRDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPGAGSALDDGRRDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 44 2 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 GPGAGSALDDGRRDPSSNDINGGMEPTPS(0.001)T(0.002)VS(0.025)T(0.006)PS(0.958)PS(0.008)ADLLGLR 130.29 1.23E-09 58254000 25680 9973.7 30240 16481 45238 23237 44687 29727 54177 TRUE FALSE 24466.15729 10990.03137 31626.53391 14824.29857 53127.49288 22432.29686 37869.17742 27123.94629 62578.49246 0.390967509 0.175619944 0.505389834 0.23689127 0.848973677 0.358466559 0.605146847 0.433438794 1 15.93337928 -5 0.105206594 2.863685066 0.066174761 0.511891184 0.17938486 124.1454256 0.878295614 50.02810433 2.283414308 1.00E-05 5 -2.797510305 GPGAPGLAHLQESQAGS(ph)DTDVEEGKAPQAVPLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEK 34 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(1)DTDVEEGKAPQAVPLEK 394.47 5.33E-167 4989920000 1954520 1870920 1930560 2290430 1162880 2207790 2346680 2335050 1255070 TRUE FALSE 1862133.713 2061568.875 2019078.086 2060191.625 1365685.904 2131333.679 1988650.866 2130580.643 1449699.846 1.284496042 1.42206601 1.39275595 1.421115986 0.942047354 1.470189629 1.371767316 1.469670187 1 20.4673228 GPGASVHDR ddPTM_SK-BR-3_Trastuzumab_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 0 103.01 0.0034925 45844000 38050 38423 41286 42451 63696 38339 48240 42216 59952 FALSE TRUE 36251.45191 42338.34738 43179.00394 38183.74483 74804.56223 37011.31082 40880.10201 38519.34324 69249.04997 0.523493852 0.611392465 0.623532077 0.551397382 1.080225104 0.534466694 0.590334482 0.556243634 1 16.07950666 GPGLLES(ph)PSIFNFTADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.803)PS(0.197)IFNFTADR;GPGLLES(0.921)PS(0.079)IFNFTADR 194.37 8.16E-11 69511000 75739 67191 75327 86829 85854 66634 83794 68963 89651 TRUE FALSE 72158.96757 74037.83929 78780.81746 78100.78396 100826.9104 64326.44787 71009.68632 62924.23412 103553.6192 0.696827094 0.714971045 0.760773192 0.754206222 0.973668629 0.62118976 0.685728677 0.607648816 1 16.66001845 3.86698974 3.705711128 0.753199582 0.702932882 0.028152687 0.130301517 1.118652716 27.45729675 0.032511135 0.062696952 7361.897059 -3.86698974 -0.0502667 GPGQVPTATSALSLELQEVEPLGLPQAS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GPGQVPTATSALSLELQEVEPLGLPQASPSR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GPGQVPTATSALSLELQEVEPLGLPQAS(0.825)PS(0.175)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.886)PS(0.114)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.786)PS(0.214)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.784)PS(0.216)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.836)PS(0.164)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.806)PS(0.194)R 184.5 1.58E-18 1069502000 697989 597504 659298 708443 808334 653922 795781 729580 845086 TRUE FALSE 664996.4433 658390.3369 689527.4654 637228.9637 949307.1937 631276.5172 674369.9929 665694.1075 976137.6208 0.681252755 0.674485158 0.706383455 0.652806479 0.972513684 0.646708521 0.690855448 0.681967474 1 19.89672503 -2.140801818 2.327284967 1.618149185 0.709327356 0.478386831 0.093975988 10262491.56 2272247.266 33542666.48 0.022754073 0.007230997 2.140801818 -0.908821828 GPGS(ph)PPRT(ph)PPAPGPPSFEEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPGSPPRTPPAPGPPSFEEQLR 22 1 A0A6E1YH78;Q6ZTN6-2;Q6ZTN6;Q6ZTN6-3 A0A6E1YH78 ANKRD13D Ankyrin repeat domain-containing protein 13D 2 GPGS(1)PPRT(1)PPAPGPPSFEEQLR 92.449 0.0047475 120700000 118370 113020 119600 133300 128820 117660 134150 126740 146340 TRUE FALSE 112774.8847 124536.8665 125083.7783 119900.4307 151286.1672 113585.4047 113682.9537 115641.9737 169033.6598 0.667174129 0.736757795 0.739993315 0.709328727 0.895006163 0.67196915 0.672546248 0.684135774 1 17.36695103 -1.151147618 4.008645389 1.000105287 0.71969453 0.631257706 0.066723563 142255.6478 34708039.54 7667.91053 0.015218475 0.070607752 1.151147618 -0.280410757 GPHGGAASAQDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPHGGAASAQDGR 13 0 O75638-2;O75638 O75638-2 CTAG2 Cancer/testis antigen 2 0 ; 91.62 0.0064481 25631000 14344.2 13227.6 16122.6 15031.7 20028.5 16408.7 16054.5 15169 20323.3 FALSE TRUE 13666.17809 14575.50748 16861.83716 13520.68496 23521.46406 15840.4626 13605.09116 13840.72194 23474.93357 0.582160459 0.620896644 0.718291156 0.575962651 1.001982135 0.674781999 0.579558239 0.589595788 1 14.51883345 3.814911219 1.427530243 0.715251822 0.584617288 0.105121218 0.155817429 1.112852501 4.31613539 0.045633907 0.124237305 6529.970495 -3.814911219 -0.130634534 GPHHLDNS(ph)SPGPGSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.822)S(0.175)PGPGS(0.003)EAR 64.2 0.030601 24105000 25134 26202 25187 32791 28628 22719 23899 23848 2708.2 TRUE FALSE 23945.96563 28872.01359 26341.84886 29494.78638 33620.71414 21932.23533 20252.76861 21759.74269 3128.173824 7.654934468 9.229670475 8.420839231 9.428755573 10.74771289 7.01119457 6.474310493 6.956052929 1 11.61110497 0.678625746 0.700476378 0.963410054 8.904499224 0.837301404 1.058098178 0.461058719 0.43192547 1.112789913 0.400433433 4.771179395 -0.678625746 7.94108917 GPHHLDNSS(ph)PGPGSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.152)S(0.848)PGPGSEAR 139.95 4.38E-07 231580000 79202 78787 75223 98660 91654 78639 87952 86233 10437 TRUE FALSE 75458.27842 86815.48487 78672.04896 88742.50936 107638.4286 75915.71171 74533.30705 78681.98137 12055.51666 6.259232232 7.201307696 6.525813136 7.361153561 8.928562057 6.29717613 6.182506249 6.526637026 1 13.55740586 0.057065614 0.786835746 0.859266265 7.056364601 0.850499011 0.784357318 1.71264098 1.121645524 1.454656179 0.264449549 1.140422072 -0.057065614 6.197098335 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_SK-BR-3_Trastuzumab_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 172.8 3.10E-12 404360000 441130 390650 412800 440070 507860 388660 499630 413380 453680 TRUE FALSE 420278.6591 430457.6791 431727.2883 395833.3275 596430.6232 375200.6067 423402.2672 377182.2557 524034.3773 0.802005894 0.82143023 0.823852989 0.755357558 1.138151711 0.71598472 0.807966587 0.719766244 1 18.99930193 -2.296125216 2.358634223 1.883373179 0.823141836 0.180110557 0.118638361 12635279.91 2368912.329 59283050.06 0.028106235 0.005056788 2.296125216 -1.060231342 GPIKFNVWDTAGQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPIKFNVWDTAGQEK 15 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 255.16 9.33E-25 3318800000 6560600 4605300 6059500 5959000 4965800 6334300 7970500 7115300 5991700 FALSE TRUE 6250493.44 5074585.306 6337334.069 5359989.999 5831833.948 6114941.603 6754453.837 6492246.611 6920862.235 0.903137966 0.733230215 0.915685626 0.77446853 0.842645577 0.88355199 0.97595554 0.938069043 1 22.72252036 1.949885277 2.226201354 0.971161315 0.826710744 0.560932128 0.05527667 0.210211871 1.917859593 0.028970151 0.014859937 89.1015537 -1.949885277 -0.144450571 GPKPEPPGS(ph)GSPAPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.873)GS(0.127)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR 126.91 4.18E-05 2466050000 2620120 2140280 2232230 2555520 1993890 2342130 2716750 2575940 2260600 TRUE FALSE 2496272.12 2358376.965 2334579.953 2298634.274 2341623.785 2261021.451 2302259.891 2350377.038 2611162.302 0.956000367 0.903190492 0.894076922 0.880310761 0.896774506 0.865906133 0.881699268 0.90012675 1 21.3162607 -1.030616808 3.295184863 1.000062639 0.898058259 0.651248132 0.023621447 3014942.323 4899269.409 2202.738201 0.006325976 0.093192979 1.030616808 -0.10200438 GPKPEPPGSGS(ph)PAPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.356)GS(0.644)PAPPR 122.19 5.73E-05 680200000 742850 596270 668970 784280 598980 742370 814430 786560 702500 TRUE FALSE 707736.9527 657030.5909 699642.9362 705442.6844 703441.9224 716661.5408 690173.7455 717684.6366 811440.1121 0.872198628 0.809709282 0.86222375 0.869371225 0.866905532 0.883197084 0.850554138 0.884457923 1 19.6301251 -5 0.228378489 1.762610707 0.84186035 0.835706025 0.019508606 59.41538606 0.594334857 20.88611845 0.033607232 1.00E-05 5 -0.920750357 GPKPEPPGSGS(ph)PAPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPKPEPPGSGSPAPPRR 17 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.134)GS(0.866)PAPPRR 94.632 0.0014439 77566000 75490 70988 69615 79930 61379 72956 81881 80320 72583 TRUE FALSE 71921.73731 78221.75791 72806.91661 71895.28454 72083.47817 70429.51543 69388.5496 73286.755 83838.80094 0.857857418 0.933001868 0.868415528 0.857541899 0.859786607 0.840058716 0.827642438 0.874138873 1 16.35533046 0.946780578 22.13460244 1 0.865785619 0.705480006 0.027504585 2976.6968 1238046.382 0.030713684 0.007678421 8.846685298 -0.946780578 -0.134214382 GPLDKWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPLDKWR 7 1 P27635;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ; 87.323 0.017717 663790000 1103880 397870 435340 378210 1587350 556480 1808910 887810 1858430 FALSE TRUE 1051701.78 438413.4053 455300.7696 340191.6122 1864183.337 537208.9581 1532927.557 810068.6498 2146625.833 0.489932509 0.204233732 0.212100666 0.158477368 0.868424906 0.250257381 0.714110272 0.377368351 1 21.03363931 0.291281358 0.312193152 1.126379007 0.273156594 0.432318192 0.223291412 3.503430786 0.620811776 0.893275672 0.245194579 1.955605987 -0.291281358 -0.853222414 GPLINSEFYTGWLDHWGQPHSTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPLINSEFYTGWLDHWGQPHSTIK 24 0 P16278-3;P16278;E7EQ29;P16278-2;C9J4G9 P16278-3 GLB1 Beta-galactosidase 0 133.95 2.22E-05 64772000 132470 108480 129130 127160 149780 127510 169960 148120 58283 FALSE TRUE 126208.4056 119534.2353 135050.7382 114377.6352 175901.5846 123094.2967 144029.4805 135149.8276 67321.22997 1.874719248 1.775580086 2.006064629 1.698983148 2.612869442 1.828461791 2.13943626 2.007536517 1 16.03877391 GPLLVQDVVFTDEMAHFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GPLLVQDVVFTDEMAHFDR 19 0 P04040 P04040 CAT Catalase 0 ;;;;;;;; 221.41 2.67E-19 601676000 962928 822342 849597 943024 1057070 716394 967785 918247 814235 FALSE TRUE 917412.3018 906139.5847 888551.8628 848229.4359 1241422.673 691585.0961 820131.6237 837840.4247 940502.4053 0.975449182 0.963463336 0.944762988 0.901889704 1.319956936 0.735335808 0.872014382 0.890843468 1 19.84307211 GPLLYCARPPQDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPLLYCARPPQDLK 14 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 124.07 9.05E-05 252910000 275010 242510 250540 278540 224190 256120 319560 303060 245020 FALSE TRUE 262010.8223 267222.0447 262027.5068 250540.63 263288.665 247250.5002 270805.2529 276522.4598 283016.4502 0.925779481 0.944192624 0.925838433 0.885251122 0.930294564 0.873625897 0.956853401 0.977054371 1 18.11052639 1.433719891 3.351888997 0.988035719 0.918293537 0.661203249 0.022110535 0.152315949 3.080696046 0.016584252 0.005705438 27.14687799 -1.433719891 -0.069742182 GPLPLSSQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPLPLSSQHR 10 0 P43243;A0A0R4J2E8;D6REM6;D6R991;D6R8Z5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 109.42 0.0020212 198909000 418520 276160 167137 212867 637260 204490 488710 354780 562350 FALSE TRUE 398737.389 304301.018 174800.3968 191469.2047 748397.9422 197408.46 414148.3137 323713.5824 649556.3659 0.613861106 0.468475153 0.269107357 0.294769191 1.15216782 0.303912748 0.637586414 0.498361034 1 19.3090952 -4.999999999 0.250783484 3.878073088 0.487475495 0.255533095 0.254259344 253.901119 2.514426034 374.4515354 0.33546911 1.00E-05 4.999999999 -3.390597593 GPLPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPLPVKR 7 1 P38159;P38159-2;H3BUY5;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 69.432 0.095812 187870000 461780 381720 444350 445950 453420 432260 518640 477850 485240 FALSE TRUE 439952.5746 420617.702 464723.887 401122.2588 532496.3044 417290.7278 439511.9425 436006.9208 560488.5409 0.784944816 0.750448352 0.829140746 0.715665405 0.950057433 0.744512505 0.784158659 0.777905147 1 19.09632535 -1.552849937 2.648025437 1.013804887 0.78899341 0.511906567 0.06373331 13325235.57 12727101.63 1303047.541 0.014958621 0.027999486 1.552849937 -0.224811477 GPLQSVQVFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPLQSVQVFGR 11 0 P62249;M0R210;M0R3H0;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 160.53 6.37E-05 235580000 258000 258120 203178 247120 252370 247570 264970 225280 231860 FALSE TRUE 245804.8513 284422.7215 212493.9123 222279.0281 296383.2481 238996.5888 224543.96 205553.2889 267815.6646 0.91781357 1.062009281 0.793433471 0.829970228 1.10666883 0.89239212 0.838427283 0.767517797 1 18.03088082 2.006889387 24.99165774 0.854374276 0.948908567 0.083580788 0.10851063 326.3365513 1183799.579 0.03930614 0.028962908 101.5989892 -2.006889387 0.094534291 GPLS(ph)PFNSR ddPTM_SK-BR-3_Trastuzumab_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 81.799 0.021253 139220000 259880 221841 228750 278000 288880 247710 289680 259340 304700 TRUE FALSE 247595.9874 244446.8501 239238.4138 250054.9118 339260.5805 239131.7406 245483.9957 236630.8148 351951.3198 0.703494982 0.694547332 0.679748591 0.710481529 0.963941777 0.6794455 0.697494176 0.672339615 1 18.42501637 -2.084063437 2.387238634 1.440409096 0.722560778 0.502526842 0.08589481 8999697.179 2974397.623 21535191.87 0.020664111 0.008240177 2.084063437 -0.717848318 GPNGYGFHLHGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPNGYGFHLHGEK 13 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;; 151.99 2.38E-05 851500000 1016680 950680 857310 985210 958670 926380 1170660 969840 75384 FALSE TRUE 968623.5513 1047555.373 896618.5115 886174.819 1125861.744 894299.2283 992054.3164 884915.6682 87074.16571 11.12412095 12.03061051 10.29718177 10.17724157 12.9299171 10.27054605 11.3932107 10.1627809 1 16.40995712 0.44048209 1.677454394 0.99903929 11.23917639 0.932737574 0.851828504 0.89953765 2.457381518 0.745895845 0.211079123 2.757287742 -0.44048209 10.2401371 GPPAS(ph)SPAPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.595)S(0.405)PAPAPK 128.85 0.0002567 108740000 298720 271040 267470 309610 252380 275380 316840 319760 292760 TRUE FALSE 284600.0976 298659.2841 279733.7641 278487.4146 296394.9921 265843.5215 268500.2388 291760.1192 338159.7256 0.841614409 0.883189988 0.827223773 0.82353809 0.876494064 0.786147792 0.794004189 0.862787899 1 18.36734532 0.970192279 23.16896794 1.000000001 0.834815046 0.745225493 0.030445455 775.8282463 603037.5408 0.032106225 0.008026556 9.336675795 -0.970192279 -0.165184955 GPPASS(ph)PAPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.032)S(0.968)PAPAPK;GPPAS(0.018)S(0.982)PAPAPK;GPPASS(1)PAPAPK;GPPASS(1)PAPAPK;GPPAS(0.035)S(0.965)PAPAPK;GPPAS(0.07)S(0.93)PAPAPK 211.52 3.24E-08 3598070000 8299380 7293250 7785790 8682340 6722320 8086740 9369660 8990090 7759620 TRUE FALSE 7907084.755 8036440.467 8142776.173 7809574.688 7894690.48 7806694.166 7940146.281 8202870.06 8962942.239 0.882197446 0.896629729 0.908493657 0.871318199 0.880814611 0.870996818 0.885886138 0.915198362 1 23.09554097 0.830934628 2.547382243 0.999938893 0.885581248 0.913786172 0.01109381 0.184009238 2.124503519 0.010889601 0.002910527 6.77539514 -0.830934628 -0.114357645 GPPASSPAPAPKFS(ph)PVTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASSPAPAPKFS(1)PVTPK;GPPASSPAPAPKFS(0.998)PVT(0.002)PK 213.14 2.98E-17 1081630000 2115060 1268910 1908360 1870470 1230160 2082420 2510400 2288600 1487290 TRUE FALSE 2015085.305 1398213.372 1995860.194 1682446.802 1444699.515 2010305.273 2127392.373 2088198.051 1717931.337 1.17297197 0.81389363 1.16178112 0.979344614 0.840953002 1.170189535 1.238345403 1.215530566 1 20.71224094 2.115324025 9.786584971 1.184284325 0.992664637 0.26460666 0.130869365 0.325786546 26.49225574 0.045603077 0.033673077 130.4139428 -2.115324025 -0.191619688 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_SK-BR-3_Trastuzumab_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" 2 GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(0.999)S(0.999)DEEREPT(0.002)PVLGSGAAAAGR 192.09 2.75E-18 3333545000 2240240 2102800 2381300 2730610 2617830 2371550 2904530 2452520 2923580 TRUE FALSE 2134348.295 2317077.711 2490484.96 2456123.895 3074378.723 2289422.629 2461390.603 2237764.347 3376953.855 0.632033598 0.686144321 0.737494519 0.727319354 0.91039998 0.677954964 0.728878957 0.662657662 1 21.68729103 -5 0.30667882 3.423821312 0.703417526 0.562652072 0.076407328 217.941131 1.987804184 341.1431981 0.072903906 1.00E-05 5 -2.720403786 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_SK-BR-3_Trastuzumab_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 GPPDFS(0.976)S(0.024)DEEREPTPVLGSGAAAAGR;GPPDFS(0.933)S(0.067)DEEREPTPVLGSGAAAAGR;GPPDFS(0.936)S(0.064)DEEREPTPVLGSGAAAAGR;GPPDFS(0.912)S(0.088)DEEREPTPVLGSGAAAAGR;GPPDFS(0.921)S(0.079)DEEREPTPVLGSGAAAAGR 310.84 5.80E-82 4776740000 1079600 974417 1038093 1268870 1226280 1130860 1337260 1108890 1229440 TRUE FALSE 1028569.448 1073711.2 1085690.591 1141320.777 1440142.844 1091698.035 1133236.427 1011789.713 1420095.276 0.724296084 0.756083918 0.764519543 0.803693102 1.014117058 0.768749853 0.798000279 0.712480162 1 20.43755629 -5 0.204279931 1.915148084 0.760079913 0.348127408 0.085606665 168.2932643 1.670658879 63.6268531 0.193623798 1.00E-05 5 -1.155068172 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_SK-BR-3_Trastuzumab_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 GPPDFSSDEEREPT(0.999)PVLGS(0.001)GAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(0.998)PVLGS(0.002)GAAAAGR 309.19 1.71E-81 4691220000 2861210 2466750 2610390 3692830 4644720 3162980 3617700 3002780 3918200 TRUE FALSE 2725966.274 2718114.629 2730078.964 3321619.712 5454757.697 3053445.209 3065753.421 2739840.664 4525814.445 0.602315077 0.600580219 0.603223795 0.733927507 1.205254383 0.674673089 0.677392646 0.605380688 1 22.10974601 3.140347126 4.792539305 0.804172646 0.602140065 0.256989774 0.174137079 0.320832044 12.41352194 0.051001242 0.061972731 1381.488028 -3.140347126 -0.20203258 GPPLREGEELVMDEEAYVLYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GPPLREGEELVMDEEAYVLYHR 22 1 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ;;; 92.812 0.0012115 32780900 38303.6 19849.6 36377.5 31334.5 47291.8 30799.6 49774.4 35300.2 53754.7 FALSE TRUE 36493.06474 21872.29681 38045.44436 28184.69653 55539.47495 29733.00213 42180.40111 32209.12735 62090.70434 0.587737973 0.352263629 0.612739777 0.453927795 0.894489369 0.478863985 0.679335201 0.518743147 1 15.92208968 -4.999999998 0.157871961 2.607446167 0.440629566 0.458701048 0.145872067 108.1922925 0.988364434 54.47903104 0.578418299 1.00E-05 4.999999998 -2.166816601 GPPPPPTASEPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPPPPPTASEPTRR 14 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 111.95 0.00099713 50961000 79380 79276 67952 87607 68334 72057 77829 78791 67977 FALSE TRUE 75627.86472 87354.31453 71067.66641 78800.57792 80251.42796 69561.64802 65954.75662 71891.64234 78518.52598 0.963184978 1.112531259 0.905106986 1.003592171 1.022069976 0.885926565 0.839989745 0.915601018 1 16.26074547 2.235989583 24.99451863 0.890534953 1.008732689 0.297632943 0.065809739 61.82183673 600995.3159 0.022873127 0.017681976 172.1827274 -2.235989583 0.118197735 GPPPSWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPPPSWGR 8 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 92.822 0.026766 187066000 174106 160569 167291 184183 174705 192414 188570 200705 175899 FALSE TRUE 165876.3544 176931.1637 174961.4578 165668.5749 205173.4967 185750.6549 159800.1832 183130.2062 203176.5186 0.816414985 0.870824862 0.861130307 0.81539233 1.009828784 0.914232886 0.786509112 0.901335487 1 17.63237415 -5 0.239987646 1.746335143 0.85309235 0.30278561 0.062197077 225.5502487 2.248734344 82.41456759 0.097825101 1.00E-05 5 -0.893242794 GPPPTDPYGRPPPYDRGDYGPPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPPPTDPYGRPPPYDRGDYGPPGR 24 2 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ; 83.115 0.0076924 490090000 276580 181880 280250 248720 322490 269690 368560 297250 426890 FALSE TRUE 263506.6115 200413.7788 293099.7397 223718.1931 378732.1539 260350.5677 312329.4029 271221.2142 493089.9209 0.534398698 0.406444687 0.59441438 0.453706684 0.768079285 0.527998153 0.633412669 0.550044125 1 18.91149124 -5 0.170242042 2.764573406 0.442839247 0.689307153 0.094689501 67.81991042 0.639994124 40.35032041 0.306127625 1.00E-05 5 -2.321734158 GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;;; 348.57 3.66E-110 4556230000 3236375 2977502 2744127 3352732 2089097 3300765 3174192 3480479 2053473 FALSE TRUE 3083397.968 3280912.839 2869947.937 3015709.01 2453434.855 3186458.68 2689910.712 3175709.808 2371915.105 1.299961352 1.383233671 1.209970766 1.271423671 1.034368747 1.343411775 1.134067027 1.338880047 1 21.17762094 -4.999999949 0.067960132 0.179708494 1.566772392 0.34601518 0.106213792 321.0084199 1.575431234 42.57463958 5.63391921 1.00E-05 4.999999949 1.387063898 GPPQEEEEEEDEEEEATKEDAEAPGIRDHESL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPPQEEEEEEDEEEEATKEDAEAPGIRDHESL 32 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 85.412 0.00010787 61759000 19619 12594 20258 16747 17014 18870 29064 20432 23048 FALSE TRUE 18691.64875 13877.34292 21186.84934 15063.55974 19981.23621 18216.52717 24629.753 18642.86576 26622.16613 0.702108486 0.52127024 0.795834916 0.565827727 0.750548852 0.684261644 0.925159616 0.700276066 1 14.70034034 1.399257719 0.422221362 1.000938399 0.609430957 0.498043882 0.102775103 0.720425938 0.369813378 0.113434562 0.076384425 25.07596868 -1.399257719 -0.391507442 GPPQS(ph)PVFEGVYNNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR 266.39 3.62E-27 7465945000 3221716 2753946 2701625 3127220 3010600 2729404 2974652 2763376 2723521 TRUE FALSE 3069431.87 3034576.228 2825497.179 2812865.904 3535647.687 2634884.055 2520814.204 2521400.148 3145870.727 0.975701844 0.964622037 0.898160612 0.894145421 1.123901137 0.837569081 0.801308898 0.801495156 1 21.58502796 GPPS(ph)PPAPVMHS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.992)PS(0.008)R;GPPS(1)PPAPVMHS(0.983)PS(0.017)R;GPPS(1)PPAPVMHS(0.997)PS(0.003)R;GPPS(1)PPAPVMHS(0.899)PS(0.101)R;GPPS(1)PPAPVMHS(0.892)PS(0.108)R;GPPS(1)PPAPVMHS(0.985)PS(0.015)R;GPPS(1)PPAPVMHS(0.924)PS(0.076)R;GPPS(1)PPAPVMHS(0.897)PS(0.103)R;GPPS(1)PPAPVMHS(0.904)PS(0.096)R;GPPS(1)PPAPVMHS(0.998)PS(0.002)R;GPPS(1)PPAPVMHS(0.981)PS(0.019)R;GPPS(1)PPAPVMHS(0.983)PS(0.017)R 156.05 1.16E-06 7933840000 3208510 2878273 2958580 3255070 3572260 3022030 3580670 3123910 3371570 TRUE FALSE 3056850.091 3171572.291 3094233.819 2927864.179 4195261.013 2917376.343 3034373.028 2850363.88 3894415.856 0.784931606 0.814389733 0.794530922 0.751810872 1.077250393 0.749117827 0.779159992 0.731910506 1 21.89297552 -2.198560118 2.313929806 1.547516154 0.809930746 0.269882936 0.098009025 6391265.856 1339336.929 18327122.05 0.022222499 0.006330527 2.198560118 -0.737585408 GPPS(ph)PPAPVMHS(ph)PSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.977)PS(0.023)RK;GPPS(1)PPAPVMHS(0.887)PS(0.113)RK;GPPS(1)PPAPVMHS(0.83)PS(0.17)RK;GPPS(1)PPAPVMHS(0.962)PS(0.038)RK;GPPS(1)PPAPVMHS(0.923)PS(0.077)RK;GPPS(1)PPAPVMHS(0.954)PS(0.046)RK;GPPS(1)PPAPVMHS(0.802)PS(0.198)RK 93.804 0.0018066 2386568000 1457444 1174216 1365960 1427712 1192952 1395061 1653812 1520662 1311299 TRUE FALSE 1388553.51 1293869.945 1428590.617 1284195.677 1401002.451 1346749.688 1401492.605 1387504.774 1514648.552 0.916749637 0.854237733 0.943182902 0.847850596 0.924968666 0.889149952 0.925292276 0.916057241 1 20.53055165 0.239276296 0.489751475 1.008541043 0.889907497 0.532685098 0.029766249 1.997593509 0.716293023 0.060683453 0.013513746 1.734907384 -0.239276296 -0.118633546 GPPS(ph)PPAPVMHSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 1 GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR 136.35 1.51E-05 638860000 665270 628990 587920 740280 646930 650730 704480 662010 657150 TRUE FALSE 633824.0055 693084.7961 614876.7135 665865.648 759754.3872 628195.0569 596998.6373 604040.8949 759057.4657 0.83501452 0.913086067 0.810052916 0.877226927 1.000918141 0.827598812 0.786499922 0.795777556 1 19.53384959 -0.398943881 7.483157886 0.999998033 0.856768273 0.335948728 0.063712332 0 0 0.062633438 0.014762843 0.399076467 0.398943881 -0.14322976 GPQAAAPPAS(ph)PEPFAHIQAVFAGSDDPFATALSMSEMDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GPQAAAPPASPEPFAHIQAVFAGSDDPFATALSMSEMDRR 40 1 H7C2F7;Q8WVT3 H7C2F7 TRAPPC12 Trafficking protein particle complex subunit 12 1 GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR;GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR;GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR;GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR;GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR;GPQAAAPPAS(1)PEPFAHIQAVFAGSDDPFATALSMSEMDRR 212.36 2.38E-32 203029000 170510.4 124713.2 168165.9 198276.2 217743.6 165471.2 200478.2 169589.8 199963.7 TRUE FALSE 162450.7113 137421.6169 175876.4729 178345.0997 255718.0149 159740.8909 169891.5686 154739.6181 230973.0493 0.70333189 0.594968189 0.761458851 0.772146795 1.107133562 0.691599697 0.735547152 0.669946639 1 17.817365 3.521730767 3.410856644 0.812810091 0.649806827 0.216020832 0.137743144 0.369122199 8.672151837 0.037501992 0.058072019 3324.533912 -3.521730767 -0.163003264 GPQLFHMDPSGTFVQCDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GPQLFHMDPSGTFVQCDAR 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 234.47 3.89E-24 1592120000 1075517 1159823 945084 1184399 983621 1010782 1019387 1087506 856248 FALSE TRUE 1024679.443 1278010.282 988417.0362 1065340.962 1155164.191 975778.3659 863860.7908 992278.2094 989030.5667 1.036044261 1.292184817 0.999379665 1.077156762 1.167976228 0.986600818 0.873441954 1.003283663 1 19.91565558 2.118542652 5.096749905 0.941644719 1.124214958 0.414374524 0.086849467 0.173339711 7.036043969 0.032651641 0.02379069 131.3840521 -2.118542652 0.182570239 GPREPGPAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GPREPGPAGR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;;;;; 138.22 6.43E-05 4746518000 1843281 1054647 1849158 1561002 2333974 1623704 2378233 1790161 2737895 FALSE TRUE 1756152.76 1162116.728 1933943.723 1404087.113 2741018.327 1567474.723 2015389.877 1633405.013 3162473.773 0.555309826 0.367470788 0.611528778 0.443983797 0.86673235 0.495648292 0.637282716 0.516495987 1 21.59262208 -5 0.171453902 2.741582167 0.448493475 0.51622983 0.13317451 98.17599712 0.928994299 58.23015997 0.427520289 1.00E-05 5 -2.293088692 GPRIS(ph)APNVDFNLEGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GPRISAPNVDFNLEGPK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPRIS(1)APNVDFNLEGPK;GPRIS(1)APNVDFNLEGPK;GPRIS(1)APNVDFNLEGPK;GPRIS(1)APNVDFNLEGPK 237.22 1.98E-20 1956340000 2252290 1290240 2122160 1903020 2037100 1979610 2796440 2397650 2212810 TRUE FALSE 2145828.715 1421716.923 2219463.135 1711724.814 2392369.595 1911055.609 2369791.718 2187699.055 2555961.273 0.839538822 0.556235706 0.868347716 0.669699041 0.935996026 0.747685667 0.927162607 0.855920267 1 21.28543455 1.878144005 0.473896739 0.989746832 0.702645073 0.353765237 0.106746186 0.87065511 0.459393745 0.099052112 0.076345445 75.53426451 -1.878144005 -0.287101759 GPRPWEDPDLLQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPRPWEDPDLLQGR 14 1 A0A087WX56;A0A087X1F5;A0A087WYV9;Q9P0S2 A0A087WX56 SYNJ2BP-COX16;COX16 "Cytochrome c oxidase assembly protein COX16 homolog, mitochondrial" 0 61.165 0.088872 0 91912 73998 87654 85010 93614 81522 90688 81639 72227 FALSE TRUE 87567.50191 81538.48033 91673.0226 76464.63329 109940.252 78698.8727 76851.88 74490.25636 83427.59428 1.049622762 0.977356246 1.098833346 0.916538874 1.317792427 0.943319454 0.921180584 0.89287312 1 16.34823702 2.037374576 24.9998467 0.930006666 1.057842868 0.270908087 0.106521956 213.7592054 142982.6321 0.03665657 0.027072613 108.9869693 -2.037374576 0.127836201 GPS(ph)PAPAS(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.5)S(0.5)PK 97.69 0.0041311 0 201080 217320 170970 221380 113050 211550 194020 217880 130540 TRUE FALSE 191575.3469 239465.1551 178809.1436 199126.4618 132765.8842 204223.9705 164418.6856 198801.2721 150783.4765 1.270532762 1.588139235 1.185866965 1.320611956 0.880506852 1.354418768 1.090429067 1.318455289 1 17.20211881 3.636599942 7.561077875 1.168370557 1.428731679 0.305709105 0.166064125 0.274494431 17.94573289 0.039514489 0.061365473 4331.117259 -3.636599942 0.260361122 GPS(ph)PAPAS(ph)SPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.5)S(0.5)PKR;GPS(1)PAPAS(0.5)S(0.5)PKR;GPS(1)PAPAS(0.593)S(0.407)PKR 80.387 0.019257 549534000 2984640 3069370 2556710 3397570 1883830 3104450 2877940 2913630 1946220 TRUE FALSE 2843561.982 3382142.293 2673937.682 3056039.809 2212369.356 2996942.118 2438857.396 2658497.111 2248029.858 1.264912907 1.504491713 1.18945826 1.359430258 0.984136998 1.333141599 1.084886568 1.182589769 1 21.10022977 2.529252495 0.357606295 1.019918005 1.426469415 0.365359116 0.129862364 1.477054506 0.414177961 0.137338528 0.218718451 338.261441 -2.529252495 0.40655141 GPS(ph)PSPVGSPASVAQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GPSPSPVGSPASVAQSR 17 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 GPS(0.892)PS(0.108)PVGSPASVAQSR;GPS(0.828)PS(0.172)PVGSPASVAQSR;GPS(0.977)PS(0.023)PVGSPASVAQSR;GPS(0.974)PS(0.026)PVGSPASVAQSR;GPS(1)PSPVGSPASVAQSR;GPS(0.999)PS(0.001)PVGSPASVAQSR;GPS(0.933)PS(0.067)PVGSPASVAQSR 279.82 7.19E-36 1204557000 1040311 961627 966507 1160838 872285 1038286 1166676 1078549 969910 TRUE FALSE 991137.5607 1059617.885 1010822.302 1044148.359 1024411.228 1002329.895 988678.1487 984105.5318 1120318.689 0.884692517 0.94581827 0.902263179 0.932010123 0.914392697 0.89468283 0.882497238 0.878415706 1 20.09547775 2.361164712 6.454367336 0.901535187 0.917449344 0 0.037949004 0.793321391 41.86158317 0.011823145 0.00984498 229.7019661 -2.361164712 0.015914157 GPS(ph)PSS(ph)PTPPAAAAPAEQAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPSPSSPTPPAAAAPAEQAPR 21 0 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 GPS(0.997)PS(0.01)S(0.989)PT(0.004)PPAAAAPAEQAPR;GPS(1)PS(0.006)S(0.99)PT(0.005)PPAAAAPAEQAPR 200.6 1.08E-21 247140000 277220 228390 242170 277390 264990 243180 302930 249650 285310 TRUE FALSE 264116.36 251663.2007 253273.734 249506.2302 311204.1721 234758.6156 256712.4648 227789.3225 329554.4176 0.801434743 0.763646873 0.768533876 0.757101762 0.944318011 0.712351597 0.778968362 0.691203972 1 18.33015718 -2.200587421 2.493617996 1.700290943 0.778677491 0.519485132 0.06732989 6131225.766 2039931.871 24058097.35 0.014778594 0.006301045 2.200587421 -0.921613453 GPS(ph)PTPEDVSMKEENLCQAFSDALLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.8)PT(0.198)PEDVS(0.001)MKEENLCQAFSDALLCK 61.099 0.070143 29860000 114290 116630 106730 127010 75455 125200 129370 135070 105690 TRUE FALSE 108887.7382 128514.7296 111623.6761 114242.7135 88614.32811 120864.2926 109632.2305 123242.5547 122079.8654 0.891938551 1.052710282 0.9143496 0.935803075 0.725871771 0.990042807 0.898036954 1.009524006 1 16.89746575 -0.419345227 6.33582493 1 0.930639448 0.062258956 0.08783528 0 0 0.080315184 0.01893047 0.380763029 0.419345227 -0.069360552 GPS(ph)WDPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR 138.08 0.00075595 11434535000 9914860 9500300 7312840 11440770 9427960 8899990 8914760 8391250 7267190 TRUE FALSE 9446204.217 10468391.37 7648140.947 10290722.06 11072193.24 8591781.115 7554649.631 7656467.665 8394148.71 1.125332007 1.24710578 0.911127645 1.225939928 1.31903706 1.023544068 0.899989968 0.912119612 1 23.00095259 2.008754613 23.27449151 0.935134943 1.164885799 0.486463468 0.108617779 66.44942031 176656.5858 0.039387577 0.029031669 102.0362792 -2.008754613 0.229750856 GPS(ph)WDPFRDWYPHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR;GPS(1)WDPFRDWYPHSR 127.49 4.71E-05 11489379000 4858908 2685435 3905444 4376477 5889432 4182812 5706906 4248379 4990713 TRUE FALSE 4629237.048 2959083.88 4084512.47 3936545.217 6916547.076 4037960.172 4836212.675 3876368.413 5764647.283 0.80303908 0.513315687 0.70854508 0.68287703 1.199821383 0.700469599 0.83894338 0.672438091 1 22.45880091 2.961457925 24.99992921 0.86328894 0.663258931 0.276545102 0.163143833 702.1696865 455455.2792 0.046452457 0.049279882 915.0776007 -2.961457925 -0.20003001 GPSAGGGPGSGT(ph)SPQVEWTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPSAGGGPGSGTSPQVEWTAR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 1 GPSAGGGPGS(0.003)GT(0.553)S(0.444)PQVEWTAR;GPSAGGGPGSGT(0.586)S(0.414)PQVEWTAR 271.29 1.31E-43 387540000 510780 473510 516150 561180 619450 519010 634410 542640 709590 TRUE FALSE 486636.4417 521761.2073 539815.988 504769.1202 727481.8839 501036.5536 537619.1028 495123.5649 819629.5931 0.593727271 0.636581709 0.658609685 0.615850287 0.88757396 0.611296319 0.655929346 0.604082099 1 19.64461255 -2.19221472 2.38161097 1.987892259 0.655748707 0.618201317 0.084460734 3596043.543 674624.7544 19225486.58 0.019233812 0.0064237 2.19221472 -1.332143552 GPSAGGGPGSGTS(ph)PQVEWTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPSAGGGPGSGTSPQVEWTAR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 1 GPSAGGGPGS(0.019)GT(0.055)S(0.926)PQVEWTAR 335.66 7.09E-68 109390000 161410 149400 163260 169600 184420 162240 194160 161240 219970 TRUE FALSE 153780.4692 164624.0299 170745.6325 152551.4858 216582.7896 156621.5881 164537.326 147120.9708 254081.8241 0.605239945 0.64791738 0.672010417 0.600402986 0.85241355 0.61642185 0.647576136 0.57902989 1 17.95493365 -1.40069104 3.039906447 1.00523599 0.652379681 0.673326401 0.076040042 12044740.67 14786748.1 548511.1264 0.017617157 0.039747421 1.40069104 -0.352856309 GPSFPEPLREEQDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPSFPEPLREEQDLER 16 1 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C1D8;A0A494C0S8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ;; 185.14 1.56E-09 348283000 519317 525993 442791 588326 563450 503636 525644 533800 528129 FALSE TRUE 494769.9146 579592.2847 463093.4053 529186.3527 661715.5016 486194.959 445447.3537 487057.6421 610028.548 0.811060263 0.950106821 0.759133989 0.867478013 1.084728746 0.797003617 0.73020739 0.798417785 1 19.21851723 -0.79427206 5.294735423 1.00000004 0.849978209 0.174331147 0.102749376 13388489.52 2528642.076 9.641377501 0.024350458 0.160593491 0.79427206 -0.150021831 GPSPAPASS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.034)S(0.966)PKR;GPSPAPAS(0.082)S(0.918)PKR 117.08 0.00047299 391600000 256330 269560 239560 306970 175565 283090 277880 310750 192944 TRUE FALSE 244213.7889 297028.4705 250544.063 276112.7924 206183.4804 273286.5223 235484.3024 283539.0826 222864.7701 1.095793601 1.332774446 1.124197704 1.238925256 0.925150621 1.226243709 1.056624168 1.272247213 1 17.76580905 -4.999999875 0.1102532 0.506555542 1.250487442 0.117576997 0.119961991 301.765366 2.210718342 34.01728293 1.347241639 1.00E-05 4.999999875 0.743931899 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDRASEPK 127.53 1.19E-05 64576000 33496 28327 37072 35687 31118 38486 39107 36054 27477 TRUE FALSE 31912.71046 31213.55351 38771.78787 32099.67496 36544.96935 37153.22017 33140.5089 32896.92063 31737.99283 1.005505 0.983475977 1.221620664 1.011395873 1.151458114 1.170622867 1.044190446 1.036515472 1 14.95392327 GPSS(ph)VEDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 GPS(0.025)S(0.975)VEDIK;GPS(0.037)S(0.963)VEDIK;GPS(0.035)S(0.965)VEDIK 134.13 0.00027015 1169530000 3431840 3786230 2987440 4341360 2375640 3883700 3782210 4037000 2445450 TRUE FALSE 3269623.724 4172051.142 3124417.079 3904958.245 2789950.864 3749206.495 3205164.399 3683498.879 2824677.896 1.157520908 1.477000669 1.106114465 1.382443729 0.987705843 1.32730408 1.134700846 1.304042094 1 21.42965493 -4.999999996 0.14376848 0.154811298 1.325366619 0.18691007 0.146122972 194.1283287 1.690301147 46.93840056 0.733117839 1.00E-05 4.999999996 1.170555321 GPSSVEDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 115.71 0.0033294 1118120000 1112460 952490 928430 1157480 779900 1063210 1204280 1158760 975810 FALSE TRUE 1059876.22 1049549.814 970999.4338 1041127.911 915914.3131 1026390.771 1020544.968 1057292.831 1127133.631 0.940328805 0.931167153 0.861476765 0.923695188 0.812604901 0.910620305 0.905433872 0.938036806 1 20.10422714 0.903556745 1.97177067 0.999842255 0.900858021 0.439053386 0.037180402 0.451147437 3.605853242 0.035454041 0.009890778 8.008602621 -0.903556745 -0.098984234 GPSTPKS(ph)PGASNFSTLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPSTPKSPGASNFSTLPK 18 1 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 GPS(0.012)T(0.01)PKS(0.977)PGASNFSTLPK 92.01 0.001462 285410000 60614 47968 75869 77182 52813 64802 84435 80076 74524 TRUE FALSE 57748.89635 52855.99374 79347.66869 69423.51872 62023.57048 62557.89049 71552.88999 73064.12093 86080.8013 0.67086848 0.614027669 0.921781251 0.806492478 0.720527336 0.726734528 0.831229367 0.848785325 1 16.39340389 -4.063715637 0.039462131 2.180943635 2.25E-10 0.531738437 0.079271611 545.4691208 1.888704401 85.6614052 31.01223965 8.64E-05 4.063715637 -2.180943635 GPSWDPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;; 132.08 0.0022738 16625008000 26347160 20719080 12364940 18538050 25422760 15756090 22389510 19139740 19056600 FALSE TRUE 25101781.96 22830377.81 12931884.73 16674569.99 29856481.29 15210452.65 18973579.04 17463762.9 22011800.2 1.140378421 1.037188126 0.587497824 0.757528682 1.356385258 0.691013571 0.861973072 0.793381856 1 24.3917738 3.981883548 24.25636263 0.859764052 1.101682144 0.176059225 0.206899148 757.9874957 1014882.677 0.050546023 0.091932025 9591.434119 -3.981883548 0.241918092 GPSWDPFRDWYPHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 201.3 3.90E-09 43806566000 5072792 2504011 3855250 4234345 6123773 4015414 6013454 4347417 5258688 FALSE TRUE 4833011.175 2759172.568 4032017.026 3808700.596 7191757.072 3876359.206 5095991.148 3966734.12 6074178.477 0.795664993 0.454246213 0.663796272 0.627031394 1.183988435 0.63817012 0.838959732 0.653048661 1 22.53425787 2.926009571 24.99987395 0.840408935 0.624114342 0.286472083 0.176188713 172.5007708 58283.84081 0.049428642 0.052427009 843.3533434 -2.926009571 -0.216294593 GPTEADELMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GPTEADELMKR 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 167.11 3.15E-05 2439440000 2790450 1588110 2528200 2306000 2465990 2555680 3603900 2994870 3198210 FALSE TRUE 2658550.959 1749940.215 2644120.471 2074196.499 2896057.875 2467176.161 3054058.865 2732623.306 3694172.073 0.719660835 0.473702952 0.71575455 0.561478041 0.783953161 0.667856319 0.8267235 0.739711971 1 21.81681964 1.122967482 0.402959797 1.014468993 0.589703721 0.607022675 0.089338104 0.712487051 0.331077498 0.115548817 0.067181537 13.27295071 -1.122967482 -0.424765272 GPTEQLVSPEPEVHDIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPTEQLVSPEPEVHDIER 18 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 139.17 2.50E-06 0 111020 101090 98210 108460 114900 95775 127600 101880 111730 FALSE TRUE 105772.3046 111391.1859 102713.0256 97557.39474 134938.5236 92458.28773 108132.2765 92958.8471 129056.5178 0.819581269 0.863119414 0.795876314 0.755927685 1.045576976 0.716417034 0.837867613 0.72029564 1 16.97764348 2.676844364 0.009558682 1.665899117 9.89E-07 0.073108483 0.105186331 11419.40632 44.78401162 3804.976864 3996.688996 475.1649126 -2.676844364 -1.665898128 GPTSS(ph)PCEEEGDEGEEDRT(ph)SDLRDEAS(ph)SVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 3 GPT(0.047)S(0.186)S(0.767)PCEEEGDEGEEDRT(0.756)S(0.244)DLRDEAS(0.6)S(0.39)VT(0.011)R;GPT(0.017)S(0.118)S(0.866)PCEEEGDEGEEDRT(0.589)S(0.411)DLRDEAS(0.534)S(0.393)VT(0.073)R 192.15 4.84E-18 459220000 204493 168345 201081 210329 229225 185768 231787 194863 229381 TRUE FALSE 194827.0212 185499.5469 210300.7627 189186.3293 269201.7674 179334.8076 196423.6361 177799.7627 264952.234 0.735328849 0.700124487 0.793730853 0.714039382 1.016038866 0.676857126 0.741354897 0.671063459 1 18.01537277 -2.17332477 2.442393707 1.654712152 0.753031305 0.374760781 0.098949979 17699516.57 4138272.678 64104797.73 0.022929247 0.006709269 2.17332477 -0.901680847 GPTSTSIDNIDGT(ph)PVRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 209.24 3.76E-16 2120050000 1632160 1453540 1495500 1598500 1760030 1467250 1797970 1678190 2015990 TRUE FALSE 1555011.031 1601657.379 1564070.154 1437815.743 2066978.675 1416438.765 1523656.655 1531238.787 2328619.433 0.667782382 0.687814143 0.671672723 0.617454154 0.887641255 0.608274046 0.65431759 0.657573653 1 21.15104345 -1.725982427 2.589423354 1.062443194 0.680043614 0.62698418 0.077181324 11895648.88 9317311.048 4796281.442 0.019312685 0.018793929 1.725982427 -0.38239958 GPVEGYEENEEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GPVEGYEENEEFLR 14 0 F5GYQ2;Q9UI30;Q9UI30-2;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 259.47 4.70E-24 480990000 368045 371707 367413 420250 464682 359772 472822 432384 477688 FALSE TRUE 350648.2422 409584.3659 384259.2495 378005.6716 545722.3937 347313.0054 400684.3199 394522.1647 551765.4153 0.635502394 0.742316127 0.696417787 0.685084025 0.989047843 0.629457729 0.726186 0.715017929 1 19.07369551 -5 0.33605623 3.883595064 0.7143715 0.423157489 0.099893483 359.9044706 3.062537654 743.7272518 0.075965665 1.00E-05 5 -3.169223563 GPVS(ph)PSVSFQPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GPVSPSVSFQPLAR 14 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 GPVS(0.987)PS(0.012)VS(0.001)FQPLAR;GPVS(0.987)PS(0.013)VSFQPLAR;GPVS(0.997)PS(0.003)VSFQPLAR 235.22 3.28E-17 345670000 382227 276112 328005 455292 516144 325871 422605 340559 424482 TRUE FALSE 364159.8872 304248.1267 343044.3537 409525.1832 606159.3502 314586.0056 358128.8456 310737.8485 490308.5006 0.742715835 0.620523867 0.699650023 0.835239819 1.236281544 0.641608304 0.730415331 0.633759864 1 18.90333025 3.271518127 5.919396596 0.82999023 0.679596284 0.145799556 0.178129806 0.376254753 36.27847366 0.050164788 0.066708207 1868.607671 -3.271518127 -0.150393946 GPVSGTEPEPVYS(ph)MEAADYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVSGTEPEPVY(0.002)S(0.998)MEAADYR 99.021 0.00075171 36744000 46676 34539 44194 58161 56826 57982 56562 45321 88210 TRUE FALSE 44469.71798 38058.56337 46220.33861 52314.54578 66736.43641 55974.0688 47932.42807 41352.45298 101889.1563 0.436451921 0.373529085 0.45363354 0.513445667 0.654990569 0.549362374 0.470436991 0.405857252 1 16.63664099 -5 0.297721296 5.251183134 0.44885925 0.793674064 0.082145157 124.8490391 1.159314804 331.1540428 0.088812373 1.00E-05 5 -4.802323884 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR 29 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 238.71 2.42E-45 203080000 294840 260270 251380 320510 324680 262090 289000 299630 262350 FALSE TRUE 280903.4975 286791.8089 262906.0216 288291.7259 381304.0892 253013.7576 244907.7422 273392.8088 303033.8981 0.926970544 0.946401742 0.867579579 0.951351409 1.258288566 0.834935495 0.808185961 0.902185566 1 18.20911966 -0.894697134 4.389008537 1.000000893 0.931414739 0.023403472 0.123338369 15642593.7 3564111.188 144.033621 0.028896061 0.12743915 0.894697134 -0.068586154 GPWALEEESLVGREPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GPWALEEESLVGREPEER 18 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63 O00515 LAD1 Ladinin-1 0 ; 169.64 1.62E-11 322920000 224200 184894 205510 226110 246450 200187 255190 211380 267850 FALSE TRUE 213602.5103 203734.9088 214932.8368 203380.9932 289430.802 193254.474 216256.0786 192870.4466 309386.81 0.690406001 0.658511941 0.694705882 0.657368015 0.935498194 0.624637081 0.698982864 0.623395828 1 18.23905217 -1.796033983 2.467064838 1.09522339 0.696634723 0.534412235 0.088598102 9369599.325 6152147.064 5343447.824 0.02126448 0.015994329 1.796033983 -0.398588667 GQAALDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQAALDR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 81.215 0.064689 217740000 433710 359320 366400 403220 443030 358100 451880 410740 498280 FALSE TRUE 413209.3878 395935.1165 383199.8024 362687.5595 520294.2917 345698.9072 382937.4067 374773.4281 575550.7175 0.717937404 0.687923939 0.665796759 0.630157427 0.90399382 0.600640216 0.665340855 0.651156217 1 19.13458354 -1.287391007 3.277325534 1.0014313 0.689798527 0.583414881 0.082225091 48800119.58 69674332.39 691430.3196 0.018160052 0.051595164 1.287391007 -0.311632772 GQAS(ph)SPTPEPGVGAGDLPGPTSAPVPS(ph)GS(ph)QSGGRGSPVSPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQASSPTPEPGVGAGDLPGPTSAPVPSGSQSGGRGSPVSPRR 42 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 3 GQAS(0.501)S(0.437)PT(0.062)PEPGVGAGDLPGPT(0.013)S(0.013)APVPS(0.395)GS(0.395)QS(0.395)GGRGS(0.395)PVS(0.395)PRR 81.128 0.00043874 81377000 13197 12564 15290 13685 20960 13323 17506 16291 22550 TRUE FALSE 12573.20396 13844.28588 15991.06162 12309.3578 24615.41736 12861.62117 14835.13818 14864.47368 26046.93883 0.482713306 0.531512973 0.613932475 0.472583664 0.945040702 0.493786285 0.569553999 0.570680254 1 14.66882621 -5 0.259412114 3.689256891 0.542873026 0.479800845 0.135637695 164.5701991 1.617216878 236.1181203 0.169119192 1.00E-05 5 -3.146383865 GQASSPT(ph)PEPGVGAGDLPGPTSAPVPS(ph)GS(ph)QSGGRGSPVSPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQASSPTPEPGVGAGDLPGPTSAPVPSGSQSGGRGSPVSPRR 42 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 3 GQAS(0.309)S(0.282)PT(0.41)PEPGVGAGDLPGPT(0.001)S(0.003)APVPS(0.412)GS(0.412)QS(0.39)GGRGS(0.312)PVS(0.471)PRR 84.858 0.0018072 88889000 21689 15356 20424 23659 27889 18063 26749 24604 38410 TRUE FALSE 20663.80395 16920.79386 21360.4606 21280.75237 32752.83277 17437.47378 22667.94877 22449.54333 44366.42663 0.465753172 0.381387349 0.481455511 0.479658922 0.738234635 0.393033091 0.510925727 0.506002963 1 15.43718074 -5 0.272941973 4.596086315 0.44936715 0.733083256 0.096070131 107.9668482 1.044098774 219.1624386 0.110726983 1.00E-05 5 -4.146719164 GQDHCGIESEVVAGIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GQDHCGIESEVVAGIPR 17 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ;;; 236.02 3.55E-20 297810000 495712 416618 436090 448701 550022 406131 492273 448600 515107 FALSE TRUE 472280.6762 459071.8479 456085.1579 403596.723 645945.6627 392066.5816 417167.7126 409318.2058 594987.1628 0.793766161 0.771565971 0.766546215 0.678328455 1.085646385 0.658949648 0.701137333 0.6879446 1 19.18249902 -0.076823771 9.957844836 0.999999999 0.766824261 0.265416861 0.121289913 0 0 0.108978746 0.025686537 0.837869205 0.076823771 -0.233175738 GQDS(ph)PLLQRPQHLMDQGQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQDSPLLQRPQHLMDQGQMR 20 1 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR 202.98 6.69E-22 1095830000 507820 444090 473810 552090 564330 536820 574700 539720 583220 TRUE FALSE 483816.355 489343.2759 495534.6572 496592.8643 662748.9733 518229.7888 487018.9599 492459.2556 673662.7789 0.718187749 0.726392034 0.735582657 0.737153484 0.983799304 0.769271815 0.722941767 0.731017463 1 19.36166706 -2.585093318 2.182230785 5.515617613 0.761288553 0.463985033 0.079078251 2163513.528 190997.1323 48410161.97 0.019531524 0.002599601 2.585093318 -4.75432906 GQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDTPKPAGQHGS(0.362)LS(0.638)PAAAHTAS(1)PEPPTQSGPLTR;GQDT(0.046)PKPAGQHGS(0.45)LS(0.504)PAAAHT(0.217)AS(0.777)PEPPT(0.004)QS(0.001)GPLT(0.001)R;GQDTPKPAGQHGS(0.053)LS(0.947)PAAAHTAS(1)PEPPTQSGPLTR 209.43 7.92E-28 379867000 202656 185649 191916 244826 197833 193454 260036 240360 122702 TRUE FALSE 193076.8525 204566.8442 200715.5384 220215.6253 232335.0126 186754.6395 220362.7323 219312.8042 141729.9995 1.362286412 1.443355993 1.416182454 1.553768617 1.639279005 1.317678968 1.554806556 1.54739861 1 17.11278564 -1.65747693 9.968393011 0.999817799 1.473102099 0.701250973 0.098250578 0.000386079 1.33E-05 0.092317666 0.021751487 0.022005086 1.65747693 0.4732843 GQECVEECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 91.867 0.024341 72843000 75534 61456 65981 96729 115450 69505 90517 79988 101850 FALSE TRUE 71963.65751 67718.43627 69006.29411 87005.61715 135584.4434 67098.02442 76706.96919 72983.82668 117644.3778 0.611705029 0.575619826 0.586566867 0.739564599 1.152494033 0.570346205 0.652024097 0.620376664 1 16.84407285 3.206689159 5.910261819 0.766661703 0.590441813 0.214208416 0.175573073 0.305659029 29.81710717 0.050263922 0.061914231 1609.493247 -3.206689159 -0.17621989 GQEETPSWEHILFTCCHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQEETPSWEHILFTCCHNR 19 0 Q8TCD5;J3KSY6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 294.59 6.97E-50 270200000 236552 186871 232170 263980 301560 218532 291710 241491 120297 FALSE TRUE 225370.6558 205913.3674 242815.2241 237444.2289 354151.9685 210964.182 247204.2819 220344.7678 138952.0444 1.621931198 1.481902395 1.747475003 1.708821414 2.548735214 1.518251732 1.779061855 1.585761252 1 17.08422754 0.716691265 1.973706233 0.999982618 1.748310297 0.40037607 0.295218981 1.27903534 7.233174071 0.277660973 0.076847692 5.208243311 -0.716691265 0.748327678 GQELAFPLSPDWQVDYESYTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQELAFPLSPDWQVDYESYTWR 22 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 135.68 5.66E-06 7916200 41513 45303 40049 45485 45658 39247 44265 49806 41292 FALSE TRUE 39550.76276 49919.42721 41885.28626 40912.76138 53620.74074 37887.86655 37511.56127 45444.7226 47695.35247 0.829237247 1.046630848 0.878183808 0.857793459 1.124234081 0.794372294 0.786482526 0.952812386 1 15.54156107 GQEPNDTNQYLKPPSRPS(ph)PDSSESDWETLDPSVLEDPNLKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQEPNDTNQYLKPPSRPSPDSSESDWETLDPSVLEDPNLKER 42 3 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 GQEPNDT(0.04)NQY(0.009)LKPPS(0.165)RPS(0.737)PDS(0.011)S(0.011)ES(0.011)DWET(0.011)LDPS(0.003)VLEDPNLKER 40.35 0.071801 56026000 35811 25493 30931 33736 26956 39392 47444 40178 33096 TRUE FALSE 34118.285 28090.76568 32349.21694 30344.79319 31657.11787 38027.84516 40205.54643 36659.80132 38228.35865 0.892486264 0.734814851 0.846209937 0.793777035 0.8281056 0.99475485 1.051720447 0.95896875 1 15.22235564 2.235673645 4.648962411 1.012555569 0.812976645 0.799441194 0.045318723 0.073165232 3.995586766 0.016022927 0.012342213 172.0575146 -2.235673645 -0.199578924 GQETSTNPIASIFAWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQETSTNPIASIFAWTR 17 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 146.2 1.07E-05 20354000 202995 172254 189732 201340 208956 209297 285252 224130 221991 FALSE TRUE 193399.8286 189806.8784 198431.3999 181100.9207 245397.8602 202048.9924 241731.5684 204503.989 256416.2305 0.754241759 0.740229579 0.773864429 0.706277135 0.957029357 0.787972711 0.942731152 0.797546975 1 17.96812806 2.745667298 24.99966464 0.888590419 0.745937519 0.559372249 0.067407914 389.8389612 1371364.069 0.017912766 0.018640928 556.7590669 -2.745667298 -0.1426529 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER 39 1 P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;F8VWU4 P51148 RAB5C Ras-related protein Rab-5C 0 ;;;; 301.11 5.03E-93 98163400 89638 92539.4 106477.3 120769.2 95701.5 106744.6 121259 108623.9 108880.6 FALSE TRUE 85400.98939 101969.2701 111359.3895 108629.2506 112391.8113 103048.0077 102758.7125 99112.21546 125765.2474 0.679050781 0.810790518 0.885454383 0.863746169 0.893663501 0.819367909 0.817067629 0.788073156 1 16.94037379 8 0.039618792 1.334264523 1.73E-14 0.484810327 0.059340583 760.9446489 2.296705869 21.30499537 68.50802451 99999999.91 -8 -1.334264523 GQFQGRPVSVWDVLFSSYLSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQFQGRPVSVWDVLFSSYLSEAR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 243.72 1.91E-37 2360220000 1001434 1021514 512346 719517 867468 643881 938110 903643 618207 FALSE TRUE 954098.1995 1125607.438 535837.5709 647189.7842 1018754.145 621583.2395 794984.0899 824515.2284 714075.3842 1.336130919 1.576314578 0.750393562 0.906332578 1.426675904 0.870472857 1.113305552 1.154661324 1 19.44571686 3.753841777 24.99807858 1.041827184 1.456222769 0.459295544 0.191252479 643.2556602 1052283.336 0.046475811 0.083384552 5673.378738 -3.753841777 0.414395585 GQFQGRPVSVWDVLFSSYLSEARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQFQGRPVSVWDVLFSSYLSEARR 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 191.5 5.25E-18 157191000 262122 160958 191917 184432 293020 187242 362620 259376 275350 FALSE TRUE 249732.0125 177359.8032 200716.5843 165892.545 344122.5952 180757.7626 307295.659 236663.6624 318049.8717 0.785197652 0.557647775 0.631085255 0.521592869 1.08197684 0.568331506 0.966187024 0.744108655 1 18.27889348 2.759601218 24.93349714 0.852765415 0.631166366 0.379038292 0.156676006 842.5268252 998408.2131 0.042612916 0.045154915 574.9117935 -2.759601218 -0.221599049 GQFSTDELVAEVEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 297.49 6.42E-44 1971420000 2901876 2659598 2688482 3382296 2525728 3177924 3582119 3659660 2957769 FALSE TRUE 2764710.072 2930614.06 2811751.559 3042301.18 2966214.164 3067871.695 3035600.956 3339200.769 3416444.71 0.809236006 0.857796425 0.823005141 0.890487462 0.868216645 0.897972002 0.888526294 0.977390548 1 21.70406435 1.523560918 0.359280152 1.014366764 0.815159998 0.8510518 0.023129475 0.40744965 0.167040847 0.030488849 0.025063478 33.38573318 -1.523560918 -0.199206765 GQGEAPPQYLTDDLEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQGEAPPQYLTDDLEFLR 18 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 76.759 0.034201 8126900 5826.8 4615 5703.9 5572.7 7013.6 5133.6 4111.6 5489.3 7579.7 FALSE TRUE 5551.378712 5085.273747 5965.429457 5012.521609 8236.769619 4955.822145 3484.299905 5008.627791 8755.121164 0.634072174 0.580834194 0.68136458 0.572524528 0.940794475 0.566048379 0.39797278 0.57207978 1 13.09591143 3.766269551 23.04268327 0.636526091 0.607453238 0 0.182039217 3091.664838 2570995.46 0.045984968 0.082862936 5838.073402 -3.766269551 -0.029072853 GQGPRS(ph)PHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQGPRSPHK 9 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHK;GQGPRS(1)PHK;GQGPRS(1)PHK 57.019 0.071539 442410000 663480 629150 536470 700800 506610 649240 769680 704050 500570 TRUE FALSE 632118.6153 693261.1003 561067.6801 630354.2526 594962.6236 626756.656 652251.1799 642399.6496 578195.839 1.093260402 1.199007418 0.970376544 1.090208905 1.028998452 1.083986798 1.128080031 1.111041634 1 19.1411987 -1.152296431 0.009806768 1.57E-05 2.090906604 0.093524224 0.062454763 12457.09153 22.16532762 2510.233009 2220.839206 0.070421224 1.152296431 2.090890907 GQGPRS(ph)PHKVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GQGPRSPHKVGR 12 2 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHKVGR;GQGPRS(1)PHKVGR;GQGPRS(1)PHKVGR;GQGPRS(1)PHKVGR 72.315 0.022031 877908000 733398 493331 727498 626595 645883 691292 979490 793310 778421 TRUE FALSE 698731.73 543601.9898 760854.5029 563608.4801 758524.7907 667352.3847 830050.8109 723843.5708 899134.5531 0.777115869 0.604583583 0.846207612 0.626834413 0.843616551 0.742216371 0.923166403 0.805044771 1 19.7781775 1.507997544 0.491804693 0.995130317 0.694530415 0.487118409 0.086454984 0.616149408 0.38286489 0.080793972 0.05012042 32.21050576 -1.507997544 -0.300599902 GQGTYEDYLEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQGTYEDYLEGFR 13 0 P14649 P14649 MYL6B Myosin light chain 6B 0 ; 173.19 5.14E-05 36650000 281300 242140 231070 296280 250810 249170 296680 270540 281680 FALSE TRUE 268003.5065 266814.3413 241664.7881 266497.3715 294551.1846 240541.1804 251416.0171 246850.0834 325361.4958 0.823709966 0.820055061 0.742757798 0.819080853 0.905304372 0.739304385 0.772728243 0.758694826 1 18.311684 -1.280830003 5.395365531 1.000026499 0.798900329 0.625233864 0.049212956 1.54E-05 2.05E-06 0.046696035 0.011004912 0.052380543 1.280830003 -0.20112617 GQHFYAVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQHFYAVER 9 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 107.83 0.0027098 303960000 340620 231940 192724 189134 423570 260630 413450 214650 300390 FALSE TRUE 324519.5676 255574.9497 201560.586 170121.891 497440.4739 251604.3177 350370.609 195854.1081 346972.947 0.93528781 0.736584659 0.580911531 0.490303041 1.433657806 0.725141023 1.009792296 0.564465068 1 18.40446366 GQHHQQQQAAGGSESHPVPPTAPLT(ph)PLLHGEGASQQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPR 38 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 GQHHQQQQAAGGSESHPVPPT(0.043)APLT(0.957)PLLHGEGASQQPR 175.58 5.75E-19 336300000 37672 31691 31680 42500 60197 40624 43504 35720 3074.8 TRUE FALSE 35891.31922 34920.34893 33132.55934 38227.81926 70695.33774 39217.18069 36866.66579 32592.16744 3551.62428 10.10560701 9.832219338 9.328846951 10.76347503 19.90507221 11.04204094 10.38022687 9.176693497 1 11.79426325 0.700773306 1.51951875 1.015238044 11.53093478 0.552549405 3.006656799 0.854457447 3.063923111 2.898017078 0.840651778 5.020804439 -0.700773306 10.51569673 GQHPNPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GQHPNPLR 8 0 M0R1K3;Q15102;M0R389;M0QZT2 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;; 101.6 0.0052792 1736320000 1986100 1617060 1489820 1634920 2019280 1531050 2000670 1683660 1897710 FALSE TRUE 1892220.989 1781840.252 1558129.721 1470574.735 2371441.793 1478029.355 1695431.047 1536229.805 2191997.175 0.863240615 0.812884375 0.710826519 0.6708835 1.081863526 0.674284334 0.773464066 0.700835668 1 21.06381451 -1.065503032 4.068165061 1.000032396 0.789962288 0.233552357 0.121628227 9830262.431 7724004.769 2502.237568 0.026204581 0.085999706 1.065503032 -0.210070108 GQKPALDCS(ph)QVSPPRPATSPENNASLSDTSPMDSSPSGIPK ddPTM_SK-BR-3_Trastuzumab_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(0.569)QVS(0.417)PPRPAT(0.007)S(0.007)PENNASLSDTSPMDSSPSGIPK 127.12 8.26E-09 215720000 34349 37182 32224 38588 22595 41175 43272 40168 32545 TRUE FALSE 32725.39084 40970.88807 33701.50227 34709.06093 26535.56085 39749.09943 36670.06166 36650.67698 37591.91238 0.87054339 1.089885709 0.896509386 0.923311923 0.705884834 1.057384339 0.975477419 0.974961758 1 15.19813469 -0.648511108 7.333329217 1 0.945641566 0.028109367 0.105976036 0 0 0.097946536 0.02308622 0.224640932 0.648511108 -0.054358434 GQKPALDCSQVS(ph)PPRPATSPENNASLSDTSPMDSSPSGIPK ddPTM_SK-BR-3_Trastuzumab_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(0.274)QVS(0.718)PPRPAT(0.004)S(0.004)PENNASLSDTSPMDSSPSGIPK 217.28 5.37E-44 143030000 37386 36086 38012 41558 30962 43460 47823 54776 34628 TRUE FALSE 35618.83787 39763.20443 39754.8878 37380.51088 36361.763 41954.9693 40526.72302 49979.52305 39997.93338 0.890516956 0.994131473 0.993923546 0.934561057 0.909091043 1.048928426 1.013220424 1.249552635 1 15.28763784 1.721126444 1.904323523 1.115085674 0.951238846 0.436338354 0.074794077 0.266428387 1.967357762 0.048281965 0.019443987 52.61704382 -1.721126444 -0.163846828 GQKPEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQKPEQR 7 1 Q92522 Q92522 H1FX Histone H1x 0 ; 80.18 0.027919 65042000 150311 130324 114489 151054 112747 114330 137661 147071 157284 FALSE TRUE 143206.0969 143604.1638 119738.4339 135869.7649 132410.0411 110370.7234 116658.2861 134192.6836 181674.7994 0.788255154 0.790446249 0.65908114 0.747873483 0.728829984 0.60751807 0.642126957 0.738642255 1 17.47099879 0.955322274 22.44845939 1.000000001 0.712684221 0.696916653 0.059785176 1988.95392 999357.8184 0.066914878 0.01672872 9.022404084 -0.955322274 -0.28731578 GQLAEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQLAEWR 7 0 Q8WZA9 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 82.671 0.055501 74994000 330840 234200 217240 259370 416160 228970 342300 289070 375980 FALSE TRUE 315201.8489 258065.2463 227200.6689 233297.6348 488738.1722 221040.7115 290075.8482 263757.4983 434285.0582 0.725794827 0.594230083 0.523160225 0.537199313 1.125385649 0.508976091 0.667938818 0.607337262 1 18.72828279 GQLGHGDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GQLGHGDTK 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;;;; 123.79 0.00054777 1316740000 2744430 2532120 2305350 2883800 2034460 2605410 2892740 2763560 2115390 FALSE TRUE 2614706.233 2790145.907 2411052.578 2593914.945 2389269.18 2515183.998 2451399.384 2521568.036 2443433.877 1.070094942 1.141895401 0.986747626 1.061585897 0.97783255 1.029364462 1.003259964 1.031977194 1 21.22047863 3.735283814 24.99957631 1.01399685 1.105995172 0.634115598 0.029370051 144.2019606 1100152.657 0.006872231 0.011133584 5436.054644 -3.735283814 0.091998322 GQLGHGDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQLGHGDTKR 10 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 127.83 0.0002244 170239000 228742 198582 196052 235520 219557 211153 272640 242630 232720 FALSE TRUE 217929.819 218817.7316 205041.1781 211845.0821 257847.6713 203840.7187 231043.7606 221384.0309 268809.029 0.810723582 0.814026718 0.76277638 0.788087673 0.959222509 0.758310535 0.859508929 0.823573642 1 18.03622207 -4.999999965 0.224538278 1.936622231 0.799600473 0.508217639 0.0559547 122.8877571 1.229428566 52.1038575 0.09275132 1.00E-05 4.999999965 -1.137021758 GQLITGMDQALVGMCVNERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQLITGMDQALVGMCVNERR 20 1 O95302;O95302-3 O95302 FKBP9 Peptidyl-prolyl cis-trans isomerase FKBP9 0 53.034 0.036573 0 96613 57809 74598 85124 71207 95920 112520 99624 89048 FALSE TRUE 92046.29496 63699.80282 78018.39209 76567.17379 83625.47826 92598.26635 95353.00743 90900.39442 102857.109 0.894894828 0.619303842 0.758512395 0.744403323 0.81302575 0.900261219 0.927043433 0.883754125 1 16.65028198 2.337554659 1.877848496 0.930211426 0.746528364 0.574461116 0.071097999 0.244440282 1.757171036 0.032191714 0.022751838 217.5477815 -2.337554659 -0.183683062 GQMQKPFEDASFALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQMQKPFEDASFALR 15 1 K7EN45;Q13526 K7EN45 PIN1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 0 ; 191.96 1.40E-07 639450000 637310 579180 585150 799220 668990 705940 863590 787470 807100 FALSE TRUE 607185.6193 638199.1005 611979.7063 718880.8872 785661.6442 681493.1208 731833.4846 718514.9522 932260.9459 0.651304361 0.684571314 0.656446791 0.771115523 0.84274864 0.731011123 0.78500927 0.770722999 1 19.83037431 -5 0.08274881 1.896991924 0.471026362 0.814761747 0.044001229 96.62045126 0.563298959 15.62491461 1.349762534 1.00E-05 5 -1.425965562 GQNQDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GQNQDYR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 163.67 0.0028529 4118300000 10905650 9639780 9713040 11539610 12404560 10299150 12708670 10956310 13077480 FALSE TRUE 10390161.54 10622084.54 10158392.49 10379626.48 14567911.34 9942487.853 10769728.98 9996917.413 15105468.81 0.687841051 0.703194629 0.672497664 0.687143617 0.964413056 0.65820452 0.712968867 0.661807822 1 23.84856762 -1.824061744 2.403983601 1.106741459 0.717312856 0.495717174 0.08921789 9992661.098 6108850.726 6168446.048 0.023864682 0.014994716 1.824061744 -0.389428603 GQPDEELKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQPDEELKPK 10 1 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 99.522 0.005085 0 218020 191440 200700 229000 138660 229400 234890 230540 151810 FALSE TRUE 207714.6267 210947.9536 209902.2935 205980.4849 162842.2601 221455.8205 199053.2164 210352.6954 175351.9195 1.184558614 1.202997688 1.197034479 1.17466912 0.928659695 1.262922135 1.135164172 1.199603039 1 17.4198937 -5 0.24684385 0.052375478 1.1781498 0.236501766 0.088959548 258.1184539 2.563477296 123.630693 0.122715797 1.00E-05 5 1.125774322 GQPDVVVKEDEEYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GQPDVVVKEDEEYKR 15 2 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ;;;;; 188.27 1.72E-07 4242230000 5517550 3994430 4906040 4580580 3018110 4496120 5190250 5323540 3287800 FALSE TRUE 5256746.346 4401466.958 5130986.787 4120131.396 3544467.428 4340418.237 4398382.037 4857382.616 3797655.232 1.384208419 1.15899593 1.351093365 1.084914544 0.933330493 1.142920558 1.158183608 1.279047812 1 21.85667751 4.6984275 0.671383536 1.117010002 1.524055498 0.345451222 0.115542604 3.575120657 1.261062567 0.048654738 1.108071405 49937.58089 -4.6984275 0.407045496 GQPIYIQFSNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQPIYIQFSNHK 12 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 291.22 3.98E-36 3781000000 3467900 2519300 2593800 2925300 4057000 2642800 4739900 3737800 4448300 FALSE TRUE 3303979.24 2776019.534 2712728.296 2631243.286 4764539.516 2551279.173 4016741.201 3410498.417 5138119.645 0.643032757 0.540279271 0.527961294 0.512102378 0.927292442 0.496539464 0.781753147 0.663763916 1 22.29280905 -0.431317895 0.259640845 1.173328613 0.547154334 0.474930688 0.127796629 7.804243568 0.65828932 1.330933324 0.191200844 0.37040949 0.431317895 -0.626174279 GQPSNKEDVDDLVSQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQPSNKEDVDDLVSQLR 17 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 166.76 2.10E-09 422370000 429450 356550 365660 407260 336910 389550 457240 417750 372160 FALSE TRUE 409150.7496 392882.8504 382425.8727 366321.4511 395666.9973 376059.7858 387479.6402 381169.5954 429872.6721 0.951795209 0.913951679 0.889625923 0.852162686 0.920428357 0.874816685 0.901382352 0.886703483 1 18.71354987 -0.841209715 4.904453353 1.000000152 0.901276179 0.580399707 0.026956734 6.30E-08 1.49E-08 0.027256752 0.006424465 0.144141914 0.841209715 -0.098723973 GQRGDS(ph)RS(ph)PSHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQRGDSRSPSHKR 13 3 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GQRGDS(0.992)RS(0.892)PS(0.116)HKR 65.231 0.084916 53161000 44310 11388 52347 28241 41973 40743 85295 45515 81257 TRUE FALSE 42215.55411 12548.45015 54747.16173 25402.16103 49293.07791 39332.05969 72281.6812 41529.46531 93857.92056 0.449781477 0.13369623 0.58329826 0.270644831 0.525188259 0.419059569 0.770118076 0.442471611 1 16.51819088 0.802763235 0.302290774 1.092476657 0.264032954 0.584410241 0.156250652 1.463729581 0.360623861 0.417294636 0.200886675 6.34984662 -0.802763235 -0.828443703 GQS(ph)PLAPLLETLEDPSASHGGQTDAYLTLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQSPLAPLLETLEDPSASHGGQTDAYLTLTSR 32 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(0.988)PLAPLLET(0.011)LEDPSASHGGQTDAYLTLTSR 175.37 4.13E-15 62774000 15464.9 13290.3 14152.8 15597.6 17411.3 13630 19923.8 16979.2 21408.8 TRUE FALSE 14733.90483 14644.59668 14801.71988 14029.69961 20447.82521 13157.98968 16884.05838 15492.41124 24728.76736 0.595820431 0.592208923 0.598562786 0.567343265 0.826884127 0.532092421 0.682769915 0.626493468 1 14.59390271 -5 0.258233145 3.397501851 0.59408186 0.686089706 0.079625055 101.408789 0.997706304 128.8155514 0.095123423 1.00E-05 5 -2.80341999 GQSQLS(ph)NPTDDSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GQSQLS(0.921)NPT(0.079)DDSWK 202.63 1.09E-07 0 154360 134800 140920 162150 120000 161200 171420 152280 141330 TRUE FALSE 147063.7087 148536.2733 147381.3214 145850.3739 140927.962 155617.6036 145266.7307 138945.5559 163246.7346 0.90086769 0.909888174 0.902813289 0.893435169 0.863281966 0.953266257 0.889859947 0.851138348 1 17.31669461 -2.069332185 2.591937893 1.15381247 0.898309225 0.58879215 0.027342127 3839885.212 1758159.315 3494844.567 0.006363445 0.008524478 2.069332185 -0.255503245 GQSQT(ph)SPDHRS(ph)DT(ph)S(ph)SPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 4 GQS(0.113)QT(0.471)S(0.418)PDHRS(0.96)DT(0.919)S(0.586)S(0.533)PEVR 57.738 0.055685 379970000 177370 132210 180750 173390 205890 157260 223080 167030 199650 TRUE FALSE 168986.0716 145682.3493 189037.5663 155960.5078 241797.1508 151814.0468 189045.0489 152403.9677 230610.7023 0.732776363 0.631724147 0.819725903 0.676293451 1.048507933 0.658313102 0.81975835 0.660871183 1 17.81509994 -5 0.171040633 1.918321934 0.696125485 0.254220876 0.124660621 171.6362018 1.622612628 54.08722971 0.401569658 1.00E-05 5 -1.222196449 GQSQT(ph)SPDHRSDTSSPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.097)QT(0.465)S(0.361)PDHRS(0.07)DT(0.005)S(0.001)S(0.001)PEVR;GQS(0.094)QT(0.451)S(0.451)PDHRS(0.004)DTSSPEVR 86.551 0.0046212 547961000 87866 32200 81394 57363 155776 67568 172785 95440 200256 TRUE FALSE 83712.74831 35481.21661 85125.99541 51596.76226 182943.2851 65228.10322 146423.4748 87082.76764 231310.6777 0.361906113 0.153392039 0.368015849 0.223062605 0.790898574 0.281993481 0.633016497 0.376475347 1 17.81947234 -4.999999962 0.113589642 3.051853145 0.044547482 0.560067599 0.176549197 104.2991283 0.780783411 49.11678582 1.771550655 1.00E-05 4.999999962 -3.007305663 GQSQTS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.001)QT(0.013)S(0.986)PDHR;GQS(0.005)QT(0.035)S(0.959)PDHR;GQS(0.06)QT(0.231)S(0.709)PDHR;GQS(0.314)QT(0.17)S(0.517)PDHR 177.41 2.44E-06 617682000 921104 908251 829475 1014572 907696 810898 898922 911051 830938 TRUE FALSE 877565.2394 1000802.809 867507.2492 912585.295 1065997.895 782816.3989 761774.9391 831274.5447 959795.6212 0.914325113 1.042724917 0.903845808 0.950812105 1.110650926 0.815607387 0.793684533 0.866095371 1 19.87236771 2.205477641 24.99996913 0.844155414 0.980843726 0.311728147 0.081694385 179.822944 135886.643 0.02815352 0.020794046 160.5009626 -2.205477641 0.136688312 GQSQTS(ph)PDHRS(ph)DT(ph)SSPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.131)QT(0.419)S(0.472)PDHRS(0.762)DT(0.439)S(0.404)S(0.373)PEVR 54.072 0.095574 454370000 227510 166620 220760 227700 236920 215160 259250 206510 250700 TRUE FALSE 216756.0532 183598.7674 230882.0644 204811.1634 278238.773 207708.9552 219696.651 188426.8896 289577.2756 0.74852577 0.634023395 0.797307261 0.707276367 0.96084464 0.717283339 0.758680565 0.650696396 1 18.14358887 -1.851849088 2.720180696 1.101428222 0.7433636 0.437951185 0.090058092 16451398.42 11126969.91 10833232.16 0.020531333 0.014065362 1.851849088 -0.358064622 GQSQTS(ph)PDHRS(ph)DTS(ph)SPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.088)QT(0.426)S(0.496)PDHRS(0.916)DT(0.167)S(0.625)S(0.284)PEVR 68.153 0.041631 275320000 288140 251420 298510 301420 416330 246390 350890 272940 388890 TRUE FALSE 274520.1932 277039.9838 312196.9788 271120.6889 488937.8202 237857.4525 297355.286 249039.9267 449197.075 0.611135309 0.616744853 0.695011157 0.603567352 1.088470623 0.529516922 0.661970664 0.554411283 1 18.77698901 -2.147969343 2.425353544 1.762299673 0.666423356 0.305448409 0.156250037 7676222.098 2443534.836 32077382.42 0.034696443 0.007112637 2.147969343 -1.095876317 GQSQTS(ph)PDHRSDT(ph)SSPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GQS(0.051)QT(0.44)S(0.509)PDHRS(0.011)DT(0.378)S(0.327)S(0.283)PEVR 110.94 0.00051773 105880000 59918 31696 64556 55559 106540 57450 92431 69710 125780 TRUE FALSE 57085.79489 34925.85844 67515.95645 49974.10376 125120.5423 55460.49209 78328.95334 63605.82284 145285.32 0.392921975 0.240394958 0.464712859 0.343972149 0.861205676 0.381735003 0.539138802 0.437799379 1 17.14852941 -5 0.133058701 2.854837163 0.222583894 0.548209777 0.158649022 101.0974111 0.841248295 50.02490526 1.049647812 1.00E-05 5 -2.632253269 GQSQTS(ph)PDHRSDTSSPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQS(0.019)QT(0.396)S(0.585)PDHRS(0.001)DTSSPEVR 138.93 5.79E-07 91291000 24104 9078 24775 16819 46526 21414 43947 30525 58386 TRUE FALSE 22964.65169 10003.05852 25910.95826 15128.32217 54640.11967 20672.42781 37242.07801 27852.06918 67440.20269 0.340518723 0.148324859 0.384206411 0.224322015 0.810201 0.30652974 0.552223696 0.412989108 1 16.04132125 -5 0.115320217 3.050048712 0.048712635 0.582189225 0.169796801 100.9567712 0.763949795 48.25536131 1.658193792 1.00E-05 5 -3.001336076 GQSS(ph)PPPAPPICLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GQSSPPPAPPICLR 14 0 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 GQS(0.028)S(0.972)PPPAPPICLR;GQS(0.017)S(0.983)PPPAPPICLR;GQS(0.023)S(0.977)PPPAPPICLR;GQS(0.03)S(0.97)PPPAPPICLR;GQS(0.002)S(0.998)PPPAPPICLR 235.38 3.25E-17 626904000 1208340 1108090 999690 1269040 1199900 1094880 1229140 1142020 1317700 TRUE FALSE 1151224.163 1221005.631 1045526.775 1141473.688 1409162.18 1056964.031 1041612.118 1042018.675 1522042.186 0.756368104 0.802215367 0.686923651 0.749961925 0.92583648 0.694438065 0.684351674 0.684618787 1 20.53757692 GQSTGKGPPQS(ph)PVFEGVYNNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQSTGKGPPQSPVFEGVYNNSR 22 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GQSTGKGPPQS(1)PVFEGVYNNSR 254.09 2.92E-37 540080000 233490 57298 233560 129140 294460 181050 362730 235430 430210 TRUE FALSE 222453.3904 63136.73134 244268.957 116158.6019 345813.7308 174780.1931 307388.8765 214814.5011 496924.7696 0.447660097 0.127054909 0.491561242 0.233754904 0.695907614 0.351723649 0.618582319 0.432287771 1 18.92266793 -4.999999976 0.13225883 3.067886267 0.163925804 0.590510879 0.156840954 85.55581244 0.709277405 46.36891514 0.994701967 1.00E-05 4.999999976 -2.903960462 GQTEHDEGMLEYLEDIIGCGR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 141.47 1.55E-07 105598200 102829 89492.2 93059 115445 112697.8 95994 108603.2 106065 105418 FALSE TRUE 97968.47696 98611.55692 97325.8472 103840.2493 132352.2606 92669.70371 92033.78721 96777.38631 121765.685 0.804565563 0.809846854 0.79928797 0.85278746 1.086942192 0.761049418 0.755826957 0.794783738 1 16.8937481 -2.429064529 2.215742865 2.536561228 0.827891702 0.234281547 0.094382327 4828055.365 682011.5811 36922117.46 0.023119723 0.003723364 2.429064529 -1.708669526 GQTHTLEDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GQTHTLEDFQR 11 0 Q99714;Q99714-2;Q5H928 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 ;;; 155.99 3.13E-05 1737550000 770698 568593 582221 677158 778064 508665 729020 650250 825670 FALSE TRUE 734268.6329 626533.2731 608916.4087 609088.7913 913758.1153 491049.8035 617794.6096 593310.6628 953710.6867 0.769907104 0.6569427 0.638470783 0.638651532 0.95810829 0.514883403 0.647779896 0.622107596 1 19.86319216 -1.749188179 2.730970819 1.066098017 0.679950046 0.427878834 0.115972881 35523041.45 29732149.29 15900882.98 0.027151625 0.017816066 1.749188179 -0.386147971 GQVEFFEPFWDSGEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQVEFFEPFWDSGEPR 16 0 H0YJT0;Q9H7Z3 H0YJT0 NRDE2 Protein NRDE2 homolog 0 133.71 8.01E-05 0 6747.8 5731.1 7783.4 7414.8 6601.6 5711.6 9013.8 7879.4 7909.3 FALSE TRUE 6428.844867 6315.105606 8140.276589 6669.450217 7752.91695 5513.80586 7638.57926 7189.437965 9135.833849 0.703695467 0.691245672 0.891027215 0.730031908 0.848627184 0.603536136 0.836111885 0.78694929 1 13.1573207 -4.99999997 0.206956045 2.163454948 0.718410076 0.450571406 0.08393603 124.6693384 1.239945691 60.02818866 0.170127667 1.00E-05 4.99999997 -1.445044872 GQVLFDLVCEHLNLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQVLFDLVCEHLNLLEK 17 0 Q9H4G0-2;A0A1B0GTW6;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1;Q4VXN5;Q4VXN6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 164.68 2.56E-09 60591000 120470 132510 122710 134790 96848 118060 142700 134110 88548 FALSE TRUE 114775.6218 146012.9197 128336.3749 121240.6531 113738.2605 113971.5526 120928.4941 122366.6174 102279.5716 1.122175426 1.427586344 1.254760583 1.185384835 1.112033017 1.114313942 1.182332818 1.196393527 1 16.6421585 3.157872204 3.083015308 1.136717141 1.283340657 0.349090842 0.089920582 0.268601477 5.141110834 0.026051387 0.032782095 1438.375257 -3.157872204 0.146623516 GQVLNSDELQELYEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQVLNSDELQELYEGLR 17 0 O00764;F2Z2Y4;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 258.81 8.22E-27 187370000 146596 121835 130228 146364 146320 143651 153021 151797 141463 FALSE TRUE 139666.6976 134250.125 136199.0826 131651.2126 171838.1617 138676.3299 129674.836 138504.85 163400.3595 0.854751471 0.821602384 0.833529883 0.805697203 1.051638822 0.848690482 0.793601901 0.847641035 1 17.31805163 -2.221728617 2.098506235 1.430329444 0.852602106 0.278076831 0.072007697 5843842.414 1058484.892 11919724.43 0.017265308 0.00600166 2.221728617 -0.577727338 GQVQEVGWHDVAGWLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GQVQEVGWHDVAGWLGR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;; 191.47 2.41E-10 1274421000 1500172 1311778 1382309 1670310 1670581 1416936 1686920 1473329 1459080 FALSE TRUE 1429261.843 1445449.67 1445689.235 1502407.265 1961929.797 1367867.151 1429549.372 1344316.502 1685346.674 0.848052133 0.857657176 0.857799322 0.89145295 1.164110522 0.811623609 0.848222739 0.797649838 1 20.68461395 3.168570683 5.301080516 0.911761946 0.854248557 0.076648301 0.104776924 0.647206019 33.495218 0.030604736 0.037240786 1474.248459 -3.168570683 -0.057513389 GQVWINGFNLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GQVWINGFNLGR 12 0 P16278-3;P16278;E7EQ29;P16278-2;Q6UWU2-2;Q6UWU2 P16278-3 GLB1;GLB1L Beta-galactosidase;Beta-galactosidase-1-like protein 0 109.29 0.0037545 41946000 150810 127940 137100 154660 124150 141300 156580 167770 129810 FALSE TRUE 143681.5102 140977.2315 143386.1706 139113.283 145801.7207 136406.7456 132690.8452 153079.1694 149940.2718 0.958258301 0.940222595 0.956288587 0.927791322 0.972398669 0.909740551 0.884958014 1.02093432 1 17.1940284 1.217876168 24.99950458 1.010467253 0.9354589 0.598831853 0.02545284 206.3990701 249450.1708 0.026115505 0.006557328 16.51490835 -1.217876168 -0.075008353 GQVYILGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GQVYILGR 8 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;;; 134.66 0.0020169 975960000 1144174 1095550 1027140 1104230 1463520 979272 1231480 1104835 1586500 FALSE TRUE 1090091.163 1207187.791 1074235.385 993230.7025 1718757.425 945359.5651 1043595.108 1008089.79 1832526.317 0.59485703 0.658756046 0.586204615 0.542000785 0.937916912 0.515877756 0.569484377 0.550109311 1 20.80540249 -1.521921575 5.852029563 1.000606512 0.619312572 0.500104929 0.119585644 0.000876446 7.16E-05 0.107241588 0.025238572 0.030066192 1.521921575 -0.38129394 GQYISPFHDIPIYADKDVFHMVVEVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GQYISPFHDIPIYADKDVFHMVVEVPR 27 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 261.86 2.69E-53 3974436000 2302330 1805988 2396687 2424375 3377560 2114879 3230990 2523028 1860883 FALSE TRUE 2193503.424 1990020.23 2506577.47 2180672.219 3966605.395 2041640.21 2738043.134 2302098.293 2149459.232 1.020490825 0.925823668 1.166143294 1.014521321 1.845396896 0.949839001 1.273828828 1.071012773 1 21.03554232 3.429654671 2.156276125 1.226432766 0.977632788 0.1010496 0.25530983 0.558881719 5.24354504 0.070282378 0.109539621 2689.395482 -3.429654671 -0.248799978 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 GRAEGEWEDQEALDYFSDKESGK 23 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.994)DKES(0.006)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK 238.59 2.72E-37 7857562000 5751259 4880050 5114366 5787706 2952313 6196916 6145671 6614978 3265357 TRUE FALSE 5479408.385 5377332.643 5348864.74 5205914.797 3467195.452 5982315.245 5208036.016 6035735.458 3771731.886 1.452756598 1.425693237 1.418145537 1.380245191 0.919258197 1.586092391 1.38080759 1.600255702 1 21.8467957 3.120788398 5.146364274 1.33165231 1.432921989 0.06302294 0.216249286 0.743071183 30.49926138 0.05958259 0.071960448 1320.652014 -3.120788398 0.101269679 GRAEGSEKEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GRAEGSEKEESR 12 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;;;;; 145.31 3.59E-05 390083000 639615 462417 586970 617392 568353 615859 766609 639350 657742 FALSE TRUE 609381.6665 509537.818 613883.1551 555330.5832 667473.5833 594531.6484 649648.7173 583365.1246 759741.2701 0.802091041 0.670672817 0.80801607 0.730946975 0.878553804 0.78254489 0.855092046 0.767847092 1 19.53514867 -5 0.136572945 1.760088689 0.698343501 0.58817926 0.057033551 86.39454504 0.730345724 17.79344304 0.338809988 1.00E-05 5 -1.061745188 GRAEGSEKEESRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GRAEGSEKEESRR 13 3 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;;; 85.42 0.0040712 97098000 214282 119200 208710 171680 201129 193530 267013 224030 259437 FALSE TRUE 204153.3145 131346.6155 218279.5599 154422.4002 236205.8339 186828.0076 226275.2628 204412.7455 299669.1649 0.681262333 0.438305408 0.728401803 0.515309609 0.788222018 0.623447553 0.75508357 0.682128058 1 18.19301112 -0.68356461 0.219375335 1.234894163 0.534487363 0.56971712 0.100173715 8.742596708 0.511950703 1.542814679 0.218552754 0.207221775 0.68356461 -0.7004068 GRAS(ph)PGGVSTSSSDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGK 103.95 0.00084757 272170000 270980 274960 232460 300420 198980 263870 260340 292250 198580 TRUE FALSE 258171.3124 302978.7366 243118.5209 270221.2108 233682.049 254732.1157 220620.3515 266659.0407 229374.7722 1.125543624 1.320889537 1.05991831 1.178077294 1.018778337 1.110549836 0.96183355 1.162547381 1 17.8073472 3.166917903 1.292415831 1.04527675 1.214133122 0.31014933 0.08609158 0.402555702 1.417869544 0.029510149 0.041491132 1468.648625 -3.166917903 0.168856372 GRAS(ph)PGGVSTSSSDGKAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GRASPGGVSTSSSDGKAEK 19 2 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK 121.94 1.78E-05 1000425000 1198100 723771 1139590 1022016 795847 1208960 1477110 1289980 994195 TRUE FALSE 1141468.187 797524.0878 1191841.329 919281.01 934642.4648 1167093.412 1251749.741 1177022.513 1148369.683 0.99399018 0.694483753 1.037855097 0.800509647 0.813886398 1.016304618 1.090023325 1.024950876 1 20.13115572 2.149223476 5.566622868 1.048752977 0.860872794 0.405370312 0.098638382 0.179829638 8.812402746 0.035029789 0.025744062 141.0014167 -2.149223476 -0.187880183 GRAS(ph)SHSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.715)S(0.285)HS(0.119)S(0.87)QT(0.011)QGGGSVTK 73.649 0.011299 55992000 42000 30386 41996 35062 35187 39006 52927 44067 44328 TRUE FALSE 40014.74324 33482.36795 43921.55814 31537.50115 41323.60166 37655.21244 44852.01408 40208.25987 51202.15984 0.781504986 0.653924913 0.857806746 0.615940836 0.807067549 0.735422345 0.875978947 0.785284449 1 15.64391705 0.77221928 0.495009149 1.00821949 0.722630477 0.514270939 0.076440424 0.951422923 0.521890001 0.089496855 0.037063892 5.918603953 -0.77221928 -0.285589013 GRAS(ph)SHSS(ph)QTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRASSHSSQTQGGGSVTKK 19 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 2 GRAS(0.925)S(0.075)HS(0.022)S(0.978)QTQGGGSVTKK 149.62 4.49E-08 68261000 96924 42525 124750 62925 95571 98851 192440 137290 161570 TRUE FALSE 92342.5946 46858.34585 130469.9109 56599.65945 112238.5521 95427.76508 163079.7436 125268.1598 186625.4504 0.494801724 0.251082292 0.699100314 0.303279426 0.60141075 0.511333073 0.873834427 0.671227635 1 17.50978622 1.666930524 0.605522 0.982517131 0.396205174 0.59786041 0.146234604 0.425722816 0.340371541 0.12536889 0.067967905 46.44409707 -1.666930524 -0.586311956 GRAS(ph)SHSSQT(ph)QGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.914)S(0.085)HS(0.081)S(0.324)QT(0.555)QGGGS(0.041)VT(0.001)K 78.352 0.027638 324810000 149170 112000 156320 158810 166740 142050 231010 188010 239550 TRUE FALSE 142119.0297 123412.9273 163487.4266 142846.1171 195819.4032 137130.7729 195765.1817 171546.8477 276698.1905 0.513624717 0.446020001 0.590851087 0.516252444 0.707700339 0.495596927 0.70750438 0.619978206 1 18.07795368 -5 0.132637188 2.520476544 0.385005042 0.795391394 0.072057241 52.59828589 0.436823453 21.03462946 0.446534527 1.00E-05 5 -2.135471502 GRAS(ph)SHSSQTQGGGS(ph)VTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.782)S(0.209)HS(0.012)S(0.017)QT(0.453)QGGGS(0.52)VT(0.006)K;GRAS(0.7)S(0.237)HS(0.029)S(0.034)QT(0.029)QGGGS(0.903)VT(0.068)K 111.09 0.00017914 459250000 616410 448730 633590 667600 702030 577720 936700 787420 1000870 TRUE FALSE 587273.5209 494456.0972 662640.7282 600491.5796 824463.8097 557713.4115 793789.2113 718469.3304 1156079.808 0.507987007 0.42770066 0.573179052 0.519420524 0.713154753 0.482417743 0.686621465 0.621470357 1 20.14080956 -5 0.133971205 2.55680142 0.375424776 0.79397744 0.073815495 53.55953239 0.447548747 22.14348297 0.453051055 1.00E-05 5 -2.181376644 GRAS(ph)SHSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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 1 GRAS(0.241)S(0.241)HS(0.241)S(0.241)QT(0.036)QGGGSVTK 147.92 4.42E-08 136790000 108420 45749 142920 64928 194590 102870 297370 199450 546740 TRUE FALSE 103295.2015 50410.87511 149473.0234 58401.31408 228526.4344 99307.58611 252000.7449 181985.1006 631525.6468 0.163564539 0.079823955 0.236685595 0.092476552 0.36186406 0.157250282 0.399034855 0.288167395 1 19.2684818 -4.999999999 0.186548537 4.40533888 0.059143616 0.89857536 0.084768454 33.14149036 0.322518008 41.67982256 0.203724068 1.00E-05 4.999999999 -4.346195264 GRASS(ph)HS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.032)S(0.967)HS(0.659)S(0.328)QT(0.014)QGGGSVTK 147.22 4.45E-08 183680000 227980 162900 289140 210890 245400 245510 395850 295540 369020 TRUE FALSE 217203.8372 179499.6952 302397.355 189690.9365 288197.6823 237007.9271 335455.8122 269660.9508 426245.7369 0.509574216 0.421117866 0.709443705 0.445027176 0.676130357 0.556035889 0.787000979 0.632641989 1 18.70132588 -1.014999699 0.135303668 1.506843089 0.305777278 0.679918351 0.097503995 15.92920864 0.444891816 3.637203565 0.807605382 0.096605155 1.014999699 -1.20106581 GRASS(ph)HSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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(0.451)S(0.549)HS(0.185)S(0.814)QT(0.002)QGGGSVTK 99.078 0.00062758 563150000 139330 111330 141210 146570 129590 134060 180610 167660 175850 TRUE FALSE 132744.147 122674.6536 147684.6182 131836.5051 152190.455 129417.4686 153054.6274 152978.8016 203119.9199 0.653525991 0.603951861 0.72708092 0.649057489 0.749264056 0.637148088 0.753518549 0.753145244 1 17.63197221 -5 0.161557097 2.231305404 0.595997853 0.852368694 0.042684051 41.33159447 0.381582296 16.17976666 0.155381898 1.00E-05 5 -1.63530755 GRASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRASSHSSQTQGGGSVTKK 19 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 2 GRAS(0.348)S(0.515)HS(0.199)S(0.937)QT(0.001)QGGGSVTKK 72.805 0.0097275 58170000 104610 39833 125730 70769 93276 96858 198050 140390 175740 TRUE FALSE 99665.29262 43892.02799 131494.8449 63655.16567 109543.3049 93503.78317 167833.8351 128096.7073 202992.8616 0.490979298 0.21622449 0.647780635 0.313583272 0.539641168 0.460625967 0.826796734 0.631040453 1 17.63106947 1.447946057 0.574891389 0.990820764 0.374807414 0.632103874 0.138705088 0.412231156 0.327323818 0.124317132 0.065010053 28.05085198 -1.447946057 -0.61601335 GRASS(ph)HSSQTQGGGS(ph)VTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRASSHSSQTQGGGSVTKK 19 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 2 GRAS(0.396)S(0.602)HS(0.002)S(0.001)QT(0.016)QGGGS(0.973)VT(0.011)KK 87.952 0.0014129 24480000 37316 22176 34721 37882 30764 36298 53464 43291 44018 TRUE FALSE 35552.14663 24435.75961 36312.99219 34074.02939 36129.23186 35040.99116 45307.08487 39500.21054 50844.08663 0.699238574 0.480601801 0.714202862 0.670167008 0.710588669 0.689185183 0.891098412 0.776888979 1 15.63379237 1.613427906 0.471710587 0.99804139 0.589408476 0.691283795 0.076282646 0.449376016 0.255843463 0.076922086 0.052241714 41.06084718 -1.613427906 -0.408632914 GRASS(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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 1 GRAS(0.013)S(0.49)HS(0.49)S(0.006)QTQGGGSVTK 265.53 2.84E-31 196480000 63333 19626 80247 33082 99230 54115 161780 112580 312920 TRUE FALSE 60339.3746 21625.91171 83926.40433 29756.53451 116535.6806 52240.98398 137097.4897 102721.8984 361446.0354 0.16693882 0.059831647 0.232196223 0.082326355 0.322415158 0.144533288 0.37930279 0.284197054 1 18.46342074 -3.143484362 0.221798789 2.662673431 0.071680785 0.909797762 0.080619152 13.99434883 0.29253918 10.85643199 0.135129733 0.000718647 3.143484362 -2.590992647 GRASSHS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Trastuzumab_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 1 GRAS(0.016)S(0.093)HS(0.744)S(0.146)QT(0.001)QGGGSVTK 97.253 0.001343 0 9906 5540.8 13109 6425.4 13467 9849.5 21935 14627 36790 TRUE FALSE 9437.763012 6105.413819 13710.06062 5779.506585 15815.64054 9508.409345 18588.41289 13346.18234 42495.2053 0.222090067 0.143673004 0.322626059 0.136003734 0.372174706 0.223752522 0.437423769 0.314063251 1 15.37501245 -5 0.198355238 4.373897056 0.140733825 0.894779719 0.080427353 35.09814716 0.346616873 46.7153533 0.166469338 1.00E-05 5 -4.233163231 GRASSHSS(ph)QTQGGGS(ph)VTK ddPTM_SK-BR-3_Trastuzumab_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(0.372)S(0.13)HS(0.132)S(0.365)QT(0.003)QGGGS(0.963)VT(0.035)K 100.27 0.00050208 217370000 425270 341170 460520 502060 527410 445540 706770 575280 763090 TRUE FALSE 405168.3299 375935.6109 481635.2975 451591.9749 619390.137 430110.8381 598939.2558 524905.4334 881426.0999 0.459673624 0.426508372 0.546427315 0.512342413 0.702713633 0.487971525 0.679511596 0.595518369 1 19.74948009 -5 0.118605761 2.541186699 0.305581875 0.823693296 0.069949949 53.48808911 0.412790304 19.65636349 0.616207125 1.00E-05 5 -2.235604824 GRDIVVLGVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GRDIVVLGVEK 11 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 ;; 135.94 1.00E-04 824880000 1178140 1026790 887850 1009800 1054430 918300 1331070 1179910 1090420 FALSE TRUE 1122451.657 1131421.068 928558.8007 908292.9855 1238322.258 886499.0407 1127990.825 1076590.825 1259516.765 0.891176433 0.898297744 0.737234173 0.721144022 0.98317251 0.703840604 0.895574284 0.854764983 1 20.26443889 0.572930962 1.358709821 0.999735747 0.836664111 0.254588251 0.089589255 2.422083592 6.012104047 0.080401339 0.023780862 3.740511224 -0.572930962 -0.163071636 GRDS(ph)PYQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(0.997)PY(0.003)QSR;GRDS(1)PYQSR;GRDS(0.999)PYQS(0.001)R;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR 145.31 5.90E-05 7513120000 605066 655258 540804 696163 703785 546742 634506 645319 638747 TRUE FALSE 576465.7293 722029.5352 565600.3983 626183.3726 826524.8812 527808.1874 537700.4562 588811.4473 737800.6225 0.781329958 0.978624188 0.766603309 0.848716243 1.120255061 0.715380513 0.728788293 0.798063094 1 19.49287148 GRDVIAQSQSGTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRDVIAQSQSGTGK 14 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 193.96 1.81E-07 261670000 244530 224890 249460 236760 239620 250470 263180 267060 239170 FALSE TRUE 232971.5515 247806.5467 260897.9877 212960.435 281409.6521 241796.1611 223027.0574 243674.8106 276259.2621 0.843307659 0.897007198 0.944395441 0.770871656 1.018643321 0.875250876 0.807310697 0.882051189 1 18.07566331 4.591944203 3.164145953 0.888273411 0.842707847 0.032480083 0.076931762 1.167118763 20.14105798 0.017421672 0.108033245 39079.06848 -4.591944203 -0.045565565 GRDWNVDLIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 127.56 0.00025913 6973728000 25058540 20941230 22488280 24731710 19159260 25204350 27593190 26887680 20934550 FALSE TRUE 23874072.48 23075165.15 23519389.88 22245631.52 22500628.88 24331517.04 23383342.08 24533252.2 24180973.1 0.987308177 0.954269502 0.97264034 0.919964281 0.930509653 1.006225719 0.967014106 1.014568442 1 24.52736897 2.228016314 24.99992751 0.991719496 0.95564115 0.474301567 0.022631141 235.2233342 557696.6725 0.008610726 0.006426279 169.0504433 -2.228016314 -0.036078346 GRECS(ph)PTSSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GRECSPTSSLER 12 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 GRECS(0.732)PT(0.151)S(0.048)S(0.07)LER;GRECS(0.611)PT(0.281)S(0.083)S(0.025)LER;GRECS(0.979)PT(0.014)S(0.004)S(0.004)LER 70.784 0.02807 854090000 1249960 1217510 1090170 1373830 1148300 1223420 1412620 1453080 1331970 TRUE FALSE 1190876.868 1341575.653 1140155.373 1235729.998 1348563.156 1181052.659 1197098.874 1325840.612 1538525.105 0.774037982 0.871988146 0.741070373 0.803191313 0.876529835 0.76765251 0.778082119 0.861760791 1 20.55311655 0.913912691 4.38038395 0.999946192 0.804810588 0.678001542 0.04320583 0.246484009 10.84911921 0.039623553 0.010077401 8.201866409 -0.913912691 -0.195135604 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFT(0.045)S(0.045)EAPILT(0.911)PPREPR 239.34 2.34E-43 3386020000 919777 816195 930326 965483 1057179 882068 1056484 939017 1134352 TRUE FALSE 876300.964 899366.1984 972982.3673 868430.8145 1241550.683 851521.764 895297.9621 856791.6934 1310261.515 0.668798522 0.686402057 0.742586389 0.662791973 0.947559452 0.649886877 0.683297153 0.653908921 1 20.32142336 -2.274676223 2.371541566 2.304939486 0.708847452 0.51468045 0.087874891 3246461.829 448982.3474 23018112.18 0.020910233 0.005312804 2.274676223 -1.596092035 GREEYEGPNKKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 121.56 0.00010744 229538000 368160 290850 303670 338860 250256 329020 352330 367390 286538 FALSE TRUE 350757.8064 320487.9457 317593.5699 304797.149 293900.5672 317625.9549 298575.5875 335219.3839 330972.8496 1.059778187 0.968320955 0.959575899 0.920912846 0.887989959 0.959673747 0.902115046 1.012830461 1 18.33635335 4.428564175 1.290901012 0.939010899 1.078569875 0.418380032 0.039686648 0.630526576 1.360036098 0.010388391 0.100776226 26826.5099 -4.428564175 0.139558976 GREFSFEAWNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GREFSFEAWNAK 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 85.536 0.010597 248160000 927040 781740 916450 925430 704460 1018600 1102400 970020 708530 FALSE TRUE 883220.6564 861400.1948 958470.139 832404.0182 827317.601 983325.6266 934208.633 885079.9064 818405.2137 1.07919725 1.052535077 1.171143735 1.01710498 1.010889944 1.201514372 1.141498878 1.081469047 1 19.64245581 2.252381665 24.9993519 1.123425115 1.068039172 0.054707556 0.066894976 448.8613883 811894.5256 0.021766724 0.018125565 178.8058258 -2.252381665 -0.055385943 GRES(ph)PAAGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 99.669 0.0027482 1016670000 308600 257546 278190 300000 278400 261830 305180 224370 257760 TRUE FALSE 294013.0896 283790.2302 290945.2867 269843.43 326952.8719 252762.7614 258619.186 204722.9733 297732.1043 0.987508855 0.953173091 0.977204952 0.906329637 1.098144497 0.848960383 0.868630498 0.687607988 1 18.18365527 2.105284585 12.54126732 0.842816322 0.97657732 0.357414953 0.088093625 0.491118767 55.13634462 0.029253 0.021604585 127.4337856 -2.105284585 0.133760998 GRGFGS(ph)EEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRGFGSEEGSR 11 1 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 1 GRGFGS(0.998)EEGS(0.002)R;GRGFGS(0.933)EEGS(0.067)R 105.99 0.0018066 210780000 229701 226651 211322 243122 242051 230987 237127 232947 248347 TRUE FALSE 218843.489 249746.9946 221011.3227 218682.9147 284264.6178 222987.8623 200948.921 212548.9258 286859.3844 0.762894648 0.87062515 0.770451778 0.762334881 0.99095457 0.777342051 0.700513673 0.740951621 1 18.12998419 -0.260703505 7.560631669 0.99999999 0.797414121 0.383222339 0.080930336 0 0 0.078381659 0.018474734 0.548651404 0.260703505 -0.20258587 GRKDDDS(ph)DDESQSSHTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.986)DDES(0.012)QS(0.001)SHTGK;GRKDDDS(0.944)DDES(0.055)QS(0.001)SHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(1)DDESQSSHTGK 229.78 8.83E-20 1395160000 977535 794227 914429 1007288 628821 1090430 1184590 1063976 715081 TRUE FALSE 931328.8578 875159.6343 956356.4741 906033.4965 738487.1833 1052668.136 1003859.039 970808.6209 825972.1094 1.12755485 1.059551072 1.157855651 1.096929892 0.89408247 1.274459662 1.215366751 1.175352787 1 19.65573354 2.191718338 24.99999946 1.190798743 1.077110488 0.177848306 0.0986073 167.2147681 89242.41171 0.033925082 0.025055402 155.4956837 -2.191718338 -0.113688255 GRKDDDSDDES(ph)QSSHTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.053)DDES(0.316)QS(0.316)S(0.316)HTGK;GRKDDDS(0.08)DDES(0.305)QS(0.305)S(0.305)HT(0.006)GK 106.03 0.0002405 98451000 72485 60156 73379 75203 46509 76578 93830 89826 56824 TRUE FALSE 69058.7777 66285.96479 76743.49973 67643.45156 54620.15487 73926.08466 79514.51019 81960.35924 65635.9757 1.052148261 1.009902939 1.169229206 1.030584993 0.832167943 1.126304346 1.211447066 1.248710914 1 16.00219917 2.01295211 24.99685178 1.174879051 1.023932986 0.268435093 0.103437078 254.4593285 491090.4575 0.036624525 0.027034076 103.0272506 -2.01295211 -0.150946064 GRLDS(ph)SEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRLDS(0.943)S(0.058)EMDHS(0.999)ENEDYT(0.001)MSSPLPGK 102.51 0.0027924 101520000 159070 156710 150550 188960 160160 169340 166610 165950 101770 TRUE FALSE 151551.0763 172678.9272 157452.8664 169965.3818 188091.8533 163475.7133 141190.5845 151418.5382 117551.9718 1.289226152 1.468958151 1.339431946 1.445874358 1.600073996 1.390667556 1.201090737 1.288098667 1 16.84293921 1.1303045 1.040882558 1.01904261 1.419393107 0.643293156 0.097136339 0.317307421 0.731364852 0.091546466 0.030501251 13.49909023 -1.1303045 0.400350497 GRLDS(ph)SEMDHS(ph)ENEDYTMSSPLPGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGKK 26 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRLDS(0.749)S(0.252)EMDHS(0.754)ENEDY(0.032)T(0.138)MS(0.037)S(0.039)PLPGKK 47.487 0.075943 130770000 46937 41305 58352 56095 37626 56252 72053 55777 31839 TRUE FALSE 44718.38103 45514.02646 61027.49692 50456.22403 44187.96249 54303.97914 61059.99151 50892.87019 36776.42951 1.215952218 1.237586875 1.659418756 1.371971796 1.201529433 1.476597371 1.660302327 1.383844785 1 15.1664938 3.953478111 24.88571526 1.432041203 1.224064937 0.08553845 0.197647629 597.4530116 319592.686 0.047965908 0.086472944 8984.1731 -3.953478111 -0.207976266 GRLDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDS(0.145)S(0.119)EMDHS(0.644)ENEDY(0.022)T(0.024)MS(0.024)S(0.024)PLPGK;GRLDS(0.006)S(0.004)EMDHS(0.985)ENEDY(0.004)TMSSPLPGK 119.18 0.0004234 367435000 390418 378549 363818 443154 337311 420323 470092 445930 374380 TRUE FALSE 371963.7149 417123.5735 380499.4152 398607.318 396137.9316 405767.1091 398370.8316 406882.0052 432436.9383 0.860157128 0.964588213 0.879895729 0.921769818 0.916059422 0.938326663 0.921222949 0.940904833 1 18.72213024 -5 0.130235273 1.279684468 0.883234853 0.546698027 0.026488618 112.8387198 0.926481162 8.197134612 0.185976426 1.00E-05 5 -0.396449615 GRLDSSEMDHS(ph)ENEDYTMSSPLPGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRLDSSEMDHSENEDYTMSSPLPGKK 26 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDSSEMDHS(0.999)ENEDYTMSSPLPGKK;GRLDS(0.031)S(0.031)EMDHS(0.938)ENEDYTMSSPLPGKK 129.01 5.44E-05 263151000 163428 115979 163519 164739 121747 160432 205204 186706 158595 TRUE FALSE 155703.0823 127797.392 171016.5079 148179.1227 142979.6383 154876.1996 173896.361 170357.0328 183189.1026 0.849958213 0.697625514 0.933551753 0.808886122 0.780502968 0.845444393 0.94927241 0.929951784 1 17.48297416 1.798135855 2.670015853 0.960735151 0.80647622 0.546281606 0.060724454 0.193623723 2.640214692 0.034507532 0.016476454 62.82548575 -1.798135855 -0.154258931 GRLESAQATFQAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GRLESAQATFQAHR 14 1 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ;;; 130.07 3.86E-05 495290000 673429 575711 601053 623937 1116430 536011 802215 647539 980340 FALSE TRUE 641597.3458 634376.6054 628611.8746 561217.6674 1311135.039 517448.8047 679822.3681 590837.0523 1132366.12 0.566598854 0.56022217 0.555131298 0.495615029 1.157872012 0.456962457 0.600355623 0.521772103 1 20.11090906 GRLGS(ph)VDSFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;GRLGS(1)VDSFER;GRLGS(0.988)VDS(0.012)FER 230.23 1.18E-12 774591000 878939 608404 795261 843080 1010114 758480 1065011 849823 1010185 TRUE FALSE 837393.2954 670401.0593 831724.5035 758331.9967 1186277.562 732213.6474 902524.0117 775407.9929 1166839.33 0.71765947 0.574544448 0.712801224 0.64990267 1.016658876 0.627518827 0.773477537 0.664537073 1 20.15417449 -5 0.158293333 2.041979952 0.631592723 0.346999788 0.120365382 140.9130881 1.288883408 46.34291304 0.486416046 1.00E-05 5 -1.41038723 GRLGSVDS(ph)FER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLGSVDSFER 11 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 GRLGS(0.033)VDS(0.967)FER 101.39 0.0087355 127080000 196320 135000 184680 176480 195380 156930 197190 164210 224790 TRUE FALSE 187040.3427 148756.6535 193147.7607 158739.8951 229454.2101 151495.4748 167105.0439 149830.9019 259649.2851 0.720357626 0.57291378 0.743879424 0.611362727 0.88370823 0.583461937 0.643579834 0.577051086 1 17.98620473 -1.547568873 5.948411501 1.000684765 0.663652594 0.54145522 0.096250442 0.000788863 6.00E-05 0.08410923 0.019786205 0.028342041 1.547568873 -0.337032171 GRLPNNSS(ph)RPS(ph)TPTINVLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 2 GRLPNNS(0.472)S(0.53)RPS(0.524)T(0.466)PT(0.008)INVLESK;GRLPNNS(0.457)S(0.541)RPS(0.513)T(0.433)PT(0.057)INVLESK 100.7 0.0012288 503010000 448100 425150 424590 483490 320450 436620 444910 470950 367380 TRUE FALSE 426919.201 468473.2684 444057.8715 434888.6666 376336.3785 421499.7399 377030.8082 429711.1213 424351.4141 1.006051086 1.103974802 1.046439005 1.02483143 0.88685077 0.993279923 0.88848722 1.012630351 1 18.69489996 2.933901951 5.639978969 0.947559124 1.054519203 0.456461945 0.04847399 0.157698469 9.736889215 0.013488052 0.014509441 858.819608 -2.933901951 0.106960079 GRLPNNSS(ph)RPST(ph)PTINVLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 2 GRLPNNS(0.449)S(0.551)RPS(0.447)T(0.548)PT(0.005)INVLESK 158.2 4.56E-11 359900000 185610 221380 189940 218430 148740 195300 192530 220550 168620 TRUE FALSE 176836.5831 243938.8737 198648.9369 196473.0014 174680.2089 188536.712 163156.0124 201237.4728 194768.7284 0.907931086 1.252454004 1.019922133 1.008750239 0.896859626 0.968002993 0.837691008 1.033212438 1 17.57140253 3.123240951 2.408110385 0.931792142 1.083109658 0.19904876 0.099463638 0.33597234 3.969414508 0.02990952 0.037563878 1328.131114 -3.123240951 0.151317516 GRLS(ph)PVPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;GRLS(1)PVPVPR 129.54 0.00018197 54297020000 3977690 2907120 3242990 3796240 4132520 2860760 3538760 3275730 4694290 TRUE FALSE 3789672.477 3203358.833 3391684.299 3414634.743 4853230.18 2761691.164 2998857.168 2988889.715 5422256.518 0.698910585 0.590779655 0.625511591 0.629744228 0.895057282 0.509325067 0.553064422 0.551226174 1 22.37046194 -1.830662581 2.626767719 1.133337933 0.628554969 0.538398593 0.107137184 9609295.676 6881631.065 8106747.211 0.025903294 0.014768535 1.830662581 -0.504782965 GRLSPVPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLSPVPVPR 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM0 Q9UKM9 RALY RNA-binding protein Raly 0 90.306 0.0099597 133170000 50790 44595 41485 50261 60243 42551 54937 48990 63266 FALSE TRUE 48389.25736 49139.2812 43387.12828 45208.66879 70749.36013 41077.4482 46555.35166 44700.17589 73076.96816 0.662168376 0.672431854 0.593718231 0.61864456 0.968148541 0.562112102 0.63707284 0.61168624 1 16.15712916 -1.444483482 5.692452353 1.000230643 0.664887282 0.46686254 0.112250642 0.000305054 2.98E-05 0.100906896 0.023767844 0.035934906 1.444483482 -0.335343361 GRLT(ph)PS(ph)PDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(1)PS(1)PDIIVLS(0.997)DNEAS(0.002)S(0.001)PR;GRLT(1)PS(1)PDIIVLS(0.677)DNEAS(0.236)S(0.087)PR;GRLT(1)PS(1)PDIIVLS(0.95)DNEAS(0.04)S(0.009)PR;GRLT(1)PS(1)PDIIVLS(0.893)DNEAS(0.084)S(0.023)PR 114.35 6.98E-06 230670000 466880 405084 414888 473399 467965 438456 552500 433411 544646 TRUE FALSE 444811.5077 446362.5201 433911.0252 425812.0331 549577.9478 423272.1588 468205.9776 395459.2352 629106.92 0.707052321 0.70951774 0.689725405 0.676851612 0.873584331 0.672814343 0.744239115 0.628604173 1 19.26294571 -1.146201198 4.143091778 1.000078967 0.715550156 0.661684801 0.064512625 12153644.16 32019879.14 13666.62658 0.013965638 0.071416539 1.146201198 -0.28452881 GRLT(ph)PS(ph)PDIIVLSDNEAS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(1)PS(1)PDIIVLSDNEAS(0.662)S(0.338)PR;GRLT(1)PS(1)PDIIVLSDNEAS(0.567)S(0.433)PR 210.58 1.64E-22 119073000 193323 169715 177090 212756 198410 172030 216926 185288 219270 TRUE FALSE 184185.0049 187009.1514 185209.7517 191369.3627 233012.6412 166072.558 183829.9546 169063.2004 253273.2717 0.727218485 0.738369075 0.731264497 0.755584517 0.920004861 0.655705029 0.725816638 0.667512996 1 17.95033531 -1.588966083 2.779566489 1.018727382 0.739970152 0.569012894 0.071061974 24472831.41 24254248.19 3363412.718 0.01652572 0.025765224 1.588966083 -0.27875723 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(0.998)PS(0.002)PDIIVLS(1)DNEASSPR;GRLT(0.998)PS(0.002)PDIIVLS(1)DNEASSPR 170.73 1.79E-11 363240000 484530 427430 460100 491510 537120 444730 520870 480090 566760 TRUE FALSE 461627.2271 470985.6029 481196.0401 442102.481 630793.5579 429328.8886 441401.7151 438050.7745 654650.2462 0.705150926 0.719446156 0.735042938 0.675326227 0.963558116 0.655814141 0.674255784 0.669137111 1 19.32036481 -1.588401791 3.07084595 1.015112149 0.722364513 0.488702368 0.088461592 28469445.86 32887970.21 3511361.734 0.020613455 0.025798723 1.588401791 -0.292747637 GRLT(ph)PSPDIIVLSDNEASS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PSPDIIVLSDNEAS(0.196)S(0.804)PR 226.17 5.79E-25 65265000 96427 76613 87968 95713 114260 90206 94800 87743 115720 TRUE FALSE 91869.08681 84419.9518 92001.41981 86091.7474 134186.9078 87082.1436 80336.51888 80059.75777 133665.2666 0.6873071 0.631577327 0.688297133 0.644084657 1.003902594 0.651494183 0.601027634 0.59895708 1 17.0282651 -1.370140671 3.443900453 1.002134583 0.68348289 0.414062118 0.116390032 35292240.85 52274392.16 760021.5761 0.02742863 0.042644137 1.370140671 -0.318651693 GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.948)PS(0.052)PDIIVLSDNEASSPR 128.06 3.04E-05 76309000 300420 263350 249880 320610 192930 253040 311690 333210 225390 TRUE FALSE 286219.742 290185.6644 261337.2452 288381.6737 226576.9309 244277.1614 264135.9659 304032.3659 260342.3301 1.099397635 1.114631126 1.003821565 1.107701823 0.870303845 0.938292137 1.014571721 1.167817642 1 17.99005038 3.551730462 1.570802584 1.002003282 1.109249788 0.159919523 0.082266888 0.593020181 2.918287884 0.025189692 0.04819609 3562.299764 -3.551730462 0.107246506 GRLTPS(ph)PDIIVLSDNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.074)PS(0.916)PDIIVLSDNEAS(0.005)S(0.005)PR 185.16 9.72E-17 57956000 60487 47623 56676 55651 57956 55168 63059 56742 62463 TRUE FALSE 57627.89938 52475.83784 59274.65066 50056.85575 68063.50805 53257.51833 53438.19139 51773.36967 72149.44302 0.79872965 0.727321455 0.821553822 0.69379407 0.943368447 0.738155641 0.740659791 0.717585161 1 16.13870064 -1.090505902 4.649562553 1.000011051 0.770570196 0.500778535 0.071312534 56832253612 11116211956 8559294.317 0.01503177 0.081188422 1.090505902 -0.229440855 GRLTPSPDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.015)PS(0.033)PDIIVLS(0.581)DNEAS(0.186)S(0.186)PR 141.22 4.15E-07 74492000 62579 48633 54765 64097 59596 51981 61529 54640 70446 TRUE FALSE 59621.01469 53588.75799 57276.02942 57653.84778 69989.52353 50180.88494 52141.62099 49855.43194 81370.40589 0.732711285 0.658577985 0.703892635 0.708535826 0.86013487 0.616696997 0.640793424 0.612697348 1 16.31221657 -1.844564279 2.925665814 1.108761292 0.690079723 0.647026219 0.071540341 9835763.054 7278611.956 7403969.102 0.016978486 0.014303283 1.844564279 -0.418681569 GRNDLMEYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRNDLMEYAK 10 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ; 122.7 0.00043924 1517150000 1704200 1170930 941740 1176030 1487720 1188090 1793680 1533260 1551850 FALSE TRUE 1623645.843 1290249.098 984919.7105 1057813.23 1747177.897 1146946.145 1520021.173 1398999.626 1792502.972 0.905798132 0.719803045 0.549466152 0.590131925 0.974714086 0.639857319 0.847988091 0.780472695 1 20.77354408 0.531760433 0.703083959 1.002641727 0.736462744 0.273513448 0.133020356 2.228674588 1.858016524 0.144257426 0.048236575 3.40220464 -0.531760433 -0.266178983 GRNDS(ph)GEENVPLDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GRNDSGEENVPLDLTR 16 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR 138.09 5.13E-06 522825000 280418 312649 304372 371360 302324 326623 327728 342830 298930 TRUE FALSE 267163.1969 344508.2886 318327.7573 334030.1873 355049.2099 315311.9636 277727.0745 312809.9877 345286.5377 0.77374345 0.997746077 0.921923454 0.967399973 1.028274118 0.913189277 0.804337975 0.905943191 1 18.39743456 -0.072001526 7.355604548 0.999999997 0.910461787 0.105351683 0.078069516 5245820.218 713173.157 0.077370489 0.0187651 0.847224437 0.072001526 -0.08953821 GRNDS(ph)GEENVPLDLTREPSDNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRNDSGEENVPLDLTREPSDNLR 23 2 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 GRNDS(1)GEENVPLDLTREPSDNLR;GRNDS(1)GEENVPLDLTREPSDNLR 138.34 2.10E-06 125511000 33808 23816.8 35708 29239 41589 29537 41400 31094 47679 TRUE FALSE 32209.96284 26243.759 37345.24712 26299.84017 48842.10843 28514.12628 35083.66964 28371.24452 55072.81581 0.584861376 0.476528367 0.678106731 0.477546677 0.886864195 0.517753194 0.637041508 0.515158778 1 15.74905275 -2.4172487 2.269575348 4.60622252 0.592573372 0.51824443 0.122133173 3623767.008 353133.784 67329073.97 0.027731613 0.003826056 2.4172487 -4.013649148 GRNS(ph)ATSADEQPHIGNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.983)AT(0.013)S(0.004)ADEQPHIGNYR;GRNS(0.981)AT(0.019)SADEQPHIGNYR 234.99 5.34E-24 423220000 109051 100590 104447 127460 124721 91857 117886 110347 108047 TRUE FALSE 103896.3753 110840.2354 109235.9983 114647.4786 146472.3029 88675.96906 99900.32558 100684.4317 124802.3769 0.832487152 0.888125996 0.875271777 0.918632172 1.17363392 0.710531091 0.800468132 0.806750914 1 16.92928589 -0.622840169 7.166248121 0.999999854 0.871710017 0.094381817 0.120394755 0 1.18E-10 0.113804185 0.026823904 0.238319638 0.622840169 -0.128289837 GRPPAEKLS(ph)PNPPNLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 151.82 1.23E-07 3040900000 1608300 1654060 1374980 1946280 858230 1834230 1785460 1947750 1095950 TRUE FALSE 1532278.846 1822610.595 1438024.193 1750636.237 1007905.04 1770710.155 1513055.285 1777194.684 1265904.329 1.210422314 1.43976962 1.135965934 1.38291354 0.796193691 1.398770914 1.195236678 1.403893362 1 20.27173695 -1.845299891 2.51717652 0.897717073 1.250860358 0.141590074 0.189465074 28803654.3 16353723.43 17676890.03 0.042119484 0.014279076 1.845299891 0.353143285 GRPSKT(ph)PS(ph)PSQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.408)KT(0.596)PS(0.605)PS(0.391)QPK;GRPS(0.428)KT(0.577)PS(0.572)PS(0.423)QPK 77.746 0.027712 146980000 284850 273010 269780 338680 144887 359110 327350 314960 178056 TRUE FALSE 271385.705 300830.0294 282149.6798 304635.243 170155.2469 346673.9307 277406.7453 287380.4327 205668.0151 1.319532864 1.462697198 1.371869514 1.481198925 0.82732965 1.685599632 1.348808395 1.397302505 1 17.64995792 -2.226306939 1.911844724 0.000184472 1.369194294 0.216815962 0.215689227 3069057.038 503563.0415 13246115.95 0.050166135 0.005938723 2.226306939 1.369009822 GRPSKT(ph)PSPS(ph)QPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.294)KT(0.708)PS(0.284)PS(0.714)QPK 81.346 0.016906 56278000 133540 114610 124560 152580 59919 161120 144850 145800 70444 TRUE FALSE 127227.8289 126288.8893 130271.1992 137242.3685 70368.85463 155540.374 122750.4721 133032.9791 81368.09574 1.563608288 1.552068881 1.60101079 1.68668527 0.864821205 1.911564632 1.508582338 1.634952592 1 16.31217561 -1.813438258 2.659101807 0.826766628 1.542906259 0.291799494 0.264558346 22968584.98 17020736.24 25624676.55 0.05685373 0.015366032 1.813438258 0.716139631 GRPVS(ph)PQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GRPVSPQSR 9 1 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GRPVS(0.998)PQS(0.002)R;GRPVS(1)PQSR;GRPVS(1)PQSR;GRPVS(1)PQSR 77.74 0.019225 347411000 235450 236036 302898 399214 305108 279001 385498 457662 455600 TRUE FALSE 224320.7451 260088.3368 316786.1729 359084.2503 358318.7386 269339.1254 326683.1999 417586.6891 526252.1211 0.42626098 0.494227626 0.601966548 0.682342618 0.68088797 0.511806251 0.620773175 0.7935107 1 19.00539462 -5 0.080187689 2.427060919 0.151979271 0.799840628 0.073289177 115.0026548 0.652724423 28.83003615 2.680383438 1.00E-05 5 -2.275081648 GRPVSLWELLFSEAISSEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRPVSLWELLFSEAISSEQR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 280.63 9.22E-45 390520000 475880 478390 281510 329090 522710 334030 477610 413320 359430 FALSE TRUE 453386.0955 527138.4849 294417.512 296009.248 613870.4585 322462.4573 404741.8226 377127.5097 415168.5687 1.092053035 1.269697479 0.709151738 0.712985689 1.47860533 0.776702481 0.974885512 0.908372016 1 18.6633377 3.762580147 24.99783896 0.941383314 1.180875267 0.172210384 0.221923696 1236.48381 1286841.033 0.053759051 0.096852058 5788.688058 -3.762580147 0.239491953 GRPYDYNGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GRPYDYNGPR 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;; 132.25 0.00020851 1725340000 683194 539532 600273 646277 728969 584929 701339 652536 779048 FALSE TRUE 650900.7736 594510.9242 627796.1108 581312.0081 856100.9628 564672.7621 594336.8546 595396.4885 899858.785 0.723336577 0.660671357 0.697660701 0.646003593 0.951372568 0.62751264 0.660477916 0.661655471 1 19.77933909 -1.059545246 4.496840489 1.000014855 0.700062786 0.504905561 0.092185643 1.52E-05 3.18E-06 0.082898549 0.019538223 0.087187606 1.059545246 -0.299952069 GRRPS(ph)GPDGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GRRPSGPDGAAR 12 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR 108.63 0.0013268 1854520000 1061200 753596 1012492 957106 1373015 988169 1276302 1088146 1456283 TRUE FALSE 1011039.179 830388.2892 1058915.76 860895.8865 1612468.381 953948.4598 1081578.689 992862.1676 1682115.93 0.601052021 0.493656991 0.629514138 0.511793433 0.958595274 0.567112196 0.642987008 0.590245981 1 20.68184571 -5 0.196103801 2.678546225 0.551655803 0.45843892 0.127992163 120.5704333 1.187920609 79.38750078 0.300423094 1.00E-05 5 -2.126890422 GRRT(ph)PPVQPPPTREDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRRTPPVQPPPTREDR 16 3 Q9Y6R9 Q9Y6R9 CCDC61 Coiled-coil domain-containing protein 61 1 GRRT(1)PPVQPPPTREDR;GRRT(1)PPVQPPPTREDR 83.423 0.0080566 154449000 67075 57388 84400 75460 66364 74292 102397 69474 94274 TRUE FALSE 63904.49768 63235.90244 88269.82348 67874.61744 77937.86059 71719.24941 86774.457 63390.48826 108893.5304 0.586853024 0.580713126 0.810606683 0.623311754 0.715725354 0.658618094 0.796874311 0.582132731 1 16.73255872 -5 0.153984319 2.178375156 0.571757985 0.582149508 0.086201805 87.13406907 0.78649837 31.51431525 0.372045262 1.00E-05 5 -1.606617171 GRS(ph)IDQDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER 201.3 1.48E-07 5119300000 2895510 2151100 2376050 2854770 3304100 2639610 3339910 2802020 3779660 TRUE FALSE 2758644.981 2370299.536 2484994.243 2567803.096 3880333.994 2548199.644 2830345.388 2556660.274 4365790.369 0.631877563 0.542925641 0.569196877 0.588164543 0.88880447 0.583674301 0.6483008 0.585612239 1 22.05781143 -5 0.2847689 3.803311146 0.602868868 0.582643124 0.097802889 167.2563834 1.589141644 277.9735337 0.103706735 1.00E-05 5 -3.200442278 GRS(ph)KDRDPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GRSKDRDPNR 10 3 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 GRS(1)KDRDPNR;GRS(1)KDRDPNR;GRS(1)KDRDPNR 86.291 0.075474 1645870000 1442600 1114068 1360440 1379370 941042 1444370 1656400 1490610 1089500 TRUE FALSE 1374411.157 1227592.796 1422817.52 1240713.107 1105159.427 1394351.105 1403685.758 1360084.286 1258454.096 1.092142464 0.975476817 1.130607405 0.985902554 0.878188112 1.10798726 1.115404815 1.080757964 1 20.26322116 GRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 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(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 354.99 5.15E-132 9539869900 1555034.3 1424565 1349505.5 1670561.2 1223583.8 1449412.5 1569548.4 1637555.8 1170734.9 TRUE FALSE 1481530.91 1569729.793 1411381.662 1502633.214 1436976.427 1399218.982 1330084.965 1494162.733 1352286.489 1.095574734 1.160796773 1.043700187 1.11117964 1.062627216 1.034706028 0.983582233 1.104915819 1 20.3669694 2.782514876 0.972279526 1.021896278 1.121114501 0.381298646 0.042319704 0.455080198 0.91728671 0.021948011 0.021226083 606.0589595 -2.782514876 0.099218223 GRS(ph)RT(ph)PPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRSRTPPTSR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GRS(1)RT(0.998)PPT(0.002)SR 67.997 0.067649 840370000 154570 121830 139520 149400 150970 130480 154260 125730 169550 TRUE FALSE 147263.7824 134244.6155 145917.13 134382.0282 177299.1202 125961.4449 130724.8038 114720.4147 195842.9481 0.751948354 0.685470765 0.745072169 0.686172413 0.905312762 0.6431758 0.667498141 0.585777613 1 17.57933765 GRSECDSS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRSECDSSPEPK 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GRSECDS(0.275)S(0.725)PEPK 76.391 0.018921 463740000 795520 605570 737200 802420 646040 694520 837520 843330 703490 TRUE FALSE 757917.3462 667278.2715 771001.3492 721759.2171 758709.1715 670468.5983 709740.9419 769483.5544 812583.6363 0.932725337 0.821181035 0.948827068 0.888227605 0.933699791 0.825107187 0.873437404 0.946959205 1 19.63215679 1.029114374 3.850811681 0.999331557 0.885199951 0.426572427 0.042921514 0.16498582 5.71976551 0.038417796 0.009879512 10.69336458 -1.029114374 -0.114131606 GRSPGQLQR ddPTM_SK-BR-3_Trastuzumab_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 60.828 0.084968 97501000 60674 50113 56250 56774 64504 42373 59554 54783 72289 FALSE TRUE 57806.06026 55219.57167 58829.11814 51066.96966 75753.47718 40905.61239 50467.94352 49985.9101 83499.20892 0.692294706 0.661318501 0.704547012 0.611586269 0.907235867 0.489892215 0.604412235 0.598639325 1 16.34947491 -1.825155802 7.387776588 1.017528322 0.656876705 0.502878618 0.106617431 0.027629781 0.000653905 0.092663262 0.022626435 0.01495699 1.825155802 -0.360651617 GRVEDVVVSDECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GRVEDVVVSDECR 13 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 121.76 0.00022153 172680000 70023 74805 61565 78851 65425 60059 80140 74366 78437 FALSE TRUE 66713.15156 82427.71455 64387.81615 70924.74767 76835.09929 57979.14177 67913.17113 67854.1188 90600.60936 0.736343299 0.909792055 0.710677518 0.782828594 0.848063825 0.639942073 0.749588459 0.748936671 1 16.46723313 -1.455039098 3.074146536 1.004826566 0.771000956 0.501264441 0.073260098 17534203 21452643.1 730022.9062 0.01759101 0.03507203 1.455039098 -0.23382561 GRVS(ph)VPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRVSVPLR 8 1 Q6A1A2 Q6A1A2 PDPK2P Putative 3-phosphoinositide-dependent protein kinase 2 1 GRVS(1)VPLR;GRVS(1)VPLR 73.616 0.026104 1468740000 2133900 2913200 4706900 3125700 1890910 3804500 2413600 3587200 2395900 TRUE FALSE 2033034.776 3210058.392 4922716.021 2811498.698 2220684.105 3672749.211 2045360.991 3273085.751 2767443.935 0.734625461 1.159936196 1.778795212 1.015918936 0.80243147 1.327126871 0.739079468 1.182710771 1 21.40012266 3.031626693 24.9994507 0.990538318 1.172740008 0.091079898 0.29969217 557.1701292 440413.9181 0.087469015 0.104544747 1075.540312 -3.031626693 0.18220169 GRWES(ph)QQDVSQTTVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.663)QQDVS(0.042)QT(0.087)T(0.024)VS(0.183)R;GRWES(0.996)QQDVS(0.003)QT(0.001)TVSR 148.33 2.48E-06 500880000 471970 372590 456100 482380 609580 404180 546580 463170 600120 TRUE FALSE 449660.9135 410557.3446 477012.6361 433890.2459 715890.559 390183.1453 463189.1824 422612.3794 693183.5446 0.648689538 0.592277973 0.688147663 0.625938468 1.032757579 0.562885758 0.668205681 0.609668799 1 19.40287788 -1.725211923 2.627182864 1.062017921 0.672822608 0.371152663 0.131297729 29182885.13 23133641.4 11863784.76 0.029441646 0.018827301 1.725211923 -0.389195314 GRYPDHSVDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;;;; 117.86 0.00044887 269447000 186288 125438.8 119412.6 124323.6 223271 126446.2 204182 160972 213158 FALSE TRUE 177482.5354 138221.1563 124887.7858 111826.3555 262209.3917 122067.3364 173030.2858 146876.4383 246213.454 0.720848242 0.561387504 0.5072338 0.454184585 1.064967765 0.495778498 0.702765357 0.596541074 1 17.90955007 GS(ph)FKDDPQLYQEIQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GS(1)FKDDPQLYQEIQER 115.66 0.00029594 202910000 467460 470060 392970 559020 317060 450960 508770 435520 325840 TRUE FALSE 445364.0922 517959.6484 410988.0632 502826.2475 372355.1636 435343.1421 431147.7923 397383.56 376369.603 1.183315785 1.37619947 1.091979958 1.335990589 0.989333784 1.156690494 1.145543606 1.0558333 1 18.52179059 2.337587651 0.396832917 1.01021076 1.294186068 0.355542585 0.102755699 1.268018377 0.452840852 0.102754193 0.127911584 217.5643087 -2.337587651 0.283975308 GS(ph)FMLGLETHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 1 GS(1)FMLGLETHDR 102.64 0.0015025 16465000 17313 15197 13349 19446 18387 15645 16678 16680 16487 TRUE FALSE 16494.6488 16745.59158 13961.06485 17491.25114 21593.68698 15103.20973 14133.46479 15219.41077 19043.71976 0.866146373 0.879323567 0.733105981 0.918478709 1.13390069 0.793080864 0.742158831 0.799182669 1 14.21702768 -0.865750718 4.219405976 1.000002262 0.855469452 0.132138178 0.114041801 4447738.869 1756880.863 91.40818037 0.027088185 0.136222636 0.865750718 -0.14453281 GS(ph)GFSLDVIDGPISQR ddPTM_SK-BR-3_Trastuzumab_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 146.78 6.93E-06 0 92717 118300 76668 109050 87774 82486 83582 86464 83547 TRUE FALSE 88334.45116 130354.9045 80183.30364 98088.08682 103081.7578 79629.48914 70830.03081 78892.75379 96503.04206 0.915354058 1.350785444 0.830888871 1.016424816 1.068171071 0.825150041 0.733966819 0.817515719 1 16.5582868 2.227044175 7.818179874 0.81201073 1.058157197 0.273130737 0.149488634 0.148511619 53.98788337 0.053427522 0.040977282 168.6724586 -2.227044175 0.246146466 GS(ph)GGGGGGGGQGSTNYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GS(1)GGGGGGGGQGSTNYGK 348 2.80E-90 339512000 342605 428475 378546 452221 331476 394897 396052 397477 371174 TRUE FALSE 326410.7406 472137.0896 395902.7085 406762.8859 389285.3095 381221.6179 335626.9934 362671.8067 428733.7682 0.761336673 1.101236069 0.923423201 0.94875402 0.907988449 0.889180294 0.78283312 0.84591379 1 18.70972253 2.259921936 2.608441781 0.850547199 0.94058072 0.033629125 0.097797371 0.533899887 7.4616001 0.039519829 0.028567577 181.9373799 -2.259921936 0.090033522 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR 250.35 4.19E-31 2281050000 1348250 1490550 1196910 1629650 1517540 1285500 1432360 1435040 1343790 TRUE FALSE 1284520.894 1642438.74 1251789.507 1465834.486 1782198.496 1240982.813 1213827.175 1309380.29 1552178.09 0.827560254 1.058150962 0.806472862 0.944372618 1.148192019 0.799510585 0.782015403 0.843576068 1 20.56586266 GS(ph)GSQSSVPSVDQFTGVGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGSQSSVPSVDQFTGVGIR 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GS(0.471)GS(0.471)QS(0.029)S(0.029)VPSVDQFTGVGIR 71.685 0.017926 46103000 38728 36787 36356 35052 37868 34278 37705 40022 38284 TRUE FALSE 36897.40419 40535.63712 38022.95856 31528.50637 44472.16721 33090.94426 31952.40975 36517.46151 44220.88719 0.834388601 0.916662684 0.859841604 0.712977698 1.005682383 0.748310275 0.722563743 0.825796673 1 15.43244035 GS(ph)GTAS(ph)DDEFENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 GS(0.996)GT(0.004)AS(1)DDEFENLR 261.17 2.50E-24 68050000 184540 175150 165490 207510 167000 183210 181250 176690 172700 TRUE FALSE 175817.1599 192997.9841 173077.8802 186650.7006 196124.7471 176865.3918 153596.9836 161218.0869 199481.434 0.881371045 0.96749848 0.867639042 0.935679561 0.983172936 0.886625829 0.769981349 0.808185923 1 17.60589495 1.994763987 24.69486066 0.832449487 0.926851592 0.133193178 0.069154389 226.5049686 1068278.567 0.023778236 0.017053702 98.80160218 -1.994763987 0.094402105 GS(ph)GVFCANCLTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGVFCANCLTTK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)GVFCANCLTTK 148.03 4.52E-05 383230000 408080 378640 401980 465400 492430 436460 509650 462220 582120 TRUE FALSE 388790.8671 417223.8465 420411.1806 418617.1078 578309.6361 421345.2808 431893.5321 421745.5664 672392.1965 0.578220374 0.620506675 0.625246966 0.622578772 0.860077852 0.626636185 0.642323832 0.627231501 1 19.35894346 -5 0.27534622 3.491770184 0.622131753 0.670208873 0.076883032 131.9337598 1.271637299 187.6122591 0.089108379 1.00E-05 5 -2.869638431 GS(ph)IGLLLGK ddPTM_SK-BR-3_Trastuzumab_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 138.22 0.00014974 61478000 313740 348362 276172 346984 293999 279032 328366 327782 282326 TRUE FALSE 298910.132 383860.4839 288834.7594 312104.5091 345272.3325 269369.0519 278267.7358 299079.6704 326107.6742 0.916599503 1.177097365 0.885703656 0.957059689 1.058767885 0.826012612 0.853300176 0.917119388 1 18.31498887 2.239949482 24.99990543 0.881110945 1.008769945 0.210980048 0.092128579 44.44060778 799960.212 0.03193264 0.025379426 173.7598696 -2.239949482 0.127659 GS(ph)KSPDLLMYQGPPDTAEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSKSPDLLMYQGPPDTAEIIK 21 1 P82909 P82909 MRPS36 "28S ribosomal protein S36, mitochondrial" 1 GS(0.5)KS(0.5)PDLLMYQGPPDTAEIIK 120.93 1.85E-05 98837000 224990 181190 201260 199950 136630 196910 215990 213120 144570 TRUE FALSE 214355.1686 199653.467 210487.9701 179850.6461 160458.2287 190090.9573 183036.7586 194458.083 166989.1772 1.283647073 1.195607226 1.260488695 1.077019775 0.960889989 1.138342978 1.096099529 1.164495126 1 17.34939508 3.234614581 24.99740244 1.078145228 1.240953213 0.628640367 0.062822351 64.07179694 405883.3757 0.017298197 0.021414929 1716.384489 -3.234614581 0.162807985 GS(ph)LDESSLGFGYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(1)LDESSLGFGYPK;GS(0.876)LDES(0.101)S(0.023)LGFGYPK;GS(1)LDESSLGFGYPK;GS(0.993)LDES(0.007)SLGFGYPK;GS(1)LDESSLGFGYPK 366.33 5.75E-97 1005369000 1131837 1186818 1012878 1317170 856696 1172076 1234152 1263650 910917 TRUE FALSE 1078337.308 1307756.104 1059319.458 1184765.569 1006103.511 1131486.714 1045859.446 1152998.107 1052177.356 1.024862683 1.242904626 1.006787926 1.126013179 0.956210952 1.075376416 0.993995394 1.095821061 1 20.00494648 3.698910332 24.99957516 1.03626507 1.133883812 0.238496425 0.072481371 596.1051839 375845.2407 0.017501274 0.027113175 4999.31305 -3.698910332 0.097618742 GS(ph)LTLTISGESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSLTLTISGESPK 13 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)LTLTISGESPK;GS(1)LTLTISGESPK 281.94 1.84E-32 456020000 1329650 1269920 1386520 1432560 995290 1443060 1589490 1416730 1105940 TRUE FALSE 1266800.08 1399326.292 1450093.313 1288556.347 1168868.261 1393086.47 1346984.108 1292673.611 1277443.527 0.991668166 1.09541147 1.135152579 1.008699265 0.915005819 1.090526854 1.054437303 1.011922315 1 20.28482808 GS(ph)PDGSLQTGKPSAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.997)PDGS(0.002)LQT(0.001)GKPSAPK;GS(0.539)PDGS(0.456)LQT(0.005)GKPSAPK;GS(0.999)PDGS(0.001)LQTGKPSAPK;GS(0.835)PDGS(0.019)LQT(0.146)GKPSAPK;GS(0.986)PDGS(0.014)LQTGKPSAPK;GS(0.811)PDGS(0.189)LQTGKPSAPK 227.73 1.25E-14 1962913000 3365069 3838708 2978404 4159665 2129490 3734445 3480392 3658973 2381108 TRUE FALSE 3206008.857 4229876.709 3114966.769 3741527.571 2500872.382 3605120.233 2949394.279 3338573.927 2750358.068 1.165669625 1.537936736 1.132567721 1.360378351 0.909289743 1.31078214 1.072367381 1.213868829 1 21.39118802 2.782315995 24.99982676 1.120333999 1.314854178 0.282691435 0.154078887 561.9111077 321049.3986 0.042688387 0.04527768 605.781484 -2.782315995 0.194520179 GS(ph)PEEELPLPAFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 290.38 1.95E-43 1182144000 1443240 1261720 1152071 1428370 1066672 1337890 1404670 1412760 1154337 TRUE FALSE 1375020.905 1390290.702 1204894.595 1284787.534 1252699.259 1291558.534 1190361.793 1289051.245 1333345.686 1.031256125 1.042708366 0.903662574 0.963581723 0.93951574 0.968659926 0.892763073 0.966779477 1 20.34661943 3.751130021 24.76794722 0.942033945 1.036982257 0.570702739 0.031828631 373.2085772 735403.6147 0.007405142 0.013230316 5638.064253 -3.751130021 0.094948312 GS(ph)PHYFS(ph)PFRPY ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 GS(0.995)PHY(0.017)FS(0.987)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(0.999)PHY(0.189)FS(0.812)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 179.81 1.15E-05 3955128000 1366849.2 1141624.9 1231558.9 1368945.1 1537981.6 1216406.4 1433607.1 1307797.7 1391246.1 TRUE FALSE 1302240.947 1257957.775 1288027.094 1231336.138 1806205.104 1174281.941 1214884.007 1193280 1606993.44 0.810358596 0.78280206 0.801513598 0.766235946 1.12396545 0.730732256 0.755998112 0.742554369 1 20.61593261 -2.346727877 2.346030342 2.23128592 0.810817033 0.209988577 0.113038581 6101682.475 1112607.339 39769354.48 0.026308196 0.004500618 2.346727877 -1.420468887 GS(ph)PHYFSPFRPY ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 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;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY 175.15 1.72E-05 27393635100 5155393.3 3777427.6 3113275.8 3695293.3 5868510.7 3461355.8 5389941.4 3942935.5 4799893.3 TRUE FALSE 4911708.076 4162351.767 3256022.575 3323835.397 6891977.108 3341488.181 4567606.846 3597671.165 5544236.239 0.88591248 0.75075296 0.587280634 0.599511863 1.243088644 0.602695852 0.823847803 0.648902935 1 22.4025573 4.586619723 3.250060141 0.772396207 0.886340385 0.022268325 0.206765991 1.193184143 22.01987309 0.046433243 0.276731497 38602.88142 -4.586619723 0.113944178 GS(ph)PIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSPIEK 6 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)PIEK 93.162 0.048181 177900000 1056000 1329600 875190 1356000 711210 1017700 950040 1211100 862610 TRUE FALSE 1006084.973 1465087.752 915318.3272 1219692.304 835244.7988 982456.7938 805093.9493 1105049.664 996379.1532 1.009741091 1.470411888 0.918644599 1.224124672 0.838280083 0.986027047 0.808019665 1.10906542 1 19.92633531 2.744991984 24.85836089 0.929070352 1.178784963 0.270730758 0.165636905 512.9392472 1982599.995 0.048040995 0.049857537 555.8939969 -2.744991984 0.24971461 GS(ph)PLAEGPQAFFPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSPLAEGPQAFFPER 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER 180.64 6.51E-07 46347000 26334 35113 28809.6 30653 35467 27195.9 32515 28771 29093 TRUE FALSE 25089.24401 38691.05462 30130.54866 27571.7022 41652.43357 26254.09916 27554.23957 26251.65872 33604.59385 0.746601614 1.151362066 0.896619932 0.820474198 1.239486296 0.781265183 0.819954548 0.78119256 1 15.03637085 GS(ph)PPFEMLSPSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSPPFEMLSPSFR 13 0 H3BMK1;P13631 H3BMK1 RARG Retinoic acid receptor gamma 1 GS(1)PPFEMLSPSFR;GS(1)PPFEMLSPSFR 86.756 0.0091054 48199000 26860 20318 20885.1 26844 22046.7 20471.4 25676 23407.2 24109 TRUE FALSE 25590.38103 22388.4273 21842.70249 24145.59012 25891.6375 19762.47028 21758.65463 21357.54148 27847.70059 0.918940541 0.803959639 0.784362875 0.867058666 0.929758542 0.709662553 0.781344749 0.766940933 1 14.76527059 2.242572308 24.9976018 0.79157414 0.855155547 0.035454639 0.08709557 218.5025062 1361537.456 0.028172981 0.022766045 174.8124292 -2.242572308 0.063581407 GS(ph)PQQIDHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 GS(1)PQQIDHAK;GS(1)PQQIDHAK 142.45 0.0022649 0 1144140 1012750 976900 1155230 935510 1040130 1145350 1167630 983050 TRUE FALSE 1090058.77 1115950.376 1021691.831 1039104.086 1098662.648 1004110.037 970605.8217 1065386.127 1135496.373 0.959984369 0.982786385 0.899775513 0.91511 0.967561565 0.884291717 0.854785488 0.938255861 1 20.11489167 3.739351287 24.9983367 0.912515895 0.97138538 0.155297293 0.042037626 89.2018327 2820254.693 0.010748031 0.018039889 5487.206287 -3.739351287 0.058869485 GS(ph)PRPQAPK ddPTM_SK-BR-3_Trastuzumab_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 91.937 0.027398 2323000000 3292300 2894980 2893480 3263350 2669690 3029390 3569130 3333640 3077540 TRUE FALSE 3136679.504 3189981.753 3026148.92 2935311.858 3135283.091 2924481.465 3024593.667 3041728.809 3554789.185 0.8823813 0.89737579 0.851287872 0.82573444 0.881988475 0.822687735 0.850850363 0.85567066 1 21.76133257 -1.35692808 7.341251879 1.000002651 0.860583005 0.775485241 0.023904434 1.12E-06 9.85E-08 0.02508302 0.005912012 0.043961441 1.35692808 -0.139419646 GS(ph)PRYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.116)S(0.884)PR;GS(1)PRY(0.095)S(0.905)PR;GS(1)PRY(0.03)S(0.97)PR;GS(0.999)PRY(0.327)S(0.674)PR 88.441 0.0083148 5434660000 5949980 5308130 5256130 6190010 5489430 5118460 5774700 5315510 5181810 TRUE FALSE 5668736.237 5849034.482 5497128.76 5567778.435 6446784.854 4941206.447 4893663.455 4850055.765 5985378.63 0.94709735 0.977220464 0.918426235 0.930229945 1.077088895 0.825546177 0.817602989 0.810317286 1 22.51301108 2.202484215 24.99754756 0.844084179 0.964759238 0.355258901 0.069056414 154.0860263 106766.2342 0.02321395 0.01714519 159.3984943 -2.202484215 0.120675059 GS(ph)PRYS(ph)PRHS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(0.999)PRY(0.42)S(0.581)PRHS(1)R;GS(1)PRY(0.311)S(0.689)PRHS(1)R;GS(1)PRY(0.243)S(0.773)PRHS(0.985)R;GS(0.999)PRY(0.035)S(0.966)PRHS(1)R;GS(1)PRY(0.187)S(0.813)PRHS(1)R;GS(1)PRY(0.032)S(0.969)PRHS(1)R 95.554 0.0050658 3654156000 2726440 1940230 2570000 2506990 2829860 2219590 2839300 2115530 2704310 TRUE FALSE 2597566.584 2137941.643 2687837.042 2254982.602 3323386.688 2142725.042 2406112.638 1930282.978 3123680.583 0.831572408 0.684430301 0.860471156 0.721899228 1.063932947 0.685961636 0.770281267 0.61795146 1 21.57481551 -1.565197386 7.730522696 1.000096399 0.778524608 0.239050216 0.12358847 0.000185178 1.04E-05 0.107917532 0.025425415 0.027214641 1.565197386 -0.221571791 GS(ph)PSPASVSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 GS(0.98)PS(0.019)PAS(0.001)VSSGR;GS(0.956)PS(0.044)PASVSSGR 104.17 0.0022726 47264000 143155 135611 134990 161500 155979 122214 123806 125474 150445 TRUE FALSE 136388.3469 149429.9151 141179.425 145265.7132 183181.6882 117981.6985 104917.1208 114486.8314 173775.2422 0.78485488 0.859903362 0.812425425 0.835940214 1.054129955 0.678932724 0.603751832 0.658821302 1 17.40686303 GS(ph)PTSAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.971)PT(0.028)SAYPER;GS(0.962)PT(0.038)SAYPER;GS(1)PTSAYPER;GS(0.822)PT(0.164)S(0.014)AYPER;GS(0.997)PT(0.003)SAYPER;GS(0.984)PT(0.011)S(0.005)AYPER;GS(0.759)PT(0.118)S(0.122)AY(0.001)PER;GS(0.998)PT(0.002)S(0.001)AYPER 185.96 1.46E-06 7659801000 1850522 1887625 1630845 1980865 1951935 1781151 1838118 1750118 1878416 TRUE FALSE 1763051.492 2079976.134 1705620.856 1781744.687 2292351.846 1719469.294 1557679.34 1596868.39 2169711.16 0.812574284 0.958641948 0.78610503 0.821189806 1.056523969 0.792487648 0.71792014 0.735982014 1 21.04907157 2.033328357 24.99935868 0.778769531 0.88593693 0.072778587 0.10974869 294.387586 220816.7972 0.037614563 0.027780031 107.9762791 -2.033328357 0.1071674 GS(ph)PTSAYPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSPTSAYPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.785)PT(0.175)S(0.04)AYPERR;GS(0.865)PT(0.126)S(0.009)AYPERR;GS(0.873)PT(0.126)S(0.001)AYPERR 185.57 2.70E-06 1144100000 296644 242178 296070 281750 326232 264823 359577 293622 322028 TRUE FALSE 282622.226 266856.2135 309645.1024 253427.9547 383126.7575 255652.1131 304716.9246 267910.9011 371966.4575 0.759805677 0.717420101 0.832454368 0.681319376 1.030003512 0.687298835 0.819205384 0.720255538 1 18.50481301 -2.757471196 2.104085994 9.680429337 0.778830524 0.314091785 0.101677167 2994088.882 134718.2125 124797291.4 0.021684653 0.001747949 2.757471196 -8.901598813 GS(ph)PVFLPR ddPTM_SK-BR-3_Trastuzumab_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 135.86 0.00085549 764759000 853813 878147 673522 871844 867441 755990 877225 813879 833316 TRUE FALSE 813454.9516 967631.1777 704403.6499 784204.5847 1018722.436 729809.8767 743388.2149 742611.4401 962542.3893 0.845110782 1.00528682 0.731815718 0.814722129 1.058366309 0.758210636 0.772317379 0.771510375 1 19.87649055 GS(ph)QSFDDKIGAFYDDVFVSGPNAPVPQSGHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSQSFDDKIGAFYDDVFVSGPNAPVPQSGHPR 32 1 F5H212 F5H212 HIVEP1 1 GS(0.5)QS(0.5)FDDKIGAFYDDVFVSGPNAPVPQSGHPR 119.05 4.42E-07 33560000 33538 20872 27397 34682 30250 32080 37293 30683 30822 TRUE FALSE 31952.72521 22998.88053 28653.17955 31195.69947 35525.59042 30969.06156 31603.26792 27996.23386 35601.71834 0.89750514 0.646004789 0.804825747 0.876241398 0.997861678 0.869875472 0.887689398 0.786373107 1 15.11965926 3.276900244 3.781218366 0.900065741 0.76607099 0.309359169 0.08552676 0.244323143 7.324828595 0.023567898 0.031432708 1891.909002 -3.276900244 -0.133994751 GS(ph)SFQSGRDDTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSSFQSGRDDTWR 13 1 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.628)S(0.372)FQSGRDDTWR;GS(0.563)S(0.436)FQSGRDDTWR 119.46 0.0002102 1012800000 1152770 1037980 1098910 1149920 961310 1147420 1185210 1106380 1061490 TRUE FALSE 1098280.847 1143751.342 1149296.11 1034327.857 1128962.16 1107684.558 1004384.447 1009499.502 1226100.448 0.895751118 0.932836575 0.937358854 0.843591452 0.920774608 0.903420727 0.81916979 0.823341598 1 20.22564575 3.250352684 24.99905187 0.875214757 0.920560831 0.075237361 0.054081137 430.6561938 912980.8041 0.014093424 0.018932769 1779.72411 -3.250352684 0.045346074 GS(ph)SGEGLPFAEEGNLTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSSGEGLPFAEEGNLTIK 18 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 GS(0.5)S(0.5)GEGLPFAEEGNLTIK;GS(0.5)S(0.5)GEGLPFAEEGNLTIK 165.02 3.06E-11 33391000 172390 165312 149678 188088 131000 158902 171122 180496 142532 TRUE FALSE 164241.4663 182157.4807 156540.8844 169181.0369 153846.3585 153399.1839 145014.196 164690.8134 164635.1346 0.997608844 1.106431389 0.950835219 1.027611981 0.934468568 0.931752413 0.880821681 1.000338195 1 17.32891273 3.102591268 1.339530557 0.935580326 1.045078711 0.267598897 0.052949755 0.37868524 1.424723729 0.018811577 0.024729559 1266.459389 -3.102591268 0.109498385 GS(ph)SLSGTDDGAQEVVKDILEDVVTSAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSLSGTDDGAQEVVKDILEDVVTSAIK 28 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GS(0.452)S(0.452)LS(0.048)GT(0.048)DDGAQEVVKDILEDVVTSAIK 72.37 0.0063751 399620000 111610 130620 137410 152550 78955 132200 146440 135150 99649 TRUE FALSE 106334.4165 143930.3265 143710.3844 137215.3842 92724.727 127621.8809 124097.8884 123315.5495 115102.058 0.92382724 1.250458324 1.24854748 1.192119295 0.805587047 1.108771495 1.078155253 1.071358338 1 16.8125541 GS(ph)SPLGPAGLGAEEPAAGPQLPSWLQPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSPLGPAGLGAEEPAAGPQLPSWLQPER 29 0 O43482;H0YKL4 O43482 OIP5 Protein Mis18-beta;Protein yippee-like 1 GS(0.5)S(0.5)PLGPAGLGAEEPAAGPQLPSWLQPER 112.8 0.0001767 36265000 10448 13770 11856 12828 14785 11616 14570 13882 17955 TRUE FALSE 9954.143746 15173.17866 12399.60933 11538.50507 17363.49932 11213.73501 12347.0789 12666.41849 20739.3697 0.479963658 0.731612333 0.597877829 0.556357557 0.837224061 0.540697966 0.595344945 0.610742692 1 14.34008443 -0.988771333 4.137852025 1.000021985 0.619308231 0.587390394 0.100424466 24669440.14 50826005.87 8773.443266 0.022196103 0.10261921 0.988771333 -0.380713754 GS(ph)SPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.5)S(0.5)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 405.77 2.90E-199 579510000 167990 154210 171460 203850 145130 195020 217860 209680 136020 TRUE FALSE 160049.4456 169924.1743 179321.6106 183358.6107 170440.6261 188266.4085 184621.4557 191319.3076 157113.2869 1.018688163 1.081539173 1.141352295 1.167047131 1.084826302 1.198284449 1.17508493 1.217715646 1 17.26144567 4.044108321 1.308708663 1.154270444 1.016623127 0.274234747 0.062705122 0.536572395 1.597768514 0.016978762 0.070314669 11068.99831 -4.044108321 -0.137647317 GS(ph)SPTPPCSPVQPSK ddPTM_SK-BR-3_Trastuzumab_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 1 GS(0.491)S(0.491)PT(0.018)PPCSPVQPSK 70.889 0.030912 0 46053 37590 43460 50337 33897 40992 46013 46929 43918 TRUE FALSE 43876.16596 41420.46374 45452.68399 45277.02913 39808.62607 39572.43676 38992.87176 42819.64797 50728.57914 0.864920065 0.816511411 0.895997577 0.892534936 0.784737652 0.78008171 0.768656888 0.844093186 1 15.63051113 2.735270158 24.96395713 0.812470728 0.860292439 0 0.070045749 652.3717647 4949374.565 0.020212444 0.019792196 543.5883725 -2.735270158 0.047821711 GS(ph)VSDEEMMELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSVSDEEMMELR 12 0 P13796;Q5TBN3;Q5TBN5 P13796 LCP1 Plastin-2 1 GS(1)VSDEEMMELR;GS(1)VSDEEMMELR;GS(0.999)VS(0.001)DEEMMELR;GS(1)VSDEEMMELR;GS(1)VSDEEMMELR 201.48 1.55E-07 504578000 639919 585647 573988 748830 649904 606828 640357 518013 458476 TRUE FALSE 609671.2971 645325.0951 600305.9176 673556.1857 763247.0518 585813.3942 542658.7787 472653.0356 529574.1165 1.151248292 1.218573709 1.133563554 1.271882754 1.441246896 1.10619718 1.024707896 0.892515364 1 19.01447309 1.786484178 2.744071239 0.958150062 1.228761396 0.639947305 0.091597826 0.166845336 2.435124809 0.053387561 0.025437854 61.16235205 -1.786484178 0.270611335 GS(ph)WACSIFDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSWACSIFDLK 11 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 GS(0.998)WACS(0.002)IFDLK;GS(1)WACSIFDLK 162.32 2.65E-05 151141000 431130 461830 407950 491830 371210 466950 447760 466750 309990 TRUE FALSE 410751.3393 508891.0021 426654.911 442390.314 435948.9065 450779.4044 379445.9883 425878.8956 358061.666 1.147152511 1.421238436 1.191568245 1.235514315 1.217524655 1.258943493 1.059722457 1.189400978 1 18.44984855 1.41399253 0.568897914 1.00701807 1.276070379 0.450114698 0.084168955 0.609256383 0.480628916 0.079485093 0.04143461 25.9413474 -1.41399253 0.269052308 GS(ph)YGDLGGPIITTQVTIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 267.38 1.29E-31 358400000 233569 325994 225654 317623 182460 273773 239990 268952 220651 TRUE FALSE 222528.6563 359213.1592 236000.4591 285694.9326 214280.9662 264292.1724 203375.1178 245401.1371 254868.4302 0.873111888 1.409406253 0.92596976 1.120950651 0.840751309 1.036974929 0.797961198 0.962854195 1 17.95939316 2.992179194 1.693210417 0.914458441 1.124439649 0.145767806 0.160863935 0.493161708 2.871446507 0.053561137 0.062988445 982.1531048 -2.992179194 0.209981207 GS(ph)YHLDWDKMDDPNFIPFGGDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSYHLDWDKMDDPNFIPFGGDTK 23 1 Q9Y6A5;A0A494BZT8;A0A494C117;H0Y8F2 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 GS(0.524)Y(0.476)HLDWDKMDDPNFIPFGGDTK 78.489 0.0081541 30704000 80584 68257 72787 85794 53485 83093 100720 97673 50771 TRUE FALSE 76774.95402 75212.4659 76124.35595 77169.82412 62812.76707 80215.46857 85353.31415 89120.23432 58644.30738 1.309162943 1.282519468 1.298068975 1.315896249 1.071080381 1.367830437 1.45544074 1.519674088 1 15.83970345 2.03154636 24.99164633 1.384641313 1.264539337 0.02122002 0.154451732 377.6597861 299188.0568 0.051745784 0.038216435 107.5341385 -2.03154636 -0.120101975 GSAADSEESPAIEAIHLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSAADSEESPAIEAIHLLR 19 0 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;;; 193.8 4.51E-15 359327000 305965 279130 271564 319638 581446 259955 363678 296547 578392 FALSE TRUE 291502.6408 307573.6643 284015.478 287507.381 682849.9983 250952.6932 308192.2417 270579.7726 668086.0773 0.436324975 0.460380293 0.425118091 0.430344817 1.02209883 0.375629281 0.461306188 0.405007351 1 19.34967447 -1.905093576 2.480685262 1.292365382 0.497130315 0.411610947 0.187028928 23587340.74 12351524.43 40184688.36 0.044507633 0.012442465 1.905093576 -0.795235067 GSALGDLAPSRPPS(ph)FSPCPAEDLFPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSALGDLAPSRPPSFSPCPAEDLFPGHR 28 1 O75427 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 GSALGDLAPS(0.038)RPPS(0.481)FS(0.481)PCPAEDLFPGHR 98.75 0.0010039 83623000 93859 99925 96442 134660 124610 96900 103210 95287 109890 TRUE FALSE 89422.47108 110107.4711 100863.9611 121123.721 146341.9445 93544.3287 87463.41892 86943.16513 126931.18 0.704495705 0.867458028 0.794635023 0.954247183 1.152923534 0.736968873 0.689061734 0.684963026 1 16.95368698 -1.682873815 6.920368892 1.001154194 0.819320506 0.128790247 0.144302379 0.002662969 0.000122031 0.144791283 0.033922464 0.020755165 1.682873815 -0.181833688 GSALGDLAPSRPPSFS(ph)PCPAEDLFPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSALGDLAPSRPPSFSPCPAEDLFPGHR 28 1 O75427 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 GSALGDLAPS(0.053)RPPS(0.178)FS(0.769)PCPAEDLFPGHR;GSALGDLAPS(0.001)RPPS(0.026)FS(0.973)PCPAEDLFPGHR 118.86 9.33E-05 87167000 65688 65106 62526 94219 91249 71215 79573 65860 72735 TRUE FALSE 62583.05842 71740.37542 65392.87895 84747.92712 107162.7967 68748.80669 67432.67739 60092.94925 84014.37232 0.744908957 0.853905986 0.778353479 1.008731301 1.275529338 0.818298165 0.802632639 0.715269871 1 16.35834853 3.257391891 24.7417838 0.925951924 0.79878861 0.161520765 0.15350801 474.0364961 622816.4301 0.044801877 0.060557032 1808.805587 -3.257391891 -0.127163314 GSAPHSESDLPEQEEEILGS(ph)DDDEQEDPNDYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSAPHSESDLPEQEEEILGSDDDEQEDPNDYCK 33 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBM8 H3BLV9 SRPK1 SRSF protein kinase 1 1 GSAPHSESDLPEQEEEILGS(1)DDDEQEDPNDYCK 74.838 0.0044567 52238000 15098 11642 14618 14634 14561 16108 19495 16148 21196 TRUE FALSE 14384.34746 12828.33304 15288.24976 13162.96252 17100.43379 15550.17592 16520.6797 14733.99551 24482.96743 0.587524674 0.523969697 0.624444312 0.537637546 0.698462465 0.635142614 0.674782571 0.601805952 1 14.57949081 -5 0.193218698 2.737216046 0.536567775 0.86187785 0.049699126 42.85319408 0.420813692 28.61322628 0.116962428 1.00E-05 5 -2.200648271 GSASYS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSASYSPPR 9 0 A0A087WTY1;P0DPB5 A0A087WTY1 POLR1D 1 GSAS(0.001)YS(0.999)PPR;GSAS(0.001)YS(0.999)PPR;GSAS(0.001)YS(0.999)PPR;GSASYS(1)PPR;GSAS(0.002)YS(0.998)PPR;GSAS(0.002)YS(0.998)PPR 136.02 0.00021441 2567880000 2695580 2432330 2377130 2826570 2978570 2474760 2893030 2577960 3033510 TRUE FALSE 2568165.276 2680187.192 2486123.762 2542437.813 3498031.665 2389058.441 2451645.139 2352220.156 3503931.238 0.732938263 0.764908616 0.70952413 0.725595807 0.998316299 0.681822296 0.699684147 0.67130888 1 21.74054303 -1.651997142 2.862953029 1.025413306 0.747729937 0.420607445 0.092945279 18245809.27 17350657.37 3411505.363 0.021189553 0.022284498 1.651997142 -0.27768337 GSAVHQLSEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;;;;; 223.22 2.30E-11 24182910000 15163040 11823740 12919650 15140820 18625460 12434840 17151890 14787780 17468750 FALSE TRUE 14446313.15 13028592.55 13512028.73 13618836.01 21873734.33 12004218.37 14535054.16 13492883.59 20177714.53 0.715953887 0.645692183 0.6696511 0.674944429 1.084054108 0.594924581 0.720351859 0.668702274 1 24.26625944 -1.777052953 2.439738911 1.080850459 0.717047878 0.298765634 0.133777543 13178355.22 8840372.352 6353357.096 0.030602182 0.016708869 1.777052953 -0.363802581 GSCFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 111.69 0.064292 1425990000 1310500 779380 943860 1158040 1710990 1023250 1588720 1222330 1633340 FALSE TRUE 1248555.262 858799.7081 987136.9146 1041631.619 2009386.114 987814.5959 1346331.585 1115296.305 1886630.025 0.66179126 0.455203032 0.523227608 0.552112288 1.065066329 0.52358681 0.713617173 0.591157933 1 20.8473801 2.947471903 24.99955227 0.743344364 0.542823811 0.29774585 0.171246931 440.172227 209489.6135 0.047885303 0.050790403 886.0778959 -2.947471903 -0.200520553 GSDALS(ph)ETSS(ph)VSHIEDLEK ddPTM_SK-BR-3_Trastuzumab_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 2 GS(0.001)DALS(0.728)ET(0.249)S(0.208)S(0.81)VS(0.004)HIEDLEK 138.35 1.10E-06 81568000 435650 478530 387220 503550 333770 504060 482920 536810 309950 TRUE FALSE 415057.6879 527292.751 404974.42 452932.1973 391979.3823 486604.2758 409241.6846 489804.0706 358015.463 1.159328942 1.472821164 1.131164606 1.265119092 1.094867185 1.359171114 1.143083824 1.368108703 1 18.44966237 -2.314949622 1.895478829 5.55E-05 1.252937048 0.291827602 0.12187998 1199467.66 147563.6324 5129170.327 0.027523427 0.004842285 2.314949622 1.2528815 GSDALS(ph)ETSSVSHIEDLEK ddPTM_SK-BR-3_Trastuzumab_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 GSDALS(0.992)ET(0.007)SSVSHIEDLEK 270.68 1.69E-39 216900000 345320 339120 332930 368980 229380 349220 369260 358040 222360 TRUE FALSE 328997.408 373676.7135 348195.1698 331889.4294 269383.7994 337126.4238 312922.6051 326688.1195 256842.4531 1.280930796 1.454886873 1.355676079 1.2921907 1.048828946 1.31258061 1.218344558 1.271939726 1 17.97052416 -5 0.0834387 0.020449535 1.568424568 0.492276197 0.096253589 188.6093517 1.107357582 33.36646066 2.82595596 1.00E-05 5 1.547975033 GSDALSET(ph)S(ph)SVSHIEDLEK ddPTM_SK-BR-3_Trastuzumab_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 2 GSDALS(0.396)ET(0.587)S(0.555)S(0.459)VS(0.002)HIEDLEK 125.04 4.99E-05 83002000 189740 207900 186220 236110 157770 238570 233740 230200 158460 TRUE FALSE 180771.3662 229085.2464 194758.3712 212375.7742 185285.038 230308.2611 198078.6701 210042.4676 183033.1675 0.98764267 1.251605102 1.064060541 1.160313058 1.012303074 1.258287032 1.082200963 1.147565059 1 17.48174558 -0.671947208 6.923275581 1.000000003 1.123656744 0.150179004 0.089802962 0 0 0.07590491 0.017890959 0.212839775 0.671947208 0.123656741 GSDALSETSS(ph)VSHIEDLEK ddPTM_SK-BR-3_Trastuzumab_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 GSDALSET(0.001)S(0.026)S(0.973)VSHIEDLEK;GSDALSET(0.001)S(0.076)S(0.922)VS(0.001)HIEDLEK;GSDALSET(0.003)S(0.154)S(0.842)VSHIEDLEK 249.38 3.25E-25 399678000 1075640 1075330 990380 1261420 816060 1196150 1159250 1240390 759390 TRUE FALSE 1024796.629 1184907.35 1035789.903 1134619.665 958380.6056 1154727.026 982385.1214 1131774.876 877152.3228 1.168322311 1.350856993 1.180855224 1.293526376 1.092604535 1.316449829 1.119970951 1.290283166 1 19.74246787 -4.505337186 0.242022645 4.82E-12 1.251056103 0.386004561 0.087609345 123.9433012 1.540290371 60.86544424 0.118419715 3.12E-05 4.505337186 1.251056103 GSDALSETSS(ph)VSHIEDLEKVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSDALSETSSVSHIEDLEKVER 22 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALSETS(0.248)S(0.751)VS(0.001)HIEDLEKVER;GSDALSETS(0.042)S(0.957)VSHIEDLEKVER 173.35 2.33E-12 249090000 251720 146359 281850 237140 269100 266470 376710 307330 308550 TRUE FALSE 239821.6945 161273.1485 294773.1013 213302.2367 316030.9548 257242.0771 319235.9707 280418.5559 356398.3581 0.672903477 0.452508113 0.827088831 0.598493881 0.886735159 0.721782441 0.89572795 0.786812143 1 18.44313117 2.525625015 0.339241517 0.988752696 0.508876905 0.500649241 0.112222583 1.206089106 0.308908264 0.124748509 0.208980148 335.4478517 -2.525625015 -0.479875791 GSDEPPVFLEIHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSDEPPVFLEIHYK 14 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 182.17 1.55E-06 290780000 592440 517690 530230 587940 519400 540670 632910 624760 548080 FALSE TRUE 564436.5353 570443.1996 554541.57 528839.1542 609983.1956 521946.4623 536347.9553 570052.7023 633073.4472 0.891581439 0.90106954 0.875951396 0.835351975 0.963526741 0.824464309 0.847212843 0.900452712 1 19.27201336 -1.045368672 6.93132904 1.000000029 0.878743418 0.474861618 0.039656564 1.70E-08 2.33E-09 0.03617744 0.008527102 0.090080612 1.045368672 -0.121256611 GSDFDCELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSDFDCELR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 209.37 1.98E-05 15578680000 14053860 11734560 11725930 13645540 15471500 11972470 15313300 13084680 16205700 FALSE TRUE 13389561.89 12930325.01 12263575.49 12273864.39 18169724.7 11557860.36 12976974.84 11938916.05 18718797.19 0.715300334 0.690766873 0.655147623 0.65569728 0.97066732 0.617446743 0.693259012 0.63780359 1 24.1579844 -1.279204142 5.131678818 1.000059166 0.704222152 0.468292783 0.098950806 6.16E-05 8.65E-06 0.088063967 0.020752735 0.052577007 1.279204142 -0.295837013 GSDHSASLEPGELAELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSDHSASLEPGELAELVR 18 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 237.59 7.44E-24 2665920000 2549650 1789890 2146110 2577480 3659000 2035700 3293140 2673250 3824200 FALSE TRUE 2429133.097 1972281.826 2244511.266 2318386.814 4297128.442 1965203.199 2790711.01 2439166.058 4417237.405 0.549921337 0.446496678 0.508125568 0.524849946 0.972809031 0.444894177 0.631777456 0.552192657 1 22.07471294 -5 0.18436013 2.772399312 0.486265195 0.442274956 0.149479536 122.0694024 1.183896937 79.48314728 0.412023275 1.00E-05 5 -2.286134116 GSDIDNPTLTVMDISPPS(ph)RSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 GSDIDNPT(0.148)LT(0.148)VMDIS(0.015)PPS(0.345)RS(0.345)PR 60.943 0.01802 0 20387 14112 21275 19626 18597 17438 23396 19452 26298 TRUE FALSE 19423.34691 15550.02884 22250.47979 17653.15719 21840.31091 16834.11769 19826.5105 17748.67976 30376.15953 0.639427341 0.511915564 0.732498122 0.581151715 0.718995135 0.55418848 0.65269971 0.58429637 1 14.89065186 -1.874984695 2.389997469 1.192154118 0.617660985 0.747776213 0.068972334 6560261.105 3601890.21 7136465.298 0.01488966 0.013335684 1.874984695 -0.574493133 GSDRT(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSDRTPER 8 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 GS(0.029)DRT(0.971)PER;GS(0.003)DRT(0.997)PER;GSDRT(1)PER 78.342 0.049914 472114000 614290 518584 548789 595485 618465 510354 645513 570300 728728 TRUE FALSE 585253.7291 571428.2992 573951.5185 535625.7165 726325.1002 492680.313 547028.1362 520361.5086 841735.4164 0.695294172 0.67886926 0.681866899 0.636335012 0.862890032 0.585314938 0.649881335 0.618200801 1 19.6830073 -1.056002286 3.911383862 1.000064369 0.676025588 0.654823023 0.073908952 22417176.58 35500895.72 18322.55118 0.016401158 0.087901789 1.056002286 -0.324038781 GSDS(ph)DSEGDNPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GS(0.001)DS(0.991)DS(0.008)EGDNPEK;GSDS(0.998)DS(0.002)EGDNPEK 298.12 9.33E-41 205246000 624180 663180 569200 704230 433360 660350 657590 676190 482410 TRUE FALSE 594676.2484 730758.796 595298.383 633439.4625 508937.8468 637481.9139 557262.568 616979.2189 557219.679 1.067220471 1.311437524 1.068336969 1.136785879 0.913352249 1.144040561 1.00007697 1.107245925 1 19.08788668 3.552993914 11.24104792 1.051612477 1.189604549 0.285645979 0.090153999 0.844427635 123.0081615 0.021751958 0.033695743 3572.678315 -3.552993914 0.137992072 GSEEDS(ph)PKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSEEDSPKK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKK;GSEEDS(1)PKK 76.655 0.021326 185481000 809810 1191210 593530 1128850 275415 879560 586840 961260 254512 TRUE FALSE 771531.8862 1312595.653 620743.9376 1015375.853 323447.2888 849100.6167 497306.7799 877086.9784 293980.4211 2.62443289 4.464908406 2.111514553 3.453889377 1.100234116 2.888289681 1.691632314 2.983487727 1 18.16536055 3.17438714 1.558112495 2.058228749 3.450188661 0.258001953 0.916161362 0.430400792 2.169381199 0.281356873 0.384885089 1494.125713 -3.17438714 1.391959912 GSEEDS(ph)PKKESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GSEEDSPKKESK 12 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(0.999)PKKES(0.001)K;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK 164.93 3.22E-05 4362604000 10121490 10403240 8626330 11930460 3449331 12156810 9944650 12011070 3313516 TRUE FALSE 9643067.227 11463341.98 9021855.763 10731187.49 4050893.234 11735816.62 8427410.996 10959317.04 3827359.138 2.519509374 2.995104867 2.357201255 2.803809914 1.058404265 3.066296158 2.201886651 2.863414861 1 21.86791785 -1.935605794 2.775244081 0.007032947 2.498466437 0.39616767 0.575194616 123997777.1 112684779.6 803383640.4 0.125554519 0.011598296 1.935605794 2.491433489 GSEGDCS(ph)PEDKNSVTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSEGDCSPEDKNSVTAK 17 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GSEGDCS(0.999)PEDKNS(0.001)VTAK;GSEGDCS(1)PEDKNSVTAK;GSEGDCS(1)PEDKNSVTAK 156.51 3.65E-08 362305000 911750 683454 795380 885900 527674 903330 1000490 1045580 651818 TRUE FALSE 868653.3844 753098.7396 831848.9597 796847.6489 619700.1785 872047.4556 847846.8752 954023.4722 752898.6064 1.153745507 1.000265817 1.104861867 1.058373122 0.823085836 1.158253513 1.1261103 1.267134066 1 19.52209606 GSEGYLAATYPTVGQT(ph)SPR ddPTM_SK-BR-3_Trastuzumab_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 310.75 1.81E-60 274710000 365250 332420 381900 411010 444530 383380 444380 399580 439020 TRUE FALSE 347985.3564 366293.9759 399410.4928 369694.4939 522055.8913 370103.4545 376581.6694 364590.6569 507100.9794 0.686224974 0.722329459 0.787635025 0.729035259 1.029490994 0.729841727 0.742616727 0.718970524 1 18.95191354 -5 0.263082487 2.515872008 0.744948329 0.348831769 0.097463687 230.880471 2.260030268 190.138878 0.123855427 1.00E-05 5 -1.770923679 GSEGYLAATYPTVGQTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSEGYLAATYPTVGQTSPR 19 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 GSEGYLAATYPTVGQT(0.02)S(0.98)PR;GSEGYLAATYPTVGQT(0.085)S(0.915)PR;GSEGYLAATYPTVGQT(0.001)S(0.999)PR 387.69 6.97E-127 377550000 804640 706130 744950 824550 874630 799470 888730 785500 935370 TRUE FALSE 766606.2618 778085.4498 779106.6944 741664.6675 1027165.195 771784.1534 753137.9159 716717.4558 1080422.402 0.709543101 0.720167823 0.72111305 0.686458061 0.95070705 0.714335571 0.697077286 0.663367822 1 20.04316403 -2.17458146 2.496205417 1.731936884 0.731677047 0.527060026 0.079524205 4481245.964 1153198.005 18641542.56 0.018524472 0.006689883 2.17458146 -1.000259837 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDET(ph)SSVKSDGAGGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDETSSVKSDGAGGAR 45 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 GSESATYVPVAPPT(0.001)PAWQPEIKPEPAWHDQDET(0.25)S(0.25)S(0.25)VKS(0.25)DGAGGAR 88.245 6.34E-05 360610000 405240 375070 416730 423420 241500 471860 466920 472530 231670 TRUE FALSE 386085.1083 413290.0594 435837.4827 380857.0172 283617.5235 455519.3699 395682.7784 431152.7682 267596.2004 1.442789949 1.54445414 1.62871327 1.423252709 1.059871265 1.702263968 1.478656191 1.611206615 1 18.02969811 -1.217409082 3.52458474 0.999176802 1.487623342 0.434501662 0.174383165 26465136.36 38490870.89 241482.7048 0.039492232 0.060616509 1.217409082 0.48844654 GSET(ph)PGAT(ph)PGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSETPGATPGSK 12 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 GSET(1)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK;GS(0.023)ET(0.977)PGAT(1)PGSK;GS(0.001)ET(0.999)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK 270.84 1.65E-27 1399810000 3758100 3470670 3651130 4058580 3094897 3950060 4243260 3954690 3373970 TRUE FALSE 3580462.061 3824335.219 3818537.922 3650603.828 3634646.057 3813268.432 3595872.754 3608396.378 3897188.036 0.918729614 0.981306312 0.979818753 0.93672766 0.932632971 0.978466627 0.922683925 0.925897428 1 21.89400211 1.724398203 24.99999978 0.941900434 0.954370477 0 0.029830573 3.593133041 6316.434911 0.012902619 0.007155231 53.01493134 -1.724398203 0.012470043 GSET(ph)PGATPGSK ddPTM_SK-BR-3_Trastuzumab_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 281.01 5.24E-27 2187490000 5319560 4920640 4759020 5523870 3860460 5194020 5509400 5354660 4501250 TRUE FALSE 5068114.941 5422058.81 4977225.774 4968600.093 4533723.002 5014149.785 4668839.843 4885777.584 5199280.861 0.974772296 1.042847839 0.957291192 0.955632178 0.871990401 0.964392946 0.897978003 0.939702569 1 22.30988066 3.439500369 2.711862411 0.92920352 1.008380206 0.327832682 0.039217185 0.223607327 3.328150263 0.010138329 0.015249863 2751.06194 -3.439500369 0.079176686 GSFAGIEDDADEALEISQAQLLFENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSFAGIEDDADEALEISQAQLLFENRR 27 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 ; 129.84 8.13E-05 23428700 28937 20622.8 26300.2 27523.6 34416.5 26422.7 32409.5 29899.1 38404.9 FALSE TRUE 27569.20536 22724.28677 27506.09018 24756.87544 40418.7267 25507.67527 27464.83553 27280.9763 44360.53575 0.621480442 0.512263578 0.620057664 0.558083328 0.911141537 0.575008278 0.619127679 0.614983021 1 15.43698917 -5 0.25768133 3.394555962 0.589584721 0.542667667 0.106674843 145.0625226 1.427958869 183.8192891 0.137694699 1.00E-05 5 -2.804971242 GSFKDDPQLYQEIQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 65.225 0.052849 132270000 90319 79441 78281 96391 88078 96381 96823 100940 96131 FALSE TRUE 86049.79987 87536.12822 81870.26128 86701.59355 103438.7753 93043.3018 82050.87307 92101.15848 111038.5045 0.7749546 0.788340302 0.737314156 0.780824579 0.931557713 0.837937274 0.738940725 0.82945244 1 16.76070052 -5 0.270606336 2.3881404 0.783113778 0.564306851 0.055250929 165.8933918 1.609255371 128.7891985 0.069097548 1.00E-05 5 -1.605026621 GSFLDKIS(ph)PSVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSFLDKISPSVLR 13 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 GSFLDKIS(0.903)PS(0.097)VLR;GSFLDKIS(0.999)PS(0.001)VLR 126.63 0.00011281 528500000 553750 523320 552800 654600 509970 600960 700100 688190 606740 TRUE FALSE 527575.3349 576646.903 578146.4268 588798.3643 598908.6065 580148.6045 593286.8868 627928.4353 700830.1404 0.752786309 0.822805513 0.824945152 0.840144181 0.854570276 0.827802018 0.846548761 0.895978068 1 19.4187053 -5 0.09412679 1.571683358 0.692632662 0.912130072 0.018754947 56.84579208 0.368685296 6.415624586 0.400593621 1.00E-05 5 -0.879050696 GSFMLGLETHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 0 ; 134.08 0.00015189 172924000 294130 255330 249330 292770 316930 253860 330430 290410 262240 FALSE TRUE 280227.0578 281348.4173 260762.0271 263340.2034 372202.4917 245068.7645 280016.8347 264980.1608 302906.8399 0.925126214 0.928828208 0.860865431 0.86937688 1.228768858 0.809056556 0.924432195 0.874790945 1 18.20851463 GSFS(ph)DTGLGDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GSFS(0.971)DT(0.029)GLGDGK;GSFS(1)DTGLGDGK;GSFS(1)DTGLGDGK;GSFS(0.998)DT(0.002)GLGDGK;GSFS(0.922)DT(0.078)GLGDGK;GSFS(0.719)DT(0.281)GLGDGK;GS(0.001)FS(0.993)DT(0.006)GLGDGK;GSFS(1)DTGLGDGK 330.56 3.97E-58 3462480000 6208850 5728180 6057400 7347260 4737500 7326530 7896940 7031140 5294260 TRUE FALSE 5915369.965 6311888.054 6335137.782 6608699.466 5563718.5 7072810.429 6692116.766 6415456.107 6115266.801 0.967311837 1.032152522 1.035954438 1.080688657 0.909807974 1.156582478 1.094329484 1.049088505 1 22.54398401 2.223846993 24.99999938 1.086722566 1.010248642 0.241396599 0.059544282 295.1254835 501445.9234 0.020532635 0.015228508 167.4352877 -2.223846993 -0.076473923 GSFSEQGINEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 279.49 5.48E-32 861860000 796220 635840 656430 745140 881260 648490 808150 704570 864860 FALSE TRUE 758584.2586 700632.8189 686527.9648 670237.1115 1034951.465 626032.6287 684851.8748 642874.1156 998978.0717 0.75936027 0.701349548 0.687230265 0.670922746 1.036010193 0.626673044 0.68555246 0.643531759 1 19.93009348 -2.189056264 2.374442051 1.77300725 0.725075388 0.355488798 0.115795815 7273989.36 1879361.024 30134595.79 0.027812243 0.006470588 2.189056264 -1.047931862 GSGEKPVSAPGDDTES(ph)LHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.136)ES(0.864)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.026)ES(0.975)LHS(1)QGEEEFDMPQPPHGHVLHR 174.92 5.59E-19 317960000 161552 139260 139498 156898 141220 154419 178032 167086 93238 TRUE FALSE 153915.7571 153450.7523 145894.1213 141126.315 165848.7233 149071.4313 150869.9486 152455.0641 107696.8728 1.429157162 1.424839443 1.354673701 1.31040309 1.539958579 1.384176043 1.400875853 1.415594158 1 16.71661683 -1.799519396 2.290033361 0.858176956 1.408204345 0.825516537 0.05887012 2162927.848 1287755.682 1701849.024 0.014029203 0.015866481 1.799519396 0.550027389 GSGIFDEST(ph)PVQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGIFDESTPVQTR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 GSGIFDES(0.14)T(0.86)PVQTR 234.57 3.63E-16 85547000 251610 279890 275630 282840 293160 241760 305570 306500 387070 TRUE FALSE 239716.8939 308411.1092 288267.9081 254408.3858 344287.0112 233387.7906 258949.6843 279661.2351 447094.8387 0.536165648 0.689811383 0.644757853 0.569025549 0.770053647 0.522009584 0.579182898 0.625507635 1 18.77022137 0.924722388 20.68825587 1 0.615150047 0.727793453 0.07362129 3626.989723 996794.3025 0.065980364 0.016495091 8.408574717 -0.924722388 -0.384849953 GSGIQWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGIQWDLR 9 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 93.598 0.013985 0 152120 140810 100160 113870 155700 105450 129080 127600 137400 FALSE TRUE 144929.5891 155158.6991 104752.4351 102423.5713 182854.0307 101798.2401 109386.4753 116426.6675 158707.2903 0.913187975 0.977640654 0.660035433 0.645361477 1.152146385 0.641421323 0.689234093 0.733593695 1 17.27600887 3.75575904 24.61139677 0.771080855 0.945414333 0.124485963 0.167578912 1106.863977 1583945.878 0.040732333 0.073196639 5698.480154 -3.75575904 0.174333478 GSGPQRPHS(ph)FSEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.983)FS(0.017)EALR;GSGPQRPHS(0.981)FS(0.019)EALR;GSGPQRPHS(0.993)FS(0.007)EALR;GSGPQRPHS(0.979)FS(0.021)EALR;GSGPQRPHS(0.97)FS(0.03)EALR 176.1 4.95E-07 1539650000 818790 688926 739890 902610 942550 720080 905200 819950 892260 TRUE FALSE 780087.4194 759128.3426 773814.6884 811877.928 1106930.422 695143.449 767095.1149 748150.8312 1030627.124 0.756905579 0.736569342 0.750819254 0.787751369 1.074035794 0.674485886 0.744299366 0.725918049 1 19.97509104 -2.083173098 2.453615292 1.357278179 0.776693243 0.286737243 0.108156084 9386634.677 2881371.88 18759775.84 0.025041565 0.008257088 2.083173098 -0.580584936 GSGS(ph)PTHSLSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GSGS(0.999)PT(0.001)HSLSQK;GS(0.011)GS(0.978)PT(0.011)HSLSQK;GS(0.003)GS(0.935)PT(0.062)HSLSQK;GSGS(1)PTHSLSQK 277.1 7.31E-28 568030000 1018990 909290 949670 1097090 909080 1017290 1224640 1116100 1026460 TRUE FALSE 970824.3621 1001947.685 993213.3089 986808.4289 1067623.264 982060.9922 1037798.676 1018368.367 1185638.174 0.818820095 0.845070365 0.837703551 0.832301498 0.900462964 0.828297379 0.875308082 0.858920022 1 20.17723237 -5 0.198342287 1.688144239 0.823064593 0.838458251 0.021310445 47.53162388 0.469399445 12.92738116 0.046082406 1.00E-05 5 -0.865079646 GSGS(ph)QSSVPSVDQFTGVGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSGSQSSVPSVDQFTGVGIR 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GS(0.156)GS(0.794)QS(0.05)S(0.001)VPSVDQFTGVGIR 123.59 2.98E-05 48862000 27561 26937 27280 29096 28395 25472 29683 30967 29391 TRUE FALSE 26258.24615 29681.91092 28530.81498 26171.2148 33347.07901 24589.89825 25154.31318 28255.36531 33948.80617 0.773465966 0.874313835 0.840407019 0.77090236 0.982275454 0.724322915 0.740948387 0.832293341 1 15.05107322 GSGTAEVELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GSGTAEVELKK 11 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 171.67 2.29E-05 5664450000 9304150 7099450 9011230 9478730 6994110 10411010 12148350 10994140 6521740 FALSE TRUE 8864361.269 7822892.026 9424403.809 8525910.052 8213880.57 10050474.11 10294896.09 10031434.82 7533098.131 1.176721863 1.038469417 1.251066115 1.131793308 1.090372172 1.334175387 1.366621795 1.331647968 1 22.84481189 2.237161411 24.99998454 1.298641275 1.132589994 0.172118337 0.116802768 40.93188252 731318.064 0.038189441 0.029747255 172.6479441 -2.237161411 -0.166051281 GSGTAS(ph)DDEFENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 GSGTAS(1)DDEFENLR;GSGT(0.001)AS(0.999)DDEFENLR;GSGT(0.001)AS(0.999)DDEFENLR;GSGTAS(1)DDEFENLR;GSGT(0.001)AS(0.999)DDEFENLR;GSGTAS(1)DDEFENLR 354.93 4.71E-82 16598410000 5796390 4961760 5240140 5944000 6150120 5530100 6545330 5752400 6656280 TRUE FALSE 5522406.132 5467368.985 5480405.602 5346497.827 7222698.981 5338591.25 5546719.695 5248689.361 7688501.907 0.718268162 0.711109791 0.71280539 0.695388763 0.939415645 0.694360399 0.72143049 0.682667368 1 22.87427109 -1.163533454 3.559573037 1.000279128 0.733025843 0.559794171 0.074001287 20048977.82 33016907.33 64050.31899 0.017062378 0.068622502 1.163533454 -0.267253286 GSIDEVDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;; 127.4 0.00071603 1240530000 2082210 1988430 1905170 2188240 1499050 2191430 2125640 2264000 1653810 FALSE TRUE 1983788.06 2191053.278 1992523.929 1968273.958 1760483.845 2115540.23 1801334.578 2065752.158 1910274.408 1.038483294 1.146983527 1.04305639 1.030361894 0.921586887 1.107453579 0.942971633 1.08139027 1 20.86534846 3.432296485 3.351651497 1.008844213 1.093243032 0.211085183 0.061105476 0.284346072 6.585854589 0.015556458 0.022615977 2705.804941 -3.432296485 0.084398819 GSIEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSIEILK 7 0 A0A087WZQ1;Q9NS40 A0A087WZQ1 KCNH7 Potassium voltage-gated channel subfamily H member 7 0 92.467 0.015648 358040000 647290 583280 709870 656430 1904600 331960 749860 386550 1997100 FALSE TRUE 616693.8845 642716.8951 742418.2417 590444.4093 2236761.637 320464.142 635455.0849 352701.6328 2306800.068 0.267337379 0.278618379 0.321839006 0.255958207 0.969638274 0.138921507 0.275470377 0.15289649 1 21.13746154 -1.408531743 3.042729921 1.010639016 0.327696178 0.445674183 0.233866169 46060906.58 57085859.62 4269827.871 0.055126375 0.039036265 1.408531743 -0.682942838 GSIFVVFDSIESAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSIFVVFDSIESAKK 15 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 142.45 7.35E-06 40528000 189720 172030 188000 188980 133980 192660 216680 190530 144410 FALSE TRUE 180752.3116 189560.0526 196619.986 169983.3714 157346.0696 185988.1359 183621.4864 173846.1831 166804.3653 1.083618593 1.136421414 1.178746046 1.019058291 0.943297073 1.115007606 1.100819431 1.042216029 1 17.34779752 6.832320454 0.013272556 0.117407476 2.171264261 0.182029096 0.063025874 10268.64075 12.85957473 845.801231 1167.172664 6797049.834 -6.832320454 2.053856785 GSIHDFPGFDPNQDAEALYTAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSIHDFPGFDPNQDAEALYTAMK 23 0 E5RK69;P08133;E7EMC6;E5RFF0;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;; 235.92 4.16E-37 263910000 415484 296545 279110 662800 536000 381634 471979 376329 360600 FALSE TRUE 395844.8947 326763.2726 291907.4696 596174.0848 629478.2303 368417.9189 399969.9351 343375.6377 416520.0063 0.95036226 0.784507989 0.700824607 1.431321607 1.5112797 0.884514341 0.960265843 0.824391704 1 18.66802627 3.275768958 24.99982049 1.094275199 0.8258095 0.265046217 0.22706268 259.2250834 174168.3864 0.066341052 0.089823917 1886.987216 -3.275768958 -0.268465699 GSITISAEEIKDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSITISAEEIKDNR 14 1 O75131;A0A087WYQ3;H0YB26;E5RHZ0;A0A087WXR6 O75131 CPNE3 Copine-3 0 121.09 0.00071156 0 1949200 1431700 1355000 1990200 1769600 1528900 1920200 1672700 1572700 FALSE TRUE 1857065.179 1577591.858 1417128.09 1790141.315 2078217.68 1475953.81 1627238.223 1526229.52 1816586.284 1.022282947 0.868437614 0.780105026 0.985442492 1.144023655 0.812487589 0.895767098 0.840163517 1 20.79279846 GSKPS(ph)PLSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSKPSPLSVK 10 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 GS(0.289)KPS(0.703)PLS(0.007)VK;GS(0.003)KPS(0.997)PLS(0.001)VK;GSKPS(0.993)PLS(0.007)VK;GS(0.005)KPS(0.977)PLS(0.017)VK;GS(0.001)KPS(0.999)PLSVK;GS(0.01)KPS(0.99)PLSVK 141.65 2.25E-05 7699600000 8639530 7810940 7528010 8787390 5180670 8857040 9507720 9443850 5984810 TRUE FALSE 8231156.539 8606883.666 7873176.705 7904064.862 6084177.208 8550318.484 8057142.693 8616896.429 6912903.769 1.190694506 1.24504607 1.138910213 1.143378402 0.880118892 1.236863519 1.165522183 1.246494486 1 22.72086041 3.622428147 4.669088737 1.122649607 1.217486508 0.13130199 0.108565492 0.455219482 15.47669113 0.028348982 0.044764223 4192.06634 -3.622428147 0.094836901 GSLAEAVGSPPPAAT(ph)PTPTPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 GSLAEAVGSPPPAAT(0.996)PT(0.004)PTPPTR;GSLAEAVGSPPPAAT(0.998)PT(0.002)PTPPTR 233.34 5.41E-36 117418000 165370 162197 173717 188433 202602 165277 202413 200932 229360 TRUE FALSE 157553.2878 178725.0587 181682.0963 169491.3568 237935.7247 159553.416 171531.1793 183337.3289 264927.9774 0.594702339 0.674617534 0.6857792 0.639763903 0.898114752 0.602252045 0.647463439 0.692027058 1 18.01524068 -2.540129106 1.464894258 3.015983633 0.673973716 0.587522694 0.084331098 227783.9596 14922.5855 1511554.953 0.022293799 0.002883174 2.540129106 -2.342009917 GSLAPQDS(ph)DSEVSQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSLAPQDSDSEVSQNR 16 0 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 GSLAPQDS(1)DSEVSQNR;GSLAPQDS(0.901)DS(0.099)EVSQNR;GSLAPQDS(0.996)DS(0.004)EVSQNR;GSLAPQDS(0.996)DS(0.004)EVSQNR;GSLAPQDS(0.985)DS(0.015)EVSQNR;GSLAPQDS(0.997)DS(0.003)EVSQNR 359.6 1.12E-87 919064000 947950 773780 802390 955870 995620 908110 1017140 1106900 1044230 TRUE FALSE 903142.2822 852629.0617 839180.3752 859784.1316 1169255.813 876661.923 861956.6119 1009973.968 1206163.855 0.748772464 0.706893229 0.695743262 0.712825316 0.969400474 0.726818267 0.714626465 0.837343918 1 20.20199448 -5 0.197040295 2.105047878 0.713193778 0.487441524 0.079738921 121.4652069 1.197935385 52.6774317 0.194421007 1.00E-05 5 -1.3918541 GSLAS(ph)LDSLR ddPTM_SK-BR-3_Trastuzumab_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 GSLAS(1)LDSLR 162 7.24E-06 39567000 132880 111950 110710 129920 166790 115840 161910 144690 177000 TRUE FALSE 126599.0257 123357.8323 115786.163 116860.1948 195878.1232 111828.4318 137207.6558 132020.1766 204448.256 0.619222821 0.603369452 0.566334804 0.571588122 0.958081654 0.546976697 0.671111892 0.645738825 1 17.64137623 -4.999999999 0.241881271 3.052839539 0.608104049 0.481732869 0.115704865 145.5864438 1.450141791 147.1985271 0.16629146 1.00E-05 4.999999999 -2.444735489 GSLDES(ph)SLGFGYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.371)LDES(0.602)S(0.027)LGFGYPK;GS(0.054)LDES(0.682)S(0.264)LGFGYPK 356.01 4.14E-82 807790000 797300 803050 704300 877190 583450 814400 825430 848800 624990 TRUE FALSE 759613.2091 884881.708 736592.8516 789013.1946 685203.4953 786197.1238 699495.4934 774474.5722 721910.2572 1.052226647 1.225750291 1.020338531 1.09295191 0.949153289 1.08905105 0.968950761 1.072812811 1 19.46145998 3.706655782 24.57445517 1.026070511 1.138988478 0.351507534 0.062867759 455.1198674 350552.4672 0.015112836 0.023414617 5089.273401 -3.706655782 0.112917967 GSLDYRPLTTADPIDEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSLDYRPLTTADPIDEHR 18 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;D6R9M0 O00139-1 KIF2A Kinesin-like protein KIF2A 0 141.86 7.02E-08 343150000 298090 240230 271140 294870 336820 274470 319310 302280 310760 FALSE TRUE 283999.8765 264709.7101 283572.0372 265229.1074 395561.3014 264965.0351 270593.395 275810.7607 358951.0737 0.791193835 0.737453457 0.790001919 0.738900443 1.10199225 0.738164765 0.753844785 0.768379818 1 18.45342769 -2.568841779 2.154684478 4.420803134 0.796591543 0.244640321 0.108630161 2489472.131 237547.8906 41631177.79 0.025035493 0.002698722 2.568841779 -3.624211591 GSLEEEKRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSLEEEKRR 9 2 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 58.699 0.060248 134741000 256360 203028 218513 252269 216023 250154 297750 272370 240146 FALSE TRUE 244242.3709 223716.784 228532.0372 226910.4408 253697.3428 241491.1043 252322.7689 248519.8389 277386.6152 0.88051246 0.806516147 0.823875503 0.818029524 0.914598358 0.870593933 0.909642914 0.89593306 1 18.08153865 1.054677727 0.454729766 1.003288625 0.831447061 0.721752333 0.030050329 0.565474487 0.311121868 0.037352277 0.01947783 11.34168882 -1.054677727 -0.171841564 GSLESPATDVFGSTEEGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSLESPATDVFGSTEEGEKR 20 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 171 1.36E-11 172680000 184161 166815 166452 200230 152585 186271 203801 205490 179564 FALSE TRUE 175456.0745 183813.6382 174083.9888 180102.5 179195.7757 179820.3886 172707.4144 187496.2062 207409.868 0.845938895 0.886233813 0.83932356 0.868341037 0.863969383 0.866980874 0.832686583 0.903988841 1 17.66212501 0.933218909 4.863306713 0.999968361 0.859071152 0.893954407 0.015584434 0.100108817 6.24943201 0.01436989 0.003637163 8.574699496 -0.933218909 -0.140897209 GSLEVLNLKDVEEGDEKFE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSLEVLNLKDVEEGDEKFE 19 2 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 159.7 1.31E-10 83918000 87539 72096 70974 105720 47456 90929 96461 97172 48352 FALSE TRUE 83401.20496 79442.66437 74228.2281 95092.82475 55732.31137 87780.10593 81744.10282 88663.10454 55850.18121 1.493302316 1.422424469 1.329059754 1.702641293 0.997889535 1.571706734 1.463631828 1.587516864 1 15.76927434 -2.134608883 2.364177852 0.0748886 1.444572965 0.356403685 0.188353381 5008769.525 1806714.865 24721623.66 0.039827888 0.007334848 2.134608883 1.369684365 GSLIITFDVDFPKEQLTEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSLIITFDVDFPKEQLTEEAR 21 1 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 143.95 1.21E-07 59374000 175890 136470 187260 178230 167860 184220 248090 201060 213640 FALSE TRUE 167576.0283 150376.4482 195846.0562 160313.9818 197134.7309 177840.4152 210239.314 183454.1205 246770.2001 0.679077248 0.609378475 0.793637385 0.649648871 0.798859549 0.720672168 0.851963948 0.743420885 1 17.91280866 -5 0.079361856 1.978380357 0.428297865 0.696169989 0.061470098 117.1818314 0.659204023 19.82876118 1.887780796 1.00E-05 5 -1.550082492 GSLLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSLLPAK 7 0 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 0 ;; 88.734 0.01839 1300490000 2540650 3094110 2722160 3076120 8298000 1177990 2427090 1277960 7137300 FALSE TRUE 2420558.51 3409403.327 2846973.729 2766902.573 9745168.573 1137195.911 2056792.844 1166055.048 8244116.032 0.293610437 0.413555961 0.34533402 0.335621498 1.18207562 0.137940309 0.249486159 0.141440883 1 22.97493338 -1.303642777 4.59512962 1.000333045 0.383853901 0.297558842 0.295763872 0.001119211 0.000169608 0.272023161 0.06407714 0.049700095 1.303642777 -0.616479145 GSLLPTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSLLPTSPR 9 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 GSLLPTS(1)PR;GSLLPT(0.013)S(0.987)PR;GSLLPT(0.136)S(0.864)PR;GSLLPTS(1)PR 144.7 0.00010378 458093000 1082220 1032520 1080060 1192570 1293320 1074470 1255480 1122860 1330670 TRUE FALSE 1031065.605 1137734.962 1129581.819 1072690.598 1518874.599 1037260.834 1063933.468 1024536.426 1537023.507 0.670819672 0.740219623 0.734915123 0.697901231 0.988192172 0.674850339 0.692203771 0.666571735 1 20.5517078 -2.161964743 2.419190518 1.662731528 0.731197575 0.442200023 0.094143867 6390088.549 1627938.292 23214264 0.021551704 0.006887082 2.161964743 -0.931533953 GSLS(ph)PVTKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSLSPVTKPR 10 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 GS(0.226)LS(0.774)PVTKPR;GS(0.012)LS(0.988)PVTKPR;GS(0.004)LS(0.996)PVTKPR 124.38 0.00026476 681000000 1564930 1274370 1333140 1450110 1282980 1394800 1690110 1536970 1419430 TRUE FALSE 1490958.86 1404229.752 1394265.788 1304342.188 1506731.306 1346497.726 1432252.679 1402384.759 1639547.955 0.909371913 0.85647373 0.850396467 0.795549885 0.918991909 0.821261569 0.873565591 0.855348424 1 20.64486667 -1.328062152 3.659385104 1.000481262 0.861438558 0.593634403 0.03635662 8096514.287 16260626.6 42107.87686 0.008029617 0.046982687 1.328062152 -0.139042704 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR 42 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 204.26 6.78E-36 47454000 36175 30589 37939 36466 38983 38963 51815 41180 23979 FALSE TRUE 34465.07944 33706.05388 39678.54068 32800.3684 45781.62286 37613.70154 43909.6701 37574.06089 27697.54085 1.244337164 1.216933086 1.432565472 1.184233957 1.65291291 1.358015924 1.585327388 1.356584727 1 14.75747027 3.451482744 1.31279926 1.423678805 1.228824885 0.01769179 0.190167179 0.790230869 2.787581819 0.057578057 0.107684738 2828.021745 -3.451482744 -0.19485392 GSNEEQVNGS(ph)PLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSNEEQVNGSPLER 14 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GSNEEQVNGS(1)PLER;GSNEEQVNGS(1)PLER;GSNEEQVNGS(1)PLER;GSNEEQVNGS(1)PLER 373.55 3.20E-97 1515180000 1461810 1436690 1475850 1659990 1660220 1478640 1656870 1536670 1756710 TRUE FALSE 1392713.138 1583090.344 1543519.182 1493124.651 1949761.842 1427434.326 1404084.051 1402111.028 2029131.615 0.686359193 0.780181203 0.760679677 0.735844161 0.960884857 0.703470547 0.691963025 0.690990677 1 20.95243101 -2.427135656 2.262956415 3.318463062 0.749636225 0.48323571 0.080809733 4782657.274 393570.7467 57075128.34 0.019291569 0.003739937 2.427135656 -2.568826837 GSNKLVIEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSNKLVIEEAER 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 78.373 0.023623 172150000 142410 78222 174490 122640 165610 136070 221700 147650 228920 FALSE TRUE 135678.5615 86192.91073 182490.5391 110311.9942 194492.3316 131357.8618 187875.5932 134720.9833 264419.7444 0.513118118 0.325970025 0.690154737 0.417185163 0.735543906 0.496777811 0.710520289 0.509496685 1 18.01247038 -5 0.123507716 2.532139479 0.324622987 0.561181758 0.12754067 94.68207715 0.751090729 35.99060021 0.984222933 1.00E-05 5 -2.207516492 GSNMDFREPTEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSNMDFREPTEEER 14 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 216.54 5.55E-12 7721520000 12517440 8251880 11940590 11602280 16125700 11533280 15520310 13112200 16778840 FALSE TRUE 11925765.42 9092755.954 12488077.86 10435996.77 18938016.97 11133879.62 13152401.66 11964026.26 19380816.81 0.615338638 0.46916268 0.644352505 0.53847043 0.977152674 0.57447938 0.678629894 0.617312798 1 24.20812604 -4.999999999 0.137898251 2.246740104 0.492290889 0.431795824 0.131931232 125.1090913 1.06368847 43.0796994 0.790846277 1.00E-05 4.999999999 -1.754449214 GSNWVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSNWVPR 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 93.195 0.055349 0 368470 349180 346030 432940 349000 366860 423390 367530 364730 FALSE TRUE 351053.1533 384761.839 361895.8178 389420.0487 409865.4895 354155.5462 358794.0794 335347.1248 421290.4656 0.833280556 0.913293488 0.859017346 0.924350491 0.972881 0.840644579 0.851654876 0.795999796 1 18.68445574 -0.408594829 7.653616748 1 0.875726691 0.375539567 0.051057657 0 0 0.048447502 0.011419186 0.390305949 0.408594829 -0.124273309 GSNYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSNYWR 6 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 136.89 0.03018 6651630000 7441780 6077170 5602350 6828920 8265660 5968970 7894180 6943210 8030420 FALSE TRUE 7090021.808 6696440.532 5859223.289 6142463.988 9707188.487 5762263.072 6689777.854 6335225.724 9275736.52 0.764362139 0.72193087 0.631672027 0.662207683 1.046514039 0.621218925 0.721212579 0.682988969 1 23.14503041 -1.848194019 2.482001485 1.112836475 0.731280336 0.330507444 0.120089728 30419659.82 18724626.43 20356997.81 0.026642155 0.014184237 1.848194019 -0.381556139 GSPDGS(ph)LQTGKPSAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.005)PDGS(0.994)LQT(0.001)GKPSAPK 164.93 1.90E-08 206670000 122560 132180 107590 154890 75875 131640 121190 125440 82657 TRUE FALSE 116766.8317 145649.2923 112523.1079 139320.1629 89107.57598 127081.2738 102700.2397 114455.8086 95475.02541 1.223009171 1.525522425 1.178560649 1.459231483 0.933307696 1.331042053 1.075676485 1.198803646 1 16.54283578 2.753013597 24.99437958 1.127902431 1.353339857 0.393868111 0.145922413 786.8484442 1360741.417 0.039671179 0.041899941 566.2570169 -2.753013597 0.225437426 GSPHSEGGKRS(ph)PEPNK ddPTM_SK-BR-3_Trastuzumab_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;GSPHS(0.001)EGGKRS(0.999)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHS(0.007)EGGKRS(0.993)PEPNK 150.61 3.77E-07 1807211000 1477870 1449730 1421817 1808217 866130 1672075 1711011 1827566 905146 TRUE FALSE 1408014.014 1597459.135 1487008.716 1626451.592 1017182.798 1614170.623 1449964.847 1667534.633 1045511.419 1.346722751 1.52792127 1.42227879 1.555651677 0.972904532 1.543905303 1.386847452 1.594946361 1 19.99577739 GSPQQIDHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;; 154.15 1.50E-05 1379590000 1710490 1357660 1489130 1762650 1377160 1535920 1836980 1675480 1411790 FALSE TRUE 1629638.528 1496007.098 1557408.083 1585465.073 1617336.268 1482730.705 1556714.963 1528766.089 1630723.183 0.999334862 0.917388747 0.955041358 0.972246602 0.991790811 0.909247333 0.954616319 0.937477375 1 20.63708047 4.731965302 4.756813748 0.951969576 1.001711024 0.184343596 0.028968278 0.258278197 14.77382122 0.006375397 0.041262058 53946.75199 -4.731965302 0.049741448 GSPS(ph)GGSTAEASDTLSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSPSGGSTAEASDTLSIR 18 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GS(0.168)PS(0.832)GGSTAEASDTLSIR 164.77 3.13E-11 50097000 44444 39651 34978 49067 40404 40330 38873 41466 45906 TRUE FALSE 42343.2202 43691.48198 36581.7759 44134.69194 47450.44481 38933.36199 32942.2099 37835.01721 53024.86802 0.798553995 0.823980966 0.689898481 0.832339496 0.894871531 0.734247221 0.62125963 0.713533454 1 15.6943815 2.030093057 24.98214316 0.721574881 0.80580591 0 0.110605672 406.0177719 337059.2633 0.037731009 0.02786588 107.1748926 -2.030093057 0.084231029 GSPT(ph)SAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.384)PT(0.615)S(0.001)AYPER 149.23 0.00026512 464000000 418820 445110 360020 481970 453300 403750 399790 374010 466030 TRUE FALSE 399023.2086 490467.215 376527.2731 433521.4599 532355.3765 389768.0363 338794.6929 341259.7016 538299.5522 0.741266098 0.911141785 0.69947536 0.805353558 0.988957494 0.724072748 0.629379481 0.633958732 1 19.0380497 2.028724211 24.96149157 0.704130893 0.828016679 0.049957198 0.131412969 334.2339829 290449.6785 0.044656689 0.032980637 106.8376215 -2.028724211 0.123885786 GSPT(ph)SAYPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSPTSAYPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.486)PT(0.497)S(0.017)AYPERR 146.67 2.09E-05 317050000 111170 85912 111370 95065 124980 109750 119560 104160 149130 TRUE FALSE 105915.2144 94666.53047 116476.4247 85508.88559 146776.4724 105949.33 101318.9261 95039.19821 172256.3187 0.614869836 0.549567825 0.676180854 0.496404928 0.85208179 0.615067887 0.588186993 0.551731274 1 17.39419738 -2.114562623 2.371546773 1.720331778 0.614679281 0.609519592 0.096052766 5713863.213 1643956.887 22167051.57 0.021366258 0.007681347 2.114562623 -1.105652497 GSQFGQSCCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSQFGQSCCLR 11 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 113.22 0.0033044 39706000 29412 31704 20408 25304 44208 28363 41254 27917 41148 FALSE TRUE 28021.75305 34934.67364 21343.72699 22760.39385 51917.8612 27380.7822 34959.94462 25472.43948 47529.02169 0.589571425 0.73501773 0.449067248 0.478873603 1.092340203 0.576085542 0.735549426 0.535934437 1 15.53652109 GSQQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 132.96 0.034132 1230263000 1217593 956905 898777 1101118 1251788 948339 1284765 1175330 1421529 FALSE TRUE 1160039.792 1054414.707 939986.8145 990431.5267 1470099.431 915497.7826 1088750.503 1072411.874 1641972.457 0.706491627 0.642163456 0.572474167 0.603196188 0.895325268 0.557559768 0.663074766 0.653124155 1 20.6469985 -1.039961224 4.951155143 0.999997062 0.660686778 0.562026748 0.093856349 5.68E-06 1.10E-06 0.083188245 0.019607311 0.091209227 1.039961224 -0.339310285 GSQS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSQSPKR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GS(0.001)QS(0.999)PKR 56.432 0.07451 123230000 36120 39390 43104 51851 54075 39729 49642 66355 55937 TRUE FALSE 34412.67918 43403.88578 45080.36104 46638.83897 63505.66288 38353.17477 42068.20116 60544.60443 64611.42427 0.532609822 0.671767977 0.697715018 0.721835798 0.982885977 0.59359742 0.6510954 0.937057264 1 15.97950166 -2.54368941 0.049769836 2.021247236 4.49E-13 0.461369408 0.120522641 322.0951569 1.941401486 61.57754381 24.25476295 0.002859635 2.54368941 -2.021247236 GSRPIDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 102.52 0.0032565 1358630000 1145297 995343 972809 1141399 1321402 1034738 1259800 1189199 1320243 FALSE TRUE 1091161.081 1096769.583 1017413.255 1026663.404 1551854.09 998904.7636 1067594.372 1085066.431 1524979.542 0.715525062 0.719202818 0.667165183 0.673230936 1.017622891 0.655028305 0.700071275 0.711528517 1 20.54035846 -1.607684182 2.740093652 1.022733171 0.729375643 0.395627885 0.103874371 18509911.83 17446721.41 3017512.561 0.023361856 0.024678333 1.607684182 -0.293357528 GSRPMS(ph)MYETGSGQKPYLPMGEASRPEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSRPMSMYETGSGQKPYLPMGEASRPEESR 30 3 Q14161-3;Q14161;F8VXI9;Q14161-4;R4GNG3;Q14161-9;Q14161-5;F8WAK2;Q14161-10;Q14161-8 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 GS(0.174)RPMS(0.825)MYETGSGQKPYLPMGEASRPEESR 78.228 0.0023829 81258000 56584 35535 56741 52704 60106 53091 51651 40035 54877 TRUE FALSE 53909.38646 39156.0569 59342.63097 47406.09379 70588.46737 51252.44536 43770.69131 36529.32316 63387.04489 0.850479567 0.617729648 0.936194945 0.747883008 1.11361032 0.808563413 0.690530555 0.576290048 1 15.95190039 -1.147942971 4.588243694 1.000026297 0.786523677 0.148515378 0.15540651 4.03E-05 7.49E-06 0.14517357 0.034213527 0.071130691 1.147942971 -0.21350262 GSRPPLILQSQSLPCS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.651)S(0.349)PR 170.04 7.85E-12 505510000 95392 80080 95343 107210 104750 94105 111810 100430 112200 TRUE FALSE 90883.00921 88240.24304 99714.57086 96433.04711 123018.3668 90846.12025 94751.33097 91635.81679 129599.403 0.701261018 0.680869209 0.769406097 0.744085581 0.949220166 0.700976379 0.731109317 0.707069745 1 16.98369955 -2.676525122 2.136596928 8.175461514 0.742751993 0.519309941 0.076045521 1769649.626 102223.328 62377977.9 0.01841588 0.00210608 2.676525122 -7.432709521 GSRPPLILQSQSLPCSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.345)S(0.655)PR 220.5 1.75E-19 443290000 211790 179320 196590 219710 250540 206430 241430 211760 256200 TRUE FALSE 201779.1064 197592.9119 205603.846 197624.3334 294234.0967 199281.2773 204595.4193 193217.1718 295930.1875 0.681846986 0.6677011 0.694771452 0.667807279 0.994268612 0.673406383 0.691363801 0.652914707 1 18.17489735 -2.149984243 2.282908764 1.633432371 0.712066793 0.443372122 0.100110866 6631079.81 1593003.838 21734368.3 0.023149465 0.007079715 2.149984243 -0.921365578 GSS(ph)FQSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSSFQSGR 8 0 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.048)S(0.952)FQSGR;GS(0.013)S(0.987)FQSGR;GS(0.009)S(0.991)FQSGR;GS(0.002)S(0.998)FQSGR 175.41 0.00027933 483450000 1760380 1728820 1614710 2003310 1769040 1727760 1834620 1813380 1853270 TRUE FALSE 1677170.326 1904988.724 1688746.051 1801933.473 2077560.016 1667927.238 1554715.024 1654590.834 2140665.646 0.78348075 0.889904842 0.788888285 0.841763157 0.970520557 0.779162893 0.72627644 0.772932866 1 21.02962805 -1.522018103 8.697348532 1.000012608 0.81891869 0.403581755 0.069104999 1.75E-05 9.62E-07 0.069289224 0.016330491 0.03005951 1.522018103 -0.181093918 GSS(ph)GSPAHAESYSSGGGGQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.081)S(0.54)GS(0.38)PAHAESYSSGGGGQQK 258.87 1.01E-36 125290000 238430 181900 203650 219490 187430 212570 255100 236560 201380 TRUE FALSE 227159.8864 200435.8168 212987.5539 197426.4482 220117.7327 205208.6476 216179.8098 215845.5523 232608.9819 0.976574011 0.861685629 0.915646301 0.848748172 0.946299368 0.882204315 0.929370001 0.927933008 1 17.82754728 0.657577535 1.055720706 0.999906147 0.905531634 0.370429762 0.037738858 1.161727591 2.134002802 0.03299709 0.010445602 4.5454568 -0.657577535 -0.094374513 GSS(ph)PGPRPVEGTPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 GS(0.033)S(0.967)PGPRPVEGTPASR;GS(0.037)S(0.963)PGPRPVEGTPASR;GS(0.012)S(0.988)PGPRPVEGTPASR;GS(0.11)S(0.89)PGPRPVEGTPASR;GS(0.117)S(0.883)PGPRPVEGTPASR;GS(0.071)S(0.929)PGPRPVEGTPASR;GS(0.046)S(0.954)PGPRPVEGTPASR 124.63 4.93E-05 8636020000 4936800 4654170 4988370 5475510 5512880 5129650 5825290 5373570 6211370 TRUE FALSE 4703447.248 5128435.214 5217091.699 4925101.332 6474324.527 4952008.934 4936535.022 4903031.724 7174597.536 0.65556949 0.714804585 0.727161583 0.686463778 0.902395499 0.690214177 0.688057413 0.683387702 1 22.77446647 -1.942447926 2.608130406 1.201071447 0.715866696 0.626774284 0.06823837 10220456.99 5448325.346 12485789.61 0.015791388 0.011417002 1.942447926 -0.485204751 GSS(ph)PLPTATTPKPLIPTEASIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSSPLPTATTPKPLIPTEASIR 22 1 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3 Q9BUK6-2 MSTO1 Protein misato homolog 1 1 GS(0.043)S(0.956)PLPTATTPKPLIPTEASIR;GS(0.173)S(0.827)PLPTATTPKPLIPTEASIR 93.446 0.0011627 231290000 273320 249497 320910 292660 396350 258150 388930 292010 330730 TRUE FALSE 260400.7053 274921.028 335624.0409 263241.2608 465473.3145 249210.2008 329591.5853 266440.0564 382017.9193 0.681645264 0.719654797 0.878555754 0.689080924 1.218459373 0.652352123 0.862764726 0.697454342 1 18.54328079 3.829478806 4.423492207 0.84767576 0.695407832 0.131785916 0.16606071 0.414717031 14.22126949 0.038984338 0.072393838 6752.720999 -3.829478806 -0.152267929 GSS(ph)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.442)S(0.558)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.013)S(0.987)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.16)S(0.84)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 432.93 4.03E-221 4483520000 1365910 1261860 1367980 1489980 975048 1628840 1727740 1667460 1126150 TRUE FALSE 1301346.141 1390444.969 1430703.236 1340204.38 1145096.062 1572432.862 1464141.531 1521448.363 1300787.59 1.000429394 1.068925456 1.099874604 1.030302249 0.880309799 1.208831383 1.125580796 1.169636283 1 20.31095397 2.210288812 24.99999936 1.137893756 1.026242405 0.321730296 0.077766595 238.8416631 211199.9356 0.027113411 0.020028572 162.2888984 -2.210288812 -0.111651351 GSS(ph)PTPPCSPVQPSK ddPTM_SK-BR-3_Trastuzumab_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 GS(0.045)S(0.924)PT(0.031)PPCSPVQPSK;GS(0.004)S(0.995)PT(0.001)PPCSPVQPSK;GS(0.022)S(0.97)PT(0.008)PPCSPVQPSK;GS(0.006)S(0.992)PT(0.002)PPCSPVQPSK 225.85 9.90E-13 389352000 710780 605860 666360 750170 562680 722130 807840 754210 680480 TRUE FALSE 677182.838 667597.8228 696913.2651 674761.4864 660811.2138 697122.457 684589.171 688167.3741 786005.363 0.861549895 0.849355302 0.886652048 0.858469316 0.840720999 0.886918194 0.870972646 0.875525036 1 19.58417963 -4.999994051 0.288042255 2.045046924 0.857052539 0.902115421 0.013940381 64.99862221 0.61420965 40.7401438 0.013980243 1.00E-05 4.999994051 -1.187994384 GSSAGFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSSAGFDR 8 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;; 122.18 0.0032608 1618320000 1300000 1160560 1123080 1318680 1431860 1137480 1353730 1181230 1498780 FALSE TRUE 1238551.576 1278822.383 1174574.329 1186123.781 1681575.931 1098088.782 1147193.626 1077795.239 1731203.148 0.715428214 0.73868996 0.678472847 0.685144192 0.971333684 0.634292275 0.662656851 0.622570055 1 20.7233436 -1.436755919 3.033812518 1.005575106 0.714325605 0.458043079 0.097910981 18711016.23 22797890.12 895001.5051 0.024062408 0.036580032 1.436755919 -0.291249501 GSSANASKWS(ph)PPQNYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSSANASKWSPPQNYK 16 1 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GS(0.001)S(0.001)ANAS(0.011)KWS(0.987)PPQNYK;GSSANAS(0.013)KWS(0.987)PPQNYK;GSSANAS(0.03)KWS(0.97)PPQNYK 141.83 9.49E-07 1012130000 1258660 667350 1324990 1028760 997630 1271630 1862710 1524350 1564020 TRUE FALSE 1199165.636 735353.7237 1385742.102 925347.0903 1171616.356 1227593.134 1578519.378 1390869.833 1806560.234 0.663783921 0.407046336 0.767061112 0.512214912 0.648534344 0.679519626 0.873770688 0.769899507 1 20.78481393 1.638111735 0.656064889 0.983282219 0.555509655 0.6208078 0.103650431 0.388977319 0.355394138 0.089504931 0.044722053 43.46220292 -1.638111735 -0.427772564 GSSCFECTHYQSFLEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSSCFECTHYQSFLEYR 17 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 267.38 9.01E-28 4292110000 2086100 1531687 1752661 2081590 2681510 1794964 2406600 2010950 2637440 FALSE TRUE 1987494.187 1687767.647 1833022.24 1872344.618 3149164.495 1732803.947 2039428.97 1834860.557 3046440.725 0.652398772 0.554012961 0.60169306 0.614600705 1.033719274 0.568796213 0.669446464 0.602296491 1 21.53869324 2.962097514 24.99921649 0.739895278 0.600465038 0.213585843 0.153483541 969.6416784 639543.4559 0.043816673 0.046484579 916.4262366 -2.962097514 -0.13943024 GSSDGRGS(ph)DS(ph)ESDLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 GSSDGRGS(1)DS(0.973)ES(0.027)DLPHR;GSSDGRGS(1)DS(0.997)ES(0.003)DLPHR 143.95 3.02E-07 290200000 366630 304970 334510 367190 415450 318300 415900 340760 369870 TRUE FALSE 349300.1265 336046.7897 349847.6144 330279.3636 487904.3485 307277.1912 352446.8165 310921.2479 427227.5506 0.817597381 0.786575653 0.818878871 0.773075995 1.142024544 0.71923543 0.824962753 0.727764976 1 18.70464516 -1.938999734 2.541056832 1.122412103 0.82501411 0.176168742 0.118044189 25050398.83 12350720.99 18156869.19 0.025990772 0.011508011 1.938999734 -0.297397993 GSSDGRGS(ph)DSESDLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 GS(0.001)S(0.001)DGRGS(0.954)DS(0.043)ESDLPHR;GS(0.046)S(0.046)DGRGS(0.903)DS(0.005)ESDLPHR;GS(0.002)S(0.002)DGRGS(0.991)DS(0.005)ESDLPHR;GSSDGRGS(0.992)DS(0.007)ESDLPHR 168.78 1.24E-09 713200000 926100 730096 838420 930060 992090 861800 1019470 910170 953320 TRUE FALSE 882325.0884 804493.6125 876862.3863 836568.6018 1165110.182 831955.6499 863931.1276 830470.6897 1101155.997 0.801271655 0.730590048 0.796310776 0.759718518 1.058079133 0.755529328 0.784567428 0.754180781 1 20.07058743 -2.227722593 2.160792738 1.618955821 0.800663259 0.303135542 0.092691693 4722444.548 796947.1816 14288421.97 0.021707965 0.005919396 2.227722593 -0.818292562 GSSERGS(ph)PIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GSSERGSPIEK 11 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.003)S(0.002)ERGS(0.995)PIEK;GS(0.005)S(0.005)ERGS(0.99)PIEK;GSSERGS(0.999)PIEK;GS(0.004)S(0.004)ERGS(0.992)PIEK;GSSERGS(0.999)PIEK;GSSERGS(1)PIEK;GS(0.024)S(0.024)ERGS(0.953)PIEK;GS(0.005)S(0.005)ERGS(0.99)PIEK 115.26 0.00069479 15475550000 13519540 12245730 12524100 13799040 9773440 13685140 14689390 14245700 11130690 TRUE FALSE 12880498.14 13493583.81 13098342.37 12411934.28 11477924.84 13211220.17 12448253.77 12998270.99 12856780.56 1.001844753 1.049530538 1.018788671 0.96539987 0.892752644 1.027568302 0.968224799 1.011005121 1 23.61602609 3.305074873 5.855861564 0.97502868 1.026692843 0.246780468 0.037643655 0.248572098 15.75339834 0.010044266 0.013563309 2018.714364 -3.305074873 0.051664163 GSSGCSEAGGAGHEEGRAS(ph)PLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSSGCSEAGGAGHEEGRASPLRR 23 2 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR 193.06 3.79E-18 294297000 80067 82274 76694 80736 85994 76902 87483 79031 84386 TRUE FALSE 76282.39159 90657.81414 80210.49576 72620.26389 100991.3264 74238.86446 74135.86161 72110.62667 97472.1499 0.782607049 0.930089407 0.822906808 0.745036033 1.036104431 0.761641808 0.760585067 0.739807491 1 16.57270245 GSSGENNNPGS(ph)PTVSNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(0.999)PT(0.001)VSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(0.998)PT(0.002)VSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(1)PTVSNFR 555.49 0 1492874000 2057830 1695690 1992870 2097920 2454680 1705690 2168870 1862660 2156520 TRUE FALSE 1960560.454 1868482.739 2084245.061 1887033.096 2882775.415 1646621.528 1837969.047 1699555.616 2490942.108 0.787075881 0.750110865 0.836729627 0.75755799 1.157303257 0.661043676 0.737861005 0.682294306 1 21.24826006 -1.593554781 7.603595579 1.000168665 0.792283974 0.177420148 0.137642728 0.000369219 1.97E-05 0.125032942 0.029446893 0.025494425 1.593554781 -0.207884691 GSSGGSGAKPSDAASEAARPATSTLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 196.55 3.53E-25 1070080000 469960 384860 459200 478760 379160 467330 547310 499470 463640 FALSE TRUE 447745.9222 424077.6715 480254.7742 430634.1352 445285.384 451146.2449 463807.8075 455733.7589 535538.9233 0.836066069 0.791870867 0.89676913 0.804113607 0.83147156 0.842415416 0.866058072 0.85098158 1 19.03063191 -5 0.218828887 1.832860155 0.816052349 0.766850606 0.028102212 65.26036626 0.652436982 23.87735155 0.049411198 1.00E-05 5 -1.016807807 GSSGPTQINQVVSHPNQPLTITAHDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSSGPTQINQVVSHPNQPLTITAHDDR 27 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317 F5GYK2 STRN4 Striatin-4 0 ; 375.28 2.60E-127 669400000 103864 98442 84007 107707 125324 91481 122026 104208 96176 FALSE TRUE 98954.55456 108473.3517 87858.80404 96880.08773 147180.4659 88312.99003 103408.6925 95082.99508 111090.4829 0.890756364 0.976441446 0.790876066 0.872082695 1.324870161 0.794964499 0.930851049 0.855905858 1 16.7613757 4.736454681 5.029690963 0.939105604 0.888568082 0.010981798 0.152077536 1.259571695 90.3999771 0.033983356 0.216699487 54507.30136 -4.736454681 -0.050537522 GSSGS(ph)PAHAESYSSGGGGQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.121)S(0.121)GS(0.758)PAHAESYSSGGGGQQK 276.96 5.14E-45 139070000 252020 201150 226870 256880 192940 230920 276740 230210 181540 TRUE FALSE 240107.5141 221647.4137 237272.2139 231057.9344 226588.6749 222923.1825 234518.2303 210051.592 209692.296 1.145046903 1.05701267 1.131525661 1.101890431 1.080577013 1.063096674 1.11839221 1.001713444 1 17.67791433 1.23089165 24.9958721 1.000856633 1.098124467 0.685161122 0.027826503 102.9938596 335679.6246 0.023155745 0.006228735 17.01733898 -1.23089165 0.097267835 GSSMGVRNS(ph)PQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSSMGVRNSPQALR 14 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 GS(0.001)S(0.001)MGVRNS(0.998)PQALR;GS(0.004)S(0.004)MGVRNS(0.992)PQALR 74.793 0.048622 343590000 337580 219400 312300 306660 430030 279230 391240 313130 497690 TRUE FALSE 321623.2624 241757.1094 326619.2639 275833.9542 505027.0958 269560.1951 331549.1524 285710.6772 574869.2234 0.559472049 0.420542794 0.568162724 0.479820354 0.878507799 0.468906986 0.576738394 0.497001171 1 19.13287427 -5 0.339365738 5.821284447 0.533798321 0.546743937 0.125939738 287.5029516 2.425115873 1004.446341 0.094466911 1.00E-05 5 -5.287486126 GSSPSIRPIQGSQGS(ph)SSPVEKEVVEATDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEKEVVEATDSR 30 2 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.013)S(0.012)PS(0.112)IRPIQGS(0.085)QGS(0.259)S(0.259)S(0.259)PVEKEVVEATDSR 43.069 0.071836 50950000 63323 39025 60059 51399 50647 57592 71056 66169 61399 TRUE FALSE 60329.84728 43001.69187 62812.76456 46232.27487 59479.82076 55597.5746 60215.10217 60374.89158 70920.44334 0.850669348 0.606337043 0.885679243 0.651889254 0.838683713 0.783942852 0.849051407 0.851304486 1 16.11391393 0.990998354 0.530930233 1.00412796 0.740659138 0.42550701 0.085531758 0.828639135 0.577435059 0.085922663 0.039740984 9.794862742 -0.990998354 -0.263468822 GSSPSIRPIQGSQGSS(ph)SPVEKEVVEATDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEKEVVEATDSR 30 2 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.006)S(0.006)PS(0.023)IRPIQGS(0.017)QGS(0.015)S(0.466)S(0.466)PVEKEVVEATDSR 58.635 0.020624 47248000 63725 47169 62303 62290 58439 66717 81889 72742 71698 TRUE FALSE 60712.84554 51975.57473 65159.65418 56028.49086 68630.7431 64406.57356 69395.32906 66372.32485 82816.55966 0.73310031 0.627598815 0.786794989 0.67653729 0.828707971 0.777701632 0.837940254 0.801437842 1 16.33763165 0.763966385 0.230306694 1.078869995 0.638239626 0.738615012 0.051266238 1.673034152 0.266808311 0.250926139 0.128357005 5.807194667 -0.763966385 -0.440630369 GSSPT(ph)PPCS(ph)PVQPSK ddPTM_SK-BR-3_Trastuzumab_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 GSS(0.006)PT(0.994)PPCS(1)PVQPSK;GS(0.003)S(0.02)PT(0.977)PPCS(1)PVQPSK 196.18 4.81E-08 395320000 388710 340600 384030 400540 332200 374800 428410 400240 398890 TRUE FALSE 370336.4486 375307.5272 401638.1554 360276.9582 390135.5748 361820.582 363048.1862 365192.8638 460747.824 0.80377254 0.814561692 0.871709283 0.781939576 0.846744259 0.785289834 0.787954207 0.792608982 1 18.81361783 -0.924070863 5.837757036 1.0000001 0.809810685 0.811533677 0.028686489 3.52E-08 6.46E-09 0.026213816 0.006178653 0.119104765 0.924070863 -0.190189414 GSSSSS(ph)PEHSASSDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.005)S(0.004)S(0.01)S(0.053)S(0.927)PEHSASSDSTK;GSS(0.003)S(0.016)S(0.142)S(0.838)PEHSASSDSTK;GSSSS(0.019)S(0.968)PEHS(0.013)ASSDSTK;GS(0.089)S(0.089)S(0.089)S(0.089)S(0.548)PEHS(0.069)AS(0.012)S(0.012)DS(0.001)T(0.001)K 223.86 1.87E-15 1089631000 2004912 1801310 1808195 2188121 1547814 2025685 2118886 2053474 1643658 TRUE FALSE 1910143.783 1984865.537 1891102.529 1968166.92 1817752.272 1955535.021 1795611.025 1873660.93 1898548.088 1.006107665 1.045464979 0.996078288 1.036669512 0.957443366 1.03001606 0.945781166 0.986891479 1 20.85646511 2.747006047 24.99816968 0.981659623 1.022091661 0.325117332 0.026387682 657.5913713 1946449.301 0.007350085 0.007675517 558.4779703 -2.747006047 0.040432038 GSST(ph)PTKGIENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSSTPTKGIENK 12 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;H0YBE9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 GSS(0.032)T(0.95)PT(0.018)KGIENK;GS(0.016)S(0.177)T(0.805)PT(0.002)KGIENK;GS(0.007)S(0.102)T(0.889)PT(0.002)KGIENK 119.54 0.00081816 833060000 2066240 1185110 2135990 1837710 1392490 2215970 2647820 2436170 1736230 TRUE FALSE 1968572.93 1305874.056 2233927.254 1652979.899 1635339.815 2139230.403 2243846.428 2222846.04 2005475.681 0.981599004 0.651154272 1.113913909 0.82423333 0.81543737 1.066694762 1.118859954 1.108388429 1 20.93551304 2.194648513 7.259104736 1.087998726 0.864337954 0.383539526 0.122457594 0.192762784 25.43084386 0.043507805 0.032334655 156.5483567 -2.194648513 -0.223660772 GSTAPVGGGAFPTIVEREPWDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GSTAPVGGGAFPTIVEREPWDGR 23 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;; 278.58 6.99E-52 1502254000 1252228 985688 1130545 1203625 1427333 1144752 1352750 1259659 1441474 FALSE TRUE 1193037.664 1086130.728 1182381.607 1082634.328 1676259.423 1105108.951 1146363.143 1149356.58 1665010.426 0.716534651 0.652326683 0.710134656 0.650226756 1.006756112 0.663724944 0.688502081 0.69029993 1 20.66709978 -1.7359038 2.492474639 1.062164483 0.7169313 0.413184251 0.10382485 18495434.19 13527119.93 7111170.494 0.025126067 0.018369452 1.7359038 -0.345233182 GSTDDKGPVAGWINALEAYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSTDDKGPVAGWINALEAYQK 21 1 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;A0A087WVS2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 219.78 4.50E-25 500300000 1055870 857500 871280 1040610 679860 1016220 1146500 1101730 774110 FALSE TRUE 1005961.118 944880.2249 911229.0498 936005.9058 798427.3687 981028.0466 971580.3681 1005256.681 894155.0252 1.12504106 1.05672976 1.01909515 1.046804949 0.892940649 1.097156554 1.086590514 1.124253236 1 19.77016546 -1.476627396 7.284981162 0.999991078 1.057976636 0.064504335 0.066765804 9.55E-06 6.86E-07 0.063821727 0.015040611 0.03337126 1.476627396 0.057985558 GSTDNLMDDIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GSTDNLMDDIER 12 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 216.06 9.30E-11 974850000 1240760 1149090 1138570 1302510 1400280 1181300 1425970 1319620 1445790 FALSE TRUE 1182111.734 1266183.577 1190774.561 1171579.22 1644488.389 1140391.285 1208412.087 1204067.077 1669995.729 0.707853148 0.758195698 0.713040483 0.701546237 0.984726104 0.682870779 0.723601903 0.721000094 1 20.67141298 -1.535219575 2.892476745 1.011412492 0.747261679 0.456005886 0.086099797 22504784.07 24177188.59 2009694.162 0.019039028 0.029159524 1.535219575 -0.264150813 GSTIYTGYPLS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GSTIYTGYPLSPTK 14 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 GSTIYTGYPLS(0.982)PT(0.018)K;GSTIYTGYPLS(0.984)PT(0.016)K 140.27 1.13E-05 0 175788 154002 143861 185044 133234 168042 188011 175390 137752 TRUE FALSE 167478.8496 169694.9789 150457.1691 166443.0256 156469.9674 162222.6634 159326.4689 160031.9218 159113.8766 1.052572241 1.066500185 0.945594265 1.046062286 0.983383541 1.019538125 1.001336101 1.005769737 1 17.27970014 3.786102428 24.99951384 1.00258248 1.059536251 0.47889305 0.025624689 281.1108775 147819.2024 0.005639467 0.010166677 6110.861323 -3.786102428 0.05695377 GSTTNDPPKQSPGS(ph)TSPKPPHTLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSTTNDPPKQSPGSTSPKPPHTLSR 25 2 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 GSTTNDPPKQS(0.034)PGS(0.321)T(0.321)S(0.321)PKPPHT(0.001)LSR 54.003 0.059761 96825000 97632 55700 95866 85000 62753 95719 136030 118130 79824 TRUE FALSE 93017.12885 61375.89333 100261.5509 76455.63851 73697.10333 92404.22703 115276.1251 107785.911 92202.69824 1.008833045 0.66566266 1.087403654 0.829212593 0.799294432 1.002185715 1.250246764 1.169010376 1 16.49252135 1.985531055 4.954642304 1.160834602 0.86950391 0.459699762 0.128770221 0.140504042 9.626315855 0.05139108 0.032998806 96.72328877 -1.985531055 -0.291330692 GSTTNDPPKQSPGSTS(ph)PKPPHTLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSTTNDPPKQSPGSTSPKPPHTLSR 25 2 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 GSTTNDPPKQS(0.012)PGS(0.033)T(0.033)S(0.918)PKPPHT(0.002)LS(0.002)R 61.186 0.035982 110880000 113730 64487 109480 95297 71658 112260 148460 133400 87855 TRUE FALSE 108354.2083 71058.29862 114499.7663 85717.56451 84155.13251 108372.4081 125809.7003 121718.7888 101479.1047 1.067748958 0.700225912 1.128308795 0.844681915 0.829285327 1.067928303 1.23975966 1.199446814 1 16.63082317 2.045743712 5.007970807 1.169562433 0.906542267 0.387885639 0.134351752 0.163440123 9.312553357 0.049257778 0.034820982 111.1075861 -2.045743712 -0.263020166 GSVIS(ph)PTELEAPILVPHTAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSVISPTELEAPILVPHTAQR 21 0 Q8N1B4-2;Q8N1B4 Q8N1B4-2 VPS52 Vacuolar protein sorting-associated protein 52 homolog 1 GS(0.032)VIS(0.954)PT(0.013)ELEAPILVPHTAQR 174.47 1.91E-12 48496000 34324 23378 30191 36041 35990 26754 35324 30969 36597 TRUE FALSE 32701.57254 25760.24478 31575.28721 32418.09021 42266.64461 25827.50227 29934.67503 28257.19018 42272.27585 0.773593848 0.609388642 0.746950255 0.766887743 0.999866786 0.610979697 0.70813966 0.668456799 1 15.36742417 -2.32104484 2.177974346 2.358202791 0.728574092 0.360716287 0.110301307 4742361.013 537692.9879 31784053.23 0.027383136 0.0047748 2.32104484 -1.629628699 GSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.071)VPLS(0.306)S(0.306)S(0.306)PPAT(0.012)HFPDETEITNPVPK 119.85 0.00050578 124170000 116350 132470 99259 152990 85399 115980 105410 121270 79134 TRUE FALSE 110850.3661 145968.8436 103810.1233 137611.1545 100292.5586 111963.5835 89327.76851 110650.9559 91405.69656 1.212729296 1.59693377 1.135707371 1.505498669 1.097224378 1.224908159 0.977266974 1.210547702 1 16.47999646 2.719919443 24.18118429 1.100576144 1.37247636 0.426580427 0.150014406 460.3244991 597128.2712 0.044152281 0.041703222 524.7101225 -2.719919443 0.271900216 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.003)VPLS(0.068)S(0.464)S(0.464)PPATHFPDETEITNPVPK;GS(0.008)VPLS(0.104)S(0.453)S(0.4)PPAT(0.034)HFPDETEITNPVPK;GS(0.002)VPLS(0.05)S(0.474)S(0.474)PPATHFPDETEITNPVPK;GSVPLS(0.069)S(0.606)S(0.325)PPATHFPDETEITNPVPK 259.7 6.12E-53 11709490000 1621870 1939960 1477330 2058950 1201378 1720460 1658810 1788570 1116770 TRUE FALSE 1545207.419 2137644.13 1545067.042 1851980.434 1410897.943 1660880.039 1405728.068 1631953.329 1289952.988 1.197878864 1.657148865 1.19777004 1.435696069 1.093759196 1.287550829 1.089751395 1.265126206 1 20.29888706 2.829313231 1.516391775 1.151680383 1.406297461 0.296231231 0.158150717 0.427647237 1.986154122 0.057371935 0.059404251 675.0147009 -2.829313231 0.254617078 GSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.001)S(0.044)S(0.954)PPATHFPDETEITNPVPK;GSVPLS(0.001)S(0.046)S(0.952)PPATHFPDETEITNPVPK;GS(0.003)VPLS(0.017)S(0.069)S(0.911)PPATHFPDETEITNPVPK;GSVPLS(0.022)S(0.166)S(0.811)PPAT(0.001)HFPDETEITNPVPK 298.18 1.13E-70 7863960000 2249640 2597400 2046110 2722240 1585840 2343380 2240040 2529090 1488280 TRUE FALSE 2143303.976 2862078.013 2139926.167 2448595.263 1862409.994 2262228.163 1898280.757 2307629.472 1719074.861 1.246777568 1.664894344 1.24481267 1.424368024 1.083379227 1.315956747 1.104245545 1.342367063 1 20.71320094 2.990936219 1.705304212 1.181156338 1.438367048 0.299870627 0.158635838 0.382258516 2.256106898 0.051016649 0.059923779 979.3461464 -2.990936219 0.25721071 GSYGS(ph)DAEEEEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR;GSYGS(1)DAEEEEYR 407.98 2.35E-126 6175320000 4928870 5030300 4092120 5492840 4918440 4936450 4567020 4557590 4122590 TRUE FALSE 4695892.083 5542893.289 4279747.75 4940689.287 5776214.379 4765499.499 3870237.22 4158503.258 4761900.202 0.986138282 1.164008705 0.898747888 1.037545744 1.213006181 1.000755853 0.812750594 0.87328652 1 22.18310595 1.958263886 7.603584669 0.881706412 1.062959303 0.370819103 0.097227914 0.250394301 40.02976961 0.03889368 0.024685402 90.83723076 -1.958263886 0.181252891 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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 GS(0.001)YGS(0.999)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.053)Y(0.002)GS(0.945)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.001)YGS(0.999)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GS(0.01)YGS(0.99)DAEEEEYRQQLSEHSK;GS(0.012)YGS(0.988)DAEEEEYRQQLSEHSK;GS(0.009)YGS(0.991)DAEEEEYRQQLSEHSK;GS(0.015)YGS(0.985)DAEEEEYRQQLSEHSK;GS(0.001)YGS(0.999)DAEEEEYRQQLSEHSK 336.79 1.54E-80 21424900000 7415260 6025481 7034615 7630703 6594709 6877712 8776589 8113736 7165783 TRUE FALSE 7064755.355 6639484.364 7357159.056 6863650.237 7744824.162 6639535.109 7437559.155 7403254.262 8277016.03 0.853538924 0.802159177 0.888866112 0.82924211 0.935702448 0.802165308 0.898579769 0.894435173 1 22.98067932 -5 0.146533863 1.521241936 0.809942573 0.561747266 0.040390776 87.947751 0.77378595 13.23110858 0.191543175 1.00E-05 5 -0.711299362 GSYGS(ph)DAEEEEYRQQLSEHSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GSYGSDAEEEEYRQQLSEHSKR 22 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 GS(0.009)YGS(0.991)DAEEEEYRQQLSEHSKR 141.36 6.41E-08 185550000 49565 20045 55207 32261 61394 47278 90661 57257 104810 TRUE FALSE 47222.16068 22087.60829 57738.29556 29018.06299 72101.09416 45640.75101 76828.99935 52243.27354 121063.3995 0.390061413 0.182446622 0.476926105 0.239693112 0.595564757 0.376998756 0.634617892 0.431536482 1 16.88540324 -2.404587335 0.159622508 1.946201677 0.176616489 0.709453722 0.123831681 22.60430522 0.456383337 8.125248716 0.534075174 0.003939242 2.404587335 -1.769585189 GSYSLSHVYTPNDVR ddPTM_SK-BR-3_Trastuzumab_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 0 138.77 8.55E-06 193030000 227760 179670 199000 221250 295560 195670 265840 254030 270030 FALSE TRUE 216994.2362 197978.5773 208124.3468 199009.5297 347105.5704 188893.8988 225281.2255 231785.7865 311904.8733 0.695706463 0.63474025 0.66726866 0.638045592 1.112857157 0.605613811 0.722275427 0.743129737 1 18.25074657 -5 0.160914914 2.03185238 0.643326293 0.27788912 0.141883381 173.2300545 1.596447005 57.28456786 0.559828027 1.00E-05 5 -1.388526086 GT(ph)PPPVFTPPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 GT(1)PPPVFTPPLPK 112.44 0.01007 31458000 63700 54829 56948 66162 54818 54974 72377 67615 65853 TRUE FALSE 60689.02724 60416.13744 59559.12213 59511.27006 64378.24184 53070.2366 61334.55936 61694.27215 76065.14691 0.797855913 0.794268333 0.783001474 0.78237238 0.846356636 0.697694526 0.806342482 0.811071491 1 16.21494794 0.620873011 2.147799343 0.999956964 0.786723903 0.768039268 0.036553608 1.064331883 5.496565567 0.031402322 0.008560054 4.177082097 -0.620873011 -0.213233061 GT(ph)PS(ph)QSPVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.883)PS(0.613)QS(0.505)PVVGR 107.65 0.011509 309230000 150450 191240 145280 194740 221890 152560 148550 158430 208770 TRUE FALSE 143338.5267 210727.5734 151941.2317 175164.3652 260587.5457 147276.8089 125885.9692 144557.0293 241144.9854 0.594408076 0.873862557 0.630082485 0.726386099 1.08062602 0.610739671 0.522034365 0.599461063 1 17.87954128 GT(ph)PSQS(ph)PVVGR ddPTM_SK-BR-3_Trastuzumab_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 2 GT(0.997)PS(0.125)QS(0.878)PVVGR;GT(0.999)PS(0.005)QS(0.996)PVVGR;GT(1)PS(0.013)QS(0.987)PVVGR 153.18 0.00017292 690990000 681670 700630 630490 708340 716430 662440 719760 692050 728270 TRUE FALSE 649448.81 772024.9936 659398.5901 637136.3174 841375.1652 639499.5367 609947.3927 631450.4332 841206.3921 0.77204455 0.917759305 0.783872539 0.757407841 1.000200632 0.760217163 0.725086493 0.750648639 1 19.68210029 GT(ph)PTAENPEYLGLDVPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.875)PT(0.125)AENPEYLGLDVPV;GT(0.9)PT(0.1)AENPEYLGLDVPV 133.32 0.00023118 61269000 158762 189997 132508 228970 180956 152520 162435 184018 161261 TRUE FALSE 151257.6349 209357.9103 138583.6229 205953.5006 212514.6691 147238.1942 137652.5574 167904.4084 186268.5323 0.81204073 1.123957481 0.743999113 1.10568059 1.140904835 0.790461987 0.739000602 0.901410487 1 17.50702444 2.20201506 24.99942161 0.823953583 0.982972108 0.141592102 0.145881737 255.9719591 175099.1995 0.051483212 0.038023976 159.2263939 -2.20201506 0.159018525 GT(ph)RESGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.5)RES(0.5)GQK;GT(0.651)RES(0.349)GQK;GT(0.651)RES(0.349)GQK 81.548 0.036498 1081210000 655270 650400 508570 531500 2387000 446850 645720 802890 1622320 TRUE FALSE 624296.6857 716676.4994 531888.4375 478072.6102 2803292.044 431375.4725 547203.5545 732584.6952 1873901.1 0.333153487 0.382451614 0.283840186 0.25512158 1.495965846 0.230201835 0.292013039 0.39094096 1 20.83761338 GT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Trastuzumab_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(0.864)S(0.136)PRPPEGGLGYSQLGDDDLK 136.53 7.08E-06 89838000 187230 249030 157300 247390 111800 218790 158540 216760 102730 TRUE FALSE 178380.009 274406.4401 164512.3606 222521.8872 131297.8846 211213.2474 134351.8112 197779.3453 118660.8437 1.503276088 2.312527296 1.386408148 1.875276462 1.106497143 1.779974259 1.132233743 1.666761663 1 16.85648442 2.111220341 0.332677344 1.030339068 1.960441061 0.262738944 0.344949705 1.659699289 0.49882471 0.425154094 0.547525297 129.1874546 -2.111220341 0.930101993 GT(ph)SPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTSPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLK 45 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 GT(0.499)S(0.499)PRPPEGGLGY(0.002)SQLGDDDLKETGFHLTTTNQGASAAGPGFSLK 160.31 2.52E-20 284220000 122690 118760 102370 141720 78136 117680 134490 140830 77385 TRUE FALSE 116890.6868 130861.779 107063.7658 127474.0363 91762.89366 113604.7121 113971.0804 128498.1786 89385.47057 1.307714622 1.464016223 1.197775937 1.42611585 1.026597422 1.270952778 1.275051523 1.437573442 1 16.44775272 -4.39371158 0.204377112 1.52E-26 1.35211396 0.311189045 0.132341151 128.0897081 1.592128598 53.50659416 0.285712744 4.04E-05 4.39371158 1.35211396 GT(ph)SPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTSPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF 46 3 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(0.468)S(0.468)PRPPEGGLGY(0.006)S(0.026)QLGDDDLKET(0.007)GFHLT(0.007)T(0.007)T(0.007)NQGAS(0.002)AAGPGFSLKF 43.155 0.029154 102770000 69679 47106 70331 67992 50775 77373 103150 78859 65659 TRUE FALSE 66385.41176 51906.15496 73555.74592 61157.31498 59630.14392 74693.55361 87412.57302 71953.6879 75841.06238 0.875322809 0.684407013 0.96986703 0.806387899 0.786251432 0.984869558 1.152575798 0.948743143 1 16.21069155 2.118050286 4.51491226 1.054549237 0.816206218 0.551043774 0.088141501 0.135120251 4.722217253 0.032736869 0.023602474 131.2351845 -2.118050286 -0.238343019 GT(ph)SPTQIWCNNSQLPVDHILAGSFETAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTSPTQIWCNNSQLPVDHILAGSFETAMR 29 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 GT(0.5)S(0.5)PTQIWCNNSQLPVDHILAGSFETAMR 124.48 8.70E-05 45799000 12610 10001 12474 13810 14988 13886 14261 10756 14036 TRUE FALSE 12013.95029 11020.11327 13045.94524 12421.79256 17601.90245 13405.12434 12085.22253 9814.147619 16212.63119 0.741024091 0.679723923 0.804677852 0.766179926 1.085690672 0.826832127 0.745420184 0.605339596 1 13.98483063 3.5402873 2.741953296 0.830143606 0.710824618 0.129708906 0.132657013 0.566216014 8.369395211 0.037250115 0.059937335 3469.663043 -3.5402873 -0.119318988 GTCADRDNLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTCADRDNLTR 11 1 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 105.46 0.002246 67388000 121890 101370 117180 129340 124420 110340 134400 125550 123150 FALSE TRUE 116128.5013 111699.7182 122552.8189 116338.4975 146118.8086 106518.8981 113894.8116 114556.1764 142247.473 0.81638358 0.785249227 0.861546545 0.817859854 1.027215496 0.748828052 0.800680737 0.805330133 1 17.1180435 -2.420755173 2.205989925 2.457790128 0.82803782 0.328306829 0.074835447 4450511.849 247851.6405 32780033.45 0.017536463 0.003795289 2.420755173 -1.629752309 GTCSGFEPHSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTCSGFEPHSWR 12 0 Q9NZU5;F8WB09;C9IYS1;H7C3D2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 112.5 0.0012672 98479000 106820 84134 87022 102810 118030 105070 112800 100760 123100 FALSE TRUE 101770.8303 92707.35025 91012.04478 92475.34347 138614.3946 101431.3996 95590.28829 91936.92024 142189.7193 0.715739723 0.651997562 0.64007472 0.650365891 0.974855252 0.713352555 0.672272853 0.646579237 1 17.11745763 GTDDS(ph)PKDSQEDLQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 GT(0.014)DDS(0.986)PKDSQEDLQER;GTDDS(0.997)PKDS(0.003)QEDLQER;GTDDS(1)PKDSQEDLQER 214.52 1.03E-14 903150000 981660 829660 874690 978610 677843 935950 1085040 1012910 865290 TRUE FALSE 935258.8773 914203.2972 914795.4017 880238.2636 796058.6046 903537.8168 919497.2199 924214.2306 999474.7539 0.935750376 0.914683731 0.915276147 0.880700848 0.796476951 0.904012646 0.919980436 0.924699926 1 19.9308106 0.825543804 1.356950933 0.99921601 0.896078744 0.440248488 0.037747603 0.714745862 2.452558201 0.037966242 0.011350633 6.691813118 -0.825543804 -0.103137266 GTDIMYTGTLDCWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTDIMYTGTLDCWR 14 0 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 199.43 4.80E-08 98219000 80257 83371 140093 103593 118967 96505 107151 84380 113839 FALSE TRUE 76463.41066 91866.59968 146516.4026 93179.63483 139714.8071 93163.00765 90803.14699 76991.23987 131492.5707 0.581503656 0.698644792 1.114256127 0.708630414 1.062530045 0.708503965 0.690557242 0.585517794 1 17.00462176 3.990802634 24.18109669 0.820828467 0.625431499 0.188224032 0.175150234 569.6875331 1497795.87 0.042948935 0.081367511 9790.449564 -3.990802634 -0.195396967 GTDLWLGVDALGLNIYEKDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTDLWLGVDALGLNIYEKDDK 21 1 P15311;E7EQR4 P15311 EZR Ezrin 0 168.75 9.48E-12 57045000 311260 327190 253450 356740 161910 284230 259490 322730 139230 FALSE TRUE 296547.3567 360531.033 265070.9332 320879.8174 190147.0527 274387.0438 219900.0346 294470.0503 160821.0773 1.843958277 2.241814562 1.64823503 1.995259718 1.182351567 1.706163448 1.367358299 1.831041398 1 17.29509697 2.756672245 24.84294763 1.457688058 1.958299933 0.457622365 0.275991473 641.4644537 879868.3002 0.075700002 0.080143761 571.0475139 -2.756672245 0.500611875 GTDLWLGVDALGLNIYEKDDKLTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTDLWLGVDALGLNIYEKDDKLTPK 25 2 P15311;E7EQR4 P15311 EZR Ezrin 0 256.12 3.90E-45 248590000 453630 357020 399690 422310 246790 459640 515730 503740 240140 FALSE TRUE 432187.8089 393400.7439 418016.1818 379858.5965 289830.0979 443722.5515 437045.9165 459629.8551 277379.6847 1.558109093 1.418275258 1.507018015 1.369453559 1.044885815 1.599693763 1.57562338 1.657042244 1 18.0815026 4.719354453 1.406841569 1.423706408 1.61253787 0.03750965 0.221492078 5.045961166 9.279858044 0.058227269 1.34051004 52402.79522 -4.719354453 0.188831462 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.999)PS(0.001)KTQATLKPK;GTDTQTPAVLS(0.999)PS(0.001)KTQATLKPK 171.08 3.36E-12 1376360000 1021910 1171540 978710 1091340 536125 1216420 1108400 1274280 615680 TRUE FALSE 973606.3395 1290921.258 1023584.822 981636.4298 629625.0303 1174295.07 939293.2228 1162697.288 711156.5099 1.369046512 1.81524213 1.439324266 1.380338106 0.885353676 1.651247024 1.320796772 1.634938683 1 19.43980757 3.483343854 5.063132704 1.335246523 1.598553383 0.161044244 0.259711224 0.296914066 22.52132017 0.066269085 0.096938024 3043.293606 -3.483343854 0.263306859 GTEAPAVVT(ph)EEEDDDEETAPPVIAPRPDHTK ddPTM_SK-BR-3_Trastuzumab_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;GT(0.219)EAPAVVT(0.78)EEEDDDEET(0.001)APPVIAPRPDHTK 191.34 1.35E-18 322003000 411962 366016 369999 424784 324982 389487 448511 450988 340607 TRUE FALSE 392489.3727 403313.4465 386963.8201 382083.9053 381658.7579 375998.9675 380082.4095 411497.0999 393426.594 0.997617799 1.025130107 0.983573114 0.971169492 0.970088865 0.955702978 0.966082149 1.045931074 1 18.58573496 3.631086188 6.122396009 0.979246349 1.011231108 0.130233095 0.0261169 0.324615231 15.78530632 0.006659767 0.010387298 4276.477469 -3.631086188 0.031984758 GTEAS(ph)PPQNNSGSSSPVFTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEAS(1)PPQNNSGSSSPVFTFR;GT(0.002)EAS(0.998)PPQNNSGSSSPVFTFR 302.61 3.24E-55 268716000 130149 109338 142385 137886 148338 132362 160278 147389 203909 TRUE FALSE 123997.1147 120479.6665 148913.4931 124025.4373 174208.1002 127778.2708 135824.6474 134482.8378 235530.1663 0.52645959 0.511525417 0.63224807 0.52657984 0.739642412 0.542513398 0.576676226 0.57097925 1 17.84555232 -5 0.321633959 5.084899921 0.554322929 0.794756404 0.067222008 137.845624 1.215981205 383.609676 0.056227643 1.00E-05 5 -4.530576992 GTEASPPQNNSGSS(ph)SPVFTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGS(0.002)S(0.917)S(0.081)PVFTFR;GTEASPPQNNSGSS(0.5)S(0.5)PVFTFR 388.98 4.05E-131 279710000 211897 202940 189888 213424 224004 204452 244710 216680 300010 TRUE FALSE 201881.0487 223619.8167 198594.5526 191970.214 263070.2267 197371.776 207374.9951 197706.3505 346534.0186 0.582572094 0.645304082 0.573088188 0.553972204 0.759146902 0.569559597 0.598426082 0.570525085 1 18.40263746 -1.751835818 2.505342969 1.093606926 0.608206969 0.811280234 0.059628627 4331501.691 3142415.888 2506994.802 0.013534084 0.017707783 1.751835818 -0.485399958 GTEASPPQNNSGSSS(ph)PVFTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGSS(0.004)S(0.996)PVFTFR;GTEASPPQNNSGSS(0.267)S(0.733)PVFTFR 420.35 1.03E-173 174703000 159220 130402 147288 175724 181681 149969 192375 171513 224800 TRUE FALSE 151693.9861 143690.1121 154041.3005 158059.8897 213366.1089 144775.5359 163024.6605 156494.4125 259660.8359 0.584200485 0.553376144 0.593240409 0.60871671 0.821710783 0.557556304 0.627836924 0.602687779 1 17.98626891 -5 0.298827473 4.177000883 0.593001499 0.711769553 0.076084216 143.089058 1.325867079 284.7047964 0.07423954 1.00E-05 5 -3.583999384 GTEDELDKYSEALKDAQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 162.85 1.51E-11 78042000 183140 208600 159040 220580 76821 211190 160810 221370 74967 FALSE TRUE 174483.3351 229856.5772 166332.1413 198406.8793 90218.55808 203876.4373 136275.481 201985.6692 86592.49948 2.014993633 2.654462898 1.92086084 2.291270959 1.041874973 2.354435298 1.573756178 2.332600057 1 16.40195445 GTEDFIVESLDASFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTEDFIVESLDASFR 15 0 C9J3L8;C9J5W0;A0A3B3IRT8;E9PAL7;C9IZQ1;P43307-2;P43307 C9J3L8 SSR1 Translocon-associated protein subunit alpha 0 123.8 0.0015047 0 10558 7377.3 9895.8 10349 12413 8018.4 14458 10370 10528 FALSE TRUE 10058.94426 8129.055257 10349.53222 9308.698858 14577.82327 7740.720797 12252.16656 9461.947825 12160.62847 0.82717306 0.668473285 0.851068861 0.765478436 1.198772194 0.636539535 1.007527414 0.778080495 1 13.56993017 2.896934546 20.99943893 0.915032377 0.769197757 0.179993327 0.153777915 15.64295167 3176.243546 0.041510775 0.044028878 788.7412352 -2.896934546 -0.14583462 GTEDITSPHGIPLDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GTEDITSPHGIPLDLLDR 18 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;;; 184.01 6.04E-14 981687000 1321459 1115901 1190641 1374739 1645132 1165069 1562408 1333331 1567303 FALSE TRUE 1258996.252 1229612.581 1245233.068 1236547.624 1932042.5 1124722.368 1324033.964 1216577.469 1810352.345 0.695442661 0.679211748 0.687840172 0.683042518 1.067219045 0.621272633 0.731368105 0.672011431 1 20.78783908 -2.08286834 2.53780616 1.444586163 0.726088234 0.321667636 0.12327076 9289318.049 3200979.292 23892757.11 0.028922408 0.008262884 2.08286834 -0.718497928 GTEKRES(ph)PSPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTEKRESPSPAPKPR 15 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 GTEKRES(0.994)PS(0.006)PAPKPR;GTEKRES(0.979)PS(0.021)PAPKPR;GT(0.007)EKRES(0.987)PS(0.006)PAPKPR 112.82 0.0040558 387823000 467340 180502 585670 300037 456630 510140 888200 636890 734890 TRUE FALSE 445249.7644 198895.359 612523.5488 269876.7107 536266.1274 492473.7239 752688.7771 581120.5352 848852.9879 0.524531068 0.234310725 0.721589672 0.317931037 0.631753831 0.58016374 0.886712762 0.684595028 1 19.69515519 1.852174428 0.593004669 0.973763338 0.399092743 0.573641974 0.15093142 0.46668071 0.342841248 0.128269285 0.076891568 71.1499219 -1.852174428 -0.574670595 GTEPS(ph)PGGTPQPS(ph)RPVSPAGPPEGVPEEAQPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 2 GT(0.033)EPS(0.773)PGGT(0.236)PQPS(0.741)RPVS(0.216)PAGPPEGVPEEAQPPR 77.077 0.0011817 200640000 101860 87586 91424 110640 89541 99603 120060 110230 98771 TRUE FALSE 97045.27967 96511.11298 95615.88083 99518.257 105156.9221 96153.72314 101742.6419 100577.6768 114087.9022 0.850618495 0.845936432 0.838089569 0.872294565 0.921718429 0.842803849 0.89179168 0.881580561 1 16.79978629 -5 0.169361572 1.529453689 0.833272431 0.783466156 0.022710053 56.6118397 0.533140317 10.03126297 0.077941344 1.00E-05 5 -0.696181258 GTEPS(ph)PGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 2 GT(0.171)EPS(0.785)PGGT(0.045)PQPS(0.085)RPVS(0.914)PAGPPEGVPEEAQPPR 113.75 2.86E-06 242590000 89203 86780 89520 94611 111610 91155 106860 92443 106710 TRUE FALSE 84986.55097 95622.98066 93624.58055 85100.52253 131074.7487 87998.27949 90556.54438 84348.20085 123258.0418 0.689501064 0.775795066 0.759581924 0.690425722 1.063417419 0.713935401 0.73469076 0.684322091 1 16.91132225 -2.301081335 2.272097416 2.145972673 0.762845854 0.309446093 0.110803462 6361227.455 980820.6799 37402715.69 0.025627805 0.004999409 2.301081335 -1.383126819 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GTEPSPGGTPQPS(0.001)RPVS(0.999)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.008)RPVS(0.992)PAGPPEGVPEEAQPPR 330.03 2.63E-117 311720000 78029 71357 79441 84387 89903 82477 98168 92480 98948 TRUE FALSE 74340.72381 78628.35943 83083.44843 75904.25844 105582.0547 79620.80081 83190.66862 84381.96093 114292.3505 0.650443564 0.687958197 0.726937963 0.664123698 0.923789338 0.696641555 0.727876085 0.738299288 1 16.80236932 -5 0.168915438 2.064603302 0.654311102 0.595376319 0.072637623 90.12991301 0.847906957 32.24070958 0.253551581 1.00E-05 5 -1.4102922 GTEVQVDDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 159.44 4.59E-05 825380000 726787 765276 672668 816220 555982 736750 759990 798460 615203 FALSE TRUE 692433.2189 843258.4944 703510.4932 734172.0149 652945.0848 711236.1628 644039.5673 728542.6095 710605.5392 0.974426993 1.186675938 0.990015493 1.033163935 0.918857297 1.000887445 0.906325003 1.025241951 1 19.43868941 3.285955648 2.114599116 0.965139731 1.077970263 0.231419525 0.066994901 0.324262718 2.972139566 0.019284108 0.027262825 1931.771026 -3.285955648 0.112830532 GTFHDDRDDGVDYWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTFHDDRDDGVDYWAK 16 1 E9PK91;Q9NYF8-3;H0YF63 E9PK91 BCLAF1 Bcl-2-associated transcription factor 1 0 96.303 0.0020782 618970000 629190 545510 536340 660180 521730 618650 710890 655520 509070 FALSE TRUE 599449.4356 601098.0892 560931.7195 593817.4521 612719.5468 597225.9954 602430.6741 598119.1937 588013.9756 1.019447599 1.022251365 0.953942836 1.009869623 1.042015279 1.015666328 1.024517612 1.017185337 1 19.16549092 2.989116537 24.99822933 1.021741606 1.003524201 0.160141135 0.021112574 1067.469106 2451880.248 0.006344638 0.007104038 975.251297 -2.989116537 -0.018217404 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR 34 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ;; 266.81 2.42E-60 181546000 187678 156277.6 181529 238708 284038 197311 262542 197731 147723 FALSE TRUE 178806.8329 172202.4651 189852.2842 214712.6183 333574.1373 190478.0706 222486.396 180416.6254 170631.1284 1.047914496 1.009208969 1.112647417 1.258343776 1.954943043 1.116314898 1.303902741 1.057348839 1 17.38052134 3.288523621 3.714267269 1.318006352 1.035645541 0.137918865 0.262294398 0.362769457 10.26287681 0.072469033 0.097342237 1943.22738 -3.288523621 -0.282360811 GTGQS(ph)DDSDIWDDTALIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 GT(0.005)GQS(0.995)DDSDIWDDTALIK 273.78 5.35E-39 76397000 159540 142490 138920 166160 107830 144170 158040 171960 149020 TRUE FALSE 151998.8604 157009.893 145289.6194 149457.2811 126635.5179 139177.3568 133928.0954 156902.2708 172129.2605 0.883050679 0.912162712 0.844072757 0.868285152 0.735700121 0.808563032 0.778066989 0.911537471 1 17.39313284 3.474336546 2.157232939 0.826495123 0.897168431 0.002226535 0.074927352 0.575660232 5.364645875 0.020199743 0.03253674 2980.825456 -3.474336546 0.070673308 GTHDRDPS(ph)EKPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTHDRDPSEKPPR 13 2 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 1 GTHDRDPS(1)EKPPR 101.15 0.001083 53429000 84206 67740 73848 85026 65427 89185 104730 88342 78812 TRUE FALSE 80225.74926 74642.78301 77234.00385 76479.02494 76837.44809 86096.50109 88751.515 80606.30615 91033.76244 0.881274673 0.81994615 0.848410543 0.840117149 0.844054404 0.945764503 0.974929659 0.885455066 1 16.47411409 2.225992818 6.576290922 0.952590586 0.845835535 0.725214871 0.032055968 0.072721516 13.06307691 0.010768818 0.00826051 168.2646236 -2.225992818 -0.106755051 GTHDRDPSEKPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTHDRDPSEKPPR 13 2 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 145.81 2.52E-05 52310000 48250 42464 46664 48625 44507 49077 59162 47867 45351 FALSE TRUE 45969.31812 46791.12988 48803.59056 43737.12262 52269.00671 47377.45118 50135.75032 43675.51172 52383.80146 0.877548342 0.893236622 0.931654237 0.834936018 0.997808583 0.90442942 0.957084994 0.833759874 1 15.67683314 2.746125921 24.9987751 0.934922513 0.887699251 0.206650971 0.052381429 984.9740929 3254748.367 0.014343121 0.014963238 557.3473243 -2.746125921 -0.047223262 GTHTGVWVGVSGSETSEALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 271.92 1.13E-44 4406000000 1615470 1635370 1484640 1946880 1837080 1621680 1820270 1720610 1579180 FALSE TRUE 1539109.935 1802016.062 1552712.213 1751175.924 2157466.17 1565520.815 1542554.38 1569944.267 1824071.169 0.843777349 0.987908856 0.851234447 0.960037061 1.182775216 0.858256433 0.845665677 0.860681476 1 20.79873059 -2.049317202 8.854344529 1.211224291 0.922719066 0.049689049 0.104644746 0.083069094 0.000462681 0.019289615 0.023457795 0.008926533 2.049317202 -0.288505225 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR 36 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 ;;; 302.08 3.09E-92 397797000 205815 173656 221217 217403 233259 209863 242116 228134 239392 FALSE TRUE 196086.5328 191351.7438 231360.0183 195549.2374 273939.2957 202595.3917 205176.7574 208157.3775 276515.6887 0.709133481 0.692010442 0.836697619 0.707190389 0.990682652 0.732672322 0.742007654 0.752786862 1 18.07700181 -5 0.214101238 2.128842999 0.731055609 0.392560637 0.088564172 152.1484633 1.518900931 74.25138031 0.174112607 1.00E-05 5 -1.39778739 GTINFLHADCDKFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTINFLHADCDKFR 14 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 101.01 0.00093592 649160000 1767010 1468660 1244190 1647470 2222500 1503490 2359500 1801130 2128500 FALSE TRUE 1683486.939 1618318.124 1301237.342 1481863.186 2610103.296 1451423.764 1999514.94 1643413.509 2458576.909 0.684740401 0.658233679 0.529264445 0.602732085 1.061631746 0.590351174 0.813281428 0.66844096 1 21.22939206 GTITDAPGFDPLRDAEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTITDAPGFDPLRDAEVLR 19 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ;; 87.352 0.0024901 205169000 101921 74044 79947 117868 128222 84380 115058 98578 107294 FALSE TRUE 97103.39632 81589.16778 83612.64903 106019.6847 150583.8762 81457.89944 97503.78891 89945.98773 123932.6055 0.783517751 0.658334967 0.674662238 0.855462404 1.215046481 0.657275776 0.786748479 0.725765325 1 16.91919627 3.230068525 23.9651117 0.858578535 0.706541808 0.200382181 0.156228591 192.2636506 542577.1267 0.044542177 0.05410774 1698.511631 -3.230068525 -0.152036727 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTLDEEDEEADSDTDDIDHR 20 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 GTLDEEDEEADS(1)DTDDIDHR;GTLDEEDEEADS(1)DTDDIDHR 324.61 2.19E-67 9263800000 4674000 4919300 4490000 5246300 4744500 4573400 4813100 4851500 4060700 TRUE FALSE 4453069.283 5420582.263 4695870.941 4718931.957 5571939.298 4415022.011 4078773.196 4426676.941 4690412.617 0.949398197 1.155672796 1.001163719 1.006080348 1.187942246 0.941286486 0.86959795 0.943771327 1 22.16128341 2.028779095 24.93476007 0.918836004 1.058460874 0.370615493 0.077295023 176.6919418 153088.5401 0.026963638 0.019913668 106.8511239 -2.028779095 0.13962487 GTLS(ph)DSEIETNSATSTIFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.023)LS(0.977)DSEIETNSATSTIFGK;GT(0.014)LS(0.984)DS(0.002)EIETNSATSTIFGK;GT(0.001)LS(0.999)DSEIETNSATSTIFGK;GT(0.001)LS(0.998)DS(0.002)EIETNSATSTIFGK;GT(0.008)LS(0.724)DS(0.267)EIETNSATSTIFGK;GT(0.024)LS(0.962)DS(0.013)EIETNSATSTIFGK 340.8 2.54E-80 851054000 1161359 1013788 1115359 1271188 997025 1173939 1326643 1231501 1197397 TRUE FALSE 1106463.862 1117094.15 1166499.313 1143405.767 1170905.844 1133285.198 1124239.245 1123664.244 1383083.211 0.799998043 0.807683978 0.843405013 0.826707864 0.846591033 0.819390467 0.812850041 0.812434302 1 20.39945653 -1.016833721 4.62204639 1.00000515 0.819670693 0.935265524 0.014784392 8.43E-07 1.79E-07 0.015389061 0.003627133 0.096198052 1.016833721 -0.180334457 GTLTLCPYHSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GTLTLCPYHSDR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;;;; 200.82 1.56E-07 2226750000 3182330 2526380 2702100 3109070 3625590 2868070 3606310 3153980 3244460 FALSE TRUE 3031907.568 2783820.994 2825993.958 2796540.377 4257891.748 2768748.017 3056101.175 2877800.791 3747594.286 0.809027695 0.742828807 0.75408215 0.74622282 1.136166677 0.738806766 0.815483465 0.767906174 1 21.83753334 GTPCERPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTPCERPVR 9 1 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;C9JPY0;C9JVS0;F8WAZ5 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ;; 150.08 7.85E-05 273383000 199098 172164 147120 189950 220189 152746 204711 176567 240060 FALSE TRUE 189687.0321 189707.7073 153865.5975 170855.8651 258589.8919 147456.3677 173478.5772 161105.8574 277287.2787 0.684081264 0.684155826 0.554895984 0.616169144 0.93257034 0.531781942 0.625627609 0.581007027 1 18.08102191 -1.109667293 4.840358752 1.000017002 0.653246523 0.491693204 0.11141041 1.91E-05 3.51E-06 0.100620149 0.023715235 0.077684202 1.109667293 -0.346770479 GTPGPPPAHGAALQPHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 215.23 5.57E-19 520990000 402960 333160 382520 414340 444180 359180 461120 410490 242640 FALSE TRUE 383912.8794 367109.3828 400058.9204 372689.756 521644.8514 346741.5065 390767.675 374545.3195 280267.372 1.369809396 1.309854159 1.427418816 1.32976505 1.861240028 1.237181139 1.394267453 1.336385741 1 18.09644427 0.520941387 1.148691647 1.000040509 1.413515232 0.381430096 0.166974741 1.888582863 3.398732356 0.149991837 0.045986535 3.318496673 -0.520941387 0.413474724 GTPGS(ph)PSGTQEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTPGSPSGTQEPR 13 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 GT(0.024)PGS(0.942)PS(0.023)GT(0.011)QEPR;GT(0.035)PGS(0.959)PS(0.006)GTQEPR;GT(0.001)PGS(0.994)PS(0.002)GT(0.003)QEPR 122.66 0.00015941 0 148370 150285 159961 168286 152042 155854 170681 146249 169865 TRUE FALSE 141356.8441 165599.2124 167295.3701 151369.5716 178558.0767 150456.7369 144640.4787 133442.6622 196206.7966 0.720448254 0.844003445 0.85264819 0.771479756 0.910050415 0.766827345 0.737183834 0.680112333 1 17.58201549 -0.118563247 7.968500445 1.000000243 0.787459405 0.495302126 0.06806689 0 0 0.06467581 0.015244235 0.761091291 0.118563247 -0.212540838 GTPKPPGPPAQPPGPPNAS(ph)SNPDLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTPKPPGPPAQPPGPPNASSNPDLRR 26 2 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.565)S(0.435)NPDLRR 102.58 0.0019748 340370000 65862 55050 62550 66400 66571 67570 89883 83454 78880 TRUE FALSE 62748.83379 60659.65759 65417.97937 59725.34585 78180.96132 65230.03396 76169.69754 76146.32534 91112.30754 0.688697669 0.665767987 0.717992784 0.655513481 0.858072454 0.715929996 0.835997897 0.835741377 1 16.47535833 1.120769487 0.331611434 1.0306069 0.649913243 0.791186506 0.049435404 0.602438345 0.208776148 0.086182016 0.054230682 13.20594508 -1.120769487 -0.380693657 GTPS(ph)QSPVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.003)PS(0.671)QS(0.326)PVVGR 79.492 0.028319 44189000 42876 38886 38365 39922 44647 35752 50136 41693 47223 TRUE FALSE 40849.33645 42848.52761 40124.0732 35908.96471 52433.42266 34513.89928 42486.83239 38042.13989 54546.10166 0.748895617 0.78554702 0.735599282 0.65832321 0.961268011 0.632747313 0.77891602 0.697430957 1 15.73518847 -1.144599539 4.999108619 1.000013084 0.752839336 0.435772008 0.089399572 1.12E-05 1.92E-06 0.074672265 0.01759949 0.071680407 1.144599539 -0.247173748 GTPSQS(ph)PVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.004)QS(0.996)PVVGR;GTPS(0.004)QS(0.996)PVVGR;GTPS(0.001)QS(0.999)PVVGR;GTPS(0.006)QS(0.994)PVVGR;GTPSQS(1)PVVGR;GTPS(0.024)QS(0.976)PVVGR;GT(0.001)PS(0.194)QS(0.805)PVVGR;GTPS(0.033)QS(0.967)PVVGR;GT(0.002)PS(0.16)QS(0.838)PVVGR 228.87 3.10E-12 6431730000 2650528 2266277 2456192 2725887 2784066 2389359 2891088 2659257 2946478 TRUE FALSE 2525242.794 2497213.203 2568810.833 2451875.66 3269606.229 2306614.899 2449999.427 2426398.359 3403402.76 0.741975891 0.733740136 0.754777208 0.720418896 0.960687424 0.677737859 0.719867615 0.712933065 1 21.69854646 -1.53889536 2.740761233 1.013609294 0.750104049 0.50540402 0.076822335 9309355.584 9367585.959 935087.4491 0.017900431 0.028913765 1.53889536 -0.263505245 GTPTAENPEY(ph)LGLDVPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 GTPTAENPEY(1)LGLDVPV 92.856 0.033035 41233000 112890 100990 109710 154140 203390 77021 83073 80827 83542 TRUE FALSE 107553.9134 111280.9958 114740.312 138645.5544 238861.1516 74353.74346 70398.68811 73749.35939 96497.26669 1.114579896 1.153203605 1.189052457 1.436782192 2.475315206 0.770526938 0.729540748 0.764263714 1 16.55820046 GTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.005)PT(0.192)S(0.192)HT(0.192)ANT(0.192)S(0.192)PRPVS(0.036)GMER;GTQEVAPPTPLT(0.002)PT(0.48)S(0.48)HT(0.011)ANT(0.012)S(0.015)PRPVSGMER;GTQEVAPPTPLT(0.001)PT(0.284)S(0.284)HT(0.284)ANT(0.073)S(0.073)PRPVSGMER;GTQEVAPPTPLT(0.011)PT(0.297)S(0.297)HT(0.297)ANT(0.047)S(0.047)PRPVS(0.002)GMER 129.07 1.54E-05 521753000 197742.2 181311.6 199832.7 217166.1 196147 203706.5 219277.1 184783.2 178694.9 TRUE FALSE 188395.3181 199787.4582 208995.227 195336.151 230354.9747 196652.0928 185822.3511 168602.6034 206405.9924 0.912741514 0.967934389 1.012544377 0.946368605 1.116028522 0.952744106 0.900275951 0.816849363 1 17.65512533 -0.892337558 4.498594793 1.000000473 0.954458173 0.03500792 0.076985677 1.93907E+12 4.76833E+11 10096518.72 0.017767409 0.128133427 0.892337558 -0.0455423 GTQEVAPPTPLTPTS(ph)HTANTSPRPVSGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.063)S(0.297)HT(0.297)ANT(0.297)S(0.047)PRPVS(0.001)GMER 136.39 1.84E-06 265890000 26083 25106 19860 26700 23059 16833 27991 24265 24398 TRUE FALSE 24850.10828 27664.32994 20770.60064 24016.06527 27080.4823 16250.06899 23720.45886 22140.22796 28181.51723 0.881787452 0.981647997 0.737029184 0.852192062 0.960930601 0.576621509 0.84170269 0.785629382 1 14.78246166 3.74501639 24.97751325 0.809408766 0.931717725 0.121649052 0.118854456 817.5720203 3163191.423 0.028062312 0.049085373 5559.252377 -3.74501639 0.122308958 GTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.003)PT(0.1)S(0.1)HT(0.271)ANT(0.208)S(0.047)PRPVS(0.271)GMER;GTQEVAPPTPLT(0.003)PT(0.101)S(0.101)HT(0.232)ANT(0.232)S(0.232)PRPVS(0.101)GMER;GTQEVAPPTPLTPT(0.02)S(0.077)HT(0.298)ANT(0.298)S(0.298)PRPVS(0.007)GMER 128.82 1.58E-05 510430000 111546 111427 115768 132962 107630 131660 122335 123044 104149 TRUE FALSE 106273.4416 122781.538 121076.0773 119596.4071 126400.6379 127100.5812 103670.5489 112269.6151 120299.895 0.883404276 1.020628804 1.006452061 0.994152216 1.050712787 1.056531107 0.861767576 0.933247823 1 16.87627586 -0.697476524 5.81433595 1.000000001 0.973331044 0.011878838 0.065674011 9.71E-10 1.67E-10 0.065135505 0.015352585 0.200688957 0.697476524 -0.026668957 GTS(ph)AEQDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTSAEQDNR 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;M0R1E7;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 GT(0.008)S(0.992)AEQDNR 96.067 0.0079918 55037000 161930 127170 135450 176930 142610 144820 160000 150110 173890 TRUE FALSE 154275.8898 140128.7676 141660.5165 159144.6603 167481.1388 139804.8471 135589.0614 136965.5726 200855.9731 0.768092118 0.697657956 0.705284061 0.792332226 0.833836984 0.696045255 0.675056157 0.681909383 1 17.61580184 -1.369992031 3.457092433 1.001795722 0.728971169 0.725344364 0.051950044 2593183.801 1382635.983 33526.0939 0.012722797 0.042658735 1.369992031 -0.272824554 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.007)S(0.993)PRPPEGGLGYSQLGDDDLK;GT(0.267)S(0.733)PRPPEGGLGYSQLGDDDLK;GT(0.116)S(0.884)PRPPEGGLGYSQLGDDDLK 169.13 5.23E-12 551814000 739770 907430 669830 898210 448580 811000 699610 784220 413490 TRUE FALSE 704802.5382 999898.1487 700542.3681 807920.2243 526812.21 782914.8666 592871.6453 715549.5394 477611.9174 1.475680385 2.093536849 1.466760653 1.691583051 1.103013118 1.639228081 1.241325067 1.49818192 1 18.86547931 1.945923778 0.286778182 0.980738226 1.8697439 0.371460269 0.247228125 1.607373674 0.434513926 0.415186668 0.526595854 88.29249266 -1.945923778 0.889005674 GTS(ph)PSSSSRPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.001)S(0.357)PS(0.027)S(0.185)S(0.185)S(0.245)RPQR;GT(0.233)S(0.767)PSSSSRPQR;GT(0.12)S(0.875)PS(0.004)SSSRPQR;GT(0.201)S(0.792)PS(0.007)SSSRPQR 92.939 0.0047433 1637630000 1056220 1046620 1056790 1193060 1177980 1134390 1245280 1121410 1308140 TRUE FALSE 1006294.574 1153271.768 1105244.867 1073131.342 1383419.339 1095105.79 1055289.665 1023213.395 1510999.67 0.665979347 0.76325084 0.731465988 0.710212824 0.915565613 0.72475581 0.69840496 0.677176452 1 20.52707191 -1.701570143 2.850802535 1.037310517 0.735348257 0.587327649 0.069583462 20782407.55 19151278.17 5579839.772 0.016140404 0.019880617 1.701570143 -0.30196226 GTS(ph)SPDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.035)S(0.482)S(0.482)PDYR;GT(0.071)S(0.859)S(0.071)PDYR;GT(0.071)S(0.464)S(0.464)PDYR 114.89 0.0026941 305445000 818060 821700 826610 928340 888990 854140 948870 915830 982260 TRUE FALSE 779391.925 905432.1642 864510.8861 835021.4995 1044029.575 824560.9176 804102.4543 835635.0701 1134583.864 0.68694078 0.798030179 0.761962966 0.735971598 0.920187222 0.726751846 0.708720157 0.736512387 1 20.11373182 -2.345986016 2.256438925 2.463145673 0.757590372 0.57943165 0.064407182 3587585.842 465937.0119 26772107.06 0.015032473 0.004508312 2.345986016 -1.705555301 GTSPSSSS(ph)RPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GTSPSSS(0.005)S(0.994)RPQR;GTS(0.001)PS(0.048)S(0.048)S(0.048)S(0.855)RPQR;GTS(0.002)PS(0.004)S(0.004)S(0.074)S(0.916)RPQR 151.68 0.00018194 765330000 1049930 1048150 1057340 1216680 1233080 1146710 1290220 1145700 1363270 TRUE FALSE 1000301.89 1154957.677 1105820.085 1094377.015 1448128.762 1106999.145 1093373.242 1045376.434 1574678.949 0.6352418 0.73345597 0.702251139 0.694984216 0.919634293 0.702999901 0.69434677 0.663866393 1 20.58662629 -1.917617159 2.560782448 1.17397862 0.717178593 0.574363028 0.076191893 8371027.133 4612730.362 8738644.622 0.017854569 0.01208879 1.917617159 -0.456800027 GTSYQSPHGIPIDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTSYQSPHGIPIDLLDR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 71.872 0.029593 245620000 225140 218300 226460 266220 254360 194220 244140 226750 245750 FALSE TRUE 214498.0784 240545.0182 236843.415 239459.0598 298720.3035 187494.1127 206891.9591 206894.5679 283859.6549 0.755648345 0.847408267 0.834368009 0.843582579 1.052352098 0.660516947 0.728852993 0.728862184 1 18.11481829 -1.575145339 8.942285181 1.00003109 0.80420851 0.249093773 0.105547383 6.48E-05 3.08E-06 0.101176884 0.023843844 0.026598348 1.575145339 -0.19582258 GTTITLVLKEEASDYLELDTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GTTITLVLKEEASDYLELDTIK 22 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;; 308.37 3.63E-67 605081000 1280437 911252 1299027 1221678 930092 1336453 1661788 1481030 1102723 FALSE TRUE 1219913.281 1004109.615 1358588.673 1098872.606 1092299.75 1290171.298 1408251.72 1351343.162 1273727.651 0.957750489 0.788323637 1.06662415 0.862721796 0.857561465 1.012909861 1.105614468 1.060935719 1 20.2806254 2.07779854 4.843790616 1.065715274 0.900999582 0.449700428 0.076619496 0.161513799 6.932851321 0.028291839 0.0202921 119.6185518 -2.07779854 -0.164715692 GTVGEPTYDAEFQHFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 255.16 4.65E-27 827581000 799205 846749 676392 894176 855829 772463 825409 884402 789089 FALSE TRUE 761428.1635 933033.6858 707405.2422 804291.7297 1005085.307 745712.4126 699477.6974 806959.0724 911456.892 0.835396792 1.023672863 0.776125836 0.882424322 1.102723909 0.818154341 0.767428173 0.885350782 1 19.7978149 GTVIIIANHGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTVIIIANHGDR 12 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 125.53 0.00030366 325320000 455280 560970 423280 550310 480340 466720 468410 477600 394600 FALSE TRUE 433759.8167 618133.4808 442687.8067 494991.7933 564111.1439 450557.3694 396945.4516 435778.8121 455792.5527 0.951660606 1.35617284 0.971248442 1.086002372 1.237648884 0.98851411 0.870890604 0.956090242 1 18.79801783 2.053181503 7.05015749 0.928260493 1.128478811 0.322879757 0.120560232 0.211188904 22.53515285 0.04349413 0.03188127 113.0268185 -2.053181503 0.200218318 GTVLLADNVICPGAPDFLAHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTVLLADNVICPGAPDFLAHVR 22 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 204.31 1.18E-22 865510000 838250 817390 702440 916490 878950 727400 858350 811220 830490 FALSE TRUE 798627.5838 900682.9703 734647.5688 824362.684 1032238.602 702209.9556 727392.9428 740185.2763 959278.1476 0.832529737 0.938917427 0.765833737 0.859357305 1.076057663 0.732019131 0.758271149 0.771606523 1 19.87158967 GTVMYVGLTDFKPGYWIGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GTVMYVGLTDFKPGYWIGVR 20 1 K7EP07;Q99426-2;Q99426 K7EP07 TBCB Tubulin-folding cofactor B 0 135.27 6.82E-06 57518000 107510 115730 89683 103310 72529 103780 118760 104350 81381 FALSE TRUE 102428.2154 127523.0186 93795.05426 92925.08252 85178.03464 100186.0726 100640.9808 95212.56081 94001.14984 1.089648537 1.356611263 0.997807521 0.988552615 0.90613822 1.065796246 1.070635636 1.012887193 1 16.52039078 3.716122634 24.8551322 1.011362545 1.223129901 0.575226452 0.077472941 454.7947367 503787.8497 0.020480358 0.031753471 5201.428508 -3.716122634 0.211767356 GTVQALHATGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GTVQALHATGAR 12 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;;;; 175.21 2.83E-05 2370270000 2050620 1736500 1864780 1969420 3065670 1687160 2287030 2032310 2841490 FALSE TRUE 1953691.257 1913451.324 1950282.008 1771450.16 3600321.877 1628733.226 1938101.569 1854350.162 3282133.757 0.595250347 0.58299005 0.594211617 0.539725158 1.096945507 0.496242185 0.590500483 0.564983118 1 21.6462026 -2.119509826 2.295186087 1.70147345 0.627042025 0.319722178 0.168245139 9189700.946 2673587.381 33553553.38 0.037783518 0.007594342 2.119509826 -1.074431426 GTVRPANDFNPDADAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GTVRPANDFNPDADAK 16 1 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;; 161.99 7.51E-09 1499200000 2010166 1718176 1520119 3079940 1915832 2189540 1962320 1783406 1215071 FALSE TRUE 1915149.437 1893260.088 1589817.96 2770338.58 2249952.494 2113715.681 1662932.044 1627241.516 1403498.005 1.364554442 1.348958161 1.132753986 1.973881381 1.60310345 1.506033976 1.184848171 1.159418475 1 20.42059558 1.628232848 3.485644862 1.1013535 1.472363165 0.398199804 0.21780321 0.224696704 6.445930726 0.136242956 0.059135916 42.48472862 -1.628232848 0.371009665 GTVTDFPGFDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;;;;; 254.24 9.73E-21 2759160000 4491380 3715400 3936280 4433760 4713460 3894890 4573850 4332670 4648830 FALSE TRUE 4279081.368 4094003.484 4116762.332 3988070.021 5535485.932 3760008.983 3876025.178 3953278.446 5369746.813 0.796886989 0.762420208 0.766658555 0.742692376 1.030865351 0.700220907 0.721826431 0.736213193 1 22.35642264 -2.36988236 2.206334959 2.446179093 0.779152787 0.353981341 0.092375761 3546529.893 437761.5015 25575787.75 0.02166235 0.004266951 2.36988236 -1.667026307 GTVTDFPGFDERADAETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GTVTDFPGFDERADAETLR 19 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;; 142.26 1.43E-07 172776000 199428 71729 201334 127687 325437 162773 341358 191158 457637 FALSE TRUE 190001.4337 79038.26665 210565.363 114851.6602 382193.1098 157136.1302 289277.5676 174419.1921 528605.0087 0.359439337 0.149522357 0.398341596 0.217273121 0.723022112 0.297265685 0.547247118 0.329961293 1 19.01183057 -4.999999999 0.156494276 3.338757059 0.186339888 0.612612016 0.157930547 79.06910086 0.719325635 57.27899212 0.631429064 1.00E-05 4.999999999 -3.152417171 GTWERPGGAAPLGYDFWYQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTWERPGGAAPLGYDFWYQPR 21 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 205.78 4.17E-22 8594800000 1291530 1084650 1089440 1278950 1313260 1080690 1390190 1339700 1511330 FALSE TRUE 1230481.936 1195177.068 1139391.902 1150387.516 1542292.128 1043265.434 1178090.983 1222388.766 1745699.338 0.704864755 0.684640844 0.652685074 0.658983762 0.883480961 0.597620342 0.674853314 0.700228693 1 20.73537367 0.917669263 18.70479595 1 0.691587683 0.62968344 0.073585852 1755.172945 398761.9334 0.065186261 0.016296565 8.273118846 -0.917669263 -0.308412317 GTWESHPETTELVVLQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTWESHPETTELVVLQGR 18 0 P36915;A0A140T8Y2;P36915-2 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 ; 153.72 3.12E-08 217900000 371290 321490 337250 389160 402850 338940 415480 366500 381180 FALSE TRUE 353739.8575 354250.1965 352713.2461 350040.8974 473106.9125 327202.4228 352090.8952 334407.3171 440291.4476 0.80342205 0.804581144 0.801090387 0.795020888 1.074531234 0.743149622 0.799676889 0.759513542 1 18.7480993 -2.278685794 2.274440303 1.771448725 0.820780666 0.268212099 0.092032593 5182108.129 892262.9174 20532000.85 0.020915881 0.00526398 2.278685794 -0.950668059 GTYFPTWEGLFWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTYFPTWEGLFWEK 14 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 158.4 1.18E-05 99795000 250817 207574 230060 267735 247372 230419 282149 278094 245527 FALSE TRUE 238961.3775 228726.0266 240608.4786 240821.7691 290513.5985 222439.5323 239101.988 253742.6151 283602.0732 0.842593902 0.806503366 0.848401691 0.849153768 1.024370503 0.784336764 0.843089704 0.894713541 1 18.11350855 -5 0.189909802 1.618275409 0.828249251 0.329233048 0.063816943 160.6935978 1.571317734 37.62961352 0.168069747 1.00E-05 5 -0.790026158 GTYLATFHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GTYLATFHQR 10 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 125.75 0.00040089 660010000 1179200 1011300 580960 721460 1235020 725700 1181910 940730 1026140 FALSE TRUE 1123461.553 1114352.62 607597.5906 648937.4701 1450407.097 700568.827 1001587.922 858354.6941 1185268.55 0.947854014 0.940168892 0.512624409 0.547502479 1.223694914 0.591063373 0.84503037 0.724185834 1 20.17678254 3.938085637 24.99996292 0.769838001 0.944976042 0.093238213 0.214543242 436.901193 176412.9315 0.051090867 0.092105434 8671.32845 -3.938085637 0.175138041 GTYVPSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 GTYVPS(0.001)S(0.997)PT(0.002)R;GTYVPS(0.004)S(0.988)PT(0.009)R;GTYVPS(0.001)S(0.999)PTR;GTYVPSS(0.995)PT(0.005)R;GTYVPSS(1)PTR;GTYVPS(0.011)S(0.985)PT(0.004)R;GTYVPS(0.002)S(0.971)PT(0.027)R;GTYVPS(0.026)S(0.972)PT(0.002)R 211.84 5.40E-08 7316400000 9471110 7585080 8348940 9516740 11176090 8392420 10199960 8539670 10325390 TRUE FALSE 9023429.4 8358008.276 8731747.157 8560099.215 13125196.56 8101788.391 8643768.767 7791891.223 11926598.75 0.756580278 0.700787245 0.73212383 0.717731802 1.100497873 0.679304181 0.724747177 0.65332048 1 23.50767933 -2.145196084 2.511151652 1.566533458 0.755332739 0.268919238 0.1252511 18673497.77 7673467.025 59747942.54 0.02936836 0.007158201 2.145196084 -0.811200718 GVAGAHGLLCLLSDHVDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVAGAHGLLCLLSDHVDKR 19 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 ; 208.26 1.13E-16 1288160000 726980 539930 649390 696380 656500 642910 805220 726640 377630 FALSE TRUE 692617.0961 594949.4808 679165.1738 626378.5594 770993.3921 620645.8655 682368.9001 663011.5494 436190.9317 1.587875964 1.363965726 1.557036436 1.436019215 1.767559424 1.42287659 1.564381216 1.520003056 1 18.73460025 -0.913291571 4.519758188 0.999994042 1.520352361 0.691741876 0.110566992 0.031911965 30138374.05 480.9228676 0.023420088 0.122097966 0.913291571 0.520358319 GVAPADS(ph)PEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GVAPADSPEAPR 12 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPR;GVAPADS(1)PEAPR;GVAPADS(1)PEAPR;GVAPADS(1)PEAPR;GVAPADS(1)PEAPR 165.58 6.52E-05 719740000 693734 656000 627871 760450 753620 634777 760120 676709 801000 TRUE FALSE 660942.5687 722847.1458 656659.5064 684008.1212 885051.0894 612794.5133 644149.7334 617452.7725 925214.9891 0.714366473 0.781274789 0.709737212 0.739296411 0.956589657 0.662326617 0.696216275 0.667361402 1 19.81942911 -2.096948683 2.299889293 1.431917711 0.741492156 0.484813144 0.083938508 5471887.017 1664599.85 12357188.32 0.019580336 0.007999288 2.096948683 -0.690425555 GVAPADS(ph)PEAPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR 239.75 4.92E-17 539100000 559350 496880 564590 571140 676080 526970 647760 557400 776360 TRUE FALSE 532910.634 547512.6369 590477.01 513727.9221 793988.1379 508720.8968 548932.3151 508591.101 896753.9437 0.594266284 0.610549461 0.658460455 0.572875007 0.885402449 0.567291508 0.612132591 0.567146768 1 19.77435266 -1.081514677 4.569996493 1.000023407 0.631182255 0.601381313 0.093752454 2.06E-05 4.14E-06 0.083626474 0.019709699 0.08288679 1.081514677 -0.368841152 GVCLIDEFDKMNDQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVCLIDEFDKMNDQDR 16 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 191.44 6.34E-10 147992000 307855 319122 315893 352150 257614 345649 364604 388451 287812 FALSE TRUE 293303.3043 351640.8946 330377.0065 316751.213 302541.8 333679.0885 308976.9634 354436.1711 332444.415 0.882262691 1.057743426 0.99378119 0.952794508 0.910052287 1.003713924 0.929409397 1.066151679 1 18.34275362 1.237221184 24.99985745 1.033075838 0.965104403 0.244483881 0.052070706 53.02605573 989518.8722 0.039844702 0.012053239 17.26717075 -1.237221184 -0.067971435 GVDDLDFFIGDEAIEKPTYATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVDDLDFFIGDEAIEKPTYATK 22 1 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 254.73 4.22E-37 681893000 1346510 1249169 1267243 1451409 937005 1363707 1513547 1557637 1090744 FALSE TRUE 1282863.141 1376460.741 1325347.345 1305510.61 1100418.375 1316481.485 1282627.607 1421242.047 1259891.009 1.018233428 1.092523664 1.051953967 1.036209165 0.873423469 1.044916961 1.01804648 1.128067457 1 20.2648675 -0.564521419 6.238783547 1.000002637 1.032728885 0.024100836 0.065827241 0 0 0.061150331 0.014413271 0.272570331 0.564521419 0.032726249 GVDLLLEGVQGES(ph)SPTRR ddPTM_SK-BR-3_Trastuzumab_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(0.017)RR 103.26 0.00033114 27073000 13283 15934 14979 16102 23154 10095 16489 15673 22071 TRUE FALSE 12655.13891 17557.69272 15665.80197 14483.39637 27192.05027 9745.407619 13973.30021 14300.58903 25493.65796 0.496403417 0.688708256 0.614498005 0.568117623 1.066620189 0.382267921 0.548108876 0.560946925 1 14.63785077 -1.941060556 2.530066375 1.275281546 0.611912641 0.313406092 0.178676839 23235706.01 11538756.57 37694331.3 0.040482992 0.011453532 1.941060556 -0.663368905 GVDLLLEGVQGESSPT(ph)RR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVDLLLEGVQGESSPTRR 18 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.272)S(0.272)PT(0.456)RR 60.602 0.03887 31124000 17984 20005 19597 17144 22301 17689 21598 18265 25355 TRUE FALSE 17133.93196 22043.53224 20495.54183 15420.65255 26190.28734 17076.42549 18302.82843 16665.61977 29286.9239 0.585036927 0.752674891 0.699818865 0.526537119 0.894265558 0.583073373 0.624948816 0.569046439 1 14.83796905 -1.748021171 3.537226614 1.043911878 0.658108559 0.505431571 0.107375294 17718466.79 9986121.819 6082620.097 0.022758332 0.017864005 1.748021171 -0.385803318 GVDLVLNSLAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GVDLVLNSLAEEK 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 ;; 178.1 3.46E-05 192098000 835240 928220 834640 932000 1079870 724010 829700 730330 889730 FALSE TRUE 795759.8605 1022806.673 872909.0696 838313.5893 1268198.986 698937.3522 703114.0265 666378.4335 1027704.784 0.774307829 0.995233932 0.849377256 0.815714398 1.234010978 0.680095454 0.684159534 0.648414256 1 19.97099447 GVDLVLNSLAEEKLQASVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVDLVLNSLAEEKLQASVR 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 ; 151.44 4.97E-10 11781000 39095 23309 54184 38095 49629 40829 75481 46234 72683 FALSE TRUE 37247.05683 25684.2136 56668.39 34265.61822 58284.28189 39415.08149 63964.98715 42185.50586 83954.30843 0.44365867 0.305930858 0.67499085 0.408146036 0.694238128 0.469482534 0.761902377 0.502481727 1 16.35731674 -4.999999933 0.079505087 2.637057433 0.025088872 0.58787026 0.130663725 147.3767351 0.830352125 42.09035159 3.990718587 1.00E-05 4.999999933 -2.611968561 GVEEEEEDGEMRE ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ;;; 293.8 2.64E-39 3186690000 2331410 1791699 1780632 2298210 2660700 1946626 2671690 2096610 2867320 FALSE TRUE 2221208.87 1974275.165 1862275.738 2067189.564 3124725.238 1879213.854 2264074.622 1913019.714 3311969.341 0.67066106 0.596103092 0.562286527 0.624157216 0.943464421 0.56740074 0.683603738 0.577607917 1 21.65925789 -1.430102131 2.959312694 1.007141482 0.652652892 0.490819436 0.111020138 22634783.14 26807822.54 1354034.369 0.02515724 0.037144787 1.430102131 -0.35448859 GVEFVHVYCVDNILVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVEFVHVYCVDNILVR 16 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 126.88 6.93E-05 86804000 125860 131970 132930 143120 133620 124730 142580 136570 124980 FALSE TRUE 119910.8472 145417.893 139024.972 128733.3057 156923.2857 120410.5688 120826.8023 124611.2068 144361.2601 0.830630372 1.007319366 0.963035179 0.891744126 1.087017982 0.834091977 0.836975254 0.863190074 1 17.13932412 GVEKPPHLAALILAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVEKPPHLAALILAR 15 1 Q8NFW8;Q8NFW8-2;F5H296 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 107.98 0.00067002 59403000 149720 125230 128800 152160 154070 138290 165170 148510 155710 FALSE TRUE 142643.0323 137991.0794 134705.6074 136864.5877 180939.7592 133500.9826 139970.2829 135505.6771 179856.7115 0.79309263 0.767227857 0.748960693 0.760964584 1.006021725 0.742263002 0.778232192 0.753409066 1 17.45648847 -2.267603539 2.165784302 1.789892035 0.792036276 0.414406399 0.077018974 3968675.521 626677.6225 15333680.8 0.019005421 0.005400034 2.267603539 -0.997855759 GVEPSPS(ph)PIKPGDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GVEPSPSPIKPGDIKR 16 2 Q92890;Q92890-1;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.002)PS(0.998)PIKPGDIKR;GVEPSPS(1)PIKPGDIKR;GVEPS(0.022)PS(0.978)PIKPGDIKR 218.69 6.83E-15 808050000 1656330 1661020 1696360 1897640 980570 1941710 2096200 2211590 1240360 TRUE FALSE 1578038.563 1830279.826 1774139.784 1706885.622 1151581.098 1874468.096 1776386.191 2017931.455 1432708.694 1.101437138 1.27749614 1.238311592 1.191369627 0.803778956 1.308338606 1.239879536 1.40847296 1 20.45031387 GVGDDQLGEESEERDDHLLPM ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVGDDQLGEESEERDDHLLPM 21 1 P20645;F5GX30;H0YF90 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ; 116.43 0.00011873 211940000 520600 499220 476680 607860 647300 537540 631700 575200 574510 FALSE TRUE 495992.2697 550091.0856 498536.2495 546756.7579 760188.9151 518924.855 535322.563 524832.4387 663602.0766 0.747424228 0.828947203 0.75125782 0.823922614 1.145549331 0.781981964 0.806692116 0.790884262 1 19.33995888 2.992170406 24.7604261 0.8867249 0.783734868 0.215083958 0.110955681 608.7281419 1925060.183 0.0323404 0.037078291 982.1332319 -2.992170406 -0.102990032 GVGFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVGFDR 6 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 114.67 0.058367 544190000 1009450 965140 957080 1088930 1179560 956760 1126940 1036570 1158950 FALSE TRUE 961735.299 1063488.863 1000963.065 979468.6876 1385274.891 923627.1613 955004.6053 945802.4356 1338674.047 0.718423802 0.794434512 0.747727251 0.731670783 1.034811195 0.689956725 0.713395922 0.706521829 1 20.35237329 -2.146175928 2.44459303 1.533637244 0.76565587 0.351427345 0.099408467 17704167.47 5200050.018 52256070.94 0.024696171 0.00714207 2.146175928 -0.767981375 GVGTDEACLIEILASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVGTDEACLIEILASR 16 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 185.59 3.81E-09 25942000 55904 51381 56925 64880 49871 65372 65169 60389 34972 FALSE TRUE 53261.52871 56616.78232 59535.06756 58358.13914 58568.48661 63108.15125 55226.27214 55101.01902 40395.27915 1.318508742 1.40156928 1.473812505 1.444677209 1.449884438 1.562265507 1.367146689 1.364046002 1 15.30189908 0.617195227 1.67868248 1.000276507 1.428110781 0.817616289 0.063661904 0.748448578 2.729671286 0.06398459 0.018164215 4.141858203 -0.617195227 0.427834274 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.44)PPAS(0.336)S(0.041)T(0.182)S(0.001)SSSLTNDVAK 296.61 7.27E-71 320700000 158210 171240 158950 180500 155100 190010 202050 162220 1088.8 TRUE FALSE 150731.7268 188689.5507 166238.0147 162355.7971 182149.3909 183429.9061 171223.5616 148015.1568 1257.645543 119.8523126 150.0339676 132.1819297 129.0950363 144.8336472 145.8518317 136.1461204 117.6922684 1 10.29650965 0.664444131 2.237614809 1.012012762 137.3415468 0.958784028 8.782825836 0.343933356 2.068141904 8.106459557 2.198045304 4.617895823 -0.664444131 136.329534 GVHPHIVEMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVHPHIVEMDR 11 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 ; 145.89 2.08E-05 125259000 71336 81075 65361 85239 80821 65230 73445 78456 4917.8 FALSE TRUE 67964.08865 89336.63467 68357.8665 76670.61378 94916.15681 62971.06874 62239.61634 71585.97672 5680.427307 11.96460847 15.7270976 12.03393034 13.49733209 16.70933394 11.08562179 10.95685465 12.60221685 1 12.47178374 -0.078820368 0.531050045 1.71E-13 13.85304142 0.819885808 1.794715425 1.876920279 0.60202158 6.334483371 0.79024071 0.834026081 0.078820368 13.85304142 GVIDYDRDRFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GVIDYDRDRFDR 12 2 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 ;; 172.09 2.06E-05 411510000 671280 482580 603600 599530 824530 594130 842000 692460 860590 FALSE TRUE 639549.9247 531755.4506 631275.657 539264.1054 968327.7709 573555.1291 713537.4356 631824.5314 994045.9019 0.643380676 0.534940539 0.635056848 0.542494169 0.974127824 0.576990588 0.717811355 0.63560901 1 19.92295295 -5 0.160780127 2.299246372 0.556819138 0.440130223 0.123212626 115.8061191 1.066838921 48.00402507 0.470855704 1.00E-05 5 -1.742427233 GVILTSDRPGVFSAGLDLTEMCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVILTSDRPGVFSAGLDLTEMCGR 24 1 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 ; 267.25 1.46E-44 705430000 287060 243945 197236 257350 294510 200097 265050 248420 298680 FALSE TRUE 273491.2427 268803.2728 206279.4657 231480.6891 345872.4508 193167.5907 224611.7545 226667.0278 344997.769 0.792733366 0.77914496 0.597915361 0.670962858 1.002535326 0.559909681 0.651052774 0.657010127 1 18.39622751 -1.18622671 5.160805024 1.000017896 0.716544583 0.341739158 0.124736545 2.48E-05 3.92E-06 0.116825497 0.027534296 0.065128832 1.18622671 -0.283473314 GVIS(ph)TPVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVISTPVIR 9 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 GVIS(0.5)T(0.5)PVIR;GVIS(0.5)T(0.5)PVIR 160.59 6.84E-05 115160000 301560 322820 339530 347270 430600 302300 383040 377040 514700 TRUE FALSE 287305.8564 355715.725 355097.7863 312361.7598 505696.5037 291831.2752 324600.213 344024.3788 594517.0473 0.48325924 0.598327208 0.597287812 0.52540421 0.85060051 0.490871164 0.545989748 0.578661925 1 19.18135865 -1.868223192 2.459620395 1.199554842 0.579091085 0.617262982 0.10293643 11988264.31 6981002.619 13971381.7 0.023706965 0.013544931 1.868223192 -0.620463757 GVIVDKDFSHPQMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVIVDKDFSHPQMPK 15 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 180.11 3.86E-07 6078850000 17941200 15110500 15503600 17828700 12694500 17250000 19951200 18509700 12980800 FALSE TRUE 17093155.03 16650277.13 16214455.4 16036525.2 14908416.78 16652628.17 16907278.01 16888892.54 14993796.17 1.140015166 1.110477756 1.081410953 1.069544032 0.994305686 1.110634558 1.127618238 1.126392033 1 23.83786236 4.004912845 2.079855898 1.079813604 1.134683604 0.182615439 0.046259588 0.601742941 5.089976844 0.012851061 0.034953681 10113.7647 -4.004912845 0.05487 GVKEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVKEEVK 7 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 ; 84.498 0.019609 219332000 330330 273330 268300 314150 237990 329650 367440 367480 267320 FALSE TRUE 314715.9556 301182.6378 280601.8204 282571.0452 279495.3806 318234.1378 311380.2795 335301.5031 308774.6203 1.019241657 0.975412543 0.908759341 0.915136888 0.905176016 1.03063567 1.008438709 1.085910178 1 18.23619465 2.214152821 24.87822722 1.029383499 0.952718026 0.5199672 0.040885064 220.0225564 224261.7071 0.016824866 0.012432076 163.7392589 -2.214152821 -0.076665472 GVLRPGTALVLLEAQAATGFVIDPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVLRPGTALVLLEAQAATGFVIDPVR 26 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 262.55 6.35E-53 3545930000 1583021 1269244 1407567 1617020 1964640 1394252 1982640 1401333 1872450 FALSE TRUE 1508194.735 1398581.407 1472105.339 1454474.077 2307272.594 1345968.704 1680151.854 1278624.854 2162819.983 0.697327908 0.646647163 0.68064164 0.672489661 1.066789013 0.622321189 0.776833887 0.591184132 1 21.04448216 GVLTGPEYEALDALPDAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVLTGPEYEALDALPDAERR 20 1 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 141.86 2.98E-07 23689000 15507 11527 14691 14824 15964 13245 17160 15593 19443 FALSE TRUE 14774.01484 12701.61441 15364.59688 13333.86336 18748.11655 12786.32233 14541.92683 14227.59426 22458.12114 0.657847322 0.565568879 0.684144359 0.593721232 0.834803429 0.569340696 0.647513064 0.633516676 1 14.45494962 -1.909695152 2.428546394 1.215263749 0.643256413 0.675821362 0.076478451 9424932.83 4778253.729 11560121.67 0.016801793 0.012311326 1.909695152 -0.572007337 GVMLAVDAVIAELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVMLAVDAVIAELKK 15 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 107.69 0.0011941 223640000 437210 382520 402960 454590 340080 396910 470110 451550 386610 FALSE TRUE 416543.9498 421499.2229 421436.1146 408893.7495 399389.8443 383164.9072 398386.0853 412009.8882 446563.5043 0.932776516 0.943872974 0.943731654 0.915645246 0.89436293 0.858030053 0.89211519 0.922623287 1 18.76850583 3.072990819 3.748619137 0.901236158 0.939787716 0.04888819 0.036976274 0.355310872 9.961144823 0.01007655 0.012101438 1183.016545 -3.072990819 0.038551558 GVNCIDYYSGGDKPYLISGADDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GVNCIDYYSGGDKPYLISGADDR 23 1 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;; 259.93 9.60E-44 3080710000 4045720 3464820 3471530 4158400 3382660 3727510 4447390 4046360 3793870 FALSE TRUE 3854486.833 3817889.097 3630703.084 3740389.732 3972594.833 3598425.394 3768858.974 3692039.267 4382203.983 0.879577228 0.871225783 0.828510744 0.853540763 0.906528963 0.821145115 0.860037321 0.842507396 1 22.06322521 -1.439882248 6.368142929 1.000038158 0.859234533 0.765275449 0.024725142 1.26E-05 1.11E-06 0.022601824 0.005325859 0.036317651 1.439882248 -0.140803625 GVNIGGAGS(ph)YIYEKPLAEGPQVTGPIEVPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVNIGGAGSYIYEKPLAEGPQVTGPIEVPAAR 32 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 GVNIGGAGS(1)YIYEKPLAEGPQVTGPIEVPAAR;GVNIGGAGS(1)YIYEKPLAEGPQVTGPIEVPAAR 251.17 2.24E-48 230530000 147610 126436 154440 203934 134246 161918 222800 175167 161127 TRUE FALSE 140632.7678 139319.9721 161521.2268 183434.1669 157658.4599 156310.7391 188807.768 159828.4489 186113.7522 0.755628029 0.748574302 0.867862932 0.985602432 0.847108062 0.839866679 1.014475103 0.858767538 1 17.50582514 5.611914716 0.256924226 0.983068523 0.356346873 0.487258567 0.06736998 10.82162883 0.421976619 0.086927662 2.315609523 409180.2999 -5.611914716 -0.62672165 GVNTGAVGSYIYDRDPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GVNTGAVGSYIYDRDPEGK 19 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;;;;;; 293.33 1.21E-49 9522300000 7826170 6721280 6795240 8082260 5934030 7605740 8192730 8251200 6487830 FALSE TRUE 7456242.454 7406186.073 7106808.475 7269815.87 6968922.953 7342351.317 6942778.569 7528681.186 7493929.541 0.994970985 0.988291394 0.948342046 0.970093971 0.929942417 0.979773199 0.926453676 1.004637306 1 22.83729098 3.833141104 5.846855173 0.96018221 0.992318606 0.120420741 0.026352882 0.306335727 15.37311855 0.005981444 0.010918933 6809.905796 -3.833141104 0.032136396 GVNWAAFHPTMPLIVSGADDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVNWAAFHPTMPLIVSGADDR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 142.88 1.42E-07 867180000 172665 155768 164936 178349 215405 166073 216305 176526 190331 FALSE TRUE 164503.4676 171640.9363 172498.4787 160421.0197 252971.5638 160321.8504 183303.6995 161068.4476 219846.5594 0.748264918 0.7807306 0.784631241 0.729695384 1.15067329 0.7292443 0.83378016 0.732640293 1 17.74613743 GVPAGNS(ph)DTEGGQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.6)DT(0.4)EGGQPGR;GVPAGNS(0.957)DT(0.043)EGGQPGR;GVPAGNS(0.986)DT(0.014)EGGQPGR;GVPAGNS(0.999)DT(0.001)EGGQPGR;GVPAGNS(0.999)DT(0.001)EGGQPGR;GVPAGNS(0.996)DT(0.004)EGGQPGR;GVPAGNS(0.853)DT(0.147)EGGQPGR;GVPAGNS(0.563)DT(0.437)EGGQPGR 259.22 1.02E-26 1296628000 477406 465376 502802 566280 620517 550316 608608 557021 657055 TRUE FALSE 454839.9645 512798.3435 525855.969 509356.4585 728734.9683 531258.4189 515753.6717 508245.2883 758947.7336 0.59930341 0.675670169 0.692875077 0.671135094 0.960191244 0.699993419 0.67956415 0.669671001 1 19.53364101 -5 0.187892426 2.219434798 0.646027643 0.484374013 0.094890917 122.2750538 1.192281901 56.21043318 0.265014527 1.00E-05 5 -1.573407156 GVPAGNS(ph)DTEGGQPGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVPAGNSDTEGGQPGRK 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 GVPAGNS(0.999)DT(0.001)EGGQPGRK 136.46 6.26E-06 387420000 124270 97484 109140 128880 99125 133240 131870 140640 124830 TRUE FALSE 118396.0034 107417.7304 114144.177 115924.7375 116412.3686 128625.8654 111750.8095 128324.816 144187.9989 0.821122453 0.744983849 0.791634379 0.803983261 0.807365173 0.892070536 0.775035443 0.889982641 1 17.13759156 -0.307279108 0.31635002 1.064991466 0.776613511 0.725448372 0.038657978 3.591091881 0.435161201 0.296581137 0.038429734 0.492856957 0.307279108 -0.288377955 GVPEKS(ph)PVLEK ddPTM_SK-BR-3_Trastuzumab_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 166.9 1.20E-05 7256400000 17210360 16021850 14930570 18682320 9509150 18478680 18533800 19525660 10954850 TRUE FALSE 16396860.39 17654494.73 15615151.4 16804337.7 11167542.75 17838758.68 15706128.41 17815889.7 12653672.19 1.295818332 1.395207215 1.234041089 1.328020629 0.882553506 1.409769307 1.24123086 1.407962008 1 23.59305279 -2.244434618 2.271713224 8.74E-06 1.278428143 0.240780313 0.152934009 2216516.816 516879.7756 11383378.56 0.035664567 0.00569594 2.244434618 1.278419406 GVPHPEDDHSQVEGPESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;;;; 188.84 8.85E-15 2268770000 2344100 1488612 2414916 2079290 2482580 2175100 3610800 2499520 2354174 FALSE TRUE 2233299.039 1640303.255 2525642.287 1870275.819 2915541.166 2099775.742 3059906.143 2280648.778 2719247.28 0.821293104 0.603219599 0.928801991 0.68779174 1.072186846 0.772190068 1.125276897 0.838705915 1 21.37477592 2.887712878 1.266876187 0.973807545 0.730515647 0.283547393 0.139269818 0.443343263 1.477716491 0.052848528 0.057082593 772.1699163 -2.887712878 -0.243291897 GVPLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 148.49 0.02503 15737960000 8493710 6930530 6650790 7296630 8341990 7483870 8706930 7976970 8507320 FALSE TRUE 8092229.161 7636758.886 6955735.3 6563158.89 9796830.415 7224701.705 7378527.915 7278464.218 9826591.736 0.823503141 0.777152353 0.707848203 0.667897789 0.996971349 0.735219484 0.75087356 0.740690609 1 23.22825969 GVQDIVVGEGTHFLIPWVQKPIIFDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVQDIVVGEGTHFLIPWVQKPIIFDCR 27 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 260.76 2.84E-53 2077320000 3310200 2345000 2486100 3085200 3189200 2124810 3142600 2763200 2761500 FALSE TRUE 3153733.406 2583958.166 2600090.144 2775069.835 3745395.47 2051227.297 2663138.652 2521239.559 3189739.316 0.988711958 0.810084433 0.815141893 0.869998943 1.174201118 0.643070513 0.834907931 0.790421821 1 21.60500709 2.179944399 24.99999998 0.801001372 0.912160229 0.13932736 0.134139439 150.0134091 63979.80652 0.046837272 0.034591632 151.3367484 -2.179944399 0.111158857 GVQKPAGPST(ph)SPDGNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.092)T(0.454)S(0.454)PDGNSR 80.98 0.016603 254650000 78382 66712 73217 81871 59224 73541 74483 77024 72514 TRUE FALSE 74677.0382 73510.02865 76574.07187 73641.17154 69552.64685 70994.25673 63119.25038 70279.37023 83759.10077 0.891569245 0.877636316 0.914217932 0.879202031 0.83038913 0.847600512 0.753580803 0.839065482 1 16.35395833 2.798848144 3.988140456 0.831242153 0.891023379 0.012604244 0.062883577 0.390170103 12.61044955 0.018206676 0.019034061 629.2861078 -2.798848144 0.059781226 GVQKPAGPSTS(ph)PDGNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.003)T(0.201)S(0.796)PDGNSR 178.56 5.85E-10 226600000 92089 68815 81756 98516 71838 91972 109930 105410 86859 TRUE FALSE 87736.13547 75827.32674 85504.59347 88612.98451 84366.52446 88786.98658 93158.1595 96179.74159 100328.6501 0.874487351 0.755789365 0.85224503 0.883227118 0.84090162 0.884961439 0.92852998 0.958646822 1 16.61437412 1.681454562 0.658149909 1.002599136 0.821050947 0.745226876 0.033796597 0.321494664 0.29109741 0.031288296 0.015856098 48.02358333 -1.681454562 -0.181548188 GVQLQTHPNVDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVQLQTHPNVDKK 13 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 166.38 2.19E-05 1674240000 3337200 2818800 3027500 3567500 2218700 3323800 3731700 3770000 2423200 FALSE TRUE 3179457.17 3106038.925 3166313.87 3208888.122 2605640.578 3208695.973 3162360.628 3439878.814 2798977.48 1.135935245 1.109704864 1.131239495 1.146450139 0.930925881 1.146381489 1.129827107 1.228976953 1 21.41646845 -0.362654806 6.662466413 1 1.117557337 0.204205352 0.07427308 0 0 0.066953464 0.015781083 0.433855586 0.362654806 0.117557336 GVQVETIS(ph)PGDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVQVETISPGDGR 13 0 P62942;A0A087WZM5;Q1JUQ3;A0A087WTS4;A0A087WV48 P62942 FKBP1A;FKBP12-Exin Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 1 GVQVET(0.001)IS(0.999)PGDGR 123.92 0.00022847 149410000 216780 176240 193550 236340 202950 191180 254650 230320 228630 TRUE FALSE 206533.239 194199.0564 202424.4589 212582.6542 238344.4157 184559.3887 215798.4655 210151.9598 264084.7727 0.782071745 0.735366354 0.76651318 0.804978841 0.902529946 0.698864182 0.817156034 0.795774621 1 18.01064159 -5 0.261819412 2.411047453 0.766978816 0.615941933 0.052874049 126.7856004 1.242784728 96.28450471 0.06480038 1.00E-05 5 -1.644068637 GVQVETISPGDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVQVETISPGDGR 13 0 P62942;A0A087WZM5;Q1JUQ3;A0A087WTS4;A0A087WV48 P62942 FKBP1A;FKBP12-Exin Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ;;; 203.51 1.98E-07 718000000 656320 510232 625080 671080 693670 629120 840550 606870 783170 FALSE TRUE 625297.0543 562225.2209 653740.5363 603621.7634 814645.8284 607333.4167 712308.6597 553729.2456 904620.0037 0.691226207 0.621504299 0.722668671 0.667265549 0.90053926 0.671368546 0.787412015 0.612112537 1 19.78695237 -5 0.215302708 2.408918726 0.670067857 0.510656403 0.086832978 114.7669045 1.146227437 70.21472044 0.159494439 1.00E-05 5 -1.738850869 GVS(ph)QEKEAQISSAIVSSVQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVSQEKEAQISSAIVSSVQSK 21 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 GVS(1)QEKEAQISSAIVSSVQSK 84.404 0.001848 77274000 148710 107370 147960 137070 100600 155480 188570 176780 123600 TRUE FALSE 141680.773 118311.1251 154744.1124 123291.4632 118144.6081 150095.6886 159800.1832 161300.206 142767.2567 0.992389826 0.828699295 1.083890774 0.863583612 0.827532943 1.051331321 1.119305552 1.129812323 1 17.12330561 2.078296119 6.497306422 1.093680767 0.918933702 0.46312346 0.083658576 0.165130172 10.97858126 0.029691607 0.021785885 119.7556793 -2.078296119 -0.174747064 GVS(ph)RS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVSRSPPK 8 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 GVS(1)RS(1)PPK 48.741 0.094629 280300000 376630 374880 310380 459530 266090 369620 366200 376210 266400 TRUE FALSE 358827.4463 413080.6982 324611.23 413337.1714 312496.0118 356819.9667 310329.4643 343267.058 307711.9514 1.166114753 1.342426566 1.054919149 1.34326005 1.015547204 1.159590861 1.008506374 1.11554672 1 18.23122095 2.724182683 24.99543604 1.064345868 1.229699443 0.43086348 0.095176725 696.5514374 1210923.856 0.027393504 0.02592871 529.8862898 -2.724182683 0.165353575 GVSFYEVPPHLFAVADTVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVSFYEVPPHLFAVADTVYR 20 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 163.45 1.96E-11 222520000 475680 471690 385600 493760 543670 412480 510460 509740 473240 FALSE TRUE 453195.5491 519755.7473 403280.1414 444126.3067 638485.8759 398195.7142 432579.9518 465104.4633 546627.6422 0.829075433 0.950840585 0.737760242 0.812484171 1.16804535 0.728458796 0.791361282 0.850861587 1 19.06019889 -0.591610644 11.7560097 0.999969605 0.858519878 0.110265575 0.126219868 0 0 0.115111696 0.027132087 0.256088075 0.591610644 -0.141449727 GVSMSLPSS(ph)PLLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMSLPS(0.03)S(0.97)PLLPR;GVSMSLPS(0.265)S(0.735)PLLPR 194.59 1.32E-07 201490000 553540 531120 502100 593750 594150 527970 616210 588790 650160 TRUE FALSE 527375.2612 585241.7318 525121.7816 534065.1219 697769.5719 509686.2665 522195.847 537232.4262 750983.4922 0.702246143 0.779300395 0.699245439 0.711154276 0.929141025 0.678691705 0.695349302 0.715371818 1 19.51842167 -1.584665106 3.561923827 1.008686105 0.738051259 0.560268033 0.072716731 0.004871426 0.000568028 0.068380257 0.01567989 0.026021654 1.584665106 -0.270634846 GVSSESSGDREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVSSESSGDREK 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 0 80.69 0.017931 639450000 87571 74708 102850 87771 172920 84239 116780 92085 162300 FALSE TRUE 83431.69238 82320.83014 107565.7742 78948.09233 203077.1933 81321.78231 98963.06619 84021.54923 187468.6551 0.445043425 0.439117836 0.57378005 0.421126893 1.083259456 0.43378869 0.527891269 0.448189854 1 17.51628987 -2.638054622 2.021189918 9.999948938 0.538128052 0.342593744 0.197111591 6851707.779 191425.7067 284586488.9 0.048564905 0.002301152 2.638054622 -9.461820886 GVTDHTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GVTDHTQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 109.11 0.0036814 154594000 220685 219507 206339 232628 233106 212941 231315 217389 143108 FALSE TRUE 210253.6574 241875.0129 215799.8472 209243.7915 273759.6126 205566.7998 196023.6484 198353.2667 165300.4577 1.271948428 1.463244665 1.305500603 1.265839153 1.656133421 1.243594861 1.185862707 1.199955943 1 17.33473119 2.010609982 24.99790815 1.165625368 1.387195747 0.475514742 0.125527454 193.7203789 456417.6894 0.043693437 0.03223859 102.4731253 -2.010609982 0.221570379 GVTECYECHPKPTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVTECYECHPKPTQR 15 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 299.27 1.99E-44 1302390000 1359250 1125190 1192840 1377900 1152570 1260490 1467480 1325920 1179340 FALSE TRUE 1295000.946 1239848.14 1247532.894 1239390.874 1353577.843 1216838.915 1243588.974 1209815.416 1362226.024 0.95065057 0.910163305 0.915804626 0.909827629 0.993651435 0.893272404 0.912909423 0.888116505 1 20.37753467 4.692777686 3.745552355 0.923602776 0.952228139 0.021985565 0.038687001 0.803533138 19.6542188 0.008364604 0.057705288 49292.14141 -4.692777686 0.028625363 GVTIPYRPKPSS(ph)SPVIFAGGQDR ddPTM_SK-BR-3_Trastuzumab_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(0.186)S(0.579)S(0.236)PVIFAGGQDR;GVTIPYRPKPS(0.089)S(0.603)S(0.308)PVIFAGGQDR;GVT(0.004)IPYRPKPS(0.074)S(0.512)S(0.41)PVIFAGGQDR 223.87 1.10E-32 3044930000 1889630 1859620 1891960 2125830 1529420 2028610 2139720 2146880 1756000 TRUE FALSE 1800310.935 2049117.392 1978708.237 1912137.53 1796150.364 1958358.727 1813266.415 1958887.806 2028311.512 0.887590947 1.010257734 0.975544548 0.942723797 0.885539698 0.965511814 0.89397827 0.965772661 1 20.95184781 0.995411043 24.94594504 1.000000007 0.939476164 0.205064058 0.040374136 251.9625457 1369697.637 0.038163144 0.009540786 9.894891658 -0.995411043 -0.060523843 GVTIPYRPKPSSS(ph)PVIFAGGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 GVT(0.013)IPYRPKPS(0.084)S(0.256)S(0.647)PVIFAGGQDR 54.003 0.055831 182390000 383320 369190 475320 356790 181010 509510 423680 276630 128260 TRUE FALSE 365201.2233 406810.8807 497113.8922 320924.7913 212578.0867 491865.5409 359039.8346 252406.8107 148149.9057 2.465079012 2.745940868 3.355478964 2.166216642 1.434885062 3.320053013 2.423490132 1.70372576 1 17.17669818 3.148473103 17.65669506 2.164358391 2.776237312 0.244073847 0.661318806 3.927800271 763.0041554 0.183133504 0.218889228 1407.58005 -3.148473103 0.61187892 GVTLGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVTLGFR 7 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 98.133 0.026723 101030000 303860 245140 154570 155560 302420 180960 282030 248540 270310 FALSE TRUE 289497.14 270120.0447 161657.1874 139922.8133 355161.9523 174693.3098 239001.1437 226776.52 312228.2942 0.927197007 0.865136343 0.517753164 0.448142644 1.137507262 0.559505058 0.765469203 0.726316366 1 18.25224176 -1.599911599 9.400855401 1.000042619 0.754089385 0.13241373 0.204811312 0.000174502 7.43E-06 0.189152059 0.044575881 0.025123978 1.599911599 -0.245953234 GVTSEEFDKFLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVTSEEFDKFLEER 14 1 O60784;O60784-3 O60784 TOM1 Target of Myb protein 1 0 ; 155.57 5.30E-06 141560000 222780 204185 194199 236270 158761 205164 209567 217572 163619 FALSE TRUE 212249.6309 224991.6836 203103.2162 212519.6907 186448.8681 198059.1192 177593.7052 198520.2423 188992.1989 1.123060275 1.190481327 1.074664549 1.124489222 0.986542668 1.047975104 0.93968802 1.050415009 1 17.52796716 2.926515341 1.308697351 0.994148153 1.151467453 0.648467962 0.04378492 0.212315427 0.754184929 0.016224391 0.018172407 844.3360675 -2.926515341 0.1573193 GVVCIDEFDKMSDMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVVCIDEFDKMSDMDR 16 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 158.17 8.74E-09 75419000 148900 108630 143150 141460 141760 156040 195270 172040 157820 FALSE TRUE 141861.7921 119699.5205 149713.5691 127240.172 166482.8991 150636.2957 165477.9751 156975.2656 182293.9196 0.778203642 0.656629254 0.821275715 0.697994603 0.913266331 0.826337467 0.907753673 0.861110815 1 17.47590692 2.097475736 0.431279081 0.987308443 0.700820678 0.620812149 0.062628387 0.609066879 0.264640825 0.059672819 0.057948232 125.1629343 -2.097475736 -0.286487766 GVVDSDDLPLNVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;;;;; 331.48 4.51E-68 3094531000 4622100 4068216 4103017 4482920 4987390 4043500 4783590 4265123 4740680 FALSE TRUE 4403622.493 4482771.836 4291144.388 4032288.365 5857189.237 3903472.581 4053765.489 3891646.219 5475840.442 0.804191163 0.818645445 0.78365037 0.736377987 1.069642057 0.712853602 0.740300148 0.710693867 1 22.38464898 -0.622790585 7.279772466 0.999999998 0.797307882 0.275154998 0.10352238 0 0 0.094062948 0.022170849 0.238346849 0.622790585 -0.202692115 GVVDSEDLPLNISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GVVDSEDLPLNISR 14 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;; 358.78 5.95E-82 2413200000 3812420 3407400 3406330 3928180 4118060 3505460 4032170 3843140 4134740 FALSE TRUE 3632214.462 3754617.934 3562513.6 3533311.883 4836248.36 3384065.041 3416988.411 3506614.288 4775934.362 0.760524368 0.786153588 0.745930185 0.739815838 1.012628733 0.70856607 0.715459668 0.734225813 1 22.18735158 -1.050694195 4.22585147 1.00002045 0.773313759 0.395271672 0.087266695 11016124.44 2738993.32 2233.542762 0.01955046 0.088982746 1.050694195 -0.226706691 GVVPLAGTDGETTTQGLDGLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GVVPLAGTDGETTTQGLDGLSER 23 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 ;; 309.87 8.91E-73 204272000 214989 188738 191336 220212 238272 189733 237831 223031 241112 FALSE TRUE 204826.896 207970.6168 200108.9449 198075.8714 279826.5614 183162.4986 201545.5129 203501.2233 278502.4175 0.735458234 0.746746181 0.718517802 0.711217781 1.004754515 0.657669331 0.723675991 0.730698229 1 18.08733033 -1.629288231 2.862754485 1.021640592 0.750765368 0.411265449 0.092597254 25046241.53 25522972.26 4044089.969 0.020564112 0.023480739 1.629288231 -0.270875224 GVVPLAGTNGETTTQGLDGLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GVVPLAGTNGETTTQGLDGLSER 23 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 370.44 4.48E-118 454804000 121638 106338.6 135848 139594 137337 113571 142217 121182 137033 FALSE TRUE 115888.4128 117174.6242 142076.7652 125561.7459 161288.5293 109638.0078 120519.1847 110570.6617 158283.3778 0.73215782 0.740283824 0.897610142 0.793271837 1.018985895 0.692669119 0.761414031 0.698561423 1 17.27215023 -2.41956043 2.355718813 3.071024321 0.787289889 0.301937982 0.099238148 13137126.97 686256.0005 147829291.7 0.025057149 0.003805744 2.41956043 -2.283734432 GVWDHGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GVWDHGGR 8 0 Q9Y3S2;D6RBR7;D6R8Y9 Q9Y3S2 ZNF330 Zinc finger protein 330 0 122.18 0.0014016 42505000 52451 49322 49247 53334 58285 55796 60912 59911 65974 FALSE TRUE 49971.74518 54347.96787 51505.02366 47972.76499 68449.88555 53863.77053 51618.75567 54664.87523 76204.91097 0.655754918 0.713181961 0.675875387 0.629523273 0.898234571 0.706828075 0.677367836 0.717340583 1 16.21759635 -5 0.310470833 3.60764982 0.692192673 0.619468205 0.071905637 194.5050565 1.759797048 331.8539878 0.064436659 1.00E-05 5 -2.915457147 GVYSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GVYSGR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 116.87 0.053984 352260000 299060 222510 241090 260050 323220 241010 291100 270210 317750 FALSE TRUE 284924.0265 245184.022 252144.215 233909.2799 379589.4657 232663.7633 246687.3486 246548.9799 367025.0472 0.776306763 0.668030762 0.686994571 0.637311491 1.034233136 0.633917944 0.67212674 0.67174974 1 18.485519 -1.015794887 4.722564615 1.000005285 0.719123673 0.354088768 0.117668506 14177637.82 3049524.323 930.3272704 0.025644461 0.096428434 1.015794887 -0.280881612 GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 GWAFGS(0.011)NS(0.989)LPIAGSVGMGVAR 126.25 2.28E-05 59691000 173040 152720 177700 169420 238260 158150 216500 148610 228920 TRUE FALSE 164860.7421 168282.3416 185847.7208 152389.5797 279812.4686 152673.2258 183468.9487 135596.9206 264419.7444 0.62348121 0.63642124 0.702851147 0.576316947 1.058213218 0.577389658 0.693854951 0.512809362 1 18.01247038 GWDLVDAVT(ph)PGPQPTLEQLEEGGPRPLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 GWDLVDAVT(0.988)PGPQPT(0.012)LEQLEEGGPRPLER 53.089 0.048146 0 12273 10113 10842 12040 13186 11440 12868 10009 14606 TRUE FALSE 11692.87961 11143.5262 11339.11642 10829.71633 15485.63423 11043.82993 10904.75026 9132.558899 16871.02388 0.693074688 0.660512739 0.672106003 0.641912216 0.917883487 0.65460342 0.646359719 0.541316221 1 14.04225991 -2.232742717 2.485282495 2.212338651 0.680019424 0.53559669 0.094081866 3651628.967 977475.4587 25073714.28 0.021851144 0.005851366 2.232742717 -1.532319227 GWEEGVAQMSVGQR ddPTM_SK-BR-3_Trastuzumab_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 ; 184.31 3.04E-06 319960000 288520 210610 223410 327360 311980 265950 373290 265160 332650 FALSE TRUE 274882.2314 232071.3984 233653.5695 294453.1509 366389.2132 256740.0848 316337.7546 241941.1847 384235.6631 0.715400099 0.603981933 0.608099643 0.766334776 0.953553375 0.668183902 0.823290977 0.629668737 1 18.5516319 3.138465039 5.601646699 0.799472755 0.645247781 0.314317046 0.114925729 0.24539563 11.50268196 0.030256292 0.036519621 1375.514077 -3.138465039 -0.154224973 GWEFMWNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 GWEFMWNER 9 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;;;;;;;;;; 172.23 0.00013109 4522771000 3397387 2667080 2467972 2852556 3907193 2093126 3297202 2774718 3197357 FALSE TRUE 3236799.249 2938858.484 2581130.957 2565811.651 4588606.222 2020640.522 2794153.278 2531748.982 3693186.794 0.876424462 0.795751379 0.698889902 0.694741911 1.242451703 0.547126543 0.756569714 0.685518801 1 21.8164348 -1.083378196 4.673341729 1.000011013 0.788353442 0.118094407 0.182744173 1.92E-05 3.76E-06 0.161734872 0.038119292 0.082531893 1.083378196 -0.211657571 GWENHVEGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GWENHVEGQK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 158.41 8.00E-06 869830000 2092720 1906350 1949300 2407060 1808290 2298470 2429440 2425770 1834240 FALSE TRUE 1993801.273 2100609.232 2038677.333 2165097.756 2123655.203 2218873.408 2058784.308 2213356.719 2118684.571 0.94105621 0.991468603 0.962237306 1.021906604 1.002346094 1.047288227 0.971727616 1.044684399 1 21.01473739 4.50764233 0.608249361 1.012992068 0.911369751 0.449403925 0.025293618 2.458269407 0.833203358 0.011401003 0.168249805 32184.17124 -4.50764233 -0.101622318 GWGS(ph)PGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;GWGS(1)PGRPK 73.951 0.025719 803880000 1145990 999020 1018810 1222070 933180 1105750 1285390 1235940 1140180 TRUE FALSE 1091821.324 1100821.274 1065523.446 1099225.202 1095926.297 1067457.6 1089280.148 1127714.541 1316993.291 0.829025729 0.835859439 0.809057611 0.834647533 0.832142657 0.810526225 0.827096201 0.85627964 1 20.32881657 0.723180156 2.359705955 0.99997378 0.82598287 0.972509657 0.009159506 0.203129405 1.522868825 0.008590692 0.002314252 5.286645096 -0.723180156 -0.17399091 GWLRDPSAS(ph)PGDAGEQAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GWLRDPSASPGDAGEQAIR 19 1 P18206;P18206-2 P18206 VCL Vinculin 1 GWLRDPS(0.1)AS(0.9)PGDAGEQAIR;GWLRDPS(0.002)AS(0.998)PGDAGEQAIR 122.39 2.02E-05 206576000 105413 55431 57369 108320 127203 75383 138561 91702 168086 TRUE FALSE 100430.3364 61079.48192 59999.4254 97431.46781 149387.1629 72772.46781 117420.9746 83672.08674 194151.9184 0.517277075 0.314596335 0.309033389 0.501831085 0.76943439 0.374822296 0.604789155 0.430961937 1 17.56682644 -5 0.195399672 3.342867961 0.38199083 0.592111766 0.136908437 94.05095518 0.925917756 85.78825852 0.330811136 1.00E-05 5 -2.96087713 GWMDPQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GWMDPQSK 8 0 J3KN30;F5H8E7;Q99572-7;Q99572-5;Q99572-2;Q99572-8;Q99572 J3KN30 P2RX7 P2X purinoceptor 7 0 78.496 0.070896 65390000 194610 149910 153430 189790 184520 178760 227490 182280 193470 FALSE TRUE 185411.171 165185.9994 160464.9173 170711.9486 216700.2296 172569.4964 192782.2224 166318.5969 223472.3395 0.829682865 0.739178727 0.718052702 0.763906392 0.969695981 0.772218597 0.862667043 0.744246904 1 17.76973675 2.905497907 24.99994959 0.854754621 0.763701847 0.287122119 0.081943918 73.61285377 19468.42605 0.022630859 0.024003656 804.447872 -2.905497907 -0.091052774 GWNYILEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GWNYILEK 8 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 120.07 0.0036567 143500000 235240 176850 133650 124750 219380 132260 251550 183080 214260 FALSE TRUE 224120.6714 194871.2161 139777.9847 112209.893 257639.8025 127679.803 213171.4275 167048.5446 247486.3465 0.905588024 0.787401886 0.564790691 0.453398317 1.041026328 0.515906452 0.861346214 0.67498085 1 17.91698941 -1.484694745 10.65680021 1.000000844 0.738142737 0.178694771 0.183148592 3.39E-06 1.64E-07 0.163623865 0.03856639 0.032757086 1.484694745 -0.261858107 GWQDVTATSAYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GWQDVTATSAYKK 13 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 198.16 2.05E-07 7065300000 1938390 1324850 1461250 1662350 1352230 1616620 1982800 1684990 1536790 FALSE TRUE 1846766.146 1459853.721 1528249.758 1495247.42 1588058.484 1560636.044 1680287.443 1537443.343 1775107.544 1.040368597 0.822402973 0.860933617 0.842341876 0.894626632 0.879178306 0.946583461 0.866112787 1 20.759475 1.743185318 24.46490622 0.929759046 0.890977086 0.09854406 0.066423269 2.247886119 11949.77671 0.030449466 0.016885019 55.358628 -1.743185318 -0.03878196 GWS(ph)QEGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;GWS(1)QEGPVK;GWS(1)QEGPVK 145.14 0.00010268 2395930000 4345480 3425870 3396800 6166060 3706910 5778530 5689770 3607750 3534150 TRUE FALSE 4140077.772 3774970.048 3552546.64 5546235.934 4353393.93 5578418.057 4821691.087 3291836.284 4082207.932 1.014176113 0.924737326 0.870251271 1.358636313 1.066431207 1.366519822 1.181147841 0.806386235 1 21.96091824 3.263468279 24.99892238 1.154838507 0.945004139 0.220209599 0.167009038 293.2597114 294332.137 0.043253536 0.058541599 1834.291186 -3.263468279 -0.209834368 GWSQEGPVKS(ph)PAECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 200.39 4.20E-09 2997050000 2252530 2809590 2119720 2784460 1610520 2265480 2118380 2352440 1456090 TRUE FALSE 2146057.371 3095890.415 2216911.259 2504560.791 1891394.178 2187025.86 1795182.224 2146447.883 1681893.001 1.275977348 1.840717819 1.318104813 1.489132061 1.124562726 1.300335907 1.067358164 1.276209534 1 20.6816545 2.872009596 1.487742834 1.148863705 1.541111779 0.44247532 0.176785409 0.319005399 1.433538819 0.064474765 0.069062899 744.7484291 -2.872009596 0.392248074 GWSQEGPVKS(ph)PAECREEHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GWSQEGPVKSPAECREEHSK 20 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECREEHSK;GWSQEGPVKS(1)PAECREEHSK 134.68 4.45E-06 236080000 142650 116190 146672 151561 83697 132470 155272 147431 83246 TRUE FALSE 135907.2172 128029.8931 153397.0563 136325.8003 98293.7303 127882.5307 131582.4046 134521.1601 96155.36452 1.41341274 1.331489863 1.595304194 1.417765936 1.022238653 1.329957318 1.368435399 1.398997973 1 16.55307973 2.953282961 24.99331928 1.26074582 1.428436923 0.326958978 0.148265577 593.8139096 317686.4045 0.043613595 0.046260639 898.0136966 -2.953282961 0.167691103 GWSQEGPVKS(ph)PAECREEHSKTPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GWSQEGPVKSPAECREEHSKTPEER 25 3 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECREEHSKTPEER 142.38 2.49E-07 146530000 123240 61342 127940 98249 103360 118120 159620 129330 100330 TRUE FALSE 117414.6894 67592.81954 133806.1755 88372.82386 121385.9513 114029.4748 135267.0374 118005.1796 115888.664 1.01316803 0.583256526 1.1546097 0.762566595 1.047435936 0.983957109 1.167215435 1.018263353 1 16.82237993 2.674790651 1.159415433 1.077565232 0.841813788 0.16707653 0.160069882 0.602483678 1.670609646 0.075676955 0.065953207 472.9232344 -2.674790651 -0.235751444 GWVTFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GWVTFDR 7 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;; 177.65 0.0016917 442076000 989413 866691 786098 903073 1205390 794158 1164290 919985 1223210 FALSE TRUE 942645.4083 955007.7982 822141.3709 812294.3863 1415609.634 766656.1093 986656.1768 839426.2363 1412899.16 0.667171045 0.675920707 0.581882554 0.574913207 1.001918378 0.54261205 0.698320308 0.594116169 1 20.43022707 -1.666231791 2.647801432 1.043198044 0.669197233 0.396663927 0.129002642 14380081.43 12329475.57 4199234.202 0.030010888 0.021565931 1.666231791 -0.374000811 GYAAGAQPRPSANRENFS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYAAGAQPRPSANRENFSPER 21 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 GYAAGAQPRPS(0.001)ANRENFS(0.999)PER;GYAAGAQPRPS(0.002)ANRENFS(0.998)PER 89.297 0.0012161 249470000 87199 41422 102048 66851 153732 75662 144305 92877 217739 TRUE FALSE 83077.27608 45642.94889 106727.0017 60131.01047 180542.8121 73041.80597 122288.6219 84744.19751 251504.8521 0.330320769 0.181479397 0.424353649 0.239084892 0.717850215 0.290419073 0.486227685 0.336948559 1 17.94022671 -5 0.18459569 3.64823661 0.24094562 0.643281986 0.146995742 77.05226969 0.747576803 74.90391586 0.385835167 1.00E-05 5 -3.40729099 GYADS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(1)PSK;GYADS(1)PSK;GYADS(0.99)PS(0.01)K;GYADS(1)PSK;GYADS(0.999)PS(0.001)K;GYADS(0.986)PS(0.014)K;GYADS(0.983)PS(0.017)K;GYADS(1)PSK;GYADS(0.999)PS(0.001)K;GYADS(0.999)PS(0.001)K 166.66 0.00033271 4502989000 9325360 11671180 9460460 12080320 6755590 11458240 10743340 12017560 8107210 TRUE FALSE 8884568.714 12860486.51 9894231.449 10865983.28 7933762.757 11061438.28 9104246.168 10965238.74 9364434.721 0.948756543 1.373332923 1.056575409 1.160345884 0.847222816 1.181217938 0.972215242 1.170945077 1 23.15876048 GYAFIEFASFEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYAFIEFASFEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 154.66 6.47E-07 0 129030 132610 119200 140550 94362 136030 130260 151720 120760 FALSE TRUE 122931.0076 146123.1098 124665.4379 126421.647 110818.7029 131319.247 110386.4446 138434.5925 139486.844 0.881308975 1.047576284 0.89374334 0.90633384 0.794474229 0.941445395 0.791375311 0.992456267 1 17.08976953 3.51726854 24.04626048 0.885975513 0.965478881 0.063122494 0.080950838 538.3859985 322464.9124 0.019427532 0.030090727 3290.550343 -3.51726854 0.079503367 GYAFIEFASFEDAKEALNSCNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYAFIEFASFEDAKEALNSCNKR 23 2 P19338;H7BY16 P19338 NCL Nucleolin 0 134.29 1.11E-05 40311000 82734 27525 81415 53506 81589 77409 131610 92303 119470 FALSE TRUE 78823.32778 30329.82879 85147.95828 48127.47523 95818.09577 74728.30692 111530.4773 84220.45999 137996.7974 0.57119679 0.219786469 0.61702851 0.348757914 0.694350141 0.541522038 0.808210621 0.610307352 1 17.07427526 1.499518889 0.415336914 1.000218611 0.382236087 0.569432313 0.142519475 0.633793491 0.313708525 0.15516872 0.1121619 31.58776434 -1.499518889 -0.617982523 GYAFIEYEHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 190.56 2.22E-06 2875130000 2963340 2488670 2208360 2435690 3512550 2290480 3173650 2680980 2748460 FALSE TRUE 2823268.791 2742268.302 2309615.49 2190849.814 4125137.608 2211160.103 2689451.404 2446219.178 3174677.14 0.889308949 0.86379439 0.727511929 0.690101613 1.299388072 0.696499205 0.847157454 0.770541088 1 21.59817845 4.220536648 4.447319103 0.851890965 0.883769641 0 0.180965444 2.047399572 95.7070655 0.042290384 0.105368322 16616.38891 -4.220536648 0.031878675 GYAFNHSADFETVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYAFNHSADFETVR 14 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 167.89 3.58E-06 741830000 630040 746800 486270 640980 725330 598450 683710 659560 565050 FALSE TRUE 600259.2578 822899.769 508565.9605 576547.4726 851827.3224 577725.5264 579397.4823 601805.4299 652675.0681 0.919690803 1.260810791 0.779202371 0.88336065 1.305132315 0.885165613 0.88772731 0.92205978 1 19.3160054 GYAFVQYSNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYAFVQYSNER 11 0 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 144.65 0.0035452 0 30758 20900 14259 17809 32690 17570 30897 19867 32043 FALSE TRUE 29304.1303 23029.73376 14912.78925 16018.80549 38391.12565 16961.54649 26183.09519 18127.34016 37012.06479 0.791745353 0.622222345 0.402916977 0.432799564 1.037259766 0.458270745 0.707420549 0.489768411 1 15.175708 -1.484194599 3.190751702 1.008407019 0.627952852 0.276666358 0.193597806 140997672.4 189126664.6 10599835.13 0.043114008 0.032794831 1.484194599 -0.380454167 GYAVLGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 163.77 0.00014601 6840600000 4531890 3180240 1950710 2193940 7550950 2064850 4977540 2925270 6827490 FALSE TRUE 4317676.541 3504310.072 2040151.983 1973400.983 8867833.289 1993343.727 4218124.854 2669117.851 7886262.279 0.547493399 0.444356268 0.258696948 0.250232735 1.124465935 0.252761531 0.534869968 0.33845157 1 22.91091026 -1.632235805 2.789412451 1.049622811 0.473104263 0.295713816 0.257503336 43468006.57 41976133.1 15623593.98 0.06298554 0.023321914 1.632235805 -0.576518548 GYDDRDYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 GYDDRDYYSR 10 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;;;; 174.4 2.84E-06 20224930000 23166990 17893910 19344980 22354340 25563010 20558310 24583060 21813590 25882210 FALSE TRUE 22071932.3 19717319.77 20231966.47 20107239.27 30021190.85 19846370.57 20832462.7 19903476.42 29895890.94 0.738293177 0.65953277 0.6767474 0.672575349 1.004191208 0.663849444 0.696833646 0.665759601 1 24.83344387 -1.285863936 3.649231896 1.000693037 0.718886241 0.417530886 0.103040755 34105126.36 51965541.89 257882.1091 0.023577166 0.051776902 1.285863936 -0.281806795 GYDELVPHQISVVSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYDELVPHQISVVSEER 17 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 112.16 0.00047443 173965000 179480 185207 190509 205507 205247 183914 246119 184973 172388 FALSE TRUE 170996.3361 204079.8039 199244.0261 184849.0459 241042.0118 177545.0121 208569.0263 168775.7835 199121.0506 0.858755694 1.02490321 1.000617592 0.928324983 1.210530032 0.891643608 1.047448402 0.847603922 1 17.60328622 4.605656481 2.852829884 0.998139783 0.852049627 0.154248285 0.098492179 0.53114079 7.104702781 0.021482783 0.154606837 40332.62427 -4.605656481 -0.146090156 GYDRYEDYDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYDRYEDYDYR 11 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 130.56 0.00020207 852690000 1711200 1059990 1521970 1498020 2160100 1456970 2114600 1683230 2378600 FALSE TRUE 1630314.967 1168004.186 1591753.83 1347436.184 2536820.756 1406514.764 1791978.933 1535837.458 2747461.14 0.593389637 0.425121276 0.579354447 0.490429569 0.923332716 0.511932541 0.652230857 0.559002432 1 21.38966765 -4.999999993 0.177148542 2.668785021 0.493349264 0.485398769 0.132557574 107.4460012 1.028850707 63.1241578 0.397356577 1.00E-05 4.999999993 -2.175435757 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GYDSEDDTWEPEQHLVNCEEYIHDFNR 27 0 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(0.995)EDDT(0.005)WEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(0.994)EDDT(0.006)WEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR 280.88 7.14E-61 723573000 168057.9 182898 134352.2 190115 154498.3 166925 147077.7 153615 82873 TRUE FALSE 160114.1361 201535.5141 140512.3813 171004.279 181442.7546 161144.3454 124638.2956 140163.6562 95724.52158 1.672655381 2.105369772 1.467882826 1.786420827 1.895467866 1.683417611 1.302051904 1.46423982 1 16.54660092 1.383528545 0.769729696 1.02606948 1.829299765 0.648711882 0.184730606 0.335391559 0.43448617 0.166494016 0.06809522 24.18402288 -1.383528545 0.803230285 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GYDSEDDTWEPEQHLVNCEEYIHDFNRR 28 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNRR;GYDS(0.981)EDDT(0.019)WEPEQHLVNCEEYIHDFNRR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNRR;GY(0.046)DS(0.719)EDDT(0.235)WEPEQHLVNCEEYIHDFNRR 230.36 2.46E-35 360533000 36956.8 34761.9 33900.7 38544.5 37611.6 30150.3 41530.5 36453.7 32552.7 TRUE FALSE 35209.92531 38304.17713 35455.08063 34669.93363 44171.05113 29106.18755 35194.25947 33261.62077 37600.80646 0.936414099 1.018706266 0.942934048 0.922052926 1.174736802 0.77408413 0.935997463 0.884598601 1 15.19847598 2.209914429 24.99999984 0.89364844 0.989930587 0.232428994 0.08953162 306.12125 267155.2133 0.030185119 0.022297214 162.1490576 -2.209914429 0.096282146 GYDVDFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 151.56 0.0010961 697820000 2336600 2436980 2204570 2597850 2682600 2215930 2615250 2473170 2696230 FALSE TRUE 2226153.549 2685311.033 2305651.715 2336709.182 3150444.591 2139191.788 2216245.58 2256606.124 3114347.578 0.714805748 0.862238708 0.740332175 0.750304558 1.011590554 0.686882801 0.711624353 0.724583903 1 21.57049854 -2.211376137 2.3928077 1.717994775 0.77597301 0.349996491 0.09623272 5254084.588 1006041.85 20521642.1 0.02285114 0.006146443 2.211376137 -0.942021765 GYDYGPHFQGILEASLEGDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 322.79 8.05E-68 9991117000 4957673 5697745 4871727 6013208 5437446 5039106.7 5186904 5451760 4745364 FALSE TRUE 4723333.622 6278351.693 5095100.502 5408748.907 6385734.861 4864601.171 4395546.531 4974374.993 5481250.813 0.861725505 1.145423172 0.929550695 0.986772744 1.165014169 0.887498372 0.801923992 0.90752552 1 22.38607372 2.036874415 24.9752007 0.872033713 1.016417401 0.233078818 0.101995704 185.6169027 125718.3661 0.035757699 0.026408744 108.8615253 -2.036874415 0.144383688 GYEEWLLNEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 255.14 4.34E-20 1444035000 1527201 901858 740816 1187251 1753323 859203 1612818 1163095 1559377 FALSE TRUE 1455013.235 993758.3555 774783.1464 1067906.274 2059101.976 829448.5847 1366752.993 1061248.236 1801197.221 0.807803398 0.551721013 0.430148979 0.592886921 1.143185184 0.460498481 0.758802521 0.589190469 1 20.78052473 GYEEWLLNEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 238.13 6.38E-16 323612000 504393 319116 256612 380187 588230 287358 564257 368780 577291 FALSE TRUE 480551.3425 351634.2832 268377.914 341969.8805 690817.1258 277406.7204 478169.2314 336487.6682 666814.3399 0.720667379 0.527334615 0.402477718 0.512841221 1.035996205 0.416017929 0.717095003 0.504619724 1 19.3469256 GYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYEVIYLTEPVDEYCIQALPEFDGKR 26 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 216.8 6.20E-34 482830000 704600 572870 649670 705760 580630 689660 842630 773120 699730 FALSE TRUE 671294.9544 631246.1043 679458.0121 634815.6639 681891.6882 665776.9013 714071.3175 705421.5142 808240.5547 0.830563315 0.781012658 0.840663102 0.785429115 0.843674181 0.823736074 0.883488602 0.872786586 1 19.62442522 0.756782856 0.533211335 1.005576213 0.805168152 0.869237357 0.022307439 0.37087045 0.229181533 0.024242205 0.009752301 5.711929728 -0.756782856 -0.200408061 GYFDEEMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 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 ;;;;;;;;;;;;;;;;;; 255.1 1.41E-14 27383220000 15285310 12686978 11286507 12882057 17144340 11813190 16314510 13753850 16595200 FALSE TRUE 14562803.69 13979795.48 11804004.51 11587128.16 20134307.47 11404096.27 13825431.86 12549489.98 19168698.86 0.759717902 0.729303308 0.615795814 0.604481725 1.050374239 0.594933248 0.721250407 0.654686584 1 24.19224908 -1.029469222 4.994660056 1.000004 0.718476474 0.315869072 0.131170837 5.30E-06 1.03E-06 0.115176146 0.027146893 0.093439559 1.029469222 -0.281527526 GYFEDRRPS(ph)ANCDPFSVTEALIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GYFEDRRPSANCDPFSVTEALIR 23 2 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 GYFEDRRPS(1)ANCDPFSVTEALIR;GYFEDRRPS(0.594)ANCDPFS(0.35)VT(0.055)EALIR;GYFEDRRPS(1)ANCDPFSVTEALIR;GYFEDRRPS(1)ANCDPFSVTEALIR;GYFEDRRPS(1)ANCDPFSVTEALIR 241.84 1.35E-37 365084000 285172 192706 261397 270936 335005 244370 326561 282726 348975 TRUE FALSE 271692.4847 212342.9605 273382.311 243700.9985 393429.7659 235907.4056 276738.1217 257969.0126 403092.2607 0.674020593 0.52678501 0.678212751 0.604578709 0.976029074 0.585244195 0.686537919 0.639975107 1 18.62075056 -5 0.221551305 2.702350751 0.621227909 0.422106925 0.119617959 144.4425901 1.444743046 110.0331038 0.211914147 1.00E-05 5 -2.081122842 GYFEHREDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 151.83 4.92E-05 603083000 682400 489108 538265 541044 864140 541263 799010 632236 734030 FALSE TRUE 650144.3044 538948.6613 562944.9827 486657.2292 1014845.742 522518.9266 677106.3497 576874.0641 847859.6235 0.76680654 0.635657892 0.663960126 0.573983258 1.196950196 0.616279997 0.798606669 0.680388649 1 19.6934659 GYFEYIEENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYFEYIEENK 10 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 208.03 2.82E-07 165947000 508620 629220 396130 631510 334000 503120 428010 529150 345910 FALSE TRUE 484578.5406 693338.2334 414292.9523 568029.415 392249.4943 485696.8282 362709.2136 482814.8208 399551.9561 1.212804826 1.735289298 1.036893816 1.421665959 0.981723373 1.21560368 0.907789858 1.208390582 1 18.60802359 3.084080484 1.17796307 1.050452323 1.443986526 0.297459846 0.204372141 0.444707538 1.313846695 0.076520895 0.100601638 1213.613737 -3.084080484 0.393534203 GYFEYIEENKYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GYFEYIEENKYSR 13 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;; 257.02 6.31E-24 7560170000 8369560 6899320 7734140 8376590 7190000 7803030 9452570 8665570 8294910 FALSE TRUE 7973947.486 7602368.552 8088757.969 7534559.259 8443933.724 7532809.115 8010406.838 7906766.752 9581242.278 0.832245679 0.793463763 0.844228518 0.786386466 0.881298424 0.786203803 0.836050963 0.825233986 1 23.19178129 -4.999999957 0.405563889 3.991811347 0.818263136 0.783793173 0.029195275 308.7200498 2.114082555 819.3234098 0.015141846 1.00E-05 4.999999957 -3.173548211 GYFSEEMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYFSEEMNR 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 ; 104.44 0.011586 353360000 303980 219330 221630 264290 373320 246000 326330 272160 402110 FALSE TRUE 289611.4678 241679.9764 231791.9547 237723.0671 438426.8898 237480.9583 276542.365 248328.2276 464467.1651 0.623534858 0.52033813 0.499049173 0.511818886 0.943935164 0.511297625 0.595397018 0.534651847 1 18.82521709 -2.106587223 2.421461978 1.742959432 0.589955399 0.487819296 0.131199686 11762312.09 3405904.427 48109030.64 0.029623075 0.007823711 2.106587223 -1.153004034 GYGFVHFETQEAAER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 253.15 1.16E-24 3427492000 2906700 2660034 2773600 3104800 3273440 2736530 3249830 2980820 2974010 FALSE TRUE 2769306.052 2931094.489 2900772.303 2792699.605 3844326.9 2641763.28 2754008.746 2719803.598 3435204.282 0.806154693 0.853251873 0.844424979 0.812964638 1.119097027 0.769026545 0.801701593 0.791744355 1 21.71196446 -2.362161899 2.268379706 2.012982949 0.847262296 0.185066709 0.098929306 7192944.542 1072472.977 37243134.3 0.023125968 0.004343483 2.362161899 -1.165720653 GYGYGQGAGTLS(ph)TDKGESLGIKHEEAPGHRPTTNPNASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYGYGQGAGTLSTDKGESLGIKHEEAPGHRPTTNPNASK 39 3 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 1 GYGYGQGAGT(0.001)LS(0.498)T(0.498)DKGES(0.003)LGIKHEEAPGHRPTTNPNASK 122.46 7.26E-09 164080000 124650 49513 103050 166400 71865 210450 234030 123940 20898 TRUE FALSE 118758.0415 54558.43099 107774.9444 149673.1559 84398.23325 203162.0637 198324.4252 113087.1566 24138.75511 4.919808043 2.260200692 4.464809554 6.200533341 3.496378868 8.416426731 8.216017121 4.6848794 1 14.55906365 3.38718655 4.007943328 5.984577488 3.553283921 0.04305725 2.292210373 0.360332846 10.95134073 0.621472337 0.864693942 2438.858196 -3.38718655 -2.431293567 GYIFLEYASPAHAVDAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYIFLEYASPAHAVDAVK 18 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 211.78 2.65E-16 356170000 555890 453310 497890 610100 535160 509220 681280 616060 582880 FALSE TRUE 529614.1814 499502.8044 520718.749 548771.5889 628491.7346 491585.5837 577338.2234 562114.5205 673270.0535 0.786629642 0.741905572 0.773417362 0.815083912 0.933491296 0.730146219 0.857513594 0.834902009 1 19.36082577 -5 0.132454785 1.676713408 0.722659455 0.576479201 0.054632722 96.43594309 0.800209779 17.20151929 0.367010573 1.00E-05 5 -0.954053953 GYIPIYTPFFMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYIPIYTPFFMR 12 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 133.13 0.00039225 30740000 73263 55234 45505 42069 82818 47199 90591 60744 68251 FALSE TRUE 69800.00318 60862.4074 47591.44926 37840.14419 97261.43298 45564.4868 76769.67913 55424.93334 78835.0165 0.885393399 0.772022511 0.603684142 0.479991581 1.233733908 0.577972693 0.973801777 0.703049683 1 16.26654896 2.773098317 24.99967504 0.87595249 0.717434159 0.201275855 0.203351243 1257.283088 910066.2137 0.058052674 0.061571375 593.0595684 -2.773098317 -0.158518331 GYISPYFINTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYISPYFINTSK 12 0 P10809;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 136.5 0.0002532 91013000 320990 292470 368160 433500 295340 314340 330240 332040 358340 FALSE TRUE 305817.4388 322273.0255 385040.5002 389923.7564 346847.2025 303454.327 279855.8227 302964.8173 413909.5371 0.738850912 0.778607393 0.930252786 0.942050669 0.837978281 0.733141665 0.676127989 0.731959016 1 18.65895597 2.243632354 24.86641659 0.748612624 0.83495672 0.02034996 0.106425503 245.6907264 1204610.132 0.037269927 0.030290507 175.2396408 -2.243632354 0.086344096 GYIWNYGAIPQTWEDPGHNDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 GYIWNYGAIPQTWEDPGHNDK 21 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 304.91 1.70E-55 6376539000 8594753 8289417 7554660 9396061 6238137 8744077 9126633 9186253 5502570 FALSE TRUE 8188496.059 9134118.017 7901048.634 8451551.097 7326066.118 8441267.421 7734197.514 8381855.988 6355880.452 1.28833387 1.437112936 1.24310844 1.329721533 1.152643788 1.328103555 1.216856983 1.31875608 1 22.59966056 -4.779362745 0.156884311 2.58E-16 1.380993055 0.589053746 0.075947561 78.03082231 0.757308112 24.46385149 0.312317 1.66E-05 4.779362745 1.380993055 GYIWNYGTLPQTWEDPHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYIWNYGTLPQTWEDPHEK 19 0 Q9H2U2-2;Q9H2U2;H0Y9D8;D6RGV9;D6RGI1 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 231.86 2.39E-20 139540000 375970 336700 294210 354400 286930 285250 287240 350540 219540 FALSE TRUE 358198.6432 371010.1128 307699.8195 318775.0387 336970.5012 275371.721 243416.2625 319844.8593 253585.1419 1.412537976 1.463059349 1.213398455 1.257073014 1.328825887 1.085914257 0.959899545 1.261291797 1 17.95211069 2.90602369 0.576801028 1.029559896 1.468812285 0.596851506 0.104790835 0.544253909 0.389062783 0.081862877 0.110918524 805.4223748 -2.90602369 0.439252389 GYIWNYGTLPQTWEDPHEKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYIWNYGTLPQTWEDPHEKDK 21 1 Q9H2U2-2;Q9H2U2;H0Y9D8;D6RGV9;D6RGI1 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ; 197.86 5.33E-22 576030000 1418450 1094650 1176430 1232560 776880 1199210 1320090 1364290 623580 FALSE TRUE 1351402.68 1206196.08 1230370.479 1108660.727 912367.626 1157681.057 1118686.025 1244825.535 720281.6016 1.876214354 1.674617367 1.708179796 1.539204562 1.266681842 1.607261735 1.553123144 1.728248413 1 19.45820153 -2.803459988 0.120293526 2.42E-21 1.963430783 0.610468782 0.156365212 56.33288401 0.762797997 17.6720338 1.745127129 0.001572317 2.803459988 1.963430783 GYKIPVIENLGATLDQFDAIDFSDNEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYKIPVIENLGATLDQFDAIDFSDNEIR 28 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 94.606 0.0021274 71116000 76469 64247 59513 76519 60978 70435 87278 77212 77753 FALSE TRUE 72854.46192 70793.84234 62241.72992 68827.16474 71612.54389 67995.81829 73962.13813 70450.90795 89810.53813 0.811201708 0.788257635 0.693033704 0.766359563 0.797373509 0.757102894 0.823535185 0.784439214 1 16.45459712 -0.298739782 0.60678357 1.020903267 0.772695265 0.80378725 0.034762649 3.367625909 1.131313031 0.196849275 0.01406459 0.50264367 0.298739782 -0.248208002 GYLGPEQLPDCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GYLGPEQLPDCLK 13 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ;; 189.58 7.73E-07 147334000 739734 534431 495188 543660 547245 494425 679030 658890 624774 FALSE TRUE 704768.2398 588890.1265 517892.8596 489010.2639 642684.3547 477302.9383 575431.5023 601194.0986 721660.761 0.976592158 0.81602071 0.71764032 0.67761792 0.890562976 0.661395165 0.797371193 0.833070233 1 19.46096129 -0.997931326 5.009171269 1.000001916 0.799538901 0.310600864 0.095271385 12446425.27 2484727.579 264.1578554 0.022728498 0.100477466 0.997931326 -0.200463016 GYLPSHYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYLPSHYER 9 0 Q6P2Q9;I3L1T8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 148.52 8.98E-05 532540000 445340 432410 370040 431490 570620 384910 510610 421820 516180 FALSE TRUE 424289.6608 476473.0706 387006.7 388115.8054 670135.9473 371580.4702 432707.0665 384883.2046 596226.5581 0.711624893 0.79914768 0.64909336 0.650953568 1.123961921 0.623220259 0.725742691 0.645531802 1 19.18550111 -2.226446761 2.307767896 1.852981196 0.743936592 0.237749034 0.145579151 5643422.098 1031858.272 25169873.3 0.032204928 0.005936811 2.226446761 -1.109044605 GYLS(ph)EGLVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYLSEGLVTK 10 0 K7ELV1;P31152 K7ELV1 MAPK4 Mitogen-activated protein kinase 4 1 GY(0.001)LS(0.999)EGLVTK 69.672 0.059033 21120000 29488 30421 25755 32306 23089 27885 31798 33758 25811 TRUE FALSE 28094.16068 33520.93449 26935.89223 29058.5395 27115.71429 26919.33546 26946.63109 30801.97056 29813.63806 0.942325812 1.124349012 0.903475523 0.974672713 0.90950706 0.902920181 0.903835722 1.033150349 1 14.86368481 3.714812686 24.99222494 0.937724383 1.033337437 0.239094348 0.06257862 808.2078835 850555.0018 0.015577351 0.024147376 5185.763253 -3.714812686 0.095613054 GYNDDYYEESYFTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 ; 264.28 9.48E-25 138172000 142770 123810 138925 180204 193847 152915 171740 150278 189392 FALSE TRUE 136021.545 136426.3798 145294.8487 162089.5516 227653.8554 147619.5152 145537.9088 137118.8616 218761.9441 0.621778827 0.623629399 0.664168758 0.740940351 1.040646518 0.674795225 0.665279829 0.626794858 1 17.73900226 3.281753021 3.590712671 0.77201405 0.626771919 0.220605358 0.136103927 0.384848473 10.2439365 0.039031014 0.052293175 1913.167615 -3.281753021 -0.145242131 GYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 31 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK 254.78 1.39E-58 288880000 112610 104800 106630 136240 108130 105700 118280 138620 116670 TRUE FALSE 107287.1485 115479.2391 111519.091 122544.8964 126987.8378 102039.5825 100234.2136 126481.6979 134762.5877 0.796119682 0.856908739 0.82752263 0.909339145 0.942307801 0.757180344 0.743783682 0.938552013 1 17.04006051 1.034394312 7.159698781 0.999879656 0.831279887 0.477396592 0.061004587 0.145774644 21.69800536 0.062414132 0.015649677 10.82416271 -1.034394312 -0.168599769 GYNPGLLVHPDLAYLQAEGGGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 158.77 2.09E-11 358330000 464090 338130 446900 474070 611420 475580 664930 504800 606160 FALSE TRUE 442153.3854 372585.8314 467390.807 426415.5829 718051.4544 459110.5454 563482.7162 460597.0359 700160.197 0.631503172 0.532143691 0.667548383 0.609025741 1.025553091 0.655722144 0.80479113 0.657845216 1 19.41732552 2.942725593 24.999754 0.803093866 0.601849444 0.421420193 0.12522566 260.1783081 113565.1669 0.034236113 0.036312991 876.4468672 -2.942725593 -0.201244422 GYPHWPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 140.53 0.00064813 4006630000 6056345 4939789 3332522 4523763 7064922 3849523 6146511 4903700 5887935 FALSE TRUE 5770073.574 5443159.115 3485321.43 4069025.749 8297042.16 3716213.053 5208747.859 4474306.032 6801005.888 0.84841473 0.800346185 0.512471462 0.598297636 1.219972795 0.54642109 0.76587904 0.657888863 1 22.69731671 3.987889584 23.97043657 0.741721798 0.8303891 0.014595773 0.21464096 1587.174471 3141552.261 0.051076386 0.094866242 9724.999428 -3.987889584 0.088667302 GYPTLLWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYPTLLWFR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 130.22 0.00085448 55618000 127400 38018 23830 23880 204270 27193 147660 45210 113760 FALSE TRUE 121378.0545 41892.07742 24922.62907 21479.53703 239894.6233 26251.29959 125131.755 41251.17273 131401.3198 0.923720208 0.318810172 0.189668027 0.163465154 1.825663728 0.199779573 0.952286897 0.313932712 1 17.00362024 GYRDDRS(ph)PAREPGDVSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GYRDDRSPAREPGDVSAR 18 3 A0A1W2PR91;A0A1W2PQT1;C9J366;P0DPB3-2;P0DPB3;B3KU38-2;B3KU38 A0A1W2PR91 IQCJ-SCHIP1 1 GYRDDRS(1)PAREPGDVSAR;GYRDDRS(1)PAREPGDVSAR;GYRDDRS(1)PAREPGDVSAR;GYRDDRS(1)PAREPGDVSAR 180.66 4.28E-13 1597590000 452646 407883 436685 480829 505011 435942 547353 463697 522517 TRUE FALSE 431250.3206 449446.7414 456707.4392 432495.1554 593084.7585 420845.2192 463844.247 423093.2325 603546.2677 0.714527359 0.744676532 0.756706592 0.716589893 0.982666599 0.697287419 0.768531382 0.701012093 1 19.20310485 -2.107643628 2.41769561 1.438445162 0.759230571 0.454670546 0.082510139 5858890.864 1699173.011 14123713.55 0.01847808 0.007804703 2.107643628 -0.679214591 GYS(ph)FSLTTFSPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYSFSLTTFSPSGK 14 0 A0A024RA52;P25787;H3BT36 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 1 GYS(0.999)FS(0.001)LTTFSPSGK;GYS(1)FSLTTFSPSGK 141.46 1.01E-05 67025000 189830 153829 183524 178328 174380 179898 245740 216363 171982 TRUE FALSE 180857.1121 169504.35 191938.7569 160402.1306 204791.8168 173668.0872 208247.8497 197417.1087 198652.0902 0.91042139 0.853272421 0.966205574 0.807452519 1.030906932 0.874232368 1.048304347 0.993783194 1 17.59988445 2.187433652 1.044348763 1.014749738 0.888497576 0.336907786 0.065029441 0.504398527 1.03952927 0.041154555 0.022219573 153.9691286 -2.187433652 -0.126252162 GYS(ph)PDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYSPDTR 7 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 GY(0.004)S(0.996)PDTR 73.665 0.050642 141240000 354770 358920 345020 394440 388090 357110 396980 335670 374880 TRUE FALSE 338000.7252 395494.3561 360839.5083 354790.1418 455772.7731 344743.1912 336413.41 306276.9553 433014.4758 0.780576041 0.91335135 0.833319735 0.819349379 1.052557821 0.796147035 0.776910309 0.707313433 1 18.72405573 -1.205178738 6.254773384 1.000001726 0.838375131 0.236302913 0.093072394 2.17E-06 2.75E-07 0.08711487 0.020532952 0.062347818 1.205178738 -0.161626596 GYSDRDGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 192.38 6.28E-07 5973426000 3345768 2108093 3076869 2804629 4426284 2912796 4213700 3256723 4774881 FALSE TRUE 3187620.177 2322910.073 3217946.487 2522702.364 5198226.528 2811925.144 3570822.675 2971547.069 5515345.159 0.577954794 0.421172203 0.583453328 0.457397006 0.942502487 0.509836658 0.647434126 0.538778079 1 22.39501974 -5 0.174823248 2.6690424 0.482886516 0.456687051 0.142397583 112.8600369 1.075678948 65.47604679 0.438863324 1.00E-05 5 -2.186155884 GYSFTTTAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 215.42 1.91E-08 26552870000 8914030 8082970 6904560 8446990 9073320 7661930 9332720 8289250 7959800 FALSE TRUE 8492681.468 8906633.833 7221140.906 7597882.517 10655704.14 7396595.443 7908842.157 7563399.326 9194165.131 0.923703387 0.968726764 0.785404743 0.826380907 1.158963754 0.804487992 0.860202318 0.822630355 1 23.13228715 GYSYDLEVEQAYDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 GYSYDLEVEQAYDLAR 16 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 276.71 6.12E-35 205684000 245862 271106 224720 261819 265415 225431 266373 259376 272356 FALSE TRUE 234240.5905 298732.0096 235023.6343 235500.4567 311703.292 217624.2679 225732.9066 236663.6624 314591.5775 0.744586338 0.949586801 0.747075418 0.748591105 0.990818936 0.691767624 0.717542753 0.752288616 1 18.26312052 GYT(ph)SDDDTWEPEIHLEDCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.583)S(0.417)DDDTWEPEIHLEDCK;GYT(0.572)S(0.427)DDDT(0.001)WEPEIHLEDCK;GYT(0.565)S(0.433)DDDT(0.002)WEPEIHLEDCK 205.96 1.42E-15 374304000 561820 521510 453440 621020 350119 534400 557650 534740 291404 TRUE FALSE 535263.882 574652.4619 474230.6725 558593.8897 411179.6427 515893.594 472570.2506 487915.3308 336593.444 1.590238585 1.707259818 1.408912386 1.659550712 1.221591359 1.532690559 1.403979367 1.449568729 1 18.36064755 -2.935801689 0.121223627 5.15E-18 1.813792556 0.639594065 0.125678151 45.85929798 0.603014092 13.36512731 1.207586474 0.001159307 2.935801689 1.813792556 GYT(ph)SDSEVYTDHGRPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.586)S(0.414)DSEVYTDHGRPGK;GYT(0.499)S(0.499)DS(0.002)EVYTDHGRPGK;GYT(0.5)S(0.5)DSEVYTDHGRPGK 197.09 2.26E-11 2519490000 2467550 2497770 2508530 3017140 2361570 2967800 3090550 2979950 2540040 TRUE FALSE 2350913.802 2752295.603 2623548.582 2713851.355 2773427.06 2865024.342 2619029.836 2719009.78 2933936.43 0.801283142 0.938089719 0.894207712 0.92498642 0.945292145 0.976512072 0.892667547 0.926744612 1 21.48440618 6.030630896 0.741344211 0.937340677 3.26E-15 0.632489116 0.032642188 9.661019379 0.912266434 0.010829915 11.6387546 1073077.023 -6.030630896 -0.937340677 GYTS(ph)DDDTWEPEIHLEDCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.123)S(0.877)DDDTWEPEIHLEDCK 245.66 8.68E-25 238090000 312730 314980 241360 349310 199440 312320 289150 312010 152880 TRUE FALSE 297947.8727 347076.8201 252426.5947 314196.6952 234222.2729 301504.2801 245034.8569 284688.7503 176587.8496 1.687250133 1.965462635 1.429467516 1.779265651 1.326378193 1.707389726 1.387608816 1.612164999 1 17.43002655 -1.988380123 0.118278433 1.49E-14 2.065075594 0.558209438 0.180771985 38.6195991 0.655160791 12.89570306 2.03498673 0.010271169 1.988380123 2.065075594 GYTS(ph)DSEVYTDHGRPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.427)S(0.572)DS(0.001)EVYTDHGRPGK;GYT(0.41)S(0.59)DSEVYTDHGRPGK;GYT(0.146)S(0.845)DS(0.009)EVYTDHGRPGK 230.99 3.69E-16 2122700000 1443350 1400360 1499470 1725950 1327610 1626670 1844450 1716210 1535620 TRUE FALSE 1375125.706 1543058.276 1568222.183 1552454.227 1559144.764 1570338.01 1563045.277 1565929.554 1773756.107 0.775262 0.869938246 0.884125037 0.875235451 0.879007411 0.885317888 0.881206425 0.882832509 1 20.75837622 -5 0.019642197 2.103819308 6.92E-15 0.794588927 0.024139383 1526.221125 2.26890739 162.8998428 90.07479264 1.00E-05 5 -2.103819308 GYWAGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GYWAGLDASAQTTSHELTIPNDLIGCIIGR 30 0 F8VZX2;Q15366-2;Q15366-3;Q15366-5;Q15366-4;F8VRH0 F8VZX2;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ;; 334.45 1.87E-105 521574000 460099 417948 441383 442347 524278 420674 528818 458755 491711 FALSE TRUE 438351.0321 460537.3764 461620.8471 397881.4392 615711.9172 406105.9539 448137.1017 418583.9802 567963.0306 0.771795009 0.810858016 0.81276566 0.700541088 1.084070413 0.71502181 0.789025126 0.736991596 1 19.1154375 -1.899846087 2.57910581 1.109078174 0.802273414 0.251728647 0.106938096 30504757.08 16294872.28 20169274.07 0.024436287 0.012593717 1.899846087 -0.306804761 GYWAS(ph)LDASTQTTHELTIPNNLIGCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 GYWAS(0.99)LDAS(0.002)T(0.002)QT(0.003)T(0.003)HELTIPNNLIGCIIGR;GY(0.004)WAS(0.934)LDAS(0.016)T(0.016)QT(0.016)T(0.016)HELTIPNNLIGCIIGR 91.942 0.00094437 48347000 35634 20142 31127.3 53109 48567 48325 59550 34313 37527 TRUE FALSE 33949.65144 22194.4927 32554.51749 47770.38242 57037.06942 46651.49313 50464.55379 31308.37182 43346.4955 0.783215599 0.512025077 0.751029976 1.102058699 1.315840387 1.076246017 1.164213005 0.722281501 1 15.40362774 3.317865566 4.205221197 1.090808276 0.646371985 0.549760049 0.162937055 0.135493567 4.533684943 0.043993296 0.05970589 2079.053026 -3.317865566 -0.444436291 GYWASLDASTQTTHELTIPNNLIGCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;; 342.71 6.68E-106 631944000 673740 508708 628617 670992 735207 565374 713095 616862 738757 FALSE TRUE 641893.6454 560545.9236 657439.7112 603542.6094 863426.868 545794.9566 604299.2609 562846.2931 853319.6625 0.752231167 0.656900278 0.770449505 0.707287826 1.011844571 0.639613712 0.708174542 0.659596067 1 19.70272677 -2.200484191 2.412499339 1.811139056 0.733691527 0.376307997 0.105751242 13151520.63 2243230.581 58456772.18 0.025988128 0.006302543 2.200484191 -1.077447529 GYWGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GYWGLDASAQTTSHELTIPNDLIGCIIGR 29 0 Q15366;Q15366-6 Q15366 PCBP2 Poly(rC)-binding protein 2 0 144.44 6.62E-08 84795000 104840 96281 92845 115530 108970 97942 118750 116760 90108 FALSE TRUE 99884.42097 106092.1434 97102.03509 103916.7049 127974.3335 94550.24398 100632.5065 106535.8754 104081.4884 0.959675178 1.019318084 0.932942414 0.998416784 1.229559026 0.908425172 0.966862677 1.023581398 1 16.66735397 5.705634316 0.807004631 1.008301345 0.783364062 0.033135383 0.086139575 49.21186989 7.690759937 0.028377585 14.28291576 507731.7431 -5.705634316 -0.224937283 GYWGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYWGNK 6 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 142.27 0.026864 2466800000 3217400 3055800 2766100 3363300 2622300 3289300 3521400 3545400 2761900 FALSE TRUE 3065319.878 3367189.494 2892928.421 3025214.694 3079628.29 3175390.716 2984145.755 3234945.981 3190201.346 0.960854675 1.055478676 0.906816877 0.948283311 0.965339788 0.995357462 0.935409848 1.014025646 1 21.60521605 -0.836471373 8.019522293 1 0.974579028 0.039015448 0.041664869 0 0 0.039497217 0.009309583 0.145723176 0.836471373 -0.025420972 GYYS(ph)PYSVSGSGSTAGSR ddPTM_SK-BR-3_Trastuzumab_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(0.765)PYS(0.233)VS(0.002)GSGSTAGSR;GYYS(0.88)PYS(0.12)VSGSGSTAGSR;GYY(0.005)S(0.959)PYS(0.035)VS(0.001)GSGSTAGSR;GYYS(0.887)PYS(0.11)VS(0.003)GSGSTAGSR 313.04 3.39E-61 2305970000 1008216 853086 926001 972497 988935 887508 1110792 984263 1183310 TRUE FALSE 960559.6278 940016.4333 968459.0618 874739.7539 1161404.951 856773.3754 941320.2793 898075.7138 1366811.671 0.702773943 0.687743932 0.708553404 0.639985575 0.849718345 0.626840839 0.688697865 0.657058857 1 20.38238304 -1.093699581 4.659429752 1.000018269 0.694810034 0.712136787 0.060906906 7444516.467 1747438.158 1392.56144 0.012612025 0.080593575 1.093699581 -0.305208236 GYYSPYS(ph)VSGSGSTAGSR ddPTM_SK-BR-3_Trastuzumab_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(0.496)PYS(0.5)VS(0.003)GSGSTAGSR;GYYS(0.001)PYS(0.989)VS(0.011)GSGSTAGSR 430.78 5.60E-169 1216750000 543510 505670 517310 621970 579900 552050 640850 568990 658450 TRUE FALSE 517819.3594 557198.3479 541029.1752 559448.3939 681034.3764 532932.3701 543076.5625 519166.2192 760559.0631 0.68084043 0.732616801 0.711357213 0.735575212 0.89543917 0.700711353 0.714049163 0.682611311 1 19.53670076 -2.022469711 2.761195573 1.310906096 0.730491521 0.656279997 0.061027466 30607140.32 29581511.81 60027175.04 0.014286855 0.009495772 2.022469711 -0.580414575 GYYSPYSVS(ph)GSGS(ph)TAGSR ddPTM_SK-BR-3_Trastuzumab_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 GYYSPYS(0.008)VS(0.992)GSGS(0.948)T(0.034)AGS(0.018)R 257.29 1.87E-30 107410000 459740 399760 424330 488360 453810 429090 451120 441140 501680 TRUE FALSE 438009.0013 440495.9985 443785.9502 439269.125 532954.3203 414230.5057 382293.3586 402511.443 579477.9722 0.755868251 0.76016004 0.765837481 0.758042835 0.919714546 0.714833912 0.65972026 0.694610429 1 19.1443943 -2.139586935 2.488015202 1.55350602 0.751214618 0.564185512 0.068030356 11507816.25 3581008.222 35869902.49 0.017018733 0.007251253 2.139586935 -0.802291402 GYYSPYSVS(ph)GSGSTAGS(ph)R ddPTM_SK-BR-3_Trastuzumab_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 GYYSPYS(0.011)VS(0.987)GS(0.019)GS(0.061)T(0.424)AGS(0.498)R 130.09 2.89E-05 111970000 460080 443900 431000 473150 451300 421720 447800 464220 494930 TRUE FALSE 438332.9302 489133.9147 450761.7763 425588.0631 530006.5771 407115.7307 379479.8856 423570.4358 571681.2166 0.766743628 0.855606062 0.788484497 0.744449967 0.927101611 0.712137672 0.663796316 0.74092068 1 19.12485136 GYYSPYSVS(ph)GSGSTAGSR ddPTM_SK-BR-3_Trastuzumab_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 GYYSPYS(0.046)VS(0.918)GS(0.036)GSTAGSR;GYYSPYS(0.025)VS(0.911)GS(0.064)GSTAGSR;GYYSPYSVS(0.939)GS(0.061)GSTAGSR 353.57 1.82E-90 712080000 568560 447963 489216 525018 525333 469480 577770 523033 608997 TRUE FALSE 541685.2956 493610.939 511647.0375 472242.1932 616950.9089 453221.7899 489620.575 477233.4577 703437.1444 0.770055008 0.701712929 0.727352887 0.67133531 0.877051935 0.644296073 0.696040263 0.678430847 1 19.42406199 -0.893197332 12.96976261 1 0.720176647 0.646088131 0.064943333 0 0 0.05731013 0.013508127 0.127880012 0.893197332 -0.279823353 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.999)T(0.001)AGS(1)R;GYYSPYSVSGSGS(0.998)T(0.002)AGS(1)R;GYYSPYSVSGS(0.001)GS(0.997)T(0.005)AGS(0.998)R;GYYSPYSVSGSGS(0.998)T(0.003)AGS(0.999)R;GYYSPYSVSGS(0.01)GS(0.984)T(0.007)AGS(0.999)R;GYYSPYSVSGS(0.021)GS(0.973)T(0.3)AGS(0.706)R 286.05 1.46E-39 3061318000 4685200 4527820 4308140 5129500 5102270 4528170 4724730 4647690 4950280 TRUE FALSE 4463739.881 4989210.006 4505672.48 4613872.915 5992104.273 4371358.337 4003885.663 4240713.625 5717944.14 0.780654685 0.872553121 0.787988195 0.806911156 1.047947326 0.764498259 0.700231686 0.741650062 1 22.4470651 -1.442074483 7.326076589 1.000015385 0.811845708 0.278634468 0.094647107 2.41E-05 1.83E-06 0.092691711 0.021845861 0.036134789 1.442074483 -0.188169678 GYYSPYSVSGSGS(ph)TAGS(ph)RTGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYYSPYSVSGSGSTAGSRTGSR 22 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 3 GYYSPYSVSGS(0.015)GS(0.96)T(0.035)AGS(0.981)RT(0.069)GS(0.939)R;GYYSPYSVSGS(0.014)GS(0.957)T(0.033)AGS(0.994)RT(0.044)GS(0.957)R 130.62 0.00011737 379340000 456940 313260 505650 455190 626200 394410 572650 452970 681910 TRUE FALSE 435341.3518 345181.5501 528834.5527 409433.4364 735409.0817 380751.4828 485281.7251 413305.5455 787657.1201 0.552704141 0.438238342 0.671401983 0.519811763 0.933666519 0.4833975 0.616107838 0.524727746 1 19.58720821 -5 0.267543158 3.777246114 0.553000785 0.448636787 0.13956261 183.520154 1.787124129 281.6985477 0.163544251 1.00E-05 5 -3.224245329 GYYSPYSVSGSGS(ph)TAGSR ddPTM_SK-BR-3_Trastuzumab_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 GYYSPYSVSGSGS(0.82)T(0.155)AGS(0.025)R;GYYSPYSVSGSGS(0.384)T(0.384)AGS(0.232)R 396.56 5.68E-127 2239030000 1438500 1259130 1280720 1503650 1471950 1410230 1518800 1435200 1594440 TRUE FALSE 1370504.956 1387436.779 1339442.279 1352500.245 1728657.614 1361393.381 1287079.165 1309526.28 1841697.612 0.744153083 0.753346678 0.727286754 0.734376934 0.938621847 0.739205705 0.698854772 0.711043046 1 20.81260477 -1.14062112 3.718963564 1.000151631 0.754034547 0.567329414 0.066987085 17606892.32 25394256.98 31384.83966 0.015926817 0.072340063 1.14062112 -0.246117084 GYYSPYSVSGSGST(ph)AGSR ddPTM_SK-BR-3_Trastuzumab_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(0.247)T(0.661)AGS(0.092)R 393.61 9.82E-126 1428800000 466520 441470 429950 462690 499880 417990 442680 487610 529080 TRUE FALSE 444468.5242 486456.2949 449663.6328 416179.5221 587058.9137 403514.9015 375141.0356 444912.2834 611127.0242 0.727293192 0.795998664 0.735794057 0.681003303 0.960616845 0.660279918 0.613851165 0.728019325 1 19.22111275 GYYSPYSVSGSGSTAGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 GYYSPYSVSGSGST(0.049)AGS(0.95)R;GYYSPYSVSGSGS(0.055)T(0.055)AGS(0.89)R;GYYSPYSVSGS(0.005)GS(0.02)T(0.041)AGS(0.934)R;GYYSPYSVSGSGS(0.001)T(0.013)AGS(0.986)R;GYYSPYSVSGSGST(0.005)AGS(0.995)R;GYYSPYSVSGSGS(0.033)T(0.033)AGS(0.933)R;GYYSPYSVSGSGS(0.145)T(0.145)AGS(0.71)R 396.43 5.84E-127 7803610000 2403604 2146249 2230205 2442412 2453405 2212169 2573278 2419889 2638715 TRUE FALSE 2289990.402 2364954.213 2332462.105 2196896.105 2881278.055 2135561.033 2180677.18 2207990.691 3047913.446 0.751330523 0.775925647 0.765265204 0.720786907 0.945328044 0.70066328 0.715465586 0.724426966 1 21.5393905 -0.948131237 4.448955931 1.000004859 0.76108482 0.538593721 0.069103815 11948506.27 38745491.62 993.2863326 0.015737248 0.112685689 0.948131237 -0.238920039 GYYSPYSVSGSGSTAGS(ph)RTGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 GYYSPYSVSGSGSTAGSRTGSR 22 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 2 GYYSPYSVSGSGSTAGS(0.999)RT(0.005)GS(0.996)R;GYYSPYSVSGSGS(0.002)T(0.012)AGS(0.985)RT(0.082)GS(0.918)R 177.35 3.65E-17 954760000 1135010 531940 1209690 975560 1637600 1021460 1642080 1180750 2115200 TRUE FALSE 1081360.327 586145.2908 1265155.483 877494.8554 1923196.922 986086.5841 1391550.537 1077357.27 2443214.413 0.442597392 0.23990743 0.517824173 0.359155893 0.787158471 0.403602148 0.569557272 0.440958953 1 21.22034905 -5 0.15189086 2.949157114 0.292582854 0.590908165 0.140392365 85.29892189 0.764686384 50.1356526 0.626739839 1.00E-05 5 -2.65657426 HAAENPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 141.39 0.0006343 1944689000 4605720 4828070 3747049 5200300 2585280 4097843 3948688 4511130 2326976 FALSE TRUE 4388016.743 5320055.822 3918854.903 4677555.964 3036152.013 3955933.669 3346243.123 4116111.542 2687831.554 1.632549011 1.97931147 1.457998697 1.740271245 1.129591625 1.471793745 1.244960131 1.531387462 1 21.3580113 3.039741248 1.471496881 1.30138441 1.780665733 0.47212915 0.209736966 0.297753131 1.3323228 0.068815358 0.084715659 1095.825111 -3.039741248 0.479281323 HAAENPGKYNILGTNTIMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HAAENPGKYNILGTNTIMDK 20 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 198.07 9.57E-22 1319920000 1397470 949540 1453400 1237010 1081740 1350500 1812610 1546500 1062480 FALSE TRUE 1331414.363 1046299.206 1520039.828 1112663.405 1270395.114 1303731.846 1536063.054 1411080.261 1227243.972 1.084881566 0.852560069 1.238579991 0.906635869 1.035161013 1.062324913 1.251636259 1.149796042 1 20.22699065 1.96054628 6.555545091 1.16137693 1.013091542 0.134839187 0.119228952 0.286635007 35.27427826 0.046601251 0.029422262 91.31587395 -1.96054628 -0.148285388 HADGEKEDQFNGS(ph)PPRPQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 205.02 4.73E-22 1902512000 997572 886616 940169 1059534 673072 1071073 1114637 1008894 372811 TRUE FALSE 950418.7486 976963.1784 983276.6786 953027.6293 790455.5437 1033981.473 944578.6539 920549.8929 430624.6258 2.207070129 2.26871182 2.283373081 2.213128493 1.835602277 2.401120167 2.193508214 2.13770843 1 18.7160713 0.561410413 2.709451723 1.000010157 2.20704593 0.872333633 0.143551298 2.186815767 13.11140463 0.128311703 0.03390119 3.642591022 -0.561410413 1.207035773 HADIVTTTTHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HADIVTTTTHK 11 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ; 146.16 2.08E-05 776580000 1467020 1231320 1230890 1111130 1035310 1105380 1274370 1254640 554670 FALSE TRUE 1397676.872 1356792.908 1287327.524 999437.1014 1215867.736 1067100.413 1079941.451 1144777.07 640685.3907 2.181533858 2.117721002 2.009297453 1.559949885 1.897760982 1.665560709 1.685603366 1.786800646 1 19.28925657 0.484092454 0.096689977 4.07E-15 2.974782663 0.817780477 0.143644173 9.35251565 0.405347924 7.295584001 4.609836579 3.048543902 -0.484092454 2.974782663 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.461)S(0.461)DT(0.077)EMEDMIAEETLEEMDSELLK;HADNS(0.456)S(0.456)DT(0.087)EMEDMIAEETLEEMDSELLK 191.02 2.83E-18 95582000 57222 49693 50059 57305 36036 53890 63305 43446 11477.5 TRUE FALSE 54517.22946 54756.7732 52354.25467 51544.59253 42320.66699 52023.77579 53646.65957 39641.63792 13257.37208 4.112219913 4.130288632 3.949067307 3.887994711 3.192236495 3.924139375 4.046553061 2.990158055 1 13.69450721 0.890411232 2.865394622 1.001803671 3.915959232 0.92110406 0.268103594 0.115190409 1.997116232 0.270434688 0.071324805 7.769824906 -0.890411232 2.914155561 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.306)S(0.306)DT(0.388)EMEDMIAEETLEEMDSELLK 130.12 9.27E-05 24640000 24318 22207 23162 25298 15715 23852 21241 18700 9497.3 TRUE FALSE 23168.53633 24469.91855 24224.00061 22754.99698 18455.69102 23025.99926 18000.29533 17062.52887 10970.09278 2.111972688 2.230602698 2.208185573 2.074275709 1.682364169 2.098979446 1.640851695 1.555367781 1 13.42128811 1.088422331 0.433520441 0.943664314 2.222724584 0.875500986 0.135893555 0.341992709 0.176219235 0.168075428 0.091886062 12.25807661 -1.088422331 1.27906027 HAEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HAEELER 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 147.34 0.0041813 447320000 237819 207360 220087 259628 257718 209699 265114 236396 204024 FALSE TRUE 226577.7672 228490.2197 230178.2066 233529.7002 302663.9376 202437.071 224665.9901 215695.913 235662.9999 0.9614482 0.969563401 0.976726116 0.990947668 1.284308261 0.859010838 0.953335866 0.915272712 1 17.84636574 3.302159585 4.538793198 0.998339604 0.967261004 0.017722596 0.110667234 1.320303553 53.60058047 0.031261444 0.042137746 2005.208721 -3.302159585 -0.0310786 HAEFESLCAQYSADKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAEFESLCAQYSADKR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 73.279 0.023051 155260000 100590 80354 87719 95657 63082 93200 103290 103750 65035 FALSE TRUE 95835.31005 88542.16395 91741.00292 86041.37662 74083.48083 89972.46063 87531.21345 94665.09999 75120.29565 1.275757892 1.178671665 1.221254551 1.14538123 0.98619794 1.197711748 1.16521391 1.260180077 1 16.19691512 -4.999999989 0.023420315 2.86E-07 1.943977373 0.297707462 0.081440151 3176.325656 5.620058654 330.5296202 163.1494853 1.00E-05 4.999999989 1.943977087 HAEMVHTGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 182.64 1.02E-06 2277161000 2126430 1791919 1613810 2182232 1548225 1955791 2353075 1937305 340345 FALSE TRUE 2025917.868 1974517.583 1687804.785 1962869.893 1818234.95 1888061.467 1994070.192 1767664.304 393123.9644 5.153381762 5.022633475 4.293314419 4.993004933 4.625093138 4.802712728 5.072369971 4.496455226 1 18.58462479 0.776414018 4.31733166 1.000022707 4.872004193 0.958762584 0.249171934 0.609000762 11.61608367 0.238423222 0.06065244 5.976047194 -0.776414018 3.871981486 HAEQQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HAEQQALR 8 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55;K7EK20;K7EPK1 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 ; 83.168 0.018384 29695000 54250 42979 35988 40797 55513 41099 53191 45604 50399 FALSE TRUE 51685.71001 47358.60896 37638.0854 36696.00805 65194.44962 39675.73132 45075.73603 41610.672 58214.61952 0.887847596 0.813517452 0.646540091 0.63035726 1.119898235 0.681542397 0.774302682 0.714780451 1 15.82909388 4.251116583 3.296810922 0.782241284 0.875593392 0.025555148 0.155730694 0.783661357 17.61230392 0.036494401 0.107288668 17828.57295 -4.251116583 0.093352108 HAGVYSTGLAMVGAICDFCEAWVCHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAGVYSTGLAMVGAICDFCEAWVCHGR 27 0 Q9Y3S2;D6RBR7;D6R8Y9;D6R9C8 Q9Y3S2 ZNF330 Zinc finger protein 330 0 120 0.00010346 76638000 80801 62598 75548 86506 88544 66455 94781 75701 43106 FALSE TRUE 76981.69686 68976.80737 79011.95053 77810.25253 103986.0456 64153.64669 80320.41768 69072.21912 49790.65833 1.546107231 1.38533632 1.586883026 1.562748016 2.088464966 1.288467533 1.613162396 1.387252578 1 15.60358747 0.774542824 1.64123022 0.999475712 1.569632906 0.4406663 0.207548288 0.750365814 3.459198794 0.186556248 0.053447812 5.950354283 -0.774542824 0.570157193 HAHGDQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HAHGDQYK 8 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;; 160.88 0.00035078 484903000 1262820 1235260 1155670 1262824 1088060 1111914 1498565 1037942 182235.93 FALSE TRUE 1203129.001 1361134.398 1208658.613 1135882.532 1277817.32 1073408.139 1269931.386 947054.296 210496.1473 5.715681815 6.466315018 5.741951234 5.396215308 6.070502173 5.099419411 6.033038621 4.499152636 1 17.6834343 0.824811236 2.363304887 1.000205014 5.831624018 0.939759007 0.381355367 0.141461162 1.405120904 0.352128575 0.095099037 6.680534876 -0.824811236 4.831419004 HAHLTDTEIMTLVDETNMYEGVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HAHLTDTEIMTLVDETNMYEGVGR 24 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;;; 118.22 0.0003262 113412500 85871.5 86077.2 83815.3 93259 97529.5 88471.1 104186.7 80212.7 63795 FALSE TRUE 81812.52438 94848.56454 87658.31441 83884.42814 114538.6139 85407.32362 88291.10539 73188.85075 73688.00278 1.11025569 1.287164273 1.189587329 1.138372937 1.55437262 1.159039741 1.198174765 0.993226143 1 16.16914213 1.313330596 2.549980368 0.985393409 1.239851123 0.387939148 0.124075512 0.28506233 3.067348289 0.103697905 0.03085463 20.57456189 -1.313330596 0.254457714 HAIPS(ph)AERGPGLLESPSIFNFTADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAIPSAERGPGLLESPSIFNFTADR 25 1 Q92615 Q92615 LARP4B La-related protein 4B 1 HAIPS(0.995)AERGPGLLES(0.005)PSIFNFTADR 148.17 1.33E-07 38078000 18657 14129 15418 16990 23923 18425 24939 18718 18438 TRUE FALSE 17775.12058 15568.76116 16124.93055 15282.13292 28095.16363 17786.93763 21134.09751 17078.95269 21297.27087 0.834619642 0.731021419 0.757136003 0.717562969 1.319190792 0.835174504 0.992338297 0.801931515 1 14.37838095 HAIVICNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HAIVICNR 8 0 P53621;A0A3B3IT15;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 102.72 0.004911 257320000 344710 367000 331680 372790 297590 365480 373630 370680 217476 FALSE TRUE 328416.2414 404397.7172 346887.8561 335316.4409 349489.6018 352823.336 316625.8813 338221.2941 251201.0674 1.307383941 1.609856684 1.380917126 1.334852771 1.39127435 1.404545529 1.260447993 1.346416628 1 17.93848307 -0.168891366 0.312518396 0.879605482 1.459029273 0.670734913 0.086451254 3.58673173 0.465520342 0.59392297 0.093135789 0.677811033 0.168891366 0.579423791 HALIIYDDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HALIIYDDLSK 11 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 155.11 3.17E-05 1313070000 2597220 2338680 2284590 2303780 1586210 2046170 2247530 2362000 1170540 FALSE TRUE 2474454.558 2576994.151 2389340.711 2072199.658 1862844.522 1975310.62 1904628.02 2155170.758 1352061.365 1.830134802 1.905974254 1.76718363 1.532622491 1.377781046 1.460962254 1.408684598 1.593988863 1 20.3667292 7.999999998 0.067883453 0.320997132 4.476144978 0.792013707 0.119125516 108.4043607 0.54473605 6.003561847 43.29349885 99999999.61 -7.999999998 4.155147845 HAPEHHPGHGDRLS(ph)PGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HAPEHHPGHGDRLSPGER 18 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER 95.926 0.00084626 94512000 31815.4 38210.3 33221.9 39451.7 48989.7 33357.2 34304.7 24206.4 25306.8 TRUE FALSE 30311.54909 42103.97301 34745.15698 35485.94016 57533.48817 32202.0318 29070.88797 22086.75929 29231.24929 1.036957018 1.440375421 1.188630586 1.213972752 1.968218587 1.101630364 0.994514045 0.755587251 1 14.83522387 1.854409682 3.463331155 0.910193255 1.343592033 0.383759605 0.256801782 0.259931793 5.268280234 0.127594711 0.06812796 71.51706481 -1.854409682 0.433398777 HAPEHHPGHGDRLS(ph)PGERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HAPEHHPGHGDRLSPGERR 19 2 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR 159.46 2.08E-11 344334000 182275 152070 194114 173901 188560 184741 194295 171342 88637 TRUE FALSE 173659.222 167566.1059 203014.3189 156420.1411 221444.8043 178343.3728 164651.7293 156338.3861 102382.3733 1.696182814 1.636669483 1.982903037 1.52780343 2.162919233 1.74193435 1.608203874 1.527004905 1 16.64360783 0.831383907 1.236964556 1.003944092 1.771749043 0.652188179 0.180050423 0.40927277 1.184076516 0.158577459 0.048538274 6.782407924 -0.831383907 0.767804951 HAPHCLS(ph)EEEGEQDRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;HAPHCLS(1)EEEGEQDRPR;HAPHCLS(1)EEEGEQDRPR;HAPHCLS(1)EEEGEQDRPR 241.8 1.35E-20 4277870000 1522656 1379008 1522700 1756965 1781322 1676738 2058520 1378981 447650 TRUE FALSE 1450683.068 1519530.483 1592517.301 1580351.54 2091983.993 1618672.143 1744454.967 1258230.113 517069.2757 2.805587446 2.93873675 3.079891566 3.056363266 4.045848576 3.130474423 3.373735491 2.433387889 1 18.97999806 4.047751921 2.266410806 3.060925658 2.830083229 0 0.79694912 2.011686519 20.3530176 0.189622222 0.518608754 11162.25452 -4.047751921 -0.230842429 HAPINSAQHLDNVDQTGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAPINSAQHLDNVDQTGPK 19 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 57.745 0.048831 30618000 50691 47000 52142 63501 72324 57085 69349 56524 47151 FALSE TRUE 48294.93689 51789.35343 54532.76228 57117.75884 84937.2827 55108.13214 58768.53637 51574.45891 54462.93627 0.886748681 0.95091005 1.001282083 1.048745491 1.559542847 1.011846513 1.0790556 0.946964348 1 15.73298714 3.349780145 2.686184667 1.124429694 0.924237404 0.180929745 0.168980591 0.416529552 6.081163858 0.048926013 0.069630006 2237.588105 -3.349780145 -0.20019229 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK 166.88 1.71E-12 213040000 88986 92993 89572 87326 65718 100620 97096 92758 41560 TRUE FALSE 84779.80813 102469.0924 93678.9648 78547.82457 77179.19839 97135.50417 82282.22191 84635.61778 48004.91254 1.766065256 2.134554299 1.95144538 1.636245551 1.607735423 2.023449248 1.714037534 1.763061597 1 15.55089443 -2.144750824 0.280822606 9.67E-11 1.930692029 0.719345003 0.163574143 18.99521138 0.751766466 12.37584321 0.19580052 0.007165544 2.144750824 1.930692029 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 125.52 3.06E-06 138370000 52377 50274 57846 54003 35512 69503 70933 67351 29173 TRUE FALSE 49901.24301 55396.97776 60498.29632 48574.51584 41705.28156 67096.09368 60110.86808 61453.38939 33696.99984 1.480880887 1.643973588 1.795361504 1.441508623 1.23765563 1.991159272 1.783864093 1.823705068 1 15.04033253 2.23004911 24.99772146 1.732244545 1.542213322 0.009566707 0.297273987 458.1398695 1345515.004 0.100075947 0.075073857 169.8435701 -2.23004911 -0.190031223 HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 HAPTYTIPLS(0.999)PVLS(0.971)PT(0.029)LPAEAPTAQVPPSLPR;HAPTYTIPLS(0.999)PVLS(0.956)PT(0.045)LPAEAPTAQVPPSLPR 141.25 3.34E-10 179213000 134430 117906 132672 154594 134601 130438 149227 125067 97709 TRUE FALSE 128075.7603 129920.7554 138755.1424 139053.9174 158075.3718 125920.8994 126459.6804 114115.4705 112861.2127 1.134807586 1.151155055 1.22943161 1.232078888 1.400617342 1.11571457 1.120488407 1.011113276 1 16.78419023 1.534412978 1.892212164 1.004777809 1.209028656 0.553036006 0.07709956 0.272495542 1.957785337 0.066881531 0.022674396 34.23047911 -1.534412978 0.204250847 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPT(0.005)YT(0.005)IPLS(0.989)PVLS(0.001)PTLPAEAPTAQVPPSLPR 105.24 3.60E-06 60969000 124440 107250 113610 125170 115790 113110 129780 113400 93718 TRUE FALSE 118557.9678 118178.8969 118819.1309 112587.6738 135983.7393 109192.9723 109979.6774 103470.0948 108251.3088 1.09521048 1.091708712 1.097623042 1.040058315 1.256185637 1.008698865 1.015966261 0.955832276 1 16.72402494 2.037829894 24.99992697 0.99736296 1.108769695 0.52648873 0.056891442 128.9843715 85238.9213 0.019543155 0.014433545 109.1012921 -2.037829894 0.111406736 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR 32 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;; 231.07 9.55E-37 390522000 192195.6 200162.5 187210.2 210520 184332 174340.7 217506 188152.1 101291.6 FALSE TRUE 183110.8949 220559.2863 195793.9728 189358.1296 216479.4424 168303.2378 184321.4649 171676.5047 116999.384 1.565058624 1.88513203 1.67346157 1.618454074 1.850261386 1.438496786 1.575405431 1.467328278 1 16.83614141 0.576102921 0.516240232 0.968864698 1.730717603 0.761843942 0.119907402 0.744479169 0.3808996 0.161572053 0.055935182 3.767930826 -0.576102921 0.761852905 HAQPTCPGAQLCTVYYASLNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 255.35 4.45E-37 1705311000 885481 924597 896343 1037714 764179 916139 989018 866059 519634 FALSE TRUE 843626.068 1018814.485 937441.2132 933401.0172 897451.5757 884412.8767 838125.1395 790222.2827 600216.1868 1.405537016 1.697412545 1.561839274 1.555108039 1.495213884 1.473490546 1.396372104 1.316562765 1 19.1951227 0.891053316 0.659861207 0.994977763 1.564870489 0.855262198 0.070615901 0.307040551 0.298785126 0.069871726 0.027683546 7.78132072 -0.891053316 0.569892726 HAS(ph)APSHVQPSDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 HAS(1)APSHVQPSDSEK;HAS(0.996)APS(0.004)HVQPSDSEK;HAS(1)APSHVQPSDSEK;HAS(1)APSHVQPSDSEK;HAS(1)APSHVQPSDSEK;HAS(0.999)APS(0.001)HVQPSDSEK;HAS(0.994)APS(0.006)HVQPSDSEK;HAS(1)APSHVQPSDSEK 197.38 5.45E-09 3195289000 4873620 3897172 4362245 5048819 3217965 5036645 5715060 4575392 965162 TRUE FALSE 4643253.641 4294298.258 4562258.248 4541302.122 3779177.077 4862224.721 4843122.633 4174746.421 1114834.394 4.164971648 3.851960688 4.092319249 4.073521725 3.38989997 4.361387439 4.344252977 3.744723382 1 20.08839799 2.792535788 24.73489791 3.717971566 4.029248191 0.046451337 0.963657298 1316.961936 603513.402 0.262601357 0.278530623 620.20575 -2.792535788 0.311276624 HAS(ph)PDKWNDKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HASPDKWNDKPK 12 2 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 HAS(1)PDKWNDKPK;HAS(1)PDKWNDKPK 97.417 0.0025741 259480000 830800 868810 798430 951700 352180 1046120 984610 955580 251660 TRUE FALSE 791529.7305 957342.7268 835038.8053 856033.3079 413600.0805 1009892.602 834389.6609 871904.3494 290686.1475 2.722970246 3.293389572 2.872647398 2.944871351 1.422840696 3.474168311 2.870414253 2.999469899 1 18.1491028 2.961726001 24.99914436 2.552784074 2.988166733 0.108963457 0.74640705 1471.285186 960988.386 0.210231931 0.223030232 915.6426228 -2.961726001 0.435382659 HAS(ph)PILPITEFSDIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 227.04 3.48E-15 971898800 357973.5 351931.6 384575.3 567482.6 510435.9 471702 584920 402324.5 306990.5 TRUE FALSE 341052.8021 387793.8302 402208.4579 510438.1709 599455.7594 455366.8415 495679.7112 367094.8339 354597.0188 0.961803918 1.093618416 1.134269146 1.439488049 1.690526788 1.284181246 1.397867678 1.035245122 1 18.43582088 3.418762929 4.055902396 1.347116942 1.03714818 0.244088042 0.200260479 0.239196617 8.065574478 0.053528634 0.075469558 2622.786434 -3.418762929 -0.309968762 HAS(ph)SSPESPKPAPAPGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;HAS(0.25)S(0.25)S(0.25)PES(0.25)PKPAPAPGSHR;HAS(0.317)S(0.317)S(0.317)PES(0.049)PKPAPAPGSHR 111.67 0.0001278 191955000 200628 175136 200736 222918 197528 194922 225546 172062 93686 TRUE FALSE 191144.712 192982.5575 209939.9442 200509.8591 231976.8207 188171.8023 191134.8153 156995.3391 108214.3464 1.766352784 1.783336165 1.940038 1.852895349 2.143678989 1.738880366 1.766261329 1.450781198 1 16.72353225 0.982378855 1.491077293 1.000966288 1.865938402 0.86522465 0.112486835 0.150135581 0.681536515 0.105931935 0.031317326 9.602379259 -0.982378855 0.864972114 HASSS(ph)PESPKPAPAPGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.29)S(0.29)S(0.42)PESPKPAPAPGSHR 119.83 3.15E-05 96307000 165580 129580 159380 175090 156700 153670 201940 158930 132960 TRUE FALSE 157753.3615 142784.3493 166687.7306 157489.6206 184028.4304 148348.3694 171130.3441 145013.2467 153578.7577 1.027182169 0.929714183 1.08535668 1.025464868 1.198267476 0.965943282 1.114283946 0.944227241 1 17.22861916 3.729627996 24.93610006 1.056114908 0.978448175 0.114114704 0.07741243 954.4372749 2664384.616 0.018237348 0.028710487 5365.719878 -3.729627996 -0.077666733 HASSSPES(ph)PKPAPAPGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.001)S(0.001)S(0.001)PES(0.997)PKPAPAPGSHR 93.34 0.0010702 116900000 94008 60623 82010 87870 86004 85024 128740 108930 73988 TRUE FALSE 89564.42815 66800.55262 85770.23962 79037.14066 101003.0704 82079.59756 109098.3485 99391.51173 85461.68116 1.04800686 0.781643325 1.003610489 0.924825484 1.181852135 0.960425731 1.276576204 1.162995045 1 16.38299008 2.746699715 24.44367045 1.132090359 0.928822911 0.375648271 0.111902692 403.8603242 1212889.222 0.032546209 0.033967389 558.0841847 -2.746699715 -0.203267448 HASTSS(ph)PADKAK ddPTM_SK-BR-3_Trastuzumab_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(0.007)T(0.007)S(0.318)S(0.669)PADKAK 51.939 0.091909 31740000 59394 43185 69238 61704 52626 64748 109150 96215 61862 TRUE FALSE 56586.56333 47585.6006 72412.63079 55501.39669 61803.95774 62505.76052 92497.16282 87789.90453 71455.24301 0.791916183 0.665949741 1.013398426 0.776729521 0.864932441 0.874754012 1.294476919 1.228599902 1 16.12475225 1.845809227 4.902134654 1.19718156 0.810219936 0.666642706 0.114058448 0.117040647 4.082191936 0.051718107 0.029734028 70.11472372 -1.845809227 -0.386961623 HAVSDPSILDSLDLNEDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 294.38 1.23E-49 305239000 334350 367219 283131 391907 277167 318388 304955 313674 154214 FALSE TRUE 318545.9381 404639.0336 296112.8364 352511.7638 325504.837 307362.1437 258428.5139 286207.0417 178128.7195 1.788290732 2.271610298 1.662353141 1.978972087 1.827357419 1.725505828 1.45079645 1.606742823 1 17.44256061 1.186455501 0.438720275 0.973823483 2.024410326 0.735607407 0.17066114 0.477177425 0.256912697 0.199557448 0.115342874 15.3622738 -1.186455501 1.050586843 HAVSDPSILDSLDLNEDEREVLINNINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;;;;; 353.19 3.64E-111 1144772000 400387.9 332395 374654 449240.8 372313.2 362856.8 446984.6 394926.3 222652.3 FALSE TRUE 381462.3575 366266.4284 391832.2565 404082.2613 437244.5042 350290.978 378788.8898 360344.4595 257180.0815 1.483250006 1.42416328 1.523571554 1.571203566 1.700149178 1.362045521 1.472854692 1.401136734 1 17.97241939 0.444597677 0.919050662 0.997754817 1.508668005 0.769096992 0.087175622 0.955232831 1.126225294 0.08779825 0.027704508 2.783541351 -0.444597677 0.510913188 HAVSDPSILDSLDLNEDEREVLINNINRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HAVSDPSILDSLDLNEDEREVLINNINRR 29 2 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 173.44 8.32E-13 287870000 107420 61573 83745 80117 106225 92524 139172 104258 80830 FALSE TRUE 102342.4695 67847.3587 87584.79109 72063.48695 124750.6064 89319.87068 117938.7553 95128.61681 93364.70358 1.096158029 0.726691738 0.938093174 0.771849363 1.336164542 0.956677066 1.263204946 1.01889272 1 16.51058962 2.752885735 24.93713554 1.12876922 0.883825632 0.366626028 0.150781542 733.0885156 1276157.849 0.041509062 0.043846948 566.090328 -2.752885735 -0.244943588 HAVSEGTK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;;;;;;;;; 161.02 0.00034996 1.63006E+11 171982721.9 142948391.3 138918359.8 168479784.2 109946641.3 156838295.5 188362673.9 162506540.4 92354003.1 FALSE TRUE 163853439.5 157514994.9 145287904 151543876.2 129121300.7 151406946 159624488.5 148276606.2 106675790.2 1.535994616 1.476576781 1.361957607 1.420602331 1.210408664 1.41931872 1.496351592 1.389974294 1 26.66865756 -3.101505692 0.326712857 3.86E-26 1.447015643 0.681900488 0.088712626 53.533877 1.474317699 36.99111841 0.081618228 0.000791579 3.101505692 1.447015643 HAVTGEAVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HAVTGEAVELR 11 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 0 135.99 0.0001086 116040000 54485 54195 50745 57981 55939 52850 58301 63625 52398 FALSE TRUE 51909.60203 59717.53211 53071.70844 52152.63972 65694.74389 51019.79125 49406.11168 58053.6577 60523.61423 0.857675185 0.986681527 0.876876061 0.86169077 1.085439869 0.842973307 0.816311324 0.959190201 1 15.88521052 HAYGDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;;;;; 161.02 0.00034996 2652817000 2234760 1651391 1492858 1710078 2112853 1590971 2305686 1829126 1771210 FALSE TRUE 2129127.324 1819669.62 1561307.016 1538177.711 2481333.894 1535875.275 1953911.254 1668958.031 2045880.201 1.040690126 0.88943117 0.763146843 0.751841535 1.21284418 0.750716134 0.955046758 0.815765278 1 20.96429024 0.98729016 0.001835442 0.422617914 1.391313793 0 0.149273574 2006909.411 2839.530283 750768.8662 747820.4171 9.711585988 -0.98729016 0.968695878 HCAPS(ph)PDRS(ph)PELSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(0.744)PELS(0.232)S(0.024)S(0.001)R;HCAPS(1)PDRS(0.999)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR 189.51 5.73E-10 11374760000 5024871 4309588 4745320 5168262 4764987 4620152 5794780 3832003 2431795 TRUE FALSE 4787355.306 4748739.917 4962897.616 4648738.485 5595999.224 4460154.978 4910679.883 3496452.503 2808905.349 1.704349101 1.690601614 1.766844019 1.655000047 1.992234885 1.587862325 1.748253954 1.244774056 1 21.42157658 1.108878949 3.040178701 1.002625212 1.733197745 0.856384797 0.106598714 0.07286963 1.271850034 0.089819705 0.023998284 12.84928463 -1.108878949 0.730572532 HCAPS(ph)PDRSPELSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HCAPS(0.996)PDRS(0.004)PELSSSR;HCAPS(0.987)PDRS(0.013)PELSSSR;HCAPS(0.99)PDRS(0.01)PELSSSR;HCAPS(0.997)PDRS(0.003)PELSSSR 96.633 0.0020212 418010000 306693 282381 311878 364697 273374 296238 348619 296194 217716 TRUE FALSE 292196.2297 311155.9449 326177.9148 328036.9647 321050.339 285979.2038 295430.7687 270257.6831 251478.2853 1.161914355 1.237307406 1.297042066 1.304434553 1.27665233 1.137192435 1.174776456 1.074676021 1 17.94007431 1.32395777 1.060500132 1.00343929 1.244728651 0.754182735 0.048823202 0.253129011 0.579143432 0.048638006 0.016682505 21.0842312 -1.32395777 0.24128936 HCCGVAQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HCCGVAQMR 9 0 O00170;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 105.57 0.0038731 0 13112 13362 9134.2 11054 24521 10894 13528 13004 15335 FALSE TRUE 12492.22175 14723.60299 9553.012105 9942.830919 28797.45464 10516.73805 11464.05514 11865.30082 17713.07348 0.705254329 0.83122802 0.539319848 0.561327255 1.625774018 0.593727456 0.647208693 0.669861209 1 14.11252694 -2.50978229 2.053411227 3.581022306 0.768342495 0.049209543 0.315047196 11034696.23 592348.6695 133010733.8 0.07384652 0.003091845 2.50978229 -2.812679811 HCECAEEGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HCECAEEGTR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 90.05 0.011095 277470000 103868 114640 96358 95790 90507 92292 99714 78810 71654 FALSE TRUE 98958.36549 126321.9463 100776.1096 86161.00721 106291.3921 89095.9049 84500.79793 71908.9786 82765.73636 1.195644114 1.526258956 1.217606633 1.041022662 1.284243901 1.07648296 1.020963525 0.868825456 1 16.33674602 2.495809924 0.671537117 0.938546825 1.352292762 0.539179666 0.123972166 0.520636785 0.478718343 0.098496164 0.080344111 313.1914689 -2.495809924 0.413745936 HCNGVDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HCNGVDWR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;; 105.52 0.004372 697870000 539310 496340 462070 547820 492590 486287 619570 525440 446010 FALSE TRUE 513817.8851 546917.6103 483256.3665 492752.0928 578497.54 469446.7593 525043.2173 479429.6881 515174.9529 0.997365812 1.061615296 0.93804321 0.956475252 1.122914724 0.911237545 1.019155171 0.93061529 1 18.97470293 HCNMVLENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HCNMVLENVK 10 0 P62316;P62316-2 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 116.77 0.0010468 104770000 280960 154780 108540 141900 228110 139640 330530 217100 204980 FALSE TRUE 267679.5776 170552.258 113516.6664 127635.9424 267892.3118 134804.2318 280101.5779 198089.5731 236767.2515 1.130559974 0.720337196 0.479444119 0.539077687 1.131458468 0.569353367 1.183025001 0.836642618 1 17.85311002 1.732585705 25 1.01184955 0.780106378 0.189774114 0.236381705 1.098218414 4560.983642 0.108152661 0.059976101 54.02387167 -1.732585705 -0.231743172 HCPFCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HCPFCPR 7 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 86.113 0.020315 43964000 59517 47374 40778 47155 42447 39114 47270 48785 41746 FALSE TRUE 56703.74936 52201.46446 42647.71163 42414.88981 49849.74336 37759.47237 40058.09333 44513.12677 48219.75647 1.175944333 1.082574204 0.884444774 0.879616425 1.0338033 0.783070574 0.830740266 0.923130477 1 15.55733674 3.858276635 2.770385497 0.889820885 1.149418093 0.611900782 0.074873222 0.152065863 2.265067146 0.019800942 0.04065327 7215.66954 -3.858276635 0.259597208 HCQHAIVFQHIPLFLESIDEDDDYYFNLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HCQHAIVFQHIPLFLESIDEDDDYYFNLSK 30 0 Q9BRF8 Q9BRF8 CPPED1 Serine/threonine-protein phosphatase CPPED1 0 88.518 0.00040748 99489000 25689 25543 22047 28739 24135 23669 32688 23290 17388 FALSE TRUE 24474.73188 28145.86074 23057.87676 25850.10112 28344.13636 22849.3366 27700.84524 21250.60413 20084.44223 1.218591564 1.40137627 1.148046657 1.287070899 1.41124837 1.137663487 1.379219045 1.058062947 1 14.29379078 1.129177804 5.627751483 1.005307671 1.287450083 0.547108882 0.096612407 0.136857589 5.844950516 0.081856995 0.020689363 13.46411474 -1.129177804 0.282142412 HCSQVDSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HCSQVDSVR 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 100.48 0.0046337 60026000 72665 75443 64042 75400 66808 68584 87518 78628 73459 FALSE TRUE 69230.26946 83130.72747 66978.38905 67820.64875 78459.29405 66208.91888 74165.52172 71742.91549 84850.64654 0.815907389 0.979730042 0.789368046 0.799294425 0.924675265 0.780299521 0.87407138 0.845519963 1 16.37263803 -1.655769807 5.453154237 1.001892191 0.857404679 0.352713425 0.062876304 0.001383031 8.73E-05 0.058210789 0.013548343 0.022091754 1.655769807 -0.144487511 HCVTFVLHEEDHTLGNSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HCVTFVLHEEDHTLGNSLR 19 0 A0A0R4J2F3;P0DPB6 A0A0R4J2F3 0 ; 216.19 1.35E-19 198705000 69067 56077 66968 64972 135732 51557 84651 57473 50049 FALSE TRUE 65802.33979 61791.31005 70038.54904 58440.89112 159403.6178 49771.56816 71735.93523 52440.35944 57810.34331 1.138245096 1.068862534 1.211522801 1.01090718 2.757354631 0.860945729 1.24088409 0.907110327 1 15.81904002 HDAATCFVDAGNAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDAATCFVDAGNAFK 15 0 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 220.4 1.67E-12 362110000 797070 851930 769070 966400 558190 860070 804630 849300 420510 FALSE TRUE 759394.0807 938742.6356 804332.6202 869255.636 655538.1593 830285.5602 681868.9155 774930.7896 485720.5431 1.56343826 1.932680528 1.65595759 1.789620901 1.34962 1.709389426 1.403829682 1.59542519 1 18.88976698 -0.378200631 0.250361668 0.694836949 1.799253697 0.631773827 0.157523013 5.487313435 0.453165777 1.633802818 0.260512336 0.418600139 0.378200631 1.104416748 HDADGQATLLNLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;; 210.07 2.07E-09 372726700 934593.4 895586 826809 944371 829541 894376 1000370 940470 561447 FALSE TRUE 890417.0222 986847.2316 864719.0105 849441.0329 974212.6878 863403.5349 847745.1834 858117.4611 648513.3333 1.373012668 1.521706927 1.333386634 1.309828171 1.502224608 1.331358186 1.30721319 1.323207122 1 19.30677671 -1.148074011 0.268958753 0.737068965 1.4464041 0.751609738 0.070096928 7.784488665 0.471979167 1.573033489 0.094435521 0.071109232 1.148074011 0.709335135 HDDPALTLVAGLTSNKPTDK ddPTM_SK-BR-3_Trastuzumab_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 ; 179.87 3.40E-17 242080000 699480 675530 614820 815550 389970 719540 732620 754830 318640 FALSE TRUE 666416.9666 744367.275 643010.1051 733569.3646 457980.6445 694622.1494 620845.3635 688733.0836 368053.0638 1.810654583 2.022445534 1.747058151 1.993107616 1.244333194 1.887288051 1.686836559 1.871287462 1 18.48955426 -2.303803054 0.266674324 2.24E-18 1.883018185 0.554512336 0.218714562 27.77003895 0.969532847 17.17860841 0.26810252 0.004968176 2.303803054 1.883018185 HDDSSDNFCEADDIQSPEAEYVDLLLNPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDDSSDNFCEADDIQSPEAEYVDLLLNPER 30 0 Q96HE7;G3V3E6;G3V5B3 Q96HE7 ERO1L ERO1-like protein alpha 0 189.23 2.96E-18 24896000 19602 15881 17009 20621 17020 16932 22389 16859 11636 FALSE TRUE 18675.45231 17499.29196 17788.87947 18548.1379 19988.28261 16345.64059 18973.14685 15382.73658 13440.45145 1.389495909 1.301986917 1.323532884 1.380023429 1.487173454 1.216152646 1.411645056 1.144510409 1 13.71429398 1.050569768 3.836615629 1.001517904 1.354315162 0.745992717 0.071954384 0.087118585 2.691103806 0.062098823 0.015994236 11.2349144 -1.050569768 0.352797258 HDDYLVMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDDYLVMLK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 97.431 0.006696 228930000 845420 728910 693900 815960 649730 754040 994910 816220 429810 FALSE TRUE 805458.6721 803186.7577 725716.0014 733938.1506 763042.7063 727927.4057 843118.2067 744747.4497 496462.7396 1.622395011 1.617818808 1.461773349 1.478334811 1.536958658 1.46622767 1.698250723 1.500107441 1 18.92132592 0.962538994 23.90975488 0.999999999 1.563696065 0.836881256 0.076281317 1575.073139 1005302.839 0.075595276 0.018898819 9.173582983 -0.962538994 0.563696066 HDEES(ph)HSLSPPGENTVMADSFQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.287)HS(0.267)LS(0.267)PPGENT(0.179)VMADSFQIK;HDEES(0.349)HS(0.303)LS(0.303)PPGENT(0.046)VMADSFQIK;HDEES(0.388)HS(0.329)LS(0.279)PPGENT(0.004)VMADSFQIK 119.79 0.00032057 177409000 161216 137820 157121 207506 141685 170098 202433 130268 51313.2 TRUE FALSE 153595.6392 151864.0147 164325.1533 186647.1026 166394.8191 164207.4636 171548.1279 118861.0433 59270.58898 2.591430958 2.56221538 2.772456898 3.14906779 2.807375833 2.770471264 2.894321296 2.005396696 1 15.85502877 0.970976857 3.170903934 1.003379421 2.772143211 0.92545326 0.165959425 0.068359695 1.731131589 0.178573089 0.046688675 9.353558294 -0.970976857 1.76876379 HDEESHSLS(ph)PPGENTVMADSFQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.101)HS(0.086)LS(0.727)PPGENT(0.086)VMADSFQIK 118.35 0.00090496 42564000 25446 21079 30092 34469 25343 28806 33842 23997 5974.3 TRUE FALSE 24243.21801 23226.97406 31471.74797 31004.11063 29762.81118 27808.441 28678.78135 21895.69546 6900.763932 3.513120902 3.365855476 4.560617966 4.492851942 4.312973385 4.029762686 4.155885005 3.172937907 1 12.75254037 HDGGS(ph)PSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HDGGS(0.939)PS(0.061)IK;HDGGS(0.593)PS(0.407)IK 80.245 0.025866 125545000 252270 235590 243680 278120 206890 250110 283460 252500 180396 TRUE FALSE 240345.6971 259596.8888 254852.969 250162.8492 242971.5505 241448.628 240212.9709 230389.7614 208370.8903 1.153451409 1.245840474 1.223073763 1.200565246 1.166053234 1.158744523 1.152814438 1.105671531 1 17.66879422 0.905668945 0.589059449 0.996510131 1.207862724 0.86363734 0.025090629 0.335431406 0.269545885 0.027230444 0.011472095 8.047647502 -0.905668945 0.211352592 HDGGSPSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 76.035 0.085084 482890000 1460400 1330100 1444700 1649100 1268900 1739500 1798800 1683000 1454900 FALSE TRUE 1391369.786 1465638.702 1510940.924 1483329.335 1490195.758 1679260.679 1524360.023 1535627.598 1680518.461 0.827940792 0.872134842 0.899092131 0.882661731 0.886747627 0.999251551 0.907077225 0.913782046 1 20.68047496 7.999999995 0.114504062 1.030985898 0.400710855 0.658274491 0.03121557 56.73823622 0.450259062 0.233778843 5.675659478 99999998.78 -7.999999995 -0.630275044 HDGITVAVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDGITVAVHK 10 0 R4GMU8;E9PLX3;A0A0C4DGV4;O43504 R4GMU8 LAMTOR5 Ragulator complex protein LAMTOR5 0 ; 162.36 3.93E-06 87989000 138757 124687 132025 163314 106762 130887 160008 142375 48983 FALSE TRUE 132198.2316 137392.7471 138078.4768 146897.3664 125381.259 126354.3504 135595.8409 129907.8902 56579.03347 2.336523328 2.428333229 2.440453086 2.596321595 2.216037484 2.233236282 2.396574005 2.296042938 1 15.78797991 -1.683576589 0.463171827 1.21E-13 2.407133412 0.945020265 0.104060443 8.818189585 0.788506976 10.03120052 0.05288351 0.020721606 1.683576589 2.407133412 HDGSEPCVDVLFGDGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDGSEPCVDVLFGDGHR 17 0 Q96EL3 Q96EL3 MRPL53 "39S ribosomal protein L53, mitochondrial" 0 ; 178.12 5.72E-10 97465000 273541 206549 236482 212680 362830 212163 241354 359700 187100 FALSE TRUE 260611.259 227596.5779 247324.9336 191301.0023 426107.4371 204815.7421 204531.0145 328202.7611 216114.5124 1.205894302 1.053129544 1.144416128 0.885183508 1.971674333 0.947718595 0.94640111 1.518652114 1 17.72143643 -1.142300169 4.192800615 0.99996005 1.177201133 0.031124566 0.325964131 0.00012521 2.56E-05 0.288817557 0.068057717 0.072060925 1.142300169 0.177241083 HDIITVLEQQENWWFGEVHGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDIITVLEQQENWWFGEVHGGR 22 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 0 231.06 8.63E-27 55263000 41458 32640 35139 37560 37147 32292 44107 33066 20830 FALSE TRUE 39498.3625 35966.05311 36750.15791 33784.39744 43625.42504 31173.71994 37377.66707 30170.56575 24060.21002 1.641646622 1.494835377 1.527424652 1.404160538 1.813177234 1.295654524 1.553505437 1.253961031 1 14.55436162 0.949600854 1.261889814 0.996402261 1.546651496 0.625366933 0.137428275 0.306241811 0.990136658 0.113266698 0.034768952 8.904321946 -0.949600854 0.550249235 HDLDLICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 143.73 0.00059669 2158180000 2210500 2375660 1676780 2263520 1764570 1845080 1981970 1965800 1017480 FALSE TRUE 2106014.046 2617742.455 1753662.022 2035986.669 2072310.449 1781184.417 1679584.075 1793664.131 1175265.602 1.79194732 2.227362437 1.492141027 1.732363022 1.763269891 1.515559048 1.429110213 1.526177681 1 20.1645554 1.650078087 0.225295079 0.83746805 2.188345021 0.668685604 0.180736357 1.216805388 0.286339973 0.61270955 0.655448689 44.67639143 -1.650078087 1.350876971 HDMLAWINESLQLNLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HDMLAWINESLQLNLTK 17 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 251.35 5.77E-22 178878000 452104 503175 402810 516603 318099 451577 473796 453092 231526 FALSE TRUE 430733.9399 554449.1046 421279.2369 464673.085 373575.3649 435938.7753 401509.7183 413416.8625 267429.8696 1.610642598 2.073250476 1.575288645 1.737551178 1.396909647 1.630105029 1.501364522 1.545888883 1 18.02880109 -1.989915785 0.137401463 3.70E-10 2.021635785 0.640977525 0.160578622 27.77369632 0.551110241 10.10388874 1.213003597 0.010234914 1.989915785 2.021635785 HDPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDPLAK 6 0 Q9BYN8 Q9BYN8 MRPS26 "28S ribosomal protein S26, mitochondrial" 0 68.033 0.097205 69797000 257330 205050 225240 230470 183600 206180 251010 238120 143950 FALSE TRUE 245166.5209 225944.8281 235567.4768 207302.7177 215619.7819 199039.9349 212713.8144 217268.9504 166273.0308 1.474481578 1.358878388 1.416750965 1.246760925 1.296781449 1.19706686 1.279304367 1.306699886 1 17.34319466 -0.276343151 0.04564677 4.03E-13 2.271104202 0.804388456 0.057053525 69.6601927 0.84728924 25.10143076 17.12159007 0.529245104 0.276343151 2.271104202 HDS(ph)LKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HDSLKK 6 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 HDS(1)LKK 68.735 0.058407 113180000 349030 290720 302280 372710 141410 340550 366060 278220 77556 TRUE FALSE 332532.0436 320344.6985 316139.837 335244.4827 166071.8592 328756.6681 310210.8238 253857.5819 89582.98838 3.711999897 3.57595459 3.529016421 3.742278403 1.853832544 3.669856008 3.462831833 2.833769965 1 16.45093717 HDS(ph)PDLAPNVTYSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR 190.23 5.73E-10 379830000 342510 301840 324860 376990 255050 324110 368960 257700 126109 TRUE FALSE 326320.2311 332597.8392 339755.1523 339094.249 299530.6392 312885.9894 312668.3756 235134.4218 145665.3396 2.240205061 2.283301161 2.332436482 2.327899346 2.056293144 2.147978306 2.146484375 1.614209821 1 17.15229811 0.987893153 1.569218262 0.996114562 2.247328594 0.960411972 0.082541178 0.073490598 0.370678625 0.07905238 0.023132433 9.725079345 -0.987893153 1.251214032 HDS(ph)PDPS(ph)PPRRPQHNS(ph)SGASPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HDSPDPSPPRRPQHNSSGASPR 22 2 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 3 HDS(1)PDPS(0.984)PPRRPQHNS(0.384)S(0.354)GAS(0.277)PR;HDS(1)PDPS(0.97)PPRRPQHNS(0.398)S(0.362)GAS(0.27)PR;HDS(1)PDPS(0.98)PPRRPQHNS(0.378)S(0.353)GAS(0.289)PR 79.017 0.005957 214916000 161321 114083 193194 190691 226072 150834 275773 93831 150235 TRUE FALSE 153695.676 125708.1874 202052.136 171522.3784 265498.8852 145610.5808 233698.7639 85614.66021 173532.6765 0.885687233 0.724406434 1.164346336 0.988415449 1.529964791 0.839096035 1.346713303 0.493363336 1 17.40484782 3.738307644 24.99878567 1.085750206 0.80504683 0.108188522 0.28150372 36.32588295 3589825.464 0.065567651 0.109113073 5474.035928 -3.738307644 -0.280703376 HDS(ph)PEDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK 150.1 0.00041487 2197603000 5396540 5136570 5045930 6495410 2924014 5668410 5965270 4301840 1783315 TRUE FALSE 5141456.249 5659992.323 5277290.882 5842479.046 3433961.116 5472111.54 5055158.502 3925148.084 2059862.382 2.496019294 2.747752652 2.561962841 2.836344358 1.667082784 2.656542295 2.454124385 1.90553899 1 20.97411652 -0.746621569 0.306014451 0.305189221 2.67249433 0.687293236 0.321597107 6.194516222 0.552399782 4.286684095 0.328405713 0.179216681 0.746621569 2.36730511 HDS(ph)PEDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;HDS(1)PEDVKR 147.71 5.62E-05 1951283000 2859500 2708130 2869100 3590070 1641578 3132750 3287780 2347450 880372 TRUE FALSE 2724337.102 2984091.526 3000651.073 3229189.343 1927868.683 3024262.082 2786168.777 2141894.833 1016895.593 2.679072581 2.934511217 2.95079563 3.175536765 1.895837386 2.974014345 2.73987693 2.106307518 1 19.95574013 0.919829289 2.326896883 1.002257982 2.78120315 0.73469569 0.340473071 0.18240171 2.14168875 0.30090627 0.081813731 8.314368882 -0.919829289 1.778945168 HDS(ph)PEDVKRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HDSPEDVKRR 10 2 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 HDS(1)PEDVKRR;HDS(1)PEDVKRR;HDS(1)PEDVKRR;HDS(1)PEDVKRR 115.34 0.00064472 479982000 381580 191156 429391 328384 310430 408597 633590 331784 248635 TRUE FALSE 363543.4696 210635.0137 449079.0021 295374.2164 364568.8937 394447.1834 536924.2088 302731.2341 287192.0459 1.265854938 0.733429135 1.563688857 1.028490241 1.269425455 1.373461379 1.86956504 1.054107307 1 18.13165627 2.397996301 2.954533688 1.447381359 1.115780699 0 0.318874495 0.431568503 7.66862002 0.11498372 0.093678199 250.0324066 -2.397996301 -0.33160066 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK 32 0 P35637-2;P35637 P35637-2 FUS RNA-binding protein FUS 0 ;; 195.51 6.19E-27 215114000 99547 83348 78643 89909 176461 57741 91230 142547 166408 FALSE TRUE 94841.61059 91841.25596 82248.85934 80871.1765 207235.7425 55741.41469 77311.18795 130064.829 192213.7027 0.493417531 0.477808058 0.427903204 0.420735751 1.078152804 0.289997091 0.402214758 0.676667829 1 17.55235166 0.947518427 5.183289597 0.999859082 0.505902586 0.35156928 0.210635615 0.304952543 24.8839757 0.190508242 0.048106415 8.861728226 -0.947518427 -0.493956496 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HDSIPAADTFEDLSDVEGGGSEPTQR 26 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDSIPAADTFEDLS(1)DVEGGGSEPTQR;HDS(0.001)IPAADT(0.029)FEDLS(0.971)DVEGGGSEPTQR 301.85 6.97E-71 325048000 160877 137303 159505 207510 243190 166838 250866 210444 166450 TRUE FALSE 153272.663 151294.3318 166818.462 186650.7006 285602.259 161060.3582 212591.7842 192016.4077 192262.2159 0.797206369 0.786916613 0.867661185 0.970813218 1.48548303 0.837711963 1.10573876 0.998721495 1 17.55271574 3.195029681 3.407435504 1.083594579 0.801941272 0.352847703 0.164344316 0.230723636 5.504985784 0.045199468 0.057579116 1566.858151 -3.195029681 -0.281653307 HDT(ph)PDPS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDTPDPSPLR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDT(1)PDPS(1)PLR;HDT(1)PDPS(1)PLR 113.22 0.0080451 197730000 653070 484400 598070 696550 462730 625690 730070 415790 330050 TRUE FALSE 622200.6754 533760.9107 625492.1011 626531.4706 543429.9655 604022.1984 618684.4128 379381.2234 381232.4683 1.632076822 1.400093001 1.640710467 1.643436807 1.425455623 1.584393378 1.622853414 0.995144052 1 18.54031147 1.234621704 24.99859022 0.997571626 1.557248902 0.881450621 0.086354234 32.07234806 203535.3121 0.070887696 0.020286762 17.16412638 -1.234621704 0.559677276 HDVTCTVSGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HDVTCTVSGGGR 12 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 118.31 0.00063921 154689000 126063 131849 138516 152556 114018 110246 123259 134772 105038 FALSE TRUE 120104.2518 145284.563 144867.0956 137220.781 133902.7031 106428.1534 104453.5757 122970.6492 121326.7566 0.989923865 1.197465152 1.1940243 1.131001808 1.103653529 0.877202658 0.860927784 1.0135493 1 16.88853822 2.287311439 6.542635372 0.917670975 1.125998732 0.601893025 0.074127335 0.122692439 12.05852134 0.026209978 0.021621092 193.7811098 -2.287311439 0.208327757 HEAMITDLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEAMITDLEER 11 0 P35579 P35579 MYH9 Myosin-9 0 ; 172.11 1.37E-05 287320000 401840 379610 353720 438610 339910 351280 401130 366210 261630 FALSE TRUE 382845.8196 418292.6906 369938.4119 394520.0895 399190.1964 339115.0855 339930.2512 334142.711 302202.2442 1.266853 1.384148194 1.224141842 1.305483652 1.320937233 1.122146152 1.12484357 1.105692355 1 18.20515485 1.871732767 0.877754317 1.025931864 1.316336565 0.791072843 0.053866321 0.233984484 0.334606466 0.043812514 0.020013999 74.42738618 -1.871732767 0.290404701 HEAPSS(ph)PISGQPCGDDQNASPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.102)S(0.898)PISGQPCGDDQNASPSK;HEAPS(0.144)S(0.856)PISGQPCGDDQNASPSK;HEAPS(0.045)S(0.955)PISGQPCGDDQNASPSK 249.19 4.11E-38 1164250000 704050 544150 576060 717440 447000 633180 693240 640090 278922 TRUE FALSE 670770.9518 599599.5036 602472.9208 645321.5682 524956.6585 611252.8178 587473.5058 584040.3263 322175.7992 2.082002911 1.861094176 1.870012963 2.003010685 1.629410588 1.897264845 1.823456346 1.812800116 1 18.2974886 -2.104002877 0.292725684 1.62E-14 1.962034077 0.869509926 0.107916019 11.26658734 0.474568389 7.715241114 0.111242049 0.007870406 2.104002877 1.962034077 HECQANGPEDLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 HECQANGPEDLNR 13 0 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;;;;;;;; 246.63 3.37E-17 23771235000 7526852 7114890 6261005 8454493 5852832 6892565 7604474 6722445 4112617 FALSE TRUE 7171072.623 7839905.38 6548078.272 7604631.301 6873564.048 6653873.746 6444271.826 6133792.078 4750380.64 1.50957853 1.650374143 1.378432334 1.600846727 1.446950164 1.40070328 1.356580096 1.291221176 1 22.17961169 0.904220462 0.405225242 0.962486103 1.579816197 0.84026403 0.071902132 0.479501236 0.202904678 0.104312833 0.050907981 8.020851244 -0.904220462 0.617330094 HEDEQALLDQNS(ph)QTPPPS(ph)PFSVQAFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 2 HEDEQALLDQNS(0.595)QT(0.407)PPPS(0.988)PFS(0.009)VQAFNK 82.336 0.0053456 47941000 92602 50135 88394 94538 87715 79415 101260 73937 72288 TRUE FALSE 88224.88698 55243.8135 92446.95233 85034.86063 103012.4682 76664.83864 85810.92723 67462.68432 83498.05384 1.056610099 0.661617977 1.107174935 1.018405301 1.233711009 0.91816318 1.027699728 0.80795517 1 16.34945495 5.075678984 18.62848444 0.966240218 3.37949036 0.027232174 0.156063263 482.1735687 128053.8319 0.035988957 3790.998204 119036.1807 -5.075678984 2.413250143 HEDEQALLDQNS(ph)QTPPPSPFSVQAFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 HEDEQALLDQNS(0.724)QT(0.276)PPPSPFSVQAFNK;HEDEQALLDQNS(0.65)QT(0.349)PPPS(0.001)PFSVQAFNK 142.22 1.29E-07 110093000 140965 95803 115127 151017 113966 126482 166998 130437 83345 TRUE FALSE 134301.8638 105565.4346 120405.6868 135836.4842 133841.6343 122101.8966 141519.388 119015.2448 96269.71693 1.39505826 1.096559105 1.250711965 1.410999103 1.390277634 1.268331315 1.470030166 1.236268773 1 16.55479443 0.980674599 24.02170412 0.999999992 1.317397839 0.488583701 0.104893971 787.9859384 979477.7691 0.105786883 0.026446721 9.564771494 -0.980674599 0.317397847 HEDEQALLDQNSQT(ph)PPPS(ph)PFSVQAFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 2 HEDEQALLDQNS(0.218)QT(0.783)PPPS(0.964)PFS(0.035)VQAFNK 100.17 0.0055755 59674000 62605 42248 52427 70419 62592 48020 60100 53033 50360 TRUE FALSE 59645.78572 46553.11923 54830.82981 63340.34833 73508.02498 46357.05536 50930.64119 48389.14937 58169.5716 1.025377772 0.800300191 0.942603294 1.088891436 1.26368517 0.796929633 0.875554689 0.831863602 1 15.82797706 HEDEQALLDQNSQT(ph)PPPSPFSVQAFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 HEDEQALLDQNS(0.004)QT(0.996)PPPSPFSVQAFNK;HEDEQALLDQNSQT(1)PPPSPFSVQAFNK;HEDEQALLDQNS(0.009)QT(0.991)PPPSPFSVQAFNK;HEDEQALLDQNSQT(1)PPPSPFSVQAFNK 198.81 2.01E-24 1162720000 952950 619100 742060 864330 738900 812940 1098580 808220 492418 TRUE FALSE 907905.9421 682186.9939 776084.185 777445.9063 867763.9261 784787.684 930971.4442 737447.9722 568779.6685 1.596234873 1.199387094 1.364472445 1.366866555 1.525659186 1.379774502 1.636787487 1.296544186 1 19.11751037 0.985913493 23.98781904 0.999999986 1.432745612 0.54948303 0.12616487 355.7558414 605816.0607 0.121333899 0.030333475 9.680850049 -0.985913493 0.432745625 HEDGEFWMSFSDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HEDGEFWMSFSDFLR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 170.56 1.13E-06 38582000 76912.7 94490 58898.1 83027 70624.7 66387.1 75178.1 77561.3 36825.7 FALSE TRUE 73277.1891 104118.6384 61598.63614 74680.96822 82941.62532 64088.09808 63708.3001 70769.62139 42536.44148 1.722692039 2.4477515 1.448137973 1.755693839 1.949895723 1.506663366 1.497734599 1.663740993 1 15.37641172 0.989884083 0.219914827 0.75797929 2.190829139 0.480997952 0.268238657 2.5523053 0.457357498 1.363065282 0.859293026 9.769764217 -0.989884083 1.432849849 HEEAPGHRPTTNPNASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 HEEAPGHRPTTNPNASK 17 1 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;;;;;;;; 144.97 3.17E-07 3122090000 1470133 1260732 1036710 1430167 1102083 1218368 1237302 1193930 372071 FALSE TRUE 1400642.727 1389202.024 1084244.179 1286403.896 1294285.926 1176175.611 1048528.855 1089383.16 429769.8704 3.259052863 3.232432331 2.522848281 2.993238904 3.011579023 2.736756789 2.439744913 2.534805799 1 18.71320482 -0.623724954 0.246229284 1.21E-13 3.319579537 0.906959754 0.197176333 3.214959206 0.226653969 2.838199974 0.358116021 0.237834606 0.623724954 3.319579537 HEEEEWT(ph)DDDLVESL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEEEEWTDDDLVESL 15 0 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL 303 2.07E-43 218113000 403540 396460 384890 466080 367090 417690 447270 307470 143285 TRUE FALSE 384465.4639 436859.7247 402537.5872 419228.7529 431110.3798 403225.2906 379030.7468 280546.2968 165504.906 2.322985301 2.639557553 2.432179184 2.533029159 2.604819339 2.436334368 2.290148105 1.695093539 1 17.33651446 1.04652194 1.608430633 1.000769658 2.505681965 0.969004954 0.088870059 0.054518586 0.285618448 0.079018859 0.023126309 11.13068622 -1.04652194 1.504912307 HEEEFDLFMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 158.79 7.88E-06 66881000 80217 69477 63052 77632 75250 69400 85700 73308 41882 FALSE TRUE 76425.30138 76556.78529 65942.99657 69828.28387 88373.57617 66996.6606 72624.89101 66888.76289 48376.84666 1.579790885 1.582508795 1.363110685 1.443423635 1.826774217 1.384891022 1.501232429 1.382660663 1 15.56202911 0.628428445 0.980036314 0.999071015 1.543141248 0.626498067 0.128491618 0.764296769 1.203852089 0.11620273 0.03748853 4.250386708 -0.628428445 0.544070233 HEENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEENLK 6 0 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 128.38 0.01665 879020000 1332010 1381720 1019610 1479940 880160 1267530 1378020 1288570 635130 FALSE TRUE 1269048.527 1522518.839 1066360.127 1331173.619 1033659.625 1223635.118 1167777.74 1175735.98 733622.7166 1.729838101 2.075343095 1.453553854 1.814520719 1.40897985 1.667935153 1.591796047 1.602643911 1 19.48467879 -2.159013032 0.143573842 1.31E-12 2.022532912 0.610601161 0.175406241 30.4736602 0.598738076 11.43682835 1.130242925 0.00693405 2.159013032 2.022532912 HEERQDEHGYISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HEERQDEHGYISR 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;; 198.48 8.10E-08 5174801000 2211288 403328 2364450 1103459 3216341 1749066 3955324 1893339 1068729 FALSE TRUE 2106764.799 444427.5817 2472862.371 992537.2049 3777269.852 1688495.406 3351866.679 1727548.2 1234462.035 1.706625833 0.360017213 2.003190298 0.804024082 3.059850967 1.36779857 2.715244847 1.399434046 1 20.23545104 2.774851881 24.98991544 2.025933841 1.173225873 0.158860373 0.759626726 781.7335126 538295.0274 0.205349845 0.217800168 595.4590238 -2.774851881 -0.852707968 HEFPELAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEFPELAAR 9 0 Q70J99;Q70J99-3;K7EN29 Q70J99 UNC13D Protein unc-13 homolog D 0 ; 137.95 0.0001502 337750000 328770 266870 255090 297790 304840 269970 358380 295160 246000 FALSE TRUE 313229.6937 294064.3564 266786.1288 267855.5834 358003.9995 260620.8712 303702.5489 269314.2257 284148.4236 1.102345351 1.034897019 0.938897093 0.942660811 1.259919006 0.917199779 1.068816589 0.947794192 1 18.11628519 1.599411648 0.008513343 1.64E-07 2.038688592 0.030191858 0.101480405 5210.177878 45.2109658 5406.02339 5414.366318 39.75682073 -1.599411648 2.038688428 HEFQAETKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEFQAETKK 9 1 Q12931-2;Q12931 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 71.221 0.032583 136850000 353750 292980 278730 288100 449130 244830 362050 287870 439390 FALSE TRUE 337028.9386 322834.9951 291510.0462 259139.6406 527458.1298 236351.4757 306812.623 262662.5767 507528.3571 0.664059326 0.636092527 0.574371938 0.510591452 1.039268294 0.465691173 0.604523114 0.51753281 1 18.95312891 -1.053503594 4.608119333 1.00001304 0.627968455 0.353969554 0.158557977 2.38E-05 4.90E-06 0.138868408 0.032730175 0.088408985 1.053503594 -0.372044586 HEGVFICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEGVFICR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 103.56 0.0047486 164720000 91579 85822 67120 91797 100690 71173 69055 73359 61847 FALSE TRUE 87250.24216 94567.35937 70197.51839 82569.39116 118250.3041 68708.26116 58519.39147 66935.29706 71437.91689 1.221343594 1.323769834 0.982636693 1.155820253 1.655287686 0.961789819 0.819164304 0.936971569 1 16.12440239 2.026277891 24.99955792 0.896583399 1.25775449 0.486218236 0.172599963 169.6563944 161402.4385 0.061744912 0.045600467 106.2375119 -2.026277891 0.361171092 HEHPPNPPVS(ph)PGKTVNDVNSNNNMSYR ddPTM_SK-BR-3_Trastuzumab_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(0.804)PGKT(0.196)VNDVNSNNNMSYR 103.73 0.0011412 57771000 46193 37166 39250 39403 38926 49293 54538 38191 19778 TRUE FALSE 44009.54844 40953.25765 41049.65132 35442.13558 45714.68208 47585.97105 46217.22644 34846.79358 22845.07123 1.92643516 1.792651782 1.796871234 1.551412785 2.001074176 2.082986329 2.02307211 1.525352809 1 14.47959532 0.963437511 4.234438199 1.000954759 1.880927397 0.783348144 0.150086359 0.100721891 5.489687386 0.152961352 0.03899666 9.192581972 -0.963437511 0.879972638 HEHQVMLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HEHQVMLMR 9 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 88.496 0.0070642 127520000 115218 119824 97970 110745 145749 105995 157981 95749 31491.6 FALSE TRUE 109771.8735 132034.2018 102462.0214 99612.7022 171167.5795 102324.3666 133878.0969 87364.70996 36375.15649 3.01777048 3.62979062 2.816813212 2.73848175 4.705617679 2.813028903 3.680481676 2.401768635 1 15.15066583 0.957982932 3.767772391 1.002254008 3.344008465 0.624709262 0.586872063 0.13995934 5.49826766 0.505752218 0.129984066 9.077848537 -0.957982932 2.341754457 HEIEGTGLPQAQLLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEIEGTGLPQAQLLWR 16 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 204.52 2.50E-11 270820000 287770 299370 254570 325960 264290 281820 317450 286800 176511 FALSE TRUE 274167.6824 329876.1434 266242.2863 293193.8815 310382.0923 272060.5027 269017.1721 261686.2716 203883.4244 1.344727671 1.617964503 1.305855477 1.43804668 1.522350791 1.334392453 1.319465636 1.283509301 1 17.63738496 0.81091392 0.605922776 0.993090777 1.460710855 0.689261627 0.090897702 0.564484836 0.451795254 0.092801531 0.037028663 6.470143611 -0.81091392 0.467620078 HEIVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEIVPK 6 0 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 71.359 0.088439 924740000 2042430 2125050 1783160 2396430 1338660 2082220 2028130 2114260 1036260 FALSE TRUE 1945888.382 2341595.011 1864919.65 2155536.303 1572121.88 2010112.199 1718701.519 1929124.186 1196957.908 1.625694912 1.956288517 1.558049483 1.800845534 1.313431215 1.679350782 1.43589136 1.611689244 1 20.19094099 -2.341942974 0.149346455 1.25E-13 1.918903497 0.605413893 0.165627957 30.29813458 0.583940493 11.14168591 0.895836259 0.004550478 2.341942974 1.918903497 HEIVQTLSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEIVQTLSLK 10 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 170.52 4.30E-06 1873830000 6007400 6949600 5034300 6487500 3760600 5917000 5364200 6226200 2483800 FALSE TRUE 5723442.108 7657772.141 5265127.635 5835364.175 4416447.449 5712092.806 4545792.77 5681000.921 2868975.019 1.994943166 2.669166546 1.83519466 2.033954335 1.539381633 1.990987293 1.58446579 1.980150013 1 21.45210398 0.01513974 0.119980651 2.92E-15 2.882562531 0.563882837 0.282964692 14.59589813 0.588941362 9.466926496 4.235654837 1.03547529 -0.01513974 2.882562531 HEIVQTLSLKDGLIPLEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEIVQTLSLKDGLIPLEIR 19 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 217.36 2.17E-19 366910000 674160 309160 667330 502150 565050 642930 898090 657470 481160 FALSE TRUE 642293.7929 340663.7555 697927.7406 451672.928 663594.5411 620665.1729 761069.8759 599898.4413 555775.8354 1.1556706 0.612951722 1.255772015 0.812689036 1.19399675 1.116754514 1.369382811 1.079389213 1 19.08414358 2.719187897 23.88397537 1.187619969 0.939845478 0.173829833 0.198447816 585.7836181 722191.3831 0.059743261 0.056419345 523.8270211 -2.719187897 -0.247774491 HEKEDGAISTIVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 179.39 1.13E-06 797550000 1072240 1168060 892540 1227850 685140 1077390 1065410 1125480 509980 FALSE TRUE 1021557.34 1287086.642 933463.8418 1104424.185 804628.1991 1040079.714 902862.1369 1026927.005 589065.0938 1.734201111 2.18496505 1.584653125 1.874876303 1.365941061 1.765644791 1.53270351 1.743316682 1 19.16806754 -1.877680486 0.142353281 1.27E-16 2.120016293 0.559681783 0.208280881 29.57156379 0.632760733 11.6139866 1.396798958 0.013253162 1.877680486 2.120016293 HELIEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 133.79 0.0032373 586800000 530100 650540 418100 585920 412400 481890 469600 511730 229050 FALSE TRUE 505043.2236 716830.7656 437270.2986 527022.2084 484322.4294 465202.0285 397953.8952 466920.2083 264569.9042 1.908921671 2.709419153 1.652759031 1.991996066 1.830602883 1.758333133 1.504154059 1.764827371 1 18.01328943 1.603785561 0.257108316 0.863229536 2.451225663 0.575671945 0.277065392 1.177425505 0.323343858 0.689828652 0.69825934 40.15924704 -1.603785561 1.587996128 HELQANCYEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HELQANCYEEVK 12 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 136.51 0.00010858 475710000 533410 767430 402610 725510 255429 512630 406470 520840 206013 FALSE TRUE 508196.7664 845631.9895 421070.0667 652580.3564 299975.7367 494877.4946 344455.5362 475232.4885 237960.4439 2.135635479 3.553666213 1.769496055 2.742390062 1.260611772 2.079662849 1.447532752 1.997107085 1 17.86036225 3.014932122 1.314203065 1.599831244 2.765373064 0.381595791 0.579939098 0.379042736 1.367557592 0.206826424 0.251219171 1034.980392 -3.014932122 1.165541819 HELQANCYEEVKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 HELQANCYEEVKDR 14 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;; 264.85 6.13E-25 36949130000 25529910 26300140 21277370 29117620 13954180 25653570 24593140 25440890 10127610 FALSE TRUE 24323161.75 28980154.17 22252958.46 26190661.52 16387784.57 24765180.44 20841004.81 23213150.8 11698148.03 2.07923183 2.477328384 1.902263366 2.238872464 1.400887091 2.117017186 1.781564462 1.98434408 1 23.47977682 -1.374702382 0.170877711 2.86E-16 2.419341584 0.594431024 0.269024834 17.80553746 0.56195451 9.190187031 1.10958121 0.042198559 1.374702382 2.419341584 HELS(ph)PPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 158.3 3.15E-05 3347930000 1019750 1133420 784511 1261010 580801 1065380 929280 939810 354017 TRUE FALSE 971548.4384 1248916.787 820481.6053 1134250.879 682092.5105 1028485.623 787501.2686 857515.2542 408916.1483 2.375911156 3.054212439 2.006478856 2.773798207 1.668049827 2.515150423 1.9258258 2.097044242 1 18.64144551 -0.545630026 0.182425295 9.14E-17 2.928451431 0.587591457 0.371943328 9.696325296 0.479814349 6.63047768 1.367751415 0.284688533 0.545630026 2.928451431 HELTEISNVDVETQSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HELTEISNVDVETQSGK 17 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 243.01 1.96E-20 110270000 136050 114560 140510 142700 102680 120700 157470 136740 65012 FALSE TRUE 129619.1861 126233.7942 146952.5225 128355.5249 120587.3595 116520.1287 133445.0594 124766.3207 75093.72892 1.726098677 1.681016458 1.956921365 1.70927089 1.60582463 1.551662574 1.777046649 1.661474566 1 16.19640481 -2.356605804 0.380681595 1.46E-16 1.737056398 0.8208745 0.104743069 24.55354005 1.164933261 20.72243007 0.070333229 0.004399408 2.356605804 1.737056398 HEMPPHIYAITDTAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEMPPHIYAITDTAYR 16 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 189.86 5.49E-10 199400000 86378 82559 70195 82822 69333 70915 93440 84615 24875 FALSE TRUE 82295.08312 90971.85596 73413.51018 74496.57521 81424.65325 68459.19577 79184.01186 77205.66203 28732.48796 2.864182289 3.166167027 2.555069728 2.592764515 2.833888015 2.382640719 2.755905161 2.687051053 1 14.8103953 -1.306177691 0.354656808 1.01E-14 2.885886042 0.87432619 0.206409557 6.605183508 0.528330162 6.609268611 0.164057008 0.049410848 1.306177691 2.885886042 HENAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HENAIK 6 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 79.146 0.067919 232670000 330930 288320 292680 368690 225040 280000 378130 358590 202320 FALSE TRUE 315287.5947 317700.1358 306099.6675 331628.5807 264286.9047 270303.5298 320439.3237 327189.9586 233694.7523 1.34914281 1.359466281 1.309826877 1.419067298 1.130906459 1.156652116 1.371187502 1.400074051 1 17.83426581 -1.995951125 2.842438957 0.694664912 1.313566728 0.509492396 0.096210085 982409.4224 5142398.553 1948715.106 0.022519947 0.010093665 1.995951125 0.618901816 HENVIGLLDVFTPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HENVIGLLDVFTPAR 15 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33;H7C4E2 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 83.418 0.0086585 0 43565 49167 41964 48078 44591 41468 48464 45673 38157 FALSE TRUE 41505.76879 54177.1732 43888.09091 43245.1081 52367.65628 40031.95276 41069.9267 41673.62999 44074.19268 0.941724993 1.229226672 0.995777534 0.981188888 1.188170516 0.90828556 0.931836165 0.945533598 1 15.42764652 2.211065636 24.99830873 0.938621319 1.070743796 0.302785991 0.090660048 244.8551057 222619.6562 0.032341867 0.023891802 162.5794448 -2.211065636 0.132122477 HEPLVLFCESCDTLTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HEPLVLFCESCDTLTCR 17 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 339.3 2.18E-72 778292000 432671 447272 388608 459870 351713 414385 417838 407638 266105 FALSE TRUE 412219.4993 492849.5253 406426.0612 413642.9939 413051.6358 400034.7435 354089.139 371943.0557 307371.2043 1.341112939 1.603434279 1.322264596 1.34574413 1.343820208 1.301471113 1.151991904 1.210077751 1 18.22962249 1.742088472 0.46332562 1.001366122 1.474425682 0.728760676 0.080972524 0.435127156 0.232318229 0.082979324 0.061170961 55.21899163 -1.742088472 0.47305956 HEQEYMEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEQEYMEVR 9 0 Q15363;E7EQ72;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 124.67 0.0016419 0 111540 103770 80904 109120 98682 106790 104700 95542 63459 FALSE TRUE 106267.7253 114344.281 84613.52842 98151.05029 115892.1096 103091.8355 88726.09205 87175.83598 73299.89762 1.449766353 1.559951442 1.154347157 1.339033934 1.581067823 1.406439011 1.210453151 1.189303653 1 16.16152356 1.36103756 1.330569643 1.025433114 1.430063992 0.561062718 0.122823691 0.297627972 1.005774116 0.114679894 0.036986563 22.9634724 -1.36103756 0.404630878 HEQILVLDPPTDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEQILVLDPPTDLK 14 0 Q9P0L0-2;Q9P0L0;J3QKM9 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 82.908 0.0094023 58246000 108840 81275 94700 138390 99703 115440 145170 101990 67842 FALSE TRUE 103695.3489 89557.0149 99042.08867 124478.7743 117091.1716 111442.2839 123021.6503 93059.21492 78362.59087 1.323276167 1.142854185 1.263895024 1.588497431 1.494222822 1.422136285 1.569902793 1.187546429 1 16.25787748 3.446567716 21.35492257 1.424646158 1.228116699 0.069270821 0.184288302 58.00708426 40542.15168 0.045666135 0.061834777 2796.196682 -3.446567716 -0.196529459 HEQISDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HEQISDLER 9 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 152.54 8.02E-05 100420000 53625 60823 54134 62889 48977 52807 60585 58843 43961 FALSE TRUE 51090.25252 67020.93285 56616.09745 56567.27824 57518.57329 50978.28035 51341.64553 53690.39497 50778.24736 1.006144465 1.319874874 1.114967538 1.114006118 1.132740421 1.003939344 1.011095266 1.057350298 1 15.63192298 2.292723833 4.972079148 1.017400085 1.149877317 0.363990683 0.077695661 0.203364871 10.47515184 0.027612896 0.022435736 196.2112176 -2.292723833 0.132477232 HEQNIDCGGGYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HEQNIDCGGGYVK 13 0 P27797 P27797 CALR Calreticulin 0 ;;;;; 196.84 1.39E-07 6428120000 6883000 5786820 5439600 7020850 4595240 6139530 7197120 6673200 3499820 FALSE TRUE 6557654.231 6376503.537 5689011.04 6315100.819 5396648.401 5926916.537 6099067.16 6088859.231 4042554.211 1.622156164 1.577345214 1.407281324 1.562156124 1.334960057 1.466131616 1.508716233 1.506191114 1 21.94683569 -3.079526772 0.247810546 1.33E-15 1.565839615 0.783361604 0.082445931 28.1331107 0.655541274 14.90430927 0.126085862 0.000832671 3.079526772 1.565839615 HERGSPS(ph)HSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.44)PS(0.56)HSK 78.324 0.018325 7147800 25356 24957 27223 28003 18641 30103 31585 22606 7948 TRUE FALSE 24157.47213 27500.14667 28471.20148 25188.08524 21891.9845 29060.52556 26766.12815 20626.4988 9180.535247 2.631379487 2.995484025 3.101257248 2.743640165 2.38460873 3.165450029 2.915530242 2.246764295 1 13.16436255 0.904026784 2.991922951 1.001818684 2.854880552 0.868329728 0.228683238 0.128538735 2.541646701 0.214783785 0.056381059 8.017275061 -0.904026784 1.853061868 HERPAGPGT(ph)PPPDSGPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HERPAGPGTPPPDSGPLAK 19 1 Q9P2K8-2;Q9P2K8;H0YME5 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 HERPAGPGT(0.978)PPPDS(0.022)GPLAK 69.779 0.032888 88313000 135550 141930 125990 161940 84582 151650 145930 134750 65919 TRUE FALSE 129142.8201 156392.8284 131766.7661 145661.4835 99333.07402 146398.3225 123665.6983 122950.5756 76141.38185 1.696092414 2.053979381 1.730553911 1.913039664 1.304587224 1.92271691 1.624158839 1.614766802 1 16.21639313 -2.224606632 0.215906879 6.96E-11 1.908369581 0.601190414 0.195110082 23.03232655 0.673144996 11.63735526 0.392180913 0.005962019 2.224606632 1.908369581 HES(ph)EEGDSHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HESEEGDSHRR 11 1 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 HES(1)EEGDSHRR;HES(1)EEGDSHRR 62.891 0.036726 41963000 14840.1 14963.6 20906 15586.2 36847 13898.5 19691.3 14124.1 26043.8 TRUE FALSE 14138.63788 16488.40785 21864.56078 14019.44556 43273.10513 13417.19146 16687.03053 12887.31893 30082.53949 0.469994825 0.548105583 0.726818984 0.466032649 1.438479127 0.446012594 0.554708173 0.428398637 1 14.87663874 3.900022396 1.841751658 0.701648032 0.480722787 0.075343064 0.307562697 1.016036003 6.675018578 0.083570968 0.214253231 7943.691986 -3.900022396 -0.220925245 HESGASIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HESGASIK 8 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 137.84 0.0007308 2136300000 2921020 2059950 2284270 3090320 3246430 2431680 4216180 3346220 3473440 FALSE TRUE 2782949.174 2269861.247 2389006.039 2779675.162 3812606.364 2347470.312 3572924.306 3053207.237 4012083.335 0.693641916 0.565756256 0.595452746 0.692825879 0.95028095 0.585100088 0.8905409 0.761002946 1 21.93592014 1.480527489 0.293629014 1.029667598 0.574831742 0.473063508 0.111915517 1.258401777 0.406426294 0.216040636 0.190887981 30.23621946 -1.480527489 -0.454835855 HESGASIKIDEPLEGSEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HESGASIKIDEPLEGSEDR 19 1 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 247.31 5.85E-25 166806000 217495 88147 235354 174985 298749 215400 436330 304260 365230 FALSE TRUE 207214.4424 97129.27951 246145.2137 157395.1754 350850.731 207940.644 369759.8447 277617.3814 421868.0031 0.491183121 0.230236185 0.583464998 0.373091048 0.831659971 0.492904516 0.876482317 0.658066929 1 18.68643214 2.122892085 0.412304698 0.979835994 0.31730761 0.571675555 0.154750083 0.693776981 0.280391088 0.149484399 0.155309799 132.7064664 -2.122892085 -0.662528385 HESQQDYSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HESQQDYSK 9 0 Q14247 Q14247 CTTN Src substrate cortactin 0 109.42 0.0029941 0 266590 195610 235330 268790 300370 217850 405320 331870 301110 FALSE TRUE 253988.819 215542.8814 246120.1133 241770.7185 352754.4329 210305.7999 343480.9898 302809.7034 347804.6009 0.730262965 0.619724066 0.707639038 0.695133756 1.014231646 0.604666526 0.98756885 0.870631678 1 18.40791749 2.108999759 0.483527115 0.995476169 0.653110228 0.418821151 0.11946534 0.823442635 0.422307233 0.106646622 0.091219797 128.5285948 -2.108999759 -0.342365941 HETWSGHVISS ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;; 213.31 2.97E-09 470680000 504510 388950 494450 565800 624820 435780 682300 523520 175926 FALSE TRUE 480662.8121 428584.4472 517121.0216 508924.7091 733788.4102 420688.8293 578202.6037 477677.8134 203207.7056 2.365376897 2.10909545 2.544790416 2.504455762 3.611026502 2.070240536 2.845377354 2.3506875 1 17.63259558 0.958993181 20.68090016 0.999999986 2.542320487 0.564280348 0.431697978 582.2681326 293655.727 0.399019151 0.099754788 9.098989853 -0.958993181 1.542320502 HEWAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HEWAQK 6 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 107.74 0.031005 257570000 571090 475840 417290 516060 559500 472530 607600 513100 434160 FALSE TRUE 544095.7075 524328.637 436423.1593 464184.6684 657076.6229 456166.1676 514899.4607 468170.2439 501487.3154 1.084964047 1.045547157 0.870257623 0.925615971 1.310255719 0.909626532 1.026744735 0.933563481 1 18.93585368 3.989223927 24.41255437 1.000398941 1.070182743 0.055681034 0.121179313 1380.39971 3127231.135 0.029489408 0.055274873 9754.924837 -3.989223927 0.069783802 HFADLLPGFLQAVNDSCYQNDDSVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFADLLPGFLQAVNDSCYQNDDSVLK 26 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 278.26 1.02E-60 222496000 317920 308240 299330 361440 243390 353700 350420 372680 222990 FALSE TRUE 302892.5517 339650.0064 313054.5766 325107.3645 285837.1389 341451.2803 296956.9931 340046.1635 257570.1503 1.175961389 1.318669908 1.215414815 1.26220901 1.109744815 1.325663241 1.152916954 1.320207963 1 17.97460588 -1.547116424 2.926490298 0.988961407 1.23356813 0.497850038 0.074188565 24632677.56 29459285.42 2171734.597 0.015513181 0.028371584 1.547116424 0.244606723 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 31 2 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ; 300.89 8.30E-82 902010000 2790520 2261050 2421910 2807770 1752090 2816070 3213720 2882450 1262700 FALSE TRUE 2658617.65 2491453.566 2532956.969 2525527.625 2057653.941 2718548.79 2723407.99 2630047.397 1458513.067 1.822827447 1.708214772 1.736670741 1.731576962 1.410788829 1.863918021 1.867249634 1.80323883 1 20.47606688 -1.601554527 2.899206208 0.94768217 1.748522017 0.76339127 0.129975931 23446050.33 24723152.88 9382334.008 0.031979026 0.025029114 1.601554527 0.800839847 HFCPNVPIILVGNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFCPNVPIILVGNKK 15 1 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 127.71 4.96E-05 525840000 1226500 1039000 956030 1214000 1190600 1134000 1434700 1302000 958310 FALSE TRUE 1168525.776 1144875.281 999864.9211 1091966.414 1398240.263 1094729.296 1215810.165 1187989.978 1106919.82 1.055655301 1.034289259 0.903285769 0.986490976 1.26318116 0.988986985 1.098372387 1.073239412 1 20.07811929 HFEALANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HFEALANR 8 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 140.09 0.00065515 442690000 279526 225472 233752 228623 729970 170931 340333 213408 514907 FALSE TRUE 266313.3599 248447.8531 244469.7604 205641.3817 857276.5369 165011.6166 288408.9502 194720.8642 594756.1478 0.447768991 0.417730618 0.411042007 0.345757471 1.441391636 0.277444155 0.484919662 0.327396135 1 19.18193875 HFEELETIMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 193.28 1.02E-06 395543000 389290 348422 358894 410895 374208 343052 439588 348740 236415 FALSE TRUE 370889.0332 383926.5979 375349.6449 369591.054 439469.7567 331172.0232 372520.777 318202.4768 273077.0308 1.358184656 1.405927832 1.374519284 1.353431495 1.609325235 1.212742142 1.364160054 1.165248047 1 18.05894844 1.052773791 1.174835549 0.998855696 1.398041264 0.65719247 0.094870616 0.26906238 0.772820559 0.079622585 0.025192416 11.29207595 -1.052773791 0.399185569 HFELGGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 176.44 0.00026027 4780440000 8767520 8894210 5998530 8611000 5447330 7555620 8150320 8304400 3426500 FALSE TRUE 8353096.705 9800540.111 6273568.534 7745405.92 6397342.627 7293966.985 6906838.993 7577222.712 3957864.12 2.110506185 2.476219449 1.585089418 1.956966102 1.61636237 1.842904851 1.7450925 1.914472676 1 21.91629065 0.118454503 0.100931366 2.33E-13 2.949447378 0.608669154 0.239204424 18.54074415 0.654530967 12.17578419 6.410705083 1.313573876 -0.118454503 2.949447378 HFFHHADEDDEEEDDS(ph)PPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HFFHHADEDDEEEDDSPPER 20 0 A0A087WZV0;O43314-2;O43314;D6RFG4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER 204.82 1.55E-21 1471710000 540831 535893 739888 754424 594789 624498 821521 462601 197450 TRUE FALSE 515266.9905 590501.106 773812.5966 678587.8662 698520.0133 602871.4777 696182.8832 422093.204 228069.5376 2.259253892 2.589127475 3.392880105 2.97535512 3.062750163 2.643366949 3.052502717 1.850721532 1 17.79911424 1.023251287 3.698174077 1.006609074 2.815907384 0.798245938 0.313754028 0.091965713 2.9957407 0.327030236 0.084377252 10.5499715 -1.023251287 1.80929831 HFGAGGNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFGAGGNQR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 105.57 0.0030769 105528000 64240 95642 75213 89386 66494 91441 78939 87547 70251 FALSE TRUE 61203.50251 105388.0285 78661.59045 80400.74946 78090.53255 88274.37524 66895.40574 79880.92056 81145.16629 0.754247053 1.298759167 0.969393422 0.99082611 0.962355937 1.087857469 0.824391751 0.98441995 1 16.30821754 1.748805747 25 0.920696138 1.019910561 0.051783064 0.141140285 6.399804791 15648.00419 0.062492106 0.034655283 56.07970847 -1.748805747 0.099214423 HFHPLFEYFDYESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 171.29 1.76E-06 518833000 607230 824380 625551 836161 671714 656934 684186 591224 107987.1 FALSE TRUE 578527.4413 908385.2592 654233.1321 752108.5077 788860.7089 634184.2109 579800.8598 539453.2923 124733.1879 4.63811958 7.282626815 5.24506062 6.029738517 6.324385049 5.084326163 4.648328719 4.324857732 1 16.92848585 0.712802251 0.683147376 0.95247598 5.984135763 0.811755326 0.719967331 0.440126206 0.405539274 0.706062072 0.259353058 5.161812813 -0.712802251 5.031659783 HFIDVGAGVIDEDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HFIDVGAGVIDEDYR 15 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;; 166.09 1.39E-06 447222000 549872 611601 495084 637870 503637 500906 533978 547931 281695 FALSE TRUE 523880.6403 673923.8372 517784.0911 573750.0957 591471.1333 483559.4996 452509.8489 499951.2569 325378.8219 1.610063732 2.071197607 1.591326959 1.763329563 1.81779235 1.486143126 1.390716969 1.536520582 1 18.31176083 1.208455677 0.471180926 0.994064008 1.840026763 0.689212156 0.157147444 0.498742275 0.300769556 0.174298934 0.097187643 16.16053286 -1.208455677 0.845962755 HFIEITDDQFDFHTYCMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HFIEITDDQFDFHTYCMR 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;;; 188.44 2.19E-14 201709000 103114 102035 106172 119377 107842 104628 113393 105233 58430 FALSE TRUE 98240.00557 112432.4825 111040.0912 107376.9972 126649.6107 101004.7061 96092.81524 96018.24064 67491.02598 1.45560101 1.665887885 1.645257123 1.590981847 1.876540011 1.496564983 1.423786553 1.422681597 1 16.04240806 0.904443246 0.917699351 1.00739088 1.624425464 0.738265978 0.115885312 0.356118588 0.62507329 0.109011584 0.037095505 8.024966837 -0.904443246 0.617034584 HFILDECDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 183.47 4.51E-05 1068900000 3950100 3916920 3250460 4622080 2318010 3871920 3634720 3834820 1543830 FALSE TRUE 3763386.601 4316058.601 3399496.806 4157459.737 2722270.21 3737834.44 3080176.708 3499022.831 1783239.272 2.110421558 2.420347437 1.906360442 2.331408804 1.52658718 2.096092487 1.727292998 1.962172372 1 20.76606886 -1.278013206 0.175997574 1.65E-14 2.426306504 0.665557068 0.237876611 13.46276651 0.457329957 7.123128837 0.877504913 0.052721383 1.278013206 2.426306504 HFIMQVVCEATQCPDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFIMQVVCEATQCPDTR 17 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 146.88 4.20E-07 531670000 982150 901340 935760 1045840 651870 1238450 1023500 992960 267670 FALSE TRUE 935725.7159 993187.5707 978665.5216 940710.1762 765555.9216 1195562.166 867346.2771 906011.1584 309178.8965 3.026486369 3.212339464 3.165369734 3.042607975 2.476093712 3.866894472 2.805321731 2.930378394 1 18.23808232 2.983260578 22.67770402 2.828420627 3.131909899 0.066663598 0.712999588 776.2961498 1051689.974 0.19087855 0.207684477 962.1894215 -2.983260578 0.303489272 HFKDEDEDEDVAS(ph)PDGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HFKDEDEDEDVASPDGLGR 19 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR 287.91 9.69E-41 2041880000 3381240 3158430 3244270 3640610 2255430 2967690 3459330 2858540 742905 TRUE FALSE 3221415.486 3480277.608 3393022.989 3274648.966 2648776.278 2864918.151 2931545.674 2608231.084 858110.9132 3.754078216 4.055743325 3.954061108 3.81611388 3.086752816 3.338633861 3.416278279 3.039503453 1 19.71080461 -0.526880508 0.306281243 2.70E-20 4.013675061 0.940792987 0.212799388 2.083315084 0.210866166 2.401376811 0.244386487 0.297248377 0.526880508 4.013675061 HFLLEEDKPEEPTAHAFVSTLTR ddPTM_SK-BR-3_Trastuzumab_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 6729141000 7065360 6791040 6864070 7983700 4507489 7861420 7893070 7731920 1816135 FALSE TRUE 6731394.435 7483054.697 7178794.399 7181163.308 5293593.654 7589177.054 6688837.205 7054872.095 2097771.94 3.208830429 3.567144051 3.42210431 3.42323356 2.523436201 3.61773218 3.188543558 3.363031014 1 21.00042641 2.827986204 24.99012229 2.970887875 3.411398679 0.130827076 0.72798928 167.4932285 46800.64845 0.196068761 0.207962323 672.9552789 -2.827986204 0.440510804 HFLPLDFSTQVNSSLTS(ph)PTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HFLPLDFSTQVNSSLTSPTGR 21 0 P19793 P19793 RXRA Retinoic acid receptor RXR-alpha 1 HFLPLDFSTQVNSSLTS(1)PTGR;HFLPLDFSTQVNSSLTS(1)PTGR;HFLPLDFSTQVNSSLTS(0.999)PTGR 303.71 1.56E-55 1544150000 1046060 922520 1004050 1098380 1102210 1025190 1290400 1140330 832250 TRUE FALSE 996614.8169 1016525.837 1050086.686 987968.7556 1294435.075 989687.4132 1093525.78 1040476.66 961311.0795 1.036724571 1.05743693 1.092348469 1.027730541 1.346530902 1.029518368 1.137535813 1.082351678 1 19.87464384 HFLQQATQVNAWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFLQQATQVNAWDR 14 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 198.16 2.24E-08 660880000 764840 660940 622600 713890 751040 644370 791010 757450 664060 FALSE TRUE 728687.529 728290.5374 651146.8258 642128.4209 882021.1382 622055.3053 670326.8966 691123.6625 767039.0333 0.950000583 0.94948302 0.848909635 0.837152209 1.149903851 0.810982595 0.873914974 0.901028021 1 19.54894047 HFLVEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFLVEDK 7 0 P53992;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 81.958 0.02579 113370000 179710 170990 156690 181960 121060 182590 177040 189370 91851 FALSE TRUE 171215.4645 188414.0754 163874.3915 163669.0351 142172.8257 176266.8625 150029.2964 172787.7589 106094.784 1.613797192 1.775903285 1.544603659 1.542668065 1.340054811 1.661409316 1.414106244 1.628616907 1 16.6949942 -2.946446371 0.186339878 4.04E-14 1.712190682 0.676823589 0.122571158 30.85340778 0.600840294 12.80708867 0.35662476 0.001131237 2.946446371 1.712190682 HFNALGGWGELQNSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFNALGGWGELQNSVK 16 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 264.3 5.29E-27 442730000 746720 636760 551290 670820 568020 646640 820740 745410 505230 FALSE TRUE 711424.0255 701646.5679 576567.1918 603387.8991 667082.5082 624246.6947 695521.0391 680137.9487 583578.488 1.21907171 1.202317396 0.987985684 1.033944725 1.143089613 1.069687638 1.1918209 1.165460967 1 19.15456718 3.95750792 23.55180062 1.097406721 1.212788891 0.361047692 0.068254933 247.3363078 137089.4333 0.017745275 0.031992444 9067.92502 -3.95750792 0.115382171 HFNKPAY(ph)CNLCLNMLIGVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFNKPAYCNLCLNMLIGVGK 20 1 B5MCD5;B5MBY2;Q9Y6T7-2;Q9Y6T7 B5MCD5 DGKB Diacylglycerol kinase;Diacylglycerol kinase beta 1 HFNKPAY(1)CNLCLNMLIGVGK 40.515 0.079982 935550000 1132500 1333500 1211300 948150 289950 1647400 805760 786750 47309 TRUE FALSE 1078968.969 1469385.166 1266839.303 852840.1606 340517.1882 1590350.125 682826.5132 717857.9992 54645.4381 19.74490473 26.88943885 23.18289225 15.60679519 6.231392776 29.1030721 12.49558128 13.13665009 1 15.73781344 0.825499054 0.300252847 4.32E-16 24.20765049 0.471531274 6.391317665 2.158374617 0.53505757 18.12277087 8.939737179 6.691123619 -0.825499054 24.20765049 HFPIEIDSTDYVSSGPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFPIEIDSTDYVSSGPSVR 19 0 P82673;H0YG82;P82673-2 P82673 MRPS35 "28S ribosomal protein S35, mitochondrial" 0 156.13 1.90E-08 72188000 80523 80491 83093 85188 93548 71037 89101 85135 68880 FALSE TRUE 76716.83737 88693.12441 86902.89624 76624.74039 109862.7416 68576.97088 75507.006 77680.12807 79561.55861 0.964245029 1.114773591 1.092272421 0.963087473 1.380852053 0.861935991 0.949038799 0.976352518 1 16.27978392 HFPNIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HFPNIDR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 133.12 0.0033029 554010000 475970 425510 409420 499860 466290 447300 557150 464090 355460 FALSE TRUE 453471.8414 468869.9528 428192.312 449613.1231 547610.8284 431809.8888 472146.5347 423451.8193 410582.9214 1.104458607 1.141961656 1.042888756 1.095060461 1.333739909 1.051699587 1.149941973 1.031342994 1 18.64731409 1.134790383 4.308616732 1.001523501 1.130343987 0.267577509 0.080156917 0.27209755 8.233636284 0.070483712 0.018177662 13.63924664 -1.134790383 0.128820486 HFRHDT(ph)PDS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFRHDTPDSSPR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.557)S(0.443)PR;HFRHDT(1)PDS(0.689)S(0.311)PR 115.8 0.0020863 385730000 525590 365690 524740 545750 557770 474520 714430 324810 146581 TRUE FALSE 500746.4023 402954.2268 548799.848 490890.1731 655044.9114 458087.2534 605430.5821 296367.9145 169312.0328 2.957535822 2.37995032 3.241351715 2.899322422 3.868862126 2.705580021 3.575827258 1.750424406 1 17.36932498 5.085402087 16.93700319 2.841218852 6.215884566 0 0.854417835 41834508.76 97082083.85 0.178384182 5253407494 121731.2515 -5.085402087 3.374665714 HFRHDT(ph)PDS(ph)SPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFRHDTPDSSPRR 13 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.555)S(0.445)PRR;HFRHDT(1)PDS(0.54)S(0.46)PRR 79.393 0.039 216340000 146710 107656 171323 154539 186343 157152 215042 96978 52264 TRUE FALSE 139775.3091 118626.2688 179178.329 139004.4461 218841.1602 151709.7868 182233.3934 88486.09221 60368.83419 2.315355447 1.965025006 2.968060116 2.302586226 3.625068516 2.513048146 3.018666764 1.465757843 1 15.88151632 3.758894208 23.72838368 2.573979164 2.140190234 0 0.767545393 1207.63723 1409249.518 0.175017888 0.314926428 5739.766279 -3.758894208 -0.43378893 HFRPELEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFRPELEER 9 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 ; 177.78 3.11E-05 366410000 467040 375000 383460 387490 422710 329970 436700 390190 310670 FALSE TRUE 444963.9448 413212.9263 401042.0203 348538.769 496430.4902 318543.0562 370073.3945 356022.8951 358847.1169 1.239981942 1.151501313 1.117584624 0.971273706 1.38340387 0.887684591 1.031284291 0.992129735 1 18.4530098 3.776331468 0.306462773 0.9659562 1.332461362 0.250910082 0.125469279 5.235624714 0.629331051 0.1389234 0.68872005 5974.91138 -3.776331468 0.366505162 HFS(ph)ESTSIDNALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFSESTSIDNALSR 14 0 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 HFS(0.989)ES(0.011)TSIDNALSR;HFS(0.704)ES(0.296)TSIDNALSR 214.63 4.38E-12 294800000 282090 264610 262170 293630 261950 255480 308990 263350 164877 TRUE FALSE 268756.1647 291574.0598 274190.7538 264113.7545 307633.9971 246632.6635 261847.9005 240289.6779 190445.2831 1.411198851 1.531012242 1.439735074 1.386822242 1.615340596 1.29503162 1.374924578 1.261725541 1 17.53901703 0.888755506 0.745291154 0.998409622 1.47116034 0.767702101 0.079878633 0.348926029 0.420052929 0.070230495 0.026190477 7.740259235 -0.888755506 0.472750718 HFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.969)QS(0.03)EET(0.001)GNEVFGALNEEQPLPR;HFS(0.929)QS(0.067)EET(0.004)GNEVFGALNEEQPLPR;HFS(0.989)QS(0.011)EETGNEVFGALNEEQPLPR 303.94 1.21E-62 1357050000 729760 688900 750190 859910 715040 758940 842840 704180 316366 TRUE FALSE 695265.691 759099.6932 784586.9535 773470.2131 839742.7496 732657.7175 714249.2782 642518.2661 365426.4235 1.902614716 2.077298313 2.14704494 2.116623658 2.297980375 2.00493908 1.954563853 1.758269859 1 18.47922143 0.732777039 1.196575091 1.000925742 2.085776505 0.920659993 0.100206273 0.24578062 0.60697392 0.100297154 0.030799086 5.404767782 -0.732777039 1.084850763 HFSGLEEAVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 247.22 4.32E-16 2903300000 2346202 1453315 1697293 1900853 3921110 1518483 3441610 2295876 3682060 FALSE TRUE 2235301.681 1601409.451 1775115.563 1709775.645 4604950.343 1465897.553 2916529.185 2094836.926 4253055.059 0.525575533 0.376531559 0.417374226 0.402011171 1.082739414 0.34466931 0.685749219 0.492548744 1 22.0200681 HFSQS(ph)EETGNEVFGALNEEQPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.466)QS(0.485)EET(0.049)GNEVFGALNEEQPLPR 217.84 7.84E-33 257800000 123750 120990 142690 174850 132020 136440 159070 137380 66522 TRUE FALSE 117900.5827 133319.0186 149232.4776 157273.7458 155044.2462 131715.0486 134800.95 125350.2789 76837.89201 1.534406784 1.735068663 1.942172979 2.046825358 2.017809731 1.714193937 1.754355129 1.6313602 1 16.22953032 0.603334565 1.234234824 1.000164896 1.81475695 0.7444642 0.151259078 0.820963256 1.828156834 0.162978276 0.049340535 4.011756502 -0.603334565 0.814592054 HFSQSEET(ph)GNEVFGALNEEQPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.211)QS(0.211)EET(0.578)GNEVFGALNEEQPLPR 191.99 4.80E-24 75638000 87054 77298 82910 98761 86790 77952 102410 78052 63615 TRUE FALSE 82939.12994 85174.75408 86711.50551 88833.35665 101926.1485 75252.50269 86785.47361 71217.3531 73480.0893 1.128729303 1.159154199 1.180068047 1.208944593 1.387126084 1.024121002 1.181074689 0.969206132 1 16.16506576 1.343215743 1.738691558 0.979769407 1.186382016 0.423226554 0.091890312 0.332549402 1.798559406 0.078608241 0.024008434 22.04021075 -1.343215743 0.206612609 HFSTLKDDDLVEFS(ph)DLES(ph)EDDERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFSTLKDDDLVEFSDLESEDDERPR 25 2 Q9HCK8-2;Q9HCK8;H0YJG4;A0A2R8Y840 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 2 HFSTLKDDDLVEFS(1)DLES(1)EDDERPR;HFSTLKDDDLVEFS(1)DLES(1)EDDERPR 131.23 4.45E-05 107728000 136103 97465 124956 138293 108301 121092 181730 118760 59903 TRUE FALSE 129669.6809 107396.7943 130685.3562 124391.5249 127188.6601 116898.5537 154003.7508 108360.7448 69192.4513 1.87404375 1.552146113 1.88872274 1.797761498 1.838186937 1.689469754 2.225730523 1.566077553 1 16.07832703 0.986408708 24.48302245 0.999999979 1.829176182 0.710601713 0.170014986 313.6873114 565070.0143 0.167289585 0.041822396 9.691895179 -0.986408708 0.829176203 HFSVEGQLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 170.68 1.54E-05 499590000 380260 234690 403840 338750 450140 320180 563940 427450 477020 FALSE TRUE 362285.8634 258605.1778 422356.4635 304698.2064 528644.2735 309092.0863 477900.5955 390020.2119 550993.8253 0.657513472 0.46934315 0.766535747 0.552997497 0.959437745 0.56097196 0.867342924 0.707848607 1 19.07167663 0.770751042 0.115773639 1.310790039 0.326063605 0.382198866 0.138449613 11.61168968 0.780686567 3.65167111 2.46152063 5.898628455 -0.770751042 -0.984726434 HFTILDAPGHK ddPTM_SK-BR-3_Trastuzumab_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 ; 183.33 3.12E-06 812440000 629470 486480 539100 649160 502760 569990 764930 651390 209057 FALSE TRUE 599716.2006 536052.8651 563818.2682 583905.2035 590441.1848 550251.1034 648225.8796 594350.8384 241476.4918 2.48353865 2.219896691 2.334878497 2.418062309 2.445129049 2.278694291 2.684426441 2.461319666 1 17.88152322 -1.12960502 4.516452225 0.999834198 2.41477171 0.925498568 0.126235202 0.000220483 4.25E-05 0.127870674 0.030135968 0.074198475 1.12960502 1.414937511 HFVALSTNTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFVALSTNTTK 11 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 ; 186.74 3.90E-06 3942000000 6472400 5453500 5346700 6386100 4574300 5988300 6911800 6448400 3705900 FALSE TRUE 6166462.479 6009217.85 5591851.484 5744157.095 5372056.472 5780923.669 5857277.966 5883743.911 4280592.045 1.440562991 1.403828673 1.306326654 1.341907156 1.254979782 1.350496289 1.36833361 1.374516387 1 22.02937892 -3.327568656 0.324308787 4.36E-25 1.378498687 0.821444655 0.051738395 43.9064213 1.061229422 29.84314696 0.04902635 0.000470361 3.327568656 1.378498687 HFVDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HFVDEK 6 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;H0Y562 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ;;; 117.7 0.022498 1507220000 3773070 3430540 3207050 3834230 2955420 3639460 4087460 3883100 2206670 FALSE TRUE 3594724.459 3780115.926 3354096.415 3448805.916 3470844.312 3513424.588 3463842.906 3543075.178 2548869.113 1.410321322 1.483056115 1.315915516 1.353072976 1.361719319 1.378424874 1.358972451 1.390057716 1 21.28142586 -3.33655518 0.291229526 6.85E-13 1.414737805 0.876969044 0.044761452 28.41250713 0.650049946 17.2605303 0.050014086 0.000460728 3.33655518 1.414737805 HFVDSELECNDVVLFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFVDSELECNDVVLFWR 17 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" 0 132.59 2.31E-05 23982000 22866 21425 20659 25893 21739 18265 21484 18859 13673 FALSE TRUE 21785.1695 23608.23186 21606.23558 23290.18645 25530.27472 17632.47847 18206.22122 17207.60598 15793.33901 1.379389722 1.49482208 1.368060014 1.474684133 1.616521668 1.116450325 1.152778473 1.08954832 1 13.9470286 2.22061756 24.97730879 1.108321455 1.458473737 0.850718488 0.07825922 88.52922879 123234.7365 0.027847562 0.020608953 166.1948495 -2.22061756 0.350152282 HFVDSHHQKPVNAIIEHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFVDSHHQKPVNAIIEHVR 19 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 204.29 1.56E-16 3845500000 1485630 1224080 1458440 1733160 1488120 1455840 1855910 1509940 88931 FALSE TRUE 1415407.214 1348815.144 1525310.917 1558939.464 1747647.657 1405423.896 1572756.843 1377721.649 102721.9653 13.77901221 13.13073733 14.84892654 15.176301 17.01337832 13.68182445 15.31081341 13.41214262 1 16.64838518 0.788474815 4.869107674 1.0000348 14.56536209 0.940128902 1.07848995 1.037030204 23.73659527 1.090461298 0.275903097 6.144334 -0.788474815 13.56532729 HFVGMLPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HFVGMLPEK 9 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 78.516 0.022415 2869470000 6183800 6529800 3304250 4658560 4024990 4395700 5802660 5085730 2607650 FALSE TRUE 5891504.029 7195194.044 3455753.131 4190272.698 4726946.982 4243475.807 4917357.644 4640396.52 3012031.044 1.955990474 2.388818023 1.147316572 1.391178456 1.569355333 1.408841989 1.632572033 1.540620416 1 21.52230521 8 0.206638964 1.194013061 6.294729537 0.377056868 0.30958915 47.52699678 0.585937347 0.539012953 79.34292903 100000000 -8 5.100716477 HFVGMLPEKDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HFVGMLPEKDCR 12 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;;; 150.06 4.07E-05 15967480000 14570760 9411790 11082760 11920820 13257590 11700240 19083710 12864870 11438010 FALSE TRUE 13882029.05 10370862.1 11590915.51 10722516.53 15569709.5 11295057.76 16172139.54 11738353.78 13211758.17 1.050732905 0.784972141 0.87731817 0.811588918 1.178473697 0.854924652 1.224071719 0.888477796 1 23.65531913 2.753076378 24.95455425 1.043356111 0.883752046 0.235000886 0.131308527 1002.276709 1723047.964 0.03664491 0.03871232 566.3388802 -2.753076378 -0.159604064 HFVLDECDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HFVLDECDK 9 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 168.83 5.89E-05 362910000 1155830 1273980 963790 1311540 691810 1150820 1087960 1137650 437470 FALSE TRUE 1101196.207 1403800.01 1007980.725 1179701.507 812461.445 1110966.815 921971.7202 1038031.335 505310.6133 2.179246146 2.778093263 1.994774498 2.334606629 1.607845597 2.198581992 1.824564329 2.054244078 1 18.94681096 -0.777066158 0.162616707 1.21E-17 2.720285878 0.639313628 0.281436884 12.3183682 0.473247992 7.211076544 1.457320973 0.167083607 0.777066158 2.720285878 HFWTAES ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HFWTAES 7 0 Q14157-4;Q14157-1 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 116 0.012922 84390000 103870 90746 88476 107520 107230 92710 115350 97904 92988 FALSE TRUE 98960.27095 99993.12057 92532.71211 96711.88533 125930.878 89499.42945 97751.23895 89331.00674 107408.1041 0.92134827 0.930964394 0.861505869 0.900415161 1.172452294 0.833265145 0.910091839 0.831697082 1 16.71274333 -1.016852681 3.829177794 1.000013113 0.921675293 0.063570928 0.096087033 37608547.31 99504836.37 7478.908072 0.021530772 0.096193853 1.016852681 -0.07833782 HFYWYLTNEGIQYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HFYWYLTNEGIQYLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;; 270.8 2.21E-33 676635000 505135 734101 417465 543126 527488 550642 590304 569482 244609 FALSE TRUE 481258.2696 808906.7265 436606.1832 488529.9426 619481.7402 531573.1295 500242.2831 519615.1371 282541.7144 1.703317581 2.862963892 1.545280434 1.729054216 2.192531964 1.881396984 1.770507708 1.839074057 1 18.10810436 -1.583392572 0.206275535 7.29E-10 2.244734534 0.399984525 0.365206512 24.46730751 0.881324616 13.40762915 0.927543436 0.026098012 1.583392572 2.244734534 HGAGS(ph)GCLGTMEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HGAGSGCLGTMEVK 14 0 Q9BYG5-2;Q9BYG5 Q9BYG5-2 PARD6B Partitioning defective 6 homolog beta 1 HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK 176.04 5.84E-06 1467050000 1680820 1572770 1547330 1868900 1098120 1782970 1905410 1804170 724540 TRUE FALSE 1601370.97 1733037.051 1618276.611 1681034.621 1289631.78 1721225.302 1614704.709 1646187.31 836897.9628 1.913460232 2.070786557 1.933660593 2.008649437 1.540966567 2.05667283 1.929392568 1.967010775 1 19.67469221 -1.575084572 2.727598747 0.935105617 1.935912397 0.796244341 0.147409408 14881781.97 14432782.86 6982096.1 0.033096552 0.02660207 1.575084572 1.00080678 HGAPS(ph)PSHPISAPQAAAAAALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGAPSPSHPISAPQAAAAAALRR 23 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 HGAPS(0.997)PS(0.003)HPISAPQAAAAAALRR;HGAPS(0.956)PS(0.041)HPIS(0.003)APQAAAAAALRR 118.01 0.00015231 130740000 116091 103351 124208 127942 189102 103585 128611 110059 129692 TRUE FALSE 110603.6085 113882.5844 129903.0597 115081.0271 222081.3289 99997.82548 108989.0298 100421.6505 149803.973 0.738322264 0.760210708 0.867153635 0.768210781 1.482479566 0.667524522 0.727544321 0.67035372 1 17.19271636 -2.461335791 2.146281196 2.7003281 0.826129648 0.044245401 0.237353239 12624234.98 1221240.851 104027233.1 0.056411509 0.00345672 2.461335791 -1.874198452 HGDEIYIAPSGVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGDEIYIAPSGVQK 14 0 Q96GX9 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 0 116.84 0.00033825 254690000 294670 217180 237450 270400 216630 275330 315200 286210 163180 FALSE TRUE 280741.5331 239310.8889 248337.3174 243218.8783 254410.2034 265795.2531 267110.451 261147.9351 188485.121 1.489462572 1.269654006 1.317543348 1.290387681 1.349762793 1.410165703 1.41714343 1.38550955 1 17.52409112 -1.447118623 4.485704633 0.998786711 1.366460427 0.759234309 0.064808737 0.000806533 9.94E-05 0.064359266 0.015121972 0.035717527 1.447118623 0.367673715 HGDLPDIQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGDLPDIQIK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 109.79 0.001972 279110000 632890 531460 688290 734520 504750 772290 876340 688240 330110 FALSE TRUE 602974.544 585616.3782 719848.7773 660684.6541 592778.2402 745545.4037 742638.2379 627974.057 381301.7728 1.58135783 1.535834397 1.887871572 1.732708057 1.554617058 1.955263408 1.94763909 1.64692142 1 18.54057371 HGDPGDAAQQEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGDPGDAAQQEAK 13 0 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ; 171.49 5.82E-05 136362000 280650 259670 255950 322700 182191 309050 315230 302680 136348 FALSE TRUE 267384.2307 286130.6682 267685.5607 290261.5829 213965.0527 298347.521 267135.8739 276175.7346 157492.1515 1.697762258 1.81679319 1.69967556 1.843022527 1.358575972 1.894364374 1.696185311 1.753584112 1 17.26492041 -1.195473257 5.101226235 0.999942929 1.725252164 0.709741752 0.144667214 8.25E-05 1.30E-05 0.123023767 0.028994712 0.063756834 1.195473257 0.725309235 HGEAQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HGEAQVK 7 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;;; 130.77 0.0035314 4599603000 8511930 7250210 7098330 8389730 5139090 7711960 8991000 8480570 4768790 FALSE TRUE 8109587.938 7989014.642 7423795.452 7546378.401 6035345.669 7444892.891 7619257.819 7737966.332 5508309.598 1.472246212 1.450356865 1.34774477 1.369998957 1.095680183 1.351574881 1.38322977 1.404780577 1 22.39317822 -4.451755156 0.149495099 6.97E-21 1.481752606 0.542781898 0.10287937 91.97742101 0.951893462 28.55100301 0.552983062 3.53E-05 4.451755156 1.481752606 HGEEVS(ph)PAASDLAMVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGEEVSPAASDLAMVLTR 18 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 HGEEVS(1)PAASDLAMVLTR 135.21 1.66E-06 0 14787 15499 13491 15784 13783 14738 18562 14442 11356 TRUE FALSE 14088.04782 17078.36572 14109.57569 14197.36233 16186.75084 14227.61936 15730.02599 13177.38192 13117.03048 1.074027222 1.301999393 1.075668438 1.082361008 1.234025556 1.084667706 1.19920633 1.004600998 1 13.67915353 1.228285645 24.93521543 1.002300328 1.1571183 0.388665507 0.076784836 212.6006529 515919.4716 0.065641261 0.017158024 16.91553136 -1.228285645 0.154817972 HGEIDYEAIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGEIDYEAIVK 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 69.01 0.055672 217870000 548550 514670 544490 573430 423330 591830 648260 577480 254370 FALSE TRUE 522621.1286 567115.4581 569455.4051 515787.727 497158.618 571334.7787 549356.0309 526912.7898 293816.4005 1.778733685 1.930169511 1.938133488 1.755476298 1.692072387 1.94452991 1.86972555 1.793340293 1 18.1645554 0.71157512 3.981839809 1.000002765 1.848874408 0.909314893 0.083283068 1.622434707 22.15642485 0.079306451 0.020265177 5.14724831 -0.71157512 0.848871644 HGEKLYTGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGEKLYTGLR 10 1 Q13618;Q13618-2;A0A087X1R9;H7C1L6 Q13618 CUL3 Cullin-3 0 52.79 0.088821 180690000 659650 464350 262770 293860 741660 294110 734030 448120 524760 FALSE TRUE 628469.6518 511667.7929 274818.2644 264320.6345 871005.2692 283924.897 622040.2421 408880.2372 606137.1007 1.036844059 0.844145314 0.453392911 0.436074007 1.436977324 0.468416958 1.026236872 0.67456725 1 19.20928462 HGESAWNLENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;; 208.74 1.85E-08 5511180000 4710040 5038330 4385140 5244750 3863599 4743960 5090050 4694620 2919070 FALSE TRUE 4487405.744 5551741.555 4586203.006 4717537.766 4537409.442 4579675.476 4313469.387 4283534.185 3371744.467 1.330885477 1.646548726 1.360187004 1.39913858 1.345715693 1.358251054 1.279299018 1.270420765 1 21.68506377 0.82473637 0.348673403 0.95308696 1.493169232 0.701988621 0.085721097 0.98031443 0.307899815 0.181807465 0.085872935 6.679383362 -0.82473637 0.540082272 HGEVCPAGWKPGSDTIKPDVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGEVCPAGWKPGSDTIKPDVQK 22 2 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 179.47 3.19E-17 1192300000 1555500 1413300 1249600 1764700 730770 1668700 1594200 1633300 503260 FALSE TRUE 1481974.598 1557316.877 1306895.396 1587309.003 858216.0566 1610912.501 1350975.511 1490279.593 581302.9905 2.549401297 2.679010606 2.248217225 2.73060526 1.476366148 2.771209725 2.324047068 2.563688159 1 19.1489308 HGFCGIPITDTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGFCGIPITDTGR 13 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 80.96 0.01637 655410000 1233630 1065570 1142910 1217170 1144210 1166630 1542350 1284440 1031670 FALSE TRUE 1175318.755 1174152.794 1195313.554 1094817.759 1343759.862 1126229.311 1307036.18 1171967.624 1191656.115 0.986290206 0.985311769 1.003069207 0.918736325 1.127640638 0.945095902 1.09682329 0.983478044 1 20.18453654 2.762643651 24.99603217 1.034378678 0.978433758 0.19899802 0.056392507 1161.593884 1205628.368 0.014949082 0.015850278 578.9534558 -2.762643651 -0.05594492 HGFESGDFVSFSEVQGMVELNGNQPMEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGFESGDFVSFSEVQGMVELNGNQPMEIK 29 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 121.3 2.87E-05 32731000 47127 42831 46821 49145 31535 45511 55271 44219 31747 FALSE TRUE 44899.40011 47195.52759 48967.78916 44204.85123 37034.69402 43934.94266 46838.39383 40346.94994 36670.16262 1.224412353 1.287028042 1.33535784 1.205471917 1.009940818 1.198111476 1.277288959 1.100266458 1 15.16231904 -4.999999999 0.113116031 0.272772853 1.340148198 0.424701659 0.085979226 167.6393786 1.251189598 27.89016426 1.019378925 1.00E-05 4.999999999 1.067375345 HGFSDNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HGFSDNQK 8 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;;; 160.63 0.00035223 615850000 866110 750590 734720 973680 815510 851520 1059450 867160 728540 FALSE TRUE 825170.6968 827075.9743 768407.6387 875803.8365 957734.6858 822031.6489 897811.4444 791226.8733 841518.2623 0.980573725 0.98283782 0.913120574 1.040742519 1.13810327 0.976843505 1.066894784 0.940237317 1 19.68263506 3.207871795 24.99676546 1.034503198 0.96708978 0.23548051 0.056337066 260.9242275 212528.1835 0.015127713 0.018082937 1613.882064 -3.207871795 -0.067413418 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 HGGPGPGGPEPELS(1)PITEGSEAR 203.5 1.22E-24 298060000 117290 93838 115210 113670 100200 99685 116760 88294 49831 TRUE FALSE 111745.9341 103400.1989 120492.4925 102243.6756 117674.8483 96232.88345 98946.11756 80562.50928 57558.53698 1.941431107 1.796435495 2.093390464 1.776342503 2.044437792 1.671913299 1.71905199 1.399662214 1 15.8127423 1.064381876 0.959643769 0.998162619 1.912136646 0.87363455 0.114018624 0.161485667 0.322473939 0.093791787 0.031982001 11.59796719 -1.064381876 0.913974026 HGGPKDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 HGGPKDEER 9 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;;;;; 151.22 5.01E-05 1284732000 1875910 1582641 1544720 1799085 1118889 1863816 1964758 1866883 891676 FALSE TRUE 1787239.452 1743913.917 1615546.94 1618237.558 1314022.887 1799271.585 1664998.082 1703408.828 1029952.56 1.735263857 1.693198294 1.56856442 1.571176791 1.275809138 1.746946077 1.616577449 1.653871153 1 19.97414646 -1.272607861 3.414793405 0.997995962 1.616993256 0.673352812 0.132871757 15683864.69 22673486.86 326275.3747 0.031592641 0.053381668 1.272607861 0.618997295 HGGS(ph)PQPLAT(ph)TPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(1)PQPLAT(0.756)T(0.244)PLSQEPVNPPS(0.145)EAS(0.687)PT(0.167)R 104.39 8.77E-10 0 57293 64181 55879 67538 46151 57514 63059 52658 26467 TRUE FALSE 54584.87343 70721.11687 58441.10742 60748.95193 54199.71979 55522.27576 53438.19139 48046.98636 30571.36719 1.785490099 2.313312206 1.911628848 1.98711924 1.77289159 1.816152854 1.747981733 1.571633551 1 14.89989345 0.654664084 0.426064967 0.92455771 2.055480735 0.822057349 0.140430537 0.684972233 0.266881045 0.242637969 0.092386571 4.5150658 -0.654664084 1.130923025 HGGS(ph)PQPLATTPLSQEPVNPPS(ph)EASPTRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTRDR 30 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATT(0.001)PLS(0.009)QEPVNPPS(0.452)EAS(0.292)PT(0.246)RDR 80.816 0.003145 74465000 17972 21202 14280 20940 12147 16995 16305 16145 10106 TRUE FALSE 17122.49918 23362.5079 14934.75212 18835.07142 14265.43295 16406.45889 13817.37279 14731.25821 11673.18687 1.466823017 2.001382157 1.279406583 1.613532931 1.222068414 1.405482417 1.183684708 1.26197399 1 13.51091086 2.532516875 0.480881121 1.059344101 1.748831393 0.49344646 0.195742461 0.757526449 0.366818088 0.171600916 0.196369357 340.8135672 -2.532516875 0.689487293 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPS(0.14)EAS(0.787)PT(0.073)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.066)EAS(0.806)PT(0.128)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.022)EAS(0.972)PT(0.006)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.001)EAS(0.993)PT(0.007)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.009)EAS(0.863)PT(0.128)R 286.35 1.60E-62 3312720000 1266770 1383550 1174090 1437860 946940 1253220 1190160 1096750 484258 TRUE FALSE 1206892.293 1524535.318 1227923.188 1293323.581 1112086.036 1209820.677 1008579.233 1000712.756 559354.2574 2.157652823 2.725527334 2.195251349 2.312172588 1.988160493 2.162888118 1.803113537 1.789050039 1 19.09340275 0.927301508 0.391448867 0.903353705 2.470603725 0.848360129 0.173895927 0.489304525 0.198228442 0.27253848 0.137165213 8.458658814 -0.927301508 1.567250019 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPS(0.008)EAS(0.908)PT(0.084)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.941)PT(0.059)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.99)PT(0.01)R;HGGSPQPLATTPLSQEPVNPPS(0.007)EAS(0.973)PT(0.02)R 225.55 9.78E-35 1651960000 868750 910480 784300 983900 626780 834860 825330 843960 510530 TRUE FALSE 827685.9092 1003258.947 820260.9308 884996.5027 736090.2336 805948.5889 699410.7503 770058.3883 589700.385 1.403570237 1.701302853 1.390979134 1.50075619 1.248244451 1.366708602 1.186044249 1.305846847 1 19.16962261 1.850343507 0.388696622 1.007004764 1.584177295 0.659588556 0.1087041 0.602877858 0.247432757 0.120718927 0.113738357 70.85059592 -1.850343507 0.577172531 HGGTIPIVPTAEFQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HGGTIPIVPTAEFQDR 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;;; 119.47 0.0001915 772426000 1246350 977380 1082360 1070850 1023750 892060 1096100 1025970 866280 FALSE TRUE 1187437.506 1076976.133 1131987.277 963206.1235 1202291.676 861167.7385 928869.8137 936130.6278 1000618.278 1.186703793 1.076310674 1.131287826 0.962610962 1.201548785 0.860635626 0.928295869 0.935552196 1 19.93246028 2.23263154 24.9999897 0.923179172 1.107801117 0.602286518 0.072747799 89.76013499 378470.3925 0.024617001 0.018661976 170.8565135 -2.23263154 0.184621945 HGGVCAPAAVATS(ph)PPGAIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGGVCAPAAVATSPPGAIPK 20 0 Q9Y6A5;A0A494BZT8;E7EMT0 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 HGGVCAPAAVAT(0.002)S(0.998)PPGAIPK;HGGVCAPAAVAT(0.051)S(0.949)PPGAIPK 187.06 1.97E-17 711130000 381470 315590 384150 425810 255320 409360 445380 410000 247030 TRUE FALSE 363438.6691 347748.9798 401763.6575 383006.7698 299847.7272 395183.7606 377429.101 374098.2265 285338.1507 1.273712149 1.218725848 1.408026429 1.342290783 1.050850461 1.384966432 1.322743209 1.31106978 1 18.12231313 -1.231566872 3.295032213 0.99916435 1.286839791 0.452613916 0.099871477 27821264.13 42617621.06 241365.9706 0.022780146 0.058672302 1.231566872 0.287675442 HGHFGWPGWEMGPPGNWS(ph)PRPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGHFGWPGWEMGPPGNWSPRPPR 23 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8 Q13501 SQSTM1 Sequestosome-1 1 HGHFGWPGWEMGPPGNWS(1)PRPPR;HGHFGWPGWEMGPPGNWS(1)PRPPR 182.95 2.29E-17 1218540000 397560 567040 559320 598280 597550 525040 614380 376100 107672 TRUE FALSE 378768.1267 624822.0207 584965.3752 538139.7577 701762.5308 506857.7331 520645.0471 343166.6902 124369.2238 3.045513311 5.023927957 4.703457633 4.326952771 5.642573855 4.075427324 4.186285248 2.759257311 1 16.92427 0.999097085 1.772010997 1.002571982 4.471250925 0.748504978 0.661708644 0.181344072 1.181462002 0.612073704 0.17516155 9.979231204 -0.999097085 3.468678943 HGINCFINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGINCFINR 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 147.19 9.30E-05 1847150000 1478350 928960 362230 420040 1598460 567810 1764050 921620 1214130 FALSE TRUE 1408471.325 1023622.08 378838.6038 377816.7812 1877230.918 548146.5973 1494911.773 840918.067 1402411.079 1.004321305 0.729901592 0.270133778 0.26940516 1.338573936 0.390860145 1.065958331 0.599623091 1 20.41947787 2.759324946 24.96682002 0.857568583 0.627209325 0.167141246 0.331279989 1927.708548 2317853.876 0.099406864 0.10533347 574.546186 -2.759324946 -0.230359258 HGITQANELVNLTEFFVNHILPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGITQANELVNLTEFFVNHILPDLK 25 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 94.446 0.006163 72896000 47668 46923 47904 63093 48208 54806 54404 48867 22866 FALSE TRUE 45414.82811 51704.50705 50100.44578 56750.77177 56615.45994 52908.05448 46103.6706 44587.94642 26411.9425 1.719480804 1.957618492 1.896886069 2.148678454 2.143555323 2.003186796 1.745561524 1.68817369 1 14.68890279 0.774815253 1.189392349 1.003795554 1.959494645 0.842573628 0.130652714 0.3300196 0.842506737 0.134153412 0.041360534 5.954088048 -0.774815253 0.955699092 HGIVEDWDLMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 HGIVEDWDLMER 12 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;;;;; 245.58 1.78E-16 1237173000 1507003 1557685 1408824 1754056 1382078 1447646 1600571 1498628 749184 FALSE TRUE 1435769.955 1716414.872 1473419.974 1577734.958 1623111.966 1397513.656 1356374.497 1367400.188 865363.6284 1.659152185 1.983460844 1.702659929 1.823204612 1.875641536 1.614943834 1.567404098 1.580145204 1 19.72294696 0.614881107 0.540457212 0.973134411 1.827782597 0.844856511 0.104227121 0.535891827 0.305793669 0.132399967 0.04750965 4.11984718 -0.614881107 0.854648186 HGLAHDEMKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 167.32 2.99E-05 2185412000 3797620 4098200 3657890 4682410 2335500 4221580 4065540 3361590 323866.1 TRUE FALSE 3618114.029 4515811.239 3825607.875 4211725.251 2742810.461 4075385.626 3445267.204 3067231.359 374089.6007 9.671784572 12.07146959 10.22644807 11.25860019 7.331961261 10.89414306 9.209737982 8.199189052 1 18.51302434 -0.089390129 0.474493442 8.07E-12 10.73784461 0.849032753 1.210827067 1.649770787 0.43812755 4.667892202 0.595219163 0.81397276 0.089390129 10.73784461 HGLAHDEMKS(ph)PREPGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGLAHDEMKSPREPGYK 17 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 HGLAHDEMKS(1)PREPGYK 83.776 0.0035736 153160000 65128 47333 67008 67984 45680 69237 84711 68405 23067 TRUE FALSE 62049.52851 52156.28651 70080.38308 61150.11916 53646.57754 66839.30533 71786.78113 62415.09556 26644.11255 2.328826993 1.957516371 2.630238967 2.295070592 2.013449592 2.508595668 2.694283061 2.342547362 1 14.70152916 2.222585484 24.87003202 2.330448674 2.233219006 0 0.497689537 1814.030347 2824058.466 0.167776764 0.124304574 166.949639 -2.222585484 -0.097229668 HGLEAISIMDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HGLEAISIMDSR 12 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;; 157.03 7.37E-05 1034476000 738050 615250 623940 692050 719400 610110 819370 679070 593550 FALSE TRUE 703163.8392 677944.6745 652548.2662 622483.8192 844863.1322 588981.7377 694360.0577 619607.0308 685594.7026 1.025626127 0.988841763 0.951798874 0.907947242 1.232306972 0.859081518 1.012785039 0.903751194 1 19.38699644 4.40423826 2.65157759 0.982602068 1.023791027 0.0181816 0.100879756 1.568864946 20.36208252 0.023138822 0.101501551 25365.19819 -4.40423826 0.041188958 HGLEVIYMIEPIDEYCVQQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HGLEVIYMIEPIDEYCVQQLK 21 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 285.47 2.35E-45 1398617000 1697659 1617509 1570380 1859239 1257617 1670487 1891640 1747888 974468 FALSE TRUE 1617414.024 1782335.006 1642383.476 1672344.763 1476945.007 1612637.616 1603035.576 1594833.661 1125583.521 1.436956027 1.583476458 1.45913959 1.485758038 1.312159409 1.432712533 1.42418181 1.416894998 1 20.10224168 -3.277249221 0.232162075 4.94E-16 1.514838705 0.838436559 0.062164995 24.48401636 0.501626015 11.90616849 0.107178089 0.000528142 3.277249221 1.514838705 HGLLLPAS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGLLLPASPVR 11 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 HGLLLPAS(1)PVR 101.89 0.0030919 48705000 68558 56616 59576 70196 66740 59063 82041 67922 67279 TRUE FALSE 65317.39921 62385.23477 62307.61853 63139.76472 78379.43487 57017.6335 69524.13866 61974.3896 77712.28371 0.840502892 0.802771863 0.801773099 0.812481138 1.008584887 0.733701685 0.894635125 0.797485116 1 16.24585504 -5 0.295137555 2.308932158 0.827589888 0.322959692 0.073484866 290.8168766 2.713613167 235.0879094 0.067328792 1.00E-05 5 -1.48134227 HGLLVPNNTTDQELQHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HGLLVPNNTTDQELQHIR 18 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;;; 153.72 1.80E-08 4151540000 2321340 1865980 1886450 2399360 2194260 1962890 2683820 2130790 1289722 FALSE TRUE 2211614.859 2056125.483 1972945.598 2158171.774 2576938.249 1894914.627 2274353.967 1944206.732 1489725.501 1.484578775 1.380204261 1.324368548 1.448704324 1.729807436 1.271989119 1.526693318 1.305077164 1 20.50661509 0.927961339 4.563244438 1.000097513 1.446474251 0.573670237 0.123890741 0.244590536 12.95077086 0.109120055 0.027697273 8.471519979 -0.927961339 0.446376738 HGLQLGAQS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;HGLQLGAQS(1)PGR 190.18 4.49E-06 5017180000 5012068 3890205 3963382 5176398 3897640 4477635 4746564 4426721 2888547 TRUE FALSE 4775157.479 4286621.312 4145106.985 4656056.639 4577387.182 4322573.377 4022388.485 4039093.842 3336488.116 1.431192713 1.284770442 1.242356286 1.395496245 1.371917724 1.295545863 1.205575547 1.210582415 1 21.66989893 0.994035053 0.733104145 1.001056978 1.346976971 0.781230693 0.057142261 0.339864494 0.415445795 0.056356195 0.021682972 9.863590935 -0.994035053 0.345919993 HGLQLGAQS(ph)PGRGTTLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGLQLGAQSPGRGTTLAR 18 1 Q8N1G0;A6PVV7 Q8N1G0 ZNF687 Zinc finger protein 687 1 HGLQLGAQS(1)PGRGTTLAR;HGLQLGAQS(1)PGRGTTLAR 209.24 3.30E-16 605530000 90526 45706 99712 78079 115021 88242 150630 86198 111089 TRUE FALSE 86247.01539 50363.49336 104283.8938 70230.35058 135080.626 85186.15741 127648.627 78650.04616 128316.1148 0.672144848 0.392495467 0.812710812 0.54732292 1.05271755 0.663877312 0.994798099 0.612939741 1 16.96934284 3.135568181 1.497191848 0.854341483 0.551297402 0.280039535 0.183112008 0.403796681 1.881477798 0.057302976 0.076346058 1366.369569 -3.135568181 -0.303044082 HGLYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HGLYEK 6 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ;; 117.56 0.022615 4636600000 14451600 12636000 12485900 15466300 10668700 13881500 15956900 14583600 8097400 FALSE TRUE 13768501.51 13923622.77 13058390.87 13911598.14 12529317.9 13400780.17 13522381.84 13306582.67 9353103.436 1.472078396 1.4886634 1.396155934 1.487377771 1.339589366 1.432762961 1.445764171 1.422691705 1 23.15701371 -2.939530919 0.365298801 4.72E-14 1.456859948 0.906604233 0.044001185 25.05811027 0.807575087 19.44099831 0.030271446 0.001149394 2.939530919 1.456859948 HGLYLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HGLYLPTR 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 ;;;;;;; 113.26 0.0028837 12609720000 15181570 10096520 4403289 5518354 15713530 7307130 17012490 11086090 11664110 FALSE TRUE 14463967.27 11125366.87 4605184.156 4963638.572 18453964.66 7054082.256 14416922.19 10115333.19 13472920.61 1.073558414 0.825757621 0.341810383 0.36841593 1.369707816 0.52357484 1.070066589 0.750789935 1 23.68355929 2.757457357 24.99748996 0.922385982 0.710823785 0.1740885 0.300855488 2004.21751 2651269.539 0.092478208 0.097940778 572.0807802 -2.757457357 -0.211562196 HGNRNS(ph)NSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGNRNSNSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK 52 1 P46109 P46109 CRKL Crk-like protein 1 HGNRNS(0.265)NS(0.265)Y(0.237)GIPEPAHAY(0.054)AQPQT(0.06)T(0.06)T(0.06)PLPAVSGSPGAAITPLPSTQNGPVFAK;HGNRNS(0.305)NS(0.305)Y(0.276)GIPEPAHAY(0.11)AQPQT(0.001)T(0.001)T(0.001)PLPAVS(0.001)GS(0.001)PGAAITPLPSTQNGPVFAK 137.41 7.39E-15 1454680000 383810 306130 385970 388920 293240 386560 475810 346460 100213 TRUE FALSE 365668.0619 337324.995 403667.1063 349825.0227 344380.9632 373173.3303 403216.4456 316122.1257 115753.5202 3.159023252 2.91416619 3.487298749 3.022154506 2.975123024 3.223861612 3.483405471 2.730993624 1 16.82069654 0.894364568 5.656041352 1.000047077 3.16673683 0.927255418 0.191041033 0.278897099 14.71997641 0.18764126 0.047251984 7.840875682 -0.894364568 2.166689753 HGPICQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGPICQK 7 0 Q96GY0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 0 64.776 0.072379 90420000 90404 73393 83384 90515 83349 81825 94970 82919 89305 FALSE TRUE 86130.78208 80871.83014 87207.23888 81416.26023 97885.03921 78991.37973 80480.58226 75658.17278 103153.9633 0.834973076 0.783991497 0.845408515 0.789269337 0.948921748 0.765761947 0.780198644 0.733449015 1 16.65443973 -2.278855388 2.422262662 1.90129257 0.809738365 0.508047708 0.058679577 4513847.54 1633152.34 21813386.8 0.013286015 0.005261924 2.278855388 -1.091554205 HGS(ph)ASQVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGSASQVQK 9 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 HGS(0.89)AS(0.11)QVQK 97.299 0.0027922 0 182810 200530 182800 241240 132550 211220 202600 194460 114650 TRUE FALSE 174168.9336 220964.235 191181.5608 216990.0969 155666.678 203905.3984 171689.649 177432.0515 132429.3364 1.315183918 1.668544455 1.443649617 1.638534955 1.175469743 1.53972982 1.296462352 1.339824364 1 17.01486323 0.602475465 0.461137545 0.971601178 1.505368348 0.496988707 0.145481847 1.370488598 0.588654403 0.219261763 0.078335075 4.003828487 -0.602475465 0.533767169 HGS(ph)DPAFAPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HGSDPAFAPGPR 12 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR;HGS(1)DPAFAPGPR 150.06 7.20E-05 2679800000 2108220 1860720 1883190 2187680 1489310 1991620 2123770 1868410 1147420 TRUE FALSE 2008568.619 2050329.483 1969536.124 1967770.25 1749045.192 1922649.7 1799749.881 1704802.115 1325356.033 1.515493624 1.547002792 1.486043052 1.484710674 1.319679504 1.450666577 1.357936913 1.286297472 1 20.33794854 -0.441587464 0.204920114 0.70899168 1.607694837 0.921154257 0.0449536 2.977858496 0.180726193 0.665151052 0.128919677 0.361753329 0.441587464 0.898703157 HGS(ph)FVNKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGSFVNKPTR 10 1 P29353-2;P29353-7;P29353;P29353-6;Q5T181;Q5T182 P29353-2 SHC1 SHC-transforming protein 1 1 HGS(1)FVNKPTR;HGS(1)FVNKPTR 126.56 0.00022968 805060000 772330 797020 779920 1002060 609900 915020 1037020 795290 470220 TRUE FALSE 735823.4915 878237.2441 815680.1034 901331.025 716266.3669 883332.628 878803.5528 725650.1915 543139.316 1.354760132 1.616964963 1.501787993 1.659484037 1.318752566 1.62634632 1.618007621 1.336029579 1 19.05096277 0.947985164 4.390605868 1.000335165 1.529837134 0.685922398 0.114475478 0.1359182 7.650794169 0.102710278 0.02612619 8.871257059 -0.947985164 0.529501969 HGS(ph)GADS(ph)DYENTQSGDPLLGLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 HGS(0.98)GADS(0.8)DY(0.22)ENTQSGDPLLGLEGK;HGS(1)GADS(0.885)DY(0.115)ENTQSGDPLLGLEGK 227.57 2.27E-33 265070000 305390 293090 317360 384860 171331 314330 350240 181411 58830 TRUE FALSE 290954.8199 322956.2042 331911.2699 346173.1416 201211.0722 303444.6733 296804.4554 165525.6911 67953.05594 4.281703242 4.752636946 4.884420065 5.094298363 2.961030514 4.465504444 4.367786721 2.435882961 1 16.05225081 1.067399054 2.665511252 1.012299945 4.441137059 0.803898439 0.574745823 0.101019734 1.479183141 0.527336467 0.142442532 11.67882239 -1.067399054 3.428837114 HGS(ph)GADS(ph)DYENTQSGDPLLGLEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 HGS(1)GADS(0.964)DY(0.025)ENT(0.01)QSGDPLLGLEGKR 120.33 0.00092487 165640000 219840 143270 255920 219470 157780 249230 378330 146340 81755 TRUE FALSE 209448.5989 157869.3759 267654.1851 197408.4586 185296.782 240599.1026 320608.81 133525.6938 94433.14785 2.217956339 1.671758058 2.834324506 2.090457251 1.962200628 2.547824658 3.395087607 1.41397059 1 16.52700574 2.235046163 24.97076737 2.416591412 2.123002684 0 0.725119917 361.1074333 2565688.98 0.250191339 0.192114037 171.8091 -2.235046163 -0.293588728 HGS(ph)GADSDYENTQSGDPLLGLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.975)GADS(0.025)DYENTQSGDPLLGLEGK 277.75 2.74E-52 218800000 433490 415710 381550 525410 216000 430810 450950 352560 100550 TRUE FALSE 412999.7868 458071.3216 399044.4449 472594.7886 253670.3316 415890.9417 382149.2952 321687.9774 116142.7805 3.555966072 3.944036123 3.435809297 4.069084507 2.184124838 3.580859181 3.290340508 2.769763011 1 16.82553995 2.751765147 24.94520503 2.837355682 3.744141002 0.362751066 0.733422195 948.9373067 1792674.019 0.20309631 0.214242027 564.6315571 -2.751765147 0.90678532 HGS(ph)GADSDYENTQSGDPLLGLEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.696)GADS(0.304)DYENTQSGDPLLGLEGKR;HGS(0.874)GADS(0.126)DYENTQSGDPLLGLEGKR 163.76 8.28E-12 281540000 513970 321770 535990 497040 367180 481970 705910 456950 200560 TRUE FALSE 489675.6567 354558.7288 560565.6717 447076.5949 431216.0757 465279.258 598210.4646 416937.0356 231661.8205 2.113752088 1.530501349 2.419758554 1.929867399 1.861403294 2.008441689 2.582257462 1.79976586 1 17.82166077 2.007879098 24.38142821 2.051197952 1.94184695 0 0.457533266 909.2528312 2813610.148 0.158593444 0.116866419 101.8307865 -2.007879098 -0.109351002 HGS(ph)GPPSSGGGLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HGSGPPSSGGGLYR 14 0 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 HGS(1)GPPSSGGGLYR;HGS(1)GPPSSGGGLYR;HGS(1)GPPSSGGGLYR 187 6.43E-07 912490000 256108 230995 242434 264378 209364 248303 279698 217366 191901 TRUE FALSE 244002.2824 254533.6531 253549.8387 237802.2212 245877.0153 239704.2048 237024.9331 198332.2807 221660.027 1.100795149 1.148306515 1.143868122 1.07282411 1.109252844 1.081404745 1.069317442 0.894758895 1 17.7579891 1.419639103 3.532729712 0.948856849 1.111704937 0.771391376 0.035571927 0.098322708 2.138422708 0.025362087 0.008710698 26.28083155 -1.419639103 0.162848088 HGS(ph)PTAPICLGSPEFTDQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGSPTAPICLGSPEFTDQGR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HGS(0.998)PT(0.002)APICLGSPEFTDQGR;HGS(0.666)PT(0.334)APICLGSPEFTDQGR 222.51 4.58E-25 234917000 401460 302233 454300 395870 321885 431380 536300 327049 145588 TRUE FALSE 382483.7814 333030.8863 475130.1044 356076.3955 378021.6421 416441.2024 454477.5852 298410.8558 168165.0435 2.274454747 1.980381174 2.825379725 2.117422195 2.247920461 2.476383878 2.702568713 1.77451181 1 17.35951832 0.976621998 5.201660358 1.000795063 2.350840144 0.758935821 0.252808771 0.083320756 8.734104723 0.248882793 0.062847416 9.475933357 -0.976621998 1.350045081 HGSGPNIILTGDSS(ph)PGFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGSGPNIILTGDSSPGFSK 19 0 Q53ET0;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HGSGPNIILTGDS(0.013)S(0.987)PGFSK 150.03 5.13E-08 95941000 100660 71156 99303 105380 99246 77545 135940 120630 100700 TRUE FALSE 95902.00129 78406.8773 103856.1408 94787.00219 116554.471 74859.59721 115199.8563 110066.9977 116316.0417 0.824495056 0.674084814 0.892878912 0.814909111 1.00204984 0.643587902 0.990403857 0.946275304 1 16.82769055 1.989113988 0.343987197 1.017778933 0.73918732 0.271478889 0.110094133 1.615546149 0.536954278 0.13604564 0.157023 97.52455731 -1.989113988 -0.278591613 HGT(ph)PDPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGTPDPSPR 9 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HGT(1)PDPS(1)PR;HGT(1)PDPS(1)PR 98.898 0.030252 106216000 274724 220075 239897 277564 173200 256640 270942 182832 108486 TRUE FALSE 261738.341 242500.8927 250896.5147 249662.7394 203406.0252 247752.4924 229604.8217 166822.2608 125309.4548 2.088735773 1.935216246 2.002215357 1.992369528 1.623229671 1.977125292 1.832302455 1.331282313 1 16.93513575 1.127091652 2.194271405 1.000507171 1.943194758 0.878491743 0.12094952 0.089347814 0.810829036 0.112139931 0.031489133 13.39959437 -1.127091652 0.942687588 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK 263.55 9.45E-38 3406580000 6006720 4921890 5893790 6661220 3221390 6362970 7258610 5670980 932977 TRUE FALSE 5722794.25 5423436.187 6164026.101 5991621.51 3783199.396 6142618.753 6151175.731 5174398.927 1077658.308 5.310397745 5.032612049 5.719833508 5.559852752 3.510574147 5.699968818 5.707909162 4.801520935 1 20.03946839 HGVESTLER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 155.84 0.00035508 867450000 571687 476926 397754 474364 1383310 424570 501116 473302 1056840 FALSE TRUE 544664.4885 525525.3016 415991.4143 426680.0295 1624558.826 409867.0344 424661.5506 431857.1677 1220729.35 0.446179564 0.430501079 0.340772846 0.349528771 1.33081 0.335755862 0.347875269 0.353769792 1 20.21931194 HGVIVAADSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HGVIVAADSR 10 0 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 120.68 0.00053504 1205046000 870740 1016122 779324 861211 723889 834654 835673 894886 538450 FALSE TRUE 829581.8458 1119665.987 815056.7763 774640.4341 850135.0124 805749.7227 708175.7357 816525.0378 621950.076 1.33383993 1.800250583 1.310485854 1.245502596 1.366886259 1.295521544 1.13863759 1.312846592 1 19.24643925 2.397567801 0.363905687 1.028922221 1.602822092 0.433385225 0.153441143 1.225114036 0.372063108 0.17702171 0.252640482 249.7858321 -2.397567801 0.573899871 HGVVPLATYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGVVPLATYMR 11 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 112.13 0.0015674 511710000 471550 228590 105770 140850 460570 189300 513940 297160 348830 FALSE TRUE 449260.766 251883.5809 110619.6591 126691.4904 540893.2622 182744.4935 435529.0138 271139.0951 402924.7748 1.114999112 0.625137983 0.274541716 0.314429636 1.342417483 0.453544942 1.080918923 0.672927335 1 18.62015099 2.758586365 24.97498897 0.890669016 0.631515562 0.192495997 0.325317771 1716.846393 2141151.851 0.098809325 0.104679148 573.5699164 -2.758586365 -0.259153454 HGVVSCSGVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGVVSCSGVAR 11 0 P07199 P07199 CENPB Major centromere autoantigen B 0 72.582 0.0459 29841000 82233 73729 78650 92900 80091 76471 94989 81188 86427 FALSE TRUE 78346.00906 81242.06892 82256.1803 83561.5155 94058.84504 73822.7901 80496.68346 74078.74832 99829.65775 0.784796931 0.813806946 0.823965364 0.837040989 0.942193404 0.739487561 0.806340373 0.74205151 1 16.60718086 4.195183765 1.681953168 0.829890811 0.786037154 0.037089363 0.080336591 1.765535703 8.926083206 0.020436567 0.088883416 15674.14156 -4.195183765 -0.043853658 HGVYNPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HGVYNPNK 8 0 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;;;;; 142.64 0.0006143 10851400000 30490820 19448790 13957680 15249250 21610440 15055990 27695560 21147300 16289590 FALSE TRUE 29049579.37 21430643.81 14597653.43 13716366.42 25379293.89 14534597.29 23470093.66 19295530.3 18815696.42 1.543901364 1.138976912 0.77582318 0.728985317 1.348836276 0.772471928 1.24736779 1.025501787 1 24.16543335 4.317796924 2.349680741 1.001138266 1.517297192 0.423467479 0.201929003 0.280295196 2.894220685 0.049589212 0.203087325 20787.24447 -4.317796924 0.516158926 HGVYNPNKIFGVTTLDIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HGVYNPNKIFGVTTLDIVR 19 1 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 316.07 6.43E-62 597900000 1048890 801010 1232280 753570 1020540 900100 1232710 989170 873040 FALSE TRUE 999311.0484 882633.8297 1288781.257 677819.7119 1198521.853 868929.3113 1044637.449 902553.0309 1008426.584 0.990960635 0.875258391 1.278011981 0.672155735 1.1885068 0.86166839 1.035908281 0.895011144 1 19.94367463 HGWQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGWQIER 7 0 O15541 O15541 RNF113A RING finger protein 113A 0 119.29 0.0048148 75170000 62219 63669 64140 62122 88108 60835 75457 58504 66265 FALSE TRUE 59278.03118 70156.94349 67080.88244 55877.37854 103474.0073 58728.2687 63944.64879 53381.07961 76541.03777 0.774460772 0.91659253 0.876404141 0.73003163 1.3518762 0.767278187 0.835429603 0.697417767 1 16.22394584 -1.274164297 7.592802831 1.000000399 0.870693747 0.047800155 0.183994378 1.13E-06 1.08E-07 0.162770446 0.038365244 0.0531907 1.274164297 -0.129306652 HGYIGEFEIIDDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 HGYIGEFEIIDDHR 14 0 P62244;I3L3P7;I3L246;H3BN98 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;;;;;;;;;; 227.56 1.15E-12 7162909200 4695626.2 5078708 4657938 5473344 4347997.8 5056167 5094136 4366318.4 1162689.9 FALSE TRUE 4473673.255 5596234.119 4871509.065 4923153.062 5106287.24 4881070.669 4316931.993 3983980.414 1342993.911 3.331119536 4.166983984 3.627350074 3.665804454 3.802167081 3.634469693 3.214409206 2.966491791 1 20.35702133 0.571384944 0.78787013 0.97723457 3.759400622 0.939668082 0.212824683 0.293556869 0.305865082 0.205681299 0.069261199 3.727219277 -0.571384944 2.782166052 HGYPLIIYDVFPDACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HGYPLIIYDVFPDACK 16 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 122.93 9.06E-05 141670000 480940 412210 379920 446910 320220 418440 457400 460380 250080 FALSE TRUE 458206.9193 454214.6676 397339.7078 401985.7577 376066.2666 403949.3179 387615.2293 420066.6866 288861.1292 1.5862533 1.572432639 1.375538858 1.391622884 1.301892947 1.398420476 1.341873967 1.45421673 1 18.14001655 -2.383643837 0.069956722 1.15E-13 2.047433723 0.763224528 0.079050299 78.36095172 0.692780962 18.19245899 5.223180482 0.004133864 2.383643837 2.047433723 HHAISAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HHAISAK 7 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 77.741 0.037226 23080000 35384 36914 27586 53158 52085 42181 58738 26574 10045 FALSE TRUE 33711.46844 40675.57857 28850.84539 47814.45685 61168.60751 40720.26139 49776.4393 24247.03968 11602.7273 2.905477961 3.505691164 2.486557225 4.120967047 5.27191633 3.509542227 4.290063709 2.089770712 1 13.50217634 3.229763935 24.99690452 3.686734885 3.07294342 0 1.221327379 581.146226 1651399.496 0.319865689 0.387756066 1697.320808 -3.229763935 -0.613791465 HHEDNLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HHEDNLLR 8 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 99.802 0.0092003 0 26617 26410 30133 36806 44619 32389 40668 24379 29004 FALSE TRUE 25358.86716 29101.20903 31514.62786 33106.19095 52400.53947 31267.36081 34463.34968 22244.24552 33501.79219 0.756940614 0.868646336 0.940684835 0.98819164 1.564111531 0.933304124 1.028701673 0.663971808 1 15.03195065 3.6746022 1.883425911 1.045066093 0.7939419 0.144209193 0.220031332 0.597343421 4.145381436 0.063184314 0.125653031 4727.180664 -3.6746022 -0.251124193 HHEEEIVHHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HHEEEIVHHKK 11 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ;; 152.62 1.34E-05 136649000 166919 193068 282868 303249 197451 259255 326032 106479 18792.6 FALSE TRUE 159029.0697 212741.8487 295837.7776 272765.8344 231886.3919 250276.9343 276289.8304 97155.13428 21706.86043 7.326212383 9.800673358 13.62876859 12.56588143 10.68263154 11.52985413 12.72822624 4.475780116 1 14.40586346 1.077752743 4.277122047 1.093572914 10.98513007 0.802757304 1.778640136 0.093124957 3.039937484 1.936586726 0.495248939 11.96059385 -1.077752743 9.891557159 HHFET(ph)LTESPCRELFPAALGDVEASEAEDHFFNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHFETLTESPCRELFPAALGDVEASEAEDHFFNPR 35 1 O43379-4 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFET(0.345)LT(0.345)ES(0.309)PCRELFPAALGDVEASEAEDHFFNPR;HHFET(0.333)LT(0.333)ES(0.333)PCRELFPAALGDVEASEAEDHFFNPR 80.593 0.00093528 25983000 11780.4 8151.5 15430.2 13737 18427.3 13011.4 21439.1 8345.5 3913.7 TRUE FALSE 11223.56384 8982.147117 16137.68993 12356.13066 21641.01529 12560.81196 18168.17154 7614.723778 4520.616608 2.482750654 1.986929638 3.5697984 2.733284358 4.787182184 2.778561653 4.018958721 1.684443614 1 12.14230385 3.74421763 24.91720611 3.171245874 2.234840112 0.03486634 1.09962275 833.9259259 3673146.267 0.251327105 0.437840953 5549.037118 -3.74421763 -0.936405762 HHFETLT(ph)ESPCRELFPAALGDVEASEAEDHFFNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HHFETLTESPCRELFPAALGDVEASEAEDHFFNPR 35 1 O43379-4 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFET(0.07)LT(0.502)ES(0.427)PCRELFPAALGDVEASEAEDHFFNPR;HHFET(0.17)LT(0.415)ES(0.415)PCRELFPAALGDVEASEAEDHFFNPR;HHFET(0.035)LT(0.508)ES(0.457)PCRELFPAALGDVEASEAEDHFFNPR 181.18 2.01E-20 132807000 45576.9 43387.1 71567.2 68132.6 78576.1 63255 103997.5 40906.2 15312 TRUE FALSE 43422.57026 47808.29482 74848.62691 61283.7816 92279.74696 61064.46349 88130.77133 37324.23627 17686.50676 2.455124172 2.703094256 4.231962136 3.465002018 5.217522501 3.452601711 4.982938267 2.110322676 1 14.11036151 3.826766843 5.927872643 3.794556723 2.555117048 0.044852945 1.270216523 0.38427532 20.73124771 0.288446829 0.52586395 6710.68484 -3.826766843 -1.239439674 HHGPQTLYLPVTLSSIPVFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHGPQTLYLPVTLSSIPVFQR 21 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 156.92 6.08E-09 522900000 505620 433500 534770 623780 538530 572870 704210 382640 77593 FALSE TRUE 481720.3446 477674.1428 559289.7335 561076.4493 632449.4615 553031.3683 596769.8308 349134.0131 89625.72615 5.374799908 5.329654368 6.240281195 6.260216496 7.056561644 6.170453418 6.658465782 3.895466493 1 16.45162528 0.972137611 3.618856792 1.008721278 6.07871144 0.910148086 0.52828857 0.070484955 2.507430711 0.593168744 0.153027993 9.378591319 -0.972137611 5.069990162 HHGT(ph)PTSTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HHGTPTSTKK 10 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 HHGT(1)PTSTKK;HHGT(1)PTSTKK;HHGT(1)PTSTKK 91.961 0.0074637 105514000 201809 252048 351186 444603 220234 419845 549967 154445 16484.7 TRUE FALSE 192269.8885 277731.9778 367288.2255 399910.6617 258642.7399 405305.6624 466059.4333 140920.977 19041.06308 10.09764464 14.58594914 19.28927097 21.00253857 13.58341909 21.28587362 24.47654478 7.400898596 1 14.21682641 1.033458364 6.138418957 1.025187622 17.44684265 0.659366662 4.186702728 0.104594393 10.7731058 4.581761384 1.151884248 10.80086068 -1.033458364 16.42165503 HHHHDS(ph)DSNSPCCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.904)DS(0.085)NS(0.01)PCCK 89.013 0.01056 18982000 8614.1 11724 14013 16765 14662 14421 18039 6670.3 5955.7 TRUE FALSE 8206.928565 12918.68893 14655.50991 15079.75035 17219.04816 13921.59715 15286.81924 6086.213171 6879.279538 1.192992452 1.877913066 2.130384414 2.192053727 2.503030741 2.023699877 2.222154101 0.884716653 1 12.74804177 4.45227 2.142283099 1.969407264 1.173836644 0.101381742 0.531973792 0.628322183 4.831858097 0.125080618 0.764355379 28331.52813 -4.45227 -0.79557062 HHIEVLHYLLQS(ph)WPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HHIEVLHYLLQSWPDPR 17 0 M0QXZ8;Q6ZW31-2;Q6ZW31 M0QXZ8 SYDE1 Rho GTPase-activating protein SYDE1 1 HHIEVLHY(0.384)LLQS(0.616)WPDPR;HHIEVLHY(0.466)LLQS(0.534)WPDPR;HHIEVLHY(0.419)LLQS(0.581)WPDPR;HHIEVLHY(0.397)LLQS(0.603)WPDPR;HHIEVLHY(0.403)LLQS(0.597)WPDPR 55.885 0.074223 1201259000 704585 536897 802806 683357 1974136 423672 985484 485436 2070789 TRUE FALSE 671280.6634 591607.4147 839615.4492 614664.6561 2318424.693 409000.1324 835130.3161 442928.6504 2391916.382 0.280645539 0.247336161 0.351022074 0.256975813 0.969274976 0.170992655 0.349146953 0.185177314 1 21.18973553 -1.188447376 4.503493867 1.000144869 0.345601201 0.444574392 0.227782698 62800547.57 16572780.71 89864.69676 0.049630105 0.064796661 1.188447376 -0.654543668 HHISIAEIYETELVDIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HHISIAEIYETELVDIEK 18 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 147.24 4.51E-08 110389000 91500 167555 168016 196718 113865 169171 179716 89572 9267.8 FALSE TRUE 87174.97634 184629.045 175719.6998 176943.5329 133723.0199 163312.5659 152297.0235 81728.60083 10705.00309 8.143386377 17.24698661 16.41472668 16.52905015 12.49163768 15.25572337 14.22671457 7.63461721 1 13.38599759 1.016985255 2.66098571 1.046065297 14.38148658 0.745189109 2.596723691 0.12813436 2.038951624 2.464276366 0.661623449 10.39884859 -1.016985255 13.33542129 HHPDLIFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHPDLIFCR 9 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 135.71 0.00021314 374320000 559780 480240 340130 390700 867780 343890 621430 406170 427290 FALSE TRUE 533320.3088 529177.002 355725.2969 351426.0937 1019120.557 331981.0031 526619.4402 370603.6016 493551.9509 1.08057583 1.072180955 0.720745397 0.712034656 2.064869879 0.672636391 1.066999004 0.750890764 1 18.91284242 HHPEDVEPALRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHPEDVEPALRK 12 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 46.592 0.077314 348430000 487710 406240 459970 508910 435890 455050 608200 419240 112328 FALSE TRUE 464656.9148 447636.3179 481060.0795 457753.3999 511909.078 439291.5044 515407.9196 382529.1231 129747.2525 3.58124666 3.450063944 3.707670644 3.528039253 3.945432893 3.385748028 3.972399488 2.948263763 1 16.98534446 0.894898925 4.249613727 1.000424024 3.634646001 0.949697728 0.192149859 0.103114775 3.757515012 0.170998549 0.043556734 7.850529059 -0.894898925 2.634221976 HHVLHDQNVDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHVLHDQNVDKR 12 1 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 189.33 3.28E-06 159543000 113333 115469 132755 142436 114349 122533 171864 80144 14644.9 FALSE TRUE 107975.9737 127235.4224 138841.9481 128118.0627 134291.4294 118289.6515 145642.9903 73126.16649 16915.9563 6.38308422 7.521621607 8.207750459 7.573799579 7.938742986 6.992785357 8.609799396 4.322910583 1 14.04609712 1.002725618 3.945870204 1.015963677 7.55334784 0.923758943 0.630185776 0.046546819 1.949692506 0.619978255 0.158956065 10.06295703 -1.002725618 6.537384163 HHYDS(ph)DEKSETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HHYDSDEKSETR 12 1 Q9BQ39 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 HHYDS(1)DEKSETR;HHYDS(1)DEKSETR 171.08 2.38E-05 359694000 209199 315114 280424 371778 239022 336370 305948 195285 68353 TRUE FALSE 199310.5779 347224.4749 293281.7178 334406.1691 280707.3611 324721.4226 259270.0135 178184.8101 78952.83414 2.524425881 4.397872206 3.714644585 4.23551824 3.555380427 4.112853276 3.283859488 2.256851348 1 16.26870343 1.069999415 1.90999347 1.016413478 3.747551497 0.76054412 0.513636288 0.148174845 1.084513323 0.464987292 0.132276714 11.74895971 -1.069999415 2.731138019 HHYEQQQEDLAR ddPTM_SK-BR-3_Trastuzumab_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 ; 208.08 7.10E-08 402990000 371820 427580 461020 533400 401620 461270 487760 285437 68629 FALSE TRUE 354244.8055 471150.8881 482158.223 479781.6186 471662.4008 445296.1042 413343.2537 260442.6231 79271.63481 4.468746057 5.943499074 6.082354983 6.052374468 5.949951732 5.617344783 5.214264278 3.285445339 1 16.27451711 1.020754066 1.891979542 1.007059809 5.666571501 0.917727259 0.463560178 0.093543763 0.696113481 0.466610068 0.132264404 10.48948259 -1.020754066 4.659511691 HIADLAGNSEVILPVPAFNVINGGSHAGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HIADLAGNSEVILPVPAFNVINGGSHAGNK 30 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 ; 341.2 6.90E-106 567630000 514130 445430 435250 500710 435460 474150 581770 540450 371510 FALSE TRUE 489828.0938 490819.8234 455206.643 450377.6795 511404.0861 457730.0666 493010.3016 493125.3329 429121.8734 1.141466153 1.14377722 1.06078639 1.049533262 1.191745557 1.066666826 1.14888178 1.149149842 1 18.71102792 -1.107099542 3.826296515 0.999956393 1.120682082 0.395709207 0.046173962 2401419.238 1390532.337 846.3477947 0.010168249 0.078144867 1.107099542 0.120725689 HIAEDADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 166.52 0.00031801 7962190000 3698580 3382550 3249031 3904240 3721010 3357689 4175490 3588360 2863310 FALSE TRUE 3523755.453 3727235.691 3398002.285 3511778.378 4369952.966 3241411.388 3538442.312 3274144.175 3307337.491 1.065435706 1.126959586 1.027413227 1.061814341 1.321290306 0.980066714 1.069876395 0.989963735 1 21.65723884 HIAEEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 187 0.00020453 18362167000 4354664 3811537 3750946 4437651 4009603 3792000 4380091 4016592 3069313 FALSE TRUE 4148827.663 4199936.954 3922930.584 3991569.89 4708876.494 3660682.089 3711827.672 3664877.911 3545286.384 1.170237666 1.184653791 1.106520083 1.125880806 1.328207649 1.03254905 1.046975412 1.033732543 1 21.75747074 2.110571895 23.22303489 1.033766557 1.176432527 0.623801394 0.059537199 3.376824417 692.3856311 0.02088604 0.015425375 128.9947085 -2.110571895 0.14266597 HIAEEADRK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 135.55 0.00014132 1022904000 810471 729709 714797 860889 624041 774243 826666 835638 511641 FALSE TRUE 772161.642 804067.1767 747571.1495 774350.8021 732873.5528 747430.7708 700542.9189 762465.1067 590983.6732 1.306570176 1.360557344 1.264960748 1.310274441 1.240091031 1.264723214 1.185384556 1.290162726 1 19.17275875 -4.999999999 0.13813043 0.011406862 1.387500005 0.835518999 0.040057603 46.43750034 0.395206449 12.56748368 0.229238887 1.00E-05 4.999999999 1.376093143 HIAEEADRKYEEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HIAEEADRKYEEVAR 15 2 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 ;; 165.34 8.59E-07 1578590000 670740 192164 758070 408590 787590 650480 1327230 796390 801100 FALSE TRUE 639035.4495 211745.7301 792828.2593 367517.7569 924945.4466 627953.7145 1124736.687 726653.8697 925330.4965 0.690602387 0.228832542 0.856805501 0.397174586 0.999583879 0.678626412 1.215497264 0.785291172 1 19.81960921 2.630804396 1.20993282 0.994548481 0.500550911 0.383836651 0.227757506 0.382296439 1.145994812 0.103795757 0.087110519 427.3703571 -2.630804396 -0.493997569 HIAELIFYMEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HIAELIFYMEELR 13 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 150.21 4.23E-05 47447000 102972 128749 87629 115053 93571 88324 111782 101430 56001 FALSE TRUE 98104.71763 141868.6695 91646.87633 103487.6539 109889.7528 85265.31773 94727.60288 92548.25149 64685.34907 1.516645099 2.193211779 1.416810416 1.599862339 1.698835275 1.318155022 1.464436758 1.430745181 1 15.98115136 1.430004114 0.30074297 0.939299823 1.883600532 0.482160954 0.217772353 1.176843428 0.390501899 0.42319797 0.356086212 26.91560298 -1.430004114 0.944300708 HIAFTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 125.74 0.00040116 253060000 183061 154922 133546 152193 177842 145275 194833 174474 160797 FALSE TRUE 174408.0693 170708.7279 139669.2162 136894.2705 208857.5885 140244.0903 165107.6475 159196.1316 185732.5775 0.939027884 0.919110316 0.751990943 0.7370504 1.124507027 0.755086115 0.888953622 0.857125517 1 17.50286736 HIDCAAIYGNEPEIGEALKEDVGPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIDCAAIYGNEPEIGEALKEDVGPGK 26 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 228.18 6.80E-35 284350000 539060 459440 441680 550260 302150 522340 560160 573310 256440 FALSE TRUE 513579.7021 506257.4583 461931.4649 494946.8194 354844.8643 504251.2348 474697.304 523107.9371 296207.4055 1.733851661 1.709131672 1.55948655 1.67094681 1.197960813 1.702358636 1.602584186 1.766019105 1 18.17624818 -1.83482184 2.59868985 0.76831805 1.622514147 0.59185842 0.161186021 23557588.26 17745648.02 34221585.57 0.03819561 0.014627771 1.83482184 0.854196098 HIDFSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 176.65 0.00074396 7419250000 1722707 1492412 1039654 1161943 1704710 1176868 1890249 1412802 1397688 FALSE TRUE 1641278.054 1644490.48 1087323.164 1045142.282 2002010.884 1136112.766 1601856.798 1289089.567 1614434.317 1.016627333 1.018617148 0.673501023 0.647373678 1.24006958 0.703721888 0.992209334 0.798477556 1 20.62259732 3.895187728 21.48273915 0.867201205 1.017786312 0.111048904 0.179378506 20.03450191 4088.435218 0.04258128 0.076764591 7855.75134 -3.895187728 0.150585107 HIDIHPENTHILDGNAVDLQAECDAFEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIDIHPENTHILDGNAVDLQAECDAFEEK 29 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 56.156 0.0195 119730000 13084 15264 13498 15563 14107 13889 18949 16481 3200.3 FALSE TRUE 12465.54525 16819.41895 14116.89665 13998.57767 16567.25633 13408.02045 16057.98203 15037.83627 3696.586179 3.372177638 4.549986971 3.818900999 3.786893364 4.481771973 3.627135903 4.344003156 4.068033461 1 11.85197783 -1.117638692 6.078541396 0.999986897 4.025814018 0.863270346 0.375908172 5.99E-05 8.69E-06 0.326456701 0.076946252 0.076271328 1.117638692 3.025827121 HIDLVEGDEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;; 153.34 3.25E-05 3099390000 2716410 2200790 2252690 2760280 2468970 2074220 2549920 2126860 1830530 FALSE TRUE 2588010.683 2425053.003 2355978.065 2482811.41 2899557.586 2002389.241 2160882.872 1940620.863 2114399.243 1.223993383 1.146922943 1.114254118 1.174239642 1.371338736 0.947025141 1.021984319 0.917811936 1 21.01181638 2.209919464 24.99799072 0.977781133 1.194068054 0.71516857 0.073254836 119.007135 103868.6896 0.026397246 0.019498977 162.1509375 -2.209919464 0.216286921 HIDMVEGDEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIDMVEGDEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 75.739 0.028266 84646000 59448 37377 50261 53603 56302 57025 82540 66688 62877 FALSE TRUE 56638.01085 41185.75879 52565.51656 48214.7246 66121.05097 55050.20995 69947.00705 60848.44518 72627.64403 0.779840949 0.567081025 0.723767338 0.663861884 0.910411619 0.757978738 0.96309068 0.837813838 1 16.14823116 2.475015634 0.986378527 0.92763846 0.667484085 0.576044076 0.087082945 0.349195343 0.682877727 0.051049286 0.035897266 298.549009 -2.475015634 -0.260154375 HIDSSPYSPAYLS(ph)PPPESSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HIDSSPYSPAYLSPPPESSWR 21 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR 274.48 6.20E-45 252300000 320240 298410 305410 352650 369370 279250 356970 301790 282200 TRUE FALSE 305102.8899 328818.3183 319413.3506 317200.952 433788.0111 269579.5025 302507.6703 275363.6677 325962.1347 0.936007153 1.008762317 0.979909372 0.973122084 1.330792644 0.827027049 0.928045432 0.844771949 1 18.31434486 HIEIFTDLSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 223.71 6.74E-12 1316520000 1558694 1590055 1428360 1676043 1440409 1445492 1565720 1530861 1048278 FALSE TRUE 1485017.624 1752083.412 1493851.719 1507563.973 1691615.874 1395434.25 1326840.658 1396810.695 1210839.598 1.226436289 1.446998772 1.233732132 1.245056716 1.397060251 1.152451779 1.095802168 1.153588549 1 20.20757633 2.093281215 5.400344319 1.100790815 1.313998281 0.637414221 0.07938917 0.129432233 5.986951642 0.028972494 0.021099759 123.9598995 -2.093281215 0.213207466 HIEPELAGRDS(ph)PIRAEMPGNLQHYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 198.7 2.86E-25 736120000 67426 59247 60002 78450 85220 69455 86394 75692 55158 TRUE FALSE 64238.90661 65284.33666 62753.15105 70564.05695 100082.341 67049.75593 73213.00857 69064.00721 63711.62093 1.00827613 1.024684912 0.984956122 1.107553943 1.570864774 1.052394445 1.149131155 1.084009576 1 15.95926892 3.003370645 23.31195298 1.184951862 1.014804158 0.190181482 0.153915942 65.62197171 453833.3844 0.042505764 0.050512091 1007.791393 -3.003370645 -0.170147703 HIGHLLPMDYSANAIAFYSYTFS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIGHLLPMDYSANAIAFYSYTFS 23 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H7C286;H0YF44 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 83.871 0.0076031 37333000 56245 57425 64779 65389 52035 49482 64510 56680 30478 FALSE TRUE 53586.41032 63276.67279 67749.18123 58815.97349 61109.88753 47768.42593 54667.81469 51716.79872 35204.37258 1.522152119 1.797409474 1.924453591 1.670700802 1.73586072 1.356889001 1.552870018 1.46904475 1 15.10346701 0.802350033 0.515067479 0.984428002 1.734987032 0.720336651 0.136198532 0.673039941 0.40342583 0.170591746 0.071502762 6.343808042 -0.802350033 0.75055903 HIGLVYSGMGPDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HIGLVYSGMGPDYR 14 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ; 186.13 1.56E-07 546200000 2355420 2036260 1549460 1855720 2401190 1777920 2590200 2030220 1920450 FALSE TRUE 2244083.965 2243757.209 1620504.274 1669179.5 2819956.776 1716350.185 2195017.418 1852443.174 2218263.578 1.011639909 1.011492607 0.730528279 0.75247122 1.271245133 0.773735909 0.98952056 0.835087044 1 21.08099937 3.90965632 24.99966048 0.909210867 1.011677788 0.069247221 0.158501264 157.5127984 43579.8954 0.037928729 0.068376995 8121.87535 -3.90965632 0.102466921 HIIKEYAENIGDGRS(ph)PEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIIKEYAENIGDGRSPEFR 19 2 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 1 HIIKEYAENIGDGRS(1)PEFR 107.74 0.00015054 61434000 54876 29076 59064 50365 61586 52741 82647 60873 55202 TRUE FALSE 52282.12023 32038.87746 61772.14282 45302.21451 72326.5789 50914.56595 70037.68223 55542.63741 63762.44423 0.819951632 0.502472542 0.968785679 0.710484284 1.134313149 0.798503987 1.098415895 0.871087018 1 15.96041931 3.265003346 1.438705027 0.97480928 0.675883653 0.313744313 0.155281438 0.368096417 1.588279982 0.047860322 0.072068045 1840.786182 -3.265003346 -0.298925626 HIISATSLST(ph)SPTELGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATS(0.001)LS(0.028)T(0.679)S(0.277)PT(0.015)ELGSR 111.4 0.0010546 0 129100 120280 136610 130890 80784 173180 116690 94107 29949 TRUE FALSE 122997.6989 132536.6687 142873.7036 117732.6885 94872.70402 167182.7332 98886.79734 85866.49219 34593.33796 3.555531385 3.83127725 4.130093019 3.403334152 2.742513721 4.83280143 2.858550321 2.482168453 1 15.07820661 1.039468375 1.622756557 1.033588743 3.704342203 0.706949838 0.564265362 0.187836489 1.004593642 0.482487942 0.140869755 10.95136805 -1.039468375 2.67075346 HIISATSLSTS(ph)PTELGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.002)T(0.298)S(0.7)PTELGSR;HIISATSLST(0.01)S(0.99)PTELGSR 251.38 7.64E-26 682020000 234283 197947 224522 244056 253642 229457 249745 237864 162843 TRUE FALSE 223208.9069 218118.0243 234816.5558 219523.0272 297877.0845 221510.8466 211641.8134 217035.3672 188095.8608 1.186676336 1.159610974 1.248387683 1.167080585 1.58364508 1.177648704 1.1251806 1.153855094 1 17.52110858 1.831898527 3.993749322 1.105957285 1.249748203 0.269445783 0.127619733 0.37275594 9.798497365 0.063149076 0.034351863 67.90449549 -1.831898527 0.143790919 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEK;HIKEEPLS(0.95)EEEPCT(0.03)S(0.007)T(0.013)AIAS(1)PEK;HIKEEPLS(0.96)EEEPCT(0.003)S(0.018)T(0.02)AIAS(1)PEK;HIKEEPLS(0.719)EEEPCT(0.089)S(0.095)T(0.102)AIAS(0.995)PEK 182.79 2.18E-17 669618000 1283420 1302590 1205950 1453980 744406 1482520 1507440 1427500 457596 TRUE FALSE 1222755.28 1435325.402 1261244 1307823.168 874230.1707 1431179.961 1277452.342 1302500.532 528557.6506 2.313381102 2.715551275 2.386199498 2.474324544 1.653992085 2.707708344 2.416864727 2.464254431 1 19.01170131 2.952693257 24.99827727 2.198024981 2.49245965 0.114961667 0.49474033 1039.78399 549452.2508 0.136802997 0.145105519 896.7951633 -2.952693257 0.294434669 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEKK;HIKEEPLS(1)EEEPCTSTAIAS(1)PEKK;HIKEEPLS(0.998)EEEPCT(0.001)STAIAS(1)PEKK;HIKEEPLS(1)EEEPCT(0.007)S(0.005)T(0.003)AIAS(0.986)PEKK;HIKEEPLS(0.99)EEEPCT(0.041)S(0.196)T(0.183)AIAS(0.591)PEKK 135.11 1.62E-05 2011080000 1610710 1523630 1447390 1700670 619109 1863200 1773530 1726110 364397 TRUE FALSE 1534574.93 1678889.629 1513754.263 1529715.421 727081.4136 1798676.917 1502945.425 1574962.658 420905.8257 3.645886649 3.988753604 3.596420317 3.634341288 1.727420647 4.27334764 3.570740374 3.741840957 1 18.68313795 2.975973538 24.85059862 3.131934228 3.761373971 0.129844858 0.970533193 1709.273329 1767905.102 0.271870839 0.289866464 946.1795085 -2.975973538 0.629439742 HIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(0.999)EEEPCT(0.001)STAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(0.665)EEEPCT(0.111)S(0.111)T(0.111)AIAS(0.001)PEK;HIKEEPLS(0.758)EEEPCT(0.225)S(0.016)T(0.001)AIASPEK 187.43 1.47E-17 5386440000 6651650 5568230 5666240 6782400 3732450 6709100 6649850 6142300 1951755 TRUE FALSE 6337239.687 6135638.968 5926042.709 6100620.266 4383388.098 6476762.185 5635293.25 5604447.65 2254423.197 2.811024875 2.721600352 2.628629228 2.706067021 1.944350157 2.87291321 2.499660781 2.485978523 1 21.10432693 -1.446517544 0.383199654 7.71E-14 2.690196414 0.799978657 0.250628478 9.988518663 0.815465204 10.1700731 0.160823277 0.035766995 1.446517544 2.690196414 HIKEEPLS(ph)EEEPCTSTAIASPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(0.998)EEEPCTS(0.001)T(0.001)AIASPEKK 66.124 0.019404 687240000 806600 624000 738540 780650 488610 817120 894410 815950 257180 TRUE FALSE 768473.6165 687586.3094 772402.7895 702177.5789 573823.4293 788822.9295 757951.3275 744501.0924 297062.1609 2.586911824 2.314620978 2.600138594 2.363739551 1.93166113 2.655413692 2.551490655 2.506213144 1 18.18040532 3.00487473 24.17911741 2.2795792 2.474161231 0.067915983 0.480619548 352.2302976 1747061.352 0.125745139 0.149740397 1011.287711 -3.00487473 0.194582031 HILANFK ddPTM_SK-BR-3_Trastuzumab_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 1011740000 3372800 2914500 1397130 1792310 2769600 1887180 3554900 2644200 2041960 FALSE TRUE 3213374.428 3211490.864 1461189.792 1612143.594 3252617.363 1821826.483 3012534.715 2412659.83 2358616.728 1.362397879 1.361599291 0.619511333 0.683512321 1.379035994 0.772413111 1.277246396 1.02291305 1 21.16950957 3.848483147 19.13994402 0.987622922 1.362092669 0.320289385 0.238697696 4.968694707 856.1579123 0.059481115 0.107231789 7054.774677 -3.848483147 0.374469747 HILGFDTGDAVLNEAAQILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HILGFDTGDAVLNEAAQILR 20 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;; 276.46 1.51E-44 614168000 717017 673407 629170 769171 713283 662398 769461 686964 483897 FALSE TRUE 683125.0274 742027.9389 658018.0668 691852.4698 837679.3294 639458.9912 652065.5923 626809.7903 558937.2754 1.222185489 1.327569249 1.177266387 1.23779984 1.498700062 1.144062168 1.166616758 1.121431363 1 19.09232687 1.402614829 1.230318057 1.021836845 1.279197715 0.480599505 0.095288612 0.355533433 1.041104649 0.082383513 0.027463569 25.27055784 -1.402614829 0.25736087 HILLAVANDEELNQLLK ddPTM_SK-BR-3_Trastuzumab_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 ; 238.32 3.03E-20 363760000 719790 611580 606980 685860 522770 572800 724000 630800 410870 FALSE TRUE 685766.9532 673900.6973 634810.6334 616916.0498 613940.9225 552963.7924 613540.5028 575563.8079 474585.6212 1.444980468 1.419977065 1.337610339 1.299904637 1.293635743 1.16515075 1.292792018 1.212771273 1 18.85630887 8 0.03564008 1.26E-11 3.315504259 0.893224339 0.041714737 265.0493144 0.721805853 19.64525528 56.24852535 100000000 -8 3.315504259 HILRPGTALVLLEAQAATGFIIDPVENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HILRPGTALVLLEAQAATGFIIDPVENR 28 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 248.95 4.06E-46 642491000 407599 420964.1 398276 442551 437755 412015.4 481722 437539 309327.9 FALSE TRUE 388332.6031 463860.8204 416537.3485 398064.9327 514099.3334 397747.2034 408226.4615 399225.7656 357296.8909 1.086862531 1.298250369 1.165801772 1.114101306 1.438857562 1.113212047 1.14254132 1.117350237 1 18.44676383 1.137329493 1.137723169 1.007452454 1.208338302 0.286150612 0.103142377 0.573393571 1.54384058 0.089874401 0.029036782 13.71922231 -1.137329493 0.200885848 HILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPR 39 1 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 62.605 0.0032722 98774000 81445 69690 79291 82479 88542 88955 111370 87913 25682 FALSE TRUE 77595.25626 76791.49023 82926.57078 74188.05422 103983.6968 85874.46605 94378.46105 80214.87166 29664.63339 2.615749712 2.588654618 2.795469261 2.500892333 3.505308675 2.894843328 3.181514492 2.704057407 1 14.85645633 HIMGQNVADYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HIMGQNVADYMR 12 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 177.1 2.37E-05 1882290000 2215050 1750930 1283490 1433784 2248120 1535950 2529410 1980900 1865590 FALSE TRUE 2110348.976 1929351.758 1342339.286 1289657.308 2640191.416 1482759.666 2143502.049 1807441.895 2154896.169 0.979327453 0.895333977 0.622925274 0.598477702 1.225205861 0.688088683 0.99471245 0.838760549 1 21.03918693 2.767751006 24.99698094 0.931067787 0.808654245 0.181882768 0.175812781 1710.345243 1464639.267 0.053020689 0.056228824 585.8022104 -2.767751006 -0.122413542 HINMDGTINVDDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HINMDGTINVDDFK 14 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 195.54 2.61E-08 80167000 239880 244630 231340 292770 185970 269290 288610 277910 154530 FALSE TRUE 228541.3478 269558.0751 241947.1678 263340.2034 218403.1091 259964.4198 244577.2438 253574.7271 178493.7232 1.280388709 1.510182377 1.355493983 1.475347137 1.223589856 1.456434519 1.370228821 1.420636662 1 17.44551382 -1.50206724 2.82139899 0.984661403 1.389802379 0.660050692 0.087151204 9064515.417 9886504.234 1077474.728 0.018637102 0.03147261 1.50206724 0.405140976 HIPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIPESK 6 0 O95202 O95202 LETM1 "LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 94.669 0.044219 482650000 1023100 1028100 884840 1134300 721820 1069800 1063300 1077200 781780 FALSE TRUE 974740.0906 1132864.559 925410.7892 1020278.009 847705.1795 1032752.558 901074.0562 982874.6574 903014.4496 1.079429118 1.254536469 1.024801751 1.129857899 0.938750404 1.143672239 0.997851204 1.088437353 1 19.78438955 3.717502152 24.96287637 1.048032965 1.166982803 0.311481307 0.074620333 746.7732682 885231.4278 0.017596842 0.027294167 5217.976901 -3.717502152 0.118949838 HIPGAAFFDIDQCSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HIPGAAFFDIDQCSDR 16 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;; 246.77 3.16E-20 801420000 793620 609970 684130 746970 831860 657250 780770 712200 647230 FALSE TRUE 756107.1554 672126.6365 715498.0372 671883.1564 976936.1206 634489.2677 661649.1967 649835.9924 747599.1228 1.011380474 0.89904685 0.957061098 0.898721167 1.306764669 0.848702531 0.885032067 0.869230544 1 19.51190535 HIQSNLDFS(ph)PVNSASSEENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIQSNLDFSPVNSASSEENVK 21 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 HIQS(0.002)NLDFS(0.967)PVNS(0.011)AS(0.011)S(0.011)EENVK 71.418 0.0044562 0 137050 139720 148710 176010 112880 177320 190420 158130 97737 TRUE FALSE 130571.9181 153957.6268 155528.5006 158317.1404 132566.2363 171179.3639 161367.9317 144283.2989 112893.5548 1.156593203 1.36374151 1.377656155 1.402357652 1.174258677 1.516289962 1.429381261 1.278047265 1 16.7846036 0.971622247 21.68592114 0.999999996 1.345454558 0.498389745 0.108430411 459.7899519 351367.2387 0.105307405 0.026326851 9.367468621 -0.971622247 0.345454562 HISDLYEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 296500000 370244 370646 325349 418638 500997 306200 439314 380011 380669 FALSE TRUE 352743.2999 408415.2488 340266.5735 376555.7129 588370.7182 295596.2172 372288.5807 346735.2223 439701.2043 0.8022341 0.928847237 0.773858634 0.856389997 1.338114866 0.672266108 0.846685379 0.788570099 1 18.74616396 -1.970978056 7.612964399 1.075066635 0.875149591 0.046208218 0.177205675 0.12279859 0.00046813 0.093320469 0.037376477 0.010691089 1.970978056 -0.199917044 HISEGCVFIYCQVGEKPYWKDPNNDFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HISEGCVFIYCQVGEKPYWKDPNNDFRK 28 3 Q9BRA2;I3L2R6 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 97.441 0.0011235 829580000 690760 328900 1033500 637990 689810 678130 1121500 880070 747960 FALSE TRUE 658109.1438 362415.2839 1080886.997 573858.0331 810112.6456 654646.1881 950394.5772 803006.4053 863949.8167 0.761744642 0.419486499 1.251099284 0.664226118 0.93768484 0.757736358 1.100057618 0.929459547 1 19.72058799 3.753501568 24.99949515 0.938825044 0.590615577 0.403183925 0.180773228 692.1503215 1158116.34 0.042306779 0.075890626 5668.936188 -3.753501568 -0.348209467 HITIFSPEGR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 208.6 1.11E-07 1494810000 1459950 1115720 1043980 1271550 1638740 1052650 1754040 1261180 1368190 FALSE TRUE 1390941.057 1229413.136 1091847.516 1143731.378 1924535.737 1016196.467 1486428.983 1150744.393 1580361.917 0.880140835 0.777931386 0.690884476 0.723714844 1.217781646 0.643015031 0.94056239 0.728152444 1 20.59182356 HITLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HITLDK 6 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 144.29 0.011291 2820550000 7228830 5361780 5624990 7025620 5763760 6453000 8575720 7094880 4987990 FALSE TRUE 6887137.532 5908151.478 5882901.355 6319391.33 6768957.919 6229530.992 7267336.41 6473614.695 5761502.014 1.195371887 1.025453339 1.02107078 1.096830534 1.174859941 1.081233848 1.261361428 1.123598443 1 22.45801354 2.870751854 5.720143834 1.149635303 1.082264834 0.032917258 0.082105035 0.47449177 20.14784328 0.024241855 0.025823938 742.5947141 -2.870751854 -0.067370469 HIYLLPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HIYLLPSGR 9 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 93.111 0.0096207 347760000 317970 270090 270460 316650 301370 243220 306970 296150 249780 FALSE TRUE 302940.1883 297612.4781 282860.8585 284819.7404 353928.8326 234797.2304 260136.0886 270217.536 288514.6067 1.049999484 1.031533486 0.980403945 0.987193486 1.226727605 0.813814015 0.901639233 0.936581822 1 18.13828483 2.211255335 24.99999478 0.9012222 1.044989763 0.424650817 0.081236564 196.5752102 179977.8586 0.028137114 0.020785837 162.6504747 -2.211255335 0.143767563 HIYYITGETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 171.85 3.89E-06 12110910000 8639430 7756190 7635800 8882410 6072350 8499600 9125970 8583960 5070410 FALSE TRUE 8231061.266 8546554.579 7985908.983 7989533.271 7131365.917 8205256.721 7733635.667 7832302.956 5856703.287 1.405408617 1.459277372 1.363550208 1.364169035 1.217641661 1.401002632 1.320475921 1.33732282 1 22.48165738 -3.984337343 0.183621618 8.31E-21 1.447413276 0.798085026 0.058062085 37.32504263 0.50668877 14.0218294 0.173121863 0.000103672 3.984337343 1.447413276 HKAAAYDIS(ph)EDEED ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HKAAAYDISEDEED 14 1 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED 212.69 1.27E-09 2020720000 2756720 1223000 3546710 2373270 2377530 2825040 4790760 2048240 836838 TRUE FALSE 2626415.309 1347625.09 3709330.162 2134704.391 2792170.479 2727208.156 4059841.574 1868885.247 966610.5631 2.717139052 1.394175837 3.837460818 2.208443061 2.88861987 2.821413567 4.200079876 1.93344178 1 19.88257523 2.711893116 19.33810158 2.903500772 2.440329601 0 1.023567569 160.4317507 116334.6316 0.312981384 0.295380247 515.101857 -2.711893116 -0.463171171 HKADSLDCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKADSLDCSR 10 1 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 100.55 0.002364 45610000 46802 35812 36220 39348 34745 34908 49918 44003 43138 FALSE TRUE 44589.76221 39461.28351 37880.72283 35392.66428 40804.517 33699.12721 42302.09229 40149.86405 49827.62072 0.894880421 0.791956006 0.760235433 0.710302113 0.818913615 0.676314195 0.848968738 0.80577526 1 15.60465807 0.489485368 1.362115164 0.999837011 0.787792484 0.53560244 0.062416502 1.926785183 4.27747715 0.059150056 0.017437006 3.086635649 -0.489485368 -0.212044528 HKAEEVEDETVELDVS(ph)DEEMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKAEEVEDETVELDVSDEEMAR 22 1 H3BNT4;Q99547;H3BSB3 H3BNT4 MPHOSPH6 M-phase phosphoprotein 6 1 HKAEEVEDETVELDVS(1)DEEMAR 87.489 0.0017071 115280000 72550 68980 70029 75113 51587 77994 85474 70901 23097 TRUE FALSE 69120.70528 76009.14042 73239.89892 67562.49853 60583.75647 75293.04822 72433.37146 64692.53257 26678.7648 2.590851031 2.849050209 2.745250744 2.532444776 2.270860624 2.822208929 2.71501968 2.424869857 1 14.70340425 0.766180854 3.300595349 1.000083079 2.659495393 0.906080585 0.16522321 0.502612877 6.748059034 0.160206791 0.041530302 5.836881201 -0.766180854 1.659412314 HKASVEDADTQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKASVEDADTQSK 13 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6 Q13561 DCTN2 Dynactin subunit 2 0 108.17 0.00074347 26117000 77395 49804 69483 69964 52495 78337 92509 92517 45753 FALSE TRUE 73736.69173 54879.08422 72668.86428 62931.0858 61650.11138 75624.17005 78395.05301 84415.72102 52848.14157 1.395256097 1.038429784 1.375050515 1.190790895 1.166552116 1.430971228 1.483402267 1.597326198 1 15.68956512 2.22881932 24.73416039 1.425649373 1.22590369 0.108646943 0.184041378 253.7944306 644404.7733 0.061274612 0.045829771 169.3633052 -2.22881932 -0.199745683 HKDAAIYLVTSLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKDAAIYLVTSLASK 15 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 109.79 0.00058405 82881000 235420 207780 214750 251590 194050 258180 289130 263770 146900 FALSE TRUE 224292.1632 228953.0182 224596.4999 226299.6952 227892.2586 249239.1619 245017.9083 240672.9005 169680.5017 1.321849952 1.349318371 1.32364354 1.3336812 1.343066859 1.46887332 1.443995661 1.418388666 1 17.37246127 -1.128480992 5.756001191 0.999996386 1.37538329 0.837478647 0.051964861 2.78E-06 4.21E-07 0.057985927 0.013667282 0.074390762 1.128480992 0.375386905 HKEEDKNSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HKEEDKNSER 10 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;;;; 179.19 1.28E-06 346542000 234010 200861 212190 238063 137719.4 236376 253248 232219 111025.6 FALSE TRUE 222948.8111 221328.9643 221919.1214 214132.4549 161737.6198 228190.2398 214610.3664 211884.6733 128242.883 1.738488763 1.725857678 1.730459548 1.669741431 1.261182032 1.779359872 1.673468042 1.652213895 1 16.96851924 -2.416465232 0.413331787 5.51E-21 1.681115431 0.666722693 0.14513297 45.37443165 2.225957137 41.37394589 0.084700802 0.003832964 2.416465232 1.681115431 HKELAPYDENWFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HKELAPYDENWFYTR 15 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;; 263.6 2.72E-25 5771100000 10159600 6697820 9218600 9635500 8999300 9497000 12958100 9965900 7441060 FALSE TRUE 9679375.842 7380335.473 9641281.928 8666921.234 10568775.07 9168116.509 10981103.85 9093232.963 8594981.581 1.126165978 0.858679615 1.121733867 1.00836996 1.229644877 1.066682508 1.277618079 1.057970035 1 23.03506312 2.760189608 24.41078879 1.149434192 1.016386256 0.141764461 0.109794926 775.7949864 875571.6119 0.030897529 0.032743694 575.691222 -2.760189608 -0.133047936 HKGPPVFTQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HKGPPVFTQEER 12 1 Q99447-3;Q99447;Q99447-4;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 142.91 3.71E-05 175582000 182036 160534 167288 197577 155831 172286 213142 212069 160469 FALSE TRUE 173431.519 176892.5971 174958.3203 177716.1846 183007.8771 166319.6926 180623.2733 193499.1141 185353.713 0.935678688 0.954351517 0.943915919 0.958794846 0.987344004 0.897309743 0.974478851 1.043945174 1 17.49992149 1.430773812 5.825582334 1.019761308 0.947532078 0.614341588 0.024555659 0.116355137 7.484291037 0.014473172 0.0055556 26.96334767 -1.430773812 -0.07222923 HKHEIESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HKHEIESGR 9 1 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 ;; 113.93 0.0010341 24568900 55935.2 66010.2 71666.6 88747 65357.8 74298.7 88526.4 53990.8 19039 FALSE TRUE 53291.25395 72736.71443 74952.5845 79825.98295 76756.17963 71725.71739 75020.07178 49263.07933 21991.47088 2.423269195 3.307496566 3.408256997 3.629861021 3.490270389 3.261524332 3.41132579 2.240099336 1 14.42465648 0.980998429 3.205835634 1.005000553 3.252049549 0.83893401 0.32685942 0.097496731 2.521603302 0.34131123 0.08917118 9.571906089 -0.980998429 2.247048997 HKLDVTSVEDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HKLDVTSVEDYK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 151.78 4.08E-05 2417400000 6648500 5861440 5649130 6823700 3757400 6823200 6979700 6985500 3126880 FALSE TRUE 6334238.581 6458727.4 5908148.198 6137768.712 4412689.37 6586910.873 5914818.574 6373812.588 3611780.581 1.753771703 1.78823914 1.635799315 1.699374747 1.221749016 1.823729522 1.637646153 1.764728628 1 21.78427882 -1.752850654 2.585734222 0.84547889 1.673166899 0.60399675 0.169284257 8017246.33 5986596.293 7902327.135 0.038759051 0.017666452 1.752850654 0.827688009 HKMS(ph)PPPSGFGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HKMSPPPSGFGER 13 1 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 HKMS(1)PPPSGFGER;HKMS(0.998)PPPS(0.002)GFGER;HKMS(1)PPPSGFGER;HKMS(0.999)PPPS(0.001)GFGER;HKMS(1)PPPSGFGER;HKMS(0.989)PPPS(0.011)GFGER;HKMS(0.998)PPPS(0.002)GFGER 141.13 5.00E-05 2818600000 2336280 1952360 1980980 2335330 1585070 2289490 2512000 2193870 1181750 TRUE FALSE 2225848.674 2151307.704 2071809.892 2100578.192 1861505.706 2210204.387 2128748.264 2001763.112 1365009.754 1.630646717 1.576038337 1.517798599 1.538874125 1.363730699 1.619185782 1.559511393 1.466482643 1 20.38047983 -2.719754293 0.344929218 2.95E-11 1.569582674 0.840494976 0.073684953 26.317423 0.930915086 19.52467037 0.058459938 0.001906539 2.719754293 1.569582674 HKPGGGDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 107.83 0.0016282 145105000 533020 474120 450290 553400 312100 524940 566430 558190 230920 FALSE TRUE 507825.2009 522433.367 470936.2419 497771.1806 366530.1412 506761.1962 480010.7003 509311.9244 266729.8942 1.903893084 1.958660721 1.765592279 1.866199445 1.374162211 1.899904012 1.799613432 1.909466976 1 18.02502 -1.890836496 2.560001231 0.569908135 1.818641346 0.704020135 0.164899279 10852252.11 7094511.639 28281415.52 0.039703016 0.012857706 1.890836496 1.248733211 HKS(ph)DNETNLQQQVVWGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKSDNETNLQQQVVWGNR 18 1 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 HKS(0.5)DNET(0.5)NLQQQVVWGNR 110.37 0.0002027 143220000 186790 151460 190900 207170 144760 185020 191300 167310 118880 TRUE FALSE 177960.8069 166893.9462 199652.9538 186344.878 170006.0982 178612.711 162113.6715 152659.4494 137315.3032 1.296001266 1.215406748 1.453974532 1.357058344 1.238071024 1.300748764 1.180594353 1.11174389 1 17.06713289 1.285776096 1.143402017 1.002948663 1.308939941 0.740146653 0.064591039 0.239734298 0.630425147 0.06151703 0.020362243 19.30972533 -1.285776096 0.305991277 HKSDFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HKSDFGK 7 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;; 136.8 0.0017696 2263198000 6020150 3948860 5292750 6216450 6599550 5199450 9540110 6887280 6499860 FALSE TRUE 5735589.44 4351253.323 5535427.823 5591560.636 7750509.431 5019391.743 8084591.003 6284193.251 7507825.092 0.763948197 0.579562426 0.737287797 0.744764371 1.032324186 0.668554699 1.07682197 0.837019133 1 22.83996361 2.923853623 4.573170323 0.91866445 0.684633039 0.43921771 0.122214555 0.186091969 7.185723214 0.034250819 0.037090237 839.1770984 -2.923853623 -0.234031411 HKSES(ph)PCESPYPNEKDKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HKSESPCESPYPNEKDKEK 19 3 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H0Y594;B7ZBA0;B7ZB98 Q8NI27 THOC2 THO complex subunit 2 1 HKS(0.134)ES(0.866)PCESPYPNEKDKEK 91.729 0.0014486 64527000 131390 85444 119460 129350 58185 150020 178210 162660 43596 TRUE FALSE 125179.4551 94150.84074 124937.3592 116347.4923 68332.44558 144824.7698 151020.7914 148416.6281 50356.64502 2.485857726 1.869680569 2.4810501 2.310469496 1.356969781 2.875981307 2.999024089 2.947309695 1 15.61989455 3.638822463 23.01700348 2.399669558 2.177187142 0 0.677965116 108.0028685 24891.23891 0.175216955 0.27144494 4353.33875 -3.638822463 -0.222482415 HKSETDTSLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HKSETDTSLIR 11 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 199.43 3.02E-08 689030000 684360 547410 650420 717700 1082020 587920 1099540 800650 1278430 FALSE TRUE 652011.6591 603191.7014 680242.4004 645555.4325 1270723.945 567560.183 931784.9786 730540.8415 1476682.395 0.441538181 0.408477614 0.460655861 0.437166065 0.860526237 0.384348175 0.630998908 0.494717648 1 20.49392813 -5 0.158134481 2.814552186 0.370589471 0.569000771 0.135843278 89.66579475 0.819757548 51.03361755 0.537973756 1.00E-05 5 -2.443962715 HLAAVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 126.41 0.0012203 592079000 394867 354769 362458 396342 556450 329088 447020 335568 510007 FALSE TRUE 376202.4195 390920.3644 379077.0578 356500.9492 653494.7038 317691.6 378818.8889 306183.887 589096.2808 0.638609395 0.663593333 0.643489138 0.605165846 1.109317314 0.539286379 0.643050892 0.519751859 1 19.16814392 HLAEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLAEIK 6 0 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;; 103.28 0.034817 1272720000 4087700 3229410 2996480 3854400 2667010 3607800 4116700 3981200 2403340 FALSE TRUE 3894482.522 3558490.551 3133871.572 3466948.389 3132135.7 3482860.981 3488621.807 3632585.022 2776037.693 1.402892523 1.281859594 1.128900944 1.248883759 1.128275638 1.254615883 1.25669108 1.308550324 1 21.40459573 4.185991714 2.379665168 1.206805517 1.387294092 0.352339191 0.090377082 0.30278832 3.338894572 0.021390102 0.068847185 15345.87704 -4.185991714 0.180488575 HLAEYTHVEAECPFLTFDDLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLAEYTHVEAECPFLTFDDLLNR 23 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 136.49 6.46E-06 35140000 23203 46054 20523 32915 22811 23454 21341 21911 5272.1 FALSE TRUE 22106.24017 50746.95496 21463.99985 29606.32167 26789.23118 22641.7821 18085.0385 19992.35668 6089.670342 3.630120997 8.333284416 3.524657107 4.86172814 4.399126664 3.718063676 2.969789411 3.282994901 1 12.57214842 1.697206078 0.438967492 1.04956327 5.876501325 0.480862793 1.330471042 0.744627569 0.37567914 1.411880954 1.07710641 49.79733233 -1.697206078 4.826938055 HLAFLAESCATLSQEQHSQELLAELLTHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLAFLAESCATLSQEQHSQELLAELLTHLER 31 0 Q969Z0;Q969Z0-2;C9J7P5;C9IZN7 Q969Z0 TBRG4 Protein TBRG4 0 ; 235.57 3.40E-46 160479000 23601 27698 25940 28623 15146.9 25395 29027 36236 13974.1 FALSE TRUE 22485.4275 30520.45769 27129.37466 25745.76166 17788.51456 24515.56478 24598.39803 33062.98374 16141.13206 1.393051455 1.890849885 1.680760343 1.595040643 1.10206115 1.518825612 1.523957424 2.048368331 1 13.97845415 2.989198842 24.32062708 1.468243584 1.664277475 0.096912758 0.301978517 926.1318187 2085350.914 0.0845816 0.09507303 975.4361391 -2.989198842 0.196033891 HLAPPPLLS(ph)PLLPSIKPTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLAPPPLLSPLLPSIKPTVR 20 1 Q14676;Q14676-3;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 HLAPPPLLS(1)PLLPSIKPTVR;HLAPPPLLS(1)PLLPSIKPTVR 146.06 8.32E-08 137699000 711120 707970 771410 879470 664850 782180 942350 844320 616410 TRUE FALSE 677506.7669 780112.9479 806779.9115 791064.0047 780799.6295 755092.9105 798577.2001 770386.8648 711999.7146 0.951554829 1.095664692 1.133118307 1.111045396 1.096629133 1.060524176 1.121597641 1.082004457 1 19.44151714 4.525463338 2.435789221 1.09469019 0.946692595 0.552472594 0.037847827 0.218688589 2.174611329 0.008485253 0.055829779 33532.2996 -4.525463338 -0.147997595 HLCEPGADGAETFADGVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 318.55 8.14E-62 444330000 304780 392420 349630 367040 289230 328190 352430 354960 235936 FALSE TRUE 290373.6534 432408.0441 365660.8813 330144.4419 339671.6204 316824.698 298660.3307 323877.8206 272523.7499 1.065498525 1.586680223 1.341757852 1.211433653 1.246392729 1.162558119 1.095905699 1.188438882 1 18.05602244 2.422482316 1.068838422 1.094128454 1.338022698 0.326918427 0.134330093 0.58090731 1.321128474 0.083693866 0.056017792 264.5344979 -2.422482316 0.243894244 HLDDDEDRKNPAYIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLDDDEDRKNPAYIPR 16 2 O15234;J3KSY7 O15234 CASC3 Protein CASC3 0 ; 154.69 1.99E-07 224390000 257490 228190 261370 316290 258970 259890 309010 318060 211500 FALSE TRUE 245318.958 251442.8204 273354.073 284495.9283 304134.286 250889.9441 261864.8491 290208.9803 244298.3398 1.004177753 1.0292449 1.118935451 1.164543028 1.244929811 1.026981781 1.071905971 1.187928581 1 17.89828453 3.784575675 4.212416835 1.118556095 1.013853261 0.246827213 0.072769175 0.276413391 10.74814203 0.018710868 0.034045823 6089.416439 -3.784575675 -0.104702835 HLDGEEDGS(ph)SDQSQASGTTGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.5)S(0.5)DQSQASGTTGGR 101.76 0.00042115 146840000 39912 46291 47749 50214 44915 53644 57870 49280 46005 TRUE FALSE 38025.43886 51008.10553 49938.33888 45166.39332 52748.16178 51786.29483 49040.86864 44964.78195 53139.22044 0.715581421 0.959895631 0.939764236 0.849963416 0.992640866 0.97453998 0.922875199 0.846169394 1 15.69748944 4.5843115 2.593415667 0.933517116 0.703147094 0.62564167 0.053222198 0.214801042 2.341493173 0.012460392 0.092791459 38398.25606 -4.5843115 -0.230370022 HLDGEEDGSS(ph)DQSQASGTTGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.122)S(0.878)DQSQASGTTGGR 187.51 1.81E-17 196640000 39215 57585 55263 60045 52556 52566 65777 58284 55126 TRUE FALSE 37361.38467 63452.97697 57796.86321 54009.16252 61721.74976 50745.62624 55741.51057 53180.34398 63674.65854 0.586754378 0.996518528 0.907690195 0.848204981 0.96932989 0.796951682 0.875411221 0.835188522 1 15.9584317 4.650156075 3.278957041 0.893455651 0.571556649 0.668731544 0.069559001 0.154572767 2.712925081 0.015609056 0.109937531 44684.4148 -4.650156075 -0.321899002 HLDGEEDGSSDQSQASGTTGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 253.83 4.90E-37 79274000 36056 32422 32922 39643 36480 32604 41236 34091 25273 FALSE TRUE 34351.70434 35725.83866 34431.50626 35658.01032 42842.10045 31474.9153 34944.69085 31105.81131 29192.20776 1.176742253 1.223814209 1.179475925 1.221490701 1.467586857 1.078195783 1.197055431 1.065551861 1 14.8332957 1.245229139 1.353623961 1.001692187 1.230326428 0.414522166 0.096281285 0.38806602 1.374421153 0.084004686 0.026248337 17.5885136 -1.245229139 0.22863424 HLDHVAALFPGDVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLDHVAALFPGDVDR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 118.13 0.00018252 317580000 748850 682850 668490 795930 716610 684510 825620 684850 25533.9 FALSE TRUE 713453.3446 752433.1913 699140.9277 715921.6042 841586.5571 660805.2471 699656.5054 624880.9034 29493.5668 24.19013439 25.51177334 23.70486189 24.27382246 28.53458053 22.40506384 23.72234291 21.18702385 1 14.84811268 0.203061038 0.89785339 0.750992904 24.95711874 0.958435512 1.536750552 0.612445316 0.551880047 1.709274106 0.446151101 1.596103457 -0.203061038 24.20612584 HLDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLDLEK 6 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ;;; 126.24 0.017575 1382940000 4033900 4760520 3746950 4604570 2535670 4360360 3855600 4470610 1750490 FALSE TRUE 3843225.541 5245622.4 3918751.364 4141709.875 2977890.045 4209359.64 3267357.407 4079139.688 2021947.049 1.900754791 2.594342123 1.938107808 2.048377022 1.472783398 2.081834755 1.61594608 2.01743151 1 20.94731379 -1.204826584 0.159557527 1.02E-11 2.439149164 0.541743145 0.285875822 19.45360069 0.607521789 9.758033267 1.50057686 0.062398395 1.204826584 2.439149164 HLDRS(ph)PESDRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(1)PESDRPR;HLDRS(0.998)PES(0.002)DRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(0.917)PES(0.083)DRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR 184.48 7.45E-06 25506199000 4270518 3430473 3983307 4507967 4052807 4109959 4603467 3885712 2312740 TRUE FALSE 4068659.077 3780042.099 4165945.566 4054817.593 4759615.258 3967630.089 3901123.561 3545458.458 2671387.907 1.523050646 1.41501056 1.559468602 1.517869262 1.781701281 1.485231732 1.460335861 1.327197165 1 21.34915805 0.903481986 1.427177792 1.001867363 1.536256974 0.77527345 0.093759391 0.255529279 1.031850173 0.090197197 0.026775462 8.007224144 -0.903481986 0.53438961 HLDSVLSDHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDSVLSDHTR 11 0 Q2M389;A0A087X256;F8W1W1 Q2M389 KIAA1033 WASH complex subunit 7 0 147.63 2.04E-05 58228000 28129 27003 22314 26776 51190 21837 33580 22666 51788 FALSE TRUE 26799.39792 29754.6364 23337.11897 24084.42561 60117.51979 21080.77921 28456.75426 20681.24488 59819.01854 0.448007984 0.497410976 0.390128751 0.402621544 1.004990073 0.352409313 0.475714162 0.345730261 1 15.86831662 -2.080252561 2.551202847 1.816508432 0.490414661 0.416330977 0.189910852 13972225.1 4451169.049 66377499.77 0.044494641 0.008312802 2.080252561 -1.326093771 HLDVDLDRQS(ph)LS(ph)SIDKNPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HLDVDLDRQS(1)LS(0.624)S(0.376)IDKNPSER 187.26 1.58E-17 494590000 1114300 1180400 1107100 1485400 781190 1436100 1412600 1180000 436880 TRUE FALSE 1061629.247 1300684.102 1157861.63 1336084.77 917429.2887 1386367.497 1197081.926 1076672.944 504629.1191 2.103781187 2.577505048 2.294480414 2.647656901 1.818026852 2.747299837 2.372201445 2.13359258 1 18.94486393 0.773910725 2.862695937 1.000261234 2.37518758 0.717126911 0.267658466 0.5969444 6.843246295 0.225985467 0.059446735 5.941700065 -0.773910725 1.374926346 HLDVDLDRQS(ph)LSS(ph)IDKNPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HLDVDLDRQS(0.999)LS(0.13)S(0.871)IDKNPSER 152.99 2.54E-08 549790000 725390 752110 646240 837560 456390 807530 742990 654500 231480 TRUE FALSE 691102.2523 828750.8641 675870.7432 753366.8775 535984.2715 779565.0336 629633.2296 597188.5103 267376.7362 2.584750873 3.099562348 2.527784402 2.817623135 2.00460324 2.915605317 2.354854198 2.233509612 1 18.02851442 -1.065848096 0.280781624 4.66E-11 2.855698758 0.763717046 0.286466693 6.673269109 0.446084176 5.522913595 0.333746252 0.085931403 1.065848096 2.855698758 HLDVDLDRQS(ph)LSSIDKNPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 HLDVDLDRQS(1)LSSIDKNPSER;HLDVDLDRQS(0.977)LS(0.02)S(0.003)IDKNPSER;HLDVDLDRQS(0.967)LS(0.029)S(0.003)IDKNPSER;HLDVDLDRQS(0.988)LS(0.01)S(0.002)IDKNPSER 248.02 9.73E-31 1329960000 1414930 1444010 1245290 1721460 1053230 1523080 1468990 1537010 744380 TRUE FALSE 1348049.063 1591156.261 1302387.778 1548415.57 1236912.979 1470335.358 1244868.596 1402421.256 859814.6486 1.567836818 1.850580545 1.514730855 1.800871354 1.438580955 1.710060837 1.447833667 1.631073928 1 19.71366616 -2.615934725 0.242997519 5.06E-14 1.715084699 0.678986492 0.135187076 23.27292342 0.649771157 12.42140527 0.189699799 0.002421393 2.615934725 1.715084699 HLDYLIQCTNEMNVNIPQLADSLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLDYLIQCTNEMNVNIPQLADSLFER 26 0 Q13492-3;Q13492-2;Q13492-5;Q13492;E9PK13;E9PKP6;E9PLJ8 Q13492-3 PICALM Phosphatidylinositol-binding clathrin assembly protein 0 180.83 2.10E-17 41575000 15881 16133 20619 23294 20966 16182 21433 20106 17769 FALSE TRUE 15130.3366 17776.97104 21564.40154 20952.44286 24622.46376 15621.61328 18163.00221 18345.41205 20524.52577 0.73718325 0.866133096 1.050665033 1.020849061 1.199660545 0.761119329 0.884941382 0.893828791 1 14.32506127 4.122686392 2.716900329 0.961678604 0.761435459 0.292958155 0.116690599 0.346697034 5.032158577 0.031460893 0.085770363 13264.36279 -4.122686392 -0.200243144 HLEAADKGHS(ph)PAQKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK;HLEAADKGHS(1)PAQKPK 183.09 9.68E-10 2215620000 3050153 2362840 2652751 2994529 1289211 3255864 3307269 2860269 338677 TRUE FALSE 2905978.313 2603616.082 2774382.257 2693513.256 1514048.99 3143112.613 2802684.372 2609808.683 391197.2994 7.4284212 6.655506278 7.092028144 6.885306365 3.870295098 8.03459691 7.164375562 6.671336144 1 18.57753689 2.967095138 24.84024587 5.997012453 7.020536422 0.102608506 1.993516929 1788.926331 1350480.744 0.554846593 0.588924862 927.0328807 -2.967095138 1.023523969 HLECTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLECTK 6 0 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 88.643 0.05107 105560000 635260 627880 508870 685750 495030 606420 646200 586880 486450 FALSE TRUE 605232.5188 691861.6858 532202.1928 616817.1072 581363.0753 585419.5233 547610.3217 535489.676 561886.1816 1.077144337 1.231319987 0.947170816 1.09776166 1.034663415 1.041882756 0.974592969 0.953021615 1 19.0999184 3.100383146 0.641480324 0.978021968 1.150947336 0.33407105 0.068497752 0.781822647 0.7046219 0.044891314 0.071347086 1260.036559 -3.100383146 0.172925368 HLEDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLEDEL 6 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 103.41 0.080751 124240000 327270 350750 313530 379720 311080 322190 342080 265020 125050 FALSE TRUE 311800.5957 386491.8238 327905.6606 341549.8242 365332.2535 311032.4795 289889.4133 241813.4438 144442.1153 2.158654316 2.675755772 2.270152717 2.364613834 2.529264077 2.153336503 2.006959069 1.674120067 1 17.14013193 1.076546885 0.921481159 1.003320194 2.414917745 0.902916349 0.147634046 0.148544644 0.276327099 0.130481601 0.045366398 11.92743024 -1.076546885 1.411597551 HLEEIVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLEEIVEK 8 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 123.72 0.0013355 610590000 2333060 1942910 2052390 2423600 1731240 2077160 2437000 2224620 1259700 FALSE TRUE 2222780.877 2140894.738 2146494.112 2179975.123 2033167.708 2005227.428 2065190.891 2029820.479 1455047.842 1.527634221 1.471356938 1.475205178 1.498215426 1.397320176 1.378117867 1.419328514 1.395019751 1 20.47263516 -3.353326294 0.208838081 1.52E-13 1.530652715 0.959793692 0.029696854 11.85939404 0.218903708 5.182091855 0.066718654 0.000443275 3.353326294 1.530652715 HLEFSHDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;; 229.53 9.13E-10 6975260000 353554 373420 597444 447994 414657 362692 372917 398728 370184 FALSE TRUE 336842.2031 411471.9225 624837.3984 402960.792 486973.0495 350131.8851 316021.6626 363813.2625 427590.2441 0.787768682 0.962304281 1.461299473 0.942399406 1.13887783 0.818849097 0.739075942 0.850845564 1 18.70586941 2.219379849 23.99861956 0.820244563 1.033822624 0.221400778 0.184880573 233.6223844 292300.9772 0.070879422 0.05244353 165.7218793 -2.219379849 0.21357806 HLEGLSEEAIMELNLPTGIPIVYELDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HLEGLSEEAIMELNLPTGIPIVYELDK 27 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;; 255.42 7.36E-53 1763940000 3235430 2893470 2895090 3464230 2469980 3219880 3794730 3386920 1457522 FALSE TRUE 3082497.636 3188317.883 3027832.74 3115999.019 2900743.73 3108374.748 3215774.244 3090343.33 1683547.068 1.830954236 1.893809768 1.798484164 1.850853521 1.722995327 1.846324827 1.910118407 1.835614453 1 20.68307263 0.907875753 22.3817 1 1.842843793 0.963288312 0.051286203 11134.94045 2705250.631 0.049633618 0.012408405 8.088644588 -0.907875753 0.842843792 HLEIFHTEFQNLLDADKNEDLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLEIFHTEFQNLLDADKNEDLGR 23 1 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UK34;A0A590UJ50;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 56.48 0.057349 129170000 458450 468410 391720 496900 376350 464800 531540 496650 195600 FALSE TRUE 436779.9771 516141.5115 409680.7495 446950.668 441985.3208 448703.8595 450443.8106 453160.6931 225932.649 1.933230894 2.284492807 1.813287063 1.978247367 1.956270255 1.986007164 1.993708358 2.005733545 1 17.78553324 -1.983899984 0.503844388 1.50E-12 2.023318796 0.873320617 0.118677979 24.61401622 1.969054672 28.73276845 0.054569665 0.010377674 1.983899984 2.023318796 HLEIIYAINQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLEIIYAINQR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 113.47 0.0013871 246240000 386990 308890 333550 370730 354540 301240 442360 407760 315860 FALSE TRUE 368697.7496 340366.2422 348843.5974 333463.5161 416371.6637 290807.9833 374869.8575 372054.3727 364841.9556 1.010568395 0.932914203 0.956149895 0.913994432 1.141238439 0.797079335 1.027485605 1.019768607 1 18.47691212 1.578754949 25 1.017745672 0.961122141 0.090178159 0.08515042 1.944099028 1661.547292 0.040600931 0.018800983 37.91010167 -1.578754949 -0.056623531 HLEINPDHPIVETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 228.49 3.41E-13 11521170000 2104091 1912117 1903090 2148712 1931754 1845501 2195426 1925864 508722 FALSE TRUE 2004634.788 2106963.896 1990348.559 1932719.387 2268651.286 1781590.838 1860473.442 1757225.139 587612.0096 3.411493904 3.585637907 3.387181553 3.289108044 3.860798025 3.031916994 3.166159663 2.990451369 1 19.16450436 -0.08856071 0.530564 0.758909118 3.505514707 0.936129909 0.196798664 1.004648637 0.319436343 0.674275738 0.082486527 0.815528777 0.08856071 2.746605589 HLEINPDHSIIETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 HLEINPDHSIIETLR 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;; 266.45 1.51E-25 10277816000 2019163 1908975 1853468 2128731 1875883.2 1846668 2219793 1946473 763206.7 FALSE TRUE 1923721.167 2103501.723 1938451.341 1914746.916 2203036.636 1782717.424 1881122.809 1776029.505 881560.8971 2.182176152 2.386110511 2.198885349 2.171996197 2.499018098 2.022228334 2.133854638 2.014641882 1 19.74970071 0.012158142 0.575965616 0.911767684 2.282676476 0.908857939 0.122335952 1.043354233 0.408349138 0.316919219 0.04720956 1.028390704 -0.012158142 1.370908792 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 184.3 1.60E-17 83302000 65098 65451 52834 74008 58254 61986 71429 66869 36034 FALSE TRUE 62020.94655 72120.53131 55256.49116 66568.57523 68413.47916 59839.40928 60531.19417 61013.59587 41621.96868 1.490101226 1.732751563 1.327579951 1.599361523 1.643686767 1.437688105 1.454308772 1.465898846 1 15.34505758 -1.058189466 0.321732915 0.708192498 1.587678099 0.691479964 0.110802992 7.967243046 0.641478448 2.185195222 0.099413706 0.087460214 1.058189466 0.879485601 HLEQQEGQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLEQQEGQPK 10 0 P07476 P07476 IVL Involucrin 0 ; 136.02 0.00012868 162943000 647500 541990 592450 717690 519430 651740 775160 724010 431860 FALSE TRUE 616893.9582 597219.3972 619614.4185 645546.4377 610018.4275 629170.0804 656895.1052 660611.8462 498830.6432 1.236680157 1.197238793 1.242133832 1.29411945 1.222896861 1.261289957 1.316869992 1.3243209 1 18.92819057 -0.930387776 4.659453315 0.999998216 1.258194072 0.804455765 0.040549089 1.26E-06 2.89E-07 0.043808688 0.0103257 0.117384897 0.930387776 0.258195856 HLEQQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLEQQEK 7 0 P07476 P07476 IVL Involucrin 0 ; 130.22 0.0035843 325340000 560710 475760 474530 572600 425510 547270 625130 603990 370410 FALSE TRUE 534206.3495 524240.4849 496287.6699 515041.1601 499718.8093 528317.9027 529754.9372 551101.4336 427851.291 1.248579497 1.225286673 1.159953658 1.203785453 1.167973125 1.234816661 1.238175386 1.288067712 1 18.70674992 -2.045872891 2.677545414 0.706889956 1.220897478 0.774821032 0.037413051 12914754.81 10414163.51 23018254.37 0.0090514 0.008997609 2.045872891 0.514007521 HLFLTSKPMVYLVNLSEKDYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLFLTSKPMVYLVNLSEKDYIR 22 2 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 200.74 9.67E-23 195040000 319290 268010 277400 329670 271130 328680 444500 351260 209310 FALSE TRUE 304197.7945 295320.5237 290119.0644 296530.9453 318414.9862 317297.7292 376683.3612 320501.8123 241768.7258 1.258218132 1.221500104 1.19998591 1.226506631 1.317023056 1.312401876 1.558031792 1.325654554 1 17.88326811 2.520664095 2.433151008 1.366447713 1.227613661 0 0.14024286 0.501790437 5.948576613 0.048824341 0.042290168 331.6378529 -2.520664095 -0.138834052 HLFS(ph)STENLAAGSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.333)S(0.333)T(0.333)ENLAAGSWK;HLFS(0.524)S(0.415)T(0.061)ENLAAGSWK 249.47 9.45E-19 1098060000 1859240 1994650 1355510 2203620 1285390 1661350 1628950 1585390 687820 TRUE FALSE 1771357.41 2197907.103 1417661.474 1982107.931 1509561.609 1603817.033 1380423.76 1446564.847 794483.6127 2.229570732 2.766459959 1.784381014 2.49483803 1.900053802 2.018691144 1.737510677 1.820761088 1 19.59965794 0.940885565 0.250350835 0.713063734 2.635282699 0.69597706 0.262257494 1.355613441 0.279586608 0.94807034 0.551194657 8.727413737 -0.940885565 1.922218966 HLFS(ph)STENLAAGSWKEPAEGGGLSSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.384)S(0.308)T(0.308)ENLAAGSWKEPAEGGGLSSDR 194.93 3.90E-19 386980000 381370 267280 336730 376430 319220 347730 432540 389810 236110 TRUE FALSE 363343.3959 294516.1359 352169.4036 338590.5412 374891.8669 335688.0229 366548.0789 355676.1699 272724.7329 1.332271525 1.079902555 1.291299839 1.241510213 1.374616313 1.230867547 1.344022139 1.304158101 1 18.05708602 4.770319557 22.71434081 1.247384619 1.332272043 0.055905392 0.115583161 2673.073879 2987814.735 0.025488834 0.891290652 58927.70908 -4.770319557 0.084887424 HLFSS(ph)TENLAAGSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.092)S(0.76)T(0.148)ENLAAGSWK 289.61 4.56E-44 612290000 954200 1071100 697170 1178800 623070 911040 830990 829010 351540 TRUE FALSE 909096.857 1180246.308 729135.9341 1060304.784 731733.2107 879490.4564 704207.2133 756417.4895 406055.0278 2.238851374 2.906616658 1.795657938 2.611234222 1.802054305 2.165939088 1.734265469 1.862844782 1 18.63131573 0.995267129 0.258290486 0.730007728 2.697850918 0.625054435 0.319415012 1.414169989 0.317293674 1.02973517 0.622854479 9.891613291 -0.995267129 1.96784319 HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.1)S(0.52)T(0.381)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.131)S(0.842)T(0.026)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.25)S(0.574)T(0.175)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.003)S(0.92)T(0.077)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.041)S(0.924)T(0.035)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.004)S(0.879)T(0.116)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.038)S(0.537)T(0.425)ENLAAGSWKEPAEGGGLSSDR 356.02 1.25E-110 4220140000 2728540 1992960 2507980 3009310 2296310 2643580 3276960 2650390 1665810 TRUE FALSE 2599567.322 2196044.89 2622973.364 2706808.441 2696785.737 2552032.162 2776999.567 2418307.801 1924135.307 1.351031454 1.141315209 1.363195901 1.406766162 1.401557223 1.326326767 1.443245471 1.256828349 1 20.87577882 0.978206032 23.24188866 0.999999996 1.336831619 0.641937763 0.081402895 511.9499134 545963.5963 0.086780749 0.021695187 9.510558737 -0.978206032 0.336831622 HLGEITYPFACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLGEITYPFACR 12 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 61.235 0.086294 131980000 230920 200500 210620 236210 240590 218930 258300 235800 229690 FALSE TRUE 220004.8692 220931.1779 220277.1353 212465.722 282548.8198 211348.3992 218891.591 215152.1019 265309.1521 0.829239653 0.832731084 0.830265875 0.800823192 1.064979544 0.796611792 0.825043498 0.810948662 1 18.01731492 -2.517536165 2.228315266 3.181388334 0.846727708 0.270177026 0.07801408 2634163.899 323947.3851 29780637.6 0.017952012 0.003037133 2.517536165 -2.334660626 HLHPSCLGS(ph)PPLR ddPTM_SK-BR-3_Trastuzumab_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 159.4 2.62E-05 2547590000 5377420 4465600 4851510 5637510 5310520 5256020 6902570 5945170 2001350 TRUE FALSE 5123240.014 4920649.717 5073956.532 5070816.784 6236673.007 5074002.709 5849456.172 5424579.397 2311709.137 2.216213075 2.128576489 2.194894008 2.193535815 2.697862334 2.194913983 2.530359931 2.346566578 1 21.14052846 2.969427023 24.84489291 2.290938816 2.176602 0 0.460188071 3736.79846 3036681.398 0.121860753 0.129406579 932.0238432 -2.969427023 -0.114336815 HLIEQDFPGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLIEQDFPGMR 11 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 131.17 0.001224 0 293830 276910 280010 290940 284350 290040 367500 308530 217070 FALSE TRUE 279941.2382 305127.4438 292848.7355 261694.1585 333940.55 279995.8421 311431.1254 281513.4776 250732.107 1.116495377 1.216946037 1.167974612 1.043720175 1.331861938 1.116713154 1.242087139 1.122765971 1 17.93578722 -0.722735002 7.397316659 1.000000008 1.174537955 0.306270566 0.080042717 0 0 0.067425585 0.015892363 0.189349864 0.722735002 0.174537947 HLIPAANTGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 115.57 0.00093493 454910000 751230 801490 631060 816900 402470 732780 682170 683030 296440 FALSE TRUE 715720.8467 883162.7422 659994.7252 734783.66 472660.6406 707403.6449 578092.4376 623220.2722 342410.4012 2.090242715 2.579252088 1.927496136 2.145915128 1.380392181 2.06595256 1.688302796 1.820097375 1 18.385367 0.194835409 0.120052371 1.12E-12 2.950381985 0.619847626 0.267932106 11.74402229 0.530667343 8.3253297 4.09361727 1.566157409 -0.194835409 2.950381985 HLLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLLDEK 6 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 0 95.957 0.042755 277590000 953620 847320 806790 935880 821740 960360 1057100 919530 530860 FALSE TRUE 908544.2725 933662.8713 843782.1195 841803.5643 965051.1958 927102.4924 895819.98 839011.0785 613183.0575 1.481685218 1.522649492 1.376068874 1.372842178 1.573838651 1.511950601 1.460934005 1.368288096 1 19.22595831 0.756690078 2.058291366 1.000196578 1.47653134 0.852699162 0.061351585 0.346567546 2.292851013 0.059014862 0.016242059 5.710709627 -0.756690078 0.476334762 HLLGAEHGDEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLLGAEHGDEPR 12 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ; 77.279 0.016684 233175000 230354 198733 198445 243877 246098 221252 254303 194001 178571 FALSE TRUE 219465.6229 218984.1186 207543.8995 219362.0206 289017.4133 213589.9878 215504.4068 177013.244 206262.8787 1.064009309 1.061674888 1.006210622 1.063507026 1.401209055 1.035523159 1.044804611 0.858192444 1 17.65412468 1.507833843 2.931596817 0.93208948 1.102532788 0.27509301 0.115107911 0.322219358 5.749634304 0.083145868 0.029936949 32.19836678 -1.507833843 0.170443309 HLLIGVSSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLLIGVSSDR 10 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 119.22 0.0007208 667030000 411620 372000 379490 343560 399730 305986 404860 367520 258228 FALSE TRUE 392163.5384 409907.2229 396889.9919 309024.6961 469442.7854 295389.6281 343091.1712 335338.0005 298272.6794 1.314781961 1.374270093 1.330628044 1.036047608 1.573871219 0.990334176 1.150260131 1.124266564 1 18.18627231 1.928053356 0.567387386 1.006171867 1.345833489 0.317051614 0.155450117 0.862070031 0.582302754 0.132985752 0.086446059 84.73315072 -1.928053356 0.339661621 HLLQAPLDDAQEILQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLLQAPLDDAQEILQAR 17 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 316.97 2.50E-58 460318000 438908 416093 403324 484557 434887 430769 499284 453138 351033 FALSE TRUE 418161.6887 458493.3498 421816.8043 435848.4098 510731.1551 415851.3615 423109.0558 413458.8345 405469.4048 1.031302692 1.130771753 1.040317221 1.074923051 1.259604668 1.025604784 1.043504271 1.019704149 1 18.62923353 2.092368093 21.62964177 1.027615529 1.102755089 0.304833 0.063465254 8.872693336 2069.323065 0.022896769 0.016910376 123.6995425 -2.092368093 0.07513956 HLLQAPVDDAQEILHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HLLQAPVDDAQEILHSR 17 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;;; 225.11 1.45E-15 438017000 329263 270645 295944 347832 330832 319637 358658 320669 175706 FALSE TRUE 313699.3905 298224.0332 309513.3251 312867.2665 388528.9961 308567.8905 303938.1349 292589.5224 202953.5891 1.545670574 1.469419854 1.525044846 1.541570503 1.914373615 1.520386468 1.497574575 1.441657296 1 17.63079033 0.667632704 1.284500485 1.000918631 1.572522757 0.683590066 0.123051165 0.683359798 1.763649015 0.117703264 0.035389834 4.651925001 -0.667632704 0.571604125 HLLQEAR ddPTM_SK-BR-3_Trastuzumab_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 79.116 0.033497 88427000 113350 102460 91373 119390 96402 97403 120930 110370 93108 FALSE TRUE 107992.1701 112900.7905 95562.54243 107388.6904 113214.4783 94029.90969 102479.9075 100705.4177 107546.7131 1.004141986 1.049783738 0.888567764 0.99853066 1.052700496 0.874316908 0.952887397 0.936387685 1 16.71460391 2.244300794 24.99999497 0.936439495 1.001177608 0.220622787 0.053627979 189.5291193 825452.5665 0.01821042 0.014845466 175.5095665 -2.244300794 0.064738114 HLLTDLPLPPELPGGDLS(ph)PPDS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 77.149 0.011761 44506000 55207 47444 53314 60615 38694 54425 57730 59093 32892 TRUE FALSE 52597.47452 52278.59754 55758.49963 54521.86504 45442.22135 52540.2486 48922.22822 53918.50365 37992.72337 1.384409167 1.37601606 1.467609971 1.435060722 1.196076967 1.382902934 1.287673635 1.41917975 1 15.21343551 -3.55854983 0.260154383 1.11E-10 1.400543713 0.691179742 0.077353814 46.66947799 0.907106804 25.09132593 0.097696951 0.000276344 3.55854983 1.400543713 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(1)PPDSPEPK;HLLTDLPLPPELPGGDLS(0.996)PPDS(0.004)PEPK;HLLTDLPLPPELPGGDLS(0.999)PPDS(0.001)PEPK;HLLTDLPLPPELPGGDLS(1)PPDSPEPK;HLLTDLPLPPELPGGDLS(1)PPDSPEPK 217.57 2.37E-34 1257770000 978624 920657 915063 1082565 664275 1063278 1083562 1043802 394562 TRUE FALSE 932366.383 1014472.995 957019.5437 973743.5095 780124.3497 1026456.416 918244.7159 952401.1633 455748.6598 2.045790729 2.225948389 2.099884493 2.136580083 1.711742499 2.252242314 2.014805082 2.089750881 1 18.79787889 -1.931502108 0.537933265 1.89E-12 2.092350822 0.838249032 0.147884959 30.26581194 2.702830683 38.02158153 0.059630456 0.011708409 1.931502108 2.092350822 HLLVSNVGGDGEEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLLVSNVGGDGEEIER 16 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 142.35 1.52E-06 101710000 76779 75419 72008 85015 83471 68215 92740 74189 77966 FALSE TRUE 73149.80883 83104.28184 75309.63803 76469.13068 98028.31597 65852.69745 78590.80971 67692.61786 90056.56908 0.812265108 0.922800887 0.836248136 0.849123295 1.088519327 0.731237023 0.872682698 0.751667741 1 16.4585439 -0.189145368 7.680946229 0.999999999 0.86219496 0.168470396 0.098719093 11650656.23 1516825.497 0.085788352 0.020806732 0.646926039 0.189145368 -0.137805039 HLMLPDFDLLEDIESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;;;;; 219.52 1.23E-14 2260131700 3289327 2849978.1 2892319.7 3463791 2167770.2 3173208 3538930 3398814 1332050 FALSE TRUE 3133847.032 3140394.109 3024935.419 3115604.148 2545828.637 3063319.011 2999001.232 3101195.828 1538617.511 2.036794076 2.041049245 1.966008704 2.024937404 1.654620865 1.99095551 1.949153191 2.015572945 1 20.5532032 -1.436460534 2.93428703 0.97859713 1.964969308 0.877461282 0.112717213 9328321.948 10905016.91 1653417.322 0.028146285 0.03660492 1.436460534 0.986372178 HLMTLVMDPLQTASVQWFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLMTLVMDPLQTASVQWFER 20 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 170.53 9.17E-12 69314000 169970 152510 168410 171760 176830 164010 193960 169480 139740 FALSE TRUE 161935.8549 168050.9424 176131.7651 154494.3585 207669.096 158330.2926 164367.8397 154639.4327 161410.1655 1.003256855 1.041142247 1.091206149 0.957153832 1.286592423 0.980918966 1.018323965 0.958052625 1 17.30037192 HLNEIDLFHCIDPNDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;;;; 234.49 2.26E-20 6883894000 9620662 8404242 8497252 9915566 6345369 9673648 10356707 9648082 1693452 FALSE TRUE 9165912.374 9260643.815 8886859.409 8918834.467 7451999.345 9338647.144 8776601.133 8803244.792 1956063.887 4.685896219 4.734325844 4.543235764 4.559582397 3.809691183 4.774203545 4.486868343 4.500489401 1 20.89952206 -1.26461173 0.745857248 6.06E-13 4.54849088 0.94401068 0.268726353 16.87737225 3.841463827 35.57458018 0.09021032 0.054373623 1.26461173 4.54849088 HLNRPTLDDSSEEEHAIEITTQEITQLFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 280.47 5.18E-72 366424000 201769 168868 178310.5 233499 226528 195064 244196 168215.5 32194.5 FALSE TRUE 192231.7792 186075.8412 186486.2128 210027.2369 266034.4115 188308.8848 206939.4152 153485.6591 37187.05863 5.169319282 5.003779487 5.014814821 5.647858277 7.153951435 5.063828431 5.564823432 4.12739444 1 15.18251302 0.850284215 2.338213685 1.001573981 5.477845232 0.836570257 0.632025682 0.221192017 2.299396284 0.610407308 0.165271042 7.084092364 -0.850284215 4.476271251 HLNSSQPSGFGPANS(ph)LEDVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLNSSQPSGFGPANSLEDVVR 21 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 HLNSSQPSGFGPANS(1)LEDVVR 50.226 0.088517 214050000 42058 43389 42828 56984 73176 28041 51889 37516 62196 TRUE FALSE 40070.00169 47810.38843 44791.70616 51255.86006 85937.87123 27069.93314 43972.38004 34230.90016 71841.03803 0.557759225 0.665502472 0.62348356 0.713462131 1.196222571 0.376803202 0.612078851 0.476481146 1 16.13252058 4.37657221 1.364440018 0.692402441 0.546285569 0.036942099 0.237056516 3.09028282 8.108292822 0.064905632 0.522057377 23799.73983 -4.37657221 -0.146116872 HLPDNECIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLPDNECIEK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;; 189.58 9.95E-07 754200000 3902720 3793610 3384550 4425820 2717440 4046710 4160110 4052220 2020750 FALSE TRUE 3718246.16 4180183.172 3539734.965 3980928.165 3191360.676 3906571.418 3525408.814 3697386.135 2334117.589 1.592998646 1.790905133 1.516519554 1.705538823 1.367266452 1.673682352 1.510381838 1.584061639 1 21.15444581 -2.712677689 0.252996687 1.08E-18 1.67635323 0.728957696 0.114362002 23.19759722 0.64368078 12.81208057 0.150848877 0.00193786 2.712677689 1.67635323 HLPDQLASVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLPDQLASVTR 11 0 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 107.97 0.0021263 46216000 58964 51245 43252 55304 78781 51137 58935 54425 70551 FALSE TRUE 56176.88858 56466.92376 45235.14698 49744.73685 92520.38146 49366.11287 49943.38333 49659.25847 81491.68876 0.689357276 0.692916353 0.555089085 0.61042712 1.135335184 0.605780953 0.612864749 0.609378198 1 16.31436531 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALS(0.004)ELS(0.163)VQHADS(0.833)LENIDESAVAESR 355.11 7.30E-155 819426000 495815 447550 500310 561666 468204 480203 624563 453258 77921.7 TRUE FALSE 472378.8076 493155.8538 523249.7084 505206.2666 549858.6294 463573.4497 529274.4435 413568.3266 90005.39927 5.24833856 5.479180781 5.813536884 5.613066224 6.109173826 5.150507119 5.880474369 4.594927971 1 16.45772393 0.827796852 3.190402318 1.00057645 5.586956485 0.961506871 0.288940631 0.143066748 2.35253897 0.263626865 0.068606206 6.726619347 -0.827796852 4.586380035 HLPNDPMFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HLPNDPMFK 9 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;;;;; 150.61 8.48E-05 1757240000 4157470 3204130 3348450 3462440 2911850 3151110 3877390 3579900 2255960 FALSE TRUE 3960954.632 3530634.49 3501979.745 3114388.953 3419675.718 3041986.271 3285822.942 3266424.978 2605802.755 1.520051594 1.35491241 1.343915896 1.19517448 1.312330993 1.167389306 1.260963799 1.253519658 1 21.31329645 8 0.110668855 0.928792059 2.641989676 0.797202268 0.061218466 43.60591979 0.336418644 0.515733512 11.42074897 100000000 -8 1.713197617 HLPNLLDETQIFSYFSQFGTVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLPNLLDETQIFSYFSQFGTVTR 23 0 Q9BYG3 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 196.81 3.08E-24 61048000 115290 125420 111990 116160 107410 109330 137980 117930 88581 FALSE TRUE 109840.4702 138200.4406 117124.8523 104483.3761 126142.27 105543.8747 116928.6168 107603.424 102317.6891 1.073523759 1.350699394 1.14471753 1.021166301 1.232849091 1.031531064 1.142799626 1.051660031 1 16.64269606 1.798060901 0.394922917 1.000280307 1.20746632 0.2289526 0.09520822 1.47441196 0.628940951 0.109123926 0.09811994 62.81464376 -1.798060901 0.207186014 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(0.994)PPLT(0.006)QEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR 293.3 1.19E-61 561612000 303059 279152 299294 333606 340569 298364 375771 316115 192819 TRUE FALSE 288734.0017 307597.9062 313016.9259 300071.2911 399964.1258 288031.5799 318440.2324 288434.2948 222720.3857 1.296396828 1.381094529 1.405425574 1.347300518 1.795812828 1.293243 1.429775866 1.295051164 1 17.76487409 0.80156689 1.979722901 0.999967439 1.415108083 0.468678853 0.141632304 0.644131275 4.39520545 0.127718549 0.035429775 6.332378857 -0.80156689 0.415140645 HLPS(ph)PPTLDSIITEYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 HLPS(0.999)PPT(0.001)LDSIITEYLR;HLPS(1)PPTLDSIITEYLR;HLPS(0.997)PPT(0.003)LDSIITEYLR 299.06 1.84E-46 825380000 421170 351480 396480 447250 381730 397250 488760 406820 275476 TRUE FALSE 401262.1288 387296.2116 414659.0002 402291.5803 448303.5911 383493.1329 414190.6853 371196.6841 318195.4111 1.261055674 1.217164667 1.303158329 1.264290955 1.408893955 1.205212644 1.301686545 1.166568313 1 18.2795535 0.945241791 3.160645986 1.00021837 1.27477469 0.722501382 0.056069996 0.144826651 3.581677307 0.050388481 0.013164224 8.815395285 -0.945241791 0.27455632 HLPSTEPDPHVVR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 126.1 0.0001113 475504000 613160 534380 536420 670130 600420 560160 668520 602890 194903 FALSE TRUE 584177.142 588833.9295 561015.3876 602767.2592 705133.0579 540761.5187 566524.9958 550097.7555 225127.5618 2.594871713 2.615556819 2.491988911 2.677447641 3.132148957 2.402022722 2.516462184 2.443493596 1 17.78038317 0.140937269 0.854214304 0.976240044 2.652397889 0.878914509 0.189638904 1.296796665 1.028519753 0.259402185 0.059466513 1.383366547 -0.140937269 1.676157846 HLPTLDHPIIPADYVAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLPTLDHPIIPADYVAIK 18 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 49.049 0.092344 154530000 494730 389840 409710 438540 388870 394960 483530 445030 86794 FALSE TRUE 471345.0934 429565.1392 428495.6088 394457.126 456688.8049 381282.4362 409758.6179 406060.8139 100253.5702 4.701529255 4.284786449 4.274118196 3.9345943 4.55533707 3.803180628 4.0872222 4.050337689 1 16.61329409 -0.879879077 0.448274152 3.79E-13 4.380566203 0.945594796 0.243638322 2.859874841 0.408605684 4.239022461 0.126074575 0.131862384 0.879879077 4.380566203 HLQDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLQDIK 6 0 Q99733;Q99733-2;C9JZI7;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 138.07 0.012461 334000000 773550 649630 647350 753620 614260 734820 809680 828910 673020 FALSE TRUE 736985.8245 715828.0356 677031.6378 677864.6858 721386.7495 709372.9991 686148.4452 756326.2461 777388.5043 0.948027686 0.920811192 0.870905132 0.87197673 0.927961689 0.912507704 0.882632611 0.972906394 1 19.56827625 1.091787632 4.919393548 0.998984639 0.907283317 0.656638388 0.024808588 0.128710939 4.822195026 0.025693643 0.006517759 12.35343209 -1.091787632 -0.091701322 HLQENKPTMEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLQENKPTMEHK 12 1 Q8NI77 Q8NI77 KIF18A Kinesin-like protein KIF18A 0 ; 53.237 0.085911 101901000 56546 40196 64284 50397 136680 40635 74160 47937 109303 FALSE TRUE 53873.18264 44292.0181 67231.48499 45330.99781 160516.9487 39227.79976 62845.52996 43739.38215 126253.151 0.426707628 0.35081911 0.532513323 0.359048447 1.271389644 0.310707491 0.497773952 0.346441905 1 16.94595987 HLQGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLQGGEK 7 0 Q8N163-2;Q8N163;E5RHH8;E5RGU7;E5RFJ3;H0YC58 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 110.31 0.0068323 19875000 88558 79401 77454 83982 68074 91463 88627 88233 68478 FALSE TRUE 84372.03885 87492.05217 81005.34251 75539.9698 79946.08405 88295.61338 75105.3234 80506.85077 79097.2185 1.066687811 1.106133108 1.024123781 0.95502688 1.010731927 1.116292267 0.949531789 1.017821515 1 16.27133934 3.631038963 5.237331975 1.008065956 1.086009752 0.324363963 0.045910057 0.229438809 9.233360681 0.011858122 0.018617661 4276.012471 -3.631038963 0.077943796 HLQLAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 153.88 0.001716 22767541000 13188529 8614501 3966732 4253900 12848678 5999165 12844710 8274926 7933224 FALSE TRUE 12565133.37 9492328.446 4148610.586 3826289.89 15089483.38 5791412.412 10885013.58 7550329.611 9163467.861 1.371220324 1.035888224 0.452733687 0.417559154 1.646700093 0.632010992 1.187870547 0.823959851 1 23.12746225 HLQLAIRGDEELDSLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLQLAIRGDEELDSLIK 17 1 Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2;Q71UI9-3;C9J386 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z;Histone H2A 0 ;;; 91.657 0.0021039 512096000 1119340 632828 1081520 938660 959350 1073520 1504170 1188910 855470 FALSE TRUE 1066431.017 697313.8927 1131108.762 844304.1135 1126660.336 1036343.733 1274681.241 1084802.738 988131.9185 1.079239519 0.705689068 1.144694084 0.854444733 1.140192231 1.048790869 1.289990958 1.097831896 1 19.91434413 2.724428492 24.021022 1.140476781 0.931802367 0.252975241 0.140033814 509.3324628 865733.7742 0.04242362 0.040193613 530.1862885 -2.724428492 -0.208674414 HLQLAIRNDEELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLQLAIRNDEELNK 14 1 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;P16104 A0A0U1RR32;Q7L7L0;Q99878;P16104 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;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 H2AX 0 ;;; 228.25 1.04E-12 2078490000 2136210 627740 2407940 1355560 2290370 1991030 3956990 2355630 2381020 FALSE TRUE 2035235.587 691707.4197 2518346.431 1219296.533 2689809.803 1922080.132 3353278.5 2149358.549 2750256.421 0.740016666 0.251506519 0.915676957 0.443339219 0.978021461 0.698873064 1.219260311 0.781512056 1 21.3911347 2.604379919 1.122597485 1.001374159 0.540716532 0.328560248 0.228489645 0.445922886 1.152784417 0.112627956 0.091020832 402.14245 -2.604379919 -0.460657627 HLQLAIRNDEELNKLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLQLAIRNDEELNKLLGK 18 2 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 ; 216.72 5.29E-19 756390000 1221370 238940 1911390 769720 1761270 1315930 3452200 1607620 2119260 FALSE TRUE 1163638.261 263288.2577 1999029.122 692346.2832 2068434.93 1270359.014 2925503.486 1466848.27 2447904.017 0.475361065 0.10755661 0.816628883 0.282832284 0.84498204 0.518957853 1.195105472 0.59922622 1 21.22311556 2.620484667 0.752758557 0.952045762 0.321430389 0.370240564 0.25981639 0.567838403 0.673806147 0.169513342 0.145763096 417.334864 -2.620484667 -0.630615373 HLQQGSES(ph)PMMIGELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLQQGSESPMMIGELR 16 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 HLQQGSES(1)PMMIGELR;HLQQGSES(1)PMMIGELR 192.64 3.23E-10 97941000 111432 108960 108569 121050 119438 112940 133979 120739 87322 TRUE FALSE 106164.8302 120063.1479 113546.996 108881.824 140267.9494 109028.8595 113538.0429 110166.4531 100863.4498 1.052559975 1.190353375 1.125749677 1.079497323 1.390671742 1.08095509 1.125660912 1.092233642 1 16.62204395 0.969818619 1.31952418 1.002158915 1.152614536 0.213615052 0.093844761 0.762746877 2.706286027 0.08291087 0.025196413 9.328646123 -0.969818619 0.150455621 HLS(ph)ESSGKPLSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLSESSGKPLSTK 13 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 HLS(0.723)ES(0.125)S(0.152)GKPLSTK;HLS(0.767)ES(0.115)S(0.118)GKPLSTK 100.77 0.0013613 595480000 797100 561440 690620 921640 663080 720060 791220 595260 359630 TRUE FALSE 759422.6627 618651.3743 722285.6101 828994.9962 778720.9421 695124.1416 670504.8572 543135.8787 415399.5837 1.828173866 1.489292235 1.738773072 1.995656782 1.874631012 1.673386708 1.614120196 1.307502222 1 18.66414024 1.112074731 1.551321202 1.001752361 1.753172176 0.798997944 0.130713917 0.177011968 0.838232957 0.132299202 0.039276284 12.94418559 -1.112074731 0.751419815 HLS(ph)LPAGQVVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLSLPAGQVVPK 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 HLS(1)LPAGQVVPK 54.7 0.075883 0 154090 124810 136470 161630 123810 144630 187810 143500 93381 TRUE FALSE 146806.4711 137528.2809 142727.2845 145382.6453 145402.4248 139621.4268 159156.1351 130934.3793 107862.0486 1.361057694 1.275038651 1.323239141 1.347857261 1.348040638 1.29444442 1.475552683 1.21390592 1 16.71882781 0.989752848 21.16563442 0.999999996 1.343721111 0.815924381 0.052999864 25.18538909 52021.7881 0.051612105 0.012903026 9.766812452 -0.989752848 0.343721115 HLS(ph)QDHTVPGRPAASELHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLSQDHTVPGRPAASELHSR 20 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 HLS(0.999)QDHT(0.001)VPGRPAASELHSR;HLS(0.97)QDHT(0.03)VPGRPAASELHSR;HLS(0.949)QDHT(0.05)VPGRPAAS(0.001)ELHSR 161.04 1.16E-11 328634000 92157 84150 91087 113060 100463 91564 117608 72578 42642.8 TRUE FALSE 87800.92125 92724.98067 95263.42905 101694.994 117983.7154 88393.11572 99664.73958 66222.68556 49255.62763 1.782556135 1.882525614 1.934061824 2.064637055 2.395334727 1.794579015 2.023418325 1.344469429 1 15.58800095 1.09219313 3.298548754 1.005724373 1.970266105 0.795657668 0.174877064 0.097515407 2.023181835 0.168239803 0.044294774 12.36497179 -1.09219313 0.964541732 HLSPDGQYVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLSPDGQYVPR 11 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;; 202.03 4.14E-08 870570000 785501 676123 688644 848294 1005680 648547 954710 851153 863910 FALSE TRUE 748371.9244 745020.7024 720219.0086 763021.8755 1181070.274 626087.6548 809051.455 776621.5311 997880.7506 0.749961279 0.74660294 0.721748574 0.764642343 1.183578572 0.627417309 0.810769678 0.778270881 1 19.92850789 -5 0.167197901 1.755409571 0.74280305 0.160517345 0.145355516 247.2430056 2.316376931 62.66031357 0.516268742 1.00E-05 5 -1.012606521 HLSVNDLPVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HLSVNDLPVGR 11 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;;; 212.2 6.74E-09 3100592000 1599153 1081722 1371900 1374632 2192880 998430 1944639 1539049 1989040 FALSE TRUE 1523564.207 1191950.702 1434802.972 1236451.38 2575317.578 963854.1187 1647948.605 1404281.711 2297490.165 0.663142864 0.518805573 0.624508864 0.53817483 1.120926486 0.419524807 0.717282115 0.611224253 1 21.13162725 -5 0.247217335 3.099803661 0.611708081 0.25268849 0.186585287 238.2288297 2.365347454 252.7165923 0.24841673 1.00E-05 5 -2.48809558 HLTASEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLTASEAK 8 0 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ;; 143.89 0.00059424 482210000 1209080 845660 842960 992070 884050 1014710 1370760 1152830 780000 FALSE TRUE 1151929.185 931833.7154 881610.5498 892345.2388 1038228.04 979570.3383 1161625.386 1051882.094 900958.4163 1.278559769 1.034269394 0.978525239 0.990439983 1.152359555 1.087253663 1.289321866 1.167514587 1 19.78110099 1.869616142 18.22284666 1.185451502 1.090182035 0.044814961 0.110759135 4.677388454 651.7538304 0.045540563 0.029359494 74.0655312 -1.869616142 -0.095269467 HLTDAYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HLTDAYFK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 116.25 0.0023075 5088900000 8294130 6652800 6648940 8244410 7246960 7195980 10088260 7799060 5404960 FALSE TRUE 7902082.912 7330727.884 6953800.476 7415666.243 8510827.53 6946781.408 8549110.653 7116132.961 6243133.592 1.265723822 1.174206474 1.11383176 1.187811559 1.363230084 1.112707474 1.36936212 1.139833524 1 22.57383891 0.991709698 24.86732255 0.999999986 1.226819428 0.405063438 0.088516995 299.0751799 897099.6515 0.079141174 0.019785293 9.810919181 -0.991709698 0.226819442 HLTGEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HLTGEFEK 8 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;;;; 208.37 5.58E-05 7452590000 11367410 10595890 9705760 12361690 8472230 10686960 12367210 11054120 6231600 FALSE TRUE 10830095.06 11675623.24 10150778.7 11119069.44 9949784.23 10316867.9 10480364.98 10086162.65 7197964.701 1.504605191 1.622072867 1.410229019 1.54475187 1.382305227 1.433303486 1.456017834 1.40125203 1 22.7791576 -3.227419534 0.201337839 4.13E-13 1.577620259 0.860294992 0.061445273 20.24035949 0.380627065 8.629895783 0.143658293 0.000592353 3.227419534 1.577620259 HLTGEFEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 163.64 4.08E-05 142120000 169440 133110 137050 164980 123080 170520 203690 200750 109110 FALSE TRUE 161430.907 146674.0603 143333.8781 148395.897 144545.113 164614.8496 172613.3495 183171.2658 126030.2215 1.280890449 1.163800702 1.137297676 1.177462795 1.146908347 1.306153775 1.36961871 1.453391603 1 16.9434102 2.181413067 7.168211053 1.319957085 1.185878921 0.110657371 0.123036885 0.319414816 32.70692451 0.041590182 0.030787502 151.8493953 -2.181413067 -0.134078164 HLTSNSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLTSNSPR 8 0 P14923 P14923 JUP Junction plakoglobin 0 ; 111.95 0.0031354 59623000 25102 17075.6 24658 23392 30141 25786 32420 27711 31431 FALSE TRUE 23915.47821 18815.62305 25788.59369 21040.59172 35397.58086 24893.02435 27473.73357 25284.47793 36305.15895 0.658734981 0.518263068 0.710328626 0.57954826 0.975001401 0.685660801 0.756744616 0.696443113 1 15.14788695 -4.999999986 0.063698793 2.143775085 0.23075685 0.456987903 0.112469615 292.0084154 1.351624997 50.74844907 7.601328837 1.00E-05 4.999999986 -1.913018235 HLTYENVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 224.64 3.02E-07 1180620000 516720 418858 417327 613390 546230 476668 614560 493505 463335 FALSE TRUE 492295.6696 461540.1064 436461.8557 551730.8718 641492.3391 460160.8676 520797.5848 450291.086 535186.6254 0.919857945 0.862390958 0.815532069 1.030913042 1.198632979 0.85981384 0.973113976 0.841372083 1 19.02968254 3.235490766 24.99991457 0.983303475 0.87287369 0.235460963 0.100008761 122.9614079 1001360.195 0.028298461 0.035224736 1719.850775 -3.235490766 -0.110429785 HLVQQEGQLEQQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLVQQEGQLEQQER 14 0 P07476 P07476 IVL Involucrin 0 125.28 9.22E-05 175870000 86177 60772 75829 82306 69596 83049 89349 75550 64617 FALSE TRUE 82103.584 66964.73589 79305.83466 74032.44451 81733.52037 80172.99231 75717.16904 68934.44148 74637.47434 1.100031649 0.897199918 1.062547137 0.991893753 1.095073501 1.074165398 1.014465853 0.923590222 1 16.18761255 1.398110048 7.808276948 0.962931951 1.028421412 0.189528767 0.06174173 0.445205368 36.70973007 0.040232834 0.014871737 25.00979016 -1.398110048 0.065489461 HLVYESDQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HLVYESDQNK 10 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;; 201.33 2.44E-07 838590000 1947000 1911110 1400140 2045590 1109350 1640680 1677930 1660570 689160 FALSE TRUE 1854969.169 2105854.282 1464337.804 1839963.407 1302820.289 1583862.84 1421930.961 1515161.688 796031.4131 2.330271316 2.645441181 1.839547761 2.311420601 1.636644318 1.989698917 1.786274936 1.903394342 1 19.60246584 1.070136291 0.109945899 5.19E-14 3.405159135 0.718410767 0.237382073 5.166710667 0.432379658 6.859331997 5.438859244 11.75266322 -1.070136291 3.405159135 HLWDYTFGPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLWDYTFGPEK 11 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 172.34 1.35E-05 961810000 1816540 1386900 934480 1004500 1529540 1164740 2033230 1562530 1187810 FALSE TRUE 1730675.754 1528226.687 977326.8323 903525.7516 1796291.292 1124404.762 1723023.421 1425706.59 1372009.508 1.261416735 1.113860128 0.712332405 0.658541902 1.309241139 0.819531319 1.255839271 1.039137543 1 20.38785905 0.67715716 11.87370434 0.999999995 1.039531428 0 0.229710609 1268377.594 46652316.3 0.21781798 0.054454495 4.755072684 -0.67715716 0.039531434 HLWFQGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLWFQGIR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 138.9 0.00068575 303410000 371710 303890 120616 152611 322490 175874 298930 222450 157350 FALSE TRUE 354140.005 334856.7365 126146.3629 137270.2523 378732.1539 169783.4393 253322.7383 202971.0987 181751.0344 1.948489626 1.842392466 0.69406132 0.755265316 2.083796415 0.934153909 1.393789802 1.116753472 1 17.47160405 3.860798842 7.623357969 1.17992764 1.90748425 0.389699561 0.391359406 0.249366894 14.46467891 0.095418725 0.172872704 7257.697147 -3.860798842 0.72755661 HLWNHSIIEEEFVSLVTGCCYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLWNHSIIEEEFVSLVTGCCYR 22 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 0 109.66 0.00022117 30469000 27630 30398 32349 35805 34033 32244 45289 32220 12549 FALSE TRUE 26323.98466 33495.59076 33832.23365 32205.81337 39968.34442 31127.38219 38379.33126 29398.64599 14495.03483 1.816069086 2.31083203 2.334056734 2.221851396 2.757381745 2.147451356 2.647757092 2.02818733 1 13.82327118 4.558186992 2.443429325 2.283387029 1.79066448 0.015294313 0.482704795 0.863566584 8.363176378 0.104038789 0.757890807 36156.55069 -4.558186992 -0.49272255 HLYDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLYDPK 6 0 Q15417;E9PDU6;Q15417-3;Q15417-2;U3KPS3;K7EQ72;K7ER02;B7Z7E1;P51911;P51911-2;B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;Q99439-2;H3BQH0 Q15417;P51911-2;B4DDF4 CNN3;CNN2;CNN1 Calponin-3;Calponin;Calponin-1;Calponin-2 0 ;; 101.52 0.036428 659610000 1632550 1342580 1352670 1673560 1175750 1506720 1740880 1627020 995050 FALSE TRUE 1555382.597 1479390.428 1414691.257 1505330.569 1380800.428 1454541.909 1475276.783 1484549.503 1149357.272 1.353262936 1.287145837 1.230854228 1.309715095 1.201367461 1.265526346 1.283566754 1.291634498 1 20.13239589 -3.644269367 0.327687806 4.48E-22 1.293288265 0.813708535 0.041663523 54.08414646 1.092918383 36.92240806 0.035619386 0.000226846 3.644269367 1.293288265 HLYISS(ph)SNPDLITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HLYISSSNPDLITR 14 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 HLYIS(0.001)S(0.84)S(0.158)NPDLITR 237.3 1.76E-17 249900000 295190 236470 272780 301120 288350 237500 338130 277170 231630 TRUE FALSE 281236.9537 260566.5618 285287.2328 270850.8455 338638.1487 229275.3154 286542.0583 252899.5254 267549.9974 1.05115663 0.973898577 1.066295031 1.012337313 1.265700437 0.856943815 1.070985091 0.945242115 1 18.02944899 HLYISSS(ph)NPDLITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HLYISSSNPDLITR 14 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 HLYISS(0.038)S(0.962)NPDLITR;HLYISS(0.007)S(0.993)NPDLITR;HLYISS(0.02)S(0.98)NPDLITR 251.35 3.07E-19 424447000 497610 451396 436416 526320 511640 466008 540830 475494 409962 TRUE FALSE 474088.9615 497393.7656 456426.1053 473413.3137 600869.854 449870.0261 458316.4505 433857.2246 473536.8132 1.001166009 1.050380354 0.963866151 0.999739198 1.268897871 0.950021231 0.967858122 0.916205905 1 18.85311706 HLYTADMFTHGIQSAAHFVMFFAPWCGHCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HLYTADMFTHGIQSAAHFVMFFAPWCGHCQR 31 0 Q8NBS9 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 212.86 3.68E-27 209966000 40745 34728 35944 38979 54215 30834 81660 28198 16495.6 FALSE TRUE 38819.0646 38266.82268 37592.06795 35060.75686 63670.07883 29766.21085 69201.26721 25728.83363 19053.6534 2.03735545 2.008371932 1.972958527 1.840106783 3.341620502 1.562231149 3.631915925 1.350335975 1 14.21778003 HLYTLDGGDIINALCFSPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 282.33 8.07E-45 3259284000 2240248 2136477 2029469 2147569 2219007 2104739 2555321 2212449 1539804 FALSE TRUE 2134355.917 2354186.435 2122522.161 1931691.284 2606001.118 2031851.361 2165459.85 2018715.237 1778588.94 1.200027656 1.323625927 1.193374204 1.086080792 1.465207086 1.14239514 1.217515639 1.13500944 1 20.76230169 0.930698177 1.14793258 1.000666066 1.24460401 0.355414276 0.102376008 0.59539771 1.594812101 0.087896922 0.027681593 8.525074389 -0.930698177 0.243937944 HMAAASAECQNYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HMAAASAECQNYAK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 189.3 7.34E-07 430706000 534407 463500 500096 546762 429020 491284 573159 504058 364738 FALSE TRUE 509146.6402 510731.177 523025.8963 491800.445 503840.9522 474270.7119 485713.0678 459920.0093 421299.7062 1.208514112 1.212275179 1.241458013 1.167341058 1.195920493 1.125732358 1.152892016 1.091669428 1 18.68448738 1.090557952 0.454955523 0.991706391 1.222193034 0.906000403 0.021520525 0.270264166 0.150584784 0.024321993 0.012968848 12.31850354 -1.090557952 0.230486643 HMDFLSDFEMMLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HMDFLSDFEMMLQR 14 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 0 ; 156.81 5.47E-06 58075000 152156 126055 123078 139184 156149 117143 171926 138125 108354 FALSE TRUE 144963.8874 138900.1478 128721.248 125192.9599 183381.3362 113086.3085 145695.5311 126030.0428 125156.9849 1.158256469 1.109807398 1.02847834 1.000287439 1.465210562 0.903555711 1.164102276 1.006975702 1 16.93337928 1.194836372 1.381911957 0.995215658 1.122490009 0.082471706 0.14730215 1.028802827 3.830316239 0.123889249 0.038174939 15.66160882 -1.194836372 0.127274351 HMESEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HMESEK 6 0 A0A087X0W9;Q8N6M0;Q8N6M0-2 A0A087X0W9 OTUD6B OTU domain-containing protein 6B 0 72.234 0.065337 13100000 29416 21177 23623 29068 18897 24954 26397 32079 17653 FALSE TRUE 28025.56398 23334.96038 24706.13792 26146.02941 22192.63082 24089.83672 22369.65284 29269.9927 20390.53708 1.374439715 1.144401459 1.211647237 1.28226291 1.088378924 1.181422374 1.097060501 1.435469433 1 14.31561216 -5 0.028151501 5.41E-09 1.936740789 0.212439793 0.118046527 2529.125927 5.364449664 280.1657125 120.0013672 1.00E-05 5 1.936740784 HMGIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HMGIGK 6 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;; 74.849 0.060109 1017980000 3695780 3369810 3239130 4076850 2922910 3581280 3775080 3861360 2665010 FALSE TRUE 3521087.804 3713197.47 3387647.314 3667037.292 3432664.579 3457259.376 3199122.212 3523238.848 3078286.14 1.143846817 1.206254812 1.100497862 1.191259398 1.115121994 1.123111764 1.039254334 1.144545597 1 21.55369591 1.386355437 0.335839883 0.992528436 1.185193386 0.541964971 0.042201086 0.88388684 0.335276281 0.065015708 0.050417328 24.34195398 -1.386355437 0.19266495 HMLPSGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HMLPSGFR 8 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 103.83 0.0046967 844360000 1239290 1219780 793800 1020850 1093350 906180 1269680 1002230 802120 FALSE TRUE 1180711.218 1344076.969 830196.5152 918232.2185 1284029.894 874798.7594 1075966.997 914469.428 926508.6729 1.274366071 1.45069011 0.896048293 0.991067051 1.385880058 0.944188419 1.161313464 0.987005794 1 19.82144496 3.74888516 24.99846393 1.068962407 1.362528101 0.440820886 0.144344829 583.9052519 1413785.855 0.034656019 0.061646419 5608.996383 -3.74888516 0.293565693 HMQLYCDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HMQLYCDR 8 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 85.67 0.012575 21588000 8006 6862 4781 5013.8 9423.2 5873 9476.5 6770.2 10408 FALSE TRUE 7627.572246 7561.245601 5000.213579 4509.803298 11066.6031 5669.616537 8030.685877 6177.365397 12022.01948 0.634466801 0.628949704 0.415921267 0.375128597 0.920527796 0.471602674 0.667998075 0.51383758 1 13.55339164 -1.570099924 2.661092867 1.029624311 0.586946026 0.42295278 0.154428624 25979261.52 24757369.01 5445829.191 0.036164993 0.026909156 1.570099924 -0.442678285 HNDDEQYAWESSAGGSFTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 272.71 1.97E-44 3243726400 1854484.1 1948895.1 1794014.5 2139019.1 1626346.6 1776041.6 1950313.3 1863897.3 1054402.5 FALSE TRUE 1766826.312 2147489.726 1876271.839 1924000.836 1909980.932 1714536.834 1652757.186 1700684.571 1217913.855 1.450698919 1.763252564 1.540562029 1.57975117 1.568239761 1.407765276 1.357039482 1.396391514 1 20.21598066 0.9415479 0.477380605 0.984622552 1.620140587 0.80188249 0.088141517 0.460445087 0.261890754 0.107421868 0.050850327 8.740733917 -0.9415479 0.635518035 HNDIVDS(ph)DS(ph)DAEDRGTLSAELTAAHFGGGGGLLHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNDIVDSDSDAEDRGTLSAELTAAHFGGGGGLLHKK 36 2 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 2 HNDIVDS(1)DS(0.999)DAEDRGTLSAELTAAHFGGGGGLLHKK 98.595 0.00039831 52510000 62167 30747 78834 64572 40468 63453 113650 44907 14524 TRUE FALSE 59228.48911 33880.15426 82448.61688 58081.09988 47525.60639 61255.6067 96310.60517 40974.70501 16776.30774 3.530484182 2.019523889 4.914586579 3.462090752 2.83290025 3.651316347 5.7408702 2.442414961 1 14.03413761 3.754826221 24.77703181 3.74064156 2.775004203 0.001377223 1.359192401 1745.794412 2659321.084 0.32800742 0.589071107 5686.253557 -3.754826221 -0.965637357 HNESVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNESVVK 7 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 72.547 0.051308 73471000 163190 159980 144270 188090 300700 150970 191430 179100 234650 FALSE TRUE 155476.3321 176282.1439 150884.9222 169182.8359 353141.9848 145741.871 162223.8376 163417.0545 271038.3236 0.573632282 0.65039564 0.556692206 0.624202635 1.302922702 0.537716841 0.598527306 0.602929698 1 18.04813733 2.968075484 24.99877532 0.767815378 0.601343885 0.161793215 0.224649951 1486.024122 1163644.761 0.067679827 0.071847542 929.1278621 -2.968075484 -0.166471493 HNGAAEPEPEAETAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNGAAEPEPEAETAR 15 0 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 ; 103.77 0.0014466 483060000 299890 251860 284780 297880 261740 288690 356200 282060 154832 FALSE TRUE 285714.794 277524.8203 297837.4447 267936.5365 307387.3731 278692.5929 301855.1479 257361.3311 178842.5558 1.597577225 1.551782903 1.665361152 1.498169914 1.718759675 1.558312515 1.687826181 1.439038544 1 17.44833054 0.903311198 4.262587562 1.000121386 1.606329318 0.892725144 0.066818804 0.130398826 5.069354384 0.056747831 0.014453144 8.0040759 -0.903311198 0.606207932 HNGPNDASDGTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HNGPNDASDGTVR 13 0 P31942;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;; 182.72 1.10E-05 1507007000 1219884 965242.2 984352 1184245 1093521.5 1092437.5 1311329 1120233.6 847997 FALSE TRUE 1162222.501 1063601.478 1029485.513 1065202.443 1284231.303 1054606.115 1111261.677 1022140.007 979500.0438 1.186546655 1.085861593 1.051031615 1.087496064 1.31110898 1.076677967 1.134519272 1.043532375 1 19.90168603 1.110942781 2.513342893 0.999335919 1.132666266 0.291108057 0.073764419 0.339545925 4.114764279 0.06665761 0.01830431 12.91049164 -1.110942781 0.133330348 HNGS(ph)LSPGLEARDPLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNGSLSPGLEARDPLEAR 18 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGS(0.584)LS(0.416)PGLEARDPLEAR 121.26 2.34E-05 189940000 114990 80309 124910 117110 118420 117710 147290 105530 62225 TRUE FALSE 109554.6506 88492.5784 130637.2471 105337.8803 139072.4105 113633.6732 124818.2053 96289.23375 71874.5352 1.524248474 1.231209053 1.817573452 1.465579986 1.934933007 1.58100046 1.736612348 1.339684959 1 16.1331931 0.974381153 5.151869783 1.000328761 1.58654563 0.510935975 0.195087918 0.153247719 15.44620236 0.191749714 0.048436264 9.427165962 -0.974381153 0.586216868 HNGSLS(ph)PGLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR 176.26 1.64E-05 2691580000 2462560 2511420 2370180 3050310 2284090 2477720 2721500 2096190 969750 TRUE FALSE 2346159.669 2767336.553 2478855.097 2743687.044 2682434.573 2391915.935 2306285.191 1912636.491 1120133.877 2.094535052 2.470540897 2.212998953 2.449427787 2.394744617 2.135383978 2.058937095 1.707507049 1 20.09523974 0.952347824 1.038529023 1.001158927 2.321110052 0.927550336 0.117338549 0.136005933 0.305252504 0.104923134 0.034227157 8.960821461 -0.952347824 1.319951125 HNGSLS(ph)PGLEARDPLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNGSLSPGLEARDPLEAR 18 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGSLS(1)PGLEARDPLEAR;HNGS(0.232)LS(0.768)PGLEARDPLEAR 150.59 3.25E-08 481000000 204347 126306 225523 183245 230412 192896 282491 190477 120150 TRUE FALSE 194687.9223 139176.725 235863.4526 164824.8645 270595.7798 186215.9632 239391.8096 173797.8241 138782.2484 1.40283015 1.002842414 1.699521772 1.187650916 1.949786684 1.341785173 1.724945463 1.252305869 1 17.08246352 3.738820452 24.99999992 1.497325638 1.202836288 0.09099732 0.2990483 36.88012963 3548278.255 0.068378406 0.114179351 5480.503401 -3.738820452 -0.29448935 HNGSS(ph)EILNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNGSSEILNK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2 Q8TDM6-4 DLG5 Disks large homolog 5 1 HNGS(0.366)S(0.634)EILNK 110.38 0.0012198 323800000 402770 347920 385820 425870 298700 375200 469300 387090 125210 TRUE FALSE 383731.8603 383373.4436 403510.2286 383060.7385 350793.1854 362206.7299 397699.6657 353194.3475 144626.9273 2.653253218 2.650775002 2.790007616 2.648612852 2.425503963 2.504421111 2.749831398 2.442106419 1 17.14197666 0.814412077 4.726173018 1.000011521 2.632368905 0.959185209 0.104951848 0.479673502 12.08475297 0.102088972 0.025861947 6.522469798 -0.814412077 1.632357384 HNGVGGS(ph)PPKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNGVGGSPPKSK 12 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 HNGVGGS(0.99)PPKS(0.01)K 66.246 0.035374 30185000 82490 43990 85420 72290 58075 102680 120900 100470 48388 TRUE FALSE 78590.86118 48472.63101 89336.59149 65023.27186 68203.26161 99124.16585 102454.4845 91672.31418 55891.76391 1.406125978 0.867258924 1.598385616 1.163378418 1.220273916 1.773502193 1.833087334 1.640175721 1 15.77034809 2.247715001 24.9356144 1.657840372 1.224639074 0.182075953 0.294631916 199.2694844 542790.0879 0.094376104 0.077922209 176.8947733 -2.247715001 -0.433201298 HNGYDPR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 68.214 0.063057 1202483000 1882190 1460190 1519678 1807910 1665400 1403442 1798860 1564161 1157415 FALSE TRUE 1793222.609 1608985.021 1589356.739 1626175.452 1955845.233 1354840.452 1524410.869 1427194.771 1336901.007 1.341327892 1.203518445 1.188836519 1.216376862 1.462969377 1.013418678 1.140257103 1.067539603 1 20.35046121 2.209872853 24.99960373 1.072928392 1.269887037 0.618192259 0.087967292 155.7014306 135683.1714 0.031462947 0.023240895 162.1335355 -2.209872853 0.196958645 HNIMDFAMPYFIQVMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNIMDFAMPYFIQVMK 16 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 135.45 2.28E-05 70318000 182090 235760 155390 188300 155670 190610 229660 210670 90530 FALSE TRUE 173482.9666 259784.212 162514.7852 169371.7263 182818.7987 184009.1279 194621.149 192222.618 104568.93 1.659029757 2.48433461 1.55414027 1.619713678 1.748308973 1.759692175 1.861175676 1.838238355 1 16.67409473 -2.192257044 0.285680499 1.25E-15 1.932329638 0.47786271 0.261640137 32.57128369 1.282497291 21.77387605 0.305289489 0.006423074 2.192257044 1.932329638 HNIQFSSFDIFSDEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HNIQFSSFDIFSDEEVR 17 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ;;;; 299.79 2.62E-46 686695000 612934 520342 541018 650228 571475 542636 671539 553924 376746 FALSE TRUE 583961.8245 573365.4414 565824.2104 584865.8461 671140.0591 523844.3793 569083.3919 505419.478 435169.8455 1.341917025 1.317567031 1.300237634 1.343994424 1.54224854 1.203769941 1.307727081 1.161430378 1 18.73121906 1.030156881 1.193473663 1.00057566 1.347837829 0.66337531 0.08149434 0.28171929 0.832376635 0.071483163 0.022455022 10.71906442 -1.030156881 0.347262168 HNKPEVEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 159.83 3.95E-05 1531270000 4890570 4633130 4279960 5062110 3579210 4707100 5571990 5093370 3200360 FALSE TRUE 4659402.448 5105251.214 4476200.399 4553257.085 4203423.091 4544091.947 4721880.589 4647367.521 3696655.484 1.260437298 1.381045985 1.210878433 1.231723407 1.137088135 1.229244101 1.277338559 1.257181672 1 21.81778916 -4.789056021 0.194455819 8.72E-13 1.301614092 0.607852532 0.061858236 90.1586635 0.95535461 35.23600026 0.168006159 1.63E-05 4.789056021 1.301614092 HNKS(ph)PTLSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HNKSPTLSCR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 HNKS(0.949)PT(0.048)LS(0.004)CR;HNKS(0.968)PT(0.027)LS(0.006)CR;HNKS(0.844)PT(0.152)LS(0.005)CR 75.483 0.023533 368890000 506189 470608 444452 533086 329306 520430 550162 474138 215250 TRUE FALSE 482262.4491 518563.4902 464830.5638 479499.1825 386736.8621 502407.3786 466224.6825 432619.9632 248629.8707 1.939680248 2.085684592 1.869568458 1.928566271 1.555472241 2.020704018 1.875175663 1.740016041 1 17.92364011 -2.059460867 0.2957861 4.86E-17 1.981550477 0.808859295 0.136432108 14.02721273 0.610429645 9.722203218 0.143340001 0.008720455 2.059460867 1.981550477 HNLLLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNLLLHLK 8 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 159.04 0.00020904 712360000 980750 791570 438740 559120 740140 569380 1082110 771930 140764 FALSE TRUE 934391.8912 872231.8829 458856.663 502916.1953 869220.1817 549662.2278 917014.2452 704335.7169 162592.9622 5.746816335 5.364511915 2.822118847 3.093099409 5.345988965 3.380602828 5.639938118 4.331895473 1 17.31090529 -1.722084761 2.102045685 0.065468632 4.588724055 0.501186384 1.080371739 1095121.499 652424.8818 5345051.565 0.289641189 0.018963358 1.722084761 4.523255423 HNMCGETEEEKIRVDIIENQVMDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HNMCGETEEEKIRVDIIENQVMDFR 25 2 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;; 189.62 5.99E-18 304920000 477360 352069 427414 475422 313168 491070 526110 481750 163826 FALSE TRUE 454796.1388 387945.2314 447011.3547 427631.6773 367784.4 474064.1228 445842.2568 439565.4161 189231.2994 2.403387496 2.050111333 2.362248508 2.259835866 1.943570653 2.50520989 2.356070366 2.322900163 1 17.52979121 -0.807254443 7.227229454 0.999999997 2.271687711 0.854232491 0.165569458 4.55E-09 1.26E-09 0.152755851 0.036004899 0.155863907 0.807254443 1.271687714 HNNCMASHLTPAVYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HNNCMASHLTPAVYAR 16 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J8F6;C9J6W7;C9JT96;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 231.23 8.86E-16 330423000 365288 252903 280470 331134 352942 270883 383867 344080 176733 FALSE TRUE 348021.5602 278674.1032 293329.8269 297847.7812 414494.9731 261502.2538 325301.0389 313950.5311 204139.851 1.704819311 1.36511368 1.436906246 1.459037908 2.030446143 1.280995614 1.593520507 1.53791888 1 17.63919832 -1.250102826 0.996983076 0.902747285 1.543937687 0.411893003 0.20678937 268.5218237 92.75632674 75.48518952 0.057785799 0.05622082 1.250102826 0.641190403 HNQLPLVIEFTEQTAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HNQLPLVIEFTEQTAPK 17 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ;; 153.95 1.56E-07 1198025000 1107468 873035 800988 1207888 726470 987917 1143494 1081471 608557 FALSE TRUE 1055120.182 961998.2591 837714.0921 1086468.803 853166.138 953705.1866 969032.9886 986771.666 702928.9115 1.501033981 1.368556967 1.191747954 1.545631124 1.213730328 1.356759085 1.378564707 1.403800085 1 19.42301927 -1.735849497 2.58453797 0.922603135 1.372774207 0.53508027 0.108354331 15252720.7 11256950.55 7555216.287 0.023617361 0.018371749 1.735849497 0.450171071 HNS(ph)ISEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HNSISEAK 8 0 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HNS(0.998)IS(0.002)EAK;HNS(0.997)IS(0.003)EAK;HNS(0.997)IS(0.003)EAK 114.72 0.0016759 429955000 709680 586594 590905 728110 456566 726660 791580 680040 334884 TRUE FALSE 676134.8329 646368.5955 617998.5787 654918.9995 536190.9658 701495.582 670809.9326 620492.0925 386816.1004 1.747949044 1.670997135 1.597654746 1.693101706 1.386165067 1.813511851 1.73418307 1.604100998 1 18.56128832 0.906139913 10.25784027 1.000000011 1.669907363 0.76687285 0.11407285 6.894533191 753.8604404 0.104618895 0.026167104 8.056379456 -0.906139913 0.669907352 HNS(ph)SDGFFNNGPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNSSDGFFNNGPLR 14 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 HNS(0.633)S(0.367)DGFFNNGPLR;HNS(0.5)S(0.5)DGFFNNGPLR 88.574 0.0041817 187988000 260026 182666 265799 222213 230363 275626 335540 277251 114808 TRUE FALSE 247735.0863 201279.8731 277986.1471 199875.7271 270538.2343 266081.0025 284347.2104 252973.4326 132611.8383 1.868121953 1.517812253 2.0962393 1.507223862 2.040076043 2.006464928 2.144206838 1.907623301 1 17.01685005 2.711280419 24.94798693 1.925851533 1.741895035 0 0.360791558 2121.900888 1940495.483 0.103171486 0.097289737 514.3756706 -2.711280419 -0.183956498 HNS(ph)TTSSTSSGGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.854)T(0.127)T(0.019)SSTSSGGYR;HNS(0.731)T(0.237)T(0.032)SS(0.001)TSSGGYR;HNS(0.858)T(0.102)T(0.004)S(0.007)S(0.011)T(0.018)SSGGYR;HNS(0.968)T(0.03)T(0.001)SSTSSGGYR;HNS(0.697)T(0.228)T(0.075)SSTSSGGYR 157.07 5.66E-06 406439000 351686 293138 285691 388346 343723 288646 373166.1 278011.5 197404.1 TRUE FALSE 335062.4998 323009.0955 298790.2149 349308.7223 403668.1824 278650.1166 316232.7578 253667.3392 228016.5196 1.469465898 1.41660392 1.310388455 1.531944803 1.770346215 1.222061091 1.386885294 1.112495444 1 17.79877882 1.261129757 1.366425477 0.997969527 1.466212451 0.582861348 0.140542061 0.278042091 0.996878465 0.124653027 0.038979759 18.2444072 -1.261129757 0.468242925 HNS(ph)TTSSTSSGGYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.963)T(0.037)TSSTSSGGYRR;HNS(0.787)T(0.212)TSSTSSGGYRR;HNS(0.938)T(0.061)T(0.001)SSTSSGGYRR;HNS(0.838)T(0.14)T(0.02)S(0.001)ST(0.001)SSGGYRR 161.95 9.94E-07 1380990000 187162.4 124908.5 158539 163661 202915 161850.1 248535 156687 126172 TRUE FALSE 178315.6043 137636.8182 165808.17 147209.4853 238303.3118 156245.1905 210616.4211 142966.6556 145738.1094 1.223534497 0.944411992 1.137713195 1.010096028 1.635147545 1.072095632 1.445170532 0.980983329 1 17.15301865 HNS(ph)WDTVNTVLPEDPEVADLFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HNSWDTVNTVLPEDPEVADLFSR 23 0 Q8N961 Q8N961 ABTB2 Ankyrin repeat and BTB/POZ domain-containing protein 2 1 HNS(0.469)WDT(0.469)VNT(0.062)VLPEDPEVADLFSR;HNS(0.479)WDT(0.479)VNT(0.042)VLPEDPEVADLFSR;HNS(0.49)WDT(0.49)VNT(0.019)VLPEDPEVADLFSR;HNS(0.499)WDT(0.499)VNT(0.001)VLPEDPEVADLFSR;HNS(0.464)WDT(0.464)VNT(0.072)VLPEDPEVADLFSR 92.01 0.0032336 151874000 147264.5 136399 126907.7 171682.5 129137 148382.9 166673 138747.8 60773 TRUE FALSE 140303.5989 150298.2132 132726.5436 154424.6489 151658.4519 143244.363 141243.9727 126598.3071 70197.36645 1.998701747 2.14108051 1.890762436 2.199863851 2.160457857 2.040594544 2.012097887 1.803462344 1 16.09912929 0.678691124 1.402360667 1.000100835 2.076299473 0.936465616 0.087112038 0.233984878 0.709768205 0.076722316 0.022617644 4.771897687 -0.678691124 1.076198638 HNS(ph)WSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HNSWSSSSR 9 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(1)WSSSSR;HNS(1)WSSSSR;HNS(1)WSSSSR;HNS(1)WSSSSR 93.348 0.0060933 940476000 436848 393233 384335 459647 587101 352574 477168 355209 477150 TRUE FALSE 416199.0608 433303.8898 401957.1399 413442.4103 689491.2285 340364.274 404367.2578 324105.0169 551143.9851 0.755154863 0.78619 0.72931421 0.750153175 1.251018331 0.617559627 0.733687147 0.588058703 1 19.07206974 -1.117529328 4.487018175 1.00001999 0.777592526 0.132365243 0.179893287 4.10E-05 8.07E-06 0.16269669 0.038343772 0.076290537 1.117529328 -0.222427465 HNST(ph)TSSTSSGGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.084)T(0.907)T(0.008)SS(0.001)TSSGGYR;HNS(0.082)T(0.835)T(0.082)SSTSSGGYR 252.68 3.68E-23 447450000 405780 335040 360750 463860 427400 368540 468100 318350 216192 TRUE FALSE 386599.5836 369180.9569 377290.7443 417231.9115 501938.4247 355777.3674 396682.7478 290473.5863 249717.9512 1.548144944 1.478391742 1.510867531 1.670812649 2.010021395 1.424716828 1.588523155 1.163206669 1 17.92994001 1.147261468 2.721675389 0.997267214 1.598624709 0.652832094 0.160511161 0.160530042 2.162706337 0.150230932 0.041193794 14.03658527 -1.147261468 0.601357495 HNTEDFTLFTLDDVDAAFDKIQQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNTEDFTLFTLDDVDAAFDKIQQLK 25 1 Q9P2I0 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 157.83 2.80E-09 22865000 79112 60324 86866 75523 57426 87380 105890 83384 49714 FALSE TRUE 75372.53254 66471.08418 90848.89202 67931.28456 67441.07622 84354.00869 89734.5357 76082.45491 57423.39322 1.312575387 1.157561065 1.582088535 1.182989732 1.174452996 1.468983353 1.56268257 1.324938334 1 15.80935096 2.227191303 24.99288477 1.407929343 1.276905236 0 0.191177311 510.6041883 1122440.114 0.066064019 0.049212367 168.7296102 -2.227191303 -0.131024108 HNVEVLGILSDDVETDTVAPGENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNVEVLGILSDDVETDTVAPGENLK 25 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 145.14 2.87E-07 65095000 184953 192904 158296 198665 119051 184230 166820 178131 70340 FALSE TRUE 176210.6382 212561.1369 165554.0282 178694.8168 139813.4567 177850.0689 141368.5451 162532.9053 81247.96795 2.168800558 2.6162025 2.037639 2.199375828 1.720824043 2.188978671 1.739964072 2.000455019 1 16.31004411 -0.926796412 0.169225732 1.95E-17 2.608437328 0.738290364 0.216956147 10.04769593 0.378535578 5.683168881 0.973628575 0.118359627 0.926796412 2.608437328 HNVMISTEWAAPNVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HNVMISTEWAAPNVLR 16 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;; 207.79 1.25E-11 2905570000 3653610 2829180 2937000 3424230 3019140 2981750 3964300 3138830 2242390 FALSE TRUE 3480911.096 3117476.659 3071664.355 3080019.895 3545677.06 2878491.25 3359473.226 2863977.405 2590128.389 1.343914499 1.203599278 1.185912007 1.189137924 1.368919423 1.111331493 1.297029615 1.10572797 1 21.30459218 -5 0.167799344 0.073093401 1.292527477 0.471842098 0.082412547 112.1149063 1.051924256 34.37833053 0.278666435 1.00E-05 5 1.219434076 HNWGQGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HNWGQGFR 8 0 E5RGY0;B4E1G1;Q9BUN8-2;Q9BUN8 E5RGY0 DERL1 Derlin-1 0 ;;; 187.55 0.00020166 1281010000 781700 576420 670000 899450 823710 742060 905210 739570 607360 FALSE TRUE 744750.5902 635157.8533 700720.1627 809035.5772 967364.7632 716362.2761 767103.5892 674809.3301 701546.2868 1.061584395 0.90536842 0.998822424 1.153217674 1.378903689 1.021119047 1.093446867 0.961888535 1 19.42017877 3.321763957 6.308141302 1.112019032 0.979136707 0.160997528 0.119728278 0.330110447 20.04831937 0.032911881 0.044568388 2097.799402 -3.321763957 -0.132882325 HNYECLVYVQLPFMEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNYECLVYVQLPFMEDLR 18 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 147.53 7.59E-08 353520000 565950 603660 545070 603260 544690 559130 600860 522340 310890 FALSE TRUE 539198.6651 665173.6403 570061.9986 542619.1587 639683.7635 539767.1879 509187.7714 476601.1405 359101.2334 1.501522732 1.852329033 1.587468785 1.511047883 1.781346607 1.503105915 1.417950494 1.327205524 1 18.45403108 1.12838065 0.795141309 1.003157199 1.661858157 0.764443744 0.114124669 0.271666001 0.390976462 0.103108182 0.038960611 13.43942382 -1.12838065 0.658700958 HNYEGTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HNYEGTLR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 118.5 0.0018756 218840000 149181 109361 116226 133238 124560 123473 141460 114301 109348 FALSE TRUE 142129.5098 120505.0102 121555.0771 119844.6631 146283.2246 119197.099 119877.6789 104292.1985 126305.1294 1.125286918 0.954078515 0.962392245 0.948850325 1.158173269 0.943723344 0.949111723 0.825716256 1 16.9465537 2.026286485 24.99050009 0.926070583 1.023845531 0.275955541 0.080739611 293.9809478 279485.7451 0.029067384 0.021467122 106.2396143 -2.026286485 0.097774948 HNYYESFSLSPAAVADNVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HNYYESFSLSPAAVADNVER 20 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 197.72 1.63E-21 158700000 132820 124060 124910 139110 122700 133000 146690 142530 111840 FALSE TRUE 126541.8618 136701.855 130637.2471 125126.3985 144098.8412 128394.1767 124309.7464 130049.3176 129183.576 0.979550696 1.058198412 1.011252754 0.968593705 1.115457906 0.993889321 0.962272064 1.006701638 1 16.97906314 2.019758436 24.99989416 0.983619553 1.025918774 0.147599831 0.042120597 378.8893941 479398.0196 0.014743972 0.010887726 104.6546273 -2.019758436 0.042299221 HPAKPDPSGECNPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HPAKPDPSGECNPDLR 16 1 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 264.52 3.07E-27 1911080000 2076140 2200490 1767630 2417860 1515540 1978320 2110760 2075130 1307230 FALSE TRUE 1978004.977 2424722.433 1848677.584 2174812.119 1779849.696 1909810.282 1788724.795 1893420.616 1509948.552 1.309981704 1.605831159 1.224331506 1.440322001 1.17874857 1.264818116 1.184626319 1.253963662 1 20.52606796 1.852082289 0.305354405 0.986306133 1.496140084 0.513358534 0.112521985 1.076905486 0.328933378 0.172457904 0.197818102 71.13482857 -1.852082289 0.509833951 HPALFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPALFK 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 84.566 0.055705 737830000 2662900 2762900 2071400 2984600 2050410 2395000 2551200 2613100 1688140 FALSE TRUE 2537029.994 3044442.651 2166375.739 2684582.338 2408000.855 2312060.549 2161967.584 2384283.111 1949928.129 1.301088977 1.561310186 1.111002865 1.376759634 1.234917748 1.185715778 1.10874219 1.222754354 1 20.89498952 2.409432912 0.356660142 1.011724318 1.460912632 0.456164169 0.115310161 1.164035207 0.340426907 0.127933423 0.188013682 256.7041631 -2.409432912 0.449188314 HPDADSLYVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPDADSLYVEK 11 0 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 87.363 0.01378 114190000 183970 203530 152730 223770 139010 166600 174980 181720 118720 FALSE TRUE 175274.1027 224269.9384 159732.8216 201276.2145 163253.3 160830.6002 148283.5873 165807.6334 137130.4913 1.278155581 1.635449099 1.16482352 1.46777141 1.19049599 1.172828878 1.081331992 1.209123018 1 17.06518987 2.566634524 0.981878658 1.088284427 1.4290745 0.468066491 0.134457099 0.414174486 0.818447085 0.076108002 0.058659668 368.6672201 -2.566634524 0.340790072 HPDASVNFSEFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPDASVNFSEFSK 13 0 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 199.13 1.20E-07 680430000 933100 1093620 881740 1056960 691050 1006120 891170 992160 529290 FALSE TRUE 888994.2122 1205061.121 922168.6512 950712.3727 811568.9012 971277.8121 755205.649 905281.2106 611369.59 1.454102767 1.971084498 1.508365261 1.555053422 1.327460369 1.588691731 1.235268586 1.480742951 1 19.22168527 1.333961453 0.296243663 0.94369637 1.758914793 0.514059127 0.175314355 1.154476306 0.370624457 0.363115093 0.284068068 21.57552902 -1.333961453 0.815218422 HPDASVNFSEFSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPDASVNFSEFSKK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 154.65 3.93E-06 200770000 658210 493800 624580 573900 449390 673100 773110 731530 452330 FALSE TRUE 627097.7177 544118.7814 653217.6108 516210.4817 527763.4737 649790.3782 655157.8704 667473.3551 522475.0262 1.200244387 1.041425435 1.250237003 0.988009868 1.010121914 1.243677392 1.253950596 1.277522028 1 18.99500255 2.215938092 24.9721337 1.220154698 1.101505786 0.137372934 0.110637989 345.0613879 380897.5768 0.038148115 0.02819415 164.4137338 -2.215938092 -0.118648911 HPDGRPTGDAFALFACEELAQAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPDGRPTGDAFALFACEELAQAALR 25 1 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 0 112.88 0.0013255 16046000 18017 19013 18663 23366 19887 18620 19813 21110 16476 FALSE TRUE 17165.37212 20950.44632 19518.71701 21017.20529 23355.2865 17975.18473 16790.16296 19261.49649 19031.01393 0.901968344 1.100858125 1.025626752 1.104366029 1.227222395 0.944520602 0.882252676 1.012110892 1 14.21606481 2.067109442 24.99999996 0.942115482 1.0620158 0.274797684 0.087792921 67.03882058 24972.79996 0.03324888 0.024555923 116.7103691 -2.067109442 0.119900317 HPDVEVDGFSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 228.7 7.00E-12 1292240000 1643650 1601430 1317230 1853070 1563070 1425540 1618220 1544080 1003030 FALSE TRUE 1565957.922 1764617.538 1377626.298 1666795.883 1835668.913 1376173.192 1371330.818 1408872.17 1158574.77 1.351624395 1.523093359 1.189069825 1.438660608 1.584419894 1.187815606 1.183636011 1.216039056 1 20.14391972 2.121062894 8.127912785 1.16188199 1.416058729 0.563440662 0.118187139 0.184727921 12.36669338 0.041827477 0.030864924 132.1486995 -2.121062894 0.254176738 HPDYAILAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPDYAILAAR 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 132.78 0.0002146 282420000 116809 116798 86308 103185 126515 89568 125201 131102 122887 FALSE TRUE 111287.6701 128699.849 90265.30717 92812.64776 148579.1759 86466.2377 106099.288 119622.0139 141943.6883 0.784026901 0.906696525 0.63592336 0.653869495 1.046747324 0.609158735 0.747474504 0.842742747 1 17.11495917 0.919405365 4.491091174 0.999918199 0.775936277 0.238207888 0.130670677 0.601712308 28.87320269 0.11806918 0.029990715 8.306257023 -0.919405365 -0.223981922 HPEHYVDY(ph)T(ph)Y(ph)MAT(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPEHYVDYTYMATK 14 0 H3BLX4;Q96JM2-2;Q96JM2;Q96JM2-3 H3BLX4 ZNF462 Zinc finger protein 462 4 HPEHY(0.108)VDY(0.976)T(0.97)Y(0.976)MAT(0.97)K 41.86 0.070971 217990000 69842 102100 86149 97965 284340 71959 90488 128790 280670 TRUE FALSE 66540.70707 112504.1061 90099.01686 88117.37208 333928.806 69467.04179 76682.39367 117512.4648 324194.8701 0.205249105 0.347026176 0.277916232 0.271803721 1.030024953 0.214275574 0.236531792 0.362474782 1 18.30650174 -2.263111271 2.160016331 3.387324098 0.354999188 0.402416442 0.241501151 14324096.65 2177196.441 166932811 0.061000315 0.005456181 2.263111271 -3.03232491 HPELADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 120.46 0.0045528 434500000 5485620 5506240 4597220 5699580 3427030 5201950 5088400 5348690 2703110 FALSE TRUE 5226325.614 6067332.116 4808007.084 5126647.39 4024702.947 5021805.167 4312071.125 4880330.348 3122294.493 1.673873373 1.943228651 1.53989545 1.641948702 1.289020929 1.608370119 1.381058428 1.563058949 1 21.57417519 -0.356965058 0.083628291 3.00E-18 2.449657367 0.642648128 0.150521112 30.62510459 0.674087679 13.37402801 6.527145207 0.439576981 0.356965058 2.449657367 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPTAPLS(0.003)HS(0.028)AS(0.028)S(0.028)DPADRLS(0.912)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASS(0.002)DPADRLS(0.998)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSAS(0.014)S(0.045)DPADRLS(0.94)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR 258.18 1.18E-62 2331870000 818305 778190 624408 962721 633165 704959 826174 831766 433211 TRUE FALSE 779625.3444 857488.4457 653037.7244 865946.456 743588.7755 680546.0931 700125.9826 758932.1596 500391.1493 1.558031842 1.713636316 1.305054506 1.730539114 1.486015043 1.360028238 1.399157406 1.516677824 1 18.93269675 -3.053771466 0.156111119 6.58E-11 1.704779968 0.614053239 0.130932292 39.17393066 0.629709831 13.59543609 0.599022586 0.000883545 3.053771466 1.704779968 HPENYDLATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPENYDLATLK 11 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 126.12 0.00031413 617050000 565290 518870 449340 528860 429640 527010 589320 561650 337070 FALSE TRUE 538569.862 571743.4429 469942.6835 475697.988 504569.08 508759.5116 499408.4104 512468.9485 389341.0941 1.383285428 1.468489845 1.207020504 1.221802669 1.295956393 1.306719273 1.282701513 1.316246747 1 18.5706751 -4.990739563 0.123100841 1.48E-15 1.465449558 0.635629685 0.074049856 99.56210667 0.789795767 25.0180336 0.69554069 1.02E-05 4.990739563 1.465449558 HPEQIFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPEQIFPR 8 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 99.136 0.0070277 250060000 87456 82940 75689 78220 72023 67104 81136 86709 80984 FALSE TRUE 83322.1282 91391.68029 79159.41552 70357.17699 84583.7884 64780.17165 68757.21304 79116.30029 93542.58511 0.890740063 0.977006143 0.84623934 0.75214061 0.904227612 0.692520648 0.735036486 0.845778425 1 16.51333568 3.537513022 4.989172055 0.798439806 0.932534009 0.17161511 0.091445094 0.243573276 12.36550508 0.022829218 0.035197392 3447.569441 -3.537513022 0.134094203 HPFPGPGLAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPFPGPGLAIR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 67.726 0.059186 254980000 324920 301410 230490 282090 316680 278780 334680 275290 217480 FALSE TRUE 309561.6755 332124.0217 241058.1945 253733.7773 371908.8917 269125.7787 283618.4192 251184.1482 251205.6877 1.232303609 1.322119832 0.959604843 1.010063823 1.480495506 1.071336327 1.129028653 0.999914256 1 17.9385096 7.999999832 0.07198055 0.804890398 1.994154978 0.149920963 0.15390328 407.1891904 2.158640416 6.044631423 48.84098193 99999961.28 -7.999999832 1.189264581 HPGAHQGNLASGLHSNAIASPGS(ph)PSLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HPGAHQGNLASGLHSNAIASPGSPSLGR 28 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HPGAHQGNLASGLHSNAIAS(0.001)PGS(0.997)PS(0.002)LGR;HPGAHQGNLASGLHSNAIAS(0.025)PGS(0.975)PSLGR;HPGAHQGNLASGLHSNAIAS(0.075)PGS(0.92)PS(0.006)LGR 307.98 2.26E-82 656449000 201064 201661 227943 245905 282518 223202 261923 235612 24822.8 TRUE FALSE 191560.1032 222210.4852 238394.412 221186.1622 331789.0498 215472.4588 221961.8358 214980.5642 28672.19305 6.681041205 7.750034495 8.314481269 7.714309186 11.5718058 7.515032367 7.741362352 7.497876562 1 14.80736464 0.294139674 1.288915766 0.993463031 8.128893162 0.754140728 1.280302921 2.349025894 3.794297761 1.234528725 0.361727642 1.968519286 -0.294139674 7.135430131 HPGASEAADGCS(ph)PLWGLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPGASEAADGCSPLWGLSK 19 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 HPGASEAADGCS(1)PLWGLSK;HPGASEAADGCS(1)PLWGLSK 188.24 1.07E-14 382380000 871760 774610 773070 973610 648120 822590 851160 775100 399060 TRUE FALSE 830553.6325 853543.6397 808516.0242 875740.8731 761151.9228 794103.502 721299.9094 707228.1349 460944.1867 1.801852928 1.85172883 1.754043217 1.899884842 1.651288691 1.722775826 1.56483134 1.534303188 1 18.81423255 0.536395843 0.452960378 0.94190331 1.844276219 0.947812471 0.058238782 0.351457727 0.139195103 0.092688718 0.030800572 3.438712307 -0.536395843 0.902372908 HPGDFGADAQGAMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPGDFGADAQGAMNK 15 0 B0QYF8;P02144;Q8WVH6 B0QYF8 MB Myoglobin 0 ; 196.33 8.98E-09 216260000 420350 235890 328980 405960 347630 356730 468900 385520 311410 FALSE TRUE 400480.8886 259927.4592 344064.0584 365152.1295 408256.5619 344376.3507 397360.6931 351761.825 359701.8723 1.11336893 0.722619144 0.956525625 1.015152151 1.134985924 0.957393823 1.104694536 0.977926033 1 18.45644214 3.291855887 3.825796576 1.042085914 0.907994821 0.16280155 0.10712391 0.305309452 9.124313343 0.029321167 0.039421054 1958.194773 -3.291855887 -0.134091094 HPGSFDVVHVK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 186.87 2.22E-06 1887620000 3738440 3410710 3369550 3782170 3207280 3498030 3951820 3753900 1394630 FALSE TRUE 3561731.35 3758265.227 3524047.2 3401979.086 3766628.617 3376892.344 3348897.279 3425188.615 1610902.098 2.211016644 2.333019016 2.187623448 2.111847201 2.338210759 2.096274099 2.078895598 2.126254985 1 20.61943739 -1.728622032 0.360562987 1.15E-12 2.261836512 0.958017166 0.078559514 5.188858754 0.334720404 4.576648431 0.055161752 0.018680047 1.728622032 2.261836512 HPHDIIDDINSGAVECPAS ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HPHDIIDDINSGAVECPAS 19 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 218.37 3.38E-19 4096618000 2228216 2183886 2806670 3135600 2746920 2658891 3281130 1411509 109529.7 FALSE TRUE 2122892.646 2406426.466 2935358.596 2820403.531 3225981.978 2566812.938 2780533.356 1287909.789 126515.0065 16.77976949 19.02087771 23.2016634 22.2930355 25.49880894 20.28860457 21.97789364 10.17989743 1 16.94894899 1.035606417 3.099514471 1.082508939 21.03404114 0.890213711 2.407439763 0.075893128 1.62019402 2.567192461 0.676141928 10.85441488 -1.035606417 19.9515322 HPHLSTLSLPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPHLSTLSLPRR 12 1 O95140-2 O95140-2 MFN2 Mitofusin-2 0 ; 68.536 0.084028 726122000 1118610 940910 935570 925640 5040360 387552 999710 367877 3369240 FALSE TRUE 1065735.522 1036789.799 978466.8099 832592.9086 5919397.188 374130.9771 847185.8786 335663.7396 3891724.532 0.273846598 0.266408835 0.251422423 0.213939322 1.521021629 0.09613501 0.217689066 0.086250642 1 21.89197816 HPHVYS(ph)PVIQGNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPHVYSPVIQGNAR 14 0 F8VZC1 F8VZC1 ATXN2 1 HPHVY(0.429)S(0.571)PVIQGNAR;HPHVY(0.426)S(0.574)PVIQGNAR 72.643 0.039917 52205000 7250.3 6214.1 8952.9 7462.4 7640.8 7181.7 9966.4 5000.5 6465.9 TRUE FALSE 6907.592688 6847.323855 9363.399321 6712.265374 8973.353101 6932.995928 8445.842635 4562.629711 7468.598749 0.924884697 0.916815066 1.253702285 0.898731556 1.201477466 0.928286036 1.130847019 0.6109084 1 12.86662188 1.25347043 24.99987163 0.805454025 1.025220554 0.274149705 0.155398573 260.4664337 436738.305 0.094141542 0.034075546 17.925465 -1.25347043 0.21976653 HPIS(ph)RWIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPISRWIAR 9 1 E7EWP0;H0Y886;O43674-2;O43674 E7EWP0 NDUFB5 "NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial" 1 HPIS(1)RWIAR 51.066 0.094898 59395000 77124 93708 69694 84874 33081 88360 59030 71748 24852 TRUE FALSE 73478.50137 103256.9517 72889.53884 76342.30427 38850.31593 85300.07104 50023.88934 65465.36476 28705.92123 2.559698425 3.59706107 2.539181315 2.659461915 1.35339032 2.971514844 1.742633129 2.280552651 1 14.80906074 1.447038315 0.180640102 0.420354433 3.684814068 0.480842825 0.552103619 2.540362975 0.474960489 3.567247725 3.314974778 27.9922827 -1.447038315 3.264459634 HPKGEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPKGEEGSDDDETENGPKPK 20 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 HPKGEEGS(0.987)DDDET(0.013)ENGPKPK;HPKGEEGS(1)DDDETENGPKPK 217.94 5.34E-25 173484000 217765 196652 213146 247153 89162 267913 263508 203344 25037.6 TRUE FALSE 207471.68 216691.0624 222918.9549 222308.7109 104711.8246 258635.1056 223305.0149 185538.1214 28920.30313 7.173910974 7.492696787 7.708043512 7.686942625 3.62070287 8.943028862 7.721392612 6.415497117 1 14.81979505 HPLLSSGGPQS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HPLLSSGGPQSPLR 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR 131.57 3.57E-05 1084140000 1648620 1415420 1540170 1854410 1567530 1679200 1970250 1801470 1670990 TRUE FALSE 1570693 1559652.907 1610788.318 1668001.184 1840906.736 1621048.883 1669652.176 1643723.737 1930118.595 0.813780565 0.808060661 0.834554064 0.864196215 0.953779079 0.839870093 0.865051599 0.851617999 1 20.88025807 -5 0.102208702 1.457922043 0.75420395 0.61584253 0.037800865 123.1459804 0.852216243 12.10714263 0.601348026 1.00E-05 5 -0.703718093 HPLLSSGGPQSPLRGS(ph)TGSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPLLSSGGPQSPLRGSTGSLK 21 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(0.141)PLRGS(0.397)T(0.397)GS(0.065)LK 128.14 1.13E-05 441940000 451950 402720 442440 446380 391170 472760 538320 513360 514540 TRUE FALSE 430587.2192 443757.6259 462726.3116 401509.0343 459389.9242 456388.2027 456189.3971 468407.4769 594332.2353 0.724489088 0.746649095 0.778565059 0.67556328 0.772951385 0.767900806 0.767566304 0.788123963 1 19.18091011 -0.964598022 0.381416335 1.107640823 0.732623354 0.891043553 0.027817664 3.989312989 0.428792792 0.494905247 0.017857437 0.108493065 0.964598022 -0.37501747 HPNGTQETILLNHTFNETQIEWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPNGTQETILLNHTFNETQIEWFR 24 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 332.63 4.04E-87 211460000 109530 87763 94260 96660 97890 94109 104030 97780 61505 FALSE TRUE 104352.734 96706.14948 98581.91424 86943.55316 114961.985 90849.98173 88158.31286 89217.86484 71042.88128 1.468869676 1.361236309 1.387639584 1.223817948 1.618205553 1.278804858 1.240916912 1.255831172 1 16.11640247 0.986947366 0.708328056 1.001531733 1.404255076 0.576504836 0.106460224 0.516540309 0.593043195 0.096622245 0.037832031 9.703923534 -0.986947366 0.402723343 HPNNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HPNNLK 6 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 91.26 0.048095 39244000 69985 82221 61638 86301 55287 69372 67344 81988 50038 FALSE TRUE 66676.94775 90599.41338 64464.16327 77625.85952 64929.0353 66969.63025 57069.43594 74808.69607 57797.63748 1.153627564 1.56752797 1.115342531 1.343062847 1.123385628 1.158691482 0.987400842 1.294321002 1 15.8187229 2.769705872 1.268634922 1.090191731 1.334783715 0.249957913 0.148938065 0.495141536 1.639562226 0.062697054 0.060614809 588.4449933 -2.769705872 0.244591985 HPNYS(ph)PPGS(ph)PIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 HPNY(0.018)S(0.99)PPGS(0.992)PIEK;HPNY(0.024)S(0.986)PPGS(0.989)PIEK;HPNY(0.205)S(0.796)PPGS(0.999)PIEK;HPNY(0.003)S(0.997)PPGS(1)PIEK;HPNY(0.001)S(0.999)PPGS(1)PIEK;HPNY(0.005)S(0.996)PPGS(1)PIEK;HPNY(0.001)S(0.999)PPGS(1)PIEK;HPNY(0.001)S(0.999)PPGS(1)PIEK;HPNYS(1)PPGS(1)PIEK 152.13 2.38E-05 4182250000 4752850 4409120 4482310 5294690 3474120 4945400 5296720 4136640 2251500 TRUE FALSE 4528192.2 4858414.341 4687828.347 4762457.702 4080005.428 4774139.558 4488608.083 3774413.872 2600651.121 1.74117634 1.868153057 1.802559486 1.831255897 1.568839971 1.835747794 1.725955491 1.451334184 1 21.31044144 0.941127529 1.919887019 1.0007899 1.781082728 0.901908275 0.08225589 0.106000319 0.821138687 0.07414101 0.020827993 8.732277508 -0.941127529 0.780292828 HPNYS(ph)PPGSPIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK;HPNYS(0.905)PPGS(0.095)PIEK;HPNYS(1)PPGSPIEK 217.4 1.67E-11 7068450000 4057020 3990280 3939930 4299130 2936410 4549360 4755700 4597330 2297690 TRUE FALSE 3865252.705 4396894.069 4120579.688 3866973.285 3448518.974 4391814.522 4030130.621 4194763.413 2654004.03 1.456385394 1.656702107 1.552589838 1.45703369 1.299364634 1.654788189 1.518509608 1.580541463 1 21.33973913 -1.099034435 4.850379189 0.999979192 1.527724065 0.710647874 0.104619885 7022216.832 1591145.465 1691.161279 0.023593411 0.079609623 1.099034435 0.527744873 HPQHLHQQHHGDAAQHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPQHLHQQHHGDAAQHTR 18 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ; 101.54 0.00019873 29278000 6129.09 9249.44 11201.7 13835.1 10545.7 8884.9 7351 5068.4 4905.9 FALSE TRUE 5839.380062 10191.96845 11715.30902 12444.36946 12384.86674 8577.213685 6229.46994 4624.584027 5666.681916 1.030476061 1.798577828 2.067401911 2.19605929 2.185558837 1.513621871 1.099315266 0.816100867 1 12.46828851 1.767777816 2.727738577 0.929269578 1.7985383 0.58749823 0.335764382 0.213689454 3.173322284 0.225225097 0.105366482 58.58383747 -1.767777816 0.869268722 HPQPFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPQPFLR 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 74.415 0.046243 213026000 61014 52815 46909 69644 45588 56184 59482 55584 50163 FALSE TRUE 58129.98914 58196.90855 49059.82405 62643.25281 53538.53277 54238.33399 50406.92844 50716.77029 57942.02184 1.003244058 1.004398996 0.846705422 1.081136813 0.924001805 0.936079416 0.8699546 0.875302046 1 15.82232241 2.501728604 24.65576115 0.909188452 0.983899254 0.168930924 0.067271586 900.096182 901866.2471 0.020139584 0.018896292 317.4889421 -2.501728604 0.074710802 HPSKPDPSGECNPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HPSKPDPSGECNPDLR 16 1 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;; 183.74 1.16E-09 936140000 1009250 890970 876700 1142670 1022340 894900 1199050 1123180 1006090 FALSE TRUE 961544.7526 981760.8559 916897.5622 1027806.641 1200635.772 863909.3886 1016112.9 1024828.405 1162109.299 0.827413354 0.844809397 0.788994256 0.884431991 1.033152195 0.743397708 0.874369478 0.881869206 1 20.14831433 -5 0.194311718 1.62900519 0.831006203 0.272005738 0.074526158 187.1439668 1.840118842 45.65957144 0.181265211 1.00E-05 5 -0.797998986 HPTGNSITKS(ph)PPLMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HPTGNSITKSPPLMAK 16 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HPTGNSITKS(1)PPLMAK;HPTGNSITKS(1)PPLMAK;HPTGNSIT(0.001)KS(0.999)PPLMAK 243.23 3.30E-20 1772250000 3195350 2118870 2955190 3218830 2552530 3234480 4200430 3698710 2497130 TRUE FALSE 3044312.138 2334785.262 3090688.385 2895267.093 2997690.424 3122469.147 3559577.257 3374831.344 2884372.167 1.055450532 0.809460474 1.071528986 1.003777226 1.039286975 1.082547246 1.234090836 1.170040185 1 21.45982589 2.552122408 1.19703193 1.156607581 0.953282268 0.311369919 0.092751046 0.410159667 1.195446851 0.04763727 0.036880331 356.5516149 -2.552122408 -0.203325313 HPTLLQDPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HPTLLQDPDLR 11 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ;;; 150.06 3.41E-05 1243330000 506242 439133 412085 553584 513691 420058 545955 508845 480330 FALSE TRUE 482312.9439 483881.152 430979.5049 497936.6846 603278.5478 405511.2861 462659.5376 464287.8342 554817.1232 0.869318779 0.87214531 0.776795609 0.897478942 1.087346663 0.7308918 0.833895563 0.836830398 1 19.08165279 -2.442493737 2.129477792 2.213459103 0.861441125 0.175677605 0.093143327 3769295.881 456623.0333 21915803.72 0.021507716 0.003609992 2.442493737 -1.352017978 HPVSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HPVSCK 6 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;;; 106.76 0.031846 595299000 1948303 1778481 1282795 1698677 1130018 1230411 1320747 1637615 999830 FALSE TRUE 1856210.578 1959710.236 1341612.42 1527922.761 1327092.781 1187801.559 1119242.788 1494216.749 1154878.53 1.607277761 1.69689728 1.161691368 1.323015989 1.149118931 1.028507785 0.969143299 1.293830226 1 20.13930969 3.537466425 1.178546535 1.075138631 1.685679037 0.722057682 0.129494096 0.213813279 0.598357942 0.042908875 0.093328527 3447.199551 -3.537466425 0.610540405 HPVSCKDTPGFIVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPVSCKDTPGFIVNR 15 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 96.993 0.0020943 731160000 867430 506450 755870 737350 662280 721350 943180 842900 667330 FALSE TRUE 826428.303 558057.8308 790527.3872 663230.1771 777781.4223 696369.4686 799280.5683 769091.2075 770816.1282 1.072147134 0.723983075 1.025571934 0.860425921 1.009036259 0.903418394 1.036927666 0.997762215 1 19.55602723 2.144584976 1.075989748 1.012952568 0.91123507 0.089956395 0.099053311 0.995660832 2.163659039 0.067506133 0.035140213 139.503459 -2.144584976 -0.101717498 HPWDDISYVLPEHMS(ph)M ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 HPWDDISYVLPEHMS(1)M;HPWDDISYVLPEHMS(1)M 94.922 0.0025301 28631000 43118 40374 46304 42078 48078 42028 52002 41871 19989.5 TRUE FALSE 41079.89759 44488.1565 48427.0842 37848.2395 56462.78798 40572.55982 44068.13982 38204.55327 23089.36957 1.779169304 1.92678091 2.097375767 1.639206276 2.44540189 1.757196519 1.908589998 1.654638216 1 14.49494116 0.761318192 1.491757042 1.000214853 1.938508598 0.648215239 0.218558551 0.471482099 1.790600655 0.184481893 0.053842147 5.771891941 -0.761318192 0.938293744 HPWDDISYVLPEHMSM ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;;;;; 169.04 5.76E-09 577044000 629605 487597 554399 641131 894852 537005 842551 669203 508210 FALSE TRUE 599844.8194 537283.6887 579818.7425 576683.2938 1050913.905 518408.3822 714004.3704 610604.0377 587020.6112 1.021846266 0.915272272 0.987731489 0.982390197 1.790250437 0.883117854 1.216319081 1.040174784 1 19.16305163 2.949254842 24.99987525 1.196384989 0.970883923 0.156722073 0.240405256 587.1711271 289272.6466 0.067114478 0.071186528 889.7230493 -2.949254842 -0.225501066 HQAS(ph)DS(ph)ENEELPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;HQAS(1)DS(1)ENEELPKPR 98.684 0.0016122 1432490000 2557710 2646380 2526130 3253240 1532170 2926920 2753660 1608320 543063 TRUE FALSE 2436812.117 2916049.131 2641955.559 2926218.134 1799379.963 2825560.026 2333538.593 1467486.975 627278.4365 3.884737583 4.648731666 4.211774876 4.664942973 2.868550644 4.504474986 3.720100129 2.339450696 1 19.25874644 1.081671235 1.968777269 1.006640836 4.158922519 0.807427187 0.514497959 0.119235035 0.918204646 0.447776904 0.126933466 12.06899855 -1.081671235 3.152281683 HQAS(ph)INELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HQASINELKR 10 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR 103.14 0.0017483 2294780000 2380430 2038980 2110930 2773860 1845580 2469030 2797190 2240840 1253490 TRUE FALSE 2267911.791 2246754.38 2207718.228 2495026.323 2167448.568 2383526.872 2370427.292 2044620.17 1447874.827 1.566372831 1.551760095 1.524799097 1.723233442 1.496986153 1.646224402 1.637176949 1.412152578 1 20.46550545 0.899707958 3.498813799 1.000305834 1.589526027 0.891098792 0.065547354 0.120963927 3.232360263 0.059076508 0.015259839 7.937942675 -0.899707958 0.589220193 HQAVQLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQAVQLPR 8 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ; 95.741 0.0094349 293270000 120544 108754 76783 102987 177149 93419 143279 111634 151260 FALSE TRUE 114846.124 119836.1562 80303.5765 92634.5511 208043.7295 90183.87661 121419.1571 101858.7352 174716.6283 0.657327955 0.685888673 0.45962183 0.530198825 1.190749453 0.516172258 0.694949063 0.582993938 1 17.41465739 HQDDLQDVIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQDDLQDVIGR 11 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;E5RID7 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ; 207.47 2.29E-08 350130000 455190 395820 382990 486470 462980 399740 500840 429490 340290 FALSE TRUE 433674.0708 436154.508 400550.4703 437569.1114 543723.5654 385896.9036 424427.6594 391881.5787 393060.4352 1.103326695 1.109637269 1.019055683 1.113236215 1.383307799 0.981774987 1.079802548 0.997000826 1 18.58439163 HQEGEIFDTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQEGEIFDTEK 11 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 168.98 1.74E-05 1102150000 4241600 4807200 3511600 5126900 2429200 4497400 4106900 4225700 1348900 FALSE TRUE 4041107.974 5297059.145 3672610.333 4611534.272 2852851.711 4341653.91 3480316.977 3855675.306 1558080.523 2.593645139 3.399733883 2.357137696 2.959753494 1.831004027 2.786540135 2.233720867 2.474631606 1 20.57133836 -0.781424274 0.220893573 4.00E-11 3.069398562 0.62519692 0.398767126 8.723845871 0.490824443 6.749473668 0.862377382 0.165415319 0.781424274 3.069398562 HQEGEIFDTEKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 220.21 1.27E-11 722110000 1657780 1538400 1463110 1846320 771000 1821100 1628170 1757900 487910 FALSE TRUE 1579420.025 1695164.709 1530195.041 1660724.406 905462.1559 1758034.85 1379762.763 1603968.957 563572.5909 2.802513909 3.007890619 2.715169377 2.94677994 1.6066469 3.11944704 2.4482432 2.846073394 1 19.10424192 HQEGEIFDTEKEKYEITEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HQEGEIFDTEKEKYEITEQR 20 2 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 247.55 2.30E-30 3516040000 4913450 3417280 4909200 4847070 3229290 5397040 6562650 5502730 2040990 FALSE TRUE 4681200.956 3765504.717 5134291.676 4359833.315 3792477.154 5210139.152 5561397.211 5020881.789 2357496.305 1.985666296 1.597247346 2.177857783 1.849348949 1.608688482 2.210030675 2.359026904 2.129751711 1 21.16882408 3.737879507 24.99804071 1.987490926 1.791456835 0 0.402380155 209.7541312 7698472.864 0.098801781 0.163532871 5468.642175 -3.737879507 -0.196034091 HQEVQDQDPVFQGSDSSGYQS(ph)DHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HQEVQDQDPVFQGSDSSGYQSDHKK 25 1 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 HQEVQDQDPVFQGS(0.025)DS(0.022)S(0.119)GY(0.249)QS(0.585)DHKK 67.283 0.020577 102490000 102570 76511 87222 114580 52227 99773 112620 105580 48124 TRUE FALSE 97721.71937 84307.55789 91221.21497 103062.2007 61335.37226 96317.83599 95437.75059 96334.85549 55586.82414 1.758001485 1.516682401 1.641058225 1.854076075 1.10341566 1.732745799 1.716913173 1.733051977 1 15.76245534 -1.913372343 2.610543025 0.625002971 1.631217672 0.479393901 0.206976124 10159676.2 5101553.025 23274403.12 0.046618959 0.012207526 1.913372343 1.006214702 HQGVMVGMGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 26 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 ;;;;;;;;;;;;;;;;;;;;;;;;; 164.64 1.71E-05 41545820000 76800350 65376370 62577920 71604740 55229520 68120820 83456510 74257820 49798740 FALSE TRUE 73170149.66 72038296.43 65447179.53 64406895.5 64861530.8 65761778.92 70723686.62 67755411.62 57521274.26 1.272053698 1.252376575 1.13779085 1.119705645 1.127609422 1.14326012 1.229522251 1.17791917 1 25.7775923 -5 0.027902611 6.20E-10 1.903087012 0.55395953 0.052325211 1434.275348 3.015751965 155.582434 67.13774368 1.00E-05 5 1.903087011 HQHMHDRDDLYAEQMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 HQHMHDRDDLYAEQMER 17 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;;;;;;;;;;;;;;;;; 162.37 2.23E-09 6665070000 4695293.6 6185643.7 6033638 7580325 5689997.5 6404351 7476501 4915306.9 2084664.4 FALSE TRUE 4473356.377 6815967.826 6310286.27 6818336.329 6682331.262 6182566.719 6335823.457 4484896.57 2407943.508 1.857749719 2.830617829 2.620612256 2.83160145 2.775119615 2.567571331 2.631217649 1.862542271 1 21.19937012 0.982503982 2.824782935 1.003481646 2.582870248 0.777184892 0.278921949 0.12250056 2.326964559 0.27052706 0.071810213 9.605146242 -0.982503982 1.579388602 HQIVEVAGDDKYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQIVEVAGDDKYGR 14 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 132.44 3.03E-05 853280000 1127210 1114150 1025450 1286500 803440 1117250 1216560 1160720 591100 FALSE TRUE 1073929.017 1227683.152 1072467.897 1157178.576 943559.6816 1078559.352 1030951.428 1059081.203 682764.7691 1.572912174 1.798105595 1.570772168 1.694842248 1.381968907 1.579693917 1.509965767 1.551165572 1 19.38102909 -2.758886957 0.209140563 1.28E-12 1.71116954 0.776498228 0.100575669 20.93859587 0.483050129 9.654405488 0.216464934 0.00174226 2.758886957 1.71116954 HQKPVLTGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQKPVLTGQR 10 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 147.91 1.57E-05 587110000 1015270 832360 590730 755220 893240 776380 1130340 914050 638860 FALSE TRUE 967280.1992 917178.4303 617815.5548 679303.8508 1049020.773 749493.7659 957885.8729 834010.9363 737931.146 1.310800072 1.242905162 0.83722656 0.920551808 1.421569992 1.015668969 1.298069445 1.130201565 1 19.49312668 7.054023061 0.013865801 7.41E-07 2.480530474 0.039335445 0.184309296 22126.18806 27.78042056 2082.15732 2956.452824 11324604.94 -7.054023061 2.480529732 HQLEETKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HQLEETKK 8 1 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 83.948 0.011555 40033000 221800 223640 176290 267910 169570 243320 198620 254370 174170 FALSE TRUE 211315.9536 246429.1703 184373.0709 240979.1778 199142.9543 234893.7674 168316.8711 232096.0143 201179.3941 1.050385675 1.22492252 0.916461011 1.197832307 0.989877493 1.167583631 0.836650651 1.153676873 1 17.61812302 1.764689392 25 0.980981784 1.096957723 0.115860074 0.11961497 27.35560579 26190.82268 0.049026933 0.027190369 58.16870451 -1.764689392 0.115975939 HQNVQLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HQNVQLPR 8 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45;A0A087WUW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;; 130.27 0.001055 2314579000 945608 714263 638572 774848 948624 792667 1067708 885657 879867 FALSE TRUE 900910.9839 787047.2117 667851.1578 696958.8069 1114063.725 765216.743 904809.5348 808104.1779 1016312.281 0.886450947 0.774414741 0.657131839 0.685772297 1.096182489 0.752934662 0.890286925 0.795133733 1 19.95491233 HQPST(ph)PDPFLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HQPSTPDPFLKPR 13 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 HQPS(0.144)T(0.856)PDPFLKPR;HQPST(1)PDPFLKPR;HQPS(0.152)T(0.848)PDPFLKPR;HQPS(0.171)T(0.829)PDPFLKPR 130.06 0.00021474 977030000 1156830 1071130 1121350 1315550 930430 1188730 1330170 1182840 684171 TRUE FALSE 1102148.939 1180279.365 1172765.007 1183308.415 1092696.697 1147563.982 1127228.136 1079264.259 790268.7444 1.394650802 1.493516444 1.484007833 1.49734938 1.382690009 1.45211865 1.426385827 1.365692705 1 19.59198382 0.208044632 0.809135119 0.992469641 1.456689846 0.932953717 0.037523455 0.750811633 0.584015896 0.048538798 0.012142992 1.614524473 -0.208044632 0.464220206 HQPTAIIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HQPTAIIAK 9 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;; 130.98 0.00034591 2287300000 3694100 2571940 2163870 2456480 2756470 2284790 3692400 2723710 1949820 FALSE TRUE 3519487.214 2834023.61 2263085.58 2209549.963 3237197.495 2205667.149 3129056.564 2485207.513 2252188.127 1.562696815 1.25834231 1.004838607 0.981068116 1.437356612 0.979344098 1.389340671 1.103463553 1 21.10289591 4.322235575 2.275537257 1.155341225 1.545806213 0.392827524 0.166392826 0.313456268 3.006378309 0.040230751 0.170886223 21000.78722 -4.322235575 0.390464988 HQPWQS(ph)PERPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(1)PERPLSR;HQPWQS(1)PERPLSR 164.93 2.19E-05 3632230000 1319800 1342320 1106908 1624360 1207874 1295690 1407589 1210472 834776 TRUE FALSE 1257415.67 1479103.934 1157660.827 1461076.247 1418526.843 1250819.93 1192835.446 1104476.655 964228.7986 1.304063591 1.533976102 1.200608018 1.515279619 1.471151707 1.297223161 1.237087554 1.145450806 1 19.87901599 1.369541954 1.131648345 1.012094142 1.408015607 0.644313331 0.101001804 0.257351458 0.652546427 0.085911146 0.029113591 23.41757686 -1.369541954 0.395921465 HQQQLLAS(ph)PGSSTVDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HQQQLLASPGSSTVDNK 17 0 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 HQQQLLAS(0.997)PGS(0.003)STVDNK 186.92 3.19E-10 303000000 197140 194690 219030 232420 150130 245350 239220 209750 143830 TRUE FALSE 187821.5829 214529.1323 229072.7422 209056.7 176312.6245 236853.468 202722.5954 191383.178 166134.4218 1.130539841 1.291298516 1.378839735 1.25835873 1.061264863 1.425673653 1.220232347 1.151977874 1 17.34199149 0.962944577 2.508554715 1.001463224 1.253568288 0.376792499 0.105221489 0.318527967 4.58818863 0.094667866 0.025520988 9.182154104 -0.962944577 0.252105064 HQS(ph)FGAAVLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HQSFGAAVLSR 11 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR 156.11 2.01E-05 5896130000 2860780 2145000 2290740 2421040 2627350 2337540 2976510 2326820 1653200 TRUE FALSE 2725556.599 2363577.939 2395772.695 2177672.46 3085559.008 2256590.404 2522388.732 2123071.306 1909569.813 1.427314456 1.237754139 1.254613829 1.1403995 1.615839854 1.181727104 1.320919882 1.111806068 1 20.86481623 1.089400478 2.505373955 0.99863491 1.311511946 0.396607214 0.134186104 0.251905061 3.136423173 0.115184389 0.031514162 12.28571618 -1.089400478 0.312877036 HQTLEVSLSRDS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HQTLEVSLSRDSPLK 15 1 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 HQTLEVSLS(0.215)RDS(0.784)PLK;HQTLEVSLS(0.01)RDS(0.99)PLK;HQTLEVSLS(0.001)RDS(0.999)PLK 211.96 6.75E-10 376988000 1120280 1126640 1121070 1350790 775290 1275280 1351230 1414430 598160 TRUE FALSE 1067326.585 1241445.897 1172472.168 1215006.023 910500.3305 1231116.734 1145075.046 1290575.011 690919.5978 1.544791301 1.796802263 1.696973385 1.758534606 1.317809385 1.781852386 1.657320258 1.86790911 1 19.39815831 -0.636655114 6.255051951 0.999999998 1.675982335 0.654269509 0.154827694 4.04E-09 6.46E-10 0.135631771 0.031968715 0.230857977 0.636655114 0.675982337 HQVLFIADEIQTGLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HQVLFIADEIQTGLAR 16 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 200.58 3.52E-11 130880000 219030 215110 222310 213290 189930 194300 213310 226800 122580 FALSE TRUE 208676.886 237029.9536 232503.1334 191849.684 223053.7319 187571.3423 180765.6418 206940.1897 141589.0803 1.473820477 1.674069448 1.642097913 1.35497514 1.575359705 1.324758532 1.276691969 1.461554727 1 17.11135048 0.874068304 0.303702391 0.929671876 1.632273272 0.673027057 0.113225558 1.212669253 0.316882802 0.300091355 0.154643528 7.482871786 -0.874068304 0.702601396 HQYYNQEWTLWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 222.1 1.80E-11 453350000 379680 586220 339210 485570 323330 389190 343620 414970 206919 FALSE TRUE 361733.2789 645956.4845 354763.114 436759.5811 379718.6496 375712.2527 291194.458 378633.0269 239006.9417 1.513484404 2.702668298 1.484321382 1.82739287 1.588734816 1.571972136 1.218351467 1.584192594 1 17.86669299 2.375769882 0.595716007 1.153735979 2.071080482 0.369572619 0.35452713 0.75281199 0.540625776 0.295609264 0.241103371 237.5581212 -2.375769882 0.917344503 HRAEAPPLEREDS(ph)GTFSLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRAEAPPLEREDSGTFSLGK 20 2 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 HRAEAPPLEREDS(0.942)GT(0.058)FSLGK 258.09 1.59E-36 301280000 692480 387880 678970 634420 624640 745330 1034200 721070 431490 TRUE FALSE 659747.8428 427405.413 710101.4461 570646.8963 733577.0182 719519.0352 876413.7956 657929.2882 498403.2655 1.323722954 0.857549383 1.424752796 1.144950155 1.471854358 1.443648317 1.758443125 1.320074192 1 18.926954 2.942944808 1.490133371 1.479609779 1.12497843 0.085990281 0.244044001 0.487216358 2.210583332 0.086723848 0.098467273 876.8893757 -2.942944808 -0.354631349 HRDILQDYTHEFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRDILQDYTHEFHK 14 1 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 83.633 0.0028419 114250000 65801 51132 60196 72942 89380 70773 89854 63976 33729 FALSE TRUE 62690.71714 56342.40893 62956.04614 65609.73158 104967.8437 68322.11326 76145.12202 58373.92228 38959.52106 1.609124431 1.446178172 1.615934807 1.68404872 2.694279623 1.753669229 1.95446761 1.498322379 1 15.24968832 0.953279562 4.77429107 1.000350112 1.791664213 0.376830303 0.339710817 0.281123689 20.10695724 0.33681944 0.085328691 8.980066688 -0.953279562 0.791314102 HRDLLHNEDRHDDYFQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HRDLLHNEDRHDDYFQER 18 2 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ;;;;;;; 217.42 5.06E-19 948416000 433592 256992.8 498826 397259 617857 416556 654978 339509 177936.7 FALSE TRUE 413096.9655 283180.6585 521697.6655 357325.7706 725611.0652 402130.5613 555049.0766 309779.7921 205530.2147 2.009908695 1.377805492 2.538301565 1.738555916 3.530435009 1.956552042 2.700571678 1.507222637 1 17.64899097 3.735997741 24.99295368 2.264237104 1.693857095 0.041140826 0.715767724 439.7200161 4288123.886 0.166801717 0.272067144 5444.998205 -3.735997741 -0.570380008 HRDLVDEDLSHFQS(ph)GSPPAPNGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRDLVDEDLSHFQSGSPPAPNGFK 24 1 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 HRDLVDEDLS(0.105)HFQS(0.496)GS(0.399)PPAPNGFK 52.721 0.072221 184350000 98156 69372 89446 82005 90039 102180 135240 116350 66409 TRUE FALSE 93516.36041 76441.08567 93547.18757 73761.7016 105741.7731 98641.48098 114606.6541 106161.7772 76707.36855 1.219131384 0.996528588 1.219533264 0.961598644 1.378508676 1.285945312 1.494076206 1.383984084 1 16.22707755 2.721622994 24.9025754 1.349536201 1.102097634 0.299922269 0.151844243 731.3418223 1075255.51 0.043965473 0.041549638 526.7723779 -2.721622994 -0.247438567 HRDTHPGS(ph)PGSPGPALRPLPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDT(0.006)HPGS(0.882)PGS(0.112)PGPALRPLPAR;HRDTHPGS(0.953)PGS(0.047)PGPALRPLPAR;HRDTHPGS(0.842)PGS(0.157)PGPALRPLPAR 137.62 1.29E-06 397570000 234748 195993 224509 264754 266931 230091 311528 237094 60738 TRUE FALSE 223651.9273 215964.9095 234802.9597 238140.4249 313483.6819 222122.891 263998.682 216332.7924 70156.93883 3.187880358 3.07831147 3.346824471 3.394395891 4.468320413 3.166085845 3.76297322 3.083555184 1 16.09829818 3.67695836 5.946057242 3.373863711 3.133445616 0 0.889370754 1.255412103 91.19933978 0.20795279 0.327221106 4752.896535 -3.67695836 -0.240418096 HRDTHPGSPGS(ph)PGPALRPLPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDT(0.001)HPGS(0.156)PGS(0.843)PGPALRPLPAR 73.109 0.0069098 98775000 57849 41309 46331 57154 54661 52978 68144 54895 15212 TRUE FALSE 55114.59242 45518.43406 48455.32218 51408.77133 64193.86109 51143.35858 57747.38125 50088.10278 17570.99927 3.136679455 2.590543279 2.757687337 2.925773916 3.653398427 2.910668756 3.286516627 2.850612081 1 14.10090862 4.752964333 22.5606148 2.883121548 3.136680067 0 0.699775484 273.0185673 2077034.583 0.144022695 0.992376965 56619.27879 -4.752964333 0.253558519 HRDYETATLSDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ; 111.39 0.00059097 704640000 1697980 1020520 1133480 1501190 1633700 1120100 2014010 1394570 1830580 FALSE TRUE 1617719.85 1124512.148 1185451.179 1350287.529 1918616.763 1081310.656 1706735.785 1272454.058 2114456.997 0.765075787 0.53182077 0.56064095 0.638597773 0.907380365 0.511389287 0.807174507 0.601787627 1 21.01185579 -5 0.244133151 2.969408475 0.632984287 0.397588695 0.128152441 169.8088899 1.68930415 166.2174057 0.177062188 1.00E-05 5 -2.336424189 HREELEQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HREELEQLK 9 1 A0A087X0W9;Q8N6M0;A0A0C4DH76 A0A087X0W9 OTUD6B OTU domain-containing protein 6B 0 66.435 0.038297 121380000 126840 97268 96570 123360 89407 114320 138720 122700 70879 FALSE TRUE 120844.5246 107179.7198 100997.83 110959.6184 104999.5525 110361.0697 117555.7162 111955.7375 81870.55332 1.476043824 1.30913638 1.233628282 1.355305588 1.282506936 1.347994673 1.435872991 1.367472589 1 16.32105703 -1.076710697 3.740279783 0.999876768 1.355180441 0.715449768 0.069520911 7017227.696 10783711.39 10365.40558 0.017087165 0.083808738 1.076710697 0.355303673 HREQEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HREQEELRR 9 2 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 82.029 0.01103 24913000 32112 27393 32242 36988 33263 31646 37874 33965 28747 FALSE TRUE 30594.1294 30184.37784 33720.32759 33269.89597 39064.05667 30550.09108 32095.6257 30990.84454 33204.93794 0.921372883 0.909032804 1.015521476 1.001956276 1.176453235 0.920046625 0.966591949 0.933320357 1 15.01911018 3.742166705 24.64437334 1.000639581 0.915202837 0.212386793 0.069439453 372.2532308 2544003.605 0.018021369 0.030881635 5522.893966 -3.742166705 -0.085436744 HRGS(ph)ADYSMEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 125.98 0.00044855 70309000 117150 104020 108370 128890 87435 107690 141960 112040 53649 TRUE FALSE 111612.5517 114619.7563 113338.8717 115933.7323 102683.6363 103960.6683 120301.3947 102229.1836 61968.61292 1.801114248 1.849642115 1.828972222 1.870846012 1.657026541 1.677634264 1.94132786 1.649692947 1 15.91925006 0.910917918 6.930064226 1.000004067 1.806358595 0.899153892 0.084118726 0.447868901 34.74853859 0.079160423 0.019855381 8.145503186 -0.910917918 0.806354528 HRGS(ph)EEDPLLSPVETWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 HRGS(1)EEDPLLSPVETWK 136.56 5.99E-06 36697000 139340 107580 122720 151610 105710 118510 125990 88707 38570 TRUE FALSE 132753.6743 118542.5243 128346.8334 136369.8748 124145.7905 114405.969 106767.9115 80939.34481 44551.23861 2.97979761 2.660813212 2.880881371 3.06096708 2.78658449 2.567963822 2.396519488 1.816769799 1 15.44317792 1.085923167 0.986607666 0.997200251 2.86800615 0.966903574 0.113716708 0.086922687 0.182557149 0.107955089 0.036502083 12.18773962 -1.085923167 1.870805899 HRHPLDHDCSGEGHPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRHPLDHDCSGEGHPTSR 18 1 A0A087X0D9;E9PFU9;Q8WV99;B8ZZ56;E7EV05;B4DEN4;Q8WV99-2 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 0 64.83 0.011591 12952000 9978.1 9301.8 11118 9552.6 11167 10658 13013 7797.7 3079.9 FALSE TRUE 9506.454988 10249.664 11627.7713 8592.354499 13114.52126 10288.91079 11027.62785 7114.89205 3557.515162 2.672217701 2.881130095 3.268509273 2.415268553 3.686427371 2.892162175 3.099811905 1.999961132 1 11.79665419 1.006003095 3.158245964 1.005849566 2.972135397 0.788858106 0.341507916 0.091416021 2.189062122 0.297563109 0.07799518 10.13918612 -1.006003095 1.96628583 HRHS(ph)PTGPPGFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.874)PT(0.126)GPPGFPR;HRHS(0.872)PT(0.128)GPPGFPR;HRHS(0.878)PT(0.122)GPPGFPR;HRHS(0.877)PT(0.123)GPPGFPR;HRHS(0.718)PT(0.282)GPPGFPR;HRHS(0.5)PT(0.5)GPPGFPR;HRHS(0.5)PT(0.5)GPPGFPR 111.43 0.00059184 4410680000 980106 960111 1009806 1112427 1018312 1051011 1225714 900770 318969 TRUE FALSE 933778.3318 1057947.402 1056106.604 1000603.724 1195905.29 1014614.226 1038708.818 821893.8035 368433.0835 2.534458423 2.871477753 2.866481463 2.715835709 3.245922649 2.75386297 2.819260442 2.230781763 1 18.49104309 0.864906734 2.183943977 1.001000975 2.828455956 0.913833499 0.178638891 0.133459481 1.250985895 0.165198326 0.045228492 7.326671745 -0.864906734 1.827454982 HRHSPT(ph)GPPGFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.381)PT(0.619)GPPGFPR;HRHS(0.386)PT(0.614)GPPGFPR;HRHS(0.386)PT(0.614)GPPGFPR 102.66 0.0024508 876530000 311941 336986 329075 388944 388119 317852 393628 244279 154654 TRUE FALSE 297196.1671 371325.2565 344163.4142 349846.6102 455806.8307 306844.7055 333572.8191 222888.6358 178636.9525 1.663688073 2.078658706 1.926608182 1.958422406 2.55158199 1.717700069 1.867322603 1.24771853 1 17.44667102 1.193294786 1.938571097 0.988773356 1.987736241 0.69172713 0.238064645 0.1729597 1.166161262 0.211786696 0.061278018 15.6061144 -1.193294786 0.998962885 HRLDLGEDYPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRLDLGEDYPSGK 13 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 89.959 0.0043324 1021680000 690210 589890 617540 766620 559230 628620 800420 759970 494970 FALSE TRUE 657585.1412 650000.4616 645854.8198 689557.9011 656759.5349 606850.7318 678301.2283 693422.9979 571727.4196 1.150172475 1.136906224 1.129655143 1.206095558 1.148728419 1.061433667 1.186406677 1.212855942 1 19.12496796 2.452775236 24.99686173 1.13056155 1.153201593 0.065336991 0.062665735 1010.752267 1037767.695 0.020215593 0.016914404 283.6450678 -2.452775236 0.022640043 HRLVNACLAEELPHIHAFEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRLVNACLAEELPHIHAFEQK 21 1 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 130.85 4.77E-06 109370000 129590 132210 208360 177870 148190 193280 293450 98486 13075 FALSE TRUE 123464.5375 145682.3493 217913.5121 159990.1697 174034.2891 186586.6651 248678.8129 89862.04373 15102.60422 8.175049528 9.646174075 14.42886994 10.59354846 11.52346221 12.35460205 16.46595576 5.950102539 1 13.88250972 1.009431339 7.065243327 1.003102482 11.6933711 0.715203996 2.322752103 0.069597416 19.28798482 2.51361323 0.630349694 10.21953979 -1.009431339 10.69026861 HRNLS(ph)STTDDEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRNLSSTTDDEAPR 14 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 HRNLS(0.441)S(0.441)T(0.095)T(0.023)DDEAPR;HRNLS(0.968)S(0.023)T(0.004)T(0.005)DDEAPR 100.02 0.0011804 310190000 149913 92077 162536 118813 201517 130079 208730 138722 155136 TRUE FALSE 142826.9096 101459.751 169988.4364 106869.6915 236661.501 125574.3316 176884.4049 126574.7663 179193.6986 0.797053193 0.566201556 0.948629543 0.596392018 1.320702139 0.700774261 0.987112864 0.70635724 1 17.45116038 HRNWYIQATCATSGDGLYEGLDWLANQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRNWYIQATCATSGDGLYEGLDWLANQLK 29 1 P61204;P61204-2;H0YGG7 P61204 ARF3 ADP-ribosylation factor 3 0 ; 241.05 1.19E-45 301370000 261630 197082 248080 245920 198255 260550 341050 281760 151315 FALSE TRUE 249263.2684 217164.8799 259454.7134 221199.6544 232830.6092 251527.0882 289016.5587 257087.6007 174780.1574 1.426153129 1.242503057 1.484463209 1.265587912 1.332134109 1.439105514 1.653600517 1.470919837 1 17.41518188 2.157913814 5.410974956 1.470197587 1.344821334 0 0.18198486 0.476379561 23.66129492 0.062381044 0.045880025 143.8513078 -2.157913814 -0.125376253 HRNWYIQATCATSGDGLYEGLDWLSNQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRNWYIQATCATSGDGLYEGLDWLSNQLR 29 1 P84077 P84077 ARF1 ADP-ribosylation factor 1 0 ; 325.32 2.09E-93 591850000 363210 178204 382750 259080 481200 314320 616120 382960 402370 FALSE TRUE 346041.7831 196363.1902 400299.4661 233036.7862 565121.1276 303435.0196 522119.5782 349425.9922 464767.4846 0.744548176 0.422497693 0.86128974 0.501405098 1.215922254 0.652874888 1.12339954 0.751829686 1 18.82614961 2.755939393 24.97559072 0.945549479 0.622616735 0.383101331 0.199291737 750.9473434 1079209.108 0.053526642 0.056655113 570.0847105 -2.755939393 -0.322932744 HRPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRPDGK 6 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 69.432 0.085289 4157900 16337 18840 13565 24311 12730 15752 17248 21210 13203 FALSE TRUE 15564.78239 20759.81742 14186.96867 21867.21209 14950.10797 15206.50429 14616.50082 19352.73996 15250.45381 1.020611097 1.361258995 0.930265345 1.433872878 0.980305777 0.99711815 0.958430549 1.268994366 1 13.89656455 HRPELIEYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRPELIEYDK 10 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 120.09 0.00036402 151450000 316750 258450 121510 185300 220360 150870 267060 173610 117660 FALSE TRUE 301777.8552 284786.3488 127081.3537 166673.292 258790.7142 145645.3341 226315.0921 158407.788 135906.1119 2.22048774 2.095463882 0.935067246 1.226385551 1.904187462 1.0716614 1.665231158 1.165567802 1 17.05225081 3.828506223 7.005989005 1.339581747 2.168678676 0.58757306 0.302624667 0.160891756 10.79170178 0.07200248 0.130595914 6737.615501 -3.828506223 0.829096929 HRPELIEYDKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HRPELIEYDKLR 12 2 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 109.22 0.00097374 287920000 992470 542450 345500 467500 887270 450310 1074810 558130 434210 FALSE TRUE 945557.91 597726.2717 361341.5167 420506.0118 1042009.607 434715.6518 910827.9943 509257.1784 501545.0692 1.885290013 1.19176981 0.720456723 0.838421186 2.077599145 0.866752917 1.816044161 1.015376702 1 18.93601982 1.053625319 24.99772814 0.999966905 1.353735162 0.081657134 0.465502572 201.8897941 94111.0377 0.422708423 0.105677106 11.31423823 -1.053625319 0.353768257 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR 36 2 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;; 334.91 2.48E-129 1888919000 2352280 1669760 2155780 2165530 1943770 2124840 2838770 2138770 1458580 FALSE TRUE 2241092.386 1839910.442 2254624.645 1947846.81 2282762.873 2051256.258 2405663.499 1951487.96 1684769.137 1.330207408 1.092084608 1.338239522 1.156150577 1.354941055 1.217529579 1.427889107 1.158311793 1 20.68411948 0.993443798 24.67135739 0.999999983 1.267395724 0.44732349 0.09887285 188.8043876 710485.1086 0.090758928 0.022689732 9.850171629 -0.993443798 0.267395741 HRPS(ph)PPAT(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_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 118.31 0.0014657 11512850000 7576580 6291940 6774950 7839770 5324560 7385260 8444100 6510220 3961960 TRUE FALSE 7218450.079 6933095.839 7085588.159 7051701.425 6253161.578 7129506.594 7155797.458 5940150.624 4576360.522 1.577334225 1.514980257 1.548302002 1.540897268 1.36640493 1.557898806 1.563643735 1.298007575 1 22.12576928 0.972493755 3.25588197 1.001080215 1.525951112 0.88984876 0.060062291 0.070745711 1.913479967 0.056493268 0.014727905 9.386285387 -0.972493755 0.524870897 HRPS(ph)PPATPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HRPS(0.994)PPAT(0.006)PPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK 142.91 3.74E-05 879220000 1974870 1719050 1820980 2061670 1438904 1931630 2114660 1875910 1000570 TRUE FALSE 1881521.809 1894223.149 1904473.734 1854427.015 1689848.402 1864737.169 1792029.779 1711645.376 1155733.285 1.627989635 1.638979489 1.647848823 1.604545822 1.462143925 1.613466699 1.550556518 1.48100379 1 20.14037707 -2.715613586 0.263135518 1.70E-12 1.651441063 0.941850517 0.046449416 10.64569704 0.304967786 6.0551507 0.060839386 0.001924804 2.715613586 1.651441063 HRPSAGGPDS(ph)AGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR 111.73 0.00057946 259576000 131519 126507 137097 152922 140695 132697 165930 128399 81829.8 TRUE FALSE 125302.3575 139398.2071 143383.0331 137549.99 165232.1635 128101.6696 140614.331 117155.7029 94519.54746 1.325676655 1.474808237 1.516966986 1.455254429 1.7481269 1.355292879 1.487674611 1.239486498 1 16.5283251 0.999150203 2.338922667 0.99986861 1.476830746 0.666582345 0.112970496 0.174411619 2.110643347 0.102987074 0.028146139 9.980451827 -0.999150203 0.476962136 HRPSAGGPDSAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 71.879 0.024677 17836000 48239 47229 43238 48201 60348 44388 56449 53759 41593 FALSE TRUE 45958.83807 52041.68879 45220.50507 43355.7439 70872.67209 42850.83243 47836.66829 49051.57697 48043.03001 0.956618225 1.083230778 0.941250064 0.902435668 1.475191554 0.891926101 0.995704648 1.020992576 1 15.55203952 HRS(ph)EDCGGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRSEDCGGGPR 11 1 Q9UGU0;Q9UGU0-2;A9JX13 Q9UGU0 TCF20 Transcription factor 20 1 HRS(1)EDCGGGPR;HRS(1)EDCGGGPR;HRS(1)EDCGGGPR 148.85 2.10E-05 226400000 56333.1 44295.2 47814.1 61683.3 50440.8 49298.3 63660.3 45949.5 31466.6 TRUE FALSE 53670.346 48808.93124 50006.42378 55482.77749 59237.65955 47591.08751 53947.75203 41925.91819 36346.27962 1.476639331 1.342886583 1.375833354 1.526504998 1.629813565 1.309379887 1.484271639 1.153513334 1 15.14952008 1.090292667 3.525724115 1.002626089 1.442560293 0.740605384 0.09368582 0.105402634 2.453003889 0.086622835 0.022609289 12.31098116 -1.090292667 0.439934204 HRS(ph)EPQHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRSEPQHPK 9 1 A0A087WZ32;A0A087X038;A8K727;Q9HB19 A0A087WZ32 PLEKHA2 Pleckstrin homology domain-containing family A member 2 1 HRS(1)EPQHPK;HRS(1)EPQHPK;HRS(1)EPQHPK 96.82 0.0042935 141070000 389449 347144 350813 405480 307377 366425 429342 352604 133125 TRUE FALSE 371040.5176 382518.3683 366898.1231 364720.38 360983.4515 353735.6104 363837.9925 321728.1245 153769.3451 2.412968055 2.487611351 2.386029041 2.371866641 2.347564472 2.300429973 2.366128257 2.092277393 1 17.2304084 -0.163628666 0.577632695 0.875079083 2.428560503 0.986517448 0.050511581 0.579306748 0.199233078 0.208775649 0.021146095 0.686074589 0.163628666 1.55348142 HRS(ph)IHEVDISNLEAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HRSIHEVDISNLEAALR 17 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 HRS(0.535)IHEVDIS(0.465)NLEAALR;HRS(0.988)IHEVDIS(0.012)NLEAALR;HRS(1)IHEVDISNLEAALR;HRS(0.981)IHEVDIS(0.019)NLEAALR;HRS(0.96)IHEVDIS(0.04)NLEAALR 158.44 2.02E-09 1459690000 1136701 820808 1051247 1096770 1052206 990192 1276993 1064882 507213 TRUE FALSE 1082971.396 904449.2684 1099447.715 986520.5959 1235710.393 955901.4028 1082164.264 971635.2868 585869.0016 1.848487279 1.543773891 1.87661015 1.683858667 2.109192311 1.631595801 1.847109612 1.658451436 1 19.16021859 0.838161401 4.617023879 1.000012329 1.775548727 0.718014741 0.154540936 0.848830659 23.75680553 0.135441903 0.034347537 6.889082739 -0.838161401 0.775536397 (ac)SCINLPTVLPGS(ph)PSKTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SCINLPTVLPGSPSKTR 17 1 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.791)PS(0.082)KT(0.127)R;SCINLPTVLPGS(0.773)PS(0.179)KT(0.048)R;SCINLPTVLPGS(0.98)PS(0.017)KT(0.003)R;SCINLPTVLPGS(0.925)PS(0.057)KT(0.018)R;SCINLPTVLPGS(0.984)PS(0.011)KT(0.005)R;SCINLPTVLPGS(0.405)PS(0.405)KT(0.189)R 162.59 6.76E-27 2999200000 2439540 1151731 3066280 1967890 2688030 2887750 4504640 3385540 4448610 TRUE FALSE 2324227.779 1269093.698 3206871.971 1770073.958 3156821.581 2787746.493 3817374.435 3089084.17 5138477.718 0.452318353 0.246978535 0.624089886 0.344474386 0.614349571 0.542523807 0.742899871 0.601167182 1 22.29290959 1.240196997 0.281788087 1.07664759 0.292831584 0.702810334 0.113525829 0.857733025 0.250394237 0.260558826 0.191121365 17.38589277 -1.240196997 -0.783816006 HRS(ph)NSFSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.493)NS(0.493)FS(0.013)DER 68.44 0.036317 52759000 95519 73705 94292 81204 92016 78486 109620 107620 66934 TRUE FALSE 91004.00617 81215.6233 98615.38147 73041.21964 108063.5613 75768.01014 92895.45569 98196.22227 77313.78287 1.177073515 1.050467592 1.27552136 0.944737367 1.397726993 0.980006505 1.201538099 1.270099827 1 16.23843801 HRS(ph)SSLESQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HRSSSLESQGK 11 1 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 HRS(0.333)S(0.333)S(0.333)LESQGK 54.898 0.077975 31319000 78598 55870 68652 67572 58486 53384 88022 75544 85181 TRUE FALSE 74882.82831 61563.21652 71799.76211 60779.53418 68685.93988 51535.29869 74592.62727 68928.96688 98390.43444 0.761078338 0.62570327 0.729743318 0.617738244 0.698095707 0.523783628 0.758128854 0.700565734 1 16.58623044 0.467526025 1.284269954 0.99986027 0.669837684 0.673796148 0.071201441 1.302157368 2.58391825 0.061368766 0.018297834 2.934445346 -0.467526025 -0.330022586 HRSNS(ph)FSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.019)NS(0.98)FS(0.001)DER;HRSNS(0.991)FS(0.009)DER;HRSNS(0.997)FS(0.003)DER 142.38 2.17E-05 1410820000 1982210 1361270 1997100 1936350 2311510 1632310 2764410 2247540 1933260 TRUE FALSE 1888514.862 1499984.961 2088669.01 1741704.419 2714636.612 1575782.695 2342648.483 2050733.483 2233060.087 0.845707141 0.671717241 0.935339368 0.779963078 1.215657665 0.705660678 1.049075435 0.918351232 1 21.09059064 3.319471545 1.80447083 0.959285613 0.766344768 0.205121751 0.145783534 0.444792308 2.974840284 0.041041979 0.061279742 2086.755397 -3.319471545 -0.192940845 HRWPT(ph)GDNIHAEHQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRWPTGDNIHAEHQVR 16 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 HRWPT(1)GDNIHAEHQVR;HRWPT(1)GDNIHAEHQVR;HRWPT(1)GDNIHAEHQVR 218.42 7.40E-15 2447910000 804850 689860 922390 909890 860750 767280 916490 688750 130890 TRUE FALSE 766806.3356 760157.5183 964682.4939 818426.1285 1010864.527 740708.9012 776662.618 628439.3987 151187.7527 5.071881299 5.027904078 6.380692064 5.413309702 6.686153537 4.899265238 5.137073633 4.156681923 1 17.20598175 0.716763218 1.175622038 1.001159487 5.5490395 0.866566392 0.564573833 0.326709656 0.768605484 0.531643727 0.163891699 5.209106275 -0.716763218 4.547880013 HS(ph)CSGSSPPRVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSCSGSSPPRVK 12 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HS(0.319)CS(0.267)GS(0.189)S(0.224)PPRVK 68.809 0.031291 217890000 89558 18238 102270 55233 105640 82507 172320 86237 105700 TRUE FALSE 85324.77083 20096.47293 106959.1807 49680.8739 124063.5826 79649.7619 146029.4191 78685.63111 122091.4162 0.698859703 0.16460185 0.876058154 0.406915371 1.016153195 0.652378066 1.196066224 0.644481271 1 16.89760225 2.82473348 1.213599866 0.93926456 0.472992491 0.287405584 0.256490591 0.450879202 1.380399138 0.10501346 0.106614933 667.9338908 -2.82473348 -0.466272069 HS(ph)EKSPPSTENKHEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.596)EKS(0.401)PPS(0.002)TENKHEAK;HS(0.5)EKS(0.5)PPS(0.001)TENKHEAK 104.86 0.00063092 154891000 150682 137319 130644 168355 71240 176374 178293 159219 40020 TRUE FALSE 143559.5605 151311.9622 136634.1566 151431.6355 83664.23344 170266.1242 151091.1283 145276.9403 46226.09721 3.105595522 3.273301692 2.955779633 3.275890562 1.809891782 3.683333321 3.268524435 3.142747259 1 15.49641994 HS(ph)FSAGPELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSFSAGPELLR 11 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 HS(1)FSAGPELLR 221.86 5.22E-12 90256000 75066 75498 69209 91980 68357 83256 88262 69150 33115 TRUE FALSE 71517.77895 83191.33203 72382.30111 82733.99565 80278.43916 80372.82384 74796.01086 63094.85941 38250.30507 1.869730942 2.174919439 1.892332649 2.162963027 2.098765984 2.101233538 1.955435668 1.649525652 1 15.22318363 0.900303961 1.751398831 1.001570971 2.05136992 0.915522072 0.101487137 0.114659879 0.707444314 0.088823422 0.025295607 7.948843767 -0.900303961 1.049798949 HRS(ph)NS(ph)FSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 HRS(1)NS(0.727)FS(0.273)DER;HRS(1)NS(0.929)FS(0.072)DER;HRS(1)NS(0.996)FS(0.004)DER 125.36 0.000234 1193040000 2030940 1721200 1800440 2343410 1701510 1630680 1758100 852990 613470 TRUE FALSE 1934941.491 1896592.237 1882991.955 2107845.975 1998252.805 1574209.143 1489869.555 778297.6736 708603.7944 2.730639472 2.676520013 2.657326943 2.974646751 2.819986036 2.221564653 2.102542446 1.098353805 1 19.43461967 1.442097031 1.369300035 0.93465729 2.747826103 0.943535028 0.165012554 0.079447279 0.283414495 0.140274149 0.046185253 27.67559911 -1.442097031 1.813168813 HS(ph)LSPVPWEEDSFLQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSLSPVPWEEDSFLQVK 17 0 P10073 P10073 ZSCAN22 Zinc finger and SCAN domain-containing protein 22 1 HS(0.576)LS(0.424)PVPWEEDSFLQVK 205.62 4.97E-12 46567000 139090 129680 122090 140700 85142 129140 142680 133480 62932 TRUE FALSE 132515.4913 142894.5394 127687.9473 126556.5687 99990.73784 124667.8494 120911.5455 121791.7836 72691.17315 1.822992884 1.965775668 1.756581188 1.741017007 1.375555429 1.71503422 1.663359391 1.675468675 1 16.14949257 -2.277270038 0.166865957 3.04E-15 1.983156095 0.753072125 0.133559167 22.07343181 0.486551606 9.211226646 0.595526978 0.005281168 2.277270038 1.983156095 HS(ph)PIKEEPCGSLSETVCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSPIKEEPCGSLSETVCK 18 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 HS(0.936)PIKEEPCGS(0.053)LS(0.011)ETVCK 75.239 0.0104 150640000 194430 286450 171590 263640 89645 222020 180710 187620 41337 TRUE FALSE 185239.6792 315639.5807 179457.5712 237138.4063 105279.0596 214331.3917 153139.3705 171190.9982 47747.33084 3.879581873 6.610622523 3.758483837 4.966526969 2.204920312 4.488866455 3.207286519 3.58535221 1 15.54313247 3.028704424 1.692921682 3.176056326 5.134081167 0.330278867 1.235012541 0.39192604 2.291774099 0.392549316 0.474383074 1068.32754 -3.028704424 1.95802484 HS(ph)PIKEEPCGSLSETVCKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSPIKEEPCGSLSETVCKR 19 2 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 HS(1)PIKEEPCGSLSETVCKR;HS(1)PIKEEPCGSLSETVCKR 164.58 1.23E-11 591560000 601000 548950 546590 681810 261730 696920 668760 650230 161305 TRUE FALSE 572591.9211 604888.6291 571651.6922 613273.1634 307375.6291 672785.4857 566728.3794 593292.4141 186319.3556 3.073174654 3.246515249 3.068128324 3.291516126 1.649724626 3.610926431 3.04170427 3.184276869 1 17.50741803 HS(ph)PQQPSNGSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSPQQPSNGSLR 12 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR;HS(1)PQQPSNGSLR 86.873 0.0069994 947090000 958460 993280 856570 1082440 824530 895480 952210 834230 639193 TRUE FALSE 913155.4953 1094496.361 895844.5818 973631.0747 968327.7709 864469.3031 806932.876 761180.3987 738315.7859 1.236808846 1.48242308 1.213362356 1.318719027 1.311536052 1.170866612 1.092937319 1.030968609 1 19.49387848 1.887825945 1.101722809 1.00136126 1.335683036 0.749527525 0.072399461 0.224831582 0.502218191 0.056072536 0.024225433 77.23709744 -1.887825945 0.334321776 HS(ph)PS(ph)PRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;HS(1)PS(1)PRPR 70.977 0.028414 239665000 160910 129956 153167 151739 134824 137480 183123 82588 84236 TRUE FALSE 153304.1032 143198.6641 160189.8585 136485.9074 158337.2629 132719.0331 155184.2231 75356.15689 97298.88866 1.575599735 1.471739977 1.64636884 1.402748883 1.627328586 1.36403442 1.594922873 0.774481168 1 16.57013571 1.240784996 24.99996803 0.887240398 1.522797901 0.861754041 0.106374929 15.69195764 176380.4604 0.066674339 0.021681023 17.40944779 -1.240784996 0.635557503 HS(ph)PTPQQSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.999)PT(0.001)PQQSNR;HS(0.627)PT(0.371)PQQS(0.001)NR;HS(0.841)PT(0.157)PQQS(0.002)NR;HS(0.954)PT(0.044)PQQS(0.001)NR 149.82 1.46E-05 343630000 361764 328131 334054 420266 347631 377048 459224 330556 182835 TRUE FALSE 344664.1327 361567.922 349370.7063 378020.0632 408257.7363 363990.7332 389160.9446 301610.7643 211188.118 1.632024263 1.712065647 1.65431043 1.789968426 1.933147282 1.723537937 1.842721779 1.428161618 1 17.68816914 0.971207183 3.696953097 1.001160698 1.748317006 0.884567797 0.088901872 0.0716645 2.700336715 0.089928629 0.023156564 9.35852022 -0.971207183 0.747156308 HS(ph)PVQMNR ddPTM_SK-BR-3_Trastuzumab_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 132.32 0.00062308 1025650000 978550 962690 776390 1001730 829350 820710 997080 819480 734362 TRUE FALSE 932295.8808 1060789.205 811988.2495 901034.1972 973988.3774 792288.6069 844957.1334 747721.9869 848243.1084 1.099090428 1.250572147 0.957258882 1.062235801 1.148242017 0.934034829 0.99612614 0.881494915 1 19.69411828 2.8010517 0.626629444 0.942558649 1.166245961 0.371028912 0.086336653 0.730838112 0.620065301 0.063690579 0.072867855 632.4871411 -2.8010517 0.223687311 HS(ph)QPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.515)QPS(0.452)PEPHS(0.516)PT(0.516)EPPAWGS(0.002)SIVK 69.152 0.011729 292480000 333480 297490 329880 385200 261010 352030 381010 308010 153200 TRUE FALSE 317717.0613 327804.5692 345005.3243 346478.9642 306530.0614 339839.1128 322879.9268 281039.0115 176957.4736 1.795443023 1.85244829 1.949651051 1.957978701 1.732224445 1.920456401 1.824618764 1.588172604 1 17.43304317 0.842513634 1.924970032 1.000562015 1.864511779 0.941221127 0.068452072 0.123021332 0.859092314 0.063345128 0.017686546 6.958467999 -0.842513634 0.863949764 HS(ph)QPSPEPHSPTEPPAWGSSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HS(0.272)QPS(0.272)PEPHS(0.228)PT(0.228)EPPAWGSSIVK;HS(0.309)QPS(0.256)PEPHS(0.217)PT(0.217)EPPAWGS(0.001)SIVK 62.663 0.07302 481770000 212708 166965 206942 232114 172004 239050 265000 175959 53267 TRUE FALSE 202653.7144 183978.9233 216430.4954 208781.4597 202001.4431 230771.6386 224569.3829 160551.0971 61527.37431 3.293716279 2.99019624 3.517629313 3.393310085 3.283114962 3.750714883 3.649910068 2.609425462 1 15.90894081 0.921436364 3.861630223 1.001398875 3.385110719 0.928830806 0.212328209 0.096253374 3.497380094 0.236461065 0.060619451 8.345192594 -0.921436364 2.383711844 HS(ph)S(ph)ISPVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.797)S(0.838)IS(0.365)PVRLPLNSSLGAELSR 170.27 1.12E-11 253470000 83459 71977 84246 89659 68824 85060 106560 69557 51736 TRUE FALSE 79514.05847 79311.53813 88108.76243 80646.30698 80826.88381 82114.35087 90302.31489 63466.22034 59758.95465 1.330579809 1.327190855 1.474402672 1.349526735 1.352548489 1.374092826 1.511109346 1.06203699 1 15.86686729 1.153684346 6.392923215 1.011742674 1.384079324 0.854824843 0.061338928 0.082306748 4.839226581 0.061970489 0.015637409 14.2457181 -1.153684346 0.37233665 HS(ph)SADNLANEMTYITETEDVFYTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.405)S(0.405)ADNLANEMT(0.088)Y(0.079)IT(0.021)ET(0.003)EDVFYTYK;HS(0.388)S(0.388)ADNLANEMT(0.124)Y(0.1)ITETEDVFYTYK;HS(0.459)S(0.459)ADNLANEMT(0.043)Y(0.038)ITETEDVFYTYK 156.88 1.66E-08 94808000 61396 55191.7 55617 62435 41767.7 63066 72082 59768 35029.5 TRUE FALSE 58493.93276 60815.79698 58167.09446 56158.91518 49051.97366 60882.00861 61084.56702 54534.39707 40461.69595 1.445661912 1.503046166 1.437584191 1.387952577 1.212306417 1.504682569 1.509688746 1.347803046 1 15.30426917 0.911048079 6.689094522 1.00000361 1.436060257 0.70593515 0.086347132 0.768866615 57.55846907 0.085026304 0.021337786 8.147944824 -0.911048079 0.436056648 HS(ph)SIS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.5)S(0.5)IS(1)PVRLPLNSSLGAELSR;HS(0.582)S(0.582)IS(0.835)PVRLPLNSSLGAELSR;HS(0.502)S(0.502)IS(0.996)PVRLPLNSSLGAELSR 179.81 7.45E-17 284615000 239467 215142 225894 274298 209326 226293 277727 165483 137952 TRUE FALSE 228147.8695 237065.2144 236251.4633 246725.0439 245832.3881 218456.4167 235354.6453 150992.4312 159344.8916 1.43178653 1.487749071 1.482642217 1.548371218 1.542769182 1.370965925 1.47701406 0.947582503 1 17.28179324 1.240231795 25 0.973791043 1.474889647 0.942028651 0.051928366 8.755387892 130993.7989 0.038776211 0.012474832 17.38728591 -1.240231795 0.501098604 HS(ph)SISPVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HS(0.348)S(0.348)IS(0.305)PVRLPLNSSLGAELSR 191.8 7.94E-18 331100000 128210 91617 125430 115380 189800 108530 188310 147610 165090 TRUE FALSE 122149.7674 100952.8765 131181.0896 103781.7832 222901.0599 104771.5789 159579.8509 134684.4859 190691.314 0.640562828 0.529404692 0.68792378 0.544239698 1.168910399 0.549430263 0.836849081 0.706295861 1 17.54087961 HS(ph)SNPPLESHVGWVMDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.5)S(0.5)NPPLESHVGWVMDSR;HS(0.561)S(0.439)NPPLESHVGWVMDSR;HS(0.55)S(0.45)NPPLESHVGWVMDSR;HS(0.511)S(0.489)NPPLESHVGWVMDSR 190.19 4.83E-14 1562900000 775818 657236 758105 824409 759113 715390 872813 719118 534839.8 TRUE FALSE 739146.6207 724209.0956 792864.8641 741537.841 891502.0669 690615.8649 739649.3465 656148.2156 617780.0246 1.196456006 1.172276647 1.283409681 1.200326672 1.443073637 1.117899313 1.197269768 1.062106558 1 19.2367337 1.235671097 1.498649596 0.999670627 1.23493025 0.502371753 0.085038605 0.311610193 1.315565729 0.074839341 0.022801057 17.2056505 -1.235671097 0.235259623 HS(ph)SPHQS(ph)EDEEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.5)S(0.5)PHQS(1)EDEEDPR 63.578 0.035899 231710000 293960 277680 288550 343840 232310 278610 274320 212470 163570 TRUE FALSE 280065.0934 305975.9077 301780.3029 309276.5499 272824.7904 268961.6658 232467.4458 193865.0004 188935.6002 1.48233098 1.619471965 1.597265431 1.636941633 1.444009441 1.423562661 1.230405734 1.026090373 1 17.52753504 1.64688646 1.162293859 0.980899667 1.574317405 0.946628402 0.053290661 0.091978153 0.23529503 0.04571637 0.017081615 44.34926843 -1.64688646 0.593417737 HS(ph)TSPASSEYSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSTSPASSEYSWK 13 0 Q96N46 Q96N46 TTC14 Tetratricopeptide repeat protein 14 1 HS(0.369)T(0.369)S(0.262)PASSEYSWK 134.08 6.43E-05 219500000 215780 183610 202850 233230 168060 205510 242960 197930 118520 TRUE FALSE 205580.507 202320.0677 212150.8731 209785.2773 197369.6108 198393.1372 205891.9897 180598.1999 136899.4763 1.501689507 1.477873205 1.549683599 1.532403797 1.441711949 1.44918843 1.503964773 1.319203001 1 17.0627574 0.890831546 2.294362588 1.000129544 1.494227663 0.955289739 0.034124561 0.0835082 0.910345271 0.032646204 0.008881087 7.777348245 -0.890831546 0.494098119 HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(0.639)Y(0.34)PPALGS(0.021)PGALAGAGVGAAGPLER;HS(0.997)Y(0.002)PPALGSPGALAGAGVGAAGPLER;HS(0.961)Y(0.039)PPALGSPGALAGAGVGAAGPLER 251.91 1.06E-52 699035000 452412 441872 414005 512713 350687 436542 428911 381425 157999 TRUE FALSE 431027.3814 486899.2592 432987.5388 461174.1151 411846.7018 421424.4411 363472.7495 348025.4049 182500.678 2.361785097 2.667931235 2.372525645 2.526972065 2.256685873 2.309166441 1.991624105 1.906981436 1 17.4775423 0.767589985 0.522126246 0.949130161 2.526558271 0.951304006 0.102661128 0.223915582 0.134363439 0.116127923 0.047318395 5.855850564 -0.767589985 1.577428109 HSAS(ph)PVVFTSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSASPVVFTSAR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 HS(0.204)AS(0.796)PVVFTSAR 101.75 0.001606 72091000 125900 118790 117750 145230 121320 128780 134520 120240 110170 TRUE FALSE 119948.9565 130894.8361 123148.954 130631.2045 142478.1696 124320.3163 113996.5034 109711.1482 127254.6009 0.942590332 1.028605921 0.96773675 1.026534236 1.119630792 0.976941623 0.895814395 0.862138951 1 16.95735829 1.895653867 4.869164593 0.911069403 1.012698879 0.370789366 0.05729964 0.227458953 8.158689556 0.025616705 0.015030407 78.64187629 -1.895653867 0.101629477 HSCDALNR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 182.73 0.00022702 574974000 290716 268470 249878 285535 684051 229450 310154 249826 381718 FALSE TRUE 276974.4308 295827.3982 261335.1535 256832.4793 803349.2778 221504.089 262834.3109 227949.911 440912.8779 0.628184035 0.670942975 0.592713814 0.582501651 1.822013641 0.502376093 0.596113936 0.516995358 1 18.75013409 HSCSGS(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCS(0.004)GS(0.721)S(0.274)PPR;HSCSGS(0.791)S(0.209)PPR;HSCS(0.002)GS(0.599)S(0.399)PPR 115.92 0.00074649 2809988000 28645.3 17094.9 20125.5 20642.1 20256.8 22991.4 28454.1 23159.6 20979.6 TRUE FALSE 27291.29344 18836.88975 21048.27408 18567.11689 23789.57951 22195.20205 24112.90445 21131.62265 24233.00922 1.126203238 0.777323591 0.868578636 0.766191137 0.981701418 0.915907796 0.995043753 0.8720181 1 14.56468595 HSCSGS(ph)SPPRVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSCSGSSPPRVK 12 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.833)S(0.167)PPRVK 133.47 9.82E-05 114100000 63894 26472 83123 44123 81816 60924 126620 74574 86379 TRUE FALSE 60873.85725 29169.5269 86934.27177 39687.67221 96084.6845 58814.1866 107301.7935 68043.90522 99774.21416 0.610116128 0.292355366 0.871310012 0.397774841 0.963021211 0.589472812 1.07544614 0.681978864 1 16.60637939 2.730317825 0.714229129 0.925389392 0.466678088 0.312218889 0.214836827 0.677782165 0.743260032 0.137039557 0.134989921 537.4249505 -2.730317825 -0.458711304 HSCSGSS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.408)S(0.591)PPR;HSCSGS(0.103)S(0.897)PPR;HSCSGS(0.453)S(0.547)PPR;HSCSGS(0.286)S(0.713)PPR 125.23 0.00043499 3712770000 241606 208199.2 214328.9 254580 220418 212728.2 239541.7 213109.7 149636 TRUE FALSE 230185.7632 229414.9352 224156.0921 228989.1347 258858.8294 205361.3691 202995.2142 194448.6849 172840.7866 1.331779192 1.327319434 1.296893496 1.324855893 1.497672132 1.188153405 1.17446361 1.125016199 1 17.39908418 1.589301799 1.316238312 1.038797824 1.343019602 0.741445901 0.069767492 0.203972824 0.677906035 0.057669427 0.020475607 38.84201924 -1.589301799 0.304221778 HSCSGSS(ph)PPRVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSCSGSSPPRVK 12 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.049)S(0.951)PPRVK 158.93 4.37E-05 441220000 297580 89914 356420 183700 364370 269960 580090 313640 354230 TRUE FALSE 283513.9831 99076.33882 372762.2095 165234.127 427916.0126 260611.2175 491586.6164 286176.0189 409162.1792 0.692913464 0.242144421 0.911037795 0.403835289 1.045834719 0.636938678 1.201446862 0.699419529 1 18.64231327 2.779837992 1.113112909 0.956801781 0.507499166 0.280176495 0.249019995 0.489531579 1.270745269 0.110292425 0.106505792 602.3348509 -2.779837992 -0.449302614 HSCSPMGDGDPEAMEES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSCSPMGDGDPEAMEESPR 19 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR 195.97 4.58E-16 346173000 285140 320196 289731 322182 257743 293948 303607 257853 129600 TRUE FALSE 271661.9973 352824.3364 303015.4529 289795.6533 302693.2976 283768.5071 257286.176 235274.0244 149697.7061 1.814737209 2.356912111 2.024182339 1.935872371 2.0220303 1.895610257 1.718704867 1.571660852 1 17.19169259 0.966784524 0.647750751 0.989609573 2.081841013 0.85439804 0.135453111 0.283287207 0.276085849 0.132792706 0.054388206 9.263700891 -0.966784524 1.09223144 HSDENDGGQPHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 78.964 0.0088659 44254000 41741 37346 55161 56241 49459 54468 61465 44765 22521 FALSE TRUE 39767.98565 41151.59986 57690.18641 50587.54783 58084.63394 52581.7595 52087.38537 40845.13929 26013.44166 1.528747567 1.581936001 2.217706798 1.944669548 2.232870018 2.021330364 2.0023258 1.570155146 1 14.66696966 3.874942686 8.349343077 1.9298106 1.548917467 0.07977249 0.362552323 0.442697734 27.92803605 0.081861739 0.148072873 7497.952516 -3.874942686 -0.380893133 HSDGNLCVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSDGNLCVK 9 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 78.556 0.029436 296650000 407740 321960 335420 369590 295800 373840 464560 375130 243040 FALSE TRUE 388466.9383 354768.09 350799.3388 332438.111 347387.4263 360893.8271 393682.8398 342281.6285 280729.4019 1.383777173 1.26373685 1.249599566 1.184194134 1.237445825 1.285557639 1.402356992 1.219258212 1 18.09882065 0.98015303 24.36120668 0.999999997 1.291279303 0.657813902 0.064797043 693.7643614 851564.1187 0.066685793 0.016671448 9.553291514 -0.98015303 0.291279306 HSDSKHDGTSNS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSDSKHDGTSNSPSK 15 1 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 HSDSKHDGT(0.009)S(0.028)NS(0.962)PSK;HSDSKHDGT(0.015)S(0.015)NS(0.97)PSK 115.42 0.00031945 46084000 77934 52337 73039 78728 40604 63262 76216 61691 9957.9 TRUE FALSE 74250.21427 57670.1998 76387.9104 70814.11187 47685.32474 61071.22108 64587.8494 56289.009 11502.12027 6.455350188 5.013875566 6.641202541 6.156613753 4.145785612 5.30956203 5.615299428 4.893794157 1 13.48961221 2.747546818 24.56335745 4.660884183 5.966369821 0.285444558 1.361832005 831.9454215 2274083.257 0.378717579 0.396287495 559.1738048 -2.747546818 1.305485638 HSDSKHDGTSNS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSDSKHDGTSNSPSKK 16 2 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 HSDSKHDGT(0.006)S(0.303)NS(0.683)PS(0.007)KK 103.73 0.00067245 20646000 45843 36641 44153 54231 21163 42609 49018 41319 3989 TRUE FALSE 43676.09224 40374.75956 46177.45872 48779.59685 24853.8205 41133.43965 41539.40382 37700.88931 4607.593747 9.479154335 8.762656123 10.02203346 10.58678337 5.394099798 8.927314756 9.015422388 8.18233798 1 12.1697978 -0.554941939 0.577516042 7.06E-17 9.077880252 0.768359794 1.353904534 5.341843194 1.386239468 13.68463862 0.537570719 0.278649367 0.554941939 9.077880252 HSEAATAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSEAATAQR 9 0 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 144.5 9.94E-05 151248000 59063.6 57721.6 43311.8 55245.1 55890 50150.2 63701 52386.9 38619.2 FALSE TRUE 56271.78068 63603.49666 45297.68887 49691.75759 65637.1983 48413.486 53982.2425 47799.62532 44608.0683 1.261470914 1.425829432 1.015459548 1.113963448 1.471419876 1.085307834 1.210145262 1.071546631 1 15.44501705 0.067129994 0.036233814 1.83E-08 2.187600174 0.234051242 0.14211985 294.7264694 3.42784845 115.8981305 90.47398833 1.167158922 -0.067129994 2.187600155 HSEAATAQREEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSEAATAQREEWK 13 1 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 225.86 7.05E-12 1113770000 977030 496470 933490 744430 838060 914040 1400260 1024880 759970 FALSE TRUE 930847.7282 547060.8574 976291.4398 669598.4821 984217.3987 882386.5656 1186624.619 935136.074 877822.2662 1.060405693 0.623202302 1.112174386 0.762795053 1.121203502 1.005199571 1.35178232 1.065290902 1 19.74356934 2.525721548 2.144361055 1.159541879 0.875504204 0.243885167 0.172952629 0.330096442 3.046292677 0.062754319 0.053653583 335.5224215 -2.525721548 -0.284037675 HSEEAEFTPPLKCS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSEEAEFTPPLKCSPK 16 1 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 HSEEAEFT(0.001)PPLKCS(0.999)PK;HSEEAEFT(0.002)PPLKCS(0.998)PK;HSEEAEFTPPLKCS(1)PK;HSEEAEFTPPLKCS(1)PK 159.8 5.44E-09 1074460000 2778320 2542570 2395790 2837950 1349790 3129280 3094720 3340810 1239570 TRUE FALSE 2646994.32 2801660.774 2505639.341 2552673.874 1585192.949 3020912.249 2622563.626 3048270.966 1431796.185 1.848722847 1.956745523 1.749997219 1.782847239 1.107135894 2.10987589 1.831659878 2.128983858 1 20.44939471 3.615417171 4.440159647 1.718609808 1.902029119 0.052299364 0.370422543 0.778582886 24.583483 0.0928065 0.146862152 4124.935589 -3.615417171 0.183419311 HSEKS(ph)PPSTENKHEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.126)EKS(0.874)PPSTENKHEAK 150.29 3.58E-07 78056000 167990 165470 151020 185090 76497 211560 195130 173850 36036 TRUE FALSE 160049.4456 182331.5811 157944.4164 166484.4016 89838.05258 204233.6242 165359.3347 158626.7724 41624.27883 3.845098344 4.380414177 3.794526195 3.999694558 2.158308927 4.906598502 3.972665457 3.810919415 1 15.34513766 2.95744741 24.9931345 3.499752213 4.042863176 0.086619081 1.083340642 1471.191282 864099.5445 0.30245575 0.320827752 906.6661672 -2.95744741 0.543110963 HSELSELNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSELSELNVK 10 0 O75886;Q92783;Q92783-2 O75886;Q92783 STAM2;STAM Signal transducing adapter molecule 2;Signal transducing adapter molecule 1 0 61.65 0.090212 235350000 806250 659940 776270 737690 609730 902560 987000 938130 464370 FALSE TRUE 768140.1603 727188.6363 811862.7473 663535.9997 716066.719 871304.1209 836415.0225 855982.3639 536382.1279 1.432076351 1.355728684 1.513590228 1.237058368 1.334993621 1.624409307 1.559364078 1.595844304 1 19.03290164 2.263886072 24.98574377 1.503533527 1.377378584 0 0.189530349 501.5145439 494785.7332 0.058156662 0.048639723 183.6056628 -2.263886072 -0.126154943 HSETFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSETFTR 7 0 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;; 91.516 0.029553 195250000 68064 84944 74554 80431 92991 63405 82342 77884 79981 FALSE TRUE 64846.74961 93599.89017 77972.37464 72345.92307 109208.601 61209.26895 69779.21559 71064.06407 92384.04499 0.701925853 1.01316077 0.844002605 0.783099756 1.182115385 0.662552381 0.755316739 0.769224427 1 16.49535609 HSEVQQANLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSEVQQANLK 10 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;; 145.25 3.08E-05 1382520000 2341740 1842630 1765560 2143180 1691670 1939990 2584810 2079890 1432000 FALSE TRUE 2231050.591 2030396.092 1846512.672 1927743.475 1986696.712 1872807.66 2190449.761 1897763.805 1654067.246 1.348827018 1.227517259 1.116346797 1.165456531 1.20109791 1.132243966 1.32428096 1.147331712 1 20.65758646 -5 0.181843871 0.135861826 1.261967086 0.440827933 0.075533091 137.311255 1.326170511 43.23810395 0.239830417 1.00E-05 5 1.126105261 HSGNITFDEIVNIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;;;; 274.48 1.77E-33 3183843000 2324616 1968048 2110988 2380653 2192586 2107282 2509235 2262107 1876957 FALSE TRUE 2214736.009 2168594.329 2207778.888 2141345.237 2574972.304 2034306.296 2126405.115 2064024.919 2168025.905 1.021544993 1.000262185 1.018336027 0.987693566 1.187703661 0.93832195 0.980802448 0.952029638 1 21.04795056 HSGPNSADSANDGFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HSGPNSADSANDGFVR 16 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;;; 300.18 7.13E-46 5062382000 3345051 2074980 2433624 3293206 3514883 2604002 3660910 2928304 2923794 FALSE TRUE 3186937.068 2286422.821 2545208.068 2962166.676 4127877.482 2513824.758 3102370.942 2671886.178 3377201.041 0.943662231 0.67701709 0.753644227 0.877107001 1.222277689 0.744351529 0.918621931 0.791154019 1 21.68739663 3.018190665 12.92402148 0.927071049 0.791969672 0.17442509 0.142240211 1.765975559 1248.022776 0.039550739 0.047081447 1042.775132 -3.018190665 -0.135101377 HSGSRS(ph)DEDRYQNGAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HSGSRSDEDRYQNGAER 17 2 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 HS(0.002)GS(0.035)RS(0.963)DEDRYQNGAER;HSGS(0.001)RS(0.999)DEDRYQNGAER;HS(0.01)GS(0.044)RS(0.947)DEDRYQNGAER 206.49 3.62E-12 409482000 147616 114620 164470 161271 148517 145998 196266 128190 66292.6 TRUE FALSE 140638.4842 126299.9083 172011.1122 145059.7327 174418.3178 140942.0527 166322.017 116965.004 76572.91783 1.836660901 1.649407021 2.246370088 1.894399963 2.277806863 1.840625336 2.172073649 1.527498329 1 16.22454661 0.983867503 4.555222086 1.001097273 1.960569258 0.7245415 0.200095842 0.093142204 6.363295564 0.194216632 0.04932573 9.635350177 -0.983867503 0.959471985 HSHS(ph)HS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.028)HS(0.972)HS(0.993)PMS(0.006)T(0.001)R 70.26 0.0276 24804000 60239 58252 69381 78355 76151 60736 87319 34951 22490 TRUE FALSE 57391.62185 64187.94503 72562.18748 70478.60654 89431.71029 58632.69709 73996.88283 31890.50515 25977.63434 2.209270525 2.470892622 2.793256173 2.713049449 3.442642587 2.257045285 2.848484272 1.227613906 1 14.66498244 1.202189022 6.542265274 1.072303582 2.645635938 0.775654017 0.349206598 0.092164916 10.78673538 0.318191979 0.083849984 15.92901869 -1.202189022 1.573332356 HSHSHS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 HSHS(0.149)HS(0.85)PMSTR 73.022 0.050901 9283800 3467.7 2999.9 3160.4 5244.9 4722.4 4143.8 5950.4 1054.4 0 TRUE FALSE 3303.788693 3305.593221 3305.307466 4717.672687 5545.985065 4000.299167 5042.557193 962.0711463 0 0 HSLASSEYPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSLASSEYPVR 11 0 P51570;P51570-2 P51570 GALK1 Galactokinase 0 136.02 0.0014057 0 56781 40988 37614 40348 54583 41654 52396 43114 36302 FALSE TRUE 54097.07466 45164.7238 39338.63911 36292.14238 64102.25792 40211.51154 44402.02788 39338.7096 41931.52876 1.290128843 1.077106539 0.938163722 0.865509641 1.528736486 0.958980336 1.058917459 0.938165404 1 15.35574781 4.437854798 2.434891792 1.049591714 1.287302964 0.150917049 0.18243881 0.599845443 6.338048173 0.043900385 0.225863661 27406.57708 -4.437854798 0.23771125 HSLASSEYPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSLASSEYPVRR 12 1 P51570;P51570-2 P51570 GALK1 Galactokinase 0 115.33 0.00062429 78258000 44247 27255 39064 40935 62879 35941 50529 41323 48191 FALSE TRUE 42155.532 30032.31549 40855.12304 36820.13603 73845.07769 34696.35416 42819.87302 37704.53905 55664.21415 0.757318371 0.539526443 0.733956702 0.661468712 1.326616729 0.623315261 0.769253167 0.677356891 1 15.76446251 HSLDS(ph)DEEEDDDDGGSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HS(0.001)LDS(0.999)DEEEDDDDGGSSK;HS(0.001)LDS(0.999)DEEEDDDDGGSSK 340.53 1.41E-75 1039750000 434760 534990 428220 593860 257969 513650 441880 309127 98241 TRUE FALSE 414209.7564 589506.0892 447854.3106 534164.0645 302958.7119 495862.1717 374463.0903 282058.2011 113475.7125 3.650206261 5.194997908 3.946697496 4.707298616 2.669811056 4.369764777 3.299940419 2.485626173 1 16.79202402 0.927495832 0.550663206 0.898425412 4.392856188 0.707386743 0.657929083 0.507140754 0.366242311 0.674721794 0.296730526 8.462444479 -0.927495832 3.494430776 HSLDS(ph)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSLDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 42 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HS(0.201)LDS(0.799)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR;HS(0.093)LDS(0.324)DEEEDDDDGGS(0.107)S(0.107)KY(0.262)DILAS(0.107)EDVEGQEAATLPSEGGVR;HS(0.03)LDS(0.97)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR;HS(0.21)LDS(0.661)DEEEDDDDGGS(0.039)S(0.039)KY(0.037)DILAS(0.014)EDVEGQEAATLPSEGGVR;HS(0.149)LDS(0.849)DEEEDDDDGGS(0.001)S(0.001)KYDILASEDVEGQEAATLPSEGGVR 294.93 1.12E-96 1363685000 836100 719320 900319 973774 543420 900596 1094609 677432 312553 TRUE FALSE 796579.21 792619.5258 941599.5167 875888.3875 638192.2759 869408.1347 927606.2932 618112.4628 361022.1229 2.206455393 2.19548741 2.608149077 2.426134942 1.767737309 2.408185204 2.56938906 1.712117966 1 18.46172772 0.985143717 4.462661924 1.001799869 2.303282393 0.768686109 0.236225946 0.080907253 5.168710996 0.226556039 0.057602503 9.66370618 -0.985143717 1.301482525 HSLSGRPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSLSGRPLK 9 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 94.309 0.005293 1983710000 2549200 1903110 1935690 2146310 1860500 2137740 2907100 2351000 1498420 FALSE TRUE 2428704.368 2097039.073 2024443.301 1930558.841 2184970.611 2063709.528 2463568.502 2145133.977 1730787.321 1.403236746 1.211609912 1.169666126 1.115422339 1.262414269 1.192353042 1.423380258 1.239397788 1 20.72299703 -2.217134895 2.220376951 0.20845784 1.260784104 0.40053084 0.096450181 2847558.074 534539.1277 11324314.03 0.025500771 0.006065479 2.217134895 1.052326264 HSLSGS(ph)SPGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.001)GS(0.5)S(0.5)PGMK 155.88 3.29E-05 31548000 125630 111730 109790 141840 75295 122730 123550 119550 50046 TRUE FALSE 119691.7189 123115.414 114823.9801 127581.9737 88426.42416 118479.8293 104700.1783 109081.5682 57806.87808 2.070544593 2.129771026 1.98633768 2.20703795 1.529686901 2.049580141 1.811206241 1.886999815 1 15.81895354 -1.830030714 0.23716167 2.30E-14 2.144047486 0.764121278 0.172907994 12.18207866 0.46323163 7.249686053 0.278090788 0.014790038 1.830030714 2.144047486 HSLSGSS(ph)PGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.001)GS(0.038)S(0.962)PGMK;HSLSGS(0.153)S(0.847)PGMK;HSLSGS(0.112)S(0.888)PGMK;HSLSGS(0.136)S(0.864)PGMK;HSLSGS(0.016)S(0.983)PGMK 231.66 9.48E-13 808560000 1761410 1607620 1544260 1990680 1075530 1746280 1808090 1695920 648210 TRUE FALSE 1678151.64 1771438.306 1615065.848 1790573.064 1263102.091 1685805.886 1532232.663 1547416.254 748731.0962 2.241327559 2.365920575 2.157070618 2.391476825 1.686990293 2.251550516 2.046439196 2.066718294 1 19.51408815 -1.663402734 0.287273431 1.18E-18 2.30114977 0.796863285 0.186021753 9.971861685 0.509541922 7.31441195 0.198051044 0.021706873 1.663402734 2.30114977 HSLSTLGSANCFLDSLYEGQDFDCNVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSLSTLGSANCFLDSLYEGQDFDCNVSR 28 0 Q0VDF9 Q0VDF9 HSPA14 Heat shock 70 kDa protein 14 0 164.46 7.37E-12 36193000 17982 17343 20364 23129 18642 20523 21732 16798 19283 FALSE TRUE 17132.0265 19110.27142 21297.70954 20804.02898 21893.1589 19812.28336 18416.38426 15327.07807 22273.30916 0.769172931 0.857989771 0.956198713 0.934034042 0.982932475 0.889507851 0.826836468 0.688136548 1 14.4430283 -0.70263701 7.115550492 1.00000051 0.863923882 0.193216953 0.087899743 0 0 0.086630007 0.020418889 0.198318391 0.70263701 -0.136076628 HSMDQTGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSMDQTGSK 9 0 Q14008;Q14008-3;Q14008-2;H0YDX5 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 125.75 0.00037389 67289000 115993 98386 104763 115607 84445 104967 137301 113339 74647 FALSE TRUE 110510.2408 108411.6453 109566.4872 103985.9647 99172.18126 101331.9665 116353.2107 103414.4363 86222.87552 1.281681226 1.257342029 1.270735713 1.206013649 1.150184109 1.175232975 1.349447117 1.199385148 1 16.39578306 -2.30412479 1.481759899 0.31245948 1.243580572 0.618449521 0.058065427 117240.1589 14557.98327 268018.0464 0.016499347 0.004964497 2.30412479 0.931121092 HSPFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSPFLK 6 0 H0YAF2 H0YAF2 LIFR 0 ; 94.669 0.044219 786290000 3653300 2770500 3236400 3608100 3395200 3433100 4434100 3720200 3636400 FALSE TRUE 3480615.749 3052817.1 3384792.141 3245406.933 3987321.805 3314210.886 3757596.607 3394439.566 4200314.34 0.828656017 0.726806818 0.805842579 0.772658109 0.949291287 0.789038776 0.894598905 0.808139413 1 22.00206587 -5 0.110256649 1.609942291 0.710069465 0.491253082 0.059560214 124.0008197 0.908445073 16.90898607 0.669609572 1.00E-05 5 -0.899872826 HSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_SK-BR-3_Trastuzumab_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(0.44)S(0.44)PHT(0.12)HR;HSPTSEPTPPGDALPPVS(0.61)S(0.374)PHT(0.016)HR 147.67 2.91E-07 1796150000 424860 370330 488740 514800 470090 437180 523380 362260 80543 TRUE FALSE 404777.7098 408067.048 511149.2124 463051.3259 552073.5472 422040.347 443528.7685 330538.5939 93033.19708 4.350895406 4.386252014 5.494266869 4.97726984 5.934156457 4.536448926 4.767424773 3.55291019 1 16.50545799 0.850284077 1.783000825 1.001364357 4.89515374 0.868626291 0.487454248 0.204690165 1.239907692 0.486915372 0.137839808 7.084090121 -0.850284077 3.893789382 HSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_SK-BR-3_Trastuzumab_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(0.241)S(0.241)PHT(0.518)HR;HSPTSEPTPPGDALPPVS(0.248)S(0.248)PHT(0.503)HR 143.15 4.66E-07 2038190000 438670 335960 429590 459550 449100 390980 509970 315350 28214 TRUE FALSE 417934.9385 370194.706 449287.1264 413355.1609 527422.8978 377440.2646 432164.7103 287736.2822 32589.28302 12.82430602 11.35940013 13.78634584 12.68377585 16.18393683 11.58172962 13.26094563 8.829168841 1 14.99210999 0.887807928 2.329171762 1.004475824 12.99693944 0.89299536 1.337189109 0.130184325 1.457278724 1.218319506 0.330620212 7.723389329 -0.887807928 11.99246361 HSQAVEELAEQLEQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSQAVEELAEQLEQTK 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 163.41 7.74E-09 426651000 512758 535317 426667 631576 347096 530951 519773 522242 278682 FALSE TRUE 488520.9455 589866.4109 446230.104 568088.7806 407629.4325 512564.0337 440472.0826 476511.7219 321898.5812 1.517623792 1.832460425 1.386244395 1.764806724 1.266328764 1.592315293 1.368356707 1.480316316 1 18.29624669 -2.772636059 0.146729316 7.89E-11 1.777861146 0.534468651 0.163261437 40.92529909 0.676957551 13.82810054 0.87225532 0.001687967 2.772636059 1.777861146 HSQAVEELAEQLEQTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 282.5 3.16E-36 1647960000 5364150 4732220 4680100 5973100 3603520 5250650 5812620 5763560 2927920 FALSE TRUE 5110597.26 5214438.598 4894687.214 5372672.64 4231972.747 5068818.674 4925798.063 5258872.132 3381966.88 1.51113167 1.541836092 1.447290109 1.588623671 1.25133477 1.49877833 1.456489149 1.554974463 1 21.6894311 -1.451685822 3.014968478 0.989296084 1.482660704 0.729168698 0.092181735 12104237.38 14858753.6 1102411.017 0.021059714 0.035343876 1.451685822 0.49336462 HSQDLAFLSMLNDIAAVPATAMPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 202.2 3.13E-25 3580790000 1797650 1530000 1622570 1928480 1814670 1703920 2105320 1937580 1664200 FALSE TRUE 1712678.647 1685908.739 1696966.439 1734625.527 2131147.873 1644912.823 1784114.767 1767915.223 1922275.636 0.890964134 0.877037979 0.88279038 0.902381268 1.108658838 0.855711216 0.9281264 0.919699126 1 20.87438379 2.982148374 24.99000423 0.952575479 0.884411937 0.240991403 0.064783686 1162.55586 1627432.163 0.018683278 0.02019684 959.7284605 -2.982148374 -0.068163541 HSQFIGYPITLFVEK ddPTM_SK-BR-3_Trastuzumab_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 ; 184.41 4.65E-07 1371220000 1973960 1594640 1390970 1708790 1427220 1582680 2053590 1841380 1069560 FALSE TRUE 1880654.823 1757135.629 1454747.35 1537019.183 1676126.716 1527871.395 1740277.129 1680139.005 1235421.902 1.522277385 1.422295999 1.177530808 1.244124926 1.356724139 1.23672034 1.408650054 1.359971846 1 20.23657238 -4.724685748 0.142735625 8.81E-32 1.466402739 0.513167496 0.102708568 113.5605691 1.059617965 33.54658213 0.644405262 1.89E-05 4.724685748 1.466402739 HSQFLGYPITLYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 ; 184.41 4.65E-07 1908020000 2364000 1779860 1356110 1560330 1695310 1697670 2443040 2041440 1254200 FALSE TRUE 2252258.405 1961229.758 1418288.985 1403482.664 1990971.527 1638879.262 2070309.378 1862680.691 1448694.93 1.554680946 1.353790723 0.979011492 0.968791037 1.374320767 1.131279766 1.429085817 1.285764623 1 20.46632239 4.093423235 3.294680299 1.195429719 1.506945205 0.36021036 0.163963553 0.264512909 5.580276323 0.042903129 0.104800922 12400.04425 -4.093423235 0.311515486 HSQPS(ph)PEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.45)QPS(0.531)PEPHS(0.509)PT(0.509)EPPAWGSSIVK;HS(0.165)QPS(0.827)PEPHS(0.814)PT(0.194)EPPAWGSSIVK;HS(0.001)QPS(0.999)PEPHS(0.925)PT(0.075)EPPAWGSSIVK;HS(0.186)QPS(0.75)PEPHS(0.532)PT(0.532)EPPAWGSSIVK;HS(0.29)QPS(0.724)PEPHS(0.492)PT(0.492)EPPAWGS(0.002)SIVK 141.78 9.49E-08 909130000 1024436 867905 992260 1125714 807190 1060000 1223580 824075 429071 TRUE FALSE 976012.9405 956345.5062 1037756.102 1012555.09 947963.6804 1023291.934 1036900.398 751914.6243 495609.1393 1.9693199 1.929636543 2.093900254 2.043051691 1.912724373 2.064715626 2.092173683 1.517152459 1 18.91884327 1.0031881 3.381200839 1.003201916 2.009366285 0.961753221 0.067091939 0.039530811 1.120158541 0.06983451 0.018159975 10.07367883 -1.0031881 1.006164369 HSQPS(ph)PEPHSPTEPPAWGSSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HS(0.138)QPS(0.507)PEPHS(0.177)PT(0.177)EPPAWGSSIVK 61.345 0.089126 175570000 60602 54108 57216 67641 47272 67362 70332 70786 32957 TRUE FALSE 57737.46356 59621.66672 59839.41019 60841.59817 55516.22183 65029.23705 59601.56166 64587.60258 38067.80324 1.516700693 1.566196671 1.571916557 1.598242951 1.458351076 1.708247693 1.565668533 1.696646433 1 15.2162837 -1.257407469 5.419438689 0.999945165 1.58008213 0.859712167 0.074271539 4.45E-05 6.10E-06 0.06510253 0.015343371 0.055283118 1.257407469 0.580136965 HSQPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HSQPSPEPHS(0.976)PT(0.024)EPPAWGSSIVK 246.76 8.26E-38 303310000 370950 293840 347360 439180 291590 372800 463000 305510 41031 TRUE FALSE 353415.9287 323782.6301 363286.7996 395032.792 342443.2037 359889.8425 392360.8464 278757.9248 47393.87792 7.456995379 6.831739547 7.665268501 8.335101691 7.225473388 7.593593483 8.278724249 5.881728548 1 15.53241309 0.88640802 3.984143363 1.001317737 7.570338937 0.955622347 0.449200443 0.116293857 3.622239338 0.466118263 0.119190809 7.698533793 -0.88640802 6.569021201 HSS(ph)IS(ph)PSTLTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.027)S(0.973)IS(0.916)PS(0.032)T(0.051)LT(0.001)LK;HS(0.013)S(0.987)IS(0.854)PS(0.13)T(0.015)LTLK;HS(0.004)S(0.996)IS(0.969)PS(0.012)T(0.019)LTLK;HS(0.026)S(0.971)IS(0.475)PS(0.291)T(0.23)LT(0.007)LK 183.89 2.20E-05 498514000 1398200 1259150 1331300 1529720 993090 1434210 1601380 1046870 665560 TRUE FALSE 1332109.857 1387458.817 1392341.422 1375949.639 1166284.582 1384542.948 1357060.07 955200.513 768771.6456 1.732777041 1.80477366 1.811124838 1.789802794 1.517075439 1.800980767 1.765231688 1.242502268 1 19.5521956 1.117230885 3.422411512 1.008494514 1.752565494 0.901322387 0.087736573 0.059979085 1.271027714 0.080920885 0.021323216 13.09878111 -1.117230885 0.74407098 HSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.366)S(0.635)IS(0.999)PVRLPLNSSLGAELSR;HS(0.042)S(0.958)IS(1)PVRLPLNSSLGAELSR;HS(0.468)S(0.533)IS(0.999)PVRLPLNSSLGAELSR;HS(0.473)S(0.528)IS(0.999)PVRLPLNSSLGAELSR;HS(0.032)S(0.968)IS(1)PVRLPLNSSLGAELSR;HS(0.064)S(0.936)IS(1)PVRLPLNSSLGAELSR;HS(0.498)S(0.539)IS(0.962)PVRLPLNSSLGAELSR;HS(0.13)S(0.88)IS(0.99)PVRLPLNSSLGAELSR 251.76 3.37E-36 2399586000 1751729 1609496 1721734 1995625 1564105 1750380 2071999 1249000 1038797 TRUE FALSE 1668928.242 1773505.472 1800677.207 1795020.984 1836884.417 1689763.902 1755877.498 1139630.939 1199888.333 1.390902966 1.478058768 1.500703988 1.49599003 1.530879471 1.408267632 1.463367423 0.949780831 1 20.19446872 1.240406751 24.99994374 0.974890216 1.464235012 0.957422114 0.043131121 8.365770281 113301.0298 0.032782158 0.010584209 17.39429178 -1.240406751 0.489344796 HSS(ph)NPPLESHVGWVMDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.233)S(0.767)NPPLESHVGWVMDSR;HS(0.202)S(0.798)NPPLESHVGWVMDSR;HS(0.233)S(0.767)NPPLESHVGWVMDSR;HS(0.007)S(0.993)NPPLESHVGWVMDSR;HS(0.023)S(0.977)NPPLESHVGWVMDSR;HS(0.038)S(0.962)NPPLESHVGWVMDSR;HS(0.087)S(0.913)NPPLESHVGWVMDSR 260.41 6.26E-31 4290680000 1448652 1349016 1449250 1566199 1419029 1467358 1716428 1399265 989434 TRUE FALSE 1380177.091 1486482.264 1515699.546 1408761.701 1666507.208 1416543.025 1454555.384 1276737.939 1142870.371 1.207640976 1.300656926 1.326221752 1.23265222 1.458176929 1.2394608 1.27272123 1.117132766 1 20.12423035 1.08360251 2.046287502 0.999754537 1.292849033 0.682880062 0.068605834 0.167439593 1.392065261 0.060508689 0.017052409 12.12278798 -1.08360251 0.293094497 HSS(ph)PHQS(ph)EDEEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.106)S(0.894)PHQS(1)EDEEDPR 115.76 0.00021169 311690000 363800 386890 394280 457170 326910 395430 408680 306520 233430 TRUE FALSE 346603.895 426314.5309 412358.128 411214.403 383923.0005 381736.1599 346328.3601 279679.4838 269629.1322 1.28548385 1.581114501 1.529353021 1.525111176 1.423892876 1.415782326 1.284461947 1.037274725 1 18.04061686 1.411512803 1.62269854 0.985304774 1.471523222 0.840155041 0.079323534 0.13487435 0.658133718 0.071801577 0.022707525 25.79365006 -1.411512803 0.486218447 HSS(ph)PTEERDEPAYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.02)S(0.969)PT(0.01)EERDEPAYPR;HS(0.158)S(0.838)PT(0.004)EERDEPAYPR 224.19 7.07E-13 871430000 340610 309610 351490 359050 331270 310010 388530 318170 218799 TRUE FALSE 324510.0403 341159.611 367606.1642 322957.6118 389043.3831 299274.276 329252.6127 290309.3481 252729.2314 1.284022582 1.349901668 1.454545491 1.277879927 1.539368362 1.184169612 1.302788011 1.148697151 1 17.94723301 1.107378986 1.037801752 1.001276388 1.359273504 0.617190222 0.094045192 0.31427652 0.721741616 0.079398099 0.026395783 12.80498239 -1.107378986 0.357997116 HSS(ph)YPAGTEDDEGMGEEPSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.145)S(0.855)YPAGTEDDEGMGEEPSPFR;HS(0.116)S(0.884)YPAGTEDDEGMGEEPSPFR;HS(0.17)S(0.83)YPAGTEDDEGMGEEPSPFR;HS(0.334)S(0.666)YPAGTEDDEGMGEEPSPFR;HS(0.108)S(0.892)YPAGTEDDEGMGEEPSPFR 305.67 9.07E-56 1083710000 748580 618942 661138 793040 653665 678054 821829 656582 393582 TRUE FALSE 713196.1069 682012.8935 691451.8313 713322.1125 767663.969 654572.82 696443.8921 599088.1993 454616.6864 1.568785591 1.50019327 1.52095568 1.56906276 1.688596112 1.439834567 1.531936493 1.317787528 1 18.79429111 0.899050576 1.550977033 0.999378193 1.55053316 0.888152667 0.062935701 0.147486036 0.70398672 0.055790703 0.016264412 7.925936264 -0.899050576 0.551154966 HSSDINHLVT(ph)QGRESPEGSYTDDANQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSDINHLVTQGRESPEGSYTDDANQEVR 29 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 HSSDINHLVT(0.5)QGRES(0.5)PEGS(0.001)YTDDANQEVR 116.73 0.00022166 77237000 14237 13465 17312 15712 21851 12318 19808 15125 6235.5 TRUE FALSE 13564.04523 14837.09881 18105.77232 14132.59991 25661.80748 11891.42457 16785.9258 13800.57482 7202.469493 1.883249244 2.060001618 2.513828395 1.962188097 3.5629179 1.65102047 2.330579229 1.916089312 1 12.81427593 0.693552179 1.495236136 0.999623035 2.258098405 0.376558656 0.518264551 1.148782483 3.964984511 0.455375021 0.132496988 4.938012436 -0.693552179 1.258475371 HSSDINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSSDINHLVTQGRESPEGSYTDDANQEVR 29 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 HSSDINHLVT(0.001)QGRES(0.999)PEGSYTDDANQEVR;HSSDINHLVT(0.002)QGRES(0.998)PEGSYTDDANQEVR;HSSDINHLVT(0.006)QGRES(0.994)PEGSYTDDANQEVR;HSSDINHLVTQGRES(1)PEGSYTDDANQEVR;HSSDINHLVT(0.03)QGRES(0.97)PEGSYTDDANQEVR 279.11 1.68E-71 1193603000 395515 321421 433851 429896 682346 333011 602713 402679 134162 TRUE FALSE 376819.7898 354174.1653 453743.4975 386682.0373 801346.9264 321478.7456 510758.0623 367418.292 154967.1578 2.431610641 2.285478875 2.927997803 2.495251529 5.171075846 2.074495979 3.295911661 2.370942962 1 17.24160297 3.7337908 22.32637063 2.924033832 2.35854475 0.006901087 1.05995642 267.4595415 1251929.164 0.250842533 0.404175346 5417.398707 -3.7337908 -0.565489082 HSSSPLS(ph)PGGPTHLTKPTTTSSSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSSSPLSPGGPTHLTKPTTTSSSER 25 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 HSSSPLS(1)PGGPTHLTKPTTTSSSER 175.07 1.38E-12 104130000 100440 90418 113290 117120 130580 93495 171710 128460 101550 TRUE FALSE 95692.40025 99631.697 118484.4586 105346.8751 153353.1107 90257.24471 145512.4858 117211.3614 117297.8554 0.815806904 0.849390611 1.010116154 0.898114247 1.307382051 0.769470545 1.240538332 0.999262613 1 16.83981711 3.583803172 1.239288904 1.063308035 0.812455238 0.232547593 0.152082578 0.549417802 1.679576199 0.045390773 0.101537389 3835.333837 -3.583803172 -0.250852796 HSSVSDSQPCEPPSVGTEYS(ph)QGASPQPQHQLK ddPTM_SK-BR-3_Trastuzumab_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 1 HSSVSDSQPCEPPS(0.07)VGT(0.07)EY(0.198)S(0.356)QGAS(0.305)PQPQHQLK 63.282 0.018189 57159000 39630 28477 35001 36535 46984 33924 61639 42573 50683 TRUE FALSE 37756.76844 31378.83868 36605.83047 32862.43239 55177.99472 32749.20337 52234.83847 38845.08243 58542.66079 0.644944523 0.53599953 0.625284707 0.561341626 0.942526253 0.559407498 0.892252552 0.663534624 1 15.8372007 0.99605157 0.220874969 1.09587993 0.50642707 0.43964127 0.127200219 2.673976375 0.484292047 0.588809797 0.372637324 9.909496081 -0.99605157 -0.58945286 HSSVYPTQEELEAVQNMVSHTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 217.11 1.41E-32 238083000 213665 149228 209436 231560 422395 170278 348325 246447 260920 FALSE TRUE 203565.4789 164434.5029 219038.8478 208283.1489 496060.5543 164381.2302 295181.6238 224866.7942 301382.141 0.675439753 0.54560135 0.726781113 0.691093202 1.645952055 0.545424588 0.979426395 0.746118511 1 18.2012344 2.970465695 24.99915777 0.96772562 0.640563792 0.247774421 0.280135907 930.4584579 787582.1262 0.078598593 0.083490994 934.2555678 -2.970465695 -0.327161829 HST(ph)SPASSEYSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSTSPASSEYSWK 13 0 Q96N46 Q96N46 TTC14 Tetratricopeptide repeat protein 14 1 HS(0.078)T(0.545)S(0.377)PASSEYSWK 148.7 0.00015967 200290000 294820 264420 280260 296930 230510 296150 339550 282180 150190 TRUE FALSE 280884.4429 291364.6986 293110.1982 267082.0323 270710.871 285894.2512 287745.4112 257470.8233 173480.6981 1.619110632 1.679522285 1.689583921 1.539548982 1.560466807 1.647988821 1.658659518 1.484146802 1 17.40441563 0.832230959 2.998508336 1.000147877 1.631074629 0.943630029 0.048070736 0.167110701 2.544602469 0.048002127 0.012574351 6.795649318 -0.832230959 0.630926752 HSTENDS(ph)PTNVQQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HSTENDSPTNVQQ 13 0 P49354;P49354-2;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 HSTENDS(1)PTNVQQ;HSTENDS(1)PTNVQQ;HSTENDS(1)PTNVQQ;HS(0.059)T(0.059)ENDS(0.873)PT(0.01)NVQQ;HSTENDS(0.998)PT(0.002)NVQQ;HS(0.001)T(0.001)ENDS(0.998)PTNVQQ 220.97 2.09E-11 1138518000 2024719 3030472 2423610 2394530 1776886 2074735 1973796 1711093 584632 TRUE FALSE 1929014.545 3339280.542 2534734.916 2153827.295 2086774.356 2002886.407 1672657.169 1561260.626 675293.7447 2.856556218 4.944930363 3.753529387 3.189467268 3.090172791 2.965948408 2.476932716 2.311972587 1 19.36515567 1.433625106 0.486016487 0.994545233 3.964928965 0.716133381 0.537053909 0.447823601 0.278541448 0.577197655 0.350046107 27.14095384 -1.433625106 2.970383732 HSTPHAAFQPNS(ph)QIGEEMSQNSFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSTPHAAFQPNSQIGEEMSQNSFIK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 HS(0.302)T(0.302)PHAAFQPNS(0.397)QIGEEMSQNSFIK 76.421 0.04946 31909000 19953 20370 20583 22798 18052 21735 25768 20112 11673 TRUE FALSE 19009.86123 22445.72616 21526.75091 20506.30173 21200.26308 20982.3115 21836.61834 18350.88666 13483.18922 1.409893529 1.664719362 1.596562249 1.520879177 1.572347813 1.556183122 1.61954401 1.361019738 1 13.71887416 0.933227197 3.481364377 1.000492938 1.564357222 0.87705408 0.067407304 0.09338197 2.832231512 0.0627924 0.016238537 8.574863144 -0.933227197 0.563864284 HSTPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HSTPSPTR 8 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 HS(0.009)T(0.301)PS(0.68)PT(0.01)R;HS(0.001)T(0.012)PS(0.985)PT(0.003)R 94.804 0.010594 282390000 220286 207050 185340 257894 203507 196151 232838 207153 145348 TRUE FALSE 209873.5173 228148.6304 193838.0223 231970.0052 238998.5564 189358.2417 197314.2867 189013.5851 167887.8255 1.250081813 1.35893493 1.154568664 1.381696406 1.423560974 1.127885486 1.175274539 1.125832588 1 17.35713809 1.524039453 1.065203807 1.027230582 1.30512256 0.559957168 0.08838943 0.340652789 0.749504376 0.075948477 0.027593692 33.42254006 -1.524039453 0.277891979 HSTPSNSSNPSGPPS(ph)PNSPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 HSTPSNSSNPS(0.001)GPPS(0.967)PNS(0.033)PHR;HSTPSNSSNPSGPPS(0.978)PNS(0.022)PHR;HSTPSNSSNPS(0.001)GPPS(0.892)PNS(0.107)PHR;HSTPSNSSNPS(0.001)GPPS(0.983)PNS(0.016)PHR;HSTPSNSSNPS(0.001)GPPS(0.945)PNS(0.054)PHR;HSTPSNSSNPSGPPS(0.964)PNS(0.036)PHR;HSTPSNSSNPS(0.001)GPPS(0.833)PNS(0.166)PHR;HSTPSNSSNPSGPPS(0.901)PNS(0.098)PHR;HSTPSNSSNPS(0.223)GPPS(0.642)PNS(0.135)PHR;HSTPSNSSNPS(0.001)GPPS(0.845)PNS(0.154)PHR 221.29 7.29E-25 1591699000 675544 479743.9 662879 733560 806685 592121 923738 707813 398886.4 TRUE FALSE 643612.3739 528630.3488 693272.6578 659821.1551 947370.6086 571615.7013 782804.8025 645833.1414 460743.6657 1.396899018 1.147341544 1.504681908 1.432078625 2.056177174 1.240637135 1.699002853 1.401718981 1 18.81360481 3.650327564 7.085008041 1.52423887 1.27277566 0.06334899 0.283557009 0.45820139 31.71628468 0.067129358 0.104426113 4470.206274 -3.650327564 -0.25146321 HSTS(ph)PASSEYSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSTSPASSEYSWK 13 0 Q96N46 Q96N46 TTC14 Tetratricopeptide repeat protein 14 1 HS(0.2)T(0.125)S(0.675)PASSEYSWK 169.98 1.78E-05 120430000 157100 133120 145810 169470 122980 148210 178610 163860 87031 TRUE FALSE 149674.1943 146685.0793 152495.5327 152434.5536 144427.6731 143077.4505 151359.7641 149511.5497 100527.323 1.488890681 1.459156327 1.516956069 1.516349477 1.436700678 1.423269279 1.50565796 1.487272766 1 16.61722815 -1.569656911 2.734823903 0.968162759 1.478529589 0.957758631 0.031632203 3403778.409 3389031.349 789377.5182 0.007828411 0.026936619 1.569656911 0.510366831 HSVGVVIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HSVGVVIGR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 161.79 6.43E-05 1001420000 973610 839310 912403 990320 895570 930720 1058000 972010 707159 FALSE TRUE 927589.3848 924836.6432 954237.58 890771.1521 1051757.124 898488.933 896582.6685 886895.6515 816821.6061 1.135608287 1.132238222 1.168232541 1.090533288 1.287621577 1.09998184 1.097648081 1.085788678 1 19.6396615 1.149570332 1.139003483 1.005545481 1.151725288 0.455404798 0.05396147 0.405929683 1.09290719 0.046739377 0.015121586 14.11140744 -1.149570332 0.146179807 HSVTAAT(ph)PPPS(ph)PTSGESGDLLSNLLQSPSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HS(0.027)VT(0.11)AAT(0.767)PPPS(0.575)PT(0.175)S(0.167)GES(0.138)GDLLS(0.04)NLLQSPSSAK;HS(0.005)VT(0.018)AAT(0.949)PPPS(0.738)PT(0.131)S(0.131)GES(0.024)GDLLS(0.003)NLLQSPSSAK;HSVT(0.004)AAT(0.995)PPPS(0.908)PT(0.038)S(0.033)GES(0.021)GDLLSNLLQSPSSAK;HSVTAAT(1)PPPS(0.873)PT(0.069)S(0.056)GES(0.002)GDLLSNLLQSPSSAK;HSVTAAT(1)PPPS(0.88)PT(0.1)S(0.018)GES(0.002)GDLLSNLLQSPSSAK 220.68 1.14E-35 350010000 620458 795113 541822 764772 395980 705860 630762 656368 279372 TRUE FALSE 591130.18 876135.9187 566665.0746 687895.6656 465038.7866 681415.8912 534527.6722 598892.9383 322695.5829 1.831850856 2.715053955 1.756036043 2.131717017 1.441106762 2.111636872 1.65644558 1.855906836 1 18.2998143 -1.075716488 0.159290488 1.27E-09 2.454051627 0.476063314 0.326393273 20.17886046 0.663484498 10.25984357 1.731590796 0.084000817 1.075716488 2.454051626 HSVVAGGGGGEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HSVVAGGGGGEGR 13 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ;;; 134.68 9.27E-05 304810000 247460 246360 238872 262843 267189 238479 299285 251686 239937 FALSE TRUE 235763.0562 271464.3641 249824.5175 236421.5223 313786.677 230220.4124 253623.5765 229647.0396 277145.2045 0.850684235 0.979502296 0.901421036 0.853060123 1.132210379 0.830685174 0.915128865 0.82861632 1 18.08028252 -0.347177606 7.598626501 0.999999969 0.914842836 0.085017797 0.090713637 0 0 0.078626538 0.018532453 0.449595954 0.347177606 -0.085157133 HSWDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HSWDGLR 7 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R2A8;M0R145;M0QXG6;M0R0I1;M0R3C4;M0R2G6 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 143.11 0.002444 83811000 40812 40915 30265 33218 42573 37815 48706 43334 38551 FALSE TRUE 38882.89764 45084.28502 31652.68019 29878.86353 49997.71772 36505.45707 41275.00515 39539.44523 44529.29219 0.873198197 1.012463545 0.71082828 0.670993453 1.12280513 0.81980771 0.926918061 0.88794237 1 15.44246706 2.742500173 24.99933743 0.93441258 0.849836998 0.205275443 0.121767074 869.2594478 5516088.621 0.038604743 0.039579509 552.7136278 -2.742500173 -0.084575582 HT(ph)GEKHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;HT(1)GEKHFK;HT(1)GEKHFK;HT(1)GEKHFK;HT(1)GEKHFK;HT(1)GEKHFK 73.931 0.068369 5634670000 8355880 3546210 7459240 5288150 6865380 8704550 14555650 10607230 9377250 TRUE FALSE 7960914.112 3907572.831 7801253.532 4756575.115 8062700.098 8403109.251 12334918.26 9678404.709 10831426.04 0.73498301 0.360762546 0.720242515 0.439145787 0.744380294 0.77580821 1.138808336 0.89354852 1 23.36871986 2.17428685 1.908342751 1.019543684 0.560953034 0.657687979 0.135658387 0.176156871 1.267012146 0.064100039 0.03874023 149.378072 -2.17428685 -0.45859065 HTADRWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTADRWR 7 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 71.342 0.049773 69652000 103612 77184 58845 77669 122888 74012 122206 123853 136466 FALSE TRUE 98714.4661 85049.13735 61543.10146 69861.56456 144319.6283 71448.94588 103561.2302 113007.7747 157628.4503 0.626247774 0.539554485 0.390431431 0.443204031 0.915568402 0.453274429 0.656995803 0.716924987 1 17.26616842 0.405130617 0.509509633 1.027397255 0.54084173 0.48579851 0.142990197 1.905617111 0.83279811 0.242122057 0.068676472 2.541737034 -0.405130617 -0.486555525 HTAFIGDRN ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTAFIGDRN 9 1 Q9HAB8;Q9HAB8-2 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 ;; 148.91 0.00014251 371060000 286596 219075 233469 230314 252221 221586 304797 246335 219209 FALSE TRUE 273049.1751 241398.9916 244173.7846 207162.3992 296208.2625 213912.4213 258294.6197 224764.6015 253202.8122 1.078381289 0.953381953 0.964340729 0.818167845 1.169845864 0.844826404 1.020109601 0.887686039 1 17.9499339 4.552656193 2.328489455 0.957977519 1.085976736 0.12804665 0.098869504 0.741419459 6.394007979 0.021798688 0.164466239 35699.01166 -4.552656193 0.127999217 HTDVQFYTEVGEITTDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTDVQFYTEVGEITTDLGK 19 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 217.97 3.47E-19 288257000 436340 441710 434040 501060 318390 477410 482790 511580 259784 FALSE TRUE 415715.0729 486720.7512 453941.1633 450692.4968 373917.1152 460877.172 409131.5185 466783.3431 300069.9759 1.385393762 1.622024162 1.512784349 1.501957986 1.246099727 1.535898987 1.363453698 1.555581633 1 18.19493945 -2.95140894 0.333228876 1.25E-10 1.489823242 0.629272983 0.110910962 49.04492138 1.486303183 34.74325717 0.086614043 0.001118384 2.95140894 1.489823242 HTENTFSRPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTENTFSRPGGR 12 1 Q05682-5;Q05682-4;C9J813;E9PGZ1;E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682 Q05682-5 CALD1 Caldesmon 0 ; 59.155 0.060708 40657000 63177 47542 61828 56957 52126 63419 89413 65623 71875 FALSE TRUE 60190.74841 52386.58385 64662.87496 51231.57415 61216.7579 61222.78413 75771.40467 59876.70223 83021.00791 0.725006236 0.631003949 0.778873644 0.617091691 0.737364668 0.737437254 0.912677485 0.721223504 1 16.34118883 1.113067555 0.451350999 1.002786352 0.670375427 0.597785654 0.073848809 0.654851107 0.362570608 0.085509736 0.04644379 12.97381064 -1.113067555 -0.332410925 HTGCCGDNDPIDVCEIGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HTGCCGDNDPIDVCEIGSK 19 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 304.37 3.09E-50 6852860000 7247920 6054660 6256650 7544820 4719140 7048010 7793370 6962900 2863330 FALSE TRUE 6905325.186 6671636.738 6543523.591 6786400.359 5542156.522 6803935.646 6604348.271 6353191.563 3307360.593 2.087865835 2.017208753 1.978472987 2.051908212 1.675703742 2.057210109 1.996863688 1.920924975 1 21.65724892 -2.000415796 0.44795194 5.54E-13 2.006570778 0.879012484 0.113729722 17.92164297 1.250427499 18.59742145 0.058617037 0.009990431 2.000415796 2.006570778 HTGMASIDSSAPETTSDSS(ph)PTLSR ddPTM_SK-BR-3_Trastuzumab_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(0.006)S(0.981)PT(0.012)LS(0.001)R 171.63 4.15E-12 184620000 97860 85367 95863 101320 92506 89101 111760 95709 74401 TRUE FALSE 93234.35174 94065.99435 100258.4134 91135.1211 108639.0171 86015.41003 94708.95939 87328.21257 85938.72709 1.084893329 1.094570487 1.166626697 1.060466267 1.264145058 1.000892298 1.102052155 1.016168327 1 16.39102079 1.418327078 1.276641203 1.002088303 1.117096113 0.293674903 0.067878475 0.519786403 1.626309294 0.055336579 0.018357709 26.20155573 -1.418327078 0.11500781 HTGPGILSMANAGPNTNGSQFFICTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 300.5 7.34E-71 5518000000 5250240 3592020 4704600 5430810 4145150 5111830 5777920 5191220 3486080 FALSE TRUE 5002071.56 3958050.922 4920310.563 4884894.661 4868062.848 4934806.045 4896392.185 4736649.256 4026683.482 1.242231127 0.982955561 1.221926329 1.213131025 1.208950957 1.225526185 1.215986359 1.176315267 1 21.94116064 4.779853421 22.95875232 1.164040423 1.24223181 0.076065502 0.090742713 6805.369143 5233196.697 0.021327499 2.080735783 60235.62508 -4.779853421 0.078191387 HTGPNS(ph)PDTANDGFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.99)PDT(0.01)ANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR 356.53 1.92E-87 14572790000 5105500 4131970 4572200 5398680 4630760 4629320 5711410 4032000 1416780 TRUE FALSE 4864173.133 4553022.441 4781839.893 4855994.43 5438363.078 4469005.488 4840029.507 3678936.705 1636487.006 2.972326156 2.782192845 2.922015191 2.967328436 3.323193558 2.730853022 2.95757283 2.248069609 1 20.64217072 0.886094349 2.123655356 1.000446722 2.947536916 0.939238518 0.158776719 0.097656151 0.895854695 0.143572356 0.039525987 7.692975497 -0.886094349 1.947090194 HTGPNSPDTANDGFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 300.32 7.00E-46 7179540000 3459633 2846438 3091560 3457456 3197904 3084965 3823898 3325943 2635144 FALSE TRUE 3296103.004 3136493.268 3233311.084 3109905.954 3755617.445 2978131.889 3240492.129 3034705.799 3043788.673 1.082894826 1.030456975 1.062265299 1.021722034 1.233862744 0.978429257 1.064624544 0.997015931 1 21.53743677 1.525920231 1.617178038 1.001683406 1.07089104 0.158572343 0.066156083 0.69500711 3.536941177 0.052243362 0.017559595 33.56759535 -1.525920231 0.069207634 HTGYVIELQHVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTGYVIELQHVVK 13 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 149.82 2.54E-05 320290000 433580 403560 363150 445150 400770 467020 524640 461020 273470 FALSE TRUE 413085.5327 444683.2228 379800.7867 400402.6763 470664.1611 450846.9803 444596.5323 420650.6448 315878.3309 1.307736214 1.40776742 1.202364169 1.267585134 1.490017247 1.427280494 1.407492977 1.331685664 1 18.26900945 0.949435667 20.44307466 0.999999999 1.362376815 0.644477143 0.083116684 844.8523227 341573.8415 0.08088212 0.02022053 8.900935757 -0.949435667 0.362376816 HTHVQDGEAGGITQQIGATNVPLEAINEQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTHVQDGEAGGITQQIGATNVPLEAINEQTK 31 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 60.093 0.016835 88601000 78536 65826 83212 76768 77414 74421 103230 72262 90511 FALSE TRUE 74823.75892 72533.74424 87027.35251 69051.13479 90914.97709 71843.78211 87480.36755 65934.3562 104546.9836 0.715695052 0.693790885 0.832423371 0.660479455 0.869608801 0.687191343 0.836756495 0.630667227 1 16.67379191 -2.095243986 2.439876891 1.437445827 0.743827514 0.504545497 0.080664506 7239681.809 2515866.197 17555436.17 0.016873761 0.008030748 2.095243986 -0.693618313 HTIAVVWGGVNIPHSPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTIAVVWGGVNIPHSPYR 18 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 90.654 0.0015415 209190000 86978 52391 52104 57557 72745 57374 94116 64192 31004 FALSE TRUE 82866.72231 57729.70246 54493.01994 51771.26101 85431.70497 55387.12399 79756.87564 58571.00818 35811.94197 2.313941042 1.612023791 1.521643813 1.445642379 2.38556471 1.546610458 2.227102783 1.635516114 1 15.12815313 0.981460815 23.59998744 0.99999998 1.867575912 0.385630894 0.343646528 614.7354471 782547.138 0.310042861 0.077510715 9.582102554 -0.981460815 0.867575932 HTIPEEETHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTIPEEETHR 10 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81 Q70J99 UNC13D Protein unc-13 homolog D 0 123.75 0.00026244 421560000 164900 153310 159590 172250 152770 162030 212890 203010 152180 FALSE TRUE 157105.5038 168932.4633 166907.3594 154935.1027 179413.0396 156418.8605 180409.7205 185233.3682 175779.2972 0.893765684 0.96104869 0.949527971 0.881418377 1.020672187 0.889859403 1.026342257 1.053783757 1 17.42340564 1.641082178 6.62590256 1.031574686 0.93526887 0.517219701 0.042657989 0.093404776 8.421995463 0.01975977 0.009817649 43.76049014 -1.641082178 -0.096305816 HTLADNFNPVSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTLADNFNPVSEER 14 0 P20645;H0YGT2 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 127.03 0.00033197 0 127920 100890 82277 116620 121190 107110 134430 111280 99750 FALSE TRUE 121873.4751 111170.8057 86049.48183 104897.136 142325.4976 103400.7538 113920.2345 101535.7333 115218.7205 1.057757581 0.964867559 0.746835943 0.91041747 1.235263653 0.897430152 0.988730251 0.881243367 1 16.81401562 -2.675433863 2.141519747 1.956583518 0.965784554 0.007971967 0.126679348 7287050.476 1558441.88 32940489.54 0.029780351 0.002111379 2.675433863 -0.990798964 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR 32 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 280.69 3.85E-74 2790500000 1583070 1602840 1419420 1907770 1433800 1695860 1971830 1542430 138905 FALSE TRUE 1508241.418 1766171.218 1484501.811 1715997.335 1683854.266 1637131.943 1670991.118 1407366.652 160445.678 9.400324381 11.00790773 9.252363976 10.69519202 10.49485587 10.2036525 10.41468452 8.771608373 1 17.2917254 0.721925328 2.556347766 1.000605396 10.23764608 0.965860499 0.539954075 0.23877363 1.992782876 0.466276067 0.124257951 5.271392179 -0.721925328 9.237040683 HTLGDS(ph)DNES ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HTLGDSDNES 10 0 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 HTLGDS(1)DNES;HTLGDS(0.995)DNES(0.005);HTLGDS(1)DNES;HTLGDS(1)DNES;HT(0.001)LGDS(0.999)DNES 134.01 0.00019085 2134148000 2331688 2275949 2027353 2415965 1808059 2102931 2328385 1961032 1344481 TRUE FALSE 2221473.729 2507870.791 2120309.14 2173107.608 2123383.917 2030105.972 1973147.105 1789313.642 1552976.247 1.430462142 1.614880328 1.36531975 1.399317995 1.367299675 1.307235688 1.270558457 1.152183522 1 20.56660433 1.59897706 0.39894344 0.979447989 1.537162024 0.858542882 0.061778695 0.346487183 0.159251704 0.073783995 0.058518933 39.71705698 -1.59897706 0.557714035 HTLQQHQET(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTLQQHQETPK 11 0 Q7Z417;Q7Z417-2 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 HTLQQHQET(1)PK 83.351 0.031305 87336000 69985 75829 55724 62490 47241 62280 61368 66825 51025 TRUE FALSE 66676.94775 83556.06131 58279.00052 56208.38648 55479.81544 60123.22798 52005.1845 60973.44874 58937.6964 1.131312417 1.417701512 0.988823861 0.953691608 0.941329893 1.020114997 0.882375588 1.034540752 1 15.84690305 3.659258126 7.285240296 0.963957653 1.273807365 0.705902907 0.080368088 0.114729438 9.212286858 0.019980759 0.031081696 4563.080457 -3.659258126 0.309849712 HTMDKDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTMDKDSR 8 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 0 ; 80.165 0.015714 56426000 50904 35280 35271 37228 38894 37821 52466 41923 34310 FALSE TRUE 48497.8688 38875.07211 36888.21024 33485.77071 45677.10129 36511.24929 44461.3481 38251.99987 39630.61957 1.223747429 0.98093526 0.930800745 0.844946939 1.152570961 0.921288884 1.121893843 0.965213269 1 15.2743279 4.549592554 2.632548667 0.995819454 1.230477389 0.391377976 0.091045003 0.331074609 3.901026573 0.021668492 0.141713088 35448.06665 -4.549592554 0.234657935 HTNFVEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTNFVEFR 8 0 M0R0N4;M0QYZ2;P53680;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 ;; 140.83 0.00064319 482440000 269098 306436 231676 232681 225346 257087 256765 277881 173327 FALSE TRUE 256378.2708 337662.1768 242298.5738 209291.4638 264646.2711 248184.0127 217590.7834 253548.2665 200205.6659 1.280574501 1.686576527 1.210248335 1.045382321 1.321872035 1.2396453 1.086836291 1.266439016 1 17.61112328 3.596052537 7.277258245 1.16832961 1.482309311 0.479137408 0.137828301 0.189100002 10.584801 0.034126772 0.052978826 3945.05023 -3.596052537 0.313979701 HTNPSSS(ph)SPGTRT ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.129)S(0.129)S(0.469)S(0.272)PGTRT 73.877 0.0093608 0 44794 37750 41479 43760 32720 45346 46780 38623 29559 TRUE FALSE 42676.67639 41596.76792 43380.85318 39361.16166 38426.35764 43775.65665 39642.85183 35240.96537 34142.85875 1.249944438 1.218315321 1.270568862 1.152837316 1.12545812 1.282132143 1.161087656 1.032162117 1 15.05929624 1.281720004 2.97976701 1.002565521 1.215846221 0.742175246 0.048323436 0.123471302 1.828396768 0.041299752 0.01217533 19.13022174 -1.281720004 0.2132807 HTNPSSSS(ph)PGTRT ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPSS(0.005)S(0.167)S(0.81)PGT(0.015)RT(0.002);HTNPSS(0.005)S(0.253)S(0.722)PGT(0.01)RT(0.01) 90.334 0.0043112 68001000 69528 58828 68985 72846 80379 73972 94182 79103 69689 TRUE FALSE 66241.54923 64822.64008 72148.03049 65523.38168 94397.07215 71410.33109 79812.80613 72176.32197 80496.0142 0.822917133 0.80529006 0.896293204 0.813995355 1.1726925 0.887128783 0.991512523 0.896644669 1 16.29662973 HTNYTMEHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 204.17 1.11E-07 1819104000 663908.9 397536.6 272701 363723.2 731556.9 354980.7 792649.6 473776 416730 FALSE TRUE 632527.242 438046.0315 285204.6106 327161.0529 859140.1917 342687.6293 671716.3455 432289.6618 481354.36 1.314057365 0.910028179 0.592504471 0.679667788 1.784839326 0.711923809 1.395471614 0.898069484 1 18.87673983 HTPLRTS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTPLRTSLR 9 1 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4;J3KRP9 Q9HCD6 TANC2 Protein TANC2 1 HT(0.001)PLRT(0.25)S(0.749)LR 79.286 0.016576 410060000 323910 288700 296620 410420 281390 322440 396540 343390 268660 TRUE FALSE 308599.4162 318118.8582 310220.3204 369163.8019 330464.3269 311273.8219 336040.54 313320.9512 310322.4207 0.994447696 1.025123668 0.999670986 1.189613696 1.064906384 1.003065848 1.082875479 1.009662629 1 18.24340841 HTPLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTPLSK 6 0 P61956;P61956-2;A8MUA9;A8MU27;P55854;P55854-2 P61956;A8MUA9 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 0 76.847 0.073978 341200000 464410 348840 402100 466820 352490 414960 512420 451260 320010 FALSE TRUE 442458.2597 384387.1926 420536.6827 419894.3667 413964.1444 400589.8312 434240.9178 411745.2821 369635.5164 1.1970123 1.039908709 1.137706373 1.135968672 1.11992524 1.083742804 1.174781368 1.113922401 1 18.49574386 -1.207533628 2.821220715 0.999285477 1.124411734 0.450349672 0.043516445 2278157.156 2891425.667 14511.44531 0.010536288 0.062010663 1.207533628 0.125126257 HTPLYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTPLYER 7 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52;Q5T035 Q9NZB2 FAM120A;C9orf129 Constitutive coactivator of PPAR-gamma-like protein 1;Putative uncharacterized protein C9orf129 0 78.77 0.034434 360190000 219480 193000 164520 191450 212450 181120 260130 199330 186930 FALSE TRUE 209105.6154 212666.9194 172063.4047 172205.0823 249501.2127 174847.769 220442.3909 181875.6085 215918.1497 0.968448533 0.984942302 0.796891808 0.797547971 1.155536082 0.80978727 1.020953501 0.842335898 1 17.72012499 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.001)PS(0.999)PGLPAEGAPEAPRPS(0.528)S(0.472)PPPEVLEPHSLDQPPATSPR 153.07 1.54E-13 65756000 15111 15649 13771 15222 9163.3 13437 15416 15401 7327.8 TRUE FALSE 14396.73298 17243.65089 14402.41397 13691.85564 10761.37662 12971.67332 13064.00607 14052.40679 8464.157799 1.70090555 2.037255366 1.701576733 1.617627644 1.271405481 1.532541527 1.543450202 1.660225049 1 13.04715081 -0.744337244 0.089696125 6.48E-11 2.431584567 0.600002417 0.173701944 39.46299464 0.783069802 15.79629234 6.281324196 0.180161818 0.744337244 2.431584566 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.141)PS(0.859)PGLPAEGAPEAPRPS(0.502)S(0.479)PPPEVLEPHS(0.013)LDQPPAT(0.003)S(0.003)PRPLIEVGELLDLT(0.002)R;HT(0.033)PS(0.967)PGLPAEGAPEAPRPS(0.529)S(0.471)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.225)PS(0.756)PGLPAEGAPEAPRPS(0.517)S(0.489)PPPEVLEPHS(0.009)LDQPPAT(0.001)S(0.001)PRPLIEVGELLDLT(0.001)R 168.31 1.38E-24 195290000 878.88 0 0 1041.4 889.28 819.03 1795.93 998.37 0 TRUE FALSE 837.3370842 0 0 936.7164935 1044.37015 790.6667857 1521.927894 910.9474301 0 0 HTPSPGLPAEGAPEAPRPS(ph)S(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.002)PS(0.008)PGLPAEGAPEAPRPS(0.734)S(0.734)PPPEVLEPHS(0.282)LDQPPAT(0.105)S(0.105)PRPLIEVGELLDLT(0.031)R 48.299 0.0025002 60157000 3575.9 3970.9 3447.1 3961.2 4075.4 4119.2 3530.3 2944.7 3109.4 TRUE FALSE 3406.874294 4375.539225 3605.152945 3563.01265 4786.14847 3976.551071 2991.687897 2686.846457 3591.589871 0.948569969 1.218273628 1.003776342 0.992043295 1.332598833 1.107184064 0.832970357 0.748093895 1 11.8104069 1.733307383 5.934771841 0.843954324 1.103702484 0.438529197 0.127380906 0.125981732 11.55825354 0.060966641 0.031543696 54.11371905 -1.733307383 0.25974816 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.478)S(0.478)PPPEVLEPHS(0.027)LDQPPAT(0.008)S(0.008)PR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.498)S(0.498)PPPEVLEPHS(0.004)LDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.498)S(0.498)PPPEVLEPHS(0.004)LDQPPATSPR 244.75 3.49E-51 776480000 316345.5 395614 293134 394026 254332.7 346400 319376 332833 177474.2 TRUE FALSE 301392.4752 435927.5164 306574.4838 354417.7579 298688.2424 334404.0811 270649.3255 303688.3781 204995.9925 1.470235937 2.12651726 1.495514522 1.728900909 1.4570443 1.631271309 1.320266421 1.481435682 1 17.64523618 1.210860437 0.387960234 0.97129742 1.795902892 0.524507658 0.198073718 0.841884938 0.378746925 0.268264138 0.169464723 16.25026462 -1.210860437 0.824605472 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.497)S(0.497)PPPEVLEPHS(0.003)LDQPPAT(0.001)S(0.001)PRPLIEVGELLDLT(0.001)R;HTPSPGLPAEGAPEAPRPS(0.49)S(0.49)PPPEVLEPHS(0.019)LDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.454)S(0.454)PPPEVLEPHS(0.084)LDQPPAT(0.003)S(0.003)PRPLIEVGELLDLT(0.003)R;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 137.09 6.69E-15 618494000 154177 117051 149422 154681 143003 137566 200904 168606 110340 TRUE FALSE 146889.3588 128978.63 156273.1465 139132.172 167942.6779 132802.0549 170252.4049 153841.9648 127450.9637 1.152516658 1.011986307 1.22614331 1.09165257 1.317704261 1.041985491 1.335826737 1.207067882 1 16.95958276 3.72681163 24.90139022 1.191270873 1.08225148 0.087245605 0.114025488 1135.116296 2405821.631 0.027055914 0.042296798 5331.036177 -3.72681163 -0.109019393 HTQENCETWGVNGETGTLVDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTQENCETWGVNGETGTLVDMK 22 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 268.13 6.47E-38 489400000 566227 628590 529053 647381 348137 579653 590633 630184 305108 FALSE TRUE 539462.5719 692644.0356 553310.6034 582305.0319 408851.9826 559579.4713 500521.0881 575001.7481 352422.5904 1.530726425 1.96537922 1.57002025 1.652292015 1.160118544 1.587808178 1.420229866 1.631568929 1 18.42694688 -2.476937075 0.120857277 2.39E-12 1.941328795 0.46071472 0.196209177 57.93041032 0.865396395 18.13298077 2.116277855 0.003334747 2.476937075 1.941328795 HTQLEQMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HTQLEQMFR 9 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 154.84 7.47E-05 1375470000 1018840 809930 763380 875730 935380 804410 1093890 897230 775530 FALSE TRUE 970681.4523 892462.7878 798381.7281 787699.9566 1098509.976 776553.08 926996.9898 818663.7847 895795.2315 1.083597476 0.996279905 0.89125472 0.879330375 1.226295851 0.86688682 1.034831351 0.913896118 1 19.77280946 4.370602715 2.679667179 0.976491292 1.077576994 0.094977547 0.105009513 0.644322028 8.64400938 0.02440795 0.099203686 23474.84399 -4.370602715 0.101085702 HTSKLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTSKLSR 7 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HTSKLS(1)R 99.257 0.0064566 128060000 136140 92644 123190 131590 196720 100350 212480 171630 184430 TRUE FALSE 129704.932 102084.5289 128838.3834 118362.3232 231027.9057 96874.85434 180062.2735 156601.1673 213030.4625 0.608856266 0.479201555 0.604788545 0.555612197 1.084482956 0.454746487 0.845241903 0.735111615 1 17.70070022 1.578840365 0.154535874 1.173937466 0.336066744 0.343455787 0.172258657 4.375895024 0.702315288 1.593408034 1.624889629 37.91755846 -1.578840365 -0.837870722 HTTDLDASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 193.38 3.36E-05 4268830000 8041650 5224080 5873270 7064420 6249740 5657900 8447400 6745170 4244310 FALSE TRUE 7661537.142 5756419.691 6142565.239 6354291.08 7339692.677 5461965.504 7158593.983 6154527.156 4902495.918 1.562782972 1.174181435 1.252946528 1.296133885 1.497133868 1.114119338 1.460193767 1.255386493 1 22.225085 0.977040789 22.37234816 0.999999989 1.333642658 0.362554465 0.140153482 503.2124667 490351.6394 0.122832196 0.030708049 9.485075431 -0.977040789 0.333642669 HTTEAAAGALQNITAGDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HTTEAAAGALQNITAGDRR 19 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;; 221.13 1.78E-19 615590000 442810 374674 404090 478100 460360 401830 539460 486420 448440 FALSE TRUE 421879.2489 412853.7066 422617.9262 430040.4797 540646.6382 387914.5263 457155.4691 443826.4861 517981.7849 0.814467345 0.797042905 0.815893413 0.83022317 1.043756082 0.748896076 0.882570551 0.856838018 1 18.98254184 -4.999999993 0.106288502 1.487299946 0.749639809 0.305030683 0.076012158 206.6413588 1.473251186 22.19928144 0.982833435 1.00E-05 4.999999993 -0.737660137 HTTENKPHS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTTENKPHSPK 11 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(1)PK 81.656 0.012729 23683000 60017 53686 49981 62240 35972 63462 58011 51350 20455 TRUE FALSE 57180.11535 59156.66444 52272.67829 55983.51695 42245.50541 61264.29503 49160.3565 46853.52178 23627.05693 2.420111634 2.503767804 2.212407514 2.369466376 1.788013866 2.592971914 2.080680495 1.983045197 1 14.52815231 -1.426887278 0.267777317 6.68E-18 2.463686132 0.781529935 0.215597978 8.721173796 0.459054459 6.284783863 0.274680802 0.03742077 1.426887278 2.463686132 HTTFEQPVFSVSKQS(ph)PPISTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTTFEQPVFSVSKQSPPISTSK 22 1 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 HTTFEQPVFSVS(0.003)KQS(0.997)PPISTSK;HTTFEQPVFSVS(0.001)KQS(0.999)PPISTSK 206.4 5.63E-23 279960000 500240 420910 485360 586020 412650 597060 775640 694160 401900 TRUE FALSE 476594.6466 463801.2075 507614.2361 527112.1562 484616.0294 576383.6625 657301.8724 633375.6704 464224.5994 1.026646686 0.999087959 1.093466905 1.135467954 1.043925785 1.24160517 1.415913489 1.364373347 1 18.82446345 2.149173299 4.124535798 1.31090436 1.052945919 0.383194132 0.117108234 0.164869984 5.23947343 0.042287369 0.030528454 140.9851266 -2.149173299 -0.257958441 HTTSIFDDFAHYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTTSIFDDFAHYEK 14 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 187.16 5.66E-07 105400000 234630 152920 185940 241960 205520 208230 290250 218800 38910 FALSE TRUE 223539.5049 168502.7219 194465.5329 217637.7211 241362.6229 201018.9429 245967.0317 199640.7121 44943.96408 4.973738065 3.749173561 4.326844259 4.842423796 5.370301172 4.472657164 5.472748939 4.441991626 1 15.45583976 0.952284528 23.18375182 0.999999995 4.711502252 0.846308261 0.497829273 2277.419526 1106542.513 0.506311428 0.126577858 8.959515564 -0.952284528 3.711502258 HTVDDGLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTVDDGLDIR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 142.72 3.53E-05 209990000 261212 251314 231482 311531 258355 246973 254339 251051 187438 FALSE TRUE 248865.0264 276923.1823 242095.6787 280215.312 303412.0302 238420.2631 215534.9143 229067.6435 216504.9277 1.149465876 1.279061799 1.118199392 1.294267594 1.401409351 1.101223263 0.99551967 1.05802508 1 17.72404034 2.010720477 24.55354039 1.025105674 1.240767906 0.646486474 0.078939307 106.7338267 244455.5376 0.028962533 0.021368682 102.4992002 -2.010720477 0.215662231 HTVDDGLDIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HTVDDGLDIRK 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 101.93 0.0019065 87929000 39767 29798 39954 43256 36515 44467 58888 49021 34692 FALSE TRUE 37887.29272 32834.45008 41785.93042 38907.8247 42883.20444 42927.09664 49903.55405 44728.46136 40071.85818 0.945483799 0.819389256 1.042774963 0.970951348 1.070157622 1.071252959 1.245351634 1.11620632 1 15.29030179 2.944364915 1.022599178 1.141797112 0.890025509 0.497183609 0.079510529 0.322704341 0.72827074 0.036763706 0.042294399 879.7614236 -2.944364915 -0.251771602 HTVLYIS(ph)PPPEDLLDNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HTVLYISPPPEDLLDNSR 18 0 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 1 HTVLYIS(1)PPPEDLLDNSR;HTVLYIS(1)PPPEDLLDNSR 138.35 1.42E-06 60368000 69970 60379 58738 77684 69140 64436 75598 69284 56897 TRUE FALSE 66662.65677 66531.68875 61431.1954 69875.05673 81197.99411 62204.56516 64064.13665 63217.12566 65720.29617 1.014338958 1.012346149 0.934737044 1.063218835 1.235508646 0.946504638 0.974799877 0.961911759 1 16.00405136 HVAEDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 126.41 0.0012203 1562810000 2003120 1600400 1656440 1686760 1418450 1520380 1803380 1817970 1237880 FALSE TRUE 1908436.487 1763482.58 1732389.412 1517203.68 1665827.231 1467728.859 1528241.26 1658778.909 1429844.108 1.334716475 1.233339054 1.21159321 1.06109727 1.165041155 1.026495721 1.068816699 1.160111721 1 20.44742643 3.81318252 0.726841238 1.067627229 1.362641236 0.72758774 0.054061705 0.488674172 0.424808042 0.023180336 0.097777107 6504.029761 -3.81318252 0.295014007 HVAEVLEYTKDEQLESLFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVAEVLEYTKDEQLESLFQR 20 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 238.65 7.37E-30 403970000 245840 228660 237390 264270 185260 264380 257520 277650 159020 FALSE TRUE 234219.6304 251960.714 248274.5663 237705.0775 217569.2853 255224.4543 218230.5943 253337.4941 183680.0094 1.275150361 1.371737266 1.351668954 1.294126009 1.18450171 1.389505886 1.188102042 1.379232802 1 17.4868351 -3.683591683 0.296685965 2.00E-09 1.320924267 0.610913851 0.075185725 68.8658691 1.327475062 42.27222221 0.069549879 0.000207209 3.683591683 1.320924265 HVAVTNMNEHSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 113.8 0.00045886 89584000 43309 37609 38688 47195 55344 34115.3 53992 49760 56895 FALSE TRUE 41261.8694 41441.39986 40461.88307 42450.86894 64995.97608 32933.87861 45754.52877 45402.75061 65717.98602 0.627862658 0.63059449 0.615689639 0.645955111 0.989013511 0.501139499 0.696225364 0.69087252 1 16.00400065 -5 0.263038416 3.173273182 0.642459102 0.410913783 0.12327361 192.6258246 1.885657761 226.6507076 0.147807433 1.00E-05 5 -2.53081408 HVCEMLVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVCEMLVQR 9 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 141.02 0.00010771 584760000 88663 75777 53800 72453 102959 76580 90461 81228 103903 FALSE TRUE 84472.0757 83498.76245 56266.78322 65169.88679 120915.017 73928.0154 76659.51302 74115.2457 120015.7466 0.703841605 0.695731725 0.46882834 0.543011135 1.007492937 0.615985964 0.638745458 0.617546012 1 16.87286418 HVDAHATLNDGVVVQVMGLLSNNNQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVDAHATLNDGVVVQVMGLLSNNNQALR 28 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 154.69 1.46E-08 133256000 124551 105172 133036 135919 121127 127895 148843 121429 50624 FALSE TRUE 118663.7211 115889.1464 139135.8322 122256.1639 142251.5104 123465.9641 126134.2667 110796.033 58474.51137 2.029323859 1.981874558 2.379427018 2.090759906 2.43270969 2.111449266 2.157081157 1.894774842 1 15.83552028 0.757015712 2.146420295 1.000209164 2.154195844 0.869874434 0.141669121 0.343165345 2.43219283 0.136912706 0.037433987 5.714993118 -0.757015712 1.15398668 HVDAHATLNDGVVVQVMGLLSNNNQALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVDAHATLNDGVVVQVMGLLSNNNQALRR 29 1 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 83.788 0.00087959 10627000 12167 8060.5 11472 10028 15929 9732.6 16886 11946 3360.6 FALSE TRUE 11591.89002 8881.874114 11998.00255 9019.966388 18707.01256 9395.557622 14309.73057 10899.94491 3881.744684 2.986257718 2.288113937 3.09087885 2.323688733 4.81922797 2.420447089 3.686417251 2.808001504 1 11.92248951 HVDNIMFENHTVADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HVDNIMFENHTVADR 15 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 157.42 1.37E-06 429199000 320532 317166 298259 362824 301476 304414 364462 387081 207610 FALSE TRUE 305381.0876 349485.576 311934.4702 326352.2422 354053.3189 293872.0668 308856.6281 353186.1356 239805.0985 1.273455358 1.457373418 1.300783312 1.360906187 1.476421149 1.22546213 1.287948547 1.472804948 1 17.87150281 -1.688434992 2.944199404 0.957392093 1.35224087 0.61709467 0.088283488 16103591.6 16020227.31 5135804.854 0.020620792 0.020491087 1.688434992 0.394848777 HVDSLSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVDSLSQR 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 74.301 0.041332 61369000 122570 113190 138700 178200 121500 169990 180520 187250 163360 FALSE TRUE 116776.359 124724.1897 145059.5322 160286.9974 142689.5615 164103.2037 152978.3585 170853.3973 188693.0345 0.618869474 0.660989898 0.768759338 0.849459006 0.756199411 0.869683421 0.81072605 0.905456833 1 17.52568164 6.010534502 0.149919746 1.044510595 8.03E-13 0.863004291 0.041544284 12.03716136 0.205576135 0.165826303 2.505767388 1024553.172 -6.010534502 -1.044510595 HVDSLSQRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 HVDSLSQRSPK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 HVDSLSQRS(1)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK;HVDSLS(0.434)QRS(0.566)PK;HVDSLS(0.001)QRS(0.999)PK;HVDSLS(0.01)QRS(0.99)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK;HVDSLS(0.042)QRS(0.958)PK;HVDSLS(0.003)QRS(0.997)PK 174.39 6.70E-06 13600980000 7764900 3334400 7547080 6121200 6273970 7241950 11476270 8396150 6414460 TRUE FALSE 7397868.566 3674179.151 7893121.083 5505885.346 7368148.382 6991159.456 9725354.235 7660938.595 7409181.696 0.998473093 0.495895404 1.065316172 0.743116524 0.994461829 0.943580512 1.312608414 1.033979042 1 22.82088278 2.363418387 1.550733262 1.138962017 0.798290475 0.285650661 0.179857803 0.376214828 1.825084985 0.086348444 0.059029607 230.8970513 -2.363418387 -0.340671542 HVDWVK ddPTM_SK-BR-3_Trastuzumab_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 ; 99.511 0.038715 1280130000 2770900 3023700 2491000 3214600 2286300 2721300 3050600 3112100 2282300 FALSE TRUE 2639925.048 3331818.468 2605214.814 2891462.301 2685029.996 2627060.699 2585174.942 2839588.026 2636227.428 1.001402618 1.26385851 0.988235987 1.09681823 1.018512276 0.996522785 0.980634263 1.077140764 1 21.33004341 3.690382776 24.99936641 1.020588186 1.132631045 0.285515252 0.072342628 404.1121901 209692.6888 0.018276656 0.028314114 4902.106877 -3.690382776 0.112042859 HVEDGNVTVQHAALSALR ddPTM_SK-BR-3_Trastuzumab_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 ; 206.7 4.77E-16 474270000 89334 94359 82149 99517 133801 82673 105162 91054 96350 FALSE TRUE 85111.35886 103974.2894 85915.61291 89513.36209 157135.852 79810.01328 89117.60547 83080.82905 111291.4659 0.764760875 0.934252133 0.771987431 0.804314701 1.411930832 0.717126085 0.800758663 0.746515722 1 16.76398344 -1.253763392 3.342553142 1.000418163 0.868139895 0.039999699 0.201721322 71878657.75 106904559.6 311073.0301 0.045747945 0.055748939 1.253763392 -0.132278268 HVENDGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HVENDGYK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;;; 130.56 0.0010426 976160000 1341090 1134580 1124790 1432220 988020 1264180 1511440 1386650 968510 FALSE TRUE 1277699.333 1250194.992 1176362.734 1288250.525 1160330.375 1220401.13 1280842.068 1265227.575 1118701.584 1.142127044 1.117541094 1.051542923 1.151558684 1.037211703 1.090908556 1.144936314 1.130978621 1 20.09339382 -2.51029285 1.875031949 3.34E-05 1.11045305 0.433872381 0.038830471 503795.184 38372.1652 2134864.551 0.009177493 0.003088212 2.51029285 1.110419693 HVFAIFNTEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVFAIFNTEQR 11 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 116.74 0.00094881 320570000 848670 755620 672650 754780 721540 730240 945370 781660 727860 FALSE TRUE 808555.051 832618.5371 703491.6678 678908.0804 847376.3476 704951.6057 801136.4436 713213.7066 840732.8114 0.961726532 0.990348569 0.836760096 0.80751943 1.007902078 0.838496602 0.952902554 0.848323863 1 19.68128785 3.762162358 24.83576778 0.897351407 0.976037562 0.174218644 0.06981118 1054.249502 1109367.535 0.016197131 0.029179422 5783.12205 -3.762162358 0.078686156 HVFGESDELIGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HVFGESDELIGQK 13 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;;; 283.82 2.99E-32 5484190000 9365280 6478460 7507720 8915680 7631540 8179190 11830530 9629540 6253190 FALSE TRUE 8922601.775 7138622.439 7851956.388 8019458.908 8962478.16 7895942.599 10025565.37 8786326.428 7222902.768 1.235320765 0.988331516 1.087091525 1.110281997 1.240841591 1.09318135 1.388024412 1.216453649 1 22.78414732 2.789518251 5.917729454 1.218070015 1.098370286 0.077141155 0.117216367 0.346891815 28.82630035 0.034368011 0.036189502 615.911412 -2.789518251 -0.119699729 HVGDLGNVTADKDGVADVS(ph)IEDSVISLSGDHCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 1 HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR;HVGDLGNVT(0.018)ADKDGVADVS(0.449)IEDS(0.449)VIS(0.079)LS(0.004)GDHCIIGR 178.1 4.48E-23 164076000 264801 187918 232597 248689 181915 249716 321556 291421 129801 TRUE FALSE 252284.3815 207067.0578 243261.8025 223690.3092 213640.9184 241068.2723 272496.7264 265902.6323 149929.8761 1.682682518 1.381092703 1.622503858 1.491966211 1.424938937 1.607873484 1.817494508 1.773513319 1 17.19392837 2.016733371 23.20861198 1.644047494 1.519394862 0 0.242152042 306.1309162 424589.1639 0.080804648 0.059656367 103.9281918 -2.016733371 -0.124652632 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;; 388.89 2.16E-179 2580039000 684668 558040 621030 700217 585659.3 647690 812274 715446 389173.6 FALSE TRUE 652305.1005 614904.9104 649504.8398 629829.8568 687798.0965 625260.3329 688346.6829 652797.7554 449524.6543 1.451099721 1.367900302 1.444870339 1.401101921 1.53005645 1.390936686 1.531276819 1.452195668 1 18.77804072 -0.798175103 6.338691884 0.999999989 1.444578885 0.873728397 0.053303017 8.24E-09 1.42E-09 0.050271274 0.011849053 0.159156689 0.798175103 0.444578896 HVGMAVAGLLADAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HVGMAVAGLLADAR 14 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;; 172.09 2.91E-06 1551620000 1866890 1652590 1614610 1824850 1857850 1680690 2044850 1686760 1473560 FALSE TRUE 1778645.81 1820990.8 1688641.466 1641412.611 2181858.452 1622487.284 1732870.576 1539058.352 1702072.159 1.044988487 1.06986698 0.99210921 0.964361354 1.281883638 0.953242361 1.01809466 0.904226266 1 20.69886077 HVGNQQYNVTYVVK ddPTM_SK-BR-3_Trastuzumab_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 0 127.76 7.77E-05 900070000 482450 394180 411170 484560 419340 407880 565400 493860 421690 FALSE TRUE 459645.5446 434347.3901 430022.5512 435851.1082 492472.7632 393755.0133 479137.8457 450615.0003 487083.5315 0.943668827 0.891730806 0.882851756 0.894817993 1.011064286 0.808393197 0.983687221 0.925128794 1 18.89380968 0.899291572 0.963030428 0.998690896 0.910800017 0.193994961 0.055331843 1.043615474 1.992200344 0.046544619 0.015528569 7.9303357 -0.899291572 -0.087890879 HVINFDLPSDIEEYVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 314.41 1.83E-58 1655338000 1324620.4 1281704.5 1285215.5 1414728.9 1330911.3 1281422 1457342.5 1315605.9 437252.7 FALSE TRUE 1262008.219 1412311.646 1344143.902 1272517.663 1563021.809 1237046.035 1234998.136 1200404.473 505059.6155 2.498731199 2.796326616 2.661356918 2.519539524 3.094727357 2.449306966 2.445252199 2.376757983 1 18.94609416 0.283734727 0.754848176 0.969986227 2.686701028 0.88804101 0.182949413 0.766469234 0.574218645 0.218665033 0.059087152 1.921917439 -0.283734727 1.7167148 HVIPMNPNTDDLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVIPMNPNTDDLFK 14 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;U3KQI3 P13797 PLS3 Plastin-3 0 ; 202.13 1.69E-08 239119000 447220 319850 364040 454690 330150 410280 497350 468440 257120 FALSE TRUE 426080.7969 352443.0786 380731.5941 408983.6973 387728.0555 396071.9007 421470.123 427420.9102 296992.8564 1.434649985 1.186705576 1.281955393 1.377082608 1.305513069 1.3336075 1.419125457 1.439162259 1 18.1800687 -0.838598347 6.489156809 0.99999999 1.340988839 0.662571148 0.077760179 1.15E-08 1.95E-09 0.077059175 0.018163021 0.145011235 0.838598347 0.340988849 HVLTGSADNSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 HVLTGSADNSCR 12 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;;;;;; 278.38 6.22E-28 1556360000 1081802 901515 910108 1148339 1055962 977176 1148449 1065711 922760 FALSE TRUE 1030667.363 993380.4034 951837.352 1032905.782 1240121.438 943336.1501 973232.0123 972391.6952 1065856.908 0.966984738 0.932001656 0.893025457 0.96908485 1.163497116 0.885049525 0.913098189 0.912309793 1 20.02358234 -1.062621374 4.037431057 1.000007231 0.951973767 0.030827786 0.07937074 0.051951035 41629229.12 708.6419914 0.018107026 0.086572234 1.062621374 -0.048033464 HVLVILTDMSSYAEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 349.36 1.26E-87 167311000 217896 277364 237097 268406 194427 253632 241327 255309 101873.9 FALSE TRUE 207596.4879 305627.7069 247968.132 241425.3189 228335.0072 244848.6602 204508.1339 232952.7905 117671.9841 1.764196376 2.597285235 2.107282662 2.051680532 1.940436451 2.080772769 1.737950927 1.979679294 1 16.84441135 -0.228593609 0.348712798 0.718173883 2.197799582 0.687436171 0.223996298 3.42836333 0.506873117 1.461036245 0.189036393 0.59075362 0.228593609 1.479625699 HVSDDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HVSDDMK 7 0 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;;; 182.13 0.00050202 782610000 1923830 1223010 1382520 1644490 1510360 1421850 2110850 1799390 1367870 FALSE TRUE 1832894.369 1347636.109 1445909.909 1479182.741 1773766.306 1372610.978 1788801.064 1641825.872 1579992.293 1.160065385 0.852938407 0.915137318 0.936196174 1.122642378 0.868745363 1.132158094 1.039135367 1 20.59148609 1.720551743 24.99999067 1.064674174 0.977695447 0.118299818 0.103670218 1.865016165 2578.764711 0.045825183 0.025412387 52.54746174 -1.720551743 -0.086978727 HVTAQQPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVTAQQPSR 9 0 A0A087WUK2;O14979 A0A087WUK2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 96.143 0.0075677 5946400 8402 5308.8 7254.6 6488.8 9067.6 6080.8 8935.9 8507.6 11313 FALSE TRUE 8004.854111 5849.772756 7587.230586 5836.533496 10648.98657 5870.220371 7572.564336 7762.629442 13067.36226 0.612583776 0.447662859 0.580624493 0.446649705 0.81493008 0.449227645 0.579502136 0.59404716 1 13.67368033 -5 0.326831252 5.388836784 0.540258531 0.613461579 0.108657607 211.0450753 1.838455668 642.4428649 0.082651541 1.00E-05 5 -4.848578253 HVTLPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.5)S(0.5)PR;HVTLPS(0.661)S(0.339)PR;HVTLPS(0.654)S(0.346)PR 116.54 0.00083572 2541670000 2395060 2164060 2272640 2582290 2757120 2218640 2671250 2424390 2349580 TRUE FALSE 2281850.26 2384580.174 2376842.792 2322713.303 3237960.855 2141807.94 2263701.752 2212097.559 2713940.866 0.840788496 0.878641169 0.875790192 0.855845215 1.193084527 0.789187402 0.834101354 0.815086867 1 21.37195786 HVTLPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPSS(1)PR;HVTLPS(0.246)S(0.754)PR;HVTLPS(0.244)S(0.756)PR 177.57 5.45E-05 3246370000 2905890 2529750 2725310 3252420 3040630 2796920 3372550 3097330 2443940 TRUE FALSE 2768534.339 2787534.401 2850268.159 2925480.562 3570914.909 2700061.959 2858005.556 2826111.365 2822933.733 0.980729482 0.987460091 1.009682985 1.036326332 1.2649659 0.956473731 1.012423892 1.001125649 1 21.42876383 3.393790633 3.294447069 1.047216328 0.985590721 0.088641329 0.082552414 0.591894506 12.83673137 0.023557419 0.033537709 2476.228018 -3.393790633 -0.061625608 HVTSNAS(ph)DSESSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HVTSNASDSESSYR 14 0 Q12959;Q12959-3;Q12959-5;A0A590UK48;C9JUA9;Q12959-8;A0A590UJ64 Q12959 DLG1 Disks large homolog 1 1 HVTS(0.001)NAS(0.765)DS(0.234)ESSYR;HVTS(0.044)NAS(0.934)DS(0.022)ESSYR;HVTSNAS(0.982)DS(0.018)ESSYR 198.51 2.30E-08 154157000 384315 372143 358241 454926 374481 350968 418134 361899 259434 TRUE FALSE 366149.1916 410064.7948 374666.7042 409195.9742 439790.3678 338813.8902 354339.9787 330209.205 299665.6997 1.221858865 1.368407513 1.250282246 1.365508213 1.467603293 1.130639544 1.182450908 1.101925263 1 18.19299443 1.628935041 1.297246292 1.038151049 1.321469838 0.629565911 0.085075648 0.270613343 0.870982123 0.069817824 0.025380876 42.55347597 -1.628935041 0.283318789 HVVFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 123.07 0.018947 63318597300 72149576 48654306 54067062 60362152 52229326 58427099 78176875 61008102 40678544 FALSE TRUE 68739208.53 53612235.1 56546090.27 54294433.8 61338103.92 56403753.91 66249556.9 55665909.16 46986764.85 1.462948316 1.14100716 1.203447193 1.155526114 1.30543365 1.200417907 1.409962084 1.184714661 1 25.4857511 0.986068348 24.30881149 0.99999999 1.269405861 0.401988534 0.103857511 534.2599173 932212.2296 0.097422343 0.024355586 9.684302538 -0.986068348 0.269405871 HVVFIAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HVVFIAQR 8 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 132.29 0.00096878 1671330000 1384130 838750 399900 432730 1397800 562380 1553520 814860 831150 FALSE TRUE 1318704.918 924219.5786 418235.8106 389231.1583 1641575.877 542904.6396 1316501.992 743506.5386 960040.4971 1.373593012 0.962688117 0.435643925 0.40543202 1.709902741 0.565501811 1.371298394 0.774453308 1 19.87273574 2.771969544 24.996404 1.085554449 0.866831597 0.098846005 0.409719012 1996.344457 1493652.314 0.123391019 0.130868306 591.5201512 -2.771969544 -0.218722852 HVVLPVDDDSDLNVVASFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVVLPVDDDSDLNVVASFDR 20 0 Q15291;Q15291-2 Q15291 RBBP5 Retinoblastoma-binding protein 5 0 92.31 0.0016706 42712000 11598 10689 8497.3 9702.3 10062 7350.8 9861.1 8696.3 11539 FALSE TRUE 11049.78553 11778.22125 8886.90961 8727.006371 11816.80961 7096.239953 8356.608083 7934.80587 13328.40919 0.829040088 0.883692951 0.666764464 0.654767291 0.886588148 0.532414623 0.626977156 0.595330302 1 13.70221698 3.736603995 24.89217058 0.684459466 0.856366525 0.14287762 0.140426296 216.8942827 2759340.551 0.033629057 0.055181122 5452.604464 -3.736603995 0.171907058 HVYEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HVYEIAR 7 0 Q9Y3B7-2;Q9Y3B7-3;Q9Y3B7 Q9Y3B7-2 MRPL11 "39S ribosomal protein L11, mitochondrial" 0 102.71 0.0085387 199740000 64763 37050 32283 35402 65463 30419 57759 44903 59084 FALSE TRUE 61701.78134 40825.43712 33763.20748 31843.3237 76879.72647 29365.5824 48946.80373 40971.05527 68246.44496 0.904102498 0.598206063 0.49472478 0.46659315 1.126501556 0.430287357 0.717206644 0.600339773 1 16.05846628 -1.116867652 3.748255564 1.000153996 0.670638216 0.195351491 0.212137881 57569751.51 96650570.18 111685.9991 0.04679602 0.076406859 1.116867652 -0.32951578 HWDHLTQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HWDHLTQVK 9 0 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 ;;;;; 148.52 5.19E-05 1457627000 2512475 1846105 1829932 1902667 2044759 1680535 2514451 1938957 163959 FALSE TRUE 2393715.286 2034225.198 1913836.192 1711407.298 2401364.322 1622337.652 2130825.319 1769171.646 189384.9243 12.63941834 10.74122032 10.10553611 9.036660676 12.67980717 8.566350554 11.25129324 9.34167095 1 17.53096197 -0.399366221 0.578659394 4.06E-11 10.99661405 0.839595363 1.323627256 3.12470239 0.907535392 8.878768555 0.51211837 0.398688565 0.399366221 10.99661405 HWDQDDDFEFTGSHLTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HWDQDDDFEFTGSHLTVR 18 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 267.38 1.67E-31 124590000 27404 25748 24606 32159 36085 27969 34086 22606 19370 FALSE TRUE 26108.66723 28371.75047 25734.20944 28926.31622 42378.21258 27000.42652 28885.55467 20626.4988 22373.80067 1.166930358 1.268079165 1.150193917 1.292865555 1.894099854 1.206787658 1.291043712 0.92190411 1 14.44952273 1.2710031 5.88133849 0.959095854 1.315224718 0.336962862 0.211504083 0.196196656 18.37643509 0.155875981 0.052254187 18.66393013 -1.2710031 0.356128863 HWGGNVLGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HWGGNVLGPK 10 0 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 93.111 0.0090088 2683300000 7215800 4620500 2313200 3167300 5930900 3898600 8207400 5402200 4588500 FALSE TRUE 6874723.434 5091334.203 2419262.508 2848916.987 6965247.082 3763590.504 6955210.391 4929154.729 5300061.145 1.297102665 0.960618012 0.456459358 0.537525306 1.314182401 0.710103224 1.312288708 0.930018465 1 22.33757757 1.740222933 25 1.105042653 0.908159574 0.086659697 0.295170519 0.710640376 10747.60685 0.139555656 0.077391061 54.98230381 -1.740222933 -0.196883079 HWLDSPWPGFFTLDGQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HWLDSPWPGFFTLDGQPR 18 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 210.09 4.50E-16 257450000 380420 287970 297520 303800 402200 266150 337640 321830 288010 FALSE TRUE 362438.3005 317314.4704 311161.5863 273261.4468 472343.5527 256933.1588 286126.8168 293648.8591 332673.1198 1.089472755 0.953832611 0.935337326 0.821411261 1.419842856 0.772329183 0.860083968 0.882694878 1 18.34374577 HWMLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 118.03 0.016853 5233990000 11599500 11478720 8772070 11771370 8479290 10394050 11380780 10627180 5880390 FALSE TRUE 11051214.62 12648414.62 9174278.086 10588089.52 9958075.491 10034101.44 9644432.989 9696607.781 6792290.848 1.627023175 1.862172116 1.350689817 1.558839243 1.466084965 1.477277941 1.419908718 1.42759019 1 22.69546681 -1.591185597 0.092027709 3.25E-14 2.144006579 0.70502714 0.118116326 39.45290505 0.584980235 12.17247113 3.334512128 0.025633883 1.591185597 2.144006579 HWMLDKLTGVFAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HWMLDKLTGVFAPR 14 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" 0 187.16 5.89E-07 42255000 140740 79301 92289 86978 142330 104150 176870 128450 105470 FALSE TRUE 134087.4991 87381.86206 96520.54194 78234.80619 167152.3069 100543.2594 149885.2331 117202.237 121825.7489 1.100649906 0.717269238 0.792283592 0.64218613 1.372060573 0.825303848 1.230324741 0.962048155 1 16.89445957 2.753630905 24.99973838 1.082387775 0.827919886 0.329262035 0.18724597 938.5731987 1556975.187 0.052937816 0.055940245 567.0624693 -2.753630905 -0.254467889 HWMLDKLTGVFAPRPSTGPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HWMLDKLTGVFAPRPSTGPHK 21 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" 0 155.93 6.37E-09 78873000 350980 158840 405600 311260 464570 369290 685360 450710 361830 FALSE TRUE 334389.871 175025.9766 424197.1612 279971.5534 545590.8609 356501.3947 580795.7445 411243.443 417940.7484 0.800089181 0.418781794 1.014969617 0.669883361 1.305426338 0.852995062 1.389660488 0.983975467 1 18.6729389 3.060869323 1.321765582 1.134967512 0.635293842 0.37182445 0.223955522 0.337691475 1.235822953 0.077583908 0.098279318 1150.454172 -3.060869323 -0.49967367 HWPFMVVNDAGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 187.57 7.93E-07 8305400000 14935980 14091330 12832340 16250540 10324590 14811450 15556980 15070870 7056180 FALSE TRUE 14229985.83 15527252.55 13420715.48 14617004.85 12125195.23 14298525.77 13183476.98 13751184.73 8150416.356 1.745921337 1.905087037 1.646629435 1.793405908 1.487678015 1.754330717 1.617521903 1.687175738 1 22.95844233 -2.419778464 0.247085634 1.21E-14 1.815002501 0.818001139 0.105654296 15.31328416 0.471925175 8.582305794 0.153248096 0.003803834 2.419778464 1.815002501 HWPFQVINDGDKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HWPFQVINDGDKPK 14 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 242.79 1.01E-17 3014800000 11816700 10337200 9937300 12277900 6066400 12357100 11983400 12441800 4096600 FALSE TRUE 11258148.01 11390572.43 10392935.03 11043702.17 7124378.239 11929170.53 10155112.24 11352330.03 4731879.805 2.37921259 2.407198175 2.196364967 2.333893214 1.505612681 2.521021458 2.146105281 2.399116313 1 22.173982 2.935605153 24.99969648 2.035093341 2.341169853 0.149364128 0.442154567 451.1777271 175157.766 0.120991469 0.128330903 862.1943103 -2.935605153 0.306076513 HWVAPGGPYSAETPGVPS(ph)PIAALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HWVAPGGPYSAETPGVPSPIAALK 24 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 HWVAPGGPYSAETPGVPS(1)PIAALK;HWVAPGGPYSAETPGVPS(1)PIAALK 177.12 2.78E-17 926180000 1207790 1197200 1180170 1352560 841160 1282710 1490720 1282570 643590 TRUE FALSE 1150700.16 1319196.041 1234281.962 1216598.099 987858.0377 1238289.431 1263283.285 1170261.371 743394.6502 1.547899437 1.774556813 1.660332048 1.63654406 1.328847386 1.665722817 1.699344063 1.574212797 1 19.50376878 0.948396952 20.1412089 0.999999998 1.626649742 0.727105599 0.117760548 600.6636272 234446.4348 0.112057027 0.028014257 8.879672571 -0.948396952 0.626649743 HYAHTDCPGHADYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HYAHTDCPGHADYVK 15 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;; 100.19 0.00078334 2237980000 1942540 1414810 1610670 1572230 1374580 1410900 1866930 1378960 40831.5 FALSE TRUE 1850719.984 1558980.748 1684520.813 1414186.453 1614306.317 1362040.179 1582095.54 1258210.952 47163.44048 39.24056356 33.0548563 35.71666519 29.98480261 34.2279168 28.87915227 33.54495609 26.67767532 1 15.52538134 0.012517885 0.561694731 6.00E-16 34.93356378 0.933460588 2.725295543 0.94837599 0.356696155 7.533560658 1.12285321 1.029242913 -0.012517885 34.93356378 HYCDSEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HYCDSEKPR 9 1 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ;;;;; 203.29 1.11E-05 1944953000 3158110 2629230 2524720 3201030 2098890 2694310 3204690 2994380 1900480 FALSE TRUE 3008832.399 2897151.526 2640480.909 2879256.383 2464935.751 2601005.369 2715755.682 2732176.213 2195196.732 1.370643622 1.319768513 1.20284477 1.311616558 1.122876923 1.184862081 1.237135443 1.244615652 1 21.06591881 7.999999997 0.027374046 2.04E-13 2.979455941 0.682594893 0.059764893 913.3808949 1.920624382 69.31701106 155.7541352 99999999.33 -7.999999997 2.979455941 HYCTVANPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HYCTVANPVSR 11 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7 Q14764 MVP Major vault protein 0 ; 155.99 3.13E-05 301730000 270920 223780 219665 261470 252440 223110 301530 265460 245610 FALSE TRUE 258114.1485 246583.4364 229736.8575 235186.5388 296465.4561 215383.6448 255526.0605 242214.9151 283697.9444 0.909820299 0.869175971 0.809793874 0.829003324 1.045003892 0.759200583 0.90069761 0.853777477 1 18.11399617 -1.085858865 4.881800111 1.000004374 0.873081489 0.221955717 0.075258568 3.18E-06 5.96E-07 0.06474087 0.015259043 0.082061818 1.085858865 -0.126922885 HYEDGYPGGSDNYGS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 HYEDGYPGGSDNYGS(0.977)LS(0.023)R;HYEDGYPGGS(0.001)DNYGS(0.939)LS(0.059)R 131.26 1.12E-05 292840000 396130 413150 398060 506420 436300 428760 480970 454690 284760 TRUE FALSE 377405.72 455250.4547 416311.4447 455513.6995 512390.5819 413911.9337 407589.1929 414874.9331 328919.1264 1.1474119 1.384080213 1.265695459 1.384880546 1.557801115 1.258400319 1.239177537 1.261328089 1 18.32737338 0.703411009 1.016232038 1.002193896 1.327128747 0.469541664 0.107924968 0.939026562 1.694120871 0.103587952 0.033293569 5.051391263 -0.703411009 0.324934852 HYEDGYPGGSDNYGSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 192.62 1.65E-14 997220000 867590 712630 754020 902790 859130 771470 931170 808050 604791 FALSE TRUE 826580.7401 785247.8072 788592.5628 812039.834 1008962 744753.8005 789102.9144 737292.8583 698578.8994 1.183231759 1.124064594 1.128852537 1.162416779 1.444306435 1.066098333 1.129583094 1.055418162 1 19.41406354 1.421227668 1.554381666 1.014312157 1.185502601 0.315895789 0.098463799 0.471436315 2.128776305 0.085869537 0.027425878 26.3771378 -1.421227668 0.171190443 HYELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 138.38 0.012327 1859810000 333364 264095 215998 280951 312626 249733 355286 274036 237869 FALSE TRUE 317606.5444 291006.5808 225901.722 252709.2717 367147.8754 241084.6836 301080.5954 250039.9551 274756.5097 1.155956395 1.059143534 0.822188789 0.919757177 1.33626634 0.877448487 1.095808779 0.910041969 1 18.06779414 4.187308337 3.459195706 1.004250222 1.136528995 0.10785425 0.143514042 0.487453752 11.58314515 0.034275958 0.089716246 15392.47074 -4.187308337 0.132278772 HYFQNTQGLIFVVDSNDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 305.98 3.77E-50 3396920000 2438319 3118480 2256365 3103720 2113068 2385960 2300030 2286849 958703 FALSE TRUE 2323064.493 3436256.657 2359821.567 2791728.169 2481586.39 2303333.607 1949118.181 2086600.378 1107373.765 2.097814276 3.103068509 2.131007291 2.521035135 2.240965489 2.079996547 1.760126745 1.884278321 1 20.07871082 1.268496125 0.478496796 0.986936761 2.595190749 0.707390091 0.289396337 0.451254969 0.279439586 0.306768366 0.174348508 18.55650252 -1.268496125 1.608253988 HYFQNTQGLIFVVDSNDRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 257.47 1.92E-36 6354374000 1598088 1201428 1556143 1646179 1565242 1317472 1728106 1389152 799853 FALSE TRUE 1522549.547 1323854.879 1627493.696 1480701.959 1838219.709 1271847.614 1464451.691 1267510.487 923890.1182 1.647976872 1.432913777 1.761566299 1.602681889 1.989651879 1.376622165 1.585092926 1.371927745 1 19.81736175 0.859699168 1.112991225 1.00099791 1.632904043 0.607282893 0.165271358 0.454573346 1.103392961 0.147273617 0.046559421 7.239343229 -0.859699168 0.631906133 HYGEHVCTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HYGEHVCTAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ; 120.68 0.00030941 126297000 198526 204288 176675 234670 178060 216171 231380 186910 23654.6 FALSE TRUE 189142.0694 225105.1795 184775.7235 211080.5258 209113.6076 208684.9441 196078.7314 170543.1695 27322.83456 6.922490748 8.238719851 6.762685003 7.725425607 7.653437537 7.637748698 7.176368579 6.241781729 1 14.73781954 0.59130474 1.435413816 0.999881718 7.523466077 0.959363652 0.414704123 0.262553574 0.727207334 0.35818126 0.10476568 3.902157013 -0.59130474 6.52358436 HYGGLTGLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HYGGLTGLNK 10 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 147.4 2.69E-05 3651900000 4940000 4120100 3481900 4283400 4326500 4159100 5514800 4692100 3274800 FALSE TRUE 4706495.99 4539942.874 3641548.559 3852824.494 5081040.23 4015069.324 4673415.974 4281234.85 3782639.259 1.244236013 1.200205085 0.962700461 1.018554567 1.343252656 1.061446532 1.235490792 1.131811562 1 21.85096177 -2.521558406 1.536484077 2.88E-05 1.157988924 0.141933598 0.114083323 1194313.091 79905.22383 4129349.519 0.0295989 0.003009134 2.521558406 1.157960142 HYGPGWVSMANAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HYGPGWVSMANAGK 14 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 151.66 5.22E-06 618590000 2022430 1582140 1737310 1686730 1690390 1867920 2425740 2065540 1299100 FALSE TRUE 1926833.742 1743361.865 1816967.382 1517176.696 1985193.481 1803233.462 2055648.811 1884670.367 1500557.793 1.284078328 1.16180921 1.210861315 1.01107515 1.322970358 1.201708771 1.369923118 1.25597986 1 20.51706745 HYLDFINHYANLFHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HYLDFINHYANLFHEK 16 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 199.08 1.36E-11 105450000 233830 195290 140250 152700 188400 173300 258070 198330 56295 FALSE TRUE 222777.3193 215190.273 146680.6012 137350.3059 221256.9004 167298.5775 218696.6817 180963.1738 65024.94108 3.426028776 3.309349758 2.255759079 2.112271132 3.402646687 2.572837049 3.363273816 2.782980973 1 15.98870557 3.850055117 7.009790785 2.664476774 3.380081734 0.186386224 0.691359571 0.410627355 22.893786 0.163096141 0.296056501 7080.356372 -3.850055117 0.71560496 HYLFYDGESVSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HYLFYDGESVSGK 13 0 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;; 173.19 2.21E-05 1152660000 2151050 1844030 1971600 2311250 1672350 2073440 2414510 2213040 1435640 FALSE TRUE 2049374.129 2031938.753 2061999.81 2078918.759 1964007.311 2001636.253 2046132.154 2019254.486 1658271.719 1.235849412 1.225335227 1.243463171 1.253665931 1.184370021 1.207061684 1.23389438 1.217686138 1 20.66124899 -3.626010689 0.391353122 3.23E-11 1.231511168 0.934410709 0.018790998 46.69195849 0.970904143 38.51971373 0.011887177 0.000236586 3.626010689 1.231511168 HYLGHNDDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HYLGHNDDIK 10 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ERY9;K7EKU5;K7ERR2;K7EIM1;K7EQR0 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;;; 149.96 1.30E-05 418647000 465934 405754 429819 521510 300910 463685 467111 435054 49233.2 FALSE TRUE 443910.2232 447100.7939 449526.6263 469086.824 353388.6087 447627.4722 395844.6379 396958.3654 56868.03321 7.805971091 7.86207591 7.904733133 8.248690829 6.214187282 7.871337321 6.960758365 6.980342787 1 15.79533029 -0.484774554 0.519642319 7.05E-13 7.800091578 0.936938872 0.533590375 1.901357948 0.440699074 4.230223899 0.224365016 0.327510665 0.484774554 7.800091578 HYLILPSEEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HYLILPSEEEGR 12 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 82.85 0.013841 73316000 97249 114470 91999 119470 102220 75623 78467 86947 64435 FALSE TRUE 92652.2325 126134.6231 96217.24515 107460.6486 120047.1356 73004.15655 66495.418 79333.45974 74427.25071 1.244869743 1.694737101 1.292769036 1.443834719 1.612945991 0.980879394 0.89342838 1.065919525 1 16.18354332 2.226616741 24.98213984 0.967477868 1.462637458 0.745048621 0.137236993 100.3981192 209994.0011 0.048420441 0.03603806 168.5065322 -2.226616741 0.49515959 HYNGEAYEDDEHHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;; 179.17 2.37E-07 1425160000 719764 694887 836932 861129 759412 755418 960417 449676 43812.6 FALSE TRUE 685742.1822 765696.7753 875306.16 774566.6769 891853.2124 729257.6852 813887.7474 410299.9856 50606.83424 13.55038687 15.13030378 17.29620462 15.3055746 17.6231773 14.41026091 16.08256591 8.107600321 1 15.62704461 1.017249243 2.875980684 1.039484191 15.55422505 0.937608298 1.260416167 0.053587814 1.013835676 1.204975811 0.319977269 10.4051715 -1.017249243 14.51474086 HYPVFENPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HYPVFENPK 9 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISU1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 129.1 0.00039879 213940000 686390 560740 505640 664970 453640 593300 724230 675560 389100 FALSE TRUE 653945.705 617880.0435 528824.0941 598125.9522 532754.6724 572753.8722 613735.4121 616404.385 449439.6408 1.455024537 1.374778697 1.176629843 1.330825984 1.185375352 1.274373287 1.365556921 1.371495367 1 18.77776785 -2.226333071 2.16378335 0.000122515 1.323745802 0.569425061 0.086373818 1159078.038 227017.2334 5665870.099 0.0236512 0.005938366 2.226333071 1.323623287 HYQEEGQGTEVVQGVLLGLVVEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HYQEEGQGTEVVQGVLLGLVVEDR 24 0 A0A087WZK9;B3KS98;O15372;E5RGU4;E5RFH0;E5RFW7 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;; 155.49 4.27E-08 264118000 287260 294423 313371 351754 236877 308421 263096 300986 187136 FALSE TRUE 273681.7891 324425.0384 327739.3703 316395.0196 278188.2738 297740.3034 222955.8731 274630.0702 216156.0951 1.266130335 1.500883138 1.516216187 1.463733972 1.286978624 1.377431912 1.03145772 1.270517355 1 17.72171399 1.957561543 1.576306663 1.095300144 1.425310545 0.610277613 0.110932836 0.250028096 1.15663614 0.070694363 0.033078426 90.69044704 -1.957561543 0.330010401 HYQGEEKS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D 153.81 4.68E-05 2715825000 5306280 4809060 4963500 5875400 2977729 5699670 5846800 4652200 1311726 TRUE FALSE 5055462.66 5299108.681 5191081.385 5284793.629 3497043.995 5502288.999 4954763.276 4244828.705 1515141.769 3.336626819 3.497434228 3.426135753 3.487986232 2.308063884 3.6315341 3.270164798 2.801604967 1 20.53102136 2.790317054 24.72727943 2.869822378 3.435347057 0.206560768 0.7128501 587.4301599 280650.7616 0.196162222 0.208061259 617.0453074 -2.790317054 0.565524678 HYS(ph)PEDEPSPEAQPIAAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HYSPEDEPSPEAQPIAAYK 19 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 HYS(1)PEDEPSPEAQPIAAYK;HYS(1)PEDEPSPEAQPIAAYK 265.41 1.33E-31 377380000 437410 371450 428450 501860 343330 445460 514830 425350 275990 TRUE FALSE 416734.4962 409301.1773 448094.8563 451412.0793 403206.6433 430033.6085 436283.228 388104.0991 318789.1196 1.307241905 1.283924551 1.405615276 1.416020973 1.264806791 1.348959491 1.368563734 1.217432074 1 18.28224287 0.930646423 3.471536926 1.000298312 1.337396299 0.835411991 0.048613967 0.122455308 3.659057616 0.047983936 0.0124114 8.524058537 -0.930646423 0.337097987 HYTEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 HYTEAIK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 141.78 0.0025335 698420000 1595830 1388090 1240610 1528900 1238120 1405610 1766650 1511810 1058730 FALSE TRUE 1520398.279 1529537.949 1297493.196 1375212.067 1454047.736 1356933.373 1497115.096 1379427.902 1222912.441 1.243260128 1.25073382 1.060986177 1.124538455 1.189003961 1.109591601 1.224221003 1.127985827 1 20.22188968 -5 0.087818089 0.488790381 1.315701388 0.444960707 0.06033147 215.2483771 1.319100684 21.34885422 1.595319958 1.00E-05 5 0.826911007 HYTEAIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 HYTEAIKR 8 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 194.2 0.00010818 1758470000 3789240 2951220 3045890 3382080 3293220 3206050 4519400 3899410 3060540 FALSE TRUE 3610130.135 3251952.673 3185547.069 3042106.893 3867556.525 3095023.685 3829882.526 3557956.988 3535152.912 1.021209047 0.919890244 0.901105878 0.860530497 1.094028072 0.875499239 1.083371107 1.006450662 1 21.75334119 2.073933196 1.299982236 1.027241597 0.943278635 0.145331605 0.076199891 0.783473669 2.480763251 0.049131196 0.024389555 118.5586365 -2.073933196 -0.083962962 HYYDGTIFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 HYYDGTIFHR 10 0 Q13356;Q13356-2 Q13356 PPIL2 Peptidyl-prolyl cis-trans isomerase-like 2 0 135.86 7.69E-05 22039000 24641 26314 20589 22331 26251 20229 27368 19434 6359 FALSE TRUE 23476.26876 28995.42652 21533.02602 20086.24545 30829.16609 19528.46466 23192.50895 17732.25593 7345.121243 3.196171716 3.947576297 2.931609337 2.734637699 4.197230389 2.658698749 3.157539295 2.414154287 1 12.84257059 0.71082048 0.789071083 0.979460492 3.401926532 0.696004335 0.481532624 0.5544429 0.653324693 0.439470674 0.153940021 5.138312101 -0.71082048 2.422466039 HYYEVSCHDQGLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 HYYEVSCHDQGLCR 14 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;;; 198.29 1.29E-08 869590000 487831 318149 348188 416176 568472 359719 597272 440678 325051 FALSE TRUE 464772.1954 350568.7448 364152.7642 374341.1978 667613.3368 347261.8408 506147.1867 402089.8981 375458.2489 1.237879835 0.933708996 0.969888836 0.997024833 1.778129362 0.924901349 1.348078483 1.070931054 1 18.51829296 HYYFCMMTEAEQDKWQAVLQDCIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 HYYFCMMTEAEQDKWQAVLQDCIR 24 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 287.46 3.54E-53 468380000 511610 443810 469340 546010 405110 537230 572270 526740 333320 FALSE TRUE 487427.2092 489034.7436 490859.7032 491124.0374 475761.0557 518625.5904 484959.701 480615.8532 385009.5632 1.266013252 1.270188562 1.274928599 1.275615165 1.235712307 1.347045996 1.259604299 1.248321858 1 18.55453476 0.574120363 2.109697064 1.000025536 1.27574001 0.904528996 0.027936714 0.836122993 3.831059648 0.024304064 0.006638501 3.750769387 -0.574120363 0.275714474 HYYTGTQGLIFVVDCADRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 HYYTGTQGLIFVVDCADRDR 20 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;; 282.5 4.72E-45 401014000 260356 237556 291158 275722 281635 263105.5 340526.5 262286 174036.6 FALSE TRUE 248049.4879 261763.2265 304507.8823 248005.9007 330752.0548 253994.0906 288572.9282 239318.8474 201025.3071 1.233921696 1.302140662 1.51477387 1.233704872 1.645325455 1.263493111 1.435505472 1.190491142 1 17.61701761 -0.319406569 7.606576889 0.99998354 1.353059476 0.375182112 0.142926144 0 0 0.123978303 0.029221966 0.479284551 0.319406569 0.353075937 IAAAILNTPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IAAAILNTPDLR 12 0 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ;; 162.36 0.00047378 0 311344 240272 218344 221998 324750 204940 308556 258061 347830 FALSE TRUE 296627.3861 264755.99 228355.2884 199682.3393 381386.2972 197842.8764 261480.1152 235463.8108 401769.6999 0.738302033 0.658974507 0.568373594 0.497006965 0.949265953 0.492428564 0.650820894 0.586066622 1 18.61600924 -1.456688392 3.613694673 1.003850868 0.646044072 0.420835656 0.131691911 30129937.68 54214538.28 1151331.74 0.028731354 0.034939091 1.456688392 -0.357806796 IAAAILNTPDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAAAILNTPDLRK 13 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 206.69 8.79E-07 0 492290 337910 437690 363240 384110 367040 488820 445300 422350 FALSE TRUE 469020.4273 372343.4132 457758.5194 326726.4251 451098.6624 354329.3128 414241.5312 406307.1713 487845.8809 0.961411064 0.763239842 0.938326093 0.669732876 0.924674534 0.72631404 0.849123765 0.832859694 1 18.89606592 0.298919837 2.500728053 0.99999989 0.831850162 0.23792132 0.093787075 51.30187948 179.7304001 0.078076842 0.020809696 1.990305929 -0.298919837 -0.168149728 IAAPELHKGDS(ph)DS(ph)EEDEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(0.999)EEDEPT(0.001)K;IAAPELHKGDS(1)DS(0.941)EEDEPT(0.059)K;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK 209.17 6.58E-22 1645814000 3872950 3594500 3107690 4090470 1627617 4211140 3755630 4495800 1774795 TRUE FALSE 3689883.329 3960783.637 3250180.66 3679288.184 1911472.889 4065307.166 3182639.667 4102123.918 2050021.144 1.799924522 1.932069651 1.585437628 1.794756212 0.932416183 1.983056213 1.552491142 2.001015419 1 20.96720736 3.728955161 22.59542173 1.581942374 1.865997075 0.114020178 0.357764081 353.9517107 832621.8857 0.084884741 0.133760105 5357.413417 -3.728955161 0.284054701 IAAPELHKGDS(ph)DS(ph)EEDEPTKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAAPELHKGDSDSEEDEPTKKK 22 3 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTKKK;IAAPELHKGDS(1)DS(0.999)EEDEPT(0.001)KKK 117.03 6.91E-05 647930000 282202 126703 250333 214682 114100 325339 348782 324619 138052 TRUE FALSE 268862.8707 139614.1797 261811.0157 193101.7575 133999.0039 314072.4289 295568.9001 296193.6394 159460.3991 1.686079254 0.875541392 1.641856017 1.210969988 0.840327784 1.969595151 1.853556756 1.85747459 1 17.28283866 2.223485825 24.9995778 1.761469223 1.255269574 0.216233794 0.379213858 282.1802045 467956.1401 0.129076378 0.095702016 167.296103 -2.223485825 -0.506199649 IAAPELHKGDS(ph)DSEEDEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 IAAPELHKGDS(0.982)DS(0.018)EEDEPTK;IAAPELHKGDS(0.925)DS(0.075)EEDEPTK 87.196 0.0014479 263970000 226237 214985 185495 242896 109609 225420 219242 242072 109391 TRUE FALSE 215543.2254 236892.2159 194000.1292 218479.6326 128724.7749 217613.6489 185792.6062 220874.8924 126354.7976 1.705857075 1.874817739 1.535360215 1.729096455 1.018756528 1.722242867 1.470404051 1.748053074 1 16.94712092 -2.765990925 0.120964805 1.26E-12 1.949645659 0.376799189 0.238241035 78.1761078 1.075573603 24.47432327 2.437000693 0.001713993 2.765990925 1.949645659 IAASS(ph)SFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAAS(0.007)S(0.525)S(0.468)FR;IAAS(0.116)S(0.767)S(0.116)FR;IAAS(0.016)S(0.66)S(0.324)FR 118.71 0.0019237 7354660000 3783880 3025050 3126380 3447250 3614140 3077320 3825100 3357410 3644600 TRUE FALSE 3605023.491 3333306.034 3269727.615 3100725.881 4244444.872 2970751.637 3241510.742 3063417.382 4209785.954 0.856343655 0.79179941 0.77669688 0.736551909 1.008232941 0.705677597 0.769994194 0.727689582 1 22.00531545 IAASSS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAAS(0.003)S(0.157)S(0.84)FR;IAAS(0.003)S(0.15)S(0.847)FR;IAASS(0.021)S(0.979)FR;IAAS(0.002)S(0.093)S(0.906)FR;IAASS(0.03)S(0.97)FR;IAAS(0.005)S(0.219)S(0.777)FR;IAAS(0.002)S(0.158)S(0.84)FR;IAAS(0.004)S(0.257)S(0.739)FR 137.95 0.00076162 11162080000 12115170 9902270 9993530 11336210 11721200 9830480 12255180 11002160 11812690 TRUE FALSE 11542509.92 10911322.57 10451743.24 10196672.63 13765373.57 9490048.013 10385427.21 10038752.54 13644541.63 0.845943399 0.799684069 0.766001784 0.747307818 1.008855698 0.695519737 0.761141524 0.735733952 1 23.70182059 IAAYLQSDQFCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAAYLQSDQFCK 12 0 P21266 P21266 GSTM3 Glutathione S-transferase Mu 3 0 162.38 0.00048346 0 183820 146540 160830 178510 150800 158390 196410 186770 149920 FALSE TRUE 175131.1929 161472.5926 168204.2146 160565.8357 177099.4723 152904.9146 166444.0472 170415.4287 173168.8279 1.011332091 0.932457617 0.971330791 0.927221357 1.022698337 0.882981749 0.961166332 0.984099914 1 17.40181973 1.111081888 3.800870884 0.998619875 0.957402666 0.114482109 0.040078962 0.433017147 10.90641241 0.034389524 0.008933084 12.91462763 -1.111081888 -0.041217209 IACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IACDEEFSDSEDEGEGGR 18 0 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 IACDEEFS(1)DS(1)EDEGEGGR;IACDEEFS(1)DS(1)EDEGEGGR 208.43 9.25E-16 157842000 340940 342550 328170 394340 308000 345500 325190 334960 267580 TRUE FALSE 324824.4419 377456.2344 343216.9191 354700.194 361715.1025 333535.2484 275576.293 305629.1267 309074.9398 1.050956904 1.221245031 1.110465052 1.147618743 1.170315208 1.079140381 0.891616425 0.988851205 1 18.23759716 1.935879765 4.906800535 0.953277989 1.141183596 0.71763173 0.051413122 0.102068437 4.765279795 0.02176302 0.013059903 86.2739665 -1.935879765 0.187905608 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;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;IACDEEFS(1)DS(1)EDEGEGGRR 190.19 4.33E-14 15135270000 5010780 3880355 4952472 4831660 4779370 4543503 5720030 5069512 5443360 TRUE FALSE 4773930.36 4275767.586 5179547.74 4345972.357 5612890.615 4386160.352 4847334.368 4625598.654 6287488.468 0.759274611 0.680043806 0.82378644 0.691209595 0.892707898 0.697601335 0.770949226 0.735683044 1 22.58405242 -1.854152297 2.668566508 1.100941037 0.752609097 0.584431762 0.06448311 21985157.22 13674312.6 14101082.49 0.013889175 0.013990966 1.854152297 -0.34833194 IACDEEFS(ph)DSEDEGEGGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 IACDEEFS(0.975)DS(0.025)EDEGEGGRR;IACDEEFS(0.997)DS(0.003)EDEGEGGRR 263.02 1.88E-31 595260000 275115 218937 274942 288650 240445 265778 305470 274440 273300 TRUE FALSE 262110.8592 241246.9292 287548.3627 259634.3536 282378.5319 256574.0412 258864.9412 250408.5787 315681.9682 0.830300383 0.764208772 0.91087991 0.822455445 0.894503204 0.812761155 0.820018142 0.793230542 1 18.26811233 -1.656965729 2.940147694 1.016885787 0.827647927 0.599068033 0.043359096 10066953.7 10377327.78 1287736.103 0.009915819 0.022031003 1.656965729 -0.18923786 IACEEEFS(ph)DS(ph)EEEGEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IACEEEFSDSEEEGEGGR 18 0 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGR;IACEEEFS(1)DS(1)EEEGEGGR 223.97 7.10E-19 406970000 814140 703200 795840 781950 781530 801080 924760 851550 875040 TRUE FALSE 775657.2157 774856.8795 832330.0512 703346.9004 917828.5846 773338.3987 783670.8776 776983.7676 1010736.734 0.767417656 0.766625822 0.823488474 0.69587547 0.908078784 0.765123471 0.775346192 0.768730117 1 19.94697584 -1.131310709 3.637738383 1.000145699 0.78222956 0.615057113 0.053730249 12700500.52 18471588.79 21551.95867 0.011616475 0.073907633 1.131310709 -0.217916139 IACEEEFS(ph)DS(ph)EEEGEGGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IACEEEFSDSEEEGEGGRK 19 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK 163.71 8.80E-11 7325950000 9540960 7594200 8522450 8912460 5826650 9254700 10601090 9969290 7217660 TRUE FALSE 9089977.729 8368057.614 8913212.762 8016562.588 6842815.915 8934207.418 8983699.018 9096326.117 8336937.85 1.090325716 1.003732757 1.069123091 0.96157159 0.820782887 1.07164136 1.077577785 1.091087193 1 22.99108615 -0.625285225 7.567306142 1.000014153 1.025062803 0.007285193 0.082800665 0 0 0.080426644 0.018956742 0.236981681 0.625285225 0.02504865 IADDKYNDTFWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IADDKYNDTFWK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;; 200.13 1.49E-07 5438470000 11773400 11535620 9662790 12870590 6519940 12083090 11937050 12929290 6820730 FALSE TRUE 11216894.71 12711112.79 10105838.48 11576813.84 7657015.472 11664649.56 10115833.78 11797132.83 7878453.973 1.423743129 1.613401923 1.282718477 1.469427108 0.971893153 1.480575961 1.283987165 1.497391857 1 22.90948112 -4.452442182 0.093992286 4.56E-13 1.67107759 0.291840655 0.17750087 205.9783357 1.494082589 43.96449054 3.481153416 3.53E-05 4.452442182 1.67107759 IADGVNEINTENMVSSIEPEKQDS(ph)PPPKPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IADGVNEINTENMVSSIEPEKQDSPPPKPPR 31 2 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 IADGVNEINTENMVS(0.005)S(0.009)IEPEKQDS(0.986)PPPKPPR;IADGVNEINTENMVS(0.037)S(0.402)IEPEKQDS(0.561)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR 360.76 2.15E-121 520550000 318096 301015 302686 350820 157965 363199 368572 356966 182358 TRUE FALSE 303060.2325 331688.7707 316564.4525 315554.9071 185514.046 350621.3276 312339.5721 325708.1646 210637.1473 1.43877866 1.574692665 1.502889954 1.498097136 0.88072806 1.664574991 1.482832331 1.546299733 1 17.68440036 -1.234596833 3.528673824 0.999091993 1.457054844 0.307383317 0.211293452 32555913.86 47130764.43 315909.2103 0.047771525 0.058264385 1.234596833 0.457962851 IADGYEQAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IADGYEQAAR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 225.72 5.72E-07 929330000 1408030 1244470 1286550 1460230 1549450 1251720 1580730 1394190 1537110 FALSE TRUE 1341475.212 1371282.908 1345539.59 1313444.906 1819673.589 1208372.623 1339560.606 1272107.333 1775477.168 0.755557569 0.772346123 0.757846743 0.739770091 1.0248927 0.680590347 0.754479207 0.716487576 1 20.75977538 -2.253921826 2.307615529 1.871248312 0.77399049 0.367864031 0.092578446 5090461.662 1165984.493 22998276.84 0.020675238 0.005572861 2.253921826 -1.097257822 IADMGHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IADMGHLK 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;;;; 96.711 0.0087474 1948378000 4923840 4250930 2654100 3040190 4342430 3339190 5574510 4362080 4117210 FALSE TRUE 4691099.841 4684104.6 2775793.11 2734584.325 5099748.417 3223553.013 4724016.117 3980113.15 4755685.899 0.986419192 0.98494827 0.583678815 0.575013654 1.072347612 0.677831354 0.993340649 0.836916742 1 22.181222 -0.981137234 6.551640316 1.000000031 0.855286411 0.068543756 0.177743194 7.90E-08 1.19E-08 0.168401694 0.039692651 0.104439015 0.981137234 -0.14471362 IADPEHDHTGFLTEY(ph)VATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.342)EY(0.658)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR 302.44 3.69E-50 2255200000 3622740 3130810 3539620 4076270 4055160 3221190 3694890 2771090 635545 TRUE FALSE 3451500.26 3449843.098 3701915.078 3666515.595 4762378.62 3109639.383 3131166.669 2528438.669 734102.0727 4.7016626 4.699405201 5.042779766 4.994558293 6.487352096 4.235976846 4.265301496 3.44426036 1 19.48562115 0.894061081 1.092512492 1.018463812 5.028022972 0.836770156 0.56760585 0.24257676 0.581384896 0.530181059 0.169071234 7.835398354 -0.894061081 4.00955916 IADPEHDHTGFLTEYVATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;; 167.05 1.08E-11 373565000 404223 400124 402720 452223 443262 420344 492417 391145 41115.8 FALSE TRUE 385116.1799 440897.0905 421185.1103 406764.6849 520566.7525 405787.3819 417289.7428 356894.2702 47491.82827 8.109104111 9.283641134 8.868580673 8.564940531 10.96118577 8.544362191 8.786558824 7.514856412 1 15.53539168 0.591250766 1.490861717 1.00013641 9.045413506 0.916969442 0.754083484 0.418459172 1.22691201 0.678458754 0.196906625 3.901672082 -0.591250766 8.045277097 IADREDEYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IADREDEYKK 10 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 101.38 0.0018958 458830000 663180 614820 552580 580610 335160 585630 649440 636250 251690 FALSE TRUE 631832.7957 677470.857 577916.3396 522245.9797 393611.7979 565349.4863 550356.0002 580536.577 290720.7997 2.173331926 2.330314369 1.987874071 1.796383266 1.353916879 1.944647534 1.893074045 1.99688697 1 18.14927477 -1.042612522 0.116869286 2.98E-15 2.642703677 0.594312005 0.247119817 31.34833775 0.734393508 14.53051122 3.831720592 0.090654106 1.042612522 2.642703677 IAEFTTNLTEEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAEFTTNLTEEEEK 14 0 P35579 P35579 MYH9 Myosin-9 0 200.44 2.36E-07 0 23803 20071 21908 27956 17450 23971 24153 22938 19316 FALSE TRUE 22677.87936 22116.25772 22912.50347 25145.80977 20493.27448 23140.87826 20468.01625 20929.42712 22311.42663 1.016424442 0.991252513 1.026940314 1.127037288 0.918510269 1.037176091 0.917378193 0.938058667 1 14.44549514 2.697913469 24.99969086 0.9601433 1.028806276 0.363685261 0.050320007 609.8079137 375056.8119 0.01561799 0.014724897 498.7850976 -2.697913469 0.068662977 IAEFTTNLTEEEEKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAEFTTNLTEEEEKSK 16 1 P35579 P35579 MYH9 Myosin-9 0 ; 239.58 7.17E-20 269688000 451349 264617 423602 408008 257489 497827 568428 538329 308742 FALSE TRUE 430014.6273 291581.7731 443024.5707 366994.2607 302395.0001 480587.1262 481703.8687 491190.0589 356620.1325 1.205805809 0.817625665 1.242287045 1.029090136 0.84794708 1.347616364 1.350747826 1.377348091 1 18.44402863 2.220183393 24.99948361 1.305558269 1.025642395 0.324027134 0.168846728 232.7602791 316633.8625 0.057961292 0.042886571 166.0287863 -2.220183393 -0.279915874 IAELVATEFFDQGDRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IAELVATEFFDQGDRER 17 1 O76074-2;G5E9C5;O76074;H0YA14 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 0 ;;; 123.02 5.01E-05 71397000 54509 40457.8 48908.1 50551.7 50447.8 50509.1 62736 50835.1 57231 FALSE TRUE 51932.4676 44580.49582 51150.58476 45470.14707 59245.88035 48759.9572 53164.47097 46383.70915 66106.09118 0.785592775 0.674378034 0.773765077 0.687835966 0.896224225 0.737601578 0.804229535 0.701655601 1 16.01249559 -5 0.28399167 2.816371205 0.741561412 0.563186805 0.066077748 161.7141197 1.538420765 173.5751191 0.06605759 1.00E-05 5 -2.074809792 IAESHLQSISNLNENQAS(ph)EEEDELGELR ddPTM_SK-BR-3_Trastuzumab_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 297.94 1.39E-71 221290000 66236 78501 77601 84562 77033 82818 87918 76735 71214 TRUE FALSE 63105.15555 86500.34115 81159.08261 76061.6671 90467.53081 79949.99189 74504.49438 70015.6766 82257.50341 0.767165948 1.051579948 0.986646558 0.924677555 1.099808857 0.971947708 0.90574709 0.851176777 1 16.32785966 -0.220777458 15.17855106 1 0.94718737 0.03210095 0.094405135 0 0 0.088456364 0.020849365 0.601481871 0.220777458 -0.05281263 IAESNHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAESNHIK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 127.46 0.0011753 990700000 1805790 791170 782740 1309240 1834240 1085170 2362000 1533630 2232280 FALSE TRUE 1720433.885 871791.1225 818629.4032 1177632.708 2154130.875 1047590.291 2001633.519 1399337.227 2578450.581 0.667235547 0.338106586 0.317488886 0.45672107 0.835436169 0.406286744 0.776293148 0.542704691 1 21.29807296 0.548284921 0.379759771 1.049029195 0.450607416 0.448688893 0.167931055 2.078745263 0.615085251 0.384093486 0.132485381 3.534149535 -0.548284921 -0.598421779 IAETDFEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAETDFEKR 9 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7EJV7;K7EN19;K7EJL5 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 127.4 0.00071603 217100000 223370 186140 183170 239620 161740 214040 252420 245920 177230 FALSE TRUE 212811.7428 205107.8776 191568.5257 215532.9424 189947.4048 206627.7411 213908.693 224385.9411 204713.9232 1.03955676 1.001924414 0.9357865 1.052849454 0.927867542 1.009348743 1.044915214 1.096095163 1 17.6432497 1.739218504 3.894748352 1.053902257 0.99580894 0.232266475 0.044984886 0.268515639 8.862350277 0.022549646 0.011157829 54.8552886 -1.739218504 -0.058093317 IAGDYVSEEVWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 206.49 1.43E-07 129919000 71666 89128 64839 79073 58991 67145 61289 76125 60625 FALSE TRUE 68278.49021 98210.24453 67811.93228 71124.43181 69279.01172 64819.75181 51938.2374 69459.09144 70026.41537 0.97503906 1.402474252 0.968376461 1.015680032 0.989326833 0.92564715 0.741694932 0.99189843 1 16.09561162 3.158512662 1.392177032 0.893452001 1.177741605 0.291281777 0.13640243 0.379776469 1.540715902 0.048542192 0.066774067 1440.498008 -3.158512662 0.284289604 IAGEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 25064590000 8845090 7284910 7221940 8515540 8416070 7789250 9522640 8289550 9239330 FALSE TRUE 8427000.125 8027250.611 7553073.092 7659541.741 9883829.943 7519506.319 8069786.373 7563673.056 10672118.11 0.789627705 0.752170331 0.707738896 0.717715234 0.926135735 0.704593619 0.756156022 0.708732135 1 23.3473432 -1.504311753 5.838233115 1.000307688 0.758979049 0.573535134 0.065613184 0.000242055 2.06E-05 0.058520124 0.013775976 0.031310373 1.504311753 -0.241328639 IAGHPLAQNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IAGHPLAQNER 11 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;;; 97.214 0.0064334 828430000 825061 593499 522748 572712 1072500 569653 989080 732584 1078150 FALSE TRUE 786062.0016 653977.2229 546716.5129 515141.9017 1259543.66 549925.7738 838177.6803 668435.0613 1245343.996 0.6312007 0.525137813 0.43900843 0.413654302 1.011402203 0.441585438 0.67304912 0.536747327 1 20.24811288 -5 0.265994312 3.785226603 0.552722852 0.364026366 0.172827592 216.4333822 2.111559528 330.3834191 0.19962514 1.00E-05 5 -3.232503751 IAGYVTHLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IAGYVTHLMK 10 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 156.83 1.03E-05 2648380000 6999110 5047290 2104830 2556810 6550950 3184400 7882030 5000250 5578020 FALSE TRUE 6668275.941 5561614.589 2201338.537 2299794.601 7693433.606 3074123.43 6679481.56 4562401.602 6443030.853 1.034959492 0.863198503 0.341661958 0.356942975 1.194070583 0.47712381 1.036698677 0.708114194 1 22.61930807 2.73312067 24.96416666 0.864191871 0.710636963 0.126902266 0.283020713 1436.925974 6594098.032 0.092406144 0.089458652 540.9045945 -2.73312067 -0.153554908 IAHFLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IAHFLDR 7 0 P60228;H0YBR5;E5RHS5;E5RIP5;E5RJ25;E5RII3 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;; 117.16 0.0052935 1260650000 1601270 1445230 1274850 1494220 1782180 1390950 1974060 1634680 1707470 FALSE TRUE 1525581.141 1592500.58 1333303.133 1344018.167 2092991.628 1342781.053 1672880.891 1491538.753 1972255.727 0.773520959 0.807451366 0.676029541 0.681462423 1.061217163 0.680835165 0.848206887 0.756260323 1 20.9114152 IAHIMGPPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IAHIMGPPDR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;; 116.3 0.0011079 834190000 930830 788840 815370 925900 1031160 819430 1062600 895520 948090 FALSE TRUE 886831.5106 869223.6928 852755.521 832826.7729 1210993.978 791052.9336 900480.854 817103.5213 1095114.955 0.809806776 0.793728265 0.778690417 0.760492557 1.105814483 0.722346937 0.822270621 0.746134931 1 20.06265089 -2.316658518 2.165700161 1.889124113 0.816745771 0.22395161 0.106811816 7046582.502 1051483.063 30571421.41 0.023791184 0.004823269 2.316658518 -1.072378342 IAHIPLYFVNAQFPRFS(ph)PVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAHIPLYFVNAQFPRFSPVLGR 22 1 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 IAHIPLYFVNAQFPRFS(1)PVLGR 56.909 0.049937 198910000 160350 69389 175170 133410 186860 131590 260460 198770 237740 TRUE FALSE 152770.5733 76459.81799 183201.7178 119999.3733 219448.3248 127033.0053 220722.0433 181364.6451 274607.505 0.556323372 0.278433097 0.667140244 0.436985046 0.799134477 0.462598447 0.8037728 0.660450431 1 18.06701153 1.257188202 0.263374387 1.079779967 0.362359844 0.52735457 0.143536603 1.339384377 0.361089594 0.376992877 0.285396616 18.07957436 -1.257188202 -0.717420123 IAIVNHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAIVNHDK 8 0 P61221;D6R9I9;D6RGF4 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 91.853 0.012192 144210000 183560 154040 153930 195680 154580 182180 213730 217600 171300 FALSE TRUE 174883.4826 169736.8511 160987.8428 176009.8746 181538.7031 175871.0609 181121.5631 198545.7904 197864.3291 0.883855536 0.857844625 0.813627416 0.889548285 0.917490807 0.888846725 0.915382595 1.003444084 1 17.59415202 1.458756163 0.930628092 1.010091605 0.864632932 0.777107122 0.027452124 0.240105975 0.420431642 0.025301217 0.009510375 28.75783334 -1.458756163 -0.145458674 IAIWTTECENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IAIWTTECENR 11 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;; 191.67 4.03E-06 771620000 979030 891110 870131 1008399 919855 913464 1081971 1078789 1025726 FALSE TRUE 932753.1922 981915.1221 910027.367 907032.8167 1080277.421 881830.5126 916896.4522 984324.5161 1184790.349 0.78727278 0.828766982 0.768091475 0.765563981 0.911787829 0.744292451 0.773889197 0.830800586 1 20.17620036 0.876400719 5.72605156 0.99999767 0.797749995 0.650056443 0.046454989 1.013127709 46.58915027 0.041620861 0.010477507 7.523167281 -0.876400719 -0.202247674 IALESEGRPEEQMES(ph)DNCS(ph)GGDDDWTHLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 2 IALESEGRPEEQMES(1)DNCS(1)GGDDDWTHLSSK 112.9 0.0001072 42722000 51892 52067 45411 60550 38696 51740 58885 49423 38104 TRUE FALSE 49439.168 57372.6865 47493.13927 54463.39896 45444.57015 49948.23083 49901.01175 45095.26011 44012.97371 1.123286246 1.303540335 1.079071357 1.237439654 1.032526692 1.134852445 1.133779601 1.024590168 1 15.42564123 1.748302119 0.394748098 0.994136499 1.212333122 0.378519479 0.074657739 1.048618931 0.454741133 0.083160925 0.072669038 56.01471346 -1.748302119 0.218196623 IALLEEARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IALLEEARR 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 174.92 8.71E-05 663860000 974980 418214 577026 499671 1152780 623238 1269430 854450 1381080 FALSE TRUE 928894.6276 460830.4821 603483.2129 449443.1218 1353824.467 601655.1118 1075755.139 779629.8283 1595250.833 0.582287505 0.288876503 0.378299889 0.281738215 0.848659307 0.377153924 0.674348583 0.488719274 1 20.60535186 -0.469116499 0.286230082 1.216241425 0.388638256 0.484295342 0.171176728 7.325618924 0.69509164 1.70316581 0.205138697 0.339534181 0.469116499 -0.827603169 IANDNSLNHEYLPILGLAEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IANDNSLNHEYLPILGLAEFR 21 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;;; 209.75 2.41E-22 591602000 1173366 1005279 1042792 1334054 1256974 999203 1258234 1179903 1069779 FALSE TRUE 1117903.315 1107718.073 1090605.045 1199952.357 1476189.868 964600.3496 1066267.294 1076584.438 1235674.864 0.904690504 0.896447849 0.882598713 0.971090691 1.194642629 0.780626343 0.862902796 0.871252196 1 20.23686775 -3.088851917 9.566463411 0.99922583 0.920210801 0 0.11138178 0 0 0 0.023943446 0.000814982 3.088851917 -0.079015028 IANS(ph)MVST(ph)WT(ph)GPPAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IANSMVSTWTGPPAMK 16 0 Q6P1X5 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 3 IANS(1)MVS(0.058)T(0.974)WT(0.968)GPPAMK;IANS(1)MVS(0.092)T(0.959)WT(0.949)GPPAMK;IANS(0.999)MVS(0.037)T(0.983)WT(0.981)GPPAMK;IANS(0.999)MVS(0.03)T(0.987)WT(0.985)GPPAMK;IANS(1)MVS(0.12)T(0.946)WT(0.934)GPPAMK 48.824 0.059753 2817387000 457702 342527 474128 478457 963887 349999 512057 251597 194834 TRUE FALSE 436067.3335 377430.8907 495867.2378 430361.5934 1131988.588 337878.4469 433933.3001 229565.8329 225047.8616 1.937664861 1.677113872 2.203385689 1.912311409 5.029990418 1.501362619 1.928182285 1.020075602 1 17.77987233 1.466109528 2.04029436 1.004776804 2.339534452 0.245169237 0.984105282 0.489820183 3.886151061 0.823320669 0.266148284 29.24889932 -1.466109528 1.334757648 IAQFLSDIPETVPLSTVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAQFLSDIPETVPLSTVNR 19 0 P09110;H7C131;P09110-2;B4DVF4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 157.68 6.96E-10 0 52839 47904 49000 52169 55632 51605 56353 55650 53878 FALSE TRUE 50341.40519 52785.47206 51246.69847 46924.87301 65334.20319 49817.90591 47755.31486 50776.99098 62233.12507 0.808916556 0.84818932 0.823463363 0.754017622 1.049830024 0.800504649 0.767361671 0.815915815 1 15.92539507 -2.428707527 2.21238903 2.501856435 0.83092973 0.291090148 0.081556412 3190139.157 321616.9439 24100037.75 0.018600162 0.003726426 2.428707527 -1.670926704 IAQLEEQLDNETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 171.57 5.78E-05 48673000 76747 82467 67033 80094 51921 81874 85914 75032 64753 FALSE TRUE 73119.32141 90870.48106 70106.52935 72042.79895 60976.00596 79038.68285 72806.24138 68461.80031 74794.56453 0.977602074 1.214934289 0.937321178 0.963209017 0.815246487 1.056743673 0.973416208 0.915331224 1 16.19064581 3.706924485 24.84127076 0.953112095 1.096268211 0.343078614 0.083199331 571.7231811 448927.5474 0.02099305 0.032525227 5092.423162 -3.706924485 0.143156116 IAQLEEQLDNETKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IAQLEEQLDNETKER 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 226.25 8.12E-13 896620000 709316 310306 807567 518389 653899 719434 1079403 855291 1032637 FALSE TRUE 675788.0384 341926.5342 844594.7457 466279.5528 767938.7786 694519.8202 914720.2478 780397.1859 1192773.072 0.566568825 0.286665202 0.708093405 0.39092059 0.643826388 0.582273222 0.766885394 0.654271298 1 20.18588816 1.175643753 0.358832602 1.03353705 0.420532451 0.607645661 0.122336771 0.786534696 0.312599288 0.183347515 0.117131302 14.98455164 -1.175643753 -0.613004599 IAQVS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 130.56 0.00037515 579750000 841230 780880 773190 897230 856900 736380 884780 784000 903150 TRUE FALSE 801466.7251 860452.5598 808641.5263 807038.7358 1006343.089 710878.976 749790.5609 715348.8038 1043205.889 0.768272815 0.824815665 0.775150461 0.773614053 0.964663926 0.681436889 0.718736894 0.685721593 1 19.99259249 -0.05169917 9.182537336 1.000000029 0.775573764 0.437159943 0.080555551 0 0 0.076237562 0.017969366 0.887770747 0.05169917 -0.224426264 IAS(ph)HDFDPTGLVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IASHDFDPTGLVQR 14 0 Q9NZN5-2 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 IAS(1)HDFDPTGLVQR 70.748 0.027919 151960000 112010 77496 89842 135510 172040 120130 149260 86760 159340 TRUE FALSE 106715.5093 85392.93051 93961.34457 121888.2773 202043.7215 115969.868 126487.6457 79162.83446 184049.6334 0.57981919 0.46396686 0.51052177 0.662257648 1.097767585 0.630101054 0.687247474 0.430116773 1 17.48973535 3.11838069 4.739604662 0.745834163 0.516374537 0.267103541 0.186533636 0.291847684 10.84493366 0.052314346 0.063329869 1313.350639 -3.11838069 -0.229459626 IASEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IASEASR 7 0 Q99880;Q96A08 Q99880 HIST1H2BL;HIST1H2BA Histone H2B type 1-L;Histone H2B type 1-A 0 91.626 0.037841 95632000 75728 62719 60746 75263 63420 68298 84839 83401 93997 FALSE TRUE 72148.48752 69110.13741 63531.26419 67697.42025 74480.42792 65932.82313 71895.25237 76097.9663 108573.5747 0.664512408 0.636528157 0.585144814 0.623516546 0.685990381 0.607263999 0.662180025 0.700888467 1 16.72831349 0.504434404 1.271481291 1.000192982 0.635512786 0.942042251 0.02809398 0.42940132 0.880764793 0.026005306 0.007784338 3.194731792 -0.504434404 -0.364680196 IASHYYITNDTVQTYNQLLKPTLSEIELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IASHYYITNDTVQTYNQLLKPTLSEIELFR 30 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 249.46 1.59E-46 233940000 137049 129442 141157 159530 117020 156095 178011 154135 133030 FALSE TRUE 130570.9654 142632.287 147629.1881 143493.7413 137428.251 150689.391 150852.1526 140638.1223 153659.613 0.8497416 0.928235365 0.960754653 0.933841616 0.894368066 0.980670119 0.981729354 0.915257559 1 17.2293785 7.348248347 0.378192087 0.965900745 2.75E-16 0.523950773 0.031211606 30.51852465 0.67239252 0.023078563 19.98101948 22297098.25 -7.348248347 -0.965900745 IASLEVENQSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 264.12 3.75E-21 561907000 331567 287770 312549 314154 322596 296353 382902 307234 375270 FALSE TRUE 315894.485 317094.0902 326879.6808 282574.6431 378856.6403 286090.2213 324483.2674 280330.9622 433464.955 0.728765916 0.731533395 0.75410867 0.651897321 0.874019078 0.660007731 0.748580165 0.646721169 1 18.72555583 -1.300652756 4.644052269 1.000154163 0.727236651 0.631050683 0.066183262 8.99E-05 1.35E-05 0.054521705 0.012843666 0.05004345 1.300652756 -0.272917512 IATPFQVYSWTAPQAEHAMDCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IATPFQVYSWTAPQAEHAMDCVR 23 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 208.65 9.79E-25 73315000 81393 70124 66329 85400 89491 77801 101120 87374 84119 FALSE TRUE 77545.7142 77269.71532 69370.25026 76815.42975 105098.2021 75106.73186 85692.2868 79723.06936 97163.7449 0.798093098 0.795252544 0.713952003 0.79057708 1.081660677 0.772991324 0.881936847 0.82050223 1 16.56813048 2.966198787 24.93212082 0.895392011 0.775522791 0.363565846 0.088881907 701.4592959 517403.814 0.024986025 0.026517161 925.1215282 -2.966198787 -0.11986922 IAVDEVHCCSQWGHDFRPDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAVDEVHCCSQWGHDFRPDYK 21 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 235.84 5.29E-30 140150000 207320 188770 198870 227080 150000 220220 245940 245190 33326 FALSE TRUE 197520.3945 208005.8776 207988.3862 204253.487 176159.9525 212593.7262 208417.336 223719.8638 38494.02587 5.131196075 5.403588554 5.403134161 5.306108736 4.576293295 5.522771946 5.414277444 5.811807383 1 15.23234694 2.779674789 18.56965264 4.877518095 5.311579951 0.042284812 1.364333734 121.5089073 54877.43335 0.365330962 0.387450915 602.108543 -2.779674789 0.434061856 IAVHCTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAVHCTVR 8 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 133.55 0.0009147 587590000 133450 114180 63206 83174 176680 83681 170900 123610 180490 FALSE TRUE 127142.083 125815.0718 66104.05762 74813.1915 207492.9361 80783.10599 144826.0662 112786.0531 208479.4674 0.60985422 0.603489031 0.317077065 0.358851605 0.995267969 0.387487108 0.694677841 0.540993578 1 17.66954578 -3.308603723 0.296280634 2.120391028 0.540349772 0.337401573 0.193934911 98.1841001 2.298572681 67.79592215 0.186521032 0.000491356 3.308603723 -1.580041256 IAVMELFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAVMELFRPK 10 1 Q16531;F5GY55;Q16531-2;F5H2L3;F5GWI0;F5GZY8;F5GYG8;F5H198 Q16531 DDB1 DNA damage-binding protein 1 0 90.05 0.010119 105090000 158950 144880 125950 134630 115410 143230 176850 150520 127870 FALSE TRUE 151436.7485 159643.4367 131724.9321 121096.7366 135537.4675 138269.9092 149868.2844 137339.6708 147699.4265 1.025303565 1.080867004 0.891844574 0.819886302 0.917657371 0.936157387 1.014684268 0.929859202 1 17.1723047 3.741840383 24.9980585 0.931106066 1.053085289 0.462302914 0.055171028 250.1603354 1906688.791 0.015425711 0.026442502 5518.745706 -3.741840383 0.121979223 IAWALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAWALSR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 154.35 0.003919 495320000 743670 336120 174751 227754 789730 255040 796270 395600 689670 FALSE TRUE 708518.1929 370371.0101 182763.5062 204859.7352 927458.662 246207.9009 674784.387 360959.1668 796620.5013 0.88940492 0.464927791 0.229423554 0.257161013 1.164241518 0.309065484 0.847058776 0.453113077 1 19.60353308 IAWDDEETRDGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IAWDDEETRDGFR 13 1 A0A1B0GWA1;A0A1B0GUX9;A0A1B0GWI4;A0A1B0GU58;P05165-3;P05165-2;P05165 A0A1B0GWA1 PCCA "Propionyl-CoA carboxylase alpha chain, mitochondrial" 0 ; 155.98 4.28E-05 152894000 122612 78684 109432 92082 144872 90021 132474 107635 147376 FALSE TRUE 116816.3738 86701.98906 114449.5654 82825.74242 170137.6309 86903.5502 112262.6582 98209.90879 170230.3174 0.686225436 0.509321667 0.672321871 0.486551066 0.999455523 0.510505717 0.659475116 0.576923725 1 17.37712847 -2.053736459 2.438878494 1.496751347 0.632653639 0.374947044 0.146927495 13234999.56 4486773.756 36647016.3 0.031792817 0.008836159 2.053736459 -0.864097708 IAYVYPDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IAYVYPDER 9 0 Q8WTS6;D6RJA0 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 79.116 0.064797 46085000 169850 127840 143240 151890 149530 162220 194010 199020 144540 FALSE TRUE 161821.5271 140867.0413 149807.6957 136621.7286 175607.9847 156602.2807 164410.2113 181592.7537 166954.525 0.969255114 0.843744974 0.897296409 0.818317016 1.051831238 0.937993629 0.984760439 1.087677939 1 17.34909567 2.732791053 24.9907353 1.003093404 0.886271227 0.574687796 0.055325012 363.5218086 1574581.795 0.017028307 0.016448235 540.4942185 -2.732791053 -0.116822177 ICANHYITPMMELKPNAGSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ICANHYITPMMELKPNAGSDR 21 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 212.18 6.56E-23 2272800000 2412570 2178580 2239020 2456030 2062180 2362010 2753100 2662400 2131310 FALSE TRUE 2298532.597 2400579.779 2341681.282 2209145.198 2421823.539 2280213.001 2333064.031 2429266.142 2461822.67 0.933671066 0.975122948 0.951198196 0.897361628 0.983752229 0.92622959 0.947697842 0.986775437 1 21.23129541 1.170744632 3.916493884 0.998594087 0.946098607 0.415402725 0.024089316 0.205515492 5.660342341 0.020682421 0.005492744 14.81646611 -1.170744632 -0.05249548 ICDDELILIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ICDDELILIK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 185.97 3.24E-06 48135000 240619 244548 223602 260465 172431 237789 252847 259184 190416 FALSE TRUE 229245.4167 269467.7192 233854.3729 234282.5633 202502.9118 229554.3073 214270.5463 236488.4749 219944.7408 1.042286421 1.225161003 1.063241485 1.065188295 0.920699041 1.043690822 0.974201727 1.075217685 1 17.74678158 3.265336707 2.444493472 1.003310925 1.132742971 0.384604612 0.062213949 0.234929333 2.872471456 0.01742152 0.02382316 1842.199701 -3.265336707 0.129432046 ICDECNYGSYQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICDECNYGSYQGR 13 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 131.43 1.46E-05 0 24177 22955 24461 30161 25201 24140 27319 25746 32888 FALSE TRUE 23034.20112 25294.1406 25582.56105 27129.15898 29596.04642 23304.02575 23150.9848 23491.54375 37988.10307 0.606353023 0.665843739 0.673436128 0.71414882 0.779087241 0.613455894 0.60942724 0.618392124 1 15.21326005 -1.129261587 4.482754082 1.000042822 0.657252612 0.793496311 0.054490461 1.296461131 34163057.26 2933.097013 0.013383377 0.074257173 1.129261587 -0.34279021 ICDQISDAVLDAHLQQDPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ICDQISDAVLDAHLQQDPDAK 21 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 266.18 5.66E-37 327106000 298236 386644 249084 360815 194928 310389 279821 337168 173299 FALSE TRUE 284138.9753 426043.4632 260504.7478 324545.1907 228923.3815 299640.1511 237129.1672 307643.7825 200173.3238 1.419464741 2.128372827 1.301395924 1.621320886 1.143625819 1.49690351 1.184619222 1.536887017 1 17.6108902 3.706281582 24.88935711 1.339465606 1.773918857 0.351134917 0.252431849 547.3201252 422021.4837 0.060539885 0.093796122 5084.89023 -3.706281582 0.43445325 ICDQWDALGSLTHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ICDQWDALGSLTHSR 15 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 266.17 2.80E-25 1793510000 2840810 1451290 1483070 2239320 3304240 1710280 3414480 2178130 3660060 FALSE TRUE 2706530.541 1599178.101 1551070.226 2014219.299 3880498.41 1651052.575 2893538.365 1987401.39 4227643.412 0.640198398 0.378267026 0.366887667 0.476440206 0.917886877 0.390537331 0.684432929 0.470096741 1 22.01142226 -5 0.218518609 3.331619252 0.478551814 0.415238315 0.170742603 144.3631634 1.443160826 147.9155842 0.308611263 1.00E-05 5 -2.853067439 ICEDSAEILDSDVLDRPLNIMIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICEDSAEILDSDVLDRPLNIMIPK 24 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 105.92 0.0025374 21402000 16365 13384 16588 19754 18255 18035 20849 19436 19004 FALSE TRUE 15591.45888 14747.84482 17348.57621 17768.29039 21438.66622 17410.44343 17668.10213 17734.0808 21951.04326 0.710283274 0.671851658 0.790330373 0.809450839 0.976658192 0.793148791 0.804886671 0.80789239 1 14.42200189 7.502849138 0.087309862 1.105953926 4.88E-15 0.541323914 0.068840828 114.9071009 0.799572524 1.514208283 15.27360953 31830916.14 -7.502849138 -1.105953926 ICEEAFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICEEAFAR 8 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 122.74 0.0032044 86839000 60822 48516 48246 53745 63113 45769 57898 53249 71138 FALSE TRUE 57947.0646 53459.83556 50458.12682 48342.45049 74119.88722 44184.00805 49064.59673 48586.23527 82169.71772 0.705211922 0.650602643 0.614072048 0.588324408 0.902034098 0.53771644 0.597112879 0.591291252 1 16.32631919 -1.443927206 3.356321107 1.004761932 0.647919896 0.548534414 0.100273991 53008990.74 81824613.87 2462189.787 0.022758193 0.035980964 1.443927206 -0.356842035 ICGDIHGQYTDLLR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 207.31 9.61E-09 1023740000 3386950 3276620 2580860 3141300 3182220 2767790 3372240 3250030 2651530 FALSE TRUE 3226855.586 3610511.303 2699194.984 2825530.556 3737198.16 2671940.738 2857742.853 2965440.144 3062715.73 1.053592912 1.178859425 0.881307709 0.922557235 1.220223648 0.87240899 0.933074795 0.968238781 1 21.54638004 3.744353049 24.99964829 0.968365955 1.116226169 0.261384729 0.101329863 570.9914285 2464343.535 0.02531891 0.044152989 5550.767658 -3.744353049 0.147860214 ICGDIHGQYYDLLR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 157.35 5.32E-06 885150000 2553830 2454540 1802790 2080750 3100390 1977970 2572190 2447020 2431800 FALSE TRUE 2433115.517 2704660.417 1885449.705 1871589.057 3641097.034 1909472.403 2179755.174 2232745.956 2808911.124 0.866213066 0.962885722 0.671238648 0.666304121 1.296266373 0.679790965 0.776014291 0.794879531 1 21.42157955 -1.11717546 4.828976217 1.000008554 0.843205355 0.067741501 0.186945599 1.61E-05 2.93E-06 0.168746338 0.039771724 0.076352725 1.11717546 -0.1568032 ICHQIEYYFGDFNLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ICHQIEYYFGDFNLPR 16 0 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 ; 245.96 3.68E-20 1142480000 797810 745900 721380 822510 838620 748240 891990 748640 744970 FALSE TRUE 760099.1024 821908.058 754455.9865 739829.7321 984875.0625 722328.2612 755900.543 683085.1128 860496.1428 0.883326565 0.955156005 0.876768586 0.85977112 1.144543262 0.839432306 0.878447334 0.793827048 1 19.7148092 -1.329735609 5.330600818 1.000024788 0.907285766 0.091430202 0.094665663 2.59E-05 3.25E-06 0.085028357 0.020036021 0.046801998 1.329735609 -0.092739021 ICKPLHELIMQLLEETPEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICKPLHELIMQLLEETPEEK 20 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 170.19 5.81E-12 110980000 554110 490870 460160 552440 351490 586430 636220 637430 362120 FALSE TRUE 527918.3184 540890.2111 481258.7912 496907.6816 412789.7447 566121.7821 539152.954 581613.25 418275.7201 1.262129961 1.293142741 1.15057788 1.187990738 0.986884308 1.353465561 1.288989363 1.390502059 1 18.67409473 ICNAVSPDKDVDGFHVINVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICNAVSPDKDVDGFHVINVGR 21 1 P13995-2;P13995;B8ZZU9 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 153.82 2.38E-08 131200000 256860 232350 266210 232900 194230 200510 226940 267640 193530 FALSE TRUE 244718.7368 256026.7292 278415.9918 209488.4495 228103.6505 193566.2884 192316.135 244204.0228 223541.644 1.094734442 1.14532006 1.24547707 0.937133886 1.02040786 0.865907063 0.860314577 1.092431899 1 17.77018409 3.222353763 24.99572133 0.945392714 1.148715978 0.578337398 0.078981355 155.9482496 240517.4828 0.022628927 0.027122491 1668.605855 -3.222353763 0.203323264 ICNHPYMFQHIEESFSEHLGFTGGIVQGLDLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICNHPYMFQHIEESFSEHLGFTGGIVQGLDLYR 33 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 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 57.262 0.013967 18766000 58352 60662 71237 73744 71722 65433 85395 57824 41659 FALSE TRUE 55593.8166 66843.52677 74503.28691 66331.11302 84230.29409 63167.0388 72366.42436 52760.62402 48119.26496 1.15533387 1.389121942 1.548304759 1.378473114 1.750448478 1.312718282 1.503897128 1.096455319 1 15.55432698 1.135457182 4.890545434 1.008381607 1.421366679 0.516452141 0.155793421 0.171916713 6.233183801 0.147992213 0.037756738 13.6602039 -1.135457182 0.412985072 ICQGCPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 101.28 0.0055038 21835000 34076 31547 36287 46180 31832 34579 36942 35902 43824 FALSE TRUE 32465.29501 34761.67517 37950.79484 41537.89866 37383.49072 33381.52056 31305.81941 32758.23055 50620.0021 0.641353095 0.686718169 0.749719346 0.820582713 0.738512232 0.659453164 0.618447612 0.647140047 1 15.62741995 -0.944325463 8.304878275 1 0.690909803 0.713013783 0.060707985 9.66E-10 5.82E-11 0.064853411 0.015286096 0.113677506 0.944325463 -0.309090198 ICRDPQT(ph)PVLQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ICRDPQTPVLQTK 13 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK 234.04 1.92E-16 1946180000 3167000 3033350 3287670 3694940 2738660 3405910 4017000 3912970 3696330 TRUE FALSE 3017302.186 3342451.814 3438412.921 3323517.611 3216281.437 3287962.483 3404132.873 3570329.603 4269537.978 0.706704613 0.782860307 0.805336067 0.778425588 0.753309012 0.770097959 0.797307083 0.836233246 1 22.02564853 -5 0.191716169 1.999223098 0.733666848 0.894313071 0.025131397 42.6370366 0.417910296 16.19990519 0.068937778 1.00E-05 5 -1.26555625 ICSWNVDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 200.07 6.21E-07 640560000 1231860 856710 676290 773210 1328150 824530 1390350 1021100 1326530 FALSE TRUE 1173632.419 944009.723 707298.5654 695485.4618 1559778.939 795976.3194 1178226.572 931687.0708 1532241.497 0.76595786 0.616097217 0.461610371 0.453900683 1.017971999 0.519484899 0.768956182 0.608054979 1 20.54721227 2.782668248 24.99997996 0.746946396 0.596362067 0.241800317 0.175312619 849.171533 481304.6395 0.050544761 0.053610577 606.2730287 -2.782668248 -0.150584329 ICTEQSNS(ph)PPPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ICTEQSNSPPPIR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ICTEQS(0.016)NS(0.984)PPPIR;ICTEQS(0.067)NS(0.933)PPPIR 145.49 4.39E-05 207390000 441580 373660 344920 472670 411950 387740 473140 432260 439860 TRUE FALSE 420707.3885 411736.3788 360734.9232 425156.3136 483793.9496 374312.4666 400953.8032 394409.0228 508071.2423 0.828048025 0.810391033 0.710008544 0.836804523 0.952216755 0.736732244 0.789168467 0.776286847 1 18.95467128 -1.612838561 2.811352326 1.0158782 0.805091328 0.470836808 0.064981751 9215190.114 9304684.199 1079506.243 0.01490852 0.024387172 1.612838561 -0.210786872 ICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ICTLPSPPSPLASLAPVADSSTR 23 0 Q9UER7-3;Q9UER7;Q9UER7-2 Q9UER7-3 DAXX Death domain-associated protein 6 1 ICT(0.002)LPS(0.043)PPS(0.955)PLASLAPVADSSTR 85.537 0.0045569 13937000 34599 32366 36078 38329 35684 36131 41564 34384 37783 TRUE FALSE 32963.57384 35664.1322 37732.21199 34476.0961 41907.2783 34879.77441 35222.64842 31373.15468 43642.19467 0.755314303 0.81719383 0.864580993 0.78997164 0.960246812 0.799221365 0.807077845 0.718872067 1 15.41343603 -2.562662088 2.253687181 4.434622938 0.814749245 0.451715738 0.064375262 2107642.75 260999.3171 37823120.14 0.015515756 0.002737398 2.562662088 -3.619873693 ICYIFHETFGR ddPTM_SK-BR-3_Trastuzumab_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 ; 123.42 0.00037033 306290000 901580 576940 516160 640360 1003550 538660 1041250 748880 907540 FALSE TRUE 858964.1002 635730.8419 539826.4466 575989.7962 1178568.802 520006.0691 882388.1886 683304.0971 1048276.668 0.819405913 0.606453297 0.514965622 0.549463528 1.124291743 0.49605804 0.841751243 0.651835644 1 19.9995881 IDAHLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDAHLNK 7 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 67.757 0.064296 1955400000 9658300 8336800 7224700 8731200 7275600 8054800 9972900 9399700 7036100 FALSE TRUE 9201771.3 9186329.398 7555959.641 7853523.188 8544462.336 7775860.256 8451350.94 8576612.437 8127222.453 1.132216 1.130315978 0.929709958 0.966323148 1.051338558 0.956767248 1.039881828 1.055294412 1 22.95433095 3.761868152 23.9029314 1.001940874 1.131266043 0.637332233 0.041174973 254.7361693 261242.0295 0.010283487 0.018521462 5779.205697 -3.761868152 0.12932517 IDASKNEEDEGHS(ph)NS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 IDASKNEEDEGHS(0.998)NS(0.869)S(0.134)PR;IDASKNEEDEGHS(0.745)NS(0.716)S(0.539)PR 69.72 0.035001 377320000 977540 752990 877030 962120 566400 932650 966860 969370 557630 TRUE FALSE 931333.6215 829720.5371 917242.693 865405.8697 665179.9807 900352.0966 819347.7494 884486.8238 644104.4124 1.445935789 1.288177074 1.424059012 1.343580098 1.032720733 1.397835629 1.272072871 1.373204106 1 19.29693505 -4.450438537 0.179632679 8.68E-14 1.390436703 0.434920161 0.115972274 102.6651605 1.181392372 37.50401822 0.34601878 3.54E-05 4.450438537 1.390436703 IDASKNEEDEGHS(ph)NSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 IDASKNEEDEGHS(0.81)NS(0.538)S(0.652)PR 52.462 0.075169 204680000 502820 393430 459650 512900 319610 504920 524620 528670 292370 TRUE FALSE 479052.6951 433520.9643 480725.4072 461342.3176 375349.8828 487434.4938 444579.5837 482376.8521 337709.2464 1.418535916 1.283710674 1.423489029 1.366093237 1.111458708 1.443355487 1.316456652 1.428379167 1 18.36542215 -1.704751375 2.755018902 0.947010699 1.344996009 0.551954971 0.098743081 16695585.58 14853817.67 6148734.718 0.021854962 0.019735522 1.704751375 0.39798531 IDASKNEEDEGHSNS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.094)NS(0.544)S(0.362)PR;IDASKNEEDEGHS(0.003)NS(0.629)S(0.368)PR;IDASKNEEDEGHS(0.02)NS(0.579)S(0.401)PR 148.52 4.15E-08 20508600000 5565600 4249300 4989000 5229500 3206970 5348200 5858300 5503900 3110090 TRUE FALSE 5302525.118 4682308.501 5217750.585 4703820.725 3766264.553 5162990.493 4964508.74 5021949.338 3592386.873 1.476045121 1.30339762 1.452446735 1.309385902 1.048401713 1.437203362 1.3819527 1.397942236 1 21.7765113 -2.015376563 2.701988703 0.611688554 1.352875845 0.452933765 0.121159479 16588556.42 3128765.017 40061650.11 0.028644506 0.009652136 2.015376563 0.741187291 IDASKNEEDEGHSNSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.013)NS(0.12)S(0.867)PR;IDASKNEEDEGHS(0.002)NS(0.338)S(0.66)PR;IDASKNEEDEGHSNS(0.12)S(0.88)PR;IDASKNEEDEGHSNS(0.125)S(0.875)PR;IDASKNEEDEGHS(0.031)NS(0.17)S(0.799)PR;IDASKNEEDEGHS(0.001)NS(0.049)S(0.951)PR;IDASKNEEDEGHSNS(0.433)S(0.567)PR;IDASKNEEDEGHSNS(0.018)S(0.982)PR 245.53 1.95E-24 48301550000 19959760 15703960 18422980 19004650 11944580 20708340 22009540 20901120 11937690 TRUE FALSE 19016301.7 17304211.38 19267691.86 17094266.48 14027710.97 19991204.99 18651580.44 19070907.13 13788926 1.379099555 1.254935401 1.397330863 1.239709785 1.017317155 1.449801457 1.352649252 1.383059648 1 23.71700676 3.212563241 24.97620884 1.268238837 1.329793136 0.074121371 0.149665464 871.5547536 837318.2075 0.041962274 0.050168765 1631.410455 -3.212563241 0.061554299 IDASKNEEDEGHSNSSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 237 4.66E-24 1201290000 2647880 2126150 2432890 2630240 1836120 2650470 2966600 2803800 1840020 FALSE TRUE 2522719.96 2342807.102 2544440.413 2365843.278 2156338.747 2558683.559 2513990.685 2558284.408 2125360.904 1.186960744 1.102310247 1.197180398 1.113148959 1.014575333 1.203881917 1.182853547 1.203694113 1 21.01927641 IDASKNEEDEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDASKNEEDEGK 12 1 Q14103-2;Q14103-4;D6RBQ9 Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 89.959 0.0083265 205410000 316070 316490 286270 352090 148740 358600 341360 364660 182000 FALSE TRUE 301129.9975 348740.6908 299395.7627 316697.2443 174680.2089 346181.5921 289279.2625 332728.4372 210223.6305 1.432426967 1.658903378 1.424177491 1.506477857 0.83092566 1.646730157 1.376054927 1.582735663 1 17.68156532 -2.170670949 2.081261075 3.46E-05 1.441352073 0.252056971 0.233570894 3337717.91 668921.9385 15734020.51 0.053087818 0.006750393 2.170670949 1.441317447 IDDDDDERENFEITDWDLQNEFNPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDDDDDERENFEITDWDLQNEFNPNR 26 1 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 87.102 0.011352 29173000 12843 14272 9457.8 11949 7527.9 12687 9735.6 11317 9665 FALSE TRUE 12235.93684 15726.33303 9891.449485 10747.86382 8840.763377 12247.64601 8250.255413 10326.02348 11163.79884 1.096037023 1.408690111 0.886028997 0.962742519 0.791913533 1.097085874 0.739018638 0.924956069 1 13.44654041 3.723716963 24.82700969 0.902041071 1.252363563 0.55813349 0.124581506 404.7292507 676937.0901 0.030277806 0.047128836 5293.18366 -3.723716963 0.350322492 IDDGDKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDDGDKTK 8 1 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 80.067 0.024085 220270000 287680 249430 272400 300500 202290 300160 351700 334090 242670 FALSE TRUE 274081.9365 274847.2006 284889.8094 270293.1691 237569.312 289765.3839 298041.7056 304835.3085 280302.0242 0.977809337 0.980539478 1.016367293 0.964292605 0.847547614 1.033761296 1.063287739 1.087524463 1 18.09662264 2.020751254 24.99544337 1.055108205 0.963286442 0.455879569 0.048163241 206.1651686 248330.5013 0.017596241 0.012994421 104.8941466 -2.020751254 -0.091821763 IDDIFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDDIFER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 157.21 0.0034697 244180000 431730 361833 380430 431060 386970 363089 454270 423940 405360 FALSE TRUE 411322.9785 398704.1941 397873.0918 387729.0298 454457.4455 350515.1369 384962.7683 386817.5662 468221.1585 0.878480118 0.851529639 0.849754618 0.82808951 0.970604248 0.748610204 0.822181487 0.826142858 1 18.8368306 2.219202463 24.99915034 0.830040247 0.869307682 0 0.07328528 694.8156899 897280.3857 0.024331116 0.017996508 165.6542043 -2.219202463 0.039267435 IDDIRKPGESEE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDDIRKPGESEE 12 2 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 84.718 0.04799 314710000 785990 438970 792140 601550 677000 758690 1191600 876430 939680 FALSE TRUE 748837.8104 483701.5421 828460.4025 541081.0511 795068.5857 732416.3751 1009799.535 799685.143 1085400.775 0.689918256 0.445643262 0.763276037 0.498508075 0.732511533 0.674788881 0.930347166 0.736764853 1 20.04979641 1.801697944 0.689464088 0.96417151 0.57816739 0.537720848 0.11382236 0.443594308 0.41878183 0.093344879 0.047897743 63.34290027 -1.801697944 -0.38600412 IDDIVSGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDDIVSGHK 9 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 152.97 7.92E-05 843840000 2727560 3340110 2652840 3205450 1684110 2866710 2640510 3228250 1575600 FALSE TRUE 2598633.644 3680471.006 2774475.338 2883232.076 1977818.251 2767435.114 2237651.703 2945567.316 1819936.001 1.427870894 2.02230793 1.524490607 1.584249157 1.086751539 1.520622216 1.229522193 1.618500494 1 20.79545629 3.104392603 2.352628579 1.31963652 1.715576051 0.330199749 0.239057638 0.296862328 3.345385011 0.068628132 0.085355247 1271.723225 -3.104392603 0.39593953 IDDRDS(ph)DEEGASDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR;IDDRDS(0.998)DEEGAS(0.002)DR;IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR 255.96 7.05E-24 2291227000 2297188 2173835 2069690 2411919 1722020 2033769 2265934 2158272 1964461 TRUE FALSE 2188604.476 2395351.258 2164587.334 2169468.32 2022339.743 1963339.07 1920224.152 1969282.262 2269099.579 0.964525531 1.05563955 0.953941094 0.956092161 0.89125209 0.86525029 0.846249398 0.867869476 1 21.11368849 3.014404883 1.596786525 0.877299055 1.006729078 0.439264344 0.049667549 0.251933017 1.314078212 0.016367438 0.019632036 1033.724676 -3.014404883 0.129430023 IDDVVNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDDVVNTR 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 167.23 0.00073018 568210000 565050 600250 560830 643460 505620 608850 615580 597300 544610 FALSE TRUE 538341.2063 661416.1574 586544.6102 578778.1783 593799.9679 587765.3718 521661.9651 544997.2455 629065.3373 0.855779479 1.051426804 0.932406501 0.920060515 0.943940053 0.934347097 0.829265156 0.866360318 1 19.26285034 1.937023483 10.50679166 0.880036101 0.94614918 0.05669306 0.064360593 1.16575757 191.0660941 0.025259583 0.016106928 86.50146906 -1.937023483 0.06611308 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDEDGENTQIEDTEPMSPVLNSK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 IDEDGENTQIEDTEPMS(1)PVLNSK;IDEDGENTQIEDTEPMS(1)PVLNSK;IDEDGENTQIEDTEPMS(1)PVLNSK;IDEDGENTQIEDTEPMS(1)PVLNSK 291.92 9.81E-62 466098000 616034 564447 499568 657679 353984 598213 615647 649001 391320 TRUE FALSE 586915.2937 621964.791 522473.6869 591567.8574 415718.6975 577496.7338 521718.743 592171.0319 452003.907 1.298473939 1.376016405 1.155905245 1.308767133 0.919723682 1.277636597 1.15423503 1.310101578 1 18.78597572 3.733207119 24.44589512 1.169601574 1.337245175 0.247550873 0.127110044 380.2764828 1736474.23 0.029991833 0.048012721 5410.122752 -3.733207119 0.1676436 IDEDGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDEDGKK 7 1 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 83.867 0.035218 327890000 612440 633080 634480 1156390 492160 1082090 1003500 1227770 556360 FALSE TRUE 583491.1749 697591.5718 663571.5356 1040147.48 577992.5482 1044616.952 850397.6445 1120259.95 642637.4673 0.907963206 1.085513384 1.032575238 1.618560282 0.899406862 1.62551517 1.323292973 1.743222278 1 19.29364557 3.606563595 0.834496333 1.401758682 0.899512671 0.240359595 0.275952539 0.899303377 1.203932246 0.107303541 0.308512371 4041.695538 -3.606563595 -0.502246011 IDEPLEGSEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IDEPLEGSEDR 11 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 237.44 3.25E-15 8344655000 3329580 3463010 2746490 3800010 2510570 3153210 2970210 3191060 2399270 FALSE TRUE 3172197.352 3815894.656 2872419.283 3418025.775 2948412.613 3044013.547 2517049.913 2911633.87 2771336.538 1.144645303 1.37691493 1.036474367 1.233349226 1.063895551 1.098391879 0.908244047 1.05062443 1 21.40215048 2.607214338 0.922179026 0.976974879 1.238634336 0.453851681 0.095721056 0.413682003 0.729097723 0.05621714 0.045306047 404.7756119 -2.607214338 0.261659457 IDEPSTPYHSMMGDDEDACS(ph)DTEATEAMAPDILAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDEPSTPYHSMMGDDEDACSDTEATEAMAPDILAR 35 0 P41236;H7C416 P41236 PPP1R2 Protein phosphatase inhibitor 2 1 IDEPS(0.003)T(0.002)PY(0.002)HS(0.002)MMGDDEDACS(0.813)DT(0.176)EAT(0.002)EAMAPDILAR 80.93 0.0026597 19665000 11567 9771.3 8593.3 11217 9348.4 9796.8 13462 10322 9782.9 TRUE FALSE 11020.25083 10767.00658 8987.311305 10089.44585 10978.758 9457.53436 11408.12465 9418.15096 11299.98217 0.975244976 0.952833944 0.795338539 0.892872723 0.971573038 0.836951264 1.009570147 0.833466002 1 13.46403288 1.724540407 25 0.946189915 0.913196532 0.063495496 0.073458316 3.435913661 6101.228732 0.032706228 0.01813727 53.03229319 -1.724540407 -0.032993383 IDEYDYSKPIQGQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDEYDYSKPIQGQQK 15 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 172.91 9.12E-07 265310000 393520 310390 313360 343160 245810 297190 349560 352420 242900 FALSE TRUE 374919.0895 342019.0939 327727.866 308664.9048 288679.1862 286898.2358 296228.2019 321560.2365 280567.6914 1.336287466 1.219025227 1.168088401 1.100144152 1.028911008 1.02256334 1.055817227 1.146105722 1 18.09798936 3.773918538 0.958082733 1.04960854 1.337176375 0.845410528 0.040667343 0.233138778 0.386262554 0.014744573 0.050516243 5941.806963 -3.773918538 0.287567835 IDFSSIAVPGTS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.1)S(0.45)S(0.45)PR 139.71 1.76E-05 0 171800 143220 160360 179810 172800 153190 189590 165050 178030 TRUE FALSE 163679.3545 157814.2808 167712.6646 161735.1572 202936.2653 147884.9919 160664.5634 150597.347 205637.9831 0.795958762 0.767437408 0.815572406 0.786504296 0.986861776 0.719152122 0.78129809 0.732342074 1 17.64974724 -2.351077776 2.356669019 2.368413335 0.796403402 0.430517746 0.072937454 2708507.556 570680.2493 19758121.91 0.016499697 0.004455764 2.351077776 -1.572009933 IDFSSIAVPGTSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.015)S(0.363)S(0.622)PR;IDFSSIAVPGT(0.01)S(0.446)S(0.544)PR;IDFSSIAVPGTS(0.009)S(0.991)PR 292.63 6.19E-44 1071480000 2419520 2068620 2213750 2487900 2295860 2073350 2488700 2195260 2323980 TRUE FALSE 2305154.085 2279414.73 2315252.627 2237811.565 2696257.257 2001549.37 2109003.107 2003031.397 2684370.949 0.858731572 0.849142974 0.862493549 0.833644682 1.004427968 0.745630692 0.785660085 0.746182787 1 21.35615262 IDFVAHDDIPYSSAGSDDVYK ddPTM_SK-BR-3_Trastuzumab_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 ; 220.63 4.61E-25 354950000 562930 514420 487020 594760 416440 536490 658020 650680 398800 FALSE TRUE 536321.4145 566839.9828 509350.3487 534973.5948 489067.0042 517911.2168 557626.9636 593703.0097 460643.8672 1.164286454 1.230538434 1.105735656 1.161360506 1.061703062 1.124320226 1.210538126 1.288854692 1 18.81329228 -2.337325274 2.284563423 0.000121235 1.169550682 0.402084903 0.064529909 1526772.302 323330.3887 8034363.48 0.016207744 0.00459912 2.337325274 1.169429448 IDFYFDENPYFENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IDFYFDENPYFENK 14 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;; 393.79 7.65E-114 2134530000 3014000 2720950 2515470 3084220 2058110 2758230 3095790 3006110 2132250 FALSE TRUE 2871534.193 2998217.898 2630806.788 2774188.346 2417043.732 2662711.803 2623470.377 2742879.072 2462908.44 1.165911873 1.217348501 1.068170763 1.126387121 0.981377827 1.081124966 1.065192004 1.113674803 1 21.23193157 3.730285665 24.10927599 1.065392871 1.191630188 0.577866068 0.045903666 216.9819187 632182.6671 0.011068105 0.017493304 5373.851547 -3.730285665 0.126237318 IDGATQS(ph)SPAEPK ddPTM_SK-BR-3_Trastuzumab_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(0.795)S(0.205)PAEPK;IDGATQS(0.982)S(0.018)PAEPK 272.96 4.16E-32 1573540000 2459100 2752200 2524400 3094500 1588600 3009500 2951800 3234600 1833350 TRUE FALSE 2342863.216 3032652.309 2640146.237 2783434.981 1865651.337 2905280.26 2501448.696 2951361.276 2117656.555 1.106347113 1.432079391 1.246730133 1.314393958 0.88099807 1.371931749 1.181234365 1.393692131 1 21.0140372 IDGATQSS(ph)PAEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDGATQSSPAEPK 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 IDGATQS(0.003)S(0.997)PAEPK;IDGATQS(0.053)S(0.947)PAEPK;IDGATQS(0.092)S(0.908)PAEPK;IDGATQS(0.004)S(0.996)PAEPK 249.73 1.33E-17 1080280000 2512040 2790290 2582650 3069420 1570600 2967600 2945300 3181560 1837210 TRUE FALSE 2393300.848 3074623.723 2701067.057 2760876.07 1844512.143 2864831.268 2495940.391 2902965.74 2122115.144 1.127790287 1.448848679 1.272818332 1.301002011 0.869185703 1.349988608 1.17615691 1.367958637 1 21.01707151 -2.310998271 1.974924951 5.12E-05 1.243104332 0.180002805 0.160268233 1931646.095 229793.98 8624243.311 0.036375401 0.004886543 2.310998271 1.243053098 IDGDKDGFVTVDELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDGDKDGFVTVDELK 15 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 190.24 2.05E-07 127440000 232020 297650 171060 314040 95946 228140 203920 245220 85548 FALSE TRUE 221052.8744 327980.8734 178903.2702 282472.1026 112678.952 220239.4546 172808.2588 223747.2368 98814.34692 2.237052425 3.319162486 1.810498938 2.858614274 1.140309637 2.228820626 1.748817496 2.26431934 1 16.5924329 3.053187572 1.583093236 1.785179624 2.690779958 0.286377987 0.594200795 0.424022218 2.184812034 0.189626732 0.234637907 1130.283979 -3.053187572 0.905600335 IDGDKDGFVTVDELKDWIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDGDKDGFVTVDELKDWIK 19 2 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ; 188.19 9.40E-15 759440000 2841700 2301570 2316170 2823100 1248710 2962700 2972300 3060500 1153380 FALSE TRUE 2707378.473 2536102.6 2422368.686 2539316.624 1466484.629 2860100.956 2518821.045 2792506.395 1332240.28 2.032199832 1.903637533 1.818267112 1.906050029 1.100765869 2.146835672 1.890665733 2.096098157 1 20.34542288 -1.885331012 2.703300066 0.575097302 1.867524249 0.467714698 0.28887667 37280264.65 24443454.26 101334976.1 0.064822002 0.013021739 1.885331012 1.292426947 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR 31 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 315.82 5.39E-93 671440000 363231 349140 368447 359396 307309 353400 430370 392251 321078 FALSE TRUE 346061.7905 384717.7629 385340.6594 323268.8313 360903.5923 341161.6694 364709.1522 357903.423 370869.1364 0.933110244 1.037341006 1.039020564 0.871652018 0.973129217 0.91989771 0.98339041 0.965039654 1 18.50055069 4.761823179 23.14172719 0.973045706 0.933110116 0.060963093 0.049988452 1206.143466 2360578.993 0.011621843 0.173829657 57786.07265 -4.761823179 -0.03993559 IDHILDAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDHILDAL 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 107.32 0.0093669 43908000 211290 140877 118817 167503 282540 148483 254800 167606 188663 FALSE TRUE 201302.7404 155232.5265 124264.877 150665.2802 331814.8865 143340.9965 215925.5803 152929.5301 217919.8945 0.923746503 0.712337563 0.570231907 0.69137919 1.522646142 0.657769208 0.990848407 0.701769476 1 17.73343838 IDHYLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IDHYLGK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 110.61 0.0067645 7428480000 10955530 9636980 8725060 10677140 7838510 9842300 11494390 10129950 7074910 FALSE TRUE 10437683.81 10618999.22 9125112.631 9603853.602 9205543.662 9501458.683 9740709.697 9242917.876 8172050.909 1.277241653 1.299428912 1.116624545 1.175207265 1.126466754 1.162677373 1.191954113 1.131040173 1 22.96226676 8 0.063351657 0.784941261 2.048545416 0.683191696 0.047355364 177.3554967 0.836211365 3.212453179 20.40346532 100000000 -8 1.263604155 IDIIPNPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IDIIPNPQER 10 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;; 134.68 0.00038235 1046359000 988068 832683 844489 971895 1163375 811350 995055 853326 1215037 FALSE TRUE 941363.9838 917534.3444 883209.656 874198.2681 1366267.232 783252.7461 843241.0843 778604.2517 1403458.732 0.670745753 0.653766529 0.629309317 0.622888474 0.973500111 0.558087479 0.600830694 0.554775309 1 20.42055521 -1.103421831 4.612046897 1.000025117 0.657205776 0.452718173 0.11817489 2.89E-05 5.61E-06 0.108183408 0.025497207 0.078809427 1.103421831 -0.342819341 IDILDSALLRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 248.77 1.75E-17 1133300000 453770 352940 360100 435060 446370 366660 546910 395460 486660 FALSE TRUE 432321.1914 388904.9873 376610.9412 391326.9422 524216.7867 353962.4723 463468.8348 360831.4259 562128.7473 0.769078602 0.691843264 0.669972747 0.696151805 0.932556446 0.629682211 0.824488762 0.641901749 1 19.10054107 -1.861322516 2.716407893 1.110975097 0.735698332 0.45750043 0.091648705 13807789.8 9120435.217 9903344.62 0.019763215 0.013761871 1.861322516 -0.375276764 IDILTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDILTELR 8 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 ; 114.6 0.0061059 5800400 32520 33481 30124 32827 33791 28570 37664 37249 35470 FALSE TRUE 30982.84405 36892.75196 31505.2152 29527.16759 39684.1397 27580.61374 31917.66505 33987.28009 40970.50644 0.756223116 0.900470977 0.768973047 0.720693254 0.968602616 0.673182153 0.779040042 0.829554795 1 15.32229811 0.863373374 5.416833226 0.999996863 0.798717331 0.363562954 0.084421656 1.945340135 76.44001446 0.074652937 0.018821242 7.300849129 -0.863373374 -0.201279531 IDINMSGFNETDDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDINMSGFNETDDLKR 16 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2 P13797 PLS3 Plastin-3 0 ;;; 320.73 6.93E-58 850000000 1124790 501597 707090 1007270 812280 895000 1348490 1234060 1030150 FALSE TRUE 1071623.406 552710.3046 739510.7759 906017.3059 953941.3748 864005.9256 1142753.084 1125999.164 1189900.401 0.900599248 0.464501318 0.621489644 0.761422809 0.801698507 0.726116173 0.96037709 0.946296987 1 20.18240939 1.89824723 0.94752519 1.004840601 0.66843759 0.520731094 0.115055094 0.42560738 0.703567349 0.09663124 0.043477726 79.11288639 -1.89824723 -0.336403011 IDIS(ph)PSTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.664)PS(0.333)T(0.004)FR;IDIS(0.998)PS(0.002)TFR;IDIS(0.991)PS(0.009)TFR;IDIS(0.994)PS(0.006)TFR;IDIS(0.999)PS(0.001)TFR;IDIS(0.999)PS(0.001)TFR;IDIS(0.995)PS(0.005)TFR;IDIS(0.994)PS(0.006)TFR 209.96 7.93E-06 21315323000 2877445 2700569 2534664 2948254 2522384 2693053 2812756 2578755 2527005 TRUE FALSE 2741433.877 2975760.051 2650880.852 2651889.907 2962286.971 2599791.899 2383618.412 2352945.541 2918880.029 0.939207453 1.019486934 0.908184244 0.908529943 1.014871095 0.890681314 0.816620892 0.806112453 1 21.47698348 2.038992401 7.196242039 0.853716911 0.95991914 0.258538836 0.064433016 0.194164979 28.14349841 0.022449861 0.016390672 109.3937226 -2.038992401 0.106202229 IDIS(ph)PSTFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDISPSTFRK 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.922)PS(0.078)TFRK;IDIS(0.999)PS(0.001)TFRK;IDIS(0.92)PS(0.08)TFRK;IDIS(0.739)PS(0.259)T(0.003)FRK 150.69 1.29E-05 1548448000 4655120 2157270 4604650 3634350 4221690 4505910 6751040 5383110 5936090 TRUE FALSE 4435081.703 2377098.266 4815777.757 3269018.233 4957951.399 4349869.207 5721044.857 4911736.351 6856628.52 0.646831266 0.346686168 0.702353605 0.476767587 0.723088816 0.634403511 0.834381626 0.716348616 1 22.70906793 1.565664583 0.448507262 0.996997991 0.494407322 0.599017899 0.112747959 0.553149957 0.298408143 0.113623999 0.079265853 36.78447682 -1.565664583 -0.502590669 IDIS(ph)PSTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.953)PS(0.047)TLR;IDIS(0.891)PS(0.109)TLR;IDIS(0.991)PS(0.008)TLR;IDIS(0.899)PS(0.101)TLR;IDIS(0.998)PS(0.002)TLR;IDIS(0.837)PS(0.163)TLR;IDIS(0.661)PS(0.336)T(0.002)LR;IDIS(0.581)PS(0.419)TLR;IDIS(0.964)PS(0.036)TLR;IDIS(0.946)PS(0.053)T(0.001)LR 208.82 9.88E-06 24205080000 2614060 2492960 2269630 2614760 2190500 2329670 2526560 2450100 2358470 TRUE FALSE 2490498.564 2746995.458 2373694.78 2351919.357 2572522.506 2248992.944 2141086.869 2235556.255 2724209.482 0.914209638 1.008364253 0.871333426 0.863340126 0.944318902 0.825558004 0.785947954 0.820625679 1 21.37740622 3.302121881 1.144025449 0.84734883 0.959934354 0.121502381 0.070164763 0.601468932 1.666502094 0.025804242 0.043203517 2005.034644 -3.302121881 0.112585524 IDIS(ph)PSTLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.969)PS(0.028)T(0.003)LRK;IDIS(0.993)PS(0.005)T(0.002)LRK;IDIS(0.974)PS(0.022)T(0.004)LRK;IDIS(0.858)PS(0.141)TLRK;IDIS(0.922)PS(0.077)T(0.002)LRK;IDIS(0.962)PS(0.032)T(0.005)LRK;IDIS(0.431)PS(0.431)T(0.138)LRK 141.37 2.31E-05 4787721000 6571743 4229648 6233737 5705054 4966151 6464989 8124090 7138400 6534050 TRUE FALSE 6261109.732 4660653.94 6519560.007 5131571.133 5832246.162 6241104.81 6884610.861 6513323.853 7547317.103 0.829580849 0.617524595 0.863824842 0.679919906 0.772757535 0.826930249 0.912193137 0.862998568 1 22.84753246 1.677609838 0.795430777 0.979212248 0.73376151 0.545231429 0.07374871 0.401431819 0.498351115 0.061500858 0.027126904 47.60031622 -1.677609838 -0.245450737 IDISPS(ph)TFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.147)PS(0.482)T(0.371)FR;IDIS(0.057)PS(0.94)T(0.003)FR;IDIS(0.321)PS(0.679)TFR;IDIS(0.283)PS(0.708)T(0.01)FR;IDIS(0.013)PS(0.917)T(0.07)FR 211.86 4.67E-06 12566710000 1678400 1636390 1503890 1759130 1450480 1466400 1670300 1586400 1411670 TRUE FALSE 1599065.358 1803140.001 1572844.844 1582298.91 1703443.253 1415618.2 1415465.058 1447486.406 1630584.574 0.98066999 1.105824273 0.964589552 0.970387514 1.044682551 0.868166069 0.868072151 0.887710107 1 20.63695784 2.237754627 24.99998797 0.891150586 1.018738712 0.467847571 0.055674773 15.53223177 481749.8551 0.019294324 0.015097226 172.8839303 -2.237754627 0.127588126 IDISPSTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 93.429 0.021881 20772000 26136 23120 24100 24841 25728 24554 23911 27887 26385 FALSE TRUE 24900.60308 25475.95429 25205.00884 22343.93549 30214.95505 23703.68882 20262.93779 25445.06644 30476.65104 0.817038691 0.835917117 0.827026854 0.733149303 0.99141323 0.777765536 0.664867599 0.834903625 1 14.89541676 IDIVENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDIVENR 7 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;; 143.11 0.0056859 1099620000 2084450 2045800 1980360 2123850 1964360 1896740 2144940 2073200 1927310 FALSE TRUE 1985922.179 2254269.346 2071161.465 1910356.563 2306943.762 1831055.418 1817690.008 1891659.617 2226187.391 0.892073231 1.012614371 0.930362589 0.858129271 1.036275639 0.822507317 0.816503595 0.849730631 1 21.08614361 2.211040855 24.9983144 0.851338354 0.945402182 0.178326071 0.07273222 263.4102854 239274.1801 0.024790922 0.018313454 162.5701683 -2.211040855 0.094063828 IDKDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDKDKR 6 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 81.381 0.034887 766030000 2266900 1678580 1768700 2383300 1466640 2081600 2667900 2658400 1932650 FALSE TRUE 2159748.13 1849629.21 1849796.644 2143726.156 1722421.552 2009513.67 2260862.856 2425616.403 2232355.491 0.967475 0.828554958 0.828629961 0.96029784 0.771571355 0.900176373 1.012770083 1.086572641 1 21.09013536 1.708295687 3.454853693 1.044166946 0.87375432 0.590474863 0.062235989 0.133927417 3.603943268 0.033488271 0.015681368 51.08526924 -1.708295687 -0.170412626 IDKEACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDKEACR 7 1 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 72.485 0.046948 390390000 685090 572620 578025 677790 630480 698820 937870 724780 586400 FALSE TRUE 652707.1534 630970.629 604528.018 609657.2615 740435.5124 674619.6882 794780.7063 661314.4209 677335.9171 0.963638775 0.931547572 0.892508433 0.900081106 1.093158496 0.995989835 1.173392236 0.976346306 1 19.36951197 2.739356173 24.98500985 1.063562556 0.926542017 0.510904427 0.060010293 50.81821687 1596002.72 0.01774305 0.017839071 548.7268009 -2.739356173 -0.137020539 IDKLMIEMDGTENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDKLMIEMDGTENK 14 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ;; 196.22 2.29E-08 1222723000 640224 470126 487086 539267 417208 618203 703329 711275 460730 FALSE TRUE 609961.8803 518032.3739 509419.3749 485058.8566 489968.9431 596794.4751 596023.2435 648991.9903 532177.6553 1.14616214 0.973420001 0.957235558 0.911460396 0.920686801 1.121419641 1.119970441 1.219502517 1 19.02154841 2.215832565 23.80319696 1.124522557 0.991280701 0.387110146 0.082582303 149.908508 156998.1315 0.031753231 0.023471733 164.3737887 -2.215832565 -0.133241856 IDKTDYMVGSYGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IDKTDYMVGSYGPR 14 1 P52565;J3KTF8;J3QQX2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;; 160.79 4.29E-06 7060330000 5325340 4256350 4329100 4981720 4168750 4485950 5997170 5036280 5022920 FALSE TRUE 5073621.732 4690076.904 4527593.517 4480948.041 4895778.68 4330600.427 5082191.571 4595276.624 5801848.78 0.874483621 0.808376275 0.780370825 0.772331064 0.843830797 0.746417322 0.875960709 0.792036607 1 22.46808126 -1.330281372 3.955431248 1.000413748 0.815599394 0.656620965 0.04270648 0.000146498 2.48E-05 0.038876395 0.009142872 0.04674322 1.330281372 -0.184814355 IDKYTEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDKYTEVLK 9 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 100.55 0.0041784 153730000 715130 614880 530290 531180 535430 606090 808090 700210 635930 FALSE TRUE 681327.2222 677536.9711 554604.321 477784.7772 628808.8225 585100.9513 684801.0289 638895.9004 734546.7765 0.927547767 0.922387781 0.755029276 0.650448402 0.856050074 0.796546891 0.932276951 0.869782457 1 19.48649484 1.045609595 1.104500332 0.992351101 0.833972176 0.289097551 0.085361388 0.796570854 2.043832167 0.088118387 0.028420087 11.10732794 -1.045609595 -0.158378924 IDLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDLFER 6 0 Q9UHG3;F8W8W4 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ;; 118.69 0.050377 242800000 322592 259672 242720 304227 255630 205315 262918 258925 269537 FALSE TRUE 307343.7155 286132.872 253848.9521 273645.524 300211.7911 198204.8901 222805.0303 236252.1544 311335.4214 0.987178761 0.91905017 0.815355191 0.878941184 0.964271234 0.63662814 0.715643049 0.758834807 1 18.2481102 2.251338678 24.99999187 0.745767107 0.914554286 0.274430367 0.103547635 218.5333791 427555.3563 0.033338271 0.027722963 178.3769269 -2.251338678 0.168787179 IDLGERPVVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDLGERPVVQR 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 145.91 3.28E-05 355010000 167411 116767 131280 157219 151569 126649 170199 152842 160883 FALSE TRUE 159497.8138 128665.6901 137299.3179 141415.0474 178002.5856 122263.1134 144232.0166 139458.3442 185831.914 0.858290755 0.692376715 0.738836053 0.760983646 0.957868763 0.657923124 0.77614234 0.750454221 1 17.50363876 -1.406709561 3.224589454 1.002789504 0.771035208 0.417837621 0.083725271 167683773.3 208398722.2 4278004.742 0.018579766 0.039200395 1.406709561 -0.231754295 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR 31 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 137.88 4.06E-07 134133000 48552 47766 55855 54265 52149 52359 66961 48296 33814.9 FALSE TRUE 46257.04318 52633.40971 58416.007 48810.1791 61243.76909 50545.7947 56744.86963 44066.94621 39058.74199 1.184294241 1.347544929 1.495593663 1.249660809 1.567991337 1.294096843 1.45280843 1.128222364 1 15.25335786 1.065355441 4.639570942 1.002384593 1.362319602 0.563412793 0.114678986 0.130443997 5.18312904 0.104356403 0.026525306 11.6239957 -1.065355441 0.359935009 IDLPEVQIEHDPELEKES(ph)PGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDLPEVQIEHDPELEKESPGLK 22 1 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 IDLPEVQIEHDPELEKES(1)PGLK;IDLPEVQIEHDPELEKES(1)PGLK;IDLPEVQIEHDPELEKES(1)PGLK 212.28 1.38E-23 172909000 419052 352303 335347 452908 195025 444974 463263 496143 189260 TRUE FALSE 399244.2424 388203.0762 350722.9917 407380.8274 229037.2983 429564.4388 392583.7209 452698.0887 218609.4742 1.826289752 1.775783404 1.604335736 1.863509479 1.047700696 1.964985463 1.795822081 2.070807271 1 17.7379964 3.904175001 5.181972452 1.669068259 1.808255718 0.029829742 0.356091642 0.951203516 39.86061159 0.084214361 0.156516087 8020.011685 -3.904175001 0.139187459 IDNSQVESGSLEDDWDFLPPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;; 226.71 8.08E-26 752335000 1820077 1492524 1570975 1793529 1064483 1766322 1966245 1877378 1311312 FALSE TRUE 1734045.567 1644613.892 1643005.758 1613240.057 1250128.498 1705153.826 1666258.213 1712984.83 1514663.568 1.144838764 1.085794844 1.084733133 1.065081442 0.825350609 1.125764072 1.100084697 1.1309342 1 20.53056595 4.053109676 1.390030965 1.049143478 1.139852614 0.119940155 0.087371579 1.167492528 3.994048361 0.025992843 0.103626391 11300.81267 -4.053109676 0.090709136 IDPHAPNEMLYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDPHAPNEMLYGR 13 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ;;; 79.646 0.019943 903220000 2065230 2133020 1957380 2343600 1985200 2080710 2215820 2228220 1683750 FALSE TRUE 1967610.671 2350377.163 2047127.809 2108016.875 2331418.251 2008654.491 1877755.963 2033105.244 1944857.351 1.011699223 1.208508769 1.052585069 1.083892798 1.198760542 1.032802992 0.965498041 1.045374996 1 20.89123291 2.015378073 24.50611286 0.999630717 1.111804419 0.39896313 0.061894044 167.0755357 266245.9193 0.021812485 0.016103657 103.6043696 -2.015378073 0.112173702 IDQLEGDHQLIQEALIFDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDQLEGDHQLIQEALIFDNK 20 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 247.74 3.65E-30 121360000 390940 238120 229180 345550 240620 299370 392510 376400 212270 FALSE TRUE 372461.041 262384.6987 239688.1297 310814.6575 282584.0518 289002.7418 332625.3906 343440.4206 245187.7475 1.519085047 1.07013789 0.977569769 1.267659827 1.152521098 1.178699771 1.356615059 1.400724237 1 17.90352736 1.758671773 25 1.289628199 1.197821237 0.009132748 0.175129606 30.33313584 37740.78945 0.079063896 0.043845973 57.36827259 -1.758671773 -0.091806961 IDRDSYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.032)YS(0.968)PR;IDRDS(0.253)YS(0.747)PR;IDRDS(0.149)Y(0.002)S(0.849)PR 113.01 0.0049191 1595390000 1593080 1392850 1385910 1644570 1539230 1525340 1748970 1598190 1733900 TRUE FALSE 1517778.266 1534782.999 1449455.344 1479254.699 1807671.225 1472517.093 1482132.504 1458244.011 2002784.356 0.757834093 0.766324639 0.723720125 0.738599088 0.902579061 0.735234969 0.74003599 0.728108349 1 20.93357566 -1.118395966 4.453349917 1.000024456 0.761383104 0.676589204 0.051809006 1.38E-05 2.73E-06 0.047602364 0.011218656 0.07613845 1.118395966 -0.238641352 IDRLDGAHAPELTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDRLDGAHAPELTK 14 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 71.031 0.025569 183100000 210360 195600 193030 234470 157780 214120 237230 255460 176070 FALSE TRUE 200416.6997 215531.8624 201880.6164 210900.6301 185296.782 206704.9707 201036.2065 233090.5681 203374.0364 0.985458632 1.05978062 0.992656782 1.037008627 0.911113264 1.016378366 0.988504777 1.146117628 1 17.63377598 1.280712261 24.99973161 1.073059735 1.002220771 0.259782796 0.051918868 160.7099514 95315.23979 0.031226955 0.011403293 19.08588318 -1.280712261 -0.070838963 IDRPEAISEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDRPEAISEER 11 1 Q9Y6B6;D6RD69;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 128.21 0.00024669 365870000 280040 260350 242020 290580 255790 281200 301400 283170 226510 FALSE TRUE 266803.0642 286879.961 253116.8564 261370.3463 300399.695 271461.9735 255415.8944 258374.1336 261636.0139 1.019749002 1.096484986 0.967438896 0.998984591 1.148158812 1.037555837 0.976226058 0.987532755 1 17.99720161 1.80269284 5.77974326 0.98662567 1.04841781 0.222564444 0.049925861 0.306698769 18.31836689 0.022788945 0.013068265 63.48817449 -1.80269284 0.061792139 IDRTDAISEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDRTDAISEEK 11 1 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;; 177.42 7.29E-06 463110000 954600 876980 859450 1064170 660540 949000 992770 976680 717270 FALSE TRUE 909477.9498 966345.259 898856.6326 957197.6098 775737.9669 916135.892 841304.703 891156.7215 828500.5683 1.097739681 1.166378511 1.084919754 1.1553373 0.936315552 1.105775816 1.015454588 1.075625963 1 19.66014316 2.770917514 24.98990853 1.033156407 1.127370029 0.487801152 0.050389504 517.8954806 399980.6521 0.013510462 0.014328971 590.0889926 -2.770917514 0.094213621 IDRTDAISEEKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDRTDAISEEKLR 13 2 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 94.059 0.0029973 92075000 131240 81504 124650 111240 190270 115910 191300 114460 183290 FALSE TRUE 125036.5453 89809.35026 130365.3258 100057.9439 223453.0278 111896.0076 162113.6715 104437.2756 211713.6771 0.590592667 0.424201929 0.615762418 0.47260973 1.055449184 0.528525172 0.765721298 0.493294893 1 17.69175495 IDRVETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDRVETR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 149.65 0.0018257 667270000 958390 833870 887170 996300 892000 899050 1132930 1006440 1057320 FALSE TRUE 913088.804 918842.301 927847.622 896150.0312 1047564.518 867915.6731 960080.7208 918310.7781 1221283.786 0.74764671 0.752357734 0.759731385 0.733777065 0.857756837 0.710658475 0.786124185 0.751922517 1 20.21996704 -4.999999998 0.424939306 5.545574714 0.758253647 0.785351219 0.038985876 397.5677025 2.535423232 1689.511121 0.019551162 1.00E-05 4.999999998 -4.787321067 IDS(ph)FFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDSFFR 6 0 R4GMW8;A0A1W2PS85;P28715;A0A090HNM7;P28715-2 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 IDS(1)FFR 100.45 0.039489 11494000 23528 21171 17017 23667 16215 18645 20551 19874 15490 TRUE FALSE 22415.87807 23328.34897 17797.24628 21287.9482 19042.89087 17999.31897 17415.5675 18133.7272 17892.11009 1.252835912 1.303834419 0.994698009 1.189795284 1.064317779 1.005991964 0.97336577 1.013504115 1 14.12703592 3.471321796 0.646409233 0.985298068 1.320415358 0.644793405 0.070669479 0.51692597 0.42362478 0.039994684 0.104143684 2960.205054 -3.471321796 0.33511729 IDS(ph)LSAQLSQLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.97)LS(0.03)AQLSQLQK 220.46 2.18E-11 72049000 195496 200943 154452 215188 119423 197942 190099 201363 126001 TRUE FALSE 186255.2915 221419.3202 161533.777 193556.8934 140250.3334 191087.2189 161095.9061 183730.5882 145540.5916 1.279748073 1.521357841 1.109888144 1.329916907 0.963650978 1.312947933 1.106879561 1.262400999 1 17.15106205 3.728591801 24.99146801 1.164893928 1.400552959 0.364927886 0.13413422 579.6790474 1453234.466 0.031150466 0.048889028 5352.932914 -3.728591801 0.235659031 IDS(ph)PGFKPASQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDSPGFKPASQQK 13 1 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK 137.81 3.41E-05 659080000 2071100 1766200 1729150 2069800 974000 2032350 2220400 2271100 1021720 TRUE FALSE 1973203.208 1946177.788 1808433.238 1861739.772 1143865.292 1961969.21 1881637.2 2072230.444 1180163.119 1.67197498 1.649075247 1.532358712 1.577527497 0.969243381 1.662455959 1.594387393 1.755884767 1 20.17055485 3.522597507 2.098725935 1.460857265 1.663351791 0.114291235 0.260677905 0.756914919 6.619357795 0.073439895 0.123582723 3331.17545 -3.522597507 0.202494526 IDS(ph)PGFKPASQQVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDSPGFKPASQQVYR 15 1 A0A087X0K9;G5E9E7;Q07157-2 A0A087X0K9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR 226.23 5.41E-13 811330000 1260950 1177680 1153610 1327510 741780 1253650 1380380 1442130 830510 TRUE FALSE 1201347.392 1297686.931 1206504.16 1194066.173 871146.1971 1210235.786 1169777.679 1315849.452 959301.2491 1.252315051 1.352741834 1.257690596 1.244724922 0.908104934 1.261580538 1.219405979 1.371674907 1 19.87162441 -5 0.201582517 4.86E-08 1.271936658 0.219591136 0.128262141 221.7788764 2.196796703 90.66850823 0.296457058 1.00E-05 5 1.271936609 IDSDLGDAWAFFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDSDLGDAWAFFYK 14 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 168.3 8.17E-06 50059000 201837 193322 193366 218122 151223 173014 227110 228479 175562 FALSE TRUE 192296.565 213021.7316 202232.0224 196195.9622 177596.2433 167022.4818 192460.1983 208472.1675 202787.2583 0.948267493 1.050469015 0.997261978 0.967496497 0.875776145 0.823634005 0.949074414 1.028033858 1 17.62960748 5.104357262 18.68744326 0.958892182 0.001027963 0.002435372 0.068070596 2761.635033 549817.7648 0.01701709 12583.83854 127161.9742 -5.104357262 -0.957864219 IDSIEDRYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDSIEDRYPR 10 1 Q13158 Q13158 FADD FAS-associated death domain protein 0 ; 109.83 0.0028886 0 337220 251910 266130 316380 362000 298120 396120 341370 759160 FALSE TRUE 321280.2789 277579.9154 278332.3237 284576.8813 425132.6854 287796.0296 335684.6188 311477.8331 876886.6555 0.366387465 0.316551647 0.317409693 0.324530975 0.484820567 0.328202086 0.382814149 0.355208773 1 19.74203085 -4.770182334 0.411224284 10 0.346052829 0.943053232 0.04947178 138.0827274 1.12914798 1112.679746 0.027691239 1.70E-05 4.770182334 -9.653947171 IDSNIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDSNISPK 8 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 IDSNIS(1)PK 157.28 0.00039804 284320000 778350 807470 728070 910590 429920 872960 876710 922400 491700 TRUE FALSE 741558.938 889752.111 761452.7297 819055.7632 504897.9119 842729.1763 742951.7876 841629.7661 567950.3247 1.3056757 1.566601994 1.340703045 1.442125706 0.888982522 1.483807896 1.308128115 1.481872145 1 19.11540523 -2.234068464 1.89953021 4.73E-05 1.359241507 0.263351387 0.184809966 1848148.901 304615.9235 7919585.302 0.043947836 0.005833531 2.234068464 1.359194165 IDTHPS(ph)PSHSSTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDT(0.003)HPS(0.895)PS(0.101)HS(0.001)STVK 126.63 5.43E-05 137550000 207210 162360 169160 235130 190470 203370 256980 234680 41618 TRUE FALSE 197415.594 178904.6686 176916.1533 211494.2857 223687.9077 196327.2459 217772.9812 214130.1751 48071.90688 4.106672831 3.721605407 3.680239974 4.399540176 4.653193979 4.08403283 4.530150671 4.454372397 1 15.55290641 3.255386037 24.87971349 4.112204184 3.850265547 0 1.078311744 1413.321662 2089861.916 0.25886267 0.349532238 1800.470611 -3.255386037 -0.261938637 IDTIEIITDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 246.93 2.74E-12 3098242000 2022077 2143165 1552555 2210138 1529490 1772849 1746110 1829394 1424716 FALSE TRUE 1926497.428 2361555.95 1623741.182 1987970.729 1796232.572 1711454.795 1479708.85 1669202.563 1645653.681 1.170657867 1.43502608 0.986684623 1.208012811 1.09150096 1.039984788 0.899161754 1.014309744 1 20.65022933 2.902757454 0.790917376 0.958259921 1.286866619 0.455335402 0.11077397 0.46506316 0.643652619 0.065381345 0.075028472 799.3876865 -2.902757454 0.328606698 IDVDAPDIDIHGPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 234.77 1.10E-19 1287780000 2405690 2135340 2114330 2574740 1594560 2250850 2583630 2606390 1564620 FALSE TRUE 2291977.801 2352933.574 2211274.122 2315922.244 1872650.759 2172902.5 2189449.792 2378160.674 1807253.279 1.26821062 1.301939026 1.223555186 1.2814597 1.036186118 1.202323175 1.21147922 1.315897834 1 20.78536728 -5 0.166356813 0.162198481 1.287494775 0.424675768 0.080927349 127.0272947 1.187623779 35.54160419 0.299591694 1.00E-05 5 1.125296294 IDVTAPDVS(ph)IEEPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDVTAPDVSIEEPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IDVTAPDVS(1)IEEPEGK 182.31 2.27E-09 20028000 77351 49132 68006 107990 52541 99114 114370 74298 52624 TRUE FALSE 73694.77152 54138.60666 71124.14237 97134.64003 61704.13376 95681.65733 96920.75595 67792.07324 60784.66115 1.212390924 0.890662309 1.17010017 1.598012363 1.015126721 1.574108591 1.594493645 1.115282572 1 15.89141969 3.468560408 24.38474469 1.367571218 1.048002364 0.153767925 0.240834054 174.3037321 496484.7362 0.06229532 0.084490128 2941.442804 -3.468560408 -0.319568854 IDYANLTGISVSSLSDSLFVLHVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IDYANLTGISVSSLSDSLFVLHVQR 25 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 254.25 7.84E-45 85145000 93089 95428 78991 96008 87964 80189 95441 103520 76373 FALSE TRUE 88688.86745 105152.2217 82612.81548 86357.09344 103304.8937 77412.03482 80879.72256 94455.24001 88216.53478 1.005354242 1.191978601 0.936477676 0.97892185 1.171037765 0.877522961 0.916831779 1.070720361 1 16.42876147 2.227004986 24.99918605 0.951861893 1.061516112 0.181445695 0.092989891 315.5525896 682654.1052 0.033833387 0.025197254 168.6572387 -2.227004986 0.109654219 IDYGEYMDKNNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IDYGEYMDKNNVR 13 1 A0A0G2JLD8;E7EUY5;Q04837 A0A0G2JLD8 SSBP1 "Single-stranded DNA-binding protein, mitochondrial" 0 110.25 0.00097877 414200000 371890 217260 332410 259540 465650 243500 380020 319500 486810 FALSE TRUE 354311.4967 239399.041 347651.3273 233450.5461 546859.2126 235067.5339 322040.9695 291522.8862 562302.0085 0.630108894 0.425748152 0.618264424 0.415169326 0.972536474 0.418044984 0.572718867 0.518445394 1 19.10098567 -1.760620569 2.579009206 1.105140576 0.564316849 0.405432195 0.162924219 17522077.85 13210877.69 11706036.35 0.037156614 0.017353194 1.760620569 -0.540823727 IDYIAGLDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;; 161.27 1.66E-05 243422000 572650 477110 407340 458590 573120 451590 642270 518320 624040 FALSE TRUE 545581.9694 525728.0514 426016.9419 412491.6619 673071.9465 435951.3251 544279.9154 472933.153 720812.936 0.756898138 0.729354351 0.591022886 0.572258961 0.933767851 0.604805079 0.75509177 0.656110801 1 19.45926538 -1.492768464 2.800200477 1.011187429 0.705327098 0.440924401 0.106038822 16319296.38 17391722.85 1405134.728 0.024072439 0.032153743 1.492768464 -0.305860332 IEAPWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEAPWAR 7 0 E9PKV2;Q9NRX2 E9PKV2 MRPL17 "39S ribosomal protein L17, mitochondrial" 0 96.51 0.029496 31007000 83214 77484 95740 80709 110250 85258 111420 83539 82655 FALSE TRUE 79280.63913 85379.70769 100129.7737 72595.97798 129477.5651 82305.49408 94420.83263 76223.88229 95472.71526 0.83040101 0.894283853 1.048778946 0.760384554 1.356173486 0.862083935 0.988982374 0.798383937 1 16.54280087 3.959100326 5.516454992 0.974336283 0.852932426 0.078792411 0.164016303 0.43109906 34.42321126 0.038129406 0.072452937 9101.234959 -3.959100326 -0.121403857 IECDDKGDGSCDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IECDDKGDGSCDVR 14 1 Q60FE5;P21333-2;P21333;A0A087WWY3;Q14315-2;Q14315 Q60FE5;Q14315-2 FLNA;FLNC Filamin-A;Filamin-C 0 ;; 119.32 0.00017737 1311240000 3200070 1633340 2089590 2740220 1935440 2683680 3588780 3050230 2441730 FALSE TRUE 3048809.033 1799779.203 2185399.768 2464767.88 2272980.123 2590743.489 3041245.699 2783135.691 2820381.018 1.080991899 0.638133356 0.774859763 0.873913086 0.805912431 0.918579253 1.078310228 0.986794222 1 21.42745865 1.987382471 4.111801582 1.026286271 0.830307853 0.371138946 0.11084185 0.221083731 8.491800477 0.049200411 0.030673265 97.13650457 -1.987382471 -0.195978418 IEDFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 IEDFLER 7 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;;;;;; 197.65 0.00097132 6106072000 7118720 7489170 6242160 7374350 6474220 6805500 7685220 7429370 6187400 FALSE TRUE 6782232.214 8252324.937 6528369.21 6633066.328 7603321.918 6569823.829 6512698.54 6778814.977 7146910.391 0.94897401 1.154670268 0.913453346 0.92810263 1.063861375 0.919253701 0.911260696 0.948495868 1 22.76888827 3.711547649 24.97628341 0.950087657 1.05182218 0.261090914 0.067393869 790.8377386 731211.2077 0.017291977 0.026796082 5146.92274 -3.711547649 0.101734523 IEDFLERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IEDFLERR 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 185.72 0.00033878 1115707000 2260277 1218734 2195030 1652495 2529631 2103063 3129543 2513811 3091893 FALSE TRUE 2153438.186 1342924.38 2295674.297 1486383.063 2970797.845 2030233.401 2652073.737 2293688.382 3571367.975 0.602972923 0.376025206 0.642799709 0.416194319 0.83183751 0.568474998 0.742593246 0.642243644 1 21.76804536 0.242668221 0.221512366 1.172930765 0.430143268 0.553682208 0.12253123 4.328338758 0.441892663 0.91899579 0.302234961 1.748510404 -0.242668221 -0.742787497 IEDGEDLKHDFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEDGEDLKHDFER 13 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 0 ; 106.52 0.00082143 52150000 120866 106980 108084 133295 112518 113622 139477 153841 92426 FALSE TRUE 115152.9037 117881.3836 113039.7583 119895.9334 132141.1036 109687.2416 118197.222 140369.8665 106758.952 1.078625272 1.10418266 1.058831659 1.123052738 1.237751974 1.027428984 1.107141085 1.31482994 1 16.70399752 3.05324651 8.945672131 1.136513227 1.085874197 0.07469951 0.091021526 0.902326929 140.8229938 0.024465248 0.029246077 1130.437381 -3.05324651 -0.05063903 IEDRLPELEQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEDRLPELEQLER 13 1 Q9NYH9 Q9NYH9 UTP6 U3 small nucleolar RNA-associated protein 6 homolog 0 127.71 0.00015845 28051000 29175 31339 31466 35796 36041 31980 38660 39441 41254 FALSE TRUE 27795.95557 34532.47973 32908.74722 32197.71807 42326.53899 30872.52458 32761.70696 35987.33695 47651.45962 0.58331803 0.724688813 0.690613624 0.675692168 0.888252728 0.647882034 0.687527879 0.755220034 1 15.54023279 -4.999999999 0.199363933 2.344409824 0.65154027 0.618564957 0.074909569 94.30471213 0.932236653 50.54391928 0.17533035 1.00E-05 4.999999999 -1.692869554 IEDTVFHVFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEDTVFHVFDK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 109.6 0.0019071 19408000 94042 91108 71017 97180 65299 76508 87409 93884 67348 FALSE TRUE 89596.82103 100392.0088 74273.1997 87411.28177 76687.12493 73858.50878 74073.15167 85663.01925 77791.98387 1.151748761 1.290518686 0.954766751 1.123654102 0.985797265 0.949435984 0.952195175 1.101180546 1 16.24733388 3.735389401 24.9957615 1.004430103 1.221133727 0.624281495 0.068141739 147.0886071 1159365.596 0.017353682 0.028176092 5437.376444 -3.735389401 0.216703624 IEDVGS(ph)DEEDDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 392.37 4.10E-114 28303190000 11444920 16138140 8646240 14027730 4997690 12816540 8698290 11600180 3979990 TRUE FALSE 10903941.31 17782634.81 9042678.656 12617635.93 5869285.554 12372700.01 7371206.105 10584406.74 4597186.522 2.371872723 3.86815604 1.967002777 2.744643026 1.276712512 2.691363499 1.603416801 2.302366174 1 22.13231977 2.367964081 0.222396697 0.833538921 3.628504312 0.359028504 0.657138761 3.177080539 0.466967495 1.674244822 3.072812038 233.3265077 -2.367964081 2.794965391 IEDVGS(ph)DEEDDSGKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(1)DEEDDSGKDK;IEDVGS(0.997)DEEDDS(0.003)GKDK 301.57 3.52E-46 99498910000 20861010 24342230 16412770 23360260 6175970 23821090 17213370 22793630 5576930 TRUE FALSE 19874951.4 26822730.91 17165311.74 21012042.28 7253057.213 22996159.68 14587154.26 20797698.92 6441771.821 3.08532372 4.163874731 2.664687948 3.261842062 1.125941342 3.569850084 2.264463049 3.228568086 1 22.61902613 3.383938577 2.047595046 2.44402311 3.597267165 0.229359888 0.887620874 0.416883896 3.552527742 0.240344582 0.366380215 2420.686662 -3.383938577 1.153244055 IEDVGS(ph)DEEDDSGKDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 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(0.998)DEEDDS(0.002)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.997)DEEDDS(0.003)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 278.58 4.06E-36 3.42189E+11 21261740 23711641 17314830 23580664 5464248.5 24991309 18317116 24358636 4847487.2 TRUE FALSE 20256739.69 26127884.18 18108732.08 21210290.85 6417211.708 24125853.7 15522503.54 22225664.7 5599210.757 3.617784821 4.666351261 3.234157967 3.788085817 1.146092188 4.308795426 2.772266344 3.969428132 1 22.41679205 3.333174654 2.133892936 2.895974461 4.108091972 0.184829952 1.114954409 0.483144583 4.492512214 0.305203191 0.445048302 2153.647663 -3.333174654 1.212117511 IEDVGS(ph)DEEDDSGKDKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK 253.83 1.15E-30 8601472000 9896598 5944929 10080862 8260414 3270557 12436900 11884480 12806580 3129394 TRUE FALSE 9428805.426 6550724.024 10543079.49 7430061.491 3840941.105 12006207.03 10071284.3 11685167.96 3614684.439 2.60847263 1.812253361 2.916735796 2.055521475 1.062593753 3.321509038 2.786213976 3.232693797 1 21.78543828 2.198332479 24.99996851 2.760537692 2.136025949 0.066590946 0.798196606 303.2805039 188473.3458 0.268966983 0.198647744 157.8819491 -2.198332479 -0.624511742 IEDVGSDEEDDSGKDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ;;; 179.78 5.04E-10 414298000 833210 923220 691640 975820 297662 954140 776370 989210 293951 FALSE TRUE 793825.8146 1017297.168 723352.3781 877728.7197 349574.1586 921097.8926 657920.4975 902589.5283 339535.4198 2.337976448 2.996144462 2.130418024 2.585087353 1.029566102 2.712818277 1.937707995 2.658307427 1 18.37320256 3.279908853 2.042777933 2.005174708 2.638499353 0.164012957 0.620041843 0.526939342 4.512705763 0.173041579 0.24498755 1905.060855 -3.279908853 0.633324646 IEDVTPIPSDS(ph)TR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEDVTPIPSDSTR 13 0 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPSDS(0.925)T(0.075)R 104.97 0.00092481 0 343110 362890 307650 366090 188970 351860 316820 300080 116410 TRUE FALSE 326891.8703 399868.9036 321756.0568 329289.9377 221926.3082 339675 268483.2902 273803.4044 134462.2683 2.431104833 2.973837261 2.392909632 2.448939334 1.650472739 2.52617336 1.996718438 2.036284289 1 17.03684187 -0.408897503 0.173744871 3.40E-15 3.006211772 0.701690418 0.296638953 8.058323442 0.40215989 5.637557596 1.370352517 0.390034027 0.408897503 3.006211772 IEDVTPIPSDSTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;;;; 222.74 6.06E-12 8171480000 6449880 5014340 6268970 6027870 6434520 6216220 7667640 6590010 7293430 FALSE TRUE 6145006.955 5525306.947 6556408.475 5421937.055 7556698.251 6000950.743 6497800.692 6012953.789 8424457.875 0.729424617 0.655864986 0.7782588 0.643594773 0.896995197 0.712324856 0.771301939 0.713749642 1 23.00615242 -5 0.216207538 2.316336633 0.698433138 0.573102939 0.070957662 98.87834084 0.98783655 56.61319837 0.125557055 1.00E-05 5 -1.617903495 IEDYFPEFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 173.39 7.97E-06 200665000 306217 272411 244418 298860 278588 233343 312387 290999 309078 FALSE TRUE 291742.7293 300169.9906 255624.8071 268818.025 327173.659 225262.2734 264726.6258 265517.5849 357008.2377 0.817187668 0.840792898 0.716019352 0.752974292 0.91643168 0.630972201 0.741514054 0.743729575 1 18.44559784 3.767069709 24.46111059 0.768252795 0.828990296 0.006914409 0.104916068 1558.295604 1337027.898 0.024292586 0.043784164 5848.83957 -3.767069709 0.060737501 IEEACEIYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEEACEIYAR 10 0 P54920;M0R0Y2;M0R2M1 P54920 NAPA Alpha-soluble NSF attachment protein 0 111.06 0.0041956 195750000 148740 143510 131160 139560 117190 138380 157270 152450 118640 FALSE TRUE 141709.355 158133.8322 137173.8157 125531.1637 137627.8989 133587.8659 133275.573 139100.6698 137038.0853 1.034087383 1.153940759 1.000990458 0.916031214 1.004304012 0.974822916 0.97254404 1.015051177 1 17.06421737 3.582839479 6.344104546 0.977753745 1.093210872 0.585613746 0.038963071 0.134682218 6.928342351 0.009674172 0.015036773 3826.83272 -3.582839479 0.115457128 IEEAMDGSET(ph)PQLFTVLPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 IEEAMDGSETPQLFTVLPEKR 21 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 IEEAMDGS(0.142)ET(0.858)PQLFTVLPEKR;IEEAMDGS(0.006)ET(0.994)PQLFTVLPEKR;IEEAMDGS(0.014)ET(0.986)PQLFTVLPEKR;IEEAMDGS(0.131)ET(0.868)PQLFT(0.001)VLPEKR;IEEAMDGS(0.004)ET(0.996)PQLFTVLPEKR;IEEAMDGS(0.002)ET(0.998)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGS(0.002)ET(0.998)PQLFTVLPEKR 279.48 3.70E-45 1352671000 2471493 1898074 2140244 2334583 1875574 2203408 2700860 2638887 2240136 TRUE FALSE 2354670.424 2091489.899 2238376.304 2099906.281 2202673.512 2127103.428 2288794.202 2407812.065 2587524.85 0.910008816 0.808297512 0.86506466 0.811550189 0.851266612 0.822061063 0.884549651 0.930546451 1 21.30314129 1.109561267 1.689723318 0.998323968 0.845358628 0.748177585 0.029903581 0.160851196 0.895767371 0.02626335 0.007667088 12.86948794 -1.109561267 -0.15296534 IEEAPLS(ph)PSENDHPEFIVSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEEAPLSPSENDHPEFIVSVK 21 0 P17861-2 P17861-2 XBP1 "X-box-binding protein 1;X-box-binding protein 1, cytoplasmic form;X-box-binding protein 1, luminal form" 1 IEEAPLS(0.996)PS(0.004)ENDHPEFIVSVK;IEEAPLS(0.997)PS(0.003)ENDHPEFIVSVK 220.05 3.11E-25 78967000 93999 101499 87284 124349 81130 101927 103130 115974 58036 TRUE FALSE 89555.85356 111841.8635 91286.05774 111849.2023 95279.04631 98397.24243 87395.62439 105818.7017 67035.92647 1.335938179 1.668386929 1.361748282 1.668496404 1.421313187 1.467828486 1.303713232 1.578537171 1 16.03264686 -2.985733412 0.302334345 8.28E-13 1.505738738 0.556904641 0.131489332 48.58693592 1.358222061 31.03037097 0.11966818 0.001033396 2.985733412 1.505738738 IEEDFPHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEEDFPHIR 9 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ;;; 193.1 3.40E-05 306223000 712410 603530 625620 757890 675290 686830 786210 727520 641170 FALSE TRUE 678735.7912 665030.3932 654305.2958 681705.4573 793060.3622 663044.9049 666259.2248 663814.492 740599.369 0.916468228 0.897962409 0.883480763 0.920478042 1.07083586 0.895281488 0.899621648 0.896320629 1 19.49833379 2.996634167 24.9939288 0.943473452 0.901532285 0.159062054 0.054208397 314.3769998 2334526.638 0.015889709 0.018631 992.2798369 -2.996634167 -0.041941167 IEEEEQEPEPPEPFEYIDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 218.5 7.80E-19 933582000 4221150 3628370 3837960 4327360 3675510 4037650 4557440 4246280 3883880 FALSE TRUE 4021624.605 3998105.028 4013934.262 3892365.551 4316517.78 3897825.168 3862118.825 3874453.212 4486172.274 0.89644899 0.891206308 0.894734758 0.867636219 0.962182796 0.868853207 0.860894007 0.86364343 1 22.09705359 -0.984998591 4.575566985 1.000002273 0.887871796 0.589383536 0.02932559 0.002755096 17286513.95 102.7718851 0.006634626 0.103514552 0.984998591 -0.112130477 IEEELGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;;; 174.52 0.00063155 4183663000 8231610 6251650 6274260 7256900 5188420 7783410 8642600 8417010 6018960 FALSE TRUE 7842518.109 6888700.243 6561941.027 6527422.625 6093278.805 7513868.56 7324012.638 7679971.983 6952349.576 1.128038517 0.990844918 0.943845092 0.938880094 0.876434468 1.080766794 1.053458627 1.10465849 1 22.72906919 -0.016316785 7.759024516 1.000000003 1.016481922 0.002820352 0.079783388 0 0 0.079545005 0.018748938 0.963126239 0.016316785 0.016481919 IEEIKDFLLTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEEIKDFLLTAR 12 1 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 132.31 0.00016712 425540000 1401800 1259260 1143840 1327790 1020210 1301720 1509140 1417170 1043400 FALSE TRUE 1335539.692 1387580.026 1196286.195 1194318.027 1198134.301 1256641.11 1278892.976 1293075.082 1205205.143 1.108143041 1.151322689 0.992599644 0.990966586 0.99413308 1.042678184 1.061141319 1.072908699 1 20.2008473 3.742378142 24.999425 1.025586645 1.129732869 0.674556499 0.031017147 196.7280854 1288288.272 0.008748577 0.015073121 5525.583445 -3.742378142 0.104146224 IEEVLSGVLDTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 170.62 7.32E-06 16647500 42850 38556 34729 40842 38074 35380 42971 42304 42254 FALSE TRUE 40824.56542 42484.90023 36321.359 36736.48457 44714.09355 34154.78173 36414.98473 38599.63749 48806.53452 0.836456959 0.870475658 0.744190493 0.752696026 0.916149733 0.699799362 0.746108797 0.790870277 1 15.5747867 3.755909051 24.13381273 0.7897408 0.853466314 0.016284394 0.090804078 1222.43669 1700551.994 0.021064333 0.037843474 5700.44882 -3.755909051 0.063725514 IEEVPELPLVVEDKVEGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IEEVPELPLVVEDKVEGYK 19 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 176.46 5.38E-13 80897000 258403 252046 219386 290798 145867 246929 225040 261316 137611 FALSE TRUE 246188.8023 277729.774 229445.0651 261566.4326 171306.1586 238377.7868 190706.0149 238433.7857 158951.0111 1.548834453 1.747266482 1.443495474 1.645578917 1.077729279 1.499693429 1.199778558 1.500045732 1 17.27822267 2.55970561 0.131719642 0.753021166 2.104461315 0.469168267 0.176539591 8.511479801 0.554256676 1.899079597 3.342224282 362.832023 -2.55970561 1.351440149 IEFVGQIELFNDKSNTHEFVNLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEFVGQIELFNDKSNTHEFVNLVK 24 1 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 289.38 5.46E-62 122350000 332390 209490 301330 318410 263140 336270 426510 419300 282850 FALSE TRUE 316678.5834 230837.2692 315146.2786 286402.8219 309031.5327 324624.8856 361438.0661 382583.8692 326712.9334 0.969286952 0.706544632 0.964596887 0.876619174 0.945880928 0.993608922 1.106286373 1.171009256 1 18.31766404 2.229387495 1.310151766 1.106475465 0.859975687 0.54387704 0.083984605 0.291218119 0.969001233 0.049744081 0.028439135 169.5850233 -2.229387495 -0.246499778 IEGCIIGFDEYMNLVLDDAEEIHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEGCIIGFDEYMNLVLDDAEEIHSK 25 0 A6NHK2;P62304 A6NHK2 SNRPE Small nuclear ribonucleoprotein E 0 172.61 5.60E-12 524120000 53294 45663 46190 56672 37181 33061 53617 53137 42107 FALSE TRUE 50774.89824 50316.11161 48307.85719 50975.22289 43665.35463 31916.08928 45436.74191 48484.04258 48636.73851 1.043961824 1.034528901 0.993238006 1.048080617 0.897785418 0.6562136 0.934206184 0.996860482 1 15.56975887 2.692856268 5.95318374 0.875348575 1.030274858 0.306495545 0.09660396 0.219792886 19.96984273 0.030317615 0.028857001 493.0106125 -2.692856268 0.154926283 IEGDMIVCAAYAHELPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IEGDMIVCAAYAHELPK 17 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;; 235.16 3.75E-20 1115592000 2044834 2091614 1862185 2264472 1398814 2165416 2063575 2224786 1447175 FALSE TRUE 1948178.749 2304751.845 1947568.024 2036842.972 1642766.719 2090427.101 1748738.734 2029971.944 1671595.508 1.165460627 1.378773653 1.165095273 1.218502301 0.982753729 1.25055798 1.046149457 1.214391839 1 20.67279436 3.221067223 2.108336496 1.111145857 1.267404465 0.269180823 0.103703608 0.345920624 3.157662027 0.029026656 0.039293253 1663.670145 -3.221067223 0.156258608 IEGDNENKLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEGDNENKLPR 11 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;;; 132.03 0.00017423 624150000 1876730 1646060 1723420 1978730 1184700 1963460 2058300 2108100 1233160 FALSE TRUE 1788020.692 1813795.385 1802440.512 1779824.301 1391311.305 1895464.888 1744268.532 1923503.588 1424392.155 1.255286816 1.273382038 1.265410306 1.249532508 0.976775462 1.330718427 1.224570443 1.350403105 1 20.44191496 -1.622450172 3.023606187 0.98267788 1.240504975 0.35893212 0.101118417 18582301.73 16940211.22 2492662.926 0.022577244 0.023853375 1.622450172 0.257827095 IEGVYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEGVYAR 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 138.48 0.0064712 1159250000 1095030 964640 704920 832100 1096800 875510 1228340 987270 1117440 FALSE TRUE 1043270.102 1062937.913 737241.2793 748455.7271 1288081.573 845190.8692 1040934.173 900819.405 1290726.888 0.808281064 0.823518842 0.571183018 0.579871493 0.997950523 0.654817744 0.806471286 0.697916355 1 20.29975233 2.764412809 24.99876477 0.803881892 0.722603641 0.167332078 0.137600738 2140.897986 2070219.33 0.041157487 0.043640449 581.3167123 -2.764412809 -0.081278251 IEGYEDQVLITEHGDLGNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEGYEDQVLITEHGDLGNGK 20 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 292.52 1.67E-54 232340000 530260 571820 432650 650750 331560 508450 492330 538990 324270 FALSE TRUE 505195.6607 630089.1081 452487.4304 585335.3737 389383.959 490842.249 417216.0162 491793.1782 374556.1355 1.348784903 1.682228773 1.208063058 1.562744054 1.03958772 1.31046378 1.113894492 1.313002596 1 18.51482243 2.742509166 24.99957737 1.171182091 1.4643212 0.459066268 0.158325396 288.0711325 1823876.751 0.044461598 0.045568376 552.725073 -2.742509166 0.293139109 IEHAPS(ph)PSSGGTLKNDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEHAPSPSSGGTLKNDK 17 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 IEHAPS(0.999)PS(0.001)SGGTLKNDK 83.936 0.0032655 117150000 368420 287880 369770 379690 212720 407710 479450 432960 239680 TRUE FALSE 351005.5167 317215.2993 386724.3203 341522.8398 249818.3007 393590.9005 406301.0968 395047.7271 276848.3503 1.267862049 1.145808884 1.396881433 1.233609807 0.902365141 1.42168411 1.46759443 1.426946293 1 18.0787364 IEHSFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 128.86 0.0037165 1141480000 873890 801975 482055 636326 864010 589736 897040 750382 679458 FALSE TRUE 832582.9516 883697.1643 504157.6986 572361.3015 1014693.07 569313.2944 760180.0727 684674.5741 784824.8764 1.060851888 1.125980064 0.642382414 0.729285371 1.292891065 0.725401693 0.96859834 0.872391529 1 19.58201125 IEIESFYEGEDFSETLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IEIESFYEGEDFSETLTR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;; 233.37 2.25E-23 146823000 187238.6 151126.7 163334.8 184840.3 174093.2 161029.1 203998.4 180029.9 193589.3 FALSE TRUE 178388.2024 166526.6825 170823.8621 166259.8019 204454.999 155452.6219 172874.6974 164265.5276 223610.1399 0.79776437 0.744718833 0.763936118 0.743525325 0.914336886 0.695194869 0.773107595 0.734606792 1 17.77062609 -1.159229997 4.838586311 1.000018039 0.770239367 0.609925606 0.057576976 1.09E-05 1.89E-06 0.049803758 0.011737856 0.069305867 1.159229997 -0.229778672 IEINFPAEYPFKPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEINFPAEYPFKPPK 15 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 133.48 3.74E-05 225780000 381890 302610 326660 398800 260310 365970 433350 404320 306140 FALSE TRUE 363838.8165 333446.303 341637.6841 358711.8663 305707.9816 353296.3671 367234.4985 368915.5974 353614.6277 1.028913365 0.942965242 0.966129954 1.014414671 0.864523008 0.999099979 1.038516141 1.043270183 1 18.43181843 2.002192535 24.99999195 1.028358286 0.96590537 0.297643143 0.045040207 83.68180143 954155.931 0.016131754 0.011840533 100.5061264 -2.002192535 -0.062452916 IEKDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEKDLEK 7 1 D6RDN4 D6RDN4 CCDC110 0 67.125 0.060202 138010000 131960 113820 108530 134770 99037 112180 136940 120780 109190 FALSE TRUE 125722.5123 125418.3874 113506.2079 121222.6636 116309.0214 108295.1785 116047.2879 110203.8629 126122.6275 0.99682757 0.994416227 0.899967041 0.961149208 0.922189965 0.858649876 0.920114734 0.873783436 1 16.94446761 3.745682876 24.11827276 0.914583215 0.995621912 0.378603342 0.040225172 280.0351676 948283.6848 0.009460423 0.016594254 5567.790372 -3.745682876 0.081038697 IEKLS(ph)DDEEVDITDEVDELSSQTPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEKLSDDEEVDITDEVDELSSQTPQK 26 1 A0A590UK32;A0A590UJW2;A0A590UJD8;Q5VVJ2 A0A590UK32 MYSM1 Histone H2A deubiquitinase MYSM1 1 IEKLS(1)DDEEVDITDEVDELSSQTPQK 117.88 0.00042417 11743000 46934 37866 43020 53715 26850 52714 53209 55057 42565 TRUE FALSE 44715.52283 41724.58845 44992.50955 48315.46615 31532.6315 50888.50096 45090.9898 50235.9172 49165.76281 0.909484981 0.848651299 0.915118712 0.982705513 0.641353448 1.035039386 0.917121737 1.021766252 1 15.58536641 IELENYRLS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IELENYRLSLR 11 1 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 IELENYRLS(1)LR 85.837 0.0090345 37175000 24570 11976 22992 21237 29608 20607 35516 26251 33339 TRUE FALSE 23408.62479 13196.36802 24046.20594 19102.21641 34771.62583 19893.37442 30097.3819 23952.32327 38509.04185 0.607873467 0.342682326 0.624430128 0.496044968 0.902947052 0.516589701 0.781566626 0.62199219 1 15.23290961 -0.302411303 0.134999777 1.397846518 0.300397235 0.467299209 0.142429016 17.0264812 0.660244879 4.00282099 1.360684213 0.498412238 0.302411303 -1.097449284 IELGDVTPHNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IELGDVTPHNIK 12 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;F8WCK0;C9JZU6;C9J5J3;A0A0D9SF32 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 171.05 3.95E-05 189049000 561740 471670 501720 580120 447200 562160 685410 619510 477070 FALSE TRUE 535187.6635 519733.7092 524724.3583 521805.2354 525191.5384 542692.2582 580838.1161 565262.4202 551051.5791 0.971211559 0.943167081 0.952223672 0.946926305 0.95307147 0.984830239 1.054053991 1.025788586 1 19.07182784 1.976139641 3.969830574 1.03106867 0.953721295 0.830372802 0.015047856 0.073871364 2.507219244 0.006389152 0.003890448 94.6541459 -1.976139641 -0.077347375 IELPELFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IELPELFDR 9 0 H0YHS6;Q9Y2Z4 H0YHS6 YARS2 "Tyrosine--tRNA ligase;Tyrosine--tRNA ligase, mitochondrial" 0 ;;; 160.88 0.00015112 105426000 184239 141529 164106 160915 162618 130642 160811 157250 174797 FALSE TRUE 175530.3876 155950.966 171630.4224 144739.5185 190978.5277 126117.8348 136276.3285 143480.3564 201903.626 0.869377094 0.772402998 0.85006112 0.71687429 0.945889539 0.624643734 0.674957311 0.710637838 1 17.62330729 2.227715976 24.99918424 0.716459446 0.822123362 0.061647956 0.116648916 359.1065109 827810.0183 0.038262178 0.028532427 168.9335762 -2.227715976 0.105663916 IENFDVSFGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IENFDVSFGDR 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 186.87 8.93E-06 70423000 171620 175040 153390 188210 174400 171740 182520 194640 192520 FALSE TRUE 163507.8627 192876.775 160423.0832 169290.7732 204815.3048 165792.6007 154673.2218 177596.2897 222375.0183 0.735279817 0.867349113 0.721407847 0.761285033 0.921035584 0.745554073 0.695551249 0.798634177 1 17.7626352 0.956201646 22.91344581 1.000000001 0.778663739 0.508779523 0.067987903 3103.523554 1623634.918 0.06491544 0.01622886 9.040691411 -0.956201646 -0.221336262 IENHEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IENHEGVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 162.49 0.0003414 50275000000 30322130 24716530 26906030 29750310 28231500 27033090 32723400 28412400 27853240 FALSE TRUE 28888863.01 27235172.51 28139698.09 26759752.32 33155064.66 26096927.31 27730844.32 25924459.63 32172578.2 0.897934347 0.846533726 0.874648526 0.83175654 1.030538008 0.811154367 0.861940381 0.805793663 1 24.93932822 2.002548567 0.007211752 1.763466241 4.37E-05 0.077196064 0.07249137 9527.230853 52.11788514 6322.659187 6416.28299 100.5885543 -2.002548567 -1.763422503 IEPADAHVLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEPADAHVLQK 11 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;B0AZT5 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 104.79 0.002552 109850000 321430 277380 280710 343560 250110 274250 336350 328610 263500 FALSE TRUE 306236.6409 305645.3374 293580.8312 309024.6961 293729.1048 264752.6537 285033.63 299835.1663 304362.2342 1.006158473 1.004215711 0.964577067 1.015318792 0.965064229 0.869860396 0.936494735 0.985126052 1 18.21542983 2.479138364 24.99487878 0.936595951 0.997036719 0.266260931 0.037045762 79.61648007 986581.1304 0.011920823 0.010122265 301.3966108 -2.479138364 0.060440768 IEPEPFENCLLRPGS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 1 IEPEPFENCLLRPGS(1)PAR 94.201 0.0012159 42997000 74605 58877 25079 33328 79844 35100 75924 41987 63980 TRUE FALSE 71078.5695 64876.63324 26228.89696 29977.80612 93768.76832 33884.4782 64340.39936 38310.39569 73901.69164 0.961798951 0.877877513 0.354916056 0.405644383 1.268831149 0.458507477 0.870621469 0.518396736 1 16.17331977 3.977840996 24.69627242 0.692940561 0.930328523 0.097345988 0.286883724 1283.838722 1430844.882 0.067967029 0.122949193 9502.568226 -3.977840996 0.237387962 IEPEPFENCLLRPGSPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 80.238 0.0081492 60809000 139040 153690 112210 177280 65079 167280 152870 185400 100100 FALSE TRUE 132467.8548 169351.1857 117354.9395 159459.4776 76428.757 161487.0517 129546.8738 169165.3931 115622.9968 1.145687782 1.46468428 1.014979224 1.379132889 0.661016918 1.396668969 1.120424807 1.463077397 1 16.81906884 3.734119475 24.96812915 1.155466002 1.305186027 0.065499813 0.245701699 953.9754947 5363259.506 0.058275993 0.093729224 5421.500155 -3.734119475 0.149720025 IEPPDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEPPDRR 7 1 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 108.09 0.018036 365090000 860370 736020 808280 879750 786760 762300 944500 856610 883510 FALSE TRUE 819702.0152 811021.2748 845340.4375 791315.8586 923970.6949 735901.3599 800399.1781 781600.6872 1020520.218 0.80321977 0.794713579 0.828342665 0.775404391 0.905391856 0.721104145 0.784305067 0.765884569 1 19.96087333 -2.157892392 2.355642754 1.478979563 0.796589893 0.64460929 0.047298392 5951239.276 1475678.403 15207874.93 0.010392347 0.006951966 2.157892392 -0.68238967 IEPSELPLPGGGNRSS(ph)SVPHPFQVTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEPSELPLPGGGNRSSSVPHPFQVTLLR 28 1 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 IEPSELPLPGGGNRS(0.259)S(0.709)S(0.031)VPHPFQVTLLR 74.446 0.0056215 157950000 44514 16208 46853 31171 67312 37771 92759 51224 88426 TRUE FALSE 42409.91144 17859.61363 49001.25639 28037.63186 79051.19149 36462.9808 78606.91091 46738.555 102138.6525 0.415219023 0.174856562 0.479752329 0.274505598 0.773959609 0.356994927 0.76960983 0.457599096 1 16.6401694 0.796317849 0.201039445 1.21527365 0.153189384 0.541999547 0.171741642 3.051423248 0.414028024 1.110372745 0.616166506 6.256304078 -0.796317849 -1.062084267 IEQHYFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEQHYFEDR 9 0 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 ; 91.937 0.0087837 0 529830 559870 439340 610790 260600 631550 494900 688520 241210 FALSE TRUE 504785.9859 616921.3895 459484.1736 549392.2288 306048.5575 609679.2651 419393.9155 628229.5387 278615.6149 1.81176488 2.214238386 1.64916878 1.971864459 1.098461612 2.18824514 1.505277856 2.254825305 1 18.08791659 3.719652418 24.35854517 1.696900669 2.013001648 0.101613665 0.420594074 1151.701347 1483683.096 0.097441152 0.151265709 5243.876056 -3.719652418 0.316100978 IEQLQNHENEDIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEQLQNHENEDIYK 14 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ;;; 268.56 3.26E-25 1699270000 1657980 1521010 1401290 1810290 1007430 1684190 1662560 1761000 953290 FALSE TRUE 1579610.571 1676002.648 1465540.533 1628316.21 1183125.473 1625866.078 1408905.937 1606797.504 1101121.344 1.434547227 1.522087149 1.330952796 1.478779989 1.074473289 1.476554865 1.279519232 1.459237451 1 20.07054203 -4.124617132 0.155306655 9.05E-13 1.505725843 0.446142515 0.132216133 83.12022236 0.968228721 26.87255923 0.567239629 7.51E-05 4.124617132 1.505725843 IERPGEGS(ph)PMVDNPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IERPGEGSPMVDNPMR 16 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 IERPGEGS(1)PMVDNPMR 83.082 0.0049657 101970000 75054 82151 63660 84715 71505 74378 87475 78493 80289 TRUE FALSE 71506.34616 90522.2803 66578.87397 76199.28725 83975.44936 71802.27121 74129.08216 71619.7368 92739.80806 0.771042637 0.976088717 0.717910414 0.821645945 0.905495182 0.774233554 0.799323222 0.772265312 1 16.50090112 3.736841279 24.99467758 0.81767002 0.873565669 0.034078515 0.092033895 405.2668923 5891530.654 0.021912499 0.035995519 5455.584405 -3.736841279 0.055895649 IES(ph)DEEEDFENVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK 341.27 5.78E-69 1861403000 3096694 2620369 2645171 3220340 1570405 3191655 3115472 3360792 1630225 TRUE FALSE 2950319.412 2887387.58 2766454.707 2896625.305 1844283.135 3081127.187 2640149.527 3066503.236 1883031.967 1.566791995 1.533371515 1.469149093 1.538277287 0.979422106 1.636258567 1.402073663 1.628492394 1 20.84462606 -1.834142935 2.591723115 0.825157469 1.470600803 0.382372771 0.187409197 12770659.96 8743767.97 13909471.48 0.04240431 0.014650656 1.834142935 0.645443335 IES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(1)DVQEPTEPEDDLDIMLGNK;IES(1)DVQEPTEPEDDLDIMLGNK 149.94 3.84E-08 81463000 222751 202439 184220 224853 116683 224270 222386 242679 119388 TRUE FALSE 212222.0017 223067.7643 192666.6692 202250.3492 137032.4783 216503.4737 188456.9313 221428.7402 137902.0813 1.538932551 1.617580838 1.397126624 1.466622892 0.993694054 1.56997974 1.366599616 1.605695419 1 17.07328471 -3.87107755 0.162368529 1.85E-24 1.573007414 0.336368661 0.185821386 100.2515501 1.298681017 35.06703609 0.756938622 0.000134562 3.87107755 1.573007414 IES(ph)DVQEPTEPEDDLDIMLGNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IESDVQEPTEPEDDLDIMLGNKK 23 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(0.846)DVQEPT(0.154)EPEDDLDIMLGNKK;IES(1)DVQEPTEPEDDLDIMLGNKK 143.5 6.90E-08 172320000 228843 175540 194402 236887 110515 244389 242520 266380 129802 TRUE FALSE 218026.0449 193427.7256 203315.524 213074.6687 129788.781 235925.7477 205519.1198 243054.355 149931.0312 1.454175584 1.290111353 1.356060332 1.421151225 0.865656562 1.573561829 1.370757729 1.621107739 1 17.19393948 IES(ph)PKLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER;IES(1)PKLER 152.67 0.00027455 28910720000 41882930 32099460 35436950 39252010 20955820 39862950 42549630 41985990 22756790 TRUE FALSE 39903206.9 35370431.47 37061769.21 35306323.38 24610508.37 38482486.05 36057902.47 38309474.13 26285796.77 1.518052021 1.345610018 1.409954187 1.343171131 0.936266402 1.464003027 1.371763724 1.457421073 1 24.64778013 -2.200791872 2.215125569 0.000104352 1.359068461 0.330347065 0.159131761 1744130.698 440022.9991 8712319.138 0.038887346 0.006298079 2.200791872 1.358964109 IES(ph)S(ph)IQSLQDLS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.931)S(0.565)IQS(0.565)LQDLS(0.939)K 53.278 0.068944 503160000 785070 1028400 674380 974490 910670 1034800 702700 760430 525990 TRUE FALSE 747961.297 1133195.129 705300.9901 876532.4138 1069490.56 998964.6165 595490.209 693842.7179 607557.8428 1.231094793 1.865164186 1.160878752 1.442714343 1.76031068 1.644229646 0.980137473 1.142019194 1 19.21266224 1.72014889 7.611486173 1.051030447 1.528036237 0.512799191 0.218349798 0.095012286 14.51219883 0.103047859 0.054274012 52.49874118 -1.72014889 0.47700579 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(0.002)DVQEPT(0.998)EPEDDLDIMLGNK 92.833 0.0074073 76607000 63079 59148 55411 68247 41460 60777 65973 77103 48181 TRUE FALSE 60097.38068 65175.24845 57951.64916 61386.6819 48690.61087 58672.27725 55907.60717 70351.45257 55652.66341 1.079865311 1.171107445 1.041309537 1.103032239 0.874901719 1.054258209 1.004580981 1.264116545 1 15.76416311 3.715703026 22.79759085 1.04220657 1.125486368 0.090639791 0.099129772 484.416936 483144.8565 0.024548336 0.038072249 5196.405409 -3.715703026 0.083279798 IESDVQEPT(ph)EPEDDLDIMLGNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IESDVQEPTEPEDDLDIMLGNKK 23 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IESDVQEPT(1)EPEDDLDIMLGNKK;IESDVQEPT(1)EPEDDLDIMLGNKK 164.96 8.03E-12 46075000 119759 90683 100857 108428 75929 117964 143181 131148 83431 TRUE FALSE 114098.2294 99923.7008 105481.3932 97528.61144 89170.99356 113878.8771 121336.1088 119663.9859 96369.05337 1.183971674 1.036885777 1.094556702 1.012032473 0.925307352 1.181695504 1.25907752 1.241726277 1 16.55628231 2.031442661 24.76004155 1.201887424 1.060435532 0.252132452 0.096147386 192.922071 151918.7944 0.034331428 0.025355261 107.5084649 -2.031442661 -0.141451892 IESFVETLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IESFVETLKR 10 1 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 195.4 5.74E-07 265280000 617590 483700 536180 589370 490700 539810 703850 595810 543190 FALSE TRUE 588397.7446 532989.5799 560764.3834 530125.4079 576277.9246 521116.2443 596464.7554 543637.7178 627425.131 0.93779754 0.84948714 0.893755056 0.844922177 0.918480782 0.830563232 0.950654869 0.866458309 1 19.25908379 -0.429313329 0.572319165 1.014380326 0.884251071 0.432304859 0.04041893 8.137973319 2.275011148 0.280080352 0.015174981 0.372123135 0.429313329 -0.130129255 IESGAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IESGAFR 7 0 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 104.25 0.019063 147300000 228350 202510 187640 201090 232950 193580 267220 228840 273990 FALSE TRUE 217556.348 223145.9992 196243.4796 180876.0512 273576.4062 186876.2761 226450.6812 208801.5564 316478.9699 0.687427503 0.705089502 0.620083792 0.571526289 0.864437869 0.590485605 0.715531529 0.659764396 1 18.27175011 -1.320236147 3.067216375 1.002630886 0.679549114 0.608424542 0.081460124 22638650.89 29799119.39 544176.504 0.017127837 0.047836991 1.320236147 -0.323081772 IESLIDRDYMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IESLIDRDYMER 12 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ;;; 150.49 6.22E-05 409875000 432438 372240 390578 449824 460390 389279 490700 443174 473720 FALSE TRUE 411997.5127 410171.6792 408486.3876 404606.8369 540681.8702 375798.1706 415834.7027 404367.3351 547182.0782 0.752944092 0.749607298 0.746527352 0.739437297 0.988120576 0.686788156 0.75995673 0.738999597 1 19.06166145 -1.859807179 2.323072354 1.109599901 0.767944791 0.447724247 0.080137439 10088790.94 5472378.638 6109166.675 0.02016409 0.013809973 1.859807179 -0.34165511 IESWLETHALLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IESWLETHALLEK 13 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 169.62 2.82E-05 61625000 303880 312100 297680 347510 256960 338190 362220 358560 232070 FALSE TRUE 289516.1946 343903.3448 311328.9224 312577.6346 301773.7426 326478.3955 306956.6864 327162.5856 268058.2304 1.080049638 1.282942681 1.161422733 1.166081094 1.125776822 1.217938338 1.145111963 1.220490731 1 18.03218691 -1.156776173 4.444603705 0.999969817 1.176426038 0.491160156 0.055953558 1.60E-05 3.03E-06 0.049569403 0.011681534 0.069698564 1.156776173 0.176456222 IET(ph)DEEESCDNAHGDANQPAR ddPTM_SK-BR-3_Trastuzumab_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 412.46 2.90E-151 825710000 511610 450000 484140 529930 346230 507290 566690 507220 383930 TRUE FALSE 487427.2092 495855.5116 506338.2979 476660.4296 406612.4024 489722.4201 480231.0325 462805.1279 443467.9036 1.09912624 1.118131679 1.141769886 1.07484764 0.916892517 1.104301836 1.082899188 1.043604563 1 18.75847017 8 0.101083744 0.969322948 1.421607496 0.226800403 0.057481996 194.7430876 1.392265837 0.699588662 12.22602948 100000000 -8 0.452284547 IETELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IETELR 6 0 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104;REV__P53355-4 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 128.75 0.038361 1471280000 3548310 3518630 3087670 3682810 2921080 3309850 3357740 3468450 3024720 FALSE TRUE 3380588.418 3877182.397 3229242.724 3312606.942 3430515.427 3195229.065 2845455.094 3164734.131 3493778.129 0.96760249 1.109739157 0.924283857 0.948144621 0.981892753 0.914548362 0.814434972 0.905820007 1 21.73635656 3.026691003 0.984387126 0.891196953 1.031833244 0.231872114 0.066339496 0.521840422 1.103534441 0.031390589 0.039793432 1063.386158 -3.026691003 0.140636292 IETIEVMEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IETIEVMEDR 10 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 285.32 4.77E-24 431110000 631300 589370 537580 659540 560640 557790 602650 602970 548740 FALSE TRUE 601459.7001 649427.4731 562228.5747 593241.7862 658415.4385 538473.5924 510704.6741 550170.7503 633835.7966 0.948920372 1.024598921 0.887025595 0.935955005 1.038779195 0.849547462 0.80573656 0.868002018 1 19.27374961 2.216324399 24.98129063 0.857783751 0.96820252 0.268249371 0.066055238 225.945878 253837.3478 0.023033124 0.01702417 164.5600455 -2.216324399 0.110418769 IETLDPALIRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IETLDPALIRPGR 13 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 164.48 3.37E-05 893850000 2181300 1959910 2033330 2316180 2111100 2126090 2515850 2263970 2369730 FALSE TRUE 2078194.272 2159627.057 2126560.192 2083353.186 2479275.172 2052462.97 2132010.876 2065724.785 2737215.625 0.759236595 0.788986822 0.776906347 0.761121326 0.905765387 0.749836056 0.778897671 0.754681058 1 21.38427766 -1.283388986 3.514930243 1.000652406 0.784097743 0.695426818 0.044834105 783163777.1 1283299373 5528166.039 0.009983003 0.05207281 1.283388986 -0.216554662 IETMLGDVAVAVHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IETMLGDVAVAVHPK 15 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 77.754 0.024947 34648000 152650 107000 166880 116660 149690 156480 194080 165640 175910 FALSE TRUE 145434.537 117903.4216 174531.6131 104933.1152 175795.8886 151061.0584 164469.5315 151135.6835 203189.2244 0.715759103 0.580264145 0.858960969 0.516430512 0.865183127 0.743450145 0.809440225 0.743817414 1 17.63246437 -2.133226721 0.142824696 1.431016765 0.581903263 0.424217594 0.105816175 40.70595217 0.802214369 6.388922417 0.648940706 0.007358229 2.133226721 -0.849113502 IETWHKPDLGTLENVHGLDPNTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IETWHKPDLGTLENVHGLDPNTWK 24 1 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 98.766 0.0033509 102290000 367800 315050 333110 356970 296200 386210 398560 387910 268780 FALSE TRUE 350414.8229 347153.9532 348383.423 321086.6974 347857.1862 372835.4509 337752.3519 353942.544 310461.0297 1.128691815 1.1181885 1.122148643 1.034225448 1.120453625 1.20090902 1.087905791 1.140054661 1 18.24405266 -0.913131428 4.434721077 0.999998207 1.118545482 0.449775015 0.041385391 6.91E-07 1.69E-07 0.037683991 0.008882067 0.122142997 0.913131428 0.118547275 IEVEKPFAIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 152.14 0.0016802 0 774960 747070 573120 866730 441120 740230 819810 860650 492960 FALSE TRUE 738329.1766 823197.2823 599398.1189 779604.6537 518051.1883 714595.6495 694732.9277 785286.9234 569405.7191 1.296666247 1.445713056 1.052673162 1.369154941 0.9098103 1.254985023 1.220101773 1.37913424 1 19.11909746 3.749314132 24.95752953 1.183433672 1.371189652 0.222922565 0.154911702 952.2355357 2210010.826 0.035951304 0.063976493 5614.539372 -3.749314132 0.18775598 IEVEKPFAIAKE ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEVEKPFAIAKE 12 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 151.54 0.00027433 847580000 2256000 1608270 1965500 2087670 1619240 2121000 2910800 2720000 2126800 FALSE TRUE 2149363.351 1772154.541 2055620.119 1877813.445 1901634.943 2047549.238 2466703.999 2481822.38 2456613.282 0.874929468 0.721381161 0.836769928 0.764391147 0.774088033 0.833484559 1.004107573 1.010261729 1 21.22823934 1.790484524 3.355488689 1.009040209 0.792801017 0.846663534 0.041162194 0.078828559 1.671470444 0.021045709 0.010615389 61.72832953 -1.790484524 -0.216239192 IEVIEIMTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 249.69 1.12E-12 1677442600 960433 915176 844443 1056443 830920 847092 989893 938765 862233 FALSE TRUE 915035.2355 1008433.475 883161.5468 950247.3425 975832.1849 817756.9916 838866.6422 856561.7599 995943.69 0.918762019 1.012540654 0.886758514 0.954117539 0.979806584 0.821087577 0.842283204 0.860050391 1 19.92570465 2.244687889 24.99881413 0.86332252 0.953271731 0.235563973 0.058452682 147.3048756 600994.5287 0.018653472 0.015237686 175.6660714 -2.244687889 0.089949211 IEVLEEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEVLEEELR 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 138.1 0.00034 60417000 79859 76538 64811 79873 76785 71850 82968 81120 77053 FALSE TRUE 76084.22334 84337.30922 67782.64846 71844.01429 90176.27969 69361.81648 70309.70779 74016.70276 89001.98571 0.854859841 0.947589074 0.7615858 0.807218106 1.01319402 0.779328865 0.789979091 0.831629791 1 16.4415499 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEVLPVDTGAGGYSGNSGSPK 21 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 IEVLPVDTGAGGYSGNS(0.13)GS(0.87)PK;IEVLPVDTGAGGYSGNSGS(1)PK 316.97 1.01E-66 83935000 159372 143391 149068 174408 99185 152741 184422 170023 100274 TRUE FALSE 151838.8014 158002.7059 155902.9152 156876.1765 116482.8326 147451.5409 156285.0368 155134.8848 115823.9798 1.310944432 1.364162294 1.34603314 1.354436074 1.005688397 1.273065743 1.349332298 1.339402126 1 16.82157445 -1.844109641 2.63141726 0.884139345 1.29812934 0.430774574 0.105653984 13404300.4 9329274.032 9799006.448 0.026867437 0.014318264 1.844109641 0.413989996 IEVLQQHENEDIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEVLQQHENEDIYK 14 0 O00505;H0Y4S9 O00505 KPNA3 Importin subunit alpha-4 0 ; 194.55 1.31E-07 314920000 391670 421440 341600 463990 262950 404490 384120 432120 249621 FALSE TRUE 373156.5353 464385.2151 357262.6979 417348.8437 308808.3967 390482.4099 325515.4392 394281.282 288330.9498 1.294195214 1.610597875 1.239071623 1.447464603 1.071020634 1.354285449 1.128964613 1.367460837 1 18.13736618 3.009246722 1.663444095 1.20202577 1.43310018 0.27292717 0.154966459 0.415694867 2.344091254 0.049078247 0.05850655 1021.519642 -3.009246722 0.231074411 IEVPLYSLLEQTHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEVPLYSLLEQTHLK 15 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 260.49 6.63E-25 220918000 593670 622120 521160 657590 402530 601160 599970 668480 387620 FALSE TRUE 565608.3956 685514.7353 545055.7015 591487.8039 472731.1046 580341.6785 508433.5573 609944.3474 447730.1299 1.263279726 1.53108913 1.217375524 1.321081081 1.055839384 1.29618634 1.135580394 1.362303554 1 18.77226988 3.620212047 7.86561402 1.203753594 1.396799325 0.288641691 0.129701969 0.293471726 17.84986717 0.030677527 0.047605633 4170.729725 -3.620212047 0.193045731 IEVPLYSLLEQTHLKVEDVSAVEIVGGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IEVPLYSLLEQTHLKVEDVSAVEIVGGATR 30 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 209.58 4.47E-26 50437000 108470 69638 111930 101620 91989 98722 166490 110370 95760 FALSE TRUE 103342.8381 76734.19137 117062.1012 91404.96453 108031.8525 95303.23239 141088.8927 100705.4177 110609.9717 0.934299471 0.693736651 1.058332259 0.826371828 0.976691801 0.861615195 1.275553103 0.910455144 1 16.75512193 1.776287618 25 1.090208013 0.87939786 0.258139177 0.132034208 48.43296506 32107.56461 0.056200708 0.031201243 59.74308132 -1.776287618 -0.210810152 IEWLESHQDADIEDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 260.25 8.86E-27 1246520000 2609150 2481760 1806970 2996090 1227280 2496630 2164280 2586730 1032520 FALSE TRUE 2485820.65 2734654.166 1889821.362 2694917.341 1441317.243 2410171.077 1834079.336 2360222.208 1192637.928 2.084304542 2.292945831 1.584572582 2.2596274 1.208511996 2.020874081 1.537834151 1.978993081 1 20.18572469 -0.207253996 0.10375696 1.57E-11 2.785865492 0.431370482 0.329164972 28.08229784 0.846358017 15.64857579 6.974591727 0.620506027 0.207253996 2.785865492 IEWLESHQDADIEDFKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IEWLESHQDADIEDFKAK 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 212.76 9.38E-17 1082620000 1957600 1322030 1666290 1857940 1133790 2019290 2247340 2108280 1033790 FALSE TRUE 1865068.128 1456746.36 1742691.045 1671176.341 1331522.617 1949361.481 1904467.008 1923667.827 1194104.873 1.561896421 1.219948425 1.459412053 1.399522252 1.11508013 1.632487669 1.59489091 1.610970585 1 20.18749812 IEYAKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEYAKPTR 8 1 A0A3B3ITJ4;M0R1W6;B4DVF8;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 113.62 0.0025657 711950000 1097620 885490 912840 1131800 935700 1011800 1225280 1115350 1069410 FALSE TRUE 1045737.678 975722.4377 954694.6169 1018029.314 1098885.784 976761.1123 1038341.032 1017684.041 1235248.641 0.846580715 0.789899625 0.772876476 0.824149309 0.889606956 0.790740487 0.840592734 0.823869792 1 20.23637004 -5 0.314363547 2.637151372 0.81303466 0.742657136 0.032972 151.5978334 1.359890471 164.6222675 0.028974504 1.00E-05 5 -1.824116713 IEYDCELVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IEYDCELVPR 10 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 154.49 3.35E-05 235096000 203533 175373 178421 204097 193808 177466 213622 200018 209876 FALSE TRUE 193912.3985 193243.7081 186601.7793 183580.7818 227608.0538 171320.3079 181030.0405 182503.3636 242422.4982 0.799894399 0.797136031 0.769737878 0.757276174 0.938889977 0.706701355 0.74675429 0.752831791 1 17.88716407 -0.923571556 4.685586051 1.000001961 0.783102899 0.552703173 0.061163622 7394152.767 1578063.543 148.7881351 0.013576455 0.119241778 0.923571556 -0.216899062 IEYDDFVECLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IEYDDFVECLLR 12 0 O43920 O43920 NDUFS5 NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 0 ;; 120.68 0.00077864 25175600 47111 37933 42392 53658 50815 37617 56696 44536 46711 FALSE TRUE 44884.1564 41798.41583 44335.71513 48264.1959 59677.11991 36314.31386 48045.98391 40636.19174 53954.70331 0.83188589 0.774694573 0.821721044 0.894531763 1.106059643 0.673051868 0.890487408 0.753153835 1 15.71946111 -2.533180855 2.139429345 3.196124376 0.841186735 0.157948699 0.113695338 4505273.526 316405.5026 48139682.6 0.025803902 0.002929673 2.533180855 -2.354937641 IEYDTFGELKVPNDKYYGAQTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IEYDTFGELKVPNDKYYGAQTVR 23 2 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 199.89 1.42E-24 1027010000 1815850 988280 1556960 1289530 1185000 1382960 1859300 1706500 1419240 FALSE TRUE 1730018.369 1088986.856 1628348.156 1159903.994 1391663.625 1335067.748 1575629.637 1557069.813 1639328.491 1.055321358 0.664288373 0.993301931 0.707548244 0.848922978 0.814399162 0.961143325 0.949821724 1 20.64467354 1.671822309 5.443764444 0.968749859 0.842622346 0.19996635 0.11560858 0.227916688 14.90345579 0.056218958 0.02757463 46.97018917 -1.671822309 -0.126127513 IEYQFFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IEYQFFEDR 9 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;;;;; 217.64 1.30E-06 1230060000 1091401 948155 852931 969643 1114258 864752 1200237 1046704 1158238 FALSE TRUE 1039812.638 1044773.072 892038.73 872172.6434 1308584.242 834805.4214 1017118.802 955049.0488 1337851.634 0.777225674 0.780933436 0.666769549 0.651920304 0.97812359 0.623989537 0.76026278 0.713867685 1 20.3514867 -1.086448936 5.005674979 1.000006765 0.746944001 0.399534282 0.098524076 6.67E-06 1.22E-06 0.085545846 0.02016281 0.081950397 1.086448936 -0.253062765 IFAPNHVVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFAPNHVVAK 10 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 131.44 0.00025009 2213290000 5721200 5483700 4662900 5730700 4621100 5242200 6304500 5871500 4898000 FALSE TRUE 5450770.214 6042495.264 4876698.577 5154639.148 5427018.377 5060661.3 5342632.735 5357360.333 5657556.824 0.963449486 1.068039695 0.861979602 0.911106916 0.959251236 0.894495885 0.944335674 0.946938846 1 22.43174774 3.744027117 24.99963595 0.927971755 1.015744588 0.380254783 0.044750649 379.75498 1736704.728 0.01061905 0.01849938 5546.603447 -3.744027117 0.087772833 IFAQDGEGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IFAQDGEGQR 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 0 ;;; 199.86 6.30E-07 691250000 971990 620922 699910 905260 1054520 762940 1109480 948390 1119810 FALSE TRUE 926045.959 684194.6577 732001.5658 814261.5449 1238427.954 736519.1965 940208.449 865343.9439 1293464.416 0.715942354 0.528962876 0.565923235 0.629519865 0.957450347 0.569415894 0.726891624 0.669012563 1 20.30280893 -5 0.184983527 2.423359898 0.596804019 0.439010363 0.118957951 123.0143697 1.194242947 64.28666982 0.327711808 1.00E-05 5 -1.826555879 IFCCHGGLSPDLQSMEQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 195.77 8.66E-16 535410000 444593 412737 390553 485712 439820 395459 442004 469815 409050 FALSE TRUE 423577.97 454795.3695 408460.2414 436887.307 516524.4687 381764.1557 374568.1718 428675.508 472483.3849 0.896492837 0.962563731 0.864496519 0.924661736 1.093211921 0.80799488 0.792764749 0.907281656 1 18.84990407 IFCCHGGLSPDLQSMEQIRR ddPTM_SK-BR-3_Trastuzumab_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 ; 197.09 1.10E-21 821550000 299220 205468 290440 250911 352530 267470 365330 307850 432960 FALSE TRUE 285076.4636 226405.4228 303756.9613 225688.9496 414011.1204 258207.4468 309592.1988 280893.022 500101.2255 0.570037522 0.452719192 0.607390956 0.451286536 0.827854641 0.516310366 0.619059068 0.561672333 1 18.93186061 -5 0.227709195 3.286972448 0.518709256 0.616597386 0.105401369 96.91643606 0.96951784 102.0119445 0.167057839 1.00E-05 5 -2.768263192 IFCGDLGNEVNDDILAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFCGDLGNEVNDDILAR 17 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 110.29 0.0013151 8541100 14399 12884 12153 13868 15177 12814 16013 16999 18420 FALSE TRUE 13718.38781 14196.89425 12710.22707 12473.96229 17823.86399 12370.24797 13569.92275 15510.47744 21276.47952 0.644767749 0.667257674 0.597383935 0.58627943 0.837726184 0.58140483 0.637789853 0.728996422 1 14.37697184 0.836846431 3.192358334 0.999906443 0.650500703 0.695074187 0.072535393 0.413045864 7.065894181 0.063920111 0.01663584 6.868255314 -0.836846431 -0.34940574 IFCSEDEQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFCSEDEQSR 10 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 187.22 0.00053897 217770000 335040 318640 299590 342970 305710 332420 354310 349140 310410 FALSE TRUE 319203.3232 351109.7783 313326.4978 308494.004 359025.7272 320908.212 300253.5022 318567.4507 358546.7974 0.890269626 0.979257884 0.873878947 0.860400947 1.001335752 0.895024623 0.837417889 0.888496154 1 18.45180191 2.01727673 24.99759066 0.884485283 0.923515938 0 0.059898817 584.0355073 845033.3868 0.020919312 0.015446792 104.0583009 -2.01727673 0.039030656 IFDEVMGCFSDS(ph)PPQS(ph)PTFPEAGHTSLYDEDKVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFSDS(1)PPQS(0.973)PT(0.027)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.033)DS(0.966)PPQS(0.975)PT(0.023)FPEAGHT(0.001)S(0.001)LY(0.001)DEDKVPR 137.44 8.45E-09 143466000 71271 48125 79692 76755 76705 71417 110130 83478 90197 TRUE FALSE 67902.16108 53028.99221 83345.95703 69039.44158 90082.32771 68943.81138 93327.64582 76168.22378 104184.2901 0.65175048 0.508992211 0.799985842 0.662666526 0.864644061 0.661748631 0.895793845 0.731091259 1 16.66877823 4.350782291 0.093265988 1.242988497 7.17E-08 0.525230153 0.098207184 37.23551135 0.637044546 2.237336824 7.107318913 22427.57361 -4.350782291 -1.242988426 IFDFDDDGTLNREDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFDFDDDGTLNREDLSR 17 1 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 ; 165.58 2.24E-09 84036000 114913 92359 104292 108031 117650 95502 130319 117305 141489 FALSE TRUE 109481.2902 101770.4871 109073.8914 97171.51863 138168.1228 92194.74179 110436.4431 107033.1523 163430.3915 0.669895539 0.622714577 0.667402742 0.594574349 0.845424902 0.564122382 0.675739941 0.654915841 1 17.31831677 -1.035600957 3.503208416 1.000139454 0.65931225 0.671508462 0.074308722 10179451.26 17184654.93 17138.82525 0.015488062 0.09212957 1.035600957 -0.340827204 IFDIDEAEEGVKDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFDIDEAEEGVKDLK 15 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 168.5 1.14E-06 77964000 228229 141195 234964 207050 145952 244516 303670 284050 187002 FALSE TRUE 217441.0675 155582.931 245737.3318 186236.9406 171405.9826 236048.3496 257339.5642 259177.0762 216001.3151 1.00666548 0.720286962 1.137665906 0.862202809 0.793541384 1.09280978 1.191379618 1.199886566 1 17.72068057 2.099516907 5.837399701 1.149278317 0.897812458 0.426314695 0.124723183 0.170709173 8.439376421 0.044575389 0.032638504 125.7525808 -2.099516907 -0.25146586 IFDIKDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFDIKDGK 8 1 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 72.928 0.040936 183130000 393920 295610 359180 380310 267720 382650 453660 448870 319000 FALSE TRUE 375300.1823 325732.9951 375648.7583 342080.5163 314410.2832 369398.7346 384445.835 409564.5632 368468.8908 1.01853967 0.884017629 1.019485682 0.928383711 0.853288544 1.002523534 1.043360361 1.111530915 1 18.49118329 1.915332184 3.53640731 1.055066087 0.942286467 0.428411251 0.058023639 0.22017217 4.856518266 0.027042125 0.015128055 82.28718089 -1.915332184 -0.11277962 IFDLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IFDLGR 6 0 P27635;X1WI28;Q96L21;A6QRI9;B8A6G2 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ;;;;;; 175.34 0.009844 4750374000 5789438 4979446 4594378 5559375 5809985 4703043 6240360 5458945 5889910 FALSE TRUE 5515782.739 5486857.209 4805034.776 5000536.063 6823244.544 4540175.442 5288278.47 4980930.836 6803287.161 0.810752598 0.806500899 0.70628134 0.735017638 1.002933491 0.667350258 0.777312253 0.73213591 1 22.69780055 -1.420949825 4.567077337 1.000494664 0.781788876 0.368471739 0.090569257 0.000417322 5.29E-05 0.080224635 0.018866875 0.037935881 1.420949825 -0.218705787 IFDLGS(ph)DNEEVVAGPAPAHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFDLGSDNEEVVAGPAPAHAK 21 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 IFDLGS(1)DNEEVVAGPAPAHAK 104.96 0.00025891 35184000 34804 29347 31739 32625 37102 29423 42920 38018 42367 TRUE FALSE 33158.88389 32337.49266 33194.26454 29345.47302 43572.57705 28404.07413 36371.76572 34688.94237 48937.05798 0.677582292 0.660797645 0.678305274 0.599657483 0.890379987 0.580420551 0.743235642 0.708848137 1 15.57863975 -4.999999969 0.259105033 3.004182696 0.66408436 0.578776413 0.083427061 126.013561 1.238707514 134.2454735 0.096920358 1.00E-05 4.999999969 -2.340098336 IFDLQDWTQEDERDKDAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IFDLQDWTQEDERDKDAAK 19 2 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ;; 197.72 4.36E-16 247147000 293916 220144 237602 262699 158895 230190 267605 285346 141416 FALSE TRUE 280023.1732 242576.9239 248496.2867 236291.9974 186606.2377 222218.4626 226776.9423 260359.5915 163346.071 1.7142939 1.485049027 1.521287198 1.446572886 1.142398079 1.360415106 1.38832199 1.593914013 1 17.31757223 7.999999993 0.038440212 2.24E-10 3.72732869 0.529070529 0.142532925 659.9611087 1.934432864 52.59672038 163.420888 99999998.47 -7.999999993 3.72732869 IFDSEEILAGYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFDSEEILAGYKR 13 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 212.68 1.92E-08 893080000 2669600 1959990 2442700 2399800 2353500 2444600 3438000 2876300 2916300 FALSE TRUE 2543413.299 2159715.209 2554700.211 2158567.545 2763949.655 2359942.889 2913469.957 2624435.924 3368544.91 0.75504806 0.641141878 0.758398739 0.640801178 0.820517383 0.700582285 0.864904591 0.779100767 1 21.6836941 0.817988144 0.443952205 1.013631695 0.691732128 0.665686346 0.061828546 0.737293122 0.345233072 0.080356465 0.035484483 6.576398845 -0.817988144 -0.321899568 IFEGTNDILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IFEGTNDILR 10 0 P49748;P49748-3;P49748-2;J3KSR4;G3V1M7;J3QRJ8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;; 230.24 2.90E-09 331732000 693592 482043 427478 432171 605727 383943 605778 520978 600000 FALSE TRUE 660807.2807 531163.7297 447078.2891 388728.35 711365.597 370646.9576 513355.4402 475358.4044 693044.9356 0.953484034 0.766420332 0.645092787 0.5608992 1.026435027 0.534809417 0.740724611 0.685898388 1 19.40258937 4.384099454 2.274775371 0.723495255 0.948902528 0.130822588 0.162930869 0.544004306 5.050076264 0.037265301 0.180628261 24215.83532 -4.384099454 0.225407272 IFEPNCLDAFPNLKDFISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFEPNCLDAFPNLKDFISR 19 1 A0A0A0MR85;Q03013-3;Q03013-2;Q03013;A6NNT0 A0A0A0MR85 GSTM4 Glutathione S-transferase Mu 4 0 105.06 0.00031088 66849000 112010 124110 115150 141960 97328 133180 161310 148470 121190 FALSE TRUE 106715.5093 136756.9501 120429.7414 127689.9111 114301.9724 128567.9432 136699.1968 135469.1797 139983.5262 0.762343342 0.976950315 0.860313671 0.912178129 0.816538742 0.918450525 0.976537743 0.967750873 1 17.09489753 1.888335274 3.315229907 0.978759093 0.872920951 0.460432967 0.056595511 0.240032366 4.541135877 0.027771129 0.015021351 77.32773229 -1.888335274 -0.105838143 IFGGLDMLAEKLPNLTHLNLSGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IFGGLDMLAEKLPNLTHLNLSGNK 24 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ;; 177.91 2.48E-17 403750000 1280970 656430 1245840 1049280 1170140 1264400 1882680 1409650 1450040 FALSE TRUE 1220421.087 723320.9633 1302962.996 943804.3809 1374212.046 1220613.511 1595442.588 1286213.573 1674904.797 0.728651019 0.431857957 0.777932572 0.56349733 0.820471735 0.728765905 0.952557179 0.767932348 1 20.67564766 2.23975027 0.702892321 0.944472244 0.589659848 0.496628115 0.117405183 0.50067043 0.478994283 0.089502965 0.057928177 173.6801839 -2.23975027 -0.354812395 IFGPIWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFGPIWNR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 182.31 0.00053332 3921900000 1246980 1126800 942380 1216420 1260530 1015580 1233760 1115540 1143000 FALSE TRUE 1188037.727 1241622.201 985589.0551 1094143.151 1480366.033 980410.2099 1045527.252 1017857.404 1320250.602 0.899857743 0.940444336 0.746516649 0.82873899 1.121276544 0.742594026 0.791915755 0.770957727 1 20.33238037 IFGSEAAWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFGSEAAWK 9 0 P49748;P49748-3;P49748-2;J3KSR4;G3V1M7;J3QRJ8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 101.72 0.0088196 43859000 409980 321080 272690 301290 263740 287180 382880 349120 274640 FALSE TRUE 390601.0579 353798.417 285193.1062 271003.7568 309736.1725 277234.8846 324464.6239 318549.202 317229.7685 1.231287529 1.115274959 0.899011173 0.854282239 0.976378018 0.873924556 1.022806357 1.004159236 1 18.27516863 3.929791551 3.290756782 0.946164821 1.196427406 0.729679798 0.058809056 0.113870769 2.41797429 0.015678021 0.032406847 8507.296138 -3.929791551 0.250262585 IFGVTTLDIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFGVTTLDIVR 11 0 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 232.83 9.43E-14 153191000 315370 167856 116622 101960 323540 112887 358320 193160 273080 FALSE TRUE 300463.0851 184960.7172 121969.2341 91710.78709 379965.2736 108977.6949 303651.703 176245.8864 315427.8517 0.952557244 0.586380423 0.386678708 0.290750441 1.204602801 0.345491669 0.96266611 0.558751821 1 18.26695053 2.762854416 24.99697007 0.785524588 0.594446449 0.155073464 0.290930973 1923.997231 1979683.401 0.08460949 0.089703652 579.2344931 -2.762854416 -0.191078139 IFHELTQTDK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 204.5 1.86E-07 1394310000 5618400 4982700 4637180 5437300 5462170 5068750 6305600 5708600 5580330 FALSE TRUE 5352829.367 5490442.795 4849799.29 4890732.274 6414770.719 4893217.917 5343564.91 5208724.721 6445699.076 0.830449778 0.851799429 0.75240858 0.758759014 0.995201706 0.759144642 0.82901247 0.808093065 1 22.61990541 -1.344048614 5.133428777 1.000075257 0.824681148 0.38711462 0.069923728 5.48E-05 7.00E-06 0.06155874 0.01450332 0.045284689 1.344048614 -0.175394109 IFHGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFHGLK 6 0 P13796;Q5TBN3 P13796 LCP1 Plastin-2 0 84.566 0.055705 673370000 1556900 1424800 1361500 1625300 1344900 1514700 1747700 1610000 1287500 FALSE TRUE 1483308.422 1569988.74 1423926.122 1461921.756 1579450.134 1462245.559 1481056.266 1469019.865 1487158.924 0.997410834 1.055696681 0.957480803 0.983029945 1.062058741 0.983247678 0.995896432 0.987802878 1 20.5041274 IFHIVENDLYIDFGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFHIVENDLYIDFGGK 16 0 H0YC42;U3KQQ8;E5RGC7;E5RK86;E5RFH3;H0YAT2;Q9Y2Q9;H7C5V3 H0YC42;E5RGC7 MRPS28 "28S ribosomal protein S28, mitochondrial" 0 ; 198.13 4.15E-11 230960000 535860 446250 471750 500260 435030 445360 585920 510130 354260 FALSE TRUE 510530.9598 491723.3823 493380.2041 449972.9144 510899.0943 429937.0715 496527.1428 465460.3128 409196.8315 1.247641527 1.20167935 1.20572831 1.099649068 1.248541179 1.050685241 1.213418836 1.137497353 1 18.64243545 -5 0.09680582 0.428244446 1.311365798 0.520824531 0.058265523 142.0375614 0.942098891 16.56750198 0.958764642 1.00E-05 5 0.883121353 IFHTVTTTDDPVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFHTVTTTDDPVIR 14 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 105.19 0.001014 136420000 49085 44744 47529 52428 51510 49206 48863 47462 52739 FALSE TRUE 46764.84933 49303.46447 49708.25166 47157.83783 60493.32769 47501.98388 41408.05192 43305.97567 60917.49477 0.767675189 0.809348196 0.815993039 0.774126349 0.993037024 0.779775729 0.679739902 0.710895545 1 15.89456899 -0.430069532 7.402407598 1.000000019 0.789092712 0.385760531 0.082710699 0 0 0.081733523 0.019264776 0.37147575 0.430069532 -0.210907307 IFILGPSHHVPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFILGPSHHVPLSR 14 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 122.64 6.22E-05 88001000 93819 82632 76879 93842 107960 76106 118400 101940 39697 FALSE TRUE 89384.3618 91052.29474 80403.97819 84408.82387 126788.1898 73470.43014 100335.9054 93013.59318 45853.00802 1.949367461 1.98574311 1.753515891 1.840856849 2.765100815 1.602303389 2.188207705 2.028516715 1 15.48472876 -0.500062678 7.147446086 1 2.011951331 0.513254906 0.310385444 0 0 0.268018058 0.063172462 0.316182131 0.500062678 1.011951331 IFLDHIGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFLDHIGGTR 10 0 P62699 P62699 YPEL5 Protein yippee-like 5 0 92.538 0.0093988 96888000 66617 56915 60369 69770 114760 57005 75755 69994 80112 FALSE TRUE 63468.14643 62714.70321 63136.97836 62756.58705 134774.1077 55030.90256 64197.18341 63864.9543 92535.3598 0.685879934 0.677737714 0.682301106 0.678190339 1.456460622 0.594701341 0.693758403 0.690168109 1 16.49771714 IFLLGLADNEAAIVQAESEETKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFLLGLADNEAAIVQAESEETKER 24 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 168.78 9.16E-12 22818000 28491 26253 27607 31411 23897 31817 34982 31531 25247 FALSE TRUE 27144.28689 28928.21055 28872.80826 28253.5066 28064.62923 30715.16931 29644.85341 28769.97848 29162.17582 0.930804583 0.991977098 0.990077299 0.968840829 0.962364037 1.053253691 1.016551495 0.986551164 1 14.83181074 2.263493364 24.99665973 1.016933915 0.969484083 0.47451656 0.023585246 187.7950377 188275.8043 0.008100497 0.006774497 183.4397139 -2.263493364 -0.047449832 IFPGLS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IFPGLSPVR 9 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR;IFPGLS(1)PVR 134.84 0.00024911 232767000 349737 248252 148342 185407 373781 207289 378058 295359 379330 TRUE FALSE 333205.6251 273549.161 155143.6274 166769.5361 438968.2881 200110.53 320378.3086 269495.8002 438154.5591 0.760475084 0.624321157 0.354084248 0.380618055 1.001857173 0.456712194 0.731199304 0.615070172 1 18.74108034 -0.490290886 0.515569999 1.065082806 0.605217673 0.288645531 0.191476388 12.27327461 2.79977332 1.61842964 0.085617363 0.32337699 0.490290886 -0.459865133 IFPMGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IFPMGDR 7 0 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ;;; 100.82 0.022129 304296000 346501 318751 313285 338608 350861 321854 369307 337922 347287 FALSE TRUE 330122.5844 351232.0893 327649.4271 304570.4805 412051.0473 310708.1153 312962.4344 308331.7582 401142.4943 0.822955905 0.875579362 0.816790621 0.759257583 1.027193711 0.774557968 0.780177714 0.768633996 1 18.61375528 -0.250740394 7.5967373 0.999999999 0.829544823 0.320990282 0.078529142 9694912.682 1276194.255 0.071413971 0.017320432 0.561383451 0.250740394 -0.170455176 IFQGNVHNFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFQGNVHNFEK 11 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 ; 96.745 0.0067836 672550000 782510 691650 755580 904180 716690 750010 959280 897060 822320 FALSE TRUE 745522.3031 762129.9213 790224.0904 813290.1086 841680.5091 724036.9656 812924.2176 818508.6708 949841.1858 0.784891532 0.802376158 0.831953912 0.856237991 0.88612762 0.762271605 0.855852778 0.861732133 1 19.85732679 -5 0.180030633 1.718452329 0.78915959 0.718776569 0.034701097 70.89709371 0.682550777 18.17845803 0.105876168 1.00E-05 5 -0.929292739 IFQGSFGGPTLYENPHYQS(ph)PNMHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFQGSFGGPTLYENPHYQSPNMHR 24 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 1 IFQGSFGGPTLYENPHY(0.451)QS(0.549)PNMHR;IFQGSFGGPTLYENPHY(0.44)QS(0.56)PNMHR 168.78 1.14E-11 211100000 120208 113824 112101 142857 132172 118266 150106 130591 106098 TRUE FALSE 114526.0061 125422.795 117240.9417 128496.7429 155222.755 114170.4188 127204.5728 119155.7597 122551.136 0.934516071 1.023432333 0.956669563 1.048515315 1.266595807 0.931614529 1.037971389 0.972294208 1 16.90302433 4.433895803 1.027160845 1.038676099 0.915581507 0.101449228 0.091444386 2.715311452 3.259298353 0.028029298 0.328721256 27157.87612 -4.433895803 -0.123094592 IFQKGESPVDYDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IFQKGESPVDYDGGR 15 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;; 178.03 6.65E-07 1490610000 1787350 1141170 1853640 1435230 1883000 1685180 2346860 1790800 2427340 FALSE TRUE 1702865.508 1257456.52 1938631.228 1290957.954 2211394.604 1626821.794 1988803.404 1633988.058 2803759.49 0.607350778 0.448489439 0.691439916 0.460438193 0.788724786 0.580228725 0.709334524 0.582784673 1 21.41893117 -5 0.165632025 2.537980627 0.500568253 0.59338907 0.102970767 79.85739369 0.745255577 40.22528974 0.345807899 1.00E-05 5 -2.037412373 IFRDGEEAGAYDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IFRDGEEAGAYDGPR 15 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 209.33 2.22E-09 2229410000 1952920 990210 2117420 1568810 2746790 1783660 2817550 2091060 3553330 FALSE TRUE 1860609.342 1091113.525 2214505.801 1411110.238 3225829.306 1721891.407 2387681 1907955.701 4104362.269 0.453324833 0.265842402 0.539549303 0.343807429 0.785951409 0.41952715 0.581742264 0.464860452 1 21.96872664 -4.999999997 0.152155741 2.9178266 0.308363822 0.59638479 0.136448581 83.09122958 0.74555082 48.07766846 0.596675014 1.00E-05 4.999999997 -2.609462777 IFSIVEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFSIVEQR 8 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 80.438 0.059203 59830000 215370 217490 220880 205590 231140 231970 248890 221460 224470 FALSE TRUE 205189.8869 239652.4783 231007.5665 184923.7026 271450.7428 223936.8207 210917.2593 202067.7884 259279.6612 0.79138443 0.924301109 0.890959073 0.713221013 1.046941907 0.863688342 0.813473985 0.779342998 1 17.98414951 4.726248125 4.492809774 0.870331263 0.787064359 0.066277873 0.098650863 0.565360991 25.90388381 0.021647187 0.142594527 53241.23544 -4.726248125 -0.083266904 IFSNTDPDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFSNTDPDKK 10 1 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 147.62 4.26E-05 3668300000 9892300 9024500 8375400 10529500 5234900 10271300 10503200 11255900 5760300 FALSE TRUE 9424710.584 9944106.81 8759420.374 9471054.655 6147864.903 9915602.306 8900743.935 10270273.72 6653577.904 1.416487598 1.494550294 1.316497755 1.423452884 0.923993826 1.490266207 1.33773799 1.543571575 1 22.66569892 -1.743053619 2.639195726 0.921909241 1.372221923 0.310067128 0.172577264 15707414.56 12591543.04 8035321.363 0.039620778 0.01806951 1.743053619 0.450312682 IFTIESTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFTIESTR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 89.296 0.032585 34735000 46878 29830 44111 38653 76668 43813 77459 45100 118980 FALSE TRUE 44662.16984 32869.71091 46133.53298 34767.527 90038.87493 42295.74482 65641.20692 41150.80491 137430.8107 0.324979309 0.239172793 0.335685519 0.252982041 0.655157853 0.30776028 0.477630937 0.299429252 1 17.06834595 -5 0.218361234 4.225466759 0.274152454 0.729306501 0.122321421 72.46470896 0.724383901 102.7261367 0.21522069 1.00E-05 5 -3.951314305 IFTLPGDCLIYPAHDYHGFTVSTVEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IFTLPGDCLIYPAHDYHGFTVSTVEEER 28 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 ;; 276.23 8.39E-62 210749000 132797 102522 132602 129196 139238 113488 136983 119144 46292 FALSE TRUE 126519.949 112969.1084 138681.9329 116208.9726 163521.0631 109557.8821 116083.7275 108711.1197 53470.72693 2.366153524 2.112728119 2.593604778 2.173319483 3.058141763 2.048931974 2.170977171 2.033095976 1 15.70646167 0.616574855 0.944676553 0.999539803 2.379349541 0.698637339 0.284205402 0.680690415 0.997247484 0.255423632 0.083155313 4.135945957 -0.616574855 1.379809738 IFTPLLHQIELEKPKPIPYIYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFTPLLHQIELEKPKPIPYIYGSR 24 2 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 178.69 2.37E-17 1558000000 2596800 1488300 2203500 2305300 1983300 2155100 2974200 2613300 2165300 FALSE TRUE 2474054.41 1639959.462 2304532.655 2073566.864 2329186.892 2080468.347 2520431.165 2384465.598 2501083.665 0.989192983 0.655699561 0.92141366 0.829067373 0.931271082 0.83182677 1.007735647 0.953372984 1 21.25412189 1.921859384 0.941466175 1.001166233 0.835233487 0.257261555 0.092271215 0.658896796 1.07474973 0.072964031 0.033346966 83.53325103 -1.921859384 -0.165932746 IFTPYFNYMHECFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFTPYFNYMHECFER 15 0 Q96L92-3;Q96L92;A0A2R8Y8A7;Q96L92-2 Q96L92-3 SNX27 Sorting nexin-27 0 104.45 0.0013925 48631000 109930 110040 112310 112310 186030 106340 137250 110480 147710 FALSE TRUE 104733.8268 121253.2011 117459.5246 101020.3854 218473.5731 102657.4191 116309.9917 100805.7855 170616.1124 0.613856601 0.71067849 0.68844333 0.592091708 1.280497897 0.601686545 0.68170579 0.590833914 1 17.38039437 IFTSIGEDYDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IFTSIGEDYDER 12 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;;;;; 326.07 1.56E-47 3311230000 3937657 2996289 3216020 3678885 4183080 2625333 3487676 3405703 3895850 FALSE TRUE 3751531.757 3301614.256 3363477.698 3309076.49 4912607.828 2534417.06 2955566.971 3107481.591 4499998.521 0.833673998 0.733692298 0.747439734 0.735350573 1.091690987 0.563203976 0.656792876 0.690551692 1 22.1014931 IFVGGIKEDTEEYNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IFVGGIKEDTEEYNLR 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 248.2 2.02E-20 1600200000 2092930 1803060 1885000 2165010 1538310 2083660 2177960 2280160 1661670 FALSE TRUE 1994001.347 1986793.864 1971429.115 1947379.082 1806590.777 2011502.332 1845672.201 2080497.103 1919353.297 1.038892292 1.03513713 1.02713196 1.014601681 0.941249732 1.04801046 0.961611499 1.083957344 1 20.87218886 3.229007282 3.449528902 1.002450542 1.03566789 0.078947803 0.039771158 0.451501109 11.30478222 0.010470138 0.013603587 1694.366209 -3.229007282 0.033217348 IFVGGIPHNCGETELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFVGGIPHNCGETELR 16 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 188.19 1.22E-09 785960000 524640 501420 404510 569810 513180 451310 525830 518450 449450 FALSE TRUE 499841.3069 552515.2681 423057.1836 512531.6162 602678.4295 435681.0215 445604.976 473051.7695 519148.4105 0.96281005 1.064272291 0.814906056 0.987254523 1.16089815 0.83922249 0.858338323 0.9112072 1 18.9857875 IFVGGLNPEATEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IFVGGLNPEATEEK 14 0 Q99729-3;D6R9P3;D6RD18;D6RBZ0;Q99729-2 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 140.39 2.32E-05 22623000 49206 38549 39200 50478 36635 42443 49368 45781 44384 FALSE TRUE 46880.1299 42477.18693 40997.35877 45403.85554 43024.1324 40973.18827 41836.00489 41772.17294 51266.84404 0.9144337 0.828550845 0.799685636 0.885637811 0.839219445 0.799214171 0.816044086 0.814798994 1 15.64573847 -1.154617997 3.386359783 1.000220571 0.838076343 0.658847851 0.036811761 6964472.599 11294941.36 16931.54112 0.009449452 0.070045784 1.154617997 -0.162144228 IFVGGLS(ph)PDTPEEK ddPTM_SK-BR-3_Trastuzumab_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(0.993)PDT(0.007)PEEK 132.31 5.37E-05 31980000 150280 120710 129410 147310 99279 141060 165120 155590 116580 TRUE FALSE 143176.5622 133010.4862 135343.5765 132502.1189 116593.2262 136175.0568 139927.9114 141965.7148 134658.631 1.063255739 0.987760571 1.005086533 0.983985341 0.865842949 1.01126126 1.039130655 1.054263761 1 17.03894718 -0.820272787 7.375941992 0.999998115 1.002532969 0 0.054804525 0 6.71E-19 0.05347236 0.012603556 0.151261086 0.820272787 0.002534854 IFVGGLSPDTPEEK ddPTM_SK-BR-3_Trastuzumab_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 0 149.23 2.66E-06 0 101560 81060 86773 109000 76117 92688 105420 110390 110440 FALSE TRUE 96759.46007 89320.10616 90751.62788 98043.11291 89391.7807 89478.19132 89336.24283 100723.6664 127566.4712 0.758502287 0.700184816 0.711406587 0.768564906 0.700746677 0.701424054 0.700311312 0.7895779 1 16.96088966 0.865074888 3.46426433 0.999926169 0.719937312 0.926628341 0.02472463 0.151822844 3.361843793 0.023488094 0.006069053 7.329509098 -0.865074888 -0.279988858 IFVGLCQVGAWGCFDEFNRLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFVGLCQVGAWGCFDEFNRLEER 23 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 163.62 1.39E-11 97837000 35045.7 30332.5 29783.1 31153.8 35872.6 35011.4 44398.1 33649.5 36665 FALSE TRUE 33389.15921 33423.41624 31148.68459 28022.16084 42128.77008 33798.94644 37624.35442 30702.97139 42350.82094 0.788394616 0.789203503 0.735491872 0.661667477 0.99475687 0.798070632 0.888397287 0.724967562 1 15.37010232 2.748662119 24.99810535 0.868704237 0.755786896 0.365473895 0.088578465 852.6374 2110014.2 0.024848204 0.026090973 560.6116509 -2.748662119 -0.112917341 IFVNDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 4476910000 7997050 7413070 6898330 8390310 7699440 7053830 7925760 7493630 7535230 FALSE TRUE 7619045.295 8168470.261 7214625.254 7546900.098 9042219.898 6809554.098 6716539.745 6837448.031 8703754.984 0.875374515 0.938499564 0.828909507 0.867085541 1.038887229 0.782369691 0.771682999 0.785574507 1 23.05320651 IFYDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IFYDMK 6 0 P60981;F6RFD5 P60981 DSTN Destrin 0 ;; 116.35 0.055015 4440422000 6625310 5664595 5623690 6725611 5340307 6093776 7738670 6687050 5631636 FALSE TRUE 6312144.726 6241823.671 5881541.749 6049539.804 6271654.85 5882747.009 6557993.761 6101496.452 6504961.348 0.970358529 0.959548157 0.904162444 0.929988586 0.964134068 0.904347727 1.00815261 0.93797582 1 22.63310905 1.728370206 25 0.980285084 0.942894552 0.323834462 0.029041503 1.085142432 2649.159144 0.012914561 0.007161775 53.50202332 -1.728370206 -0.037390532 IFYGEKQPEDDSSQAFISTQNGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFYGEKQPEDDSSQAFISTQNGSPR 25 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 IFYGEKQPEDDSSQAFIS(0.002)T(0.002)QNGS(0.996)PR;IFYGEKQPEDDSSQAFIS(0.04)T(0.031)QNGS(0.93)PR 153.69 5.87E-08 217400000 147074 61674 154134 102178 144608 119665 229902 150449 217093 TRUE FALSE 140122.1035 67958.65072 161201.1964 91906.87331 169827.5894 115520.971 194826.2275 137274.888 250758.6737 0.558792649 0.271012164 0.64285392 0.366515231 0.677255095 0.460685843 0.776947113 0.547438244 1 17.93594008 0.451274503 0.288062967 1.11161786 0.394767415 0.555749953 0.13779322 2.369612274 0.415653141 0.526468603 0.179996179 2.826666053 -0.451274503 -0.716850445 IFYPEIEEVQALDDTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFYPEIEEVQALDDTER 17 0 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ; 167.32 5.20E-09 26649000 13297.8 11944.2 13213.4 15642.9 14661.6 13148.7 12640.4 14222.8 15894.8 FALSE TRUE 12669.23935 13161.32756 13819.24746 14070.44597 17218.5784 12693.35722 10711.87482 12977.37623 18359.6844 0.690057578 0.716860229 0.752695262 0.766377333 0.937847188 0.69137121 0.583445477 0.706840921 1 14.16425364 3.948534568 2.618063478 0.750600916 0.696919676 0.028317398 0.120629802 1.283043527 17.40450001 0.032651117 0.074256726 8882.486753 -3.948534568 -0.05368124 IFYPETTDIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFYPETTDIYDR 12 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 143.89 0.00014561 123571000 133682 139294 104315 136054 124364 100293 136270 126734 132237 FALSE TRUE 127363.1168 153488.217 109097.9459 122377.5934 146053.0422 96819.82826 115479.5087 115636.4991 152743.6386 0.833835818 1.004874693 0.714255251 0.801196008 0.956197218 0.633871428 0.756034816 0.757062619 1 17.22075277 3.735111471 24.90476825 0.786697671 0.919355254 0.139680449 0.11522324 401.6566372 2900191.454 0.028132574 0.045571872 5433.897865 -3.735111471 0.132657583 IFYPETTDIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 179.43 2.21E-05 355830000 300352 266951 304577 305909 239575 282097 331168 305941 272803 FALSE TRUE 286154.9562 294153.6104 318542.1567 275158.4461 281356.8041 272327.9102 280642.2393 279151.1841 315107.896 0.908117378 0.933501236 1.010898682 0.873219775 0.892890365 0.864237024 0.890622682 0.885890794 1 18.26548638 IGADFLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGADFLAR 8 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 135.84 0.0018994 114225000 440010 370960 321170 385350 449410 318010 460700 398770 440060 FALSE TRUE 419211.5993 408761.2457 335895.9622 346613.8859 527786.9617 306997.234 390411.7537 363851.5848 508302.2573 0.824728974 0.804169645 0.66081934 0.681905069 1.038332909 0.603965907 0.768070077 0.71581737 1 18.95532711 -0.982655593 9.460216117 0.999999616 0.765627113 0.284810264 0.118303932 0 0 0.104418482 0.024611672 0.104074518 0.982655593 -0.234372503 IGAEVYHNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;;; 140.45 3.93E-05 35001745000 20526805 14635673 11601299 13436774 16126194 14966425 21939036 17573274 15654406 FALSE TRUE 19556543.61 16127064.72 12133230.03 12086083.95 18938597.13 14448133.95 18591833.12 16034464.97 18082011.33 1.081546917 0.891884449 0.671011085 0.668403737 1.047372263 0.799033564 1.028194971 0.886763351 1 24.10805183 1.733190024 24.99999988 0.968681522 0.873203297 0.120964718 0.138904392 1.53884334 7104.503054 0.067037572 0.037175711 54.09909795 -1.733190024 -0.095478224 IGALEGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGALEGYR 8 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 133.79 0.0021038 443570000 510400 425830 316820 372990 506160 375480 538440 457740 488210 FALSE TRUE 486274.4035 469222.5611 331346.5104 335496.3366 594434.1437 362477.0335 456291.0889 417657.859 563919.1134 0.862312328 0.832074228 0.587578081 0.594936984 1.054112424 0.642781961 0.809142797 0.740634338 1 19.10512872 -1.242798576 5.504122426 1.000015452 0.772645116 0.216140707 0.139780412 2.48E-05 3.41E-06 0.126533694 0.029822252 0.057174375 1.242798576 -0.227370335 IGDEDVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IGDEDVGR 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 147.34 0.0012538 2671490000 4414980 4188020 3892580 4982090 4185140 4281060 5552880 4862910 4713040 FALSE TRUE 4206292.645 4614783.999 4071058.643 4481280.848 4915027.091 4132805.819 4705686.17 4437087.82 5443914.172 0.772659618 0.847695951 0.7478183 0.823172575 0.902848013 0.759160723 0.864393894 0.815054698 1 22.37621289 -4.999999993 0.229538606 1.981822231 0.796923132 0.610324563 0.046803929 102.4980449 1.025150345 46.69516552 0.072880061 1.00E-05 4.999999993 -1.1848991 IGDEYAEDS(ph)S(ph)DEEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IGDEYAEDSSDEEDIR 16 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 2 IGDEYAEDS(1)S(1)DEEDIR;IGDEYAEDS(1)S(1)DEEDIR;IGDEYAEDS(1)S(1)DEEDIR 216.29 2.24E-14 839060000 583760 673520 533467 671340 430371 617580 548100 551653 375405 TRUE FALSE 556166.8217 742152.4537 557926.9896 603855.6277 505427.5661 596193.0497 464477.2785 503347.3388 433620.8901 1.282610765 1.711523754 1.286669998 1.392588876 1.165597824 1.37491773 1.071159829 1.160800483 1 18.72607474 2.220202921 0.566304806 1.021602637 1.492066088 0.509305952 0.13944568 0.600143966 0.391411224 0.119940138 0.092285256 166.0362517 -2.220202921 0.470463452 IGDEYFTFITDCKDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGDEYFTFITDCKDPK 16 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 216.71 1.36E-14 1200640000 4063900 3575800 3218800 4310700 1983140 4111400 4089400 4291000 2129300 FALSE TRUE 3871807.501 3940178.085 3366385.164 3877380.246 2328998.988 3969021.187 3465486.923 3915257.292 2459500.969 1.574224832 1.602023392 1.368726911 1.576490636 0.946939651 1.613750609 1.409020353 1.591890933 1 21.22993419 -3.40368751 0.224736121 1.33E-33 1.532501844 0.318437723 0.204157161 82.68643478 1.575363839 39.7053057 0.360054917 0.000394741 3.40368751 1.532501844 IGDPLLEDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGDPLLEDTR 10 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 95.502 0.017166 30178000 67602 68872 58552 81070 66620 66079 75850 65524 63919 FALSE TRUE 64406.58743 75890.1351 61236.66712 72920.68958 78238.50691 63790.66766 64277.68942 59786.3712 73831.23207 0.87234881 1.027886614 0.82941413 0.987667245 1.059693909 0.864006544 0.870602963 0.809770737 1 16.17194361 IGDYVQCHGGVSLVEQMFQDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGDYVQCHGGVSLVEQMFQDPR 22 0 A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;D6RJE6;A0A2R8Y6I1;D6RB22;B4DQ67 A0A2R8Y3N3 HARS2 "Probable histidine--tRNA ligase, mitochondrial" 0 127.92 1.74E-05 53638000 87618 73371 75637 80010 81941 75920 86437 78414 79220 FALSE TRUE 83476.47078 80847.58832 79105.03127 71967.24279 96231.48446 73290.87136 73249.44813 71547.65446 91505.033 0.912260977 0.883531601 0.864488309 0.786483983 1.051652366 0.800949073 0.800496385 0.78189857 1 16.48156348 IGDYVQQHGGVSLVEQLLQDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGDYVQQHGGVSLVEQLLQDPK 22 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 192.63 1.00E-17 429750000 350760 312750 343890 375930 261106 364720 404730 409200 277934 FALSE TRUE 334180.2699 344619.5806 359657.6967 338140.8022 306642.8037 352089.6549 342981.0051 373368.2787 321034.5852 1.040947877 1.07346559 1.120308257 1.053284654 0.95517062 1.096734343 1.068361544 1.163015749 1 18.2923692 IGEEFLTDLSQLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGEEFLTDLSQLKK 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 177.84 3.29E-06 240940000 551900 474170 496640 579960 343100 579530 662390 643170 356020 FALSE TRUE 525812.7808 522488.4621 519411.4352 521661.3189 402936.5314 559460.7308 561330.2399 586850.6251 411229.7633 1.27863503 1.270551183 1.263068682 1.268539793 0.979833094 1.36045778 1.365003922 1.427062624 1 18.64958516 IGEEQS(ph)AEDAEDGPPELLFIHGGHTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 1 IGEEQS(1)AEDAEDGPPELLFIHGGHTAK 145.06 2.75E-07 11175000 47192 34410 36139 41746 31536 40677 46380 42925 9621.4 TRUE FALSE 44961.32769 37916.41812 37796.0089 37549.61277 37035.86842 39268.34529 39303.87917 39166.25944 11113.43757 4.045672403 3.411763271 3.400928709 3.3787577 3.332530387 3.533411245 3.536608625 3.524225442 1 13.44001752 0.705993446 8.945367872 1 3.530112103 0.940297998 0.199582064 283.6944965 8634.167595 0.200330615 0.050132852 5.081517739 -0.705993446 2.530112103 IGEEQSAEDAEDGPPELLFIHGGHTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 319.24 1.41E-82 613050000 767410 643906 617908 778850 509894 712560 814840 757470 48434.5 FALSE TRUE 731136.0502 709520.7535 646239.693 700558.5183 598819.3522 687883.8685 690521.1924 691141.9112 55945.47489 13.06872543 12.6823618 11.55124153 12.52216591 10.70362444 12.29561229 12.34275326 12.35384832 1 15.77173382 -0.682296004 8.707096653 1 12.24507968 0.966745856 0.652159207 0 0 0.636536893 0.150033168 0.20782797 0.682296004 11.24507968 IGEEQSPEDAEDGPPELLFIHGGHTAK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 206.33 1.61E-25 578362000 1104570 922920 949170 1138170 708380 1085260 1144840 1088080 66787 FALSE TRUE 1052359.165 1016966.597 992690.3834 1023758.989 831921.2477 1047677.174 970173.6316 992801.9469 77143.98686 13.64149311 13.18270728 12.86802023 13.27075552 10.7840064 13.58080152 12.57614068 12.8694664 1 16.23526609 -0.823342545 0.908254601 6.16E-11 12.92904655 0.955390619 0.804391025 10.56736262 4.379802825 34.50793558 0.23971642 0.150195685 0.823342545 12.92904655 IGEGT(ph)Y(ph)GVVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 2 IGEGT(1)Y(1)GVVYK;IGEGT(1)Y(1)GVVYK;IGEGT(1)Y(1)GVVYK;IGEGT(1)Y(1)GVVYK 225.97 8.87E-11 519053000 1273520 966150 1334650 1531840 1026260 1939670 1885000 1404640 1045990 TRUE FALSE 1213323.233 1064601.783 1395845.023 1377856.533 1205239.419 1872498.742 1597408.63 1281642.275 1208196.787 1.004243056 0.881149325 1.155312642 1.140423934 0.997552246 1.549829268 1.322142756 1.060789342 1 20.20442402 3.249915991 1.152679632 1.249700059 0.943607329 0.179671555 0.173568168 0.5427298 1.533993329 0.065648084 0.103453424 1777.935456 -3.249915991 -0.306092731 IGEGT(ph)YGVVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.856)Y(0.144)GVVYK;IGEGT(0.858)Y(0.142)GVVYK;IGEGT(0.969)Y(0.031)GVVYK 205.02 3.49E-07 3864580000 3605440 3060710 3145840 3790860 2110650 3579550 3757880 4004700 2535350 TRUE FALSE 3435017.996 3372599.829 3290079.876 3409795.551 2478746.692 3455589.286 3184546.388 3654027.238 2928519.129 1.172953921 1.15164002 1.123461972 1.164341225 0.846416425 1.17997839 1.087425503 1.2477389 1 21.48173989 IGEGTY(ph)GVVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.358)Y(0.642)GVVYK;IGEGT(0.193)Y(0.807)GVVYK;IGEGT(0.008)Y(0.992)GVVYK 228.05 3.66E-11 6961000000 5684530 4800520 5000120 6016610 3392870 5563890 6062740 6038430 3919130 TRUE FALSE 5415833.533 5289698.446 5229380.448 5411808.932 3984585.454 5371211.094 5137757.663 5509673.057 4526888.664 1.196369943 1.168506415 1.155182032 1.195480899 0.880203988 1.186512745 1.134942351 1.217099307 1 22.11008839 -4.999999994 0.017710158 1.53E-05 1.966743844 0.146210455 0.097773396 8203.246131 11.00421411 796.1532629 466.5761089 1.00E-05 4.999999994 1.966728501 IGEHMEEHGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IGEHMEEHGIK 11 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 ;;; 134.13 8.52E-05 1107840000 1235390 1027700 1028370 1204970 782990 1180490 1217830 1175450 316933 FALSE TRUE 1176995.563 1132423.798 1075521.782 1083844.126 919543.2081 1139609.335 1032027.667 1072521.367 366081.351 3.215120246 3.09336653 2.937931088 2.960664681 2.511854826 3.112994782 2.819121116 2.929735054 1 18.48180476 -1.324149534 0.434387346 2.38E-15 3.038656961 0.913923167 0.188084566 6.475065244 0.670425834 7.747956037 0.104894635 0.047407872 1.324149534 3.038656961 IGEHTPSALAIMENANVLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;; 304.13 3.00E-55 13906482000 2959838 2468033 2664340 3056544 2586026 2645332 3302330 2991600 2566511 FALSE TRUE 2819932.324 2719528.369 2786502.624 2749294.39 3037028.116 2553723.49 2798498.907 2729639.645 2964512.418 0.951229722 0.917361099 0.939953096 0.92740188 1.024461256 0.8614312 0.943999725 0.920771871 1 21.49936341 -0.93379447 4.528396712 1.000000966 0.93495374 0.202907532 0.039939604 4493593.203 992314.3057 42.9111548 0.008276104 0.116467708 0.93379447 -0.065047226 IGELGAPEVWGLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;IGELGAPEVWGLS(1)PK 225.86 9.89E-13 1941746000 3946297 4174744 3225217 4390144 1691409 4116935 3460158 4214253 1607460 TRUE FALSE 3759763.362 4600155.16 3373096.39 3948838.384 1986390.194 3974364.509 2932247.347 3845230.666 1856736.687 2.02493083 2.477548482 1.816679992 2.126762729 1.069828699 2.140510572 1.57924781 2.070961754 1 20.8243378 -0.185131693 0.106499518 2.15E-12 2.84256908 0.385777323 0.371909466 29.82192418 0.936640497 17.2185393 7.605061519 0.652932531 0.185131693 2.84256908 IGEWELIQESGVPLKPLFGPGYTGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGEWELIQESGVPLKPLFGPGYTGIR 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 156.43 2.63E-08 140410000 183080 169470 159940 184570 145210 164710 198770 199710 149690 FALSE TRUE 174426.1712 186739.1857 167273.4072 166016.6729 170534.578 159006.0514 168443.9858 182222.3337 172903.1607 1.00880846 1.080021816 0.967439846 0.960171418 0.986301103 0.919624897 0.974209986 1.053898222 1 17.39960472 3.723352952 24.55319075 0.974860429 1.044415138 0.325342116 0.037812038 561.342423 906302.6904 0.009600748 0.014941799 5288.748952 -3.723352952 0.069554709 IGEYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGEYLEK 7 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 101.99 0.045273 0 91828 84536 77580 96538 68310 91506 92547 98660 76895 FALSE TRUE 87487.47243 93150.31451 81137.11974 86833.81683 80223.24237 88337.12428 78427.25541 90020.80737 88819.48387 0.985003162 1.048759917 0.913505868 0.97764379 0.903216714 0.994569214 0.882996072 1.01352545 1 16.43858857 3.739651865 24.99778224 0.947560609 1.016881539 0.221172815 0.046599007 105.9087079 2426088.391 0.010716407 0.018007845 5491.005333 -3.739651865 0.06932093 IGFFNQQYAEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGFFNQQYAEQLR 13 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 117.94 0.0010851 116320000 52188 51092 50804 53897 58351 44251 74151 56388 51981 FALSE TRUE 49721.17667 56298.33289 53133.41365 48479.17116 68527.39593 42718.57677 62837.90307 51450.36779 60041.948 0.82810732 0.937650006 0.884938204 0.807421691 1.141325327 0.711478861 1.046566695 0.856907038 1 15.87368316 7.99999998 0.058012889 1.120856287 0.487028872 0.076249694 0.120319864 927.7219155 4.029579993 9.184979039 50.16081127 99999995.32 -7.99999998 -0.633827415 IGFPS(ph)TSPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGFPSTSPAK 10 0 Q9UDT6;Q9UDT6-2 Q9UDT6 CLIP2 CAP-Gly domain-containing linker protein 2 1 IGFPS(0.485)T(0.274)S(0.241)PAK 84.658 0.015494 49171000 245150 167610 166840 194520 159740 193900 239060 237900 174350 TRUE FALSE 233562.2453 184689.6496 174489.779 174966.48 187598.6054 187185.1944 202587.0064 217068.2148 201387.3075 1.159766463 0.91708684 0.86643881 0.868805895 0.931531424 0.929478608 1.005957172 1.077864427 1 17.61961323 1.549655117 4.52516285 1.040124895 0.952485655 0.181625389 0.083482839 0.327248797 14.75546349 0.054123065 0.023501235 35.45317361 -1.549655117 -0.08763924 IGFPSTS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGFPSTSPAK 10 0 Q9UDT6;Q9UDT6-2 Q9UDT6 CLIP2 CAP-Gly domain-containing linker protein 2 1 IGFPS(0.256)T(0.147)S(0.596)PAK 74.611 0.043504 51035000 309760 220140 206090 271640 193480 263630 311830 298190 208340 TRUE FALSE 295118.2587 242572.5163 215539.4304 244334.2311 227222.8507 254500.427 264254.6063 272078.9028 240648.3031 1.226346726 1.007995956 0.895661542 1.015316659 0.944211315 1.057561693 1.098094617 1.130608025 1 17.87656673 -0.334347244 7.722238084 1.00000001 1.04974554 0.023799688 0.093055045 0 0 0.092991437 0.021918292 0.463076514 0.334347244 0.04974553 IGFPWSEIR ddPTM_SK-BR-3_Trastuzumab_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 ; 169.97 0.00013507 919730000 613510 432420 375290 421270 636620 377570 632260 484400 579340 FALSE TRUE 584510.5982 476484.0896 392497.4177 378923.1392 747646.3264 364494.6562 535797.1247 441983.368 669181.0883 0.873471484 0.712040579 0.586533936 0.566249026 1.117255612 0.544687623 0.800675832 0.660483949 1 19.35203715 IGGIFAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGGIFAFK 8 0 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 114.54 0.006134 23917000 188420 167400 147480 168870 360890 119830 216110 149940 328010 FALSE TRUE 179513.76 184458.2503 154242.1039 151894.8668 423829.1017 115680.2571 183138.4504 136810.4587 378876.1156 0.473805956 0.48685637 0.407104321 0.400909058 1.118648245 0.305324755 0.48337291 0.361095496 1 18.53136667 -1.779297611 2.932608708 1.111920426 0.503128149 0.321942199 0.225917536 40224871.92 23592821.1 31674283.6 0.050213969 0.016622731 1.779297611 -0.608792276 IGGIGTVPVGR ddPTM_SK-BR-3_Trastuzumab_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 ; 129.38 0.00057254 1464230000 1237960 966840 1009360 1125740 1092660 1025370 1321750 1167610 1275480 FALSE TRUE 1179444.084 1065362.095 1055640.154 1012578.476 1283219.558 989861.1798 1120092.762 1065367.879 1473274.924 0.800559397 0.723125112 0.716526248 0.687297707 0.870998031 0.671878116 0.760274097 0.723129038 1 20.49059524 -2.186177569 2.350047058 1.698799896 0.744866159 0.662387607 0.057385731 5480104.667 908456.9263 20458077.62 0.012398014 0.00651362 2.186177569 -0.953933738 IGGVQQDTILAEGLHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IGGVQQDTILAEGLHFR 17 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2 Q99623-2 PHB2 Prohibitin-2 0 ;; 196.66 1.58E-11 778070000 540294 436017 437644 483544 500577 382887 470375 474944 429794 FALSE TRUE 514755.3734 480447.628 457710.4103 434937.2384 587877.4703 369627.5272 398610.6547 433355.3855 496444.2584 1.036884534 0.96777759 0.921977448 0.876104882 1.18417619 0.744549908 0.802931342 0.872918516 1 18.92127221 2.208567987 24.99999886 0.831485929 0.987997798 0.304511237 0.103628883 215.6911306 179785.5172 0.035688906 0.026361437 161.6471258 -2.208567987 0.156511869 IGHHS(ph)TSDDSSAY(ph)RSVDEVNYWDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGHHSTSDDSSAYRSVDEVNYWDK 24 1 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.584)T(0.22)S(0.197)DDS(0.007)S(0.006)AY(0.869)RS(0.119)VDEVNYWDK 174.05 7.06E-12 197770000 216130 174560 199340 193080 168630 167860 210410 165170 69319 TRUE FALSE 205913.9632 192347.8625 208479.9362 173671.2316 198039.0186 162046.9661 178308.0901 150706.8392 80068.63649 2.571718119 2.402287224 2.603765286 2.169029463 2.473365693 2.023850701 2.226940509 1.882220627 1 16.28894962 -0.54255153 0.261483368 0.32776029 2.613211045 0.913683857 0.137397054 2.392569527 0.191521425 1.490613622 0.187684351 0.286713716 0.54255153 2.285450755 IGHHS(ph)TSDDSSAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IGHHSTSDDSSAYR 14 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 IGHHS(0.631)T(0.369)SDDSSAYR;IGHHS(0.98)T(0.018)S(0.003)DDSSAYR;IGHHS(0.977)T(0.022)SDDSSAYR;IGHHS(0.97)T(0.029)S(0.001)DDSSAYR;IGHHS(0.96)T(0.039)SDDSSAYR 176.42 1.44E-06 6601460000 4886120 4833910 4625420 5168470 4307520 4340220 4542020 4159740 1221892 TRUE FALSE 4655162.791 5326490.925 4837500.082 4648925.576 5058750.124 4189917.093 3849051.429 3795491.113 1411376.771 3.298313312 3.77396811 3.427504393 3.29389407 3.584266249 2.968673695 2.727160818 2.689211833 1 20.42867174 0.618230781 0.491448103 0.877495214 3.575031536 0.945069067 0.182622403 0.327879138 0.159105102 0.262785242 0.095044153 4.15174605 -0.618230781 2.697536321 IGHHS(ph)TSDDSSAYRS(ph)VDEVNYWDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IGHHSTSDDSSAYRSVDEVNYWDK 24 1 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.956)T(0.034)S(0.011)DDS(0.114)S(0.281)AYRS(0.606)VDEVNYWDK;IGHHS(0.743)T(0.192)S(0.065)DDS(0.007)S(0.018)AY(0.405)RS(0.571)VDEVNYWDK;IGHHS(0.922)T(0.036)S(0.042)DDSS(0.002)AY(0.373)RS(0.625)VDEVNYWDK 227.4 5.90E-33 501720000 549410 452930 519780 555410 446250 444422 555920 469026 153785 TRUE FALSE 523440.4781 499084.0819 543612.4271 499579.1316 524075.8587 429031.5547 471104.1938 427955.597 177633.1924 2.94674926 2.809633015 3.06030883 2.812419936 2.950326185 2.415266815 2.652118039 2.409209626 1 17.43854166 -0.331464224 0.385692067 0.556647573 2.959345431 0.950003967 0.132576236 1.253230677 0.202631383 0.874511256 0.087082064 0.466160827 0.331464224 2.402697858 IGHHS(ph)TSDDSSAYRS(ph)VDEVNYWDKQDHPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGHHSTSDDSSAYRSVDEVNYWDKQDHPISR 31 2 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.999)T(0.001)SDDS(0.002)S(0.002)AYRS(0.996)VDEVNYWDKQDHPISR 227.37 4.93E-35 221640000 111570 46166 115860 92639 135870 79690 157320 92234 26257 TRUE FALSE 106296.3072 50870.36789 121172.2956 83326.75172 159565.685 76930.31532 133317.9446 84157.502 30328.80146 3.50479749 1.677295687 3.99528797 2.747446246 5.261193233 2.536543207 4.395753812 2.77483771 1 14.88840087 3.722249667 24.81358798 3.459077873 2.591046444 0.023893767 1.245218571 1570.120658 2388599.575 0.289503584 0.449974096 5275.330417 -3.722249667 -0.868031429 IGHHST(ph)SDDSSAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGHHSTSDDSSAYR 14 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 IGHHS(0.379)T(0.619)S(0.002)DDSSAYR 182.7 5.49E-06 320540000 437410 429200 427580 426190 391150 392230 450490 383910 214290 TRUE FALSE 416734.4962 472935.968 447184.9659 383348.5715 459366.4362 378646.9768 381759.4767 350292.8052 247520.9988 1.683632897 1.910690286 1.80665466 1.548751716 1.855868546 1.529756985 1.542331675 1.415204394 1 17.9171914 0.920533374 0.502744968 0.974480533 1.804664385 0.831597355 0.10731307 0.393004701 0.241690241 0.119776795 0.05471421 8.327859205 -0.920533374 0.830183852 IGHHSTS(ph)DDS(ph)SAYRSVDEVNYWDKQDHPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGHHSTSDDSSAYRSVDEVNYWDKQDHPISR 31 2 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.279)T(0.342)S(0.377)DDS(0.369)S(0.331)AY(0.129)RS(0.173)VDEVNYWDKQDHPISR 88.346 0.00033017 58123000 51906 26951 52936 41776 45108 37905 56901 43664 50574 TRUE FALSE 49452.50625 29697.33754 55363.16796 37576.59711 52974.82092 36592.34035 48219.70739 39840.54868 58416.75762 0.846546578 0.508370179 0.947727505 0.643250304 0.906842883 0.626401427 0.825443064 0.682005478 1 15.83409466 -5 0.342553239 3.838895944 0.73201443 0.239168514 0.137814631 530.5791271 4.437150088 1103.049137 0.095823304 1.00E-05 5 -3.106881514 IGHKVESESYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IGHKVESESYR 11 1 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ;; 147.71 2.11E-05 298039000 250476 128833 206691 182428 203261 193964 326408 222518 251324 FALSE TRUE 238636.4959 141961.2292 216167.9868 164089.9908 238709.654 187246.978 276608.4647 203033.1443 290298.0423 0.822039632 0.489018899 0.744641559 0.565246632 0.822291642 0.645016331 0.952843025 0.699395499 1 18.14717532 1.437407799 0.577650185 0.978788533 0.647324055 0.352511279 0.1286089 0.707648039 0.567738934 0.11521981 0.059765796 27.37838325 -1.437407799 -0.331464478 IGHPAPNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 144.38 9.97E-05 21931820000 15937970 12679670 12898670 14709980 11779700 14022980 16799910 14431850 11697630 FALSE TRUE 15184613.74 13971742.79 13490086.78 13231304.86 13834075.95 13537360.69 14236775.18 13168120.71 13511638.72 1.12381733 1.034052426 0.998404935 0.979252416 1.023863666 1.00190369 1.053667544 0.97457614 1 23.68769932 4.387649839 1.813762944 1.009169533 1.127839498 0.725711881 0.022782781 0.231829888 1.244572229 0.006030634 0.037212369 24414.6127 -4.387649839 0.118669965 IGIIGGTGLDDPEILEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 97.121 0.0034108 30700400 108851 95767 99856 106876 96714 97038 118561 112347 116569 FALSE TRUE 103705.829 105525.7662 104434.4964 96132.62143 113580.891 93677.54973 100472.3419 102509.3011 134645.9252 0.770211418 0.783727885 0.775623148 0.713966066 0.843552383 0.695732527 0.746196677 0.761324941 1 17.03881104 -0.474947086 7.449341346 1 0.76124566 0.779582441 0.039889783 0 0 0.035134778 0.008281347 0.335006253 0.474947086 -0.23875434 IGITNHDEYSLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGITNHDEYSLVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 208.68 4.40E-08 620790000 758800 645320 595670 692700 712640 625040 765860 667800 667600 FALSE TRUE 722933.0278 711078.8417 622982.0587 623068.48 836924.1904 603394.7081 649013.991 609323.8918 771127.9984 0.937500686 0.922128159 0.807884113 0.807996184 1.085324605 0.782483206 0.841642363 0.79017218 1 19.55661083 IGKPAPDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGKPAPDFK 9 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 117.67 0.0010155 9698000000 18724700 16092600 17713000 20781600 13640500 21645100 24021100 22684000 16236200 FALSE TRUE 17839620.54 17732454.24 18525158.57 18692594.09 16019398.88 20895524.76 20356240.02 20697668.7 18754026.97 0.951242129 0.94552782 0.987796306 0.996724283 0.854184486 1.114188691 1.085433014 1.103638634 1 24.16069708 2.219184773 24.9999988 1.084318452 0.951364228 0.631765768 0.048578907 138.2710309 178405.3252 0.016404106 0.012133325 165.6474569 -2.219184773 -0.132954224 IGKPHTVPCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGKPHTVPCK 10 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 110.14 0.0011573 3939500000 16571800 14716000 14180000 17067600 11674200 15557800 17354600 17608900 12519600 FALSE TRUE 15788483.86 16215577.13 14830167.03 15351932.42 13710176.78 15019029.48 14706837.03 16066971.37 14461075.63 1.091791805 1.121325795 1.025523094 1.061603771 0.948074482 1.038583151 1.016994684 1.111049536 1 23.78567153 3.732783422 24.50109783 1.027520221 1.106558801 0.371460968 0.042006766 308.6487415 1308984.428 0.010272228 0.016432951 5404.847223 -3.732783422 0.07903858 IGLDDEEKLDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 224.05 1.35E-11 321912000 985989 919476 812182 1078327 674896 957331 957173 1047565 665872 FALSE TRUE 939383.254 1013171.65 849421.3481 969931.5213 792597.6487 924178.3874 811138.6792 955834.6551 769132.029 1.221355006 1.317292235 1.104389515 1.261072852 1.030509222 1.201586142 1.054615656 1.242744573 1 19.55287175 7.999999966 0.075873 0.852001796 1.971159238 0.318910498 0.088654815 199.0018325 1.10647459 2.612774777 23.49705994 99999992.11 -7.999999966 1.119157442 IGLEVDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGLEVDRR 8 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 160.75 0.0005637 193514000 273020 236470 217800 249230 282430 232000 320310 272730 306940 FALSE TRUE 260114.8857 260566.5618 227786.3454 224176.9269 331685.7026 223965.7818 271440.8266 248848.3154 354538.6876 0.733671373 0.734945356 0.64248657 0.632305965 0.935541633 0.631710416 0.765616944 0.70189326 1 18.43558354 -4.999999093 0.437202403 6.721934024 0.720446799 0.49140996 0.088720984 924.3046094 5.623678385 5104.23641 0.043990843 1.00E-05 4.999999093 -6.001487224 IGLIHGHQVIPWGDMASLALLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGLIHGHQVIPWGDMASLALLQR 23 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 194.18 2.24E-18 282250000 296510 344270 280930 345580 317140 290530 355010 311310 124687 FALSE TRUE 282494.5599 379351.5044 293810.9184 310841.6418 372449.1156 280468.8733 300846.7043 284050.046 144022.8231 1.961456898 2.633967979 2.040030267 2.158280438 2.586042319 1.947391859 2.088882149 1.972257173 1 17.13593793 0.2683414 0.613869871 0.950203071 2.275797794 0.731802571 0.229546106 1.269544678 0.676542931 0.355094265 0.086426677 1.854989262 -0.2683414 1.325594722 IGNFLNYGSHTGDADGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGNFLNYGSHTGDADGFK 18 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 105.77 0.00046817 230470000 183920 209440 183630 203530 131600 189410 200670 210840 133900 FALSE TRUE 175226.4661 230782.1741 192049.6171 183070.7777 154550.9983 182850.6842 170054.1059 192377.7319 154664.5281 1.132945403 1.492146757 1.24171728 1.183663636 0.999265961 1.182240598 1.099502956 1.24383874 1 17.23878283 3.246773886 3.007277913 1.116061054 1.317276225 0.349622446 0.113693796 0.244390582 4.550686568 0.031637776 0.04195302 1765.118577 -3.246773886 0.201215171 IGNLQTDLSDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGNLQTDLSDGLR 13 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 137.62 0.00013632 50051000 89030 76083 56338 78455 91336 58907 102890 83731 108320 FALSE TRUE 84821.72834 83835.9442 58921.15303 70568.55435 107264.9695 56867.03582 87192.2408 76399.06975 125117.7124 0.677935416 0.670056562 0.470925754 0.5640173 0.857312426 0.454508277 0.696881674 0.61061754 1 16.93292651 -1.53665947 2.469920421 1.026504695 0.630250746 0.50757073 0.115900928 3448470.091 3081093.512 607135.6121 0.026842581 0.029063006 1.53665947 -0.396253948 IGPLGLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IGPLGLSPK 9 0 P30050 P30050 RPL12 60S ribosomal protein L12 1 IGPLGLS(1)PK;IGPLGLS(1)PK;IGPLGLS(1)PK;IGPLGLS(1)PK 136.94 0.00018736 398609000 1459800 1470830 1340570 1681600 880540 1709180 1765540 1911180 1040320 TRUE FALSE 1390798.147 1620709.249 1402036.461 1512562.373 1034105.897 1649990.668 1496174.447 1743826.947 1201647.512 1.157409417 1.34873932 1.166761838 1.258740486 0.86057341 1.373107048 1.245102604 1.451196736 1 20.19658233 IGRPGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGRPGYK 7 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 83.801 0.020076 606780000 1510570 1265350 1195230 1426540 1167690 1366170 1697400 1546550 1401440 FALSE TRUE 1439168.35 1394290.604 1250032.478 1283141.489 1371334.766 1318859.19 1438430.455 1411125.883 1618768.158 0.889051556 0.861328163 0.772212174 0.792665388 0.84714711 0.814730129 0.888595719 0.871728219 1 20.62646494 0.691929374 0.969853103 0.99939365 0.835924214 0.675677747 0.035945548 0.697294248 1.148843629 0.037351063 0.012170381 4.919595258 -0.691929374 -0.163469436 IGRPSETGIIGIIDPECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IGRPSETGIIGIIDPECR 18 1 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 152.71 3.51E-08 377719000 542067 470662 491777 547575 474106 528399 569094 558347 540770 FALSE TRUE 516444.5672 518622.9929 514325.4619 492531.7207 556789.9363 510100.4101 482268.2582 509455.1767 624629.8497 0.826800972 0.830288519 0.823408395 0.788517745 0.891391816 0.816644306 0.772086474 0.815611321 1 19.25264199 -1.021314429 6.099730135 1.000000194 0.819367132 0.769073507 0.030888852 8.10E-08 1.30E-08 0.029758984 0.007014252 0.095210659 1.021314429 -0.180633062 IGSIS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IGSISR 6 0 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 IGSIS(1)R;IGSIS(1)R 106.14 0.033961 258080000 319950 289290 286970 335720 375930 329790 357170 301420 364140 TRUE FALSE 304826.5976 318768.9799 300127.8584 301972.7878 441492.073 318369.2896 302677.1566 275026.0669 420608.9714 0.724726809 0.757874895 0.713555532 0.717941861 1.049649682 0.756924629 0.719616502 0.653875893 1 18.6821201 IGTLQDRPPS(ph)PFREPPGSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;IGTLQDRPPS(1)PFREPPGSER 105.79 0.00013091 524089000 755801 664070 598100 752907 648968 645958 759727 704472 739662 TRUE FALSE 720075.7846 731739.488 625523.4766 677223.3579 762147.8137 623588.3125 643816.6928 642784.697 854365.0053 0.842819849 0.856471746 0.732150161 0.792662801 0.892063473 0.729885129 0.753561638 0.752353728 1 19.70449303 3.805392839 24.9934214 0.793133835 0.849645912 0.020174275 0.084078327 450.1855442 168354.8009 0.019435414 0.035037688 6388.410858 -3.805392839 0.056512077 IGVDHVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGVDHVAR 8 0 Q7L5N1;E7EM64;H7C3T0 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 182.39 0.00022882 208430000 288210 268350 217770 242350 242010 233000 259040 266550 247080 FALSE TRUE 274586.8845 295695.1701 227754.9699 217988.5176 284216.4674 224931.1516 219518.6904 243209.4689 285395.9045 0.962126226 1.036087643 0.798031669 0.763810952 0.995867365 0.788137279 0.769172532 0.852182758 1 18.12260511 3.7390236 24.99999316 0.837170122 0.99910694 0.316854428 0.087305463 37.6506173 2033004.263 0.021370111 0.035740062 5483.067602 -3.7390236 0.161936818 IGVLDEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IGVLDEGK 8 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 107.9 0.0091081 64207000 140210 141550 140360 156010 117220 156670 175080 167470 130450 FALSE TRUE 133582.5512 155974.1059 146795.6448 140327.5784 137663.1309 151244.4786 148368.3304 152805.439 150679.5198 0.886534224 1.035138061 0.974224268 0.931298285 0.913615408 1.003749407 0.984661556 1.01410888 1 17.20112381 2.198199914 24.99800395 0.997934915 0.95483794 0.292051006 0.039747267 246.4482749 152639.9556 0.015170188 0.011204065 157.8337642 -2.198199914 -0.043096974 IHAEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHAEIK 6 0 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 106.84 0.03178 172330000 493960 389240 351820 477400 360900 404190 493680 486320 308150 FALSE TRUE 470611.4897 428903.9985 367951.295 429410.845 423840.8457 390192.799 418360.0489 443735.2427 355936.3282 1.322178863 1.205002031 1.033755944 1.206426012 1.190777148 1.096243255 1.175378897 1.246670282 1 18.44125966 8 0.019224021 1.81E-08 2.666188855 0.346999462 0.078361989 3846.976081 5.70314375 296.6324132 524.1929572 99999999.97 -8 2.666188837 IHAENAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHAENAIR 8 0 Q7LBR1 Q7LBR1 CHMP1B Charged multivesicular body protein 1b 0 66.299 0.062043 557090000 360180 423730 688860 827710 266330 667840 391330 629050 329050 FALSE TRUE 343155.0052 466908.5687 720444.9124 744507.0183 312777.8677 644712.5333 331625.4212 573967.0472 380077.3934 0.902855606 1.228456564 1.895521609 1.958830046 0.822932048 1.696266456 0.872520773 1.510132034 1 18.53593369 1.72891981 25 1.130467117 1.372427782 0.094540694 0.40732748 2.402182313 6197.647569 0.189436058 0.105051939 53.56977343 -1.72891981 0.241960665 IHDDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHDDLK 6 0 A0A669KBH7;A0A669KB27;A0A669KB18;A0A669KAY5;O95620-2;O95620 A0A669KBH7 DUS4L tRNA-dihydrouridine(20a/20b) synthase [NAD(P)+]-like 0 101.33 0.036648 134280000 202860 179250 197890 197330 145770 260950 237490 255870 125870 FALSE TRUE 193271.2098 197515.7788 206963.4522 177494.0135 171192.2418 251913.2361 201256.5387 233464.6663 145389.2767 1.32933607 1.358530582 1.423512496 1.220819152 1.177475022 1.732680991 1.384259852 1.605790135 1 17.14956134 IHDENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IHDENLR 7 0 O95232;J3KPP4;D6RDI2 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 194.25 0.00048478 834570000 660650 593600 649726 738510 655251 691835 755740 725450 579327 FALSE TRUE 629422.3838 654088.5149 679516.5798 664273.5717 769526.5669 667876.5805 640437.9829 661925.7521 669166.0724 0.940607137 0.977468138 1.015467771 0.99268866 1.149978456 0.998072987 0.957068819 0.989180085 1 19.35200478 4.046764848 1.83730081 1.013467157 0.945096409 0.186996017 0.050951493 0.634894585 4.101956395 0.014674688 0.045981834 11136.91353 -4.046764848 -0.068370748 IHDPQLLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IHDPQLLTER 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;; 158.3 8.03E-06 1885410000 1588340 1329140 1279550 1512320 1611000 1385950 1692110 1438560 1195580 FALSE TRUE 1513262.316 1464580.877 1338218.633 1360298.72 1891957.89 1337954.204 1433947.542 1312592.06 1380984.44 1.095785204 1.060533946 0.969032376 0.985021033 1.370006667 0.968840897 1.0383517 0.950475633 1 20.39726563 IHEAAVQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IHEAAVQELR 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;; 145.75 2.99E-05 627570000 362034 315543 301981 355000 389240 308592 398710 345576 307448 FALSE TRUE 344921.3703 347697.1904 315827.1275 319314.7255 457123.3328 297905.3817 337879.4667 315315.5334 355125.4656 0.971266225 0.979082674 0.889339566 0.899160315 1.287216426 0.838873611 0.951436885 0.887898965 1 18.43796929 IHEDIFDIIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IHEDIFDIIDR 11 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;;;; 199.7 4.94E-08 518419000 662263 746919 617218 768474 564651 634868 708452 657282 339131 FALSE TRUE 630959.1405 823030.8953 645518.0558 691225.5335 663125.9556 612882.362 600364.6358 599726.9036 391721.7034 1.610733168 2.101060238 1.647899644 1.764583191 1.692849668 1.564586176 1.532630514 1.531002491 1 18.57946954 0.627587717 0.350189637 0.903673577 1.867540112 0.748475222 0.135761944 1.074574657 0.294691093 0.332484208 0.127855233 4.24216657 -0.627587717 0.963866535 IHEGCEEPATHNALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IHEGCEEPATHNALAK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 288.12 1.12E-36 2166930000 3218020 3176430 3326070 4007280 2661850 3846720 4340990 3762700 747115 FALSE TRUE 3065910.572 3500111.828 3478573.599 3604460.601 3126075.797 3713507.122 3678692.248 3433218.041 862973.7785 3.552727381 4.055872746 4.030914596 4.176790409 3.622445867 4.303151746 4.262808836 3.978357311 1 19.7189572 0.906148201 21.63214584 1.000000005 4.006101883 0.936784518 0.244745864 10121.55847 2332947.586 0.241940344 0.060485086 8.056533204 -0.906148201 3.006101879 IHEKDPNSATATAPPS(ph)PLKR ddPTM_SK-BR-3_Trastuzumab_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;IHEKDPNS(0.006)AT(0.004)AT(0.007)APPS(0.983)PLKR 198.55 8.06E-22 390380000 495210 481810 424200 554020 251496 543520 519880 496840 180031 TRUE FALSE 471802.4047 530906.9868 443649.9896 498328.857 295356.8228 524697.7661 440562.7577 453334.0557 207949.288 2.268833951 2.553059892 2.133452794 2.396396072 1.420331012 2.52320059 2.118606714 2.180022158 1 17.66587222 -1.704510542 0.325244935 2.53E-15 2.320614284 0.590290099 0.314310886 18.29309756 1.059214833 15.09776234 0.265200934 0.019746469 1.704510542 2.320614284 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR 39 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 219.07 9.64E-40 129580000 18219 16823 12994 17363 18624 15524 17554 16909 9292 FALSE TRUE 17357.82398 18537.28283 13589.78775 15617.63825 21872.0197 14986.39999 14875.8149 15428.35832 10732.9559 1.617245439 1.727136773 1.266173818 1.455110632 2.03783747 1.396297546 1.385994225 1.437475236 1 13.38975983 0.837469683 0.729823381 1.001935958 1.607676381 0.424165313 0.209424395 0.852921364 0.96105114 0.202285042 0.075290648 6.878118955 -0.837469683 0.605740423 IHFPLATYAPVISAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 268.59 1.52E-27 7522700000 5640400 5030800 4955900 5768900 4361900 5443900 6309900 5937300 3727000 FALSE TRUE 5373789.47 5543444.24 5183132.917 5188999.212 5122613.979 5255376.378 5347208.866 5417398.536 4304964.125 1.24827741 1.287686512 1.203989805 1.205352486 1.189931862 1.220771236 1.242103003 1.258407359 1 22.03756978 -1.413785771 3.187625241 0.996820468 1.235135053 0.862317601 0.029118924 4191856.455 4801387.853 118034.0723 0.007734636 0.038566855 1.413785771 0.238314585 IHFVPGWDCHGLPIEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHFVPGWDCHGLPIEIK 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 136.81 5.24E-06 352720000 561190 466750 478930 467550 382130 451460 520540 535630 142890 FALSE TRUE 534663.6609 514312.3557 500889.4142 420550.9857 448773.351 435825.827 441122.0626 488727.3976 165048.6514 3.239430654 3.116125768 3.034798588 2.548042544 2.719036764 2.640590052 2.672678988 2.961111124 1 17.33253183 -1.12156773 0.292287041 3.01E-18 3.120893317 0.875371658 0.221627062 5.488784209 0.375906222 5.112565534 0.264297089 0.075584417 1.12156773 3.120893317 IHGVGFK ddPTM_SK-BR-3_Trastuzumab_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 2196210000 8359000 7748900 7163100 9053000 6552700 7979000 9152500 8072100 4816500 FALSE TRUE 7963886.636 8538521.72 7491535.22 8142975.24 7695488.805 7702685.229 7756118.028 7365264.131 5563418.221 1.431473659 1.534761792 1.346570566 1.463664049 1.383230327 1.384523853 1.394128164 1.323873892 1 22.40754013 -3.487043551 0.20690905 1.31E-09 1.494633473 0.887700719 0.047356637 19.81982423 0.34593522 8.479635661 0.099919308 0.000325804 3.487043551 1.494633472 IHGVGFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHGVGFKK 8 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 121.52 0.00092812 254830000 1061500 637420 933530 864890 962930 977210 1564600 1143100 893420 FALSE TRUE 1011324.999 702373.8227 976333.2739 777949.614 1130864.687 943368.9727 1325891.534 1043004.104 1031967.011 0.979997411 0.680616546 0.946089617 0.753851243 1.095834145 0.914146444 1.284819689 1.0106952 1 19.97696542 2.728569079 24.65803089 1.083319756 0.834977696 0.421490596 0.127095942 475.260066 1172888.033 0.038499816 0.036700533 535.2652867 -2.728569079 -0.24834206 IHIPEPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IHIPEPDLR 9 0 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 0 ;;; 96.331 0.0059812 145758000 340971 305423 303220 368330 349626 305920 376729 333578 258104 FALSE TRUE 324853.9766 336545.9509 317122.9369 331304.7686 410600.6637 295325.9137 319252.0719 304368.1419 298129.4501 1.089640679 1.128858457 1.063708858 1.111278233 1.377256301 0.990596245 1.070850504 1.020926117 1 18.18557937 IHLAQSLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHLAQSLHK 9 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 117.53 0.0006577 210640000 568440 385990 192950 256380 705280 335160 917680 493690 158460 FALSE TRUE 541570.9677 425322.8198 201796.9484 230608.1953 828280.6087 323553.3252 777671.0617 450459.8864 183033.1675 2.958867921 2.323747251 1.102515741 1.25992572 4.525303365 1.767730568 4.248798577 2.461083379 1 17.48174558 2.771950889 24.99667508 3.015686725 2.051481463 0.106439594 1.161993407 1208.314193 904567.7849 0.329158841 0.349107549 591.4947431 -2.771950889 -0.964205262 IHLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 IHLDEK 6 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;;; 166.13 0.0070625 11489640000 21485290 18379040 18057690 21060050 15201710 20290450 23380570 20739290 10328960 FALSE TRUE 20469722.92 20251885.07 18885652.95 18943053.76 17852883.41 19587786.63 19813434.63 18923247.82 11930722.36 1.715715302 1.697456738 1.582942958 1.587754135 1.496379085 1.641793852 1.660707041 1.586094056 1 23.50817806 -2.485239334 0.391542558 3.47E-17 1.651857762 0.906672259 0.062693794 22.10744108 0.992333835 18.96027388 0.044867618 0.003271604 2.485239334 1.651857762 IHLGSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 IHLGS(0.01)S(0.99)PK;IHLGS(0.017)S(0.983)PK;IHLGS(0.01)S(0.99)PK;IHLGS(0.026)S(0.974)PK;IHLGS(0.017)S(0.983)PK;IHLGS(0.025)S(0.975)PK 121.41 0.00092391 1980640000 4207900 4035950 4064520 4732480 2625070 4620250 4920390 4640720 1754730 TRUE FALSE 4009000.906 4447217.893 4250882.262 4256762.119 3082881.377 4460249.584 4169694.136 4234353.955 2026844.566 1.977951824 2.194158332 2.097290701 2.100191692 1.521025059 2.200587878 2.057234287 2.089136002 1 20.95080403 IHMGSCAENTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IHMGSCAENTAK 12 0 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ;; 138.63 5.39E-05 60861000 352300 275791 314520 345366 293192 302269 356254 337983 270799 FALSE TRUE 335647.4772 303894.4164 328941.0531 310649.1535 344324.592 291801.3487 301900.9092 308387.4168 312793.1259 1.073065389 0.971550815 1.051624943 0.993145718 1.100806135 0.932889263 0.96517757 0.985914943 1 18.25484928 2.21619337 24.99999944 0.966523855 1.030733347 0.396358091 0.040392302 236.1994327 263999.8438 0.013883058 0.0102606 164.5104045 -2.21619337 0.064209492 IHNAENIQPGEQKYEYK ddPTM_SK-BR-3_Trastuzumab_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 ; 270.96 8.09E-36 391080000 1534520 1331680 1407210 1640590 843660 1647180 1720590 1641050 652510 FALSE TRUE 1461986.281 1467379.706 1471731.97 1475674.776 990794.0369 1590137.744 1458082.395 1497350.962 753697.9182 1.939750987 1.946906938 1.952681485 1.957912767 1.314577118 2.10978126 1.934571344 1.986672546 1 19.52362688 IHNFGLIQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHNFGLIQEK 10 0 P49748;P49748-3;P49748-2;J3KSR4 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ; 136.02 0.00012868 959710000 1825300 1501800 1209950 1328580 1321940 1229340 1712220 1547320 944590 FALSE TRUE 1739021.686 1654835.127 1265427.404 1195028.614 1552485.917 1186767.648 1450989.392 1411828.458 1091072.193 1.593864914 1.516705437 1.159801718 1.095279141 1.422899353 1.08770772 1.329874779 1.293982623 1 20.05731513 3.804119801 5.177917756 1.217141336 1.562549469 0.57531885 0.126950567 0.13334365 7.091521124 0.029845455 0.054407429 6369.712063 -3.804119801 0.345408133 IHNQNNEQAWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHNQNNEQAWK 11 0 P53701 P53701 HCCS Cytochrome c-type heme lyase 0 103.44 0.002734 42357000 214620 137450 232520 220770 198510 205700 307550 252770 195700 FALSE TRUE 204475.3379 151456.3113 243181.272 198577.7802 233130.0811 198576.5574 260627.599 230636.1188 226048.1565 0.904565386 0.670017901 1.075794095 0.878475557 1.031329274 0.878470148 1.152973787 1.020296393 1 17.78627063 3.730567904 24.99924718 1.008537013 0.787291641 0.457937769 0.098576425 440.1878579 1376799.736 0.024934668 0.039396678 5377.345034 -3.730567904 -0.221245372 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IHPMAYQLQLQAASNFKSPVK 21 1 P67870;Q5SRQ6 P67870 CSNK2B Casein kinase II subunit beta 1 IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAAS(0.032)NFKS(0.968)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK 340.62 8.35E-81 4902587000 7042120 6432630 6609200 7587040 4008345 7819790 7930070 9073330 4862110 TRUE FALSE 6709252.944 7088122.31 6912238.357 6824376.325 4707399.099 7548988.712 6720192.176 8278821.124 5616101.187 1.194646022 1.262107301 1.230789498 1.215144831 0.838196988 1.344168928 1.196593856 1.474122501 1 22.4211375 -0.276072777 7.143146413 0.999999462 1.214855363 0.156964612 0.159527638 9576181.337 1340611.026 0.141393626 0.034292991 0.529574693 0.276072777 0.214855901 IHPQTIIAGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHPQTIIAGWR 11 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 157.68 3.05E-05 735970000 375440 280820 207526 277000 409680 263930 420660 356220 400160 FALSE TRUE 357693.6953 309435.8773 217041.2724 249155.4337 481128.0623 254790.0379 356480.591 325027.4884 462214.7691 0.773869031 0.669463414 0.469568017 0.53904689 1.040918842 0.551237336 0.771244484 0.703195809 1 18.81820383 IHPTSVISGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHPTSVISGYR 11 0 P17987;E7ERF2;F5H136;F5H676 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 172.61 1.32E-05 1851810000 506350 476030 499420 534350 680690 479260 657480 552310 660960 FALSE TRUE 482415.839 524537.9982 522318.901 480636.1228 799402.1205 462663.106 557169.3506 503946.8084 763458.3011 0.631882368 0.687055203 0.684148565 0.629551243 1.047080265 0.606009661 0.729796702 0.660084261 1 19.54218984 -5 0.254040807 2.791858633 0.68148455 0.340610515 0.125835567 210.4713171 2.078754957 196.7124903 0.161938447 1.00E-05 5 -2.110374084 IHPVSTMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHPVSTMVK 9 0 A0A5F9ZHM4;P07195;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 62.463 0.062544 509820000 445230 542510 339360 446560 426420 453130 466860 517020 369720 FALSE TRUE 424184.8603 597792.3858 354919.9917 401670.9404 500787.513 437437.9945 395631.9325 471746.9879 427054.2893 0.99328088 1.399804195 0.831088694 0.940561775 1.172655387 1.024314719 0.926420697 1.104653436 1 18.70405996 3.732223042 24.99994223 0.998647126 1.196542538 0.271254923 0.133946054 574.4304621 2265966.765 0.034042304 0.054167646 5397.877717 -3.732223042 0.197895412 IHQESELHSYLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHQESELHSYLSR 13 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 203.32 5.02E-08 558050000 216555 166747 178096 223442 256158 176395 248622 182801 107335 FALSE TRUE 206318.8743 183738.7089 186261.8778 200981.1856 300831.8741 170286.3969 210690.1476 166793.9754 123979.9636 1.664130786 1.482003249 1.502354674 1.621077953 2.426455577 1.37349933 1.699388688 1.345330088 1 16.91974746 0.976007673 2.062774051 0.998693574 1.670537437 0.384546961 0.28502692 0.365959326 3.353731377 0.258039338 0.071808068 9.46253879 -0.976007673 0.671843863 IHQETFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHQETFGK 8 0 Q15393;Q15393-2;J3QL37 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 138.4 0.00070713 501140000 1567750 1428770 1440870 1686030 1236900 1524780 1768660 1556530 964920 FALSE TRUE 1493645.564 1574363.287 1506935.315 1516547.061 1452614.968 1471976.486 1498818.433 1420231.982 1114554.865 1.340127445 1.412548934 1.352051264 1.360675107 1.303314008 1.320685533 1.344768642 1.274259371 1 20.08803621 -3.696420796 0.244900798 7.99E-16 1.384507644 0.943550415 0.026712559 17.84301684 0.316707053 8.935236598 0.040045897 0.000201177 3.696420796 1.384507644 IHQIGPGMVQQIQSVCMECQGHGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHQIGPGMVQQIQSVCMECQGHGER 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 257.51 3.61E-45 255440000 27367 34533 34356 41134 43228 33442 53168 37031 23810 FALSE TRUE 26073.41615 38051.95196 35931.25658 36999.13217 50766.94951 32283.89515 45056.2451 33788.36933 27502.3332 0.948043788 1.383589955 1.306480302 1.345308847 1.845914278 1.173860229 1.638269916 1.22856374 1 14.7472664 4.750126183 1.161575086 1.415614243 0.704763991 0.20948742 0.239529134 1.952807581 2.169158195 0.061330589 1.70512696 56250.4735 -4.750126183 -0.710850252 IHQPYTLTFAELVEDYEHYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHQPYTLTFAELVEDYEHYIK 21 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 115.76 8.44E-05 29781000 52606 58850 59611 58398 45272 54556 66968 55773 22929 FALSE TRUE 50119.41864 64846.88191 62344.22331 52527.72209 53167.42247 52666.71204 56750.80165 50889.22045 26484.71221 1.892390532 2.448464661 2.3539702 1.983322366 2.007475937 1.988570297 2.142775847 1.921456425 1 14.69287221 -1.767801177 0.332518975 6.32E-10 2.196806559 0.807924468 0.17020431 12.32569955 0.708250925 9.946653938 0.148185376 0.017068636 1.767801177 2.196806559 IHRAS(ph)DPGLPAEEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 120.31 8.67E-05 1519550000 2980980 3016760 2707240 3731690 1834214 3175710 3148710 3122580 1052923 TRUE FALSE 2840074.983 3324171.274 2831369.632 3356573.431 2154100.341 3065734.366 2668316.459 2849150.341 1216204.921 2.335194451 2.733232875 2.328036651 2.759874897 1.771165618 2.520738334 2.193969464 2.342656481 1 20.2139549 -1.479621642 0.317168863 4.36E-11 2.520693579 0.718274218 0.272709157 10.66538638 0.673747212 8.962127524 0.233922142 0.033141973 1.479621642 2.520693579 IHRAS(ph)DPGLPAEEPKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IHRASDPGLPAEEPKEK 17 2 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 IHRAS(1)DPGLPAEEPKEK;IHRAS(1)DPGLPAEEPKEK;IHRAS(1)DPGLPAEEPKEK;IHRAS(1)DPGLPAEEPKEK;IHRAS(1)DPGLPAEEPKEK;IHRAS(1)DPGLPAEEPKEK 188.24 2.20E-10 6089590000 7421590 4263410 7461580 6991350 4502449 7947700 10308090 8226320 2968241 TRUE FALSE 7070786.149 4697856.326 7803700.824 6288566.215 5287674.68 7672469.156 8735401.549 7505979.81 3428540.655 2.062331138 1.370220394 2.276099837 1.834181609 1.542252291 2.23782359 2.547848321 2.189263762 1 21.7091632 3.726410214 24.93576577 2.037892231 1.716275738 0.012221712 0.469464232 1748.144819 3587646.458 0.120178583 0.187770161 5326.111015 -3.726410214 -0.321616493 IHSEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHSEIVK 7 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 117.17 0.0052914 457800000 770450 736520 693830 827720 935120 738540 859870 847210 707830 FALSE TRUE 734032.3554 811572.2254 725642.7918 744516.013 1098204.632 712964.1746 728681.0389 773023.8011 817596.6613 0.897792751 0.992631531 0.887531501 0.91061528 1.343210759 0.872024322 0.891247572 0.94548307 1 19.64102978 -2.614994752 2.322952325 1.989256309 0.963127873 0.004503057 0.138183655 23741787.52 5380440.419 121112140.1 0.033438932 0.002426639 2.614994752 -1.026128436 IHSEVVEDTEAVSAVQQLLDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHSEVVEDTEAVSAVQQLLDDER 23 0 Q96GA7;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 158.37 2.13E-11 29301000 31667 28717 28149 33425 28804 27892 36642 28155 22853 FALSE TRUE 30170.16367 31643.29495 29439.65949 30065.0555 33827.40848 26926.09305 31051.58992 25689.59894 26396.92652 1.142942291 1.198749215 1.115268456 1.138960457 1.281490421 1.02004652 1.176333536 0.973204169 1 14.68808234 1.236743776 24.9982447 0.986601998 1.15418108 0.52655722 0.065750361 34.73876057 477909.5774 0.047818205 0.014321079 17.24819988 -1.236743776 0.167579083 IHTDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IHTDFEK 7 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;; 192.31 0.00051313 2304404000 4759960 4194031 4192240 4906760 3675070 4521034 5251410 4721690 2788042 FALSE TRUE 4534966.124 4621407.527 4384458.351 4413523.163 4316001.044 4364469.459 4450210.956 4308233.792 3220397.314 1.408200816 1.43504266 1.361465038 1.370490263 1.340207628 1.355258073 1.381882582 1.337795735 1 21.61880726 -3.398038518 0.279963406 3.96E-18 1.410204298 0.959824549 0.024285995 16.19281614 0.352202082 9.411166865 0.030825247 0.000399909 3.398038518 1.410204298 IHVFYIDYGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 192.12 1.53E-06 6048600000 6546000 5805400 5575000 6383600 6582400 5598800 7359000 5892800 4710300 FALSE TRUE 6236583.553 6396976.86 5830619.264 5741908.4 7730368.476 5404912.152 6236249.393 5376795.192 5440749.267 1.146272921 1.175752924 1.071657409 1.055352511 1.420827922 0.993413202 1.146211503 0.988245355 1 22.37537391 1.386437322 1.56854298 0.990987358 1.154748856 0.22115643 0.113373715 0.532658644 2.422206933 0.093355756 0.029370154 24.34654403 -1.386437322 0.163761499 IHVS(ph)DQELQSANASVDDSRLEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 IHVS(1)DQELQSANASVDDSRLEELK;IHVS(1)DQELQSANASVDDSRLEELK 232.47 2.05E-34 104439000 155392 133168 157822 163341 125024 164415 198593 181226 128311 TRUE FALSE 148046.9281 146737.9706 165058.2948 146921.6524 146828.146 158721.2673 168293.9904 165356.8907 148208.8146 0.998907714 0.990075867 1.113687437 0.991315212 0.990684302 1.07093001 1.135519442 1.115702134 1 17.17727173 2.066181627 5.319450064 1.099933151 1.015281531 0.261937921 0.050890611 0.200341323 10.87488669 0.018574802 0.013407506 116.4612983 -2.066181627 -0.08465162 IHVSDQELQSANASVDDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHVSDQELQSANASVDDSR 19 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 157.22 3.55E-10 0 60601 50552 50278 65310 56810 56139 68493 65089 59433 FALSE TRUE 57736.51083 55703.30627 52583.29603 58744.91472 66717.64601 54194.89235 58043.13489 59389.4621 68649.5661 0.841032422 0.811415271 0.76596691 0.855721573 0.971858233 0.789442606 0.845498933 0.865110524 1 16.06696298 -5 0.213254829 1.786730232 0.817349853 0.471072142 0.053610259 133.1938374 1.3292203 44.83344241 0.107512859 1.00E-05 5 -0.969380379 IHVSDQELQSANASVDDSRLEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 284.12 1.11E-52 435400000 594560 383310 567840 597120 611940 537550 917580 745800 620350 FALSE TRUE 566456.3271 422369.7248 593876.0257 537096.3631 718662.1423 518934.5087 777586.3185 680493.7983 716550.7097 0.790532086 0.589448477 0.828798322 0.749558065 1.002946662 0.724211841 1.085179748 0.949679889 1 19.45070928 2.619290354 0.746655642 1.006320462 0.690492864 0.480671501 0.109652895 0.488523951 0.570252906 0.07273917 0.062694654 416.1887671 -2.619290354 -0.315827598 IHWWENVYGFDMSCIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IHWWENVYGFDMSCIK 16 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;; 157.11 9.82E-08 206402000 649372 604035 430461 473251 499204 480145 715779 586581 325072 FALSE TRUE 618677.4725 665586.8532 450198.0626 425678.9104 586265.0195 463517.4583 606573.7674 535216.858 375482.5055 1.647686546 1.772617481 1.198985455 1.133685069 1.561364407 1.234458201 1.615451475 1.425410905 1 18.51838617 8 0.037503374 1.02E-12 3.749344408 0.309836813 0.209440048 1087.873493 3.113203977 88.52227523 267.6310647 100000000 -8 3.749344408 IHYFDPQYFEFEFEA ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IHYFDPQYFEFEFEA 15 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 122.42 0.00025357 25894000 119390 116680 112450 118280 128110 108000 134620 125070 102700 FALSE TRUE 113746.6713 128569.8247 117605.9437 106390.2697 150452.3434 104259.9329 114081.2465 114118.2078 118626.1915 0.958866418 1.083823252 0.991399473 0.896853118 1.268289419 0.878894716 0.961686834 0.961998411 1 16.85606305 IIAEGANGPTTPEADKIFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIAEGANGPTTPEADKIFLER 21 1 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ; 195.53 9.25E-22 193796000 192682 147479 167198 177328 153939 154537 181621 175358 162196 FALSE TRUE 183574.3037 162507.2778 174864.1937 159502.6525 180785.9129 149185.3449 153911.3808 160002.7239 187348.5273 0.979854533 0.867406219 0.933363054 0.851368595 0.964971091 0.796298466 0.821524369 0.854037799 1 17.51536511 2.239462089 24.99999926 0.84768158 0.915343172 0.094190758 0.066588122 36.60336488 1015138.494 0.02146756 0.017006622 173.5649745 -2.239462089 0.067661591 IIALDGDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IIALDGDTK 9 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 119.86 0.0017637 495981000 5032080 4057630 4092430 4760760 3575340 4426100 5539800 4787460 3959980 FALSE TRUE 4794223.551 4471107.11 4280071.963 4282199.36 4198878.164 4272823.047 4694601.765 4368244.622 4574073.474 1.048129983 0.977489132 0.935724358 0.936189457 0.917973484 0.934139574 1.026350318 0.955000974 1 22.12504811 -0.333304577 6.102570028 0.999999995 0.971630475 0.046749236 0.042146906 0 0 0.043740007 0.010309618 0.464189618 0.333304577 -0.02836952 IIANALSSEPACLAEIEEDKAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIANALSSEPACLAEIEEDKAR 22 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 263.32 1.89E-37 140460000 188940 154380 175297 211554 167926 213507 248550 237650 140481 FALSE TRUE 180009.1806 170111.4975 183334.5408 190288.19 197212.2412 206113.1991 210629.1326 216840.1061 162266.076 1.109345743 1.048349117 1.129838999 1.172692375 1.215363347 1.270217436 1.298047859 1.336324335 1 17.30800189 3.043477454 1.499777881 1.254502897 1.079694159 0.267886705 0.092366298 0.357016577 1.657063441 0.030271471 0.037325955 1105.293089 -3.043477454 -0.174808738 IIAPPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 127.95 0.0088528 2615252000 2682680 3087210 2293580 3001040 2257260 2488730 2421370 2712070 2137420 FALSE TRUE 2555875.033 3401800.209 2398742.912 2699369.758 2650925.429 2402544.656 2051945.535 2474586.773 2468880.177 1.035236565 1.377871733 0.971591466 1.093357945 1.073735961 0.973131332 0.831123986 1.002311411 1 21.23542539 2.799387732 0.985048904 0.9247502 1.183343574 0.310275339 0.115464472 0.486147748 1.006716114 0.060788819 0.059838258 630.0684485 -2.799387732 0.258593374 IIAPPERK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 126.41 0.0019566 17383830000 7391120 7258830 7750470 9032210 6625690 9582390 9714680 10465770 7174190 FALSE TRUE 7041756.405 7998513.03 8105836.716 8124275.091 7781208.238 9250549.432 8232527.144 9549331.696 8286726.745 0.849763317 0.965219836 0.978171112 0.980396161 0.9389966 1.116309216 0.993459468 1.152364738 1 22.98237092 4.975197299 0.365161646 1.061764238 0.665940469 0.516938581 0.059100999 5.277805026 0.493540853 0.047349855 0.95547168 94448.98579 -4.975197299 -0.395823769 IIAPSRGS(ph)PLPVLSWANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIAPSRGSPLPVLSWANR 18 1 I3L413;C9J2U0;P24864-2;P24864-3;P24864;I3L1Q9 I3L413 CCNE1 G1/S-specific cyclin-E1 1 IIAPS(0.03)RGS(0.97)PLPVLSWANR;IIAPS(0.079)RGS(0.921)PLPVLSWANR 75.868 0.006437 63352000 191216 180457 216514 188042 251520 172913 242930 198357 262870 TRUE FALSE 182177.5986 198845.7735 226441.3811 169139.6609 295385.0084 166924.9795 205866.5668 180987.8095 303634.537 0.599989713 0.654885229 0.745769514 0.557050138 0.97283073 0.549756234 0.678007742 0.596071222 1 18.21197637 -1.436680275 2.861785034 1.008080867 0.667306131 0.417928889 0.122633541 12082159.21 13717824.12 791473.4284 0.027850115 0.036586404 1.436680275 -0.340774736 IIDDSEITKEDDALWPPPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IIDDSEITKEDDALWPPPDR 20 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;;;; 181.87 4.51E-17 584527000 796780 735304 706116 798599 519152 790912 851122 791669 577184 FALSE TRUE 759117.7885 810232.3136 738492.117 718322.3113 609691.9444 763522.5191 721267.707 722346.2655 666690.7469 1.138635555 1.215304573 1.107698165 1.077444549 0.914504884 1.145242412 1.081862483 1.083480263 1 19.34665818 3.461676982 3.158608393 1.056884364 1.17645277 0.399898976 0.063442005 0.236084819 4.860496167 0.017492128 0.026150136 2895.189413 -3.461676982 0.119568406 IIDINYYPVPEACLSNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIDINYYPVPEACLSNKR 18 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 131.11 2.83E-05 108260000 102850 97473 112410 110430 106470 124850 130880 116940 126380 FALSE TRUE 97988.48433 107405.6095 117564.1097 99329.3666 125038.3343 120526.4132 110911.8522 106700.1137 145978.3649 0.671253472 0.735763889 0.80535297 0.680438958 0.856553876 0.825645727 0.759782809 0.73093101 1 17.15539504 -5 0.15187447 1.850361907 0.682809421 0.637794656 0.057888217 84.40856366 0.75666312 21.80142691 0.272659198 1.00E-05 5 -1.167552485 IIDKNGIHDLDNISFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIDKNGIHDLDNISFPK 17 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 191.99 1.27E-10 484640000 1609100 1105500 1548600 1607100 1292500 1573200 2040700 1884900 1397000 FALSE TRUE 1533041.032 1218151.707 1619604.842 1445551.255 1517911.591 1518719.69 1729353.735 1719848.164 1613639.625 0.950051677 0.754909391 1.003696747 0.89583277 0.940675704 0.941176497 1.071710008 1.065819243 1 20.62188699 2.172417511 1.108393731 1.056078611 0.881208035 0.433824182 0.068304602 0.400261453 0.929438007 0.046753733 0.024897255 148.7364841 -2.172417511 -0.174870575 IIDKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 416980000 1010550 819470 866080 1069910 918910 932950 1157060 1078360 1038930 FALSE TRUE 962783.3042 902974.9247 905790.6247 962360.6141 1079167.613 900641.7076 980529.2461 983933.0817 1200041.958 0.802291368 0.752452794 0.754799129 0.801939138 0.899274901 0.750508515 0.817079136 0.819915566 1 20.19465342 -4.999999981 0.227146842 2.087929243 0.771932797 0.697717484 0.042166895 86.60844819 0.86643422 43.1886625 0.071780654 1.00E-05 4.999999981 -1.315996446 IIDPLPPIDHSEIDYPPFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIDPLPPIDHSEIDYPPFEK 20 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 244.46 6.77E-30 52123000 202450 178240 185920 216600 155870 198890 227920 227110 165320 FALSE TRUE 192880.5897 196402.8586 194444.6159 194826.9565 183053.6786 192002.3894 193146.618 207223.0444 190956.9813 1.010073517 1.02851887 1.018263981 1.020266215 0.958612131 1.005474574 1.011466649 1.08518182 1 17.54288814 1.433543519 24.99475497 1.04450214 1.008778213 0.219140059 0.027439129 82.59644519 47378.79594 0.014416739 0.006353489 27.13585557 -1.433543519 -0.035723927 IIECTHCGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IIECTHCGCR 10 0 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ;; 174.98 2.22E-05 412050000 495930 394847 403010 475220 477040 429810 575520 487440 529730 FALSE TRUE 472488.3717 435082.3582 421488.4071 427449.9827 560235.625 414925.5719 487713.8539 444757.1695 611877.8229 0.772193981 0.711060839 0.688844066 0.698587147 0.915600474 0.678118337 0.797077187 0.726872511 1 19.22288409 -4.999999998 0.30027635 3.097489956 0.735148695 0.561074658 0.069807648 190.4884107 1.760097785 251.498061 0.063212359 1.00E-05 4.999999998 -2.362341261 IIELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIELKR 6 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 129.16 0.026159 719800000 1199100 961110 1142690 1098780 1065650 1146830 1439340 1288540 1308070 FALSE TRUE 1142420.919 1059048.202 1195083.467 988328.5469 1251499.023 1107114.99 1219742.248 1175708.607 1510918.815 0.756110062 0.700929918 0.790964713 0.654124191 0.828303288 0.732742871 0.807285101 0.778141483 1 20.52699471 -1.103867581 0.307285107 1.146128182 0.723430147 0.730829271 0.047804773 7.016220581 0.518218348 0.908598292 0.043006029 0.07872858 1.103867581 -0.422698034 IIEVVDAIMTTAQSHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIEVVDAIMTTAQSHQR 17 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 117.48 0.00082397 0 14976 15921 12884 14894 15141 13448 15686 12525 15319 FALSE TRUE 14268.11416 17543.368 13474.74414 13396.82682 17781.58561 12982.29239 13292.81261 11428.2446 17694.59228 0.806354503 0.991453644 0.761517639 0.757114186 1.004916379 0.733687003 0.75123588 0.645860861 1 14.1110209 IIFDDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IIFDDFR 7 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 ;;;;; 107.66 0.017281 244333000 1135530 916202 1018508 1533900 1808790 1048525 1492550 1116000 1453260 FALSE TRUE 1081855.747 1009564.025 1065207.599 1379709.458 2124242.403 1012214.316 1264834.085 1018277.124 1678624.139 0.644489569 0.601423512 0.634571835 0.821928761 1.265466375 0.60300236 0.753494517 0.606614131 1 20.6788478 3.24306495 6.771824587 0.827899043 0.623080497 0.218221236 0.19065264 0.224794413 49.50672561 0.05324326 0.068472195 1750.108401 -3.24306495 -0.204818546 IIFEDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IIFEDDR 7 0 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;;;;;;; 173.93 0.0019657 7246760000 16056580 12993900 14280990 16767740 17071290 14428830 17630380 15894410 18449270 FALSE TRUE 15297617.28 14317993.18 14935787.52 15082214.92 20048517.57 13929156 14940541.73 14502611.2 21310288.57 0.71785125 0.671881713 0.700872138 0.707743345 0.940790525 0.65363526 0.701095233 0.680545041 1 24.34504679 -1.143684938 4.0690642 1.000091968 0.718255226 0.54230099 0.080261766 11818756618 57047855.78 10219607.01 0.018465492 0.071831521 1.143684938 -0.281836742 IIFVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIFVGR 6 0 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 123.07 0.044078 57474000 98468 84192 85766 93852 108480 92689 109670 100290 115470 FALSE TRUE 93813.61278 92771.26052 89698.45593 84417.81865 127398.8777 89479.15669 92937.82727 91508.07593 133376.4979 0.70337439 0.695559278 0.672520702 0.632928739 0.955182357 0.67087649 0.696808124 0.686088459 1 17.02514495 -1.440980188 2.96811049 1.006269604 0.71228914 0.509535453 0.088114336 14204552.29 17230620.68 751758.5306 0.019847264 0.036225952 1.440980188 -0.293980464 IIGATDS(ph)SGELMFLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIGATDSSGELMFLMK 16 0 P83916;J3KS05;K7ELA4;B5MD17;Q13185 P83916;Q13185 CBX1;CBX3 Chromobox protein homolog 1;Chromobox protein homolog 3 1 IIGATDS(0.99)S(0.01)GELMFLMK 263.6 7.71E-22 0 54956 46699 43931 51861 43678 48305 61233 53223 53528 TRUE FALSE 52358.33879 51457.68119 45945.2798 46647.83375 51295.42937 46632.18574 51890.78123 48562.51197 61828.84886 0.846827003 0.832260056 0.743104241 0.754467124 0.829635847 0.754214038 0.839264877 0.785434516 1 15.91599252 -1.196180942 4.605607805 1.000039148 0.802854104 0.728635438 0.038617751 1.56E-05 2.73E-06 0.037631559 0.008868084 0.063653026 1.196180942 -0.197185044 IIGDPYKVQQACEMVMDILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIGDPYKVQQACEMVMDILR 20 1 A0A087WTP3;Q92945;M0R0I5;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 92.474 0.0015024 31697000 87608 71614 106280 88576 108620 98822 140120 111160 126170 FALSE TRUE 83466.94346 78911.54802 111153.0431 79672.1722 127563.2936 95399.76936 118742.1205 101426.2411 145735.7992 0.572727799 0.541469896 0.762702395 0.546689095 0.875305136 0.654607652 0.814776611 0.695959686 1 17.15299579 0.71897163 0.067700601 1.629087255 1.59E-11 0.585235914 0.09642446 23.67197044 0.846545471 11.16835377 8.642534526 5.235662335 -0.71897163 -1.629087255 IIGLKDEFYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIGLKDEFYNR 11 1 Q5MIZ7-3;Q5MIZ7-2;Q5MIZ7;Q5MIZ7-5;Q6IN85-2;Q6IN85;G3V5Z3;Q6IN85-4 Q5MIZ7-3;Q6IN85-2 SMEK2;SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3B;Serine/threonine-protein phosphatase 4 regulatory subunit 3A 0 ; 104.87 0.0023188 257650000 347630 345740 307010 368230 302850 347310 414500 401020 341030 FALSE TRUE 331198.2188 380971.2991 321086.7122 331214.8208 355666.9441 335282.5676 351260.4122 365904.5629 393915.1907 0.840785597 0.96714041 0.815116349 0.840827743 0.902902332 0.851154197 0.891715833 0.92889173 1 18.58752553 0.961410909 1.955693045 0.999555139 0.876434011 0.495192657 0.042099416 0.328501664 2.668038136 0.03907535 0.01095872 9.149785409 -0.961410909 -0.123121128 IIGVHQEDELLECLSPATSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 217.42 1.06E-24 100390000 79066 76653 73652 73064 96206 75617 90921 89934 65797 FALSE TRUE 75328.70687 84464.02785 77029.01705 65719.46791 112984.2959 72998.36433 77049.33157 82058.90219 76000.46272 0.991161161 1.111362021 1.013533527 0.864724576 1.486626422 0.960498946 1.013800822 1.079715824 1 16.21372058 IIIEELSLVAAS(ph)PTLSPR ddPTM_SK-BR-3_Trastuzumab_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(0.989)PT(0.011)LSPR 181.41 7.72E-14 24896000 66121 52014 71152 66063 72633 63533 87793 64031 83157 TRUE FALSE 62995.59137 57314.28574 74414.38958 59422.22173 85300.1722 61332.83628 74398.56542 58424.10619 96052.56285 0.655844982 0.5966971 0.774725706 0.618642751 0.888057223 0.638534095 0.774560961 0.608251404 1 16.55153649 -5 0.206687261 2.4186441 0.646849651 0.489748462 0.095451231 111.9568802 1.113311487 65.97872656 0.188332368 1.00E-05 5 -1.771794449 IIIEELSLVAASPT(ph)LSPR ddPTM_SK-BR-3_Trastuzumab_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(0.217)PT(0.392)LS(0.392)PR 143.56 1.17E-06 158230000 51982 61823 45699 73788 67490 40294 54892 40901 70327 TRUE FALSE 49524.91388 68122.83399 47794.34435 66370.69005 79260.23463 38898.60868 46517.21724 37319.49161 81232.95198 0.609665323 0.838610839 0.588361535 0.817041465 0.975715306 0.47885258 0.572639749 0.459413215 1 16.30977745 2.210792927 24.99999176 0.585981642 0.755852485 0.102050316 0.184824909 365.9563184 329478.0374 0.062464668 0.04614321 162.4773872 -2.210792927 0.169870843 IIIHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIIHLK 6 0 Q12931-2;Q12931;I3L0K7;I3L239;I3L2D5 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 89.775 0.049783 278520000 469230 484490 459410 483860 361080 379720 409430 479580 369510 FALSE TRUE 447050.4278 533860.0818 480474.4029 435221.4735 424052.2377 366570.2012 346963.9338 437585.4328 426811.7236 1.047418342 1.25080932 1.12572916 1.019703653 0.993534653 0.858856917 0.812920345 1.025242299 1 18.70324028 2.906556624 1.68311253 0.901905484 1.152947175 0.552276959 0.081934327 0.222530437 1.267946467 0.029604422 0.032675229 806.411336 -2.906556624 0.251041691 IIILYDDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IIILYDDDER 10 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 ;;; 154.84 3.20E-05 104748000 237699 220361 202199 259364 237488 193564 230802 226832 230818 FALSE TRUE 226463.4393 242816.0364 211470.0242 233292.238 278905.832 186860.8301 195588.9159 206969.3876 266612.0766 0.849411783 0.910746578 0.793174964 0.875025021 1.046111022 0.70087159 0.733608614 0.776294121 1 18.02438261 2.204142959 24.99997635 0.772627208 0.887394509 0.136820131 0.102519674 256.685819 186447.6116 0.03500411 0.025853438 160.0084649 -2.204142959 0.114767301 IIKPCNHVLSLSFPIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIKPCNHVLSLSFPIRR 17 2 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 56.215 0.067595 39463000 98533 74641 75441 82518 101160 61597 104810 85780 113890 FALSE TRUE 93875.54036 82247.00276 78900.04447 74223.13387 118802.272 59463.88044 88819.30953 78268.64845 131551.4795 0.713603075 0.625207737 0.599765542 0.5642136 0.903085791 0.452019853 0.675167697 0.594965931 1 17.00526795 -1.491342034 3.221848193 1.008213057 0.642220305 0.486677721 0.115862898 37178981.58 43629279.69 2684589.844 0.025061653 0.032259525 1.491342034 -0.365992751 IILDLISES(ph)PIKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIKGR;IILDLIS(0.001)ES(0.999)PIKGR;IILDLIS(0.04)ES(0.96)PIKGR;IILDLIS(0.209)ES(0.791)PIKGR 184.27 7.94E-07 1683395000 510011 447869 491569 551679 425769 566363 656531 599835 517629 TRUE FALSE 485903.7908 493507.3603 514107.9249 496223.1788 500022.9788 546749.7073 556365.1379 547310.2675 597900.2616 0.81268369 0.82540081 0.859855661 0.82994307 0.836298311 0.914449687 0.930531685 0.915387235 1 19.18954532 1.713500882 0.51891605 0.997688223 0.814106455 0.893256074 0.019397457 0.239219754 0.150448165 0.019379298 0.01248603 51.70123085 -1.713500882 -0.183581768 IILDLISESPIKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 144.27 8.12E-06 57045000 91552 28966 114780 49551 131430 81723 177510 102700 224630 FALSE TRUE 87224.5184 31917.66833 120042.7765 44570.03934 154351.3504 78892.91202 150427.5893 93707.04355 259464.4731 0.336171335 0.123013636 0.462655928 0.171777041 0.594884334 0.304060556 0.579761797 0.361155585 1 17.98517749 -5 0.141507042 3.303021906 0.12225137 0.675752912 0.14273055 68.27611865 0.589223843 43.99056795 0.73115606 1.00E-05 5 -3.180770537 IILLAEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IILLAEGR 8 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 81.297 0.052878 0 27728 25156 24729 23799 32927 21643 33837 26481 30670 FALSE TRUE 26417.35239 27719.425 25862.84911 21406.6793 38669.45837 20893.49748 28674.54419 24162.18326 35426.14696 0.745702106 0.782456671 0.730049732 0.604262138 1.091551345 0.589776176 0.809417525 0.682043782 1 15.11252694 -1.249767942 4.121689884 1.000185329 0.757739554 0.236162382 0.138692446 41.37332911 65756563.28 22253.02478 0.028016741 0.056264188 1.249767942 -0.242445775 IILLFDAHKLDISDEFSEVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IILLFDAHKLDISDEFSEVIK 21 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 ;;; 254.26 1.32E-36 387471000 609569 721434 616316 791867 459581 751706 784444 803520 345160 FALSE TRUE 580755.8814 794948.9448 644574.6982 712267.0247 539731.7809 725674.2327 664762.6605 733159.5291 398685.65 1.456676159 1.993924148 1.616749181 1.786537902 1.353777797 1.820166421 1.667385472 1.838941354 1 18.60489215 -0.959942141 5.089803048 0.999996447 1.698704952 0.574676403 0.186945766 6.79E-06 1.39E-06 0.162926524 0.038401956 0.109662428 0.959942141 0.698708505 IILPPEKELAMPGEDLKFNLILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IILPPEKELAMPGEDLKFNLILR 23 2 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 105.51 0.00086252 136311000 355740 160505 338720 248450 341700 262390 466130 333180 425120 FALSE TRUE 338924.8752 176860.642 354250.647 223475.334 401292.3718 253303.3685 395013.3074 304004.9929 491045.4384 0.690210821 0.360171642 0.721421317 0.45510113 0.817220445 0.51584507 0.80443331 0.619097479 1 18.905497 -0.056207028 0.266858892 1.141138745 0.514912814 0.421329533 0.143437133 5.589565232 0.614479199 0.984007004 0.20586041 0.878603588 0.056207028 -0.626225931 IILTARPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IILTARPFR 9 1 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 209.21 8.01E-06 582660000 442120 260330 167400 151800 551080 191248 506460 303260 506000 FALSE TRUE 421221.8638 286857.923 175075.4556 136540.7756 647188.1775 184625.0338 429190.2252 276704.9467 584467.8957 0.720692902 0.490801847 0.299546745 0.233615527 1.107311766 0.315885672 0.734326433 0.473430532 1 19.15676426 -2.484623789 0.334005868 1.681260485 0.529305486 0.231979833 0.258505213 80.51274232 3.16470433 40.1130557 0.200484524 0.003276244 2.484623789 -1.151954999 IILWDHDLNPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IILWDHDLNPER 12 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 174.9 2.91E-05 46993000 51783 49444 43309 52955 61578 45589 55106 55249 50388 FALSE TRUE 49335.32021 54482.39981 45294.76049 47631.86279 72317.1837 44010.2415 46698.56761 50411.10467 58201.91369 0.847658042 0.936092928 0.7782349 0.818389977 1.242522438 0.756164853 0.802354504 0.866141703 1 15.82877897 -0.871529398 3.858115662 1.000005216 0.878487605 0.068242976 0.137987137 139176179.7 301769609.9 10871.86771 0.03142253 0.134422077 0.871529398 -0.121517611 IINDLLQSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IINDLLQSLR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 142.83 8.16E-05 67148000 81497 67471 62272 61787 94182 57849 102660 66964 98493 FALSE TRUE 77644.79832 74346.37161 65127.2328 55576.05337 110607.311 55845.67462 86997.33152 61100.27716 113766.7914 0.682490886 0.653498008 0.572462596 0.488508577 0.972228447 0.490878524 0.764698823 0.537066014 1 16.79571997 -1.896524561 2.772854712 1.179445838 0.652562108 0.371596149 0.144709764 36735297.74 27959552.69 43274183.79 0.030303596 0.012690404 1.896524561 -0.52688373 IINEPTAAAIAYGLDKK ddPTM_SK-BR-3_Trastuzumab_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 ; 197.6 2.40E-11 3513900000 5311000 4266600 4714100 5505900 3335100 5447300 6156700 6232000 4180000 FALSE TRUE 5059959.555 4701371.391 4930246.148 4952436.471 3916740.384 5258658.635 5217382.339 5686293.042 4828213.052 1.047998401 0.973729067 1.021132683 1.025728653 0.81121946 1.089152152 1.080603172 1.177722064 1 22.20305791 2.059648499 24.99999935 1.092523448 0.98349329 0.336549284 0.076808968 81.15817684 34014.56423 0.026803081 0.019795393 114.7224728 -2.059648499 -0.109030158 IINEPTAAAIAYGLDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 252.51 8.77E-27 1807720000 2288070 1839470 1774800 2105660 2026800 1947600 2507100 2145160 2173890 FALSE TRUE 2179917.466 2026914.084 1856176.336 1893995.056 2380273.278 1880154.124 2124595.849 1957318.418 2511005.759 0.868145148 0.807212041 0.73921628 0.754277464 0.947936209 0.748765357 0.846113491 0.77949579 1 21.25983391 -1.453824457 3.06938932 1.003894137 0.814202041 0.463256145 0.063737474 23070390.61 25557375.05 763622.6671 0.014112225 0.035170257 1.453824457 -0.189692097 IINEPTAAAIAYGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 256.57 2.82E-26 207757000 120610 103589 103282 112898 124796 103998 135107 120985 141811 FALSE TRUE 114909.0043 114144.8369 108017.5819 101549.2785 146560.3829 100396.5232 114493.9457 110390.912 163802.3256 0.701510213 0.696845032 0.659438634 0.619950164 0.894739329 0.612912685 0.698976314 0.673927623 1 17.32159631 -1.304586214 5.024757497 1.00009782 0.694705373 0.605113307 0.077485878 7.55E-05 1.04E-05 0.066697953 0.015715843 0.049592247 1.304586214 -0.305392447 IINYRDDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IINYRDDEK 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1;H3BQD1;H3BUV0;H3BTM1;H3BRA2 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 111.06 0.0019942 926970000 536330 492900 521290 625320 582330 555010 665990 601530 656710 FALSE TRUE 510978.7438 543127.0704 545191.6621 562461.6456 683888.1676 535789.8645 564380.9938 548856.8443 758549.2328 0.673626341 0.716007672 0.718729436 0.741496559 0.90157387 0.70633499 0.744026847 0.723561267 1 19.53288329 -5 0.233459937 2.423117115 0.708719169 0.643648244 0.060596385 105.3434788 1.052777752 71.09298865 0.100109077 1.00E-05 5 -1.714397946 IIPAIWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIPAIWFR 8 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 91.584 0.028809 11571000 40270 24818 14550 17879 47933 17099 48347 20216 27668 FALSE TRUE 38366.51691 27346.98242 15217.13189 16081.76895 56292.50002 16506.85734 40970.7772 18445.77987 31958.61213 1.200506353 0.855699938 0.476151212 0.503206112 1.761418794 0.516507327 1.281994882 0.577177125 1 14.96391714 IIPELVGS(ph)PTQSTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IIPELVGSPTQSTSSR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 IIPELVGS(0.987)PT(0.012)QS(0.001)TSSR;IIPELVGS(0.991)PT(0.008)QSTSSR;IIPELVGS(0.877)PT(0.123)QSTSSR;IIPELVGS(0.866)PT(0.134)QSTSSR 172.24 4.87E-09 202291000 187285 172068 166708 181966 200544 178328 212308 190637 225717 TRUE FALSE 178432.4092 189601.9248 174351.7267 163674.432 235518.8101 172152.4566 179916.5153 173943.8136 260720.0396 0.684383178 0.72722421 0.66873159 0.627778487 0.903339883 0.66029622 0.690075514 0.667167027 1 17.99214195 -2.006398865 2.88886903 1.308624477 0.704247511 0.604055433 0.075407566 57333361.07 58014776.85 117438208.7 0.016624872 0.009853741 2.006398865 -0.604376966 IIPGFMCQGGDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 270.74 1.42E-32 15858817000 907175 636385.3 696224 836764.2 966407 751780.6 897873 722928.1 948686 FALSE TRUE 864294.6356 701233.6856 728146.5591 752651.0729 1134948.075 725746.2493 760885.9833 659624.6831 1095803.38 0.788731493 0.639926559 0.664486506 0.686848651 1.035722371 0.662296049 0.694363603 0.601955328 1 20.06355753 IIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.84)PT(0.157)AT(0.002)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.421)PT(0.421)AT(0.078)S(0.078)QLPLES(0.001)DAVECLNY(0.001)QHY(0.001)K;IIPTLEEGLQLPS(0.671)PT(0.11)AT(0.11)S(0.11)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.454)PT(0.454)AT(0.057)S(0.008)QLPLES(0.01)DAVECLNY(0.009)QHY(0.009)K;IIPTLEEGLQLPS(0.88)PT(0.101)AT(0.016)S(0.003)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.622)PT(0.088)AT(0.088)S(0.013)QLPLES(0.013)DAVECLNY(0.088)QHY(0.088)K;IIPTLEEGLQLPS(0.822)PT(0.173)AT(0.005)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.811)PT(0.18)AT(0.007)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.785)PT(0.213)AT(0.002)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.956)PT(0.038)AT(0.005)S(0.001)QLPLESDAVECLNYQHYK 202.25 6.00E-30 6862316800 2585088 2111824 2386220.6 2573314 2144307.1 2380874 2765373 2405229 2125941 TRUE FALSE 2462896.013 2327021.267 2495631.175 2314639.588 2518273.579 2298423.736 2343464.559 2194614.398 2455621.072 1.002962567 0.947630436 1.016293272 0.942588257 1.025513915 0.935984693 0.95432662 0.893710525 1 21.22765652 2.184305633 24.99998498 0.943276659 0.982394154 0.229597381 0.03662752 130.2883058 60034.11113 0.012035067 0.008888491 152.8641455 -2.184305633 0.039117496 IIQLLDDYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIQLLDDYPK 10 0 F8VWS0;P05388;P05388-2;F8VU65;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ; 148.96 5.63E-05 84415000 518930 505490 467340 530520 383220 505340 563660 551400 411970 FALSE TRUE 494401.2073 557000.0057 488768.0013 477191.1217 450053.4467 487839.9491 477663.3147 503116.4928 475856.2035 1.038971865 1.170521686 1.027133822 1.002805297 0.945776147 1.025183544 1.003797599 1.057286821 1 18.86016615 3.553768299 7.052551616 1.005238703 1.104554084 0.489037765 0.041285308 0.187469219 14.84937323 0.010509277 0.016280291 3579.054399 -3.553768299 0.099315381 IIREEYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IIREEYGR 8 1 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ;;;;; 215.38 7.66E-06 581500000 491228 367398 417468 460849 527903 423521 557729 497029 593203 FALSE TRUE 468008.626 404836.2739 436609.3207 414523.583 619969.1161 408854.3616 472637.1977 453506.5058 685193.8916 0.683030937 0.590834622 0.637205506 0.604972677 0.904808294 0.596698784 0.689786064 0.66186595 1 19.38615276 -5 0.283411552 3.489609821 0.64556009 0.569091634 0.089905487 163.6258913 1.558057921 240.0579471 0.09272446 1.00E-05 5 -2.844049731 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 38 2 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 157.78 2.54E-15 118970000 128120 91823 151250 130960 149940 156690 241380 169200 89607 FALSE TRUE 122064.0215 101179.8681 158184.9621 117795.652 176089.4885 151263.786 204553.0478 154383.951 103502.7959 1.179330669 0.977556859 1.528315836 1.138091497 1.701301757 1.461446376 1.976304562 1.491592084 1 16.65931021 3.154071941 1.173026269 1.612587695 1.095834676 0.167734749 0.289277261 0.485984149 1.425974591 0.105650563 0.149507912 1425.843766 -3.154071941 -0.516753019 IIS(ph)NASCTTNCLAPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 IIS(0.999)NAS(0.001)CTTNCLAPLAK;IIS(0.993)NAS(0.007)CTTNCLAPLAK 205.23 8.46E-12 179249000 281610 205691 213738 289494 234747 230415 301313 267376 239747 TRUE FALSE 268298.8534 226651.1468 223538.0987 260393.5131 275686.8025 222435.6708 255342.1679 243963.14 276925.7403 0.968847652 0.818454603 0.807213148 0.940300865 0.995526101 0.803232197 0.922060071 0.880969533 1 18.07913963 -1.5537086 2.387225832 1.009415636 0.890441943 0.203339298 0.067065665 3987614.732 3367913.198 239155.1132 0.016253 0.027944182 1.5537086 -0.118973692 IIS(ph)PGSSTPS(ph)STRSPPPGRDESYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IISPGSSTPSSTRSPPPGRDESYPR 25 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 2 IIS(0.932)PGS(0.048)S(0.01)T(0.011)PS(0.291)S(0.265)T(0.242)RS(0.202)PPPGRDESYPR 67.69 0.02313 148280000 35199 28752 38346 41265 45497 40725 51419 36373 48250 TRUE FALSE 33535.21303 31681.86149 40104.20203 37116.9638 53431.6624 39314.68304 43574.08718 33187.98729 55732.36357 0.601718838 0.568464344 0.719585524 0.665985819 0.958718758 0.705419267 0.781845312 0.595488602 1 15.76622772 -2.165907844 0.049057774 1.9348591 5.76E-18 0.431607431 0.110480802 270.0779938 1.770084348 51.95354908 22.5656872 0.006824835 2.165907844 -1.9348591 IIS(ph)PGSSTPSS(ph)TRSPPPGRDESYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IISPGSSTPSSTRSPPPGRDESYPR 25 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 2 IIS(0.994)PGS(0.005)S(0.001)T(0.001)PS(0.09)S(0.434)T(0.295)RS(0.179)PPPGRDESYPR;IIS(0.789)PGS(0.198)S(0.008)T(0.009)PS(0.162)S(0.327)T(0.286)RS(0.22)PPPGRDESYPR 113.47 0.0011008 432520000 170868 127636 195443 183125 206888 162956 228660 189887 266990 TRUE FALSE 162791.4083 140642.2535 204404.2549 164716.9271 242969.2017 157312.7929 193773.7174 173259.4876 308393.4456 0.527869222 0.456048128 0.662803499 0.534112931 0.787854623 0.510104203 0.628332801 0.561813132 1 18.23441258 -5 0.212287488 3.045857419 0.516203527 0.661933807 0.093312864 84.16900823 0.839616578 73.47101906 0.18076049 1.00E-05 5 -2.529653893 IIS(ph)PGSSTPSSTR ddPTM_SK-BR-3_Trastuzumab_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 IIS(0.696)PGS(0.086)S(0.168)T(0.05)PSSTR 111.83 0.00099508 168590000 173790 163820 140720 173340 152200 151610 160800 162140 120300 TRUE FALSE 165575.2911 180513.4442 147172.1512 155915.5339 178743.6318 146359.7077 136267.0067 147942.162 138955.5096 1.191570537 1.299073673 1.059131456 1.122053629 1.286337133 1.053284667 0.98065206 1.064672876 1 17.08426351 2.09362492 6.340893654 1.013984643 1.196586385 0.571759926 0.07229305 0.148317397 8.368644918 0.027738608 0.020365378 124.0580413 -2.09362492 0.182601742 IISPGSSTPS(ph)STRSPPPGRDESYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IISPGSSTPSSTRSPPPGRDESYPR 25 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGSST(0.001)PS(0.353)S(0.215)T(0.215)RS(0.215)PPPGRDESYPR 206.4 1.97E-25 651030000 200930 131650 197410 194230 249930 187610 248530 195200 310620 TRUE FALSE 191432.4371 145065.2847 206461.4438 174705.6314 293517.7129 181113.0187 210612.1839 178107.2532 358789.3632 0.533551038 0.4043188 0.575439143 0.486930911 0.818078079 0.504789264 0.587007881 0.496411743 1 18.45277759 -5 0.235375819 3.510706116 0.495277209 0.620612321 0.109340937 105.4686529 1.053435951 126.6256101 0.169576381 1.00E-05 5 -3.015428907 IISPGSSTPSSTRS(ph)PPPGRDESYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IISPGSSTPSSTRSPPPGRDESYPR 25 2 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGSSTPS(0.037)S(0.037)T(0.037)RS(0.888)PPPGRDESYPR;IISPGSSTPSSTRS(0.999)PPPGRDESYPR;IISPGSSTPS(0.013)S(0.007)T(0.007)RS(0.974)PPPGRDESYPR;IISPGSSTPS(0.035)S(0.128)T(0.128)RS(0.708)PPPGRDESYPR;IISPGSSTPS(0.008)S(0.038)T(0.038)RS(0.916)PPPGRDESYPR 218.67 7.35E-34 2532900000 584360 344302 600515 526766 739690 577401 794369 637309 891293 TRUE FALSE 556738.4609 379386.7652 628049.2067 473814.4809 868691.7018 557405.4586 673173.4195 581502.8454 1029510.166 0.540779954 0.368511917 0.610046629 0.460232931 0.843791281 0.541427833 0.653877389 0.564834486 1 19.97352665 -4.999999997 0.12261127 2.448699883 0.35335733 0.578422593 0.118542064 97.56581248 0.770203096 34.90709128 0.978705408 1.00E-05 4.999999997 -2.095342553 IISSDRDLLAVVFYGTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IISSDRDLLAVVFYGTEK 18 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 174.78 4.54E-12 428181000 182595 194567 161441 185857 144116 180974 183349 198207 143550 FALSE TRUE 173964.0962 214393.5985 168843.2295 167174.3013 169249.7848 174706.825 155375.7426 180850.9443 165811.0008 1.049171016 1.292999846 1.018287259 1.008222014 1.020739178 1.053650386 0.937065344 1.090705342 1 17.3391802 3.63626348 9.751219404 1.012664245 1.170942802 0.453438556 0.069497997 0.292151191 25.89676702 0.017328542 0.026858305 4327.763105 -3.63626348 0.158278557 IISSIEQKEENKGGEDKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IISSIEQKEENKGGEDKLK 19 3 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 96.131 0.00058065 465610000 819250 772430 870540 742980 340840 989630 845510 1051700 323410 FALSE TRUE 780525.6761 851141.4952 910455.1201 668294.2388 400282.3881 955358.865 716511.9206 959607.5726 373562.7711 2.089409697 2.278443039 2.43722124 1.788974412 1.071526445 2.557425255 1.918049592 2.568798732 1 18.51099116 3.228771117 24.77816622 1.882595955 2.244955044 0.134824059 0.520190402 411.2846486 1040999.21 0.140064954 0.169393124 1693.445082 -3.228771117 0.362359089 IISVT(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IIS(0.212)VT(0.788)PVK 97.284 0.093239 177330000 620910 744060 602000 825430 518330 730580 721070 756490 621890 TRUE FALSE 591560.8148 819880.5599 629602.2955 742456.2082 608726.5879 705279.8314 611057.5281 690247.7252 718329.525 0.823522902 1.1413711 0.87648116 1.033587208 0.847419696 0.981833277 0.850664642 0.9609068 1 19.45428629 2.746553646 24.86089007 0.917882486 0.976251515 0.032668401 0.097752148 1472.276401 4579250.448 0.027682878 0.028861804 557.8965121 -2.746553646 0.058369029 IISVT(ph)PVKNIDPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IISVTPVKNIDPVK 14 1 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IIS(0.081)VT(0.919)PVKNIDPVK 150.68 1.16E-05 204860000 813500 753060 775950 874750 623780 965410 1038700 968470 756260 TRUE FALSE 775047.4672 829797.6702 811528.075 786818.4681 732567.0345 931977.6096 880227.238 883665.6326 873536.9384 0.887252082 0.949928542 0.929014034 0.900727186 0.838621703 1.066901202 1.007658863 1.011595038 1 19.73650918 2.231022057 24.99999999 1.022218794 0.907757345 0.75663093 0.033821359 86.86390211 288062.7447 0.012344326 0.009293614 170.224496 -2.231022057 -0.114461449 IITDVIGNPEEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 154.19 9.92E-06 256030000 262604 206427 236255 244004 270040 241749 291160 256640 478370 FALSE TRUE 250191.2294 227462.146 247087.5254 219476.2543 317134.8905 233377.1715 246738.1945 234167.2411 552553.1764 0.452791224 0.411656571 0.447174201 0.39720386 0.573944561 0.422361469 0.446541989 0.423791322 1 19.07575379 -2.008843042 2.821816354 1.587385871 0.445421321 0.928166305 0.048352253 5266123.959 3255841.191 20064613.84 0.010692573 0.00979844 2.008843042 -1.14196455 IITYNEAMDS(ph)PDQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IITYNEAMDSPDQ 13 0 Q7Z417;Q7Z417-2 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 IITYNEAMDS(1)PDQ 115.8 0.0002815 0 35137 28749 33509 35399 35673 27325 38008 26162 44396 TRUE FALSE 33476.14364 31678.55578 35045.42079 31840.62527 41894.35991 26378.7284 32209.18154 23871.11659 51280.70494 0.65280194 0.617748056 0.683403647 0.620908494 0.816961466 0.514398709 0.62809553 0.465498995 1 15.64612847 -1.50806208 3.538058108 1.006754483 0.628372474 0.612967183 0.093617124 7051207.067 37634603.27 675962.8405 0.019859076 0.031041158 1.50806208 -0.378382009 IIVDELKQEVISTSSK ddPTM_SK-BR-3_Trastuzumab_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 ; 225.69 6.06E-15 516600000 1748290 1587320 1751070 1782340 1193010 1945510 2103370 2038500 1360160 FALSE TRUE 1665651.796 1749069.713 1831358.292 1603175.797 1401070.566 1878136.501 1782462.275 1859998.133 1571086.666 1.060190906 1.113286587 1.165663442 1.0204248 0.891784391 1.195437872 1.134541024 1.183892763 1 20.58333134 IIVEKPFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIVEKPFGR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 132.39 0.00027941 11480100000 10076900 8430800 7277900 7236300 5712900 6651900 7187500 6534200 6089500 FALSE TRUE 9600584.907 9289908.105 7611598.914 6508893.376 6709227.951 6421543.035 6090914.868 5962030.808 7033828.559 1.364915967 1.320747019 1.08214166 0.925369921 0.953851504 0.912951315 0.865945881 0.847622423 1 22.74587874 3.569946515 1.80737397 0.904031505 1.361728638 0.941812675 0.043370647 0.063766772 0.412359256 0.012533154 0.023022857 3714.894762 -3.569946515 0.457697133 IIVWDVAAGVAQCEIQEHAKPIQDVQWLWNQDASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIVWDVAAGVAQCEIQEHAKPIQDVQWLWNQDASR 35 1 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 120.98 3.64E-08 26598000 39094 24016 26605 28260 21734 25966 29649 26868 26450 FALSE TRUE 37246.1041 26463.2577 27824.86557 25419.25111 25524.40272 25066.79091 25125.50051 24515.29548 30551.73091 1.219116004 0.866178672 0.910745962 0.832006906 0.835448662 0.820470401 0.822392046 0.8024192 1 14.8989665 4.747322602 1.202906674 0.842918111 1.410428064 0.778415646 0.059490244 0.565441604 0.684365283 0.014843236 0.404960517 55888.51908 -4.747322602 0.567509953 IIWELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIWELIK 7 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 123.96 0.009755 46659000 372910 329310 310780 358130 348520 299100 440580 357390 360070 FALSE TRUE 355283.2833 362867.0634 325029.5704 322130.092 409301.7777 288742.092 373361.4292 326095.037 415907.8166 0.854235648 0.872469929 0.781494258 0.774522813 0.984116579 0.694245408 0.897702362 0.784056043 1 18.66590427 -1.704216552 6.290911476 1.002265997 0.835560219 0.308283111 0.079521475 0.002210059 0.000103912 0.06733102 0.015671178 0.019759841 1.704216552 -0.166705779 IIWQFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IIWQFIK 7 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 145.87 0.0052517 60925000 422540 313690 258060 242900 421440 212420 404240 311450 399260 FALSE TRUE 402567.3716 345655.3676 269892.3063 218483.2305 494939.0026 205063.8421 342565.7636 284177.7869 461175.2017 0.872916345 0.749509875 0.585227274 0.473753206 1.073212525 0.444654963 0.74281046 0.616203529 1 18.81495541 -1.087178673 4.615230911 1.000014567 0.703484124 0.209350023 0.185724621 3.15E-05 6.24E-06 0.163426821 0.038517713 0.081812813 1.087178673 -0.296530444 IIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IIYDRK 6 1 Q13541;O60516;Q13542 Q13541;Q13542 EIF4EBP1;EIF4EBP3;EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 1;Eukaryotic translation initiation factor 4E-binding protein 3;Eukaryotic translation initiation factor 4E-binding protein 2 0 ;; 103.29 0.055824 3142550000 3866660 3255030 2758840 3506120 3243500 3247940 4243220 3829670 3392820 FALSE TRUE 3683890.645 3586721.258 2885335.543 3153678.156 3809165.373 3135463.023 3595838.857 3494323.792 3918961.197 0.940017127 0.915222447 0.736250092 0.804722986 0.971983437 0.800075037 0.917548982 0.891645417 1 21.90203986 0.581912416 1.072759619 0.999842526 0.871706976 0.249109143 0.071690355 2.219136205 3.85255029 0.068566556 0.021480874 3.818672518 -0.581912416 -0.12813555 IIYGGS(ph)VTGATCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIYGGSVTGATCK 13 0 P60174;P60174-3;P60174-4 P60174 TPI1 Triosephosphate isomerase 1 IIYGGS(0.99)VT(0.01)GATCK 123.76 0.00023044 63977000 170400 73760 333540 123640 158810 176900 283300 212140 237460 TRUE FALSE 162345.5297 81276.22786 348833.1389 111211.4723 186506.4137 170773.9086 240077.3818 193563.897 274284.084 0.591888262 0.296321342 1.271795045 0.405460903 0.679975342 0.622616909 0.875287324 0.705705902 1 18.06531138 3.332780647 0.099832804 1.270058567 2.40E-11 0.149276154 0.259612638 51.29847993 1.476423263 5.904046264 12.92190602 2151.694684 -3.332780647 -1.270058567 IIYIVHDEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IIYIVHDEVK 10 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;; 171.85 3.89E-06 597250000 3074861 3408830 2394709 3211905 2099689 2973441 3118008 3285717 1803940 FALSE TRUE 2929518.414 3756193.653 2504508.776 2889038.207 2465874.097 2870469.993 2642298.613 2998002.201 2083685.802 1.405930977 1.802667969 1.201960859 1.386503764 1.18341935 1.377592529 1.268088793 1.438797633 1 20.99070632 8 0.03942474 2.26E-10 3.614232439 0.352496855 0.168808569 730.2212724 2.193518243 55.55222372 177.6261574 100000000 -8 3.614232439 IIYIVHDEVKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IIYIVHDEVKDK 12 1 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 140.24 3.58E-05 287950000 454690 362050 449550 434620 298590 492760 547340 558360 258380 FALSE TRUE 433197.7048 398943.3066 470162.3122 390931.1719 350664.0015 475695.5976 463833.2304 509467.0383 298448.2508 1.451500231 1.33672523 1.575356233 1.309879253 1.174957469 1.593896417 1.554149603 1.707053189 1 18.18712127 2.182326682 24.99999709 1.517687065 1.379252728 0.018482011 0.211615873 200.5328996 89149.53147 0.070871711 0.052342249 152.1691735 -2.182326682 -0.138434337 IKAEYEGDGIPTVFVAVAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKAEYEGDGIPTVFVAVAGR 20 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 146.72 1.19E-07 826600000 1885550 1601510 1790370 1899610 1561010 1779810 2203320 1981170 1885540 FALSE TRUE 1796423.788 1764705.69 1872460.235 1708657.594 1833249.65 1718174.733 1867163.067 1807688.252 2177939.913 0.824827066 0.810263717 0.859739162 0.784529262 0.841735641 0.788899052 0.85730697 0.829999139 1 21.05453272 -0.23834697 0.69649567 1.010618355 0.819937949 0.832963224 0.024763232 2.644562228 1.144748873 0.097414649 0.007682499 0.577634375 0.23834697 -0.190680406 IKDAFDRNPELQNLLLDDFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 199.7 4.43E-22 661870000 2594800 2276500 2248180 2602800 1449950 2543900 2781500 2961400 1538910 FALSE TRUE 2472148.946 2508477.938 2351261.277 2341161.599 1702820.821 2455804.105 2357131.089 2702084.117 1777556.303 1.390757042 1.411194646 1.322749256 1.317067479 0.957956053 1.381561923 1.326051437 1.52011169 1 20.76146383 3.465358184 2.578362181 1.266365969 1.400103637 0.118948686 0.166621845 0.625691407 8.368461848 0.046098238 0.07116579 2919.834152 -3.465358184 0.133737668 IKDHIQNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKDHIQNGK 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 123.86 0.00032799 1137770000 3181900 3398600 2914900 3660700 2139600 3402300 3242700 3236800 1994050 FALSE TRUE 3031497.893 3744921.204 3048551.048 3292719.481 2512745.563 3284477.498 2747966.559 2953368.633 2303277.09 1.316167259 1.625909979 1.323571125 1.429580269 1.090943671 1.426001896 1.19306816 1.282246346 1 21.13525655 1.226318261 0.243870833 0.92633542 1.527349049 0.45567963 0.131320955 1.837424586 0.442760846 0.437389966 0.328079734 16.83907615 -1.226318261 0.601013629 IKDIAWTEDSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKDIAWTEDSKR 12 2 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 118.52 0.00034675 2051930000 2006830 1540900 1749770 2013410 1511490 1944860 2401520 2146390 1759480 FALSE TRUE 1911971.123 1697919.462 1829998.685 1811018.202 1775093.377 1877509.011 2035124.017 1958440.713 2032331.172 0.940777344 0.835454125 0.900443151 0.891103884 0.873427226 0.923820407 1.001374208 0.96364251 1 20.95470408 1.927929905 3.543917696 0.986774874 0.886800961 0.728238832 0.027818767 0.119882223 2.727539371 0.013001189 0.007350949 84.70906831 -1.927929905 -0.099973914 IKDLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKDLHK 6 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 60.151 0.078573 303050000 2015200 1959700 1627000 2209500 1387600 1927300 2172400 2090400 1314200 FALSE TRUE 1919945.49 2159395.658 1701599.559 1987396.862 1629597.001 1860557.118 1840960.481 1907353.494 1517999.424 1.264786705 1.422527324 1.120948752 1.309221091 1.073516218 1.225663915 1.2127544 1.25649158 1 20.53373981 -4.999999994 0.062091565 0.149857013 1.599301798 0.387632504 0.094441077 346.141617 1.565271411 44.69677443 7.015989113 1.00E-05 4.999999994 1.449444785 IKDMDLWEQQEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IKDMDLWEQQEEER 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 268.92 2.37E-25 1123769000 1314661 1201657 1229229 1406392 988277 1317437 1497026 1462504 1094199 FALSE TRUE 1252519.58 1324107.214 1285590.366 1265018.804 1160632.196 1271813.826 1268627.189 1334439.397 1263881.793 0.991010067 1.047651151 1.01717611 1.000899619 0.918307553 1.00627593 1.00375462 1.05582611 1 20.26943011 -1.406230616 3.470264954 0.999950982 1.005635022 0.001710817 0.036944469 1.39E-05 2.38E-06 0.035481244 0.008290872 0.039243649 1.406230616 0.00568404 IKDPDASKPEDWDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;;;;;; 159.88 9.79E-07 42186247000 57367420 48510840 47272350 58859360 30140270 57050140 59677710 59752060 31277760 FALSE TRUE 54655775.75 53454149.75 49439834.01 52942705.31 35396723.55 55074479.35 50572779.28 54519852.86 36128155.28 1.512830515 1.479570416 1.368457194 1.465414021 0.979754523 1.524419914 1.399816262 1.509068272 1 25.10662026 -1.99720718 2.803200735 0.596737727 1.410615608 0.389124244 0.159298845 81550333.07 87443106.88 212498113.3 0.036296913 0.010064514 1.99720718 0.813877881 IKDYLLMEEEFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKDYLLMEEEFIR 13 1 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 160.48 3.99E-05 50159000 99822 77381 80750 96176 90313 86807 112083 91210 97620 FALSE TRUE 95103.61189 85266.21187 84452.46737 86508.20576 106063.5586 83800.85182 94982.6798 83223.16887 112758.411 0.843428096 0.756184936 0.748968229 0.767199582 0.940626581 0.743189364 0.842355607 0.738066173 1 16.78287553 -1.923509273 2.441136855 1.130574583 0.79924817 0.502284594 0.063327568 10113025.07 5071444.626 7539626.979 0.013931377 0.011925888 1.923509273 -0.331326413 IKEDEDDKTVLDLAVVLFETATLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKEDEDDKTVLDLAVVLFETATLR 24 2 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 131.43 3.17E-05 349680000 196270 190520 172190 225940 91488 227180 219980 242510 85787 FALSE TRUE 186992.7061 209934.2046 180085.0818 203228.0819 107443.4782 219312.6996 186418.0108 221274.5388 99090.40982 1.887091863 2.118612739 1.817381542 2.050935931 1.084297445 2.213258579 1.881292157 2.233057055 1 16.59645782 IKEEEPDPEEWQLS(ph)GDSTLNTNDLTHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.759)GDS(0.102)T(0.114)LNT(0.02)NDLT(0.005)HLR 61.555 0.019119 23824000 40269 30991 31771 39760 25710 28990 37393 37070 29545 TRUE FALSE 38365.56418 34149.01813 33227.73178 35763.24926 30193.81586 27986.06903 31688.01108 33823.95428 34126.68771 1.124210017 1.000654339 0.973658272 1.047955476 0.884756708 0.820064029 0.928540483 0.99112913 1 15.05861277 4.344895426 0.670651627 0.922105394 1.183964652 0.44977154 0.062276083 1.688595548 0.807848324 0.028281118 0.311873268 22125.6188 -4.344895426 0.261859258 IKEEPVS(ph)EEGEEDEEQEAEEEPMDTSPSGLHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK 137.97 6.41E-09 304521000 74275 54915 64883 79274 55305 74848 89726 88846 53352 TRUE FALSE 70764.16795 60510.90093 67857.94973 71305.22691 64950.17449 72255.99499 76036.65077 81066.17324 61625.55568 1.148292574 0.981912459 1.101133271 1.157072356 1.053948703 1.172500502 1.233849333 1.315463566 1 15.91124113 2.098522701 4.682292898 1.207869612 1.083387916 0.179382311 0.092331831 0.256965569 9.676484208 0.033072102 0.023799212 125.4650317 -2.098522701 -0.124481696 IKEEVLS(ph)ESEAENQQAGAAALAPEIVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.646)ES(0.354)EAENQQAGAAALAPEIVIK 156.96 4.94E-09 154530000 229160 207980 225690 236710 150170 275710 292790 275630 184880 TRUE FALSE 218328.061 229173.3985 236038.1097 212915.4611 176359.6005 266162.0936 248119.508 251494.376 213550.2462 1.022373258 1.07315914 1.105304789 0.997027467 0.825845924 1.246367533 1.16187882 1.177682445 1 17.70421604 2.20278915 24.99991225 1.163261903 1.019894422 0.340442047 0.095502759 192.2958997 134390.4143 0.034056521 0.025153267 159.5104535 -2.20278915 -0.143367481 IKEEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKEEYK 6 1 Q5VWI1 Q5VWI1 TCERG1L Transcription elongation regulator 1-like protein 0 102.72 0.032194 1664600000 3188700 2643400 2986900 3968600 2375300 3730600 4220000 4026700 2781000 FALSE TRUE 3037976.47 2912765.465 3123852.319 3569668.788 2789551.568 3601408.387 3576161.494 3674100.801 3212263.277 0.9457433 0.906764239 0.972477051 1.111262833 0.868406892 1.121143591 1.113284058 1.143773248 1 21.61515871 2.752390831 0.779986759 1.103794706 0.92697997 0.308289427 0.081561868 0.632785489 0.83070498 0.051203832 0.049821883 565.4456031 -2.752390831 -0.176814736 IKENKGEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKENKGEER 9 2 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 85.29 0.0083888 354030000 736660 609190 599790 727560 511030 676240 818810 810370 578800 FALSE TRUE 701839.5417 671267.1536 627290.9648 654424.2865 600153.4702 652821.6392 693885.496 739409.7068 668557.3479 1.049782108 1.004053214 0.938275477 0.97886036 0.897684353 0.976463188 1.03788478 1.105977982 1 19.35069179 1.637508563 4.304810828 1.057984438 0.979398427 0.353074975 0.046766592 0.197712447 8.388430282 0.027959232 0.012851821 43.40188215 -1.637508563 -0.078586011 IKESYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IKESYR 6 1 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ;;; 114.19 0.023257 993180000 1008320 853500 836510 1032160 916410 937260 1192480 1012670 980070 FALSE TRUE 960658.7119 940472.6203 874864.8109 928405.3158 1076231.614 904802.4512 1010545.275 923995.2463 1132054.25 0.84859777 0.830766388 0.772811737 0.820106736 0.95068908 0.799257148 0.89266506 0.816211101 1 20.11051167 -4.999999953 0.237300526 1.885167067 0.826382626 0.499749056 0.049827583 136.0865829 1.35832886 58.02277607 0.073885748 1.00E-05 4.999999953 -1.058784441 IKETVDQVEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKETVDQVEELRR 13 2 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 164.68 2.06E-05 296730000 485290 386720 456850 496270 424910 486010 604880 520520 516250 FALSE TRUE 462351.3035 426127.2077 477797.0244 446383.9967 499014.1695 469179.3518 512594.4466 474940.5093 596307.4134 0.775357296 0.714609945 0.801259575 0.748580324 0.836840459 0.786807847 0.859614412 0.796469235 1 19.18569675 -5 0.131286406 1.748591317 0.695281162 0.803111598 0.034387719 51.97288036 0.428892004 10.12739984 0.223178145 1.00E-05 5 -1.053310155 IKEWVDKYDPGALVIPFSGALELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKEWVDKYDPGALVIPFSGALELK 24 2 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 158.53 1.29E-11 330130000 1360160 1227720 1117480 1457820 811260 1413710 1553700 1553580 915980 FALSE TRUE 1295867.932 1352826.064 1168717.563 1311277.164 952743.4871 1364752.868 1316654.529 1417540.299 1058025.5 1.224798393 1.278632758 1.104621357 1.239362533 0.900491989 1.289905459 1.244444987 1.339797858 1 20.01294297 -2.250006317 2.443752582 0.155980861 1.206725211 0.21021708 0.123295752 7491430.173 1353326.64 35648465.69 0.028899127 0.005623331 2.250006317 1.05074435 IKFPLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKFPLPHR 8 1 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 73.931 0.02541 1049450000 3274700 2695400 2118700 2430300 2938900 2474900 3810900 2955300 3021700 FALSE TRUE 3119911.421 2970064.324 2215844.491 2186001.627 3451443.23 2389193.592 3229477.213 2696518.265 3490289.803 0.893883201 0.850950635 0.634859744 0.62630949 0.988870101 0.684525849 0.925274804 0.772577183 1 21.7349154 1.657206197 12.38702663 0.886245683 0.79360171 0.157045145 0.126484875 0.280478657 58.43931395 0.057977619 0.03166152 45.41571932 -1.657206197 -0.092643973 IKFSDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IKFSDDR 7 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;; 86.833 0.034094 492780000 4072840 1794690 2790610 3745980 4473800 2996910 6000200 3780300 5476900 FALSE TRUE 3880324.925 1977570.951 2918562.229 3369426.974 5254029.304 2893126.255 5084759.289 3449276.891 6326229.68 0.613370858 0.312598665 0.461343071 0.532612179 0.830515104 0.457322355 0.803758249 0.545234218 1 22.5929145 0.376427473 0.228675389 1.160210564 0.391278834 0.487238741 0.147492173 4.327786165 0.507995264 0.991496734 0.359946004 2.379180944 -0.376427473 -0.76893173 IKGDVDVSVPEVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKGDVDVSVPEVEGK 15 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 123.97 9.07E-05 269460000 310390 274730 257080 353510 209600 285450 302740 313270 193100 FALSE TRUE 295718.4798 302725.2993 268867.3723 317974.5032 246154.1736 275564.7949 256551.4528 285838.4181 223044.9618 1.325824522 1.357238903 1.20544024 1.425607199 1.103607863 1.235467471 1.150223035 1.281528243 1 17.76697503 -4.738546555 0.060365622 4.13E-11 1.700288378 0.516893733 0.087348148 256.5362067 1.183465498 38.42219292 6.816322005 1.83E-05 4.738546555 1.700288378 IKGEHPGLSIGDVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKGEHPGLSIGDVAK 15 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 189.37 1.57E-07 9501300000 20092400 16657100 17205800 20006600 13107400 19713100 22987000 21355900 14087200 FALSE TRUE 19142672.07 18354477.43 17994702.95 17995498.56 15393326.41 19030430.4 19479910.96 19485864.18 16271771.03 1.176434454 1.127995066 1.10588472 1.105933615 0.946014197 1.169536516 1.19715985 1.197525712 1 23.95586795 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.622)S(0.377)PGIQDTLEAEDGAFETDEAPEDR;IKGS(0.596)S(0.404)PGIQDTLEAEDGAFETDEAPEDR 199.22 2.93E-25 188924000 143458 144930 149964 164228 100231 157275 178600 174075 132333 TRUE FALSE 136677.0246 159698.5318 156839.9977 147719.4894 117711.2547 151828.5273 151351.2898 158832.0702 152854.5258 0.894164068 1.044774638 1.026073627 0.966405729 0.770086813 0.993287746 0.990165577 1.0391061 1 17.22179974 1.777062678 3.372154232 1.012510004 0.951578612 0.132300234 0.076741898 0.554671726 12.25316018 0.04282249 0.021365626 59.84979645 -1.777062678 -0.060931392 IKGSEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IKGSEADR 8 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 107.24 0.0036849 692480000 1688850 1333580 1468300 1750580 1409910 1601230 1934930 1709590 1645720 FALSE TRUE 1609021.407 1469473.318 1535623.007 1574608.373 1655797.858 1545779.004 1639720.891 1559889.236 1900929.852 0.846439128 0.773028692 0.807827288 0.828335864 0.87104627 0.813169935 0.862588848 0.82059274 1 20.85827386 -4.999999998 0.226893964 1.925476518 0.805629844 0.79330331 0.027707288 65.9101866 0.659377523 27.92505923 0.046721883 1.00E-05 4.999999998 -1.119846673 IKIIAPPER ddPTM_SK-BR-3_Trastuzumab_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 ; 112.13 0.0018355 3737300000 4244500 3641100 4695000 3353500 3779900 4053700 4715200 4274500 4489800 FALSE TRUE 4043870.897 4012132.23 4910270.394 3016399.809 4439113.363 3913319.353 3995809.639 3900202.119 5186055.253 0.779758545 0.773638543 0.946821843 0.581636651 0.855971089 0.754584971 0.770491143 0.752055643 1 22.30620615 -1.758916211 3.136656582 1.039113901 0.776884525 0.372883397 0.090938639 40284538.61 32911080.83 12020222.67 0.018960109 0.01742143 1.758916211 -0.262229376 IKISFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKISFR 6 1 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 108.98 0.027312 609970000 1129410 763540 1060580 943480 1261850 1043180 1517490 1131550 1528310 FALSE TRUE 1076025.028 841345.5941 1109208.642 848639.5979 1481916.24 1007054.415 1285969.03 1032465.483 1765312.509 0.609537984 0.47659867 0.62833557 0.480730519 0.839463966 0.570468067 0.72846537 0.584862724 1 20.75149217 -5 0.154081337 2.43967522 0.492766146 0.582095152 0.1045553 83.72110125 0.755926532 36.72275715 0.432386503 1.00E-05 5 -1.946909074 IKKPEGKPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKKPEGKPDQK 11 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 64.827 0.029402 934040000 1226900 982950 1004900 1222500 593930 1361200 1257800 1323200 602580 FALSE TRUE 1168906.868 1083113.723 1050975.659 1099611.977 697511.204 1314061.303 1065899.509 1207333.593 696025.0288 1.679403498 1.556141917 1.509968199 1.579845454 1.002135232 1.88795122 1.531409741 1.734612325 1 19.40877966 4.288498684 1.420329301 1.498000479 1.688616777 0.048751382 0.280832446 2.112246653 6.637997879 0.072758471 0.454785588 19431.15804 -4.288498684 0.190616299 IKLEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IKLEAER 7 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 92.062 0.014542 577630000 1097800 905770 758820 1058500 888260 957070 1155760 1068970 972590 FALSE TRUE 1045909.17 998068.9928 793612.6476 952097.569 1043172.263 923926.4259 979427.585 975365.3198 1123414.29 0.931009316 0.88842469 0.706429191 0.847503523 0.928573076 0.822427162 0.871831161 0.868215162 1 20.09945863 0.28049071 1.553287473 1.000034894 0.860526857 0.333491319 0.063116173 9.725567065 19.48968515 0.061122548 0.017439243 1.907614916 -0.28049071 -0.139508037 IKLNGLENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKLNGLENR 9 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 ; 145.25 8.90E-05 974940000 2321100 1785210 1573480 1913500 1809310 1906540 2511900 2155800 2084900 FALSE TRUE 2211386.203 1967124.929 1645625.614 1721151.345 2124853.091 1840516.042 2128663.521 1967026.723 2408215.644 0.918267518 0.816839195 0.683338146 0.714699844 0.882335059 0.764265462 0.883917321 0.816798416 1 21.19953315 0.346780603 0.746488957 1.002453833 0.805945513 0.403686206 0.073618312 2.592983836 2.019999337 0.092122472 0.026707475 2.222187004 -0.346780603 -0.196508319 IKLYSESLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKLYSESLAR 10 1 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 221.32 4.95E-09 2444500000 4836400 2803200 3300600 3086100 4899200 3559200 6261000 4367400 5713500 FALSE TRUE 4607792.957 3088849.267 3451935.775 2775879.365 5753618.929 3435944.012 5305769.459 3984967.303 6599520.399 0.698201184 0.468041476 0.523058581 0.420618348 0.871823796 0.52063541 0.803962885 0.603826803 1 22.65392975 0.401264809 0.380493718 1.048162525 0.545033629 0.452451941 0.139100632 2.381072052 0.632519647 0.355319448 0.102635376 2.519212539 -0.401264809 -0.503128896 IKNENTEGS(ph)PQEDGVELEGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENT(0.003)EGS(0.997)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.003)EGS(0.997)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.005)EGS(0.995)PQEDGVELEGLK;IKNENT(0.023)EGS(0.977)PQEDGVELEGLK;IKNENT(0.011)EGS(0.989)PQEDGVELEGLK;IKNENT(0.046)EGS(0.954)PQEDGVELEGLK 320.91 9.20E-67 7549660000 4213670 4096370 3894290 4827981 2294359 4949177 4627243 4927329 2449760 TRUE FALSE 4014498.17 4513794.76 4072847.048 4342663.177 2694494.483 4777785.76 3921272.095 4495865.951 2829656.269 1.418722908 1.59517423 1.439343391 1.53469636 0.95223385 1.6884686 1.38577683 1.588838192 1 21.43219538 -1.529255455 3.119878245 0.984627079 1.454337505 0.335132177 0.199304961 21066840.95 24073529.16 2731287.518 0.04312445 0.029562731 1.529255455 0.469710426 IKNENTEGS(ph)PQEDGVELEGLKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKNENTEGSPQEDGVELEGLKQR 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENT(0.001)EGS(0.999)PQEDGVELEGLKQR 76.237 0.0084666 442930000 98490 31918 125670 73609 77501 100400 191360 135180 150850 TRUE FALSE 93834.57289 35170.48049 131432.0938 66209.68347 91017.14986 96923.12283 162164.5174 123342.9226 174243.0476 0.538526927 0.201847253 0.754303231 0.37998465 0.522357426 0.556252454 0.930679988 0.707878588 1 17.41074157 1.886197418 3.096176524 0.869425984 0.456839749 0.576199761 0.156384652 0.173224872 2.900868624 0.077313729 0.04109272 76.94801449 -1.886197418 -0.412586235 IKNEVDSTLTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKNEVDSTLTFR 12 1 P21912;A0A087WWT1;A0A087WXX8 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 67.275 0.050891 308540000 337490 251150 290090 294630 250490 234590 310970 261610 298530 FALSE TRUE 321537.5165 276742.4705 303390.9134 265013.2326 294175.3767 226466.0895 263525.8151 238702.0415 344824.5077 0.932467123 0.802560329 0.879841504 0.768545236 0.853116209 0.656757523 0.764231687 0.6922421 1 18.39550279 4.463381257 0.632482761 0.768347202 0.984706117 0.127880631 0.097775627 3.806782716 1.452802142 0.041331088 0.567667374 29065.73145 -4.463381257 0.216358916 IKPHLMSQELPEDWDKQPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IKPHLMSQELPEDWDKQPVK 20 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;; 139.98 5.78E-06 2094630000 3172830 2466250 2325600 3231840 1539160 2964860 3376730 3232670 1579370 FALSE TRUE 3022856.614 2717563.679 2432231.06 2906969.303 1807589.017 2862186.155 2861547.821 2949600.277 1824290.633 1.657003856 1.489655009 1.333247574 1.593479268 0.990844871 1.568931015 1.568581107 1.616847789 1 20.79890416 4.297685412 1.979043916 1.417609224 1.652733167 0.111741313 0.231297762 0.849545739 5.986171624 0.056993311 0.261591937 19846.56778 -4.297685412 0.235123943 IKPNLSS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKPNLSSSPR 10 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 IKPNLS(0.088)S(0.456)S(0.456)PR 73.435 0.027251 80680000 356560 308960 306740 345270 279720 325250 381680 342080 345880 TRUE FALSE 339706.1154 340443.3753 320804.3324 310562.8036 328503.0794 313986.5109 323447.706 312125.6617 399517.3039 0.850291369 0.852136746 0.802979819 0.777345063 0.822249941 0.785914672 0.809596237 0.781256929 1 18.60789846 -1.657520437 7.13964919 1.000666939 0.814103965 0.837435778 0.026228112 0.000312579 1.50E-05 0.028508965 0.00669641 0.022002882 1.657520437 -0.186562974 IKPS(ph)SSANAIYSLAARPLPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKPSSSANAIYSLAARPLPVPK 22 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 IKPS(0.482)S(0.342)S(0.176)ANAIYSLAARPLPVPK 151.66 2.45E-08 97143000 142440 122490 138150 145100 114580 159800 177640 173830 135040 TRUE FALSE 135707.1435 134971.8703 144484.3141 130514.2723 134562.7157 154266.0859 150537.7554 158608.5237 155981.3135 0.870021802 0.865307948 0.926292457 0.836730179 0.862684848 0.989003634 0.965101216 1.016843108 1 17.25101368 2.23633394 24.9996618 0.98714993 0.87191371 0.845778939 0.025524955 21.47940922 241151.6533 0.008844555 0.006848604 172.3193072 -2.23633394 -0.11523622 IKPSSS(ph)ANAIYSLAARPLPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKPSSSANAIYSLAARPLPVPK 22 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 IKPS(0.007)S(0.045)S(0.948)ANAIYSLAARPLPVPK 149.04 3.46E-08 178250000 243710 182460 208780 234240 144790 219540 283990 253710 188660 TRUE FALSE 232190.3113 201052.8814 218352.7695 210693.7502 170041.3302 211937.2748 240662.1097 231493.8074 217916.4293 1.065501633 0.92261461 1.002002328 0.966855739 0.780305233 0.972562167 1.104377997 1.062305436 1 17.73341544 1.852200591 6.39368292 1.063739501 0.951966876 0.295266612 0.075855001 0.291306065 14.15465759 0.033476142 0.020279428 71.15420827 -1.852200591 -0.111772625 IKPY(ph)KIELY(ph)QS(ph)S(ph)QNLGFIS(ph)ASTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKPYKIELYQSSQNLGFISASTWK 24 2 A0A075B6G4;F5H0L2;P82279-4;P82279-3;P82279-2;P82279 A0A075B6G4 CRB1 Protein crumbs homolog 1 5 IKPY(0.999)KIELY(0.999)QS(0.999)S(0.999)QNLGFIS(0.377)AS(0.338)T(0.289)WK 42.59 0.0847 587150000 239060 269390 226140 326130 173060 234230 276070 295100 175060 TRUE FALSE 227760.1076 296841.1473 236508.7427 293346.7928 203241.6092 226118.5564 233950.4511 269259.4796 202207.4107 1.126368746 1.468003305 1.169634396 1.450722265 1.005114543 1.11825059 1.156982577 1.331600452 1 17.62547635 2.734818696 24.99948091 1.133648716 1.303920439 0.295785348 0.138395893 421.2221317 2814142.411 0.040638623 0.039688815 543.0235898 -2.734818696 0.170271723 IKQEILPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKQEILPEER 10 1 O75534-2;O75534;O75534-3;O75534-4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 138.45 5.87E-05 551790000 1435170 1324110 1262330 1506880 1215910 1468780 1691160 1595220 1467960 FALSE TRUE 1367332.358 1459038.314 1320209.079 1355405.56 1427964.319 1417915.78 1433142.482 1455534.08 1695603.739 0.806398527 0.860483072 0.778607082 0.799364573 0.842156859 0.836230628 0.845210734 0.858416413 1 20.69336762 0.108905944 0.591402524 1.010104485 0.818830188 0.863862573 0.022157653 1.248675697 0.550179412 0.05095766 0.009253865 1.285008332 -0.108905944 -0.191274296 IKSDFFELLSNHHLDSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKSDFFELLSNHHLDSQSR 19 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 107.72 0.00018636 221745000 440120 294590 421730 431800 495440 420340 640790 502260 108670 FALSE TRUE 419316.3998 324609.0559 441066.7376 388394.6436 581844.5791 405783.5204 543025.7166 458279.4518 125521.9886 3.340581236 2.586073242 3.513860341 3.094235902 4.635399627 3.232768417 4.326140166 3.650989415 1 16.93758059 3.375404483 2.231327764 3.611790786 2.981374056 0 1.006773898 0.804671682 8.138296575 0.266825714 0.397370475 2373.583329 -3.375404483 -0.630416731 IKSDYAQLLEDMQNAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKSDYAQLLEDMQNAFR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 228.46 1.30E-15 968330000 2083100 1474620 2019890 1928830 1848990 1878430 2548800 2247600 2343900 FALSE TRUE 1984635.991 1624885.455 2112503.954 1734940.344 2171453.271 1813379.498 2159933.748 2050788.229 2707380.041 0.733046695 0.600168957 0.780276105 0.640818916 0.802049671 0.669791263 0.797794811 0.757480737 1 21.36846599 -1.053010706 0.257244178 1.191821589 0.662392996 0.67556346 0.062812448 8.048348488 0.482864235 1.173325688 0.086163776 0.088509379 1.053010706 -0.529428593 IKSEEIEITFSYWDGSGHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKSEEIEITFSYWDGSGHRR 20 2 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ; 111.4 0.00010128 121713000 522880 247560 558910 405910 544860 512500 819250 591090 718620 FALSE TRUE 498164.4986 272786.6455 584536.5763 365107.1556 639883.4115 494751.9965 694258.3659 539331.026 830059.9194 0.600154865 0.328634884 0.704210097 0.439856385 0.770888217 0.596043713 0.836395481 0.64974951 1 19.66285596 1.538015437 0.319524661 1.025863222 0.42981609 0.536075252 0.129827834 0.905545994 0.321657476 0.199257295 0.177513802 34.51560075 -1.538015437 -0.596047132 IKSESTNHEQQS(ph)PQSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IKSESTNHEQQSPQSGK 17 1 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 IKS(0.001)ES(0.001)T(0.001)NHEQQS(0.996)PQS(0.001)GK;IKSESTNHEQQS(1)PQSGK 96.718 0.0013602 123850000 103904 98147 113133 138025 83837 114288 158497 146002 109004 TRUE FALSE 98992.66384 108148.2909 118320.26 124150.4648 98458.14626 110330.1779 134315.3717 133217.2909 125907.7836 0.786231486 0.858948413 0.939737454 0.98604281 0.781986176 0.876277659 1.066775761 1.058054451 1 16.94200795 1.76087161 6.203519014 1.045770424 0.866649525 0.614484718 0.063361701 0.110954567 11.11085545 0.031940669 0.017193769 57.65959793 -1.76087161 -0.179120899 IKT(ph)EDGEGIVIALSVDTPPAAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IKTEDGEGIVIALSVDTPPAAVR 23 1 Q01167 Q01167 FOXK2 Forkhead box protein K2 1 IKT(1)EDGEGIVIALSVDTPPAAVR;IKT(1)EDGEGIVIALSVDTPPAAVR;IKT(1)EDGEGIVIALSVDTPPAAVR 201.6 3.60E-24 155886000 319423 282764 280023 344591 189358 332112 330758 358449 220127 TRUE FALSE 304324.5078 311577.9731 292862.3315 309952.058 222381.9752 320610.8782 280294.7923 327061.3053 254263.1709 1.196887881 1.225415273 1.15180791 1.219020658 0.874613395 1.260941083 1.102380621 1.286310181 1 17.95596298 -5 0.258928477 2.07E-11 1.177110779 0.147085328 0.116830405 366.3561203 3.601906662 196.1352454 0.142251824 1.00E-05 5 1.177110779 IKTEPSS(ph)PLSDPSDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.042)S(0.958)PLSDPSDIIR;IKTEPS(0.007)S(0.993)PLSDPSDIIR;IKTEPS(0.005)S(0.995)PLSDPSDIIR;IKTEPS(0.006)S(0.994)PLSDPSDIIR 235.25 2.26E-20 2568520000 3096120 2448930 2870270 3015560 2295550 2886910 3496740 3233270 2765290 TRUE FALSE 2949772.544 2698478.751 3001874.719 2712430.18 2695893.193 2786935.583 2963248.091 2950147.738 3194117.05 0.923501706 0.84482776 0.939813623 0.849195611 0.844018285 0.872521432 0.92772057 0.92361917 1 21.60698575 1.032859256 1.178460441 0.997288253 0.879310719 0.558410687 0.033525386 0.34909385 1.007714911 0.029882437 0.0094256 10.78597119 -1.032859256 -0.117977534 IKVDEFVTHNLSFDEINKAFELMHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKVDEFVTHNLSFDEINKAFELMHSGK 27 2 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 133.62 9.84E-06 49057000 120660 65398 135020 98728 106170 119080 195030 149850 87519 FALSE TRUE 114956.6409 72062.13055 141210.8006 88803.67387 124686.0144 114956.2297 165274.5915 136728.3396 101090.9995 1.137159999 0.712844179 1.39686818 0.878452822 1.233403715 1.137155931 1.634909065 1.352527329 1 16.62529503 2.294289626 1.902940861 1.383746423 1.011967125 0.159062705 0.242574635 0.390366777 2.871926359 0.107137338 0.072913395 196.9199086 -2.294289626 -0.371779297 IKVDFVIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKVDFVIPK 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 91.855 0.0082784 0 568060 506740 478900 552950 393000 530600 656230 622670 464770 FALSE TRUE 541208.9296 558377.3821 500858.0387 497366.4155 461539.0756 512225.189 556110.061 568145.7138 536844.1579 1.008130426 1.040110755 0.932967289 0.92646331 0.859726363 0.954141312 1.035887329 1.058306597 1 19.03414382 -0.804128862 8.015439864 1 0.981218903 0.009539789 0.061412681 0 0 0.06390632 0.015062864 0.156989692 0.804128862 -0.018781097 IKVFGPGIEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKVFGPGIEGK 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 0 134.99 0.001274 0 1030600 752850 822900 989270 755240 903960 1126900 1032900 889610 FALSE TRUE 981885.5805 829566.2709 860630.779 889826.7001 886953.6169 872655.6385 954970.7081 942453.8003 1027566.175 0.955544863 0.807311773 0.837542924 0.865955616 0.863159608 0.849245197 0.929352027 0.917170906 1 19.97079988 1.121825725 1.040108169 0.996374584 0.862484289 0.53941066 0.039962435 0.385698109 0.88846595 0.036947802 0.012298335 13.23810207 -1.121825725 -0.133890295 IKVPVDWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IKVPVDWSK 9 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2 P13797 PLS3 Plastin-3 0 106.62 0.0033868 0 1560400 1397600 1211900 1482100 1132400 1433500 1592600 1610800 1143400 FALSE TRUE 1486642.984 1540017.029 1267466.814 1333116.492 1329890.201 1383857.536 1349619.62 1469749.813 1320712.632 1.125636984 1.166050048 0.959684024 1.009391793 1.006948952 1.047811236 1.021887417 1.112846032 1 20.33288516 3.751650327 24.98218796 1.023787865 1.145843526 0.61948955 0.040131264 436.8972903 833831.8606 0.009772422 0.017482028 5644.82298 -3.751650327 0.122055661 IKWDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IKWDEQTSNTKGDDDEESDEEAVKK 25 3 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQTSNTKGDDDEES(1)DEEAVKK;IKWDEQTSNTKGDDDEES(1)DEEAVKK;IKWDEQTSNTKGDDDEES(1)DEEAVKK 215.47 1.23E-33 1801010000 2353280 1976620 2021520 2340610 732690 2666050 2357780 2735720 568836 TRUE FALSE 2242045.118 2178039.825 2114208.692 2105327.436 860470.904 2573724.02 1998057.357 2496165.854 657048.1817 3.412299403 3.31488601 3.21773768 3.204220778 1.309600921 3.917100894 3.040960181 3.799060592 1 19.32563964 2.977583498 24.7632277 2.809602175 3.314124423 0.095720657 0.931110508 1978.004299 2185078.97 0.260138644 0.277964509 949.6935717 -2.977583498 0.504522248 IKWGDAGAEYVVESTGVFTTMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;; 309.21 3.63E-73 13707879200 19479594 14170617 18169607 18700185 13926140 19502386 24795815 21150335 16727789 FALSE TRUE 18558832.2 15614618.98 19002701.45 16820406.88 16354854.41 18827013.48 21012758.02 19298299.54 19321849.08 0.960510152 0.808132747 0.983482552 0.870538156 0.846443544 0.974389842 1.08751279 0.998781196 1 24.20372983 2.026102213 5.476388287 1.037238959 0.891897785 0.552227706 0.055867826 0.111973929 9.684399807 0.02058503 0.014457326 106.1945461 -2.026102213 -0.145341174 IKYPENFFLLR ddPTM_SK-BR-3_Trastuzumab_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 ; 162.49 2.29E-05 1236790000 3165400 2760100 1442180 1804790 3122500 1870800 3769700 3018600 3072200 FALSE TRUE 3015777.815 3041357.328 1508305.38 1623369.08 3667063.011 1806013.727 3194563.03 2754275.381 3548621.085 0.84984498 0.857053276 0.425039852 0.457464756 1.033376887 0.508933945 0.900226582 0.776153699 1 21.7588271 0.926307109 0.99051756 0.99446851 0.716589788 0.177246873 0.199735272 1.227380953 2.499105202 0.184675549 0.061133192 8.439313284 -0.926307109 -0.277878722 ILAT(ph)PPQEDAPSVDIANIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 1 ILAT(0.967)PPQEDAPS(0.033)VDIANIR;ILAT(1)PPQEDAPSVDIANIR;ILAT(0.941)PPQEDAPS(0.059)VDIANIR;ILAT(1)PPQEDAPSVDIANIR;ILAT(0.891)PPQEDAPS(0.109)VDIANIR 203.56 5.59E-15 311177000 135318 102638 105076 115318 143703 102510.5 145154 104935 137599 TRUE FALSE 128921.7863 113096.9289 109893.8385 103726.0156 168764.7577 98960.53568 123008.0914 95746.3351 158937.1502 0.811149478 0.711582715 0.691429527 0.652622848 1.061833294 0.622639424 0.77394172 0.602416333 1 17.27809686 ILATPPQEDAPSVDIANIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 181.71 7.18E-14 88246000 51946 40412 43749 42285 57394 33483 51738 35480 56920 FALSE TRUE 49490.61553 44530.02874 45754.93492 38034.43146 67403.49543 32323.47531 43844.41787 32373.18311 65746.86289 0.752744897 0.67729511 0.695925751 0.578498042 1.025197134 0.491635249 0.666867071 0.492391297 1 16.00463444 4.589285268 2.627186148 0.686290839 0.756536743 0 0.182868947 2.272670258 25.42303467 0.040522245 0.302525128 38840.54077 -4.589285268 0.070245904 ILCLFRPQS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILCLFRPQSGR 11 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 ILCLFRPQS(1)GR 77.527 0.019606 91630000 38036 32312 26965 29927 44099 29224 44828 32455 44709 TRUE FALSE 36238.11366 35604.62954 28201.37192 26918.6811 51789.85164 28211.96555 37988.66528 29613.06815 51642.24338 0.701714552 0.68944777 0.546091147 0.521253132 1.002858285 0.546296282 0.73561222 0.573427222 1 15.65626405 -1.147759906 4.376912069 1.000061265 0.67084866 0.358127023 0.140898242 18072037.82 4739042.772 10588.66859 0.029552357 0.071160681 1.147759906 -0.329212605 ILCLFRPQSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILCLFRPQSGR 11 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 224.58 5.57E-12 876610000 828030 524910 343030 382870 1045890 436730 976360 610320 1104870 FALSE TRUE 788890.6629 578398.9258 358758.2648 344383.1802 1228292.885 421605.9306 827398.3499 556877.1453 1276207.597 0.618152301 0.453216959 0.28111278 0.269848872 0.962455394 0.330358424 0.64832583 0.436353103 1 20.2834316 -5 0.294289993 4.979453675 0.477614158 0.365057155 0.20710273 275.684679 2.576443234 674.5721941 0.19740793 1.00E-05 5 -4.501839517 ILDAVVAQEPLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILDAVVAQEPLHR 13 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 148.68 4.34E-05 351363000 535237 486214 495660 558636 560006 493498 581691 558885 551656 FALSE TRUE 509937.4077 535759.7594 518386.5013 502480.8479 657670.8691 476408.0405 492943.3545 509946.0666 637203.995 0.8002734 0.840797866 0.813533037 0.788571402 1.032119814 0.747653882 0.773603678 0.800286989 1 19.28139579 5.458876414 0.866687985 0.837318588 0.706941719 0.01184303 0.094767635 45.39841173 10.81060054 0.028865738 7.571447419 287657.972 -5.458876414 -0.130376868 ILDDDTIITTLENLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILDDDTIITTLENLKR 16 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 320.56 7.13E-58 695610000 456830 351630 414890 462450 402650 448660 536460 490970 479810 FALSE TRUE 435236.5512 387461.4968 433913.1169 415963.6474 472872.0325 433122.7917 454613.1742 447978.064 554216.4843 0.785318668 0.699115793 0.78293073 0.750543622 0.853226214 0.781504708 0.82028086 0.808308805 1 19.0800901 -5 0.154113246 1.825765593 0.712910482 0.799030951 0.035378703 51.97332361 0.469320425 13.03430723 0.153336754 1.00E-05 5 -1.112855111 ILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVR 36 1 P38606;C9JVW8 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 207.05 1.29E-30 72583000 160100 142380 142240 168000 116690 150990 194250 180630 134810 FALSE TRUE 152532.3903 156888.6839 148761.8447 151112.3208 137040.6991 145761.1784 164613.5949 164813.0796 155715.6463 0.97955725 1.007533203 0.955342949 0.970437618 0.880070194 0.936072783 1.05714229 1.058423373 1 17.24855439 1.719128741 8.080300887 1.042336203 0.960608123 0.531409021 0.036656147 0.100323572 17.26878779 0.019253465 0.010204745 52.37556744 -1.719128741 -0.08172808 ILDEIEEHNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ILDEIEEHNIK 11 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;C9J2Q4 Q15019-2 2-Sep Septin-2 0 ;;;;; 185.99 4.22E-06 926787000 2224870 1901090 1981380 2266940 2250110 2031350 2523860 2206130 1781230 FALSE TRUE 2119704.804 2094813.232 2072228.233 2039062.884 2642528.472 1961003.84 2138798.803 2012949.562 2057454.051 1.030256206 1.018157966 1.007180808 0.991061202 1.284368159 0.953121572 1.039536607 0.978369145 1 20.97242878 ILDILEYIHEHEYVHGDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDILEYIHEHEYVHGDIK 19 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 102.99 0.00013258 15360000 71314 87855 70638 96912 55176 82417 84644 64636 4648.6 FALSE TRUE 67943.12855 96807.52438 73876.82217 87170.22164 64798.67693 79562.87862 71730.00321 58976.12918 5369.481146 12.65357428 18.02921395 13.75865194 16.23438453 12.06795874 14.8176102 13.35883324 10.98358064 1 12.39056697 0.255172265 0.620211965 0.42618579 15.14396075 0.864128444 1.679998061 0.848000897 0.454475532 2.590040868 0.619625738 1.799584586 -0.255172265 14.71777496 ILDKCNEIINWLDKNQTAEKEEFEHQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDKCNEIINWLDKNQTAEKEEFEHQQK 28 3 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 136.67 4.41E-06 226050000 143250 80216 143740 136740 92736 151670 260270 205130 113480 FALSE TRUE 136478.8564 88390.1016 150330.6212 122994.6354 108909.129 146417.6299 220561.0313 187167.7297 131077.8988 1.041204182 0.67433261 1.146880004 0.93833237 0.83087332 1.117027593 1.682671398 1.427912191 1 17.00006493 1.969195277 6.126182949 1.43816478 0.916773183 0.478462483 0.207436208 0.12614568 15.00399885 0.080904627 0.051518718 93.15266342 -1.969195277 -0.521391598 ILDPNTGEPAPVLSSPPPADVS(ph)TFLAFPSPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDPNTGEPAPVLSSPPPADVSTFLAFPSPEK 32 0 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 1 ILDPNTGEPAPVLS(0.012)S(0.097)PPPADVS(0.527)T(0.364)FLAFPSPEK 167.88 2.65E-14 54406000 181500 160530 165770 184190 141530 157580 188390 191040 164540 TRUE FALSE 172920.8547 176888.1895 173370.7185 165674.8713 166212.7872 152122.9651 159647.6455 174311.5248 190056.0228 0.909841488 0.930716043 0.912208494 0.871715975 0.874546277 0.800411178 0.840003085 0.917158647 1 17.53606522 3.257219103 3.573822261 0.866986314 0.920553114 0.022541578 0.053383804 0.380298053 10.27152509 0.014379117 0.018985524 1808.08608 -3.257219103 0.0535668 ILDQMPATPSS(ph)PMYVD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.002)PS(0.157)S(0.839)PMY(0.001)VD 106.49 0.0012603 24373000 74053 73953 70983 79006 67800 66987 72464 77303 70990 TRUE FALSE 70552.66145 81488.89478 74237.64076 71064.16678 79624.29853 64667.22339 61408.28591 70533.93951 81998.76663 0.860411252 0.993781957 0.9053507 0.866649216 0.971042636 0.788636537 0.7488928 0.860182932 1 16.32331459 2.231717578 24.99725761 0.818549068 0.921176164 0.113699391 0.078229624 194.9906499 712284.3231 0.026666816 0.020133716 170.4973282 -2.231717578 0.102627096 ILDSVGIEADDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILDSVGIEADDDR 13 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;; 164.04 8.77E-05 313122000 556530 603470 413834 594760 399400 481742 485970 540070 403910 FALSE TRUE 530223.9298 664964.2791 432808.6982 534973.5948 469055.2335 465059.1537 411826.351 492778.6077 466546.2999 1.136487268 1.425291079 0.927686488 1.146667748 1.005377673 0.996812436 0.882712715 1.056226591 1 18.83166074 3.729064819 24.99324128 0.996172949 1.280889177 0.584706247 0.097537674 382.3434009 1006339.956 0.025217503 0.039623485 5358.766315 -3.729064819 0.284716228 ILDSVGIEADDDRLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;;;;; 314.84 7.99E-58 21725010000 18625020 15660520 12630600 16375180 12396560 16421590 20229040 19061390 14857750 FALSE TRUE 17744652.22 17256344.79 13209725.5 14729115.8 14558516.14 15852906.22 17142728.42 17392273.64 17161813.99 1.033961342 1.005508206 0.769716157 0.858249356 0.848308702 0.923731386 0.998887905 1.01342863 1 24.03269872 1.717443704 4.384347708 1.006194909 0.918115361 0.261552267 0.075744527 0.332801 14.89267984 0.047452369 0.023359512 52.17274708 -1.717443704 -0.088079548 ILDSVGIEADDDRLNKVISELNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILDSVGIEADDDRLNKVISELNGK 24 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 78.008 0.011667 132610000 225210 205370 228230 211480 180630 242930 282630 266750 199180 FALSE TRUE 214564.7696 226297.4365 238694.5713 190221.6286 212131.8148 234517.2732 239509.6026 243391.9559 230067.8171 0.932615314 0.983611873 1.03749657 0.826806769 0.922040368 1.019339759 1.041039141 1.057913962 1 17.81169966 2.143041382 5.44718169 1.035472994 0.945101714 0.398004379 0.054333775 0.221456894 10.22606462 0.020704454 0.015192172 139.0085079 -2.143041382 -0.09037128 ILDWHVANTDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILDWHVANTDKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 137.16 6.31E-05 4435300000 19540900 16514300 15927700 19321000 12055300 18751600 22578500 21405400 12214600 FALSE TRUE 18617240.38 18197125.95 16658000.8 17378816.37 14157740.5 18102227.39 19133735.14 19531029.7 14108777.78 1.319550188 1.289773375 1.180683476 1.231773343 1.003470373 1.283047169 1.356158232 1.384317621 1 23.75008968 3.911778404 5.821228296 1.225843264 1.308742765 0.079010146 0.128251905 0.629500828 32.86879038 0.032927139 0.060618392 8161.658222 -3.911778404 0.082899502 ILEDMERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILEDMERR 8 1 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 84.476 0.02794 27058000 36751 20005 30362 27208 42242 30188 45100 34304 48921 FALSE TRUE 35013.85306 22043.53224 31754.12773 24473.00015 49608.99143 29142.58199 38219.16668 31300.1599 56507.41883 0.619632852 0.39009979 0.561946173 0.433093577 0.87791997 0.515730193 0.676356618 0.553912399 1 15.78615267 -5 0.168399132 2.681401166 0.465308672 0.506694627 0.132486042 99.44993024 0.934440287 55.67754635 0.444036439 1.00E-05 5 -2.216092494 ILEFFGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILEFFGLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 124.08 0.0030712 69259000 544900 451100 344200 469770 433040 362850 571660 456690 445320 FALSE TRUE 519143.6569 497067.6029 359981.9105 422547.8271 508562.0389 350284.4135 484442.7677 416699.8025 514377.9512 1.009264988 0.966347025 0.69983931 0.821473444 0.988693309 0.680986447 0.941803136 0.810104324 1 18.97246928 3.973336866 24.48295991 0.845751432 0.99317079 0.227131392 0.107500873 631.0877164 579486.3018 0.024636249 0.044472272 9404.525024 -3.973336866 0.147419358 ILEFFGLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILEFFGLKK 9 1 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 129.38 0.0021403 0 341570 256620 233820 319170 227830 285750 402210 324290 264450 FALSE TRUE 325424.663 282769.8698 244540.8783 287086.4252 267563.4799 275854.4058 340845.4774 295893.4484 305459.5554 1.065360888 0.925719509 0.800567126 0.939850858 0.875937502 0.903079969 1.115844869 0.968682902 1 18.22062185 1.757452082 25 1.037888686 0.925222315 0.317379302 0.074991421 9.808552226 12992.76794 0.035826938 0.019868135 57.20738307 -1.757452082 -0.11266637 ILEFFGLKKEECPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILEFFGLKKEECPAVR 16 2 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 152.68 2.95E-07 92742000 257390 110540 273040 178830 247320 230670 462000 298590 400010 FALSE TRUE 245223.6848 121804.1517 285559.1541 160853.6686 290452.5297 222681.8401 391513.4148 272443.8767 462041.5078 0.530739513 0.263621665 0.61803788 0.348136836 0.628628651 0.481952024 0.847355504 0.589652384 1 18.81766294 1.392095277 0.461435661 0.999341662 0.394100123 0.597980279 0.136450446 0.540477017 0.314414095 0.137483771 0.08561596 24.66580403 -1.392095277 -0.605241539 ILEFVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILEFVGR 7 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;P50225;H3BRY5;P50225-2;E9PKW4;P50226 A0A0A6YYL2;P50225;P50226 SULT1A4;SULT1A3;SULT1A1;SULT1A2 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A1;Sulfotransferase 1A2 0 ; 134.44 0.0073853 237600000 400840 363920 349350 425940 414950 360230 459460 400450 430620 FALSE TRUE 381893.0876 401003.8617 365368.0431 383123.702 487317.1486 347755.1448 389360.9384 365384.4751 497398.3503 0.76778117 0.806202637 0.734558212 0.770255273 0.979732137 0.699148167 0.782794994 0.734591248 1 18.9240422 -1.025747523 4.06428915 1.000022907 0.785267142 0.445885396 0.075533713 29476235.02 37591700.83 8406.332538 0.016713718 0.094243732 1.025747523 -0.214755764 ILELDQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILELDQFK 8 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 152.59 0.0010576 39750000 388400 335170 290690 331320 329100 328620 438300 382370 313350 FALSE TRUE 370041.1017 369324.2041 304018.424 298015.0841 386494.9358 317239.807 371429.2851 348887.6557 361942.7176 1.022374767 1.020394074 0.839962815 0.823376379 1.067834541 0.876491753 1.026210135 0.963930586 1 18.46540186 -0.346457284 8.496857569 0.999999999 0.962197045 0.021285433 0.084212691 0 0 0.079447301 0.018725909 0.450342273 0.346457284 -0.037802955 ILELT(ph)PEPDRPR ddPTM_SK-BR-3_Trastuzumab_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 169.3 7.15E-05 2647830000 1434480 1243070 1326010 1410630 1792250 1255440 1469000 1357010 1946940 TRUE FALSE 1366674.973 1369740.246 1386808.87 1268830.792 2104817.833 1211963.798 1244877.07 1238183.01 2248861.512 0.607718602 0.609081635 0.61667153 0.564210284 0.935948177 0.538923269 0.553558796 0.550582152 1 21.10076339 -1.093808365 4.527614749 1.000028395 0.618941037 0.515862924 0.115020724 3.30E-05 6.60E-06 0.105210432 0.024796382 0.08057339 1.093808365 -0.381087358 ILENEKDLEEAEEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILENEKDLEEAEEYK 15 1 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 262.36 4.90E-25 256411000 707840 876110 544464 860040 291367 731600 559700 774690 275826 FALSE TRUE 674381.806 965386.6051 569428.2129 773587.1452 342181.3125 706264.5086 474307.4854 706854.0367 318599.6874 2.1167058 3.030092757 1.78728428 2.428085073 1.074016473 2.216777155 1.488725521 2.218627528 1 18.28138533 3.249812069 1.627041564 1.687455642 2.53317562 0.290225472 0.523227398 0.391169678 2.144785981 0.154044582 0.222478948 1777.510069 -3.249812069 0.845719978 ILENEKDLEEAEEYKEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 156.29 7.12E-09 1341830000 1332520 1109810 1174590 1329040 642980 1274920 1424380 1515110 678950 FALSE TRUE 1269534.42 1222900.901 1228446.113 1195442.374 755115.5084 1230769.201 1207064.67 1382438.936 784238.0984 1.618812479 1.559349008 1.566419836 1.52433601 0.962865117 1.569382058 1.539155867 1.762779619 1 19.5809322 2.986537002 24.80843361 1.409585617 1.577510797 0.133277197 0.244164705 1398.649053 2577313.673 0.069996072 0.077358761 969.4758665 -2.986537002 0.167925181 ILENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 177.57 0.0084773 2527680000 2105540 1621720 1671570 1971100 2157110 1558700 2055870 1843200 1945720 FALSE TRUE 2006015.297 1786975.112 1748213.138 1772961.283 2533309.301 1504721.828 1742209.273 1681799.637 2247452.32 0.892573017 0.795111467 0.777864394 0.788876039 1.127191566 0.66952336 0.775192985 0.748313822 1 21.09985908 -1.393064017 6.881156232 1.000011971 0.820294997 0.175169235 0.121462798 2.09E-05 1.84E-06 0.109957465 0.025915498 0.040451626 1.393064017 -0.179716974 ILEPDDFLDDLDDEDYEEDT(ph)PKRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILEPDDFLDDLDDEDYEEDTPKRR 24 2 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 1 ILEPDDFLDDLDDEDYEEDT(1)PKRR;ILEPDDFLDDLDDEDYEEDT(1)PKRR 315.3 6.31E-72 197293000 220333 174808 216787 217795 159441 204719 278900 261960 192528 TRUE FALSE 209918.2957 192621.1339 226726.8984 195901.8328 187247.4599 197629.5297 236348.6827 239021.3937 222384.2589 0.94394404 0.866163526 1.019527639 0.880915914 0.841999613 0.888684886 1.062794119 1.074812556 1 17.76269515 1.724965743 6.671187447 1.05051986 0.905849639 0.611515039 0.052066558 0.083418142 9.844976769 0.025075365 0.013042017 53.08425698 -1.724965743 -0.14467022 ILEPDDFLDDLDDEDYEEDTPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 144.88 2.33E-07 30546000 31101 25342 21225 26073 23943 27522 30664 36841 22734 FALSE TRUE 29630.91737 27924.37861 22198.18724 23452.0925 28118.65162 26568.90624 25985.64362 33615.00673 26259.47261 1.12838966 1.063402111 0.845340178 0.893090766 1.070800318 1.011783695 0.989572182 1.280109743 1 14.68055032 1.293900586 24.99997997 1.14006075 1.008293205 0.228922126 0.105822758 119.6836019 54066.92327 0.070380403 0.025701054 19.67435873 -1.293900586 -0.131767545 ILEQEEEEEQAGKPGEPSKKEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILEQEEEEEQAGKPGEPSKKEEGR 24 3 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 110.9 0.00082544 79974000 84245 47437 86615 75351 41392 88931 108530 99734 53283 FALSE TRUE 80262.90581 52270.88423 90586.38342 67776.57432 48610.75169 85851.29717 91971.75521 91000.76224 61545.85551 1.304115527 0.849299824 1.471851885 1.101237017 0.789829815 1.394915977 1.494361472 1.478584731 1 15.90937409 2.093768022 24.99999138 1.395684179 1.102618199 0.183470821 0.238541716 20.66803519 5498.521899 0.08286861 0.061202526 124.0989257 -2.093768022 -0.29306598 ILEQQNSSRT(ph)LEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILEQQNSSRTLEK 13 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 1 ILEQQNSS(0.008)RT(0.992)LEK;ILEQQNS(0.004)S(0.203)RT(0.793)LEK;ILEQQNS(0.001)S(0.093)RT(0.906)LEK 144.97 6.72E-05 1153430000 863800 615410 731040 820150 767760 792590 977160 935840 805040 TRUE FALSE 822969.8859 678120.9787 764558.9071 737706.9638 901657.1009 765142.4096 828076.2952 853892.8884 929881.4916 0.885026633 0.72925527 0.822211125 0.793334388 0.969647325 0.822838627 0.890518096 0.918281411 1 19.82668734 1.318067174 0.41730385 1.004755391 0.799243561 0.472654606 0.059293789 0.874964513 0.443174614 0.071829902 0.046521858 20.80018386 -1.318067174 -0.20551183 ILESDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILESDRK 7 1 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;; 104.37 0.013096 1490220000 2316089 1800984 1801070 1784304 1487192 1630972 2005895 1845088 1656455 FALSE TRUE 2206612.063 1984506.317 1883650.841 1604942.372 1746557.814 1574491.031 1699858.877 1683522.313 1913329.581 1.153283828 1.037200457 0.984488433 0.8388217 0.912836884 0.822906334 0.888429727 0.879891436 1 20.86765398 3.818196243 1.326361878 0.880872216 1.138447151 0.735054845 0.051787426 0.190036717 0.629614738 0.014288834 0.04121467 6579.550785 -3.818196243 0.257574934 ILEVHIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;;; 104.17 0.0046324 497520000 1947210 1683520 1687710 2056160 1614460 1907940 2160680 2091250 1561220 FALSE TRUE 1855169.242 1855072.602 1765093.173 1849470.89 1896021.313 1841867.559 1831028.582 1908129.064 1803326.024 1.028748666 1.028695076 0.978798703 1.025588754 1.051402402 1.021372472 1.015361925 1.058116524 1 20.78222882 3.016359828 24.99891172 1.029310742 1.016043592 0.110077125 0.021455847 649.4807613 992441.4446 0.006019202 0.007191649 1038.3884 -3.016359828 -0.01326715 ILEVHVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 107.69 0.0039539 524740000 3554800 3074500 3154400 3720500 2806200 3549300 4037200 3897500 2693700 FALSE TRUE 3386771.649 3387795.045 3299032.36 3346508.272 3295600.392 3426386.851 3421250.992 3556214.238 3111425.238 1.088495268 1.088824184 1.060296201 1.075554775 1.05919318 1.10122744 1.099576795 1.142953459 1 21.56914415 2.211349016 24.99507301 1.095059202 1.077109301 0 0.036910601 682.9601593 627325.6632 0.012285281 0.009075254 162.6855635 -2.211349016 -0.017949902 ILFEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILFEDFR 7 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 76.035 0.097366 15982000 124550 115040 109810 131520 125970 115290 138380 136890 133530 FALSE TRUE 118662.7683 126762.7068 114844.8971 118299.3597 147939.1281 111297.4784 117267.5895 124903.1859 154237.1504 0.769352701 0.821868833 0.744599448 0.766996534 0.959166632 0.72159968 0.760307028 0.809812588 1 17.23479078 0.95114605 20.64546293 1.000000001 0.791168425 0.498222008 0.065138335 1071.922742 452991.6627 0.058708775 0.014677194 8.936059462 -0.95114605 -0.208831575 ILFIFIDSDHTDNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ILFIFIDSDHTDNQR 15 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 344.45 3.60E-70 2127158200 1724678.9 1358633.7 1309193.8 1888735.7 1575249.6 1437366 2013894.7 1668901.3 1333684.9 FALSE TRUE 1643156.746 1497080.019 1369221.631 1698876.399 1849972.631 1387589.655 1706638.076 1522763.455 1540505.943 1.066634474 0.971810609 0.888812949 1.102804184 1.200886397 0.900736321 1.107842578 0.988482688 1 20.55497282 4.754720566 22.22314048 1.024318231 1.066634605 0.021116077 0.095788808 355.0731679 1671054.43 0.021605135 0.168821173 56848.70365 -4.754720566 0.042316374 ILFQEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILFQEFR 7 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 77.058 0.090912 8836000 32808 26135 17713 25356 37132 23466 33286 28070 36203 FALSE TRUE 31257.23086 28798.18621 18525.15857 22807.16671 43607.80904 22653.36654 28207.60936 25612.04199 41817.17634 0.747473493 0.688668837 0.443003574 0.545401883 1.042820507 0.541723964 0.674546008 0.6124766 1 15.35180803 ILFRPVASQLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILFRPVASQLPR 12 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 170.23 3.80E-05 582780000 1180940 677150 392050 545080 1443860 521880 1258200 822210 1282290 FALSE TRUE 1125119.307 746152.3549 410025.8803 490287.5228 1695668.727 503807.1647 1066238.482 750212.9336 1481140.984 0.759630122 0.503768624 0.276831095 0.331020158 1.144839516 0.340148014 0.719876428 0.506510144 1 20.49827754 ILGADTSVDLEETGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILGADTSVDLEETGR 15 0 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4;K7ESA0 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 212.9 1.50E-09 280605000 479609 422207 382591 443195 434381 379537 469166 444320 466576 FALSE TRUE 456938.8331 465230.3733 400133.1758 398644.1966 510136.9089 366393.5385 397586.1099 405412.9853 538930.2231 0.847862698 0.863247881 0.742458223 0.739695381 0.946573206 0.679853389 0.737732071 0.752255056 1 19.03973897 3.756380001 23.23506171 0.78254157 0.855555313 0.029290253 0.100678476 748.3727522 975811.047 0.023552206 0.042313345 5706.633752 -3.756380001 0.073013743 ILGETS(ph)LMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILGETSLMR 9 0 O96017-13;O96017-4;O96017-12;O96017;O96017-9;H0Y820 O96017-13 CHEK2 Serine/threonine-protein kinase Chk2 1 ILGET(0.194)S(0.806)LMR;ILGET(0.041)S(0.959)LMR 111.27 0.0022581 96381000 306070 235948 244416 285360 330710 270150 356630 300540 351590 TRUE FALSE 291602.6777 259991.3695 255622.7154 256675.0707 388385.7193 260794.6378 302219.5435 274223.1243 406112.7815 0.718033736 0.640194993 0.62943775 0.632029038 0.956349411 0.642172937 0.74417639 0.675238842 1 18.63152091 -5 0.240186267 2.69550587 0.672409525 0.476646195 0.097195794 145.3459273 1.448963429 120.4235639 0.142201397 1.00E-05 5 -2.023096344 ILGQGT(ph)HRPTPNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILGQGTHRPTPNSR 14 1 K7ELA6 K7ELA6 TPGS2 1 ILGQGT(1)HRPTPNSR;ILGQGT(1)HRPTPNSR 55.755 0.072159 1155130000 162605 90628 161267 127109 188792 119732 247712 170716 284395 TRUE FALSE 154918.9839 99863.09624 168661.2515 114331.7618 221717.265 115585.6508 209918.9849 155767.202 328497.5241 0.471598635 0.30399954 0.513432337 0.348044516 0.674943489 0.351861559 0.639027601 0.474180749 1 18.32552297 -5 0.179736279 3.23090252 0.351035239 0.68534673 0.11473137 65.92866587 0.634379766 52.27286607 0.306874901 1.00E-05 5 -2.879867281 ILGQS(ph)SPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILGQSSPEKK 10 1 P29374;P29374-3;P29374-2;H7C485 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 ILGQS(0.5)S(0.5)PEKK 55.291 0.080581 166870000 269330 222070 207490 262940 219990 231310 247930 269400 189290 TRUE FALSE 256599.3047 244699.1855 217003.6217 236508.7716 258356.1863 223299.6767 210103.725 245809.9078 218644.1264 1.173593404 1.119166517 0.992496918 1.081706495 1.181628752 1.021292821 0.960939259 1.124246564 1 17.73822507 8 0.260499573 1.016291965 2.113156631 0.253986804 0.06677526 60.54620859 0.837713096 0.08122799 29.5068394 100000000 -8 1.096864667 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGS(0.082)AS(0.918)PEEEQEKPILDRPTR;ILGSAS(1)PEEEQEKPILDRPTR;ILGSAS(1)PEEEQEKPILDRPTR;ILGS(0.001)AS(0.747)PEEEQEKPILDRPT(0.252)R;ILGS(0.029)AS(0.644)PEEEQEKPILDRPT(0.327)R;ILGS(0.032)AS(0.968)PEEEQEKPILDRPTR 364.26 1.73E-112 2518842000 1502437 1182464 1245878 1479417 936964 1415414 1560497 1531099 1064314 TRUE FALSE 1431419.781 1302958.426 1303002.739 1330703.192 1100370.225 1366397.858 1322414.522 1397027.855 1229362.379 1.164359512 1.059865218 1.059901263 1.082433638 0.895073937 1.111468743 1.075691386 1.136384095 1 20.22947881 4.564184709 1.70384528 1.054042493 1.182925108 0.218811977 0.066336283 0.982088644 3.708329748 0.016748454 0.18597332 36659.34566 -4.564184709 0.128882615 ILGSASPEEEQEKPILDRPT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGSAS(0.351)PEEEQEKPILDRPT(0.649)R;ILGSAS(0.118)PEEEQEKPILDRPT(0.882)R 155.06 4.49E-08 1149490000 1155680 984350 957540 1161740 788330 1118670 1282600 1180150 844500 TRUE FALSE 1101053.297 1084656.384 1001444.156 1044959.688 925814.5024 1079930.177 1086915.813 1076809.81 975460.7469 1.128752028 1.111942626 1.026637063 1.071247297 0.949104826 1.107097524 1.114258894 1.103898658 1 19.89572429 3.887891809 6.191725718 1.061007069 1.122520765 0.215048767 0.052047931 0.363924627 17.4404606 0.013582555 0.024823629 7724.88119 -3.887891809 0.061513697 ILHDWPDDKVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILHDWPDDKVHK 12 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 165.58 3.50E-05 167430000 203280 202180 195450 241480 159520 236430 254190 239520 80835 FALSE TRUE 193671.3573 222782.3719 204411.5758 217205.9716 187340.2375 228242.3698 215408.647 218546.359 93370.47895 2.074224738 2.386004381 2.189252729 2.326281005 2.006418298 2.444481086 2.307031616 2.340636585 1 16.51067886 -0.750911408 5.193196378 0.99999959 2.263491851 0.894080732 0.13620908 0.000125469 21530820.03 25.51531552 0.02912324 0.177455144 0.750911408 1.263492262 ILHGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILHGFK 6 0 O14787-2;O14787;K7ESG1;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 89.775 0.049783 422330000 1290000 1193300 1101400 1344200 1107600 1282300 1477100 1319300 1040600 FALSE TRUE 1229024.257 1314898.627 1151900.279 1209078.462 1300765.089 1237893.629 1251741.266 1203775.098 1201970.933 1.022507469 1.0939521 0.958342875 1.005913229 1.082193465 1.029886493 1.041407268 1.001501005 1 20.19697058 -4.999999999 0.13430181 0.876946543 1.048564488 0.048372131 0.038880387 396.1131077 3.31493867 12.92250798 0.261987746 1.00E-05 4.999999999 0.171617944 ILHLLGQEGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILHLLGQEGPK 11 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 162.36 2.52E-05 406960000 475150 420450 362020 469490 378460 479860 491940 516140 357150 FALSE TRUE 452690.6012 463294.333 378618.9751 422295.9732 444463.3042 463242.3279 416885.5179 470944.0454 412534.9979 1.097338658 1.123042494 0.917786314 1.023660963 1.077395388 1.122916432 1.01054582 1.141585678 1 18.65415699 ILHVNGFNGEGGEEDPQAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILHVNGFNGEGGEEDPQAAR 20 0 P63092-4;P63092;A0A590UJ58;B0AZR9;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJ22;S4R3E3;Q5JWD1;S4R3V9;Q5JWE9;A0A590UJY8;A0A590UJB7;H0Y7E8;A0A590UJX3;Q5JWF2 P63092-4;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 109.5 0.00019655 60856000 45872 45662 39228 45311 42051 36973 44116 53321 38233 FALSE TRUE 43703.72147 50315.00971 41026.6426 40756.25219 49384.68109 35692.61574 37385.29395 48651.93057 44161.97837 0.989623271 1.139328707 0.929003729 0.922881032 1.118262426 0.808220489 0.846549347 1.101670087 1 15.43051718 3.719253365 24.46626408 0.944215719 1.064475993 0.130421876 0.104414709 893.9355304 1132800.014 0.027220353 0.042253002 5239.059913 -3.719253365 0.120260274 ILIEDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILIEDWK 7 0 K7ELL7;P14314-2;P14314;K7EPW7 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 102.72 0.019862 36342000 174598 158144 147500 177212 126900 163861 185695 184155 142592 FALSE TRUE 166345.0986 174259.0534 154263.0209 159398.3131 149031.3198 158186.4525 157363.8172 168029.4119 164704.4391 1.009961234 1.058010667 0.93660512 0.967783953 0.904840942 0.960426163 0.955431548 1.020187512 1 17.32951991 3.73786936 24.9965355 0.959141104 1.033985952 0.428298737 0.033494574 46.13113466 1668159.121 0.008194379 0.01355895 5468.514396 -3.73786936 0.074844848 ILIEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ILIEELR 7 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ;;;; 131.04 0.0081542 104760400 388937 412745 395750 498765 384935 384024 405717 423842 414759 FALSE TRUE 370552.7188 454804.1848 413895.529 448628.1946 452067.5421 370725.1526 343817.4201 386728.1476 479077.7074 0.773471011 0.949332807 0.863942368 0.936441391 0.943620492 0.77383094 0.717665245 0.807234696 1 18.86990016 2.225590655 24.99895061 0.791233639 0.890715839 0.076248374 0.089655792 333.5233786 642845.2722 0.031157933 0.02315226 168.10888 -2.225590655 0.0994822 ILIPS(ph)DIESSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ILIPS(1)DIESSK;ILIPS(1)DIESSK 124.12 0.00037319 49060000 401740 381270 348200 406960 290740 390430 409070 412390 271240 TRUE FALSE 382750.5464 420121.8465 364165.3144 366051.6076 341444.9639 376909.3112 346658.8584 376278.9454 313302.5139 1.22166446 1.340946299 1.162344055 1.168364732 1.089825165 1.203020386 1.106466891 1.201008382 1 18.25719682 7.999999996 0.051657333 0.671482677 2.141840254 0.522804981 0.062308773 311.9926979 1.214681101 7.937380193 36.15173181 99999999.19 -7.999999996 1.470357577 ILIRPMYSNPPLNGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILIRPMYSNPPLNGAR 16 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 213.51 1.59E-12 1024830000 232760 203110 189663 196326 232850 149628 211420 195469 230000 FALSE TRUE 221757.8961 223807.1399 198359.2362 176590.9375 273458.9663 144446.3448 179163.996 178352.6981 265667.2253 0.834720564 0.842434138 0.746645492 0.664707275 1.029328951 0.543711572 0.674392544 0.671338732 1 18.01926073 2.217784394 24.99970008 0.687583366 0.816436743 0.083886068 0.146426769 422.298056 508141.4828 0.049028512 0.036248821 165.1141883 -2.217784394 0.128853377 ILIVTQT(ph)PHYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ILIVTQTPHYMR 12 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 ILIVTQT(1)PHYMR;ILIVTQT(1)PHYMR;ILIVTQT(1)PHYMR;ILIVTQT(1)PHYMR;ILIVTQT(1)PHYMR;ILIVTQT(1)PHYMR 228.9 2.69E-11 1212174000 732617 628536 706065 890162 977222 837768 1025341 889726 1015363 TRUE FALSE 697987.6463 692584.533 738438.7786 800681.2246 1147649.207 808755.8841 868906.3988 811816.8747 1172820.308 0.595136051 0.59052911 0.629626528 0.682697272 0.978537973 0.689582094 0.740869162 0.692192034 1 20.16155056 -1.734137791 0.052584824 1.909822555 1.64E-12 0.532055325 0.098791677 182.8262015 1.455410756 38.35597368 17.42332303 0.018444301 1.734137791 -1.909822555 ILKEDILNYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILKEDILNYLEK 12 1 Q5VVL7;P11182 Q5VVL7 DBT "Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial" 0 ; 161.63 5.91E-05 108156000 644370 505050 471350 451380 457570 418260 610610 587130 477130 FALSE TRUE 613911.9071 556515.1692 492961.8637 406006.4248 537370.0631 403775.5513 517450.2299 535717.7846 551120.8836 1.113933305 1.009787845 0.894471392 0.736692143 0.975049357 0.732644259 0.938905139 0.972051324 1 19.07200927 3.940239928 2.391226481 0.880739976 1.088695473 0.379053673 0.093441873 0.250503783 2.820073605 0.02324996 0.054457565 8714.448902 -3.940239928 0.207955497 ILKEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILKEQER 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 105.14 0.0072912 1752370000 3013420 2244330 2668070 2472690 2489500 2630840 3381220 2989930 3020780 FALSE TRUE 2870981.609 2473029.779 2790403.649 2224130.503 2923668.012 2539733.351 2865352.789 2728115.879 3489227.134 0.822813047 0.708761477 0.799719692 0.637427837 0.837912781 0.727878482 0.821199847 0.78186824 1 21.73447608 0.052351736 0.612209146 1.013164858 0.754173018 0.601571743 0.060345543 2.456113752 1.092991831 0.130600777 0.021309178 1.128110745 -0.052351736 -0.258991839 ILKGEYAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILKGEYAVR 9 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 84.213 0.014268 429530000 1031300 765640 598010 710850 1256000 717010 1167800 846640 1323000 FALSE TRUE 982552.4928 843659.5865 625429.35 639394.0075 1475046.002 692179.7639 989630.6619 772503.7133 1528164.083 0.642962692 0.552073953 0.409268453 0.418406645 0.965240591 0.452948588 0.647594504 0.505510973 1 20.54336803 -1.645014246 2.484786228 1.055328332 0.578208083 0.407037089 0.16142997 8515098.296 6934257.226 3009549.825 0.03804127 0.0226457 1.645014246 -0.477120249 ILKS(ph)PEIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 1 ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR 177.42 3.16E-05 4737950000 5404770 5150350 5162420 6046860 3899440 5892130 6419570 6322860 4669200 TRUE FALSE 5149297.233 5675176.52 5399122.063 5439018.145 4579501.101 5688084.061 5440146.693 5769196.859 5393275.689 0.954762473 1.052268945 1.001084012 1.008481386 0.849113111 1.054662211 1.008690638 1.069701827 1 22.36273035 ILKSPEIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 115.78 0.0012953 1559510000 2318740 1186680 1738130 1326700 2604360 1867420 3232900 2316790 3428200 FALSE TRUE 2209137.755 1307604.041 1817824.98 1193337.595 3058559.559 1802750.777 2739661.729 2113919.586 3959827.747 0.557887337 0.330217405 0.459066681 0.301360986 0.772397123 0.455259898 0.691863865 0.533841298 1 21.91700624 0.08705069 0.309732909 1.127516856 0.404051165 0.591333526 0.13430017 3.142114014 0.476375603 0.659605323 0.142961658 1.221942274 -0.08705069 -0.72346569 ILLDHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILLDHEK 7 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 76.774 0.051659 0 66827 65399 43030 59503 45486 60537 59073 69782 46116 FALSE TRUE 63668.22015 72063.23245 45002.96806 53521.64539 53418.744 58440.58851 50060.3289 63671.51814 53267.43375 1.195256007 1.352857222 0.844849562 1.004772365 1.002840577 1.097116651 0.93979239 1.19531792 1 15.70096616 3.750335588 24.99142355 1.009878355 1.274056624 0.55162546 0.098170594 461.7021978 979922.92 0.023057905 0.041153302 5627.760252 -3.750335588 0.264178269 ILLDHEKEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILLDHEKEWK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 178.54 1.32E-06 956810000 2034780 1399810 1878480 1819570 1385500 2054910 2584500 2193800 1385820 FALSE TRUE 1938599.982 1542452.23 1964610.166 1636663.367 1627130.761 1983747.951 2190187.057 2001699.242 1600725.888 1.211075548 0.96359548 1.227324541 1.022450739 1.016495562 1.239280233 1.368246165 1.250494702 1 20.61029485 2.156328596 7.004839092 1.260228725 1.085988534 0.16405096 0.124343762 0.25422675 18.04424577 0.042812408 0.031593392 143.3271931 -2.156328596 -0.17424019 ILLWDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILLWDTR 7 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 ;; 114.19 0.013869 508458300 1608025 1304694 1082255 1230882 1792949 1023825 1832174 1370443 1825878 FALSE TRUE 1532016.845 1437643.802 1131877.462 1107151.403 2105638.738 988369.6835 1552642.206 1250439.746 2109025.835 0.72640971 0.68166249 0.536682597 0.524958673 0.998393999 0.468638016 0.736189278 0.592899207 1 21.00814534 -1.701186037 2.552939772 1.057984458 0.663854839 0.341198536 0.149066796 15091503.53 11863216.93 5621015.557 0.034111058 0.019898208 1.701186037 -0.39412962 ILMEHIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ILMEHIHK 8 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;;; 127.02 0.00069057 6119100000 11464500 10676110 10145660 11580350 10782240 11017270 14331840 9721350 595324.1 FALSE TRUE 10922595.81 11764017.75 10610848.55 10416271.22 12662659.24 10635739.18 12145254.59 8870097.058 687643.9209 15.88408691 17.10771722 15.43073126 15.14776892 18.41455855 15.46692824 17.66212747 12.89925903 1 19.39130217 0.852697612 3.496835648 1.00244732 16.45355914 0.954546907 1.056053276 0.126975177 2.683283926 0.921007019 0.23774771 7.12356861 -0.852697612 15.45111182 ILNDDTALKEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILNDDTALKEYK 12 1 P54727;Q5W0S4;Q5W0S5 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 109.84 0.0014178 247780000 186490 135590 158700 188050 130690 169160 218910 206720 147540 FALSE TRUE 177674.9873 149406.7752 165976.552 169146.8567 153482.2946 163301.9468 185511.2589 188618.5009 170419.7497 1.042572751 0.876698713 0.973927918 0.992530837 0.900613309 0.958233697 1.088554932 1.106787806 1 17.37873301 1.758655301 6.720961503 1.072365464 0.954254005 0.475699093 0.052999657 0.120602737 15.39223073 0.02414551 0.013011855 57.36609678 -1.758655301 -0.118111459 ILNDLS(ph)SDAPGVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILNDLSSDAPGVPR 14 0 P16220-1;P16220;P16220-3;H7C3I0;C9J896;E7EWP8;C9J4L5;C9JBT4 P16220-1 CREB1 Cyclic AMP-responsive element-binding protein 1 1 ILNDLS(0.76)S(0.24)DAPGVPR 105.46 0.0021975 0 59532 53325 58927 69062 67230 59353 73366 56900 74192 TRUE FALSE 56718.04034 58758.87813 61628.86124 62119.75655 78954.89071 57297.59073 62172.66924 51917.53435 85697.31644 0.661841499 0.685655987 0.719145754 0.724874 0.92132279 0.668604259 0.725491437 0.605824505 1 16.38696241 -2.294787971 2.373641432 2.433037741 0.713914144 0.545466154 0.082020535 3178529.366 616893.5119 24458652.72 0.018978014 0.005072383 2.294787971 -1.719123597 ILNDVQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILNDVQDR 8 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 125.16 0.0029635 167733000 501990 568960 472040 600640 531250 474780 500830 488910 529590 FALSE TRUE 478261.9275 626937.6709 493683.5009 540262.5261 623899.8318 458338.2496 424419.1851 446098.4485 611716.1124 0.781836407 1.02488337 0.807046751 0.88319159 1.019917277 0.749266269 0.693817241 0.729257313 1 19.22250275 2.205750152 24.99091144 0.759014066 0.90359946 0.161643214 0.11358312 235.3803153 179281.969 0.038822891 0.028674543 160.6017053 -2.205750152 0.144585394 ILNDVQDRFEVNISELPDEIDISSYIEQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILNDVQDRFEVNISELPDEIDISSYIEQTR 30 1 Q13838-2;Q13838;A0A0G2JJZ9 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 253.26 4.27E-58 96675000 155056 139928 233738 196887 128575 184131 192079 219660 200015 FALSE TRUE 147726.8102 154186.8223 244455.1185 177095.5447 150998.4393 177754.4973 162773.8208 200425.4059 231032.3047 0.63942058 0.66738209 1.058099294 0.766540181 0.653581496 0.769392391 0.704550046 0.86752113 1 17.81773507 -5 0.187889012 2.05908993 0.703478437 0.275638355 0.122534147 184.7109578 1.801074032 73.15689203 0.344943286 1.00E-05 5 -1.355611493 ILNDVQDRFEVNVAELPEEIDISTYIEQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILNDVQDRFEVNVAELPEEIDISTYIEQSR 30 1 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;; 214.44 1.77E-34 60559000 70608.7 47377.8 66541.9 60934 80719 60702.2 80548 67609.3 84851 FALSE TRUE 67271.16668 52205.65168 69592.91193 54808.79855 94796.36804 58600.06759 68258.92323 61689.07127 98009.25972 0.686375623 0.532660402 0.710064663 0.559220616 0.967218488 0.597903379 0.696453819 0.629420847 1 16.58063044 -5 0.246566515 2.967652555 0.634398961 0.414929648 0.120734742 164.9744836 1.638725274 163.5133981 0.163478757 1.00E-05 5 -2.333253594 ILNEDGSPNLDFKPEDQPHFDIKDEF ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILNEDGSPNLDFKPEDQPHFDIKDEF 26 2 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 256.46 6.98E-53 117128000 218480 212750 193377 257490 118061 220779 232940 256240 106162 FALSE TRUE 208152.8834 234429.4669 202243.5267 231606.616 138650.801 213133.3679 197400.7248 233802.2672 122625.0608 1.697474253 1.911758212 1.649283804 1.888738033 1.130688949 1.738089804 1.609791045 1.906643436 1 16.90389433 ILNHVLQHAEPGNAQSVLEAIDTYCEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILNHVLQHAEPGNAQSVLEAIDTYCEQK 28 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 273.88 9.93E-62 2024860000 1302600 1356130 1196700 1553270 868300 1320910 1281850 1425690 104061 FALSE TRUE 1241028.68 1494321.189 1251569.879 1397132.349 1019731.245 1275166.555 1086280.24 1300849.026 120198.2484 10.32484829 12.43213781 10.41254673 11.62356662 8.483744635 10.60886138 9.037404905 10.82252897 1 16.87505635 -0.379426167 0.50063244 5.24E-16 11.00161515 0.86933193 1.149638221 2.454092162 0.577459735 7.492356859 0.519440349 0.417420557 0.379426167 11.00161515 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK 38 2 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 106.5 5.45E-06 1482170000 293778 136060 288430 235978 223102 280276 394025 317773 83121 FALSE TRUE 279891.6962 149924.6687 301654.8008 212257.0431 262010.9182 270569.9718 333909.2495 289947.1115 96010.98016 2.91520507 1.561536696 3.141878151 2.210758007 2.728968267 2.81811488 3.477823567 3.019937001 1 16.55091179 2.5587583 4.457921352 2.853531679 2.397689564 0 0.775447215 0.617838961 22.19172101 0.237101714 0.219048923 362.0414538 -2.5587583 -0.455842115 ILPEAHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ILPEAHQR 8 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;;; 174.16 0.00027356 982260000 1514305 1273197 1153763 1235043 1593070 1209169 1649456 1393045 1521812 FALSE TRUE 1442726.804 1402937.222 1206664.175 1110894.131 1870900.904 1167295.174 1397801.193 1271062.595 1757806.833 0.820753895 0.798117971 0.686460055 0.631977366 1.064338168 0.664063396 0.795196131 0.723095719 1 20.74534511 ILPKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILPKPTR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 82.452 0.022299 1596690000 3047700 2909100 2667500 3280900 2405300 2864600 3207900 3017400 2827500 FALSE TRUE 2903641.261 3205540.597 2789807.514 2951097.699 2824783.558 2765398.184 2718475.938 2753180.46 3265974.259 0.88905822 0.981495977 0.854203767 0.903588781 0.864912989 0.846729939 0.83236294 0.842989026 1 21.63908199 3.719732315 24.49166981 0.867456395 0.935277103 0.146196384 0.053320435 757.0195278 984723.1411 0.012874027 0.019985376 5244.840858 -3.719732315 0.067820708 ILQALHECLAALPRPQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILQALHECLAALPRPQLR 18 1 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 94.882 0.0011305 25997000 21844 19933 20747 24227 23953 20690 26593 21443 19816 FALSE TRUE 20811.47741 21964.19536 21698.27047 21791.65593 28130.39562 19973.50011 22535.74944 19565.33724 22888.96407 0.909236318 0.959597616 0.947979577 0.95205951 1.22899383 0.872625779 0.984568343 0.85479348 1 14.48236455 4.145754741 1.297396692 0.981164565 0.910870165 0.045452014 0.100645397 2.044206818 5.650071585 0.02855968 0.143949266 13987.97159 -4.145754741 -0.0702944 ILQEHEQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILQEHEQIK 9 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 157.78 6.77E-05 629300000 1153410 949690 885660 1053360 908160 1036260 1271540 1144590 950720 FALSE TRUE 1098890.595 1046464.491 926268.387 947474.2515 1066542.816 1000374.056 1077543.22 1044363.632 1098152.802 1.000671849 0.952931585 0.843478599 0.862789085 0.971215312 0.91096071 0.9812325 0.951018501 1 20.06664738 1.508081495 1.363659718 0.987072962 0.928846322 0.195907984 0.048513399 0.824462986 2.936513889 0.046397298 0.015726557 32.2167328 -1.508081495 -0.05822664 ILQEKLDQPVS(ph)APPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ILQEKLDQPVSAPPSPR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 ILQEKLDQPVS(1)APPS(1)PR;ILQEKLDQPVS(1)APPS(1)PR;ILQEKLDQPVS(1)APPS(1)PR;ILQEKLDQPVS(1)APPS(1)PR;ILQEKLDQPVS(1)APPS(1)PR;ILQEKLDQPVS(1)APPS(1)PR 127.3 2.32E-05 1197263000 3633210 1209270 4292590 2433290 4396080 3239690 6596640 3887230 6525400 TRUE FALSE 3461475.364 1332495.988 4489409.497 2188691.066 5162754.96 3127498.723 5590201.412 3546843.534 7537325.705 0.459244499 0.176786309 0.595623657 0.290380322 0.684958454 0.414934799 0.741669079 0.470570554 1 22.84562131 -0.353448519 0.16820476 1.415794953 0.189975907 0.554404972 0.156947514 10.04045236 0.495310642 2.850979581 0.74872602 0.443150742 0.353448519 -1.225819045 ILQEKLDQPVSAPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILQEKLDQPVSAPPSPR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 ILQEKLDQPVSAPPS(1)PR;ILQEKLDQPVSAPPS(1)PR;ILQEKLDQPVSAPPS(1)PR 183.01 4.33E-10 517660000 773510 215766 923150 456121 999040 674930 1380580 867880 1563000 TRUE FALSE 736947.7152 237752.8007 965477.3406 410270.8505 1173272.26 651557.0049 1169947.165 791883.8263 1805382.057 0.408194882 0.131691129 0.534777299 0.227248769 0.649874776 0.36089702 0.648033008 0.438623959 1 20.78387274 -4.022030119 0.123883672 2.582644236 0.103053259 0.612570359 0.151906921 63.12390055 0.636810732 26.08261448 1.222490834 9.51E-05 4.022030119 -2.479590976 ILQGGVGIPHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILQGGVGIPHIR 12 0 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;P48729-3;A0A590UK94;A0A590UJQ7;E5RG27;D6RGE5 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ; 121.08 0.00022937 210710000 185607 174768 163619 186755 246780 163993 196768 188373 213572 FALSE TRUE 176833.7249 192577.0579 171121.093 167982.0326 289818.3539 158313.8813 166747.4277 171878.0615 246691.655 0.716820863 0.78063872 0.69366389 0.680939258 1.174820258 0.641748021 0.67593461 0.69673237 1 17.91234939 -1.807098981 2.611818696 1.076902083 0.754481495 0.198762588 0.152791745 31957280.18 22367570.34 15551091.44 0.036851444 0.015591971 1.807098981 -0.322420589 ILQINKDDVTALHCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILQINKDDVTALHCK 15 1 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 150.39 1.92E-06 162860000 914450 870840 951470 905210 532820 950480 933220 987530 599560 FALSE TRUE 871225.7608 959579.5861 995095.8406 814216.571 625743.6393 917564.6393 790840.1492 901056.638 692536.7027 1.258021066 1.385601055 1.436885347 1.175701689 0.903553035 1.324932867 1.141946912 1.301095862 1 19.40153101 3.144486327 6.936545611 1.147591797 1.350373172 0.383838514 0.130770542 0.230797528 14.49164182 0.035660854 0.042822915 1394.717745 -3.144486327 0.202781375 ILQLCMGNHELYMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ILQLCMGNHELYMR 14 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 225.55 2.73E-12 997330000 1272640 1130910 1021020 1180990 1203620 1068780 1256600 1214370 1037020 FALSE TRUE 1212484.829 1246151.015 1067834.777 1062274.641 1413530.947 1031767.881 1064882.591 1108033.325 1197835.765 1.01222961 1.040335454 0.891470106 0.886828288 1.180070748 0.861360055 0.889005506 0.925029422 1 20.19199868 ILRLS(ph)TFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILRLSTFEK 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 ILRLS(0.898)T(0.102)FEK 118.61 0.00058258 129150000 252630 180000 183780 257530 214160 204660 269120 228510 200510 TRUE FALSE 240688.6806 198342.2046 192206.4948 231642.5951 251509.4362 197572.5729 228060.8013 208500.453 231604.0667 1.03922476 0.85638481 0.829892573 1.000166355 1.085945682 0.85306176 0.984701195 0.900245216 1 17.82130106 4.738787785 5.243757854 0.937522177 1.043409489 0.132140272 0.080812561 0.311765421 26.62045502 0.018639077 0.117241384 54800.91186 -4.738787785 0.105887312 ILRLST(ph)FEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILRLSTFEK 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 ILRLS(0.283)T(0.717)FEK 134.18 0.00041398 111540000 262540 178870 184480 278800 244000 206630 284710 256410 208810 TRUE FALSE 250130.2545 197097.0564 192938.5905 250774.4943 286553.5227 199474.3513 241272.2604 233957.3811 241191.1883 1.037062159 0.817181829 0.799940461 1.039733234 1.188076251 0.827038304 1.000336132 0.970007995 1 17.87981768 3.220126822 24.99940248 1.000229541 0.892015906 0.215702458 0.106912225 400.5442302 543205.8607 0.030764053 0.036833603 1660.071608 -3.220126822 -0.108213635 ILRPWQSSETR ddPTM_SK-BR-3_Trastuzumab_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 ; 173.72 1.08E-05 2371700000 3489800 2848800 2717200 3175800 3641200 3015800 3875800 3274700 3792100 FALSE TRUE 3324844.07 3139095.959 2841786.308 2856562.55 4276224.127 2911362.09 3284475.526 2987949.908 4380159.501 0.759069178 0.716662477 0.648786033 0.652159482 0.976271327 0.664670337 0.749852951 0.682155503 1 22.06255197 -1.659309307 2.654369303 1.033347654 0.732385064 0.441351401 0.095031057 22111987.96 19202690.53 5010294.287 0.020812254 0.021912438 1.659309307 -0.30096259 ILS(ph)DVTHSAVFGVPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ILSDVTHSAVFGVPASK 17 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 ILS(0.999)DVT(0.001)HSAVFGVPASK;ILS(0.977)DVT(0.022)HS(0.001)AVFGVPASK;ILS(1)DVTHSAVFGVPASK;ILS(1)DVTHSAVFGVPASK 252.55 3.51E-27 483654000 1969330 1787919 1676501 2133820 1199104 1910385 2024200 2158852 1198581 TRUE FALSE 1876243.674 1970109.979 1753370.229 1919324.36 1408227.358 1844227.888 1715371.113 1969811.474 1384450.82 1.355225947 1.423026337 1.266473466 1.386343474 1.017173985 1.332100687 1.239026398 1.422810724 1 20.40088237 -5 0.137992255 0.017568441 1.417018598 0.362988519 0.121683998 143.3224239 1.219028177 39.39802818 0.721386671 1.00E-05 5 1.399450156 ILS(ph)PSMASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILSPSMASK 9 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 ILS(0.998)PS(0.002)MASK;ILS(0.988)PS(0.012)MASK 95.477 0.008411 199187000 682650 609410 613040 712600 587600 689350 790890 755100 686500 TRUE FALSE 650382.4874 671509.5718 641148.4904 640968.0941 690077.254 665477.6366 670225.2048 688979.441 792958.9138 0.820196956 0.846840309 0.808551968 0.80832447 0.870256002 0.83923344 0.845220595 0.868871551 1 19.59688659 -0.583809635 0.417946531 1.044645747 0.825549752 0.90393149 0.017099066 2.613814908 0.406137079 0.174939599 0.010265947 0.260729616 0.583809635 -0.219095994 ILSDDVPIRDYR ddPTM_SK-BR-3_Trastuzumab_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 75.479 0.030736 124360000 487590 319130 421720 507830 663210 383320 635850 488280 720410 FALSE TRUE 464542.587 351649.7098 441056.2791 456781.9636 778873.614 370045.5323 538839.4043 445523.6147 832127.5035 0.558258903 0.422591139 0.530034493 0.54893266 0.936002729 0.444698115 0.647544279 0.535403064 1 19.66644508 -5 0.183508932 2.765863008 0.484460583 0.466230203 0.141713866 115.3955957 1.117627287 74.5187744 0.395230596 1.00E-05 5 -2.281402425 ILSGRPPLGFLNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILSGRPPLGFLNPR 14 1 A0A2R8Y7U1;A0A2R8YGD1;A0A2R8YD45;O14773-2;O14773 A0A2R8Y7U1 TPP1 Tripeptidyl-peptidase 1 0 162.93 3.98E-06 127110000 104430 83304 64287 75307 109310 70163 123670 86725 119270 FALSE TRUE 99493.80086 91792.77231 67234.62254 67736.99729 128373.6294 67733.23772 104801.8701 79130.89924 137765.7825 0.722195302 0.666295873 0.488035718 0.491682304 0.931825212 0.491655014 0.760724966 0.57438718 1 17.07185808 -1.568949908 2.818505037 1.021341578 0.649292252 0.389058159 0.141087419 20871275.31 22035825.5 3362963.728 0.033049645 0.026980506 1.568949908 -0.372049326 ILSHGGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILSHGGFR 8 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 193.86 0.00016842 2176200000 2361800 2544500 2006140 2598400 2294400 2211500 2241600 2372500 2026740 FALSE TRUE 2250162.395 2803787.443 2098123.503 2337203.895 2694542.634 2134915.2 1899602.75 2164751.323 2341036.488 0.961182111 1.197669262 0.896236993 0.998362865 1.151004116 0.91195298 0.811436626 0.924697814 1 21.15871599 2.090371156 7.837666242 0.883880063 1.046178468 0.284565827 0.09795878 0.239550967 18.07258014 0.035154916 0.025920006 123.1320629 -2.090371156 0.162298405 ILSISADIETIGEILKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILSISADIETIGEILKK 17 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 229.68 1.66E-15 675400000 506780 461000 475400 619520 474540 611830 756390 719730 526640 FALSE TRUE 482825.5137 507976.4241 497197.5602 557244.6726 557299.6258 590642.1737 640988.8134 656706.6257 608308.6415 0.793717992 0.835063633 0.817344233 0.916055822 0.91614616 0.970958052 1.053723011 1.07956156 1 19.21444397 2.535759446 0.874685019 1.055970961 0.808348169 0.90133794 0.030507473 0.149857722 0.234056473 0.019451449 0.014695258 343.3677055 -2.535759446 -0.247622792 ILSQS(ph)TDS(ph)LNMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 2 ILS(0.015)QS(0.782)T(0.207)DS(0.996)LNMR;ILSQS(0.593)T(0.441)DS(0.965)LNMR 128.71 0.00036139 198983000 265803 222513 250309 255446 250383 242357 274962 267413 291159 TRUE FALSE 253239.019 245187.3277 261785.9152 229768.0828 294049.7159 233964.1163 233011.4969 243996.9001 336310.4507 0.752991822 0.729050576 0.778405532 0.683202328 0.874340108 0.695678995 0.692846435 0.725510907 1 18.35943409 -1.164191328 5.403349745 1.000007955 0.738911056 0.683567482 0.055247248 4.88E-06 7.55E-07 0.049323035 0.011625197 0.06851863 1.164191328 -0.261096898 ILSQS(ph)TDSLNMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.629)T(0.37)DSLNMR;ILSQS(0.916)T(0.082)DS(0.001)LNMR;ILSQS(0.988)T(0.012)DSLNMR;ILSQS(0.998)T(0.002)DSLNMR;ILSQS(0.998)T(0.002)DSLNMR;ILSQS(0.991)T(0.009)DSLNMR;ILSQS(0.658)T(0.342)DSLNMR;ILS(0.001)QS(0.788)T(0.206)DS(0.005)LNMR;ILS(0.005)QS(0.886)T(0.108)DS(0.001)LNMR;ILS(0.028)QS(0.538)T(0.413)DS(0.021)LNMR;ILSQS(0.938)T(0.062)DSLNMR;ILSQS(0.923)T(0.077)DSLNMR;ILSQS(0.577)T(0.423)DSLNMR;ILS(0.001)QS(0.558)T(0.441)DS(0.001)LNMR;ILSQS(0.605)T(0.394)DSLNMR;ILS(0.001)QS(0.931)T(0.064)DS(0.005)LNMR;ILS(0.004)QS(0.847)T(0.14)DS(0.01)LNMR 333.15 3.27E-58 9067347000 11621690 10747730 10996960 11601180 11342550 10619810 12352180 11874390 12076430 TRUE FALSE 11072355.75 11842935.91 11501181.49 10435007.35 13320687.13 10252043.32 10467628.08 10834605.46 13949181.09 0.793763854 0.849005819 0.824505856 0.748073115 0.954944025 0.734956644 0.750411656 0.776719823 1 23.73367709 ILSQST(ph)DSLNMR ddPTM_SK-BR-3_Trastuzumab_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(0.444)T(0.555)DS(0.001)LNMR 233.19 6.08E-15 641540000 351430 348020 318780 373950 343980 315550 418330 384020 366320 TRUE FALSE 334818.6004 383483.6337 333396.3783 336359.8355 403970.0031 304622.4244 354506.0753 350393.173 423127.0347 0.791295694 0.906308513 0.787934476 0.794938182 0.954725106 0.719931367 0.837824214 0.82810396 1 18.69073134 -2.192934713 2.014818166 1.416348848 0.829909894 0.409307472 0.065023734 5129652.798 987678.0246 9725370.747 0.015139073 0.00641306 2.192934713 -0.586438954 ILTDYGFEGHPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILTDYGFEGHPFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 176.05 1.72E-05 158810000 408740 352350 295460 329720 374990 260950 343100 328510 318010 FALSE TRUE 389419.6702 388254.8656 309007.1332 296575.9192 440388.1373 251913.2361 290753.7935 299743.9229 367325.3666 1.060149136 1.056978093 0.841235486 0.807392971 1.198904778 0.685804083 0.791542921 0.816017488 1 18.486699 3.902655382 0.729709414 0.843526675 1.121452174 0.158949527 0.144547513 1.623978946 1.336972482 0.063833655 0.311711779 7991.998292 -3.902655382 0.277925499 ILTEAEIDAHLVALAERD ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 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 1357170600 1152361.9 992900.5 1013438.4 1159454.9 1228934.7 1007507.8 1303224.9 1147314.1 1192034.4 FALSE TRUE 1097892.037 1094078.19 1059905.553 1042904.291 1443260.523 972617.5523 1104394.006 1046849.195 1376889.007 0.797371488 0.794601587 0.769782857 0.757435266 1.04820397 0.706387768 0.802093706 0.760300351 1 20.39298084 -2.091078573 2.190933772 1.310991053 0.80353657 0.312942985 0.091015244 6549816.561 1795493.609 10159912.13 0.020868159 0.008108144 2.091078573 -0.507454482 ILTTEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILTTEGR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 108.98 0.016588 62226000 188720 132540 151950 174130 147580 143140 190090 199600 186990 FALSE TRUE 179799.5796 146045.9767 158917.0578 156626.1216 173317.9053 138183.0259 161088.2793 182121.9659 215987.4542 0.832453812 0.676178055 0.735769855 0.725163052 0.802444318 0.639773391 0.74582239 0.843206225 1 17.72058799 0.959428352 2.674141048 0.999095842 0.734358249 0.709193025 0.054576691 0.150688371 2.522013945 0.048724287 0.013011345 9.108111777 -0.959428352 -0.264737593 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR 39 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 72.348 0.0019119 561730000 79624 39004 58560 46695 97300 54148 105880 54575 70548 FALSE TRUE 75860.33132 42978.55194 61245.03392 42001.12989 114269.0892 52272.84118 89726.06138 49796.12368 81488.22353 0.930936128 0.527420406 0.75158141 0.515425764 1.402277338 0.641477246 1.101092373 0.611083682 1 16.31430396 ILVDVEKVDWDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILVDVEKVDWDK 12 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 131.26 0.00018414 89388000 301780 253120 258360 319480 246660 298710 301820 317230 249890 FALSE TRUE 287515.4575 278913.2158 270206.0616 287365.2634 289677.4259 288365.5978 255771.8157 289451.6595 288641.6649 0.996098251 0.966295756 0.936129791 0.995577903 1.003588397 0.999043564 0.886122299 1.002806229 1 18.13892004 ILVDVEKVDWDKAWEITKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILVDVEKVDWDKAWEITKK 19 3 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 144.88 5.74E-08 178294000 587070 266660 612550 446740 382380 572740 887590 739800 453500 FALSE TRUE 559320.3646 293832.9572 640636.0234 401832.8464 449066.9509 552905.8702 752171.8438 675019.1901 523826.4638 1.067758892 0.560935687 1.222992857 0.767110626 0.857281909 1.055513435 1.435917991 1.288631325 1 18.99872942 1.992752556 4.478226566 1.284044949 0.877549407 0.368388539 0.203625949 0.168989851 8.47072116 0.081612296 0.052201929 98.3450615 -1.992752556 -0.406495542 ILVLDDTNHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILVLDDTNHER 11 0 K7EN66;C9K0L8;K7ERZ0;K7ERC4;P09543-2;P09543 K7EN66 CNP "2,3-cyclic-nucleotide 3-phosphodiesterase" 0 ; 244.95 6.57E-16 179936000 315080 294420 268940 326090 321270 266220 290800 272900 287180 FALSE TRUE 300186.7928 324421.7327 281271.165 293310.8137 377299.3863 257000.7346 246433.1191 249003.4293 331714.4077 0.904955546 0.9780152 0.84793171 0.884226934 1.137422366 0.774765065 0.742907493 0.750656057 1 18.33958215 ILVTLLHTLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ILVTLLHTLER 11 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 231.05 1.35E-12 204470000 324281 304619 278245 305935 340670 296663 366080 331336 294022 FALSE TRUE 308952.8798 335660.0224 291002.8085 275181.8326 400082.7401 286389.4859 310227.7725 302322.4633 339617.4301 0.90970855 0.988347454 0.856854751 0.810270051 1.178039478 0.843270871 0.913462458 0.890185357 1 18.37355098 4.799487061 19.51958377 0.93148378 0.90970643 0.004725385 0.104770526 13400.4133 5282050.883 0.022850353 8.074076848 63021.25691 -4.799487061 -0.02177735 ILYDFTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILYDFTAR 8 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 126.28 0.0028522 26502000 58670 52662 46168 49796 65423 39756 65050 56179 66928 FALSE TRUE 55896.78537 58028.31767 48284.84847 44790.41147 76832.75049 38379.23975 55125.42777 51259.66894 77306.85242 0.72305085 0.750623209 0.624586915 0.579384751 0.993867272 0.496453271 0.713072982 0.663067598 1 16.23830868 -1.470589433 2.961754615 1.00819756 0.695985921 0.354607611 0.130099772 28532849.67 32454000.08 1924489.04 0.027632117 0.033838458 1.470589433 -0.312211639 ILYLINQGEHLGTTEATEAFFAMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ILYLINQGEHLGTTEATEAFFAMTK 25 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 95.835 8.98E-06 0 26643 25208 28668 25718 30917 26984 30173 28470 29346 FALSE TRUE 25383.63819 27776.72386 29982.45616 23132.77778 36308.91501 26049.53731 25569.55468 25977.01587 33896.8278 0.748849961 0.819449065 0.884521004 0.682446685 1.071159674 0.768494842 0.754334737 0.766355366 1 15.04886265 -2.440113248 2.275569856 2.918039577 0.808877433 0.237583986 0.105739461 5894858.691 504492.7486 58730823.67 0.024018104 0.003629834 2.440113248 -2.109162144 IMAT(ph)PEQVGK ddPTM_SK-BR-3_Trastuzumab_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 158.01 9.11E-05 576940000 1969930 1904930 1876980 2173630 1623310 2150520 2430530 2245710 1873660 TRUE FALSE 1876815.313 2099044.533 1963041.39 1955132.583 1906414.75 2076046.953 2059708.009 2049063.727 2164217.623 0.867202675 0.969886073 0.90704436 0.903390011 0.880879413 0.959259795 0.95171021 0.946791905 1 21.04541415 1.291852468 0.754560995 0.996192162 0.911632172 0.471850893 0.03031728 0.561111206 0.722046367 0.028338475 0.011461354 19.58179358 -1.291852468 -0.08455999 IMDPNIVGSEHYDVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 IMDPNIVGSEHYDVAR 16 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;;;;;;;;;;;;;; 205.78 2.17E-11 14157476000 11160100 8338835 9467897 9492955 11758930 7773521 10880857 9845593 10829720 FALSE TRUE 10632584.19 9188571.767 9902009.442 8538705.128 13809683.67 7504322.019 9220782.424 8983460.682 12509137.67 0.849985385 0.734548776 0.791582098 0.682597422 1.103967678 0.599907221 0.737123747 0.718151876 1 23.576479 -0.145930841 8.962093761 1 0.774389642 0.216246031 0.133183513 0 0 0.116175496 0.027382827 0.714610114 0.145930841 -0.225610357 IMDYSLLLGIHDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMDYSLLLGIHDIIR 15 0 Q8TBX8;Q8TBX8-3;Q8TBX8-2;H0YIJ6 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 177.88 7.35E-07 92577000 120668 119364 85635 94601 133802 82333 132915 113357 114456 FALSE TRUE 114964.2628 131527.3273 89561.44945 85091.52775 157137.0264 79481.78757 112636.3756 103430.8601 132205.2519 0.869589227 0.994872181 0.677442448 0.643631978 1.188583843 0.601199925 0.851981097 0.782350615 1 17.01241996 3.762271098 24.92470022 0.811520678 0.932230695 0.063060932 0.175889915 1817.035276 1910079.605 0.041072908 0.073991714 5784.570228 -3.762271098 0.120710017 IMEEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMEEFFR 7 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;Q08499-4;D6RHE0;Q08499-5;Q08499-8 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 0 ; 139.92 0.0061873 42648000 80846 64645 67129 84263 78850 60742 87478 77521 82420 FALSE TRUE 77024.5698 71232.399 70206.93105 75792.72315 92601.41504 58638.48931 74131.62446 70732.85028 95201.27266 0.8090708 0.748229483 0.737457905 0.796131407 0.972690936 0.615942284 0.778683125 0.742982192 1 16.53869324 -1.007568315 5.163571807 1.000001701 0.773424887 0.393684078 0.0876716 1.57E-06 3.02E-07 0.077744476 0.018324411 0.098272428 1.007568315 -0.226576814 IMEIVDAITTTAQSHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMEIVDAITTTAQSHQR 17 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 226.06 2.20E-15 191295000 287200 292410 284320 320030 301570 281520 311250 290330 275060 FALSE TRUE 273624.6252 322206.9114 297356.3532 287859.9764 354163.7125 271770.8918 263763.096 264907.1661 317714.9 0.861226921 1.014138498 0.935921964 0.906032347 1.11472176 0.85539234 0.830187996 0.833788929 1 18.27737322 IMEVIDAITTTAQSHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMEVIDAITTTAQSHQR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 103.61 0.00089073 92137000 87291 82300 86112 94615 107780 80552 98447 82708 85985 FALSE TRUE 83164.92742 90686.46357 90060.32038 85104.12044 126576.7979 77762.46404 83427.10205 75465.64906 99319.11465 0.837350672 0.913081675 0.906777318 0.856875544 1.274445491 0.782955671 0.839990392 0.759830062 1 16.59978378 -0.887775868 4.011944713 1.000003469 0.895565964 0.049493694 0.142619197 3.3018E+11 7.56922E+11 17974417.73 0.032412027 0.129486393 0.887775868 -0.104437504 IMGLDLPDGGHLTHGYMSDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMGLDLPDGGHLTHGYMSDVKR 22 1 P34897-3;P34897-2;P34897;G3V540;G3V5L0;G3V4W5 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 ; 76.704 0.0043118 174445000 560500 425970 489720 475240 506390 428430 634560 527090 59755 FALSE TRUE 534006.2758 469376.8273 512174.1464 427467.9723 594704.2557 413593.3617 537746.2175 480935.2053 69021.50021 7.736810619 6.800443714 7.420501508 6.193258202 8.616217466 5.992239525 7.790995789 6.967904259 1 16.07475821 0.93663813 21.9246006 0.999999996 7.211473052 0.865061157 0.768914308 2257.865672 781272.541 0.622237531 0.155559383 8.642474962 -0.93663813 6.211473056 IMGPNYT(ph)PGKKEDLYLKPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMGPNYTPGKKEDLYLKPIQR 21 3 P13639 P13639 EEF2 Elongation factor 2 1 IMGPNY(0.006)T(0.994)PGKKEDLYLKPIQR;IMGPNY(0.002)T(0.998)PGKKEDLYLKPIQR 58.812 0.036888 590410000 1392550 1168840 1388130 1435930 731730 1573670 1526160 1818430 846500 TRUE FALSE 1326726.921 1287946.125 1451777.134 1291587.588 859343.4803 1519173.413 1293316.262 1659198.629 977770.8967 1.356889355 1.317226898 1.484782518 1.320951148 0.878880199 1.553711016 1.322719122 1.696919631 1 19.89913694 IMKDILEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMKDILEK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 108.67 0.0034351 7049300000 15466600 10700600 14752300 14323500 11217900 15897200 20019300 17303300 14172400 FALSE TRUE 14735524.47 11791003.31 15428707.55 12883674.57 13174298.21 15346675.98 16964988.11 15788131.32 16370183.41 0.900144128 0.720273134 0.942488374 0.787020783 0.804774014 0.937477339 1.036334638 0.964444376 1 23.96456715 2.076928587 3.916506785 1.001497476 0.825565828 0.610036677 0.062474296 0.134170829 4.028949189 0.023977297 0.016525139 119.3791788 -2.076928587 -0.175931647 IMLFTNEDNPHGNDSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IMLFTNEDNPHGNDSAK 17 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 296.47 3.70E-46 882170000 1416760 1353530 1229500 1490740 1057864 1384570 1469680 1512450 1018015 FALSE TRUE 1349792.563 1491456.246 1285873.791 1340887.983 1242355.147 1336621.994 1245453.323 1380011.86 1175883.567 1.147896442 1.268370686 1.093538363 1.140323771 1.056529049 1.13669587 1.059163814 1.173595668 1 20.16531378 8 0.0683569 0.859814243 1.751100771 0.364750098 0.058920342 227.6715536 1.151373365 2.684144712 19.61330097 99999999.96 -8 0.891286528 IMMEFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMMEFER 7 0 O43633;M0R1L7;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ; 100.45 0.022762 78789000 161835 115747 77565 91169 165454 91789 167682 127626 163975 FALSE TRUE 154185.3803 127541.7509 81121.43197 82004.51891 194309.1252 88610.32391 142099.0312 116450.3909 189403.4055 0.81405812 0.673386788 0.428299754 0.43296222 1.025900905 0.467839127 0.750245387 0.614827334 1 17.53110275 -1.398978437 2.765094033 1.007376115 0.659315844 0.25789145 0.185604992 14921109.72 16765928.07 877053.7946 0.047056885 0.039904472 1.398978437 -0.34806027 IMNMIEEIKTPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMNMIEEIKTPASTPVSGTPQASPMIER 28 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 IMNMIEEIKTPAS(0.002)T(0.012)PVS(0.426)GT(0.561)PQAS(0.999)PMIER 118.74 0.00036941 46961000 90195 49194 98876 78568 91203 85667 131870 101200 130750 TRUE FALSE 85931.6611 54206.92453 103409.5624 70670.19537 107108.7743 82700.33031 111750.8095 92338.39151 151026.0422 0.568985718 0.358924353 0.68471345 0.467933837 0.709207318 0.547589867 0.739943972 0.61140708 1 17.20443782 -4.201732609 0.117198567 2.203795009 0.330384468 0.641040521 0.103546412 66.66494453 0.615126139 19.75099719 0.984322916 6.28E-05 4.201732609 -1.873410541 IMNTFSVVPSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMNTFSVVPSPK 12 0 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;P68371;M0R2D3;P04350;M0QYM7;M0R042 Q13509;Q5JP53;P68371;P04350 TUBB3;TUBB;TUBB4B;TUBB4A Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-4A chain 0 ; 171.67 8.80E-05 99575000 775830 642110 632910 730240 674860 655260 902790 797650 779660 FALSE TRUE 739158.0534 707541.739 661929.5495 656834.8878 792555.3703 632568.1819 765052.8046 727803.5374 900565.6908 0.820770834 0.785663663 0.735015287 0.729358107 0.880063918 0.702412038 0.849524707 0.80816263 1 19.78047199 0.289336788 0.794462745 1.003031258 0.781372888 0.613057742 0.053644872 1.705930225 1.389127483 0.059120999 0.016404272 1.946869262 -0.289336788 -0.22165837 IMNVIGEPIDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IMNVIGEPIDER 12 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;; 202.16 3.26E-07 712270000 1119041 882151 927854 918899 1079795 779397 1015719 915159 1085130 FALSE TRUE 1066146.15 972043.1898 970397.0237 826529.5267 1268110.906 752406.2865 860752.4116 835022.8264 1253406.418 0.850598923 0.775521152 0.774207798 0.659426595 1.01173162 0.60028916 0.686730496 0.666202769 1 20.25742286 IMPDSNDS(ph)PPAEREPGEVVDSLVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IMPDSNDSPPAEREPGEVVDSLVGK 25 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 1 IMPDSNDS(1)PPAEREPGEVVDSLVGK;IMPDS(0.045)NDS(0.955)PPAEREPGEVVDSLVGK;IMPDS(0.158)NDS(0.842)PPAEREPGEVVDSLVGK;IMPDS(0.098)NDS(0.902)PPAEREPGEVVDSLVGK 199.8 4.22E-25 314379000 505478 444534 451201 515055 396174 497605 568650 536900 459270 TRUE FALSE 481585.0567 489832.52 471889.0121 463280.6929 465266.6202 480372.8141 481891.9985 489886.1897 530491.246 0.907809621 0.923356462 0.889532138 0.873305067 0.877048629 0.905524488 0.90838822 0.923457632 1 19.01696942 0.658114158 1.269982216 0.999935431 0.89859978 0.828015337 0.014695073 0.542332018 1.35674512 0.016064945 0.004841548 4.551076735 -0.658114158 -0.101335651 IMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDR 33 2 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82 F8W0W8 PPP1CC Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit 0 98.258 5.73E-05 131310000 26934 30089 27897 29991 23749 30607 32698 28648 28709 FALSE TRUE 25660.8832 33155.10331 29176.10504 26976.2477 27890.81808 29547.07192 27709.31956 26139.42925 33161.04509 0.77382613 0.99982082 0.879830686 0.813492085 0.841071746 0.891017513 0.835598501 0.7882571 1 15.01720185 3.467530793 24.16562898 0.852842821 0.895657187 0.008476844 0.078145969 396.6475797 999449.9238 0.020020232 0.027147643 2934.477559 -3.467530793 0.042814366 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR ddPTM_SK-BR-3_Trastuzumab_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 ; 149.49 1.33E-10 252807000 239647 269422 216988 274157 156398 237671 234243 247613 169946 FALSE TRUE 228319.3612 296876.4081 226937.1144 246598.2175 183673.7617 229440.3937 198504.9282 225930.693 196300.3577 1.163112304 1.512357958 1.156070814 1.256229079 0.935677162 1.168823105 1.011230598 1.150943868 1 17.58270328 3.142464559 1.886638577 1.062664476 1.327251429 0.42171809 0.121788127 0.265233164 1.939038417 0.036462072 0.047403297 1388.240017 -3.142464559 0.264586953 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR 33 2 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 192.63 1.15E-19 125028000 382788 330247 311914 396878 256943 362187 364398 383272 255501 FALSE TRUE 364694.3699 363899.5448 326215.5654 356983.0694 301753.7778 349644.3734 308802.3925 349710.6718 295122.7902 1.23573774 1.233044539 1.105355385 1.209608615 1.022468572 1.18474203 1.04635224 1.184966677 1 18.17095581 7.999999998 0.124739853 0.976597554 1.885825646 0.434600059 0.066275153 66.55468298 0.566367302 0.343681009 10.58004194 99999999.62 -7.999999998 0.909228092 IMSCS(ph)PDTQCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMSCSPDTQCSR 12 0 Q9C0C9;K7EQ12 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 IMSCS(1)PDTQCSR 143.21 0.00024244 84174000 94921 86011 93649 94418 102140 99250 118150 105000 120920 TRUE FALSE 90434.27245 94775.61869 97942.89928 84926.92326 119953.1837 95812.94761 100124.0475 95805.64336 139671.656 0.647477627 0.678560142 0.701236758 0.608046941 0.858822664 0.685987052 0.716853014 0.685934756 1 17.09167975 -5 0.240582047 2.738234723 0.665116093 0.69063451 0.063872127 91.53503615 0.912346976 77.89336859 0.091033726 1.00E-05 5 -2.07311863 IMSS(ph)IGEGIDFSQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IMSSIGEGIDFSQER 15 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 IMS(0.022)S(0.978)IGEGIDFSQER;IMS(0.017)S(0.983)IGEGIDFSQER;IMS(0.003)S(0.997)IGEGIDFSQER;IMS(0.009)S(0.991)IGEGIDFSQER;IMS(0.019)S(0.981)IGEGIDFSQER 214.53 2.58E-12 227366000 315893 277833 272687 302979 335802 280067 330769 309108 367036 TRUE FALSE 300961.3639 306144.4986 285189.9687 272522.9753 394365.7625 270368.2096 280304.1141 282040.8648 423954.0683 0.70989144 0.722117138 0.672690723 0.642812502 0.930208699 0.637729957 0.661166232 0.665262786 1 18.69354844 -1.409081536 5.709685427 1.000124852 0.704638755 0.546933242 0.084311039 0.000124933 1.29E-05 0.076112629 0.017932387 0.038986878 1.409081536 -0.295486097 IMVGS(ph)TDDPSVFSLPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IMVGSTDDPSVFSLPDSK 18 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 IMVGS(0.916)T(0.084)DDPSVFSLPDSK;IMVGS(0.882)T(0.118)DDPSVFSLPDSK;IMVGS(0.867)T(0.133)DDPSVFSLPDSK;IMVGS(0.974)T(0.026)DDPSVFSLPDSK;IMVGS(0.938)T(0.062)DDPSVFSLPDSK 363.75 2.18E-92 189020000 695274 596922 591686 789658 499050 678413 676676 735012 549907 TRUE FALSE 662409.7759 657749.0304 618815.3884 710280.0776 586084.162 654919.3877 573436.6482 670650.4527 635183.769 1.042863197 1.035525564 0.97423048 1.118227688 0.922700155 1.031070723 0.902788573 1.055836886 1 19.27681452 2.721542915 24.99935881 0.974487034 1.037726361 0.209522215 0.056604281 1106.401262 1625325.547 0.016221944 0.015334928 526.6752564 -2.721542915 0.063239327 IMVGST(ph)DDPSVFSLPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMVGSTDDPSVFSLPDSK 18 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 IMVGS(0.218)T(0.782)DDPSVFSLPDSK 326.56 9.83E-74 35313000 148990 126060 121030 146010 99666 138020 142640 143270 104800 TRUE FALSE 141947.538 138905.6573 126579.3452 131332.7974 117047.7188 133240.3328 120877.6482 130724.5193 121051.8488 1.172617679 1.147488938 1.045662223 1.084930125 0.966922191 1.100688128 0.998560943 1.079905186 1 16.88526559 3.759319239 1.790189147 1.035617285 1.170905436 0.583117768 0.042446086 0.202796525 1.264306903 0.010733428 0.023803506 5745.386364 -3.759319239 0.135288151 IMVIKDIEREDIEFICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IMVIKDIEREDIEFICK 17 2 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 83.966 0.003037 37498000 57474 21547 69092 37247 73886 50411 81562 68909 82979 FALSE TRUE 54757.31792 23742.6638 72259.93654 33502.8608 86771.69501 48665.25443 69118.21891 62874.96265 95846.95952 0.571299478 0.247714314 0.753909534 0.349545369 0.905315051 0.507739157 0.721131054 0.655993294 1 16.54844505 -0.130463004 0.122435202 1.468973946 0.183517531 0.391847058 0.180100644 20.57102522 0.780978079 5.720129696 2.33216291 0.740520347 0.130463004 -1.285456415 IMYTVFEHTFHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IMYTVFEHTFHVR 13 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 213.38 3.70E-09 463240000 253050 246020 200673 210580 259250 199599 267750 243960 60084 FALSE TRUE 241088.828 271089.7177 209874.0555 189412.0983 304463.1179 192686.8366 226899.8199 222597.5691 69401.51985 3.473826344 3.906106354 3.024055611 2.729221186 4.386980553 2.776406583 3.269378256 3.207387526 1 16.08267964 -1.02951746 0.396788075 4.54E-17 3.525685767 0.692346274 0.494114881 8.452214871 0.9241819 10.19280662 0.301283313 0.093429181 1.02951746 3.525685767 INEKPQVIADYESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 INEKPQVIADYESGR 15 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;;;; 195.92 8.38E-09 4843430000 5088010 4280300 4510550 5084570 3749290 4800650 5424880 5328310 4440080 FALSE TRUE 4847509.851 4716467.436 4717363.179 4573459.364 4403164.989 4634402.287 4597214.921 4861734.929 5128624.93 0.945187047 0.919635868 0.919810523 0.891751576 0.858546891 0.903634473 0.896383531 0.94796071 1 22.29014064 0.977269445 3.653411073 0.999823791 0.907182632 0.65764505 0.02242115 0.149722017 5.444956014 0.023884063 0.006157535 9.490070636 -0.977269445 -0.092641159 INENEKS(ph)PSQNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 INENEKSPSQNRK 13 2 K7EQT1;Q9UM11-3;Q9UM11-2;Q9UM11 K7EQT1 FZR1 Fizzy-related protein homolog 1 INENEKS(0.884)PS(0.116)QNRK 92.236 0.0032172 90634000 166730 161270 160110 183270 102780 188490 202100 206280 114640 TRUE FALSE 158849.0033 177703.5963 167451.2019 164847.3514 120704.7995 181962.544 171265.9332 188217.0296 132417.7857 1.19960474 1.341991904 1.264567301 1.244903398 0.911545219 1.374154862 1.293375601 1.421387834 1 17.01473739 3.189207958 5.230482384 1.224044844 1.274741408 0.025755894 0.157989481 1.029763789 61.39844303 0.04457014 0.054725509 1545.994548 -3.189207958 0.050696563 INETDTFGPGDDDEIQFDDIGDDDEDIDDI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 66.012 0.0011708 11385000 41662 40824 41653 47894 41502 44920 43248 42151 39882 FALSE TRUE 39692.71983 44984.01201 43562.83125 43079.60413 48739.93566 43364.40914 36649.7233 38460.03498 46066.69687 0.8616359 0.97649745 0.945646947 0.935157219 1.058029748 0.941339668 0.795579579 0.834877202 1 15.49143654 -0.701338163 4.945209528 1.00000003 0.917745768 0.10584924 0.074318949 91.9750385 52006064.28 4.85855974 0.018468148 0.198912391 0.701338163 -0.082254262 INFDDNAEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 INFDDNAEFR 10 0 E9PDQ8;Q96I99;Q96I99-2 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 ;;;; 280.96 1.04E-23 1859110000 2532350 1851190 2088110 1981850 2242360 1796620 2246250 2073160 2239280 FALSE TRUE 2412650.834 2039828.366 2183851.909 1782630.673 2633426.874 1734402.599 1903543.307 1891623.12 2586536.106 0.932772919 0.788633246 0.844315262 0.689196129 1.018128789 0.670550314 0.735943064 0.731334512 1 21.3025899 INFDKYHPGYFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 INFDKYHPGYFGK 13 1 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 153.39 2.36E-05 8115700000 10142500 5851200 8862800 8379800 8465300 9281300 13527500 10509200 9810000 FALSE TRUE 9663084.125 6447443.932 9269168.147 7537446.583 9941645.64 8959886.254 11463631.43 9588958.735 11331284.7 0.85277922 0.568994964 0.818015644 0.665189057 0.877362621 0.790721131 1.011679764 0.846237562 1 23.4338081 2.251428705 1.183338033 0.954570308 0.717109417 0.456649281 0.098815114 0.374008802 1.011569686 0.058796573 0.033745629 178.4139076 -2.251428705 -0.237460892 INFDSNSAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 INFDSNSAYR 10 0 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5;Q5T9Q8 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ; 130.79 0.00062194 233910000 361890 304720 274990 310400 317030 269150 349020 335790 351850 FALSE TRUE 344784.1769 335771.3144 287598.5635 279198.0023 372319.9316 259829.268 295770.5888 306386.4475 406413.101 0.848358914 0.82618231 0.707650818 0.686980812 0.916112032 0.639323062 0.7277585 0.753879358 1 18.63258738 3.890650441 6.459022933 0.756928996 0.840120994 0.031579258 0.108791672 0.503660697 25.71093186 0.024984359 0.045569917 7774.10569 -3.890650441 0.083191998 INFS(ph)DLDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;INFS(1)DLDQR 125.28 0.00053068 61788000 133868 142895 134554 144223 126827 135811 166966 149978 152632 TRUE FALSE 127540.3249 157456.163 140723.434 129725.43 148945.5886 131107.831 141492.2702 136845.1312 176301.391 0.723422114 0.893107888 0.798198092 0.735816259 0.844835017 0.743657383 0.802559012 0.776199952 1 17.42768433 -1.155485454 5.378843433 1.00000591 0.793896889 0.622911485 0.05132499 3.37E-06 5.29E-07 0.04606703 0.010857792 0.069906015 1.155485454 -0.206109021 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTASPHSNR 40 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPT(0.278)AS(0.709)PHS(0.013)NR 115.1 2.50E-06 66648000 313800 234290 292490 300020 243520 282570 345050 323660 270480 TRUE FALSE 298967.2959 258164.4174 305900.9558 269861.4196 285989.8109 272784.53 292406.2852 295318.6146 312424.657 0.956926059 0.826325361 0.979119122 0.863764794 0.915388093 0.873121004 0.935925762 0.945247464 1 18.25314879 1.066960209 1.407307817 0.99842308 0.900092149 0.323948942 0.044428904 0.431008962 1.729376261 0.03722112 0.01123297 11.66702715 -1.066960209 -0.09833093 INHEGEVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 143.91 0.00023454 2205296000 1842075 1629776 1541499 1837432 1838339 1620036 1954219 1786454 1873290 FALSE TRUE 1755003.765 1795852.027 1612178.254 1652729.844 2158944.74 1563933.747 1656067 1630022.617 2163790.246 0.811078509 0.829956615 0.745071412 0.763812411 0.99776064 0.722775117 0.765354684 0.75331822 1 21.04512922 -1.221060056 5.158736804 1.000019216 0.799544542 0.401156942 0.077309636 1.61E-05 2.43E-06 0.070399249 0.016591672 0.060109061 1.221060056 -0.200474674 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.998)PEPT(0.002)R;INHTVILDDPFDDPPDLLIPDRS(1)PEPTR;INHTVILDDPFDDPPDLLIPDRS(0.956)PEPT(0.044)R;INHTVILDDPFDDPPDLLIPDRS(0.973)PEPT(0.027)R;INHTVILDDPFDDPPDLLIPDRS(0.964)PEPT(0.036)R;INHTVILDDPFDDPPDLLIPDRS(0.909)PEPT(0.091)R;INHTVILDDPFDDPPDLLIPDRS(0.984)PEPT(0.016)R;INHTVILDDPFDDPPDLLIPDRS(0.937)PEPT(0.063)R;INHTVILDDPFDDPPDLLIPDRS(0.996)PEPT(0.004)R;INHTVILDDPFDDPPDLLIPDRS(0.954)PEPT(0.046)R;INHTVILDDPFDDPPDLLIPDRS(0.978)PEPT(0.022)R;INHTVILDDPFDDPPDLLIPDRS(0.817)PEPT(0.183)R;INHTVILDDPFDDPPDLLIPDRS(0.996)PEPT(0.004)R;INHTVILDDPFDDPPDLLIPDRS(0.977)PEPT(0.023)R;INHTVILDDPFDDPPDLLIPDRS(0.998)PEPT(0.002)R;INHTVILDDPFDDPPDLLIPDRS(0.992)PEPT(0.008)R 278.59 7.15E-62 3855902000 892093.7 848721.4 818867.1 1019566.3 803862.1 836707.2 952905.1 914494.8 717607.6 TRUE FALSE 849926.1988 935207.0756 856412.9665 917077.5585 944055.3957 807731.8199 807521.9257 834416.7873 828890.5216 1.025378113 1.128263686 1.033203957 1.106391658 1.138938583 0.974473466 0.974220243 1.006667063 1 19.66082204 2.222433181 24.99997535 0.984919231 1.085075951 0.62981453 0.037117305 147.8344627 229164.3627 0.013244876 0.009813063 166.8911016 -2.222433181 0.10015672 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTREQLDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 INHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGR 35 2 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.794)PEPT(0.175)REQLDS(0.031)GR;INHTVILDDPFDDPPDLLIPDRS(0.89)PEPT(0.051)REQLDS(0.06)GR;INHTVILDDPFDDPPDLLIPDRS(0.997)PEPT(0.003)REQLDSGR;INHTVILDDPFDDPPDLLIPDRS(0.924)PEPT(0.057)REQLDS(0.019)GR;INHTVILDDPFDDPPDLLIPDRS(0.937)PEPT(0.034)REQLDS(0.029)GR;INHTVILDDPFDDPPDLLIPDRS(0.997)PEPT(0.003)REQLDSGR;INHTVILDDPFDDPPDLLIPDRS(0.966)PEPT(0.034)REQLDS(0.001)GR;INHTVILDDPFDDPPDLLIPDRS(0.974)PEPT(0.022)REQLDS(0.004)GR;INHTVILDDPFDDPPDLLIPDRS(0.722)PEPT(0.214)REQLDS(0.064)GR;INHTVILDDPFDDPPDLLIPDRS(0.977)PEPT(0.017)REQLDS(0.006)GR 318.57 2.72E-105 1337826000 176585.4 88651.6 171136.7 133430 206397.7 148099 242742.7 170691 225597.1 TRUE FALSE 168238.5581 97685.29883 178983.487 120017.3629 242393.3935 142970.2945 205707.8428 155744.3912 260581.5461 0.645627293 0.374874201 0.686861712 0.460575066 0.930201686 0.548658555 0.789418307 0.597680049 1 17.99137539 -5 0.09427958 2.283148796 0.317199133 0.390221552 0.15236768 173.5263242 1.126910771 43.87025514 2.727416616 1.00E-05 5 -1.965949663 INHTVILDDPFDDPPDLLIPDRSPEPT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.428)PEPT(0.572)R 116.72 0.00041061 22983000 7424.1 8978.7 7457.3 9500.3 7783.7 6276.8 9366.2 9127 6356 TRUE FALSE 7073.177506 9893.639738 7799.224581 8545.311795 9141.174816 6059.432842 7937.214168 8327.791495 7341.656018 0.963430797 1.347603281 1.06232498 1.163948811 1.245110748 0.825349598 1.08112041 1.134320578 1 12.84188981 2.272102811 24.99994051 1.016988526 1.16105457 0.245107048 0.127179189 261.7183003 195065.0678 0.041694528 0.034882235 187.1125039 -2.272102811 0.144066044 INISEGNCPER ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 221.32 1.98E-11 1613070000 940470 785691 835080 892650 851404 840190 1009170 925420 1002340 FALSE TRUE 896015.8469 865753.8062 873369.244 802919.1261 999888.588 811094.0096 855202.5818 844385.3188 1157777.768 0.773910047 0.747772008 0.754349641 0.693500211 0.863627387 0.700561051 0.738658666 0.729315541 1 20.14292693 -1.707090143 2.559752463 1.044443699 0.750144032 0.737903864 0.046784785 6285589.367 4980538.18 1796087.908 0.011027266 0.019629528 1.707090143 -0.294299666 INPPSSGGTSSS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.009)S(0.991)PIK;INPPSSGGTSS(0.048)S(0.952)PIK;INPPSSGGTSS(0.063)S(0.937)PIK;INPPSSGGTSSS(1)PIK 270.73 2.33E-33 904830000 1655210 1731640 1491690 1925150 922430 1746660 1549460 1857920 1030200 TRUE FALSE 1576971.504 1908096.085 1560085.462 1731630.264 1083301.5 1686172.726 1313061.419 1695230.675 1189958.154 1.325232738 1.603498474 1.311042288 1.455202654 0.910369407 1.417001699 1.103451759 1.424613688 1 20.18247941 INPYMS(ph)SPCHIEMILTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 1 INPYMS(0.913)S(0.087)PCHIEMILTEK;INPYMS(0.631)S(0.369)PCHIEMILTEK;INPYMS(0.5)S(0.5)PCHIEMILTEK;INPYMS(0.5)S(0.5)PCHIEMILTEK;INPYMS(0.847)S(0.153)PCHIEMILTEK;INPYMS(0.5)S(0.5)PCHIEMILTEK;INPYMS(0.63)S(0.37)PCHIEMILTEK 261.49 5.58E-31 771981000 1849623 1632544 1622507 2018722 1433359 1878792 2042447 2053106 1347859 TRUE FALSE 1762194.986 1798902.09 1696900.551 1815796.229 1683336.356 1813728.962 1730834.198 1873325.154 1556878.09 1.131877311 1.155454689 1.089937974 1.166305982 1.081225542 1.164978153 1.11173393 1.203257446 1 20.57022455 -1.441855179 3.093526317 0.997442678 1.13635287 0.577635602 0.037084267 4203420.019 5401629.79 93968.66082 0.007543878 0.03615304 1.441855179 0.138910192 INPYMSSPCHIEMILTEK ddPTM_SK-BR-3_Trastuzumab_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 0 220.34 6.84E-19 209250000 208160 183230 195170 242470 205310 202080 313440 258660 241340 FALSE TRUE 198320.6893 201901.3453 204118.7375 218096.4549 241115.999 195081.9189 265618.9713 236010.3592 278765.7746 0.711424096 0.724268772 0.732223092 0.782364533 0.864941183 0.699805847 0.952839249 0.846626023 1 18.08869392 1.685114755 0.34354591 1.016318984 0.684379123 0.67208307 0.05939383 0.664304781 0.248461627 0.077691103 0.073487333 48.43003187 -1.685114755 -0.331939861 INS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.576)S(0.411)PNVNT(0.004)T(0.006)AS(0.002)GVEDLNIIQVTIPDDDNER;INS(0.466)S(0.466)PNVNT(0.021)T(0.021)AS(0.025)GVEDLNIIQVTIPDDDNER 145.29 1.19E-08 83312000 57566 55742 59296 70966 59687 60924 70537 66645 73762 TRUE FALSE 54844.96926 61422.17317 62014.78025 63832.36285 70096.3939 58814.1866 59775.28515 60809.21049 85200.63424 0.643715505 0.720912159 0.727867589 0.74920056 0.822721504 0.690302216 0.701582631 0.713717815 1 16.37857655 -1.915908225 2.258500078 1.182069407 0.718039629 0.787479354 0.045481487 4209191.212 1920500.58 4053241.66 0.011470347 0.012136453 1.915908225 -0.464029778 INSSPNVNT(ph)TASGVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.183)S(0.152)PNVNT(0.221)T(0.221)AS(0.221)GVEDLNIIQVTIPDDDNER 102.99 0.00063746 51961000 52607 48967 54757 53622 48864 50929 60664 52895 57226 TRUE FALSE 50120.37137 53956.79297 57267.66261 48231.81468 57385.86613 49165.31596 51408.59263 48263.23339 66100.31581 0.758247079 0.816286463 0.866375023 0.72967601 0.868163267 0.743798503 0.777735961 0.730151328 1 16.01236954 -1.452189854 4.735496135 1.00054024 0.787802956 0.637650838 0.050614444 0.000260216 3.01E-05 0.044173932 0.010385818 0.035302881 1.452189854 -0.212737284 INSSPNVNTTAS(ph)GVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.154)S(0.128)PNVNT(0.224)T(0.224)AS(0.271)GVEDLNIIQVTIPDDDNER 103.82 0.0001066 29348000 31989 27049 27765 28698 27770 27297 32378 29534 35217 TRUE FALSE 30476.94337 29805.32385 29038.05271 25813.22252 32613.07921 26351.69805 27438.14144 26947.84639 40678.2725 0.749219214 0.732708692 0.713846752 0.634570274 0.801732158 0.647807698 0.674515896 0.662462901 1 15.31197079 -1.018125184 6.330008835 1.00000018 0.704314048 0.773394041 0.050662829 1.24E-07 1.93E-08 0.047269511 0.011141524 0.095912413 1.018125184 -0.295686132 INVYYNEATGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 ; 206.27 2.14E-07 75692000 213308 173771 179577 197764 166020 190204 229062 209155 189426 FALSE TRUE 203225.3536 191478.4625 187810.7831 177884.387 194973.8354 183617.1878 194114.3849 190840.2794 218801.2166 0.928812722 0.875125218 0.858362609 0.81299542 0.891100326 0.839196375 0.887172329 0.872208493 1 17.73926123 -0.085543125 1.411441531 1.000251996 0.872293253 0.633808201 0.030882328 18.85859741 23.23073505 0.051255589 0.008761577 0.821215003 0.085543125 -0.127958743 INYTEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 190.54 0.0012539 8452150000 8515700 7683830 7542270 8841000 8856650 7826300 9144140 8301200 9414120 FALSE TRUE 8113179.737 8466821.013 7888090.54 7952285.883 10401246.96 7555273.269 7749033.499 7574302.921 10874013.65 0.746107187 0.778628875 0.725407453 0.731311008 0.956523257 0.69480079 0.712619438 0.696550801 1 23.37438121 -1.053074455 4.937591762 1.000003808 0.755303859 0.508244818 0.075661407 4.09E-06 7.85E-07 0.069667121 0.016420351 0.088496388 1.053074455 -0.244699949 IPAS(ph)QTS(ph)VPFDHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPASQTSVPFDHLGK 15 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 2 IPAS(0.975)QT(0.099)S(0.925)VPFDHLGK 161.51 8.71E-07 90486000 169760 136260 153720 171780 126370 174290 185260 180880 134530 TRUE FALSE 161735.7812 150145.0489 160768.214 154512.348 148408.888 168254.2936 156995.1845 165041.1883 155392.2253 1.040822866 0.966232697 1.034596253 0.994337701 0.955059931 1.082771633 1.010315569 1.062094245 1 17.2455548 2.239078462 25 1.038051356 0.999201192 0.252077737 0.034704068 19.63732999 948094.1856 0.011350118 0.00897598 173.4117263 -2.239078462 -0.038850163 IPASQTS(ph)VPFDHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPASQTSVPFDHLGK 15 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IPAS(0.003)QT(0.356)S(0.641)VPFDHLGK;IPAS(0.005)QT(0.319)S(0.676)VPFDHLGK 137.99 8.59E-06 472610000 392650 334851 322228 373110 603271 348885 444620 388660 534408 TRUE FALSE 374090.2127 368972.6976 337002.4725 335604.2739 708481.2714 336803.025 376785.053 354626.87 617281.2633 0.606028783 0.597738372 0.545946382 0.543681291 1.147744656 0.545623276 0.610394443 0.57449803 1 19.23556848 IPDHDPAPNVTVLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPDHDPAPNVTVLLR 15 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 179.79 6.56E-07 401050000 533070 481960 394100 504390 452310 404370 417760 426100 356340 FALSE TRUE 507872.8375 531072.2719 412169.8748 453687.7589 531192.7208 390366.5655 354023.0393 388788.4251 411599.3873 1.233900859 1.290264972 1.001386026 1.102255671 1.290557608 0.948413865 0.860115564 0.944579698 1 18.65088131 2.161343298 6.816819901 0.917057976 1.190396483 0.632693258 0.092366844 0.13406138 9.664563028 0.036067631 0.026622696 144.9917522 -2.161343298 0.273338508 IPDWFLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPDWFLNR 8 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 127.12 0.0027686 1157810000 1141760 863990 500150 518650 1201340 576830 1229080 802860 1049990 FALSE TRUE 1087791.268 952031.5633 523082.3722 466514.3166 1410853.316 556854.2325 1041561.272 732557.3222 1212817.087 0.896912881 0.784975388 0.431295352 0.384653483 1.163286147 0.45914115 0.858795019 0.604013029 1 20.20993055 -1.685856137 12.66345469 1.00003005 0.71424732 0.13038723 0.241942083 0.000189293 4.70E-06 0.216035 0.050914623 0.020613126 1.685856137 -0.28578273 IPESETESTAS(ph)APNS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPESETESTASAPNSPR 17 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 2 IPESETESTAS(1)APNS(1)PR;IPESETEST(0.004)AS(0.996)APNS(1)PR 244.1 2.50E-20 144380000 258880 220183 255960 271910 263450 268650 295950 269130 284540 TRUE FALSE 246643.2555 242619.898 267696.0192 244577.0902 309395.5966 259346.5831 250797.392 245563.5505 328665.01 0.750439651 0.738198137 0.814495036 0.744153113 0.941370658 0.789090944 0.763079076 0.747154528 1 18.32625835 -2.572066929 2.245493012 5.188320701 0.78252139 0.556287015 0.059993795 2919459.669 336838.3332 61703754.55 0.014255804 0.002678755 2.572066929 -4.405799312 IPFTVSLDNGHSFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPFTVSLDNGHSFPR 15 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ; 199.84 7.22E-09 474550000 308690 215060 227270 276630 315310 235670 306020 292150 359710 FALSE TRUE 294098.8355 236974.8585 237690.5543 248822.6268 370299.9642 227508.6888 259331.0286 266567.7972 415491.9897 0.707832745 0.570347599 0.572070125 0.598862633 0.891232499 0.547564561 0.624154099 0.641571447 1 18.66446114 -1.357146345 3.717208381 1.001468811 0.639764243 0.561671185 0.098709132 36549199.77 62921719.43 590233.0684 0.022294555 0.043939353 1.357146345 -0.361704568 IPGLLSPHPLLQLSYTATDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 251.7 4.64E-36 10204016000 3346302 3380217.9 3281181 3786069 3409017 3326089 3527704 3396513 3236430 FALSE TRUE 3188128.936 3724665.947 3431626.394 3405486.151 4003548.485 3210905.704 2989487.964 3099096.316 3738319.035 0.852824199 0.9963478 0.917959747 0.910967234 1.070948854 0.858916982 0.799687757 0.829007981 1 21.83395827 2.035757436 24.98590618 0.847806625 0.945859546 0.17013863 0.077945483 212.6727814 148606.6259 0.026811033 0.019801206 108.5818998 -2.035757436 0.09805292 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IPGTPGAGGRLSPENNQVLTK 21 1 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK 165.48 8.87E-12 3479600000 2510700 1867140 2134960 2359020 1844840 2192480 2623770 2426000 2110190 TRUE FALSE 2392024.187 2057403.689 2232850.028 2121886.828 2166579.512 2116553.868 2223465.698 2213566.579 2437427.488 0.981372451 0.844088162 0.916068289 0.87054357 0.888879576 0.868355624 0.912218193 0.908156895 1 21.21692787 0.512387045 1.484109253 0.999960413 0.896001475 0.434206784 0.036610695 2.223028538 5.748845311 0.03288973 0.00953487 3.253771456 -0.512387045 -0.103958939 IPIFSAAGLPHNEIAAQICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 220.82 8.26E-25 197410000 126130 109650 105090 149430 135020 105590 139640 136440 122390 FALSE TRUE 120168.0849 120823.4597 109908.4804 134409.0125 158567.4453 101933.3918 118335.3533 124492.5903 141369.6161 0.850027666 0.854663562 0.777454756 0.950763086 1.121651523 0.721041725 0.837063554 0.880617729 1 17.10911256 -2.759306539 1.785743759 3.983808896 0.868555167 0.118796132 0.106744177 4914734.782 109027.8593 59742348.62 0.026717307 0.001740578 2.759306539 -3.115253728 IPIHNEDITYDELVLMMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IPIHNEDITYDELVLMMQR 19 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;; 200.99 6.21E-16 230444000 208520 160994 170581 203504 192547 195838 213351 210451 159209 FALSE TRUE 198663.6728 177399.4716 178402.3076 183047.3913 226127.1358 189056.081 180800.3865 192022.7948 183898.3186 1.080290861 0.96466065 0.970113859 0.995372838 1.22963134 1.028046816 0.983154103 1.044179176 1 17.48854876 4.752186216 23.18787304 1.025665815 1.080290944 0.046141188 0.076115149 157.3449456 1668255.269 0.018042962 0.118584663 56517.92594 -4.752186216 0.054625129 IPLFNTDVDNLEGKT(ph)PPVFASEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPLFNTDVDNLEGKTPPVFASEGK 24 1 Q96PZ0;Q96PZ0-2 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 1 IPLFNTDVDNLEGKT(0.999)PPVFASEGK 66.98 0.058206 43183000 79745 73179 65848 96484 47357 88456 83191 87549 46798 TRUE FALSE 75975.61189 80636.0233 68867.19593 86785.24501 55616.04581 85392.74654 70498.68504 79882.74543 54055.19483 1.405519157 1.491734949 1.274016237 1.60549315 1.028875134 1.579732472 1.304198149 1.477799603 1 15.72214565 -1.750588105 2.5440908 0.907681357 1.397967456 0.356258357 0.167236929 11665074.42 8408269.04 6754125.948 0.036220472 0.01775873 1.750588105 0.490286099 IPLSQEEITLQGHAFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPLSQEEITLQGHAFEAR 18 0 G5E9X5;F5GYT8;E9PG35;E9PHF7;Q96RQ3 G5E9X5 MCCC1 "Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial" 0 228.01 2.66E-19 81187000 35872 38596 30505 30091 38111 31022 34314 17430 35021 FALSE TRUE 34176.40165 42528.97628 31903.68442 27066.19551 44757.54633 29947.70036 29078.76908 15903.7368 40451.87782 0.84486564 1.051347393 0.788682408 0.669096145 1.106439274 0.740329052 0.718848435 0.393152003 1 15.30391906 2.018972806 24.66384206 0.686967939 0.897067252 0.182278056 0.188389477 289.4355642 376252.1515 0.065199785 0.048145644 104.4654805 -2.018972806 0.210099313 IPMPDFDLHLKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPMPDFDLHLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 148.91 4.58E-06 51739000 271990 149350 266920 239490 222420 254470 367810 314600 270190 FALSE TRUE 259133.5717 164568.9348 279158.546 215416.0102 261209.9776 245657.6401 311693.8292 287051.9562 312089.6853 0.830317643 0.527312957 0.894481808 0.690237519 0.836970877 0.787137966 0.998731595 0.91977393 1 18.25160115 2.072043291 0.851962427 0.999086623 0.707192393 0.4731987 0.103384261 0.453340288 0.611928847 0.079246454 0.041217469 118.0438298 -2.072043291 -0.29189423 IPMPPSS(ph)PQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.483)S(0.517)PQPR 98.406 0.005816 270260000 92471 76383 88908 99145 96109 76556 86292 77991 94589 TRUE FALSE 88100.07909 84166.51454 92984.51974 89178.75624 112870.3792 73904.84652 73126.57054 71161.69458 109257.379 0.806353583 0.770350848 0.851059403 0.816226392 1.033068706 0.67642888 0.669305553 0.651321634 1 16.73737119 IPMTPTSSFVSPPPPT(ph)ASPHSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.653)AS(0.345)PHS(0.002)NR 138.11 1.80E-05 172930000 61103 76101 54707 74523 50293 57355 52861 55254 39367 TRUE FALSE 58214.78228 83855.77842 57215.37006 67031.80646 59064.08328 55368.78197 44796.08359 50415.66684 45471.8333 1.280238294 1.844125744 1.258259584 1.474139079 1.298915812 1.217650091 0.985139158 1.108722987 1 15.47268555 2.358617377 0.986129258 1.006839415 1.52637493 0.567885439 0.163241451 0.348789719 0.663840118 0.106790996 0.067209456 228.3586025 -2.358617377 0.519535515 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.226)AS(0.688)PHS(0.086)NR;IPMTPTSSFVSPPPPT(0.071)AS(0.915)PHS(0.014)NR;IPMTPTSSFVSPPPPT(0.013)AS(0.974)PHS(0.013)NR 149.16 3.29E-07 436841000 162636 169516 142672 180700 115792 139171 147286 155570 121571 TRUE FALSE 154948.5186 186789.8731 149213.6523 162535.6927 135986.0881 134351.4734 124814.8156 141947.4661 140423.6098 1.103436373 1.330188516 1.062596614 1.157466988 0.968399035 0.956758437 0.888844944 1.010851852 1 17.09942599 2.885544183 1.488542778 0.943805045 1.202274782 0.604998292 0.077919047 0.215975985 0.972625086 0.028618772 0.030998839 768.3236174 -2.885544183 0.258469737 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR 32 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 359.53 2.41E-132 5451130000 1635709 1493740 1404919 1664260 1829040 1318010 1853510 1502270 929955 FALSE TRUE 1558392.277 1645953.804 1469335.926 1496965.423 2148023.997 1272366.983 1570723.007 1370723.275 1074167.672 1.450790522 1.532306219 1.367883213 1.393604986 1.999710151 1.184514314 1.462269857 1.276079434 1 20.03478778 0.939511809 1.04274318 1.002993534 1.504505448 0.37986231 0.204338657 0.612080188 1.376835121 0.176184864 0.057316448 8.699850882 -0.939511809 0.501511913 IPNIYAIGDVVAGPMLAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPNIYAIGDVVAGPMLAHK 19 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 192.69 6.91E-15 155078000 394710 334060 351090 346580 310040 294120 363400 346720 288380 FALSE TRUE 376052.8405 368101.0938 367187.8238 311741.1199 364110.8778 283934.5507 307956.6557 316359.3587 333100.4976 1.128947099 1.105075184 1.102333459 0.935877077 1.093096169 0.852399059 0.924515748 0.949741478 1 18.34559798 3.130171787 1.00609497 0.932325524 1.129309872 0.537985147 0.06407975 0.332054941 0.731810029 0.026435986 0.037624319 1349.496575 -3.130171787 0.196984347 IPNYQLS(ph)PTKLPSINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.982)PT(0.018)KLPSINK;IPNYQLS(0.979)PT(0.021)KLPSINK 212.18 3.14E-12 5577900000 4336320 5060510 4308220 5280960 2403640 5415580 5262270 5656250 2888160 TRUE FALSE 4131350.747 5576181.722 4505756.148 4750107.868 2822834.055 5228037.107 4459414.063 5160958.764 3336041.102 1.238399235 1.671496709 1.350629687 1.423875702 0.846162852 1.567138098 1.336738345 1.547030929 1 21.66970563 -1.907573747 2.465815754 0.77404797 1.381914571 0.211463846 0.225545246 12322036.79 6153182.943 16102802.81 0.051296272 0.012371611 1.907573747 0.607866601 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR ddPTM_SK-BR-3_Trastuzumab_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 ; 291.62 1.26E-89 825020000 357712 289515 324823 343415 270040 364391 418476 386600 320626 FALSE TRUE 340803.6627 319016.9077 339716.4558 308894.2718 317134.8905 351772.0483 354629.8004 352747.2545 370347.0425 0.92022785 0.861399906 0.917292207 0.834067068 0.85631814 0.949844356 0.957560773 0.952477579 1 18.49851829 2.152722604 5.737455107 0.9621759 0.879406362 0.68935641 0.029098894 0.124128536 6.477881161 0.010649174 0.007836027 142.1420595 -2.152722604 -0.082769538 IPQSHIQQICETILTSGENLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPQSHIQQICETILTSGENLAR 22 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 220.69 9.96E-26 457380000 262850 198980 278390 254400 227650 277420 324910 206940 134700 FALSE TRUE 250425.6014 219256.2882 291154.4569 228827.2287 267352.0879 267812.8758 275339.0121 188819.2365 155588.588 1.609537078 1.409205463 1.871309847 1.470719874 1.718327104 1.721288683 1.769660716 1.213580243 1 17.24737672 1.079530039 4.519228687 1.006263735 1.637761491 0.740041107 0.137170845 0.097310331 3.420801387 0.132166882 0.033672313 12.00964137 -1.079530039 0.631497756 IPRPLS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPRPLSPTK 9 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 IPRPLS(0.824)PT(0.176)K;IPRPLS(0.873)PT(0.127)K 74.392 0.024963 684960000 2590110 2092590 1916770 2082410 2318200 2005410 2840020 2643550 2582930 TRUE FALSE 2467680.633 2305827.3 2004655.8 1873082.19 2722493.346 1935962.149 2406722.788 2412066.748 2983477.593 0.827115524 0.772865634 0.671919174 0.627818421 0.912523477 0.648894483 0.806683715 0.8084749 1 21.50856351 0.691676489 1.350568051 0.999647727 0.752524518 0.453751906 0.08585046 0.952872077 2.7620813 0.07638689 0.022720795 4.916731461 -0.691676489 -0.247123209 IPRPLSPT(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPRPLSPTK 9 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 IPRPLS(0.359)PT(0.641)K 77.597 0.051979 204570000 1007900 803200 652490 834910 684910 859120 1010200 1012300 772150 TRUE FALSE 960258.5645 885046.9932 682407.3119 750983.2606 804358.0871 829368.459 856075.4364 923657.6455 891891.0784 1.076654524 0.992326322 0.765124048 0.842012303 0.90185686 0.929898817 0.959843031 1.035617093 1 19.76650801 1.43299144 3.361888426 1.01700786 0.929796758 0.186703886 0.082916196 0.527517121 10.71560933 0.071883842 0.024729658 27.10138212 -1.43299144 -0.087211102 IPS(ph)AKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPSAKK 6 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 IPS(1)AKK 59.35 0.082844 2268600000 4150900 3314200 3476400 4359700 1973700 4124000 4722200 4242600 2234600 TRUE FALSE 3954695.183 3651920.748 3635796.379 3921454.673 2317912.655 3981184.846 4001741.661 3871095.453 2581130.355 1.532156319 1.414853279 1.408606261 1.519278042 0.898022314 1.542419133 1.550383402 1.499767513 1 21.29957157 4.437083145 1.065005374 1.375727285 1.565290185 0.054915461 0.227000355 4.074795336 5.335920545 0.067552258 0.780086413 27357.92437 -4.437083145 0.1895629 IPS(ph)PNILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;IPS(1)PNILK 132.32 0.0010147 1851373000 5339280 4757920 4716320 5325540 3798460 5254200 5813890 5567520 4219610 TRUE FALSE 5086902.816 5242757.457 4932567.937 4790206.601 4460910.221 5072245.737 4926874.301 5079998.434 4873965.568 1.043688706 1.075665674 1.01202355 0.982815027 0.915252715 1.040681487 1.010855377 1.042272122 1 22.21666463 3.615615056 4.869424031 0.998974158 1.059342657 0.324293607 0.035859831 0.24480011 8.667718993 0.00971892 0.015286002 4126.815525 -3.615615056 0.060368499 IPSIVS(ph)SPLNSPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.579)S(0.421)PLNSPLDR;IPSIVS(0.767)S(0.233)PLNSPLDR 202.93 5.94E-09 121440000 101926 93167 85652 106111 93370 92954 107656 94829 100249 TRUE FALSE 97108.15998 102660.8232 89579.22892 95444.52068 109653.6984 89734.97967 91231.09996 86525.27004 115795.1029 0.838620611 0.886573099 0.773601186 0.824253516 0.946963176 0.77494624 0.787866651 0.747227369 1 16.82121472 IPSIVSS(ph)PLNSPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.494)S(0.506)PLNSPLDR 135.14 3.24E-05 33138000 30727 30084 30190 39330 29325 30934 31617 30721 31970 TRUE FALSE 29274.59561 33149.5938 31574.24136 35376.47368 34439.27072 29862.74782 26793.24596 28030.90638 36927.74432 0.79275342 0.897688023 0.855027621 0.95799173 0.932612358 0.808680529 0.725558695 0.759074427 1 15.17241752 2.090251573 7.230099087 0.790245777 0.881523397 0.068018181 0.085940835 0.344092598 23.47949098 0.030255636 0.022281744 123.0981632 -2.090251573 0.09127762 IPSKEEEADMS(ph)SPTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.606)S(0.394)PTQR;IPSKEEEADMS(0.494)S(0.494)PT(0.011)QR;IPSKEEEADMS(0.499)S(0.499)PT(0.001)QR 137.09 8.44E-06 866410000 1210332 984434 1126775 1267789 874780 1171637 1331251 1267595 991013 TRUE FALSE 1153122.005 1084748.944 1178438.748 1140348.441 1027341.355 1131062.917 1128144.21 1156597.662 1144694.235 1.007362464 0.94763205 1.029479063 0.996203533 0.897481025 0.988091739 0.985541969 1.010398783 1 20.12653085 1.470995346 2.765665533 1.004647797 0.976345621 0.087529449 0.035654925 0.648969994 9.617760323 0.026871802 0.009149585 29.57980769 -1.470995346 -0.028302176 IPSKEEEADMSS(ph)PTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.005)S(0.992)PT(0.003)QR;IPSKEEEADMS(0.007)S(0.991)PT(0.002)QR;IPSKEEEADMS(0.001)S(0.997)PT(0.003)QR;IPSKEEEADMS(0.001)S(0.988)PT(0.01)QR;IPSKEEEADMS(0.016)S(0.984)PTQR;IPSKEEEADMS(0.025)S(0.975)PTQR;IPSKEEEADMS(0.009)S(0.985)PT(0.006)QR;IPSKEEEADMS(0.034)S(0.954)PT(0.012)QR;IPSKEEEADMS(0.023)S(0.977)PTQR;IPSKEEEADMS(0.058)S(0.942)PTQR;IPSKEEEADMS(0.005)S(0.994)PTQR;IPSKEEEADMS(0.153)S(0.847)PTQR;IPSKEEEADMS(0.294)S(0.693)PT(0.013)QR;IPSKEEEADMS(0.001)S(0.962)PT(0.036)QR;IPSKEEEADMS(0.047)S(0.953)PTQR;IPSKEEEADMS(0.156)S(0.843)PT(0.001)QR;IPSKEEEADMS(0.254)S(0.603)PT(0.143)QR;IPSKEEEADMS(0.145)S(0.523)PT(0.333)QR 215.32 9.82E-15 26125590000 24450900 20655370 21753020 25012530 17980760 23255900 26012970 24087190 18988420 TRUE FALSE 23295154.41 22760175.69 22750417.48 22498222.96 21116598.85 22450542.35 22044213.67 21977987.95 21933047.19 1.062102963 1.037711517 1.037266609 1.025768228 0.962775426 1.023594312 1.005068446 1.002048997 1 24.38660293 3.10744308 3.040017973 1.001130396 1.04700394 0.622194241 0.016630296 0.158729759 2.943815206 0.004815518 0.005913301 1280.687234 -3.10744308 0.045873544 IPTPVIHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPTPVIHTK 9 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ; 185.81 4.24E-05 1432220000 1730770 1463900 1242730 1777180 1244410 1381790 1523260 1582050 1152510 FALSE TRUE 1648959.932 1613073.074 1299710.4 1598534.49 1461434.71 1333938.266 1290858.71 1443517.315 1331235.365 1.238668966 1.211711405 0.976319015 1.200790283 1.0978034 1.002030371 0.969669785 1.084344176 1 20.34433423 4.234792133 0.39860632 0.994293052 1.379841199 0.490568814 0.072332992 2.734033609 0.463649942 0.060753068 0.486578316 17170.86338 -4.234792133 0.385548147 IPTPVIHTKH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPTPVIHTKH 10 1 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 75.652 0.024896 128070000 238660 136060 183380 144570 265060 170910 313790 207900 134520 FALSE TRUE 227379.0148 149924.6687 191788.1544 130037.5489 311286.3801 164991.3438 265915.5724 189695.1739 155380.6746 1.463367407 0.9648862 1.234311506 0.83689654 2.003378998 1.061852411 1.711381245 1.220841487 1 17.24544755 2.787366467 24.99992915 1.43686905 1.141894063 0.136266624 0.335110705 652.1096216 334030.3282 0.090086997 0.095551545 612.8673239 -2.787366467 -0.294974987 IPVEGPLS(ph)PSRGDFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IPVEGPLSPSRGDFPK 16 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.979)PS(0.021)RGDFPK 132.14 2.47E-05 98699000 168130 130060 151220 172350 140550 155140 203050 178860 166010 TRUE FALSE 160182.8281 143313.2619 158153.5866 155025.0506 165061.8755 149767.4629 172070.9932 163198.0702 191753.9829 0.835355937 0.747380887 0.824773411 0.808458047 0.860800245 0.781039646 0.897352903 0.851080471 1 17.54889702 0.410295524 0.376031762 1.025164843 0.789888262 0.722813953 0.036183506 1.31926056 0.345954187 0.092527214 0.027116581 2.572145454 -0.410295524 -0.23527658 IPVHPNDHVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IPVHPNDHVNK 11 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ;;;;; 154.66 1.84E-05 2326390000 4611740 3649790 4001380 4100520 3437200 3689640 4252570 3856940 265526 FALSE TRUE 4393752.19 4021707.75 4184847.231 3688327.939 4036646.592 3561866.842 3603762.343 3519205.887 306702.416 14.32578278 13.1127358 13.64465036 12.02575444 13.16144374 11.61342936 11.7500292 11.47433376 1 18.22648001 -0.165176444 0.495962563 4.43E-17 13.46911918 0.969983093 0.654230893 0.810015915 0.218589628 2.846811127 0.307327958 0.683633846 0.165176444 13.46911918 IPWFQYPIIYDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IPWFQYPIIYDIR 13 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5 Q99623-2 PHB2 Prohibitin-2 0 ; 125.22 0.00047166 262460000 297170 268150 210141 260859 248930 243963 270700 270680 165884 FALSE TRUE 283123.363 295474.7899 219776.1727 234636.9577 292343.3132 235514.5001 229399.7433 246977.8242 191608.4435 1.477614232 1.54207604 1.147006722 1.224564813 1.525732937 1.229144686 1.197231912 1.288971507 1 17.54780161 7.999999995 0.061691979 0.562481347 2.926564697 0.479773821 0.1261691 251.959366 1.159045331 8.769348922 53.15141234 99999998.83 -7.999999995 2.36408335 IQAIAWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQAIAWAR 8 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6 P17812 CTPS1 CTP synthase 1;CTP synthase 0 75.243 0.090481 69154000 306620 298740 276600 290510 229790 302350 324000 283670 152380 FALSE TRUE 292126.6803 329181.9456 289282.3836 261307.3829 269865.3032 291879.5437 274567.8493 258830.351 176010.3122 1.659713438 1.870242383 1.643553608 1.484614053 1.533235752 1.658309335 1.559953198 1.470540833 1 17.42530043 -2.56186098 0.178518101 1.35E-12 1.816801045 0.827262393 0.092728343 19.45533651 0.415819904 8.004565526 0.347730887 0.002742452 2.56186098 1.816801045 IQALGLHLPDPPLES(ph)EDEDEEGATALNNHSSIPMDPEHVELVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.25)EDEDEEGAT(0.25)ALNNHS(0.25)S(0.25)IPMDPEHVELVK 104.51 2.37E-06 59087000 34767 26776 28648 39048 34329 33228 42362 38589 19314 TRUE FALSE 33123.63281 29504.50484 29961.53914 35122.82085 40315.96673 32077.30603 35898.89887 35209.94259 22309.11648 1.484757715 1.322531301 1.343017737 1.574370769 1.807152102 1.437856405 1.609158252 1.578275976 1 14.44534576 -1.003724005 4.222024339 0.999969838 1.50868586 0.575936151 0.139850279 21530978.74 41490831.55 9400.262555 0.035516244 0.099146182 1.003724005 0.508716022 IQDFNDTFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQDFNDTFYR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 133.23 0.00047165 165134000 211590 207933 170384 220700 223473 196081 232220 218540 216259 FALSE TRUE 201588.56 229121.6091 178196.2749 198514.8167 262446.6204 189290.6658 196790.574 199403.479 249795.3412 0.807014891 0.917237319 0.713369089 0.794709844 1.050646578 0.757783011 0.787807223 0.798267406 1 17.93038704 -1.45462233 3.157751186 1.003177166 0.83086572 0.246956534 0.094105741 43061852.59 53081237.02 1216692.197 0.021439769 0.035105703 1.45462233 -0.172311446 IQDPTEDAEAEDT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQDPTEDAEAEDTPR 15 0 O96028;O96028-5;O96028-3;H0Y9L4 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 1 IQDPTEDAEAEDT(1)PR;IQDPTEDAEAEDT(1)PR 138.28 0.00012874 325320000 239190 230930 251440 253970 227070 246630 236160 261460 267780 TRUE FALSE 227883.9627 254462.0295 262968.7727 228440.4531 266670.9361 238089.1413 200129.4546 238565.1763 309305.9548 0.736759054 0.822687134 0.850189816 0.738558213 0.862159076 0.769752853 0.647027487 0.771291896 1 18.23867508 3.207018828 24.98677837 0.772760289 0.797892167 0 0.096440456 1204.694181 954331.3485 0.026702174 0.031917716 1610.715463 -3.207018828 0.025131879 IQDRQEAIDWLLGLAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQDRQEAIDWLLGLAVR 17 1 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 233.79 3.70E-20 135575000 215440 125154 222980 173437 245110 187622 322640 223560 307990 FALSE TRUE 205256.5782 137907.3349 233203.8536 156002.7833 287857.1064 181124.6031 273415.3423 203983.9012 355751.5162 0.576966137 0.38765073 0.655524553 0.438516144 0.809152156 0.509132343 0.768557068 0.573388705 1 18.44051038 -5 0.11536417 2.416069991 0.352427654 0.536860996 0.125199631 103.6975374 0.78490122 34.09444824 1.170144357 1.00E-05 5 -2.063642337 IQEAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQEAYR 6 0 Q96PZ0;Q96PZ0-2 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 97.602 0.095116 46814000 89143 71477 79332 94536 93645 77937 105400 87761 107200 FALSE TRUE 84929.38705 78760.58756 82969.45067 85033.06167 109976.6584 75238.02215 89319.2942 80076.18159 123824.0285 0.685887772 0.63606869 0.670059371 0.686725046 0.888168958 0.607620533 0.721340561 0.646693397 1 16.91793178 -1.836005984 2.67463635 1.112628449 0.690761393 0.616205311 0.076171688 15044186.43 9768062.875 10848893.28 0.017077358 0.014587942 1.836005984 -0.421867056 IQEHFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 104.45 0.0081492 345900000 1051860 871190 897050 1035430 902350 942560 1192730 1066850 944690 FALSE TRUE 1002140.662 959965.2515 938180.6298 931346.6092 1059719.554 909918.9109 1010757.133 973430.9583 1091187.7 0.91839439 0.879743468 0.85977933 0.85351641 0.971161565 0.833879369 0.926290804 0.892083881 1 20.05746786 -0.501264857 0.555309249 1.016329595 0.888561303 0.427449039 0.039545214 9.13822548 2.318915346 0.326168102 0.015365851 0.315308111 0.501264857 -0.127768292 IQEIIEQLDVTTSEYEKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IQEIIEQLDVTTSEYEKEK 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;;; 247.35 8.79E-25 1802448000 3630014 2387269 3244201 2860967 1989224.9 3026325 3565344 3482341 2121529.9 FALSE TRUE 3458430.432 2630534.425 3392950.825 2573377.162 2336145.093 2921522.606 3021385.291 3177408.761 2450525.922 1.411301305 1.07345709 1.384580671 1.050132602 0.953323967 1.192202286 1.232953818 1.2966232 1 21.22465998 4.657961349 3.160997108 1.159900501 1.427740102 0.268657971 0.13486606 0.403792088 6.503150725 0.03155748 0.238821057 45494.75694 -4.657961349 0.267839601 IQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 IQEQES(0.995)S(0.987)GEEDS(0.018)DLSPEER;IQEQES(1)S(1)GEEDSDLSPEER;IQEQES(1)S(1)GEEDSDLSPEER 250.86 5.93E-29 3717200000 986310 836530 885470 1020760 888810 924290 1002050 906040 883320 TRUE FALSE 939689.081 921773.3581 926069.6753 918151.2655 1043818.183 892281.6055 849168.8686 826702.3344 1020300.754 0.920992244 0.903432987 0.907643821 0.899882963 1.023049506 0.874528027 0.832273097 0.810253576 1 19.96056305 2.021956573 24.99999087 0.860004514 0.925933018 0.11851993 0.061299174 335.7891575 382331.6087 0.020805245 0.015364577 105.1856688 -2.021956573 0.065928504 IQEQES(ph)S(ph)GEEDSDLSPEEREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQEQESSGEEDSDLSPEEREK 21 1 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 IQEQES(1)S(1)GEEDSDLSPEEREK;IQEQES(1)S(1)GEEDSDLSPEEREK 128.71 1.01E-05 440650000 554000 180062 663000 407020 593080 499030 1059850 628960 972340 TRUE FALSE 527813.5179 198410.5225 693399.2058 366105.5763 696512.9642 481748.466 898150.417 573884.9281 1123125.521 0.469950605 0.176659259 0.617383536 0.325970312 0.620155941 0.428935553 0.79968837 0.510971318 1 20.09908774 1.047141344 0.281365942 1.088210388 0.279028671 0.569772734 0.152494582 1.306337732 0.342820566 0.39460725 0.244264564 11.14657248 -1.047141344 -0.809181717 IQEQES(ph)SGEEDSDLSPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 IQEQES(0.5)S(0.5)GEEDSDLSPEER 269.71 2.65E-32 403910000 495260 417390 467930 508800 426630 423550 467000 453480 434780 TRUE FALSE 471850.0413 459922.5155 489385.0533 457654.4573 501034.1369 408882.3573 395750.573 413770.8872 502203.4619 0.939559516 0.91580913 0.974475667 0.911292916 0.997671611 0.8141767 0.788028365 0.823910862 1 18.93791245 2.226325515 24.99529092 0.832536195 0.942215526 0.306967546 0.063432562 200.1376871 408861.7754 0.021046486 0.015658247 168.393574 -2.226325515 0.10967933 IQESHPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQESHPELR 9 0 Q9H9B4 Q9H9B4 SFXN1 Sideroflexin-1 0 98.254 0.0061384 74090000 97902 74136 74327 134830 148520 55944 104060 79829 94763 FALSE TRUE 93274.36648 81690.54269 77734.96647 121276.6322 174421.841 54006.64525 88183.73581 72838.74956 109458.3621 0.852144731 0.746316144 0.710178419 1.107970464 1.593499461 0.49339899 0.805637268 0.6654471 1 16.74002265 -2.474550404 2.055795329 2.305462294 0.862023809 0.016797822 0.299962114 27167031.98 1976059.732 165103882.9 0.071994268 0.003353124 2.474550404 -1.443438485 IQEY(ph)IIAFAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQEYIIAFAKEK 12 1 V9GZ60;P31513 V9GZ60 FMO3 Dimethylaniline monooxygenase [N-oxide-forming] 3 1 IQEY(1)IIAFAKEK;IQEY(1)IIAFAKEK;IQEY(1)IIAFAKEK 76.655 0.036561 1754760000 1216870 1646660 1906130 1437950 8204270 1230680 2352910 1378710 12505500 TRUE FALSE 1159350.967 1814456.526 1993527.946 1293404.534 9635092.09 1188061.243 1993930.365 1257982.843 14444789.07 0.080260844 0.125613224 0.13801018 0.089541254 0.667028923 0.082248431 0.13803804 0.087089042 1 23.7840458 -1.963723969 2.616171277 1.666906382 0.170108312 0.682891958 0.176428733 32056699.26 16222876.75 129696026.2 0.042524894 0.010871164 1.963723969 -1.49679807 IQFKPDDGISPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQFKPDDGISPER 13 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 107.74 0.0011597 488100000 861910 726660 741080 849120 666390 842030 939120 889290 719050 FALSE TRUE 821169.2224 800707.4801 775059.251 763764.8444 782608.205 812870.29 795839.9959 811419.0532 830556.6016 0.988697484 0.964061304 0.933180532 0.919581932 0.942269562 0.978705471 0.958200795 0.976958165 1 19.66371896 0.971328421 1.112612629 0.999760263 0.955073552 0.363182357 0.020075582 0.743071032 1.906158063 0.021066475 0.006724975 9.361133124 -0.971328421 -0.044686711 IQFKPDDGTTPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;;; 125.22 0.00018489 2829950000 3292430 2883430 2868470 3322570 2465990 3371060 3747530 3542590 2891520 FALSE TRUE 3136803.359 3177254.795 2999992.187 2988578.951 2896057.875 3254319.347 3175775.47 3232382.039 3339922.154 0.939184572 0.951296063 0.898222189 0.894804973 0.867103406 0.97436982 0.950853141 0.96780161 1 21.67138305 2.194042393 24.99999981 0.967385177 0.917141621 0.569732343 0.026664823 132.6296502 74479.73579 0.010944445 0.008083045 156.3300233 -2.194042393 -0.050243556 IQFTSLYHKEEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 IQFTSLYHKEEAPAS(1)PLRPLYPQIS(1)PLK 107.98 0.0014 573710000 129190 91633 119710 127950 79200 132260 158640 166900 110350 TRUE FALSE 123083.4447 100970.5069 125198.8219 115088.2229 93012.45492 127679.803 134436.5544 152285.3512 127462.5144 0.965644255 0.792158442 0.982240328 0.902918191 0.729723993 1.001704726 1.054714439 1.194746172 1 16.9597135 1.932095464 3.280670595 1.087760958 0.877130353 0.53090259 0.089116752 0.185246761 3.628987412 0.041501832 0.023177312 85.52546898 -1.932095464 -0.210630605 IQFTSLYHKEEAPAS(ph)PLRPLYPQISPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 IQFTSLYHKEEAPAS(1)PLRPLYPQISPLK 176.86 9.61E-18 349870000 174630 122460 160560 162580 159960 169570 235060 207050 207800 TRUE FALSE 166375.586 134938.8132 167921.8348 146237.1495 187856.9734 163697.7484 199197.2798 188919.6044 240024.5627 0.693160667 0.562187518 0.699602711 0.609259102 0.782657288 0.682004152 0.82990373 0.787084464 1 17.87282252 1.168768086 0.433092885 1.01159647 0.618407984 0.777049012 0.057957324 0.425217842 0.223647192 0.065928138 0.037995678 14.74918715 -1.168768086 -0.393188486 IQHEELNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQHEELNNR 9 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 135.86 0.00020901 777510000 733180 691070 689250 828240 971310 675720 882860 697320 1077760 FALSE TRUE 698524.0344 761490.8187 720852.7943 744983.7416 1140706.156 652319.647 748163.4922 636258.9641 1244893.516 0.561111473 0.611691529 0.579047754 0.598431699 0.916308216 0.523996341 0.600985934 0.51109509 1 20.24759091 -1.407457191 3.49592014 1.00328089 0.612431907 0.537809837 0.112796111 443117345.7 551137426.9 14197635.93 0.025571623 0.03913297 1.407457191 -0.390848983 IQHILCTGNLCTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQHILCTGNLCTK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 209.79 3.50E-08 416410000 695150 561340 596820 701600 534340 613090 716240 715760 614700 FALSE TRUE 662291.6372 618541.1842 624184.7873 631073.835 627528.7268 591858.5396 606964.4333 653084.2599 710024.5365 0.932772888 0.871154661 0.879103123 0.888805672 0.883812734 0.83357477 0.854849941 0.919805199 1 19.43750936 0.943424391 4.934682692 0.999959401 0.878253039 0.705420955 0.02521718 0.176127781 12.46860148 0.026314882 0.006656965 8.778582421 -0.943424391 -0.121706362 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK 32 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 261.79 1.25E-59 1046250000 520710 376050 439790 487710 635950 417100 647950 519260 169424 FALSE TRUE 496097.0702 414369.9225 459954.8065 438684.4642 746859.4787 402655.7224 549093.3271 473790.8416 195697.4086 2.535021152 2.117401173 2.350336725 2.241646771 3.81639943 2.057542434 2.805828299 2.421037892 1 17.57826513 IQIISTDSAVAS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQIISTDSAVASPQR 15 0 P49116;P49116-2;C9J2Y1;C9JMI6;C9JKS0 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 IQIISTDS(0.002)AVAS(0.998)PQR 100.04 0.0024226 48225000 54896 54904 58376 60857 62669 56222 74193 61485 72698 TRUE FALSE 52301.17487 60498.78002 61052.59734 54739.53874 73598.45376 54275.01804 62873.4952 56101.04745 83971.63455 0.622843358 0.720466862 0.727062152 0.651881305 0.876468038 0.646349429 0.74874683 0.668095217 1 16.35761445 -5 0.30418675 3.482081571 0.693044612 0.614220572 0.072397865 175.4568218 1.608569632 278.4225917 0.063374771 1.00E-05 5 -2.789036959 IQLLCLMEMTFTRPANHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQLLCLMEMTFTRPANHR 18 1 Q9UNM6;A0A087WUL9;Q9UNM6-2;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 155.22 1.23E-08 31391000 42554 42717 32454 31840 46987 36852 50189 43449 33622 FALSE TRUE 40542.55675 47069.91087 33942.048 28639.38271 55181.51792 35575.806 42531.74627 39644.37522 38835.92804 1.043944584 1.212019726 0.873985758 0.73744556 1.420888355 0.916053968 1.095164926 1.020816991 1 15.24510432 0.992457119 0.007400516 2.53E-07 2.066977685 0 0.186975101 22419.29041 110.7286292 15606.61553 15307.98884 9.827818309 -0.992457119 2.066977432 IQLVEEELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 196.07 7.91E-07 2943729000 2759922 2803151 2273450 3109239 2502506 2428468 2688810 2548160 2400003 FALSE TRUE 2629465.957 3088795.274 2377689.931 2796692.389 2938942.254 2344369.544 2278582.651 2325029.602 2772183.208 0.948518103 1.114210369 0.857695813 1.008841111 1.06015441 0.845676266 0.821945189 0.838699836 1 21.40259117 2.227387799 24.99746741 0.856904604 1.003384712 0.333591457 0.082950089 198.2609094 443575.2885 0.028898618 0.021539034 168.8059689 -2.227387799 0.146480108 IQLVEEELDRAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 274.38 4.47E-33 10049502000 3835844 2592017 3760430 3398912 4178338 3544176 4839637 3970569 4973838 FALSE TRUE 3654531.256 2856146.479 3932849.435 3057246.908 4907038.824 3421440.296 4101261.49 3622884.929 5745155.394 0.636106599 0.497139987 0.684550576 0.532143467 0.854117685 0.595534857 0.713864327 0.630598249 1 22.45391448 -4.999999999 0.164872933 2.395890465 0.541999196 0.581377817 0.096600216 84.06736101 0.783023866 38.30222882 0.336132568 1.00E-05 4.999999999 -1.853891269 IQNS(ph)DDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQNSDDEER 9 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 IQNS(1)DDEER 149.83 9.09E-05 202090000 199010 326220 229390 314250 241140 255280 197070 245010 256270 TRUE FALSE 189603.1917 359462.1889 239907.7584 282660.993 283194.7397 246439.5896 167003.3521 223555.6255 296011.0428 0.640527427 1.214353983 0.810468948 0.954900163 0.956703294 0.832535122 0.564179466 0.755227317 1 18.17529147 1.99121061 9.212705424 0.718028407 0.925543319 0.092825235 0.177727818 0.240280459 197.1269001 0.065772311 0.045104788 97.99651011 -1.99121061 0.207514912 IQNTGDY(ph)YDLYGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNTGDY(0.925)Y(0.074)DLYGGEK 209.79 2.27E-08 59218000 89788 86847 78614 101470 67344 96654 96742 104680 77579 TRUE FALSE 85543.89918 95696.80804 82218.52966 91270.04282 79088.77228 93306.84774 81982.23111 95513.66426 89609.5551 0.954629214 1.067930847 0.917519673 1.018530253 0.882593069 1.041260027 0.914882693 1.065887049 1 16.45136496 1.218709607 24.99896498 1.032943492 0.976810776 0.147544399 0.060632935 548.2345375 690389.9722 0.051660902 0.012985637 16.54663197 -1.218709607 -0.056132715 IQNTGDYY(ph)DLYGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNT(0.017)GDY(0.314)Y(0.591)DLY(0.078)GGEK 155.98 2.27E-05 58905000 35497 29339 33017 35455 28442 34075 34302 35324 32207 TRUE FALSE 33819.12716 32328.67746 34530.86211 31890.99604 33402.27579 32894.97421 29068.5999 32230.8433 37201.49707 0.909079737 0.869015497 0.928211627 0.857250341 0.897874506 0.884237915 0.78138253 0.866385652 1 15.18307306 1.972011028 24.94529159 0.85192648 0.890711491 0 0.058210929 1652.191161 1472520.336 0.021289427 0.013777909 93.7585815 -1.972011028 0.038785011 IQPAGNTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IQPAGNTSPR 10 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IQPAGNTS(1)PR;IQPAGNT(0.343)S(0.657)PR;IQPAGNT(0.009)S(0.991)PR;IQPAGNT(0.001)S(0.999)PR 142.47 3.74E-05 4298150000 5073600 4458240 4756520 5360400 5149360 4701850 5829100 5121010 5759900 TRUE FALSE 4833780.983 4912539.725 4974611.147 4821562.408 6047406.754 4539023.756 4939763.736 4672587.216 6653115.875 0.726543934 0.738381807 0.747711484 0.724707415 0.908958579 0.682240298 0.742473727 0.702315622 1 22.66559873 -1.014884259 4.482561502 1.000008799 0.745809837 0.630442538 0.060952398 10387863.02 33441474.87 1644.526846 0.013481083 0.096630837 1.014884259 -0.254198962 IQPEDMFVCDINEKDISGPS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQPEDMFVCDINEKDISGPSPSK 23 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 IQPEDMFVCDINEKDIS(0.011)GPS(0.987)PS(0.002)K;IQPEDMFVCDINEKDIS(0.019)GPS(0.955)PS(0.026)K 146.03 8.04E-08 363880000 158370 86731 155733 142934 105505 164647 226810 199477 148414 TRUE FALSE 150884.164 95568.9875 162873.5121 128566.0028 123905.0386 158945.2331 192205.9688 182009.7364 171429.2851 0.880153959 0.55748344 0.950091532 0.749965227 0.722776383 0.927176666 1.121196817 1.061719042 1 17.38725406 2.026268809 3.644852452 1.06818298 0.760484488 0.607026577 0.106157852 0.139144027 3.89444204 0.044820766 0.02869865 106.2352902 -2.026268809 -0.307698492 IQPEDMFVCDINEKDISGPS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQPEDMFVCDINEKDISGPSPSKK 24 2 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 IQPEDMFVCDINEKDIS(0.001)GPS(0.998)PS(0.002)KK;IQPEDMFVCDINEKDIS(0.094)GPS(0.901)PS(0.004)KK;IQPEDMFVCDINEKDIS(0.098)GPS(0.805)PS(0.098)KK 252.77 4.77E-44 1087935000 1037352 537037 1113949 885379 560018 1184976 1489838 1315146 741695 TRUE FALSE 988318.4268 591761.6809 1165024.663 796379.0208 657684.9619 1143939.984 1262535.85 1199984.844 856713.2725 1.153616336 0.690734812 1.359876987 0.929574744 0.767683872 1.335265859 1.473697083 1.400684316 1 19.70845291 2.174348861 9.468925163 1.3570811 0.971724025 0.326921868 0.223485497 0.329055951 45.62457575 0.07804004 0.057662553 149.3994026 -2.174348861 -0.385357076 IQPFDDDEDEDIWEDSDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 210.36 4.18E-16 111059000 135537 113581 127557 134244 119116 129955 143582 140115 137868 FALSE TRUE 129130.4346 125155.033 133405.6146 120749.5381 139889.7927 125454.6258 121675.9288 127845.7878 159247.8653 0.810877021 0.785913411 0.837723095 0.758249022 0.878440615 0.787794709 0.76406631 0.802810057 1 17.28091451 0.905644732 20.51197866 1 0.800522585 0.756604271 0.035045768 8944.667929 1944493.64 0.031078179 0.007769545 8.047198839 -0.905644732 -0.199477415 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 270.14 9.15E-55 2007550000 3438440 3373690 3018910 3793540 1735470 3744720 3624880 3885970 1504480 TRUE FALSE 3275911.756 3717472.847 3157330.01 3412206.152 2038135.419 3615039.407 3071837.981 3545693.866 1737787.075 1.885105375 2.139199273 1.816868163 1.963535235 1.1728338 2.080254515 1.767672246 2.040350005 1 20.72881989 2.930075034 24.99999506 1.692963118 1.968247398 0.169448654 0.347377308 314.8123795 112552.7893 0.096122158 0.101952983 851.2851037 -2.930075034 0.275284281 IQQFDDGGS(ph)DEEDIWEEKHIAFTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IQQFDDGGSDEEDIWEEKHIAFTPESQR 28 1 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)DEEDIWEEKHIAFTPESQR;IQQFDDGGS(1)DEEDIWEEKHIAFTPESQR;IQQFDDGGS(1)DEEDIWEEKHIAFTPESQR 338.57 1.92E-96 368214000 180029 81095.2 198267 145455 198310 157762 297106 188041 214074 TRUE FALSE 171519.386 89358.89308 207357.7381 130833.5871 232895.2012 152298.6624 251777.023 171575.1332 247271.5026 0.693648011 0.361379666 0.838583241 0.529109039 0.941860258 0.615916759 1.018220945 0.69387346 1 17.91573646 2.700661774 0.656245438 0.911699205 0.535603589 0.297502735 0.177327513 0.768843881 0.70578148 0.121749173 0.12199456 501.9515205 -2.700661774 -0.376095616 IQQYISHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IQQYISHR 8 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;;;;; 178.94 0.00024695 2653270000 2638979 2104857 1749622 2152913 2482420 1936329 2750840 2336433 2284649 FALSE TRUE 2514239.693 2319344.321 1829843.899 1936498.095 2915353.262 1869273.441 2331148.835 2131842.54 2638940.699 0.95274581 0.878892172 0.693400917 0.73381645 1.104743757 0.708342344 0.883365373 0.80784026 1 21.3315275 IQRPNTTQEGEEMETDMDVADVAMES(ph)SPGSSISMEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.415)S(0.359)PGS(0.099)S(0.106)IS(0.02)MEHR;IQRPNTTQEGEEMET(0.001)DMDVADVAMES(0.437)S(0.437)PGS(0.099)S(0.021)IS(0.005)MEHR 59.954 0.020783 184181000 38083 31943.3 29611.8 36806 40843 34806 46120 42497 41716 TRUE FALSE 36282.89206 35198.35859 30969.53032 33106.19095 47966.00627 33600.65949 39083.54695 38775.73739 48185.10422 0.752989801 0.730482151 0.642720003 0.687062765 0.995452994 0.69732462 0.811112637 0.804724572 1 15.55629961 -2.328392961 0.181933945 1.351938001 0.690449073 0.433407347 0.091416629 39.8270539 0.941288405 5.997830312 0.298505427 0.004694691 2.328392961 -0.661488928 IQRPPEDSIQPYEK ddPTM_SK-BR-3_Trastuzumab_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 ; 198.16 2.05E-08 898130000 691960 602020 642140 682270 508760 692360 787890 700070 598860 FALSE TRUE 659252.4221 663366.5224 671582.7542 613686.9234 597487.5829 668383.3996 667682.9099 638768.1595 691728.1502 0.953051313 0.958998882 0.970876715 0.887179339 0.863760688 0.966251553 0.965238887 0.923438144 1 19.39984564 IQSQNDREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQSQNDREK 9 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 100.88 0.0039781 158407000 102429 52557 85640 79918 116104 90995 168877 113987 155494 FALSE TRUE 97587.38416 57912.61805 89566.67871 71884.49081 136352.5008 87843.82033 143111.712 104005.694 179607.2154 0.543337772 0.322440376 0.498680849 0.400231642 0.759170507 0.489088482 0.796803802 0.579073028 1 17.45448578 1.137359239 0.334897933 1.039633523 0.388227411 0.621804375 0.124221681 0.875301264 0.310035177 0.214929285 0.136704887 13.720162 -1.137359239 -0.651406112 IQSSLSSAS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 IQS(0.007)S(0.041)LS(0.277)S(0.185)AS(0.487)PS(0.003)K;IQSSLSSAS(0.964)PS(0.036)K 212.39 8.80E-05 100910000 328928 364226 336014 406452 236753 367022 385757 438970 303599 TRUE FALSE 313380.2253 401341.0435 351420.5743 365594.6728 278042.6482 354311.9361 326902.6847 400531.4597 350679.5824 0.89363693 1.144466526 1.002113017 1.042531961 0.792868083 1.010358042 0.932197656 1.142157912 1 18.41979391 -1.737342639 7.805910756 1.000053142 0.994033558 0.000135116 0.106262502 9.21E-05 3.10E-06 0.09641487 0.022524553 0.018308694 1.737342639 -0.006019584 IQTYLQSTKPIIDLYEEMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQTYLQSTKPIIDLYEEMGK 20 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 ; 240.28 9.77E-30 306190000 752870 639850 658300 744700 483300 752100 807760 812310 524250 FALSE TRUE 717283.3271 705051.4424 688483.7061 669841.3412 567587.367 726054.5884 684521.3765 741179.8301 605548.0125 1.184519332 1.164319638 1.136959732 1.106173792 0.937311915 1.199004164 1.130416354 1.223981938 1 19.20788183 0.074184728 0.012281302 7.18E-07 2.179192531 0.137296448 0.082811568 4468.830096 17.55770198 1622.572241 1491.851748 1.186273224 -0.074184728 2.179191813 IQVLQQQADDAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 364.95 1.38E-96 512170000 503400 498610 455810 574900 474910 453600 527340 518750 488220 FALSE TRUE 479605.2796 549418.9259 476709.3394 517109.9598 557734.1536 437891.7183 446884.5977 473325.4999 563930.6641 0.850468524 0.974266804 0.845333247 0.91697436 0.989011928 0.776499215 0.792445998 0.839332794 1 19.10515827 2.229020648 24.99982075 0.828157053 0.914282261 0.112887078 0.075729642 276.1579392 723675.8972 0.025579055 0.019136985 169.4418359 -2.229020648 0.086125208 IQVLQQQADDAEERAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 282.19 4.65E-36 1736400000 816140 391179 828970 665080 1016850 684360 1120180 837050 1300950 FALSE TRUE 777562.6796 431040.5848 866979.0945 598224.8948 1194188.318 660660.4416 949275.9675 763753.4645 1502694.682 0.517445552 0.286845086 0.576949599 0.398101425 0.794697907 0.439650482 0.631715796 0.508255918 1 20.51912048 -4.999999978 0.149218736 2.776181379 0.349733507 0.573821637 0.13280766 86.37802423 0.76732651 45.34741189 0.609898915 1.00E-05 4.999999978 -2.426447872 IQVTPPGFQLVFLPFADDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IQVTPPGFQLVFLPFADDKR 20 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 140.95 3.15E-07 697390000 1393550 1594750 1156430 1659210 957790 1366170 1340960 1539320 935760 FALSE TRUE 1327679.653 1757256.838 1209453.459 1492423.059 1124828.273 1318859.19 1136371.924 1404528.98 1080872.882 1.228340239 1.625775674 1.118959944 1.380757242 1.040666569 1.220179739 1.051346502 1.299439559 1 20.04376543 3.198900951 1.404663634 1.131081224 1.408058128 0.279203485 0.159101674 0.419177827 1.730564393 0.051472258 0.073344234 1580.887446 -3.198900951 0.276976904 IQVWHAEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IQVWHAEHR 9 0 P15311;E7EQR4 P15311 EZR Ezrin 0 66.595 0.063283 106300000 580570 477110 417740 541630 553080 476380 644660 556530 396050 FALSE TRUE 553127.6067 525728.0514 436893.7922 487184.3234 649536.9769 459882.8412 546305.277 507797.2828 457467.4113 1.209108219 1.149214214 0.955027137 1.064959626 1.419854094 1.005280004 1.19419496 1.110018485 1 18.80330945 0.976027977 21.17681542 0.999999991 1.144177678 0.110752096 0.126529113 604.0652417 533633.2846 0.112859228 0.028214807 9.462981189 -0.976027977 0.144177687 IQYQLVDISQDNALRDEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 IQYQLVDISQDNALRDEMR 19 1 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ;;;;;;;;;;;;;; 318.9 7.09E-62 6867603000 3972639 3277836 3522355 3949635 4033161 3555472 4309648 3998997 4469096 FALSE TRUE 3784860.227 3611851.215 3683858.461 3552610.186 4736543.001 3432345.113 3652132.045 3648823.623 5162140.583 0.733195884 0.699680909 0.713630015 0.68820485 0.917554051 0.66490733 0.707484034 0.706843133 1 22.299538 -1.141359899 4.421625888 1.000043727 0.726260975 0.600293168 0.069481684 2.76E-05 5.37E-06 0.062102773 0.014635429 0.072217109 1.141359899 -0.273782752 IRAEEEDLAAVPFLAS(ph)DNEEEEDEKGNSGSLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRAEEEDLAAVPFLASDNEEEEDEKGNSGSLIR 33 2 O95714;A0A3B3IRP6;A0A0J9YVP0 O95714 HERC2 E3 ubiquitin-protein ligase HERC2 1 IRAEEEDLAAVPFLAS(0.995)DNEEEEDEKGNS(0.002)GS(0.002)LIR 112.68 3.02E-06 21091000 39072 34625 33301 45646 28759 42670 45200 47831 30859 TRUE FALSE 37225.14399 38153.32687 34827.88379 41057.57736 33774.56049 41192.3272 38303.90985 43642.66407 35644.45611 1.044345967 1.070386002 0.977091183 1.151864324 0.947540352 1.155644711 1.074610585 1.224388554 1 15.12139009 2.197338155 24.99999863 1.116305721 1.045567242 0.184076005 0.077967087 243.5841092 147723.9136 0.025303804 0.018688298 157.5208893 -2.197338155 -0.070738479 IRDGWQVEEADDWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IRDGWQVEEADDWLR 15 1 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 108.63 0.00096973 110469000 113712 69484 91076 96565 104315 93241 130976 107058 132485 FALSE TRUE 108337.0591 76564.4986 95251.92469 86858.10274 122507.503 90012.04079 110993.2057 97683.43397 153030.0972 0.707946091 0.500323139 0.622439157 0.567588366 0.800545156 0.588198286 0.725303112 0.638328249 1 17.2234559 -5 0.212407473 2.781054783 0.587911973 0.644248552 0.083894244 85.03528384 0.848304066 64.40311978 0.157947765 1.00E-05 5 -2.19314281 IRDIDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IRDIDLK 7 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 122.19 0.0039811 1480880000 2939600 2814230 2770300 3570730 2434170 3353520 3613290 3576890 2691800 FALSE TRUE 2800650.934 3101003.237 2897320.995 3211793.436 2858688.477 3237386.762 3062016.248 3263678.549 3109230.596 0.90075369 0.997353892 0.931845003 1.032986566 0.919419898 1.041217967 0.984814781 1.04967401 1 21.56812619 8 0.318164888 1.012398533 0.024086976 0.366315063 0.041314104 56.15249318 0.803190577 0.033770055 32.2247102 100000000 -8 -0.988311558 IRDPNQGGK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 156.16 6.53E-05 2306900000 2292130 2270220 1978750 2680650 1660840 2377140 2211310 2442280 1799880 FALSE TRUE 2183785.557 2501557.999 2069477.645 2411185.969 1950489.97 2294819.046 1873934.046 2228421.016 2078996.198 1.050403825 1.203252801 0.995421563 1.159783732 0.93818833 1.103811083 0.901364826 1.071873541 1 20.98745569 2.740740379 24.99999996 0.997491224 1.107365188 0.273641401 0.079804045 222.1488316 2547864.827 0.022470376 0.022797028 550.4785229 -2.740740379 0.109873964 MQAS(ph)IEKGGSLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQASIEKGGSLPK 13 1 P06748;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEKGGSLPK 121.19 0.00015113 160880000 103250 45567 136740 89602 95532 121530 201730 162590 186440 TRUE FALSE 98369.57712 50210.32911 143009.6643 80595.03673 112192.7506 117321.3856 170952.3835 148352.7577 215352.163 0.456784718 0.233154515 0.664073498 0.374247631 0.520973409 0.544788518 0.793827102 0.688884456 1 17.71633829 1.558310917 0.475338541 1.006331133 0.357281985 0.715189492 0.115729792 0.417757221 0.244228696 0.115065316 0.075536943 36.16686933 -1.558310917 -0.649049148 IRDTPEDIVLEAPASGLAFHPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IRDTPEDIVLEAPASGLAFHPAR 23 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ;; 205.73 8.99E-25 228357000 503013 396394 424237 442531 350562 433092 470456 492747 375667 FALSE TRUE 479236.5724 436786.9993 443688.6861 398046.9431 411699.9018 418093.9154 398679.2967 449599.4605 433923.5197 1.104426358 1.006599042 1.022504349 0.917320507 0.948784482 0.963519829 0.9187778 1.036126045 1 18.72708126 4.289814492 1.001960704 0.9586781 1.124931366 0.531592842 0.039117328 0.659885012 0.853719493 0.01185211 0.1009749 19490.11906 -4.289814492 0.166253265 IRDTS(ph)QEPCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IRDTSQEPCGR 11 1 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IRDT(0.001)S(0.999)QEPCGR;IRDT(0.07)S(0.93)QEPCGR;IRDT(0.249)S(0.751)QEPCGR;IRDT(0.028)S(0.972)QEPCGR 185.57 2.67E-06 2371890000 527614 427244 505332 552303 531937 561366 617670 584017 578194 TRUE FALSE 502674.7319 470780.6493 528501.972 496784.4531 624706.6444 541925.7547 523433.0972 532877.3754 667857.3725 0.752667789 0.70491196 0.791339579 0.743848123 0.935389306 0.811439354 0.783749823 0.797890983 1 19.34918051 -4.999999999 0.113967493 1.685837811 0.667507748 0.598510421 0.05651873 110.0672666 0.825924956 17.61660236 0.628711128 1.00E-05 4.999999999 -1.018330062 IRDVTNNQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRDVTNNQEK 10 1 Q9Y2L1;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 123.67 0.00041576 58050000 152930 126360 110610 154140 117050 139440 182610 164210 130180 FALSE TRUE 145701.302 139236.2277 115681.5779 138645.5544 137463.4829 134611.1578 154749.4906 149830.9019 150367.6495 0.968967078 0.925971963 0.769324906 0.922043769 0.914182561 0.895213553 1.02914085 0.996430431 1 17.19813469 1.747675563 8.430843882 1.00839172 0.904143715 0.496342386 0.051679371 0.110271982 29.48662721 0.025656293 0.013805379 55.93395947 -1.747675563 -0.104248005 IREDLPNLESSEETEQINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IREDLPNLESSEETEQINK 19 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 260.53 3.75E-31 517603000 410463 415484 357116 459400 289476 407073 412326 419622 312170 FALSE TRUE 391061.2274 457822.292 373490.1218 413220.2392 339960.5227 392975.9599 349418.0958 382877.6731 360579.7293 1.084534697 1.269683942 1.035804543 1.145988545 0.942816512 1.089844847 0.969045311 1.06183915 1 18.45995877 3.19181776 1.543152558 1.015881905 1.168942569 0.357751152 0.074918543 0.326627647 1.616456427 0.023215071 0.032278768 1555.312851 -3.19181776 0.153060664 IREEFPDR ddPTM_SK-BR-3_Trastuzumab_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 ; 152.28 0.00041923 284620000 165637 144786 142096 158919 184333 142916 197775 169058 199193 FALSE TRUE 157807.6673 159539.858 148611.2422 142944.1602 216480.6168 137966.7831 167600.7914 154254.3853 230082.8331 0.685873279 0.693401832 0.645903217 0.621272601 0.940881221 0.599639622 0.728436751 0.670429789 1 17.81179382 -2.263670573 2.190993141 2.141196336 0.698279865 0.505701735 0.093761836 6892017.612 905227.3699 39056035.33 0.020568251 0.005449158 2.263670573 -1.442916471 IREESGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 IREESGAR 8 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;;;;;;; 155.42 0.00037329 9285728000 3756776 2877404 3104238 3415244 3913304 3105985 4094881 3541597 4233090 FALSE TRUE 3579200.644 3170614.739 3246570.383 3071937.185 4595782.979 2998423.961 3470131.696 3231475.991 4889535.978 0.732012334 0.648449005 0.66398333 0.628267631 0.939922111 0.613232825 0.709705729 0.66089625 1 22.22126613 -1.814147386 2.639310252 1.097596183 0.697918498 0.510678368 0.092411795 28317763.19 20289984.2 17647598.93 0.020012832 0.015340963 1.814147386 -0.399677685 IREESNTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IREESNTK 8 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 ; 119.62 0.0015137 215450000 244532 239320 228162 274194 213363 252110 293187 275099 294735 FALSE TRUE 232973.457 263706.9801 238623.4534 246631.4982 250573.4396 243379.3675 248455.9384 251009.8732 340440.9985 0.684328439 0.774604061 0.700924549 0.724447112 0.736026039 0.714894412 0.729806162 0.737308004 1 18.37704526 0.179623408 1.588465002 1.000093728 0.725271773 0.931570027 0.023425303 2.851094098 5.214565067 0.020914832 0.005879605 1.512249356 -0.179623408 -0.274821955 IREEYPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 223.84 3.97E-06 1.27005E+11 24903520 20575130 19591000 21428910 23529770 19547080 26851830 22448430 24946120 FALSE TRUE 23726379.96 22671759.14 20489266.73 19274835.25 27633354.44 18870159.72 22755090.17 20482726.46 28814636.88 0.823414158 0.78681398 0.711071488 0.668925148 0.959004084 0.654881052 0.789705949 0.710844511 1 24.7802985 -0.895102794 5.444929836 1.000000224 0.767134404 0.41747422 0.087835465 2.13E-07 4.33E-08 0.07589826 0.017889374 0.127320169 0.895102794 -0.23286582 IREHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 IREHLEK 7 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 160.88 0.0012129 5330260000 5492640 4800010 4821100 5922040 4385500 5676370 7917170 5971440 5386530 FALSE TRUE 5233013.793 5289136.476 5042152.204 5326745.288 5150329.811 5479795.884 6709260.308 5448549.057 6221845.562 0.841070988 0.850091251 0.810394947 0.85613589 0.827781686 0.880734796 1.078339255 0.875712681 1 22.56891115 1.941557939 7.323463354 0.990825815 0.840049179 0.64559611 0.049883571 0.145804386 15.97062032 0.018761976 0.011746853 87.40935981 -1.941557939 -0.150776635 IREIADGLCLEVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IREIADGLCLEVEGK 15 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;; 143.02 4.09E-06 573913000 1729660 1415690 1576190 1717170 1387080 1788770 2038860 1907780 1688100 FALSE TRUE 1647902.4 1559950.421 1648459.871 1544556.809 1628986.313 1726824.446 1727794.461 1740724.669 1949881.926 0.845129327 0.800023016 0.845415227 0.792128379 0.835428182 0.885604622 0.886102095 0.892733373 1 20.89495533 1.032648161 0.549930091 1.001222987 0.816957933 0.864023977 0.021658596 0.296792823 0.22278895 0.022546384 0.01041946 10.7807298 -1.032648161 -0.184265054 IRELESQISELQEDLESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 IRELESQISELQEDLESER 19 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;; 232.54 7.32E-21 513574700 339334.4 271327.2 221460.5 375293.4 308932.2 326072.4 372916.9 314648.8 312525.2 FALSE TRUE 323294.7354 298975.7502 231614.683 337568.1944 362809.8779 314780.431 316021.5778 287096.483 360990.0119 0.895578063 0.828210588 0.641609672 0.935117824 1.00504132 0.871992079 0.875430254 0.795303121 1 18.46159939 IRELETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRELETR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 146.81 0.0092582 0 128740 106310 124140 128850 133680 112650 147040 127210 131800 FALSE TRUE 122654.7153 117143.1099 129831.9418 115897.7532 156993.7497 108748.9023 124606.3474 116070.818 152238.8709 0.805672787 0.769469119 0.852817293 0.761288839 1.031233014 0.71433072 0.818492325 0.762425637 1 17.21597724 -2.350867624 2.292383596 2.198672783 0.811944672 0.315771686 0.085758683 3095854.755 567194.3351 19173393.71 0.018571874 0.004457921 2.350867624 -1.386728111 IRELTAVVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRELTAVVQK 10 1 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 144.1 2.99E-05 392770000 743120 661100 547440 592360 586020 592440 826600 801980 676150 FALSE TRUE 707994.1903 728466.8416 572540.6655 532814.8474 688221.7025 571923.6542 700486.9884 731754.3796 781003.8887 0.906518137 0.932731389 0.733082989 0.682217919 0.881201377 0.732292966 0.896905891 0.936940763 1 19.57497021 1.267087574 2.322063654 0.988978906 0.82734192 0.378701481 0.08252235 0.365384683 3.301360512 0.081068824 0.023563721 18.49641554 -1.267087574 -0.161636986 IRES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRESPK 6 1 P51587;A0A590UJI7;A0A087WW77;Q15334 P51587;A0A087WW77 BRCA2;LLGL1 Breast cancer type 2 susceptibility protein;Lethal(2) giant larvae protein homolog 1 1 IRES(1)PK 60.436 0.078228 418810000 951810 838290 787960 982590 513390 921240 972920 999790 577120 TRUE FALSE 906819.8276 923712.7041 824088.7454 883818.1864 602925.0535 889337.2278 824483.1851 912243.0874 666616.8221 1.360331449 1.385672659 1.236225547 1.325826408 0.904455203 1.334105589 1.236817251 1.368466947 1 19.3464982 7.999981813 0.025445111 2.96E-08 2.982734324 0.249124624 0.141100406 2598.99514 5.085301297 203.5153251 432.0623693 99995812.27 -7.999981813 2.982734295 IRETTDFKVDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IRETTDFKVDTK 12 2 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 79.633 0.01266 450240000 679420 425790 600950 652660 467150 692370 942820 832820 642730 FALSE TRUE 647305.1631 469178.4851 628504.1519 587053.3768 548620.8121 668393.0533 798975.4929 759893.8657 742401.2858 0.871907384 0.631974236 0.84658279 0.790749407 0.738981495 0.900312359 1.07620435 1.023562163 1 19.50183968 1.996515896 3.428745903 1.036607762 0.769556447 0.753181287 0.067124197 0.108009827 2.582719421 0.030164319 0.018261324 99.20096477 -1.996515896 -0.267051314 IREYFGGFGEVESIELPMDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IREYFGGFGEVESIELPMDNK 21 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 221.14 4.03E-25 633056000 2061098 1694279 1759344 2082632 1404313 2044253 2257304 2165103 1537688 FALSE TRUE 1963673.982 1866927.956 1840011.663 1873281.875 1649224.743 1973460.006 1912910.817 1975515.103 1776144.802 1.105582146 1.051112474 1.035958139 1.054689839 0.928541829 1.111091846 1.077001613 1.112248901 1 20.76031777 -0.639893416 7.328462221 0.999992389 1.060319825 0.109115014 0.053413264 0 0 0.049557765 0.011680877 0.229142994 0.639893416 0.060327435 IRIDS(ph)LSAQLSQLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.897)LS(0.103)AQLSQLQK;IRIDS(0.902)LS(0.098)AQLSQLQK 265.63 1.91E-25 246120000 559480 409690 489760 515400 486270 502860 643580 544830 576920 TRUE FALSE 533034.4892 451437.8768 512215.9804 463591.0128 571075.334 485445.8321 545390.0508 497121.7969 666385.8071 0.799888718 0.677442214 0.768647794 0.695679602 0.856974035 0.728475647 0.818429872 0.745996976 1 19.34599815 -4.999999999 0.235953744 2.352924705 0.733750153 0.656299848 0.054296018 91.70291117 0.915765812 59.32108826 0.07824927 1.00E-05 4.999999999 -1.619174553 IRIDSLSAQLSQLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 198.95 6.99E-09 1403840000 3901500 2613100 3174200 2911300 3524400 3336900 5017800 3996100 4275400 FALSE TRUE 3717083.827 2879377.861 3319740.21 2618650.593 4139054.244 3221342.316 4252242.452 3646180.299 4938407.196 0.752688808 0.583058008 0.672228935 0.530262186 0.838135472 0.652303909 0.861055454 0.738331238 1 22.23561437 1.055209886 0.531190037 0.999061075 0.644922762 0.549057372 0.093059598 0.636851959 0.453723387 0.09262154 0.044170414 11.35559476 -1.055209886 -0.354138313 IRIEDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IRIEDPPR 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;;; 133.86 0.00082194 899766000 1492800 1251064 1317230 1504880 1597110 1323990 1759570 1479230 1843200 FALSE TRUE 1422238.302 1378548.844 1377626.298 1353606.603 1875645.478 1278139.894 1491115.28 1349700.779 2129034.042 0.668020461 0.647499672 0.647066355 0.635784387 0.880984259 0.600337932 0.700371741 0.633949835 1 21.02176759 -2.194327308 2.351610742 1.928018115 0.675995973 0.634777927 0.077054049 7106418.304 1464955.54 35110193.36 0.016913937 0.006392529 2.194327308 -1.252022142 IRLDETDDPDDYGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 162.81 1.44E-06 1081320000 671310 785690 619610 838530 592580 669230 666020 671760 609480 FALSE TRUE 639578.5067 865752.7043 648019.7314 754239.3713 695925.7644 646054.3973 564406.4167 612937.1332 703995.0456 0.908498591 1.229771018 0.920489051 1.071370283 0.988537872 0.917697364 0.801719302 0.870655464 1 19.42520575 2.279013866 2.523350298 0.867689059 1.044769589 0.272326698 0.100975787 0.281405921 3.678498472 0.040125813 0.029231509 190.1138978 -2.279013866 0.177080531 IRLDETDDPDDYGDRESGCSFVLALMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IRLDETDDPDDYGDRESGCSFVLALMQK 28 2 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 148.15 4.20E-08 373400000 550170 420030 537190 521150 484950 535620 685800 554650 629830 FALSE TRUE 524164.5544 462831.5345 561820.6929 468763.0119 569525.1265 517071.3451 581168.6144 506081.9056 727500.8197 0.720500294 0.636193832 0.772261251 0.644347057 0.782851525 0.710750189 0.798856302 0.695644447 1 19.47258935 -5 0.198178025 2.279843105 0.670930908 0.730040696 0.053641171 62.97442019 0.621802985 31.81839934 0.113921792 1.00E-05 5 -1.608912196 IRLEETLEQLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRLEETLEQLAK 12 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 118.67 0.00054805 71237000 260550 214230 220290 269470 219220 250410 308020 282820 261000 FALSE TRUE 248234.3179 236060.2806 230390.5144 242382.3636 257451.8986 241738.2389 261025.8918 258054.7815 301474.547 0.823400583 0.783018941 0.764212159 0.803989478 0.853975572 0.801852897 0.865830613 0.855975352 1 18.20167668 0.425957468 0.453575675 1.015708349 0.79215913 0.86688036 0.023934216 0.762708007 0.277979451 0.047766022 0.013865314 2.6665975 -0.425957468 -0.223549219 IRLESEEEGVPSTAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IRLESEEEGVPSTAIR 16 1 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ;;; 89.041 0.0054037 547909000 1522966 1598710 1442164 1493429 1333400 1808229 1745351 1720957 1244480 FALSE TRUE 1450978.415 1761620.367 1508288.646 1343306.68 1565944.538 1745609.576 1479065.649 1570260.882 1437467.602 1.009399038 1.225502657 1.049267923 0.934495273 1.089377274 1.214364465 1.028938424 1.092380015 1 20.45509801 0.369766131 1.34471302 1.000060049 1.087216738 0.071245617 0.087932559 10.43919079 19.49482222 0.08276632 0.024318627 2.342966782 -0.369766131 0.087156688 IRNPFRGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRNPFRGSPK 10 2 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 IRNPFRGS(1)PK 82.55 0.0092237 199460000 426850 326380 335120 375520 309190 393170 513510 468940 381180 TRUE FALSE 406673.6464 359638.4931 350485.5835 337772.0162 363112.6381 379554.4243 435164.6182 427877.1276 440291.4476 0.923646482 0.816819166 0.796030869 0.767155524 0.824709724 0.862052684 0.988355828 0.971804313 1 18.7480993 1.809269102 3.259654689 0.987520398 0.829943584 0.769433558 0.040341482 0.128083424 2.477049161 0.024019702 0.012218681 64.45685362 -1.809269102 -0.157576814 IRPVS(ph)LPVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IRPVSLPVDR 10 1 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 IRPVS(1)LPVDR;IRPVS(1)LPVDR;IRPVS(1)LPVDR 116.19 0.00068033 120018000 377235 288118 328039 369072 376820 319424 424606 358799 392064 TRUE FALSE 359403.8492 317477.5518 343079.9126 331972.1814 442537.2887 308362.2668 359824.5563 327380.6574 452863.2827 0.7936255 0.701045026 0.757579441 0.73305166 0.97719843 0.680916909 0.794554494 0.722912786 1 18.78871605 -1.495497136 3.19520421 1.005648093 0.768017498 0.436684073 0.082026058 20244912.44 21307131.38 980859.2472 0.01776906 0.031952354 1.495497136 -0.237630595 IRQNEINNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRQNEINNPK 10 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 80.763 0.021005 83855000 143210 124070 114330 146890 141340 136410 154920 159280 142470 FALSE TRUE 136440.7471 136712.8741 119572.1436 132124.3381 165989.6513 131686.0875 131284.1087 145332.5988 164563.52 0.829106883 0.830760512 0.726601762 0.802877443 1.008666145 0.800214334 0.797771637 0.883139829 1 17.32828503 -4.999999994 0.242433721 1.987608116 0.813893991 0.361678002 0.071529558 198.7732941 1.97934157 96.7949801 0.107784719 1.00E-05 4.999999994 -1.173714124 IRS(ph)EDEEDLGNARPSAPSTLFDFLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRSEDEEDLGNARPSAPSTLFDFLESK 27 2 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 IRS(0.799)EDEEDLGNARPS(0.155)APS(0.023)T(0.023)LFDFLESK 120 9.34E-05 48318000 73969 57710 71846 94735 52386 77536 85758 73590 50132 TRUE FALSE 70472.63196 63590.71461 75140.21017 85212.05782 61522.10181 74850.90888 72674.04205 67146.06947 57906.21452 1.217013278 1.098167358 1.297619103 1.471552898 1.062443856 1.292623072 1.255030097 1.159565861 1 15.82143057 0.914562716 3.786418519 1.000138645 1.232754674 0.319755372 0.111934437 0.470626779 15.83116687 0.10419896 0.026748814 8.214151645 -0.914562716 0.23261603 IRS(ph)IEALLEAGQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IRSIEALLEAGQAR 14 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR;IRS(1)IEALLEAGQAR 173.36 1.64E-06 280248000 286940 209909 240612 263906 237806 244684 282002 250229 235300 TRUE FALSE 273376.9149 231298.9657 251644.2982 237377.6675 279279.2911 236210.5317 238977.4156 228317.6222 271789.1223 1.005842002 0.851023631 0.925880683 0.873389139 1.027558751 0.869094869 0.879275129 0.840054305 1 18.05212819 IRS(ph)SVEKENQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.5)S(0.5)VEKENQK;IRS(0.5)S(0.5)VEKENQK;IRS(0.5)S(0.5)VEKENQK;IRS(0.627)S(0.373)VEKENQK 127.66 0.00022203 2994060000 1173480 894943 1085035 1106710 592292 1166490 1311490 1270300 717051 TRUE FALSE 1118011.926 986138.7092 1134784.928 995461.4082 695587.5373 1126094.159 1111398.113 1159065.798 828247.6069 1.349852287 1.19063273 1.370103479 1.201888662 0.839830422 1.359610519 1.341866978 1.399419435 1 19.6597026 -2.001837211 2.629043744 0.740573679 1.256586725 0.195526888 0.163605199 14121474.42 6040025.25 22173072.98 0.038522477 0.009957786 2.001837211 0.516013046 IRSS(ph)VEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.013)S(0.987)VEK;IRS(0.061)S(0.939)VEK;IRS(0.005)S(0.995)VEK;IRS(0.026)S(0.974)VEK;IRS(0.023)S(0.977)VEK;IRS(0.147)S(0.853)VEK 116.13 0.0033457 3406550000 3930710 4452240 3126710 4649940 2399790 3921600 3665100 3863110 2220290 TRUE FALSE 3744913.128 4905928.318 3270072.746 4182519.197 2818312.616 3785794.009 3105921.681 3524835.609 2564601.234 1.460232132 1.912940013 1.275080392 1.630865314 1.0989282 1.476172576 1.211073925 1.374418589 1 21.29030309 2.447877662 0.277599388 0.995703605 1.79903983 0.392276111 0.205528825 2.053969121 0.394990254 0.313360007 0.578794579 280.4643479 -2.447877662 0.803336224 IRSS(ph)VEKENQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.182)S(0.818)VEKENQK;IRS(0.13)S(0.87)VEKENQK;IRSS(1)VEKENQK;IRS(0.001)S(0.999)VEKENQK;IRS(0.002)S(0.998)VEKENQK;IRSS(1)VEKENQK 200.97 2.35E-08 8752589000 7274029 5245093 6028817 6313615 3590950 6994611 7781290 7160710 4247224 TRUE FALSE 6930200.065 5779573.94 6305244.223 5678958.425 4217210.543 6752385.867 6594111.297 6533680.271 4905861.806 1.412636625 1.178095545 1.285247011 1.157586302 0.859626852 1.376391373 1.344129035 1.331810909 1 22.22607516 4.611328641 2.523923446 1.210780745 1.429891971 0.144414843 0.162427374 0.819358897 8.062326736 0.040450652 0.341445855 40862.84885 -4.611328641 0.219111225 IRT(ph)SPTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.642)S(0.358)PTFR 91.937 0.019615 1830800000 132220 95725 126110 152050 151170 110510 152510 134890 133920 TRUE FALSE 125970.2226 105479.4863 131892.2682 136765.6451 177534.0001 106683.011 129241.7985 123078.3165 154687.6296 0.814352272 0.681887017 0.852636171 0.884140803 1.147693585 0.689667372 0.835501835 0.795657137 1 17.2389983 3.584093263 5.90354551 0.877814133 0.748810992 0.175008671 0.124979905 0.392856465 18.37531482 0.032503258 0.050586904 3837.896536 -3.584093263 -0.129003141 IRTPS(ph)GEFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IRTPSGEFLER 11 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 IRT(0.163)PS(0.837)GEFLER 88.075 0.034854 100640000 173880 135340 169780 171150 154100 154170 171900 162920 173420 TRUE FALSE 165661.037 149131.2999 177564.5809 153945.6768 180974.9912 148831.0542 145673.4978 148653.8611 200313.0879 0.82701055 0.744491044 0.886435244 0.768525304 0.903460643 0.742992162 0.727229056 0.742107581 1 17.61189716 IRTS(ph)PTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.031)S(0.969)PTFR;IRT(0.167)S(0.829)PT(0.004)FR;IRT(0.168)S(0.832)PTFR;IRT(0.252)S(0.748)PTFR;IRT(0.173)S(0.71)PT(0.117)FR 101.3 0.0033284 3587790000 271749 241584 307895 298098 311981 311474 278194 265198 471213 TRUE FALSE 258903.9633 266201.6843 322012.2903 268132.6227 366390.3876 300687.5773 235750.3959 241975.8572 544286.3054 0.475676056 0.489083928 0.591622988 0.49263158 0.673157461 0.552443768 0.43313674 0.444574583 1 19.05400621 -1.832310641 2.558496661 1.180510821 0.51512513 0.814960659 0.072002034 7929579.26 5093202.617 8788283.635 0.018111338 0.014712598 1.832310641 -0.665385691 IRVDIIENQVMDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IRVDIIENQVMDFR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;; 174.62 2.29E-06 506395000 1258911 1031549 1102017 1192957 1181433 1131216 1320906 1294342 789327 FALSE TRUE 1199404.772 1136665.016 1152545.569 1073038.696 1387474.541 1092041.706 1119377.53 1181002.553 911731.7998 1.315523679 1.246709851 1.264127861 1.176923626 1.521801194 1.19776639 1.227748697 1.295339872 1 19.79824997 -0.890791919 0.551462136 0.930942091 1.283071891 0.460092892 0.095332398 16.72901512 3.218383992 2.044480134 0.037923399 0.128590262 0.890791919 0.3521298 IRVDVADQAQDKDRDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IRVDVADQAQDKDRDDR 17 3 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 239.75 1.18E-20 9681339000 6122220 5029860 5258140 5948390 4640120 5990250 7020050 6933710 5375860 FALSE TRUE 5832834.794 5542408.452 5499230.92 5350446.536 5449355.459 5782806.14 5949012.44 6326557.594 6209520.913 0.93933733 0.892566195 0.885612755 0.861652068 0.87758066 0.931280564 0.958046929 1.018847941 1 22.56605053 1.631459293 1.831382405 1.008874536 0.895095422 0.819657588 0.022137669 0.142761232 0.988240324 0.018615031 0.006841254 42.80152991 -1.631459293 -0.113779113 IRYESLTDPSK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 171.62 1.31E-05 1705260000 2931830 3171080 2290390 3419810 1861900 2848180 2623270 3072210 1872130 FALSE TRUE 2793248.206 3494216.657 2395406.647 3076044.202 2186614.771 2749546.812 2223041.982 2803191.006 2162450.359 1.291705123 1.615859824 1.107727924 1.422480839 1.011174551 1.271495922 1.028019891 1.296303055 1 21.04423558 3.225877399 1.235411509 1.130224381 1.436427413 0.298866898 0.165672013 0.440216905 1.42144201 0.055686259 0.083926631 1682.19911 -3.225877399 0.306203031 IRYESLTDPSKLDSGK ddPTM_SK-BR-3_Trastuzumab_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 ; 174.23 2.22E-09 3935200000 8196000 6332700 6991000 7587900 4789800 8275600 9331500 9115800 5453100 FALSE TRUE 7808591.323 6978009.33 7311544.265 6825149.876 5625139.603 7989013.897 7907808.29 8317572.226 6298738.897 1.239707099 1.107842291 1.160794944 1.083574028 0.89305807 1.268351336 1.255458977 1.320513894 1 22.58663158 IS(ph)AFFS(ph)S(ph)IWDT(ph)ILTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISAFFSSIWDTILTK 15 0 Q15053 Q15053 KIAA0040 Uncharacterized protein KIAA0040 4 IS(0.999)AFFS(0.999)S(0.999)IWDT(1)ILT(0.002)K 41.092 0.079621 50216000 97286 71251 98442 82071 263890 71437 108800 76778 218080 TRUE FALSE 92687.48358 78511.55791 102955.6631 73821.06716 309912.3324 68963.11878 92200.56175 70054.91129 251898.7326 0.367955339 0.311679051 0.408718464 0.29305851 1.230305247 0.273773187 0.366022333 0.278107439 1 17.94248434 IS(ph)APNVDFNLEGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK 274.79 5.00E-33 9291783000 10791173 9459230 9012711 10778460 5599708 9559283 10063996 10887209 5410664 TRUE FALSE 10281095.64 10423136.29 9425952.714 9694988.723 6576295.302 9228242.633 8528548.572 9933867.263 6249722.139 1.645048437 1.667775952 1.508219486 1.551267161 1.052254029 1.476584467 1.36462844 1.589489427 1 22.57536062 7.999999996 0.041479777 7.95E-09 3.892773885 0.478394183 0.167320252 576.9525956 1.82044016 45.74955934 155.2944238 99999999 -7.999999996 3.892773877 IS(ph)ASSATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ISASSATR 8 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 IS(1)ASSATR;IS(0.999)AS(0.001)SATR;IS(1)ASSATR;IS(0.998)AS(0.002)SATR;IS(1)ASSATR;IS(0.858)AS(0.054)S(0.088)ATR;IS(0.946)AS(0.038)S(0.016)ATR 172.26 0.00029853 2599120000 2834170 2440847 2430918 2705743 2464138 2507903 3160968 2761463 2788457 TRUE FALSE 2700204.401 2689572.084 2542377.995 2433756.573 2893882.887 2421053.69 2678704.276 2519654.66 3220876.67 0.838344549 0.835043487 0.789343479 0.755619299 0.898476776 0.751675379 0.83166931 0.782288463 1 21.61902199 -1.34246407 5.80950186 1.000028259 0.813314658 0.647760596 0.043910913 1.43E-05 1.62E-06 0.037866385 0.008923843 0.045450214 1.34246407 -0.186713601 IS(ph)DAELEAELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ISDAELEAELEK 12 0 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK 268.35 5.35E-22 804436000 2381449 2368816 1805191 2704294 1195101 2504558 2180739 2426611 1061344 TRUE FALSE 2268882.625 2610201.044 1887960.793 2432453.229 1403526.236 2417824.528 1848027.214 2214124.077 1225931.807 1.850741299 2.1291568 1.540021054 1.984166832 1.144864851 1.972234112 1.507446991 1.80607442 1 20.2254473 -1.890817972 0.134074528 4.34E-12 2.170505076 0.417379508 0.280917612 42.50509892 0.849498573 16.36058248 2.184008223 0.012858255 1.890817972 2.170505076 IS(ph)DAELEAELEKLSLSEGGLVPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK 265.65 1.38E-45 485221000 501678 328681 447282 451938 272925 514383 587089 590562 295351 TRUE FALSE 477964.6752 362173.9676 467790.3221 406508.3336 320523.0336 496569.7877 497517.7904 538849.2605 341152.5246 1.401029278 1.061618899 1.371205805 1.191573576 0.939530006 1.455565332 1.458344155 1.579496623 1 18.38005737 IS(ph)DS(ph)ESEDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISDSESEDPPR 11 0 Q96ST2;Q96ST2-3;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 IS(1)DS(1)ESEDPPR;IS(1)DS(0.997)ES(0.003)EDPPR 230.06 3.04E-12 517900000 1236940 1194650 1033600 1381040 790740 1229210 1076920 1044930 693240 TRUE FALSE 1178472.298 1316386.193 1080991.582 1242215.235 928644.8056 1186642.149 912616.075 953430.3897 800744.1186 1.471721453 1.643953621 1.349983793 1.551326081 1.159727289 1.481924278 1.139709994 1.190680478 1 19.61098177 1.941013312 0.428187283 0.991857478 1.581937631 0.640007122 0.124029447 0.560505515 0.25284403 0.118740869 0.106208064 87.29981276 -1.941013312 0.590080154 IS(ph)EDETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 143.4 0.00063157 202510000 240110 372770 204810 320950 218730 345310 220620 237410 140760 TRUE FALSE 228760.4762 410755.6868 214200.7411 288687.4962 256876.4427 333351.8281 186960.367 216621.1218 162588.3419 1.406991876 2.52635387 1.317442189 1.775573161 1.579919198 2.050281245 1.149900201 1.332328747 1 17.31086429 1.678059793 6.826622188 1.180150593 1.807996066 0.406319178 0.347996769 0.125294457 11.68441273 0.168074814 0.085927531 47.64965851 -1.678059793 0.627845472 IS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.894)EDET(0.106)ERNGDDGTHDK 141.1 3.85E-07 204550000 194330 197980 157300 221740 88789 201650 179810 199670 71961 TRUE FALSE 185144.406 218154.3871 164512.3606 199450.2739 104273.7735 194666.8099 152376.6821 182185.8363 83120.34435 2.227425878 2.624560675 1.979206918 2.399536184 1.254491596 2.34198753 1.833205616 2.191832068 1 16.34291401 -1.260623316 0.169767891 9.22E-15 2.57034445 0.480946017 0.367109049 21.3566979 0.700600303 11.70365604 1.557056708 0.054875272 1.260623316 2.57034445 IS(ph)FVEEDVHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISFVEEDVHPK 11 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 IS(1)FVEEDVHPK;IS(1)FVEEDVHPK 141.54 2.45E-05 45273000 111347 124734 104348 145316 78192 133116 118848 129561 69896 TRUE FALSE 106083.848 137444.5364 109132.459 130708.5596 91828.66004 128506.1595 100715.5548 118215.952 80735.1147 1.313974079 1.702413342 1.351734737 1.618980292 1.137406696 1.59170096 1.247481411 1.464244554 1 16.30090867 -2.460944761 0.217260312 0.350609957 1.520071937 0.373112996 0.174854239 39.22035322 1.050890348 12.48851271 0.32839378 0.003459834 2.460944761 1.169461979 IS(ph)LQQELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISLQQELSR 9 0 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 IS(1)LQQELSR 61.679 0.091882 35432000 3122.4 3039.1 2949.3 4060.1 4430.5 4342 5581.8 5126.6 7138.1 TRUE FALSE 2974.81034 3348.787745 3084.528322 3651.971034 5203.177797 4191.635451 4730.193893 4677.687726 8245.040092 0.360799985 0.406157849 0.374107134 0.442929445 0.631067616 0.508382665 0.573701746 0.567333533 1 13.00931079 -4.999999998 0.119887355 2.790006997 0.205556762 0.918513819 0.052956783 37.99039376 0.295366295 16.33827978 0.494200017 1.00E-05 4.999999998 -2.584450235 IS(ph)MPDFDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MPDFDLHLK;IS(1)MPDFDLHLK 131.13 0.00013509 35744000 112564 127316 83868 128423 72975 96022 93955 101674 57435 TRUE FALSE 107243.3228 140289.6451 87713.43076 115513.6761 85701.8169 92696.73406 79620.43915 92770.88555 66341.72646 1.616528971 2.114651708 1.322145736 1.74119189 1.291823735 1.397261407 1.200156273 1.398379127 1 16.01762894 2.746426952 0.521855905 1.118998851 1.892213393 0.521475607 0.214568614 0.67162172 0.383209886 0.172341951 0.2168472 557.7337841 -2.746426952 0.773214542 IS(ph)MPDVDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MPDVDLHLK 176.87 0.00041873 0 136110 152600 100920 150290 73831 116960 98986 112510 52058 TRUE FALSE 129676.35 168150.1135 105547.2818 135182.5637 86707.10302 112909.6459 83883.8677 102658.0279 60130.88876 2.156567992 2.796401599 1.75529223 2.24813846 1.44197275 1.877731199 1.395021251 1.707242817 1 15.87581866 2.565081002 0.346499026 1.050792521 2.681502521 0.61040073 0.31320307 0.975142734 0.254938704 0.342591681 0.577961993 367.3508105 -2.565081002 1.63071 IS(ph)MSEVDLNVAAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(0.999)MS(0.001)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.952)MS(0.048)EVDLNVAAPK;IS(0.997)MS(0.003)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(0.898)MS(0.102)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(0.5)MS(0.5)EVDLNVAAPK;IS(0.983)MS(0.017)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(0.968)MS(0.032)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.752)MS(0.248)EVDLNVAAPK;IS(0.995)MS(0.005)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(1)MSEVDLNVAAPK 366.69 5.63E-97 4709931000 6017712 5484332 5087267 6228812 3623442 5453770 5802480 6006813 3477874 TRUE FALSE 5733266.68 6043191.666 5320523.224 5602679.984 4255369.138 5264904.577 4917205.106 5480824.61 4017204.937 1.427178043 1.504327452 1.324434105 1.394671188 1.059286047 1.310588994 1.224036409 1.364337816 1 21.93776063 7.999999993 0.051276931 0.44622409 2.940263436 0.536713825 0.107506958 317.6744075 1.228154087 13.79275881 62.13858478 99999998.48 -7.999999993 2.494039347 IS(ph)PGATLPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ISPGATLPESR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 IS(1)PGATLPESR;IS(1)PGATLPESR;IS(0.987)PGAT(0.013)LPESR 244.94 6.90E-16 934170000 1219340 1056153 1185220 1253830 1044120 1179760 1369720 1231140 1148170 TRUE FALSE 1161704.215 1163776.191 1239563.509 1127792.626 1226214.197 1138904.615 1160744.057 1123334.855 1326222.34 0.875949816 0.877512131 0.934657389 0.850379754 0.924591723 0.858758431 0.875225837 0.847018499 1 20.33889123 -2.013495803 2.826009372 1.130327702 0.88062633 0.630558202 0.028743291 4573051.56 8265551.532 3851073.584 0.00615663 0.009694026 2.013495803 -0.249701372 IS(ph)PPIKEEETKGDSVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 148.29 1.92E-07 807320000 1378010 1208270 941220 1360580 411790 1360830 1135230 1361040 293040 TRUE FALSE 1312874.198 1331394.087 984375.868 1223811.913 483606.0456 1313704.116 962029.8136 1241860.122 338483.1466 3.878698871 3.93341323 2.908197581 3.6155771 1.42874483 3.881150743 2.842179362 3.668897949 1 18.36872448 3.631173171 1.708631312 2.832386981 3.950428563 0.20096586 0.930177335 0.553907805 3.179843798 0.24927802 0.496254284 4277.334071 -3.631173171 1.118041582 IS(ph)RESSVDCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISRESSVDCLK 11 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BMM1 H3BRD5 MYO9A Unconventional myosin-IXa 1 IS(0.996)RES(0.004)SVDCLK 55.314 0.076378 159220000 21582 19743 24184 20112 89909 12672 29474 10496 78694 TRUE FALSE 20561.86163 21754.83415 25292.86032 18090.30355 105589.1011 12233.16546 24977.19997 9576.914597 90897.46361 0.22620941 0.239333786 0.278257053 0.199018794 1.161628685 0.134582033 0.274784345 0.105359536 1 16.47195242 -2.183500836 2.312061123 2.80372831 0.320991096 0.328212908 0.302288843 19802493.03 4088197.799 187047539.7 0.06907842 0.00655389 2.183500836 -2.482737214 IS(ph)TYGLPAGGIQPHPQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISTYGLPAGGIQPHPQTK 18 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 IS(0.967)T(0.033)YGLPAGGIQPHPQTK;IS(0.799)T(0.201)YGLPAGGIQPHPQTK 235.76 5.42E-24 336600000 1163180 969110 990860 1232920 767480 987270 1175710 1335670 667330 TRUE FALSE 1108198.787 1067863.411 1036291.911 1108984.539 901328.269 953080.5923 996333.8461 1218711.654 770816.1282 1.43769538 1.385367238 1.344408703 1.438714758 1.169316827 1.236456475 1.292570056 1.581066625 1 19.55602723 2.75869971 24.69491218 1.273574423 1.399692194 0.194918105 0.144618704 1251.55418 1534675.947 0.040579179 0.042990047 573.7196299 -2.75869971 0.126117771 IS(ph)WYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;IS(1)WYLR 126.52 0.018309 29411000 110789 100342 86550 106413 88857 90165 116539 95690 85961 TRUE FALSE 105552.2235 110566.9639 90518.40311 95716.16307 104353.6327 87042.56344 98758.83516 87310.87632 99291.39285 1.06305512 1.113560407 0.911644006 0.963992551 1.050983672 0.876637551 0.994636416 0.879339828 1 16.59938104 3.743529804 24.95479594 0.955700986 1.08830777 0.501414286 0.055701964 278.4235977 1398213.247 0.012983797 0.02251792 5540.255633 -3.743529804 0.132606784 ISAEDGLKHEYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISAEDGLKHEYFR 13 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 0 171.76 1.47E-05 219300000 289100 178690 243210 256540 231340 259430 312300 271870 223860 FALSE TRUE 275434.8159 196898.7142 254361.4191 230752.1118 271685.6228 250445.874 264652.8992 248063.6215 258575.0655 1.065202538 0.761476029 0.983704359 0.89239893 1.0507031 0.96856158 1.023505104 0.959348579 1 17.98022364 2.749344339 24.79166093 1.000997791 0.917049059 0.175295776 0.079559858 990.8452906 2277941.676 0.023088395 0.024250247 561.4929902 -2.749344339 -0.083948731 ISDDKYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ISDDKYGR 8 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 180.44 0.00021805 3705980000 5477230 4291710 4241720 5427040 4060900 4810680 5889260 5171650 4719250 FALSE TRUE 5218332.193 4729040.128 4436207.058 4881503.628 4769119.674 4644084.945 4990745.223 4718792.909 5451087.187 0.957301179 0.867540725 0.813820602 0.895510099 0.874893303 0.851955727 0.915550431 0.865660876 1 22.37811256 -1.498391752 3.117793948 1.003175842 0.883193251 0.491702271 0.03815218 11595922.12 11044487.98 303905.622 0.009430364 0.031740097 1.498391752 -0.119982591 ISDEDWDIIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 225.31 5.57E-12 514623000 838152 860232 774211 867302 752020 762894 857602 826058 624900 FALSE TRUE 798534.216 947890.6188 809709.3401 780119.1552 883172.0499 736474.7895 726759.064 753723.9823 721806.3005 1.10629987 1.313220206 1.121782034 1.080787401 1.223558245 1.020321919 1.006861624 1.044219179 1 19.46125221 2.227352152 24.96898922 1.017251604 1.176898773 0.563482026 0.06596493 154.1364779 343365.8874 0.024781686 0.018468069 168.7921138 -2.227352152 0.159647169 ISDYFEYQGGNGS(ph)SPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.5)S(0.5)PVR;ISDYFEYQGGNGS(0.622)S(0.378)PVR 187.39 4.92E-10 187765000 212990 182020 204062 215849 201652 186960 241806 237791 242394 TRUE FALSE 202922.3848 200568.0449 213418.4445 194151.4484 236820.045 180485.5283 204914.0536 216968.7594 279983.2235 0.724766228 0.716357367 0.762254402 0.693439578 0.845836554 0.644629796 0.731879757 0.774934857 1 18.09498086 0.765889984 2.843214425 0.999948851 0.729197848 0.730426412 0.050915105 0.615985127 6.806651168 0.043080228 0.011339998 5.832973233 -0.765889984 -0.270751003 ISDYFEYQGGNGSS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.114)S(0.886)PVR;ISDYFEYQGGNGS(0.039)S(0.961)PVR;ISDYFEYQGGNGS(0.143)S(0.857)PVR 263.92 2.06E-27 483830000 363091 314459 341415 390567 344693 343015 396188 371297 398813 TRUE FALSE 345928.408 346502.7296 357069.2155 351306.4631 404807.3501 331136.3045 335742.2441 338784.2663 460658.8832 0.750942662 0.752189401 0.775127168 0.762617364 0.878757286 0.718831909 0.7288305 0.735434133 1 18.81333931 -1.220902479 4.328456591 1.000101564 0.760651965 0.738105118 0.044379185 4.25E-05 7.66E-06 0.042014808 0.009898795 0.060130875 1.220902479 -0.239449599 ISEDKNPDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISEDKNPDYR 10 1 P14923 P14923 JUP Junction plakoglobin 0 111.06 0.0016452 368930000 925760 899670 874140 897140 613690 875610 970570 957580 588940 FALSE TRUE 882001.1595 991347.3958 914220.1836 806957.7827 720717.3417 845287.4061 822491.7208 873729.2187 680269.8073 1.296546091 1.457285602 1.343908217 1.186231954 1.059458077 1.242576691 1.20906692 1.284386297 1 19.37574753 7.999996345 0.043473619 0.418329192 2.677461644 0.470374934 0.095968668 542.5952718 1.79132684 24.18581678 86.98928222 99999158.38 -7.999996345 2.259132452 ISEDVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISEDVEER 8 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 75.043 0.091687 71697000 204740 183270 179620 221360 201210 195010 249940 199690 221020 FALSE TRUE 195062.346 201945.4214 187855.7547 199108.4722 236300.9603 188256.7548 211807.0625 182204.085 255294.6528 0.764067495 0.791028794 0.735838971 0.779916344 0.9256009 0.737409706 0.829657262 0.713701141 1 17.96180379 -2.173588429 2.525499596 1.582802889 0.78762492 0.561795737 0.059719835 5082116.758 1684295.193 16906583 0.013740028 0.006705197 2.173588429 -0.795177968 ISEQFTAMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 214.05 2.56E-08 3365960000 751450 638264 478587 526881 703865 508675 810390 625647 723758 FALSE TRUE 715930.4477 703303.8272 500530.6873 473917.9209 826618.8331 491059.4572 686750.1217 570862.0319 835994.6942 0.856381569 0.84127786 0.598724718 0.566891063 0.988784784 0.587395423 0.821476651 0.682853654 1 19.67313426 -1.234574196 5.284867005 1.000022137 0.754364978 0.253596078 0.137348267 3.35E-05 4.85E-06 0.124229489 0.029278535 0.058267422 1.234574196 -0.245657159 ISESVLRDS(ph)PPPHEDYEDEVFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISESVLRDSPPPHEDYEDEVFVR 23 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.06)ES(0.052)VLRDS(0.888)PPPHEDYEDEVFVR 154.7 2.23E-08 100430000 86499 112680 70908 108560 72705 108220 93867 96722 65712 TRUE FALSE 82410.36369 124162.2201 74159.20194 97647.34255 85384.72898 104472.3143 79545.86516 88252.50892 75902.28135 1.085742908 1.635816709 0.977035217 1.286487584 1.124929679 1.376405457 1.048003614 1.162712205 1 16.21185563 1.482926546 0.396436809 0.989395423 1.314896918 0.129243802 0.186695053 1.765718289 0.824818736 0.223892219 0.16661167 30.40370749 -1.482926546 0.325501495 ISESVLRDS(ph)PPPHEDYEDEVFVRDPHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.078)ES(0.072)VLRDS(0.847)PPPHEDY(0.004)EDEVFVRDPHPK;IS(0.008)ES(0.007)VLRDS(0.985)PPPHEDYEDEVFVRDPHPK 130.56 1.14E-05 516710000 278630 217593 228140 275824 206445 264125 304680 314591 161470 TRUE FALSE 265459.7121 239765.9741 238600.4447 248097.6475 242448.9426 254978.285 258195.4702 287043.7443 186509.9429 1.423300592 1.285539904 1.279290749 1.330211374 1.299925027 1.367102906 1.384352309 1.539026498 1 17.50889302 -1.232460058 4.003387007 0.999700631 1.356956424 0.686490454 0.07710361 5617921.513 1729521.943 14711.24737 0.017527166 0.058551758 1.232460058 0.357255793 ISEVFDCWFESGSMPYAQVHYPFENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISEVFDCWFESGSMPYAQVHYPFENKR 27 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 177.52 1.41E-17 343230000 577470 511890 595180 608260 507370 602740 739890 653220 525090 FALSE TRUE 550174.1375 564052.173 622469.5917 547116.5492 595855.1674 581866.9627 627006.1915 596020.5939 606518.2754 0.907102325 0.929983804 1.026299811 0.902061111 0.982419148 0.959356026 1.033779553 0.982691896 1 19.21019159 6.093435257 0.2548293 1.012004025 0.701712196 0.354628219 0.036652894 17.48722009 0.551801176 0.045077523 1.921269667 1240038.752 -6.093435257 -0.310291829 ISFDEFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISFDEFIK 8 0 P13796;Q5TBN3 P13796 LCP1 Plastin-2 0 82.426 0.047235 26562000 87906 81385 99862 90543 116460 86985 127780 93504 102070 FALSE TRUE 83750.85759 89678.22403 104440.7715 81441.44562 136770.5871 83972.68764 108284.8142 85316.29406 117898.4943 0.710364098 0.760639265 0.88585331 0.69077596 1.160070686 0.712245632 0.918457991 0.723641931 1 16.84718577 3.866755816 1.132446418 0.873548956 0.705215758 0.139523542 0.142212935 1.04946878 2.415065031 0.041728285 0.146030963 7357.932776 -3.866755816 -0.168333198 ISGLIYEETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISGLIYEETR 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;; 144.79 7.35E-05 236494000 326604 303060 289893 399053 390687 325672 363289 393334 323612 FALSE TRUE 311166.0762 333942.1586 303184.8808 358939.4343 458822.6891 314393.897 307862.5908 358891.5898 373796.0962 0.832448705 0.893380541 0.811096969 0.960254636 1.227467846 0.84108395 0.823611038 0.96012664 1 18.51189198 3.225041521 24.63315722 0.953897918 0.853986979 0.206488504 0.110856307 383.87397 699455.5605 0.033782062 0.040594642 1678.964527 -3.225041521 -0.099910939 ISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYR 33 1 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;;; 277.9 7.23E-74 1014230000 1426556 914108 1343996 1272288 1354892 1381648 2005278 1624052 985938 FALSE TRUE 1359125.525 1007256.644 1405619.546 1144395.193 1591184.736 1333801.183 1699336.012 1481841.397 1138832.23 1.193437883 0.88446447 1.234263932 1.004884796 1.397207327 1.171200769 1.492174148 1.301193766 1 20.1191238 2.742090088 24.96203582 1.309586921 1.068093682 0.24132528 0.162316378 319.3625844 2258683.286 0.045877374 0.046911303 552.1919709 -2.742090088 -0.241493239 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK 29 0 Q96PZ0;Q96PZ0-2;E7EUH7 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 ;;; 139.81 8.87E-08 86839500 88690 81643 82280 96903 69987 86056 99730 103613 58538 FALSE TRUE 84497.79947 89962.51452 86052.61939 87162.12634 82192.71064 83075.85914 84514.35683 94540.09643 67615.77407 1.249675843 1.330495964 1.272670772 1.289079768 1.215584851 1.22864613 1.249920717 1.398195876 1 16.04507223 -1.268797127 4.06657434 0.99970655 1.276076548 0.73206743 0.053067358 0.000133904 2.41E-05 0.048731552 0.01147403 0.053852128 1.268797127 0.276369998 ISHQSQDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ISHQSQDKK 9 1 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;; 150.1 5.59E-05 269572000 889930 504378 617674 840650 698210 714910 1266490 1053590 984720 FALSE TRUE 847864.7726 555774.6916 645994.9639 756146.2649 819977.6029 690152.4874 1073263.69 961332.0742 1137425.348 0.745424545 0.488625203 0.567944934 0.664787598 0.720906743 0.606767282 0.943590444 0.845182566 1 20.11734043 1.718884677 1.160070496 0.974881168 0.610021616 0.691944001 0.089887046 0.243793518 0.615241249 0.072866401 0.02828299 52.34614178 -1.718884677 -0.364859552 ISICS(ph)SDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 IS(0.03)ICS(0.878)S(0.092)DKR 79.152 0.016998 229900000 468800 402260 414950 469140 401310 445300 520130 478420 394660 TRUE FALSE 446640.7531 443250.7513 433975.8679 421981.1559 471298.3369 429879.1493 440774.6157 436527.0085 455861.8572 0.979772153 0.972335685 0.951989865 0.925677701 1.033862188 0.943003111 0.966903918 0.957586167 1 18.79823718 ISICSSDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 91.867 0.013617 0 363830 319990 220720 237870 287400 260030 446440 326650 289600 FALSE TRUE 346632.4769 352597.3448 230840.2303 213958.8557 337522.469 251025.0959 378327.3786 298046.7943 334509.6889 1.036240469 1.054072143 0.690085334 0.639619308 1.009006555 0.750426981 1.130990794 0.890995999 1 18.35168847 -0.305163604 7.97204309 1.0000087 0.920301077 0.022408318 0.165022894 0 0 0.161726641 0.038119335 0.495263583 0.305163604 -0.079707623 ISIPDVGLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISIPDVGLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 95.477 0.0077288 162230000 677510 579710 573690 701390 555390 584070 661190 722910 574030 FALSE TRUE 645485.445 638783.1081 599994.254 630884.9446 652249.8402 563843.5094 560313.3219 659608.168 663047.6407 0.97351292 0.963404541 0.904903686 0.951492632 0.983714895 0.850381594 0.84505741 0.994812631 1 19.33875301 2.25340337 24.9987905 0.900613503 0.955669171 0.016423325 0.055896991 388.0743057 653610.2204 0.018587099 0.015491267 179.2269729 -2.25340337 0.055055668 ISKEEAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 ISKEEAMR 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;;;;; 128.27 0.0010404 5902410000 8157390 6214640 6294200 7218220 6964100 7210140 9925860 8662180 8243690 FALSE TRUE 7771806.341 6847918.881 6582795.296 6492630.812 8178636.835 6960451.044 8411487.756 7903673.598 9522079.342 0.816187942 0.719162132 0.691319097 0.681850106 0.858912906 0.730980156 0.883366695 0.83003652 1 23.18284522 1.101318991 0.662816528 0.996400001 0.73937295 0.646415832 0.059011592 0.440625787 0.461985812 0.055445002 0.023266134 12.62754691 -1.101318991 -0.257027051 ISKSDMSRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISKSDMSRLR 10 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 52.579 0.083916 86658000 43905 41173 48550 41257 182190 23472 53706 21892 167060 FALSE TRUE 41829.69766 45368.57551 50776.06552 37109.76798 213963.8783 22659.15875 45512.16332 19975.02042 192966.8116 0.216771461 0.235110769 0.263133671 0.192311661 1.108811803 0.11742516 0.235854876 0.103515316 1 17.55799321 -2.044958725 2.742419642 1.92657809 0.302436429 0.359887376 0.289447084 47882367.35 22774026.88 278034681.7 0.069262265 0.009016568 2.044958725 -1.624141661 ISLFS(ph)SLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISLFSSLR 8 0 A0A2R8YFA9;Q6ZW33 A0A2R8YFA9 MICALCL MICAL C-terminal-like protein 1 IS(0.005)LFS(0.498)S(0.498)LR 66.962 0.063281 14718000 75317 57635 59983 66422 76637 60106 83921 72550 89265 TRUE FALSE 71756.91467 63508.07203 62733.27988 59745.13437 90002.46854 58024.51415 71117.31014 66197.13739 103107.7603 0.69594097 0.615938818 0.608424426 0.579443625 0.872897135 0.562756033 0.689737707 0.642018963 1 16.65379339 -4.91818143 0.485191088 10 0.654304063 0.601916828 0.08724287 1187.227618 6.46570113 11549.4995 0.038151083 1.21E-05 4.91818143 -9.345695937 ISLPGQMAGT(ph)PITPLK ddPTM_SK-BR-3_Trastuzumab_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(0.998)PIT(0.002)PLK;ISLPGQMAGT(1)PITPLK 227.64 5.42E-14 126467000 575070 596200 457530 644310 368690 550590 506460 597590 375980 TRUE FALSE 547887.5808 656953.4578 478508.2031 579542.7347 432989.4193 531522.9302 429190.2252 545261.8516 434285.0582 1.261585151 1.512724063 1.101829764 1.334475418 0.997016616 1.223903333 0.988268459 1.255539055 1 18.72828279 3.261792172 1.280879442 1.097205377 1.375630061 0.337474815 0.137618286 0.390188637 1.346847974 0.044742184 0.069284632 1827.225603 -3.261792172 0.278424684 ISLSKS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISLSKSPTK 9 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 ISLSKS(0.999)PT(0.001)K;ISLS(0.005)KS(0.995)PTK 132.5 0.00018365 2330900000 4875900 5242900 3913400 5673400 2481100 5332100 4995400 6022300 2789100 TRUE FALSE 4645425.87 5777157.471 4092833.261 5103099.053 2913803.054 5147448.04 4233259.983 5494955.486 3221619.383 1.441953663 1.793246434 1.270427314 1.584016746 0.904452919 1.5977828 1.314016176 1.705650119 1 21.61935463 3.726184239 24.85865912 1.357662403 1.617600057 0.156816202 0.265524445 1093.841647 2197044.016 0.062798687 0.098070792 5323.340417 -3.726184239 0.259937654 ISLSKS(ph)PTKTDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.01)LS(0.036)KS(0.93)PT(0.02)KT(0.004)DPK 82.59 0.0062283 4776700000 7498900 7066300 6488600 7851700 2661200 8835200 7660200 8359700 2565000 TRUE FALSE 7144441.858 7786364.004 6786108.728 7062432.199 3125312.437 8529234.809 6491495.801 7627680.35 2962767.1 2.411408531 2.628071577 2.290463104 2.383728441 1.054862678 2.878807048 2.191024668 2.574512303 1 21.49851379 2.97538891 24.9861374 2.06659922 2.460691065 0.125324118 0.591965299 1768.281243 1795229.283 0.16575814 0.176610004 944.9066592 -2.97538891 0.394091845 ISLSKSPT(ph)KTDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 ISLS(0.003)KS(0.387)PT(0.61)KTDPK 165.16 5.76E-05 1546900000 2361500 2299600 2101800 2672700 913060 2794400 2348800 2918200 949580 TRUE FALSE 2249876.575 2533931.854 2198169.609 2404035.118 1072297.375 2697629.227 1990447.421 2662666.938 1096836.017 2.051242429 2.310219409 2.0041005 2.191790825 0.977627794 2.459464484 1.814717416 2.427588899 1 20.06491642 ISMFCHVEPEQVICVHDVSSIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISMFCHVEPEQVICVHDVSSIYR 23 0 P17812;B4E1E0;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 P17812 CTPS1 CTP synthase 1;CTP synthase 0 112.48 0.00049695 174730000 205620 141930 199840 200330 190340 196620 269890 249270 193820 FALSE TRUE 195900.7501 156392.8284 209002.8617 180192.4478 223535.2357 189811.0001 228713.3236 227442.5973 223876.6157 0.875038911 0.698567056 0.933562717 0.804873913 0.998475142 0.847837544 1.021604346 1.015928335 1 17.77234432 2.542999104 0.710090871 1.015158592 0.793891235 0.475108997 0.076748227 0.521323494 0.540661901 0.05407872 0.044442356 349.1395955 -2.542999104 -0.221267357 ISMPDFDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 156.01 3.13E-05 1853220000 6735900 6819300 5353500 7492500 4647700 5921600 6165700 6591500 3826500 FALSE TRUE 6417507.356 7514194.423 5598963.27 6739339.665 5458257.408 5716533.507 5225009.224 6014313.316 4419894.077 1.451959537 1.700084729 1.266764129 1.524774021 1.234929461 1.293364367 1.182157114 1.36073698 1 22.07558037 2.460031742 0.253210586 0.977751809 1.710364388 0.559113853 0.128225409 1.788694756 0.297091923 0.233972924 0.452088919 288.4242303 -2.460031742 0.732612579 ISMPDFDLHLKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISMPDFDLHLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 202.13 1.01E-08 478070000 2215480 1094350 2173590 1791080 1809360 2054140 3166400 2524700 2181540 FALSE TRUE 2110758.651 1205865.509 2273251.251 1611037.236 2124911.811 1983004.617 2683307.525 2303623.884 2519842.081 0.837655132 0.478548048 0.902140364 0.639340555 0.843271817 0.786955909 1.064871305 0.914193751 1 21.26490189 2.14395835 1.2705587 1.003434211 0.695993584 0.444816947 0.126232239 0.355939197 1.089691557 0.078279683 0.041141659 139.3023202 -2.14395835 -0.307440627 ISMPDIDFNLKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISMPDIDFNLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 80.522 0.014648 54076000 100160 98697 106990 103870 71498 107550 110920 99792 60534 FALSE TRUE 95425.6353 108754.3365 111895.5973 93428.79026 83967.22856 103825.5165 93997.11681 91053.68345 69921.30356 1.36475767 1.555381993 1.600307655 1.336199206 1.20088191 1.484891031 1.344327294 1.30223092 1 16.09344446 -1.021863317 0.2365468 0.70620916 1.504742876 0.602743727 0.109233038 11.38841875 0.622553596 2.382049031 0.213002616 0.095090402 1.021863317 0.798533716 ISMPDLDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISMPDLDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 145.23 3.63E-05 192060000 655230 591640 560620 637050 484470 568970 669180 618740 440610 FALSE TRUE 624258.5764 651928.7886 586324.9815 573012.5237 568961.4146 549266.4262 567084.3007 564559.8455 508937.5485 1.226591707 1.280960288 1.152056835 1.125899485 1.117939551 1.079241309 1.114251252 1.109291007 1 18.95712911 4.511712733 0.203704475 0.995312619 1.483330662 0.778722789 0.036021524 5.335438633 0.225082428 0.080620992 0.671393296 32487.23376 -4.511712733 0.488018044 ISMPDLDLHLKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK 211.49 2.27E-09 2523600000 5399010 5070200 5129700 6390630 3026740 5825230 6033220 6115710 2432940 TRUE FALSE 5143809.497 5586859.144 5364901.819 5748231.731 3554602.498 5623500.824 5112741.481 5580186.011 2810227.909 1.830388731 1.988044858 1.909062892 2.045468167 1.264880505 2.001083544 1.819333394 1.98567027 1 21.42225571 ISMPDVDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 183.99 5.11E-06 2184793000 4278790 4286780 3319190 4715230 2714730 3582640 3768200 4051100 2384980 FALSE TRUE 4076540.076 4723607.756 3471378.145 4241246.122 3188178.052 3458572.278 3193291.882 3696364.208 2754830.518 1.479778901 1.714663652 1.260105884 1.539566988 1.157304608 1.255457371 1.159160922 1.341775541 1 21.39353213 3.047225547 0.941029154 1.176008849 1.589434539 0.527500293 0.143526532 0.370377379 0.720793944 0.063835759 0.083535914 1114.873382 -3.047225547 0.413425691 ISMPDVDLHLKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISMPDVDLHLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 151.54 4.15E-06 1633480000 3430500 2050080 3220700 2965100 2482700 3259600 4529300 3963900 2983200 FALSE TRUE 3268347.064 2258985.483 3368372.281 2667042.515 2915682.094 3146719.235 3838272.099 3616799.902 3445819.42 0.948496327 0.655572799 0.977524319 0.773993698 0.846150578 0.913199112 1.11389241 1.049619687 1 21.71641567 1.955744408 3.380529724 1.062854335 0.829329235 0.52321602 0.092541255 0.169659156 3.696026038 0.042049976 0.024178977 90.31178126 -1.955744408 -0.2335251 ISMPDVDLHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISMPDVDLHVK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 112.13 0.00089889 0 426300 347760 333830 446910 349210 364320 444990 414290 337380 FALSE TRUE 406149.6438 383197.1394 349136.4357 401985.7577 410112.1134 351703.507 377098.6027 378012.5713 389699.1673 1.042213271 0.983315263 0.895912707 1.031528398 1.052381293 0.902500022 0.967665919 0.970011237 1 18.57200132 2.23905834 24.99996576 0.956496177 0.998993913 0.144240962 0.049175164 26.25994431 1319090.884 0.017536662 0.013851585 173.403692 -2.23905834 0.042497736 ISMQDVDLSLGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ISMQDVDLSLGSPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMQDVDLSLGS(1)PK;ISMQDVDLS(0.006)LGS(0.994)PK;ISMQDVDLS(0.03)LGS(0.97)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK 263.15 1.40E-24 1808934000 3674956 2986875 3213729 3885809 2322602 3363188 3505999 3499519 2325498 TRUE FALSE 3501248.113 3291240.958 3361081.653 3495200.097 2727663.053 3246719.956 2971094.46 3193082.564 2686124.353 1.303457194 1.225274978 1.251275523 1.301205617 1.015464176 1.20870054 1.106089693 1.18873222 1 21.35709466 8 0.059560723 0.713511711 2.173440958 0.547633234 0.07190085 234.9205709 1.045830185 5.225425214 29.81847273 100000000 -8 1.459929246 ISMS(ph)EVDLNVAAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(0.102)MS(0.898)EVDLNVAAPK;IS(0.126)MS(0.874)EVDLNVAAPK 129.01 0.00016882 20508000 57901 48775 56520 63364 47843 57185 70341 61887 44873 TRUE FALSE 55164.13448 53745.22795 59111.49791 56994.53034 56186.80405 55204.66911 59609.18855 56467.8462 51831.67566 1.064293866 1.036918588 1.140451223 1.099608099 1.084024457 1.06507591 1.150053279 1.089446665 1 15.66154641 3.763464258 24.9646882 1.097783024 1.050606223 0.109502573 0.041926998 1099.79426 1102487.104 0.009747911 0.017567498 5800.484328 -3.763464258 -0.047176801 ISNDNPEEHVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISNDNPEEHVLK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 117.7 0.00070489 107370000 293100 246930 267530 306440 229680 287220 298960 290030 346180 FALSE TRUE 279245.7439 272092.4477 279796.5151 275636.069 269736.1193 277273.4994 253348.1612 264633.4357 399863.8264 0.698352103 0.680462772 0.6997295 0.689324842 0.674569945 0.693419812 0.633586097 0.661808891 1 18.60914925 -1.99166219 3.008026679 1.303626991 0.67832149 0.963201508 0.019723483 547778.5723 3877115.507 1129375.627 0.005010001 0.01019384 1.99166219 -0.625305501 ISNLS(ph)PEEEQGLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 306.26 1.66E-44 988160000 2075230 1748280 1795090 2044370 1316853 2027610 2266980 2238490 1537525 TRUE FALSE 1977137.991 1926431.72 1877396.652 1838866.044 1546511.746 1957393.357 1921110.565 2042475.949 1775956.524 1.113280626 1.084729098 1.057118587 1.035422894 0.870804958 1.10216288 1.08173288 1.150070917 1 20.76016483 -0.833938136 7.413813807 1.000001797 1.063545558 0.063179138 0.074693568 1.07E-09 3.67E-19 0.071490407 0.016850451 0.146575662 0.833938136 0.063543761 ISNYGWDQSDKFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISNYGWDQSDKFVK 14 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 205.28 1.14E-08 1534270000 1726130 1461650 1444620 1826790 1095200 1791370 2036220 1729110 1331920 FALSE TRUE 1644539.256 1610593.797 1510857.256 1643157.599 1286202.533 1729334.408 1725557.241 1577699.962 1538467.351 1.068946478 1.046882013 0.982053506 1.068048404 0.836028488 1.124063118 1.121607969 1.025501101 1 20.5530624 ISPDTVLHLILPESPGSHEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISPDTVLHLILPESPGSHEESR 22 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 110.38 0.00020774 5782200 7239.2 8965.3 9115.4 9722.7 8486.8 8177.1 8978.8 10609 7144.3 FALSE TRUE 6897.017363 9878.874263 9533.350106 8745.355724 9966.895233 7893.924977 7608.919153 9680.019718 8252.201556 0.835779073 1.197119847 1.155249304 1.059760315 1.207786209 0.956584122 0.922047178 1.173022696 1 13.01056334 ISPFEHQTYCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISPFEHQTYCQR 12 0 P28482;P28482-2;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P28482;P27361 MAPK1;MAPK3 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 165.58 5.42E-05 1289860000 951470 766030 797160 839160 1147210 799060 1205140 1072890 1196070 FALSE TRUE 906495.8987 844089.3279 833710.5745 754806.0425 1347283.061 771388.3518 1021273.759 978942.0639 1381550.427 0.65614391 0.610972507 0.603460111 0.546347081 0.975196442 0.558349762 0.739222933 0.708582217 1 20.39785679 -5 0.169705334 2.314925772 0.588473548 0.449765231 0.11835314 114.0991522 1.075385076 50.27088908 0.386976374 1.00E-05 5 -1.726452224 ISQAEEEDQQLLGHLLLVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISQAEEEDQQLLGHLLLVAK 20 0 Q9BX68 Q9BX68 HINT2 "Histidine triad nucleotide-binding protein 2, mitochondrial" 0 106.94 0.00023394 9733800 21304 18159 18954 21718 17052 19903 17397 23547 18071 FALSE TRUE 20297.00214 20009.42275 19823.05965 19534.86538 20025.8634 19213.75412 14742.76813 21485.09985 20873.35839 0.972387949 0.958610607 0.949682331 0.935875532 0.959398245 0.920491747 0.706295933 1.029307285 1 14.34937512 1.990791126 24.60095343 0.862773934 0.954746664 0 0.089305508 565.6866945 1511198.122 0.032046697 0.022399238 97.90190124 -1.990791126 0.09197273 ISQMPVILTPLHFDRDPLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISQMPVILTPLHFDRDPLQK 20 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 231.6 5.29E-26 267970000 599220 536470 506820 649170 434000 595920 667020 676310 466810 FALSE TRUE 570896.0581 591136.9029 530058.1983 583914.1983 509689.4626 575283.141 565253.8483 617088.7111 539200.5107 1.058782488 1.096321111 0.983044689 1.0829259 0.94526888 1.066918761 1.048318459 1.144451273 1 19.04046234 -0.618717927 6.798510856 1.000000078 1.053251021 0.082910385 0.0556616 0 0 0.049032599 0.011557094 0.240592494 0.618717927 0.053250943 ISQRDPS(ph)PESNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 ISQRDPSPESNK 12 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 IS(0.001)QRDPS(0.976)PES(0.023)NK;ISQRDPS(1)PESNK;ISQRDPS(0.978)PES(0.022)NK;IS(0.002)QRDPS(0.998)PESNK;ISQRDPS(0.999)PESNK 131.39 0.00012089 1681200000 1868880 1656780 1634420 1973740 1228120 1833890 1830610 1952130 1270110 TRUE FALSE 1780541.746 1825607.766 1709359.774 1775335.905 1442303.739 1770381.929 1551316.823 1781191.148 1467072.172 1.213670179 1.244388518 1.165150431 1.210121724 0.9831171 1.206744946 1.057423658 1.214112831 1 20.48450841 7.999999949 0.071940532 0.857523659 1.862031573 0.344427022 0.077623049 223.3945756 1.183687173 2.802841092 22.62210215 99999988.32 -7.999999949 1.004507914 ISQRDPS(ph)PESNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISQRDPSPESNKK 13 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 IS(0.002)QRDPS(0.954)PES(0.044)NKK;ISQRDPS(0.999)PES(0.001)NKK 78.441 0.012116 216335000 545630 498500 487240 572510 300860 628360 602460 628750 345180 TRUE FALSE 519839.1512 549297.7167 509580.4359 514960.2071 353329.8887 606599.7356 510543.6621 573693.3168 398708.7515 1.303806724 1.377691648 1.278076877 1.291569862 0.886185436 1.521410637 1.280492741 1.438878165 1 18.60497575 3.544799038 3.984292201 1.257151642 1.34051597 0.042566963 0.185947234 0.876149595 26.97385955 0.047753556 0.07427926 3505.896077 -3.544799038 0.083364328 ISQRDPS(ph)PESNKKGESPSLESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISQRDPSPESNKKGESPSLESR 22 3 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.964)PES(0.028)NKKGES(0.006)PS(0.001)LESR;IS(0.001)QRDPS(0.772)PES(0.226)NKKGES(0.001)PSLESR 114.91 0.0011755 931310000 835130 428450 876200 648510 600930 897890 1265310 983630 766080 TRUE FALSE 795655.06 472109.5421 916374.6367 583320.5427 705732.0017 866795.8442 1072263.72 897498.1426 884879.7738 0.899167416 0.533529589 1.035592251 0.65920881 0.797545636 0.979563405 1.211762041 1.014259981 1 19.75512193 2.137871508 3.352434877 1.09833256 0.764939973 0.461090477 0.144278645 0.178085708 3.942353523 0.055792684 0.038703678 137.3635505 -2.137871508 -0.333392587 ISQTVEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISQTVEILK 9 0 E7EQM7;C9JM82;E7EPG2;B4DJ62;E7EX32;G3XAH0;Q99719-2;Q99719;F8W9E5 E7EQM7 5-Sep Septin-5 0 ; 126.41 0.0011033 133222000 448790 379250 426050 372270 382030 444320 519500 485310 442460 FALSE TRUE 427576.5861 417896.0062 445584.8139 334848.7123 448655.911 428933.087 440240.7337 442813.6836 511074.437 0.836622917 0.817681292 0.871858934 0.655185797 0.877868034 0.839277131 0.861402375 0.866436768 1 18.96317391 0.672399105 0.69318353 1.00129965 0.81209647 0.47194948 0.060982356 1.036221245 0.948827505 0.058980099 0.021227527 4.703261277 -0.672399105 -0.18920318 ISQTYQQQYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISQTYQQQYGR 11 0 P09525;Q6P452;P09525-2;B4E1S2 P09525 ANXA4 Annexin A4;Annexin 0 ; 179.42 7.12E-05 72961000 80938 56655 41785 65922 91090 52412 73447 57010 102739 FALSE TRUE 77112.22114 62428.20891 43700.88358 59295.39532 106976.0672 50596.9593 62241.3112 52017.90217 118671.2394 0.649797049 0.526060141 0.368251683 0.499661044 0.901448975 0.426362441 0.524485221 0.438336217 1 16.85661081 -1.360186368 5.276636767 1.000191622 0.544475035 0.485708831 0.148151881 0.000316034 3.83E-05 0.135741408 0.031981279 0.043632855 1.360186368 -0.455716587 ISRPGDSDDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 ISRPGDSDDSR 11 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;;;;;; 144.57 3.34E-05 12277450000 9946670 8873710 7985270 10455080 8289400 8524470 9988520 9595370 8740010 FALSE TRUE 9476510.622 9777951.138 8351402.528 9404115.495 9735068.735 8229265.466 8464587.822 8755148.535 10095366.11 0.938699054 0.968558349 0.827251081 0.93152793 0.964310618 0.815152752 0.838462689 0.867244282 1 23.2671899 2.244424868 24.99987816 0.861879447 0.928767874 0.085739544 0.062446674 211.0903279 899901.2717 0.020562648 0.016776372 175.5597155 -2.244424868 0.066888427 ISS(ph)LLEEQFQQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISSLLEEQFQQGK 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 1 IS(0.021)S(0.979)LLEEQFQQGK 121.76 0.0002548 17233000 68045 59019 54074 77557 48333 60495 73169 67192 51494 TRUE FALSE 64828.6477 65033.1032 56553.34639 69760.82301 56762.2599 58400.04298 62005.72521 61308.31227 59479.42653 1.089933974 1.093371389 0.950805172 1.172856349 0.954317538 0.981852825 1.042473488 1.030748207 1 15.86010312 3.913969041 0.619913022 1.012606325 1.115605864 0.146252746 0.063979286 2.611126276 1.469324144 0.032614565 0.168973808 8202.930662 -3.913969041 0.102999539 ISS(ph)PTETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 IS(0.051)S(0.934)PT(0.015)ETER;IS(0.027)S(0.905)PT(0.069)ETER 175.66 0.00083959 714850000 1453740 1288080 1193020 1487860 1135590 1356980 1468910 1419580 1218980 TRUE FALSE 1385024.591 1419336.816 1247721.147 1338297.486 1333636.536 1309987.442 1244800.801 1295274.05 1408013.193 0.983673021 1.008042271 0.886157284 0.950486468 0.947176165 0.930380091 0.884083194 0.919930336 1 20.42522942 3.752562073 24.98352749 0.925310822 0.995857652 0.378896728 0.033788025 641.461132 1144589.687 0.008141428 0.014592839 5656.68602 -3.752562073 0.07054683 ISSDLDGHPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 ISSDLDGHPVPK 12 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;;;;; 118.61 0.00060734 6962420000 16960580 14510340 13556660 16130200 12752620 14520370 17891090 15802550 12102230 FALSE TRUE 16158887 15988960.14 14178246.27 14508761.65 14976672.89 14017525.95 15161475.63 14418794.95 13978982.02 1.155941611 1.143785729 1.014254561 1.037898298 1.071370782 1.002757277 1.084590824 1.031462443 1 23.73675597 3.749803116 23.49386787 1.040457101 1.149863704 0.749935857 0.027506368 135.5444873 283250.2837 0.006480783 0.011528729 5620.864497 -3.749803116 0.109406603 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR 34 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;; 250.08 4.30E-48 1904019000 558832 439926.3 477024 523545 616710 457298 747124 566945 368892.1 FALSE TRUE 532417.1189 484755.2901 498896.0222 470917.2619 724264.0287 441461.6556 633136.5119 517300.2902 426098.0028 1.249517987 1.137661493 1.170848065 1.10518533 1.699759266 1.036056618 1.485894108 1.214040636 1 18.70082576 ISSIQSIVPALEIANAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 215.81 9.31E-19 1272760000 923490 775120 798990 825920 867820 682290 867050 823780 831690 FALSE TRUE 879838.4579 854105.6092 835624.4818 742896.9525 1019167.533 658662.1262 734765.598 751645.4561 960664.2375 0.915864694 0.889078177 0.869840314 0.773315924 1.060898796 0.685631983 0.76485162 0.782422647 1 19.87367276 2.212938742 24.99999768 0.782404626 0.894050792 0.140925911 0.105684434 327.0820243 319141.1998 0.035200272 0.026006395 163.282162 -2.212938742 0.111646166 ISSLPVSRPIS(ph)PSPSAILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.911)PS(0.076)PS(0.012)AILER;ISSLPVSRPIS(0.98)PS(0.019)PS(0.002)AILER;ISSLPVSRPIS(0.991)PS(0.007)PS(0.002)AILER;ISSLPVSRPIS(0.967)PS(0.023)PS(0.01)AILER;ISSLPVSRPIS(0.908)PS(0.092)PSAILER 297.95 6.50E-55 2589818000 1723842 1456803 1465461 1703258 1546209 1572722 1750039 1684382 1707095 TRUE FALSE 1642359.405 1605252.882 1532653.836 1532043.27 1815867.36 1518258.243 1483038.409 1536888.583 1971822.574 0.832914394 0.814096006 0.777277762 0.776968116 0.92090809 0.769977108 0.752115545 0.779425392 1 20.91109831 -1.094784333 5.346249265 1.000002858 0.802488126 0.627369417 0.047722432 1.62E-06 2.74E-07 0.045994658 0.010840888 0.080392525 1.094784333 -0.197514732 ISSLPVSRPISPS(ph)PSAILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.25)PS(0.543)PS(0.208)AILER 123.65 1.71E-05 103620000 63508 53687 53348 63284 59276 51777 67265 61677 65846 TRUE FALSE 60506.1027 59157.76634 55794.05857 56922.57209 69613.71563 49983.94951 57002.48884 56276.23491 76057.06139 0.795535636 0.777807678 0.733581571 0.748419293 0.915282741 0.657190123 0.74947004 0.739921237 1 16.21479458 -1.580881772 6.890803504 1.00030435 0.764801754 0.568067721 0.06449436 0.000279637 1.70E-05 0.057907772 0.013631672 0.02624933 1.580881772 -0.235502595 ISSPTETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;; 193.29 7.85E-05 5341412000 2318088 1861594 1876032 2273611 2019600 2037941 2357737 2094417 2201362 FALSE TRUE 2208516.574 2051292.545 1962049.923 2045063.303 2371817.601 1967366.592 1998020.918 1911018.744 2542737.976 0.868558458 0.806725885 0.771628827 0.804276069 0.932780972 0.77371975 0.785775387 0.751559446 1 21.27795137 -1.187409441 4.847812347 1.00002148 0.813224248 0.553889531 0.053045846 1.20E-05 2.01E-06 0.050007693 0.011785572 0.064951705 1.187409441 -0.186797232 ISTAS(ph)GDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.002)T(0.146)AS(0.852)GDGR;IST(0.004)AS(0.996)GDGR;IST(0.001)AS(0.999)GDGR;IST(0.001)AS(0.999)GDGR;IS(0.027)T(0.147)AS(0.826)GDGR;IS(0.005)T(0.132)AS(0.863)GDGR;IST(0.001)AS(0.999)GDGR;IST(0.009)AS(0.991)GDGR 155.53 7.67E-05 3121340000 4405720 3608460 3756820 4397430 3994340 3559250 4269660 3886310 3899510 TRUE FALSE 4197470.347 3976166.176 3929073.913 3955391.982 4690951.631 3435992.28 3618244.949 3546004.094 4504226.095 0.931896015 0.882763452 0.872308323 0.878151296 1.041455631 0.762837435 0.803300028 0.787261567 1 22.10284782 2.202685507 24.99996873 0.81784759 0.912830604 0.185993644 0.080283856 229.3215325 159803.9214 0.026996393 0.019938841 159.4723915 -2.202685507 0.094983014 ISTKNEEPVRS(ph)PERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISTKNEEPVRSPERR 15 3 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 ISTKNEEPVRS(1)PERR 92.474 0.028894 541420000 351980 237730 337710 320770 230960 315910 445030 414570 388680 TRUE FALSE 335342.603 261954.9573 353194.3375 288525.5902 271239.3509 304969.9575 377132.5 378268.053 448954.5093 0.746941162 0.583477728 0.786704065 0.642661081 0.60415776 0.679289218 0.84002386 0.842553188 1 18.77620974 1.34311791 1.264848217 0.98035447 0.667479265 0.726327613 0.066626294 0.202397195 0.626798357 0.057982884 0.018857881 22.03524636 -1.34311791 -0.312875205 ISTLYYQLGDHELSLSEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISTLYYQLGDHELSLSEVR 19 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 161.22 3.00E-11 71177000 61737 56182 62164 65994 71772 58374 66382 57348 67157 FALSE TRUE 58818.81436 61907.00967 65014.28089 59360.15774 84289.01408 56352.49374 56254.20671 52326.3051 77571.36457 0.758254218 0.79806524 0.838122176 0.765232867 1.086599605 0.726460003 0.72519295 0.674556976 1 16.24323656 -0.72907712 7.042239074 0.999999994 0.795021758 0.245162537 0.112156795 7.77E-10 1.10E-10 0.104268969 0.024576431 0.18660483 0.72907712 -0.204978236 ISVAGVTSSNVGYLAHAIHQVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISVAGVTSSNVGYLAHAIHQVTK 23 0 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 310.4 2.15E-73 202251000 722660 486240 629310 586560 625930 533290 691290 640530 90548 FALSE TRUE 688501.294 535788.4088 658164.486 527597.8744 735091.9938 514822.0336 585821.0141 584441.7975 104589.7214 6.582877216 5.122763516 6.292821869 5.044452432 7.028338771 4.922300459 5.601133709 5.587946787 1 16.67438155 -0.800903029 0.56190247 1.13E-18 5.868208121 0.832649041 0.674844426 5.841209643 1.228125323 11.27494542 0.250867489 0.158160115 0.800903029 5.868208121 ISVSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISVSSPGR 8 0 O75864;O75864-2 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 IS(0.006)VS(0.158)S(0.836)PGR;IS(0.005)VS(0.157)S(0.838)PGR 128.27 0.0011966 358100000 1506170 1615540 1536970 1662170 1481200 1494940 1746480 1722860 1706210 TRUE FALSE 1434976.329 1780165.363 1607441.595 1495085.514 1739520.811 1443169.853 1480022.4 1571997.245 1970800.333 0.728118575 0.903270277 0.815628843 0.75861846 0.882646903 0.732276035 0.750975315 0.797644094 1 20.91035019 -1.39289315 5.721749327 1.000068066 0.797398056 0.539584796 0.059168467 5.03E-05 5.34E-06 0.056113285 0.013221597 0.040467544 1.39289315 -0.202670009 ISVYYNEATGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISVYYNEATGGK 12 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;; 208.74 1.47E-07 461390000 799360 683740 679890 814500 654240 778970 874550 848930 770170 FALSE TRUE 761575.837 753413.8833 711063.629 732624.9126 768339.2489 751994.0736 741121.3353 774593.1887 889604.0301 0.856084068 0.846909252 0.799303516 0.82354046 0.86368679 0.84531325 0.833091252 0.870716816 1 19.7628038 0.786182837 2.82996156 0.999983635 0.83945592 0.888486316 0.017902964 0.349139268 4.109194804 0.017631725 0.004645214 6.111992838 -0.786182837 -0.160527715 ISWYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ISWYLR 6 0 M0QYT0;M0R076;Q13011;M0R248;M0QZW4 M0QYT0;Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ; 140.72 0.027321 1075040000 1055700 775520 505370 535370 1101460 582520 1120390 815820 1043350 FALSE TRUE 1005799.153 854546.3697 528541.7144 481553.5905 1293554.275 562347.1863 949453.9281 744382.4759 1205147.389 0.834586012 0.709080381 0.438570186 0.399580661 1.073357738 0.466621088 0.787832208 0.617669243 1 20.20077817 -1.516274938 2.812072243 1.014057547 0.676647956 0.206900083 0.204606389 28092643.6 29453344.81 3027944.211 0.050302396 0.030459661 1.516274938 -0.337409591 ISY(ph)TPPESPVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.102)Y(0.447)T(0.447)PPES(0.004)PVPSYASSTPLHVPVPR 120.32 0.0015418 81662000 95050 66728 73379 89884 100860 72776 99716 88386 99015 TRUE FALSE 90557.17487 73527.65906 76743.49973 80848.68955 118449.9521 70255.74887 84502.49279 80646.45328 114369.7405 0.791793131 0.642894342 0.671012275 0.706906295 1.035675621 0.614286161 0.738853585 0.705138028 1 16.80334587 -1.637182207 2.671036502 1.028581887 0.733725137 0.331224382 0.116694077 19418649.12 17562519.09 3833753.965 0.026706634 0.023057796 1.637182207 -0.29485675 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.394)Y(0.149)T(0.458)PPES(0.998)PVPSYAS(0.001)S(0.001)T(0.001)PLHVPVPR;IS(0.039)Y(0.067)T(0.895)PPES(0.959)PVPS(0.011)YAS(0.012)S(0.014)T(0.004)PLHVPVPR;IS(0.019)Y(0.095)T(0.888)PPES(0.996)PVPS(0.002)YASSTPLHVPVPR;IS(0.016)Y(0.008)T(0.975)PPES(0.999)PVPS(0.001)YASSTPLHVPVPR 145.33 5.02E-07 446929000 261637 196655 220014 241678 248716 223387 258562 229880 261578 TRUE FALSE 249269.9375 216694.3681 230101.8595 217384.0683 292091.9917 215651.0522 219113.6181 209750.4885 302142.1803 0.825008734 0.717193369 0.761568144 0.719476069 0.96673689 0.713740306 0.725200361 0.69421121 1 18.20486808 -1.141826108 3.851576532 1.000104251 0.763955425 0.457882381 0.080212496 4791062.342 2132410.772 4472.779821 0.017646176 0.072139627 1.141826108 -0.236148826 ISYT(ph)PPESPVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.015)Y(0.014)T(0.949)PPES(0.022)PVPSYASSTPLHVPVPR 123.62 0.00059014 109050000 115750 97080 114720 137770 131750 111360 129140 116980 127990 TRUE FALSE 110278.7269 106972.5624 119980.0255 123921.0979 154727.1583 107503.5753 109437.3212 106736.6111 147838.0355 0.745942859 0.723579436 0.811563987 0.838222027 1.046599123 0.727171292 0.740251457 0.721983424 1 17.17365797 3.662444525 4.5188117 0.827392846 0.734706597 0.132861448 0.10906001 0.468859625 17.8731959 0.029331334 0.04700997 4596.682688 -3.662444525 -0.092686249 IT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 33 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IT(0.996)PEPAVS(0.004)NTEEPSTTSTASNYPDVLTRPSLHR 136 3.71E-08 163670000 46050 50139 39865 50282 25608 45587 42959 43633 28188 TRUE FALSE 43873.30776 55248.2211 41692.84968 45227.55783 30074.02709 44008.31076 36404.81555 39812.26321 32559.25108 1.347491306 1.696851717 1.28052238 1.38908471 0.923670726 1.351637685 1.118109734 1.222763482 1 14.99077989 3.237060045 1.913119254 1.15277112 1.511494847 0.4555942 0.160563809 0.253117595 1.907371294 0.046143731 0.064054533 1726.076522 -3.237060045 0.358723726 ITADLLSNGIDVYPQKEFDEDSEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITADLLSNGIDVYPQKEFDEDSEDR 25 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 169.41 9.06E-12 93113000 82766 117660 78416 115300 57975 97301 88745 97750 58748 FALSE TRUE 78853.81521 129649.6878 82011.45116 103709.8249 68085.82164 93931.44197 75205.32034 89190.49179 67858.3398 1.162035727 1.910593276 1.208568489 1.528328357 1.003352305 1.384228413 1.108269382 1.314363011 1 16.05023851 2.755493864 24.42950297 1.182091962 1.482944318 0.269526972 0.233837005 750.2369668 1082361.084 0.06646748 0.070320345 569.5001775 -2.755493864 0.300852355 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK ddPTM_SK-BR-3_Trastuzumab_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 ; 270.85 1.84E-71 538790000 155551 145577 152959 153518 129949 179322 204392 189069 142629 FALSE TRUE 148198.4125 160411.4618 159972.3214 138086.079 152612.0645 173112.0342 173208.2465 172513.116 164747.1769 0.899550544 0.973682614 0.971017073 0.838169622 0.926340999 1.050773904 1.051357903 1.047138527 1 17.32989422 2.241191535 24.97603072 1.04297092 0.925255357 0.667638957 0.040387393 39.91069951 378886.9266 0.014336043 0.011485963 174.2575224 -2.241191535 -0.117715563 ITDDSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITDDSRR 7 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 73.324 0.078893 349630000 528140 354880 403070 507810 506640 460820 670030 536810 712570 FALSE TRUE 503175.8689 391042.6755 421551.1582 456763.974 594997.8556 444861.6879 567804.6176 489804.0706 823071.7163 0.611339035 0.475101583 0.512168199 0.554950395 0.722899164 0.540489582 0.689860441 0.595092822 1 19.65065862 -5 0.189884772 2.828618418 0.50540224 0.781551273 0.07003667 57.50389499 0.562274033 39.59126083 0.176950006 1.00E-05 5 -2.323216178 ITDFENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ITDFENRR 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 118.5 0.0030073 675890000 1245250 1181190 1117240 1236540 1236070 1173060 1266330 1264520 1113450 FALSE TRUE 1186389.5 1301554.604 1168466.559 1112240.65 1451640.217 1132436.638 1073128.101 1153791.925 1286118.139 0.922457638 1.012002369 0.908521949 0.864804419 1.128698968 0.880507477 0.8343931 0.897111929 1 20.29459174 ITDFIKFDTGNLCMVTGGANLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITDFIKFDTGNLCMVTGGANLGR 23 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 121.46 6.32E-05 21662000 24777 14255 19042 21090 21773 22914 29636 23358 29747 FALSE TRUE 23605.84031 15707.60071 19915.09454 18969.99313 25570.20431 22120.48243 25114.4839 21312.64969 34360.01283 0.687014886 0.457147696 0.579600905 0.552095054 0.744184946 0.643785628 0.730921843 0.620274788 1 15.06844295 -1.247471485 0.234771805 1.300879622 0.539888518 0.69072734 0.080572577 10.33146678 0.50302023 2.06986462 0.149089372 0.056562489 1.247471485 -0.760991104 ITDKEAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ITDKEAAER 9 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;; 110.39 0.0020932 2916340000 4783110 3707940 4220950 4882500 3646690 4664000 5638170 5043350 4393130 FALSE TRUE 4557021.87 4085783.302 4414484.733 4391701.824 4282671.581 4502484.511 4777963.614 4601727.538 5074394.163 0.898042549 0.805176573 0.86995306 0.865463281 0.843976925 0.887294988 0.941583066 0.906852599 1 22.27480416 1.347738312 0.694161875 0.994541094 0.849915349 0.708504096 0.028696923 0.32184615 0.354975485 0.026269611 0.011413969 22.27092788 -1.347738312 -0.144625745 ITDLYTDLRDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITDLYTDLRDGR 12 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 126.12 0.00026737 134910000 88650 48096 102180 87447 101810 84366 122730 103300 146100 FALSE TRUE 84459.69019 52997.03708 106865.0541 78656.66142 119565.6318 81444.38427 104005.2844 94254.50437 168756.4418 0.500482762 0.314044528 0.633250221 0.466095757 0.708510031 0.482614965 0.616304085 0.55852389 1 17.36458305 -5 0.145896986 2.705573149 0.360310309 0.685330999 0.101841417 70.1174503 0.615461061 34.59247862 0.509614474 1.00E-05 5 -2.345262839 ITDQY(ph)RPKWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITDQYRPKWR 10 2 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 1 ITDQY(1)RPKWR 62.303 0.069274 295290000 49074 36208 23661 31119 69281 25671 66540 36285 24318 TRUE FALSE 46754.36928 39897.63637 24745.88025 27990.859 81363.58446 24782.00683 56388.10091 33107.69304 28089.11124 1.664501553 1.420395114 0.880977687 0.996502123 2.896623669 0.882263829 2.007471879 1.17866645 1 14.77772336 ITEAEKNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 ITEAEKNER 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 192.12 3.20E-05 6173090000 4674650 3621420 3944080 4512410 3246790 4264210 4876930 4672750 3627170 FALSE TRUE 4453688.559 3990446.815 4124919.969 4058813.974 3813029.148 4116539.338 4132864.758 4263579.238 4189652.999 1.063020866 0.95245282 0.98454931 0.968770916 0.910106195 0.982548994 0.986445598 1.017644955 1 21.99839933 -1.026742583 7.037226475 1.000000002 0.982871752 0.01748027 0.039535804 1.37E-09 2.39E-10 0.037678242 0.008880845 0.094028047 1.026742583 -0.017128251 ITEFCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;;;; 186.43 0.00059898 11710410000 7977330 6015520 5136940 7000970 6986260 5975370 8344080 6960440 7233900 FALSE TRUE 7600257.42 6628508.327 5372473.78 6297219.195 8204661.532 5768441.439 7071037.346 6350946.974 8355696.266 0.909589959 0.793292159 0.642971406 0.753643861 0.981924339 0.690360355 0.846253516 0.760073939 1 22.99432862 -1.331881702 4.690977838 1.000145572 0.801752748 0.292894273 0.098778053 0.000141501 2.02E-05 0.08999121 0.021195621 0.046571293 1.331881702 -0.198392825 ITES(ph)EEVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ITES(1)EEVVSR 146.5 2.99E-05 112550000 113450 115090 112300 136170 105930 115390 144140 116490 98508 TRUE FALSE 108087.4433 126817.8018 117449.0661 122481.9329 124404.1585 111394.0154 122148.7957 106289.518 113784.1175 0.949934364 1.114547483 1.032209667 1.076441383 1.093335003 0.978994413 1.073513583 0.934133167 1 16.79593967 1.24106783 24.99999129 0.967066575 1.046287093 0.27948908 0.05239074 75.97428292 757619.9046 0.035927031 0.011744565 17.42078937 -1.24106783 0.079220518 ITESEEVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 204.86 4.17E-07 1511500000 1109318 907679 909512 1131422 942143 940186 1157586 1014095 1050717 FALSE TRUE 1056882.737 1000172.522 951214.0248 1017689.311 1106452.441 907627.1231 980974.9952 925295.4657 1213656.826 0.870825026 0.824098296 0.783758641 0.838531362 0.911668288 0.747844946 0.808280376 0.762402885 1 20.21092911 2.23082957 24.99973673 0.810729174 0.841949082 0 0.075667661 655.2496327 2118847.374 0.024971268 0.018798567 170.1490663 -2.23082957 0.031219909 ITFDAFPGEPDKELNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ITFDAFPGEPDKELNPK 17 1 Q12904;Q12904-2 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 150.28 2.68E-07 310940000 650990 554240 570360 677890 399350 671120 722310 729620 475100 FALSE TRUE 620218.9928 610717.6861 596511.5702 609747.2093 468996.5136 647878.9461 612108.3434 665730.6048 548776.0815 1.130185906 1.112872275 1.086985367 1.111103836 0.854622731 1.180588892 1.115406382 1.213118843 1 19.06585808 -1.51407571 7.31711111 0.999971976 1.100715349 0.099860789 0.094929488 4.05E-05 2.69E-06 0.085843568 0.020227899 0.030614297 1.51407571 0.100743373 ITFDDYIACCVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITFDDYIACCVK 12 0 C9J0K6;P30626-3;P30626-2;P30626;B4DHQ6 C9J0K6 SRI Sorcin 0 86.189 0.018233 0 91583 72590 67465 93032 81664 79463 98320 97083 89034 FALSE TRUE 87254.05309 79987.00353 70558.33698 83680.24661 95906.17574 76711.17639 83319.47823 88581.89785 102840.938 0.848436963 0.777773959 0.686091924 0.813686147 0.932568077 0.745920621 0.810178124 0.861348599 1 16.65005515 0.86223635 2.342782206 0.999770279 0.800985283 0.491603506 0.063732006 0.44642712 4.792437977 0.059164858 0.016022585 7.281759814 -0.86223635 -0.198784997 ITFHGEGDQEPGLEPGDIIIVLDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ITFHGEGDQEPGLEPGDIIIVLDQK 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;;; 242.43 1.17E-38 265190000 376102 399613 350458 452700 268895 427555 406867 435567 249841 FALSE TRUE 358324.4038 440334.019 366526.846 407193.7359 315790.2029 412748.6631 344791.9665 397426.4444 288585.0663 1.241659551 1.525837857 1.270082512 1.411000719 1.094270771 1.430249557 1.194767182 1.377155268 1 18.13863712 -4.18414752 0.194401282 1.41E-12 1.384905061 0.37546579 0.12668254 92.16161691 1.20722131 36.21705185 0.295305018 6.54E-05 4.18414752 1.384905061 ITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTR 32 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 122.68 1.04E-07 27275000 60478 32319 68349 50360 66427 60998 94261 70870 54397 FALSE TRUE 57619.3248 35612.34284 71482.86926 45297.71712 78011.84777 58885.62397 79879.75323 64664.24709 62832.60894 0.917029004 0.566781221 1.137671513 0.720926886 1.241582183 0.937182539 1.271310464 1.029151076 1 15.93922586 3.068624872 1.175964392 1.11418759 0.769493043 0.258087008 0.187094346 0.457034243 1.345197206 0.069390934 0.08981163 1171.183303 -3.068624872 -0.344694547 ITGMLLEIDNSELLHMLESPESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 170.55 5.92E-12 251650000 125329 110886 116846 135591 116853 113518 139102 141035 115330 FALSE TRUE 119404.9465 122185.4095 122203.5047 121961.1351 137232.1262 109586.8432 117879.4351 128685.2277 133214.7874 0.896334025 0.917206054 0.917341889 0.915522499 1.030156854 0.822632722 0.884882508 0.965998072 1 17.02339471 1.049019988 5.06987318 0.999512183 0.910319829 0.266252925 0.05060684 0.217931013 11.68151758 0.046422207 0.011742593 11.19489407 -1.049019988 -0.089192354 ITITNDKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 214.71 6.08E-07 12472360000 8363510 5081710 5456550 6706770 7308600 7162990 10969360 8391920 8702970 FALSE TRUE 7968183.457 5599542.026 5706738.215 6032592.738 8583217.526 6914933.86 9295782.666 7657078.996 10052582.14 0.79265042 0.557025245 0.567688792 0.6001038 0.853832121 0.687876385 0.924715913 0.761702704 1 23.26106279 1.858058722 0.75812272 0.94692676 0.635766928 0.521043501 0.103826803 0.49168054 0.539478568 0.08880573 0.043670519 72.12049876 -1.858058722 -0.311159832 ITKFENAFLSHVVSQHQALLGTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ITKFENAFLSHVVSQHQALLGTIR 24 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 212.9 9.19E-26 183526000 529160 356840 476560 443630 519790 405890 601280 520900 306420 FALSE TRUE 504147.6555 393202.4017 498410.7474 399035.4696 610441.2114 391833.9275 509543.6927 475287.2345 353938.0486 1.424395194 1.110935666 1.408186402 1.127416143 1.724712033 1.107069243 1.439640905 1.342854311 1 18.43313734 -0.808939425 6.351547694 0.999999991 1.326590216 0.235961714 0.189190194 2.13E-08 3.73E-09 0.158863165 0.037444407 0.155260355 0.808939425 0.326590225 ITKPGS(ph)IDSNNQLFAPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;ITKPGS(1)IDSNNQLFAPGGR 280.89 7.05E-40 1958850000 1426920 1182080 1218570 1927210 1279900 1817570 1983820 1665730 1404340 TRUE FALSE 1359472.319 1302535.296 1274442.64 1733483.189 1503114.155 1754627.095 1681151.824 1519869.851 1622117.875 0.838084791 0.802984368 0.785665863 1.068654268 0.926636823 1.08168902 1.036393131 0.936966341 1 20.62944723 3.243646402 24.99999507 1.013235094 0.811809093 0.773640388 0.050811919 51.31942411 252267.1311 0.013244444 0.017397642 1752.45309 -3.243646402 -0.201426001 ITKPGSIDSNNQLFAPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 191.64 8.40E-15 514420000 391500 377320 395890 432660 356300 410000 453920 445820 422150 FALSE TRUE 372994.5709 415769.337 414041.9481 389168.1948 418438.6072 395801.5972 384666.1672 406781.6374 487614.866 0.764936832 0.852659273 0.849116746 0.798105681 0.858133409 0.811709455 0.788872928 0.834227309 1 18.89538258 -2.535819773 1.405414394 2.029385242 0.818227414 0.780137397 0.030068208 88122.42674 5949.010441 286005.3346 0.00807581 0.002911925 2.535819773 -1.211157828 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_SK-BR-3_Trastuzumab_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 124.13 6.20E-05 7394900000 3175210 2568550 2913900 3328000 1971480 3175770 3515040 3262900 2406310 TRUE FALSE 3025124.116 2830288.165 3047505.197 2993463.117 2315305.488 3065792.289 2978756.09 2977183.178 2779468.265 1.088382319 1.018284037 1.096434608 1.076991292 0.83300303 1.103013957 1.071699982 1.071134078 1 21.40637748 -0.965405813 7.163006328 0.999999998 1.045795735 0.030862459 0.078863941 2.13E-09 2.97E-10 0.071360686 0.016819874 0.108291455 0.965405813 0.045795737 ITLDNAYMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ITLDNAYMEK 10 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 167.67 1.20E-05 759685000 1594770 1273377 1229642 1482500 1305900 1437290 1811440 1487030 1455610 FALSE TRUE 1519388.383 1403135.564 1286022.302 1333476.283 1533648.547 1387516.287 1535071.559 1356817.77 1681338.565 0.903677828 0.834534813 0.764880036 0.793103966 0.912159263 0.825245026 0.91300562 0.806986647 1 20.68117883 -2.087225978 0.373944415 1.169760447 0.842015358 0.466604731 0.051761472 42.18570879 2.308847648 6.132625618 0.035650685 0.00818039 2.087225978 -0.327745089 ITLQDVVSHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITLQDVVSHSK 11 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 132.59 0.00017941 135610000 772000 714200 698420 813210 481490 850630 902750 910770 512180 FALSE TRUE 735509.09 786977.792 730443.2478 731464.5858 565461.7036 821172.4698 765018.9074 831018.1505 591606.2585 1.243240888 1.330239125 1.234678027 1.236404408 0.955807508 1.388038848 1.293121728 1.404681135 1 19.17427779 3.623016559 9.599813461 1.232347994 1.286685739 0.029919811 0.14601904 1.656143863 127.2888457 0.037112996 0.057523293 4197.749895 -3.623016559 0.054337745 ITLY(ph)EGKHFT(ph)GQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITLYEGKHFTGQK 13 1 A0A2R8Y702;Q8WXF5-2;Q8WXF5 A0A2R8Y702 CRYGN Gamma-crystallin N 2 IT(0.002)LY(0.998)EGKHFT(1)GQK 56.404 0.056253 0 90237 70346 78533 97113 71973 78407 98094 92298 70665 TRUE FALSE 85971.67584 77514.33738 82133.81573 87351.01674 84525.06841 75691.74593 83127.95868 84215.89782 81623.36729 1.05327284 0.949658657 1.006253705 1.070171688 1.035549883 0.927329372 1.018433341 1.031762112 1 16.31669461 4.751526227 23.80127088 1.003546612 1.053272894 0.119553969 0.041114644 87.06969861 1357342.818 0.009627531 0.060783425 56432.10192 -4.751526227 0.049726282 ITNDFYPEEDGKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 ITNDFYPEEDGKTK 14 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 211.7 3.16E-09 531790000 761570 634520 705990 809850 461141 829260 856780 905230 535585 FALSE TRUE 725572.0954 699178.3094 738360.3398 728442.3394 541563.8444 800542.5183 726062.4752 825963.2623 618640.7864 1.172848786 1.130184632 1.193520305 1.177488383 0.875409214 1.294034496 1.173641459 1.33512578 1 19.23874243 ITPAHDQNDYEVGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 ITPAHDQNDYEVGQR 15 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;;;; 263.99 4.26E-25 3826160000 2040290 1748270 1826360 2182720 2014560 1866610 2214430 2012400 2060450 FALSE TRUE 1943849.535 1926420.701 1910100.413 1963308.839 2365898.626 1801968.828 1876578.033 1836183.588 2379974.063 0.816752403 0.809429284 0.802571945 0.82492867 0.994085887 0.757138011 0.788486758 0.771514117 1 21.18251442 -1.780030337 2.827006426 1.043195433 0.819028452 0.428848206 0.065037505 30018697.14 23340984.49 8952882.281 0.01512436 0.01659471 1.780030337 -0.224166981 ITPFNLQEEMEEGHFDADGNYFLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITPFNLQEEMEEGHFDADGNYFLNR 25 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 252.04 8.92E-45 71986000 16089 12665 13622 13177 14162 17662 19522 17819 13932 FALSE TRUE 15328.50486 13955.5779 14246.58217 11852.42293 16631.84832 17050.36051 16543.56035 16258.6739 16092.50341 0.952524568 0.867209877 0.885293097 0.73651828 1.03351529 1.059521945 1.028029011 1.010325957 1 13.97410115 2.694580926 24.76227063 1.03075185 0.873144952 0.688285307 0.055132608 238.325995 134186.5061 0.017505641 0.016504583 494.9723351 -2.694580926 -0.157606898 ITPLEIEVLEETVQTMDTS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ; 110.38 0.00055114 52976000 21891.7 19365.7 19223.2 20865.1 22542.7 18728.4 26065.2 25077.5 23034.3 FALSE TRUE 20856.92273 21339.08685 20104.60273 18767.70051 26474.13974 18079.83081 22088.47502 22881.58116 26606.3416 0.783907951 0.802030101 0.755631986 0.705384483 0.99503119 0.679530883 0.830195874 0.860004788 1 14.69948253 0.88234219 1.842758001 0.999286714 0.790626175 0.382468659 0.084175559 0.480619435 3.24582832 0.070825983 0.019966231 7.626797059 -0.88234219 -0.208660539 ITPPAAKPGS(ph)PQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 136.43 1.64E-05 3217390000 4747100 4026170 4217430 4879050 2530120 4775260 5053840 5213510 2901070 TRUE FALSE 4522713.991 4436441.3 4410803.337 4388598.624 2971372.127 4609891.549 4282783.888 4756987.426 3350953.119 1.349679876 1.323934159 1.316283213 1.309656826 0.88672447 1.375695626 1.278079321 1.419592354 1 21.67614007 -1.611758432 3.19465493 0.983694922 1.283930723 0.269412016 0.146159603 41385562.98 40459405.61 5532057.332 0.03336112 0.0244479 1.611758432 0.300235801 ITPSYVAFTPEGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 220.5 1.07E-11 324720000 192686 180056 171544 195274 208101 158341 186260 179379 239750 FALSE TRUE 183578.1146 198403.9111 179409.4621 175644.6865 244393.7485 152857.6115 157842.6161 163671.6238 276929.2055 0.662906299 0.716442712 0.647853164 0.634258442 0.88251345 0.551973603 0.569974611 0.591023339 1 18.07915769 -1.787933178 4.573017342 1.036737045 0.657319433 0.572667958 0.093084534 0.033292008 0.001543867 0.086063138 0.021063134 0.016295467 1.787933178 -0.379417612 ITQDIFQQLLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 ITQDIFQQLLKR 12 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 187.44 1.68E-05 114695000 323870 177998 299310 262970 417380 320760 535480 397690 529360 FALSE TRUE 308561.3069 196136.1986 313033.6596 236535.756 490170.9399 309652.0008 453782.6912 362866.1553 611450.4452 0.50463829 0.320772027 0.511952623 0.386843706 0.801652765 0.506422071 0.742141403 0.593451453 1 19.22187606 0.920192887 0.237388491 1.124677702 0.321191032 0.638237506 0.121920237 1.740474946 0.327848978 0.505909213 0.293593559 8.321332712 -0.920192887 -0.80348667 ITS(ph)PLMEPSSIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.001)S(0.999)PLMEPSSIEK;ITS(1)PLMEPSSIEK;IT(0.012)S(0.987)PLMEPS(0.001)SIEK;IT(0.014)S(0.986)PLMEPSSIEK;IT(0.158)S(0.842)PLMEPSSIEK;IT(0.14)S(0.86)PLMEPSSIEK;IT(0.001)S(0.999)PLMEPSSIEK;IT(0.017)S(0.983)PLMEPSSIEK;IT(0.014)S(0.986)PLMEPSSIEK;IT(0.002)S(0.998)PLMEPSSIEK 217.68 2.67E-11 1118041000 4892410 3682765 4001212 4874230 3478029 4437490 5115690 4733750 3633864 TRUE FALSE 4661155.475 4058042.94 4184671.528 4384263.14 4084596.156 4283818.609 4335197.534 4319237.755 4197385.07 1.110490317 0.966802634 0.99697108 1.044522498 0.973128767 1.020592235 1.032832933 1.029030619 1 22.00105939 4.677645135 3.549959675 1.01029443 1.11608227 0.617648418 0.025235548 0.165175734 3.480891856 0.005958356 0.041579833 47604.18511 -4.677645135 0.105787839 ITSEIPQTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITSEIPQTER 10 0 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 117.52 0.0022026 139780000 107420 83707 101460 108060 116070 98387 118570 103110 126610 FALSE TRUE 102342.4695 92236.83847 106112.0414 97197.6035 136312.5713 94979.83352 100479.9688 94081.14178 146244.0322 0.699806125 0.630704974 0.725582027 0.664626119 0.932089804 0.649461261 0.687070558 0.643316109 1 17.15801823 -2.138719367 2.490998301 1.664569936 0.700107342 0.538868252 0.08595913 3264126.038 1018426.517 12304373.56 0.019406135 0.007265753 2.138719367 -0.964462594 ITVGNDHFCVS(ph)TPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.586)T(0.414)PERR 83.395 0.0036877 98536000 42519 36535 41759 48877 43238 39010 45590 45910 47026 TRUE FALSE 40509.21113 40257.95804 43673.69146 43963.7911 50778.69351 37659.07392 38634.40818 41889.87702 54318.5519 0.745771191 0.741145642 0.804029009 0.809369719 0.934831503 0.693300403 0.711256225 0.771189134 1 15.7291574 -1.988389974 2.753284819 1.213828524 0.769832755 0.520448802 0.067205574 23373948.96 10638232.94 31742220.51 0.016497268 0.010270936 1.988389974 -0.443995769 ITVGNDHFCVST(ph)PERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.242)T(0.758)PERR 107.57 0.00085172 93982000 55247 41859 49107 52652 50611 49224 57999 51088 59339 TRUE FALSE 52635.5838 46124.47969 51358.60452 47359.32093 59437.54238 47519.36054 49150.18733 46614.46389 68540.98906 0.767943161 0.67294739 0.749312276 0.690963489 0.867182444 0.693298436 0.717091889 0.680096166 1 16.06467939 -1.279942605 5.221585621 1.000047269 0.728093606 0.687761594 0.057192822 2.86E-05 3.95E-06 0.050403059 0.011878054 0.052487682 1.279942605 -0.271953662 ITVNGDS(ph)SAEAEELANEI ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 ITVNGDS(0.5)S(0.5)AEAEELANEI;ITVNGDS(0.5)S(0.5)AEAEELANEI;IT(0.001)VNGDS(0.499)S(0.499)AEAEELANEI 211.09 3.57E-16 116629200 231178 267564 221493 300510 196201 255153 253754 257766 210391 TRUE FALSE 220250.6741 294829.0758 231648.6731 270302.1639 230418.3923 246316.9876 215039.1668 235194.6425 243017.3618 0.906316621 1.213201697 0.953218616 1.112275115 0.948156093 1.013577737 0.884871621 0.96781004 1 17.89069986 2.716671415 23.5891809 0.954210653 1.053360727 0.172499757 0.08902002 560.9120574 604472.7386 0.026979064 0.025461139 520.8005273 -2.716671415 0.099150074 ITVTSEVPFSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ITVTSEVPFSKR 12 1 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4 P35268 RPL22 60S ribosomal protein L22 0 107.65 0.0028726 766290000 1069100 681410 1030700 845610 1168400 990000 1465500 1154100 1352600 FALSE TRUE 1018565.762 750846.4537 1077958.615 760607.6762 1372168.59 955716.0518 1241911.059 1053040.886 1562354.3 0.65194288 0.480586544 0.689957851 0.486834309 0.878269795 0.611715314 0.794897201 0.674009017 1 20.57529022 -0.148666494 0.195353894 1.209278607 0.500633826 0.516797784 0.112357503 7.655579999 0.513318139 1.378736678 0.361748725 0.71012288 0.148666494 -0.708644781 IVADKDYSVTANSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVADKDYSVTANSK 14 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 197.88 2.08E-08 1947010000 3016180 2668060 2723790 2981600 2073210 3023900 3521700 3428200 2553610 FALSE TRUE 2873611.149 2939938.347 2848678.466 2681883.903 2434777.168 2919181.585 2984399.985 3128008.634 2949610.797 0.974234008 0.996720771 0.965781136 0.909233146 0.825457098 0.989683652 1.011794501 1.060481823 1 21.49209317 2.007770313 24.99828631 1.019236746 0.943460996 0.411711354 0.048881753 224.7184936 722950.4225 0.020080691 0.014805782 101.8052823 -2.007770313 -0.07577575 IVAHAVEVPAVQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVAHAVEVPAVQSPR 15 0 Q96FF9;B5MBX0;H0YCL8 Q96FF9 CDCA5 Sororin 1 IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR 137.46 1.07E-05 382580000 252761 245380 233977 266954 259813 250040 269798 270267 260308 TRUE FALSE 240813.4885 270384.501 244705.0769 240119.2767 305124.3049 241381.0521 228635.3599 246600.9887 300675.2352 0.800908955 0.899257635 0.813851785 0.798600113 1.014796928 0.802796585 0.760406356 0.820157299 1 18.19784652 -2.369757315 2.237060162 2.088924964 0.837899371 0.333595024 0.071570282 3908552.556 431506.9952 21612398.06 0.016968694 0.00426818 2.369757315 -1.251025593 IVALNAHTFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVALNAHTFLR 11 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;A6NHQ2 P22087;A6NHQ2 FBL;FBLL1 rRNA 2-O-methyltransferase fibrillarin;rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 ; 176.45 8.64E-06 854100000 977480 893530 603280 699070 1112600 674960 1013550 890840 1003950 FALSE TRUE 931276.4576 984581.7229 630940.9847 628798.1555 1306637.088 651585.966 858914.3324 812833.327 1159637.439 0.803075536 0.849042718 0.544084697 0.542236853 1.126763456 0.561887659 0.74067489 0.700937465 1 20.14524239 -2.268493929 2.227364973 2.027549285 0.740749796 0.18491612 0.175207701 11587068.73 1816784.505 59927997.9 0.042073781 0.005388974 2.268493929 -1.286799489 IVATKPLYVALAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 106.14 0.00087462 698190000 1500090 1037630 726120 942360 1519150 948080 1730990 1375380 1597560 FALSE TRUE 1429183.719 1143365.677 759413.3202 847632.1824 1784089.279 915247.7519 1466895.684 1254944.436 1845301.446 0.77449878 0.619609159 0.411538896 0.459346187 0.966828094 0.495988205 0.794935531 0.680075572 1 20.81542508 0.413076602 0.56234286 1.013835961 0.621913172 0.325294353 0.165262612 2.534333672 1.316950494 0.243937419 0.070941301 2.588669472 -0.413076602 -0.391922789 IVDAVIQEHQPSVLLELGAYCGYSAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IVDAVIQEHQPSVLLELGAYCGYSAVR 27 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;; 260.97 4.61E-53 1072530000 543132 373718 564535 523830 561393 584671 772869 609707 686663 FALSE TRUE 517459.2267 411800.2891 590419.4882 471173.6132 659299.7615 564423.6967 654953.6393 556317.8228 793147.1911 0.652412607 0.519197816 0.744400907 0.594055704 0.831245157 0.711625412 0.825765566 0.701405526 1 19.5972291 -0.33206444 0.09576908 1.46593716 0.309270097 0.626324977 0.082167662 23.01884944 0.594660982 4.995247092 2.235690989 0.465517016 0.33206444 -1.156667063 IVDDLKDEAEQYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IVDDLKDEAEQYRK 14 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 160.47 2.67E-06 258357000 638085 611011 617127 716204 413553 724050 768832 735510 474179 FALSE TRUE 607923.9866 673273.7156 645422.8834 644209.8132 485676.5123 698975.9669 651532.5578 671104.8452 547712.2575 1.109933141 1.229247121 1.178397734 1.17618294 0.886736613 1.276173679 1.189552633 1.225287249 1 19.06305864 -2.34784152 2.267996494 0.000170659 1.162544455 0.180753704 0.106093356 2714478.553 491151.703 14289217.84 0.024010543 0.004489092 2.34784152 1.162373796 IVDDWANDGWGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVDDWANDGWGLK 13 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 151.1 0.00010368 7281700 43130 37788 38995 57621 45240 42556 56378 43257 39265 FALSE TRUE 41091.33038 41638.64016 40782.95932 51828.82761 53129.84168 41082.27505 47776.50065 39469.18776 45354.01566 0.906013057 0.918080561 0.899213856 1.142761602 1.171447355 0.905813398 1.0534128 0.870246817 1 15.46894267 3.28914162 24.9999139 1.027034221 0.9097276 0.26379405 0.091375657 137.7987073 68106.64579 0.024475722 0.033140237 1945.994551 -3.28914162 -0.117306621 IVDDWANDGWGLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVDDWANDGWGLKK 14 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 185.67 1.85E-06 644680000 1214010 878870 1014300 1594640 1277260 1297550 1734240 1273430 1190990 FALSE TRUE 1156626.153 968427.8522 1060806.658 1434343.758 1500013.74 1252615.518 1469649.836 1161921.718 1375682.646 0.840765242 0.703961669 0.771112917 1.042641456 1.090377743 0.910541048 1.068305863 0.844614651 1 20.39171627 3.245639488 24.97632849 0.999836198 0.767209581 0.633438383 0.079029894 88.04068838 310631.3341 0.020290943 0.026905986 1760.514021 -3.245639488 -0.232626617 IVDNVRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVDNVRPDR 9 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 105.2 0.0036896 521700000 746100 607360 652090 757690 808180 678290 788560 722530 833110 FALSE TRUE 710833.3316 669250.6745 681988.9715 681525.5617 949126.3361 654800.6472 668250.6891 659261.4428 962304.4439 0.738678218 0.695466678 0.708703961 0.708222399 0.986305677 0.680450611 0.694427521 0.685086146 1 19.87613387 -2.152290539 2.462558298 1.631403672 0.733771023 0.455450808 0.090251095 11314983.66 4100865.077 39617507.71 0.020898259 0.007042218 2.152290539 -0.897632649 IVDQIRPDR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 132.88 0.00026701 8004670000 7594700 6911980 7089920 7787200 7380090 7272940 8201610 7963590 8132600 FALSE TRUE 7235713.582 7616318.62 7414999.845 7004415.861 8667175.359 7021076.264 6950303.762 7266255.842 9393762.072 0.770267921 0.810784706 0.789353593 0.745645441 0.922652212 0.747419001 0.739885012 0.773519255 1 23.16327162 -2.522798809 2.13615588 3.79900227 0.786110097 0.616785217 0.052645313 1577861.58 114694.7265 21438403.17 0.012189307 0.003000552 2.522798809 -3.012892173 IVDS(ph)PEKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVDSPEKLK 9 1 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEKLK;IVDS(1)PEKLK 125.82 0.0002973 121570000 979010 1017130 988470 1247620 558100 1222270 1253890 1374710 673750 TRUE FALSE 932734.1375 1120776.703 1033792.327 1122206.867 655432.4633 1179942.483 1062586.051 1254333.105 778231.709 1.198530112 1.440158105 1.328386283 1.441995815 0.842207347 1.516184023 1.365385192 1.611773319 1 19.56984024 IVEDEPNKICEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IVEDEPNKICEADR 14 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;; 136.81 2.27E-05 944410000 1069910 1088070 981660 1252080 1009130 1220510 1216870 1244270 1208390 FALSE TRUE 1019337.475 1198945.57 1026670.082 1126218.54 1185121.952 1178243.433 1031214.132 1135315.123 1395780.95 0.730299031 0.858978316 0.735552439 0.806873414 0.849074457 0.844146378 0.738808 0.813390613 1 20.41264112 0.955742794 23.00555057 1.000000001 0.795495872 0.643232949 0.047672918 2432.39941 1264399.022 0.043282312 0.010820578 9.031144563 -0.955742794 -0.204504129 IVEGQGQSSEVIT(ph)PPEEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVEGQGQSSEVITPPEEISR 20 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 IVEGQGQSSEVIT(1)PPEEISR 163.78 2.14E-10 36716000 89613 79727 89367 93422 119140 88560 111880 101950 123620 TRUE FALSE 85377.17109 87851.27194 93464.56535 84031.04307 139917.9783 85493.14499 94810.65118 93022.71753 142790.3582 0.59791972 0.615246527 0.654557958 0.588492417 0.979883936 0.598731918 0.663984966 0.651463577 1 17.12353904 -5 0.222178413 2.705932245 0.621017526 0.45651 0.113696477 138.4461029 1.384866525 106.0718225 0.200934774 1.00E-05 5 -2.084914718 IVEIDAHIGCAMSGLIADAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVEIDAHIGCAMSGLIADAK 20 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 180.83 5.32E-17 40058000 116106 95327 104442 120017 92463 117560 139464 126254 95677 FALSE TRUE 110617.8995 105040.9297 109230.769 107952.6631 108588.5179 113488.8677 118186.2054 115198.5304 110514.1005 1.000939237 0.950475362 0.988387622 0.976822529 0.982576137 1.026917535 1.069421955 1.042387622 1 16.75387093 2.172601367 3.564538265 1.045599607 0.977528436 0.614001885 0.021331915 0.122426822 3.129565618 0.007922025 0.005687962 148.799464 -2.172601367 -0.068071171 IVELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 162.47 0.019043 152183000 455208 407744 380209 405944 448906 373339 487359 398340 448638 FALSE TRUE 433691.22 449293.5772 397641.9587 365137.7379 527195.0643 360410.1768 413003.4336 363459.2379 518210.4897 0.836901662 0.867009808 0.767336761 0.704612788 1.017337693 0.695489929 0.796980072 0.701373757 1 18.98317869 IVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR 179.07 8.71E-17 173994000 618163 571953 580188 643508 626316 593578 703712 621796 700457 TRUE FALSE 588943.6601 630235.661 606790.1937 578821.3533 735545.3121 573022.245 596347.8098 567348.2459 809080.2941 0.727917444 0.778953171 0.749975247 0.715406564 0.909112875 0.708239033 0.737068761 0.701226133 1 19.62592336 -2.022547461 2.768360834 1.283656085 0.754331034 0.627675858 0.059663894 15435932.53 5852023.602 27838166.85 0.013676336 0.009494072 2.022547461 -0.529325051 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 IVEPEVVGES(0.998)DS(0.002)EVEGDAWR;IVEPEVVGES(0.903)DS(0.097)EVEGDAWR;IVEPEVVGES(0.996)DS(0.004)EVEGDAWR;IVEPEVVGES(0.987)DS(0.013)EVEGDAWR 339.29 3.42E-80 249679000 205578 193372 172960 222867 184923 183179 213000 192264 216889 TRUE FALSE 195860.7354 213076.8266 180890.3871 200463.9857 217173.5127 176835.4653 180502.938 175428.3449 250523.0384 0.78180728 0.850527872 0.722050907 0.80018184 0.866880404 0.705865083 0.720504346 0.700248352 1 17.93458376 2.22778572 24.99948381 0.752431928 0.80462618 0 0.094600103 596.1794574 1383221.583 0.03129692 0.023340119 168.9607077 -2.22778572 0.052194252 IVEPYIAWGYPNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVEPYIAWGYPNLK 14 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 223.78 7.89E-12 146039000 431770 412170 381700 447900 375190 414780 520010 478570 445520 FALSE TRUE 411361.0878 454170.5916 399201.3226 402876.241 440623.0172 400416.0646 440672.9239 436663.8737 514608.9662 0.799366344 0.882554758 0.775737208 0.782878394 0.856228799 0.778097723 0.856325779 0.8485353 1 18.97311707 0.482803329 1.078587254 1.000183648 0.819443344 0.715750365 0.035917285 1.025515072 1.60549844 0.033007802 0.010226777 3.039508268 -0.482803329 -0.180740304 IVEVLLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVEVLLMK 8 0 P38159;P38159-2;H3BT71;H0Y6E7;H3BR27;P38159-3;O75526 P38159 RBMX;RBMXL2 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2" 0 124.08 0.0030712 12715000 92852 74705 79191 76887 83907 71248 136120 80494 81128 FALSE TRUE 88463.06997 82317.52443 82821.98568 69158.17268 98540.35423 68780.66389 115352.394 73445.51863 93708.9159 0.944019778 0.878438552 0.883821832 0.738010594 1.051557937 0.733982068 1.230964982 0.783762334 1 16.5158987 1.753543653 25 1.025752589 0.88023933 0.160707446 0.139995607 7.591967994 12683.96255 0.056566078 0.031368985 56.69485549 -1.753543653 -0.145513259 IVEYS(ph)PPSAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 IVEYS(0.973)PPS(0.027)APR;IVEYS(0.997)PPS(0.003)APR;IVEY(0.007)S(0.764)PPS(0.229)APR 153.49 3.40E-05 470494000 598430 640450 602690 675070 676590 607650 704780 669800 770430 TRUE FALSE 570143.3999 705712.5831 630323.9326 607210.6811 794587.0818 586606.9281 597252.8668 611148.7612 889904.3496 0.640679417 0.793020714 0.708305261 0.682332524 0.892890435 0.659179752 0.671142766 0.686757809 1 19.76329075 -1.714870047 3.084563524 1.037343003 0.717041716 0.58691627 0.074669397 21913374.57 29084682.43 6505783.503 0.017038691 0.019281018 1.714870047 -0.320301287 IVFAAGNFWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVFAAGNFWGR 11 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 110.12 0.004274 147410000 226970 195841 172915 138436 227550 146610 223180 180087 206010 FALSE TRUE 216241.5779 215797.4206 180843.3238 124520.1503 267234.648 141532.8589 189129.792 164317.6276 237956.9786 0.908742325 0.90687578 0.759983274 0.523288499 1.123037658 0.594783392 0.794806663 0.690535022 1 17.86034124 3.741222595 22.49192372 0.768646974 0.907809087 0.07474304 0.175248686 116.5858255 985038.9813 0.040553436 0.068987246 5510.900816 -3.741222595 0.139162113 IVFSGNLFQHQEDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVFSGNLFQHQEDSK 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 136.81 2.06E-05 229640000 274330 157810 264680 221220 245100 252120 372040 303340 347450 FALSE TRUE 261362.9646 173891.0184 276815.8398 198982.5453 287845.3624 243389.0212 315278.465 276777.9415 401330.7715 0.65124078 0.433286034 0.689744868 0.495806849 0.717227242 0.606454921 0.785582585 0.689650436 1 18.61443225 0.810076495 0.381380106 1.033986551 0.537261048 0.663955765 0.089777295 0.896331441 0.322983754 0.151095797 0.068755471 6.457679616 -0.810076495 -0.496725503 IVFSGNLFQHQEDSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVFSGNLFQHQEDSKK 16 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 178.12 1.84E-09 141370000 468430 441610 444670 531730 344580 525370 561130 593470 375830 FALSE TRUE 446288.2422 486610.5611 465058.5593 478279.4902 404674.6429 507176.3052 475519.3126 541502.6206 434111.7969 1.0280491 1.120933742 1.071287541 1.10174267 0.932189924 1.168308046 1.095384452 1.24738057 1 18.7277071 IVGAPMHDLLLWNNATVTTCHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 232.39 4.42E-34 231540000 509950 453370 452790 506840 433360 496680 550850 532960 312230 FALSE TRUE 485845.6741 499568.9184 473550.8694 455891.4803 508937.8468 479479.8471 466807.7154 486291.197 360649.0338 1.347142592 1.385194113 1.313051818 1.264086238 1.411172079 1.329491562 1.294354544 1.348377928 1 18.46023603 -3.275917316 0.358488761 9.01E-17 1.350016899 0.861230774 0.042389259 40.05936556 1.038129428 30.13748465 0.0300007 0.000529764 3.275917316 1.350016899 IVGCICEEDNTSVVWFWLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IVGCICEEDNTSVVWFWLHK 20 0 P10606 P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" 0 ;;; 221.91 7.52E-25 274804000 422161.1 330981 313653 328423.9 381612.7 278973.9 422012 347999.4 310511.3 FALSE TRUE 402206.3814 364708.3402 328034.3003 295410.1056 448165.8341 269312.9639 357626.3186 317526.7277 358663.8065 1.121402199 1.016852923 0.914601067 0.823640691 1.249542959 0.750878564 0.997107353 0.885304628 1 18.45227264 4.148170304 2.251436608 0.945080683 1.107204748 0.151847655 0.131852704 0.50681108 4.996397746 0.031358156 0.099000429 14065.99 -4.148170304 0.162124065 IVGCSVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVGCSVHK 8 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;G3V2H6;E5RG71;B3KT61;Q86SE5;Q86SE5-3;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4 B4DY08;P07910;P07910-2 HNRNPC;RALYL RNA-binding Raly-like protein;Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 111.95 0.0031354 1561020000 2769400 1412790 1231410 1503300 3103400 1391120 3295000 2187300 3481500 FALSE TRUE 2638495.95 1556754.907 1287871.367 1352185.428 3644631.977 1342945.166 2792287.233 1995768.416 4021393.239 0.656114882 0.387118298 0.320255019 0.336247999 0.906310764 0.333950222 0.694358166 0.496287803 1 21.93926399 -0.867732412 0.347053157 1.212008078 0.469195864 0.40052394 0.1883316 12.35076624 1.228805425 2.864401604 0.146534291 0.135602466 0.867732412 -0.742812213 IVGCTHITAQTAVLIETLCALGAQCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVGCTHITAQTAVLIETLCALGAQCR 26 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 ; 198.99 5.91E-25 48983000 29921 31330 26872 33627 31135 27496 35012 31523 27111 FALSE TRUE 28506.69363 34522.56262 28104.10778 30246.75007 36564.93414 26543.80663 29670.27636 28762.67901 31315.23542 0.910313886 1.102420664 0.897457976 0.965879696 1.167640404 0.847632351 0.947470966 0.918488353 1 14.9345771 IVGELEQMVSEDVPLDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 IVGELEQMVSEDVPLDHR 18 0 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ;;;;;;;;;;;;;;;; 211.13 2.55E-16 817932900 711643.1 678064.8 675253.2 795160 723440.3 717076.9 813391.6 774496.1 703760.4 FALSE TRUE 678005.141 747160.374 706214.2271 715229.0061 849608.0593 692244.3471 689293.7725 706677.1156 812895.9685 0.834061389 0.919134063 0.868763353 0.879853061 1.045162102 0.85157803 0.847948322 0.869332784 1 19.63271121 4.635531599 2.950192613 0.901218394 0.829805152 0.10369993 0.065541618 0.792572207 11.07604018 0.01547248 0.118197809 43204.76016 -4.635531599 -0.071413241 IVGHLTHALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVGHLTHALK 10 0 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ; 142.83 2.03E-05 1099350000 1325650 713040 608850 662700 1345740 667390 1401520 1023450 145678 FALSE TRUE 1262989.152 785699.5867 636766.3747 596084.137 1580436.63 644278.117 1187692.383 933831.2924 168269.0002 7.505774385 4.669306798 3.784216783 3.542447725 9.392321984 3.828858055 7.058295834 5.54963357 1 17.36040989 4.608362114 3.117296901 5.190078194 7.571277709 0.104075893 2.253127724 0.671464721 10.96049805 0.499293441 3.292474253 40584.67887 -4.608362114 2.381199515 IVGNKWEAYLGLLQAEYTEGDALDALGLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVGNKWEAYLGLLQAEYTEGDALDALGLKR 30 2 P62875 P62875 POLR2L "DNA-directed RNA polymerases I, II, and III subunit RPABC5" 0 110.03 0.0001306 49945000 67056 47112 64228 65199 58706 66148 97931 68013 70634 FALSE TRUE 63886.39577 51912.76636 67172.91733 58645.07265 68944.30781 63857.27817 82989.82732 62057.42116 81587.55997 0.783040892 0.636282864 0.823323033 0.718799198 0.84503456 0.782684005 1.017187269 0.76062357 1 16.31606157 2.271012747 0.762522439 0.945164544 0.716361531 0.415443721 0.089082176 0.540166982 0.605334996 0.065363978 0.041178269 186.6434472 -2.271012747 -0.228803013 IVGVNS(ph)RVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVGVNSRVQK 10 1 A0A2R8YDK5;H0Y4P9;A0A2R8YGB3;Q9UNA1-2;Q9UNA1 A0A2R8YDK5 ARHGAP26 Rho GTPase-activating protein 26 1 IVGVNS(1)RVQK 77.058 0.089809 989090000 329040 289430 338410 312350 258130 347890 398920 359080 306210 TRUE FALSE 313486.9313 318923.2461 353926.4332 280951.9846 303147.7903 335842.4821 338057.4273 327637.0516 353695.4829 0.88631873 0.901688773 1.000652964 0.794332973 0.857086972 0.949524374 0.955786669 0.926325236 1 18.43214827 2.155418975 7.997876257 0.954756033 0.890664603 0.297263247 0.053245885 0.351576005 29.59027324 0.019412448 0.014332819 143.0273113 -2.155418975 -0.06409143 IVGWYHTGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVGWYHTGPK 10 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 145.17 3.09E-05 299150000 678660 550800 459500 599810 553950 566260 749300 687830 627330 FALSE TRUE 646581.0868 606927.1462 480568.5295 539515.9592 650558.7046 546650.2742 634980.5232 627599.9588 724613.1324 0.892312129 0.837587837 0.663207038 0.744557247 0.897801427 0.754402935 0.876302809 0.866117285 1 19.46685143 0.844129528 0.996418335 0.998867564 0.806132595 0.431790656 0.071639323 0.772996142 1.516920619 0.069528659 0.022777147 6.984406826 -0.844129528 -0.19273497 IVHKGDECILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVHKGDECILK 11 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 57.802 0.066305 214110000 341810 337770 301920 404970 297010 324520 427230 418110 364510 FALSE TRUE 325653.3187 372189.147 315763.3306 364261.6462 348808.45 313281.791 362048.2169 381498.0719 421036.3491 0.773456542 0.883983408 0.749966912 0.865154866 0.828452106 0.744073028 0.859897768 0.90609296 1 18.68358526 1.060143936 1.943551863 0.997540363 0.814507074 0.644805096 0.046382484 0.188884701 1.445812749 0.039939084 0.011316215 11.48534212 -1.060143936 -0.183033289 IVHSLDYYNTCEYPNEDEMPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVHSLDYYNTCEYPNEDEMPNR 22 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 206.43 9.29E-23 118670000 74291 66817 81009 76511 64896 87627 93611 76732 77347 FALSE TRUE 70779.41166 73625.72826 84723.34278 68819.96892 76213.84185 84592.45502 79328.92267 70012.9393 89341.57773 0.792233733 0.824092546 0.948308111 0.770301697 0.853061293 0.946843084 0.887928383 0.783654611 1 16.44704411 -5 0.098479783 1.434354128 0.754165908 0.330800514 0.063969354 211.4030564 1.421292765 19.32819664 1.066728839 1.00E-05 5 -0.680188219 IVIFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVIFRK 6 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 175.51 0.0067035 611460000 1474430 781710 1308420 1201270 1401270 1202870 1868100 1417970 1807560 FALSE TRUE 1404736.616 861367.1377 1368412.351 1080516.057 1645651.044 1161214.31 1583087.035 1293805.03 2087867.173 0.672809379 0.412558399 0.655411594 0.517521455 0.788197193 0.556172502 0.75823168 0.619677845 1 20.9935985 -1.970739051 0.196329628 1.476875513 0.511088117 0.566409761 0.106542835 21.57153763 0.630040817 4.978748068 0.274613549 0.010696974 1.970739051 -0.965787396 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 250.46 7.88E-47 404890000 311960 309020 283280 358680 167400 370260 346520 414550 175520 FALSE TRUE 297214.269 340509.4893 296268.6682 322624.805 196594.507 357437.8034 293652.0097 378249.8043 202738.7452 1.465996393 1.679548174 1.461332258 1.59133275 0.969693814 1.763046344 1.448425704 1.865700629 1 17.6292623 3.672014 24.77005647 1.466355851 1.572773092 0.028977131 0.288757993 704.0734668 262069.677 0.069271872 0.10731554 4699.092562 -3.672014 0.106417242 IVLDNSVFSEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 160.69 6.66E-05 751840000 795950 806046 806354 907570 921070 819341 907220 924000 838640 FALSE TRUE 758327.0209 888183.0038 843326.1285 816339.3393 1081704.316 790967.0157 768806.9268 843089.6616 968692.008 0.782836046 0.916888956 0.870582313 0.842723314 1.116664851 0.81653096 0.793654661 0.870338203 1 19.88567851 IVLHPDTEHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVLHPDTEHSK 11 0 Q9NW13;Q9NW13-2;H7C5G8 Q9NW13 RBM28 RNA-binding protein 28 0 101.95 0.0016964 138160000 235170 242130 244510 239130 421790 191550 263520 180020 349720 FALSE TRUE 224053.9802 266803.3223 255721.0254 215092.1981 495350.0425 184916.5755 223315.1841 164256.4945 403952.7915 0.554653873 0.660481442 0.633046808 0.532468651 1.226257258 0.457767787 0.552824956 0.406622996 1 18.62382717 4.707323426 1.232356366 0.664924655 0.506961549 0.020893389 0.25122213 7.99481599 10.84468045 0.067704954 1.593004769 50971.03191 -4.707323426 -0.157963106 IVLLDS(ph)SLEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVLLDSSLEYK 11 0 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 1 IVLLDS(0.76)S(0.24)LEYK;IVLLDS(0.707)S(0.293)LEYK 166.04 2.19E-05 37337000 216550 189166 187368 231940 149319 217480 231670 239650 184304 TRUE FALSE 206314.1107 208442.2305 195959.0081 208624.9505 175360.1863 209948.6131 196324.4866 218664.9755 212884.923 0.96913444 0.979131014 0.920492656 0.979989318 0.823732296 0.986207055 0.922209444 1.027151066 1 17.69971425 1.234488729 24.9998069 1.013575562 0.943912174 0.285025896 0.048071969 141.1594614 866605.1801 0.037737491 0.01076396 17.15887177 -1.234488729 -0.069663388 IVLQNGAHEVFNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVLQNGAHEVFNHR 14 0 A6NP24;Q08257;C9JH92;Q08257-2;Q08257-3 A6NP24 CRYZ Quinone oxidoreductase 0 ; 100.73 0.00096532 1010110000 1324570 1123150 1018390 1573620 1364290 1298310 1661130 1345720 287590 FALSE TRUE 1261960.201 1237600.262 1065084.189 1415436.728 1602221.744 1253349.199 1407694.11 1227881.623 332187.9884 3.798933872 3.725602084 3.20626942 4.26095096 4.823238046 3.773011797 4.237643018 3.69634564 1 18.34164038 0.945672787 18.717972 0.999999996 3.955649096 0.829064983 0.42135337 227.9641941 78543.87402 0.407523885 0.101880868 8.824148073 -0.945672787 2.955649101 IVLVDDRECPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IVLVDDRECPVRR 13 2 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 ; 182.02 6.50E-06 140345000 125157 80174 138260 124185 184999 124836 187058 143975 238710 FALSE TRUE 119241.0766 88343.82175 144599.3578 111701.6879 217262.767 120512.898 158518.8665 131367.7857 275727.9276 0.432459191 0.320402153 0.524427681 0.405115611 0.787960686 0.437071787 0.574910449 0.476439898 1 18.07288588 -5 0.153148405 2.85677308 0.329953618 0.641980598 0.120675352 77.93187327 0.701540917 44.02500906 0.531749942 1.00E-05 5 -2.526819462 IVNGWQVEEADDWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IVNGWQVEEADDWLR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 281.25 2.20E-33 415620000 185669 187282 161948 199158 165150 164210 192517 188618 167682 FALSE TRUE 176892.7943 206366.2487 169373.476 179138.2595 193952.1077 158523.3665 163144.9958 172101.608 193685.2682 0.913300201 1.065472096 0.874477845 0.924893572 1.001377697 0.818458564 0.842320107 0.888563233 1 17.5633547 2.242616087 24.99999324 0.868789661 0.961861471 0.16659246 0.070315508 126.2799161 778458.3945 0.023640162 0.019104934 174.8300523 -2.242616087 0.09307181 IVNHWAS(ph)PELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 167.03 1.27E-05 532990000 938540 990170 915250 1051520 1049230 952200 1085630 1052510 1023350 TRUE FALSE 894177.0742 1091069.449 957215.1178 945819.2118 1232215.38 919225.0752 919997.2045 960346.6447 1182045.891 0.756465617 0.923034763 0.809795224 0.800154392 1.042442928 0.777655996 0.77830921 0.812444467 1 20.17285462 4.727888478 4.554987627 0.85467332 0.751181652 0.107937652 0.094039166 0.43811843 21.16625711 0.021226337 0.139348031 53442.7107 -4.727888478 -0.103491667 IVPEGEWGQFMDALREPLPATLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVPEGEWGQFMDALREPLPATLR 23 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 169.9 7.25E-12 126860000 39578 26960 32024 42269 40182 42909 71775 39880 46687 FALSE TRUE 37707.22638 29707.25465 33492.33208 38020.03981 47189.72808 41423.05057 60824.40551 36387.89578 53926.98152 0.699227461 0.550879241 0.621068177 0.705028146 0.875067114 0.768132193 1.127903024 0.674762332 1 15.71871966 2.716908839 1.470866304 0.929391893 0.615770685 0.489172568 0.12597282 0.286601747 1.251928647 0.049319892 0.046330075 521.0853202 -2.716908839 -0.313621208 IVQIPFCGEIDCEDWIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVQIPFCGEIDCEDWIKK 18 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 146.76 1.31E-07 151750000 502960 330920 462780 478850 343680 489990 662010 540140 445540 FALSE TRUE 479186.0776 364641.1242 483998.9208 430715.0882 403617.6832 473021.5234 561008.2159 492842.4781 514632.0677 0.931123627 0.708547226 0.940475635 0.836937912 0.784283974 0.919145061 1.090115154 0.957659868 1 18.97318183 1.984592994 5.578957874 1.022178063 0.835710573 0.544688064 0.073210509 0.115598183 11.98708548 0.028861511 0.018784126 96.51459538 -1.984592994 -0.18646749 IVSGIITPIHEQWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVSGIITPIHEQWEK 15 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 224.59 1.11E-12 214470000 488900 296090 380380 456840 461410 397840 629610 474470 524370 FALSE TRUE 465790.6659 326261.9076 397820.7992 410917.5753 541879.7579 384062.701 533551.4309 432922.8915 605686.6215 0.769029147 0.538664544 0.656809619 0.678432643 0.894653669 0.63409474 0.880903444 0.714763834 1 19.20821202 0.756462894 0.294875601 1.04864065 0.625897227 0.453789534 0.10277214 2.141024582 0.490308496 0.307123592 0.142355246 5.70772308 -0.756462894 -0.422743423 IVSGS(ph)PISTPSPSPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVSGSPISTPSPSPLPR 17 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 IVSGS(0.999)PISTPSPSPLPR 117.4 0.00023 55031000 51000 45234 45241 51523 52464 50815 60059 52454 61921 TRUE FALSE 48589.33107 49843.39603 47315.3446 46343.81015 61613.70499 49055.26381 50895.89649 47860.84968 71523.39243 0.679348804 0.696882437 0.661536638 0.647953188 0.861448302 0.685863214 0.711597909 0.669163585 1 16.12612755 -2.399351662 2.227226303 3.310941814 0.701929298 0.712235073 0.059583599 1921642.991 185284.2247 22458947.44 0.013558114 0.003987019 2.399351662 -2.609012516 IVSRPEELREDDVGTGAGLLEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IVSRPEELREDDVGTGAGLLEIK 23 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;;; 216.67 1.41E-32 2385203000 2132172 1932170 1873083 2247973 1556813 2057555 2281533 2267407 1840658 FALSE TRUE 2031388.455 2129060.32 1958965.708 2022002.483 1828320.694 1986301.354 1933443.238 2068860.823 2126097.842 0.955453891 1.001393387 0.921390196 0.951039244 0.859941936 0.934247388 0.909385824 0.973078841 1 21.01977656 3.726870316 24.79222873 0.928194887 0.978423639 0.151558829 0.039218491 798.464696 1693345.937 0.009413892 0.014721339 5331.756608 -3.726870316 0.050228752 IVTDRETGSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 IVTDRETGSSK 11 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 165.35 1.98E-05 4637950000 4447990 2340740 4487920 3624700 4198800 4279420 6313460 4819640 5645000 FALSE TRUE 4237742.328 2579264.067 4693695.571 3260338.27 4931069.391 4131222.612 5350225.722 4397606.771 6520397.769 0.64992083 0.395568516 0.719848043 0.500021377 0.756252849 0.633584447 0.820536708 0.67443842 1 22.63652855 1.131987541 0.308351853 1.043703178 0.499296715 0.569950449 0.108382771 1.069504874 0.335683173 0.220048496 0.14315239 13.55150536 -1.131987541 -0.544406463 IVVAGNNEDVSFSRPADLDLIQSTPFKPLALKT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IVVAGNNEDVSFSRPADLDLIQSTPFKPLALKTPPR 36 3 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 IVVAGNNEDVSFSRPADLDLIQS(0.122)T(0.122)PFKPLALKT(0.756)PPR 47.91 0.041001 45734000 72962 46375 60569 88347 60003 77179 98278 69430 66148 TRUE FALSE 69513.23086 51100.66522 63346.14856 79466.19171 70467.5042 74506.27188 83283.8861 63350.34113 76405.894 0.909788855 0.668805279 0.82907411 1.040053163 0.922278381 0.975137754 1.09001913 0.829128982 1 16.22139631 3.353844788 5.394387976 0.984902398 0.783428824 0.455745169 0.089501634 0.156027136 6.757336395 0.023774602 0.032347789 2258.628416 -3.353844788 -0.201473574 IVYGHLDDPASQEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IVYGHLDDPASQEIER 16 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;; 180.62 2.44E-09 1105970000 560641 415281 443300 476450 589502 393177 494392 469045 561008 FALSE TRUE 534140.611 457598.606 463625.7435 428556.3408 692310.9622 379561.1819 418963.4203 427972.9332 648006.2554 0.824283109 0.706163871 0.71546492 0.661345994 1.068370801 0.58573691 0.646542247 0.660445682 1 19.30564821 4.648431199 3.29741047 0.735697076 0.828424622 0.004544581 0.157579237 1.2065678 21.45175588 0.035495378 0.24697109 44507.29488 -4.648431199 0.092727546 IWDDGDDFCIFSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWDDGDDFCIFSESR 15 0 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 0 ; 136.53 5.19E-05 25087000 38897 33950 34666 40837 34880 35433 42032 38820 38462 FALSE TRUE 37058.4159 37409.5436 36255.47039 36731.98717 40963.06096 34205.94633 35619.24643 35420.715 44426.49052 0.834151324 0.84205489 0.816077749 0.82680371 0.922041342 0.769944822 0.801756925 0.797288163 1 15.43913256 -0.997156922 4.770456012 1.000002855 0.826362679 0.653895737 0.039722698 1.17E-06 2.45E-07 0.037212318 0.008770883 0.10065679 0.997156922 -0.173640176 IWDILGDRPSLVHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IWDILGDRPSLVHSR 15 1 Q13610;B4DJV5 Q13610 PWP1 Periodic tryptophan protein 1 homolog 0 112.24 0.00046846 31605000 77495 69848 63972 75393 90577 63493 100760 76094 89694 FALSE TRUE 73831.96493 76965.59061 66905.17948 67814.3524 106373.6001 61294.22149 85387.21142 69430.80596 103603.2874 0.712641141 0.742887533 0.645782399 0.654557921 1.026739622 0.591624291 0.82417473 0.670160259 1 16.66071026 -5 0.307524659 3.28578276 0.724005657 0.316288593 0.12199188 333.6812676 3.038052852 493.7245976 0.103277502 1.00E-05 5 -2.561777103 IWDLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 158.08 0.0033356 1736473000 5319383 5041458 4890870 5599449 3889784 5302828 5829768 5796908 4275028 FALSE TRUE 5067946.308 5555188.302 5115121.227 5036581.748 4568161.098 5119189.737 4940329.821 5289300.004 4937977.508 1.026320249 1.12499263 1.03587374 1.019968548 0.925107717 1.036697662 1.000476372 1.071147043 1 22.23548883 3.450151576 3.851690078 1.006913318 1.076563967 0.281127224 0.043406147 0.235931813 7.659083696 0.011572661 0.01675975 2819.366768 -3.450151576 0.06965065 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 3 IWDPTPS(0.003)HT(0.011)PAGAAT(0.986)PGRGDT(0.998)PGHAT(0.983)PGHGGAT(0.007)S(0.006)S(0.006)AR 84.903 0.00038032 109070000 78167 77720 68889 76447 85959 76040 92653 77300 61657 TRUE FALSE 74472.20082 85639.75636 72047.62879 68762.40232 100950.2224 73406.71573 78517.08316 70531.20221 71218.45266 1.04568687 1.202493921 1.011642715 0.965513849 1.41747284 1.030726069 1.102482295 0.990350107 1 16.11996347 1.351231373 2.158066778 0.991394401 1.118971919 0.121141734 0.126927499 0.635132487 5.079625273 0.105388102 0.03185109 22.45077684 -1.351231373 0.127577518 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPTPSHTPAGAAT(1)PGRGDT(0.918)PGHAT(0.079)PGHGGAT(0.001)S(0.001)S(0.001)AR;IWDPTPS(0.001)HT(0.007)PAGAAT(0.992)PGRGDT(0.993)PGHAT(0.007)PGHGGATSSAR 125.05 1.35E-08 538770000 215757 199879 236254 243096 260119 224204 270853 252659 121870 TRUE FALSE 205558.5942 220246.8973 247086.4796 218659.5282 305483.6712 216439.7593 229529.4003 230534.8385 140768.9772 1.460254939 1.564598264 1.755262307 1.553321851 2.170106492 1.537552972 1.630539661 1.637682131 1 17.1029699 -0.022446724 1.28448023 0.998136899 1.653736531 0.530291089 0.196179089 12.74567562 14.87373687 0.269975568 0.054211773 0.949627485 0.022446724 0.655599632 IWDPTPSHTPAGAAT(ph)PGRGDTPGHATPGHGGATSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.012)PAGAAT(0.988)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHT(0.03)PAGAAT(0.97)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHT(0.008)PAGAAT(0.989)PGRGDT(0.002)PGHATPGHGGATSSAR 138.04 9.58E-10 2367380000 787730 635820 836370 881540 1210150 805370 1183960 835560 199313 TRUE FALSE 750495.564 700610.7809 874718.3918 792925.9244 1421199.777 777479.835 1003325.157 762393.9368 230221.4421 3.259885601 3.043203858 3.799465349 3.444187983 6.173185972 3.377095669 4.358087361 3.311567897 1 17.81266268 3.61837095 2.912598981 3.904245325 3.147972969 0 1.276696871 0.759600033 12.35091439 0.318216633 0.532446031 4153.086244 -3.61837095 -0.756272357 IWDPTPSHTPAGAATPGRGDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHTPAGAAT(0.044)PGRGDT(0.912)PGHAT(0.044)PGHGGATSSAR 155.38 4.52E-14 118580000 77720 56395 82615 87326 96310 83612 123790 87399 45459 TRUE FALSE 74046.32963 62141.71462 86402.97947 78547.82457 113106.4335 80716.49547 104903.5619 79745.88023 52508.54955 1.410176633 1.183458982 1.64550307 1.495905433 2.154057472 1.537206725 1.99783774 1.518721826 1 15.68026472 3.636008328 4.653411414 1.697595111 1.298016173 0.119795128 0.318161169 0.288457147 10.14488341 0.076238982 0.120781372 4325.221247 -3.636008328 -0.399578938 IWDPVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWDPVHR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4;A0A494C159 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 77.674 0.037406 215250000 367360 316470 311340 364820 390900 328290 430130 372630 393290 FALSE TRUE 349995.6208 348718.6528 325615.247 328147.6005 459072.8362 316921.235 364505.7686 340000.5418 454279.4046 0.770441313 0.767630338 0.716773078 0.722347518 1.010551726 0.69763505 0.802382333 0.748439261 1 18.79322037 -1.49506274 3.059450204 1.006260584 0.77929045 0.385070471 0.087559249 31718670.28 38730346.3 1689303.677 0.018925616 0.03198433 1.49506274 -0.226970134 IWDTTQKEHLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IWDTTQKEHLLK 12 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 108.91 0.00099414 108610000 944180 566350 881440 842220 955660 923140 1330100 1026200 1240500 FALSE TRUE 899550.4826 624061.7089 921854.8959 757558.4455 1122326.801 891171.4303 1127168.816 936340.4878 1432870.404 0.627796122 0.435532555 0.643362368 0.528699904 0.783271675 0.621948382 0.786650916 0.65347186 1 20.4504767 0.382016196 0.218824746 1.150970733 0.46901073 0.655485099 0.090733593 3.183021485 0.352264487 0.64323644 0.241449559 2.409995304 -0.382016196 -0.681960003 IWEQIQPDLHTNDECVATYK ddPTM_SK-BR-3_Trastuzumab_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 ; 205.02 9.06E-22 546250000 467700 409670 411830 504530 366460 477160 567360 533530 442470 FALSE TRUE 445592.7479 451415.8388 430712.8129 453813.6859 430370.508 460635.8296 480798.8117 486811.2848 511085.9878 0.871854754 0.883248317 0.842740406 0.887939988 0.842070646 0.901288317 0.940739569 0.952503681 1 18.96320651 1.53293447 1.228600614 0.990753446 0.867755562 0.873395038 0.017677768 0.13363797 0.386714281 0.014674186 0.005135458 34.11414337 -1.53293447 -0.122997885 IWFDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWFDKFK 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 ; 84.568 0.019562 296810000 1670750 546590 208248 228547 2007190 362190 2342430 842990 1716540 FALSE TRUE 1591776.959 602288.1424 217796.3768 205573.0213 2357243.301 349647.2695 1985049.282 769173.3266 1982732.256 0.802819924 0.303766754 0.10984659 0.103681685 1.188886343 0.176346185 1.001168602 0.387936053 1 20.91905844 2.760881817 24.98190986 0.723914114 0.365951784 0.25722269 0.351362584 1244.816633 1393197.959 0.10062444 0.106654511 576.6095316 -2.760881817 -0.357962331 IWGDCTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IWGDCTVR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 77.058 0.063193 0 82709 79757 71731 82460 114720 77834 96504 80006 98867 FALSE TRUE 78799.50948 87884.32898 75019.9373 74170.96414 134727.1317 75138.58906 81780.54238 73000.2505 114198.7894 0.690020532 0.76957321 0.656924103 0.649489933 1.179759719 0.657963096 0.716124425 0.639238392 1 16.80118783 IWGEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IWGEDLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 139.92 0.0061873 1494520000 3905900 3419770 3364480 3947350 3903320 3422520 4155660 3806410 3960690 FALSE TRUE 3721275.848 3768248.451 3518744.736 3550554.879 4584057.772 3303997.274 3521637.743 3473100.561 4574893.577 0.813412549 0.823680024 0.769142424 0.776095623 1.002003149 0.722201996 0.76977479 0.759165323 1 22.12530675 -1.053811996 4.606634294 1.00000669 0.804424277 0.397422201 0.075678978 1.00316E+11 20604385359 9495056.783 0.016673912 0.088346227 1.053811996 -0.195582413 IWGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWGLGR 6 0 P41743 P41743 PRKCI Protein kinase C iota type 0 ; 119.58 0.048604 94679000 180754 172774 159653 184952 170231 161932 207120 195284 173219 FALSE TRUE 172210.1166 190379.867 166973.248 166360.2736 199919.2325 156324.2542 175520.04 178183.8977 200080.9178 0.860702352 0.951514363 0.834528599 0.831464966 0.9991919 0.781305164 0.877245276 0.890559178 1 17.61022406 -1.373799948 6.486108407 1.000010399 0.880159433 0.278779696 0.061446427 8.42E-06 8.13E-07 0.0542185 0.012778315 0.042286336 1.373799948 -0.119850966 IWHHTFYNELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 168.74 1.02E-05 35634280000 5200229 3082170 1826296 2031954 6706859 2401523 6174457 3788566 1099419 FALSE TRUE 4954424.481 3396246.627 1910033.478 1827698.123 7876533.086 2318357.656 5232430.183 3456819.077 1269911.283 3.901394173 2.674396764 1.504068436 1.439232919 6.20242783 1.825605998 4.120311593 2.722094938 1 20.27629628 0.97143921 22.66934667 0.999999927 3.109861873 0.172923423 1.430618083 1611.905454 1279409.221 1.266442042 0.316610511 9.363521451 -0.97143921 2.109861947 IWLGLFDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWLGLFDAR 9 0 O95081;A0A0C4DG34;O95081-2 O95081 AGFG2 Arf-GAP domain and FG repeat-containing protein 2 0 ; 96.19 0.017531 25312000 111645 73007 47052 54022 129404 51332 128453 74156 99369 FALSE TRUE 106367.7621 80446.4963 49209.38074 48591.60592 151972.0166 49554.35997 108855.1356 67662.50751 114778.637 0.926720903 0.700883879 0.428732925 0.423350609 1.324044444 0.43173853 0.948391952 0.589504365 1 16.80849462 IWLS(ph)TETLANED ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 IWLS(0.494)T(0.494)ET(0.011)LANED;IWLS(0.492)T(0.492)ET(0.017)LANED;IWLS(0.489)T(0.489)ET(0.021)LANED 155.06 7.55E-05 39861000 152680.6 139266.9 146859 167194 168011 153368 176505 163822 183508 TRUE FALSE 145463.6906 153458.3554 153592.6304 150387.3415 197312.0652 148056.8277 149575.9205 149476.8772 211965.4834 0.686261217 0.723978041 0.724611517 0.709489767 0.930868847 0.698494988 0.705661687 0.705194425 1 17.69346983 -2.30452923 2.272973978 2.316240108 0.732639022 0.581032155 0.07052825 3074367.188 561242.3208 20692319 0.016430724 0.004959875 2.30452923 -1.583601086 IWSEPFYQETYLPYMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWSEPFYQETYLPYMIR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 196.38 3.73E-11 28885000 73224 58241.9 55443 74225 59888 65020 84043 78164 60135 FALSE TRUE 69762.84664 64176.81583 57985.11639 66763.76198 70332.44824 62768.3411 71220.69679 71319.54579 69460.42867 1.004353817 0.923933483 0.834793529 0.961176936 1.012554192 0.903656115 1.025342028 1.026765126 1 16.08390369 1.668268819 7.453295551 1.019525712 0.942867197 0.338852748 0.050635771 0.150292147 15.5426906 0.025466281 0.013150515 46.58743706 -1.668268819 -0.076658515 IWSTVPTDEEDEMEESTNRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IWSTVPTDEEDEMEESTNRPR 21 1 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 ; 196.3 8.87E-22 132404000 99452 96978 88266 111812 107795 94835 115247 101859 115118 FALSE TRUE 94751.10105 106860.1685 92313.08341 100572.4453 126594.4139 91550.84017 97663.95349 92939.68597 132969.9115 0.712575499 0.803641721 0.694240391 0.756354909 0.952053081 0.688507942 0.734481601 0.698952755 1 17.0207403 -1.924949015 2.748732797 1.15147022 0.75639206 0.49357388 0.077950186 18510251.71 13619251.36 18095560.09 0.017690455 0.011886418 1.924949015 -0.395078161 IWYEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 7186440000 4805160 3941230 3781594 3912050 4721440 3353460 4512550 3947200 4023550 FALSE TRUE 4578029.61 4342845.818 3954983.825 3518803.302 5544857.641 3237328.839 3824077.619 3601562.243 4647501.585 0.985051759 0.93444741 0.850991388 0.757138699 1.19308354 0.696574015 0.822824382 0.774945888 1 22.14802393 IY(ph)T(ph)EMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYTEMR 6 0 C9J466;C9JB88;C9J6S4;F8WDG5;A0A3B3IRY8;P54762-6;P54762 C9J466 EPHB1 Ephrin type-B receptor 1 2 IY(1)T(1)EMR;IY(1)T(1)EMR 66.993 0.050826 676280000 35585 30959 29874 29989 41538 38872 39326 34666 47390 TRUE FALSE 33902.96757 34113.7573 31243.75245 26974.44874 48782.21405 37525.85289 33326.09643 31630.46126 54738.99917 0.619356731 0.623207545 0.570776831 0.492783009 0.891178406 0.685541451 0.608818154 0.577841425 1 15.74028144 -2.280099181 2.299913348 2.61361386 0.633942847 0.55186554 0.103738573 5789463.707 847464.8213 48627499.07 0.024505195 0.005246876 2.280099181 -1.979671013 IYAMHWGTDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IYAMHWGTDSR 11 0 P62879;E7EP32;C9JZN1;C9JIS1;C9JXA5;P62873-2;P62873;F6X3N5;F6UT28;B1AKQ8 P62879;P62873-2 GNB2;GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 ;; 140.17 0.00040201 1038440000 1684370 1271610 635283 779506 1812810 742895 1616530 1242874 1577510 FALSE TRUE 1604753.168 1401188.505 664411.3539 701148.5759 2128963.49 717168.3599 1369898.659 1134041.364 1822142.194 0.880695905 0.768978683 0.364632001 0.384793557 1.168384936 0.393585288 0.751806672 0.622367106 1 20.79720412 -1.972647945 2.473320758 1.274251235 0.679493482 0.147267852 0.250272471 26068598.15 12588841.59 40934057.83 0.059519393 0.01065006 1.972647945 -0.594757753 IYCKPHFNQLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYCKPHFNQLFK 12 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 113.63 0.00068802 934680000 1646390 1149600 863530 1064200 1570200 1012600 1817710 1472610 1578570 FALSE TRUE 1568568.408 1266745.547 903123.7046 957224.5942 1844042.383 977533.4081 1540384.955 1343660.462 1823366.573 0.860259495 0.694728951 0.495305616 0.524976496 1.01133936 0.536114582 0.844802673 0.736911865 1 20.7981732 0.464708739 0.685407419 1.004483827 0.697869292 0.248156803 0.162523679 2.64544429 1.99498966 0.182330891 0.058015138 2.915471086 -0.464708739 -0.306614535 IYDALDVSLIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYDALDVSLIER 12 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 220.82 6.67E-11 67096000 147255 137369 141125 167614 167102 134448 161004 165930 168893 FALSE TRUE 140294.548 151367.0573 147595.7208 150765.1223 196244.5359 129792.032 136439.8828 151400.2895 195084.0639 0.719149198 0.775906828 0.756574976 0.772821312 1.005948574 0.66531335 0.699390202 0.776077177 1 17.57373641 -1.379326502 2.68286118 1.005045839 0.765593165 0.381994528 0.091114396 6268225.154 6886030.603 246059.0656 0.022533955 0.041751636 1.379326502 -0.239452673 IYDDDFFQNLDGVANALDNVDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IYDDDFFQNLDGVANALDNVDAR 23 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 249.32 6.04E-38 170348000 192337 167688 179282 204043 194653 182553 218101 204198 239119 FALSE TRUE 183245.6112 184775.5978 187502.257 183532.21 228600.4216 176231.1438 184825.6868 186317.3406 276200.3533 0.663451763 0.668991171 0.678863205 0.664489411 0.827661583 0.638055461 0.669172521 0.674573144 1 18.07535564 -1.894080279 2.488065167 1.17274756 0.683074456 0.784278662 0.051794692 5914468.011 3193400.543 5987655.907 0.011879359 0.012762029 1.894080279 -0.489673104 IYEDGDDDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYEDGDDDMK 10 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 129.38 0.0079433 0 88493 123000 77407 115190 46040 104430 77524 97058 88973 FALSE TRUE 84310.11127 135533.8398 80956.18752 103610.8824 54069.36142 100813.5629 65696.28997 88559.08698 102770.4784 0.82037286 1.318801293 0.78773777 1.008177484 0.526117639 0.980958389 0.639252546 0.861717181 1 16.64906637 3.691153504 24.81463301 0.808297884 1.069587375 0.20250638 0.194994892 420.4983042 220104.2032 0.046923645 0.072693963 4910.814209 -3.691153504 0.261289492 IYEDGDDDMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;;;; 194.5 7.78E-07 5001860000 7678620 6943727 6907953 8341780 5237310 7801430 8635310 8598180 5769547 FALSE TRUE 7315666.85 7651300.676 7224689.478 7503248.426 6150695.206 7531264.523 7317834.861 7845277.777 6664258.882 1.097746498 1.148109762 1.084094962 1.1258939 0.922937616 1.130097833 1.098071817 1.177216839 1 22.66801301 -1.505157108 2.920922154 0.996455751 1.099043965 0.170727869 0.067858726 11204066.56 12388880.67 316921.2501 0.015328785 0.031249487 1.505157108 0.102588214 IYEKDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYEKDEEK 8 1 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 64.297 0.061902 920650000 1715370 1292980 1446880 2139260 1172740 1996780 2242150 2268690 1143320 FALSE TRUE 1634287.86 1424736.132 1513220.879 1924217.52 1377265.485 1927631.008 1900068.838 2070031.477 1320620.226 1.237515394 1.078838642 1.145841059 1.457055921 1.04289292 1.459640682 1.438770056 1.56746916 1 20.33278422 2.221869279 24.99215458 1.408884697 1.19094887 0.164483484 0.184183033 316.7299507 474240.8226 0.061841113 0.04579688 166.6745453 -2.221869279 -0.217935827 IYEKDEEKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYEKDEEKQR 10 2 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 81.017 0.012527 240720000 418250 344160 555400 376350 362490 455100 574090 517890 486040 FALSE TRUE 398480.1514 379230.2953 580865.6394 338518.583 425708.1412 439339.7729 486502.0266 472540.8061 561412.6009 0.709781275 0.675493024 1.034650164 0.602976461 0.758280346 0.782561297 0.866567701 0.841699679 1 19.09870192 -4.999999856 0.087331566 1.789754382 0.567522487 0.313119803 0.112271711 243.6537426 1.486303306 35.52957712 2.692123238 1.00E-05 4.999999856 -1.222231895 IYFMAGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYFMAGSSR 9 0 P14625 P14625 HSP90B1 Endoplasmin 0 126.28 0.001112 147170000 225030 141270 77744 76045 246790 98800 237210 143900 223050 FALSE TRUE 214393.2779 155665.5736 81308.6393 68400.81212 289830.0979 95378.53123 201019.2578 131299.3531 257639.4548 0.832144588 0.604199282 0.315590791 0.26549044 1.12494454 0.370201572 0.780234759 0.509624402 1 17.97499402 -4.78140271 0.48997681 9.981356047 0.610287862 0.184757844 0.261986029 2977.066755 18.37838272 29117.60852 0.117170498 1.65E-05 4.78140271 -9.371068184 IYGADDIELLPEAQHK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 232.93 1.22E-19 1554423000 3868130 3677320 3292150 4079210 2628480 3697820 4010170 3997620 2652120 FALSE TRUE 3685291.161 4052043.089 3443098.334 3669160.061 3086886.08 3569763.566 3398344.915 3647567.2 3063397.224 1.203007932 1.322728589 1.123947723 1.197742177 1.007667584 1.165295685 1.109338641 1.190693512 1 21.54670102 8 0.09818802 0.931648809 1.90979205 0.378325304 0.075172192 116.8623462 0.815030469 0.948180418 15.3978558 99999999.99 -8 0.978143241 IYGFYDECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYGFYDECK 9 0 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;H0Y3Y6;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 ; 160.75 0.00015136 196747000 658210 487210 336030 424210 519800 439710 697530 585590 521240 FALSE TRUE 627097.7177 536857.2529 351437.3079 381567.6049 610452.9554 424482.7324 591108.9875 534312.6352 602071.2371 1.041567308 0.89168394 0.58371383 0.633758235 1.013921473 0.705037388 0.981792438 0.887457501 1 19.19957467 1.637607512 12.67374145 0.950754282 0.831136342 0.16156153 0.150886113 0.266081784 89.58811073 0.074762986 0.040617307 43.41177183 -1.637607512 -0.119617939 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 307.21 3.51E-56 29952630000 11218220 9632528 9393906 10986110 6678688 10781560 11608040 11882760 6699171 TRUE FALSE 10687956.97 10614093.55 9824625.882 9881765.351 7843449.073 10408191.87 9837020.302 10842242.54 7738044.224 1.381222007 1.371676518 1.26965233 1.277036557 1.013621639 1.34506751 1.271254081 1.401160581 1 22.88353754 -4.565555805 0.197874903 3.29E-34 1.343071087 0.373252285 0.112929441 128.4308837 1.481868178 51.91923538 0.277306088 2.72E-05 4.565555805 1.343071087 IYHPNIDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IYHPNIDEK 9 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;; 138.11 0.00014568 4469760000 2203810 1748100 1836870 2237370 1527890 2028270 2464490 2177230 1492570 FALSE TRUE 2099640.269 1926233.377 1921092.306 2012465.317 1794353.532 1958030.501 2088486.787 1986580.199 1724030.133 1.217867501 1.117285215 1.114303207 1.167302867 1.040790122 1.1357287 1.211398077 1.15228856 1 20.71735356 4.58289069 2.728245125 1.129168885 1.221669108 0.187766377 0.061209928 0.57619253 7.127367366 0.014531757 0.101934789 38272.84001 -4.58289069 0.092500223 IYHPNVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IYHPNVDK 8 0 P61088;F8VSD4;F8VV71;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;; 105.57 0.0043629 2079350000 5125500 4753500 3645470 4286140 3874880 4086700 5068900 4682000 3313910 FALSE TRUE 4883227.773 5237887.054 3812618.405 3855289.064 4550657.845 3945176.554 4295546.208 4272019.259 3827814.238 1.275722245 1.368375456 0.996030154 1.00717768 1.188839782 1.0306604 1.122192965 1.116046651 1 21.86808939 3.743056329 24.99950001 1.07424359 1.322048862 0.720087298 0.066247042 174.2149031 968760.9785 0.016255656 0.028113168 5534.218849 -3.743056329 0.247805273 IYHPNVDKLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYHPNVDKLGR 11 1 P61088;F8VSD4;F8VV71;F8VQQ8 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 141.73 2.28E-05 663620000 545890 177335 487760 291500 662960 392190 873190 508950 874740 FALSE TRUE 520086.8615 195405.6381 510124.2785 262197.8662 778580.0141 378608.362 739968.8283 464383.6399 1010390.212 0.514738618 0.193396211 0.504878484 0.25950159 0.770573591 0.374714994 0.732359458 0.459608213 1 19.94648114 0.022405917 0.239621319 1.218724572 0.297675352 0.503620975 0.171928901 5.134152849 0.507026093 1.313510364 0.329464098 1.052945559 -0.022405917 -0.921049219 IYIDSNNNPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 IYIDSNNNPER 11 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 198.25 1.26E-07 904410000 574591 513614 521695 613872 635019 561653 653467 572958 687796 FALSE TRUE 547431.2222 565951.8505 545615.2318 552164.4203 745766.1125 542202.8158 553768.6074 522786.7601 794455.8909 0.689064338 0.712376681 0.686778508 0.695022123 0.93871305 0.682483222 0.697041351 0.658043783 1 19.5996076 -1.42298534 3.016563593 1.005105997 0.718907493 0.552947855 0.079134049 22889952.09 27552821.71 999010.3382 0.018638759 0.037758494 1.42298534 -0.286198504 IYITLTGVHQVPTENVQVHFTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 IYITLTGVHQVPTENVQVHFTER 23 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 264.63 3.33E-44 2023006000 567901 485140.8 493480 639184 588423 538186 659315 613826 486745.2 FALSE TRUE 541057.4452 534577.1991 516106.5461 574932.0099 691043.7849 519548.4839 558724.3876 560076.1413 562227.1597 0.962346688 0.95082066 0.917968009 1.022597361 1.229118468 0.924089978 0.993769828 0.996174112 1 19.10079362 3.216178852 18.0849361 1.027134096 0.947897745 0.202184542 0.078427192 17.0762301 13796.83801 0.022522628 0.026996717 1645.049049 -3.216178852 -0.079236351 IYKDGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYKDGER 7 1 P13861-2;P13861;H7C4A9 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ; 72.547 0.046793 568880000 903590 617630 834520 895600 913640 868880 1184740 1013200 1173000 FALSE TRUE 860879.0914 680567.1992 872783.5675 805572.5865 1072978.527 838790.4677 1003986.154 924478.8367 1354902.849 0.635380678 0.50229963 0.644166899 0.594561143 0.791922851 0.619077942 0.741002319 0.682321125 1 20.36975798 -5 0.127359885 2.237191672 0.480634232 0.74333087 0.068306221 64.80224779 0.524535413 20.31531979 0.499164481 1.00E-05 5 -1.756557439 IYKVPSTETEALASNLMGMFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYKVPSTETEALASNLMGMFEK 22 1 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 87.102 0.0026317 69352000 190410 141660 157180 185860 151400 172970 211520 191380 152770 FALSE TRUE 181409.6967 156095.3151 164386.8585 167176.9997 177804.1121 166980.0055 179248.7392 174621.7526 176460.7914 1.028045354 0.884589227 0.931577248 0.947388926 1.007612573 0.946272564 1.015799248 0.989578202 1 17.42898813 2.756347931 21.31092388 0.990927473 0.945346514 0.237308259 0.039014955 174.2596244 208778.1002 0.011741864 0.012410569 570.6212375 -2.756347931 -0.04558096 IYLTADNLVLNLQDESFTRGS(ph)DSLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYLTADNLVLNLQDESFTRGSDSLIK 26 1 Q99623-2;Q99623 Q99623-2 PHB2 Prohibitin-2 1 IYLTADNLVLNLQDES(0.17)FT(0.17)RGS(0.648)DS(0.012)LIK 99.319 0.0032745 17094000 44267 23386 31582 32192 30875 29596 33252 36541 29901 TRUE FALSE 42174.58664 25769.05999 33030.06594 28955.999 36259.59022 28571.0831 28178.79669 33341.27632 34537.89437 1.221110534 0.746109757 0.956342781 0.838383449 1.049849474 0.827238708 0.815880563 0.965353474 1 15.07589251 4.677913467 3.524396633 0.88958953 1.240239891 0.527421933 0.094886142 0.177045495 3.669819229 0.020910296 0.14743824 47633.60679 -4.677913467 0.350650361 IYNDDKNTYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYNDDKNTYIR 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 176.18 8.16E-06 795210000 1784610 1586530 1555550 1894620 1570080 1807970 2188720 1944920 1688840 FALSE TRUE 1700255.022 1748199.211 1626873.506 1704169.198 1843901.455 1745359.546 1854790.565 1774612.494 1950736.682 0.871596376 0.896173854 0.83397904 0.873602888 0.945233394 0.894718166 0.950815445 0.909714012 1 20.89558762 1.250289263 0.372817048 1.004618279 0.864704408 0.653934606 0.027723524 0.7493161 0.321032929 0.040442604 0.026853307 17.79464231 -1.250289263 -0.139913871 IYNEIPDINLDVPHSYSVLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYNEIPDINLDVPHSYSVLER 21 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 0 158.52 2.37E-11 47512000 56361 43604 40490 57127 45287 44777 65595 61846 51109 FALSE TRUE 53696.92723 48047.29717 42346.50655 51384.48543 53185.03846 43226.36126 55587.27802 56430.43637 59034.72269 0.909582103 0.813881983 0.717315245 0.870411227 0.900911125 0.732219265 0.941603102 0.955885516 1 15.84927614 1.581461839 6.747240705 0.96789765 0.829944549 0.525091856 0.063889507 0.106171371 9.946075976 0.033803478 0.015900574 38.14712731 -1.581461839 -0.137953101 IYNISGNGS(ph)PLADSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 IYNIS(0.005)GNGS(0.995)PLADSK;IYNIS(0.001)GNGS(0.999)PLADSK 245.1 4.70E-18 254360000 624300 779740 658760 800300 474230 759820 748940 754310 540250 TRUE FALSE 594790.5762 859196.3925 688964.7976 719852.3235 556935.5619 733507.2429 634675.4478 688258.6176 624029.2108 0.953145407 1.376852842 1.104058569 1.153555492 0.89248316 1.175437352 1.017060479 1.102926923 1 19.25125404 2.955988326 24.79356294 1.045778454 1.162289775 0.15362866 0.124573389 703.6380159 396387.7658 0.035785055 0.037958226 903.6251838 -2.955988326 0.116511321 IYNYYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYNYYKK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 123.96 0.0067234 1389850000 1997460 1481110 1288450 1280140 1721530 1447180 2183500 1941760 1590820 FALSE TRUE 1903044.024 1632036.793 1347526.707 1151457.895 2021764.287 1397063.794 1850366.972 1771729.2 1837516.241 1.035661064 0.888175438 0.733341386 0.626638214 1.100270159 0.760300107 1.006993534 0.964197846 1 20.80932557 1.631633805 11.56250746 0.989218784 0.870768861 0.16598471 0.138236402 0.212466085 70.19165926 0.065867337 0.035264956 42.81873223 -1.631633805 -0.118449923 IYPHGLVLLDLQSYDGDAQGKEEIDSILNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYPHGLVLLDLQSYDGDAQGKEEIDSILNK 30 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 226.03 4.33E-35 41025000 214080 221680 182890 265950 123380 223630 211940 241680 122980 FALSE TRUE 203960.8627 244269.444 191275.6874 239216.2007 144897.4329 215885.637 179604.6605 220517.218 142051.1103 1.435827303 1.719588418 1.346527225 1.684015001 1.020037314 1.519774372 1.264366467 1.552379404 1 17.11605058 -3.469732987 0.114246441 2.83E-15 1.726555514 0.318901012 0.203442651 108.1158044 1.168419901 28.47327787 2.22542705 0.000339053 3.469732987 1.726555514 IYPTFLHLHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYPTFLHLHGK 11 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 232.88 2.85E-15 1041670000 1695030 1534260 1263900 1586880 1442180 1343240 1786410 1492310 52353 FALSE TRUE 1614909.291 1690602.838 1321851.065 1427363.808 1693695.735 1296723.262 1513860.345 1361635.425 60471.63586 26.70523574 27.95695559 21.85902608 23.60385637 28.00810184 21.44349568 25.0342218 22.51692725 1 15.88397099 -0.207056093 0.659316782 1.23E-15 25.66288281 0.918308957 2.228422869 1.785179591 0.728660715 9.351834639 0.817542916 0.620788849 0.207056093 25.66288281 IYQDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYQDAYR 7 0 Q00059;Q00059-2;H7BYN3 Q00059 TFAM "Transcription factor A, mitochondrial" 0 86.095 0.047292 321040000 494950 308860 196120 216900 598970 226110 477830 341070 546310 FALSE TRUE 471554.6944 340333.1851 205112.296 195096.7999 703430.1784 218279.754 404928.2575 311204.1027 631028.9646 0.747279001 0.539330529 0.325044186 0.309172496 1.114735167 0.345910832 0.6416952 0.493169284 1 19.2673467 -1.215984194 4.299979141 1.00018274 0.570378216 0.245053612 0.240007521 15668961277 2856924149 29292697.52 0.05143232 0.060815713 1.215984194 -0.429804525 IYQNIQDGS(ph)LDLNAAESGVQHKPSAPQGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYQNIQDGSLDLNAAESGVQHKPSAPQGGR 30 1 P61106 P61106 RAB14 Ras-related protein Rab-14 1 IYQNIQDGS(1)LDLNAAESGVQHKPSAPQGGR 179.54 4.58E-18 130310000 51322 39303 42864 51599 43685 48027 46701 57436 49148 TRUE FALSE 48896.11077 43308.02038 44829.3568 46412.17049 51303.65017 46363.81295 39575.90473 52406.59935 56769.62083 0.861307686 0.762873166 0.789671591 0.817552941 0.903716626 0.816701121 0.697131743 0.923145136 1 15.79283149 1.022826299 8.299943388 0.999969787 0.804519345 0.598546926 0.05464773 0.112708531 33.03478559 0.053905934 0.013496445 10.53965267 -1.022826299 -0.195450443 IYQY(ph)IQSR ddPTM_SK-BR-3_Trastuzumab_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 9034540000 1707445 1357053 1475099 1642367 1652709 1493376 1842229 1580568 1657034 TRUE FALSE 1626737.459 1495338.244 1542733.748 1477273.149 1940940.926 1441660.015 1561163.131 1442165.087 1913998.37 0.849915802 0.781264116 0.806026678 0.771825709 1.014076583 0.75321904 0.815655413 0.753482923 1 20.86815817 -1.930437536 2.76415456 1.116974924 0.8178033 0.36348102 0.07561232 10133263.51 7333070.733 7659549.409 0.016582136 0.011737145 1.930437536 -0.299171624 IYSAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYSAER 6 0 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" 0 107.49 0.07263 291830000 195040 200480 184520 208250 210820 188710 234060 214060 227000 FALSE TRUE 185820.8457 220909.1399 192980.4245 187316.3144 247586.9413 182174.9254 198349.8482 195315.7716 262202.0006 0.70869347 0.842515081 0.735999054 0.714396968 0.944260306 0.694788464 0.756477249 0.744905726 1 18.00031917 -0.919387788 4.274262417 1.000005271 0.769418703 0.488981033 0.074597084 14028898.38 26486107.84 1102.065204 0.016324451 0.120396043 0.919387788 -0.230586569 IYSHDGTDSPPDADEVVIVLNNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYSHDGTDSPPDADEVVIVLNNFK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 258.95 5.92E-44 104395000 179210 165091 168144 190151 146957 179758 194179 197028 148186 FALSE TRUE 170739.0985 181913.9606 175853.5687 171036.6602 172586.2543 173532.9354 164553.4272 179775.1838 171165.9281 0.99750634 1.062793061 1.027386529 0.999244781 1.008297949 1.01382873 0.961367891 1.050297719 1 17.38503602 3.286097898 5.425107623 1.001402233 1.0323336 0.137166766 0.026568351 0.280303814 18.44035494 0.007146422 0.009575768 1932.403868 -3.286097898 0.030931368 IYSQS(ph)TLSLSTVANEAHNNLGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYSQSTLSLSTVANEAHNNLGVK 23 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 IYS(0.03)QS(0.683)T(0.194)LS(0.091)LS(0.001)TVANEAHNNLGVK;IYS(0.139)QS(0.823)T(0.037)LS(0.001)LSTVANEAHNNLGVK 172.06 3.51E-12 167378000 117010 70910 139789 128463 128287 135068 168079 131277 132034 TRUE FALSE 111479.1692 78135.80962 146198.4639 115549.6552 150660.2122 130390.5613 142435.4616 119781.6899 152509.1584 0.730967047 0.512335196 0.958620882 0.757657156 0.987876491 0.854968729 0.933946939 0.785406537 1 17.21853636 3.733000143 24.99782734 0.892241707 0.621651119 0.590254452 0.095288674 248.7237825 1118170.612 0.02239089 0.035807145 5407.545013 -3.733000143 -0.270590588 IYVASVHQDLSDDDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 179.81 2.57E-09 221470000 248750 177120 190560 309750 182380 230870 274080 308840 192720 FALSE TRUE 236992.0805 195168.7294 199297.3645 278613.3415 214187.0143 222874.914 232264.0622 281796.3323 222606.0333 1.064625594 0.876745012 0.895291837 1.251598339 0.962179735 1.001207877 1.043386195 1.265897101 1 17.76413317 IYVASVHQDLSDDDIKSVFEAFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 IYVASVHQDLSDDDIKSVFEAFGK 24 1 A0A0J9YVP6;A0A0J9YXX5;Q9UHX1-2;Q9UHX1;A0A0J9YYL3;A0A0J9YXJ8;Q9UHX1-4;Q9UHX1-6;Q9UHX1-3;Q9UHX1-5;A0A0J9YVR6;E9PQ56;A0A0J9YWM1;H0YEM1 A0A0J9YVP6 PUF60 Poly(U)-binding-splicing factor PUF60 0 202.73 7.67E-25 69457000 149360 117450 162360 143100 133340 144530 244790 207030 173720 FALSE TRUE 142300.0488 129418.2885 169804.3666 128715.3161 156594.4538 139524.8899 207442.7896 188901.3557 200659.6104 0.709161393 0.644964317 0.84623092 0.641461009 0.780398474 0.695331211 1.033804408 0.941401986 1 17.61439073 1.746174842 7.736259866 0.987746902 0.714252614 0.799416123 0.064142451 0.048917729 9.861855388 0.028451854 0.015209722 55.74101109 -1.746174842 -0.273494287 IYVDDGLISLQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYVDDGLISLQVK 13 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 210.38 7.07E-08 188719000 1002210 758420 734350 899840 912430 812540 1103170 942090 1000980 FALSE TRUE 954837.5195 835703.8603 768020.6739 809386.3736 1071557.503 784401.5361 934861.1554 859595.6053 1156206.866 0.82583623 0.72279787 0.664258876 0.700035951 0.926787009 0.678426637 0.80855873 0.743461772 1 20.14096811 -4.999999989 0.364443041 4.058216738 0.753151426 0.481916862 0.078591239 429.1256341 3.368564569 1031.150525 0.052083923 1.00E-05 4.999999989 -3.305065312 IYVLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYVLLR 6 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 131.47 0.035629 319860000 680920 571600 349690 472830 669500 407370 664820 524100 623090 FALSE TRUE 648734.2611 629846.6899 365723.6324 425300.2301 786260.588 393262.6748 563389.4987 478207.0256 719715.6149 0.901375832 0.875132729 0.508150198 0.590928168 1.092460094 0.546413982 0.782794603 0.664438864 1 19.45706743 3.96171591 24.84523533 0.728529855 0.891534927 0.095250498 0.186773192 899.882778 583997.6939 0.043716303 0.07881767 9156.213487 -3.96171591 0.163005072 IYVVDVGSEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 IYVVDVGSEPR 11 0 Q13228;Q13228-4;Q13228-2;A6PVX1;F2Z2W8;F8WCR4 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 166.33 4.78E-05 385690000 834640 655570 691770 789310 812030 699050 866760 750460 939110 FALSE TRUE 795188.2213 722373.3283 723488.3388 709967.0592 953647.7749 674841.7232 734519.8429 684745.744 1084742.382 0.733066426 0.665939987 0.666967891 0.654502922 0.879146782 0.622121652 0.67713759 0.63125195 1 20.04892102 -1.050462622 4.590082713 1.000011802 0.691138957 0.637332049 0.073190894 9.32E-06 1.93E-06 0.065141327 0.015353286 0.089030206 1.050462622 -0.308872845 KAAALEFLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAAALEFLNR 10 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 161.19 1.15E-05 1624750000 2317200 2129600 1474350 1830200 2059720 1674580 2289100 2024910 2013700 FALSE TRUE 2207670.548 2346608.661 1541950.406 1646224.819 2418934.516 1616588.875 1939855.753 1847598.146 2325974.311 0.949137975 1.008871272 0.66292667 0.707757094 1.039966135 0.69501579 0.833997067 0.794332997 1 21.14940373 3.768999472 24.75834338 0.81066255 0.979004662 0.222932489 0.123294413 739.0610153 601134.5441 0.028865379 0.052029841 5874.886376 -3.768999472 0.168342112 KAAALEFLNRFEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAAALEFLNRFEEAKR 16 3 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 206.81 8.35E-12 630860000 1207670 610820 1240740 910490 1050680 1187580 1652350 1318210 1422410 FALSE TRUE 1150585.832 673063.2524 1297629.156 818965.8154 1233918.259 1146453.807 1400253.66 1202780.544 1642990.078 0.700299927 0.409657527 0.789797317 0.498460597 0.751019909 0.697784985 0.852259352 0.732068051 1 20.64789234 1.524871045 0.438970711 0.997252794 0.557806826 0.50516637 0.116743193 0.675011525 0.357535666 0.120434191 0.083971891 33.4865993 -1.524871045 -0.439445968 KAADKLIQNLDANHDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAADKLIQNLDANHDGR 17 2 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 205.31 4.80E-12 692310000 1814400 1056300 1925200 1484600 1872400 1676500 2624600 2182500 2377400 FALSE TRUE 1728636.908 1163938.171 2013472.324 1335365.187 2198945.967 1618442.385 2224169.066 1991388.73 2746075.05 0.629493687 0.423855193 0.733218243 0.486281388 0.800759603 0.589365678 0.809944749 0.725176368 1 21.38893962 1.109750423 0.310573669 1.047989833 0.505399912 0.5732516 0.109304008 1.062260252 0.333029169 0.216736898 0.137962797 12.87509444 -1.109750423 -0.542589921 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 219.67 2.73E-35 386950000 103270 85698 106330 92461 94849 109140 132130 104140 10485 FALSE TRUE 98388.63176 94430.72363 111205.3357 83166.64462 111390.6356 105360.4544 111971.1418 95020.94952 12110.96025 8.123933175 7.797129351 9.182206314 6.867056195 9.197506496 8.699595429 9.245438797 7.845864205 1 13.56402564 -0.250200556 13.64950445 0.999009289 8.386757415 0.903708001 0.75601664 0 0 0.691633919 0.163019678 0.562081698 0.250200556 7.387748126 KAAEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAAEVLNK 8 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 113.62 0.0045108 218300000 528990 435530 454180 531130 393090 499370 577190 509100 468250 FALSE TRUE 503985.6911 479911.0022 475004.6022 477739.8033 461644.7715 482076.6917 489129.0647 464520.5051 540863.8185 0.931816242 0.887304689 0.878233274 0.883290372 0.85353236 0.89130882 0.904347912 0.858849287 1 19.04490586 -1.329225007 4.643319665 1.000085241 0.889013457 0.722990944 0.022093649 1.97E-05 2.84E-06 0.02160776 0.005089093 0.046857055 1.329225007 -0.111071784 KAAGGAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAAGGATPK 9 1 P16403 P16403 HIST1H1C Histone H1.2 1 KAAGGAT(1)PK 51.013 0.092287 104390000 221540 155430 113970 140340 135070 133860 192770 177540 124350 TRUE FALSE 211068.2432 171268.4937 119195.6372 126232.7566 158626.1652 129224.3946 163359.396 161993.6564 143633.5629 1.469491106 1.192398839 0.829859225 0.878852784 1.104380912 0.89968105 1.137334427 1.127825928 1 17.13203338 4.152053354 2.556216105 1.004685123 1.424627525 0.64825816 0.110378632 0.161935545 2.077260485 0.028959683 0.084748292 14192.31865 -4.152053354 0.419942403 KAALEEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 152.54 0.00012864 2394310000 3012880 2592710 2779680 3201150 2443620 2905620 3380980 3133490 2912640 FALSE TRUE 2870467.133 2856910.097 2907131.077 2879364.32 2869786.554 2804997.651 2865149.405 2859105.004 3364317.335 0.853209388 0.849179733 0.864107273 0.855853962 0.853007094 0.833749427 0.851628761 0.849832141 1 21.68188236 -2.025331318 2.529495891 1.172611307 0.851064602 0.974863901 0.007502799 885886.787 462553.0849 886219.0096 0.001831195 0.009433409 2.025331318 -0.321546705 KAALLAQYADVT(ph)DEEDEADEKDDSGATTMNIGSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAALLAQYADVTDEEDEADEKDDSGATTMNIGSDK 35 2 Q96MW1 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 1 KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK;KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK 313.03 1.31E-104 749110000 404750 365520 354100 409970 200375 444360 421780 480220 212244 TRUE FALSE 385618.2696 402766.9036 370335.8353 368759.0367 235320.3366 428971.7018 357429.7145 438169.391 245157.7155 1.572939562 1.642888957 1.510602407 1.504170635 0.959873264 1.749778508 1.457958252 1.787295946 1 17.90335064 3.431148847 2.848167254 1.437037077 1.605842897 0.080695947 0.268029041 0.719357394 11.84220922 0.07170707 0.106471045 2698.664195 -3.431148847 0.16880582 KAALSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAALSSPR 8 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 KAALS(0.107)S(0.893)PR 64.297 0.041574 74379000 298450 285290 262250 300070 250510 298190 353180 321090 325520 TRUE FALSE 284342.86 314361.3753 274274.4219 269906.3935 294198.8647 287863.6055 299295.9044 292973.6574 375999.9791 0.756231053 0.836067534 0.72945329 0.717836193 0.782443833 0.765594738 0.79599979 0.779185302 1 18.52037306 -0.377088752 0.769871739 1.012868851 0.770829464 0.830191241 0.032716908 5.202027236 2.350421382 0.234592435 0.011417362 0.419673211 0.377088752 -0.242039386 KAAS(ph)LTEDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.5)LT(0.5)EDRDR;KAAS(0.802)LT(0.198)EDRDR;KAAS(0.955)LT(0.045)EDRDR 121.79 0.00031843 4903701000 4085420 3568620 3610150 4199860 2816650 4139130 4491040 4168000 3500650 TRUE FALSE 3892310.293 3932266.435 3775678.948 3777682.094 3307872.868 3995790.89 3805849.364 3803027.824 4043512.923 0.962606122 0.972487664 0.933762058 0.934257455 0.818069073 0.988197878 0.941223495 0.9405257 1 21.94717779 -0.289724808 6.815314196 1 0.93993077 0.156625034 0.045736412 0 0 0.042849262 0.010099668 0.513186463 0.289724808 -0.06006923 KAAS(ph)PS(ph)PQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.994)PS(0.611)PQS(0.395)VR;KAAS(0.957)PS(0.859)PQS(0.185)VR;KAAS(0.926)PS(0.926)PQS(0.149)VR 133.48 0.00010744 1526725000 3826570 3435220 3553490 3988300 2623650 3855670 4307120 3597740 3057000 TRUE FALSE 3645695.62 3785272.824 3716421.031 3587388.507 3081213.729 3722147.181 3649989.738 3282702.813 3531063.947 1.032463777 1.071992148 1.052493268 1.015951158 0.872602076 1.054114917 1.033679875 0.929663938 1 21.75167152 3.074506568 5.108148912 0.986730814 1.052789649 0.292309044 0.051741194 0.280663549 13.36997463 0.015060942 0.018063215 1187.152655 -3.074506568 0.066058835 KAAS(ph)PSPQS(ph)VR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.981)PS(0.333)PQS(0.686)VR;KAAS(0.792)PS(0.491)PQS(0.716)VR 161.09 1.79E-05 1002090000 2529600 2141090 2242460 2545300 1713800 2440900 2790900 2205750 1874140 TRUE FALSE 2410030.821 2359269.505 2345279.009 2289441.608 2012686.177 2356371.021 2365096.947 2012602.837 2164772.059 1.113295421 1.089846617 1.083383814 1.057590151 0.929745083 1.088507684 1.092538559 0.929706584 1 21.04578369 8 0.192084868 0.994312338 1.593898835 0.299661651 0.056494388 71.21307614 0.837651453 0.110884016 12.71018851 100000000 -8 0.599586497 KAAS(ph)PSPQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.77)PS(0.23)PQSVR;KAAS(0.856)PS(0.144)PQSVR;KAAS(0.499)PS(0.499)PQS(0.003)VR;KAAS(0.819)PS(0.181)PQSVR;KAAS(0.78)PS(0.219)PQSVR;KAAS(0.901)PS(0.099)PQSVR;KAAS(0.708)PS(0.292)PQSVR;KAAS(0.962)PS(0.038)PQSVR;KAAS(0.801)PS(0.199)PQSVR 154.81 1.95E-05 10958510000 7110190 5564980 6108200 6731020 4945350 6642540 7768130 7106290 5483670 TRUE FALSE 6774105.41 6132057.789 6388267.012 6054405.081 5807817.474 6412507.174 6582959.097 6484025.575 6334049.537 1.06947465 0.968110172 1.008559686 0.955850605 0.916920122 1.012386647 1.039297066 1.023677749 1 22.59469672 2.011344561 24.98675983 1.02547894 0.987239278 0.156642871 0.039939583 408.7717687 900330.1062 0.015585171 0.011501531 102.6465981 -2.011344561 -0.038239662 KAASLT(ph)EDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.328)LT(0.672)EDRDR;KAAS(0.078)LT(0.922)EDRDR;KAAS(0.102)LT(0.898)EDRDR;KAAS(0.079)LT(0.921)EDRDR;KAAS(0.07)LT(0.93)EDRDR;KAAS(0.011)LT(0.989)EDRDR;KAAS(0.085)LT(0.915)EDRDR;KAAS(0.082)LT(0.918)EDRDR 160.78 4.35E-05 44333370000 30652030 27926510 27980390 31749900 20754030 30327240 34898290 32782520 27277220 TRUE FALSE 29203169.29 30772253.12 29263318.56 28558339.73 24373526.26 29277000.07 29573914.91 29911908.76 31507231.96 0.926871942 0.976672694 0.928781005 0.906405861 0.773585134 0.929215239 0.938638943 0.949366444 1 24.90917968 -0.881049337 6.029676207 1.000000014 0.920043499 0.189148196 0.054011955 1.07E-08 1.91E-09 0.053422914 0.012591899 0.131507543 0.881049337 -0.079956515 KAASLTEDRDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 109.72 0.0010634 863330000 1638450 1350590 1468080 1605530 1930610 1409410 1951430 1632840 2251040 FALSE TRUE 1561003.716 1488216.656 1535392.92 1444139.074 2267307.773 1360601.778 1653703.513 1489859.873 2600119.786 0.600358385 0.572364652 0.590508533 0.555412517 0.872001276 0.523284268 0.636010511 0.572996629 1 21.31014666 -2.252092782 2.310237177 2.478314042 0.613319331 0.613337705 0.095964276 4479327.441 772333.8449 34587588.88 0.021537221 0.00559638 2.252092782 -1.864994711 KAASPS(ph)PQSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.322)PS(0.678)PQSVR 150.34 2.08E-05 910710000 598180 471260 502550 594280 455910 566900 654160 564420 501290 TRUE FALSE 569905.2169 519281.9298 525592.4146 534541.8453 535420.5597 547268.1109 554355.8775 514996.3926 579027.493 0.984245522 0.896817398 0.907715818 0.923171787 0.924689356 0.945150476 0.957391288 0.889416131 1 19.14327233 2.23140868 21.58329034 0.945851969 0.927261386 0.079109662 0.034689189 93.53989845 282273.6224 0.012155043 0.009202349 170.3761028 -2.23140868 -0.018590583 KACGNFGIPCELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KACGNFGIPCELR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 67.102 0.086687 226010000 273600 204160 260110 271840 257700 264270 314350 317260 262940 FALSE TRUE 260667.4702 224964.1361 272036.3008 244514.1267 302642.7984 255118.2636 266390.1341 289479.0325 303715.3923 0.858262297 0.740707063 0.895694811 0.805076506 0.996468424 0.839991222 0.877104489 0.953125985 1 18.2123605 1.772047632 0.232530154 1.028278255 0.764580813 0.414548309 0.062690683 2.038372264 0.473715645 0.182028547 0.213515849 59.16265186 -1.772047632 -0.263697442 KACQIFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KACQIFVR 8 1 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 148.38 0.00083722 1287150000 2886700 1465280 625460 774620 2923400 1121420 3041200 1935010 2861100 FALSE TRUE 2750251.412 1614593.698 654137.9597 696753.7259 3433240.034 1082584.944 2577209.085 1765570.266 3304784.776 0.832202881 0.488562435 0.197936629 0.210831801 1.038869478 0.327581073 0.779841732 0.534246671 1 21.65612489 0.252034232 0.565342133 1.021085647 0.52759495 0.219547524 0.27036123 4.400010152 2.022325366 0.495449167 0.114681911 1.786628394 -0.252034232 -0.493490697 KADGYNQPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 199.8 7.86E-08 2694760000 4433650 4025890 3971140 4891600 2924300 4620910 5091070 5092350 3491530 FALSE TRUE 4224080.151 4436132.768 4153220.697 4399887.075 3434296.994 4460886.728 4314333.768 4646436.838 4032978.64 1.047384707 1.09996436 1.029814702 1.090977034 0.85155348 1.106102245 1.069763605 1.15211045 1 21.94341433 -0.521658449 6.992602931 1.000135811 1.056766162 0.045970564 0.080039324 0 0 0.071515645 0.016856399 0.300844136 0.521658449 0.056630351 KADIDLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KADIDLTK 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 85.958 0.026254 464380000 524300 484680 438770 555310 316660 481680 500820 563940 359240 FALSE TRUE 499517.3781 534069.443 458888.0385 499489.1838 371885.4037 464999.3008 424410.7108 514558.424 414949.1045 1.203803967 1.287072167 1.105889936 1.203736021 0.896219319 1.120617675 1.022801848 1.240051897 1 18.66257487 3.347767608 1.726149535 1.064490387 1.241590741 0.308224219 0.100147923 0.353012763 2.157787636 0.028849397 0.044530101 2227.243029 -3.347767608 0.177100353 KADKVEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KADKVEQR 8 2 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 94.692 0.0057253 3744490000 8665770 7792960 7792140 9205960 5819560 9400150 9907800 10377730 7138400 FALSE TRUE 8256156.226 8587071.484 8149417.326 8280559.411 6834489.421 9074620.448 8396183.141 9469000.945 8245386.614 1.001306138 1.041439521 0.98836085 1.004265755 0.828886472 1.10056943 1.018288594 1.148399874 1 22.97515571 KADLVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KADLVNR 7 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 83.206 0.035997 194960000 221610 216420 200350 227730 206170 209340 252120 254980 246320 FALSE TRUE 211134.9345 238473.444 209536.2457 204838.1477 242125.9827 202090.5033 213654.4635 232652.5995 284518.0476 0.742079233 0.838166317 0.736460296 0.719947819 0.851003951 0.71029063 0.750934661 0.817707704 1 18.11816064 0.856711425 3.829519828 0.999962405 0.767442172 0.716549154 0.046448663 0.425258942 10.47723015 0.042208467 0.010819533 7.189710854 -0.856711425 -0.232520233 KADRDQS(ph)PFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KADRDQSPFSK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KADRDQS(0.994)PFS(0.006)K;KADRDQS(1)PFSK;KADRDQS(1)PFSK;KADRDQS(1)PFSK;KADRDQS(1)PFSK 120.53 0.00022961 1434010000 3136280 1786270 3072130 2527020 2325580 3222800 4162330 3526230 2927460 TRUE FALSE 2988034.26 1968292.944 3212990.199 2272999.149 2731160.416 3111193.628 3527290.112 3217454.607 3381435.545 0.883658499 0.582087967 0.950185256 0.67219946 0.807692585 0.920080713 1.043133919 0.951505526 1 21.68920442 2.1695278 2.712290914 1.000263525 0.761201012 0.490690845 0.103282497 0.201744488 2.999627209 0.042047168 0.028369435 147.7501055 -2.1695278 -0.239062513 KADS(ph)DSEDKGEESKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KADSDSEDKGEESKPK 16 3 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 KADS(0.822)DS(0.178)EDKGEESKPK;KADS(0.797)DS(0.203)EDKGEESKPK;KADS(1)DSEDKGEESKPK 194.08 1.50E-09 3414010000 3289790 3245150 2814810 3670410 843150 4195640 3117880 3936840 662030 TRUE FALSE 3134288.146 3575834.474 2943871.823 3301453.413 990195.093 4050343.935 2642190.142 3592109.419 764694.2312 4.098746948 4.676162482 3.849737192 4.317351013 1.294890235 5.296684308 3.455224369 4.697445426 1 19.54452347 KADSEEERDDVSTLGSMLPAKAS(ph)PVAESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KADSEEERDDVSTLGSMLPAKASPVAESPK 30 3 H0YGZ1;H0YGK7;J3KQH6;P78364 H0YGZ1 PHC1 Polyhomeotic-like protein 1 1 KADSEEERDDVSTLGSMLPAKAS(1)PVAESPK 108.6 0.00018625 57331000 96451 79907 84076 93319 45925 101350 97073 112460 51761 TRUE FALSE 91891.95238 88049.61415 87930.96776 83938.39683 53934.30546 97840.22409 82262.73098 102612.4062 59787.83152 1.536967474 1.472701249 1.470716792 1.403937803 0.902095026 1.636457145 1.375910932 1.716275764 1 15.86756427 3.210601013 4.431957331 1.357453983 1.49695334 0.079372607 0.246226811 0.590198882 26.54271102 0.067024032 0.08451698 1624.056046 -3.210601013 0.139499358 KADTTTPTPTAILAPGS(ph)PAS(ph)PPGSLEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KADTTTPTPTAILAPGSPASPPGSLEPK 28 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHL0;A0A140T9F7;A0A140T9V2;U3KQA6;H0YDJ7;U3KPW0;E9PIQ3 H0Y6K2 BRD2 Bromodomain-containing protein 2 2 KADTTTPTPTAILAPGS(1)PAS(0.998)PPGS(0.002)LEPK;KADTTTPTPTAILAPGS(1)PAS(0.999)PPGS(0.001)LEPK 147.36 2.83E-07 200878000 391660 321090 331420 388030 218205 394230 424310 395630 254650 TRUE FALSE 373147.008 353809.436 346615.9348 349024.4872 256259.8829 380577.7162 359573.7165 360986.5398 294139.8214 1.268604183 1.202861395 1.178405335 1.186593796 0.871217918 1.293866687 1.222458472 1.227261709 1 18.16614259 4.03981124 1.463889047 1.151671771 1.263066742 0.105792307 0.122081534 1.178027862 4.570848305 0.034811642 0.129641071 10960.01731 -4.03981124 0.111394971 KADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KADYQAVDDEIEANLEEFDISEDDIDDGFRR 31 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;;;;; 311.13 7.77E-93 1343261000 341245.4 262135.6 294152.3 349956.3 278867.6 337935.8 392725.2 367226.6 334419.9 FALSE TRUE 325115.4062 288847.5157 307639.4739 314778.0279 327502.0211 326232.9985 332807.7578 335070.2921 386280.0301 0.841657298 0.747767146 0.796415683 0.814895939 0.847835755 0.844550515 0.861571223 0.867428461 1 18.55928757 0.492833827 0.355321107 1.026183127 0.785956551 0.842930711 0.025585873 0.981685049 0.249257343 0.072609309 0.023886932 3.110525938 -0.492833827 -0.240226576 KAEAAASALADADADLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KAEAAASALADADADLEER 19 1 O43633;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;;; 237.15 5.26E-24 577096000 1736380 1562320 1554850 1812640 1456720 1653320 1898870 1824780 1689120 FALSE TRUE 1654304.759 1721522.184 1626141.41 1630429.983 1710771.507 1596065.114 1609162.506 1664992.589 1951060.103 0.84790046 0.882352205 0.833465565 0.835663638 0.876842033 0.818050203 0.824763165 0.853378421 1 20.89582679 0.939257939 22.10071886 1 0.846714772 0.847289147 0.020494671 2902.979172 1056237.458 0.020924229 0.005231057 8.694766813 -0.939257939 -0.153285228 KAEAGAGS(ph)ATEFQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 KAEAGAGS(0.998)AT(0.002)EFQFR 211.11 9.46E-10 333240000 220080 187840 228380 252350 183970 244230 277940 269000 234780 TRUE FALSE 209677.2546 206981.1096 238851.4489 226983.2986 216054.3098 235772.2539 235535.1483 245444.9339 271188.4833 0.773179052 0.763237093 0.880758084 0.836994609 0.796694266 0.869403638 0.868529317 0.905071377 1 18.04893639 -4.999999999 0.042142104 1.867156845 0.34883654 0.80482965 0.030687023 292.9471313 0.920070592 30.75285802 8.680712227 1.00E-05 4.999999999 -1.518320305 KAEAGAGSATEFQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;;; 213.71 3.80E-10 2776120000 3710250 2959060 3498500 3632560 3238680 3392590 4289830 4058450 4107720 FALSE TRUE 3534873.836 3260591.578 3658909.685 3267408.167 3803504.767 3275103.758 3635337.645 3703070.603 4744724.238 0.74501144 0.6872036 0.771153286 0.688640267 0.801628203 0.690262193 0.766185233 0.780460658 1 22.17789281 0.082862884 0.675480781 1.010815617 0.725801075 0.828470952 0.03767694 1.324831024 0.704610213 0.067556773 0.012115454 1.210215983 -0.082862884 -0.285014542 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR 190.8 2.80E-09 6431660000 6334760 5195800 5485250 6218230 3603260 6499730 7076970 6332000 4306160 TRUE FALSE 6035328.449 5725257.927 5736754.138 5593161.707 4231667.403 6274642.72 5997248.249 5777536.512 4973937.3 1.213390537 1.151051487 1.153362777 1.12449381 0.850768144 1.261504185 1.20573459 1.161561991 1 22.24595689 -1.069002436 0.011937005 6.23E-07 2.167127391 0.089733453 0.113161756 11783.39026 26.31663534 2564.835872 2219.88231 0.085309533 1.069002436 2.167126768 KAEDS(ph)DSEPEPEDNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 KAEDS(0.93)DS(0.07)EPEPEDNVR 108.08 0.00066028 239450000 147830 128380 129290 148070 93565 120820 147110 164410 106600 TRUE FALSE 140842.3689 141462.068 135218.0744 133185.7223 109882.7064 116635.9731 124665.6676 150013.3888 123130.9836 1.143841824 1.148874669 1.098164495 1.081658884 0.892405008 0.947251209 1.012463833 1.218323646 1 16.90983431 3.148460231 2.767887271 1.008352063 1.139915869 0.277830441 0.084307131 0.307731126 4.780963151 0.025408964 0.032058166 1407.538333 -3.148460231 0.131563806 KAEEDAALQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAEEDAALQAK 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 103.75 0.0035254 0 412620 400650 406050 459410 358980 421610 499210 458290 287140 FALSE TRUE 393116.2703 441476.6905 424667.7941 413229.234 421585.9983 407009.54 423046.3459 418159.6981 331668.2047 1.185269691 1.331079326 1.280399472 1.245911511 1.271107668 1.227158752 1.275510706 1.260777163 1 18.33938119 -1.354929112 2.848504613 0.996205141 1.261732052 0.824731761 0.037606556 2997209.929 3554391.337 94878.79974 0.009499834 0.044164253 1.354929112 0.265526911 KAEEVQAWAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KAEEVQAWAQR 11 1 Q9BYN8 Q9BYN8 MRPS26 "28S ribosomal protein S26, mitochondrial" 0 ;;; 215.72 2.02E-11 948720000 1358600 1007290 999830 1082860 1127970 955410 1299080 1195940 1239040 FALSE TRUE 1294381.67 1109933.996 1045673.194 974008.8555 1324687.611 922323.9121 1100881.487 1091217.154 1431183.995 0.904413182 0.775535501 0.730635053 0.68056159 0.925588614 0.644448174 0.769210312 0.762457628 1 20.44877773 -1.381872278 3.280734717 1.002095105 0.776124064 0.401473213 0.086649129 31639480.34 37626073.97 613539.0354 0.019848296 0.04150761 1.381872278 -0.225971041 KAEGAPNQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KAEGAPNQGR 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 125.72 0.00064392 1099987000 1034205 836801 850524 1054590 926099 903371 1133750 946308 1015498 FALSE TRUE 985320.1792 922071.9733 889521.3667 948580.6096 1087610.372 872087.0358 960775.6148 863444.2548 1172976.243 0.840017166 0.786096034 0.758345595 0.8086955 0.927222847 0.743482266 0.819092134 0.736114017 1 20.16174236 -1.154527451 4.87358735 1.000014833 0.804242689 0.558552667 0.055190031 8.13E-06 1.41E-06 0.048819965 0.011506104 0.07006039 1.154527451 -0.195772145 KAEGAQNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KAEGAQNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 171.92 6.21E-06 4037430000 4579620 4567690 4397870 5376790 2844860 4185440 4709550 6219070 4064490 FALSE TRUE 4363150.439 5033142.804 4599516.69 4836304.854 3341002.683 4040497.163 3991021.651 5674495.261 4694790.351 0.929360017 1.072069768 0.979706514 1.03014288 0.711640443 0.860634205 0.85009582 1.208679161 1 22.1626293 5.166795476 9.65100532 0.952248577 0.000762951 0 0.135784176 902212.9942 816331.3551 0.031459298 18328044.61 146823.4674 -5.166795476 -0.951485626 KAEGAQNQGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAEGAQNQGKK 11 2 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 93.623 0.0051248 721720000 529040 348300 456220 450280 299930 445670 580620 577060 432360 FALSE TRUE 504033.3277 383792.166 477138.1383 405016.9989 352237.697 430236.3362 492035.7552 526529.5672 499408.1806 1.009261256 0.768493951 0.955407133 0.810993922 0.705310227 0.861492368 0.985237676 1.054307053 1 18.92985993 1.66503837 3.66206676 1.024222915 0.850657767 0.441443247 0.086443447 0.177935273 5.612936874 0.049929939 0.022691328 46.2421875 -1.66503837 -0.173565148 KAEGDAKGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KAEGDAKGDK 10 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;; 123.84 0.00025393 488155000 661020 490343 734710 700200 384760 723470 874390 1178860 554371 FALSE TRUE 629774.8946 540309.5092 768397.1802 629814.5657 451862.0222 698416.0525 740985.7462 1075632.769 640340.0233 0.983500752 0.843785316 1.199983059 0.983562705 0.705659502 1.09069561 1.157175437 1.679783755 1 19.28847866 1.638479685 2.875431333 1.351355276 0.950254864 0.348131363 0.208553849 0.206463045 3.984745305 0.121923002 0.050660329 43.49904127 -1.638479685 -0.401100412 KAEGEPQEES(ph)PLK ddPTM_SK-BR-3_Trastuzumab_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 208.59 2.74E-08 10980820000 17175510 19202110 13223510 19556740 7426620 18914830 15907100 18832980 6752500 TRUE FALSE 16363657.68 21158826.84 13829821.01 17590859.34 8721820.177 18259804.69 13480179.74 17183864.43 7799643.213 2.098000797 2.712794196 1.773135083 2.255341541 1.118233224 2.341107689 1.728307228 2.203160319 1 22.8949767 -1.104320563 0.139717283 1.03E-14 2.636270948 0.356193023 0.429389021 32.86510381 0.917910379 16.6063786 3.341070029 0.078646507 1.104320563 2.636270948 KAEGEPQEES(ph)PLKSK ddPTM_SK-BR-3_Trastuzumab_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(1)PLKSK;KAEGEPQEES(0.998)PLKS(0.002)K;KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK 213.15 2.71E-10 17810330000 7465020 5992450 6838690 7255860 3010959 8395010 8223050 8671160 3349304 TRUE FALSE 7112163.299 6603087.468 7152250.701 6526487.168 3536069.296 8104288.699 6968472.696 7911867.262 3868696.958 1.838387285 1.706798837 1.848749276 1.686998811 0.91402075 2.094836785 1.801245425 2.045098737 1 21.88341629 3.013939894 22.36094343 1.640599848 1.782170571 0.05104171 0.38691326 304.1227144 487829.265 0.106914043 0.12768663 1032.618483 -3.013939894 0.141570723 KAEGS(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KAEGSPNQGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGK;KAEGS(1)PNQGK;KAEGS(1)PNQGK;KAEGS(1)PNQGK 83.169 0.0096908 598745000 809240 939752 831772 1100180 475030 900418 923901 1281070 663835 TRUE FALSE 770988.829 1035513.797 869909.5689 989587.8162 557875.0816 869236.2989 782942.9338 1168892.719 766779.1414 1.005490091 1.350472048 1.134498217 1.290577381 0.727556413 1.133620168 1.021080115 1.524419036 1 19.54845157 -2.214379097 2.424062996 0.537384598 1.139758308 0.04352786 0.215303087 11020003.35 4271786.518 29185850.31 0.047820902 0.00610409 2.214379097 0.60237371 KAEGS(ph)PNQGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAEGSPNQGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGKK 50.102 0.083039 198160000 507120 537250 492050 563480 224230 548470 517660 669180 313090 TRUE FALSE 483149.4426 591996.3858 514610.9792 506837.9199 263335.641 529476.3464 438681.4595 610583.0517 361642.3982 1.335986724 1.63696621 1.422982985 1.401489213 0.728165841 1.464088141 1.213025524 1.688361361 1 18.4642043 2.985366529 24.91961442 1.231963699 1.474697071 0.162641039 0.262129073 1133.128945 1929630.455 0.073219185 0.080334246 966.8665351 -2.985366529 0.242733372 KAEGS(ph)PSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.951)PS(0.049)EGK;KAEGS(0.987)PS(0.013)EGK;KAEGS(0.671)PS(0.329)EGK;KAEGS(0.855)PS(0.145)EGK 153.75 1.66E-05 203744000 530913 498888 446811 546341 295117 499765 518932 600523 298879 TRUE FALSE 505817.7947 549725.2544 467297.7263 491421.7647 346585.3114 482458.0127 439759.3926 547938.0225 345227.6289 1.465171824 1.592355908 1.353593071 1.423471714 1.003932717 1.397506956 1.273824445 1.587178942 1 18.3971884 3.425438613 2.120969787 1.28410238 1.525966331 0.237673574 0.180273426 0.406132147 3.689671179 0.049272592 0.076837757 2663.413599 -3.425438613 0.24186395 KAEGS(ph)PSEGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.682)PS(0.318)EGKK;KAEGS(0.523)PS(0.477)EGKK;KAEGS(0.967)PS(0.033)EGKK;KAEGS(0.952)PS(0.048)EGKK;KAEGS(0.964)PS(0.036)EGKK;KAEGS(0.774)PS(0.226)EGKK 125.98 0.00024974 3270350000 8086060 8333520 7332490 9117930 3326880 9259290 8848740 10453350 4084790 TRUE FALSE 7703847.969 9182715.162 7668691.919 8201378.353 3907086.819 8938638.466 7498702.195 9537999.257 4718238.371 1.632780577 1.94621688 1.62532948 1.738228913 0.828081693 1.894486408 1.589301261 2.021517038 1 22.16981688 2.955417464 24.99999028 1.519072725 1.755048407 0.107261499 0.367203346 1091.629524 612139.2435 0.104324969 0.110658902 902.438187 -2.955417464 0.235975682 KAEGSPS(ph)EGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.367)PS(0.633)EGK 107.37 0.0024286 37732000 123990 113610 103120 132160 62508 131890 126440 155030 84304 TRUE FALSE 118129.2384 125186.9882 107848.154 118875.0257 73409.37541 127322.6162 107149.2558 141454.7513 97377.43375 1.213106917 1.285585205 1.107527174 1.220765645 0.753864346 1.307516653 1.100349964 1.452644066 1 16.57129986 7.999884702 0.012960927 2.57E-08 2.538774131 0.03062899 0.187540203 29054.60681 29.10191678 2348.98651 3449.169018 99973455.09 -7.999884702 2.538774105 KAEGT(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KAEGTPNQGK 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK 133.48 0.00011493 1489976000 3082477 3626570 3258968 3757686 1713814 3449061 3701674 4374316 2924880 TRUE FALSE 2936774.421 3996121.606 3408394.906 3379956.264 2012702.619 3329619.153 3136915.645 3991277.701 3378455.452 0.869265397 1.182825011 1.008861876 1.00044423 0.595746384 0.985544785 0.928505848 1.181391248 1 21.6879324 -0.338632395 6.68899879 0.999999307 0.970816513 0.003364936 0.164860857 0 0 0.153444577 0.036167234 0.458529842 0.338632395 -0.029182794 KAEPSEVDMNS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK 134.21 6.02E-05 757420000 1746850 1916090 1804750 2109270 997018 2188060 2103180 2325110 1185455 TRUE FALSE 1664279.862 2111341.749 1887499.573 1897242.172 1170897.624 2112286.934 1782301.263 2121511.042 1369289.307 1.21543333 1.541925245 1.378451992 1.385567069 0.855113392 1.542615518 1.301625051 1.549351939 1 20.38499586 2.941586179 24.99999254 1.277739379 1.389260595 0.069078637 0.224572286 838.5965387 358902.2248 0.064024729 0.067908645 874.1504369 -2.941586179 0.111521217 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;KAEQGS(1)EEEGEGEEEEEEGGESK 276.2 5.76E-52 8330600000 6911470 7170880 5271450 7630970 2961860 7602140 6335400 7388800 2468710 TRUE FALSE 6584778.51 7901600.825 5513151.197 6863890.398 3478407.446 7338875.986 5368818.372 6741797.502 2851544.938 2.309196822 2.770989409 1.933390957 2.407077758 1.219832589 2.573649072 1.882775298 2.364261356 1 21.44331234 -1.453262694 0.190923583 1.96E-17 2.558174122 0.410172721 0.43750721 24.36842655 0.846925266 14.33923821 1.312486094 0.03521578 1.453262694 2.558174122 KAEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KAEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 33 2 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 280 4.74E-74 3061090000 4304182 2824437 3716507 4071747 1956295 4447589 5329704 5290994 1968043 TRUE FALSE 4100731.847 3112250.341 3886912.522 3662447.256 2297472.229 4293567.878 4516559.768 4827686.516 2273237.057 1.803917385 1.369083058 1.70985798 1.611115411 1.010661084 1.888746211 1.986840639 2.123705709 1 21.11631671 KAEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAEQGSEEEGEGEEEEEEGGESKADDPYAHLSKK 34 3 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSKK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSKK 217.49 2.73E-36 172523000 196329 48040 221486 123855 150495 207462 462400 296970 199854 TRUE FALSE 187048.9173 52935.33062 231641.3522 111404.8601 176741.2804 200277.5389 391852.3874 270965.7325 230846.3376 0.810274571 0.229309813 1.003443912 0.482593145 0.765623064 0.867579451 1.697459841 1.173792642 1 17.81657332 1.956413279 4.883482838 1.357137871 0.632578667 0.528139326 0.269204812 0.131055283 7.124625512 0.111729401 0.068369658 90.45098047 -1.956413279 -0.724559204 KAERS(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KAERSPNQGK 10 2 Q9P2E9;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK;KAERS(1)PNQGK 128.76 0.00025279 3923060000 3170360 2080500 3585400 2798170 2015475 2973700 3589630 3503280 2786850 TRUE FALSE 3020503.366 2292505.315 3749794.136 2516892.635 2366973.202 2870720.023 3041966.015 3196514.231 3219020.465 0.938329967 0.712174819 1.164886703 0.781881527 0.735308529 0.891799246 0.944997414 0.99300836 1 21.61819032 1.635417618 2.625077576 0.991424969 0.859395108 0.147931328 0.126227883 0.439039447 6.939349267 0.08157287 0.032883375 43.19342255 -1.635417618 -0.132029861 KAESVQGGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAESVQGGETR 11 1 Q9UBS8;E7EP22;D6R988;D6RBK4;D6RAS4;D6R996;D6RDU6;D6RBU3;D6RA38 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 71.548 0.078134 21799000 69008 56457 59469 75813 58504 58164 84396 76488 77731 FALSE TRUE 65746.1286 62210.03249 62195.71247 68192.1332 68707.07908 56149.7661 71519.84016 69790.30523 89785.12649 0.732260801 0.692876815 0.692717323 0.759503671 0.765238985 0.625379373 0.79656668 0.777303636 1 16.45418885 0.626718741 1.031331421 0.999951355 0.71496399 0.791653588 0.044926375 0.499470486 0.854206164 0.039397714 0.012523647 4.233686944 -0.626718741 -0.284987366 KAEVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 97.635 0.019004 4835580000 6988000 6010400 5500060 6886400 3857900 6399000 7163200 7290200 5347180 FALSE TRUE 6657691.089 6622866.593 5752243.191 6194165.989 4530716.539 6177401.025 6070322.279 6651831.44 6176393.365 1.077925368 1.072287046 0.931327209 1.002877508 0.733553754 1.000163147 0.982826371 1.076976651 1 22.55833321 3.747824323 22.86292245 0.956804456 1.075106252 0.219343394 0.089127199 274.3608078 677117.974 0.022204413 0.039219656 5595.312195 -3.747824323 0.118301796 KAFEEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KAFEEAEK 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 114.5 0.0042411 3624920000 5259280 4318600 4459530 5287740 3272210 5324650 5729970 5717780 3769680 FALSE TRUE 5010684.257 4758670.25 4664003.862 4756206.329 3842882.388 5140256.035 4855757.838 5217100.871 4354262.722 1.150753773 1.092876235 1.071135152 1.092310371 0.88255639 1.180511229 1.115173371 1.198159414 1 22.05399703 -0.216351039 7.302928989 0.99999582 1.09820184 0.112704243 0.086355035 0 4.13E-18 0.078928626 0.018603656 0.607643646 0.216351039 0.09820602 KAGEQQETASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KAGEQQETASR 11 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;;;; 193.15 1.73E-06 608913000 701349 618134 624615 688182 568147 654374 767571 705071 712852 FALSE TRUE 668197.6227 681122.5574 653254.2156 619004.6379 667231.6569 631712.8643 650463.9465 643331.2454 823397.4474 0.811512866 0.827209945 0.793364392 0.751768954 0.81033972 0.767202845 0.789975666 0.78131314 1 19.65122945 -1.405696773 3.663968976 1.001367103 0.793998185 0.898515824 0.021999045 3818524.739 1465253.419 41353.58757 0.005472721 0.039291918 1.405696773 -0.207368918 KAGSEPETSRPS(ph)PLGS(ph)YSPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAGSEPETSRPSPLGSYSPIR 21 2 Q8N2Y8 Q8N2Y8 RUSC2 Iporin 2 KAGSEPET(0.005)S(0.019)RPS(0.973)PLGS(0.566)Y(0.313)S(0.124)PIR 71.882 0.0087751 74873000 72126 73162 73740 76643 65759 77593 86819 82098 80299 TRUE FALSE 68716.74692 80617.29098 77121.05194 68938.70003 77227.34878 74905.93495 73573.16701 74909.06389 92751.35881 0.740870514 0.869176387 0.83148164 0.743263505 0.832627681 0.807599327 0.793230072 0.807633062 1 16.5010808 -1.45616397 2.135326267 1.013463835 0.804687785 0.715887135 0.038946318 193794.2134 154396.735 15440.53027 0.009569368 0.034981307 1.45616397 -0.20877605 KAGSEPETSRPS(ph)PLGSYS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAGSEPETSRPSPLGSYSPIR 21 2 Q8N2Y8 Q8N2Y8 RUSC2 Iporin 2 KAGSEPET(0.004)S(0.004)RPS(0.992)PLGS(0.272)Y(0.023)S(0.705)PIR 70.465 0.0096584 80480000 59653 50896 56808 64903 56176 60122 74857 62744 72694 TRUE FALSE 56833.32091 56082.36026 59412.70299 58378.82713 65973.07661 58039.96006 63436.18981 57249.80273 83967.01425 0.676852945 0.667909426 0.707571938 0.695259057 0.785702305 0.69122334 0.755489407 0.68181301 1 16.35753507 -5 0.243130806 2.70535611 0.677804407 0.861003854 0.036851173 56.01490215 0.557571152 47.30938608 0.051731013 1.00E-05 5 -2.027551703 KAGTQIENIDEDFRDGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAGTQIENIDEDFRDGLK 18 2 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ; 230.01 8.80E-20 754110000 1566050 1229770 847700 1153200 1091140 1102120 1604020 1171200 813580 FALSE TRUE 1492025.92 1355084.961 886567.8835 1037278.145 1281434.471 1063953.308 1359297.289 1068643.519 939745.8312 1.587690917 1.441969643 0.943412414 1.103785844 1.363596866 1.132171352 1.446452055 1.137162287 1 19.84191108 3.955665347 9.504527631 1.197912856 1.53333082 0.475248877 0.153838261 0.400377545 84.13760763 0.039006415 0.070842919 9029.534203 -3.955665347 0.335417964 KAGTQIENIEEDFRDGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAGTQIENIEEDFRDGLK 18 2 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ; 227.95 1.51E-19 305130000 351215 296382 307152 362416 207658 336480 354113 357066 228686 FALSE TRUE 334613.763 326583.6628 321235.223 325985.2551 243873.4895 324827.6132 300086.5581 325799.4081 264149.4569 1.266759231 1.236359395 1.216111616 1.234093982 0.923240548 1.229711456 1.136048363 1.233390414 1 18.01099492 7.999999985 0.047613041 0.691248284 2.045640579 0.300369559 0.095856377 638.9690754 2.30184141 15.97916114 64.78307613 99999996.57 -7.999999985 1.354392295 KAHELASDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAHELASDIK 10 1 A0A0A0MRM2;Q86VF7-4;Q86VF7-3;Q86VF7;Q86VF7-2 A0A0A0MRM2 NRAP Nebulin-related-anchoring protein 0 60.398 0.063847 231060000 390920 424220 342900 451200 235640 437290 374710 416740 246720 FALSE TRUE 372441.9863 467448.5003 358622.3042 405844.5188 276735.5414 422146.5377 317541.1075 380248.0363 284980.0775 1.306905344 1.640284838 1.258411842 1.424115406 0.971069781 1.481319471 1.114257215 1.334296908 1 18.12050154 1.975137215 0.175563518 0.896763426 1.62701002 0.274189194 0.1788269 4.524494918 0.672787778 0.987119648 1.325701709 94.43591988 -1.975137215 0.730246594 KAIS(ph)SANLLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAISSANLLVR 11 1 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 KAIS(0.5)S(0.5)ANLLVR 127.57 0.00017388 342810000 385880 292180 348780 406200 418590 435910 527970 445560 489440 TRUE FALSE 367640.2171 321953.4742 364771.908 365368.0043 491591.9635 420814.3274 447418.4797 406544.4043 565339.8555 0.650299485 0.569486604 0.645225884 0.646280287 0.869551224 0.744356378 0.791415067 0.71911506 1 19.10875888 -3.462722017 0.058697292 2.043992427 0.128733867 0.712293637 0.06744673 149.6382265 0.86046048 26.69558485 6.98378069 0.00034457 3.462722017 -1.91525856 KAIVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KAIVER 6 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;; 94.262 0.071645 1408290000 4731600 4012500 3816900 4653400 3989500 4373300 5293300 4641100 4642400 FALSE TRUE 4507946.645 4421378.312 3991908.64 4185631.391 4685267.537 4221851.524 4485709.867 4234700.68 5362319.682 0.840670999 0.824527177 0.7444369 0.780563569 0.873738944 0.787318134 0.836524141 0.789714327 1 22.3544258 -1.620720763 2.74742029 1.016993614 0.812734251 0.726659617 0.036640057 11947036.29 11314077.35 1452570.024 0.008426267 0.023948551 1.620720763 -0.204259363 KAKS(ph)S(ph)S(ph)GGSSLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAKSSSGGSSLAK 13 2 O94762-4;O94762;J3KS37 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 3 KAKS(1)S(1)S(1)GGSSLAK 61.641 0.054602 4715000000 3449900 3079900 3109000 3541300 2436000 3375900 4002000 3578100 2602200 TRUE FALSE 3286830.064 3393745.312 3251550.725 3185321.796 2860837.629 3258991.737 3391421.398 3264782.595 3005735.886 1.093519254 1.129089661 1.081781916 1.059747735 0.951792751 1.08425752 1.128316501 1.086184122 1 21.51928681 KALEEAGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KALEEAGFK 9 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 115.18 0.0024349 349880000 502260 436830 403720 477640 373490 466400 601670 565360 385760 FALSE TRUE 478519.1652 481343.4736 422230.9613 429626.7197 438626.5377 450248.4511 509874.1911 515854.0812 445581.6906 1.073920171 1.080258646 0.947594953 0.964192939 0.984390847 1.010473412 1.144288919 1.157709332 1 18.76533043 1.753924186 14.47500244 1.112919127 1.017971356 0.328836628 0.05942384 0.318105774 297.7344319 0.029014606 0.01600565 56.74455386 -1.753924186 -0.09494777 KALELDQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KALELDQER 9 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P35241-2 A0A2R8Y5S7 RDX Radixin 0 90.653 0.018094 165000000 349200 256560 215840 255560 417240 222800 365660 250710 398680 FALSE TRUE 332694.008 282703.7557 225736.4775 229870.6233 490006.5239 215084.3801 309871.8512 228756.5033 460505.2582 0.722454309 0.613899083 0.490193051 0.499170464 1.06406282 0.467061725 0.672895359 0.496751121 1 18.8128581 KALERPYTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KALERPYTSK 10 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 132.56 0.00012389 1576500000 2598500 1867500 2458600 3056900 2291200 2702800 3570900 3138300 2856200 FALSE TRUE 2475674.055 2057800.373 2571329.242 2749614.604 2690784.555 2609201.358 3026093.621 2863493.815 3299124.909 0.75040325 0.623741274 0.779397359 0.833437557 0.815605541 0.790876802 0.9172413 0.867955562 1 21.65365197 2.237051793 0.331582998 1.005936505 0.648060452 0.736596531 0.051383605 0.745930791 0.210110382 0.0677187 0.095131477 172.6043725 -2.237051793 -0.357876053 KALNIPEQLPQWDMCNFLVNLQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KALNIPEQLPQWDMCNFLVNLQYR 24 1 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 77.959 0.0001836 0 81575 82619 64504 103280 41391 85411 80926 95012 49519 FALSE TRUE 77719.11142 91037.97003 67461.5722 92898.09818 48609.5773 82453.19565 68579.25239 86692.24559 57198.15361 1.358769584 1.591624279 1.179436187 1.624145052 0.849845217 1.441535967 1.198976681 1.515647623 1 15.80368096 2.802959644 24.99998396 1.232088063 1.44076498 0.208525146 0.225277346 335.9351474 130410.534 0.0610604 0.064764331 635.2718978 -2.802959644 0.208676917 KALVVPEPEPDSDS(ph)NQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.084)DS(0.916)NQER;KALVVPEPEPDS(0.022)DS(0.978)NQER;KALVVPEPEPDS(0.003)DS(0.997)NQER;KALVVPEPEPDS(0.035)DS(0.965)NQER;KALVVPEPEPDS(0.035)DS(0.965)NQER;KALVVPEPEPDS(0.035)DS(0.965)NQER 160.36 2.50E-11 2356390000 2110570 1607684 1847935 2157660 2036040 1908288 2462450 2148620 2375500 TRUE FALSE 2010807.539 1771508.827 1932664.648 1940767.918 2391124.731 1842203.508 2086758.027 1960475.442 2743880.408 0.73283352 0.645621734 0.704354549 0.707307765 0.871439121 0.671386225 0.760513476 0.71449012 1 21.38778617 -5 0.241272448 2.59874941 0.694305979 0.671045606 0.060312221 97.36457393 0.970121025 76.41759151 0.087712955 1.00E-05 5 -1.904443431 KANLQIDQINTDLNLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KANLQIDQINTDLNLER 17 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 295.82 6.28E-46 1341390000 2181860 1451150 2086340 2017970 2069840 2004550 2560790 2315430 2630420 FALSE TRUE 2078727.802 1599023.835 2182000.753 1815119.822 2430819.441 1935131.931 2170094.453 2112678.674 3038332.099 0.68416741 0.526283429 0.718157424 0.597406657 0.800050607 0.636905996 0.714238728 0.69534159 1 21.53484814 -5 0.184220466 2.429661864 0.595254504 0.688600314 0.070809682 68.67359539 0.665885386 35.84355362 0.186503916 1.00E-05 5 -1.83440736 KAPAQKVPAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAPAQKVPAQK 11 2 P50914 P50914 RPL14 60S ribosomal protein L14 0 ; 114.83 0.00067735 946030000 668760 454980 684330 667740 571360 717960 964800 865920 777780 FALSE TRUE 637149.0402 501342.9793 715707.2074 600617.5066 671005.0031 693096.8652 817602.0402 790095.4543 898394.1501 0.709208803 0.558043459 0.796651678 0.668545656 0.74689378 0.77148417 0.91007053 0.879453027 1 19.77698901 1.851397662 0.61568694 0.997419414 0.646288276 0.763719177 0.061337633 0.308703407 0.24035798 0.053457472 0.030913857 71.02277914 -1.851397662 -0.351131138 KAPDFVFYAPR ddPTM_SK-BR-3_Trastuzumab_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 ; 163.45 3.84E-05 1167780000 3199500 2728700 2096900 2555900 3064800 2327600 3595800 2996000 3150300 FALSE TRUE 3048265.976 3006757.632 2193044.939 2298976.076 3599300.15 2246994.628 3047194.669 2733654.357 3638832.434 0.837704409 0.826297359 0.602678188 0.631789487 0.989135997 0.617504287 0.83741 0.751244913 1 21.79504419 -0.923916031 0.79370555 1.03252109 0.76752904 0.27693977 0.120569515 65.05986996 20.7847853 5.538887115 0.0376428 0.119147235 0.923916031 -0.26499205 KAPKS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAPKSPAK 8 2 P10412 P10412 HIST1H1E Histone H1.4 1 KAPKS(1)PAK;KAPKS(1)PAK 88.338 0.011566 6126600000 6481700 5797200 4794600 5692600 2864100 6681300 6635100 7066000 3670600 TRUE FALSE 6175322.886 6387941.271 5014437.153 5120369.033 3363598.133 6449924.906 5622793.633 6447263.581 4239817.901 1.456506631 1.50665463 1.182701066 1.207686073 0.793335519 1.52127404 1.326187531 1.520646342 1 22.01557087 7.999999932 0.024439629 8.89E-11 3.077089561 0.106310136 0.229564571 4879.901149 9.175630045 400.4534482 825.356887 99999984.34 -7.999999932 3.077089561 KAPT(ph)PQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 103.91 0.0072532 1279570000 5128280 5637310 4296635 6250470 2169497 5664220 4874533 6068570 2435739 TRUE FALSE 4885876.368 6211758.298 4493639.965 5622160.88 2547856.59 5468066.641 4130833.464 5537173.839 2813460.964 1.736607129 2.207870796 1.597192931 1.998307761 0.905595145 1.943537412 1.468239125 1.968100468 1 21.42391452 KAPTSSSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAPTSSSQR 9 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 105.98 0.0048277 42614000 62962 45584 39574 47060 75698 52572 93235 73479 96444 FALSE TRUE 59985.91104 50229.06142 41388.50704 42329.43939 88899.70723 50751.41846 79010.28837 67044.78922 111400.043 0.538472961 0.450889067 0.371530441 0.379976868 0.798022199 0.455578087 0.709248276 0.601838091 1 16.76539026 0.500599243 0.372693162 1.059131903 0.443960544 0.629290328 0.121373108 1.568112255 0.433688456 0.294889369 0.09662736 3.166644006 -0.500599243 -0.615171359 KAQCPIVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KAQCPIVER 9 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;; 205.83 2.29E-05 6043690000 8669320 7738160 7532950 9108650 8074850 8285920 10149330 9133680 9318870 FALSE TRUE 8259538.425 8526687.302 7878343.209 8193031.197 9483101.283 7998976.513 8600863.303 8333886.559 10763992.77 0.767330358 0.792149111 0.731916435 0.761151682 0.881002198 0.74312355 0.799040234 0.774237473 1 23.35970999 -4.999999996 0.395974873 4.426850583 0.777276382 0.740668947 0.04068911 340.3854616 2.410832704 1007.212677 0.023498919 1.00E-05 4.999999996 -3.649574201 KAQPQDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KAQPQDSR 8 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;; 90.657 0.020911 289477000 625350 526450 488290 573500 505840 545900 639810 589720 618390 FALSE TRUE 595790.9448 580095.8535 510678.5795 515850.6904 594058.3358 526995.3461 542195.2336 538080.9905 714286.7629 0.834106098 0.812133003 0.714948962 0.722189906 0.831680449 0.737792401 0.759072213 0.753312281 1 19.44614386 -1.930153335 5.27238087 1.09668131 0.774264044 0.738232917 0.042871535 0.030813267 0.000408203 0.026252624 0.010275994 0.011744828 1.930153335 -0.322417266 KAQVS(ph)PQS ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.999)PQS(0.001);KAQVS(0.643)PQS(0.357);KAQVS(0.979)PQS(0.021);KAQVS(0.984)PQS(0.016);KAQVS(0.974)PQS(0.026) 86.276 0.017105 26572440000 19214920 16024990 16805420 18908660 13890130 17959100 20246140 18701680 16830600 TRUE FALSE 18306668.81 17657954.7 17575965.13 17007925.57 16312564.27 17337171.86 17157219.5 17064061.76 19440603.49 0.941671838 0.908302806 0.904085366 0.874866132 0.839097628 0.891802144 0.882545622 0.877753706 1 24.21256967 -1.440834085 2.954130331 1.002392522 0.892520672 0.630112495 0.026420617 6713837.647 8115743.537 134359.95 0.007283565 0.036238141 1.440834085 -0.10987185 KAQVS(ph)PQS(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAQVS(1)PQS(1) 84.718 0.0071377 0 250010 257020 253880 283170 203630 246950 290420 275280 266070 TRUE FALSE 238192.5228 283210.6302 265520.6491 254705.2136 239143.0075 238398.0596 246111.0951 251175.0238 307330.7767 0.775036348 0.921517309 0.863957238 0.828765724 0.778129057 0.775705128 0.800801982 0.817279111 1 18.22943272 -1.344492962 3.11489221 1.001600034 0.823183749 0.607857497 0.045339767 10506548.06 14435126.74 155921.6245 0.011747682 0.045238379 1.344492962 -0.178416285 KAQVSPQS(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.258)PQS(0.742) 61.815 0.088532 538450000 997790 871720 902290 1038800 740460 922050 1070900 950520 860170 TRUE FALSE 950626.4441 960549.2591 943660.889 934377.8504 869595.9896 890119.1773 907514.5366 867287.4298 993560.7705 0.956787418 0.966774542 0.949776719 0.940433518 0.875231808 0.895888006 0.913396104 0.872908287 1 19.92224869 2.967221709 4.476182537 0.90541017 0.958501497 0.258416217 0.035352836 0.214375086 10.06284086 0.009486855 0.010547444 927.3030947 -2.967221709 0.053091327 KAS(ph)DVHEVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KASDVHEVRK 10 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 1 KAS(1)DVHEVRK;KAS(1)DVHEVRK 77.894 0.016505 255670000 517310 230430 535540 443030 383310 541610 793910 592320 497360 TRUE FALSE 492857.7815 253911.079 560095.0387 398495.7827 450159.1426 522853.9099 672784.4483 540453.3207 574488.0486 0.857907806 0.441978 0.974946372 0.693653739 0.783583129 0.910121474 1.171102602 0.940756421 1 19.13191735 2.139959808 2.704883756 1.054477565 0.72099643 0.436534364 0.147342099 0.215950631 3.161428055 0.063715785 0.041806879 138.0256522 -2.139959808 -0.333481135 KAS(ph)GPPKGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASGPPKGPSR 11 2 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 KAS(1)GPPKGPSR 60.657 0.048138 274490000 315720 208200 252490 269910 546470 208640 288310 226390 502850 TRUE FALSE 300796.5413 229415.8167 264066.9162 242778.134 641774.195 201414.7445 244323.0143 206566.0914 580829.4098 0.517874158 0.394979684 0.454637647 0.417985264 1.104927168 0.346770913 0.420645047 0.355639862 1 19.14775498 -1.419539264 4.432677789 1.001350596 0.494732935 0.335176961 0.220365788 6135.13456 246595799.5 445058.6787 0.048847606 0.038059295 1.419539264 -0.506617661 KAS(ph)GS(ph)ENEGDYNPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGR 97.271 0.011822 464980000 436380 374060 416210 483900 255200 442150 493240 359210 296850 TRUE FALSE 415753.1822 412177.1393 435293.6402 435257.4527 299706.7992 426838.2346 417987.179 327755.6681 342883.9819 1.212518532 1.202089223 1.269507073 1.269401534 0.874076408 1.244847404 1.219033846 0.955879205 1 18.38736098 1.29998768 0.323951963 0.974266032 1.240724155 0.259850004 0.123034818 2.199730813 0.786142714 0.224768736 0.16557452 19.95205715 -1.29998768 0.266458123 KAS(ph)GS(ph)ENEGDYNPGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGRK 106.47 0.0059192 143540000 554520 383420 549310 542850 303960 582460 729290 529720 357570 TRUE FALSE 528308.9386 422490.9339 574496.4068 488281.6867 356970.5278 562289.2642 618023.4162 483334.9086 413020.1294 1.279136054 1.022930612 1.390964667 1.182222492 0.864293293 1.361408862 1.496351805 1.170245405 1 18.65585257 KAS(ph)GSENEGDYNPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.5)GS(0.5)ENEGDYNPGR;KAS(0.53)GS(0.47)ENEGDYNPGR;KAS(0.897)GS(0.103)ENEGDYNPGR 135.81 1.64E-05 795718000 382350 361581 343990 474740 317632 374790 400584 361370 310029 TRUE FALSE 364277.0732 398426.515 359762.2818 427018.2333 373026.9202 361810.9283 339467.5536 329726.5271 358106.7139 1.017230504 1.112591581 1.004623113 1.192432916 1.041664135 1.010343884 0.947950821 0.920749358 1 18.45003004 2.085336514 2.35581257 0.952502696 1.077369773 0.490429809 0.05531813 0.232052152 2.503949159 0.025576872 0.01519447 121.7128731 -2.085336514 0.124867078 KAS(ph)GSENEGDYNPGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.971)GS(0.029)ENEGDYNPGRK;KAS(0.973)GS(0.027)ENEGDYNPGRK;KAS(0.5)GS(0.5)ENEGDYNPGRK 140.97 8.61E-07 323990000 346860 237480 325781 326124 237080 345234 415844 385631 293891 TRUE FALSE 330464.6152 261679.482 340718.3811 293341.3959 278426.6769 333278.46 352399.3603 351863.1053 339466.1153 0.973483362 0.770855971 1.003688927 0.864125704 0.820189893 0.981772392 1.03809878 1.036519079 1 18.37290805 2.062578709 5.671400575 1.024815959 0.883281163 0.479682394 0.067191364 0.156249779 9.835212106 0.024381866 0.017684235 115.4991289 -2.062578709 -0.141534797 KAS(ph)IS(ph)LTDDEVDDEEETIEEEEANEGVVDHQTELSNLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASISLTDDEVDDEEETIEEEEANEGVVDHQTELSNLAK 39 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80 Q96L91-4 EP400 E1A-binding protein p400 2 KAS(0.724)IS(0.664)LT(0.611)DDEVDDEEET(0.001)IEEEEANEGVVDHQTELSNLAK 59.918 0.017384 20571000 19534 15763 21587 20630 20188 20130 22449 23094 27732 TRUE FALSE 18610.66653 17369.26762 22576.7853 18556.23321 23708.78081 19432.89305 19023.99275 21071.76693 32032.53692 0.580992588 0.542238277 0.704807907 0.579293274 0.740146835 0.606661068 0.593895912 0.657823855 1 14.96725044 -5 0.29307839 4.046728716 0.595055896 0.795688428 0.059774662 107.8942963 1.010569709 201.26672 0.060743803 1.00E-05 5 -3.45167282 KAS(ph)PEAASTPRDPIDVDLPEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASPEAASTPRDPIDVDLPEEAER 24 2 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BT29 P29590-2 PML Protein PML 1 KAS(1)PEAASTPRDPIDVDLPEEAER 115.27 0.00057172 100150000 39145 39354 40292 41588 32377 37904 41339 44007 35128 TRUE FALSE 37294.69343 43364.21734 42139.42805 37407.49523 38023.53855 36591.37498 35031.97631 40153.51378 40575.47083 0.919143824 1.068729862 1.038544401 0.921923873 0.937106527 0.901810237 0.863378184 0.989600686 1 15.30832022 3.226134554 24.68991935 0.922260245 1.00883796 0.261561283 0.05497331 204.7228869 406772.6257 0.015613987 0.018791178 1683.195473 -3.226134554 0.086577715 KAS(ph)PEPEGEAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 189.84 3.01E-06 2942090000 6096420 5757760 5598440 6791890 3125035 6594950 6757180 6987210 3833860 TRUE FALSE 5808254.309 6344482.29 5855134.012 6109156.313 3670040.115 6366565.228 5726248.087 6375372.851 4428395.428 1.311593421 1.432681971 1.322179581 1.379541735 0.828751672 1.437668639 1.293075151 1.439657536 1 22.07835262 -1.967650889 2.678863672 0.745777048 1.310454047 0.225192818 0.177972489 52081774.01 49879615.02 82625057.83 0.04004718 0.010773309 1.967650889 0.564676999 KAS(ph)PEPPDSAEGALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(1)PEPPDSAEGALK;KAS(0.998)PEPPDS(0.002)AEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(0.907)PEPPDS(0.093)AEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK 196.76 1.27E-11 8181210000 9305860 8413810 7997250 10059960 4585411 10056680 9745830 10503640 5000970 TRUE FALSE 8865990.44 9271186.805 8363931.823 9048713.708 5385105.227 9708414.65 8258924.639 9583885.598 5776494.886 1.534839139 1.604984855 1.44792508 1.566471344 0.932244438 1.680675711 1.429746724 1.659117819 1 22.46176292 -1.974222427 2.710486414 0.586323105 1.485963039 0.339154263 0.211382673 24899734.61 7609344.515 64458640.25 0.047864003 0.010611519 1.974222427 0.899639935 KAS(ph)PEPPDSAEGALKLGEEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KASPEPPDSAEGALKLGEEQQR 22 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(1)PEPPDSAEGALKLGEEQQR;KAS(1)PEPPDSAEGALKLGEEQQR;KAS(1)PEPPDSAEGALKLGEEQQR 158.77 1.06E-11 613640000 275923 77113.9 315581 161753 236214 291846 493776 315285 360798 TRUE FALSE 262880.6666 84971.89408 330050.701 145493.2811 277409.6468 281739.2998 418441.4024 287676.974 416748.7111 0.630789393 0.203892398 0.791965739 0.349115132 0.665652081 0.676041203 1.004061659 0.690288815 1 18.66881821 2.21037583 1.584434096 0.898904798 0.475222683 0.461012962 0.182732271 0.300564312 1.481278913 0.094290873 0.055606171 162.3214186 -2.21037583 -0.423682116 KAS(ph)PSPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASPSPSSAR 10 1 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 KAS(0.716)PS(0.282)PS(0.002)S(0.001)AR 69.345 0.035071 89703000 30227 28680 25105 39633 33073 36035 35715 34662 37005 TRUE FALSE 28798.22961 31602.52461 26256.08908 35649.01554 38840.92073 34787.09891 30266.0208 31626.81153 42743.5464 0.673744507 0.739351955 0.614270253 0.834021005 0.908696727 0.813856169 0.708083988 0.739920156 1 15.38341899 -5 0.143652287 1.823312709 0.667540572 0.484410316 0.081588961 129.1715549 1.124209166 30.80720752 0.4827077 1.00E-05 5 -1.155772137 KAS(ph)SPSPLTIGTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.492)S(0.492)PS(0.015)PLTIGTPESQR 122.34 3.51E-05 484640000 85652 75215 80882 105280 60855 90755 103520 100250 80782 TRUE FALSE 81603.39971 82879.49401 84590.5197 94697.05438 71468.09273 87612.13159 87726.12272 91471.57854 93309.25998 0.874547711 0.888223677 0.906560825 1.014873062 0.76592712 0.93894359 0.940165239 0.980305476 1 16.50973264 1.533099185 1.856634838 0.991822319 0.894142531 0.288553174 0.060759246 0.403899627 2.780991713 0.046854254 0.015847988 34.12708429 -1.533099185 -0.097679788 KAS(ph)VHSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.957)VHS(0.042)S(0.001)GR;KAS(0.657)VHS(0.111)S(0.232)GR;KAS(0.969)VHS(0.03)S(0.001)GR;KAS(0.516)VHS(0.303)S(0.181)GR;KAS(1)VHSSGR 131.69 0.00019968 666135000 493113 289767 449581 573679 539010 440867 782878 587087 716930 TRUE FALSE 469804.5257 319294.5867 470194.7335 516011.697 633013.1733 425599.6652 663435.5826 535678.5499 828107.8428 0.567322879 0.385571263 0.567794083 0.623121374 0.764409103 0.513942319 0.801146358 0.646870519 1 19.65945913 0.165140448 0.14675042 1.325009597 0.304801159 0.656045971 0.099901805 7.637468722 0.430302187 1.957890658 0.82634429 1.462650108 -0.165140448 -1.020208439 KASATCSSATAAASSGLEEWTSRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASATCSSATAAASSGLEEWTSRSPR 26 2 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 KASATCSSATAAASSGLEEWT(0.001)S(0.02)RS(0.979)PR 215.72 2.15E-34 167420000 146540 117220 147010 148850 142780 129520 185840 153960 179290 TRUE FALSE 139613.3446 129164.8513 153750.5539 133887.3152 167680.7868 125034.6899 157486.6948 140478.4462 207093.3775 0.674156491 0.623703437 0.742421393 0.646506985 0.809686861 0.603759963 0.760462245 0.678333841 1 17.65992189 -5 0.254739328 2.944475559 0.662642962 0.699069125 0.063401678 92.57347967 0.913757239 93.91067221 0.075920986 1.00E-05 5 -2.281832596 KASDSELER ddPTM_SK-BR-3_Trastuzumab_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 ; 112.94 0.0034697 0 1532150 1125590 1204770 1500850 1222960 1290130 1580350 1568810 1441740 FALSE TRUE 1459728.306 1240288.901 1260009.896 1349981.707 1436243.837 1245452.475 1339238.582 1431436.68 1665317.676 0.876546455 0.744776158 0.75661834 0.810645156 0.86244436 0.747876812 0.80419406 0.859557729 1 20.66736598 0.870032833 2.506979068 0.999773581 0.798473469 0.67107828 0.044185059 0.290303724 3.633885833 0.0408361 0.010954012 7.413662865 -0.870032833 -0.201300112 KASDVHEVR ddPTM_SK-BR-3_Trastuzumab_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 21859870000 54021070 45747740 46679970 57358120 47927220 50778410 62580480 55229730 48978480 FALSE TRUE 51467601.08 50409486.72 48820292.8 51592372.8 56285711.99 49019940.93 53032678.41 50393522.05 56573812.53 0.90974249 0.891039236 0.862948608 0.911947958 0.994907528 0.866477593 0.937406832 0.890757045 1 25.75363106 -5 0.215135163 1.450157468 0.895764278 0.365717804 0.03779919 158.8529146 1.586440617 30.95249055 0.070621657 1.00E-05 5 -0.554393191 KASDVHEVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KASDVHEVRK 10 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 94.767 0.0047322 1383570000 2703000 1353930 2644300 2154510 2690200 2651700 4382600 3188300 3554000 FALSE TRUE 2575234.547 1491897.006 2765543.771 1937934.561 3159370.028 2559870.964 3713953.878 2909115.55 4105136.169 0.627320128 0.363422051 0.673678937 0.472075586 0.769613942 0.623577601 0.904709058 0.708652632 1 21.96899865 1.911672637 0.524136266 0.972564988 0.48879515 0.588311092 0.119300132 0.504514014 0.304080942 0.104149847 0.073014387 81.59670788 -1.911672637 -0.483769838 KASEPAGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASEPAGGPR 10 1 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 73.781 0.070487 24715000 188280 174430 149470 200060 131850 173410 192480 199080 157970 FALSE TRUE 179380.3775 192204.6153 156323.3473 179949.5887 154844.5983 167404.7682 163113.6409 181647.4998 182467.1808 0.983082967 1.053365402 0.856720352 0.986202494 0.84861616 0.917451388 0.893934132 0.995507789 1 17.47727747 3.749213812 24.98564201 0.920812615 1.018224187 0.298108337 0.056420603 651.4036942 1527775.321 0.012844943 0.022878226 5613.242595 -3.749213812 0.097411572 KASFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KASFLR 6 1 P46777;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ; 134.44 0.022501 1662340000 4193300 3390700 2769300 3491300 4001900 3325200 4705100 4058600 4271900 FALSE TRUE 3995091.019 3736216.185 2896275.144 3140347.891 4699830.093 3210047.49 3987250.58 3703207.468 4934364.434 0.809646525 0.757182862 0.586960121 0.636423988 0.952469189 0.650549333 0.808057579 0.750493304 1 22.23443284 -0.593872204 0.510205259 1.050166363 0.736800924 0.38287288 0.103200648 11.53397789 2.412702193 1.08812249 0.046483964 0.25475798 0.593872204 -0.313365439 KASGPPKGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASGPPKGPSR 11 2 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 59.185 0.057138 293860000 560590 200460 453850 306560 698480 462810 1092500 693690 1045600 FALSE TRUE 534092.0217 220887.1019 474659.4714 275744.0064 820294.6909 446782.7737 925819.0599 632946.8261 1207746.308 0.442222028 0.18289197 0.393012563 0.228312854 0.679194534 0.369930979 0.766567493 0.524072665 1 20.20388601 1.303909831 0.426429727 1.008462934 0.276882944 0.643625595 0.148777277 0.560735024 0.292850727 0.165031221 0.104340604 20.133062 -1.303909831 -0.73157999 KASGS(ph)ENEGDYNPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.094)GS(0.906)ENEGDYNPGR;KAS(0.243)GS(0.757)ENEGDYNPGR 209.85 1.34E-09 572020000 319450 246496 262139 342620 249520 314794 335870 298895 265199 TRUE FALSE 304350.2316 271614.2226 274158.3324 308179.1867 293036.209 303892.6048 284626.8628 272722.1693 306324.7065 0.993554307 0.886687286 0.894992557 1.006053969 0.95661957 0.99206038 0.929167177 0.890304189 1 18.22470221 4.751636243 24.19833105 0.942452342 0.99355435 0.103372954 0.04506374 121.1626711 1791379.179 0.010366185 0.066221075 56446.39926 -4.751636243 0.051102008 KASS(ph)PNLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.005)S(0.995)PNLHR;KAS(0.082)S(0.918)PNLHR;KAS(0.414)S(0.586)PNLHR;KAS(0.102)S(0.898)PNLHR 165.44 3.77E-05 318048000 552264 512430 478601 616867 439751 558240 596351 598078 496440 TRUE FALSE 526159.5752 564647.1996 500545.3293 554858.3572 516443.4352 538908.0088 505366.7022 545707.1197 573425.3797 0.917572877 0.984691678 0.872904038 0.967620857 0.900628841 0.939804947 0.881312059 0.951661958 1 19.12924623 0.988654725 24.44261477 1.000000004 0.926136173 0.3303547 0.034806412 472.5859794 1018157.35 0.031336046 0.007834011 9.742148048 -0.988654725 -0.073863831 KASS(ph)PSPLTIGTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.189)S(0.81)PSPLTIGTPESQR 140.63 4.01E-07 230920000 128420 73318 94125 110350 74357 97911 130770 120850 98278 TRUE FALSE 122349.8411 80789.18756 98440.72435 99257.40835 87324.83726 94520.31752 110818.6347 110267.7333 113518.4503 1.077796964 0.71168332 0.867178191 0.874372475 0.769256777 0.832642775 0.976216945 0.971363977 1 16.79256727 1.685268328 5.492153083 0.981857272 0.853949002 0.289122982 0.093761035 0.195064803 13.27737435 0.048388891 0.023963048 48.44716046 -1.685268328 -0.12790827 KASSPS(ph)PLTIGTPESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.002)S(0.007)PS(0.99)PLTIGTPESQR;KASSPS(0.999)PLTIGTPESQR;KASSPS(0.997)PLT(0.003)IGTPESQR;KASSPS(1)PLTIGTPESQR 195.13 2.16E-11 3586260000 2025040 1602900 1849500 2014970 1734340 1926290 2334520 2066560 2207380 TRUE FALSE 1929320.372 1766237.332 1934301.404 1812421.387 2036808.347 1859582.094 1978346.098 1885601.051 2549689.217 0.756688447 0.692726518 0.75864203 0.710840119 0.798845731 0.729336769 0.775916565 0.739541525 1 21.28188998 -5 0.290918844 3.018258592 0.728557416 0.874574571 0.030329808 72.41538237 0.680888395 88.69544901 0.028282951 1.00E-05 5 -2.289701177 KASVVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 KASVVDPSTESSPAPQEGSEQPASPAS(1)PLSSR 311.12 3.11E-104 138410000 122180 106110 125640 138820 120480 117990 158520 141230 148010 TRUE FALSE 116404.7935 116922.7296 131400.7183 124865.5499 141491.6739 113903.9767 134334.8626 128863.1525 170962.6349 0.680878565 0.683908093 0.768593198 0.730367486 0.827617532 0.666250709 0.785755687 0.753750389 1 17.38332152 -5 0.184356242 2.123844623 0.678928159 0.761396342 0.047275802 60.18418962 0.583696109 24.76734302 0.128401937 1.00E-05 5 -1.444916464 KASWEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KASWEER 7 1 G5E9W7;G5E9V5;P82650;H7C5L9;H7C5H3 G5E9W7 MRPS22 "28S ribosomal protein S22, mitochondrial" 0 ; 91.069 0.026738 296390000 754730 595380 629980 629970 712120 556530 715560 674020 802950 FALSE TRUE 719055.4086 656049.8989 658865.2061 566644.2187 836313.5025 537257.2266 606388.1798 614999.2356 927467.3851 0.775289159 0.707356301 0.71039178 0.610958647 0.901717425 0.579273444 0.653810786 0.663095269 1 19.82293702 -1.969300588 5.592000726 1.201955566 0.700134184 0.524131737 0.089764373 0.045413921 0.000249317 0.017464262 0.019007882 0.010732463 1.969300588 -0.501821381 KATDAEADVASLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KATDAEADVASLNR 14 1 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKX5;H0YKP3 P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;;; 174.39 4.09E-06 1077500000 968780 780530 831720 972550 810970 881990 1065280 1027180 951300 FALSE TRUE 922987.6893 860066.8944 869855.1847 874787.4263 952402.9112 851446.4651 902751.9708 937234.6738 1098822.745 0.839978689 0.782716683 0.791624662 0.796113322 0.86674845 0.774871533 0.821562872 0.852944369 1 20.06752725 0.73457065 1.813110457 0.999908297 0.808529848 0.825891659 0.027286722 0.365711056 1.871081825 0.024110217 0.006773011 5.427135316 -0.73457065 -0.191378449 KATDAEADVASLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KATDAEADVASLNRR 15 2 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKX5;H0YKP3 P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ; 203.99 2.88E-09 398630000 584160 340160 533530 512610 587460 539970 790600 645970 775630 FALSE TRUE 556547.9145 374822.6907 557992.8782 461081.4689 689912.838 521270.7035 669979.4496 589405.4423 895910.739 0.621209112 0.418370575 0.622821955 0.514651124 0.770068722 0.581833302 0.74781942 0.657884113 1 19.77299548 -0.096093355 0.226475151 1.189183069 0.473551522 0.679611361 0.0892853 4.358566487 0.368969065 0.838181354 0.198146928 0.801505754 0.096093355 -0.715631547 KATGAAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 1 KAT(0.001)GAAT(0.999)PK;KAT(0.067)GAAT(0.933)PK 88.092 0.0076286 1145470000 2964800 3472300 2860700 4166700 1665420 3808400 3639900 4360900 2456600 TRUE FALSE 2824659.78 3826131.318 2991865.925 3747855.4 1955868.721 3676514.153 3084566.404 3979036.477 2837556.981 0.995454822 1.348389246 1.054380914 1.320803573 0.689279099 1.295661788 1.087050031 1.402275444 1 21.43621793 -0.337018089 6.911148529 1.000000082 1.148376208 0.046807199 0.211514485 0 0 0.178937751 0.042176032 0.460237403 0.337018089 0.148376126 KATKS(ph)PAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KATKSPAKPK 10 3 P16401 P16401 HIST1H1B Histone H1.5 1 KAT(0.129)KS(0.871)PAKPK 99.011 0.027555 854460000 1574300 1312400 1578700 1895400 915670 2217100 2303100 2260000 1191400 TRUE FALSE 1499885.959 1446135.052 1651084.957 1704870.791 1075362.558 2140321.271 1951719.796 2062102.419 1376156.227 1.089909655 1.050850931 1.199780173 1.238864278 0.781424766 1.555289457 1.418239991 1.498450814 1 20.39221283 2.220231505 24.99984911 1.409941819 1.084250192 0.363321959 0.190666892 219.0280471 298739.6877 0.063476909 0.046967822 166.0471802 -2.220231505 -0.325691627 KATLELTHNWGTEDDETQSYHNGNSDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KATLELTHNWGTEDDETQSYHNGNSDPR 28 1 Q04760 Q04760 GLO1 Lactoylglutathione lyase 0 ;;;; 137.32 2.28E-06 1076670000 629074 262178 470710 565168 693456 466109 881213 616893 336133 FALSE TRUE 599338.9187 288894.2363 492292.5191 508356.2389 814394.5068 449967.5285 746767.7723 562874.5786 388258.7889 1.543658343 0.744076488 1.267949453 1.309323197 2.097555883 1.158937135 1.92337635 1.449740726 1 18.56665906 2.98723461 21.77527441 1.592127798 1.16024142 0.137917586 0.373501379 149.3558675 254774.8438 0.100627247 0.111768537 971.0343872 -2.98723461 -0.431886378 KATQAS(ph)QEY ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KATQASQEY 9 1 P16104 P16104 H2AFX Histone H2AX 1 KAT(0.001)QAS(0.999)QEY;KAT(0.006)QAS(0.994)QEY;KAT(0.002)QAS(0.998)QEY;KAT(0.012)QAS(0.988)QEY 86.911 0.014637 1155390000 3215570 2864240 2844500 3205000 2709370 2989570 3445660 3179480 2882520 TRUE FALSE 3063576.379 3156109.312 2974923.139 2882827.311 3181883.27 2886040.441 2919961.283 2901067.876 3329526.48 0.920123747 0.947915366 0.893497366 0.865837028 0.955656394 0.866802069 0.876989957 0.871315454 1 21.66688558 3.7275884 23.94683249 0.896325621 0.934019556 0.050503243 0.044049562 734.2423313 1602484.51 0.010467627 0.016410705 5340.579692 -3.7275884 0.037693935 KAVAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAVAVR 6 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 106.29 0.051713 987800000 3099000 3005100 2748900 3381900 2863400 3043500 3446100 3251300 3288400 FALSE TRUE 2952516.412 3311323.107 2874939.784 3041944.987 3362776.053 2938102.832 2920334.153 2966598.936 3798348.277 0.777315874 0.871779749 0.756892095 0.800859944 0.885325886 0.773521177 0.768843176 0.781023413 1 21.85694076 -1.334371398 3.395457111 1.001076127 0.803947849 0.674115286 0.043256654 18802232.12 29213579.28 206247.4777 0.01024972 0.046305076 1.334371398 -0.197128278 KAVEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAVEEAR 7 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 0 70.919 0.089348 97841000 436570 358630 314370 429270 331090 393710 456710 434310 379940 FALSE TRUE 415934.2013 395174.8047 328784.1755 386118.964 388831.9912 380075.724 387030.5014 396279.514 438859.1547 0.94776239 0.900459294 0.749179257 0.879824335 0.886006335 0.866053994 0.881901397 0.902976524 1 18.74339848 0.711181023 1.858763183 0.999963019 0.87668796 0.391281779 0.049550513 1.332597318 6.777663157 0.048825464 0.013647305 5.142579598 -0.711181023 -0.123275059 KAVIFCLSADKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAVIFCLSADKK 12 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 100.55 0.0017826 400850000 1892600 1408100 1239500 1468500 1193400 1550100 2180600 1715100 1415700 FALSE TRUE 1803140.549 1551586.991 1296332.301 1320883.59 1401528.582 1496419.648 1847909.421 1564916.752 1635239.526 1.102676715 0.948843865 0.792747656 0.807761535 0.857078465 0.915107313 1.130054277 0.956995429 1 20.64107054 1.768945552 25 1.041375707 0.914696837 0.266549237 0.095931185 37.51138608 30880.05581 0.04944023 0.027423069 58.74157026 -1.768945552 -0.12667887 KAVLFCLSEDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAVLFCLSEDKK 12 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 172.57 1.99E-05 1789300000 2147200 1603200 1772000 2016300 1056300 2076100 2202800 2061000 1262300 FALSE TRUE 2045706.111 1766567.903 1853247.953 1813617.693 1240518.386 2004204.136 1866722.403 1880527.914 1458051.037 1.403041498 1.211595382 1.271044638 1.243864342 0.850805873 1.374577491 1.28028605 1.289754519 1 20.47560979 4.79580791 1.105253034 1.200861108 1.52442952 0.157426218 0.154057196 3.660190022 3.406617631 0.04358664 1.426577695 62489.62375 -4.79580791 0.323568412 KAVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAVSPLLLTTTNSSEGLSMGNYIGLINR 28 1 P19525-2;P19525;C9JZT2 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KAVS(0.957)PLLLT(0.035)T(0.007)TNSSEGLSMGNYIGLINR 240.46 1.74E-45 75642000 49357 40572 49210 50805 51636 50818 69096 56073 70542 TRUE FALSE 47023.99243 44706.33293 51466.32718 45697.98488 60641.30205 49058.15992 58554.13616 51162.95086 81481.29308 0.577113969 0.5486699 0.631633658 0.560840202 0.744235882 0.602078809 0.718620605 0.627910394 1 16.31418126 -4.999999999 0.162402162 2.445124939 0.521046454 0.823902 0.055926985 45.43597581 0.420445921 21.0687683 0.197735687 1.00E-05 4.999999999 -1.924078485 KAVVLPGGTATS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAVVLPGGTATSPK 14 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 KAVVLPGGTAT(0.039)S(0.961)PK;KAVVLPGGTAT(0.067)S(0.933)PK 144.01 5.49E-06 1371740000 2205900 2103750 2027090 2549800 1332990 2541600 2628700 2442400 1395050 TRUE FALSE 2101631.479 2318124.517 2120034.082 2293489.26 1565463.034 2453583.755 2227643.536 2228530.508 1611387.229 1.304237393 1.438589356 1.315657741 1.423301127 0.971500212 1.522653097 1.382438371 1.382988811 1 20.6198718 -1.936396601 2.467371097 0.756227044 1.349968775 0.351595161 0.145946252 15765627.33 9083039.717 22161644.37 0.032029094 0.011577196 1.936396601 0.593741731 KAVVVCPKDEDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KAVVVCPKDEDYK 13 2 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 136.17 4.24E-05 437600000 454690 316270 428930 452310 302100 475330 514700 549070 353310 FALSE TRUE 433197.7048 348498.2726 448596.8648 406842.9395 354786.1444 458869.2029 436173.0619 500990.52 408099.5103 1.061500183 0.853954155 1.099234019 0.99692092 0.869361848 1.124405179 1.068790946 1.227618528 1 18.63856145 2.211344903 24.92799356 1.106901781 0.973815023 0.324270046 0.092489608 235.0587482 215298.4994 0.032093325 0.023708269 162.6840229 -2.211344903 -0.133086758 KAYGQALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAYGQALAK 9 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 138.98 0.00019483 3055500000 11539100 7385000 5320400 6327700 9778900 6337500 12636200 8222600 9439100 FALSE TRUE 10993669.61 8137539.896 5564345.603 5691627.574 11484337.06 6118030.786 10708315.61 7502585.553 10902867.42 1.008328285 0.746366949 0.510356165 0.522030339 1.053331809 0.561139611 0.982155904 0.688129578 1 23.37820427 1.709680145 24.9999943 0.876535864 0.751773545 0.112598524 0.201684159 2.227169783 1917.924107 0.091200404 0.050575204 51.24838035 -1.709680145 -0.124762319 KAYS(ph)FCGTVEYMAPEVVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)FCGTVEYMAPEVVNR;KAYS(1)FCGTVEYMAPEVVNR;KAYS(0.996)FCGT(0.004)VEYMAPEVVNR;KAYS(1)FCGTVEYMAPEVVNR 240.95 1.48E-24 1928220000 1647170 1255590 1591890 1666470 1442140 1582100 2000680 1780260 1744110 TRUE FALSE 1569311.538 1383536.048 1664879.731 1498953.27 1693648.759 1527311.48 1695439.521 1624370.997 2014577.671 0.778977927 0.686762327 0.826416253 0.744053352 0.84069668 0.758129856 0.841585582 0.806308449 1 20.942046 -5 0.145196377 1.802119447 0.703434296 0.725002688 0.043351565 61.39814753 0.537517085 14.10569929 0.211839378 1.00E-05 5 -1.098685151 KAYWQVHLDQVEVASGLTLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KAYWQVHLDQVEVASGLTLCK 21 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 150.69 4.48E-08 392730000 810780 495250 691630 708030 766580 691540 1055300 793360 745640 FALSE TRUE 772456.0362 545716.5381 723341.9196 636857.4792 900271.3093 667591.7964 894294.6031 723889.1925 861270.043 0.896880186 0.63361839 0.839854962 0.739439952 1.045283435 0.775124831 1.038344025 0.840490388 1 19.71610613 2.756411518 24.78640919 0.936459746 0.770213933 0.363860695 0.106457631 723.9908628 1005277.656 0.029232794 0.030943318 570.7047903 -2.756411518 -0.166245812 KCEAEEAEPPAATQPQTSETQTSHLPESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCEAEEAEPPAATQPQTSETQTSHLPESER 30 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 233.6 1.44E-45 260370000 110110 93031 107640 111000 85424 103770 123880 116130 94840 FALSE TRUE 104905.3185 102510.9647 112575.4005 99842.06911 100321.9186 100176.4189 104979.8308 105961.0416 109547.3028 0.957625754 0.935768951 1.027641919 0.911406 0.915786295 0.914458104 0.958305938 0.967262898 1 16.74119444 0.990665421 2.09630292 0.999339454 0.944818512 0.217371124 0.033514384 0.509993663 4.831314607 0.030684779 0.00852709 9.787356793 -0.990665421 -0.054520942 KCEPIVMTVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCEPIVMTVPR 11 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 81.565 0.034194 450510000 1112500 956240 1008200 1112200 1109200 1173500 1453900 1251200 1346000 FALSE TRUE 1059914.33 1053681.943 1054426.967 1000399.543 1302644.129 1132861.401 1232080.852 1141638.295 1554730.806 0.681734951 0.677726292 0.67820549 0.64345515 0.837858312 0.728654373 0.792472142 0.734299656 1 20.56823338 -5 0.136726061 1.992936512 0.609143612 0.783828471 0.048775593 57.56925238 0.486992779 15.47406958 0.293403917 1.00E-05 5 -1.3837929 KCLELFSELAEDKENYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KCLELFSELAEDKENYKK 18 3 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 244.46 1.66E-24 1034280000 2049480 1818250 1858620 2074220 972980 2245850 2158910 2452610 1084300 FALSE TRUE 1952605.142 2003531.742 1943839.565 1865715.465 1142667.404 2168075.651 1829528.628 2237846.466 1252447.706 1.559031273 1.599692931 1.552032517 1.489655381 0.912347396 1.731070799 1.460762489 1.786778366 1 20.25631894 3.138442244 4.774602978 1.419341622 1.574620189 0.082524589 0.27283213 0.612783011 23.48051314 0.074743777 0.090802813 1375.44188 -3.138442244 0.155278567 KCLELFTELAEDKENYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KCLELFTELAEDKENYK 17 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 210.75 1.74E-12 2739400000 689020 808390 614110 779920 362992 745350 660820 786130 336129 FALSE TRUE 656451.3901 890765.8601 642267.5509 701520.9598 426297.6899 719538.3426 559999.7722 717292.2897 388254.1686 1.690777442 2.294285373 1.654245087 1.806860084 1.097986124 1.853266238 1.442353534 1.847481232 1 18.56664189 3.301249762 2.178195756 1.512363638 1.981565838 0.267345885 0.323945078 0.355578445 3.452306621 0.08888945 0.126381333 2001.012316 -3.301249762 0.4692022 KCLELFTELAEDKENYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCLELFTELAEDKENYKK 18 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 154.75 1.04E-08 782980000 577270 550030 494760 645330 299370 608470 627940 700040 318230 FALSE TRUE 549983.5911 606078.6823 517445.2354 580460.2024 351580.0332 587398.5313 532136.2201 638740.7865 367579.4831 1.496230384 1.648837082 1.407709786 1.579142006 0.956473496 1.59801773 1.44767661 1.737694338 1 18.48769672 3.466474011 2.231634171 1.403872643 1.568444893 0.076036983 0.249706407 0.814507621 8.133547246 0.068062721 0.108154395 2927.345686 -3.466474011 0.164572249 KCS(ph)LPAEEDSVLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)LPAEEDSVLEK 189.48 3.56E-08 1133200000 812859 693594 663977 820687 465654 866570 884131 897771 554751 TRUE FALSE 774436.766 764272.0172 694421.0022 738189.9836 546863.9102 836560.4636 749240.5778 819157.4119 640778.9518 1.208586462 1.192723349 1.083713815 1.152019712 0.853436132 1.30553674 1.169265276 1.278377527 1 19.28946723 3.888390354 7.183527085 1.131394063 1.202652745 0.057927403 0.129370559 0.797875849 45.40760993 0.031698875 0.05756126 7733.753999 -3.888390354 0.071258682 KCSASNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCSASNR 7 1 Q8WVC2;P63220;Q9BYK1;Q9BYK2 Q8WVC2 RPS21 40S ribosomal protein S21 0 78.334 0.057108 15556000 24039 23436 21261 35406 24652 21124 32347 39498 33873 FALSE TRUE 22902.72411 25824.15504 22235.83788 31846.92161 28951.30099 20392.47058 27411.87106 36039.34573 39125.85184 0.585360396 0.660027931 0.568315751 0.813961105 0.739953244 0.521201958 0.700607649 0.921113382 1 15.25583454 1.210789524 3.309619636 0.992303618 0.648540282 0.703193352 0.083732922 0.124432501 2.43374603 0.073795393 0.020565291 16.24761142 -1.210789524 -0.343763336 KCSTPEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KCSTPEEIK 9 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 143.28 0.00016407 1907990000 4328430 3397360 3548000 4446000 2957760 4199940 5053500 4574100 3318660 FALSE TRUE 4123833.692 3743554.846 3710679.309 3999079.633 3473592.408 4054495.025 4282495.761 4173567.555 3833300.843 1.07579182 0.976587802 0.968011503 1.043247007 0.906162221 1.057703319 1.117182276 1.088765981 1 21.8701558 2.01467115 24.99940084 1.083112971 0.998577997 0.294508924 0.05376522 240.8987612 410486.0475 0.018832309 0.01390358 103.4358649 -2.01467115 -0.084534974 KCSTPEEIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KCSTPEEIKK 10 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 144.1 1.84E-05 3509910000 8795460 6850700 7832820 9942280 5325220 9294220 11182950 10038710 6599130 FALSE TRUE 8379716.037 7548794.119 8191962.545 8942863.125 6253936.682 8972358.831 9476785.589 9159667.334 7622489.377 1.099341124 0.990331865 1.074709605 1.173220805 0.820458563 1.177090369 1.243266487 1.201663509 1 22.8618308 2.052092508 24.99995465 1.184052105 1.037055837 0.217505014 0.110868968 113.7585703 54593.79686 0.037554423 0.027735776 112.7437583 -2.052092508 -0.146996268 KCSTPEEIKKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCSTPEEIKKR 11 3 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 51.841 0.064889 304030000 179090 117220 193640 156570 163640 165250 289440 193620 232810 FALSE TRUE 170624.7706 129164.8513 202518.5855 140831.2861 192178.7642 159527.3511 245280.6121 176665.6064 268912.9858 0.634498071 0.480322105 0.753100803 0.523705784 0.714650368 0.593230374 0.912118882 0.656961975 1 18.0367799 1.184992308 0.378798365 1.018986227 0.550954004 0.530954418 0.110620346 0.842444713 0.363491929 0.151066635 0.094802372 15.31060345 -1.184992308 -0.468032223 KCYEMASHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KCYEMASHLR 10 1 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 105.13 0.001681 271950000 1064700 842050 581580 618090 1087400 623360 1150500 860800 998020 FALSE TRUE 1014373.741 927855.8523 608246.0183 555958.4189 1277042.216 601772.8869 974970.0946 785423.7886 1152787.844 0.879930983 0.804879976 0.527630493 0.482272971 1.107785983 0.522015295 0.845749805 0.68132553 1 20.1366956 -1.171791418 4.447380864 1.000053302 0.742898942 0.159137787 0.192408002 25870402.52 6816310.826 13428.17545 0.041462505 0.067329995 1.171791418 -0.25715436 KDAAEQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDAAEQVR 8 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 0 67.113 0.096103 41181000 119300 108390 96042 115140 99954 112960 129760 120310 110650 FALSE TRUE 113660.9254 119435.0642 100445.6207 103565.9084 117385.946 109048.1669 109962.7288 109775.0186 127809.0369 0.88930273 0.93448059 0.785903901 0.810317572 0.918447935 0.85321171 0.8603674 0.858898723 1 16.96363032 -0.894415545 5.083123253 1.000000316 0.868340122 0.477245222 0.044557959 1.64E-07 3.56E-08 0.044301098 0.010441844 0.127521806 0.894415545 -0.131660194 KDAENHEAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KDAENHEAQLK 11 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;;;; 164.11 1.50E-05 883695000 2022000 1868240 1765370 2187900 1274360 1948360 2086760 2263000 1354930 FALSE TRUE 1926424.067 2058615.78 1846313.961 1967968.135 1496607.981 1880887.805 1768386.436 2064839.723 1565045.624 1.230906011 1.315371097 1.179718937 1.257450968 0.956271151 1.201810206 1.129926443 1.319347942 1 20.57777328 5.563669272 0.022229567 1.18E-09 2.569469634 0.232022363 0.106000222 2024.999499 5.581982587 261.8915951 394.2825167 366158.6281 -5.563669272 2.569469633 KDDDS(ph)DDESQSSHTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.673)DDES(0.327)QSSHTGK;KDDDS(0.999)DDES(0.001)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.998)DDES(0.002)QSSHTGK;KDDDS(0.917)DDES(0.083)QSSHTGK;KDDDS(0.986)DDES(0.014)QSSHTGK;KDDDS(0.995)DDES(0.003)QS(0.002)SHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.982)DDES(0.016)QS(0.001)S(0.001)HTGK 304.8 1.70E-46 7012312000 6254365 5397954 5836149 7009378 3220970 7053187 7547237 7530488 3089010 TRUE FALSE 5958733.561 5948011.65 6103742.204 6304782.006 3782706.148 6808933.366 6395767.381 6871078.549 3568037.894 1.670030907 1.667025919 1.710671911 1.767016549 1.06016423 1.908313075 1.792516663 1.925730262 1 21.76669951 -1.97304406 2.781626772 0.422168003 1.686865613 0.448124739 0.239833277 61378090.32 57502633.29 229240005.4 0.053924974 0.010640351 1.97304406 1.264697611 KDDDS(ph)DDESQSSHTGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KDDDSDDESQSSHTGKK 17 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.995)DDES(0.003)QS(0.001)SHTGKK;KDDDS(1)DDESQSSHTGKK;KDDDS(0.999)DDESQSSHTGKK;KDDDS(1)DDESQSSHTGKK 172.81 8.12E-10 164047000 187492 156641 173856 192452 85398 216191 220198 248754 77618.3 TRUE FALSE 178629.6247 172602.896 181827.4696 173106.3593 100291.3842 208704.2515 186602.7509 226971.781 89654.94954 1.992412306 1.925190933 2.028080664 1.9308065 1.11863745 2.327860899 2.081343549 2.53161462 1 16.45209561 3.003347161 23.25023097 1.896148308 1.972271076 0.010257891 0.475842214 433.2789941 3009536.717 0.130253596 0.154796473 1007.7369 -3.003347161 0.076122768 KDDEDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDDEDSFR 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 109.29 0.009917 0 245280 233980 223820 254160 159560 209790 266170 256700 162260 FALSE TRUE 233686.1005 257822.828 234082.3684 228611.3539 187387.2135 202524.9197 225560.878 234221.9871 187422.4521 1.246841549 1.375624025 1.248955852 1.219765035 0.999811983 1.080579821 1.203489099 1.249700794 1 17.51593426 3.143700921 2.73476461 1.12368094 1.307099191 0.479966593 0.086413138 0.229022781 3.47442604 0.026226009 0.03303042 1392.19773 -3.143700921 0.183418251 KDDEENYLDLFSHK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 288.53 1.08E-34 5248270000 19147150 17930330 16455400 21419530 10320300 20006830 20345750 21375370 9870440 FALSE TRUE 18242102.17 19757451.01 17209896.37 19266398.15 12120157.05 19313988.46 17241632.16 19503629.28 11401097.42 1.600030373 1.732942916 1.50949472 1.689872249 1.063069335 1.694046436 1.512278294 1.710679995 1 23.44266936 -1.950133169 2.558971999 0.575169485 1.570009283 0.453125123 0.194642758 10056313.81 4389042.759 25384515.07 0.043120308 0.011216745 1.950133169 0.994839798 KDDEVQVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 154.84 0.00011983 5401065000 11268620 10392080 11124130 11716290 8466760 12232090 12941940 12150510 6939790 FALSE TRUE 10735974.66 11451044.77 11634182.36 10538546.27 9943360.263 11808489.66 10967409.36 11086546.93 8015977.19 1.339322008 1.428527614 1.451374185 1.314692647 1.240442684 1.473119169 1.368193683 1.383056197 1 22.93444697 -0.935717495 5.321223856 0.99999918 1.377696775 0.750415563 0.06791942 6.31E-07 1.26E-07 0.06278311 0.014798089 0.115953138 0.935717495 0.377697595 KDDPTLLSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KDDPTLLSSGR 11 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ;;;; 158.25 4.82E-05 6644100000 8475750 5857960 6610350 8138700 7216660 7439050 10188660 8581940 8351160 FALSE TRUE 8075118.095 6454892.784 6913441.086 7320582.413 8475243.219 7181433.833 8634192.789 7830459.838 9646215.241 0.837128127 0.669163254 0.716699857 0.758907222 0.878608139 0.744482023 0.89508606 0.811764992 1 23.20153157 0.964541671 0.425911382 1.00870712 0.737254941 0.565704699 0.063733066 0.886973457 0.421354347 0.087518024 0.044112854 9.215983132 -0.964541671 -0.27145218 KDDPVTNLNNAFEVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDDPVTNLNNAFEVAEK 17 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 226.23 3.44E-15 277570000 837130 547800 354520 485260 582560 460540 862690 530810 444830 FALSE TRUE 797560.5239 603621.4428 370775.0927 436480.7429 684158.2796 444591.3843 731070.7961 484329.4624 513811.9645 1.552242024 1.174790555 0.721616308 0.849495094 1.331534349 0.865280326 1.422837237 0.942620055 1 18.97088096 4.317221773 2.593985217 1.051142908 1.518897103 0.363033584 0.21670959 0.307103777 3.938502064 0.054751655 0.206946605 20759.73345 -4.317221773 0.467754195 KDDRVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDDRVEER 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 68.626 0.031508 41500000 70932 53652 49434 58346 43819 50001 54368 70652 32962 FALSE TRUE 67579.18493 59119.1998 51700.5978 52480.94923 51461.01973 48269.45283 46073.16306 64465.33633 38073.57861 1.77496278 1.552761835 1.357912749 1.378408627 1.351620247 1.267793956 1.210108551 1.693177754 1 15.21650256 8 0.294731882 1.232909708 6.00410445 0.467334489 0.166425831 40.0470482 0.570856278 0.155449876 100.1282231 100000000 -8 4.771194742 KDDS(ph)DDDGGGWITPSNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;KDDS(1)DDDGGGWITPSNIK 232.96 6.06E-24 1467300000 3839060 4593050 3437510 4700690 1707090 4676350 3823750 4812410 1738310 TRUE FALSE 3657595.242 5061087.017 3595123.234 4228167.71 2004805.956 4514406.827 3240366.71 4391009.868 2007878.237 1.821622036 2.52061451 1.790508592 2.105788903 0.998469887 2.248346909 1.613826302 2.186890514 1 20.93724035 3.243667206 2.219835123 1.701004201 2.150657376 0.145008392 0.465435165 0.524096352 5.296655412 0.129137611 0.176255261 1752.53704 -3.243667206 0.449653175 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;KDDS(1)HS(1)AEDS(1)EDEKEDHKNVR 60.521 0.036891 442390000 248370 177784 227110 211243 75868 245160 271450 264900 70393 TRUE FALSE 236630.0423 195900.3917 237523.2181 190008.4523 89099.35518 236670.0477 230035.317 241703.9517 81309.18692 2.910249767 2.40932666 2.921234698 2.336863268 1.095809201 2.910741783 2.829143 2.972652425 1 16.31113075 4.658756709 0.813255908 2.367286174 3.145230013 0.066181424 0.717736252 7.881568421 4.333345255 0.246685565 5.426930803 45578.15164 -4.658756709 0.777943838 KDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.401)HS(0.599)AEDS(1)EDEKEDHK;KDDS(0.023)HS(0.977)AEDS(1)EDEKEDHK;KDDS(0.024)HS(0.976)AEDS(1)EDEKEDHK;KDDS(0.367)HS(0.633)AEDS(1)EDEKEDHK;KDDS(0.17)HS(0.83)AEDS(1)EDEKEDHK 184.59 3.08E-14 2991180000 2590150 3015080 1860640 3118320 758620 3149970 2192150 2910440 463391 TRUE FALSE 2467718.743 3322320.08 1945952.184 2804860.549 890923.0878 3040885.749 1857697.256 2655586.444 535251.3096 4.610392723 6.2070284 3.635586031 5.240268447 1.664494924 5.681229909 3.470701001 4.961382432 1 19.02985689 3.724454268 24.2840693 3.848628726 5.408710574 0.177108505 1.523201145 783.9372558 1349547.634 0.352517492 0.549288891 5302.177571 -3.724454268 1.560081849 KDDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.121)HS(0.879)AEDS(1)EDEKEDHKNVR;KDDS(0.064)HS(0.936)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.054)HS(0.946)AEDS(1)EDEKEDHKNVR;KDDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;KDDS(0.035)HS(0.965)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.47)HS(0.531)AEDS(0.998)EDEKEDHKNVR;KDDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;KDDS(0.012)HS(0.988)AEDS(1)EDEKEDHKNVR;KDDS(0.144)HS(0.856)AEDS(1)EDEKEDHKNVR;KDDS(0.045)HS(0.955)AEDS(1)EDEKEDHKNVR 230.8 4.41E-26 21049115000 6991088 5507298 5754599 6678886 2316701 7568650 7133609 7644403 1782500 TRUE FALSE 6660633.125 6068497.927 6018453.056 6007511.69 2720732.921 7306545.753 6045245.929 6975018.548 2058920.996 3.235011512 2.947416602 2.923110244 2.917796118 1.321436289 3.548725651 2.936123309 3.387705774 1 20.97345704 2.98310571 24.86727772 2.624230196 3.029362357 0.085266846 0.811757764 2202.410165 3241807.916 0.227991208 0.247354195 961.8463696 -2.98310571 0.40513216 KDDSHSAEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK 349.92 1.12E-90 1163690000 1421910 1767960 1027460 1646410 425070 1628510 1098730 1530700 291971 TRUE FALSE 1354699.132 1948117.134 1074570.057 1480909.739 499202.0734 1572114.29 931098.5589 1396663.793 337248.3715 4.016918232 5.776505681 3.186286868 4.391154603 1.480220857 4.66159194 2.760868955 4.141350741 1 18.36345195 3.718122798 23.6641505 3.216551968 4.896711859 0.261895614 1.247560767 448.0771631 518810.9507 0.289736746 0.449598812 5225.439193 -3.718122798 1.680159891 KDDSHSAEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 256.75 7.55E-37 814652000 1277460 944750 994970 1134750 404560 1272800 1076700 1313140 387835 TRUE FALSE 1217076.997 1041021.099 1040590.359 1020682.774 475115.1359 1228722.617 912429.64 1198154.5 447978.471 2.716820285 2.323819483 2.322857963 2.278419255 1.060575824 2.742816221 2.036771182 2.674580538 1 18.77306988 3.993432769 1.029134618 2.03896558 2.717248174 0.147829065 0.57915781 1.457141399 2.513989271 0.178445458 0.830868389 9849.921489 -3.993432769 0.678282594 KDDTDDEIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDDTDDEIAK 10 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 90.926 0.016833 119810000 202570 207360 157910 301800 123690 227420 206120 214980 116760 FALSE TRUE 192994.9176 228490.2197 165150.3297 271462.4906 145261.4968 219544.3884 174672.6083 196155.2115 134866.5445 1.431006617 1.694194959 1.224546312 2.012823059 1.077075841 1.627863969 1.295151507 1.454439367 1 17.04117299 -0.033533816 0.34795007 0.88747928 1.561940259 0.265285489 0.258534806 6.094433691 1.022340318 1.18037485 0.200588482 0.925691303 0.033533816 0.674460979 KDDVS(ph)PVMQFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;KDDVS(1)PVMQFSSK;KDDVS(0.999)PVMQFS(0.001)SK;KDDVS(1)PVMQFSSK 251 2.48E-18 2460260000 3886540 3302890 3396480 3965870 2316920 4297470 4494610 4358790 2791330 TRUE FALSE 3702830.957 3639458.246 3552211.968 3567213.213 2720990.114 4148647.536 3808874.695 3977111.24 3224195.2 1.148451234 1.128795876 1.101736014 1.106388724 0.843928468 1.286723439 1.181341221 1.233520613 1 21.62050766 KDEDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDEDLFR 7 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ; 155.1 0.0026194 1454090000 1966330 1384640 1291740 1636420 1488740 1499360 2003060 1703220 1456400 FALSE TRUE 1873385.478 1525736.39 1350967.557 1471923.953 1748375.785 1447436.787 1697456.408 1554077.027 1682251.074 1.113618239 0.906961163 0.8030713 0.874972812 1.039307278 0.860416623 1.009038683 0.923808016 1 20.68196161 -0.217687842 7.785125533 1.000064528 0.946452079 0.036295416 0.091666921 0 0 0.087330856 0.02058408 0.605776133 0.217687842 -0.053612449 KDEEGQKEEDKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KDEEGQKEEDKPR 13 3 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ;; 115.78 0.00027912 666490000 761430 705750 679430 853580 301443 829840 846940 939650 284961 FALSE TRUE 725438.7129 777666.7274 710582.5375 767776.5167 354014.5638 801102.4327 717723.7479 857369.2646 329151.2965 2.203967357 2.362642152 2.158832565 2.332594539 1.075537504 2.433842556 2.180528394 2.604787749 1 18.32839135 KDEEKEDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 52.278 0.083913 115560000 320730 415630 274410 398690 124820 339540 268190 401510 137330 FALSE TRUE 305569.7285 457983.1695 286991.9699 358612.9237 146588.5685 327781.6447 227272.6899 366351.6559 158626.435 1.92634808 2.887180623 1.80923167 2.260738721 0.924111851 2.066374653 1.432754193 2.309524613 1 17.27527369 3.182922408 1.993441289 1.616508691 2.367956629 0.25439743 0.519977784 0.376333588 3.073086325 0.149224357 0.198257712 1523.780489 -3.182922408 0.751447938 KDEESGGGSNPFQHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KDEESGGGSNPFQHLEK 17 1 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 213.69 2.90E-13 634560000 1677750 1484220 1417770 1840840 964790 1710030 1674710 1858020 956320 FALSE TRUE 1598446.082 1635463.705 1482776.157 1655795.266 1133049.071 1650811.232 1419202.231 1695321.919 1104621.221 1.447053571 1.480565169 1.34233901 1.498971081 1.025735382 1.494459096 1.284786318 1.534754073 1 20.07512032 -3.532208311 0.258135517 4.31E-22 1.425621891 0.373772673 0.152772852 83.95030771 1.644846406 45.31984657 0.189191069 0.000293624 3.532208311 1.425621891 KDEKKEES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDEKKEESEESDDDMGFGLFD 21 3 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 2 KDEKKEES(1)EES(1)DDDMGFGLFD;KDEKKEES(1)EES(1)DDDMGFGLFD 61.801 0.01887 311223000 1457930 569391 1305900 987400 554560 1401600 1902310 1727240 662540 TRUE FALSE 1389016.538 627412.5902 1365776.807 888144.6761 651275.0884 1353062.241 1612077.671 1575993.709 765283.3194 1.815035691 0.819843546 1.784668203 1.160543623 0.851024806 1.768054009 2.106510923 2.059359807 1 19.54563443 2.071581544 9.609665558 1.867910955 1.288268378 0.175300686 0.446931782 0.418102128 52.58293253 0.15344695 0.113266653 117.9183909 -2.071581544 -0.579642577 KDEKTDTLEDLFPTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDEKTDTLEDLFPTTK 16 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 105.6 0.00071482 274760000 1543500 976220 1402300 1321700 811730 1607900 1833700 1831300 966890 FALSE TRUE 1470541.814 1075697.928 1466596.842 1188840.205 953295.455 1552218.02 1553935.387 1670941.664 1116830.363 1.316710095 0.963170382 1.313177803 1.064476974 0.853572294 1.389842246 1.391379961 1.496146343 1 20.09097864 2.185460895 24.99995253 1.357534644 1.110630799 0.233993075 0.189350256 116.649089 54918.84084 0.065011886 0.048014505 153.2713189 -2.185460895 -0.246903846 KDELSDWSLAGEDDRDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 188.19 2.20E-14 1802890000 2276380 2531750 2032040 2671760 1569920 2185990 2233540 2424250 1659010 FALSE TRUE 2168780.029 2789738.203 2125211.044 2403189.609 1843713.551 2110288.618 1892772.451 2211969.818 1916280.798 1.131765257 1.455808672 1.109029035 1.254090534 0.962131204 1.101241854 0.987732306 1.154303597 1 20.86987755 3.019577369 1.752689868 1.041722758 1.277922808 0.394768156 0.112651204 0.292593362 1.827745341 0.03596047 0.043078683 1046.110037 -3.019577369 0.236200049 KDENKVDGMNAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDENKVDGMNAPK 13 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 97.273 0.018509 103950000 289990 297340 255550 345070 144050 337280 298580 378450 168330 FALSE TRUE 276282.7474 327639.284 267267.2203 310382.908 169172.2744 325599.909 253026.1372 345310.9117 194433.7567 1.420960805 1.685094654 1.374592688 1.596342699 0.870076664 1.674605864 1.301348806 1.775982307 1 17.56891919 -1.430867886 3.151028199 0.992595443 1.461125331 0.2414086 0.257579115 60087986.98 76649470.92 3979848.076 0.057073506 0.03707935 1.430867886 0.468529888 KDEPDAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KDEPDAFK 8 1 P13674;P13674-2 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 107.24 0.0064785 1091210000 2600990 2441070 2178080 2933900 1353230 2679220 2652840 2788990 1418220 FALSE TRUE 2478046.357 2689817.808 2277947.122 2638978.798 1589232.884 2586437.94 2248100.535 2544771.25 1638150.314 1.512709997 1.641984734 1.390560501 1.610950335 0.970138619 1.578877052 1.372340814 1.553441847 1 20.64363631 -3.671373818 0.161127637 8.81E-12 1.597377791 0.339801575 0.194710662 88.13980594 1.205763446 30.63938212 0.786127962 0.000213121 3.671373818 1.597377791 KDEPDAFKELGTGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDEPDAFKELGTGNR 15 2 P13674;P13674-2 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 161.91 9.14E-07 740960000 1099210 745150 1002700 1057310 899500 1117810 1466010 1292990 1013980 FALSE TRUE 1047252.522 821081.6322 1048674.787 951027.19 1056372.515 1079099.959 1242343.249 1179768.941 1171222.84 0.89415309 0.701046466 0.895367432 0.811995086 0.901939818 0.921344703 1.060723209 1.007296734 1 20.15958416 2.243673282 1.347947373 1.030603715 0.812784286 0.667465121 0.058998514 0.22439869 0.79502269 0.033923664 0.019785722 175.2561561 -2.243673282 -0.217819429 KDEQEHEFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDEQEHEFYK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 119.03 0.00048474 671060000 2595200 2026960 1661840 2343900 1489950 2185100 2703400 2428500 1257580 FALSE TRUE 2472530.039 2233509.528 1738037.008 2108286.719 1749796.808 2109429.439 2290946.679 2215847.666 1452599.084 1.702142089 1.537595303 1.196501517 1.451389267 1.204597213 1.45217594 1.577136255 1.525436503 1 20.47020514 4.019877491 4.038351275 1.383020137 1.652420342 0.291352695 0.177922784 0.259165471 9.784074187 0.043549715 0.094870018 10468.33209 -4.019877491 0.269400205 KDETNVK ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 106.93 0.012174 3578670000 4637890 3575520 3555980 4881390 2515800 3689170 4245240 5052410 3591930 FALSE TRUE 4418666.131 3939869.553 3719025.2 4390703.403 2954554.723 3561413.118 3597550.669 4609994.196 4148948.159 1.065008759 0.949606841 0.896377843 1.058269044 0.712121388 0.858389399 0.86709945 1.111123595 1 21.9843142 4.56094638 1.030576662 0.909166636 1.119014012 0.106619621 0.112730347 2.487586173 2.628101788 0.033076137 0.538926085 36387.0108 -4.56094638 0.209847377 KDFSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KDFSELR 7 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;; 101.64 0.014284 434580000 1116510 893660 804940 938980 958930 908230 1240930 1055090 1041140 FALSE TRUE 1063734.785 984724.97 841847.2952 844591.9465 1126167.088 876777.7674 1051603.337 962700.7262 1202594.674 0.884533092 0.818833637 0.700025797 0.702308072 0.93644776 0.72907172 0.874445364 0.800519699 1 20.19771904 -0.251569395 0.651001897 1.01397533 0.804671027 0.376267181 0.078755388 8.276684739 3.205157341 0.368575828 0.028715232 0.560312879 0.251569395 -0.209304303 KDFSSVFQFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDFSSVFQFLR 11 1 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 164.48 3.64E-05 83246000 277910 164710 74025 80016 234170 91932 232970 156610 191560 FALSE TRUE 264773.7451 181494.1363 77419.11947 71972.63966 275009.1739 88748.37179 197426.1477 142896.3982 221266.1464 1.196630164 0.82025262 0.34989139 0.325276328 1.242888613 0.401093313 0.892256456 0.645812296 1 17.75542321 4.301135175 2.64716544 0.68734464 1.158746928 0.215317696 0.295487847 0.375668585 5.071487007 0.069899541 0.253012042 20004.84425 -4.301135175 0.471402288 KDFVSEQLTSLLVNGVQLPALGENKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDFVSEQLTSLLVNGVQLPALGENKK 26 2 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 132.35 3.16E-05 43844000 144100 132410 139840 148200 98548 151170 174130 172830 106600 FALSE TRUE 137288.6786 145902.7295 146251.8023 133302.6544 115734.74 145934.945 147563.2704 157696.089 123130.9836 1.114980768 1.184939203 1.187774174 1.082608541 0.939931905 1.185200839 1.198425174 1.280718178 1 16.90983431 -0.266217976 7.210749069 1.000000004 1.147019286 0.207606151 0.090144985 0 0 0.087142117 0.020539594 0.541728924 0.266217976 0.147019282 KDGADFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 4977700000 7713400 6865000 6360100 7807700 4510800 7393600 8250700 7594900 4952200 FALSE TRUE 7348802.868 7564551.305 6651716.876 7022855.162 5297482.092 7137557.778 6991904.18 6929850.293 5720161.884 1.284719387 1.322436578 1.162854655 1.227737135 0.926107023 1.247789472 1.222326277 1.211478003 1 22.44762455 8 0.048617996 0.684995643 2.131786892 0.294102608 0.104053521 652.1466936 2.396649326 17.14250475 71.54290713 100000000 -8 1.446791248 KDGNASGTTLLEALDCILPPTRPTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 163.62 8.26E-12 57284000 143810 172290 126470 166070 106670 145950 140890 150910 92905 FALSE TRUE 137012.3863 189846.5469 132268.7746 149376.3281 125273.2142 140895.7149 119394.6429 137695.5204 107312.2329 1.276763912 1.769104432 1.232560082 1.391978566 1.167371238 1.312951106 1.112591171 1.283129767 1 16.71145502 3.156158063 1.37771151 1.183565522 1.50668889 0.354421184 0.163823992 0.382904441 1.522661147 0.055439208 0.076238002 1432.709245 -3.156158063 0.323123368 KDGS(ph)SPPLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 KDGS(0.726)S(0.274)PPLLEK 107.61 0.0013318 257070000 705070 648210 666080 751960 378790 756860 773130 784800 442830 TRUE FALSE 671742.7384 714263.336 696620.4268 676371.5522 444850.8561 730649.7484 655174.819 716078.7515 511501.8147 1.313275377 1.396404305 1.361911936 1.322324834 0.869695558 1.428440188 1.280884642 1.399953492 1 18.96437983 -1.86885 2.632616681 0.864199204 1.300923303 0.256818352 0.158420429 17427555.53 10305280.01 14769274.41 0.038049042 0.013525396 1.86885 0.436724099 KDHRDNLEFFLAGIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDHRDNLEFFLAGIGR 16 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 0 137.52 6.97E-06 121030000 206120 71176 230680 137180 331730 182030 540820 200600 385660 FALSE TRUE 196377.1161 78428.91532 241256.9062 123390.4058 389583.607 175726.2555 458307.9762 183034.4006 445466.1831 0.44083507 0.176060312 0.541582987 0.276991634 0.874552596 0.394477206 1.028827762 0.410882818 1 18.76495639 2.711049775 1.051130995 0.780196664 0.317180633 0.345590752 0.241607603 0.4812228 1.112111667 0.114216742 0.102405489 514.1025701 -2.711049775 -0.463016031 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(0.997)PPDY(0.002)S(0.001)EYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK 311.16 2.23E-92 762244000 1020309 1000367 937738 1129603 690003 1086390 1088933 1164992 628327 TRUE FALSE 972081.0156 1102305.535 980734.2148 1016053.16 810339.3047 1048768.042 922796.2712 1062979.124 725764.7421 1.339388591 1.518819351 1.351311462 1.399975917 1.11653165 1.445052344 1.271481263 1.464633183 1 19.46914245 -3.632115714 0.251969298 4.01E-19 1.40361023 0.483781406 0.11483499 70.02062656 1.296161577 36.56875604 0.153196235 0.000233284 3.632115714 1.40361023 KDIHFMPCSGLTGANLK ddPTM_SK-BR-3_Trastuzumab_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 ; 163.34 1.77E-09 575830000 1037470 859890 920290 1079990 786800 1029380 1191020 1128030 790510 FALSE TRUE 988430.8492 947513.7686 962486.2068 971427.3534 924017.6709 993732.3125 1009308.024 1029253.713 913098.2534 1.082502179 1.037690922 1.054088323 1.06388042 1.011958645 1.088308195 1.105366285 1.127210253 1 19.80041058 2.044470856 24.94787478 1.091134025 1.051944715 0.10817584 0.037553418 185.2339159 103914.257 0.012558102 0.009274769 110.7824222 -2.044470856 -0.03918931 KDISENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 107.57 0.0022367 103100000 272810 239440 227180 256770 212160 266800 307280 278410 257140 FALSE TRUE 259914.812 263839.2082 237596.4277 230958.9918 249160.6368 257560.6491 260398.7924 254030.9445 297015.9579 0.875087028 0.888299774 0.799944991 0.777597922 0.83887963 0.86716098 0.876716505 0.855277091 1 18.18018092 0.064019325 0.731687563 1.004463203 0.846325022 0.66544694 0.034303355 3.064083645 1.81228963 0.076093955 0.013548058 1.158828919 -0.064019325 -0.158138181 KDKS(ph)PVREPIDNLTPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER;KDKS(1)PVREPIDNLTPEER 226.56 2.46E-19 34464510000 10901630 9160810 9389220 10618200 5819982 11189850 11872400 11888880 6426470 TRUE FALSE 10386331.55 10094306.95 9819725.024 9550838.363 6834985.018 10802342.69 10061047.33 10847826.64 7423054.146 1.399199218 1.359858995 1.32286857 1.286645385 0.920778009 1.455242341 1.35537841 1.461369731 1 22.82358146 3.577948874 2.427732539 1.271063798 1.382126516 0.082634414 0.174577898 0.858315829 9.895879479 0.048535385 0.08207584 3783.980359 -3.577948874 0.111062719 KDLSLGLDDS(ph)RTNT(ph)PQGVLPSSQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDLSLGLDDSRTNTPQGVLPSSQLK 25 2 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 KDLS(0.002)LGLDDS(0.914)RT(0.325)NT(0.759)PQGVLPSSQLK 101.85 0.0096415 65131000 89163 74936 79954 82804 58069 85542 93108 99330 67103 TRUE FALSE 84948.44169 82572.0636 83619.96999 74480.3846 68196.21521 82579.65909 78902.66455 90632.13862 77508.99053 1.095981784 1.065322397 1.078842202 0.960925747 0.879849096 1.065420392 1.017980805 1.169311302 1 16.24207604 3.286177989 20.74997509 1.013790727 1.079170301 0.146579875 0.073234464 42.05043289 18322.3955 0.020041837 0.027136327 1932.760269 -3.286177989 0.065379574 KDLYANTVLSGGTTMYPGIADR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 290.36 3.64E-55 11050358000 6420529 5769727 6175414 6776159 5308342 6154865 7638018 6540330 5857667 FALSE TRUE 6117043.318 6357668.741 6458562.84 6095006.623 6234115.164 5941720.482 6472698.072 5967624.033 6766044.082 0.904079732 0.939643411 0.954555241 0.900822778 0.921382582 0.878167569 0.956644384 0.881996032 1 22.68988115 -1.751896528 3.519599967 1.010694799 0.920127439 0.471951387 0.0273781 0.002321085 0.000163618 0.026779925 0.00560657 0.017705307 1.751896528 -0.090567361 KDNDFIYHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;;;;; 143.17 2.24E-05 3432187000 8988720 9247610 7783960 9771860 6636220 8828800 9008250 9134250 6051853 FALSE TRUE 8563841.02 10189951.97 8140862.265 8789574.067 7793574.667 8523056.442 7633876.015 8334406.646 6990343.455 1.225095888 1.457718357 1.164586879 1.257388013 1.114905829 1.219261471 1.092060221 1.192274271 1 22.73693191 2.382158174 0.314035562 1.00655436 1.381218875 0.473088406 0.087329579 1.386610183 0.334797361 0.114147664 0.185445184 241.07833 -2.382158174 0.374664516 KDNDFIYHDRVPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KDNDFIYHDRVPDLK 15 2 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 133.45 2.48E-05 669513000 1017940 572340 979600 883850 749380 1026510 1342730 1200760 885370 FALSE TRUE 969823.9936 630662.0967 1024515.629 795003.7188 880071.6347 990961.7013 1137871.878 1095615.089 1022668.658 0.9483267 0.616682727 1.001806031 0.777381523 0.860563808 0.968995866 1.112649604 1.071329487 1 19.96390736 2.121797735 2.532687967 1.071080243 0.821261359 0.475615453 0.105633597 0.214069457 2.72310154 0.047000944 0.02967468 132.372489 -2.121797735 -0.249818883 KDNVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDNVIR 6 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 82.305 0.095553 52925000 173590 161420 168850 193090 158720 170550 198050 192400 159730 FALSE TRUE 165384.7447 177868.8815 176591.9395 173680.2264 186400.7177 164643.8107 167833.8351 175552.436 184500.1126 0.896393733 0.96405839 0.957137299 0.941355666 1.010301377 0.892377833 0.909667927 0.951503138 1 17.49326217 1.781800847 0.004569861 1.891590094 4.92E-08 0.126925382 0.037115199 16023.56708 68.33538633 14107.64662 14173.58454 60.50633495 -1.781800847 -1.891590045 KDPAFGGKHEAPS(ph)SPISGQPCGDDQNASPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDPAFGGKHEAPSSPISGQPCGDDQNASPSK 31 2 O75376;O75376-2;E7EVU5;E7EW50;J3KS51 O75376 NCOR1 Nuclear receptor corepressor 1 1 KDPAFGGKHEAPS(0.333)S(0.333)PIS(0.333)GQPCGDDQNASPSK 47.757 0.044056 169570000 124130 34725 121840 75313 100760 111830 199580 130540 127300 TRUE FALSE 118262.6209 38263.51698 127426.4845 67742.39415 118332.5121 107957.2991 169130.4055 119109.2256 147041.0338 0.804283116 0.260223395 0.866604928 0.460704012 0.804758434 0.734198449 1.1502259 0.810040724 1 17.16585929 2.239352685 1.588887527 0.994087326 0.579418726 0.387406791 0.196528216 0.329501757 1.645670435 0.099575812 0.06050152 173.5212569 -2.239352685 -0.4146686 KDPEDTGAEKS(ph)PTTSADLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDTGAEKS(0.79)PT(0.203)T(0.006)S(0.001)ADLK;KDPEDTGAEKS(0.867)PT(0.115)T(0.016)S(0.002)ADLK 185.28 1.20E-14 1263960000 1261800 1474590 1126370 1666110 525970 1506740 1243810 1544200 441050 TRUE FALSE 1202157.215 1624852.397 1178015.179 1498629.457 617699.0015 1454561.216 1054043.94 1408981.662 509445.7814 2.359735341 3.189451079 2.312346518 2.941685871 1.212492132 2.855183552 2.069001214 2.765714651 1 18.95856909 KDPEDTGAEKS(ph)PTTSADLKSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDPEDTGAEKSPTTSADLKSDK 22 3 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDT(0.052)GAEKS(0.9)PT(0.039)T(0.008)S(0.001)ADLKSDK;KDPEDT(0.005)GAEKS(0.955)PT(0.034)T(0.005)S(0.001)ADLKSDK 140.71 7.05E-07 188719000 365510 261765 385270 392330 146703 465370 460510 495490 148657 TRUE FALSE 348233.0667 288439.1511 402935.0106 352892.243 172287.9568 449254.1202 390250.7417 452102.2688 171709.9683 2.02803058 1.679804346 2.346602323 2.055164569 1.003366074 2.616354336 2.272732011 2.632941309 1 17.38961427 KDPEDTGAEKSPT(ph)TSADLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDTGAEKS(0.26)PT(0.571)T(0.068)S(0.101)ADLK 150.59 3.53E-06 950430000 979310 1029200 842200 1271900 395510 1117100 941640 1101500 347060 TRUE FALSE 933019.9571 1134076.65 880815.703 1144046.196 464486.8188 1078414.547 797975.5236 1005046.821 400880.2923 2.327427851 2.828965833 2.197203804 2.853834967 1.158667133 2.690116146 1.990558127 2.5070996 1 18.61281197 KDPEDTGAEKSPTTSADLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 203.48 2.83E-16 1008730000 1062090 905310 876740 1077440 469210 1207870 1124290 1233830 519100 FALSE TRUE 1011887.111 997562.1183 916939.3962 969133.6842 551040.0754 1166041.159 952758.9115 1125789.304 599599.3768 1.687605341 1.663714401 1.529253418 1.61630202 0.919013756 1.944700419 1.588992498 1.87756917 1 19.19363936 -1.825107755 2.711464145 0.796897417 1.605608557 0.323503858 0.274201592 14364923.76 10600393.04 19074220.47 0.060663322 0.014958645 1.825107755 0.808711139 KDPELWGSVLLESNPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 141.6 9.90E-07 344880000 242260 258830 186730 255550 190440 242760 229140 249540 219190 FALSE TRUE 230808.8499 285205.0713 195291.7552 229861.6285 223652.6757 234353.1603 194180.4846 227688.9547 253180.8657 0.91163623 1.126487464 0.771352743 0.907894946 0.883371163 0.925635354 0.766963506 0.899313438 1 17.94980885 3.736017026 24.99570435 0.867720054 1.019061844 0.308127735 0.085782912 208.7171029 2051053.152 0.020863701 0.033991378 5445.239997 -3.736017026 0.151341791 KDPELWGSVLLESNPYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDPELWGSVLLESNPYRR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 163.45 1.86E-11 453590000 197383 214490 188458 228060 114650 194356 191085 215380 162419 FALSE TRUE 188053.0968 236346.7749 197098.9857 205134.9755 134644.9237 187625.403 161931.4737 196520.1854 187606.109 1.002382586 1.259803191 1.05060004 1.093434412 0.717700103 1.000102843 0.86314606 1.047514851 1 17.51734728 2.964200953 24.54761126 0.917727226 1.116660467 0.379376567 0.111206808 411.7738099 282355.5483 0.030945149 0.032835262 920.8755736 -2.964200953 0.198933241 KDPNAEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDPNAEGR 8 1 H0YER2;H0YE76;H0YCB3;A0A5F9ZH79;A0A5F9ZHP1;Q8N9N2-2;Q8N9N2 H0YER2 ASCC1 Activating signal cointegrator 1 complex subunit 1 0 67.993 0.092453 27218000 41486 36238 31921 30921 38093 30500 36704 29956 39289 FALSE TRUE 39525.039 39930.6934 33384.60942 27812.76233 44736.40714 29443.77735 31104.13068 27332.89383 45381.73746 0.870945918 0.879884633 0.735639737 0.61286244 0.985779956 0.648802338 0.685388714 0.602288395 1 15.46982422 3.737123934 23.97519516 0.734523164 0.875415287 0.106502411 0.139721446 115.4021272 1925847.596 0.033368286 0.05495529 5459.136257 -3.737123934 0.140892123 KDPSGASNPSADS(ph)PLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 KDPSGASNPS(0.342)ADS(0.658)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.002)ADS(0.998)PLHR;KDPSGASNPS(0.001)ADS(0.999)PLHR;KDPSGASNPS(0.013)ADS(0.987)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.001)ADS(0.999)PLHR 188.07 2.64E-10 3428127000 2645569 2490035 2500137 2760005 2116646 2578718 2945771 2816010 2450346 TRUE FALSE 2520518.196 2743772.397 2614770.754 2482564.054 2485788.392 2489416.349 2496339.531 2569425.236 2830333.143 0.89053764 0.969416764 0.92383851 0.87712786 0.878267068 0.879548881 0.881994947 0.907817245 1 21.43254044 -1.093173592 2.619132977 1.000406455 0.9032921 0.542416655 0.028491531 575334.2764 712696.4842 2021.219176 0.008273942 0.080691243 1.093173592 -0.097114355 KDQGELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDQGELER 8 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 137.95 0.0011642 836540000 1732630 1537720 1556350 1860880 1306120 1707850 1966900 1950270 1604890 FALSE TRUE 1650732.014 1694415.416 1627710.187 1673820.807 1533906.914 1648706.726 1666813.28 1779494.02 1853768.145 0.890473827 0.91403848 0.878054891 0.902928887 0.827453487 0.889381302 0.899148734 0.959933433 1 20.82202938 1.130333527 2.292984565 0.999516793 0.886280932 0.761015868 0.022654281 0.136031315 1.340020204 0.021222788 0.00592667 13.49999248 -1.130333527 -0.113235862 KDRHDT(ph)PDPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDRHDTPDPSPR 12 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 KDRHDT(1)PDPS(1)PR;KDRHDT(1)PDPS(1)PR 108.63 0.0018592 368760000 930370 694210 890200 926370 715520 888050 1111210 833790 740040 TRUE FALSE 886393.2539 764950.7883 931016.5505 833249.5276 840306.4615 857296.6058 941674.5057 760778.9274 854801.6236 1.03695785 0.894886915 1.089160952 0.97478702 0.98304266 1.002918785 1.10162929 0.890006414 1 19.70523012 1.996484801 24.58170939 1.019446534 0.989374663 0 0.070937538 452.0168963 3160940.875 0.02542869 0.018353408 99.19386239 -1.996484801 -0.030071871 KDRNNTEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDRNNTEVER 10 2 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 52.79 0.083144 195230000 541170 758210 475360 688700 325650 604090 402250 573770 267760 FALSE TRUE 515589.9666 835472.461 497155.7262 619470.5676 382443.2569 583170.2118 340879.3747 523527.6571 309282.8533 1.667049955 2.701321629 1.607446779 2.002925675 1.236548528 1.885556233 1.102160599 1.69271478 1 18.23856733 2.972940325 1.236094816 1.375888463 2.148884759 0.355730687 0.395273757 0.415709995 1.333695728 0.150475332 0.176295087 939.5941961 -2.972940325 0.772996296 KDS(ph)DDEKSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)DDEKSDR;KDS(0.981)DDEKS(0.019)DR;KDS(0.998)DDEKS(0.002)DR 148.57 1.30E-05 1531066000 1604700 1829960 1340440 1983620 566107 1795260 1440810 2167640 672553 TRUE FALSE 1528849.011 2016435.004 1401900.5 1784222.749 664835.8816 1733089.696 1220987.972 1977829.95 776849.0843 1.96801289 2.595658597 1.804598252 2.296743068 0.855810858 2.230921978 1.571718364 2.545964191 1 19.56727483 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 41 1 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(0.915)LDLEEEAAS(0.068)GAS(0.011)S(0.005)ALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 308 5.39E-114 401419000 147405 138069 122243 159825 94415.4 128153 136687 138563 83111.1 TRUE FALSE 140437.4578 152138.3881 127847.9625 143759.0874 110881.4159 123715.0295 115832.8877 126429.6892 95999.54492 1.46289712 1.584782388 1.331755922 1.497497592 1.155020224 1.288704333 1.2065983 1.316982172 1 16.55073995 2.66687032 0.197949193 0.933389339 1.752383492 0.665290874 0.099367146 2.748273012 0.278332399 0.310747786 0.694866367 464.3765923 -2.66687032 0.818994152 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 48 3 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR;KDS(0.996)LDLEEEAAS(0.002)GAS(0.001)SALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 158.69 1.90E-21 125742000 278291 150607 238001 238148 154109 236292 294777 265259 144121 TRUE FALSE 265136.7359 165954.0245 248913.5813 214208.9106 180985.5608 228109.1488 249803.3547 242031.5157 166470.5486 1.592694553 0.996897204 1.49524095 1.286767614 1.087192674 1.370267298 1.50058588 1.453899911 1 17.34490744 2.026562939 24.98749103 1.389193798 1.282997017 0 0.218386406 700.0410003 658518.6653 0.075669863 0.055884708 106.3072635 -2.026562939 -0.106196781 KDS(ph)LSQLEEYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDSLSQLEEYLR 12 1 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 KDS(1)LSQLEEYLR 133.96 9.43E-05 53997000 40165 46986 41751 45843 40548 45207 57661 54899 45345 TRUE FALSE 38266.48005 51773.92682 43665.32465 41234.77454 47619.55836 43641.47025 48863.75543 50091.75252 52376.87101 0.730598818 0.98848835 0.833675701 0.787270674 0.9091715 0.833220263 0.932926204 0.956371611 1 15.67664226 1.422332011 1.486802824 0.995235618 0.852231803 0.397124473 0.068774696 0.402196115 1.670815888 0.059368675 0.019101505 26.44429608 -1.422332011 -0.143003814 KDS(ph)LTQAQEQGNLLN ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KDSLTQAQEQGNLLN 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 KDS(0.997)LT(0.003)QAQEQGNLLN;KDS(0.996)LT(0.004)QAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN;KDS(0.99)LT(0.01)QAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN 222.64 1.46E-12 1347860000 4698700 3858130 4084920 4661900 2831950 4630500 5105610 5041910 3201380 TRUE FALSE 4476601.763 4251277.833 4272217.623 4193276.955 3325841.183 4470144.624 4326655.424 4600413.632 3697833.66 1.210601172 1.149667136 1.155329854 1.133982039 0.899402593 1.208854977 1.170051393 1.244083443 1 21.8182489 4.213418226 1.317918663 1.12228012 1.212092238 0.084272505 0.100086588 1.745338443 4.800355211 0.028747391 0.163840674 16346.25335 -4.213418226 0.089812118 KDS(ph)PHSR ddPTM_SK-BR-3_Trastuzumab_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(0.991)PHS(0.009)R 66.056 0.042208 51419000 62177 70817 64824 73211 48954 66648 68916 91515 54548 TRUE FALSE 59238.01643 78033.33281 67796.24452 65851.69119 57491.5621 64339.96305 58401.59847 83501.46145 63007.02525 0.940181134 1.238486224 1.076010877 1.045148393 0.912462727 1.021155384 0.926906139 1.325272239 1 15.94322508 4.759395739 23.54085823 1.059571577 0.940180861 0.086600098 0.127954541 901.3182102 2258034.704 0.029399456 0.356346882 57463.98484 -4.759395739 -0.119390717 KDS(ph)QNSSQHSVSSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.969)QNS(0.031)SQHSVSSHR;KDS(0.99)QNS(0.009)SQHSVSSHR;KDS(0.783)QNS(0.177)S(0.04)QHSVSSHR;KDS(0.781)QNS(0.109)S(0.109)QHSVSSHR 196.3 4.23E-09 139266000 111958.9 65481.2 102853.8 114827.8 107627.4 96479.4 151318.5 121785.3 22735 TRUE FALSE 106666.8247 72153.80873 107569.7485 103285.0914 126397.5845 93138.29419 128232.0837 111121.1335 26260.62769 4.061853584 2.747604116 4.09623676 3.933077786 4.813197384 3.546689565 4.883054785 4.231472866 1 14.68061378 3.676612161 24.98769481 4.030197844 3.404723812 0 1.138920749 606.9224133 244809.2115 0.264695466 0.41006453 4749.109259 -3.676612161 -0.625474032 KDS(ph)SSVVEWTQAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.915)S(0.078)S(0.007)VVEWTQAPK 214.82 2.92E-08 0 55908 43961 45030 64093 29738 57100 63521 61410 38182 TRUE FALSE 53265.33964 48440.67588 47094.67004 57650.24987 34924.29778 55122.61268 53829.70481 56032.61485 44103.06955 1.207746766 1.098351574 1.067832024 1.307170917 0.791879072 1.24985887 1.220543272 1.270492404 1 15.42859145 KDSETGENIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KDSETGENIR 10 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;;;;;; 174.77 4.82E-06 10495240000 12606440 9335750 10389380 10915860 9575710 9713420 12540610 12121400 11334500 FALSE TRUE 12010558.56 10287073.54 10865743.35 9818577.014 11245710.79 9377041.83 10627309.62 11059985.96 13092196.37 0.917383014 0.785740853 0.82994045 0.749956442 0.858962887 0.716231377 0.811728553 0.844776968 1 23.64220381 -1.571843433 4.802331371 1.001640599 0.813296623 0.519047332 0.056157352 0.000939507 8.38E-05 0.05178808 0.012104229 0.026801344 1.571843433 -0.188343976 KDSLSVNEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 182.08 2.91E-06 2331400000 6046700 6160400 4860400 6799300 4189400 6042200 6621100 6314300 4467000 FALSE TRUE 5760884.474 6788151.764 5083254.148 6115821.446 4920030.034 5832957.099 5610929.59 5761386.418 5159719.546 1.116511164 1.315604793 0.985180319 1.185301137 0.953546019 1.130479486 1.08744856 1.116608445 1 22.29886122 3.735974791 24.99994713 1.074187681 1.216057977 0.347226281 0.085173043 216.9723673 2097705.958 0.020006731 0.032717842 5444.710482 -3.735974791 0.141870295 KDSNELS(ph)DS(ph)AGEEDSADLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDSNELSDSAGEEDSADLKR 20 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 2 KDS(0.002)NELS(0.998)DS(1)AGEEDSADLKR 145.54 7.07E-07 416110000 1686600 1356400 1322300 1670500 663900 1689900 1747200 1647900 829730 TRUE FALSE 1606877.761 1494618.702 1382928.763 1502578.166 779683.9498 1631378.339 1480632.55 1503601.14 958400.2907 1.676624868 1.559493164 1.442955283 1.567798112 0.813526412 1.702188903 1.544899939 1.568865488 1 19.87026882 3.889414224 1.480005188 1.404304724 1.661473024 0.122905098 0.273624539 0.983253213 4.062080203 0.077706522 0.227917274 7752.008216 -3.889414224 0.257168301 KDSPHS(ph)R ddPTM_SK-BR-3_Trastuzumab_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(0.368)PHS(0.632)R;KDS(0.225)PHS(0.775)R 54.157 0.082903 156799000 114965 111253 121533 146692 90084 112475 121586 183392 111143 TRUE FALSE 109530.8323 122589.8072 127105.4083 131946.2415 105794.6211 108579.9625 103035.8226 167333.2243 128378.4888 0.853186802 0.954909256 0.990083381 1.027790892 0.824083708 0.845780033 0.802594138 1.303436626 1 16.97004396 1.246245297 24.99697202 1.15171834 0.899403285 0.512608926 0.102133173 120.8007521 392953.7228 0.068653336 0.024019836 17.62971522 -1.246245297 -0.252315055 KDSS(ph)SVVEWTQAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.23)S(0.385)S(0.385)VVEWTQAPK 151.57 4.23E-06 844420000 573740 431530 492930 597320 301500 588430 643110 659590 407760 TRUE FALSE 546620.4472 475503.3976 515531.3281 537276.2588 354081.5045 568052.5216 544991.758 601832.8029 470993.3383 1.160569381 1.009575633 1.094561825 1.140730059 0.751776035 1.206073368 1.157111394 1.277794725 1 18.84534713 KDT(ph)PRKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDTPRKEK 8 3 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 KDT(1)PRKEK;KDT(1)PRKEK 89.301 0.014403 657180000 836800 680050 902000 939410 338645 931680 1102540 1296240 486380 TRUE FALSE 797246.1224 749347.8682 943357.5922 844978.722 397704.5808 899415.688 934327.2735 1182734.354 561805.3263 1.419078967 1.333821224 1.679153878 1.504041849 0.707904611 1.600938343 1.663080127 2.105238769 1 19.09971078 2.026944727 24.99988381 1.655339484 1.344319293 0.106157404 0.362136789 395.2316347 366702.496 0.125504356 0.092688885 106.4007593 -2.026944727 -0.311020192 KDTEVLFCFEQFDELTLLHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDTEVLFCFEQFDELTLLHLR 21 1 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 208.92 1.86E-22 110965000 252046 328488 235826 272107 142463 243159 187396 232768 103064 FALSE TRUE 240132.2851 361961.3007 246638.8554 244754.2874 167308.5021 234738.3429 158805.2984 212385.5999 119046.6387 2.017127805 3.040499963 2.071783445 2.055952944 1.40540299 1.971818317 1.333975492 1.78405373 1 16.86116736 3.118443634 1.729505257 1.536407498 2.515582614 0.54401826 0.372747378 0.235423826 1.448856114 0.115806264 0.149395821 1313.541001 -3.118443634 0.979175116 KDTFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDTFFK 6 1 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 91.626 0.076449 3296600000 6866000 6342200 6030500 7461500 4907600 7244000 7992700 7541600 5924800 FALSE TRUE 6541457.787 6988477.39 6307004.39 6711455.844 5763483.886 6993138.464 6773266.819 6881217.523 6843587.724 0.955852113 1.021171595 0.92159327 0.980692601 0.842172866 1.021852681 0.989724556 1.005498549 1 22.70632142 KDVGRPQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KDVGRPQPGR 10 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;; 204.56 1.04E-07 9422906000 7646549 5277716 5068615 7599003 5546109 5960484 8564901 7257036 6940396 FALSE TRUE 7285111.783 5815521.261 5301016.011 6835136.781 6513348.654 5754070.945 7258168.047 6621571.456 8016677.165 0.908744562 0.725427897 0.661248533 0.852614698 0.81247486 0.717762587 0.905383602 0.825974568 1 22.93457295 0.821426103 0.793358426 0.998245865 0.783312322 0.417651413 0.077666087 0.859597083 1.109674474 0.073478886 0.026274504 6.628665487 -0.821426103 -0.214933543 KDVHMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KDVHMPK 7 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;; 82.543 0.011552 504936000 1978700 2067590 1690220 2163240 1420860 2010850 2235630 2265720 1564580 FALSE TRUE 1885170.772 2278279.772 1767718.259 1945787.005 1668657.534 1941213.76 1894543.583 2067321.545 1807207.076 1.043140434 1.260663375 0.978149257 1.076681821 0.923334994 1.074151262 1.048326785 1.143931746 1 20.78533039 3.722424335 24.99732885 1.037145704 1.151901918 0.275287531 0.078833285 888.3299548 1376145.847 0.019587151 0.030444756 5277.452525 -3.722424335 0.114756214 KDWDDDQND ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KDWDDDQND 9 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 142.98 0.0021123 7512020000 15097900 13024100 13150900 15110600 9959680 15150700 16552000 15521700 10985120 FALSE TRUE 14384252.19 14351270.6 13753881.77 13591653.78 11696645.04 14626027.46 14026688.4 14162537.66 12688636.31 1.133632633 1.131033332 1.083952715 1.071167417 0.921820498 1.152687106 1.10545279 1.116159162 1 23.59703369 3.663475544 3.128164555 1.06937817 1.133338785 0.162775085 0.064145881 0.478771373 9.13931633 0.017518577 0.029772739 4607.608212 -3.663475544 0.063960615 KDWSALSSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDWSALSSLAR 11 1 O00515 O00515 LAD1 Ladinin-1 0 ; 133.48 0.0002579 335850000 627500 484550 349080 339770 694860 381740 738520 483260 693810 FALSE TRUE 597839.3186 533926.1959 365085.6633 305615.6741 816043.364 368520.2481 625845.2101 440943.1925 801402.5113 0.745991322 0.666239734 0.455558422 0.381351031 1.018269038 0.459844139 0.780937421 0.550214388 1 19.61216751 -4.876024512 0.486245635 9.999999997 0.64011114 0.272097434 0.187787264 2408.432879 13.65291521 23461.94301 0.083108202 1.33E-05 4.876024512 -9.359888858 KDWYDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDWYDVK 7 1 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 119.77 0.0075461 4412900000 5363300 4675300 4689900 5808900 3678110 5645200 6404600 5978800 4114100 FALSE TRUE 5109787.438 5151718.385 4904936.554 5224978.336 4319571.219 5449705.308 5427460.641 5455264.576 4752093.616 1.075270786 1.084094465 1.032163284 1.099510817 0.90898277 1.146800915 1.142119891 1.147970772 1 22.18013183 KDYEEIGPSICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDYEEIGPSICR 12 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 169.04 7.20E-05 1463900000 1502370 1265380 1352400 1505790 1093990 1355420 1590150 1525120 1370490 FALSE TRUE 1431355.948 1394323.661 1414408.878 1354425.128 1284781.51 1308481.466 1347543.412 1391572.408 1583018.59 0.904194023 0.88080056 0.893488483 0.855596477 0.811602288 0.826573657 0.851249266 0.879062581 1 20.59424677 0.843019514 5.499216481 0.999999247 0.862558557 0.705610267 0.028070922 1.828848841 63.76450392 0.030760883 0.007751819 6.966578168 -0.843019514 -0.13744069 KDYNEAYNYYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KDYNEAYNYYTK 12 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;K7EIH8;K7EK03;K7ESP1;K7ELJ8 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 156.24 0.00010899 478190000 661910 569170 567660 684850 478470 605900 734840 661090 572770 FALSE TRUE 630622.8261 627169.0701 593687.7725 616007.5769 561915.0165 584917.5311 622726.6617 603201.4549 661592.2463 0.953189566 0.947969196 0.897362047 0.931098543 0.849337367 0.884105783 0.941254474 0.911742026 1 19.3355828 -1.12666512 1.395670858 1.004940747 0.918199597 0.410050219 0.03195376 1658.045179 981.8160721 36.07098635 0.009528213 0.074702456 1.12666512 -0.086741149 KDYQTSPLLETQAEDHPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KDYQTSPLLETQAEDHPPR 19 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 277.07 1.11E-39 661950000 407170 295610 366400 445410 337260 379470 475410 393170 318520 FALSE TRUE 387923.881 325732.9951 383199.8024 400636.5406 396078.0372 366328.8587 402877.473 358741.9505 367914.4548 1.054386083 0.885349817 1.041545928 1.088939386 1.076549269 0.995690313 1.095030292 0.975068921 1 18.48901083 3.521634491 24.98281253 1.047165868 0.968797894 0.192793313 0.057019154 527.3889634 295992.9476 0.013996182 0.021681621 3323.796996 -3.521634491 -0.078367973 KEAAENSLVAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEAAENSLVAYK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 147.68 0.00010549 377710000 623260 577530 498570 585770 448290 567740 676490 655850 482120 FALSE TRUE 593799.735 636380.9636 521429.9277 526887.2867 526471.6341 548079.0214 573279.0259 598420.2971 556884.7073 1.066288457 1.142751732 0.936333717 0.946133517 0.945387128 0.984187596 1.029439341 1.074585618 1 19.08701915 3.742605192 24.99992995 0.988061582 1.104520097 0.532558995 0.045380156 258.9809712 1600782.717 0.012383738 0.021325016 5528.472993 -3.742605192 0.116458515 KEAEDSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEAEDSLRR 9 2 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 51.436 0.087018 58375000 40000 27265 32846 44712 36711 35709 46026 51173 42788 FALSE TRUE 38109.27927 30043.3345 34352.02159 40217.46481 43113.38678 34472.38838 39003.88837 46692.02083 49423.34451 0.771078519 0.607877407 0.695056596 0.813734182 0.872328395 0.69749202 0.789179461 0.944736163 1 15.59290502 1.129142063 0.379643433 1.025388682 0.683475178 0.592674227 0.075439194 0.929889237 0.395322352 0.12042196 0.072352052 13.46300672 -1.129142063 -0.341913505 KEAESSPFVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEAESSPFVER 11 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;; 152 5.32E-05 4287650000 4025640 3412790 3650940 4190370 3622260 3919740 4333740 4106560 3960440 FALSE TRUE 3835355.975 3760557.181 3818339.21 3769146.046 4253980.997 3783998.421 3672548.368 3746967.836 4574604.808 0.838401597 0.822050721 0.834681764 0.823928231 0.929912238 0.827174932 0.80281216 0.819080116 1 22.12521569 -1.852390383 2.633221751 1.067266483 0.835372101 0.68830049 0.03439749 10328856.05 7047771.401 4373143.607 0.008169639 0.014047842 1.852390383 -0.231894382 KEAPAPPKAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEAPAPPKAEAK 12 2 P62750 P62750 RPL23A 60S ribosomal protein L23a 0 70.889 0.02591 176100000 476520 393480 414020 497070 363910 502240 626320 602890 466090 FALSE TRUE 453995.844 433576.0593 433003.2265 447103.5792 427375.7888 484847.3029 530763.3808 550097.7555 538368.8567 0.843280287 0.805351301 0.804287286 0.830478163 0.793834531 0.900585717 0.985873113 1.02178599 1 19.03823543 1.888857937 2.212181534 1.009060382 0.816559994 0.960490109 0.017301814 0.050377194 0.454411905 0.009700397 0.004719031 77.42085037 -1.888857937 -0.192500388 KEAPPMEKPEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEAPPMEKPEVVK 13 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 122.34 0.00013284 251120000 326140 271240 269340 330780 175990 298100 310050 336600 198970 FALSE TRUE 310724.0085 298879.6644 281689.5054 297529.366 206682.6003 287776.7223 262746.178 307125.5196 229825.2514 1.352001169 1.300464864 1.225668214 1.294589538 0.899303271 1.252154498 1.143243297 1.336343668 1 17.81017779 3.34659924 1.672599417 1.149181597 1.326223221 0.256887404 0.127780914 0.471374415 2.708956284 0.03786791 0.058877681 2221.259202 -3.34659924 0.177041624 KECSEAMEVETSVISIDS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KECSEAMEVETSVISIDSPQK 21 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVIS(0.009)IDS(0.991)PQK 118.54 4.91E-05 78767000 141780 133570 124140 156040 65532 156520 130100 148040 70204 TRUE FALSE 135078.3404 147180.9349 129831.9418 140354.5627 76960.76005 151099.6732 110250.8555 135076.8328 81090.87777 1.665764931 1.81501223 1.601067165 1.730830478 0.949068035 1.863337496 1.359596277 1.665746339 1 16.30725201 -2.710232842 0.128361194 1.23E-15 1.900684508 0.338770163 0.260044563 74.26378432 1.099957692 23.82958708 2.149069934 0.001948799 2.710232842 1.900684508 KECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KECSEAMEVETSVISIDSPQKLAILDQELEHK 32 2 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVIS(0.192)IDS(0.807)PQKLAILDQELEHK 93.983 4.54E-05 31415000 19991 15408 17011 17781 10018 17804 21036 21186 12622 TRUE FALSE 19046.06505 16978.09272 17790.97118 15993.6201 11765.13603 17187.44302 17826.57185 19330.84153 14579.3553 1.306372241 1.164529732 1.220285178 1.097004619 0.80697231 1.178889098 1.222727033 1.325905099 1 13.8316393 4.368812693 1.175996093 1.12422843 1.328444976 0.151686067 0.140544797 1.814082177 3.271437188 0.043116102 0.38936693 23378.28738 -4.368812693 0.204216546 KEDEVEEWQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDEVEEWQHR 11 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 221.8 5.29E-12 420050000 1425390 1332740 1202690 1580560 978640 1335530 1436620 1429510 875800 FALSE TRUE 1358014.64 1468547.721 1257834.526 1421679.106 1149314.506 1289280.261 1217437.234 1304334.526 1011614.591 1.342422946 1.451686971 1.243393025 1.405356465 1.136118949 1.274477724 1.203459543 1.289359147 1 19.94822832 -4.232769954 0.068561836 1.07E-08 1.723217862 0.607524161 0.081456249 156.2558091 0.891861871 26.5446773 4.386413848 5.85E-05 4.232769954 1.723217852 KEDGTFYEFGEDIPEAPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 193.47 8.38E-15 800350000 1500780 1443240 1362994 1669340 1161005 1504080 1624120 1637550 1280840 FALSE TRUE 1429841.104 1590307.797 1425488.623 1501534.772 1363483.904 1451993.332 1376330.665 1494157.441 1479466.126 0.96645748 1.074920047 0.963515554 1.014916628 0.921605355 0.981430603 0.930288731 1.009930146 1 20.49664523 3.232588442 1.887009178 0.96438422 1.017410402 0.102517832 0.041961493 0.459693578 3.371724382 0.012318605 0.017082409 1708.39559 -3.232588442 0.053026183 KEDIAMWEVNEAFSLVVLANIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEDIAMWEVNEAFSLVVLANIK 22 1 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 179.03 9.33E-17 370880000 264370 218680 193700 242950 169440 192620 261130 229240 139310 FALSE TRUE 251873.754 240963.7406 202581.3366 218528.2044 198990.2824 185949.5211 221289.8225 209166.5303 160913.4833 1.565274388 1.497473895 1.258945692 1.358047815 1.236629015 1.155586948 1.375209945 1.299869508 1 17.29592569 8 0.132244963 1.001316214 2.935437954 0.682017467 0.091062561 46.76186827 0.416989428 0.46543456 16.92642624 100000000 -8 1.934121739 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLSPK 33 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(1)PK 80.816 0.00056971 68269000 29374 29673 24587 30336 13470 29405 28793 35534 12824 TRUE FALSE 27985.54923 32696.71244 25714.33827 27286.56765 15819.16374 28386.69748 24400.09903 32422.45458 14812.68042 1.889296767 2.207346105 1.735967937 1.842108711 1.067947413 1.916378175 1.647244005 2.188831032 1 13.85454511 3.489022481 2.670814995 1.637859373 2.045276181 0.184431418 0.367273286 0.424357715 6.068549212 0.096159212 0.150033883 3083.347553 -3.489022481 0.407416808 KEDLELIMTEMEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDLELIMTEMEISR 15 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ; 114.29 0.00099047 91717000 199725 184490 185293 213377 162862 194703 211954 226309 169697 FALSE TRUE 190284.3951 203289.7407 193788.8673 191927.9386 191265.0812 187960.3863 179616.5245 206492.1842 196012.7441 0.97077563 1.03712512 0.988654428 0.979160511 0.975778805 0.958919213 0.916351257 1.053463055 1 17.58058793 3.283153604 2.706520617 0.969928352 1.004715644 0.00862349 0.038320529 0.528080993 7.894157169 0.011049877 0.01510667 1919.347466 -3.283153604 0.034787291 KEDLISAFGTDDQTEICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDLISAFGTDDQTEICK 18 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 197.1 3.01E-15 180312000 400830 316260 353480 386150 269280 360670 472660 434390 317420 FALSE TRUE 381883.5603 348487.2536 369687.4076 347333.4684 316242.3467 348179.9075 400547.036 396352.5088 366643.8724 1.041565369 0.95047887 1.008301067 0.947331987 0.862532748 0.949640601 1.092468922 1.081028591 1 18.4840199 1.750052002 10.73951879 1.06407758 0.962774884 0.440492054 0.05175033 0.106717142 63.59639598 0.024957012 0.013619963 56.2408663 -1.750052002 -0.101302697 KEDLVFIFWAPESAPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDLVFIFWAPESAPLK 17 1 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ; 212.69 2.15E-12 5546000000 29685000 25386000 23445000 28305000 17948300 28033000 32173000 28986000 19446100 FALSE TRUE 28281848.88 27972862.26 24519976.44 25459727.62 21078477.84 27062210.18 27264417.95 26447832.18 22461701.87 1.259114249 1.245358095 1.091634845 1.133472778 0.938418556 1.204815661 1.213817996 1.177463414 1 24.42096391 3.750668431 21.717087 1.122789603 1.25223629 0.31027762 0.087084254 161.3088403 289324.467 0.022643944 0.040285268 5632.075013 -3.750668431 0.129446687 KEDLVFIFWAPESAPLKS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDLVFIFWAPESAPLKSK 19 2 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 1 KEDLVFIFWAPES(0.155)APLKS(0.845)K;KEDLVFIFWAPES(0.008)APLKS(0.992)K 164.96 1.19E-11 163946000 1228580 815570 892860 1206750 501350 1232240 1287370 1192130 472620 TRUE FALSE 1170507.458 898677.5102 933798.5142 1085445.197 588785.2813 1189567.22 1090958.062 1087740.777 545911.4958 2.144134108 1.646196347 1.710530959 1.988317164 1.078536147 2.179047756 1.998415624 1.992522205 1 19.05830755 -0.978978653 7.280681616 0.999999972 1.846720921 0.408671671 0.318342963 1.46E-07 2.18E-08 0.287930267 0.067865812 0.104959402 0.978978653 0.846720949 KEDLYLKPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 188.59 1.73E-06 7754900000 9619900 9268400 8769200 10762400 6693200 9692600 10920000 10820100 8373500 FALSE TRUE 9165186.392 10212860.5 9171276.494 9680543.105 7860491.961 9356942.832 9253953.44 9872634.683 9672019.614 0.947597995 1.055918092 0.948227657 1.000881252 0.812704303 0.967423889 0.956775711 1.020741797 1 23.20538574 1.242364772 24.96318804 1.010370908 0.961864046 0.116492929 0.060808006 223.1287939 1464273.696 0.044110221 0.014747768 17.47289116 -1.242364772 -0.048506862 KEDMAVHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEDMAVHVR 9 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 59.542 0.065952 21079000 79179 56282 46456 69128 75786 56126 85786 73653 87327 FALSE TRUE 75436.36559 62017.19979 48586.05355 62179.12211 89003.05441 54182.34255 72697.77013 67203.55286 100869.2252 0.747863042 0.61482776 0.481673706 0.61643303 0.882360842 0.537154345 0.720713082 0.666244365 1 16.62212655 -1.672490253 0.413820638 1.259049108 0.645782081 0.487252176 0.110782785 29.42772233 2.311666513 7.758563099 0.06360196 0.021257381 1.672490253 -0.613267027 KEDMEYALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEDMEYALR 9 1 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;; 138.71 0.00020664 1497480000 1113369 979637 909169 1133244 1075260 924763 1228803 1160760 1139280 FALSE TRUE 1060742.254 1079463.124 950855.2979 1019328.16 1262785.004 892738.2254 1041326.534 1059117.701 1315953.724 0.806063492 0.820289577 0.722559829 0.774592709 0.959596816 0.678396367 0.791309387 0.804828986 1 20.32767733 0.72546536 4.50380495 0.999999493 0.793713063 0.443731484 0.07234861 7.339768278 119.7896651 0.063898348 0.016220235 5.31453608 -0.72546536 -0.20628643 KEDMMFHKIY(ph)IQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDMMFHKIYIQK 13 2 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK 49.423 0.063885 219770000 241874 185320 244445 207027 389960 209475 345640 255150 433870 TRUE FALSE 230441.0954 204204.3187 255653.045 186216.2526 457968.9005 202220.8282 292906.2699 232807.7134 501152.3437 0.459822444 0.407469547 0.510130399 0.371576138 0.913831705 0.403511688 0.584465529 0.464544796 1 18.9348897 -5 0.206126377 3.283486861 0.43480706 0.494634795 0.154236913 113.7635792 1.130848022 107.3910178 0.311144636 1.00E-05 5 -2.848679801 KEDMTYAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KEDMTYAVR 9 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 164.33 1.00E-04 4291150000 3987950 2958120 2441200 2917130 3355760 2725200 4400560 3506090 3612140 FALSE TRUE 3799447.507 3259555.791 2553131.435 2623894.55 3941003.482 2630825.641 3729173.75 3199078.173 4172292.223 0.910637919 0.781238613 0.611925363 0.628885613 0.944565546 0.630546831 0.893794958 0.766743555 1 21.99240878 0.296739652 0.767031518 1.002993387 0.768502504 0.266964952 0.119949569 3.733216741 2.900196558 0.144522856 0.039942736 1.980339509 -0.296739652 -0.234490883 KEDQDRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEDQDRSPR 9 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KEDQDRS(1)PR 58.116 0.087372 84448000 159290 148730 157260 168870 108190 169080 156480 170310 151080 TRUE FALSE 151760.6774 163885.7561 164470.5266 151894.8668 127058.3017 163224.7172 132606.102 155396.7535 174508.7148 0.869645264 0.939126486 0.942477439 0.870414219 0.728091442 0.935338487 0.759882406 0.890481336 1 17.41293956 3.010353202 18.10409866 0.842130274 0.913957752 0.056188623 0.081054473 13.54100688 23671.42136 0.020776408 0.024739872 1024.125552 -3.010353202 0.071827478 KEDQYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEDQYMK 7 1 P53004 P53004 BLVRA Biliverdin reductase A 0 92.439 0.025123 182710000 365050 358380 290870 341480 220810 336830 372490 365980 251200 FALSE TRUE 347794.81 394899.3294 304206.6772 307153.7816 259319.1941 325165.4926 315659.8093 333932.851 290154.813 1.198652562 1.360995275 1.048428851 1.058585858 0.893727012 1.120662067 1.087901338 1.150878207 1 18.14646333 3.726540287 24.88660214 1.055138809 1.279823916 0.587640101 0.079485331 416.7745659 862880.1665 0.020629966 0.032232 5327.706447 -3.726540287 0.224685107 KEDS(ph)DEEEDDDS(ph)EEDEEDDEDEDEDEDEIEPAAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEDSDEEEDDDSEEDEEDDEDEDEDEDEIEPAAMK 35 1 P19338;C9J1H7;C9JWL1 P19338 NCL Nucleolin 2 KEDS(1)DEEEDDDS(1)EEDEEDDEDEDEDEDEIEPAAMK;KEDS(1)DEEEDDDS(1)EEDEEDDEDEDEDEDEIEPAAMK 252.28 1.02E-59 284700000 297370 176110 135393 256632 114065 227565 301520 312170 143617 TRUE FALSE 283313.9094 194055.8092 141600.903 230834.8638 133957.8999 219684.367 255517.5862 284834.7399 165888.3909 1.707858567 1.169797405 0.853591395 1.39150704 0.807518231 1.32429018 1.540298178 1.71702636 1 17.3398534 1.995745547 24.960213 1.467429569 1.212201444 0.098458223 0.308777706 369.0387775 2165099.34 0.11537726 0.083183383 99.02515872 -1.995745547 -0.255228125 KEECPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KEECPAVR 8 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;; 172.23 0.0004566 6613800000 9906586 8057464 6711913 10238710 6948707 8432311 9859461 9260342 7938755 FALSE TRUE 9438321.313 8878528.742 7019660.85 9209495.419 8160559.301 8140297.956 8355219.143 8449457.362 9169856.58 1.029276874 0.968229837 0.765514792 1.004322733 0.889933145 0.887723585 0.911161376 0.921438333 1 23.12846774 3.991476765 24.63894994 0.906348973 1.006384265 0.247403182 0.06632826 471.6459398 1363442.337 0.01493054 0.028453693 9805.658532 -3.991476765 0.100035292 KEEELQAALAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 191.79 2.69E-06 2086300000 3868780 3325150 2712460 3863640 2736980 3414660 4142440 3945410 3116590 FALSE TRUE 3685910.437 3663986.565 2836828.974 3475259.567 3214308.445 3296409.468 3510434.697 3599928.984 3599894.86 1.023893914 1.017803772 0.788031063 0.965378074 0.892889534 0.91569604 0.975149229 1.000009479 1 21.77952334 1.501076033 4.575180297 0.99738643 0.944496355 0.137338141 0.066766721 0.45630442 20.70458128 0.044516006 0.018362401 31.70122413 -1.501076033 -0.052890075 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 190.77 8.71E-18 850637000 618100 534155 528702 620592 356073 588949 652356 659803 430835 TRUE FALSE 588883.638 588586.0018 552943.5097 558208.9131 418172.0185 568553.5485 552827.1109 602027.1515 497646.6914 1.183336789 1.182738702 1.11111662 1.121697226 0.840299003 1.142484333 1.110882721 1.209748124 1 18.92476233 3.536758778 2.272073082 1.073407666 1.184190865 0.181516554 0.098089053 0.50683624 5.170936808 0.027988471 0.046649355 3441.587199 -3.536758778 0.110783198 KEEEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEEEVER 7 1 D6RCC6;E7EUJ7;Q8TC20-2;Q8TC20-4;Q8TC20;Q8TC20-3;Q8TC20-5 D6RCC6 CAGE1 Cancer-associated gene 1 protein 0 ; 87.616 0.030803 756680000 1462640 1219870 1256760 1493560 988270 1398810 1543250 1523720 1053320 FALSE TRUE 1393503.906 1344176.14 1314383.689 1343424.511 1160623.975 1350368.859 1307798.869 1390294.999 1216663.486 1.14534867 1.104805195 1.080318185 1.104187416 0.953940008 1.109895114 1.07490599 1.142711206 1 20.21449876 4.029127735 1.242331855 1.067256821 1.145085151 0.19562812 0.053988399 0.912235641 2.417101258 0.015552658 0.065712667 10693.69357 -4.029127735 0.07782833 KEELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEELLK 6 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ; 102.72 0.056601 2521600000 3774900 3302400 3207300 4129400 2746000 4209700 4570400 4158900 3283800 FALSE TRUE 3596467.958 3638918.315 3354357.877 3714304.867 3224901.531 4063917.033 3873101.539 3794724.668 3793034.933 0.948176862 0.959368521 0.884346687 0.979243517 0.85021667 1.071415662 1.02110885 1.000445484 1 21.85492123 2.224368184 24.99999973 1.026242136 0.931913909 0.578570233 0.041655404 164.1419446 289134.5109 0.014163837 0.010510873 167.6363453 -2.224368184 -0.094328226 KEELMFFLWAPELAPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEELMFFLWAPELAPLK 17 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 136.2 1.16E-05 752660000 3511600 2840200 2614900 3283400 2694600 3034200 4399300 3514500 3136000 FALSE TRUE 3345613.627 3129619.609 2734795.751 2953346.394 3164537.387 2929124.893 3728105.986 3206751.748 3622314.864 0.923612042 0.863983316 0.754985653 0.815320177 0.873622947 0.80863343 1.029205391 0.885276921 1 21.78848052 1.744965336 25 0.969165071 0.846291266 0.539037699 0.057101692 1.093524527 4282.363922 0.026417208 0.014649706 55.58598883 -1.744965336 -0.122873805 KEELTLEGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KEELTLEGIR 10 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;; 101.71 0.005043 4151780000 8235150 8932880 7885860 8524340 6517370 8766340 9481380 9184640 5300670 FALSE TRUE 7845890.78 9843150.628 8247434.481 7667457.148 7653997.265 8462759.448 8034821.344 8380384.231 6122670.832 1.28144906 1.607656348 1.347032154 1.252305956 1.250107588 1.382200625 1.3123066 1.368746493 1 22.54572969 -3.94678843 0.196078755 8.45E-10 1.430600002 0.524118236 0.103464895 69.6109176 0.995487773 27.93200888 0.270712434 0.000113035 3.94678843 1.430600002 KEENLADWYSQVITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEENLADWYSQVITK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 133.71 6.35E-05 430520000 1244160 1091920 1166170 1328190 910490 1254980 1310870 1452010 974680 FALSE TRUE 1185351.022 1203187.889 1219640.048 1194677.818 1069279.168 1211519.728 1110872.706 1324864.307 1125828.396 1.05287007 1.068713396 1.083326777 1.061154454 0.949771005 1.076114026 0.986715835 1.176790629 1 20.10255551 2.972455672 24.93708841 1.033003033 1.066943294 0.049756677 0.060701742 1919.116747 1737462.395 0.016657336 0.017709339 938.5462349 -2.972455672 0.033940261 KEEPSNNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEEPSNNVK 9 1 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 120.06 0.0011641 507420000 685728 686030 627308 786010 566802 693569 841090 786610 644491 FALSE TRUE 653314.9964 755937.237 656070.6923 706998.7815 665652.0893 669550.5316 712766.2728 717730.2583 744435.3727 0.877598003 1.015450454 0.881299729 0.949711429 0.894170419 0.899407197 0.9574589 0.964127021 1 19.50578708 1.186951328 1.821672588 0.996458016 0.926795788 0.287979461 0.04106355 0.448649537 2.716810728 0.03656164 0.010661479 15.37982266 -1.186951328 -0.069662228 KEEPSQNDIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEEPSQNDISPK 12 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KEEPSQNDIS(1)PK;KEEPSQNDIS(1)PK 99.891 0.0021691 308861000 428080 517740 457230 523080 242220 553190 524270 606210 288330 TRUE FALSE 407845.5068 570498.2946 478194.4478 470499.0046 284463.0913 534032.8916 444282.9826 553127.0387 333042.7438 1.224604092 1.712988213 1.435835059 1.412728586 0.854133881 1.603496553 1.334011897 1.660828975 1 18.34534782 -2.025600788 2.674647446 0.520431641 1.40963963 0.21164576 0.245387911 63813706.92 55993672.88 186899022.4 0.054610163 0.009427558 2.025600788 0.889207989 KEEQEVQATLESEEVDLNAGLHGNWTLENAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEEQEVQATLESEEVDLNAGLHGNWTLENAK 31 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 377.06 1.44E-137 184953000 266900 248510 250470 325850 186909 330890 361460 333620 201528 FALSE TRUE 254284.1659 273833.4515 261954.2972 293094.9389 219505.8704 319431.1963 306312.6383 304406.4642 232779.933 1.092380098 1.176361931 1.125330237 1.259107412 0.942975916 1.372245418 1.315889366 1.307700626 1 17.82860717 2.211479692 24.99973498 1.283096563 1.131215751 0.180730276 0.126992388 278.1638371 256785.0497 0.041867967 0.030929518 162.7345219 -2.211479692 -0.151880812 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 41 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 173.37 1.33E-20 1423506000 328437 296205 289333 366362 250561 322362 383451 362926 185172.1 FALSE TRUE 312912.4339 326388.6263 302599.2042 329534.5957 294258.7591 311198.5231 324948.5074 331146.2754 213887.6435 1.462975742 1.525981683 1.414757764 1.540690197 1.375763247 1.454962605 1.51924862 1.548225367 1 17.70649361 -1.635321523 2.894848105 0.957629141 1.481763581 0.879682565 0.05582414 4469899.148 4727571.325 1429245.988 0.012535272 0.023156796 1.635321523 0.52413444 KEES(ph)DEEETASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(1)DEEETASK 120.29 0.00026072 111760000 145010 143500 121880 151720 60114 152840 142080 146240 63740 TRUE FALSE 138155.6647 158122.8131 127468.3186 136468.8174 70597.86257 147547.1125 120403.0865 133434.4503 73624.47366 1.876491034 2.147693631 1.731330796 1.853579531 0.958891236 2.00404981 1.635367705 1.812365423 1 16.16789779 -1.806764608 0.121098564 4.23E-14 2.25996264 0.371215668 0.312290535 57.17177627 1.054767427 21.45378133 3.586215442 0.01560398 1.806764608 2.25996264 KEES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 37 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 225.69 1.55E-15 37125981000 35286739 31002606 31384768 36583292 19000495 36782088 37727724 38991391 22582103 TRUE FALSE 33618804.78 34161806.8 32823790.66 32905869.98 22314175.31 35508315.07 31971666.79 35577098.1 26084020.2 1.288865923 1.309683344 1.258386951 1.26153368 0.855473011 1.361305305 1.225718526 1.363942284 1 24.63666291 -2.308736302 1.987569679 4.89E-05 1.243421038 0.216283783 0.143854547 4310509.187 527284.3868 19353746.93 0.033238269 0.00491206 2.308736302 1.243372107 KEES(ph)EESDDDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.799)EES(0.201)DDDMGFGLFD;KEES(0.649)EES(0.351)DDDMGFGLFD;KEES(0.778)EES(0.222)DDDMGFGLFD;KEES(0.818)EES(0.182)DDDMGFGLFD 146.88 3.01E-06 660553000 2386166 2022617 2059013 2466363 1483731 2397782 2584545 2588615 1671676 TRUE FALSE 2273376.662 2228723.972 2153420.783 2218439.505 1742493.217 2314746.208 2190225.192 2361942.147 1930910.976 1.177359645 1.154234452 1.115235663 1.148908227 0.902420276 1.19878453 1.134296308 1.223226848 1 20.88085022 1.141983682 0.010723616 4.24E-07 2.210337893 0.09919532 0.091723131 2941.718361 24.53867963 2552.794506 2500.704646 13.86703724 -1.141983682 2.21033747 KEESEES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.029)EES(0.971)DDDMGFGLFD;KEES(0.004)EES(0.996)DDDMGFGLFD;KEES(0.35)EES(0.65)DDDMGFGLFD;KEES(0.484)EES(0.516)DDDMGFGLFD;KEES(0.027)EES(0.973)DDDMGFGLFD;KEES(0.007)EES(0.993)DDDMGFGLFD;KEES(0.446)EES(0.554)DDDMGFGLFD;KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.148)EES(0.852)DDDMGFGLFD;KEES(0.291)EES(0.709)DDDMGFGLFD;KEES(0.183)EES(0.817)DDDMGFGLFD;KEES(0.166)EES(0.834)DDDMGFGLFD;KEES(0.432)EES(0.568)DDDMGFGLFD;KEES(0.006)EES(0.994)DDDMGFGLFD;KEES(0.036)EES(0.964)DDDMGFGLFD 250.1 3.61E-21 8181982800 11058256 9225906 9728154 11272356 6556870 10875270 11828346 11793848 7369773 TRUE FALSE 10535554.15 10166036.31 10174199.48 10139237.36 7700386.052 10498656.67 10023714.58 10761116.15 8512639.757 1.237636556 1.194228418 1.195187365 1.191080282 0.904582629 1.233302122 1.177509546 1.264133859 1 23.02117515 -2.392986352 1.919941444 5.80E-05 1.175986627 0.232642946 0.09969257 1864752.589 197975.1489 8067206.029 0.025767276 0.004045886 2.392986352 1.175928626 KEESEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KEESEKPR 8 2 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ;; 95.099 0.005563 142584000 366295 319620 347943 391413 250408 368935 448400 382033 280234 FALSE TRUE 348980.9613 352189.6414 363896.5307 352067.4216 294079.0759 356158.6884 379988.3446 348580.1652 323691.2575 1.078129091 1.088041871 1.124208709 1.08766429 0.908517203 1.100303701 1.173922174 1.076890887 1 18.30425888 0.957147975 22.97117786 0.999999998 1.084861373 0.118567013 0.067395241 7960.531803 4267314.906 0.065911583 0.016477896 9.060412591 -0.957147975 0.084861375 KEEVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEEVSR 6 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 112.17 0.043649 119331000 345050 326070 315450 415070 284300 406580 441410 472900 357910 FALSE TRUE 328740.1703 359296.9037 329913.6945 373346.375 333881.83 392500.0327 374064.7974 431490.369 413412.8548 0.795186135 0.869099496 0.798024761 0.903083614 0.807623242 0.949414195 0.904821398 1.043727509 1 18.65722372 1.728265689 0.990448986 1.018750551 0.833029359 0.704696858 0.045793424 0.256397982 0.470956529 0.034762022 0.014108753 53.48914908 -1.728265689 -0.185721192 KEEWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEEWDR 6 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 91.065 0.077472 86664000 202290 199080 162740 235830 164100 186850 227000 209070 184450 FALSE TRUE 192728.1526 219366.4783 170201.79 212123.9204 192718.988 180379.3376 192366.9809 190762.7225 213053.564 0.904599524 1.029630644 0.798868542 0.995636573 0.904556509 0.846638443 0.902904309 0.895374473 1 17.70085666 2.506168482 24.66585491 0.897907904 0.939167926 0.005149989 0.070972482 1589.566876 1349801.4 0.021086013 0.019845464 320.7513419 -2.506168482 0.041260022 KEFSPFGTITSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEFSPFGTITSAK 13 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YAP2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 135.45 0.00013436 383920000 1500600 1321400 1437900 1734200 1079300 1503200 1583000 1536900 1297500 FALSE TRUE 1429669.612 1456052.162 1503829.137 1559874.921 1267529.578 1451143.807 1341484.276 1402320.888 1498709.673 0.953933665 0.971537175 1.003415914 1.040811939 0.845747246 0.968262121 0.895092826 0.935685486 1 20.5152895 2.751723797 24.98043162 0.923582678 0.985277265 0.306802479 0.046471845 917.003955 1740243.657 0.013053993 0.013770716 564.5777998 -2.751723797 0.061694587 KEGDLIAAQAR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 113.07 0.002311 2480950000 6515260 5238100 4616460 5708330 4656530 5081520 6662980 5658290 4830040 FALSE TRUE 6207296.572 5771868.345 4828129.257 5134517.823 5468627.358 4905545.688 5646420.027 5162820.131 5579057.935 1.112606581 1.034559672 0.865402244 0.920319861 0.980206232 0.879278499 1.012074098 0.925392816 1 22.4115901 3.967202571 4.625378791 0.942076415 1.086436605 0.584563634 0.048475683 0.117389182 6.171958596 0.011775427 0.023269183 9272.622319 -3.967202571 0.14436019 KEGGLGPLNIPLLADVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEGGLGPLNIPLLADVTR 18 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 152.32 6.62E-08 1032450000 1316610 1132520 1163140 1357510 1176400 1204630 1437970 1318350 1342820 FALSE TRUE 1254376.455 1247925.076 1216471.12 1221050.516 1381563.788 1162913.361 1218581.266 1202908.285 1551057.667 0.808723287 0.804563945 0.784284908 0.787237342 0.890723676 0.749755077 0.785645364 0.775540659 1 20.5648209 -2.137863887 2.485392061 1.443818318 0.798376475 0.750147376 0.036581106 8005776.561 2190486.231 20031923.15 0.008724151 0.007280079 2.137863887 -0.645441843 KEGVFAK ddPTM_SK-BR-3_Trastuzumab_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 1552280000 2921400 2769700 2797400 3608400 2547700 3130400 3827400 3811600 3105700 FALSE TRUE 2783311.212 3051935.579 2925663.557 3245676.776 2992018.073 3021993.463 3243459.835 3477836.097 3587316.094 0.775875651 0.850757363 0.815557782 0.904764646 0.834054763 0.8424107 0.904146652 0.969481363 1 21.77447344 1.420127062 0.31619344 1.02449527 0.79051473 0.765416395 0.033446422 0.674254668 0.237664992 0.059963632 0.049071357 26.31037646 -1.420127062 -0.23398054 KEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVR 35 1 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 ;; 98.636 0.00012137 69326000 103539 81265 89971 102740 87836 79764 102137 98581 77707 FALSE TRUE 98644.91666 89545.99589 94096.25934 92412.38001 103154.5706 77001.75268 86554.12478 89948.72503 89757.40469 1.099017034 0.997644665 1.048339796 1.029579457 1.149259729 0.857887468 0.964311803 1.002131527 1 16.45374334 2.238607833 25 0.950908272 1.056382236 0.474673527 0.056316086 1.096433287 580678.1424 0.019064961 0.015009454 173.2239084 -2.238607833 0.105473963 KEIHTVPDMGK ddPTM_SK-BR-3_Trastuzumab_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 ; 85.813 0.009696 567120000 1320760 1135200 1187940 1392280 968780 1286140 1394180 1463000 974440 FALSE TRUE 1258330.292 1250878.171 1242408.224 1252325.369 1137734.925 1241600.649 1181472.235 1334891.964 1125551.178 1.117968082 1.111347218 1.103822063 1.112632987 1.010824694 1.103104571 1.049683264 1.185989575 1 20.10220023 KEKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_SK-BR-3_Trastuzumab_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(0.621)S(0.379)DPEAAFLSR 235.14 3.44E-45 853770000 663060 504320 607250 684010 520400 673320 804490 773550 574100 TRUE FALSE 631718.4679 555710.7814 635093.0132 615252.0153 611157.5952 650002.7596 681750.275 705813.8612 663128.4959 0.952633572 0.838013726 0.957722398 0.927802106 0.921627707 0.980206346 1.028081705 1.064369674 1 19.33892893 2.04550328 1.756916873 1.037368618 0.910821957 0.663956796 0.036089495 0.198529272 1.154487462 0.021084597 0.010960445 111.0460923 -2.04550328 -0.12654666 KEKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.007)S(0.993)DPEAAFLSR;KEKPELSEPSHLNGPS(0.168)S(0.832)DPEAAFLSR 197.8 3.03E-25 1992490000 1459540 1052920 1259670 1417570 1051010 1409240 1806350 1568830 1189450 TRUE FALSE 1390550.437 1160213.745 1317427.115 1275073.17 1234305.811 1360437.665 1530758.132 1431454.928 1373903.831 1.012116282 0.844465034 0.958893254 0.928065809 0.898393165 0.990198611 1.11416687 1.041888738 1 20.38984959 1.994179878 5.255199646 1.062699088 0.926742599 0.553449481 0.050513283 0.110529662 9.576512136 0.019811549 0.013054826 98.6688071 -1.994179878 -0.135956489 KEKT(ph)PELPEPSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 191.99 0.00014762 2141080000 2740190 2324810 2134950 2766610 1082966 2989260 2856970 3105510 1037723 TRUE FALSE 2610666.649 2561710.782 2232839.569 2488505.107 1271834.928 2885741.177 2421086.755 2833575.081 1198647.783 2.178009826 2.137167247 1.862798731 2.076093697 1.06105809 2.407497196 2.019848357 2.363976409 1 20.19297636 3.774585624 5.588046194 1.890993854 2.160873998 0.06524851 0.474406188 0.578264892 51.06929303 0.112877685 0.201620432 5950.940715 -3.774585624 0.269880145 KELNYFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KELNYFAK 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 145.72 0.0009056 1660580000 6162800 4882300 3735200 4600800 4987400 4389700 6796300 5479800 5437500 FALSE TRUE 5871496.657 5379811.921 3906462.615 4138318.843 5857200.981 4237683.588 5759399.612 4999959.662 6280719.729 0.934844558 0.856559782 0.621976904 0.658892455 0.932568437 0.674713054 0.916996755 0.796080685 1 22.58249846 -0.999331705 5.545322814 1.000000539 0.809312934 0.224887567 0.115850242 7.58E-07 1.37E-07 0.110218475 0.02597867 0.100153999 0.999331705 -0.190687605 KELQAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KELQAAGK 8 1 P06744;A0A2U3TZU2;P06744-2 P06744 GPI Glucose-6-phosphate isomerase 0 ;;; 113.22 0.004635 2517690000 5014960 4249320 3972160 4794340 3889520 4873940 6266210 5386020 4664180 FALSE TRUE 4777912.779 4682330.539 4154287.465 4312403.835 4567851.057 4705154.236 5310184.578 4914391.536 5387477.213 0.886855311 0.869113753 0.771100703 0.800449573 0.847864571 0.873350188 0.985653278 0.912187902 1 22.36117843 1.894178774 3.677845782 0.962283178 0.840813034 0.693114592 0.039583059 0.155047235 3.534941014 0.020828952 0.011571196 78.37522024 -1.894178774 -0.121470144 KELS(ph)PAGSISK ddPTM_SK-BR-3_Trastuzumab_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 151.59 2.04E-05 927810000 2757400 2226560 2234410 2670600 1516680 2722800 2988000 3053800 1887560 TRUE FALSE 2627063.167 2453448.995 2336859.909 2402146.214 1781188.512 2628508.753 2532125.722 2786393.083 2180273.164 1.204923864 1.125294314 1.071819782 1.101763877 0.816956582 1.205586894 1.161380034 1.278001825 1 21.05607747 -0.262243791 7.428635317 0.999984503 1.121813413 0.087056167 0.122808266 0 0 0.115029351 0.027112678 0.546708982 0.262243791 0.12182891 KELSDIAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KELSDIAHR 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;; 169.37 3.80E-05 10274617000 13661460 11912170 12077720 14069000 12386920 12761790 16192100 13999300 12440550 FALSE TRUE 13015709.86 13126033.67 12631495.41 12654757.39 14547194.93 12319846.01 13721697.76 12773447.08 14369766.96 0.905770421 0.913447915 0.879032725 0.880651539 1.01234731 0.857344872 0.954900507 0.88891122 1 23.77653333 -4.999999996 0.229043762 1.463944151 0.902988104 0.279330333 0.044286302 200.1066215 2.001526855 43.02913323 0.068036905 1.00E-05 4.999999996 -0.560956047 KEMQPTHPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 100.72 0.001823 1136150000 1764800 1823610 1578150 1943610 1444110 1728450 1884990 1882980 1507790 FALSE TRUE 1681381.401 2009437.932 1650509.739 1748234.63 1695962.327 1668593.343 1597400.155 1718096.289 1741610.372 0.965417655 1.15378156 0.947691725 1.003803524 0.973789749 0.958074992 0.917197199 0.986498654 1 20.73199047 3.698967668 24.99565952 0.964187152 1.059599694 0.343528405 0.05131605 458.4889306 289451.3635 0.013141659 0.020359224 4999.973098 -3.698967668 0.095412542 KENPLQFK ddPTM_SK-BR-3_Trastuzumab_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 ; 149.72 0.0008028 3529100000 6413900 5192900 4875300 5699700 4819100 5451300 6894100 6489000 5622700 FALSE TRUE 6110727.658 5722062.414 5098837.327 5126755.327 5659549.514 5262520.114 5842278.426 5920788.76 6494639.599 0.940887876 0.881043871 0.785083953 0.789382574 0.871418564 0.810286704 0.899553907 0.911642389 1 22.63081804 0.982883329 1.500280986 0.998266198 0.854870169 0.504900397 0.047804182 0.419605727 1.928964271 0.049376421 0.014578757 9.61353981 -0.982883329 -0.143396029 KENQWCEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KENQWCEEK 9 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 187.42 6.50E-05 2109570000 2703690 2284560 2267250 2744000 1643100 2724870 2966770 2874760 1870940 FALSE TRUE 2575891.932 2517359.261 2371205.655 2468167.907 1929656.12 2630507.069 2514134.748 2623030.774 2161075.82 1.191948893 1.164863925 1.097233902 1.142101487 0.892914585 1.217221092 1.163371838 1.213761567 1 21.04331826 -2.444638408 1.929063424 5.44E-05 1.138757027 0.171963715 0.093138503 2259011.854 194929.415 9840121.963 0.022587695 0.003592209 2.444638408 1.138702662 KENSESEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KENSESEKR 9 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ; 58.223 0.062003 40477000 88447 81007 75202 83878 63536 76032 93669 93549 87560 FALSE TRUE 84266.2856 89261.7054 78650.08608 75446.42408 74616.65828 73398.99278 79378.0737 85357.35363 101138.3576 0.833178307 0.882570248 0.777648441 0.745972407 0.737768143 0.725728542 0.784846379 0.843966183 1 16.62597073 0.861234864 3.236793422 0.99990199 0.791159754 0.679177721 0.046616733 0.453176606 8.817205389 0.053834171 0.01399743 7.264987377 -0.861234864 -0.208742237 KENSETTLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KENSETTLTR 10 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ; 199.82 4.35E-07 534120000 640650 581790 595090 743610 589850 623200 788580 710880 732730 FALSE TRUE 610367.7441 641075.0624 622375.4651 668860.91 692719.6532 601618.4277 668267.6377 648631.5786 846358.0261 0.721169677 0.757451389 0.735357196 0.790281287 0.818471181 0.71083207 0.789580316 0.766379663 1 19.69090856 -5 0.28463562 2.812291735 0.744882327 0.847166916 0.032045482 82.74373998 0.786338074 88.77483364 0.03323328 1.00E-05 5 -2.067409408 KEPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEPAITSQNSPEAR 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KEPAITSQNS(1)PEAR;KEPAITS(0.001)QNS(0.999)PEAR 174.02 1.60E-06 876730000 843430 810840 757000 959670 614620 772940 930590 829640 776170 TRUE FALSE 803562.7354 893465.5178 791709.1988 863202.1483 721809.5334 746172.894 788611.404 756992.3234 896534.4795 0.896298752 0.996576862 0.883077246 0.962820916 0.805110735 0.832285775 0.879621947 0.844353832 1 19.77399954 2.754903775 24.92689382 0.862866685 0.937873705 0.200987309 0.060092067 962.0186582 1467288.02 0.016407063 0.017350599 568.7269064 -2.754903775 0.075007019 KEPAVLELEGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEPAVLELEGKK 12 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 119.32 0.00029853 313250000 558540 418260 462660 494150 330170 528220 554770 558030 410960 FALSE TRUE 532138.9211 460881.1695 483873.4186 444477.1032 387751.5435 509927.609 470129.6474 509165.9349 474689.5779 1.121025078 0.970910656 1.019347045 0.936353196 0.816852869 1.074233842 0.990393869 1.072629269 1 18.85662485 -1.261938619 5.262355026 0.999999936 1.000553004 0 0.084550986 6.93E-08 9.66E-09 0.07932513 0.01869467 0.054709328 1.261938619 0.000553068 KEPEDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KEPEDGR 7 1 Q13867;J3KSD8;K7ES02;K7EMJ3 Q13867 BLMH Bleomycin hydrolase 0 ;; 79.906 0.050273 179221000 613760 582130 508360 646070 398435 552330 584090 636050 495340 FALSE TRUE 584748.7812 641449.7088 531668.8088 581125.8161 467921.9379 533202.6736 494976.343 580354.0901 572154.7974 1.022011497 1.121112174 0.929239449 1.015679356 0.817824022 0.931920306 0.865109137 1.01433055 1 19.126046 3.725299817 24.36874228 0.927556341 1.071561832 0.388637057 0.067836977 414.3349125 761403.7119 0.01674352 0.026129084 5312.510691 -3.725299817 0.144005492 KEPEKPIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEPEKPIDR 9 2 O00422;O00422-2;U3KQ12 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;;; 131.28 0.00018979 1393710000 3104090 2841210 2608410 3579530 1858860 3236460 3237220 3508590 2072590 FALSE TRUE 2957365.817 3130732.529 2728008.179 3219708.844 2183044.595 3124380.579 2743322.633 3201359.259 2393996.672 1.235325785 1.307743058 1.139520456 1.34490949 0.911882887 1.305089775 1.14591748 1.337244657 1 21.19098972 -4.642616672 0.24591617 3.44E-33 1.236954752 0.192769821 0.131483664 227.8201188 2.666007154 114.8177318 0.174522855 2.28E-05 4.642616672 1.236954752 KEPFFHGHDNYDQLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEPFFHGHDNYDQLVR 16 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 191.37 2.87E-10 170350000 266570 252170 203900 295390 230020 255300 298270 302920 93683 FALSE TRUE 253969.7644 277866.4097 213249.0167 265696.836 270135.4152 246458.897 252763.4334 276394.7189 108210.8812 2.346989153 2.567823186 1.970679976 2.455361541 2.496379405 2.277579614 2.335841189 2.554222976 1 16.72348605 -1.472579816 7.668116899 0.999875613 2.37751312 0.863538645 0.17185331 0.000336622 2.32E-05 0.153271757 0.036123412 0.03368373 1.472579816 1.377637507 KEQQLQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEQQLQER 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 110.38 0.0055105 141665000 154599 133479 128689 157342 152186 143941 168491 161614 156527 FALSE TRUE 147291.4117 147080.6619 134589.5179 141525.6832 178727.1902 138956.2871 142784.6034 147462.2214 180800.4077 0.81466305 0.813497401 0.744409372 0.782773031 0.988533115 0.768561801 0.78973607 0.815607792 1 17.46403841 0.90549123 19.20300483 1 0.812789605 0.439069917 0.065789401 7431.573133 1510009.777 0.06010854 0.015027135 8.044355043 -0.90549123 -0.187210395 KEQSEVSVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KEQSEVS(0.015)VS(0.985)PR 107.74 0.0013214 360220000 518600 501460 492200 555530 385530 507950 537260 516320 436650 TRUE FALSE 494086.8058 552559.3441 514767.8569 499687.069 452766.3099 490359.5641 455291.1195 471108.2836 504363.4519 0.979624523 1.09555786 1.020628784 0.990728149 0.897698491 0.972234531 0.902704424 0.934065071 1 18.94410421 3.052066943 2.912811707 0.93537918 1.038621563 0.498062244 0.041147509 0.174792123 3.021894585 0.011824007 0.014117978 1127.371219 -3.052066943 0.103242383 KEQT(ph)PEHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 KEQT(1)PEHGK;KEQT(1)PEHGK 68.676 0.042548 151111000 335852 348026 337268 405640 186163 371480 408540 430790 235115 TRUE FALSE 319976.9416 383490.2451 352732.0714 364864.2965 218629.7683 358615.5545 346209.7196 393067.7438 271575.4334 1.178224914 1.412094755 1.298836448 1.343509948 0.805042509 1.320500717 1.274819726 1.447361195 1 18.05099345 -1.045152663 3.968618493 0.999958694 1.262474834 0.174410939 0.177738799 36379285.87 44451891.92 18164.11673 0.040480564 0.090125427 1.045152663 0.26251614 KEQTPEHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 86.898 0.0089755 244630000 550720 503750 459360 609520 350930 551300 516790 500970 366350 FALSE TRUE 524688.557 555082.6977 480422.1104 548249.8916 412132.0809 532208.3428 437944.194 457102.411 423161.6869 1.239924533 1.311750839 1.135315708 1.295603805 0.973935244 1.257695012 1.034933472 1.08020746 1 18.69084949 2.558007416 0.398028944 1.00210007 1.309073473 0.435944791 0.093277373 1.101049232 0.371398578 0.086917679 0.125671894 361.4160345 -2.558007416 0.306973403 KES(ph)APQVLLPEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KESAPQVLLPEEEK 14 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK 110.38 0.00061006 489360000 3555470 3770100 2842260 4007630 1559780 3906350 3324010 4171980 1586320 TRUE FALSE 3387409.979 4154277.476 2972580.432 3604775.418 1831805.138 3771072.12 2816871.225 3806659.314 1832318.404 1.848701608 2.267224663 1.622305614 1.967330247 0.999719882 2.058087782 1.537326274 2.077509731 1 20.80523879 -2.191719974 0.148395819 5.83E-14 2.139045036 0.297237726 0.364155448 56.6945634 1.140288095 23.10197484 2.082074161 0.006431022 2.191719974 2.139045036 KES(ph)APQVLLPEEEKIIVEETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KESAPQVLLPEEEKIIVEETK 21 2 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 KES(1)APQVLLPEEEKIIVEETK;KES(1)APQVLLPEEEKIIVEETK 176.68 4.76E-14 348920000 341980 215880 294220 306440 159089 363530 413930 424730 189801 TRUE FALSE 325815.2831 237878.4174 307710.278 275636.069 186834.0712 350940.8649 350777.3762 387538.3896 219234.3697 1.486150568 1.085041628 1.403567691 1.257266684 0.852211592 1.600756603 1.600010877 1.767689939 1 17.74211446 KES(ph)PPKPKDPVSAAVPAPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KESPPKPKDPVSAAVPAPGR 20 3 Q68EM7-2 Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 KES(1)PPKPKDPVSAAVPAPGR 77.053 0.05801 392390000 373500 352390 362310 418350 161300 445380 418520 452270 163380 TRUE FALSE 355845.3952 388298.9416 378922.2719 376296.6632 189430.6689 429956.3789 354667.0874 412666.8412 188716.136 1.885611919 2.057582091 2.007895456 1.99398245 1.003786284 2.278323349 1.879368108 2.186706712 1 17.52585826 2.906820845 19.81088135 1.757924954 1.988504345 0.101398491 0.425362946 27.78002388 5898.047661 0.119984222 0.127262875 806.9020992 -2.906820845 0.230579391 KES(ph)PTSSSFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KESPTSSSFGK 11 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 KES(0.807)PT(0.135)S(0.055)S(0.002)SFGK 65.038 0.040755 117520000 296200 289840 294190 342340 234570 313970 370900 333110 194020 TRUE FALSE 282199.213 319375.0255 307678.9025 307927.3328 275478.9337 303097.1402 314312.393 303941.1225 224107.6307 1.259212871 1.425096613 1.372906855 1.374015387 1.229226033 1.352462383 1.40250643 1.356228351 1 17.77383225 -1.159984361 4.067712481 0.999866039 1.350549674 0.766814298 0.060004608 5.18557234 15889630.23 4124.977998 0.013719789 0.069185588 1.159984361 0.350683635 KESYSIYVYK ddPTM_SK-BR-3_Trastuzumab_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 ; 149.38 3.76E-05 10349300000 20833500 17594400 16093300 20338300 14998000 19064400 23226600 20617100 17895400 FALSE TRUE 19848741.74 19387289.36 16831193.72 18293855.44 17613646.45 18404195.05 19682955.58 18811757.43 20670527.23 0.960243612 0.937919442 0.814260494 0.88502123 0.852114039 0.890359246 0.9522232 0.910076323 1 24.30107185 0.793513357 0.993130452 0.998064774 0.89930623 0.349711846 0.043919786 1.104389251 2.074404437 0.045630156 0.014894989 6.216033646 -0.793513357 -0.098758544 KESYSVYVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 157.68 1.40E-05 45230640000 49701740 41964780 37463820 46665350 34716840 44046600 53701760 45872540 40933270 FALSE TRUE 47352437.25 46241038.79 39181573.2 41974460.36 40771445.9 42521255.2 45508570.21 41855697.21 47280992.45 1.001511068 0.978004826 0.828696082 0.88776606 0.862322125 0.899330851 0.962513007 0.885254201 1 25.49475698 3.938203015 11.41690237 0.903170962 0.992709165 0.360760953 0.048031345 0.8601899 157.6985238 0.011825259 0.021341321 8673.672401 -3.938203015 0.089538203 KET(ph)ES(ph)EAEDNLDDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;KET(1)ES(1)EAEDNLDDLEK 297.99 7.96E-46 3004031000 7092040 6345640 6088310 7094830 2997540 7735820 7638330 8541450 3330140 TRUE FALSE 6756813.324 6992267.93 6367465.036 6381644.209 3520310.027 7467926.614 6472962.471 7793515.357 3846561.103 1.756585465 1.817797181 1.655365628 1.659051823 0.915183701 1.941455345 1.682792057 2.026099456 1 21.8751378 3.495572634 2.833626864 1.579182414 1.785815705 0.070718164 0.353779247 0.806000236 13.00675145 0.095429105 0.14822828 3130.203944 -3.495572634 0.206633292 KET(ph)ESEAEDNLDDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.686)ES(0.314)EAEDNLDDLEK;KET(0.784)ES(0.216)EAEDNLDDLEK;KET(0.78)ES(0.22)EAEDNLDDLEK 244.31 2.79E-20 3048810000 4011300 3222331 3211552 3861610 1764076 4227620 4088160 4436060 1661564 TRUE FALSE 3821693.799 3550690.192 3358804.836 3473433.626 2071730.296 4081216.459 3464436.108 4047615.069 1919230.859 1.991263209 1.850058932 1.75007859 1.809805011 1.079458621 2.12648543 1.805116926 2.108977693 1 20.87209683 4.001614421 1.562296409 1.712260999 1.97637874 0.071367854 0.373464303 1.270582707 5.780056337 0.099462749 0.329816809 10037.2426 -4.001614421 0.264117742 KET(ph)PPPLVPPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 87.429 0.0049058 5638490000 3682830 3130170 3005970 3820910 2148810 3541090 3822690 3803790 2313550 TRUE FALSE 3508749.925 3449137.882 3143796.698 3436824.868 2523561.784 3418461.165 3239468.432 3470709.982 2672323.518 1.312995938 1.290688743 1.176428182 1.286081137 0.944332438 1.279209326 1.212229137 1.298761156 1 21.34966324 -5 0.097356 0.384837002 1.373864521 0.272947907 0.110263502 255.7690226 1.704082847 33.6046561 1.914626435 1.00E-05 5 0.989027519 KETES(ph)EAEDNLDDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.287)ES(0.713)EAEDNLDDLEK;KET(0.254)ES(0.746)EAEDNLDDLEK 245.09 2.61E-20 9918700000 7510150 6674120 6467280 7612340 3001030 8432140 7965530 8709670 3569030 TRUE FALSE 7155160.093 7354220.416 6763811.185 6847133.121 3524408.682 8140132.877 6750242.102 7947005.122 4122496.944 1.735637452 1.7839238 1.640707386 1.660918907 0.854920872 1.974563714 1.637415914 1.927716437 1 21.97508699 3.406582962 2.704387205 1.549056258 1.755738338 0.073622484 0.354085049 0.813962547 12.04309361 0.097311371 0.143289275 2550.251207 -3.406582962 0.20668208 KETKPEPMEEDLPENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KETKPEPMEEDLPENK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 145.1 7.05E-07 1296110000 564960 480780 459207 659460 288810 580800 628380 652510 317055 FALSE TRUE 538255.4604 529772.0286 480262.0952 593169.8279 339178.3726 560686.7504 532509.09 595372.7652 366222.2701 1.469750762 1.446586054 1.311395113 1.619698954 0.926154416 1.531001242 1.454059825 1.625714256 1 18.48236 3.961822151 17.32570175 1.379983542 1.461064639 0.023909451 0.236001152 68.47037336 31072.85447 0.054998774 0.099235349 9158.453628 -3.961822151 0.081081098 KETKPEPMEEDLPENKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KETKPEPMEEDLPENKK 17 3 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 138.07 2.13E-06 313666000 905520 796470 757880 892690 398561 951640 917200 1039190 386332 FALSE TRUE 862717.8642 877631.1985 792629.5476 802955.1052 468069.9122 918684.4682 777264.2945 948193.0145 446242.3934 1.933294274 1.96671408 1.776230944 1.799369842 1.048914041 2.058711771 1.741798417 2.124838492 1 18.76746805 3.48799072 2.394206239 1.673670152 1.949581789 0.108333134 0.367552573 0.685987129 7.85405329 0.099102381 0.157596876 3076.031086 -3.48799072 0.275911636 KETQS(ph)PEQVK ddPTM_SK-BR-3_Trastuzumab_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 KET(0.002)QS(0.998)PEQVK;KET(0.002)QS(0.998)PEQVK;KETQS(1)PEQVK;KET(0.005)QS(0.995)PEQVK;KETQS(1)PEQVK;KET(0.003)QS(0.997)PEQVK;KET(0.002)QS(0.998)PEQVK;KETQS(1)PEQVK;KET(0.004)QS(0.996)PEQVK;KET(0.032)QS(0.968)PEQVK 201.08 1.52E-07 12116490000 13710110 14160740 11406320 15616070 6285750 14691100 13350360 14377910 6435140 TRUE FALSE 13062060.27 15603735.51 11929311.05 14046312.98 7381982.81 14182343.52 11313517.39 13118903.98 7433068.645 1.757290413 2.099231993 1.6048972 1.889705806 0.993127221 1.908006531 1.522052052 1.764937821 1 22.8255265 -2.012147717 0.124591458 2.22E-11 2.137925904 0.362621798 0.292999673 57.08560931 1.014777568 20.44023607 2.906807842 0.009724164 2.012147717 2.137925904 KETQS(ph)PEQVKSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KETQSPEQVKSEK 13 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KET(0.247)QS(0.753)PEQVKSEK;KET(0.001)QS(0.999)PEQVKSEK;KETQS(1)PEQVKSEK;KET(0.005)QS(0.995)PEQVKSEK;KETQS(1)PEQVKSEK;KET(0.002)QS(0.998)PEQVKSEK;KET(0.01)QS(0.99)PEQVKSEK;KET(0.001)QS(0.999)PEQVKSEK;KET(0.031)QS(0.969)PEQVKSEK 218.66 1.24E-11 6146430000 6296982 4291081 6297165 5839645 3237370 7006341 8230428 7801300 3950086 TRUE FALSE 5999336.14 4728347.032 6585896.244 5252632.79 3801966.303 6763709.654 6974725.046 7118176.815 4562645.163 1.314881155 1.036317063 1.443438183 1.151225353 0.833281171 1.482409746 1.528658223 1.560098706 1 22.12143903 KETSFGS(ph)SENITMTSLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.279)S(0.279)FGS(0.429)S(0.014)ENITMTSLSK 239.32 3.99E-24 131930000 537950 460890 513970 616070 383090 563280 649960 632230 500260 TRUE FALSE 512522.1696 507855.215 537536.0329 554141.4731 449900.7747 543773.4724 550796.6647 576868.5895 577837.7658 0.886965512 0.878888929 0.930254242 0.958991443 0.77859358 0.94104869 0.953202953 0.998322754 1 19.14030497 1.689055872 2.267374334 0.993534722 0.890475851 0.457638273 0.048007499 0.242059742 2.683529201 0.0310063 0.012700319 48.87152285 -1.689055872 -0.103058871 KETTSGTSTEPVKNS(ph)SPAPPQPAPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.5)S(0.5)PAPPQPAPGK;KETTSGTSTEPVKNS(0.569)S(0.431)PAPPQPAPGK 141.78 1.52E-07 876580000 618631 554089 604497 651024 341137 643843 732905 720483 370310 TRUE FALSE 589389.5386 610551.299 632213.7854 585581.8307 400631.1848 621546.5555 621086.8815 657393.689 427735.7835 1.377928996 1.427402903 1.478047453 1.369026986 0.93663238 1.453108623 1.452033955 1.536915344 1 18.70636038 2.998548429 24.98469813 1.312573921 1.420954971 0.101251889 0.192560247 167.3606932 2880732.428 0.054961111 0.064840768 996.6632138 -2.998548429 0.108381049 KETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.141)S(0.859)PAPPQPAPGK;KETTSGTSTEPVKNS(0.157)S(0.843)PAPPQPAPGK 165.49 6.58E-12 791780000 3043300 2632000 2750300 3307400 1558660 3309600 3424100 3505900 1825950 TRUE FALSE 2899449.24 2900203.792 2876403.975 2974933.868 1830489.811 3194987.722 2901690.657 3198904.81 2109109 1.374727072 1.375084831 1.363800531 1.41051689 0.867897207 1.514851874 1.375789803 1.516709098 1 21.00820223 KEVDMMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEVDMMK 7 1 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 84.476 0.034502 267430000 616720 477250 318180 396580 389230 439430 606380 541230 372770 FALSE TRUE 587568.8678 525882.3176 332768.8677 356715.0249 457111.5888 424212.4289 513865.5941 493837.032 430577.2678 1.364607265 1.221342502 0.772843558 0.828457635 1.061624993 0.985217894 1.1934341 1.146918495 1 18.71591263 3.976382764 15.68556774 1.011109821 1.310891495 0.488266584 0.12825745 5.836459598 3877.096547 0.035665409 0.064986367 9470.714924 -3.976382764 0.299781673 KEVEGDDVPESIMLEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEVEGDDVPESIMLEMK 17 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 154.12 2.40E-07 200710000 515840 415140 422340 555610 349430 506010 579010 544280 371720 FALSE TRUE 491457.2655 457443.238 441704.7068 499759.0272 410370.4814 488486.7468 490671.3903 496619.9578 429364.4391 1.144615671 1.065396191 1.028740777 1.163950671 0.95576262 1.137697262 1.142785349 1.156639704 1 18.71184318 KEVEVVEIIQATIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEVEVVEIIQATIIR 15 1 Q14764;H3BQK6;I3L155 Q14764 MVP Major vault protein 0 ; 227.29 1.20E-12 254830000 1065490 1083120 1001330 1099040 859380 1112530 1181070 1192930 921150 FALSE TRUE 1015126.399 1193491.159 1047241.971 988562.4112 1009255.6 1074002.807 1000876.08 1088470.725 1063997.237 0.954068642 1.12170513 0.984252528 0.929102423 0.948550959 1.009403755 0.94067545 1.023001458 1 20.02106297 3.501046445 24.88289904 0.969995924 1.040402218 0.205621784 0.049797717 844.6293664 878436.8626 0.012400039 0.019085609 3169.906444 -3.501046445 0.070406294 KEVLAS(ph)PDRLWGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR 180.81 1.35E-06 3150520000 1827550 1674590 1813590 2004580 1690900 1833020 2149760 1958000 2009900 TRUE FALSE 1741165.333 1845232.625 1896744.895 1803075.81 1985792.425 1769542.058 1821774.629 1786547.14 2321585.027 0.749989905 0.794815871 0.817004277 0.776657236 0.855360627 0.762212901 0.784711569 0.769537673 1 21.14667869 -1.038864185 4.568569115 1.000006997 0.788039389 0.83185161 0.029841706 3697788.51 840854.15 319.0891804 0.00657404 0.091439915 1.038864185 -0.211967608 KEVQDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KEVQDEEK 8 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;; 137.95 0.0011642 1937436000 3528030 2840800 3129140 3770420 2479900 3662890 4170820 3853770 2808840 FALSE TRUE 3361267.014 3130280.75 3272614.164 3391410.218 2912393.775 3536043.201 3534484.807 3516313.469 3244420.562 1.036014583 0.964819662 1.008689873 1.045305365 0.897662223 1.089884352 1.089404021 1.083803225 1 21.62952941 2.143587355 23.42866955 1.075555157 0.99435703 0.366935063 0.048228154 9.109841657 2239.722303 0.016275605 0.012020336 139.1833722 -2.143587355 -0.081198127 KEVS(ph)PEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEVSPEVVR 9 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KEVS(1)PEVVR;KEVS(1)PEVVR 152.4 4.93E-05 925240000 2843100 2451800 2460800 2870200 1993780 2975800 3101800 2979300 2324800 TRUE FALSE 2708712.297 2701641.207 2573630.114 2581682.043 2341494.601 2872747.3 2628563.442 2718416.698 2685318.111 1.008711887 1.006078646 0.958407909 0.961406409 0.871961721 1.06979776 0.978864825 1.01232576 1 21.35666157 KEVVEEAENGR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;;; 207.66 3.56E-08 9525910000 13495510 13131430 11814580 14596220 10031610 13193560 13489070 13770560 10841770 FALSE TRUE 12857603.99 14469537.65 12356290.18 13128980.23 11781119.61 12736663.71 11431064.63 12564736.76 12523056.32 1.026714538 1.155431811 0.986683272 1.048384667 0.940754342 1.017057129 0.912801503 1.003328297 1 23.57808337 3.273661601 1.535606405 0.969896107 1.086687898 0.362509842 0.051801296 0.306351564 1.499181695 0.016017848 0.023916882 1877.853038 -3.273661601 0.116791791 KEWDLKPIADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEWDLKPIADR 11 2 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 138.02 3.73E-05 1707140000 5176900 3881100 3836400 4029200 4037100 3876600 5208800 5067300 4265600 FALSE TRUE 4932198.197 4276588.502 4012302.735 3624177.161 4741168.962 3742352.37 4414101.894 4623580.349 4927087.462 1.001037273 0.867974952 0.814335602 0.735561767 0.962266044 0.759546568 0.895884623 0.938400299 1 22.23230365 1.095099881 2.549887735 0.99700342 0.864865433 0.253033703 0.080959275 0.385980907 4.932186984 0.075702304 0.020680005 12.44800864 -1.095099881 -0.132137987 KEWSGLLEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KEWSGLLEELAR 12 1 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 170.95 6.38E-05 1127510000 2070870 1913280 1854960 2409440 2071450 2158380 2736000 2462370 2367860 FALSE TRUE 1972984.079 2108245.407 1940011.751 2167238.514 2432710.224 2083634.759 2318572.95 2246751.829 2735055.635 0.721368901 0.770823591 0.709313451 0.792392844 0.88945548 0.761825366 0.847724236 0.821464763 1 21.38313875 -5 0.094426672 1.716444691 0.617610412 0.755338669 0.042377241 90.95685111 0.591430158 12.87297657 0.796977888 1.00E-05 5 -1.098834279 KEY(ph)EMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KEYEMLR 7 1 Q5VTR2;H3BP71;O75150-4;O75150;O75150-3 Q5VTR2;H3BP71 RNF20;RNF40 E3 ubiquitin-protein ligase BRE1A;E3 ubiquitin-protein ligase BRE1B 1 KEY(1)EMLR 43.246 0.078726 0 123830 86228 109390 125210 100390 112870 131980 115630 75680 TRUE FALSE 117976.8013 95014.73123 114405.6397 112623.6529 117897.9842 108961.2836 111844.027 105504.8242 87416.06788 1.349600871 1.086925248 1.308748408 1.288363291 1.348699239 1.246467454 1.279444726 1.206927133 1 16.41561086 0.829591476 3.273855886 1.000034589 1.262850643 0.569763531 0.07394909 0.676146249 11.63839454 0.070125143 0.018204172 6.754473086 -0.829591476 0.262816054 KFAADAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFAADAVK 8 1 P37837 P37837 TALDO1 Transaldolase 0 ; 89.029 0.022762 1035300000 1844980 1275450 916830 1081440 1569190 1212820 2180000 1634230 1689240 FALSE TRUE 1757771.452 1405419.805 958867.5624 972731.5966 1842856.239 1170819.739 1847400.962 1491128.158 1951198.712 0.900867472 0.720285328 0.491424864 0.498530258 0.944473891 0.600051513 0.946803086 0.764211327 1 20.89592928 1.70961503 9.590545571 0.889425245 0.706424983 0.277591428 0.158749763 0.172587653 35.7552033 0.075802734 0.04081145 51.2406972 -1.70961503 -0.183000261 KFAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFAELR 6 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 101.69 0.058103 2220630000 8282600 6200630 5719220 6709330 7679260 6360140 9379550 7727430 8721850 FALSE TRUE 7891097.913 6832481.247 5981451.894 6034895.402 9018520.513 6139886.757 7948527.38 7050775.264 10074389.95 0.783282953 0.678202976 0.593728446 0.599033334 0.895192717 0.609454943 0.788983494 0.699871188 1 23.26418914 -0.916547259 0.451487654 1.098472221 0.694987552 0.486541253 0.095445516 12.83438888 1.810314158 1.779026515 0.048473545 0.121186081 0.916547259 -0.403484668 KFAETQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFAETQPK 8 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 160.59 0.00056519 2066760000 7196060 5833340 5363920 6964870 5038610 6754220 8150830 7619570 5929990 FALSE TRUE 6855916.505 6427763.978 5609861.038 6264748.035 5917341.989 6520319.668 6907271.183 6952360.057 6849582.563 1.000924719 0.938416892 0.819007726 0.914617493 0.863898192 0.951929495 1.00842221 1.015004928 1 22.70758464 1.875869283 3.557728252 1.008181358 0.915929251 0.476795893 0.047331124 0.254386425 5.385695928 0.026153532 0.014253315 75.13967001 -1.875869283 -0.092252107 KFAMEPEEFDSDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFAMEPEEFDSDTLR 15 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 96.163 0.0061019 90705000 42782 30150 36002 43062 42269 37927 43277 45030 50312 FALSE TRUE 40759.77965 33222.31928 37652.72731 38733.32595 49640.70022 36613.57848 36674.29881 41086.93448 58114.128 0.70137471 0.571673712 0.647910045 0.666504468 0.854193325 0.630028871 0.631073718 0.707004233 1 15.82660132 -4.999999996 0.350813438 4.858583081 0.656937473 0.654230128 0.073974947 272.2638701 2.225032375 790.416963 0.055924595 1.00E-05 4.999999996 -4.201645607 KFAYLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFAYLGR 7 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 151.51 0.0030086 1771590000 2426660 1975900 1666630 2225490 3125070 2328020 3739000 2966430 3415700 FALSE TRUE 2311956.591 2177246.456 1743046.634 2001779.517 3670081.219 2247400.084 3168546.879 2706673.663 3945389.311 0.58598947 0.551845784 0.441793318 0.507371861 0.930220297 0.569626951 0.803101197 0.686034622 1 21.91173623 1.154880526 0.316274833 1.037701852 0.497908622 0.534760863 0.125352656 1.23234748 0.405343633 0.252044958 0.165936575 14.28500926 -1.154880526 -0.53979323 KFDDRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFDDRPK 7 2 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 82.452 0.013752 32508000 143600 127380 123720 154960 111560 149750 153480 165200 114740 FALSE TRUE 136812.3126 140360.1668 129392.6844 139383.1264 131016.0287 144564.12 130063.8071 150734.2122 132533.2932 1.032286373 1.059055905 0.976303246 1.051683868 0.988551824 1.090775883 0.981367051 1.13733092 1 17.01599529 2.254268422 24.99988671 1.044801963 1.026971437 0.0717362 0.049908934 1001.094117 1593294.937 0.015601451 0.01300991 179.5843231 -2.254268422 -0.017830526 KFDEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KFDEGR 6 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6;H0Y4J5;Q13087-2;Q13087 P07237 P4HB;PDIA2 Protein disulfide-isomerase;Protein disulfide-isomerase A2 0 ;;;;; 121.29 0.031612 6182460000 16956570 13568830 12228480 17736830 12308600 14576560 17916550 15981400 14643620 FALSE TRUE 16155066.54 14951509.2 12789167.9 15953890.15 14455215.94 14071770.07 15183051.24 14581983.89 16914477.8 0.955102885 0.883947431 0.756107759 0.943209145 0.854606102 0.831936418 0.897636416 0.862100744 1 24.0117553 -1.002881854 5.053208796 1.000001128 0.876719651 0.334237938 0.056085276 6.79E-07 1.34E-07 0.051749701 0.01219741 0.099338625 1.002881854 -0.123281477 KFDEVLVNHFCEEFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFDEVLVNHFCEEFGK 16 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 169.64 3.60E-09 140920000 646160 610860 577070 723760 382060 661020 649640 732900 392700 FALSE TRUE 615617.2974 673107.3285 603529.2303 651006.2697 448691.143 638128.7117 550525.4865 668723.3907 453597.9104 1.357187243 1.483929518 1.330537942 1.435205619 0.989182562 1.40681581 1.213686117 1.474264708 1 18.79105447 -4.822073381 0.127832566 7.50E-13 1.479787099 0.316620822 0.148937755 153.7942335 1.303271214 40.46085311 1.087970138 1.51E-05 4.822073381 1.479787099 KFDGVEGPRT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFDGVEGPRTPK 12 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 1 KFDGVEGPRT(1)PK 128.64 0.011838 815350000 1962500 1709000 1928000 2380800 1316800 2115600 2238500 2247300 1364200 TRUE FALSE 1869736.514 1883149.043 2016400.707 2141477.461 1546449.503 2042336.242 1896975.712 2050514.498 1575753.169 1.186566876 1.195078697 1.279642489 1.359018343 0.981403391 1.296101624 1.203853338 1.301291686 1 20.58761013 KFDLGQDVIDFTGHALALYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFDLGQDVIDFTGHALALYR 20 1 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ;; 218.07 6.59E-25 4350904000 2686813 2058172 2396025 2567788 2640678 2474246 3358747 2848754 2697217 FALSE TRUE 2559812.674 2267902.067 2505885.116 2309669.072 3101211.407 2388562.241 2846308.458 2599301.998 3115487.637 0.821641095 0.727944493 0.804331587 0.741350742 0.995417658 0.766673638 0.913599664 0.834316261 1 21.57102656 0.901009402 0.229657442 1.050442479 0.736815614 0.402960261 0.07475943 3.005607155 0.532569785 0.338695706 0.195388146 7.961765869 -0.901009402 -0.313626865 KFDLNSPWEAFPVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFDLNSPWEAFPVYR 15 1 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 180.7 9.92E-07 324860000 749260 563390 614830 615860 634560 553930 699460 680310 676830 FALSE TRUE 713843.9647 620800.0815 643020.5636 553952.5827 745227.0631 534747.2652 592744.5305 620738.4498 781789.3396 0.913089919 0.79407591 0.822498506 0.708570141 0.953232572 0.684004294 0.758189579 0.793997076 1 19.57642039 4.579308129 2.027450212 0.797788151 0.927388073 0.067401646 0.099034842 1.021693966 5.96050604 0.022555554 0.218228049 37958.42018 -4.579308129 0.129599922 KFDQLLAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 136.7 0.00017763 2985500000 6836960 5519610 4703600 5825230 4797070 5873810 7655920 7248650 5355480 FALSE TRUE 6513790.45 6082064.534 4919264.712 5239666.813 5633677.489 5670398.487 6487868.793 6613919.778 6185980.486 1.052992402 0.983201377 0.795227971 0.847022849 0.910716984 0.916653148 1.048802014 1.069178895 1 22.56057085 1.719383675 6.097381458 1.043897764 0.927883009 0.385364874 0.071464718 0.181752318 16.97345361 0.0416093 0.021347968 52.40632131 -1.719383675 -0.116014755 KFDSSR ddPTM_SK-BR-3_Trastuzumab_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 3047450000 5393340 3225080 3185730 5073500 4906880 3859000 6407150 4708180 6928400 FALSE TRUE 5138407.507 3553719.319 3331798.872 4563502.141 5762638.318 3725361.862 5429621.592 4295906.8 8002820.887 0.642074536 0.444058335 0.416328057 0.570236696 0.720075883 0.46550609 0.678463465 0.536799069 1 22.93207719 -5 0.244476377 3.618624748 0.515210876 0.662905056 0.099206358 102.9002588 1.023471216 134.0515308 0.141525437 1.00E-05 5 -3.103413872 KFDSSYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFDSSYDR 8 1 Q96AY3;C9JPC3;K7ELI6;K7ESG6 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10;Peptidyl-prolyl cis-trans isomerase 0 86.18 0.026001 258880000 927660 830110 652540 811200 758110 808290 910390 920210 726070 FALSE TRUE 883811.3502 914699.1528 682459.6045 729656.6348 890324.144 780298.7146 771493.285 839631.5341 838665.2273 1.053830923 1.090660639 0.813744963 0.870021328 1.061596588 0.93040547 0.919906132 1.001152196 1 19.67773551 3.777085503 24.9984998 0.939133486 1.072245831 0.371866644 0.070056433 502.1130995 325815.6493 0.017346166 0.031270491 5985.294201 -3.777085503 0.133112345 KFDVNTSAVQVLIEHIGNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 260.01 9.15E-37 1441001000 1323175 1348570 1318580 1459620 1170498 1364994 1446123 1509843 1135362 FALSE TRUE 1260631.14 1485990.816 1379038.197 1312896.225 1374632.481 1317723.916 1225490.376 1377633.143 1311428.14 0.961265891 1.133108838 1.051554527 1.001119455 1.048195047 1.004800702 0.934470093 1.050483134 1 20.32270733 2.107566471 4.64299923 0.98371415 1.043475162 0.123877143 0.051516949 0.321089848 11.73909815 0.019689636 0.014194767 128.1051151 -2.107566471 0.059761012 KFEDEYSEYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFEDEYSEYLK 11 1 B8ZZ77;H7BZ14;Q9H2H8;Q9H2H8-2;C9K058 B8ZZ77 PPIL3 Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase-like 3 0 134.98 0.00020787 154100000 361420 310500 303200 343970 229410 329160 391450 357890 256290 FALSE TRUE 344336.3929 342140.303 317102.0199 309393.4821 269419.0314 317761.1067 331727.113 326551.2543 296034.1443 1.163164451 1.155746084 1.071167046 1.045127693 0.910094449 1.073393434 1.120570446 1.103086454 1 18.17540406 3.686544616 3.252135091 1.049491545 1.161490334 0.400605799 0.058147615 0.259449206 5.507524554 0.016988789 0.029144982 4858.974458 -3.686544616 0.111998789 KFEEDLLLLEDQNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFEEDLLLLEDQNSK 15 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;; 185.61 6.67E-07 168738000 491985 414223 405636 504534 308933 481651 518904 560761 357284 FALSE TRUE 468729.8441 456432.7946 424234.8118 453817.2838 362810.8174 464971.3051 439735.6645 511657.7941 412689.778 1.135792232 1.105994912 1.02797509 1.099657195 0.879136913 1.126684812 1.065535635 1.239812133 1 18.65469818 -0.938793769 7.262891891 1 1.083110319 0.07867091 0.091275527 2.44E-09 3.35E-10 0.081745314 0.019267555 0.115134699 0.938793769 0.083110319 KFEEETVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFEEETVK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 119.68 0.0026417 375870000 818130 705760 740310 920260 576380 868810 994090 941630 657580 FALSE TRUE 779458.6163 777677.7464 774253.9458 827753.7164 676900.4895 838722.8919 842423.3128 859175.8853 759554.1479 1.026205463 1.023860838 1.019353193 1.089788949 0.891181348 1.104230546 1.109102379 1.131158177 1 19.53479329 KFELLPTPPLS(ph)PSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFELLPTPPLSPSRR 15 2 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1 H0YBT0 MYC Myc proto-oncogene protein 1 KFELLPT(0.006)PPLS(0.975)PS(0.019)RR 61.181 0.047696 234420000 537270 479380 503680 525340 573690 579920 686790 610500 663920 TRUE FALSE 511874.3119 528229.367 526774.2262 472531.8251 673741.3544 559837.225 582007.5717 557041.3835 766877.3228 0.667478744 0.688805564 0.686908076 0.616176553 0.878551672 0.73002188 0.75893178 0.726376132 1 19.54863628 -5 0.152545486 2.037969872 0.629318063 0.681610373 0.063087663 73.18408653 0.657502969 22.93306224 0.281596939 1.00E-05 5 -1.408651809 KFESEILEAISQNSVVIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFESEILEAISQNSVVIIR 19 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 139.17 7.70E-07 455170000 175490 148360 174380 197990 166470 185490 234170 182970 205410 FALSE TRUE 167194.9355 163478.0527 182375.4955 178087.669 195502.3153 179066.4348 198443.0657 166948.1768 237263.9337 0.704679101 0.689013497 0.768660844 0.750588875 0.823986656 0.754714094 0.836381082 0.703639083 1 17.85613329 -5 0.132217588 1.818273943 0.65335696 0.720915759 0.048197964 68.11990115 0.564620511 14.8045063 0.317947607 1.00E-05 5 -1.164916983 KFFDANYDGKDYDPVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFFDANYDGKDYDPVAAR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 178.72 4.91E-14 327970000 825760 448960 749820 698520 678140 757430 1113300 919630 902090 FALSE TRUE 786727.9613 494709.5344 784199.9887 628303.4425 796407.4013 731200.0092 943445.6378 839102.3219 1041981.51 0.755030635 0.474777652 0.752604515 0.602989052 0.76432009 0.701739908 0.905434145 0.805294829 1 19.99089825 1.702431841 0.633000203 0.983764035 0.621675091 0.592728148 0.092634016 0.42478779 0.359476105 0.079646072 0.042087229 50.40015143 -1.702431841 -0.362088944 KFFVGGNWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFFVGGNWK 9 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 145.17 0.00015682 1517110000 7752200 3515700 1655360 1956960 7374300 2698500 9120900 4389900 7373200 FALSE TRUE 7385768.869 3873953.827 1731259.893 1760242.663 8660375.585 2605050.268 7729339.188 4005497.084 8516598.199 0.867220538 0.454871034 0.203280682 0.206683775 1.016882021 0.305879203 0.9075618 0.47031655 1 23.02184586 0.610833417 0.56214939 1.003411787 0.521244404 0.188708018 0.29049501 2.599203069 1.582532476 0.357482482 0.127592528 4.08162797 -0.610833417 -0.482167384 KFGDPVVQSDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 137.68 0.00014089 2333100000 4028600 3465600 3149400 3954200 2528500 3670300 4075900 4015900 2652800 FALSE TRUE 3838176.062 3818748.58 3293803.105 3556716.304 2969469.599 3543196.591 3454046.596 3664246.506 3064182.675 1.252593748 1.246253564 1.074936926 1.16073899 0.969090265 1.156326814 1.127232597 1.195831611 1 21.54707088 3.747052942 24.13657824 1.105187407 1.249423681 0.440727686 0.070652196 319.1194947 906985.169 0.016725085 0.029528006 5585.382787 -3.747052942 0.144236275 KFGEEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFGEEIAR 8 1 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 123.35 0.0021665 853230000 1608980 1369530 1303130 1609970 1463470 1567010 1726060 1540600 1241520 FALSE TRUE 1532926.704 1509086.664 1362879.799 1448132.757 1718698.705 1512744.051 1462717.846 1405696.897 1434048.581 1.06895033 1.05232604 0.950372127 1.009821268 1.198494059 1.054876432 1.019991837 0.980229621 1 20.45166247 1.54833779 3.454920702 0.991925335 1.055796345 0.165426134 0.061493803 0.390308295 10.42565457 0.041186105 0.016418178 35.34579793 -1.54833779 0.063871011 KFGGPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KFGGPGAR 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;; 123.92 0.0021279 7357382000 8855410 8468390 7915400 9851510 8758680 8538030 10824350 9681770 9576920 FALSE TRUE 8436832.319 9331328.569 8278328.919 8861217.498 10286191.02 8242355.88 9172896.605 8833982.893 11062059.84 0.762681855 0.84354349 0.748353294 0.801045883 0.929862175 0.745101364 0.829221387 0.7985839 1 23.39911672 -1.604472636 2.415227392 1.021234105 0.808365022 0.556726121 0.054030817 3384116.768 2784197.296 453595.4836 0.012571925 0.024861502 1.604472636 -0.212869083 KFGNPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KFGNPGER 8 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 136.57 0.0012594 1589890000 2181880 1661410 1821300 2032130 1779830 1901040 2297490 2093110 2205060 FALSE TRUE 2078746.856 1830709.568 1904808.407 1827856.432 2090231.788 1835206.508 1946965.704 1909826.192 2547009.443 0.816152002 0.718768269 0.747860756 0.717648078 0.820661185 0.720533845 0.76441244 0.749830825 1 21.28037288 -1.944379104 2.21846478 1.183264368 0.756505904 0.812882872 0.036641531 2495250.207 1066756.829 2361009.398 0.008422873 0.011366347 1.944379104 -0.426758464 KFGQGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KFGQGSR 7 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;;; 128.61 0.0059987 10125087000 8287590 6945420 6893115 7654790 7078770 7368800 9025050 8151930 8582380 FALSE TRUE 7895852.045 7653166.194 7209171.141 6885315.966 8313305.247 7113616.608 7648112.866 7438103.793 9913291.658 0.79649145 0.772010595 0.727222742 0.694553959 0.838601903 0.71758371 0.771500843 0.750316247 1 23.24093275 -1.793147519 2.31644087 1.079439271 0.760537917 0.774830956 0.040895236 2482999.914 1499833.47 1108872.924 0.009410005 0.016100986 1.793147519 -0.318901354 KFGVVLDEIKPSSAPELQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFGVVLDEIKPSSAPELQAVR 21 2 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 111.97 0.00013257 135010000 171150 167970 167890 197170 135600 185790 214860 231760 187580 FALSE TRUE 163060.0787 185086.334 175587.9226 177350.097 159248.5971 179356.0457 182079.1608 211465.8658 216668.9484 0.752577053 0.854235622 0.810397262 0.818530289 0.734985785 0.827788417 0.840356508 0.975986025 1 17.72513288 1.276019772 2.300355735 1.004401182 0.801369193 0.831885065 0.034607568 0.109358209 0.969033716 0.030256975 0.008830216 18.88077303 -1.276019772 -0.203031988 KFGYVDFESAEDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 ;;;;; 258.2 1.31E-24 5153620000 9221184 7914468 8040345 9293854 5577520 9425075 10212027 9950269 6373216 FALSE TRUE 8785316.907 8720961.287 8409002.771 8359618.139 6550237.722 9098682.289 8653994.724 9078970.697 7361541.787 1.193407191 1.184665052 1.142288262 1.135579798 0.889791556 1.235975092 1.17556824 1.233297448 1 22.81157652 -2.421320278 1.941665951 5.17E-05 1.15202974 0.185436335 0.09781893 2084399.074 123855.6097 9208621.214 0.023401501 0.003790354 2.421320278 1.151978049 KFHTVSGSK ddPTM_SK-BR-3_Trastuzumab_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 ; 147.95 5.92E-05 3486400000 6823300 5714600 5612200 6886900 5497100 5973200 7972600 7171000 5634900 FALSE TRUE 6500776.131 6296924.237 5869524.921 6194615.728 6455792.5 5766346.586 6756233.443 6543069.224 6508731.513 0.998777737 0.967457979 0.901792448 0.951739324 0.991866462 0.885940152 1.038026139 1.005275638 1 22.63394497 1.647754692 12.73420586 1.016022407 0.955474592 0.406237089 0.036436375 0.123460523 32.10662175 0.016694669 0.009114793 44.43801915 -1.647754692 -0.060547815 KFIEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 110.61 0.045786 4998330000 12928310 12575320 11102710 13197150 11898940 11855790 15067210 13076160 14475560 FALSE TRUE 12317214.41 13856759.4 11611780.24 11870547.41 13974111.37 11445221.02 12768430.39 11931142.11 16720355.91 0.736659822 0.828735912 0.694469681 0.709945857 0.835754421 0.684508217 0.763645849 0.713569865 1 23.99510222 -1.435766004 6.307897739 1.000068707 0.751040088 0.701771663 0.051959718 4.64E-05 4.15E-06 0.046454347 0.010946385 0.036663506 1.435766004 -0.249028619 KFIQTFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFIQTFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 103.55 0.0076192 151320000 333370 296260 278430 355920 302570 352310 415120 320850 380130 FALSE TRUE 317612.2608 326449.2308 291196.2909 320142.2454 355338.1122 340109.4164 351785.8198 292754.6731 439078.619 0.723360799 0.743486967 0.663198521 0.72912283 0.809281292 0.774597991 0.801190959 0.666747731 1 18.74411976 -5 0.268465616 2.73507779 0.724544804 0.718206041 0.050674259 110.4127613 1.073981197 106.1911483 0.060202544 1.00E-05 5 -2.010532986 KFLDAGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFLDAGHK 8 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 78.934 0.019046 1025600000 1799400 1482300 1366500 1905700 1331300 1500800 2031100 1810800 1256500 FALSE TRUE 1714345.928 1633348.055 1429155.377 1714135.415 1563478.298 1448826.92 1721218.391 1652236.752 1451351.603 1.181206487 1.125397906 0.984706514 1.181061441 1.077256742 0.998260461 1.185941703 1.138412463 1 20.46896564 1.740995151 0.01069869 2.81E-07 2.189040644 0.13693398 0.073768827 1992.432856 20.43692912 2079.568073 2098.213915 55.08015461 -1.740995151 2.189040364 KFLDAGHKLNFAVASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFLDAGHKLNFAVASR 16 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 94.856 0.0023724 470070000 1260300 752780 338550 312990 1254100 447910 1367700 787660 858480 FALSE TRUE 1200728.117 829489.1378 354072.8524 281527.6506 1472814.643 432398.7644 1159032.245 718688.3148 991608.6939 1.210889057 0.836508537 0.357069129 0.283910026 1.485278066 0.436057859 1.168840343 0.724770082 1 19.91941139 2.753331049 24.98479294 0.94561265 0.741861357 0.118802413 0.371060729 2471.81091 4181166.295 0.112971542 0.119361884 566.6710795 -2.753331049 -0.203751293 KFLDGIYVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFLDGIYVSEK 11 1 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 202.32 6.48E-08 2741000000 11339800 9454000 8942700 10621600 8796300 10258200 12788100 11243700 9377100 FALSE TRUE 10803790.13 10417373.35 9352731.641 9553896.588 10330371.93 9902955.962 10837040.48 10259142.02 10831252.78 0.997464499 0.961788407 0.86349491 0.882067549 0.953755964 0.914294603 1.000534352 0.947179632 1 23.36869678 1.738588963 15.45007852 0.980199972 0.934547074 0.268301598 0.041067095 0.106717734 361.6614768 0.020935291 0.011558019 54.7758295 -1.738588963 -0.045652898 KFLDGNELTLADCNLLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFLDGNELTLADCNLLPK 18 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 135.28 1.40E-05 146060000 202690 196620 191310 221860 164290 208880 251630 250030 197210 FALSE TRUE 193109.2454 216655.8015 200081.7527 199558.2113 192942.124 201646.4332 213239.222 228136.0477 227792.3196 0.847742565 0.951111091 0.878351619 0.876053291 0.847008909 0.88522051 0.936112431 1.001508954 1 17.79735958 1.448151075 2.466575056 1.002621193 0.884904201 0.746409514 0.028750495 0.149308091 1.696308733 0.024375495 0.007936073 28.06409714 -1.448151075 -0.117716992 KFLMECRNS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFLMECRNSPVTK 13 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 KFLMECRNS(0.996)PVT(0.004)K 142.39 2.10E-05 712580000 1358000 509530 1174200 1116400 1221600 1302600 2075500 1516500 1613100 TRUE FALSE 1293810.031 561451.6863 1228038.231 1004177.351 1434646.653 1257490.635 1758844.356 1383707.221 1863251.309 0.694382999 0.301329017 0.65908352 0.538938224 0.769969486 0.674890515 0.943965179 0.742630483 1 20.82939084 2.291869495 0.764021032 0.928153845 0.502928639 0.555738658 0.130191838 0.432846715 0.488794299 0.096941814 0.061981103 195.8256133 -2.291869495 -0.425225206 KFLPLFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFLPLFDR 8 1 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 145.72 0.0009056 4607300000 10644800 6674000 5735200 5824000 9423000 5458800 9225300 7264600 9655200 FALSE TRUE 10141641.4 7354088.188 5998164.593 5238560.455 11066368.22 5269760.387 7817811.051 6628473.112 11152479.1 0.909362062 0.659412864 0.537832399 0.469721611 0.992278767 0.47251919 0.700993114 0.594349745 1 23.41086111 -1.837433983 7.545537142 1.019339328 0.674096287 0.270353028 0.171548118 0.049532983 0.001067171 0.147416862 0.036501785 0.014540054 1.837433983 -0.345243042 KFMTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFMTNR 6 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 125.86 0.028448 3227600000 5068600 3752800 3443600 4133800 4328400 3761700 5487000 4331100 4652900 FALSE TRUE 4829017.323 4135214.587 3601492.466 3718262.57 5083271.59 3631431.386 4649857.374 3951845.923 5374447.968 0.898514108 0.769421271 0.670113933 0.691840835 0.945822086 0.675684537 0.865178601 0.735302667 1 22.35768515 -1.587115256 2.780630464 1.015108639 0.787366008 0.339883894 0.095391296 23625077.29 23387767.36 2622904.506 0.021183465 0.025875261 1.587115256 -0.227742631 KFNALFAQGNYSEAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFNALFAQGNYSEAAK 16 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 216.99 2.35E-14 334390000 1036400 795230 880670 1031200 741260 1034000 1224000 1183600 982950 FALSE TRUE 987411.4259 876264.8411 921049.5906 927541.8168 870535.5093 998192.3207 1037256.32 1079957.709 1135380.866 0.869674182 0.771780525 0.811225218 0.816943323 0.766734349 0.879169582 0.913575656 0.951185406 1 20.1147449 1.629947059 1.350794809 0.985763182 0.808716152 0.822632755 0.031944484 0.15754572 0.552590099 0.026127309 0.009464886 42.65275216 -1.629947059 -0.17704703 ESNGPVKVWGSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ESNGPVKVWGSIK 13 1 P00441 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 154.6 4.22E-05 287980000 558750 213700 583660 484390 729180 668900 1281400 840330 1195800 FALSE TRUE 532338.9948 235476.273 610421.3883 435698.1969 856348.7611 645735.8253 1085898.895 766746.2503 1381238.557 0.38540699 0.170481972 0.441937698 0.315440222 0.61998614 0.467504923 0.786177659 0.555115006 1 20.39753108 1.686272318 0.374910254 1.008419573 0.225221989 0.745799842 0.119195971 0.487256749 0.202326991 0.138294524 0.122111371 48.55928884 -1.686272318 -0.783197585 down KFPHLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFPHLEFR 8 1 F5H345;A0A3B3IRR1;A0A3F2YNY7;P08397-2;P08397;A0A3B3IU56;F5GY90;A0A1W2PNU5;F5H226;A0A3B3IU34;F5H0P4;P08397-4;P08397-3 F5H345 HMBS Porphobilinogen deaminase 0 91.921 0.0078838 175810000 248250 135290 81433 104190 267790 116360 282670 186320 251850 FALSE TRUE 236515.7145 149076.2048 85166.7836 93716.62325 314492.4912 112330.424 239543.4999 170004.8331 290905.6117 0.813032492 0.512455583 0.29276432 0.322154745 1.081080868 0.386140451 0.823440629 0.584398603 1 18.1501916 2.76749031 24.99958124 0.736833157 0.515412117 0.253766386 0.239674088 1262.444521 1090938.713 0.070371115 0.074627968 585.450674 -2.76749031 -0.22142104 KFPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFPSLR 6 1 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 107.74 0.049715 728810000 710060 626550 567340 743260 685700 662670 795770 728340 782350 FALSE TRUE 676496.871 690396.1573 593353.1002 668546.0927 805285.8629 639721.5717 674360.6712 664562.6884 903672.8423 0.748608168 0.763989051 0.656601673 0.739809875 0.891125444 0.7079128 0.74624426 0.735401859 1 19.78544104 -1.416136704 2.969563579 1.004611355 0.749257769 0.64472573 0.058621914 11971658.93 14132332.65 466696.727 0.013224441 0.038358648 1.416136704 -0.255353586 KFPTTATKIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFPTTATKISPK 12 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 KFPTT(0.001)AT(0.265)KIS(0.735)PK 76.85 0.015656 385800000 318410 292510 264730 295120 169170 372380 372740 398110 206460 TRUE FALSE 303359.3903 322317.1016 276868.1324 265453.9769 198673.1944 359484.3872 315871.6672 363249.3779 238476.7623 1.27207107 1.351566075 1.16098579 1.113123033 0.833092468 1.507418935 1.324538559 1.523206598 1 17.86348917 KFPVTENSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFPVTENSK 9 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 143.96 0.00016146 703370000 1412160 1213280 1013090 1118320 1105900 1216390 1598350 1489120 1335690 FALSE TRUE 1345409.995 1336914.611 1059541.179 1005904.349 1298768.61 1174266.109 1354492.352 1358724.758 1542821.983 0.87204487 0.866538477 0.686755303 0.651989899 0.841813653 0.761115749 0.877931716 0.880675005 1 20.55714018 1.102549035 1.202170513 0.994931338 0.790991539 0.478966996 0.073711048 0.463684861 1.383672939 0.075163983 0.023753068 12.66336237 -1.102549035 -0.203939798 KFQEQECPPS(ph)PEPTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KFQEQECPPSPEPTRK 16 2 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(1)PEPTRK;KFQEQECPPS(0.997)PEPT(0.003)RK;KFQEQECPPS(0.981)PEPT(0.019)RK 134.07 1.58E-05 322296000 366600 227857 272737 356468 266041 282610 415091 329834 284038 TRUE FALSE 349271.5445 251075.8874 285242.2612 320635.1594 312438.4662 272823.1448 351761.2443 300951.9864 328085.1624 1.064575862 0.765276569 0.869415304 0.977292472 0.95230904 0.831561973 1.07216444 0.917298375 1 18.32371082 1.737283264 24.99999629 0.999247853 0.907895229 0.173267742 0.088830711 0.2972705 5563.302861 0.039692801 0.022011619 54.61139416 -1.737283264 -0.091352624 KFQGIKHECQANGPEDLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFQGIKHECQANGPEDLNR 19 2 P60981;P60981-2 P60981 DSTN Destrin 0 ; 214.24 2.61E-19 2558000000 1925700 927360 2005500 1462060 1906910 1919030 2963100 2011000 2313800 FALSE TRUE 1834675.977 1021859.038 2097454.159 1315090.951 2239474.5 1852573.51 2511024.674 1834906.179 2672612.287 0.686472926 0.382344661 0.784795524 0.492062002 0.837934672 0.69316957 0.939539448 0.68655906 1 21.34981913 2.235157101 0.536256382 0.943969459 0.533813675 0.409619087 0.143422074 0.725826007 0.431828475 0.119903453 0.098623216 171.8529932 -2.235157101 -0.410155785 KFS(ph)APGQLCISMTSNLGGSAPISAASATSLGHFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFSAPGQLCISMTSNLGGSAPISAASATSLGHFTK 35 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KFS(0.833)APGQLCIS(0.124)MT(0.032)S(0.01)NLGGSAPISAASATSLGHFTK 56.006 0.020794 18840000 14973 10749 13837 16488 12460 13438 20002 19648 18371 TRUE FALSE 14265.25596 11844.33532 14471.44014 14830.59491 14633.02006 12972.63869 16950.32754 17927.51696 21219.88085 0.672259004 0.558171622 0.68197556 0.698900951 0.689590114 0.611343616 0.798794661 0.844845317 1 14.37312894 1.203909645 1.038316494 0.998727853 0.640788239 0.854960362 0.047945747 0.165078958 0.37470973 0.044482238 0.015012505 15.99225276 -1.203909645 -0.357939614 KFS(ph)FKKPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFSFKKPFK 9 3 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KFS(1)FKKPFK 89.629 0.0085474 1303300000 2864800 2093900 2272200 3207200 1587400 2911100 3305000 2981000 1453700 TRUE FALSE 2729386.581 2307270.791 2376382.618 2884806.163 1864242.057 2810287.877 2800761.55 2719967.837 1679132.372 1.625474339 1.374085111 1.415244359 1.718033796 1.11024127 1.673654755 1.667981391 1.619865046 1 20.67928454 KFS(ph)GSGLAMGLGSASASAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFSGSGLAMGLGSASASAWR 20 1 Q92796-2 Q92796-2 DLG3 Disks large homolog 3 1 KFS(0.915)GS(0.085)GLAMGLGSASASAWR;KFS(0.879)GS(0.121)GLAMGLGSASASAWR 310.26 1.83E-66 548740000 755140 670190 651390 755960 708950 686570 892940 774450 711900 TRUE FALSE 719446.0287 738483.1229 681256.8758 679969.4646 832590.6555 662793.9087 756705.603 706635.0524 822297.8161 0.874921488 0.898072582 0.828479491 0.826913864 1.012517167 0.806026595 0.92023302 0.859342003 1 19.64930147 -5 0.366821126 2.54195375 0.877270764 0.296794037 0.0586621 631.5546318 4.921546482 770.9946719 0.036726322 1.00E-05 5 -1.664682986 KFS(ph)NSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFSNSLK 7 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 KFS(0.688)NS(0.312)LK 87.298 0.015387 0 1622100 1272000 1189700 1546700 898660 1556900 1651200 1516300 878290 TRUE FALSE 1545426.548 1401618.246 1244248.922 1391222.777 1055386.019 1502984.163 1399279.114 1383524.734 1014490.728 1.523352068 1.381597888 1.226476387 1.371350905 1.040311154 1.481515919 1.379292167 1.363762818 1 19.95232425 -2.266472682 1.684946582 3.55E-05 1.355642563 0.39524391 0.134012506 647110.1197 92405.90643 2453918.018 0.034951588 0.005414113 2.266472682 1.355607086 KFS(ph)PSQVPVQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KFSPSQVPVQTR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 KFS(0.949)PS(0.051)QVPVQTR;KFS(0.857)PS(0.143)QVPVQTR;KFS(0.746)PS(0.254)QVPVQTR;KFS(0.788)PS(0.212)QVPVQTR;KFS(0.997)PS(0.003)QVPVQTR 177.04 1.46E-05 3752880000 3816900 2997480 3235390 3706050 3006530 3536180 4086590 3732140 3314530 TRUE FALSE 3636482.701 3302926.62 3383735.832 3333510.813 3530867.88 3413721.2 3463105.64 3405334.036 3828530.384 0.949837754 0.862713963 0.883821073 0.870702457 0.922251498 0.891653156 0.904552215 0.889462455 1 21.86835928 -1.623112086 2.622714533 1.010577761 0.89690101 0.627463503 0.024972346 5939758.72 5388227.878 429191.4485 0.005709952 0.023817047 1.623112086 -0.113676751 KFSAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFSAPR 6 1 P39023;H7C422;H7C3M2;F8WCR1;Q92901 P39023;Q92901 RPL3;RPL3L 60S ribosomal protein L3;60S ribosomal protein L3-like 0 ; 114.02 0.041111 1876450000 3995700 2705300 1885730 2336800 4168900 2354400 4719100 3051500 4551200 FALSE TRUE 3806831.18 2980973.146 1972192.586 2101900.424 4895954.84 2272866.538 3999114.623 2784294.483 5256976.852 0.724148363 0.567050841 0.375157175 0.399830641 0.931325166 0.432352396 0.760725173 0.529637958 1 22.32580195 -1.645202827 0.381693849 1.307621491 0.578171618 0.349963523 0.175077857 33.68043402 2.438570763 9.81497988 0.111957974 0.022635869 1.645202827 -0.729449873 KFSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFSGFSAKPNNSGEAPSSPTPK 22 2 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 KFSGFSAKPNNSGEAPS(0.004)S(0.996)PTPK 159.1 1.04E-11 2197200000 1453500 1430900 1334100 1625200 776900 1677000 1672900 1817400 932370 TRUE FALSE 1384795.936 1576710.337 1395269.805 1461831.808 912391.114 1618925.07 1417668.38 1658258.821 1076957.178 1.285841224 1.464041811 1.295566652 1.357372269 0.847193494 1.503239964 1.31636467 1.539763006 1 20.03852946 3.429917679 3.080614783 1.276921046 1.374751412 0.039801515 0.212588099 0.950208622 18.39870085 0.057421631 0.084264243 2691.024667 -3.429917679 0.097830366 KFSKEEPVSS(ph)GPEEAVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFSKEEPVSSGPEEAVGK 18 2 O00567 O00567 NOP56 Nucleolar protein 56 1 KFSKEEPVS(0.138)S(0.862)GPEEAVGK;KFSKEEPVS(0.11)S(0.89)GPEEAVGK 184.38 3.05E-14 477540000 878870 442490 902280 714330 633740 884690 1350330 1059500 916700 TRUE FALSE 837327.5569 487580.2341 943650.4305 642524.1913 744264.0554 854052.9635 1144312.358 966724.5632 1058857.154 0.790784247 0.46047782 0.891197105 0.606809133 0.702893731 0.806579962 1.08070513 0.91298865 1 20.01407654 1.990974659 3.169687525 1.001677115 0.674133722 0.578082136 0.118932704 0.160280688 3.156152209 0.05360358 0.031576072 97.94328349 -1.990974659 -0.327543393 KFTNFQSPNIDPTEENDLDDS(ph)LSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFTNFQSPNIDPTEENDLDDSLSVK 25 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 KFTNFQSPNIDPTEENDLDDS(0.5)LS(0.5)VK 154.7 4.56E-08 102230000 83134 75111 76424 88844 43597 87245 89307 99536 50687 TRUE FALSE 79204.42058 82764.89629 79928.11599 79913.23233 51200.303 84223.68377 75681.57691 90820.10017 58547.28109 1.352828331 1.413642013 1.365189203 1.364934987 0.874512053 1.438558413 1.292657413 1.551226607 1 15.83731455 -2.14896337 2.661996831 0.176168109 1.330592976 0.259147529 0.176242408 48855638.33 40068841.84 235462497.2 0.039650108 0.007096376 2.14896337 1.154424868 KFVADGIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFVADGIFK 9 1 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;E9PQ96;E9PJH4;E9PK82;E9PQX2 P23396 RPS3 40S ribosomal protein S3 0 ; 121.9 0.00096357 833070000 4215500 3375600 2033120 2309530 4303900 2752000 5696900 4245100 4755200 FALSE TRUE 4016241.669 3719577.478 2126340.563 2077371.657 5054498.797 2656697.55 4827733.274 3873376.539 5492612.13 0.731207953 0.677196458 0.387127384 0.37821197 0.920235887 0.483685628 0.878950335 0.705197536 1 22.38906099 1.156331181 0.76902408 0.985233892 0.602353039 0.338773827 0.175275983 0.736886643 1.000230183 0.161189401 0.062446206 14.33280462 -1.156331181 -0.382880853 KFVETPGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFVETPGQK 9 1 P05455;E7ERC4 P05455 SSB Lupus La protein 0 90.685 0.018059 161730000 301300 271060 264950 315930 324280 292750 361210 291830 362780 FALSE TRUE 287058.1461 298681.3222 277098.2196 284172.1162 380834.3293 282611.9941 306100.7804 266275.8181 419038.0696 0.685040732 0.712778489 0.661272184 0.678153459 0.908829906 0.674430355 0.730484418 0.63544541 1 18.67672179 -1.517329942 3.344654826 1.0069811 0.712606498 0.59389611 0.075141808 28116222.25 37024271.56 1781439.369 0.016801976 0.030385757 1.517329942 -0.294374602 KFYEAFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFYEAFSK 8 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 98.943 0.011488 274560000 799830 628760 692850 1027300 927120 995460 1309200 1139200 1137200 FALSE TRUE 762023.621 692831.3588 724617.8578 924033.8523 1088809.434 960986.9706 1109457.495 1039445.609 1313551.168 0.580124809 0.527449083 0.551647987 0.703462396 0.828905231 0.731594622 0.844624497 0.791324795 1 20.32504097 2.441765439 0.350579429 0.987970896 0.466251532 0.838306346 0.059276306 0.581234907 0.163066149 0.071439476 0.109261516 276.5447633 -2.441765439 -0.521719364 KFYEQFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFYEQFSK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 117.7 0.0032532 298470000 748200 630960 607240 838960 859920 951580 1300200 1086000 1125100 FALSE TRUE 712834.0688 695255.5413 635082.5546 754626.1469 1009889.776 918626.546 1101830.61 990904.0828 1299574.762 0.548513321 0.534986952 0.488684894 0.580671593 0.777092481 0.706867025 0.847839341 0.762483323 1 20.3096082 2.011612339 0.487033812 0.975341475 0.494383921 0.856449027 0.060635651 0.312228856 0.1652435 0.058739516 0.047139206 102.7099077 -2.011612339 -0.480957554 KFYGPEGPYGVFAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFYGPEGPYGVFAGR 15 1 O00264 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 176.29 1.29E-06 237360000 292540 179370 240910 333840 353160 275020 391220 277340 384300 FALSE TRUE 278712.214 197648.0069 251955.9618 300281.7689 414750.9922 265495.9884 331532.2038 253054.6393 443895.2813 0.627878299 0.445258184 0.567602253 0.676469838 0.934344224 0.598105003 0.746870304 0.570077336 1 18.75985985 3.183612539 3.637298588 0.744349482 0.53397033 0.342261177 0.137998278 0.244625017 6.584473092 0.037037345 0.046642853 1526.203831 -3.183612539 -0.210379152 KFYPLEIDYGQDEEAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KFYPLEIDYGQDEEAVK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 193.9 1.68E-10 237350000 423350 357580 376050 444500 280100 387900 462500 487760 359780 FALSE TRUE 403339.0845 394017.8085 393292.2645 399818.0155 328949.3513 374466.9257 391937.1306 445049.1486 415572.8449 0.970561694 0.94813175 0.946385861 0.962088886 0.791556415 0.901086128 0.943124979 1.070929331 1 18.66474186 1.34260919 5.697730796 1.034123269 0.924968059 0.43756176 0.053162305 0.200043175 8.795114893 0.03812072 0.013522603 22.00944999 -1.34260919 -0.10915521 KGAAPT(ph)PPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;KGAAPT(1)PPGK;KGAAPT(1)PPGK 56.122 0.073927 2553070000 6565310 5979220 5976830 6995260 4236070 6929320 7515760 7468480 5152970 TRUE FALSE 6254980.807 6588509.316 6250873.567 6292083.175 4974839.267 6689355.911 6369092.776 6814500.298 5952066.27 1.050892333 1.106928085 1.05020228 1.05712586 0.835817184 1.123871208 1.070064157 1.144896577 1 22.50495916 -0.790650068 7.42668765 0.999999999 1.056835403 0.039968708 0.08423598 0 0 0.077111663 0.018175393 0.161938433 0.790650068 0.056835404 KGADSLEDFLYHEGYACTSIHGDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 217.21 5.16E-33 904783000 913410 823030 922200 940500 959540 888480 1145670 1047660 426732 FALSE TRUE 870234.9195 906897.6927 964483.7822 845959.1532 1126883.472 857711.7148 970876.9998 955921.3364 492907.4191 1.76551394 1.839894588 1.956724011 1.716263786 2.286197019 1.740107131 1.969694434 1.939352705 1 18.91095717 -0.81877367 6.311955726 0.999999969 1.894042669 0.75040282 0.163382069 6.54E-08 1.20E-08 0.141537413 0.033360687 0.151784117 0.81877367 0.8940427 KGAEPSGGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGAEPSGGAAR 11 1 O00762;K4DI81;A0A0A0MSE8;A0A087WVK1;O00762-3;O00762-4 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 72.29 0.074877 24133000 56464 50103 57279 57357 47654 49396 58472 59252 54181 FALSE TRUE 53795.05862 55208.55266 59905.29881 51591.36539 55964.84251 47685.40413 49551.02249 54063.58077 62583.11276 0.859577868 0.882163738 0.957211877 0.824365601 0.894248305 0.761953218 0.791763469 0.863868516 1 15.9334858 3.14497206 23.7140218 0.8375075 0.890293653 0.032756663 0.069745586 23.38386644 5908.661161 0.018798233 0.0224682 1396.278529 -3.14497206 0.052786153 KGAGDGS(ph)DEEVDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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 221.81 4.37E-12 33136604000 26348090 29287970 20400550 30739500 9427984 29962300 22678860 27737550 8110780 TRUE FALSE 25102668 32272447.44 21335935.4 27649507.06 11072221.42 28924698.04 19218783.38 25308703.08 9368558.338 2.679459005 3.444761326 2.277397933 2.951308628 1.181849013 3.087422525 2.051413108 2.70145119 1 23.15939563 3.319579105 1.747575793 2.178107759 3.029356197 0.208581108 0.702478597 0.497699282 3.125564935 0.199131184 0.299536434 2087.272276 -3.319579105 0.851248438 KGAGDGS(ph)DEEVDGKADGAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGAGDGSDEEVDGKADGAEAK 21 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK 210.91 9.29E-23 487420000 554840 637810 449800 699320 206445 683950 506770 675020 183152 TRUE FALSE 528613.8128 702803.5641 470423.7749 629023.025 242448.9426 660264.64 429452.929 615911.6703 211554.2767 2.498714849 3.322095752 2.223655235 2.973341095 1.146036593 3.121017689 2.029989351 2.91136478 1 17.69066833 3.21865255 1.876303426 2.20430233 2.862301493 0.12950329 0.739568295 0.63402554 4.598783507 0.211187291 0.290166176 1654.445823 -3.21865255 0.657999163 KGAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE 175.89 1.28E-12 72587530000 12699980 10167870 11267240 12749640 4578570 14405810 13491000 15323210 4713010 TRUE FALSE 12099677.11 11203987.51 11783854.1 11468021.96 5377071.158 13906933.19 11432700.17 13981428.5 5443879.52 2.222620297 2.058088808 2.164605968 2.106589964 0.987727803 2.554599736 2.100101615 2.568283969 1 22.37620371 2.971648112 24.95616135 1.940430644 2.139165909 0.053533216 0.537807908 2995.270444 2636525.985 0.153104459 0.162736667 936.8026539 -2.971648112 0.198735265 KGAGSVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGAGSVFR 8 1 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 89.886 0.021787 603180000 747550 410080 413480 457000 686680 457480 840030 591290 774050 FALSE TRUE 712214.793 451867.6182 432438.467 411061.4918 806436.7746 441637.3529 711867.9953 539513.513 894085.7207 0.796584462 0.505396303 0.483665556 0.459756243 0.901968073 0.493954151 0.796196583 0.603424818 1 19.77005363 -0.161326638 0.44303732 1.058571339 0.600616151 0.367367488 0.153702253 5.704804519 1.288771418 0.718883669 0.083848812 0.689720862 0.161326638 -0.457955188 KGAILSEEELAAMS(ph)PTAAAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGAILSEEELAAMSPTAAAVAK 22 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 KGAILSEEELAAMS(0.996)PT(0.004)AAAVAK 116.2 0.0001047 82913000 175970 106410 152820 179960 123440 169120 196460 179160 143910 TRUE FALSE 167652.2468 117253.3 159826.9482 161870.0789 144967.8969 163263.332 166486.4188 163471.8006 166226.8278 1.008575144 0.705381325 0.961499117 0.973790338 0.872108906 0.982171976 1.001561667 0.983426098 1 17.34279372 2.5705333 0.842920888 1.001352027 0.871206699 0.179363447 0.083750856 0.853177096 1.249543754 0.056556795 0.044571427 371.9917429 -2.5705333 -0.130145328 KGASLS(ph)NGQGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGASLSNGQGSR 12 1 O43639 O43639 NCK2 Cytoplasmic protein NCK2 1 KGAS(0.008)LS(0.992)NGQGSR;KGAS(0.005)LS(0.995)NGQGSR 103.04 0.001402 132481000 148272 134563 138026 165442 160589 148586 197764 171420 184144 TRUE FALSE 141263.4764 148275.1227 144354.6286 148811.4558 188595.6708 143440.4296 167591.4696 156409.556 212700.111 0.664143877 0.697108817 0.67867679 0.699630363 0.886674059 0.674378724 0.787923752 0.735352489 1 17.69846126 -5 0.146264573 1.976059762 0.633070395 0.679774356 0.061336791 73.48336198 0.645883983 20.82503195 0.30371399 1.00E-05 5 -1.342989367 KGAVAEDGDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 120.53 0.00064134 731620000 1028400 1049970 791960 1176710 827070 956440 992320 1035470 862440 FALSE TRUE 979789.5701 1156963.137 828272.1494 1058424.875 971310.7461 923318.243 840923.3588 944798.7574 996182.7905 0.983543963 1.16139643 0.831445953 1.062480586 0.97503265 0.926856247 0.84414564 0.948419072 1 19.92605096 3.14155087 0.848823224 0.914266135 1.057390192 0.106709657 0.091122327 0.837417568 1.337337257 0.045198557 0.068072644 1385.322442 -3.14155087 0.143124057 KGAVAEDGDELRTEPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 203.77 6.45E-16 1781710000 2166910 1763610 1951350 2220900 1412730 2220500 2592730 2487510 1531480 FALSE TRUE 2064484.459 1943323.864 2040821.328 1997650.913 1659109.665 2143603.528 2197161.42 2269690.437 1768974.097 1.167051831 1.098559819 1.153675077 1.129270867 0.937893702 1.211777794 1.242054038 1.283054648 1 20.75448149 KGAVECCPNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGAVECCPNCR 11 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 164.81 3.58E-05 336920000 294180 210696 245980 276330 267630 277230 329800 294080 340950 FALSE TRUE 280274.6944 232166.1619 257258.4263 248552.7834 314304.5873 267629.4556 279482.9528 268328.7962 393822.7847 0.711677194 0.589519375 0.653233983 0.6311285 0.798086346 0.679568237 0.709666794 0.681344012 1 18.58718706 -5 0.237455101 2.823332729 0.64394077 0.77857994 0.053676447 73.67510846 0.735333543 64.71810929 0.082078832 1.00E-05 5 -2.179391959 KGCVITISGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGCVITISGR 10 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 164.04 1.01E-05 772100000 1001360 1135720 1094240 1228460 1185960 1161610 1339320 1279990 1304260 FALSE TRUE 954027.6973 1251451.159 1144411.986 1104972.867 1392791.049 1121383.154 1134982.136 1167907.29 1506517.98 0.633266719 0.830691154 0.759640444 0.733461453 0.924510074 0.744354312 0.753381075 0.775236211 1 20.52278646 -5 0.223993945 2.185817112 0.739418787 0.508800164 0.072366943 131.5993068 1.316558035 70.74112609 0.127746372 1.00E-05 5 -1.446398325 KGDECELLGHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KGDECELLGHSK 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;; 168.76 2.96E-05 5406270000 12459510 9106760 10016680 10478110 7451280 9340380 11733840 11262880 7834540 FALSE TRUE 11870573.65 10034749.2 10475954.69 9424830.476 8750780.873 9016920.299 9943627.201 10276642.52 9049480.45 1.311740903 1.108875725 1.157630512 1.041477522 0.966992627 0.996401987 1.098806418 1.135605804 1 23.10940354 4.692178343 0.799647559 1.045826559 1.455123359 0.677009235 0.0570202 1.400618821 0.717522845 0.021202222 0.505476997 49224.16333 -4.692178343 0.4092968 KGDEVDGVDEVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGDEVDGVDEVAK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 132.44 0.00019051 967230000 1888270 1625140 1628620 2019150 1013360 1995880 1987610 2179570 1165340 FALSE TRUE 1799015.219 1790743.614 1703293.838 1816181.206 1190089.663 1926762.175 1684363.59 1988715.296 1346054.975 1.336509468 1.330364395 1.265396933 1.34926228 0.884131544 1.431414177 1.25133343 1.477439876 1 20.3603059 -2.268940586 2.002713615 3.80E-05 1.289330956 0.246776176 0.159609689 3596925.335 537211.2916 16255534.78 0.037684841 0.005383434 2.268940586 1.28929293 KGDEVQCEIEELGVIINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGDEVQCEIEELGVIINK 18 1 Q96GK7;Q6P2I3 Q96GK7 FAHD2A;FAHD2B Fumarylacetoacetate hydrolase domain-containing protein 2A;Fumarylacetoacetate hydrolase domain-containing protein 2B 0 99.569 0.0016225 21731000 59490 52303 50968 58877 45001 59014 69241 60591 47464 FALSE TRUE 56678.0256 57632.73516 53304.93321 52958.5721 52849.16015 56970.33038 58677.01375 55285.33083 54824.47471 1.033808822 1.051222752 0.972283519 0.965965883 0.963970206 1.039140469 1.070270423 1.008406029 1 15.74253246 2.089323609 24.98064154 1.039220825 1.005182897 0.129666078 0.034496147 37.75729594 10548.4661 0.014408323 0.010641242 122.8354183 -2.089323609 -0.034037928 KGDIFLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGDIFLVR 8 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 103.7 0.0075718 1478800000 2139900 1452100 1725300 1953900 1914400 1780900 2365300 1935500 2088200 FALSE TRUE 2038751.168 1600070.641 1804406.712 1757490.26 2248270.754 1719226.986 2004430.043 1766017.359 2412027.391 0.845243788 0.663371671 0.748087156 0.728636112 0.932108301 0.71277258 0.831014627 0.732171353 1 21.20181486 -4.999999944 0.275268728 2.616038355 0.756667268 0.445968948 0.078113986 192.9112272 1.859567835 177.6770824 0.084557544 1.00E-05 4.999999944 -1.859371088 KGDIIQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGDIIQLQR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 158.79 0.0001067 2360200000 1311050 1040250 892520 1031900 1129320 1017280 1383490 1092180 1220960 FALSE TRUE 1249079.265 1146252.658 933442.9248 928171.4515 1326273.05 982051.3385 1172413.191 996542.9292 1410300.241 0.885683224 0.812772078 0.661875321 0.658137483 0.940418935 0.696342034 0.831321698 0.70661757 1 20.4275709 -0.909952926 5.751759937 1.000000117 0.782567688 0.352928123 0.095505611 1.36E-07 2.58E-08 0.087741466 0.020680851 0.123040213 0.909952926 -0.217432429 KGDIVDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KGDIVDIK 8 1 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ;;;; 97.915 0.012657 3626510000 7429320 6284990 6536960 7544120 4508220 6977840 7839510 7505810 5103920 FALSE TRUE 7078150.767 6925437.626 6836686.082 6785770.725 5294452.141 6736195.651 6643448.767 6848561.486 5895409.846 1.200620644 1.174716908 1.159662561 1.151026121 0.898063456 1.142617024 1.126884973 1.161676909 1 22.49116068 2.982495846 24.97544668 1.078397734 1.17756759 0.317073976 0.076693739 949.9170729 1355371.946 0.022651858 0.024523865 960.496632 -2.982495846 0.099169856 KGDLLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGDLLLNR 8 1 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 104.2 0.0074175 1223180000 1132390 807410 579730 680000 967190 722590 1138530 883030 946110 FALSE TRUE 1078864.169 889685.9969 606311.1939 611645.1081 1135867.63 697566.5271 964826.338 805707.212 1092827.907 0.987222382 0.814113541 0.554809399 0.559690235 1.039383807 0.638313245 0.882871248 0.737268153 1 20.0596348 -1.517947724 8.554866581 1.000015921 0.788231468 0.150538225 0.164685269 4.82E-05 2.72E-06 0.153837557 0.036257138 0.030342564 1.517947724 -0.211784453 KGDRS(ph)PEPGQTWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.992)PEPGQT(0.007)WT(0.002)R;KGDRS(0.999)PEPGQT(0.001)WTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(0.965)PEPGQT(0.034)WTR;KGDRS(1)PEPGQTWTR;KGDRS(0.948)PEPGQT(0.009)WT(0.042)R;KGDRS(1)PEPGQTWTR;KGDRS(0.96)PEPGQT(0.039)WT(0.001)R;KGDRS(0.992)PEPGQT(0.006)WT(0.002)R 184.66 6.61E-07 64204730000 21837570 17662020 19339490 21650010 16572420 20079460 23023860 20395320 17030270 TRUE FALSE 20805351.34 19461799.92 20226224.75 19473709.86 19462644.8 19384103.27 19511147.29 18609397.66 19671237.29 1.057653417 0.989353116 1.028213144 0.989958566 0.989396067 0.985403357 0.991861722 0.946020699 1 24.22958437 8 0.394674078 0.980738673 2.147089376 0.592005903 0.018543298 45.76097883 0.612208594 0.01204975 41.32139836 100000000 -8 1.166350703 KGDSNANSDVCAAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGDSNANSDVCAAALR 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ; 160.25 1.42E-08 135710000 69956 55571 58903 64318 67534 68046 79918 69074 75008 FALSE TRUE 66649.31852 61233.74808 61603.76081 57852.63244 79311.90822 65689.54996 67725.04131 63025.51438 86639.85755 0.769268561 0.706761874 0.711032573 0.667736929 0.915420575 0.758190881 0.781684587 0.727442498 1 16.40274325 -5 0.237009673 2.379930317 0.727962636 0.576461342 0.066078683 118.116509 1.179092566 78.44147229 0.100649765 1.00E-05 5 -1.65196768 KGDSSAEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGDSSAEELK 10 1 P26373;P26373-2 P26373 RPL13 60S ribosomal protein L13 0 ;;;;; 130.44 0.00044365 7622130000 11374110 10888460 9345940 12816060 6243790 12640560 12037260 13188210 6596140 FALSE TRUE 10836478.36 11998006.45 9774460.593 11527765.3 7332704.999 12202814.24 10200754.91 12033380.42 7619035.703 1.422290009 1.57474081 1.282899959 1.513021562 0.962419036 1.601621874 1.338851176 1.57938365 1 22.86117699 -1.308768838 3.653343504 0.998768485 1.413955222 0.314073871 0.190035663 9795794.351 7019291.91 87966.39942 0.039784544 0.049116924 1.308768838 0.415186737 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGS(0.001)QS(0.999)QDEGEGSGESER;KGDVEGS(0.003)QS(0.997)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER 321.9 2.83E-67 4851420000 2373355 2075861 2266885 2582848 1654569 2487168 2615336 2595489 1932094 TRUE FALSE 2261171.213 2287393.596 2370823.92 2323215.212 1943125.31 2401036.749 2216318.459 2368214.224 2231713.27 1.013199699 1.024949588 1.062333568 1.041000761 0.870687707 1.07587152 0.993101797 1.061164199 1 21.08972025 -1.244106492 3.655930042 0.999971328 1.01663218 0.008906447 0.05784008 13830303264 2859365939 3480833.634 0.012225653 0.057002448 1.244106492 0.016660852 KGDVLHMHYTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGDVLHMHYTGK 12 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 143.25 2.52E-05 290460000 1152900 1146000 935300 1328900 842670 1145100 1162500 1156600 95363 FALSE TRUE 1098404.702 1262778.703 978184.4301 1195316.447 989631.3812 1105444.9 985139.2742 1055321.972 110151.407 9.971771871 11.46402699 8.880362556 10.85157675 8.984282709 10.0356857 8.943501505 9.580649047 1 16.7491284 -0.404617671 0.544818313 1.81E-15 10.27848137 0.922645453 0.80655343 1.942778564 0.51227109 5.3730436 0.324241972 0.393896688 0.404617671 10.27848137 KGDVVHCWYTGTLQDGTVFDTNIQTSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;; 330.08 4.72E-96 370334000 724822 635827.5 665585 757196 502287 712361 770131 803359 551933 FALSE TRUE 690561.1005 700619.0451 696102.7306 681081.2195 589885.6938 687691.7599 652633.3715 733012.6271 637523.9508 1.083192404 1.098968979 1.09188483 1.068322561 0.92527613 1.078691646 1.023700162 1.149780532 1 19.28212002 2.992830443 24.7720416 1.035161602 1.090352374 0.172739054 0.056374485 488.0705517 1686376.498 0.015373351 0.017707418 983.6270034 -2.992830443 0.055190772 KGDVVIVLTGWRPGS(ph)GFTNTMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 1 KGDVVIVLTGWRPGS(0.93)GFT(0.069)NT(0.001)MR 156.92 4.29E-09 132030000 159460 143930 144050 169330 145190 146770 191970 162840 143300 TRUE FALSE 151922.6418 158596.6306 150654.835 152308.6267 170511.09 141687.3181 162681.4507 148580.8663 165522.2321 0.917838286 0.958159086 0.910178851 0.920170208 1.030140108 0.856001736 0.982837463 0.897649001 1 17.33666548 -1.899405028 2.564936895 1.034791957 0.936962874 0.15485819 0.047959669 20967844.15 9702146.667 4386127.089 0.010432366 0.012606513 1.899405028 -0.097829083 KGDVVIVLTGWRPGSGFTNTMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 159.51 1.10E-11 836290000 1135560 999240 1028690 1087020 1157070 1069970 1341900 1206350 1192600 FALSE TRUE 1081884.329 1101063.692 1075856.454 977750.6844 1358862.642 1032916.671 1137168.509 1100715.599 1377542.317 0.785372845 0.79929573 0.780997027 0.709779055 0.986439854 0.749825728 0.825505319 0.799043039 1 20.39366521 -4.999999999 0.263488667 2.293808909 0.788303413 0.427557555 0.071529684 182.4628921 1.785276219 128.0194266 0.082520855 1.00E-05 4.999999999 -1.505505496 KGDYIEAESSYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 96.489 0.0067564 391850000 375290 326060 301610 316010 293300 328810 382990 356360 366800 FALSE TRUE 357550.7855 359285.8847 315439.1168 284244.0744 344451.4271 317423.2273 324557.8414 325155.2292 423681.4706 0.843914144 0.848009435 0.7445195 0.670890974 0.812996204 0.749202524 0.766042095 0.767452088 1 18.69262051 -1.917392924 5.160720288 1.082140744 0.780784811 0.647143371 0.051989758 0.037816088 0.000605318 0.038742882 0.012946381 0.012095034 1.917392924 -0.301355933 LYGKPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYGKPIR 7 1 Q5SZ64;Q15427 Q5SZ64 SF3B4 Splicing factor 3B subunit 4 0 64.803 0.09676 0 679730 620090 755060 1066800 1226500 927470 1338300 1158400 1460900 FALSE TRUE 647600.51 683277.876 789680.2479 959563.2372 1440401.212 895351.4813 1134117.755 1056964.355 1687448.911 0.383774884 0.404917667 0.467972833 0.568647282 0.853596931 0.530594719 0.672090129 0.626368211 1 20.68641239 1.802937387 0.121462363 1.303268299 1.26E-17 0.717571987 0.102828978 3.787711277 0.431411538 1.943290117 2.21929507 63.52393411 -1.802937387 -1.303268299 down KGEDEDKGPPCGPVNCNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGEDEDKGPPCGPVNCNEK 19 2 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 228.68 5.52E-20 612710000 567720 504560 472390 612050 242002 592860 550890 604610 245527 FALSE TRUE 540885.0007 555975.2376 494049.5488 550525.5712 284207.0722 572329.1095 466841.6127 551667.1432 283602.0732 1.907196921 1.960406112 1.742051965 1.941190221 1.002133267 2.018070965 1.646114951 1.945215481 1 18.11350855 -2.401823455 0.261119764 3.18E-30 1.867396103 0.383929556 0.299430766 42.20114493 1.381493752 25.70224856 0.385089911 0.003964392 2.401823455 1.867396103 KGEDFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGEDFVK 7 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;;;; 113.26 0.009894 26152400000 40762100 30476100 29867360 32679300 24865780 30647820 38400400 35531900 26487880 FALSE TRUE 38835356.32 33581649.24 31236808 29394314.68 29202364.16 29586478.31 32541713.71 32420538.47 30595485.15 1.269316572 1.097601462 1.020961356 0.96074027 0.954466452 0.967021054 1.063611626 1.059651067 1 24.86681544 4.247616548 1.475165646 1.00286592 1.276933144 0.832041999 0.038057408 0.213541844 0.760824112 0.011973607 0.065818524 17685.46763 -4.247616548 0.274067224 KGEDVLGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGEDVLGSVR 10 1 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 103.88 0.0044186 260280000 353990 252240 250200 281300 297640 264450 356430 282530 274450 FALSE TRUE 337257.5942 277943.5428 261671.9175 253023.1896 349548.3218 255292.0302 302050.0572 257790.1754 317010.3043 1.063869501 0.87676501 0.825436631 0.798154464 1.102640252 0.805311457 0.952808326 0.813191786 1 18.27417021 4.56465309 2.798076358 0.894952475 1.067973099 0.220065965 0.098323317 0.432131928 5.813828744 0.021999433 0.141797325 36698.90362 -4.56465309 0.173020624 KGEFETGFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 123.26 0.00074861 2048390000 3728700 3274150 3481770 4573420 3001120 4363050 4748390 4644170 3432290 FALSE TRUE 3552451.741 3607789.607 3641412.598 4113691.133 3524514.378 4211956.484 4023935.895 4237501.855 3964552.003 0.896053763 0.910011927 0.918492832 1.037618154 0.889006973 1.062404146 1.014978714 1.06884759 1 21.91872642 2.973377417 0.667599595 1.03913123 0.889433149 0.49488534 0.049455349 0.552714073 0.545273542 0.030913515 0.041290341 940.540318 -2.973377417 -0.149698081 KGEIFELK ddPTM_SK-BR-3_Trastuzumab_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 ; 111.06 0.0053021 1674570000 4414000 3871600 3883900 4667600 2702100 4511900 4776500 5051900 3118900 FALSE TRUE 4205358.968 4266120.442 4061980.657 4198403.98 3173345.384 4355651.772 4047757.199 4609528.854 3602563.083 1.167324172 1.184190351 1.127525199 1.165393605 0.880857687 1.209042471 1.123577049 1.27951371 1 21.78059226 -2.420150584 2.02090587 4.47E-05 1.141549304 0.158864534 0.102805368 1545637.703 165776.5051 7060000.207 0.024372154 0.003800576 2.420150584 1.141504653 KGEITGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGEITGEVR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 0 ; 91.937 0.0167 344720000 1026780 703750 679790 1105260 730880 829250 1083110 1029340 881830 FALSE TRUE 978246.1443 775462.9251 710959.0439 994157.1649 858345.2406 800532.8646 917861.6768 939205.5327 1018579.693 0.960402167 0.761317873 0.697990593 0.976022958 0.84268835 0.785930517 0.90111916 0.922073687 1 19.95812743 1.147483883 1.571069311 0.996257051 0.838668057 0.283279891 0.084268958 0.47171555 2.244011649 0.076360418 0.022714386 14.04377564 -1.147483883 -0.157588993 KGENYVYINEATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGENYVYINEATR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 173.36 3.50E-05 2218190000 1809360 1977510 1693460 1932540 1464340 1807640 1865790 1903760 1558910 FALSE TRUE 1723835.139 2179020.517 1771106.816 1738277.408 1719720.432 1745040.974 1581129.468 1737056.682 1800657.801 0.957336334 1.21012472 0.983588784 0.965356886 0.955051222 0.96911305 0.878084368 0.964678953 1 20.78009261 3.497763754 22.15411519 0.94790539 1.085918303 0.374974516 0.067194672 148.3228476 159183.1682 0.017308278 0.026388944 3146.036481 -3.497763754 0.138012913 KGEQCVHTASGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGEQCVHTASGPR 13 1 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 0 ; 92.468 0.0039333 69246000 105249 107002 106687 119312 98033 105163 132606 116759 122715 FALSE TRUE 100274.0884 117905.6255 111578.7045 107318.5311 115129.9242 101521.1789 112374.5192 106534.963 141745.0155 0.707425852 0.831814968 0.787179035 0.757123845 0.812232612 0.716223979 0.792793446 0.751595833 1 17.11293848 -2.223796192 2.331840004 1.758210894 0.772008898 0.77389545 0.039126618 3222549.818 627144.2289 12882802.33 0.00896837 0.005973155 2.223796192 -0.986201996 KGEQGGPPPKAS(ph)PSTAGETPSGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGEQGGPPPKASPSTAGETPSGVK 24 2 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 KGEQGGPPPKAS(0.944)PS(0.044)T(0.011)AGET(0.001)PSGVK 62.034 0.029267 137290000 210770 195500 223710 227000 118550 243400 254550 262710 144710 TRUE FALSE 200807.3198 215421.6723 233967.3248 204181.5287 139225.0825 234970.997 215713.7224 239705.7197 167150.8877 1.201353595 1.288785691 1.399737255 1.221540199 0.83293056 1.405741843 1.290532915 1.434067883 1 17.35079149 4.744151169 6.00449356 1.248135244 1.200022179 0 0.188714198 1.309200113 203.9708946 0.04238686 0.257483433 55481.8801 -4.744151169 -0.048113065 KGEQGGPPPKASPS(ph)TAGETPSGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGEQGGPPPKASPSTAGETPSGVK 24 2 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 KGEQGGPPPKAS(0.169)PS(0.794)T(0.036)AGETPSGVK 115.27 0.00057172 134480000 482030 454540 483460 549840 274860 554320 561000 573350 299610 TRUE FALSE 459245.3972 500858.1428 505627.1192 494569.0386 322795.497 535123.7594 475409.1465 523144.4345 346071.9886 1.327022736 1.447265769 1.461046071 1.429092948 0.932740897 1.546278743 1.373729057 1.511663618 1 18.40071265 KGESGQSWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGESGQSWPR 10 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 122.33 0.00078811 5781800000 3303500 2715700 2810400 3394100 2510200 2919700 3535900 3154800 2917100 FALSE TRUE 3147350.102 2992432.917 2939259.62 3052918.62 2947978.085 2818590.057 2996433.514 2878548.987 3369468.97 0.934078969 0.888102233 0.87232132 0.906053342 0.87490881 0.836508685 0.889289541 0.854303457 1 21.68408981 -1.116714806 4.067023942 1.000028507 0.884178724 0.658582931 0.026669878 12525107434 2720254782 3636872.758 0.006386676 0.076433755 1.116714806 -0.115849783 KGESQTDIEITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KGESQTDIEITR 12 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;;;; 209.83 8.11E-08 3097260000 3384870 4177760 3310790 4145460 2253038 3747960 3313700 3875040 2457372 FALSE TRUE 3224873.903 4603478.494 3462592.996 3728750.485 2645967.114 3618167.205 2808134.205 3535720.955 2838448.699 1.136139577 1.621829028 1.219889229 1.313657874 0.932187753 1.274698819 0.989320048 1.245652583 1 21.43667124 2.889591645 6.435919486 1.095346039 1.350995569 0.334636089 0.162824855 0.248403038 12.65512162 0.046210196 0.049198243 775.5175762 -2.889591645 0.25564953 KGESQTDIEITREEDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGESQTDIEITREEDFTR 18 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 202.07 7.50E-16 1313610000 1978630 1427500 2032410 1814530 1624400 2057500 2413780 2281190 1941040 FALSE TRUE 1885104.081 1572963.873 2125598.009 1632129.997 1907694.846 1986248.259 2045513.529 2081436.91 2242046.57 0.840796131 0.701575023 0.948061489 0.72796436 0.850872088 0.885908565 0.912342124 0.928364709 1 21.09638481 1.728094309 0.606829429 0.997173192 0.787121588 0.478190688 0.067281367 0.556571475 0.437954814 0.05827044 0.032333256 53.46804551 -1.728094309 -0.210051604 KGESVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGESVKR 7 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;;; 107.29 0.0042237 4572235000 8538727 6278496 7006564 8359962 5957418 7879004 10258585 9121929 7757703 FALSE TRUE 8135118.297 6918281.88 7327821.89 7519602.737 6996389.813 7606152.116 8693449.446 8323164.538 8960727.96 0.90786355 0.772066947 0.817770824 0.839173198 0.780783642 0.848831942 0.970172232 0.928849149 1 23.09518451 1.797836693 4.102143494 0.962808025 0.82405411 0.725400678 0.040352335 0.112568875 3.439959797 0.019659168 0.010461687 62.78222358 -1.797836693 -0.138753914 KGETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGETLR 6 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 100.74 0.059833 847897000 1403450 1434950 1307010 1510570 1173790 1421380 1657560 1483580 1281150 FALSE TRUE 1337111.7 1581173.036 1366937.701 1358724.634 1378498.604 1372157.254 1404668.779 1353669.87 1479824.199 0.90356118 1.06848708 0.923716278 0.918166249 0.931528627 0.927243422 0.949213278 0.914750462 1 20.49699437 KGFLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGFLFR 6 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 120.96 0.031844 834130000 1985010 1678570 1284690 1688510 1720180 1382720 1673210 1560590 1543240 FALSE TRUE 1891182.511 1849618.191 1343594.307 1518777.767 2020178.847 1334836.06 1417931.084 1423936.466 1782557.777 1.060937567 1.037620331 0.753745166 0.852021621 1.133303432 0.748831862 0.795447475 0.798816445 1 20.76551741 3.826969463 7.690943603 0.859534805 1.051116159 0.284125328 0.1184062 0.320962357 24.85672353 0.029680968 0.053725839 6713.816433 -3.826969463 0.191581354 KGFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGFNGCDSPEPDGEDSLEQSPLLEDKYR 28 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR 164.7 3.77E-12 307600000 305340 239850 263960 275140 190190 302610 349420 341210 233841 TRUE FALSE 290907.1833 264290.9877 276062.8271 247482.4045 223359.0758 292130.5398 296109.5615 311331.8435 270103.868 1.077019687 0.978479093 1.022061732 0.91624902 0.826937716 1.081548895 1.096280345 1.152637487 1 18.04315477 2.039559192 24.99920175 1.092481836 0.974938092 0.376730796 0.074675868 168.048341 106196.4612 0.028399585 0.020974457 109.5365837 -2.039559192 -0.117543744 KGGDGIKPPPIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGGDGIKPPPIIGR 14 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 104.94 0.00057858 1156040000 1678200 1358710 1411600 1749330 1585400 1482540 1906000 1787780 1701070 FALSE TRUE 1598874.812 1497164.094 1476323.256 1573484.025 1861893.258 1431199.268 1615204.694 1631232.506 1964863.248 0.81373338 0.761968598 0.751361835 0.800810961 0.947594322 0.728396376 0.822044331 0.830201546 1 20.90599748 -4.999999996 0.242818448 2.151361907 0.783623499 0.526382639 0.05849574 134.7328992 1.341359818 76.624868 0.084471979 1.00E-05 4.999999996 -1.367738408 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;KGGEFDEFVNDDT(1)DDDLPISK 206.88 2.33E-22 2604610000 3127350 2879100 2793870 3350740 1806860 3349390 3586450 3653670 2032312 TRUE FALSE 2979526.363 3172483.563 2921971.703 3013917.249 2121975.812 3233399.784 3039271.183 3333735.285 2347472.565 1.269248641 1.351446492 1.244730927 1.283898817 0.903940622 1.377396197 1.294699341 1.420138124 1 21.16267687 3.583545568 5.012491614 1.231844603 1.310168428 0.050151056 0.159170831 0.791297011 30.22566668 0.040806092 0.063774959 3833.059562 -3.583545568 0.078323824 KGGEFDEFVNDDT(ph)DDDLPISKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGGEFDEFVNDDTDDDLPISKK 22 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISKK 173.07 1.99E-10 98684000 215970 167880 204760 217410 126240 242740 299880 304720 148780 TRUE FALSE 205761.5261 184987.1629 214148.4485 195555.5337 148256.216 234333.8529 254127.7983 278037.1014 171852.0425 1.197317897 1.076432727 1.246121055 1.137929645 0.862696852 1.363579097 1.478759255 1.61788651 1 17.39080747 2.027703092 23.33436144 1.419350379 1.116489503 0.314945352 0.185176569 94.80322275 79852.14731 0.062405338 0.04608777 106.5867186 -2.027703092 -0.302860877 KGGHERPPS(ph)PGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 130.27 7.51E-05 656180000 277530 238230 244910 275300 223420 252300 313080 256830 242710 TRUE FALSE 264411.7069 262505.9078 256139.3657 247626.321 262384.3773 243562.7877 265313.8959 234340.6037 280348.2272 0.943154553 0.936356582 0.913647175 0.883281209 0.935923083 0.868786616 0.946372654 0.835891156 1 18.09686042 3.741373108 3.926931571 0.909005642 0.94045772 0.060757248 0.044772114 0.498990333 17.98594812 0.010310332 0.01806666 5512.811052 -3.741373108 0.031452078 KGGQAPAPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGGQAPAPPTR 11 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ; 91.914 0.016653 143932000 288423 237700 247186 313339 240468 301603 320849 279185 308468 FALSE TRUE 274789.8164 261921.9002 258519.7226 281841.5684 282405.5431 291158.4125 271897.5923 254738.0813 356303.642 0.771223709 0.735108681 0.725560146 0.791015121 0.792597969 0.817163728 0.763106408 0.714946611 1 18.4427477 -2.106622952 2.646708238 1.451025168 0.764517373 0.844191792 0.03188356 4081292.247 1185095.144 11244348.69 0.007898972 0.007823067 2.106622952 -0.686507795 KGHAVGDIPGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGHAVGDIPGVR 12 1 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 129.71 0.00014895 2188870000 3875310 3295180 3417630 3894580 3554620 3608560 4462960 3995430 3301690 FALSE TRUE 3692131.776 3630962.588 3574331.716 3503089.419 4174544.603 3483594.662 3782053.484 3645568.968 3813699.223 0.968123484 0.952084151 0.937234823 0.918554195 1.094618206 0.913442424 0.991702089 0.955914128 1 21.86275964 KGLIAAICAGPTALLAHEIGFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGLIAAICAGPTALLAHEIGFGSK 24 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 243.27 7.38E-38 270700000 510880 417760 483180 507770 446620 497760 656200 586520 481180 FALSE TRUE 486731.7149 460330.219 505334.2809 456727.9949 524510.3866 480522.4464 556084.6381 535161.1995 555798.9369 0.87573344 0.828231557 0.909203396 0.821750393 0.943705271 0.864561651 1.000514037 0.96286834 1 19.08420355 1.910976217 1.010477316 1.000010613 0.858798828 0.630250975 0.039463141 0.285862355 0.536233712 0.028303586 0.012600396 81.46596701 -1.910976217 -0.141211785 KGLIPWEQAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGLIPWEQAAR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 122.42 0.00062709 553230000 635200 450280 419680 526760 639030 456720 699470 564890 687750 FALSE TRUE 605175.3548 496164.0439 438922.7431 473809.084 750476.6297 440903.6719 592753.0049 515425.2369 794402.7575 0.761799162 0.624574927 0.552519159 0.59643434 0.944705469 0.555012766 0.746161817 0.648821057 1 19.59951111 -5 0.369298933 5.207090324 0.671263877 0.42379966 0.117530107 502.9397567 3.889269175 1687.941038 0.075647129 1.00E-05 5 -4.535826447 KGLTPSQIGVILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGLTPSQIGVILR 13 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 229.97 1.98E-08 0 2009140 1850170 2008600 2076070 2089840 2078800 2589180 2208710 2571190 FALSE TRUE 1914171.934 2038704.426 2100696.297 1867379.499 2454307.434 2006810.635 2194153.037 2015303.643 2969917.013 0.644520344 0.686451647 0.707324914 0.628764875 0.82638923 0.675712697 0.73879271 0.678572376 1 21.50199119 -5 0.244007498 2.766463401 0.668161321 0.754586957 0.054216099 77.92922789 0.775318063 68.45746464 0.073163385 1.00E-05 5 -2.09830208 KGLVGPELHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 156.69 2.01E-05 1205340000 2794112 2306874 2366389 2788490 2608829 2487185 3124322 2784565 2675505 FALSE TRUE 2662039.863 2541947.083 2474890.276 2508185.687 3063807.952 2401053.16 2647649.297 2540733.727 3090408.651 0.861387656 0.822527818 0.800829455 0.811603244 0.991392498 0.776937108 0.85673113 0.822135198 1 21.55936619 -2.123083647 2.453896044 1.315635248 0.842556937 0.417968518 0.058243757 4827832.633 1573762.788 8485319.67 0.012815685 0.007532105 2.123083647 -0.47307831 KGMWSEGNGSHTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGMWSEGNGSHTIR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 124.09 6.43E-05 409690000 337500 265760 299210 321410 373380 310010 427570 343460 382240 FALSE TRUE 321547.0439 292841.2461 312929.0745 289101.2562 438497.3538 299274.276 362336.3436 313384.8216 441515.827 0.728279768 0.663263304 0.708760718 0.654792509 0.993163386 0.677833631 0.820664451 0.709792951 1 18.75210563 -5 0.140450987 1.889871387 0.648674957 0.40762764 0.098519575 127.0196352 1.091504796 31.64300846 0.541441527 1.00E-05 5 -1.24119643 KGNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAKEK 126.25 7.29E-05 969580000 1599300 1372600 1187700 1562500 356900 1720500 1387200 1774300 307750 TRUE FALSE 1523704.259 1512469.501 1242157.22 1405434.531 419143.247 1660918.654 1175557.162 1618932.886 355474.2982 4.286397824 4.254792845 3.49436577 3.953688181 1.179109852 4.672401526 3.307010291 4.554289562 1 18.43938573 3.558564341 1.864821516 3.242837604 4.297084374 0.126395539 1.225927678 0.718853687 4.952090211 0.33346828 0.5995779 3618.797999 -3.558564341 1.05424677 KGNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.566)S(0.434)DEEGKLVIDEPAKEK 92.238 0.027341 137140000 84089 76928 67192 82148 24737 84097 76528 93641 19043 TRUE FALSE 80114.27962 84767.05066 70272.81966 73890.32697 29051.12497 81184.6998 64852.24807 85441.29762 21996.09118 3.642205288 3.853732464 3.194786705 3.359248075 1.320740341 3.690869397 2.948353302 3.884385499 1 14.42495955 3.357126863 2.172192083 2.793222636 3.730802007 0.180240912 0.924768547 0.523826328 5.033267316 0.256242713 0.378689647 2275.762113 -3.357126863 0.937579371 KGNEQHAFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGNEQHAFTR 10 1 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 116.77 0.00067951 76135000 189260 149940 153060 173990 162400 159810 199000 182530 165470 FALSE TRUE 180314.0549 165219.0565 160077.9524 156500.1946 190722.5086 154275.7396 168638.8951 166546.7055 191130.2425 0.943409335 0.864431784 0.837533351 0.818814399 0.997866722 0.807175974 0.882324497 0.871378089 1 17.54419655 -0.650362373 7.153972891 1.000000043 0.878324901 0.313351461 0.056814635 0 0 0.05026162 0.011846777 0.223685394 0.650362373 -0.121675142 KGNS(ph)PNSEPPTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(0.889)PNS(0.111)EPPTPK;KGNS(0.962)PNS(0.038)EPPTPK;KGNS(0.985)PNS(0.015)EPPTPK;KGNS(0.962)PNS(0.038)EPPTPK 123.36 0.00013738 1386230000 2176010 1740960 1803880 2173390 1141340 2164910 2283730 2195690 1228260 TRUE FALSE 2073154.32 1918365.803 1886589.682 1954916.708 1340389.335 2089938.624 1935305.045 2003423.744 1418732.288 1.461272389 1.352168989 1.329771444 1.377932063 0.944779608 1.473102883 1.364108692 1.412122471 1 20.43617095 -1.419894058 3.037722117 0.99405006 1.344367682 0.342390612 0.147682464 21191218.41 26184693.34 1090459.092 0.035874823 0.038028215 1.419894058 0.350317622 KGNYAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 84685580000 50891300 41880990 34618260 42305380 43528790 42169380 54459900 44827200 47734700 FALSE TRUE 48485769.11 46148710.5 36205541.46 38052762.83 51120197.19 40709043.8 46151042.03 40901892.72 55137153.48 0.879366562 0.836980286 0.656645096 0.690147395 0.927146107 0.738323276 0.837022572 0.741820898 1 25.71652145 -0.749467482 5.218985572 1.000000055 0.79627807 0.378830901 0.084611763 5.83E-08 1.39E-08 0.079815713 0.018812738 0.178046122 0.749467482 -0.203721985 KGNYSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 136.8 0.0047224 16851310000 16847660 14183480 12335260 14583660 14401550 14481530 18431900 15639000 16408900 FALSE TRUE 16051304.5 15628792.74 12900843.87 13117682.79 16913175.76 13980030.98 15619775.13 14269566.25 18953508.41 0.846877747 0.824585739 0.680657301 0.69209787 0.892350661 0.737595947 0.824109964 0.752872025 1 24.17596159 -1.276086549 4.345150566 1.000151947 0.787575809 0.504330684 0.067863353 9.70E-05 1.62E-05 0.063800891 0.015027301 0.05295579 1.276086549 -0.212576137 KGPEADSEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGPEADSEWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 115.33 0.0019845 1585030000 3458980 2996360 2947220 3556120 2891880 3221890 3756450 3635990 3354510 FALSE TRUE 3295480.87 3301692.491 3082352.952 3198652.061 3396222.956 3110315.141 3183334.561 3317603.44 3874710.278 0.850510266 0.852113385 0.795505401 0.825520318 0.876510168 0.802721989 0.821567119 0.856219743 1 21.88565701 0.825645506 4.565827002 0.999996839 0.833450954 0.829067672 0.02377198 0.782343563 20.1482397 0.022732021 0.005767521 6.693380381 -0.825645506 -0.166545885 KGPEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGPEFTR 7 1 Q9NQG5;E9PIQ9 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;; 93.267 0.024149 884070000 1120320 968280 1053910 1144220 1037300 1046880 1364370 1203340 1340980 FALSE TRUE 1067364.694 1066948.833 1102232.816 1029200.832 1218204.792 1010626.283 1156210.298 1097969.17 1548932.33 0.689097047 0.688828564 0.711608115 0.664458228 0.786480318 0.652466388 0.746456302 0.70885548 1 20.56284269 -4.999999999 0.310653317 3.636193945 0.691058215 0.857995677 0.037713002 89.8766467 0.812843015 155.0288651 0.029963754 1.00E-05 4.999999999 -2.94513573 KGPEQS(ph)ELY(ph)AQLS(ph)KSS(ph)VLTGGHEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPEQSELYAQLSKSSVLTGGHEER 25 2 Q9UBK2-9;Q9UBK2-4;Q9UBK2;Q9UBK2-3 Q9UBK2-9 PPARGC1A Peroxisome proliferator-activated receptor gamma coactivator 1-alpha 4 KGPEQS(0.994)ELY(0.995)AQLS(0.515)KS(0.515)S(0.55)VLT(0.431)GGHEER 53.073 0.074252 355900000 403820 438210 289490 454250 90445 480130 344510 500250 82597 TRUE FALSE 384732.2289 482864.0972 302763.4028 408587.927 106218.5794 463502.9777 291948.6721 456445.458 95405.72091 4.032590763 5.061165018 3.173430272 4.282635497 1.113335535 4.858230442 3.060075112 4.784256684 1 16.54178816 3.727427622 24.44117223 3.313438221 4.546877888 0.145638585 1.345538293 885.3993747 1943790.145 0.314639873 0.492689557 5338.602947 -3.727427622 1.233439667 KGPGAGSALDDGRRDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGPGAGSALDDGRRDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 45 3 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 KGPGAGSALDDGRRDPSSNDINGGMEPTPS(0.001)T(0.001)VS(0.02)T(0.079)PS(0.895)PS(0.003)ADLLGLR;KGPGAGSALDDGRRDPS(0.001)S(0.001)NDINGGMEPT(0.021)PS(0.107)T(0.107)VS(0.107)T(0.098)PS(0.535)PS(0.021)ADLLGLR 125.89 9.73E-10 261710000 150540 54203 171262 102446 195867 137308 281290 177884 283460 TRUE FALSE 143424.2725 59726.34732 179114.5321 92147.93345 230026.1428 132552.9895 238374.0443 162307.5339 327417.5291 0.438047019 0.182416462 0.54705236 0.281438607 0.702546817 0.4048439 0.728043013 0.495720356 1 18.32077204 0.379492693 0.20259017 1.250789822 0.203631339 0.595997952 0.149524823 3.969127107 0.393716023 1.213611587 0.477931648 2.396032436 -0.379492693 -1.047158483 KGPGLAVQSGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPGLAVQSGDK 12 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 77.078 0.047127 137620000 666030 693570 540850 597820 517090 666760 722880 674530 562770 FALSE TRUE 634548.0818 764245.5715 565648.5075 537725.9978 607270.3323 643669.934 612591.3794 615464.5773 650041.4974 0.976165498 1.175687359 0.870172919 0.827217955 0.934202408 0.990198221 0.942388112 0.946808134 1 19.31017229 3.728485911 24.99415358 0.928294277 1.075926432 0.434204494 0.069160947 549.199425 1362499.064 0.018228589 0.028591171 5351.627927 -3.728485911 0.147632155 KGPGQPS(ph)SPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.923)S(0.077)PQR;KGPGQPS(0.5)S(0.5)PQR;KGPGQPS(0.729)S(0.271)PQR;KGPGQPS(0.595)S(0.405)PQR;KGPGQPS(0.68)S(0.32)PQR 71.548 0.029847 2849120000 3385910 3867410 2955940 4039020 2808290 3519280 3588730 3381000 2816090 TRUE FALSE 3225864.745 4261503.476 3091472.773 3633010.036 3298054.887 3397406.451 3041203.327 3084941.716 3252794.855 0.991720932 1.310105207 0.950405086 1.116888767 1.013914198 1.044457644 0.934950854 0.948397257 1 21.63324841 2.638088886 0.900913387 0.959131641 1.128808949 0.22116613 0.0978691 0.679747907 1.152541253 0.05865642 0.048926638 434.5991637 -2.638088886 0.169677307 KGPGQPS(ph)SPQRLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.5)S(0.5)PQRLDR 109.35 0.00040314 1282300000 414200 337890 394560 381980 313130 427780 552970 415940 382470 TRUE FALSE 394621.5869 372321.3751 412650.9663 343582.6447 367739.7729 412965.8713 468604.2705 379518.0886 441781.4942 0.893250605 0.842772683 0.934061231 0.777720772 0.83240194 0.934774038 1.060715029 0.859062893 1 18.75297346 2.054432619 5.327902461 0.984300217 0.858477325 0.420910671 0.063456799 0.161129853 9.745025881 0.02288662 0.016427573 113.3528957 -2.054432619 -0.125822891 KGPGQPSS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.122)S(0.878)PQR;KGPGQPS(0.374)S(0.626)PQR;KGPGQPS(0.033)S(0.967)PQR 87.083 0.0085685 1035260000 2040140 2359450 1745410 2477040 1373800 2100030 1878670 2096130 1325820 TRUE FALSE 1943706.625 2599880.637 1825438.775 2228043.233 1613390.285 2027305.435 1592044.387 1912581.745 1531421.394 1.269217364 1.697691208 1.191989861 1.454885795 1.053524713 1.323806395 1.039586095 1.248893186 1 20.54643989 2.941597344 1.208639542 1.131250138 1.462237214 0.353844644 0.168799138 0.419932736 1.289046085 0.065643235 0.074659203 874.1729105 -2.941597344 0.330987076 KGPGQPSS(ph)PQRLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.344)S(0.656)PQRLDR 67.902 0.026761 471730000 334300 283970 350860 378900 308260 383360 450550 419550 430130 TRUE FALSE 318498.3015 312906.8658 366947.278 340812.2521 362020.4464 370084.1471 381810.3226 382811.9778 496832.3636 0.64105788 0.62980371 0.738573621 0.685970313 0.728657135 0.744887359 0.768489234 0.770505317 1 18.92239963 -5 0.105283432 1.991182779 0.513691448 0.944268701 0.024138362 33.22649435 0.235198396 7.077166773 0.322322337 1.00E-05 5 -1.477491331 KGPGRPTGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGPGRPTGSK 10 2 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 68.484 0.033655 1528280000 1425280 1139680 1096940 1479970 891570 1336890 1554890 1376580 1074590 FALSE TRUE 1357909.839 1255814.688 1147235.784 1331200.604 1047059.526 1290593.164 1317662.973 1256039.357 1241231.929 1.094001699 1.011748617 0.924271893 1.072483371 0.843564769 1.039767939 1.061576763 1.011929623 1 20.24334128 0.940218538 19.99919718 0.999999998 1.012686364 0 0.074335322 26848.19871 8981784.793 0.068100074 0.017025018 8.714019718 -0.940218538 0.012686367 KGPPTQELDRDS(ph)EEEEEEDDEDGEDEEEVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPPTQELDRDSEEEEEEDDEDGEDEEEVPK 31 2 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 KGPPT(0.008)QELDRDS(0.992)EEEEEEDDEDGEDEEEVPK 248.5 9.86E-47 172960000 138270 128870 125910 146600 72217 154230 156500 166260 77547 TRUE FALSE 131734.2511 142001.9995 131683.098 131863.4895 84811.62194 148888.9764 132623.0507 151701.393 89572.5927 1.470698203 1.585328673 1.470127123 1.472141037 0.946847907 1.662215773 1.480620876 1.693613955 1 16.45076975 3.2490669 3.503958616 1.403221916 1.524168478 0.057837269 0.244834943 0.799375328 20.72656329 0.067706459 0.089021295 1774.462803 -3.2490669 0.120946562 KGPQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGPQVR 6 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 113.82 0.041389 10902870000 15051410 17322880 12693110 18160140 10904330 14626010 14237260 15909160 12276480 FALSE TRUE 14339959.68 19088101.17 13275101.65 16334648.23 12806041.7 14119507.61 12065104.5 14516069.61 14180253.82 1.011262553 1.346104337 0.936168126 1.151929185 0.903089738 0.995716141 0.850838402 1.023681931 1 23.75738002 3.067857796 1.34097817 0.940368344 1.159648777 0.251427341 0.120292045 0.421040011 1.584002365 0.04254084 0.054152295 1169.116516 -3.067857796 0.219280433 KGPS(ph)STGASGQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGPSSTGASGQAK 13 1 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 KGPS(0.488)S(0.488)T(0.025)GASGQAK;KGPS(0.428)S(0.198)T(0.362)GAS(0.012)GQAK 73.887 0.027957 119100500 145345 125326 125657 150705 82010 156662 153167 158510 110183 TRUE FALSE 138474.8299 138096.8619 131418.4977 135555.8471 96312.51803 151236.7557 129798.561 144630.0241 127269.6169 1.088043111 1.08507329 1.032599146 1.065107685 0.756759707 1.188317835 1.019870761 1.136406533 1 16.95752852 -1.076421954 4.500141355 0.999996638 1.048179458 0.016045327 0.113836731 7029597.974 1681578.576 232.9298703 0.024248354 0.083864478 1.076421954 0.04818282 KGPSGYGFNLHSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGPSGYGFNLHSDK 14 1 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 128.9 4.61E-05 3141700000 8179500 6562000 5230900 5869000 5553500 6127400 9061200 7441000 5463700 FALSE TRUE 7792871.245 7230675.26 5470741.939 5279036.97 6522028.642 5915206.602 7678747.52 6789426.593 6310982.691 1.234811063 1.145728901 0.866860552 0.836484146 1.03344106 0.937287724 1.21672771 1.075811316 1 22.58943324 3.953834323 8.205224549 1.008004253 1.201780547 0.368614089 0.107659323 0.347116617 57.86662445 0.030307199 0.055307522 8991.545017 -3.953834323 0.193776294 KGPST(ph)PYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGPSTPYTK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KGPS(0.15)T(0.847)PY(0.003)TK 91.858 0.0061348 1073000000 2770900 2405300 2494100 2866000 1696900 2599000 3033000 2809800 2052800 TRUE FALSE 2639925.048 2650402.805 2608456.952 2577904.235 1992838.823 2508995.978 2570260.145 2563759.016 2371137.74 1.113357948 1.117776821 1.100086641 1.087201385 0.840456794 1.058140122 1.083977578 1.081235802 1 21.17714804 2.981428011 24.92961208 1.020812164 1.11006244 0.30864982 0.068447349 982.1265497 1318332.966 0.021009305 0.022671771 958.1378816 -2.981428011 0.089250276 KGQAVDYEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGQAVDYEGSR 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 190.68 3.47E-06 3010120000 3267570 2581470 2751660 3185050 2652620 2928200 3430240 3075030 3088980 FALSE TRUE 3113118.442 2844524.728 2877826.333 2864882.723 3115236.088 2826795.7 2906893.887 2805764.071 3568003.242 0.872509981 0.797231542 0.806564943 0.802937253 0.873103491 0.792262649 0.814711672 0.78636814 1 21.7666855 -0.977801223 5.754034523 1.000000238 0.81893229 0.776080883 0.030685339 8.79E-08 1.56E-08 0.027884311 0.006572386 0.105244347 0.977801223 -0.181067948 KGQGGAGAGDDEEED ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGQGGAGAGDDEEED 15 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;; 142.08 9.53E-05 9917460000 11304980 9972590 10234910 11516430 7046760 11818340 12674950 11943060 7461860 FALSE TRUE 10770616 10988808.26 10704190.75 10358776.58 8275712.713 11409067.92 10741153.59 10897262.35 8619007.139 1.24963535 1.274950593 1.241928516 1.201852651 0.960170073 1.32371023 1.246217043 1.264329194 1 23.03909026 -1.8154041 2.609486713 0.92562867 1.225487851 0.333481468 0.097660462 10994927.27 7742368.187 5155936.483 0.022804743 0.015296635 1.8154041 0.299859181 KGQSEEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KGQSEEIQK 9 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;;;; 140.78 0.00017363 1373875000 2594810 2205760 2286650 2902380 1850860 2630360 3180600 3113350 2233610 FALSE TRUE 2472158.474 2430529.452 2391495.164 2610627.248 2173649.398 2539269.974 2695341.054 2840728.569 2579986.831 0.95820585 0.942070488 0.926940842 1.011876191 0.842504067 0.984218192 1.044711167 1.101063205 1 21.29893227 1.828200818 3.490328607 1.05482568 0.940636377 0.523489497 0.048213264 0.168666542 3.560950721 0.022538853 0.011836399 67.32879127 -1.828200818 -0.114189303 KGQTHTLEDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGQTHTLEDFQR 12 1 Q99714;Q99714-2;Q5H928 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 ;;; 165.58 3.52E-05 1230340000 983400 551289 787871 802123 815881 645231 1003310 746074 810970 FALSE TRUE 936916.6309 607465.9759 823995.6647 721492.0721 958170.3881 622886.4887 850236.6324 680743.8054 936731.0857 1.000198077 0.648495588 0.879650176 0.770223262 1.022887361 0.664957636 0.907663518 0.726722766 1 19.83727542 -1.439667417 2.724995528 1.005157338 0.826323169 0.150493355 0.128693831 22992187.93 24723883.2 909351.927 0.026851636 0.036335621 1.439667417 -0.17883417 KGRPYDYNGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGRPYDYNGPR 11 2 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 164.9 1.25E-05 1036150000 654060 546710 599330 675060 609020 634850 725990 745740 710920 FALSE TRUE 623143.88 602420.3706 626809.8733 607201.6863 715232.8952 612864.9853 615226.8918 680439.0522 821165.8427 0.758852655 0.733615963 0.763317031 0.739438558 0.87099689 0.746335214 0.749211499 0.828625616 1 19.64731409 -5 0.248631933 2.41055839 0.746079811 0.764350573 0.040427987 83.18673495 0.825138147 59.50635046 0.056379338 1.00E-05 5 -1.664478579 KGS(ph)FSALVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.762)FS(0.238)ALVGR;KGS(1)FSALVGR;KGS(0.774)FS(0.226)ALVGR 225.72 2.06E-09 2107080000 1515640 1274050 1278800 1696400 1124830 1651390 1918700 1695590 1464850 TRUE FALSE 1443998.701 1403877.143 1337434.245 1525874.649 1320999.996 1594201.95 1625967.076 1547115.151 1692011.457 0.85342135 0.829709006 0.790440419 0.901811062 0.780727572 0.942193355 0.960966942 0.914364465 1 20.69030791 2.160988597 7.583364805 0.952913632 0.834535089 0.712712051 0.038845474 0.120304769 10.07512427 0.01288869 0.009517176 144.8733815 -2.160988597 -0.118378543 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 KGS(1)GS(1)EQEGEDEEGGER 229.77 3.51E-15 436700000 668600 575580 584780 674760 321060 690530 736040 723270 361420 TRUE FALSE 636996.603 634232.2564 611592.7414 606931.8428 377052.7623 666616.773 623743.5797 659936.6445 417467.1677 1.52586036 1.51923865 1.465008002 1.453843295 0.903191416 1.596812455 1.494114095 1.580810889 1 18.67130321 2.988984707 24.70371835 1.360616286 1.503663122 0.115038609 0.226962334 1223.047818 2742908.236 0.065237922 0.073229288 974.9553055 -2.988984707 0.143046836 KGS(ph)ITEYTAAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.98)IT(0.02)EYTAAEEK;KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.982)IT(0.018)EYTAAEEK;KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.99)IT(0.01)EYTAAEEK 230.05 2.90E-12 2947250000 3237080 3451980 2665610 3629110 1419130 3596420 3091280 3527580 1327710 TRUE FALSE 3084069.644 3803740.687 2787830.855 3264304.968 1666625.823 3471875.074 2619648.461 3218686.394 1533604.486 2.010994146 2.480261842 1.817829095 2.12851814 1.086737707 2.263866014 1.708164318 2.098772157 1 20.54849503 -1.711125887 0.165847136 1.54E-13 2.327847105 0.378512854 0.377142424 34.22329412 0.917194938 16.55956812 1.649720461 0.019447963 1.711125887 2.327847105 KGS(ph)ITEYTAAEEKEDGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGSITEYTAAEEKEDGRR 18 3 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.995)IT(0.005)EYTAAEEKEDGRR;KGS(0.992)IT(0.008)EYTAAEEKEDGRR;KGS(0.497)IT(0.497)EYT(0.005)AAEEKEDGRR;KGS(1)ITEYTAAEEKEDGRR 233.26 5.38E-23 2153140000 1748680 1401770 1632880 1558320 860034 1830390 1942110 1982930 993600 TRUE FALSE 1666023.362 1544611.957 1707749.163 1401674.713 1010023.657 1767003.135 1645805.45 1809294.137 1147682.413 1.451641449 1.34585312 1.487998024 1.221308871 0.88005501 1.539627265 1.434025155 1.576476311 1 20.13029204 3.241993374 24.98302816 1.305865305 1.414094273 0.085094643 0.22056648 310.1669148 2257319.543 0.061820016 0.080434253 1745.795518 -3.241993374 0.108228968 KGS(ph)KVGDFGDAINWPTPGEIAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGSKVGDFGDAINWPTPGEIAHK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;H0YAX9 Q6PKG0 LARP1 La-related protein 1 1 KGS(1)KVGDFGDAINWPTPGEIAHK;KGS(1)KVGDFGDAINWPTPGEIAHK 118.61 0.00013866 406710000 1039310 680910 915520 912490 513000 1120090 1317670 1252250 536290 TRUE FALSE 990183.876 750295.5031 957497.4976 820764.7716 602467.0376 1081301.002 1116635.241 1142596.351 619455.1142 1.598475585 1.211218514 1.545709246 1.324978603 0.972575775 1.745567964 1.802608801 1.844518392 1 19.24064022 2.179742098 24.99998802 1.682671765 1.348184055 0.143079017 0.292995817 104.8842576 44578.59525 0.099367375 0.073387697 151.2662699 -2.179742098 -0.33448771 KGS(ph)LAALYDLAVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGSLAALYDLAVLK 14 1 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 KGS(1)LAALYDLAVLK;KGS(1)LAALYDLAVLK 178.77 1.19E-06 132913000 801230 668900 601600 670810 490520 729570 958050 825020 485420 TRUE FALSE 763357.4458 737061.6705 629183.9551 603378.9043 576066.5327 704304.808 811881.8767 752776.8751 560696.4544 1.36144511 1.314546694 1.122147198 1.076123988 1.027412476 1.256124954 1.447988248 1.342574702 1 19.09686042 1.996245823 24.92540701 1.322987252 1.202223561 0.008164642 0.153177425 346.0497372 2297558.949 0.060163235 0.043473058 99.13929416 -1.996245823 -0.12076369 KGS(ph)PTPGFSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.909)PT(0.05)PGFS(0.033)T(0.008)R;KGS(0.708)PT(0.292)PGFSTR;KGS(0.751)PT(0.249)PGFSTR;KGS(0.753)PT(0.247)PGFSTR;KGS(0.888)PT(0.111)PGFSTR;KGS(0.957)PT(0.043)PGFSTR;KGS(0.752)PT(0.248)PGFSTR 102.63 0.0017412 9540060000 3145467 2538859 2731451 3191200 1917259 3169038 3321033 3204875 2089095 TRUE FALSE 2996787.009 2797571.619 2856690.73 2870414.513 2251628.363 3059293.419 2814348.421 2924239.155 2413061.183 1.241902621 1.159345498 1.18384513 1.189532422 0.933100403 1.267805989 1.166297996 1.211837966 1 21.20243306 -2.416659729 1.842380862 4.68E-05 1.170743866 0.257523365 0.090260214 945554.0113 81897.04783 3934712.71 0.020873926 0.003831248 2.416659729 1.170697078 KGS(ph)SGNASEVSVACLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.911)S(0.089)GNASEVSVACLTER;KGS(0.953)S(0.047)GNASEVSVACLTER;KGS(0.967)S(0.033)GNASEVSVACLTER;KGS(0.771)S(0.229)GNASEVSVACLTER;KGS(0.973)S(0.027)GNASEVSVACLTER 260.8 5.72E-31 3297390000 2164800 2101500 2121200 2387330 1450600 2277510 2334290 2334460 1447200 TRUE FALSE 2062474.194 2315645.239 2218459.118 2147351.053 1703584.181 2198639.258 1978151.188 2130042.307 1671624.385 1.233814374 1.385266487 1.327127756 1.284589452 1.019119006 1.315271109 1.183370622 1.274235005 1 20.67281928 -5 0.12739314 0.130913448 1.372925164 0.413445594 0.097231922 136.4470425 1.104643543 30.25479456 0.742699935 1.00E-05 5 1.242011716 KGS(ph)VSHDTVQPR ddPTM_SK-BR-3_Trastuzumab_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(0.935)VS(0.065)HDTVQPR;KGS(0.929)VS(0.071)HDTVQPR 144.33 3.86E-05 508500000 400200 323110 341150 448920 326680 392190 470310 398150 324620 TRUE FALSE 381283.3391 356035.2763 356792.0649 403793.7087 383652.8886 378608.362 398555.5717 363285.8753 374960.4117 1.01686292 0.949527644 0.95154596 1.07689691 1.023182386 1.009728895 1.06292707 0.968864616 1 18.51637876 3.256945359 24.99944412 1.028176968 0.974008452 0.311277787 0.035274739 256.6757192 349023.4246 0.009173393 0.01239632 1806.946771 -3.256945359 -0.054168516 KGSFS(ph)ALVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.125)FS(0.875)ALVGR 62.042 0.09286 384080000 273620 202850 220650 279050 182920 264050 323470 277530 241470 TRUE FALSE 260686.5249 223520.6456 230767.0208 250999.3638 214821.1901 254905.8823 274118.7106 253228.0019 278915.9343 0.934641922 0.801390735 0.827371234 0.899910449 0.770200493 0.913916528 0.982800467 0.907900807 1 18.08947083 2.006526818 24.8495825 0.958331657 0.849391623 0.522288601 0.051379013 116.536881 443689.0137 0.017990128 0.013253889 101.5142051 -2.006526818 -0.108940034 KGSFSALVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 0 77.597 0.052148 303880000 353990 249580 282410 264960 481570 247950 383910 330080 555420 FALSE TRUE 337257.5942 275012.4857 295358.7778 238325.7174 565555.6555 239363.4293 325337.4785 301176.4453 641551.6969 0.525690441 0.428667693 0.460381882 0.371483262 0.881543387 0.373100766 0.507110308 0.469450002 1 19.291206 -1.982760824 2.829333769 1.448557188 0.498069517 0.541254887 0.143988494 31414166.99 11985195.17 91996529.42 0.031979672 0.01040493 1.982760824 -0.950487671 KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSR 37 1 P06576;H0YH81;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 164.11 7.12E-18 298910000 630550 431170 530290 516770 598390 434950 637500 558620 624820 FALSE TRUE 600745.1511 475106.7132 554604.321 464823.2978 702749.0265 419887.5724 540237.6665 509704.2714 721713.8945 0.832386844 0.658303404 0.768454543 0.6440548 0.973722457 0.58179228 0.748548241 0.706241456 1 19.4610675 -1.326256979 5.863143701 1.000029559 0.736402411 0.362663863 0.108602327 3.64E-05 4.18E-06 0.091154648 0.021482951 0.04717838 1.326256979 -0.263627148 KGSLESPATDVFGSTEEGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGSLESPATDVFGSTEEGEKR 21 2 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 156.05 1.05E-08 204476000 137650 134619 128125 150823 100021 144213 160420 164023 116529 FALSE TRUE 131143.5573 148336.8291 133999.658 135661.9855 117464.6307 139218.8676 135944.9827 149660.2766 134599.7222 0.974322645 1.102058955 0.995541862 1.007892017 0.872695938 1.034317645 1.009994527 1.111891423 1 17.03831591 -0.35264245 6.414756702 0.999979853 1.014821105 0.003814867 0.066412758 0 0 0.061208137 0.014426896 0.443974012 0.35264245 0.014841253 KGSS(ph)SQAPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGSSSQAPASK 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 KGS(0.348)S(0.63)S(0.022)QAPASK 134.14 9.01E-05 106420000 428750 355720 355310 489160 235900 373150 368170 396690 207480 TRUE FALSE 408483.8372 391968.2724 371601.3149 439988.7075 277040.8853 360227.7219 311998.9046 361953.7206 239654.9387 1.704466594 1.63555266 1.55056815 1.835925893 1.155999066 1.503109946 1.301867202 1.510311962 1 17.87059915 -0.517517467 0.079541364 3.37E-14 2.345966235 0.578795537 0.163778953 42.01136456 0.811013441 16.48358311 7.851532987 0.303726393 0.517517467 2.345966235 KGSVS(ph)HDTVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.059)VS(0.941)HDTVQPR 157.58 4.54E-05 158020000 118170 81426 98234 117540 84627 98907 136190 124470 89635 TRUE FALSE 112584.3383 89723.40197 102738.1261 105724.6559 99385.92201 95481.82579 115411.7142 113570.7469 103535.138 1.087402214 0.866598565 0.992302015 1.021147583 0.959924562 0.922216627 1.114710584 1.096929498 1 16.65976095 1.725642888 10.59236348 1.078112063 0.972979307 0.324007177 0.064701485 0.102274796 40.10800677 0.029196221 0.015860147 53.16708967 -1.725642888 -0.105132756 KGSVSHDTVQPR ddPTM_SK-BR-3_Trastuzumab_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 0 ; 64.65 0.040814 64409000 37699 33752 38832 41574 48046 37057 50263 41329 57711 FALSE TRUE 35917.04298 37191.36717 40612.48561 37394.90253 56425.20719 35773.7068 42594.45621 37710.01366 66660.52713 0.538805265 0.557921888 0.609243391 0.5609752 0.846456061 0.536655024 0.638975688 0.565702302 1 16.02454511 -5 0.272863668 3.753942599 0.575429102 0.642398395 0.091692241 130.5492139 1.262616444 203.0466047 0.102791639 1.00E-05 5 -3.178513496 KGTAVFWYNLFASGEGDYSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGTAVFWYNLFASGEGDYSTR 21 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 160.33 3.42E-11 39566000 110187 67769.5 70127 75005.2 90862.4 81610.6 114415 88732.6 102319 FALSE TRUE 104978.6789 74675.2891 73342.39232 67465.5348 106708.7738 78784.40446 96958.89037 80962.70314 118186.1079 0.888248887 0.631844896 0.620566948 0.570841497 0.902887621 0.666613072 0.820391602 0.685044161 1 16.85070094 -1.005616615 0.445340928 1.102242886 0.714444501 0.366602091 0.113727303 18.63569664 2.436102533 2.557517684 0.060305164 0.098715053 1.005616615 -0.387798385 KGTDDSMTLQSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGTDDSMTLQSQK 13 1 O00422;O00422-2;H7BZW6 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 122.34 0.0003787 106760000 184410 159090 181490 200380 163000 196000 240790 221520 171480 FALSE TRUE 175693.3048 175301.4519 189811.496 180237.4217 191427.1484 189212.4709 204053.0631 202122.5344 198072.2426 0.887016285 0.885037952 0.958294274 0.909958 0.966451159 0.955269998 1.030195147 1.020448559 1 17.59566719 2.617763217 0.663426302 1.024023947 0.884568335 0.787415858 0.023617948 0.287862391 0.265464543 0.017539692 0.016103656 414.7278662 -2.617763217 -0.139455612 KGTDLWLGVDALGLNIYEKDDKLTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGTDLWLGVDALGLNIYEKDDKLTPK 26 3 P15311;E7EQR4 P15311 EZR Ezrin 0 127.73 4.08E-05 117030000 175890 130120 164480 160110 100630 159870 190540 209570 112850 FALSE TRUE 167576.0283 143379.3759 172021.5707 144015.4386 118179.8401 154333.6618 161469.6235 191218.9398 130350.2016 1.285583192 1.099955153 1.319687799 1.104834797 0.906633351 1.183992505 1.238737044 1.46696313 1 16.99203329 -0.262881219 6.990379077 1.000000003 1.191505002 0.149164188 0.149254062 0 0 0.138805438 0.032716755 0.545907148 0.262881219 0.191504999 KGTVEGFEPADNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGTVEGFEPADNK 13 1 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ;;; 166.9 5.26E-05 1708920000 2897300 2220790 2390030 2879240 1933730 2902740 3317080 3126360 2261970 FALSE TRUE 2760350.371 2447091.026 2499615.24 2589813.325 2270971.9 2802217.386 2810998.524 2852599.345 2612744.755 1.056494465 0.936597814 0.956700893 0.991223241 0.86919011 1.072518615 1.075879501 1.091801769 1 21.31713476 2.175869848 24.99998404 1.067611778 0.968241442 0.460534051 0.052187067 56.25889842 22434.41421 0.01856499 0.013711158 149.9235469 -2.175869848 -0.099370335 KGTVLLADNVICPGAPDFLAHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGTVLLADNVICPGAPDFLAHVR 23 1 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 186.62 1.74E-17 1845250000 1161790 712400 1014100 1093440 1202480 962930 1554830 1146520 1339770 FALSE TRUE 1106874.489 784994.3699 1060597.488 983525.3338 1412192.131 929583.4927 1317612.127 1046124.631 1547534.689 0.715250196 0.507254781 0.685346503 0.63554332 0.912543119 0.600686692 0.851426554 0.675994301 1 20.56154032 -2.601947741 0.122213445 1.581917375 0.498509255 0.443531314 0.11157208 57.94316534 0.843912281 10.18697507 1.085534733 0.002500646 2.601947741 -1.08340812 KGVAEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGVAEQKR 8 2 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 72.928 0.025245 258170000 428190 338940 436710 425600 447160 532140 652430 576010 580830 FALSE TRUE 407950.3073 373478.3713 456733.5855 382817.8794 525144.5624 513711.8584 552889.8208 525571.5108 670902.1499 0.608062304 0.556680838 0.68077526 0.570601658 0.782743896 0.765703104 0.824099045 0.783380275 1 19.35574284 1.814016676 0.351277064 1.008944934 0.536075188 0.843144963 0.053037013 0.41533159 0.152462802 0.065740517 0.066530124 65.16534161 -1.814016676 -0.472869746 KGVAINFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGVAINFVK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 107.15 0.0053919 0 1345300 1135160 1037750 1317030 1211780 1178250 1548890 1347540 1401650 FALSE TRUE 1281710.335 1250834.095 1085331.864 1184639.642 1423114.048 1137446.907 1312578.383 1229542.254 1619010.723 0.79166266 0.772591606 0.67036731 0.731705865 0.879002237 0.702556747 0.810728653 0.759440463 1 20.62668111 -3.574953615 0.373383408 1.929264816 0.76000846 0.625066847 0.057382484 108.8412276 2.342241683 79.23708258 0.036939095 0.000266101 3.574953615 -1.169256356 KGVAINFVTEEDKR ddPTM_SK-BR-3_Trastuzumab_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 ; 192.4 2.12E-07 1733540000 1654510 1407610 1430220 1649600 1063170 1558040 1702490 1763310 1246660 FALSE TRUE 1576304.591 1551047.059 1495797.002 1483779.074 1248586.511 1504084.684 1442743.882 1608905.229 1439985.666 1.094666863 1.077126736 1.038758258 1.030412392 0.867082597 1.04451365 1.001915447 1.11730642 1 20.45762302 3.565758888 2.104542252 1.005921199 1.088227857 0.206350663 0.061250244 0.444359993 3.879491397 0.017248989 0.030002999 3679.246519 -3.565758888 0.082306658 KGVAINMVTEEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;; 219.52 2.80E-12 6784860000 4998120 4680140 5254630 6147370 4487415 5829647 6620290 6420420 5191430 FALSE TRUE 4761868.773 5157051.587 5495559.983 5529424.688 5270018.755 5627764.863 5610243.171 5858213.988 5996490.45 0.79410929 0.86001164 0.916462726 0.922110147 0.878850521 0.938509768 0.935587777 0.976940435 1 22.51568695 8 0.181928888 1.004407051 0.08678566 0.875213074 0.02073843 17.12035458 0.194052308 0.045478497 4.360644023 100000000 -8 -0.917621391 KGVEGLIDIENPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KGVEGLIDIENPNR 14 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 222.27 6.34E-12 1465090000 2638090 2165100 2419510 2689250 2272060 2439560 3022300 2716700 2697240 FALSE TRUE 2513392.714 2385726.152 2530446.927 2418921.481 2668306.545 2355077.425 2561192.627 2478811.346 3115514.204 0.806734475 0.765756789 0.812208439 0.776411636 0.856457833 0.755919335 0.822077018 0.795634744 1 21.57103886 -4.999999901 0.377269453 3.806025778 0.792629699 0.825512598 0.029040088 200.9857884 1.515414939 460.9493712 0.01698444 1.00E-05 4.999999901 -3.013396079 KGVITVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGVITVK 7 1 P10809;E7EXB4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 116.73 0.023495 0 1465000 1144700 1180600 1130500 1011900 1044400 1471900 1289900 1259700 FALSE TRUE 1395752.353 1261346.231 1234731.678 1016859.992 1188375.04 1008232.166 1247334.622 1176949.518 1455047.842 0.959248427 0.866876122 0.848584934 0.698849868 0.81672575 0.692920285 0.857246467 0.808873415 1 20.47263516 4.083262548 1.586889624 0.80174324 0.951218564 0.203446723 0.086206773 0.524053896 2.415755648 0.021856884 0.081701125 12113.30209 -4.083262548 0.149475324 KGVLANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGVLANR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 79.116 0.05371 4895476000 3921460 2762540 2005213 2647770 5678590 3372380 6265670 4243740 6156210 FALSE TRUE 3736100.357 3044045.967 2097153.999 2381611.129 6668934.298 3255593.635 5309726.965 3872135.628 7110883.605 0.525405922 0.42808266 0.294921717 0.33492478 0.93784889 0.457832502 0.746704244 0.544536494 1 22.76159741 2.760413762 24.98120756 0.700793119 0.409999252 0.488304787 0.171204492 725.9868251 829903.4447 0.047409558 0.050247211 575.9884324 -2.760413762 -0.290793867 KGVNLPGAAVDLPAVSEK ddPTM_SK-BR-3_Trastuzumab_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 ; 145.05 1.50E-07 1121520000 2772600 2657300 2262800 3202700 1830720 2788700 2811200 3045200 1897570 FALSE TRUE 2641544.693 2928081.891 2366551.618 2880758.511 2149996.988 2692126.62 2382299.809 2778546.144 2191835.464 1.20517472 1.335904058 1.079712258 1.314313304 0.980911671 1.228252149 1.086897191 1.267680074 1 21.06370807 -4.034846217 0.032004122 1.02E-07 1.902224961 0.208747331 0.111782695 1355.85565 3.83990762 170.6591341 75.06205162 9.23E-05 4.034846217 1.902224859 KGVNLPGAAVDLPAVSEKDIQDLK ddPTM_SK-BR-3_Trastuzumab_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 ; 182.17 1.76E-17 1218480000 2605460 1422890 2182160 2348040 1588160 2544450 3297500 2768500 1811730 FALSE TRUE 2482305.069 1567884.109 2282214.194 2112010.558 1865134.601 2456335.058 2794405.812 2526075.463 2092683.835 1.18618256 0.749221685 1.090568081 1.009235376 0.891264399 1.173772654 1.335321545 1.207098474 1 20.99692293 2.117629971 5.795489932 1.226347431 0.977994138 0.297352029 0.141732254 0.197425541 9.262963772 0.050509831 0.037039489 131.108235 -2.117629971 -0.248353293 KGWESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGWESR 6 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 97.068 0.066531 507820000 1482100 1196700 1231300 1498200 1270800 1309500 1625100 1363800 1479500 FALSE TRUE 1412044.07 1318645.091 1287756.323 1347598.09 1492427.118 1264151.687 1377161.148 1244378.442 1708933.304 0.826272194 0.771618815 0.753543933 0.788560962 0.873309166 0.739731436 0.805860091 0.728160917 1 20.70466466 -1.057701881 4.53099013 1.000011397 0.788006523 0.712516347 0.042724008 4.44E-06 9.24E-07 0.037377464 0.008809479 0.087558461 1.057701881 -0.212004874 KGWEVVESDLYAMNFNPIISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGWEVVESDLYAMNFNPIISR 21 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 236.04 1.30E-29 675930000 2204900 1798470 1913790 2212600 2028600 1840200 2426100 2228900 2142300 FALSE TRUE 2100678.747 1981736.138 2001539.164 1990185.244 2382387.198 1776473.413 2055953.887 2033725.7 2474516.943 0.848924778 0.800857777 0.808860562 0.804272224 0.962768594 0.717907153 0.8308506 0.821867761 1 21.23871549 -0.824577438 5.118200148 1.000000171 0.822756662 0.457944596 0.059964962 3.40E-05 36505983.46 16.89921281 0.01252566 0.149769218 0.824577438 -0.177243509 KGWS(ph)MSEQSEESVGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.995)MS(0.005)EQSEESVGGR 130.89 2.04E-05 731660000 892310 565940 739890 1078570 918030 905110 1201150 682820 783020 TRUE FALSE 850132.2747 623609.9294 773814.6884 970150.0945 1078134.141 873765.8137 1017892.507 623028.6609 904446.7425 0.939947301 0.689493256 0.855566892 1.072644799 1.192037177 0.966077683 1.125431116 0.688850578 1 19.78667603 3.338476598 5.287132431 1.026333873 0.808913009 0.248253719 0.145138652 0.230477743 10.0630229 0.037974398 0.051590515 2180.10092 -3.338476598 -0.217420865 KGYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KGYEVIYLTEPVDEYCIQALPEFDGKR 27 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 179.81 1.06E-17 841920000 1294350 918530 1115280 1264910 940540 1179870 1478920 1313530 1162390 FALSE TRUE 1233168.641 1012129.251 1166416.691 1137758.844 1104569.878 1139010.806 1253283.592 1198510.35 1342647.505 0.918460457 0.753830956 0.868743797 0.847399515 0.822680469 0.848331973 0.933442015 0.892647062 1 20.35664916 1.22012214 0.803764271 0.994322207 0.835288621 0.537429659 0.045432132 0.418380363 0.608618498 0.040806455 0.015619847 16.6005371 -1.22012214 -0.159033586 KGYNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGYNAR 6 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 107.65 0.049838 552420000 743730 551390 541970 676970 662470 579000 753850 693770 776220 FALSE TRUE 708575.3568 607577.2679 566819.8606 608919.6894 778004.5583 558949.0848 638836.3371 633019.8209 896592.2332 0.790298344 0.677651719 0.632193588 0.679148967 0.867735108 0.623415042 0.712516028 0.706028669 1 19.77409248 -1.562659555 2.726663555 1.018586118 0.710444568 0.612669026 0.072182539 16068504.91 16101430.82 2176638.892 0.016633225 0.027374138 1.562659555 -0.30814155 KHDNEGSGSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHDNEGSGSKR 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 62.408 0.048747 3427300 8753.1 7105.7 5508.1 8554.3 6783.3 8446.8 10664 9090.1 7285.7 FALSE TRUE 8339.35831 7829.778909 5760.651833 7694.405512 7966.305372 8154.285198 9037.010942 8294.122654 8415.529146 0.990948776 0.930396505 0.684526396 0.914310363 0.946619664 0.96895692 1.073849402 0.985573517 1 13.03883827 2.283470497 2.067574861 1.025424792 0.892283455 0.345886661 0.082193016 0.393562143 3.431186148 0.039767789 0.027494217 192.0748477 -2.283470497 -0.133141336 KHEAFESDLAAHQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 208.51 1.16E-09 2371780000 1801670 1291710 986639 1773090 1567760 1279861 2015860 1517820 376197 FALSE TRUE 1716508.63 1423336.718 1031877.374 1594855.625 1841176.848 1235539.093 1708303.533 1384911.634 434535.7094 3.950213049 3.275534523 2.374666458 3.670252157 4.237112872 2.843354564 3.931330605 3.187106616 1 18.72911521 0.959132618 21.56231752 0.99999999 3.474615348 0.663726274 0.547972946 759.117654 400524.4458 0.498379812 0.124594953 9.101911703 -0.959132618 2.474615359 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR 40 2 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 120.95 5.44E-09 49775000 124720 72828 80654 119010 151810 98177 202210 112290 38012 FALSE TRUE 118824.7328 80249.256 84352.06568 107046.8887 178285.6159 94777.10587 171359.1507 102457.2923 43906.70682 2.706300276 1.827722045 1.921165849 2.438053237 4.06055541 2.158602016 3.902801259 2.333522592 1 15.42215371 2.989146914 24.42081796 2.942997921 2.163784246 0.030157728 0.90665811 694.716513 1563206.059 0.238153772 0.267697261 975.319514 -2.989146914 -0.779213676 KHEDFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHEDFDK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 101.6 0.0058032 499740000 1235030 1074290 1071830 1336160 755030 1221160 1325400 1270790 536190 FALSE TRUE 1176652.579 1183761.372 1120974.466 1201846.658 886706.9929 1178870.923 1123185.887 1159512.891 619339.6067 1.899850368 1.911328388 1.809951202 1.940529308 1.431697543 1.903432156 1.813521814 1.872176231 1 19.24037118 -1.970123752 2.650196662 0.309074184 1.829229939 0.759827412 0.145340875 16131177.6 7165798.117 68355927.52 0.033447813 0.01071214 1.970123752 1.520155755 KHEEEEAKAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KHEEEEAKAER 11 2 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ;;;;; 229.97 1.29E-12 2742437000 2573326 2118450 2420463 2612923 1614208 2710980 2962218 2751621 1414866 FALSE TRUE 2451689.98 2334322.463 2531443.623 2350267.016 1895725.364 2617098.083 2510277.239 2510674.478 1634276.193 1.500168692 1.428352486 1.548969283 1.438108825 1.159978572 1.601380534 1.536017749 1.536260816 1 20.64022039 -1.96974805 2.610963905 0.608142955 1.470063266 0.596557637 0.12111621 4219473.684 2335650.717 9997003.545 0.028897161 0.010721411 1.96974805 0.861920311 KHFGAGGNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHFGAGGNQR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 176.38 1.63E-06 820490000 575370 472980 510640 582120 610570 523430 753150 604710 467440 FALSE TRUE 548173.4004 521177.1997 534053.3491 523604.1916 717053.2147 505303.4879 638243.135 551758.3866 539928.2078 1.015270905 0.965271294 0.989119185 0.969766321 1.328052886 0.935871622 1.182088888 1.021910651 1 19.04240806 KHGGPKDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KHGGPKDEER 10 2 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;; 169.58 2.76E-06 6658160000 4804210 4210180 4314840 5039390 3195780 5248770 5992020 4935040 1604370 FALSE TRUE 4577124.514 4639202.129 4512679.682 4532820.943 3753123.02 5067003.779 5077827.298 4502901.735 1853167.506 2.469892495 2.503390608 2.435116992 2.445985551 2.025247588 2.734239492 2.740080043 2.429840649 1 20.82156186 2.978748519 24.0757625 2.360550841 2.47226637 0.0084594 0.500485097 3358.161636 3804459.984 0.138381208 0.148290417 952.2446009 -2.978748519 0.111715529 KHGLAHDEMKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 136.63 4.60E-05 1055442000 1449960 2225240 1845410 2675670 1174090 2372110 2337280 1532890 212446 TRUE FALSE 1381423.264 2451994.486 1930023.874 2406706.568 1378850.924 2289963.236 1980685.009 1398662.025 245391.0407 5.629477183 9.992192377 7.86509511 9.807638297 5.618994567 9.331894228 8.07154574 5.699727347 1 17.90472305 0.900760276 2.599231489 1.008863032 8.117127345 0.689157985 1.505756023 0.211893538 3.076702285 1.30404593 0.348496553 7.957200031 -0.900760276 7.108264314 KHGLEVIYMIEPIDEYCVQQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHGLEVIYMIEPIDEYCVQQLK 22 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 201.31 1.00E-22 1357120000 1800690 1745180 1827820 2079550 1451270 1985450 2500500 2013970 917060 FALSE TRUE 1715574.952 1923015.826 1911627.355 1870509.683 1704371.029 1916693.369 2119002.8 1837616.11 1059272.981 1.619577751 1.815411004 1.804659789 1.76584291 1.609000757 1.809442328 2.000431275 1.734789939 1 20.014643 0.948696464 23.23600641 0.999999999 1.782000609 0.831916336 0.10886582 3265.924598 1479179.362 0.112711013 0.028177753 8.885798568 -0.948696464 0.782000611 KHGVYNPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHGVYNPNK 9 1 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 109.21 0.0016134 359070000 1085100 884080 539590 554140 891150 550760 1079000 837170 588250 FALSE TRUE 1033809.473 974168.7571 564330.7352 498436.7944 1046566.278 531687.0431 914378.7328 763862.9567 679472.8056 1.521487637 1.433712651 0.830542048 0.733564008 1.540262199 0.782499371 1.345717923 1.124199453 1 19.37405629 3.871001831 6.656801133 1.07305625 1.488200218 0.334620817 0.249594163 0.248633128 12.32293221 0.06020899 0.109560491 7430.222705 -3.871001831 0.415143968 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK 31 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 119.97 4.74E-06 174942000 161471 235240 173691 209178 137706 205743 248420 157068 20468.4 FALSE TRUE 153838.5858 259211.2234 181654.9042 188151.03 161721.8828 198618.0683 210518.9665 143314.2933 23642.53493 6.506856657 10.96376612 7.683393708 7.958158064 6.840293702 8.400878708 8.904246818 6.061714349 1 14.52909711 0.900502288 3.401832062 1.003777823 8.305425109 0.774867283 1.2214337 0.184152602 4.675708931 1.140770468 0.295423033 7.952474557 -0.900502288 7.301647286 KHLEINPDHPIVETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KHLEINPDHPIVETLR 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;; 245.96 1.50E-20 5743763000 2790040 2558370 3014070 3119330 2900750 3130230 3715350 2923580 575001 FALSE TRUE 2658160.339 2819070.812 3152268.091 2805769.022 3406639.882 3021829.35 3148505.12 2667575.836 664169.2184 4.002233565 4.244506872 4.746182153 4.22447916 5.129174595 4.549788317 4.740516473 4.016409919 1 19.34119134 0.819543864 4.450081701 1.000057539 4.486855926 0.922294548 0.318449025 0.535877637 12.97790134 0.321319544 0.081622873 6.599998913 -0.819543864 3.486798388 KHLEINPDHSIIETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KHLEINPDHSIIETLR 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 284.25 4.15E-36 5373090000 4145000 3502920 4343640 4475430 4260140 4353090 5455440 4383530 981700 FALSE TRUE 3949074.065 3859871.53 4542800.19 4025551.274 5003107.067 4202341.402 4623112.432 3999684.875 1133937.022 3.482622039 3.403955824 4.00621913 3.550066004 4.412156028 3.705974247 4.077045146 3.527254862 1 20.11290909 0.951605898 20.85353749 0.999999997 3.774661825 0.892491252 0.303557565 453.1567359 195270.8134 0.29958075 0.074895188 8.945526321 -0.951605898 2.774661828 KHNGVGGS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHNGVGGSPPK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 KHNGVGGS(1)PPK;KHNGVGGS(1)PPK 91.969 0.0063367 114887000 139123 160244 144966 200755 77968 181878 163905 154774 38008 TRUE FALSE 132546.9315 176573.0458 151612.8345 180574.726 91565.59451 175579.5193 138898.2819 141221.1681 43902.08652 3.019148792 4.021973892 3.453431181 4.113124006 2.08567751 3.999343384 3.163819602 3.216730211 1 15.42200189 2.762061172 24.96659253 2.961404028 3.632260169 0.203322149 0.85560098 1511.067514 1605330.021 0.234162256 0.248238828 578.1774804 -2.762061172 0.670856142 KHNMCGETEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 KHNMCGETEEEK 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;;;;; 192.05 2.97E-06 2227135000 5281719 6660632 4824412 6660263 2616041 6308827 5161062 5970305 1207555 FALSE TRUE 5032062.61 7339357.973 5045616.062 5990760.71 3072277.722 6090350.739 4373647.202 5447513.444 1394816.462 3.607687998 5.261880809 3.617405013 4.29501721 2.202639419 4.366417306 3.135643521 3.905541404 1 20.41164387 2.787226252 23.97224739 3.178858678 4.275800736 0.254929905 1.027036901 345.0929503 169988.6645 0.27975392 0.296723063 612.6694871 -2.787226252 1.096942058 KHNMCGETEEEKIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHNMCGETEEEKIR 14 2 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 169.04 2.04E-06 127089000 265740 222970 283640 287540 179103 279860 332560 310170 100134 FALSE TRUE 253178.9968 245690.8965 296645.1746 258635.9329 210338.5065 270168.378 281821.8641 283009.8705 115662.2693 2.188950626 2.124209545 2.564753193 2.236130542 1.818557666 2.335838469 2.436592899 2.446864238 1 16.81955879 2.976399215 24.80709415 2.138174416 2.26157215 0.0426271 0.439326639 3845.568362 4042129.095 0.122651076 0.130890329 947.107368 -2.976399215 0.123397734 KHNMCGETEEEKIRVDIIENQVMDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHNMCGETEEEKIRVDIIENQVMDFR 26 3 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 67.614 0.020513 65556000 75546 36506 89151 76304 71128 86674 122570 87979 33643 FALSE TRUE 71975.0903 40226.0029 93238.66153 68633.77695 83532.70068 83672.45765 103869.6953 80275.09235 38860.18462 1.85215513 1.035146984 2.399336556 1.766172179 2.149570351 2.153166756 2.672907923 2.065741405 1 15.24600513 3.731293954 24.95707861 2.132632617 1.44365105 0.178236732 0.485239082 612.033929 2102008.453 0.118133343 0.187140601 5386.34236 -3.731293954 -0.688981568 KHPDADSLYVEEVDVGEIAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHPDADSLYVEEVDVGEIAPR 21 1 Q12904;Q12904-2;A0A5F9ZHC5 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 171.85 4.13E-12 501280000 442737 376044 433262 450418 402225 412757 458797 507289 381076 FALSE TRUE 421809.6994 414363.3111 453127.4913 405141.1269 472372.9127 398463.1216 388799.0913 462868.0859 440171.3198 0.958285287 0.941368264 1.029434384 0.920416912 1.073156954 0.905245534 0.883290378 1.051563482 1 18.74770562 3.4520287 0.002155375 1.923421507 4.78E-05 0 0.063991035 876790.0818 482.97826 213474.2553 217519.8297 2831.57911 -3.4520287 -1.923373737 KHPDASVNFSEFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KHPDASVNFSEFSK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;;; 177.62 1.93E-06 5793334000 5438810 4959860 4484890 5573170 3703897 5148960 5653250 5591360 3941730 FALSE TRUE 5181728.23 5465275.373 4690526.643 5012944.363 4349855.464 4970650.224 4790742.883 5101750.877 4552993.357 1.13809264 1.200369723 1.030207223 1.101021673 0.955383662 1.091732369 1.05221829 1.120526756 1 22.11838392 3.736059606 24.99911409 1.052993057 1.169231184 0.487120623 0.05073149 153.5687001 1535017.854 0.012056166 0.019685378 5445.773894 -3.736059606 0.116238127 KHPEVDVLINFASLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KHPEVDVLINFASLR 15 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 169.09 7.90E-07 466420000 1631190 1439780 1242670 1392330 1415160 1378870 1815330 1586520 1233790 FALSE TRUE 1554086.881 1586495.219 1299647.649 1252370.343 1661963.456 1331119.386 1538368.068 1447595.898 1425119.852 1.090495567 1.113236348 0.911956736 0.87878247 1.16619206 0.934040309 1.079465749 1.015771338 1 20.44265182 3.779601648 24.73172626 1.00397402 1.101866008 0.211900634 0.082635795 646.0799603 389331.8317 0.020157635 0.036339089 6020.071486 -3.779601648 0.097891988 KHPS(ph)SPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.5)S(0.5)PAR;KHPS(0.842)S(0.158)PAR;KHPS(0.678)S(0.322)PAR;KHPS(0.664)S(0.336)PAR;KHPS(0.639)S(0.361)PAR 102.52 0.0030311 1081415000 1029978 850408 780863 924437 1256854 821026 1395648 1094135 1306667 TRUE FALSE 981292.9812 937065.542 816666.3409 831510.8364 1476048.94 792593.6638 1182716.265 998326.739 1509298.245 0.650165058 0.620861745 0.541090102 0.550925464 0.977970355 0.525140519 0.783619983 0.661450938 1 20.52544649 -5 0.166065722 2.322124759 0.575900148 0.412955075 0.130858998 122.9397924 1.148570724 53.25683909 0.452479326 1.00E-05 5 -1.74622461 KHPSS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.498)S(0.502)PAR;KHPS(0.367)S(0.633)PAR;KHPS(0.261)S(0.739)PAR;KHPS(0.205)S(0.795)PAR 118.9 0.0011005 1003957000 1097954 832459 723627 959203 1253198 802829 1408106 1111627 1277312 TRUE FALSE 1046055.89 917287.5185 756806.0137 862782.0921 1471755.334 775026.8304 1193273.568 1014287.047 1475391.021 0.709002478 0.621725024 0.512952839 0.584781986 0.997535781 0.525302662 0.808784621 0.687469987 1 20.49266593 -1.105066441 0.255660203 1.221186946 0.619791742 0.360706722 0.13927735 17.62744581 1.022623251 2.918837367 0.204826969 0.078511551 1.105066441 -0.601395204 KHQEVQDQDPVFQGSDSSGYQS(ph)DHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHQEVQDQDPVFQGSDSSGYQSDHKK 26 2 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 KHQEVQDQDPVFQGS(0.001)DS(0.029)S(0.029)GY(0.012)QS(0.929)DHKK 93.125 0.0042627 59889000 44858 43930 39052 53481 24619 55215 53688 54304 14844 TRUE FALSE 42737.65124 48406.51694 40842.57283 48104.98827 28912.54581 53302.89071 45496.90955 49548.85388 17145.93171 2.492582612 2.823207147 2.382056194 2.805621129 1.686262741 3.108777733 2.653510485 2.889831519 1 14.06557868 -1.131060619 5.651983087 0.999980184 2.615311617 0.63214698 0.384761068 8.56E-05 1.32E-05 0.332087036 0.07827271 0.073950205 1.131060619 1.615331434 KHRS(ph)PT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHRSPTPK 8 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 KHRS(1)PT(1)PK 78.653 0.056839 165440000 424190 386380 370640 447640 227770 441490 492610 360190 228280 TRUE FALSE 404139.3794 425752.5613 387634.2106 402642.3767 267493.0159 426201.0906 417453.2971 328649.8541 263680.4965 1.532685901 1.614653214 1.470090567 1.527008566 1.01445886 1.616354248 1.583178516 1.246394248 1 18.00843134 -3.307923219 0.196416966 2.34E-14 1.57546704 0.409235296 0.180678016 66.62671419 1.194403539 27.78799402 0.471781588 0.000492127 3.307923219 1.57546704 KHRS(ph)PTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHRSPTPK 8 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 KHRS(0.999)PT(0.001)PK 62.303 0.042001 83562000 120820 83157 106920 113840 105350 137090 171670 137910 90247 TRUE FALSE 115109.078 91630.79284 111822.3878 102396.5869 123723.0066 132342.5389 145478.5886 125833.8693 104242.0438 1.104248092 0.879019534 1.072718681 0.982296424 1.186882011 1.269569687 1.395584576 1.20713164 1 16.66957775 2.600015113 3.069489413 1.265576761 1.000782624 0.39944387 0.116749326 0.194284817 3.493330994 0.037885363 0.034965921 398.1210248 -2.600015113 -0.264794137 KHS(ph)PS(ph)PPPPTPTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(0.999)PPPPT(0.001)PTESR 126.69 8.44E-05 2976353000 2246550 2013630 2111910 2405320 1501481 2397850 2678990 1879770 1507454 TRUE FALSE 2140360.034 2218821.186 2208743.162 2163532.664 1763338.811 2314811.853 2270260.872 1715167.374 1741222.267 1.229228499 1.274289462 1.26850156 1.242536754 1.012701735 1.329417787 1.303831748 0.985036434 1 20.73166894 1.230819811 24.97880878 0.992518007 1.241764451 0.584721593 0.085665799 130.0826874 419746.6287 0.075034647 0.020158321 17.01452429 -1.230819811 0.249246445 KHS(ph)VNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHSVNEK 7 1 E9PNQ0;E9PR18;Q96PZ2 E9PNQ0 FAM111A Protein FAM111A 1 KHS(1)VNEK 53.683 0.084654 34228000 53640 48650 46888 60296 31390 56957 58497 66780 34599 TRUE FALSE 51104.5435 53607.49031 49037.86118 54234.93153 36864.40606 54984.56481 49572.20828 60932.38918 39964.43621 1.278750518 1.341379871 1.227037482 1.357079861 0.922430279 1.37583737 1.240408047 1.524665301 1 15.28642912 3.527931555 2.196668827 1.242882094 1.308058085 0.024533065 0.174922219 1.472110286 14.07432889 0.04708748 0.078616896 3372.341559 -3.527931555 0.065175991 KHSQFIGYPITLFVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHSQFIGYPITLFVEK 16 1 P07900;P07900-2;G3V2J8;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 73.707 0.022277 92548000 123570 94960 96983 105330 101900 109090 138970 121140 76379 FALSE TRUE 117729.091 104636.532 101429.7665 94742.02829 119671.3277 105312.1859 117767.5741 110532.3394 88223.46523 1.334441927 1.186039697 1.149691482 1.073886953 1.356456895 1.193698135 1.334878128 1.252867807 1 16.42887481 -1.096521059 3.936177492 0.99993716 1.238351774 0.404350903 0.08965986 4879466.166 2721124.528 2553.539573 0.020476419 0.08007168 1.096521059 0.238414614 KHSQFIGYPITLYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KHSQFIGYPITLYLEK 16 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 104.45 0.00088286 111480000 666810 637270 496710 600830 412850 612930 662170 624070 268290 FALSE TRUE 635291.2128 702208.5375 519484.6448 540433.4269 484850.9093 591704.0804 561143.8049 569423.1224 309895.043 2.050020571 2.265956018 1.676324474 1.743924077 1.564564908 1.909369297 1.810754375 1.837470896 1 18.24142015 -1.869910961 0.15598526 5.79E-18 2.239852318 0.674698415 0.189547101 24.86206596 0.588364545 11.0441932 1.113616957 0.013492395 1.869910961 2.239852318 KIADDKYNDTFWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIADDKYNDTFWK 13 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 162.46 2.27E-05 1755050000 1795940 1308860 1767100 1749890 1183800 2055320 2306180 1979310 1394870 FALSE TRUE 1711049.475 1442234.322 1848123.283 1573987.733 1390254.345 1984143.753 1954329.885 1805991.123 1611179.316 1.061985751 0.895142029 1.147062444 0.976916546 0.862879961 1.231485368 1.212980992 1.120912555 1 20.61968564 2.225846437 24.99999592 1.16745229 0.989333478 0.348552553 0.100859016 208.9943296 410944.4882 0.035143135 0.026123675 168.2079185 -2.225846437 -0.178118812 KICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7;Q9UER7-2 Q9UER7-3 DAXX Death domain-associated protein 6 1 KICTLPSPPS(1)PLASLAPVADSSTR 157.73 3.12E-09 309880000 184100 148790 169330 201170 174870 172550 191470 182060 196060 TRUE FALSE 175397.9579 163951.8702 177093.948 180948.0094 205367.2726 166574.5502 162257.7349 166117.8612 226463.9835 0.774507077 0.723964436 0.781996083 0.799014513 0.906842976 0.735545439 0.716483621 0.733528832 1 17.7889221 -2.415216454 2.280011324 3.059348389 0.767192698 0.628389141 0.055138582 3637913.483 557893.2588 38314105.34 0.014312054 0.003844001 2.415216454 -2.29215569 KIDKYTEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIDKYTEVLK 10 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 121.68 0.00028607 897890000 3454500 1959900 2599800 1826000 1325200 1849700 2371800 2126700 1672500 FALSE TRUE 3291212.631 2159616.038 2719003.402 1642447.011 1556314.46 1785644.425 2009938.349 1940474.874 1931862.758 1.703647227 1.117893095 1.407451637 0.850188247 0.805603014 0.924312257 1.040414667 1.004457933 1 20.88156118 4.855150145 0.666615625 0.949090585 2.269046099 0.716625736 0.144332383 1.854107458 0.559106532 0.059973909 1.927792792 71639.1039 -4.855150145 1.319955514 KIDS(ph)PPIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIDSPPIRR 9 2 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 KIDS(1)PPIRR 52.693 0.076431 35090000 85195 74739 75727 94100 62864 92005 93933 100060 75705 TRUE FALSE 81168.00119 82354.98907 79199.15785 84640.88922 73827.4617 88818.84378 79601.79565 91298.21595 87444.94475 0.928218337 0.941792454 0.905703104 0.967933475 0.844273639 1.015711589 0.910307576 1.044065111 1 16.41608736 1.238612722 25 1.02203258 0.932205419 0.416026693 0.045021408 1.183783438 570408.5391 0.029944835 0.009335151 17.32258584 -1.238612722 -0.089827161 KIDTHPS(ph)PSHSSTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KIDTHPSPSHSSTVK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594 Q8NI27 THOC2 THO complex subunit 2 1 KIDT(0.001)HPS(0.984)PS(0.015)HSSTVK;KIDT(0.007)HPS(0.966)PS(0.027)HSSTVK;KIDTHPS(0.967)PS(0.032)HSSTVK 187.73 1.54E-07 1191960000 2413550 1875890 2221800 2820580 2234180 2444340 3377560 3009650 235516 TRUE FALSE 2299466.275 2067045.324 2323671.728 2537049.94 2623820.285 2359691.893 2862251.189 2746109.091 272038.6184 8.452720014 7.598352527 8.541698017 9.326065374 9.645028709 8.674106296 10.52148848 10.09455608 1 18.05345194 -0.117035124 9.015025727 1 9.0302838 0.89881176 0.854488184 8196694.415 909225.8257 0.961276321 0.233143753 0.76377401 0.117035124 8.0302838 KIDYFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KIDYFER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 124.23 0.0066809 1144810000 2996950 2529020 2318430 2844660 2569810 2717770 3263970 2873110 2855150 FALSE TRUE 2855290.113 2786730.013 2424732.309 2558709.372 3017984.05 2623652.943 2765991.43 2621525.257 3297912.08 0.865787214 0.844998273 0.73523255 0.775857364 0.91511962 0.795549693 0.838709875 0.794904532 1 21.65312151 -1.487315872 3.051523362 1.004773503 0.824482094 0.557392753 0.050095885 81191930.08 87184975.33 3221763.339 0.012011216 0.03255998 1.487315872 -0.180291409 KIEDLGAAMEEALILDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIEDLGAAMEEALILDNK 18 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 114.55 0.00034461 37650000 199640 178240 164000 218840 128100 185130 206400 200550 128440 FALSE TRUE 190203.4128 196402.8586 171519.5622 196841.7874 150440.5994 178718.9017 174909.8892 182988.7788 148357.8192 1.282058565 1.323845684 1.156120811 1.326804266 1.014038898 1.204647673 1.178973175 1.233428611 1 17.17872144 3.057549303 0.0279673 2.14E-12 2.449707478 0.418813174 0.086372783 330.0843203 2.943603443 116.3676676 141.0561023 1141.692908 -3.057549303 2.449707478 KIEDNNTLVFIVDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIEDNNTLVFIVDVK 15 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 135.45 4.64E-05 17525000 116280 103040 110110 127410 76657 129220 140470 133990 85651 FALSE TRUE 110783.6748 113539.8931 115158.6524 114602.5047 90025.95653 124745.079 119038.7216 122257.1253 98933.31964 1.119781235 1.147640588 1.164002713 1.158381273 0.909965994 1.260900569 1.203221746 1.235752785 1 16.59416887 KIEEAMDGSET(ph)PQLFTVLPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KIEEAMDGSETPQLFTVLPEKR 22 2 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 KIEEAMDGS(0.001)ET(0.999)PQLFTVLPEKR;KIEEAMDGSET(1)PQLFTVLPEKR;KIEEAMDGS(0.224)ET(0.776)PQLFTVLPEKR;KIEEAMDGSET(1)PQLFTVLPEKR 213.37 1.25E-22 907300000 1171600 924350 1081290 1122410 828040 1111600 1245120 1287310 1005750 TRUE FALSE 1116220.79 1018542.316 1130868.216 1009583.214 972449.9138 1073105.013 1055154.076 1174586.312 1161716.573 0.96083745 0.876756293 0.973445883 0.869044341 0.837080176 0.923723598 0.908271518 1.011078209 1 20.1478267 1.240948363 24.86008738 1.005539144 0.907093261 0.503284453 0.040688946 44.09361886 459126.8547 0.029023985 0.009466574 17.41599789 -1.240948363 -0.098445883 KIEEIKDFLLTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEEIKDFLLTAR 13 2 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 195.2 2.10E-07 1848900000 4570900 4168400 3986100 4553200 3076600 4577600 5237300 4838300 3618700 FALSE TRUE 4354842.616 4593164.699 4168866.628 4095503.685 3613158.066 4419076.564 4438253.695 4414632.803 4179869.514 1.0418609 1.098877533 0.997367648 0.979816157 0.864418866 1.057228353 1.061816327 1.056165219 1 21.99502647 -1.529444976 8.128986363 0.999996115 1.02597204 0.000778235 0.064798036 4.77E-06 2.76E-07 0.065557001 0.015449622 0.029549833 1.529444976 0.025975925 KIEFPLPDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEFPLPDRR 10 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 110.64 0.0010459 1017940000 1829200 1365760 1165740 1476940 1774700 1410040 2099600 1638960 1714640 FALSE TRUE 1742737.341 1504932.497 1219190.332 1328475.185 2084207.118 1361209.961 1779267.458 1495443.974 1980537.614 0.879931453 0.759860598 0.615585548 0.670764936 1.052344123 0.687293163 0.898375999 0.755069716 1 20.91746067 KIEFPMPNEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEFPMPNEEAR 12 1 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 84.753 0.019336 302450000 360100 355010 367850 427620 487610 372880 423480 388640 509340 FALSE TRUE 343078.7866 391185.9226 384716.2864 384634.8252 572649.0296 359967.0721 358870.3483 354608.6213 588325.8459 0.583144169 0.664913713 0.653917024 0.653778561 0.973353514 0.611849836 0.609985692 0.602741871 1 19.16625589 -2.192325851 2.383512301 1.962234793 0.665163074 0.465015379 0.111429024 8360676.674 2078913.153 43289373.9 0.02647021 0.006422057 2.192325851 -1.297071719 KIEFSLPDLEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KIEFSLPDLEGR 12 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 142.85 9.90E-05 508053000 1056275 1027206 989111 1102058 914149 1016780 1120518 1152653 932277 FALSE TRUE 1006346.974 1131879.459 1034462.718 991277.0361 1073576.296 981568.6536 949562.3994 1051720.593 1076849.756 0.934528674 1.05110249 0.960637928 0.920534207 0.996960152 0.911518667 0.88179655 0.976664188 1 20.03838555 3.484699567 23.92795492 0.938013448 0.994991355 0.109358171 0.046883968 284.1378344 897144.4781 0.012500465 0.017687931 3052.808534 -3.484699567 0.056977907 KIEFVVVGPEAPLAAGIVGNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEFVVVGPEAPLAAGIVGNLR 22 1 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 ; 156.29 2.06E-08 124719000 456480 361130 362120 475750 425040 415820 563680 461590 519520 FALSE TRUE 434903.0951 397929.5576 378723.5602 427926.7061 499166.8414 401420.0491 477680.2633 421170.7326 600084.5083 0.724736415 0.66312253 0.631117043 0.713110737 0.831827575 0.668939197 0.796021655 0.701852367 1 19.19480616 -5 0.201094924 2.314446449 0.669439847 0.706894323 0.058153548 73.16045892 0.724370253 38.55480347 0.127710173 1.00E-05 5 -1.645006601 KIEIDNGDELTADFLYEEVHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEIDNGDELTADFLYEEVHPK 22 1 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ; 231.89 5.27E-27 113160000 94262 89155 90493 116002 61956 105543 111928 123555 71675 FALSE TRUE 89806.42207 98239.99586 94642.19356 104341.2586 72761.10678 101888.0194 94851.3279 112735.8692 82789.99293 1.084749725 1.186616792 1.143159822 1.260312447 0.878863546 1.230680374 1.145685904 1.361708888 1 16.33716878 KIEIGDGAELTAEFLYDEVHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KIEIGDGAELTAEFLYDEVHPK 22 1 Q6IBS0 Q6IBS0 TWF2 Twinfilin-2 0 ;;; 195.13 7.64E-19 187126000 277508 233754 226498 271901 179871.8 262853 284731 290137 168332.7 FALSE TRUE 264390.7468 257573.7984 236883.1573 244568.9949 211241.385 253750.3347 241290.0565 264731.0662 194436.8754 1.359776772 1.324716815 1.218303662 1.257832365 1.086426556 1.305052523 1.240968597 1.361527054 1 17.56894233 -4.168455804 0.254921399 2.70E-40 1.296130181 0.491304999 0.083208404 103.5065098 1.510867839 54.31909534 0.115192769 6.78E-05 4.168455804 1.296130181 KIEISQHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEISQHAK 9 1 Q6P4E4;E9PEL3;P61513;G5E9R3;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 119.53 0.00052743 2206200000 4932300 3304100 3329400 4556200 4501800 4142500 6547800 5222000 5258800 FALSE TRUE 4699159.954 3640791.546 3482056.283 4098202.12 5286912.495 3999044.186 5548812.851 4764733.996 6074307.846 0.773612414 0.59937554 0.573243301 0.674678041 0.870372827 0.658353888 0.91348891 0.784407725 1 22.5342886 1.535137279 0.57503917 0.985229139 0.654227071 0.544894804 0.093370689 0.541373804 0.418490254 0.087585874 0.047311314 34.28761513 -1.535137279 -0.331002068 KIEMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KIEMVR 6 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;; 135.35 0.021868 3644020000 5749050 4612500 4497810 5623390 4744200 4930480 6047570 5533520 5413860 FALSE TRUE 5477303.8 5082518.994 4704039.037 5058116.153 5571586.978 4759736.241 5124902.125 5048975.654 6253413.759 0.875890196 0.812759109 0.752235374 0.808856786 0.890967269 0.761142062 0.819536708 0.807395104 1 22.57621255 -1.20336202 5.798630482 1.000004391 0.817194995 0.64639697 0.042739369 2.33E-06 3.20E-07 0.039773196 0.009374407 0.062609175 1.20336202 -0.182809396 KIEPELDGSAQVTSHDASTNGLINFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KIEPELDGSAQVTSHDASTNGLINFIK 27 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 ;; 222.4 1.52E-34 3410231000 2172747 1685235 1952090 2123528 1519654 2065860 2579123 2311613 1749974 FALSE TRUE 2070045.555 1856962.362 2041595.257 1910066.931 1784681.176 1994318.75 2185630.418 2109195.911 2021351.03 1.024090088 0.918673864 1.010015196 0.944945684 0.882915016 0.986626628 1.081272072 1.043458499 1 20.94688845 1.947168101 6.935058975 1.04716249 0.957172191 0.432380292 0.044509064 0.214850269 23.50762861 0.018277657 0.011435436 88.54582749 -1.947168101 -0.0899903 KIEQVDKEDEITEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIEQVDKEDEITEK 14 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 ; 165.45 2.23E-06 625670000 1077120 943450 876590 1175500 495070 1182340 1113420 1224120 570240 FALSE TRUE 1026206.672 1039588.628 916782.5186 1057336.507 581410.0513 1141395.269 943547.3296 1116929.563 658669.9068 1.557998417 1.578315051 1.391869446 1.605260079 0.882703225 1.73287903 1.432504081 1.695734922 1 19.32919611 3.7428212 23.11981167 1.418899784 1.568156758 0.06033324 0.273669855 381.6140271 2070774.703 0.064046613 0.11026424 5531.223413 -3.7428212 0.149256975 KIESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIESER 6 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 100.45 0.060363 115490000 316400 269650 253310 316890 267990 296200 345600 314850 295240 FALSE TRUE 301444.399 297127.6416 264924.5141 285035.6151 314727.3712 285942.5197 292872.3726 287280.0649 341024.3113 0.883938151 0.87127994 0.776849348 0.83582198 0.922888371 0.838481335 0.858802035 0.842403475 1 18.37951507 -1.534209005 2.842463549 1.006820796 0.855927689 0.599692537 0.037501372 11496007.42 11472244.74 598003.2559 0.009288296 0.029227455 1.534209005 -0.150893107 KIESFGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIESFGSPK 9 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KIES(0.002)FGS(0.998)PK 77.912 0.010842 0 928010 789340 809080 1018000 507430 971260 993990 1011700 550500 TRUE FALSE 884144.8064 869774.6434 846177.1183 915668.7059 595925.6313 937625.0227 842338.5696 923110.1846 635868.7284 1.390451782 1.367852521 1.330741835 1.440027894 0.937183423 1.474557532 1.324705135 1.451730748 1 19.27836943 -1.481778285 2.80426953 0.98800322 1.34077128 0.331790864 0.151476461 19089227.28 20589102.94 1774011.972 0.033157403 0.032977803 1.481778285 0.35276806 KIESFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIESFGSK 8 1 P30405 P30405 PPIF "Peptidyl-prolyl cis-trans isomerase F, mitochondrial" 0 ; 127.76 0.0018637 2423200000 3511100 2328920 2621310 2844400 2507620 2789900 3740700 3499900 2987700 FALSE TRUE 3345137.261 2566239.596 2741499.656 2558475.508 2944948.134 2693285.063 3169987.512 3193430.202 3451017.257 0.969319193 0.743618303 0.794403346 0.741368506 0.853356537 0.780432221 0.918566114 0.925359094 1 21.71859026 1.407929006 1.626343631 0.98489922 0.815087073 0.475579079 0.067212286 0.319670447 1.564319129 0.05952243 0.018790319 25.58167671 -1.407929006 -0.169812148 KIFDIDEAEEGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIFDIDEAEEGVK 13 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 195.54 2.39E-07 113660000 651280 681170 559540 763270 389870 683650 665050 755990 417350 FALSE TRUE 620495.2851 750581.9974 585195.4625 686544.6495 457863.2046 659975.0291 563584.408 689791.5078 482070.5065 1.287146334 1.556996305 1.213920899 1.424158168 0.949784727 1.369042537 1.169091244 1.430893404 1 18.87888464 -4.753450517 0.065457325 2.74E-08 1.718175977 0.219153539 0.169410461 422.7153596 2.095910648 67.89082823 10.39919731 1.76E-05 4.753450517 1.718175949 KIFTFAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIFTFAEK 8 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 ; 98.943 0.011488 293910000 918030 732000 629800 818690 941060 843850 1307490 1050250 1071530 FALSE TRUE 874636.5413 806591.6322 658676.953 736393.7258 1105180.566 814627.2629 1108008.387 958284.5423 1237697.4 0.70666428 0.651687264 0.532179314 0.59497073 0.892932769 0.658179667 0.895217512 0.774247843 1 20.23922721 1.547252511 0.573915418 0.982635262 0.63444517 0.561768541 0.097653464 0.538967546 0.413769019 0.091510611 0.049752297 35.25758089 -1.547252511 -0.348190093 KIFVGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIFVGTK 7 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 78.334 0.07574 0 3211700 2743200 2566100 3050900 2829800 3106000 4555900 3420900 3901000 FALSE TRUE 3059889.306 3022735.199 2683758.223 2744217.736 3323316.224 2998438.441 3860813.78 3121347.861 4505947.156 0.679077938 0.670832367 0.595603572 0.609021287 0.737539991 0.665440214 0.856826245 0.692717369 1 22.10339896 0.712986723 0.466097322 1.013213414 0.641788065 0.729624928 0.063198814 0.767046892 0.363922224 0.090587695 0.036078046 5.164005825 -0.712986723 -0.371425349 KIGDEYFTFITDCKDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIGDEYFTFITDCKDPK 17 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 166.91 1.29E-09 1695650000 1430730 1240170 1355450 1534250 744878 1618510 1640450 1675680 852317 FALSE TRUE 1363102.228 1366544.733 1417598.723 1380024.275 874784.4874 1562460.593 1390169.224 1528948.576 984489.9673 1.384577064 1.388073803 1.439932117 1.401765707 0.888566178 1.587076197 1.412070483 1.553036218 1 19.90901698 KIGELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 127.02 0.0062459 1017290000 2092400 1775070 1855180 2411820 2316470 2268640 2863400 2627500 2746200 FALSE TRUE 1993496.399 1955951.651 1940241.838 2169379.271 2720461.635 2190076.428 2426535.74 2397422.171 3172066.67 0.628453499 0.616617447 0.611664899 0.683900907 0.857630661 0.690425724 0.764969968 0.755791861 1 21.59699166 -5 0.081051288 2.067764024 0.377518655 0.781128217 0.056607777 106.3078652 0.608933747 19.99335063 1.813297218 1.00E-05 5 -1.690245369 KIGGIFAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIGGIFAFK 9 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 145.17 0.0025904 0 255600 196120 198250 236540 232620 219980 303530 266760 284340 FALSE TRUE 243518.2946 216104.851 207339.9586 212762.5498 273188.8543 212362.0374 257220.9238 243401.0802 328433.995 0.741452768 0.657985636 0.631298714 0.647809158 0.831792258 0.646589697 0.783173873 0.741095879 1 18.32524394 -0.197036306 0.415872674 1.05612577 0.679936657 0.702283775 0.061303964 2.994135375 0.596431053 0.317647936 0.036575586 0.635277822 0.197036306 -0.376189113 KIHPQTIIAGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIHPQTIIAGWR 12 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 163.99 3.80E-05 1957940000 3732600 2937600 2904000 3222000 3860000 3091600 4401800 3455900 4036100 FALSE TRUE 3556167.395 3236944.78 3037151.272 2898118.439 4533182.778 2984537.117 3730224.565 3153283.075 4661997.774 0.762799033 0.694325681 0.65146991 0.621647323 0.972369142 0.640184157 0.800134351 0.676380219 1 22.15251689 -4.999999936 0.309964837 3.396259192 0.716600247 0.405345004 0.103092262 283.9532039 2.571891792 444.2849851 0.087376969 1.00E-05 4.999999936 -2.679658945 KIHSQEEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KIHSQEEALR 10 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;; 192.38 4.47E-07 1541880000 1001820 673890 669770 743960 914840 761060 1093140 842160 906340 FALSE TRUE 954465.954 742560.1571 700479.617 669175.7274 1074387.806 734704.3014 926361.4161 768416.0058 1046890.578 0.911715106 0.70930064 0.669104901 0.639203123 1.026265618 0.701796651 0.884869379 0.733998397 1 19.99767923 2.766503602 24.99932422 0.850314443 0.744911595 0.223943853 0.122998692 1371.970715 1227437.992 0.035569071 0.037719216 584.1220511 -2.766503602 -0.105402848 KIIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.967)PT(0.032)AT(0.001)SQLPLESDAVECLNYQHYK 135.22 2.59E-09 101930000 117860 78716 101150 105100 95524 102270 133970 121010 104080 TRUE FALSE 112288.9914 86737.24989 105787.8276 94535.14832 112183.3554 98728.36426 113530.416 110413.7229 120220.1948 0.934027694 0.721486519 0.879950558 0.786349984 0.933149006 0.821229448 0.944353951 0.91842908 1 16.87531974 1.471747472 0.700260735 0.996147874 0.828458374 0.380871646 0.065870404 0.589089416 0.63312506 0.056716098 0.02541006 29.63107938 -1.471747472 -0.1676895 KIIPTLEEGLQLPSPT(ph)ATSQLPLESDAVECLNYQHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.484)PT(0.495)AT(0.017)S(0.003)QLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.188)PT(0.8)AT(0.011)SQLPLESDAVECLNYQHYK 251.09 2.68E-51 2001770000 3450500 2617970 3078980 3242690 2839160 3245450 4301430 3637930 2907920 TRUE FALSE 3287401.703 2884744.119 3220154.279 2916728.64 3334308.605 3133059.253 3645167.852 3319373.563 3358865.382 0.978723863 0.858844816 0.958702988 0.868367234 0.992688967 0.932773093 1.085237852 0.988242512 1 21.67954255 2.139761307 1.790616132 1.028646535 0.918922563 0.384972527 0.051499844 0.293907617 1.829969211 0.025699867 0.01469292 137.9625799 -2.139761307 -0.109723971 KIKDPDASKPEDWDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIKDPDASKPEDWDER 16 3 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 136.01 8.65E-06 1117650000 1549030 1185010 1397640 1463980 865985 1566510 1803480 1707280 952331 FALSE TRUE 1475810.422 1305763.866 1461723.176 1316817.949 1017012.51 1512261.366 1528326.003 1557781.512 1100013.628 1.341629217 1.187043354 1.328822789 1.197092396 0.924545373 1.374766028 1.389370063 1.416147467 1 20.06908997 KIKNENTEGS(ph)PQEDGVELEGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIKNENTEGSPQEDGVELEGLK 22 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KIKNENT(0.169)EGS(0.831)PQEDGVELEGLK;KIKNENT(0.008)EGS(0.992)PQEDGVELEGLK 120.57 1.55E-05 470870000 872440 677940 967820 923150 499720 1055490 1152750 1179840 619120 TRUE FALSE 831201.4902 747022.8568 1012195.504 830353.2081 586871.0098 1018938.117 976876.8158 1076526.955 715129.9676 1.162308291 1.044597333 1.415400767 1.161122098 0.820649443 1.42482928 1.366012977 1.505358471 1 19.44784594 2.140924755 21.86147033 1.358300554 1.12873006 0.202881317 0.19461217 7.701161271 1712.625001 0.06725972 0.049674647 138.3326686 -2.140924755 -0.229570493 KILDSVGIEADDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KILDSVGIEADDDR 14 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 130.29 0.00010086 248300000 264030 269340 177140 229050 222620 195600 238600 224940 254370 FALSE TRUE 251549.8252 296786.0522 185262.0442 206025.4588 261444.8575 188826.323 202197.1878 205243.0611 293816.4005 0.856146303 1.010107168 0.63053677 0.701204761 0.889823907 0.642667743 0.688175294 0.698541881 1 18.1645554 3.74278595 24.98314278 0.731858445 0.933126738 0.275420624 0.120592932 350.0351148 2069646.152 0.02830287 0.048843892 5530.77448 -3.74278595 0.201268292 KILDSVGIEADDDRLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KILDSVGIEADDDRLNK 17 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;; 245.66 7.61E-21 2274830000 5128050 3979860 3610830 4625380 3384710 4866860 5887270 5533440 3863800 FALSE TRUE 4885657.239 4385412.259 3776390.127 4160428.015 3975002.352 4698319.418 4989058.834 5048902.659 4462978.37 1.094707801 0.982620101 0.846159182 0.932208868 0.890661353 1.052731837 1.117876543 1.131285487 1 22.08957538 2.051372398 6.765763795 1.093642902 0.961831901 0.420149678 0.073189154 0.212212066 21.60318922 0.029971705 0.021917216 112.5569711 -2.051372398 -0.131811001 KILGYINTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KILGYINTGK 10 1 P05091;P05091-2;S4R3S4 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 120.96 0.0048806 0 1191500 910860 979570 1004000 856610 888590 1050300 1021500 949440 FALSE TRUE 1135180.156 1003677.67 1024484.253 903076.0125 1006002.513 857817.9055 890057.4449 932052.0447 1096674.306 1.035111473 0.915201226 0.934173663 0.823467831 0.917321129 0.782199328 0.81159688 0.849889561 1 20.0647037 4.331151256 0.760649712 0.846488988 1.082806883 0.371877147 0.064660799 1.35654096 0.872192501 0.023280486 0.247196134 21436.37057 -4.331151256 0.236317895 KINLELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KINLELR 7 1 Q9BTT0;Q5TB19;Q9BTT0-2;Q5TB25;E9PPH5;E9PLC4;E9PI45 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 107.9 0.011825 138460000 375240 279880 213190 267320 419590 317080 531440 410320 475270 FALSE TRUE 357503.1489 308400.0902 222964.9724 240448.4857 492766.3632 306099.4401 450359.0674 374390.2056 548972.4443 0.651222393 0.561776995 0.406149661 0.437997368 0.897615843 0.557586165 0.820367347 0.681983603 1 19.06637421 1.173705431 0.497064004 0.996363552 0.5440846 0.489686333 0.137117234 0.778486988 0.508905135 0.147862779 0.077971833 14.91782235 -1.173705431 -0.452278952 KINS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KINSSPNVNTTASGVEDLNIIQVTIPDDDNER 32 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 KINS(0.48)S(0.48)PNVNT(0.019)T(0.019)AS(0.001)GVEDLNIIQVTIPDDDNER 73.975 0.0011932 43516000 62684 56082 61433 70780 52550 61986 70767 70900 61384 TRUE FALSE 59721.05155 61796.81956 64249.76382 63665.05993 61714.70336 59839.40928 59970.19442 64691.62014 70903.11721 0.842290916 0.871567034 0.906162752 0.897916233 0.870408887 0.843960204 0.845804765 0.912394584 1 16.11356144 0.937273009 4.447153839 0.999939494 0.867260519 0.792960365 0.021425957 0.141739784 7.659491418 0.022579925 0.005739141 8.655118322 -0.937273009 -0.132678975 KIPDPDS(ph)DDVSEVDAR ddPTM_SK-BR-3_Trastuzumab_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(0.999)DDVS(0.001)EVDAR;KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR 146.6 6.79E-07 2159380000 1117640 1194700 1005280 1263630 815710 1198600 1176370 1158500 867300 TRUE FALSE 1064811.372 1316441.288 1051373.082 1136607.512 957969.5657 1157092.181 996893.151 1057055.598 1001796.454 1.062901917 1.314080602 1.049487725 1.13456931 0.956251703 1.155017246 0.995105489 1.055160051 1 19.93415798 3.686027798 24.50247706 1.051841661 1.18849132 0.319293348 0.084389955 252.5161878 117779.0258 0.020437626 0.031661864 4853.195634 -3.686027798 0.13664966 KIPDPDSDDVSEVDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 118.47 0.00043242 243350000 332830 347380 292440 386270 255670 349340 345880 323930 281920 FALSE TRUE 317097.7855 382778.4169 305848.6633 347441.4057 300258.7671 337242.2682 293109.6535 295564.9719 325638.7138 0.973771766 1.175469626 0.939226973 1.066953624 0.922061028 1.035633215 0.900106901 0.907646909 1 18.3129127 2.869924604 1.048728878 0.941571264 1.062944723 0.204214051 0.075700271 0.603804406 1.417261125 0.03468242 0.036759517 741.1815559 -2.869924604 0.121373458 KIPEPS(ph)PVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(0.999)PVT(0.001)R 153.7 9.67E-06 3987960000 3720040 3624080 3462800 4003290 3427720 3576660 4213030 3972940 3778980 TRUE FALSE 3544201.082 3993377.872 3621572.805 3600871.683 4025513.283 3452799.367 3570254.896 3625048.312 4365004.918 0.811958096 0.91486217 0.829683557 0.824941037 0.922224226 0.791018437 0.81792689 0.830479777 1 22.05755185 -0.962912137 4.632434585 1.000002439 0.844610527 0.571721885 0.042712047 0.003876183 25588370.36 149.0248885 0.009700342 0.108915042 0.962912137 -0.155391912 KIPGISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIPGISR 7 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 126.28 0.0063618 809050000 854110 767530 749290 922660 830980 837890 956540 888490 914860 FALSE TRUE 813737.913 845742.1796 783645.6876 829912.4639 975902.6489 808873.6592 810602.2549 810689.1054 1056731.816 0.770051493 0.800337575 0.741574802 0.785357695 0.923510236 0.765448382 0.767084176 0.767166364 1 20.01117786 -1.317508046 3.61474719 1.00071777 0.789417601 0.636725255 0.049831902 18652069.54 23220947.36 135388.3211 0.011608273 0.048138434 1.317508046 -0.211300169 KIPGIYVLSLEIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIPGIYVLSLEIGK 14 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;E9PIA8;E9PK48 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 130.98 9.44E-05 223960000 508770 402230 419190 486600 426120 486120 604320 561870 485560 FALSE TRUE 484721.4504 443217.6943 438410.2761 437686.0435 500435.1931 469285.5425 512119.8849 512669.6841 560858.1649 0.86424961 0.790249161 0.781677621 0.780386327 0.89226693 0.836727665 0.913100525 0.914080807 1 19.09727645 1.409409871 0.725228113 0.995487336 0.809953204 0.76061268 0.034273913 0.29092288 0.338343624 0.031827701 0.0136446 25.66905446 -1.409409871 -0.185534132 KIPIPET(ph)PPQT(ph)PPQVLDSPHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIPIPETPPQTPPQVLDSPHQR 22 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 KIPIPET(0.999)PPQT(0.959)PPQVLDS(0.042)PHQR 45.489 0.075414 43952000 43553 39763 38215 44846 33360 37003 37366 39328 41952 TRUE FALSE 41494.336 43814.89491 39967.19555 40337.99488 39177.97344 35721.57683 31665.13043 35884.23183 48457.7019 0.856300121 0.904188461 0.824785204 0.832437225 0.808498379 0.737170263 0.653459186 0.740526901 1 15.56443837 2.737421365 1.578630482 0.74517674 0.870472979 0.054317309 0.092807138 0.497685956 2.487576376 0.034517408 0.033293692 546.2876278 -2.737421365 0.125296239 KIPIPETPPQT(ph)PPQVLDSPHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIPIPETPPQTPPQVLDSPHQR 22 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 KIPIPET(0.064)PPQT(0.936)PPQVLDSPHQR 180.42 4.06E-17 59550000 84414 64546 75907 89046 78951 71097 92356 86723 100520 TRUE FALSE 80423.91751 71123.31078 79387.41103 80094.9269 92720.0294 68634.89306 78265.39597 79129.07437 116108.1282 0.692663974 0.612560997 0.683736895 0.689830489 0.798566223 0.591129098 0.674073359 0.681511928 1 16.82510945 0.588898665 3.751258988 0.999999787 0.672726633 0.773608868 0.054697897 8.590866359 77.83206611 0.049897182 0.012797774 3.880598082 -0.588898665 -0.327273154 KIPIPETPPQTPPQVLDS(ph)PHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIPIPETPPQTPPQVLDSPHQR 22 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 KIPIPETPPQTPPQVLDS(1)PHQR;KIPIPET(0.003)PPQT(0.089)PPQVLDS(0.908)PHQR 104.3 0.00026135 262810000 101638 105552 103157 111880 94331 102740 121337 107505 101642 TRUE FALSE 96833.77317 116307.8688 107886.8505 100633.6098 110782.2965 99182.08804 102824.8121 98091.29228 117404.1222 0.824790232 0.990662564 0.918935796 0.857155677 0.943598014 0.844792211 0.875819436 0.835501262 1 16.84112354 2.236395441 24.99986938 0.877163108 0.909231201 0.003709345 0.062913307 179.5157968 2072704.223 0.021116127 0.016359953 172.3437115 -2.236395441 0.032068092 KIPNPDFFEDLEPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KIPNPDFFEDLEPFR 15 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ;;; 213.49 5.57E-10 669876000 1066603 836445 906984 1422931 1455496 1106650 1458933 1132324 1346253 FALSE TRUE 1016186.79 921679.6965 948570.1135 1279895.272 1709334.042 1068326.433 1236345.976 1033171.708 1555023.04 0.653486646 0.59271128 0.610003897 0.823071582 1.099233901 0.687016466 0.795066018 0.66440926 1 20.56850453 3.229854966 8.839296248 0.833103513 0.617960924 0.400193958 0.129947746 0.139539134 91.74423254 0.035695151 0.044507865 1697.676614 -3.229854966 -0.21514259 KIPSVEDSLGEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIPSVEDSLGEGSR 14 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 136.34 4.43E-05 256410000 93031 86560 87025 112680 94427 103760 108790 115770 102360 FALSE TRUE 88633.609 95380.56241 91015.18233 101353.1923 110895.0389 100166.7652 92192.08743 105632.5651 118233.466 0.74964908 0.806713747 0.769792051 0.857229309 0.937932741 0.847194695 0.779746129 0.893423568 1 16.85127892 -5 0.074508275 1.572000924 0.629141292 0.60691365 0.049226988 214.3571338 1.141516549 20.86949871 2.28493363 1.00E-05 5 -0.942859632 KIQALQQQADEAEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KIQALQQQADEAEDR 15 1 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;;; 270.97 3.52E-33 4280840000 4085390 3339560 3501100 4194150 3620290 3749470 4413520 4178740 4088510 FALSE TRUE 3892281.711 3679864.961 3661628.898 3772546.074 4251667.43 3619624.914 3740156.464 3812827.373 4722535.25 0.824193258 0.779213868 0.77535237 0.798839156 0.900293424 0.766457998 0.791980635 0.807368748 1 22.17113013 -1.569056378 2.163091119 1.022986632 0.803368006 0.725337771 0.037601802 405387.8453 298385.7381 53216.59042 0.009394495 0.026973892 1.569056378 -0.219618625 KIQEESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 171.56 0.00046283 500220000 1028470 964140 803420 949500 804840 966690 1068180 1032550 870390 FALSE TRUE 979856.2613 1062386.962 840257.6017 854054.4561 945203.8412 933213.2829 905209.5225 942134.4481 1005365.636 0.974626769 1.056717003 0.835773147 0.849496368 0.940159289 0.928232724 0.90037842 0.937106277 1 19.93928885 3.748895564 24.98782468 0.907938055 1.015671888 0.415263195 0.050360955 564.089323 1363850.499 0.012235684 0.021745213 5609.130759 -3.748895564 0.107733832 KIQGIEEYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIQGIEEYKK 10 2 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 51.979 0.086111 152570000 656930 561190 604040 697610 467410 647350 722960 732740 589790 FALSE TRUE 625878.2208 618375.899 631735.8315 627484.9174 548926.156 624932.1072 612659.1739 668577.4011 681251.621 0.918718138 0.907705582 0.927316445 0.921076586 0.805761248 0.917329351 0.899314079 0.981395685 1 19.37782823 1.184205095 4.009656829 0.998778924 0.90054404 0.54552238 0.034712873 0.162608973 4.858852713 0.030993444 0.00830755 15.28287618 -1.184205095 -0.098234884 KIQNDAGVR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 172.88 8.96E-05 1253650000 2410970 2009540 1753530 1968500 2151240 1972050 2588990 2251450 2392190 FALSE TRUE 2297008.226 2214314.411 1833931.085 1770622.64 2526415.575 1903757.414 2193992.025 2054301.102 2763158.608 0.831298001 0.801370723 0.663708221 0.6407966 0.914321591 0.688978696 0.794015957 0.74346116 1 21.39788695 -1.622783013 2.705573908 1.022383466 0.764941537 0.456698652 0.082179951 13431900.16 12517135.12 2119047.053 0.019078792 0.0238351 1.622783013 -0.257441929 KIQVLQQQADDAEER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 319.28 2.76E-56 10243580000 10135790 9458590 9043500 11213900 8659140 9328620 10713960 10479390 9985180 FALSE TRUE 9656691.294 10422431.07 9458153.42 10086657.47 10169291.27 9005567.55 9079348.627 9561759.057 11533630.72 0.837263784 0.903655694 0.820049961 0.874543126 0.881707723 0.780809423 0.787206462 0.829032877 1 23.4593434 3.721233332 24.40374897 0.839058843 0.870459748 0 0.064745299 1956.756676 2755894.318 0.016110939 0.025023771 5262.999537 -3.721233332 0.031400905 KIS(ph)ADTIGDEGFFDLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KISADTIGDEGFFDLLSR 18 1 H0Y4A4;A0A2R8Y6E3;P81274 H0Y4A4 GPSM2 G-protein-signaling modulator 2 1 KIS(0.997)ADT(0.003)IGDEGFFDLLSR;KIS(0.999)ADT(0.001)IGDEGFFDLLSR 279.74 1.90E-39 88993000 120144 109544 100939 140199 94940 130184 155705 156633 126366 TRUE FALSE 114465.0312 120706.6581 105567.153 126105.9302 111497.5059 125675.6954 131949.3425 142917.3842 145962.1939 0.784210131 0.826972074 0.723249974 0.863962967 0.763879351 0.861015391 0.903996706 0.979139737 1 17.15523522 1.582626026 1.299723466 1.001332953 0.79512907 0.811098391 0.038438914 0.15428097 0.499497856 0.029340956 0.010400099 38.24952324 -1.582626026 -0.206203883 KIS(ph)ASEFDRPLRPIVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISASEFDRPLRPIVVK 17 3 O76074-2;G5E9C5;O76074;C9JGT3 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 1 KIS(0.702)AS(0.298)EFDRPLRPIVVK 109.05 0.0034589 149540000 135770 118570 122350 126040 104010 139900 152340 156780 124810 TRUE FALSE 129352.4212 130652.4178 127959.8685 113370.2197 122149.3111 135055.2279 129097.7351 143051.5121 144164.8974 0.897253239 0.906270668 0.887593796 0.786392678 0.847288857 0.936810766 0.895486609 0.992277001 1 17.1373604 1.325767275 1.484108538 1.005441584 0.87518217 0.601080502 0.039670613 0.282720388 1.157613843 0.037830656 0.011789926 21.17226274 -1.325767275 -0.130259414 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.998)ENS(0.001)YS(0.001)LDDLEIGPGQLSSSTFDSEK;KIS(0.569)ENS(0.215)YS(0.215)LDDLEIGPGQLSSSTFDSEK 348.53 5.33E-111 1721130000 658775 701321 610450 846914 368172 752800 674190 750919 352463 TRUE FALSE 627636.0113 772786.4072 638439.7363 761780.5957 432381.0802 726730.3472 571329.9332 685164.5515 407121.1619 1.541644282 1.898173024 1.568181161 1.871139766 1.062045211 1.785046849 1.403341282 1.68294998 1 18.63509869 -2.740253653 0.192733572 1.70E-15 1.75471535 0.375352671 0.24398357 48.04993198 1.036753714 20.83780569 0.62077153 0.001818638 2.740253653 1.75471535 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_SK-BR-3_Trastuzumab_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(0.716)ENS(0.225)YS(0.059)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.994)ENS(0.005)YSLDDLEIGPGQLSSSTFDSEKNESR;KIS(0.635)ENS(0.306)YS(0.059)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.985)ENS(0.014)YSLDDLEIGPGQLSSSTFDSEKNESR 218.01 4.09E-36 6078400000 1076009 834983 973177 1116997 677934 1125154 1218451 1131803 647940 TRUE FALSE 1025148.187 920068.717 1017798.128 1004714.339 796165.475 1086189.635 1032553.922 1032696.329 748419.226 1.369751272 1.229349387 1.359930494 1.342448596 1.063796128 1.451311774 1.379646441 1.379836719 1 19.51348709 -2.23044361 2.142787638 1.54E-05 1.320778402 0.472721547 0.10687079 2089846.978 371644.2844 10119628.07 0.025289479 0.005882425 2.23044361 1.320762955 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESRR ddPTM_SK-BR-3_Trastuzumab_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(0.985)ENS(0.011)YS(0.004)LDDLEIGPGQLSSSTFDSEKNESRR 241.06 3.66E-46 404390000 250320 97089 250500 156490 206550 241530 405600 277140 255630 TRUE FALSE 238487.8697 106982.4795 261985.6728 140759.3279 242572.2546 233165.7555 343718.2706 252872.1524 295271.7948 0.807689301 0.362318655 0.887269551 0.476711052 0.821521929 0.789664843 1.164074174 0.856404698 1 18.17168403 2.21968943 1.860582858 1.015606804 0.624168673 0.433711848 0.173773972 0.268625241 1.857457393 0.080698005 0.050610487 165.8400539 -2.21968943 -0.391438131 KIS(ph)GTTALQEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISGTTALQEALK 13 1 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 1 KIS(0.79)GT(0.209)T(0.002)ALQEALK 229.93 3.03E-12 127520000 307570 278780 211750 283980 159240 281060 289960 340590 199490 TRUE FALSE 293031.7756 307187.9989 221458.9469 255433.7909 187011.4056 271326.8217 245721.2765 310766.134 230425.8903 1.271696402 1.33313144 0.961085348 1.108529039 0.811590248 1.177501457 1.066378766 1.348659795 1 17.8139433 3.750406821 24.82867935 1.068213552 1.302413941 0.327383061 0.139878859 693.9196429 1454394.601 0.033516877 0.059817045 5628.683398 -3.750406821 0.23420039 KIS(ph)GTTALQEALKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISGTTALQEALKEK 15 2 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 1 KIS(0.997)GT(0.003)TALQEALKEK 192.25 7.41E-08 365750000 468130 271920 413600 368440 317240 473700 667900 609740 416310 TRUE FALSE 446002.4226 299628.9571 432563.9691 331403.7112 372566.5556 457295.6502 565999.5882 556347.9332 480869.2286 0.927492125 0.623098629 0.899545954 0.689176374 0.774777285 0.950977154 1.177034326 1.156963058 1 18.87528508 2.020013358 3.114421773 1.125035784 0.775449602 0.692690034 0.099825719 0.12485244 2.403055606 0.043443178 0.026351442 104.7160756 -2.020013358 -0.349586182 KIS(ph)LEDIQAFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISLEDIQAFEK 12 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 1 KIS(1)LEDIQAFEK 110.26 0.00092434 71048000 134500 93059 112610 191000 119090 160200 219190 132770 63612 TRUE FALSE 128142.4516 102541.8179 117773.2799 171800.3171 139859.2583 154652.2338 185748.5398 121143.9549 73476.62407 1.743989373 1.395570621 1.602867325 2.338162909 1.903452425 2.104781429 2.527995021 1.648741439 1 16.16499772 3.340492792 8.115553993 2.042523468 1.559213857 0.078966274 0.428137136 0.34341256 24.49054311 0.107512377 0.145623574 2190.245478 -3.340492792 -0.483309611 KIS(ph)PPSYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.842)PPS(0.158)YAR;KIS(0.585)PPS(0.414)YAR;KIS(0.665)PPS(0.335)YAR;KIS(0.955)PPS(0.044)YAR 112.82 0.0011645 2995150000 1116220 863190 915160 1096360 903500 1022200 1245760 1146100 1099870 TRUE FALSE 1063458.493 951150.0424 957120.9912 986151.8099 1061070.114 986800.9577 1055696.432 1045741.408 1270432.222 0.837084005 0.74868224 0.753382175 0.776233311 0.835204032 0.776744277 0.830974226 0.823138291 1 20.27688798 -0.026090202 0.524631592 1.019782183 0.782147537 0.824556159 0.030063351 1.711751101 0.560193667 0.099038676 0.01376645 0.941693988 0.026090202 -0.237634646 KIS(ph)PVKFSNTDSVLPPKR ddPTM_SK-BR-3_Trastuzumab_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(0.998)PVKFS(0.002)NTDSVLPPKR 150.14 3.15E-07 1227500000 1251300 973810 1257200 1166000 694330 1378300 1450200 1487600 906920 TRUE FALSE 1192153.529 1073042.346 1314843.864 1048791.465 815420.9322 1330569.125 1228945.355 1357337.858 1047560.522 1.138028309 1.024324919 1.255148353 1.001175057 0.77839983 1.270159669 1.173149742 1.295713068 1 19.99860217 KISELDAFLKEPALNEANLSNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KISELDAFLKEPALNEANLSNLK 23 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 253.08 9.83E-44 336730000 1306020 1082350 1142310 1387850 817890 1380340 1421460 1424750 910500 FALSE TRUE 1244287.023 1192642.696 1194686.043 1248340.681 960529.757 1332538.48 1204590.17 1299991.337 1051695.69 1.183124582 1.134018811 1.135961719 1.186978984 0.913315293 1.267038073 1.145379012 1.236090772 1 20.00428589 4.583883867 1.948524037 1.134964468 1.189931495 0.022805193 0.104268541 2.838956209 14.8349896 0.024523886 0.252191139 38360.46537 -4.583883867 0.054967026 KISENSYS(ph)LDDLEIGPGQLSSSTFDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.287)ENS(0.18)YS(0.533)LDDLEIGPGQLSSSTFDSEK 191.02 2.69E-18 504250000 295210 302600 242140 361460 159920 331780 301300 335080 140280 TRUE FALSE 281256.0083 333435.284 253242.3585 325125.3541 187809.9974 320290.3754 255331.1512 305738.6188 162033.9059 1.735784907 2.057811802 1.562897327 2.006526672 1.159078381 1.97668737 1.575788411 1.886880508 1 17.30593621 -2.379274624 0.282370603 8.71E-13 1.826993777 0.416330167 0.271764626 38.03232092 1.3546632 24.51191144 0.28260315 0.004175662 2.379274624 1.826993777 KISENSYS(ph)LDDLEIGPGQLSSSTFDSEKNESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KISENSYSLDDLEIGPGQLSSSTFDSEKNESR 32 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.273)ENS(0.327)Y(0.007)S(0.393)LDDLEIGPGQLSSSTFDSEKNESR 49.682 0.041192 158590000 157240 124930 156320 172730 115260 167130 179010 175970 102110 TRUE FALSE 149807.5768 137660.509 163487.4266 155366.8522 135361.3075 161342.2462 151698.7368 160561.1339 117944.6973 1.270151014 1.167161493 1.386136303 1.317285608 1.147667599 1.367948283 1.286185307 1.361325584 1 16.84775103 -1.105576989 5.070248931 0.999991837 1.27977348 0.56036744 0.079869949 5412802.917 1180271.574 496.0359921 0.018013182 0.078419309 1.105576989 0.279781643 KISSDLDGHPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KISSDLDGHPVPK 13 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;; 121.76 0.00015768 5766660000 10909610 8918020 9090130 10457800 7456740 9869080 11944440 11029460 7807520 FALSE TRUE 10393934.36 9826776.377 9506921.452 9406562.075 8757193.095 9527311.285 10122096.3 10063662.01 9018270.326 1.152541893 1.089652009 1.054184573 1.043056122 0.971050188 1.05644552 1.122398857 1.115919311 1 23.10441933 4.246307149 1.768304909 1.057587087 1.151101144 0.325235961 0.045683703 0.538595872 2.989811927 0.013284561 0.061019108 17632.22621 -4.246307149 0.093514057 KISSIQSIVPALEIANAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KISSIQSIVPALEIANAHR 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 199.12 4.60E-16 1069900000 1671550 1083020 1462700 1267600 1593340 1207050 1651260 1477980 1653060 FALSE TRUE 1592539.144 1193380.969 1529766.242 1140178.44 1871217.992 1165249.556 1399329.96 1348560.236 1909408.102 0.834048595 0.625000474 0.801173013 0.597137112 0.979998979 0.61026742 0.732860596 0.706271349 1 20.86469406 -1.290987163 3.645929905 1.000698103 0.731367582 0.336719278 0.116362862 53155462.58 105042518.8 430496.2928 0.024204958 0.051169696 1.290987163 -0.269330521 KITAFVPNDGCLNFIEENDEVLVAGFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KITAFVPNDGCLNFIEENDEVLVAGFGR 28 1 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ; 209.89 2.22E-25 87190000 121280 75364 124936 109410 134436 114133 175258 135922 179569 FALSE TRUE 115547.3348 83043.67728 130664.4392 98411.89893 157881.5958 110180.5456 148519.1733 124019.9491 207415.6434 0.5570811 0.40037326 0.629964245 0.474467101 0.761184611 0.531206537 0.716046152 0.597929583 1 17.66216518 -5 0.124601706 2.458874926 0.373317576 0.669646453 0.096659454 75.36085538 0.601330682 27.34188996 0.725303896 1.00E-05 5 -2.08555735 KITIADCGQLE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KITIADCGQLE 11 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 107.11 0.04594 473910000 1859300 1175800 1246200 1437100 1844100 1422200 2158900 1704500 2034400 FALSE TRUE 1771414.574 1295615.357 1303339.503 1292639.978 2165710.456 1372948.857 1829520.154 1555244.944 2349884.362 0.75383053 0.551352815 0.554639847 0.550086634 0.921624269 0.584262307 0.778557526 0.661838927 1 21.16415833 -0.912326859 0.29549239 1.17820411 0.619663582 0.44366538 0.118817945 11.96409585 0.928235826 1.957383458 0.12915747 0.122369488 0.912326859 -0.558540528 KIVDQIRPDR ddPTM_SK-BR-3_Trastuzumab_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 7617300000 8793700 7034100 7827700 8467300 8525100 8539400 10047100 8649800 10113700 FALSE TRUE 8378039.228 7750882.787 8186607.788 7616150.917 10011874.74 8243678.437 8514230.367 7892377.657 11682080.94 0.717170106 0.66348477 0.700783347 0.651951562 0.857028366 0.705668663 0.728828229 0.675596899 1 23.47779395 -5 0.351753224 4.361397141 0.702349393 0.710733557 0.057321631 230.9406681 1.882258025 585.9682719 0.040504132 1.00E-05 5 -3.659047748 KIVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 KIVEPEVVGES(1)DS(1)EVEGDAWR;KIVEPEVVGES(1)DS(1)EVEGDAWR 178.63 2.11E-16 244950000 299980 209429 282330 284500 266030 275640 362200 295210 328080 TRUE FALSE 285800.5399 230770.0532 295275.1098 255901.5195 312425.5478 266094.5177 306939.7377 269359.8474 378956.9708 0.754176759 0.608961098 0.779178462 0.675278565 0.824435416 0.702176073 0.809959339 0.710792697 1 18.53167452 -5 0.182664528 2.136753636 0.673619556 0.632853959 0.063977334 75.92889819 0.734354899 31.25258908 0.169564098 1.00E-05 5 -1.46313408 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 KIVEPEVVGES(1)DSEVEGDAWR;KIVEPEVVGES(0.892)DS(0.108)EVEGDAWR;KIVEPEVVGES(0.874)DS(0.126)EVEGDAWR 167.28 7.54E-12 253023000 176314 135065 181106 179218 149226 157900 228731 199903 220757 TRUE FALSE 167979.9866 148828.2771 189409.8892 161202.6661 175250.9672 152431.8834 193833.885 182398.4336 254990.8681 0.658768637 0.583661204 0.74281048 0.632189958 0.687283307 0.5977935 0.760160105 0.715313591 1 17.96008606 -0.034305059 0.458399743 1.045507014 0.637287572 0.806166034 0.051979471 1.707697854 0.446450714 0.185712976 0.026542902 0.92404887 0.034305059 -0.408219442 KIVLATNIAETSITINDIVHVVDSGLHKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIVLATNIAETSITINDIVHVVDSGLHKEER 31 2 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 100.68 7.14E-05 46986000 94932 57885 124160 83142 82888 106230 154520 119140 63180 FALSE TRUE 90444.7525 63783.54731 129852.8588 74784.4082 97343.64096 102551.2285 130945.136 108707.47 72977.63172 1.239348967 0.874015035 1.779351505 1.024757949 1.333883255 1.405241936 1.794318793 1.48959986 1 16.15516671 2.280463087 2.885445402 1.527399381 1.201684538 0.035075059 0.304844434 0.420224168 7.193479696 0.115183242 0.086566151 190.7493591 -2.280463087 -0.325714843 KIWCFGPDGTGPNILTDITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KIWCFGPDGTGPNILTDITK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 161.8 3.53E-11 301120000 707120 548720 695430 740880 557790 762110 910830 790280 791060 FALSE TRUE 673695.839 604635.1918 727316.1534 666405.3348 655068.3994 735717.9396 771866.155 721078.8937 913733.5446 0.737300106 0.661719377 0.795982765 0.729321298 0.716914032 0.805177772 0.844738775 0.78915664 1 19.80141399 0.410856774 0.283556745 1.062862504 0.6852413 0.800828206 0.040881723 1.563324573 0.259697249 0.181086321 0.059804413 2.57547165 -0.410856774 -0.377621204 KIYEDGDDDMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KIYEDGDDDMKR 12 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;;;; 186.13 6.84E-06 3005950000 5892490 4594090 5507500 5619720 3645540 6207610 6996040 6822420 4314670 FALSE TRUE 5613963.675 5062232.994 5760024.323 5054815.069 4281321.022 5992638.909 5928665.607 6225012.737 4983766.987 1.12644987 1.015744317 1.155757149 1.0142559 0.859053209 1.202431599 1.189595264 1.249057741 1 22.24880519 KKAEPSEVDMNS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 176.21 1.18E-06 2923230000 4017170 4421430 4210570 5118030 2047800 5465790 5184180 5557480 2361480 TRUE FALSE 3827286.335 4871978.744 4403628.799 4603555.901 2404935.672 5276508.322 4393238.127 5070837.589 2727686.258 1.40312557 1.78612138 1.614419102 1.687714593 0.88167606 1.934426405 1.610609767 1.859025236 1 21.37924628 KKAEPSEVDMNSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKAEPSEVDMNSPK 14 2 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 83.633 0.0047541 237190000 491130 479860 470210 573950 449980 555780 616000 624480 465870 FALSE TRUE 467915.2582 528758.2796 491769.5936 516255.4556 528456.3695 536533.1992 522017.8864 569797.2206 538114.7403 0.869545514 0.982612517 0.913874973 0.959378023 0.982051466 0.997060959 0.970086577 1.058876812 1 19.0375543 8 0.23812071 1.017373177 0.221678502 0.629958888 0.030877221 31.79269536 0.42383319 0.039908313 9.97606219 100000000 -8 -0.795694675 KKANEVDR ddPTM_SK-BR-3_Trastuzumab_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 ; 113.71 0.0015731 251680000 894470 757710 817490 909940 667700 886360 1088210 1038570 829520 FALSE TRUE 852190.1758 834921.5104 854972.7251 818471.1024 784146.6686 855665.1309 922183.5782 947627.305 958157.725 0.8894049 0.871382121 0.892308962 0.854213332 0.818389967 0.893031605 0.96245488 0.989009722 1 19.86990364 1.699298464 2.666562322 0.990890029 0.868166882 0.871840302 0.021034637 0.085233913 1.334999737 0.013873958 0.006027152 50.03782965 -1.699298464 -0.122723147 KKAVLFCLSEDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKAVLFCLSEDKK 13 3 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 183.81 4.40E-06 688670000 1864320 860490 2040730 1217660 1262590 2001600 2795400 2084510 1599740 FALSE TRUE 1776197.288 948174.9093 2134299.489 1095258.503 1482785.296 1932284.09 2368910.389 1901979.254 1847819.509 0.961239601 0.513131778 1.155036776 0.592730241 0.80245137 1.045710407 1.282003127 1.029310084 1 20.81739241 2.168035495 3.985279541 1.140196165 0.784340397 0.345188155 0.192148665 0.198147624 6.194935454 0.069643744 0.050552346 147.2432841 -2.168035495 -0.355855769 KKDAS(ph)DDLDDLNFFNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKDASDDLDDLNFFNQK 17 2 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 KKDAS(1)DDLDDLNFFNQK;KKDAS(1)DDLDDLNFFNQK 190.79 1.46E-10 272860000 366990 356010 330480 409500 185617 405190 402410 457320 229662 TRUE FALSE 349643.11 392287.8237 345632.8349 368336.282 217988.546 391158.1687 341014.9637 417274.6364 265276.81 1.318031192 1.47878672 1.302913869 1.388497856 0.821739925 1.474528319 1.285506124 1.57297819 1 18.01713904 -1.893120837 2.675393189 0.828376449 1.331668849 0.209203547 0.201848011 42453440.32 27268340.24 46042018.98 0.045761714 0.012790254 1.893120837 0.5032924 KKDEEFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KKDEEFQR 8 2 V9GY93;Q9HC07-2;Q9HC07 V9GY93 TMEM165 Transmembrane protein 165 0 ;;; 143.04 0.00034189 760360000 601660 487898 572466 845560 537777 747370 911340 788770 608494 FALSE TRUE 573220.7242 537615.3609 598714.1323 760562.7023 631565.1385 721488.3895 772298.3451 719701.1173 702856.1418 0.815559103 0.764900993 0.851830263 1.082102947 0.898569566 1.026509333 1.098800024 1.023966463 1 19.42286991 3.368135576 4.652411927 1.025684704 0.792719821 0.76960828 0.054965263 0.090337829 3.295055992 0.015607018 0.021385745 2334.186626 -3.368135576 -0.232964884 KKDELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 15205760000 16856290 14815820 14961780 19317450 11773160 19211320 21051080 20699720 14193070 FALSE TRUE 16059526.58 16325568.9 15647792.41 17375623.23 13826395.38 18546027.17 17839351.12 18887142.78 16394058.81 0.979594301 0.995822273 0.954479461 1.059873179 0.843378418 1.131265136 1.088159517 1.152072406 1 23.96666974 2.199431381 24.99999604 1.100037411 0.975474779 0.469936965 0.066060407 126.3309162 80713.16901 0.021558391 0.015922171 158.2819458 -2.199431381 -0.124562633 KKDELS(ph)DYAEK ddPTM_SK-BR-3_Trastuzumab_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 145.55 1.89E-05 502570000 1493280 1559400 1339360 1826890 682600 1795750 1760650 1946480 698780 TRUE FALSE 1422695.614 1718304.633 1400770.981 1643247.546 801645.2239 1733562.727 1492030.506 1776035.892 807143.2335 1.762630912 2.128872004 1.735467663 2.035880966 0.99318831 2.147775829 1.848532508 2.200397425 1 19.62246519 KKDQVTAQEIFQDNHEDGPTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKDQVTAQEIFQDNHEDGPTAK 22 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 324.67 2.36E-68 743030000 939360 762260 857640 977460 578800 1033480 1059440 1025010 547630 FALSE TRUE 894958.3144 839935.1606 896963.6423 879203.8637 679742.5367 997690.3285 897802.97 935254.6905 632553.6635 1.414833817 1.327848069 1.418004027 1.389927708 1.074600585 1.577242195 1.419330915 1.478538098 1 19.27082835 -2.203952608 2.024681589 4.52E-05 1.38641422 0.473450413 0.128435627 3489825.336 639467.0564 15969154.98 0.029455771 0.006252409 2.203952608 1.386368984 KKDTEVLFCFEQFDELTLLHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KKDTEVLFCFEQFDELTLLHLR 22 2 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 240.85 7.29E-31 571609900 1459911 1209568 1372795 1289097 1058527 1322475 1469008 1450780 873636 FALSE TRUE 1390903.9 1332824.354 1435739.009 1159514.52 1243133.774 1276677.359 1244883.849 1323742.012 1009115.009 1.378340316 1.320785384 1.422770443 1.149041001 1.231904949 1.265145546 1.233639217 1.311785079 1 19.94465918 -5 0.108881313 0.090150401 1.459725653 0.631647281 0.07244148 105.2690124 0.764119974 21.55034411 0.887013073 1.00E-05 5 1.369575252 KKEEEDDDMKELENWAGSM ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEEEDDDMKELENWAGSM 19 3 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ; 144.5 1.65E-07 116524000 397790 350760 330670 416940 141730 459260 408980 461450 133345 FALSE TRUE 378987.255 386502.8428 345831.5466 375028.3991 166447.6671 443355.711 346582.5896 421042.9917 154023.4616 2.460581337 2.509376421 2.245317324 2.434878396 1.08066437 2.878494656 2.250193484 2.733628938 1 17.2327906 3.421810645 2.200685793 2.141216438 2.478876467 0.06578636 0.616087409 0.977391167 9.561401329 0.16925691 0.261160585 2641.256903 -3.421810645 0.337660029 KKEEPSQNDIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK 188.27 3.26E-06 7483420000 9102490 11125550 9740820 11573050 4222790 12831820 11489670 12949940 4550510 TRUE FALSE 8672233.337 12259256.19 10187446.23 10409705.03 4959243.239 12387450.86 9736709.819 11815974.6 5256179.85 1.649911834 2.332350974 1.938184484 1.980469718 0.943507144 2.356740296 1.852430871 2.248015658 1 22.32558321 2.956941469 24.99903974 1.764612461 1.998556143 0.069526487 0.481602514 1519.929042 882444.1402 0.136450707 0.144737472 905.6105404 -2.956941469 0.233943682 KKEEPSQNDISPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 116.96 0.00030598 376050000 1219260 1228320 1085110 1371770 686870 1404330 1368790 1484230 692820 FALSE TRUE 1161627.996 1353487.204 1134863.367 1233877.073 806659.9105 1355697.7 1159955.946 1354262.953 800258.9872 1.451565074 1.691311471 1.418120115 1.541847193 1.007998565 1.694073696 1.449475688 1.692280842 1 19.61010745 -1.97669764 2.771304657 0.570346907 1.498606892 0.370923886 0.201803841 31898786.45 30107556.34 88145171.69 0.04425556 0.010551212 1.97669764 0.928259985 KKEGETVEPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEGETVEPYK 11 2 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 83.182 0.0095064 122351000 654560 714820 547570 783350 361040 751650 674000 711390 366840 FALSE TRUE 623620.246 787660.9707 572676.6261 704606.1697 424005.2617 725620.172 571168.9211 649096.9203 423727.6736 1.47174774 1.858884892 1.351520474 1.662875034 1.00065511 1.712468213 1.34796228 1.531872853 1 18.69277783 -3.207116318 0.137005005 3.33E-14 1.736923701 0.303720191 0.234648396 85.71655642 1.171046398 26.81860187 1.533462233 0.000620703 3.207116318 1.736923701 KKEIQNGNLHES(ph)DSESVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KKEIQNGNLHESDSESVPR 19 2 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 KKEIQNGNLHES(1)DSESVPR;KKEIQNGNLHES(0.999)DS(0.001)ESVPR;KKEIQNGNLHES(0.999)DS(0.001)ESVPR;KKEIQNGNLHES(1)DSESVPR 248.45 3.73E-25 828410000 706240 441229 727620 887130 765350 823840 1064240 791960 758330 TRUE FALSE 672857.4348 486190.7367 760982.0967 797954.007 898826.7977 795310.2142 901870.6419 722611.784 875927.9434 0.768165281 0.555057914 0.868772486 0.910981335 1.026142395 0.907963058 1.029617389 0.824967156 1 19.74045267 3.544422993 3.954910859 0.954398617 0.662688255 0.68240375 0.079929885 0.106656485 3.240010175 0.020294614 0.031571874 3502.861718 -3.544422993 -0.291710362 KKELEEIVQPIISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKELEEIVQPIISK 14 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 134.9 2.03E-05 392790000 2313100 1731700 1893900 2282900 1452600 2228800 2665300 2474700 1671600 FALSE TRUE 2203764.347 1908162.199 1980737.188 2053418.555 1705932.98 2151616.097 2258659.533 2258002.149 1930823.191 1.141359995 0.988263559 1.025851149 1.063493832 0.883526254 1.114351696 1.16979097 1.169450502 1 20.88078463 2.025550878 24.99673052 1.134477547 1.026759064 0.235916803 0.079607048 260.7887892 255131.5734 0.027965044 0.020652912 106.0598181 -2.025550878 -0.107718483 KKEPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;KKEPAITS(0.002)QNS(0.998)PEAR;KKEPAIT(0.018)S(0.214)QNS(0.768)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.001)QNS(0.999)PEAR;KKEPAITSQNS(1)PEAR 278.27 6.82E-34 53370260000 18890580 17112030 17438760 20021370 13003430 18564250 21148380 19857040 15315720 TRUE FALSE 17997659.72 18855765.31 18238344.4 18008783.85 15271224.07 17921365.37 17921806.21 18118252.31 17690803.64 1.017345514 1.065851258 1.030950587 1.017974323 0.863229528 1.013032858 1.013057778 1.024162196 1 24.07649625 2.99141902 24.79859155 0.983692238 1.038975753 0.234016904 0.046419339 538.5919379 1556510.153 0.013677573 0.015600994 980.4354831 -2.99141902 0.055283515 KKEPAITSQNS(ph)PEAREESTSSGNVSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKEPAITSQNSPEAREESTSSGNVSNR 27 3 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KKEPAIT(0.002)S(0.123)QNS(0.875)PEAREESTSSGNVSNR 186.23 6.16E-17 75198000 28462 4339.4 39714 13924 43161 21496 77251 31937 94222 TRUE FALSE 27116.65767 4781.589793 41534.92618 12524.33307 50688.26473 20751.58813 65464.94114 29140.42697 108833.4665 0.249157346 0.043934921 0.381637446 0.115077958 0.465741526 0.190672858 0.601514803 0.267752447 1 16.73176273 -5 0.139671859 3.575751435 0.011893291 0.700059247 0.151455281 65.03191967 0.557044318 46.20157313 0.807697141 1.00E-05 5 -3.563858144 KKEPAITSQNSPEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKEPAITSQNSPEAR 15 2 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 186.85 2.05E-07 94278000 121280 103240 108920 115170 104780 109600 131920 121860 128720 FALSE TRUE 115547.3348 113760.2734 113914.0897 103592.8928 123053.5988 105804.5245 111793.1811 111189.2924 148681.2402 0.777148042 0.765128628 0.766163166 0.69674488 0.827633659 0.711619868 0.751898363 0.747836729 1 17.1818631 -1.07571467 5.569662701 1.000001735 0.756108872 0.824215598 0.035481448 6.74E-07 1.12E-07 0.030310191 0.00714413 0.084001169 1.07571467 -0.243892863 KKEPELFQTVAEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKEPELFQTVAEGLR 15 2 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 153.72 1.46E-06 261990000 331830 306880 280280 369440 249630 345510 409260 400230 301010 FALSE TRUE 316145.0535 338151.4209 293131.1152 332303.1893 293165.393 333544.9021 346819.8704 365183.7394 347689.0935 0.909275153 0.972568387 0.84308401 0.955748097 0.843182598 0.959319427 0.997499999 1.050316925 1 18.40743829 1.788965133 2.693967243 1.022206431 0.913688707 0.564512978 0.04394385 0.187875894 2.638168781 0.023903287 0.011353556 61.5127485 -1.788965133 -0.108517724 KKEPPR ddPTM_SK-BR-3_Trastuzumab_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 ; 82.386 0.033398 894000000 1058400 1013560 1027470 1443500 1013960 1268590 1432530 1579510 1293370 FALSE TRUE 1008371.53 1116842.916 1074580.516 1298396.638 1190794.303 1224658.41 1213971.238 1441199.731 1493939.214 0.674974939 0.74758257 0.719293333 0.869109416 0.797083504 0.819751164 0.812597478 0.964697705 1 20.51069002 6.071762129 0.075314971 1.250097701 3.58E-14 0.801974352 0.04515719 58.42513733 0.482908262 1.790416911 8.257618867 1179674.329 -6.071762129 -1.250097701 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KKEPPRAS(0.998)PPGGLAEPPGS(0.002)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.687)PPGGLAEPPGS(0.156)AGPQAGPT(0.156)VVPGS(0.002)ATPMETGIAETPEGR 175.58 2.21E-21 459610000 163081 145382 151567 152768 117091 160312 180947 188872 141403 TRUE FALSE 155372.4843 160196.5911 158516.4969 137411.4704 137511.6333 154760.3552 153340.2118 172333.3664 163331.0551 0.951273377 0.980809137 0.970522702 0.841306452 0.841919703 0.947525596 0.938830719 1.055116961 1 17.3174396 1.313163329 5.834837677 1.026895263 0.928729599 0.42578254 0.049555946 0.209302995 11.57572827 0.03796508 0.013343851 20.56663919 -1.313163329 -0.098165663 KKEPVGDDESVPENVLSFDDLTADALANLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEPVGDDESVPENVLSFDDLTADALANLK 30 2 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 230.75 1.26E-35 164870000 608290 523820 555920 652690 368070 654630 733350 713680 422510 FALSE TRUE 579537.3372 577197.8535 581409.4819 587080.3612 432261.2915 631959.999 621463.9886 651186.3957 488030.6929 1.187501822 1.1827081 1.191337943 1.202957867 0.885725627 1.294918554 1.273411688 1.33431443 1 18.89661236 KKEQSEVS(ph)VSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.5)VS(0.5)PR 83.418 0.0066844 501640000 242470 211100 222600 261380 163950 240450 269770 291920 219400 TRUE FALSE 231008.9236 232611.33 232806.4302 235105.5858 192542.8281 232123.1562 228611.6318 266357.9372 253423.4315 0.911553136 0.917876175 0.918646034 0.927718422 0.759767268 0.915949859 0.902093506 1.051039108 1 17.9511904 1.247512759 24.19363795 1.025519556 0.895960747 0.546148395 0.050038782 84.90023705 229454.1544 0.033300977 0.011752138 17.68124162 -1.247512759 -0.129558808 KKEQSEVSVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.003)VS(0.997)PR;KKEQSEVS(0.004)VS(0.996)PR 131.18 0.00010604 1571430000 3219910 2826080 3039750 3461070 2278180 3311380 3961000 3654340 2881640 TRUE FALSE 3067711.236 3114060.765 3179125.544 3113156.668 2675493.871 3196706.08 3356676.701 3334346.617 3328510.014 0.92164699 0.935571998 0.955119718 0.935300376 0.803811273 0.960401521 1.008462251 1.001753518 1 21.66644508 2.002671448 24.99995957 0.999367115 0.914958082 0.521852954 0.040741558 69.2075245 647653.3967 0.015251482 0.011199467 100.6170193 -2.002671448 -0.084409033 KKFS(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKFSFK 6 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KKFS(1)FK;KKFS(1)FK 69.423 0.052661 2405760000 5054500 5533600 3718500 6776100 2234600 5741700 4961600 4724600 1959800 TRUE FALSE 4815583.802 6097480.131 3888996.903 6094953.554 2624313.532 5542863.489 4204616.794 4310888.977 2263715.775 2.12729171 2.693571428 1.717970492 2.692455308 1.159294626 2.448568655 1.857396075 1.904341979 1 21.1102614 -1.209710151 0.186272217 8.36E-10 2.504710359 0.387240651 0.450137331 21.36332818 0.798521532 12.12026576 1.422967137 0.061700666 1.209710151 2.504710358 KKGDDS(ph)DEEDLCISNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KKGDDSDEEDLCISNK 16 2 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 KKGDDS(1)DEEDLCISNK;KKGDDS(1)DEEDLCISNK;KKGDDS(1)DEEDLCISNK;KKGDDS(1)DEEDLCISNK;KKGDDS(1)DEEDLCISNK 228.68 2.03E-15 1222810000 2791720 1848140 2104400 2678550 997590 2736560 2801890 2835480 857888 TRUE FALSE 2659760.928 2036467.567 2200888.822 2409297.065 1171569.38 2641792.241 2374410.22 2587190.339 990924.8896 2.68411961 2.05511799 2.221045051 2.431361943 1.182298873 2.665986362 2.396155597 2.610884404 1 19.91841618 4.606433779 2.729994374 2.150758583 2.716178083 0.088357532 0.567150061 0.868106932 10.44003861 0.126912977 0.961956795 40404.87608 -4.606433779 0.5654195 KKGEDEDKGPPCGPVNCNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKGEDEDKGPPCGPVNCNEK 20 3 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 75.533 0.0054167 93358000 242790 226700 193830 255720 117390 275980 250210 293930 107340 FALSE TRUE 231313.7979 249800.9877 202717.2972 230014.5398 137862.7788 266422.7434 212035.8691 268191.931 123985.739 1.865648419 2.014755808 1.635004952 1.855169326 1.111924484 2.148817643 1.710163369 2.163086926 1 16.91981466 3.737932928 24.99021678 1.705316491 1.940202116 0.076757848 0.379234913 144.049491 5735129.135 0.088887424 0.147292835 5469.314889 -3.737932928 0.234885625 KKGEPGPPDADGPLYLPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKGEPGPPDADGPLYLPYK 19 2 Q9P2E9;A0A087WVV2 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 49.606 0.084565 308530000 451420 339850 342380 437960 283150 412140 470130 441530 306740 FALSE TRUE 430082.2712 374481.1014 358078.4617 393935.4287 332531.2704 397867.4885 398403.034 402867.2925 354307.6726 1.21386666 1.056937601 1.010642697 1.111845605 0.938538158 1.122943473 1.124455 1.137054949 1 18.43464318 4.556198632 2.706489163 1.069006576 1.217781904 0.342848497 0.064943213 0.370514871 4.64112075 0.015766823 0.102340455 35991.39099 -4.556198632 0.148775328 KKGFNGCDS(ph)PEPDGEDSLEQSPLLEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKGFNGCDSPEPDGEDSLEQSPLLEDK 27 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KKGFNGCDS(1)PEPDGEDSLEQSPLLEDK 236.31 2.61E-45 134020000 130570 116910 112080 140120 63849 140770 140810 155720 60876 TRUE FALSE 124398.2149 128823.2619 117218.9789 126034.8714 74984.24538 135895.0996 119326.8483 142084.3313 70316.33917 1.769122459 1.832053025 1.667023344 1.792398081 1.066384375 1.932624781 1.697000295 2.020644603 1 16.10157234 KKGVPEKS(ph)PVLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKGVPEKSPVLEK 13 3 O00515;E9PDI4;A0A0J9YYF6 O00515 LAD1 Ladinin-1 1 KKGVPEKS(1)PVLEK 82.248 0.0091806 233640000 553610 346100 530270 473180 326290 582050 719130 612900 379810 TRUE FALSE 527441.9524 381367.9835 554583.404 425615.0474 383194.8727 561893.4626 609413.5108 559231.2268 438708.995 1.202259262 0.86929602 1.264125902 0.970153455 0.87346026 1.280788561 1.389106487 1.27472022 1 18.74290476 2.209971838 24.26419924 1.281929309 1.035662335 0.260527375 0.159601306 158.4828925 134508.0768 0.055310482 0.040858273 162.1704933 -2.209971838 -0.246266974 KKIPDPDS(ph)DDVSEVDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKIPDPDSDDVSEVDAR 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;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KKIPDPDS(1)DDVSEVDAR 139.83 3.57E-07 73251000 133130 90355 137780 120460 100910 144930 172390 148540 136210 TRUE FALSE 126837.2087 99562.27723 144097.3493 108351.1319 118508.6721 139911.0378 146088.7393 135533.0501 157332.7511 0.806171683 0.632813426 0.915876372 0.688674997 0.753235872 0.889268361 0.928533559 0.861442066 1 17.26345949 2.190886207 4.082496629 0.918824146 0.749480558 0.496716618 0.080469858 0.170692602 5.953937598 0.029033461 0.021398671 155.1980309 -2.190886207 -0.169343588 KKKEPIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKKEPIEK 8 3 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 62.303 0.035263 1540050000 1080450 1083240 1086730 1314230 704860 1296390 1340850 1492380 874060 FALSE TRUE 1029379.27 1193623.388 1136557.645 1182121.104 827787.3608 1251495.689 1136278.706 1361699.296 1009604.761 1.019586386 1.182267986 1.125745133 1.170875128 0.819912299 1.239589727 1.125468847 1.348744923 1 19.94535919 KKLEEER ddPTM_SK-BR-3_Trastuzumab_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 1212850000 3511120 2926950 3118820 3754150 2398070 3669350 4134010 3983630 2910130 FALSE TRUE 3345156.316 3225209.533 3261820.982 3376775.71 2816292.649 3542279.489 3503290.848 3634802.239 3361418.098 0.995162226 0.959478839 0.970370507 1.00456879 0.837828728 1.053805087 1.04220622 1.081330002 1 21.68063857 KKLGAGEGGEASVS(ph)PEKTSTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKLGAGEGGEASVSPEKTSTTSK 23 3 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KKLGAGEGGEASVS(0.988)PEKT(0.008)S(0.002)T(0.001)TSK 95.459 0.0028014 281000000 658480 410460 627580 559460 340840 741360 903960 757590 434170 TRUE FALSE 627354.9554 452286.3407 656355.1638 503222.0179 400282.3881 715686.5173 766044.2996 691251.4034 501498.8662 1.250959868 0.901869119 1.308786935 1.003436003 0.79817207 1.427094986 1.527509535 1.37837082 1 18.93588691 2.209522053 24.99185777 1.395089318 1.059519122 0.301127319 0.202764186 201.7647621 173646.3772 0.07025882 0.051897892 162.0026253 -2.209522053 -0.335570196 KKMDLIDLEDETIDAEVMNSLAVTMDDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKMDLIDLEDETIDAEVMNSLAVTMDDFR 29 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 97.771 0.0046495 48024000 231260 156930 215270 204730 164750 213960 299780 252280 175740 FALSE TRUE 220328.7981 172921.3454 225140.3424 184150.1514 193482.3478 206550.5116 254043.0552 230189.0258 202992.8616 1.085401705 0.851859243 1.109104727 0.907175503 0.953148531 1.017525985 1.251487629 1.133975963 1 17.63106947 1.926320618 7.094558434 1.152491002 0.97631874 0.317926334 0.096470866 0.24127818 20.03283595 0.037625075 0.023385508 84.39575802 -1.926320618 -0.176172262 KKNDIYGED ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KKNDIYGED 9 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;; 117.31 0.0046566 13562790000 13797800 12101400 12138000 14281500 9044610 14177800 15553600 15134400 10389110 FALSE TRUE 13145605.34 13334546.42 12694539.31 12845896.49 10621987.12 13686819.23 13180612.66 13809151.7 12000200.12 1.095448843 1.111193671 1.057860634 1.070473522 0.885150832 1.140549249 1.098366071 1.150743452 1 23.51655513 -1.251141925 5.281158641 0.999991296 1.078446154 0.095227842 0.073554512 7.23E-06 1.03E-06 0.068314104 0.016100002 0.056086466 1.251141925 0.078454859 KKNLQYYDISAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKNLQYYDISAK 12 2 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 182.07 9.76E-06 1845080000 3134000 1615340 3270400 2285600 2780800 3187200 4836900 3539900 3871300 FALSE TRUE 2985862.031 1779944.982 3420351.075 2055847.146 3265770.64 3076826.465 4098942.069 3229927.59 4471641.432 0.667732884 0.398051814 0.764898332 0.459752236 0.730329274 0.688075399 0.916652673 0.722313638 1 22.09237308 1.895753485 0.640783945 0.960308881 0.543482627 0.523868802 0.124372001 0.488499903 0.401539858 0.102813443 0.05857332 78.65991723 -1.895753485 -0.416826254 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTT(0.004)GS(0.944)PT(0.052)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.001)DT(0.003)T(0.012)GS(0.979)PT(0.004)EFLEEK 165.44 2.82E-20 988780000 906910 729150 737310 890280 412281 912420 977030 961100 389223 TRUE FALSE 864042.1616 803451.214 771116.3928 800787.363 484182.6759 880822.6666 827966.1291 876940.9889 449581.715 1.921880123 1.787108299 1.715186288 1.781183123 1.076962563 1.959204828 1.841636574 1.950570852 1 18.77822384 3.981529708 1.411537435 1.662035996 1.909300187 0.078477518 0.333150687 1.398428369 5.08468352 0.093245732 0.325728859 9583.622702 -3.981529708 0.247264192 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPT(ph)EFLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.001)T(0.013)GS(0.435)PT(0.55)EFLEEK 116 4.90E-07 497070000 510090 446610 422780 498180 264710 516690 541470 598700 248770 TRUE FALSE 485979.0566 492120.0668 442164.8812 448101.9999 310875.3402 498796.8957 458858.8067 546274.6541 287347.9811 1.691256207 1.712627543 1.538778451 1.559440224 1.081877586 1.735863582 1.596874998 1.901090977 1 18.13243939 3.689136113 4.169495582 1.516417194 1.703131266 0.090718574 0.270889426 0.537788218 20.03305487 0.067807808 0.111655267 4888.055329 -3.689136113 0.186714072 KKPFVYTQGQAVLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPFVYTQGQAVLNR 15 2 Q9H4A4;A6NKB8;C9JMZ3;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 254.58 5.97E-25 1052700000 1233200 1036900 1055100 1238200 1006400 1213900 1411700 1232900 1210000 FALSE TRUE 1174909.08 1142561.289 1103477.379 1113733.784 1181915.841 1171862.339 1196319.237 1124940.74 1397640.62 0.840637474 0.817492904 0.789528698 0.796867068 0.845650752 0.838457556 0.855956259 0.804885551 1 20.41456201 -5 0.31776223 2.631461602 0.817967168 0.86126954 0.022188774 113.6352932 1.011521279 124.5017388 0.020115138 1.00E-05 5 -1.813494434 KKPGDASSLPDAGLS(ph)PGSQVDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KKPGDASSLPDAGLSPGSQVDSK 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 KKPGDAS(0.004)S(0.004)LPDAGLS(0.991)PGS(0.001)QVDSK;KKPGDASSLPDAGLS(0.999)PGS(0.001)QVDSK;KKPGDASSLPDAGLS(0.998)PGS(0.001)QVDSK 107.2 0.00071477 1274450000 1346430 1061420 1185050 1489230 670910 1524790 1577370 1514820 825978 TRUE FALSE 1282786.922 1169579.905 1239385.715 1339529.771 787916.4916 1471986.14 1336713.236 1382174.33 954066.4497 1.344546727 1.225889355 1.299055967 1.404021461 0.825850748 1.542854945 1.401069324 1.448719144 1 19.86373023 KKPGDASSLPDAGLSPGS(ph)QVDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPGDASSLPDAGLSPGSQVDSK 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 KKPGDASSLPDAGLS(0.142)PGS(0.858)QVDS(0.001)K 121.72 5.38E-05 108010000 132400 104110 116520 145660 81112 135320 148140 165120 90384 TRUE FALSE 126141.7144 114718.9274 121862.5573 131017.9801 95257.90712 130633.8345 125538.5222 150661.2174 104400.2891 1.208250623 1.098837258 1.167262642 1.25495802 0.912429534 1.251278474 1.202472937 1.443111113 1 16.67176618 KKPLKQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPLKQPK 8 3 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 55.531 0.054034 638070000 1222300 942270 826720 1143200 699290 1123900 1542300 1470000 851370 FALSE TRUE 1164524.301 1038288.384 864625.9297 1028283.364 821245.9546 1084979.061 1306993.809 1341279.007 983396.1114 1.1841864 1.055819087 0.879224475 1.045645139 0.835112062 1.1032981 1.329061396 1.363925474 1 19.90741312 1.944166777 5.987139201 1.25798056 1.016825901 0.368476565 0.135548101 0.220210786 17.176002 0.057676838 0.035593312 87.93601426 -1.944166777 -0.241154659 KKPNATRPVT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_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 KKPNATRPVT(1)PPR;KKPNAT(0.009)RPVT(0.991)PPR 86.378 0.0091067 2606500000 3009100 2976100 2632700 3573600 2032990 3207600 3239400 3275100 2623700 TRUE FALSE 2866865.806 3279367.974 2753411.899 3214374.939 2387542.812 3096520.008 2745170.034 2988314.882 3030569.996 0.945982376 1.0820961 0.908545885 1.060650288 0.787819722 1.021761587 0.905826309 0.986057041 1 21.53115773 KKPRPPPALGPEETSASAGLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKPRPPPALGPEETSASAGLPK 22 3 Q01105 Q01105 SET Protein SET 0 ; 89.831 0.0010822 1093750000 1576780 1331370 1276850 1671970 1002270 1584310 1824830 1758490 1220430 FALSE TRUE 1502248.734 1467038.117 1335394.835 1503900.399 1177065.571 1529444.947 1546418.668 1604507.293 1409688.051 1.065660401 1.040682806 0.947298116 1.066832054 0.834983009 1.084952764 1.096993528 1.138200251 1 20.42694451 2.049851887 24.99999546 1.089626907 1.002241846 0.245297967 0.075360222 148.3208314 74380.01352 0.026726787 0.019739035 112.1635864 -2.049851887 -0.087385061 KKPS(ph)SEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.5)S(0.5)EER;KKPS(0.5)S(0.5)EER;KKPS(0.927)S(0.073)EER 101.93 0.0039874 262409000 425167 473764 345572 486067 203723 445997 380212 453392 238073 TRUE FALSE 405070.1985 522041.0902 361416.818 437206.6217 239252.2267 430552.0121 322203.6763 413690.5929 274992.1449 1.473024615 1.898385462 1.314280516 1.589887674 0.870032949 1.565688402 1.1716832 1.504372399 1 18.06903088 3.360731663 1.885918874 1.267920892 1.672583981 0.273637622 0.257793399 0.364847489 2.650423064 0.07115926 0.108592013 2294.730368 -3.360731663 0.404663089 KKPS(ph)SEERETEISLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPSSEERETEISLK 15 3 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.498)S(0.498)EERET(0.004)EISLK 122.49 0.00060005 125270000 86276 84551 84290 99244 49711 97834 99396 109960 60687 TRUE FALSE 82197.90446 93166.84303 88154.77987 89267.80457 58380.58266 94445.98405 84231.31467 100331.3195 70098.03001 1.172613616 1.329093599 1.257592829 1.273470946 0.832841988 1.347341488 1.20162171 1.43130013 1 16.09708628 -2.300951103 2.124481735 3.26E-05 1.229419701 0.171463993 0.159375158 3790497.779 655509.0408 18103104.99 0.035461649 0.005000908 2.300951103 1.229387052 KKPSS(ph)EER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.167)S(0.833)EER 110.08 0.0027527 108120000 241340 297330 200700 299720 128430 276190 229950 276270 131710 TRUE FALSE 229932.3365 327628.265 209902.2935 269591.5762 150828.1513 266625.471 194866.9042 252078.3342 152134.9141 1.511371258 2.153537647 1.379711519 1.772055926 0.9914105 1.752559382 1.280882205 1.656939406 1 17.21499176 -0.174492914 0.080128729 1.18E-09 2.480256871 0.257902196 0.309379175 61.50583926 1.421488962 28.55797744 15.3166056 0.669124737 0.174492914 2.48025687 KKPSS(ph)EERETEISLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKPSSEERETEISLK 15 3 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.132)S(0.867)EERET(0.001)EISLK 169.39 6.63E-06 148190000 142820 136060 136560 161950 91101 177810 180980 172850 80332 TRUE FALSE 136069.1816 149924.6687 142821.4111 145670.4783 106988.9856 171652.3951 153368.1771 157714.3377 92789.47628 1.466429029 1.61575078 1.539198375 1.569903012 1.153029307 1.849912318 1.65286176 1.699700699 1 16.50167357 4.740144456 5.369254389 1.548780628 1.463219801 0 0.255406763 1.09720051 103.7225356 0.054625532 0.341831178 54972.36934 -4.740144456 -0.085560827 KKQDPPVTHDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKQDPPVTHDLR 12 2 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 119.01 0.00033828 336550000 272630 247290 230530 292520 200059 276990 298200 305960 245770 FALSE TRUE 259743.3202 272489.1321 241100.0285 263115.3338 234949.2263 267397.7668 252704.1132 279168.5204 283882.7564 0.914966881 0.959865036 0.849294376 0.926845072 0.827627677 0.941930289 0.890170704 0.983393722 1 18.11493569 1.169077481 5.378970636 0.997253053 0.906052647 0.465612343 0.04001041 0.184894122 9.388966167 0.035520297 0.009118866 14.75969831 -1.169077481 -0.091200405 KKQPAS(ph)PDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKQPASPDGR 10 2 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 KKQPAS(1)PDGR 52.344 0.078646 36078000 78207 91997 65232 80063 56858 76640 76799 76066 61738 TRUE FALSE 74510.3101 101371.5989 68222.95172 72014.91513 66774.0172 73985.93758 65081.90204 69405.25779 71312.01373 1.044849335 1.421522035 0.956682446 1.009856704 0.936364207 1.03749612 0.912635875 0.973261785 1 16.12185752 3.710504557 24.70345846 0.971651746 1.233185696 0.556364739 0.095739613 360.7710897 317660.1732 0.02382784 0.036922389 5134.57565 -3.710504557 0.261533949 KKQPAS(ph)PDGRT(ph)SPINEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KKQPASPDGRTSPINEDIR 19 3 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 KKQPAS(1)PDGRT(0.589)S(0.411)PINEDIR;KKQPAS(1)PDGRT(0.539)S(0.461)PINEDIR;KKQPAS(1)PDGRT(0.532)S(0.468)PINEDIR 121.35 6.69E-05 1072170000 878470 601350 837660 826570 657740 840630 1161870 857310 838620 TRUE FALSE 836946.4641 662628.2487 876067.5396 743481.6132 772449.6478 811518.7723 984605.3923 782239.3915 968668.9065 0.864017063 0.684060616 0.90440349 0.76752914 0.797434131 0.837766926 1.016451943 0.807540519 1 19.88564411 1.939997678 6.470800982 0.940455506 0.797263311 0.386436624 0.079333733 0.217193294 18.67144911 0.031255198 0.019368039 87.09589323 -1.939997678 -0.143192194 KKQPAS(ph)PDGRTS(ph)PINEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKQPASPDGRTSPINEDIR 19 3 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 KKQPAS(1)PDGRT(0.189)S(0.811)PINEDIR;KKQPAS(1)PDGRT(0.16)S(0.84)PINEDIR 109.97 0.0003516 498710000 742920 495010 743240 716950 510400 699640 912800 781330 702280 TRUE FALSE 707803.6439 545452.0818 777318.2892 644880.8239 599413.5984 675411.2914 773535.5953 712912.6031 811185.9957 0.872554072 0.67241309 0.958249148 0.794985154 0.738934846 0.832621982 0.953585983 0.878852208 1 19.62967322 1.837611213 4.280707372 0.937015574 0.800276584 0.37546192 0.08041502 0.231841132 6.728577843 0.037070269 0.02057582 68.80360805 -1.837611213 -0.13673899 KKQQEEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 98.156 0.0031322 65987000 216100 177070 208780 260060 222480 231930 309140 270360 283690 FALSE TRUE 205885.3813 195113.6343 218352.7695 233918.2747 261280.4416 223898.2059 261975.0153 246685.8451 327683.1963 0.628306192 0.59543375 0.66635327 0.713854959 0.797356851 0.683276434 0.799476501 0.752818112 1 18.32194217 -5 0.068651921 2.125531913 0.286704456 0.858949209 0.042863699 99.47653039 0.492660143 17.6348207 2.287254395 1.00E-05 5 -1.838827457 KKQSDVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKQSDVMR 8 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 95.523 0.0053937 693450000 1248420 597860 608340 584920 1035160 770090 1573670 1015180 1398880 FALSE TRUE 1189409.661 658782.6137 636232.9907 526122.7303 1215691.576 743421.5902 1333577.739 926285.4574 1615811.166 0.736106846 0.407710151 0.393754545 0.325609045 0.752372308 0.460091876 0.825330192 0.573263434 1 20.62382717 0.973496334 0.60945195 0.991121742 0.498047078 0.456144754 0.160632055 0.775657562 0.681387293 0.159334036 0.067700545 9.407978888 -0.973496334 -0.493074664 KKS(ph)IPLSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKSIPLSIK 9 2 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 KKS(1)IPLSIK 98.167 0.0032337 608420000 1093300 854300 923210 1168500 678410 1196600 1509000 1470600 981520 TRUE FALSE 1041621.876 941354.1413 965540.0917 1051040.16 796724.4892 1155161.442 1278774.335 1341826.468 1133729.109 0.918757283 0.830316637 0.851649732 0.927064633 0.702746788 1.018904281 1.127936405 1.183551218 1 20.11264454 2.035446011 7.243149755 1.107413785 0.854358761 0.717824002 0.075139064 0.092522743 14.6836374 0.026071011 0.01900578 108.5040656 -2.035446011 -0.253055024 KKS(ph)PIINESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(0.999)PIINES(0.001)R;KKS(0.992)PIINES(0.008)R;KKS(0.996)PIINES(0.004)R;KKS(1)PIINESR;KKS(1)PIINESR 162.94 3.45E-06 9662150000 14656910 12671170 12433920 14911930 8525520 15117520 16210080 15488130 10463530 TRUE FALSE 13964106.91 13962376.63 13004027.53 13412954.47 10012367.99 14593996.49 13736934.58 14131907.23 12086160.79 1.155379872 1.15523671 1.075943615 1.109777927 0.828415918 1.20749647 1.136583801 1.169263546 1 23.5268527 7.999384735 0.009142966 7.51E-08 2.339704523 0.052838821 0.106520179 54022.15541 38.20699228 4266.172187 5594.422843 99858430.23 -7.999384735 2.339704448 KKS(ph)PNELVDDLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK 179.78 7.02E-06 9618942000 4715130 4199900 3928730 4928090 2224611 5237120 4899320 5485540 2171792 TRUE FALSE 4492255.149 4627874.585 4108866.157 4432709.03 2612582.454 5055757.221 4151838.752 5005197.037 2508582.411 1.790754463 1.844816644 1.637923529 1.767017504 1.041457694 2.015384146 1.65505376 1.995229263 1 21.2584409 3.729165279 18.56053638 1.627129775 1.81778548 0.064078051 0.340664128 57.25818074 113119.6501 0.081398383 0.1291544 5360.006044 -3.729165279 0.190655705 KKSEAPSGESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 125.54 0.00018343 217484000 241040 197318 209482 243482 212225 237281 275986 289820 334220 FALSE TRUE 229646.5169 217424.9285 219086.9569 219006.7268 249236.9728 229063.8995 233879.2669 264441.8244 386049.1306 0.594863448 0.563205331 0.567510556 0.567302733 0.645609465 0.593354268 0.605827726 0.684995259 1 18.55842494 0.244881331 0.745804535 1.00915419 0.57965887 0.968519959 0.023136381 0.444070046 0.315540744 0.031098372 0.007916208 1.757443333 -0.244881331 -0.42949532 KKSPIINES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(0.31)PIINES(0.69)R 60.628 0.076279 5213200000 657370 573020 533800 677520 370840 628780 693110 726410 461600 TRUE FALSE 626297.4229 631411.3895 558275.258 609414.4024 435514.3786 607005.1909 587363.3397 662801.6895 533182.5705 1.174639715 1.184231114 1.047062093 1.142975101 0.816820359 1.138456552 1.101617668 1.243104569 1 19.02427009 3.745807471 23.78568711 1.072755133 1.179435433 0.143794116 0.110856037 514.8587441 1689862.452 0.027235838 0.047775581 5569.38795 -3.745807471 0.1066803 KKT(ph)PVTEQEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKTPVTEQEEK 11 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KKT(0.998)PVT(0.002)EQEEK 196.95 2.80E-06 161190000 417470 362730 317930 418410 166040 471860 408200 456440 192110 TRUE FALSE 397737.0204 399692.5994 332507.405 376350.6319 194997.3234 455519.3699 345921.5929 416471.6939 221901.4376 1.792403982 1.801216809 1.498446376 1.696026109 0.878756467 2.052800445 1.558897484 1.876831887 1 17.75955949 3.74538451 23.0644445 1.547557817 1.796810459 0.094510285 0.355188298 432.7573592 1462682.392 0.083195433 0.145472945 5563.966544 -3.74538451 0.249252642 KKTDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KKTDELR 7 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ;;;; 108.74 0.0040408 1387188000 3906260 2977990 3065070 4076420 3091520 3841570 4419100 4159840 3621060 FALSE TRUE 3721618.831 3281450.567 3205606.491 3666650.517 3630680.109 3708535.468 3744885.133 3795582.357 4182595.491 0.889786937 0.78454887 0.766415614 0.876644783 0.868044762 0.886658888 0.895349584 0.90747058 1 21.99596705 1.231912875 0.5039277 0.999885001 0.821641484 0.66307742 0.037453458 0.544041466 0.364878329 0.041846866 0.022450867 17.05740162 -1.231912875 -0.178243517 KKTEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKTEFLDLDNSPLSPPSPR 19 2 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KKTEFLDLDNSPLSPPS(1)PR;KKTEFLDLDNSPLS(0.002)PPS(0.998)PR 135.68 3.81E-06 1963080000 852020 747270 704450 891110 645280 844930 951490 941140 834450 TRUE FALSE 811746.7031 823417.6626 736749.7293 801533.9298 757816.6277 815669.8622 806322.7252 858728.7923 963852.2442 0.842189981 0.854298641 0.764380364 0.831594194 0.786237343 0.846260272 0.836562585 0.890934059 1 19.87845248 0.853973905 1.390937122 0.999978589 0.82288242 0.815086484 0.027266042 0.25474678 0.941692358 0.025580686 0.007615744 7.14453396 -0.853973905 -0.177096169 KKVEAQLQELQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKVEAQLQELQVK 13 2 P35579 P35579 MYH9 Myosin-9 0 ; 138.02 3.03E-05 1558880000 3943220 3375500 3415520 4102200 2601740 3878630 4513100 4361300 3211310 FALSE TRUE 3756831.805 3719467.288 3572124.97 3689839.062 3055482.632 3744312.071 3824543.706 3979401.451 3709303.554 1.012813255 1.002740065 0.963017698 0.994752521 0.823734857 1.00943803 1.031067868 1.072816337 1 21.82271691 2.0096315 24.99945948 1.033623309 0.967331885 0.281213814 0.055162442 297.0560031 771033.4287 0.020891047 0.015409334 102.2425093 -2.0096315 -0.066291423 KKVENTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKVENTR 7 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 93.162 0.0085139 2312400000 4164600 3701500 3581700 5161600 3528700 4688600 5975900 5665600 5142000 FALSE TRUE 3967747.611 4078687.058 3745924.488 4642746.162 4144104.163 4526232.606 5064166.7 5169490.029 5939395.098 0.668039008 0.686717585 0.630691245 0.781686701 0.697731687 0.762069627 0.852640145 0.870373151 1 22.50188458 1.457256412 0.581481438 1.002638128 0.666833149 0.897192716 0.035755807 0.193109494 0.155588602 0.032034891 0.016639295 28.65869511 -1.457256412 -0.335804979 KKVPVSVNLLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKVPVSVNLLSK 12 2 O76021;J3QSV6;I3L3C4 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 100.55 0.0017826 85134000 607540 552190 512000 656090 418220 578840 704730 660550 537930 FALSE TRUE 578822.7882 608458.7888 535475.7064 590138.5867 491157.4356 558794.6257 597210.4952 602708.7402 621349.437 0.931557597 0.979253786 0.861794788 0.949769247 0.790468948 0.899324265 0.961150779 0.969999656 1 19.24504532 1.602106665 3.846476882 0.97986979 0.909371971 0.317894075 0.051703689 0.263113956 8.996937533 0.032221577 0.014025678 40.00429907 -1.602106665 -0.070497819 KKWNLDELPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKWNLDELPK 10 2 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 105.46 0.0014321 561290000 3152900 3070800 2632000 3484800 1828990 3379700 3483200 3682400 2021680 FALSE TRUE 3003868.665 3383718.011 2752679.803 3134501.283 2147965.277 3262660.142 2951773.867 3359949.534 2335191.809 1.286347723 1.44901074 1.178781029 1.342288574 0.919823917 1.397170086 1.264039149 1.438832357 1 21.15510962 -1.774217644 2.777883511 0.931546253 1.290148748 0.252985314 0.153389659 32645626.66 25002122.84 15179048.9 0.034863266 0.01681831 1.774217644 0.358602495 KKWPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKWPER 6 2 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 58.981 0.077232 956780000 1222400 1177500 1019500 1349500 905950 1261300 1382700 1273700 994400 FALSE TRUE 1164619.575 1297488.589 1066245.083 1213845.696 1063947.393 1217620.865 1171743.72 1162168.076 1148606.473 1.013941329 1.129619777 0.92829451 1.056798585 0.926294095 1.060085323 1.020143754 1.011807005 1 20.13145317 3.748759267 24.99698147 1.005148071 1.071780546 0.238215503 0.052489966 904.2898347 2216413.674 0.012225549 0.021748383 5607.370682 -3.748759267 0.066632475 KKYDVDTLDMVFLDHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKYDVDTLDMVFLDHWK 17 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 272.31 7.48E-36 1153180000 2403600 1568450 1966180 2283470 1617660 2328480 2780250 2630430 1497870 FALSE TRUE 2289986.591 1728276.838 2056331.298 2053931.257 1899779.392 2247844.154 2356071.8 2400095.604 1730152.03 1.323575358 0.99891617 1.188526362 1.187139177 1.098041883 1.299217708 1.361771543 1.387216593 1 20.72246738 2.223650778 24.47130717 1.299904019 1.154916445 0.099663558 0.133157609 268.5713455 440798.5072 0.045402769 0.033679951 167.3596575 -2.223650778 -0.144987574 KKYDVDTLDMVFLDHWKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKYDVDTLDMVFLDHWKDR 19 3 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 181.14 1.92E-14 1455850000 2984600 914640 3195500 2014860 2934600 2939500 5739600 3292300 3152700 FALSE TRUE 2843523.873 1007842.856 3342016.836 1812322.445 3446393.311 2837704.378 4863918.605 3004008.758 3641604.614 0.780843659 0.276757903 0.917731931 0.497671394 0.946394152 0.779245601 1.335652582 0.824913486 1 21.79614286 2.481364916 1.372287126 1.070441834 0.581926831 0.364696041 0.226380286 0.35591208 1.355444113 0.106363792 0.079068965 302.9457862 -2.481364916 -0.488515003 KKYELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KKYELR 6 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 110.63 0.01605 3296500000 6661200 2976200 4403600 5814200 5802200 5425900 8489000 5986100 6667100 FALSE TRUE 6346338.277 3279478.164 4605509.416 5229745.57 6814101.843 5237999.722 7193847.139 5461925.35 7700999.817 0.824092771 0.42585096 0.598040453 0.679099558 0.884833399 0.680171386 0.934144567 0.709248861 1 22.87661433 2.917443825 3.714420812 0.831915781 0.60684763 0.383346204 0.133415164 0.23716327 6.168396297 0.039198494 0.042808486 826.882547 -2.917443825 -0.225068151 KKYPS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KKYPSPQK 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 KKY(0.002)PS(0.998)PQK 66.267 0.032416 417490000 1423500 1145400 1041900 1429300 636030 1436800 1566000 1525500 783800 TRUE FALSE 1356213.976 1262117.562 1089672.146 1285624.049 746953.4306 1387043.256 1327077.938 1391919.133 905347.7009 1.498003446 1.39406944 1.203595198 1.420033482 0.825045924 1.532055866 1.465821294 1.537441506 1 19.78811244 4.108672837 3.035778405 1.313111333 1.475688313 0.073975444 0.231668224 0.7181394 12.92369359 0.057487203 0.14672468 12843.18791 -4.108672837 0.16257698 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 33 1 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;; 286.33 1.76E-74 644760000 530069 428186 525557 471922 528832 536511 781720 600379 548740 FALSE TRUE 505013.6889 471818.6402 549654.3083 424483.504 621060.1334 517931.4895 662454.2567 547806.632 633835.7966 0.796757917 0.744386232 0.867187229 0.669705792 0.979843891 0.817138275 1.045151221 0.864272158 1 19.27374961 2.724071913 24.97343929 0.942100123 0.77377629 0.530258177 0.08028933 570.065501 982591.4509 0.023004266 0.021776196 529.7511555 -2.724071913 -0.168323833 KLAEVTEEEWLSIPEVGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLAEVTEEEWLSIPEVGDAR 20 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 106.03 0.00039671 22567000 51724 44363 53849 49169 46852 45412 68645 55385 58339 FALSE TRUE 49279.10903 48883.64014 56318.02991 44226.43871 55022.97397 43839.37105 58171.9445 50535.19579 67385.91417 0.731296884 0.725428166 0.835753742 0.656315778 0.816535245 0.650571734 0.863265643 0.749937081 1 16.04015943 -0.396515469 0.437588027 1.05218059 0.735689039 0.559695334 0.069266743 4.923155903 0.928053404 0.452040302 0.034978631 0.401314204 0.396515469 -0.316491551 KLALDIEIATYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLALDIEIATYR 12 1 K7EPI4 K7EPI4 GFAP 0 ; 137.81 0.00013732 627350000 1209960 1091880 997680 1286450 1032510 1067470 1300040 1178550 1132940 FALSE TRUE 1152767.589 1203143.813 1043424.615 1157133.602 1212579.417 1030503.246 1101695.021 1075349.914 1308630.549 0.880896132 0.919391508 0.797340866 0.884232454 0.926601796 0.787466904 0.84186864 0.821736826 1 20.31962642 3.794590632 24.99679385 0.856709284 0.900143824 0.034263467 0.063838434 697.6434171 311238.7875 0.014795385 0.026672752 6231.471771 -3.794590632 0.04343454 KLAPEYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLAPEYEK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 112.75 0.0047803 625150000 1031220 1009810 882940 1117500 835340 1035210 1150380 1165910 956110 FALSE TRUE 982476.2743 1112710.787 923423.6723 1005166.777 981023.0315 999360.4181 974868.4028 1063816.74 1104378.656 0.889619035 1.007544633 0.8361477 0.91016498 0.888303144 0.9049074 0.88273021 0.963271731 1 20.07480348 1.039717007 4.921255335 0.999659355 0.908879513 0.377818962 0.042888861 0.188107634 10.39878279 0.041147242 0.01042004 10.95763947 -1.039717007 -0.090779842 KLAS(ph)YMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLASYMNK 8 1 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 KLAS(0.999)Y(0.001)MNK 52.79 0.060377 188030000 730290 553740 637790 736190 795380 643840 877140 736840 910100 TRUE FALSE 695770.639 610166.7356 667033.3024 662186.7825 934094.0202 621543.6594 743316.1832 672318.3834 1051233.66 0.661861074 0.580429222 0.6345243 0.629913984 0.88856936 0.591251672 0.707089405 0.639551804 1 20.00365195 -5 0.245505616 2.983891886 0.630398978 0.591812808 0.086746963 118.4173275 1.177065783 117.6764372 0.120948665 1.00E-05 5 -2.353492908 KLAT(ph)PPAAQESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLATPPAAQESSR 13 1 H0Y760;Q9Y4B4 H0Y760 RAD54L2 Helicase ARIP4 1 KLAT(0.999)PPAAQESSR 58.427 0.062742 128210000 356430 272870 271220 374160 239790 326130 340760 334660 271550 TRUE FALSE 339582.2603 300675.7632 283655.7053 336548.7259 281609.3001 314836.0363 288770.8035 305355.3963 313660.5871 1.08264243 0.95860231 0.904339649 1.072971039 0.897815383 1.00374752 0.920647398 0.973521726 1 18.25884473 4.533508279 2.597478512 0.962667077 1.08542544 0.32149755 0.052557742 0.333103154 3.859422431 0.011584134 0.073021147 34159.24626 -4.533508279 0.122758364 KLAVNMVPFPR ddPTM_SK-BR-3_Trastuzumab_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 ; 178.54 1.20E-05 5525000000 6655900 4900900 3452800 4211000 6711300 4054000 7775700 5586300 7543700 FALSE TRUE 6341288.798 5400307.282 3611114.295 3787702.28 7881748.595 3913608.963 6589374.154 5097133.957 8713538.468 0.727751283 0.619760537 0.414425702 0.434691635 0.904540517 0.449141182 0.756222536 0.584967172 1 23.05482727 -0.783649647 0.495822808 1.098073354 0.604533345 0.382450402 0.155361493 14.69650906 2.593936618 2.385712609 0.070648104 0.16456988 0.783649647 -0.493540009 KLCERPLASSPPRLY(ph)EDDETPGALSGLT(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLCERPLASSPPRLYEDDETPGALSGLTK 29 3 O75969 O75969 AKAP3 A-kinase anchor protein 3 2 KLCERPLAS(0.21)S(0.225)PPRLY(0.565)EDDET(0.361)PGALS(0.309)GLT(0.33)K 42.241 0.060961 317780000 253270 272890 170030 257020 98802 273290 206840 261430 73534 TRUE FALSE 241298.429 300697.8013 177826.0437 231183.8613 116033.0375 263825.8988 175282.7591 238537.8033 84937.27716 2.840901393 3.540233585 2.093616014 2.721818606 1.366102628 3.106126163 2.063672924 2.80839946 1 16.37411024 0.221563602 0.130921455 8.40E-14 3.7776001 0.388192024 0.611406106 16.20485261 0.825277191 15.20876873 7.180268267 1.665572732 -0.221563602 3.7776001 KLCLNICVGESGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLCLNICVGESGDR 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 157.68 8.39E-06 1181290000 716400 635340 674840 750430 686140 701960 818670 738670 819230 FALSE TRUE 682537.1918 700081.8683 705782.0815 674995.3507 805802.5988 677650.9492 693766.8556 673988.1389 946272.0044 0.721290695 0.739831534 0.745855397 0.713320639 0.851554939 0.716127019 0.733157963 0.712256239 1 19.85189542 -1.376972187 3.196602 1.002628995 0.741113213 0.79915447 0.04069833 15150037.03 20879693.29 373314.4642 0.009341521 0.041978587 1.376972187 -0.261515782 KLCQGLFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLCQGLFFR 9 1 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 125.82 0.00078717 570790000 596860 341220 423340 354650 609590 409020 821270 565200 718530 FALSE TRUE 568647.6107 375990.7059 442750.5577 318999.9082 715902.303 394855.5348 695970.1778 515708.0917 829955.9627 0.685153955 0.453024887 0.533462711 0.384357632 0.862578661 0.475754802 0.838562778 0.621368018 1 19.66267526 0.875613035 0.474570587 1.009764014 0.533506042 0.440332274 0.14933204 1.055849878 0.574019499 0.17698865 0.080211512 7.509534808 -0.875613035 -0.476257972 KLCQPQSTGSLLGDPAASS(ph)PPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLCQPQSTGSLLGDPAASSPPGER 24 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 KLCQPQSTGSLLGDPAAS(0.097)S(0.903)PPGER;KLCQPQSTGSLLGDPAAS(0.123)S(0.877)PPGER;KLCQPQSTGSLLGDPAAS(0.031)S(0.969)PPGER;KLCQPQSTGSLLGDPAAS(0.022)S(0.978)PPGER 183.47 1.73E-17 1987430000 999700 781500 942420 1016700 961580 947300 1177260 1014920 1136670 TRUE FALSE 952446.1622 861135.7385 985630.8892 914499.3844 1129279.248 914494.7635 997647.3651 926048.2244 1312938.978 0.725430639 0.655884053 0.750705787 0.696528475 0.860115562 0.696524956 0.759858136 0.705324649 1 20.32436843 -5 0.263855431 2.791037361 0.706845134 0.69782157 0.055208407 105.5442027 1.03225371 102.7150844 0.065585595 1.00E-05 5 -2.084192227 KLDAGNQLALIEELHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDAGNQLALIEELHK 16 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 102.99 0.00095668 153300000 168270 136460 153950 185920 131880 160450 191330 211360 155380 FALSE TRUE 160316.2106 150365.4291 161008.7598 167230.9684 154879.8302 154893.5763 162139.0945 192852.1979 179475.5368 0.893248258 0.837804593 0.897106996 0.931775836 0.862957888 0.863034478 0.903404984 1.074531946 1 17.45342769 1.324934281 5.335879173 1.036060861 0.879778944 0.811209197 0.030778394 0.075041553 3.262490377 0.02124269 0.007397381 21.13169243 -1.324934281 -0.156281917 KLDALCNIHENIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDALCNIHENIR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 140.03 2.54E-05 414570000 875510 756830 780990 842280 822160 791040 973540 896950 897160 FALSE TRUE 834126.3774 833951.8374 816799.164 757612.4142 965544.4437 763646.0865 825008.5927 818408.303 1036286.991 0.804918314 0.804749886 0.788197836 0.731083591 0.931734599 0.736905986 0.796119801 0.789750629 1 19.98299217 -1.092124505 5.460588804 1.00000223 0.79780952 0.579312017 0.05411552 1.29E-06 2.14E-07 0.045971741 0.010835524 0.080886398 1.092124505 -0.20219271 KLDDDSDS(ph)PSFFEEKPEEPVVLALDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDDDSDSPSFFEEKPEEPVVLALDPK 27 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 KLDDDS(0.039)DS(0.766)PS(0.194)FFEEKPEEPVVLALDPK 80.711 0.0060554 49011000 94442 89295 76396 99067 39201 106250 100780 110440 35440 TRUE FALSE 89977.91383 98394.26202 79898.83217 89108.59695 46037.64199 102570.5359 85404.16005 100769.2881 40935.8542 2.19802214 2.40362059 1.951805666 2.176786064 1.124628834 2.505640541 2.086292365 2.461638827 1 15.32107738 3.728957209 23.85392218 1.969076266 2.300821364 0.087287429 0.501224724 852.2592987 2116930.915 0.120877337 0.190193856 5357.438678 -3.728957209 0.331745097 KLDEAVAEAHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLDEAVAEAHLGK 13 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 120.53 0.00017063 5968490000 16590700 14586500 14753600 17934000 11205210 17004300 19188000 18863600 12169600 FALSE TRUE 15806490.49 16072880.93 15430067.15 16131240.25 13159395.08 16415436.83 16260518.19 17211803.18 14056799.41 1.124472935 1.143423937 1.097694198 1.147575616 0.936158701 1.167793346 1.156772442 1.224446809 1 23.74476481 KLDELYGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 147.26 4.36E-05 8453550000 15555500 12379030 9794150 11467600 13965800 11475460 17261710 13857920 14312300 FALSE TRUE 14820222.34 13640467.23 10243221.47 10314855.06 16401431.1 11078061.94 14628119.11 12644447.06 16531778.39 0.896468728 0.82510586 0.619607959 0.623941044 0.99211535 0.670107092 0.884848488 0.764857039 1 23.97873859 -0.42661681 0.634627046 1.021055079 0.787532329 0.23324662 0.12211315 16.10481253 5.279733833 0.918141873 0.045243042 0.374440822 0.42661681 -0.23352275 KLDEMTDRDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLDEMTDRDWR 11 2 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 131.69 0.00011139 615100000 1387160 1064390 1286240 1414540 1290590 1416600 1667800 1413160 1451510 FALSE TRUE 1321591.696 1172852.551 1345215.376 1272347.752 1515668.487 1367542.787 1413346.479 1289416.219 1676602.758 0.788255709 0.699541108 0.802345917 0.758884444 0.904011687 0.815662971 0.842982318 0.769064832 1 20.67710948 -5 0.117892474 1.669364016 0.688924859 0.60537874 0.052208216 97.40571438 0.748581998 15.59144131 0.498605699 1.00E-05 5 -0.980439157 KLDEQYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDEQYQK 8 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 134.25 0.0014187 274160000 401130 309990 289730 405130 348790 357220 446180 411960 364860 FALSE TRUE 382169.3799 341578.3334 303014.4071 364405.5627 409618.8656 344849.3818 378107.0463 375886.5985 421440.6254 0.906816659 0.810501677 0.718996672 0.864666434 0.971949169 0.818263264 0.897177499 0.891908791 1 18.68496987 0.570768405 0.426407084 1.011483908 0.834192539 0.359404024 0.064601949 2.347464175 0.860325268 0.125777259 0.043691192 3.721931747 -0.570768405 -0.177291368 KLDGFPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLDGFPLLR 9 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 128.03 0.00068734 379060000 878460 740410 733160 905680 890190 848400 1071270 964940 1022920 FALSE TRUE 836936.9367 815858.6208 766776.1112 814639.3257 1045438.854 819019.6953 907828.0863 880444.7381 1181549.209 0.70833862 0.690499062 0.648958253 0.689467116 0.884803482 0.693174426 0.768337094 0.745161294 1 20.17224829 -5 0.18148626 2.146883929 0.668326746 0.68253334 0.060194763 74.99713718 0.72388536 30.92592844 0.173197119 1.00E-05 5 -1.478557183 KLDLEAWFPGSGAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLDLEAWFPGSGAFR 15 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 136.2 3.90E-05 303850000 907310 873950 831600 940990 761400 842480 1006320 1032440 912700 FALSE TRUE 864423.2544 963006.4986 869729.6826 846399.8974 894187.9189 813304.7064 852787.4017 942034.0803 1054236.855 0.819951656 0.913463132 0.824985086 0.802855538 0.848185031 0.771462981 0.808914427 0.893569672 1 20.0077676 -1.213107753 4.200092303 1.000081388 0.835721152 0.603198144 0.041948933 3.27E-05 6.12E-06 0.041497981 0.009776331 0.061219848 1.213107753 -0.164360236 KLDNTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDNTK 6 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 89.298 0.080693 1110300000 1453800 1256800 1077400 1535000 893560 1274300 1557800 1768200 1346400 FALSE TRUE 1385081.755 1384869.349 1126799.856 1380698.884 1049396.581 1230170.671 1320128.999 1613367.034 1555192.836 0.890617371 0.890480793 0.724540282 0.887799154 0.674769429 0.791008448 0.848852289 1.037406421 1 20.56866205 1.293803365 4.876875539 1.019929424 0.820610104 0.580144831 0.072041706 0.143239475 6.467241918 0.055291829 0.018362622 19.66995492 -1.293803365 -0.19931932 KLDPAQSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDPAQSASR 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 92.247 0.015389 141420000 327790 246530 208410 228120 250980 228030 318720 285880 274050 FALSE TRUE 312296.0163 271651.6873 217965.8046 205188.9442 294750.8325 220133.2639 270093.4103 260846.8317 316548.2743 0.986566794 0.858168277 0.688570503 0.648207433 0.931140229 0.695417672 0.853245562 0.824034919 1 18.27206601 0.399696686 1.761743435 0.999984208 0.816577068 0.232752347 0.107734224 9.860245281 26.94078893 0.105484502 0.029585458 2.510132726 -0.399696686 -0.18340714 KLDPELHLDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLDPELHLDIK 11 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 117.79 0.00052425 1709440000 6146200 6187400 5293600 6655700 3908000 6583000 6685300 7161300 3677500 FALSE TRUE 5855681.307 6817903.094 5536316.796 5986656.391 4589553.963 6355029.059 5665334.701 6534218.608 4247787.918 1.378524875 1.605047904 1.303341151 1.40935859 1.080457417 1.496079649 1.333714114 1.538263853 1 22.01828031 -2.185495383 2.148823109 2.24E-05 1.399392178 0.423274001 0.144037689 3853153.772 708256.3944 18764697.97 0.034530135 0.00652386 2.185495383 1.399369761 KLDPGSEETQTLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;; 180.74 2.76E-06 6608090000 2672930 2421770 2404810 2690430 2220480 2666090 2992400 2769700 2461990 FALSE TRUE 2546585.896 2668551.116 2515072.917 2419982.865 2607731.009 2573762.635 2535854.421 2527170.385 2843782.835 0.895492393 0.938380766 0.884411034 0.85097316 0.916993723 0.905048938 0.891718731 0.888665039 1 21.43937987 -1.518516248 3.930486118 1.001295039 0.898900739 0.673390725 0.02260482 0.000263536 3.23E-05 0.022485101 0.005233466 0.030302869 1.518516248 -0.1023943 KLDVEEPDSANS(ph)SFYSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KLDVEEPDSANS(0.621)S(0.379)FYSTR 158.37 2.80E-11 76830000 133870 139650 148560 179680 147450 171680 192800 183530 176880 TRUE FALSE 127542.2304 153880.4938 155371.6229 161618.225 173165.2333 165734.6786 163384.819 167459.1402 204309.647 0.624259462 0.753172922 0.7604713 0.791045491 0.847562687 0.811193602 0.799692141 0.819634034 1 17.6403978 6.109904611 0.069448254 1.237784916 1.54E-17 0.861732486 0.034502894 64.33498544 0.486026559 2.047354829 8.530182914 1287966.63 -6.109904611 -1.237784916 KLDVEEPDSANSSFYSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 291.7 5.52E-49 1305130000 1491180 1335540 1274590 1500840 1208970 1459720 1572880 1537860 1398720 FALSE TRUE 1420694.877 1471633.044 1333031.212 1349972.712 1419813.985 1409169.53 1332908.268 1403196.826 1615626.354 0.879346189 0.910874622 0.825086326 0.835572352 0.878800957 0.872212518 0.825010229 0.868515683 1 20.62366215 -1.372151336 7.181853979 1.000004225 0.863552135 0.72039318 0.027016457 1.99E-06 1.74E-07 0.028529264 0.006724204 0.042447162 1.372151336 -0.136452091 KLDVLSNDLVMNMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLDVLSNDLVMNMLK 15 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 198.15 1.29E-08 101160000 320780 263970 222370 256700 277260 263380 393430 331420 309030 FALSE TRUE 305617.3651 290868.8431 232565.8845 230896.0283 325614.0562 254259.0846 333405.0277 302399.1078 356952.7941 0.856184264 0.814866413 0.651531206 0.646853119 0.912204811 0.712304509 0.934031147 0.847168345 1 18.44537377 1.310295974 0.950011486 0.985522525 0.771276927 0.395303645 0.09198609 0.542654845 1.030175345 0.084460824 0.030244031 20.43129874 -1.310295974 -0.214245598 KLDVSIEMPEELDISQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLDVSIEMPEELDISQLR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 186.56 7.60E-14 183843000 267010 237525 229955 269020 230637 259891 283960 277530 279620 FALSE TRUE 254388.9665 261729.0675 240498.6642 241977.5985 270860.0198 250890.9095 240636.6867 253228.0019 322982.0415 0.787625731 0.810351765 0.744619308 0.749198306 0.838622539 0.776795231 0.745046646 0.784031213 1 18.30109442 -2.131244374 2.221679389 1.430804214 0.779873011 0.846006327 0.029559669 3643966.429 910337.3086 7912241.386 0.007345604 0.007391892 2.131244374 -0.650931203 KLDYGQHVVAGTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLDYGQHVVAGTPGR 15 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;; 145.1 2.67E-06 2358860000 4318410 4077590 4286880 4338020 3670420 4166680 4586770 4644790 3905880 FALSE TRUE 4114287.318 4493101.057 4483437.688 3901953.988 4310540.086 4022386.827 3886973.995 4238067.564 4511583.922 0.911938554 0.995903243 0.993761341 0.864874522 0.955438303 0.891568659 0.861554182 0.939374649 1 22.10520259 3.248070412 24.99987811 0.908413984 0.965456873 0.164064474 0.047755724 272.9036852 717420.0452 0.012504758 0.016711306 1770.395967 -3.248070412 0.057042889 KLEAAEDIAYQLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 ;;; 226.67 3.71E-12 1932050000 4780640 3583040 3783450 4271520 3962330 3445720 4470790 4192420 4113290 FALSE TRUE 4554668.622 3948155.85 3956924.925 3842138.694 4653359.097 3326393.852 3788688.874 3825309.479 4751158.005 0.958643896 0.830988118 0.832833789 0.808674157 0.979415774 0.700122759 0.797424306 0.805132028 1 22.17984776 2.238880657 24.99999995 0.803689979 0.876519409 0.062214521 0.091421957 16.96429665 1325303.339 0.029991263 0.023651457 173.3327618 -2.238880657 0.07282943 KLEAAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 153.05 0.0007173 7785480000 15850120 13582370 12708120 15125330 13135890 13808200 17501270 15722590 15003360 FALSE TRUE 15100916.24 14966428.94 13290799.87 13604903.09 15426785.06 13330018.57 14831129.83 14345836.67 17330004.44 0.871374055 0.863613682 0.766924205 0.785049025 0.89017779 0.769187256 0.855806464 0.827803404 1 24.04676869 -1.182884342 4.855110034 1.000018098 0.832190135 0.60564156 0.04335083 8.20E-06 1.38E-06 0.040522034 0.009550105 0.065632003 1.182884342 -0.167827963 KLEAAEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLEAAEERR 9 2 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 ; 59.426 0.05757 75000000 333326 233789 292072 290758 299743 299045 417845 368661 392518 FALSE TRUE 317570.3406 257612.3649 305463.7901 261530.4534 352018.0843 288688.9967 354095.071 336379.0884 453387.6867 0.700438829 0.568194445 0.673736405 0.576836251 0.77641739 0.63673762 0.780998429 0.741923741 1 18.79038568 0.523577008 0.437085035 1.02751543 0.625813155 0.751344237 0.061906519 0.904294258 0.333576129 0.106942551 0.035090588 3.33869701 -0.523577008 -0.401702276 KLEAELLQIEER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 190.27 1.10E-05 332229000 753692 656251 681140 795226 664532 699841 856470 801945 769727 FALSE TRUE 718066.4728 723123.723 712370.9427 715288.3716 780426.1704 675605.3307 725799.7713 731722.4444 889092.3319 0.807639935 0.813328039 0.801233929 0.804515286 0.877778542 0.75988208 0.816337905 0.822999387 1 19.76197372 0.575869057 2.662995243 0.999996618 0.8109875 0.811466253 0.028385596 2.236320653 13.56893679 0.024427132 0.00646738 3.765902374 -0.575869057 -0.189009118 KLEDGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 103.56 0.013385 48436100000 54847800 49193400 48337700 56057200 29782100 57987200 59286700 59380900 34083400 FALSE TRUE 52255253.19 54206263.39 50554031.36 50422223.75 34976088.81 55979088.72 50241425.04 54181193.6 39368879.6 1.327323859 1.376881027 1.284111508 1.280763493 0.888419715 1.421912162 1.276171066 1.376244235 1 25.23055232 -2.287995115 1.893288456 6.72E-05 1.284926783 0.261405601 0.147071268 2627040.645 357505.7342 11215345.94 0.034615268 0.005152344 2.287995115 1.284859613 KLEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEDIR 6 1 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 83.801 0.090714 920910000 3006700 2366800 2604600 2930300 2482700 2745600 3457500 2966700 2861600 FALSE TRUE 2864579.25 2607979.611 2724023.486 2635740.677 2915682.094 2650519.184 2929994.874 2706920.021 3305362.313 0.866646067 0.789014748 0.82412251 0.797413544 0.882106655 0.801884614 0.886436825 0.81894805 1 21.65637699 -2.424934478 0.311497179 1.241398893 0.821608655 0.693437268 0.03479271 24.53404017 0.93570419 4.071194954 0.029931107 0.003758941 2.424934478 -0.419790238 KLEDNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLEDNPK 7 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;; 113.5 0.0098046 6075050000 6380260 5340650 5477320 6938710 3877340 6745420 7330150 7150320 4667520 FALSE TRUE 6078677.754 5884868.307 5728460.54 6241217.688 4553546.868 6511824.414 6211800.99 6524200.075 5391335.163 1.127490236 1.091541915 1.062530962 1.1576386 0.844604672 1.207831496 1.152182308 1.210126968 1 22.36221117 KLEDQLQGGQLEEVILQAEHELNLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLEDQLQGGQLEEVILQAEHELNLAR 26 1 A0A087X1G1;H7BYD0;Q16718-2;Q16718;A0A087WXR5 A0A087X1G1 NDUFA5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 0 ;; 266.28 2.34E-53 310863000 300134 253247 269282 241171 235779 240118 300104 287489 244932 FALSE TRUE 285947.2606 279053.1572 281628.8461 216928.0329 276898.7829 231802.6535 254317.623 262314.9391 282914.8036 1.010718623 0.986350497 0.995454612 0.766760983 0.978735575 0.819337308 0.898919462 0.927187039 1 18.11000814 3.407099061 24.99999764 0.891252768 0.997268386 0.315855365 0.068149672 44.52874354 15897.3015 0.016345103 0.022131377 2553.28363 -3.407099061 0.106015619 KLEDSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLEDSTR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 146.81 0.0035178 253324000 691230 620264 609928 717289 543540 665458 799968 737807 667504 FALSE TRUE 658556.9278 683469.6068 637893.8021 645185.747 638333.2039 642413.0226 677918.1892 673200.7077 771017.1112 0.854140483 0.886451931 0.827340655 0.836798221 0.827910554 0.833202031 0.879251808 0.873133291 1 19.55640335 0.504927815 1.112196251 1.000019064 0.849748758 0.856877952 0.019352071 0.723000143 1.215892774 0.020272321 0.006253493 3.198363459 -0.504927815 -0.150270306 KLEDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLEDVK 6 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ;;; 117.17 0.0368 11509600000 14497600 12467000 12217600 14268800 7756300 14315000 15511000 15128900 9438900 FALSE TRUE 13812327.18 13737401.47 12777789.04 12834473.12 9108996.264 13819267.96 13144512.07 13804133.31 10902636.4 1.266879557 1.260007301 1.171990753 1.177189868 0.83548565 1.267516172 1.205626931 1.266128008 1 23.3781737 3.622379336 2.490390054 1.137804664 1.266112966 0.157155758 0.128989277 0.550786645 6.651873685 0.035960617 0.062422968 4191.595213 -3.622379336 0.128308303 KLEDVKNS(ph)PTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEDVKNSPTFK 12 2 H0YC42;P55327-2;P55327-3 H0YC42;P55327-2 1 KLEDVKNS(0.997)PT(0.003)FK 101.39 0.0014089 694910000 468430 419780 421810 535370 270510 418280 443230 504100 249070 TRUE FALSE 446288.2422 462556.0593 441150.4057 481553.5905 317686.8584 403794.8587 375607.123 459958.3316 287694.5035 1.551257451 1.607802908 1.533398797 1.673836603 1.104250705 1.403554304 1.305576292 1.598773442 1 18.13417813 2.754792046 24.99337959 1.311429791 1.586567212 0.461139688 0.164364048 740.0229748 1139496.482 0.044750271 0.047333867 568.5806116 -2.754792046 0.275137421 KLEEEGEQFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 1261530000 2634100 2426190 2108580 2950830 1584120 2667450 2731060 2768390 1668560 FALSE TRUE 2509591.313 2673421.519 2205260.479 2654206.962 1860390.026 2575075.538 2314386.638 2525975.095 1927311.763 1.302120063 1.38712458 1.144215752 1.377154964 0.965277161 1.336097038 1.200836669 1.310620909 1 20.87815853 -5 0.111087937 0.225502971 1.39911209 0.271231984 0.127337575 200.1141084 1.474130338 35.88300429 1.38823407 1.00E-05 5 1.173609119 KLEEEGEQFVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEEEGEQFVKK 12 2 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 172.57 1.99E-05 532110000 709760 542810 620680 697440 443040 612410 665700 791870 462220 FALSE TRUE 676211.0514 598122.9561 649138.7919 627332.0062 520306.0357 591202.0881 564135.2386 722529.6648 533898.7169 1.266553056 1.120292927 1.215846323 1.175001899 0.974540712 1.107330041 1.056633441 1.353308487 1 19.02620656 8 0.446359852 1.104621181 4.67576092 0.154535268 0.107870637 149.8426784 1.817819233 0.060550733 486.5581993 99999999.98 -8 3.571139739 KLEEEQIILEDQNCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLEEEQIILEDQNCK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 235.88 1.73E-17 1880950000 3749940 3097270 3428260 3822140 2186320 3911150 4165940 3980060 2402410 FALSE TRUE 3572687.768 3412885.334 3585449.112 3437931.226 2567613.516 3775705.895 3530349.34 3631544.847 2774963.473 1.287471998 1.229884778 1.292070741 1.238910443 0.925278311 1.360632647 1.272214706 1.308682036 1 21.40403735 2.992026631 24.8823778 1.199304893 1.263991397 0.084065324 0.133592208 1243.893686 3881814.064 0.038068978 0.04361872 981.8081457 -2.992026631 0.064686504 KLEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEELK 6 1 Q15172;Q15172-2;Q9Y2C4-3;Q9Y2C4-4;Q9Y2C4;Q9Y2S6 Q15172;Q9Y2S6 PPP2R5A;EXOG;TMA7 "Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform;Nuclease EXOG, mitochondrial;Translation machinery-associated protein 7" 0 88.942 0.081342 631910000 793390 753020 738590 787850 542310 818660 825910 895780 623260 FALSE TRUE 755888.027 829753.5941 772455.0821 708653.8212 636888.6923 790309.5989 699902.2606 817340.7544 719911.9776 1.049972845 1.152576454 1.072985457 0.98436176 0.884675783 1.097786429 0.972205328 1.135334291 1 19.457461 3.396121324 5.164235645 1.008843984 1.10306043 0.217952988 0.072021746 0.258624527 11.99130208 0.018778475 0.025745135 2489.552702 -3.396121324 0.094216446 KLEELQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEELQQK 8 1 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 107.21 0.0064904 339870000 1258100 1005800 1028400 1166600 772830 1343100 1341900 1296600 959630 FALSE TRUE 1198632.106 1108292.163 1075553.157 1049331.152 907611.3073 1296588.11 1137168.509 1183062.83 1108444.519 1.081364097 0.99986255 0.97032656 0.946669981 0.818815278 1.169736588 1.025913782 1.067318039 1 20.08010513 2.211836086 24.99999811 1.067039756 0.978655609 0.289015653 0.077726474 338.01566 316201.3465 0.029388827 0.021710938 162.8681209 -2.211836086 -0.088384147 KLEEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEEQAR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 74.301 0.074644 202760000 1326700 1159000 1179000 1417700 942320 1388900 1505200 1473800 1178000 FALSE TRUE 1263989.52 1277103.418 1233058.316 1275190.103 1106660.31 1340802.045 1275554.095 1344746.259 1360678.224 0.928940802 0.938578567 0.906208606 0.937172419 0.813315221 0.985392447 0.937439927 0.988291159 1 20.3758945 1.501971713 1.477213531 0.996011128 0.915855715 0.365771638 0.042186425 0.420327825 1.758137467 0.034484252 0.011518234 31.76667156 -1.501971713 -0.080155413 KLEEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEEQQR 7 1 Q02818;H7BZI1;C9JKZ2 Q02818 NUCB1 Nucleobindin-1 0 85.161 0.033695 94414000 173760 145610 134430 167410 174000 153220 192340 161330 189930 FALSE TRUE 165546.7092 160447.8245 140593.7485 150581.6287 204345.5449 147913.953 162995.0004 147203.0899 219383.3744 0.754600068 0.731358176 0.64085872 0.686385781 0.931454106 0.6742259 0.742968791 0.670985622 1 17.74309467 -1.411545598 5.330686677 1.000196016 0.731367933 0.529888952 0.080163261 0.000172744 1.91E-05 0.07179796 0.016910701 0.038766304 1.411545598 -0.268828083 KLEEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEEVER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 96.668 0.020143 236560000 531030 465510 477480 562060 456680 497250 659790 563290 467990 FALSE TRUE 505929.2643 512945.9982 499372.9303 505560.661 536324.8474 480030.1078 559126.9176 513965.3414 540563.499 0.935929387 0.948909793 0.923800684 0.9352475 0.992158828 0.888017982 1.034340866 0.950795498 1 19.04410457 1.730328722 24.99999973 0.995101235 0.94007616 0.414756981 0.032202212 0.669362418 2021.298141 0.012957015 0.007185294 53.74384352 -1.730328722 -0.055025075 KLEEVVQILGDKFPCTLVAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEEVVQILGDKFPCTLVAQK 21 2 Q9BY32 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 182.39 2.64E-17 194820000 892620 702790 765880 956800 533790 922430 1038200 971070 585010 FALSE TRUE 850427.6216 774405.1 800996.3556 860620.6462 626882.807 890486.0178 879803.5221 886037.9628 675730.363 1.258531018 1.146026792 1.185378665 1.273615473 0.927711468 1.317812646 1.302003832 1.311230058 1 19.36608816 SAPGGGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAPGGGGKR 9 1 Q14847;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 78.264 0.048527 36939000 49449 36978 44431 54658 83453 86258 135990 107220 135530 FALSE TRUE 47111.64377 40746.10024 46468.2053 49163.674 98007.17678 83270.86383 115242.2279 97831.24839 156547.3002 0.300941912 0.260279802 0.296831726 0.314049964 0.626054724 0.53192143 0.736149571 0.62493092 1 17.2562391 1.846602323 0.421596238 0.991206088 0.209469019 0.887027096 0.079788742 0.291729919 0.133022497 0.083536983 0.072107723 70.24288224 -1.846602323 -0.78173707 down KLEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLEGAR 6 1 Q96JK9 Q96JK9 MAML3 Mastermind-like protein 3 0 83.229 0.091757 125210000 575010 548090 516520 656730 510150 596110 714390 619790 491920 FALSE TRUE 547830.4169 603940.9941 540202.9529 590714.2527 599119.9985 575466.5612 605396.6848 565517.9019 568204.4412 0.964143145 1.062893829 0.950719343 1.039615691 1.054409214 1.012780822 1.065455743 0.995271879 1 19.11605058 KLEGDSTDLSDQIAELQAQIAELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLEGDSTDLSDQIAELQAQIAELK 24 1 P35579 P35579 MYH9 Myosin-9 0 ; 184.26 4.23E-17 163581000 291450 292190 207236 325440 158900 286260 307500 331680 177267 FALSE TRUE 277673.7361 321964.4932 216737.9756 292726.1529 186612.1097 276346.7444 260585.2274 302636.3409 204756.661 1.356115766 1.572425002 1.058514895 1.429629451 0.911384806 1.349634943 1.272658121 1.478029283 1 17.64355086 3.748723515 24.99457821 1.232564092 1.464270382 0.225796059 0.190126048 931.4596495 2290821.192 0.044077679 0.078315253 5606.909097 -3.748723515 0.231706289 KLEHLITELVHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLEHLITELVHQR 13 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 202.13 3.92E-08 211360000 612730 577340 552650 678020 574320 620280 726550 633070 340720 FALSE TRUE 583767.4672 636171.6024 577989.5491 609864.1414 674481.2262 598799.5481 615701.4535 577635.0347 393557.1174 1.483310659 1.616465753 1.46862939 1.549620409 1.71380772 1.521506083 1.564452595 1.467728594 1 18.58621351 0.649092745 1.957535154 1.000023421 1.56156069 0.864741167 0.069044872 0.565268539 2.733409345 0.061671677 0.017063798 4.457514295 -0.649092745 0.561537269 KLEKEEEEGISQES(ph)S(ph)EEEQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLEKEEEEGISQESSEEEQ 19 2 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 KLEKEEEEGIS(0.11)QES(0.891)S(0.999)EEEQ;KLEKEEEEGIS(0.131)QES(0.878)S(0.991)EEEQ;KLEKEEEEGIS(0.004)QES(0.997)S(1)EEEQ;KLEKEEEEGIS(0.008)QES(0.992)S(0.999)EEEQ;KLEKEEEEGIS(0.008)QES(0.993)S(0.999)EEEQ;KLEKEEEEGIS(0.017)QES(0.984)S(0.999)EEEQ 144.45 6.65E-07 8053360000 10198830 5765550 8791020 8432180 5548870 9187310 11774940 9144270 6512200 TRUE FALSE 9716751.518 6353066.1 9194096.963 7584561.246 6516591.171 8869151.151 9978456.641 8343549.242 7522078.716 1.291764137 0.844589154 1.222281408 1.008306551 0.8663285 1.17908247 1.326555732 1.109207914 1 22.84269997 2.032806782 24.95124624 1.199358851 1.045545933 0.070914613 0.159790943 304.750406 231777.1383 0.056267206 0.04155583 107.8466806 -2.032806782 -0.153812918 KLELSDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLELSDNR 8 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 130.66 0.0016652 6261300000 23890200 17792300 16033400 18649800 20462500 18599600 25412800 21256200 21704800 FALSE TRUE 22760957.59 19605355.6 16768547.25 16775086.67 24031153.52 17955491.19 21535610.62 19394894.44 25070669.53 0.907871948 0.782003671 0.668851194 0.669112034 0.958536568 0.716195121 0.85899623 0.773608954 1 24.57949719 -1.044477896 0.568098227 1.059249572 0.792832088 0.317562985 0.095626015 32.4294413 5.868671663 3.288416393 0.038627091 0.090265565 1.044477896 -0.266417483 KLELSENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KLELSENR 8 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ;;;;;;; 132.01 0.0015722 12920160000 17951410 13578720 10823340 12547290 16151140 13060430 19824480 15962100 17658110 FALSE TRUE 17102882.43 14962407.01 11319600.84 11286012.57 18967893.7 12608144.03 16799891.47 14564373.9 20396439.51 0.83852294 0.733579358 0.554979257 0.553332485 0.92996102 0.618154165 0.82366785 0.714064526 1 24.281814 -0.171422216 0.602179878 1.021870119 0.716145759 0.343814885 0.121889916 7.123424692 2.598926261 0.485934435 0.04770396 0.673872578 0.171422216 -0.30572436 KLEMDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLEMDLK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 109.71 0.01117 925610000 2306680 2054550 1869480 2432300 1477340 2273660 2434320 2556830 1696730 FALSE TRUE 2197647.808 2263910.981 1955197.507 2187800.583 1734987.628 2194922.584 2062919.775 2332940.411 1959850.223 1.121334571 1.155144896 0.997625984 1.116310092 0.885265419 1.119944044 1.052590525 1.190366684 1 20.90231197 3.756491211 24.42145101 1.053818311 1.138239743 0.157823874 0.082972847 987.1494955 1344490.903 0.019419438 0.034916128 5708.095246 -3.756491211 0.084421433 KLENCNYAVELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLENCNYAVELGK 13 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;P13796 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 149.3 2.74E-06 0 1172800 886760 735490 1035900 692080 920390 1187000 1137200 865650 FALSE TRUE 1117364.068 977121.8522 769212.944 931769.3639 812778.5329 888516.6635 1005901.349 1037620.739 999890.5809 1.117486343 0.97722878 0.76929712 0.931871328 0.812867476 0.888613895 1.006011426 1.037734287 1 19.9314107 1.614987273 6.042346188 1.019510179 0.92992284 0.187268417 0.093916791 0.292361461 22.67671995 0.056538604 0.027075843 41.20854431 -1.614987273 -0.08958734 KLENEVEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLENEVEQR 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 114.89 0.0025081 424320000 1024520 852590 913960 1055040 903280 942720 1063240 1051040 1041270 FALSE TRUE 976092.97 939469.8903 955865.97 948985.3748 1060811.746 910073.37 901023.2103 959005.3657 1202744.834 0.81155449 0.781104906 0.794737124 0.78901638 0.881992353 0.756663712 0.749139123 0.797347317 1 20.19789917 -2.084404035 2.923327133 1.366494916 0.792352199 0.760626313 0.036076141 2020147.832 11197762.62 5781198.603 0.008428771 0.008233718 2.084404035 -0.574142718 KLENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLENLK 6 1 P39687;H0YN26 P39687;REV__Q9Y2X3 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 97.602 0.065557 868690000 1389600 1121400 1144300 1438100 1183400 1466700 1532300 1480900 1343800 FALSE TRUE 1323916.362 1235671.935 1196767.287 1293539.456 1389784.585 1415907.811 1298519.492 1351224.545 1552189.641 0.852934672 0.796083096 0.771018731 0.833364314 0.895370352 0.912200271 0.836572709 0.870528001 1 20.5658734 2.858461128 4.134600751 0.88896942 0.810223505 0.467602901 0.046727369 0.233212961 6.752219467 0.013816887 0.014756367 721.873548 -2.858461128 -0.078745915 KLEPLSQDEDQHADLTQSR ddPTM_SK-BR-3_Trastuzumab_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 ; 133.26 7.82E-06 155447000 234090 188897 208307 242310 187947 220000 256090 228353 187838 FALSE TRUE 223025.0296 208145.8191 217858.082 217952.5384 220724.8973 212381.3448 217018.7671 208357.2007 216966.9577 1.027921634 0.959343401 1.004107189 1.004542538 1.017320331 0.978864925 1.000238789 0.960317658 1 17.72711582 -0.749693631 4.740312409 1.000000007 0.994075202 0.006853177 0.022388824 1.62E-09 3.73E-10 0.019780709 0.004662352 0.177953432 0.749693631 -0.005924804 KLERPPET(ph)PTVDPTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLERPPETPTVDPTVK 16 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 1 KLERPPET(0.869)PT(0.131)VDPTVK;KLERPPET(0.999)PT(0.001)VDPTVK 165.74 3.30E-07 474300000 758130 688980 553700 803850 432550 717720 709640 757740 469770 TRUE FALSE 722294.6974 759187.8453 579087.6927 723045.4708 507986.583 692865.1764 601371.3846 691388.2686 542619.5323 1.331125502 1.399116324 1.067207607 1.332509111 0.936174525 1.276889487 1.108274488 1.274167676 1 19.04958145 3.746918663 24.96995034 1.151552798 1.365120927 0.347314475 0.126554093 565.9619674 1690826.786 0.028147149 0.049696407 5583.656114 -3.746918663 0.213568128 KLES(ph)TESR ddPTM_SK-BR-3_Trastuzumab_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(0.79)T(0.201)ES(0.009)R;KLES(0.883)T(0.117)ESR;KLES(0.83)T(0.17)ESR;KLES(0.905)T(0.094)ES(0.001)R 119.45 0.0010365 2415300000 2331090 1916410 2108510 2697860 1806100 2272900 2413570 2307350 1728710 TRUE FALSE 2220903.995 2111694.358 2205187.269 2426665.987 2121083.268 2194188.903 2045335.568 2105306.202 1996789.518 1.112237407 1.057544793 1.104366409 1.215283817 1.062246796 1.098858384 1.024312052 1.05434558 1 20.92925084 1.822550685 1.790843111 1.023432585 1.108445343 0.432072995 0.044413701 0.361200528 2.219027163 0.030372598 0.013148841 66.45852293 -1.822550685 0.085012758 KLEST(ph)ESR ddPTM_SK-BR-3_Trastuzumab_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(0.057)T(0.937)ES(0.006)R 84.507 0.010198 64346000 128220 102190 111230 132150 92667 117140 129950 111640 90631 TRUE FALSE 122159.2947 112603.2772 116330.0055 118866.0309 108828.0955 113083.4124 110123.7408 101864.2098 104685.5926 1.166916017 1.075632992 1.11123224 1.135457401 1.039570898 1.080219442 1.051947437 0.973048986 1 16.67570338 1.973282405 0.574349374 0.98637359 1.128503998 0.697098289 0.032333486 0.450989055 0.307751676 0.029127199 0.019140372 94.0334576 -1.973282405 0.142130407 KLESTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 175.73 0.00042398 14685760000 24213300 18961030 19838610 23441100 18705680 20870190 24826760 22602580 20991030 FALSE TRUE 23068785.3 20893180.51 20748229.89 21084756.09 21967944.67 20147450.09 21038981.79 20623378.27 24246211.73 0.951438747 0.861709068 0.855730789 0.869610326 0.906036164 0.830952493 0.867722431 0.850581464 1 24.53125602 -1.630441196 6.368008216 1.000552033 0.875457257 0.584687811 0.033299809 0.000263607 1.53E-05 0.03256663 0.007642653 0.023418485 1.630441196 -0.125094776 KLEVEANNAFDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLEVEANNAFDQYR 14 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 267.47 8.49E-25 4035340000 4422950 4211240 3796600 4683590 3728160 4195540 4660610 4540990 3921600 FALSE TRUE 4213885.919 4640370.144 3970677.865 4212786.635 4378349.924 4050247.398 3949548.347 4143356.842 4529741.699 0.930270686 1.024422683 0.876579313 0.930028005 0.966578276 0.894145332 0.871914694 0.914700466 1 22.11099735 3.733507927 24.99674848 0.914594203 0.977346684 0.192797216 0.045156319 497.1927717 2459718.611 0.01140119 0.018296257 5413.871298 -3.733507927 0.062752481 KLFADAEEEQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLFADAEEEQRR 12 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 112.43 0.00071692 259850000 435670 299330 385120 388360 459690 364160 539710 420640 476300 FALSE TRUE 415076.7425 329832.0673 402778.1329 349321.315 539859.7905 351549.0479 457367.327 383806.5316 550162.1714 0.754462528 0.599517896 0.732108011 0.634942446 0.98127392 0.638991676 0.831331834 0.697624358 1 19.06949742 -4.999999998 0.148546089 1.972031458 0.641790407 0.371027669 0.109728181 129.1647033 1.144701607 36.96518145 0.506409488 1.00E-05 4.999999998 -1.330241051 KLFAPQQILQCS(ph)PAN ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLFAPQQILQCSPAN 15 1 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN 273.99 1.94E-33 1562746000 1975060 2044160 2247150 2454530 2156550 2312270 2800540 2486840 2969640 TRUE FALSE 1881702.828 2252462.228 2350184.05 2207795.981 2532651.637 2232195.51 2373266.188 2269079.106 3430156.604 0.548576361 0.656664546 0.685153572 0.643642911 0.738348691 0.650756151 0.691882751 0.661508895 1 21.70984301 -5 0.203542634 2.581489274 0.603150711 0.858298894 0.04411122 49.46257866 0.490738376 31.8708749 0.098908195 1.00E-05 5 -1.978338564 KLFDQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLFDQHK 7 1 Q6ZPD8;Q6E213 Q6ZPD8 DGAT2L6;AWAT2 Diacylglycerol O-acyltransferase 2-like protein 6;Acyl-CoA wax alcohol acyltransferase 2 0 64.836 0.046879 1231000000 2537600 2230300 1987500 2654500 1944100 2431200 2723400 2590400 1945500 FALSE TRUE 2417652.677 2457570.106 2078628.841 2387664.617 2283150.424 2347006.934 2307895.311 2363570.843 2247198.204 1.075851998 1.093615197 0.924986874 1.062507354 1.015998687 1.044414743 1.027010126 1.051785659 1 21.09969595 KLFEAEEQDLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLFEAEEQDLFK 12 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8 A0A024R571 EHD1 EH domain-containing protein 1 0 98.531 0.0069053 69178000 222840 201460 212020 249390 259140 214670 260790 244520 295320 FALSE TRUE 212306.7948 221989.003 221741.3267 224320.8434 304333.934 207235.9241 221001.6958 223108.5325 341116.7173 0.622387541 0.650771398 0.650045323 0.6576073 0.892169508 0.60752204 0.64787706 0.654053352 1 18.37990593 -1.616215081 2.62028588 1.032691526 0.66875521 0.623995438 0.079765773 14013377.19 12489278.46 3125349.15 0.019032199 0.024198303 1.616215081 -0.363936316 KLFIGGLSFETTDDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLFIGGLSFETTDDSLR 17 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 266.7 1.78E-27 713210000 786350 675200 716770 804030 663940 679830 797940 745930 687660 FALSE TRUE 749180.7939 744003.6476 749634.6135 723207.3768 779730.9258 656287.3166 676199.5978 680612.4148 794298.8007 0.94319769 0.936679807 0.943769036 0.910497883 0.981659452 0.826247397 0.851316403 0.856872016 1 19.5993223 2.238748519 24.99999999 0.867480155 0.940823332 0.234389423 0.049726102 5.159644598 686598.0935 0.015703403 0.012367051 173.2800319 -2.238748519 0.073343177 KLFIGGLSFETTDDSLREHFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLFIGGLSFETTDDSLREHFEK 22 2 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 201.32 9.26E-23 183880000 433790 205560 436830 331590 432000 409350 650590 488030 469740 FALSE TRUE 413285.6064 226506.7977 456859.0876 298257.9432 507340.6632 395174.1069 551330.5466 445295.506 542584.8801 0.76169761 0.417458735 0.842004826 0.549698221 0.935043865 0.72831758 1.016118522 0.820692803 1 19.04948932 2.56417223 0.957179013 0.941391595 0.609212316 0.403538901 0.145828713 0.461673279 0.867214928 0.082125571 0.06318225 366.582923 -2.56417223 -0.332179279 KLFIGGLSFETTDESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 286.28 3.28E-36 2458367000 1987330 1480017 1919980 1896070 2093990 1834370 2376240 2089490 2345390 FALSE TRUE 1893392.849 1630832.415 2008012.982 1705473.441 2459181.193 1770845.307 2013700.945 1906523.179 2709101.103 0.698900771 0.601982855 0.741210057 0.629534808 0.907748031 0.653665271 0.743309633 0.703747519 1 21.3693828 -4.999999999 0.192720463 2.290898468 0.65075295 0.551015167 0.082796528 95.67968383 0.9389927 47.44785113 0.196555859 1.00E-05 4.999999999 -1.640145518 KLFIGGLSFETTEESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 286.28 3.28E-36 3393234000 2584610 1808836 2445916 2360075 2644784 2330429 3305189 2701047 3104309 FALSE TRUE 2462440.608 1993158.445 2558063.668 2122835.777 3106033.492 2249725.659 2800921.714 2464529.006 3585709.385 0.686737363 0.555861681 0.713405185 0.592026723 0.866225664 0.627414388 0.781134613 0.687319786 1 21.77382713 -5 0.146817988 2.149081982 0.576164409 0.580692134 0.085668836 83.97509214 0.739602814 28.00426355 0.402262355 1.00E-05 5 -1.572917573 KLFVGGIKEDTEEHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLFVGGIKEDTEEHHLR 17 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 205.06 4.94E-12 3643640000 3786470 2151900 3559900 3248770 3110230 3700420 4952740 3983390 874406 FALSE TRUE 3607491.067 2371181.057 3723124.936 2922197.467 3652653.127 3572273.528 4197108.55 3634583.254 1010004.417 3.571757715 2.34769375 3.686246193 2.893252167 3.61647243 3.536889016 4.155534848 3.598581545 1 19.94593017 2.735509591 24.74673172 3.467589118 3.076094022 0 0.930254414 856.5458905 6947376.106 0.263866044 0.258630962 543.8881426 -2.735509591 -0.391495096 KLFVGGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLFVGGLK 8 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;; 117.04 0.0071619 0 4638790 4494500 3409940 4750120 3325830 4303840 4746270 4755600 3681820 FALSE TRUE 4419523.59 4952494.66 3566289.122 4272628.913 3905853.699 4154796.942 4022139.34 4339174.453 4252777.841 1.039208667 1.164531712 0.838578749 1.004667789 0.918424109 0.976960729 0.945767564 1.020315336 1 22.01997406 3.752437894 24.99864871 0.956426717 1.101870189 0.50185443 0.059654693 525.0650012 945854.0095 0.013620908 0.024402518 5655.068813 -3.752437894 0.145443472 KLFYSTFATDDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLFYSTFATDDRK 13 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 175.28 1.04E-05 710640000 1476300 1085800 1260200 1249600 1131000 1125800 1526400 1523900 1278900 FALSE TRUE 1406518.225 1196444.254 1317981.417 1123987.834 1328246.042 1086813.264 1293519.646 1390459.237 1477225.28 0.952135225 0.809926739 0.892200691 0.760877741 0.899149276 0.735712608 0.875641422 0.941264177 1 20.49445843 1.140395648 2.842404258 0.995657399 0.84495235 0.411023688 0.064462259 0.2303793 3.402485861 0.055679845 0.015149246 13.81642385 -1.140395648 -0.150705049 KLGAGEGGEASVS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 KLGAGEGGEAS(0.169)VS(0.831)PEK;KLGAGEGGEAS(0.004)VS(0.996)PEK;KLGAGEGGEASVS(1)PEK;KLGAGEGGEAS(0.002)VS(0.998)PEK;KLGAGEGGEASVS(1)PEK 227.6 2.99E-15 5098140000 5019610 5400930 3983050 5653440 2246910 5460840 4604990 5417810 2303490 TRUE FALSE 4782342.983 5951290.907 4165676.782 5085145.47 2638770.393 5271729.742 3902414.199 4943397.835 2660703.465 1.797397961 2.236735881 1.565629856 1.911203386 0.991756664 1.981329303 1.466685127 1.85792889 1 21.3433763 -0.843586553 0.096921427 4.81E-12 2.504211865 0.321772555 0.334361679 56.47301878 1.168468865 23.51634696 8.356225487 0.143355199 0.843586553 2.504211865 KLGAGEGGEASVS(ph)PEKTSTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.033)VS(0.967)PEKTSTTSK;KLGAGEGGEAS(0.002)VS(0.991)PEKT(0.003)S(0.004)TTSK;KLGAGEGGEAS(0.015)VS(0.977)PEKT(0.002)S(0.002)T(0.002)T(0.001)SK;KLGAGEGGEAS(0.004)VS(0.995)PEKTSTTSK;KLGAGEGGEAS(0.083)VS(0.911)PEKT(0.002)S(0.002)T(0.002)TSK 210.11 2.55E-23 6058400000 4142210 2838930 3888380 3918380 2127821 4718220 5108480 4862500 2510700 TRUE FALSE 3946415.942 3128220.195 4066666.069 3524496.998 2498912.309 4554826.858 4329087.552 4436713.722 2900046.533 1.360811248 1.07867931 1.402276144 1.215324291 0.861680073 1.570604749 1.492764858 1.529876735 1 21.46764462 2.195221574 24.99999966 1.449782399 1.196888014 0.177511666 0.216255592 184.3410968 106335.5338 0.07350864 0.054290043 156.7550621 -2.195221574 -0.252894385 KLGCEVLGVSVDSQFTHLAWINTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLGCEVLGVSVDSQFTHLAWINTPR 25 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 302.57 1.55E-63 1925271000 2611730 2335211 2629880 2947980 2666770 2747599 3203760 2921060 2877010 FALSE TRUE 2488278.699 2573171.656 2750462.599 2651643.45 3131853.844 2652448.958 2714967.571 2665276.501 3323162.017 0.748768398 0.774314235 0.82766431 0.797927828 0.942431885 0.79817022 0.81698321 0.802030261 1 21.6641252 -5 0.139696473 1.623939897 0.742546703 0.586389424 0.049851552 99.35392091 0.851123239 17.46055487 0.305039069 1.00E-05 5 -0.881393194 KLGEMWNNTAADDKQPYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLGEMWNNTAADDKQPYEK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 219.87 1.46E-18 1534760000 1220750 1012900 1013860 1270250 631260 1263660 1337730 1288730 664300 FALSE TRUE 1163047.567 1116115.662 1060346.484 1142562.057 741351.5441 1219899.137 1133634.719 1175881.969 767316.2512 1.515734308 1.454570602 1.381889778 1.489036698 0.966161661 1.589825754 1.477402202 1.532460661 1 19.54946178 3.936244914 1.545561691 1.375399397 1.50882622 0.060807794 0.211407022 1.405504034 6.326510659 0.058030552 0.17602496 8634.6535 -3.936244914 0.133426823 KLGEMWSEQSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLGEMWSEQSAK 12 1 P26583 P26583 HMGB2 High mobility group protein B2 0 172.57 5.68E-05 375840000 469180 409540 389220 522060 357400 435620 537880 528330 407780 FALSE TRUE 447002.7912 451272.5916 407066.122 469581.537 419730.4468 420534.3702 455816.5272 482066.6243 471016.4397 0.949017388 0.958082465 0.864229117 0.996953604 0.891116342 0.892823126 0.96772955 1.023460295 1 18.84541789 1.46399642 4.438788984 1.009373016 0.929981202 0.463436741 0.038272926 0.173914134 6.860833612 0.024011498 0.009263206 29.10693124 -1.46399642 -0.079391814 KLGGSLADSYLDEGFLLDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLGGSLADSYLDEGFLLDKK 20 2 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 232.82 2.64E-27 562620000 897340 663990 762530 868020 580650 889890 1067950 1032270 668850 FALSE TRUE 854924.5166 731651.3359 797492.7547 780764.9805 681915.1762 859072.8862 905014.6133 941878.9664 772571.842 1.106595491 0.947033397 1.032257081 1.010605018 0.882656006 1.111965049 1.17143101 1.219147418 1 19.55930957 2.020321854 24.38025257 1.147355046 1.00121725 0.393138427 0.079299811 152.4398032 182881.9624 0.027428327 0.020254643 104.7904858 -2.020321854 -0.146137796 KLGIDDLVHFDFMDPPAPETLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLGIDDLVHFDFMDPPAPETLMR 23 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 145.58 8.94E-08 48385000 237230 148980 225930 211370 227470 213390 296210 245910 210230 FALSE TRUE 226016.608 164161.2314 236289.114 190122.686 267140.696 206000.2508 251017.7242 224376.8167 242831.3947 0.930755302 0.676029685 0.973058341 0.782941128 1.100107737 0.848326268 1.03371199 0.924002504 1 17.88959543 2.75876021 24.87399952 0.976400838 0.830611739 0.313905069 0.102621987 832.896158 1025636.014 0.028403218 0.030092134 573.7995589 -2.75876021 -0.145789099 KLGINSLQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLGINSLQELK 11 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 198.32 0.001509 0 3574100 2538100 2245400 2914800 2379800 2767300 3929700 3423500 2683900 FALSE TRUE 3405159.376 2796735.276 2348353.811 2621798.766 2794836.367 2671467.707 3330152.091 3123720.191 3100105.505 1.098401126 0.902141966 0.757507707 0.845712755 0.901529436 0.861734448 1.074206051 1.007617382 1 21.56388588 1.739247783 11.94896489 1.029506404 0.904201898 0.338171356 0.08681565 0.107196425 102.9550893 0.044957545 0.02461006 54.85898693 -1.739247783 -0.125304506 KLGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLGPGRPLPTFPTSECTSDVEPDTR 25 2 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 KLGPGRPLPTFPTSECT(0.106)S(0.894)DVEPDTR;KLGPGRPLPTFPTSECT(0.276)S(0.724)DVEPDTR 216.21 8.62E-34 676770000 703640 437620 695920 639880 618910 641010 806350 678300 816770 TRUE FALSE 670380.3317 482213.9755 727828.6204 575558.0467 726847.708 618811.663 683326.4979 618904.4561 943430.5201 0.710577321 0.511128234 0.771470294 0.610069353 0.770430564 0.655916519 0.724299758 0.656014876 1 19.84755675 -4.999999995 0.223666534 2.719266222 0.628762416 0.624788157 0.078302258 92.01559556 0.920535939 71.3447347 0.12995239 1.00E-05 4.999999995 -2.090503806 KLGPIS(ph)PPQPPSVSAWNKPLTSFGSAPSSEGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(1)PPQPPSVSAWNKPLTSFGSAPSSEGAK 224.4 1.71E-36 347960000 217500 162860 189920 218900 120880 195380 244440 227770 152250 TRUE FALSE 207219.206 179455.6192 198628.0199 196895.7561 141961.4337 188613.9416 207146.1886 207825.2513 175860.1524 1.178318131 1.020445034 1.129465755 1.119615521 0.807240479 1.072522337 1.177902929 1.181764308 1 17.4240691 -0.489358231 7.113896424 0.999999405 1.085823817 0.055640544 0.111227908 7.88E-10 0 0.105710002 0.024916086 0.324072194 0.489358231 0.085824413 KLGSSLDWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLGSSLDWDR 10 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 138.24 0.00011233 343060000 598640 477380 449910 527690 601510 480500 694190 576300 651660 FALSE TRUE 570343.4736 526025.5647 470538.8185 474645.5987 706413.1536 463860.1645 588278.5658 525836.1168 752716.1046 0.757713924 0.698836602 0.625121232 0.63057718 0.938485505 0.616248492 0.781541091 0.698584916 1 19.52174631 -4.999999999 0.327704113 3.796467364 0.708663622 0.464003289 0.095171389 299.7881415 2.605890178 583.2935289 0.073418497 1.00E-05 4.999999999 -3.087803742 KLGVS(ph)VSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLGVSVSPSR 10 1 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 KLGVS(0.633)VS(0.366)PS(0.001)R 75.088 0.024527 90511000 96343 91043 87699 98903 83275 74765 99156 85656 100820 TRUE FALSE 91789.05732 100320.3852 91720.0859 88961.08254 97798.13363 72175.8693 84027.93108 78155.50655 116454.6507 0.788195721 0.86145452 0.787603461 0.763911806 0.839795861 0.619776616 0.721550669 0.671123962 1 16.82940873 2.287926921 24.99982873 0.725078589 0.810688878 0.035734488 0.103411406 196.5174813 99518.43982 0.031416112 0.02628456 194.0559309 -2.287926921 0.085610289 KLHAVVETLVNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLHAVVETLVNHR 13 1 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 146.79 1.73E-05 63372000 124940 110330 82793 105790 118350 95029 128340 110410 81440 FALSE TRUE 119034.3338 121572.7524 86589.14094 95155.78821 138990.2025 91738.1219 108759.3759 100741.9151 94069.29926 1.265389822 1.292374381 0.92048247 1.011549878 1.477529902 0.97521851 1.156162284 1.070932981 1 16.52143634 8 0.330099512 1.08337866 3.395107796 0.106591261 0.163237767 115.21232 1.642992859 0.13937819 162.4861151 100000000 -8 2.311729136 KLHS(ph)PTSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLHSPTSSAK 10 1 J3KN75;Q0IIM8 J3KN75 TBC1D8B TBC1 domain family member 8B 1 KLHS(0.931)PT(0.066)S(0.002)S(0.001)AK 74.649 0.025334 79053000 209300 186360 191610 239750 149550 221130 237730 228530 138470 TRUE FALSE 199406.8038 205350.2959 200395.508 215649.8745 175631.4727 213472.2127 201459.9223 208518.7017 159943.2204 1.246734956 1.283894968 1.252916551 1.348290187 1.098086385 1.334674969 1.259571502 1.303704534 1 17.28720032 -1.027583824 4.441524111 0.999987235 1.266083647 0.599519372 0.06831991 3851410.888 891056.1643 477.2609752 0.01386858 0.093846088 1.027583824 0.266096412 KLILDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLILDSAR 8 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 126.07 0.0019803 4999300000 9850800 5233600 3536700 3812800 10011100 5026400 10471700 7027000 8742800 FALSE TRUE 9385172.206 5766909.79 3698861.193 3429530.1 11757032.67 4852334.508 8874049.839 6411678.628 10098588.77 0.929354826 0.571060959 0.366275059 0.339604887 1.164225313 0.480496297 0.878741579 0.634908379 1 23.26765036 2.760196768 24.96810454 0.799595254 0.586503084 0.234780687 0.24394266 1516.787728 1750369.655 0.072940017 0.077301383 575.700714 -2.760196768 -0.213092171 KLKDVLLQVDDERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLKDVLLQVDDERR 14 3 P35579;P35579-2 P35579 MYH9 Myosin-9 0 209.6 2.81E-09 565240000 1318800 746670 1388600 1109500 1391800 1320600 1973600 1543000 1977800 FALSE TRUE 1256462.938 822756.5219 1452268.684 997970.9521 1634529.479 1274867.291 1672491.072 1407886.74 2284507.123 0.549993005 0.360146184 0.635703285 0.436843003 0.715484519 0.558049164 0.732101492 0.616275925 1 21.12345151 -0.264596656 0.191967737 1.282132437 0.377774322 0.686507693 0.098065195 5.982940192 0.366927866 1.340311944 0.325780108 0.543755101 0.264596656 -0.904358115 KLKDYAFVHFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLKDYAFVHFEDR 13 2 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 90.367 0.0042181 487390000 490870 277870 510920 392470 536530 439310 662650 521620 571350 FALSE TRUE 467667.5479 306185.2689 534346.1874 353018.17 630100.6621 424096.5845 561550.5721 475944.1875 659952.0399 0.708638688 0.463950788 0.809674272 0.534914886 0.954767353 0.64261728 0.850896032 0.721179963 1 19.33200166 1.156403012 0.183912292 1.120433066 0.494216208 0.353136014 0.136670251 3.629291293 0.590374955 0.918200661 0.689509974 14.33517544 -1.156403012 -0.626216858 KLKEDKAPQVDVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLKEDKAPQVDVDK 14 3 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 124.78 4.17E-05 714850000 2160860 1814560 1878030 2204740 1050600 2325900 2345890 2659810 1036300 FALSE TRUE 2058720.43 1999465.727 1964139.533 1983115.346 1233824.307 2245353.5 1987981.395 2426902.936 1197004.111 1.719894201 1.670391695 1.640879521 1.656732277 1.030760292 1.875811017 1.660797466 2.027480869 1 20.19099668 2.975428015 24.76243251 1.571887646 1.677629653 0.039547133 0.321611066 3237.097949 3262190.668 0.091411543 0.097429579 944.9917451 -2.975428015 0.105742007 KLLADQAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLLADQAEAR 10 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 146.16 4.67E-05 253220000 586030 501760 454530 515720 587590 493460 628840 568070 635080 FALSE TRUE 558329.5233 552889.9145 475370.6501 463878.8458 690065.51 476371.3565 532898.9086 518326.7793 733564.9629 0.761118035 0.753702729 0.64802802 0.632362325 0.940701294 0.649392188 0.726450874 0.706586063 1 19.48456521 -1.321625975 2.975521243 1.002566291 0.729157664 0.488442306 0.087689685 18008408.31 22782572.82 412527.9694 0.020534719 0.047684148 1.321625975 -0.273408627 KLLDIVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLLDIVAR 8 1 Q12931-2;Q12931 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 171.36 0.00046474 410960000 1260610 998420 955260 930780 1117770 848880 1168880 1068820 1202600 FALSE TRUE 1201023.464 1100160.133 999059.6159 837216.226 1312708.734 819483.0727 990545.888 975228.4546 1389093.066 0.86460979 0.791998866 0.719217193 0.60270708 0.945011365 0.589941087 0.71308821 0.702061279 1 20.40571183 4.081933061 2.402297198 0.73255671 0.851315644 0.048147751 0.131621731 0.620239486 7.061660766 0.03095535 0.085642821 12076.27685 -4.081933061 0.118758934 KLLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 107.32 0.0503 2844560000 10593800 8613200 9040000 10814600 9142000 9882100 11858700 10335100 10347800 FALSE TRUE 10093052.07 9490894.872 9454492.942 9727495.862 10736361.91 9539880.399 10049437.52 9430103.854 11952483.97 0.844431341 0.794052089 0.791006536 0.813847221 0.898253612 0.798150445 0.840782346 0.788966032 1 23.51080714 -1.477099367 3.158544525 1.003964439 0.82171602 0.737111524 0.03355873 13960561.32 16884615.26 484144.1891 0.007554852 0.033335013 1.477099367 -0.182248419 KLLEGEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 187.42 6.50E-05 11618730000 23846510 19189470 20229940 22983330 19082260 21895830 24902600 22792010 20807420 FALSE TRUE 22719332.73 21144898.81 21157502.76 20673002 22410200.1 21137571.92 21103251 20796220.78 24034128.42 0.945294638 0.879786379 0.880310797 0.860151932 0.932432402 0.879481525 0.878053517 0.865278757 1 24.51858115 -1.116710123 7.387338056 1.000000032 0.891099152 0.611373346 0.027526829 1.45E-08 1.74E-09 0.026116621 0.006155745 0.076434579 1.116710123 -0.10890088 KLLELDPEHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLLELDPEHQR 11 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 122.55 0.0002522 824590000 2202400 1698180 1780960 2148500 1903710 1966830 2250470 2078330 1846110 FALSE TRUE 2098296.917 1871226.473 1862618.778 1932528.698 2235716.421 1898718.184 1907119.469 1896340.407 2132395.31 0.984009347 0.877523255 0.873486623 0.906271313 1.048453076 0.890415663 0.894355498 0.88930059 1 21.02404348 4.712787724 4.103157205 0.917308732 0.987938919 0.095747097 0.057448784 0.458043055 15.05749871 0.013210135 0.089150857 51616.40156 -4.712787724 0.070630187 KLLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLLLNR 6 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;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 ; 94.151 0.071847 1109590000 768130 609820 678260 933740 1055530 924350 1272600 1103620 1296260 FALSE TRUE 731822.0172 671961.3513 709358.8919 839878.6812 1239614.098 892339.5277 1078441.497 1006981.182 1497277.38 0.488768499 0.448788822 0.473765851 0.560937267 0.827912125 0.59597476 0.720268343 0.672541505 1 20.51391008 0.372027018 0.091595855 1.591826225 5.05E-09 0.763417798 0.083867335 13.13377594 0.493463559 5.112656487 3.155373028 2.355195799 -0.372027018 -1.59182622 KLNAFGNAFLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNAFGNAFLNR 12 1 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1;Q9NZN3-2;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 98.105 0.0072896 289270000 296500 262110 226480 290210 238230 243830 327710 296620 284610 FALSE TRUE 282485.0326 288819.307 236864.332 261037.5394 279777.2366 235386.106 277711.8207 270646.3803 328745.8652 0.859280869 0.878548866 0.720508931 0.794040525 0.851044123 0.71601237 0.84476141 0.823269306 1 18.32661322 0.417762488 1.816377885 0.999984843 0.81437487 0.538485118 0.055032886 4.805543209 13.99118342 0.053013424 0.014797365 2.616751537 -0.417762488 -0.185609973 KLNCQVIGASVDSHFCHLAWVNTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLNCQVIGASVDSHFCHLAWVNTPK 25 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 198.05 3.18E-25 2347370000 2617130 2092710 2321050 2786600 2200390 2429050 3202100 2516320 144909 FALSE TRUE 2493423.452 2305959.528 2427472.438 2506485.674 2584137.319 2344931.389 2713560.834 2295977.681 167380.7476 14.89671594 13.77673096 14.50269803 14.97475492 15.43867712 14.00956456 16.21190533 13.71709539 1 17.35277407 0.953628278 23.18928146 0.999999994 14.78629725 0.975516409 0.68383175 723.1957921 361651.7143 0.65703429 0.164258572 8.987280117 -0.953628278 13.78629726 KLNEQSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLNEQSPTR 9 1 O75396 O75396 SEC22B Vesicle-trafficking protein SEC22b 0 ; 156.48 0.00011357 157370000 253938 209653 202173 283371 328380 290734 382320 320090 366740 FALSE TRUE 241934.854 231016.8791 211442.832 254886.0087 385649.368 280665.8087 323990.0622 292061.2227 423612.1662 0.571123479 0.545349963 0.499142491 0.60169662 0.910383126 0.662553701 0.764827094 0.689454284 1 18.6923845 2.922476912 6.439392549 0.776477194 0.545158873 0.602627105 0.100809297 0.161937552 11.04650117 0.027401758 0.029259981 836.5211242 -2.922476912 -0.231318321 KLNIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNIAR 6 1 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 137.2 0.020584 968270000 3085300 2346600 2380100 2229400 2752900 2045800 2787500 2420700 2962200 FALSE TRUE 2939463.983 2585721.208 2489229.939 2005296.476 3233004.888 1974953.433 2362215.679 2208730.675 3421562.847 0.859099808 0.755713492 0.727512558 0.586076178 0.944891277 0.577207996 0.690390849 0.645532692 1 21.70622402 4.326986893 1.717313519 0.717461795 0.861848606 0.050531976 0.139313648 1.030110031 5.062401065 0.033394478 0.188313365 21231.80383 -4.326986893 0.144386811 KLNLAPAATTSNEPSGNNPPTHLSLDPT(ph)NAENTASQSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNLAPAATTSNEPSGNNPPTHLSLDPTNAENTASQSPR 39 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 KLNLAPAATTSNEPSGNNPPT(0.001)HLS(0.004)LDPT(0.345)NAENT(0.217)AS(0.217)QS(0.217)PR 74.258 0.0019469 134990000 18455 15836 22833 25300 30703 18262 27000 24200 36472 TRUE FALSE 17582.66872 17449.7064 23879.91563 22756.79593 36057.59348 17629.58236 22880.65411 22080.91971 42127.89149 0.417364081 0.414207922 0.566843362 0.540183596 0.855907861 0.418477682 0.543123648 0.524140158 1 15.36248809 -5 0.194373068 3.05330965 0.44119451 0.569545399 0.127218274 102.2800767 1.005754858 81.71898331 0.323886907 1.00E-05 5 -2.61211514 KLNQGTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLNQGTER 8 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 102.62 0.0079046 93622000 162885 123589 133998 205794 205568 161781 210262 166340 199926 FALSE TRUE 155185.7489 136182.8596 140141.9408 185107.1961 241418.9941 156178.4834 178182.6702 151774.3878 230929.503 0.672004862 0.589716159 0.606860271 0.801574479 1.045422915 0.676303726 0.771589025 0.657232557 1 17.81709297 3.229337161 12.91341781 0.8111684 0.622768725 0.369547549 0.123758495 0.630738778 876.7934791 0.033841619 0.041714031 1695.653695 -3.229337161 -0.188399675 KLNQNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNQNSR 7 1 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 96.253 0.020632 190300000 201100 151490 147880 179610 207810 201330 237410 203720 237310 FALSE TRUE 191594.4015 166927.0032 154660.4443 161555.2616 244051.9982 194357.8916 201188.7442 185881.1968 274110.8228 0.698966935 0.608976331 0.564225968 0.589379361 0.890340614 0.709048587 0.733968627 0.678124253 1 18.06439977 2.76025924 24.97719566 0.774052268 0.620763025 0.449513541 0.100025487 819.2289816 943009.873 0.028250503 0.02994106 575.7835324 -2.76025924 -0.153289244 KLNTTTMSNATANSSIRPIFGGTVYHS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNTTTMSNATANSSIRPIFGGTVYHSPVSR 31 2 O43663-2;O43663-4;O43663;O43663-3;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 KLNTTTMSNATANSSIRPIFGGT(0.001)VY(0.019)HS(0.959)PVS(0.021)R 60.574 0.012646 138510000 45866 24719 38738 42640 47519 47720 58786 45972 45179 TRUE FALSE 43698.00508 27237.8942 40514.17562 38353.74619 55806.29855 46067.44443 49817.11602 41946.44797 52185.12858 0.837365094 0.521947439 0.776354811 0.734955479 1.069390841 0.882769588 0.954622847 0.803800797 1 15.67135111 2.885788729 5.978052576 0.93521508 0.69682273 0.527837512 0.105136695 0.170265201 7.829662875 0.030454388 0.032452998 768.7563721 -2.885788729 -0.23839235 KLNVTEQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 222.3 6.23E-07 14594130000 20356840 18584500 13836770 20334730 12412400 20131870 21264650 21367210 13479880 FALSE TRUE 19394612.52 20478281.68 14471199.59 18290644.31 14577118.63 19434698.29 18020337.09 19496183.82 15570270.94 1.245618177 1.315216784 0.929412188 1.174715865 0.936214834 1.248192685 1.157355396 1.25214159 1 23.89229071 3.790262004 24.99998637 1.114257623 1.280417589 0.284845401 0.117287458 408.1936499 197378.9161 0.027972332 0.05042778 6169.670977 -3.790262004 0.166159966 KLNVTEQEKIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLNVTEQEKIDK 12 2 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 182.57 9.40E-06 20962450000 4754770 3775400 3830120 4443810 3083200 4467460 5186710 5009930 3465670 FALSE TRUE 4530021.445 4160117.552 4005734.791 3997109.776 3620909.104 4312750.74 4395382.129 4571233.97 4003108.403 1.131625974 1.039221808 1.000656087 0.998501508 0.904524369 1.077350475 1.097992282 1.141921105 1 21.93268925 -0.342337681 7.63168499 1.000000012 1.050582958 0.045254379 0.07035002 0 0 0.070302816 0.016570533 0.454634427 0.342337681 0.050582946 KLNVTEQEKIDKLMIEMDGTENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLNVTEQEKIDKLMIEMDGTENK 23 3 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 88.168 0.0027333 278750000 226690 81533 233420 123460 144790 218940 413110 282700 222960 FALSE TRUE 215974.813 89841.3054 244122.5379 111049.5662 170041.3302 211358.0529 350082.4822 257945.2893 257535.4981 0.838621528 0.348850182 0.947918014 0.431201008 0.660263659 0.820694834 1.359356224 1.001591203 1 17.97441178 1.96544973 4.591927148 1.151169588 0.632117449 0.541149072 0.198335411 0.132210219 6.452516697 0.080784642 0.049634913 92.35272833 -1.96544973 -0.519052139 KLPEEEAECYFHSRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPEEEAECYFHSRPK 16 2 J3QQZ9;Q9NVS9-3;Q9NVS9;J3QQV6 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 156.49 9.49E-08 125300000 388990 306110 340370 383770 259690 356400 421930 394740 281530 FALSE TRUE 370603.2136 337302.957 355976.3012 345192.7105 304979.8538 344057.7786 357556.8292 360174.473 325188.2345 1.13965751 1.037254492 1.094677677 1.061516604 0.937856359 1.058026528 1.099538025 1.107587651 1 18.31091554 4.622934062 2.600868033 1.053941023 1.147102933 0.229835502 0.051018319 0.594819951 6.216142358 0.012724118 0.108146674 41969.52579 -4.622934062 0.093161911 KLPEYNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLPEYNPR 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;;; 124.92 0.0020589 1628850000 2788670 2295880 2350400 2647560 3763240 2242350 3396520 2501620 4968340 FALSE TRUE 2656855.096 2529832.782 2458168.165 2381422.239 4419547.865 2164696.857 2878318.493 2282564.891 5738804.792 0.462963142 0.44082921 0.428341485 0.41496833 0.770116431 0.377203431 0.50155365 0.397742208 1 22.45231887 -1.690332995 2.571346229 1.084084807 0.473963414 0.68996336 0.110765353 10469555.2 8470567.709 5720344.849 0.025134641 0.02040173 1.690332995 -0.610121393 KLPGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPGDDR 7 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 77.674 0.059979 52308000 321720 243520 255850 318530 263120 287710 322800 310670 293960 FALSE TRUE 306512.9332 268334.9649 267580.9756 286510.7592 309008.0447 277746.5306 273550.9314 283466.0878 339545.8155 0.902714506 0.790276165 0.788055583 0.843805891 0.910062886 0.817994267 0.805637763 0.834838996 1 18.37324673 -1.244995391 3.392578267 1.00045388 0.834428496 0.601683603 0.041727302 8377508.088 13689496.96 40488.25153 0.01036328 0.056885897 1.244995391 -0.166025384 KLPIQEFHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLPIQEFHLSR 11 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 184.34 3.21E-06 719790000 971250 683370 733350 872100 1338240 717930 1368550 1077840 1613940 FALSE TRUE 925340.9373 753006.1799 766974.8229 784434.8511 1571628.632 693067.9041 1159752.562 983458.6156 1864221.572 0.496368539 0.403925258 0.411418275 0.420784129 0.843048195 0.371773353 0.622110901 0.527543845 1 20.83014191 -5 0.182247587 3.072600873 0.403949998 0.582715047 0.133356093 88.84019545 0.858622782 66.4920072 0.364828737 1.00E-05 5 -2.668650874 KLPLGFTFSFPCHQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPLGFTFSFPCHQTK 16 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 104.45 0.00088286 49509000 86321 72518 78529 82047 78505 74506 110250 98497 87691 FALSE TRUE 82240.7774 79907.66665 82129.63233 73799.47968 92196.24714 71925.83854 93429.33762 89872.08051 101289.6724 0.811936454 0.78890241 0.810839154 0.728598266 0.910223569 0.710100416 0.92239747 0.887277828 1 16.62812756 1.228575256 1.121084137 0.993899596 0.795804174 0.542382522 0.060956671 0.302653553 0.779864838 0.048594749 0.016012679 16.92681534 -1.228575256 -0.198095422 KLPS(ph)GHS(ph)DLLEERIRNS(ph)GISDEYITPMFSFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPSGHSDLLEERIRNSGISDEYITPMFSFYK 32 3 Q96RI1-5;Q96RI1-2;Q96RI1-1;Q96RI1-4;Q96RI1 Q96RI1-5 NR1H4 Bile acid receptor 3 KLPS(0.973)GHS(0.973)DLLEERIRNS(0.525)GIS(0.525)DEY(0.001)IT(0.001)PMFS(0.001)FY(0.001)K 43.291 0.08367 86617000 40680 35310 46591 40764 120220 25557 46516 26697 125180 TRUE FALSE 38757.13702 38908.12914 48727.24343 36666.32527 141186.3299 24671.95468 39419.12988 24359.26915 144592.2751 0.268044313 0.269088574 0.336997557 0.253584261 0.976444488 0.170631209 0.272622655 0.168468676 1 17.14163095 -1.143656972 4.646479875 1.000059997 0.333209147 0.443760166 0.232308658 28.0334126 271312560.6 37440.11843 0.051270751 0.071836147 1.143656972 -0.666850849 KLPS(ph)PFSLLNSDSSWY ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPSPFSLLNSDSSWY 16 1 Q8IUC4;Q8IUC4-2 Q8IUC4 RHPN2 Rhophilin-2 1 KLPS(0.967)PFS(0.033)LLNSDSSWY 143.67 1.47E-06 24849000 93500 79388 85367 96551 76055 88572 101550 92237 68627 TRUE FALSE 89080.4403 87477.72746 89281.16139 86845.51005 89318.96792 85504.72943 86056.68241 84160.2393 79269.32466 1.123769386 1.10355081 1.126301527 1.095575248 1.126778464 1.078661005 1.085624014 1.061699966 1 16.27447506 0.877384133 0.582249971 0.997673366 1.116808561 0.894273432 0.012389626 0.264255468 0.205056023 0.011708131 0.00489753 7.540222013 -0.877384133 0.119135195 KLPS(ph)TTL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPSTTL 7 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 KLPS(0.913)T(0.086)T(0.001)L 71.223 0.058153 510470000 1546800 1098800 1260100 1649600 1126400 1399500 1446900 1130100 804970 TRUE FALSE 1473685.829 1210768.969 1317876.831 1483779.074 1322843.803 1351034.964 1226148.831 1031142.453 929800.6364 1.584948183 1.302181265 1.417375704 1.595803461 1.422717679 1.453037255 1.318722297 1.10899306 1 19.82656189 1.281262352 1.74493707 0.999829916 1.457634137 0.80416915 0.08339062 0.143934376 0.779936248 0.075455434 0.022606949 19.11007325 -1.281262352 0.457804221 KLPVDSVFNKFEDEDS(ph)DDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLPVDSVFNKFEDEDSDDVPR 21 2 P49756 P49756 RBM25 RNA-binding protein 25 1 KLPVDSVFNKFEDEDS(1)DDVPR 122.04 1.50E-05 121220000 233380 205230 200640 237490 153880 245250 255960 265460 183030 TRUE FALSE 222348.5899 226143.1703 209839.5425 213617.054 180716.6233 236756.931 216908.601 242214.9151 211413.3576 1.051724415 1.069673047 0.992555744 1.010423638 0.854802295 1.119876879 1.025992886 1.145693526 1 17.68970701 -0.580892653 7.601276967 0.999999999 1.034090958 0.017882366 0.078801227 0 0 0.071194353 0.01678067 0.262486727 0.580892653 0.034090958 KLQDVFEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLQDVFEFR 9 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHL0;A0A140T9F7;A0A140T9V2;U3KQA6 H0Y6K2 BRD2 Bromodomain-containing protein 2 0 112.13 0.0032271 99598000 171160 145740 172490 184880 162520 161220 195980 191770 179040 FALSE TRUE 163069.606 160591.0717 180398.8371 166295.5112 190863.4365 155636.911 166079.6516 174977.6022 206804.6088 0.788520174 0.776535265 0.872315362 0.80411898 0.922916746 0.752579509 0.803075195 0.846101077 1 17.65790881 0.828308347 3.80909022 0.999981772 0.812814989 0.576795171 0.048741783 0.81204608 17.08869274 0.044652761 0.011448072 6.734546358 -0.828308347 -0.187166783 KLQELSSK ddPTM_SK-BR-3_Trastuzumab_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 8090300000 17687300 15899700 13949200 17718100 12181700 16535100 18606300 18633600 13920700 FALSE TRUE 16851256.38 17519897.51 14588784.62 15937042.93 14306184.62 15962485.34 15767567.21 17001943.2 16079451.06 1.047999482 1.089583061 0.907293698 0.99114347 0.889718472 0.992725764 0.980603576 1.057370873 1 23.93871482 3.755790066 24.89171121 0.972231809 1.06879128 0.401347801 0.048024858 654.5239639 945600.0379 0.011557526 0.02077179 5698.887262 -3.755790066 0.096559471 KLQNLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLQNLEGK 8 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6;Q8N6H7-3;H0YDN9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 87.913 0.024031 259590000 308860 258100 273080 295640 262150 293720 340960 353410 309810 FALSE TRUE 294260.7999 284400.6834 285600.9881 265921.7055 307868.877 283548.4028 288940.2898 322463.5469 357853.7525 0.822293459 0.794739978 0.798094155 0.743101626 0.860320382 0.792358333 0.807425625 0.901104277 1 18.44901058 1.01427763 2.444759068 0.999488542 0.801501313 0.837873155 0.028911776 0.095475501 1.260455492 0.025123368 0.006829545 10.33421827 -1.01427763 -0.197987229 KLQQELEFLEVQEEYIKDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLQQELEFLEVQEEYIKDEQK 21 2 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 172 3.47E-12 24642000 76318 70607 68081 83361 41585 82551 78994 89985 41014 FALSE TRUE 72710.59939 77801.93357 71202.58119 74981.3939 48837.41083 79692.23817 66942.01448 82105.43636 47374.24165 1.534812946 1.642283462 1.502980918 1.582746051 1.030885332 1.682184989 1.413046671 1.733124025 1 15.53181523 -1.695325033 3.03796725 0.938895849 1.514865998 0.408564433 0.194827194 24996967.39 33802056.32 12091220.63 0.04293926 0.020168563 1.695325033 0.575970149 KLRPLYDIPYMFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLRPLYDIPYMFEAR 15 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 131.69 2.93E-05 564210000 1262620 728680 1167520 944200 1475690 1108900 1702390 1332540 1784560 FALSE TRUE 1202938.455 802933.3204 1221051.947 849287.2221 1733049.869 1070498.515 1442659.139 1215855.733 2061300.451 0.583582299 0.389527553 0.592369708 0.412015251 0.840755586 0.519331626 0.699878147 0.589848866 1 20.97512337 -5 0.134696491 2.516833464 0.39497916 0.560905292 0.122737558 91.47560978 0.766894246 37.0270492 0.742533897 1.00E-05 5 -2.121854304 KLS(ph)ASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(1)ASSPR 134.2 0.00054329 260190000 426710 369600 323230 360220 299610 360430 409900 371180 350140 TRUE FALSE 406540.264 407262.6602 338050.4152 324010.0012 351861.8891 347948.2187 347362.2267 338677.5115 404437.9229 1.00519818 1.006984353 0.835852417 0.801136547 0.870002216 0.860325402 0.858876497 0.837402954 1 18.62555876 3.743592833 24.50685073 0.85767716 1.006091283 0.549757814 0.052176996 177.4988218 864413.763 0.01182941 0.020502392 5541.059752 -3.743592833 0.148414122 KLS(ph)DASDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(1)DASDER;KLS(0.998)DAS(0.002)DER;KLS(1)DASDER;KLS(0.999)DAS(0.001)DER;KLS(0.901)DAS(0.099)DER 132.79 0.00018079 631850000 3621192 4237287 3170130 4344548 2282766 3716874 3261405 3635734 1887112 TRUE FALSE 3450025.431 4669071.363 3315483.596 3907825.781 2680879.668 3588157.721 2763817.767 3317369.857 2179755.691 1.58275785 2.142015907 1.521034495 1.792781548 1.229899148 1.646128388 1.267948412 1.521899849 1 21.05573501 1.906797631 0.315416387 0.987474838 1.940822714 0.482371612 0.227411717 1.108672793 0.343273454 0.323118011 0.377499542 80.68589682 -1.906797631 0.953347876 KLS(ph)DASDERGEPDLASGSDVNGSTESFEMVIEEATIDSATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSDASDERGEPDLASGSDVNGSTESFEMVIEEATIDSATK 41 2 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.307)DAS(0.307)DERGEPDLAS(0.077)GS(0.077)DVNGS(0.077)T(0.077)ES(0.077)FEMVIEEAT(0.001)IDSATK;KLS(0.667)DAS(0.271)DERGEPDLAS(0.012)GS(0.012)DVNGS(0.012)T(0.012)ES(0.012)FEMVIEEAT(0.001)IDSATK 44.6 0.028012 30406000 52023 35495 40999 47564 27444 47141 47282 48400 30363.9 TRUE FALSE 49563.97589 39111.98085 42878.8447 42782.77635 32230.22491 45508.49535 40068.26251 44161.83942 35072.57853 1.413183118 1.115172664 1.222574629 1.219835499 0.918957951 1.297552026 1.142438457 1.259155764 1 15.09805588 4.607442817 2.567451106 1.156339373 1.433109373 0.335245559 0.116548883 0.401287142 4.142759291 0.025993717 0.212116063 40498.86176 -4.607442817 0.27677 KLS(ph)DGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSDGHK 7 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 KLS(1)DGHK 59.426 0.063459 100690000 141210 137160 130300 161870 80414 157480 172940 191690 102590 TRUE FALSE 134535.2832 151136.7599 136274.3839 145598.5201 94438.17614 152026.4281 146554.8267 174904.6074 118499.1332 1.135327149 1.275425025 1.150003212 1.228688481 0.796952463 1.282932828 1.236758639 1.475999044 1 16.85451698 KLS(ph)FLSWGTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLS(0.971)FLS(0.029)WGTNK 191.51 1.10E-06 379520000 1548000 1148800 761500 865360 1101900 986520 1691500 1226800 989610 TRUE FALSE 1474829.108 1265864.026 796415.5282 778372.3687 1294071.011 952356.565 1433430.608 1119374.888 1143073.665 1.290231027 1.107421215 0.696731587 0.680946813 1.132097651 0.833154148 1.254014201 0.979267499 1 20.12448695 KLS(ph)FTESLTSGASLLTLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.482)FT(0.107)ES(0.411)LTSGASLLTLNK;KLS(0.552)FT(0.335)ES(0.113)LTSGASLLTLNK;KLS(0.781)FT(0.195)ES(0.024)LTSGASLLTLNK 229.71 4.53E-20 695507000 1436270 1207381 1233912 1411543 929334 1398149 1594668 1694930 1162246 TRUE FALSE 1368380.364 1330414.497 1290488.086 1269652.016 1091409.555 1349730.75 1351372.109 1546512.944 1342481.174 1.019292032 0.99101166 0.9612709 0.945750332 0.812979412 1.005400132 1.006622763 1.151981103 1 20.35647043 1.570648184 2.941905071 1.075751003 0.958905252 0.34307768 0.067164468 0.256180763 5.038833502 0.045854248 0.017775442 37.20901587 -1.570648184 -0.116845751 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_SK-BR-3_Trastuzumab_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 285.55 2.56E-45 1101130000 1304200 1152020 1203760 1539790 812710 1461450 1560220 1502480 1006310 TRUE FALSE 1242553.051 1269412.148 1258953.587 1385007.384 954446.3667 1410839.62 1322179.784 1370914.886 1162363.415 1.068988437 1.092095752 1.083098083 1.191544198 0.821125609 1.213768088 1.1374926 1.179420195 1 20.14862977 KLS(ph)GDQPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;KLS(1)GDQPAAR 167.22 3.25E-06 55177360000 40356660 33802710 34418150 39758630 27629800 38704370 41893260 38629970 30544300 TRUE FALSE 38449080.66 37247244.58 35996256.22 35762016.98 32448428.37 37364027.96 35501673.76 35247325.04 35280954.05 1.089797079 1.055732352 1.020274457 1.013635202 0.919715162 1.059042449 1.006256059 0.999046823 1 25.07238624 3.831364284 1.607305543 1.001071343 1.083970739 0.455446289 0.033698363 0.332765755 1.652526554 0.009524324 0.024430846 6782.101486 -3.831364284 0.082899396 KLS(ph)GDQPAART(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSGDQPAARTPR 13 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 2 KLS(1)GDQPAART(1)PR 61.684 0.090898 216510000 379880 224320 386700 372990 338020 371220 499010 406550 421930 TRUE FALSE 361923.8252 247178.463 404430.5775 335496.3366 396970.581 358364.5583 422876.8596 370950.3267 487360.7495 0.74261997 0.507177616 0.829838221 0.688394248 0.814531292 0.735316824 0.86768756 0.761141161 1 18.89463054 1.352815523 0.207625462 1.078434967 0.562861045 0.499873855 0.089993344 1.95698356 0.41336335 0.419445366 0.358441844 22.53281872 -1.352815523 -0.515573922 KLS(ph)HDAESEREDPAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSHDAESEREDPAPAKK 18 3 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 KLS(1)HDAESEREDPAPAKK;KLS(1)HDAESEREDPAPAKK 86.557 0.0024447 240100000 711470 614860 669800 706030 391820 733810 770820 743720 328700 TRUE FALSE 677840.2231 677514.933 700510.9925 635058.523 460153.2839 708397.9757 653217.2519 678595.9341 379673.1172 1.78532583 1.784469066 1.845037114 1.672645479 1.211972255 1.865810202 1.72047275 1.787316255 1 18.53439833 -1.627952028 2.842713728 0.937383613 1.715909939 0.59059227 0.185474625 22380595.63 21961127.54 10361657.69 0.04465061 0.023553094 1.627952028 0.778526325 KLS(ph)LGQYDNDAGGQLPFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSLGQYDNDAGGQLPFSK 19 1 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 KLS(1)LGQYDNDAGGQLPFSK 266.28 1.04E-31 435280000 1431900 1189600 1290100 1610900 963870 1574300 1809700 1720300 1189200 TRUE FALSE 1364216.925 1310821.592 1349252.361 1448969.271 1131968.623 1519781.596 1533597.028 1569661.412 1373615.062 0.993158099 0.954285977 0.982263807 1.054858316 0.824079943 1.106410113 1.11646783 1.142722918 1 20.38954633 2.119756259 20.37645292 1.103006765 0.968406791 0.467481615 0.068062266 1.794535769 306.3920032 0.022664279 0.016738691 131.7517094 -2.119756259 -0.134599974 KLS(ph)LQER ddPTM_SK-BR-3_Trastuzumab_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 92.611 0.0095199 296440000 741540 702850 653710 839860 598620 803060 883240 895190 788450 TRUE FALSE 706488.8738 774471.2141 683683.2501 755435.6772 703019.1385 775249.8308 748485.5162 816802.4179 910718.7992 0.775748644 0.85039555 0.750707299 0.829493888 0.771938758 0.851250497 0.821862376 0.896876641 1 19.79664614 0.899157102 1.048672863 1.00065988 0.802490965 0.79810495 0.032202636 0.252626714 0.563037 0.026841919 0.008681387 7.92788063 -0.899157102 -0.198168915 KLS(ph)PIIEDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLSPIIEDSR 10 1 O60566-3;O60566 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 KLS(1)PIIEDSR;KLS(0.978)PIIEDS(0.022)R;KLS(1)PIIEDSR 100.11 0.0025944 478620000 1478360 1261730 1344350 1589050 1212410 1556660 1743810 1673070 1483620 TRUE FALSE 1408480.853 1390301.721 1405989.777 1429315.675 1423853.92 1502752.474 1477759.757 1526567.121 1713692.212 0.82189838 0.811290214 0.820444749 0.834056235 0.830869108 0.876909204 0.86232507 0.890805893 1 20.70867659 0.395651824 0.353582466 1.026889618 0.808048847 0.968390862 0.009870978 0.435509829 0.101974372 0.0286879 0.008420995 2.48686279 -0.395651824 -0.218840771 KLS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSPLR 6 1 Q8IZD2-6;Q8IZD2-5;Q8IZD2-7;Q8IZD2;Q8IZD2-8;Q8IZD2-4;Q8IZD2-3 Q8IZD2-6 KMT2E Histone-lysine N-methyltransferase 2E 1 KLS(1)PLR;KLS(1)PLR 79.474 0.041071 166880000 645480 569600 580860 673420 498330 595830 712730 677300 584950 TRUE FALSE 614969.4396 627642.8876 607493.0055 605726.5422 585238.5942 575196.2577 603989.9483 617992.0214 675661.0585 0.910174461 0.92893157 0.899109099 0.896494677 0.866171858 0.851308878 0.893924462 0.914647979 1 19.36594018 -1.460906664 7.379357927 1.000010916 0.896193963 0.682915499 0.022453638 4.53E-06 3.31E-07 0.024430383 0.005757691 0.034601373 1.460906664 -0.103816952 KLS(ph)PPPLPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSPPPLPPR 10 1 F5GWN5;O00750 F5GWN5 PIK3C2B Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta 1 KLS(1)PPPLPPR;KLS(1)PPPLPPR 68.657 0.035443 50133000 147927 123290 141791 156224 128790 140808 174776 145224 138497 TRUE FALSE 140934.7839 135853.3912 148292.2576 140520.0667 151250.9352 135931.7837 148110.7112 132507.4167 159974.4074 0.880983316 0.849219531 0.926974883 0.878390919 0.945469576 0.849709562 0.925840037 0.828303844 1 17.2874816 -1.741731896 2.888099678 1.020407731 0.886230557 0.474330012 0.037839382 25417605.85 29689533.15 3810390.263 0.008145843 0.018124586 1.741731896 -0.134177175 KLS(ph)PTEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.637)PT(0.363)EPK;KLS(0.848)PT(0.152)EPK;KLS(0.86)PT(0.14)EPK;KLS(0.746)PT(0.254)EPK;KLS(0.882)PT(0.118)EPK;KLS(0.939)PT(0.061)EPK;KLS(0.973)PT(0.027)EPK 124.42 0.0007996 6009280000 10206910 8088970 8474610 10957220 5425920 10949970 11088080 10566290 5855690 TRUE FALSE 9724449.592 8913245.239 8863179.251 9855779.428 6372198.73 10570769.79 9396389.749 9641049.632 6763760.498 1.437728257 1.317794331 1.310392237 1.457144946 0.942108866 1.562853947 1.389225676 1.425397844 1 22.68939414 -2.197821932 2.255655941 9.76E-05 1.357882466 0.318065439 0.163473579 5685307.217 1208950.665 28986875.82 0.038006671 0.006341297 2.197821932 1.357784846 KLS(ph)PTKEAFGEQPLQLTTKPDLLAWDPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLSPTKEAFGEQPLQLTTKPDLLAWDPAR 29 3 O00257 O00257 CBX4 E3 SUMO-protein ligase CBX4 1 KLS(0.89)PT(0.11)KEAFGEQPLQLTTKPDLLAWDPAR;KLS(0.997)PT(0.003)KEAFGEQPLQLTTKPDLLAWDPAR;KLS(0.967)PT(0.033)KEAFGEQPLQLTTKPDLLAWDPAR 279.28 1.51E-70 1197050000 1098231 908366 976792 1096323 617736 1217702 1357810 1380260 738637 TRUE FALSE 1046319.797 1000929.528 1021578.879 986118.5292 725468.9628 1175532.674 1150651.147 1259397.117 853181.0535 1.226374862 1.173173647 1.197376425 1.15581391 0.850310681 1.377823229 1.348659985 1.476119414 1 19.7024924 KLS(ph)QRPTVAELLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSQRPTVAELLAR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 KLS(0.999)QRPT(0.001)VAELLAR;KLS(1)QRPTVAELLAR 140.32 5.21E-06 793750000 620410 561670 537080 635370 579090 546280 692210 671330 570000 TRUE FALSE 591084.4488 618904.8116 561705.6492 571501.4005 680083.1127 527362.1866 586600.6512 612544.7863 658392.6888 0.897768853 0.940023822 0.853146851 0.868025132 1.032944509 0.800984269 0.890958635 0.930363895 1 19.32858879 0.918855543 4.062337443 0.999928388 0.899052706 0.226633513 0.059973021 0.544531197 21.59279446 0.052940889 0.013524625 8.295747846 -0.918855543 -0.100875681 KLS(ph)SAMSAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSSAMSAAK 10 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 1 KLS(0.5)S(0.5)AMSAAK 151.22 1.24E-05 637630000 1211900 908360 732230 821240 769410 924610 1322600 1055800 817600 TRUE FALSE 1154615.889 1000922.917 765803.4698 738687.3949 903594.8604 892590.5239 1120813.079 963348.5549 944389.2323 1.222605944 1.059862695 0.810898138 0.782185321 0.956803434 0.945151102 1.186812641 1.02007575 1 19.84902207 1.762572981 25 1.087342543 0.98104631 0.110521209 0.132070355 34.35358713 35792.3838 0.069363803 0.038467016 57.88592545 -1.762572981 -0.106296233 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.69)S(0.231)S(0.079)DAPAQDTGSSAAAVETDASR;KLS(0.595)S(0.163)S(0.241)DAPAQDTGSSAAAVETDASR;KLS(0.68)S(0.16)S(0.16)DAPAQDTGSSAAAVETDASR;KLS(0.736)S(0.132)S(0.132)DAPAQDTGSSAAAVETDASR 298.29 2.68E-63 1558040000 892574 744761 850192 1025869 882875 800509 938828 829398 878592 TRUE FALSE 850383.7959 820652.9926 889174.1442 922746.6991 1036848.12 772787.1726 795592.5458 756771.5142 1014839.56 0.837949001 0.808652939 0.876172135 0.909253773 1.021686739 0.76148704 0.78395894 0.745705572 1 19.95282023 -0.420279838 7.383354683 0.999999999 0.840158216 0.272287928 0.080477796 0 0 0.079333828 0.018699163 0.3799445 0.420279838 -0.159841783 KLS(ph)TQDRPAAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSTQDRPAAIHR 13 2 H7C1N2;J3KR05;O75128-2;O75128-6;O75128-3;O75128;O75128-7 H7C1N2;O75128-3 COBL Protein cordon-bleu 1 KLS(0.93)T(0.07)QDRPAAIHR;KLS(0.965)T(0.035)QDRPAAIHR 145.33 2.18E-05 217360000 142243 134925 115970 139706 190723 138242 183266 167542 192317 TRUE FALSE 135519.4553 148674.0109 121287.3392 125662.4875 223985.0308 133454.6449 155305.4058 152871.1343 222140.5381 0.610061794 0.669279062 0.545993722 0.565689129 1.008303269 0.600766731 0.699131312 0.688173062 1 17.76111317 -4.999999992 0.174123078 2.310627578 0.595161636 0.418614606 0.125798707 129.5708011 1.233157471 58.67435317 0.400783821 1.00E-05 4.999999992 -1.715465942 KLSCS(ph)LEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.43)CS(0.57)LEDLR;KLS(0.057)CS(0.943)LEDLR;KLS(0.001)CS(0.999)LEDLR;KLS(0.034)CS(0.966)LEDLR;KLS(0.032)CS(0.968)LEDLR;KLS(0.062)CS(0.938)LEDLR 116.58 0.00065591 1657100000 7595560 7771420 6994300 8537130 5597380 7701470 8030510 8413630 6277220 TRUE FALSE 7236532.932 8563336.533 7314995.573 7678961.473 6573561.3 7434766.163 6805308.209 7676887.954 7250659.218 0.998051724 1.181042478 1.008873173 1.059070802 0.906615675 1.025391753 0.93857786 1.058784825 1 22.78968074 3.223977549 2.105781859 0.983662632 1.086067255 0.219964423 0.065489138 0.342780611 3.121541913 0.018822185 0.025533212 1674.856291 -3.223977549 0.102404623 KLSCS(ph)LEDLRSESVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSCSLEDLRSESVDK 16 2 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLSCS(1)LEDLRSESVDK 139.26 1.13E-06 324510000 980960 632650 982670 834760 659730 987160 1299600 1246500 1004800 TRUE FALSE 934591.9649 697117.7543 1027726.391 750848.3389 774786.7031 952974.4017 1101322.151 1137349.852 1160619.252 0.805252854 0.600642935 0.885498314 0.646937691 0.667563201 0.821091327 0.948909084 0.979950875 1 20.14646333 1.845218804 2.38282431 0.983190782 0.716916521 0.673531921 0.08088316 0.158463599 1.672797294 0.044828634 0.021516886 70.01946751 -1.845218804 -0.266274261 KLSELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSELLR 7 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 164.72 0.0019034 3706500000 11066000 8906600 7068200 8727100 10932800 8309900 13053000 10702300 11725000 FALSE TRUE 10542932.11 9814192.666 7392283.961 7849835.328 12839476.86 8022126.079 11061525.12 9765149.876 13543253.12 0.778463787 0.724655486 0.545827793 0.579612244 0.948034918 0.592333763 0.8167554 0.721034289 1 23.69107098 -0.11746836 0.514459364 1.031441805 0.699360793 0.37228321 0.1192338 5.508780756 1.631993178 0.460728468 0.053736892 0.763012478 0.11746836 -0.332081012 KLSEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KLSEQR 6 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ;;;;;;; 124.89 0.02912 3834750000 8933420 6373560 6692920 8444920 8077980 7450820 10423810 8059820 9701350 FALSE TRUE 8511154.941 7023033.01 6999797.002 7596020.597 9486777.154 7192796.235 8833466.338 7354059.433 11205785.81 0.759532181 0.626732755 0.624659182 0.677865946 0.846596331 0.641882359 0.788295126 0.656273425 1 23.41774049 -5 0.268957411 3.028352089 0.681681451 0.605322628 0.074963851 136.2678673 1.324657137 153.3599967 0.085848891 1.00E-05 5 -2.346670638 KLSFLS(ph)WGTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLS(0.306)FLS(0.694)WGTNK 174.48 6.71E-06 417940000 1201300 864620 583680 624310 774960 713200 1182700 868560 664010 TRUE FALSE 1144516.93 952725.761 610442.3053 561553.1727 910112.7786 688501.7052 1002257.393 792504.2819 766981.2795 1.492235809 1.24217603 0.795902484 0.732160207 1.186616679 0.897677327 1.306756006 1.033277217 1 19.54883184 4.046058975 3.371901878 1.014505731 1.426513732 0.469140665 0.172149843 0.206144638 4.815484201 0.046000756 0.106904699 11118.82705 -4.046058975 0.412008001 KLSFT(ph)ESLTSGASLLTLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.23)FT(0.346)ES(0.346)LT(0.077)S(0.001)GASLLTLNK 118.51 4.56E-05 139190000 157950 142830 138500 170690 108030 166010 195600 190370 139890 TRUE FALSE 150484.0165 157384.5394 144850.362 153531.9169 126870.3978 160261.0321 165757.6276 173700.1936 161583.4267 0.931308486 0.974014121 0.896443187 0.95017119 0.78516962 0.991816025 1.0258331 1.074987683 1 17.30191971 2.011771414 24.99996001 1.02956412 0.917482459 0.546223817 0.053078702 177.3421868 376635.3035 0.01944078 0.014348013 102.7475355 -2.011771414 -0.112081661 KLSPT(ph)EPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.381)PT(0.619)EPK 80.763 0.014419 440400000 604820 491510 488000 709950 383980 662310 716730 674340 390670 TRUE FALSE 576231.3572 541595.4278 510375.2827 638584.4772 450945.9904 639374.0386 607379.6749 615291.2147 451253.1083 1.276958201 1.200203207 1.131017766 1.415135908 0.999319411 1.416885617 1.345984468 1.363516845 1 18.78357734 KLSS(ph)AMSAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSSAMSAAK 10 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 1 KLS(0.272)S(0.728)AMSAAK 148.08 1.58E-05 681730000 1062600 842010 670920 726370 711920 810360 1213900 975940 727290 TRUE FALSE 1012373.004 927811.7763 701682.3456 653353.9076 836078.6226 782297.03 1028697.26 890481.5198 840074.4187 1.205099193 1.104439982 0.835262127 0.777733369 0.995243521 0.931223488 1.22453111 1.060003138 1 19.68015761 3.985299451 18.36344646 0.987243791 1.167353539 0.284049445 0.121738318 30.40839821 37989.24627 0.034758527 0.064421246 9667.172111 -3.985299451 0.180109747 KLSS(ph)IGIQVDCIQPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.392)S(0.608)IGIQVDCIQPVPK 124.08 3.15E-05 644890000 174390 180560 153240 220380 121010 196260 212400 222710 155620 TRUE FALSE 166146.9303 198959.2693 160266.2056 198226.9837 142114.1057 189463.467 179994.479 203208.3317 179752.7548 0.924308117 1.106849625 0.891592486 1.102775776 0.790608777 1.054022606 1.001344759 1.130487997 1 17.45565436 1.630032989 2.497266367 1.060677728 0.982098234 0.101732315 0.101515528 0.586976103 8.29665028 0.063422987 0.025043432 42.66119229 -1.630032989 -0.078579495 KLSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSSERPSSDGEGVVENGITTCNGK 25 2 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 KLS(0.106)S(0.106)ERPS(0.394)S(0.394)DGEGVVENGITTCNGK 206.94 1.83E-25 145700000 203710 165140 186510 208770 134320 202280 235970 230250 168360 TRUE FALSE 194081.032 181967.9537 195061.668 187784.043 157745.3655 195274.9929 199968.4426 210088.0894 194468.4089 0.998008021 0.935719867 1.003050671 0.965627497 0.811161907 1.004147635 1.028282402 1.080319886 1 17.56917629 2.011541173 24.99599546 1.033561225 0.946994471 0.376211783 0.05578736 238.8614063 517326.677 0.020401199 0.015055075 102.6930785 -2.011541173 -0.086566754 KLSSWDQAET(ph)PGHT(ph)PSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 KLSSWDQAET(1)PGHT(0.98)PS(0.02)LR;KLSSWDQAET(1)PGHT(0.637)PS(0.363)LR;KLSSWDQAET(1)PGHT(0.984)PS(0.016)LR;KLSSWDQAET(1)PGHT(0.966)PS(0.034)LR 153.34 1.50E-08 1210930000 2104040 1613940 2030730 1962610 2069290 1903240 2463560 2106260 2071690 TRUE FALSE 2004586.199 1778402.321 2123840.979 1765324.714 2430173.521 1837330.322 2087698.676 1921824.708 2392957.104 0.837702521 0.743181864 0.887538258 0.737716824 1.01555248 0.767807462 0.872434642 0.803117074 1 21.19036311 -5 0.18422533 1.702322751 0.795848934 0.281250101 0.082350434 157.9355539 1.531415839 40.73577673 0.211932015 1.00E-05 5 -0.906473816 KLSSWDQAET(ph)PGHTPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAET(1)PGHTPSLR;KLSSWDQAET(1)PGHTPSLR 176.48 5.82E-13 414500000 830510 644750 846490 797650 871680 749330 987310 841670 954410 TRUE FALSE 791253.4382 710450.758 885302.4038 717468.7066 1023700.716 723380.5142 836677.7263 767968.9128 1102415.028 0.717745511 0.644449449 0.803057271 0.650815426 0.928598295 0.656178023 0.758949855 0.696624133 1 20.07223603 -4.999999971 0.309315439 3.392936772 0.714569661 0.481885095 0.086411093 233.6065947 2.118833926 364.2819077 0.072828195 1.00E-05 4.999999971 -2.678367111 KLSSWDQAETPGHT(ph)PSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAET(0.001)PGHT(0.998)PS(0.001)LR;KLSSWDQAETPGHT(0.997)PS(0.003)LR;KLSSWDQAETPGHT(1)PSLR 154.79 1.79E-08 540411000 701080 533484 726560 687800 740020 701580 876190 786290 770990 TRUE FALSE 667941.3378 587846.6261 759873.4947 618661.0373 869079.2537 677284.1087 742511.1232 717438.2792 890551.1915 0.750031378 0.660093021 0.853262004 0.694694525 0.975889159 0.760522377 0.833765796 0.805611498 1 19.76433902 -4.999999995 0.052082804 1.878045177 0.360011598 0.430053374 0.082575039 422.0141107 1.621161718 50.38397653 10.60321415 1.00E-05 4.999999995 -1.518033579 KLSTDVDLIVEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLSTDVDLIVEVLR 14 1 Q92615 Q92615 LARP4B La-related protein 4B 0 93.765 0.0071068 15831000 60241 48144 61836 56692 56657 54288 73572 55941 52744 FALSE TRUE 57393.52732 53049.92834 64671.24176 50993.21245 66537.96286 52407.99295 62347.24016 51042.50948 60923.27014 0.942062486 0.870766264 1.061519541 0.837007146 1.092160068 0.860229479 1.023373171 0.837816312 1 15.89470576 KLSVEEFFMDLHNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLSVEEFFMDLHNFR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;; 261.74 3.75E-25 440629000 860906 659776 723078 767552 923980 755273 1115346 899132 846111 FALSE TRUE 820212.6795 727007.9245 756231.8415 690396.2147 1085121.819 729117.7066 945179.483 820399.2355 977321.5725 0.839245447 0.743877906 0.773779954 0.706416633 1.110301716 0.746036645 0.967112064 0.839436331 1 19.89847381 2.784590898 24.99483902 0.918083492 0.770770237 0.398816587 0.100780306 433.2118458 235236.9347 0.027089805 0.028732997 608.9629885 -2.784590898 -0.147313255 KLSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.002)VPT(0.998)S(1)DEEDEVPAPKPR;KLS(0.006)VPT(0.995)S(0.999)DEEDEVPAPKPR;KLS(0.008)VPT(0.992)S(1)DEEDEVPAPKPR 99.838 0.0013841 343245000 295486 237817 269060 286255 176667 284517 308506 277118 217429 TRUE FALSE 281518.9624 262050.8227 281396.6671 257480.1036 207477.6689 274664.1049 261437.7436 252852.0788 251146.7788 1.120933996 1.043417016 1.120447049 1.025217623 0.826121162 1.093639768 1.040975898 1.006790053 1 17.93817125 3.071138442 7.04019206 1.000119619 1.086594054 0.295638216 0.070674353 0.311447069 25.41076793 0.020267432 0.024265627 1177.981425 -3.071138442 0.086474435 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KLSVPT(0.207)S(0.793)DEEDEVPAPKPR;KLSVPT(0.206)S(0.794)DEEDEVPAPKPR;KLSVPT(0.041)S(0.959)DEEDEVPAPKPR;KLS(0.001)VPT(0.286)S(0.713)DEEDEVPAPKPR;KLSVPT(0.045)S(0.955)DEEDEVPAPKPR;KLSVPT(0.026)S(0.974)DEEDEVPAPKPR;KLSVPT(0.057)S(0.943)DEEDEVPAPKPR;KLSVPT(0.028)S(0.972)DEEDEVPAPKPR 179.06 1.91E-14 7729270000 5260490 4863230 4917130 5664860 3498070 5638410 6037330 5737310 3928290 TRUE FALSE 5011837.063 5358798.666 5142585.274 5095417.51 4108132.3 5443150.448 5116224.425 5234920.721 4537469.15 1.104544603 1.18101049 1.133359832 1.122964662 0.905379665 1.199600541 1.127550239 1.15370938 1 22.1134564 -1.11161943 3.512502635 0.999913871 1.119901652 0.170216404 0.080092789 11304824.73 17767788.5 11577.00696 0.018281523 0.077335798 1.11161943 0.119987781 KLTATEGPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLTATEGPGSPR 12 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 KLTAT(0.12)EGPGS(0.88)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR 130.01 0.00013728 565860000 955260 896730 907340 997490 847730 918600 1037600 1021110 1073710 TRUE FALSE 910106.7529 988107.8065 948942.4365 897220.4101 995573.8436 886788.6517 879295.0632 931696.1952 1240215.463 0.733829548 0.796722695 0.765143207 0.723439142 0.802742647 0.715027895 0.708985728 0.751237364 1 20.24215935 0.90061803 21.69131826 1 0.749502018 0.860085558 0.031734906 23873.76385 5210745.287 0.031512895 0.007878224 7.954594214 -0.90061803 -0.250497982 KLTDIINNDHENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLTDIINNDHENVK 14 1 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 134.14 2.63E-05 345270000 474300 385540 431100 461160 391560 467440 497850 500990 429000 FALSE TRUE 451880.779 424826.9643 450866.3614 414803.3207 459847.94 451252.4356 421893.8389 457120.6597 495527.129 0.911919353 0.857323322 0.909872205 0.837095078 0.927997506 0.910651323 0.851404119 0.92249371 1 18.91860452 0.960378058 8.086390778 0.999998872 0.885447768 0.59212192 0.029872789 0.378012252 76.37592952 0.025947211 0.006497575 9.128050994 -0.960378058 -0.114551104 KLTFEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLTFEYR 7 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-4;A6PVN9;Q5T948;Q5T949;A6PVN6;A6PVN8;A6PVN7 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ; 101.43 0.014534 1391460000 2031300 1511900 1098790 1237050 1985460 1344490 2299740 1920290 2250280 FALSE TRUE 1935284.475 1665964.329 1149170.608 1112699.384 2331723.595 1297929.974 1948872.425 1752139.228 2599241.93 0.74455727 0.640942388 0.442117602 0.428086117 0.897078325 0.499349429 0.749784929 0.674096246 1 21.30965949 0.32654927 0.670814165 1.009354553 0.616870573 0.404028057 0.143872782 2.444255949 1.578865247 0.190411981 0.052040793 2.121042007 -0.32654927 -0.39248398 KLTGIKHELQANCYEEVKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLTGIKHELQANCYEEVKDR 20 3 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 197.72 9.75E-22 5774900000 5543700 3075900 5548900 4772300 4004700 5770300 7877600 6535100 4817300 FALSE TRUE 5281660.288 3389337.707 5803322.554 4292579.337 4703118.412 5570473.064 6675727.438 5962851.999 5564342.281 0.949197591 0.609117401 1.042948521 0.771444157 0.845224498 1.001101798 1.199733428 1.071618477 1 22.40777974 2.114027314 3.328820023 1.110969831 0.825900844 0.458653239 0.122522957 0.180524004 3.925662145 0.048781254 0.033195608 130.0251351 -2.114027314 -0.285068987 KLTPQGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLTPQGQR 8 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 128.38 0.0018213 4177500000 4488900 3037300 1635000 2055770 4837600 2892300 5469900 3628500 4965800 FALSE TRUE 4276718.593 3346804.323 1709966.367 1849120.094 5681275.908 2792138.926 4635366.293 3310769.304 5735870.902 0.745609283 0.583486689 0.298118001 0.322378262 0.99048183 0.486785525 0.80813644 0.577204292 1 22.45158112 2.746661487 24.99870688 0.741019094 0.521587421 0.316738682 0.202461998 949.0824097 2928800.246 0.06112593 0.063801913 558.0350621 -2.746661487 -0.219431673 KLTS(ph)DEEGEPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.229)S(0.771)DEEGEPSGK;KLT(0.282)S(0.718)DEEGEPSGK;KLT(0.333)S(0.667)DEEGEPSGK;KLT(0.256)S(0.744)DEEGEPSGK;KLT(0.287)S(0.713)DEEGEPSGK;KLT(0.324)S(0.676)DEEGEPSGK 197.95 7.95E-08 3409020000 6336240 6480890 5895190 7330650 3869900 7247420 7076520 7527730 4212940 TRUE FALSE 6036738.492 7141300.059 6165490.293 6593759.135 4544809.335 6996440.028 5996866.905 6868562.054 4866261.218 1.240529068 1.467512683 1.266987121 1.3549949 0.93394274 1.437744444 1.232335593 1.411465958 1 22.21438233 -1.948814288 2.395951659 0.77564781 1.297597617 0.270666681 0.151096196 9674448.308 4165784.79 12084817.93 0.033661471 0.01125086 1.948814288 0.521949807 KLTS(ph)DEEGEPSGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KLTSDEEGEPSGKR 14 2 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.039)S(0.961)DEEGEPSGKR;KLT(0.045)S(0.955)DEEGEPSGKR;KLT(0.023)S(0.977)DEEGEPSGKR;KLT(0.036)S(0.964)DEEGEPSGKR;KLT(0.161)S(0.839)DEEGEPSGKR;KLT(0.218)S(0.782)DEEGEPSGKR;KLT(0.027)S(0.973)DEEGEPSGKR 173.87 1.37E-06 3825514000 2279470 1842763 2158500 2285380 1362094 2481250 2743940 2707830 1736513 TRUE FALSE 2171723.971 2030542.645 2257469.36 2055649.26 1599642.762 2395323.69 2325301.557 2470718.05 2005802.567 1.082720705 1.012334254 1.125469374 1.024851246 0.797507586 1.194197141 1.159287357 1.231785267 1 20.93574818 KLTSDLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLTSDLGR 8 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 107.57 0.0063765 1377070000 2967690 2365300 2788860 3584780 3480450 3543360 4467430 3873990 4089000 FALSE TRUE 2827413.175 2606326.759 2916731.99 3224431.104 4087439.378 3420652.555 3785841.504 3534762.898 4723101.236 0.598634887 0.551825301 0.617545939 0.682693625 0.865414306 0.724238669 0.801558407 0.748398715 1 22.17130303 3.627926536 0.101476973 1.242683228 0.042954312 0.7821444 0.062344159 15.34011142 0.388112532 1.34087287 3.385597745 4245.477424 -3.627926536 -1.199728915 KLVEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLVEESR 7 1 Q15404 Q15404 RSU1 Ras suppressor protein 1 0 92.062 0.025567 86251000 167410 135110 139750 172490 162920 150150 180270 178770 166090 FALSE TRUE 159496.8611 148877.8626 146157.6757 155150.9775 191333.1964 144950.2679 152766.5006 163115.9511 191846.3889 0.831377968 0.7760264 0.761847416 0.808725034 0.997324982 0.755553798 0.79629594 0.850242488 1 17.54959208 -5 0.309697794 2.621420238 0.808104974 0.402732814 0.068505214 298.5793239 2.705920678 315.7574045 0.062519939 1.00E-05 5 -1.813315264 KLVGYLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLVGYLDR 8 1 P07602;C9JIZ6;P07602-2;P07602-3;Q5BJH1 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 77.192 0.054277 1079100000 6910200 5266700 4401300 5064000 7653400 4874700 7961700 6151500 8098000 FALSE TRUE 6583568.541 5803382.718 4603103.958 4554957.099 8988150.537 4705887.917 6746996.438 5612842.049 9353796.481 0.70383919 0.620430723 0.492110767 0.48696346 0.960909354 0.503099242 0.721311015 0.600060313 1 23.15712061 -5 0.350495271 5.18001698 0.62802687 0.395259655 0.141332498 437.7415141 3.580618292 1375.108455 0.098064176 1.00E-05 5 -4.55199011 KLVIIEGDLER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 159.5 4.58E-05 4489740000 9093470 8316780 7791950 9312560 8344320 8244310 9859430 9259040 8911540 FALSE TRUE 8663639.695 9164269.337 8149218.615 8376443.776 9799566.766 7958807.477 8355192.873 8448269.372 10293496.11 0.841661531 0.890297061 0.79168618 0.813760814 0.952015395 0.773187981 0.811696316 0.820738579 1 23.29522973 -1.045850208 5.17219305 1.000001876 0.838495305 0.499460957 0.051296178 1.06E-06 1.96E-07 0.047627726 0.011225832 0.089980788 1.045850208 -0.161506571 KLVIIEGDLERTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KLVIIEGDLERTEER 15 2 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 ;;;; 233.52 7.00E-18 611839000 1397730 550740 1642740 968353 1928340 1331302 2367390 1616660 2796600 FALSE TRUE 1331662.073 606861.0321 1718061.254 871012.3167 2264641.885 1285198.678 2006201.175 1475096.68 3230282.445 0.412243231 0.187866245 0.531861001 0.269639678 0.701066215 0.397859537 0.621060607 0.456646348 1 21.62322888 -4.999999997 0.118436045 2.912213713 0.140340022 0.631033892 0.13968226 85.1189631 0.65624823 38.72086068 1.219623289 1.00E-05 4.999999997 -2.771873691 KLVIIESDLER ddPTM_SK-BR-3_Trastuzumab_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 844534000 3329190 3092470 2666040 3382590 3033820 2924310 3515890 3166740 3064850 FALSE TRUE 3171825.787 3407596.209 2788280.571 3042565.627 3562917.247 2823040.411 2979476.407 2889443.458 3540131.285 0.895962757 0.962562101 0.787620669 0.859449942 1.006436474 0.797439469 0.841628789 0.816196696 1 21.75537143 KLVIIESDLERAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KLVIIESDLERAEER 15 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;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 250.17 5.53E-19 329602000 523371 232067 512297 383520 610232 450000 733953 551372 808308 FALSE TRUE 498632.2901 255714.8911 535786.3242 344967.841 716656.2676 434416.3872 621974.9899 503090.9447 933656.2764 0.53406409 0.273885473 0.573858215 0.369480557 0.76758041 0.465285136 0.666171273 0.538839568 1 19.832532 -4.99999945 0.128530871 2.695523482 0.294069863 0.590506851 0.130436326 87.80143467 0.714897169 38.03861768 0.904767057 1.00E-05 4.99999945 -2.401453619 KLVILEGELER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 147.26 5.67E-05 804820000 2322680 2077030 1908290 2398040 2014290 2096970 2475430 2316750 2237690 FALSE TRUE 2212891.52 2288681.718 1995786.984 2156984.463 2365581.538 2024351.403 2097757.689 2113883.088 2584699.537 0.856150391 0.885473025 0.772154347 0.834520389 0.915224963 0.783205697 0.811606014 0.817844805 1 21.30156515 -1.080427484 4.956386486 1.00000452 0.836749501 0.589199793 0.043388169 2.16E-06 4.01E-07 0.041946943 0.009886716 0.083094545 1.080427484 -0.163255018 KLVILEGELERAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLVILEGELERAEER 15 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 258.16 4.61E-25 258772000 484883 198782 492205 366851 621150 425898 733300 492332 808080 FALSE TRUE 461963.5415 219038.1118 514773.0861 329974.4405 729478.3633 411149.0455 621421.617 449220.8001 933392.9193 0.49492934 0.234668709 0.551507383 0.353521474 0.781534066 0.440488713 0.665766371 0.481277274 1 19.832125 -5 0.117153721 2.713511624 0.21885066 0.561285034 0.14426886 100.3842058 0.768097641 40.5950071 1.325269517 1.00E-05 5 -2.494660964 KLVIPSELGYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLVIPSELGYGER 13 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 ; 138.19 8.34E-05 777710000 1039660 823840 879240 1043570 1127460 944990 1153330 1066390 1200330 FALSE TRUE 990517.3322 907790.2326 919554.0237 938668.3609 1324088.667 912264.7593 977368.3261 973011.2383 1386471.046 0.714416168 0.654748785 0.663233485 0.677019808 0.95500636 0.657976062 0.704932374 0.7017898 1 20.40298606 -2.255090607 2.134482582 2.009726321 0.711805598 0.508717888 0.087574341 4100624.041 602444.8494 19995367 0.021091227 0.005557883 2.255090607 -1.297920723 KLVNSVAGCADDALAGLVACNPNLQLLQGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLVNSVAGCADDALAGLVACNPNLQLLQGHR 31 1 H0YCY6;Q3LXA3-2;Q3LXA3;E9PJG8;E9PQR1 H0YCY6 TKFC;DAK Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing);ATP-dependent dihydroxyacetone kinase;FAD-AMP lyase (cyclizing) 0 49.095 0.055742 46753000 48400 40318 54302 44761 60568 46562 78262 54369 68014 FALSE TRUE 46112.22792 44426.45004 56791.80041 40261.53924 71131.04002 44949.54626 66321.69452 49608.16213 78561.26375 0.586958836 0.565500705 0.722898254 0.512485891 0.90542128 0.572159155 0.844203509 0.631458301 1 16.26153052 -5 0.085290184 2.121919772 0.35440835 0.462316218 0.119842228 171.6774906 1.02675848 35.39829176 2.843299063 1.00E-05 5 -1.767511422 KLVPIKPAPLPLS(ph)PGKNSFGILSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLVPIKPAPLPLSPGKNSFGILSSK 25 3 A0A1B0GVH1;Q9BRW5;Q02086-2;Q02086 A0A1B0GVH1 SP2 Transcription factor Sp2 1 KLVPIKPAPLPLS(0.973)PGKNS(0.027)FGILSSK 160.43 1.58E-11 113670000 243480 223350 232780 256680 161210 277160 315360 327720 225440 TRUE FALSE 231971.1829 246109.6189 243453.1933 230878.0387 189324.973 267561.8797 267246.04 299023.0994 260400.0838 0.890826069 0.94512112 0.934919796 0.886628128 0.727054194 1.027503048 1.026290146 1.148321825 1 17.99037039 2.029661038 24.9812633 1.052568059 0.889448622 0.601995846 0.070056779 144.1442052 121401.2319 0.025713594 0.018990505 107.0683322 -2.029661038 -0.163119437 KLVQTTYECLMQAIDAVKPGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLVQTTYECLMQAIDAVKPGVR 22 2 P53582 P53582 METAP1 Methionine aminopeptidase 1 0 193.87 3.16E-18 39443000 49832 40933 51249 52006 51562 50527 67857 52692 54680 FALSE TRUE 47476.54012 45104.11924 53598.81734 46778.25808 60554.39647 48777.23732 57504.16837 48078.00914 63159.49513 0.751692838 0.714130459 0.848626437 0.740636985 0.95875365 0.772286688 0.910459595 0.761215856 1 15.94671202 -0.661095075 0.033628139 1.869718959 1.27E-09 0.428869202 0.074680891 302.9228578 2.253631225 73.67819347 52.32017428 0.218225213 0.661095075 -1.869718958 KLVWVPSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLVWVPSDK 9 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 127.42 0.0022987 0 10039800 8865300 8563300 10318600 6846500 10183100 10716800 10107900 7414100 FALSE TRUE 9565238.551 9768684.149 8955935.775 9281354.724 8040527.432 9830456.694 9081755.332 9222798.691 8563840.762 1.116933257 1.140689607 1.045784949 1.083784132 0.938892683 1.147902789 1.060476903 1.076946542 1 23.02982654 3.737786412 24.9999992 1.056041816 1.128811434 0.25715448 0.054687743 87.14810988 2814144.978 0.01319921 0.021832024 5467.470047 -3.737786412 0.072769618 KLWGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KLWGDR 6 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 119.89 0.033075 14232820000 21099230 18711920 18633360 22435120 19735430 20088270 24627410 21530470 20779830 FALSE TRUE 20101911.21 20618685.92 19487717.99 20179899.11 23177282.74 19392608.17 20870046.29 19645147.91 24002259.91 0.837500772 0.859031025 0.811911798 0.840749962 0.965629188 0.807949262 0.869503387 0.81847076 1 24.51666691 -1.390417032 3.091666974 1.001918174 0.852452955 0.517818618 0.045070722 50846648.83 63558974.56 868207.0132 0.009869915 0.040698928 1.390417032 -0.149465219 KLYANMFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLYANMFER 9 1 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 123.11 0.00090897 652110000 3182300 1914500 2894700 1664000 1942800 3329600 3514300 3203700 1692000 FALSE TRUE 3031878.986 2109589.727 3027424.858 1496731.559 2281623.705 3214295.117 2978128.99 2923167.044 1954386.718 1.551319888 1.07941264 1.549040847 0.765831831 1.167437173 1.644656652 1.523817657 1.495695308 1 20.89828453 2.25560243 24.99692958 1.473170128 1.227039857 0.090519268 0.279537628 431.2059516 632491.625 0.090374023 0.075434939 180.1367942 -2.25560243 -0.246130271 KLYEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLYEGK 6 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 91.906 0.075939 599810000 983510 905260 771530 1190900 895690 1045700 1176700 1146200 921290 FALSE TRUE 937021.4314 997507.0232 806905.4136 1071188.469 1051898.052 1009487.147 997172.8034 1045832.652 1064158.948 0.880527701 0.93736657 0.758256476 1.006605706 0.988478323 0.948624403 0.937052501 0.98277861 1 20.02128222 3.183887671 24.99999761 0.970212076 0.878683199 0.544959063 0.049686663 79.12323313 36179.86655 0.013867123 0.016574395 1527.171007 -3.183887671 -0.091528877 KLYESLLVGS(ph)LPDMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLYESLLVGSLPDMNK 16 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 KLYESLLVGS(1)LPDMNK 130.87 2.92E-05 83272000 288190 254840 251830 302900 205470 294400 321520 370920 249710 TRUE FALSE 274567.8298 280808.4857 263376.6546 272451.9165 241303.9029 284204.8542 272466.2189 338440.2784 288433.7515 0.951926841 0.973563199 0.913127029 0.944590968 0.836600785 0.98533841 0.944640554 1.173372661 1 18.13788047 1.301353933 10.44607508 1.086409082 0.939327962 0.543006468 0.057515621 0.276164938 44.28849059 0.034644378 0.012652323 20.01492345 -1.301353933 -0.14708112 KLYGAQFHPEVGLTENGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KLYGAQFHPEVGLTENGK 18 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 136.2 4.40E-06 183850000 419860 355480 360170 448070 319730 420570 484230 470170 357990 FALSE TRUE 400014.0499 391703.8161 376684.1508 403029.1523 375490.8108 406005.5554 410351.82 428999.4223 413505.2608 0.967373545 0.9472765 0.910953708 0.974665114 0.908067796 0.981863096 0.99237388 1.037470289 1 18.65754616 1.792586927 2.197057198 1.015730214 0.945177319 0.618897265 0.024304189 0.182749778 1.723691864 0.014141304 0.006336241 62.02787838 -1.792586927 -0.070552895 KLYGDADYLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KLYGDADYLEER 12 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;;;; 202.13 2.25E-07 2790020000 4219770 3615130 3709940 4280100 3900100 4005060 4866250 4421590 4372630 FALSE TRUE 4020309.835 3983515.857 3880044.419 3849856.216 4580276.205 3866363.768 4123814.188 4034412.139 5050715.128 0.795988238 0.788703333 0.768216841 0.762239825 0.906856968 0.765508184 0.816481247 0.798780378 1 22.26805624 -5 0.312471184 2.80888722 0.790239465 0.700236272 0.041171272 158.2261543 1.425323552 188.5738903 0.034812553 1.00E-05 5 -2.018647756 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR 32 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 225.56 1.16E-36 172691000 234040 165195 290683 261059 354760 266093 410850 213350 58066 FALSE TRUE 222977.393 182028.5583 304011.1031 234816.8533 416630.0317 256878.1327 348167.2867 194667.943 67070.57872 3.324518698 2.713985205 4.532704337 3.50104111 6.21181507 3.82996744 5.191058335 2.902434222 1 16.03339243 3.739669306 24.99363195 4.190096729 3.01925192 0.026658739 1.407610576 187.7026234 4231413.245 0.323182989 0.544187325 5491.225852 -3.739669306 -1.170844809 KMASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMASER 6 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 84.244 0.089907 203210000 360730 256640 252610 262430 294860 224330 341740 322490 366280 FALSE TRUE 343679.0078 282791.9078 264192.4184 236050.0378 346283.4906 216561.3959 289601.2865 294251.066 423080.8317 0.812324696 0.668411061 0.624449038 0.557931299 0.818480689 0.511867661 0.684505808 0.695496094 1 18.6905738 0.641239878 2.946175983 0.999989692 0.671175213 0.539862011 0.095556759 3.531980022 28.09882148 0.086762246 0.022723026 4.377638326 -0.641239878 -0.328814479 KMAVDALEYDESAEDANPAGALEEILENPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KMAVDALEYDESAEDANPAGALEEILENPER 31 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 129.03 7.79E-06 22415700 34112.8 33069.9 31712.9 32759.6 30201.3 30062.8 43432.9 35704.2 40780.3 FALSE TRUE 32500.35555 36439.76041 33166.96783 29466.54277 35468.39716 29021.7177 36806.41341 32577.75097 47104.30065 0.68996578 0.773597313 0.704117615 0.6255595 0.752975772 0.616116093 0.781381167 0.691608845 1 15.52357116 -0.664915446 0.805855715 1.024510953 0.707807075 0.736063222 0.055522382 13.40693246 5.256856564 1.006845042 0.016882121 0.216313963 0.664915446 -0.316703878 KMDADGFLPITLIASFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMDADGFLPITLIASFHR 18 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 86.213 0.0022653 37517000 132110 113460 98960 107230 147820 93868 156800 132730 116410 FALSE TRUE 125865.4221 125021.703 103497.4139 96451.03668 173599.7612 90617.32762 132877.2802 121107.4576 134462.2683 0.936064992 0.929790227 0.769713431 0.717309309 1.291066732 0.673923836 0.988212395 0.900679864 1 17.03684187 KMEDSVGCLETAEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KMEDSVGCLETAEEVKR 17 2 P35579 P35579 MYH9 Myosin-9 0 ; 192.6 9.97E-11 1634500000 710730 578660 685130 781950 471060 764600 804740 864790 569600 FALSE TRUE 677135.2014 637626.1119 716543.8882 703346.9004 553212.7149 738121.7103 681962.1329 789064.4031 657930.6589 1.029189311 0.969138774 1.089087244 1.069028918 0.840837416 1.121883743 1.036525846 1.199312408 1 19.32757602 KMEES(ph)DEEAVQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 141.13 1.70E-05 196990000 207660 195340 208140 247850 141440 239750 242670 279990 185920 TRUE FALSE 197844.3233 215245.3681 217683.4249 222935.6471 166107.0912 231447.3974 205646.2346 255472.5913 214751.5241 0.92127087 1.002299607 1.013652526 1.038109732 0.77348504 1.077745075 0.957600815 1.189619456 1 17.71230884 1.265912099 24.99923434 1.094809843 0.971256147 0.238410178 0.093301567 249.1272206 227702.6712 0.055571728 0.020283004 18.44642027 -1.265912099 -0.123553696 KMEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMEEVK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 91.626 0.076449 205420000 533170 487900 516810 737440 480780 687390 777800 783070 557560 FALSE TRUE 507968.1107 537617.5647 540506.2497 663311.1302 564627.8798 663585.5119 659132.3247 714500.2395 644023.5572 0.788741507 0.834779347 0.839264719 1.029948552 0.876719296 1.030374595 1.023459961 1.109431839 1 19.29675393 3.151709436 0.630891408 1.053220712 0.772770871 0.709228164 0.057699295 0.408344804 0.352215898 0.035998885 0.061517842 1418.108421 -3.151709436 -0.280449841 KMEIYRPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 133.23 0.0001699 583430000 1128700 1283100 1021900 1204200 813920 1272900 1193500 1373400 830710 FALSE TRUE 1075348.588 1413849.349 1068755.126 1083151.528 955867.3903 1228819.154 1011409.655 1253137.815 959532.2641 1.120700812 1.473477653 1.113829275 1.128832837 0.996180562 1.280643913 1.054065291 1.305988201 1 19.87197179 3.671259299 24.99968119 1.12768303 1.297091107 0.225843241 0.131919275 215.4272218 80021.97961 0.031726776 0.049150915 4690.933741 -3.671259299 0.169408077 KMENCLGESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KMENCLGESR 10 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 149.49 3.73E-05 1204130000 2267940 1809910 1858020 2131020 1963170 1962720 2489260 2227360 2263190 FALSE TRUE 2160738.971 1994341.887 1943212.055 1916805.821 2305546.226 1894750.514 2109477.669 2032320.55 2614153.946 0.826553835 0.762901469 0.743342624 0.73324137 0.881947381 0.724804489 0.806944699 0.777429559 1 21.31791267 KMEVEELS(ph)PLALGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMEVEELSPLALGR 14 1 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 KMEVEELS(1)PLALGR 81.003 0.0090147 30672000 29059 23172 28604 25759 24821 22150 27588 21600 25175 TRUE FALSE 27685.43866 25533.25314 29915.52169 23169.65638 29149.77454 21382.93995 23378.94391 19708.58949 29079.01042 0.952076369 0.87806472 1.028766841 0.796782836 1.002433512 0.735339327 0.803980038 0.677759979 1 14.82769055 2.231994096 24.99885218 0.787775552 0.924466793 0.264814419 0.103457328 176.3366158 671310.436 0.033112642 0.025022145 170.6059196 -2.231994096 0.136691241 KMGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMGAPESGLAEYLFDKHTLGDSDNES 26 2 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 KMGAPESGLAEYLFDKHTLGDS(1)DNES 189.31 4.60E-18 347010000 559400 241850 517830 407020 467750 503940 749140 545410 590150 TRUE FALSE 532958.2706 266494.79 541573.0177 366105.5763 549325.4519 486488.4314 634844.9341 497651.009 681667.4479 0.781844978 0.390945454 0.794482734 0.53707358 0.805855485 0.713674143 0.931311794 0.730049543 1 19.37870857 1.994891147 0.628737367 0.95041229 0.595663178 0.380860292 0.138041553 0.662939318 0.520781886 0.114609896 0.069848523 98.83053522 -1.994891147 -0.354749112 KMGAPESGLAEYLFDKHTLGDSDNES(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMGAPESGLAEYLFDKHTLGDSDNES 26 2 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 KMGAPESGLAEYLFDKHT(0.005)LGDS(0.165)DNES(0.83) 82.992 0.0077988 269130000 311900 135630 288570 254130 265850 272780 421240 305030 312650 TRUE FALSE 297157.1051 149450.8512 301801.2199 228584.3696 312214.1558 263333.5602 356972.1014 278319.9561 361134.1652 0.822844067 0.413837475 0.835703871 0.63296246 0.864537853 0.729184845 0.988475021 0.770682984 1 18.46217539 2.39810262 0.768030213 0.93405049 0.635350798 0.32390651 0.14033175 0.653492672 0.762816327 0.100218754 0.06962035 250.0936239 -2.39810262 -0.298699692 KMGS(ph)CDGEGLLTSPDQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KMGSCDGEGLLTSPDQPR 18 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KMGS(1)CDGEGLLTSPDQPR;KMGS(1)CDGEGLLTSPDQPR;KMGS(1)CDGEGLLTSPDQPR;KMGS(1)CDGEGLLTSPDQPR 208.69 3.70E-16 954570000 769540 619050 751600 1202470 658270 1114600 1168940 758130 764840 TRUE FALSE 733165.3693 682131.8988 786061.6034 1081595.431 773072.0796 1076001.123 990596.7339 691744.1181 883447.4809 0.82989129 0.772125014 0.889766082 1.224289451 0.87506286 1.217957089 1.121285368 0.783005366 1 19.75278485 3.46378816 21.82220613 1.053503058 0.805997639 0.342357889 0.137597766 44.82212288 73358.83848 0.035133854 0.047621605 2909.297676 -3.46378816 -0.247505419 KMGSCDGEGLLTS(ph)PDQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KMGSCDGEGLLTSPDQPR 18 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KMGSCDGEGLLT(0.002)S(0.998)PDQPR;KMGSCDGEGLLT(0.177)S(0.823)PDQPR;KMGSCDGEGLLT(0.015)S(0.985)PDQPR;KMGSCDGEGLLT(0.131)S(0.869)PDQPR;KMGSCDGEGLLT(0.018)S(0.982)PDQPR;KMGSCDGEGLLT(0.033)S(0.967)PDQPR 223.15 2.28E-19 2069430000 2400600 1929050 2223240 2323280 2058840 2241380 2706320 2485640 2412940 TRUE FALSE 2287128.396 2125622.388 2325177.753 2089739.48 2417901.044 2163760.449 2293421.179 2267984.184 2787126.412 0.820604471 0.76265733 0.834256295 0.749782813 0.867524714 0.77634098 0.822862275 0.813735672 1 21.41034701 -5 0.314535154 2.800775654 0.794812608 0.756303684 0.034721709 128.9244765 1.156058533 154.0729702 0.027000762 1.00E-05 5 -2.005963046 KMKDTDSEEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KMKDTDSEEEIR 12 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 124.47 0.00018136 395500000 981120 827820 579440 1185100 643570 871400 985790 933560 645690 FALSE TRUE 934744.402 912175.7992 606007.8971 1065971.496 755808.4042 841223.1995 835389.6302 851812.5373 745820.3075 1.253310473 1.223050365 0.812538746 1.429260488 1.013392095 1.127916726 1.120095044 1.142114969 1 19.50846855 3.968007083 24.99544333 1.103796742 1.241963192 0.132986606 0.15353215 1085.535311 848108.5309 0.034815439 0.062788498 9289.815383 -3.968007083 0.13816645 KMKDTDSEEEIREAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KMKDTDSEEEIREAFR 16 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;; 216.93 6.45E-15 3089350000 4323970 2157060 2593840 3814680 3115220 3394360 4799020 3623460 3115790 FALSE TRUE 4119584.507 2376866.866 2712770.13 3431221.119 3658513.382 3276812.462 4066841.359 3306170.633 3598970.8 1.144656274 0.660429606 0.753762751 0.953389541 1.016544336 0.910485982 1.13000121 0.918643361 1 21.77915297 3.032963377 8.735713822 1.004452367 0.853109658 0.186344395 0.135039268 0.418685544 100.8862282 0.03927763 0.046793155 1078.855742 -3.032963377 -0.15134271 KMLGEDS(ph)DEEEEMDTSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KMLGEDSDEEEEMDTSER 18 1 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER 187.56 2.59E-14 1150040000 645950 528157 576510 640800 415016 622810 715590 708680 478070 TRUE FALSE 615417.2236 581976.7988 602943.5537 576385.5666 487394.659 601241.9335 606413.6028 646624.2223 552206.654 1.114469047 1.053911239 1.091880276 1.043785986 0.882630905 1.088798784 1.098164244 1.170982308 1 19.07484875 -0.455411209 7.488885669 1 1.067262393 0.076270794 0.074408222 0 0 0.070564622 0.016632241 0.350419924 0.455411209 0.067262393 KMLGEDS(ph)DEEEEMDTSERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMLGEDSDEEEEMDTSERK 19 2 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(0.999)DEEEEMDTSERK 61.222 0.029369 29206000 26388 17904 24747 25251 17740 22648 28390 27656 26724 TRUE FALSE 25140.69154 19728.43796 25881.67443 22712.72151 20833.85038 21863.69408 24058.58408 25234.29403 30868.22143 0.814452222 0.639118065 0.838456938 0.735796248 0.674928759 0.708291345 0.779396511 0.817484547 1 14.91383474 0.825058019 1.419693854 0.999198052 0.733039856 0.659418674 0.059125059 0.377735527 1.413262801 0.052497844 0.015532676 6.684332107 -0.825058019 -0.266158196 KMNLGVGAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KMNLGVGAYR 10 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 163.64 0.00046846 519470000 1360290 1027220 1078290 1080520 1323340 998090 1196980 1142730 1173700 FALSE TRUE 1295991.788 1131894.886 1127730.663 971904.0767 1554130.077 963525.893 1014358.717 1042666.503 1355711.402 0.955949611 0.834908436 0.831836821 0.716895997 1.146357606 0.71071608 0.748211394 0.769091786 1 20.37061867 KMPFTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMPFTEK 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 109.21 0.01135 980660000 1257200 1123600 1071700 1258700 915870 1153300 1343000 1310100 1071100 FALSE TRUE 1197774.648 1238096.117 1120838.505 1132173.085 1075597.438 1113360.932 1138100.684 1195380.699 1237200.718 0.968132843 1.00072373 0.905947183 0.915108655 0.869379902 0.899903238 0.919899793 0.966197871 1 20.23864814 3.736251125 24.99127232 0.917823184 0.984428288 0.289649423 0.037185451 188.2679352 2037268.985 0.009039152 0.014764929 5448.175959 -3.736251125 0.066605104 KMPLDLS(ph)PLATPIIR ddPTM_SK-BR-3_Trastuzumab_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 208.28 1.82E-09 321220000 1212210 1038290 1119870 1243600 1133300 1190730 1537440 1399900 1370030 TRUE FALSE 1154911.236 1144092.931 1171217.147 1118590.965 1330947.161 1149494.722 1302875.291 1277317.335 1582487.255 0.729807606 0.72297134 0.740111583 0.706856224 0.841047634 0.726384821 0.823308552 0.807158055 1 20.59376245 -0.812524747 0.246296645 1.150519819 0.703762553 0.834051547 0.03583842 4.561270973 0.291575123 0.542515408 0.056090893 0.153983878 0.812524747 -0.446757266 KMQANNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMQANNAK 8 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 111.04 0.0053081 308890000 442470 371870 298340 374740 358870 362610 479830 488590 500070 FALSE TRUE 421555.32 409763.9758 312019.1841 337070.4232 421456.8144 350052.7248 406623.1208 445806.4694 577618.3016 0.729816418 0.709402688 0.540182302 0.583552187 0.729645881 0.606027759 0.703965092 0.77180115 1 19.13975693 0.838060218 1.56175821 0.999447465 0.658716305 0.751449922 0.063137398 0.324857421 1.485819509 0.062250128 0.018061038 6.887477892 -0.838060218 -0.340731161 KMQQNIQELEEQLEEEESAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KMQQNIQELEEQLEEEESAR 20 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 273.94 2.91E-44 499799000 520063 407006 477379 486187 484660 512124 606840 533390 556066 FALSE TRUE 495480.6527 448480.3741 499267.2993 437314.5591 569184.5506 494389.0175 514255.4126 486683.5439 642297.8753 0.771418794 0.69824359 0.777314263 0.68085942 0.886169132 0.769719217 0.800649406 0.757722488 1 19.292883 -5 0.195538651 2.049097891 0.724111384 0.64687993 0.054476485 79.03719812 0.778230082 32.29286403 0.124063982 1.00E-05 5 -1.324986507 KMS(ph)DDEDDDEEEYGKEEHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMSDDEDDDEEEYGKEEHEK 20 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KMS(1)DDEDDDEEEYGKEEHEK 246.44 2.55E-30 396640000 376940 422970 255880 393920 140700 419290 319730 449530 87695 TRUE FALSE 359122.7932 466071.1239 267612.3511 354322.4132 165238.0355 404769.8822 270949.3163 410166.7701 101294.2927 3.545340844 4.601158776 2.641929214 3.497950415 1.631266985 3.995979155 2.674872483 4.049258444 1 16.62819336 3.730256864 24.81619519 2.895543724 4.073249819 0.221708459 0.9869585 703.7969866 2103334.627 0.228410212 0.360601527 5373.495184 -3.730256864 1.177706095 KMS(ph)GADTVGDDDEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KMSGADTVGDDDEASR 16 1 P49796-1;P49796-4;P49796-6;P49796;C9J582;P49796-2 P49796-1 RGS3 Regulator of G-protein signaling 3 1 KMS(0.999)GADT(0.001)VGDDDEASR;KMS(0.98)GADT(0.02)VGDDDEASR 168.68 3.61E-09 130000000 221092 198646 188458 225971 155496 193494 229573 247522 189332 TRUE FALSE 210641.4193 218888.2532 197098.9857 203255.9658 182614.4532 186793.2543 194547.4225 225847.6615 218692.6396 0.963184768 1.000894468 0.901260262 0.929413839 0.835027889 0.85413599 0.889592914 1.032717251 1 17.73854514 3.732450715 24.22487678 0.907541244 0.98203962 0.123812628 0.061354143 437.6256055 1735123.971 0.015453543 0.024643308 5400.708229 -3.732450715 0.074498375 KMS(ph)GGSTMSSGGGNTNNSNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.928)GGS(0.033)T(0.033)MS(0.005)S(0.001)GGGNTNNSNSK;KMS(0.905)GGS(0.022)T(0.029)MS(0.038)S(0.006)GGGNTNNSNSK;KMS(0.981)GGS(0.014)T(0.005)MSSGGGNTNNSNSK;KMS(0.654)GGS(0.16)T(0.16)MS(0.023)S(0.003)GGGNTNNSNSK;KMS(0.888)GGS(0.062)T(0.05)MSSGGGNTNNSNSK;KMS(0.573)GGS(0.198)T(0.198)MS(0.027)S(0.004)GGGNTNNSNSK;KMS(0.983)GGS(0.016)T(0.001)MSSGGGNTNNSNSK;KMS(0.96)GGS(0.026)T(0.012)MS(0.001)SGGGNTNNSNSK 246.21 1.72E-30 1508628000 1210770 1141864 1151156 1315944 792480 1321679 1428700 1366995 961501 TRUE FALSE 1153539.302 1258221.24 1203937.641 1183662.809 930688.2611 1275908.925 1210725.575 1247293.671 1110605.664 1.038657859 1.132914481 1.084037008 1.065781354 0.838000643 1.148840642 1.090148929 1.123075193 1 20.08291523 -0.787095674 7.416284641 0.999985136 1.068802216 0.050990571 0.08713785 0 0 0.080237805 0.018912232 0.163269223 0.787095674 0.06881708 KMSGGSTMS(ph)SGGGNTNNSNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.224)GGS(0.224)T(0.224)MS(0.278)S(0.05)GGGNTNNSNSK 56.529 0.031443 47919000 70643 65500 67163 76893 44203 79834 82532 80394 52659 TRUE FALSE 67303.84539 72174.52447 70242.48998 69163.56955 51911.9892 77069.32856 69940.2276 73354.27516 60825.08878 1.106514544 1.186591354 1.154827579 1.137089496 0.853463435 1.267064794 1.149858208 1.205987145 1 15.8923789 -2.421953677 2.057011718 0.000267071 1.135489338 0.128323221 0.10845102 2977438.161 298227.7629 13840084.12 0.024616228 0.00378483 2.421953677 1.135222267 KMTPSYEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KMTPSYEIR 9 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 76.143 0.058151 397800000 451120 271310 202970 273640 460640 315380 548640 430180 538670 FALSE TRUE 429796.4516 298956.7975 212276.3753 246133.1873 540975.4702 304458.3115 464934.8915 392511.1587 622204.1925 0.690764313 0.480480204 0.341168346 0.395582656 0.869450056 0.489322179 0.747238442 0.630839784 1 19.24702859 0.682988092 0.490243956 1.015880789 0.517907261 0.462842971 0.152982562 1.380534709 0.699803735 0.213039544 0.081962316 4.819345836 -0.682988092 -0.497973528 KGDYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KGDYQK 6 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 81.784 0.097755 370500000 436610 420060 553600 873220 515280 815710 990050 1313100 1008600 FALSE TRUE 415972.3106 462864.5916 578983.1076 785442.2666 605144.6689 787461.7582 838999.689 1198118.003 1165008.537 0.357055161 0.397305751 0.496977567 0.67419443 0.519433678 0.675927887 0.72016613 1.028419934 1 20.1519091 2.079339441 0.410530059 1.050350938 0.323610614 0.858560576 0.085206586 0.37629284 0.153241933 0.090144867 0.091676134 120.0437188 -2.079339441 -0.726740324 down KNDKEAAGEGPALYEDPPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 172.81 2.88E-12 1034300000 1121430 718990 1082050 1056630 702280 1229170 1535150 1377570 808610 FALSE TRUE 1068422.226 792255.8984 1131663.063 950415.5449 824757.4096 1186603.535 1300934.673 1256942.668 934005.109 1.143914756 0.84823508 1.211624061 1.017569964 0.883033082 1.270446514 1.392856056 1.345755666 1 19.83307092 2.152169474 7.443319671 1.299036315 1.017458617 0.354764115 0.14951063 0.19795551 14.60027908 0.051627039 0.038102534 141.9611387 -2.152169474 -0.281577698 KNDMDEPPPLDYGS(ph)GEDDGKSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNDMDEPPPLDYGSGEDDGKSDK 23 2 Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5;H7C2H0 Q12873-3;H7C2H0 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 KNDMDEPPPLDYGS(0.999)GEDDGKS(0.001)DK 100.68 0.0020118 47699000 52613 58742 48619 56116 34777 60128 52406 65679 29555 TRUE FALSE 50126.08776 64727.87658 50848.22924 50475.11307 40842.09779 58045.75228 44410.5022 59927.79857 34138.23845 1.468326722 1.896052038 1.489480171 1.478550603 1.196373909 1.700314806 1.300901986 1.755444958 1 15.059101 -3.175302482 0.183678322 1.04E-11 1.66902199 0.351699496 0.21480005 65.14495783 1.158990636 26.41296735 0.637631191 0.000667879 3.175302482 1.66902199 KNEGSCGPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNEGSCGPAR 10 1 Q9NQZ5 Q9NQZ5 STARD7 "StAR-related lipid transfer protein 7, mitochondrial" 0 83.182 0.025305 22144000 29369 20843 18320 19225 29363 18834 34654 22010 31951 FALSE TRUE 27980.78557 22966.9254 19159.99012 17292.46647 34483.8979 18181.77386 29366.89584 20082.68772 36905.7979 0.758167745 0.622312122 0.519159352 0.468556906 0.934376165 0.492653591 0.795725808 0.544160779 1 15.17155986 -2.057466497 2.455754736 1.482928868 0.651083237 0.36083762 0.149340539 6772388.774 2424982.673 18345329.78 0.033900197 0.008760593 2.057466497 -0.83184563 KNELEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNELEQK 7 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ; 93.143 0.024294 257688000 494740 533450 499740 552050 327480 557820 547710 610770 371400 FALSE TRUE 471354.6207 587809.1615 522653.5733 496556.8852 384592.4083 538502.5535 464146.7801 557287.7409 428994.8152 1.098741999 1.370201086 1.218321422 1.157489246 0.896496635 1.255265879 1.081940303 1.299054723 1 18.71060069 -4.999999999 0.096936289 0.487434037 1.294294015 0.107838151 0.13374545 384.8397331 2.555271313 41.06834182 2.367861385 1.00E-05 4.999999999 0.806859978 KNFEWVAERVELLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNFEWVAERVELLLK 15 2 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 189.81 1.36E-07 81531000 294413 190962 318010 271740 351380 277256 421450 273041 285148 FALSE TRUE 280496.681 210421.2449 332591.0731 244424.1789 412660.5607 267654.5552 357150.062 249132.0826 329367.2955 0.851622747 0.638865023 1.009787789 0.742102152 1.252888694 0.812632459 1.084351928 0.756395932 1 18.32933778 KNGFVVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 130.22 0.0033168 0 5523000 4279600 4211800 5419200 4095000 5210600 6181900 5499500 4944400 FALSE TRUE 5261938.736 4715696.106 4404915.196 4874451.72 4809166.703 5030155.615 5238737.617 5017934.625 5711152.3 0.921344496 0.825699589 0.771283091 0.853497064 0.842065918 0.880760195 0.917282072 0.878620349 1 22.44535043 0.918767111 0.659565212 0.99768549 0.844775862 0.573262081 0.040336648 0.671681467 0.662058523 0.042330408 0.016919429 8.294058828 -0.918767111 -0.152909628 KNGSTAVAESVAS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KNGSTAVAESVASPQK 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KNGSTAVAESVAS(1)PQK;KNGSTAVAES(0.001)VAS(0.999)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK 204.82 1.48E-11 3550410000 4538380 4289510 4125410 5159500 2661230 4991410 5103330 5268010 3157130 TRUE FALSE 4323859.772 4726615.946 4314564.129 4640857.258 3125347.669 4818556.22 4324723.279 4806715.117 3646721.596 1.185684089 1.296127445 1.183135048 1.272610792 0.857029413 1.321339207 1.185920879 1.318092152 1 21.79816863 -1.240315613 3.835534682 0.999769099 1.204976495 0.183924561 0.133955988 29.99338849 31074246.74 13586.7435 0.028454995 0.05750219 1.240315613 0.205207397 KNHLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KNHLEGK 7 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 119.89 0.0030386 3051810000 10684400 9648000 9345860 11694400 7639630 11125300 12353600 11896200 7317650 FALSE TRUE 10179369.59 10631142.17 9774376.925 10518856.69 8971979.053 10740028.07 10468831.43 10854505.66 8452433.789 1.204312254 1.25776107 1.156397929 1.244476675 1.061466943 1.270643266 1.23855823 1.284187009 1 23.01093538 -1.225564126 3.957115564 0.999826801 1.216667218 0.516835392 0.065222509 9.89E-05 1.94E-05 0.05811226 0.013685436 0.059488891 1.225564126 0.216840417 KNLQYYDISAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNLQYYDISAK 11 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 91.914 0.0090541 0 648540 664520 738230 772320 411740 695000 649210 704390 422900 FALSE TRUE 617884.7995 732235.3435 772078.5757 694684.9263 483547.3256 670931.9757 550161.0909 642709.8774 488481.1721 1.264910164 1.49900423 1.580569774 1.42213245 0.989899618 1.373506317 1.126268774 1.315731115 1 18.89794343 2.864008138 8.609050364 1.183188336 1.441151866 0.487244018 0.142144887 0.273167074 17.88350182 0.040285354 0.042768498 731.1527837 -2.864008138 0.25796353 KNLS(ph)PGAVESDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNLSPGAVESDVR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 KNLS(1)PGAVESDVR 104.89 0.00091615 117660000 287110 233610 272890 309320 239610 301640 341960 306520 321220 TRUE FALSE 273538.8793 257415.1246 285402.2764 278226.5659 281397.9081 291194.1312 289787.7215 279679.4838 371033.157 0.737235673 0.693779302 0.769209627 0.749869818 0.758417146 0.7848197 0.781029178 0.753785689 1 18.50118859 -5 0.204901685 2.171509246 0.711965894 0.921702066 0.022819772 34.78513168 0.345474805 16.68723543 0.04994821 1.00E-05 5 -1.459543352 KNLTQDEMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNLTQDEMQR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 103.88 0.0044186 65225000 92982 83547 96238 105360 82541 94780 100330 96551 108380 FALSE TRUE 88586.92513 92060.53429 100650.6075 94769.01263 96936.12427 91497.74483 85022.81581 88096.48259 125187.0169 0.707636681 0.73538404 0.804001964 0.757019498 0.774330491 0.730888451 0.679166402 0.703719002 1 16.93372542 -0.981382099 4.61694629 1.000004858 0.73409627 0.840709507 0.036029618 4987944.471 1080355.832 266.1170555 0.009170351 0.104380146 0.981382099 -0.265908588 KNNIDTHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNNIDTHAR 9 1 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 122.26 0.00038356 77939000 254900 269380 241490 269150 245390 255210 305940 312640 271450 FALSE TRUE 242851.3822 296830.1283 252562.5554 242094.5306 288185.9383 246372.0137 259263.234 285263.5842 313545.0796 0.774534183 0.946690436 0.805506359 0.772120331 0.919121227 0.785762653 0.826877061 0.909800864 1 18.25831335 0.981367103 3.440515308 0.999539877 0.83770058 0.467189231 0.058443636 0.196055015 6.060953113 0.052792496 0.013689258 9.580035168 -0.981367103 -0.161839298 KNPDSQYGELIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KNPDSQYGELIEK 13 1 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;; 235.38 1.76E-16 2231750000 3427020 2705190 2871770 3431480 2183370 3397230 3637620 3617160 2635820 FALSE TRUE 3265031.556 2980851.937 3003443.495 3086541.111 2564149.037 3279583.073 3082634.26 3300422.295 3044569.504 1.072411568 0.979071732 0.986492012 1.013785728 0.842204139 1.077191067 1.012502508 1.084035786 1 21.53780682 KNQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNQKPSQVNGAPGSPTEPAGQK 22 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 KNQKPSQVNGAPGS(0.991)PT(0.009)EPAGQK;KNQKPSQVNGAPGS(0.999)PT(0.001)EPAGQK 142.21 6.08E-08 242648000 473702 459103 488694 581697 306426 576220 532355 551607 380012 TRUE FALSE 451311.0452 505886.1177 511101.1033 523223.7124 359866.5974 556265.3569 451134.4674 503305.3668 438942.3201 1.028178475 1.152511605 1.164392404 1.192010176 0.819849399 1.267285772 1.027776194 1.146632129 1 18.74367185 KNQTALDALHAQTVSQTAASS(ph)PQDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNQTALDALHAQTVSQTAASSPQDAYR 27 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 KNQTALDALHAQTVSQTAAS(0.109)S(0.891)PQDAYR 197.36 2.81E-25 168810000 152840 124610 145050 183830 150390 150320 156640 154160 147500 TRUE FALSE 145615.5561 137307.9007 151700.686 165351.0591 176617.9684 145114.3807 132741.6911 140660.9331 170373.5467 0.854684069 0.805922653 0.89040047 0.970520731 1.036651357 0.851742442 0.779121487 0.825603128 1 17.37834182 KNREELDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KNREELDK 8 2 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 166.09 0.00018026 8498620000 10624820 11917130 9374010 12895800 5202890 11309080 9941520 11583350 5474710 FALSE TRUE 10122605.81 13131499.1 9803817.631 11599489.68 6110272.369 10917443.72 8424758.535 10569050.47 6323700.066 1.600740976 2.076553119 1.550329321 1.834288401 0.966249554 1.726432881 1.332251443 1.67133962 1 22.59233751 2.800570583 24.99996374 1.389392442 1.787067351 0.356116184 0.27964791 243.3721212 98117.39101 0.076282644 0.080909952 631.7868513 -2.800570583 0.397674909 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 287.11 2.03E-77 798444000 1368592 1213917 1303235 1434757 940674 1416586 1502574 1487057 1009502 FALSE TRUE 1303901.368 1337616.522 1362989.614 1290532.5 1104727.248 1367529.272 1273328.74 1356842.406 1166050.414 1.118220407 1.147134383 1.168894241 1.106755321 0.947409507 1.172787433 1.092001447 1.163622421 1 20.15319873 -2.370347681 2.279445124 0.196437184 1.115015646 0.233427119 0.065264156 1044139.543 551347.929 4195375.986 0.015080009 0.004262382 2.370347681 0.918578462 KNS(ph)FGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KNSFGYR 7 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR 134.84 0.0019202 6381210000 8964370 7625930 7692520 9727660 6380380 8977900 10052010 8991750 7091100 TRUE FALSE 8540641.996 8403020.937 8045229.651 8749817.135 7493116.252 8666993.072 8518391.257 8204384.702 8190751.572 1.042717743 1.025915737 0.982233386 1.06825571 0.914826458 1.05814381 1.040001175 1.001664454 1 22.96556441 1.078653913 13.54800865 1.000000931 1.020998478 0.026851377 0.043773741 3.014947173 506.4147431 0.037875447 0.009469578 11.98543808 -1.078653913 0.020997547 KNS(ph)FGYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNSFGYRK 8 2 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 KNS(1)FGYRK 68.786 0.043793 452820000 778740 491710 714260 686070 482830 816040 1001500 844820 723760 TRUE FALSE 741930.5035 541815.808 747009.5275 617104.9402 567035.3991 787780.3302 848702.7812 770843.0821 835997.0043 0.887479859 0.648107356 0.893555268 0.738166449 0.678274439 0.942324346 1.015198352 0.922064407 1 19.67313825 2.119675718 6.157004469 0.979919725 0.768179146 0.606465518 0.080700036 0.13274897 6.645751449 0.028675252 0.021072658 131.7272781 -2.119675718 -0.211740579 KNS(ph)GCGYSIHQHQGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNSGCGYSIHQHQGNK 16 1 Q8TDY4-3;Q8TDY4;H0YER8 Q8TDY4-3 ASAP3 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3" 1 KNS(0.982)GCGYS(0.018)IHQHQGNK;KNS(0.996)GCGYS(0.004)IHQHQGNK 149.47 3.91E-07 57306000 118508 96780 105685 128052 86179 115453 152593 129616 24469 TRUE FALSE 112906.3617 106641.992 110530.7618 115179.9697 101208.5903 111454.8337 129312.1353 118266.1359 28263.52755 3.994772468 3.773131002 3.910720684 4.075215646 3.580890253 3.943415537 4.575229863 4.184408181 1 14.78665392 2.753587076 23.41993821 3.789168239 3.915620894 0 0.981654036 4175.953309 6508545.56 0.268101321 0.283114998 567.0052448 -2.753587076 0.126452655 KNS(ph)IHELLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNSIHELLLER 11 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 KNS(1)IHELLLER;KNS(1)IHELLLER 155.1 1.94E-05 330390000 408630 347620 355100 413250 273380 372570 452990 439620 289750 TRUE FALSE 389314.8697 383042.8732 371381.6862 371709.3249 321057.3854 359667.8075 383878.0558 401124.5422 334682.9502 1.163234845 1.144494732 1.109652243 1.110631195 0.959288142 1.074652316 1.146990176 1.198520994 1 18.35243553 3.646055674 2.008334196 1.087325867 1.157386907 0.163065013 0.067182027 0.638539589 5.044364299 0.019872512 0.037539405 4426.451136 -3.646055674 0.07006104 KNS(ph)LISSLEEEVSILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.65)LIS(0.34)S(0.01)LEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.842)LIS(0.158)SLEEEVSILNR;KNS(0.982)LIS(0.014)S(0.004)LEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.751)LIS(0.249)SLEEEVSILNR;KNS(0.998)LIS(0.002)SLEEEVSILNR;KNS(0.933)LIS(0.065)S(0.002)LEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR 262.98 1.38E-27 5711296600 2035162 1930308.1 1979914 2260461 1408885.3 2027146 2372866 2271813 1525029.9 TRUE FALSE 1938963.926 2127008.69 2070695.015 2033235.166 1654594.45 1956945.426 2010841.711 2072881.01 1761523.748 1.100731073 1.207482268 1.175513539 1.154247945 0.939297271 1.110938997 1.141535397 1.176754507 1 20.74839249 -5 0.189863808 0.476483471 1.151543459 0.203495293 0.07437218 227.4138145 2.223594148 45.48905759 0.20342456 1.00E-05 5 0.675059988 KNS(ph)TGSGHSAQELPTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.971)T(0.029)GSGHSAQELPTIR;KNS(0.973)T(0.014)GS(0.014)GHSAQELPTIR;KNS(0.889)T(0.04)GS(0.071)GHSAQELPTIR;KNS(0.923)T(0.039)GS(0.039)GHSAQELPTIR 269.41 1.31E-28 4208760000 1464190 1249230 1228480 1461900 1168850 1401470 1703810 1489190 1100990 TRUE FALSE 1394980.64 1376527.957 1284807.023 1314947.035 1372697.07 1352936.742 1443862.492 1358788.629 1271725.906 1.09691926 1.082409307 1.010286113 1.033986198 1.079396954 1.063858758 1.135356672 1.068460289 1 20.27835633 1.902791639 24.35309575 1.087135867 1.064042811 0 0.04178501 118.2387613 29606.97656 0.016810602 0.010848752 79.94506123 -1.902791639 -0.023093056 KNS(ph)WEPKPITVPQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNSWEPKPITVPQFK 15 2 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 KNS(1)WEPKPITVPQFK;KNS(1)WEPKPITVPQFK 154.19 1.32E-06 719890000 1652830 1423160 1401020 1911420 811430 1869110 1969460 2118600 1020400 TRUE FALSE 1574704.001 1568181.622 1465258.153 1719280.43 952943.1351 1804382.252 1668982.705 1933084.153 1178638.421 1.336036544 1.330502718 1.243178677 1.45870048 0.808511854 1.530903983 1.416026049 1.640099388 1 20.16868977 KNSLIS(ph)SLEEEVSILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.151)LIS(0.757)S(0.092)LEEEVSILNR 264.1 1.17E-27 1342100000 238490 231220 234380 249290 153280 258550 272090 259600 196030 TRUE FALSE 227217.0503 254781.5809 245126.5548 224230.8956 180011.9835 249596.3487 230577.6732 236868.0478 226429.3312 1.003478874 1.125214563 1.082574212 0.990290853 0.795002938 1.10231456 1.018320692 1.046101433 1 17.78870133 3.235413002 24.61312253 0.993198532 1.072600319 0.16456918 0.083211824 119.4278868 933883.4562 0.023545026 0.029291513 1719.542847 -3.235413002 0.079401788 KNSLISSLEEEVSILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 205.18 1.30E-11 118745000 271040 249930 264610 293020 289690 271850 350590 323050 330360 FALSE TRUE 258228.4763 275398.1511 276742.6302 263565.0729 340211.8443 262435.7663 297101.0565 294762.0294 381590.5416 0.676716135 0.721711157 0.725234512 0.690701273 0.891562571 0.687741801 0.778586008 0.77245633 1 18.54166589 -5 0.163915386 1.99882373 0.670554761 0.686212883 0.057194829 70.4539146 0.654591791 22.82555094 0.205590989 1.00E-05 5 -1.328268969 KNT(ph)APS(ph)LS(ph)S(ph)RKNMDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNTAPSLSSRKNMDLAK 17 3 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 4 KNT(1)APS(1)LS(1)S(1)RKNMDLAK;KNT(1)APS(1)LS(1)S(1)RKNMDLAK 43.798 0.087486 1081080000 1106920 312447 1029050 602360 995510 1098170 2072470 1366640 216138 TRUE FALSE 1054598.085 344285.7045 1076232.96 541809.6284 1169126.629 1060140.098 1756276.638 1246969.757 249655.5772 4.224212002 1.379042713 4.310870891 2.170228419 4.682958186 4.246410633 7.034798333 4.994760264 1 17.92957961 3.584244047 9.595265827 4.438873171 2.800228565 0.050580588 1.769028866 0.736964805 61.29807696 0.466914055 0.723598207 3839.229258 -3.584244047 -1.638644606 KNTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 KNTFTAWS(1)DEES(1)DY(0.001)EIDDRDVNK;KNT(0.001)FT(0.001)AWS(0.997)DEES(0.997)DY(0.003)EIDDRDVNK;KNTFTAWS(1)DEES(1)DYEIDDRDVNK;KNTFTAWS(1)DEES(1)DYEIDDRDVNK;KNT(0.002)FT(0.002)AWS(0.997)DEES(0.997)DY(0.003)EIDDRDVNK 179.74 2.55E-17 810612000 794830 705850 722639 830580 424947 838110 880680 855760 503671 TRUE FALSE 757259.9611 777776.9175 755772.7129 747088.5204 499057.6223 809086.0405 746316.0912 780825.1177 581777.7263 1.301631064 1.336897035 1.299074679 1.284147685 0.857814935 1.390713333 1.28281998 1.342136494 1 19.15010854 -2.136385995 2.509432847 0.411494746 1.267606003 0.236413505 0.147608059 3035562.694 1915247.89 10172543.97 0.034215186 0.007304895 2.136385995 0.856111257 KNTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFTAWS(0.991)DEES(0.009)DYEIDDRDVNK 242.5 1.90E-37 104880000 102850 87804 99300 109150 58862 103630 115850 111910 67610 TRUE FALSE 97988.48433 96751.32742 103853.0032 98178.03463 69127.51416 100041.2671 98174.95477 102110.5671 78094.6135 1.254740627 1.238898857 1.329835677 1.257167815 0.885176468 1.281026471 1.257128378 1.307523817 1 16.25293542 -2.324445483 1.980707109 3.55E-05 1.227700371 0.24612572 0.124526067 2365929.444 307123.7884 10563887.28 0.029667689 0.004737558 2.324445483 1.227664902 KNVFIIGATNRPDIIDPAILRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KNVFIIGATNRPDIIDPAILRPGR 24 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 204.31 4.82E-25 1852270000 2633200 2321750 2351930 2830400 2457900 2479500 2704400 2627800 2626100 FALSE TRUE 2508733.854 2558338.965 2459768.317 2545882.815 2886556.982 2393634.293 2291794.11 2397695.901 3033342.176 0.827052706 0.843405991 0.810910268 0.83929958 0.951609418 0.789107906 0.755534317 0.790446894 1 21.53247682 KPAEKPLPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPAEKPLPKPR 11 3 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 54.486 0.057546 211980000 566300 511950 465100 607200 357940 551000 528670 597680 411170 FALSE TRUE 539532.1213 564118.287 486425.295 546163.1024 420364.6227 531918.7318 448011.6818 545343.9707 474932.1436 1.136019384 1.187787128 1.024199565 1.149981339 0.885104595 1.119988906 0.943317246 1.148256605 1 18.85736188 3.485065621 1.487075532 1.024066429 1.162212885 0.222531541 0.088343534 0.456073783 2.039722377 0.024961837 0.045805231 3055.382738 -3.485065621 0.138146456 KPAFNLSAFGTLS(ph)PSLGNSSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPAFNLSAFGTLSPSLGNSSILK 23 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KPAFNLSAFGTLS(0.741)PS(0.259)LGNSSILK 228.51 4.15E-33 235570000 526480 490360 470600 565750 420880 559110 598220 603120 488850 TRUE FALSE 501594.3338 540328.2415 492177.4755 508879.7351 494281.3387 539747.8805 506950.5519 550307.6155 564658.3613 0.888314719 0.956911787 0.871637629 0.901217037 0.875363534 0.955883978 0.897800487 0.974585082 1 19.10701872 1.116943281 3.96169795 0.999254618 0.909833378 0.569559446 0.029354821 0.148327015 3.950482731 0.025992362 0.006729913 13.09010953 -1.116943281 -0.08942124 KPAFNLSAFGTLSPS(ph)LGNSSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPAFNLSAFGTLSPSLGNSSILK 23 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KPAFNLSAFGTLS(0.459)PS(0.541)LGNSSILK 217.78 1.43E-32 218750000 460390 434560 395720 514090 341030 440370 521870 554860 460790 TRUE FALSE 438628.2771 478842.1581 413864.1534 462412.6965 400505.524 425119.8765 442249.1467 506273.5169 532246.9598 0.824106684 0.899661612 0.777579178 0.868793495 0.752480623 0.798726735 0.830909672 0.951200392 1 19.02173628 1.150472148 3.4488221 0.997253099 0.825654362 0.704950505 0.041943056 0.127312879 2.68998997 0.039322925 0.010476523 14.14074035 -1.150472148 -0.171598736 KPALGFYDTSEENYQALDADFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPALGFYDTSEENYQALDADFRK 23 2 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 127.01 2.69E-05 56193000 46145 46663 42421 55255 45613 50533 56489 63794 58502 FALSE TRUE 43963.8173 51418.01275 44366.04481 49700.66242 53567.89276 48783.02954 47870.56556 58207.85917 67574.19137 0.650600716 0.760911995 0.6565531 0.735497701 0.7927271 0.721918066 0.708414923 0.861391871 1 16.04418472 1.016132739 2.925957993 0.999131743 0.718050902 0.827702728 0.042887224 0.088929903 1.752187028 0.039270399 0.010402656 10.37845577 -1.016132739 -0.28108084 KPALPVS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPALPVSPAAR 11 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR 105.39 0.0011537 696410000 2108360 2596490 2049000 2749200 1867070 2318410 2264110 2364710 1931670 TRUE FALSE 2008702.001 2861075.283 2142948.677 2472845.193 2192686.417 2238122.88 1918678.436 2157643.456 2231223.518 0.900269285 1.282289856 0.960436576 1.108291112 0.982728265 1.003092188 0.85992211 0.96702255 1 21.08940362 2.425257807 1.709308296 0.931775883 1.077228505 0.163367001 0.107141443 0.486013488 2.886264046 0.046987344 0.03512249 266.2304993 -2.425257807 0.145452622 KPANDITSQLEINFGDLGR ddPTM_SK-BR-3_Trastuzumab_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 ; 240.21 4.15E-24 1175280000 1254770 1365030 906910 1406980 946060 1041670 1184580 1268820 1106720 FALSE TRUE 1195459.509 1504128.109 948492.7206 1265547.697 1111052.564 1005596.707 1003850.565 1157715.394 1278344.485 0.935162253 1.176621894 0.74196958 0.989989562 0.869133929 0.786639844 0.785273904 0.905636476 1 20.28584523 3.73728099 24.9999491 0.855315305 1.055892071 0.364163387 0.101879432 97.07067 1896470.338 0.025090265 0.041365065 5461.110828 -3.73728099 0.200576767 KPAPPQHFS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPAPPQHFSPR 11 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 KPAPPQHFS(1)PR 103.6 0.0012752 74975000 119090 124550 122090 142760 112510 122140 138500 134570 141970 TRUE FALSE 113460.8517 137241.7866 127687.9473 128409.4936 132131.7084 117910.2612 117369.2813 122786.3374 163985.9825 0.6918936 0.836911695 0.778651598 0.783051646 0.805750018 0.719026464 0.715727524 0.748761178 1 17.32321297 -1.82758428 2.74598747 1.080573057 0.760254311 0.747574222 0.04383307 10663725.28 8454457.77 5701772.446 0.010775686 0.014873587 1.82758428 -0.320318746 KPASFMTSICDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KPASFMTSICDER 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;; 163.23 6.27E-05 4127945000 5776330 5069910 4904120 5689970 5506830 5237470 6633380 5771310 6145390 FALSE TRUE 5503294.328 5586539.593 5128978.753 5118003.405 6467219.408 5056095.101 5621336.051 5265943.501 7098385.695 0.775288152 0.787015504 0.722555659 0.721009484 0.911083123 0.712288021 0.791917528 0.741850856 1 22.75905954 -1.204894541 4.430976771 1.00006827 0.772320053 0.613518317 0.05725722 3.44E-05 6.17E-06 0.049355897 0.011629815 0.062388631 1.204894541 -0.227748217 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 289.24 4.87E-89 3110350000 405367 400729 334333 443872 178532 460535 406393 388264 212868 TRUE FALSE 386206.1053 441563.7407 349662.4988 399253.1433 209667.9243 444586.5575 344390.2839 354265.5458 245878.4823 1.570719413 1.795861666 1.42209475 1.623782364 0.852729862 1.808155612 1.40065239 1.440815571 1 17.90758596 -2.790232047 0.099107127 1.56E-12 1.927433831 0.27883932 0.261464151 128.3925194 1.443885577 33.95885131 4.962829746 0.001620944 2.790232047 1.927433831 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER 186.64 4.25E-20 525510000 618950 351880 696810 543650 381330 661780 891940 661370 544260 TRUE FALSE 589693.4601 387736.9721 728759.4277 489001.2691 447833.8313 638862.3927 755858.1714 603456.9367 628661.0611 0.938014928 0.616766325 1.159224696 0.777845646 0.712361333 1.016227077 1.202330187 0.959908246 1 19.26192288 2.073089908 6.48486768 1.084550467 0.831695121 0.291527385 0.155865461 0.213753022 14.99560123 0.056063856 0.041105865 118.3286496 -2.073089908 -0.252855346 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Trastuzumab_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 424.32 6.07E-208 1.34024E+11 3418263 3626542 2968405 3911138 1493179.4 3577887 3050624 3665132 1448680 TRUE FALSE 3256688.482 3996090.753 3104509.305 3517982.978 1753589.415 3453983.876 2585195.28 3344193.612 1673333.896 1.946227523 2.388101241 1.855283822 2.102379559 1.047961449 2.064133097 1.544936899 1.998521407 1 20.67429392 -0.539687015 0.112568249 3.32E-10 2.665182714 0.395594222 0.350991003 32.13635136 0.897893319 16.16656471 5.735489472 0.28861107 0.539687015 2.665182714 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER 382.73 6.17E-166 28144960000 3079372 1692306 3038183 2550543 1824777 3075676 3690327 3464676 2133121 TRUE FALSE 2933816.188 1864753.905 3177486.696 2294157.572 2143017.531 2969164.569 3127299.839 3161290.602 2463914.51 1.190713467 0.756825733 1.289609149 0.931102748 0.869761318 1.205059898 1.2692404 1.283035831 1 21.23252077 2.15690984 8.854656782 1.218991976 0.999585392 0.213963784 0.168594122 0.3567533 35.00585865 0.058681133 0.043335911 143.5191454 -2.15690984 -0.219406584 KPATSYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPATSYVR 8 1 P46779;H0YKD8;P46779-2;P46779-3 P46779 RPL28 60S ribosomal protein L28 0 ; 105.94 0.0068822 1819320000 1774720 981070 258330 375400 1948090 675440 2000690 1078660 1782270 FALSE TRUE 1690832.503 1081042.148 270174.686 337664.0788 2287836.279 652049.3434 1695447.995 984206.8121 2058655.329 0.821328602 0.525120516 0.131238426 0.164021667 1.111325557 0.316735558 0.823570596 0.478082367 1 20.97327088 0.11275913 0.501428886 1.035783831 0.525077399 0.178587212 0.306731772 6.442810612 2.177611522 0.820444957 0.148257993 1.296460025 -0.11275913 -0.510706432 KPDHVPISSEDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPDHVPISSEDER 13 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 141.85 2.60E-05 203760000 806610 728210 711550 875400 675090 753150 847590 860320 735210 FALSE TRUE 768483.1438 802415.4269 744175.2713 787403.1288 792825.4823 727068.2267 718274.5784 784985.82 849222.6119 0.904925438 0.944882314 0.876301762 0.92720462 0.933589699 0.856157404 0.845802465 0.924358124 1 19.69578326 3.740888332 24.8950505 0.898068416 0.924903874 0 0.045889 588.2092786 6290923.348 0.011516183 0.019657975 5506.660876 -3.740888332 0.026835458 KPDIYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPDIYER 7 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 78.516 0.056318 292410000 512360 514270 512610 566540 502920 529070 631830 573520 603130 FALSE TRUE 488141.7582 566674.6977 536113.6755 509590.3228 590629.0888 510748.1732 535432.7291 523299.5484 696660.32 0.700688333 0.813416067 0.769548172 0.731476027 0.847800674 0.733138028 0.768570728 0.75115452 1 19.41009587 -2.504006341 2.157116124 3.866243727 0.765526695 0.75838115 0.041775707 2191366.366 166931.3142 30680236.75 0.009334761 0.00313324 2.504006341 -3.100717031 KPDQPYEWLSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPDQPYEWLSYK 12 1 E7EPM6;P33121-2;P33121;P33121-3;D6RER0 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 146.47 0.00010385 264510000 625890 468970 464350 570140 479810 538060 639220 586380 503260 FALSE TRUE 596305.4201 516758.5762 485640.9068 512828.444 563488.7121 519426.8473 541695.2489 535033.4586 581302.9905 1.025808279 0.888965969 0.835435074 0.882205068 0.969354573 0.893556124 0.931863861 0.920403761 1 19.1489308 -0.156360553 1.016659657 1.001072477 0.91921159 0.197867528 0.051628012 23.56317866 18.3959306 0.152413872 0.015943448 0.69765297 0.156360553 -0.081860887 KPEASHSFENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPEASHSFENR 11 1 P56181-2 P56181-2 0 ; 151.26 2.17E-05 262470000 334410 253120 269620 263650 257610 245720 297420 292480 262510 FALSE TRUE 318603.102 278913.2158 281982.3437 237147.4011 302537.1024 237210.6548 252043.1165 266868.9007 303218.7101 1.050736948 0.919841707 0.929963536 0.782100158 0.997752092 0.782308766 0.831225476 0.880120163 1 18.20999925 4.5032267 0.941988705 0.866749614 1.109552937 0.296869191 0.076972361 1.447385855 1.309517798 0.022800406 0.332337749 31858.60098 -4.5032267 0.242803323 KPEDRPNTSEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPEDRPNTSEILR 13 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ; 157.38 2.68E-05 525250000 308100 229880 252110 295990 244130 248730 331890 313030 280160 FALSE TRUE 293536.7236 253305.0334 263669.4929 266236.5229 286706.1947 240116.4177 281254.0849 285619.4337 323605.7819 0.907081208 0.782758058 0.8147861 0.822718683 0.885973647 0.742002866 0.869125648 0.88261536 1 18.30387786 0.876602734 1.750059917 0.999142329 0.828909063 0.559626464 0.047591523 0.361761934 2.178062827 0.041639999 0.011844068 7.526667555 -0.876602734 -0.170233266 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;;;; 283.93 3.08E-52 2626585000 3508389 3434632 2786071 3893486 1686585 3659420 3250978 3882063 1736463 FALSE TRUE 3342554.405 3784624.906 2913815.111 3502105.39 1980724.89 3532693.368 2754981.598 3542128.984 2005744.813 1.666490364 1.88689253 1.452734711 1.746037366 0.987525869 1.76128755 1.373545418 1.765991845 1 20.93570664 -2.671867804 0.107835044 8.63E-13 1.990772682 0.310046166 0.263489006 97.85046834 1.234617826 28.6063447 3.774189249 0.002128787 2.671867804 1.990772682 KPEDWDERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPEDWDERPK 10 2 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 122.7 0.00027088 365220000 1433270 1643970 1175610 2185800 982390 1729300 1552520 1547330 720630 FALSE TRUE 1365522.168 1811492.412 1229512.881 1966079.231 1153718.505 1669413.907 1315654.56 1411837.582 832381.6199 1.640500144 2.176276324 1.477102391 2.361992606 1.386045147 2.005587182 1.580590595 1.696142188 1 19.66688558 0.119354933 0.47032583 0.912889428 1.886164672 0.416205561 0.302902943 3.040357904 0.929432124 0.77095197 0.142008496 1.316300155 -0.119354933 0.973275244 KPEEES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 81.017 0.01467 3225530000 3916700 4997520 3168320 4767950 2477930 4345370 3556610 4111200 2424430 TRUE FALSE 3731565.353 5506772.97 3313590.606 4288666.607 2910080.207 4194888.747 3013983.823 3751201.533 2800398.222 1.332512399 1.966424963 1.183256931 1.53144884 1.039166567 1.497961509 1.076269724 1.339524323 1 21.41720057 3.712975037 24.94353591 1.2504275 1.649468736 0.347828645 0.233641442 656.407031 639935.2573 0.055890551 0.086620559 5163.866871 -3.712975037 0.399041235 KPEEES(ph)PRKDDAK ddPTM_SK-BR-3_Trastuzumab_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 137.81 0.00031128 6913380000 5667120 5557670 4992260 6093140 2176297 6713790 6031860 6661360 2397922 TRUE FALSE 5399246.469 6124002.892 5221160.059 5480645.991 2555842.508 6481289.769 5111588.974 6078056.004 2769779.497 1.949341626 2.211007374 1.885045385 1.978730075 0.922760281 2.340002075 1.845485888 2.194418729 1 21.4013397 3.315243987 2.687654006 1.763038163 2.070972148 0.092364331 0.458815595 0.690194521 10.12574125 0.126095408 0.175813727 2066.540813 -3.315243987 0.307933985 KPEENPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPEENPASK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 136.5 0.00030625 545950000 1203420 1032660 1080420 1276670 754520 1240360 1327290 1358410 920480 FALSE TRUE 1146536.722 1137889.228 1129958.326 1148336.706 886108.0491 1197406.022 1124787.533 1239460.419 1063223.337 1.078359251 1.070225971 1.06276667 1.080052202 0.833416666 1.126203668 1.057903353 1.165757349 1 20.02001325 -0.959872649 4.377968787 0.999998368 1.058381978 0.044044033 0.086773696 1.27E-06 3.02E-07 0.077264498 0.018210908 0.109679977 0.959872649 0.05838361 KPEGAQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPEGAQAR 8 1 P40222 P40222 TXLNA Alpha-taxilin 0 69.954 0.084315 48702000 85884 84323 86267 91232 88216 92984 119490 111130 109970 FALSE TRUE 81824.43353 92915.60957 90222.42728 82061.18603 103600.8425 89763.94076 101259.6059 101398.8681 127023.586 0.644167246 0.731483125 0.710280903 0.646031093 0.815603194 0.706671443 0.797171684 0.798268033 1 16.95473688 -4.999999242 0.127191707 1.958690944 0.601831417 0.827128539 0.042955416 51.86302653 0.419441532 12.53978921 0.309554816 1.00E-05 4.999999242 -1.356859528 KPES(ph)PYGNLCDAPDSPRPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPES(0.953)PY(0.009)GNLCDAPDS(0.038)PRPVK;KPES(0.53)PYGNLCDAPDS(0.47)PRPVK 85.467 0.0013793 260730000 304950 253430 281480 341550 237460 285380 345480 322300 250900 TRUE FALSE 290535.6179 279254.8051 294386.1364 307216.7451 278872.9488 275497.219 292770.6808 294077.7034 289808.2906 1.002509684 0.963584598 1.015796118 1.060068863 0.962266981 0.950618833 1.010221896 1.014731852 1 18.14473934 4.065871 0.004056625 1.250637364 0.736758172 0 0.032272981 346958.9946 275.8762613 17067.33849 17884.74103 11637.80297 -4.065871 -0.513879193 KPESPYGNLCDAPDS(ph)PRPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPES(0.102)PYGNLCDAPDS(0.898)PRPVK 104.96 0.00013724 115750000 129070 115080 133290 145790 93047 119820 145960 136690 99408 TRUE FALSE 122969.1169 126806.7828 139401.4783 131134.9122 109274.3673 115670.6034 123691.1213 124720.699 114823.6849 1.070938604 1.104360855 1.214048116 1.142054553 0.951670968 1.007375816 1.077226544 1.086193141 1 16.80906074 2.767366888 24.91136939 1.031751625 1.125734136 0.510494155 0.052251733 693.4746605 599708.836 0.017007359 0.018035211 585.2843185 -2.767366888 0.093982511 KPFEEHWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPFEEHWR 8 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 ; 147.2 0.00035126 1300200000 4379100 3245900 3325700 3554700 4192000 3139800 4717100 3865400 3880800 FALSE TRUE 4172108.622 3576660.9 3478186.635 3197374.803 4923083.473 3031067.939 3997419.76 3526925.084 4482614.644 0.930731047 0.797896135 0.775928094 0.713283442 1.098261587 0.676183027 0.891760742 0.786800866 1 22.09590905 KPFSQHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPFSQHVR 8 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 158.76 0.00023573 1364230000 3762700 1892030 850060 1048620 4557300 1312260 4866300 2545200 4653800 FALSE TRUE 3584844.628 2084830.008 889036.0918 943210.7254 5352091.677 1266816.107 4123856.559 2322328.795 5375487.536 0.666887348 0.387840172 0.165387062 0.17546515 0.995647677 0.235665342 0.767159543 0.432021985 1 22.35796418 0.126308416 0.436195616 1.060822533 0.428842944 0.282708384 0.265947739 4.697730988 1.27470296 0.806021063 0.152836232 1.337545044 -0.126308416 -0.631979589 KPGDGEVS(ph)PSTEDAPFQHSPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPGDGEVSPSTEDAPFQHSPLGK 23 1 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KPGDGEVS(0.956)PS(0.017)T(0.026)EDAPFQHSPLGK;KPGDGEVS(0.794)PS(0.182)T(0.024)EDAPFQHSPLGK 228.3 3.35E-33 718730000 1285110 1079620 1050480 1265940 772650 1305650 1420160 1390130 822130 TRUE FALSE 1224365.397 1189634.505 1098645.547 1138685.306 907399.9154 1260435.013 1203488.509 1268402.848 949621.7215 1.289319072 1.252745676 1.156929672 1.199093576 0.955538289 1.327302214 1.267334647 1.335692749 1 19.85699341 3.92869546 4.802813727 1.193953362 1.276629358 0.080403134 0.124418634 0.576493515 25.17004896 0.031185366 0.059114685 8485.852143 -3.92869546 0.082675996 KPGDLSDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KPGDLSDELR 10 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;;;; 136.53 0.00018476 1986177000 5520660 4695360 4815260 5466250 4527210 5080710 6130230 5501510 5075380 FALSE TRUE 5259709.343 5173822.522 5036044.434 4916772.165 5316753.991 4904763.739 5194950.824 5019768.619 5862444.009 0.897187135 0.882536791 0.859034974 0.838689829 0.906917658 0.836641464 0.8861408 0.856258689 1 22.48307081 -1.511701626 3.306386983 1.003098634 0.872421203 0.750442591 0.02345758 3684483.212 1767940.648 80778.94188 0.005077786 0.030782109 1.511701626 -0.130677431 KPGGEREER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPGGEREER 9 2 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 78.098 0.017286 35354000 54794 37366 48049 45982 58611 43120 64352 52441 66127 FALSE TRUE 52203.99621 41173.63788 50252.09418 41359.802 68832.73984 41626.74359 54533.92049 47848.98803 76381.63743 0.683462648 0.539051522 0.657908051 0.541488811 0.901168686 0.54498365 0.713966371 0.62644622 1 16.22093823 -5 0.259692825 3.276510934 0.6181115 0.507421238 0.107780259 146.4963701 1.439196173 177.8563052 0.126467134 1.00E-05 5 -2.658399433 KPGGFDISLFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPGGFDISLFYR 12 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 196.11 3.37E-07 1787270000 3310700 2857000 2092900 2421500 3216400 2407900 3521300 2954400 3246400 FALSE TRUE 3154209.772 3148131.548 2188861.535 2178086.219 3777339.142 2324513.819 2984061.012 2695697.074 3749835.132 0.841159587 0.839538656 0.583722073 0.580848529 1.007334725 0.619897606 0.79578459 0.718884159 1 21.83839574 -1.502372812 9.680002237 1.000003702 0.757046059 0.258879559 0.133073917 9.99E-06 5.14E-07 0.121058744 0.028533385 0.031450473 1.502372812 -0.242957643 KPGINVASDWSIHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPGINVASDWSIHLR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 171.08 7.17E-07 376980000 233570 191890 216250 233960 255930 210160 288640 271470 285830 FALSE TRUE 222529.609 211443.8092 226165.2764 210441.8963 300564.111 202882.1065 244602.6668 247698.6476 330155.0566 0.67401545 0.640437894 0.68502745 0.63740322 0.910372581 0.614505525 0.74087209 0.750249444 1 18.33278422 -5 0.179857567 2.244613232 0.635853001 0.590136901 0.07993046 87.00969275 0.837410046 38.57257855 0.225706618 1.00E-05 5 -1.608760231 KPGMFFNPEESELDLTYGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 295.17 2.21E-54 7085750000 6868440 5578570 5768820 6744610 6078110 5990580 7362050 6478190 7165690 FALSE TRUE 6543782.453 6147032.625 6033326.103 6066628.989 7138130.46 5783124.712 6238834.059 5910925.341 8276908.608 0.790607069 0.742672526 0.728934725 0.732958315 0.862415039 0.69870588 0.753763797 0.714146503 1 22.9806606 -1.36111394 5.274219097 1.000105093 0.753850546 0.741124325 0.04587044 5.17E-05 6.26E-06 0.040473279 0.009535588 0.043539763 1.36111394 -0.246254547 KPGMTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KPGMTR 6 1 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ;;;; 97.068 0.066531 14280159000 15257574 11013079 11379042 12337782 12950195 10668215 13586422 12586034 14263095 FALSE TRUE 14536378.71 12135324.27 11900782.33 11097564.71 15208704.91 10298772.04 11513563.79 11483934.14 16474942.93 0.882332569 0.736592796 0.722356513 0.67360262 0.923141584 0.625117312 0.698853031 0.697054563 1 23.97377013 -1.110250318 4.879063898 1.00001158 0.745986271 0.435148141 0.091339095 1.11E-05 2.03E-06 0.085484574 0.020147989 0.077579983 1.110250318 -0.254025309 KPGPPLS(ph)PEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KPGPPLSPEIR 11 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR 132.44 0.00011178 3235690000 2691080 2592810 2489560 2925990 2305110 2600200 2881240 2808690 2589320 TRUE FALSE 2563877.982 2857020.287 2603708.789 2631863.926 2707120.454 2510154.422 2441653.92 2562746.214 2990858.521 0.857238135 0.955250898 0.870555652 0.879969383 0.905131565 0.839275547 0.816372257 0.856859726 1 21.51212824 2.247109372 24.983265 0.857006499 0.897054135 0 0.056218002 402.5966005 1176566.733 0.017940725 0.014780098 176.6482631 -2.247109372 0.040047636 KPGPSGPSES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPSGPS(0.005)ES(0.995)PK;KPGPSGPS(0.002)ES(0.998)PK 144.46 3.86E-05 891560000 1366270 1464150 1260390 1566310 688210 1499340 1470370 1736610 820900 TRUE FALSE 1301689.125 1613348.55 1318180.128 1408861.543 808233.6061 1447417.48 1246038.051 1584543.222 948200.9794 1.372798756 1.701483741 1.390190642 1.485825868 0.852386386 1.526488067 1.314107535 1.671104815 1 19.85483336 2.962659266 24.98802863 1.300273701 1.507468175 0.150910312 0.247022105 1051.655342 703756.8742 0.069753108 0.07400443 917.6123843 -2.962659266 0.207194474 KPIDSLRDS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KPIDSLRDSR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R 147.73 2.08E-05 3776640000 5919190 7296100 4945450 6683590 4207110 6099190 5681240 6334920 4393670 TRUE FALSE 5639401.619 8039580.885 5172203.774 6011742.835 4940828.652 5887973.521 4814462.495 5780200.821 5075017.904 1.111208222 1.58414828 1.019149858 1.18457569 0.973558861 1.160187734 0.948659214 1.138951809 1 22.27498148 3.709709893 24.99629053 1.059435118 1.3476783 0.431451609 0.136939491 523.267374 453359.3607 0.033547236 0.05198083 5125.189087 -3.709709893 0.288243182 KPIETGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KPIETGSPK 9 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KPIET(0.001)GS(0.999)PK;KPIET(0.012)GS(0.988)PK;KPIET(0.006)GS(0.994)PK;KPIET(0.001)GS(0.999)PK;KPIET(0.033)GS(0.967)PK;KPIET(0.034)GS(0.966)PK;KPIET(0.057)GS(0.943)PK;KPIETGS(1)PK 106.32 0.0018096 26125100000 34853800 29743400 29087100 35245400 16466070 36180700 35430600 36368400 17800530 TRUE FALSE 33206329.95 32774286.28 30420772.31 31702465.43 19337747.39 34927753.29 30025011.24 33183790.09 20560945.28 1.615019616 1.594006785 1.479541524 1.541877817 0.940508675 1.698742583 1.46029333 1.61392337 1 24.29340326 -2.097596805 2.446820069 0.133250204 1.50012711 0.355254006 0.208523325 11483926.93 5899611.334 54939245.91 0.049629476 0.007987359 2.097596805 1.366876906 KPIFQANLELAQLELISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPIFQANLELAQLELISR 18 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 157.12 1.06E-08 35410000 91636 94655 95776 98978 89128 89731 112390 101640 104460 FALSE TRUE 87304.54789 104300.4521 100167.4243 89028.54339 104671.895 86623.59297 95242.84132 92739.86277 120659.1233 0.723563586 0.864422426 0.830168674 0.737851734 0.867500875 0.71791996 0.789354661 0.768610448 1 16.88057748 -2.277467583 2.269540475 1.897187956 0.789565537 0.607493397 0.053674856 2260627.569 432728.7382 10370555.05 0.011955363 0.005278766 2.277467583 -1.107622419 KPIKS(ph)PSKDASSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPIKSPSKDASSGK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.865)PS(0.135)KDASSGK;KPIKS(0.703)PS(0.194)KDAS(0.051)S(0.051)GK 104.45 0.0058414 2955500000 7533400 7795100 5975900 8864500 2769900 8459400 6896400 8321100 2494500 TRUE FALSE 7177311.112 8589429.552 6249900.926 7973423.619 3252969.683 8166448.857 5844227.519 7592460.371 2881334.32 2.490967835 2.981059675 2.169099532 2.767267777 1.128980299 2.834259392 2.028305941 2.635050129 1 21.45830563 3.193006961 1.905008669 2.079309972 2.691098394 0.163254513 0.626329767 0.573311869 4.282748144 0.180379064 0.242771286 1559.577498 -3.193006961 0.611788422 KPITDDDVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KPITDDDVDR 10 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;;; 149 3.87E-05 2253760000 5263510 5152170 4625020 6079730 4366390 5392610 5586690 5552700 4487030 FALSE TRUE 5014714.314 5677181.981 4837081.742 5468583.99 5127887.034 5205862.564 4734337.834 5066476.151 5182855.696 0.967558159 1.095377204 0.933285051 1.05512951 0.989394136 1.004439033 0.913461248 0.977545286 1 22.3053158 1.9137368 8.370391717 0.954923922 1.013598348 0.137489767 0.049252389 0.468043151 41.66446458 0.019155552 0.012045645 81.98545296 -1.9137368 0.058674426 KPLFHGDSEIDQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPLFHGDSEIDQLFR 15 1 P06493;A0A024QZP7;A0A087WZZ9;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 233.78 7.96E-18 1330210000 2827500 2747800 2756100 3173200 2840400 3051200 3382600 3345400 2947000 FALSE TRUE 2693849.679 3027803.944 2882469.911 2854223.907 3335764.861 2945536.179 2866522.244 3052459.041 3404005.709 0.791376369 0.889482628 0.846787625 0.838489753 0.979952781 0.8653147 0.842102655 0.896725594 1 21.69880203 -5 0.12996195 1.430142246 0.81064662 0.484704431 0.046020792 133.8249673 1.097334733 15.15337757 0.346412693 1.00E-05 5 -0.619495626 KPLHYAADCGQLEILEFLLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPLHYAADCGQLEILEFLLLK 21 1 P58546 P58546 MTPN Myotrophin 0 ;; 159.35 3.63E-11 3279430000 5739920 4964210 4401487 6323310 4203766 5694660 7035700 5834910 3530269 FALSE TRUE 5468605.357 5470068.643 4603299.533 5687678.865 4936901.459 5497452.496 5962274.746 5323974.348 4077725.086 1.341092212 1.341451061 1.128889132 1.394816655 1.210699926 1.348166534 1.462157114 1.305623659 1 21.95933308 0.950696265 23.57765021 1 1.32664786 0.537193519 0.092167124 6384.837373 3053310.145 0.08693052 0.02173263 8.926809453 -0.950696265 0.326647861 KPLPDHVSIVEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KPLPDHVSIVEPK 13 1 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;; 120.53 0.00017063 2374930000 7207750 6542660 6358580 8094900 6726590 6843540 8624010 8290830 6801090 FALSE TRUE 6867053.942 7209364.492 6650127.182 7281185.273 7899705.166 6606546.494 7308258.884 7564840.973 7855768.302 0.874141609 0.917716029 0.846527918 0.926858455 1.005592943 0.840980314 0.93030479 0.962966407 1 22.90532095 -4.999999956 0.091783519 1.31038622 0.833915294 0.340216706 0.046429877 242.9653757 1.543987089 14.49524144 0.967432238 1.00E-05 4.999999956 -0.476470925 KPLPDHVSIVEPKDEILPTT(ph)PISEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KPLPDHVSIVEPKDEILPTTPISEQK 26 2 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 KPLPDHVSIVEPKDEILPT(0.035)T(0.965)PISEQK;KPLPDHVSIVEPKDEILPT(0.022)T(0.978)PISEQK;KPLPDHVSIVEPKDEILPT(0.018)T(0.982)PISEQK;KPLPDHVSIVEPKDEILPT(0.113)T(0.886)PIS(0.001)EQK 194.98 6.89E-19 1056830000 2135500 800981 2043380 1671810 1678870 1988690 3517970 2670160 2367810 TRUE FALSE 2034559.147 882601.8745 2137070.994 1503756.483 1971664.396 1919821.167 2981239.065 2436346.635 2734997.882 0.743897888 0.322706603 0.781379396 0.549819981 0.720901617 0.701946126 1.090033409 0.890803847 1 21.38310828 2.0142392 1.8965265 1.003335926 0.587250721 0.581262252 0.140533588 0.214356609 1.442871689 0.077990883 0.040339352 103.3330384 -2.0142392 -0.416085205 KPLPDHVSIVEPKDEILPTTPISEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPLPDHVSIVEPKDEILPTTPISEQK 26 2 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 112.23 0.001105 96434000 154030 93031 175320 142610 167010 180570 286330 241130 229790 FALSE TRUE 146749.3072 102510.9647 183358.5954 128274.5719 196136.4911 174316.8156 242645.0997 220015.3789 265424.6596 0.552884978 0.386214924 0.690812209 0.483280536 0.738953537 0.656746875 0.914176927 0.82891838 1 18.01794289 2.08105974 0.59967436 0.991285095 0.47319928 0.757393989 0.093278693 0.318502314 0.229763391 0.075959472 0.050744087 120.5201713 -2.08105974 -0.518085815 KPLSLAGDEETECQSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPLSLAGDEETECQSSPK 18 1 Q86TN4;Q86TN4-4;F5H1K3;Q86TN4-2 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 1 KPLSLAGDEETECQS(0.028)S(0.972)PK 153.83 9.04E-10 0 144300 148290 126980 162320 72475 150320 141070 167140 84811 TRUE FALSE 137479.225 163400.9196 132802.1586 146003.2852 85114.61705 145114.3807 119547.1806 152504.3355 97963.05673 1.403378269 1.667985106 1.355635104 1.490391277 0.868844031 1.481317402 1.22032922 1.556753542 1 16.57995017 2.9352304 24.99971486 1.250688231 1.496112871 0.251184895 0.214556602 271.3315374 104727.871 0.059277464 0.062873296 861.4506432 -2.9352304 0.245424641 KPLTSSSAAPQRPISTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPLTSSSAAPQRPISTQR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 158.44 2.56E-11 1032790000 479170 411700 450580 476040 456150 479620 535340 506810 518750 FALSE TRUE 456520.5837 453652.6981 471239.5387 428187.5548 535702.4156 463010.6391 453664.0508 462431.0296 599195.1006 0.761889714 0.757103484 0.786454259 0.714604566 0.894036709 0.772721003 0.75712243 0.77175369 1 19.1926663 -1.365541664 2.98279596 1.002872979 0.77469807 0.701637004 0.045687651 13594375.9 16614377.86 339482.0353 0.010595676 0.043098121 1.365541664 -0.228174909 KPLVIIAEDVDGEALSTLVLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 314.27 4.30E-67 1764350000 1706900 1309380 1439340 1429200 1556650 1284210 1642010 1546070 1701380 FALSE TRUE 1626218.22 1442807.311 1505335.163 1285534.101 1828129.267 1239737.486 1391491.217 1410687.915 1965221.321 0.827498767 0.734170394 0.7659876 0.65414215 0.930240909 0.63083861 0.708058274 0.717826486 1 20.90626037 -0.973197037 5.075846344 1.000001564 0.745293682 0.468269812 0.085025882 1.37E-06 2.78E-07 0.075120109 0.017705871 0.106366033 0.973197037 -0.254707882 KPLVLCGDLNVAHEEIDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPLVLCGDLNVAHEEIDLR 19 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;; 218.79 2.13E-19 2165877000 4350838 4069633 3969058 4898275 3791654 4159991 4655750 4435616 3399062 FALSE TRUE 4145182.51 4484333.229 4151043.235 4405891.091 4452917.257 4015929.469 3945429.829 4047209.948 3926171.175 1.055782421 1.142164473 1.057275154 1.122185176 1.134162791 1.022861533 1.0049052 1.030828705 1 21.90469164 2.166209041 6.951557677 1.013315235 1.102259779 0.686889042 0.02943719 0.120121253 9.443804026 0.010412506 0.007690231 146.6253431 -2.166209041 0.088944544 KPLVLCGDLNVAHEEIDLRNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPLVLCGDLNVAHEEIDLRNPK 22 2 P27695;G3V3M6;G3V5Q1 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 128.55 9.90E-06 216971000 296750 121665 313320 213363 294550 283730 478510 332900 405930 FALSE TRUE 282723.2156 134062.8018 327686.0319 191915.3459 345919.4267 273904.359 405504.5111 303749.5112 468879.5512 0.602976212 0.285921622 0.698870384 0.409306282 0.737757545 0.584167849 0.86483727 0.647819915 1 18.83885784 1.693824149 0.415402871 0.993522184 0.434015397 0.52074957 0.141450957 0.690367767 0.324860439 0.146867779 0.118312368 49.41105756 -1.693824149 -0.559506787 KPNEGADGQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPNEGADGQWK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 166.7 3.22E-05 2769260000 6763040 6673650 5822410 7745770 4360870 6929950 6976560 7300540 4824130 FALSE TRUE 6443364.502 7353702.522 6089373.258 6967150.484 5121404.347 6689964.094 5912157.639 6661266.015 5572231.442 1.156334687 1.319705148 1.092806952 1.25033401 0.919093975 1.200589775 1.061003603 1.19543958 1 22.40982375 3.203236966 1.766044556 1.09218012 1.227592263 0.198831139 0.106694973 0.467003091 3.007010371 0.031213061 0.042802433 1596.75015 -3.203236966 0.135412143 KPNEGADGQWKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPNEGADGQWKK 12 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 153.39 3.97E-05 1520790000 1964110 1283110 1814660 1648490 1331960 1992350 2519000 2187530 1682680 FALSE TRUE 1871270.413 1413860.368 1897863.956 1482780.653 1564253.402 1923354.42 2134680.285 1995978.276 1943621.42 0.962775154 0.727436091 0.976457625 0.762895818 0.804813831 0.989572558 1.098300452 1.026937785 1 20.89031581 2.099949237 4.541626547 1.050868528 0.843769017 0.558308897 0.081089118 0.138846563 4.998626552 0.02955289 0.021196818 125.877827 -2.099949237 -0.207099511 KPNFEVGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPNFEVGSSR 10 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 ; 91.043 0.016705 842580000 1437830 1251740 1311890 1479110 1250180 1415090 1577760 1447070 1525140 FALSE TRUE 1369866.625 1379293.729 1372041.454 1330427.053 1468210.996 1366085.078 1337043.734 1320356.879 1761650.922 0.777603899 0.782955188 0.778838439 0.755216051 0.833429017 0.775457306 0.758972006 0.749499724 1 20.74849665 -0.979268658 4.432303951 1.000006457 0.776891326 0.902794579 0.023047911 0.013913085 13026244.02 204.3028489 0.005161115 0.104889337 0.979268658 -0.223115131 KPNIFYSGPAS(ph)PARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KPNIFYSGPASPARPR 16 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR 249.2 8.20E-21 24221880000 2933090 2829600 2728940 3089390 2881740 2839350 3465810 3151200 3244600 TRUE FALSE 2794448.649 3117939.457 2854064.598 2778838.648 3384314.544 2741022.598 2937037.031 2875264.222 3747755.997 0.745632493 0.83194836 0.761539599 0.741467334 0.903024249 0.731377016 0.783678829 0.767196217 1 21.8375956 -1.306744863 5.538722295 1.000031147 0.784638782 0.641681397 0.050896553 1.75E-05 2.19E-06 0.044000934 0.010369622 0.049346362 1.306744863 -0.215392366 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(0.998)PVQS(0.336)QS(0.577)PS(0.044)T(0.044)NWS(1)PAVPVKK;KPPAPPS(1)PVQS(0.018)QS(0.936)PS(0.037)T(0.009)NWS(1)PAVPVKK 153.63 5.85E-08 1371530000 1904480 1520870 1703370 1929050 1201160 1936570 2128180 1849040 1447420 TRUE FALSE 1814459.005 1675848.382 1781471.199 1735138.229 1410641.924 1869506.095 1803487.054 1687128.255 1671878.501 1.085281618 1.002374503 1.065550635 1.037837515 0.843746673 1.118206912 1.07871897 1.009121329 1 20.67303858 1.018674867 24.59616872 0.999999899 1.035388273 0.024833513 0.074504288 707.5261468 931859.9228 0.068356703 0.017089176 10.43938385 -1.018674867 0.035388374 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQSQSPS(0.001)T(0.004)NWS(0.995)PAVPVKK 181.32 1.09E-17 675690000 643730 501490 561800 612710 366800 612760 695750 646170 421740 TRUE FALSE 613302.1586 552592.4011 587559.0857 551119.2267 430769.8039 591539.9676 589600.5592 589587.9292 487141.2853 1.258982101 1.134357563 1.206136912 1.131333441 0.884281043 1.214308837 1.210327634 1.210301707 1 18.89398073 4.853989663 1.023254881 1.13036776 1.349500017 0.136646824 0.106856127 5.043131537 3.662340346 0.032357733 1.279269078 71447.93198 -4.853989663 0.219132257 KPPAPPS(ph)PVQSQSPSTNWSPAVPVKK ddPTM_SK-BR-3_Trastuzumab_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 314.68 3.77E-82 2385400000 2331200 1857030 1959010 2287900 1505790 2194700 2604400 2432400 1763540 TRUE FALSE 2221008.796 2046263.468 2048832.546 2057915.945 1768399.299 2118696.989 2207050.947 2219406.161 2037020.776 1.090322112 1.004537358 1.005798552 1.01025771 0.868130222 1.040095915 1.083470023 1.089535358 1 20.95802926 -0.642248265 7.543301176 0.999994341 1.02565843 0.012861644 0.06472601 0 0 0.063553384 0.014979676 0.227903888 0.642248265 0.025664089 KPPLS(ph)PAQTNPVVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 162.42 9.78E-07 1438900000 808770 652340 697050 841650 677560 741830 877030 765160 776380 TRUE FALSE 770541.0449 718814.1876 729010.432 757045.743 795726.2495 716140.2411 743222.9657 698158.534 896777.0452 0.859233685 0.80155284 0.812922717 0.844185015 0.887317816 0.798571111 0.828771175 0.778519631 1 19.77438982 -1.159960912 4.585121985 1.000024348 0.826959945 0.748964244 0.031586926 7.37E-06 1.35E-06 0.028681242 0.006759283 0.069189324 1.159960912 -0.173064403 KPPPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPPPGER 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 77.282 0.061682 77440000 95440 79561 73332 93439 75795 87526 96282 86708 92261 FALSE TRUE 90928.74034 87668.35635 76694.34474 84046.3342 89013.624 84494.95267 81592.41256 79115.38785 106568.3647 0.853243274 0.822648979 0.719672719 0.788661198 0.835272496 0.792870876 0.765634462 0.742390935 1 16.70141971 -0.900950567 7.628918473 1.000000001 0.793961588 0.721805641 0.040898185 6.21E-10 8.14E-11 0.041699126 0.009828578 0.125617294 0.900950567 -0.206038412 KPPPNLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPPPNLFK 8 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 84.498 0.033821 0 693440 624870 576810 725070 523240 716070 756890 760150 591660 FALSE TRUE 660662.4655 688544.9634 603257.309 652184.5861 614492.8903 691272.3163 641412.5293 693587.2362 683411.611 0.966712381 1.007511363 0.882714457 0.954307149 0.899154888 1.011502154 0.938544969 1.014889453 1 19.38239523 1.231537212 24.98831155 1.007444756 0.956204628 0.240572688 0.040664485 273.5975242 973380.0973 0.034551258 0.009376318 17.04265341 -1.231537212 -0.051240128 KPPQHLS(ph)PDTTGPPPPPLETLEAEFGSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPPQHLSPDTTGPPPPPLETLEAEFGSLK 29 1 A0A3B3ISF0;A0A3B3IT29;A0A3B3ISF8 A0A3B3ISF0 1 KPPQHLS(0.639)PDT(0.18)T(0.18)GPPPPPLET(0.001)LEAEFGSLK 98.326 0.00043298 60144000 107360 97396 97790 109550 74650 105230 128980 112670 74873 TRUE FALSE 102285.3056 107320.7631 102273.7682 98537.82587 87668.93636 101585.8587 109301.7321 102804.0175 86483.92244 1.182708909 1.240933113 1.182575505 1.13937739 1.01370213 1.174621315 1.263838746 1.188706694 1 16.40014434 3.453207118 4.78766352 1.149323176 1.212101837 0.130719191 0.080147212 0.447799383 26.20585219 0.023007437 0.032664031 2839.272772 -3.453207118 0.062778661 KPQSSSTEPAR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 142.91 6.00E-05 215903000 369821 328749 330123 431446 359153 381516 441702 412461 408575 FALSE TRUE 352340.2942 362248.8969 345259.4661 388076.2284 421789.1695 368304.0053 374312.2475 376343.7282 471934.7243 0.746586924 0.76758263 0.731583095 0.822309121 0.893744723 0.780413024 0.793144111 0.797448691 1 18.8482278 -5 0.186380011 1.885473854 0.747533199 0.714161113 0.042303634 76.33597241 0.742678635 25.10533208 0.123267181 1.00E-05 5 -1.137940655 KPRPPPALGPEETSASAGLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPRPPPALGPEETSASAGLPK 21 2 Q01105 Q01105 SET Protein SET 0 111.66 0.00013678 713110000 656480 608220 614410 667580 438090 689660 691600 739350 575240 FALSE TRUE 625449.4914 670198.3095 642581.3062 600473.5901 514492.7573 665776.9013 586083.7179 674608.5945 664445.2813 0.941310758 1.008658393 0.967094393 0.903721656 0.774319228 1.002004108 0.882064685 1.015295937 1 19.34179087 -0.435716999 6.327197628 1.000001095 0.937369648 0.070160833 0.072270759 0 0 0.066962051 0.015783107 0.366676435 0.435716999 -0.062631447 KPRPS(ph)EGDEDCLPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPRPSEGDEDCLPASK 16 2 P78346;P78346-2;Q5VU10 P78346 RPP30 Ribonuclease P protein subunit p30 1 KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK 126.45 5.64E-05 421980000 303810 260910 274770 337910 205714 303580 330410 276890 219390 TRUE FALSE 289449.5034 287497.0256 287368.4763 303942.6448 241590.4565 293066.9485 279999.8861 252644.0437 253411.8807 1.142209681 1.134504921 1.133997646 1.199401717 0.953350947 1.156484643 1.104920122 0.996970004 1 17.95112464 1.433357178 0.406768265 0.990008664 1.150265928 0.345196148 0.065332166 1.216607382 0.591717357 0.077105365 0.054564085 27.12421502 -1.433357178 0.160257264 KPS(ph)DEEFASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 1 KPS(1)DEEFASR;KPS(1)DEEFASR;KPS(0.957)DEEFAS(0.043)R;KPS(1)DEEFASR;KPS(1)DEEFASR;KPS(1)DEEFASR 144.88 1.92E-05 2668460000 4257540 3533530 3397110 3910600 2673850 3605320 3711250 3790330 2646720 TRUE FALSE 4056294.522 3893600.724 3552870.854 3517499.058 3140168.593 3480466.864 3145030.651 3458428.611 3057159.82 1.326817949 1.273600647 1.162147569 1.15057742 1.027152252 1.138464153 1.028742636 1.131255418 1 21.54376054 3.594261563 1.000244678 1.066038496 1.334549871 0.803374936 0.04629343 0.205383073 0.404802979 0.01529003 0.039250101 3928.814854 -3.594261563 0.268511375 KPS(ph)FSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSFSK 6 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 KPS(0.981)FS(0.019)K;KPS(1)FSK;KPS(0.956)FS(0.044)K 95.775 0.026315 2832900000 6034150 5257010 5352630 6545220 4154920 6065880 6855310 6362150 4266060 TRUE FALSE 5748927.688 5792705.296 5598053.38 5887282.05 4879536.733 5855817.055 5809406.553 5805046.418 4927618.797 1.1666746 1.17555873 1.136056503 1.194751926 0.990242333 1.18836649 1.178948046 1.17806321 1 22.23245922 -2.396306625 2.051509663 1.18E-05 1.153805051 0.388831709 0.05944035 817245.4932 72438.75128 3826077.617 0.014458689 0.004015072 2.396306625 1.153793262 KPS(ph)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KPSLIGLDPEQGHLNPMSYTQHCITTMAAPSWK 33 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(0.855)LIGLDPEQGHLNPMS(0.03)Y(0.029)T(0.032)QHCIT(0.038)T(0.015)MAAPSWK;KPS(0.998)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK 236.13 4.57E-47 2062470000 2980040 2814610 3017090 3340440 2268490 3213240 3869070 3858140 1371520 TRUE FALSE 2839179.415 3101421.959 3155426.561 3004652.625 2664113.938 3101964.693 3278772.311 3520300.808 1584208.317 1.792175552 1.957710944 1.991800275 1.896627226 1.681668951 1.958053534 2.069659827 2.222119888 1 20.59533063 2.991563712 23.98916586 1.874201662 1.910685733 0 0.331732006 3385.362675 9626594.262 0.088794398 0.101431451 980.7621846 -2.991563712 0.036484071 KPS(ph)LVASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPSLVASK 8 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 KPS(0.993)LVAS(0.007)K 90.793 0.0079288 878950000 1893200 1952100 1277100 2115700 858230 1666600 1687700 1707100 999020 TRUE FALSE 1803712.188 2151021.209 1335656.298 1903025.816 1007905.04 1608885.224 1430210.368 1557617.274 1153942.919 1.563086144 1.864062055 1.157471722 1.649150738 0.873444452 1.394250268 1.239411711 1.34982177 1 20.13814043 3.734720611 24.98827483 1.257813526 1.713574106 0.437070515 0.223639873 250.1624308 1627898.383 0.052336083 0.084576097 5429.009623 -3.734720611 0.45576058 KPS(ph)PAASPATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 KPS(0.997)PAAS(0.003)PATK;KPS(0.998)PAAS(0.002)PATK 95.767 0.0046018 594430000 1111980 957560 946030 1253720 722980 1039270 1203790 1233040 772630 TRUE FALSE 1059418.909 1055136.453 989406.4113 1127693.684 849067.4831 1003279.819 1020129.726 1125068.481 892445.5144 1.187096458 1.182297895 1.108646293 1.263599475 0.951394197 1.124191677 1.143072277 1.260657892 1 19.76740457 -2.230163312 2.387552129 0.46325828 1.151432312 0.229702867 0.087809232 3438638.412 940825.879 10252852.99 0.019803387 0.005886223 2.230163312 0.688174032 KPS(ph)PAQAAETPALELPLPSVPAPAPL ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.882)PAQAAET(0.118)PALELPLPSVPAPAPL;KPS(0.5)PAQAAET(0.5)PALELPLPSVPAPAPL;KPS(0.5)PAQAAET(0.5)PALELPLPSVPAPAPL 122.01 8.52E-05 116807300 277531 238672 256720 287701 216591 276901 325812 308629 264287 TRUE FALSE 264412.6596 262992.9481 268490.8659 258780.7489 254364.4018 267311.8489 276103.3955 281603.8086 305271.2782 0.866156362 0.861505706 0.879515648 0.84770749 0.833240531 0.875653453 0.904452581 0.922470697 1 18.21973233 1.04877003 1.038462745 0.998344058 0.859321016 0.913496584 0.013874512 0.14488838 0.332660998 0.01342389 0.00442711 11.1884527 -1.04877003 -0.139023042 KPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 156.73 3.36E-06 3349190000 4769220 4220590 3923770 4909990 2217016 4751440 4507950 5135760 2311860 TRUE FALSE 4543788.422 4650672.919 4103678.736 4416428.477 2603662.888 4586896.441 3820179.433 4686045.628 2670371.441 1.701556702 1.74158278 1.536744541 1.653862983 0.975018998 1.717699781 1.430579797 1.754829143 1 21.348609 -3.255094421 0.138043641 1.31E-20 1.797757836 0.340006722 0.237124083 87.80532945 1.191474746 28.67958892 1.559867842 0.000555783 3.255094421 1.797757836 KPS(ph)PQPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(1)PQPS(0.58)S(0.42)PR;KPS(1)PQPS(0.574)S(0.427)PR;KPS(0.987)PQPS(0.877)S(0.136)PR 136.99 0.00036087 1321494000 1830680 1578910 1637320 1879280 1368900 1767740 2024270 1748000 1577460 TRUE FALSE 1744147.384 1739802.724 1712392.742 1690371.204 1607635.727 1706522.721 1715430.433 1594935.853 1822084.44 0.95722643 0.954841985 0.939798784 0.92771288 0.882305831 0.936577188 0.941465936 0.875335862 1 20.79715839 3.493846763 2.551459712 0.924215107 0.956130399 0.105345081 0.033912992 0.512357854 6.662587965 0.008848628 0.013960823 3117.789302 -3.493846763 0.031915292 KPS(ph)PQPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(0.978)PQPS(0.188)S(0.833)PR;KPS(1)PQPS(0.179)S(0.821)PR;KPS(1)PQPS(0.135)S(0.865)PR 115.34 0.00082582 1815510000 2278690 1904950 2060790 2298890 1708530 2201910 2469430 2172880 2004760 TRUE FALSE 2170980.84 2099066.571 2155279.26 2067801.21 2006497.091 2125657.305 2092673.099 1982611.108 2315647.942 0.937526297 0.90647051 0.930745655 0.892968733 0.866494882 0.917953574 0.903709524 0.85617985 1 21.1429845 -1.171298098 4.012744116 1.000042281 0.904361796 0.593116556 0.025540394 0.477787097 13257616.04 1143.747582 0.005802002 0.067406519 1.171298098 -0.095680485 KPS(ph)PSES(ph)PEPWKPFPAVSPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.767)PS(0.465)ES(0.767)PEPWKPFPAVSPEPR 63.706 0.016064 156290000 164990 148720 139780 152210 109160 157190 188190 153330 133930 TRUE FALSE 157191.2497 163874.7371 146189.0513 136909.5616 128197.4694 151746.4709 159478.1592 139903.6123 154699.1804 1.016109131 1.059312252 0.944989178 0.885005087 0.828688744 0.980913218 1.030892076 0.904359105 1 17.23910603 3.728613428 23.08149596 0.941801374 1.037710687 0.32499056 0.058896894 276.0843086 640628.5201 0.016838197 0.026480189 5353.199494 -3.728613428 0.095909312 KPS(ph)VSEEVQATPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(0.85)VS(0.15)EEVQATPNK;KPS(0.997)VS(0.003)EEVQATPNK;KPS(0.999)VS(0.001)EEVQATPNK 204.81 1.39E-08 177876000 1237369 964921 1041762 1179735 734612 1194389 1302852 1247555 771130 TRUE FALSE 1178881.02 1063247.547 1089527.818 1061145.796 862728.1002 1153027.009 1104077.999 1138312.47 890712.902 1.323525254 1.193703992 1.223208753 1.191344365 0.968581569 1.294499054 1.239544186 1.277979097 1 19.76460097 -1.785394489 2.684983798 0.942633984 1.216362918 0.324976191 0.096899012 167086293.9 117379656.2 62621871.02 0.02269719 0.016391002 1.785394489 0.273728933 KPSAS(ph)ERLPDEKVELFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPSASERLPDEKVELFSK 18 3 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 KPS(0.229)AS(0.771)ERLPDEKVELFSK 110.89 0.0017718 254300000 216630 154220 206710 236530 158240 232710 283840 290480 160370 TRUE FALSE 206390.3292 169935.1933 216187.858 212753.555 185837.0059 224651.1943 240534.9949 265044.0313 185239.3605 1.114181827 0.917381667 1.167073009 1.148533197 1.003226341 1.21276166 1.298509098 1.430819187 1 17.49903116 2.091428096 4.768585825 1.27190287 1.06180693 0.285515101 0.127326969 0.210423194 8.305217713 0.04612553 0.033187321 123.4320939 -2.091428096 -0.21009594 KPSDGS(ph)PDTKPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 KPSDGS(1)PDTKPSR;KPSDGS(1)PDTKPSR;KPS(0.023)DGS(0.977)PDTKPSR;KPSDGS(1)PDTKPSR;KPSDGS(1)PDTKPSR;KPS(0.002)DGS(0.997)PDTKPSR;KPSDGS(0.999)PDT(0.001)KPSR 164.01 1.97E-05 1796416000 2669563 2498710 2550612 2896340 1493670 3009550 3096890 3152530 1931604 TRUE FALSE 2543378.048 2753331.39 2667560.083 2605194.401 1754165.575 2905328.529 2624402.552 2876477.761 2231147.283 1.139941799 1.234042867 1.195600175 1.167647882 0.786216844 1.30216797 1.176256974 1.289237059 1 21.08935432 -2.406091312 1.934384007 6.91E-05 1.163852954 0.111483073 0.143036841 1859140.316 189226.5514 8112925.519 0.033665803 0.003925624 2.406091312 1.163783893 KPSGS(ph)PDLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.082)GS(0.918)PDLWK;KPS(0.289)GS(0.711)PDLWK;KPS(0.341)GS(0.659)PDLWK;KPS(0.019)GS(0.981)PDLWK 101.72 0.0019217 2666800000 10291600 9567600 8738100 10997700 5972230 10671700 10873000 11311500 6188390 TRUE FALSE 9805136.464 10542549.32 9138750.528 9892190.302 7013785.021 10302136.35 9214124.154 10321005.09 7148053.915 1.371721112 1.474883855 1.278494907 1.383899789 0.981216021 1.44125051 1.289039543 1.443890214 1 22.76911909 -3.757023835 0.26065652 2.83E-31 1.368893447 0.332514692 0.142939205 109.4195046 1.943625536 59.23317317 0.180508215 0.000174975 3.757023835 1.368893447 KPSKYPLCSADAAVS(ph)TTPPGS(ph)PPPPPPLPEPPVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPSKYPLCSADAAVS(0.682)T(0.131)T(0.187)PPGS(1)PPPPPPLPEPPVLK 161.14 8.53E-15 82950000 163430 137920 147770 172030 111730 167340 194890 185330 137160 TRUE FALSE 155704.9878 151974.2048 154545.4007 154737.2176 131215.6766 161544.9738 165155.9511 169101.5227 158430.0723 0.982799449 0.959250997 0.975480213 0.976690948 0.828224558 1.01966105 1.042453296 1.06735748 1 17.27348668 2.022371906 24.99917688 1.038754827 0.950447789 0.465765213 0.046799451 200.9460422 224543.4371 0.016775292 0.012388525 105.2863102 -2.022371906 -0.088307038 KPSPQPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPS(0.002)PQPS(0.499)S(0.499)PR;KPS(0.036)PQPS(0.482)S(0.482)PR 74.611 0.026471 46747000 276950 233141 245420 284320 252650 263060 312930 271100 298220 TRUE FALSE 263859.1224 256898.333 256672.7498 255739.6134 296712.08 253950.1662 265186.7811 247361.0468 344466.4345 0.765993711 0.745786257 0.74513138 0.742422448 0.861367176 0.73722761 0.769847958 0.71809913 1 18.39400389 -1.112483968 4.370152503 1.000031571 0.761287653 0.791395976 0.038604383 14286209037 2901353505 4725814.691 0.008298802 0.077182001 1.112483968 -0.238743918 KPSPQPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPS(0.001)PQPS(0.06)S(0.94)PR;KPSPQPS(0.065)S(0.935)PR;KPSPQPS(0.074)S(0.926)PR 93.649 0.0052932 1273100000 1658440 1412470 1558890 1740450 1441700 1544240 1861410 1700870 1701550 TRUE FALSE 1580048.828 1556402.299 1630366.648 1565496.659 1693132.024 1490762.582 1577417.717 1551932.806 1965417.684 0.803925212 0.791893912 0.829526803 0.796521102 0.861461682 0.758496575 0.802586509 0.789619845 1 20.90640451 -0.966167326 4.402473177 1.000005377 0.803259661 0.840897059 0.026755479 3486.254823 14136073.72 186.1807462 0.005639118 0.108101737 0.966167326 -0.196745716 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.011)PS(0.03)ES(0.959)PEPWKPFPAVSPEPR;KPSPS(0.001)ES(0.999)PEPWKPFPAVSPEPR 194.21 2.30E-18 957340000 988700 899300 888830 1036540 680140 965770 1126420 1086190 758100 TRUE FALSE 941966.1104 990939.6924 929583.7347 932345.0299 798756.2007 932325.1427 954563.9409 991077.4453 875662.2762 1.0757185 1.131645977 1.061577916 1.064731296 0.912173817 1.064708585 1.090105132 1.13180329 1 19.74001504 3.55320172 4.690369631 1.047606361 1.103581311 0.142193291 0.059332936 0.430642594 17.35569642 0.016254109 0.025252576 3574.388216 -3.55320172 0.05597495 KPSQTAS(ph)YER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 KPSQT(0.037)AS(0.963)YER;KPS(0.001)QT(0.031)AS(0.968)YER;KPS(0.001)QT(0.022)AS(0.977)YER;KPS(0.003)QT(0.012)AS(0.985)YER;KPSQT(0.026)AS(0.974)YER;KPS(0.001)QT(0.001)AS(0.998)YER 94.09 0.0044102 340045000 740741 699014 669902 810614 634466 703297 755733 804663 658066 TRUE FALSE 705727.6409 770244.3213 700617.6693 729129.5407 745116.6695 678941.6485 640432.0509 734202.4419 760115.5143 0.928447884 1.013325352 0.921725259 0.959235178 0.980267677 0.893208513 0.84254569 0.965909034 1 19.53585916 2.234830821 24.99850982 0.904139864 0.963038016 0.038631228 0.050178898 133.6612178 895835.8162 0.017252774 0.013234023 171.7239307 -2.234830821 0.058898152 KPSQTASYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 68.069 0.097942 60180000 65835 56202 40748 51669 61851 54021 75089 64060 74511 FALSE TRUE 62723.11002 61929.0477 42616.33611 46475.13396 72637.79482 52150.23922 63632.79395 58450.5668 86065.78533 0.728781011 0.719554785 0.495160021 0.539995467 0.843979922 0.605934623 0.739350646 0.67913825 1 16.3931522 -0.450734967 0.564651762 1.044624605 0.663138798 0.521291274 0.100538112 7.834839874 2.113176825 0.806061659 0.042052576 0.354213438 0.450734967 -0.381485808 KPTDGASSSNCVTDISHLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPTDGASSSNCVTDISHLVR 20 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 232.29 2.65E-26 1468640000 1292380 1099440 1129720 1361680 1188590 1262000 1508730 1394550 1300600 FALSE TRUE 1231291.759 1211474.186 1181518.779 1224801.339 1395879.72 1218296.624 1278545.529 1272435.809 1502290.405 0.81960968 0.806418108 0.786478284 0.815289331 0.929167699 0.810959465 0.851064165 0.846997228 1 20.51873229 -5 0.183059276 1.711042931 0.796286283 0.690370598 0.036316552 74.65450145 0.722505786 19.26683065 0.103430089 1.00E-05 5 -0.914756649 KPTETQELVQQVLSLATQDSDNPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPTETQELVQQVLSLATQDSDNPDLR 26 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 235.68 1.02E-44 156399000 223860 318450 180644 297170 179326 243350 210542 240670 170568 FALSE TRUE 213278.5814 350900.417 188926.7061 267297.907 210600.3976 234922.7285 178419.951 219595.6589 197018.8143 1.082529007 1.781050294 0.958927231 1.356712596 1.068935464 1.192387282 0.905598542 1.114592328 1 17.58797388 2.873718283 0.954392396 1.016330931 1.388432129 0.207069169 0.224588171 0.654969422 1.291236874 0.112578574 0.120495122 747.6843377 -2.873718283 0.372101198 KPTTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KPTTEEK 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 86.136 0.032547 1605710000 2327150 2119410 1695770 2386870 1178090 2101720 2022760 2537140 1633690 FALSE TRUE 2217150.231 2335380.289 1773522.732 2146937.293 1383548.523 2028936.909 1714150.811 2314974.571 1887034.301 1.174939019 1.237592919 0.939846579 1.137730931 0.733186737 1.075198743 0.908383494 1.226779275 1 20.84768922 3.742132747 24.97506616 0.99300199 1.20626598 0.281959062 0.134104471 308.8510617 2159370.464 0.031065225 0.053341096 5522.462135 -3.742132747 0.213263989 KPTTEEKKPAA ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPTTEEKKPAA 11 3 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 75.819 0.0453 220800000 300060 102710 322800 212700 276190 313420 528100 399150 455220 FALSE TRUE 285876.7585 113176.2658 337600.6993 191318.9919 324357.4486 302566.1868 447528.6458 364198.31 525813.1927 0.543685024 0.215240445 0.642054448 0.363853541 0.616868221 0.575425248 0.851117188 0.692638213 1 19.00419081 1.792481153 0.576877578 0.976913989 0.389557006 0.649150521 0.130989574 0.408782832 0.292551967 0.113584969 0.06805228 62.0127731 -1.792481153 -0.587356983 KPVCGVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVCGVCR 8 1 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 84.568 0.033693 0 356870 238380 161260 217670 368920 187410 408250 283240 353160 FALSE TRUE 340001.4623 262671.193 168653.9305 195789.3981 433259.5312 180919.9447 345963.9645 258438.0041 407926.2491 0.83348758 0.64391834 0.413442211 0.479962735 1.062102603 0.443511407 0.848104198 0.633541001 1 18.63794882 -0.383455863 0.488170476 1.054106488 0.659159715 0.209535263 0.201955455 12.15497634 2.742089554 1.347333146 0.095015636 0.413565342 0.383455863 -0.394946773 KPVGEVHSQFSTGHANS(ph)PCTIIIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVGEVHSQFSTGHANSPCTIIIGK 25 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 KPVGEVHSQFS(0.002)T(0.001)GHANS(0.995)PCT(0.002)IIIGK 101.14 0.0026514 225370000 135010 125190 145500 171860 127920 143610 196330 177580 77054 TRUE FALSE 128628.3449 137947.0033 152171.3189 154584.3063 150229.2075 138636.7497 166376.2527 162030.1538 89003.14078 1.445211301 1.549911634 1.709729764 1.736841025 1.687909058 1.557661319 1.869330129 1.820499281 1 16.44156863 3.977834459 2.758708328 1.675915397 1.47148876 0.021987078 0.243996733 0.571259092 8.71573536 0.056910855 0.130828588 9502.425182 -3.977834459 -0.204426637 KPVIAAVNGYAFGGGCELAMMCDIIYAGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVIAAVNGYAFGGGCELAMMCDIIYAGEK 30 1 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 219.24 2.30E-34 25948000 96002 69884 80743 83300 64717 72591 85500 86881 73027 FALSE TRUE 91464.17572 77005.25905 84445.14642 74926.52574 76003.62431 70077.15547 72455.40468 79273.23905 84351.65419 1.084319882 0.912907515 1.001108363 0.888263858 0.901033003 0.830773933 0.858968391 0.939794718 1 16.36412874 5.724881095 0.599570235 0.891088496 1.601067688 0.462853913 0.055378311 7.691168728 0.860015289 0.022899058 4.919914365 530739.1144 -5.724881095 0.709979192 KPVTDCVISVPSFFTDAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPVTDCVISVPSFFTDAER 19 1 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 121.26 5.69E-05 408160000 1262360 1545940 1023730 1545590 937820 1142580 1118300 1332460 985360 FALSE TRUE 1202690.745 1703473.044 1070669.033 1390224.357 1101375.511 1103012.168 947682.796 1215782.739 1138164.596 1.056693161 1.496684266 0.940697889 1.221461607 0.967676832 0.969114811 0.832641253 1.068195885 1 20.11827778 2.997844437 1.20726857 0.93857034 1.248619454 0.287258653 0.154938575 0.427755137 1.316253648 0.06097313 0.07329388 995.0489297 -2.997844437 0.310049113 KPVTDCVISVPSFFTDAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPVTDCVISVPSFFTDAERR 20 2 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 146.64 7.38E-08 173785000 374070 297220 396700 413420 345160 392040 459490 443050 410920 FALSE TRUE 356388.4524 327507.0559 414889.0874 371862.2362 405355.7947 378463.5565 389386.3614 404254.1932 474643.3749 0.750855213 0.690006589 0.874106981 0.783456076 0.854021811 0.797364035 0.820376691 0.851700908 1 18.85648442 -5 0.075999393 1.706307856 0.563689898 0.694072555 0.045469422 142.492807 0.772081889 17.10389249 1.79382619 1.00E-05 5 -1.142617958 KPVTVHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPVTVHSR 8 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 94.692 0.016321 595260000 433610 349960 390000 420590 523610 424500 602390 478120 591000 FALSE TRUE 413114.1146 385621.3219 407881.8858 378311.4941 614927.4182 409799.4586 510484.3418 436253.2781 682649.2616 0.605163058 0.564889385 0.597498465 0.554181357 0.900795552 0.600307481 0.747798863 0.639059181 1 19.380785 -4.999999998 0.12972214 2.197817232 0.495635703 0.579063223 0.097767394 94.66462077 0.775321558 29.38849635 0.676312688 1.00E-05 4.999999998 -1.702181529 KPVTVSPT(ph)TPTS(ph)PTEGEAS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.009)PT(0.727)T(0.264)PT(0.015)S(0.715)PT(0.263)EGEAS(0.006) 175.38 5.91E-12 405450000 664090 519210 613440 662250 547380 590370 737630 583520 587930 TRUE FALSE 632699.7818 572118.0893 641566.8308 595679.3718 642842.8987 569925.3389 625090.996 532423.8954 679103.1817 0.931669588 0.842461212 0.944726587 0.877155914 0.946605635 0.83923232 0.920465421 0.784010309 1 19.37327127 4.753656519 23.45506918 0.891062639 0.931669659 0.031561911 0.062715225 310.2648207 1989822.684 0.012691969 0.092744735 56709.59157 -4.753656519 0.04060702 KPVTVSPTT(ph)PTS(ph)PTEGEAS ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.138)PT(0.071)T(0.79)PT(0.006)S(0.972)PT(0.02)EGEAS(0.003);KPVTVSPT(0.04)T(0.96)PT(0.031)S(0.957)PT(0.012)EGEAS;KPVTVS(0.003)PT(0.258)T(0.718)PT(0.027)S(0.972)PT(0.019)EGEAS(0.002);KPVTVSPT(0.211)T(0.788)PT(0.209)S(0.78)PT(0.011)EGEAS;KPVTVS(0.008)PT(0.106)T(0.887)PT(0.067)S(0.931)PT(0.002)EGEAS 214.54 9.47E-19 1737400000 2127890 1658830 1936880 2148210 1830690 1944420 2334480 1988480 1893210 TRUE FALSE 2027308.857 1827866.663 2025687.864 1932267.849 2149961.756 1877084.248 1978312.2 1814358.15 2186799.338 0.927066705 0.835863918 0.926325442 0.883605467 0.983154567 0.858370595 0.904661057 0.829686619 1 21.06038941 2.276341737 0.007515041 1.80330778 1.71E-06 0.103448073 0.053894006 7921.456039 34.32202861 4065.377048 4167.435857 188.9477555 -2.276341737 -1.803306071 KPVTVSPTTPT(ph)SPTEGEAS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.001)T(0.005)PT(0.604)S(0.379)PT(0.011)EGEAS 203.06 1.01E-15 858330000 761440 701300 746960 811660 689040 787810 889970 800680 792020 TRUE FALSE 725448.2402 772763.2673 781208.8548 730070.3947 809208.3578 760527.9422 754188.7311 730568.2145 914842.4165 0.792976175 0.844695494 0.853927235 0.79802858 0.884533055 0.831321251 0.824391958 0.798572739 1 19.80316373 -1.077002834 4.356141591 1.000015543 0.829161915 0.784827211 0.028210285 0.085770405 15164826.81 524.9701057 0.006113492 0.083752382 1.077002834 -0.170853628 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPTTPT(0.001)S(0.917)PT(0.032)EGEAS(0.05);KPVTVSPTTPTS(0.996)PT(0.003)EGEAS;KPVTVSPTTPT(0.003)S(0.973)PT(0.024)EGEAS;KPVTVSPTTPTS(1)PTEGEAS;KPVTVSPT(0.016)T(0.011)PT(0.141)S(0.777)PT(0.026)EGEAS(0.029);KPVTVSPTTPT(0.002)S(0.998)PTEGEAS;KPVTVSPTTPTS(0.998)PT(0.002)EGEAS;KPVTVSPTTPT(0.025)S(0.815)PT(0.159)EGEAS 272.32 2.53E-39 3790780000 5518340 4876620 5546010 5991790 5233410 5429540 6415860 5541720 5695410 TRUE FALSE 5257499.004 5373553.122 5800300.044 5389483.886 6146115.047 5241513.668 5437002.722 5056457.618 6578625.095 0.799178997 0.816820087 0.881688797 0.819241682 0.934255252 0.796749107 0.826464899 0.768619209 1 22.64935467 -2.406245975 2.388095963 2.588740261 0.829842889 0.565269563 0.046746531 3460609.721 831562.7196 29207473.12 0.010613694 0.003924226 2.406245975 -1.758897372 KPVVDCVVSVPCFYTDAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVVDCVVSVPCFYTDAER 19 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 61.345 0.088657 420840000 828110 771970 666270 843150 716490 728190 842300 792230 717880 FALSE TRUE 788966.8815 850634.6207 696819.1385 758394.9601 841445.6292 702972.5977 713791.6651 722858.1413 829205.164 0.951473671 1.025843371 0.840345874 0.914604724 1.014761685 0.847766787 0.860814303 0.871748239 1 19.66136958 3.747628358 24.99415736 0.900122199 0.988658521 0.223239678 0.062144502 802.0521919 2210757.189 0.015464893 0.027388419 5592.788005 -3.747628358 0.088536323 KPVWVDEEDEDEEMVDMMNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPVWVDEEDEDEEMVDMMNNR 21 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 63.225 0.031944 0 26025 19821 22458 28548 36335 20503 31540 26862 36674 FALSE TRUE 24794.84983 21840.78243 23487.72151 25678.3008 42671.8125 19792.97597 26727.99373 24509.82088 42361.21662 0.585319587 0.5155844 0.554462865 0.606174772 1.007332081 0.467242859 0.630954346 0.578591052 1 15.3704564 -4.999999926 0.285067538 3.911001747 0.58687594 0.396333567 0.146809225 241.4605942 2.29305554 417.4139222 0.154545267 1.00E-05 4.999999926 -3.324125808 KPWTSLS(ph)SESVSCPQGS(ph)LSPATSLMQVSERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.126)S(0.137)LS(0.67)S(0.062)ES(0.007)VS(0.038)CPQGS(0.502)LS(0.42)PAT(0.029)S(0.008)LMQVS(0.002)ERPR 72.366 0.0015783 93798000 28925 26456 28440 27760 28828 27974 33656 28091 33786 TRUE FALSE 27557.77257 29151.89648 29744.00213 24969.51206 33855.59407 27005.25337 28521.15907 25631.20312 39025.36033 0.706150368 0.746998778 0.762171108 0.639827841 0.867528033 0.691992416 0.730836534 0.656783253 1 15.25212433 -1.671389458 3.792489393 1.015449105 0.727632472 0.653087875 0.062902009 0.007417476 0.000642707 0.054981013 0.012487423 0.021311329 1.671389458 -0.287816633 KPYCNAHYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KPYCNAHYPK 10 1 Q14847;Q14847-2;C9J9W2;F6S2S5;O76041-2 Q14847;O76041-2 LASP1;NEBL LIM and SH3 domain protein 1;Nebulette 0 58.223 0.073026 567460000 932470 732670 586310 779920 981910 700230 1177200 934210 1105900 FALSE TRUE 888393.9911 807329.906 613192.8934 701520.9598 1153154.793 675980.8595 997596.5192 852405.6198 1277397.324 0.695471937 0.632011584 0.480033019 0.54917992 0.902737756 0.529186062 0.780960239 0.667298736 1 20.2847759 -0.293090903 0.386781379 1.081385815 0.619598491 0.464012395 0.120356721 5.746694865 0.957089407 0.766624088 0.080869884 0.509224274 0.293090903 -0.461787324 KPYIWEYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KPYIWEYSR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 130.79 0.00056338 1602140000 2417900 1752270 1148270 1494990 2458500 1411240 2542300 2209300 2347800 FALSE TRUE 2303610.659 1930828.305 1200919.315 1344710.765 2887261.622 1362368.405 2154425.442 2015841.98 2711884.833 0.849450032 0.711987575 0.442835662 0.49585836 1.064669704 0.502369565 0.794438398 0.743336131 1 21.37086448 0.400487362 0.827926786 1.002839832 0.691347881 0.215694261 0.185013294 3.411961942 3.28129127 0.18889553 0.058437367 2.514706835 -0.400487362 -0.31149195 KQALYLMFDTSQES(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQALYLMFDTSQESPVK 17 1 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 KQALYLMFDTSQES(1)PVK 233.56 2.52E-20 256560000 382850 379580 369620 393790 240300 409190 428410 505710 271370 TRUE FALSE 364753.4392 418259.6335 386567.4426 354205.481 282208.2439 395019.6477 363048.1862 461427.3515 313452.6736 1.163663513 1.334362948 1.233256166 1.130012633 0.9003217 1.260221019 1.158223288 1.472079807 1 18.25788811 -2.040289523 2.809819036 0.735487448 1.203786648 0.163041934 0.146933147 1954805.707 11781393.66 3634235.764 0.03281826 0.00911403 2.040289523 0.4682992 KQALYLMFDTSQES(ph)PVKSSPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQALYLMFDTSQESPVKSSPVR 22 2 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 KQALYLMFDT(0.003)S(0.014)QES(0.384)PVKS(0.3)S(0.3)PVR 91.175 0.0011821 1550000000 131060 100340 115660 133140 102840 128810 149410 135240 117120 TRUE FALSE 124865.0535 110564.7601 120963.1254 119756.5143 120775.2634 124349.2774 126614.7604 123397.6686 135282.3714 0.922995747 0.817288749 0.894152905 0.8852337 0.892764239 0.919183158 0.935929486 0.912148917 1 17.04561433 1.133306556 0.429907937 1.002331977 0.867947923 0.608667034 0.028572335 0.691864732 0.356640197 0.036191501 0.020476702 13.5927258 -1.133306556 -0.134384054 KQALYLMFDTSQESPVKSS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQALYLMFDTSQESPVKSSPVR 22 2 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 KQALYLMFDTSQES(0.006)PVKS(0.143)S(0.851)PVR 202.03 7.60E-23 1413800000 1821900 1284600 1648100 1753000 1271700 1649500 2056400 1866400 1431700 TRUE FALSE 1735782.398 1415502.2 1723667.015 1576785.11 1493484.077 1592377.401 1742658.412 1702968.122 1653720.724 1.04962245 0.855949968 1.042296314 0.953477263 0.903105377 0.962905875 1.053780355 1.029779755 1 20.65728419 1.769296335 11.55305797 1.031467171 0.956447646 0.221782631 0.058249946 0.482188537 179.0984679 0.025444774 0.014119471 58.78903544 -1.769296335 -0.075019524 KQAS(ph)FLEAEGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQASFLEAEGGAK 13 1 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 KQAS(1)FLEAEGGAK 114.55 0.00044975 166340000 672630 556160 575340 594390 418940 715610 749020 684180 450130 TRUE FALSE 640836.1129 612833.3363 601719.9081 534640.7879 492003.0034 690828.2463 634743.2423 624269.5721 519933.8615 1.232533906 1.178675562 1.157300866 1.028286149 0.946279979 1.328684853 1.220815356 1.200671121 1 18.98796859 2.202794016 24.99986488 1.211920857 1.12799526 0.07630511 0.113562567 409.4161878 286168.3602 0.042474376 0.031370621 159.5122408 -2.202794016 -0.083925597 KQDADSLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQDADSLQR 9 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 129.88 0.0006044 378660000 593230 594280 600350 677270 755000 544200 698310 610330 819120 FALSE TRUE 565189.1936 654837.8076 627876.6413 609189.5329 886671.761 525354.2175 591769.9842 556886.2696 946144.9461 0.597360051 0.69211151 0.663615701 0.643864912 0.937141571 0.555257648 0.625453834 0.588584521 1 19.85170169 -1.580998784 2.83585851 1.021891526 0.661732419 0.504348178 0.105009691 29455235.39 30398086.19 4860251.32 0.025069104 0.026242259 1.580998784 -0.360159107 KQDAETPPPPDPPAPETLLAPPPLPS(ph)TPDPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQDAETPPPPDPPAPETLLAPPPLPSTPDPPRR 33 2 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KQDAETPPPPDPPAPET(0.001)LLAPPPLPS(0.499)T(0.499)PDPPRR;KQDAETPPPPDPPAPET(0.019)LLAPPPLPS(0.49)T(0.49)PDPPRR 91.911 0.0001336 526740000 231656 217439 218539 225570 200198 221827 275399 268996 247279 TRUE FALSE 220706.08 239596.2813 228559.2293 202895.275 235112.4678 214145.0754 233381.8245 245441.2842 285625.7644 0.772710685 0.83884688 0.800205226 0.710353548 0.823148669 0.749740052 0.81708954 0.85931073 1 18.1237666 0.858284062 1.639718379 0.999533537 0.787640725 0.776792674 0.036560979 0.252834497 1.304567287 0.03297383 0.009485213 7.215792932 -0.858284062 -0.211892813 KQDDS(ph)PPRPIIGPALPPGFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQDDSPPRPIIGPALPPGFIK 21 2 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 KQDDS(1)PPRPIIGPALPPGFIK;KQDDS(1)PPRPIIGPALPPGFIK 153.24 2.35E-08 1310900000 1921710 1621310 1652070 1987300 1245740 1902840 2112570 2100810 1263220 TRUE FALSE 1830874.577 1786523.332 1727819.044 1787532.828 1462996.662 1836944.174 1790258.646 1916851.939 1459113.706 1.254785401 1.224389384 1.184156544 1.22508124 1.002661174 1.258945184 1.226949373 1.313709776 1 20.47666088 3.956515225 1.789334919 1.184410873 1.250404212 0.064316994 0.101565594 1.159963056 7.147860254 0.026878096 0.075482281 9047.221532 -3.956515225 0.065993339 KQDEDKDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQDEDKDKR 9 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 44.318 0.087563 83380000 254010 237610 216690 300680 137140 275690 281060 338330 166030 FALSE TRUE 242003.4507 261822.7291 226625.4508 270455.0751 161057.1726 266142.7862 238179.135 308704.0316 191777.0844 1.261899728 1.365245123 1.18171288 1.410257518 0.839814481 1.387771573 1.241958265 1.609702392 1 17.54907082 3.746650043 24.51448232 1.248087552 1.313572413 0.019159934 0.214629825 2543.722106 7708552.693 0.050396922 0.08867651 5580.20357 -3.746650043 0.065484862 KQEAEWK ddPTM_SK-BR-3_Trastuzumab_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 ;; 147.29 0.0034659 1371250000 3397210 2839290 2921660 3442730 2261470 3328560 3886910 3686130 2658910 FALSE TRUE 3236630.616 3128616.879 3055621.001 3096660.24 2655869.652 3213291.133 3293890.492 3363352.916 3071240.183 1.053851351 1.018681931 0.994914373 1.008276805 0.864754788 1.046251983 1.072495245 1.095112305 1 21.55038991 2.019375888 24.9997232 1.062786631 0.995807682 0.25753589 0.05406252 330.0622588 425860.594 0.020312723 0.014999979 104.5624832 -2.019375888 -0.066978949 KQEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQEEEAR 7 1 Q9NQS7-2;Q9NQS7;Q7Z3H0 Q9NQS7-2 INCENP;ANKRD33 Inner centromere protein;Ankyrin repeat domain-containing protein 33 0 ; 95.099 0.021992 327450000 869790 823270 681730 901800 527290 775190 827950 891610 664490 FALSE TRUE 828676.7505 907162.149 712987.9948 811149.3507 619249.2091 748344.9759 701631.0212 813535.9017 767535.7155 1.079658879 1.181915227 0.928931358 1.056822939 0.806801816 0.974996943 0.914134687 1.059932307 1 19.54987436 3.733608162 24.96128219 0.955242959 1.130787056 0.448251117 0.076968187 281.8029249 1420340.449 0.018484557 0.029630351 5415.120963 -3.733608162 0.175544097 KQEELNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQEELNR 7 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 95.741 0.021235 99061000 132370 111470 121240 143090 127490 106660 168660 127340 180540 FALSE TRUE 126113.1324 122828.9197 126798.9739 128706.3213 149724.2156 102966.3375 142927.8193 116189.4345 208537.2211 0.604751189 0.589002381 0.60804001 0.617186326 0.717973582 0.493755201 0.685382775 0.557164011 1 17.66994538 -1.53326815 2.901339864 1.01719791 0.610932377 0.798828652 0.061634064 12157302.22 13274509.03 1643432.61 0.01270887 0.029290842 1.53326815 -0.406265533 KQEELQQLEQQR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 166.6 8.25E-05 1094470000 1392170 1381390 1213650 1603110 1120430 1368770 1479320 1523990 1222700 FALSE TRUE 1326364.883 1522155.212 1269297.053 1441962.337 1315832.637 1321369.152 1253622.564 1390541.356 1412310.071 0.939145666 1.077776929 0.898738229 1.020995578 0.931688206 0.93560839 0.887639754 0.984586448 1 20.42962544 2.71844613 23.55784923 0.935615566 0.990018309 0.066603257 0.056215708 640.7005758 750379.0688 0.016981041 0.016033787 522.9330972 -2.71844613 0.054402743 KQEELVQQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQEELVQQVR 10 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 105.36 0.0041043 183180000 49053 24908 37734 26002 166310 22906 26052 36319 400000 FALSE TRUE 46734.3619 27446.15352 39464.14122 23388.22956 195314.4113 22112.75948 22077.28892 33138.71582 462029.9571 0.101150069 0.059403407 0.085414681 0.050620591 0.422731055 0.047860012 0.047783241 0.071724171 1 18.81762687 -1.291230756 3.78886648 1.001844869 0.105294069 0.860376082 0.112549668 509114057.2 818709550.3 10665935.55 0.025934032 0.051141003 1.291230756 -0.8965508 KQEFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQEFLEK 7 1 Q9H444;P59074 Q9H444 CHMP4B;CHMP4BP1 Charged multivesicular body protein 4b;Putative charged multivesicular body protein 4B-like protein CHMP4BP1 0 ; 146.81 0.0035178 1956400000 3213200 2722500 2767500 3427400 2214620 3004400 3527200 3473200 2609200 FALSE TRUE 3061318.404 2999925.845 2894392.612 3082871.24 2600849.027 2900356.875 2989060.859 3169068.195 3013821.41 1.015759724 0.995389387 0.960372968 1.022911056 0.862973837 0.962351938 0.991784334 1.051511607 1 21.5231625 1.440056335 5.320098052 1.025616944 0.974270089 0.198058109 0.045462427 0.329652071 18.14213332 0.029711111 0.011454339 27.54585995 -1.440056335 -0.051346855 KQEGPATQVDSAVGTLPATS(ph)PQSTSVQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQEGPATQVDSAVGTLPATSPQSTSVQAK 29 1 Q13428-6 Q13428-6 TCOF1 Treacle protein 1 KQEGPATQVDSAVGTLPAT(0.215)S(0.783)PQS(0.002)TSVQAK;KQEGPATQVDSAVGTLPAT(0.084)S(0.914)PQS(0.001)TSVQAK 192.32 1.42E-18 909610000 1176590 1102320 1088200 1242620 815890 1252580 1390260 1395700 1017690 TRUE FALSE 1120974.922 1214647.661 1138095.046 1117709.477 958180.9577 1209202.841 1178150.303 1273485.109 1175508.168 0.953608791 1.033295808 0.968172811 0.95083089 0.81512063 1.028663921 1.002247654 1.083348584 1 20.16485313 KQEKT(ph)PKT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQEKTPKTPK 10 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 2 KQEKT(1)PKT(1)PK 116.84 0.0017711 884420000 1744500 1755900 1862400 2206200 526940 2544100 2436500 1940200 635300 TRUE FALSE 1662040.942 1934828.206 1947792.882 1984428.584 618838.1692 2455997.179 2064767.176 1770305.802 733819.0793 2.264919227 2.636655629 2.65432303 2.704247737 0.843311637 3.346870159 2.813727843 2.412455402 1 19.48506489 0.942787273 21.35236458 0.999999993 2.497086245 0.338144887 0.641039564 4020.323335 1500428.867 0.578394985 0.144598746 8.765713514 -0.942787273 1.497086252 KQELEEICHDLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 KQELEEICHDLEAR 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;; 228.9 9.65E-13 8919851000 11563132 9592150 10255558 11746363 9407606 11117309 12958482 12019632 9530990 FALSE TRUE 11016565.67 10569600.99 10725785.48 10565596.27 11048289.51 10732313.8 10981427.57 10967129.3 11009007.25 1.000686566 0.960086659 0.974273632 0.959722892 1.003568192 0.97486663 0.997494808 0.996196029 1 23.39218104 1.962157834 1.043552025 0.999188431 0.976003217 0.276294954 0.014387528 0.674022962 1.34883339 0.010981535 0.005016724 91.65535292 -1.962157834 -0.023185215 KQELEEILHDLESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;; 154.6 3.94E-06 100125000 451311 351988 392015 451572 360347 415003 483065 459088 348855 FALSE TRUE 429978.4234 387855.9774 409989.2755 406179.1246 423191.4027 400631.3421 409364.5622 418887.8209 402953.6517 1.0670667 0.962532479 1.017460132 1.008004576 1.050223521 0.994236782 1.015909796 1.039543429 1 18.62025438 KQELELVVSELEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQELELVVSELEAR 14 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;;; 176.04 3.67E-06 288422000 686820 549765 581472 666370 550663 619482 732610 687190 630360 FALSE TRUE 654355.3797 605786.6785 608133.0664 599385.2216 646698.4529 598029.183 620836.8892 627016.0006 728113.0094 0.8987003 0.831995406 0.835217966 0.82320356 0.888184175 0.821341159 0.852665563 0.861152036 1 19.47380286 0.595338657 2.660928114 0.999997223 0.850275152 0.768927504 0.025642684 2.293417847 14.52280496 0.023314806 0.00617417 3.938570799 -0.595338657 -0.149722071 KQELLEALTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQELLEALTK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 158.42 0.0072323 0 2591100 2009500 2010200 2258200 1706400 2270500 2733900 2434300 1956400 FALSE TRUE 2468623.838 2214270.335 2102369.658 2031201.446 2003995.62 2191872.016 2316793.343 2221139.787 2259788.52 1.092413656 0.979857325 0.930339118 0.898845811 0.886806709 0.969945637 1.025225734 0.98289719 1 21.10775634 1.834406562 8.356398576 1.004531468 0.965827429 0.106490635 0.056897882 0.938229505 73.89622791 0.028091432 0.017509858 68.297776 -1.834406562 -0.038704039 KQELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQELLR 6 1 O94804;H0YB71 O94804 STK10 Serine/threonine-protein kinase 10 0 99.919 0.061332 534600000 1439800 1184500 1257700 1354000 1307800 1304600 1549500 1512400 1567300 FALSE TRUE 1371743.507 1305201.897 1315366.789 1217893.348 1535879.906 1259421.375 1313095.316 1379966.238 1810348.879 0.757723289 0.720967053 0.726581933 0.672739582 0.848388906 0.695678821 0.725327218 0.762265359 1 20.78783632 0.7565944 3.806892763 0.999995921 0.73463076 0.761801042 0.046151565 1.278358257 19.56526761 0.039761823 0.010191106 5.709451661 -0.7565944 -0.265365161 KQEQANNPFYIKSS(ph)PSPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQEQANNPFYIKSSPSPQKR 20 3 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 KQEQANNPFYIKS(0.212)S(0.783)PS(0.005)PQKR;KQEQANNPFYIKS(0.14)S(0.532)PS(0.328)PQKR 121.58 2.29E-05 1263120000 1403690 859660 1405490 1285550 1008390 1498250 1962650 1753740 1372870 TRUE FALSE 1337340.356 947260.3314 1469933.107 1156324.072 1184252.897 1446365.227 1663211.696 1600173.228 1585767.668 0.843339401 0.597351271 0.926953637 0.729188831 0.74680101 0.91209151 1.048836932 1.009084282 1 20.59674999 2.057371298 3.097183421 1.020446741 0.757209531 0.646821263 0.08480428 0.145109057 2.768174758 0.036901505 0.023313618 114.1225055 -2.057371298 -0.26323721 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR 29 1 P60510;H3BTA2;H3BV22 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 176.21 1.07E-13 28144000 44734 33415 41231 44492 38176 36816 42011 33900 37624 FALSE TRUE 42619.51247 36820.02649 43121.48213 40019.57963 44833.88231 35541.05269 35601.45037 30931.53628 43458.53776 0.98069366 0.847244946 0.992244202 0.920868066 1.031647281 0.817815199 0.819204976 0.711748206 1 15.40735201 2.207807236 24.85016143 0.821658831 0.942469499 0.306743238 0.085200643 207.8169712 167924.4764 0.028870641 0.021324718 161.3642173 -2.207807236 0.120810668 KQEVQAWDGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQEVQAWDGEVR 12 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 138.77 0.00010997 2089390000 3070080 2543970 2811110 3092330 2615630 2942530 3613120 3060770 2913470 FALSE TRUE 2924963.403 2803203.435 2940002.174 2781483.113 3071795.044 2840629.448 3061872.184 2792752.753 3365276.048 0.869160022 0.83297875 0.873628829 0.826524503 0.912791403 0.844099981 0.909842801 0.829873304 1 21.68229342 -5 0.260178455 1.882738597 0.852225864 0.646166853 0.031567343 109.0442117 1.070728339 51.45302032 0.036129493 1.00E-05 5 -1.030512733 KQFS(ph)LENVQEGEILHDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQFSLENVQEGEILHDAK 18 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 KQFS(1)LENVQEGEILHDAK 173.36 4.00E-12 154290000 162800 184450 199720 216040 133600 211650 235880 237180 155860 TRUE FALSE 155104.7666 203245.6647 208877.3596 194323.2488 156899.7977 204320.5074 199892.1738 216411.2618 180029.9728 0.861549687 1.128954593 1.160236578 1.079393868 0.871520421 1.134924948 1.11032719 1.202084622 1 17.45787759 KQFY(ph)S(ph)T(ph)AK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQFYSTAK 8 1 C9JF76;Q5FBZ4;Q3BDU3;Q5FBZ9;E9PC65;P54277-2;P54277-3;P54277 C9JF76 PMS1 PMS1 protein homolog 1 3 KQFY(1)S(1)T(1)AK 45.718 0.093731 301080000 436600 257140 317980 389810 376240 378130 538360 430720 400490 TRUE FALSE 415962.7833 283342.8583 332559.6975 350625.5582 441856.1369 365035.2633 456223.2943 393003.8734 462595.9438 0.899192457 0.612506145 0.718898862 0.757952081 0.955166475 0.789101738 0.986224156 0.849561866 1 18.81939309 2.806368855 5.900620407 0.910359057 0.738530314 0.451773751 0.092206107 0.200143139 13.29142509 0.026936992 0.028508731 640.278406 -2.806368855 -0.171828743 KQGGLGPMNIPLVSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQGGLGPMNIPLVSDPK 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 140.02 1.09E-06 956890000 3477900 3490700 2858100 4001900 2180500 3447100 3499300 3718600 2211500 FALSE TRUE 3313506.56 3846406.299 2989146.712 3599621.409 2560778.51 3327726.063 2965417.516 3392979.67 2554448.125 1.297151634 1.505768021 1.17017319 1.409158156 1.002478181 1.3027182 1.160883827 1.32826329 1 21.28458021 5.326234755 0.03304684 2.98E-06 2.814111033 0.304266806 0.13602684 659.0242907 2.871903697 91.12458115 161.2785083 211950.6512 -5.326234755 2.814108056 KQGGLGPMNIPLVSDPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KQGGLGPMNIPLVSDPKR 18 2 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 257.15 7.27E-31 10925850000 10020610 6733410 9233080 9371440 7916830 9490910 12408820 10730420 10490610 FALSE TRUE 9546955.624 7419552.134 9656425.851 8429405.047 9297522.645 9162237.407 10515626.61 9790807.539 12117440.22 0.78786901 0.612303589 0.796903114 0.695642388 0.767284383 0.756119877 0.867809241 0.807993055 1 23.53058163 1.063765744 0.486012475 1.005096227 0.703469052 0.678630303 0.057514032 0.523612774 0.322371453 0.062484762 0.031574676 11.58152488 -1.063765744 -0.301627175 KQGGS(ph)PDEPDSK ddPTM_SK-BR-3_Trastuzumab_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(0.98)PDEPDS(0.02)K;KQGGS(0.986)PDEPDS(0.014)K;KQGGS(1)PDEPDSK 157.68 7.86E-05 2298881000 5718040 4652471 4855560 6104120 2658898 5856270 6153850 6171670 3070873 TRUE FALSE 5447759.581 5126563.084 5078192.229 5490522.261 3122608.969 5653465.901 5214967.159 5631245.857 3547088.301 1.535839855 1.445287698 1.43165092 1.547895568 0.880330204 1.593832863 1.470210696 1.587568557 1 21.75820381 KQGLEQFINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQGLEQFINK 10 1 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ; 117.98 0.0014212 480130000 1704910 1541250 1284090 1602400 1364580 1523960 1945180 1839330 1530550 FALSE TRUE 1624322.283 1698305.127 1342966.797 1441323.708 1602562.32 1471184.883 1648407.065 1678268.514 1767899.877 0.918786354 0.960634224 0.759639623 0.815274511 0.906477986 0.832165273 0.93240974 0.949300657 1 20.75360514 1.274990222 1.832202194 0.993136627 0.876485766 0.38032159 0.058062026 0.416281628 2.455713651 0.057439702 0.017069035 18.83606679 -1.274990222 -0.116650861 KQGSSKEEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQGSSKEEQER 11 2 P78316 P78316 NOP14 Nucleolar protein 14 0 ; 124.38 0.00019708 70244000 144121 107496 135354 162707 125697 165016 204207 181808 151662 FALSE TRUE 137308.686 118449.9646 141560.1148 146351.3832 147618.517 159301.4545 173051.4716 165887.9277 175180.9684 0.78381052 0.676157723 0.808079303 0.835429696 0.842662981 0.909353659 0.987844018 0.946951768 1 17.41848652 2.538406435 0.754926097 0.994491747 0.729226885 0.861450075 0.036986288 0.209845107 0.245251532 0.027129336 0.021525819 345.4668939 -2.538406435 -0.265264862 KQIS(ph)VR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KQISVR 6 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 1 KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR 119.29 0.012947 53763330000 43697100 31193400 34894800 42616300 35311800 40224600 46455500 39451400 39466900 TRUE FALSE 41631624.68 34372042.92 36494761.1 38332428.56 41470166.74 38831612.02 39367860.26 35996826.27 45587225.28 0.913230064 0.753984098 0.80054798 0.840858998 0.909688328 0.851809071 0.863572196 0.789625296 1 25.44212626 2.991664751 22.22770007 0.871563814 0.820819092 0.144506849 0.065434438 191.3730087 510345.3829 0.017994442 0.020522488 980.9903851 -2.991664751 -0.050744722 KQIT(ph)MEELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 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;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR;KQIT(1)MEELVR 194.55 2.65E-07 10045185000 20019750 14975010 15736620 19928730 17657780 20477740 22831340 17119400 21438990 TRUE FALSE 19073456.09 16500980.54 16458159.59 17925456.2 20737291.24 19768590.73 19347999.76 15620334.58 24763639.07 0.770220243 0.666339083 0.664609896 0.723861955 0.837408879 0.798291021 0.781306806 0.630777025 1 24.56172 2.904993264 5.915580506 0.793718638 0.702023732 0.225233903 0.093416983 0.375564767 19.080707 0.026066542 0.027828939 803.5136588 -2.904993264 -0.091694907 KQITMEELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 127.87 0.00055271 289110000 472890 412460 374990 482470 644130 540080 761910 682440 744240 FALSE TRUE 450537.4269 454490.1429 392183.6624 433971.199 756466.0681 521376.8942 645666.6361 622681.9358 859652.9381 0.524092232 0.528690269 0.456211623 0.504821399 0.879966827 0.606496961 0.751078264 0.724341078 1 19.7133948 1.340904364 0.273550708 1.058692311 0.431718127 0.685771222 0.098955698 1.006873706 0.293290794 0.246504066 0.198467837 21.92322111 -1.340904364 -0.626974184 KQITTS(ph)PITVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQITTSPITVR 11 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 KQIT(0.023)T(0.312)S(0.663)PIT(0.002)VR;KQIT(0.009)T(0.051)S(0.94)PIT(0.001)VR 111.35 0.0010239 577250000 362840 332290 373260 443200 348540 359890 410150 398710 402370 TRUE FALSE 345689.2723 366150.7288 390374.3402 398648.694 409325.2656 347426.9191 347574.0846 363796.8387 464767.4846 0.743789709 0.787814856 0.839934705 0.857737917 0.880709773 0.747528454 0.747845097 0.782750194 1 18.82614961 -2.270984778 2.338851207 1.886420086 0.794017885 0.634817921 0.047918429 2474892.736 680611.3993 11475405.14 0.01259918 0.005358154 2.270984778 -1.0924022 KQLLHSCTVIATNILLVDEIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQLLHSCTVIATNILLVDEIMR 22 1 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 ; 241.68 7.27E-31 108215000 213190 165157 227289 204980 228882 210455 301714 232221 253163 FALSE TRUE 203112.9312 181986.6861 237710.4255 184375.021 268798.9483 203166.8906 255681.9879 211886.4982 292422.2251 0.694587873 0.622342184 0.812901363 0.630509603 0.91921518 0.694772398 0.874358944 0.724590951 1 18.15769344 -5 0.061831451 1.978576006 0.341073149 0.466473732 0.09186413 275.815207 1.242469382 40.10900525 6.343800141 1.00E-05 5 -1.637502856 KQLQDEMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 195.36 5.03E-05 5479540000 7151120 5222440 4923440 6194050 6343490 5815250 7861970 6430280 6961550 FALSE TRUE 6813100.73 5754612.573 5149184.594 5571412.326 7449792.648 5613866.434 6662482.082 5867210.594 8041111.619 0.847283442 0.715648886 0.640357309 0.692865936 0.926463032 0.698145567 0.828552369 0.729651679 1 22.93896353 -4.092880133 0.324388326 2.184249888 0.751666613 0.436805738 0.085499352 167.9564922 2.596927559 134.1642288 0.070762432 8.07E-05 4.092880133 -1.432583275 KQMVIDVLHPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQMVIDVLHPGK 12 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 125.61 0.00019615 2137210000 8511100 7455600 7546900 8878900 6751600 8378600 10397000 8904500 7202700 FALSE TRUE 8108797.17 8215334.116 7892932.83 7986376.103 7929076.902 8088446.981 8810746.696 8124774.774 8319657.93 0.974655117 0.987460565 0.948708817 0.959940441 0.953053235 0.97220908 1.059027519 0.976575581 1 22.98809278 1.907162994 10.64458204 1.017866019 0.967384646 0.462148828 0.02305545 0.431700188 47.57503213 0.009108406 0.00580519 80.75380489 -1.907162994 -0.050481373 KQNGAIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQNGAIGR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 131.06 0.0016373 155355000 208570 191530 224330 208630 197061 216430 247340 226440 259730 FALSE TRUE 198711.3094 211047.1248 234615.7524 187658.116 231428.376 208934.9748 209603.7403 206611.7132 300007.6019 0.662354248 0.70347259 0.782032692 0.625511203 0.771408373 0.696432269 0.69866143 0.688688259 1 18.19463953 -1.05581129 4.353497872 1.000022548 0.702529547 0.805521099 0.045771816 5388641.767 1306854.781 1180.270326 0.009490026 0.087940455 1.05581129 -0.297493001 KQNS(ph)PVAPTAQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQNSPVAPTAQPK 13 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK 144.68 2.54E-05 547920000 1223090 1122550 1035040 1341420 662900 1241280 1223270 1316190 723430 TRUE FALSE 1165276.96 1236939.121 1082497.608 1206577.913 778509.5501 1198294.162 1036637.695 1200937.426 835615.8296 1.394512787 1.480272486 1.295448901 1.443938554 0.931659649 1.434025206 1.240567325 1.437188458 1 19.6724803 -5 0.095364644 0.01161177 1.573209518 0.285708222 0.161334539 234.6924121 1.538176151 47.67591382 2.874112001 1.00E-05 5 1.561597749 KQPDVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQPDVSSR 8 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 0 ; 83.005 0.030151 45511000 62181 64543 77786 87543 70490 82826 85244 82363 85185 FALSE TRUE 59241.82736 71120.00508 81352.56504 78743.01132 82783.43368 79957.71485 72238.46219 75150.85909 98395.05474 0.60208135 0.722800605 0.826795262 0.800274074 0.841337341 0.812619243 0.73416761 0.763766627 1 16.58629819 -1.295882221 0.038201068 1.855110393 1.71E-24 0.629133356 0.061684427 280.6259698 1.861296714 57.34075038 34.7987573 0.050596186 1.295882221 -1.855110393 KQPPKEPSEVPT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPKEPSEVPT(1)PK;KQPPKEPSEVPT(1)PK;KQPPKEPS(0.001)EVPT(0.999)PK 117.26 0.014957 1249540000 3244230 3329890 3169570 3754450 1597710 4111830 3848190 4406840 1922920 TRUE FALSE 3090881.677 3669209.577 3314897.92 3377045.553 1876350.118 3969436.296 3261077.939 4020953.727 2221116.613 1.391589104 1.651966203 1.492446592 1.520426948 0.844777851 1.787135477 1.468215545 1.81032986 1 21.08285371 KQPPVS(ph)PGTALVGSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.881)PGT(0.119)ALVGSQK;KQPPVS(0.978)PGT(0.022)ALVGSQK;KQPPVS(0.995)PGT(0.005)ALVGSQK 191.44 4.26E-10 1592300000 2027400 2774200 1866740 2897350 1370500 2407010 2201160 2443310 1571150 TRUE FALSE 1931568.82 3056894.134 1952331.875 2606102.873 1609514.766 2323654.64 1865332.615 2229360.824 1814795.918 1.064344922 1.684428593 1.075785909 1.436030822 0.886884718 1.280394461 1.027847042 1.228436102 1 20.79137589 2.756056015 24.98121795 1.097827554 1.33552957 0.232038489 0.206072429 1099.065474 1569325.163 0.057635903 0.061002173 570.2378168 -2.756056015 0.237702016 KQPPVS(ph)PGTALVGSQKEPSEVPTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.967)PGT(0.033)ALVGSQKEPSEVPTPK;KQPPVS(0.934)PGT(0.066)ALVGSQKEPSEVPTPK 146.5 1.34E-07 1008910000 846290 652880 846270 932420 481610 997850 1153670 990930 560760 TRUE FALSE 806287.5489 719409.2143 885072.3166 838691.3701 565602.6315 963294.2043 977656.4529 904158.9159 647719.7968 1.24480918 1.110679676 1.366443207 1.294836709 0.873221159 1.487208217 1.509381769 1.395910578 1 19.30501031 KQPPVSPGTALVGSQKEPSEVPT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVSPGTALVGSQKEPS(0.003)EVPT(0.997)PK;KQPPVSPGTALVGSQKEPS(0.068)EVPT(0.932)PK 166.19 6.82E-10 1818590000 2382900 2043920 2242300 2455700 1198080 2680400 2810200 2725800 1243660 TRUE FALSE 2270265.039 2252197.772 2345111.673 2208848.37 1407024.773 2587577.076 2381452.377 2487114.502 1436520.441 1.58039174 1.567814636 1.632494468 1.537637967 0.979467283 1.801281069 1.657792196 1.731346405 1 20.45414709 3.001663104 24.96228201 1.493658431 1.58602892 0.043713595 0.276622672 271.8675969 4080454.147 0.077339884 0.091786059 1003.83678 -3.001663104 0.092370489 KQPSNNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQPSNNLDR 9 1 P17252 P17252 PRKCA Protein kinase C alpha type 0 ; 147.75 0.00014695 69705000 195942 164263 143373 178761 172311 148140 199104 182966 185660 FALSE TRUE 186680.21 181001.5865 149946.7939 160791.6047 202361.9838 143009.8747 168727.028 166944.5271 214451.2046 0.870502035 0.844022242 0.699211712 0.749781774 0.943627173 0.666864404 0.786785173 0.778473254 1 17.71028989 -1.46322115 2.981483034 1.005116468 0.795854285 0.396275006 0.080425581 18455788.99 22693276.53 792550.8029 0.019768903 0.034417463 1.46322115 -0.209262183 KQQDTPGS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KQQDTPGSPDHR 12 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KQQDT(0.028)PGS(0.972)PDHR;KQQDT(0.057)PGS(0.943)PDHR;KQQDT(0.055)PGS(0.945)PDHR;KQQDT(0.038)PGS(0.962)PDHR;KQQDT(0.018)PGS(0.982)PDHR;KQQDT(0.204)PGS(0.796)PDHR;KQQDT(0.093)PGS(0.907)PDHR;KQQDT(0.061)PGS(0.939)PDHR;KQQDT(0.01)PGS(0.99)PDHR 154.88 4.40E-05 4402227000 6545450 5758474 6255630 7048190 5529283 6431590 7276060 6492860 4962922 TRUE FALSE 6236059.55 6345269.047 6542456.823 6339692.551 6493588.205 6208862.426 6165963.413 5924310.758 5732546.597 1.08783408 1.106884862 1.141282799 1.105912084 1.132758033 1.083089744 1.075606331 1.033451828 1 22.45074475 1.298267925 1.230540911 1.000716166 1.111622261 0.853829427 0.016293809 0.153835572 0.457710214 0.015195624 0.004927528 19.87320559 -1.298267925 0.110906095 KQQDTPGSPDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQQDTPGSPDHR 12 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 91.914 0.0052125 67357000 45735 31824 37260 44097 46633 32915 54379 49972 54175 FALSE TRUE 43573.19719 35066.90178 38968.40786 39664.28578 54765.78044 31775.1453 46082.48481 45596.18676 62576.18231 0.696322396 0.560387363 0.622735463 0.633855955 0.875185708 0.507783379 0.73642212 0.728650823 1 15.93332602 -1.904161681 0.272802996 1.357261252 0.62064343 0.543957487 0.097917673 21.18173655 0.90988293 4.936157987 0.115671293 0.012469192 1.904161681 -0.736617823 KQQLAEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQQLAEEEAR 10 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 86.772 0.021374 90284000 89508 81977 84235 97372 88743 87349 106680 93398 103740 FALSE TRUE 85277.13423 90330.5495 88097.25807 87583.98157 104219.7511 84324.08223 90404.00669 85219.57599 119827.4694 0.711665987 0.753838414 0.735200856 0.730917393 0.869748411 0.703712452 0.754451439 0.711185644 1 16.87059915 -1.215972442 3.724057687 1.000294166 0.746515915 0.741209018 0.047103982 2450247.151 1603480.773 5523.705563 0.010092195 0.060817359 1.215972442 -0.253778251 KQQLEVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQQLEVELR 9 1 P15924 P15924 DSP Desmoplakin 0 103.34 0.0055125 167050000 852140 765550 772680 858740 822600 826800 1009900 981910 974310 FALSE TRUE 811861.031 843560.4154 808108.1423 772417.8237 966061.1796 798167.7087 855821.2069 895928.755 1125401.019 0.7213971 0.74956429 0.718062387 0.686348964 0.858415057 0.709229595 0.760458888 0.796097338 1 20.10200774 -5 0.241255554 2.474442191 0.721405944 0.762321385 0.045128993 76.61691537 0.763402204 55.34742704 0.063556474 1.00E-05 5 -1.753036247 KQQMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQQMAR 6 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 79.027 0.071602 165150000 136500 92966 67875 108830 112240 99639 142200 120510 137490 FALSE TRUE 130047.9155 102439.3411 70987.13589 97890.20164 131814.6205 96188.47645 120504.7783 109957.5055 158811.247 0.818883536 0.645038327 0.446990608 0.616393382 0.830008094 0.605677987 0.75879247 0.692378579 1 17.27695356 -0.067892176 0.590636741 1.023540973 0.664712322 0.463963207 0.110773037 4.665521473 1.786357272 0.367560166 0.046047546 0.85527903 0.067892176 -0.358828651 KQQNVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KQQNVDR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;;; 202.17 0.00050507 15880500000 15741520 12481810 11607150 12053360 11877400 10100270 13876270 13550940 16141720 FALSE TRUE 14997449.55 13753720.63 12139349.31 10841733.35 13948814.8 9750495.117 11759190.16 12364347.86 18644895.5 0.804372947 0.737666812 0.651081649 0.581485338 0.74813049 0.522957885 0.6306922 0.663149217 1 24.15227738 -1.7880372 8.521196441 1.00512928 0.671728354 0.619695502 0.081812837 0.008647848 0.000215113 0.08592805 0.020143816 0.016291565 1.7880372 -0.333400926 KQREEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQREEAAR 8 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 101.64 0.0029522 15662000 12364 6465.1 11839 7826.3 21908 11226 17338 13438 34281 FALSE TRUE 11779.57822 7123.90104 12381.82986 7039.585455 25728.74826 10837.24081 14692.76967 12261.29748 39597.1224 0.297485714 0.179909564 0.312695194 0.177780228 0.649763081 0.273687585 0.3710565 0.309651226 1 15.27310797 -4.999999999 0.240141256 4.927750685 0.243499716 0.733304578 0.129187041 82.24886894 0.819961881 157.742479 0.186488446 1.00E-05 4.999999999 -4.684250969 KQS(ph)AGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Trastuzumab_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 2 KQS(1)AGPNS(0.891)PT(0.108)GGGGGGGS(0.001)GGT(0.001)R;KQS(1)AGPNS(0.919)PT(0.081)GGGGGGGSGGTR;KQS(1)AGPNS(0.859)PT(0.141)GGGGGGGSGGTR;KQS(1)AGPNS(0.993)PT(0.006)GGGGGGGS(0.001)GGT(0.001)R 92.801 0.0070625 355022000 485406 386608 433833 506588 370476 476680 574684 493925 433691 TRUE FALSE 462461.8204 426003.7947 453724.6722 455664.8118 435086.8971 460172.4521 487005.401 450674.3085 500945.5853 0.923177754 0.850399339 0.905736442 0.909609397 0.868531253 0.91860766 0.972172258 0.899647231 1 18.93429438 1.231923112 0.526576284 0.996971005 0.885326356 0.503673774 0.030832551 0.640464227 0.460420731 0.031716031 0.016444023 17.05780367 -1.231923112 -0.111644649 KQS(ph)FDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 KQS(1)FDDNDS(0.999)EELEDKDS(0.001)K;KQS(1)FDDNDS(0.999)EELEDKDS(0.001)K;KQS(1)FDDNDS(1)EELEDKDSK 140.09 6.95E-08 389592000 944843 749935 681238 971685 344990 1043203 893777 848936 287570 TRUE FALSE 900182.1439 826354.2291 712473.4361 874009.3777 405156.1468 1007076.619 757414.9033 774598.6633 332164.8869 2.710046063 2.487783212 2.144939048 2.631251563 1.219744057 3.031857545 2.280237717 2.331970337 1 18.34154005 4.064937081 1.019508888 2.170135394 2.764267018 0.104421632 0.602547477 1.904092244 3.066810861 0.182246908 0.972439997 11612.80359 -4.064937081 0.594131624 KQS(ph)LGELIGTLNAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK;KQS(0.974)LGELIGT(0.026)LNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK 269.49 5.85E-26 1.29655E+11 43356913 37778848 39358903 42235179 26727123.7 43452761 48420962 47111742 32026508 TRUE FALSE 41307517.65 41628555.56 41163547.63 37989618.57 31388325.61 41947980.99 41033454.93 42986388.12 36993015.29 1.116630189 1.125308527 1.112738373 1.026940309 0.8484933 1.133943277 1.10922169 1.162013634 1 25.14074956 3.31770053 6.963815491 1.05302835 1.120286509 0.129822514 0.086266641 0.512349578 37.28292118 0.02469738 0.033431115 2078.263115 -3.31770053 0.067258158 KQS(ph)LPATSIPTPASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQSLPATSIPTPASFK 16 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KQS(1)LPATSIPTPASFK;KQS(1)LPATSIPTPASFK 184.62 1.10E-09 1185640000 3084700 2661320 2617630 3233200 1938340 3380100 3613700 3757500 2661670 TRUE FALSE 2938892.344 2932511.534 2737650.925 2908192.593 2276385.882 3263046.289 3062363.695 3428473.38 3074428.19 0.955915105 0.953839658 0.890458568 0.945929589 0.740425777 1.061350628 0.996075857 1.115158062 1 21.55188668 KQS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 77.058 0.044972 411160000 398970 340978 321101 409180 266426 372465 402570 394538 328123 TRUE FALSE 380111.4788 375724.0459 335823.7985 368048.449 312890.61 359566.4437 341150.5528 359990.1611 379006.639 1.002915093 0.991338956 0.886063103 0.971087076 0.825554431 0.948707507 0.900117617 0.949825476 1 18.53186359 3.81635493 7.029138579 0.919841112 0.997972487 0.264509493 0.048600507 0.261948247 20.35609001 0.010894905 0.019742912 6551.713978 -3.81635493 0.078131375 KQS(ph)SEGIPVAQPSVMDDIEVWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.815)S(0.185)EGIPVAQPSVMDDIEVWLR;KQS(0.817)S(0.183)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR;KQS(0.846)S(0.154)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR;KQS(0.854)S(0.146)EGIPVAQPSVMDDIEVWLR 165.37 8.10E-12 576721000 413436 351355 360309 412001 313701 408682 480647 439833 379789 TRUE FALSE 393893.6996 387158.474 376829.524 370585.8767 368410.3551 394529.2399 407315.4725 401318.8908 438684.7384 0.897896975 0.88254375 0.858998481 0.844765829 0.839806637 0.899345715 0.928492461 0.914823005 1 18.74282499 1.114597598 0.903058385 0.995486104 0.870176881 0.776605581 0.022041558 0.289227991 0.519915614 0.022934745 0.008097163 13.01959869 -1.114597598 -0.125309222 KQS(ph)SSEISLAVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.478)S(0.478)S(0.044)EISLAVER;KQS(0.898)S(0.099)S(0.003)EISLAVER;KQS(0.976)S(0.023)S(0.001)EISLAVER;KQS(0.955)S(0.022)S(0.022)EISLAVER 214.81 1.85E-11 1036990000 1024730 1005880 837600 1060870 753550 1017280 1114670 1135690 975150 TRUE FALSE 976293.0437 1108380.316 876004.7885 954229.3321 884968.8814 982051.3385 944606.6192 1036242.963 1126371.282 0.866759531 0.984027499 0.777722943 0.847171219 0.785681325 0.871871784 0.83862811 0.919983472 1 20.10325103 -2.004252525 8.618763701 1.145796792 0.866002574 0.343895933 0.059840174 0.038284792 1.89E-05 0.013231761 0.013893434 0.00990256 2.004252525 -0.279794218 KQS(ph)VFSAPSLSAGASAAEPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQSVFSAPSLSAGASAAEPLDR 22 1 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 KQS(0.999)VFS(0.001)APSLSAGASAAEPLDR;KQS(0.999)VFS(0.001)APSLSAGASAAEPLDR;KQS(1)VFSAPSLSAGASAAEPLDR;KQS(0.999)VFS(0.001)APSLSAGASAAEPLDR 331.7 5.45E-81 1019060000 472681 348809 443693 628510 542430 542330 661240 566020 576730 TRUE FALSE 450338.3059 384353.0337 464036.7629 565330.9807 637029.6203 523548.9761 560355.6935 516456.2881 666166.3429 0.676014798 0.576962553 0.696577916 0.848633358 0.956262091 0.785913281 0.841164822 0.775266258 1 19.34552294 3.336472591 3.468248763 0.85815752 0.627547375 0.673031692 0.072553368 0.125528333 2.951189877 0.019371424 0.02670533 2170.064243 -3.336472591 -0.230610146 KQSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Trastuzumab_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(0.966)PT(0.034)GGGGGGGSGGTR;KQSAGPNS(0.985)PT(0.015)GGGGGGGSGGTR;KQSAGPNS(0.864)PT(0.136)GGGGGGGSGGTR;KQSAGPNS(0.933)PT(0.067)GGGGGGGSGGTR 195.58 1.37E-22 665740000 654950 461012 644980 683850 607790 624800 783030 655910 692020 TRUE FALSE 623991.8115 507989.6469 674552.971 615108.0988 713788.3836 603163.0193 663564.3922 598475.0432 799334.9273 0.780638741 0.635515389 0.843892776 0.769524861 0.892977848 0.754581088 0.830145624 0.748716242 1 19.6084406 -5 0.133836269 1.742906145 0.687709945 0.485576613 0.069366966 111.4193823 0.930458497 22.25598877 0.457054364 1.00E-05 5 -1.0551962 KQSDS(ph)VKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQSDSVKGK 9 2 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 1 KQS(0.001)DS(0.999)VKGK;KQS(0.001)DS(0.999)VKGK 86.911 0.00721 674290000 2041890 1509510 1230750 2680600 1056250 1879420 2568000 1976390 1077630 TRUE FALSE 1945373.906 1663330.785 1287181.105 2411140.995 1240459.666 1814335.214 2176204.435 1803326.814 1244743.357 1.562871492 1.336284123 1.034093573 1.937058738 0.996558575 1.457597829 1.748315766 1.448753917 1 20.24741688 KQSDVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQSDVMR 7 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 72.485 0.054021 73530000 105090 88640 42862 65534 92659 65929 111390 92727 103320 FALSE TRUE 100122.604 97672.51678 44827.2651 58946.39781 108818.7003 63645.8622 94395.40968 84607.3323 119342.3379 0.838952929 0.818423021 0.37561913 0.493926957 0.911819746 0.533304972 0.790963302 0.708946496 1 16.86474642 0.309592252 0.980467777 1.001272137 0.688958028 0.258335735 0.169525973 4.652127295 5.267214593 0.176975635 0.052514086 2.039821909 -0.309592252 -0.312314109 KQSEPFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQSEPFFK 8 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 128.28 0.0018283 1785700000 3581800 3248100 3068400 3676400 2716900 3438700 4221500 3973100 3321400 FALSE TRUE 3412495.412 3579085.083 3209089.175 3306841.287 3190726.5 3319616.957 3577432.642 3625194.301 3836465.749 0.889489347 0.932912039 0.836470175 0.861949905 0.831683823 0.865279967 0.932481319 0.944930709 1 21.87134644 1.2949703 1.607935694 0.992102692 0.87604165 0.675256768 0.030405334 0.248155371 1.167475357 0.0312127 0.00950575 19.72287851 -1.2949703 -0.116061043 KQSFDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQS(0.033)FDDNDS(0.967)EELEDKDSK;KQS(0.038)FDDNDS(0.962)EELEDKDSK;KQSFDDNDS(0.666)EELEDKDS(0.333)K;KQSFDDNDS(1)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQS(0.063)FDDNDS(0.937)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK 222.72 2.89E-19 5082870000 5525060 5025040 4801830 5644380 1945658 6163780 5419740 6472380 1752690 TRUE FALSE 5263901.363 5537097.289 5021998.655 5076996.199 2284980.139 5950326.753 4592859.123 5905624.095 2024488.214 2.600114601 2.735060274 2.480626274 2.507792421 1.128670507 2.939175794 2.268651945 2.917094827 1 20.94912581 2.980189752 24.88934269 2.173881831 2.615077207 0.132111456 0.636848483 1636.919627 2056607.792 0.176490825 0.189650511 955.4099334 -2.980189752 0.441195376 KQSFDDNDSEELEDKDS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQSFDDNDS(0.003)EELEDKDS(0.997)K 107.2 0.00033638 421150000 553540 491500 486260 600700 187280 593560 566490 659050 173830 TRUE FALSE 527375.2612 541584.4088 508555.502 540316.4947 219941.5727 573004.8684 480061.5462 601340.0882 200786.6686 2.626545203 2.697312588 2.532815079 2.690997856 1.095399282 2.85379937 2.390903487 2.994920392 1 17.61530396 KQSHAASAAPQAS(ph)SPPDYTMAWAEYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQSHAASAAPQASSPPDYTMAWAEYYR 27 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 KQS(0.001)HAAS(0.001)AAPQAS(0.561)S(0.436)PPDY(0.002)TMAWAEYYR 96.134 0.0021707 57084000 51153 27208 54575 45515 65316 47388 77791 53324 75941 TRUE FALSE 48735.09907 29980.52613 57077.31773 40939.74573 76707.08972 45746.94168 65922.55422 48654.66787 87717.54243 0.55559125 0.341784839 0.650694447 0.466722443 0.874478327 0.521525574 0.751532161 0.554674316 1 16.42057777 -4.999999999 0.079849306 2.430032087 0.144875102 0.482241331 0.140743453 183.8993285 1.039982062 46.12907714 4.330596012 1.00E-05 4.999999999 -2.285156985 KQSLGELIGTLNAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 177.58 1.20E-06 453980000 2664800 1441810 1830040 2180220 2089330 2146070 3436600 2714100 2948200 FALSE TRUE 2538840.185 1588732.078 1913949.144 1961060.143 2453708.49 2071751.058 2912283.553 2476439.016 3405391.799 0.745535414 0.4665343 0.562034931 0.575869168 0.720536325 0.608373773 0.855197794 0.727211188 1 21.69938936 1.303513363 0.62978427 0.988061087 0.581266294 0.643979938 0.092114839 0.407502052 0.387452289 0.085622764 0.039509972 20.11469088 -1.303513363 -0.406794793 KQTDFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQTDFEHR 8 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 168.8 0.00019783 423312000 1692490 1458030 1411940 1777730 1456830 1529200 1835050 1675320 1455220 FALSE TRUE 1612489.352 1606604.915 1476678.846 1599029.203 1710900.691 1476243.421 1555079.419 1528620.099 1680888.085 0.959307979 0.955807188 0.878511103 0.951300219 1.017855207 0.878252058 0.925153455 0.909412181 1 20.68079224 KQTIDNSQGAYQEAFDISKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQTIDNSQGAYQEAFDISKK 20 2 P27348 P27348 YWHAQ 14-3-3 protein theta 0 211.93 1.25E-22 853000000 517650 403650 480700 523590 332960 561580 599070 599660 386170 FALSE TRUE 493181.7104 444782.3939 502740.5705 470957.7384 391028.1186 542132.3438 507670.8688 547150.5914 446055.2713 1.105651569 0.997146368 1.127081335 1.055828209 0.876636022 1.215392752 1.138134445 1.226643034 1 18.76686296 2.188969009 24.99992939 1.156681645 1.03966564 0.270259117 0.090601943 133.2888278 67192.1281 0.030805159 0.022751153 154.5144174 -2.188969009 -0.117016005 KQVAPEKPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQVAPEKPVKK 11 3 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 85.845 0.0065327 251550000 268700 200960 253540 295700 223160 314390 379990 336770 268330 FALSE TRUE 255999.0835 221438.0525 265165.0598 265975.6742 262079.0333 303502.5955 322015.5465 307280.6335 309941.246 0.825960039 0.714451708 0.855533309 0.85814869 0.845576498 0.979226222 1.03895674 0.991415752 1 18.24163523 2.43121936 1.09417744 1.025710524 0.783957904 0.817299775 0.042870037 0.183235701 0.437828058 0.026256068 0.017761104 269.910239 -2.43121936 -0.241752621 KQVEELFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQVEELFER 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 179.57 0.0001032 539920000 929370 786690 713200 880840 834220 775770 1004140 883310 918550 FALSE TRUE 885440.5219 866854.6054 745900.9255 792296.2897 979707.7039 748904.8904 850940.0007 805962.6937 1060994.043 0.834538637 0.817021181 0.703020842 0.746749046 0.923386621 0.705852116 0.802021469 0.759629801 1 20.01698513 -1.486811525 6.460214802 1.000101686 0.789827454 0.514903052 0.065047185 8.85E-05 7.03E-06 0.05849362 0.013780442 0.032597814 1.486811525 -0.210274233 KQVEIAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KQVEIAQR 8 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;; 158.76 0.00058226 5144900000 7311690 5767427 5514817 6694190 6641710 5941750 7762190 6680830 7554720 FALSE TRUE 6966080.904 6355134.368 5767676.814 6021277.303 7800022.121 5735985.708 6577925.353 6095821.108 8726267.393 0.798288729 0.728276373 0.660955773 0.690017511 0.893855502 0.657324082 0.753807448 0.698559972 1 23.05693325 -1.156479342 3.786640157 1.000161203 0.737222119 0.583198214 0.070349552 4321138687 7066621183 8638646.853 0.015607171 0.069746217 1.156479342 -0.262939084 KQVENER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KQVENER 7 1 Q9H307 Q9H307 PNN Pinin 0 133.86 0.0051797 265540000 154220 147690 116320 169580 118680 136020 133740 144700 111130 FALSE TRUE 146930.3262 162739.7789 121653.3871 152533.4962 139377.7544 131309.5933 113335.5067 132029.3009 128363.4728 1.14464281 1.267804425 0.947725894 1.188293623 1.085805419 1.022951393 0.88292646 1.028558187 1 16.9698752 2.619238236 0.817994843 0.951032485 1.180967454 0.373237572 0.090382353 0.526033311 0.735125409 0.059694651 0.049787035 416.1388241 -2.619238236 0.229934969 KQVENERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KQVENERR 8 2 Q9H307 Q9H307 PNN Pinin 0 ;;;;; 148.94 0.00028861 298372000 504376 343246 437629 411936 522901 418507 659417 524003 668460 FALSE TRUE 480535.1461 378223.1576 457694.7225 370527.4107 614094.7688 404013.9977 558810.8256 478118.5194 772121.3628 0.622357014 0.489849363 0.592775624 0.479882346 0.795334514 0.523251936 0.723734445 0.619227161 1 19.5584681 -2.649515005 0.214681862 1.651384887 0.525257534 0.65088456 0.093360127 25.37126501 0.624771436 7.828875432 0.178345769 0.002241223 2.649515005 -1.126127353 KQVEVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KQVEVFR 7 1 A0A087X1Z3;Q9UL46;H0YLG1;H0YLD2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 155 0.0026311 3540620000 5469520 4713590 4524460 5482330 5224510 5110660 6134500 5500200 6093570 FALSE TRUE 5210986.629 5193910.18 4731910.966 4931235.773 6135662.89 4933676.563 5198569.357 5018573.33 7038529.714 0.740351585 0.737925446 0.672286849 0.700605947 0.871725082 0.700952722 0.738587399 0.713014441 1 22.74684266 -1.145230406 4.118519456 1.000074525 0.735092872 0.710815872 0.053232406 3.248431899 27243048.88 4285.683927 0.011616317 0.071576358 1.145230406 -0.264981653 KQVS(ph)AR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQVSAR 6 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 KQVS(1)AR;KQVS(1)AR 75.213 0.04795 282590000 688370 405890 417440 741470 572550 573390 642540 603980 990330 TRUE FALSE 655832.1143 447250.6525 436580.0369 666936.0269 672402.5387 553533.3605 544508.7219 551092.3093 1143905.318 0.573327271 0.390985727 0.381657494 0.583034291 0.587813106 0.483897882 0.476008559 0.481763919 1 20.12553621 -1.469257655 2.691289927 1.018977579 0.490651369 0.828406093 0.072235901 4460294.784 4636065.4 632591.3093 0.018841659 0.033942384 1.469257655 -0.52832621 KQVVNIPSFIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQVVNIPSFIVR 12 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ; 185.59 0.0001909 0 1896030 1774340 1427690 1793170 1795970 1759330 2198500 1999540 1941240 FALSE TRUE 1806408.419 1955147.263 1493150.999 1612917.145 2109186.599 1698403.961 1863078.447 1824449.677 2242277.585 0.8056132 0.871947022 0.665908186 0.719320906 0.940644733 0.757445899 0.830886621 0.813659152 1 21.09653346 -0.720221487 0.536940304 1.041286257 0.798665166 0.4106592 0.075799012 14.41170064 2.990322628 1.107841861 0.032661211 0.190448919 0.720221487 -0.24262109 KQWLQEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KQWLQEVK 8 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 123.86 0.0021318 1345340000 3961400 2159400 1138730 1220690 3019400 1702520 3608100 2752600 3014800 FALSE TRUE 3774152.473 2379445.315 1190941.897 1097983.922 3545982.404 1643561.306 3057618.078 2511567.752 3482319.787 1.083804103 0.683293167 0.341996706 0.315302439 1.018281669 0.471973112 0.878040578 0.721234093 1 21.73161726 0.781579555 0.960419329 0.995396123 0.682825711 0.133638398 0.258488729 1.97931875 3.47058978 0.24870698 0.082047772 6.04755122 -0.781579555 -0.312570412 KRAPS(ph)PLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRAPSPLPK 9 2 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 KRAPS(1)PLPK 68.536 0.045515 187570000 732840 573490 629270 720130 605400 683280 801770 769430 829260 TRUE FALSE 698200.1055 631929.283 658122.6519 647741.1642 710981.5683 659617.8423 679445.261 702054.6302 957857.4055 0.728918628 0.659732106 0.687077897 0.676239658 0.742262433 0.688638871 0.709338631 0.732942739 1 19.86945138 -0.628427363 0.57021808 1.050924791 0.691732281 0.940433146 0.023653005 2.644604496 0.639736936 0.281349677 0.0093691 0.235273296 0.628427363 -0.359192511 KRAQEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KRAQEEAER 9 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 132.78 0.00016618 101598000 134842 91050 113325 84856 94364 110062 142477 152602 180326 FALSE TRUE 128468.2859 100328.0985 118521.0633 76326.11366 110821.0517 106250.5253 120739.5169 139239.3599 208290.0351 0.616775958 0.48167498 0.569019364 0.366441504 0.532051625 0.510108538 0.579670155 0.66848786 1 17.66823429 0.767354872 1.235684565 0.999553284 0.513664912 0.848781851 0.064415394 0.284209111 0.771627429 0.057979998 0.017686608 5.852681251 -0.767354872 -0.485888373 MAVTFIGNSTAIQELFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MAVTFIGNSTAIQELFKR 18 1 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 ;; 312.5 5.39E-61 512791000 510891 290307 585410 514007 671738 658538 1040585 807087 909914 FALSE TRUE 486742.1949 319889.6134 612251.6275 462338.0398 788888.8945 635732.6639 881824.6466 736414.1836 1051018.816 0.463114635 0.304361452 0.582531557 0.439895112 0.750594454 0.604872771 0.839018896 0.700666984 1 20.00335707 2.196137667 0.385743204 0.989991481 0.322361303 0.756708509 0.100416731 0.515093402 0.18437097 0.101898262 0.119511803 157.0860674 -2.196137667 -0.667630178 down KRDAEDDGEEEDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KRDAEDDGEEEDD 13 2 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;;;;;;; 202.32 3.77E-07 2246815000 4299907 3561616 3788518 4390972 2816191 4412174 4731316 4653285 3026420 FALSE TRUE 4096658.918 3924548.72 3962225.298 3949583.152 3307333.819 4259379.308 4009466.848 4245818.697 3495741.757 1.171899758 1.122665515 1.133443364 1.129826923 0.946103588 1.21844793 1.146957392 1.21456875 1 21.73716718 4.593973992 1.581101852 1.120663363 1.18308819 0.039255595 0.084556962 3.182976493 9.493530476 0.021356145 0.283138384 39262.14224 -4.593973992 0.062424827 KRDFTNEAPPAPLPDASAS(ph)PLSPHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRDFTNEAPPAPLPDASASPLSPHRR 26 3 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 KRDFTNEAPPAPLPDAS(0.005)AS(0.592)PLS(0.403)PHRR 133.79 3.19E-05 497820000 710780 415230 680080 578090 671470 637970 909350 740250 795750 TRUE FALSE 677182.838 457542.4091 711262.3407 519979.2949 788574.1554 615876.9389 770611.9561 675429.7857 919150.8459 0.736748316 0.497788161 0.773825476 0.565717039 0.857937692 0.670049907 0.838395525 0.734841064 1 19.80994212 0.815984498 0.292733316 1.0526577 0.600848381 0.478981579 0.103845797 1.841869078 0.436005285 0.288104852 0.14192016 6.546128078 -0.815984498 -0.451809319 KRDFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRDFTNEAPPAPLPDASASPLSPHRR 26 3 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 KRDFTNEAPPAPLPDASAS(0.065)PLS(0.934)PHRR 149.58 1.08E-07 463870000 517640 292060 503450 439620 539570 468080 701690 536760 634400 TRUE FALSE 493172.1831 321821.246 526533.6805 395428.5624 633670.8372 451870.2722 594634.3031 489758.4489 732779.5119 0.673015791 0.439178826 0.718543125 0.5396283 0.864749665 0.616652438 0.811477796 0.668357181 1 19.48301964 -0.282688562 0.162344234 1.271704075 0.464118079 0.491288906 0.114569606 11.61416324 0.569263598 2.169622738 0.622338551 0.5215686 0.282688562 -0.807585997 KRDS(ph)DAGSSTPTTSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.998)DAGS(0.002)STPTTSTR;KRDS(1)DAGSSTPTTSTR;KRDS(0.999)DAGS(0.001)STPTTSTR 175.02 2.89E-09 229203000 170855 154172 171220 185822 134179 185285 203865 194329 156438 TRUE FALSE 162779.0228 169882.3021 179070.6064 167142.8195 157579.7751 178868.534 172761.65 177312.5226 180697.6061 0.900836631 0.940146944 0.990996009 0.924986352 0.872063435 0.989877718 0.956081565 0.981266584 1 17.46321787 2.188665445 24.99999699 0.976201509 0.928417064 0.425710208 0.031947518 125.557967 62910.015 0.011981114 0.008848655 154.4064526 -2.188665445 -0.047784445 KRDS(ph)QGTYSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KRDSQGTYSSR 11 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KRDS(1)QGTYSSR;KRDS(0.984)QGT(0.015)YS(0.001)SR;KRDS(1)QGTYSSR;KRDS(0.989)QGT(0.011)YSSR;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR;KRDS(0.997)QGT(0.003)YSSR;KRDS(0.925)QGT(0.062)YS(0.013)SR;KRDS(0.86)QGT(0.064)YS(0.021)S(0.054)R;KRDS(1)QGTYSSR 207.52 1.18E-08 4920526000 2609147 2309603 2357662 2601266 2131491 2511987 2997987 2691513 2369586 TRUE FALSE 2485817.792 2544954.172 2465763.135 2339781.8 2503222.356 2424996.26 2540589.021 2455829.853 2737049.295 0.908210823 0.92981671 0.900883714 0.854855557 0.914569701 0.885989253 0.928221872 0.897254521 1 21.38418999 -0.723272002 0.759643518 1.010250923 0.904240819 0.665689758 0.021645358 16.94387816 5.86039104 0.480995497 0.007351772 0.18911588 0.723272002 -0.106010104 KRDS(ph)SLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.5)S(0.5)LR;KRDS(0.5)S(0.5)LR 96.89 0.0097654 105862000 150096 123067 129749 148346 117250 147601 182602 147353 161268 TRUE FALSE 143001.2595 135607.6672 135698.12 133433.9782 137698.3629 142489.5404 154742.7112 134449.9902 186276.6178 0.767682285 0.727990817 0.7284764 0.716321672 0.739214425 0.764935192 0.830714628 0.72177599 1 17.50708707 -2.109581033 0.309955371 1.287916193 0.732779538 0.845903977 0.033554983 13.66238359 0.608866465 2.802967055 0.032659384 0.007769963 2.109581033 -0.555136655 KREAEEVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KREAEEVYR 9 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 90.108 0.0065543 56353000 75871 47073 62547 58697 62724 66131 95573 78588 90601 FALSE TRUE 72284.72819 51869.79222 65414.84182 52796.66604 73663.04574 63840.86689 80991.58353 71706.4181 104650.9404 0.690722204 0.495645735 0.625076484 0.504502548 0.703892822 0.610036247 0.773921221 0.685196118 1 16.67522575 0.701473842 0.503118848 1.013718501 0.578005653 0.728420846 0.074619798 0.680850234 0.365869835 0.092798263 0.036159806 5.028909756 -0.701473842 -0.435712849 KREEGS(ph)DIEDEDMEELLNDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KREEGSDIEDEDMEELLNDTR 21 2 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR 242.67 2.42E-30 412180000 617798 543259 529252 609260 392484 609693 657726 642909 444845 TRUE FALSE 588595.9129 598617.7097 553518.7277 548016.0273 460933.0853 588579.1785 557377.8187 586612.4797 513829.2906 1.145508681 1.165012818 1.077242457 1.066533258 0.897054905 1.145476113 1.084752911 1.141648579 1 18.97092961 3.661034158 4.160743303 1.061469029 1.155476425 0.243759218 0.070817946 0.302589668 9.875192115 0.018666267 0.030203955 4581.779217 -3.661034158 0.094007396 KREELSNVLAAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KREELSNVLAAMR 13 2 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 174.39 1.13E-05 1414500000 4237300 3164100 2267700 2755000 3769100 2894100 4860400 3792300 4094200 FALSE TRUE 4037011.227 3486525.387 2371676.288 2478062.166 4426429.847 2793876.591 4118856.713 3460226.108 4729107.626 0.853651798 0.737248053 0.501506093 0.524002066 0.935996851 0.590783042 0.870958548 0.731686902 1 22.17313654 0.62656903 0.701469327 1.000394625 0.703577857 0.290496581 0.143480403 1.789769955 1.611221655 0.149064108 0.052448296 4.232227742 -0.62656903 -0.296816768 KREENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KREENLK 7 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 63.486 0.044513 153520000 85465 78544 76007 90888 67307 90453 100290 110670 99996 FALSE TRUE 81425.23883 86547.7229 79491.99613 81751.76556 79045.31949 87320.58993 84988.91855 100979.1481 115502.869 0.704962912 0.749312322 0.688225296 0.707789913 0.684358061 0.756003645 0.735816515 0.874256622 1 16.81756916 1.044590487 1.791521746 1.000746846 0.715058421 0.946055656 0.022912603 0.068007536 0.444512096 0.02051858 0.005884992 11.08129425 -1.044590487 -0.285688425 KREGELTVAQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KREGELTVAQGR 12 2 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 137.16 5.46E-05 126437000 175490 138453 178373 183277 232580 172977 229490 200153 291460 FALSE TRUE 167194.9355 152561.5181 186551.5785 164853.6478 273141.8784 166986.7631 194477.0856 182626.5422 336658.1282 0.496631216 0.453164517 0.554127653 0.489676719 0.811333087 0.496012866 0.57766936 0.542468834 1 18.36092477 -5 0.216433759 3.248968351 0.484524737 0.675973168 0.097816079 84.9842 0.849087906 83.26013683 0.183553581 1.00E-05 5 -2.764443613 KREHS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(1)PSK;KREHS(0.997)PS(0.003)K;KREHS(0.999)PS(0.001)K;KREHS(0.999)PS(0.001)K 89.548 0.007215 253361000 437623 503887 354706 510342 237082 448287 382242 510388 233903 TRUE FALSE 416937.4281 555233.6582 370969.621 459041.4526 278429.0257 432762.7088 323923.9625 465695.721 270175.4826 1.54320971 2.055085283 1.373069152 1.699049255 1.030548823 1.601783791 1.198939146 1.723678686 1 18.04353724 3.351957596 1.784799576 1.351312378 1.782705074 0.246795272 0.286201351 0.395383161 2.57952159 0.080028367 0.122906473 2248.83502 -3.351957596 0.431392696 KREHS(ph)PSKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KREHSPSKEK 10 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.999)PS(0.001)KEK;KREHS(0.992)PS(0.008)KEK;KREHS(0.999)PS(0.001)KEK;KREHS(1)PSKEK 99.844 0.003153 1760010000 2741920 1835860 2408650 2560870 1363630 2910540 3390740 3108970 1394430 TRUE FALSE 2612314.876 2022936.221 2519088.985 2303446.482 1601446.64 2809747.27 2873420.338 2836732.105 1610671.083 1.621879789 1.255958614 1.563999635 1.430115998 0.99427292 1.744457512 1.783989524 1.761211296 1 20.61923048 KREPEDEGEDDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 KREPEDEGEDDD 12 2 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;;;;;;; 262 8.59E-21 22808480000 10834230 8442097 9222780 10613360 6901011 10147700 11117440 10867411 7424666 FALSE TRUE 10322117.42 9302356.282 9645653.586 9546484.889 8104545.133 9796282.605 9421270.342 9915802.881 8576045.283 1.203598754 1.084690667 1.124720459 1.113157006 0.945021262 1.142284384 1.098556506 1.15622091 1 23.03188109 5.031605824 1.007763273 1.084649433 1.334921385 0.254973775 0.064725646 4.277501003 2.364301036 0.018321986 1.327508754 107548.8633 -5.031605824 0.250271952 KRES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.718)ES(0.842)ES(0.439)DETPPAAPQLIK;KRES(0.999)ES(0.984)ES(0.016)DETPPAAPQLIK;KRES(0.826)ES(0.932)ES(0.24)DET(0.002)PPAAPQLIK;KRES(0.484)ES(0.774)ES(0.351)DET(0.391)PPAAPQLIK 179.44 2.86E-16 791560000 1543190 1298670 1384400 1783090 788010 1666540 1654750 1368170 894390 TRUE FALSE 1470246.467 1431005.949 1447876.109 1603850.406 925438.6945 1608827.302 1402287.496 1248365.782 1033087.433 1.423157827 1.385174094 1.401503941 1.552482737 0.895799005 1.557300234 1.357375427 1.208383474 1 19.97853093 -3.97230776 0.18130778 1.58E-09 1.444589444 0.296225536 0.18273159 108.7412503 1.470377487 40.10470083 0.526465663 0.000106584 3.97230776 1.444589443 KRET(ph)DDEGEDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 190.86 3.35E-06 62832869600 2949341 2506913 2551513 2978089 1654594 2923719 3135836 2910362 2045844 TRUE FALSE 2809931.496 2762370.285 2668502.395 2678725.836 1943154.67 2822469.878 2657406.625 2655515.274 2363103.039 1.189085474 1.168958881 1.12923658 1.133562859 0.822289438 1.194391371 1.124541157 1.123740789 1 21.17225111 3.286116119 2.686268126 1.072031612 1.174220476 0.185070516 0.10063642 0.481100191 7.082113858 0.029427543 0.040332641 1932.484945 -3.286116119 0.102188864 KREVS(ph)PPGAR ddPTM_SK-BR-3_Trastuzumab_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 52.495 0.078132 46000000 48546 36559 47963 57629 51230 44332 65853 53529 76218 TRUE FALSE 46251.32679 40284.40366 50162.15099 51836.02343 60164.49578 42796.77172 55805.91538 48841.71698 88037.49817 0.525359395 0.457582331 0.56978165 0.588794826 0.683396246 0.486119808 0.63388802 0.554783109 1 16.42583053 -5 0.223349396 3.297809387 0.501929605 0.821409654 0.064384582 59.65299362 0.596764818 61.73704871 0.113395827 1.00E-05 5 -2.795879781 KRFDTEEEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KRFDTEEEFK 10 2 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 219.03 3.66E-09 482310000 1042950 941400 873910 1104150 594924 1105430 1108090 1142740 685402 FALSE TRUE 993651.8204 1037329.73 913979.6379 993158.7443 698678.5572 1067148.682 939030.519 1042675.628 791690.6416 1.255101132 1.310271558 1.154465633 1.254478318 0.882514609 1.347936461 1.186107893 1.317024066 1 19.59457727 -2.083130137 2.60095297 0.64156779 1.217870804 0.206056137 0.131447255 20185965.69 3976347.532 43153829.12 0.029424943 0.008257905 2.083130137 0.576303014 KRFPQHTIMAGNVVTGEMVEELILSGADIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRFPQHTIMAGNVVTGEMVEELILSGADIIK 31 2 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YNH0;H0YLB8 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 150.26 6.75E-09 49722000 42748 44796 44875 42597 35675 47684 58056 51233 39378 FALSE TRUE 40727.38676 49360.76333 46932.56314 38315.06863 41896.7087 46032.69112 49198.49093 46746.76692 45484.53913 0.895411662 1.085220699 1.031835521 0.842375659 0.921119781 1.012051392 1.08165306 1.0277507 1 15.47308861 2.010631147 12.70924069 1.045872743 0.965897947 0.214581793 0.070340281 1.02306516 1214.259671 0.027663342 0.020200192 102.4781193 -2.010631147 -0.079974796 KRGHT(ph)ASESDEQQWPEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KRGHTASESDEQQWPEEK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KRGHT(0.464)AS(0.464)ES(0.072)DEQQWPEEK;KRGHT(0.496)AS(0.496)ES(0.007)DEQQWPEEK;KRGHT(0.333)AS(0.333)ES(0.333)DEQQWPEEK 177.93 4.35E-12 433903000 434095 308061 419404 354238 257697 448431 531391 523650 314688 TRUE FALSE 413576.1896 339452.7661 438634.0882 318629.3232 302639.2752 432901.722 450317.5433 477796.43 363488.2078 1.137798093 0.933875594 1.206735401 0.876587786 0.832597231 1.190964969 1.238877998 1.314475737 1 18.47154904 2.088716102 10.69884684 1.211961173 1.005698687 0.31550414 0.135738563 0.415422622 46.96939996 0.047928241 0.035392581 122.6637118 -2.088716102 -0.206262487 KRGHTAS(ph)ESDEQQWPEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRGHTASESDEQQWPEEKR 19 3 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KRGHT(0.036)AS(0.963)ES(0.002)DEQQWPEEKR 144.22 9.81E-08 61212000 40497 20516 48164 31899 34889 39412 73355 55133 50747 TRUE FALSE 38582.78707 22606.60372 50372.36704 28692.45192 40973.63055 38047.15256 62163.34749 50305.26224 58616.58558 0.658223039 0.385669064 0.859353484 0.489493744 0.699010871 0.649085104 1.060507822 0.858208675 1 15.83902131 1.822000074 5.285096427 0.97058252 0.602130908 0.601260078 0.133701099 0.135922194 5.922622005 0.058518883 0.033644147 66.37431838 -1.822000074 -0.368451612 KRHNS(ph)ISEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRHNSISEAK 10 2 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 KRHNS(0.632)IS(0.368)EAK;KRHNS(0.994)IS(0.006)EAK 170.95 2.18E-06 328710000 472630 353600 436450 434080 335690 545800 677490 578230 380410 TRUE FALSE 450289.7166 389632.242 456461.6642 390445.4537 394234.2297 526898.8091 574126.4575 527597.1158 439402.0399 1.024778393 0.886732893 1.038824636 0.888583616 0.897206189 1.199126907 1.306608539 1.200716128 1 18.74518204 2.229615956 24.02576728 1.213245818 0.947524587 0.58681619 0.093423873 66.33390314 178173.7405 0.031720581 0.02379451 169.674257 -2.229615956 -0.265721231 KRHNSIS(ph)EAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRHNSISEAK 10 2 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 KRHNS(0.319)IS(0.681)EAK 147.26 1.42E-05 238510000 201000 139950 188980 181620 126000 215640 286150 249220 168450 TRUE FALSE 191499.1283 154211.0641 197644.9199 163363.2125 147974.3601 208172.3327 242492.562 227396.9756 194572.3657 0.984205171 0.79256406 1.015791319 0.839601307 0.76051067 1.069896704 1.246284698 1.168701294 1 17.5699473 2.053008696 6.004285012 1.164288346 0.881881402 0.603328756 0.098234483 0.109701474 8.607231326 0.034861677 0.02531086 112.9818536 -2.053008696 -0.282406944 KRKPEEES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRKPEEESPR 10 3 P49321;P49321-3;P49321-4;P49321-2;Q5T624 P49321 NASP Nuclear autoantigenic sperm protein 1 KRKPEEES(1)PR 83.204 0.087106 70523000 169390 216460 150790 205000 85766 194060 162610 197150 99600 TRUE FALSE 161383.2704 238517.5201 157703.8707 184393.0105 100723.5632 187339.6535 137800.858 179886.5008 115045.4593 1.40277827 2.073245841 1.370796132 1.602783905 0.875510984 1.628396763 1.197794844 1.563612349 1 16.81184452 3.34793037 2.211689513 1.301067373 1.72716237 0.237208932 0.298128786 0.360228504 3.590214841 0.081143754 0.118774513 2228.077898 -3.34793037 0.426094998 KRKPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRKPSPEPEGEVGPPK 16 3 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KRKPS(1)PEPEGEVGPPK 124.31 0.00045968 895710000 1165600 690260 1067000 993060 677140 1201700 1487700 1439000 861770 TRUE FALSE 1110504.398 760598.2788 1115923.005 893235.7221 795233.0016 1160084.828 1260724.042 1312993.531 995408.8903 1.115626361 0.764106375 1.121069961 0.89735558 0.798900843 1.16543547 1.26653886 1.319049432 1 19.92492975 2.099458124 6.384910639 1.222502049 0.938642717 0.432435218 0.140392268 0.169589391 9.313166472 0.049037534 0.036026388 125.735561 -2.099458124 -0.283859331 KRKS(ph)ELEFETLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRKSELEFETLK 12 3 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 KRKS(1)ELEFETLK;KRKS(1)ELEFETLK 144.73 0.0003324 1103000000 1068120 1084560 869930 1268060 532720 1195630 1098840 1344180 590890 TRUE FALSE 1017632.084 1195077.897 909817.151 1140592.2 625626.1993 1154225.033 931191.7764 1226476.473 682522.2034 1.490987516 1.750972922 1.333022056 1.671142996 0.916638603 1.691117194 1.36433917 1.796976666 1 19.38051645 3.730435713 24.32246781 1.417500592 1.620980222 0.091146844 0.289084971 907.7597026 2717444.223 0.067810681 0.107139292 5375.708532 -3.730435713 0.20347963 KRLEEALMADMLAHVEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRLEEALMADMLAHVEELAR 20 2 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 164.65 1.07E-11 28870000 188370 114920 183920 166300 199940 170710 257150 204180 217780 FALSE TRUE 179466.1234 126630.4787 192352.9139 149583.2081 234809.4727 164798.2699 217917.0446 186300.9168 251552.2101 0.71343489 0.503396407 0.764663979 0.594640802 0.933442296 0.65512551 0.866289525 0.740605366 1 17.94049834 1.401282878 0.22742652 1.064896864 0.543657594 0.434498652 0.113553055 1.864135166 0.444042039 0.394350047 0.345990213 25.1931735 -1.401282878 -0.52123927 VLKGDVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLKGDVEK 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 67.334 0.054141 856510000 959660 822900 891870 1079100 1244000 1448200 2066100 1607800 1739600 FALSE TRUE 914298.7737 906754.4456 932763.1217 970626.8178 1460953.206 1398048.471 1750878.498 1467012.509 2009368.283 0.455018018 0.451263441 0.464207149 0.483050731 0.7270709 0.695765173 0.871357686 0.730086426 1 20.93831058 2.248452077 0.623184854 0.940526834 0.418380632 0.873870033 0.067568024 0.228530816 0.1760035 0.054670508 0.039124108 177.1952504 -2.248452077 -0.522146202 down KRLS(ph)QSDEDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KRLSQSDEDVIR 12 2 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 KRLS(0.942)QS(0.058)DEDVIR;KRLS(0.761)QS(0.239)DEDVIR;KRLS(0.999)QS(0.001)DEDVIR 122.16 0.00028626 812890000 1028140 884630 963790 1122090 877490 1057730 1250300 1161410 1123350 TRUE FALSE 979541.8598 974774.8027 1007980.725 1009295.381 1030523.978 1021100.545 1059543.772 1059710.783 1297553.381 0.754914499 0.751240617 0.776831797 0.777844978 0.794205459 0.786942996 0.816570468 0.816699181 1 20.30736246 -5 0.177120731 1.905952536 0.73246742 0.989496157 0.007292457 10.91306113 0.104492508 3.457743842 0.021782276 1.00E-05 5 -1.173485116 KRLS(ph)VER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRLSVER 7 2 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 1 KRLS(1)VER 60.398 0.076982 1344600000 2180500 2146200 2082900 2519300 1955100 2272000 2696300 2359700 2572700 TRUE FALSE 2077432.086 2364900.22 2178403.025 2266055.178 2296068.821 2193320.07 2284929.914 2153072.158 2971661.176 0.699081074 0.795817585 0.733059018 0.76255503 0.772654985 0.738078785 0.768906608 0.724534875 1 21.5028382 -1.224180775 4.279785187 1.000118669 0.751870347 0.89072204 0.027579715 3.51365514 14173188.26 3004.576665 0.005815665 0.059678682 1.224180775 -0.248248322 KRNDS(ph)EEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRNDSEEEER 10 2 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 KRNDS(1)EEEER 98.531 0.0041847 29460000 35806 41775 28931 45017 23119 37088 31072 40208 21541 TRUE FALSE 34113.52134 46031.91999 30257.51497 40491.80563 27150.94628 35803.63326 26331.39572 36687.17436 24881.46826 1.37104133 1.850048378 1.216066297 1.627388111 1.091211579 1.438967865 1.058273388 1.474477871 1 14.602784 2.950042266 1.16103474 1.210655566 1.579703328 0.253694026 0.230964377 0.528725354 1.5081318 0.090837816 0.104323441 891.3376789 -2.950042266 0.369047762 KRNDS(ph)EEEERER ddPTM_SK-BR-3_Trastuzumab_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 167.71 0.00026794 407010000 317781 373634 279029 363294 237339 337592 311800 317729 216099 TRUE FALSE 302760.1219 411707.7294 291822.7556 326774.9969 278730.8465 325901.1044 264229.1834 289906.9644 249610.5292 1.212930091 1.649400491 1.169112363 1.309139474 1.116663016 1.30563845 1.058565855 1.161437241 1 17.92931927 2.526701314 0.54608671 1.043492909 1.423812217 0.368138646 0.142902827 0.83244226 0.51486945 0.119782111 0.119335273 336.2802132 -2.526701314 0.380319308 KRNEDEDSPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;; 184.03 2.86E-06 3125763000 4111227 4418679 3614276 5024418 2107712 4416140 4106043 4447095 2197370 FALSE TRUE 3916897.447 4868947.414 3779994.13 4519353.957 2475296.305 4263207.964 3479590.728 4057683.786 2538126.917 1.543223635 1.918323068 1.489284915 1.780586277 0.975245284 1.679666976 1.370928579 1.598692232 1 21.27533278 -2.359287733 0.109234544 7.81E-12 1.980983574 0.338764025 0.248048056 79.17547145 1.105527052 23.54121397 3.532855839 0.004372323 2.359287733 1.980983574 KRNEDEDSPNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 39.124 0.095729 286790000 697900 435300 626720 557530 452950 679150 891290 759670 555410 FALSE TRUE 664911.6501 479657.5649 655455.7319 501486.0252 531944.3366 655630.8652 755307.3408 693149.2675 641540.1462 1.036430306 0.747665704 1.021690904 0.781690792 0.829167652 1.021963893 1.17733449 1.080445661 1 19.29118002 2.060219467 4.829393605 1.104842435 0.88143888 0.463581269 0.100799279 0.150735003 7.151703183 0.036935016 0.026237404 114.8733978 -2.060219467 -0.223403555 KRNS(ph)LIELPDDYSCLLNQASHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRNSLIELPDDYSCLLNQASHFR 23 2 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 KRNS(1)LIELPDDYSCLLNQASHFR;KRNS(1)LIELPDDYSCLLNQASHFR 203.21 1.01E-24 407970000 210521 157968 207502 205071 211208 237565 274910 241884 240480 TRUE FALSE 200570.0895 174065.1188 217016.1719 184456.8735 248042.6083 229338.0645 232967.4304 220703.3547 277772.4102 0.722066275 0.626646537 0.781273316 0.664057576 0.892970645 0.825632986 0.838698956 0.79454743 1 18.08354378 1.832462325 0.184345021 1.074742462 0.55954378 0.64424133 0.064565103 1.906090637 0.331929423 0.336346017 0.411501536 67.99270586 -1.832462325 -0.515198682 KRPAS(ph)MAVMEGDLVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRPASMAVMEGDLVKK 16 3 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 KRPAS(1)MAVMEGDLVKK;KRPAS(1)MAVMEGDLVKK 119.01 0.0012584 636360000 1177580 778390 959780 1172930 773050 1131740 1402800 1347150 832630 TRUE FALSE 1121918.127 857708.826 1003786.862 1055024.848 907869.6752 1092547.56 1188777.096 1229186.404 961750.0079 1.166538204 0.891820971 1.043708712 1.096984496 0.94397678 1.135999533 1.236056237 1.278072674 1 19.87530241 2.041790369 6.473160951 1.195059786 1.026676656 0.28811725 0.103540385 0.187934231 20.4642777 0.036574963 0.026564279 110.1007731 -2.041790369 -0.16838313 KRPAS(ph)PSHNGSSGGGYGASKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRPASPSHNGSSGGGYGASKK 21 3 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.993)PS(0.007)HNGSSGGGYGASKK 130.01 1.11E-05 381030000 334580 255530 349160 325400 232140 354330 443470 399260 280260 TRUE FALSE 318765.0665 281568.7975 365169.3314 292690.1738 272625.1425 342059.4633 375810.5066 364298.6778 323721.2894 0.984689845 0.869787705 1.128036194 0.904142493 0.842160066 1.056648032 1.160907604 1.125346678 1 18.30439272 2.033727019 8.937904475 1.112233994 0.945468336 0.391391998 0.086998588 0.241082792 59.24349806 0.030969967 0.022746776 108.0754418 -2.033727019 -0.166765659 KRPCGPGEHGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRPCGPGEHGQR 12 2 Q5T280 Q5T280 C9orf114 Putative methyltransferase C9orf114 0 63.408 0.042575 7183200 12027 9931.3 12230 10001 12862 14405 12223 12371 12307 FALSE TRUE 11458.50755 10943.31076 12790.7576 8995.680479 15105.12873 13906.15124 10358.15686 11287.72966 14215.5067 0.80605692 0.769815033 0.899775004 0.632807586 1.062581098 0.978238168 0.728651963 0.794043427 1 13.7951779 2.74608378 24.9982697 0.88775173 0.785927657 0.234016416 0.116675504 1133.230161 3765544.586 0.035771575 0.037277332 557.2932463 -2.74608378 -0.101824074 KRPIYEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRPIYEDK 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 131.06 0.00057435 339930000 668680 579580 628390 756330 497910 753640 886030 816420 603600 FALSE TRUE 637072.8216 638639.8609 657202.3031 680302.2715 584745.3464 727541.2578 750849.8504 744929.9367 697203.2052 0.913754866 0.916002474 0.942626623 0.975758956 0.83870146 1.043513932 1.076945494 1.06845455 1 19.41121968 2.130867336 7.806991829 1.057547817 0.920868187 0.723833993 0.039676792 0.108575272 7.167998003 0.013539856 0.009990018 135.165961 -2.130867336 -0.136679631 KRPPS(ph)DIHDSDGSSSSSHQSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRPPSDIHDSDGSSSSSHQSLK 22 2 O43665 O43665 RGS10 Regulator of G-protein signaling 10 1 KRPPS(0.998)DIHDS(0.001)DGSSSSSHQSLK 73.341 0.0067889 43577000 33218 22330 34860 42867 64384 32797 79585 50921 57654 TRUE FALSE 31647.85097 24605.45239 36458.36548 38557.92772 75612.54922 31661.23167 67442.84657 46462.08729 66594.68786 0.475230863 0.369480707 0.547466572 0.578994045 1.135414124 0.47543179 1.012736132 0.697684587 1 16.02311948 2.955419623 6.467896295 0.847309709 0.458397446 0.503153973 0.185823501 0.159676851 17.57607538 0.050184476 0.054219586 902.442673 -2.955419623 -0.388912263 KRPQS(ph)PS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 89.283 0.060068 1204530000 1290480 1185400 1130720 1355070 986070 1262030 1428720 1039640 1064000 TRUE FALSE 1229481.568 1306193.608 1182564.63 1218855.789 1158040.296 1218325.585 1210742.524 948603.6101 1228999.686 1.000392093 1.062810367 0.962217195 0.991746217 0.942262483 0.991314806 0.985144698 0.771850165 1 20.22905312 2.754683438 0.663381551 0.925413472 1.030099353 0.219520304 0.06691448 1.087429005 1.031259561 0.047304191 0.049742748 568.4384387 -2.754683438 0.104685882 KRPQS(ph)PSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.93)PS(0.07)PR;KRPQS(0.983)PS(0.017)PR;KRPQS(0.996)PS(0.004)PR;KRPQS(0.903)PS(0.097)PR;KRPQS(1)PSPR;KRPQS(0.998)PS(0.002)PR;KRPQS(0.997)PS(0.003)PR;KRPQS(0.987)PS(0.013)PR;KRPQS(0.999)PS(0.001)PR;KRPQS(0.987)PS(0.013)PR 111.5 0.0016659 3885455000 3295810 2840600 2878330 3308800 2593760 3024760 3555140 3164170 2896310 TRUE FALSE 3140023.593 3130060.369 3010304.278 2976193.138 3046110.923 2920011.803 3012738.098 2887098.5 3345454.962 0.938593892 0.935615755 0.899819101 0.889622838 0.910522173 0.872829506 0.900546602 0.862991292 1 21.67377099 3.742240769 5.61279136 0.898742155 0.937394715 0.094504174 0.037162752 0.246286846 30.2711046 0.008394931 0.014309016 5523.835906 -3.742240769 0.038652561 KRPYEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 1911166000 1928670 1533480 1583966 1791513 1760460 1597633 2023780 1743226 1957960 FALSE TRUE 1837505.591 1689743.355 1656592.408 1611426.71 2067483.667 1542306.569 1715015.192 1590579.89 2261590.437 0.8124838 0.747148258 0.732490013 0.712519245 0.914172448 0.681956619 0.758322623 0.703301475 1 21.10890626 -0.992289537 5.275877018 1.000001162 0.759208862 0.572118394 0.065815852 8.13E-07 1.55E-07 0.057555312 0.013565852 0.101791254 0.992289537 -0.2407923 KRQEEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KRQEEIER 8 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;;;; 182.76 0.00012758 597773000 704161 569611 593018 645320 679900 637548 727049 660192 701608 FALSE TRUE 670876.705 627655.0085 620208.4619 580451.2076 798474.3447 615469.5529 616124.3219 602382.0886 810409.7853 0.827824043 0.774490906 0.765302287 0.716244076 0.985272339 0.75945474 0.760262688 0.743305547 1 19.62829207 -1.019032363 4.507305059 1.000007912 0.791173561 0.436705981 0.074410698 0.061099995 41641524.71 744.1182027 0.016224211 0.095712275 1.019032363 -0.20883435 KRQS(ph)PEPSPVTLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KRQSPEPSPVTLGR 14 2 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 KRQS(0.981)PEPS(0.016)PVT(0.003)LGR;KRQS(0.994)PEPS(0.006)PVTLGR;KRQS(0.975)PEPS(0.025)PVTLGR 157.54 4.15E-06 1041720000 843240 739940 805610 903290 712700 865640 1043170 897980 818990 TRUE FALSE 803381.7163 815340.7272 842548.0154 812489.5731 836994.6544 835662.6697 884015.2574 819348.1107 945994.7864 0.849245395 0.861887126 0.890647631 0.858873204 0.884777238 0.883369213 0.934482166 0.866123284 1 19.85147271 -5 0.12463704 1.411197671 0.82221611 0.780225331 0.021022853 60.56051034 0.48332433 6.207188575 0.164497876 1.00E-05 5 -0.588981561 KRQS(ph)VSGLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KRQSVSGLHR 10 2 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KRQS(0.997)VS(0.003)GLHR;KRQS(1)VSGLHR;KRQS(0.998)VS(0.002)GLHR;KRQS(1)VSGLHR;KRQS(1)VSGLHR 173.72 1.74E-06 2070802000 957752 840372 939740 1030358 921511 955022 1286035 1042259 1046488 TRUE FALSE 912480.961 926006.8622 982828.0085 926784.4563 1082222.227 921949.3487 1089826.741 950993.2766 1208772.014 0.7548826 0.766072387 0.813079718 0.766715679 0.89530715 0.762715663 0.901598257 0.786743294 1 20.20511073 -4.999999994 0.103262879 1.636340555 0.676280909 0.631804537 0.048984591 97.22573355 0.678157542 13.18240656 0.635564815 1.00E-05 4.999999994 -0.960059646 KRS(ph)EGFSMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(0.563)EGFS(0.437)MDR;KRS(1)EGFSMDR;KRS(0.524)EGFS(0.476)MDR;KRS(0.999)EGFS(0.001)MDR;KRS(0.829)EGFS(0.171)MDR;KRS(0.993)EGFS(0.007)MDR;KRS(0.918)EGFS(0.082)MDR;KRS(0.993)EGFS(0.007)MDR 211.94 2.59E-08 5115220000 6613100 4982990 5677270 6755180 5735370 6466520 7925030 6884990 6147160 TRUE FALSE 6300511.869 5490762.346 5937578.445 6076136.472 6735616.712 6242582.791 6715921.12 6282103.776 7100430.177 0.887342275 0.773299956 0.836227989 0.855742021 0.948620935 0.879183744 0.945847076 0.884749743 1 22.759475 2.90614622 3.567050958 0.925395673 0.82856157 0.533835002 0.043475041 0.179762151 4.268533139 0.01254837 0.013664469 805.6496456 -2.90614622 -0.096834103 KRS(ph)FVPEEEKHEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRSFVPEEEKHEER 14 3 A0A0U1RRH6;O94880;O94880-2;B4DG57 A0A0U1RRH6 PHF14 PHD finger protein 14 1 KRS(1)FVPEEEKHEER 114.34 0.00034499 100500000 76016 75713 73930 108380 63215 95097 93991 101180 53872 TRUE FALSE 72422.87433 83428.24078 77319.76363 97485.43649 74239.67599 91803.76704 79650.94669 92320.14281 62226.19462 1.163864748 1.340725418 1.242559731 1.566630212 1.193061482 1.475323497 1.280022781 1.483621863 1 15.9252344 -0.879666228 7.712951881 1.000015231 1.333406349 0.398801547 0.131949513 1.69E-09 2.20E-10 0.113618326 0.026780096 0.131927026 0.879666228 0.333391118 KRS(ph)GEAAV ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KRSGEAAV 8 2 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 1 KRS(1)GEAAV;KRS(1)GEAAV;KRS(1)GEAAV;KRS(1)GEAAV 97.452 0.0064751 5841810000 5940570 5271910 5075310 6419520 4365560 5574650 6887760 6315080 5562700 TRUE FALSE 5659771.029 5809123.623 5308017.984 5774217.653 5126912.282 5381598.473 5836905.71 5762098.117 6425335.106 0.880852272 0.9040966 0.826107572 0.898664048 0.797921384 0.837559191 0.908420435 0.896777837 1 22.61534027 0.791180668 1.276352465 0.999000857 0.865068446 0.603074605 0.034989143 0.54284076 1.603267846 0.033065017 0.010015713 6.1827355 -0.791180668 -0.133932412 KRS(ph)GNSDSIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.551)GNS(0.435)DS(0.014)IER;KRS(0.968)GNS(0.032)DSIER;KRS(0.975)GNS(0.024)DSIER;KRS(0.946)GNS(0.053)DSIER;KRS(0.703)GNS(0.268)DS(0.029)IER;KRS(0.959)GNS(0.041)DSIER;KRS(0.863)GNS(0.112)DS(0.025)IER 105.58 0.0024047 904527000 1227080 964127 1206902 1246306 1058419 1205414 1479614 1295144 1270961 TRUE FALSE 1169078.36 1062372.637 1262239.65 1121024.953 1243006.938 1163670.211 1253871.709 1181734.325 1468055.141 0.796344993 0.723659901 0.859803978 0.763612294 0.846703168 0.792661106 0.85410396 0.804965898 1 20.48547473 -4.999999996 0.163182712 1.763608639 0.748589697 0.706686488 0.040136296 63.09554464 0.585088063 15.53040216 0.142696302 1.00E-05 4.999999996 -1.015018941 KRS(ph)HPSGSGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRSHPSGSGAK 11 2 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 KRS(0.999)HPS(0.001)GSGAK 110.44 0.00093631 20019000 30715 22958 26673 30452 25920 27702 42958 31272 31770 TRUE FALSE 29263.16282 25297.4463 27895.98343 27390.9071 30440.43979 26742.67279 36403.96812 28533.6579 36696.72934 0.797432451 0.689365149 0.760176286 0.746412762 0.829513702 0.728748128 0.992022144 0.777553161 1 15.16336387 1.575099367 0.58612608 0.983322916 0.734811059 0.493879721 0.074386398 0.533821568 0.419016567 0.065625018 0.035364915 37.59234064 -1.575099367 -0.248511858 KRS(ph)PGGSGGASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KRSPGGSGGASR 12 2 E7ER77;Q7Z2K6 E7ER77 ERMP1 Endoplasmic reticulum metallopeptidase 1 1 KRS(0.997)PGGS(0.001)GGAS(0.002)R;KRS(1)PGGSGGASR;KRS(1)PGGSGGASR;KRS(0.969)PGGS(0.009)GGAS(0.022)R;KRS(1)PGGSGGASR 121.32 0.00019741 1584556000 1199146.3 672474.2 1047423.3 1429819 1353892 1163731.2 1602336.9 1147530.3 1423560.1 TRUE FALSE 1142465.031 741000.0855 1095448.694 1286090.878 1590010.336 1123430.897 1357870.977 1047046.463 1644318.53 0.694795449 0.450642666 0.666202244 0.782142179 0.966972218 0.683219751 0.825795582 0.636766201 1 20.64905837 3.363040175 3.464510464 0.806986199 0.57091203 0.405267712 0.124114046 0.207443656 4.847899161 0.032552899 0.045411918 2306.960586 -3.363040175 -0.236074169 KRS(ph)PS(ph)PSPTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(1)PS(0.989)PS(0.012)PTPEAK;KRS(0.997)PS(0.926)PS(0.077)PTPEAK;KRS(0.999)PS(0.931)PS(0.07)PTPEAK;KRS(0.999)PS(0.999)PS(0.002)PTPEAK;KRS(0.989)PS(0.996)PS(0.015)PTPEAK;KRS(0.994)PS(0.901)PS(0.106)PTPEAK 189.42 2.83E-06 5347370000 7795000 6557570 6969190 7980760 4131160 8210200 8429600 7143460 4948860 TRUE FALSE 7426545.798 7225793.838 7288734.255 7178518.842 4851632.996 7925878.715 7143509.7 6517940.773 5716303.934 1.299186657 1.264067468 1.275078152 1.255797264 0.848736011 1.386539066 1.249672828 1.140236917 1 22.4466512 -5 0.115307013 0.302419683 1.342335057 0.216953863 0.140284805 257.0633751 1.945065201 42.56748753 1.46328061 1.00E-05 5 1.039915374 KRS(ph)PSPS(ph)PTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.918)PS(0.393)PS(0.689)PTPEAK;KRS(0.912)PS(0.222)PS(0.539)PT(0.327)PEAK;KRS(0.98)PS(0.157)PS(0.796)PT(0.067)PEAK 195.15 2.21E-07 3693880000 5785200 5101350 5135670 5854610 3155210 6141740 6343900 5421430 3617880 TRUE FALSE 5511745.061 5621183.365 5371145.549 5266093.48 3705477.625 5929050.004 5376021.541 4946700.848 4178922.353 1.318939333 1.345127497 1.285294412 1.260155857 0.886706503 1.418798796 1.286461218 1.183726432 1 21.99469952 -5 0.132883261 0.156392966 1.363996874 0.257296731 0.139570922 203.5185097 1.692134703 46.12761384 0.972579045 1.00E-05 5 1.207603908 KRS(ph)PTESVNTPVGK ddPTM_SK-BR-3_Trastuzumab_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(0.476)PT(0.476)ES(0.047)VNTPVGK;KRS(0.543)PT(0.39)ES(0.067)VNTPVGK 141.32 5.07E-06 306080000 1412890 1337930 1183540 1590270 817230 1486090 1425620 1489770 959110 TRUE FALSE 1346105.49 1474266.588 1237806.48 1430413.038 959754.6533 1434626.331 1208115.486 1359317.841 1107843.88 1.215067857 1.330753019 1.117311294 1.291168425 0.866326628 1.294971571 1.090510592 1.226994042 1 20.07932316 7.999999893 0.067009433 0.826238463 1.961830035 0.16772549 0.132758292 405.088157 2.011503216 6.217794679 43.75762413 99999975.34 -7.999999893 1.135591572 KRS(ph)S(ph)SEDAESLAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 2 KRS(0.993)S(0.759)S(0.214)EDAES(0.034)LAPR;KRS(0.987)S(0.641)S(0.335)EDAES(0.037)LAPR 97.713 0.014095 926210000 1243730 867550 1133170 1278250 791280 1146310 1285720 862320 767510 TRUE FALSE 1184941.348 955954.3313 1185126.965 1149757.881 929278.9815 1106612.997 1089559.8 786810.6894 886531.5309 1.336603726 1.078308326 1.336813101 1.296917077 1.048218759 1.248250016 1.229014155 0.887515742 1 19.75781242 1.24452043 24.99983159 0.943757829 1.21963606 0.577013861 0.099985978 87.57306825 367357.6298 0.065844096 0.022644136 17.55983496 -1.24452043 0.275878232 KRS(ph)SITEPEGPNGPNIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRSSITEPEGPNGPNIQK 18 2 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 KRS(0.333)S(0.333)IT(0.333)EPEGPNGPNIQK 176.83 5.06E-14 230140000 205780 152580 180940 209010 152550 199340 253540 240790 193370 TRUE FALSE 196053.1872 168128.0755 189236.278 187999.9177 179154.6717 192436.8058 214857.8164 219705.1511 223356.832 0.877757736 0.752733077 0.847237473 0.841702114 0.802100702 0.861566687 0.96194871 0.98365091 1 17.76899086 1.758576748 2.290792795 0.990830168 0.820950403 0.831200021 0.03269681 0.103811544 1.10117455 0.020394923 0.00897733 57.35572164 -1.758576748 -0.169879765 KRS(ph)SSEDAESLAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 KRS(0.932)S(0.055)S(0.01)EDAES(0.002)LAPR;KRS(0.818)S(0.091)S(0.091)EDAESLAPR 170.89 2.44E-06 1443990000 896930 607120 871150 793640 743780 832290 999160 793430 857940 TRUE FALSE 854533.8964 668986.2182 911093.0892 713861.7994 873494.9965 803467.5886 846719.7912 723953.063 990984.9534 0.86230764 0.675072024 0.919381355 0.720355841 0.88144123 0.810776779 0.854422449 0.730538905 1 19.91850363 -2.179707482 2.399611682 1.525929384 0.805169992 0.379282395 0.077654657 8094348.126 1642062.5 23185950.09 0.017942349 0.006611386 2.179707482 -0.720759392 KRS(ph)VSHGSNHTQKPDEQR ddPTM_SK-BR-3_Trastuzumab_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(0.967)VS(0.033)HGSNHTQKPDEQR;KRS(0.96)VS(0.04)HGSNHTQKPDEQR 120.25 2.05E-05 269610000 71259 33486.8 62532 60900 80944 64578 129916 92091 10188.1 TRUE FALSE 67890.72829 36899.14299 65399.15405 54778.2163 95060.60797 62341.64767 110094.9281 84027.02383 11768.01851 5.769087481 3.135544267 5.557363287 4.654837705 8.07787716 5.297548401 9.355434646 7.140286509 1 13.5225838 2.764287108 21.99298759 6.830463554 4.658480045 0.041559406 2.32695398 275.803204 235776.1809 0.636068203 0.674220566 581.1484824 -2.764287108 -2.171983509 KRSEGFS(ph)MDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(0.14)EGFS(0.86)MDR 82.515 0.014003 459480000 815020 647620 714350 848770 710460 815850 1032800 887310 769370 TRUE FALSE 776495.6198 713613.2143 747103.6541 763450.027 834363.9991 787596.9099 875227.3913 809612.4325 888679.9702 0.873762936 0.803003599 0.840689201 0.859083194 0.938880167 0.886254823 0.984862291 0.911028109 1 19.76130445 2.502906387 0.940648334 0.964177772 0.833089764 0.674715016 0.035215394 0.295875374 0.52959538 0.021183623 0.015346002 318.3511233 -2.502906387 -0.131088008 KRSPS(ph)PS(ph)PTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.11)PS(0.925)PS(0.949)PT(0.016)PEAK;KRS(0.56)PS(0.72)PS(0.72)PTPEAK 118.21 0.0021934 2590790000 1578040 1375270 1453390 1727910 982470 1628040 1880890 1477170 1132380 TRUE FALSE 1503449.177 1515411.577 1520029.369 1554217.204 1153812.457 1571660.567 1593925.686 1347821.164 1307983.707 1.149440294 1.158585974 1.16211644 1.188254254 0.882130604 1.201590324 1.218612799 1.030457151 1 20.31891314 -4.999999952 0.229546155 0.277711361 1.149898275 0.146308457 0.098983871 316.8856939 3.169380362 106.2691082 0.165828342 1.00E-05 4.999999952 0.872186914 KRSS(ph)ISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KRSSISK 7 2 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 KRS(0.006)S(0.994)ISK;KRS(0.076)S(0.924)ISK;KRS(0.002)S(0.998)ISK;KRS(0.079)S(0.921)ISK 101.97 0.004542 1685880000 2880760 2197070 2319410 2980460 1747850 2702080 3160560 3305540 2569460 TRUE FALSE 2744592.184 2420953.931 2425757.243 2680858.498 2052674.487 2608506.292 2678358.524 3016089.394 2967918.734 0.924753145 0.815707621 0.817326032 0.903278944 0.691620853 0.878900848 0.902436611 1.016230451 1 21.50102016 1.454490657 2.273222792 1.009976502 0.83843144 0.544601647 0.063406545 0.219919752 2.141749279 0.050313385 0.016276488 28.47676536 -1.454490657 -0.171545062 KRT(ph)EEPDRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER 218.68 1.07E-11 15336352000 15740710 12410285 12968558 15310374 10672841 14478536 16464054 16105569 12002970 TRUE FALSE 14996677.83 13674907.15 13563179.21 13771346.12 12534181.09 13977140.67 13952160.18 14695280 13864329.28 1.081673518 0.986337447 0.978278785 0.993293353 0.90405968 1.008136808 1.006335027 1.059934433 1 23.72487449 -0.153819717 6.712960532 1.000000001 1.002227256 0.000223206 0.047418147 0 0 0.045508829 0.010726534 0.701746545 0.153819717 0.002227255 KRTEEPDRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;;;;;;; 199.4 2.21E-08 935553000 958134 676382 883623 843528 852313 896631 1156335 992120 1048019 FALSE TRUE 912844.9047 745306.0948 924137.9886 758734.9628 1000956.117 865580.4436 979914.8582 905244.7132 1210540.434 0.754080474 0.615680463 0.763409435 0.626773746 0.826867149 0.715036375 0.809485442 0.747802129 1 20.20721984 -0.758741092 0.260825464 1.15320116 0.672184503 0.65198567 0.063802491 6.751849389 0.479364681 0.887464165 0.088237889 0.174284557 0.758741092 -0.481016657 KRTS(ph)ESR ddPTM_SK-BR-3_Trastuzumab_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(0.14)S(0.836)ES(0.024)R 80.688 0.023023 127210000 176150 202400 202880 254120 161160 176470 229020 292450 240080 TRUE FALSE 167823.7386 223024.7901 212182.2487 228575.3748 189266.253 170358.7997 194078.7928 266841.5276 277310.3802 0.60518376 0.804242488 0.76514355 0.824258272 0.682506918 0.614325362 0.699861262 0.962248609 1 18.08114209 1.216478463 6.710459317 0.986600997 0.713941997 0.705817254 0.071839133 0.097311392 15.89612555 0.065000854 0.017871302 16.4618433 -1.216478463 -0.272659 KRVDIIPGFEFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRVDIIPGFEFDR 13 2 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 113.59 0.00045569 93368000 218340 162960 194180 194510 215910 192790 237430 215760 228590 FALSE TRUE 208019.5009 179565.8093 203083.3451 174957.4853 253564.6356 186113.634 201205.6928 196866.9106 264038.5697 0.787837554 0.680074163 0.769142725 0.66262094 0.960331803 0.704872906 0.762031445 0.745599065 1 18.01038916 -5 0.355560626 3.928820198 0.747659228 0.458178132 0.082005888 390.329615 3.146455451 873.5451274 0.054948479 1.00E-05 5 -3.181160971 KRVPDHHPC ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KRVPDHHPC 9 2 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;; 83.005 0.0094755 1068890000 2809370 1912770 1963840 2146060 2756190 2154920 3535300 2596020 348062 FALSE TRUE 2676576.648 2107683.438 2053884.007 1930333.972 3236868.663 2080294.58 2995925.055 2368698.726 402037.6773 6.657526891 5.242502274 5.108685386 4.801375793 8.051157506 5.174377173 7.451851465 5.891733189 1 18.61697119 4.692330226 3.760190347 5.711940673 6.711468905 0.013218723 1.898503073 1.099202492 27.12616583 0.402476652 2.757543516 49241.38121 -4.692330226 0.999528232 KRYS(ph)YLTEPGMSPQSPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KRYSYLTEPGMSPQSPCER 19 2 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 KRY(0.22)S(0.28)Y(0.22)LT(0.28)EPGMSPQSPCER;KRY(0.226)S(0.274)Y(0.226)LT(0.274)EPGMSPQSPCER;KRY(0.22)S(0.28)Y(0.22)LT(0.28)EPGMSPQSPCER;KRY(0.171)S(0.412)Y(0.171)LT(0.245)EPGMSPQSPCER 134.21 9.02E-06 719258000 453886 363588 454082 428907 441870 432420 586850 510955 614126 TRUE FALSE 432431.7083 400638.0306 474902.1088 385792.4535 518931.9881 417445.187 497315.2543 466213.0715 709361.5236 0.609606941 0.564786808 0.669478246 0.543858725 0.731547978 0.588480166 0.70107447 0.65722915 1 19.43616155 -5 0.210307964 2.809232607 0.575004281 0.82472586 0.05421878 49.1154046 0.489466532 37.38064395 0.096922405 1.00E-05 5 -2.234228326 KRYST(ph)VVMADVSQYPVNHLVTFCLGEDDGVHTVEDASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KRYSTVVMADVSQYPVNHLVTFCLGEDDGVHTVEDASR 38 2 Q8TE68 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 KRY(0.11)S(0.381)T(0.479)VVMADVS(0.028)QY(0.001)PVNHLVTFCLGEDDGVHTVEDASR 98.19 0.00017793 62083000 200310 135330 168220 198670 139960 186810 246640 210360 28900 TRUE FALSE 190841.7433 149120.2809 175933.0534 178699.3142 164368.9797 180340.7229 209010.5381 191939.7632 33381.6644 5.716963091 4.467131389 5.270349953 5.353217623 4.923930027 5.40238859 6.261237775 5.749855996 1 15.02676827 2.250845746 22.96431014 5.185338509 5.120621528 0 1.48841035 2897.859834 5416894.138 0.46093244 0.382430805 178.1745808 -2.250845746 -0.064716981 KS(ph)KS(ph)PTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSKSPTLR 8 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 KS(0.995)KS(0.991)PT(0.014)LR;KS(0.99)KS(0.941)PT(0.068)LR 85.554 0.081948 1067160000 4949600 4243200 4463900 5063700 2144500 5507000 5797600 4857000 2382000 TRUE FALSE 4715642.217 4675586.904 4668574.23 4554687.256 2518500.121 5316291.209 4913069.64 4431695.331 2751388.394 1.713913683 1.699355465 1.696806689 1.655414141 0.915356089 1.932221281 1.785669246 1.610712374 1 21.39172838 2.982673234 24.97030994 1.533257647 1.700521465 0.097571829 0.315391009 2316.932401 3339030.967 0.092906184 0.100672534 960.8890282 -2.982673234 0.167263818 KS(ph)KSPIPGQGYLGTERPSSVSSVHSEGDYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSKSPIPGQGYLGTERPSSVSSVHSEGDYHR 31 3 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 KS(0.5)KS(0.5)PIPGQGYLGTERPSSVSSVHSEGDYHR;KS(0.5)KS(0.5)PIPGQGYLGTERPSSVSSVHSEGDYHR 104.48 6.48E-05 368730000 150380 109201 133281 138618 113104 134473 172953 156476 52037 TRUE FALSE 143271.8354 120328.7061 139392.0657 124683.8553 132829.3018 129816.1663 146565.8434 142774.1319 60106.63219 2.383627733 2.001920614 2.319079619 2.074377664 2.209894265 2.159764431 2.438430469 2.37534739 1 15.87523657 -0.644769364 6.794990644 1 2.238872729 0.886675367 0.139896226 2.00E-09 2.94E-10 0.134077496 0.031602369 0.226584729 0.644769364 1.238872729 KS(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.563)KS(0.437)PPKVPIVIQDDSLPAGPPPQIR;KS(0.498)KS(0.498)PPKVPIVIQDDS(0.004)LPAGPPPQIR 116.94 0.0049213 1267610000 1749240 1413440 1618370 1729010 790860 1846270 2002430 2057690 985640 TRUE FALSE 1666556.892 1557471.143 1692573.865 1555206.63 928785.7336 1782333.207 1696922.526 1877507.755 1138488.017 1.463833494 1.368017159 1.486685709 1.366028106 0.815806332 1.56552654 1.49050539 1.649123861 1 20.11868768 KS(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLPEEDVAEIQHAEEFLIKPESK 24 2 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 KS(1)LPEEDVAEIQHAEEFLIKPESK 102.51 0.0017727 26549000 38721 38534 40643 54272 27135 51759 52145 51404 26999 TRUE FALSE 36890.73507 42460.65841 42506.52175 48816.47545 31867.33541 49966.57285 44189.32254 46902.79325 31185.86703 1.182931199 1.361535287 1.363005932 1.565339691 1.021851834 1.602218492 1.416966298 1.503975926 1 14.92860475 4.496324299 1.799742764 1.382321923 1.16340656 0.051304476 0.203957041 1.260715803 5.970404996 0.047636322 0.400773939 31356.26302 -4.496324299 -0.218915363 KS(ph)LSDSESDDS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.971)LS(0.037)DS(0.374)ES(0.05)DDS(0.568)K;KS(0.609)LS(0.389)DS(0.151)ES(0.01)DDS(0.842)K 214.63 2.90E-11 433590000 1790750 1722800 1645540 2051220 820760 2111000 1892500 1961610 874710 TRUE FALSE 1706104.796 1898355.279 1720989.637 1845027.469 963900.2841 2037895.541 1603764.367 1789841.029 1010355.559 1.68861821 1.878898236 1.703350489 1.826117005 0.954020864 2.017008292 1.587326711 1.771496195 1 19.94643166 -2.365294185 0.436012384 4.72E-43 1.70372121 0.357152185 0.283864626 86.31241953 4.584380701 83.51606286 0.143929272 0.004312269 2.365294185 1.70372121 KS(ph)LVGTPYWMAPELISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSLVGTPYWMAPELISR 17 1 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 KS(0.998)LVGT(0.002)PYWMAPELISR;KS(0.935)LVGT(0.065)PYWMAPELISR 62.611 0.037023 194466000 129514 117717 116829 132803 115746 120727 144561 132423 114833 TRUE FALSE 123392.1299 129712.4961 122185.7252 119453.3901 135932.0658 116546.1937 122505.5644 120827.3401 132640.7152 0.930273406 0.977923679 0.921178124 0.900578604 1.024814029 0.878660776 0.923589444 0.910937037 1 17.01716416 KS(ph)PAKSPNPSTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSPAKSPNPSTPR 13 2 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 KS(1)PAKSPNPSTPR;KS(0.994)PAKS(0.006)PNPSTPR;KS(0.993)PAKS(0.007)PNPSTPR 106.38 0.00071942 430711000 589981 464209 594829 552687 409700 631916 726010 602667 577281 TRUE FALSE 562093.7674 511512.4249 622102.498 497129.8527 481151.5503 610032.5905 615243.8404 549894.2825 666802.7891 0.842968531 0.767112006 0.932963251 0.745542551 0.721579991 0.914862086 0.922677365 0.824673039 1 19.34690061 2.205499804 24.95587869 0.910768812 0.804376257 0.386526782 0.070916614 200.6733186 151476.6324 0.024907334 0.018396541 160.5091532 -2.205499804 -0.106392555 KS(ph)PEIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPEIHR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHR;KS(1)PEIHR 102.52 0.0052562 393640000 317300 325530 279260 403780 222230 350020 340790 331540 240387 TRUE FALSE 302301.8578 358701.8771 292064.3472 363191.2673 260986.8416 337898.7196 288796.2265 302508.6 277664.9882 1.088728758 1.291851304 1.051858749 1.308019674 0.939934283 1.216929516 1.040088735 1.089473332 1 18.08298575 1.755569497 0.499603719 1.006009613 1.185280665 0.170418419 0.111024912 1.300181107 0.76552312 0.099078807 0.067775311 56.95993658 -1.755569497 0.179271051 KS(ph)PEIHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPEIHRR 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHRR;KS(1)PEIHRR 83 0.0098187 122604000 203211 162914 180519 201467 129892 195454 213520 214020 152108 TRUE FALSE 193605.6188 179515.1218 188795.9747 181215.1544 152545.1237 188685.379 180943.6024 195279.2742 175696.1318 1.101934441 1.021736335 1.074559655 1.031412317 0.868232682 1.073930183 1.02986674 1.111460294 1 17.4227229 5.01471158 0.991048944 1.023945872 1.183057102 0.119376195 0.064606215 6.660283948 3.648863229 0.019046184 1.282550555 103445.4944 -5.01471158 0.15911123 KS(ph)PEKNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPEKNER 8 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KS(1)PEKNER 84.479 0.013721 105020000 201950 202680 188450 230300 86901 217470 207870 277960 127930 TRUE FALSE 192404.2237 223333.3224 197090.6189 207149.8065 102056.5069 209938.9594 176155.6137 253620.3488 147768.731 1.302063179 1.511370646 1.333777569 1.401851427 0.690650222 1.42072655 1.192103448 1.716332996 1 17.17298149 KS(ph)PENTEGKDGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPENTEGKDGSK 13 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 KS(1)PENTEGKDGSK 90.654 0.0035958 71770000 138370 101940 122240 131560 74822 134170 155650 143230 74078 TRUE FALSE 131829.5243 112327.8019 127844.8249 118335.3389 87870.93311 129523.6593 131902.7338 130688.0219 85565.6379 1.540683007 1.312767656 1.494114087 1.382977346 1.026941834 1.513734513 1.541538602 1.527342343 1 16.38474392 3.02288852 23.33844638 1.368151972 1.433715976 0.05066996 0.199520921 564.057703 575136.6953 0.056738497 0.0678089 1054.116278 -3.02288852 0.065564004 KS(ph)PESEILSLHLLVEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPESEILSLHLLVEELR 18 1 A0A0A6YYJ5;O94854-2;O94854 A0A0A6YYJ5 MACF1;KIAA0754 Uncharacterized protein KIAA0754 1 KS(0.996)PES(0.004)EILS(0.001)LHLLVEELR 126.31 1.31E-05 5314200 10159 8799 10721 12993 9838.5 9476.7 12792 11233 8681.6 TRUE FALSE 9678.804203 9695.628104 11212.56845 11686.91895 11554.33129 9148.519503 10840.34546 10249.37897 10027.89819 0.965187721 0.966865431 1.118137445 1.165440528 1.152218647 0.91230678 1.0810187 1.022086461 1 13.29173163 3.760256358 22.7759819 1.067011216 0.966026504 0.230358449 0.074686267 346.9991593 364272.7971 0.019146727 0.034457706 5757.797113 -3.760256358 -0.100984712 KS(ph)PGVEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPGVEIK 8 1 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 KS(1)PGVEIK;KS(1)PGVEIK 81.431 0.014013 705120000 1655820 1423750 1503690 1940350 1207290 1897140 1833850 1815840 1417040 TRUE FALSE 1577552.67 1568831.744 1572635.674 1745302.332 1417840.994 1831441.566 1554062.502 1656835.423 1636787.326 0.963810414 0.958482338 0.960806361 1.06629756 0.866234099 1.118924577 0.949459027 1.012248444 1 20.64243545 3.391226753 24.69690478 0.999369456 0.96084261 0.078578282 0.065971057 53.68164808 15425.05004 0.01597925 0.021636014 2461.652541 -3.391226753 -0.038526846 KS(ph)PMMPENAENEGDALLQFTAEFSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPMMPENAENEGDALLQFTAEFSSR 26 1 Q9UNN5;B3KT28 Q9UNN5 FAF1 FAS-associated factor 1 1 KS(1)PMMPENAENEGDALLQFTAEFSSR 63.724 0.026156 19808000 16601 13713 13659 11994 14227 12263 21579 17823 16492 TRUE FALSE 15816.30363 15110.37029 14285.27866 10788.34033 16708.1843 11838.32924 18286.72722 16262.32363 19049.49513 0.830274163 0.793216313 0.749903268 0.566332087 0.877093287 0.621451075 0.959958629 0.853687907 1 14.21746514 1.661198409 8.855701636 0.929483592 0.752249785 0.469800521 0.098312167 0.108974214 14.27690031 0.044698268 0.023624327 45.83512387 -1.661198409 -0.177233808 KS(ph)PPKADEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPPKADEK 9 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEK;KS(1)PPKADEK 69.716 0.028413 1471840000 2559270 2555620 2089320 2822490 804170 2962550 2373980 2860640 704820 TRUE FALSE 2438298.379 2816040.583 2185117.389 2538767.943 944416.9934 2859956.151 2011785.75 2610147.196 814119.8859 2.995011449 3.458999875 2.684024093 3.118420256 1.160046585 3.512942259 2.471117319 3.206096844 1 19.63488173 3.277366877 2.120636278 2.473757509 3.194979515 0.142730457 0.817482757 0.597000932 5.505462093 0.227930237 0.320211844 1893.942883 -3.277366877 0.721222007 KS(ph)PPKADEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPPKADEKER 11 3 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEKER;KS(1)PPKADEKER 61.641 0.06139 578410000 1188280 1026140 1039480 1188040 534460 1308750 1311650 1338700 613280 TRUE FALSE 1132112.359 1130704.833 1087141.186 1068615.962 627669.6548 1263427.659 1111533.702 1221476.331 708384.3302 1.598161211 1.596174258 1.534677067 1.508525692 0.886058073 1.783534171 1.569111081 1.72431303 1 19.43417277 -1.95932251 2.753995921 0.589817753 1.530940243 0.316835345 0.242170112 37216670.35 7442469 97034973.82 0.055441454 0.0109819 1.95932251 0.94112249 KS(ph)PPPAKDEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPPPAKDEAR 11 2 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 KS(1)PPPAKDEAR 71.344 0.025717 115630000 172130 153360 112520 163400 89611 168010 156650 175820 94924 TRUE FALSE 163993.756 168987.5584 117679.1533 146974.7216 105239.13 162191.7716 132750.1654 160424.2687 109644.3291 1.495688444 1.541233913 1.0732808 1.340468064 0.959822828 1.479253627 1.21073444 1.463133297 1 16.74247167 3.757758986 24.45799754 1.235618715 1.518461234 0.329106389 0.176919266 624.4597318 795534.8637 0.040176625 0.07227462 5724.782427 -3.757758986 0.282842519 KS(ph)PRPAGPQLFLPDPDPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSPRPAGPQLFLPDPDPQR 19 2 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR 136.4 3.08E-06 4463470000 9033800 7527100 8179900 9089100 6407990 8613800 9580000 9546900 7333440 TRUE FALSE 8606790.177 8294120.048 8554956.506 8175446.4 7525541.427 8315501.946 8118395.051 8710922.825 8470672.421 1.016069298 0.979157219 1.009950106 0.965147274 0.888423144 0.981681445 0.958412113 1.028362613 1 23.01404507 1.2381163 24.99999924 1.014181313 0.973118528 0.202832075 0.035223843 20.8824453 1174332.345 0.028281306 0.00871323 17.3027965 -1.2381163 -0.041062786 KS(ph)PSSDSWTCADTSTER ddPTM_SK-BR-3_Trastuzumab_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 1 KS(0.906)PS(0.087)S(0.006)DS(0.001)WTCADTSTER;KS(0.995)PS(0.004)S(0.001)DSWTCADTSTER;KS(0.994)PS(0.005)S(0.001)DSWTCADTSTER;KS(0.945)PS(0.045)S(0.01)DS(0.001)WTCADTSTER 185.41 3.56E-10 994720000 509710 468392 448418 524370 380411 490524 527440 519130 427761 TRUE FALSE 485617.0184 516121.6773 468978.4088 471659.3314 446754.558 473537.0309 446969.3409 473672.2251 494095.9912 0.982839422 1.044577747 0.94916457 0.954590484 0.904185757 0.958390757 0.904620456 0.958664376 1 18.91443183 3.628648061 5.766417441 0.939523101 1.013388048 0.42132317 0.031646395 0.158867079 7.107185359 0.007661528 0.011972311 4252.536608 -3.628648061 0.073864947 KS(ph)RDSESHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSRDSESHSR 10 2 Q15424;Q15424-3;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 KS(0.995)RDS(0.005)ESHSR 115.24 0.00065176 48469000 20615 13520 16869 18391 14706 20184 25320 23323 21861 TRUE FALSE 19640.5698 14897.70337 17642.46034 16542.30174 17270.72174 19485.02302 21456.96897 21280.71448 25251.09223 0.777810703 0.589982534 0.698681078 0.655112325 0.683959394 0.771650701 0.849744192 0.842764118 1 14.62405817 1.457584787 0.819918065 0.98518255 0.670837558 0.803104738 0.051727857 0.224956949 0.316192448 0.046223767 0.018571265 28.68037243 -1.457584787 -0.314344992 KS(ph)REDLSAQPVQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSREDLSAQPVQTK 14 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 KS(0.595)REDLS(0.405)AQPVQTK 83.106 0.0046178 257430000 381870 378090 359950 424880 681990 287930 476350 330230 797520 TRUE FALSE 363819.7619 416617.8009 376454.0635 382170.2552 800928.8401 277958.9119 403674.0587 301313.3105 921195.3284 0.394943125 0.452257831 0.408658242 0.414863432 0.869445182 0.301737214 0.438206802 0.32708949 1 19.81314757 -0.996668708 4.307729502 1.000024517 0.450259816 0.550156608 0.156040971 77225926.75 168986019.2 30230.24193 0.034871393 0.100770008 0.996668708 -0.549764701 KS(ph)SGTGTEPVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.431)S(0.431)GT(0.042)GT(0.096)EPVAK 62.165 0.048818 142510000 60568 56331 56840 72575 51377 67544 86418 79191 67743 TRUE FALSE 57705.07067 62071.19294 59446.17022 65279.62312 60337.13253 65204.93434 73233.34692 72256.61622 78248.23846 0.737461594 0.79325994 0.759712569 0.834263166 0.771098925 0.833308655 0.935910487 0.923428024 1 16.25577065 1.702706522 0.900013988 0.994150819 0.769217699 0.886530741 0.02876729 0.155616747 0.239588219 0.023931395 0.009978794 50.43203835 -1.702706522 -0.22493312 KS(ph)SLGNDETDKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.682)S(0.318)LGNDETDKEK 98.165 0.0017975 212440000 460900 427790 388030 477680 209560 539780 533680 549270 204190 TRUE FALSE 439114.1704 471382.2874 405821.5593 429662.6989 246107.1977 521087.2833 452257.3143 501173.0069 235854.7423 1.861799199 1.998612717 1.720641931 1.821725926 1.043469363 2.209356819 1.917524786 2.124922323 1 17.84753908 3.730157582 22.98917738 1.74946022 1.930205951 0.04278574 0.402250324 741.9131958 2029746.834 0.099646822 0.157609935 5372.266918 -3.730157582 0.180745732 KS(ph)SLLSEEQQETSTLVETIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSSLLSEEQQETSTLVETIR 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 KS(0.403)S(0.403)LLS(0.193)EEQQETSTLVETIR;KS(0.659)S(0.34)LLS(0.001)EEQQETSTLVETIR;KS(0.488)S(0.488)LLS(0.024)EEQQETSTLVETIR 249.91 9.78E-31 142818000 98152 88300 102944 123257 92055 117299 129208 111605 92527 TRUE FALSE 93512.54948 97297.87039 107664.0842 110866.9722 108109.3629 113236.9062 109494.9465 101832.2745 106875.6146 0.874966192 0.910384195 1.007377451 1.037345821 1.011543777 1.059520515 1.024508228 0.952811125 1 16.70557319 3.780368802 2.96276515 1.019706897 0.886245 0.766231455 0.027903298 0.101672699 1.789730414 0.007275453 0.013800467 6030.714955 -3.780368802 -0.133461898 KS(ph)SMCSAPSSSSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSMCSAPSSSSSAK 15 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 KS(0.5)S(0.5)MCS(0.001)APSSSSSAK 149.94 3.32E-08 0 116990 87816 99827 123550 70907 123730 150990 138330 97184 TRUE FALSE 111460.1146 96764.55024 104404.1667 111130.5193 83273.15835 119445.1991 127953.7024 126217.0919 112254.7984 0.992920714 0.862008143 0.930064177 0.989984579 0.741822707 1.064054284 1.139850628 1.124380371 1 16.77641759 2.023870716 24.88497448 1.103200107 0.91034129 0.554037527 0.079392233 137.613769 143460.2849 0.026999604 0.01993956 105.6502955 -2.023870716 -0.192858817 KS(ph)SMCSLAQPATTTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSMCSLAQPATTTAR 16 1 H3BPV0 H3BPV0 MTSS1L 1 KS(0.478)S(0.478)MCS(0.044)LAQPATTTAR 49.125 0.080324 146860000 148210 113510 138290 135600 122350 145370 174650 155860 166880 TRUE FALSE 141204.407 125076.7981 144630.7333 121969.2304 143687.8013 140335.8004 148003.9348 142212.0721 192758.8981 0.73254417 0.648876909 0.750319361 0.632755383 0.745427592 0.728037989 0.76781895 0.737771763 1 17.55643793 -0.886253304 0.34360342 1.129141859 0.686558073 0.839031606 0.039614522 4.281156265 0.415526399 0.591273841 0.030012945 0.129941147 0.886253304 -0.442583785 KS(ph)SPPASSPQPEAPTSSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSSPPASSPQPEAPTSSWR 19 1 P43250-2 P43250-2 GRK6 G protein-coupled receptor kinase 6 1 KS(0.5)S(0.5)PPASSPQPEAPTSSWR;KS(0.498)S(0.498)PPAS(0.002)S(0.002)PQPEAPTSSWR 83.857 0.0020149 507940000 155463 137136 142157 161003 124080 156524 175534 170509 149025 TRUE FALSE 148114.5721 151110.3143 148675.0391 144818.6726 145719.5127 151103.5346 148753.0644 155578.328 172135.0359 0.860455696 0.877859139 0.863711669 0.841308522 0.846541856 0.877819753 0.864164948 0.903815584 1 17.39318124 0.773526963 1.600691678 1.000029175 0.861665843 0.935748462 0.011481012 0.18721938 0.823135601 0.011284534 0.003248517 5.936452029 -0.773526963 -0.138363333 KS(ph)SPQKEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSSPQKEVK 9 2 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 KS(0.5)S(0.5)PQKEVK;KS(0.5)S(0.5)PQKEVK 88.101 0.0067896 1982260000 3099900 2300990 2962700 3104500 1456330 3566400 3563800 3826100 1680140 TRUE FALSE 2953373.87 2535463.497 3098542.726 2792429.762 1710313.491 3442894.674 3020076.856 3491066.401 1940687.53 1.521818337 1.306476935 1.596621134 1.438886847 0.881292565 1.774059255 1.556189139 1.798881245 1 20.88813642 KS(ph)SPSKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.836)S(0.146)PS(0.018)KDR;KS(0.627)S(0.263)PS(0.11)KDR;KS(0.571)S(0.415)PS(0.014)KDR;KS(0.97)S(0.029)PS(0.001)KDR 89.266 0.011047 1443460000 1521720 1647530 1597500 2108390 803810 1655780 1776420 2527610 1108470 TRUE FALSE 1449791.311 1815415.18 1670746.955 1896450.632 943994.2095 1598439.923 1505394.503 2306279.069 1280365.866 1.132325806 1.41788783 1.304898076 1.481178686 0.737284736 1.248424349 1.175753386 1.801265661 1 20.28812469 -0.680386928 8.930344396 0.999997528 1.270854227 0.097168462 0.271167092 0 0 0.238789946 0.05628333 0.208743553 0.680386928 0.270856699 KS(ph)SPSTGSLDSGNESK ddPTM_SK-BR-3_Trastuzumab_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(0.465)S(0.465)PS(0.06)T(0.01)GSLDSGNESK 122.64 5.65E-05 343300000 327890 289370 306580 370670 167240 339660 365540 384300 219830 TRUE FALSE 312391.2895 318857.132 320636.9962 333409.5474 196406.603 327897.489 309770.1594 350648.6547 253920.1137 1.230273904 1.255737985 1.26274753 1.313048984 0.773497618 1.29134114 1.219951247 1.380940839 1 17.95401515 -2.159544949 2.459006716 0.468845907 1.215182317 0.146169589 0.164011188 20750717.56 7762182.254 60925385.12 0.037301579 0.006925562 2.159544949 0.74633641 KS(ph)SPSVKPAVDPAAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.607)S(0.393)PSVKPAVDPAAAK;KS(0.632)S(0.367)PS(0.001)VKPAVDPAAAK;KS(0.499)S(0.499)PS(0.001)VKPAVDPAAAK;KS(0.5)S(0.5)PSVKPAVDPAAAK 162.65 4.18E-09 2177280000 4009720 4113550 4060550 4890600 2187730 5179160 5346020 5405650 2807600 TRUE FALSE 3820188.482 4532725.422 4246730.234 4398987.596 2569269.419 4999804.391 4530386.463 4932302.629 3242988.269 1.177984058 1.397700222 1.309511439 1.35646115 0.792253689 1.54172756 1.396978986 1.52091288 1 21.62889237 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_SK-BR-3_Trastuzumab_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(0.332)S(0.332)S(0.332)LES(0.005)LQTAVAEVTLNGDIPFHRPRPR 157.5 1.85E-09 367050000 133500 119650 132610 125130 119320 126260 156820 161780 138230 TRUE FALSE 127189.7196 131842.471 138690.2997 112551.6947 140129.3702 121887.5845 132894.2288 147613.6856 159666.0024 0.796598635 0.825739162 0.86862762 0.704919601 0.877640625 0.76339097 0.832326399 0.924515447 1 17.28469763 1.107252521 2.457935546 0.998207864 0.807970071 0.644232534 0.049151058 0.146630267 1.709829426 0.040355667 0.01110879 12.80125418 -1.107252521 -0.190237793 KS(ph)STTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.638)S(0.343)T(0.016)T(0.004)LR 63.216 0.049472 134720000 286640 278060 248190 306940 253910 270180 319690 272920 281350 TRUE FALSE 273091.0953 306394.6301 259569.757 276085.8081 298191.8236 260823.5989 270915.419 249021.678 324980.3211 0.840331176 0.942809796 0.798724539 0.849546235 0.917568863 0.802582747 0.833636382 0.766266945 1 18.30999283 2.227074901 24.97904583 0.83520291 0.87292293 0 0.072240579 647.5271111 1408226.507 0.024248388 0.018059157 168.6843924 -2.227074901 0.03772002 KS(ph)STVATLQGTPDHGDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.435)S(0.435)T(0.13)VATLQGTPDHGDPR;KS(0.646)S(0.32)T(0.034)VATLQGTPDHGDPR;KS(0.593)S(0.303)T(0.104)VATLQGTPDHGDPR;KS(0.326)S(0.326)T(0.326)VAT(0.021)LQGTPDHGDPR 272.18 3.45E-39 1725190000 3004950 2686250 2895550 3221740 2528430 3315930 3928630 3946640 3291220 TRUE FALSE 2862911.969 2959981.929 3028313.832 2897884.574 2969387.391 3201098.513 3329245.339 3601051.279 3801605.588 0.753079693 0.778613631 0.796588116 0.762279123 0.781087707 0.842038565 0.875747171 0.94724484 1 21.85817743 1.484544611 0.938238292 1.000769092 0.769345848 0.972046602 0.013769282 0.072981963 0.128627721 0.012304826 0.004644034 30.5171949 -1.484544611 -0.231423244 KS(ph)TAALEEDAQILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSTAALEEDAQILK 14 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;Q15052-2;Q15052 B1ALK7;Q15052-2 ARHGEF7;ARHGEF6 Rho guanine nucleotide exchange factor 7;Rho guanine nucleotide exchange factor 6 1 KS(0.954)T(0.046)AALEEDAQILK;KS(0.927)T(0.073)AALEEDAQILK;KS(0.5)T(0.5)AALEEDAQILK;KS(0.5)T(0.5)AALEEDAQILK 227.08 1.33E-12 158141000 466914 421575 421948 515974 271168 474584 501646 555562 302300 TRUE FALSE 444843.9006 464533.9718 441294.7332 464107.3132 318459.6133 458149.0371 425110.6893 506914.0461 349179.1401 1.273970434 1.330360032 1.263806117 1.329138141 0.912023591 1.312074476 1.217457289 1.45173061 1 18.41360785 -1.620880181 3.037147633 0.981731073 1.259095162 0.260351261 0.138377816 153222589.8 193992959.2 22681855.79 0.030822264 0.023939761 1.620880181 0.277364089 KS(ph)TGSPTQETQAPFIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSTGSPTQETQAPFIAK 17 1 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 KS(0.333)T(0.333)GS(0.333)PTQETQAPFIAK;KS(0.394)T(0.394)GS(0.211)PTQETQAPFIAK 210.38 2.10E-12 339090000 550340 420610 510540 577480 386820 548910 687010 610130 499980 TRUE FALSE 524326.5189 463470.6372 533948.764 519430.6133 454281.2855 529901.1091 582194.0067 556703.7827 577514.3449 0.907902156 0.802526623 0.924563639 0.899424608 0.786614721 0.917554886 1.008103109 0.96396529 1 19.13949726 1.960463187 5.112077084 0.986678676 0.863039788 0.625450541 0.044577447 0.126159674 8.030706268 0.018645186 0.011528697 91.29840436 -1.960463187 -0.123638888 KS(ph)VKEDSVPTGAEENVVCESPVEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSVKEDSVPTGAEENVVCESPVEIIK 26 2 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KS(0.759)VKEDS(0.202)VPT(0.04)GAEENVVCESPVEIIK 155.79 2.10E-08 58549000 103290 73221 76549 145360 49185 116390 131400 94445 46414 TRUE FALSE 98407.6864 80682.30315 80058.84737 130748.1366 57762.84843 112359.3851 111352.5167 86174.89512 53611.64607 1.835565472 1.50493986 1.493310749 2.438801011 1.077430981 2.095801815 2.077021036 1.607391331 1 15.71025881 KS(ph)VMLY(ph)AAEMIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSVMLYAAEMIPK 13 1 A0A087WYR0;P09132 A0A087WYR0 SRP19 Signal recognition particle 19 kDa protein 2 KS(1)VMLY(1)AAEMIPK 53.252 0.049939 365630000 291530 430040 343490 348160 481400 398020 408110 470920 296800 TRUE FALSE 277749.9547 473861.5649 359239.3563 313162.2953 565356.0076 384236.4676 345845.324 429683.7483 342826.2282 0.810177086 1.382220863 1.047875941 0.913472394 1.649103718 1.120790756 1.00880649 1.253357278 1 18.38711796 4.713162201 4.087122978 1.16828449 0.788685683 0.216528658 0.215981461 0.31699741 10.31464922 0.048757119 0.331305112 51660.92779 -4.713162201 -0.379598807 KS(ph)VSNGALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSVSNGALR 9 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 KS(0.595)VS(0.405)NGALR 65.395 0.070633 45560000 102450 83189 95555 101980 89382 92794 113740 107080 96010 TRUE FALSE 97607.39154 91666.05368 99936.29127 91728.77665 104970.1925 89580.52051 96386.87402 97703.50753 110898.7404 0.880148784 0.826574344 0.90114902 0.827139932 0.94654089 0.807768602 0.869143091 0.881015484 1 16.75888345 0.698605333 2.573012814 0.999978989 0.862861831 0.522532849 0.040038744 1.407024001 11.09350458 0.033255941 0.008851935 4.995803324 -0.698605333 -0.137117158 KS(ph)YSTSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSYSTSLK 8 1 A0A0B4J2B6 A0A0B4J2B6 IGHV2OR16-5 1 KS(0.804)Y(0.039)S(0.052)T(0.052)S(0.052)LK;KS(0.836)Y(0.034)S(0.043)T(0.043)S(0.043)LK 65.038 0.040001 1539550000 1620560 1330910 1842660 1468960 3435600 839270 1964080 1242120 4413000 TRUE FALSE 1543959.34 1466531.242 1927147.784 1321297.35 4034767.552 810205.8695 1664423.523 1133353.388 5097345.502 0.302894779 0.287704893 0.378068895 0.259212829 0.791542883 0.158946626 0.326527508 0.222341881 1 22.28131471 -1.541033563 2.846469937 1.032694968 0.337060788 0.594869979 0.170911058 42106436.49 44386180.3 10569475.09 0.038875834 0.028771761 1.541033563 -0.69563418 KSADTLWGIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSADTLWGIQK 11 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 109.6 0.0030577 3761800000 14351700 9864500 6989500 7266000 11635700 8714300 16043100 11271900 11525400 FALSE TRUE 13673323.58 10869703.77 7309975.489 6535607.876 13664962.4 8412521.606 13595430.44 10284872.68 13312700.17 1.027088676 0.816491292 0.549097884 0.490930299 1.026460615 0.631917004 1.021237636 0.772560979 1 23.66629988 1.727095717 24.99970501 0.922950975 0.776772799 0.154131604 0.188360941 1.981225601 4300.455297 0.088196327 0.048909316 53.3452454 -1.727095717 -0.146178176 KSAEFLLHMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSAEFLLHMLK 11 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 113.83 0.00086952 383720000 2038320 1337910 677140 755380 1797310 940100 2410650 1487570 1609030 FALSE TRUE 1941972.653 1474244.55 708187.5388 679447.7673 2110760.295 907544.1013 2042861.068 1357310.485 1858550.155 1.044885794 0.793222904 0.381043007 0.365579463 1.135702628 0.488307565 1.09916919 0.730306084 1 20.82574619 1.724389942 24.99999963 0.938178988 0.729920858 0.146172104 0.269496893 2.070359544 3637.405626 0.124146047 0.068845302 53.01392291 -1.724389942 -0.20825813 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSAEPSANTTLVSETEEEGSVPAFGAAAK 29 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KSAEPSANTT(0.001)LVS(0.788)ET(0.211)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.991)ET(0.008)EEEGSVPAFGAAAK;KSAEPSANT(0.002)T(0.002)LVS(0.976)ET(0.019)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.961)ET(0.039)EEEGSVPAFGAAAK 263.45 1.74E-58 1457490000 1261630 1497770 1029810 1505680 641542 1309340 1143960 1389290 733436 TRUE FALSE 1201995.25 1650394.466 1077027.807 1354326.186 753426.7217 1263997.227 969427.8917 1267636.403 847173.509 1.418830071 1.948118595 1.271319034 1.598640859 0.889341692 1.492016941 1.144308552 1.496312608 1 19.69229795 3.327914028 1.813396328 1.244701069 1.665922619 0.272891961 0.261708182 0.366399555 2.472527538 0.073760484 0.110735379 2127.717805 -3.327914028 0.42122155 KSATQFTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSATQFTGR 9 1 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ; 141.08 0.00017246 2672400000 635630 444460 535710 609850 760890 463620 627660 603670 781170 FALSE TRUE 605585.0296 489750.9793 560272.8334 548546.7194 893588.9751 447564.7231 531898.9392 550809.4545 902309.8539 0.671149746 0.542774721 0.620931746 0.607936084 0.99033494 0.496021097 0.589485903 0.610443798 1 19.78326342 -1.5707055 2.946325554 1.01989436 0.633189081 0.417213488 0.132999274 43069064.24 47268197.13 6754532.133 0.031708245 0.02687166 1.5707055 -0.386705279 KSDASDMNSDT(ph)SPSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSDASDMNSDTSPSCR 16 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KSDASDMNS(0.001)DT(0.588)S(0.41)PS(0.002)CR;KSDASDMNS(0.027)DT(0.485)S(0.485)PS(0.003)CR 94.057 0.0024738 351723000 209648 190574 205771 220484 184700 224822 265880 236168 224105 TRUE FALSE 199738.3545 209993.7073 215205.8039 198320.5294 216911.6215 217036.3578 225315.1228 215487.8779 258858.0588 0.771613429 0.811231098 0.831366058 0.7661362 0.837955838 0.838437709 0.87041958 0.832455744 1 17.98180171 -5 0.139106227 1.646060698 0.750431619 0.867960684 0.023494209 43.18589914 0.369048367 7.672331874 0.136234413 1.00E-05 5 -0.895629079 KSDASDMNSDTS(ph)PSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSDASDMNSDTSPSCR 16 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KSDASDMNSDT(0.032)S(0.968)PSCR 180.04 1.55E-09 271150000 161490 139980 159290 188170 129340 184110 180750 205310 170950 TRUE FALSE 153856.6877 154244.1211 166593.6041 169254.7941 151896.855 177734.2245 153173.2678 187331.968 197460.0529 0.779178803 0.781140888 0.843682566 0.857159672 0.769253592 0.900102182 0.775717749 0.948708183 1 17.59120129 -5 0.121698154 1.62448678 0.731496338 0.599181906 0.050223005 95.33699014 0.748826993 14.41220329 0.414486712 1.00E-05 5 -0.892990442 KSDGIYIINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSDGIYIINLK 11 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 147.24 0.0021146 0 3864700 4516000 3343000 4509300 3001800 3926600 4303700 4033100 3097500 FALSE TRUE 3682023.29 4976185.534 3496279.857 4056016.597 3525312.97 3790620.857 3647091.522 3679940.383 3577844.48 1.029117758 1.390833381 0.977202859 1.1336481 0.985317553 1.05947055 1.019354402 1.02853559 1 21.77065925 3.708010178 24.99926074 1.03335171 1.209975669 0.379701415 0.0960047 580.3158712 474869.4226 0.023656345 0.036652849 5105.169643 -3.708010178 0.176623958 KSDGIYIINLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSDGIYIINLKR 12 2 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 128.9 0.0001371 679770000 1741820 1185810 1734060 1563280 1765370 1927960 2677300 2151000 2378800 FALSE TRUE 1659487.621 1306645.387 1813568.366 1406136.124 2073249.969 1861194.262 2268828.713 1962647.037 2747692.155 0.603956894 0.475542861 0.660033317 0.511751697 0.754542304 0.67736637 0.825721582 0.714289275 1 21.38978895 1.491121791 0.360954768 1.014478369 0.507628329 0.744213829 0.076419496 0.512259588 0.212162586 0.098328618 0.07882948 30.98288042 -1.491121791 -0.50685004 KSDIDEIVLVGGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 256.98 1.44E-24 3463240000 6071550 5034700 5430690 6163980 5100110 5948320 7070270 6327210 5660490 FALSE TRUE 5784559.864 5547741.654 5679692.508 5544365.02 5989567.569 5742328.187 5991570.457 5773165.95 6538289.879 0.884720618 0.848500412 0.86868166 0.847983972 0.916075561 0.878261486 0.916381893 0.882977974 1 22.64048191 -1.033942949 0.256726721 1.079897855 0.856631565 0.778326073 0.02076585 6.529217393 0.394407484 0.400453054 0.030160144 0.092481966 1.033942949 -0.22326629 KSDLFQDDLYPDTAGPEAALEAEEWVSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSDLFQDDLYPDTAGPEAALEAEEWVSGR 29 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 216.8 4.16E-34 658026000 276251 241319 251399 287992 233784 268435 307279 312555 273761 FALSE TRUE 263193.1627 265909.6805 262925.8928 259042.497 274555.8556 259139.0286 260397.945 285186.0272 316214.4577 0.832324887 0.840915632 0.83147967 0.819198777 0.868258389 0.81950405 0.82348526 0.901875358 1 18.27054381 0.958407206 3.187025811 0.999706642 0.833785613 0.933421593 0.0143927 0.057251339 1.465306096 0.013171242 0.003439725 9.086721252 -0.958407206 -0.165921029 KSDLFQEDLYPPTAGPDPALTAEEWLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSDLFQEDLYPPTAGPDPALTAEEWLGGR 29 1 P31146 P31146 CORO1A Coronin-1A 0 172.18 3.07E-12 230150000 308650 274040 277130 331170 266680 284650 346800 325360 299630 FALSE TRUE 294060.7262 301964.9876 289836.6846 297880.1624 313188.9076 274792.4991 293889.2906 296869.7536 346095.0901 0.849652984 0.872491394 0.837448126 0.860688784 0.904921556 0.793979767 0.849157642 0.85776933 1 18.40080895 -2.145412776 1.891060935 1.276675222 0.853111933 0.734773643 0.027705727 814639.6048 173133.5584 965401.4275 0.006620357 0.007154631 2.145412776 -0.42356329 KSDPVVSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSDPVVSYR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 138.25 0.00022762 1180800000 601880 539315 602310 845640 846190 803600 978770 895570 979740 FALSE TRUE 573430.3252 594271.8117 629926.5093 760634.6606 993765.2681 775771.1305 829440.6602 817149.1431 1131673.075 0.506710231 0.525126757 0.556632938 0.67213286 0.878138121 0.685508163 0.732933104 0.722071737 1 20.11002581 3.726844232 0.117757749 1.177233923 6.62E-13 0.762212585 0.074971665 13.35985409 0.382548615 1.001206603 3.021995632 5331.43639 -3.726844232 -1.177233923 KSDVEAIFSK ddPTM_SK-BR-3_Trastuzumab_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 ; 134.56 0.00026837 2477900000 6324600 4529800 5112300 6026600 4423100 5246100 6728600 5776000 5392600 FALSE TRUE 6025648.692 4991391.77 5346704.012 5420794.718 5194487.24 5064426.242 5702028.491 5270222.819 6228856.866 0.967376329 0.801333515 0.858376445 0.870271197 0.833939092 0.813058696 0.915421339 0.846097917 1 22.57053599 -1.152133921 5.703724939 1.000001975 0.864641803 0.439786781 0.048487315 1.15E-06 1.72E-07 0.044517187 0.010492649 0.07044758 1.152133921 -0.135360171 KSDVETIFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSDVETIFSK 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 ; 134.99 0.00025021 899560000 1522040 1098680 1216700 1617380 1270000 1272500 1671630 1503260 1608210 FALSE TRUE 1450096.186 1210636.741 1272486.898 1454797.89 1491487.598 1228433.006 1416592.142 1371626.585 1857602.993 0.78062761 0.651719848 0.68501553 0.78315867 0.802909773 0.661300079 0.76259144 0.738385215 1 20.82501077 -5 0.34065355 3.938774703 0.720328774 0.72014092 0.052278645 206.7485243 1.737926251 441.9237734 0.040249719 1.00E-05 5 -3.218445928 KSDYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSDYIK 6 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 95.541 0.069313 1427500000 1765200 1828800 1581600 2175300 1397900 2080500 2122000 2091600 1602000 FALSE TRUE 1681762.494 2015156.799 1654117.924 1956634.711 1641693.317 2008451.763 1798249.927 1908448.416 1850429.978 0.908849572 1.089020835 0.893910034 1.057394624 0.887195591 1.085397333 0.971801121 1.03135403 1 20.81942911 KSEAPSGESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 87.363 0.020728 191272000 324525 321327 316187 380481 316361 354289 395135 364690 363443 FALSE TRUE 309185.3464 354070.5866 330684.4867 342234.327 371534.2582 342019.8831 334849.8986 332755.8103 419803.8842 0.736499489 0.843419034 0.787711832 0.815224298 0.885018629 0.814713479 0.797634112 0.792645859 1 18.67935599 -2.297480891 2.320927122 1.936232747 0.809054625 0.711388707 0.038211356 1768536.509 283536.2816 8723825.277 0.00901966 0.005041028 2.297480891 -1.127178122 KSEEEIDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSEEEIDFLR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;;; 153.95 2.46E-05 1288044000 2174360 1822170 1992960 2385450 1840070 2294630 2665890 2457710 2113860 FALSE TRUE 2071582.312 2007851.195 2084339.187 2145660.034 2160977.625 2215166.388 2259159.518 2242499.883 2441666.613 0.848429635 0.822328152 0.853654294 0.878768634 0.88504205 0.907235401 0.925253065 0.918430007 1 21.2194348 1.711681068 0.31570569 1.009324191 0.813803214 0.939439085 0.012203815 0.296971167 0.099761102 0.019899365 0.020254265 51.48504164 -1.711681068 -0.195520976 KSEEWPDWS(ph)EPEEPENQTVNIQIWPR ddPTM_SK-BR-3_Trastuzumab_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 108.04 0.0016437 31109000 56190 54164 49868 57500 48893 60383 70523 59197 57476 TRUE FALSE 53534.01006 59683.37318 52154.49713 51719.99076 57419.92372 58291.92157 59763.42111 54013.39686 66389.08453 0.80636765 0.898993767 0.785588437 0.77904359 0.864900068 0.878034725 0.900199506 0.813588517 1 16.01865844 2.474378562 4.499395251 0.889148057 0.827384313 0.304200955 0.055739997 0.298961265 15.46228347 0.018263226 0.015893815 298.1113847 -2.474378562 -0.061763744 KSEIEYYAMLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSEIEYYAMLAK 12 1 E5RI99;P62888 E5RI99 RPL30 60S ribosomal protein L30 0 ; 145.17 9.86E-05 3431800000 2912880 3196430 2432840 3094080 2176300 2920500 3026170 3284350 2215530 FALSE TRUE 2775193.935 3522149.851 2544388.12 2783057.2 2555846.031 2819362.353 2564472.187 2996754.903 2559103.077 1.084440076 1.376321994 0.994249955 1.08751274 0.99872727 1.101699411 1.002098044 1.171017662 1 21.28720683 3.719513165 24.98435511 1.050382669 1.230381054 0.411245193 0.08935036 622.2369904 816182.0127 0.021658083 0.033610376 5242.194913 -3.719513165 0.179998385 KSES(ph)DKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSESDKDVK 9 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KS(0.056)ES(0.944)DKDVK 101.53 0.0020449 266120000 649050 582680 536060 641220 190630 693300 601940 812920 233120 TRUE FALSE 618370.6928 642055.7545 560638.8812 576763.3474 223875.8116 669290.8472 510102.9976 741736.4152 269271.059 2.29646177 2.384421693 2.082061412 2.141943325 0.83141431 2.485565473 1.894384787 2.75460875 1 18.03869965 3.390807984 2.445818585 1.888784109 2.332181963 0.1068101 0.584517247 0.654492221 7.930176529 0.159676968 0.236440589 2459.280035 -3.390807984 0.443397854 KSFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSFSKEELMSSDLEETAGSTSIPK 24 2 O00567 O00567 NOP56 Nucleolar protein 56 1 KSFS(0.014)KEELMS(0.493)S(0.493)DLEETAGSTSIPK;KS(0.089)FS(0.089)KEELMS(0.397)S(0.397)DLEET(0.02)AGS(0.006)T(0.001)SIPK 95.654 0.0035841 687141000 1392570 1079930 1412710 1317150 865000 1467000 1686160 1634270 1020920 TRUE FALSE 1326745.976 1189976.095 1477484.151 1184747.58 1015855.726 1416197.422 1428905.324 1491164.655 1179239.059 1.125086525 1.009105054 1.252913172 1.00467125 0.861450202 1.200941752 1.211718109 1.264514301 1 20.16942479 KSFYGSTLFLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSFYGSTLFLCR 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 0 117.08 0.0012382 393280000 479360 244010 182040 200710 611510 264350 717350 391520 707750 FALSE TRUE 456701.6028 268874.8964 190386.7141 180534.2495 718157.1504 255195.4932 607905.0825 357236.4332 817504.2553 0.558653487 0.328897244 0.232887735 0.220835853 0.878475122 0.312164116 0.743610909 0.436984188 1 19.64086671 0.345274724 0.36575759 1.076479622 0.370574104 0.415684291 0.208381036 2.939717971 0.701128784 0.614106861 0.167364884 2.214495104 -0.345274724 -0.705905517 KSHEAEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSHEAEVLK 9 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ; 84.17 0.010174 215218000 818090 664330 566610 657660 598200 655930 886750 769110 592390 FALSE TRUE 779420.507 732025.9823 592589.629 591550.7673 702525.8906 633214.9796 751460.0012 701762.6511 684254.8157 1.139079315 1.069814878 0.866036476 0.864518238 1.02670215 0.925408145 1.098216606 1.025586719 1 19.38417416 3.983125955 19.38512925 0.977861671 1.113105688 0.371795615 0.073345528 41.78312296 48003.31147 0.019835208 0.036421024 9618.912087 -3.983125955 0.135244016 KSHS(ph)LDSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSHSLDSLSR 10 1 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 KS(0.003)HS(0.991)LDS(0.006)LSR 123.1 0.00028855 180140000 97868 96545 90119 96891 81763 87572 93220 93629 75078 TRUE FALSE 93241.9736 106383.0453 94251.04529 87151.3326 96022.44131 84539.35968 78997.5769 85430.3484 86720.71279 1.075198423 1.226731675 1.086834301 1.004965593 1.107260748 0.974846227 0.910942431 0.985120459 1 16.40408899 2.769168196 0.941591246 0.953133141 1.147363302 0.535162368 0.059934396 0.35948909 0.680588942 0.033885348 0.032362935 587.7169226 -2.769168196 0.194230161 KSHS(ph)PVKRPR ddPTM_SK-BR-3_Trastuzumab_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 98.942 0.0035918 602160000 740580 674440 645820 655870 452220 832420 854050 703070 426430 TRUE FALSE 705574.2511 743166.2028 675431.4858 589940.7015 531087.0248 803593.0867 723748.9868 641505.4636 492558.5865 1.432467671 1.508787428 1.371271366 1.197706664 1.078221027 1.631467015 1.469366298 1.302394235 1 18.90993581 0.917053142 5.997914855 1.000014126 1.398222342 0.373232345 0.154998415 0.885032009 62.79822591 0.153335297 0.038559126 8.261390339 -0.917053142 0.398208216 KSLDFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSLDFYTR 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 129.28 0.0017597 2900200000 2755600 1203660 1399610 1810800 2958100 1662920 3351700 2251300 3253000 FALSE TRUE 2625348.249 1326314.322 1463783.503 1628774.944 3473991.703 1605332.663 2840336.607 2054164.237 3757458.626 0.698703169 0.35298175 0.389567431 0.433477812 0.924558871 0.427238946 0.755919596 0.546689782 1 21.84132579 -0.1198327 0.307777814 1.129693077 0.479257272 0.383706793 0.178107932 6.1660436 0.806843964 1.146009528 0.194006038 0.758869853 0.1198327 -0.650435804 KSLDQDPVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLDQDPVVR 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 75.78 0.044282 0 796600 654560 698700 772930 688190 718230 906460 855720 832570 FALSE TRUE 758946.2967 721260.4082 730736.0861 695233.6079 808210.1181 693357.515 768162.8787 780788.6203 961680.7034 0.789187403 0.749999876 0.759853123 0.722936007 0.840414199 0.720985159 0.79877123 0.81190006 1 19.87519845 0.488769652 1.05986324 1.0004762 0.764637147 0.814722071 0.034609084 0.676204498 1.037923126 0.029284842 0.00911377 3.081553076 -0.488769652 -0.235839053 KSLDS(ph)DES(ph)EDEEDDYQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.002)LDS(0.998)DES(1)EDEEDDYQQK;KS(0.01)LDS(0.99)DES(1)EDEEDDYQQK;KS(0.017)LDS(0.983)DES(1)EDEEDDYQQK;KS(0.004)LDS(0.996)DES(1)EDEEDDYQQK;KS(0.037)LDS(0.963)DES(1)EDEEDDYQQK;KS(0.011)LDS(0.989)DES(1)EDEEDDYQQK;KS(0.083)LDS(0.917)DES(1)EDEEDDYQQK;KS(0.073)LDS(0.927)DES(1)EDEEDDYQQK 296.55 8.40E-49 13017690000 17191860 15682460 14691820 17387900 6620040 19565360 17157050 20719780 7155540 TRUE FALSE 16379234.85 17280520.5 15365454.48 15640035.26 7774572.88 18887806.68 14539426.91 18905446.22 8265184.598 1.981714341 2.090760382 1.859057629 1.892279001 0.940641166 2.285225025 1.759117021 2.287359223 1 22.97861561 3.415383781 2.61966755 1.738558599 2.031675532 0.085879352 0.448618656 0.726884187 10.08998927 0.120722282 0.179662927 2602.45831 -3.415383781 0.293116933 KSLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.017)LDS(0.983)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR;KS(0.003)LDS(0.997)DES(1)EDEEDDYQQKR;KS(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;KS(0.055)LDS(0.945)DES(1)EDEEDDYQQKR;KS(0.008)LDS(0.992)DES(1)EDEEDDYQQKR;KS(0.018)LDS(0.982)DES(1)EDEEDDYQQKR;KS(0.018)LDS(0.982)DES(1)EDEEDDYQQKR 183.15 1.49E-14 7501930000 7075290 4795432 5970622 6159541 2739296 7197291 7705480 7881350 3423694 TRUE FALSE 6740855.064 5284091.973 6244380.924 5540372.236 3217028.355 6948047.008 6529867.505 7191217.212 3954622.98 1.704550623 1.336180971 1.579007899 1.400986204 0.813485476 1.756942961 1.651198493 1.818433072 1 21.91510873 KSLESINSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KSLESINSR 9 1 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;;;; 183.33 7.26E-05 1949840000 2614650 2387930 2281550 2521700 2725940 2229350 2804440 2508840 2811260 FALSE TRUE 2491060.676 2631262.782 2386161.324 2268213.925 3201343.073 2152147.051 2376571.171 2289152.669 3247215.843 0.767137387 0.810313484 0.734832989 0.698510365 0.9858732 0.662766861 0.731879643 0.70495858 1 21.63077185 -1.231560847 3.374246086 1.000581396 0.763808297 0.413763364 0.088995709 42666903.29 65866993.93 270142.6368 0.019806787 0.058673116 1.231560847 -0.236773098 KSLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLPAPVAQRPDSPGGGLQAPGQK 24 2 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 KSLPAPVAQRPDS(1)PGGGLQAPGQK 142.55 1.36E-07 724030000 285100 173250 217390 286870 214020 278120 262020 284970 236390 TRUE FALSE 271623.888 190904.372 227357.5465 258033.2826 251345.0202 268488.6347 222044.0367 260016.5161 273048.1539 0.994783829 0.69916009 0.832664654 0.945010171 0.920515362 0.98330141 0.81320468 0.952273481 1 18.05879588 3.248169603 24.05299123 0.921427022 0.833348077 0.192382844 0.086468439 209.8941689 525396.87 0.023579359 0.031496756 1770.800365 -3.248169603 -0.088078945 KSLQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLQAER 7 1 P54136;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 71.614 0.086328 131230000 387770 227050 127810 161250 341530 181170 467270 310940 324850 FALSE TRUE 369440.8806 250186.6531 133670.2149 145040.8436 401092.7239 174896.0375 395979.3795 283712.4452 375226.0789 0.9845821 0.666762433 0.356239138 0.386542545 1.06893616 0.466108427 1.055308791 0.756110679 1 18.51740058 1.714717613 12.67700291 0.927326263 0.675763211 0.227549731 0.242853032 0.197933492 81.3659125 0.112501619 0.061700788 51.84628139 -1.714717613 -0.251563052 KSLS(ph)DSESDDS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.034)LS(0.954)DS(0.086)ES(0.027)DDS(0.899)K 234.82 3.31E-16 81093000 459270 437770 435150 504840 186140 531880 493470 486610 199050 TRUE FALSE 437561.2173 482379.2607 455102.0579 454092.5241 218602.7571 513460.8622 418182.0883 443999.8487 229917.6574 1.903121414 2.09805226 1.979413252 1.975022402 0.950787162 2.233238056 1.818834156 1.93112549 1 17.81075774 2.957040141 24.99949752 1.68123538 1.999788386 0.183268953 0.394846964 914.7810371 532335.5004 0.111556522 0.118331318 905.8163192 -2.957040141 0.318553006 KSLS(ph)DSESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.963)DS(0.037)ESDDSK;KS(0.154)LS(0.821)DS(0.026)ESDDSK;KSLS(0.5)DS(0.5)ESDDSK;KSLS(0.902)DS(0.098)ESDDSK;KS(0.319)LS(0.397)DS(0.284)ESDDSK 219.85 1.90E-11 6100090000 6533640 5857970 5475040 6760910 2860550 7142790 6732540 7177450 3140790 TRUE FALSE 6224807.786 6454903.803 5726076 6081290.482 3359429.014 6895433.391 5705367.371 6548954.428 3627847.672 1.715840451 1.77926539 1.578367263 1.676280547 0.926011596 1.900695402 1.572659022 1.805190024 1 21.79068245 3.478864935 2.250450459 1.515290456 1.746018198 0.103207043 0.312060374 0.726564996 7.360817894 0.085093301 0.13619619 3012.069126 -3.478864935 0.230727742 KSLS(ph)DSESDDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSLSDSESDDSKSK 14 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KS(0.027)LS(0.952)DS(0.004)ES(0.017)DDSKSK;KS(0.035)LS(0.79)DS(0.164)ES(0.011)DDSKSK;KS(0.002)LS(0.742)DS(0.244)ES(0.012)DDSKSK;KS(0.145)LS(0.485)DS(0.145)ES(0.223)DDS(0.001)KSK 114.55 0.0002458 1169450000 2409410 1014982 2707120 1645555 1322064 2838210 3812960 3332270 1866304 TRUE FALSE 2295521.964 1118409.82 2831244.13 1480140.685 1552631.543 2739922.076 3231222.922 3040478.773 2155720.893 1.064851193 0.518810122 1.313363033 0.686610539 0.72023774 1.271000381 1.498905973 1.410423206 1 21.03973897 2.148400645 5.527809783 1.362854732 0.846262947 0.415880411 0.251576474 0.165361935 7.991162357 0.088556798 0.065061319 140.734523 -2.148400645 -0.516591785 KSLS(ph)PGVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSLSPGVSR 9 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSLS(0.999)PGVS(0.001)R;KS(0.003)LS(0.995)PGVS(0.002)R 116.98 0.00075076 1263040000 1031450 838530 1007080 996710 940180 976200 1297980 1169510 1187380 TRUE FALSE 982695.4026 923977.1603 1053255.614 896518.8172 1104147.094 942393.9492 1099949.312 1067101.504 1371512.826 0.716504712 0.673691957 0.767951706 0.653671479 0.805057797 0.687120041 0.801997102 0.778047047 1 20.38733668 -0.499408918 0.317325668 1.102943934 0.691188513 0.7811228 0.046136684 3.396013647 0.367929783 0.404596567 0.040549444 0.31665845 0.499408918 -0.411755422 KSLSDS(ph)ESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KS(0.001)LS(0.104)DS(0.895)ESDDSK;KSLS(0.08)DS(0.753)ES(0.134)DDS(0.033)K;KS(0.011)LS(0.012)DS(0.978)ESDDSK 225.17 1.12E-11 3462210000 2943660 2777030 2581090 3035930 1308750 3237540 3014670 3346610 1547010 TRUE FALSE 2804519.026 3060012.514 2699435.53 2730752.549 1536995.586 3125423.178 2554726.723 3053563.087 1786912.41 1.569477614 1.712458035 1.510670313 1.528196085 0.860140417 1.749063446 1.429687717 1.708848777 1 20.76903749 -2.146698307 1.958411889 6.69E-05 1.516077217 0.286741253 0.251827367 2791935.444 595822.2593 12388554.73 0.05869486 0.007133484 2.146698307 1.516010341 KSLSDS(ph)ESDDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSLSDSESDDSKSK 14 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.057)DS(0.942)ES(0.001)DDSKSK 169.43 1.74E-06 724910000 1360200 536720 1502000 912820 692210 1567900 2179400 1750700 1004300 TRUE FALSE 1295906.042 591412.3782 1570868.186 821061.5994 812931.2048 1513603.23 1846892.503 1597399.427 1160041.715 1.117120208 0.509819923 1.354148015 0.707786271 0.700777562 1.304783449 1.592091456 1.377018953 1 20.14574525 2.138814958 5.795796372 1.401343825 0.864626651 0.375535079 0.275137645 0.175247705 8.576280133 0.096788291 0.071118519 137.6622801 -2.138814958 -0.536717174 KSMS(ph)EDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.421)MS(0.579)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 138.7 4.34E-10 54985000 30299 19208 25448 30255 29799 24731 27638 25824 27330 TRUE FALSE 28866.82632 21165.31704 26614.81597 27213.70992 34995.93617 23874.55927 23421.31549 23562.71366 31568.19682 0.914427469 0.670463288 0.843089522 0.862060956 1.108582044 0.756285175 0.741927568 0.746406701 1 14.94618424 -0.669656213 5.784517091 1.000000003 0.821470894 0.158644459 0.121199058 5.21E-09 1.35E-09 0.116465807 0.027451254 0.213965517 0.669656213 -0.178529109 KSNLDEEVNVIPPHT(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR 97.974 0.00099686 1245620000 1325190 1393510 1386240 1534080 1244690 1584800 1781430 1692210 1370710 TRUE FALSE 1262550.895 1535510.253 1449800.475 1379871.364 1461763.542 1529917.979 1509640.135 1544031.121 1583272.706 0.7974311 0.969833085 0.915698521 0.871531075 0.923254431 0.966300987 0.953493438 0.975214892 1 20.59447834 8 0.258500519 0.979040661 5.96E-15 0.619548809 0.036573592 37.56192115 0.51828878 0.046032019 16.1724422 100000000 -8 -0.979040661 KSPENTEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSPENTEGK 9 1 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 0 104.42 0.0052312 231270000 539460 550100 469380 602380 345830 580880 586780 627560 403550 FALSE TRUE 513960.7949 606155.8154 490901.5373 541827.618 406142.6425 560763.9799 497255.934 572607.5195 466130.473 1.102611446 1.30039946 1.053141911 1.162394757 0.871306782 1.203019353 1.066774139 1.22842756 1 18.83037431 3.716004858 24.83283626 1.086936898 1.201505475 0.158589682 0.112719761 1100.531044 1211633.316 0.027201779 0.042174407 5200.018136 -3.716004858 0.114568577 KSPSDLWK ddPTM_SK-BR-3_Trastuzumab_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 ; 117.53 0.0033064 1227720000 2464600 2367400 1850160 2829000 1849900 2615600 3085700 3038400 2105320 FALSE TRUE 2348103.242 2608640.752 1934991.666 2544623.545 2172521.974 2525021.116 2614919.792 2772341.588 2431802.273 0.965581482 1.072719102 0.795702713 1.046394098 0.893379367 1.038333233 1.075301155 1.140035775 1 21.2135945 2.01304806 22.05816461 1.074313665 0.968519081 0.295388637 0.083189982 71.23564267 120424.0855 0.029145851 0.021502409 103.0500152 -2.01304806 -0.105794584 KSPSGPVKS(ph)PPLSPVGTTPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.044)PS(0.036)GPVKS(0.897)PPLS(0.023)PVGTTPVK;KS(0.01)PS(0.05)GPVKS(0.94)PPLS(0.001)PVGTTPVK 137.03 2.07E-06 1284590000 2135800 1824590 1886340 2241300 1171360 2175200 2311600 2264100 1278090 TRUE FALSE 2034844.967 2010517.795 1972830.555 2016000.266 1375644.813 2099872.279 1958922.965 2065843.401 1476289.67 1.378350746 1.361872156 1.336343805 1.365585838 0.931825807 1.422398545 1.326923167 1.399348274 1 20.4935444 -1.41480382 3.540426583 0.99730465 1.319303449 0.335302023 0.139428941 10653826.08 4260152.786 219495.0821 0.030674258 0.038476555 1.41480382 0.321998799 KSPVGKS(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSPVGKSPPSTGSTYGSSQK 20 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.007)PVGKS(0.929)PPS(0.052)T(0.012)GSTYGSSQK;KS(0.041)PVGKS(0.926)PPS(0.027)T(0.006)GSTYGSSQK 175.71 7.98E-13 969710000 811120 805130 690790 933590 454370 877450 861180 938540 507710 TRUE FALSE 772779.9651 887173.6624 722463.4048 839743.7595 533611.9841 847063.6865 729791.1743 856356.4621 586443.0738 1.3177408 1.5128044 1.231941235 1.43192715 0.909912672 1.444409056 1.244436514 1.460255054 1 19.16163155 -4.277757306 0.202418767 2.32E-20 1.376929913 0.223969427 0.175459684 146.7268809 1.895119618 60.93402551 0.379326479 5.28E-05 4.277757306 1.376929913 KSRVS(ph)VS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSRVSVSPGR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KS(0.003)RVS(0.997)VS(1)PGR 87.647 0.062633 778880000 1785800 1307800 1692900 1663700 1366100 1594000 2143500 1421500 1687600 TRUE FALSE 1701388.773 1441066.307 1770521.14 1496461.715 1604347.407 1538799.38 1816469.707 1297025.924 1949304.389 0.872818418 0.739272078 0.908283565 0.767690117 0.823035857 0.789409488 0.931855341 0.665378856 1 20.89452796 -1.569422072 2.874826011 1.01046671 0.818595732 0.352240714 0.079611791 23326443.94 24519224.88 1874287.998 0.016731187 0.026951189 1.569422072 -0.191870978 KSS(ph)DSKPGVSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSSDSKPGVSSK 12 2 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 KS(0.051)S(0.948)DSKPGVSSK;KS(0.198)S(0.801)DS(0.001)KPGVSSK 106.6 0.00099386 395586000 656880 534661 575330 696130 358617 733160 777830 851280 444945 TRUE FALSE 625830.5842 589143.5638 601709.4496 626153.6898 421159.6913 707770.4854 659157.7477 776737.4103 513944.7981 1.217700007 1.146316814 1.170766689 1.218328685 0.819464839 1.37713328 1.28254581 1.511324588 1 18.97125388 KSS(ph)GTGTEPVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.211)S(0.789)GTGTEPVAK;KS(0.199)S(0.788)GT(0.013)GTEPVAK;KS(0.227)S(0.77)GT(0.003)GTEPVAK 181.81 1.08E-05 1173310000 1195160 1093000 1125540 1295480 736700 1333240 1433520 1381060 950550 TRUE FALSE 1138667.155 1204377.943 1177147.122 1165255.889 865180.2468 1287069.564 1214810.196 1260127.065 1097956.439 1.037078626 1.09692689 1.072125524 1.061295191 0.787991414 1.172241009 1.106428408 1.14770224 1 20.06638939 KSS(ph)LGNDETDKEK ddPTM_SK-BR-3_Trastuzumab_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(0.152)S(0.848)LGNDETDKEK;KS(0.248)S(0.752)LGNDETDKEK;KS(0.001)S(0.999)LGNDETDKEK 182.49 5.82E-06 1331920000 1587410 1478470 1449950 1720630 675900 1775510 1679310 1971220 645500 TRUE FALSE 1512376.275 1629127.774 1516431.642 1547669.003 793776.746 1714023.644 1423100.417 1798609.527 745600.8432 2.028399363 2.184986496 2.033838421 2.075733977 1.06461353 2.298848853 1.908662564 2.412295457 1 19.50804397 2.951602434 24.99973536 1.820677038 2.091440139 0.109604026 0.45308669 1007.451644 520397.9586 0.126639242 0.134323854 894.5454973 -2.951602434 0.270763101 KSS(ph)LVTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.012)S(0.986)LVT(0.001)SK;KSS(1)LVTSK;KS(0.163)S(0.83)LVT(0.006)S(0.001)K;KS(0.004)S(0.996)LVTSK;KS(0.012)S(0.988)LVTSK 145.15 0.00035154 19505490000 19583750 15868410 15782700 20036940 11357770 20737050 23832920 21040840 15610560 TRUE FALSE 18658064.95 17485419.02 16506352.41 18022788.72 13338561.49 20018920.76 20196770.33 19198392.51 18031365.92 1.034756049 0.969722377 0.915424404 0.999524318 0.739742156 1.110227636 1.120090981 1.064722029 1 24.10400535 KSS(ph)PSTGSLDSGNESK ddPTM_SK-BR-3_Trastuzumab_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(0.197)S(0.797)PS(0.006)T(0.001)GSLDSGNESK 186.15 9.47E-10 335820000 340190 313490 326230 367420 187190 401640 411350 390760 242480 TRUE FALSE 324109.8929 345434.9874 341187.9682 330486.2435 219835.8767 387731.1061 348591.0025 356542.9829 280082.56 1.157194125 1.233332727 1.218169272 1.179960093 0.784896699 1.384345766 1.244600887 1.272992445 1 18.09549263 KSS(ph)TPEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.012)S(0.894)T(0.095)PEEVK;KS(0.008)S(0.496)T(0.496)PEEVK;KS(0.002)S(0.701)T(0.297)PEEVK 130.56 0.00021906 1487190000 5705800 5402000 4976400 6448300 2814450 6309400 6166800 6538100 3119720 TRUE FALSE 5436098.142 5952469.942 5204572.862 5800104.633 3305289.189 6090903.896 5225941.399 5965589.303 3603510.244 1.508556317 1.651853204 1.444306387 1.609570735 0.917241513 1.690269621 1.45023631 1.655493921 1 21.78097152 -1.83832095 2.717556981 0.819351248 1.496871393 0.327012495 0.221191153 50036217.82 36336839.37 59003578.02 0.049181809 0.014510389 1.83832095 0.677520144 KSS(ph)TTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.266)S(0.73)T(0.002)T(0.002)LR;KS(0.004)S(0.904)T(0.046)T(0.046)LR;KS(0.026)S(0.954)T(0.017)T(0.004)LR;KS(0.041)S(0.951)T(0.004)T(0.005)LR 105.4 0.0048609 844630000 845750 793260 765310 937850 724150 771770 919930 893990 859020 TRUE FALSE 805773.0736 874094.0959 800400.2205 843575.5362 850441.5307 745043.4114 779577.7828 815707.4963 992232.4343 0.812080966 0.880936831 0.806666052 0.85017936 0.857099104 0.750875889 0.785680609 0.822093159 1 19.92031859 -1.029643211 4.067680861 1.00002018 0.821340783 0.700769488 0.036818801 4303699.006 2179396.089 715.1886127 0.009220761 0.093402132 1.029643211 -0.178679397 KSS(ph)TVATLQGTPDHGDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.131)S(0.854)T(0.015)VATLQGTPDHGDPR;KS(0.171)S(0.792)T(0.037)VATLQGTPDHGDPR;KS(0.168)S(0.664)T(0.168)VATLQGTPDHGDPR 246.17 1.77E-24 5012620000 4837310 4315770 4358540 5073600 3931200 5363200 6282800 6312700 5187030 TRUE FALSE 4608659.943 4755551.87 4558383.37 4563592.089 4616800.035 5177471.039 5324243.468 5759926.522 5991408.121 0.769211486 0.793728582 0.760820041 0.761689405 0.770570113 0.864149284 0.888646435 0.961364408 1 22.51446368 1.619011134 1.08584642 0.996526192 0.771023834 0.960607283 0.017206601 0.084105912 0.188567215 0.015206312 0.005704489 41.59212731 -1.619011134 -0.225502358 KSS(ph)VNGSSATSSG ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.296)S(0.698)VNGS(0.005)S(0.001)ATSSG 100.19 0.0026637 103040000 260400 219990 240150 284370 201720 239630 297610 252490 247510 TRUE FALSE 248091.4081 242407.2311 251161.115 255784.5873 236899.9041 231331.553 252204.1285 230380.6371 285892.5867 0.867778388 0.847896176 0.878515662 0.894687723 0.828632553 0.809155479 0.882163932 0.805829349 1 18.12511369 -1.199290723 4.810116333 1.000020551 0.854005614 0.702401684 0.030280102 6.18E-06 1.03E-06 0.02714782 0.006397902 0.063198865 1.199290723 -0.146014937 KSSEAS(ph)PTAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KSSEAS(1)PTAQR 172.82 7.91E-06 106940000 221560 214560 254460 254910 227670 284690 324610 279570 275480 TRUE FALSE 211087.2979 236423.9079 266127.2427 229285.9625 267375.5759 274831.1139 275084.7826 255089.3687 318200.0314 0.663379249 0.743004037 0.836352031 0.720571778 0.84027514 0.863705489 0.864502688 0.801663556 1 18.27957445 7.027461319 0.086119325 1.143910673 5.46E-14 0.767651389 0.044703818 58.31375091 0.442617062 0.977569386 7.980430013 10652739.79 -7.027461319 -1.143910673 KSSLLS(ph)EEQQETSTLVETIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSLLSEEQQETSTLVETIR 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 KS(0.304)S(0.304)LLS(0.392)EEQQETSTLVETIR 92.833 0.00097774 12765000 15711 12679 15122 15204 10684 12235 18077 15742 9640.1 TRUE FALSE 14968.37217 13971.00451 15815.35866 13675.66503 12547.28622 11811.29888 15319.02164 14363.54703 11135.03747 1.344258805 1.254688594 1.420323793 1.228165156 1.126829276 1.060732747 1.375749447 1.289941508 1 13.44281879 -4.999999999 0.174496692 5.46E-12 1.323141815 0.374351765 0.107687489 155.5283332 1.481354534 54.47586978 0.368368183 1.00E-05 4.999999999 1.323141815 KSSMCS(ph)APSSSSSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSMCSAPSSSSSAK 15 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 KS(0.333)S(0.333)MCS(0.334)APSSSSSAK 81.317 0.0061623 51001000 90309 70176 79748 95426 60134 94628 114180 109390 80576 TRUE FALSE 86040.27255 77327.01418 83404.52468 85833.59718 70621.35056 91351.00863 96759.74394 99811.23169 93071.31455 0.924455327 0.830836166 0.896135668 0.922234714 0.758787505 0.981516261 1.039630142 1.072416696 1 16.50604896 2.034223991 9.360903914 1.034047576 0.870570528 0.712536326 0.050515059 0.160179766 41.52121555 0.017643106 0.012974595 108.1991853 -2.034223991 -0.163477048 KSSSISEEKGDS(ph)DDEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KSSSISEEKGDSDDEKPR 18 3 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KS(0.005)S(0.005)S(0.005)IS(0.035)EEKGDS(0.949)DDEKPR;KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR 176.53 4.63E-13 895849000 2052480 1795720 1748030 2029210 690357 2252980 2037300 2414900 651212 TRUE FALSE 1955463.338 1978705.91 1828178.905 1825229.956 810755.0422 2174958.738 1726472.467 2203438.554 752198.631 2.599663516 2.630563029 2.430446998 2.426526559 1.077847006 2.89146862 2.295234791 2.929330715 1 19.52075416 2.987531614 24.82977517 2.158065399 2.558125796 0.110898817 0.639688081 1406.691988 2801320.025 0.176626746 0.196368798 971.6986833 -2.987531614 0.400060397 KSST(ph)PEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.001)S(0.07)T(0.928)PEEVK 126.34 0.00027902 386690000 1267200 1205700 1127600 1441100 655950 1414200 1400300 1497800 687250 TRUE FALSE 1207301.967 1328562.201 1179301.575 1296237.89 770347.4723 1365225.899 1186658.517 1366644.692 793825.22 1.520866227 1.673620549 1.485593485 1.632900867 0.970424538 1.719806659 1.494861195 1.721593944 1 19.59846187 -1.189480632 4.371833953 0.999847983 1.531316066 0.370245565 0.21613587 14497114.69 3944363.325 21065.72992 0.045975153 0.064642682 1.189480632 0.531468083 KSST(ph)PEEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.052)S(0.096)T(0.853)PEEVKK 109.44 0.096176 200690000 772850 755010 721780 922200 398080 917620 915940 973190 428900 TRUE FALSE 736318.9121 831946.3774 754874.3269 829498.7039 467505.026 885842.5893 776196.5306 887972.3244 495411.6215 1.486277027 1.679303313 1.523731568 1.674362627 0.943669881 1.788094084 1.566770937 1.792393004 1 18.91826819 KSST(ph)VATLQGTPDHGDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.273)S(0.273)T(0.358)VAT(0.078)LQGT(0.018)PDHGDPR 62.362 0.039717 287540000 765730 693960 723460 862990 663520 844200 1033700 1007900 870260 TRUE FALSE 729535.4604 764675.313 756631.3566 776240.6056 779237.6779 814965.1423 875990.0798 919642.9328 1005215.476 0.725750327 0.760707859 0.752705638 0.772213146 0.775194669 0.810736764 0.871445079 0.914871443 1 19.93907336 1.426566555 0.696510079 1.00186208 0.743320272 0.988680183 0.009066096 0.056863035 0.061531255 0.008393603 0.003723088 26.70339962 -1.426566555 -0.258541808 KSSTPEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;; 147.3 0.00014867 7418940000 13470600 11312140 11127730 13610100 8253620 13712900 14674800 14832300 9630980 FALSE TRUE 12833871.43 12464859.93 11637947.43 12241986.89 9693048.715 13238018.83 12435889.74 13533505.18 11124503.19 1.15365794 1.120486885 1.046154352 1.100452459 0.871324189 1.189987419 1.117882707 1.216549175 1 23.40723757 -0.287376734 7.338287428 1.000000003 1.103218911 0.10308484 0.094556866 0 0 0.086449931 0.020376444 0.515968592 0.287376734 0.103218908 KSSTPEEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 98.407 0.003036 782380000 878610 729260 784460 957520 471910 852410 956540 944920 529620 FALSE TRUE 837079.8465 803572.4231 820428.2669 861268.2704 554210.9546 822890.828 810602.2549 862177.7955 611750.7647 1.368334778 1.31356178 1.341115229 1.407874448 0.905942398 1.345140661 1.325053113 1.409361206 1 19.22258447 -1.46188589 3.050803631 0.993115353 1.303105044 0.301270828 0.144554072 221790234.4 245031040.5 12875274.27 0.03273508 0.034523444 1.46188589 0.309989691 KSTDEPSEKDALQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSTDEPSEKDALQPGR 16 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 79.805 0.0097466 111090000 82874 68334 70456 89300 66465 80783 90154 89928 83270 FALSE TRUE 78956.71026 75297.31229 73686.47729 80323.39434 78056.47496 77985.46445 76399.35151 82053.42758 96183.08632 0.820900153 0.782853984 0.766106393 0.835109346 0.811540552 0.810802267 0.794311707 0.853096222 1 16.5534956 0.836717209 2.741600527 0.999948919 0.80236108 0.91019676 0.019428142 0.178102163 2.379135605 0.018170232 0.00481077 6.866212005 -0.836717209 -0.197587839 KSVKEDSVPTGAEENVVCES(ph)PVEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KSVKEDSVPTGAEENVVCESPVEIIK 26 2 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KSVKEDSVPTGAEENVVCES(1)PVEIIK;KSVKEDSVPTGAEENVVCES(1)PVEIIK;KSVKEDSVPTGAEENVVCES(1)PVEIIK;KSVKEDSVPTGAEENVVCES(1)PVEIIK 139.3 2.75E-07 460699000 531905 298629 532878 423492 331109 511598 713550 595540 467766 TRUE FALSE 506762.9048 329059.6346 557310.9834 380921.7796 388854.3048 493881.233 604684.8423 543391.3604 540304.7623 0.937920485 0.609025975 1.031475238 0.705012812 0.719694387 0.914078993 1.119155122 1.005712698 1 19.04341387 1.988939373 4.996353929 1.04840016 0.79387651 0.447698094 0.12210257 0.149716382 10.68554417 0.048297943 0.031255556 97.48535399 -1.988939373 -0.25452365 KSVS(ph)NGALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSVSNGALR 9 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 KS(0.135)VS(0.865)NGALR 64.439 0.073629 45997000 115490 89586 99366 108080 93325 114230 127750 112530 117620 TRUE FALSE 110031.0166 98714.91525 103922.0294 97215.59306 109600.8505 110274.1865 108259.3912 102676.2766 135859.9089 0.809885841 0.726593416 0.7649205 0.71555762 0.806719593 0.811675699 0.796845752 0.755751108 1 17.05176027 -5 0.295667389 2.837499989 0.760978537 0.812015724 0.034194658 105.7950441 0.986201132 120.1808691 0.03395884 1.00E-05 5 -2.076521452 KSVYRGS(ph)LTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSVYRGSLTQR 11 2 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 KS(0.023)VYRGS(0.975)LT(0.001)QR 68.168 0.04566 128280000 143890 98950 138660 152300 162220 140350 209520 164760 197550 TRUE FALSE 137088.6049 109033.1175 145017.6982 136990.5146 190511.1166 135489.6443 177553.8759 150332.741 228185.0451 0.600778219 0.477827622 0.635526742 0.600348347 0.834897469 0.593770921 0.778113552 0.658819428 1 17.79984472 -5 0.083961681 2.23866012 0.289732314 0.656515943 0.087142644 123.6922237 0.730062192 27.7107949 2.312062937 1.00E-05 5 -1.948927806 KSYESSEDCSEAAGS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KSYESSEDCSEAAGSPAR 18 1 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KSYESSEDCSEAAGS(1)PAR;KSYESSEDCSEAAGS(1)PAR 193.5 7.37E-15 1025380000 560100 524230 549740 600290 494870 592070 766400 644880 640740 TRUE FALSE 533625.183 577649.633 574946.1228 539947.7087 581175.1713 571566.4674 649471.6041 588410.8885 740102.6868 0.72101506 0.780499305 0.77684642 0.729557828 0.785262885 0.772279952 0.877542557 0.795039525 1 19.49736593 -0.194583738 0.271718136 1.086796746 0.728539484 0.838942753 0.032487682 2.688395912 0.278403908 0.268533093 0.04738177 0.638875542 0.194583738 -0.358257262 KSYS(ph)GGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSYSGGTR 8 1 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 KS(0.266)Y(0.001)S(0.716)GGT(0.017)R 51.013 0.093057 44734000 101670 73147 79648 109330 84077 87006 112080 93913 92109 TRUE FALSE 96864.26059 80600.76246 83299.93958 98339.94069 98740.00218 83992.9604 94980.13751 85689.47986 106392.7933 0.910440055 0.757577275 0.7829472 0.924310168 0.9280704 0.789460995 0.892730932 0.805406806 1 16.69904091 -5 0.385828316 3.227010407 0.844223261 0.35313736 0.063487719 722.4407759 5.29628981 1349.290376 0.0403192 1.00E-05 5 -2.382787146 KSYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KSYSPR 6 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 KS(0.077)Y(0.007)S(0.917)PR 60.91 0.077495 123450000 438370 415700 381470 482450 368610 431870 491150 433570 412850 TRUE FALSE 417649.1189 458060.3026 398960.7768 433953.2094 432895.4673 416914.2336 416216.0469 395604.3123 476872.6695 0.875808461 0.960550545 0.836619086 0.909998071 0.90777999 0.87426741 0.872803315 0.829580594 1 18.86324458 2.242712064 24.87264001 0.882078282 0.902370645 0 0.053030108 399.2848773 2392255.756 0.016978278 0.013724525 174.8686928 -2.242712064 0.020292363 KT(ph)ASFGNILDVPEIVISGNGQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTASFGNILDVPEIVISGNGQPR 23 1 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR;KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 74.382 0.010824 525900000 378790 300357 333060 375820 327660 333330 436700 433780 453840 TRUE FALSE 360885.3474 330963.7198 348331.1304 338041.8596 384803.8003 321786.6985 370073.3945 395795.9236 524219.1893 0.688424527 0.63134606 0.664476115 0.644848312 0.734051344 0.613839984 0.705951636 0.755019907 1 18.99981064 0.716913411 1.336534718 0.999854002 0.662497127 0.906638127 0.033577027 0.235572009 0.693318498 0.028337706 0.008458085 5.21090806 -0.716913411 -0.337356875 KT(ph)GSYGALAEITASK ddPTM_SK-BR-3_Trastuzumab_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(0.676)GS(0.324)YGALAEITASK 175.8 1.62E-06 123100000 286010 223110 235990 259260 182290 281750 298120 295890 228050 TRUE FALSE 272490.8741 245845.1627 246810.3749 233198.6922 214081.3183 271992.9269 252636.3187 269980.303 263414.8293 1.03445533 0.933300389 0.936964618 0.885290676 0.812715514 1.032564976 0.95908161 1.024924465 1 18.00697704 -0.293772001 7.077436084 1 0.953006302 0.044575589 0.069189938 0 0 0.065821547 0.015514287 0.50842629 0.293772001 -0.046993698 KT(ph)LDELSQGTTTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTLDELSQGTTTVK 14 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 KT(1)LDELSQGTTTVK;KT(1)LDELSQGTTTVK 167.05 7.17E-06 106519000 214130 133204 156941 275400 120400 276590 280610 164807 149599 TRUE FALSE 204008.4993 146777.639 164136.9001 247716.2688 141397.7219 267011.6189 237797.7907 150375.6254 172798.0489 1.180618072 0.849417224 0.949877045 1.433559409 0.818283093 1.545223576 1.376160161 0.87023914 1 17.3987274 3.276933502 24.99989035 1.21395098 0.989230145 0.089910471 0.249993997 294.4595006 191838.1082 0.065409162 0.088562704 1892.053892 -3.276933502 -0.224720835 KT(ph)MELLQSDMNQHFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTMELLQSDMNQHFLK 16 1 A0A6I8PIP2;A0A6I8PU78;A0A6I8PIF8;A0A5F9ZHQ6;O75071 A0A6I8PIP2 EFCAB14 EF-hand calcium-binding domain-containing protein 14 1 KT(0.823)MELLQS(0.177)DMNQHFLK 44.089 0.077369 333140000 889760 660650 759840 930030 560060 815720 1013000 897340 642860 TRUE FALSE 847702.8081 727970.9861 794679.4156 836541.6175 657734.2867 787471.4119 858448.245 818764.1525 742551.4455 1.141608185 0.980364378 1.070201156 1.12657732 0.88577605 1.06049408 1.156079151 1.102636265 1 19.50213146 1.985736739 24.76983704 1.104757114 1.040872485 0.04527782 0.081432868 1270.128822 2205727.928 0.030703671 0.020699576 96.76910829 -1.985736739 -0.063884629 KT(ph)MEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTMEVK 6 1 Q68D51-2;Q68D51 Q68D51-2 DENND2C DENN domain-containing protein 2C 1 KT(1)MEVK;KT(1)MEVK 58.661 0.067537 552320000 670440 531010 697080 611860 549940 774950 876670 801670 621770 TRUE FALSE 638749.6299 585120.5227 729041.8075 550354.6703 645849.3619 748113.2872 742917.8904 731471.5249 718190.916 0.889386952 0.814714458 1.015108645 0.766306922 0.89927253 1.041663533 1.034429528 1.018491753 1 19.45400788 2.30442509 4.986997023 1.028041342 0.86875309 0.56726396 0.063816024 0.13038987 6.238721901 0.020799511 0.016990238 201.5696258 -2.30442509 -0.159288252 KT(ph)NHRLSLPMPASGTSLSAAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTNHRLSLPMPASGTSLSAAIHR 23 2 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 KT(0.913)NHRLS(0.087)LPMPASGTSLSAAIHR;KT(0.5)NHRLS(0.5)LPMPASGTSLSAAIHR 178.85 5.06E-17 3029000000 597030 378890 543110 550270 511690 511660 615140 517180 397910 TRUE FALSE 568809.5751 417499.3218 568012.1307 494955.8142 600928.574 493941.0859 521289.0952 471892.9775 459615.8506 1.237576064 0.908365804 1.23584104 1.076890219 1.307458333 1.074682445 1.134184329 1.026711713 1 18.81006903 1.164245979 3.821865813 1.0007924 1.127357609 0.178542544 0.110471403 0.40404907 10.4763342 0.096903648 0.025690601 14.59640748 -1.164245979 0.126565208 KT(ph)SDANETEDHLESLICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.499)S(0.499)DANET(0.002)EDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK 274 3.83E-39 779877000 1660070 1683350 1597430 2059100 1007240 1739990 1673360 1523420 776346 TRUE FALSE 1581601.781 1854885.279 1670673.746 1852115.356 1182902.337 1679733.71 1418058.199 1390021.269 896737.7727 1.763728293 2.068481261 1.86305718 2.065392373 1.319117331 1.873160428 1.581352143 1.550086671 1 19.77432664 0.544602775 0.332011471 0.867611223 1.972105865 0.649571367 0.196965941 1.581564402 0.373353563 0.550691031 0.196385485 3.504312077 -0.544602775 1.104494642 KT(ph)SDFNTFLAQEGCTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTSDFNTFLAQEGCTK 16 1 Q9UHD1-2;Q9UHD1;E9PHZ2 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 1 KT(0.5)S(0.5)DFNTFLAQEGCTK;KT(0.449)S(0.449)DFNT(0.102)FLAQEGCTK 154.65 1.96E-07 130618000 214910 181988 189173 227950 135569 211577 241198 239337 181012 TRUE FALSE 204751.6302 200532.7841 197846.7692 205036.0329 159212.1907 204250.0354 204398.8152 218379.3835 209082.4165 0.979286703 0.959108793 0.946262113 0.980646945 0.761480537 0.976887674 0.977599258 1.044465561 1 17.67371221 1.628677229 2.735668249 1.018215928 0.935497104 0.243009682 0.064657945 0.354549196 6.144060456 0.042384599 0.017164389 42.52822223 -1.628677229 -0.082718823 KT(ph)SETLSQAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSETLSQAGQK 12 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 KT(0.379)S(0.379)ET(0.212)LS(0.029)QAGQK 62.377 0.045824 115310000 114180 105560 109130 143920 85599 136870 148130 132100 76305 TRUE FALSE 108782.9377 116316.684 114133.7184 129452.8882 100527.4385 132130.1576 125530.0479 120532.6237 88137.98969 1.234234387 1.319711108 1.294943518 1.468752449 1.14056877 1.499128333 1.42424451 1.367544507 1 16.42747637 2.223690632 24.99606061 1.370209019 1.298451261 0 0.154603208 788.1638638 1324874.468 0.051384763 0.038109325 167.3750163 -2.223690632 -0.071757758 KT(ph)SFDQDSDVDIFPSDFPTEPPSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.349)S(0.349)FDQDS(0.301)DVDIFPSDFPTEPPSLPR;KT(0.359)S(0.359)FDQDS(0.283)DVDIFPSDFPTEPPSLPR 81.967 0.012371 84469000 101444 84526 90896 104046 72056 97805 113585 107899 88213 TRUE FALSE 96648.94316 93139.2955 95063.67151 93587.09841 84622.54359 94417.98833 96255.52212 98450.79155 101892.6215 0.948537212 0.914092641 0.932978955 0.918487492 0.83050708 0.926642056 0.944676079 0.966221009 1 16.63669006 1.285188976 1.664479031 0.995470172 0.913471956 0.481707302 0.031343335 0.322208554 1.609520227 0.029303146 0.008851107 19.28363827 -1.285188976 -0.081998217 KT(ph)SLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTSLDLR 7 1 Q5T457;A0A0A0MRN9;Q9GZV1-2;Q9GZV1 Q5T457 ANKRD2 Ankyrin repeat domain-containing protein 2 1 KT(0.673)S(0.327)LDLR;KT(0.657)S(0.343)LDLR 88.496 0.010879 493040000 966680 975700 745260 1124140 662960 958460 916900 950810 657460 TRUE FALSE 920986.9522 1075124.939 779430.9082 1011139.311 778580.0141 925268.2899 777010.065 867552.0358 759415.539 1.212757581 1.415726811 1.026356281 1.3314704 1.025235822 1.218395256 1.023168509 1.14239437 1 19.53452999 2.80046239 0.442131951 1.025448036 1.328476305 0.292570473 0.119418259 1.290740174 0.511676572 0.102072928 0.15914321 631.629477 -2.80046239 0.303028269 KT(ph)SLDVSNSAEPGFLAPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTSLDVSNSAEPGFLAPGAR 20 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 KT(0.5)S(0.5)LDVSNSAEPGFLAPGAR;KT(0.647)S(0.353)LDVSNSAEPGFLAPGAR;KT(0.707)S(0.293)LDVSNSAEPGFLAPGAR;KT(0.498)S(0.498)LDVS(0.003)NSAEPGFLAPGAR 250.83 4.28E-31 2116630000 1473680 1276820 1348740 1638610 1144470 1623600 1843850 1727160 1543520 TRUE FALSE 1404022.067 1406929.41 1410581.063 1473893.81 1344065.206 1567374.325 1562536.818 1575920.714 1782881.198 0.787501752 0.789132451 0.791180626 0.826692104 0.753872556 0.879124378 0.876411069 0.883917961 1 20.76577914 1.181799379 0.555618874 1.0008862 0.783220538 0.852551196 0.027338987 0.267015199 0.209174485 0.026221309 0.012787937 15.19845281 -1.181799379 -0.217665662 KT(ph)SLFEEDEEDDLFAIAK ddPTM_SK-BR-3_Trastuzumab_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 121.26 2.26E-05 21612000 37246 28153 34494 38353 24963 36238 39223 39833 23892 TRUE FALSE 35485.45539 31021.82271 36075.58402 34497.68357 29316.5393 34983.06897 33238.81097 36345.01135 27597.04934 1.285842373 1.124099259 1.307226131 1.250049712 1.062307022 1.26763802 1.204433509 1.316989034 1 14.7522264 -2.323859499 2.028412741 3.50E-05 1.220329493 0.436507977 0.080823196 1806725.655 229416.3046 8270597.938 0.018038641 0.004743954 2.323859499 1.22029454 KT(ph)SPAPGGPAGEGPLQSLTCLIGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSPAPGGPAGEGPLQSLTCLIGEK 25 1 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHI7;A0A5F9ZHQ1;A0A5F9ZHB0;A0A5F9ZHL4;Q07912-2 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 KT(0.5)S(0.5)PAPGGPAGEGPLQSLTCLIGEK 70.345 0.0038284 0 77281 70713 73742 74136 40881 87600 73915 69530 28635 TRUE FALSE 73628.08029 77918.73509 77123.14364 66683.70843 48010.63346 84566.39003 62637.90921 63441.5846 33075.56955 2.226056309 2.355779089 2.331725339 2.016101592 1.451543665 2.556762927 1.893781726 1.918079884 1 15.01347838 -1.580357204 0.237375727 9.32E-11 2.329494841 0.605939797 0.289171241 15.96537584 0.677780434 10.09832135 0.502236544 0.026281055 1.580357204 2.329494841 KT(ph)SPASLDFPESQK ddPTM_SK-BR-3_Trastuzumab_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(0.5)S(0.5)PAS(0.001)LDFPESQK;KT(0.5)S(0.5)PASLDFPESQK 163.18 2.53E-06 2442140000 3755300 3409110 3365100 3900900 2294810 3906480 4163480 4085420 2754270 TRUE FALSE 3577794.411 3756502.185 3519393.164 3508774.121 2695024.137 3771197.618 3528264.658 3727678.967 3181388.125 1.124601674 1.180774567 1.106244515 1.102906651 0.847122084 1.185393756 1.109033076 1.171714617 1 21.60122496 3.444808221 3.120442401 1.075190547 1.152116316 0.11113479 0.095869924 0.560458335 11.20521886 0.026702174 0.039510625 2784.891124 -3.444808221 0.076925769 KT(ph)SPGPTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSPGPTHR 9 1 Q14678;Q14678-2;Q5W0W3 Q14678 KANK1 KN motif and ankyrin repeat domain-containing protein 1 1 KT(0.448)S(0.448)PGPT(0.105)HR 63.473 0.044441 34233000 29389 27214 26442 30764 23023 25784 31222 32030 30500 TRUE FALSE 27999.84021 29987.13754 27654.39185 27671.54427 27038.20391 24891.09361 26458.51047 29225.2834 35229.78423 0.794777511 0.851187091 0.784971934 0.785458806 0.767481394 0.706535511 0.751026753 0.829561805 1 15.10450802 0.894933744 5.184930245 0.999987945 0.781297526 0.787614414 0.036219232 0.460034656 22.03588447 0.041049412 0.010364017 7.851158477 -0.894933744 -0.218690419 KT(ph)SSDDES(ph)EEDEDDLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSSDDESEEDEDDLLQR 18 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 KT(0.356)S(0.287)S(0.356)DDES(1)EEDEDDLLQR 110.36 0.00029077 380610000 323480 273830 294160 339270 171360 315600 322370 389140 197700 TRUE FALSE 308189.7415 301733.5883 307647.527 305165.935 201245.1297 304670.6929 273186.5358 355064.8386 228358.3063 1.349588489 1.321316458 1.347214086 1.336346989 0.881269147 1.334178282 1.196306542 1.554858435 1 17.80093974 -2.173334855 2.660031948 0.182104613 1.282867378 0.223619754 0.169416144 10257931.15 20391851.16 57727683.97 0.039181451 0.006709114 2.173334855 1.100762766 KT(ph)STSPPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.293)S(0.293)T(0.207)S(0.207)PPPEK 68.034 0.035855 172380000 589130 668740 527670 721340 324230 634290 628960 671120 399810 TRUE FALSE 561282.9924 736885.3663 551864.1914 648829.5327 380775.6093 612324.3783 533000.6004 612353.175 461810.4929 1.215396794 1.595644486 1.195001413 1.40496923 0.824527843 1.32592132 1.154154374 1.325983676 1 18.81694143 KTAESVTSLPSQNNGT(ph)TSPDPFESQPLTVASSKPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTAESVTSLPSQNNGTTSPDPFESQPLTVASSKPSSAR 38 2 I3L2B2;O95208-3;O95208-2;O95208;I3L356;I3L2H1;O95208-5 I3L2B2 EPN2 Epsin-2 1 KTAESVTSLPS(0.002)QNNGT(0.35)T(0.35)S(0.297)PDPFESQPLTVASSKPSSAR 78.239 0.094667 39950000 61055 48954 55711 56731 55487 56147 73140 65522 55653 TRUE FALSE 58169.05115 53942.46826 58265.40446 51028.2921 65163.91523 54202.61531 61981.14969 59784.54633 64283.383 0.904884722 0.839135492 0.906383605 0.793802219 1.013697665 0.843182371 0.964186183 0.930015558 1 15.97215823 1.480780896 0.535047314 0.998218575 0.867455985 0.305125025 0.059084083 0.867366391 0.612834971 0.052586053 0.029748463 30.25386719 -1.480780896 -0.13076259 KTAFVVEHDFIMATYLADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTAFVVEHDFIMATYLADR 19 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 166.06 1.34E-11 25926000 67334 68833 60886 78071 59670 67974 75434 75239 46725 FALSE TRUE 64151.25526 75847.16096 63677.68332 70223.15475 70076.42911 65620.04334 63925.15786 68650.67429 53970.87436 1.188627311 1.405335041 1.179852728 1.301130574 1.298411966 1.215841769 1.184438062 1.271994851 1 15.71989344 -1.090466251 0.305119798 0.848016204 1.291146009 0.568903637 0.069755011 10.54905917 0.777343992 1.423718266 0.06969107 0.081195834 1.090466251 0.443129805 KTAPTLS(ph)PEHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTAPTLSPEHWK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.001)APT(0.022)LS(0.977)PEHWK;KT(0.087)APT(0.228)LS(0.685)PEHWK 110.38 0.00070331 530890000 785330 715250 741770 871000 603610 796860 934300 888990 649840 TRUE FALSE 748209.0073 788134.7882 775780.8882 783445.4252 708879.3929 769264.5384 791755.3754 811145.3228 750613.8683 0.996796141 1.049986979 1.033528584 1.043739609 0.944399541 1.024847223 1.054810481 1.080642601 1 19.51771142 1.813680113 5.471436968 1.050535257 1.01683367 0.130407979 0.035370739 0.397378219 19.49001818 0.015815619 0.009088636 65.11486034 -1.813680113 -0.033701587 KTEAAATTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTEAAATTR 9 1 E7EVA0;P27816-4;B5MEG9;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ;;; 127.83 0.00069652 471303000 453075 361914 357909 433426 416694 395386 527867 456182 522050 FALSE TRUE 431659.0427 398793.4481 374319.4817 389857.195 489365.3017 381693.6837 447331.1942 416236.2857 603006.8477 0.715844346 0.661341491 0.620754943 0.646522003 0.811541865 0.632983995 0.741834352 0.690267925 1 19.20181486 -5 0.294430513 3.499610189 0.672640517 0.75496094 0.055768552 118.101543 1.103446005 181.5890485 0.052950744 1.00E-05 5 -2.826969672 KTEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTEFLDLDNSPLSPPSPR 18 1 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KTEFLDLDNSPLS(0.001)PPS(0.999)PR;KTEFLDLDNSPLS(0.001)PPS(0.999)PR 158.67 2.75E-11 213260000 426520 411040 375550 458740 357560 419500 457970 467800 409370 TRUE FALSE 406359.2449 452925.4433 392769.339 412626.5837 419918.3508 404972.6098 388098.2653 426836.952 472853.0088 0.859377518 0.957856744 0.830637284 0.872631824 0.888052615 0.856445031 0.820758794 0.902684225 1 18.85103225 0.978195679 23.61319904 1.000000003 0.872946326 0.548816785 0.037130516 730.5671852 791176.4646 0.037928128 0.009482032 9.510332011 -0.978195679 -0.127053677 KTEITDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTEITDK 7 1 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 ; 81.972 0.041294 500730000 1090300 1069540 866090 1241690 724090 1109710 1165020 1243250 806300 FALSE TRUE 1038763.68 1178527.342 905801.0832 1116872.962 850371.0667 1071280.464 987274.8019 1134384.439 931336.886 1.115346869 1.265414653 0.972581562 1.199214784 0.913064949 1.150260964 1.060061957 1.2180173 1 19.82894359 3.74819269 24.97825392 1.077978099 1.190380754 0.18142195 0.103010601 981.8251263 2546097.935 0.023367739 0.041455163 5600.060129 -3.74819269 0.112402654 KTEKEESTEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTEKEESTEVLK 12 2 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;H0Y9H6 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 91.307 0.0047086 289770000 396970 330010 350940 411270 261803 371110 427040 443090 203805 FALSE TRUE 378206.0148 363638.3942 367030.9461 369928.3582 307461.3603 358258.3676 361887.2049 404290.6906 235410.0385 1.606584057 1.544702157 1.559113403 1.57142134 1.306067329 1.521848303 1.537263267 1.71738934 1 17.84481632 -1.049126095 4.650905506 0.999986583 1.541749302 0.741462925 0.101218024 0.295515799 30044531.71 1347.312616 0.022688812 0.089304615 1.049126095 0.541762719 KTENWLSEWWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTENWLSEWWLK 12 1 P43155-2;P43155;P43155-3 P43155-2 CRAT Carnitine O-acetyltransferase 0 95.651 0.0030918 0 232760 205860 213460 208690 178130 215900 259200 234060 175420 FALSE TRUE 221757.8961 226837.368 223247.3521 187712.0847 209195.8156 208423.3289 219654.2795 213564.4656 202623.2377 1.094434669 1.119503225 1.101785534 0.926409463 1.032437434 1.028625005 1.084052757 1.053997893 1 17.62844011 3.433118411 24.99999967 1.028761173 1.10758194 0.475039861 0.041265577 119.2462673 67748.84115 0.011590395 0.015693476 2710.93067 -3.433118411 0.078820767 KTEPATGFIDGDLIESFLDISRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTEPATGFIDGDLIESFLDISRPK 24 2 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 228.63 1.94E-33 278380000 383810 351060 366320 417520 255990 413300 465310 454480 284720 FALSE TRUE 365668.0619 386833.4131 383116.1343 375550.0964 300634.575 398987.3174 394318.4135 414683.3218 328872.9235 1.111882541 1.176239774 1.164936688 1.141930726 0.914135988 1.213196006 1.198999326 1.260922661 1 18.32717071 KTERDELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTERDELLK 9 2 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 149.96 4.86E-05 451410000 1177620 690120 1082540 1058250 933000 1283080 1616120 1405550 1235640 FALSE TRUE 1121956.236 760444.0126 1132175.53 951872.6995 1095714.905 1238646.618 1369551.212 1282472.591 1427256.74 0.786092792 0.532801136 0.793252887 0.666924648 0.76770694 0.8678513 0.959568922 0.89855774 1 20.44481345 2.24010967 1.371360791 0.959075116 0.677669437 0.695788223 0.075709599 0.218360602 0.801342456 0.042952695 0.025066427 173.823972 -2.24010967 -0.28140568 KTES(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTESPIK 7 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.013)ES(0.987)PIK;KT(0.01)ES(0.99)PIK 55.426 0.078221 524940000 1701170 1960070 1361850 1900240 820380 1799300 1550460 1818260 778740 TRUE FALSE 1620759.065 2159803.361 1424292.17 1709224.265 963454.0123 1736989.79 1313908.851 1659043.515 899503.0219 1.801838377 2.401107399 1.583421217 1.900187352 1.071095915 1.93105498 1.460705321 1.844400157 1 19.7787686 1.77267393 0.078562281 2.89E-18 3.21421391 0.353090599 0.335094736 15.84030515 1.177383555 22.09654497 23.86366974 59.24803212 -1.77267393 3.21421391 KTES(ph)PIKLSPATPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTESPIKLSPATPSR 15 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.005)ES(0.995)PIKLSPATPSR 146.13 2.06E-06 652040000 1451200 1153800 1448600 1564800 805610 1601400 1848300 1855900 1087200 TRUE FALSE 1382604.652 1271373.532 1515019.743 1407503.331 946108.1289 1545943.116 1566307.889 1693387.557 1255797.423 1.100977456 1.012403361 1.20642049 1.120804443 0.753392316 1.231044982 1.247261588 1.34845599 1 20.26017233 KTESASVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTESASVQGR 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 161.93 1.11E-05 807270000 916930 688250 744970 950680 820100 841490 1015490 907660 868140 FALSE TRUE 873588.5361 758383.4575 779127.6114 855115.8402 963125.1803 812348.9903 860558.3497 828180.4786 1002766.717 0.871178232 0.756291014 0.776977933 0.852756504 0.960467837 0.810107651 0.858183997 0.825895459 1 19.93555459 -5 0.195286264 1.726338228 0.807156847 0.450094594 0.055869958 128.445543 1.264366638 36.3431183 0.140569354 1.00E-05 5 -0.919181381 KTESHHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 53.166 0.091737 33248000 80147 68262 66669 107340 83551 78527 130550 123900 16509 FALSE TRUE 76358.61015 75217.97541 69725.83959 96549.97927 98122.26795 75807.5903 110632.1998 113050.6592 19069.1314 4.004304576 3.944488808 3.656476958 5.06315559 5.145607625 3.975408669 5.801638126 5.928464007 1 14.21895151 3.239605714 24.99967868 4.788892668 3.904134695 0.011599802 1.399095088 67.49445735 1614494.485 0.349433986 0.447492531 1736.223833 -3.239605714 -0.884757973 KTETLLYAMLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTETLLYAMLPK 12 1 O75343 O75343 GUCY1B2 Guanylate cyclase soluble subunit beta-2 0 41.54 0.090525 2060100000 7938000 9021800 4563500 7468900 3146400 6554200 5482300 6030600 1855000 FALSE TRUE 7562786.472 9941131.677 4772740.989 6718111.982 3695131.164 6327226.411 4645874.446 5502528.694 2142663.926 3.529618612 4.639613127 2.227479975 3.135401637 1.724550042 2.952971921 2.16827025 2.568078282 1 21.03097415 7.999999997 0.103754227 0.147225918 12.20661384 0.548844377 0.673727742 75.52429666 0.55200045 6.953097148 129.9240221 99999999.25 -7.999999997 12.05938792 KTFEINPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTFEINPR 8 1 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 156.92 0.00061773 1067720000 978580 962280 915260 1101260 1005990 903130 1177340 1065160 1165130 FALSE TRUE 932324.4628 1060337.426 957225.5763 990559.2525 1181434.337 871854.3816 997715.1597 971888.9436 1345812.41 0.692759597 0.787879067 0.71126226 0.736030702 0.877859595 0.647827569 0.741347867 0.722157811 1 20.3600459 -0.994965089 5.166218077 1.000001668 0.740299816 0.644809955 0.060726438 1.05E-06 2.05E-07 0.05310071 0.012515877 0.101166077 0.994965089 -0.259701852 KTFPTVNPSTGEVICQVAEGDKEDVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTFPTVNPSTGEVICQVAEGDKEDVDK 27 2 P05091;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ;;; 325.62 1.58E-83 870980000 1643150 1366080 1381740 1473810 790367 1427854 1396980 1647720 679284 FALSE TRUE 1565481.556 1505285.105 1445094.146 1325659.819 928206.7546 1378407.058 1183845.044 1503436.902 784623.8934 1.995199954 1.918479819 1.841766683 1.689548113 1.18299578 1.756774258 1.508805752 1.916124291 1 19.58164174 3.50057374 0.060576207 1.07E-14 3.591392408 0.515684447 0.22872335 78.41708191 1.211764299 26.72927314 45.60800199 3166.458057 -3.50057374 3.591392408 KTGEGFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTGEGFYK 8 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 75.509 0.06126 829930000 986650 685330 726220 789860 693630 696430 947580 893750 830860 FALSE TRUE 940013.0099 755165.9062 759517.9053 710461.7722 814598.8524 672312.4545 803009.2675 815488.5119 959705.5254 0.979480669 0.786872521 0.791407244 0.740291426 0.848800836 0.70054036 0.836724648 0.849727849 1 19.87223227 0.762124248 2.341086493 0.999845004 0.814544194 0.390451705 0.073487028 1.161782501 9.566281639 0.070714954 0.019088295 5.782614599 -0.762124248 -0.18530081 KTGNQHFGYLYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTGNQHFGYLYGR 13 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 95.651 0.0029852 685290000 506420 356560 415650 463980 479350 432530 572550 480660 549630 FALSE TRUE 482482.5302 392893.8694 434707.9636 417339.8489 562948.4882 417551.3776 485196.9819 438570.8623 634863.8133 0.759977999 0.618863229 0.684726322 0.657369093 0.886723225 0.65770228 0.764253643 0.690810932 1 19.27608762 -4.999999984 0.259328172 2.852029197 0.68876065 0.581038124 0.075810153 130.6494814 1.283989704 128.8214903 0.092468802 1.00E-05 4.999999984 -2.163268547 KTGS(ph)PEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTGSPEIK 8 1 Q9BZ95-3;Q9BZ95-4;Q9BZ95-2;Q9BZ95-5;Q9BZ95;E9PKA2 Q9BZ95-3 WHSC1L1 Histone-lysine N-methyltransferase NSD3 1 KT(0.278)GS(0.722)PEIK;KT(0.006)GS(0.994)PEIK 97.779 0.0048939 455390000 1306040 1373310 1217250 1511720 750220 1528620 1539320 1622040 904210 TRUE FALSE 1244306.078 1513251.85 1273062.117 1359759.034 881058.1305 1475683.506 1304468.462 1480005.579 1044430.269 1.191373053 1.448877819 1.218905804 1.301914617 0.843577745 1.41290764 1.248976118 1.417045851 1 19.99428474 3.587041384 22.78423865 1.219871299 1.322424516 0.057942185 0.184639539 38.89770968 8020.265923 0.045764962 0.070898722 3864.037957 -3.587041384 0.102553217 KTGS(ph)YGALAEITASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.001)GS(0.999)YGALAEITASK;KT(0.356)GS(0.644)YGALAEITASK 262.8 3.10E-25 676270000 2298910 1913710 2108950 2230850 1530650 2277090 2628300 2556290 1915150 TRUE FALSE 2190245.08 2108719.225 2205647.444 2006600.72 1797594.875 2198233.802 2227304.563 2332447.696 2212141.681 0.990101628 0.953247815 0.997064276 0.907085083 0.812603863 0.993712935 1.00685439 1.054384408 1 21.07701236 2.015709043 24.99868589 1.015951857 0.938780038 0.376531584 0.052683076 289.7606149 461110.5022 0.020555087 0.015176169 103.6833553 -2.015709043 -0.077171819 KTIQMGSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTIQMGSFR 9 1 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2;H0YIH9 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 82.489 0.030556 0 67306 55183 50611 43290 71407 50753 87359 55604 62132 FALSE TRUE 64124.57877 60806.21044 52931.56441 38938.40695 83860.35819 48995.41088 74030.78009 50735.01898 71767.11323 0.89350924 0.847271232 0.737546238 0.542566159 1.168506777 0.682700037 1.031541841 0.706939665 1 16.13103527 2.743208849 24.99823124 0.909553862 0.784947632 0.174861106 0.169738006 855.6308821 4601595.173 0.04854856 0.049968216 553.6162746 -2.743208849 -0.12460623 KTKPPRPDS(ph)PATTPNISVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTKPPRPDSPATTPNISVK 19 3 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 KTKPPRPDS(1)PATTPNISVK;KTKPPRPDS(0.999)PAT(0.001)TPNISVK 245.41 7.76E-24 1783240000 1328870 957300 1092680 1270200 761060 1287010 1440380 1384000 944130 TRUE FALSE 1266056.949 1054849.958 1142780.459 1142517.083 893788.623 1242440.521 1220623.577 1262809.623 1090540.858 1.160944075 0.967272294 1.04790247 1.04766096 0.819582885 1.139288374 1.119282755 1.157966355 1 20.05661239 KTLEEAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTLEEAIR 8 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 96.342 0.014445 102630000 264350 204550 156890 251170 277180 183690 278910 203800 237950 FALSE TRUE 251854.6994 225393.8776 164083.5617 225921.9144 325520.1042 177328.7692 236357.157 185954.1916 274850.0707 0.916334854 0.820061195 0.596992976 0.821982377 1.184355177 0.645183641 0.859949413 0.676565922 1 18.06828533 -0.963081564 7.751475399 1.000000002 0.821614152 0.109335941 0.16487254 4.40E-09 7.10E-10 0.147685851 0.034809889 0.10887256 0.963081564 -0.178385849 KTLEEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KTLEEEAK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 144.65 0.0009332 712170000 1719090 1468120 1501150 1820640 1006280 1758390 1845370 1941070 1105510 FALSE TRUE 1637832.023 1617723.097 1569979.212 1637625.808 1181774.913 1697496.513 1563824.914 1771099.621 1276946.845 1.282615662 1.266868002 1.229478908 1.282454172 0.925469152 1.329339996 1.224659367 1.386979911 1 20.28426704 -2.282874941 2.190580492 1.83E-05 1.24006921 0.279274349 0.121655125 1756825.307 327319.1594 8690281.906 0.02700632 0.005213448 2.282874941 1.24005096 KTNSNKDGDQHS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTNSNKDGDQHSPGR 15 2 A0A2R8YFA9;Q6ZW33 A0A2R8YFA9 MICALCL MICAL C-terminal-like protein 1 KTNSNKDGDQHS(1)PGR;KTNSNKDGDQHS(1)PGR 63.918 0.035981 9298400 34281 24342 29011 32668 21604 30285 44160 38670 24451 TRUE FALSE 32660.60507 26822.47747 30341.18305 29384.15057 25371.73076 29236.22286 37422.58095 35283.8498 28242.7362 1.15642496 0.949712425 1.074300409 1.04041444 0.898345351 1.035176714 1.325033831 1.249307062 1 14.78559225 1.761028265 25 1.222817057 1.0245449 0.336292798 0.106748142 10.29444093 11463.72187 0.045284643 0.025113629 57.68040015 -1.761028265 -0.198272157 KTPCGEGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KTPCGEGSK 9 1 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 110.93 0.0035385 3960260000 4739430 4061370 3875480 4680850 3067350 4511740 5058430 4732260 3935440 FALSE TRUE 4515406.537 4475228.22 4053174.591 4210322.065 3602294.869 4355497.313 4286673.599 4317878.227 4545727.936 0.993329693 0.984490995 0.891644781 0.926215146 0.792457208 0.95815178 0.943011474 0.949876079 1 22.11607991 -0.179661811 8.23195428 1.000000555 0.935076037 0.125459974 0.056720316 0 0 0.056667253 0.0133566 0.661208137 0.179661811 -0.064924518 KTPEKLDNTPAS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTPEKLDNTPASPPR 15 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 1 KTPEKLDNT(0.003)PAS(0.997)PPR 99.343 0.0013457 103650000 106230 143030 95910 135510 56331 139680 121010 174640 85310 TRUE FALSE 101208.7184 157604.9196 100307.5684 121888.2773 66155.10856 134842.8466 102547.702 159347.5958 98539.4391 1.027088436 1.599409547 1.017943367 1.236949169 0.671356659 1.368415 1.040676738 1.617094609 1 16.58841364 0.953700157 0.0147334 5.85E-05 2.310635463 0 0.291743985 4055.701542 38.40648239 3068.731681 2945.22329 8.988767707 -0.953700157 2.310576981 KTPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 KTPEKLDNT(0.097)PAS(0.932)PPRS(0.97)PAEPNDIPIAK;KTPEKLDNT(0.07)PAS(0.931)PPRS(1)PAEPNDIPIAK;KTPEKLDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;KTPEKLDNT(0.067)PAS(0.934)PPRS(1)PAEPNDIPIAK;KT(0.003)PEKLDNT(0.04)PAS(0.962)PPRS(0.995)PAEPNDIPIAK 154.51 2.14E-08 4114560000 4169100 3259330 3908340 4128410 2166090 4224500 4760290 4434400 2556960 TRUE FALSE 3972034.905 3591459.433 4087541.255 3713414.383 2543855.41 4078204.506 4034020.332 4046100.428 2953480.298 1.344865889 1.216009274 1.383974445 1.257301221 0.86130773 1.380813175 1.365853138 1.36994326 1 21.49398456 3.006266146 24.92846805 1.226910681 1.300849011 0.07503144 0.171479957 635.3700413 2527647.448 0.049677168 0.059232998 1014.532925 -3.006266146 0.07393833 KTPEKLDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 KT(0.014)PEKLDNT(0.208)PAS(0.765)PPRS(0.014)PAEPNDIPIAK 59.971 0.037723 582650000 273180 245860 259850 257520 150710 356300 385650 440270 244890 TRUE FALSE 260267.3228 270913.4135 271764.3795 231633.6003 176993.7763 343961.2417 326812.0096 401717.6248 282866.2905 0.920107243 0.957743721 0.960752089 0.818880185 0.625715337 1.215985267 1.155358629 1.420167897 1 18.10976073 2.205192224 24.99836659 1.205066363 0.879212416 0.596327964 0.138764413 132.5066017 99268.3031 0.049856184 0.036823421 160.3955164 -2.205192224 -0.325853947 KTPESFLGPNAALVDLDSLVS(ph)RPGPTPPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KTPESFLGPNAALVDLDS(0.018)LVS(0.635)RPGPT(0.347)PPGAK 141.78 1.23E-08 62389000 254030 239200 280980 318830 193300 300820 337780 331700 219780 TRUE FALSE 242022.5053 263574.7519 293863.2109 286780.6027 227011.4588 290402.528 286245.4572 302654.5895 253862.3599 0.953361126 1.038258496 1.15756905 1.129669648 0.894230475 1.143936927 1.127561634 1.192199543 1 17.95368698 KTPESFLGPNAALVDLDSLVSRPGPT(ph)PPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KTPESFLGPNAALVDLDS(0.007)LVS(0.099)RPGPT(0.894)PPGAK 131.4 0.00017849 84087000 131360 129120 132180 145640 94092 146110 161010 153810 111420 TRUE FALSE 125150.8731 142277.4748 138240.5837 130999.9905 110501.615 141050.1741 136444.9673 140341.581 128698.4445 0.972435009 1.105510446 1.074143392 1.017883246 0.858608784 1.095974194 1.06019127 1.090468354 1 16.97363509 KTPSKPPAQLS(ph)PSVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.975)PS(0.025)VPK 133.21 1.82E-05 1629300000 3722900 3014200 3250100 3773200 2175300 3864300 4094400 4277900 2588000 TRUE FALSE 3546925.895 3321350.407 3399120.3 3393910.767 2554671.631 3730478.322 3469724.081 3903304.397 2989333.822 1.186527202 1.111067082 1.137082876 1.135340169 0.854595633 1.247929654 1.160701443 1.305743898 1 21.51139258 KTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR 37 2 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 215.27 3.13E-39 180797000 134142 114547 127139 131974 114102 139589 162679 141434 98797 FALSE TRUE 127801.3735 126219.4695 132968.4489 118707.7228 134001.3527 134754.9979 137859.3307 129049.2892 114117.9342 1.119906125 1.106044115 1.165184507 1.040219696 1.174235703 1.180839794 1.208042642 1.130841441 1 16.80016601 3.760311154 23.87752185 1.142458197 1.112975117 0 0.065216595 1741.088216 1911337 0.015896403 0.028623439 5758.523635 -3.760311154 -0.02948308 KTQMAEVLPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KTQMAEVLPSPR 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR 162.81 3.78E-05 3145290000 6188260 5903950 6072700 7153610 6048060 6348520 7563250 6684680 7365500 TRUE FALSE 5895753.214 6505569.217 6351139.302 6434515.532 7102839.749 6128669.161 6409337.304 6099333.981 8507704.122 0.692989922 0.764668014 0.746516241 0.756316327 0.834871506 0.720366984 0.753356865 0.716918912 1 23.02033843 -1.250713004 3.413242946 1.000696016 0.748323469 0.816276095 0.037534883 1351415761 1835689364 9612848.826 0.008644195 0.056141886 1.250713004 -0.252372547 KTQNDVLHAENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTQNDVLHAENVK 13 1 A0A2R8Y5S7;P35241;P35241-5;P35241-4;P35241-3;P35241-2;A0A2R8Y4H6 A0A2R8Y5S7 RDX Radixin 0 98.531 0.0021271 88805000 192660 147970 164610 206450 156480 169910 205110 178890 161190 FALSE TRUE 183553.3436 163048.3112 172157.5313 185697.2538 183770.0625 164025.9741 173816.7024 163225.4432 186186.522 0.98585731 0.875725641 0.92465088 0.997372161 0.987021297 0.880976627 0.933562218 0.876677009 1 17.50638911 -0.205508961 7.572830996 0.999999998 0.931912106 0.173846228 0.04605532 0 0 0.042863159 0.010102944 0.623004292 0.205508961 -0.068087893 KTQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 KTQQLHPVLQKPS(0.009)VFGNDS(0.99)DDDDET(0.001)SVSESLQR 101.86 6.78E-06 2085700000 962760 712630 939920 962930 667840 995960 1249400 952930 771530 TRUE FALSE 917252.2428 785247.8072 983016.2617 866134.447 784311.0846 961469.6555 1058781.083 869486.3974 891174.932 1.029261719 0.881137675 1.103056456 0.971901717 0.880086565 1.078878704 1.188073234 0.975662988 1 19.76534913 2.107804145 9.495185998 1.089871853 0.971628866 0.168097351 0.086881115 0.346250127 28.15303958 0.030831875 0.02276389 128.1752418 -2.107804145 -0.118242987 KTRPDGNCFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTRPDGNCFYR 11 2 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 127.52 0.00016026 760950000 1008900 848880 746510 906080 884060 901780 1171230 978270 996020 FALSE TRUE 961211.2964 935381.8371 780738.2219 814999.117 1038239.784 870551.1325 992537.3524 892607.4927 1150477.695 0.835488859 0.813037785 0.678620912 0.708400624 0.902442341 0.756686667 0.862717597 0.775858147 1 20.13380158 -0.801247416 0.442429631 1.062569081 0.785800094 0.488562838 0.0671997 11.46310007 1.688724995 1.041361232 0.037053395 0.158034747 0.801247416 -0.276768987 KTS(ph)LDVSNSAEPGFLAPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSLDVSNSAEPGFLAPGAR 20 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 KT(0.239)S(0.761)LDVSNSAEPGFLAPGAR 234.1 1.02E-29 489350000 523610 479210 455730 521640 405910 592420 733140 659730 577520 TRUE FALSE 498859.993 528042.0438 476625.6713 469203.7561 476700.5755 571904.3469 621286.028 601960.5438 667078.852 0.747827624 0.791573653 0.714496749 0.703370756 0.714609036 0.857326454 0.931353207 0.902382892 1 19.34749778 2.019059518 2.844381132 0.935445298 0.741102906 0.879343477 0.035650819 0.095750787 1.501490536 0.018036656 0.010633001 104.4863403 -2.019059518 -0.194342392 KTSATVGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTSATVGPK 9 1 P16104 P16104 H2AFX Histone H2AX 0 ; 94.465 0.013955 1056000000 1606590 1369310 1347390 1537580 1118160 1534710 1716860 1556460 1283190 FALSE TRUE 1530649.675 1508844.246 1409169.164 1383019.537 1313166.75 1481562.608 1454921.475 1420168.111 1482180.552 1.032701227 1.017989505 0.950740558 0.933097885 0.885969492 0.999583085 0.981608801 0.958161345 1 20.49928977 3.789950171 5.037871089 0.957650549 1.026685739 0.411689099 0.03331519 0.190961038 10.94712419 0.008879951 0.016086473 6165.242605 -3.789950171 0.06903519 KTSAVS(ph)SPLLDQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KT(0.005)S(0.005)AVS(0.604)S(0.385)PLLDQQR 53.779 0.089367 696570000 565940 397470 563350 453710 432170 556200 672980 575410 452310 TRUE FALSE 539189.1378 437972.6449 589180.1547 408102.2088 507540.3112 536938.6545 570304.5409 525024.05 522451.9247 1.032035891 0.83830229 1.127721283 0.781128731 0.971458401 1.02772835 1.091592382 1.004923181 1 18.99493876 2.272439142 4.115549785 1.045239295 0.941172115 0.141856943 0.097474694 0.32113887 11.84352079 0.032896379 0.025905595 187.2574661 -2.272439142 -0.10406718 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.06)S(0.06)FDQDS(0.881)DVDIFPSDFPTEPPSLPR;KT(0.006)S(0.023)FDQDS(0.971)DVDIFPSDFPTEPPSLPR;KT(0.057)S(0.057)FDQDS(0.886)DVDIFPSDFPTEPPSLPR;KT(0.051)S(0.116)FDQDS(0.834)DVDIFPSDFPTEPPSLPR;KT(0.097)S(0.067)FDQDS(0.836)DVDIFPSDFPTEPPSLPR 213.35 1.97E-26 3654358000 869041 737158 811427 908855 587441 859015 922486 927151 710900 TRUE FALSE 827963.1542 812275.2383 848631.7306 817495.1687 689890.5244 829267.0952 781743.8181 845964.7433 821142.7412 1.008306002 0.989201021 1.033476505 0.995557931 0.840159073 1.009893961 0.952019398 1.030228608 1 19.64727351 2.980406453 24.97080606 0.961375483 1.006637522 0.127980276 0.052062729 1362.164052 1735999.043 0.014623658 0.015737814 955.8867742 -2.980406453 0.045262038 KTSS(ph)DDES(ph)EEDEDDLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KTSSDDESEEDEDDLLQR 18 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 KT(0.029)S(0.152)S(0.819)DDES(1)EEDEDDLLQR;KT(0.029)S(0.152)S(0.819)DDES(1)EEDEDDLLQR;KT(0.059)S(0.301)S(0.641)DDES(1)EEDEDDLLQR;KT(0.05)S(0.277)S(0.673)DDES(1)EEDEDDLLQR 283.08 6.96E-39 1884840000 3201680 2679800 2818650 3233360 1645420 3200230 3197590 3940010 1974770 TRUE FALSE 3050342.932 2952874.667 2947887.891 2908336.51 1932380.727 3089405.233 2709738.918 3595001.837 2281007.246 1.337278931 1.294548569 1.292362353 1.275022916 0.847161152 1.354403954 1.187957172 1.576058929 1 21.1212396 2.98485768 24.85085161 1.201021347 1.306134945 0.072225283 0.1918537 1872.486741 3073041.523 0.053770164 0.058823369 965.734352 -2.98485768 0.105113599 KTSYAQHQQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KTSYAQHQQVR 11 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;; 178.71 4.82E-06 1353530000 2086380 1243180 756823 960269 2165620 1170160 2521830 1676750 2397530 FALSE TRUE 1987760.952 1369861.455 791524.0832 863740.9357 2543303.442 1129637.066 2137078.517 1529924.881 2769326.708 0.717777699 0.494655055 0.285818239 0.311895644 0.918383315 0.407910364 0.771696063 0.552453734 1 21.40110383 0.366529834 0.496149452 1.026473072 0.516310004 0.345484015 0.197485639 2.750705435 1.114441585 0.367261205 0.098661603 2.325572236 -0.366529834 -0.510163068 KTTHFVEGGDAGNREDQINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KTTHFVEGGDAGNREDQINR 20 2 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;; 163.85 1.14E-11 1498790000 812490 617730 834110 762420 771020 815430 985930 822250 895140 FALSE TRUE 774085.2079 680677.3893 872354.7685 685780.0931 905485.6439 787191.4546 835508.2707 750249.431 1033953.739 0.748665224 0.658324801 0.843707736 0.663259938 0.875750635 0.761341078 0.808071231 0.725612184 1 19.97974021 -4.999999999 0.172326352 1.952469285 0.700561608 0.530259253 0.070293473 92.53196504 0.877273891 30.16373739 0.216293317 1.00E-05 4.999999999 -1.251907677 KTTPGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTTPGFR 7 1 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 113.5 0.0098046 1394670000 1258780 1002460 1015500 1292110 1168340 1099930 1315090 1203740 1198340 FALSE TRUE 1199279.964 1104611.814 1062061.679 1162224.648 1372098.126 1061839.148 1114448.867 1098334.144 1384172.447 0.866423809 0.798030488 0.767290002 0.839653073 0.991276867 0.767129234 0.8051373 0.793495165 1 20.40059226 -2.193262787 2.259011662 1.472685711 0.827055664 0.405434902 0.065225631 4312875.703 861583.9239 10428489.52 0.016453766 0.006408217 2.193262787 -0.645630048 KTTPS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTTPSPGR 8 1 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KT(0.001)T(0.033)PS(0.966)PGR;KT(0.018)T(0.093)PS(0.888)PGR 66.056 0.038388 147847000 398820 373830 346400 433760 330800 400230 432450 418490 356750 TRUE FALSE 379968.569 411923.702 362282.7826 390157.6207 388491.4153 386369.9347 366471.81 381844.797 412072.968 0.9220905 0.999637768 0.879171435 0.946816829 0.942773357 0.937625044 0.889337177 0.926643645 1 18.6525403 3.747272869 24.9774815 0.926402813 0.960864128 0.079947394 0.037769366 1142.263059 3274788.902 0.008945395 0.015817135 5588.211947 -3.747272869 0.034461315 KTTT(ph)TPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KT(0.06)T(0.06)T(0.44)T(0.44)PGR 79.974 0.015617 343640000 484570 591540 426880 625750 353040 551260 513480 567790 436520 TRUE FALSE 461665.3364 651818.5985 446452.8702 562848.4212 414610.0642 532169.728 435139.1953 518071.2976 504213.2922 0.915615164 1.292743783 0.885444468 1.116290328 0.822291024 1.055445654 0.863006196 1.027484411 1 18.94367463 3.701420732 24.99985601 0.961121217 1.104179779 0.16683278 0.126767762 768.0513834 516996.1208 0.030487176 0.047232012 5028.294798 -3.701420732 0.143058562 KTTTT(ph)PGRKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTTTTPGRKPR 11 3 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KT(0.002)T(0.037)T(0.17)T(0.791)PGRKPR 68.972 0.057367 759140000 160890 145930 158690 174220 126800 197430 221730 193100 163510 TRUE FALSE 153285.0486 160800.4329 165966.0935 156707.0746 148913.8799 190592.9496 187901.0161 176191.1403 188866.2957 0.811606158 0.851398246 0.878749132 0.829724933 0.788461908 1.009142202 0.994889085 0.932888209 1 17.52700574 2.233207475 24.99999022 0.985896615 0.834804644 0.85753839 0.030818696 45.85142604 214130.8815 0.011177589 0.008495711 171.0832435 -2.233207475 -0.151091972 KTTTTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ;;;;;; 129.38 0.0017527 3483743000 3365016 2888689 2662291 3317360 2731213 2750557 3156477 3096933 2887802 FALSE TRUE 3205958.362 3183049.693 2784359.676 2983892.67 3207535.682 2655304.521 2674898.461 2825749.129 3335627.585 0.961125989 0.954258115 0.834733376 0.894552103 0.96159886 0.796043459 0.801917598 0.847141672 1 21.66952679 2.240599119 24.99806818 0.838437422 0.924232598 0.122864543 0.068198342 69.67948504 854491.1002 0.023124948 0.018452869 174.0199819 -2.240599119 0.085795176 KTVEDEDQDS(ph)EEEKDNDSYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 241.69 2.69E-30 306610000 795750 859480 670460 935460 316220 945210 796970 1083380 318510 TRUE FALSE 758136.4745 947061.9891 701201.2542 841425.7835 371368.6679 912477.1407 675377.5891 988513.5038 367902.9041 2.060697173 2.574217215 1.905941069 2.28708655 1.009420322 2.480211846 1.835749546 2.686886928 1 18.48896554 3.713272983 23.74817586 1.931618681 2.317457209 0.087686017 0.563501641 892.3385957 838014.6839 0.133259941 0.206565083 5167.410735 -3.713272983 0.385838529 KTVEDLDGLIQQIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTVEDLDGLIQQIYR 15 1 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 92.575 0.008321 139913000 208077 137605 176643 178417 206610 177146 228860 188499 225000 FALSE TRUE 198241.6126 151627.1059 184742.2563 160482.1842 242642.7186 171011.3896 193943.2037 171993.0283 259891.8509 0.762785027 0.583423857 0.71084282 0.617496023 0.933629576 0.658009818 0.746245806 0.661786923 1 17.98755187 -5 0.280901538 3.157627106 0.686545646 0.461966979 0.097446187 194.6087666 1.860398037 245.0213181 0.100921647 1.00E-05 5 -2.47108146 KTVGVEPAADGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KTVGVEPAADGK 12 1 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 121.76 0.00059414 197400000 648200 578660 565510 703300 459030 663980 729780 729800 508590 FALSE TRUE 617560.8706 637626.1119 591439.1929 632602.9478 539084.6867 640986.2061 618438.6577 665894.8431 587459.5397 1.051239837 1.085395791 1.006774344 1.076845136 0.917654154 1.091115494 1.052734045 1.133516094 1 19.16412997 -0.852887791 7.269801361 0.99999999 1.052063159 0.073924479 0.057737781 0 5.20E-11 0.050692477 0.011948331 0.14031762 0.852887791 0.052063169 KTVT(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KTVTPAK 7 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KT(0.147)VT(0.853)PAK;KT(0.002)VT(0.998)PAK;KT(0.012)VT(0.988)PAK;KT(0.002)VT(0.998)PAK;KTVT(1)PAK 96.143 0.0075877 2947400000 12076410 12422830 11848190 15027840 7001180 13832110 14749000 15254620 10031680 TRUE FALSE 11505582.03 13688730.5 12391441.23 13517212.97 8222183.575 13353100.56 12498769.17 13918844.6 11587341.7 0.992944053 1.181352104 1.069394651 1.166549958 0.709583249 1.152386881 1.078657167 1.201211198 1 23.46604629 -0.645557451 7.241925507 1 1.071025925 0.022600975 0.142073143 0 0 0.125627695 0.029610732 0.226173932 0.645557451 0.071025925 KTYVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KTYVTPR 7 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 138.1 0.0045197 4190200000 3331500 3146300 2922900 3370600 3399500 3133200 4080800 3422400 3674700 FALSE TRUE 3174026.597 3466911.547 3056917.856 3031780.884 3992371.724 3024696.498 3458199.011 3122716.513 4244553.708 0.747788063 0.816790595 0.720197709 0.714275538 0.940586926 0.712606485 0.814737956 0.735699611 1 22.01718144 -1.690659588 2.835805111 1.029326448 0.778744759 0.506032934 0.069686117 19602835.76 18715894.15 4146791.017 0.016057917 0.020386394 1.690659588 -0.250581689 KVACIGAWHPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVACIGAWHPAR 12 1 P39023;H7C422;G5E9G0;B5MCW2;Q92901 P39023;Q92901 RPL3;RPL3L 60S ribosomal protein L3;60S ribosomal protein L3-like 0 ; 122.42 0.00023292 2497300000 3347000 2211000 2216400 2496200 3628900 2478700 4245200 3044000 4039000 FALSE TRUE 3188793.943 2436303.414 2318024.132 2245277.234 4261779.011 2392861.997 3597516.772 2777451.223 4665347.492 0.683506202 0.522212636 0.496859909 0.48126688 0.913496587 0.512901129 0.77111443 0.595336409 1 22.15355311 -1.503658817 0.255270645 1.32450632 0.559660818 0.445837428 0.134997207 19.50388495 0.934383771 4.248856104 0.191574024 0.031357482 1.503658817 -0.764845502 KVAECQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVAECQR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 93.162 0.024272 483899000 388450 320064 234801 275919 385952 293149 415188 315753 410240 FALSE TRUE 370088.7383 352678.8855 245566.8581 248183.0979 453261.9066 282997.1766 351843.4451 288103.9934 473857.924 0.781012028 0.744271368 0.518228873 0.523750022 0.956535459 0.597219467 0.742508308 0.607996572 1 18.85409504 -1.187291878 3.810579015 1.000242075 0.693333855 0.358076637 0.132462222 5303037750 11326779073 16616063.89 0.030018263 0.06496929 1.187291878 -0.306908221 KVAGAAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVAGAATPK 9 1 P16402 P16402 HIST1H1D Histone H1.3 1 KVAGAAT(1)PK;KVAGAAT(1)PK 71.513 0.028929 713910000 1661340 1756940 1653750 2281100 986720 2098200 1928140 2115500 1170770 TRUE FALSE 1582811.751 1935974.183 1729576.073 2051799.494 1158803.656 2025538.808 1633966.83 1930255.605 1352327.032 1.170435637 1.431587284 1.278962878 1.517236175 0.856896023 1.497817288 1.208263084 1.427358589 1 20.36701265 KVAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVATPK 6 1 P07305-2;P07305 P07305-2 H1F0 "Histone H1.0;Histone H1.0, N-terminally processed" 1 KVAT(1)PK 56.563 0.088397 137940000 369050 396950 334960 443400 229330 444620 396470 507690 319260 TRUE FALSE 351605.7379 437399.6563 350318.2473 398828.5896 269325.0794 429222.6979 335981.2198 463233.9722 368769.2102 0.953457415 1.186106769 0.949966097 1.081512714 0.730335049 1.163933121 0.911088048 1.256162281 1 18.49235868 -0.323405436 7.338913817 1.000001245 1.026343147 0.003246462 0.153610708 0 0 0.130008444 0.030643284 0.474891684 0.323405436 0.026341902 KVCGDSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVCGDSDK 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 98.044 0.01251 278900000 684920 876110 575490 845500 360190 677100 621440 880400 514470 FALSE TRUE 652545.189 965386.6051 601876.7857 760508.7337 423007.022 653651.8572 526627.9145 803307.5087 594251.3801 1.098096211 1.624542471 1.012831953 1.279776134 0.711831787 1.099958501 0.88620394 1.351797464 1 19.18071382 3.705155249 24.68485608 1.034009751 1.361319388 0.258260477 0.218978085 563.2923111 416244.0732 0.053462146 0.082828841 5071.719764 -3.705155249 0.327309636 KVDEAIALFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVDEAIALFQK 11 1 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 110.29 0.0018497 0 995210 769830 745980 895740 696990 873880 1089300 920060 759720 FALSE TRUE 948168.3956 848276.5522 780183.9209 805698.5134 818544.8353 843617.3165 923107.2786 839494.6689 877533.4975 1.080492538 0.966660025 0.889064546 0.918139895 0.932779019 0.961350557 1.05193395 0.956652562 1 19.74309467 1.794041919 25 1.008431404 0.963323374 0.122519268 0.054647482 377.9533291 170350.6168 0.026896096 0.015625128 62.23603537 -1.794041919 -0.04510803 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_SK-BR-3_Trastuzumab_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 352.25 3.84E-132 2441800000 1046040 961470 1046540 1124060 716730 1168480 1338060 1237340 810170 TRUE FALSE 996595.7623 1059444.886 1094524.894 1011067.353 841727.4851 1128015.245 1133914.372 1128991.95 935807.0258 1.064958624 1.13211897 1.16960534 1.080422913 0.899466943 1.205393007 1.211696793 1.206436711 1 19.83585153 KVDHPLSEQVHQPLLEEQCS(ph)IDEPLFEDQCSFDQPQPEEQCIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVDHPLSEQVHQPLLEEQCSIDEPLFEDQCSFDQPQPEEQCIK 43 1 F8VNY5;Q9P031 F8VNY5 CCDC59 Thyroid transcription factor 1-associated protein 26 1 KVDHPLS(0.167)EQVHQPLLEEQCS(0.833)IDEPLFEDQCSFDQPQPEEQCIK 103.53 2.09E-06 71882000 57032 42112 53317 55295 34181 52238 56737 51464 22026 TRUE FALSE 54336.21039 46403.26068 55761.63719 49736.64155 40142.15558 50428.98496 48080.7286 46957.53933 25441.67959 2.135716323 1.823907125 2.191743552 1.954927597 1.577810751 1.982140558 1.889840977 1.84569337 1 14.6349063 -2.030038323 0.306009113 1.88E-14 2.00748757 0.775784779 0.159324141 15.61340252 0.714636461 11.26511065 0.153409696 0.00933172 2.030038323 2.00748757 KVDIIADAAYSIFQKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVDIIADAAYSIFQKPK 17 2 Q6YN16-2;Q6YN16 Q6YN16-2 HSDL2 Hydroxysteroid dehydrogenase-like protein 2 0 ; 205.06 4.62E-12 174496000 485530 359320 396890 449090 304740 403170 519370 500730 378690 FALSE TRUE 462579.9591 395935.1165 415087.7991 403946.62 357886.5595 389208.1218 440130.5676 456883.4267 437415.3111 1.057530332 0.90516977 0.948955806 0.923485323 0.818184802 0.889790805 1.006207502 1.044507165 1 18.7386442 1.61101591 5.709919546 1.022855725 0.929086136 0.347798366 0.059985847 0.1765541 12.25111805 0.034787038 0.016479751 40.83343453 -1.61101591 -0.093769589 KVDLTLLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVDLTLLSPK 10 1 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 KVDLTLLS(1)PK;KVDLT(0.001)LLS(0.999)PK 115.91 0.00071069 1232220000 6176200 5293500 4992300 6487300 3667300 6464600 6914100 7201700 3933600 TRUE FALSE 5884263.266 5832913.668 5221201.893 5835184.279 4306875.959 6240729.281 5859227.059 6571080.969 4543602.598 1.295065565 1.283764049 1.149132606 1.284263787 0.947898912 1.373520053 1.289555354 1.446227047 1 22.11540523 KVDNDYNALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVDNDYNALR 10 1 O94763-3;O94763;O94763-4 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 0 105.2 0.0041372 313800000 277100 231560 179850 232270 250020 219280 290190 254610 271220 FALSE TRUE 264002.0322 255156.2273 188096.3004 208921.7783 293623.4088 211686.2786 245916.1858 232314.9986 313279.4124 0.842704697 0.814468545 0.600410665 0.666886396 0.937257276 0.675710788 0.784973976 0.74155846 1 18.25709044 -1.616725824 2.572257642 1.02435906 0.763924522 0.382231139 0.096426957 11846914.49 10326309.99 1933171.96 0.02290779 0.024169862 1.616725824 -0.260434539 KVDQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVDQYK 6 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 85.265 0.088045 873010000 2975400 2310900 2527600 2748600 1979300 2760700 3144000 2820500 2414800 FALSE TRUE 2834758.739 2546383.337 2643492.96 2472305.506 2324489.293 2665096.267 2664325.056 2573522.068 2789274.851 1.016306707 0.912919477 0.947734842 0.88636138 0.833366885 0.955479976 0.955203484 0.922649149 1 21.41145867 -0.474864968 7.99402771 1 0.93194799 0.176263047 0.047964242 0 0 0.047053918 0.011090715 0.335069603 0.474864968 -0.06805201 KVDSSVLGSLSSVPLTGFSFS(ph)PGNSSLFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVDSSVLGSLSSVPLTGFSFSPGNSSLFGK 30 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 KVDSSVLGSLSSVPLTGFS(0.007)FS(0.98)PGNS(0.01)S(0.003)LFGK;KVDSSVLGSLSSVPLTGFS(0.047)FS(0.953)PGNSSLFGK 244.25 5.56E-46 245960000 330230 378190 369610 452640 288268 406130 462250 483360 417860 TRUE FALSE 314620.6824 416727.991 386556.9841 407139.7672 338541.8479 392065.6163 391725.2727 441034.4359 482659.5947 0.651847981 0.863399372 0.800889464 0.843533977 0.701409133 0.812302543 0.811597401 0.913758767 1 18.88064653 -5 0.112551535 1.697872315 0.676464764 0.574714715 0.063904819 123.0018008 0.914730637 19.47433782 0.723129232 1.00E-05 5 -1.021407551 KVDTT(ph)PNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.089)T(0.911)PNQGK;KVDT(0.095)T(0.905)PNQGK;KVDT(0.175)T(0.825)PNQGK;KVDT(0.471)T(0.529)PNQGK 147.73 1.55E-05 1431590000 3340690 3890860 3635210 4250150 2146540 4225320 4468900 4431900 2975540 TRUE FALSE 3182782.204 4287343.058 3801887.974 3822916.847 2520895.896 4078996.109 3787087.228 4043819.341 3436971.546 0.92604264 1.247418839 1.106173829 1.11229226 0.73346429 1.186799499 1.101867495 1.176564684 1 21.71270648 -0.456353457 7.163049731 0.999993599 1.079250299 0.023130068 0.147077574 0 0 0.133310333 0.031421547 0.349660475 0.456353457 0.0792567 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR 35 2 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ; 195.66 1.31E-27 387850000 50287 47754 44002 52567 33264 52279 60393 57752 39848 FALSE TRUE 47910.03317 52620.18689 46019.53522 47282.86529 39065.23107 50468.56512 51178.93866 52694.92872 46027.42432 1.040901894 1.143235531 0.9998286 1.027275933 0.848738152 1.096489014 1.111922716 1.144859385 1 15.49020609 -0.611670137 7.675291344 0.999991709 1.056990196 0.030782655 0.086612241 0 0 0.083994579 0.019797712 0.244528713 0.611670137 0.056998487 KVDWLTEK ddPTM_SK-BR-3_Trastuzumab_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 ; 152.97 0.00071916 2818900000 10744900 11643600 9142000 10304400 7175600 10704500 11569300 11717100 7790200 FALSE TRUE 10237009.87 12830096.08 9561169.743 9268582.135 8427022.368 10333800.48 9804190.8 10691088.61 8998264.429 1.13766493 1.425841192 1.062557098 1.030041094 0.936516418 1.148421516 1.089564646 1.188127854 1 23.10121533 3.710997076 24.31916578 1.068414864 1.281753058 0.458227003 0.097915508 389.4794286 343635.5168 0.025151593 0.038975348 5140.401901 -3.710997076 0.213338194 KVEAPETNIDKT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVEAPETNIDKTPK 14 2 O75152;E9PBY7;E9PQ61 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 KVEAPET(0.012)NIDKT(0.988)PK;KVEAPETNIDKT(1)PK;KVEAPETNIDKT(1)PK;KVEAPETNIDKT(1)PK 217.26 2.77E-10 458750000 1867640 1950980 1747520 2241670 816547 2379210 2170190 2598590 948725 TRUE FALSE 1779360.359 2149787.08 1827645.521 2016333.073 958952.5383 2296817.361 1839087.657 2371043.684 1095848.428 1.623728532 1.961755865 1.66779043 1.839974418 0.875077715 2.095926137 1.67823178 2.163660251 1 20.06361683 KVEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVEDAK 6 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 94.662 0.070915 204660000 330390 296480 309170 369780 190920 318550 375880 465590 264420 FALSE TRUE 314773.1195 326691.6491 323345.7503 332609.0119 224216.3876 307518.5336 318532.6025 424820.4714 305424.9031 1.03060725 1.069630033 1.058675134 1.089004231 0.734112986 1.006854813 1.042916276 1.390916284 1 18.22045817 -1.015450136 5.381902887 0.999999785 1.042711691 0.007459515 0.156714284 3.76E-07 6.90E-08 0.14152199 0.033356885 0.096505011 1.015450136 0.042711906 KVEDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVEDLAR 7 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 77.732 0.059727 103510000 423540 355380 300590 368120 384760 334890 415230 414040 404450 FALSE TRUE 403520.1036 391593.626 314372.3488 331115.8782 451862.0222 323292.6753 351879.0373 377784.4626 467170.0404 0.863754241 0.838225041 0.672929173 0.708769505 0.967232449 0.692023562 0.753214048 0.80866586 1 18.83358823 -1.283822308 7.201064142 1.000001465 0.789628523 0.360487426 0.088676365 2.02E-06 2.01E-07 0.08336529 0.01964925 0.05202088 1.283822308 -0.210372942 KVEDMMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVEDMMK 7 1 P13639 P13639 EEF2 Elongation factor 2 0 ;; 111.17 0.010646 1795680000 7075600 5535200 3716980 4737990 4474650 5194170 7862700 6733100 4734860 FALSE TRUE 6741150.41 6099243.173 3887407.21 4261718.244 5255027.543 5014294.59 6663100.707 6143514.07 5469117.906 1.232584582 1.115215155 0.710792357 0.779233199 0.960854681 0.916837903 1.218313597 1.12330986 1 22.38287673 -0.673266858 8.217758227 1.00000001 1.023726659 0 0.174118634 0 0 0.182714231 0.043066157 0.212194021 0.673266858 0.023726648 KVEEAEPEEFVVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KVEEAEPEEFVVEK 14 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;;;;; 216.71 9.67E-12 5842600000 10572180 9380050 8465430 11072650 5867100 10505480 10920000 11774160 6992380 FALSE TRUE 10072454 10335887.76 8853578.339 9959606.185 6890320.382 10141672.59 9253953.44 10743152.13 8076722.578 1.247096691 1.279713109 1.096184529 1.23312471 0.853108463 1.255666825 1.145756011 1.330137568 1 22.94533856 3.745716689 24.48108709 1.137540682 1.263404911 0.143111728 0.134293428 744.2286395 2546011.864 0.031816134 0.055838005 5568.223889 -3.745716689 0.125864229 KVEEDEAGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVEEDEAGGR 10 1 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 0 ;; 158.3 1.29E-05 520430000 941920 801516 883810 1002520 902310 907180 1054170 992930 993940 FALSE TRUE 897397.3083 883191.3916 924333.5627 901744.7849 1059672.578 875764.1291 893337.0053 905983.7853 1148075.139 0.781653812 0.76928013 0.805115912 0.785440564 0.922999325 0.762810812 0.778117194 0.789132832 1 20.13078564 -1.426544223 2.73206826 1.005520381 0.796051796 0.656222873 0.045593544 6005540.912 6489417.08 256327.62 0.011579519 0.037450341 1.426544223 -0.209468586 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR 226.03 2.21E-25 8268577000 8022001 6836766 7374824 8421219 6061217 8039769 9133416 8496919 5829085 TRUE FALSE 7642816.911 7533440.228 7712966.975 7574702.067 7118291.326 7761349.784 7739945.643 7752883.727 6733029.731 1.135123001 1.118878206 1.145541797 1.125006478 1.057219649 1.152727686 1.14954871 1.151470295 1 22.6828244 -1.178581996 3.613134846 0.999867774 1.129559981 0.678071735 0.028029108 872322.5752 427247.8193 899.6292263 0.006441927 0.066285419 1.178581996 0.129692207 KVEEEQEADEEDVS(ph)EEEAESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KVEEEQEADEEDVSEEEAESK 21 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK 301.8 2.19E-55 1307300000 1175493 1097453 1014491 1671900 777655 1469060 1335430 1307630 594233 TRUE FALSE 1119929.775 1209284.708 1061006.416 1503837.436 913277.7858 1418186.084 1131685.627 1193126.985 686383.6187 1.631638263 1.761820468 1.545792159 2.190957643 1.330564659 2.066171227 1.648765495 1.738280099 1 19.3886556 0.073669324 1.723712121 0.999808046 1.740062065 0.475621481 0.243950568 22.554715 40.39614477 0.205305341 0.055523058 1.184866236 -0.073669324 0.740254019 KVEEVLEEEEEEYVVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVEEVLEEEEEEYVVEK 17 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;; 164.2 4.21E-09 87936000 305049 265605 267659 308969 186371 306948 337062 342041 221069 FALSE TRUE 290629.9383 292670.4515 279931.4299 277910.8491 218874.0434 296318.3138 285637.0013 312090.0768 255351.2515 1.138157486 1.146148491 1.096260262 1.088347316 0.857148896 1.160434155 1.118604274 1.222199128 1 17.9621236 3.611982485 3.260287793 1.079514127 1.142401076 0.073716847 0.096806526 0.717710833 14.25111803 0.026424442 0.04321811 4092.441543 -3.611982485 0.06288695 KVEEVVYDLSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVEEVVYDLSIR 12 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ; 228.07 1.83E-11 354870000 1301060 1158930 1144670 1359110 1134590 1236300 1522630 1395190 1303270 FALSE TRUE 1239561.472 1277026.285 1197154.252 1222489.681 1332462.137 1193486.621 1290324.828 1273019.767 1505374.455 0.823424011 0.848311382 0.795253465 0.81208345 0.885136673 0.792817107 0.857145426 0.845649906 1 20.52169097 -0.479892034 0.58044148 1.02258223 0.827661285 0.789779695 0.027428119 4.157482386 1.145922886 0.218435243 0.010288249 0.331213451 0.479892034 -0.194920945 KVEGAPTQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVEGAPTQGR 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 136.7 0.00017763 639810000 815430 698640 678820 864900 708420 734520 836940 741620 739890 FALSE TRUE 776886.2399 769832.2103 709944.5684 777958.6088 831968.2237 709083.3882 709249.4315 676679.8212 854628.3624 0.909034001 0.900780087 0.830705602 0.910288779 0.973485389 0.829697936 0.829892223 0.791782547 1 19.70493767 KVEGAQNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KVEGAQNQGK 10 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 164.65 9.77E-06 1593010000 4040900 3751450 3570370 4477360 2547340 4043960 4365170 4619150 3038370 FALSE TRUE 3849894.665 4133727.02 3734074.996 4027287.266 2991595.289 3903916.651 3699183.145 4214672.738 3509544.902 1.096978319 1.177852723 1.063976983 1.147524075 0.852416873 1.112371194 1.054034995 1.200917172 1 21.74285253 KVEGNFNPFAS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVEGNFNPFASPQK 14 1 Q5TH58;Q9H6K1-2;Q9H6K1 Q5TH58 C6orf106 Uncharacterized protein C6orf106 1 KVEGNFNPFAS(1)PQK;KVEGNFNPFAS(1)PQK 149.34 4.60E-06 617520000 862550 931280 815540 1023570 537350 1029190 996260 1149730 698120 TRUE FALSE 821778.9709 1026178.491 852933.3157 920678.7989 631063.6699 993548.8922 844262.2394 1049053.546 806380.8841 1.019095302 1.272572938 1.057730078 1.141741846 0.782587586 1.232108687 1.046977001 1.300940494 1 19.62110191 -1.69091834 7.946679874 0.999624461 1.107356563 0.047961169 0.149402531 0.000896415 3.49E-05 0.130452272 0.030642151 0.020374251 1.69091834 0.107732102 KVELS(ph)ES(ph)EEDKGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 99.86 0.0012583 724650000 3174160 2551080 2655180 3096820 1216110 3276140 3250820 3109700 1257440 TRUE FALSE 3024123.747 2811037.952 2776922.629 2785521.77 1428199.199 3162686.45 2754847.704 2837398.182 1452437.373 2.08210268 1.93539357 1.911905243 1.917825733 0.983312069 2.177502802 1.896706705 1.953542531 1 20.47004453 2.976269748 24.95395587 1.697117593 1.97427027 0.153649714 0.387137558 1672.766247 1759027.853 0.111166521 0.118566338 946.8250691 -2.976269748 0.277152678 KVELS(ph)ESEEDKGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.927)ES(0.073)EEDKGGK;KVELS(0.997)ES(0.003)EEDKGGK;KVELS(0.991)ES(0.009)EEDKGGK;KVELS(0.5)ES(0.5)EEDKGGK 191.21 2.68E-07 3352610000 1738800 1579220 1529020 1833710 727177 1947910 1823790 2028610 810375 TRUE FALSE 1656610.37 1740144.313 1599127.079 1649381.987 853996.4386 1880453.388 1545537.339 1850974.154 936043.8162 1.769800026 1.859041514 1.708389129 1.762077756 0.912346649 2.008937355 1.651137813 1.977443921 1 19.83621654 2.965041771 24.9411237 1.573263678 1.787430742 0.106790907 0.355335004 1534.670715 1094918.535 0.100451597 0.106591923 922.6601655 -2.965041771 0.214167064 KVELSES(ph)EEDKGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.094)ES(0.906)EEDKGGK 171.35 1.58E-06 205420000 420340 385400 353480 411230 155510 464650 424570 466710 140700 TRUE FALSE 400471.3612 424672.6982 369687.4076 369892.3791 182630.8948 448559.054 359794.0487 425842.3982 162519.0374 2.464150463 2.613064321 2.274732939 2.275994154 1.123750778 2.760040062 2.213857862 2.620261632 1 17.3102492 3.422385308 2.573809164 2.079591874 2.533276202 0.125841144 0.567657791 0.604914233 8.100997915 0.153589694 0.230300141 2644.754154 -3.422385308 0.453684328 KVELSSSSQHGPSYDVYNPFYMYQHIS(ph)PDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVELSSSSQHGPSYDVYNPFYMYQHISPDLSR 32 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 KVELSSSSQHGPSYDVYNPFYMY(0.001)QHIS(0.982)PDLS(0.018)R 129.09 3.76E-08 78925000 61434 44240 60437 72570 86516 61227 93486 77601 68794 TRUE FALSE 58530.13657 48748.1063 63208.09623 65275.12573 101604.363 59106.69364 79222.99371 70805.84505 79462.22217 0.73657815 0.613475246 0.795448384 0.821461116 1.278649907 0.743833888 0.996989406 0.891062987 1 16.27798152 3.227027153 2.575759647 0.966683304 0.682864546 0.428164323 0.139811982 0.228869108 3.109211807 0.038663756 0.051360854 1686.658477 -3.227027153 -0.283818758 KVENTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVENTR 6 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 100.45 0.060363 255662000 403810 373850 321060 436960 313650 334290 394900 454220 428160 FALSE TRUE 384722.7016 411945.74 335780.9186 393035.9506 368350.4607 322713.4535 334650.7522 414446.0888 494556.8661 0.777913983 0.832959298 0.678953102 0.794723474 0.744809113 0.652530529 0.676667892 0.838015034 1 18.91577689 0.960095757 5.650645724 0.999939783 0.742422867 0.692056894 0.056441887 0.153512845 17.48817944 0.060622306 0.015268071 9.122119486 -0.960095757 -0.257516916 KVEQNSRPVS(ph)CSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 KVEQNSRPVS(0.988)CS(0.012)GR;KVEQNS(0.013)RPVS(0.981)CS(0.005)GR;KVEQNSRPVS(0.957)CS(0.043)GR;KVEQNSRPVS(1)CSGR;KVEQNSRPVS(1)CSGR;KVEQNSRPVS(0.999)CS(0.001)GR;KVEQNSRPVS(1)CSGR;KVEQNSRPVS(1)CSGR;KVEQNSRPVS(0.998)CS(0.002)GR;KVEQNS(0.012)RPVS(0.969)CS(0.02)GR;KVEQNS(0.01)RPVS(0.965)CS(0.025)GR 238.45 1.31E-17 12270280000 4603960 3686450 4267680 4368490 3935950 4094210 5138360 4752180 4596480 TRUE FALSE 4386339.935 4062103.446 4463357.349 3929361.086 4622378.434 3952426.481 4354408.81 4336053.926 5309278.643 0.826164952 0.76509517 0.840671144 0.740093212 0.870622686 0.744437568 0.82015074 0.816693607 1 22.34008443 0.371003903 1.415057536 1.000062129 0.798425511 0.690713885 0.041589995 1.996606302 3.990925072 0.033482102 0.009750208 2.349653937 -0.371003903 -0.201636618 KVEQNSRPVSCSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 ;;; 166.92 2.10E-06 543410000 347878 305639 311848 339517 313146 322604 385690 345435 352854 FALSE TRUE 331434.4964 336783.9616 326146.5393 305388.1061 367758.5633 311432.1426 326845.9068 315186.8801 407572.7962 0.813190918 0.826316096 0.800216654 0.749284812 0.902313812 0.764114155 0.801932587 0.773326589 1 18.63669824 -2.150510745 2.402959946 1.447189267 0.805562082 0.683661626 0.041920245 2907923.169 818886.2025 7077342.618 0.009313898 0.007071137 2.150510745 -0.641627185 KVESLWPIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVESLWPIFR 10 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 130.01 0.0004619 131680000 492070 489890 425210 523680 455370 493260 567200 523860 473320 FALSE TRUE 468810.8263 539810.348 444706.2991 471038.6915 534786.3838 476178.2825 480663.2227 477988.0412 546720.0482 0.857497046 0.987361539 0.813407704 0.861572011 0.978172258 0.870972784 0.879176142 0.874282995 1 19.06044275 -2.044202038 2.60754033 1.137566455 0.894498823 0.28993164 0.053593887 10108565.36 3273206.658 8320536.596 0.012397445 0.009032292 2.044202038 -0.243067632 KVEWTSDTVDNEHMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVEWTSDTVDNEHMGR 16 1 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 ; 128.26 4.01E-05 138897000 144463 137005 141140 158089 157502 127778 165775 149529 159557 FALSE TRUE 137634.5203 150965.9653 147611.4086 142197.5934 184970.2989 123353.0158 140482.9791 136435.4481 184300.2847 0.746794941 0.819130397 0.800928815 0.771553846 1.003635449 0.669304532 0.762250473 0.740288862 1 17.49169877 4.615655556 2.903798522 0.806181793 0.743743921 0.029417166 0.106970139 1.386421585 19.09521401 0.024087785 0.175548105 41272.00389 -4.615655556 -0.062437872 KVFASLPQVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVFASLPQVER 11 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 86.803 0.022765 262660000 551850 495840 579730 518620 368080 629000 513110 496000 297080 FALSE TRUE 525765.1442 546366.6597 606311.1939 466487.3323 432273.0355 607217.5723 434825.6456 452567.6105 343149.6491 1.532174506 1.59221104 1.76690023 1.359428265 1.25972163 1.76954158 1.267160397 1.318863684 1 18.38847835 0.764281771 0.419845821 0.956571063 1.593455165 0.522095315 0.166693231 1.260977281 0.51793615 0.265232136 0.112989476 5.811413407 -0.764281771 0.636884102 KVFIEDVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KVFIEDVSR 9 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;;; 177.57 8.33E-05 5017640000 13442800 10350050 8045910 9294050 13081020 9395740 14378480 11234370 13525970 FALSE TRUE 12807385.49 11404731.86 8414822.932 8359794.436 15362345.75 9070363.168 12184778.8 10250629.01 15623508.35 0.819750929 0.729972527 0.538600086 0.535077926 0.983283998 0.580558666 0.779900297 0.656102892 1 23.89721512 -1.171377389 3.262075919 1.000570968 0.710464225 0.312371155 0.1381241 20644158.17 30820216.84 122675.8298 0.032071032 0.067394214 1.171377389 -0.290106743 KVFSDVMEDLYNYINPHNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVFSDVMEDLYNYINPHNGK 20 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 159.06 1.69E-11 228130000 340660 353490 338580 389050 299960 373700 442710 420440 317580 FALSE TRUE 324557.6769 389511.0329 354104.2279 349941.9549 352272.929 360758.6753 375166.4586 383624.0447 366828.6844 0.884766352 1.061833628 0.965312264 0.953965624 0.960320019 0.983452741 1.022729341 1.045785297 1 18.48474693 1.790114694 3.316249155 1.026519137 0.970709565 0.25954896 0.043723255 0.33944437 7.044296933 0.02334474 0.011736899 61.67578615 -1.790114694 -0.055809572 KVFVGR ddPTM_SK-BR-3_Trastuzumab_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 ; 136.58 0.021019 4008800000 5611800 4869300 4767700 5210800 5532900 5130200 5862500 5291300 5953000 FALSE TRUE 5346541.336 5365487.206 4986303.761 4687000.484 6497836.008 4952539.888 4968067.953 4827965.721 6876160.836 0.777547452 0.780302749 0.725158105 0.681630432 0.944980224 0.720247825 0.722506071 0.702131005 1 22.71317186 -1.183615911 5.150937454 1.000015072 0.758275568 0.519717248 0.073457661 1.19E-05 1.88E-06 0.066454783 0.015662567 0.065521539 1.183615911 -0.241739505 KVGAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVGAER 6 1 P11142;E9PKE3;P11142-2;E9PN89;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 86.113 0.0865 409780000 422510 393810 347770 406790 306150 379330 416650 408800 405290 FALSE TRUE 402538.7896 433939.6867 363715.5985 365898.6963 359542.4631 366193.707 353082.3902 373003.3048 468140.3033 0.859867836 0.926943661 0.776937162 0.781600503 0.768022878 0.782230678 0.754223441 0.79677674 1 18.83658145 3.732087364 24.89800873 0.79184239 0.89340575 0.161570078 0.073033878 527.5471102 2029099.102 0.016733396 0.026631097 5396.191632 -3.732087364 0.10156336 KVGDDIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KVGDDIAK 8 1 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;;;; 107.21 0.0064904 8964240000 18678200 15709100 15911100 19961400 11862480 19327600 21743500 20432800 13869880 FALSE TRUE 17795318.5 17309875.15 16640639.67 17954842.15 13931292.76 18658280.37 18426129.73 18643595.71 16020750.15 1.11076687 1.080465957 1.038692915 1.120724184 0.869578055 1.164632129 1.150141507 1.163715527 1 23.93343837 KVGFNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVGFNPK 7 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 93.262 0.024154 266540000 478870 371090 401130 601070 570330 546470 786690 679350 678930 FALSE TRUE 456234.7641 408904.4929 419522.2073 540649.3016 669795.3714 527545.6069 666665.9919 619862.5125 784214.9969 0.581772557 0.521418864 0.534958154 0.689414642 0.854096611 0.672705328 0.85010615 0.790424201 1 19.58088971 2.272120339 0.340018039 0.998036891 0.467549276 0.77593406 0.073025549 0.679156164 0.195338082 0.091302314 0.128305014 187.120056 -2.272120339 -0.530487615 KVGIVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVGIVGK 7 1 Q6P4E4;E9PEL3;P61513;G5E9R3 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 102.71 0.033418 0 1260300 1075000 1169000 1356100 967260 1158900 1355100 1309700 1100700 FALSE TRUE 1200728.117 1184543.722 1222599.806 1219782.252 1135949.838 1118767.002 1148354.607 1195015.725 1271390.934 0.944420858 0.931691182 0.961623819 0.9594077 0.893470141 0.879955152 0.90322699 0.939927832 1 20.27797628 2.745096462 24.91571436 0.912652253 0.94649832 0.07874534 0.034186541 816.4157915 3112307.627 0.009678617 0.010057615 556.027744 -2.745096462 0.033846067 KVGLIAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVGLIAAR 8 1 P62917;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 141.39 0.0010171 1570030000 2763200 1675770 801130 1021380 2855900 1424190 3373300 2190300 3103200 FALSE TRUE 2632589.012 1846532.868 837862.6029 918708.9419 3353968.056 1374869.943 2858641.13 1998505.72 3584428.407 0.734451554 0.515154066 0.233750687 0.256305563 0.935705132 0.383567416 0.797516593 0.557552138 1 21.77331165 0.644303644 0.569508975 1.006388589 0.510281146 0.305662577 0.221835777 1.825003865 1.166061615 0.265680643 0.097321431 4.408629923 -0.644303644 -0.496107442 KVGTLWR ddPTM_SK-BR-3_Trastuzumab_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 ; 128.61 0.0059987 1581070000 1699710 1397620 1158220 1421160 1668290 1366230 1931570 1613480 1824990 FALSE TRUE 1619368.077 1540039.067 1211325.533 1278302.297 1959239.248 1318917.113 1636873.521 1472195.138 2108000.128 0.768201128 0.730568773 0.574632571 0.606405227 0.929430327 0.625672216 0.776505418 0.698384748 1 21.00744352 -3.939625213 0.377523405 2.564020127 0.710151212 0.4412738 0.101338539 223.8582049 3.734060616 278.7339338 0.064187213 0.000114914 3.939625213 -1.853868915 KVGWIFTDLVSEDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVGWIFTDLVSEDTR 15 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 148.03 5.78E-06 212640000 380460 285540 341190 357230 402990 331650 444340 385870 455520 FALSE TRUE 362476.4098 314636.8506 356833.899 321320.5617 473271.3284 320164.8773 376547.7721 352081.1772 526159.7151 0.688909469 0.597987344 0.678185518 0.610690162 0.899482258 0.60849371 0.715652988 0.669152668 1 19.00514127 -5 0.260808571 3.078204262 0.653305877 0.572440607 0.085863031 133.3332045 1.308369953 148.5433652 0.102618596 1.00E-05 5 -2.424898385 KVGYTPDWIFLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 232.37 1.38E-12 566330000 819550 616250 572270 575000 820720 621910 993360 793370 825670 FALSE TRUE 780811.4957 679046.5756 598509.1456 517199.9076 963853.3082 600373.1008 841804.6877 723898.3169 953710.6867 0.818708972 0.712004788 0.627558393 0.542302728 1.010634904 0.629512817 0.88266253 0.759033454 1 19.86319216 0.641011665 0.521492183 1.00729366 0.717725619 0.286328342 0.132356949 1.94889988 1.066308209 0.167884519 0.061802313 4.375338568 -0.641011665 -0.28956804 KVICIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVICIPK 7 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 92.925 0.04214 0 574240 445480 406100 484610 425550 415980 597590 520020 497020 FALSE TRUE 547096.8132 490874.9185 424720.0867 435896.0821 499765.7853 401574.5083 506416.67 474484.292 574095.3232 0.952972078 0.85504079 0.739807606 0.759274748 0.870527533 0.699490994 0.882112516 0.826490433 1 19.13093078 0.233265757 1.471707818 1.000055381 0.827934896 0.355011572 0.074622289 10.13711014 18.00741354 0.073858414 0.02111183 1.711062043 -0.233265757 -0.172120485 KVIDDTNITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVIDDTNITR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 171.09 6.62E-06 551590000 632220 287290 406090 615560 636320 575570 862780 661820 902180 FALSE TRUE 602336.2135 316565.1776 424709.6282 553682.7393 747294.0065 555637.8666 731147.065 603867.5323 1042085.467 0.578010377 0.303780436 0.407557385 0.531321813 0.717113932 0.533197981 0.701619098 0.579479852 1 19.99104217 0.338537698 0.251066278 1.150062294 0.377890316 0.683195145 0.10590886 2.785057957 0.364783125 0.642439444 0.211842662 2.180407655 -0.338537698 -0.772171977 KVIEINPYLLGTMAGGAADCSFWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVIEINPYLLGTMAGGAADCSFWER 25 1 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 133.15 0.00010154 95310000 128710 112050 128120 119300 116340 133150 140480 137800 118390 FALSE TRUE 122626.1334 123468.0224 133994.4287 107307.7373 136629.6592 128538.9821 119047.1959 125733.5015 136749.3165 0.896722093 0.902878534 0.979854467 0.784704012 0.999124987 0.939960691 0.870550573 0.919445191 1 17.0611741 KVIIWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVIIWR 6 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 119.7 0.033331 588590000 581070 577920 550220 606210 582380 551580 583960 614780 591290 FALSE TRUE 553603.9727 636810.705 575448.1312 545272.6191 683946.8876 532478.6463 494866.1768 560946.604 682984.2333 0.810566256 0.932394445 0.842549657 0.798367799 1.001409482 0.779635342 0.724564569 0.821317062 1 19.38149275 KVIQYLAYVASSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVIQYLAYVASSHK 14 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 128.96 4.59E-05 131500000 360670 277620 291440 336910 338000 318540 481890 413630 334100 FALSE TRUE 343621.8439 305909.7936 304802.8123 303043.1667 396947.093 307508.8799 408368.83 377410.3644 385910.5217 0.890418438 0.792696173 0.789827681 0.785267956 1.028598783 0.796839844 1.058195636 0.977973761 1 18.55790685 2.192616214 1.028703025 1.011249419 0.822333961 0.450550129 0.080120849 0.444749884 0.88963253 0.053806395 0.029203794 155.8174934 -2.192616214 -0.188915458 KVISSANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVISSANR 8 1 P62917;E9PKZ0;G3V1A1;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 97.431 0.015182 0 424270 336900 225090 215370 557080 304380 507570 367570 537890 FALSE TRUE 404215.5979 371230.493 235410.5991 193720.5984 654234.5756 293839.2443 430130.8743 335383.6222 621303.234 0.650593101 0.597502914 0.378898075 0.311797183 1.053003654 0.472940149 0.692304258 0.539806658 1 19.24493804 2.772224696 24.99982032 0.706352259 0.516053771 0.27814776 0.203873484 1092.355195 811209.5858 0.059052735 0.062631776 591.8677763 -2.772224696 -0.190298487 KVLVTVEEDDTIMEELVDNHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVLVTVEEDDTIMEELVDNHGK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 259.93 2.00E-37 99412000 165731 172785 127470 189318 109495 154441 161084 164308 99011 FALSE TRUE 157897.2241 190391.9879 133314.6256 170287.395 128590.8933 149092.6694 136507.6773 149920.3205 114365.1202 1.380641439 1.664773207 1.165693048 1.48898016 1.124389089 1.303655076 1.193612852 1.310891994 1 16.80328759 3.126221401 0.156736306 0.894819022 1.824282603 0.413035653 0.145610545 9.202170183 0.509034136 0.787209601 2.138106259 1337.277079 -3.126221401 0.929463581 KVMDS(ph)DEDDDY ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY 116.81 0.0064179 31320620000 32915970 29082960 28718080 32633670 21122250 32070940 34384320 33300920 22612560 TRUE FALSE 31360097.33 32046546.69 30034832.37 29353271.49 24805963.71 30960315.31 29138360.47 30384914.91 26119200.32 1.200653043 1.226934451 1.149913933 1.123819686 0.949721408 1.185346984 1.1155916 1.163317197 1 24.63860739 3.45390989 2.606109681 1.0966501 1.213248756 0.345913795 0.070439566 0.299015779 4.095683861 0.019413134 0.029679164 2843.870982 -3.45390989 0.116598656 KVMDSDEDDDY(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(0.012)DEDDDY(0.988) 107.15 0.0023458 110470000 413310 367110 349640 439760 288890 401030 432660 427330 319260 TRUE FALSE 393773.6554 404518.9264 365671.3398 395554.4893 339272.3245 387142.2305 366649.7707 389910.7198 368769.2102 1.067805132 1.096943332 0.991599433 1.072634261 0.920012613 1.049822544 0.994252667 1.057329921 1 18.49235868 3.741408487 24.96098831 1.011921795 1.082374235 0.311357946 0.043363465 238.1770391 2087564.654 0.009945232 0.017007712 5513.260161 -3.741408487 0.070452441 KVNAEGSVDSVFSQVCTHLDALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVNAEGSVDSVFSQVCTHLDALK 23 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 208.46 6.58E-25 275760000 323200 273230 289240 347170 260210 337700 375300 369940 259040 FALSE TRUE 307922.9765 301072.4476 302501.9401 312271.812 305590.5416 326005.3643 318041.0921 337546.0924 299210.6002 1.029117873 1.006222532 1.011000078 1.043652236 1.021322578 1.08955152 1.062933906 1.128122106 1 18.19080176 2.248872331 24.56503835 1.074566651 1.021159149 0.341059935 0.032802196 154.6989524 368531.1988 0.010107239 0.008364615 177.3668001 -2.248872331 -0.053407502 KVNEEKDGPIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVNEEKDGPISPK 13 2 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 KVNEEKDGPIS(1)PK;KVNEEKDGPIS(1)PK 97.214 0.0020251 473760000 1690780 1568800 1657640 1928940 764810 1754260 1727530 2130900 813330 TRUE FALSE 1610860.18 1728662.504 1733644.434 1735039.286 898192.6219 1693509.536 1463963.57 1944307.099 939457.0625 1.714671425 1.840065473 1.845368461 1.846853205 0.956076289 1.802647086 1.558308121 2.069607199 1 19.8414677 KVNELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KVNELR 6 1 P50502;Q3KNR6;Q8IZP2;F8WAQ7 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;;; 110.36 0.046126 2444030000 7383310 6621030 6588150 7745010 6264430 7068070 8021080 7608870 7821520 FALSE TRUE 7034315.569 7295720.484 6890223.194 6966466.88 7356944.609 6823300.964 6797316.929 6942597.006 9034441.375 0.778611015 0.807545279 0.762661786 0.771101011 0.814322026 0.75525433 0.752378221 0.768458914 1 23.10700397 -0.720075561 5.904685194 1.000000006 0.777021319 0.92279903 0.020333954 1.86E-09 3.67E-10 0.020753273 0.004891593 0.190512923 0.720075561 -0.222978687 KVNLGVGAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVNLGVGAYR 10 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 98.943 0.0080698 495040000 862800 669700 808390 946360 893990 984640 1182400 1171100 1020600 FALSE TRUE 822017.1539 737943.1914 845455.4811 851230.0948 1049901.573 950541.6699 1002003.164 1068552.276 1178869.435 0.697292787 0.625975336 0.717174825 0.722073259 0.890600385 0.806316324 0.849969584 0.906421223 1 20.16897251 2.280597594 0.382834859 0.997069964 0.61723409 0.846385564 0.044459615 0.463159691 0.159137146 0.049682313 0.062047744 190.8084458 -2.280597594 -0.379835875 KVNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(1)PATETVPAFSER;KVNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;KVNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER;KVNVTVDYIRPAS(0.976)PAT(0.024)ETVPAFSER 220.69 6.30E-34 3175560000 2084750 1696690 1908760 2120420 1881900 1912990 2268710 2058900 2097330 TRUE FALSE 1986207.999 1869584.64 1996278.534 1907271.353 2210102.764 1846742.677 1922576.622 1878611.801 2422573.225 0.819875321 0.771735038 0.824032278 0.787291519 0.912295547 0.762306236 0.793609292 0.775461308 1 21.20810884 -1.8255741 2.75991946 1.064656841 0.804052147 0.67179995 0.042636366 17593211.07 14962071.65 7617474.997 0.009772599 0.014942591 1.8255741 -0.260604694 KVNVTVDYIRPASPAT(ph)ETVPAFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(0.412)PAT(0.588)ETVPAFSER 204.99 2.12E-23 1339600000 972510 750420 873520 980260 860380 852460 953080 903250 884160 TRUE FALSE 926541.3796 826888.6512 913571.756 881722.4024 1010430 822939.0965 807670.1415 824156.6416 1021271.017 0.90724339 0.809666227 0.894543897 0.863357902 0.989384779 0.805798934 0.790848 0.80699112 1 19.96193434 -1.630149698 8.657987127 1.000091032 0.855002588 0.347012019 0.060844336 0.000106963 4.57E-06 0.058938684 0.01388331 0.023434209 1.630149698 -0.145088444 KVNVTVDYIRPASPATETVPAFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 229.77 1.74E-34 2353000000 534450 457150 465930 554040 489850 469410 553980 496590 560800 FALSE TRUE 509187.6077 503734.1047 487293.3514 498346.8466 575279.6849 453154.214 469460.1765 453105.947 647765.9998 0.786067203 0.777648263 0.752267565 0.76933159 0.888097994 0.699564679 0.724737292 0.699490166 1 19.30511322 -1.03644621 4.758090968 1.000005061 0.762988357 0.658525514 0.053823649 3.47E-06 7.03E-07 0.051373614 0.012108562 0.091950435 1.03644621 -0.237016704 KVPAPFKPVIRDELDVS(ph)NFAEEFTEMDPTYSPAALPQSSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVPAPFKPVIRDELDVSNFAEEFTEMDPTYSPAALPQSSEK 41 3 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 KVPAPFKPVIRDELDVS(0.5)NFAEEFT(0.5)EMDPTYSPAALPQSSEK 90.094 0.00017286 189160000 308010 180620 264670 297570 207380 317050 390170 342160 225560 TRUE FALSE 293450.9777 199025.3833 276805.3813 267657.6983 243547.0063 306070.479 330642.4005 312198.6565 260538.6928 1.126323981 0.763899524 1.062434828 1.027324177 0.934782484 1.17476017 1.269072156 1.19828135 1 17.99113812 2.20951324 8.196841862 1.192597177 0.97173915 0.34690336 0.116924701 0.194108431 46.32724736 0.041419859 0.030991468 161.999338 -2.20951324 -0.220858028 KVPDKLLDSSTVTHLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVPDKLLDSSTVTHLFK 17 2 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 124.25 3.06E-05 363650000 452400 176256 415990 319980 423770 402230 719710 466680 573010 FALSE TRUE 431015.9486 194216.6868 435063.553 287815.0025 497675.3538 388300.6742 609905.0211 425815.0252 661869.4643 0.651209901 0.293436542 0.657325313 0.43485161 0.751923726 0.586672592 0.921488381 0.643351972 1 19.33618719 1.878264143 0.552514153 0.958489797 0.468922753 0.489183988 0.147481661 0.58152034 0.381728735 0.127826553 0.083315263 75.55516227 -1.878264143 -0.489567044 KVPGVTAIELDEDTGTFR ddPTM_SK-BR-3_Trastuzumab_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 ;; 261.63 1.37E-30 600410000 893430 766330 800650 901950 786440 819940 979300 954240 956350 FALSE TRUE 851199.3345 844419.8982 837360.5945 811284.2724 923594.887 791545.2722 829889.7989 870681.6869 1104655.874 0.770556111 0.764418964 0.758028463 0.73442263 0.836092858 0.716553717 0.751265456 0.788192692 1 20.07516558 0.778819985 4.032655887 0.999995942 0.76146332 0.853529068 0.030791051 0.861656681 15.40397566 0.026847368 0.006856022 6.009246025 -0.778819985 -0.238532622 KVPLDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KVPLDER 7 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 98.392 0.018113 1618480000 6544000 5909200 5757200 6546700 5971760 6153400 7287900 6835400 6725800 FALSE TRUE 6234678.089 6511354.198 6021173.315 5888613.278 7013233.053 5940306.215 6175997.004 6236856.139 7768802.713 0.802527535 0.838141273 0.775045208 0.757982085 0.902743101 0.764635998 0.794974108 0.802807893 1 22.88926084 -1.773336552 2.450458043 1.054066737 0.805728057 0.68578327 0.041508535 8640801.613 5792746.672 2799678.307 0.009475706 0.016852466 1.773336552 -0.24833868 KVPLQEGPKS(ph)FDGNTLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVPLQEGPKSFDGNTLLNR 19 2 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KVPLQEGPKS(0.996)FDGNT(0.004)LLNR 152.07 3.10E-08 498110000 291770 119140 261950 325650 276280 445330 516740 289920 298200 TRUE FALSE 277978.6103 131280.5015 273960.6666 292915.0433 324463.1445 429908.1104 437901.8224 264533.0678 344443.333 0.807037279 0.38113817 0.795372244 0.850401257 0.941992814 1.248124348 1.271331974 0.768001707 1 18.39390713 2.997313162 1.517898703 1.109113604 0.604114129 0.485441561 0.182003142 0.264413646 1.249612547 0.066143506 0.078467356 993.8324253 -2.997313162 -0.504999475 KVPS(ph)PEAFLGKPWSSWIDAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVPSPEAFLGKPWSSWIDAAK 21 2 Q9ULK2;C9IZF2;Q9ULK2-2 Q9ULK2 ATXN7L1 Ataxin-7-like protein 1 1 KVPS(1)PEAFLGKPWSSWIDAAK 122.04 1.50E-05 50352000 162090 152150 144200 148220 94633 163220 181980 174070 106290 TRUE FALSE 154428.3269 167654.258 150811.7126 133320.644 111136.9652 157567.6505 154215.6087 158827.508 122772.9103 1.257837144 1.36556393 1.228379389 1.085912549 0.905223839 1.283407309 1.256104529 1.293668999 1 16.90563274 3.487631536 6.458037554 1.156309075 1.309964532 0.240648737 0.126159809 0.230352129 44.02290045 0.035391774 0.051650823 3073.488101 -3.487631536 0.153655457 KVQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVSRPDPEPVS(1)DNEEDS(0.243)Y(0.757)DEEIHDPR 143.72 1.06E-07 210280000 264590 221270 258160 283420 241340 260680 300150 289830 262310 TRUE FALSE 252083.3551 243817.6646 269996.8914 254930.0831 283429.6196 251652.5862 254356.6049 264450.9487 302987.6951 0.831992055 0.80471144 0.891115038 0.841387579 0.935449275 0.830570318 0.839494834 0.872810853 1 18.20889968 -5 0.227718193 1.787897307 0.833226511 0.609878165 0.036428502 107.3528183 1.073918793 38.97060495 0.063804304 1.00E-05 5 -0.954670796 KVQVAALQAS(ph)PPLDQDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR;KVQVAALQAS(1)PPLDQDDR 216.8 5.37E-19 4920600000 5109300 4757740 4994140 5583320 4666730 5184360 5685710 5482840 4964110 TRUE FALSE 4867793.515 5242559.115 5223126.259 5022074.066 5480606.234 5004824.313 4818250.514 5002733.463 5733918.826 0.848947057 0.914306476 0.91091737 0.875853708 0.955822083 0.872845338 0.840306719 0.872480692 1 22.45109005 -2.18661755 2.370473628 1.317897281 0.885218884 0.528254074 0.033709763 2237182.635 617666.8968 3817377.374 0.008441214 0.006507025 2.18661755 -0.432678398 KVQYAPERPGPQPTAETTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVQYAPERPGPQPTAETTR 19 2 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 215.62 2.26E-19 449785000 344768 275977 327657 369000 356115 360021 417716 402304 422841 FALSE TRUE 328471.4999 304099.3701 342680.3975 331907.4189 418221.3432 347553.3825 353985.7523 367076.129 488413.0227 0.672528136 0.622627481 0.701620108 0.679563 0.856286225 0.711597288 0.724767227 0.751569086 1 18.89774214 -5 0.141354092 2.02544492 0.601486451 0.758733835 0.053140759 64.94583974 0.560139145 18.70811396 0.312254093 1.00E-05 5 -1.423958469 KVS(ph)IVSKPVLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVSIVSKPVLYR 12 2 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KVS(1)IVSKPVLYR;KVS(1)IVSKPVLYR 127.88 0.00013666 1744100000 2116820 1795090 1800610 2234130 1573340 2264850 2833500 2496900 2084170 TRUE FALSE 2016762.114 1978011.712 1883169.75 2009551.008 1847729.998 2186417.677 2401197.534 2278258.199 2407372.439 0.837744123 0.821647569 0.782251105 0.834748697 0.767529763 0.908217458 0.997435002 0.946367152 1 21.19902792 2.026884156 4.232437582 0.97645119 0.813524805 0.899266814 0.026505839 0.057170791 2.345889487 0.01039861 0.006938186 106.3859206 -2.026884156 -0.162926385 KVS(ph)PIKINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVSPIKINLK 10 2 H0Y6F5;Q9H4I2;Q9H4I2-2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 KVS(1)PIKINLK;KVS(1)PIKINLK 130.2 0.00014764 596590000 1725920 1560130 1477600 1633210 984520 1784750 2163500 2114700 1158770 TRUE FALSE 1644339.182 1719109.021 1545349.422 1469036.628 1156219.976 1722943.66 1833418.34 1929525.657 1338466.133 1.228525056 1.284387388 1.154567443 1.097552333 0.863839545 1.287252338 1.369790609 1.44159468 1 20.3521492 2.027280275 24.99977422 1.315792891 1.150001635 0.150794538 0.158938482 344.7229102 315904.2351 0.058757031 0.043394072 106.4829992 -2.027280275 -0.165791256 KVS(ph)SAEGAAKEEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVSSAEGAAKEEPK 14 2 P05114;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 KVS(0.631)S(0.369)AEGAAKEEPK;KVS(0.5)S(0.5)AEGAAKEEPK;KVS(0.918)S(0.082)AEGAAKEEPK 172.84 1.46E-06 534910000 1243920 977080 1169120 1273890 560040 1367290 1349950 1410660 512980 TRUE FALSE 1185122.367 1076645.563 1222725.308 1145836.157 657710.7987 1319940.404 1143990.334 1287135.132 592530.3185 2.00010418 1.817030335 2.063565813 1.933801733 1.11000362 2.227633529 1.93068658 2.172268814 1 19.17652945 2.951070592 24.99734635 1.77668767 1.943175674 0.074009098 0.403445015 1451.589288 741595.5162 0.114549029 0.121499745 893.4506978 -2.951070592 0.166488003 KVSAQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVSAQEVR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 90.108 0.021534 411120000 1484490 1009890 675390 862410 1493410 922000 1520790 1264920 1452580 FALSE TRUE 1414321.1 1112798.939 706357.2996 775718.9083 1753860.231 890070.9088 1288765.554 1154156.899 1677838.688 0.842942239 0.663233568 0.420992378 0.462332234 1.045309209 0.530486581 0.768110524 0.687883113 1 20.67817259 -0.279605759 0.557076463 1.03595496 0.668154248 0.238740656 0.183303836 10.51718515 3.138655942 0.970052134 0.076630226 0.525284083 0.279605759 -0.367800712 KVSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVSPNELILGWYATGHDITEHSVLIHEYYSR 31 1 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 190 3.66E-19 113460000 194090 179620 211520 177360 188150 208770 243880 182180 39887 FALSE TRUE 184915.7503 197923.4822 221218.4012 159531.4358 220963.3004 201540.2426 206671.6268 166227.3534 46072.47225 4.01358428 4.29591625 4.801530945 3.462619392 4.795993999 4.374417797 4.485794158 3.607953845 1 15.49161739 3.236878035 24.99995974 3.943292966 4.303429333 0.044095165 1.082482779 205.6133633 3055039.412 0.273623849 0.343585126 1725.353284 -3.236878035 0.360136366 KVT(ph)SSPITSEEESNLSNDFIDENGLPINKNENVNGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTSSPITSEEESNLSNDFIDENGLPINKNENVNGESK 38 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 KVT(0.409)S(0.324)S(0.258)PIT(0.004)S(0.004)EEESNLSNDFIDENGLPINKNENVNGESK 114.71 0.00033771 70530000 52932 38012 48690 58113 30720 58038 65018 62180 37756 TRUE FALSE 50430.00926 41885.46602 50922.48466 52271.37083 36077.55827 56028.12951 55098.30996 56735.18956 43611.00765 1.156359644 0.960433346 1.1676521 1.198582047 0.827258076 1.284724489 1.263403735 1.300937369 1 15.4124047 KVTAAMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTAAMGK 8 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 111.65 0.0051186 642600000 1106100 829710 608670 729840 953710 758470 1260400 1013400 1005700 FALSE TRUE 1053816.845 914258.3923 636578.1216 656475.0966 1120036.722 732203.9937 1068102.831 924661.3236 1161658.82 0.907165535 0.787028323 0.547990607 0.565118678 0.964170119 0.630308987 0.919463454 0.795983561 1 20.14775498 1.653317262 9.473083157 0.892884938 0.748740051 0.2371775 0.14250743 0.201486544 30.65729375 0.068874933 0.036604792 45.01085498 -1.653317262 -0.144144887 KVTAEADSSS(ph)PTGILATSESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVTAEADSSSPTGILATSESK 21 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 KVTAEADS(0.001)S(0.005)S(0.99)PT(0.005)GILATSESK;KVTAEADS(0.001)S(0.009)S(0.981)PT(0.009)GILATSESK;KVTAEADS(0.081)S(0.454)S(0.457)PT(0.008)GILATSESK 197.54 5.54E-22 872370000 1546750 1331390 1423610 1614700 1020530 1547340 1692050 1656230 1155270 TRUE FALSE 1473638.193 1467060.155 1488883.927 1452387.288 1198510.109 1493755.228 1433896.696 1511201.721 1334423.371 1.104325827 1.099396328 1.115750787 1.088400668 0.89814832 1.119401278 1.074544052 1.13247546 1 20.34778503 2.985259799 24.90479271 1.051285926 1.1043382 0.160420391 0.064985831 1337.551085 2259910.783 0.01883527 0.020639196 966.628952 -2.985259799 0.053052274 KVTEELLTDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTEELLTDNR 11 1 Q9UHB9;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 97.69 0.009747 205410000 327390 323300 307550 355950 282680 344070 359980 372590 349120 FALSE TRUE 311914.9235 356244.6376 321651.4717 320169.2297 331979.3025 332154.7696 305058.4395 339964.0444 403259.7465 0.773483905 0.883412343 0.797628512 0.793952862 0.823239377 0.823674499 0.756481256 0.84303987 1 18.62134988 0.971176185 23.44345561 1.000000001 0.809923485 0.758495931 0.033923374 734.5980906 597476.3567 0.032718918 0.00817973 9.357852276 -0.971176185 -0.190076516 KVTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 KVTFFEPGS(1)GDENGTSNKEDEFR;KVT(0.01)FFEPGS(0.971)GDENGT(0.009)S(0.009)NKEDEFR;KVTFFEPGS(1)GDENGTSNKEDEFR 183.47 1.90E-17 248298000 292925 239326 264865 295685 193757 302526 326734 315624 216185 TRUE FALSE 279079.0158 263713.5915 277009.3222 265962.182 227548.1595 292049.4488 276884.7274 287986.2893 249709.8657 1.117613095 1.056079986 1.109324702 1.065084799 0.911250178 1.169555107 1.108825743 1.153283586 1 17.9298933 KVTFFEPGSGDENGTSNKEDEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 57.985 0.043807 58510000 166420 150510 156110 185220 120580 167260 192490 185570 150350 FALSE TRUE 158553.6564 165847.1401 163267.7979 166601.3337 141609.1138 161467.7443 163122.1152 169320.507 173665.5101 0.912982988 0.954980295 0.940127938 0.959323089 0.815412996 0.929762877 0.939289068 0.974980622 1 17.40595174 1.211724519 2.04793523 0.998547413 0.921535723 0.33880505 0.039887637 0.368980568 2.71365441 0.036232332 0.010453692 16.28262869 -1.211724519 -0.07701169 KVTHAVVTVPAYFNDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVTHAVVTVPAYFNDAQR 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 168.2 1.38E-11 646450000 1274320 1175780 1131930 1334230 1244300 1150820 1406950 1241360 1295070 FALSE TRUE 1214085.419 1295593.319 1183830.11 1200110.666 1461305.526 1110966.815 1192293.937 1132659.938 1495902.841 0.811607135 0.866094564 0.791381684 0.802265115 0.97687195 0.74267311 0.79703969 0.757174802 1 20.51258504 -2.300685568 2.406403441 1.950462428 0.820387493 0.433254985 0.065323014 6487778.85 937657.7175 33727939.44 0.014768591 0.005003967 2.300685568 -1.130074935 KVTLGDTLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 91.961 0.015701 240160000 417540 374180 364600 399290 384930 326300 418740 328900 511360 FALSE TRUE 397803.7117 412309.3674 381317.2706 359152.6106 452061.6701 315000.1492 354853.5223 300099.7724 590659.0971 0.673491213 0.698049635 0.645579273 0.608053973 0.765351236 0.533302798 0.600775513 0.508076103 1 19.17196618 -1.843576347 5.223985956 1.055607876 0.635001334 0.705590074 0.07521061 0.03809798 0.001140781 0.056957104 0.016858883 0.014335857 1.843576347 -0.420606542 KVTQLDLDGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTQLDLDGPK 11 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 89.959 0.012096 0 2372100 2038400 1968600 2337400 1429000 2396300 2584900 2454400 1735800 FALSE TRUE 2259975.534 2246115.277 2058862.257 2102440.111 1678217.148 2313315.53 2190526.03 2239479.724 2004978.999 1.127181649 1.12026873 1.026874725 1.048609543 0.837024801 1.153785417 1.09254313 1.116959193 1 20.93515569 3.750033068 21.53151441 1.04519465 1.123725262 0.142903707 0.084939457 224.2433183 420850.7773 0.021758269 0.038635174 5623.841449 -3.750033068 0.078530611 KVTS(ph)PLQS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_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(0.444)S(0.556)PLQS(0.997)PT(0.003)K 85.493 0.053105 130120000 408990 380230 358300 424700 237720 391420 458000 465650 279950 TRUE FALSE 389657.8532 418975.8693 374728.4094 382008.3491 279178.2927 377865.0273 388123.6883 424875.2174 323363.2162 1.205016012 1.295681909 1.158846741 1.181359938 0.863358226 1.168546725 1.20027161 1.31392563 1 18.30279605 3.527290799 3.209116618 1.12836689 1.24981043 0.151904667 0.122622755 0.465793101 9.548604996 0.03404488 0.053211294 3367.369696 -3.527290799 0.12144354 KVTS(ph)SPITSEEESNLSNDFIDENGLPINKNENVNGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTSSPITSEEESNLSNDFIDENGLPINKNENVNGESK 38 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 KVT(0.172)S(0.473)S(0.351)PIT(0.003)S(0.001)EEESNLSNDFIDENGLPINKNENVNGESK 110.98 6.03E-06 90644000 59085 36847 56055 60126 23642 57870 64044 67826 32544 TRUE FALSE 56292.16915 40601.75119 58625.1772 54082.02025 27765.15731 55865.94739 54272.91155 61886.79587 37590.75731 1.497500268 1.080099314 1.559563611 1.43870526 0.738616599 1.486161796 1.443783404 1.646330117 1 15.19809036 KVTSPSSSSSSSSSDSES(ph)DDEADVSEVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVTSPSSSSSSSSSDSESDDEADVSEVTPR 30 1 P56181-2 P56181-2 1 KVTSPSSSSSSSSSDS(0.061)ES(0.939)DDEADVSEVTPR 132.99 3.99E-06 182130000 76579 58125 70001 74064 64404 59675 74653 69893 74563 TRUE FALSE 72959.26243 64048.00358 73210.61509 66618.94601 75636.03721 57608.43979 63263.31375 63772.79839 86125.84922 0.847123867 0.743655989 0.850042301 0.773506985 0.878203674 0.668886755 0.734545021 0.740460605 1 16.39415868 2.252759775 24.99998231 0.757320188 0.810289224 0 0.094785917 629.4421894 1108235.888 0.029086089 0.02422463 178.9615677 -2.252759775 0.052969036 KVVAEVYDQER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 184.1 8.11E-06 1336040000 1479040 966140 1126770 1438060 1214400 1281390 1519330 1452850 1364850 FALSE TRUE 1409128.71 1064590.764 1178433.519 1293503.477 1426190.976 1237015.143 1287528.304 1325630.752 1576503.967 0.893831376 0.675285814 0.747497972 0.820488564 0.904654225 0.784657171 0.816698423 0.840867375 1 20.58829737 -1.280474322 0.295985725 1.134268234 0.779346155 0.464799107 0.065302315 16.46179294 1.05611002 1.795800161 0.073494966 0.05242346 1.280474322 -0.354922079 KVVDYSQFQES(ph)DDADEDYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 44 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.006)QFQES(0.994)DDADEDYGR;KVVDYSQFQES(0.998)DDADEDY(0.002)GR;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;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;KVVDY(0.001)SQFQES(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;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR 305.45 1.53E-55 1.80773E+11 36489069.3 35432602.8 34246944.4 39682544.9 27494613.4 37217594.1 37831109.5 38417208.5 31011758.1 TRUE FALSE 34764303.31 39043225.31 35817200.68 35693580.09 32289665.27 35928739.48 32059278.93 35053194.06 35820903.16 0.97050326 1.089956474 0.999896639 0.996445565 0.90141963 1.00301043 0.894988013 0.978568126 1 25.09429838 3.101988412 2.616624023 0.948720994 1.029637816 0.270943887 0.046902161 0.268679874 3.734217711 0.013380595 0.016509746 1264.702602 -3.101988412 0.080916822 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 KVVDYSQFQESDDADEDYGRDSGPPTK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(0.999)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK 310.68 2.78E-82 50404770000 7869190 5050803 7121805 6944528 5712648 7706755 10087294 8568493 7641157 TRUE FALSE 7497228.984 5565485.568 7448346.804 6246450.852 6708932.003 7439868.142 8548292.034 7818190.328 8826108.602 0.849437654 0.63057071 0.843899292 0.707724223 0.760123437 0.842938658 0.968523323 0.885802643 1 23.07334607 2.004872208 2.605671049 0.947169164 0.75014737 0.621591729 0.068471548 0.172228588 2.215333167 0.032420587 0.018336304 101.1281838 -2.004872208 -0.197021794 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KVVDYSQFQESDDADEDYGRDSGPPTKK 28 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYSQFQES(1)DDADEDYGRDSGPPTKK 237.74 2.53E-45 26724200000 3817075 1950981 3839860 3162547 2605361 3886860 5704330 4447310 3677370 TRUE FALSE 3636649.429 2149788.182 4015921.379 2844641.767 3059735.134 3752257.064 4834029.691 4057879.96 4247637.758 0.85615809 0.506113822 0.945448178 0.669699708 0.720338058 0.883375014 1.138051304 0.955326276 1 22.01822931 2.028734033 3.71413287 1.042130185 0.725614097 0.537036371 0.123048791 0.151640339 4.43684918 0.050500115 0.032614339 106.8400378 -2.028734033 -0.316516088 KVVDYSQFQESDDADEDYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 295.17 2.21E-54 575630000 409730 418830 387130 457600 325300 431930 444300 404400 322166 FALSE TRUE 390362.8749 461509.2532 404880.2934 411601.1786 382032.217 416972.1558 376513.8749 368988.5921 372125.8579 1.049007659 1.240196679 1.088019778 1.106080564 1.026620991 1.120513791 1.011791755 0.991569342 1 18.50543112 2.204219427 0.693188067 0.992055402 1.140040186 0.418134879 0.056802036 0.629794276 0.58497396 0.04686088 0.029889344 160.036641 -2.204219427 0.147984784 KVVGDVAYDEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 167.32 7.94E-05 1240110000 4126880 3814330 3572580 4336650 2650720 4086800 4521390 4542650 2861670 FALSE TRUE 3931810.561 4203014.564 3736386.327 3900721.703 3113004.729 3945273.091 3831568.914 4144871.484 3305443.168 1.189495738 1.271543436 1.130373792 1.180090386 0.94178135 1.193568575 1.159169503 1.253953335 1 21.65641228 -5 0.107496843 0.555411873 1.256896323 0.198631895 0.092535274 274.5140781 1.973781494 28.38775706 1.214808999 1.00E-05 5 0.70148445 KVVNPLFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVVNPLFEK 9 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 141.95 0.0024511 0 2881200 2157600 1587500 1865000 2407200 2181200 3429200 2570000 2518100 FALSE TRUE 2745011.386 2377461.893 1660288.445 1677526.657 2827014.918 2105664.497 2906012.558 2344957.176 2908594.087 0.943758841 0.817392122 0.570821639 0.576748287 0.97195237 0.723945808 0.999112448 0.806216717 1 21.47189054 1.742251977 25 0.927675042 0.779733524 0.236240399 0.140758402 1.126605189 7669.338314 0.066586588 0.036925552 55.23978464 -1.742251977 -0.147941518 KVVVS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.827)PT(0.173)K;KVVVS(0.5)PT(0.5)K;KVVVS(0.5)PT(0.5)K;KVVVS(0.638)PT(0.362)K;KVVVS(0.5)PT(0.5)K 90.653 0.0079894 21058700000 25328330 25303410 23045460 27885870 15216840 27855390 29492730 27882400 17699220 TRUE FALSE 24131110.04 27881856.25 24102117.14 25082729.37 17870652.08 26890750.86 24993072.37 25440869.24 20443924.64 1.180356045 1.363821122 1.178937878 1.226903826 0.874130207 1.315341909 1.222518318 1.244421983 1 24.28516884 -2.315921695 2.135282754 0.004443976 1.210576389 0.188385775 0.129582572 1825631.438 249130.4733 8805054.568 0.030237489 0.004831459 2.315921695 1.206132414 KVVVSHST(ph)HR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVVVSHSTHR 10 1 Q7L2H7;Q7L2H7-2 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 1 KVVVSHS(0.332)T(0.668)HR 91.202 0.0078582 56187000 43032 35669 38369 43462 45305 37388 51994 38892 12866 TRUE FALSE 40997.96264 39303.71165 40128.2566 39093.11719 53206.17766 36093.24419 44061.36036 35486.4103 14861.19357 2.758726104 2.644721063 2.700204153 2.630550299 3.580208912 2.428690806 2.964860134 2.38785735 1 13.85926237 0.85480946 3.602074579 1.00019891 2.797427261 0.775747454 0.305928634 0.320146075 7.147422313 0.265316324 0.06832274 7.158292821 -0.85480946 1.797228351 KVVVSPT(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.481)PT(0.519)K;KVVVS(0.312)PT(0.688)K 100.04 0.0037435 6658600000 18060000 17523900 16506600 20833600 11329700 20923500 21425300 21483000 12964300 TRUE FALSE 17206339.59 19309605.33 17263443.94 18739366.95 13305596.09 20198913.95 18156476.98 19601834.63 14974737.43 1.14902446 1.289478725 1.152837839 1.251398699 0.888536187 1.348865985 1.212473812 1.308993545 1 23.83602737 KVVVVVPNEEDWKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVVVVVPNEEDWKK 14 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 128.96 3.98E-05 508390000 1014890 805260 787290 1044040 692400 943960 1193040 1065940 797350 FALSE TRUE 966918.161 887316.9095 823388.0252 939091.1157 813154.3408 911270.4285 1011019.836 972600.6427 920998.9657 1.049858031 0.96342878 0.894016232 1.01964405 0.882904727 0.989436973 1.09774264 1.056027942 1 19.81284001 1.906991555 6.448246125 1.059011836 0.967085221 0.35092979 0.054847631 0.256733667 14.84174256 0.023237907 0.014249616 80.72193343 -1.906991555 -0.091926615 KVVYENAYGQFIGPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVVYENAYGQFIGPHR 16 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 ; 199.37 2.49E-11 717170000 1335810 1135010 1223640 1278020 1362730 1235080 1489630 1439910 1360230 FALSE TRUE 1272668.909 1250668.809 1279745.104 1149551.002 1600389.681 1192308.87 1262359.585 1313823.847 1571167.521 0.810014777 0.796012387 0.814518558 0.731654 1.018599009 0.758868073 0.803453208 0.836208634 1 20.58340558 -4.999999977 0.3409082 2.983294697 0.810913645 0.354703446 0.076039727 420.4724853 3.532055718 607.2546245 0.054957925 1.00E-05 4.999999977 -2.172381052 KVWLDPNETNEIANANSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KVWLDPNETNEIANANSR 18 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 126.07 4.55E-05 82430000 85063 55176 77738 79426 91719 84145 95688 81348 95566 FALSE TRUE 81042.24057 60798.49713 81302.36419 71441.94758 107714.7646 81231.03755 81089.03817 74224.73787 110385.8872 0.734172118 0.550781433 0.736528611 0.647201824 0.975801955 0.735882454 0.734596063 0.672411481 1 16.75219621 KVYASQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVYASQR 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 103.56 0.013385 1140410000 2208730 1379520 893950 1035400 2271580 1216960 2554200 1700050 2244000 FALSE TRUE 2104327.71 1520094.656 934938.4917 931319.6249 2667742.833 1174816.37 2164509.879 1551184.609 2591988.059 0.811858567 0.586458973 0.36070324 0.359307066 1.029226513 0.453249144 0.835077103 0.598453609 1 21.30562764 0.218396892 0.501379429 1.026055022 0.604109751 0.2346827 0.213609498 4.513380612 1.65564142 0.478125721 0.103074899 1.653472177 -0.218396892 -0.42194527 KVYENYPTYDLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KVYENYPTYDLTER 14 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ;; 254.56 4.71E-24 1023970000 1649670 1434330 1364870 1628950 1480900 1498130 1728970 1575550 1613150 FALSE TRUE 1571693.368 1580489.858 1427450.64 1465204.851 1739168.491 1446249.382 1465183.872 1437586.489 1863309.063 0.8434958 0.848216696 0.766083667 0.786345583 0.933376285 0.776172569 0.786334324 0.771523371 1 20.82943556 -1.122163041 4.42203188 1.000024132 0.816171855 0.567793736 0.050982012 1.18E-05 2.35E-06 0.048152137 0.011348079 0.075480881 1.122163041 -0.183852277 KVYFAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KVYFAEK 7 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 94.302 0.022929 3082600000 5886300 4027700 2254700 2869400 6091400 3151200 5995500 4402300 6004300 FALSE TRUE 5608066.265 4438127.209 2358080.225 2580962.46 7153738.231 3042073.154 5080776.36 4016811.274 6935416.178 0.808612796 0.639922262 0.340005584 0.372142406 1.031479301 0.438628782 0.732584207 0.57917379 1 22.72555103 -2.789167625 0.523266779 1.972046991 0.62434861 0.247130475 0.20899517 353.0574515 15.17002891 387.0155011 0.089019747 0.001624921 2.789167625 -1.347698382 KWDGS(ph)EEDEDNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(0.999)EEDEDNS(0.001)K;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK 205.15 4.42E-08 4331680000 6194970 5475210 5232040 6477350 2737413 6683190 6267170 6855410 2945356 TRUE FALSE 5902146.045 6033140.124 5471934.209 5826234.472 3214816.961 6451749.455 5310998.112 6255113.958 3402106.766 1.73485033 1.773354142 1.608395793 1.712537223 0.944948875 1.89639829 1.561090959 1.838600135 1 21.69799699 -2.081970296 2.369756916 0.000142764 1.639263811 0.362497246 0.26404465 2627618.943 1012494.521 14161660.21 0.062381591 0.008279988 2.081970296 1.639121047 KWDGS(ph)EEDEDNSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KWDGSEEDEDNSKK 14 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(0.985)EEDEDNS(0.015)KK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK 165.17 2.09E-06 3139380000 2048870 1895420 1810440 2190040 761283 2251800 2019070 2436610 723492 TRUE FALSE 1952023.976 2088565.453 1893450.465 1969893.018 894050.5142 2173819.601 1711023.789 2223247.511 835687.4443 2.335830207 2.499218419 2.265739994 2.357212654 1.069838395 2.601235206 2.047444652 2.660381613 1 19.67260393 2.951910713 24.99995203 1.979210823 2.380917109 0.151477746 0.544739457 818.473923 425495.8017 0.150954105 0.160114355 895.1807063 -2.951910713 0.401706286 KWDGSEEDEDNS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(0.009)EEDEDNS(0.991)K 218.2 2.60E-11 168120000 232700 216350 220790 272280 128240 269400 278670 298290 134050 TRUE FALSE 221700.7322 238396.311 230913.4399 244909.8971 150605.0154 260070.6104 236153.7734 272170.1463 154837.7894 1.431825739 1.539651993 1.49132483 1.581719153 0.972663172 1.679632676 1.525168851 1.757775976 1 17.24039809 KWDKDEYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWDKDEYEK 9 2 Q96NC0;R4GNG8 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 58.676 0.060332 353180000 288710 255370 257730 310560 181100 304190 313320 375720 207710 FALSE TRUE 275063.2505 281392.4933 269547.1754 279341.9188 212683.7827 293655.824 265517.2795 342819.965 239920.606 1.146476141 1.172856713 1.123484889 1.164309825 0.886475681 1.223970833 1.1066881 1.428889209 1 17.87219755 KWDSNVIETFDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWDSNVIETFDIAR 14 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 174.95 3.95E-06 154740000 421750 463390 345570 427770 325690 394250 392710 421730 328300 FALSE TRUE 401814.7133 510609.9678 361414.7263 384769.7469 382490.2329 380597.0236 332794.8769 384801.0855 379211.0873 1.059606976 1.346505904 0.953070041 1.014658484 1.008647283 1.003654789 0.877597961 1.014741125 1 18.53264162 3.717854901 24.96921076 0.974611213 1.203056444 0.571298308 0.079506725 456.843644 550911.9748 0.020526639 0.031840262 5222.216842 -3.717854901 0.228445231 KWDTCAPEVILHAVGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWDTCAPEVILHAVGGK 17 1 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 106.67 0.00048159 188580000 1311200 948110 1105200 1190600 983940 1226400 1458200 1331700 1019800 FALSE TRUE 1249222.175 1044723.487 1155874.513 1070918.626 1155538.824 1183929.46 1235724.808 1215089.288 1177945.376 1.060509426 0.886903169 0.981263255 0.909141161 0.980978277 1.005080104 1.049051029 1.031532797 1 20.16784121 2.195820969 2.776843017 1.031027583 0.959115804 0.278767222 0.047227162 0.312691138 4.919350283 0.019489216 0.01354492 156.971558 -2.195820969 -0.071911779 KWENPGLGAESHTDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KWENPGLGAESHTDSLR 17 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 240.79 1.60E-20 885150000 1007180 785950 849980 983780 891830 917550 1117830 1033870 915940 FALSE TRUE 959572.5974 866039.1986 888952.4237 884888.5653 1047364.87 885775.0134 947284.5031 943338.8619 1057979.297 0.906986176 0.818578587 0.840236124 0.836394973 0.989967263 0.837232842 0.895371493 0.891642081 1 20.01287997 -2.03560597 0.239984833 1.148919575 0.852983965 0.402866214 0.0486306 31.21299075 1.100696999 2.646889313 0.078917524 0.009212851 2.03560597 -0.29593561 KWENPGLGAESHTDSLRNS(ph)STEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHTDSLRNS(0.997)S(0.003)TEIR;KWENPGLGAESHTDS(0.044)LRNS(0.952)S(0.004)T(0.001)EIR 245.43 4.39E-38 581970000 324570 265380 296060 370100 330420 324680 441170 390840 338150 TRUE FALSE 309228.2193 292422.5237 309634.6438 332896.8449 388045.1434 313436.2502 373861.4139 356615.9776 390588.575 0.791698066 0.748671473 0.79273861 0.852295398 0.993488208 0.802471629 0.957174474 0.91302204 1 18.57529022 2.843771925 0.421819209 0.979616103 0.729177829 0.593072129 0.05754657 0.897150583 0.3181617 0.053510805 0.090920835 697.8658154 -2.843771925 -0.250438273 KWNTTLYEGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KWNTTLYEGTWR 12 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 130.61 0.00034213 493100000 490780 465220 442100 480830 513900 505830 607910 588380 575130 FALSE TRUE 467581.802 512626.4469 462370.7223 432496.0549 603523.9973 488312.9803 515162.1645 536858.328 664318.223 0.703852139 0.771657963 0.696007886 0.65103747 0.908486289 0.735058837 0.775474986 0.808134279 1 19.34151496 -5 0.173880157 2.006411616 0.696144187 0.620365877 0.064030458 85.25536141 0.810983102 29.43339978 0.202373487 1.00E-05 5 -1.310267429 KWQDEDGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KWQDEDGKK 9 2 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 142.83 5.82E-05 3812700000 6645100 5803500 6005900 7966100 3597600 8137600 7930700 8550400 4010000 FALSE TRUE 6330999.292 6394883.248 6281276.456 7165332.493 4225020.301 7855792.872 6720726.058 7801681.647 4631850.32 1.366840216 1.380632535 1.356105233 1.546969785 0.912166847 1.696037723 1.450980838 1.684355303 1 22.1431572 KWQIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWQIFK 6 1 B4DZG7;F8VYN9;P40616-2;P40616;F8W1Z8 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 106.29 0.051713 127390000 641810 579790 554330 703520 569500 636880 751670 636200 487100 FALSE TRUE 611472.9132 638871.2602 579746.5788 632800.833 668820.6197 614824.6859 636988.9361 580490.9553 562636.9802 1.086798299 1.135494613 1.030409659 1.12470537 1.188724956 1.092755556 1.132149074 1.031732673 1 19.10184485 1.113967456 4.396814354 1.001592784 1.113486903 0.504518112 0.040533613 0.159079203 4.907777452 0.036508867 0.009353661 13.00072154 -1.113967456 0.111894119 KWQVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWQVSR 6 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 135.35 0.021868 253470000 302980 282940 273530 341350 294750 279650 333880 289270 349310 FALSE TRUE 288658.7358 311771.9077 286071.6211 307036.8495 346154.3067 269965.6504 282940.4739 263939.9853 403479.2108 0.715424062 0.772708728 0.709012047 0.760973159 0.857923525 0.669094325 0.701251679 0.654160061 1 18.62213482 -1.574840947 3.054774784 1.013442265 0.732091569 0.682452626 0.057851461 59614911.75 72853695.22 6605723.128 0.013645622 0.026616997 1.574840947 -0.281350696 KWS(ph)LNTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KWSLNTYK 8 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 1 KWS(0.989)LNT(0.011)YK 64.266 0.07211 60445000 206860 172260 160650 256320 164750 233020 279910 214880 188600 TRUE FALSE 197082.1378 189813.4898 168015.9614 230554.2266 193482.3478 224950.459 237204.5886 196063.968 217847.1248 0.904680922 0.871315102 0.771256272 1.058330363 0.888156537 1.032606968 1.088858018 0.900007142 1 17.73295655 3.229738763 24.99999173 1.00286769 0.861790283 0.478478919 0.070890224 158.2375206 448424.1587 0.01995603 0.024193714 1697.222433 -3.229738763 -0.141077407 KY(ph)RNLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYRNLKR 7 3 I3NI13;I3L270;Q8NBZ0;J3KNE2;H3BNM4;Q8NBZ0-2 I3NI13 INO80E INO80 complex subunit E 1 KY(1)RNLKR 46.37 0.085218 220930000 113130 103690 118590 133280 295130 91896 125680 105420 287960 TRUE FALSE 107782.5691 114256.1289 124027.4688 119882.4412 346600.5786 88713.61848 106505.2077 96188.86593 332615.3661 0.32404567 0.34350827 0.372885565 0.360423641 1.042046201 0.266715334 0.320205314 0.289189484 1 18.34349529 -2.144710246 2.384291529 2.314955616 0.405878227 0.398292893 0.22577603 18040859.1 4808237.251 128143996.3 0.056498206 0.007166214 2.144710246 -1.909077389 KYAEAVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYAEAVTR 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 136.63 0.0012547 4024290000 5829500 4080510 4522920 5254600 4797400 4694800 6276300 5458700 5349500 FALSE TRUE 5553951.088 4496318.608 4730300.356 4726397.625 5634065.041 4532217.899 5318735.163 4980707.29 6179073.139 0.898832392 0.727668779 0.765535583 0.764903978 0.911797759 0.733478597 0.860765853 0.806060582 1 22.55895902 -0.664742737 0.506480759 1.041991277 0.799873062 0.466416095 0.064434827 10.18184099 2.008125911 0.767302513 0.028367844 0.216400003 0.664742737 -0.242118215 KYAVLYQPLFDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 176.91 8.94E-06 1124910000 1808210 1334690 1240450 1416230 1563390 1402190 2154390 1732860 1871720 FALSE TRUE 1722739.497 1470696.428 1297325.859 1273867.87 1836044.721 1353631.809 1825698.237 1581121.592 2161976.778 0.796835338 0.680255423 0.60006466 0.589214409 0.849243498 0.626108394 0.844457839 0.731331441 1 21.0439196 0.520958463 0.606751667 1.006227303 0.6918583 0.510988323 0.090950722 1.36681484 0.88229995 0.109693747 0.036232974 3.318627158 -0.520958463 -0.314369003 KYCQVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYCQVIR 7 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 72.138 0.084047 343700000 360860 291110 162050 171930 344190 212050 379320 272660 357080 FALSE TRUE 343802.863 320774.44 169480.1528 154647.2698 404216.627 204706.6553 321447.7673 248784.4449 412454.1427 0.833554152 0.777721465 0.410906657 0.374944154 0.980028045 0.496313733 0.779353955 0.603180861 1 18.6538742 -1.154981589 4.793241065 1.000024268 0.67297267 0.233847173 0.193200406 5.75E-05 1.01E-05 0.17905977 0.042201039 0.069987166 1.154981589 -0.327051598 KYDAFLASESLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 198.74 1.98E-07 2201590000 5057500 4495600 4437200 4848400 3873400 4913700 6126000 5621600 4510600 FALSE TRUE 4818441.998 4953706.751 4640650.009 4361029.621 4548919.734 4743537.337 5191366.188 5129342.902 5210080.811 0.924830568 0.95079269 0.890705956 0.837036848 0.87309965 0.910453697 0.996407998 0.984503521 1 22.31287432 1.759945767 4.786867868 0.993109985 0.901932408 0.688791101 0.030296794 0.135739828 6.845015277 0.018157781 0.00950766 57.53680834 -1.759945767 -0.091177578 KYDEVLHMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYDEVLHMVR 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 130.69 0.00017529 658550000 1783250 1418440 1038650 1201350 1488600 1190560 1841650 1513040 1367920 FALSE TRUE 1698959.307 1562980.649 1086273.13 1080588.016 1748211.369 1149330.609 1560672.468 1380550.196 1580050.047 1.075256641 0.989196925 0.687492862 0.683894803 1.106427845 0.727401395 0.987736098 0.873738271 1 20.59153883 3.984511579 23.3997913 0.865268867 1.042984332 0.204707197 0.139813322 424.6647529 641584.101 0.033593507 0.061576088 9649.650385 -3.984511579 0.177715465 KYDVDTLDMVFLDHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYDVDTLDMVFLDHWK 16 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 269.24 6.11E-28 2002420000 7248700 7017900 5763900 7792600 4551800 6728300 7041000 7138400 3761000 FALSE TRUE 6906068.317 7733031.989 6028180.516 7009273.043 5345632.479 6495297.284 5966766.133 6513323.853 4344236.671 1.589708121 1.780066919 1.387627096 1.613464821 1.230511338 1.495152722 1.373490117 1.499302258 1 22.05067127 -1.920985872 0.085777662 3.06E-10 2.094717745 0.600029026 0.136515128 61.02256296 0.757311359 17.03212973 4.46441901 0.011995383 1.920985872 2.094717744 KYDVDTLDMVFLDHWKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYDVDTLDMVFLDHWKDR 18 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 200.6 8.98E-16 747880000 2376000 1061660 2439500 1768300 2264400 2257800 3787400 2634000 2470100 FALSE TRUE 2263691.189 1169844.361 2551353.488 1590547.124 2659310.643 2179611.82 3209562.57 2403352.996 2853150.492 0.793400557 0.410018456 0.894223244 0.557470462 0.93206112 0.7639316 1.124918779 0.842350588 1 21.44412441 2.489224295 1.146306151 0.990524551 0.634447324 0.382516912 0.162394136 0.407749485 1.081349595 0.084769944 0.061137144 308.4780698 -2.489224295 -0.356077227 KYDYDSSSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYDYDSSSVR 10 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 167.11 8.56E-06 1637560000 3270960 3067930 2505300 2900240 2564580 2856950 3312910 3251060 2659550 FALSE TRUE 3116348.203 3380555.555 2620170.483 2608702.365 3011841.94 2758013.105 2807464.734 2966379.951 3071979.431 1.014443056 1.10044863 0.85292579 0.849192654 0.980423863 0.897796736 0.913894379 0.965624939 1 21.55073713 3.74379757 24.99974444 0.916947024 1.057445847 0.517430174 0.053810943 285.5842898 1363294.669 0.01305206 0.022666925 5543.672553 -3.74379757 0.140498823 KYEAAYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 88.496 0.023368 838870000 2171500 1393500 1484100 1344000 1538500 1430200 1866700 1641600 1732100 FALSE TRUE 2068857.498 1535499.234 1552147.453 1208898.567 1806813.913 1380671.815 1581900.631 1497852.801 2000705.222 1.034064127 0.767478996 0.775800171 0.604236223 0.903088518 0.690092574 0.790671516 0.748662414 1 20.93207719 4.544486985 2.215657125 0.770423731 1.052844943 0.333915882 0.108387873 0.389990794 2.989812169 0.023828466 0.185016777 35033.77894 -4.544486985 0.282421212 KYEDICPSTHNMDVPNIK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;;;; 235.73 5.47E-24 7982050000 6357432 5210806 5625302 7016612 5087306 6153016 7563517 7077032 5475522 FALSE TRUE 6056928.789 5741793.056 5883227.661 6311288.831 5974530.556 5939935.513 6409563.568 6457329.56 6324637.987 0.957672012 0.907845329 0.930207812 0.997889341 0.944643878 0.939173993 1.013427738 1.020980106 1 22.59255147 1.715512704 5.536647528 1.013102122 0.943936625 0.633569955 0.023285844 0.095666464 7.156432145 0.012363238 0.006253511 51.94128675 -1.715512704 -0.069165497 KYEDICPSTHNMDVPNIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 194.27 2.09E-15 3765260000 4408490 2722850 4165980 3991190 3985440 4230950 6058450 5134380 4980190 FALSE TRUE 4200109.414 3000311.511 4356994.304 3589987.998 4680499.474 4084431.141 5134122.181 4684786.468 5752492.43 0.730137321 0.521567224 0.757409828 0.624075223 0.81364722 0.710028077 0.892503944 0.814392461 1 22.45575575 1.699802403 0.491619189 0.994230876 0.624016961 0.638037967 0.080130559 0.472828021 0.277137226 0.074342625 0.050386898 50.09592539 -1.699802403 -0.370213915 KYEEIDNAPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 KYEEIDNAPEER 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;;;; 210.14 7.54E-08 7074030000 9966280 7511649 8295980 8248230 7645315 7271564 9240590 8731430 8333260 FALSE TRUE 9495193.696 8277094.573 8676358.889 7419102.25 8978655.515 7019747.915 7830768.28 7966859.701 9625539.4 0.986458348 0.859909687 0.901389369 0.770772623 0.932795051 0.729283589 0.813540723 0.827679299 1 23.19843596 4.869925738 0.81164615 0.832495783 1.10558184 0.194011526 0.079238683 3.603314113 1.580815532 0.024504852 0.931587371 74118.34924 -4.869925738 0.273086057 KYEEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 131.06 0.0056162 30537500000 27021600 23022300 22272500 26351000 20588700 23841600 27199300 25358900 22131500 FALSE TRUE 25744342.52 25368298.54 23293716.16 23702147.42 24179362.76 23015959.41 23049547.24 23138340.28 25563539.99 1.007072672 0.992362504 0.911208548 0.927185649 0.945853461 0.900343201 0.901657096 0.905130521 1 24.6075843 3.784585242 5.470100165 0.921190531 1.000898015 0.493495889 0.030027417 0.12935053 9.539252364 0.007084316 0.012762533 6089.550584 -3.784585242 0.079707484 KYEFGESDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYEFGESDLR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 106.01 0.0039663 1000970000 3132800 2691040 2949800 3566900 2967600 3203000 3831500 3616500 3713800 FALSE TRUE 2984718.753 2965260.035 3085051.248 3208348.435 3485148.5 3092079.307 3246934.305 3299820.088 4289717.137 0.695784514 0.691248383 0.719173584 0.747916082 0.812442497 0.720811934 0.756911051 0.769239552 1 22.03245109 -5 0.183394011 2.11565313 0.680160317 0.894307673 0.029086901 40.78346907 0.394920718 16.55753145 0.088089164 1.00E-05 5 -1.435492813 KYEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYEGGR 6 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 94.262 0.071645 1538600000 1383200 1172130 1028260 1322010 981600 1157000 1273840 1379040 1354210 FALSE TRUE 1317818.877 1291571.38 1075406.738 1189119.043 1152790.729 1116932.8 1079492.312 1258283.947 1564213.97 0.842479931 0.825699939 0.687506159 0.76020229 0.736977646 0.714053717 0.690118061 0.804419325 1 20.57700644 0.973295309 22.84934959 1.000000002 0.756430992 0.698306062 0.051141561 601.5218551 514681.7613 0.057978449 0.014494612 9.40362515 -0.973295309 -0.24356901 KYELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KYELGR 6 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 118.69 0.034721 767530000 1126280 1366000 887030 1397050 938040 1066170 1073220 1141530 859130 FALSE TRUE 1073042.976 1505196.953 927701.2029 1256615.88 1101633.879 1029248.266 909480.578 1041571.582 992359.4926 1.081304693 1.516785967 0.934843885 1.266290985 1.110115726 1.037172792 0.916482973 1.049590989 1 19.92050332 2.626075273 0.950499708 0.970374545 1.256562926 0.259108088 0.151616211 0.58918072 1.1059241 0.087687033 0.071905058 422.7418783 -2.626075273 0.286188381 KYELGRPAANTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYELGRPAANTK 12 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 141.73 3.42E-05 4119200000 4478600 3590770 3894390 4289800 3415190 4199100 5349300 5001000 4385190 FALSE TRUE 4266905.454 3956673.545 4072951.634 3858581.154 4010798.055 4053684.114 4533166.038 4563085.928 5065222.869 0.84239244 0.781145005 0.80410117 0.761779147 0.791830519 0.800297286 0.894958851 0.900865776 1 22.27219432 1.279109542 1.136454407 0.992352448 0.79517496 0.876235741 0.025440502 0.142842 0.372297152 0.023465781 0.007772358 19.0155785 -1.279109542 -0.197177488 KYEMFAQTLQQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 KYEMFAQTLQQSR 13 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 254.45 1.33E-23 3954150000 5654600 4154750 3054782 3784320 5733040 3828870 6524640 5234460 6378620 FALSE TRUE 5387318.264 4578123.749 3194846.776 3403912.964 6732880.361 3696275.272 5529186.335 4776102.933 7367783.812 0.731199286 0.621370532 0.433623849 0.461999571 0.913827079 0.501680745 0.750454475 0.64824146 1 22.8127993 -0.098028146 0.514492278 1.039527303 0.612865262 0.404447856 0.142938663 5.010562492 1.506003012 0.535967443 0.064985263 0.797942972 0.098028146 -0.426662041 KYEPPVPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYEPPVPTR 9 1 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 94.465 0.013955 141610000 430840 401330 471480 445610 514060 451840 573150 467990 469320 FALSE TRUE 410475.047 442225.9833 493097.8244 400816.4362 603711.9012 436192.6675 485705.4409 427010.3146 542099.7486 0.757194682 0.815764966 0.909607181 0.739377646 1.113654642 0.804635436 0.895970607 0.787696943 1 19.04819881 4.075939071 0.999556247 0.893048179 0.743586336 0.15871262 0.106913262 1.413939043 2.154239736 0.032637252 0.180523208 11910.74895 -4.075939071 -0.149461844 KYES(ph)DEDS(ph)LGSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 KYES(1)DEDS(0.99)LGS(0.005)S(0.004)GR;KYES(1)DEDS(0.763)LGS(0.235)S(0.002)GR;KYES(1)DEDS(0.989)LGS(0.006)S(0.005)GR;KYES(1)DEDS(0.871)LGS(0.073)S(0.057)GR 174.68 4.74E-08 0 881000 982900 1004440 1090880 721330 1097410 1175530 1025440 838160 TRUE FALSE 839356.876 1083058.627 1050494.568 981222.6699 847129.7236 1059406.417 996181.3084 935647.0374 968137.5721 0.866980995 1.118703228 1.085067451 1.013515742 0.875009656 1.094272598 1.028966685 0.966440168 1 19.88485254 2.997024845 24.97475072 0.99982092 1.025056864 0.024321741 0.084209821 702.4087729 5896362.631 0.024777932 0.029085047 993.1728637 -2.997024845 0.025235945 KYESVLQLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYESVLQLGR 10 1 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 150.09 3.56E-05 624570000 1052330 1052440 799990 970380 906180 941780 1143300 1070120 939280 FALSE TRUE 1002588.446 1159684.833 836670.3328 872835.5588 1064217.505 909165.9225 968868.5869 976414.6197 1084938.745 0.924096822 1.068894293 0.771168268 0.804502155 0.980901005 0.837988252 0.893016856 0.899972117 1 20.04918216 3.749111088 24.99444294 0.878368215 0.996495551 0.261484536 0.07820934 794.5079417 1882212.27 0.018683728 0.033227329 5611.915043 -3.749111088 0.118127336 KYFDFLSSYSAVNQGHCHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYFDFLSSYSAVNQGHCHPK 20 1 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 229.46 9.55E-26 578540000 832820 623620 704110 663870 713620 602270 833020 655940 51400 FALSE TRUE 793454.2491 687167.587 736394.14 597136.5263 838075.1021 581413.2389 705927.4995 598502.4162 59370.84949 13.3643742 11.57415791 12.40329465 10.0577393 14.11593584 9.792907528 11.89013642 10.08074537 1 15.85746714 -0.248475293 0.567123718 2.82E-16 12.21679388 0.876337003 1.279270895 1.896915109 0.59543032 5.654857051 0.474777905 0.564319045 0.248475293 12.21679388 KYFLHDDRDDGVDYWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYFLHDDRDDGVDYWAK 17 2 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 55.755 0.069844 183320000 442570 350390 413360 444120 339550 440790 538770 498540 362240 FALSE TRUE 421650.5932 386095.1394 432312.9649 399476.2138 398767.4125 425525.3318 456570.7413 454885.1947 418414.3291 1.007734592 0.922757928 1.033217399 0.954738368 0.95304435 1.016995122 1.091192891 1.087164475 1 18.67457273 1.989506851 4.441249794 1.06728863 0.972492024 0.496452598 0.038931098 0.139095151 6.755072103 0.015588347 0.009899554 97.61281804 -1.989506851 -0.094796606 KYGDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYGDKR 6 2 F8WF02;C9J634;P11177-3;P11177-2;P11177 F8WF02 PDHB "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial" 0 53.466 0.094591 246260000 997020 753920 805780 823830 692700 769580 966500 998690 968740 FALSE TRUE 949892.8405 830745.3051 842725.81 741017.0432 813506.6607 742929.2516 819042.674 911239.4092 1118967.252 0.848901377 0.742421464 0.753128216 0.662233003 0.727015612 0.663941908 0.731963043 0.814357532 1 20.09373638 0.88332997 2.993083977 0.999772339 0.736300508 0.729116952 0.051544681 0.269779621 4.981893178 0.0532721 0.013974487 7.644163548 -0.88332997 -0.263471831 KYGGSVGSQPPPVAPEPGPVPS(ph)SPSQEPPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 KYGGSVGSQPPPVAPEPGPVPS(0.551)S(0.415)PS(0.032)QEPPT(0.001)KR 116.55 8.40E-07 91485000 85667 69714 83032 91645 67385 81678 97394 91332 83713 TRUE FALSE 81617.69069 76817.93586 86839.09933 82432.67049 79136.92267 78849.47038 82534.75654 83334.4859 96694.78449 0.844075418 0.794437221 0.898074284 0.852503792 0.818419764 0.815446984 0.853559548 0.861830205 1 16.56115046 0.532565367 1.364738428 0.999981746 0.835517524 0.767004173 0.027596057 0.917616886 2.16719464 0.02598339 0.007667756 3.408516238 -0.532565367 -0.164464222 KYGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 KYGGSVGSQPPPVAPEPGPVPS(0.263)S(0.662)PS(0.061)QEPPT(0.014)KR 115.24 1.08E-06 90338000 190390 163970 193790 203090 153380 180590 216650 190610 181380 TRUE FALSE 181390.642 180678.7294 202675.4632 182675.0074 180129.4234 174336.123 183596.0634 173919.1779 209507.484 0.865795524 0.862397495 0.967390087 0.871925928 0.859775603 0.832123606 0.87632222 0.830133485 1 17.67664226 -1.30010552 4.602173795 1.00007757 0.870957165 0.53850968 0.037607013 2.88E-05 4.39E-06 0.035093904 0.008266749 0.050106548 1.30010552 -0.129120405 KYGLNMCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYGLNMCR 8 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7;A0A087WTT6 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ; 132.08 0.0015671 1837100000 3263800 1597020 1045110 1250020 5013200 1718010 5434700 2983800 4482700 FALSE TRUE 3109526.642 1759758.154 1093029.327 1124365.615 5887500.493 1658514.883 4605536.7 2722522.654 5177854.222 0.600543489 0.339862437 0.211096968 0.217148951 1.137054123 0.320309304 0.889468205 0.525801333 1 22.30392292 2.766455447 24.99934714 0.740113067 0.363207035 0.416622524 0.251864 755.5117147 677088.3324 0.070096979 0.074334999 584.0572876 -2.766455447 -0.376906032 KYHNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYHNPK 6 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 97.306 0.026759 1829420000 5115800 5056000 3977400 5124600 3828500 4700200 5828000 5511600 4150500 FALSE TRUE 4873986.273 5571212.148 4159767.724 4609465.472 4496189.188 4537430.895 4938831.561 5028975.085 4794138.342 1.016655325 1.162088315 0.867677866 0.961479445 0.937851365 0.946453893 1.030181277 1.04898414 1 22.19284011 3.748158267 24.99978833 0.972013414 1.089371814 0.396599879 0.060995298 631.687011 1645403.035 0.015602325 0.027687017 5599.61627 -3.748158267 0.117358401 KYHNVGLSK ddPTM_SK-BR-3_Trastuzumab_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 ; 105.4 0.0020154 2309400000 4140400 3251100 2934100 3830400 3257400 3444700 4524600 4234700 3479100 FALSE TRUE 3944691.497 3582390.786 3068631.387 3445360.915 3825489.529 3325409.175 3834289.17 3863887.218 4018621.059 0.981603251 0.891447771 0.763603072 0.857349042 0.951940845 0.827500062 0.954130562 0.961495787 1 21.93826911 1.574767942 6.186103371 0.97322681 0.885720601 0.340417045 0.061100179 0.180719025 14.17694163 0.034919811 0.016253571 37.56366356 -1.574767942 -0.08750621 KYIEIDS(ph)DEEPRGELLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KY(0.003)IEIDS(0.996)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR 225.88 8.51E-20 738745000 597647 416583 536935 558339 561968 528250 693909 611206 736096 TRUE FALSE 569397.4107 459033.2813 561554.0009 502213.7029 659975.0413 509956.57 588040.4375 557685.5624 850246.0082 0.669685485 0.539882901 0.660460614 0.590668698 0.776216571 0.599775318 0.691612112 0.655910827 1 19.6975208 -5 0.241149135 3.069146822 0.60661493 0.761692888 0.062272231 74.44323348 0.741783336 75.49562618 0.086934296 1.00E-05 5 -2.462531892 KYKDIIRQPS(ph)EEEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYKDIIRQPSEEEIIK 16 3 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 KYKDIIRQPS(1)EEEIIK 105.32 0.0071416 261250000 133190 32349 156330 73341 213880 133280 391920 131700 332930 TRUE FALSE 126894.3727 35645.39988 163497.8851 65968.62334 251180.6043 128664.4802 332125.4059 120167.6498 384559.084 0.329973671 0.092691608 0.425156736 0.171543531 0.653165182 0.334576624 0.863652478 0.312481631 1 18.55284575 1.479324702 0.282266032 1.062547637 0.107626579 0.513382276 0.203427789 1.127523447 0.347774566 0.408905387 0.365677271 30.1525955 -1.479324702 -0.954921059 KYNPTWHCIVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYNPTWHCIVGR 12 1 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 124.12 0.00021336 1248300000 1766650 1511460 2135230 2587400 1390690 2410800 1991360 2443480 1598950 FALSE TRUE 1683143.956 1665479.492 2233132.408 2327309.636 1633225.896 2327313.392 1687541.458 2229515.937 1846907 0.911331191 0.901766842 1.209120117 1.26011198 0.884303268 1.260114013 0.9137122 1.207161995 1 20.81667979 3.761703706 23.94056727 1.097016824 0.906548945 0.267775442 0.135894356 545.506736 564301.0468 0.031807824 0.057285248 5777.017798 -3.761703706 -0.190467879 KYNWSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYNWSAK 7 1 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 101.43 0.014534 2045050000 3255600 2424300 1218570 1597570 2807200 1786290 3031700 2233290 2791400 FALSE TRUE 3101714.24 2671338.926 1274442.64 1436979.228 3296774.791 1724430.329 2569158.484 2037731.288 3224276.056 0.961987803 0.82850813 0.395264741 0.445674999 1.022485276 0.534827136 0.796817158 0.631996533 1 21.62054384 -1.007709844 9.083544853 1 0.719997054 0.16346058 0.208292072 0 1.63E-10 0.198825563 0.046863635 0.098240408 1.007709844 -0.280002946 KYPDYESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYPDYESK 8 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 114.39 0.0042726 1862770000 6760900 5704150 5770320 6830900 4437290 6713600 7543000 6984400 5067720 FALSE TRUE 6441325.656 6285409.37 6034894.88 6144244.954 5211151.971 6481106.349 6392176.813 6372808.909 5853596.135 1.100404863 1.073768881 1.030972199 1.049653036 0.890247952 1.107200804 1.092008513 1.088699794 1 22.48089178 -0.119101831 7.188197097 1.000003946 1.057852227 0.065595775 0.062803511 4062791.486 565203.0705 0.059973263 0.014545653 0.76014802 0.119101831 0.057848281 KYPS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYPSPQK 7 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 KYPS(1)PQK;KY(0.001)PS(0.999)PQK;KYPS(1)PQK;KYPS(1)PQK 82.749 0.014483 3571790000 5468090 4748480 4641070 5748040 2972230 5754870 5939530 5918610 3169360 TRUE FALSE 5209624.222 5232355.511 4853867.65 5170236.099 3490585.971 5555577.409 5033345.612 5400345.132 3660848.162 1.423064818 1.429274113 1.325886089 1.412305529 0.953491054 1.517565647 1.374912422 1.475162283 1 21.80374651 -1.86047225 2.732495127 0.846834947 1.368729168 0.35213947 0.155024628 39010506.9 23978697.13 38785382.2 0.034598879 0.013788841 1.86047225 0.521894221 KYQEDS(ph)DPERS(ph)DYEEQQLQKEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYQEDSDPERSDYEEQQLQKEEEAR 25 3 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 2 KYQEDS(1)DPERS(1)DYEEQQLQKEEEAR;KY(0.03)QEDS(0.97)DPERS(0.998)DY(0.002)EEQQLQKEEEAR 167.61 1.78E-11 867670000 1136260 908010 999350 1163800 637474 1150690 1226160 1313100 776218 TRUE FALSE 1082551.242 1000537.251 1045171.186 1046812.613 748649.2638 1110841.317 1039086.772 1198118.003 896589.9231 1.207409557 1.115936311 1.165718194 1.167548938 0.834996295 1.238962527 1.158932022 1.336305452 1 19.77408876 -0.424755607 7.167728273 0.999999986 1.149002589 0.123573694 0.127802726 0 0 0.114425007 0.026970233 0.376048961 0.424755607 0.149002603 KYS(ph)AAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 KYSAAK 6 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 1 KYS(1)AAK;KYS(1)AAK;KYS(1)AAK;KYS(1)AAK;KYS(1)AAK;KYS(1)AAK 71.223 0.05439 2837420000 7394910 6207340 6065130 7886460 3621280 7602020 8007810 9114600 5178990 TRUE FALSE 7045367.26 6839875.003 6343222.21 7093698.058 4252830.085 7338760.141 6786071.511 8316477.304 5982121.319 1.177737275 1.143386207 1.060363351 1.185816482 0.71092341 1.226782232 1.134392158 1.390222107 1 22.51222574 -0.29156812 7.407957837 0.999997688 1.125215551 0.052640345 0.171020934 0 0 0.151943788 0.035813494 0.511012919 0.29156812 0.125217863 KYS(ph)CDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 1 KY(0.001)S(0.999)CDR;KYS(1)CDR 79.906 0.040373 336586000 401600 408240 374830 441850 398260 444850 478280 468120 455390 TRUE FALSE 382617.1639 449840.1201 392016.3263 397434.3985 467716.4179 429444.733 405309.6018 427128.9311 526009.5554 0.727395843 0.855193818 0.745264648 0.755564979 0.889178558 0.816420022 0.770536576 0.812017437 1 19.00472948 -5 0.315904088 2.875283947 0.787209343 0.633614205 0.049113487 201.8637497 1.804526227 252.6152348 0.042768818 1.00E-05 5 -2.088074604 KYSSCSTIFLDDSTVSQPNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYSSCSTIFLDDSTVSQPNLK 21 1 Q8ND76-3;Q8ND76-2;Q8ND76;R4GNF3 Q8ND76-3 CCNY Cyclin-Y 0 60.034 0.024403 1258700000 1564400 1790800 1328300 1754900 661910 1648900 1174400 1409600 411420 FALSE TRUE 1490453.912 1973284.556 1389203.869 1578494.118 777346.8944 1591798.18 995223.7107 1286167.951 475220.9124 3.136339066 4.152352105 2.923280169 3.321600706 1.635759021 3.349596237 2.094233828 2.706463284 1 18.8582388 1.036389872 0.164141206 1.09E-11 4.473355266 0.559935644 0.607488803 3.488780566 0.448412222 5.986811475 4.240051203 10.87401359 -1.036389872 4.473355266 KYTELPHGAIS(ph)EDQAVGPADIPCDSTGQTST ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYTELPHGAISEDQAVGPADIPCDSTGQTST 31 1 Q9H773;H3BPN2;H3BSA6 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 KYT(0.044)ELPHGAIS(0.956)EDQAVGPADIPCDSTGQTST 87.016 0.00039964 81979000 78265 55873 67887 113750 69510 133920 129720 73131 68197 TRUE FALSE 74565.56856 61566.52222 70999.6861 102315.6339 81632.52199 129282.3168 109928.8315 66727.26195 78772.64246 0.946592195 0.781572387 0.901324164 1.298872688 1.036305492 1.641208328 1.395520426 0.847086753 1 16.26540705 3.272599524 6.292239804 1.256818236 0.862936521 0.296157352 0.227519591 0.17856601 20.05372751 0.061843921 0.082420248 1873.266316 -3.272599524 -0.393881715 KYTGEDFDEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYTGEDFDEDLR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 139.3 9.49E-05 1037170000 3603750 3134030 3301280 3855310 3144160 3673430 4171830 4115670 3716270 FALSE TRUE 3433407.879 3453391.22 3452646.953 3467766.914 3692500.509 3546218.198 3535340.713 3755280.116 4292570.172 0.799848981 0.804504314 0.804330929 0.807853285 0.860207373 0.826129348 0.823595322 0.874832552 1 22.03341029 -5 0.185468866 1.773020567 0.785252555 0.931935621 0.015718904 30.96310955 0.300822846 8.781292335 0.044184221 1.00E-05 5 -0.987768012 KYTLENKEEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYTLENKEEGS(0.484)LS(0.484)DT(0.032)EADAVSGQLPDPTTNPSAGK 225.28 4.60E-37 1613300000 795920 692630 707890 885320 368980 882070 832460 932680 386510 TRUE FALSE 758298.439 763209.7845 740347.4567 796325.9516 433329.9952 851523.6947 705452.9378 851009.5948 446447.9968 1.698514596 1.709515531 1.658306145 1.783692518 0.970616955 1.907330083 1.580145824 1.906178549 1 18.76813261 -1.799973222 2.677949438 0.810724074 1.649790326 0.377696296 0.262917806 32381335.63 24338815.33 39912663.25 0.05657351 0.015849909 1.799973222 0.839066252 KYTLENKEEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYT(0.006)LENKEEGS(0.13)LS(0.734)DT(0.13)EADAVSGQLPDPTTNPSAGK;KYTLENKEEGS(0.154)LS(0.817)DT(0.029)EADAVSGQLPDPTTNPSAGK 256.21 4.10E-60 1106640000 1106280 945520 967280 1249380 556160 1233340 1174710 1291030 553430 TRUE FALSE 1053988.337 1041869.563 1011630.745 1123789.949 653154.1279 1190629.127 995486.4145 1177980.569 639253.0979 1.648780961 1.629823252 1.582519894 1.757973411 1.021745737 1.862531649 1.557264905 1.842745186 1 19.28602772 -1.860941933 2.702091909 0.743492049 1.609621818 0.404573641 0.233650661 42851211.88 32728430.38 71096091.99 0.051330041 0.013773936 1.860941933 0.86612977 KYVATLGVEVHPLVFHTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 KYVATLGVEVHPLVFHTNR 19 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;; 233.89 1.64E-24 2706080000 3677570 2987460 3466900 3648380 3731150 3550040 4377780 3641360 1048970 FALSE TRUE 3503738.554 3291885.57 3625860.794 3281637.911 4381861.379 3427101.225 3709869.258 3322503.214 1211638.91 2.891734926 2.716886642 2.992525879 2.708428958 3.616474629 2.828483962 3.061860449 2.742156253 1 20.20852838 0.780017603 4.151898961 1.000016577 2.952902663 0.852541813 0.255823154 0.976061958 18.11823865 0.230824174 0.058844832 6.025840092 -0.780017603 1.952886085 KYVIS(ph)DEEEEDDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD;KYVIS(1)DEEEEDDD 183.96 1.05E-05 5073580000 9361710 8088140 8829950 9506840 6861710 9094570 10087930 9633710 7932430 TRUE FALSE 8919200.521 8912330.661 9234811.942 8551194.381 8058390.052 8779622.76 8548831.001 8790131.281 9162550.731 0.973440779 0.972691003 1.007886582 0.93327662 0.879491998 0.958207274 0.933018681 0.959354173 1 23.12731785 3.217982837 24.99955691 0.938154347 0.980500693 0.254148593 0.031673155 278.4733887 338311.2578 0.008479788 0.010145781 1651.896515 -3.217982837 0.042346347 KYYLHDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 KYYLHDDR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;; 135.71 0.00053365 521817000 2274520 1926010 1420530 1854990 1962500 1667570 2401740 2048620 1970550 FALSE TRUE 2167007.947 2122272.609 1485662.706 1668522.881 2304759.379 1609821.633 2035310.452 1869231.972 2276132.83 0.952056892 0.932402793 0.652713535 0.73305163 1.012576836 0.707261726 0.894196694 0.821231498 1 21.11815332 -1.080190875 7.058974376 1.000000049 0.847570092 0.159449492 0.114977804 8.67E-08 1.12E-08 0.108305172 0.025527765 0.083139829 1.080190875 -0.152429957 LAAAEETAVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR 234.47 5.31E-16 6436230000 3615330 3634600 3048290 4048980 3449050 3213110 3828660 3726050 3825380 TRUE FALSE 3444440.516 4004969.872 3188057.112 3641968.838 4050563.228 3101839.195 3244527.599 3399777.309 4418600.393 0.779532026 0.906388792 0.721508357 0.824235847 0.916707298 0.701995863 0.734288533 0.769424027 1 22.07515803 2.228470937 24.9999247 0.77170321 0.830413261 0 0.097803598 539.4886731 1336719.585 0.03296083 0.024619874 169.2274993 -2.228470937 0.058710051 LAAAEETAVS(ph)PRKS(ph)PRPAGPQLFLPDPDPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAAAEETAVSPRKSPRPAGPQLFLPDPDPQR 31 3 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 2 LAAAEET(0.205)AVS(0.84)PRKS(0.955)PRPAGPQLFLPDPDPQR 62.27 0.025665 99168000 103410 48006 107620 93853 106920 106430 180550 121980 149720 TRUE FALSE 98522.01424 52897.86598 112554.4835 84418.71813 125566.8141 102744.3024 153003.7815 111298.7845 172937.8129 0.569696196 0.305877963 0.650837903 0.488144939 0.726080734 0.594111263 0.88473295 0.643576917 1 17.39989382 1.909230168 0.381912791 0.99321329 0.405837974 0.598747284 0.122684315 0.681362012 0.267562005 0.134039495 0.13316813 81.13909659 -1.909230168 -0.587375317 LAAAILGGVDQIHIKPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAAAILGGVDQIHIKPGAK 19 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 227.29 7.83E-20 384330000 467380 460110 421800 521090 326570 467740 506950 499270 357300 FALSE TRUE 445287.8737 506995.7321 441139.9472 468709.0432 383523.7046 451542.0465 429605.4667 455551.272 412708.2592 1.078941029 1.228460349 1.068890524 1.13569097 0.929285266 1.094095009 1.040942257 1.103809439 1 18.65476278 3.180523009 2.128623807 1.043128212 1.147975889 0.279501741 0.067251668 0.340536453 3.164820229 0.019486101 0.025650264 1515.385088 -3.180523009 0.104847677 LAADCAHELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAADCAHELRR 11 1 Q96LJ7 Q96LJ7 DHRS1 Dehydrogenase/reductase SDR family member 1 0 125.22 0.0002161 84602000 86710 56488 81392 77775 139900 69861 86876 82907 98129 FALSE TRUE 82611.39014 62244.19142 85123.90371 69956.90924 164298.5157 67441.69605 73621.47061 75647.22356 113346.3441 0.728840359 0.549150411 0.751007051 0.617195991 1.449526378 0.595005481 0.649526645 0.667398884 1 16.79037833 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK 36 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 298.18 2.33E-92 311540000 226651 246152 247865 268163 112656 289129 222063 254473 96623 FALSE TRUE 215937.6564 271235.1687 259229.8554 241206.7458 132303.1707 279116.3902 188183.2109 232189.9951 111606.8014 1.934807322 2.430274547 2.322706612 2.161219055 1.185440037 2.500890509 1.686126729 2.080428722 1 16.76806542 2.970486967 24.69278644 1.783598447 2.231733244 0.247271917 0.437136727 883.9470313 739575.7823 0.118923176 0.126337889 934.3013293 -2.970486967 0.448134797 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 37 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 234.87 6.51E-50 9472656000 9152316 7124358 7320899 8522610 2838373 9372144 9045630 9583730 3314519 FALSE TRUE 8719704.161 7850338.18 7656569.461 7665901.051 3333384.353 9047584.303 7665553.009 8744527.795 3828517.678 2.277566644 2.050490252 1.999878309 2.002315699 0.870672316 2.363208182 2.002224791 2.28405052 1 21.86835449 3.765900275 1.485577538 1.826509799 2.221121176 0.105309736 0.49055749 1.063127618 4.520533486 0.141095971 0.351407019 5833.111463 -3.765900275 0.394611377 LAAELEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LAAELEDRR 9 1 Q9NQG5;A2A2M0;A0A087X2D2 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;; 209.6 1.31E-05 1723240000 1785550 1496530 1498640 1673120 1788320 1580480 1923980 1685340 1842580 FALSE TRUE 1701150.59 1649028.108 1567354.126 1504934.799 2100202.442 1525747.581 1630441.515 1537762.695 2128317.896 0.799293467 0.774803478 0.73642858 0.707100571 0.986789824 0.716879553 0.766070481 0.722524909 1 21.02128222 -1.46409866 5.716160424 1.00019272 0.777041235 0.435227316 0.080102392 0.000179512 1.68E-05 0.070769753 0.016666293 0.034347991 1.46409866 -0.223151485 LAAFADALEFADEEKES(ph)PVEFTGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAAFADALEFADEEKESPVEFTGHK 25 1 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 1 LAAFADALEFADEEKES(1)PVEFTGHK;LAAFADALEFADEEKES(1)PVEFTGHK 259.42 3.21E-45 274670000 456110 401650 391950 478050 240272 474590 457550 482210 216030 TRUE FALSE 434550.5842 442578.5916 409921.2952 429995.5058 282175.3607 458154.8293 387742.344 439985.136 249530.8291 1.741470526 1.773642933 1.642768137 1.723215954 1.130823641 1.836065031 1.553885528 1.763249606 1 17.92885854 -2.548249416 0.328355579 3.40E-26 1.688689816 0.496421586 0.2015042 45.65894547 1.708928328 33.15391795 0.162534795 0.002829766 2.548249416 1.688689816 LAAFGQLHK ddPTM_SK-BR-3_Trastuzumab_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 ; 120.07 0.00072403 1259170000 1620240 1205210 732970 818540 1390060 887570 1727980 1241880 1244540 FALSE TRUE 1543654.466 1328022.269 766577.3995 736258.8041 1632486.024 856833.2283 1464344.914 1133134.404 1437536.907 1.073819016 0.92381786 0.533257543 0.512166888 1.135613295 0.596042595 1.01864857 0.788247173 1 20.45516757 -0.370695696 7.91704071 1.000011034 0.841268151 0.053548576 0.222391599 0 0 0.207790655 0.048976727 0.425896728 0.370695696 -0.158742882 LAAGRPFNT(ph)YPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAAGRPFNTYPR 12 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 LAAGRPFNT(1)YPR;LAAGRPFNT(1)YPR;LAAGRPFNT(1)YPR;LAAGRPFNT(1)YPR;LAAGRPFNT(1)YPR;LAAGRPFNT(1)YPR 181.72 2.88E-05 2890600000 1735820 1546401 1790208 1955360 1960170 1729980 2262190 1837840 2146300 TRUE FALSE 1653771.229 1703981.02 1872290.808 1758803.498 2302023.027 1670070.359 1917051.368 1676908.987 2479137.242 0.667075304 0.687328233 0.755218701 0.709441764 0.928558124 0.673649821 0.773273595 0.676408292 1 21.24140671 -5 0.223487975 2.359152779 0.699071128 0.519770778 0.079019512 121.2237039 1.212724911 74.5565166 0.136442869 1.00E-05 5 -1.660081651 LAAPSVSHVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAAPSVSHVSPR 12 0 A0A0U1RRM7;Q8WXE1-3;A0A0U1RQW3;A0A0U1RQJ8;Q8WXE1-5;Q8WXE1-2;Q8WXE1 A0A0U1RRM7 ATRIP ATR-interacting protein 1 LAAPSVSHVS(1)PR;LAAPSVSHVS(1)PR;LAAPSVSHVS(1)PR;LAAPSVSHVS(1)PR;LAAPSVSHVS(1)PR;LAAPSVSHVS(1)PR 217.01 2.43E-11 1662310000 983583 954024 1037448 1187745 1269032 1100444 1409449 1252482 1447013 TRUE FALSE 937090.9809 1051240.13 1085016.017 1068350.616 1490350.779 1062335.348 1194411.669 1142808.036 1671408.386 0.560659495 0.628954682 0.649162722 0.639191849 0.891673628 0.635592927 0.714613902 0.683739561 1 20.67263285 -5 0.114028368 2.040698876 0.493489211 0.648950727 0.07922552 97.78378681 0.734032093 23.79301922 0.847692765 1.00E-05 5 -1.547209665 LAAQENRPVTDHLDEQAVQGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAAQENRPVTDHLDEQAVQGLK 22 1 Q9BTW9-4;Q9BTW9;J3KR97;I3L439;I3L500;I3L4D2;I3L163;I3L143;I3L131;I3L3H4;I3L1S3;Q9BTW9-3;Q9BTW9-5;I3L0V3 Q9BTW9-4 TBCD Tubulin-specific chaperone D 0 71.592 0.0097442 87464000 98098 88804 94093 96383 62202 104590 107470 110840 72693 FALSE TRUE 93461.10195 97853.22856 98407.25712 86694.39772 73050.00911 100968.0221 91073.47768 101134.262 83965.85918 1.113084566 1.165393048 1.171991308 1.032495809 0.869996566 1.202489 1.084648911 1.204468852 1 16.35751522 -4.999766054 0.010728603 6.68E-06 2.012711921 0.053116441 0.101747996 37922.00079 30.88405369 3403.21954 2461.459019 1.00E-05 4.999766054 2.01270524 LAAQLGAPTS(ph)PIPDSAIVNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAAQLGAPTSPIPDSAIVNTR 21 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LAAQLGAPT(0.058)S(0.942)PIPDSAIVNTR;LAAQLGAPT(0.026)S(0.974)PIPDSAIVNTR 189.51 2.24E-17 101948000 204667 191602 186681 223985 210876 186871 196113 200473 215121 TRUE FALSE 194992.7965 211126.4616 195240.5085 201469.6023 247652.7076 180399.6104 166192.36 182918.5213 248480.866 0.784739685 0.84966889 0.785736591 0.810805297 0.996667114 0.726010068 0.668833632 0.736147311 1 17.92277524 LAASTEPQGPRPVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAASTEPQGPRPVLGR 16 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;F5GWK5;F5H3G8;F5H5A8;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;; 144.18 1.22E-06 851080000 759920 648690 713440 751860 674640 718030 865440 816150 760480 FALSE TRUE 724000.0876 714792.2485 746151.9297 676281.6044 792297.0024 693164.4411 733401.2331 744683.5793 878411.3544 0.824215311 0.813732934 0.849433384 0.769891693 0.901965803 0.789111431 0.834917752 0.847761787 1 19.74453718 0.556638755 1.741720586 0.999984987 0.824569933 0.705544339 0.035026259 1.179647215 4.077301978 0.028556166 0.008043324 3.602788394 -0.556638755 -0.175415054 LADALQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 224.7 6.98E-07 2537169000 2436470 1838223 1642859 1874513 2387800 1783294 2514630 1999421 2471450 FALSE TRUE 2321302.892 2025540.014 1718185.71 1686083.392 2804231.564 1721538.082 2130977.009 1824341.098 2854709.844 0.813148453 0.70954322 0.60187753 0.590632143 0.982317545 0.60305186 0.74647762 0.639063582 1 21.44491268 -1.157028927 4.344769764 1.000059871 0.71552393 0.365614552 0.119588598 4.71209154 63379980.58 7612.095843 0.025617649 0.069658011 1.157028927 -0.284535941 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 326.52 9.29E-118 2906538000 1880411 1685670 1732749 1852570 1912281 1671492 2042784 1764192 214964.7 FALSE TRUE 1791527.699 1857441.689 1812197.256 1666346.144 2245782.201 1613607.813 1731119.782 1609709.996 248300.3278 7.215164453 7.480625201 7.298408632 6.711010649 9.044620363 6.498613301 6.971878764 6.482915308 1 17.92172664 0.115660337 0.812438794 0.87921373 7.418519384 0.898424093 0.664284836 1.102969041 0.79572982 0.938649739 0.198523136 1.305149727 -0.115660337 6.539305654 LADELHMPSLPEMMFGDNVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LADELHMPSLPEMMFGDNVLR 21 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 157.97 5.90E-10 140599000 359040 293560 305150 356490 315910 299740 405450 361910 319810 FALSE TRUE 342068.8907 323474.0978 319141.4293 320654.9479 371004.604 289359.9286 343591.1559 330219.2418 369404.5014 0.926000873 0.87566366 0.863934868 0.868032053 1.004331573 0.783314571 0.930121735 0.893923167 1 18.49484192 0.336182553 1.436559439 1.000007013 0.891885208 0.261881996 0.056415651 6.348782085 12.3813157 0.047745924 0.013840385 2.168615479 -0.336182553 -0.108121804 LADFGVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 143.37 0.00010209 1371000000 2277400 1860590 1585250 1747110 2384830 1680770 2407230 1964850 2166040 FALSE TRUE 2169751.815 2050186.236 1657935.281 1571487.184 2800743.597 1622564.513 2039962.852 1792797.318 2501938.421 0.867228305 0.819439127 0.662660306 0.628107859 1.119429469 0.648522961 0.815352942 0.716563327 1 21.25461485 4.133558007 4.062513558 0.786957788 0.85529952 0.012496715 0.157060138 0.919680138 26.56981604 0.03618336 0.085389322 13600.59808 -4.133558007 0.068341732 LADHFGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 109.86 0.0035366 1415450000 6222340 5375590 5486310 6086770 5569910 5748420 6689280 6167140 5273270 FALSE TRUE 5928222.32 5923368.733 5737862.74 5474916.315 6541300.541 5549350.774 5668707.479 5627112.528 6091021.779 0.973272225 0.972475382 0.942019738 0.898850228 1.073924996 0.911070585 0.930666099 0.923837204 1 22.53825283 LADILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 118.4 0.0019859 78787000 381517 323063 329624 388882 378448 330569 414188 398696 477677 TRUE FALSE 363483.4475 355983.487 344737.5864 349790.8425 444449.2114 319121.3126 350996.0135 363784.0646 551752.7095 0.658779633 0.645186659 0.624804519 0.633963072 0.805522481 0.578377427 0.636147331 0.659324473 1 19.07366228 -1.790831958 2.110007 1.125659967 0.652823854 0.776375294 0.058132139 750207.2115 406115.7997 482585.3303 0.013865249 0.016187062 1.790831958 -0.472836114 LADINYEGR ddPTM_SK-BR-3_Trastuzumab_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 84.615 0.035763 56213000 224840 175730 203780 216060 180140 196710 255310 210200 233920 FALSE TRUE 214212.2588 193637.0868 213123.5146 194341.2383 211556.359 189897.8834 216357.7704 191793.7737 270195.1189 0.792805805 0.716656495 0.788776331 0.71926258 0.782976243 0.702817594 0.800746406 0.709834339 1 18.04364209 -1.884850708 2.501979045 1.126980708 0.753453222 0.809420956 0.037850843 6603487.427 3748527 4957183.604 0.007863295 0.013036148 1.884850708 -0.373527486 LADKVNSSWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LADKVNSSWQR 11 1 E5RG77;O94903;H0YBG2;E5RFX7 E5RG77 PROSC Proline synthase co-transcribed bacterial homolog protein 0 ; 110.31 0.0011208 343770000 694700 419170 433610 493270 636360 482060 753450 599060 649480 FALSE TRUE 661862.9078 461883.8996 453491.4474 443685.5624 747340.9825 465366.1413 638497.3644 546603.1306 750198.0413 0.882250914 0.615682625 0.604495643 0.591424581 0.996191594 0.620324389 0.851105081 0.72861178 1 19.51691197 0.067268326 0.444318119 1.032518099 0.708746645 0.278564414 0.135862744 5.072564291 1.357985296 0.441706761 0.075801136 1.167530746 -0.067268326 -0.323771455 LADLIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LADLIER 7 0 P05091;F8VP50;Q5SYQ7;Q5SYQ9;Q5SYQ8;P00352 P05091 ALDH2;ALDH1A1 "Aldehyde dehydrogenase, mitochondrial;Retinal dehydrogenase 1" 0 ;;;;;; 170.72 0.0022433 960342000 1586515 1284401 1331067 1305127 1504316 1113301 1436445 1364541 1548103 FALSE TRUE 1511523.58 1415282.922 1392097.739 1173933.154 1766668.234 1074747.107 1217288.933 1245054.556 1788174.907 0.845288442 0.791467835 0.778501999 0.656497947 0.987972836 0.601030192 0.680743773 0.696271126 1 20.77005643 2.199818564 24.9999987 0.709750895 0.803599431 0.03074263 0.131333118 344.0185218 221991.0259 0.043709173 0.032281955 158.4231207 -2.199818564 0.093848536 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;; 391.46 2.69E-166 1793645000 384601.2 523586 342353.3 474163 363202.6 391873.4 424970.2 455084 305110.2 FALSE TRUE 366421.8635 576940.0087 358050.5374 426499.2344 426545.0184 378302.7259 360133.1909 415234.4324 352425.1315 1.039715476 1.637056944 1.015961989 1.21018394 1.210313852 1.073427211 1.02187148 1.178220267 1 18.42695728 2.908010106 0.989230332 1.065826077 1.305452614 0.14211779 0.174660454 0.780838569 1.651772396 0.085632949 0.094909131 809.1147265 -2.908010106 0.239626537 LADS(ph)PPPQVWQLISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LADSPPPQVWQLISK 15 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 1 LADS(1)PPPQVWQLISK;LADS(1)PPPQVWQLISK 118.4 0.00030894 57410000 188917 178474 186539 209510 161432 190189 238960 217580 200941 TRUE FALSE 179987.2678 196660.7035 195091.9977 188449.6568 189585.6897 183602.7072 202502.2632 198527.5417 232101.904 0.775466572 0.847303275 0.840544581 0.811926372 0.816820915 0.79104352 0.872471357 0.855346459 1 17.82439883 0.546404144 0.806982963 1.001167816 0.81580331 0.836622178 0.025040887 0.558055213 0.591061195 0.02469092 0.008206568 3.518877468 -0.546404144 -0.185364506 LADSGDGAGPS(ph)PEEKDFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LADSGDGAGPSPEEKDFLK 19 1 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 LADSGDGAGPS(1)PEEKDFLK;LADSGDGAGPS(1)PEEKDFLK 253.66 4.23E-31 211660000 1162290 932290 944480 1157810 588700 1218720 1306600 1284790 588710 TRUE FALSE 1107350.855 1027291.411 987785.3422 1041424.739 691369.0936 1176515.421 1107254.173 1172286.976 680004.1401 1.628447225 1.510713465 1.452616659 1.531497645 1.016713065 1.730159203 1.628305046 1.72394094 1 19.375184 LAEAHQQECCQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAEAHQQECCQK 12 0 Q9Y5X3;A0A087WUY5 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 219.42 4.47E-05 0 426810 417390 395520 472110 340480 423960 461980 464350 341350 FALSE TRUE 406635.5372 459922.5155 413654.9832 424652.6058 399859.6042 409278.1589 391496.4662 423689.0523 394284.8146 1.031324368 1.16647281 1.049127351 1.077019936 1.014138991 1.038026685 0.992928086 1.074576135 1 18.58887862 3.005540484 1.72339822 1.021571259 1.09579435 0.303440603 0.041666556 0.357600622 2.158115167 0.013771111 0.016342844 1012.83916 -3.005540484 0.07422309 LAEALYIADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAEALYIADR 10 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ; 96.331 0.01585 26466000 63083 42390 42387 53123 73467 38170 67822 43590 77390 FALSE TRUE 60101.19161 46709.58919 44330.48588 47782.97511 86279.62154 36848.16333 57474.50826 39773.02851 89391.24595 0.672338672 0.522529792 0.495915292 0.534537522 0.965190949 0.412212213 0.642954549 0.44493203 1 16.44784594 -1.240801893 4.837342253 1.000087357 0.589040229 0.40930625 0.156146835 0.000131989 2.07E-05 0.135649299 0.031966082 0.057437841 1.240801893 -0.411047128 LAEDEGDS(ph)EPEAVGQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAEDEGDSEPEAVGQSR 17 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR 464.4 3.20E-206 5854630000 3377617 3466607 3181711 3577890 2793888 3257026 3354979 3000542 2703411 TRUE FALSE 3217963.738 3819858.195 3327595.596 3218233.7 3281141.183 3144234.373 2843115.335 2737798.636 3122642.171 1.030525934 1.223277592 1.065634618 1.030612386 1.050757981 1.006914722 0.910483872 0.876757081 1 21.57433583 2.427194648 0.990652249 0.919880161 1.118015362 0.552730226 0.062113372 0.352695461 0.688324956 0.040126879 0.026932974 267.42047 -2.427194648 0.198135201 LAEEENKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAEEENKAK 9 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 127.4 0.00040726 282920000 490830 261730 440120 417170 341530 458060 680050 557500 426170 FALSE TRUE 467629.4386 288400.5846 460299.9373 375235.279 401092.7239 442197.2673 576295.8825 508682.3445 492258.267 0.949967669 0.585872506 0.935078125 0.762273189 0.814801397 0.898303385 1.170718546 1.033364757 1 18.90905591 1.958759147 4.012269957 1.081105414 0.797736132 0.537589862 0.108571059 0.149442355 4.936798754 0.047422099 0.028285269 90.94087895 -1.958759147 -0.283369282 LAEIGAPIQGNREELVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAEIGAPIQGNREELVER 18 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;; 189.77 2.83E-14 487880000 229776 151653 239435 211342 265310 198953 290315 230733 322622 FALSE TRUE 218914.9439 167106.6131 250413.3316 190097.5006 311579.98 192063.2077 246022.1147 210528.7953 372652.572 0.587450511 0.448424687 0.671975321 0.510119921 0.836113859 0.515394827 0.660191646 0.564946578 1 18.50747169 -5 0.216502642 3.019649823 0.537706754 0.571434771 0.108418259 99.89191075 0.998053867 87.90310322 0.193436778 1.00E-05 5 -2.481943069 LAEIIWQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAEIIWQNR 9 0 P51692;K7EK35;P42229;P42229-2 P51692 STAT5B;STAT5A Signal transducer and activator of transcription 5B;Signal transducer and activator of transcription;Signal transducer and activator of transcription 5A 0 111.74 0.0050459 0 75195 64068 71330 67117 84843 70745 76487 67213 84997 FALSE TRUE 71640.68137 70596.60204 74600.55105 60370.27165 99639.59234 68295.08291 64817.50337 61327.4734 98177.90066 0.729702722 0.719068157 0.759850746 0.614906932 1.014888195 0.695625823 0.660204618 0.624656598 1 16.5831107 -1.596232849 3.01404093 1.016561017 0.72658104 0.369947647 0.111812259 113221044.2 127554071.2 15001335.27 0.025113483 0.025337698 1.596232849 -0.289979977 LAELEEFINGPNNAHIQQVGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LAELEEFINGPNNAHIQQVGDR 22 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 350.82 4.98E-96 2466793000 1681704 1618861 1689455 1894852 1674719 1749391 1917664 1838101 1703925 FALSE TRUE 1602213.185 1783824.776 1766918.183 1704377.877 1966789.463 1688809.151 1625089.136 1677147.132 1968160.987 0.814066123 0.906340888 0.897750842 0.865974831 0.999303145 0.85806454 0.825689132 0.852139202 1 20.9084168 4.606771749 2.912050284 0.890909568 0.810704193 0.157032848 0.059104542 0.61678474 8.645437853 0.014082374 0.099435721 40436.33153 -4.606771749 -0.080205375 LAELSDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAELSDYR 8 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;; 98.997 0.016579 51796000 829460 749790 685710 750030 785320 738960 938470 792630 627280 FALSE TRUE 790253.0696 826194.4534 717150.4818 674635.5594 922279.5594 713369.6299 795289.1653 723223.1152 724555.3787 1.090673112 1.140277856 0.989780081 0.931102824 1.272890363 0.984561913 1.097623713 0.998161268 1 19.46673644 1.451889269 0.011078417 2.57E-05 2.100977504 0.055105954 0.096472731 2233.594129 24.70742214 2346.948029 2334.081004 28.30670175 -1.451889269 2.100951808 LAELSDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LAELSDYRR 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 201.21 3.50E-05 908510000 1458825 998733 950630 977915 1490271 1033029 1583237 1221154 1571471 FALSE TRUE 1389869.233 1100505.028 994217.3258 879613.1263 1750173.791 997254.9467 1341685.118 1114223.282 1815166.697 0.765697848 0.606283175 0.547727835 0.484590825 0.964194525 0.549401302 0.739152564 0.613840748 1 20.79167061 -4.999969627 0.376553026 5.664462669 0.653403935 0.375389008 0.137905289 599.5173775 4.530867361 2280.733559 0.08553319 1.00E-05 4.999969627 -5.011058734 LAENFCVCHLATGDMLR ddPTM_SK-BR-3_Trastuzumab_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 ;; 187.31 4.74E-10 662818000 504606 444380 429226 474751 582448 394477 544367 470398 487007 FALSE TRUE 480754.2744 489662.8272 448906.4367 427028.1275 684026.7468 380816.1626 461313.8162 429207.4574 562529.5583 0.854629357 0.870465952 0.798013953 0.759121225 1.215983652 0.676970938 0.820070358 0.762995386 1 19.10156938 -1.683404006 6.764708588 1.001115703 0.845393338 0.104479213 0.142803511 0.00219251 0.000102612 0.126161884 0.029532481 0.020729842 1.683404006 -0.155722365 LAEQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 206.8 0.00048795 19664030000 10512580 8609610 8493470 10591940 9774660 9112180 10945940 9576020 10014780 FALSE TRUE 10015671.18 9486939.047 8882904.001 9527218.068 11479357.61 8796622.922 9275935.817 8737492.923 11567820.93 0.865821768 0.820114618 0.767897779 0.823596607 0.992352637 0.760439064 0.801874084 0.75532747 1 23.46361379 4.620087477 3.348550897 0.829856808 0.866556274 0 0.088500527 1.598561848 29.94660011 0.01977076 0.124891291 41695.33593 -4.620087477 0.036699467 LAEQAERYDDMAAAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAEQAERYDDMAAAMK 16 1 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 ;; 225.13 6.53E-15 906800000 1286230 726270 1416350 926420 1437760 1314110 2188790 1483160 2086630 FALSE TRUE 1225432.457 800277.7387 1481291.048 833294.5015 1688504.889 1268602.041 1854849.886 1353286.648 2410213.923 0.508433067 0.332035979 0.614589035 0.345734664 0.70056225 0.526344168 0.769578944 0.56147989 1 21.20072977 0.650419574 0.254209624 1.125364311 0.363331024 0.629715301 0.120109961 2.004445901 0.337608592 0.500814705 0.221614409 4.471153434 -0.650419574 -0.762033288 LAEQAERYDDMAACMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAEQAERYDDMAACMK 16 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 179.14 2.44E-09 497740000 445582 168056 482090 299728 557250 429465 846140 533400 835690 FALSE TRUE 424520.2219 185181.0975 504194.3034 269598.772 654434.2236 414592.5194 717045.8026 486692.6683 965284.5371 0.439787654 0.191840945 0.522327132 0.279294614 0.677970276 0.429502912 0.742833615 0.504196068 1 19.88059474 0.916007306 0.263903582 1.114790245 0.247223443 0.628640649 0.141351315 1.453229472 0.317292864 0.453627682 0.253732136 8.241519796 -0.916007306 -0.867566803 LAEQAERYDEMVESMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAEQAERYDEMVESMK 16 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 266.28 3.24E-27 528720000 689075 577001 690246 662700 605848 706913 871840 798170 699469 FALSE TRUE 656503.7904 635798.0579 721894.4618 596084.137 711507.6994 682432.4256 738824.7956 728278.0034 807939.0801 0.812565955 0.786938116 0.893501106 0.737783518 0.880645233 0.84465827 0.914456069 0.901402125 1 19.62388699 1.346759984 0.53795358 1.000758641 0.802570089 0.648818323 0.043491414 0.432723864 0.318098242 0.03962053 0.021144799 22.22081504 -1.346759984 -0.198188553 LAEQAERYDEMVESMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LAEQAERYDEMVESMKK 17 2 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 238.7 1.65E-20 684470000 922400 771620 911468 812799 689651 937230 1187309 1104421 840075 FALSE TRUE 878799.98 850248.9553 953259.7094 731094.9003 809925.916 904773.4901 1006163.206 1007712.042 970349.5405 0.905653008 0.876229564 0.982387964 0.753434582 0.834674395 0.932420177 1.036908004 1.038504168 1 19.888145 1.903886981 3.492392482 1.02726532 0.874481763 0.595688147 0.057885933 0.170150434 3.593456288 0.028392902 0.015707702 80.14694649 -1.903886981 -0.152783556 LAEQFVLLNLVYETTDKHLSPDGQYVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAEQFVLLNLVYETTDKHLSPDGQYVPR 28 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;; 240.16 1.76E-45 771910000 605659 346539 641854 512823 856809 528657 949104 698658 923588 FALSE TRUE 577030.6994 381851.7181 671283.6408 461273.0577 1006236.218 510349.4755 804300.7533 637479.8017 1066813.31 0.54089192 0.357936777 0.629241906 0.432384048 0.943216783 0.478386866 0.753928308 0.597555163 1 20.0248763 -4.99999792 0.070032505 2.523875937 0.035583112 0.448614806 0.155555554 240.4356759 1.212136129 58.62812558 7.305840691 1.00E-05 4.99999792 -2.488292825 LAERLS(ph)PFLAESK ddPTM_SK-BR-3_Trastuzumab_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 99.663 0.0016699 171400000 125396 99813 113130 114775 116222 118665 120192 126001 142138 TRUE FALSE 119468.7796 109984.0582 118317.1224 103237.5989 136491.08 114555.6013 101854.5029 114967.6845 164180.0351 0.727669351 0.669899103 0.720654752 0.628807266 0.831350048 0.697743798 0.620383001 0.700253745 1 17.32491918 -1.085366107 4.597997404 1.000018979 0.69538068 0.721528272 0.058598748 1.08E-05 2.15E-06 0.053803381 0.012680789 0.08215498 1.085366107 -0.304638299 LAETYLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAETYLHR 8 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 151.27 0.00080307 329520000 381690 349630 243720 307150 392480 277490 390360 332550 324640 FALSE TRUE 363648.2701 385257.6945 254894.8031 276274.6985 460928.3877 267880.4517 330803.4125 303430.159 374983.5132 0.969771356 1.027399021 0.67974936 0.736764921 1.229196409 0.714379279 0.882181218 0.809182666 1 18.51646764 LAFVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAFVIR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 123.06 0.044092 344090000 484210 392610 387800 444110 479070 389540 519230 463320 505580 FALSE TRUE 461322.3529 432617.4054 405581.0136 399467.219 562619.6563 376050.1321 440011.9272 422749.2446 583982.7643 0.78995885 0.740805092 0.694508534 0.684039399 0.963418256 0.643940464 0.753467318 0.723907058 1 19.15556626 -1.06889214 4.085915691 1.000035778 0.749333696 0.456283675 0.086020551 19492110878 37256231599 10352578.94 0.018706663 0.085331201 1.06889214 -0.250702082 LAGDKANYWWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAGDKANYWWLR 12 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 158.25 6.10E-05 450770000 1273090 726120 871580 763840 1509650 963200 1922310 1243460 1887340 FALSE TRUE 1212913.559 800112.4535 911542.8051 687057.352 1772932.482 929844.1425 1629026.304 1134576.05 2180019.048 0.556377505 0.367020854 0.418135248 0.315161169 0.813264675 0.426530283 0.747253243 0.520443182 1 21.05590931 0.339700838 0.324449397 1.093376321 0.412129086 0.535451576 0.148598194 2.554473169 0.498716811 0.52363305 0.149070687 2.186255114 -0.339700838 -0.681247236 LAGESESNLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAGESESNLRK 11 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 140.49 6.19E-05 668770000 659280 453140 539370 575220 565240 585380 737560 657650 675200 FALSE TRUE 628117.141 499315.4812 564100.648 517397.7928 663817.677 565108.1438 625031.6758 600062.6796 779906.5676 0.805374858 0.640224742 0.723292599 0.66340997 0.851150259 0.724584415 0.801418659 0.769403291 1 19.57294177 -0.32523023 0.359803236 1.070595692 0.71162494 0.641579483 0.061153639 4.096310277 0.597208726 0.426873294 0.046423796 0.472900497 0.32523023 -0.358970752 LAGGDWFTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAGGDWFTSR 10 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 219.54 1.46E-08 669205000 339320 316192 268281 329703 295967 287180 345493 324883 301295 FALSE TRUE 323281.0161 348412.3243 280581.9492 296560.628 347583.5511 277234.8846 292781.6974 296434.5222 348018.2898 0.928919616 1.001132223 0.806227596 0.852140927 0.998750817 0.7966101 0.841282502 0.851778573 1 18.4088036 3.748394599 24.9633701 0.868822487 0.965025921 0.191179995 0.07238494 851.019315 2160289.973 0.017308087 0.030731385 5602.664275 -3.748394599 0.096203434 LAGS(ph)PPGSGQWKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAGSPPGSGQWKPK 14 1 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 LAGS(0.889)PPGS(0.111)GQWKPK 165.16 2.43E-06 791590000 1755100 1748800 1687500 2154400 1127300 2034400 2102800 2073900 1395800 TRUE FALSE 1672139.901 1927004.708 1764873.544 1937835.619 1323900.763 1963948.218 1781979.239 1892298.322 1612253.535 1.037144509 1.195224365 1.094662536 1.201942236 0.821149239 1.218138571 1.105272341 1.173697734 1 20.6206472 -1.062208292 4.93479977 0.999997441 1.10860554 0.076061488 0.115658674 2.89E-06 5.49E-07 0.099437991 0.023437207 0.086654617 1.062208292 0.108608099 LAHCEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAHCEELR 8 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 131.03 0.0010225 135600000 199273 163815 140753 164726 283560 126594 206940 143360 281900 FALSE TRUE 189853.7602 180507.9347 147206.6643 148167.4295 333012.7742 122210.018 175367.5023 130806.6384 325615.6123 0.583060987 0.554358968 0.452087243 0.455037854 1.022717467 0.375319897 0.538572156 0.401721028 1 18.31281035 -1.415963066 5.56630279 1.000252248 0.550474402 0.380452507 0.181299931 0.000517632 5.43E-05 0.160107346 0.037716897 0.038373988 1.415963066 -0.449777846 LAHEVGWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAHEVGWK 8 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 143.61 0.00059868 8173300000 13033150 11182550 11333070 13198650 10570450 12181500 14394340 12658660 10616750 FALSE TRUE 12417098.83 12322064.56 11852702.47 11871896.63 12413933.13 11759651.6 12198219.06 11550200.62 12263141.37 1.012554488 1.004804902 0.966530689 0.968095879 1.012296341 0.958942839 0.994705899 0.941863123 1 23.54782526 3.850162959 5.510809521 0.97824608 1.009585705 0.283192066 0.020698887 0.246345415 10.38513386 0.004754702 0.00872203 7082.114745 -3.850162959 0.031339625 LAHHLVALYYQSEEQAEEELLDMAVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAHHLVALYYQSEEQAEEELLDMAVLK 27 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 184.39 7.73E-18 267100000 153609 203738 157945 192970 123839 174027 192366 156377 74942 FALSE TRUE 146348.207 224499.1338 165186.9345 173572.289 145436.4824 168000.4014 163017.0337 142683.8009 86563.62261 1.690643282 2.593458165 1.908271968 2.005141233 1.68011086 1.940773691 1.883204847 1.648311341 1 16.40147326 -0.074453138 0.323368552 0.73275833 2.13313808 0.607819277 0.246725964 3.637243832 0.52910263 1.462729832 0.25039877 0.842455291 0.074453138 1.40037975 LAHPNKPK ddPTM_SK-BR-3_Trastuzumab_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 ; 92.925 0.0068693 1535170000 2504400 2138930 1997150 2454100 1801170 2253050 2797300 2720300 1900770 FALSE TRUE 2386021.975 2356889.399 2088721.303 2207409.206 2115293.478 2175026.314 2370520.509 2482096.111 2195531.704 1.086762706 1.073493676 0.95135101 1.005409852 0.963453852 0.990660399 1.079702245 1.130521644 1 21.06613894 -0.819404984 7.395291954 0.999999965 1.037320375 0.033899883 0.058002089 0 5.89E-11 0.058495325 0.01378748 0.151563636 0.819404984 0.037320411 LAHQS(ph)EEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAHQSEEK 8 0 Q9H257;Q9H257-2;Q9H257-3 Q9H257 CARD9 Caspase recruitment domain-containing protein 9 1 LAHQS(1)EEK 53.683 0.08698 41094000 57066 53255 58771 66918 59330 43631 70676 60678 59329 TRUE FALSE 54368.60327 58681.74505 61465.70848 60191.2755 69677.13322 42120.04753 59893.07815 55364.71265 68529.43831 0.793361286 0.856299811 0.896924154 0.878327285 1.016747473 0.614627065 0.873975909 0.807896781 1 16.06443624 -2.439833116 2.061618856 2.284591906 0.840805012 0.194790877 0.100743765 3342161.089 260590.5076 20072355.37 0.022649065 0.003632176 2.439833116 -1.443786893 LAHYIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LAHYIDR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;;; 107.59 0.0074425 1475510000 2075350 1656190 1681460 2014020 2126240 1707790 2165000 1871040 1997860 FALSE TRUE 1977252.318 1824957.644 1758556.604 1811566.883 2497055.583 1648648.804 1834689.487 1707201.819 2307677.925 0.856814678 0.790819908 0.762045945 0.785017209 1.082064163 0.714418934 0.795037066 0.739792065 1 21.13801046 -2.421210366 2.239546013 2.62087476 0.815346318 0.24392768 0.101940951 3707083.715 349496.9714 30847084.46 0.023241341 0.003791313 2.421210366 -1.805528443 LAHYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 132.11 0.015041 21763110000 39199900 38138100 23662680 32768700 29373100 28254800 36376400 31428200 25297270 FALSE TRUE 37346998.41 42024415.75 24747637.28 29474728.02 34495759.34 27276329.19 30826512.08 28676180.2 29220241.43 1.278120802 1.438195364 0.84693473 1.008709257 1.180543269 0.933473779 1.054971163 0.981380673 1 24.80046476 3.746933086 24.99991651 1.009420372 1.3581581 0.719512557 0.092625196 280.9199716 838815.6612 0.022454412 0.039645496 5583.841546 -3.746933086 0.348737728 LAHYNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAHYNKR 7 1 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 ; 137.83 0.0045612 3721200000 3421400 2194960 1170230 1266550 2699400 1635550 3383900 2357600 2535600 FALSE TRUE 3259677.203 2418628.919 1223886.203 1139233.988 3170174.505 1578910.493 2867623.905 2151156.046 2928807.898 1.112970641 0.825806609 0.41787862 0.388975319 1.082411212 0.539096639 0.979109592 0.734481783 1 21.48188214 -0.314080257 8.057079358 0.999991879 0.780312124 0.075275826 0.255669839 0 0 0.243600464 0.05741718 0.485198828 0.314080257 -0.219679755 LAIQGPEDS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.905)PS(0.095)R;LAIQGPEDS(0.991)PS(0.009)R;LAIQGPEDS(0.627)PS(0.373)R;LAIQGPEDS(0.7)PS(0.3)R;LAIQGPEDS(0.999)PS(0.001)R;LAIQGPEDS(0.999)PS(0.001)R 305.46 5.75E-37 6398240000 7195800 6168590 6425790 6767190 6756000 6603780 7728160 6708310 7157940 TRUE FALSE 6855668.795 6797176.334 6720418.827 6086939.204 7934244.261 6375089.443 6549087.255 6120894.813 8267956.778 0.829185369 0.822110773 0.812827039 0.736208397 0.959637849 0.771059842 0.79210468 0.740315289 1 22.97909942 -1.618862415 4.376231369 1.00408104 0.810015987 0.48307188 0.062407707 0.002293604 0.000199756 0.055773966 0.012891369 0.024051246 1.618862415 -0.194065053 LAIRES(ph)IESEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAIRESIESEIRR 13 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(1)IESEIRR;LAIRES(1)IESEIRR 166.9 1.71E-05 361370000 259310 197779 242230 246790 268220 218381 284130 268130 307620 TRUE FALSE 247052.9302 217932.905 253336.4851 221982.2003 314997.4831 210818.4112 240780.7501 244651.1158 355324.1385 0.695288902 0.613335491 0.71297291 0.624731552 0.886507414 0.593312945 0.677636907 0.6885294 1 18.43877617 -1.850711237 1.580708807 1.185272539 0.680992974 0.596306459 0.080940191 43815.23732 14903.91627 30494.99264 0.020047676 0.014102261 1.850711237 -0.504279565 LALDMEIHAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 186.87 3.84E-06 4102950000 5416620 4523820 4233630 4977060 5482570 4347230 5631950 5076060 5020820 FALSE TRUE 5160587.107 4984802.401 4427746.123 4476756.473 6438728.472 4196684.335 4772692.59 4631573.277 5799423.123 0.889844903 0.85953418 0.763480441 0.771931342 1.110236024 0.723638239 0.822959886 0.798626549 1 22.46747797 4.208595476 3.784865839 0.844157281 0.883670917 0 0.117380759 1.222873791 36.6860654 0.027500285 0.071254855 16165.73578 -4.208595476 0.039513636 LALDMEIHAYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LALDMEIHAYRK 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 145.91 4.17E-05 325700000 354270 139500 301670 220430 392690 300360 500010 347430 506020 FALSE TRUE 337524.3592 153715.2086 315501.8679 198271.9576 461175.0117 289958.4579 423724.2912 317007.1874 584490.9972 0.577467165 0.262989865 0.539789098 0.339221577 0.789019872 0.496087124 0.724945796 0.542364534 1 19.15682128 0.351470451 0.258939628 1.142909568 0.371974044 0.537469862 0.145042845 3.254456663 0.450589804 0.754396884 0.247070464 2.246313931 -0.351470451 -0.770935524 LALLEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LALLEEAR 8 0 Q5TZA2-2;Q5TZA2;B1AKD8 Q5TZA2-2 CROCC Rootletin 0 ;;;;; 176.29 0.00060758 491306000 1109710 767789 515675 671394 1095730 615975 1073970 882340 1091200 FALSE TRUE 1057256.208 846027.572 539319.2088 603904.1996 1286824.965 594643.6313 910116.1517 805077.632 1260417.723 0.838814139 0.671227924 0.427889262 0.479130203 1.020951183 0.471782982 0.722075019 0.638738743 1 20.26547051 -1.331667789 3.031625767 1.003104998 0.665110363 0.26303006 0.1791993 30698730.75 39446959.3 866983.748 0.043378863 0.046594238 1.331667789 -0.337994634 LALPGHAESYNPPPEYLLSEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 264.72 5.67E-44 203042000 154561 138148 126444 160878 141841 136549 148502 150098 139214 FALSE TRUE 147255.2078 152225.4383 132241.5825 144706.2378 166578.0255 131820.2739 125845.2925 136954.6234 160802.5961 0.915751433 0.946660327 0.822384624 0.899899885 1.035916269 0.819764588 0.782607343 0.851694106 1 17.29493117 LALQLHPDRNPDDPQAQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LALQLHPDRNPDDPQAQEK 19 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;; 135.38 4.74E-06 1008850000 1127380 996050 973450 1182200 827020 1140920 1202580 1217380 835080 FALSE TRUE 1074090.982 1097548.627 1018083.645 1063363.01 971252.0262 1101409.654 1019104.334 1110779.753 964579.9414 1.113532363 1.13785139 1.055468398 1.102410453 1.006917088 1.141854197 1.056526567 1.151568373 1 19.87954128 0.749601777 0.009956747 3.73E-07 2.135340923 0.196393153 0.048715702 2798.844747 14.7304729 1607.899434 1549.263706 5.618259272 -0.749601777 2.13534055 LALS(ph)PLSLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 LALS(1)PLSLGK;LALS(0.998)PLS(0.002)LGK;LALS(0.991)PLS(0.009)LGK 138.63 6.26E-05 362348000 1437130 1659440 1449880 1844840 1191421 1616050 1696740 1695910 1402850 TRUE FALSE 1369199.713 1828538.823 1516358.432 1659393.178 1399204.445 1560085.783 1437871.15 1547407.13 1620396.813 0.844978034 1.128451258 0.935794504 1.024065935 0.863494938 0.962780086 0.887357429 0.954955673 1 20.62791572 2.755023482 24.93952969 0.926018222 0.989498528 0.080488298 0.079818543 1593.604047 2414140.851 0.022786365 0.02410451 568.8836895 -2.755023482 0.063480307 LALSEEDKEVIIDSTNIIFHCAATVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LALSEEDKEVIIDSTNIIFHCAATVR 26 1 E9PNW8;Q8WVX9 E9PNW8 FAR1 Fatty acyl-CoA reductase 1 0 131.56 3.76E-05 64121000 142420 139430 138060 184390 135620 184160 204290 168660 115560 FALSE TRUE 135688.0888 153638.0755 144390.1876 165854.7669 159272.0851 177782.493 173121.8085 153891.2363 133480.4546 1.016539008 1.151015525 1.081732812 1.242539721 1.193224023 1.331899068 1.296982461 1.152912138 1 17.02626898 3.526976472 1.167642999 1.233899338 1.058045657 0.188110005 0.098973266 0.557129973 1.534797044 0.032250645 0.069602723 3364.93339 -3.526976472 -0.175853681 LALVTGGEIASTFDHPELVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LALVTGGEIASTFDHPELVK 20 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 290.42 1.90E-54 235490000 482610 408340 451790 515460 477590 440970 639800 507030 558070 FALSE TRUE 459797.9817 449950.3102 472505.0184 463644.9815 560881.5448 425699.0983 542186.7593 462631.7653 644612.6454 0.713293456 0.698016574 0.733006127 0.719261381 0.870106333 0.660395202 0.841104752 0.717689559 1 19.29807296 -5 0.180133294 2.055961725 0.689338378 0.623329495 0.063058194 77.38741537 0.745173203 29.2028392 0.169615393 1.00E-05 5 -1.366623347 LAMQEFMILPVGAANFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LAMQEFMILPVGAANFR 17 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 254.4 1.14E-26 1289292000 808976 603228 591707 687775 777962 665446 834281 760566 791132 FALSE TRUE 770737.3077 664697.619 618837.3512 618638.5503 913638.3265 642401.4382 706996.1108 693966.809 913816.71 0.843426586 0.727386151 0.677200739 0.676983189 0.999804793 0.702987187 0.77367387 0.759415757 1 19.8015453 LANQAADYFGDAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LANQAADYFGDAFK 14 0 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 122.45 0.00025283 36021000 165900 125040 138470 156490 129260 162470 179200 171470 145260 FALSE TRUE 158058.2358 137781.7182 144818.9865 140759.3279 151802.9031 156843.6232 151859.7488 156455.1778 167786.1789 0.942021785 0.82117442 0.863116303 0.838920874 0.904740212 0.934782735 0.90507901 0.932467613 1 17.35626436 1.156171127 0.602594708 0.998043489 0.869064952 0.55208409 0.035402788 0.586861586 0.525422064 0.035715448 0.016263084 14.32752343 -1.156171127 -0.128978537 LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAK 38 0 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 374.1 5.38E-162 159860000 104050 77436 97667 110540 134390 97145 153000 126920 36149 FALSE TRUE 99131.76271 85326.81644 102145.1286 99428.30919 157827.5735 93780.84429 129657.04 115806.212 41754.8023 2.374140392 2.043521026 2.446308519 2.381242485 3.779866381 2.245989422 3.105200667 2.773482464 1 15.34965451 2.979109458 24.67969097 2.750335531 2.268643807 0.005062822 0.714750371 1448.885829 1711688.319 0.189363132 0.202948939 953.0363335 -2.979109458 -0.481691725 LAPEFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAPEFAK 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 91.906 0.037363 150920000 358800 310490 285250 351950 318550 325920 399270 385800 358540 FALSE TRUE 341840.2351 342129.284 298328.9947 316571.3173 374105.0191 314633.3087 338354.0284 352017.3067 414140.552 0.825420822 0.826118771 0.720356877 0.764405504 0.903328634 0.759725912 0.817002891 0.849994778 1 18.65976095 0.751900014 1.888588844 0.999895726 0.803427505 0.61867431 0.048772478 0.613151996 3.47775467 0.044471305 0.012412335 5.648069266 -0.751900014 -0.196468221 LAPGGHVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;;;;;;; 172.15 5.64E-05 7895840000 8953313 8249429 7701367 9573649 9085214 8299010 10014711 9254353 9538899 FALSE TRUE 8530107.638 9090055.194 8054482.295 8611287.614 10669672.45 8011613.203 8486782.904 8443992.791 11018142.74 0.774187433 0.825007935 0.731019963 0.781555278 0.968373046 0.72712919 0.770255306 0.766371701 1 23.39337772 -1.101908475 4.123353751 1.000036151 0.793121627 0.477561074 0.068045839 56328.58679 35126079.09 2998.491265 0.014965343 0.079084528 1.101908475 -0.206914524 LAPPS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAPPSPAR 8 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 LAPPS(1)PAR;LAPPS(1)PAR 87.258 0.016208 855620000 642780 558790 598850 630140 888180 572310 704780 584430 964900 TRUE FALSE 612397.0633 615731.3363 626307.8648 566797.13 1043078.311 552490.7612 597252.8668 533254.2109 1114531.764 0.549465778 0.552457414 0.561947075 0.508551796 0.935889263 0.495715581 0.535877833 0.478455822 1 20.0880063 -1.549748114 3.045450837 1.018041229 0.575028932 0.509076133 0.130436556 50993392.84 57627526.29 7542673.941 0.029185752 0.02820018 1.549748114 -0.443012297 LAPS(ph)EDELTCFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAPSEDELTCFSK 13 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LAPS(1)EDELTCFSK;LAPS(1)EDELTCFSK 146.84 2.63E-06 35468000 91761 83765 91689 109145 70513 102357 106810 102668 94820 TRUE FALSE 87423.63938 92300.74873 95893.03134 98173.53724 82810.44487 98812.35142 90514.1728 93677.84564 109524.2013 0.798212982 0.842742952 0.875541937 0.896363873 0.756092661 0.902196503 0.826430795 0.8553164 1 16.74089017 -4.999999977 0.30919761 2.392297349 0.834741537 0.557830159 0.043765603 207.6047491 1.883466833 188.1636392 0.037730132 1.00E-05 4.999999977 -1.557555813 LAPSEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAPSEYR 7 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;; 103.29 0.019566 165035000 525772 433505 452145 486786 739647 400923 590348 469232 668800 FALSE TRUE 500919.7995 477679.6524 472876.2955 437853.3464 868641.2026 387038.936 500279.5701 428143.5585 772514.0882 0.648428044 0.61834426 0.612126436 0.566790112 1.124434125 0.501012139 0.647599284 0.554221036 1 19.55920172 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 LAPVPS(1)PEPQKPAPVS(1)PESVK;LAPVPS(1)PEPQKPAPVS(0.967)PES(0.033)VK;LAPVPS(1)PEPQKPAPVS(0.81)PES(0.19)VK 162.07 1.09E-11 1149450000 1863350 1629830 1656870 1954240 1011670 2029230 2136720 2127850 1251890 TRUE FALSE 1775273.138 1795911.53 1732839.128 1757796.082 1188104.928 1958957.256 1810724.12 1941524.174 1446026.707 1.227690422 1.241962905 1.198345175 1.215604161 0.821634152 1.354717203 1.252206554 1.342661352 1 20.46366277 3.49708789 2.923836524 1.180182638 1.234193085 0.026824469 0.157910663 1.395727412 24.04707267 0.043916183 0.067990321 3141.144314 -3.49708789 0.054010447 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(0.999)PEPQKPAPVS(0.001)PESVK;LAPVPS(1)PEPQKPAPVSPESVK 200.12 4.63E-22 1197500000 2859860 2433384 2429510 2905450 1775269 2886260 3088350 3158240 2116396 TRUE FALSE 2724680.085 2681348.596 2540905.437 2613388.646 2084875.352 2786308.092 2617165.486 2881687.763 2444595.883 1.114572803 1.096847383 1.039396922 1.069047307 0.852850717 1.139782699 1.070592283 1.178799238 1 21.22116456 -0.237760426 7.133717945 0.999999073 1.070911264 0.060944686 0.086608464 0 0 0.078942865 0.018607012 0.578415036 0.237760426 0.070912191 LAQALHEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAQALHEMR 9 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 129.85 0.00037767 118330000 256920 146530 73234 94969 279980 121630 263700 174620 241220 FALSE TRUE 244775.9008 161461.5736 76591.85134 85422.53569 328808.4234 117417.9226 223467.7218 159329.3471 278627.1656 0.878506948 0.579489703 0.274890107 0.306583658 1.180101813 0.421415917 0.80203135 0.571837088 1 18.0879764 2.789709036 24.99999798 0.753522862 0.54937709 0.207933171 0.264974618 760.1477135 371538.6103 0.079379321 0.084194391 616.1820406 -2.789709036 -0.204145772 LAQANGWGVMVSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;; 248.69 1.29E-17 15850930000 8063179 6158500 4879922 5217511 7903369 6067193 8305037 6892302 6621125 FALSE TRUE 7682048.508 6786058.152 5103671.251 4693036.882 9281714.051 5857084.585 7037951.073 6288775.498 7647895.249 1.004465707 0.887310552 0.667330172 0.613637704 1.213629861 0.765842679 0.920246793 0.822288394 1 22.86663133 2.777373551 24.99996628 0.923078598 0.825357086 0.161254452 0.160188293 1522.315002 980542.1334 0.049289929 0.052279069 598.9265299 -2.777373551 -0.097721512 LAQFVEHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAQFVEHWK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 148.91 8.89E-05 423490000 1206820 895090 758620 1110750 912120 879810 1280500 1119540 902430 FALSE TRUE 1149776.01 986300.6886 793403.4774 999095.2997 1071193.439 849341.9591 1085136.207 1021507.143 1042374.235 1.103035715 0.946205936 0.761150315 0.958480425 1.027647656 0.814814805 1.041023627 0.979981189 1 19.9914419 1.616546911 25 1.007878559 0.9457775 0.10203201 0.097052745 1.889030473 5424.888579 0.04650237 0.025283748 41.35679844 -1.616546911 -0.062101058 LAQGHTTVDELAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 173.68 2.13E-05 3131255000 1150919 878641 996871 1148615 1210512 1044598 1370645 1161397 1259261 FALSE TRUE 1096517.34 968175.5168 1042578.521 1033154.038 1421624.91 1008423.309 1161527.932 1059698.922 1454540.764 0.753858102 0.665622814 0.716775045 0.710295691 0.977370277 0.693293261 0.798553028 0.728545358 1 20.4721323 -4.999999998 0.174957963 1.982046839 0.69612202 0.443457979 0.086293586 118.2744689 1.12759623 40.40265481 0.269821363 1.00E-05 4.999999998 -1.285924818 LAQGLTHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAQGLTHLGK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 125.22 0.00041493 523100000 1543700 1314280 1356230 1539850 1257050 1433650 1682600 1582160 1355510 FALSE TRUE 1470732.36 1448206.626 1418414.487 1385061.352 1476279.122 1384002.341 1425888.467 1443617.683 1565715.568 0.939335592 0.92494873 0.90592092 0.884618753 0.942878229 0.883942377 0.910694443 0.922017838 1 20.57839072 -1.04076633 5.837117407 1.000000214 0.914795989 0.650675988 0.019732202 5.39E-08 8.83E-09 0.018693701 0.004406137 0.091040298 1.04076633 -0.085204226 LAQMISDHNDADFEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 149.09 8.69E-07 128210000 101640 92638 81566 119670 55548 83098 103380 119190 65408 FALSE TRUE 96835.67863 102077.9175 85305.88178 107640.5442 65235.55361 80220.29542 87607.4823 108753.0917 75551.13858 1.281723617 1.351110247 1.129114443 1.424737552 0.863462217 1.061801277 1.159578584 1.439463306 1 16.20516588 2.766947854 24.99859658 1.114697927 1.294774982 0.257561355 0.16132701 1047.06723 922075.0656 0.046929241 0.049768199 584.7198725 -2.766947854 0.180077054 LAS(ph)PELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LASPELER 8 0 P05412;P17535 P05412;P17535 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER 234.28 1.55E-08 5651140000 12529530 9594790 10106360 11632060 9581450 10584850 12251400 10755970 9138030 TRUE FALSE 11937283.95 10572510.01 10569746.6 10462783.23 11252451.85 10218293.99 10382223.92 9814120.246 10555109.02 1.130948427 1.001648584 1.001386777 0.991252976 1.066066852 0.968089858 0.983620718 0.929798094 1 23.33143814 8 0.566698731 0.983932236 8.533889003 0.631036171 0.033404786 86.58451766 0.74883202 0.014539681 800.7407695 100000000 -8 7.549956766 LAS(ph)PSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.795)PS(0.165)GS(0.034)T(0.005)S(0.001)SGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.555)PS(0.189)GS(0.235)T(0.017)S(0.002)S(0.002)GLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.167)PS(0.167)GS(0.167)T(0.167)S(0.167)S(0.167)GLEVVAPEGTSAPGGGPGTLDDSATICR 256.9 1.77E-62 1365040000 399269 281343 379258 383071 342069 329308 423521 372213 397966 TRUE FALSE 380396.3456 310012.1716 396647.3544 344563.9753 401725.7253 317903.9814 358905.093 339620.0565 459680.5348 0.827523284 0.674407873 0.862876116 0.749572691 0.873923725 0.691575904 0.7807707 0.738817572 1 18.81027205 -1.275739404 5.283790004 1.000034134 0.770898248 0.532194664 0.06621884 2.35E-05 3.23E-06 0.056655071 0.013351741 0.052998136 1.275739404 -0.229135886 LAS(ph)SVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LASSVLR 7 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 1 LAS(0.711)S(0.289)VLR;LAS(0.5)S(0.5)VLR;LAS(0.525)S(0.475)VLR 101.28 0.0096213 191728000 429220 371870 401497 469849 505870 394839 478870 440429 527040 TRUE FALSE 408931.6212 409763.9758 419906.0346 422618.8859 594093.5678 381165.6264 405809.5864 401862.7019 608770.6715 0.671733446 0.673100718 0.689760618 0.694216896 0.975890587 0.626123505 0.666605021 0.660121653 1 19.21553933 -1.481885093 2.892991522 1.009419093 0.70280534 0.470245482 0.097570357 16606136.13 18662357.97 1251849.239 0.023514246 0.032969693 1.481885093 -0.306613753 LAS(ph)YLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LAS(1)YLDR;LAS(1)YLDR;LAS(0.999)Y(0.001)LDR;LAS(1)YLDR 139.02 0.0028627 181221000 605670 497960 451630 618090 523990 530270 619950 544190 495940 TRUE FALSE 577041.1794 548702.6901 472337.6822 555958.4189 615373.6901 511906.6169 525365.2413 496537.8387 572847.8423 1.007320159 0.957850671 0.824543007 0.970516737 1.074235852 0.893617081 0.917111321 0.866788355 1 19.12779246 LASDDRPS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LASDDRPSPPR 11 1 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 LAS(0.018)DDRPS(0.982)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LAS(0.014)DDRPS(0.986)PPR;LAS(0.001)DDRPS(0.999)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR 120.49 0.0011705 7241440000 7167610 6323270 6316330 7339240 6568540 6640100 7866750 7375010 7462410 TRUE FALSE 6828811.28 6967618.402 6605939.978 6601485.652 7714091.296 6410151.672 6666532.805 6729215.027 8619642.43 0.792238348 0.80834193 0.766382136 0.765865371 0.894943306 0.743667933 0.773411758 0.780683779 1 23.03919659 -1.111046104 5.513842313 1.000002627 0.79062023 0.721928741 0.040824356 1.22E-06 1.97E-07 0.036651626 0.008638763 0.077437959 1.111046104 -0.209382396 LASDLLEWIR ddPTM_SK-BR-3_Trastuzumab_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 ; 169.09 1.10E-05 770240000 989760 683470 629970 826170 1075010 655550 1089410 779760 935170 FALSE TRUE 942976.0063 753116.37 658854.7476 743121.822 1262491.404 632848.1391 923200.4961 711480.0806 1080191.387 0.872971232 0.69720642 0.609942604 0.687953848 1.168766404 0.585866677 0.854663819 0.658661131 1 20.04285552 LASDLLEWIRR ddPTM_SK-BR-3_Trastuzumab_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 ; 234.72 2.67E-15 177372000 413010 288120 299480 368400 532350 322630 625730 443470 811040 FALSE TRUE 393487.8358 317479.7556 313211.4542 331367.7321 625191.6715 311457.2422 530263.3962 404637.4158 936811.941 0.42002863 0.338893797 0.334337598 0.353718519 0.667360912 0.332465064 0.566029715 0.43193025 1 19.83739994 -4.999999999 0.205231081 3.709944049 0.338876722 0.754229762 0.103980007 63.70324037 0.632832056 70.73893656 0.209889048 1.00E-05 4.999999999 -3.371067327 LASDS(ph)DAESDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 LAS(0.113)DS(0.887)DAESDSR;LASDS(1)DAESDSR;LASDS(1)DAESDSR 318.32 1.51E-46 1332010000 900140 732110 783740 893380 819210 783190 932300 833160 806040 TRUE FALSE 857592.1661 806712.8413 819675.2542 803575.7451 962079.9646 756067.9339 790060.5121 760204.0935 931036.5665 0.92111545 0.866467409 0.880389969 0.863097943 1.033342834 0.812071149 0.848581614 0.81651368 1 19.82847831 -0.292840748 7.27351489 1.000000373 0.880076799 0.265438699 0.062632286 0 0 0.057272248 0.013499198 0.509517672 0.292840748 -0.119923574 LASELAKT(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASELAKTPQK 11 1 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 1 LASELAKT(1)PQK 79.652 0.04294 339790000 397770 302980 403300 360900 251920 407000 514790 489380 368130 TRUE FALSE 378968.2004 333854.0065 421791.7039 324621.6463 295854.7682 392905.4879 436249.3307 446527.2928 425217.7203 0.89123332 0.785136627 0.991942913 0.763424549 0.695772434 0.924010146 1.02594344 1.050114498 1 18.69784219 1.945378473 4.16759983 1.021971707 0.829117405 0.568121455 0.079277832 0.165663107 5.677833256 0.035971615 0.021272849 88.18170123 -1.945378473 -0.192854302 LASEYNWGGPESSDKGDPFATLSARPSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASEYNWGGPESSDKGDPFATLSARPSTQPRPDSWGEDNWEGLETDSR 48 3 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 1 LASEYNWGGPESSDKGDPFAT(0.005)LS(0.005)ARPS(0.018)T(0.018)QPRPDS(0.955)WGEDNWEGLETDSR 84.223 1.83E-05 84897000 50123 25285 55146 39211 55051 50289 89343 56956 91032 TRUE FALSE 47753.78512 27861.57025 57674.49865 35269.43578 64651.87697 48547.47932 75712.08445 51968.6307 105148.7776 0.454154449 0.26497284 0.548503748 0.335424116 0.614860947 0.461702746 0.720047215 0.494239038 1 16.68207255 -0.344961437 0.201906307 1.325936979 0.278705008 0.698283369 0.113260839 5.755513453 0.360881435 1.505417298 0.322994774 0.451896068 0.344961437 -1.047231971 LASFYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LASFYER 7 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 120.62 0.01051 294640000 544540 401300 324330 324580 577420 373020 634430 450000 543370 FALSE TRUE 518800.6734 442192.9262 339200.8513 291952.6017 678121.8652 360102.2239 537636.0514 410595.6144 627633.0445 0.826598724 0.704540543 0.540444539 0.465164485 1.080443216 0.573746438 0.856608899 0.654196936 1 19.25956179 2.759806096 24.9980213 0.805396082 0.662083839 0.227271094 0.174835871 1601.960999 1884909.564 0.050761174 0.053792336 575.1830721 -2.759806096 -0.143312244 LASHLNLAMCHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LASHLNLAMCHLK 13 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 160.69 2.51E-05 645760000 1154390 874730 433620 551910 1217880 619800 1406560 884270 673070 FALSE TRUE 1099824.272 963865.9815 453501.9059 496430.9582 1430277.886 598336.1706 1191963.439 806838.631 777446.258 1.414662764 1.239784707 0.583322514 0.638540546 1.83971287 0.769617404 1.533177923 1.037806308 1 19.56838342 2.786471323 24.99995815 1.25157626 1.042274417 0.093402934 0.38265139 1214.937552 633955.9151 0.115167903 0.122153718 611.605416 -2.786471323 -0.209301843 LASLEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASLEELKR 9 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 166.07 9.78E-05 284420000 545340 510220 587120 717110 597490 779720 873160 897190 792730 FALSE TRUE 519562.859 562211.9981 614040.0327 645024.7404 701692.0668 752718.1009 739943.4053 818627.2873 915662.5197 0.567417414 0.61399477 0.670596447 0.704435015 0.766321709 0.822047517 0.808096203 0.894027297 1 19.80445645 2.67356442 0.262801818 1.031270664 0.44515915 0.98450469 0.016136986 0.3111224 0.048015046 0.027565677 0.061370568 471.5898185 -2.67356442 -0.586111514 LASLSSHVTELEEDLDTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 0 ; 172.97 7.32E-12 30709000 30592 27525.5 29075 35873 37669 23686 36713 34637 38605 FALSE TRUE 29145.97679 30330.37974 30408.11751 32266.97789 44238.46167 22865.74788 31111.75757 31604.00066 44591.66623 0.65361937 0.680180453 0.681923778 0.723610051 0.992079135 0.512780746 0.69770341 0.708742313 1 15.44448649 -1.671033262 2.001118549 1.065823004 0.700298204 0.381442172 0.117303795 501341.3413 299057.3183 166960.873 0.028929508 0.021328816 1.671033262 -0.3655248 LASPS(ph)GSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.408)PS(0.481)GS(0.109)T(0.003)SSGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.382)PS(0.465)GS(0.149)T(0.004)SSGLEVVAPEGTSAPGGGPGTLDDSATICR 214.98 2.39E-39 900160000 429820 321869 357182 386596 325796 339432 471590 398180 431700 TRUE FALSE 409503.2604 354667.817 373559.148 347734.6356 382614.7192 327677.3847 399640.2842 363313.2483 498645.8312 0.821230691 0.711261972 0.74914724 0.697357952 0.767307566 0.657134512 0.801451169 0.728599791 1 18.92765596 -1.457315094 3.912969099 1.001927195 0.743885067 0.739675869 0.048144277 0.000738466 0.000102417 0.042528743 0.009952297 0.03488871 1.457315094 -0.258042128 LASPSGS(ph)TSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.309)PS(0.309)GS(0.364)T(0.013)S(0.002)S(0.003)GLEVVAPEGTSAPGGGPGTLDDSATICR 150.07 1.45E-13 261320000 189950 131810 160450 165850 169460 139110 201270 155250 183080 TRUE FALSE 180971.4399 145241.5889 167806.7912 149178.4429 199013.7703 134292.5858 170562.5649 141655.487 211471.1114 0.855773816 0.686815272 0.793521111 0.705431782 0.941091996 0.635039864 0.806552554 0.669857391 1 17.69010107 -1.062893881 4.51340366 1.000012915 0.762867524 0.394820096 0.092686551 1.12E-05 2.32E-06 0.076796233 0.018099979 0.08651793 1.062893881 -0.237145391 LASPSGST(ph)SSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.235)PS(0.235)GS(0.235)T(0.273)S(0.011)S(0.011)GLEVVAPEGTSAPGGGPGTLDDSATICR 133.47 2.58E-08 272770000 153800 93708 114730 135070 127830 118900 165400 121020 149790 TRUE FALSE 146530.1788 103256.9517 119990.484 121492.507 150123.5115 114782.4632 140165.1922 110422.8472 173018.6682 0.846903865 0.596796593 0.693511777 0.702193054 0.867672333 0.663410858 0.810116005 0.638213485 1 17.40056818 -1.919416752 2.716324204 1.163990793 0.728456524 0.479560781 0.089255609 13430771.75 10534928.27 14091743.76 0.019999626 0.012038801 1.919416752 -0.435534268 LASS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LASSPK 6 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.07)S(0.93)PK;LAS(0.012)S(0.988)PK;LAS(0.06)S(0.94)PK;LAS(0.026)S(0.974)PK;LAS(0.031)S(0.969)PK 94.806 0.046221 1805320000 9053400 8600200 7331120 9298300 4395140 8014170 7929560 10722000 5739030 TRUE FALSE 8625463.724 9476570.158 7667259.103 8363617.218 5161651.024 7736637.283 6719759.986 9783124.839 6629009.461 1.301169319 1.429560512 1.156622139 1.261669223 0.778645898 1.167087983 1.013689907 1.475804929 1 22.66036188 3.451961608 2.047592239 1.093216855 1.362909081 0.225054834 0.183919024 0.387611741 3.269460027 0.050849702 0.081562451 2831.141711 -3.451961608 0.269692225 LASS(ph)PKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASSPKDK 8 1 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.427)S(0.573)PKDK 59.067 0.061145 190680000 1044000 806230 883540 1080500 489950 1006700 1131400 1148100 544820 TRUE FALSE 994652.189 888385.7536 924051.1829 971886.0872 575397.1249 971837.7266 958784.1504 1047566.278 629307.903 1.580549337 1.411686949 1.468361002 1.544372925 0.914333226 1.544296078 1.523553329 1.664632325 1 19.26340654 LASS(ph)VLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASSVLR 7 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 1 LAS(0.394)S(0.606)VLR 103.42 0.0087905 90718000 121960 93676 106590 128000 123210 97400 130810 119320 131890 TRUE FALSE 116195.1925 103221.6909 111477.2569 115133.1968 144697.785 94027.01358 110852.532 108871.7082 152342.8276 0.762721779 0.677561868 0.731752579 0.755750688 0.949816852 0.617206698 0.727651795 0.714649386 1 17.21696205 -1.524787814 2.735527161 1.013130268 0.73754788 0.4764594 0.084826206 15442598.5 15749846.38 1506108.154 0.0193511 0.029868416 1.524787814 -0.275582388 LASTLVHLGEYQAAVDGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 269.33 4.14E-32 1273114000 1573960 1501000 1460360 1740970 1771250 1597420 1786450 1740070 1768090 FALSE TRUE 1499562.03 1653953.606 1527318.95 1565964.388 2080155.439 1542100.945 1513894.242 1587700.246 2042276.367 0.73426009 0.809857879 0.747851258 0.766773985 1.018547476 0.755089257 0.741277854 0.777416941 1 20.96174668 -2.532240564 2.09073514 3.712034732 0.790842197 0.378996798 0.082835489 4487348.771 169248.6181 58114984.51 0.019527876 0.002936023 2.532240564 -2.921192536 LASTNSS(ph)VLGADLPSSMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASTNSSVLGADLPSSMK 18 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LAS(0.033)T(0.033)NS(0.191)S(0.742)VLGADLPSSMK 94.882 0.0019736 21880000 71082 71083 72790 75348 59825 74925 93712 88067 77188 TRUE FALSE 67722.09473 78326.43851 76127.4935 67773.87589 70258.46106 72330.32846 79414.51326 80355.38661 89157.92082 0.75957463 0.878513516 0.853850031 0.76015541 0.78802265 0.811260826 0.890717421 0.901270306 1 16.44407535 1.170981293 1.190868701 0.994678848 0.811616216 0.716489571 0.03936831 0.247647963 0.717507438 0.037550839 0.01201365 14.82454227 -1.170981293 -0.183062631 LASVLLYSDYGIGEVPVEPLDVPLPSTIRPAS(ph)PVAGS(ph)PKQPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LASVLLYSDYGIGEVPVEPLDVPLPSTIRPASPVAGSPKQPVR 43 2 Q13057;Q13057-2;K7EN91 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 2 LASVLLYSDYGIGEVPVEPLDVPLPS(0.464)T(0.464)IRPAS(0.467)PVAGS(0.605)PKQPVR 111.82 1.53E-06 33047000 91657 67473 88556 88771 71639 94978 118630 96856 87472 TRUE FALSE 87324.55526 74348.57541 92616.38019 79847.57043 84132.81892 91688.88804 100530.8147 88374.77517 101036.711 0.864285411 0.735857043 0.91666068 0.790282756 0.832695543 0.907480926 0.994992946 0.874679849 1 16.62452006 2.135806112 3.202979123 0.955428122 0.820140399 0.515824133 0.057314149 0.178273203 3.626293475 0.022394251 0.015346932 136.7118349 -2.135806112 -0.135287724 LASYLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;; 225.42 3.96E-05 45438130000 14167570 11223830 7586130 8605130 15628220 8731320 16159640 11277470 15096950 FALSE TRUE 13497897.04 12367551.04 7933961.564 7740125.984 18353776.62 8428952.199 13694190.13 10289954.94 17438107.9 0.774045964 0.709225514 0.45497835 0.443862719 1.052509637 0.48336392 0.785302523 0.590084371 1 24.05574018 -1.414818281 2.999508584 1.005752637 0.672098342 0.244993681 0.185855156 45545817.24 54750657.15 2236973.577 0.040978791 0.038475274 1.414818281 -0.333654294 LAT(ph)QSNEITIPVTFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.5)QS(0.5)NEITIPVTFESR 216.34 5.95E-14 26433000 45052 33405 39049 46729 48118 36349 43153 44519 47020 TRUE FALSE 42922.48124 36809.00748 40839.43527 42031.71214 56509.76397 35090.22502 36569.21729 40620.68035 54311.62146 0.790300125 0.677737223 0.75194653 0.773899048 1.040472784 0.646090543 0.673322142 0.747918756 1 15.72897331 -2.401496797 2.148758652 2.794972846 0.753823133 0.314296013 0.10945106 5049828.918 339610.6463 44340667.66 0.027208609 0.003967375 2.401496797 -2.041149713 LATELPDAELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LATELPDAELRR 12 1 Q93034 Q93034 CUL5 Cullin-5 0 ; 103.4 0.0036082 379000000 230120 190939 241970 227467 250540 240214 296320 259640 221215 FALSE TRUE 219242.6837 210395.9012 253064.5638 204601.585 294234.0967 231895.3289 251110.9417 236904.5452 255519.8924 0.858025892 0.823403216 0.990390852 0.80072664 1.151511508 0.907543154 0.982745176 0.92714717 1 17.96307608 3.431277638 1.254690896 0.976601723 0.840346734 0.236985317 0.089078563 0.555570311 1.801284961 0.02789387 0.05205033 2699.464611 -3.431277638 -0.136254989 LATKS(ph)SPVKVGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LATKSSPVKVGEK 13 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 LAT(0.161)KS(0.643)S(0.196)PVKVGEK;LAT(0.055)KS(0.518)S(0.427)PVKVGEK 82.349 0.0065699 1800740000 1979230 1336210 2030890 2028140 1122690 2463350 2849900 2906950 1531820 TRUE FALSE 1885675.72 1472371.318 2124008.315 1824267.514 1318486.781 2378043.572 2415095.413 2652402.047 1769366.822 1.065734757 0.832145884 1.200434126 1.03102844 0.745174355 1.344008231 1.364948965 1.499068488 1 20.75480175 2.213253929 24.96821589 1.336318347 0.976496485 0.457893003 0.175090088 171.5788993 169282.9559 0.059970322 0.044307905 163.400706 -2.213253929 -0.359821861 LATNTS(ph)APDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.003)S(0.997)APDLK;LATNT(0.005)S(0.995)APDLK;LATNT(0.001)S(0.999)APDLK;LATNT(0.001)S(0.999)APDLK;LATNT(0.078)S(0.922)APDLK;LATNT(0.005)S(0.995)APDLK 239.31 1.27E-15 3625790000 8742870 6722090 7238930 7910450 5108800 7808770 8544190 8099490 5652480 TRUE FALSE 8329611.862 7407078.613 7570842.101 7115276.537 5999773.102 7538350.337 7240616.891 7390255.718 6529037.73 1.275779404 1.134482434 1.159564765 1.089789465 0.91893681 1.154588264 1.108986836 1.131905807 1 22.63843895 4.440888632 0.903712968 1.078385426 1.328786691 0.44926644 0.070833437 1.338585347 1.166914433 0.023629246 0.301402063 27598.70041 -4.440888632 0.250401265 LATQS(ph)NEITIPVTFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.003)QS(0.997)NEITIPVTFESR;LAT(0.006)QS(0.994)NEITIPVTFESR;LAT(0.014)QS(0.986)NEITIPVTFESR;LAT(0.003)QS(0.997)NEITIPVTFESR;LAT(0.022)QS(0.977)NEIT(0.001)IPVTFESR 303.86 1.34E-46 430406000 338448 236687 277808 336848 308241 283603 352512 313711 316565 TRUE FALSE 322450.2338 260805.6744 290545.7716 302987.3991 361998.1328 273781.757 298729.8201 286240.8018 365656.2834 0.881839718 0.713253638 0.794587116 0.828612587 0.989995658 0.748740742 0.816968923 0.782813847 1 18.48012863 -0.98552563 3.899113237 1.000019919 0.815350162 0.358740209 0.075609122 13243460.42 26237297.06 3672.315463 0.017184371 0.103389009 0.98552563 -0.184669757 LATQSNEITIPVTFES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LATQSNEITIPVT(0.021)FES(0.979)R;LATQSNEITIPVT(0.13)FES(0.87)R;LATQSNEITIPVT(0.121)FES(0.879)R 176.42 1.16E-09 147935000 174078 114150 120656 166324 156849 139183 170421 151228 148488 TRUE FALSE 165849.6779 125782.0148 126188.1969 149604.7955 184203.4159 134363.0578 144420.1465 137985.6746 171514.7607 0.96697029 0.733359708 0.735727913 0.872256096 1.073979961 0.783390638 0.842027508 0.80451195 1 17.38797322 4.747945957 7.246142789 0.846404095 0.968752873 0.088166557 0.10894645 0.242357759 95.81695042 0.024965594 0.147497241 55968.7951 -4.747945957 0.122348778 LATQSNEITIPVTFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 362.15 3.49E-88 758188000 1186891 845075 938148 1110480 1131920 941757 1165017 1036771 1135338 FALSE TRUE 1130789.015 931189.1033 981163.0138 998852.4406 1329326.49 909143.7189 987272.2596 945985.835 1311400.419 0.862275929 0.710072294 0.74817958 0.761668539 1.013669411 0.693261727 0.752838146 0.721355447 1 20.32267683 -0.975936759 4.574258099 1.000004357 0.780284373 0.345362939 0.093865772 0.02767388 53946250.64 578.1833726 0.020710683 0.105697141 0.975936759 -0.219719984 LATTILQHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LATTILQHWK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 145.25 3.08E-05 198558000 430430 366120 212544 264505 445030 325440 521820 372520 389270 FALSE TRUE 410084.4269 403428.0442 222289.3526 237916.4549 522643.0911 314169.9312 442206.7751 339900.1739 449636.0035 0.912036456 0.897232519 0.494376231 0.529131237 1.16236931 0.698720585 0.983477239 0.75594519 1 18.77839803 2.746520527 24.98945436 0.906017277 0.750470911 0.229172012 0.185070824 1246.951 3914694.718 0.057954876 0.060476745 557.8539689 -2.746520527 -0.155546366 LATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITR 40 2 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 255.25 3.22E-63 160219000 112978 66805 121444 102770 98107 120961 161410 144005 109438 FALSE TRUE 107637.7538 73612.50545 127012.3275 92439.36435 115216.8297 116772.0902 136783.94 131395.1588 126409.0861 0.851503299 0.582335556 1.004772137 0.731271518 0.911460033 0.923763424 1.082073641 1.039443942 1 16.94774064 2.42171408 0.953132538 1.05639926 0.753662349 0.469950336 0.110125583 0.408080994 0.735799165 0.070049344 0.046872716 264.0669686 -2.42171408 -0.302736911 LAVCNMDWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAVCNMDWDR 10 0 Q9H501;A0A087WX71 Q9H501 ESF1 ESF1 homolog 0 77.662 0.075205 53072000 91091 71140 67846 74953 92727 66175 94935 86659 101080 FALSE TRUE 86785.30895 78389.24688 70956.80621 67418.58204 108898.5594 63883.34316 80450.92215 79070.67855 116754.9702 0.743311474 0.671399657 0.607741205 0.577436506 0.932710267 0.547157376 0.689057794 0.677236082 1 16.83312444 -1.312103854 6.432238666 1.000012014 0.680562265 0.471809351 0.106153957 1.64E-05 1.75E-06 0.092144559 0.021717865 0.048741192 1.312103854 -0.319449749 LAVEALSSLDGDLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAVEALSSLDGDLAGR 16 0 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 0 74.611 0.07398 14204000 52222 51186 42926 56225 37534 48199 59580 56283 45189 FALSE TRUE 49753.56955 56401.91159 44894.19956 50573.15618 44079.91772 46529.85654 50489.97674 51354.56215 52196.67933 0.953194153 1.08056513 0.860096852 0.968896045 0.84449659 0.89143327 0.967302468 0.983866461 1 15.67167041 3.740039164 24.99654757 0.927579761 1.016879639 0.259783063 0.060159812 148.9202593 2517651.453 0.014857124 0.025099074 5495.904328 -3.740039164 0.089299878 LAVNMVPFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAVNMVPFPR 10 0 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 ; 214.11 2.31E-08 152820000 659860 481840 423460 431490 790990 462910 813570 580100 699890 FALSE TRUE 628669.7255 530940.0438 442876.0599 388115.8054 928938.4056 446879.3106 689444.9543 529303.3687 808425.3667 0.777647203 0.656758268 0.547825536 0.480088604 1.149071323 0.552777447 0.852824494 0.654733746 1 19.62475507 LAVNNIAGIEEVNMIKDDGTVIHFNNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAVNNIAGIEEVNMIKDDGTVIHFNNPK 28 1 Q96K17;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 313.03 5.90E-83 106600000 178050 143350 153480 179190 117390 192360 199800 184660 121170 FALSE TRUE 169633.9294 157957.528 160517.2098 161177.4808 137862.7788 185698.525 169316.8404 168490.1915 139960.4247 1.212013536 1.128587086 1.146875698 1.151593253 0.985012578 1.326793094 1.209747975 1.20384167 1 17.09465942 2.222370136 24.9999959 1.207779541 1.135477391 0.059386915 0.097917517 516.2564636 797155.4676 0.033299035 0.024665412 166.8668761 -2.222370136 -0.072302151 LAVYIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LAVYIDR 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;; 154.09 0.0039591 6645529000 5957594 4938998 4665174 5705003 5670123 4940793 6173443 5511082 6095892 FALSE TRUE 5675990.338 5442287.511 4879076.842 5131525.26 6658990.656 4769692.1 5231570.887 5028502.444 7041211.798 0.806109872 0.77291916 0.692931413 0.728784392 0.945716568 0.677396482 0.742992973 0.714152988 1 22.74739231 -1.509102605 3.275925005 1.005875831 0.76152773 0.498267021 0.075635391 30261111.52 31079452.01 1543003.492 0.017143709 0.030966876 1.509102605 -0.2443481 LAWVGDVFTATPAEPRPLT(ph)SPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.5)S(0.5)PLR 107.9 0.0021046 32331000 26001 20121 24899 27892 27774 20458 27440 25170 27592 TRUE FALSE 24771.98426 22171.35278 26040.64378 25088.24317 32617.77681 19749.53433 23253.52403 22965.98137 31870.82644 0.777262061 0.695662939 0.817068356 0.787185209 1.023436806 0.619674371 0.729617855 0.720595728 1 14.95994881 3.726799633 23.99492769 0.79449666 0.736462497 0.046000496 0.124173178 1528.259364 3117979.549 0.031580595 0.049422041 5330.888921 -3.726799633 -0.058034162 LAWVGDVFTATPAEPRPLTS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.003)S(0.997)PLR;LAWVGDVFTATPAEPRPLT(0.047)S(0.953)PLR;LAWVGDVFTATPAEPRPLT(0.018)S(0.982)PLR 251.76 1.14E-43 2539885000 1511320 1014602 1368921 1435492 1644134 1328465 1711111 1402856 1740332 TRUE FALSE 1439882.899 1117991.097 1431687.382 1291193.617 1930870.449 1282459.924 1450049.59 1280014.492 2010213.798 0.716283462 0.55615532 0.712206524 0.642316563 0.960529895 0.637971904 0.72134098 0.6367554 1 20.93891752 -5 0.256124882 2.914279318 0.666242525 0.429002697 0.107360925 176.4201965 1.739192289 177.6583037 0.138556866 1.00E-05 5 -2.248036793 LAYHPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LAYHPLK 7 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 72.021 0.052736 299100000 382510 216060 110480 132190 355460 147240 383930 258150 273090 FALSE TRUE 364429.5104 238076.7596 115545.6173 118902.0101 417452.1115 142141.0419 325354.4271 235545.0175 315439.4024 1.155307509 0.75474642 0.36630052 0.376940893 1.323398752 0.45061283 1.031432423 0.746720339 1 18.26700336 1.631674003 24.99999957 0.916838802 0.764465456 0.067134976 0.319976566 2.963485378 3102.60029 0.145622583 0.080694965 42.82269575 -1.631674003 -0.152373346 LAYIAHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LAYIAHPK 8 0 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ; 107.66 0.0039607 2782800000 7074400 4139600 2734600 3545900 5946200 3885400 8205000 5592700 6410800 FALSE TRUE 6740007.132 4561429.946 2859984.115 3189459.395 6983215.397 3750847.624 6953176.555 5102973.539 7404954.122 0.910202416 0.615997057 0.386225771 0.43071967 0.943046409 0.506532189 0.938989822 0.689129663 1 22.82005937 1.712383681 10.52497581 0.858159325 0.646502024 0.251169074 0.196553012 0.17926835 47.32652457 0.092158621 0.050000857 51.56840284 -1.712383681 -0.211657302 LCAGIMITAS(ph)HNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 1 LCAGIMITAS(1)HNPK;LCAGIMIT(0.002)AS(0.998)HNPK;LCAGIMIT(0.006)AS(0.994)HNPK;LCAGIMIT(0.002)AS(0.998)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK;LCAGIMITAS(1)HNPK 243.99 9.36E-18 4963990000 7341850 7104260 6985110 8244730 5197380 7693070 7701880 8282290 5110200 TRUE FALSE 6994815.301 7828192.171 7305384.203 7415954.076 6103801.426 7426657.057 6526816.751 7557048.78 5902663.717 1.185026902 1.326213477 1.237641945 1.256374144 1.034075753 1.25818739 1.10574091 1.280277709 1 22.49293472 2.882545324 23.07943503 1.148841698 1.25569521 0.272824478 0.092320817 13.65390275 2644.828271 0.024803989 0.026308623 763.0365188 -2.882545324 0.106853512 LCDDGPQLPTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LCDDGPQLPTSPR 13 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LCDDGPQLPT(0.045)S(0.955)PR;LCDDGPQLPT(0.059)S(0.941)PR;LCDDGPQLPT(0.001)S(0.999)PR;LCDDGPQLPT(0.044)S(0.956)PR;LCDDGPQLPT(0.197)S(0.803)PR;LCDDGPQLPT(0.089)S(0.911)PR 180.95 1.31E-05 884349000 2280390 2154340 2148156 2621620 2348290 2207010 2536740 2392360 2476610 TRUE FALSE 2172600.484 2373869.695 2246651.077 2358089.777 2757831.033 2130580.69 2149713.723 2182872.276 2860670.03 0.759472593 0.82982996 0.785358344 0.824313798 0.964050731 0.744783798 0.751472103 0.763063287 1 21.44792167 4.62805215 2.493393846 0.818667477 0.75334865 0.043893795 0.087169083 1.48998032 13.90139881 0.020526257 0.187036869 42467.05555 -4.62805215 -0.065318826 LCDEQLSSQSHYDFGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LCDEQLSSQSHYDFGLR 17 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 263.71 2.03E-27 564540000 732020 598170 669940 766400 800000 683880 922050 771110 862360 FALSE TRUE 697418.8653 659124.2031 700657.4117 689360.0159 939519.7467 660197.0641 781374.3379 703587.5205 996090.3845 0.700156207 0.66171124 0.703407464 0.692065727 0.943207325 0.662788312 0.784441201 0.706349074 1 19.92591713 -5 0.171948735 2.057399798 0.665251093 0.518815662 0.081792301 100.8379694 0.955229844 36.44829348 0.264040989 1.00E-05 5 -1.392148706 LCDFGSASHVADNDITPY(ph)LVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LCDFGSASHVADNDITPYLVSR 22 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 LCDFGSASHVADNDIT(0.006)PY(0.994)LVSR;LCDFGSASHVADNDITPY(0.998)LVS(0.002)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.005)PY(0.994)LVS(0.001)R;LCDFGSASHVADNDIT(0.002)PY(0.998)LVSR;LCDFGSASHVADNDIT(0.006)PY(0.993)LVS(0.001)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.016)PY(0.983)LVSR 347.44 3.64E-95 21450080000 5449610 4373520 4784960 5354870 5612570 4921170 6301130 5421140 5790200 TRUE FALSE 5192017.735 4819186.66 5004355.149 4816588.294 6591400.431 4750748.649 5339776.89 4946436.242 6688114.644 0.776305134 0.720559816 0.748246018 0.720171311 0.985539391 0.710327036 0.79839793 0.739586043 1 22.67316815 -5 0.303197379 2.91649708 0.761204682 0.433787217 0.080123048 253.6295925 2.329924139 309.6238209 0.072265677 1.00E-05 5 -2.155292398 LCDSYEIRPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 6851150000 10846900 9043700 9123200 10418200 8725700 10099500 11637700 10344800 10001800 FALSE TRUE 10334188.53 9965263.312 9541507.744 9370942.743 10247459.32 9749751.783 9862155.124 9438954.471 11552828.06 0.894515912 0.862582154 0.825902341 0.811138424 0.887008727 0.843927715 0.853657223 0.817025443 1 23.46174272 -1.976284563 4.561345117 1.115019145 0.852448229 0.746746175 0.027501178 0.023452939 0.000121937 0.019414156 0.006290767 0.010561253 1.976284563 -0.262570917 LCEEWPVDETKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LCEEWPVDETKR 12 1 Q5TAQ0;V5IRT4;Q9BRT2 Q5TAQ0 UQCC2 Ubiquinol-cytochrome-c reductase complex assembly factor 2 0 92.19 0.012626 215310000 143120 145770 133710 151240 111500 139960 157690 154270 133060 FALSE TRUE 136355.0012 160624.1287 139840.7358 136037.0679 130945.5647 135113.1501 133631.4943 140761.301 153694.2652 0.887183403 1.045088628 0.909863068 0.885114794 0.851987317 0.879103393 0.869463113 0.915852656 1 17.22970381 3.496067414 23.86321352 0.889326734 0.968026002 0.175751983 0.055113442 479.7033828 604198.0265 0.013457162 0.020447891 3133.77213 -3.496067414 0.078699268 LCFEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LCFEGLR 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 ; 117.62 0.030584 0 680360 637160 532030 616610 741560 601420 740880 673380 704610 FALSE TRUE 648200.7311 702087.3284 556424.1017 554627.1913 870887.8292 580592.6746 627845.1488 614415.2774 813877.3202 0.796435427 0.862645157 0.68367073 0.681462891 1.070048038 0.713366327 0.7714248 0.754923699 1 19.63445182 LCLPSFDKLELLECIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LCLPSFDKLELLECIR 16 1 M0QZP4;B3KSI3;M0QZ10;M0QXF9;O15382-2;O15382 M0QZP4 BCAT2 "Branched-chain-amino-acid aminotransferase;Branched-chain-amino-acid aminotransferase, mitochondrial" 0 88.992 0.0054189 59784000 109640 97197 96303 110400 99006 92535 103620 115980 92250 FALSE TRUE 104457.5345 107101.4848 100718.5878 99302.38225 116272.6151 89330.48975 87810.86589 105824.1764 106555.6589 0.980309592 1.005122449 0.94522045 0.931929691 1.091191367 0.838345806 0.824084491 0.993135207 1 16.70124769 2.217277557 24.99918937 0.889005769 0.987020832 0.187183192 0.071453498 283.0177091 332431.9924 0.025086275 0.018545235 164.9216065 -2.217277557 0.098015063 LCMVRPCEADLEENIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LCMVRPCEADLEENIK 16 1 P29279-2;P29279 P29279-2 CTGF Connective tissue growth factor 0 53.995 0.08822 8293600 13297 9586.2 12922 16305 43802 12409 23387 10438 49305 FALSE TRUE 12668.47716 10563.04468 13514.48648 14665.99042 51441.05493 11979.27322 19818.88362 9523.993385 56950.96758 0.222445337 0.185476123 0.237300384 0.257519601 0.903251641 0.210343629 0.347999068 0.167231459 1 15.79743273 -5 0.295479763 6.502368408 0.272219675 0.48662241 0.217577471 223.2853565 2.082150868 760.3449359 0.215874116 1.00E-05 5 -6.230148733 LCS(ph)SSSSDTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.561)S(0.428)S(0.006)S(0.006)SDTSSR;LCS(0.451)S(0.451)S(0.092)S(0.006)S(0.001)DTSSR 191.53 5.51E-06 396543000 457600 365000 392740 483130 435380 448730 475610 438210 438840 TRUE FALSE 435970.1549 402193.915 410747.5175 434564.8545 511310.1342 433190.3676 403046.9593 399838.0093 506893.0659 0.860083091 0.793449234 0.810323804 0.857310711 1.008714004 0.854599119 0.795132122 0.788801497 1 18.9513219 -2.176829909 2.51503341 1.436887587 0.843106448 0.363047428 0.063978309 6486610.974 2113261.565 16151134.71 0.015818195 0.006655338 2.176829909 -0.593781139 LCSDLMNCLHER ddPTM_SK-BR-3_Trastuzumab_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 ;; 183.79 1.52E-05 405490000 861710 633960 603950 711300 951630 659200 907420 739470 905060 FALSE TRUE 820978.676 698561.2448 631641.7049 639798.7726 1117593.971 636371.7387 768976.4131 674718.0866 1045412.082 0.785315848 0.668216158 0.604203563 0.612006292 1.06904635 0.608728127 0.735572533 0.645408732 1 19.99564031 LCSS(ph)SSSDTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.033)S(0.482)S(0.482)S(0.002)SDTSSR;LCS(0.003)S(0.989)S(0.008)SSDTSSR;LCS(0.004)S(0.848)S(0.143)S(0.004)SDTSSR;LCS(0.047)S(0.906)S(0.047)SSDTSSR 296.32 2.89E-36 1977490000 1955220 1563900 1821750 2013780 1720910 1872510 2260940 1920460 1791070 TRUE FALSE 1862800.625 1723263.188 1905279.039 1811351.008 2021036.159 1807664.509 1915992.078 1752294.341 2068819.988 0.90041697 0.832969131 0.920949648 0.875547906 0.976902858 0.873765973 0.926127981 0.847001842 1 20.98037669 -5 0.212261712 1.503183958 0.878569323 0.353946359 0.042619138 153.0334344 1.526545596 32.97832687 0.0811918 1.00E-05 5 -0.624614635 LCYSSDHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LCYSSDHEK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 166.07 6.10E-05 6784300000 1213690 1013510 923300 1065200 1255580 1078200 1525870 1369420 1208040 FALSE TRUE 1156321.279 1116787.821 965634.2183 958124.0723 1474552.754 1040861.664 1293070.507 1249506.325 1395376.673 0.828680385 0.800348639 0.692024051 0.686641887 1.056741726 0.745935978 0.926682043 0.895461669 1 20.41222319 2.758180604 24.99880194 0.906115203 0.765195316 0.462365232 0.090974594 855.9588019 1090618.277 0.026339098 0.027900677 573.034281 -2.758180604 -0.140919886 LCYVALDFEQEMATAAS(ph)SSSLEK ddPTM_SK-BR-3_Trastuzumab_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(0.466)S(0.466)S(0.061)S(0.008)LEK 130.87 2.12E-05 13004000 21961 22919 23420 26447 21982 22842 28840 30778 22680 TRUE FALSE 20922.94705 25254.47216 24493.83017 23788.49731 25815.65384 22050.97581 24439.92832 28082.91516 26197.09857 0.798674212 0.964017908 0.934982556 0.908058473 0.985439429 0.841733513 0.932925005 1.071985704 1 14.67711942 4.591497057 2.582431721 0.944644764 0.789398871 0.380125781 0.061172759 0.374024936 3.998315896 0.01427476 0.109451078 39038.85367 -4.591497057 -0.155245893 LCYVALDFEQEMATAASS(ph)SSLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.021)S(0.842)S(0.132)S(0.004)LEK;LCYVALDFEQEMATAAS(0.118)S(0.625)S(0.234)S(0.023)LEK;LCYVALDFEQEMATAAS(0.14)S(0.737)S(0.101)S(0.021)LEK;LCYVALDFEQEMATAAS(0.309)S(0.571)S(0.101)S(0.018)LEK 175.77 7.33E-13 54963000 174651 162012 169577 180558 141020 177790 204983 194876 154370 TRUE FALSE 166395.5934 178521.207 177352.2732 162407.9668 165613.8434 171633.0877 173709.0786 177811.6243 178308.9112 0.933187199 1.001190607 0.99463494 0.910823613 0.928802954 0.962560349 0.974203013 0.997211094 1 17.44401928 1.420983506 2.267096127 0.999925625 0.957671939 0.292120807 0.027712392 0.442172833 4.11340808 0.024855184 0.007841896 26.36231265 -1.420983506 -0.042253686 LDAENAIVHMGGQWLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDAENAIVHMGGQWLGGR 18 0 E7ETJ9;Q01085;Q01085-2 E7ETJ9 TIAL1 Nucleolysin TIAR 0 171.09 1.42E-11 208580000 134020 144020 121100 162070 117720 111590 139410 145020 127860 FALSE TRUE 127685.1402 158695.8017 126652.5548 145778.4157 138250.3307 107725.6103 118140.4441 132321.28 147687.8758 0.864560747 1.074535069 0.857569073 0.987070976 0.936098038 0.729414041 0.799933261 0.895952219 1 17.17219187 2.41471552 12.20252639 0.831513365 0.954233356 0.157802304 0.092434889 0.918687597 177.2031542 0.029527294 0.024700379 259.8456915 -2.41471552 0.122719991 LDAFIEALHQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 160.69 6.74E-05 87542000 150960 132860 128910 184660 128590 130830 159480 145920 92379 FALSE TRUE 143824.42 146398.585 134820.651 166097.626 151016.0553 126299.3243 135148.3969 133142.4712 106704.6635 1.347873797 1.371998001 1.263493521 1.556610747 1.41527137 1.18363453 1.266565045 1.247766188 1 16.7032637 0.955257709 0.642513104 1.002914837 1.380276546 0.616481107 0.091177645 0.571675333 0.546810314 0.091068426 0.037334967 9.021062858 -0.955257709 0.377361709 LDALVAEEHLTVDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDALVAEEHLTVDAR 15 0 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ;;; 238.47 9.04E-18 454324000 787900 547361 644640 758360 830200 649650 916320 731070 791500 FALSE TRUE 750657.5285 603137.7082 674197.3816 682128.212 974986.6171 627152.4576 776518.5546 667053.6352 914241.7776 0.821071129 0.659713571 0.737438824 0.746113587 1.066442861 0.685980966 0.849357986 0.729624976 1 19.80221622 2.961561819 24.99557891 0.847957158 0.734968936 0.210595099 0.117462448 877.9830971 570934.7024 0.032714983 0.034706419 915.2965363 -2.961561819 -0.112988221 LDAMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LDAMFR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EIV0;Q96L46;K7EMQ1 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ;;;; 133.82 0.033265 722263000 921409 891579 729763 804634 907317 726682 1021872 850200 849149 FALSE TRUE 877855.8226 982431.9137 763223.3554 723750.6616 1065552.798 701516.8201 865966.6584 775751.9808 980830.6901 0.895012596 1.001632518 0.778139758 0.737895611 1.086377912 0.715227233 0.882891071 0.790913242 1 19.9036446 3.74486692 24.89661862 0.849179867 0.948322554 0.094236509 0.117662027 930.9435603 3675255.733 0.027387596 0.047872415 5557.339383 -3.74486692 0.099142687 LDAQSLNLSQEDFDRYMSGQT(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMS(0.029)GQT(0.527)S(0.444)PR;LDAQSLNLSQEDFDRYMS(0.008)GQT(0.623)S(0.368)PR 161.04 3.20E-11 290920000 173424 178964 186107 187500 189471 189047 203357 208203 237850 TRUE FALSE 165226.5912 197200.6351 194640.19 168652.1438 222514.6824 182500.255 172331.1547 189971.6416 274734.5632 0.601404458 0.717786043 0.708466338 0.613873048 0.80992606 0.664278469 0.627264195 0.691473396 1 18.0676789 -1.702510331 2.108974398 1.076270803 0.676567342 0.735311442 0.060447498 547276.3002 336377.8619 220276.2386 0.014876117 0.019837625 1.702510331 -0.399703461 LDAQSLNLSQEDFDRYMSGQTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMSGQT(0.004)S(0.996)PR;LDAQSLNLSQEDFDRYMSGQT(0.118)S(0.881)PR 197.13 1.15E-24 684810000 288860 301500 319090 309790 329190 321760 353300 347210 380720 TRUE FALSE 275206.1603 332223.1928 333720.5921 278649.3206 386600.6318 310617.3705 299397.5962 316806.4517 439760.1132 0.625809736 0.755464588 0.758869625 0.633639369 0.879117092 0.706333661 0.680820264 0.720407427 1 18.74635723 -1.281666469 3.002288519 1.001966655 0.717571546 0.601134387 0.071638139 8922297.824 11654179.59 159398.1659 0.01598573 0.052279753 1.281666469 -0.284395108 LDDCGLTEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDDCGLTEAR 10 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 ; 147.24 6.34E-05 549300000 538010 440800 476570 529200 534980 463080 573650 473730 516980 FALSE TRUE 512579.3335 485718.0211 498421.2059 476003.8106 628280.3426 447043.4235 486129.1567 432247.6898 597150.618 0.858375288 0.813392813 0.834665813 0.797125208 1.05213044 0.748627582 0.814081309 0.72385036 1 19.18773534 -1.20910054 5.143276557 1.000014434 0.831270599 0.268665836 0.087986888 1.33E-05 2.05E-06 0.078011661 0.018385952 0.061787334 1.20910054 -0.168743835 LDDFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDDFFK 6 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 99.171 0.090968 135070000 538220 463880 483430 566700 408310 518430 620560 576730 450630 FALSE TRUE 512779.4072 511149.8994 505595.7437 509734.2393 479519.1347 500476.6391 525882.1746 526228.4638 520511.3989 0.985145394 0.982014804 0.971344229 0.979295056 0.921246174 0.96150947 1.010318267 1.010983554 1 18.98957023 1.710090957 6.637090449 1.007782372 0.968864341 0.520061031 0.018151767 0.119097434 12.53791558 0.009727742 0.005018577 51.29688074 -1.710090957 -0.038918031 LDDFLDLNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDDFLDLNHK 10 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 121.83 0.00050465 30125000 46701 53793 44110 55137 33499 50228 46166 58340 26902 FALSE TRUE 44493.53628 59274.56786 46132.48713 49594.52401 39341.21499 48488.59177 39122.5288 53231.44032 31073.82476 1.431865457 1.907540134 1.484609232 1.596022517 1.266056409 1.56043204 1.259018775 1.713063671 1 14.92341221 -3.007161583 0.141966214 3.63E-17 1.762476749 0.395556577 0.197915735 62.79742531 0.938789793 20.51791661 1.210625298 0.000983645 3.007161583 1.762476749 LDDGHLNNSLS(ph)SPVQADVYFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDDGHLNNSLSSPVQADVYFPR 22 0 Q3ZCW2;F8WF17;B9A055;U3KQ88 Q3ZCW2 LGALSL Galectin-related protein;Galectin 1 LDDGHLNNS(0.001)LS(0.988)S(0.012)PVQADVYFPR;LDDGHLNNSLS(0.605)S(0.395)PVQADVYFPR 173.59 2.31E-12 182666000 26198 20283 21322 27614 23881 19512.2 24635 22811.4 19586.3 TRUE FALSE 24959.67246 22349.86076 22299.63479 24838.18826 28045.83884 18836.48762 20876.4783 20813.91289 22623.64337 1.103256096 0.987898385 0.98567832 1.097886306 1.239669419 0.832601863 0.922772604 0.920007116 1 14.46554366 2.214776286 24.99998821 0.910669809 1.068042714 0.497119581 0.081036086 204.002911 214428.5168 0.02999619 0.022165499 163.974489 -2.214776286 0.157372905 LDDIEEFENIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDDIEEFENIRK 12 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 0 130.1 0.00035676 24131000 59542 51247 53780 60866 34153 60725 60903 67066 41476 FALSE TRUE 56727.56766 56469.12756 56245.8662 54747.63404 40109.27239 58622.07802 51611.12879 61193.3455 47907.88625 1.184096651 1.17870213 1.174041908 1.142768724 0.83721649 1.223641505 1.077299226 1.277312574 1 15.54797554 2.991719973 24.91791664 1.087755257 1.17697705 0.123433369 0.117869662 811.5814023 2442383.046 0.032376278 0.037010954 981.1151291 -2.991719973 0.089221793 LDDIHPFYADLMNILYDKDHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDDIHPFYADLMNILYDKDHYK 22 1 Q9BZE4-2;Q9BZE4;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 246.11 4.00E-31 104480000 486100 498180 387410 531760 268170 505050 450240 483130 134310 FALSE TRUE 463123.0164 548945.1084 405173.1317 478306.4745 314938.7631 487559.9919 381547.6188 440824.576 155138.1088 2.985230514 3.538428517 2.611693121 3.083101103 2.030054159 3.142748068 2.459406149 2.841497678 1 17.24319359 -0.918585249 0.256418754 6.10E-13 3.225255807 0.67991874 0.400521296 7.843143278 0.501177315 6.899624844 0.591972506 0.12061873 0.918585249 3.225255807 LDDLFLESFEITDVKPLKGDHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDDLFLESFEITDVKPLKGDHLSR 24 2 Q9NRX1 Q9NRX1 PNO1 RNA-binding protein PNO1 0 216.82 7.81E-33 65376000 150930 119410 130880 163370 138480 141890 222910 199160 161120 FALSE TRUE 143795.838 131578.0148 136880.9775 146947.7372 162630.8682 136976.3137 188900.9855 181720.4946 186105.6667 0.772656956 0.70700703 0.735501395 0.78959303 0.873863064 0.736013664 1.015020063 0.976437192 1 17.50576246 1.723728923 6.586842632 0.995306353 0.765701496 0.846417585 0.045675255 0.050496612 5.739502166 0.023926607 0.012418101 52.93329434 -1.723728923 -0.229604857 LDDLFLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDDLFLKR 8 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 152.47 0.00073221 225128000 612750 451180 510380 504260 509270 472290 635260 643120 577490 FALSE TRUE 583786.5219 497155.7549 533781.4278 453570.8268 598086.5268 455934.4789 538339.4196 586805.0034 667044.1998 0.875184166 0.745311563 0.800218978 0.679971173 0.896622033 0.683514644 0.807052096 0.879709326 1 19.34742284 0.992918539 2.430924511 0.998657852 0.782305949 0.507387078 0.069888607 0.216541474 2.874917724 0.059114091 0.016050689 9.838265507 -0.992918539 -0.216351903 LDDLVRPYVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDDLVRPYVHK 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 128.28 0.00016166 215150000 437860 587680 388880 581980 320560 491210 417860 497280 263320 FALSE TRUE 417163.2256 647565.2601 406710.5327 523478.2647 376465.5625 474199.2745 354107.7825 453735.527 304154.3207 1.371551206 2.129068095 1.337184794 1.72109429 1.237745239 1.559074595 1.164237225 1.49179379 1 18.21444397 1.908842342 0.407860647 1.035042248 1.751471586 0.319985642 0.260219887 1.083513807 0.463264808 0.2718297 0.251948359 81.06667146 -1.908842342 0.716429338 LDDPSCPRPECYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDDPSCPRPECYR 13 1 P41091;H7BZU1 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;;; 135.58 7.50E-05 1685520000 3530600 3489670 2716820 3961690 3040390 3124810 3386020 3503350 3083940 FALSE TRUE 3363715.535 3845271.34 2841388.884 3563453.394 3570633.053 3016597.046 2869420.46 3196578.102 3562181.665 0.944285231 1.07947087 0.797654121 1.000357009 1.002372532 0.846839754 0.805523337 0.897365267 1 21.76432966 2.234314506 24.99265356 0.86331522 0.972609707 0.135865851 0.086884513 140.7186907 828261.7428 0.030279422 0.023157508 171.5198965 -2.234314506 0.109294487 LDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDEDEDEDDADLSKYNLDASEEEDSNKK 28 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 LDEDEDEDDADLSKYNLDAS(1)EEEDSNKK 239.24 1.65E-45 81876000 202640 166410 157710 189950 53620 215270 152390 208500 51159 TRUE FALSE 193061.6088 183367.3682 164941.1595 170855.8651 62971.31102 207815.1459 129140.1067 190242.6347 59092.47644 3.267109799 3.103057771 2.791237894 2.891330258 1.065640075 3.51677842 2.185389993 3.219405348 1 15.85068684 3.276995022 2.183727161 2.361512257 3.158767767 0.178860714 0.805727871 0.519286754 5.074589558 0.222627542 0.311304946 1892.321928 -3.276995022 0.797255509 LDEEEEDNEGGEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 218.5 4.49E-12 103280000 85144 84303 91029 100830 63147 87321 96630 90621 82530 FALSE TRUE 81119.41186 92893.57154 95202.76969 90694.37684 74159.81681 84297.05187 81887.31877 82685.74483 95328.3309 0.850947573 0.974459226 0.998682855 0.95138954 0.777940997 0.884281211 0.859002964 0.867378502 1 16.54061742 LDEIYVAGLVAHSDLDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;; 219.95 7.05E-19 262620400 404073.5 461676.9 340616.3 491462.6 342005 374854.8 383301.1 392614.1 287309.3 FALSE TRUE 384973.7465 508722.301 356233.8943 442059.8457 401650.5637 361873.4843 324821.4774 358234.728 331863.7589 1.160035515 1.532925146 1.073434157 1.332052187 1.210287514 1.090427848 0.978779601 1.079463239 1 18.34023156 2.271411538 1.957963743 1.015515879 1.295867425 0.468162195 0.121163397 0.261128195 2.030923941 0.055179936 0.03706016 186.8149114 -2.271411538 0.280351546 LDELEELLTNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDELEELLTNNR 12 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ; 172.8 8.09E-05 39702000 56169 69617 47372 59987 49188 47046 50008 53791 48074 FALSE TRUE 53514.00269 76711.05145 49544.05306 53956.99279 57766.37163 45416.78522 42378.36114 49080.77488 55529.07039 0.963711481 1.381457512 0.892218305 0.971689106 1.04029063 0.81789205 0.763174331 0.88387532 1 15.76095562 3.149082212 1.143574509 0.85571661 1.156116299 0.274448337 0.14324716 0.454266463 1.270979399 0.057027003 0.080692004 1409.555601 -3.149082212 0.300399689 LDELFEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDELFEQER 9 0 Q9P0U4;Q9P0U4-2;A0A669KB29 Q9P0U4 CXXC1 CXXC-type zinc finger protein 1 0 80.231 0.057456 9183100 28519 24455 17662 35210 15700 27188 38817 14864 14950 FALSE TRUE 27170.96339 26946.9923 18471.82017 31670.62391 18438.07503 26246.47274 32894.75373 13562.42936 17268.36965 1.573452732 1.560482712 1.069691033 1.834025131 1.067736874 1.519916082 1.904913689 0.78539142 1 14.07584426 1.221691409 24.99941308 0.892695154 1.516490835 0.46034769 0.275061852 234.7027586 347809.6284 0.244145247 0.061685429 16.6606296 -1.221691409 0.623795681 LDELYGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDELYGTWR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 150.24 0.00019939 392002000 623615 722980 397381 588343 548414 450464 524831 532978 480936 FALSE TRUE 594137.9548 796652.484 415601.3119 529201.6439 644057.228 434864.3187 444758.3918 486307.6208 555517.0986 1.069522354 1.434073741 0.748134149 0.952628902 1.159383266 0.782809962 0.800620526 0.875414316 1 19.08347179 3.735015366 24.99998328 0.894028914 1.251798049 0.493190885 0.146913525 217.8767908 1536399.924 0.038182605 0.061823938 5432.695523 -3.735015366 0.357769136 LDETDDPDDYGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDETDDPDDYGDR 13 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 217.83 5.85E-11 416520000 1301120 1868610 1060530 1644320 880270 1373200 1026610 1338230 802510 FALSE TRUE 1239618.636 2059023.483 1109156.35 1479029.83 1033788.809 1325645.74 869981.7895 1221047.487 926959.1521 1.33729586 2.221266685 1.196553642 1.595571742 1.115247427 1.430101571 0.938533038 1.317261374 1 19.82214624 3.05531993 1.16247333 1.137859071 1.740530973 0.330254753 0.298521024 0.436518326 1.256841915 0.116245117 0.148628171 1135.847249 -3.05531993 0.602671902 LDETDDPDDYGDRESGCSFVLALMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDETDDPDDYGDRESGCSFVLALMQK 26 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 190.57 6.39E-18 182416000 348810 343680 323250 392680 237210 342700 373790 399120 243480 FALSE TRUE 332322.4426 378701.3827 338071.3322 353207.0604 278579.3489 330832.2131 316761.4704 364170.9369 281237.6349 1.181642858 1.346553006 1.202084253 1.255902541 0.990547901 1.176344031 1.126312524 1.294886928 1 18.10143014 2.878286866 21.77816073 1.12954104 1.25356149 0.304956219 0.095520009 7.719932279 1350.606573 0.026691789 0.028310956 755.5911563 -2.878286866 0.12402045 LDFIESDS(ph)PCSSEALSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIESDS(0.999)PCSSEALSK;LDFIESDS(0.983)PCS(0.016)S(0.002)EALSK;LDFIESDS(0.819)PCS(0.158)S(0.023)EALSK;LDFIES(0.023)DS(0.955)PCS(0.019)S(0.003)EALSK 302.96 1.65E-46 139616000 413293 378782 319898 424913 238815 357794 357471 389701 274967 TRUE FALSE 393757.459 417380.3164 334565.6397 382199.938 280464.2604 345403.5041 302932.2335 355576.7145 317607.478 1.239761297 1.31413882 1.053393459 1.203371975 0.883053076 1.087516913 0.953794399 1.119547678 1 18.27688536 3.428115855 1.349801945 1.014630366 1.279971204 0.515431404 0.091939579 0.268226804 1.003092717 0.027443607 0.049491743 2679.883134 -3.428115855 0.265340839 LDFNLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDFNLIR 7 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 87.323 0.045195 95542000 280800 242130 184642 177758 306420 196280 335390 253260 297420 FALSE TRUE 267527.1405 266803.3223 193108.0183 159889.4281 359859.551 189482.7744 284220.0956 231083.2118 343542.3746 0.778731127 0.776624201 0.562108295 0.465413992 1.047496838 0.551555757 0.8273218 0.672648351 1 18.39012854 -2.093327324 0.462486327 1.315997449 0.713718301 0.231468597 0.165216079 104.5841185 7.080336936 34.79557097 0.078144857 0.008066269 2.093327324 -0.602279148 LDFYQHSWLPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDFYQHSWLPAR 12 0 F8VR84;Q9HB07;F8VQQ3 F8VR84 C12orf10 "UPF0160 protein MYG1, mitochondrial" 0 ; 165.7 5.39E-05 400600000 535010 290600 233760 252380 604130 301260 595480 404110 520530 FALSE TRUE 509721.1376 320212.4704 244478.1272 227010.2829 709490.0807 290827.2907 504628.5893 368723.9861 601251.1339 0.847767445 0.532576909 0.406615661 0.377563168 1.180022857 0.483703521 0.839297526 0.61326119 1 19.19760818 LDGAHAPELTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDGAHAPELTK 11 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 71.241 0.04957 206350000 111630 107050 94168 113260 85344 119950 125480 120210 92657 FALSE TRUE 106353.4711 117958.5167 98485.69594 101874.8896 100227.9666 115796.1014 106335.7214 109683.7751 107025.7743 0.993718306 1.102150556 0.920205404 0.951872484 0.936484386 1.081945934 0.99355246 1.024835147 1 16.70759875 -0.007782372 7.617163564 0.999999995 1.006209573 0 0.058513676 0 2.94E-18 0.056217155 0.01325051 0.982240028 0.007782372 0.006209578 LDGLVET(ph)PTGYIESLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.99)PT(0.01)GYIESLPR;LDGLVET(0.993)PT(0.007)GYIESLPR;LDGLVET(0.913)PT(0.087)GYIESLPR;LDGLVET(0.926)PT(0.074)GYIESLPR;LDGLVET(0.583)PT(0.417)GYIESLPR 300.56 2.64E-45 733889000 356192 309842 322724 375253 335774 351382 408045 358780 355100 TRUE FALSE 339355.5101 341415.2521 337521.2146 337531.8555 394332.8793 339213.5532 345790.241 327363.3212 410167.0944 0.827359178 0.832380892 0.822887109 0.822913052 0.961395696 0.827013083 0.84304725 0.798121852 1 18.64585223 -2.184475927 2.459060446 1.449066366 0.84201525 0.560233786 0.044023798 4018206.961 1024496.386 10069238.25 0.01031493 0.006539192 2.184475927 -0.607051117 LDGLVETPTGYIES(ph)LPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.003)PT(0.077)GYIES(0.92)LPR;LDGLVET(0.038)PT(0.199)GY(0.004)IES(0.76)LPR;LDGLVETPT(0.002)GYIES(0.998)LPR;LDGLVETPTGYIES(1)LPR 153.72 1.73E-07 80881700 151488 134562 137459 159191 136734 146886 177398 167890 166529 TRUE FALSE 144327.4625 148274.0208 143761.6311 143188.8182 160580.3663 141799.301 150332.677 153188.6616 192353.4668 0.750324207 0.770841427 0.747382584 0.744404666 0.834819195 0.737180896 0.781543891 0.796391477 1 17.55340031 -5 0.294443439 2.866315102 0.755697188 0.880104896 0.026954011 75.20951063 0.702680343 86.34192667 0.025168693 1.00E-05 5 -2.110617915 LDGLVETPTGYIESLPR ddPTM_SK-BR-3_Trastuzumab_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 ; 180.28 2.02E-09 56444000 109188 77170 98697 112909 90097 97128 123643 127865 92961 FALSE TRUE 104026.8996 85033.71074 103222.3551 101559.1728 105809.8883 93764.43301 104778.9895 116668.4627 107376.9171 0.968801326 0.791917975 0.961308611 0.945819414 0.985406278 0.873227091 0.97580553 1.086532058 1 16.71232436 1.484964249 4.575925681 1.041963806 0.915151182 0.415577162 0.059367136 0.163818796 7.280114797 0.037602785 0.015143923 30.5466964 -1.484964249 -0.126812624 LDGMGCLEFDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDGMGCLEFDEER 13 0 Q13951-2;A0A494C0A9;Q13951;J3KS23;H3BSC0 Q13951-2 CBFB Core-binding factor subunit beta 0 89.301 0.017478 22544000 29857 33635 26850 32126 29769 32843 32878 35685 34902 FALSE TRUE 28445.71878 37062.44474 28081.09906 28896.63344 34960.70417 31705.63867 27861.85725 32560.23222 40314.42391 0.705596559 0.919334599 0.69655216 0.716781505 0.867200887 0.78645893 0.691113863 0.807657138 1 15.29900849 0.967223099 23.07106929 1.000000003 0.773940504 0.478550075 0.075115398 1520.626848 1070343.707 0.070742554 0.017685638 9.273060613 -0.967223099 -0.226059498 LDGQTPHDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDGQTPHDER 10 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 119.76 0.00064914 629955000 433220 396750 396460 466720 506240 343941 415860 420150 496210 FALSE TRUE 412742.5492 437179.2761 414638.0832 419804.4189 594528.0957 332030.2369 352412.9192 383359.4386 573159.7125 0.720117866 0.762752975 0.723425032 0.732438812 1.037281726 0.579297933 0.614859892 0.66885273 1 19.12857768 LDGSLETTNEILDS(ph)ASHDCPLVTQTYGAAAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDGSLETTNEILDSASHDCPLVTQTYGAAAGK 32 0 Q9Y4P8-4;Q9Y4P8;Q9Y4P8-2;Q9Y4P8-6;Q9Y4P8-3;Q9Y4P8-5 Q9Y4P8-4;Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 LDGSLETTNEILDS(0.998)AS(0.002)HDCPLVTQTYGAAAGK;LDGSLETTNEILDS(0.999)AS(0.001)HDCPLVTQTYGAAAGK 276.26 1.13E-73 219550000 199520 171256 197701 194190 164043 200561 222524 208273 142525 TRUE FALSE 190089.085 188707.1811 206765.7864 174669.6523 192652.0473 193615.5223 188573.8769 190035.512 164627.0491 1.15466496 1.146270811 1.255964846 1.061002145 1.170233253 1.176085724 1.145461077 1.154339539 1 17.32884187 -3.771359746 0.450394832 2.19E-06 1.159317922 0.5298008 0.046838927 286.6306824 5.15328016 276.469982 0.022143529 0.000169293 3.771359746 1.159315734 LDHKFDLMYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 156.36 1.87E-05 9604300000 27778000 24087000 17455400 18537000 18977500 21604000 31170000 26568000 15276100 FALSE TRUE 26464988.99 26541492.68 18255747.36 16673625.54 22287169.99 20855848.06 26414444.02 24241565.07 17645039.57 1.499854329 1.504190035 1.034610735 0.944946906 1.263084161 1.181966636 1.496989787 1.373845889 1 24.07275933 3.765722108 23.45833627 1.21576108 1.502022363 0.365196507 0.170026129 397.0137748 342882.9313 0.046874104 0.084464281 5830.718948 -3.765722108 0.286261283 LDHKFDLMYAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 193.23 1.85E-06 673750000 1149120 600500 1049260 862980 1236860 884080 1984140 1057240 1179110 FALSE TRUE 1094803.375 661691.6327 1097369.609 776231.6108 1452567.992 853464.0879 1681423.002 964662.4608 1361960.357 0.80384379 0.48583766 0.805728011 0.569937008 1.066527366 0.626643855 1.234560899 0.708289677 1 20.37725328 2.743091334 24.9173342 0.940801858 0.659275995 0.307036395 0.194014103 393.960077 2166643.517 0.054130056 0.055673492 553.4664929 -2.743091334 -0.281525863 LDHLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 139.68 0.0026756 4822817000 13407450 7105010 6803320 10293670 10296430 8833940 15501180 10678720 9584260 FALSE TRUE 12773706.41 7829018.597 7115258.951 9258930.735 12092124.13 8528018.443 13136190.29 9743634.665 11070538.09 1.153846932 0.707194044 0.642720245 0.836357787 1.09227971 0.770334592 1.186590045 0.880141018 1 23.40022201 2.765469 22.77127603 0.995000714 0.838463996 0.15904941 0.171555156 453.9909712 384188.9278 0.052024563 0.055157535 582.7321782 -2.765469 -0.156536718 LDHSTDFFSEAFEHNGRPYSLLVYIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDHSTDFFSEAFEHNGRPYSLLVYIPSR 28 1 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 110.68 0.00041016 105880000 64113 49905 79187 62498 104410 64242 88340 60040 98517 FALSE TRUE 61082.50555 54990.37624 82817.80228 56215.5823 122619.0709 62017.28343 74862.11052 54782.57931 113794.5132 0.536779005 0.483242774 0.727783792 0.494009603 1.077548183 0.544993618 0.657871003 0.481416702 1 16.79607147 3.740346075 24.91794688 0.691715172 0.510010882 0.146583052 0.197941137 268.5344648 3747657.761 0.046653816 0.078937965 5499.78959 -3.740346075 -0.18170429 LDIDPETITWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 254.57 9.53E-21 566975000 952570 829736 867426 990377 910693 854703 1051967 944548 964816 FALSE TRUE 907543.9039 914287.0417 907198.3401 890822.4224 1069517.571 825104.4208 891470.1135 861838.3698 1114434.738 0.814353567 0.820404292 0.814043487 0.799349116 0.959695112 0.740379309 0.799930299 0.773341265 1 20.0878807 -1.008620107 4.449582532 1.000006163 0.814941438 0.513680164 0.056512694 94598124598 30960561.11 6958125.17 0.01257359 0.098034716 1.008620107 -0.185064725 LDIDS(ph)PPITAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(1)PPITAR;LDIDS(0.999)PPIT(0.001)AR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR 202.72 4.10E-08 2844413000 3038697 2576910 2730517 2967495 2879583 2638135 3229138 2883607 2833232 TRUE FALSE 2895063.815 2839500.059 2855713.905 2669196.765 3381781.363 2546775.723 2736473.691 2631103.084 3272595.148 0.884638546 0.867660047 0.872614477 0.815620828 1.033363802 0.778212889 0.836178497 0.803980622 1 21.64200371 LDIDSPPITAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 275 9.02E-27 1358180000 916600 786111 880690 933750 917640 893810 1123320 1007160 1129380 FALSE TRUE 873274.1345 866216.6046 921070.5076 839887.676 1077676.125 862857.1356 951936.9028 918967.7311 1304518.482 0.669422585 0.66401252 0.706061677 0.643829649 0.826110278 0.661437264 0.729722818 0.704449759 1 20.31508595 -5 0.248134564 2.817872111 0.669577391 0.782355116 0.049999367 73.73229554 0.731616864 67.88421305 0.065154808 1.00E-05 5 -2.14829472 LDINLLDNVVNCLYHGEGAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDINLLDNVVNCLYHGEGAQQR 22 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49 O14980 XPO1 Exportin-1 0 ; 310.88 3.43E-67 864830000 1182920 1056200 1071190 1348490 1123830 1197960 1257670 1222640 1058690 FALSE TRUE 1127005.716 1163827.981 1120305.121 1212937.223 1319825.596 1156474.345 1065789.343 1115579.16 1222866.238 0.921609969 0.95172141 0.916130551 0.991880539 1.079288605 0.945707968 0.871550223 0.912265892 1 20.22183517 -0.389454305 6.209985774 0.999818137 0.945932968 0.074763586 0.055851541 0 0 0.056892863 0.013409776 0.407892477 0.389454305 -0.053885169 LDKDNLSYIEHIFEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 154.33 8.54E-08 365030000 1436960 1538330 1108290 1639310 969610 1299330 1330420 1414430 798180 FALSE TRUE 1369037.749 1695087.576 1159106.193 1474523.444 1138709.677 1254333.876 1127439.994 1290575.011 921957.6779 1.484924722 1.838574174 1.257222778 1.599339622 1.235099728 1.360511341 1.222876083 1.399820232 1 19.814341 2.470933987 0.228780225 0.953774683 1.832712765 0.482727557 0.165278727 2.516829058 0.357955505 0.377896575 0.747377969 295.7562884 -2.470933987 0.878938083 LDKENALDR ddPTM_SK-BR-3_Trastuzumab_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 5566800000 10463460 9867750 8280320 10534410 7561310 9437540 10910040 10279920 7611310 FALSE TRUE 9968872.982 10873284.94 8659980.862 9475471.093 8880000.07 9110715.623 9245513.021 9379755.708 8791633.082 1.133904576 1.236776472 0.985025283 1.07778282 1.01005126 1.036293887 1.051626352 1.06689572 1 23.06769975 3.73861794 24.99999998 1.036706413 1.185340526 0.738169862 0.037773535 2.114451642 922009.2761 0.008997513 0.01499635 5477.948434 -3.73861794 0.148634114 LDKESYPVFYLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDKESYPVFYLFR 13 1 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 89.629 0.0067139 57780000 75465 55494 47109 52988 67911 47062 87805 55910 66846 FALSE TRUE 71897.91901 61148.90169 49268.99425 47661.54557 79754.6569 45432.23114 74408.7346 51014.224 77212.13628 0.931173809 0.791959718 0.638099095 0.617280493 1.032929028 0.588407902 0.963692215 0.660702144 1 16.23654001 -0.74206052 5.41953223 1.000000032 0.79141975 0.161667414 0.1562294 5.37E-08 1.25E-08 0.13609404 0.032077668 0.18110877 0.74206052 -0.208580282 LDKSQIHDIVLVGGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDKSQIHDIVLVGGSTR 17 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 186.45 3.14E-10 2448900000 7480300 4722100 8284800 6425300 7971800 7714400 10831700 9098500 10550700 FALSE TRUE 7126721.044 5203287.359 8664666.275 5779416.637 9362079.396 7447248.394 9179125.227 8301787.106 12186848.67 0.584787851 0.426959216 0.710984973 0.474233889 0.768211672 0.611088937 0.753199246 0.681208681 1 23.53882178 -0.427078193 0.160943415 1.329020337 0.400097703 0.649043397 0.095800645 9.361066522 0.420709218 1.952659411 0.511148884 0.374043237 0.427078193 -0.928922634 LDLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 26456000000 22665140 20927790 18219380 20745400 20033230 19104460 22429620 20970440 19902550 FALSE TRUE 21593803.75 23060355.59 19054756.59 18660032.98 23527018.97 18442867.76 19007569.52 19134157.1 22988935.81 0.939312891 1.003106703 0.828866406 0.81169625 1.02340618 0.802249739 0.826813806 0.832320263 1 24.45443635 3.739837959 24.98325889 0.864675749 0.971209799 0.195725112 0.078887669 140.096469 2740089.546 0.019207729 0.032381159 5493.358716 -3.739837959 0.10653405 LDLAGRDLTDYLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDLAGRDLTDYLMK 14 1 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 ;;; 182.35 1.40E-06 660720000 1781430 620527 1783050 1302759 2125240 1525471 3288170 1942950 3326640 FALSE TRUE 1697225.334 683759.4068 1864804.606 1171803.19 2495881.183 1472643.557 2786499.275 1772814.998 3842518.341 0.441696092 0.177945646 0.485307926 0.304957084 0.649543076 0.383249584 0.72517527 0.461367999 1 21.87362072 0.249207981 0.228468391 1.223660935 0.234322198 0.636971251 0.139393376 3.432257497 0.367858341 0.978074707 0.316261952 1.775039331 -0.249207981 -0.989338736 LDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDLHLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 76.592 0.07465 69835000 404950 736650 374540 680900 285600 548170 416240 500890 233630 FALSE TRUE 385808.816 811715.4725 391713.0295 612454.6384 335408.5496 529186.7354 352734.9432 457029.4162 269860.1472 1.429662068 3.00791162 1.451540858 2.269526067 1.242897675 1.960966601 1.30710276 1.69357877 1 18.04185241 1.890600445 0.457123935 1.072075847 2.181155584 0.240145297 0.510835214 1.159549616 0.580329767 0.493609553 0.398847791 77.73210791 -1.890600445 1.109079737 LDLLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LDLLEDR 7 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 204.1 0.00063089 1565650000 2793520 2566650 2373650 2698100 2594900 2407360 2976860 2661400 2634240 FALSE TRUE 2661475.846 2828194.553 2482484.2 2426881.862 3047449.738 2323992.52 2522685.333 2428353.707 3042744.485 0.874695808 0.929488022 0.815870084 0.797596339 1.001546385 0.763781688 0.829082214 0.798080062 1 21.53694176 LDLLGNLPGS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDLLGNLPGSK 11 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LDLLGNLPGS(1)K 118.51 0.0007459 43181000 232510 279750 252010 311490 167510 268360 262450 303350 212790 TRUE FALSE 221519.7131 308256.843 263564.9078 280178.4334 196723.691 259066.6259 222408.4323 276787.0658 245788.3864 0.90126192 1.254155445 1.072324497 1.139917298 0.8003783 1.054023055 0.90487771 1.126119382 1 17.90705722 LDLLGNLPGS(ph)KR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDLLGNLPGSKR 12 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LDLLGNLPGS(1)KR;LDLLGNLPGS(1)KR 116.35 0.0005215 170715000 340370 401260 338820 433900 241870 386010 376900 440810 275480 TRUE FALSE 324281.3846 442148.8502 354355.2321 390283.5476 284052.0514 372642.3769 319396.9828 402210.3395 318200.0314 1.01911173 1.389531133 1.113624127 1.226535227 0.89268392 1.171094721 1.003761632 1.264017284 1 18.27957445 LDLRDDKDTIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 60.628 0.050955 368370000 738370 464170 607090 862240 486020 755900 913380 880860 497250 FALSE TRUE 703468.7134 511469.4507 634925.677 775565.9971 570781.7341 729722.9935 774027.1056 803727.2287 574360.9904 1.224784979 0.890501722 1.105447075 1.350311059 0.993768281 1.270495395 1.347631748 1.399341602 1 19.13159824 2.844069749 1.00418722 1.275725382 1.062864962 0.091030934 0.165653669 0.812418803 1.754278782 0.082119618 0.084776279 698.3445508 -2.844069749 -0.21286042 LDLRDPAALFETHGAEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDLRDPAALFETHGAEEIR 19 1 A0A087WVI0;E9PBL8;Q8WTW3;J3KRP4 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 127.17 1.44E-05 64877000 102394 84752 94108 111134 110437 97712 120875 110134 118294 FALSE TRUE 97554.03855 93388.32516 98422.94489 99962.59918 129697.1778 94328.20894 102433.2987 100490.0831 136638.4294 0.713957552 0.683470423 0.720316717 0.731584809 0.949199859 0.690349043 0.749666834 0.735445245 1 17.06000377 -5 0.223435699 2.321086594 0.710036108 0.530717156 0.074806553 122.5893874 1.226383542 73.14586238 0.134045931 1.00E-05 5 -1.611050486 LDNARQS(ph)AER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER;LDNARQS(1)AER 148.52 1.51E-05 4258800000 3138800 2170810 2696360 2706800 2995110 2596060 3319560 2805850 3398990 TRUE FALSE 2990435.145 2392018.007 2819990.773 2434707.321 3517456.236 2506157.791 2813100.154 2560154.899 3926088.01 0.761683166 0.609262452 0.718269882 0.620135696 0.895918845 0.638334593 0.716514797 0.652088005 1 21.90466108 -1.191938598 3.519502151 1.00042895 0.699191369 0.554719978 0.084017392 23809029.09 35150992.64 111253.6392 0.018199476 0.064277859 1.191938598 -0.301237581 LDNLHSCFCALQALIDSCAGPGSLATEPHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDNLHSCFCALQALIDSCAGPGSLATEPHVR 31 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 ; 225.57 2.15E-35 172573000 278225 242505 224241 290452 253671 263353 337300 291402 207592 FALSE TRUE 265073.8556 267216.5352 234522.6717 261255.2131 297911.1421 254233.0196 285838.6901 265885.2961 239784.3071 1.105467905 1.114403767 0.978056798 1.089542582 1.242413007 1.060257123 1.192065876 1.108851948 1 17.87137772 LDNLVAILDINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDNLVAILDINR 12 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 268.91 8.51E-22 313580000 578450 652990 353010 433990 480610 388830 551830 477350 379730 FALSE TRUE 551107.8149 719530.4234 369195.8577 390364.5007 564428.2318 375364.7196 467638.1984 435550.7034 438616.589 1.256468243 1.640454195 0.841727985 0.88999028 1.286837402 0.855792346 1.066166238 0.993010101 1 18.74260085 3.735740531 24.99811928 0.99717326 1.448461223 0.59915278 0.155653944 140.4734142 1245201.457 0.038276057 0.062311301 5441.774375 -3.735740531 0.451287963 LDNNLDSVSLLIDHVCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDNNLDSVSLLIDHVCSR 18 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 212.83 1.49E-16 122347000 155772 133756 163544 165883 163129 154146 192232 184954 171628 FALSE TRUE 148408.9663 147385.8885 171042.6542 149208.1257 191578.646 148807.8854 162903.4778 168758.4473 198243.1937 0.74862074 0.743460019 0.862792064 0.752651947 0.966381959 0.750633011 0.82173554 0.851269817 1 17.59691181 -4.999999997 0.102317168 1.615209638 0.676541727 0.484382434 0.065726982 146.4356186 1.0142162 19.2249498 0.951961145 1.00E-05 4.999999997 -0.938667911 LDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.022)PAS(0.978)PPRS(1)PAEPNDIPIAK;LDNT(0.097)PAS(0.906)PPRS(0.996)PAEPNDIPIAK;LDNT(0.064)PAS(0.937)PPRS(1)PAEPNDIPIAK;LDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;LDNT(0.003)PAS(0.997)PPRS(1)PAEPNDIPIAK;LDNT(0.004)PAS(0.996)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNT(0.004)PAS(0.996)PPRS(1)PAEPNDIPIAK 227.41 2.54E-26 4907700000 4161090 4705200 3438080 5023390 2700541 4186290 3828990 4034430 2602974 TRUE FALSE 3964403.522 5184665.229 3595719.369 4518429.293 3171514.495 4041317.728 3244807.251 3681153.921 3006629.914 1.318553875 1.724410845 1.195930152 1.502821905 1.054840332 1.344135409 1.079217378 1.224345539 1 21.51971587 2.918666082 1.029117387 1.135858108 1.501334755 0.385839242 0.171634684 0.451166025 1.027800824 0.075755427 0.084695935 829.2129624 -2.918666082 0.365476646 LDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 LDNT(0.011)PAS(0.984)PPRS(0.005)PAEPNDIPIAK 105.35 0.00031601 82415000 177700 228820 156020 211110 106510 227530 224700 274900 187970 TRUE FALSE 169300.4732 252137.0181 163173.6713 189888.8217 125085.3103 219650.579 190417.8881 250828.2987 217119.4276 0.779757367 1.161282622 0.751538787 0.874582362 0.576112933 1.011657876 0.877019114 1.155254974 1 17.7281293 1.252362291 24.90447743 1.07762746 0.880452011 0.235408517 0.159010631 300.6503754 542515.5879 0.103901966 0.037509272 17.87978496 -1.252362291 -0.197175449 LDNTPASPPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 LDNT(0.091)PAS(0.323)PPRS(0.586)PAEPNDIPIAK 110.03 0.00022437 296060000 363810 456630 385650 423360 243330 476920 510780 572270 396170 TRUE FALSE 346613.4223 503161.1161 403332.434 380803.0485 285766.675 460404.1408 432851.1299 522159.005 457606.0202 0.757449437 1.09955091 0.881396695 0.832163546 0.624481896 1.006114694 0.945903486 1.14106673 1 18.80374651 1.66858261 2.221300274 1.057286772 0.870967929 0.289621517 0.131339869 0.396368911 4.247155066 0.09252567 0.036872019 46.62111009 -1.66858261 -0.186318843 LDNVPHT(ph)PSSYIETLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 LDNVPHT(0.998)PS(0.002)SYIETLPK;LDNVPHT(0.998)PS(0.001)SYIETLPK;LDNVPHT(0.919)PS(0.081)SYIETLPK;LDNVPHT(0.994)PS(0.005)SYIETLPK 149.85 1.14E-06 605964000 602366 570808 603860 710810 488063 672645 744733 714935 540136 TRUE FALSE 573893.353 628973.9842 631547.5783 639358.0283 573181.0327 649351.135 631110.3029 652331.5013 623897.5322 0.919851936 1.008136676 1.012261703 1.024780505 0.91871021 1.040797729 1.011560826 1.045574742 1 19.25094958 4.54231295 2.179005754 1.007991487 0.913265636 0.38521915 0.034771886 0.417053039 3.070892027 0.008362722 0.065693411 34858.84153 -4.54231295 -0.094725852 LDNVPHTPSS(ph)YIETLPK ddPTM_SK-BR-3_Trastuzumab_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 LDNVPHTPS(0.046)S(0.954)YIETLPK;LDNVPHTPS(0.04)S(0.96)YIETLPK 195.03 2.65E-11 127052000 238990 204670 224360 256580 179227 249530 266510 257330 192509 TRUE FALSE 227693.4163 225526.1057 234647.1279 230788.0909 210484.1321 240888.7135 225849.0047 234796.821 222362.3125 1.023974853 1.0142281 1.055246841 1.037892115 0.946581863 1.083316281 1.01568023 1.055920036 1 17.76255277 LDPELHLDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDPELHLDIK 10 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 128.17 0.00033681 56332000 295700 296120 267510 312410 176540 287890 293020 325660 162610 FALSE TRUE 281722.847 326294.9647 279775.5981 281005.9533 207328.5201 277920.2971 248314.4173 297143.484 187826.7283 1.499908184 1.73721263 1.489540922 1.496091402 1.10382863 1.479663196 1.322039837 1.582008517 1 17.51904285 -2.804350356 0.087362199 8.08E-13 1.940468898 0.448544701 0.162857846 108.7374401 1.075978875 26.4463474 4.778108972 0.001569096 2.804350356 1.940468898 LDPFADGGKT(ph)PDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDPFADGGKTPDPK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LDPFADGGKT(1)PDPK 120.11 0.00024028 238940000 1236100 1487000 1141200 1424200 538880 1427700 1247200 1595200 542930 TRUE FALSE 1177672.003 1638526.991 1193525.149 1281036.71 632860.5014 1378258.391 1056916.734 1455515.831 627124.8115 1.877890942 2.612760587 1.903170034 2.042714124 1.00914601 2.197741766 1.685337136 2.320934852 1 19.25839307 3.311400301 2.50989233 1.728367075 2.237081559 0.17429423 0.47137828 0.439291741 5.637400334 0.128024618 0.179552586 2048.331772 -3.311400301 0.508714484 LDPHLVLDQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LDPHLVLDQLR 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 125.28 0.00033151 1886284000 7351250 5538830 3255830 4196830 6953570 4409840 7385720 5994930 5905180 FALSE TRUE 7003770.981 6103243.074 3405113.026 3774956.675 8166270.406 4257126.135 6258892.766 5469982.148 6820925.155 1.026806602 0.894782296 0.499215715 0.553437633 1.197237944 0.624127378 0.917601736 0.801941382 1 22.701536 1.596182805 25 0.894835369 0.818441814 0.045993084 0.216751715 4.29156008 9158.726351 0.114450755 0.053668386 39.46233736 -1.596182805 -0.076393555 LDPHNHVLYSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LDPHNHVLYSNR 12 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 89.013 0.0055875 3523960000 5841970 4950130 3697270 4364670 5697100 4287950 5865310 4620880 270883 FALSE TRUE 5565831.656 5454553.875 3866793.487 3925925.079 6690672.436 4139457.216 4970449.236 4216251.25 312890.1522 17.78845265 17.43280777 12.35830997 12.54729512 21.38345483 13.22974593 15.88560458 13.47518041 1 18.25529673 -0.173965257 0.645838443 8.81E-10 16.24875544 0.739144547 2.738760153 3.1190742 1.265037163 10.43715614 1.000480288 0.669938201 0.173965257 16.24875544 LDPITGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 286395000 95250 95205 94637 94186 152227 85939 101193 110026 171865 FALSE TRUE 90747.72127 104906.4977 98976.20006 84718.24434 178775.3406 82962.91088 85754.14931 100391.5402 198516.9464 0.457128335 0.528451095 0.49857809 0.42675573 0.900554556 0.417913495 0.431973949 0.505707659 1 17.59890264 -1.18939512 4.972257963 1.000045224 0.514819227 0.535607594 0.140103869 6.58E-05 1.07E-05 0.127063682 0.029946414 0.064655411 1.18939512 -0.485225997 LDQPGNLPGS(ph)NRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDQPGNLPGSNRR 13 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LDQPGNLPGS(1)NRR 64.507 0.037436 143180000 116560 111980 117730 143210 119080 120340 129910 135450 140220 TRUE FALSE 111050.4398 123390.8893 123128.037 128814.2587 139847.5143 116172.5956 110089.8435 123589.2799 161964.6015 0.685646362 0.761838625 0.760215725 0.795323531 0.863444932 0.717271518 0.67971546 0.763063526 1 17.30531901 -2.212461918 2.073446975 1.694758968 0.748070755 0.677671826 0.05335802 3689512.202 647296.125 12018205.22 0.013666787 0.006131096 2.212461918 -0.946688214 LDQPVS(ph)APPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR 182.91 2.38E-05 10838740000 10531680 9292580 9901420 11553940 10450050 9397280 10837840 9522740 9661600 TRUE FALSE 10033868.36 10239504.47 10355409.9 10392516 12272535.41 9071849.837 9184328.457 8688878.402 11159871.58 0.899102493 0.917528879 0.92791479 0.931239748 1.099702207 0.812899124 0.82297797 0.778582293 1 23.41181709 LDQPVSAPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVS(0.001)APPS(0.999)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR 224.55 2.08E-11 7167650000 3911645 3528939 3369198 3896953 3264518 3230995 3759025 3459474 3134400 TRUE FALSE 3726749.293 3888541.896 3523679.061 3505223.881 3833848.906 3119104.833 3185516.697 3156544.117 3620466.744 1.029356035 1.074044363 0.973266518 0.968169059 1.058937749 0.861520089 0.879863543 0.8718611 1 21.78774427 2.237134484 24.99996954 0.890725209 1.024254638 0.568673691 0.050245074 23.58186899 413375.695 0.017408674 0.013558021 172.6372399 -2.237134484 0.133529429 LDRAS(ph)PDLWPEQLPGVAEFAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDRASPDLWPEQLPGVAEFAASFK 24 1 Q52LA3 Q52LA3 LIN52 Protein lin-52 homolog 1 LDRAS(1)PDLWPEQLPGVAEFAASFK;LDRAS(1)PDLWPEQLPGVAEFAASFK 264.86 1.72E-44 778050000 1490530 1278960 1277430 1513010 1049690 1403400 1539710 1566210 1201490 TRUE FALSE 1420075.601 1409287.478 1336001.429 1360919.36 1232755.604 1354799.906 1304798.961 1429064.349 1387810.933 1.023248605 1.015475123 0.962668183 0.980623029 0.888273449 0.976213599 0.940184956 1.029725531 1 20.40437961 3.757377906 4.107108661 0.961875941 1.020575421 0.232761449 0.037293004 0.232638905 9.347334985 0.009109393 0.016176879 5719.761315 -3.757377906 0.05869948 LDRDPASGTALQEISFWLNLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDRDPASGTALQEISFWLNLER 22 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 149 6.07E-08 88036000 148500 176910 152890 173980 139990 142790 172760 166880 145160 FALSE TRUE 141480.6993 194937.3301 159900.1577 156491.1999 164404.2117 137845.1465 146402.289 152267.1025 167670.6714 0.843801114 1.162620323 0.953656095 0.933324824 0.980518598 0.822118414 0.873153831 0.908132002 1 17.35527083 2.824408116 1.55478935 0.891442069 1.001374644 0.093111829 0.091800667 0.596730769 2.904875443 0.034884215 0.036037084 667.4336759 -2.824408116 0.109932575 LDRETEELHHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LDRETEELHHDR 12 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;; 124.07 0.00019802 1293350000 956550 758670 770810 844810 863790 865850 1047360 940280 333333 FALSE TRUE 911335.7772 835979.3355 806152.4009 759888.0938 1014434.703 835865.3974 887565.9959 857944.0985 385024.5792 2.366954803 2.171236281 2.093768669 1.973609309 2.634727125 2.170940357 2.305219053 2.228283971 1 18.55459102 0.904704466 19.4470842 1 2.245495063 0.831784238 0.175700678 3610.421569 736786.3501 0.157334832 0.039333708 8.029795144 -0.904704466 1.245495063 LDRLDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDRLDLAR 8 1 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 143.04 0.00055437 846280000 1829420 1708570 1372340 1514340 1807230 1450790 1966380 1737980 1853090 FALSE TRUE 1742946.942 1882675.225 1435263.146 1362115.666 2122410.34 1400548.779 1666372.616 1585793.258 2140457.733 0.814287017 0.879566644 0.670540289 0.636366533 0.991568442 0.654322091 0.778512273 0.74086642 1 21.02948792 -1.612382823 7.430543656 1.000293114 0.777544505 0.305263896 0.108256834 0.000492352 2.57E-05 0.098175381 0.023110291 0.024412777 1.612382823 -0.222748609 LDS(ph)ELTARKELEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSELTARKELEQK 14 2 Q8IUG5-2;Q8IUG5;Q8IUG5-3 Q8IUG5-2 MYO18B Unconventional myosin-XVIIIb 1 LDS(0.5)ELT(0.5)ARKELEQK;LDS(0.5)ELT(0.5)ARKELEQK 92.773 0.0025181 418430000 769520 552450 746210 753080 1373160 520810 955560 639910 1617930 TRUE FALSE 733146.3146 608745.2831 780424.4666 677378.9676 1612638.669 502774.2191 809771.7719 583876.088 1868830.321 0.392302237 0.325735984 0.417600495 0.362461461 0.862913369 0.269031497 0.433304063 0.312428625 1 20.83370416 -1.678159483 2.800701652 1.073074458 0.417192453 0.548993561 0.164598269 31586853 28854265.38 16459399.15 0.038280797 0.020981692 1.678159483 -0.655882005 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 LDS(1)PPPS(0.982)PIT(0.018)EASEAAEAAEAGNLAVSSR;LDS(1)PPPS(0.996)PIT(0.005)EASEAAEAAEAGNLAVSSR 288.02 1.49E-72 182985000 56517 45052 51241 55734 38184 52178 57602 55905 39700 TRUE FALSE 53845.55342 49642.85002 53590.45053 50131.51243 44843.27751 50371.06278 48813.75697 51009.66183 45856.47324 1.174219246 1.08257017 1.168656173 1.093226515 0.977905066 1.098450431 1.064489995 1.11237647 1 15.48483778 8 0.170474878 1.01971618 1.598639085 0.392652512 0.048649484 62.5937858 0.677422906 0.118780701 9.258536666 100000000 -8 0.578922904 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.921)PPPS(0.064)PIT(0.013)EAS(0.002)EAAEAAEAGNLAVSSR;LDS(0.747)PPPS(0.168)PIT(0.039)EAS(0.045)EAAEAAEAGNLAVSSR;LDS(0.854)PPPS(0.121)PIT(0.024)EASEAAEAAEAGNLAVSSR 190.14 2.53E-18 84893000 39589 44399 39422.3 48543 33101.4 48614 47737 56984 43685 TRUE FALSE 37717.70643 48923.30858 41229.85145 43663.36541 38874.27368 46930.48499 40453.8439 51994.17887 50459.44669 0.747485534 0.969556977 0.817088854 0.865315977 0.770406261 0.930063409 0.801710018 1.030415161 1 15.62283677 1.231841712 24.99997438 1.015207693 0.84871857 0.524670094 0.067944525 128.9153595 479651.9887 0.054249024 0.014791789 17.05460685 -1.231841712 -0.166489123 LDS(ph)SPSVSSTLAAKDDPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSSPSVSSTLAAKDDPDGK 20 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.497)S(0.497)PS(0.002)VSS(0.002)T(0.002)LAAKDDPDGK 135.64 4.13E-06 227830000 807390 777400 699660 871740 405610 877930 834500 921200 526840 TRUE FALSE 769226.2748 856617.9438 731740.1031 784111.039 476348.2556 847527.064 707181.6984 840534.8444 608539.6565 1.26405283 1.407661661 1.202452618 1.288512639 0.782772742 1.392722816 1.162096325 1.381232653 1 19.21499176 3.470993392 2.565135244 1.172235101 1.333709637 0.118452818 0.182445487 0.551816302 7.294935285 0.048831619 0.075749308 2957.967458 -3.470993392 0.161474536 LDS(ph)SPVSSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSSPVSSPR 10 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 LDS(0.727)S(0.273)PVSSPR;LDS(0.605)S(0.394)PVS(0.001)SPR 113.42 0.0015636 318230000 646290 601970 583570 693190 612130 655210 761500 687240 738060 TRUE FALSE 615741.1525 663311.4274 610327.2617 623509.2242 718885.2782 632519.9134 645319.1891 627061.6223 852514.5753 0.722264663 0.778064618 0.715914167 0.731376615 0.843252771 0.741946158 0.756959714 0.73554358 1 19.70136497 -2.113716643 2.517371617 1.47521945 0.754182002 0.818443565 0.036533141 5578477.537 1399661.499 15201868.38 0.008153213 0.007696324 2.113716643 -0.721037448 LDSEDKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LDSEDKDK 8 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 102.61 0.0044983 7180890000 9415650 12290030 7079750 12177590 3226220 9912350 7917190 10959420 3191040 FALSE TRUE 8970590.885 13542398.03 7404363.54 10953475.52 3788871.747 9569082.834 6709277.256 9999755.085 3685890.186 2.433765097 3.674118693 2.008839973 2.971731377 1.0279394 2.596138884 1.820259671 2.712982368 1 21.81358166 3.263100798 1.681962201 1.970481278 2.996890575 0.240934627 0.724041894 0.437290403 2.557148604 0.211454957 0.306579597 1832.739744 -3.263100798 1.026409297 LDSEDKDKEGKPLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSEDKDKEGKPLLK 15 3 P13639 P13639 EEF2 Elongation factor 2 0 64.136 0.029424 2685000000 3919800 2684200 3147400 3759700 1532700 4074900 3905900 4436000 1435500 FALSE TRUE 3734518.822 2957723.032 3291711.403 3381767.813 1800002.395 3933785.191 3309983.218 4047560.323 1658110.008 2.252274459 1.783791797 1.985218946 2.039531633 1.085574772 2.372451267 1.99623861 2.441068628 1 20.6611083 4.641869472 3.131141338 1.892284506 2.271593465 0.059304236 0.475209875 0.92635732 14.7516755 0.104128971 0.755755637 43839.8916 -4.641869472 0.379308958 LDSGDLLQQAQEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSGDLLQQAQEIR 14 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ; 142.57 2.18E-05 72896000 88042 88754 82901 102746 91406 89140 96643 94299 104740 FALSE TRUE 83880.42914 97798.1335 86702.09285 92417.77688 107347.1775 86053.05945 81898.33538 86041.67965 120982.5443 0.693326708 0.808365654 0.716649607 0.763893481 0.887294759 0.711284921 0.676943404 0.71119086 1 16.88443938 -1.021605407 4.671019936 1.000006109 0.745714508 0.620794485 0.062357929 4.47E-06 9.36E-07 0.060689314 0.014304224 0.095146889 1.021605407 -0.2542916 LDSHPCLEVTAAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDSHPCLEVTAAALR 15 0 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 185.27 4.30E-07 2129460000 3107060 2802710 2536060 3156100 2887340 2732730 3217730 3067270 2696320 FALSE TRUE 2960195.431 3088309.335 2652340.86 2838842.832 3390891.182 2638094.875 2726806.191 2798683.578 3114451.535 0.950470861 0.991606163 0.851623739 0.911506504 1.088760298 0.847049583 0.875533352 0.898612018 1 21.57054669 LDSHPCLEVTAAALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSHPCLEVTAAALRR 16 1 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 131.4 2.91E-05 190560000 132590 61341 127100 97303 145950 116270 194900 142130 196290 FALSE TRUE 126322.7335 67591.71764 132927.6607 87521.91758 171403.6338 112243.5407 165164.4254 129684.3437 226729.6507 0.557151361 0.298115917 0.586282651 0.386018844 0.755982437 0.49505453 0.728464164 0.571977875 1 17.79061355 -0.031929048 0.221339318 1.222640606 0.369684576 0.596038218 0.12561164 4.999870859 0.426354402 1.150353827 0.295166907 0.929118167 0.031929048 -0.85295603 LDSLHPDLIYNVSWNHNGSLFCSACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSLHPDLIYNVSWNHNGSLFCSACK 26 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 249.83 4.11E-46 128645000 184705 157908 159966 201732 165002 170861 216306 202834 114753 FALSE TRUE 175974.3607 173999.0047 167300.5993 181453.5161 193778.2966 164944.0407 183304.547 185072.7797 132548.3092 1.327624334 1.312721421 1.262185843 1.368961379 1.461944689 1.244406977 1.382926332 1.39626662 1 17.01615874 -1.182480736 5.148270218 0.999978908 1.341153998 0.741695703 0.063886522 1.45E-05 2.30E-06 0.057990921 0.013667747 0.065693025 1.182480736 0.34117509 LDSQEPGRQT(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LDSQEPGRQTPDR 13 1 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 1 LDSQEPGRQT(1)PDR;LDS(0.001)QEPGRQT(0.999)PDR;LDS(0.001)QEPGRQT(0.999)PDR 133.71 0.00016812 651280000 572930 515740 572850 585800 588070 549170 662080 599620 684420 TRUE FALSE 545848.7343 568294.4923 599115.7391 526914.2711 690629.2218 530152.1052 561067.5361 547114.094 790556.3581 0.690461507 0.718853864 0.757840644 0.666510699 0.873598972 0.670606339 0.709712256 0.692062101 1 19.59250879 -2.068219375 2.599198647 1.419759388 0.720960117 0.68107138 0.059679931 3806900.985 1646431.125 9479607.078 0.013570999 0.008546349 2.068219375 -0.698799271 LDSQNAQGYEWIFIAWSPDHSHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDSQNAQGYEWIFIAWSPDHSHVR 24 0 Q12792;Q12792-3;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ; 166.91 7.17E-12 186392000 102532 94597 103563 114307 94061 103976 130827 119042 99679 FALSE TRUE 97685.51556 104236.5418 108311.466 102816.6432 110465.2086 100375.285 110866.9383 108618.0514 115136.7102 0.848430664 0.905328471 0.940720521 0.892996187 0.95942648 0.871792192 0.962915634 0.943383315 1 16.81298837 8 0.08260298 1.062039223 0.529905927 0.58039793 0.029714244 118.8024771 0.712705084 0.666791502 7.197604986 100000000 -8 -0.532133297 LDSQPQET(ph)SPELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.76)S(0.24)PELPR 137.46 4.06E-05 0 107400 74800 90615 98942 96432 85129 105370 84252 102280 TRUE FALSE 102323.4148 82422.20504 94769.78738 88996.16218 113249.7103 82180.96138 89293.87125 76874.44823 118141.06 0.866112212 0.697659264 0.802174852 0.753304246 0.958597377 0.695617268 0.755824192 0.650700512 1 16.85015094 LDSQPQETS(ph)PELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.079)S(0.921)PELPR;LDSQPQET(0.001)S(0.999)PELPR;LDSQPQET(0.019)S(0.981)PELPR;LDSQPQET(0.087)S(0.913)PELPR;LDSQPQET(0.025)S(0.975)PELPR;LDSQPQET(0.026)S(0.974)PELPR;LDSQPQETS(1)PELPR;LDSQPQET(0.107)S(0.893)PELPR;LDSQPQET(0.017)S(0.983)PELPR;LDSQPQET(0.027)S(0.973)PELPR 305.1 2.96E-44 20404290000 9648620 7215500 8224320 8961210 8817730 8202130 10078890 8660210 9070800 TRUE FALSE 9192548.854 7950767.653 8601413.207 8060412.146 10355539.32 7918088.181 8541170.219 7901876.102 10477453.34 0.87736481 0.758845437 0.820945026 0.76931024 0.988364156 0.755726409 0.815195253 0.754179078 1 23.32078476 -1.115821079 4.63666831 1.000010263 0.816701509 0.389559066 0.071793416 9.72E-06 1.85E-06 0.062469456 0.014723022 0.076591208 1.115821079 -0.183308754 LDSQPQETS(ph)PELPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSQPQETSPELPRR 15 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDS(0.001)QPQET(0.478)S(0.521)PELPRR 66.325 0.036082 70624000 23450 14294 24579 22873 27436 22602 32347 24263 33643 TRUE FALSE 22341.56497 15750.57485 25705.97146 20573.76258 32220.82971 21819.28707 27411.87106 22138.40309 38860.18462 0.57492174 0.405313948 0.661498954 0.529430387 0.829147623 0.561481817 0.705397345 0.569693719 1 15.24600513 -5 0.122729632 2.326053706 0.404782764 0.570786076 0.10964953 97.84200147 0.772883789 32.13353314 0.897978644 1.00E-05 5 -1.921270941 LDSS(ph)PSVSSTLAAK ddPTM_SK-BR-3_Trastuzumab_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(0.026)S(0.974)PSVSSTLAAK;LDS(0.03)S(0.97)PSVSSTLAAK;LDS(0.016)S(0.984)PSVSSTLAAK;LDSS(1)PSVSSTLAAK;LDS(0.034)S(0.965)PSVSSTLAAK;LDS(0.061)S(0.919)PS(0.02)VSSTLAAK;LDS(0.017)S(0.983)PSVSSTLAAK;LDS(0.116)S(0.882)PS(0.001)VSSTLAAK 375.65 2.46E-97 4336460000 5930130 6913810 4927000 6980280 3396470 5955550 5434130 6006970 3564400 TRUE FALSE 5649824.507 7618335.099 5152907.823 6278608.993 3988813.293 5749307.81 4605053.664 5480967.862 4117148.948 1.37226624 1.850390937 1.251571874 1.524989519 0.968828999 1.396429394 1.118505481 1.331253237 1 21.97321421 3.213165103 1.613790819 1.191966225 1.591597137 0.359981778 0.207001917 0.332314756 1.794275198 0.062480173 0.087703801 1633.672894 -3.213165103 0.399630912 LDSS(ph)PSVSSTLAAKDDPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSSPSVSSTLAAKDDPDGK 20 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.185)S(0.757)PS(0.018)VS(0.018)S(0.018)T(0.003)LAAKDDPDGK 94.671 0.00080854 192100000 360260 370750 347910 417370 215720 380130 405050 441190 204330 TRUE FALSE 343231.2238 408529.8465 363862.0176 375415.1746 253341.4997 366966.0028 343252.1832 402557.0647 236016.4528 1.454268207 1.730937999 1.541680731 1.590631374 1.073406098 1.554832294 1.454357013 1.705631365 1 17.84852791 -1.912427004 2.62570267 0.695921417 1.516456801 0.443716508 0.180560157 40778031.65 26556867.76 76605797.17 0.043403933 0.012234127 1.912427004 0.820535385 LDSSDIYNELKETYPNYLPLYVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSSDIYNELKETYPNYLPLYVAR 24 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0A3;A0A494C1S6 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 204.96 9.37E-25 77772000 105890 80099 102590 102360 83883 107040 118380 92923 107620 FALSE TRUE 100884.7896 88261.17917 107293.853 92070.57833 98512.16864 103333.178 100318.9568 84786.1695 124309.16 0.811563602 0.710013479 0.863121053 0.740658036 0.792477149 0.831259563 0.807011783 0.682058905 1 16.92357308 -1.64992762 5.398745909 1.002817165 0.781342594 0.610647083 0.055252895 0.001721626 0.000111636 0.049160662 0.011453926 0.022390943 1.64992762 -0.221474571 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDS(0.211)S(0.211)EMDHS(0.577)ENEDYTMSSPLPGK;LDS(0.001)S(0.004)EMDHS(0.996)ENEDYTMSSPLPGK;LDSSEMDHS(1)ENEDYTMSSPLPGK;LDS(0.159)S(0.136)EMDHS(0.704)ENEDYTMSSPLPGK 255.21 8.18E-44 585159000 488116 462391 424739 582800 369046 537453 544334 549343 349315 TRUE FALSE 465043.724 509509.1686 444213.7033 524215.8368 433407.5056 518840.8678 461285.8509 501239.6147 403484.9861 1.152567605 1.262771072 1.100942336 1.299220181 1.074160181 1.285898821 1.143254066 1.242275752 1 18.62215547 -1.169506037 4.483481185 0.999963055 1.195500682 0.385813923 0.077373931 2.35E-05 4.36E-06 0.061663043 0.014531374 0.067685238 1.169506037 0.195537627 LDSSPS(ph)VSSTLAAKDDPDGKQEAKPQQAAGMLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDSSPSVSSTLAAKDDPDGKQEAKPQQAAGMLSPK 35 3 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.285)S(0.256)PS(0.317)VS(0.048)S(0.048)T(0.048)LAAKDDPDGKQEAKPQQAAGMLSPK 109.38 1.13E-05 576900000 401110 287180 392640 382210 177410 438020 481190 510590 179980 TRUE FALSE 382150.3252 316443.9685 410642.9324 343789.5246 208350.2478 422851.2576 407775.6278 465880.0328 207890.3792 1.838229969 1.522167451 1.975285889 1.653705794 1.002212073 2.034010709 1.961493502 2.240988903 1 17.66546347 LDT(ph)PDINIVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDTPDINIVLK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 LDT(1)PDINIVLK 132.97 0.0019172 16049000 54642 43960 42621 57644 37332 48987 61293 60344 46919 TRUE FALSE 52059.18095 48439.57398 44575.21501 51849.5156 43842.68898 47290.56791 51941.62713 55059.95946 54194.95889 0.960590838 0.893802209 0.822497441 0.956722113 0.808980944 0.872600863 0.958421746 1.015960905 1 15.72587104 1.540124462 3.486317529 1.004828702 0.890141205 0.527416726 0.048520988 0.167041767 4.498228213 0.031712738 0.012560215 34.68362341 -1.540124462 -0.114687497 LDTDDLDEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 141.95 8.81E-05 28840000 139840 129440 134650 150340 102000 152470 145950 152290 103230 FALSE TRUE 133230.0403 142630.0832 140823.8357 135227.5376 119788.7677 147189.9257 123682.6469 138954.6803 119238.3812 1.117341908 1.196175944 1.181027739 1.134094041 1.00461585 1.234417343 1.037272108 1.165351952 1 16.86348917 -5 0.136152751 0.53052604 1.186741252 0.269841231 0.069435687 169.2202764 1.427891836 21.46013631 0.413394446 1.00E-05 5 0.656215212 LDTHPAMVTVLEMGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDTHPAMVTVLEMGAAR 17 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 222.5 3.34E-15 266720000 657930 607450 614960 670740 633270 546730 646480 618140 553020 FALSE TRUE 626830.9528 669349.8456 643156.5243 603315.9409 743712.0875 527796.603 547847.6026 564012.3846 638779.5172 0.981294697 1.047857402 1.006852141 0.94448229 1.164270406 0.82625787 0.857647416 0.882953147 1 19.28495853 2.212748839 24.99998902 0.875558744 1.022353117 0.463033155 0.072320813 170.6938495 165324.392 0.024229796 0.017900971 163.2107796 -2.212748839 0.146794373 LDTIPDIPPPRPPKPHPAHDRS(ph)PVETCSIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDTIPDIPPPRPPKPHPAHDRSPVETCSIPR 31 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 LDTIPDIPPPRPPKPHPAHDRS(0.833)PVET(0.078)CS(0.089)IPR;LDTIPDIPPPRPPKPHPAHDRS(0.91)PVET(0.047)CS(0.044)IPR 50.85 0.031257 403070000 194746 145430 162297 196474 140268 171764 186054 176641 36719 TRUE FALSE 185540.7425 160249.4823 169738.478 176724.0602 164730.6948 165815.7696 157668.0452 161173.3776 42413.19499 4.374599522 3.778293109 4.002020551 4.166723594 3.883949201 3.909532627 3.717429098 3.800076313 1 15.37222554 -0.986833104 0.470909146 2.57E-19 4.065676154 0.970779924 0.162155121 2.541270366 0.364299943 3.686931721 0.079166849 0.103078216 0.986833104 4.065676154 LDVATDNFFQNPELYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDVATDNFFQNPELYIR 17 0 C9JVE2;Q96GG9;C9J8R4;C9JRU6;C9J0B2 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 127.76 0.0004686 0 9471.6 6343.4 9363.4 7782.3 7934.5 8275.5 9667.6 10536 10887 FALSE TRUE 9023.896239 6989.799672 9792.721152 7000.008419 9318.274288 7988.91736 8192.630062 9613.411985 12575.30036 0.717588923 0.555835604 0.778726621 0.556647414 0.740998149 0.635286405 0.651485836 0.764467783 1 13.61830524 0.878285217 2.602182479 0.999755991 0.656608667 0.687496318 0.071948692 0.234322615 3.229102561 0.059437736 0.015866567 7.555882873 -0.878285217 -0.343147324 LDVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDVELR 6 0 A0A087X1S3 A0A087X1S3 HUWE1 0 ; 100.82 0.086601 82216000 225671 197833 189918 238974 233911 206180 259278 229475 238154 FALSE TRUE 215003.9791 217992.4076 198625.9282 214951.8795 274705.0043 199039.9349 219720.3791 209380.9525 275085.706 0.781589063 0.79245269 0.722051069 0.781399669 0.998616062 0.723556079 0.798734265 0.761148064 1 18.06952165 -1.596872934 2.530263598 1.019616112 0.794539264 0.411650962 0.077040952 6517213.144 5721195.999 849126.0612 0.018371107 0.025300381 1.596872934 -0.225076848 LDVFARPAS(ph)PSLQLLPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDVFARPASPSLQLLPWR 18 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 LDVFARPAS(0.899)PS(0.101)LQLLPWR;LDVFARPAS(0.566)PS(0.434)LQLLPWR 193.77 6.47E-15 1485220000 1712100 1177780 1516480 1598270 1639500 1517470 1956820 1648810 1959700 TRUE FALSE 1631172.426 1297797.121 1586012.108 1437608.863 1925428.281 1464919.633 1658271.17 1504431.456 2263600.267 0.720609751 0.573333172 0.700659092 0.63509838 0.850604371 0.647163572 0.732581275 0.664618872 1 21.11018778 -5 0.24671137 2.865924638 0.656593361 0.633877815 0.073517242 106.5160849 1.057944592 100.0475933 0.099649676 1.00E-05 5 -2.209331277 LDVGNFSWGSECCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LDVGNFSWGSECCTR 15 0 P62241 P62241 RPS8 40S ribosomal protein S8 0 ;;;;; 358.07 2.42E-82 1278200000 401673 334172 338849 370034 380321 367267 455639 427803 444673 FALSE TRUE 382686.7133 368224.5067 354385.5618 332837.4793 446648.862 354548.4517 386122.9022 390342.3014 513630.6178 0.745062113 0.716905289 0.68996191 0.648009421 0.869591583 0.690279044 0.751752113 0.759966964 1 18.97037168 -2.751985463 0.325627693 1.49731534 0.716915717 0.687349924 0.057130925 35.12674943 1.169910571 12.17323825 0.045859001 0.001770168 2.751985463 -0.780399622 LDVTILS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.99)PS(0.009)R;LDVTILS(0.958)PS(0.042)R;LDVTILS(0.999)PS(0.001)R;LDVTILS(1)PSR;LDVTILS(0.96)PS(0.039)R 181.49 1.97E-06 492051000 631264 661323 597295 767544 652615 625650 713075 717343 675448 TRUE FALSE 601425.4018 728712.5656 624681.5666 690389.0189 766430.8494 603983.5836 604282.3122 654528.644 780193.0261 0.770867441 0.934015739 0.800675661 0.884895142 0.982360549 0.77414635 0.774529241 0.838931677 1 19.57347158 -2.527122695 2.126647808 3.05904224 0.844181149 0.317447404 0.071393181 4632754.226 257403.2027 46172348.02 0.017234497 0.002970827 2.527122695 -2.214861091 LDVTILS(ph)PSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.992)PS(0.008)RK;LDVTILS(0.982)PS(0.018)RK 116.71 0.00058336 462800000 559010 533840 562840 657940 437820 578880 680020 613130 562840 TRUE FALSE 532586.7052 588238.9029 588646.7707 591802.6212 514175.6694 558833.2404 576270.4596 559441.0868 650122.3526 0.819209958 0.90481261 0.905439981 0.910294222 0.790890618 0.859581644 0.886403086 0.860516616 1 19.31035173 -1.628683709 2.612577688 1.014053929 0.868786358 0.539879617 0.038518844 10511496.54 9046529.222 997513.4174 0.008981422 0.023513447 1.628683709 -0.14526757 LDWELEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDWELEQR 8 0 Q13769;F8WCP5;C9JXG5;H7C072 Q13769 THOC5 THO complex subunit 5 homolog 0 ; 118.32 0.0044398 81985000 146809 120150 126035 138915 159777 121494 164796 134537 175108 FALSE TRUE 139869.6295 132393.4216 131813.8294 124951.0003 187642.0582 117286.6323 139653.3435 122756.2271 202262.8543 0.691524057 0.654561225 0.651695685 0.617765435 0.927713884 0.579872329 0.690454725 0.606914342 1 17.62587187 -1.445566079 5.60987853 1.000249918 0.677815476 0.529107548 0.095595056 0.000267229 2.64E-05 0.082778388 0.019496135 0.03584544 1.445566079 -0.322434442 LDYFLLSHSLLPALCDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDYFLLSHSLLPALCDSK 18 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 227.22 3.09E-19 1060670000 4679710 4477150 4235740 4789030 3335170 4763940 4984040 5091000 3005210 FALSE TRUE 4458509.383 4933376.675 4429952.869 4307627.606 3916822.592 4598963.563 4223633.16 4645205.051 3471242.618 1.284413068 1.421213444 1.276186471 1.240946854 1.128363247 1.324875288 1.216749627 1.338196595 1 21.72702077 -4.929897647 0.16112511 4.66E-11 1.358871365 0.53566077 0.079665377 98.12139773 0.923676661 31.64646614 0.323727423 1.18E-05 4.929897647 1.358871365 LDYGQHVVAGTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDYGQHVVAGTPGR 14 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;; 151.07 7.04E-06 312790000 2185580 2020920 2001200 2375930 1906250 2141910 2244610 2342970 1722060 FALSE TRUE 2082271.965 2226854.046 2092956.999 2137097.002 2238699.396 2067735.12 1902153.519 2137807.126 1989108.27 1.046836915 1.119523798 1.052208686 1.074399536 1.125478905 1.039528693 0.956284556 1.074756542 1 20.92369038 2.003714093 23.05673023 1.003593972 1.083300216 0.443705374 0.037685653 30.87229349 191648.9314 0.012965105 0.009518961 100.8588688 -2.003714093 0.079706244 LDYILGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDYILGLK 8 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 124.08 0.0030712 10059000 99178 93011 77281 70369 91581 71098 116240 91812 90344 FALSE TRUE 94490.05249 102488.9266 80824.41029 63295.37443 107552.6974 68635.85843 98505.45311 83772.45455 104354.0861 0.905475349 0.982126627 0.7745208 0.606544284 1.030651519 0.657720852 0.943953963 0.802771196 1 16.67112757 -1.626284373 8.340174181 1.000114045 0.850744643 0.116971389 0.135938982 0.000267842 1.20E-05 0.122295778 0.028803521 0.02364371 1.626284373 -0.149369402 LDYVPS(ph)S(ph)ASREVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LDYVPSSASREVR 13 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 LDY(0.002)VPS(0.994)S(0.666)AS(0.338)REVR;LDY(0.022)VPS(0.936)S(0.612)AS(0.429)REVR 73.208 0.021312 144724000 407840 173630 495110 344210 563450 380280 618710 433460 729330 TRUE FALSE 388562.2115 191323.0944 517811.2832 309609.3568 661715.5016 367110.8082 524314.4261 395503.9445 842430.7715 0.461239338 0.227108388 0.614663306 0.36751905 0.785483536 0.43577564 0.622382804 0.469479461 1 19.68419861 -5 0.121035054 2.691181633 0.234144961 0.541257064 0.148427117 103.2605615 0.808064317 42.68192422 1.250393598 1.00E-05 5 -2.457036672 LDYVPS(ph)SAS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 LDY(0.001)VPS(0.995)S(0.013)AS(0.992)R;LDY(0.009)VPS(0.965)S(0.042)AS(0.984)R;LDYVPS(0.996)S(0.005)AS(1)R;LDYVPS(0.996)S(0.007)AS(0.997)R 104.81 0.0038494 1975660000 2875430 2464720 2570510 2956020 2595760 2750410 2965610 2810540 2458320 TRUE FALSE 2739514.122 2715877.77 2688370.426 2658875.254 3048459.722 2655162.612 2513151.727 2564434.218 2839543.71 0.964772654 0.956448658 0.946761417 0.936374124 1.073573797 0.935066646 0.885054778 0.903114894 1 21.43722769 -0.840515312 4.495540847 1.000000298 0.949287179 0.089660497 0.049856774 6466701.381 1438470.354 19.62222789 0.011918213 0.14437257 0.840515312 -0.05071312 LDYVPS(ph)SASREVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LDYVPSSASREVR 13 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPS(0.45)S(0.361)AS(0.19)REVR 100.41 0.0014621 244900000 201480 93801 247600 149970 265010 190200 325330 216810 357420 TRUE FALSE 191956.4397 103359.4285 258952.7049 134894.7307 311227.6601 183613.3263 275694.9334 197824.967 412846.8682 0.464957965 0.250357788 0.627236694 0.326742773 0.753857384 0.444749229 0.667789814 0.479172745 1 18.65524724 -4.999999995 0.116235445 2.691691502 0.219060706 0.554630609 0.145258097 100.6788897 0.766111383 39.99857039 1.339739042 1.00E-05 4.999999995 -2.472630796 LDYVPSSAS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPS(0.003)S(0.124)AS(0.873)R 207.34 1.40E-07 5667190000 5567250 5317470 4883460 5669940 4510660 5131950 5381570 5099900 4608840 TRUE FALSE 5304097.126 5859326.238 5107371.471 5099986.859 5297317.676 4954229.285 4560512.657 4653325.72 5323555.369 0.996344878 1.100641551 0.959391068 0.95800391 0.995071397 0.930624168 0.856666709 0.874101122 1 22.34395865 2.890080858 0.910932748 0.899522993 1.04336335 0.382375112 0.054163156 0.445633 0.806782337 0.028990669 0.031783705 776.391654 -2.890080858 0.143840358 LDYVPSSAS(ph)REVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LDYVPSSASREVR 13 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPSS(0.059)AS(0.941)REVR;LDYVPS(0.304)S(0.086)AS(0.61)REVR;LDYVPS(0.096)S(0.046)AS(0.858)REVR 173.51 1.31E-05 934620000 893850 377900 1039010 662480 1177850 834480 1389740 911300 1621780 TRUE FALSE 851599.4819 416408.4396 1086649.636 595886.2518 1383266.667 805581.7484 1177709.639 831501.7409 1873277.359 0.454604054 0.222288727 0.580079416 0.318098251 0.73842064 0.430038694 0.62868941 0.443875402 1 20.83713309 -5 0.131123873 2.818745184 0.242016828 0.579472442 0.143226965 88.77324602 0.732009557 42.25472757 0.935370288 1.00E-05 5 -2.576728356 LDYWEDDLR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 133.57 0.00063549 158113000 567830 511893 502226 617810 534820 507925 607260 580380 556850 FALSE TRUE 540989.8012 564055.4787 525253.5589 555706.565 628092.4387 490335.4299 514611.3339 529558.8504 643203.454 0.841086592 0.876947217 0.816621173 0.86396701 0.976506632 0.762333328 0.800075514 0.823314687 1 19.29491563 LDYWEDDLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 108.7 0.0033944 153588000 214623 173709 192847 197212 204994 197636 235674 235272 437100 FALSE TRUE 204478.1961 191410.1446 201689.2257 177387.8751 240744.8887 190791.8158 199717.6029 214670.3364 504883.2356 0.405000962 0.379117648 0.399476971 0.351344356 0.476832804 0.377892951 0.395571864 0.425188086 1 18.94559025 0.475203777 2.456730211 0.999999161 0.396662438 0.971892716 0.032028586 1.315792507 5.971401273 0.027464097 0.007339749 2.986783733 -0.475203777 -0.603336723 LEAAEER ddPTM_SK-BR-3_Trastuzumab_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 ; 94.407 0.033089 192987000 502980 413160 400820 477120 492450 395400 495290 474930 508430 FALSE TRUE 479205.1322 455261.4737 419197.9935 429158.9911 578333.1241 381707.1989 419724.4139 433342.6114 587274.7277 0.815981192 0.775210395 0.713802201 0.730763595 0.984774411 0.649963605 0.71469858 0.737887382 1 19.16367603 -0.934130476 4.782234016 1.000001883 0.76438527 0.406911077 0.089008728 0.005187417 54102447.35 250.1748181 0.019867353 0.116377634 0.934130476 -0.235616614 LEAEIATYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEAEIATYR 9 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 190.73 8.54E-05 2241060000 2361410 2306380 1864300 2361910 2008040 2103830 2322010 2336000 2064880 FALSE TRUE 2249790.829 2541402.744 1949779.999 2124486.319 2358241.54 2030973.84 1967744.728 2131447.456 2385091.044 0.943272515 1.065536995 0.817486613 0.890735943 0.988742776 0.851528852 0.825018706 0.893654547 1 21.18561291 3.740547551 24.99993182 0.885416195 1.004404755 0.30416229 0.067319263 172.3763507 2168857.791 0.016866042 0.028595653 5502.341629 -3.740547551 0.118988559 LEAEIATYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LEAEIATYRR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 256.38 5.83E-17 4973450000 2953587 1601696 2865811 2062074 3879475 2507969 4397972 3112013 4812733 FALSE TRUE 2813976.796 1764910.643 2997211.269 1854790.404 4556054.212 2421117.405 3726980.597 2839508.644 5559067.054 0.506195872 0.317483244 0.539157243 0.333651382 0.819571732 0.43552585 0.670432747 0.510788702 1 22.40641135 -5 0.134975956 2.722623751 0.310505342 0.557011643 0.140929338 91.52996579 0.768313865 42.2225374 0.840212123 1.00E-05 5 -2.41211841 LEAFHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEAFHER 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 ; 107.29 0.0075096 118868000 135862 115226 106700 111034 156466 113894 165411 130610 148576 FALSE TRUE 129440.0725 126967.6604 111592.3005 99872.65137 183753.6209 109949.8222 140174.514 119173.096 171616.4073 0.754240661 0.739834043 0.65024261 0.581952815 1.070722921 0.640671973 0.816789701 0.694415516 1 17.38882796 LEAGDKKPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEAGDKKPDAK 11 2 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 64.65 0.03802 645330000 1940150 1788250 1593800 1963710 938200 1726100 1780300 2254480 992880 FALSE TRUE 1848442.955 1970474.708 1666877.306 1766314.14 1101821.783 1666324.724 1508682.538 2057065.779 1146850.759 1.611755444 1.718161401 1.453438726 1.540142974 0.960736847 1.4529569 1.315500317 1.793664749 1 20.12924623 3.373145493 1.9948407 1.338425913 1.660227127 0.234801833 0.240392262 0.425158521 3.445415545 0.067695197 0.102960569 2361.269148 -3.373145493 0.321801215 LEALQKQMDS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;LEALQKQMDS(1)R 69.979 0.026587 447330000 678300 585460 566910 641480 482120 588550 661390 623720 43280 TRUE FALSE 646238.1033 645119.0396 592903.3843 576997.2117 566201.5754 568168.3659 560482.8082 569103.7703 49991.64136 12.9269231 12.90453808 11.86005036 11.54187372 11.32592489 11.36526728 11.21153043 11.3839785 1 15.60939927 -0.378039155 0.557863649 2.57E-16 12.32120206 0.973885609 0.558395528 1.329102431 0.370426357 4.290126932 0.269325564 0.418755809 0.378039155 12.32120206 LEALSVKEETKEDAEEKQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEALSVKEETKEDAEEKQ 18 3 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 62.203 0.065301 59835000 128550 114340 123880 153110 66022 169030 154280 182940 75983 FALSE TRUE 122473.6963 125991.376 129560.0205 137719.0919 77536.2159 163176.4487 130741.7525 166920.8038 87766.05557 1.395456312 1.435536497 1.476197371 1.569161232 0.883441957 1.859220489 1.489661938 1.901883395 1 16.42137545 LEAPDADELPKGEFDPGQDTYQHPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEAPDADELPKGEFDPGQDTYQHPPK 26 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 199.94 3.33E-25 348320000 523314 448880 431243 451662 285689 419349 444486 481565 236161 FALSE TRUE 498577.9843 494621.3823 451015.9181 406260.0777 335513.0711 404826.839 376671.4972 439396.6157 272783.6417 1.827741507 1.813236964 1.653383301 1.489312464 1.229960378 1.484058342 1.380843421 1.610787996 1 18.05739761 8 0.098408482 0.783835447 4.000362091 0.690422625 0.141101132 69.46526467 0.485400328 1.847258909 30.16726123 99999999.96 -8 3.216526644 LEAPLEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEAPLEELR 9 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 135 0.00054241 107254000 219196 187680 195257 216498 220007 185991 243101 222547 251130 FALSE TRUE 208835.0395 206804.8054 204209.7266 194735.2097 258376.1511 179550.085 206011.4776 203059.6049 290073.9578 0.719937222 0.7129382 0.703991934 0.671329516 0.890725086 0.618980368 0.710203285 0.700027008 1 18.14606125 -2.292920986 2.134779729 2.203627496 0.714808663 0.628275666 0.068642876 2871464.103 416615.0097 16654041.59 0.015135675 0.005094235 2.292920986 -1.488818833 LEAQHQALVTLWHQLHVDMK ddPTM_SK-BR-3_Trastuzumab_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 ; 240.85 3.54E-30 83414000 192573 240060 180315 225130 147374 208290 208760 219250 49369 FALSE TRUE 183470.4559 264522.3869 188582.6211 202499.5047 173075.9789 201076.8651 176909.8279 200051.3077 57024.89238 3.217374874 4.638717863 3.307022832 3.551072106 3.035095232 3.526124411 3.102326379 3.50814003 1 15.7993042 -0.813770036 0.33357939 5.05E-14 3.807693788 0.755362396 0.444907587 5.609712942 0.544201805 6.509142723 0.388979485 0.153542979 0.813770036 3.807693788 LEAS(ph)YSDSPPGEEDLLVHVAEGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEAS(1)YSDSPPGEEDLLVHVAEGSK;LEAS(0.992)YS(0.008)DSPPGEEDLLVHVAEGSK 226.07 3.55E-33 43445000 113394 93722 92079 126577 95619 123648 133329 118329 86217 TRUE FALSE 108034.0903 103272.3784 96300.91323 113853.2395 112294.9233 119366.0388 112987.2123 107967.4855 99587.09202 1.084820213 1.037005663 0.967001961 1.143252978 1.127605205 1.198609542 1.134556798 1.084151402 1 16.60367114 3.212159893 24.99939205 1.128474539 1.039081459 0.297016848 0.058629847 227.0000081 214950.4385 0.015826944 0.018922204 1629.895996 -3.212159893 -0.08939308 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEAS(0.044)Y(0.003)S(0.257)DS(0.695)PPGEEDLLVHVAEGSK;LEAS(0.002)YS(0.143)DS(0.855)PPGEEDLLVHVAEGSK;LEASYS(0.006)DS(0.994)PPGEEDLLVHVAEGSK;LEASYS(0.003)DS(0.997)PPGEEDLLVHVAEGSK;LEAS(0.003)YS(0.152)DS(0.845)PPGEEDLLVHVAEGSK 201.16 9.35E-25 258811000 426235 368636 343097 415402 312717 393325 433646 412933 279317 TRUE FALSE 406087.7163 406200.4275 358828.3368 373645.0017 367254.7458 379704.0566 367485.3382 376774.3974 322632.0538 1.25867133 1.259020679 1.112190598 1.15811494 1.138308303 1.176895018 1.139023026 1.167814521 1 18.29953025 8 0.021689612 1.45E-15 2.702369261 0.70030944 0.040223388 1402.881371 2.344080029 105.5294723 200.5642793 100000000 -8 2.702369261 LEAVSHTSDMHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 197.43 1.36E-07 2137340000 2219940 1608610 1789700 2091470 3001990 1751160 3029650 2215880 912792 FALSE TRUE 2115007.836 1772529.188 1871759.515 1881231.462 3525536.106 1690516.89 2567421.249 2021845.8 1054343.121 2.005995764 1.681169206 1.775284988 1.78426873 3.343822361 1.603383999 2.435090813 1.917635501 1 20.00791302 LECVEPNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LECVEPNCR 9 0 H0Y5B4;H7BZ11;J3KQN4;P83881;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;;; 176.6 0.00012337 1673430000 1704080 1371910 1466170 1714530 1579460 1539360 1855930 1676860 1790500 FALSE TRUE 1623531.516 1511709.189 1533395.345 1542182.187 1854917.324 1486051.577 1572773.792 1530025.249 2068161.595 0.785011925 0.730943458 0.741429175 0.745677799 0.896891872 0.718537459 0.760469489 0.739799662 1 20.97991748 -1.074065268 3.989043811 1.000043631 0.763392097 0.683855541 0.050239173 20839468.96 24903939.85 11608.40241 0.011281448 0.084320803 1.074065268 -0.236651534 LEDAGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEDAGVR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 117.93 0.030326 0 106540 108740 98273 123020 127690 101900 113950 109150 118950 FALSE TRUE 101504.0653 119820.7296 102778.9143 110653.7959 149959.0956 98371.17745 96564.83466 99592.24736 137396.1585 0.738769311 0.872082094 0.748047947 0.805363098 1.091435869 0.715967452 0.702820484 0.724854672 1 17.06798214 -0.642145795 7.185651573 1.000013948 0.799101583 0.230520033 0.114874371 0 0 0.109216845 0.025742657 0.227957668 0.642145795 -0.200912365 LEDEHLVFFCQMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEDEHLVFFCQMGK 14 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;;; 221.86 4.11E-12 1510140000 3213060 2723800 2567460 3133760 2209930 2759470 3146380 3089130 2107200 FALSE TRUE 3061185.021 3001358.317 2685180.581 2818748.491 2595341.092 2663908.862 2666341.944 2818629.401 2433973.814 1.257690204 1.233110356 1.103208492 1.15808497 1.06629787 1.09446899 1.095468624 1.158036042 1 21.21488222 8 0.214636353 1.038168652 2.312633522 0.676017224 0.043531093 25.41837144 0.320612384 0.066100975 11.14229913 100000000 -8 1.27446487 LEDFFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LEDFFAR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 208.74 0.00038576 943617000 2703722 2265011 2228669 2710791 2671272 2160371 2954637 2643540 2829858 FALSE TRUE 2575922.419 2495818.196 2330855.678 2438297.139 3137140.991 2085556.811 2503852.86 2412057.623 3268697.926 0.788057654 0.763551192 0.713083843 0.745953647 0.959752495 0.638039017 0.766009254 0.737926134 1 21.64028463 -1.032025583 4.438757836 1.00001133 0.76374334 0.458834865 0.080530815 8.61E-06 1.88E-06 0.070574577 0.016633748 0.092891167 1.032025583 -0.23626799 LEDFRDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 105.78 0.003941 3667280000 8932210 4698758 4968228 7151900 10132080 5580799 11107330 7448530 12064790 FALSE TRUE 8510002.135 5177566.782 5196026.168 6432977.424 11899111.54 5387534.531 9412702.808 6796297.226 13935736.01 0.6106604 0.371531635 0.372856243 0.461617342 0.853855981 0.386598492 0.67543636 0.487688431 1 23.73228586 -5 0.204974651 3.243903129 0.45115649 0.493313333 0.151511988 115.3992628 1.146169857 105.9790837 0.316601403 1.00E-05 5 -2.792746639 LEDFRDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 54.982 0.07395 1129360000 1524420 1050750 1187160 1420930 1747270 1265770 2107870 1565640 2796590 FALSE TRUE 1452363.688 1157822.62 1241592.46 1278095.417 2051993.335 1221936.068 1786275.718 1428544.262 3230270.894 0.449610493 0.358428955 0.384361715 0.395661992 0.635238778 0.378276655 0.552980161 0.442236676 1 21.62322373 -5 0.234352083 4.078155491 0.386242514 0.817477777 0.082430998 61.2936267 0.612402361 89.55297319 0.123188884 1.00E-05 5 -3.691912976 LEDLCELQLLYQGMQEEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEDLCELQLLYQGMQEEQK 19 0 H0Y876;H7C4R2;Q96JN2-2;Q96JN2;Q96JN2-4 H0Y876 CCDC136 Coiled-coil domain-containing protein 136 0 ;;; 86.488 0.0016588 1603095000 2010988 1245878 1879120 1567997 1992894 1339956 2327783 1752814 2560170 FALSE TRUE 1915932.583 1372834.385 1965279.511 1410378.963 2340454.083 1293552.988 1972636.951 1599328.314 2957188.088 0.647889997 0.464236411 0.664577109 0.476932451 0.791445797 0.437426687 0.667065094 0.540827389 1 21.49579458 -1.927712467 2.345764153 1.281644534 0.583790275 0.581012273 0.110388524 6484078.243 2977701.868 10003927.19 0.024057139 0.011811023 1.927712467 -0.697854258 LEDLDTCMMT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 LEDLDTCMMTPK 12 0 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDT(0.015)CMMT(0.985)PK;LEDLDT(0.255)CMMT(0.745)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDT(0.119)CMMT(0.881)PK;LEDLDT(0.21)CMMT(0.79)PK;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK 255.15 4.41E-20 1715201000 4632919 4791010 3930385 5188690 2543297 4551806 4509490 5392530 2798233 TRUE FALSE 4413930.1 5279219.366 4110597.04 4667113.023 2986847.192 4394175.817 3821484.478 4920331.486 3232168.682 1.365624921 1.633336588 1.271776768 1.443957133 0.924100035 1.359513147 1.182328292 1.522300341 1 21.62407106 3.326147448 1.956453407 1.226483997 1.490054097 0.223477428 0.193741783 0.413893896 3.244296202 0.054369831 0.080199771 2119.080465 -3.326147448 0.2635701 LEDLFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEDLFQR 7 0 Q7L5L3-1;Q7L5L3 Q7L5L3-1 GDPD3 Glycerophosphodiester phosphodiesterase domain-containing protein 3 0 ;; 138.24 0.0065249 110593000 449808 238708 303148 527048 566858 353477 544923 392517 535873 FALSE TRUE 428546.4673 263032.6166 317047.6357 474068.1337 665717.8557 341236.0029 461784.9882 358146.1306 618973.448 0.692350324 0.424949757 0.512215244 0.765894135 1.075519245 0.551293442 0.746049753 0.578613076 1 19.239518 3.23390244 24.55885743 0.769076984 0.539149691 0.302136446 0.172792871 114.0470977 601280.1749 0.047054719 0.058046179 1713.572328 -3.23390244 -0.229927293 LEDLITVITQTESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEDLITVITQTESHR 15 0 A0A2R8YE46;A0A2R8Y6X9;Q9HBG4 A0A2R8YE46 ATP6V0A4 V-type proton ATPase 116 kDa subunit a isoform 4 0 167.32 1.32E-06 22169000 73256 61206 57485 83360 79740 66927 84327 77584 75605 FALSE TRUE 69793.33406 67442.96099 60120.74411 74980.49443 93646.63075 64609.30121 71461.36738 70790.33366 87329.43726 0.799195967 0.772282098 0.688436179 0.858593583 1.072337504 0.739834164 0.818296437 0.810612502 1 16.41418042 -5 0.158364844 1.654880655 0.765410306 0.246610614 0.100441191 199.3078649 1.823384063 41.36194273 0.433290336 1.00E-05 5 -0.889470349 LEDLLQDAQDEKEQLNEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEDLLQDAQDEKEQLNEYK 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 ;;;; 327.85 3.19E-75 361498000 676682 679943 552188 742036 324462 705897 664038 776681 342013 FALSE TRUE 644696.5829 749229.9647 577506.366 667445.1315 381048.0701 681451.6099 562726.8072 708670.6942 395050.6293 1.631934074 1.896541631 1.461854059 1.689517956 0.964555026 1.72497285 1.42444225 1.793873093 1 18.59167803 -3.134223784 0.130414562 3.87E-17 1.84781279 0.289969698 0.26506192 96.64823674 1.288402323 30.66290465 2.08114723 0.000734135 3.134223784 1.84781279 LEDLLR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 141.55 0.027076 268588000 721559 792233 468922 724356 572353 535654 657544 650553 518177 FALSE TRUE 687452.3361 872962.4434 490422.5375 651542.3587 672171.182 517104.1677 557223.5862 593587.1305 598533.2427 1.148561662 1.458502855 0.819373934 1.088565032 1.123030659 0.863952293 0.930981851 0.991736278 1 19.19107185 3.738378674 24.99999974 0.972611496 1.30353226 0.580219247 0.116543013 9.908294886 1361509.062 0.029461929 0.049060052 5474.9313 -3.738378674 0.330920764 LEDLVCDVVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEDLVCDVVDR 11 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 143.5 8.64E-05 32791000 85731 149335 71821 106999 68120 89939 73888 88714 60833 FALSE TRUE 81678.66553 164552.4063 75114.06389 96243.25724 80000.10643 86824.38988 62615.02855 80945.73186 70266.67095 1.16240978 2.341827271 1.068985664 1.369685741 1.138521369 1.235641147 0.891105665 1.151979036 1 16.10055293 3.694459772 24.87323063 1.121430184 1.752119011 0.422939969 0.305860988 332.4629618 187511.6844 0.077512396 0.120082347 4948.342734 -3.694459772 0.630688827 LEDNDS(ph)AAS(ph)DPDAETTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEDNDSAASDPDAETTAR 18 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8;F8WF85;C9J6R3;C9J9X8;C9JCX6;C9JXA0 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 2 LEDNDS(1)AAS(1)DPDAETTAR;LEDNDS(1)AAS(1)DPDAETTAR 289.86 5.61E-49 439750000 1090940 791700 849970 935740 882270 925890 1088760 922140 948550 TRUE FALSE 1039373.428 872375.1301 888941.9652 841677.6374 1036137.609 893826.1971 922649.6656 841392.533 1095646.289 0.948639573 0.796219673 0.811340278 0.768201969 0.94568623 0.815798133 0.842105408 0.767941754 1 20.06335069 -1.139299345 4.473353683 1.000022473 0.839664623 0.391432683 0.063798729 8518452.737 2169528.657 1888.866313 0.013982062 0.072560565 1.139299345 -0.160357851 LEDNDSAAS(ph)DPDAETTAR ddPTM_SK-BR-3_Trastuzumab_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(0.006)AAS(0.994)DPDAETTAR;LEDNDSAAS(1)DPDAETTAR 329.19 7.93E-75 619240000 1114730 807980 899710 1040560 995550 924120 1156790 983830 1027280 TRUE FALSE 1062038.922 890314.0806 940962.5934 935960.9319 1169173.605 892117.4927 980300.4396 897680.6296 1186585.336 0.895037963 0.750316099 0.793000356 0.788785184 0.985326187 0.751835933 0.826152498 0.756524291 1 20.17838443 -1.132185398 4.997060905 1.000008393 0.817839073 0.378149221 0.073194622 6.25E-06 1.08E-06 0.064691724 0.015247283 0.073758929 1.132185398 -0.18216932 LEDTAGDTGHSSLEAPRS(ph)PDTLAPVASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEDTAGDTGHSSLEAPRSPDTLAPVASER 29 1 O43310;O43310-2 O43310 CTIF CBP80/20-dependent translation initiation factor 1 LEDTAGDTGHS(0.001)S(0.015)LEAPRS(0.984)PDTLAPVASER;LEDTAGDTGHS(0.001)S(0.034)LEAPRS(0.965)PDTLAPVASER 104.29 0.00032666 58767000 56518 58164 56879 63030 76471 51268 66989 55295 77299 TRUE FALSE 53846.50615 64090.97773 59486.95841 56694.10465 89807.51819 49492.5763 56768.59771 50453.07666 89286.13413 0.603078033 0.717815575 0.666250801 0.634970986 1.005839474 0.554314248 0.635805305 0.565071802 1 16.44614853 -2.064622969 2.627835144 1.483096943 0.673252426 0.393989956 0.127493173 31584129.34 18291381.26 91019830.65 0.030441325 0.008617415 2.064622969 -0.809844516 LEDTENWLYEDGEDQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEDTENWLYEDGEDQPK 17 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 195.1 8.57E-11 26309000 58648 50512 50231 58035 44627 54740 59088 67635 67412 FALSE TRUE 55875.82527 55659.23023 52534.14104 52201.21154 52409.93467 52844.34007 50073.04037 61712.52084 77865.90867 0.717590358 0.714808716 0.674674475 0.670398798 0.673079343 0.678658234 0.643067566 0.792548651 1 16.2487042 0.931387864 3.980796383 0.999817298 0.684938255 0.954826299 0.02209252 0.069820401 2.855996745 0.025531568 0.006532217 8.538623494 -0.931387864 -0.314879044 LEDTHFVQCPSVPSHK ddPTM_SK-BR-3_Trastuzumab_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 ; 224.86 4.29E-15 416870000 931240 746420 818830 929170 767860 884920 1016000 1008460 585910 FALSE TRUE 887222.1307 822481.0466 856374.1654 835768.0663 901774.5409 854274.9985 860990.5399 920153.8962 676769.9304 1.310965649 1.215303768 1.265384479 1.234936762 1.332468392 1.262282735 1.272205666 1.359625856 1 19.36830594 -1.420186487 6.595196984 0.999958615 1.275946956 0.804285701 0.04358242 2.46E-05 2.16E-06 0.039074156 0.00920849 0.038002618 1.420186487 0.275988341 LEDTIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEDTIRR 7 1 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786;A0A1B0GTM0;A0A1B0GUD9 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 110.81 0.027378 0 95575 65277 86333 73170 97298 71629 90584 89114 105120 FALSE TRUE 91057.35916 71928.80051 90291.45344 65814.81259 114266.7404 69148.46977 76763.74711 81310.70574 121421.4727 0.749927975 0.592389459 0.743620147 0.542036026 0.94107523 0.569491279 0.632208994 0.669656725 1 16.88966405 -1.19090992 3.622027281 1.000381166 0.673881462 0.43308123 0.114850137 32200162.19 48960139.86 137540.9393 0.024426235 0.064430289 1.19090992 -0.326499704 LEDVKNS(ph)PTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEDVKNSPTFK 11 1 H0YC42;P55327-2;P55327-3 H0YC42;P55327-2 1 LEDVKNS(0.951)PT(0.049)FK;LEDVKNS(0.923)PT(0.077)FK;LEDVKNS(0.894)PT(0.106)FK 162.37 1.53E-05 3216550000 7356800 6564600 6722400 7989900 3563650 7221700 6984600 7151800 3192340 TRUE FALSE 7009058.644 7233540.203 7030628.689 7186740.072 4185149.432 6971610.718 5918970.989 6525550.478 3687391.783 1.900817449 1.961695591 1.906667125 1.949003658 1.134989087 1.890661782 1.605191783 1.769692743 1 21.81416928 -1.987209368 0.153703862 7.18E-14 2.105177558 0.537932432 0.234305927 31.71315596 0.70907479 13.08224577 1.254672751 0.010298895 1.987209368 2.105177558 LEDVSKPPAYAYPATPSSHPT(ph)SPPPAS(ph)PPPTPGITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEDVSKPPAYAYPATPSSHPTSPPPASPPPTPGITR 36 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 2 LEDVSKPPAYAYPATPS(0.001)S(0.001)HPT(0.531)S(0.466)PPPAS(1)PPPTPGITR 179.54 1.04E-21 105440000 114190 91569 107150 116410 89455 106080 135870 118040 93403 TRUE FALSE 108792.465 100899.9852 112062.9335 104708.2456 105055.9237 102406.423 115140.5361 107703.7918 107887.4602 1.008388415 0.935233669 1.038702119 0.970532122 0.973754721 0.949196717 1.067228164 0.998297593 1 16.71916766 1.746541121 25 1.027202557 0.978187906 0.251102006 0.034181521 2.04855315 6434.194864 0.014460787 0.0080191 55.78804218 -1.746541121 -0.04901465 LEEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 108.24 0.07115 262890000 932460 883110 776650 1116580 647740 890930 936300 968640 707440 FALSE TRUE 888384.4638 973099.913 812260.1707 1004339.257 760705.6509 860076.8707 793450.2387 883820.7465 817146.1821 1.087179361 1.190851691 0.99402064 1.229081502 0.930929701 1.052537342 0.971001586 1.081594415 1 19.64023466 2.729879235 24.99941443 1.006361065 1.124685225 0.389594863 0.073431353 602.0482337 1733690.133 0.020786359 0.019883741 536.8824842 -2.729879235 0.11832416 LEEAEKAADESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LEEAEKAADESER 13 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 ;;;;;;; 194.55 8.45E-07 5375520000 8314210 3613960 9358530 6459410 7688250 8797700 13775980 10327270 10166400 FALSE TRUE 7921213.77 3982226.633 9787627.857 5810097.835 9029078.366 8493033.443 11674201.24 9422959.49 11742953.39 0.674550388 0.339116277 0.833489458 0.494773133 0.768893316 0.723245095 0.994145242 0.802435229 1 23.48529196 2.271371457 0.798757931 0.966002313 0.538989055 0.50197805 0.143276748 0.447585186 0.54859141 0.104083681 0.064112615 186.7976707 -2.271371457 -0.427013258 LEEAGGS(ph)PHPPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEEAGGSPHPPGGR 14 0 E9PPP7 E9PPP7 MROH6 1 LEEAGGS(1)PHPPGGR 90.614 0.0059608 107290000 234950 197640 209490 244570 231380 235090 271170 236690 264750 TRUE FALSE 223844.3791 217779.7407 219095.3237 219985.3589 271732.5987 226948.7744 229798.0361 215964.1688 305806.0778 0.731981459 0.712149812 0.716451829 0.719362285 0.888578149 0.742132975 0.751450193 0.706212808 1 18.22225755 -1.749792366 2.872438404 1.048722511 0.745044113 0.697251874 0.052587647 18260764.62 16080546.41 6333271.202 0.012400003 0.017791298 1.749792366 -0.303678398 LEECVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEECVR 6 0 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;;;; 150.07 0.024564 1283966000 1375830 1405587 1214510 1595650 1256144 1267378 1363301 1399908 1234530 FALSE TRUE 1310797.243 1548817.913 1270196.485 1435252.23 1475215.116 1223488.382 1155304.394 1277324.634 1425974.607 0.919229021 1.08614691 0.890756735 1.006506163 1.034531126 0.858001521 0.810185811 0.895755526 1 20.44351686 2.228812287 24.98654697 0.86759239 0.991166888 0.276805785 0.073110768 190.8495701 489174.8001 0.025216768 0.018854181 169.3605625 -2.228812287 0.123574499 LEEEDEDEEDGESGCTFLVGLIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LEEEDEDEEDGESGCTFLVGLIQK 24 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;; 166.25 1.32E-11 129416900 259659 217462 236847 275017 192227 254084 300413 284211 232820 FALSE TRUE 247385.4337 239621.625 247706.6692 247371.7687 225751.3279 245285.0074 254579.4794 259323.9781 268924.5365 0.919906517 0.891036676 0.921101036 0.919855703 0.839459764 0.912096049 0.946657686 0.964300177 1 18.03684187 1.419902723 1.68021189 0.991461129 0.900044589 0.667915518 0.024547522 0.208786566 1.091865944 0.021376074 0.00675899 26.29678909 -1.419902723 -0.09141654 LEEEPSASS(ph)PQYACDFNLFLEDSADNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPS(0.033)AS(0.022)S(0.941)PQY(0.003)ACDFNLFLEDSADNR 168.65 4.46E-12 14572000 45435 49079 34053 49847 34520 42629 34922 41235 29842 TRUE FALSE 43287.37759 54080.2059 35614.36373 44836.28486 40540.27707 41152.74704 29594.00751 37624.2448 34469.74495 1.255807888 1.568918075 1.033206477 1.300743157 1.176111896 1.19388023 0.858550232 1.091515033 1 15.073043 2.624817297 0.694245945 0.963809813 1.386587979 0.42464078 0.146272946 0.559548746 0.565947109 0.106460169 0.095711698 421.5191373 -2.624817297 0.422778167 LEEHQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEEHQAR 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 ; 79.597 0.032193 185401000 232340 197653 204689 240670 240610 229611 267850 236810 247860 FALSE TRUE 221357.7487 217794.0654 214074.1931 216477.3944 282572.3078 221659.5135 226984.5631 216073.661 286296.8629 0.7731756 0.760728089 0.747735029 0.756129118 0.986990584 0.774229627 0.792829376 0.754718926 1 18.12715234 -5 0.292561009 2.632814507 0.779773958 0.451917395 0.070779202 234.6477491 2.199833052 234.413107 0.071685862 1.00E-05 5 -1.85304055 LEELDADKAEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEELDADKAEMR 12 1 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 72.496 0.043799 287330000 223800 195180 218490 237420 150430 231630 266910 254960 189880 FALSE TRUE 213221.4175 215069.0639 228507.9826 213554.0905 176664.9444 223608.595 226187.9774 232634.3508 219325.6206 0.972168308 0.980592524 1.041866344 0.973685108 0.805491597 1.019527926 1.031288441 1.060680235 1 17.74271483 2.027116921 24.99998412 1.031951783 0.960337382 0.262413083 0.060735559 309.5755014 285406.3007 0.022697979 0.016763184 106.4429545 -2.027116921 -0.071614401 LEELHVIDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEELHVIDVK 10 0 Q16531;F5GY55;F5H2L3;F5GWI0 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 136.96 0.00010389 670735000 3189530 3157820 2954290 3540660 2197140 3306120 3269050 3541860 1911360 FALSE TRUE 3038767.238 3479605.448 3089747.119 3184746.13 2580320.52 3191628.235 2770296.382 3231715.962 2207763.947 1.376400426 1.57607676 1.399491609 1.442521124 1.168748373 1.445638353 1.254797365 1.463795967 1 21.0741545 -3.942865943 0.155630368 2.63E-11 1.522155155 0.541444003 0.112697 63.93364674 0.786246504 20.7102692 0.493156954 0.00011406 3.942865943 1.522155155 LEELKDGAEWSRDS(ph)MEINEADFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEELKDGAEWSRDSMEINEADFR 23 2 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 LEELKDGAEWSRDS(1)MEINEADFR;LEELKDGAEWS(0.006)RDS(0.994)MEINEADFR 199.04 1.40E-24 270590000 281662 243350 231821 298489 200850 256580 300892 319173 207559 TRUE FALSE 268348.3955 268147.6417 242450.2222 268484.3186 235878.1764 247694.5703 254985.3991 291224.5201 239746.1897 1.119302025 1.118464665 1.01127873 1.119868971 0.983866216 1.033153314 1.063563928 1.214720119 1 17.87114836 3.825134893 13.57210918 1.06122271 1.118932375 0.115487365 0.066684294 2.827793283 439.2014189 0.015880259 0.028632805 6685.515396 -3.825134893 0.057709666 LEELKESILADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEELKESILADK 12 1 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 106.13 0.0017832 52935000 165340 149140 117970 155680 122430 141310 179290 153860 93725 FALSE TRUE 157524.7059 164337.5356 123379.0412 140030.7506 143781.7532 136416.3993 151936.0176 140387.2027 108259.3943 1.455067312 1.517997921 1.139661292 1.293474359 1.328122646 1.260088329 1.403444187 1.296766933 1 16.7241327 -4.817494906 0.110064501 9.79E-19 1.548184906 0.518394499 0.103558589 134.3422643 1.023482774 31.29448665 1.364968318 1.52E-05 4.817494906 1.548184906 LEELTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEELTNR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 124.59 0.0096111 452410000 659090 649970 688530 701780 646930 792600 872900 856520 689100 FALSE TRUE 627936.1219 716202.682 720099.7815 631235.7411 759754.3872 765152.0633 739723.0731 781518.5681 795962.1086 0.788902028 0.899794945 0.904691032 0.793047476 0.954510747 0.96129207 0.929344582 0.981853985 1 19.60234023 7.999994243 0.139499539 1.038025721 0.216035533 0.633736987 0.043577522 46.53786978 0.432836409 0.179605483 7.628622298 99998674.46 -7.999994243 -0.821990188 LEEPPELNRQS(ph)PNPR ddPTM_SK-BR-3_Trastuzumab_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 216.3 1.35E-12 17449400000 8094510 6903390 7297240 7916800 7076770 7007190 8528650 7370400 8410290 TRUE FALSE 7711898.554 7606853.29 7631825.672 7120988.223 8310956.447 6764529.253 7227447.803 6725008.703 9714514.819 0.793853187 0.783039959 0.785610585 0.733025617 0.855519457 0.696332177 0.743984433 0.692263981 1 23.21171051 -1.150862102 4.956630086 1.000014654 0.762953596 0.70687087 0.048454988 7.42E-06 1.27E-06 0.044356777 0.010454346 0.070654186 1.150862102 -0.237061058 LEEQRPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 191.17 0.0001665 4975880000 7952123 6921155 6965801 7904196 7391868 7128448 8404757 7790398 7985659 FALSE TRUE 7576241.905 7626428.563 7285189.866 7109651.201 8681007.439 6881588.058 7122456.956 7108229.452 9224034.213 0.821358825 0.826799683 0.789805165 0.770774591 0.941129146 0.746049711 0.772162894 0.770620456 1 23.13696643 -1.07516041 4.993428584 1.000004691 0.805289134 0.561738477 0.054173619 2.68E-06 4.96E-07 0.049665387 0.011705962 0.084108442 1.07516041 -0.194715557 LEESHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEESHNR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;; 161.68 0.0023936 215598000 656310 562740 542840 613310 590030 581640 733270 589820 638180 FALSE TRUE 625287.527 620083.8458 567729.7509 551658.9136 692931.0452 561497.661 621396.1941 538172.234 737145.695 0.848255007 0.841195777 0.770173054 0.748371614 0.940019117 0.761718701 0.842976088 0.730075801 1 19.49159027 -2.072534368 2.554031327 1.28186854 0.816028747 0.476871901 0.062173061 10340689.42 4904651.909 16916393.16 0.013982516 0.008461856 2.072534368 -0.465839793 LEETDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LEETDRR 7 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQL2;A0A0U1RQJ6;A0A0U1RRJ7 P47897 QARS Glutamine--tRNA ligase 0 ;;;;; 143.11 0.0039189 2017600000 1944160 1643493 1666714 1982492 2063110 1795723 2044196 2096640 2399710 FALSE TRUE 1852263.41 1810966.805 1743134.486 1783208.138 2422915.731 1733536.662 1732316.356 1913047.087 2771844.771 0.668242114 0.653343515 0.628871611 0.643329005 0.874116674 0.625408999 0.624968748 0.690171076 1 21.40241504 0.943046914 20.92404989 1.000000001 0.670246482 0.658923429 0.073295207 1603.480407 589105.9749 0.067844189 0.016961047 8.770955631 -0.943046914 -0.329753519 LEEVMQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEEVMQELR 9 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;; 155.84 0.0001683 106794500 192638 223328 143239 207843 170986 160559 181713 193048 156001 FALSE TRUE 183532.3835 246085.3771 149806.6498 186950.2268 200805.9043 154998.8016 153989.3445 176143.6937 180192.8383 1.018533174 1.3656779 0.831368501 1.037500871 1.114394479 0.860182918 0.854580825 0.977528826 1 17.45918215 3.730115241 24.99852472 0.946357349 1.192105541 0.404402533 0.120055073 519.9583238 1539090.143 0.031521927 0.049720652 5371.743183 -3.730115241 0.245748192 LEEWLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEEWLGR 7 0 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 162.07 0.0029913 97792000 218420 198820 209260 237050 219390 207650 241070 231240 242660 FALSE TRUE 208095.7195 219079.984 218854.778 213221.2836 257651.5465 200459.0284 204290.3439 210991.3997 280290.4735 0.742428799 0.78161766 0.780814186 0.760715414 0.91923048 0.715183167 0.728852256 0.752759796 1 18.09656319 -1.731718152 2.64135219 1.044926133 0.770282814 0.618053818 0.05612654 17212481.13 13211539.76 5070175.981 0.012994166 0.018547349 1.731718152 -0.274643319 LEFLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEFLHK 6 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 90.285 0.049203 363280000 1269400 1273700 986260 1411740 878880 1137150 1164940 1227360 842440 FALSE TRUE 1209397.978 1403491.478 1031480.997 1269829.213 1032156.394 1097770.21 987207.0074 1119885.852 973081.2926 1.242854001 1.442316781 1.060015237 1.304956968 1.060709317 1.128138233 1.01451648 1.150865668 1 19.89220081 3.094476444 0.861703382 1.056290135 1.335082999 0.440352639 0.104364267 0.453628854 0.747575388 0.049624549 0.070158632 1243.015214 -3.094476444 0.278792864 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LEGDSDDLLEDSDSEEHSR 19 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(0.999)DS(0.001)EEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR 335.14 1.30E-75 2921350000 2761770 3016700 2495110 3311130 2121870 2898870 2683760 2969860 1982640 TRUE FALSE 2631226.605 3324105.16 2609513.262 2978288.922 2491923.456 2798481.405 2274303.121 2709803.314 2290097.685 1.14895824 1.451512388 1.139476835 1.300507372 1.088129765 1.221992155 0.993103105 1.183269749 1 21.12697771 2.473975557 0.870260906 1.056765166 1.287900409 0.336004873 0.111141671 0.574798884 0.875122791 0.071091021 0.050656523 297.8348799 -2.473975557 0.231135243 LEGEIRRMHDFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEGEIRRMHDFNR 13 2 Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 Q4VCS5 AMOT Angiomotin 0 62.89 0.041178 117470000 43489 42684 38721 45023 223820 29010 42201 20904 155340 FALSE TRUE 41433.36116 47033.54813 40496.39615 40497.2025 262854.1371 28005.37643 35762.46238 19073.53494 179429.3338 0.230917433 0.262128533 0.225695516 0.22570001 1.464945177 0.156080256 0.19931224 0.106301097 1 17.45305624 LEGELQAPDLELS(ph)LPAIHVEGLDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEGELQAPDLELSLPAIHVEGLDIK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LEGELQAPDLELS(1)LPAIHVEGLDIK;LEGELQAPDLELS(1)LPAIHVEGLDIK 198.7 4.83E-25 81075000 150037 116611 129386 151903 101500 138019 157904 144427 92269 TRUE FALSE 142945.0484 128493.7935 135318.4761 136633.4218 119201.5679 133239.3674 133812.8447 131780.2062 106577.6053 1.341229689 1.20563596 1.269670826 1.282008744 1.118448548 1.250162894 1.255543736 1.236471826 1 16.7015448 -4.347123527 0.246285068 1.43E-14 1.271101427 0.664941627 0.055360854 75.77670047 1.012991751 38.0242442 0.079866627 4.50E-05 4.347123527 1.271101427 LEGENTQDKNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEGENTQDKNK 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 147.33 3.22E-05 566061000 1428680 1353570 1286690 1537420 832010 1576710 1475550 1689690 875840 FALSE TRUE 1361149.128 1491500.322 1345686.009 1382875.621 977112.2806 1522108.137 1250427.747 1541731.786 1011660.794 1.345459996 1.474308712 1.330175111 1.366936061 0.965849706 1.50456373 1.236014833 1.523961188 1 19.94829421 -1.991583239 2.684339332 0.673962279 1.343486047 0.31258898 0.160042396 6010541.987 5476583.836 12141301.18 0.035122735 0.010195693 1.991583239 0.669523767 LEGFHTQISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEGFHTQISK 10 0 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 152.54 1.79E-05 4121020000 9643720 9108850 8156260 10134240 7198230 8804910 9692130 9942200 7280900 FALSE TRUE 9187880.468 10037052.17 8530232.589 9115526.941 8453599.033 8499993.759 8213417.56 9071608.261 8409984.786 1.092496681 1.193468529 1.014298219 1.083893393 1.005186008 1.010702632 0.976626923 1.078671186 1 23.00367176 3.725404498 24.66630911 1.02133983 1.142982604 0.590591265 0.041063373 359.5484406 674114.513 0.010539071 0.016432653 5313.791351 -3.725404498 0.121642775 LEGFYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEGFYGER 8 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 0 78.334 0.07187 39102000 67672 59833 58770 75200 77885 67532 84702 74472 82464 FALSE TRUE 64473.27867 65930.05072 61464.66263 67640.75313 91468.11934 65193.34991 71779.15424 67950.83688 95252.09595 0.676869921 0.692163779 0.645284096 0.710123514 0.960274086 0.684429558 0.753570339 0.713378915 1 16.53946322 -5 0.167155399 2.034228512 0.658916069 0.507885438 0.085211915 109.2792432 1.023711908 37.60303012 0.310175211 1.00E-05 5 -1.375312443 LEGGRQDS(ph)EDEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEGGRQDSEDEEER 14 1 A0A3B3ISZ4;Q9BYE7-3;Q9BYE7 A0A3B3ISZ4 PCGF6 Polycomb group RING finger protein 6 1 LEGGRQDS(1)EDEEER 157 3.28E-06 758000000 407130 396600 391050 439590 376710 414090 481150 401910 397160 TRUE FALSE 387885.7718 437013.9909 408980.0293 395401.578 442408.1047 399749.9595 407741.7306 366716.6297 458749.5444 0.845528408 0.95262 0.891510486 0.861911653 0.964378298 0.871390423 0.888811195 0.799383093 1 18.8073472 LEGLTQDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEGLTQDLR 9 0 Q01094 Q01094 E2F1 Transcription factor E2F1 0 ; 89.298 0.028386 58263000 144076 117158 106332 115636 155411 107786 149221 126174 157050 FALSE TRUE 137265.813 129096.5334 111207.4274 104012.0496 182514.6292 104053.3438 126454.5958 115125.5357 181404.5119 0.756683566 0.711650069 0.61303562 0.573370797 1.006119568 0.573598433 0.697086277 0.634634356 1 17.46885081 -0.897134401 4.160580656 1.000007459 0.698402576 0.368609248 0.125089556 138064392.3 318054668.6 16568.32868 0.02739099 0.126725963 0.897134401 -0.301604883 LEGPVS(ph)PDVEPGKEETEESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEGPVSPDVEPGKEETEESK 20 1 O14686;O14686-3;A0A3B3ISC8 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LEGPVS(1)PDVEPGKEETEESK;LEGPVS(1)PDVEPGKEETEESK 128.07 1.24E-05 343910000 605280 589220 499430 674390 272140 656460 557530 687330 263110 TRUE FALSE 576669.6139 649262.1879 522329.3595 606599.0359 319601.1298 633726.6256 472468.5588 627143.7414 303911.755 1.897490322 2.13635102 1.718687582 1.995970955 1.051624771 2.085232358 1.554624166 2.063571846 1 18.21329295 -2.306564176 0.194680503 3.36E-19 2.012330646 0.356651477 0.330154455 41.93838258 1.069593784 20.4183315 0.859833619 0.00493669 2.306564176 2.012330646 LEGVDGGQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEGVDGGQSPR 11 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 LEGVDGGQS(1)PR;LEGVDGGQS(1)PR;LEGVDGGQS(1)PR;LEGVDGGQS(1)PR;LEGVDGGQS(1)PR 149.09 3.62E-05 1241312000 1561639 1954221 1636800 2002900 1592707 1794071 1889487 1939726 1909615 TRUE FALSE 1487823.419 2153358.342 1711848.899 1801564.687 1870474.597 1731941.871 1601211.055 1769873.308 2205748.341 0.674520929 0.976248424 0.776085316 0.816758944 0.848000001 0.785194684 0.725926447 0.802391313 1 21.07283677 2.222608263 24.70356104 0.7962822 0.824794197 0 0.102798183 1221.154048 1891043.761 0.035791882 0.026525357 166.9583956 -2.222608263 0.028511997 LEGVLAEVAQHYQDTLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 257.81 1.23E-30 415550000 837830 692760 709970 895950 742820 773990 904040 893150 705770 FALSE TRUE 798227.4363 763353.0316 742522.8268 805887.4038 872367.5728 747186.5322 766112.0942 814941.0511 815217.207 0.97915921 0.93637993 0.910828207 0.988555439 1.070104465 0.91654902 0.939764381 0.999661249 1 19.63682498 -4.999999952 0.168324616 1.14140084 0.954364949 0.05313769 0.046574485 457.2964282 4.296034293 21.59529827 0.172574022 1.00E-05 4.999999952 -0.187035891 LEHAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEHAAK 6 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 88.201 0.051572 109000000 609970 552250 497220 625240 410750 577740 646840 654110 505480 FALSE TRUE 581137.9269 608524.9029 520018.0288 562389.6873 482384.67 557732.7189 548152.678 596832.6607 583867.2568 0.995325428 1.042231596 0.890644274 0.963214979 0.82618894 0.955238905 0.938830996 1.022206082 1 19.15528088 3.74849255 24.95397568 0.936858164 1.018778515 0.242173796 0.055568858 769.7978279 1934111.9 0.013285454 0.023592741 5603.928042 -3.74849255 0.08192035 LEHALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEHALEK 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 75.854 0.042341 183700000 434350 348270 339920 393790 403350 402710 490350 400610 402350 FALSE TRUE 413819.1363 383759.109 355505.6682 354205.481 473694.1123 388764.0517 415538.1016 365530.4646 464744.3831 0.890423104 0.825742328 0.764948822 0.762151182 1.019257316 0.836511566 0.894121837 0.786519381 1 18.8260779 2.789864882 24.99992993 0.894406361 0.819601045 0.269123694 0.076789862 578.8511964 282065.6969 0.022256704 0.023606772 616.4031955 -2.789864882 -0.074805316 LEHDVNIQFPDKDDGNQPQDQITITGYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEHDVNIQFPDKDDGNQPQDQITITGYEK 29 1 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 220.55 1.19E-34 221020000 349460 316730 336100 377290 226740 389190 409640 415040 219060 FALSE TRUE 332941.7184 349005.1471 351510.5174 339364.0924 266283.3842 375712.2527 347141.8944 378696.8973 253030.706 1.315815474 1.379299582 1.38920103 1.341197271 1.052375771 1.484848454 1.371935841 1.496644037 1 17.94895295 2.992678734 24.58679983 1.313404903 1.359554785 0.031488623 0.161910835 1584.646281 5321714.411 0.044632396 0.051349957 983.2834601 -2.992678734 0.046149882 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR 29 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;;;;; 301.8 4.11E-81 289748700 182513.6 170732.3 152910.2 200058.4 167305.1 173573.6 189610.1 181706.7 154739.8 FALSE TRUE 173886.5438 188130.1155 159921.2839 179948.1495 196483.0565 167562.7027 160681.5968 165795.4981 178736.0579 0.972867735 1.052558268 0.894734313 1.006781461 1.099291653 0.937486843 0.898988143 0.927599613 1 17.44747118 2.033718502 24.99372111 0.927788537 1.005016898 0.219781264 0.058109892 221.8455685 164441.3712 0.020667873 0.01526417 108.0733222 -2.033718502 0.077228361 LEHEYIQNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEHEYIQNFK 10 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 152.04 1.87E-05 1986350000 6148300 5197500 5190200 6167500 4633900 5631800 6578400 6297400 4525900 FALSE TRUE 5857682.044 5727131.159 5428175.804 5547531.183 5442050.693 5436769.354 5574744.259 5745966.271 5227753.457 1.120496996 1.095524341 1.038338141 1.061169244 1.040992223 1.039981973 1.066374745 1.099127248 1 22.31775967 3.907171064 3.654060798 1.052608561 1.112486604 0.484865236 0.025400644 0.177091615 4.399191696 0.006140243 0.012136423 8075.530545 -3.907171064 0.059878043 LEHGDGGILDLDDILCDVADDKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 106.13 0.0016489 16301700 51337 46314 44844 55197 32719 49227 58466 53063 30030.8 FALSE TRUE 48910.40175 51033.44925 46900.14176 49648.49269 38425.18324 47522.25665 49545.9379 48416.52242 34687.82309 1.410016467 1.47122087 1.352063565 1.431294566 1.107742713 1.369998242 1.428338059 1.395778637 1 15.08214168 -2.211386508 1.992401261 1.67E-05 1.379166661 0.576626644 0.099625082 1187672.564 227880.9698 5338315.708 0.024663202 0.006146296 2.211386508 1.379149982 LEHGQATAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEHGQATAK 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 150.61 8.48E-05 926340000 2078590 1688450 1694080 1982850 1577970 1846440 2213190 2010230 1570790 FALSE TRUE 1980339.17 1860504.975 1771755.244 1783530.151 1853167.468 1782497.32 1875527.217 1834203.604 1814380.091 1.09146875 1.025421842 0.976507212 0.982996981 1.021377758 0.982427733 1.033701388 1.010925778 1 20.79104528 4.330958041 2.147745103 1.003308993 1.089103531 0.698931145 0.018420626 0.185749696 1.554982723 0.00483103 0.022021498 21426.83576 -4.330958041 0.085794539 LEHQGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEHQGIR 7 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 94.262 0.01433 76152000 108940 122240 98054 112230 109300 104910 117730 110580 104700 FALSE TRUE 103790.6221 134696.395 102549.8729 100948.4272 128361.8854 101276.9404 99768.12624 100897.029 120936.3413 0.858225253 1.113779312 0.84796573 0.834723675 1.061400436 0.837440089 0.824963987 0.834298673 1 16.88388831 2.150610918 24.77775047 0.85508689 0.949534597 0.086827751 0.102185479 35.81081592 10080.78496 0.036631382 0.027054075 141.4525947 -2.150610918 0.094447707 LEIFHPFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEIFHPFFK 9 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 102.61 0.0035568 37111000 165090 145010 143010 168700 140190 132220 175570 173660 137350 FALSE TRUE 157286.5229 159786.6839 149567.15 151741.9555 164639.0916 127641.1882 148783.5719 158453.4098 158649.5365 0.99140865 1.007167669 0.942751887 0.956460125 1.037753373 0.804548132 0.937812837 0.998763774 1 17.27548378 LEILSGDHEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEILSGDHEQR 11 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 ;; 192.6 1.32E-06 340666000 547620 394560 491000 517240 733210 457820 572150 468100 475780 FALSE TRUE 521735.0879 434766.1126 513512.8357 465246.0525 861081.5919 441965.5786 484858.0092 427110.6824 549561.5325 0.949366098 0.791114528 0.934404621 0.846576816 1.56685201 0.80421491 0.882263369 0.777184459 1 19.0679215 -2.464813904 2.136283304 1.632186516 0.935772806 0.004730965 0.229165289 10660643.92 1296574.291 32681990.05 0.053081002 0.003429147 2.464813904 -0.696413709 LEKHELIEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 146.16 1.75E-05 931000000 1659630 1599620 1611440 1822410 1215950 1760660 1717670 1777340 1131460 FALSE TRUE 1581182.579 1762623.097 1685326.118 1639217.884 1428011.295 1699687.903 1455607.894 1621706.687 1306921.038 1.209853184 1.348683696 1.289539359 1.254259314 1.092653078 1.300528382 1.113768814 1.240860496 1 20.31774055 -0.323389145 0.215047719 0.86802899 1.315099975 0.507391722 0.075310002 8.157235523 0.563210017 0.93551107 0.189830523 0.474909498 0.323389145 0.447070984 LEKPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEKPAK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 86.086 0.049227 48091010000 25202660 25525740 18872690 29745000 15372970 25783120 23487790 25344650 14092440 FALSE TRUE 24011380.21 28126841.93 19738021.5 26754976.09 18054011.1 24890244.09 19904296.25 23125338.09 16277823.62 1.475097701 1.727923989 1.212571285 1.643645779 1.109117012 1.529089187 1.222786087 1.420665233 1 23.95640449 -1.47442959 0.070881334 8.06E-14 2.131486281 0.371332602 0.185631548 107.1931788 1.258719966 29.55382571 11.18623372 0.033540568 1.47442959 2.131486281 LEKPAKYDDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEKPAKYDDIK 11 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 127.76 0.00015749 10263040000 16391280 13914670 15844560 16805960 8459460 18123370 20410580 19703950 10053610 FALSE TRUE 15616496.68 15332590.69 16571048.75 15116592.97 9934787.146 17495753.15 17296571.15 17978567.68 11612672.49 1.3447806 1.320332654 1.426979772 1.301732481 0.855512558 1.506608678 1.489456554 1.5481852 1 23.46919669 LEKPAKYDDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LEKPAKYDDIKK 12 3 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 101.2 0.0012279 29645935300 24106253 15998402 21266988 21153601 11799932 26038794 29712852 26688525 12976559 FALSE TRUE 22966798.19 17628657.35 22242100.44 19027200.84 13857836.4 25137064.03 25179610.71 24351536.27 14988897.49 1.532254004 1.176114345 1.483905033 1.269419638 0.924540074 1.677045563 1.679884109 1.624638255 1 23.83739093 2.170781773 25 1.570210223 1.295650288 0.120564608 0.25726516 77.99718228 28767.66993 0.088150093 0.065103173 148.1773327 -2.170781773 -0.274559935 LEKPETQSS(ph)PITVQSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEKPETQSSPITVQSSK 17 1 Q96CB8;A0A087WXN4;E9PGI3 Q96CB8 INTS12 Integrator complex subunit 12 1 LEKPET(0.057)QS(0.167)S(0.765)PIT(0.01)VQSSK 55.524 0.089357 0 216440 200120 194990 225830 133770 213890 237680 220450 151350 TRUE FALSE 206209.3101 220512.4555 203930.4844 203129.1394 157099.4456 206482.9357 201417.5507 201146.2293 174820.585 1.179548222 1.261364361 1.166512996 1.161929182 0.898632422 1.181113401 1.152138638 1.150586639 1 17.41551555 7.999999999 0.084029086 0.927610683 1.739078621 0.235797112 0.090278617 250.059271 1.523036336 2.092861079 23.47178764 99999999.88 -7.999999999 0.811467938 LEKVPDS(ph)PENELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEKVPDSPENELK 13 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 LEKVPDS(1)PENELK 138.66 2.82E-05 143110000 328290 301170 294630 381470 164270 365090 384280 441820 195230 TRUE FALSE 312772.3823 331859.5654 308139.0769 343123.9109 192918.636 352446.8418 325651.0282 403131.8986 225505.2713 1.386984794 1.471626643 1.366438466 1.521578227 0.855495017 1.562920635 1.444094971 1.787682817 1 17.78280163 LELAQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LELAQYR 7 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 127.31 0.022596 245180000 1215610 972850 657310 653300 1367300 626420 1046520 866370 1191770 FALSE TRUE 1158150.524 1071984.521 687448.3137 587629.0428 1605756.687 604726.9183 886854.1533 790506.0499 1376583.605 0.841322329 0.778728235 0.499387259 0.426874939 1.166479596 0.439295453 0.644242856 0.574252117 1 20.3926608 -1.448792637 5.850091412 1.000190568 0.680357495 0.178282717 0.221002347 0.000513638 4.84E-05 0.200091196 0.047134159 0.035580116 1.448792637 -0.319833073 LELASLGLGAPTPPS(ph)GLSQGPTSWLRPPPTSPGPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LELASLGLGAPTPPSGLSQGPTSWLRPPPTSPGPQAR 37 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LELASLGLGAPT(0.006)PPS(0.184)GLS(0.184)QGPT(0.184)S(0.184)WLRPPPT(0.115)S(0.145)PGPQAR 85.097 0.000526 114300000 87524 79927 87512 93449 84258 84678 80505 67080 84994 TRUE FALSE 83386.91398 88071.65217 91524.51176 84055.32898 98952.56852 81745.57963 68222.48367 61206.11959 98174.43543 0.849375029 0.897093544 0.932264203 0.856183472 1.007926026 0.832656478 0.694910884 0.623442542 1 16.58305978 1.995812261 24.19179351 0.745110158 0.901982827 0.247177188 0.105051203 122.1669345 705738.1538 0.035827434 0.025803873 99.04037148 -1.995812261 0.15687267 LELASLGLGAPTPPSGLS(ph)QGPTSWLRPPPTSPGPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LELASLGLGAPTPPSGLSQGPTSWLRPPPTSPGPQAR 37 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LELASLGLGAPTPPS(0.044)GLS(0.27)QGPT(0.27)S(0.27)WLRPPPT(0.127)S(0.017)PGPQAR 117.49 2.71E-06 89676000 56828 50670 50606 62555 62626 55867 68163 40738 54498 TRUE FALSE 54141.85306 55833.33061 52926.33516 56266.85255 73547.95457 53932.31178 57763.48245 37170.76475 62949.2715 0.860087047 0.886957534 0.840777564 0.89384438 1.168368637 0.856758315 0.917619554 0.590487608 1 15.94190206 LELKAS(ph)PNVEAPQPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 142.98 8.79E-07 454840000 361330 326620 324960 387600 252870 404270 397920 380660 233920 TRUE FALSE 344250.647 359902.9493 339859.7374 348637.7116 296970.4479 390270.0285 337209.9957 347327.3924 270195.1189 1.274081665 1.332011292 1.257830781 1.290318319 1.099096272 1.444400736 1.24802401 1.285468789 1 18.04364209 -0.031171802 2.101230843 0.999979507 1.282710424 0.517884241 0.084495845 96.17166576 192.3445647 0.07741934 0.01972071 0.930739612 0.031171802 0.282730917 LELLELDHEQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LELLELDHEQTR 12 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 0 ; 151.78 6.54E-05 36683000 62602 69912 66483 83156 66930 62522 71632 72410 69103 FALSE TRUE 59642.92753 77036.11228 69531.31131 74797.00089 78602.57081 60356.84746 60703.22279 66069.39653 79819.14031 0.747225882 0.965133325 0.871110752 0.937081013 0.984758424 0.756170102 0.760509604 0.827738764 1 16.28444712 2.223092142 24.99557037 0.808043903 0.896089641 0.071481608 0.093855268 419.0114078 677077.8659 0.033224398 0.024627182 167.1445197 -2.223092142 0.088045737 LELQGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LELQGPR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 196.94 0.0010086 1031131000 1477380 1261080 1081190 1267260 1610320 1193250 1634090 1373100 1524910 FALSE TRUE 1407547.175 1389585.486 1130763.631 1139872.617 1891159.298 1151927.453 1384779.558 1252864.085 1761385.255 0.79911375 0.78891627 0.641974053 0.647145543 1.073677262 0.653989495 0.786187777 0.71129475 1 20.74827906 LELQGPRGS(ph)PNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LELQGPRGSPNAR 13 1 P19338;H7BY16 P19338 NCL Nucleolin 1 LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR 152.37 2.74E-05 9263160000 3939490 921884 5014900 2480110 7747470 3665080 9335470 4669790 12992470 TRUE FALSE 3753278.115 1015825.028 5244838.125 2230804.631 9098626.315 3538157.361 7911172.594 4260878.431 15007275.89 0.250097229 0.067688835 0.349486353 0.148648206 0.606281005 0.235762798 0.527155804 0.283920844 1 23.83915879 -4.999999999 0.137715754 3.453562556 0.030571404 0.691456739 0.149952464 68.03684552 0.578004396 45.63454907 0.841974355 1.00E-05 4.999999999 -3.422991152 LELQMVETERVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LELQMVETERVR 12 1 Q9HA90-2;Q9HA90 Q9HA90-2 EFCC1 EF-hand and coiled-coil domain-containing protein 1 0 65.395 0.08186 82790000 182930 184990 137240 169150 132290 140210 161650 151880 90704 FALSE TRUE 174283.2614 203840.6913 143532.5897 152146.7206 155361.3341 135354.4925 136987.3236 138580.582 104769.9131 1.663485788 1.945603326 1.369979086 1.452198596 1.482881197 1.291921398 1.307506321 1.322713535 1 16.67686495 3.313404038 0.234363456 0.969329764 2.153013685 0.701972049 0.135885147 2.65516354 0.23848268 0.25742369 0.934941442 2057.804149 -3.313404038 1.183683921 LELTELEAIREDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LELTELEAIREDFLR 15 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 0 61.732 0.077175 0 6868.2 7025.4 8457.2 6859.4 8882.8 7190.6 9784.4 6669.7 4593.6 FALSE TRUE 6543.553797 7741.296247 8844.970985 6169.88008 10431.95751 6941.587719 8291.610077 6085.66571 5305.952027 1.233247825 1.45898346 1.66699038 1.162822439 1.966085908 1.30826432 1.562699782 1.14695076 1 12.37339592 1.091446694 4.388949671 1.004474488 1.468854372 0.359357613 0.229078206 0.201382067 6.47494506 0.195802646 0.050032524 12.34373798 -1.091446694 0.464379884 LELVHHGPMAVAFEVYDDFLHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LELVHHGPMAVAFEVYDDFLHYK 23 0 P53634 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 121.26 2.44E-05 115977000 204305 204241 156590 229600 162365 173061 223972 193775 27845 FALSE TRUE 194647.9075 225053.3901 163769.8064 206520.1718 190681.4046 167067.8542 189800.9579 176807.0337 32163.06039 6.05190878 6.997262928 5.091860178 6.421036099 5.928583981 5.194401657 5.901209511 5.497208027 1 14.97311707 -0.580862467 0.467461552 9.88E-14 6.223682422 0.895556053 0.52803731 2.794548154 0.515935528 5.286919497 0.2640298 0.262504971 0.580862467 6.223682422 LELVHHGPMAVAFEVYDDFLHYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LELVHHGPMAVAFEVYDDFLHYKK 24 1 P53634 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 122.18 3.66E-05 194332000 638600 438150 545490 621520 538960 577090 908570 660410 91014 FALSE TRUE 608414.6436 482797.9831 570501.2561 559043.6288 632954.4534 557105.2286 769950.9595 602580.9993 105127.9863 5.787370852 4.59247818 5.426730562 5.317743149 6.020798797 5.299304669 7.323939007 5.731879975 1 16.68178726 2.968991437 16.4954744 5.636260606 5.219765903 0 1.679028238 67.27098435 35784.02701 0.456702352 0.486759837 931.089516 -2.968991437 -0.416494704 LENGELEHIRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LENGELEHIRPK 12 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;; 196.27 1.25E-07 2542800000 3343630 3078440 2924900 3594020 2400500 3233600 3675220 3465630 2425990 FALSE TRUE 3185583.236 3392136.536 3059009.558 3232742.281 2819146.44 3121619.621 3114497.689 3162161.065 2802200.139 1.13681503 1.210526146 1.091645638 1.153644323 1.006047498 1.113988818 1.111447268 1.128456537 1 21.41812857 -4.999999999 0.020332537 9.44E-07 1.898687777 0.383500914 0.04977961 2912.841049 4.481095259 283.3629608 153.4651859 1.00E-05 4.999999999 1.898686833 LENGGFPYEKDLIEAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LENGGFPYEKDLIEAIR 17 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ; 131.71 2.37E-05 390110000 181563 117737 159252 174291 156663 166333 223710 197928 193803 FALSE TRUE 172980.8768 129734.5342 166553.8617 156770.9375 183984.9776 160572.8465 189578.9308 180596.375 223856.9794 0.772729433 0.579542056 0.74401907 0.700317399 0.821886269 0.71730105 0.846875229 0.806748914 1 17.77221777 0.995024703 0.372953447 1.021238718 0.669222599 0.669812159 0.062668892 0.78872026 0.306926934 0.100984045 0.054757902 9.886093262 -0.995024703 -0.352016119 LENGGFPYEKDLIEAIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LENGGFPYEKDLIEAIRR 18 2 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 93.804 0.0011706 181240000 556800 379590 547710 513130 586680 544610 815170 631070 673800 FALSE TRUE 530481.1675 418270.6526 572823.0453 461549.1975 688996.8063 525750.0191 690800.8449 575810.1653 778289.4627 0.681598805 0.537422993 0.736002571 0.593030254 0.885270634 0.675519899 0.887588588 0.739840629 1 19.5699473 1.657139889 0.28791806 1.026088676 0.559894232 0.549422647 0.094945375 1.019661834 0.313623543 0.167442744 0.171004626 45.40878577 -1.657139889 -0.466194443 LENLGIPEEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LENLGIPEEELLR 13 0 Q01658 Q01658 DR1 Protein Dr1 0 ; 133.71 0.00024199 26260000 30249 22561 26240 30028 28550 26518 31321 28707 36042 FALSE TRUE 28819.18972 24859.99155 27443.12995 27009.52839 33529.11096 25599.67501 26542.4062 26193.26289 41631.20928 0.692249642 0.597147956 0.65919608 0.648780779 0.805384027 0.614915479 0.637560298 0.629173722 1 15.34537785 -1.072983851 4.401456846 1.000028499 0.657188943 0.774305273 0.05756915 7413307.19 1807210.71 2031.199632 0.012854177 0.084531028 1.072983851 -0.342839556 LENNDNKPVTNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LENNDNKPVTNSR 13 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 234.22 1.07E-16 278070000 403000 355650 374430 449720 341750 409330 482200 495250 397710 FALSE TRUE 383950.9887 391891.1393 391597.9859 404513.2912 401351.0918 395154.7995 408631.5338 451883.2845 459384.8356 0.835793781 0.853078093 0.852439949 0.880554298 0.873670746 0.860182507 0.889518987 0.983670443 1 18.80934371 1.284107778 2.401684789 1.002814086 0.857914441 0.950761642 0.012330755 0.06208625 0.595906427 0.01254527 0.003670789 19.23569039 -1.284107778 -0.144899645 LENVSQLSLDKS(ph)PTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 LENVSQLSLDKS(0.968)PT(0.032)EK;LENVSQLSLDKS(0.982)PT(0.018)EK 204.31 1.55E-11 236930000 543580 534970 466920 596460 249670 552620 512330 628510 249230 TRUE FALSE 517886.0507 589484.0512 488328.7438 536502.7076 293212.369 533482.6308 434164.6489 573474.3325 287879.3155 1.7989693 2.047677688 1.696296738 1.863637569 1.01852531 1.853146795 1.508148122 1.992065083 1 18.13510461 2.932835266 24.99995481 1.527395231 1.870615765 0.245145727 0.320826744 260.1028127 96814.5522 0.087942037 0.093276664 856.7128199 -2.932835266 0.343220534 LEPQELS(ph)PLSATVFPK ddPTM_SK-BR-3_Trastuzumab_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(0.998)PLS(0.002)ATVFPK;LEPQELS(0.993)PLS(0.007)ATVFPK 236.27 1.05E-19 171559000 268470 247280 253640 285090 191263 265130 290690 296560 226300 TRUE FALSE 255779.9552 272478.1131 265269.6449 256432.2116 224619.2066 255948.4816 246339.9016 270591.6342 261393.4482 0.978524737 1.042406055 1.014828974 0.981020042 0.859314601 0.97916946 0.942410391 1.035189046 1 17.99586346 3.007235447 12.25355038 0.955674508 1.011732159 0.169806931 0.047555506 0.549109198 906.6089443 0.013025167 0.015331509 1016.799787 -3.007235447 0.056057651 LEPQIASASEYAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LEPQIASASEYAHR 14 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ;;;; 272.74 5.45E-33 1662330000 2116810 1637000 1860820 2048270 2290730 1740340 2416710 2167230 2316310 FALSE TRUE 2016752.586 1803812.161 1946140.438 1842374.008 2690232.587 1680071.589 2047996.504 1977455.852 2675511.525 0.753782059 0.674193381 0.727390041 0.688606269 1.005502149 0.627944067 0.765459795 0.7390945 1 21.35138331 -4.999999978 0.308064458 3.245681691 0.730397442 0.382100018 0.100494685 290.4886997 2.641784998 423.0352876 0.087290896 1.00E-05 4.999999978 -2.515284249 LEPTAPALS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEPTAPALSPR 11 0 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 LEPTAPALS(1)PR;LEPTAPALS(1)PR;LEPTAPALS(1)PR;LEPTAPALS(1)PR 154.1 3.37E-05 604726000 688965 568031 603261 689524 633233 578605 720735 620897 666662 TRUE FALSE 656398.9898 625914.0047 630921.1136 620211.7375 743668.6347 558567.7638 610773.6385 566527.9671 770044.5381 0.852416915 0.812828315 0.819330678 0.805423202 0.965747561 0.725370724 0.793166639 0.735708052 1 19.55458237 LEPVS(ph)PPS(ph)PPHTDPELELVPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LEPVSPPSPPHTDPELELVPPR 22 0 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(0.999)PPHT(0.001)DPELELVPPR;LEPVS(1)PPS(0.997)PPHT(0.003)DPELELVPPR;LEPVS(1)PPS(0.998)PPHT(0.002)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR 117.08 7.53E-05 671906000 443570 412379 407037 481289 435148 403849 490161 470456 410561 TRUE FALSE 422603.3252 454400.8889 425700.0491 432908.9153 511037.6734 389863.6079 415377.937 429260.3786 474228.703 0.891138226 0.958189342 0.897668248 0.912869492 1.077618605 0.822100403 0.875902143 0.905175869 1 18.85522346 -0.341618319 9.622986131 0.999999866 0.916386683 0.132669092 0.066163109 0 0 0.061035041 0.014386097 0.455388103 0.341618319 -0.083613183 LEQDEYALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEQDEYALR 9 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;; 179.28 0.00011628 1736389000 2095280 1463490 1538520 1632510 1865560 1376370 1858950 1697850 1834440 FALSE TRUE 1996240.267 1612621.295 1609062.664 1468406.993 2190913.073 1328705.962 1575333.036 1549177.253 2118915.586 0.942104669 0.761059716 0.759380258 0.692999288 1.033978459 0.627068851 0.743461913 0.731117966 1 21.01489468 LEQEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEQEKR 6 1 A0A087WUT6;O60841;CON__ENSEMBL:ENSBTAP00000034412 A0A087WUT6;REV__Q1RMZ1 EIF5B Eukaryotic translation initiation factor 5B 0 ;;; 117.17 0.0368 1135700000 1711130 1298910 1414510 1587040 1215590 1477460 1933750 1818340 1519210 FALSE TRUE 1630248.276 1431270.406 1479366.683 1427507.724 1427588.511 1426295.19 1638720.922 1659116.51 1754801.328 0.929021565 0.815631025 0.843039414 0.813486804 0.813532842 0.812795823 0.93384983 0.945472564 1 20.74287627 1.597146408 3.775890917 0.964889275 0.840797241 0.70820229 0.037267863 0.110403841 3.640546275 0.023623146 0.01018532 39.54999277 -1.597146408 -0.124092034 LEQENDDLAHELVTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 137.14 1.37E-05 216754000 460746 398920 400507 491559 356259 449003 524350 509300 388778 FALSE TRUE 438967.4497 439570.4015 418870.6421 442146.5554 418390.4568 433453.9135 444350.7772 464702.992 449067.7066 0.977508387 0.978851062 0.932756099 0.984587733 0.931686805 0.965230648 0.989496173 1.034817212 1 18.77657345 1.522757736 3.357510446 1.016965005 0.963712765 0.57372301 0.019753298 0.149186918 3.624483404 0.012842727 0.004917578 33.32404681 -1.522757736 -0.05325224 LEQLDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEQLDHR 7 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 70.525 0.056792 41592000 65642 64849 62466 72216 67689 68233 78101 66975 67983 FALSE TRUE 62539.23275 71457.18683 65330.12789 64956.71048 79493.94017 65870.0741 66185.25803 61110.31394 78525.45643 0.796419857 0.909987539 0.831961135 0.827205768 1.012333373 0.838837201 0.842850982 0.77822297 1 16.2608728 4.692883534 3.693310114 0.87247073 0.79174288 0.099756203 0.075888172 0.585351823 13.82577868 0.016776007 0.117924974 49304.15653 -4.692883534 -0.08072785 LEQQLVHVERPILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEQQLVHVERPILR 14 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6;E7EPX3;B9ZVU2;F8WAN0;C9JRG3;C9J1E2 E5RIA4 DNPEP Aspartyl aminopeptidase 0 183 8.76E-07 97507000 63556 54262 54250 64999 55134 56261 60627 56770 55844 FALSE TRUE 60551.83384 59791.35949 56737.41616 58465.17703 64749.35214 54312.66746 51377.23766 51798.91784 64504.00231 0.938729872 0.926940304 0.879595283 0.906380611 1.003803637 0.842004612 0.796496897 0.803034168 1 15.97710106 2.121480822 11.01703054 0.837778835 0.927719119 0.19228412 0.064902286 0.401584052 36.81062576 0.021930839 0.016196162 132.2759294 -2.121480822 0.089940284 LEQTSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEQTSVR 7 0 O15234 O15234 CASC3 Protein CASC3 0 ; 99.919 0.02367 1596190000 1692610 1239180 1366910 1490030 1642450 1470730 2034500 1809480 1844380 FALSE TRUE 1612603.68 1365453.851 1429584.176 1340249.354 1928892.76 1419798.251 1724099.659 1651032.339 2130397.031 0.756949834 0.640938675 0.671041198 0.629107783 0.905414687 0.666447724 0.809285609 0.774988096 1 21.02269089 0.170956918 0.349090858 1.053955236 0.678668565 0.567559963 0.078839167 2.746153128 0.534157287 0.299723524 0.066712264 1.482371027 -0.170956918 -0.375286672 LES(ph)IDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESIDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR 40 2 Q5VZ89-7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 LES(0.918)IDNHS(0.065)S(0.014)T(0.003)GGQSDQGYGSKDELIKDDAEIHVPEEQAAR 118.46 7.73E-07 84814000 60538 34645 49519 73750 50279 70781 89194 58620 41342 TRUE FALSE 57676.48871 38175.36489 51789.49513 66336.50988 59047.64168 68329.83622 75585.81714 53486.92204 47753.10621 1.207806011 0.799432077 1.084526206 1.389155913 1.236519388 1.430898252 1.582846083 1.120072102 1 15.54330696 3.340109823 4.605761601 1.346019322 0.995085192 0.271284671 0.192348902 0.199339457 7.245954787 0.051841744 0.070650885 2188.314929 -3.340109823 -0.350934129 LES(ph)LNIQR ddPTM_SK-BR-3_Trastuzumab_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 110.39 0.0036038 182640000 420720 353100 384480 433040 407760 413300 522120 451260 430420 TRUE FALSE 400833.3994 389081.2914 402108.7883 389509.9965 478873.2149 398987.3174 442461.0046 411745.2821 497167.3353 0.806234382 0.782596248 0.808799693 0.783458544 0.963203294 0.802521182 0.889963948 0.828182491 1 18.92337199 -4.999999999 0.102155482 1.556278187 0.715991438 0.541911174 0.051545967 124.8561936 0.86370499 14.64950105 0.728717723 1.00E-05 4.999999999 -0.840286749 LES(ph)VEEYNELMVR ddPTM_SK-BR-3_Trastuzumab_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 124.09 0.00022634 49633000 40976 32008 30905 47523 42386 41797 43573 32173 38570 TRUE FALSE 39039.14569 35269.65159 32322.02482 42745.89775 49778.10498 40349.55941 36925.13858 29355.76156 44551.23861 0.876275204 0.791664894 0.725502272 0.959477202 1.117322583 0.905688835 0.828824063 0.658921334 1 15.44317792 5.122412899 17.8904286 0.866636653 2.369398366 0 0.133703146 4828.409977 694635.9149 0.030879295 4641.856915 132560.1232 -5.122412899 1.502761713 LESAQATFQAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESAQATFQAHR 12 0 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 82.85 0.013841 153730000 142690 136700 159380 157470 148400 167490 149770 157750 179090 FALSE TRUE 135945.3265 150629.8854 166687.7306 141640.8164 174280.913 161689.7793 126919.8358 143936.5737 206862.3625 0.657177675 0.728164774 0.80579052 0.684710426 0.842496967 0.781629763 0.61354726 0.69580842 1 17.65831165 -2.288478344 2.343891325 2.322371047 0.721281604 0.605918076 0.069303309 4607404.641 690490.391 32340434.53 0.017083201 0.005146615 2.288478344 -1.601089443 LESDYEILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LESDYEILER 10 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 234.81 9.86E-12 395791000 554991 584280 495429 587182 512630 527520 531376 568760 518957 FALSE TRUE 528757.6753 643818.7963 518144.9097 528157.3498 602032.5097 509251.8501 450304.8318 518956.3592 599434.2011 0.882094606 1.074044149 0.864389968 0.881093119 1.004334602 0.849554212 0.751216449 0.86574366 1 19.19324187 2.131555487 7.11373031 0.834074286 0.947467108 0.1033138 0.088377507 0.288617658 17.27493481 0.03164352 0.023328493 135.3803046 -2.131555487 0.113392821 LESEST(ph)SPSLEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.016)T(0.552)S(0.416)PS(0.016)LEMK 141.54 0.00044596 34797000 135260 125020 134260 155590 103240 145010 150910 159780 120740 TRUE FALSE 128866.5279 137759.6801 140415.9538 139949.7976 121245.0233 139988.2673 127885.9078 145788.8162 139463.7425 0.924014554 0.987781323 1.006827662 1.003485171 0.869365909 1.003761012 0.916983192 1.045352817 1 17.08953058 1.22714677 24.99999989 1.022676421 0.959650767 0.248249503 0.046133167 339.0536638 742612.9735 0.039375863 0.010185695 16.87123092 -1.22714677 -0.063025654 LESESTS(ph)PSLEMK ddPTM_SK-BR-3_Trastuzumab_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 LESEST(0.006)S(0.994)PSLEMK;LESEST(0.018)S(0.982)PSLEMK;LESEST(0.002)S(0.998)PSLEMK;LESES(0.005)T(0.267)S(0.728)PSLEMK;LESES(0.022)T(0.161)S(0.804)PS(0.013)LEMK;LESEST(0.004)S(0.934)PS(0.062)LEMK;LESES(0.001)T(0.024)S(0.584)PS(0.391)LEMK 370.65 3.09E-91 970173000 3478540 3097360 3172550 3714070 2389616 3641560 3891690 3820260 2614706 TRUE FALSE 3314116.308 3412984.505 3318014.556 3340724.627 2806364.274 3515451.864 3297941.215 3485737.782 3020181.252 1.097323647 1.130059496 1.09861438 1.10613382 0.929203925 1.163987049 1.091967978 1.15414854 1 21.5262037 -2.501092371 2.017821822 2.48E-05 1.097472085 0.181964362 0.064221174 1835238.257 106286.2919 8455149.346 0.014545581 0.003154334 2.501092371 1.097447328 LESIISGAALMADS(ph)SCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESIISGAALMADSSCTR 18 0 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;H0YBB8 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 LESIISGAALMADS(0.424)S(0.424)CT(0.152)R 97.081 0.0015456 20097000 23305 25255 26853 33917 30085 31920 31207 30882 30975 TRUE FALSE 22203.41884 27828.51321 28084.23661 30507.59872 35331.81447 30814.6024 26445.79899 28177.80836 35778.4448 0.620580882 0.777801086 0.784948501 0.852680962 0.987516776 0.86126165 0.739154514 0.787563812 1 15.12680306 4.338567585 1.06673713 0.851721843 0.584449574 0.474124535 0.081431859 0.912968051 1.322358545 0.026193837 0.237954277 21805.57708 -4.338567585 -0.267272269 LESIISGAALMADSS(ph)CTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESIISGAALMADSSCTR 18 0 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;H0YBB8 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 LESIISGAALMADS(0.167)S(0.666)CT(0.167)R 90.379 0.0028497 21751000 24915 25290 27397 31050 27004 28429 31757 29499 31465 TRUE FALSE 23737.31733 27867.07975 28653.17955 27928.79501 31713.48905 27444.4966 26911.88639 26915.91118 36344.4315 0.653121162 0.76674964 0.788378807 0.768447706 0.872581789 0.755122462 0.740467942 0.740578682 1 15.14944672 -5 0.31929321 3.264714236 0.747089788 0.656033709 0.054145057 210.1273541 1.863825414 321.7197133 0.050014227 1.00E-05 5 -2.517624448 LESLSETPGPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.626)S(0.374)PR 115.82 0.00041701 47992000 81169 83494 73416 86135 72107 76048 84394 87073 77085 TRUE FALSE 77332.30223 92002.13352 76782.19622 77476.54615 84682.43797 73414.43869 71518.1453 79448.42652 89038.9481 0.86852219 1.033279654 0.862343928 0.8701422 0.95107186 0.824520508 0.80322316 0.892288467 1 16.44214893 3.683019419 24.99981046 0.872185471 0.950901262 0.105064305 0.069653945 421.7966249 189855.9158 0.017773335 0.027534357 4819.693481 -3.683019419 0.07871579 LESLSETPGPS(ph)SPRQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LESLSETPGPSSPRQPR 17 1 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.768)S(0.232)PRQPR;LESLSET(0.003)PGPS(0.696)S(0.301)PRQPR 146.15 2.71E-07 317480000 198450 147503 215130 183958 335690 178070 303810 211860 487790 TRUE FALSE 189069.6618 162533.7234 224993.9233 165466.1923 394234.2297 171903.3912 257458.2046 193308.4153 563433.9819 0.335566664 0.288469863 0.399326151 0.293674499 0.699699064 0.305099438 0.456944758 0.343089734 1 19.10388705 -5 0.261154248 4.983693415 0.335799556 0.710515495 0.122026703 99.73568703 0.978327927 213.3689485 0.146090077 1.00E-05 5 -4.647893858 LESLSETPGPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPSS(1)PR 278.85 3.57E-33 1078380000 1157310 1114790 994530 1184780 971930 1040820 1074100 1068400 1017600 TRUE FALSE 1102606.25 1228388.368 1040130.184 1065683.663 1141434.284 1004776.142 910226.3178 974845.2321 1175404.211 0.938065595 1.045077393 0.88491276 0.906652923 0.971099366 0.854834561 0.774394297 0.829370206 1 20.16472554 2.183249058 5.554912052 0.836736032 0.956413237 0.213280085 0.072068598 0.200212785 12.86411686 0.026050021 0.019305513 152.4927014 -2.183249058 0.119677205 LESLSETPGPSS(ph)PRQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESLSETPGPSSPRQPR 17 1 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.295)S(0.705)PRQPR 125.23 2.88E-05 168160000 87865 45230 80161 65459 131860 81931 114830 81145 163010 TRUE FALSE 83711.79558 49838.98842 83836.46114 58878.93696 154856.3423 79093.70893 97310.5745 74039.51362 188288.7583 0.444592637 0.264694445 0.445254735 0.312705535 0.822440722 0.420066018 0.516815637 0.39322323 1 17.52258734 -5 0.191581052 3.393987143 0.34405783 0.569590409 0.149437801 94.78127173 0.928845944 86.70462313 0.370304126 1.00E-05 5 -3.049929313 LESNKEGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LESNKEGTR 9 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 63.624 0.068259 51018000 96645 79740 104040 76709 94754 94135 140840 113140 105730 FALSE TRUE 92076.78238 87865.59666 108810.3369 68998.06558 111279.0676 90875.08135 119352.2713 103232.8618 122126.0684 0.753948633 0.71946635 0.890967329 0.5649741 0.911181937 0.744108793 0.977287428 0.845297512 1 16.89801166 1.861324541 1.036518449 0.961416198 0.745066688 0.371212634 0.104503497 0.484170202 0.957599322 0.075894139 0.032616821 72.66487667 -1.861324541 -0.216349509 LESTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LESTSPK 7 0 Q03111 Q03111 MLLT1 Protein ENL 1 LES(0.002)T(0.043)S(0.955)PK;LES(0.001)T(0.017)S(0.982)PK;LES(0.019)T(0.044)S(0.937)PK;LES(0.335)T(0.218)S(0.447)PK;LES(0.206)T(0.062)S(0.732)PK 108.3 0.0076397 1689120000 12439900 11780900 10654500 13772600 6423580 12949700 12581700 13856100 7248310 TRUE FALSE 11851890.58 12981387.1 11143019.36 12388152.08 7543850.318 12501248.64 10662130.59 12642786.43 8372340.896 1.415600574 1.550508665 1.330932352 1.479652135 0.901044333 1.493160491 1.27349456 1.510065893 1 22.99719962 -4.65144869 0.118928988 2.34E-16 1.552361086 0.253362983 0.189630911 185.3192034 1.55430712 46.83542384 1.756280301 2.23E-05 4.65144869 1.552361086 LETHMTPEMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LETHMTPEMFR 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 202.03 4.14E-08 858075000 1066400 941110 783890 938090 1249270 886700 1306510 1073170 1165050 FALSE TRUE 1015993.385 1037010.179 819832.1319 843791.4109 1467142.292 855993.3567 1107177.904 979197.5456 1345720.004 0.754981261 0.770598769 0.609214495 0.627018554 1.090228494 0.636085779 0.822740169 0.727638396 1 20.35994684 LETLLR ddPTM_SK-BR-3_Trastuzumab_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 99.511 0.090068 29935000 40345 38338 38136 45737 41395 34901 43770 43286 39998 FALSE TRUE 38437.97181 42244.68579 39884.57332 41139.42987 48614.27489 33692.36962 37092.08261 39495.64837 46200.68556 0.831978386 0.91437357 0.863289643 0.890450637 1.052241418 0.729261248 0.802847018 0.854871478 1 15.49562664 -1.392137874 8.605077427 1.000000795 0.864778022 0.201665618 0.082756499 1.24E-06 8.76E-08 0.078716471 0.018553541 0.040537982 1.392137874 -0.135222773 LEVADEWVRPEQAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEVADEWVRPEQAVVR 16 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 0 74.12 0.03025 43395000 28447 23799 29889 33363 39215 25497 34756 26003 33099 FALSE TRUE 27102.36669 26224.14516 31259.44021 30009.28785 46054.08358 24614.0325 29453.33386 23726.03947 38231.82387 0.708895468 0.685924513 0.817628798 0.784929538 1.204600747 0.643810051 0.770387883 0.62058351 1 15.22248641 3.732376128 19.30319699 0.823347699 0.697409907 0.100333909 0.168154771 48.7385036 152133.41 0.04255096 0.068329738 5399.780776 -3.732376128 -0.125937792 LEVGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LEVGPR 6 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 124.32 0.042818 49399000 144870 109620 118060 140020 136910 120540 150520 125300 157780 FALSE TRUE 138022.2822 120790.4026 123473.1678 125944.9236 160787.0607 116365.6696 127555.4095 114328.0677 182247.7166 0.757333397 0.662781432 0.677501864 0.691064481 0.882244583 0.638502757 0.699901277 0.62732236 1 17.47554121 -0.972645976 8.132805773 1.000000001 0.704757939 0.620884288 0.072547091 1.45E-09 1.79E-10 0.06498855 0.015317948 0.106501083 0.972645976 -0.295242062 LEVLDHS(ph)KR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEVLDHSKR 9 1 Q8TE67-2;Q8TE67;Q8TE67-3 Q8TE67-2 EPS8L3 Epidermal growth factor receptor kinase substrate 8-like protein 3 1 LEVLDHS(1)KR;LEVLDHS(1)KR 54.416 0.082802 490810000 479980 447970 364840 358700 3276800 164015 437330 171852 323410 TRUE FALSE 457292.2966 493618.6523 381568.2749 322642.7945 3848272.883 158335.1194 370607.2764 156803.7278 373562.7711 1.224137768 1.321380744 1.021430144 0.863690977 10.30154282 0.423851443 0.992088359 0.41975202 1 18.51099116 LEVTEIVKPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEVTEIVKPSPK 12 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK 114.01 0.00066833 1154780000 3130700 2929100 2521060 3371300 1306340 3234300 2940000 3500000 1373700 TRUE FALSE 2982718.015 3227578.62 2636653.095 3032410.519 1534165.282 3122295.38 2491449.003 3193521.445 1586726.38 1.87979355 2.034111653 1.661693615 1.911111176 0.966874504 1.967759167 1.570181875 2.012647855 1 20.59762194 -2.544802753 0.17677589 3.97E-23 1.962692979 0.325076395 0.323327953 55.09990905 1.173420248 24.2411848 1.097223647 0.002852313 2.544802753 1.962692979 LEYDAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LEYDAYR 7 0 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ;;; 133.7 0.0075516 345450000 1716680 1310140 964820 1047440 1639270 1055790 1754630 1392830 1609560 FALSE TRUE 1635535.939 1443644.756 1009057.951 942149.3412 1925158.169 1019227.728 1486928.968 1270866.421 1859162.344 0.87971658 0.776502794 0.542748703 0.506760125 1.035497613 0.548218788 0.799784361 0.683569364 1 20.82622132 -1.254045554 3.994658415 1.000281701 0.730948112 0.21913373 0.164320194 102.5340724 81703892.69 39552.20198 0.035918399 0.055712731 1.254045554 -0.269333589 LEYDDLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LEYDDLRR 8 1 P15924 P15924 DSP Desmoplakin 0 ; 175.91 0.00042234 558360000 682120 607340 622270 701950 615190 639150 747430 678050 672150 FALSE TRUE 649877.5394 669228.6365 650801.695 631388.6524 722478.9412 617016.0752 633395.826 618676.3474 776383.5891 0.837057285 0.861981945 0.838247619 0.813243172 0.930569568 0.79473096 0.815828458 0.796869429 1 19.5664101 -1.038334314 4.717162788 1.000004735 0.837204824 0.633837505 0.039149391 1.84E-06 3.75E-07 0.035738885 0.008423491 0.091551547 1.038334314 -0.162799911 LFAGSLAPLLQPGAAGGEIPAVQASSGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFAGSLAPLLQPGAAGGEIPAVQASSGSPK 30 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 LFAGSLAPLLQPGAAGGEIPAVQAS(0.005)S(0.08)GS(0.914)PK;LFAGSLAPLLQPGAAGGEIPAVQAS(0.002)S(0.014)GS(0.985)PK 156.49 3.12E-09 467330000 989810 873080 848060 1008920 548400 1016850 1065360 1063600 639100 TRUE FALSE 943023.6429 962047.8446 886944.3898 907501.4448 644040.7864 981636.2295 902819.7653 970465.5455 738208.3639 1.277449144 1.303219919 1.201482445 1.22932967 0.872437672 1.329754955 1.222987722 1.314622799 1 19.49366856 3.580832952 2.677423906 1.175194891 1.290858241 0.121104485 0.138013715 0.602015967 8.379514517 0.03732899 0.06195256 3809.192775 -3.580832952 0.115663349 LFAPQQILQCS(ph)PAN ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LFAPQQILQCSPAN 14 0 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 LFAPQQILQCS(1)PAN;LFAPQQILQCS(1)PAN;LFAPQQILQCS(1)PAN;LFAPQQILQCS(1)PAN 159.22 5.19E-06 108724000 354602 316394 378241 398338 597897 302712 470642 351936 782950 TRUE FALSE 337840.6662 348634.9083 395583.724 358296.3074 702170.0475 292229.0075 398836.919 321118.6181 904365.8872 0.373566353 0.385502055 0.437415574 0.39618512 0.776422527 0.323131391 0.441012785 0.355075996 1 19.78654705 -2.019889938 2.911053814 1.648569116 0.432384071 0.663474263 0.126202099 61807970.46 18429083.42 268223821.7 0.029362564 0.009552346 2.019889938 -1.216185045 LFAYPDTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFAYPDTHR 9 0 P04040 P04040 CAT Catalase 0 ; 116.52 0.0013002 313660000 371260 280760 209581 237283 420080 218617 385720 290820 335140 FALSE TRUE 353711.2756 309369.7632 219190.4962 213430.862 493341.819 211046.2385 326871.3298 265354.2591 387111.7995 0.913718662 0.799174201 0.566220137 0.55134166 1.274416899 0.545181621 0.844384827 0.685471896 1 18.56239076 4.344691117 3.079096517 0.77018179 0.901283537 0.029394653 0.226204335 0.909656044 16.36230965 0.052030981 0.183012421 22115.21252 -4.344691117 0.131101747 LFDANKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 166.09 0.00029229 9260170000 18956920 14533330 12226940 13017680 14032750 14450750 20375950 17006690 14937370 FALSE TRUE 18060863.96 16014292.85 12787557.29 11709118.07 16480057.16 13950316.9 17267224.6 15517494.07 17253781.05 1.046777162 0.928161358 0.741145217 0.678640701 0.95515627 0.808536799 1.000779165 0.89936774 1 24.04040922 1.713408953 11.50433122 0.961704183 0.874189455 0.168365698 0.108731883 0.265920604 86.36531554 0.05549071 0.030282576 51.69028812 -1.713408953 -0.087514729 LFDDEAS(ph)VDEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 189.3 8.50E-06 167510000 436800 385590 408160 420980 375900 384940 419140 426340 380940 TRUE FALSE 416153.3297 424882.0594 426874.5397 378662.2906 441456.841 371609.4313 355192.495 389007.4094 440014.2296 0.945772436 0.965609816 0.970138034 0.860568284 1.003278556 0.844539577 0.807229565 0.884079158 1 18.74719065 2.221738228 24.99813764 0.86056345 0.947962824 0.172732093 0.062005743 269.5394382 400534.0917 0.021024738 0.015569478 166.6242577 -2.221738228 0.087399373 LFDFPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFDFPGR 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 105.12 0.018609 218954000 1131000 1102120 1037620 1205690 1082340 1036520 1143830 1135600 1057100 FALSE TRUE 1077539.871 1214427.281 1085195.903 1084491.751 1271099.753 1000625.052 969317.7256 1036160.844 1221029.669 0.882484594 0.99459277 0.888754738 0.88817805 1.041006444 0.819492825 0.793852721 0.84859596 1 20.21966683 2.193423663 24.99988772 0.841442949 0.936851749 0.162793553 0.074355505 158.1633409 87600.53275 0.025338916 0.018714109 156.107462 -2.193423663 0.0954088 LFDHPES(ph)PTPNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.463)PT(0.463)PNPT(0.074)EPLFLAQAEVYK;LFDHPES(0.497)PT(0.497)PNPT(0.007)EPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK 274.79 3.24E-53 905212000 850079 785660 773823 928553 609287 880612 914470 901844 530476.5 TRUE FALSE 809897.4504 865719.6472 809303.55 835213.0883 715546.4599 850116.1856 774950.8061 822873.7584 612740.0863 1.32176345 1.41286602 1.320794196 1.363078909 1.167781374 1.387400963 1.26473006 1.342940958 1 19.22491571 -3.820292682 0.247811611 3.25E-15 1.360683011 0.687890181 0.068236881 49.32054829 0.833988194 25.0423741 0.09208555 0.000151254 3.820292682 1.360683011 LFDHPESPT(ph)PNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Trastuzumab_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(0.39)PT(0.61)PNPTEPLFLAQAEVYK;LFDHPES(0.182)PT(0.818)PNPTEPLFLAQAEVYK;LFDHPES(0.17)PT(0.83)PNPTEPLFLAQAEVYK;LFDHPES(0.47)PT(0.53)PNPTEPLFLAQAEVYK;LFDHPES(0.429)PT(0.571)PNPTEPLFLAQAEVYK 311.39 6.17E-74 4491200000 2818380 2570760 2606420 3152430 2057884 2812120 3013930 2942700 1736465 TRUE FALSE 2685160.763 2832723.367 2725926.935 2835541.747 2416778.318 2714735.579 2554099.624 2685021.588 2005747.124 1.338733448 1.412303342 1.35905813 1.413708495 1.204926728 1.353478486 1.273390645 1.33866406 1 20.9357083 -3.953601703 0.209290927 2.52E-10 1.395403534 0.774096327 0.058131037 37.63706206 0.556602969 16.00092478 0.115581619 0.000111275 3.953601703 1.395403533 LFDHPESPTPNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 319.73 7.48E-75 2527000000 2695480 2691160 2581320 3125250 2191980 2901680 3159300 3276270 2034610 FALSE TRUE 2568070.002 2965392.264 2699676.075 2811093.932 2574260.618 2801194.094 2677290.76 2989382.43 2350126.927 1.092736725 1.261800896 1.148736285 1.196145578 1.095370887 1.191933109 1.139211133 1.272008927 1 21.16430725 -1.052846743 4.459410426 0.999989644 1.173357972 0.45287506 0.060343901 0.03847166 16019882.88 361.7813124 0.012617282 0.088542801 1.052846743 0.173368328 LFDHPESPTPNPTEPLFLAQAEVYKELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFDHPESPTPNPTEPLFLAQAEVYKELR 28 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 0 148.02 4.55E-08 73360000 126140 60538 131790 92321 163550 132630 363690 131370 148150 FALSE TRUE 120177.6122 66706.89103 137832.7019 83040.71768 192073.0682 128036.9898 308202.4109 119866.5464 171124.3454 0.702282378 0.389815318 0.805453494 0.485265364 1.122418133 0.748210254 1.801043623 0.700464601 1 17.3846855 2.529794955 1.651713263 1.212132544 0.575836691 0.297037373 0.330834205 0.340143138 1.874868864 0.134323971 0.109554206 338.6842146 -2.529794955 -0.636295852 LFDQAFGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LFDQAFGLPR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 224.86 8.77E-09 6607485000 2941775 1868485 1755308 2333991 2876968 1916834 2916759 2226332 2823181 FALSE TRUE 2802723.126 2058885.746 1835790.608 2099373.79 3378710.308 1850453.558 2471753.845 2031382.568 3260985.491 0.859471204 0.631369183 0.562955773 0.643785076 1.036100994 0.567452251 0.757977566 0.622935175 1 21.63687659 LFDSTTLEHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFDSTTLEHQK 11 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 194.17 6.33E-07 920210000 1502900 1201820 1117940 1294250 1189250 1249100 1656340 1432610 1251020 FALSE TRUE 1431860.895 1324286.824 1169198.655 1164149.531 1396654.823 1205843.354 1403634.912 1307163.074 1445021.792 0.99089225 0.916447649 0.809121815 0.805627664 0.966528554 0.834481086 0.971358992 0.904597481 1 20.46265982 0.834072652 0.947291067 0.997585945 0.897881968 0.194608424 0.065838292 1.434862281 2.554149777 0.06369889 0.021235725 6.824528496 -0.834072652 -0.099703976 LFDVCGS(ph)QDFESDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.999)QDFES(0.001)DLDR 131.51 4.63E-05 39520000 44755 50480 35102 54206 34469 45062 37708 40819 35827 TRUE FALSE 42639.51985 55623.96939 36711.46142 48757.1099 40480.38269 43501.49164 31954.95205 37244.67196 41382.86818 1.030366471 1.344130357 0.887117376 1.17819552 0.978191809 1.051195665 0.772178282 0.900002189 1 15.33674602 2.430170351 1.102910578 0.876569583 1.14273326 0.277129819 0.134914905 0.490019303 1.18971725 0.077532071 0.052435845 269.2590758 -2.430170351 0.266163677 LFEAEAQDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFEAEAQDLFR 11 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ;; 152.62 7.64E-05 81120000 124429 109719 96161 116716 145810 99756 144040 127363 146929 FALSE TRUE 118547.4878 120899.4908 100570.077 104983.4859 171239.2178 96301.42471 122064.0525 116210.4205 169713.9989 0.698513314 0.712371941 0.59258563 0.618590609 1.008986995 0.567433596 0.719233848 0.684742692 1 17.37274605 -1.90149179 2.319638945 1.177037214 0.700303232 0.376931405 0.121091976 7711777.639 3841094.605 7447454.308 0.027432969 0.012546085 1.90149179 -0.476733982 LFECDRDQMYYNLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFECDRDQMYYNLLK 15 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 189.69 2.26E-07 320030000 210953 171598 169107 176054 194367 183176 229337 193562 191109 FALSE TRUE 200981.6698 189084.0313 176860.7232 158356.7174 228264.5433 176832.5692 194347.4286 176612.6851 220745.2077 0.910469006 0.856571399 0.801198473 0.717373297 1.034063415 0.801070932 0.880415166 0.800074833 1 17.75202259 2.761883049 24.99403796 0.886084348 0.836038205 0.150410976 0.08868695 2283.897454 2447589.039 0.025779293 0.027325437 577.9403927 -2.761883049 -0.050046142 LFEDDDS(ph)NEKLFDEEEDSSEKLFDDSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFEDDDSNEKLFDEEEDSSEKLFDDSDER 29 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEKLFDDSDER 216.83 1.35E-34 15662000 21617 23968 17098 25104 9509.2 26337 19989 25456 5387.9 TRUE FALSE 20595.20725 26410.36645 17881.96021 22580.49823 11167.60147 25424.94309 16939.31093 23226.93769 6223.428014 3.309302719 4.243700801 2.873329646 3.628305521 1.794445351 4.085359874 2.721861792 3.732177449 1 12.60349376 3.720237009 24.08580134 2.956226244 3.77650177 0.137661359 0.943023406 862.2986413 1133464.271 0.21775316 0.338151013 5250.93943 -3.720237009 0.820275526 LFEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFEEIR 6 0 F8VRQ3;G3V1Z2;Q8N4U5-2;Q8N4U5 F8VRQ3 TCP11L2 T-complex protein 11-like protein 2 0 98.133 0.093712 22855000 68159 64689 70417 79103 90379 64959 84731 75681 87863 FALSE TRUE 64937.25915 71280.88265 73645.6891 71151.41615 106141.069 62709.45354 71803.72976 69053.97043 101488.3453 0.639849423 0.702355354 0.725656615 0.701079675 1.045844906 0.617898078 0.707507148 0.680412812 1 16.63095454 -2.610511393 2.167268676 6.835974292 0.722688138 0.344462175 0.117936112 3952900.197 197453.944 114308563.3 0.027208405 0.00245182 2.610511393 -6.113286153 LFEELAMDVYDEVDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFEELAMDVYDEVDRR 16 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 80.706 0.023761 99028000 9003.6 5755.4 8286.7 8017.1 9112 4460.3 9753.9 7458.9 8006 FALSE TRUE 8578.017671 6341.881803 8666.653392 7211.205877 10701.12992 4305.838693 8265.763412 6805.759174 9247.529591 0.927600997 0.685791999 0.937185797 0.779798086 1.157187961 0.465620429 0.893834762 0.735954301 1 13.1748523 -1.233962987 8.497887558 1.000000056 0.818574733 0.085472399 0.18160276 1.68E-07 1.51E-08 0.152538937 0.035953761 0.058349483 1.233962987 -0.181425323 LFEELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFEELGK 7 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 105.95 0.018175 39928000 86271 75458 77687 86179 69302 73628 96365 95227 73513 FALSE TRUE 82193.1408 83147.25599 81249.02579 77516.12319 81388.24686 71078.2439 81662.74939 86888.41905 84913.02059 0.967968637 0.97920502 0.956850024 0.912888538 0.958489597 0.837071198 0.961722346 1.023263787 1 16.37369817 1.356807964 5.761654233 1.010049989 0.940306395 0.366682467 0.040387176 0.241887169 10.49245126 0.028819282 0.010289348 22.7409165 -1.356807964 -0.069743594 LFEFAGYDVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFEFAGYDVLR 11 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 142.83 8.72E-05 193902000 370417 305465 253979 243036 345672 253119 402231 302680 337738 FALSE TRUE 352908.1225 336592.2308 265624.1884 218605.5595 405957.0874 244353.4256 340863.2735 276175.7346 390112.6841 0.904631243 0.862807708 0.68089093 0.560365167 1.04061494 0.626366267 0.873755936 0.707938362 1 18.57353138 -0.857207129 7.805914088 0.999999999 0.793766878 0.180192318 0.144143677 9.54E-10 0 0.128015131 0.030173456 0.138928988 0.857207129 -0.20623312 LFEGNALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LFEGNALLR 9 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;; 125.98 0.0011314 564670000 1190750 980230 976115 1007524 1225370 1029648 1421120 1133480 1328110 FALSE TRUE 1134465.607 1080116.551 1020870.838 906245.7733 1439074.14 993991.0316 1204302.043 1034226.482 1534066.516 0.739515266 0.70408717 0.665467128 0.590747379 0.938078059 0.647945198 0.785039 0.674173168 1 20.54892961 -5 0.324372468 3.720888555 0.70919217 0.46676291 0.094268746 284.7220494 2.495203379 532.8494115 0.072912545 1.00E-05 5 -3.011696385 LFEHYYQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFEHYYQELK 10 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 152.07 1.87E-05 707370000 1624520 1285660 1176260 1460510 1256490 1333810 1803270 1508210 1203700 FALSE TRUE 1547732.159 1416670.216 1230192.684 1313696.76 1475621.458 1287619.825 1528148.042 1376143.137 1390363.648 1.113185145 1.018920638 0.884799229 0.944858391 1.061320511 0.926102913 1.099099537 0.989772092 1 20.40703084 -0.374024736 7.695359724 1.000011265 1.011810803 0 0.073668894 0 0 0.070799738 0.016687658 0.422644541 0.374024736 0.011799538 LFENLR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 160.17 0.020687 1632718000 2038308 1780872 1617523 1906232 1907102 1777847 2266870 2002666 1996065 FALSE TRUE 1941961.22 1962344.881 1691688.029 1714613.938 2239699.985 1716279.713 1921017.348 1827301.948 2305604.566 0.842278528 0.851119446 0.733728608 0.743672164 0.971415488 0.744394654 0.833194632 0.792547853 1 21.13671367 -1.638760194 3.225203379 1.012491808 0.817315676 0.410016082 0.070004617 30679032.28 37950354.28 3220515.693 0.015497935 0.022974169 1.638760194 -0.195176132 LFFDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFFDKR 6 1 O15371-2;O15371;O15371-3;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 95.957 0.068555 285340000 605860 514800 360720 454510 522080 467370 707760 572470 577550 FALSE TRUE 577222.1985 567258.7053 377259.3688 408821.7913 613130.5867 451184.8597 599778.2131 522341.4919 667113.5043 0.865253356 0.850318127 0.565510016 0.612821939 0.919079861 0.676323979 0.899064716 0.782987436 1 19.34757272 0.641890635 0.771341856 0.998965261 0.765314422 0.280066085 0.118754465 1.797206973 1.923656099 0.120748733 0.041818485 4.384202804 -0.641890635 -0.233650839 LFGPYVWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFGPYVWGR 9 0 Q9H4A4;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 137.83 0.00035742 228120000 560700 436380 608080 490770 478430 572930 791240 657310 608600 FALSE TRUE 534196.8222 480847.6181 635961.0695 441436.8672 561868.0405 553089.2904 670521.8059 599752.4518 702978.5797 0.759904836 0.684014609 0.904666355 0.627952088 0.799267654 0.78677972 0.95382964 0.853158928 1 19.4231212 1.893349949 2.32782023 0.933317864 0.746191368 0.511718048 0.080379162 0.222569722 2.207933688 0.042044434 0.020836999 78.22578841 -1.893349949 -0.187126496 LFHEVVQAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFHEVVQAFR 10 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 148.91 2.43E-05 72846000 138690 122450 101740 126250 140830 106380 135180 122580 124750 FALSE TRUE 132134.3986 134927.7942 106404.8796 113559.1101 165390.7074 102696.0339 114555.8082 111846.2454 144095.5929 0.916991255 0.936376967 0.738432575 0.788081772 1.147784635 0.712693788 0.794998695 0.776194769 1 17.13666669 LFHSTDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFHSTDTK 8 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 ; 93.429 0.011409 403520000 798780 651290 715950 886250 786600 843690 1075340 877890 798150 FALSE TRUE 761023.2524 717657.1915 748777.0157 797162.4662 923782.791 814472.8037 911277.133 801017.2976 921923.0256 0.825473745 0.778435044 0.812190383 0.864673562 1.002017267 0.883449899 0.988452515 0.868854856 1 19.81428677 3.007861329 3.447704915 0.94581139 0.803146863 0.668834264 0.046243565 0.121363998 3.065477562 0.012521536 0.014494448 1018.266202 -3.007861329 -0.142664526 LFIGGLS(ph)FETTEESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 LFIGGLS(0.994)FET(0.002)T(0.004)EESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(0.999)FET(0.001)TEESLR 128.96 6.08E-05 35312100 37006 27406.2 27741.4 36034 36151 33328 34655.6 25628.6 43368 TRUE FALSE 35256.79972 30198.92294 29013.37063 32411.79386 42455.72295 32173.843 29368.25173 23384.42392 50093.28795 0.703822831 0.602853679 0.57918679 0.647028678 0.847533167 0.642278523 0.586271194 0.466817509 1 15.61232969 -1.234048247 4.541779803 1.000120403 0.637400784 0.582769259 0.097170672 0.000116169 1.96E-05 0.092258573 0.021738371 0.058338029 1.234048247 -0.36271962 LFIGGLSFETTDDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 121.08 0.00023427 19928800 21885.7 22568 19601.5 26948 18505.5 16802.9 20325.9 19139.8 24272.2 FALSE TRUE 20851.20633 24867.70486 20500.24816 24239.13584 21732.85334 16221.01136 17224.81064 17463.81765 28036.20881 0.743724177 0.886985292 0.731206145 0.864565391 0.775170904 0.578573639 0.614377313 0.622902253 1 14.77500365 2.403056818 7.140633022 0.662930539 0.80992129 0.092006454 0.126591943 0.297268223 23.87133288 0.038877379 0.032467047 252.962892 -2.403056818 0.146990751 LFIGGLSFETTDDSLREHFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFIGGLSFETTDDSLREHFEK 21 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 303.83 1.42E-55 527657000 1229748 798101 1196089 1127733 1156182 1147694 1594849 1358112 1201830 FALSE TRUE 1171620.249 879428.3993 1250930.864 1014371.136 1357819.775 1107949.069 1351525.494 1239188.513 1388203.658 0.843982972 0.633500995 0.901114801 0.730707724 0.978112805 0.798117094 0.973578686 0.892656136 1 20.40478781 2.488747006 0.596735841 0.970975898 0.742207471 0.367256339 0.092345737 0.744799449 0.544259279 0.070927954 0.063070238 308.139239 -2.488747006 -0.228768426 LFIGGLSFETTDESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 245.69 8.99E-20 163415000 125826 95309 107928 118464 130262 105302 130139 107699 126984 FALSE TRUE 119878.4543 105021.0955 112876.6056 106555.7737 152979.6516 101655.3653 110283.9054 98268.30461 146676.0302 0.81730092 0.716007212 0.769564089 0.726470259 1.042976493 0.693060517 0.751887716 0.669968396 1 17.1622736 -2.24925496 2.388881691 1.897230113 0.772295868 0.318281661 0.104208641 9841459.173 1051179.961 48169247.28 0.025085612 0.005633069 2.24925496 -1.124934245 LFIGGLSFETTEESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 323.66 4.90E-58 616005700 283796.6 237111 256121.3 259405.8 283087.9 241767.8 295080.6 261115.8 283250.7 FALSE TRUE 270382.0971 261272.8805 267864.7149 233329.8361 332458.3401 233395.3205 250060.6349 238251.1163 327175.7719 0.826412346 0.79857038 0.818718065 0.713163554 1.016145964 0.713363704 0.764300588 0.728205255 1 18.31970639 -2.281090883 2.336399721 1.918269576 0.797611111 0.345351699 0.087679467 3144972.216 589797.9637 15318832.17 0.019144896 0.005234909 2.281090883 -1.120658464 LFIGGLSFETTEESLRNYYEQWGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFIGGLSFETTEESLRNYYEQWGK 24 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 207.24 7.06E-25 58935000 68110 21388 91987 34777 121490 50159 155310 72507 219850 FALSE TRUE 64890.57528 23567.46152 96204.69494 31281.14989 142677.8175 48421.98125 131614.607 66157.9027 253943.2152 0.255531833 0.092806029 0.378843337 0.123181672 0.561849299 0.19068035 0.518283613 0.260522427 1 17.9541464 -4.999999999 0.171176426 3.820703191 0.1217228 0.695148028 0.148435769 63.73662918 0.602736537 60.85113056 0.450130724 1.00E-05 4.999999999 -3.698980391 LFKDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFKDDIR 7 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 66.073 0.062803 59996000 422250 338430 357120 409050 381650 400420 484200 448210 423720 FALSE TRUE 402291.0793 372916.4018 373494.3052 367931.5169 448209.6392 386553.355 410326.3971 408962.3563 489428.3335 0.821961157 0.761942814 0.763123587 0.751757697 0.915781961 0.789805838 0.838378919 0.835591911 1 18.9007381 -1.264780049 0.264754049 1.142556014 0.775097018 0.660744849 0.044806057 10.75707103 0.603632391 1.127468566 0.061185042 0.054352553 1.264780049 -0.367458995 LFKPGQEAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFKPGQEAVK 10 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 90.913 0.0096283 0 710820 496940 341690 424640 515040 519600 814030 693630 650830 FALSE TRUE 677220.9473 547578.751 357356.8245 381954.3804 604862.8129 501606.1217 689834.7728 632892.08 751757.3924 0.9008504 0.728398226 0.475361903 0.508081975 0.804598424 0.667244681 0.917629517 0.841883414 1 19.51990762 1.71407056 5.880635434 0.909922908 0.693328907 0.424918584 0.13014184 0.170237186 14.39786698 0.071744406 0.036519346 51.76909345 -1.71407056 -0.216594001 LFLEFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LFLEFER 7 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;;; 160.03 0.0031676 103894000 268625 256119 215882 249143 283802 202473 288346 247392 292887 FALSE TRUE 255927.6286 282217.8173 225780.4032 224098.6723 333296.9789 195461.3092 244353.5219 225729.045 338306.4201 0.756496517 0.83420769 0.667384329 0.6624133 0.985192592 0.577764115 0.722284613 0.667232519 1 18.36797103 LFLLPHKDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFLLPHKDQR 10 1 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 129.16 0.00018661 429210000 1001640 716080 677150 697410 886760 729470 1117330 954170 869850 FALSE TRUE 954294.4623 789049.3661 708197.9973 627305.0218 1041410.663 704208.271 946860.7873 870617.8164 1004741.895 0.949790654 0.785325435 0.704855646 0.624344446 1.036495709 0.700884749 0.942392063 0.866508922 1 19.93839351 1.628532449 11.3621837 0.928497383 0.809106053 0.208188804 0.123826649 0.176021227 60.71082043 0.05718232 0.030417301 42.5140471 -1.628532449 -0.11939133 LFLSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFLSTR 6 0 Q8NCM8;Q8NCM8-2 Q8NCM8 DYNC2H1 Cytoplasmic dynein 2 heavy chain 1 0 122.15 0.045 71956000 156580 133620 145700 154510 210100 118290 184680 149940 214670 FALSE TRUE 149178.7737 147236.0299 152380.4891 138978.3613 246741.3735 114193.5876 156503.6741 136810.4587 247959.9272 0.601624526 0.593789616 0.614536755 0.560487184 0.995085683 0.460532429 0.631165188 0.551744228 1 17.91974746 -1.610041857 2.660111622 1.03452893 0.623620441 0.414769161 0.139542612 17612953.51 16078972.57 4224378.179 0.030912819 0.024544723 1.610041857 -0.410908489 LFNHANQEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LFNHANQEVQR 11 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;;; 178.53 7.50E-06 1211444000 1185491 985108 766235 870144 1190211 927745 1398300 1103157 1020064 FALSE TRUE 1129455.19 1085491.625 801367.6327 782675.472 1397783.422 895616.958 1184963.653 1006558.725 1178250.315 0.958586792 0.921274207 0.680133603 0.664269266 1.186321279 0.760124522 1.005697718 0.854282585 1 20.16821464 2.762097019 24.99414939 0.948539485 0.835217892 0.212559515 0.142493736 1660.527051 1763370.556 0.042946346 0.045527266 578.2252059 -2.762097019 -0.113321594 LFNHLSAVSESIQALGWVAMAPKPGPYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFNHLSAVSESIQALGWVAMAPKPGPYVK 29 1 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 152.14 1.72E-08 99198000 120890 76643 94757 103790 145910 101500 193820 145080 183460 FALSE TRUE 115175.7693 84453.00884 99101.70218 93356.83201 171356.6578 97985.02955 164249.1993 132376.0261 211910.0398 0.543512565 0.398532363 0.467659306 0.440549358 0.808629256 0.462389746 0.775089276 0.624680295 1 17.69309242 0.874154131 0.319846422 1.060878014 0.422531778 0.62909955 0.118165632 1.189285016 0.336820656 0.26656576 0.135329872 7.484350722 -0.874154131 -0.638346236 LFNIHED ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFNIHED 7 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 77.674 0.087024 28457000 125250 88196 97719 127290 141290 78116 117590 101520 109840 FALSE TRUE 119329.6807 97183.27267 102199.5128 114494.5674 165930.9313 75410.82333 99649.48581 92630.37061 126873.4262 0.94054117 0.765986035 0.805523393 0.902431429 1.307846223 0.594378394 0.785424409 0.730100647 1 16.9530304 -0.899042808 4.649827442 1.000000847 0.848518478 0.056264943 0.186668978 2.12E-06 5.02E-07 0.171954317 0.040529713 0.126170316 0.899042808 -0.151482369 LFNLSKEDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFNLSKEDDVR 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;; 95.094 0.0073095 975508000 3252160 1595930 3357370 2569580 3405710 3311680 5289080 3985170 4733270 FALSE TRUE 3098436.842 1758557.081 3511308.735 2311280.937 3999664.746 3196995.691 4482133.705 3636207.388 5467281.337 0.566723505 0.321651105 0.64224036 0.42274776 0.731563733 0.584750536 0.819810328 0.665085106 1 22.38239219 1.573591223 0.378864278 1.009161808 0.419643102 0.63738184 0.114943114 0.607144102 0.263240765 0.134753835 0.109975811 37.46202269 -1.573591223 -0.589518706 LFNVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LFNVDR 6 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;; 160.77 0.020256 2104230000 2182280 2182020 1926040 2231310 2182210 1976890 2298360 2135770 2223660 FALSE TRUE 2079127.949 2404370.319 2014350.839 2007014.48 2562786.733 1908429.804 1947702.97 1948750.656 2568493.836 0.809473599 0.936101261 0.784253717 0.781397429 0.997778035 0.743015139 0.758305487 0.758713386 1 21.29249118 LFNYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFNYHK 6 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 114.67 0.025089 1972300000 3099800 2513840 2118310 2169780 2226770 2001380 2471170 2387340 1936180 FALSE TRUE 2953278.597 2770003.154 2215436.609 1951669.592 2615117.983 1932071.709 2094147.63 2178291.854 2236432.906 1.320530828 1.238580933 0.990611703 0.872670755 1.169325481 0.863907745 0.936378473 0.974002774 1 21.09276805 3.773392812 3.349826253 0.962921291 1.292074881 0.700737553 0.084156436 0.110835886 2.57645956 0.021089788 0.038924551 5934.618584 -3.773392812 0.32915359 LFPDT(ph)PLALDANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 237.65 1.06E-15 371510000 1483850 1699590 1379780 1827320 1066150 1607340 1752820 1758490 1200990 TRUE FALSE 1413711.351 1872780.153 1443044.278 1643634.322 1252086.222 1551677.413 1485395.116 1604507.293 1387233.395 1.019086879 1.350010863 1.04023179 1.184828975 0.902577913 1.118540988 1.070760783 1.156623895 1 20.4037791 LFPDT(ph)PLALDANKK ddPTM_SK-BR-3_Trastuzumab_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 133.94 2.44E-05 1064600000 1487600 1496770 1287760 1748240 887460 1637050 1652110 1884660 1145330 TRUE FALSE 1417284.096 1649292.565 1346805.07 1572503.594 1042232.743 1580358.548 1400050.276 1719629.179 1322941.927 1.071312404 1.246685536 1.018037937 1.188641438 0.787814432 1.194578927 1.058285514 1.299852355 1 20.3353183 3.726472766 24.91860684 1.079064228 1.158998977 0.05212106 0.143259532 2008.898922 4141261.724 0.034694078 0.054206895 5326.878192 -3.726472766 0.079934748 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.5)DY(0.5)DEVPEEGPGAPAR 88.036 0.004046 13046000 19062 18576 20909 21333 19293 19845 21330 16410 19430 TRUE FALSE 18160.97704 20468.91552 21867.69833 19188.56631 22657.69309 19157.76267 18075.71675 14973.05341 22443.10517 0.809200728 0.912035806 0.974361532 0.854987141 1.009561419 0.853614619 0.805401775 0.667156051 1 14.45398468 2.002677664 24.98902595 0.809299973 0.905311396 0.144153128 0.096630791 133.2147147 1243203.627 0.03348982 0.0245894 100.6184595 -2.002677664 0.096011422 LFPNSLDQTDMHGDSEYNIMFGPDICGPGTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFPNSLDQTDMHGDSEYNIMFGPDICGPGTKK 32 1 P27797 P27797 CALR Calreticulin 0 245.12 3.61E-47 56641000 85590 56044 85649 82338 64519 84826 105310 97484 77480 FALSE TRUE 81544.33032 61754.94732 89576.09137 74061.22781 75771.09317 81888.45435 89243.02535 88947.78416 89495.20269 0.911158675 0.690036398 1.000903833 0.827544109 0.846649774 0.915003843 0.997182225 0.993883264 1 16.44952273 1.968864997 2.143775923 1.000005704 0.84205907 0.406918425 0.077104473 0.29111584 2.475368102 0.042845562 0.022094845 93.08184799 -1.968864997 -0.157946634 LFPSDGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFPSDGFR 8 0 P78545-2;P78545;Q5SR36 P78545-2 ELF3 ETS-related transcription factor Elf-3 0 81.784 0.051693 0 76404 65614 52426 73818 89217 64484 80594 71154 89627 FALSE TRUE 72792.53434 72300.1412 54829.78396 66397.67439 104776.4166 62250.90291 68297.90509 64923.37855 103525.8974 0.703133575 0.698377343 0.529623846 0.641362945 1.012079288 0.601307542 0.659718069 0.627122103 1 16.65963218 -1.313417057 3.666186646 1.000955889 0.684830441 0.380333078 0.12672183 32491351.37 39782777.31 317129.1279 0.028968389 0.048594033 1.313417057 -0.316125448 LFQCLLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFQCLLHR 8 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 191.63 0.00018018 1983870000 3239000 1751600 697820 858560 3789600 1142650 3422200 1973540 2932200 FALSE TRUE 3085898.889 1930090.031 729815.7372 772255.9176 4450505.04 1103079.744 2900080.537 1800726.375 3386910.6 0.911124991 0.569867428 0.215481252 0.228011899 1.314030857 0.325689064 0.856261319 0.531672249 1 21.69153848 LFQECCPHSTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LFQECCPHSTDR 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;; 244.58 2.07E-16 31477380000 12393900 9623400 10887420 12500860 13774930 10859780 14495760 12482800 13664920 FALSE TRUE 11808064.91 10604035.4 11386618.98 11244249.8 16177273.43 10483703.1 12284165.58 11389739.86 15784006 0.748103169 0.671821551 0.721402347 0.712382509 1.024915565 0.664197865 0.778266657 0.721600071 1 23.91196007 -5 0.227524218 2.30099425 0.721865602 0.357226744 0.102070312 171.7530413 1.718180587 103.0096612 0.169513957 1.00E-05 5 -1.579128648 LFQEDDEIPLYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFQEDDEIPLYLK 13 0 D6RIE3;D6RGV5;H0UI06;P14406 D6RIE3 COX7A2 "Cytochrome c oxidase subunit 7A2, mitochondrial" 0 89.403 0.010859 0 24845 16154 19007 23456 25864 14338 28708 19900 24163 FALSE TRUE 23670.62609 17800.11097 19878.48975 21098.15832 30374.67341 13841.47146 24328.06734 18157.4505 27910.07463 0.848103289 0.637766513 0.712233486 0.755933425 1.088304987 0.495931009 0.871658986 0.650569758 1 14.76849836 -1.139922688 4.003750198 1.000077626 0.757514621 0.187152488 0.158784686 19716709.37 5622670.037 14900.37213 0.032814804 0.072456493 1.139922688 -0.242563005 LFQEDPEAFLLYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFQEDPEAFLLYHR 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 ;; 193.98 1.97E-07 205699000 336062 287012 267614 312631 365724 243537 380725 310485 333107 FALSE TRUE 320177.0153 316258.8491 279884.3666 281204.7379 429506.1498 235103.2526 322638.4088 283297.2874 384763.5323 0.832139713 0.821956403 0.727419163 0.730850807 1.116286014 0.611033097 0.838536872 0.73628934 1 18.55361254 -1.374649252 3.092278148 1.002237161 0.804475852 0.185664193 0.130334813 37720848.61 45853444.26 761723.6851 0.028664887 0.042203721 1.374649252 -0.197761309 LFQLGPPS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 LFQLGPPS(1)PVK 157.38 3.21E-05 94202000 383210 541430 364200 532570 256170 460130 409620 470230 261090 TRUE FALSE 365096.4227 596602.3326 380898.9302 479035.0518 300845.9669 444195.5827 347124.9458 429054.1684 301578.5037 1.210618191 1.978265444 1.263017508 1.588425719 0.997570991 1.472902005 1.151026819 1.422694798 1 18.20217407 2.764311384 24.34405053 1.234416854 1.541112863 0.247892063 0.256088002 716.2294963 677101.6271 0.07206439 0.076409332 581.1809677 -2.764311384 0.306696009 LFQLMVEHTPDEESIDWTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFQLMVEHTPDEESIDWTK 19 0 Q12907;D6RBV2;D6RDX1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 138.3 2.19E-06 73962000 198260 183450 148840 191290 163890 156900 218470 184990 126210 FALSE TRUE 188888.6427 202143.7636 155664.4612 172061.1658 192472.3641 151466.5137 185138.389 168791.2949 145782.0022 1.295692471 1.386616733 1.067789294 1.180263429 1.320275214 1.038993232 1.269967391 1.157833562 1 17.15345309 7.999999971 0.026432694 0.000345027 2.897289513 0.355316683 0.103018088 1744.028824 3.54301601 130.603883 285.4496229 99999993.33 -7.999999971 2.896944486 LFQQIYSDGSDEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFQQIYSDGSDEVKR 15 1 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 266.45 4.18E-25 138900000 197570 152920 179870 204690 152100 207590 219000 229890 175600 FALSE TRUE 188231.2576 168502.7219 188117.2174 184114.1723 178626.1918 200401.1062 185587.5278 209759.6129 202831.1512 0.928019471 0.830753663 0.927457229 0.907721379 0.880664488 0.98801937 0.91498533 1.034158765 1 17.62991972 1.776297796 0.79531388 1.01015746 0.886447203 0.527554283 0.040945302 0.444345122 0.538288583 0.033672695 0.015475835 59.74448145 -1.776297796 -0.123710257 LFQVEYAIEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFQVEYAIEAIK 12 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 0 164.13 0.0001352 17714000 73620 60047 63547 57231 56919 63153 83301 68808 57255 FALSE TRUE 70140.1285 66165.85757 66460.69281 51478.03115 66845.65558 60965.99577 70591.90252 62782.80675 66133.81298 1.060578928 1.000484542 1.004942703 0.778392003 1.010763671 0.921858169 1.067410139 0.94932991 1 16.01310046 -0.556735935 7.6464801 0.999999995 0.981925028 0.001886015 0.082526924 0 0 0.07683698 0.01811065 0.277500688 0.556735935 -0.018074967 LFRPPS(ph)PAPAAPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;LFRPPS(1)PAPAAPGAR 113.49 0.00041239 5723760000 4138980 3465400 3674500 4190990 4302280 3809650 4479390 4113920 4547910 TRUE FALSE 3943338.618 3818528.2 3842979.46 3769703.723 5052596.27 3677720.865 3795976.786 3753683.356 5253176.655 0.750657912 0.726898875 0.731553441 0.717604598 0.961817316 0.700094649 0.722605965 0.714554945 1 22.32475867 -1.587133822 2.874386872 1.016191078 0.750750216 0.513431479 0.075464155 19447843.14 20047181.8 2395381.784 0.018052554 0.025874155 1.587133822 -0.265440862 LFRPWLNMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFRPWLNMDR 10 1 M0QZP4;B3KSI3;M0QZ10;M0QXF9;O15382-2;O15382;M0R2K7 M0QZP4 BCAT2 "Branched-chain-amino-acid aminotransferase;Branched-chain-amino-acid aminotransferase, mitochondrial" 0 ; 182.28 1.64E-06 265150000 527170 251060 131362 132103 573510 166735 444430 294660 470670 FALSE TRUE 502251.7189 276643.2994 137385.0776 118823.7555 673529.9624 160960.9251 376624.041 268858.0083 543659.0998 0.923835762 0.508854353 0.252704457 0.218562985 1.238882901 0.296069587 0.692757725 0.494534182 1 19.05234277 -1.354378958 3.096432811 1.004092564 0.587194152 0.149405268 0.315597893 96741214.16 127165024.4 3634530.211 0.069528986 0.044220235 1.354378958 -0.416898412 LFS(ph)TSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFSTSR 6 0 A0A0A0MRY4;Q96N96-6 A0A0A0MRY4 SPATA13 Spermatogenesis-associated protein 13 1 LFS(0.761)T(0.238)SR 73.26 0.087515 20492000 25715 21152 25179 32700 30141 27336 33862 28093 26367 TRUE FALSE 24499.50291 23307.41285 26333.48206 29412.93387 35397.58086 26389.34747 28695.72998 25633.02799 30455.8597 0.804426575 0.765285009 0.864644187 0.965756152 1.162258469 0.866478495 0.94220719 0.841645196 1 14.89443221 3.442056784 3.339791066 0.960988512 0.786529926 0.428558335 0.086018685 0.214419399 4.963705396 0.024139723 0.03534287 2767.303448 -3.442056784 -0.174458586 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LFSLS(0.908)NPS(0.092)LSTTNLSGPSR;LFSLS(0.997)NPS(0.003)LSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR 275.31 2.06E-39 160700000 383498 362114 311842 377429 374031 316609 385289 350908 394863 TRUE FALSE 365370.8096 399013.8283 326140.2642 339489.1199 439261.888 305644.7509 326506.0867 320180.6352 456096.3374 0.801082534 0.8748455 0.715068808 0.744336431 0.963090146 0.670132 0.715870881 0.702002207 1 18.79897906 LFSQDHLVIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFSQDHLVIYK 11 0 Q9BW91-2;Q9BW91;H7C386 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 87.618 0.010248 0 647790 509640 561110 615890 574600 574520 713270 652820 577740 FALSE TRUE 617170.2505 561572.8954 586837.4485 553979.5671 674810.0581 554624.2283 604447.5614 595655.62 667332.9685 0.924831051 0.841518285 0.879377277 0.830139665 1.011204436 0.831105692 0.905766072 0.892591327 1 19.34804725 -4.999990465 0.292025805 1.893493152 0.880969507 0.298618348 0.053343329 295.9742306 2.777455244 161.1524871 0.049959313 1.00E-05 4.999990465 -1.012523645 LFTEEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFTEEELAR 9 0 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 121.96 0.0013943 77896000 93824 79849 88229 95644 97936 83388 109354 90564 110881 FALSE TRUE 89389.12546 87985.70388 92274.38692 86029.68341 115016.0074 80500.25265 92670.03888 82633.73605 128075.8592 0.697938909 0.686981172 0.720466663 0.671708814 0.89803034 0.628535722 0.723555863 0.645193689 1 16.96663904 -1.297851378 3.145860924 1.001797324 0.708776497 0.607475428 0.073499786 16710040.09 22171211.37 282426.5904 0.01634417 0.050367294 1.297851378 -0.293020828 LFVGEPVWTAYNRPADHFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFVGEPVWTAYNRPADHFEAR 21 1 Q9BV57;Q9BV57-2;A0A0G2JQN5;H7C382 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ; 137.43 1.98E-06 192297000 230515 158313 227699 259110 224181 233536 302120 263378 275371 FALSE TRUE 219619.0128 174445.2747 238139.2244 233063.7705 263278.0954 225448.5898 256026.0452 240315.2261 318074.1283 0.690464874 0.5484422 0.74869096 0.732734133 0.82772559 0.708792604 0.804925715 0.755532138 1 18.2790035 -4.999999996 0.063637698 2.070808952 0.291572918 0.686154318 0.063943903 185.3287087 0.857085716 29.93387566 4.491615214 1.00E-05 4.999999996 -1.779236034 LFVGGIKEDTEEHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 295.09 7.17E-46 3311406000 4705588 3526448 4538679 4540992 3839172 4722933 5817541 5171244 982936.7 FALSE TRUE 4483164.181 3885797.06 4746781.922 4084522.857 4508722.381 4559376.646 4929968.274 4718422.461 1135365.503 3.948652806 3.422507597 4.180840362 3.597540039 3.971163795 4.015778736 4.342186071 4.155862097 1 20.11472538 2.74703642 20.73058979 3.796339166 3.766350027 0 0.98190273 3012.558654 7368268.832 0.265895384 0.27664024 558.5170306 -2.74703642 -0.029989139 LFVGGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFVGGLK 7 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 103.41 0.019501 131145000 664470 705540 520610 739670 502540 612580 672500 676980 535870 FALSE TRUE 633061.82 777435.3281 544480.4835 665316.9663 590182.8169 591366.201 569897.7737 617700.0423 618969.9828 1.022766592 1.256014588 0.879655716 1.074877595 0.953491822 0.955403683 0.920719566 0.9979483 1 19.23950992 3.732388252 24.99993155 0.965752458 1.139390591 0.469560372 0.075290642 347.4543258 1407295.25 0.018515149 0.029510267 5399.93152 -3.732388252 0.173638133 LFVGNLPADITEDEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 227 3.04E-15 1197167000 854654 716839 781569 865596 660320 839498 934300 956368 731447 FALSE TRUE 814256.1992 789885.7091 817404.7117 778584.6456 775479.5989 810425.9738 791755.3754 872623.3479 844876.065 0.963758157 0.934913109 0.967484754 0.921537108 0.917861958 0.959224681 0.937126057 1.032841838 1 19.6883802 1.243412439 24.99994099 1.016420932 0.943418214 0.734132816 0.018336017 51.94841019 267685.0738 0.012221851 0.004147447 17.51509264 -1.243412439 -0.073002718 LFVGNLPPDITEEEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFVGNLPPDITEEEMR 16 0 Q15233;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 122.39 0.00021767 17016000 50679 49115 47161 53943 50549 48628 56340 50369 54379 FALSE TRUE 48283.50411 54119.87434 49323.3785 48520.54715 59364.7296 46944.00017 47744.29824 45958.42334 62811.81759 0.768700954 0.861619301 0.785256348 0.772474815 0.945120391 0.747375286 0.760116489 0.731684341 1 15.9387484 -2.311352308 2.362268482 2.093339497 0.798986369 0.506594158 0.063061483 3606954.722 722724.7805 20997456.86 0.014804588 0.004882561 2.311352308 -1.294353128 LFVPALDKPETDLLSHLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LFVPALDKPETDLLSHLDR 19 1 V9GYV5;V9GY92;Q9UNI6 V9GYV5 DUSP12 Dual specificity protein phosphatase 12 0 132.14 8.55E-06 69330000 71420 71281 64270 78265 62614 73562 80286 76245 50245 FALSE TRUE 68044.11814 78544.61494 67216.84307 70397.65351 73533.86178 71014.52949 68036.89615 69568.5836 58036.73798 1.172431817 1.353360262 1.158177482 1.212984326 1.267022654 1.223613386 1.172307378 1.198699066 1 15.82467881 -0.201955741 0.410362891 0.95504468 1.248008833 0.616266838 0.05533892 3.610736352 0.701803804 0.299420809 0.034582243 0.628122368 0.201955741 0.292964153 LFVT(ph)PPEGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LFVTPPEGSSR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LFVT(0.999)PPEGS(0.001)SR;LFVT(0.901)PPEGS(0.05)S(0.05)R;LFVT(0.93)PPEGS(0.035)S(0.035)R;LFVT(0.997)PPEGS(0.003)SR 135.26 0.0013826 277677000 686670 744220 764060 887400 790460 752960 864800 816420 932330 TRUE FALSE 654212.4699 820056.8641 799092.9068 798196.8661 928315.9737 726884.8064 732858.8769 744929.9367 1076910.975 0.607489835 0.761489931 0.742023181 0.741191134 0.862017377 0.674972048 0.680519462 0.691728429 1 20.03846756 -2.051914859 2.566851102 1.383472946 0.717853668 0.635405298 0.066592861 13855738.26 4479633.405 31203365.34 0.016004291 0.0088733 2.051914859 -0.665619278 LFYSTFATDDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LFYSTFATDDRK 12 1 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 ; 269.81 2.09E-22 981410000 1083400 902300 960220 1108640 861130 960380 1206080 1174180 968900 FALSE TRUE 1032189.829 994245.3958 1004247.037 997197.4009 1011310.799 927121.7998 1022070.345 1071362.574 1119152.064 0.922296319 0.888391692 0.897328495 0.891029408 0.903640204 0.828414502 0.91325422 0.957298485 1 20.09397464 1.13440597 2.644476737 0.997377932 0.890968448 0.705851817 0.024367652 0.135521755 1.754213499 0.022040725 0.006043565 13.62717928 -1.13440597 -0.106409484 LGADES(ph)EEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGR;LGADES(1)EEEGR 226.42 4.99E-12 243270000 514750 638850 527490 657970 417360 608430 548190 589410 436500 TRUE FALSE 490418.7876 703949.5413 551675.9383 591829.6055 490147.4519 587359.9165 464553.5473 537798.1357 504190.1907 0.972686095 1.396198408 1.094182212 1.173822134 0.972147933 1.164957049 0.921385532 1.066657277 1 18.94360852 2.751599439 23.99638675 1.023685715 1.174378694 0.228736629 0.121015292 593.9803909 1093147.901 0.035200346 0.037099735 564.4161585 -2.751599439 0.150692978 LGADES(ph)EEEGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGADESEEEGRR 12 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGRR 83.061 0.00813 75613000 208520 215770 175050 214580 190810 189410 190880 210430 171140 TRUE FALSE 198663.6728 237757.2083 183076.2156 193010.0107 224087.2036 182850.6842 161757.7502 192003.6336 197679.5171 1.004978542 1.202740738 0.92612638 0.9763784 1.13358838 0.924985486 0.818282807 0.971287448 1 17.59280387 2.121967318 6.831321702 0.900653454 1.056532387 0.279210028 0.091382401 0.220170041 12.31409214 0.033919147 0.02498443 132.4241879 -2.121967318 0.155878933 LGADESEEEGRRGS(ph)LSNAGDPEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGADESEEEGRRGSLSNAGDPEIVK 25 2 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(0.441)EEEGRRGS(0.55)LS(0.008)NAGDPEIVK;LGADES(0.017)EEEGRRGS(0.981)LS(0.002)NAGDPEIVK;LGADES(0.072)EEEGRRGS(0.464)LS(0.464)NAGDPEIVK;LGADES(0.16)EEEGRRGS(0.568)LS(0.272)NAGDPEIVK;LGADESEEEGRRGS(0.998)LS(0.002)NAGDPEIVK;LGADES(0.005)EEEGRRGS(0.993)LS(0.002)NAGDPEIVK 152.31 6.66E-08 2742320000 1246938 692758 1380543 1152017 1163486 1276307 1882230 1537284 1707155 TRUE FALSE 1187997.712 763350.8278 1443842.262 1036214.062 1366397.59 1232108.169 1595061.244 1402671.263 1971891.878 0.602465949 0.387115965 0.732211678 0.525492332 0.692937379 0.624835561 0.808898937 0.711332745 1 20.91114902 1.268684742 0.304439995 1.047554297 0.469243603 0.660060802 0.095500595 0.836659403 0.273149712 0.18614669 0.136699255 18.56456347 -1.268684742 -0.578310694 LGADKEVWVWVMGEHHLDKPYDVLCNEIIAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGADKEVWVWVMGEHHLDKPYDVLCNEIIAER 32 2 Q9H788-2;Q9H788;H0YAT1 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 0 102.91 2.06E-06 109660000 333850 260160 302750 358030 238240 331960 429720 339520 78668 FALSE TRUE 318069.5721 286670.5998 316631.387 322040.1442 279788.9806 320464.142 364158.3217 309789.8289 90867.43166 3.500369344 3.1548223 3.484542054 3.54406566 3.079089785 3.526721688 4.007578018 3.409250413 1 16.47147568 2.771219042 23.83857856 3.29871878 3.388952377 0 0.816459645 5135.691104 3748716.687 0.224115047 0.237685653 590.4988304 -2.771219042 0.090233597 LGADVTAVEFLGHVGGVGIDMEISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGADVTAVEFLGHVGGVGIDMEISK 25 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;; 185.5 1.70E-17 120034000 207000 147005 168089 185299 178526 169962 218379 190323 175687 FALSE TRUE 197215.5202 161984.9766 175796.0469 166672.3925 209660.8779 164076.1733 185061.2727 173657.3092 202931.6427 0.971832276 0.79822434 0.866282087 0.821322837 1.033160108 0.808529272 0.911938968 0.855742884 1 17.63063431 LGAGEGGEASVS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEAS(0.002)VS(0.998)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK 319.74 1.69E-56 3087400000 3825160 4275460 3039620 4468980 1987300 4033620 3396190 4011430 1906820 TRUE FALSE 3644352.268 4711134.235 3178989.584 4019749.64 2333884.491 3893934.728 2878038.84 3660167.923 2202519.907 1.654628526 2.138974644 1.443342044 1.825068471 1.059642859 1.767945305 1.306702759 1.661809236 1 21.07072363 2.271558813 0.069502021 1.38E-10 3.091176551 0.352257922 0.282145955 30.48559672 1.25638149 24.05232257 30.1132108 186.8782734 -2.271558813 3.091176551 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEAS(0.003)VS(0.997)PEKTSTTSK;LGAGEGGEAS(0.179)VS(0.806)PEKT(0.009)S(0.003)T(0.002)T(0.001)S(0.001)K;LGAGEGGEAS(0.004)VS(0.996)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEAS(0.001)VS(0.999)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(0.999)PEKTSTTSK 283.4 2.25E-45 14391210000 7936407 6580745 7365308 7803690 3953623 8586190 9129686 9330950 4567350 TRUE FALSE 7561268.77 7251330.397 7703014.657 7019248.255 4643133.599 8288848.087 7736784.723 8513882.552 5275631.311 1.43324435 1.374495292 1.460112393 1.330503942 0.880109569 1.571157573 1.466513535 1.61381303 1 22.33091231 LGAGGGS(ph)PEKS(ph)PSAQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 LGAGGGS(1)PEKS(0.845)PS(0.155)AQELK;LGAGGGS(1)PEKS(0.976)PS(0.024)AQELK;LGAGGGS(1)PEKS(0.62)PS(0.38)AQELK;LGAGGGS(1)PEKS(0.602)PS(0.398)AQELK 157.3 3.06E-09 1269250000 2499400 2508120 2235810 2821820 1074170 2916480 2656480 3136050 1233300 TRUE FALSE 2381258.315 2763700.279 2338324.1 2538165.292 1261504.908 2815481.566 2251185.186 2861440.837 1424553.865 1.671581801 1.940046177 1.641443091 1.781726444 0.885543846 1.976395302 1.580273826 2.008657522 1 20.44207874 2.902512361 18.91964178 1.546773689 1.773047155 0.10742716 0.363755792 15.49208199 2997.060442 0.101785707 0.107960538 798.9366806 -2.902512361 0.226273466 LGAGGGS(ph)PEKSPSAQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.979)PEKS(0.02)PS(0.001)AQELK;LGAGGGS(1)PEKSPSAQELK;LGAGGGS(0.994)PEKS(0.006)PSAQELK;LGAGGGS(0.958)PEKS(0.042)PSAQELK 295.84 6.72E-49 3572020000 5176820 5081190 5050550 6437020 2961613 6711230 6861800 7357190 3387359 TRUE FALSE 4932121.978 5598969.038 5282122.713 5789958.52 3478117.37 6478818.422 5814906.384 6712955.441 3912653.333 1.260556854 1.430990318 1.350010405 1.479803608 0.888940847 1.655863137 1.486179809 1.715704119 1 21.89971586 LGAGGGSPEKS(ph)PSAQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGSPEKS(0.97)PS(0.03)AQELK 119.27 4.76E-05 803750000 521260 395680 460530 550630 254370 484880 508530 562380 264760 TRUE FALSE 496621.0728 436000.2419 481645.756 495279.6263 298732.0475 468088.484 430944.4087 513135.0258 305817.6286 1.62391251 1.42568708 1.574944382 1.619526083 0.976830698 1.530613151 1.409154896 1.677911859 1 18.22231205 -1.966970044 2.859892585 0.619402974 1.47307601 0.366942845 0.197887655 12170262.8 10303493.64 30324034.02 0.046719091 0.010790211 1.966970044 0.853673036 LGAPENSGIST(ph)LER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGAPENSGISTLER 14 0 A0A1B0GV68;M0QYB0;Q9Y4F1-3;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 LGAPENSGIS(0.016)T(0.984)LER;LGAPENSGIS(0.017)T(0.983)LER;LGAPENSGIS(0.015)T(0.985)LER 170.11 3.61E-05 416310000 614900 473680 542030 742830 754420 461120 676310 650920 694490 TRUE FALSE 585834.8956 521948.5305 566882.6116 668159.3171 885990.6091 445151.2988 573126.4882 593921.9941 802187.9622 0.730296294 0.650656149 0.706670554 0.832921146 1.104467595 0.55492144 0.714454112 0.740377595 1 19.61358079 -2.615110612 1.977881324 5.218587963 0.743873104 0.222106544 0.14329307 4251727.591 145617.7784 80895847.23 0.034814501 0.002425992 2.615110612 -4.474714859 LGASNS(ph)PGQPNSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;LGAS(0.001)NS(0.999)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK;LGASNS(1)PGQPNSVK 362.17 9.00E-83 21244140000 16330260 14837090 14258120 17008850 10886270 16265340 17609920 16555550 12214730 TRUE FALSE 15558360.97 16349006.34 14911868.91 15299088.08 12784832.04 15702067.2 14923203.28 15105858.28 14108927.94 1.10273162 1.158770277 1.056910133 1.084355108 0.906151913 1.112917102 1.05771348 1.070659538 1 23.75010503 3.615778729 4.475768217 1.043566146 1.130426709 0.295272077 0.057593386 0.259685053 8.286820994 0.014681672 0.023221083 4128.371094 -3.615778729 0.086860563 LGASNS(ph)PGQPNSVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGASNSPGQPNSVKR 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 LGAS(0.008)NS(0.992)PGQPNSVKR;LGASNS(1)PGQPNSVKR;LGAS(0.001)NS(0.999)PGQPNSVKR;LGAS(0.215)NS(0.785)PGQPNSVKR;LGAS(0.001)NS(0.999)PGQPNSVKR;LGASNS(1)PGQPNSVKR 154.46 1.52E-06 4306670000 5797780 4202110 5523890 5462590 4731210 5729270 7441060 6276620 6196170 TRUE FALSE 5523730.429 4630309.786 5777165.82 4913480.075 5556331.526 5530863.943 6305789.633 5727005.878 7157040.398 0.771789751 0.646958733 0.807200393 0.68652401 0.77634486 0.772786464 0.881061065 0.800191917 1 22.77093169 1.070812945 0.447340405 1.007098229 0.708556037 0.698257517 0.053274776 0.542043877 0.292019866 0.062320504 0.033122852 11.77098876 -1.070812945 -0.298542192 LGCEVLGVSVDSQFTHLAWINTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGCEVLGVSVDSQFTHLAWINTPR 24 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 388.09 2.87E-137 1210579000 1364376 1264519 1276799 1480630 1490069 1264943 1548847 1425030 1469371 FALSE TRUE 1299884.65 1393374.924 1335341.497 1331794.259 1749936.562 1221137.707 1312541.944 1300246.819 1697233.55 0.765884371 0.820968289 0.786775336 0.784685325 1.031052304 0.719487136 0.773341974 0.766097759 1 20.69475367 -2.28750305 2.213059414 1.847081504 0.804295823 0.344898035 0.083979629 3989425.002 607225.4252 16898235.91 0.019485402 0.005158185 2.28750305 -1.042785681 LGDAS(ph)DTEAADGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 LGDAS(0.873)DT(0.127)EAADGER;LGDAS(1)DTEAADGER 342.38 4.13E-69 431640000 724290 612260 632060 725980 575230 655610 684630 665320 553940 TRUE FALSE 690054.2471 674649.9901 661040.5762 653003.1111 675549.9299 632906.0613 580177.1194 607061.0537 639842.1861 1.078475696 1.054400608 1.033130654 1.020569017 1.055807111 0.989159632 0.906750339 0.948766847 1 19.28735659 2.059586616 3.843403126 0.94226314 1.049801001 0.721614015 0.027443557 0.101024686 3.036683393 0.011183291 0.007556136 114.706127 -2.059586616 0.107537861 LGDDIDLIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGDDIDLIVR 10 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;; 113.66 0.0033941 89963000 248941 267721 214552 283250 216586 224069 259698 255868 225571 FALSE TRUE 237174.0523 295002.0743 224389.4214 254777.1719 254358.5298 216309.4343 220076.3004 233462.8415 260551.3986 0.91027741 1.132222187 0.861209814 0.977838435 0.976231681 0.830198707 0.844655993 0.89603373 1 17.99120847 2.286929788 9.519192281 0.874305278 0.983335704 0.160355646 0.082726388 0.448234302 84.10839636 0.027489853 0.02292751 193.610893 -2.286929788 0.109030426 LGDS(ph)SGPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGDSSGPALK 10 0 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 LGDS(0.841)S(0.159)GPALK 74.611 0.029102 0 80765 76507 60140 114300 60122 90560 94566 58452 32166 TRUE FALSE 76947.39851 84303.15028 62897.47849 102810.3468 70607.25776 87423.88449 80138.21988 53333.63301 37154.139 2.071031669 2.269011005 1.692879453 2.767130382 1.900387404 2.35300526 2.156912313 1.435469491 1 15.18123532 1.099227749 3.066431466 1.011118125 2.183237126 0.67867557 0.281793858 0.115800683 2.086102269 0.23075147 0.061443143 12.56688812 -1.099227749 1.172119001 LGDS(ph)SLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.5)S(0.5)LSR;LGDS(0.5)S(0.5)LSR;LGDS(0.5)S(0.5)LSR 116.37 0.002396 548164000 1527320 1377440 1512930 1814740 1393160 1689520 1878840 1800160 1710880 TRUE FALSE 1455126.61 1517802.702 1582299.337 1632318.887 1636126.663 1631011.499 1592188.451 1642528.447 1976194.532 0.736327617 0.768043164 0.800679949 0.825990995 0.827917817 0.825329426 0.805684068 0.831157267 1 20.91429354 -5 0.129584727 1.673554183 0.711982806 0.913776128 0.020235848 43.22605088 0.353791888 7.571220924 0.174900043 1.00E-05 5 -0.961571377 LGDSHDLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGDSHDLQR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 126.55 0.00047044 353530000 597600 549700 491430 614330 574120 517960 673400 614810 542090 FALSE TRUE 569352.6323 605715.055 513962.5516 552576.3812 674246.3462 500022.9153 570660.4622 560973.9771 626154.5486 0.909284511 0.967357111 0.820823793 0.882492002 1.076804996 0.7985615 0.91137318 0.895903381 1 19.25615926 LGDSS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.114)S(0.886)LSR;LGDS(0.099)S(0.901)LSR 134.05 0.00093686 464593000 1365990 1348600 1301270 1612830 1304410 1485020 1619750 1612220 1501790 TRUE FALSE 1301422.36 1486023.873 1360934.517 1450705.264 1531898.691 1433593.385 1372627.389 1471045.47 1734679.923 0.750237748 0.856655948 0.784545032 0.836295644 0.883101643 0.82643107 0.791285684 0.848021269 1 20.72623806 -5 0.280495905 2.318851196 0.808119646 0.699351704 0.037220984 130.3308695 1.246698872 100.1188621 0.041668547 1.00E-05 5 -1.510731549 LGDTALHAAAWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGDTALHAAAWK 12 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 0 103.91 0.0011379 0 682530 536580 427680 588340 549410 539750 779090 670560 551220 FALSE TRUE 650268.1595 591258.112 447289.551 529198.9454 645226.9301 521058.3222 660225.5115 611842.2115 636700.3824 1.021309516 0.928628486 0.70251183 0.831158517 1.013391774 0.818372875 1.036948508 0.96095782 1 19.28025511 1.699767007 10.33583522 0.99814085 0.897060399 0.234606072 0.095041033 0.200020836 39.06935654 0.04683274 0.025353838 50.09184254 -1.699767007 -0.101080451 LGDVGMAELCPGLLHPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGDVGMAELCPGLLHPSSR 19 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;; 191.21 1.01E-14 661580000 259685 213777 233403 257042 267592 209297 306527 263450 302679 FALSE TRUE 247410.2047 235561.1193 244104.7584 231203.6498 314259.9601 202048.9924 259760.6764 240380.9214 349616.9134 0.707660857 0.673769232 0.698206377 0.661305677 0.898869442 0.577915383 0.742986584 0.687555184 1 18.41541545 -2.074772769 2.326154798 1.4409663 0.704559903 0.567912874 0.080574176 5970321.152 1747602.193 13969322.85 0.017241379 0.008418355 2.074772769 -0.736406397 LGDVYVNDAFGTAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;; 242.19 6.48E-18 37689460000 19860560 16523080 17393980 19702810 19318270 17845470 21946560 19383250 18663330 FALSE TRUE 18921790.69 18206800.64 18191511.19 17722246.11 22687370.17 17227476.9 18598209.2 17685949.87 21557543.9 0.877734067 0.844567485 0.843858246 0.822090225 1.052409787 0.799139131 0.862723939 0.820406534 1 24.36168948 -2.352857301 2.355633713 1.916847294 0.864773212 0.266567225 0.070177116 8839840.364 1492767.406 42970858.99 0.015466227 0.004437544 2.352857301 -1.052074082 LGEDLNKWQALLVQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGEDLNKWQALLVQIR 16 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 92.977 0.0041848 57829000 89803 61176 63503 73021 77655 69921 89273 75048 70137 FALSE TRUE 85558.19016 67409.90395 66414.67536 65680.79035 91198.00741 67499.61824 75652.76424 68476.39927 81013.48775 1.056098096 0.832082482 0.819797755 0.810738954 1.125713877 0.833189881 0.933829247 0.845246899 1 16.3058745 4.671567089 3.5195843 0.897653225 1.064360072 0.194986551 0.099283839 0.393852634 8.100205151 0.022282896 0.153921351 46942.59442 -4.671567089 0.166706848 LGEESIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGEESIR 7 0 Q02487-2;J3QRL9;Q14574-2;Q08554-2 Q02487-2 DSC2;DSC3 Desmocollin-2 0 ; 113.25 0.014357 313190000 632190 521210 504010 546690 672530 434360 557540 535610 646140 FALSE TRUE 602307.6316 574321.8916 527119.357 491735.6826 789819.0191 419318.0043 472477.0331 488709.149 746340.0912 0.807014977 0.769517675 0.706272333 0.658862747 1.058256187 0.561832346 0.633058627 0.65480758 1 19.50947366 LGEGT(ph)YAT(ph)VYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGEGTYATVYK 11 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5;Q00537;Q00537-2;F5H6Z0 E5RJM2;Q00537 CDK16;CDK17 Cyclin-dependent kinase 16;Cyclin-dependent kinase 17 2 LGEGT(0.998)Y(0.018)AT(0.982)VY(0.002)K 71.085 0.077759 325890000 151300 191840 158670 193640 463520 98034 160210 95324 317300 TRUE FALSE 144148.3488 211388.7141 165945.1764 174174.9393 544357.7412 94639.058 135767.022 86976.92522 366505.2635 0.39330499 0.576768563 0.452777062 0.475231754 1.485265822 0.258220188 0.370436759 0.23731426 1 18.48347439 LGEMWNNTAADDKQPYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LGEMWNNTAADDKQPYEK 18 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;;; 257.83 1.12E-30 1418330000 1801740 1849560 1458650 1968290 871457 1794520 1630480 1869110 768797 FALSE TRUE 1716575.321 2038032.267 1525530.545 1770433.75 1023438.825 1732375.322 1381720.33 1705440.82 888018.1123 1.933040889 2.29503457 1.717904764 1.993691035 1.152497692 1.95083332 1.555959626 1.920502292 1 19.76022958 -0.544344764 0.10415361 1.14E-09 2.639293173 0.449789561 0.293768711 33.48109944 0.855772533 16.15418829 6.140609317 0.285532295 0.544344764 2.639293172 LGEMWNNTAADDKQPYEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGEMWNNTAADDKQPYEKK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 218.25 1.92E-19 211170000 228720 230400 223220 273420 111900 272550 280320 297470 146690 FALSE TRUE 217908.8589 253878.0219 233454.8578 245935.3021 131415.3246 263111.5252 237552.0356 271421.9498 169437.936 1.286068893 1.498354075 1.377819296 1.451477207 0.775595641 1.552848974 1.402000291 1.601895987 1 17.37039739 LGETDEEKLFVETGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGETDEEKLFVETGK 15 1 J3QLR8;Q9Y3D9 J3QLR8 MRPS23 "28S ribosomal protein S23, mitochondrial" 0 87.148 0.006642 69206000 44544 29745 40305 39398 30523 42990 61598 45435 18436 FALSE TRUE 42438.4934 32776.04932 42153.02412 35437.63819 35846.20154 41501.24552 52200.09378 41456.47053 21294.96072 1.99288902 1.539145798 1.979483535 1.664132592 1.683318509 1.948876359 2.451288568 1.94677375 1 14.37822445 2.095338963 6.385137305 2.018260343 1.76624342 0 0.393807009 0.523477604 29.45463381 0.134681974 0.09891764 124.5486324 -2.095338963 -0.252016924 LGETYKDHENIVIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGETYKDHENIVIAK 15 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 164.15 9.00E-07 3881100000 9881900 8419300 8607600 10457900 5280300 9776500 10055100 10752000 4951200 FALSE TRUE 9414802.171 9277236.242 9002266.974 9406652.023 6201182.648 9437937.354 8521009.82 9810497.88 5719006.809 1.646230278 1.622176114 1.574096215 1.64480518 1.084311115 1.650275593 1.489945738 1.715419864 1 22.44733319 -2.029691146 2.744339995 0.331651466 1.554007207 0.491326195 0.176961978 36739254.75 31633684.21 153726772.8 0.042548811 0.009339182 2.029691146 1.222355741 LGEVVNTHGPVEPDKDNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGEVVNTHGPVEPDKDNIR 19 1 P30419;P30419-2;K7EN82 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 231.77 1.57E-20 257950000 501040 457950 435550 544080 326770 515730 530940 564930 321990 FALSE TRUE 477356.8322 504615.6256 455520.3983 489388.0447 383758.5845 497870.1408 449935.3516 515461.7343 371922.5647 1.28348446 1.356776043 1.224772148 1.315833163 1.031823882 1.338639244 1.209755455 1.38593832 1 18.50464275 -1.875451214 2.695095144 0.875826185 1.268976164 0.414720325 0.100194407 14718646.93 11819954.84 11757274.37 0.021922898 0.013321367 1.875451214 0.393149979 LGEWVGLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGEWVGLCK 9 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 90.709 0.026165 269860000 260760 239280 230640 281020 243250 231590 303900 290070 244520 FALSE TRUE 248434.3916 263662.904 241215.0721 252771.3357 285672.723 223569.9802 257534.4735 264669.933 282438.9128 0.879603979 0.933521877 0.854043339 0.894959314 1.011449592 0.791569327 0.911823626 0.937087353 1 18.10757934 0.959891995 2.739431288 0.999364478 0.897178476 0.264955875 0.055654348 0.377821326 6.697724353 0.048136001 0.012811659 9.117840593 -0.959891995 -0.102186002 LGEYEDVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGEYEDVSR 9 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42;K7EL99 K7EP07 TBCB Tubulin-folding cofactor B 0 ; 170.24 0.0001346 223360000 483340 414790 425510 512360 421710 446110 509400 495300 469880 FALSE TRUE 460493.4761 457057.5726 445020.0544 460856.5994 495256.0905 430661.0988 431681.6742 451928.9062 542746.5906 0.848450242 0.842119657 0.819940764 0.84911929 0.91249968 0.793484669 0.795365059 0.832670189 1 19.04991923 -1.873866209 2.482172356 1.080164796 0.835122429 0.703929458 0.033267587 10137977.66 6021416.273 4785701.691 0.008362575 0.013370073 1.873866209 -0.245042367 LGFDKENVYDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGFDKENVYDELR 13 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 154.72 4.23E-05 562580000 1625240 1397590 1420380 1637910 1538620 1399950 1829530 1674130 1772780 FALSE TRUE 1548418.126 1540006.01 1485505.828 1473264.175 1806954.841 1351469.38 1550401.597 1527534.302 2047693.668 0.756176644 0.752068551 0.725453153 0.719474889 0.882434159 0.659995878 0.757145281 0.745977939 1 20.96556848 -1.250063446 5.326025856 1.000025408 0.749304379 0.670899171 0.055061218 1.47E-05 2.07E-06 0.04710155 0.011100818 0.056225918 1.250063446 -0.250721029 LGFHLPLEVAYQR ddPTM_SK-BR-3_Trastuzumab_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 ; 134.98 8.93E-05 1358510000 1824730 1478820 1382560 1514080 1980970 1441690 2032970 1691730 1809150 FALSE TRUE 1738478.629 1629513.439 1445951.744 1361881.802 2326450.541 1391763.914 1722803.088 1543593.153 2089703.742 0.831925882 0.779782036 0.691941022 0.651710467 1.113292039 0.666010155 0.82442456 0.738666023 1 20.99486699 LGFVDVQNCIS(ph)R ddPTM_SK-BR-3_Trastuzumab_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 118.51 0.00064834 345075000 530890 451994 490472 662010 697850 579910 680610 568240 662200 TRUE FALSE 505795.8818 498052.7025 512960.6263 595463.4971 819554.8191 559827.5713 576770.4442 518481.8932 764890.594 0.661265658 0.651142407 0.670632677 0.778494992 1.071466724 0.73190542 0.754056134 0.677851051 1 19.54489388 3.184106682 4.364531005 0.825160904 0.657826736 0.327249381 0.118979477 0.257395211 10.06783351 0.033993435 0.042200847 1527.941344 -3.184106682 -0.167334168 LGGAVPFAPPEVS(ph)PEQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGGAVPFAPPEVSPEQAK 18 0 A0A096LNZ0;A0A096LP25;Q6ZSR9 A0A096LNZ0;A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK 288.92 3.67E-41 164937000 385500 416310 396260 475960 281560 441200 496640 487410 354740 TRUE FALSE 367278.179 458732.4623 414428.913 428115.5965 330663.9749 425921.1334 420868.4466 444729.7965 409751.2674 0.896344217 1.119538849 1.011415817 1.044818236 0.80698707 1.039462638 1.027131531 1.085365274 1 18.64438889 LGGHGPSFPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGGHGPSFPLK 11 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 143.96 3.69E-05 1382210000 5226400 4491300 3393700 3879800 4253400 4055800 5546600 5057300 4210900 FALSE TRUE 4979358.43 4948968.576 3549304.502 3489795.133 4995191.613 3915346.629 4700364.3 4614456.002 4863904.866 1.023736806 1.017488769 0.729723257 0.717488362 1.026992047 0.804980101 0.966376693 0.94871428 1 22.21368358 1.596678659 25 0.968177404 0.903812101 0.096337219 0.114825154 2.841732853 6333.323853 0.065042495 0.030543384 39.50741907 -1.596678659 -0.064365303 LGGLRPES(ph)PESLTSVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.8)PES(0.029)LT(0.062)S(0.062)VS(0.047)R;LGGLRPES(0.741)PES(0.094)LT(0.094)S(0.004)VS(0.067)R;LGGLRPES(0.24)PES(0.24)LT(0.042)S(0.24)VS(0.24)R;LGGLRPES(0.996)PES(0.002)LT(0.002)SVSR;LGGLRPES(0.942)PES(0.056)LT(0.001)SVSR;LGGLRPES(1)PESLTSVSR;LGGLRPES(0.999)PES(0.001)LTSVSR;LGGLRPES(0.955)PES(0.045)LTSVSR 223.06 8.32E-15 8451857000 2670417 2464212 2428611 2766239 2342689 2465459 2744788 2451677 2426344 TRUE FALSE 2544191.681 2715318.004 2539965.217 2488171.4 2751253.22 2380079.537 2326020.179 2236995.165 2802609.035 0.907794005 0.968853654 0.906285959 0.887805387 0.981675712 0.849237088 0.829948148 0.798183099 1 21.41833907 2.21372513 24.96862165 0.852256661 0.93061293 0.181143047 0.059882837 264.8286334 266246.6182 0.020004756 0.01478069 163.5780891 -2.21372513 0.078356269 LGGLRPESPESLT(ph)SVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPESPESLT(0.474)S(0.474)VS(0.052)R 228.2 9.60E-15 1556800000 504060 501340 464090 520120 467910 490130 527160 491920 489970 TRUE FALSE 480234.0828 552427.116 485368.9855 467836.5494 549513.3559 473156.6752 446732.06 448844.877 565952.0452 0.848542004 0.976102341 0.857615039 0.826636379 0.970953918 0.836036691 0.789346136 0.793079344 1 19.11032029 2.044437842 24.99915929 0.831224573 0.89817432 0.029883283 0.076223175 229.9971417 129387.2877 0.026098175 0.019274767 110.774001 -2.044437842 0.066949746 LGGLRPESPESLTSVS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.108)PES(0.003)LT(0.001)S(0.001)VS(0.887)R 134.14 4.72E-05 166270000 212920 206410 183590 237080 201690 199700 221100 221170 234270 TRUE FALSE 202855.6936 227443.4137 192007.7831 213248.268 236864.6721 192784.3389 187367.1342 201803.1823 270599.3951 0.749653167 0.840517081 0.709564717 0.788058923 0.875333339 0.712434478 0.6924152 0.745763612 1 18.04579909 LGGPEGPGS(ph)PLLAT ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGGPEGPGSPLLAT 14 0 Q9C086 Q9C086 INO80B INO80 complex subunit B 1 LGGPEGPGS(1)PLLAT;LGGPEGPGS(1)PLLAT 142.1 9.96E-06 135577000 427880 370910 371260 440890 385890 384890 465270 447140 477910 TRUE FALSE 407654.9604 408706.1507 388282.6382 396570.8996 453189.0938 371561.1628 394284.5162 407986.0512 552021.842 0.738476142 0.740380397 0.703382744 0.718397117 0.820962251 0.673091415 0.714255282 0.739075921 1 19.07436583 0.926252022 19.43685394 1 0.729471253 0.834353301 0.037689018 1051.244067 277064.9165 0.034009597 0.008502399 8.438242895 -0.926252022 -0.270528747 LGGS(ph)AVISLEGKPL ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 1 LGGS(0.999)AVIS(0.001)LEGKPL;LGGS(0.982)AVIS(0.018)LEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(1)AVISLEGKPL;LGGS(0.997)AVIS(0.003)LEGKPL 174.59 6.62E-06 541010000 2251480 1858556 1912114 2307300 1840401 2263400 2616030 2339120 1975696 TRUE FALSE 2145057.002 2047944.969 1999786.318 2075365.82 2161366.352 2185017.89 2216906.577 2134294.252 2282076.845 0.93995827 0.897404035 0.876301042 0.909419779 0.947104983 0.957469024 0.971442562 0.935242061 1 21.12191594 2.606606029 2.708196472 0.963919928 0.906231935 0.629298311 0.021953339 0.190712585 2.724427188 0.007713431 0.007105261 404.2090467 -2.606606029 -0.057687992 LGGS(ph)LIVAFEGCPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGGSLIVAFEGCPV 14 0 P60981;P60981-2 P60981 DSTN Destrin 1 LGGS(1)LIVAFEGCPV;LGGS(1)LIVAFEGCPV;LGGS(1)LIVAFEGCPV 125.56 9.49E-05 54401200 129173 103926 129643 146515 143916 135668 171808 144567 148998 TRUE FALSE 123067.2483 114516.1776 135587.2598 131787.0338 169014.9048 130969.7831 145595.5341 131907.9471 172103.8489 0.715075515 0.665389986 0.787822357 0.765741352 0.98205186 0.760992761 0.845974887 0.766443911 1 17.39291984 6.308883482 0.064354945 1.256410085 1.63E-12 0.489883699 0.076654244 165.0738868 1.104535544 5.231319264 20.88465042 2036495.63 -6.308883482 -1.256410085 LGGSLADSYLDEGFLLDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGGSLADSYLDEGFLLDKK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 226.65 2.33E-19 344290000 792680 653500 685990 765570 477680 790640 914140 894190 577430 FALSE TRUE 755211.5873 720092.393 717443.32 688613.4491 560987.2408 763259.9386 774671.1537 815889.9832 666974.8953 1.132293873 1.079639426 1.075667653 1.032442831 0.841091988 1.144360821 1.161469733 1.223269405 1 19.34727293 2.057802448 24.99999567 1.147876778 1.045019869 0.205255769 0.09382944 120.0499758 51921.76254 0.034707938 0.025633508 114.2358581 -2.057802448 -0.102856909 LGGSPTSLGTWGSWIGPDHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDK 21 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 302.49 3.16E-55 815810000 1459820 1741290 1163970 1747460 902690 1439880 1257290 1468160 724160 FALSE TRUE 1390817.202 1918729.431 1217339.176 1571802.001 1060118.85 1390016.595 1065467.319 1339600.127 836459.0343 1.662743954 2.29387137 1.455348231 1.879114142 1.267388846 1.661786815 1.273783025 1.601513131 1 19.67393536 2.209518956 0.28906368 0.98916462 2.105120365 0.440021699 0.268050235 1.532082474 0.359997866 0.40434906 0.616761948 162.0014702 -2.209518956 1.115955745 LGGSPTSLGTWGSWIGPDHDKFSAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGGSPTSLGTWGSWIGPDHDKFSAMK 26 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;; 358.45 1.55E-110 1256130000 2112260 1488684 1757495 2073087 1445259 1937060 2416420 2237640 1381917 FALSE TRUE 2012417.656 1640382.592 1838077.884 1864696.356 1697311.712 1869979.126 2047750.748 2041700.379 1596217.631 1.260741404 1.027668509 1.151520851 1.168196818 1.06333352 1.171506373 1.282876914 1.279086473 1 20.60622593 1.995986884 24.70797232 1.220861841 1.132226213 0.023291119 0.099931514 262.849766 1618317.047 0.034727193 0.025047005 99.08020207 -1.995986884 -0.088635628 LGGSVLGQIPFLQNCEDEDS(ph)DEDDELDSVQHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGGSVLGQIPFLQNCEDEDSDEDDELDSVQHKK 33 1 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;Q9NRL3-2 F5GYK2 STRN4 Striatin-4 1 LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK;LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK 277.44 5.48E-74 389030000 795360 564870 728120 776760 449060 787610 938940 875410 467330 TRUE FALSE 757764.9091 622430.8952 761505.0222 698678.6091 527375.9218 760334.8682 795687.4582 798754.4596 539801.1496 1.403785282 1.153074416 1.410713969 1.2943259 0.976981843 1.408546219 1.474038095 1.479719819 1 19.04206852 LGGVKYDIDLPNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGGVKYDIDLPNKK 14 2 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 99.927 0.0011175 1139700000 3021100 2133100 2987900 2579100 1969600 3079600 4047200 3500700 2372400 FALSE TRUE 2878298.59 2350465.315 3124898.17 2319843.968 2313097.616 2972952.68 3429725.308 3194160.15 2740299.675 1.05035906 0.857740245 1.140349064 0.846565793 0.84410389 1.08490057 1.251587678 1.165624394 1 21.38590224 2.031074677 7.159016452 1.167569365 0.949672014 0.384449093 0.111504585 0.154091013 26.29029336 0.039486109 0.028682866 107.4174101 -2.031074677 -0.217897351 LGHAEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGHAEQK 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 97.068 0.012269 347276000 1162620 1328670 986960 1418100 1111570 1080350 1146030 1160450 1054530 FALSE TRUE 1107665.257 1464062.984 1032213.092 1275549.894 1305427.456 1042937.209 971182.0752 1058834.846 1218061.127 0.909367545 1.201961832 0.847423064 1.047196948 1.071725735 0.856227316 0.797318011 0.869278908 1 20.2161551 2.22861683 24.67915985 0.856420042 1.025102998 0.266982832 0.107071823 179.9417693 446587.7217 0.037339301 0.027914431 169.2843577 -2.22861683 0.168682956 LGHDPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGHDPYR 7 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 0 ;;; 110.63 0.0067597 499830000 505542 423908 437897 528486 531220 451024 554827 502308 465422 FALSE TRUE 481646.0315 467104.7071 457975.0106 475361.5832 623864.5998 435404.9258 470177.9511 458323.2486 537597.2667 0.895923513 0.868874781 0.851892372 0.884233631 1.160468325 0.809909114 0.874591409 0.852540139 1 19.03616628 LGHDPYRLT(ph)PDPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGHDPYRLTPDPYR 14 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 1 LGHDPY(0.009)RLT(0.991)PDPYR 79.805 0.026479 39056000 39081 33059 34101 36577 38498 34432 37471 36230 31673 TRUE FALSE 37233.71858 36427.74968 35664.56458 32900.21047 45212.03901 33239.61121 31754.11075 33057.50913 36584.68708 1.017740524 0.995710298 0.974849518 0.899289104 1.235818661 0.90856623 0.867961797 0.903588681 1 15.1589523 2.054700673 24.99997808 0.903945018 1.017139992 0.236264207 0.090969316 111.8666197 51126.03168 0.031465534 0.023238834 113.4228807 -2.054700673 0.113194973 LGHEEQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGHEEQQKR 9 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 126.07 0.00031413 282660000 201930 147592 179181 203632 179883 189230 254135 211166 198392 FALSE TRUE 192385.1691 162631.7926 187396.6261 183162.5245 211254.5382 182676.9177 215362.0382 192675.1856 229157.6181 0.839532068 0.709694026 0.817763021 0.799286212 0.921874385 0.797167116 0.939798729 0.840797645 1 17.80598072 1.52680132 0.327189918 1.008432324 0.75646572 0.520300354 0.057478236 0.936679985 0.342694506 0.087498518 0.076355996 33.63576581 -1.52680132 -0.251966604 LGHELQQAGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGHELQQAGLK 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 73.499 0.031737 0 282460 191500 241400 201760 256970 246860 309340 326190 264120 FALSE TRUE 269108.6756 211014.0677 252468.4288 181478.7015 301785.4866 238311.1763 262144.5016 297627.0744 305078.3807 0.88209684 0.691671653 0.827552671 0.594859266 0.9892064 0.781147375 0.859269349 0.975575764 1 18.21882042 1.405275794 0.864533738 1.008599977 0.774568811 0.367423268 0.104008615 0.547925288 0.858630122 0.087396793 0.033583288 25.42586837 -1.405275794 -0.234031166 LGHPDTLNQGEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGHPDTLNQGEFK 13 0 P06702 P06702 S100A9 Protein S100-A9 0 ; 223.03 1.65E-11 2138750000 3562100 2297900 2539600 3282000 2571900 2980900 3855400 3518200 2659900 FALSE TRUE 3393726.592 2532058.622 2656043.172 2952087.125 3020438.546 2877670.686 3267187.921 3210127.757 3072383.707 1.10459074 0.824134895 0.864489408 0.960845847 0.98309288 0.936624771 1.06340491 1.044832958 1 21.55092697 1.754095176 9.64812416 1.039659155 0.94272344 0.243324366 0.074950789 0.183466464 72.83466375 0.035868446 0.019522919 56.76689974 -1.754095176 -0.096935715 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 LGHPEALSAGT(0.005)GS(0.995)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR;LGHPEALSAGT(0.003)GS(0.997)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR 321.87 3.28E-75 4493470000 831638 817630 876417 963972 943536 878626 1074909 956090 986966 TRUE FALSE 792328.1199 900947.4266 916601.5863 867071.7031 1108088.38 848198.9613 910911.89 872369.691 1140019.647 0.695012689 0.79029114 0.804022623 0.760576106 0.971990599 0.744021354 0.799031747 0.765223383 1 20.12062726 -5 0.190754585 1.877590257 0.751190561 0.454756315 0.071645724 125.3533841 1.227131752 42.10376781 0.183844391 1.00E-05 5 -1.126399696 LGHPEPNHVTEASELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGHPEPNHVTEASELLR 17 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 146.3 2.56E-07 85718000 54030 41368 41908 52432 49908 41339 50171 44845 40522 FALSE TRUE 51476.10898 45583.44623 43829.52325 47161.43575 58611.9394 39907.42006 42516.4925 40918.13406 46805.9448 1.099777159 0.973881553 0.936409327 1.007594996 1.252232802 0.852614347 0.908356677 0.874208057 1 15.51440416 LGIAVIHGEAQDAES(ph)DLVDGRHSPPMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAES(0.869)DLVDGRHS(0.131)PPMVR 65.301 0.018496 188240000 33708 28477 26424 30835 33398 26497 35696 28471 25343 TRUE FALSE 32114.68964 31378.83868 27635.56654 27735.40722 39222.60063 25579.40225 30249.9196 25977.92831 29273.06301 1.097073089 1.071935611 0.944061321 0.947471989 1.339887138 0.87382049 1.033370495 0.887434578 1 14.83728609 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAES(0.004)DLVDGRHS(0.996)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.105)DLVDGRHS(0.895)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.001)DLVDGRHS(0.999)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.014)DLVDGRHS(0.986)PPMVR;LGIAVIHGEAQDAES(0.009)DLVDGRHS(0.991)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.001)DLVDGRHS(0.999)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.011)DLVDGRHS(0.989)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.002)DLVDGRHS(0.998)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR 238.17 1.72E-45 5534410000 2421793 2203052 2221257 2630288 2522623 2273468 2791087 2508767 1699324 TRUE FALSE 2307319.644 2427545.503 2323103.831 2365886.453 2962567.653 2194737.233 2365255.416 2289086.062 1962846.487 1.175496739 1.236747509 1.183538217 1.205334431 1.509322136 1.118140032 1.20501294 1.166207381 1 20.90451591 0.789740896 1.09033624 1.001590955 1.237447026 0.344997965 0.103009353 0.910481221 2.014322422 0.092422327 0.029253269 6.162272457 -0.789740896 0.235856071 LGIDDLVHFDFMDPPAPETLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGIDDLVHFDFMDPPAPETLMR 22 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 135.73 5.59E-06 318250000 604770 686570 562340 674310 516200 543680 600390 619970 379810 FALSE TRUE 576183.7206 756532.2636 588123.8452 606527.0777 606225.1166 524852.2253 508789.4786 565682.1401 438708.995 1.313361994 1.724451224 1.340578497 1.382527107 1.381838812 1.196356198 1.159742527 1.289424531 1 18.74290476 2.179586062 0.559808511 1.060373781 1.519603671 0.546784213 0.12597709 0.574744727 0.368187761 0.112037106 0.085025506 151.2119318 -2.179586062 0.459229889 LGIEGLSLHNVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGIEGLSLHNVLK 13 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 130.56 2.10E-05 0 173850 142550 127950 157530 185780 134480 221710 180730 207220 FALSE TRUE 165632.455 157076.0071 133816.6341 141694.7851 218179.9732 129822.9239 187884.0675 164904.3231 239354.6193 0.691996067 0.656248071 0.559072703 0.591986842 0.911534416 0.542387376 0.78496111 0.688954003 1 17.86879012 -1.538314385 0.296651744 1.259415459 0.642907615 0.485742836 0.106537045 18.52776268 1.046417927 3.660048775 0.10634592 0.02895247 1.538314385 -0.616507845 LGIHEDSQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LGIHEDSQNR 10 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 226.39 3.05E-09 48095430000 21092710 18252170 17981330 19565350 20886330 18367170 22913740 20225580 19575330 FALSE TRUE 20095699.4 20112086.87 18805791.77 17598603.85 24528899.34 17731110.3 19417828.12 18454520.99 22610972.2 0.888758751 0.889483508 0.831710888 0.778321414 1.084822852 0.784181686 0.858779001 0.816175476 1 24.43051969 LGIHEDSQNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LGIHEDSQNRK 11 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 178.53 4.87E-06 8110530000 12813570 10663720 11580280 12746660 8784690 12552230 14500430 14584590 10266970 FALSE TRUE 12207897.94 11750365.19 12111247.29 11465341.52 10316737.15 12117543.13 12288123.08 13307485.98 11859119.27 1.029410166 0.990829498 1.021260265 0.966795363 0.869941259 1.021791151 1.036175015 1.122131052 1 23.49949353 1.751121696 3.079793669 1.062320325 0.982822873 0.291210091 0.053053788 0.291440041 5.681501147 0.029988291 0.014276474 56.37956173 -1.751121696 -0.079497452 LGIHEDSTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;;; 225.87 3.30E-09 38972651900 16232212.3 14179283.9 13930779.9 15426462.1 15227397.4 13980803.1 17128700.4 15675841 14623557.6 FALSE TRUE 15464947.79 15624169.05 14569519.94 13875764.82 17883050.69 13496644.38 14515402.56 14303181.26 16891304.23 0.915556761 0.924982988 0.862545588 0.821473856 1.058713433 0.799029146 0.859341728 0.84677779 1 24.00977739 LGIHEDSTNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;; 171.62 9.30E-06 8626260000 6516240 5289960 6029520 6419910 6531470 5889410 7527180 6537480 7185590 FALSE TRUE 6208230.249 5829012.938 6305979.456 5774568.45 7670556.3 5685458.255 6378770.445 5965023.594 8299894.598 0.747989047 0.702299634 0.759766209 0.695739974 0.924175146 0.685003669 0.768536319 0.718686668 1 22.98466158 -1.592364827 2.951406096 1.015744942 0.748277628 0.573293796 0.067688685 18962441.38 18444721.09 2303999.143 0.014767501 0.025564375 1.592364827 -0.267467314 LGIYDADGDGDFDVDDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 244.14 9.22E-24 114284000 233762 211714 198735 320526 187068 257669 264772 261487 155467 FALSE TRUE 222712.5335 233287.8973 207847.1963 288306.1175 219692.6 248745.8579 224376.1685 238589.8121 179576.0283 1.240213048 1.29910378 1.157432861 1.605482203 1.223396029 1.385184093 1.249477286 1.328628405 1 17.45423525 -0.814178439 6.589801615 0.999999995 1.306451972 0.392491123 0.121519231 6.19E-09 1.41E-09 0.103844059 0.024476279 0.153398658 0.814178439 0.306451977 LGLALNYSVFYYEIQNAPEQACHLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGLALNYSVFYYEIQNAPEQACHLAK 26 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 288.94 8.22E-63 791644000 957995 1029048 794762 1010369 719858 979804 980395 1072095 661871 FALSE TRUE 912712.4749 1133909.161 831202.6238 908804.7885 845401.0073 945873.1418 830817.7366 978216.6783 764510.5743 1.193851996 1.483183097 1.08723496 1.188740639 1.10580682 1.237227023 1.086731517 1.279533222 1 19.54417693 7.999997749 0.056465671 0.694276923 2.219301891 0.226188641 0.117427985 441.5940204 1.87002409 10.78465551 56.36032534 99999481.77 -7.999997749 1.525024968 LGLAVIHGEAQCTELDMDDGRHS(ph)PPMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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;LGLAVIHGEAQCT(0.001)ELDMDDGRHS(0.999)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 256.2 7.56E-54 3633538000 2303742 2073760 2144135 2459950 1943637 2293817 2631525 2468057 1479478 TRUE FALSE 2194848.681 2285078.502 2242445.711 2212671.152 2282606.677 2214381.542 2230037.53 2251940.845 1708907.892 1.284357508 1.337157206 1.312209816 1.294786666 1.335710771 1.295787533 1.304948933 1.317766075 1 20.70464321 -1.30222113 3.245523758 0.998317945 1.310475585 0.970750867 0.016929466 15387672.06 20440390.35 249535.576 0.003760186 0.049863054 1.30222113 0.31215764 LGLDPTQEDCVATHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGLDPTQEDCVATHR 15 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;;; 182.57 5.41E-07 926780000 915408 927120 801163 975970 478627 954706 849705 927830 443552 FALSE TRUE 872138.478 1021594.582 837897.116 877863.6414 562099.3973 921644.2918 720066.8963 846584.2865 512335.7788 1.70227908 1.993994221 1.63544525 1.713453711 1.097130867 1.798906752 1.405458932 1.65240126 1 18.96673012 -1.241626713 0.097316765 2.49E-14 2.29318044 0.462365279 0.225997577 50.64552127 0.90046638 18.04651098 5.36956558 0.057328858 1.241626713 2.29318044 LGLDYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGLDYEER 8 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H3X6;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 129.55 0.0025258 1274020000 3714960 2860750 3135540 3341650 3747340 2434510 3308390 3120080 3558660 FALSE TRUE 3539361.203 3152263.677 3279307.61 3005740.993 4400874.91 2350202.308 2803634.343 2846869.255 4110518.818 0.861049751 0.766877326 0.797784357 0.731231537 1.070637334 0.571753205 0.682063376 0.692581492 1 21.97088907 2.190967928 24.99999918 0.702159575 0.828843437 0.100997324 0.141439025 203.650139 106974.2507 0.047313668 0.034943549 155.2272372 -2.190967928 0.126683862 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;; 351.33 5.68E-132 3441290000 1908175 1904334 1834741 2069857 1750682 1900134 1996233 2017463 1887474 FALSE TRUE 1817979.349 2098387.8 1918865.69 1861791.042 2056000.387 1834331.883 1691670.993 1840803.244 2180173.828 0.833868991 0.962486464 0.880143439 0.853964495 0.943044247 0.841369555 0.775933997 0.844337833 1 21.05601174 2.125767317 10.7271586 0.838605949 0.895873321 0 0.068734923 0.653558477 59.06714614 0.023570674 0.017406963 133.5879598 -2.125767317 0.057267372 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;; 203.64 2.85E-27 859350000 420523 383250 413628 457931 421719 411112 458671 428736 448260 FALSE TRUE 400645.7112 422303.6107 432593.2529 411898.9059 495266.6601 396875.0884 388692.3149 391193.603 517773.8714 0.773785108 0.815613985 0.835486835 0.79551891 0.956530809 0.766502735 0.750698976 0.755529826 1 18.98196264 4.44893156 2.103397037 0.821757813 0.772432686 0.030641801 0.083875023 1.691041209 12.46307309 0.020430917 0.126203555 28114.57739 -4.44893156 -0.049325127 LGLGTLSSS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGLGTLSSSLSR 12 0 O95248;O95248-5;O95248-4 O95248 SBF1 Myotubularin-related protein 5 1 LGLGTLSS(0.018)S(0.978)LS(0.004)R 127.56 0.00028069 50459000 136620 123850 128160 148450 160010 130970 168720 141690 151840 TRUE FALSE 130162.2434 136470.4558 134036.2628 133527.524 187915.6933 126434.4761 142978.6652 129282.8725 175386.5717 0.742144864 0.778112341 0.764233324 0.761332653 1.071437177 0.720890287 0.815220138 0.737130963 1 17.42017877 LGLHQVLQDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGLHQVLQDLR 11 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 161.62 2.61E-05 484020000 1222650 826010 488910 516920 1249970 681680 1300400 953450 1174390 FALSE TRUE 1164857.758 910181.3581 511327.0071 464958.2195 1467964.372 658073.2507 1102000.097 869960.8634 1356508.403 0.858717686 0.670973623 0.376943487 0.342761031 1.082163862 0.485122871 0.812379852 0.641323608 1 20.37146655 -0.089128799 0.565209735 1.027521871 0.651334477 0.188899937 0.223891374 8.873605759 3.118813954 0.771553556 0.092811591 0.814462703 0.089128799 -0.376187394 LGLLGALMAEDGVRGS(ph)PPVPSGPPMEEDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGLLGALMAEDGVRGSPPVPSGPPMEEDGLR 31 1 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 LGLLGALMAEDGVRGS(0.992)PPVPS(0.008)GPPMEEDGLR;LGLLGALMAEDGVRGS(0.996)PPVPS(0.004)GPPMEEDGLR 107.63 7.87E-05 76790000 87884 63360 70920 80504 82865 72177 97992 82576 97927 TRUE FALSE 83729.89749 69816.45603 74171.75215 72411.58497 97316.62976 69677.49239 83041.52065 75345.20768 113113.019 0.740232187 0.617227412 0.655731345 0.640170209 0.86034862 0.615998874 0.734146444 0.666105532 1 16.78740546 -4.999999989 0.366023585 4.985069967 0.681243569 0.632455368 0.07375853 310.2327516 2.423512067 976.3300191 0.047430435 1.00E-05 4.999999989 -4.303826398 LGLPLLTDCAQPSRPHGS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.075)RPHGS(0.925)PSR;LGLPLLTDCAQPS(0.184)RPHGS(0.816)PSR;LGLPLLTDCAQPS(0.216)RPHGS(0.777)PS(0.007)R;LGLPLLTDCAQPS(0.001)RPHGS(0.982)PS(0.017)R 263.57 5.57E-37 826580000 1053390 868619 971670 1053480 1155160 926530 1163900 1019090 1144820 TRUE FALSE 1003598.342 957132.2636 1016222.031 947582.1889 1356619.538 894444.0338 986325.6785 929853.0771 1322352.839 0.758948983 0.723810042 0.768495367 0.71658801 1.025913431 0.676403459 0.745886914 0.703180762 1 20.33467575 -2.257877384 2.243359415 1.901364694 0.762148007 0.36802187 0.096759685 6722260.348 852204.303 30857641.74 0.02261388 0.005522333 2.257877384 -1.139216688 LGLQDGSTS(ph)LLPEQLLSAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGLQDGSTSLLPEQLLSAPK 20 0 Q5T7V8-2;Q5T7V8 Q5T7V8-2 GORAB RAB6-interacting golgin 1 LGLQDGS(0.002)T(0.002)S(0.93)LLPEQLLS(0.065)APK 62.064 0.075843 1405400000 1157300 962600 1284700 1231200 2399900 531120 1348300 648160 2953100 TRUE FALSE 1102596.723 1060690.034 1343604.766 1107437.437 2818441.8 512727.1812 1142592.072 591403.6743 3411051.666 0.323242457 0.310956895 0.393897512 0.324661584 0.826267696 0.15031352 0.334967683 0.173378691 1 21.70178518 -0.985723343 4.27757463 1.000028566 0.352781389 0.550018327 0.183420668 499846937.9 974101799 213607.8099 0.040853701 0.103341951 0.985723343 -0.647247177 LGLVLDQAEAEGVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGLVLDQAEAEGVCR 15 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 220.31 3.92E-12 88578000 135615 101793 106439 122867 127588 109270 130559 111352 151795 FALSE TRUE 129204.7477 112165.8224 111319.3334 110516.1757 149839.3068 105485.9525 110639.8267 101601.4286 175334.5933 0.736903912 0.639724428 0.634896579 0.630315864 0.854590665 0.601626584 0.631021093 0.579471664 1 17.41975114 -1.710133484 2.871779548 1.049334841 0.664400811 0.641027582 0.079118658 23465519 19186948.05 8287997.174 0.017926202 0.019492454 1.710133484 -0.38493403 LGMLS(ph)PEGTCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 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(1)PEGTCK;LGMLS(0.988)PEGT(0.012)CK;LGMLS(1)PEGTCK;LGMLS(0.919)PEGT(0.081)CK;LGMLS(0.998)PEGT(0.002)CK;LGMLS(1)PEGTCK;LGMLS(0.998)PEGT(0.002)CK;LGMLS(1)PEGTCK;LGMLS(0.996)PEGT(0.004)CK;LGMLS(0.982)PEGT(0.018)CK;LGMLS(0.998)PEGT(0.002)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK 278.35 3.10E-27 8083024000 23486930 20185540 21964870 25567670 16827280 23964840 26778450 25652810 19802580 TRUE FALSE 22376749.37 22242469.48 22971981.02 22997559.24 19761952.3 23134931.58 22692905.63 23406513.96 22873462.97 0.978284285 0.972413731 1.004307089 1.005425338 0.863968536 1.01143109 0.992106253 1.023304342 1 24.44717147 LGNDFHTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGNDFHTNK 9 0 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 117.71 0.0011081 1553950000 6398600 6564200 5120720 6532560 5148830 5858200 6843100 6360330 4730990 FALSE TRUE 6096150.859 7233099.443 5355510.077 5875894.658 6046784.322 5655329.065 5799059.413 5803385.787 5464647.767 1.115561536 1.323616773 0.980028413 1.075255883 1.106527736 1.034893612 1.061195462 1.061987165 1 22.38169708 3.731797155 24.99986737 1.051799135 1.219589156 0.582684233 0.061010944 312.5243911 1155187.646 0.015090345 0.023987941 5392.586929 -3.731797155 0.167790022 LGNDFHTNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGNDFHTNKR 10 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;;; 178.46 1.44E-06 8325080000 13903590 10875560 10154940 11401950 11553610 11340240 15682760 12943940 11356410 FALSE TRUE 13246394.85 11983791.93 10620554.04 10255804.32 13568555.93 10947524.65 13290066.93 11810499.99 13117504.06 1.009825863 0.913572572 0.809647475 0.78184114 1.034385494 0.834573757 1.01315516 0.900361832 1 23.6449899 1.723613744 24.99998739 0.967772466 0.905299133 0.139572869 0.084782841 2.175892037 3624.540354 0.038801937 0.021517623 52.91925771 -1.723613744 -0.062473334 LGNSCEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 87.251 0.038389 0 150690 127550 132580 158150 219770 113960 159240 130640 195510 FALSE TRUE 143567.1823 140547.49 138658.9241 142252.4615 258097.8184 110013.5366 134945.0134 119200.469 225828.6923 0.635734905 0.622363299 0.614000474 0.629913144 1.142892056 0.487154823 0.597554775 0.527835803 1 17.78486927 2.951167733 24.99986591 0.713186706 0.624921334 0.07080993 0.201650801 1429.877861 732030.5636 0.059554454 0.063168229 893.6505619 -2.951167733 -0.088265372 LGNSGAS(ph)PSSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGNSGASPSSAGK 13 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 LGNSGAS(0.926)PS(0.061)S(0.012)AGK;LGNS(0.001)GAS(0.971)PS(0.027)S(0.001)AGK;LGNSGAS(0.942)PS(0.056)S(0.002)AGK;LGNSGAS(0.908)PS(0.063)S(0.029)AGK 150.31 4.63E-05 342440000 791660 717260 727640 840600 535684 812280 882960 868770 661960 TRUE FALSE 754239.8007 790349.6095 761003.0137 756101.291 629107.12 784150.5399 748248.2353 792695.8932 764613.376 0.986432914 1.033659146 0.995278186 0.988867465 0.822778073 1.02555169 0.978596842 1.036727735 1 19.54437091 -0.337291677 6.4302457 1 0.9852573 0.006507936 0.06071269 0 0 0.056005343 0.013200586 0.459947564 0.337291677 -0.014742701 LGPGGLDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGPGGLDDR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 113.89 0.0040182 119580000 186080 183420 173150 206840 174090 191170 198650 195770 184860 FALSE TRUE 177284.3672 202110.7065 181089.0988 186048.0502 204451.2409 184549.735 168342.294 178627.341 213527.1447 0.830266182 0.94653402 0.848084674 0.87130866 0.957495316 0.864291682 0.78838826 0.836555658 1 17.70405996 2.006319115 24.96685889 0.845186653 0.891765887 0 0.067244488 360.4642542 1424187.793 0.022945791 0.016902896 101.465667 -2.006319115 0.046579233 LGPGGLDDRYS(ph)LVS(ph)EQLEPAATSTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGPGGLDDRYSLVSEQLEPAATSTYR 26 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 2 LGPGGLDDRY(0.028)S(0.975)LVS(0.995)EQLEPAAT(0.001)S(0.001)T(0.001)YR;LGPGGLDDRY(0.003)S(0.997)LVS(1)EQLEPAATSTYR 104.9 0.0018873 75235000 82158 67384 73343 78565 75451 74228 89359 83912 78204 TRUE FALSE 78274.55416 74250.50621 76705.8491 70667.49694 88609.63051 71657.46575 75725.64336 76564.22043 90331.47691 0.866525787 0.821978216 0.849159692 0.782313091 0.980938578 0.793272381 0.838308483 0.847591815 1 16.46294118 0.892017955 16.98123173 1 0.845357587 0.441288281 0.053881058 2713.948789 426800.0324 0.045918006 0.011479502 7.798623509 -0.892017955 -0.154642413 LGPGGLDDRYS(ph)LVSEQLEPAATSTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGPGGLDDRYSLVSEQLEPAATSTYR 26 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 LGPGGLDDRYS(1)LVSEQLEPAATSTYR;LGPGGLDDRYS(1)LVSEQLEPAATSTYR;LGPGGLDDRYS(1)LVSEQLEPAATSTYR;LGPGGLDDRYS(1)LVSEQLEPAATSTYR 300.9 7.62E-71 938830000 508410 502838 512929 514200 454748 483741 563920 529060 490330 TRUE FALSE 484378.4669 554077.7639 536447.302 462511.6391 534055.9072 466988.9279 477883.6469 482732.7017 566367.8721 0.855236483 0.978300132 0.947171138 0.816627605 0.942948803 0.824532871 0.843768989 0.852330659 1 19.1113799 3.261302204 24.9991344 0.869536224 0.927678338 0.092983049 0.063582997 406.4743747 446821.8765 0.016114122 0.0218033 1825.165304 -3.261302204 0.058142114 LGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.009)S(0.034)ECT(0.479)S(0.479)DVEPDTR 157.96 1.94E-09 315280000 167130 159410 182760 182000 162490 156890 180030 144090 184970 TRUE FALSE 159230.0961 175654.0602 191139.7268 163705.0142 190828.2046 151456.86 152563.117 131472.7157 213654.2029 0.745270133 0.822141843 0.89462189 0.766214809 0.893163822 0.70888781 0.714065602 0.615352818 1 17.70491817 2.213640132 24.99173024 0.732466164 0.817365486 0.054755708 0.108389891 445.5452164 446816.056 0.036092401 0.026667099 163.5460772 -2.213640132 0.084899322 LGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.002)S(0.006)ECT(0.285)S(0.707)DVEPDTR;LGPGRPLPTFPTS(0.003)ECT(0.126)S(0.871)DVEPDTR 136.67 1.16E-05 406690000 275197 255573 249558 258667 258756 273915 297960 272064 302420 TRUE FALSE 262188.9832 281616.1793 261000.4811 232665.3017 303882.9645 264429.2549 252500.7296 248240.6339 349317.7491 0.750574467 0.80618915 0.747172114 0.666056341 0.869932791 0.756987744 0.722839679 0.710644204 1 18.41418042 -1.393906949 5.383364636 1.000132907 0.756573553 0.666928142 0.054647778 8.24E-05 9.27E-06 0.049998203 0.011778291 0.040373189 1.393906949 -0.243559354 LGPLFSLLNENHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGPLFSLLNENHR 13 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 220.66 2.04E-11 210162000 559360 464800 456980 513210 527880 466520 585940 551890 527030 FALSE TRUE 532920.1613 512163.6484 477932.985 461621.1558 619942.1049 450364.2954 496544.0915 503563.5858 608759.1207 0.875420414 0.841323984 0.785093757 0.758298545 1.01837013 0.73980706 0.815665958 0.827196782 1 19.21551196 -1.636159352 2.59125522 1.019087812 0.832471681 0.319085705 0.076829177 14546670.23 12592974.4 1860020.245 0.016858911 0.023112166 1.636159352 -0.186616131 LGPQNFIDET(ph)SDIENLLKEEEDYKEENNDSKETSGALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGPQNFIDETSDIENLLKEEEDYKEENNDSKETSGALK 38 3 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 LGPQNFIDET(0.588)S(0.412)DIENLLKEEEDYKEENNDSKETSGALK;LGPQNFIDET(0.5)S(0.5)DIENLLKEEEDYKEENNDSKETSGALK 225.78 7.80E-40 269320000 374780 271364 328510 345420 109397 443080 409520 466780 99014 TRUE FALSE 357064.8921 299016.3001 343572.5084 310697.7253 128475.8022 427736.0285 347040.2026 425906.2686 114368.5854 3.122053935 2.614496796 3.004081122 2.716635204 1.123348704 3.739978307 3.03440146 3.723979509 1 16.8033313 3.118501176 9.363500942 2.695752616 2.878578228 0.017143997 0.928273324 2.315744113 179.3927901 0.254168416 0.304092849 1313.715052 -3.118501176 0.182825612 LGPSDYFGEIALLMNRPR ddPTM_SK-BR-3_Trastuzumab_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 ; 217.88 7.46E-19 139932000 261263 211075 249198 262621 216820 252354 311360 273660 217705 FALSE TRUE 248913.6158 232583.7825 260623.9748 236221.8381 254633.3394 243614.9177 263856.3135 249696.8796 251465.5795 0.989851638 0.924912996 1.036420075 0.939380406 1.012597191 0.968780372 1.049274076 0.992966433 1 17.94000141 2.334684789 1.310908301 1.015517707 0.969631229 0.122964622 0.036317117 0.639920977 2.179954196 0.019261086 0.012212236 216.1149391 -2.334684789 -0.045886478 LGQHSCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGQHSCLR 8 0 Q9Y3S2;D6RBR7 Q9Y3S2 ZNF330 Zinc finger protein 330 0 68.383 0.05665 65164000 83590 58121 64842 58581 94942 65343 109330 70400 59740 FALSE TRUE 79638.86636 64043.59598 67815.06984 52692.32658 111499.8547 63080.15553 92649.70052 64235.40279 69004.17409 1.154116652 0.928111912 0.982767647 0.763610713 1.615842175 0.914149852 1.342668059 0.930891553 1 16.07439601 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR 34 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 172.03 3.59E-15 139750000 63151 54368 54521 71328 67968 57773 69559 56065 3746.8 FALSE TRUE 60165.97738 59908.16101 57020.84178 64157.97393 79821.59768 55772.30652 58946.49701 51155.65138 4327.834608 13.9020972 13.84252552 13.17537451 14.82449764 18.44377267 12.88688491 13.6203211 11.82014934 1 12.07942965 0.512537566 1.174196768 0.990868761 14.46703597 0.884340768 1.51650921 0.576955504 1.062507969 1.428139224 0.435388883 3.254899372 -0.512537566 13.47616721 LGQSDPAPLQHQMDIYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LGQSDPAPLQHQMDIYQK 18 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;;;;; 227.04 3.19E-19 2893880000 5921260 5757210 4779370 5620770 4718940 5023770 6094610 5462710 4171020 FALSE TRUE 5641373.775 6343876.244 4998508.842 5055759.521 5541921.642 4849795.585 5164765.309 4984366.153 4817840.479 1.170934114 1.316746844 1.037499864 1.049382922 1.150291643 1.006632662 1.072008368 1.034564381 1 22.1999552 3.728111538 24.98626612 1.055414763 1.24384048 0.69003481 0.053903421 319.4836937 763962.8899 0.01323671 0.020755503 5347.01667 -3.728111538 0.188425717 LGS(ph)LVDEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGSLVDEFK 9 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 LGS(1)LVDEFK;LGS(1)LVDEFK;LGS(1)LVDEFK 118.28 0.0010649 29207900 133239 121134 121358 140556 71479 132550 130009 131493 64292 TRUE FALSE 126941.0565 133477.6923 126922.3843 126427.0438 83944.91497 127959.7603 110173.7393 119978.7758 74262.075 1.709365871 1.797387055 1.709114435 1.702444267 1.130387415 1.723083556 1.483580135 1.615613028 1 16.18033801 -2.58603897 0.142244712 2.19E-14 1.898391736 0.553629859 0.179785012 42.90842517 0.729291273 15.01016692 1.152852837 0.002593947 2.58603897 1.898391736 LGS(ph)PGAPQQEDAMDDKELIEYFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGSPGAPQQEDAMDDKELIEYFK 23 1 H0YGG4 H0YGG4 EIF2B1 1 LGS(1)PGAPQQEDAMDDKELIEYFK;LGS(1)PGAPQQEDAMDDKELIEYFK;LGS(1)PGAPQQEDAMDDKELIEYFK;LGS(1)PGAPQQEDAMDDKELIEYFK 295.78 6.97E-62 445308000 659511 635461 558482 689852 247660 698487 650940 725143 251624 TRUE FALSE 628337.2221 700215.1984 584088.9521 620506.7663 290851.8256 674298.22 551627.1477 661645.6347 290644.5648 2.161875012 2.409180433 2.009633149 2.134933322 1.000713107 2.320009736 1.897944137 2.276476889 1 18.1488964 3.265430472 2.413954459 1.810301988 2.267737228 0.176615319 0.46175332 0.495261856 5.906154927 0.128933655 0.176583413 1842.597477 -3.265430472 0.457435241 LGS(ph)PHRRPLSVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGSPHRRPLSVDK 13 2 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 LGS(1)PHRRPLSVDK;LGS(1)PHRRPLSVDK;LGS(0.999)PHRRPLS(0.001)VDK 94.203 0.002746 748640000 419690 375010 340146 468820 300503 482310 558600 545600 294941 TRUE FALSE 399852.0854 413223.9454 355742.0306 421693.3229 352910.6281 465607.4838 473375.3106 497824.3716 340678.9439 1.173691807 1.212942428 1.044214903 1.237802718 1.035903845 1.366704612 1.38950563 1.461271324 1 18.37805326 2.219537445 24.99934676 1.343540142 1.153722521 0.234220567 0.137992887 269.0708329 353597.7713 0.045524725 0.033674706 165.7820267 -2.219537445 -0.189817621 LGS(ph)PKPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 101.95 0.0030633 5323560000 6327540 5276870 5107450 6376000 2877980 6219040 5956880 5930260 2773950 TRUE FALSE 6028449.724 5814589.052 5341631.634 5735072.366 3379898.801 6003673.085 5048048.55 5410974.996 3204119.999 1.881468149 1.814722624 1.667113478 1.789905612 1.054860243 1.873735406 1.575486734 1.688755414 1 21.61149675 -2.543420168 0.145761356 2.17E-19 1.962102162 0.461767075 0.232791317 50.51857222 0.891234061 18.64756081 1.38937879 0.002861408 2.543420168 1.962102162 LGS(ph)PLAVDEALR ddPTM_SK-BR-3_Trastuzumab_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 222.74 2.53E-11 218241000 404607 371011 310653 423451 250036 361218 367227 375534 215523 TRUE FALSE 385482.029 408817.4427 324896.7473 380884.901 293642.1992 348708.9301 311199.7766 342650.2521 248945.2061 1.548461346 1.642198495 1.305093408 1.529994921 1.179545507 1.400745712 1.250073385 1.376408317 1 17.92546871 7.999999732 0.05593317 0.358334875 3.438849953 0.634368382 0.114593913 205.0820467 0.860759888 10.20423786 52.5237584 99999938.28 -7.999999732 3.080515078 LGS(ph)PLAVDEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGSPLAVDEALRR 13 1 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR 188.9 3.50E-06 471452000 715051 548974 593271 684060 426794 655029 698748 681954 429041 TRUE FALSE 681251.9563 604915.0747 620473.0622 615296.9892 501226.7385 632345.1815 592141.1592 622238.4925 495574.487 1.374671163 1.220634013 1.252027855 1.241583264 1.011405453 1.275984132 1.194858038 1.255590247 1 18.91874239 7.999999985 0.023476453 3.49E-12 2.843782916 0.446111629 0.085847681 2113.7894 3.819721882 162.737151 326.0243777 99999996.62 -7.999999985 2.843782916 LGS(ph)PSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LGSPSGK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LGS(0.985)PS(0.015)GK;LGS(0.999)PS(0.001)GK;LGS(0.988)PS(0.012)GK;LGS(0.957)PS(0.043)GK;LGS(0.983)PS(0.017)GK;LGS(0.845)PS(0.155)GK;LGS(0.924)PS(0.076)GK;LGS(0.884)PS(0.116)GK;LGS(0.969)PS(0.031)GK 154.35 0.0017667 12320820000 31725230 27137250 26284750 31418600 14257090 28566460 29345410 31817710 16211750 TRUE FALSE 30225641.25 29902566.63 27489931.79 28260342.64 16743521.98 27577196.33 24868228.74 29031582.64 18725785.39 1.614118747 1.596865819 1.468025571 1.509167282 0.894142576 1.472685698 1.328020599 1.550353271 1 24.15852289 8 0.076582763 0.738817778 3.11418415 0.349891176 0.198781287 223.0742099 1.250761472 6.146628331 56.36085159 100000000 -8 2.375366372 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 273.63 3.52E-52 546155000 181847 169933 152696 204386 111861 184523 190620 198500 128498 TRUE FALSE 173251.4527 187249.3659 159697.2626 183840.731 131369.523 178132.9222 161537.418 181118.2877 148424.8136 1.167267444 1.261577235 1.0759472 1.238611837 0.885091379 1.200155944 1.088345096 1.220269599 1 17.17937278 8 0.061865466 0.863891994 1.719609911 0.129131032 0.109973129 553.9105134 2.554719233 6.958761051 42.38445021 100000000 -8 0.855717916 LGS(ph)SSNLQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.498)S(0.498)S(0.004)NLQFK;LGS(0.915)S(0.066)S(0.019)NLQFK;LGS(0.8)S(0.145)S(0.055)NLQFK;LGS(0.729)S(0.135)S(0.135)NLQFK;LGS(0.86)S(0.139)S(0.001)NLQFK 252.84 4.78E-17 2232020000 3379200 2745110 2755100 3204680 1797320 3019890 3133420 3195480 1729540 TRUE FALSE 3219471.913 3024839.83 2881424.06 2882539.478 2110772.039 2915310.452 2655359.23 2915666.831 1997748.23 1.611550377 1.514124645 1.442335935 1.442894272 1.056575602 1.459298228 1.329176114 1.459476618 1 20.92994335 8 0.037778267 9.64E-11 3.620709681 0.531381423 0.133527201 648.6941038 1.86961462 50.75221396 154.6749811 100000000 -8 3.620709681 LGS(ph)VDSFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(0.976)VDS(0.024)FER;LGS(0.999)VDS(0.001)FER;LGS(1)VDSFER 117.8 0.0011461 557160000 1835570 1405240 1500630 1748130 1322650 1519090 1692670 1575810 1229580 TRUE FALSE 1748806.244 1548435.554 1569435.37 1572404.651 1553319.741 1466483.532 1434422.103 1437823.723 1420256.987 1.231330851 1.090250263 1.10503619 1.107126855 1.09368921 1.032548015 1.009973629 1.012368702 1 20.43772057 8 0.21396062 0.981415187 2.214419376 0.88328192 0.023484665 16.16615211 0.203533312 0.040969984 6.827732102 100000000 -8 1.233004189 LGS(ph)YSGPTSVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGSYSGPTSVSR 12 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 LGS(1)YSGPTSVSR;LGS(0.996)YS(0.004)GPTSVSR 185.51 1.36E-05 396500000 718390 630520 656800 710290 863270 565040 730910 612660 930910 TRUE FALSE 684433.1284 694770.7048 686914.9297 638890.2997 1013824.015 545472.5231 619396.2554 559012.2425 1075270.768 0.636521654 0.646135583 0.638829725 0.594166901 0.942854623 0.507288526 0.576037472 0.519880442 1 20.03626857 -1.105274181 4.283280248 1.000049125 0.63259646 0.48061939 0.119990937 3.825688447 64454228.44 7176.883911 0.026425838 0.078474005 1.105274181 -0.367452665 LGSLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGSLSER 7 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ; 90.706 0.039413 203510000 300030 256270 251490 282260 333170 253300 311530 281870 361770 FALSE TRUE 285848.1765 282384.2044 263021.0653 253886.6885 391274.7425 244528.1575 264000.3769 257187.9685 417871.4439 0.684057694 0.67576813 0.62943058 0.607571281 0.936351953 0.585175563 0.631774151 0.61547151 1 18.67269965 -1.141134605 4.854675554 1.000022331 0.670077081 0.521761632 0.099077084 2.22E-05 3.93E-06 0.088949229 0.020964117 0.072254582 1.141134605 -0.32994525 LGSQHS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 LGSQHS(1)PGR;LGS(0.142)QHS(0.858)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR 122.33 0.00037936 2480570000 2568230 2319042 2599700 2971050 3015760 2406930 3321350 3065230 3113200 TRUE FALSE 2446834.858 2555355.016 2718898.816 2672394.409 3541707.589 2323577.411 2814617.057 2796822.211 3595979.156 0.680436329 0.710614524 0.756094154 0.743161819 0.984907708 0.646159866 0.782712284 0.777763744 1 21.77795323 -5 0.145168716 1.841523116 0.672106038 0.43958302 0.08806328 125.5581171 1.099098463 30.69570343 0.461338267 1.00E-05 5 -1.169417078 LGSS(ph)SNLQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.246)S(0.692)S(0.061)NLQFK 149.41 2.45E-05 178240000 573290 464270 494250 542850 328230 501490 517320 537660 288350 TRUE FALSE 546191.7179 511579.6408 516911.8514 488281.6867 385473.2081 484123.2756 438393.3328 490579.6401 333065.8453 1.639891107 1.535971484 1.551980963 1.46602149 1.157348355 1.453536237 1.316236231 1.472920886 1 18.34544789 2.639007408 0.050200015 6.04E-12 2.855240349 0.670406307 0.111185786 49.22965145 1.058486305 26.07612414 33.40004872 435.5193028 -2.639007408 2.855240349 LGSSGLGS(ph)ASSIQAAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGSSGLGS(0.842)AS(0.01)S(0.148)IQAAVR;LGS(0.001)S(0.008)GLGS(0.941)AS(0.016)S(0.034)IQAAVR 221.9 3.71E-15 207344000 171318 162295 163264 184730 161638 162438 198989 182391 204314 TRUE FALSE 163220.1377 178833.045 170749.8159 166160.5894 189827.616 156812.7313 168629.5734 166419.8771 235997.9716 0.691616697 0.757773653 0.723522388 0.704076346 0.804361219 0.664466437 0.714538232 0.705175032 1 17.84841493 -1.254423919 3.743665596 1.000447634 0.721337487 0.842650205 0.037930275 3996393.613 2695267.663 13440.83629 0.008099769 0.055664214 1.254423919 -0.279110147 LGSSLDWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LGSSLDWDR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;;;; 204.62 3.79E-05 1148203000 2980890 2465350 2197540 2561330 3053200 2320200 3283500 2768200 2996480 FALSE TRUE 2839989.237 2716571.968 2298299.383 2303860.242 3585677.113 2239850.892 2782541.769 2525801.733 3461158.815 0.820531328 0.784873539 0.664025983 0.665632629 1.035975899 0.647139011 0.803933572 0.729756093 1 21.72282371 -1.757600858 2.685604013 1.050864858 0.772151788 0.294266674 0.112338169 27649984.17 21594434.14 9313055.816 0.024880592 0.017474274 1.757600858 -0.27871307 LGTGFSDEELEEHHQSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGTGFSDEELEEHHQSLK 18 0 P18858;P18858-3;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 160.25 2.37E-11 71533000 89919 70715 84495 107160 98477 89348 119880 118740 29939 FALSE TRUE 85668.70707 77920.9389 88369.17933 96388.07321 115651.3576 86253.85636 101590.1043 108342.4961 34581.78721 2.477278185 2.253236318 2.555367621 2.787249618 3.344285155 2.494198921 2.937676518 3.132935133 1 15.07772481 3.462303802 4.068105369 2.748805984 2.367324908 0 0.640198064 0.561485612 21.36433908 0.156157798 0.227122668 2899.371073 -3.462303802 -0.381481076 LGTLS(ph)PAFSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGTLSPAFSTR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 LGT(0.181)LS(0.819)PAFSTR;LGT(0.046)LS(0.954)PAFSTR;LGTLS(1)PAFSTR 140.01 0.00064655 225280000 283036 233132 259441 272587 241443 249472 323082 282861 294234 TRUE FALSE 269657.4492 256888.4158 271336.6265 245186.0369 283550.5828 240832.7221 273789.9071 258092.1913 339862.306 0.793431471 0.755860274 0.798372228 0.721427568 0.834310183 0.708618514 0.805590683 0.759402225 1 18.37459084 -1.870448791 2.600056748 1.10466009 0.77268049 0.778104571 0.038241919 7489018.085 4794334.468 4841799.142 0.007807806 0.013475696 1.870448791 -0.331979601 LGTQGWT(ph)KQRKPCPQNAS(ph)SYSAEMTEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGTQGWTKQRKPCPQNASSYSAEMTEPK 28 3 P45844-3 P45844-3 2 LGT(0.001)QGWT(0.565)KQRKPCPQNAS(0.565)S(0.384)Y(0.156)S(0.164)AEMT(0.164)EPK;LGTQGWT(0.615)KQRKPCPQNAS(0.615)S(0.615)Y(0.049)S(0.052)AEMT(0.052)EPK 55.469 0.035023 395130000 563880 597230 554870 646160 273030 649150 546480 549860 132160 TRUE FALSE 537226.5099 658088.416 580311.3383 581206.7692 320646.3456 626669.7727 463104.4392 501711.3434 152654.6978 3.519226841 4.310960785 3.801464001 3.807329728 2.100468247 4.105145676 3.033673027 3.286576506 1 17.21991246 2.955341452 21.00108912 2.961362185 3.904693474 0.293910596 0.838756216 96.12452206 45202.92592 0.227505002 0.241344551 902.2802515 -2.955341452 0.943331289 LGVADIIDCVVLTS(ph)SPEATETSQQLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.069)S(0.549)S(0.349)PEAT(0.033)ETSQQLQLR;LGVADIIDCVVLT(0.012)S(0.527)S(0.459)PEAT(0.002)ETSQQLQLR;LGVADIIDCVVLT(0.01)S(0.545)S(0.442)PEAT(0.003)ETSQQLQLR 160.92 6.11E-12 243094000 180691 138115 156603 173295 167390 155398 197028 176873 201288 TRUE FALSE 172150.0945 152189.0755 163783.4025 155875.0574 196582.763 150016.5283 166967.7599 161385.0625 232502.715 0.740421868 0.654569025 0.704436516 0.670422525 0.845507387 0.645224845 0.718132517 0.694121195 1 17.82688804 -1.407013836 3.793070518 1.001650817 0.706849818 0.725066509 0.056279078 8320621.403 3087337.909 113047.4584 0.011814492 0.03917294 1.407013836 -0.294800999 LGVADIIDCVVLTSS(ph)PEATETSQQLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.019)S(0.122)S(0.823)PEAT(0.03)ET(0.007)SQQLQLR;LGVADIIDCVVLT(0.003)S(0.026)S(0.97)PEAT(0.001)ETSQQLQLR 160.92 6.11E-12 167538000 121397 91956 102230 113789 117020 105024 140506 118998 137094 TRUE FALSE 115658.8044 101326.4209 106917.3466 102350.7135 137428.251 101386.9925 119069.2291 108577.9043 158353.8373 0.730382076 0.63987348 0.675180017 0.646341859 0.867855514 0.640255988 0.751918811 0.685666392 1 17.2727923 -5 0.287672757 3.28517057 0.68504203 0.644412514 0.068863307 141.3484821 1.336518397 193.5603458 0.067050518 1.00E-05 5 -2.60012854 LGVDLDAQTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGVDLDAQTWR 11 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 167.09 4.57E-05 158092000 340180 308930 289160 344140 375120 297550 378030 322300 363200 FALSE TRUE 324100.3656 340410.3182 302418.272 309546.3934 440540.8092 287245.7689 320354.5805 294077.7034 419523.201 0.772544557 0.811421913 0.720861853 0.737852859 1.050098798 0.684695788 0.763615885 0.700980786 1 18.67839107 -2.328571931 2.282654623 2.226349221 0.781957475 0.311337497 0.102679598 6931472.463 1145193.213 43668758.17 0.024179504 0.004692757 2.328571931 -1.444391747 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK 35 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 243.24 9.14E-48 2126470000 1214970 756920 1042550 1279050 1455650 1101760 1749560 1322510 90120 FALSE TRUE 1157540.776 834051.0085 1090351.949 1150477.464 1709514.899 1063605.775 1482632.489 1206704.013 104095.3493 11.12000472 8.012375326 10.47455007 11.05215047 16.4225867 10.21761089 14.24302333 11.59229515 1 16.66754609 -0.952242879 9.791834119 1.00000011 11.51567187 0.681735859 2.283650061 0 0 2.293513482 0.54058632 0.111623882 0.952242879 10.51567176 LGVIEDHSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;;;;;;; 242.59 2.27E-12 26506950000 14355070 11862030 12105620 13934970 15483190 11984480 15245680 12709630 14792580 FALSE TRUE 13676534.29 13070784.34 12660674.65 12534200.34 18183453.43 11569454.45 12919671.51 11596707.42 17086537.76 0.800427476 0.764975592 0.740973674 0.733571688 1.064197656 0.677109349 0.756131622 0.678704345 1 24.02635676 -2.296009047 2.32972018 2.08915317 0.777466447 0.293407907 0.108749033 8837298.152 2142735.712 50085145.1 0.026121731 0.005058141 2.296009047 -1.311686723 LGVQVVITDPEKLDQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGVQVVITDPEKLDQIR 17 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 153.21 1.68E-07 143330000 486770 523290 473060 551500 324210 544720 488150 586250 366410 FALSE TRUE 463761.3468 576613.8459 494750.2689 496062.1722 380752.1214 525856.2098 413673.752 534914.8421 423230.9914 1.095764148 1.362409317 1.168984027 1.172083761 0.899631948 1.242480396 0.977418385 1.263883914 1 18.69108575 3.106143609 3.209926154 1.078401744 1.227329117 0.175057934 0.129261068 0.34863598 7.151949415 0.035237252 0.043136378 1276.86096 -3.106143609 0.148927373 LGVS(ph)VS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 LGVS(1)VS(0.983)PS(0.017)R;LGVS(1)VS(0.92)PS(0.08)R 132.5 0.00044333 177044000 716130 516810 600580 666070 629630 621050 743530 651360 720440 TRUE FALSE 682279.9541 569473.5266 628117.1871 599115.3781 739437.2727 599542.8828 630090.8426 594323.4653 832162.1557 0.819888227 0.684329998 0.754801432 0.719950281 0.88857354 0.720464009 0.757173152 0.714191893 1 19.66650515 -1.741308561 2.832690941 1.045181912 0.755773283 0.626932454 0.058796 17517561.52 12908471.9 5507496.524 0.012828087 0.018142262 1.741308561 -0.289408629 LGVSVS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGVS(0.002)VS(0.998)PSR;LGVS(0.008)VS(0.982)PS(0.01)R;LGVSVS(0.836)PS(0.164)R;LGVSVS(0.998)PS(0.002)R;LGVSVS(1)PSR;LGVSVS(0.998)PS(0.002)R;LGVSVS(0.997)PS(0.003)R;LGVS(0.002)VS(0.997)PS(0.001)R;LGVS(0.001)VS(0.975)PS(0.024)R;LGVS(0.001)VS(0.999)PSR 176.62 5.56E-05 14275160000 11852690 10133580 10251560 12057390 11480030 10575920 12819960 11512940 12734610 TRUE FALSE 11292436.83 11166203.32 10721604.17 10845358.25 13482143.6 10209673.24 10864039.65 10504805.94 14709428.28 0.767700594 0.759118785 0.72889333 0.737306579 0.91656476 0.694090419 0.738576608 0.714154605 1 23.81023784 -1.031427104 4.497651816 1.000010698 0.757008789 0.614669587 0.060452441 0.08938196 33815875.43 806.8017713 0.013203489 0.093019263 1.031427104 -0.243001909 LGYEEHIPGQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LGYEEHIPGQTR 12 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 73.927 0.037881 1422560000 1212560 1154660 1225940 1342310 1367040 1220830 1443110 1330760 1288610 FALSE TRUE 1155244.692 1272321.167 1282150.562 1207378.449 1605451.343 1178552.351 1222937.065 1214231.6 1488441.057 0.776144064 0.854801176 0.861404995 0.811169809 1.078612643 0.791803172 0.82162277 0.815774057 1 20.50537066 -2.437530695 2.187618425 2.373565918 0.848434413 0.231804072 0.084851504 2982185.779 294227.2513 20401514.42 0.019386717 0.003651483 2.437530695 -1.525131505 LGYFSVDPDSHQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LGYFSVDPDSHQGK 14 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RR79 P47897 QARS Glutamine--tRNA ligase 0 ;;; 229.97 1.09E-12 1427120000 3766320 3163340 3410730 4108070 3301090 3725560 4600800 4179050 3458640 FALSE TRUE 3588293.518 3485687.942 3567115.344 3695118.999 3876799.051 3596542.923 3898863.461 3813110.227 3994988.227 0.898198772 0.872515198 0.892897586 0.924938645 0.970415638 0.90026371 0.975938661 0.954473458 1 21.92975982 2.338525233 0.378291129 0.998809247 0.86883022 0.682540729 0.023609171 0.719561278 0.237792166 0.025340407 0.033319155 218.0345072 -2.338525233 -0.129979027 LGYILTCPS(ph)NLGTGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LGYILTCPSNLGTGLR 16 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 1 LGYILTCPS(0.994)NLGT(0.006)GLR 130.29 5.32E-05 36149000 109540 84937 85313 91646 97331 80211 109480 96039 105370 TRUE FALSE 104362.2613 93592.17687 89224.68544 82433.56996 114305.4956 77433.27296 92776.81526 87629.31603 121710.2414 0.857464911 0.768975361 0.733091023 0.67729362 0.939160865 0.636210002 0.762276158 0.719983093 1 16.89309104 -1.065182285 4.415910065 1.000014664 0.76429922 0.432171445 0.085762652 10550793.67 2545006.471 1786.611485 0.018406722 0.086063245 1.065182285 -0.235715444 LGYLVS(ph)PPQQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LGYLVSPPQQIR 12 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LGYLVS(1)PPQQIR;LGYLVS(1)PPQQIR;LGYLVS(1)PPQQIR 116.63 0.00086054 130783000 355989 248006 395450 306386 388294 367487 619723 416068 521684 TRUE FALSE 339162.1055 273278.0934 413581.7737 275587.4972 456012.3507 354760.833 525172.8744 379634.8802 602584.0903 0.562846101 0.453510303 0.686346985 0.457342803 0.756761352 0.588732492 0.871534584 0.630011456 1 19.20080306 1.272605609 0.280779612 1.05511752 0.454276876 0.592683609 0.110342846 1.054297268 0.310316393 0.246206898 0.185844284 18.73292564 -1.272605609 -0.600840644 LHAEFAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHAEFAAER 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 135.55 0.00021771 162730000 132030 119320 62684 75810 118490 74309 126620 102070 76554 FALSE TRUE 125789.2036 131478.8437 65558.1234 68189.43477 139154.6185 71735.6607 107301.7935 93132.20969 88425.60334 1.42254278 1.486886588 0.741393001 0.771150348 1.573691479 0.81125441 1.213469735 1.053226737 1 16.43217654 3.76583179 24.68158179 1.041844409 1.454714797 0.349960708 0.2433528 630.7652423 570867.1755 0.058582269 0.105575828 5832.191699 -3.76583179 0.412870388 LHAEFAAERDWEQFHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHAEFAAERDWEQFHQPR 18 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 246.12 1.88E-24 711360000 98486 58846 60164 58592 106571 75608 113760 95059 91719 FALSE TRUE 93830.76196 64842.4743 62922.57891 52702.22084 125156.9487 72989.676 96403.82265 86735.13002 105942.3141 0.885677859 0.61205454 0.593932457 0.497461485 1.18136884 0.688956784 0.909965234 0.818701486 1 16.6929194 2.75851615 24.996317 0.894740336 0.664935062 0.415265112 0.158537992 915.8213146 1147156.955 0.0462174 0.048961127 573.4771915 -2.75851615 -0.229805274 LHCESESFK ddPTM_SK-BR-3_Trastuzumab_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 ; 166.09 0.00082221 0 539120 617160 416390 528220 390620 474990 477310 553040 254697 FALSE TRUE 513636.866 680049.3057 435481.8934 475122.322 458744.0043 458540.9772 404487.5931 504612.8858 294194.1099 1.745911453 2.311566692 1.48025361 1.614996038 1.559324231 1.558634118 1.374900378 1.715237895 1 18.16640884 6.086570385 0.062286179 1.45E-07 4.345965938 0.506343356 0.230582423 149.5620694 1.019387595 18.22353191 65.4554888 1220591.622 -6.086570385 4.345965793 LHDAFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHDAFFK 7 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 97.602 0.011877 732210000 1890580 1621120 1679760 1964730 1630770 1649030 2114620 1923310 1240610 FALSE TRUE 1801216.03 1786313.971 1756778.658 1767231.608 1915175.772 1591923.678 1791995.881 1754894.78 1432997.463 1.256956887 1.246557665 1.225946803 1.233241268 1.336482319 1.110904743 1.250522718 1.224632162 1 20.45060462 -4.196748075 0.271065277 1.39E-11 1.255030981 0.660569996 0.053575559 73.57992074 1.071114093 40.79554868 0.058586223 6.36E-05 4.196748075 1.255030981 LHDALDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHDALDAK 8 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 99.442 0.0068105 919230000 661467 531528 610125 658650 542620 594241 714437 663341 388173 FALSE TRUE 630200.7658 585691.3075 638099.8347 592441.2506 637252.7562 573662.2852 605436.5141 605255.3454 448368.8863 1.405540806 1.306271076 1.42315815 1.321325517 1.421268905 1.27944267 1.350308937 1.349904875 1 18.77432664 -3.19775485 0.364144821 1.18E-12 1.367253968 0.851282765 0.047091569 37.47985938 1.026315141 28.70272176 0.029610935 0.000634228 3.19775485 1.367253968 LHDEKEETAGSYDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHDEKEETAGSYDSR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;A0A2R8YEF8 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 246.27 2.21E-18 1054540000 888010 861570 757020 993380 597520 884380 1003810 919750 464540 FALSE TRUE 846035.5272 949364.9625 791730.1158 893523.5551 701727.2988 853753.6988 850660.3483 839211.8141 536578.4907 1.576722776 1.769293736 1.47551594 1.665224325 1.307781268 1.591106825 1.585341871 1.564005693 1 19.0334297 -2.726248628 0.29899241 2.34E-14 1.623427771 0.688027018 0.11962039 31.56954776 0.99837554 20.47283234 0.118394057 0.001878241 2.726248628 1.623427771 LHDETLTYLNQGQSYEIR ddPTM_SK-BR-3_Trastuzumab_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 0 223.06 4.38E-19 0 64238 51951 62148 64115 60386 56158 78640 55848 61747 FALSE TRUE 61201.59705 57244.86596 64997.54727 57670.03839 70917.29928 54213.23438 66642.02368 50957.65305 71322.4094 0.858097722 0.802621034 0.911320128 0.808582308 0.994320016 0.760115016 0.934377067 0.714469035 1 16.12206782 -2.387407589 2.415173994 2.277910437 0.851836202 0.246968724 0.08317834 5272009.997 1285279.1 36603078.49 0.01750519 0.004098193 2.387407589 -1.426074235 LHDFGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LHDFGYR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;;;; 163.34 0.0012385 3301990000 1798573 1502631 1346759 1654961 1725995 1485606 1987728 1620899 1286787 FALSE TRUE 1713558.019 1655750.807 1408509.232 1488601.176 2027007.982 1434159.092 1684463.586 1478964.491 1486335.356 1.152874425 1.113981983 0.947638921 1.001524434 1.363762204 0.964896035 1.133299817 0.995040914 1 20.50332823 -5 0.1161788 0.683062028 1.141711073 0.061341604 0.120890813 484.0984427 3.682459573 35.65521109 1.196150447 1.00E-05 5 0.458649045 LHDINAQMVEDQGFLDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LHDINAQMVEDQGFLDSLR 19 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ;;; 220.36 2.92E-19 285758000 214372 237987 186804 268176 246104 208541 231213 225726 165835 FALSE TRUE 204239.0604 262238.1459 195369.1482 241218.439 289024.4597 201319.1729 195937.2103 205960.2348 191551.8448 1.066233847 1.369019161 1.019928304 1.259285387 1.508857615 1.050990519 1.022893883 1.07521927 1 17.54737539 2.043595755 24.99990964 1.035670549 1.239523464 0.358824057 0.137820984 146.9252927 84253.42399 0.049284142 0.036398727 110.5594208 -2.043595755 0.203852915 LHDTFGFVDEDVFFQLSAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHDTFGFVDEDVFFQLSAVK 20 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 87.486 0.0023563 40598000 49769 46715 49687 53443 50122 53680 68387 56230 33061 FALSE TRUE 47416.518 51475.31161 51965.1981 48070.8081 58863.26093 51821.04814 57953.30714 51306.20311 38187.93103 1.241662398 1.347947119 1.360775426 1.258795824 1.541410057 1.357000674 1.517581748 1.343518796 1 15.22082914 0.955261264 23.32084202 0.999999998 1.374607093 0.604761831 0.094612413 3637.831493 1896285.067 0.09293021 0.023232552 9.021136707 -0.955261264 0.374607095 LHDVEHVLIDVGTGYYVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHDVEHVLIDVGTGYYVEK 19 0 Q99471;H3BPF6;Q99471-3 Q99471 PFDN5 Prefoldin subunit 5 0 169.25 8.38E-12 54389000 130600 146290 156940 184930 128720 173940 202980 133370 8388.7 FALSE TRUE 124426.7968 161197.1173 164135.8542 166340.4851 151168.7272 167916.4142 172011.673 121691.4158 9689.576752 12.8413036 16.63613607 16.93942454 17.16695056 15.60116929 17.32959225 17.75223804 12.5590022 1 13.24221793 0.877588939 3.982995361 1.002703562 16.24663695 0.924017032 1.379465419 0.175156514 5.161936243 1.432196736 0.366206307 7.54377868 -0.877588939 15.24393339 LHDVNSDGFLDEQELEALFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LHDVNSDGFLDEQELEALFTK 21 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;; 233.68 9.32E-30 184570300 249647 228749 206882 284518 220381 235921 328596 241990 126597 FALSE TRUE 237846.6811 252058.7832 216367.7443 255917.7101 258815.3766 227750.9966 278462.6451 220800.0727 146229.0162 1.626535466 1.723726178 1.479649867 1.750115789 1.769931737 1.55749524 1.904291312 1.509960735 1 17.15787009 0.980966182 23.73286262 0.999999995 1.690179895 0.773969472 0.116857199 294.3359194 367002.0575 0.103928952 0.025982238 9.571195379 -0.980966182 0.6901799 LHEDLCEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHEDLCEKR 9 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 125.48 0.00032484 354040000 520210 343920 452800 436170 401040 477870 615430 539780 462490 FALSE TRUE 495620.7043 378965.839 473561.3279 392325.3629 470981.249 461321.2421 521534.8504 492514.0016 534210.5871 0.927762789 0.709394101 0.88646938 0.734402074 0.881639676 0.863556907 0.976272023 0.921947287 1 19.02704904 1.993566233 1.541826294 0.969578734 0.814926557 0.459757473 0.068553386 0.323770921 1.435096915 0.041639838 0.019968352 98.5294895 -1.993566233 -0.154652176 LHEEGIIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LHEEGIIYR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;;; 198.65 2.60E-05 1918240000 959776 1012302 934881 1053638 931724 1011664 995387 967205 591897 FALSE TRUE 914409.2906 1115456.725 977746.2186 947724.3065 1094216.371 976629.822 843522.4316 882511.4027 683685.3638 1.337470917 1.631535182 1.430111379 1.386199496 1.600467742 1.428478469 1.233787465 1.290815117 1 19.38297302 1.194391358 0.885767582 1.014317206 1.485691527 0.689690653 0.100267184 0.291934955 0.504179228 0.090351432 0.03266062 15.64556885 -1.194391358 0.471374321 LHELNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHELNQK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 107.43 0.0074794 77793000 134230 125930 124410 145960 116090 126920 154040 130270 75103 FALSE TRUE 127885.2139 138762.4102 130114.3216 131287.8235 136336.0592 122524.7286 130538.3689 118862.8682 86749.58967 1.474188113 1.599574254 1.499884 1.513411464 1.571604659 1.412395483 1.504772177 1.370183636 1 16.40456931 0.338421118 0.681396721 0.98616429 1.533025482 0.91367158 0.049586342 0.553335468 0.37028838 0.059674026 0.016647462 2.179822434 -0.338421118 0.546861192 LHEVFHDQLHTFLVMELLNGGELFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHEVFHDQLHTFLVMELLNGGELFER 26 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 129.23 2.82E-05 55775000 27730 40853 38449 43936 36977 40037 43654 25368 8319.5 FALSE TRUE 26419.25786 45015.96715 40211.92468 39519.46981 43425.77709 38650.50865 36993.78054 23146.64344 9609.64557 2.749243733 4.684456551 4.184537753 4.112479437 4.518978018 4.022053505 3.849650882 2.408688569 1 13.23026751 1.042626948 2.221577146 1.007551934 4.048636439 0.798861482 0.511007303 0.123509454 1.278777434 0.478413861 0.132414642 11.03130642 -1.042626948 3.041084506 LHFFMPGFAPLT(ph)SR ddPTM_SK-BR-3_Trastuzumab_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(0.5)S(0.5)R 120.9 0.00043307 48226000 128030 116810 86938 107910 119260 91008 126830 94929 80459 TRUE FALSE 121978.2756 128713.0718 90924.19329 97062.68178 140058.9062 87856.37014 107479.7541 86616.51351 92936.17079 1.312495174 1.384962073 0.978350975 1.04440156 1.507044082 0.945340973 1.156490021 0.932000025 1 16.50395258 7.110677748 0.171328561 0.945860357 2.30760234 0.238795245 0.174682969 54.47596346 0.773082172 0.430634069 17.97158184 12902615.28 -7.110677748 1.361741983 LHFFMPGFAPLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 145 8.70E-06 8966540000 7621120 5392680 3573840 4403780 8060650 4311800 8474660 6288070 5485920 FALSE TRUE 7260884.761 5942200.223 3737704.099 3961103.668 9466424.808 4162481.285 7181694.969 5737453.256 6336648.455 1.145855702 0.937751284 0.589855051 0.625110213 1.493916678 0.656890044 1.133358592 0.905439728 1 22.59528855 LHGELQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;;; 140.35 0.00065091 3888891000 1892701 1857301 1747259 2000108 1984314 1739313 2173084 1849879 1570990 FALSE TRUE 1803236.775 2046562.083 1827372.553 1799053.344 2330377.733 1679080.155 1841540.124 1687893.788 1814611.106 0.993731808 1.12782407 1.007032608 0.991426393 1.284229842 0.925311296 1.014840105 0.930168333 1 20.79122896 LHGGFDS(ph)DCS(ph)EDGEALNGEPELDLTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 2 LHGGFDS(1)DCS(1)EDGEALNGEPELDLTSK;LHGGFDS(1)DCS(1)EDGEALNGEPELDLTSK;LHGGFDS(1)DCS(1)EDGEALNGEPELDLTSK 201.8 2.33E-25 433775000 228605 239854 274365 320058 182170 303759 335471 243547 123088 TRUE FALSE 217799.2947 264295.3953 286944.9066 287885.1618 213940.3903 293239.7497 284288.7376 222220.7336 142175.8584 1.531900684 1.858933002 2.018239312 2.024852637 1.504758914 2.062514361 1.999557033 1.562999064 1 17.11731699 0.939201756 4.66876552 1.000329396 1.85072215 0.659431556 0.196524009 0.187217003 11.38246905 0.190318893 0.048258784 8.693642069 -0.939201756 0.850392754 LHHCPGNHS(ph)WDSTISGSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHHCPGNHSWDSTISGSQR 19 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 LHHCPGNHS(0.999)WDS(0.001)TISGSQR;LHHCPGNHS(1)WDSTISGSQR 151 1.17E-07 225290000 66238 71311 82799 102816 102143 91255 105813 58778 27985 TRUE FALSE 63107.06101 78577.67197 86595.41605 92480.74034 119956.7069 88094.81647 89669.28346 53631.08672 32324.77087 1.952281774 2.43088102 2.678918171 2.860986725 3.71098398 2.725303663 2.774011417 1.659132773 1 14.98035252 1.074986874 3.355268561 1.012859257 2.69269706 0.655521816 0.435750798 0.150239281 3.34383797 0.459011076 0.120247297 11.88466307 -1.074986874 1.679837803 LHHS(ph)QSPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.5)QS(0.5)PAR;LHHS(0.593)QS(0.407)PAR 64.439 0.044772 20967000 13088.4 13854.5 11687.8 12312.1 20572.8 13001.6 22616 13885.6 4203.1 TRUE FALSE 12469.73727 15266.2893 12223.69719 11074.46432 24160.68981 12551.35133 19165.51383 12669.70325 4854.895282 2.568487382 3.144514643 2.51780862 2.281092315 4.976562501 2.585298056 3.947667811 2.609675908 1 12.24522446 LHHSQS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.005)QS(0.995)PAR;LHHS(0.077)QS(0.923)PAR;LHHS(0.023)QS(0.977)PAR;LHHS(0.121)QS(0.879)PAR;LHHS(0.048)QS(0.952)PAR;LHHS(0.156)QS(0.844)PAR 167.18 3.88E-05 421421000 308350.7 259364.6 238126.6 283153.4 482663 272550.7 475499 287506.9 93609.2 TRUE FALSE 293775.5735 285794.1476 249044.9401 254690.2823 566839.2744 263112.2009 402952.8944 262331.2717 108125.6366 2.716983526 2.643167305 2.303292243 2.355503192 5.242413289 2.433393311 3.726710028 2.426170886 1 16.7223491 LHIVQVVCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHIVQVVCK 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 109.21 0.0024854 513930000 2186170 1813480 813330 1007250 1882830 1228750 2263430 1652390 1442820 FALSE TRUE 2082834.077 1998275.674 850621.985 905999.3164 2211194.956 1186198.079 1918102.183 1507697.972 1666565.157 1.249776565 1.199038433 0.510404278 0.5436327 1.326797783 0.711762198 1.150931408 0.904673883 1 20.66844629 3.960516164 24.97949211 0.891766081 1.23075003 0.24676683 0.25115235 635.0183427 401745.4653 0.062555374 0.112780293 9130.954201 -3.960516164 0.338983949 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LHKTEDGGWEWSDDEFDEESEEGK 24 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK 325.65 5.77E-75 3374780000 3911840 4499430 3315890 4524980 1480215 4478230 3816740 4498580 885481 TRUE FALSE 3726935.076 4957927.032 3467926.836 4070120.413 1738364.027 4323147.772 3234426.214 4104660.487 1022796.871 3.643866325 4.847421001 3.390631057 3.979402488 1.699618054 4.226790181 3.162334873 4.013172706 1 19.96408822 3.273200855 2.078381494 3.098952618 4.204383619 0.182320075 1.053353785 0.50696279 4.493791675 0.293912832 0.413029748 1875.861868 -3.273200855 1.105431001 LHKTEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LHKTEDGGWEWSDDEFDEESEEGKAAISQLR 31 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKTEDGGWEWS(1)DDEFDEESEEGKAAISQLR;LHKT(0.005)EDGGWEWS(0.993)DDEFDEES(0.002)EEGKAAISQLR;LHKTEDGGWEWS(1)DDEFDEESEEGKAAISQLR 220.04 3.10E-35 117804000 139083 105794 130944 146585 91143 146144 175658 163794 92196 TRUE FALSE 132508.8222 116574.5289 136947.9119 131849.9973 107038.3103 141082.9966 148858.1459 149451.329 106493.2848 1.24429275 1.094665538 1.285976972 1.238106211 1.005117933 1.324806507 1.397817207 1.403387353 1 16.70040294 2.100092114 22.54184337 1.32404095 1.176286643 0.0969042 0.138717543 8.841986656 1973.124457 0.046800442 0.034564411 125.9192459 -2.100092114 -0.147754307 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR 30 0 Q9BPW8;H7C2U6 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 ; 233.22 1.31E-45 435960000 289820 240440 250820 255300 279510 217330 286930 261330 124231 FALSE TRUE 276120.783 264941.1094 262320.3451 229636.759 328256.4555 209803.8076 243153.5587 238446.5598 143496.109 1.924238817 1.846329571 1.82806591 1.600299552 2.287563459 1.462087084 1.694495832 1.661693557 1 17.13065209 -0.371044637 0.334735796 0.743085513 1.906106374 0.612411403 0.206624124 4.663932784 0.591611792 1.570911343 0.17447495 0.425554673 0.371044637 1.163020861 LHLGFIEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHLGFIEIR 9 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 158.37 6.69E-05 1235040000 1508300 1298750 1075650 1299730 1647940 1175880 1705140 1351770 1010610 FALSE TRUE 1437005.648 1431094.102 1124969.616 1169078.671 1935340.214 1135158.981 1444989.576 1233401.853 1167330.237 1.231018954 1.225954795 0.963711536 1.001497806 1.657920058 0.972440312 1.237858431 1.05660062 1 20.15478133 1.084819729 4.668466869 1.001100574 1.185691503 0.098543533 0.199545637 0.43739002 15.71951372 0.174579036 0.04440072 12.1568128 -1.084819729 0.18459093 LHLGIPEAVFVEDVDSFMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHLGIPEAVFVEDVDSFMK 19 0 P61758 P61758 VBP1 Prefoldin subunit 3 0 152.68 5.33E-08 83138000 93878 114180 93351 110540 80751 91811 109530 102540 59027 FALSE TRUE 89440.57299 125815.0718 97631.23569 99428.30919 94833.94883 88631.56205 92819.18684 93561.054 68180.60569 1.311818399 1.845320536 1.431950255 1.458307801 1.390922651 1.299952694 1.361372283 1.372253195 1 16.0570738 0.742490818 0.289834674 0.917760984 1.599439927 0.511205998 0.143855189 2.060612387 0.4546241 0.474782012 0.218303949 5.527017221 -0.742490818 0.681678944 LHLIYLINDVLHHCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHLIYLINDVLHHCQR 16 0 Q8IWX8 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 137.68 3.72E-06 48660000 26637.9 30098.1 25444.9 31141.6 29469.1 29199.4 37954 24474.4 8458 FALSE TRUE 25378.77926 33165.13061 26611.57383 28011.1872 34608.50171 28188.21746 32163.42023 22331.29179 9769.623443 2.597723383 3.394719439 2.723909881 2.867171633 3.542460148 2.885292112 3.292186277 2.285788385 1 13.25408724 0.942097901 3.645874238 1.00177739 3.049319312 0.827980461 0.298719163 0.097923929 3.408290834 0.263475042 0.067874504 8.751810412 -0.942097901 2.047541921 LHLSGIDANPNALFPPVEFPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 178.53 5.13E-17 2247959000 1225870 901930 1153895 1252031 2495940 956785 1689587 1419891 2038880 FALSE TRUE 1167925.555 993837.6924 1206802.227 1126174.465 2931231.146 923651.2955 1431809.472 1295557.817 2355059.097 0.495921973 0.422001169 0.5124297 0.478193718 1.244652905 0.392198776 0.60797178 0.550116903 1 21.16733183 2.939218009 24.99993995 0.710794702 0.47121457 0.243794954 0.238343511 379.3176787 156014.7867 0.068508154 0.072663971 869.3967436 -2.939218009 -0.239580132 LHNAIEGGTQLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHNAIEGGTQLSR 13 0 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 172.85 2.27E-05 503060000 283790 233760 247760 329080 301240 242600 305030 257880 237750 FALSE TRUE 270375.8091 257580.4098 259120.0411 296000.2532 353776.1606 234198.7012 258492.0712 235298.6601 274619.0557 0.984548608 0.93795534 0.943561765 1.077857661 1.288243307 0.852813001 0.941275071 0.856818401 1 18.06707221 LHNQVNGTEWSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHNQVNGTEWSWK 13 0 O14980 O14980 XPO1 Exportin-1 0 ; 201.09 1.05E-07 1388730000 1185620 1197000 1159780 1413900 1011190 1369800 1410470 1274310 786860 FALSE TRUE 1129578.092 1318975.661 1212957.06 1271772.086 1187541.216 1322363.483 1195276.896 1162724.661 908882.2301 1.242821187 1.451206347 1.33455911 1.399270493 1.306595262 1.454933806 1.315106465 1.279290784 1 19.79373384 0.72520934 1.624473631 1.000404945 1.363266397 0.752564161 0.06445433 0.438219961 1.830582658 0.055522774 0.015908852 5.31140405 -0.72520934 0.362861452 LHPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHPESK 6 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 129.16 0.016314 548300000 1368840 1362490 1201380 1441360 930980 1389600 1333500 1441210 952450 FALSE TRUE 1304137.646 1501329.28 1256464.461 1296471.754 1093342.617 1341477.804 1130050.084 1315010.012 1100151.082 1.185416865 1.364657369 1.142083558 1.17844883 0.993811337 1.219357801 1.027177178 1.195299477 1 20.06927023 3.471154146 2.706880272 1.100554946 1.273908119 0.364511274 0.090827636 0.236763075 3.497255401 0.023179988 0.035643824 2959.06255 -3.471154146 0.173353172 LHPGLPENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHPGLPENR 9 0 Q5VZK9;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 84.213 0.015645 124220000 66031 57917 57309 72080 65452 56112 69420 70477 76036 FALSE TRUE 62909.84549 63818.80815 59936.67434 64834.38146 76866.80808 54168.82737 58828.70401 64305.66026 87827.27454 0.716290535 0.72663997 0.682438054 0.738203272 0.875204297 0.616765437 0.669822721 0.732183261 1 16.42238141 0.944234459 21.47203967 1.000000001 0.715186108 0.641596564 0.06589969 2205.699426 849287.5124 0.06190558 0.015476395 8.794971953 -0.944234459 -0.284813892 LHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHPPSPVPQGVCPAHREPLAAFCGDELR 28 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHREPLAAFCGDELR 82.058 0.0029239 84518000 8746.7 10095 7251.5 8649.2 11170 8442.7 10834 10246 8902.3 TRUE FALSE 8333.260825 11123.69198 7583.988448 7779.765984 13118.04446 8150.327182 9181.07432 9348.805923 10282.82322 0.810405922 1.081774114 0.737539515 0.756578794 1.275724009 0.792615706 0.892855408 0.909167232 1 13.3279488 LHPTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHPTDK 6 0 G8JLM4 G8JLM4 USHBP1 0 ; 110.24 0.028873 840670000 2030380 1984050 1680370 2128160 1334030 1892050 1968870 1981590 1338590 FALSE TRUE 1934407.961 2186226.951 1757416.627 1914233.314 1566684.41 1826527.834 1668482.721 1808071.475 1546171.701 1.251095179 1.413961302 1.136624494 1.238047051 1.013266773 1.181322769 1.079105716 1.169385957 1 20.56026911 3.441706937 1.822207621 1.107359695 1.329442906 0.503344089 0.085814262 0.230673055 1.547946873 0.023406129 0.038435795 2765.075133 -3.441706937 0.222083211 LHPVILASIVDSYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHPVILASIVDSYER 15 0 O00303;E9PQV8;A0A1W2PP79 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 232.37 6.91E-14 556690000 601080 567730 558040 631700 631020 564330 666130 643130 573940 FALSE TRUE 572668.1396 625582.3325 583626.686 568200.3158 741069.6882 544787.1106 564499.6342 586814.1278 662943.6839 0.863826225 0.94364325 0.880356356 0.857086853 1.117847121 0.821769818 0.851504657 0.885164369 1 19.3385268 -0.984917761 7.979702151 1 0.901080135 0.120134414 0.082699892 1.12E-09 1.40E-10 0.074921617 0.017659194 0.10353382 0.984917761 -0.098919865 LHQEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHQEGK 6 0 O43488;H7C5H7;H7C4Q7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 92.191 0.047037 417970000 911480 852340 780210 971470 619980 870650 983590 1020770 547080 FALSE TRUE 868396.1468 939194.415 815983.4002 873815.9899 728104.3157 840499.1722 833525.2806 931385.9674 631918.3723 1.374222027 1.486259074 1.291279754 1.382798836 1.152212608 1.330075543 1.319039479 1.47390234 1 19.26937869 -3.489423563 0.296293729 4.03E-33 1.377156879 0.545003612 0.0977865 74.58687657 1.590668223 46.22735341 0.099623525 0.000324023 3.489423563 1.377156879 LHQLAMQQSHFPMTHGNTGFSGIESSS(ph)PEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.021)S(0.108)S(0.872)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.005)S(0.17)S(0.825)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.003)S(0.039)S(0.958)PEVK;LHQLAMQQSHFPMTHGNT(0.001)GFS(0.001)GIES(0.08)S(0.133)S(0.784)PEVK 197.35 1.47E-25 2540280000 615204 702904 679718 852277 587503 869900 1018570 900940 78599 TRUE FALSE 586124.5261 774530.7167 710883.7426 766604.4967 689963.3372 839775.1449 863168.4392 822048.9174 90787.73149 6.455988232 8.531226676 7.830174088 8.443921708 7.599742012 9.249874747 9.507544962 9.054625597 1 16.47020973 -0.38779893 8.148202883 1 8.334512858 0.870605816 0.88858322 0 0 0.936299812 0.220687982 0.409450184 0.38779893 7.334512858 LHQNICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHQNICR 7 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 151.17 0.0018992 257770000 370400 308690 225530 276740 366090 258150 442140 319880 295610 FALSE TRUE 352891.9261 340145.862 235870.7736 248921.5694 429935.9801 249210.2008 374683.4225 291869.6114 341451.689 1.033504702 0.996175661 0.690788129 0.72900963 1.259141465 0.729854936 1.097324847 0.854790358 1 18.38132194 LHS(ph)PQTHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHSPQTHWK 9 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LHS(1)PQTHWK;LHS(1)PQTHWK 146.36 0.00015875 208718000 330460 347780 337250 431870 281370 395500 421870 301610 39515 TRUE FALSE 314839.8107 383219.1774 352713.2461 388457.6071 330440.8389 381803.7358 357505.9833 275199.4295 45642.78439 6.897909822 8.396051699 7.727689071 8.51082186 7.239716931 8.36504041 7.832694437 6.029418082 1 15.47809918 0.824428903 2.346710197 1.003287421 7.873975464 0.94717197 0.509451544 0.1275165 1.249421905 0.451720009 0.122120058 6.67465624 -0.824428903 6.870688043 LHS(ph)SNPNLSTLDFGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHSSNPNLSTLDFGEEK 17 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 LHS(0.491)S(0.491)NPNLS(0.016)T(0.003)LDFGEEK 63.918 0.03208 855140000 289830 266350 271260 335750 210370 277090 324600 342170 203760 TRUE FALSE 276130.3103 293491.3678 283697.5393 301999.7721 247058.4614 267494.3038 275076.3083 312207.7808 235358.0601 1.173234986 1.246999434 1.205386971 1.283150328 1.049713196 1.13654193 1.168756694 1.326522579 1 17.84449774 2.758521637 24.99203433 1.148405975 1.223287238 0.198275548 0.088829765 1540.573494 1928860.146 0.025219157 0.026712789 573.4844368 -2.758521637 0.074881263 LHSELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHSELK 6 0 D6RBP0;A0A494C0G8;Q96NL6-2;Q96NL6 D6RBP0 SCLT1 Sodium channel and clathrin linker 1 0 ; 100.27 0.037849 353600000 962870 850810 845440 942680 866250 857070 1048490 911560 863830 FALSE TRUE 917357.0433 937508.5063 884204.2603 847920.0154 1017323.726 827389.451 888523.5937 831738.9739 997788.3446 0.919390418 0.939586548 0.88616415 0.849799479 1.019578682 0.829223407 0.890493057 0.833582571 1 19.92837429 LHSLVKPSVDYVCQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHSLVKPSVDYVCQLK 16 1 O43813 O43813 LANCL1 LanC-like protein 1 0 ; 114.69 0.00033867 785890000 1248190 1112490 1169120 1396540 906030 1264230 1426820 1429070 857550 FALSE TRUE 1189190.532 1225853.996 1222725.308 1256157.146 1064041.345 1220449.398 1209132.404 1303933.055 990534.4742 1.200554411 1.23756823 1.234409645 1.268160956 1.074209301 1.232111986 1.220686846 1.316393411 1 19.91784766 -0.995168121 4.349980546 0.99999061 1.220632302 0.565877146 0.061355437 0.033455163 16373782.24 355.7349467 0.013220429 0.101118793 0.995168121 0.220641692 LHSS(ph)NPNLSTLDFGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LHSSNPNLSTLDFGEEK 17 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 LHS(0.119)S(0.881)NPNLSTLDFGEEK;LHS(0.028)S(0.97)NPNLST(0.001)LDFGEEK;LHS(0.041)S(0.959)NPNLSTLDFGEEK;LHS(0.02)S(0.98)NPNLSTLDFGEEK 311.37 2.56E-58 1173031000 1397990 1402410 1201150 1531090 868160 1413300 1507280 1551870 734386 TRUE FALSE 1331909.783 1545317.173 1256223.916 1377181.924 1019566.829 1364357.067 1277316.753 1415980.036 848270.8302 1.570146863 1.821726173 1.480923157 1.623516777 1.201935506 1.608397953 1.505788844 1.66925466 1 19.69416543 -2.928676422 0.237088017 1.04E-13 1.647332254 0.526650216 0.162695917 42.772453 1.026562582 22.20201531 0.265459602 0.001178484 2.928676422 1.647332254 LHSS(ph)SLELGPRPLEQENER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LHSSSLELGPRPLEQENER 19 1 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 LHS(0.21)S(0.662)S(0.128)LELGPRPLEQENER;LHS(0.001)S(0.865)S(0.134)LELGPRPLEQENER;LHS(0.001)S(0.999)SLELGPRPLEQENER;LHSS(0.999)SLELGPRPLEQENER;LHS(0.002)S(0.997)S(0.001)LELGPRPLEQENER 309.82 1.04E-61 1322420000 560970 420349 510441 524619 526424 463470 635445 583840 541107 TRUE FALSE 534454.0598 463183.041 533845.2247 471883.3014 618232.1789 447419.9177 538496.1945 532715.8745 625019.11 0.85510035 0.741070207 0.854126244 0.754990198 0.989141242 0.715849981 0.861567568 0.852319339 1 19.25354078 -4.999999729 0.223916353 1.93545056 0.800547702 0.335426 0.077269769 162.7989401 1.628683037 68.63284633 0.124192848 1.00E-05 4.999999729 -1.134902858 LHSYS(ph)SPSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LHS(0.001)YS(0.497)S(0.497)PS(0.004)T(0.001)K;LHSYS(0.529)S(0.469)PS(0.001)TK;LHS(0.003)YS(0.964)S(0.033)PS(0.001)TK;LHSYS(0.714)S(0.286)PSTK 208.33 0.00045039 2129120000 2329890 2011950 2125600 2499080 1796200 2317020 2759350 2362320 1409090 TRUE FALSE 2219760.717 2216969.992 2223060.863 2247867.73 2109456.711 2236781.016 2338360.479 2155462.737 1627604.481 1.363820722 1.362106101 1.365848331 1.381089667 1.296049953 1.374277991 1.436688401 1.32431605 1 20.63431873 0.964099487 23.75654628 0.999999999 1.369824865 0.921160272 0.03361818 839.3782876 555444.8458 0.033218652 0.008304663 9.206604501 -0.964099487 0.369824865 LHSYSS(ph)PSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LHSYS(0.232)S(0.768)PSTK 136.38 7.68E-05 1468000000 1364300 1229600 1322100 1561200 1022800 1413200 1699000 1457200 739370 TRUE FALSE 1299812.243 1354897.638 1382719.593 1404265.21 1201175.996 1364260.53 1439786.346 1329599.843 854027.7234 1.521978979 1.58647969 1.619057034 1.644285275 1.406483611 1.597442908 1.68587776 1.556857941 1 19.70392338 0.942354983 23.01233337 1 1.58311045 0.85393291 0.075089949 3843.734821 1534450.37 0.072031554 0.018007888 8.756992605 -0.942354983 0.583110451 LHTDDELNWLDHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 234.85 1.85E-17 615597000 417016 391100 410566 463919 394184 423721 477416 398252 83826.4 FALSE TRUE 397304.4801 430953.5346 429390.8572 417284.9807 462929.5648 409047.4355 404577.4209 363378.9436 96825.76999 4.103292751 4.450814434 4.434675369 4.309647946 4.781057407 4.224571987 4.17840644 3.75291561 1 16.56310345 0.471132055 1.15927216 0.996035174 4.3855044 0.973201848 0.174163481 0.295594427 0.508227708 0.161725396 0.049287743 2.95891204 -0.471132055 3.389469227 LHTLEEEKEELAQYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHTLEEEKEELAQYQK 16 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 77.754 0.013845 51879000 74005 76580 67478 82514 43089 80964 78158 80443 49514 FALSE TRUE 70506.93031 84383.58906 70571.93304 74219.53595 50603.70796 78160.19638 66233.56163 73398.98446 57192.37824 1.23280291 1.475434169 1.233939473 1.297717253 0.884798106 1.366619098 1.158083711 1.283370035 1 15.80353528 -2.84756414 0.041752583 5.23E-08 1.969759072 0.209529682 0.15155159 680.854434 3.201219509 113.4316075 48.88186037 0.001420482 2.84756414 1.96975902 LHVAILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 310704000 454260 422800 338537 347236 655450 346057 558380 422370 582220 FALSE TRUE 432788.0301 465883.8007 354059.2563 312331.1776 769760.2725 334072.9593 473188.8756 385385.0437 672507.704 0.643543602 0.69275608 0.526476134 0.464427657 1.144611828 0.496757074 0.70361852 0.573056697 1 19.35919127 LHVAVK ddPTM_SK-BR-3_Trastuzumab_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 ; 72.054 0.086609 1123490000 5704600 4996000 5123800 6208500 5813800 5833200 7009700 6577000 5260200 FALSE TRUE 5434954.863 5505098.08 5358731.298 5584409.785 6827724.879 5631194.821 5940241.523 6001083.013 6075924.951 0.894506583 0.906051033 0.881961404 0.919104471 1.123734235 0.926804539 0.977668679 0.987682215 1 22.53467262 2.978085302 24.98190552 0.996244315 0.897236809 0.520248811 0.049245997 603.5729216 688050.2823 0.013955006 0.014922882 950.7915245 -2.978085302 -0.099007507 LHVENEDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LHVENEDKK 9 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 190.05 2.43E-05 1315660000 3121900 2858300 2642570 3439250 1715410 3271620 3340040 3508140 1347840 FALSE TRUE 2974333.974 3149564.02 2763734.448 3093530.056 2014576.961 3158322.979 2830455.554 3200948.664 1556856.143 1.910474508 2.023028289 1.775202198 1.987036547 1.294003283 2.028654345 1.818058506 2.056033679 1 20.57020421 -1.791473012 2.698738826 0.762814844 1.866996606 0.598943163 0.221524154 34680013.73 26105178.81 54102111.33 0.050748248 0.016163187 1.791473012 1.104181761 LHVGNIS(ph)PTCTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHVGNISPTCTNK 13 0 Q9BWF3;E9PB51;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 Q9BWF3 RBM4 RNA-binding protein 4 1 LHVGNIS(0.923)PT(0.076)CT(0.001)NK 89.344 0.0048264 316650000 798370 738140 719310 769590 625000 754750 842290 785650 362770 TRUE FALSE 760632.6323 813357.3052 752291.075 692229.3511 733999.8021 728612.8183 713783.1908 716854.321 419026.5188 1.815237457 1.941064034 1.795330465 1.651994134 1.751678639 1.738822689 1.703432023 1.710761226 1 18.67668202 -2.275480891 0.265359234 1.00E-19 1.867253189 0.930842888 0.06635554 9.362804578 0.329498387 5.690707619 0.093479565 0.005302969 2.275480891 1.867253189 LHYCVSCAIHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LHYCVSCAIHSK 12 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 179.35 1.20E-05 1414630000 1730080 1578250 1285450 1559210 1504600 1392030 1866100 1669570 766700 FALSE TRUE 1648302.547 1739075.469 1344389.154 1402475.248 1767001.764 1343823.652 1581392.172 1523373.6 885595.9202 1.861235479 1.963734735 1.518061594 1.583651433 1.995268636 1.517423038 1.78568141 1.720167816 1 19.75628905 -2.339093572 0.289142082 4.71E-11 1.827978489 0.65617038 0.168871843 25.16362783 0.934437363 16.52274153 0.183323295 0.004580432 2.339093572 1.827978489 LHYTPPLQS(ph)PIIDNDPLLGQSPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYTPPLQS(1)PIIDNDPLLGQSPWR 239.9 1.03E-37 131740000 69023 58230 56638 66770 76349 70575 83424 72635 51590 TRUE FALSE 65760.41958 64163.7032 59234.90832 60058.15275 89664.24143 68130.97005 70696.13661 66274.69434 59590.31371 1.103542094 1.076747196 0.994035853 1.007850924 1.504678124 1.143322896 1.186369599 1.112172268 1 15.86279022 LHYTPPLQSPIIDNDPLLGQS(ph)PWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYTPPLQSPIIDNDPLLGQS(1)PWR 176.84 2.82E-17 136950000 17021 18408 19025 17745 19107 18784 19608 19954 18522 TRUE FALSE 16216.45106 20283.79613 19897.31507 15961.23889 22439.25475 18133.50537 16616.43947 18206.72198 21394.29716 0.757980079 0.948093596 0.930028919 0.746051098 1.04884281 0.847585935 0.776676109 0.851008184 1 14.38493866 -2.481077197 2.191997859 2.569443609 0.861584253 0.173870182 0.09359086 6162472.425 518903.826 48088242.05 0.021708965 0.003303108 2.481077197 -1.707859356 LIALSIDSVEDHLAWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LIALSIDSVEDHLAWSK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 294.93 4.21E-46 3882830000 10115680 8167260 9209260 10295620 8787580 9498980 12071700 10386810 8480330 FALSE TRUE 9637531.854 8999513.079 9631513.68 9260684.717 10320131.17 9170027.941 10229940.45 9477285.852 9795416.265 0.983881807 0.918747385 0.98326742 0.945410023 1.053567392 0.936155003 1.044359951 0.967522522 1 23.22367537 2.795843163 24.99981899 1.001108407 0.955621817 0.234887016 0.03800255 345.8683604 150946.5591 0.010228344 0.010848796 624.9469651 -2.795843163 -0.04548659 LIAQACVSIFPDSGHFNVDNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIAQACVSIFPDSGHFNVDNIR 22 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 171.58 5.86E-12 892410000 313550 324630 335340 394980 395590 329170 395970 373560 380190 FALSE TRUE 298729.1129 357710.1661 350715.6707 355275.86 464580.7708 317770.7604 335557.504 340849.106 439147.9235 0.680247126 0.814555067 0.798627642 0.809011818 1.057914078 0.723607567 0.764110419 0.776160122 1 18.74434746 -2.674534548 2.060593672 5.951491236 0.798280603 0.278322423 0.099417508 2444909.198 102455.8003 57207672.61 0.024536317 0.002115755 2.674534548 -5.153210633 LICCDILDVLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LICCDILDVLDK 12 0 P62258;P62258-2;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 177.76 5.32E-05 107452000 446140 559110 396830 535220 298620 459870 424870 506610 284760 FALSE TRUE 425051.8464 616083.9447 415025.048 481418.6687 350699.2335 443944.5866 360048.2782 462248.5427 328919.1264 1.292268561 1.873056004 1.261784477 1.463638415 1.06621721 1.349707423 1.094640747 1.405356227 1 18.32737338 3.217688382 1.728787111 1.20071366 1.566411867 0.308418187 0.206666112 0.349044468 2.155794517 0.062024533 0.086305343 1650.776896 -3.217688382 0.365698207 LICCDILDVLDKHLIPAANTGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LICCDILDVLDKHLIPAANTGESK 24 1 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 137.16 9.42E-06 279440000 102980 85443 113970 92031 80889 111700 120470 129680 91544 FALSE TRUE 98112.33949 94149.73884 119195.6372 82779.86903 94996.01599 107831.801 102090.0889 118324.5317 105740.176 0.927862457 0.890387575 1.127250226 0.782861086 0.898390939 1.019780798 0.965480603 1.119012056 1 16.69016411 2.230014049 24.66074186 1.016886619 0.923511627 0.225049066 0.092138118 254.4284123 734135.1445 0.032180933 0.024154473 169.8298589 -2.230014049 -0.093374991 LIDLES(ph)PTPESQK ddPTM_SK-BR-3_Trastuzumab_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(0.984)PT(0.016)PESQK;LIDLES(0.714)PT(0.286)PESQK;LIDLES(0.562)PT(0.438)PESQK;LIDLES(0.52)PT(0.48)PESQK;LIDLES(0.898)PT(0.102)PESQK;LIDLES(0.652)PT(0.348)PESQK 305.75 1.93E-41 692378000 2179950 1939850 1994310 2393340 1664990 2183400 2428410 2382310 1849170 TRUE FALSE 2076908.084 2137522.92 2085751.086 2152756.916 1955363.729 2107788.311 2057911.454 2173702.307 2135929.839 0.972367184 1.000745849 0.976507303 1.007878104 0.915462527 0.986824694 0.963473339 1.01768432 1 21.02643283 1.234268134 24.99931433 1.00884217 0.976313871 0.237683336 0.025261846 166.8263993 971526.6473 0.019870595 0.005651725 17.15015835 -1.234268134 -0.032528299 LIDLESPT(ph)PESQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.343)PT(0.657)PESQK;LIDLES(0.099)PT(0.901)PESQK 315.32 1.10E-49 475670000 980100 871600 884800 1033130 706160 954610 1024950 1002410 735740 TRUE FALSE 933772.6154 960417.0309 925368.9552 929277.8096 829314.0804 921551.6163 868575.053 914633.6663 849834.8016 1.098769565 1.13012203 1.088880984 1.09348053 0.975853282 1.084389124 1.02205164 1.076248778 1 19.6968229 2.952428358 12.642731 1.036320576 1.10773103 0.528564365 0.033368192 1.266062062 335.7783817 0.009042459 0.009606627 896.2483266 -2.952428358 0.071410455 LIDLHSPSEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;; 199.7 1.69E-07 3098580000 5253670 4382520 4162600 4822930 4322690 4560760 5654000 5025010 4309260 FALSE TRUE 5005339.431 4829103.771 4353459.327 4338119.913 5076565.767 4402819.738 4791378.457 4584993.485 4977518.032 1.005589412 0.970183079 0.874624522 0.871542782 1.019899021 0.884541193 0.962603938 0.921140507 1 22.24699511 3.988674087 21.73995618 0.93116524 0.992312118 0.180362699 0.05033507 154.2971765 296178.2862 0.011780296 0.022059003 9742.582397 -3.988674087 0.061146877 LIDVLENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIDVLENR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;; 125.31 0.0029482 58839000 148008 130283 135128 160624 176820 130611 151566 135709 169793 FALSE TRUE 141011.9552 143558.9858 141323.7525 144477.7704 207657.352 126087.9083 128441.823 123825.6005 196123.6313 0.718995229 0.731982092 0.720585029 0.736666813 1.058808419 0.642900131 0.65490233 0.631365021 1 17.58140385 2.982219563 24.94831865 0.768050423 0.725367182 0.035387222 0.14360286 4165.974889 5845427.28 0.042911605 0.046396584 959.8857918 -2.982219563 -0.042683241 LIDVNHYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIDVNHYAK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 98.044 0.0055903 0 1263530 1297440 910200 1417510 1055240 1091750 1150750 1299080 1046810 FALSE TRUE 1203805.441 1429650.611 951933.5703 1275019.202 1239273.522 1053942.424 975181.9525 1185325.668 1209143.948 0.995584887 1.182365932 0.787278944 1.054480902 1.024918103 0.871643467 0.806506085 0.980301535 1 20.20555458 2.242334314 24.63784246 0.88767429 1.023359735 0.12495364 0.110956273 109.8280075 717054.4479 0.03829099 0.030888223 174.7166579 -2.242334314 0.135685445 LIDWGLAEFYHPAQEYNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIDWGLAEFYHPAQEYNVR 19 0 P19784;H3BSA1 P19784 CSNK2A2 Casein kinase II subunit alpha 0 125.18 2.78E-05 68589000 71573 70306 88183 79168 77516 93538 90485 81179 72562 FALSE TRUE 68189.88613 77470.26133 92226.27777 71209.88223 91034.76586 90298.75561 76679.85138 74070.5364 83814.54436 0.813580586 0.924305703 1.100361262 0.849612472 1.08614521 1.077363795 0.91487524 0.883743233 1 16.354913 4.212763167 2.686929286 0.984790514 0.829453839 0.282887613 0.086417892 0.317416067 4.519721891 0.021174187 0.065561288 16321.61641 -4.212763167 -0.155336676 LIDWGLAEFYHPGQEYNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 191.64 9.21E-15 409532000 434078 413703 400643 473155 457236 430840 522069 440293 424609 FALSE TRUE 413559.9932 455859.806 419012.8778 425592.5605 536977.8136 415919.9028 442417.7856 401738.6108 490455.1951 0.843216663 0.929462692 0.854334671 0.867750132 1.094856001 0.848028336 0.902055458 0.819113784 1 18.90376182 6.231957066 0.883780938 0.911834119 4.03E-08 0.068278999 0.081429468 80.88643474 5.785200058 0.023967359 125.9706704 1705913.734 -6.231957066 -0.911834079 LIEDFLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617;O43617-2 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ;;; 150.17 0.0011482 203446000 366458 319333 308408 363624 390490 297035 398257 360034 416606 FALSE TRUE 349136.2566 351873.3958 322548.8119 327071.8247 458591.3324 286748.6035 337495.5802 328507.5143 481211.1308 0.725536535 0.731224557 0.670285434 0.679684662 0.952994025 0.595889382 0.701346163 0.682668154 1 18.87631049 -1.325817801 5.513421843 1.000054282 0.717049919 0.484060349 0.091672262 5.58E-05 6.82E-06 0.080964208 0.019079796 0.047226113 1.325817801 -0.283004363 LIEDKPR ddPTM_SK-BR-3_Trastuzumab_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 3618770000 5437060 4760040 4895060 6079300 4663110 5800020 6776120 6308820 5602300 FALSE TRUE 5180060.949 5245093.488 5119503.343 5468197.214 5476354.908 5599163.853 5742298.442 5756386.276 6471076.071 0.800494522 0.810544248 0.791136325 0.845021315 0.846281955 0.865260088 0.887379221 0.889556267 1 22.62557421 0.92288891 0.29126622 1.029598746 0.780738631 0.963056309 0.01153072 0.361239871 0.091695044 0.032245979 0.017623738 8.373150747 -0.92288891 -0.248860115 LIEDTEDWRPR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 194.17 5.77E-07 1925250000 2420810 1997190 2159930 2369750 2460400 2117370 2542400 2270640 2497090 FALSE TRUE 2306383.109 2200705.932 2258964.927 2131538.228 2889492.981 2044044.946 2154510.186 2071810.724 2884325.964 0.799626373 0.762987942 0.78318642 0.739007399 1.001791412 0.708673351 0.74697181 0.718299787 1 21.45980279 -2.117492595 2.262770867 1.403483726 0.781229854 0.405837367 0.08266628 5933912.056 1684582.363 12292072.71 0.018596923 0.007629699 2.117492595 -0.622253872 LIEECISQIVLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIEECISQIVLHK 13 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 153.38 4.57E-05 169486000 932760 947970 1004600 1106870 997140 906730 1103440 977810 1016470 FALSE TRUE 888670.2834 1044569.221 1050661.904 995605.3247 1171040.9 875329.7127 935089.9619 892187.7727 1174098.976 0.756895544 0.889677312 0.894866553 0.847973931 0.997395385 0.745533154 0.796431971 0.759891449 1 20.1631226 -0.070745624 7.85483964 0.999999999 0.836067624 0.305329127 0.077701868 9957826.354 1267731.174 0.073269869 0.017770554 0.849678004 0.070745624 -0.163932376 LIEGLSHEVIVSAACGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIEGLSHEVIVSAACGR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 171.46 1.72E-09 63334000 88524 79011 86069 84842 93328 83860 99366 83480 91823 FALSE TRUE 84339.64596 87062.31073 90015.34878 76313.52097 109604.3737 80955.90717 84205.89172 76170.04864 106062.4419 0.795188612 0.820859007 0.848701455 0.719515029 1.033394779 0.763285342 0.793927523 0.718162314 1 16.69455434 -2.345833143 2.341457053 2.207726145 0.812872627 0.308129836 0.088690308 3416157.725 711511.493 21812170.49 0.019194866 0.004509899 2.345833143 -1.394853518 LIEGVHPGSLVEKLPDS(ph)PALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIEGVHPGSLVEKLPDSPALAK 22 1 G0XQ39;Q13586;H0YDB2;E9PNJ4 G0XQ39 STIM1 Stromal interaction molecule 1 1 LIEGVHPGSLVEKLPDS(1)PALAK;LIEGVHPGSLVEKLPDS(1)PALAK 227.24 2.79E-26 367960000 385990 272580 339690 532140 312660 425410 512230 448530 283850 TRUE FALSE 367745.0177 300356.2119 355265.1225 478648.2762 367187.805 410677.945 434079.9058 409254.3354 327868.0083 1.121625192 0.916088805 1.083561413 1.459881001 1.119925689 1.252570957 1.323947121 1.248228937 1 18.32275561 3.461196687 24.90596632 1.252739772 1.01568499 0.334421628 0.129382315 189.9835768 297132.6285 0.031868696 0.043162715 2891.989335 -3.461196687 -0.237054783 LIEIHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 68.915 0.061157 225980000 240680 198310 215580 244160 228560 201310 251260 246240 234820 FALSE TRUE 229303.5334 218518.0145 225464.5562 219616.5729 268420.7916 194338.5842 212925.6723 224677.9202 271234.6863 0.845406377 0.80564185 0.831252666 0.809692064 0.989625609 0.716496061 0.785023756 0.828352462 1 18.04918216 -2.302078907 2.067252895 1.747707215 0.822502342 0.390186627 0.068032614 3545021.208 452801.8924 12383631.77 0.01671367 0.004987939 2.302078907 -0.925204872 LIESAEELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIESAEELIR 10 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 75.378 0.091134 9240400 19838 20569 17378 23544 17215 19891 22013 21548 16157 FALSE TRUE 18900.29706 22665.00449 18174.79849 21177.31239 20217.29055 19202.16968 18654.51255 19661.14289 18662.54504 1.012739528 1.214464824 0.97386495 1.134749432 1.083308333 1.028914847 0.999569593 1.053508128 1 14.18785812 2.228688524 4.028526603 1.017092026 1.093188702 0.18089212 0.06591266 0.308423013 11.25194682 0.02357246 0.017862702 169.3123056 -2.228688524 0.076096676 LIEVDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LIEVDDER 8 0 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 183.9 0.00051381 7044920000 9939600 8764500 8960900 10274500 10756900 9197200 11498800 10079600 11668400 FALSE TRUE 9469774.806 9657612.514 9371766.129 9241687.74 12632899.95 8878698.658 9744446.87 9196976.789 13477875.88 0.702616265 0.716553009 0.695344445 0.685693193 0.937306447 0.658760975 0.722995742 0.682375834 1 23.68408981 -1.729087639 2.850141325 1.04658954 0.724272338 0.55283637 0.077664495 31488161.36 25845280.36 10377670.8 0.017243778 0.018660031 1.729087639 -0.322317202 LIEVDDERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LIEVDDERK 9 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;;; 173.32 8.90E-05 922792000 1318310 1137010 1189830 1339760 861467 1354750 1376820 1470350 1021870 FALSE TRUE 1255996.099 1252872.612 1244384.882 1205084.779 1011706.572 1307834.668 1166760.822 1341598.359 1180336.381 1.064100132 1.061453864 1.054262923 1.020967242 0.857134109 1.108018603 0.988498568 1.136623747 1 20.17076664 3.249455997 5.063180081 1.0145305 1.061435771 0.064147989 0.074050223 0.470517468 33.082152 0.019713031 0.025625857 1776.053307 -3.249455997 0.04690527 LIFYDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIFYDLR 7 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 95.62 0.031016 693380000 1414870 1424990 1154250 1280350 1386250 1120640 1484290 1411550 1341450 FALSE TRUE 1347991.899 1570198.101 1207173.504 1151646.785 1628011.561 1081831.956 1257834.3 1287947.199 1549475.215 0.869966739 1.013374132 0.779085391 0.743249569 1.050685771 0.698192488 0.811780845 0.831215102 1 20.56334825 3.732349122 24.97380011 0.831280911 0.941670436 0.103123787 0.113261814 799.4031811 3214063.915 0.027432905 0.043726009 5399.445009 -3.732349122 0.110389524 LIGDAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 121.29 0.010358 807300000 3177930 2507950 2366590 2781500 2473820 2684500 3513710 3166090 2852660 FALSE TRUE 3027715.547 2763512.956 2475100.492 2501898.335 2905253.425 2591535.092 2977629.006 2888850.375 3295035.943 0.918871781 0.838689776 0.751160392 0.759293185 0.881706141 0.786496759 0.903671176 0.876728031 1 21.65186277 0.885578069 1.00503992 0.997888137 0.829767189 0.495457859 0.054769288 0.626408213 1.28197288 0.05356803 0.017564293 7.683835678 -0.885578069 -0.168120947 LIGEYGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LIGEYGLR 8 0 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;;; 188.89 0.00045267 1215910000 1524400 1329430 916310 1026990 1619600 1000180 1659940 1316150 1372010 FALSE TRUE 1452344.633 1464900.428 958323.7199 923755.014 1902057.727 965543.5158 1406685.666 1200900.929 1584774.304 0.916436258 0.924359024 0.604706751 0.582893736 1.200207325 0.609262476 0.887625237 0.757774104 1 20.59584596 LIHEDGIIRPYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHEDGIIRPYDR 13 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ; 150.21 2.45E-05 495980000 22727.7 17154.1 18272.4 23712 21332.1 13357.8 21476.5 20569.1 17633.8 FALSE TRUE 21653.40666 18902.12229 19110.20761 21328.42471 25052.41149 12895.21604 18199.86548 18767.96056 20368.35964 1.063090354 0.92801397 0.938230076 1.04713512 1.229967063 0.633100371 0.893536141 0.921427198 1 14.31404218 2.240551903 24.99982345 0.849613006 1.023404404 0.334407229 0.123711539 61.66498173 774191.2553 0.04219441 0.033660192 174.0010638 -2.240551903 0.173791398 LIHEQEQQS(ph)SS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.703)S(0.225)S(0.072) 86.738 0.010005 0 62479 53143 55333 64317 57061 54129 68617 66324 66697 TRUE FALSE 59525.74149 58558.33212 57870.07278 57851.73297 67012.42033 52254.49916 58148.21641 60516.31895 77040.03012 0.772659894 0.760102664 0.751168875 0.75093082 0.869838969 0.678277242 0.754779253 0.785517852 1 16.23332065 LIHEQEQQSS(ph)S ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.046)S(0.721)S(0.234);LIHEQEQQS(0.028)S(0.924)S(0.049);LIHEQEQQS(0.236)S(0.382)S(0.382);LIHEQEQQS(0.222)S(0.753)S(0.025);LIHEQEQQS(0.208)S(0.585)S(0.208);LIHEQEQQS(0.037)S(0.482)S(0.482) 146.58 3.75E-05 2046590000 1644070 1651970 1734250 1800460 1962980 1493570 1886420 1746750 1911480 TRUE FALSE 1566358.069 1820307.621 1813767.078 1619474.34 2305323.09 1441847.296 1598611.983 1593795.31 2207902.556 0.709432608 0.824451068 0.821488735 0.733489952 1.044123566 0.653039371 0.724041004 0.721859443 1 21.07424507 -2.379789171 2.240726628 2.581689153 0.777132209 0.295892507 0.107109309 5167919.546 692473.6845 41302451.75 0.02519814 0.004170718 2.379789171 -1.804556945 LIHEQEQQSSS ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ; 110.38 0.0024358 127450000 295620 245340 261760 297320 298500 229730 301860 302580 282890 FALSE TRUE 281646.6285 270340.4249 273761.9549 267432.8287 350558.3055 221774.3925 255805.713 276084.4911 326759.1364 0.861939567 0.827338534 0.837809641 0.818440248 1.072833982 0.678709079 0.782857109 0.844917434 1 18.31786805 LIHGEDS(ph)DS(ph)EGEEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHGEDSDSEGEEEGR 16 0 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 2 LIHGEDS(1)DS(1)EGEEEGR;LIHGEDS(1)DS(1)EGEEEGR 223.97 1.20E-14 467450000 629820 695760 561000 716740 491510 624050 563120 567300 441140 TRUE FALSE 600049.6568 766658.735 586722.4049 644691.9335 577229.1884 602438.992 477205.7016 517624.2046 509549.7382 1.177607625 1.504580765 1.151452667 1.265218849 1.132822068 1.182296736 0.93652428 1.015846277 1 18.95886345 2.363045666 0.871685898 0.969630535 1.320463691 0.574566379 0.103620578 0.371285909 0.551717234 0.072464747 0.046666609 230.6989756 -2.363045666 0.350833156 LIHGEDS(ph)DS(ph)EGEEEGRGSSGCSEAGGAGHEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIHGEDSDSEGEEEGRGSSGCSEAGGAGHEEGR 33 1 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 2 LIHGEDS(1)DS(1)EGEEEGRGSSGCSEAGGAGHEEGR 157.63 1.48E-11 133940000 25270 20304 20240 23326 31821 22819 29013 27736 28440 TRUE FALSE 24075.53718 22373.00068 21168.02402 20981.22616 37370.57233 22028.77231 24586.53399 25307.2888 32850.32995 0.732885704 0.681058629 0.644377821 0.638691489 1.137601126 0.670579941 0.748441006 0.770381571 1 15.00362024 LIHLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHLNK 6 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ; 124.34 0.018396 1452610000 3522400 3160100 2896600 3608200 2962600 3315000 3800500 3710900 2946900 FALSE TRUE 3355903.133 3482117.783 3029411.975 3245496.881 3479276.502 3200200.719 3220663.924 3385953.923 3403890.201 0.985902287 1.022981817 0.889985222 0.953466971 1.022147101 0.940159796 0.946171508 0.994730653 1 21.69875307 LIHPDEDISLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIHPDEDISLEER 13 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;; 240.59 7.46E-17 628078000 1033110 979080 911660 1133630 1086280 914300 1037660 994290 936820 FALSE TRUE 984276.9377 1078849.365 953460.5128 1019675.359 1275726.888 882637.5617 879345.9091 907224.6965 1082097.261 0.909601173 0.996998518 0.881122749 0.942313963 1.178939208 0.815673039 0.81263112 0.838394781 1 20.04539875 LIHPDEDISLEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHPDEDISLEERR 14 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ; 157.56 3.42E-06 179604000 114405 60517 118943 86774 134891 98471 154295 116655 152395 FALSE TRUE 108997.3024 66683.7511 124396.6542 78051.31266 158415.9477 95060.92458 130754.4639 106440.0698 176027.6383 0.619205617 0.37882546 0.706688196 0.443403737 0.899949288 0.540034085 0.742806443 0.604678168 1 17.42544244 -5 0.111591511 2.309406079 0.377859467 0.429742717 0.144008131 133.8430372 0.989198165 39.69615888 1.514219441 1.00E-05 5 -1.931546613 LIHTLDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LIHTLDDR 8 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;;; 173.23 0.00027894 2160380000 1797850 1454290 1444339 1768750 1940080 1536546 1913180 1651070 1822450 FALSE TRUE 1712869.193 1602483.804 1510563.372 1590951.89 2278429.338 1483335.027 1621289.253 1506493.558 2105066.238 0.813688977 0.761251012 0.717584722 0.75577284 1.082355176 0.704650048 0.770184436 0.71565138 1 21.0054342 -1.743667039 2.699341996 1.042803339 0.789241546 0.268772624 0.108773981 21874424.54 16454940.51 6238023.189 0.026092888 0.018044006 1.743667039 -0.253561793 LIHTLDDRTQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIHTLDDRTQLWASEPGTPPLPTSLPSQNPILK 33 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 LIHTLDDRTQLWASEPGT(1)PPLPTSLPSQNPILK;LIHTLDDRTQLWASEPGT(1)PPLPTSLPSQNPILK 286.3 4.03E-74 534730000 459660 134322 535820 276200 667160 419290 1020870 551400 1085480 TRUE FALSE 437932.7828 148009.5645 560387.877 248435.8513 783512.4928 404769.8822 865117.5319 503116.4928 1253810.695 0.349281422 0.118047776 0.446947756 0.198144626 0.624904937 0.322831735 0.689990551 0.401269901 1 20.25788811 -0.129447182 0.1931728 1.374510977 0.112431489 0.642653306 0.153297808 5.876415083 0.392576313 1.88412923 0.507940302 0.742254464 0.129447182 -1.262079488 LIICVFLEKDEDIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIICVFLEKDEDIYR 15 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 163.23 1.41E-06 54090000 126500 119670 96452 117770 98304 108870 141130 139430 95863 FALSE TRUE 120520.5957 131864.5091 100874.4196 105931.5359 115448.1865 105099.8046 119598.0265 127220.77 110728.9444 1.088429013 1.190876602 0.911003172 0.956674304 1.042619769 0.949162887 1.080097233 1.148938705 1 16.75667286 3.754237072 24.99515513 1.014952677 1.139652808 0.347910949 0.072236533 851.859764 1358234.591 0.018479168 0.033166635 5678.545007 -3.754237072 0.124700131 LIILDEIHLLHDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIILDEIHLLHDDR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 196.58 1.43E-08 27138000 28754 47088 25917 36948 27964 28630 23507.2 30452.3 705.26 FALSE TRUE 27394.8554 51886.32073 27105.32009 33233.91684 32840.91275 27638.53592 19920.7449 27785.73517 814.6281188 33.62866414 63.69326019 33.2732439 40.79642732 40.31399357 33.92779513 24.45378994 34.10849016 1 9.669997803 0.930464884 0.373550883 5.85E-26 48.38838499 0.650513274 9.133992443 0.911273545 0.34273846 15.68073666 8.029052227 8.520496142 -0.930464884 48.38838499 LIILDEIHLLHDDRGPVLEALVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIILDEIHLLHDDRGPVLEALVAR 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 331.34 4.97E-87 164424000 168962 190146 181452 207740 212393 188716 226784 200160 18598.1 FALSE TRUE 160975.5011 209522.0936 189771.7537 186857.5805 249434.272 182180.7176 192183.9356 182632.9293 21482.19836 7.493437049 9.753289214 8.833907521 8.698252263 11.61120793 8.480543496 8.946195002 8.501594027 1 14.39085402 0.212074145 1.311580291 0.990137515 9.122143912 0.853531265 1.049955374 2.306331092 3.476433827 0.986309167 0.282219769 1.629574217 -0.212074145 8.132006398 LIKDDFLQQNGYTPYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LIKDDFLQQNGYTPYDR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 228.3 1.35E-15 1718023000 1577620 1557334 1467330 1667190 1316449 1574764 1739950 1668760 1469660 FALSE TRUE 1503049.029 1716028.105 1534608.532 1499600.894 1546037.289 1520229.528 1474488.671 1522634.528 1697567.367 0.88541348 1.010874819 0.904004496 0.883382258 0.910736928 0.895534138 0.868589194 0.896950871 1 20.6950374 3.515954823 24.96428847 0.899103234 0.949693416 0.087412787 0.046411447 782.2937692 502897.785 0.011204362 0.017353876 3280.611651 -3.515954823 0.050590182 LIKDDIER ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 112.75 0.002719 1780860000 4058530 3641510 3718780 4245590 3313890 3984470 4492630 4450920 3794450 FALSE TRUE 3866691.33 4012584.009 3889289.741 3818815.227 3891831.367 3846486.805 3807196.781 4061173.849 4382873.927 0.882227368 0.915514358 0.88738344 0.871303919 0.887963339 0.877617488 0.868653045 0.926600654 1 22.06344575 0.941331118 4.226597755 0.999931928 0.886162722 0.891308227 0.012929425 0.093455514 4.624925875 0.013907397 0.003545033 8.736371996 -0.941331118 -0.113769207 LIKPYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIKPYTR 7 1 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 69.344 0.062347 174860000 438040 298840 374070 363670 625600 373290 672680 440440 946730 FALSE TRUE 417334.7173 329292.1358 391221.4795 327113.2007 734704.4419 360362.8737 570050.3114 401872.7387 1093544.053 0.38163503 0.301123795 0.357755573 0.299131251 0.671856282 0.329536677 0.521287011 0.367495701 1 20.06057991 -5 0.221490557 4.079628464 0.32499019 0.738524424 0.112112896 71.19275074 0.71207821 97.80685499 0.188669413 1.00E-05 5 -3.754638274 LILADALCYAHTFNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LILADALCYAHTFNPK 16 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 165.34 7.06E-09 108097000 250950 231022 246887 263530 224555 275970 330130 281980 236256 FALSE TRUE 239088.0908 254563.4045 258207.0132 237039.4637 263717.3209 266413.0897 279762.6052 257288.3363 272893.3739 0.876122741 0.932831021 0.946182787 0.868615681 0.966374951 0.976253421 1.025171851 0.942816356 1 18.05797784 2.537415879 4.646070689 0.989961887 0.909367174 0.606026746 0.030694885 0.139127376 6.0956412 0.009860654 0.009050228 344.6798374 -2.537415879 -0.080594712 LILDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LILDSAR 7 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 134.66 0.0073342 129260000 386400 231530 137950 152920 454270 186600 418110 231050 348050 FALSE TRUE 368135.6378 255123.1702 144275.144 137548.1911 533494.5442 180137.9952 354319.6404 210818.0371 402023.8164 0.915706042 0.634597155 0.358872132 0.342139409 1.327022237 0.448077919 0.881339925 0.52439191 1 18.61692145 LILDVFCGSQMHFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LILDVFCGSQMHFVR 15 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 279.86 1.11E-33 1735994000 1957488 1385526 991666 1167136 2372334 1112846 2258948 1605915 2023345 FALSE TRUE 1864961.422 1526712.675 1037134.867 1049813.272 2786068.298 1074307.864 1914303.994 1465292.569 2337115.009 0.797975887 0.653246703 0.44376715 0.44919196 1.192097217 0.459672656 0.819088486 0.626966394 1 21.1562973 LILEQMQKDPQALSEHLKNPVIAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LILEQMQKDPQALSEHLKNPVIAQK 25 2 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 145.58 1.67E-07 179790000 225490 92655 234750 159620 195430 231840 346890 263010 253630 FALSE TRUE 214831.5346 102096.6498 245513.5197 143574.6943 229512.9301 223811.3227 293965.5594 239979.4501 292961.645 0.733309422 0.34849835 0.838039804 0.490080175 0.783423134 0.763961175 1.003426778 0.819149722 1 18.16035227 2.287022564 1.204374542 0.949108167 0.578958715 0.482670347 0.145739121 0.348112294 0.984391065 0.084385319 0.050211544 193.6522575 -2.287022564 -0.370149453 LILEVHQFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LILEVHQFSR 10 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 133.42 0.00019763 91534000 170590 131980 144500 150590 186490 145790 184490 164630 194530 FALSE TRUE 162526.5488 145428.912 151125.4679 135452.4071 219013.797 140741.2557 156342.6621 150214.1244 224696.7189 0.723315185 0.647223123 0.672575321 0.602823253 0.974708478 0.626360974 0.695794148 0.668519439 1 17.77761953 -1.294285537 3.081540519 1.00200461 0.698649815 0.453393509 0.102991776 15738983.57 20811708.5 293207.156 0.022711931 0.050782545 1.294285537 -0.303354795 LILFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LILFPR 6 0 P26373 P26373 RPL13 60S ribosomal protein L13 0 ; 141.66 0.027043 202510000 250240 142956 50277 58373 296060 83396 255950 153398 247290 FALSE TRUE 238411.6511 157523.3789 52582.25018 52505.23514 347692.7703 80507.97561 216900.1267 139965.6579 285638.4702 0.83466226 0.551478163 0.184086724 0.1838171 1.217247698 0.281852705 0.759351941 0.490009829 1 18.12383077 -1.743316368 0.452050505 1.332853773 0.564440513 0.155442432 0.318666804 85.60462654 7.149050323 31.19133841 0.159774715 0.018058581 1.743316368 -0.76841326 LILGLMMPPAHYDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LILGLMMPPAHYDAK 15 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 200.16 7.06E-09 319250000 1184970 774740 807490 1700850 1367940 1118260 1382040 959090 885200 FALSE TRUE 1128958.816 853686.8868 844514.2152 1529877.327 1606508.303 1079534.376 1171184.415 875106.9951 1022472.295 1.104146119 0.834924223 0.825953152 1.496253086 1.571199837 1.055807948 1.145443667 0.855873552 1 19.96363032 3.269735271 24.99972496 1.199648301 0.929152485 0.234414441 0.225547701 291.0796506 233422.0802 0.063314624 0.085719554 1860.952425 -3.269735271 -0.270495816 LILIESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LILIESR 7 0 P62277 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 170.55 0.002258 515421000 1257170 1310486 1024132 1171465 1350885 1056669 1286337 1194915 1305623 FALSE TRUE 1197746.066 1444026.013 1071089.465 1053707.113 1586478.916 1020076.288 1090082.665 1090281.908 1508092.347 0.794212681 0.957518296 0.710228036 0.698701983 1.051977301 0.67640174 0.722822225 0.722954341 1 20.52429334 LILPHVDIQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LILPHVDIQLK 11 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 150.21 0.0019188 0 459160 359910 354530 356790 377530 340040 441620 415440 366090 FALSE TRUE 437456.4168 396585.2382 370785.5512 320924.7913 443371.1125 328264.3295 374242.7581 379061.8712 422861.3675 1.034514974 0.937861126 0.876848962 0.758936181 1.048502291 0.776293024 0.885024708 0.896421145 1 18.68982524 4.195965648 1.975354674 0.881865967 1.026580245 0.201265855 0.087415064 0.451937796 3.311707927 0.020949512 0.079090644 15702.38596 -4.195965648 0.144714278 LILSTDTLEELKEIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LILSTDTLEELKEIDK 16 1 Q5TAQ0;V5IRT4;Q9BRT2 Q5TAQ0 UQCC2 Ubiquinol-cytochrome-c reductase complex assembly factor 2 0 125.52 6.99E-05 44379000 250730 229520 216570 236550 147960 246050 216350 257950 128920 FALSE TRUE 238878.4898 252908.3489 226499.9487 212771.5446 173764.1772 237529.2268 183341.834 235362.5305 148912.2552 1.604156015 1.698371626 1.521029605 1.428838374 1.166889703 1.595095223 1.231207155 1.580545068 1 17.18410296 1.914761694 0.054680076 1.79E-12 2.784775628 0.502668626 0.158389528 27.91037022 1.273193728 30.28953249 33.10858614 82.17915937 -1.914761694 2.784775628 LIMGIGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 143.02 0.00060815 3067950000 4128660 3400200 3242350 3574870 4570460 3295530 4472960 3875090 4251790 FALSE TRUE 3933506.424 3746684.246 3391014.955 3215517.276 5367546.777 3181404.97 3790527.8 3535766.576 4911135.878 0.800936183 0.76289566 0.690474676 0.654740035 1.092933877 0.647794125 0.771823035 0.71994884 1 22.22762531 LINGVRS(ph)PQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LINGVRSPQTR 11 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 LINGVRS(1)PQTR 112.42 0.00092535 117450000 69221 53014 71343 64819 70359 67091 88679 63693 70147 TRUE FALSE 65949.06051 58416.18687 74614.14712 58303.27097 82629.58732 64767.62185 75149.38985 58115.70326 81025.0385 0.813934331 0.72096463 0.920877651 0.719571037 1.019803123 0.799353176 0.927483544 0.717256102 1 16.30608018 3.407020324 1.340079976 0.876280844 0.773057476 0.102593821 0.108239353 0.81320139 3.009447196 0.032628839 0.057738647 2552.820764 -3.407020324 -0.103223368 LINQVLELQHTLEDLSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LINQVLELQHTLEDLSAR 18 0 A0A0C4DGB0;Q9UIL1-3;Q9UIL1-2;Q9UIL1 A0A0C4DGB0 SCOC Short coiled-coil protein 0 86.367 0.0038417 0 7212.5 5952.2 7079.4 7492.1 8629.7 6447.9 8400.8 5413.9 8454.5 FALSE TRUE 6871.579419 6558.735947 7403.997492 6738.979874 10134.71695 6224.607606 7119.103669 4939.830215 9765.58068 0.703652926 0.671617609 0.758172784 0.690074671 1.037799725 0.637402712 0.728999524 0.50584091 1 13.25349012 3.732184791 23.0133092 0.753128783 0.687635269 0.036341231 0.156922973 654.7157119 2363183.839 0.038276518 0.061090613 5397.402321 -3.732184791 -0.065493514 LINYHQEQAVNCLLGNVFYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LINYHQEQAVNCLLGNVFYER 21 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 189.79 2.03E-17 153290000 173323 145819 158287 156022 177957 141997 189284 176531 180034 FALSE TRUE 165130.3653 160678.1219 165544.6155 140338.3721 208992.6445 137079.6083 160405.2494 161073.0098 207952.7532 0.79407636 0.77266648 0.7960684 0.674857005 1.005000613 0.659186311 0.771354295 0.774565411 1 17.66589626 -0.802868598 4.466605535 1.000000943 0.778960222 0.356496133 0.092445474 4092304.075 2290517.275 35.55894699 0.018875852 0.157445917 0.802868598 -0.22104072 LIPDSIGKDIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIPDSIGKDIEK 12 1 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ; 110.92 0.001311 1252560000 3102800 1906530 2711600 2667500 2511000 2943400 3852900 3251700 2818700 FALSE TRUE 2956136.793 2100807.575 2835929.542 2399357.832 2948917.605 2841469.32 3265069.342 2966963.91 3255809.6 0.907957515 0.645248904 0.871036667 0.736946605 0.90574019 0.872738172 1.002844067 0.911282991 1 21.6345849 2.333774707 1.363198723 0.969619564 0.782000235 0.466704255 0.07967502 0.335090623 1.238233719 0.041704524 0.026673655 215.6625356 -2.333774707 -0.187619329 LIPGPLS(ph)PVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 179.94 7.22E-06 1946222000 2511247 2162199 2246892 2570324 2662950 2130991 2536462 2141134 2370906 TRUE FALSE 2392545.331 2382529.536 2349914.221 2311950.148 3127367.637 2057194.247 2149478.137 1953644.956 2738573.994 0.873646407 0.869989105 0.858079506 0.844216791 1.141969377 0.751191771 0.78488956 0.71338038 1 21.38499343 -0.844178607 4.52808075 1.000000792 0.855628502 0.136414649 0.114893071 12379553.72 5467903.153 96.57487747 0.025981183 0.143159902 0.844178607 -0.14437229 LIPITGGNARS(ph)PEDQLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIPITGGNARSPEDQLGK 18 1 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 LIPIT(0.014)GGNARS(0.986)PEDQLGK;LIPIT(0.008)GGNARS(0.992)PEDQLGK;LIPITGGNARS(1)PEDQLGK;LIPITGGNARS(1)PEDQLGK 177.91 5.54E-14 743070000 1253240 709560 1146680 1085260 1001840 1148880 1507400 1286940 1356000 TRUE FALSE 1194001.829 781864.9707 1199256.412 976167.6029 1176560.579 1109093.998 1277418.445 1174248.711 1566281.555 0.762316217 0.499185455 0.765671031 0.623238906 0.751180767 0.708106403 0.815573957 0.749704744 1 20.57891214 0.742965962 0.376139501 1.02950316 0.632592642 0.590904805 0.081827492 1.171469457 0.393716992 0.153937438 0.065739907 5.533067425 -0.742965962 -0.396910517 LIQNLDANHDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;; 291.57 3.90E-36 14396790000 9332430 9821760 7242040 9941070 9227380 7287650 8297580 8513200 7864340 FALSE TRUE 8891304.529 10822608.51 7574094.697 8941774.757 10836632.15 7035276.853 7031631.775 7767739.077 9083901.682 0.97879797 1.191405289 0.833793117 0.984353978 1.19294908 0.774477433 0.774076165 0.85511043 1 23.11488066 2.220616671 24.99992226 0.823815754 1.040629893 0.355954791 0.12139678 224.8415896 313252.5508 0.0433596 0.032089917 166.1945092 -2.220616671 0.216814139 LIQSHPESAEDLQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIQSHPESAEDLQEK 15 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 162.59 1.59E-06 389830000 371050 316630 296070 375070 334140 355610 402450 385870 293650 FALSE TRUE 353511.2019 348894.957 309645.1024 337367.251 392413.9102 343295.1365 341048.861 352081.1772 339187.7422 1.042228706 1.028619002 0.912901806 0.994632792 1.15692244 1.012109501 1.005486987 1.038012679 1 18.37172451 3.995036607 24.77655022 1.017327018 1.037125082 0.018068618 0.059468117 1595.309823 7963720.146 0.015092455 0.030135918 9886.364244 -3.995036607 0.019798063 LIRDFQEYVEPGEDFPAS(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIRDFQEYVEPGEDFPASPQRR 22 2 Q9Y6G9;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 LIRDFQEYVEPGEDFPAS(1)PQRR 82.089 0.0024444 18257000 11600 3973.1 15313 9614.3 27010 10825 28758 14215 46644 TRUE FALSE 11051.69099 4377.963407 16015.1162 8647.852298 31720.53545 10450.12754 24370.43892 12970.25924 53877.3133 0.205126988 0.081258013 0.297251574 0.160510088 0.58875496 0.193961556 0.452332112 0.240736934 1 15.71739029 -4.999999998 0.167187966 3.829729451 0.086246077 0.728855837 0.140755621 61.0326738 0.571790713 57.17846146 0.471230019 1.00E-05 4.999999998 -3.743483373 LIRGPGENGDDS(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LIRGPGENGDDS 12 1 Q6IBS0 Q6IBS0 TWF2 Twinfilin-2 1 LIRGPGENGDDS(1);LIRGPGENGDDS(1);LIRGPGENGDDS(1) 120.65 0.0010265 728580000 1187490 858110 1223310 1119210 1424400 1138130 1538830 1250090 1673080 TRUE FALSE 1131359.701 945552.3846 1279399.974 1006704.884 1672814.909 1098716.273 1304053.221 1140625.492 1932532.701 0.58542849 0.489281441 0.662032768 0.520925148 0.865607556 0.568536963 0.674789731 0.590223126 1 20.8820614 -5 0.177710441 2.553521562 0.529399138 0.574975576 0.103160226 88.5529364 0.848859422 48.60981377 0.301387927 1.00E-05 5 -2.024122424 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PK;LIRPEYAWIVQPVSGAVYDRPGAS(1)PK 208.7 1.11E-25 2367200000 2325610 2237300 2193900 2722500 1406290 2488400 2388000 2484300 1434470 TRUE FALSE 2215683.024 2465283.414 2294492.485 2448829.128 1651546.531 2402226.084 2023666.741 2266761.522 1656920.281 1.337229708 1.487870866 1.38479353 1.477940221 0.996756784 1.449813917 1.221342248 1.36805708 1 20.66007276 -4.409148049 0.131837124 6.00E-14 1.497410257 0.379395651 0.141579935 114.3968868 1.098239843 30.9646009 0.957010808 3.90E-05 4.409148049 1.497410257 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPKR 27 3 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR;LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR 175.34 6.67E-12 1525980000 1856630 1480480 1635970 1808930 1381040 1996750 2165580 2019110 1609370 TRUE FALSE 1768870.779 1631342.595 1710980.843 1627092.92 1621892.939 1927602.047 1835180.997 1842306.024 1858942.88 0.951546601 0.87756467 0.92040528 0.875278599 0.872481321 1.036934522 0.987217529 0.991050367 1 20.82605101 2.240643768 24.99999832 1.002294172 0.901059109 0.78769164 0.026906285 24.5991391 295219.9223 0.009419045 0.007519247 174.0378734 -2.240643768 -0.101235063 LIS(ph)PYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LISPYK 6 0 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 1 LIS(1)PYK 98.997 0.041224 109690000 399970 478360 424040 484160 274290 478820 498800 523620 321100 TRUE FALSE 381064.2108 527105.4279 443482.6534 435491.317 322126.0892 462238.3433 422698.8989 477769.0569 370894.548 1.027419283 1.421173297 1.195710899 1.174164784 0.868511254 1.246279693 1.139674069 1.288153356 1 18.50064954 -2.368954457 2.040357263 0.000287782 1.176628062 0.11468158 0.147583006 4248888.043 436816.4314 19600200.49 0.036564228 0.004276077 2.368954457 1.17634028 LIS(ph)WYDNEFGYSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR 207.39 9.97E-09 47333700 66577.3 56699.9 49897.7 76324.4 67113.8 53927.7 62373.6 59609.5 62584.3 TRUE FALSE 63430.32297 62477.68427 52185.5589 68652.12631 78818.42547 52060.17023 52857.36175 54389.77617 72289.55361 0.877447983 0.864269886 0.721896267 0.949682532 1.090315565 0.720161733 0.731189489 0.752387772 1 16.14149956 -0.81450615 5.156717978 1.000000089 0.837218611 0.157056097 0.11761348 1.73E-07 3.97E-08 0.115839527 0.027303617 0.15328295 0.81450615 -0.162781478 LISGGHDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LISGGHDNR 9 0 Q15061;C9JEE7 Q15061 WDR43 WD repeat-containing protein 43 0 ;; 135.55 0.00021771 154407000 229313 231867 234408 242541 270985 220793 246066 246172 263879 FALSE TRUE 218473.8289 255494.5109 245155.8387 218160.3179 318244.6982 213146.883 208524.1124 224615.8746 304800.0076 0.716777636 0.838236563 0.804317036 0.715749057 1.044109876 0.69930078 0.68413421 0.736928704 1 18.21750341 -0.185986245 8.900944977 1 0.777510812 0.301807528 0.105128065 13305828.03 1494878.279 0.097559055 0.023661546 0.651649034 0.185986245 -0.222489188 LISGVSRPDEVLECIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LISGVSRPDEVLECIER 17 1 Q9H974-2;Q9H974-3;Q9H974;Q9H974-4 Q9H974-2 QTRTD1 Queuine tRNA-ribosyltransferase subunit QTRTD1 0 ; 108.75 0.00058385 117480000 62917 49052 55107 58069 60799 55570 66780 59030 71107 FALSE TRUE 59943.0381 54050.45457 57633.71046 52231.7938 71402.32635 53645.59697 56591.4845 53861.02026 82133.9104 0.729820823 0.65807721 0.701704207 0.63593458 0.869340398 0.653147971 0.689014857 0.655770802 1 16.32569037 -1.420745556 5.455833947 1.000208905 0.697820669 0.669576367 0.06642366 0.000152023 1.61E-05 0.057927263 0.013644249 0.037953728 1.420745556 -0.302388235 LISGWVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LISGWVSR 8 0 O14980 O14980 XPO1 Exportin-1 0 82.75 0.04528 91482000 231840 251460 179260 216060 199020 188310 231090 223600 195490 FALSE TRUE 220881.3827 277084.0599 187479.2483 194341.2383 233729.025 181788.7775 195832.9762 204020.3986 225805.5908 0.97819271 1.227091229 0.830268408 0.860657336 1.035089628 0.805067655 0.86726363 0.903522353 1 17.78472168 3.727817773 24.99425707 0.89142748 1.102641973 0.452969765 0.092061269 499.5322578 1162209.73 0.02288954 0.035858322 5343.401072 -3.727817773 0.211214493 LISQIVSSITASLR ddPTM_SK-BR-3_Trastuzumab_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 ; 163.99 9.75E-06 218340000 219449 232340 196720 207460 214474 197994 255600 219824 166208 FALSE TRUE 209076.0807 256015.7101 205739.8066 186605.7267 251878.1977 191137.4181 216603.5256 200575.0452 191982.6878 1.089036116 1.333535399 1.071658122 0.971992469 1.311983912 0.995597157 1.128245094 1.044755897 1 17.55061669 1.985752924 0.311151319 0.991043468 1.209626829 0.134604715 0.116558564 2.707434503 0.793101047 0.170910563 0.212836653 96.77271458 -1.985752924 0.218583361 LISSDGHEFIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LISSDGHEFIVK 12 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;;; 138.75 6.88E-05 988316000 4853160 4169550 3980658 5328420 4331350 4439417 5402860 5168050 4438740 FALSE TRUE 4623760.745 4594431.885 4163175.107 4792797.098 5086736.069 4285678.876 4578554.477 4715508.144 5127077.129 0.901831712 0.896111326 0.811997753 0.934801053 0.992131762 0.835891243 0.89301455 0.919726391 1 22.28970517 0.855640885 3.341811057 0.999952257 0.894682995 0.312081766 0.048832479 0.822470803 16.43379543 0.044688613 0.011582915 7.172009971 -0.855640885 -0.105269262 LISSDGHEFIVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LISSDGHEFIVKR 13 1 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 147.26 2.77E-05 369630000 166860 106830 195010 142940 230630 176760 256720 206390 280590 FALSE TRUE 158972.8585 117716.0985 203951.4014 128571.3996 270851.799 170638.7569 217552.649 188317.3975 324102.4641 0.490501851 0.363206428 0.629280626 0.396699852 0.835698055 0.526496327 0.671246513 0.581042782 1 18.30609046 -4.999999998 0.095153731 2.48390372 0.20376665 0.58643677 0.124192898 120.2791953 0.7869162 35.59692884 2.158818181 1.00E-05 4.999999998 -2.28013707 LISVETDIVVDHYKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LISVETDIVVDHYKEEK 17 1 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 125.45 2.82E-05 121680000 243580 234120 227360 232690 187700 243010 261550 264430 192150 FALSE TRUE 232066.4561 257977.0942 237784.6809 209299.5591 220434.8206 234594.5028 221645.7438 241275.1074 221947.6406 1.045591003 1.162333123 1.071354848 0.943013219 0.993183888 1.056981287 0.998639784 1.087081199 1 17.75985985 3.468270814 24.92576834 1.013596716 1.106109055 0.403680208 0.047037886 157.7517132 444279.1185 0.012315937 0.016698289 2939.482063 -3.468270814 0.092512339 LISWYDNEFGYS(ph)NR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LISWYDNEFGYS(1)NR 199.58 2.15E-08 22259000 13561 11815 8786.7 15087 14266 10878 14654 12614 10729 TRUE FALSE 12919.99841 13018.96193 9189.578886 13570.4261 16753.98588 10501.29213 12418.26316 11509.45129 12392.79852 1.042540826 1.050526393 0.741525723 1.095025153 1.351913037 0.84737052 1.002054793 0.928720923 1 13.59721439 LISWYDNEFGYSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;; 449.61 1.52E-174 48709359400 7087029 6028976 6487422.6 7447309 7688387 6198651.6 8069411 6817373.2 7726859 FALSE TRUE 6752039.184 6643335.509 6784877.343 6698691.35 9029239.259 5983990.741 6838274.147 6220407.861 8925100.83 0.756522454 0.744342908 0.760201758 0.750545173 1.011668039 0.670467578 0.766184526 0.696956592 1 23.08943704 -2.21896365 2.374621234 1.767147586 0.768342178 0.386137468 0.09127866 3291564.169 691591.1286 13632911.19 0.020451424 0.006039992 2.21896365 -0.998805409 LIT(ph)SEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LITSEEER 8 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LIT(0.707)S(0.293)EEER 97.277 0.093291 102570000 387970 371130 362020 459220 430140 377620 391230 386570 468330 TRUE FALSE 369631.427 408948.5689 378618.9751 413058.3331 505156.2798 364542.9247 331540.6781 352719.8815 540956.2245 0.683292677 0.755973497 0.699906865 0.763570719 0.933820995 0.673886182 0.612878941 0.652030359 1 19.04515233 -2.319274526 2.387396405 2.622714308 0.719469771 0.499220464 0.087497872 4204954.146 835066.202 36765599.05 0.022026601 0.004794303 2.319274526 -1.903244537 LITLEEEMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LITLEEEMTK 10 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ; 229.48 3.73E-09 68777000 211480 160329 153867 226100 152491 180963 215990 207899 175475 FALSE TRUE 201483.7595 176666.7074 160921.9541 203371.9984 179085.3821 174696.2059 183036.7586 189694.2614 202686.7668 0.994064697 0.871624281 0.793944058 1.003380742 0.883557348 0.861902376 0.903052338 0.935898601 1 17.62889237 0.917996891 2.939849509 0.999822739 0.902186374 0.210479902 0.060839306 0.562831078 11.13141005 0.055358237 0.0145693 8.279362369 -0.917996891 -0.097636365 LITQTFSHHNQLAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LITQTFSHHNQLAQK 15 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 161.84 9.42E-07 332500000 1160500 1001700 915410 1191800 1102300 1166300 1359200 1350200 483010 FALSE TRUE 1105645.465 1103774.369 957382.454 1071998 1294540.771 1125910.739 1151829.077 1231969.33 557912.7239 1.981753449 1.978399706 1.716007563 1.921443899 2.320328459 2.018076825 2.064532726 2.208175719 1 19.08967993 -1.240532389 6.612201198 0.999990311 2.018641334 0.800546756 0.160920749 2.27E-05 2.61E-06 0.153959736 0.036288314 0.057473495 1.240532389 1.018651023 LITSEEERS(ph)PAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 237.59 4.95E-17 697410000 906628 907040 830927 970780 652681 956550 1042040 1075850 876533 TRUE FALSE 863773.4912 999468.4072 869025.8248 873195.35 766508.3598 923424.4337 883057.6596 981642.8706 1012461.261 0.853142263 0.987167061 0.858329951 0.862448158 0.75707426 0.912059028 0.872189084 0.969560919 1 19.94943528 1.146165104 3.714982715 0.998881033 0.878630853 0.405109133 0.056933158 0.242710569 5.854907477 0.054743635 0.014420813 14.00119498 -1.146165104 -0.12025018 LIVAYVDDLDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LIVAYVDDLDRR 12 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ;;; 225.55 2.79E-11 328865000 400591 318376 329234 391169 430282 332589 411772 382408 430592 FALSE TRUE 381655.8573 350818.8764 344329.7046 351847.9489 505323.0446 321071.3595 348948.6187 348922.3282 497366.0082 0.767354124 0.705353544 0.692306468 0.707422588 1.015998352 0.645543431 0.701593219 0.70154036 1 18.92394839 -1.830129103 2.638660839 1.093012287 0.73889252 0.387260796 0.101862467 30212133.7 20282590.63 17811579.57 0.023032493 0.014786688 1.830129103 -0.354119767 LIVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LIVDGR 6 0 Q99832-3;Q99832;F8WAM2;F8WBP8;A0A0D9SG95 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 105.42 0.076756 305070000 964510 835820 878550 1004370 1036550 870510 1080450 983480 1134970 FALSE TRUE 918919.5238 920991.0082 918832.3865 903408.8194 1217323.992 840364.0204 915607.5087 897361.2774 1310975.351 0.700943403 0.702523512 0.700876935 0.68911198 0.9285636 0.641021984 0.698417028 0.68449897 1 20.32220913 -1.070496299 4.573251225 1.000015943 0.715929379 0.568768708 0.077077903 0.250399822 43709778.58 1491.51509 0.016784464 0.085016594 1.070496299 -0.284086564 LIVDHNIADYMTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIVDHNIADYMTAK 14 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 138.19 1.52E-05 0 192280 168560 159370 192310 157510 198150 197100 218690 159860 FALSE TRUE 183191.3055 185736.4556 166677.2721 172978.6334 184979.6941 191288.0158 167028.775 199540.3443 184650.2723 0.992098756 1.005882381 0.902664643 0.936790568 1.001784031 1.035947651 0.904568257 1.080639317 1 17.49443586 2.691589125 24.65275488 0.993564442 0.967600945 0.129534169 0.052323019 1199.984891 629804.0594 0.016937546 0.015968887 491.5742498 -2.691589125 -0.025963497 LIVENLSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.035)S(0.965)R;LIVENLS(0.097)S(0.903)R;LIVENLS(0.147)S(0.853)R;LIVENLS(0.271)S(0.729)R 104.3 0.0034437 324062000 921100 867520 868640 1016380 1157690 1007780 1101910 939590 1091430 TRUE FALSE 877561.4284 955921.2743 908468.0032 914211.5514 1359590.769 972880.3259 933793.3915 857314.5185 1260683.39 0.696099778 0.75825642 0.720615509 0.72517141 1.078455368 0.771708689 0.740704128 0.680039513 1 20.26577457 LIVENLSSR ddPTM_SK-BR-3_Trastuzumab_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 0 ;; 177.7 0.00012055 256169000 351616 277361 303361 294158 351261 284458 397500 324955 346732 FALSE TRUE 334995.8085 305624.4012 317270.4019 264588.679 412520.8072 274607.1481 336854.0744 296500.2175 400501.4277 0.836440985 0.763104399 0.792182949 0.660643535 1.030010828 0.68565835 0.841080833 0.740322498 1 18.61144786 -2.02805147 2.34727666 1.23838824 0.795126532 0.288894615 0.10170537 12926397.55 4617833.052 16584820.06 0.021213511 0.009374509 2.02805147 -0.443261709 LIVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LIVLDR 6 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;; 116.35 0.055015 110940000 217121 185328 190613 234790 240228 201058 244965 209449 255857 FALSE TRUE 206858.1206 204213.1339 199352.7946 211188.4631 282123.6871 194095.311 207591.0902 191108.5352 295533.9968 0.699946953 0.690997097 0.67455114 0.714599557 0.954623462 0.656761365 0.702427106 0.646654995 1 18.17296458 -1.2182616 3.659273901 1.000360027 0.716098728 0.51023022 0.08695065 27218622.97 40640481.45 118069.0347 0.020069178 0.060497635 1.2182616 -0.284261299 LIVY(ph)VMGGVAMSEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIVYVMGGVAMSEMR 15 0 Q15833-2;Q15833;Q15833-3;R4GMY7 Q15833-2 STXBP2 Syntaxin-binding protein 2 1 LIVY(0.781)VMGGVAMS(0.219)EMR 53.124 0.071697 318140000 213430 167060 152940 206540 218910 161680 214380 217600 251390 TRUE FALSE 203341.5869 184083.6039 159952.4503 185778.2068 257087.8347 156080.9811 181672.3936 198545.7904 290374.2773 0.700274104 0.633952861 0.550849241 0.639788788 0.88536711 0.537516555 0.62564906 0.683758191 1 18.14755413 0.845556718 6.413772173 0.999999665 0.651485637 0.564211736 0.095050189 3.749080555 155.6469223 0.086548028 0.021734472 7.007396928 -0.845556718 -0.348514029 LIYKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LIYKPR 6 1 B7Z6D5;Q96GQ7;A0A087X059 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 101.72 0.084494 0 680870 561510 498930 665050 504340 577170 669330 627390 583130 FALSE TRUE 648686.6245 618728.5074 521806.434 598197.9105 592296.7363 557182.4582 567211.4154 572452.4056 673558.8222 0.963073459 0.9185961 0.774700615 0.888115322 0.879354136 0.827221677 0.842111181 0.849892224 1 19.36144442 3.984974856 23.07901703 0.856823638 0.946394493 0.227207011 0.057878627 271.8148734 417517.9182 0.012951083 0.023780932 9659.949505 -3.984974856 0.089570855 LKAEATEAAR ddPTM_SK-BR-3_Trastuzumab_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 1917801000 2841407 2377317 2372042 2663060 2298040 2619792 3107960 2840646 2832340 FALSE TRUE 2707099.322 2619568.305 2480802.472 2395364.149 2698817.448 2529067.946 2633783.62 2591903.977 3271564.822 0.827463147 0.800708055 0.758292318 0.732176888 0.824931675 0.773045342 0.805053167 0.792252062 1 21.64154943 -0.621098638 0.881710872 1.012772654 0.790007615 0.839029878 0.02901996 12.43855131 5.702375572 0.553921312 0.009345635 0.239277224 0.621098638 -0.22276504 LKAEGSEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LKAEGSEIR 9 1 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;;; 138.22 0.00013019 14230720000 36309800 29271300 30264700 33735300 30699900 33122600 41831500 36598000 34167900 FALSE TRUE 34593507.71 32254078.75 31652366.43 30344163.55 36053952.84 31975556.06 35449336.39 33393285.1 39466483.43 0.876528758 0.817252411 0.802006251 0.768859065 0.913533452 0.810195216 0.898213707 0.846117571 1 25.23412464 0.124044276 0.49621576 1.014158443 0.828732256 0.579736204 0.043414674 2.405662729 0.806204842 0.112100528 0.020671077 1.330590065 -0.124044276 -0.185426187 LKAEQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKAEQEAR 8 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 78.934 0.026759 70189000 106390 102820 86040 120390 80949 91171 96789 112790 80384 FALSE TRUE 101361.1555 113297.4749 89985.01911 108288.1685 95066.47997 88013.72541 82022.0604 102913.5097 92849.54018 1.091671056 1.220226559 0.969148786 1.166275765 1.023876691 0.947917731 0.883386824 1.108390084 1 16.50260714 2.52574152 4.100284606 0.96554926 1.119303194 0.323136197 0.084692024 0.208168686 7.333989024 0.027688757 0.025043766 335.5378521 -2.52574152 0.153753934 LKATVT(ph)PS(ph)PVKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.026)VT(0.976)PS(0.999)PVKGK;LKAT(0.183)VT(0.838)PS(0.979)PVKGK;LKAT(0.024)VT(0.976)PS(1)PVKGK 100.77 0.0024807 5145930000 8834340 7820840 8865210 9149930 4276270 10276730 10724160 10076260 5089400 TRUE FALSE 8416758.256 8617792.488 9271688.647 8230161.653 5022050.134 9920844.263 9087992.429 9193929.257 5878638.159 1.431753074 1.46595049 1.577183082 1.400011606 0.854288017 1.687609272 1.545934991 1.563955632 1 22.48705055 3.024917194 24.17192494 1.380295726 1.478950825 0.057436479 0.255813323 684.2840327 663810.2861 0.07287709 0.087100643 1059.051779 -3.024917194 0.098655099 LKATVT(ph)PSPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.683)PS(0.316)PVK 127.07 0.00047579 356280000 1557600 1655200 1091200 1565500 935980 1610000 1773000 1977100 1107900 TRUE FALSE 1483975.335 1823866.762 1141232.599 1408132.966 1099214.616 1554245.296 1502496.287 1803974.643 1279707.474 1.159620746 1.425221622 0.891791775 1.100355351 0.858957721 1.214531702 1.174093547 1.409677352 1 20.28738263 3.753731066 24.94649125 1.102483329 1.292421165 0.189995154 0.170465377 1251.75723 2058399.958 0.042548953 0.076346462 5671.932666 -3.753731066 0.189937836 LKATVTPS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.006)VT(0.141)PS(0.853)PVK;LKAT(0.001)VT(0.142)PS(0.857)PVK;LKAT(0.001)VT(0.178)PS(0.822)PVK 136.81 5.53E-05 14929300000 14462100 15625000 10105300 13436100 7700880 14136200 15919300 16164000 9404300 TRUE FALSE 13778505.19 17217205.26 10568638 12085477.7 9043911.034 13646659.85 13490518.41 14748594.47 10862670.81 1.268427022 1.584988219 0.972931812 1.112569635 0.832567901 1.256289552 1.241915422 1.35773188 1 23.37287553 3.737872834 24.99997852 1.125245347 1.42670762 0.372233927 0.169851765 62.07628418 2256408.256 0.044540955 0.073765502 5468.558142 -3.737872834 0.301462273 LKATVTPS(ph)PVKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.087)PS(0.913)PVKGK;LKAT(0.002)VT(0.252)PS(0.746)PVKGK 125.18 0.00016005 16377700000 6165810 5527900 6230030 6143560 3422480 7308600 8561600 7970700 4734210 TRUE FALSE 5874364.381 6091199.295 6515683.038 5525997.677 4019359.428 7055501.349 7255370.675 7272743.253 5468367.108 1.0742447 1.113897289 1.191522608 1.010538899 0.735020043 1.290239154 1.326789247 1.329966169 1 22.38267867 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVK 33 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGS(0.003)GPVHIS(0.004)GQHLVAVEEDAES(0.993)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 367.31 2.65E-148 3065830000 1400005 768990.6 1333363 1062404 1114719 1287376 2079141 1839697 693044 TRUE FALSE 1333829.538 847351.6164 1394499.012 955609.1315 1309125.641 1242793.846 1761929.854 1678603.378 800517.7239 1.666208628 1.058504504 1.741996424 1.19373888 1.635348727 1.552487608 2.200987938 2.096897205 1 19.61057382 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 40 2 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK 182.42 2.46E-24 239470000 225070 65261 250860 133050 237710 204980 485440 352210 169810 TRUE FALSE 214431.3871 71911.1701 262362.1791 119675.5612 279166.5487 197881.4912 411377.2123 321368.6252 196143.2675 1.093238579 0.366625737 1.337604815 0.610143609 1.423278771 1.00886201 2.09733027 1.638438215 1 17.58154829 2.35293187 1.504954558 1.64066117 0.821043287 0.293349329 0.414764662 0.360759909 1.642680143 0.198987134 0.133399291 225.3885607 -2.35293187 -0.819617883 LKDDEVAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LKDDEVAQLK 10 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;;; 172.17 3.46E-06 2119570000 6571030 6610940 5494380 7488310 3565760 7025410 6574330 7303910 3803330 FALSE TRUE 6260430.434 7284602.302 5746302.758 6735570.852 4187627.415 6782118.29 5571295.213 6664340.92 4393130.992 1.425049798 1.658180081 1.308019899 1.533205102 0.953221614 1.543800607 1.268183267 1.516991169 1 22.06681809 -4.103515012 0.105234048 1.85E-11 1.67132337 0.276237311 0.198029795 164.2782505 1.417569002 38.95563982 2.725417331 7.88E-05 4.103515012 1.67132337 LKDDEVAQLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 163.99 1.31E-05 5659060000 4521790 3908340 4254590 5164970 2779070 4987490 5579730 5929040 3431270 FALSE TRUE 4308053.948 4306604.289 4449667.16 4645777.403 3263738.928 4814771.971 4728439.71 5409861.826 3963373.827 1.086966341 1.086600578 1.122696812 1.172177444 0.823474916 1.214816513 1.193033995 1.364963807 1 21.91829762 LKDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDDIR 6 1 Q9UDT6;Q9UDT6-2 Q9UDT6 CLIP2 CAP-Gly domain-containing linker protein 2 0 70.268 0.083281 98071000 181010 142970 187960 212270 166900 160850 196700 190690 161100 FALSE TRUE 172454.016 157538.8055 196578.1519 190932.2163 196007.3072 155279.7242 166689.8024 173992.1727 186082.5652 0.926760741 0.846607017 1.056402848 1.026061824 1.053335152 0.834466808 0.895784095 0.935026731 1 17.50558336 -0.261616571 9.666554757 1 0.937323291 0.030985183 0.078996811 0 0 0.079628177 0.018768541 0.547499124 0.261616571 -0.062676709 LKDEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDEVVR 7 1 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 100.15 0.0091254 138910000 225790 207770 214970 241170 257130 211420 280130 253200 257630 FALSE TRUE 215117.3542 228941.9992 224826.5871 216927.1334 301973.3906 204098.4724 237391.0236 231028.4657 297581.9446 0.722884429 0.769341028 0.755511519 0.728966046 1.014757098 0.68585637 0.797733289 0.77635243 1 18.18292747 -5 0.224915794 2.143512433 0.75168264 0.380243849 0.08834163 160.9364293 1.61009865 83.72305193 0.147563426 1.00E-05 5 -1.391829793 LKDHMLIPVSMSELEKVDGLLTCCSVLINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDHMLIPVSMSELEKVDGLLTCCSVLINK 30 2 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 127.63 7.19E-06 81079000 279040 139670 280160 214190 192550 275980 426380 337280 257480 FALSE TRUE 265850.3322 153902.5318 293005.6131 192659.2143 226130.659 266422.7434 361327.9 307745.9752 297408.6834 0.893888938 0.517478273 0.98519522 0.647792835 0.760336438 0.8958136 1.214920479 1.034757868 1 18.18208724 1.994057927 3.795916927 1.101140501 0.746960668 0.530033674 0.137410825 0.148853324 4.618719186 0.057541865 0.035604023 98.64110469 -1.994057927 -0.354179833 LKDIALGMQTEIEEQDDILDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKDIALGMQTEIEEQDDILDR 21 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 ;; 151.82 5.33E-08 73629000 75859 65400 61085 77005 61299 63471 77247 74004 64149 FALSE TRUE 72273.29541 72064.33435 63885.80767 69264.3111 71989.52619 61272.98335 65461.55141 67523.81744 74096.89929 0.975388931 0.972568826 0.862192727 0.934780156 0.971559227 0.826930465 0.883458715 0.91129073 1 16.17712555 3.768707086 21.71782761 0.904846856 0.973979017 0.190181374 0.050325558 172.7481166 124447.1621 0.012193157 0.021973167 5870.932485 -3.768707086 0.06913216 LKDISTLEPLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDISTLEPLKK 12 2 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 131.53 0.00011081 138680000 611700 510970 516630 618080 383810 615430 691930 721740 468720 FALSE TRUE 582786.1533 563038.4239 540317.9965 555949.4241 450746.3425 594117.5048 586363.3703 658540.6194 541406.7037 1.076429511 1.039954659 0.997989114 1.026860991 0.832546659 1.097358974 1.083036775 1.216351063 1 19.04635323 2.044667416 24.99997692 1.10431744 1.006200883 0.279601307 0.082062285 177.1093095 99125.74124 0.029666742 0.021910334 110.8325732 -2.044667416 -0.098116557 LKDLDLDAFAEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKDLDLDAFAEELER 15 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 178.12 6.61E-07 434102000 618840 570744 575949 671982 501287 612035 682500 703723 564344 FALSE TRUE 589588.6596 628903.4625 602356.8313 604433.0927 588711.2941 590840.0745 578372.09 642101.2834 651859.5853 0.904471872 0.964783639 0.924059176 0.927244312 0.90312593 0.906391634 0.887264839 0.985030056 1 19.31420171 1.127307684 6.180310635 0.998446153 0.91890471 0.699106575 0.020704586 0.130830686 6.224439131 0.021881771 0.005509989 13.40626144 -1.127307684 -0.079541443 LKDLEALLNSKEAALSTALSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDLEALLNSKEAALSTALSEKR 23 3 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 128.12 1.91E-05 27227000 78302 61748 132430 69846 91743 101390 124690 99185 117770 FALSE TRUE 74600.81964 68040.1914 138502.0465 62824.94738 107742.9502 97878.83888 105666.2504 90499.83559 136033.1701 0.548401685 0.500173534 1.018149076 0.461835502 0.792034399 0.719521855 0.776768271 0.665277708 1 17.05359895 -0.310772054 0.060466289 1.7363246 5.05E-13 0.313477471 0.156995146 108.00054 1.725914979 31.10896485 18.62583498 0.488908903 0.310772054 -1.7363246 LKDLFDYS(ph)PPLHK ddPTM_SK-BR-3_Trastuzumab_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;LKDLFDYS(1)PPLHK;LKDLFDY(0.003)S(0.997)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK 137.45 3.66E-05 23783416000 1860181 1643792 2394386 2033979 1216279 1985060 2182650 2063085 1383429 TRUE FALSE 1772253.931 1811296.274 2504170.966 1829519.567 1428397.673 1916316.874 1849646.655 1882430.34 1597964.104 1.109069926 1.133502479 1.567100888 1.144906548 0.893885957 1.199223981 1.157502006 1.178017914 1 20.60780357 3.01242812 24.99986379 1.100863601 1.234979617 0.220368353 0.152134469 456.6434174 918557.3715 0.044708913 0.053406349 1029.030198 -3.01242812 0.134116016 LKDLFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 81.594 0.024421 180130000 1737700 1579400 1560300 2157600 1301500 1851300 2064100 2143300 1545800 FALSE TRUE 1655562.365 1740342.656 1631841.298 1940713.949 1528481.188 1787189.017 1749183.635 1955621.29 1785514.769 0.927218522 0.97470079 0.91393324 1.086921252 0.856045111 1.000937683 0.979652292 1.095270296 1 20.76790864 1.474122251 3.085200036 1.046584804 0.958746743 0.226230606 0.06429182 0.313003615 5.825107077 0.042091629 0.014804819 29.79354977 -1.474122251 -0.087838061 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(0.999)GDQEDEDDES(0.001)EDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(0.999)GDQEDEDDES(0.001)EDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 245.99 2.65E-50 2532810000 251134 226704 234443 268832 140595.7 269206 282330 286474 117894.5 TRUE FALSE 239263.3935 249805.3953 245192.4434 241808.4966 165115.5456 259883.3287 239255.3732 261388.8179 136176.9769 1.757003268 1.834417248 1.800542566 1.775692941 1.212507057 1.908423396 1.756944371 1.919478782 1 17.05512329 2.967501129 24.86125919 1.631762871 1.79808668 0.11129107 0.289233748 1638.741214 1253618.039 0.081067365 0.086049497 927.8999016 -2.967501129 0.166323809 LKDLPFIVSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDLPFIVSHR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 163.99 1.40E-05 269490000 1145970 1110410 1036380 1169250 991020 1100590 1254350 1236200 996210 FALSE TRUE 1091802.269 1223562.041 1083899.048 1051714.769 1163853.574 1062476.292 1062975.87 1127951.774 1150697.159 0.94881808 1.06332238 0.941949878 0.913980503 1.01143343 0.923332681 0.923766833 0.980233388 1 20.13407676 3.691194085 24.99925333 0.950150763 1.006070339 0.177864918 0.04280701 487.1226291 257094.6966 0.010669413 0.016529009 4911.273105 -3.691194085 0.055919576 LKDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 124.59 0.016679 25476358000 27704190 21851170 19881450 22867370 25518660 22179010 32924390 25821830 28403660 FALSE TRUE 26394667.84 24077829.07 20793034.15 20568698.52 29969106.22 21410945.32 27901169.61 23560733.68 32808354.53 0.804510565 0.733893224 0.633772539 0.62693478 0.913459595 0.652606497 0.850428801 0.718132135 1 24.9675599 -0.701270498 0.43037016 1.073449228 0.730768171 0.432305114 0.093278341 10.41896141 1.56975516 1.130219916 0.051099269 0.198943384 0.701270498 -0.342681058 LKDLYIRPNIAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDLYIRPNIAQK 13 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 180.84 7.06E-06 405130000 1117000 746060 854530 945200 826620 919600 1273900 1099600 1121300 FALSE TRUE 1064201.624 822084.3622 893711.0457 850186.7002 970782.2663 887754.0214 1079543.158 1003313.195 1295185.477 0.821659633 0.634723271 0.69002553 0.65642081 0.749531464 0.68542617 0.833504681 0.774648274 1 20.30472728 0.778304568 0.725098578 0.999549812 0.702717638 0.695669915 0.059303417 0.535599627 0.573910995 0.05681533 0.020883483 6.002118528 -0.778304568 -0.296832174 LKDNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDNEK 6 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0Y400;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 89.142 0.046059 375040000 1300210 1147730 1062450 1257220 591720 1045390 1163440 1425910 865630 FALSE TRUE 1238751.65 1264684.992 1111164.383 1130841.857 694915.7807 1009187.882 985935.86 1301049.761 999867.4794 1.238915832 1.264852611 1.111311655 1.130991737 0.695007884 1.009321638 0.986066534 1.3012222 1 19.93137737 3.372323597 2.094434525 0.997282701 1.24901788 0.292620579 0.148440845 0.339276383 3.027937353 0.043429422 0.065336418 2356.804709 -3.372323597 0.251735178 LKDPANFQYPAESVLAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDPANFQYPAESVLAYK 18 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 184.15 5.44E-14 779560000 2815000 2340690 2389680 2890000 2136500 2609700 3015900 2791700 2305500 FALSE TRUE 2681940.529 2579208.972 2499249.192 2599491.709 2509104.924 2519325.435 2555769.064 2547243.948 2663025.165 1.007102961 0.968525948 0.938500028 0.976142375 0.942200981 0.946038914 0.959723963 0.956522673 1 21.34463463 4.362869576 2.106817557 0.957292734 1.006610769 0.388289971 0.018071542 0.29345841 2.306706401 0.004096205 0.02040156 23060.54547 -4.362869576 0.049318034 LKDQDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKDQDLR 7 1 Q9UMY1 Q9UMY1 NOL7 Nucleolar protein 7 0 73.248 0.04506 296970000 1290700 1230000 1124900 1392400 1479400 1203300 1412900 1281700 1551400 FALSE TRUE 1229691.169 1355338.398 1176477.778 1252433.307 1737406.892 1161629.419 1197336.155 1169467.553 1791983.189 0.686218027 0.756334327 0.656522776 0.698909072 0.969544191 0.648236784 0.668162605 0.652610784 1 20.77312567 -2.058171302 2.666280737 1.404228015 0.717188679 0.466067036 0.095170951 25594576 14317072.7 62752910.47 0.021851155 0.008746387 2.058171302 -0.687039335 LKDSEAELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKDSEAELQR 10 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;; 141.08 3.48E-05 2104840000 3352840 2744320 2813880 3382000 2649910 3072100 3618460 3412370 2928230 FALSE TRUE 3194357.898 3023969.328 2942899.181 3042034.935 3112053.465 2965712.407 3066397.469 3113564.793 3382324.953 0.944426672 0.894050504 0.87008174 0.899391684 0.920092986 0.876826576 0.90659458 0.920539817 1 21.68958384 0.741035411 2.304226097 0.999964981 0.902186881 0.687527603 0.020727631 0.71345382 5.418257428 0.019994559 0.005406771 5.508526093 -0.741035411 -0.0977781 LKDSEAELQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDSEAELQRR 11 2 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ; 86.313 0.0081912 208673000 273630 145147 254814 188534 271245 246312 337040 282571 356010 FALSE TRUE 260696.0522 159937.6443 266497.4739 169582.2041 318550.0421 237782.1537 285618.3578 257827.5852 411218.2126 0.633960375 0.388936189 0.648068266 0.412389819 0.774649644 0.578238382 0.694566411 0.62698484 1 18.64954464 -0.874838897 0.237185403 1.27352597 0.485847396 0.591668855 0.110604047 9.046573087 0.533246198 1.862806281 0.192680362 0.13340162 0.874838897 -0.787678574 LKDSGSVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDSGSVQR 9 1 D6R9V6;A6NJ38;A6NHM7;Q7Z5H3-4;Q7Z5H3-3;Q7Z5H3;Q7Z5H3-5;Q7Z5H3-2 D6R9V6 ARHGAP22 Rho GTPase-activating protein 22 0 ; 66.692 0.03786 46921000 144675 137392 139483 153676 373560 80109 168982 91039 401430 FALSE TRUE 137836.4995 151392.401 145878.4335 138228.1965 438708.7457 77334.80524 143200.6923 83067.14253 463681.7142 0.297265334 0.326500693 0.314608985 0.298110088 0.946142003 0.166784246 0.30883403 0.179146902 1 18.82277531 -1.027005568 4.221075029 1.000048488 0.351870337 0.464312537 0.217818753 73401523.27 167821560.1 55032.67641 0.050801347 0.093971126 1.027005568 -0.648178151 LKDVLLQVDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKDVLLQVDDER 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 150.12 5.63E-05 559290000 2165350 2192720 1842340 2383680 1695440 2057230 2174290 2236360 1843510 FALSE TRUE 2062998.197 2416160.661 1926813.111 2144067.958 1991124.199 1985987.609 1842562.127 2040532.463 2129392.115 0.968820248 1.134671554 0.904865336 1.006892034 0.935066954 0.932654721 0.865299591 0.958269944 1 21.02201021 3.721643257 24.98798691 0.935128297 1.051745907 0.377152941 0.057198738 656.3330468 969444.3217 0.014760169 0.022922762 5267.969557 -3.721643257 0.116617611 LKDVLLQVDDERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LKDVLLQVDDERR 13 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 195.1 2.54E-07 2851500000 4490400 3679460 4074730 4370630 3762270 4212020 5038040 4815960 4608020 FALSE TRUE 4278147.691 4054401.157 4261560.401 3931285.969 4418408.697 4066156.691 4269394.468 4394249.011 5322608.207 0.80376904 0.761732031 0.800652657 0.738601418 0.830120972 0.763940635 0.802124504 0.825581903 1 22.34370194 0.473350219 1.102276745 1.000394674 0.782115333 0.873537057 0.025516601 0.568205927 0.909142688 0.02108349 0.006495381 2.974063376 -0.473350219 -0.218279342 LKDYAFIHFDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKDYAFIHFDER 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 152.99 4.22E-05 878520000 2802500 2474900 2369800 2933800 2445800 2648700 3068400 2820200 2209410 FALSE TRUE 2670031.379 2727095.124 2478457.674 2638888.85 2872346.746 2556974.855 2600259.225 2573248.337 2552034.019 1.046236594 1.068596697 0.971169528 1.034033571 1.125512718 1.001936039 1.018896773 1.00831271 1 21.28321613 LKDYAFVHFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKDYAFVHFEDR 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 140.35 3.53E-05 1967180000 4484110 3708490 3722910 4359300 4202220 3834240 4903260 4335550 3809990 FALSE TRUE 4272155.007 4086389.347 3893609.106 3921094.882 4935085.838 3701459.307 4155177.632 3955906.258 4400823.79 0.970762569 0.928551004 0.884745514 0.890991112 1.121400463 0.84108328 0.944181778 0.898901307 1 22.06934218 4.584665422 3.20110924 0.935063487 0.970974093 0.014589887 0.077235182 1.432997447 25.66061199 0.017319501 0.104110453 38429.5609 -4.584665422 0.035910605 LKEAETR ddPTM_SK-BR-3_Trastuzumab_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 0 105.95 0.0071249 459540000 1328900 1101300 1147500 1413500 1090000 1210600 1497800 1404100 1346000 FALSE TRUE 1266085.531 1213523.722 1200114.01 1271412.295 1280095.655 1168676.618 1269283.101 1281149.56 1554730.806 0.814343889 0.78053623 0.771911128 0.817770054 0.823355175 0.751690656 0.81640056 0.824033045 1 20.56823338 0.524802006 1.473517374 0.999976152 0.794812117 0.887045199 0.022675575 0.649132383 1.692588011 0.020232443 0.005875631 3.348127638 -0.524802006 -0.205164034 LKEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKEASR 6 1 A4D1E1;A0A087WUA7;O75131;H0YB26 A4D1E1;O75131;REV__Q1MSJ5 ZNF804B;CPNE3 Zinc finger protein 804B;Copine-3 0 76.847 0.067469 262400000 618670 389050 377470 707600 721560 420340 598980 501610 730670 FALSE TRUE 589426.6952 428694.6373 394777.3729 636470.7036 847399.8355 405783.5204 507594.6 457686.3692 843978.5719 0.698390593 0.507944931 0.467757578 0.754131355 1.004053733 0.480798369 0.601430672 0.542296196 1 19.68684684 -1.185698089 3.573731355 1.0004288 0.626159533 0.340732281 0.160637085 14558031225 21901890310 73961511.67 0.038101183 0.065208155 1.185698089 -0.374269268 LKECEDTHLGEEVDRNWNEVVTQQYLFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKECEDTHLGEEVDRNWNEVVTQQYLFDR 29 2 O43847;O43847-2;G3V1R5;H0Y5G9 O43847 NRD1 Nardilysin 0 61.911 0.014754 69141000 38965 31621 43739 44722 37973 41978 55454 52375 36604 FALSE TRUE 37123.20167 34843.21585 45744.47641 40226.45959 44595.47918 40524.29133 46993.47382 47788.76734 42280.36137 0.878024701 0.824099291 1.081932011 0.951421849 1.054756339 0.958466059 1.111472852 1.13028285 1 15.36770009 3.740957975 24.99590749 1.041829051 0.851061987 0.631747746 0.060347326 117.074412 1220663.947 0.01523069 0.02592874 5507.543995 -3.740957975 -0.190767064 LKEDILENEDEQNS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK 195.13 2.15E-11 1763600000 3503890 3883630 2974770 4291980 1722880 4184210 3762680 4388310 1749460 TRUE FALSE 3338268.064 4279376.312 3111166.147 3860542.016 2023349.727 4039309.759 3188614.06 4004046.313 2020757.322 1.651988602 2.117709171 1.539604045 1.910443166 1.001282888 1.998908882 1.577930227 1.981458273 1 20.94646464 3.714591641 24.54238991 1.610915271 1.884848949 0.102514156 0.370742263 1254.060141 1284060.988 0.087506309 0.13564676 5183.1245 -3.714591641 0.273933677 LKEDILENEDEQNS(ph)PPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKEDILENEDEQNSPPKK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK 189.57 1.67E-14 2658090000 1612780 1745060 1438980 1941530 651429 2029860 1699590 2016920 700300 TRUE FALSE 1536547.086 1922883.598 1504958.656 1746363.716 765038.0113 1959565.439 1440286.33 1840307.792 808898.9474 1.89955382 2.377161701 1.860502676 2.158939286 0.94577699 2.422509568 1.780551619 2.275077497 1 19.62559996 LKEEEEDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKEEEEDKK 9 2 P27797 P27797 CALR Calreticulin 0 ; 101.93 0.0020626 533280000 1895620 1762830 1576060 1980490 687051 2144830 1808880 2310680 601230 FALSE TRUE 1806017.799 1942464.381 1648323.91 1781407.383 806872.4769 2070553.999 1532902.134 2108344.61 694465.6777 2.600586116 2.797063186 2.373513858 2.565148199 1.161860842 2.981506597 2.207311582 3.035923411 1 19.40554387 3.388515815 2.250800684 2.221137636 2.688774325 0.096070339 0.665757346 0.733823406 7.539847142 0.180496831 0.270815378 2446.334356 -3.388515815 0.467636689 LKEEEEDKKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKEEEEDKKR 10 3 P27797 P27797 CALR Calreticulin 0 ; 145.28 1.35E-05 2345550000 1323850 1084280 1078230 1327530 658154 1383140 1408690 1607000 724858 FALSE TRUE 1261274.234 1194769.365 1127667.912 1194084.162 772935.8492 1335241.515 1193768.468 1466282.561 837265.2766 1.506421285 1.426990224 1.346846625 1.426171843 0.92316721 1.594765187 1.425794789 1.751275972 1 19.67532527 4.164521349 2.067154843 1.373534166 1.498110269 0.035278801 0.245123777 1.416184841 11.5792181 0.061121598 0.210760419 14605.66545 -4.164521349 0.124576103 LKEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKEEEK 6 1 Q7Z6E9;A0A2R8Y880;H3BSK8;Q93034;I3L121;I3L3S9;J3KNW5;Q96AJ1-2;Q96AJ1 Q7Z6E9;Q93034 RBBP6;CUL5;CLUAP1 E3 ubiquitin-protein ligase RBBP6;Cullin-5;Clusterin-associated protein 1 0 65.038 0.095851 150670000 312490 263460 289870 331320 309870 323350 286020 355180 284050 FALSE TRUE 297719.217 290306.8735 303160.8262 298015.0841 363911.2299 312152.3084 242382.3959 324078.5563 328099.0233 0.907406593 0.884814806 0.923991858 0.908308355 1.109150604 0.95139664 0.738747691 0.987746178 1 18.32377177 1.032064067 24.99948726 1.000002056 0.910113782 0.108463094 0.089149996 343.3233303 267678.8313 0.088247064 0.022061766 10.76624025 -1.032064067 -0.089888274 LKEEISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKEEISK 7 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 118.5 0.0045542 2846530000 8167380 7701760 6138750 8043820 4316800 6347120 6604650 7583280 4483360 FALSE TRUE 7781324.134 8486578.1 6420217.76 7235239.931 5069648.553 6127317.643 5596989.34 6919247.802 5178616.571 1.502587424 1.63877321 1.239755381 1.397137601 0.978958083 1.183195851 1.08078852 1.336118963 1 22.30413531 3.385868674 1.420217125 1.13063373 1.572911762 0.606264855 0.134237631 0.224178451 0.931741558 0.040311235 0.068331907 2431.468647 -3.385868674 0.442278032 LKEELIDAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKEELIDAIR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 118.87 0.00070066 90237000 543600 465090 438150 547830 429190 501030 535290 570240 484780 FALSE TRUE 517905.1053 512483.1998 458239.6109 492761.0876 504040.6001 483679.2055 453621.6792 520306.7626 559957.2065 0.924901223 0.915218509 0.818347555 0.87999776 0.900141286 0.863778874 0.810100618 0.929190225 1 19.09495705 0.995030488 24.88465695 1.000000004 0.875926822 0.555859602 0.037030431 136.9439637 685745.848 0.039613034 0.009903259 9.88622494 -0.995030488 -0.124073182 LKEENEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 111.95 0.0058957 904840000 1701830 1682340 1397960 1783210 962500 1487040 1575010 1592930 1045180 FALSE TRUE 1621387.869 1853772.359 1462057.849 1603958.343 1130359.695 1435543.432 1334713.297 1453444.605 1207261.176 1.34302991 1.535518904 1.21105348 1.328592664 0.936300875 1.189091027 1.105571291 1.203918947 1 20.20330639 3.270748428 1.660414936 1.108101425 1.431313363 0.562030069 0.114192925 0.223838545 1.275899774 0.03375545 0.049380894 1865.298873 -3.270748428 0.323211938 LKEFLEDYDDDRDDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKEFLEDYDDDRDDPK 16 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ;; 153.86 2.31E-07 490450000 1867390 1866390 1573280 2053310 1000050 2071420 1925510 2210170 956770 FALSE TRUE 1779122.176 2056577.263 1645416.444 1846907.378 1174458.403 1999686.206 1631738.085 2016635.798 1105141.005 1.609859889 1.860918429 1.488874665 1.671196136 1.062722673 1.809439879 1.476497639 1.824776919 1 20.07579902 -1.981039285 2.836325673 0.463910485 1.606764754 0.398101145 0.231950896 52370199.58 47176920.28 184444583.7 0.053298568 0.010446257 1.981039285 1.142854269 LKEIKEELLHSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKEIKEELLHSEK 13 2 H7BZN7;Q9NY93-2;Q9NY93 H7BZN7 DDX56 Probable ATP-dependent RNA helicase DDX56 0 81.311 0.0092581 90304000 154610 120940 149710 153980 97324 177100 174460 182030 89266 FALSE TRUE 147301.8917 133263.9235 156574.3516 138501.6379 114297.2748 170966.9826 147842.9228 166090.4882 103108.9154 1.428604803 1.292457815 1.518533592 1.343255696 1.108510107 1.65812027 1.433851983 1.610825675 1 16.65380956 2.223485774 24.99977156 1.465863011 1.34865713 0.026152633 0.203343714 635.8669884 1054500.526 0.067354263 0.049934553 167.2960834 -2.223485774 -0.117205882 LKEINFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKEINFR 7 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 170.66 0.00088133 808710000 1209810 959620 1108640 1397080 1213330 1243050 1582380 1395520 1443550 FALSE TRUE 1152624.679 1057406.369 1159472.241 1256642.864 1424934.368 1200002.867 1340958.869 1273320.871 1667408.361 0.691267182 0.634161609 0.695373891 0.753650331 0.854580318 0.71968145 0.804217431 0.763652684 1 20.66917604 -5 0.086405556 1.898181824 0.489052031 0.768081959 0.049285528 99.31031387 0.6004431 16.52698209 1.285836629 1.00E-05 5 -1.409129794 LKELIFEETAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKELIFEETAR 11 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 136.99 8.00E-05 370340000 1198120 964450 1059600 1256960 1100990 1139140 1404000 1271880 1281810 FALSE TRUE 1141487.242 1062728.551 1108183.708 1130607.993 1293002.307 1099691.296 1189794.014 1160507.445 1480586.548 0.770969616 0.717775366 0.748476142 0.763621684 0.873304103 0.742740299 0.803596396 0.783816013 1 20.4977374 -5 0.206205094 2.078504817 0.737276061 0.763899444 0.039840889 65.15742557 0.64772167 28.97445257 0.083772438 1.00E-05 5 -1.341228756 LKELQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKELQER 7 1 B4DH95;Q6P9H5-2;Q6P9H5 B4DH95 GIMAP6 GTPase IMAP family member 6 0 61.962 0.080551 397940000 734630 621180 662720 846190 784170 901930 1059200 984690 982070 FALSE TRUE 699905.4958 684478.9482 693106.3675 761129.3735 920928.9997 870695.9379 897599.5865 898465.3234 1134364.4 0.617002346 0.603403058 0.611008568 0.670974313 0.811845823 0.76756282 0.791279757 0.792042948 1 20.11345273 1.689879943 0.229171102 1.062116311 0.501738023 0.897543299 0.039064096 0.660669282 0.156388098 0.133806617 0.14744379 48.96434426 -1.689879943 -0.560378288 LKERPSS(ph)REDTPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKERPSSREDTPSR 14 3 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 LKERPS(0.406)S(0.594)REDTPSR 97.32 0.016696 254850000 142270 100640 122870 129050 100760 125700 148090 139160 117510 TRUE FALSE 135545.1791 110895.3304 128503.711 116077.6488 118332.5121 121346.9775 125496.1506 126974.4127 135732.8506 0.998617346 0.817011725 0.946739941 0.855192006 0.871804516 0.894013328 0.924582001 0.935472968 1 17.0504104 0.955734464 1.258283666 0.998892632 0.895674339 0.29836432 0.049328471 0.617988769 1.991159712 0.043282322 0.013302925 9.030971335 -0.955734464 -0.103218293 LKESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKESER 6 1 E9PL50;B3KRD1;B7Z4D2;A0A0C4DG86;Q9NX95-5;Q9NX95-2;Q9NX95-4;Q9NX95-3;Q9NX95 E9PL50 SYBU Syntabulin 0 92.925 0.042137 117650000 235200 213350 197570 241110 218110 223660 280790 237990 250980 FALSE TRUE 224082.5621 235090.6076 206628.7799 216873.1647 256148.3149 215914.5981 237950.3284 217150.3339 289900.6966 0.772963172 0.810934952 0.712757101 0.748094666 0.883572609 0.744788131 0.820799437 0.749050749 1 18.14519927 -1.37145484 3.015367442 1.00274833 0.783922744 0.668257802 0.048574722 16971071.87 21556901.64 409796.6519 0.010563168 0.042515291 1.37145484 -0.218825586 LKETYEALLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKETYEALLAR 11 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 101.53 0.0024848 0 177260 172140 164930 192700 157510 171990 185100 180870 177450 FALSE TRUE 168881.2711 189681.2617 172492.2036 173329.4299 184979.6941 166033.9432 156859.5954 165032.0639 204968.0397 0.823939534 0.925418724 0.841556586 0.845641253 0.902480672 0.810047964 0.765288069 0.805159986 1 17.64503944 2.220300065 24.94780122 0.818552286 0.869474702 0 0.069643588 506.139069 691489.3219 0.023483704 0.017376153 166.0733952 -2.220300065 0.050922416 LKEVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 77.282 0.066421 120520000 338730 260740 284330 327200 277780 300170 363450 328040 296080 FALSE TRUE 322718.9042 287309.7024 297366.8117 294309.2344 326224.7441 289775.0376 307999.0273 299315.0786 341994.5742 0.943637498 0.840100177 0.869507396 0.86056697 0.953888654 0.847308874 0.900596239 0.875204173 1 18.38361391 -1.252069896 3.951937827 1.000126515 0.885733955 0.473058321 0.037690632 3.82E-05 7.22E-06 0.033154603 0.007805983 0.055966752 1.252069896 -0.11439256 LKEVFSMAGVVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKEVFSMAGVVVR 13 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 202.13 8.78E-08 199583000 788400 579550 697140 711020 762750 663840 950730 743540 867830 FALSE TRUE 751133.8945 638606.8039 729104.5586 639546.9188 895773.3585 640851.0543 805678.6771 678431.6958 1002408.644 0.749329027 0.637072323 0.727352625 0.638010179 0.893620944 0.639311181 0.803742747 0.676801522 1 19.93503933 -5 0.252867025 2.732361076 0.695149058 0.527474947 0.082427174 132.2813388 1.30780465 118.5785791 0.100636597 1.00E-05 5 -2.037212018 LKFGTFGGLGS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKFGTFGGLGSK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKFGT(0.049)FGGLGS(0.951)K 56.205 0.073854 126100000 97711 83300 112560 109730 130620 93849 170230 111780 190630 TRUE FALSE 93092.39467 91788.3647 117720.9873 98699.73193 153400.0866 90598.9856 144258.287 101991.9506 220191.9268 0.422778419 0.416856177 0.53462899 0.448244099 0.696665354 0.41145462 0.655147939 0.463195686 1 17.74840205 -5 0.176643599 3.001668649 0.39406977 0.724167268 0.096716822 61.34130854 0.58679488 43.03374882 0.274606614 1.00E-05 5 -2.607598879 LKFMS(ph)SPSLSDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKFMSSPSLSDLGK 14 1 B1AHC3;B1AHC4;F8WEZ7;E9PH80;P85299;P85299-5 B1AHC3;P85299 PRR5-ARHGAP8;PRR5 Proline-rich protein 5 1 LKFMS(0.985)S(0.015)PSLSDLGK 126 0.00038223 0 151820 93431 129290 123390 110750 155680 191890 146730 129620 TRUE FALSE 144643.7695 102951.7251 135218.0744 110986.6028 130064.7649 150288.7626 162613.6562 133881.5433 149720.8076 0.966089963 0.687624698 0.903134818 0.741290436 0.868715358 1.003793427 1.086112604 0.894207996 1 17.19191521 2.304614962 3.935789265 1.013389539 0.820713972 0.450257969 0.089385945 0.171589779 5.294078585 0.030851288 0.024663937 201.6577707 -2.304614962 -0.192675567 LKFNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKFNFK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 106.29 0.029414 191200000 331600 349130 279500 344060 224560 286580 300750 344930 205200 FALSE TRUE 315925.9252 384706.7439 292315.3515 309474.4351 263723.1929 276655.6627 254865.0638 314726.1006 237021.368 1.332900607 1.623088868 1.233286914 1.305681584 1.112655771 1.167218235 1.075283068 1.327838512 1 17.8546576 3.32126124 1.691207035 1.143522689 1.471579024 0.511645448 0.121860091 0.237430969 1.397980325 0.035943787 0.05456894 2095.372503 -3.32126124 0.328056335 LKFS(ph)DDEEEEEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 224.4 1.91E-12 319286000 837560 913760 693520 990490 393310 925920 806510 972540 392716 TRUE FALSE 797970.1987 1006873.183 725318.578 890924.0634 461903.1395 893855.1582 683462.0869 887379.2418 453616.3916 1.759129991 2.219657847 1.598969066 1.964047332 1.018268184 1.970508947 1.506696186 1.956232752 1 18.79111325 -2.200224515 0.147223581 2.08E-12 2.088057845 0.316391835 0.334602451 53.94466243 1.073124046 21.32048102 1.944087866 0.006306312 2.200224515 2.088057845 LKFS(ph)DDEEEEEVVKDGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKFSDDEEEEEVVKDGRPK 19 3 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVKDGRPK 89.365 0.0017185 270150000 135380 115020 137130 134800 62060 153970 151510 164740 56418 TRUE FALSE 128980.8557 126740.6688 143417.5461 121249.6479 72883.24435 148637.9803 128394.3668 150314.4923 65167.0153 1.979235279 1.944859193 2.200768985 1.860598454 1.118406974 2.280877521 1.970235498 2.30660391 1 15.9918543 3.022990707 24.10702363 1.817714091 2.014312987 0.077051187 0.431445026 549.9349978 576630.9998 0.117182175 0.140048937 1054.364334 -3.022990707 0.196598896 LKFS(ph)DEEDGRDS(ph)DEEGAEGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;LKFS(1)DEEDGRDS(1)DEEGAEGHR 154.19 1.94E-08 2978170000 3075896 3271180 2471002 3320030 1725456 3212570 2854021 3008540 1474719 TRUE FALSE 2930504.492 3604516.961 2584299.886 2986294.277 2026374.98 3101317.895 2418587.679 2745096.288 1703410.891 1.720374402 2.116058422 1.517132419 1.753126209 1.189598465 1.820651677 1.419849839 1.61152914 1 20.69999505 -0.466825994 0.091786224 1.23E-11 2.487097689 0.476961065 0.230445441 37.44532092 0.864023263 16.57512889 7.240968425 0.341329643 0.466825994 2.487097689 LKGDDLQAIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 143.42 2.09E-05 6537800000 13639000 10448600 11405000 14135500 8528700 12442300 14851000 15078300 10706400 FALSE TRUE 12994311.5 11513324.22 11927930.53 12714572.68 10016102.58 12011420.03 12585207.19 13757964.12 12366693.83 1.050750643 0.930994523 0.964520566 1.028130304 0.809925653 0.971271723 1.017669505 1.112501393 1 23.55995652 1.593951807 3.623860811 1.058167351 0.960332943 0.257706982 0.069080443 0.246886295 7.527034059 0.040864157 0.017358666 39.26013664 -1.593951807 -0.097834408 LKGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGDLK 6 1 A0A494BZV2;H0Y2S9 A0A494BZV2 MPRIP 0 70.912 0.081731 291220000 726780 662110 638530 739300 461100 625610 737530 723700 543940 FALSE TRUE 692426.5497 729579.7618 667807.2321 664984.1594 541515.694 603944.9688 625006.2528 660328.9914 628291.4371 1.102078604 1.161212327 1.062894053 1.0584008 0.86188616 0.961249721 0.994771241 1.05099155 1 19.26107439 3.211648888 2.300511445 0.974709025 1.127231188 0.569915645 0.053475468 0.187925121 2.038332642 0.016144906 0.021495934 1627.979337 -3.211648888 0.152522163 LKGDNEKHS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKGDNEKHSPR 11 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 LKGDNEKHS(1)PR;LKGDNEKHS(1)PR 79.639 0.013877 145390000 488970 405340 401170 480870 280910 479450 543060 502930 259140 TRUE FALSE 465857.3571 446644.6068 419564.0413 432532.034 329900.6151 462846.5263 460206.223 458890.783 299326.1077 1.556353907 1.492167223 1.401695444 1.445019405 1.102144472 1.546295209 1.537474384 1.533079712 1 18.19135859 -1.932352048 2.598892993 0.693484658 1.459552413 0.529569645 0.133639541 15241614.51 7508892.495 28314874.59 0.032385881 0.011685518 1.932352048 0.766067755 LKGEATVSFDDPPSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKGEATVSFDDPPSAK 16 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;; 128.26 5.63E-05 450980000 1195030 975920 1076990 1264440 799450 1127560 1390790 1278100 916510 FALSE TRUE 1138543.3 1075367.358 1126371.057 1137336.089 938873.8269 1088512.314 1178599.442 1166182.788 1058637.69 1.075479658 1.015803015 1.063981632 1.074339313 0.886869829 1.028219876 1.113317099 1.101588201 1 20.01377749 1.761558166 24.99937432 1.082880279 1.025293779 0.10877498 0.061306326 22.60312805 24589.35231 0.02737033 0.01517873 57.75082138 -1.761558166 -0.057586499 LKGEIDASVPELEGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKGEIDASVPELEGDLR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 77.468 0.016161 159474000 99191 101911 85440 110876 76044 87913 92327 102467 83564 FALSE TRUE 94502.43801 112295.8468 89357.50851 99730.53383 89306.04952 84868.55077 78240.82045 93494.44627 96522.67833 0.979069786 1.163414119 0.925766981 1.033234216 0.925233852 0.879260214 0.810595207 0.96862673 1 16.55858033 2.924647966 1.34265206 0.889184983 1.056987503 0.277150137 0.080044317 0.375650658 1.399298241 0.030864048 0.034511041 840.7133932 -2.924647966 0.16780252 LKGEMMDLQHGSLFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKGEMMDLQHGSLFLR 16 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 195.27 4.77E-11 2247406000 5375380 3506496 4086496 5487350 7000240 4503930 7548470 6386020 7291050 FALSE TRUE 5121296.44 3863811.929 4273865.884 4935751.153 8221079.64 4347957.775 6396812.264 5826826.234 8421708.796 0.608106569 0.458791918 0.507482031 0.586074783 0.976177144 0.516279757 0.759562272 0.691881704 1 23.00568156 -0.925842435 0.123303559 1.476793347 0.336206306 0.473616961 0.135960051 29.73566109 0.775778465 6.215698179 1.634571674 0.118619903 0.925842435 -1.140587041 LKGIEEEEILPGFILCDPNNLCHSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKGIEEEEILPGFILCDPNNLCHSGR 26 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;; 123.43 7.67E-05 291440000 684738 535775 653126 645917 686480 655669 848769 712810 785861 FALSE TRUE 652371.7918 590371.0816 683072.4731 580988.196 806201.8947 632963.0181 719273.7003 650392.5776 907728.3103 0.71868618 0.650383022 0.752507623 0.640046355 0.8881533 0.697304481 0.792388749 0.716505776 1 19.79190103 -5 0.174426728 2.087517588 0.666901054 0.601246602 0.069504385 80.80950281 0.769571197 30.37368961 0.205776742 1.00E-05 5 -1.420616534 LKGIVPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGIVPLAK 9 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 72.643 0.039408 0 1207800 870860 844440 1032300 1005000 1015300 1416100 1217400 1148800 FALSE TRUE 1150709.688 959601.6241 883158.4093 928531.2428 1180271.682 980139.9064 1200047.937 1110798.002 1326950.037 0.867183885 0.723163343 0.665555134 0.699748459 0.889462036 0.738641154 0.904365578 0.837106124 1 20.33968262 1.195743143 0.699569563 0.99280866 0.755242924 0.505632199 0.074424635 0.549460907 0.632398633 0.070572248 0.029284239 15.69434313 -1.195743143 -0.237565736 LKGMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.569)GS(0.431)PQLNNR;LKGMKDDKEEEEDGT(0.571)GS(0.429)PQLNNR;LKGMKDDKEEEEDGT(0.56)GS(0.44)PQLNNR 121.23 7.23E-05 708240000 1023060 648950 983560 944360 500259 1171560 1275940 1333990 512164 TRUE FALSE 974701.9813 715078.7428 1028657.199 849431.1386 587504.0112 1130988.583 1081271.919 1217178.764 591587.7773 1.647603312 1.208744958 1.73880739 1.43584971 0.99309694 1.911784906 1.827745535 2.057477876 1 19.17423272 2.20007569 24.99996059 1.779734495 1.416744655 0.132709964 0.347210634 239.0798961 155305.8705 0.116528531 0.08606361 158.5169436 -2.20007569 -0.362989839 LKGMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.196)GS(0.804)PQLNNR 120.93 5.10E-05 272890000 486870 270250 430390 444980 212990 474540 558100 543380 231800 TRUE FALSE 463856.62 297788.7822 450123.8072 400249.765 250135.3886 458106.5608 472951.5948 495798.7666 267746.3601 1.732447902 1.112204783 1.681157522 1.494884057 0.934225169 1.710972133 1.766416524 1.851747924 1 18.03050744 LKGSGNLEAIHIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKGSGNLEAIHIIK 14 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 114.43 0.0002871 1194550000 2625600 2130280 2152500 2670000 1942160 2370100 3007200 2559600 2157090 FALSE TRUE 2501493.091 2347357.954 2251194.254 2401606.527 2280872.089 2288022.843 2548396.409 2335467.855 2491600.5 1.003970376 0.942108478 0.903513326 0.963881058 0.915424479 0.918294423 1.02279495 0.937336405 1 21.24864134 -0.762161094 4.447011122 1.000000141 0.954819015 0.133543526 0.038157791 3529809.043 793751.1648 4.783020793 0.009209651 0.172917483 0.762161094 -0.045181126 LKGTSPSS(ph)SSRPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGTSPSSSSRPQR 14 2 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 LKGT(0.14)S(0.14)PS(0.033)S(0.446)S(0.121)S(0.121)RPQR 69.935 0.035924 736970000 303230 238390 318120 329880 268730 336130 441740 382070 348910 TRUE FALSE 288896.9188 262682.212 332706.1167 296719.8357 315596.4269 324489.7338 374344.4499 348613.9253 403017.1808 0.716835243 0.651789116 0.825538296 0.73624612 0.7830843 0.805151118 0.928854817 0.865010084 1 18.62048182 1.970571314 0.41525513 1.004867723 0.671385698 0.792755019 0.046360125 0.420095727 0.180107007 0.048597983 0.045759467 93.44828048 -1.970571314 -0.333482025 LKGTSPSSSS(ph)RPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGTSPSSSSRPQR 14 2 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 LKGT(0.01)S(0.036)PS(0.036)S(0.082)S(0.112)S(0.724)RPQR 113.11 0.00043692 744570000 407270 295750 371020 357930 354620 414300 492510 415960 417440 TRUE FALSE 388019.1542 325887.2612 388031.634 321950.1964 416465.6157 399952.6871 417368.5539 379536.3373 482174.4632 0.804727715 0.675870014 0.804753598 0.667704785 0.863723916 0.829477124 0.865596554 0.787134878 1 18.87919572 0.674012871 0.306206892 1.035549366 0.722102054 0.566335643 0.06257576 1.780985526 0.406745456 0.184106932 0.077517295 4.720770314 -0.674012871 -0.313447312 LKGVGDSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGVGDSFK 9 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 87.184 0.012433 432560000 673030 431200 418580 466610 525270 454750 745850 606150 554230 FALSE TRUE 641217.2057 475139.7702 437772.307 419705.4763 616876.9217 439001.8935 632056.884 553072.2926 640177.1578 1.001624625 0.742200443 0.683829939 0.655608328 0.963603456 0.685750637 0.987315583 0.863936312 1 19.28811168 1.685818193 9.555852156 0.9428439 0.797520562 0.284398073 0.119951149 0.170118663 25.01987531 0.056534774 0.030345574 48.50853887 -1.685818193 -0.145323338 LKGVIDLIFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 97.214 0.0031562 0 101630 129820 79345 102600 77903 90240 112220 108860 78943 FALSE TRUE 96826.15131 143048.8056 82983.04673 92286.45307 91489.25853 87114.96617 95098.77794 99327.6413 91185.07726 1.061864005 1.568774298 0.910050737 1.012078466 1.003335867 0.955364285 1.042920408 1.089297112 1 16.47651012 3.718872783 24.99979967 1.003650085 1.315319186 0.507108053 0.128466804 537.7018365 682779.0072 0.032245725 0.050031722 5234.470821 -3.718872783 0.311669101 LKGYTSWAIGLSVADLAESIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKGYTSWAIGLSVADLAESIMK 22 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 175.77 1.17E-12 78375000 255880 165140 199390 189180 196350 235360 310170 272610 226310 FALSE TRUE 243785.0595 181967.9537 208532.2287 170163.267 230593.3778 227209.4242 262847.8698 248738.8232 261404.999 0.932595247 0.696115049 0.797736193 0.650956438 0.882130712 0.86918546 1.005519676 0.951545778 1 17.99592721 2.125172333 1.828925822 0.984394799 0.779153815 0.561831101 0.079311183 0.255156884 1.651809754 0.042330582 0.02402337 133.4050693 -2.125172333 -0.205240984 LKHFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKHFEK 6 1 Q9Y2X3;F8WED0 Q9Y2X3 NOP58 Nucleolar protein 58 0 ; 83.614 0.03412 436360000 1530870 1294040 1348210 1591240 1282690 1559550 1824760 1653890 1275890 FALSE TRUE 1458508.809 1425904.147 1410026.762 1431285.532 1506390.73 1505542.392 1546359.348 1509066.624 1473748.505 0.989659229 0.967535602 0.956762132 0.971187097 1.022149115 1.021573483 1.049269494 1.023964821 1 20.49105892 2.702181362 4.331688177 1.028879174 0.971654662 0.756660298 0.014538829 0.09518152 4.155272393 0.004727567 0.00457557 503.7109154 -2.702181362 -0.057224512 LKKEDIYAVEIVGGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKKEDIYAVEIVGGATR 17 2 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 143.6 3.06E-07 570080000 1191880 906450 1158450 1135880 896760 1238340 1427750 1367990 1183410 FALSE TRUE 1135542.194 998818.2855 1211566.078 1021699.184 1053154.66 1195455.975 1209920.515 1248201.543 1366927.179 0.830726181 0.730703362 0.886342811 0.747442293 0.770454108 0.874557177 0.88513897 0.91314414 1 20.38250496 1.423277707 0.854422493 0.993220269 0.788683642 0.672631889 0.047135285 0.294077732 0.448885177 0.04064062 0.015794705 26.50194247 -1.423277707 -0.204536627 LKLDKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKLDKDR 7 2 P61254;E5RIT6;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 60.478 0.054708 778600000 2041600 1105100 1533500 1363200 1651600 1693800 2863000 2061500 1892300 FALSE TRUE 1945097.614 1217710.946 1603812.492 1226168.546 1939638.517 1635143.281 2426196.767 1880984.131 2185748.219 0.889900125 0.557114006 0.733759029 0.560983436 0.887402538 0.748093155 1.110007432 0.860567615 1 21.05969579 2.117039007 1.721145872 0.992806925 0.697214152 0.458169749 0.128966802 0.288836888 1.644607815 0.068240302 0.037684657 130.9299516 -2.117039007 -0.295592773 LKLEDFFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKLEDFFAR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 162.36 5.82E-05 5141100000 5388700 4088600 4089400 4895600 3953100 4485000 5613300 4880900 4211700 FALSE TRUE 5133986.83 4505232.988 4276903.035 4403484.987 4642519.388 4329683.325 4756887.99 4453502.521 4864828.926 1.055327311 0.926082511 0.879147674 0.90516749 0.954302702 0.889997036 0.977811977 0.915448948 1 22.21395764 4.526730862 2.567942788 0.928782246 1.058078409 0.512196252 0.037926983 0.242132513 2.744211445 0.008849931 0.055276663 33630.30935 -4.526730862 0.129296163 LKLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKLEDR 6 1 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 74.415 0.073312 112140000 431690 360900 407480 442920 367430 401580 500350 450960 431940 FALSE TRUE 411284.8692 397676.1203 426163.3611 398396.8401 431509.6757 387673.1839 424012.4179 411471.5517 498923.0492 0.824345297 0.797069049 0.854166513 0.7985136 0.864882223 0.777019992 0.849855341 0.824719468 1 18.92845779 -5 0.364254741 3.256401185 0.817675062 0.802127563 0.027510059 186.1378032 1.461992157 329.8046621 0.016736154 1.00E-05 5 -2.438726123 LKLGEIVTTIPTIGFNVETVEYK ddPTM_SK-BR-3_Trastuzumab_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 ; 198.05 2.61E-24 336180000 1098590 1076320 1093720 1250780 658880 1153620 1156250 1343820 700700 FALSE TRUE 1046661.828 1185998.232 1143868.144 1125049.218 773788.4634 1113669.85 979842.8265 1226147.997 809360.9773 1.29319532 1.465351388 1.413297868 1.390046283 0.956048642 1.375986589 1.210637594 1.514958135 1 19.62642377 -4.340820108 0.192724823 2.08E-13 1.383852621 0.265332222 0.16057814 138.1992819 1.706984517 54.45760916 0.402301937 4.56E-05 4.340820108 1.383852621 LKLLLPWLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKLLLPWLEAR 11 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 63.537 0.080117 0 42498 26177 19455 19222 42301 24502 54425 32362 46759 FALSE TRUE 40489.20376 28844.46606 20347.03099 17289.76804 49678.28101 23653.4896 46121.46667 29528.21172 54010.14691 0.749659204 0.534056427 0.376726081 0.320120737 0.919795332 0.437945293 0.853940774 0.546716004 1 15.72094285 0.494602241 0.506658458 1.015740465 0.55505404 0.30665181 0.195874465 2.387183255 1.109476891 0.300618842 0.095196725 3.123217587 -0.494602241 -0.460686425 LKLS(ph)PS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.995)PS(0.901)PS(0.091)S(0.013)R;LKLS(0.96)PS(0.879)PS(0.125)S(0.036)R;LKLS(0.998)PS(0.986)PS(0.014)S(0.003)R 61.167 0.053117 1823410000 1780210 1988650 1932700 2153610 1282910 2161240 2249980 2125730 1618720 TRUE FALSE 1696063.001 2191295.696 2021316.207 1937125.031 1506649.098 2086395.717 1906704.227 1939589.812 1869742.83 0.907110312 1.171977055 1.08106643 1.036038219 0.805805522 1.115873094 1.019768172 1.037356465 1 20.83440842 2.991354581 24.81379191 1.000074188 1.057982379 0.066731405 0.099564367 1108.706319 3182184.621 0.028762683 0.032789521 980.2900194 -2.991354581 0.057908191 LKLS(ph)PSPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.91)PS(0.09)PSSR;LKLS(0.789)PS(0.211)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.767)PS(0.233)PSSR;LKLS(0.971)PS(0.029)PSSR 142.12 2.20E-05 9702170000 12339910 12471620 12097770 14151640 9226900 13275570 14446740 14427780 11228550 TRUE FALSE 11756626.91 13742492.26 12652464.72 12729090.26 10836068.44 12815833.68 12242624.48 13164407.1 12969816.19 0.906460565 1.059574944 0.975531537 0.981439527 0.835483578 0.988127626 0.943931996 1.015003367 1 23.6286547 1.231252918 24.99098332 1.007501709 0.961057479 0.115996458 0.057945254 451.5560583 1544172.294 0.050185581 0.013553534 17.03150073 -1.231252918 -0.04644423 LKLSILYPATTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKLSILYPATTGR 13 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 90.367 0.0042724 0 479250 332220 450100 474960 527470 468230 622850 536940 619190 FALSE TRUE 456596.8023 366073.5957 470737.5302 427216.1184 619460.601 452015.0777 527822.7931 489922.6871 715210.8228 0.638408687 0.511840123 0.658180099 0.597328934 0.86612308 0.632002569 0.737996093 0.685004577 1 19.44800904 -5 0.112778503 2.139433961 0.462080215 0.638740583 0.083883234 93.29434659 0.694813117 24.31084914 0.89699704 1.00E-05 5 -1.677353746 LKMPEMHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKMPEMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 59.757 0.060196 84673000 341940 233800 185930 233690 257980 213830 359790 277620 260250 FALSE TRUE 325777.1739 257624.4858 194455.0744 210199.0372 302971.6303 206425.0135 304897.4275 253310.121 300608.2408 1.08372669 0.857010723 0.646872068 0.699245758 1.007862025 0.686691133 1.01426836 0.842658606 1 18.19752503 -0.361278161 7.666848664 0.999950395 0.865921641 0.082239606 0.148361637 0 0 0.140595673 0.033138718 0.435233022 0.361278161 -0.134028754 LKNDSDLFGLGLEEAGPKES(ph)SEEGKEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNDSDLFGLGLEEAGPKESSEEGKEGK 28 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 1 LKNDSDLFGLGLEEAGPKES(0.954)S(0.046)EEGKEGK 210.21 9.16E-26 254260000 277540 282290 241000 316200 85759 322310 273460 335440 77700 TRUE FALSE 264421.2342 311055.6719 252050.0884 284414.9753 100715.3424 311148.3239 231738.6546 306067.0953 89749.31916 2.946219946 3.46582765 2.808378835 3.168993123 1.12218503 3.466859992 2.582065878 3.410244202 1 16.45361337 LKNEITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKNEITR 7 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 95.815 0.012028 1147830000 2335210 2116640 2003760 2436760 3187360 2072520 2427170 2148760 3272040 FALSE TRUE 2224829.251 2332328.022 2095634.378 2191812.255 3743234.575 2000748.113 2056860.638 1960603.183 3779451.252 0.588664624 0.617107582 0.554481124 0.579928701 0.990417477 0.529375293 0.544222032 0.518753399 1 21.84974535 -2.347700991 2.215645617 3.279575297 0.613248554 0.438757359 0.136694397 6311888.211 648473.9833 72267129.52 0.031875708 0.004490545 2.347700991 -2.666326743 LKNGELENIKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNGELENIKPK 12 2 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 123.28 0.00019328 697430000 1833700 1506800 1614600 1890200 1162400 1904100 2087600 2030600 1493300 FALSE TRUE 1747024.635 1660344.633 1688631.007 1700193.505 1365122.192 1838160.54 1769098.279 1852789.899 1724873.337 1.012842275 0.962589309 0.978988411 0.9856918 0.791433297 1.065678563 1.02563953 1.074159974 1 20.71805899 LKNGFPHPEPDCNPSEAAS(ph)EES(ph)NSEIEQEIPVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.125)EAAS(0.625)EES(0.625)NS(0.625)EIEQEIPVEQK 99.866 0.00016777 92575000 96668 87743 94782 105530 59767 120370 130340 118560 63009 TRUE FALSE 92098.69522 96684.11146 99127.84845 94921.92391 70190.34588 116201.5567 110454.2391 108178.2579 72780.11391 1.265437635 1.328441332 1.36201832 1.304228845 0.964416543 1.596611361 1.51764312 1.486371099 1 16.15125669 2.195003705 24.99999964 1.456734824 1.266183155 0.102147209 0.193887875 216.9782179 124535.8969 0.065693994 0.048518539 156.6764438 -2.195003705 -0.190551669 LKNGFPHPEPDCNPSEAAS(ph)EESNSEIEQEIPVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.07)EAAS(0.31)EES(0.31)NS(0.31)EIEQEIPVEQK 105.1 1.32E-05 115900000 108200 95196 94605 111080 64869 101180 118750 119040 64799 TRUE FALSE 103085.6004 104896.5806 98942.73283 99914.02736 76182.13306 97676.11123 100632.5065 108616.2265 74847.69797 1.377271489 1.401467025 1.321920854 1.3348978 1.017828672 1.304998201 1.344497015 1.451163222 1 16.19167032 -2.139182508 2.477629947 0.286252483 1.322624002 0.430841155 0.115260737 1963393.251 1173081.884 7847924.965 0.028170526 0.007258009 2.139182508 1.036371519 LKNGFPHPEPDCNPSEAASEES(ph)NS(ph)EIEQEIPVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.091)EAAS(0.613)EES(0.67)NS(0.626)EIEQEIPVEQK 87.091 0.0010034 95807000 105600 93396 100340 112170 65539 108330 128100 109450 64602 TRUE FALSE 100608.4973 102913.1586 104940.6882 100894.4585 76968.98085 104578.5049 108555.9923 99865.97777 74620.14822 1.348275227 1.379160469 1.406331812 1.352107452 1.031477191 1.401478119 1.454781247 1.33832457 1 16.18727761 -2.258458757 1.77759167 2.91E-05 1.347192597 0.460956754 0.114901815 1002886.835 149419.5509 4015974.643 0.030559928 0.005514946 2.258458757 1.347163499 LKNGFPHPEPDCNPSEAASEES(ph)NSEIEQEIPVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.107)EAAS(0.107)EES(0.393)NS(0.393)EIEQEIPVEQK 50.583 0.041381 65408000 73316 61983 62443 72128 56430 69234 80689 75107 56762 TRUE FALSE 69850.49798 68299.13817 65306.07331 64877.55641 66271.37413 66836.40922 68378.41109 68530.23291 65564.36106 1.065372969 1.041711336 0.996060547 0.989524726 1.010783497 1.019401518 1.042920422 1.045236037 1 16.0006242 3.99875011 3.918590624 1.017200798 1.058147492 0.446250447 0.0185167 0.207270821 7.344938174 0.005271928 0.011232913 9971.261596 -3.99875011 0.040946694 LKNGFPHPEPDCNPSEAASEESNS(ph)EIEQEIPVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.001)EAAS(0.004)EES(0.144)NS(0.85)EIEQEIPVEQK;LKNGFPHPEPDCNPSEAAS(0.002)EES(0.055)NS(0.943)EIEQEIPVEQK 183.75 1.80E-20 384010000 287790 246732 279430 281560 183555 310100 343170 308300 178118 TRUE FALSE 274186.737 271874.2713 292242.1419 253257.0539 215566.9339 299361.1592 290813.1138 281303.6176 205739.6297 1.332688007 1.321448239 1.420446524 1.230959024 1.047765733 1.455048595 1.413500715 1.367279692 1 17.65046019 3.227786231 24.98801871 1.286716 1.346676371 0.069559262 0.148917224 882.8886058 2047597.446 0.042723836 0.051549747 1689.609065 -3.227786231 0.059960371 LKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEK 34 2 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 269.93 2.59E-61 458280000 1135670 860480 916010 989770 734380 859310 1074070 1026650 800150 FALSE TRUE 1081989.13 948163.8903 958009.9646 890276.4392 862455.6395 829551.8792 910200.8949 936751.0834 924233.1754 1.170688478 1.025892508 1.036545744 0.963259557 0.933158063 0.897556917 0.984817381 1.013544102 1 19.81789735 4.464219083 0.852302702 0.961025069 1.236162876 0.743707917 0.03689237 0.759697948 0.563490152 0.013182396 0.181233957 29121.85824 -4.464219083 0.275137807 LKPEGLHQLLAGFEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPEGLHQLLAGFEDK 16 1 Q9BY32;Q9BY32-3;Q9BY32-2 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 ; 199.08 2.35E-11 649460000 2981900 2862600 2501200 3448200 1823300 3063900 3243500 3292300 1790450 FALSE TRUE 2840951.497 3154302.195 2615882.494 3101580.385 2141282.943 2957796.375 2748644.504 3004008.758 2068103.842 1.37369867 1.52521461 1.264869994 1.499721785 1.035384636 1.430197225 1.329065035 1.452542516 1 20.9798772 -3.543239041 0.268809196 3.51E-18 1.401962418 0.380493557 0.14211962 86.97469817 1.72980016 48.72463218 0.163814712 0.00028626 3.543239041 1.401962418 LKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVR 36 2 Q9BY32;Q9BY32-3;Q9BY32-2 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 198.44 2.84E-30 239950000 365860 192520 365210 275950 391020 359100 607920 438760 540530 FALSE TRUE 348566.5229 212138.0069 381955.2397 248210.9817 459213.7642 346664.277 515170.6388 400339.8484 624352.6318 0.558284702 0.339772744 0.61176204 0.397549348 0.73550385 0.555237953 0.82512768 0.641207914 1 19.25200156 1.456138888 0.391990583 1.009172397 0.424766841 0.632970866 0.116980375 0.594100135 0.274471708 0.135193283 0.09983858 28.58504549 -1.456138888 -0.584405556 LKPGGVGAPSSSS(ph)PSPSPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSSS(0.038)S(0.961)PSPSPSAR;LKPGGVGAPSS(0.001)S(0.103)S(0.893)PS(0.002)PS(0.001)PSAR;LKPGGVGAPSS(0.003)S(0.234)S(0.76)PS(0.002)PSPSAR 192.75 5.90E-18 656390000 769195 919202 699508 1004861 589264 874277 779904 805051 605030 TRUE FALSE 732836.6767 1012869.729 731581.1337 903850.4632 692031.455 844000.5683 660915.3209 734556.4666 698854.9623 1.048624845 1.449327519 1.046828274 1.293330536 0.990236161 1.207690599 0.945711709 1.051085713 1 19.41463355 2.428960183 0.947581702 1.003071447 1.230844228 0.241751253 0.136993082 0.661986377 1.181688088 0.085054595 0.057334336 268.5098258 -2.428960183 0.227772781 LKPGTMIEWGNNWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKPGTMIEWGNNWAR 15 1 Q9BPW8;C9JDV8 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 120.77 0.00010868 231810000 205860 189580 179640 200010 196670 194730 239020 211170 192150 FALSE TRUE 196129.4058 208898.4175 187876.6717 179904.6148 230969.1857 187986.4513 202553.1091 192678.8353 221947.6406 0.883674209 0.941205849 0.846490961 0.810572324 1.040647177 0.846985581 0.912616636 0.868127432 1 17.75985985 LKPGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKPGTR 6 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;A6PVL3-2;A6PVL3 A0A087X2I1 PSMC6;KNCN 26S protease regulatory subunit 10B;Kinocilin 0 69.432 0.085289 215340000 922820 725790 677380 916380 844280 825230 1017200 877630 941180 FALSE TRUE 879200.1275 799748.8262 708438.543 824263.7414 991522.1647 796652.0782 862007.4578 800780.0646 1087133.388 0.808732523 0.735649218 0.651657424 0.758199271 0.912051986 0.732800673 0.79291784 0.736597803 1 20.05209753 -4.999999988 0.381552553 4.317408451 0.761442724 0.545739775 0.066851863 473.3598159 3.519696224 1300.245798 0.043137481 1.00E-05 4.999999988 -3.555965727 LKPGYLEATVDWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPGYLEATVDWFR 14 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 212.39 2.28E-09 3869900000 5927000 4995300 4198200 5227400 5098300 4464900 6303300 5270800 5404200 FALSE TRUE 5646842.456 5504326.749 4390691.623 4701931.821 5987441.906 4310279.393 5341615.817 4809260.81 6242255.735 0.904615686 0.881784884 0.703382208 0.753242421 0.959179207 0.69050029 0.855718837 0.770436364 1 22.57363603 -1.452336455 2.826924702 1.005023458 0.822278251 0.302815898 0.087645667 11392237.76 12826332.05 454211.3655 0.022121945 0.035290966 1.452336455 -0.182745206 LKPGYLEATVDWFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPGYLEATVDWFRR 15 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 176.25 4.55E-07 573650000 793570 307440 736370 467400 978490 644090 1354700 838750 1538380 FALSE TRUE 756059.5188 338768.4855 770133.2929 420416.064 1149138.346 621785.0018 1148015.634 765304.6035 1776944.113 0.425483004 0.190646674 0.433403216 0.236594984 0.646693578 0.349918153 0.646061756 0.430685804 1 20.76096688 -0.910319486 0.216341024 1.431809571 0.243713198 0.667781736 0.134908544 8.495821008 0.437067359 2.511126336 0.294112031 0.122936407 0.910319486 -1.188096373 LKPKPIDVQVITHHMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKPKPIDVQVITHHMQR 17 2 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 90.714 0.0012014 483260000 871080 863380 934380 1035400 622610 916170 1023900 999660 150560 FALSE TRUE 829905.7747 951359.4036 977222.2472 931319.6249 731192.9869 884442.8032 867685.2498 912124.4709 173908.0758 4.772094514 5.470472829 5.619188427 5.355240809 4.204479771 5.085691385 4.989332701 5.244865521 1 17.4079654 2.748670636 23.12784295 4.481943169 5.290321538 0.152422396 1.239099261 588.312135 1345829.6 0.336505993 0.352543353 560.6226455 -2.748670636 0.808378369 LKPLEVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPLEVELR 9 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 116.77 0.0011497 977330000 2479600 2137400 1642090 2389800 2855300 2239700 3531300 2492200 2600000 FALSE TRUE 2362394.222 2355203.49 1717381.451 2149572.764 3353263.416 2162138.627 2992535.328 2273969.756 3003194.721 0.786627056 0.784232695 0.571851515 0.715762035 1.116565434 0.7199462 0.996450649 0.757183589 1 21.51806659 LKPNLGNGADLPNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPNLGNGADLPNYR 15 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 210.08 1.88E-09 1385990000 2303500 2098940 2061130 2450100 2012340 2186940 2529100 2406000 2439700 FALSE TRUE 2194618.12 2312824.372 2155634.849 2203811.293 2363291.459 2111205.719 2143239.345 2195317.885 2818036.216 0.778775698 0.820722019 0.764942209 0.78203796 0.83863062 0.74917622 0.760543577 0.779024014 1 21.42625872 -0.688356941 5.876197533 1.000000004 0.784778013 0.863939795 0.026909258 1.55E-09 3.30E-10 0.026065323 0.006143656 0.204947705 0.688356941 -0.215221991 LKPPVHYNGPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 134.56 8.61E-05 997520000 2189300 1766290 1804930 2106080 1604830 1982370 2524300 2280370 1942180 FALSE TRUE 2085816.128 1946276.959 1887687.826 1894372.837 1884711.844 1913720.03 2139171.673 2080688.714 2243363.355 0.929771864 0.867570987 0.841454338 0.844434243 0.840127766 0.853058434 0.953555592 0.927486271 1 21.09723188 1.692137865 5.37111031 0.956432616 0.866077476 0.682754363 0.031227255 0.102041279 6.784356956 0.017549746 0.00869836 49.21957561 -1.692137865 -0.09035514 LKPVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKPVELR 7 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 100.45 0.0089232 1271460000 3348600 3037000 3277500 4149500 3266400 3865200 4369300 3698900 3803400 FALSE TRUE 3190318.314 3346473.753 3427776.617 3732384.376 3836059.126 3731347.155 3702683.037 3375004.707 4393211.847 0.726192687 0.761737396 0.780243871 0.849579876 0.873178727 0.84934378 0.842819142 0.768231723 1 22.06684464 -4.999999681 0.027945334 2.147618348 5.43E-07 0.689276157 0.042927149 922.8974391 1.943435704 113.0415886 48.71797943 1.00E-05 4.999999681 -2.147617804 LKPVPVAQENQGVFFSGDSYLVLHNGPEEVSHLHLWIGQQSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKPVPVAQENQGVFFSGDSYLVLHNGPEEVSHLHLWIGQQSSR 43 1 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 127.35 1.71E-09 143770000 0 2911.2 2880.4 0 4750.6 4367.8 7146.8 3452.4 4128 FALSE TRUE 0 3207.85459 3012.469189 0 5579.103136 4216.541991 6056.4244 3150.089554 4768.149157 0 0.672767249 0.631790049 0 1.170077309 0.884314197 1.270183503 0.660652477 1 12.21921365 2.726534052 24.99873211 1.02542294 0.364653532 0.597649416 0.272170019 505.0845488 1049880.331 0.083344634 0.079126049 532.7629958 -2.726534052 -0.660769407 LKQDGDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKQDGDSFR 9 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 97.813 0.0058704 853330000 1311400 1001100 1221170 1399890 1102710 1319050 1557790 1390660 1424130 FALSE TRUE 1249412.721 1103113.228 1277161.852 1259170.398 1295022.275 1273370.968 1320120.525 1268886.438 1644976.807 0.75953212 0.670595004 0.77640113 0.765463922 0.787258683 0.774096609 0.802516193 0.771370412 1 20.64963581 -5 0.169169621 1.953198877 0.699404082 0.854302255 0.031382375 44.42320107 0.418166144 14.15524923 0.110557495 1.00E-05 5 -1.253794795 LKQFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKQFEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 134.81 0.0028621 624660000 1458580 1228350 1375590 1497570 1257370 1377890 1732710 1601250 1574520 FALSE TRUE 1389635.814 1353520.262 1438662.162 1347031.418 1476654.93 1330173.324 1468353.266 1461036.061 1818688.52 0.764086757 0.744228738 0.791043736 0.740660868 0.811933937 0.731391499 0.807369294 0.803345952 1 20.79446705 -0.329831664 0.499317523 1.035377348 0.75886015 0.888634018 0.025587912 1.84720298 0.448116206 0.139447199 0.010744644 0.467916474 0.329831664 -0.276517198 LKQGLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKQGLYR 7 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 105.39 0.0072389 2431000000 4043300 2680600 2397000 2840200 3733800 2941200 4479400 3589300 3918500 FALSE TRUE 3852181.222 2953756.188 2506904.821 2554697.7 4384973.538 2839345.507 3795985.26 3275001.864 4526160.967 0.851092405 0.652596363 0.55387001 0.564429263 0.968806361 0.62731872 0.838676593 0.723571673 1 22.10985646 0.234206897 0.487438222 1.021765693 0.697268398 0.319450538 0.130869945 3.5957329 1.274149632 0.299528356 0.066177512 1.714774029 -0.234206897 -0.324497294 LKQNLEEQLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKQNLEEQLDR 11 1 Q8WZA0-2;Q8WZA0 Q8WZA0-2 LZIC Protein LZIC 0 110.38 0.0016437 79794000 216120 183280 231460 211380 183480 222190 237940 223790 180350 FALSE TRUE 205904.4359 201956.4404 242072.6699 190131.6808 215478.8539 214495.5046 201637.8829 204193.7612 208317.7569 0.988415193 0.969463398 1.162035698 0.912700308 1.034375836 1.029655406 0.967934207 0.980203341 1 17.66842629 1.723240012 11.85134093 0.980838919 1.01092804 0.05385687 0.063372343 0.351972402 171.600783 0.027745763 0.015170912 52.87373773 -1.723240012 0.030089121 LKQSAEEQAQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 157.56 6.47E-05 848860000 1291720 960290 1125370 1219370 1304540 1124540 1518030 1269700 1624230 FALSE TRUE 1230662.956 1058144.643 1176969.328 1096796.611 1532051.363 1085596.898 1286426.643 1158518.337 1876107.293 0.655966191 0.564010729 0.627346491 0.584612946 0.816611805 0.578643291 0.685689271 0.617511771 1 20.83931091 -5 0.296911368 3.945700896 0.618831533 0.706247883 0.072527443 133.2262337 1.239009004 243.8834892 0.066767385 1.00E-05 5 -3.326869363 LKQVEDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LKQVEDEK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 125.48 0.0011493 1177940000 1970710 1896620 1589300 2257640 1061740 2113040 1949580 2118840 1154490 FALSE TRUE 1877558.444 2089887.734 1662170.977 2030697.738 1246907.12 2039864.895 1652135.765 1933303.137 1333522.413 1.407969169 1.567193558 1.246451474 1.522807355 0.935047741 1.529681748 1.238926132 1.449771761 1 20.34681064 -4.543152105 0.108088524 9.89E-11 1.588620451 0.259400087 0.188830932 185.543026 1.481816776 43.2295981 2.276466517 2.86E-05 4.543152105 1.58862045 LKQVEDEKNSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKQVEDEKNSFR 12 2 P35579 P35579 MYH9 Myosin-9 0 86.803 0.0061338 1232200000 1047800 664930 924440 901860 845280 950290 1375600 1170800 1061100 FALSE TRUE 998272.5705 732687.123 966826.4884 811203.3194 992696.5644 917381.219 1165726.955 1068278.545 1225649.969 0.81448423 0.597794755 0.788827572 0.66185562 0.809934802 0.748485491 0.951109195 0.871601658 1 20.22511559 1.801708686 1.015661026 0.974581459 0.710143223 0.623478302 0.073974498 0.295159003 0.563609883 0.056839528 0.023750704 63.34446702 -1.801708686 -0.264438237 LKRGS(ph)LPAEASCTT ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKRGSLPAEASCTT 14 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 LKRGS(1)LPAEASCTT 88.319 0.0051924 350460000 269370 196800 287270 279380 243010 273780 392030 346730 378500 TRUE FALSE 256637.4139 216854.1437 300441.6136 251296.1916 285390.8671 264298.93 332218.6234 316368.4831 437195.8469 0.587007895 0.496011445 0.687201436 0.574790894 0.652775796 0.604532115 0.759885131 0.723631035 1 18.73792017 0.456665238 0.310552982 1.080748622 0.530249028 0.849976591 0.053329 1.06863727 0.211989724 0.1822382 0.06049175 2.861971061 -0.456665238 -0.550499594 LKS(ph)DERPVHIK ddPTM_SK-BR-3_Trastuzumab_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 159.13 1.51E-05 2173980000 4902850 4010360 4318470 5360450 2658220 5000060 5255520 5192670 2307450 TRUE FALSE 4671101.997 4419020.243 4516476.121 4821607.382 3121812.726 4826906.668 4453693.9 4737972.287 2665277.561 1.752576191 1.657996266 1.694561267 1.809045126 1.171289914 1.811033394 1.671005664 1.777665619 1 21.34585435 -1.003889303 4.173244665 0.999956367 1.668989501 0.563745557 0.18471389 4551729.928 2189871.245 1804.186305 0.039221694 0.099108453 1.003889303 0.669033134 LKS(ph)EDGVEGDLGETQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR 232.81 1.40E-17 3538270000 2574560 1795580 2154280 3043470 1691690 2272560 2234760 1750470 1180750 TRUE FALSE 2452865.651 1978551.643 2253055.869 2737534.613 1986720.2 2193860.677 1893806.318 1597189.567 1363854.68 1.79848021 1.450705616 1.651976492 2.007204033 1.456694933 1.608573633 1.388568992 1.17108486 1 20.3792585 1.369935742 1.169015527 0.998405698 1.672057026 0.711390729 0.155703822 0.236616137 0.635346996 0.13781639 0.046213318 23.4388199 -1.369935742 0.673651328 LKS(ph)ISREPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKSISREPSPALGPNLDGSGLLPR 24 2 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 LKS(0.824)IS(0.204)REPS(0.972)PALGPNLDGSGLLPR 107.95 0.0012961 156500000 41326 42892 43468 49163 36708 42161 42318 42047 36393 TRUE FALSE 39372.60188 47262.74356 45461.0508 44221.04184 43109.86358 40700.954 35861.61188 38365.14177 42036.64057 0.936625795 1.124322565 1.081462509 1.051964221 1.025530656 0.968225659 0.853103659 0.912659557 1 15.35935976 2.128122619 2.937441368 0.906373232 1.048688 0.466636686 0.059351694 0.19641923 3.377473543 0.025443114 0.016927243 134.3144131 -2.128122619 0.142314768 LKS(ph)PSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKSPSQK 7 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LKS(0.89)PS(0.11)QK 79.16 0.020213 240670000 528940 606210 415520 594360 248210 528370 461260 585330 287180 TRUE FALSE 503938.0545 667983.4882 434572.003 534613.8036 291497.7454 510072.4144 390886.3154 534075.4022 331714.4077 1.519192543 2.013730705 1.310078769 1.611668927 0.878761183 1.537685438 1.178382085 1.61004584 1 18.33958215 3.716592313 23.85624692 1.312414556 1.766461596 0.336745868 0.269731725 399.1380997 433439.733 0.063819152 0.098979056 5207.056781 -3.716592313 0.45404704 LKS(ph)VEDEMDS(ph)PGEEPFYTGQGR ddPTM_SK-BR-3_Trastuzumab_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 2 LKS(1)VEDEMDS(1)PGEEPFYTGQGR 73.616 0.0012406 0 63470 53298 61675 79771 39721 62883 60413 62191 39046 TRUE FALSE 60469.89889 58729.12679 64502.85975 71752.26753 46648.32982 60705.34594 51195.88729 56745.22634 45101.05426 1.340764642 1.302167494 1.430185188 1.590922179 1.03430686 1.345985076 1.135137263 1.258179599 1 15.46087354 2.728632391 24.99452268 1.176535961 1.389463086 0.510084581 0.125043442 653.174917 1644379.658 0.037968453 0.036192749 535.3433234 -2.728632391 0.212927125 LKS(ph)VEDEMDSPGEEPFYTGQGR ddPTM_SK-BR-3_Trastuzumab_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 195.27 4.07E-19 46607000 65597 61868 56863 68737 43873 69271 70001 66684 38243 TRUE FALSE 62496.35981 68172.41954 59470.2248 61827.42617 51524.43731 66872.1279 59321.06179 60844.79545 44173.52912 1.414792095 1.54328669 1.346286475 1.399648781 1.166409801 1.513850698 1.342909724 1.377403994 1 15.43089448 -3.636580029 0.215050337 1.90E-15 1.46106053 0.594046905 0.101335373 51.78185912 0.876357684 23.05711273 0.200341911 0.000230898 3.636580029 1.46106053 LKSDGIPMYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKSDGIPMYK 10 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 98.803 0.0046771 452710000 2787100 2343900 1980700 2570700 2025000 2368500 2859400 2823300 2120700 FALSE TRUE 2655359.307 2582746.075 2071517.054 2312288.352 2378159.359 2286478.251 2423146.014 2576076.885 2449567.325 1.084011564 1.054368275 0.845666511 0.943957869 0.970848743 0.933421273 0.989213886 1.051645676 1 21.22409551 3.971444136 24.68820336 0.960438199 1.072895361 0.419253446 0.052828849 471.1207267 407311.8481 0.013121156 0.023674536 9363.627663 -3.971444136 0.112457161 LKSDTAAAAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKSDTAAAAVR 11 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 128.1 0.00024892 1341130000 3382980 2509080 2017390 2455640 3062320 2396860 3813590 3056450 3291280 FALSE TRUE 3223073.24 2764758.105 2109889.327 2208794.402 3596387.638 2313856.137 3231756.804 2788811.035 3801674.893 0.847803489 0.72724738 0.554989416 0.5810056 0.946000839 0.608641244 0.850087631 0.73357431 1 21.85820373 0.205244442 0.615603562 1.010925537 0.720527095 0.321360684 0.124862562 3.68637639 1.873007373 0.220468922 0.048397012 1.604148028 -0.205244442 -0.290398442 LKSEDEPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKSEDEPTR 9 1 O14787-2;O14787;A0A075B780;K7ENW1;K7ESC1;E7EW37;Q92973-2;Q92973 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 69.721 0.04965 149590000 234270 181140 225260 253260 200400 226220 298850 250950 278580 FALSE TRUE 223196.5214 199598.3719 235588.3938 227801.8236 235349.6966 218385.9447 253254.9437 228975.4876 321780.7636 0.693629162 0.620293052 0.732139458 0.707941087 0.731397657 0.678679304 0.787041901 0.71158849 1 18.29571856 -5 0.182541287 2.247986403 0.643111896 0.854620512 0.038554833 43.20062877 0.417733111 19.48650897 0.106077173 1.00E-05 5 -1.604874507 LKSEDGVEGDLGETQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 152.04 2.08E-07 783610000 804970 691600 705880 800370 588930 736010 841180 843180 678070 FALSE TRUE 766920.6634 762074.8263 738245.2962 719915.287 691639.2055 710521.7891 712842.5417 769346.6892 783221.6325 0.979187284 0.973000227 0.942575212 0.919171863 0.88306959 0.907178453 0.910141539 0.98228478 1 19.57906109 3.617330626 2.686613686 0.924042263 0.977106604 0.158599667 0.035544528 0.329727718 4.606938031 0.009294145 0.015796055 4143.149705 -3.617330626 0.053064342 LKSVEDEMDS(ph)PGEEPFYTGQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 LKSVEDEMDS(1)PGEEPFYTGQGR;LKSVEDEMDS(1)PGEEPFYTGQGR;LKSVEDEMDS(1)PGEEPFYTGQGR;LKSVEDEMDS(1)PGEEPFYTGQGR;LKSVEDEMDS(1)PGEEPFYTGQGR;LKSVEDEMDS(1)PGEEPFYTGQGR 220.96 1.48E-25 1445280000 1884170 1232367 1823010 1728450 1550676 1854480 2499890 2097190 1863860 TRUE FALSE 1795109.018 1357946.598 1906596.812 1554702.922 1821113.403 1790258.893 2118485.867 1913548.926 2152897.89 0.833810571 0.630752905 0.88559556 0.722144292 0.845889353 0.831557735 0.984015952 0.888824749 1 21.03784846 2.086910662 0.913245843 0.977388111 0.750592128 0.524664008 0.075590291 0.393675212 0.609342704 0.055604966 0.028487351 122.1548352 -2.086910662 -0.226795983 LKTEAEIALK ddPTM_SK-BR-3_Trastuzumab_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 0 110.98 0.002644 0 517970 471970 392290 491730 342660 486890 555810 581660 408020 FALSE TRUE 493486.5846 520064.2796 410276.8845 442300.3662 402419.7955 470028.8772 471010.9763 530726.7668 471293.6577 1.047089382 1.103482449 0.87053343 0.938481473 0.853862107 0.997316364 0.999400201 1.126106321 1 18.84626674 1.411534405 6.827585753 1.064380209 0.982618176 0.173930024 0.08032049 0.457315921 34.69908322 0.058191909 0.021816279 25.79493307 -1.411534405 -0.081762033 LKTEEGEIDYS(ph)AEEGENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKTEEGEIDYSAEEGENRR 19 2 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 LKTEEGEIDYS(1)AEEGENRR 112.88 9.81E-05 69667000 101110 91209 95529 108390 73540 99078 114180 111310 82804 TRUE FALSE 96330.73068 100503.3008 99909.09914 97494.43127 86365.35272 95646.90402 96759.74394 101563.1063 95644.82142 1.007171421 1.050797098 1.044584512 1.019338317 0.902979915 1.000021774 1.011656904 1.061877735 1 16.54539924 5.154674849 14.81081642 1.01232643 0.000396104 0.000531068 0.043824814 7558702.929 2981440.071 0.010599165 258454193.5 142782.4564 -5.154674849 -1.011930326 LKTEGSDLCDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKTEGSDLCDR 11 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 68.277 0.052602 635020000 779780 538000 755310 949130 857880 799490 974480 755830 883240 FALSE TRUE 742921.3448 592822.8117 789941.7106 853721.6492 1007494 771803.4608 825805.1784 689645.5183 1020208.348 0.728205514 0.581080142 0.774294498 0.836811079 0.987537499 0.756515532 0.80944758 0.675984978 1 19.96043238 5.970297941 0.06092153 1.263200427 9.09E-18 0.301529661 0.106935945 260.1172642 1.782285906 9.764279125 33.05478135 933894.7661 -5.970297941 -1.263200427 LKTEKEPDATPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LKTEKEPDATPPSPR 15 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 LKTEKEPDAT(0.03)PPS(0.97)PR;LKTEKEPDAT(0.272)PPS(0.728)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDAT(0.003)PPS(0.997)PR;LKTEKEPDAT(0.003)PPS(0.997)PR;LKTEKEPDAT(0.001)PPS(0.999)PR 159.06 1.41E-06 2854550000 4048730 3213930 3729840 4272640 2700860 4290500 4847850 4672220 3256120 TRUE FALSE 3857354.557 3541433.121 3900856.853 3843146.11 3171889.129 4141918.909 4108221.446 4263095.648 3761062.46 1.025602366 0.941604443 1.037168857 1.021824591 0.84334923 1.101262995 1.092303435 1.133481747 1 21.84270883 LKTPST(ph)PVACSTPAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKTPSTPVACSTPAQLK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LKT(0.013)PS(0.246)T(0.602)PVACS(0.137)T(0.002)PAQLK;LKT(0.01)PS(0.245)T(0.744)PVACS(0.001)TPAQLK 170.11 3.06E-09 646970000 1063930 898440 882240 1100560 739370 968650 1140090 1098200 785910 TRUE FALSE 1013640.137 989992.0574 922691.5767 989929.6179 868315.8939 935105.4076 966148.3313 1002035.786 907784.9089 1.116608271 1.090557959 1.016420925 1.090489177 0.956521622 1.030095784 1.064292127 1.10382512 1 19.79199098 3.901061959 4.396613379 1.040028049 1.107646998 0.296610763 0.042896917 0.254404767 8.334768531 0.010658156 0.020236655 7962.729435 -3.901061959 0.067618949 LKTVLELQYVLDKLGDDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKTVLELQYVLDKLGDDEVR 20 2 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 139 4.42E-07 25440000 98876 69807 120230 96671 83506 96687 147350 134140 121240 FALSE TRUE 94202.32743 76920.41266 125742.6644 86953.44742 98069.41996 93338.70495 124869.0512 122393.9905 140041.28 0.672675424 0.549269563 0.897897137 0.620912972 0.700289372 0.666508511 0.891658883 0.873985088 1 17.09549263 1.683831535 3.513738341 0.924160369 0.673252536 0.589914803 0.093168217 0.135259253 3.881637307 0.052354792 0.02400752 48.2871458 -1.683831535 -0.250907833 LKVDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKVDSFR 7 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;K7ENH2;B7Z8D3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 136.8 0.002686 1248710000 2973100 2294100 2026830 2449100 3242400 2658500 4322400 3086200 4428500 FALSE TRUE 2832567.455 2527871.398 2119762.16 2202911.815 3807873.533 2566435.478 3662938.494 2815955.967 5115249.162 0.553749654 0.494183434 0.414400568 0.430655819 0.744416042 0.501722477 0.716082126 0.55050221 1 22.28637308 -0.614637042 0.285738526 1.207599676 0.472529236 0.685030209 0.099500942 5.698244177 0.496497152 1.181764734 0.119743642 0.242863896 0.614637042 -0.735070441 LKVFDGIPPPYDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKVFDGIPPPYDKK 14 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 112.5 0.0003318 305510000 975790 693690 959850 954050 1033220 967530 1151790 1060870 1184500 FALSE TRUE 929666.3405 764377.7997 1003860.072 858147.0814 1213413.241 934024.1935 976063.2814 967974.5988 1368186.21 0.679488167 0.558679655 0.73371597 0.627215122 0.886877262 0.682673299 0.713399444 0.707487469 1 20.38383316 -5 0.152007024 2.116491714 0.594485486 0.589432913 0.080759695 88.2859616 0.791770594 29.758333 0.370825387 1.00E-05 5 -1.522006229 LKVPEWVDTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKVPEWVDTVK 11 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 166.45 1.86E-05 2139310000 5463800 4815900 4739500 5309100 4175100 5179600 6079800 5547000 4795500 FALSE TRUE 5205537.002 5306645.685 4956810.763 4775419.181 4903236.118 5000229.153 5152214.847 5061275.274 5539161.648 0.93976983 0.958023257 0.894866602 0.862119484 0.885194625 0.902705043 0.930143436 0.913725866 1 22.40123621 -1.469767652 5.927351674 1.000061273 0.914856965 0.500427102 0.027743498 2.57E-05 2.30E-06 0.030746414 0.007241793 0.033902549 1.469767652 -0.085204309 LKVPPAINQFTQALDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKVPPAINQFTQALDR 16 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 253.02 1.39E-26 2630800000 1683720 1447710 1490160 1680090 1580300 1682860 2009180 1776270 1897860 FALSE TRUE 1604133.892 1595233.295 1558485.31 1511204.161 1855903.82 1624582.136 1702642.69 1620730.382 2192170.436 0.73175601 0.727695835 0.710932546 0.689364356 0.846605624 0.741083864 0.776692661 0.739326813 1 21.06392854 -5 0.241471983 2.476094553 0.71930089 0.794929849 0.040981763 71.04501347 0.707806752 51.49668864 0.058801291 1.00E-05 5 -1.756793663 LKVSELKEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKVSELKEELK 11 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 67.115 0.034228 167090000 711130 635650 656210 750070 510340 788680 827250 833620 537500 FALSE TRUE 677516.2942 700423.4577 686297.8776 674671.5386 599343.1344 761367.8138 701037.819 760623.8135 620852.7548 1.091267275 1.128163566 1.105411665 1.086685262 0.965354715 1.226325901 1.12915311 1.225127548 1 19.24389163 2.207421365 24.9997877 1.155561736 1.08589838 0.160382326 0.075624246 337.8416915 271230.5055 0.025591013 0.018902052 161.2209087 -2.207421365 -0.069663356 LKVTEGGEPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LKVTEGGEPYR 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 152.4 3.01E-05 2210700000 3346130 2550430 3091220 3513200 3249680 3413280 4338540 3765890 3879920 FALSE TRUE 3187965.066 2810321.717 3232955.495 3160046.461 3816423.163 3295077.258 3676616.04 3436128.707 4481598.178 0.711345583 0.627080252 0.721384508 0.705115973 0.851576382 0.735246028 0.820380564 0.766719499 1 22.09558187 -4.99999945 0.090901421 1.905931239 0.509926638 0.761971861 0.04979221 88.07669859 0.555315221 15.24991427 1.043677128 1.00E-05 4.99999945 -1.396004602 LKVTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKVTELR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 111.74 0.0059383 1207100000 2995300 2407300 2644800 3106100 2645200 2721200 3408500 3015100 3082800 FALSE TRUE 2853718.105 2652606.607 2766066.696 2793868.927 3106522.042 2626964.162 2888470.724 2751081.86 3560864.879 0.801411511 0.744933239 0.776796309 0.784604028 0.872406606 0.737732054 0.811171112 0.772588108 1 21.76379626 -1.812857327 2.319834013 1.078586248 0.78641345 0.760528732 0.037431565 2771630.818 1631582.08 1218865.502 0.008963819 0.0153866 1.812857327 -0.292172797 LKWGMEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LKWGMEYK 8 1 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ; 129.38 0.00099688 986650000 2174400 1380000 1073860 1529760 1885950 1479380 2678700 1920760 2096900 FALSE TRUE 2071620.421 1520623.569 1123097.543 1375985.618 2214859.083 1428148.7 2270015.117 1752568.072 2422076.543 0.855307578 0.627818131 0.463692011 0.568101624 0.914446362 0.589638137 0.937218572 0.723580796 1 21.20781303 1.33207264 0.708823997 0.976314841 0.662696007 0.314646292 0.148998911 0.77096769 0.884088451 0.138430442 0.0590009 21.48189751 -1.33207264 -0.313618834 LKYALTGDEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 147.68 3.34E-05 758560000 2119700 1700710 1997410 1969410 1373180 2239520 2652030 2503090 1622240 FALSE TRUE 2019505.982 1874014.283 2088993.224 1771441.165 1612662.157 2161964.861 2247414.116 2283906.17 1873808.694 1.077754623 1.000109717 1.114838047 0.945369274 0.860633299 1.153780996 1.199382905 1.218857708 1 20.83754224 2.044326062 24.75170377 1.16532096 1.009440425 0.370717763 0.090350332 110.6932595 61810.64644 0.0322247 0.023799504 110.7454933 -2.044326062 -0.155880535 LKYEATIADMEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LKYEATIADMEDR 13 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 92.265 0.0056108 66282000 145650 128690 125340 141870 122140 143410 151610 145780 137490 FALSE TRUE 138765.4132 141803.6573 131086.963 127608.9581 143441.1773 138443.6757 128479.11 133014.7304 158811.247 0.873775729 0.892906894 0.825426193 0.80352595 0.903218003 0.871749818 0.809005108 0.837564926 1 17.27695356 -1.080479906 7.38643153 1.000000023 0.853891601 0.653329839 0.033826218 1.37E-08 1.69E-09 0.034280904 0.008080085 0.083084516 1.080479906 -0.146108421 LLAAFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLAAFEER 8 0 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 0 ; 89.55 0.032166 42587000 114667 86791 102966 112183 122222 95019 131788 106068 140497 FALSE TRUE 109246.9182 95635.10157 107687.0929 100906.1517 143537.4781 91728.4682 111681.3201 96780.12362 162284.5572 0.673181232 0.589305004 0.663569565 0.621785298 0.884480203 0.565232267 0.688182055 0.596360648 1 17.3081662 -2.115141215 2.425932974 1.650140119 0.658297357 0.591304347 0.088751492 3548115.603 856882.2463 12755600.51 0.019310656 0.00767112 2.115141215 -0.991842762 LLAAGQLADALSQFHAAVDGDPDNYIAYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLAAGQLADALSQFHAAVDGDPDNYIAYYR 30 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 234.52 2.11E-45 187244000 165574 188403 156679 182826 180431 151542 179117 188709 169975 FALSE TRUE 157747.6452 207601.4799 163862.8871 164447.9831 211898.1093 146294.0625 151789.4119 172184.6396 196333.8549 0.803466347 1.057390128 0.834613507 0.837593614 1.07927443 0.745129069 0.77311889 0.87699923 1 17.58294944 LLAAVEAFYS(ph)PPSHDRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFY(0.093)S(0.799)PPS(0.108)HDRPR;LLAAVEAFY(0.359)S(0.545)PPS(0.096)HDRPR 85.945 0.0021375 50509000 127192 128650 122302 136185 136819 122516 144279 131884 136187 TRUE FALSE 121179.8862 141759.5813 127909.6677 122495.4251 160680.1903 118273.2402 122266.5887 120335.5378 157306.1844 0.770344069 0.901169791 0.813125486 0.778706988 1.021448654 0.751866436 0.777252269 0.764976522 1 17.26321587 0.032114573 7.938410067 0.999999997 0.824029989 0.315300404 0.082234748 1135251.608 127117.7126 0.074907325 0.018167695 1.076749237 -0.032114573 -0.175970007 LLAAVEAFYSPPSHDRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 84.14 0.0023278 133360000 63790 53233 60806 68701 68598 53388 72465 65577 71693 FALSE TRUE 60774.77312 58657.50322 63594.01525 61795.04496 80561.46948 51539.16017 61409.13334 59834.73023 82810.78428 0.733899258 0.708331695 0.767943642 0.746219777 0.9728379 0.622372564 0.741559615 0.722547561 1 16.33753104 -1.350362073 3.056677565 1.002598786 0.747621911 0.440662825 0.087700302 117612770.7 149118811.6 2740569.132 0.019982862 0.044631135 1.350362073 -0.254976874 LLACIASRPGQCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLACIASRPGQCGR 14 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 231.69 4.05E-13 4362200000 1886920 1314370 1605470 1680050 2019610 1628640 2267550 1857100 2159300 FALSE TRUE 1797729.031 1448305.797 1679082.388 1511168.182 2371829.345 1572239.788 1921593.601 1694482.479 2494153.216 0.720777304 0.580680364 0.673207394 0.605884263 0.950955751 0.630370171 0.770439277 0.679381871 1 21.25011866 -5 0.172831664 2.205894796 0.626310042 0.458178907 0.103128815 110.8547326 1.05214082 45.77124098 0.323754063 1.00E-05 5 -1.579584754 LLADQAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLADQAEAR 9 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 89.047 0.028781 265950000 385630 343650 340640 389030 383020 349290 400840 401520 426870 FALSE TRUE 367402.0341 378668.3257 356258.6809 349923.9653 449818.5667 337193.9997 339684.4961 366360.7802 493066.8195 0.745136399 0.76798582 0.722536311 0.709688731 0.912287238 0.683870799 0.688921831 0.743024608 1 18.91142365 -0.910093203 4.764666025 1.000001232 0.744644682 0.605376386 0.06425721 4.35203E+11 99602036589 8223817.906 0.014443273 0.123000477 0.910093203 -0.255356551 LLAEGHPDPDAELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLAEGHPDPDAELQR 15 0 P49756 P49756 RBM25 RNA-binding protein 25 0 ;; 154.6 2.45E-06 882160000 1113170 936940 1039590 1115220 1167170 1010110 1241780 1118310 1123130 FALSE TRUE 1060552.66 1032415.251 1087256.23 1003115.967 1370724.078 975129.6374 1052323.654 1020384.848 1297299.264 0.817508103 0.795818883 0.838092073 0.773234052 1.056598208 0.751661289 0.81116492 0.786545461 1 20.30707989 -2.432627494 2.178918886 2.52461356 0.826046399 0.287504403 0.084583894 5214299.437 493472.9222 39193900.85 0.020346141 0.003692942 2.432627494 -1.69856716 LLAEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLAEKER 7 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 ; 132.08 0.0031038 395110000 866040 325300 443670 349070 936640 488210 1191740 691350 1167320 FALSE TRUE 825104.0055 358448.4398 464012.7083 313980.8204 1099989.719 471303.1653 1009918.175 630811.7289 1348342.024 0.611939694 0.265843854 0.344135761 0.232864373 0.81580912 0.34954274 0.749007416 0.467842519 1 20.36275507 0.542394479 0.403933329 1.046426087 0.386754283 0.448194813 0.189517581 1.898209217 0.620762694 0.380186843 0.128745786 3.486538613 -0.542394479 -0.659671805 LLAHVTLELQHYHQLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLAHVTLELQHYHQLLEK 18 0 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 157.12 2.31E-09 72936000 95107 95257 96034 114830 81332 93583 114380 101110 33531 FALSE TRUE 90611.48059 104963.7966 100437.2539 103287.0702 95516.27505 90342.19724 96929.23027 92256.27238 38730.81623 2.339519004 2.710084806 2.593212942 2.666793016 2.466157039 2.332566314 2.50263846 2.381986267 1 15.24119429 -1.532050235 0.429128752 0.015506809 2.563924845 0.942440771 0.117184005 6.540287328 0.585938058 7.019752861 0.066123421 0.029373099 1.532050235 2.548418036 LLALLSLGEVGHHIDLSGQLELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLALLSLGEVGHHIDLSGQLELK 23 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 158.52 1.22E-11 59277000 86800 78809 86827 92307 66886 99563 107680 104120 29501 FALSE TRUE 82697.13602 86839.7267 90808.10383 83028.12499 78550.89722 96115.10835 91251.43832 95002.70083 34075.86441 2.426853653 2.548423296 2.664880419 2.436566949 2.305176951 2.820621282 2.677890639 2.787976254 1 15.05646263 LLAS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLASPSSR 8 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 LLAS(0.494)PS(0.494)S(0.012)R 79.489 0.029271 250360000 237960 222120 213470 259100 280100 235620 280140 250410 321860 TRUE FALSE 226712.1024 244754.2805 223257.8107 233054.7757 328949.3513 227460.4203 237399.4979 228482.7729 371772.405 0.609814229 0.658344399 0.600522814 0.626874864 0.884813792 0.611827068 0.638561374 0.61457701 1 18.50406016 -1.743345518 2.551246831 1.076518442 0.65436177 0.628063113 0.083269527 15336194.57 11356715.23 7408023.221 0.019115299 0.018057369 1.743345518 -0.422156672 LLASFFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLASFFDR 8 0 Q96RE7 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 0 ; 89.55 0.032166 27657000 122663 100215 84648 77417 137146 75839 139604 98207 130885 FALSE TRUE 116864.9631 110427.0224 88529.19453 69634.89608 161064.219 73212.67641 118304.8458 89607.47445 151181.9773 0.773008563 0.730424515 0.585580346 0.460603157 1.065366533 0.484268546 0.782532732 0.592712677 1 17.20592664 -1.320197919 3.250080899 1.001884726 0.693196293 0.243215756 0.174380219 34412069.22 47989842.35 629870.2251 0.036828273 0.047841202 1.320197919 -0.308688433 LLASPS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLASPSSR 8 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 LLAS(0.002)PS(0.998)SR 167.1 0.00033002 273740000 273040 250420 288020 299510 309200 270090 334460 304000 359580 TRUE FALSE 260133.9403 275938.0827 301226.0019 269402.6858 363124.3821 260736.7156 283431.9842 277380.1484 415341.8299 0.626312886 0.664363815 0.72524841 0.648628831 0.87427838 0.627764161 0.682406548 0.667835812 1 18.66393965 -1.904815721 2.620265957 1.176874211 0.685890332 0.649493214 0.071614052 17534370.53 10185360.99 19105651.34 0.016034805 0.012450428 1.904815721 -0.490983879 LLASS(ph)PALPSSGAQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLASSPALPSSGAQAR 16 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 LLAS(0.002)S(0.99)PALPS(0.008)SGAQAR;LLAS(0.03)S(0.967)PALPS(0.002)S(0.001)GAQAR 195.6 1.33E-12 0 303530 303310 328600 342330 352680 321000 399590 362670 432220 TRUE FALSE 289182.7384 334217.6338 343666.635 307918.338 414187.2803 309883.6895 338625.2065 330912.6922 499246.4701 0.579238424 0.66944416 0.688370686 0.61676618 0.829624855 0.620702815 0.67827261 0.6628243 1 18.9293927 -5 0.287092848 3.552561114 0.645032441 0.715483174 0.06588157 123.9856947 1.173492639 189.3255899 0.066561794 1.00E-05 5 -2.907528673 LLASSDPLAQIAEDKPYAELWMGTHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLASSDPLAQIAEDKPYAELWMGTHPR 27 1 H3BPB8;P34949-2;P34949;H3BPU7;H3BUG1;H3BU66;H3BPM5;H3BQX0;H3BT46;H3BMZ9;H3BPP3;H3BP57;H3BT48;H3BUZ9 H3BPB8 MPI Mannose-6-phosphate isomerase 0 ; 195.63 3.96E-25 301690000 511270 425139 440576 551670 452856 522840 592730 554570 433601 FALSE TRUE 487103.2803 468461.1474 460776.8454 496215.0835 531833.943 504733.9197 502298.1523 506008.9108 500841.6286 0.972569476 0.935347864 0.920005086 0.990762459 1.061880468 1.007771501 1.002908152 1.010317198 1 18.93399495 3.047977894 6.18003234 1.015993262 0.945956533 0.711411676 0.021446848 0.103427182 9.205497312 0.006221898 0.007418607 1116.806399 -3.047977894 -0.07003673 LLAVAATAPPDAPNREEVFDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLAVAATAPPDAPNREEVFDER 22 1 P18206;P18206-2 P18206 VCL Vinculin 0 158.52 1.89E-11 230790000 133190 62332 65224 117990 205340 78613 270510 107710 358850 FALSE TRUE 126894.3727 68683.70167 68214.58492 106129.421 241151.231 75890.6121 229238.7312 98278.34139 414498.6252 0.306139429 0.165703087 0.164571318 0.256042878 0.581790183 0.183090142 0.553050643 0.237101731 1 18.66100779 -5 0.186228895 3.970068559 0.169865254 0.697202367 0.145278904 68.92729328 0.670445697 75.62090469 0.37280823 1.00E-05 5 -3.800203306 LLCEHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLCEHFR 7 0 Q13155;A8MU58;Q13155-2 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ;;;;; 181.2 0.00067538 1150150000 1824760 1167590 525113 676973 2088500 835762 1969790 1325440 1751090 FALSE TRUE 1738507.211 1286568.748 549189.9505 608922.3879 2452733.739 806819.3524 1669262.358 1209377.447 2022640.094 0.859523756 0.636083875 0.271521341 0.301053257 1.212639731 0.398894175 0.82528887 0.597920238 1 20.9478082 LLCGLLAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLCGLLAER 9 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ;; 142.19 0.00024409 447592000 422282 266371 170333 226653 595786 226519 607046 311822 777846 FALSE TRUE 402321.5667 293514.5077 178142.9365 203869.4098 699690.8898 218674.5902 514429.9835 284517.2126 898470.385 0.447785006 0.326682451 0.198273576 0.226907212 0.778757877 0.243385418 0.572561981 0.316668437 1 19.77711143 -5 0.250196529 4.70713188 0.338112307 0.542036208 0.17675849 134.3430241 1.331022676 254.4680075 0.231481584 1.00E-05 5 -4.369019574 LLDDAMAADKSDEWFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLDDAMAADKSDEWFAK 17 1 Q9HC38-2;F6TLX2;Q9HC38;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 201.96 1.16E-11 369290000 1048800 779010 854870 1111570 668580 998800 1176680 1153480 726590 FALSE TRUE 999225.3025 858392.0047 894066.6351 999832.8718 785180.1403 964211.3056 997155.8548 1052475.176 839265.8663 1.190594474 1.022789129 1.065296077 1.191318403 0.935555909 1.148874682 1.188128691 1.254042632 1 19.67876838 2.021007074 24.99591524 1.168345729 1.083635978 0.091068837 0.097226901 420.4229112 500251.1133 0.033128645 0.024464372 104.9559525 -2.021007074 -0.084709752 LLDDLFR ddPTM_SK-BR-3_Trastuzumab_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 380393000 1518450 1248133 1120695 1307241 1611670 1075066 1657230 1404490 1594560 FALSE TRUE 1446675.878 1375319.172 1172079.974 1175834.651 1892744.738 1037836.195 1404389.126 1281505.41 1841836.221 0.78545305 0.746710894 0.636364928 0.638403479 1.027640089 0.563479088 0.762494032 0.695775985 1 20.81271335 -1.522663778 2.833833823 1.011760421 0.734274044 0.314443433 0.124304443 20475950.41 21690259.62 1856821.842 0.026623931 0.030014853 1.522663778 -0.277486376 LLDEEEATDNDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 297.52 2.20E-40 2531720000 1503830 1392316 1462380 1644140 1522780 1447910 1734760 1591130 1648220 FALSE TRUE 1432746.936 1534194.583 1529431.569 1478867.924 1788352.35 1397768.514 1470090.501 1451802.222 1903817.54 0.752565257 0.805851691 0.803349868 0.776790786 0.939350706 0.734192476 0.772180354 0.762574245 1 20.86046379 -2.156331556 2.398622754 1.493097937 0.792068963 0.571767288 0.056192411 3689926.276 722695.886 9941422.458 0.013293862 0.006976996 2.156331556 -0.701028974 LLDEVFFSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 190.24 2.15E-06 212327000 970900 914773 842084 948794 761220 841437 991411 952453 801747 FALSE TRUE 925007.4811 1007989.409 880694.3843 853419.4245 893976.527 812297.8257 840153.0434 869051.166 926077.83 0.998844213 1.088449994 0.950993918 0.921541794 0.96533628 0.877137752 0.907216452 0.938421305 1 19.82077392 3.595920069 5.16364808 0.927004675 1.04295071 0.554711435 0.039357332 0.130569086 4.987633914 0.009936121 0.015540701 3943.847097 -3.595920069 0.115946035 LLDFGS(ph)LSNLQVTQPTVGMNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLDFGSLSNLQVTQPTVGMNFK 22 0 H3BNC9;P08708 H3BNC9 RPS17 40S ribosomal protein S17 1 LLDFGS(0.712)LS(0.288)NLQVTQPTVGMNFK;LLDFGS(0.815)LS(0.185)NLQVTQPTVGMNFK 203.72 4.20E-22 246880000 594170 516220 601470 660890 551570 645180 743830 666640 661130 TRUE FALSE 566084.7616 568823.4049 629047.9944 594456.0816 647763.6334 622837.2548 630345.0721 608265.4675 763654.6638 0.741283709 0.744869942 0.823733586 0.778435738 0.848241573 0.815600669 0.825432099 0.796519024 1 19.54256085 -5 0.124807278 1.677704943 0.698913302 0.836764111 0.029313453 53.93411674 0.430828095 9.201253931 0.242692704 1.00E-05 5 -0.978791641 LLDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLDGKR 6 1 Q68DA7-5;A0A5F9ZHS8;H0YM30;Q68DA7;H0YLM7 Q68DA7-5 FMN1 Formin-1 0 ; 103.29 0.055824 1048950000 1296710 1108480 1204660 1347200 1240340 1293310 1658610 1454970 1464270 FALSE TRUE 1235417.088 1221435.372 1259894.853 1211776.896 1456654.903 1248522.35 1405558.582 1327565.114 1691341.513 0.730436212 0.722169569 0.744908608 0.716459028 0.861242329 0.738184654 0.8310318 0.784918423 1 20.68973657 -4.999999996 0.141295862 1.849208374 0.676375592 0.790361779 0.040124622 52.75087849 0.454854533 12.50913696 0.209122781 1.00E-05 4.999999996 -1.172832782 LLDGPSTEKDLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDGPSTEKDLDEK 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 111.12 0.0014907 0 197650 162610 177520 209050 119720 205940 219350 226750 119090 FALSE TRUE 188307.4762 179180.1439 185659.4676 188035.8968 140599.1301 198808.2462 185884.1289 206894.5679 137557.869 1.368932782 1.302580108 1.349682639 1.36695849 1.022108958 1.44526989 1.351315852 1.504054762 1 17.06967915 LLDIACWIHHK ddPTM_SK-BR-3_Trastuzumab_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 ; 141.93 2.19E-05 10204700000 18501400 14676500 12718800 13935400 17663700 13468500 21316400 15864900 1801340 FALSE TRUE 17626875.49 16172052.04 13301969.56 12534587.12 20744243.69 13002082.47 18064191.68 14475685.25 2080682.607 8.471679163 7.772474273 6.393079615 6.024266783 9.969922186 6.248950427 8.681858355 6.957180879 1 20.98862548 0.95844407 21.93212301 0.999999991 7.68735299 0.743891372 1.217081097 788.0886757 415933.4589 1.064634025 0.266158508 9.0874926 -0.95844407 6.687353 LLDLELTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDLELTSR 9 0 E5RGC7;E5RK86;E5RFH3;H0YAT2;Q9Y2Q9 E5RGC7 MRPS28 "28S ribosomal protein S28, mitochondrial" 0 75.378 0.089405 10194000 41783 33664 34690 38777 43789 35241 40425 39746 47990 FALSE TRUE 39808.0004 37094.39987 36280.57081 34879.06229 51425.78774 34020.59533 34257.42379 36265.62953 55432.0441 0.718140582 0.669186938 0.654505375 0.629222011 0.927726707 0.613735176 0.618007587 0.654235833 1 15.75843259 -1.058435803 5.024194548 1.000005901 0.682644401 0.539683998 0.091217458 5.73E-06 1.07E-06 0.083877596 0.019769771 0.087410619 1.058435803 -0.3173615 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 LLDLSDSTSVAS(1)FPSADETDGNLPESR;LLDLSDSTSVAS(1)FPSADETDGNLPESR;LLDLSDSTSVAS(1)FPSADETDGNLPESR;LLDLSDSTSVAS(1)FPSADETDGNLPESR 205.89 1.90E-25 184916000 227725 223334 231074 240405 244632 213253 265557 237181 265673 TRUE FALSE 216960.8906 246091.9885 241668.9715 216239.0327 287295.7433 205867.9951 225041.4024 216412.1743 306872.212 0.707007289 0.801936373 0.787523151 0.704654981 0.936206447 0.670859032 0.733339135 0.705219195 1 18.22727849 -0.990002764 4.455565905 1.000007148 0.756335596 0.509761124 0.075246079 0.057709956 40760824.34 730.2222043 0.016065494 0.102328648 0.990002764 -0.243671552 LLDLVVQPVPRPSQCSEFIQQSSMKS(ph)PLYLVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDLVVQPVPRPSQCSEFIQQSSMKSPLYLVSR 33 2 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 LLDLVVQPVPRPS(0.004)QCS(0.004)EFIQQS(0.055)S(0.042)MKS(0.896)PLYLVSR 146.48 1.66E-10 35672000 74164 41219 80550 66725 71405 80002 113250 77779 99991 TRUE FALSE 70658.4147 45419.26296 84243.29717 60017.67623 83858.00939 77231.51068 95971.63252 70968.25843 115497.0936 0.611776561 0.393250268 0.729397551 0.519646637 0.726061642 0.668687915 0.830944135 0.614459258 1 16.81749702 0.957352206 0.187141514 1.155645019 0.394856164 0.564934874 0.10920198 2.840986556 0.401539001 0.796285178 0.513421382 9.064674328 -0.957352206 -0.760788855 LLDPEDISVDHPDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLDPEDISVDHPDEK 15 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 215 2.40E-12 183604000 257368 264473 279659 359600 173150 308790 279430 335270 215437 FALSE TRUE 245202.7247 291423.0994 292481.6418 323452.3248 203347.3052 298096.5249 236797.8214 305911.9814 248845.8697 0.985359833 1.1710988 1.175352607 1.299809899 0.817161665 1.197916306 0.951584295 1.229323122 1 17.92489292 2.767189708 24.99670248 1.04243272 1.14190174 0.150023879 0.137967799 1563.421764 1365056.219 0.038814206 0.041162551 585.0455878 -2.767189708 0.099469019 LLDPS(ph)SPLALALSARDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDPSSPLALALSARDR 17 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LLDPS(0.333)S(0.333)PLALALS(0.333)ARDR 54.501 0.076617 167010000 363260 278690 260790 330840 257710 327960 360340 339870 289600 TRUE FALSE 346089.4197 307088.8278 272747.4795 297583.3346 302654.5424 316602.663 305363.5149 310109.181 334509.6889 1.034617027 0.918026706 0.815364961 0.889610509 0.904770631 0.946467841 0.912868969 0.927055901 1 18.35168847 -0.631926246 7.475063046 1.000000105 0.92170228 0.182107793 0.053859343 0 0 0.054927663 0.012946574 0.233385437 0.631926246 -0.078297825 LLDSSTVTHLFK ddPTM_SK-BR-3_Trastuzumab_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 ; 224.24 2.05E-11 935900000 3259600 3131500 2231150 2984800 3066200 2668300 3814800 3161400 3147000 FALSE TRUE 3105525.168 3450603.41 2333450.434 2684762.233 3600944.309 2575896.102 3232782.196 2884571.056 3635020.687 0.854334936 0.949266512 0.641935943 0.738582381 0.990625534 0.708633134 0.889343548 0.793550107 1 21.79353214 -1.948092506 7.870577019 1.06600511 0.830909392 0.210401931 0.107529532 0.06719989 0.000443192 0.056178312 0.023101009 0.011269574 1.948092506 -0.235095717 LLDSVEQDFHLEIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LLDSVEQDFHLEIAK 15 0 Q6IBS0;H0Y858;H7C5I2;Q9NR96-4 Q6IBS0 TWF2 Twinfilin-2 0 ;;;;;;; 210.9 1.65E-09 343332800 709769 634391 589458 753567 566269 681353 782624 743526 524031 FALSE TRUE 676219.626 699036.1641 616485.2324 677817.0135 665026.1343 657757.5748 663220.3349 678418.9218 605295.0511 1.117173558 1.154868461 1.018487151 1.119812581 1.098680938 1.086672646 1.0956976 1.120806986 1 19.20727903 -5 0.231583879 0.44386111 1.115584613 0.429044977 0.035723765 150.7449979 1.507169649 39.4153563 0.058301603 1.00E-05 5 0.671723503 LLDTVDDMLANDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLDTVDDMLANDIAR 15 0 A0A024R571;Q9H4M9;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;; 143.17 1.04E-05 26818100 47774.4 40921 41216.8 47239.8 46061.9 42231.7 51745.6 48701.5 50124.7 FALSE TRUE 45516.19879 45090.89642 43106.63105 42491.16555 54095.08078 40769.20564 43850.85835 44436.93848 57897.78247 0.786147532 0.778801786 0.744529915 0.733899706 0.934320426 0.704158327 0.757384074 0.767506743 1 15.82122047 -1.176614301 5.382610233 1.000008331 0.774760936 0.571153002 0.061035578 5.57E-06 8.52E-07 0.053963227 0.012718784 0.066586425 1.176614301 -0.225247395 LLDVVHPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLDVVHPAAK 10 0 Q99832-3;Q99832;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 120.68 0.00053504 843340000 3701700 3265400 3181500 3710300 2952100 3570000 4167500 3807200 3122000 FALSE TRUE 3526727.977 3598147.972 3327374.922 3337333.595 3466945.305 3446370.005 3531671.334 3473821.385 3606143.815 0.977977629 0.997782717 0.922696124 0.925457709 0.961399623 0.955693999 0.979348444 0.963306391 1 21.7820255 0.542079664 0.964675436 0.99981803 0.962007469 0.22650488 0.022951877 2.919988149 4.102003675 0.024721631 0.007917248 3.484012174 -0.542079664 -0.037810561 LLDWLVDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDWLVDRR 9 1 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 99.855 0.0079502 0 48636 41888 33594 37326 56542 35294 51346 48273 47501 FALSE TRUE 46337.07267 46156.43482 35134.31813 33573.91957 66402.9069 34071.75993 43512.22467 44045.96021 54867.21248 0.844531198 0.841238925 0.640351797 0.611912252 1.210247503 0.620985802 0.793046023 0.802773792 1 15.74365666 LLDYTEKPLYENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLDYTEKPLYENLR 14 1 Q99986;H0YJ50;H0YJJ9 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 79.81 0.01646 229210000 178130 175610 166170 207830 182890 180430 213450 181680 174080 FALSE TRUE 169710.1479 193504.8587 173789.0589 186938.5335 214785.9581 174181.6639 180884.2822 165771.1361 201075.4373 0.844012328 0.96234956 0.864297804 0.929693532 1.068185955 0.86625033 0.899584179 0.824422606 1 17.61737733 LLEAHEEQNVDSYTESVKEYDSISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEAHEEQNVDSYTESVKEYDSISR 25 1 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 198.39 4.60E-25 201140000 175140 145740 182850 181100 152070 173830 214790 229440 158560 FALSE TRUE 166861.4793 160591.0717 191233.8534 162895.4839 178590.9599 167810.2235 182019.8406 209349.0173 183148.675 0.911071179 0.876834472 1.044145437 0.889416666 0.97511467 0.916251365 0.993836514 1.143055047 1 17.48265574 1.492485311 4.244933003 1.072678628 0.931600875 0.476194301 0.058316059 0.14040953 5.337797658 0.034915734 0.01389263 31.08030776 -1.492485311 -0.141077752 LLEAQIATGGIIDPVHSHR ddPTM_SK-BR-3_Trastuzumab_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 ; 118.52 4.50E-05 158562000 186754 234367 191208 217687 226719 197166 181850 193414 40472.7 FALSE TRUE 177926.5085 258249.2638 199975.0759 195804.6892 266258.7218 190338.092 154105.4426 176477.6448 46748.99961 3.805996064 5.524166633 4.277633267 4.188425224 5.695495605 4.071490162 3.296443643 3.775003664 1 15.51264787 0.737661838 0.678133319 0.983858755 4.706037374 0.736748032 0.659816266 0.535552774 0.496297512 0.657747543 0.244507471 5.465901971 -0.737661838 3.72217862 LLEAQIATGGVIDPVHSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 221.79 1.49E-19 3679094000 3698445 3479419 3330208 3957837 3886295 3547654 3952573 3226767 174858.7 FALSE TRUE 3523626.834 3833975.752 3482901.331 3559987.705 4564063.618 3424797.852 3349535.395 2944214.175 201974.8941 17.44586548 18.98243724 17.24422902 17.62589217 22.59718287 16.95655228 16.58391955 14.57712944 1 17.62381645 0.532720561 1.026103048 0.970625802 18.52410678 0.919647283 1.600380625 0.392764106 0.602027354 1.466747563 0.462349703 3.409734479 -0.532720561 17.55348098 LLEAQIATGGVIDPVHSHRVPVDVAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEAQIATGGVIDPVHSHRVPVDVAYR 27 1 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 ; 212.07 4.82E-26 330620000 143670 78952 161614 129397 196265 138438 217590 145434 86572 FALSE TRUE 136879.0038 86997.29856 169024.1618 116389.7677 230493.5539 133643.8573 184392.6492 132699.028 99997.14361 1.368829137 0.869997836 1.690289899 1.163930924 2.305001378 1.336476748 1.843979163 1.327028185 1 16.60959926 3.727676294 24.90007691 1.580142864 1.11941348 0.145389125 0.389417884 872.0880286 1995076.667 0.091656617 0.143534342 5341.660646 -3.727676294 -0.460729384 LLEAQVATGGIIDPTSHHHLPMPVAIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEAQVATGGIIDPTSHHHLPMPVAIQR 28 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 146.34 3.07E-08 91441000 33783 29335 32338 37580 46738 35852 43722 36362 11369 FALSE TRUE 32186.14454 32324.26985 33820.72929 33802.387 54889.0924 34610.43625 37051.40589 33177.95051 13132.04646 2.450961825 2.461480011 2.575434789 2.574038031 4.179782077 2.635570653 2.821449499 2.526487446 1 13.68080414 2.980922547 24.77355879 2.812533334 2.493716389 0 0.765753716 2532.860824 3289120.978 0.209316315 0.22537935 957.0233779 -2.980922547 -0.318816945 LLEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 151.7 0.024083 6038840000 4512480 4093060 3651630 4245640 4745990 3969140 4921340 4376370 4945580 FALSE TRUE 4299184.013 4510147.467 3819060.847 3818860.201 5573689.153 3831687.687 4170499.196 3993151.842 5712515.288 0.752590373 0.78952042 0.668542779 0.668507655 0.975697897 0.670753161 0.730063551 0.699018145 1 22.44569469 -1.521685831 5.957728807 1.000358045 0.746718358 0.436819131 0.091195678 0.000399447 3.21E-05 0.081325113 0.019141918 0.030082517 1.521685831 -0.253639687 LLEDFGDGGAFPEIHVAQYPLDMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLEDFGDGGAFPEIHVAQYPLDMGR 25 0 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ;;; 188.72 1.15E-17 353872000 344900 301868 292552 339480 357354 289376 365836 343094 339456 FALSE TRUE 328597.2605 332628.6924 305965.7986 305354.8254 419676.4245 279354.8366 310020.9992 313050.8705 392097.1028 0.838050723 0.848332441 0.780331699 0.778773481 1.070337989 0.712463404 0.790674037 0.798401387 1 18.58085146 -2.373088692 2.178769122 2.128947944 0.826333822 0.25019019 0.094018767 7372197.475 639496.7957 41166892 0.021128963 0.004235565 2.373088692 -1.302614121 LLEDFLQEGEEPDEDDAYQVLSTLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEDFLQEGEEPDEDDAYQVLSTLKR 26 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 171.72 9.02E-12 38676000 32032 25818 32431 33483 29052 36118 44786 35857 39994 FALSE TRUE 30517.91084 28448.88355 33917.99343 30117.22523 34118.6596 34867.2246 37953.07315 32717.17099 46196.06526 0.660617104 0.615829149 0.734218233 0.651943516 0.738562027 0.754766113 0.82156506 0.708224192 1 15.49548236 -5 0.099395399 1.991596651 0.494127655 0.819792956 0.045833881 65.61780456 0.444370442 13.33441102 0.717106988 1.00E-05 5 -1.497468996 LLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.473)S(0.311)NS(0.206)MQT(0.009)IQK;LLEDGEDFNLGDALDS(0.329)S(0.329)NS(0.329)MQT(0.014)IQK 145.13 1.85E-07 50862000 39791 38987 38408.3 51340 38006 47877 55828 47803 46025 TRUE FALSE 37910.15829 42959.81962 40169.35855 46179.20566 44634.23437 46219.00749 47310.41325 43617.1159 53162.32194 0.713102004 0.808087722 0.755598271 0.868645386 0.83958399 0.869394071 0.889923757 0.820451672 1 15.6981165 8 0.067042368 1.190739043 0.016972935 0.784699569 0.036075144 107.936652 0.536211795 1.711535324 12.05598439 100000000 -8 -1.173766108 LLEDGEDFNLGDALDSS(ph)NSMQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.086)S(0.427)NS(0.427)MQT(0.061)IQK 99.454 0.023113 37704000 19570 16313 20888 23655 16779 21988 24114 22223 20782 TRUE FALSE 18644.96488 17975.31325 21845.73546 21277.15446 19705.25229 21226.55005 20434.96642 20277.03631 24004.76642 0.77671928 0.748822668 0.910058239 0.886372068 0.820889149 0.88426397 0.851287868 0.844708753 1 14.55103328 -4.999998775 0.024353277 2.137461773 1.97E-11 0.581392223 0.045491729 1495.079541 2.749360431 173.3278232 83.19228163 1.00E-05 4.999998775 -2.137461773 LLEDGEDFNLGDALDSSNS(ph)MQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.004)S(0.121)NS(0.695)MQT(0.181)IQK;LLEDGEDFNLGDALDS(0.022)S(0.408)NS(0.57)MQTIQK 236.28 1.26E-38 61225000 45722.5 40842.7 44935 61155 41622 52018.4 59648 53977 55473 TRUE FALSE 43561.28804 45004.61756 46995.3142 55007.58321 48880.86362 50216.98976 50547.60209 49250.48773 64075.46952 0.679843447 0.702368908 0.733436907 0.858481157 0.762863916 0.783716298 0.788876031 0.768632491 1 15.96748452 -5 0.10573574 1.767924989 0.604466393 0.779232615 0.042294316 79.70190943 0.566009795 13.4294752 0.60389012 1.00E-05 5 -1.163458595 LLEDGEDFNLGDALDSSNSMQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 277.91 3.92E-53 160052000 124069 118570 111552 132494 89672 113597 129991 120571 106964 FALSE TRUE 118204.5043 130652.4178 116666.7695 119175.4514 105310.7684 109663.1074 110158.4855 110013.1641 123551.4308 0.95672307 1.057473936 0.94427696 0.964581718 0.852363811 0.887590752 0.891600241 0.890424039 1 16.91475219 3.182916554 1.982439265 0.897278451 1.003802584 0.36907804 0.048463946 0.250017476 2.019456139 0.014014662 0.018632373 1523.75995 -3.182916554 0.106524133 LLEDS(ph)EES(ph)SEETVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 LLEDS(1)EES(0.989)S(0.011)EETVSR;LLEDS(1)EES(0.932)S(0.068)EETVSR;LLEDS(1)EES(0.99)S(0.01)EETVSR;LLEDS(1)EES(0.651)S(0.349)EETVSR;LLEDS(1)EES(0.989)S(0.011)EETVSR 270.79 3.24E-33 4401250000 4057360 3342930 3757230 4023710 3722340 3870800 4541410 3973390 3753410 TRUE FALSE 3865576.634 3683578.368 3929502.712 3619239.026 4371514.917 3736753.225 3848534.496 3625458.907 4335469.653 0.891616582 0.849637678 0.906361485 0.834797454 1.008314039 0.861902752 0.887685719 0.836232103 1 22.04775686 LLEDS(ph)EESSEETVSR ddPTM_SK-BR-3_Trastuzumab_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(0.968)EES(0.023)S(0.008)EETVSR 184.48 4.85E-07 299590000 285500 233600 235227 299250 233118 236090 286810 247780 239809 TRUE FALSE 272004.9808 257404.1056 246012.3906 269168.8215 273773.7054 227914.1441 243051.8669 226083.0696 276997.3549 0.981976817 0.929265572 0.888139855 0.971737876 0.988362165 0.822802601 0.877451941 0.816192161 1 18.07951267 2.241364565 24.99998661 0.868169376 0.949548861 0.27664164 0.05721125 79.85237573 711970.4652 0.018406451 0.01475977 174.3269632 -2.241364565 0.081379485 LLEEALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLEEALLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 176.66 0.00060257 127787900 222772 203500 169318 215890 266532 199909 273229 221433 284308 FALSE TRUE 212242.0091 224236.8814 177081.3978 194188.327 313015.0964 192986.1012 231542.8979 202043.1526 328397.0326 0.646296976 0.682822496 0.539229592 0.591321808 0.953160551 0.587660917 0.705070006 0.615240494 1 18.32508157 -2.295214043 2.323423537 2.613159063 0.66753745 0.464107913 0.113068812 6670072.384 762200.482 56816242.65 0.02516041 0.005067409 2.295214043 -1.945621612 LLEEDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEEDVKR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 114.89 0.0041182 104540000 166090 130550 126620 154290 120520 144430 182500 166440 133190 FALSE TRUE 158239.2549 143853.1934 132425.6522 138780.4761 141538.6498 139428.3529 154656.2732 151865.6312 153844.425 1.028566715 0.935056265 0.860776413 0.902083232 0.920011563 0.906294478 1.005277073 0.987137696 1 17.23111264 1.698988891 7.512903761 0.996645192 0.930982766 0.384231257 0.042495708 0.162333418 19.35314119 0.023572379 0.012320766 50.00217451 -1.698988891 -0.065662426 LLEEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLEEERR 7 1 Q8NE71;Q8NE71-2;H0YGW7;Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q8NE71;Q5JSZ5;Q5JSZ5-5 ABCF1;PRRC2B ATP-binding cassette sub-family F member 1;Protein PRRC2B 0 ;; 101.28 0.014707 373251000 399775 312792 346726 393281 450129 346646 458867 389503 499690 FALSE TRUE 380878.428 344665.8604 362623.7301 353747.6467 528631.3551 334641.5621 388858.4115 355396.0524 577179.3731 0.659896119 0.59715554 0.628268692 0.612890313 0.915887469 0.579787805 0.673721948 0.615746281 1 19.13866022 -1.777859041 2.581069991 1.091445572 0.657565398 0.557524679 0.095042952 13818554.39 10000780.77 7978119.846 0.021375887 0.016677884 1.777859041 -0.433880173 LLEEGVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEEGVLR 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 96.492 0.020712 54318000 92649 67664 71690 82504 111402 74773 107494 88755 115323 FALSE TRUE 88269.66538 74559.03853 74977.05741 74210.54117 130830.4735 72183.59226 91093.81604 80983.14168 133206.7019 0.662651835 0.559724379 0.562862501 0.557108165 0.982161346 0.541891596 0.6838531 0.607950956 1 17.02330714 -5 0.265810572 3.388831902 0.614015751 0.425926935 0.129128876 190.9188066 1.863039341 249.9304381 0.151731306 1.00E-05 5 -2.774816151 LLEEHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEEHAK 7 0 P51572;P51572-2;A0A2R8Y5M6 P51572 BCAP31 B-cell receptor-associated protein 31 0 ; 112.17 0.0064142 484780000 817810 653430 672350 1045720 897950 850030 1016810 824710 696130 FALSE TRUE 779153.742 720015.2599 703177.9125 940602.2389 1054552.196 820593.248 861676.9595 752494.0203 804082.2851 0.968997522 0.895449724 0.874509892 1.169783561 1.311497859 1.020533922 1.071627836 0.935842058 1 19.61698362 3.245344202 24.99983837 1.093146551 0.917229669 0.375080011 0.104182776 164.0371509 604529.5008 0.02923886 0.03871671 1759.317418 -3.245344202 -0.175916882 LLEEHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLEEHSR 7 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ;;; 181.81 0.0006665 1010240000 2018450 1536400 1610920 1601870 2046570 1346220 1753650 1655350 1889060 FALSE TRUE 1923041.869 1692960.907 1684782.275 1440846.984 2403491.16 1299600.064 1486098.485 1510398.778 2182005.777 0.881318413 0.775873705 0.772125488 0.660331425 1.101505406 0.595598819 0.681069913 0.69220659 1 21.05722349 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 56.46 0.04365 11285000 25448 14988 21509 22938 21363 21641 28226 20971 21278 FALSE TRUE 24245.12347 16515.29424 22495.20893 20632.22866 25088.70044 20891.56674 23919.60529 19134.66807 24577.68357 0.986469022 0.67196301 0.915269694 0.839470026 1.020791905 0.850021797 0.973224561 0.778538303 1 14.58506133 2.884317536 18.16072742 0.921818599 0.841245599 0.096739879 0.105127675 5.84248186 896.5530415 0.029656649 0.03145586 766.1565808 -2.884317536 -0.080573 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 LLEENETEAVTVPTPS(1)PTPVR;LLEENETEAVTVPTPS(0.987)PT(0.013)PVR;LLEENETEAVTVPT(0.001)PS(0.999)PTPVR;LLEENETEAVTVPTPS(0.994)PT(0.006)PVR;LLEENETEAVTVPTPS(1)PTPVR;LLEENETEAVTVPT(0.001)PS(0.996)PT(0.003)PVR;LLEENETEAVTVPT(0.011)PS(0.988)PT(0.001)PVR;LLEENETEAVTVPTPS(0.999)PT(0.001)PVR;LLEENETEAVTVPT(0.002)PS(0.997)PT(0.002)PVR;LLEENETEAVTVPT(0.003)PS(0.993)PT(0.003)PVR;LLEENETEAVTVPT(0.001)PS(0.991)PT(0.008)PVR 361.31 4.72E-96 2414690000 2659820 2410181 2626912 2753360 2762460 2548894 3124900 2827900 3176490 TRUE FALSE 2534095.58 2655781.184 2747358.514 2476587.022 3244232.149 2460625.162 2648139.112 2580274.084 3669083.846 0.690661671 0.72382679 0.748785972 0.674987851 0.884207689 0.670637485 0.721743962 0.703247512 1 21.80698844 -1.148701534 4.754610858 1.000024582 0.725705504 0.666926267 0.060564083 1.41E-05 2.53E-06 0.052527822 0.012379818 0.071006559 1.148701534 -0.274319078 LLEEQLQHEISNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEEQLQHEISNK 13 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 0 110.51 0.0010528 63773000 80591 72881 75137 99733 75459 84738 92092 74651 73714 FALSE TRUE 76781.62315 80307.65676 78582.10577 89707.64936 88619.02571 81803.50181 78041.67401 68114.16269 85145.19064 0.901772873 0.943184884 0.922918901 1.053584456 1.040798958 0.960753052 0.916571722 0.79997663 1 16.37763742 -2.063888301 9.669089475 1.23020334 0.944490167 0.060260158 0.071021766 0.067543884 0.000446295 0.01317872 0.016167886 0.008632005 2.063888301 -0.285713173 LLEFQLALKDCEECIQLEPTFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEFQLALKDCEECIQLEPTFIK 23 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 299.4 7.31E-62 312240000 873980 435680 777280 730930 696090 741810 1193240 933820 897730 FALSE TRUE 832668.6975 480076.2873 812919.0568 657455.5277 817487.8756 716120.9337 1011189.323 852049.7703 1036945.383 0.803001499 0.462971623 0.78395552 0.634031009 0.788361556 0.690606222 0.975161603 0.821692043 1 19.98390848 1.890771465 0.833886141 0.97364077 0.648767294 0.48172443 0.112106152 0.445803371 0.578326952 0.089578986 0.042353027 77.76272399 -1.890771465 -0.324873476 LLEGEEER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 211.39 7.32E-05 9457080000 9076940 7518370 7774640 8816530 8496680 8241430 9934230 8425860 8913640 FALSE TRUE 8647891.035 8284500.451 8131114.934 7930275.654 9978498.302 7956027.213 8418580.759 7688047.03 10295921.77 0.839933639 0.804639025 0.789741329 0.770234646 0.969169981 0.772735787 0.817661687 0.746707988 1 23.29556966 -1.05334023 4.658393144 1.000007179 0.815518346 0.478025485 0.061108433 4.13E-06 8.39E-07 0.053614969 0.012636678 0.088442247 1.05334023 -0.184488833 LLEIVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLEIVER 7 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ;;; 114.78 0.013557 107796000 241791 225423 213057 258802 250252 244454 269890 249044 228312 FALSE TRUE 230362.0186 248393.86 222825.8742 232786.7313 293895.8696 235988.4967 228713.3236 227236.3871 263717.4589 0.873518271 0.941893878 0.844941685 0.882712628 1.114434633 0.894853521 0.867266523 0.861666073 1 18.00863356 4.692829943 3.625966537 0.919459154 0.8705104 0.034599333 0.080681127 1.126608099 25.40608037 0.018967918 0.136584639 49298.07295 -4.692829943 -0.048948753 LLELDPEHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLELDPEHQR 10 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;;;; 152.54 1.78E-05 1341990000 2618900 2183470 2187160 2530020 2588430 2248790 2658340 2439570 2393890 FALSE TRUE 2495109.787 2405968.075 2287443.449 2275697.583 3039851.372 2170913.838 2252761.409 2225948.318 2765122.235 0.902350629 0.870112737 0.827248583 0.823000717 1.099355151 0.785105921 0.814705904 0.805009012 1 21.39891183 -0.989133467 5.985621191 1.00000012 0.865548153 0.181674611 0.089466931 1.35E-07 2.29E-08 0.082137622 0.019360006 0.102533677 0.989133467 -0.134451966 LLELGPKPEVAQQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLELGPKPEVAQQTR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 123.36 0.00072342 0 256140 255800 228840 306550 229520 235840 307880 273870 264160 FALSE TRUE 244032.7698 281866.3108 239332.5404 275735.0116 269548.2153 227672.8017 260907.2514 249888.4909 305124.5837 0.799780755 0.923774504 0.784376459 0.903680091 0.883403796 0.746163416 0.855084334 0.818972001 1 18.2190389 -1.597447089 6.290669674 1.000461107 0.842916872 0.455927641 0.055014802 0.000327051 2.09E-05 0.048966707 0.011508296 0.025266955 1.597447089 -0.157544236 LLELLGHYQESGSVIIFVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLELLGHYQESGSVIIFVDK 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 76.768 0.010847 8622800 33403 30701 27248.7 41461 25327 31672 27686 30886 17577.4 FALSE TRUE 31824.10639 33829.4668 28498.07985 37293.26151 29744.02078 30575.1907 23461.99221 28181.4581 20303.21342 1.567441849 1.666212442 1.403624109 1.836815717 1.464990796 1.505928646 1.155580239 1.388029447 1 14.30942046 1.626289637 0.835618381 1.060772351 1.618775997 0.639459773 0.142693767 0.318719662 0.437777935 0.116375589 0.048903748 42.2950592 -1.626289637 0.558003647 LLELLGHYQESGSVIIFVDKQEHADGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLELLGHYQESGSVIIFVDKQEHADGLLK 29 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 125.12 1.46E-05 44163000 53715 41160 52728 62505 43452 56909 67412 65226 24694 FALSE TRUE 51175.9984 45354.2508 55145.63096 56221.87865 51030.01504 54938.22706 57127.06129 59514.46566 28523.4194 1.794174734 1.590070607 1.933345725 1.971077796 1.789056716 1.92607437 2.002812513 2.086512308 1 14.79985932 -1.553483867 8.010863824 0.99977025 1.867432185 0.800616083 0.138759849 0.000641601 3.58E-05 0.151396007 0.035675575 0.027958646 1.553483867 0.867661935 LLEMNLMHAPQVADAILGNQMFTHYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLEMNLMHAPQVADAILGNQMFTHYDR 27 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 232.02 1.12E-35 1298320000 696317 685967 644608 728720 809470 698620 854100 741460 425014 FALSE TRUE 663403.4754 755867.8172 674163.9144 655467.6811 950641.3117 674426.6142 723791.3584 676533.8317 490923.0004 1.351339161 1.539687113 1.373257952 1.335174112 1.936436693 1.373793067 1.47434803 1.378085425 1 18.90513724 -0.376911521 7.651654223 0.999993153 1.472209243 0.410896838 0.176946182 0 0 0.156569865 0.036903871 0.41984451 0.376911521 0.472216091 LLEPFEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEPFEVR 8 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ; 98.997 0.016579 23998000 43701 35994 40284 48568 53019 39731 47423 38828 46176 FALSE TRUE 41635.34034 39661.82952 42131.06125 43685.85237 62265.49681 38355.10551 40187.75037 35428.01448 53336.73825 0.780612795 0.74361183 0.789906969 0.819057442 1.167403536 0.719112319 0.753472216 0.664232865 1 15.70284198 3.301459128 3.880472847 0.841077247 0.763866617 0.065689298 0.14404993 0.746375338 22.4851055 0.04125343 0.055708923 2001.977202 -3.301459128 -0.07721063 LLEPPVLTLDPNDENLILEIPDEKEEAT(ph)SNSPSKESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEPPVLTLDPNDENLILEIPDEKEEATSNSPSKESK 37 2 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(0.326)S(0.326)NS(0.326)PS(0.019)KES(0.001)K 113.66 0.00047535 16082000 54814 43924 47315 59117 25341 67490 62743 68783 28812 TRUE FALSE 52223.05085 48399.90554 49484.43955 53174.44685 29760.46238 65152.80438 53170.403 62759.99588 33280.01781 1.569201409 1.454323306 1.48691145 1.597789014 0.894244184 1.95771543 1.597667504 1.885816175 1 15.02236859 LLEQALVIEEQLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 228.19 2.81E-12 201333000 278676 263157 253955 273578 286009 256413 289863 289583 294219 FALSE TRUE 265503.5378 289972.9975 265599.0879 246077.4197 335888.879 247533.3535 245639.0757 264225.5773 339844.9799 0.781248962 0.85325079 0.78153012 0.724087258 0.988359102 0.72837137 0.722797423 0.77748854 1 18.37451729 -2.229812742 2.27526156 1.686462863 0.794088278 0.400363125 0.0789801 8016817.703 1459760.183 28309111.18 0.018325567 0.005890976 2.229812742 -0.892374585 LLEQGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 206.51 0.00050334 5886477000 5251740 4407900 4129680 4651870 5827520 4276700 6041930 4911990 6191820 FALSE TRUE 5003500.658 4857070.021 4319029.913 4184255.19 6843837.643 4128596.807 5120122.611 4481870.116 7152015.822 0.699593063 0.679119026 0.603889871 0.585045572 0.956910305 0.577263377 0.715899229 0.626658305 1 22.7699185 -1.90955995 2.368261476 1.193844383 0.68253245 0.4596708 0.10882765 8748743.741 4428672.896 9427308.717 0.024498804 0.01231516 1.90955995 -0.511311933 LLEQWEKDDDIEEGDLPEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLEQWEKDDDIEEGDLPEHK 20 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 99.059 0.00042735 31379000 119020 129090 95463 133940 62237 127580 112650 130580 43732 FALSE TRUE 113394.1605 142244.4178 99840.07298 120476.0967 73091.1131 123161.8726 95463.17354 119145.723 50513.73521 2.244818365 2.815955248 1.976493573 2.385016595 1.446955225 2.438185814 1.889845864 2.358679723 1 15.6243881 -1.421501362 0.202087257 2.19E-15 2.542573208 0.498915775 0.371497915 18.88528267 0.710720464 11.48909619 0.961210869 0.037887735 1.421501362 2.542573208 LLESDYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLESDYFR 8 0 Q96HE7;G3V3E6;G3V503 Q96HE7 ERO1L ERO1-like protein alpha 0 77.282 0.078204 93231000 150400 124280 108940 115680 185620 101130 169730 133520 170860 FALSE TRUE 143290.8901 136944.2733 113935.0068 104051.6266 217992.0692 97627.84274 143834.5712 121828.281 197356.0962 0.726052515 0.693894316 0.577306751 0.527227832 1.104562126 0.494678627 0.728807339 0.617301838 1 17.59044156 -2.085488278 2.5851566 1.52137257 0.686567083 0.256854244 0.169004456 11560813.39 2864532.635 35733340.37 0.036983194 0.008213187 2.085488278 -0.834805487 LLESLQENHFQEDEQFLGAVMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLESLQENHFQEDEQFLGAVMPR 23 0 P49903;P49903-2;P49903-4;Q5T5U6 P49903 SEPHS1 "Selenide, water dikinase 1" 0 131.37 2.35E-05 37456000 30144 21306 24770 27979 26291 27587 36176 35250 26752 FALSE TRUE 28719.15286 23477.10562 25905.729 25166.49776 30876.14208 26631.65527 30656.68678 32163.32313 30900.56353 0.929405473 0.759763025 0.838357818 0.814434913 0.999209676 0.861850149 0.992107693 1.040865261 1 14.91534553 2.119066791 0.911069856 1.01974685 0.834761356 0.545477035 0.063252821 0.419696167 0.649110011 0.04780783 0.025067966 131.5427118 -2.119066791 -0.184985495 LLETTDRPDGHQNNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLETTDRPDGHQNNLR 16 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 203.2 1.71E-11 1628651000 2504050 2256270 2072190 2455530 2246850 2279920 2657710 2571200 2416610 FALSE TRUE 2385688.519 2486186.478 2167201.961 2208695.459 2638699.929 2200965.799 2252227.527 2346052.097 2791365.536 0.854667183 0.890670335 0.776394898 0.791259844 0.945307913 0.788490712 0.806855103 0.84046753 1 21.41253963 -1.358479079 6.554926433 1.000010087 0.838236733 0.496733835 0.051617364 7.41E-06 7.25E-07 0.048690253 0.011475687 0.043804721 1.358479079 -0.161773353 LLEVEHPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLEVEHPAAK 10 0 P17987;E7ERF2;F5H136;F5GZI8;F5H676;F5H726 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;; 140.16 3.98E-05 4437710000 9372850 8027910 8353490 9434850 8084410 8828930 10207410 9762390 8148340 FALSE TRUE 8929813.956 8845963.156 8736505.779 8486440.953 9494328.544 8523181.94 8650082.133 8907543.378 9411942.951 0.948774764 0.939865786 0.92823616 0.901667275 1.008753303 0.905570931 0.919053821 0.94640856 1 23.16606115 0.967781875 21.71308719 1.000000001 0.935704975 0.311791061 0.029672022 858.2623866 578419.5198 0.026315628 0.006578907 9.284999297 -0.967781875 -0.064295026 LLEVQGSRPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLEVQGSRPGK 11 1 P62136;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 127.17 0.00026643 2409500000 852460 777080 737130 958000 818930 843700 1002430 967710 933660 FALSE TRUE 812165.9052 856265.3355 770928.1396 861700.0199 961751.1327 814482.4574 849490.8926 882972.1822 1078447.224 0.753088224 0.793979822 0.714850131 0.799019183 0.891792487 0.755236268 0.787698158 0.818743989 1 20.04052415 -5 0.239572961 2.220239201 0.764833352 0.701353383 0.044234364 94.83067692 0.945640591 56.32187182 0.067581779 1.00E-05 5 -1.455405849 LLEVSDDPQVLAVAAHDVGEYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLEVSDDPQVLAVAAHDVGEYVR 23 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ;;;; 252.84 1.77E-43 300078000 365777.5 314887.2 328195.9 386202 396887 332835.7 425894 390190.1 386984 FALSE TRUE 348487.9225 346974.5637 343244.0066 347380.2412 466103.9671 321309.5163 360916.0482 356022.9863 446995.5023 0.779622884 0.776237259 0.76789141 0.777144825 1.042748674 0.718820468 0.807426577 0.796480019 1 18.76990079 -5 0.300006931 2.610441665 0.79434968 0.323129099 0.086823884 317.7373963 2.937419158 322.1002026 0.081513119 1.00E-05 5 -1.816091985 LLFEDWTYDDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LLFEDWTYDDFR 12 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ;;;;;;; 282.13 9.37E-28 331469400 559711 579704 531357 602029 574474 469825 612655 587726 578610 FALSE TRUE 533254.5703 638776.4967 555720.244 541511.9011 674662.0837 453554.8424 519183.2276 536261.5957 668337.8837 0.797881705 0.955768799 0.831495951 0.81023673 1.009462579 0.678631054 0.77682747 0.802380964 1 19.35021813 2.23044628 24.99999531 0.789635947 0.878151812 0.07272491 0.101871976 324.7023692 1000388.606 0.034015425 0.025557538 169.9989662 -2.23044628 0.088515865 LLFEVFDENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 152.28 4.26E-05 21355000 40620 34246 29348 37486 38917 26502 40371 38226 42074 FALSE TRUE 38699.9731 37735.70633 30693.63483 33717.83606 45704.11248 25584.22909 34211.66249 34878.72879 48598.62104 0.796318337 0.776476894 0.631574192 0.693802321 0.940440521 0.526439404 0.703963647 0.71768968 1 15.56862776 -0.685242768 12.27579391 0.999999999 0.724932433 0.395930452 0.107379384 0 0 0.098166246 0.023138006 0.206422595 0.685242768 -0.275067566 LLFGHSTEGDILELVDGHFDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLFGHSTEGDILELVDGHFDTK 22 0 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ;;; 348.88 3.31E-96 332758000 640634 564801 558441 675472 498066 613030 691362 680698 301473 FALSE TRUE 610352.5004 622354.864 584046.0722 607572.2712 584928.5527 591800.6174 585882.0292 621092.4745 348223.8931 1.752758821 1.787226196 1.67721424 1.744774794 1.679748473 1.699483089 1.682486586 1.783600973 1 18.40965567 -1.702316489 2.853630902 0.89729269 1.726284844 0.968464888 0.041166219 4682805.841 4500350.264 3475979.551 0.010308951 0.019846481 1.702316489 0.828992154 LLGELLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLGELLLDR 9 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 73.931 0.071971 0 21906 20688 20344 22989 23000 15294 23387 19613 21280 FALSE TRUE 20870.54679 22796.13072 21276.79252 20678.10204 27011.19272 14764.36495 19818.88362 17895.58174 24579.99372 0.849086742 0.927426222 0.865614238 0.841257418 1.098909667 0.600665937 0.806301411 0.728054773 1 14.58519693 2.231615759 24.99999945 0.765796689 0.906100304 0.220469723 0.121064294 213.974669 770256.1739 0.03957359 0.02986313 170.4573606 -2.231615759 0.140303615 LLGHWEEAAHDLALACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLGHWEEAAHDLALACK 17 0 P50502;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;; 195.54 9.72E-12 735782000 1686900 1623824 1410144 1738402 1301437 1581827 1727201 1711178 345186 FALSE TRUE 1607163.58 1789293.512 1474800.497 1563654.528 1528407.201 1527047.934 1463684.765 1561338.183 398715.6819 4.030851188 4.487642681 3.698877581 3.921728187 3.833326027 3.829916915 3.670998738 3.91591867 1 18.60500082 -0.946619585 0.437613735 1.02E-16 4.093495417 0.943929814 0.224070322 3.305822708 0.437291701 4.663247281 0.128346572 0.113078598 0.946619585 4.093495417 LLGIFENQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLGIFENQDR 10 0 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 96.331 0.01585 19266000 20427 20675 20375 22391 28238 16293 21673 21021 29301 FALSE TRUE 19461.45619 22781.80601 21309.2139 20140.21414 33162.69826 15728.76932 18366.3858 19180.2898 33844.84943 0.57501973 0.673124756 0.629614676 0.595074715 0.979844757 0.46473155 0.542664131 0.566712221 1 15.04664868 -1.844234144 3.486091484 1.107339041 0.625224032 0.422816032 0.136421192 0.079741111 0.003562999 0.092548648 0.029530385 0.01431416 1.844234144 -0.482115009 LLGLTPPEGGAGDRS(ph)EEEASSTEKPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLGLTPPEGGAGDRSEEEASSTEKPTK 27 2 V9GYY5;Q9UGY1 V9GYY5 NOL12 Nucleolar protein 12 1 LLGLTPPEGGAGDRS(1)EEEASSTEKPTK 117.88 0.00023564 72797000 67799 67419 73209 86266 49596 78388 89378 88173 53321 TRUE FALSE 64594.27563 74289.07275 76565.70506 77594.37779 58245.5267 75673.4039 75741.74456 80452.10469 61589.74835 1.048782912 1.206192179 1.243156647 1.259858659 0.945701651 1.228668828 1.229778439 1.306258052 1 15.91040261 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQAS(0.02)QDQDS(0.091)HT(0.016)LS(0.873)PQV;LLGPAPEDDGGHNDHSQPQASQDQDS(0.094)HT(0.29)LS(0.616)PQV 145.52 5.77E-10 166790000 164190 162610 170881 189074 172777 177555 203287 165618 40152 TRUE FALSE 156429.0641 179180.1439 178716.0629 170067.9223 202909.2541 171406.2258 172271.8345 151115.6099 46378.56709 3.372874021 3.86342561 3.853419243 3.66695077 4.375065182 3.695806847 3.714470828 3.258307003 1 15.50117063 0.630756841 1.635391992 1.0002999 3.794092873 0.925638709 0.247353525 0.374572128 1.345415903 0.23058385 0.065797768 4.273235633 -0.630756841 2.793792973 LLGPQWLDYDCDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLGPQWLDYDCDR 13 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ;;; 117.09 0.0012418 201933000 115799 111246 110347 121779 129454 95747 134584 117118 141261 FALSE TRUE 110325.4108 122582.0939 115406.5191 109537.5436 152030.7366 92431.25738 114050.739 106862.527 163167.0344 0.676150125 0.751267524 0.707290658 0.671321532 0.931749095 0.566482425 0.698981503 0.654927188 1 17.31599009 -1.229255887 3.992496347 1.00024227 0.708004213 0.496555754 0.092629065 43.37591124 44494228.48 19302.22422 0.019571001 0.058985343 1.229255887 -0.292238058 LLGSENDT(ph)GSPDFYTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.8)GS(0.2)PDFYTPR;LLGSENDT(0.5)GS(0.5)PDFYTPR 183.7 7.57E-09 93204000 141561 112536 119651 138190 133993 128871 148856 132506 155937 TRUE FALSE 134869.6921 124003.5463 125137.1167 124298.8787 157361.3368 124408.165 126145.2833 120903.0722 180118.9135 0.748781399 0.688453777 0.694747232 0.690093429 0.873652487 0.690700174 0.70034446 0.671240292 1 17.45859016 -1.459416184 5.528534003 1.000288496 0.718954679 0.69529971 0.058301555 0.000195789 1.91E-05 0.053311577 0.012552944 0.034720328 1.459416184 -0.281333817 LLGWDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLGWDDR 7 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ; 128.38 0.0087545 97563000 314820 306590 271230 429500 406210 301520 338840 316570 308640 FALSE TRUE 299939.0825 337831.8696 283666.1638 386325.844 477052.8954 291078.2868 287143.7348 288849.4526 356502.3149 0.841338387 0.947628824 0.795692347 1.08365592 1.3381481 0.816483581 0.805447041 0.810231632 1 18.44355192 4.039357163 0.002872556 1.624533644 0.22682332 0.000630762 0.17106191 1945622.399 1106.272719 264746.9811 273573.0862 10948.56404 -4.039357163 -1.397710323 LLGWIQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLGWIQNK 8 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 0 154.11 0.0010009 68520000 192040 145210 135390 151610 182180 150650 240740 137280 156460 FALSE TRUE 182962.6498 160007.0641 141597.7654 136369.8748 213952.1343 145432.9527 204010.6915 125259.0354 180723.0177 1.012392622 0.885371803 0.783507088 0.754579447 1.18386765 0.804728443 1.128858372 0.693099512 1 17.46342074 LLHDQIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLHDQIEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 ; 113.66 0.0028062 333570000 1194270 954320 1002210 1225640 910490 1097130 1266810 1182720 956600 FALSE TRUE 1137819.224 1051566.293 1048162.32 1102436.339 1069279.168 1059136.113 1073534.868 1079154.767 1104944.642 1.029752243 0.951691381 0.948610708 0.997729928 0.967721935 0.95854224 0.971573441 0.976659577 1 20.07554266 4.638961841 3.242843369 0.969954437 1.032307713 0.526533345 0.017217161 0.197856018 3.410597596 0.003873832 0.026721011 43547.36096 -4.638961841 0.062353276 LLHDQVGVIQFGPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLHDQVGVIQFGPYK 15 0 P53621;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 130.47 5.95E-05 259670000 715730 643170 486060 547470 604900 574520 787810 704070 640410 FALSE TRUE 681898.8613 708709.7542 508346.3318 492437.2755 710394.3685 554624.2283 667615.1154 642417.8983 739721.512 0.921831865 0.958076442 0.687213125 0.665706306 0.960353805 0.749774367 0.902522239 0.868459127 1 19.49662271 -0.695743925 6.974376621 0.999965222 0.848720702 0.178491005 0.106676784 0 1.11E-10 0.103707114 0.024444001 0.201491196 0.695743925 -0.15124452 LLHEDLDES(ph)DDDMDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 230.67 6.85E-15 128710000 262180 314240 233740 297570 152160 288330 280610 319360 154480 TRUE FALSE 249787.271 346261.4133 244457.2102 267657.6983 178696.6558 278345.0598 237797.7907 291395.1454 178435.9694 1.399870619 1.940535949 1.369999619 1.500020983 1.001460952 1.559915642 1.33267856 1.6330516 1 17.44504694 3.614018087 10.65544996 1.359362626 1.670051799 0.234583681 0.244729239 0.542325557 44.27776662 0.058859059 0.091203417 4111.668446 -3.614018087 0.310689174 LLHEVQELTTEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLHEVQELTTEVEK 14 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;;; 213.67 7.15E-10 297311000 577696 496933 499086 569525 412319 549541 599011 604638 417044 FALSE TRUE 550389.455 547571.0377 521969.5868 512275.265 484227.3031 530510.2574 507620.8704 551692.6913 481717.0536 1.142557547 1.136706773 1.083560532 1.063436017 1.005211046 1.101290173 1.053773925 1.145262945 1 18.87782647 3.656104069 2.784868779 1.063862446 1.141311377 0.368152786 0.041721658 0.254591838 3.847760221 0.010587349 0.018345184 4530.061194 -3.656104069 0.077448931 LLHHDDPEVLADTCWAISYLTDGPNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLHHDDPEVLADTCWAISYLTDGPNER 27 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 ;;; 270.58 5.60E-61 850143000 300914 310971 308911 346737 359675 294000 355364 322551 37935.3 FALSE TRUE 286690.3916 342659.2984 323074.8749 311882.338 422402.2061 283818.7063 301146.6951 294306.7245 43818.11258 6.542737117 7.82003784 7.373089709 7.117657965 9.639899605 6.477200627 6.872653279 6.716554118 1 15.41923972 0.132501967 0.837216342 0.897222128 7.496903504 0.840565064 0.873374011 1.483820597 1.134762417 1.210332522 0.269730487 1.356756677 -0.132501967 6.599681375 LLHIEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;;;;;;; 238.31 1.13E-08 1837145000 2485563 2146364 2204472 2537204 2602008 2219864 2665532 2463489 2392092 FALSE TRUE 2368075.363 2365080.932 2305549.222 2282159.434 3055797.371 2142989.553 2258856.138 2247772.843 2763045.41 0.85705264 0.855968897 0.83442321 0.82595799 1.105952642 0.775589697 0.817524073 0.813512813 1 21.39782784 -2.297837725 2.329131893 1.698018132 0.858707956 0.18977081 0.090338774 20232568.92 4653104.941 73534798.6 0.02142214 0.005036888 2.297837725 -0.839310176 LLHKLEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLHKLEHEVFDAGEVFGIMQVEEVEEEEDEAAR 33 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 198.48 4.25E-27 80942000 78498 52837 89140 73209 101300 72259 129790 86620 17719 FALSE TRUE 74787.55511 58221.15037 93227.15717 65849.89223 118966.6879 69756.65271 109988.1517 79035.0936 20466.77202 3.65409626 2.844666971 4.555049378 3.217404882 5.8126747 3.408287962 5.373986265 3.861629646 1 14.32099596 3.738040653 24.99906362 4.164022143 3.249381613 0.006850406 1.342975749 106.7946991 5134598.671 0.306462696 0.508327139 5470.671694 -3.738040653 -0.91464053 LLHKYPFILPHQQVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLHKYPFILPHQQVDK 16 1 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 154.69 2.14E-07 63819000 301260 252970 264670 255140 253010 277230 361320 313460 181890 FALSE TRUE 287020.0368 278747.9306 276805.3813 229492.8425 297134.8639 267629.4556 306193.9979 286011.7806 210096.5722 1.366133839 1.326760963 1.317514981 1.092320736 1.414277543 1.273840181 1.457396447 1.361334826 1 17.6806931 -1.075150327 4.711688384 0.999985467 1.331101494 0.524683655 0.097472806 1.42E-05 2.80E-06 0.090341975 0.021292874 0.084110395 1.075150327 0.331116027 LLHMDS(ph)DDEIPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 209.13 2.60E-08 99933000 140476 130466 137115 144129 156358 130452 154959 151754 146636 TRUE FALSE 133835.9779 143760.6337 143401.8584 129640.8791 183626.7857 125934.4145 131317.1585 138465.6153 169375.562 0.790172893 0.848768453 0.846650229 0.765404865 1.084139787 0.743521752 0.775301685 0.817506455 1 17.36986621 4.607897346 1.884739648 0.846773615 0.780285824 0.027264513 0.107031702 2.832046006 13.10818638 0.026050304 0.303407228 40541.2697 -4.607897346 -0.066487791 LLHSPHQNVCEQAVWALGNIIGDGPQCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLHSPHQNVCEQAVWALGNIIGDGPQCR 28 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 83.216 0.0024146 126600000 254690 223760 228940 285400 222220 240530 292320 260530 168230 FALSE TRUE 242651.3084 246561.3984 239437.1255 256711.0498 260975.0976 232200.3858 247721.2152 237716.612 194318.2492 1.248731447 1.26885354 1.232190628 1.321085646 1.343029277 1.194948939 1.274822186 1.223336527 1 17.56806187 0.260423646 0.947267009 0.998070897 1.271192214 0.804353099 0.041432307 1.36881876 1.405646464 0.043140159 0.012264522 1.821476807 -0.260423646 0.273121318 LLHVAVSDVNDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLHVAVSDVNDDVR 14 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 155.43 5.85E-06 103330000 55222 57285 48730 58816 58296 57975 55875 56085 47898 FALSE TRUE 52611.7655 63122.40663 50964.3187 52903.70394 68462.80394 55967.31121 47350.24254 51173.90007 55325.77721 0.950944897 1.140922185 0.921167696 0.956221613 1.237448571 1.011595571 0.855844146 0.924955828 1 15.75566419 1.938374269 8.376300682 0.916018031 1.044483273 0.21422568 0.099469755 0.484951651 61.58664192 0.04027646 0.025407942 86.77093339 -1.938374269 0.128465242 LLHYAGEVTYSVTGFLDKNNDLLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLHYAGEVTYSVTGFLDKNNDLLFR 25 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 267.55 8.09E-46 299990000 563320 461630 504380 562820 509330 499790 660980 673060 495290 FALSE TRUE 536692.98 508670.6218 527506.3219 506244.2643 598156.9907 482482.147 560135.3613 614123.2983 572097.0436 0.938115283 0.889133456 0.922057416 0.884892292 1.04555162 0.843357176 0.979091515 1.07346001 1 19.12590036 1.484013328 6.027663667 1.034485512 0.921145844 0.438426985 0.054661009 0.118662394 10.23995413 0.028439759 0.012348507 30.47988527 -1.484013328 -0.113339668 LLIDGDGAGDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLIDGDGAGDDRR 13 1 Q6I9Y2;H7C5E3 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 ; 102.57 0.0026926 177485000 229240 176307 192919 222670 279560 181530 259240 199481 285220 FALSE TRUE 218404.2795 194272.8837 201764.527 200286.7886 328315.1755 175243.5706 219688.1767 182013.3861 329450.4609 0.662935116 0.589687698 0.612427515 0.60794205 0.996554003 0.531926925 0.666832203 0.552475737 1 18.32970202 -1.224967481 3.48919847 1.000659699 0.651088098 0.415664797 0.129436787 131632398.8 213215405.5 991285.1405 0.028711221 0.059570675 1.224967481 -0.349571601 LLIEMEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLIEMEQR 8 0 P12277;H0YJG0 P12277 CKB Creatine kinase B-type 0 75.738 0.087503 16639000 35759 37848 26232 33662 29646 33536 35177 39249 34943 FALSE TRUE 34068.74294 41704.75423 27434.76315 30278.23181 34816.25301 32374.63991 29810.10258 35812.14949 40361.78198 0.844084212 1.033273364 0.679721306 0.750170838 0.862604457 0.802111263 0.738572509 0.887278701 1 15.30070225 3.745354788 24.99533312 0.800913488 0.93867878 0.189963539 0.099970354 641.4213627 2359742.562 0.023508545 0.041228347 5563.58578 -3.745354788 0.137765293 LLKEEDMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLKEEDMTK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 103.22 0.0031534 206090000 472670 500740 412720 563010 330030 470270 503070 540460 373310 FALSE TRUE 450327.8258 551765.9753 431643.6202 506415.1652 387587.1275 453984.432 426317.432 493134.4572 431201.0082 1.04435708 1.279602702 1.001026463 1.174429455 0.898854873 1.05283713 0.988674479 1.143630112 1 18.71800103 3.200973948 1.722759479 1.022057092 1.150400507 0.156461164 0.099924821 0.481735516 2.954621814 0.030168779 0.041464165 1588.45146 -3.200973948 0.128343416 LLKEEDMTKVEFETSEEVDVTPTFDTMGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLKEEDMTKVEFETSEEVDVTPTFDTMGLR 30 2 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 43.256 0.076273 30412000 42476 29000 45775 40518 28491 42339 49493 51450 31319 FALSE TRUE 40468.24366 31955.13297 47873.82903 36445.05366 33459.82138 40872.78981 41941.93385 46944.76525 36175.79056 1.118655405 0.883329223 1.323366491 1.007443185 0.924923018 1.129838192 1.159392323 1.297684571 1 15.14273692 2.016542543 24.54176599 1.163705763 1.043584199 0.104510788 0.137336014 355.5877881 527531.2132 0.048484493 0.035798355 103.8825359 -2.016542543 -0.120121564 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPT(0.002)VY(0.001)S(0.996)DEEEPKDES(0.001)AR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(0.999)DEEEPKDES(0.001)AR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(0.999)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR 295.25 6.27E-62 18447840000 9150930 6357450 8315380 11421070 6642090 10996580 12645400 10487830 6255480 TRUE FALSE 8718383.674 7005281.383 8696648.398 10273002.34 7800468.393 10615765.68 10716111.98 9569460.006 7225547.89 1.206605202 0.969515598 1.203597088 1.421761021 1.079567738 1.469198715 1.483086424 1.324392302 1 22.78467556 3.468743992 6.461999203 1.332007557 1.087188898 0.189350147 0.167294486 0.167908874 31.82922184 0.043617759 0.061610242 2942.686468 -3.468743992 -0.244818659 LLKEGEEPTVYS(ph)DEEEPKDESARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLKEGEEPTVYSDEEEPKDESARK 24 3 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPT(0.014)VYS(0.986)DEEEPKDESARK 120.37 0.0001262 177620000 128350 70416 112350 151100 74039 152920 171180 151050 234930 TRUE FALSE 122283.1499 77591.47046 117501.3586 135911.1409 86951.37816 147624.3421 145063.3471 137823.2612 271361.7445 0.450627814 0.28593371 0.43300635 0.500848567 0.320426073 0.544013093 0.534575525 0.507894956 1 18.04985782 -1.342338038 0.266375203 1.432016269 0.350684019 0.858773536 0.072776613 6.316912275 0.344043792 1.971987435 0.096399936 0.045463405 1.342338038 -1.08133225 LLKPGEEPSEYT(ph)DEEDTKDHNKQD ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LLKPGEEPSEYTDEEDTKDHNKQD 24 3 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPS(0.002)EYT(0.998)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPS(0.001)EYT(0.999)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPS(0.005)EYT(0.995)DEEDTKDHNKQD 245.11 4.69E-38 7450130000 2575990 1957142 2130988 3431866 1360374 3111545 3023805 2768265 930295 TRUE FALSE 2454228.058 2156576.995 2228695.908 3086888.31 1597622.795 3003791.416 2562468.011 2525861.041 1074560.397 2.283936821 2.006938838 2.074053644 2.872698749 1.486768728 2.795367691 2.384666341 2.350599415 1 20.03531514 LLLAADPGGS(ph)PAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLAADPGGSPAQR 14 0 Q5SQI0-7;Q5SQI0-6;Q5SQI0-5;Q5SQI0-4;Q5SQI0-3;Q5SQI0-2;Q5SQI0 Q5SQI0-7 ATAT1 Alpha-tubulin N-acetyltransferase 1 1 LLLAADPGGS(1)PAQR 82.362 0.011461 35420000 36779 30990 31912 38399 38316 35986 46401 40491 50451 TRUE FALSE 35040.52956 34147.91623 33375.19677 34539.05957 44998.29827 34739.7958 39321.67524 36945.39338 58274.68341 0.601299355 0.585982012 0.572722061 0.592694075 0.772175765 0.596138731 0.674764288 0.633987029 1 15.83058164 -5 0.224778241 2.96283908 0.580368667 0.820630263 0.055280397 59.43385749 0.59460837 52.88072705 0.093541393 1.00E-05 5 -2.382470413 LLLAEDS(ph)EEEVDFLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(1)EEEVDFLSER 358.02 5.35E-88 1728613400 1153350.1 1117492.7 1095439 1218004 1171827 1089114 1292404 1123899.6 1190180 TRUE FALSE 1098833.526 1231366.477 1145665.962 1095567.924 1376193.258 1051397.709 1095224.033 1025484.993 1374747.036 0.799298706 0.895704042 0.833364926 0.796923285 1.001051991 0.764793581 0.796673137 0.745944502 1 20.39073475 -1.567879959 8.684913396 1.000029648 0.832144041 0.349549761 0.073117263 3.95E-05 1.97E-06 0.066645207 0.015705657 0.027047059 1.567879959 -0.167885608 LLLAGYDDFNCNVWDALKADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLAGYDDFNCNVWDALKADR 21 1 P62873-2;P62873;B3KVK2 P62873-2 GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 132.14 1.10E-05 64432000 173620 121990 188610 143540 171280 158520 264610 195560 240530 FALSE TRUE 165413.3267 134420.9197 197257.9551 129111.0865 201151.1778 153030.4127 224238.8846 178435.7297 277830.1639 0.595375694 0.483824066 0.70999474 0.464712271 0.724007699 0.550805609 0.807107772 0.642247505 1 18.08384372 0.149417134 0.287025846 1.112240191 0.522375105 0.624672917 0.097780828 2.824228972 0.397037738 0.485515451 0.119713261 1.410643051 -0.149417134 -0.589865086 LLLAS(ph)PPNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLLASPPNER 10 0 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LLLAS(1)PPNER;LLLAS(1)PPNER;LLLAS(1)PPNER;LLLAS(1)PPNER;LLLAS(1)PPNER 132.14 0.00024278 228189000 341125 303535 332178 374832 394296 334673 417728 357549 430902 TRUE FALSE 325000.6973 334465.5616 347408.6899 337153.1752 463061.0976 323083.1901 353995.9215 326240.1141 497724.0814 0.652973624 0.671989912 0.697994537 0.677389718 0.930357029 0.649121074 0.711229243 0.655463793 1 18.92498667 -2.569600225 2.176041797 6.15013763 0.703304712 0.557363608 0.082363559 2421435.645 166950.6672 61682042.06 0.019032237 0.002694014 2.569600225 -5.446832918 LLLDIPLQT(ph)PHKLVDTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLDIPLQTPHKLVDTGR 18 1 P49792;J3KNE0;A6NKT7;O14715;Q99666;J3KQ37;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD8;RGPD5;RGPD1;RGPD2 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;RANBP2-like and GRIP domain-containing protein 2 1 LLLDIPLQT(1)PHKLVDTGR 146.06 1.27E-07 43736000 123430 104140 152880 133110 126830 153070 202340 157970 135710 TRUE FALSE 117595.7085 114751.9844 159889.6992 119729.5299 148949.1118 147769.1475 171469.3168 144137.3093 156755.2137 0.750186904 0.732045727 1.019996053 0.763799347 0.950201964 0.942674531 1.093866754 0.91950568 1 17.2581539 3.426612349 0.542968433 1.021251496 0.689027674 0.478329879 0.088566711 0.882910922 0.489841435 0.060727212 0.159230255 2670.621552 -3.426612349 -0.332223822 LLLEAQAATGFLLDPVKGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLLEAQAATGFLLDPVKGER 20 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 ; 166.29 1.41E-11 210899000 282956 282284 303757 299428 260110 287369 342361 311689 285771 FALSE TRUE 269581.2306 311049.0605 317684.5589 269328.9286 305473.1016 277417.3395 290127.5416 284395.8588 330086.9072 0.816697739 0.942324745 0.962427022 0.815933388 0.925432348 0.840437271 0.878942894 0.861578732 1 18.33248639 -0.850246289 4.658851111 1.000000519 0.882041612 0.357603282 0.050307938 5972677.361 1282006.605 31.4804633 0.010971973 0.141173672 0.850246289 -0.117958907 LLLEEIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLLEEIYR 8 0 Q9Y2P8;Q5VZU2;Q5VZU3;Q9Y2P8-2 Q9Y2P8 RCL1 RNA 3-terminal phosphate cyclase-like protein 0 ;; 98.299 0.017729 42965000 60610 49099 45842 57058 63159 43739 58624 56777 67559 FALSE TRUE 57745.08542 54102.24392 47943.90104 51322.42144 74173.9096 42224.30746 49679.8321 51805.30489 78035.70468 0.739982879 0.693301152 0.614384162 0.657678708 0.95051246 0.54108959 0.636629506 0.663866689 1 16.25184675 -1.558352205 2.80452906 1.018129238 0.685499669 0.458257052 0.106876375 13882936.11 14245547.71 1890205.765 0.024398103 0.027646986 1.558352205 -0.332629569 LLLEFTDTSYEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LLLEFTDTSYEEKR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;; 305.69 3.51E-44 3006112000 2161799 1868312 1986959 2101617 1644036 2163585 2322765 2324326 1729508 FALSE TRUE 2059615.046 2058695.117 2078063.036 1890358.466 1930755.358 2088659.509 1968384.539 2120795.693 1997711.268 1.03098735 1.030526859 1.040221913 0.946262104 0.96648369 1.045526219 0.985319836 1.06161272 1 20.92991665 -0.214827257 6.868678681 1.000000002 1.012748166 0.012628576 0.036785887 0 0 0.034198538 0.008060673 0.609779392 0.214827257 0.012748164 LLLEHLECLVSR ddPTM_SK-BR-3_Trastuzumab_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 ; 114.82 0.0010168 70780000 142564 112583 114119 138089 152332 113443 153340 129732 152040 FALSE TRUE 135825.2823 124055.3357 119351.469 124208.0314 178898.6526 109514.4405 129945.1667 118371.9783 175617.5867 0.773415037 0.706394718 0.679610005 0.707264197 1.018683014 0.62359609 0.739932538 0.674032599 1 17.4220778 -1.130574947 4.269823751 1.000040061 0.739599487 0.368824175 0.106736377 2.803469846 55840894.4 5645.925971 0.022966578 0.07403295 1.130574947 -0.260440575 LLLERPS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_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 132.06 0.00014152 4352566000 3988850 3655889 3213639 3935018 3654292 3436516 3644417 3667821 3517278 TRUE FALSE 3800304.966 4028428.246 3360987.527 3539462.515 4291599.368 3317508.589 3088394.252 3346647.149 4062719.508 0.935409141 0.99155953 0.827275307 0.871205238 1.056336614 0.816573377 0.760179049 0.823745558 1 21.95401433 2.135680774 22.53621528 0.822146348 0.935971382 0.162350653 0.087619278 6.980867091 1511.720735 0.030750508 0.022710769 136.6723853 -2.135680774 0.113825034 LLLERPS(ph)PIRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR 173.28 1.75E-05 15655137000 5246809 4351833 4643368 5119780 5598689 4596358 5662783 5062819 5875020 TRUE FALSE 4998802.737 4795289.73 4856271.016 4605129.987 6575098.589 4437184.97 4798821.449 4619491.729 6786088.096 0.736625087 0.706635349 0.71562157 0.678613352 0.968908522 0.653864923 0.707155784 0.680729702 1 22.69414873 -1.266919723 3.462643527 1.000783046 0.729151371 0.481296469 0.087736968 130044878.8 196008002.4 1072274.401 0.019523456 0.054085429 1.266919723 -0.271631674 LLLEVTYEAIVDGGINPDSLR ddPTM_SK-BR-3_Trastuzumab_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 0 222.25 9.30E-25 101800000 61036 67779 68394 76156 76469 62982 77689 70263 76827 FALSE TRUE 58150.94924 74685.75716 71529.93255 68500.65419 89805.16939 60800.91755 65836.11619 64110.39923 88740.93878 0.655288867 0.841615586 0.806053368 0.771917168 1.011992555 0.685150714 0.74189114 0.722444456 1 16.43731219 4.616967664 2.963886818 0.807046103 0.648139951 0.173979771 0.109597665 0.552725673 7.970151491 0.02512942 0.179703188 41396.88512 -4.616967664 -0.158906151 LLLIQAFRPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLLIQAFRPDR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 164.6 2.06E-05 246910000 699730 730570 587470 709970 775150 610300 791030 732890 770980 FALSE TRUE 666655.1496 805015.9136 614406.0806 638602.4667 910335.9146 589165.158 670343.8452 668714.2663 890539.6408 0.748596827 0.903964155 0.689925583 0.717096059 1.022229526 0.661582181 0.752738918 0.75090904 1 19.76432031 -1.139732393 4.191795026 1.000050087 0.784824575 0.292703086 0.10688998 14718429301 54135845899 13287354.83 0.024005408 0.072488249 1.139732393 -0.215225512 LLLPGELAK ddPTM_SK-BR-3_Trastuzumab_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 ;; 152.63 0.00018614 2365445000 8630870 7243830 7314070 8579740 6851990 7757380 9700160 8513410 7763140 FALSE TRUE 8222905.88 7981984.513 7649427.344 7717288.235 8046974.887 7488739.985 8220222.436 7767930.688 8967008.103 0.917017782 0.890150251 0.853063503 0.860631344 0.897397972 0.835143662 0.916718524 0.866278986 1 23.09619527 -1.042583679 4.448344352 1.0000055 0.882480473 0.663950518 0.026858542 3395831.442 795900.2193 213.8310397 0.006034114 0.090660126 1.042583679 -0.117525028 LLLPHAFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLPHAFSR 9 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 0 156.62 7.05E-05 126590000 117610 73383 68485 72578 138860 78492 139030 101920 135910 FALSE TRUE 112050.8084 80860.81113 71625.10499 65282.32155 163077.14 75773.80236 117818.42 92995.34449 156986.2287 0.713762024 0.515082194 0.45625088 0.415847442 1.038799017 0.482678022 0.750501627 0.592378996 1 17.26027848 2.799206591 24.99999953 0.732967899 0.54065835 0.297406304 0.182841271 358.747561 147885.0984 0.051398687 0.054516532 629.8057062 -2.799206591 -0.192309549 LLLPLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLPLFR 7 0 Q9BV86;Q9BV86-2 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 119.23 0.011231 10977000 46242 38541 47940 44936 55275 38653 63615 45656 48384 FALSE TRUE 44056.2323 42468.37172 50138.09642 40418.94791 64914.9425 37314.43692 53909.36338 41658.1186 55887.14361 0.788307104 0.759895192 0.897131132 0.723224436 1.161536237 0.667674791 0.964611177 0.745397169 1 15.77022882 6.151836808 0.032309045 1.500220701 1.31E-10 0.103400125 0.143506505 1661.444265 5.80330565 95.08463846 187.7981066 1418524.39 -6.151836808 -1.500220701 LLLPWLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLLPWLEAR 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 157.33 0.00016006 322820000 728770 590940 449600 568980 772990 424250 757970 622200 714540 FALSE TRUE 694322.4864 651157.4578 470214.6047 511785.0494 907799.2113 409558.1161 642327.7554 567716.8695 825347.2138 0.841248961 0.788949726 0.569717322 0.620084542 1.099899771 0.496225236 0.778251558 0.687852167 1 19.65464165 -1.276113633 6.364526956 1.000006399 0.740991759 0.199278381 0.166414036 1.37E-05 1.56E-06 0.146189786 0.034456412 0.052952488 1.276113633 -0.25901464 LLLSEEEIEKGVEIEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLLSEEEIEKGVEIEEK 17 1 Q9HAB8;Q9HAB8-2 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 99.891 0.0013399 21136000 30150 25274 27737 36395 23821 34425 35537 41782 26817 FALSE TRUE 28724.86925 27849.44933 29008.76889 32736.50545 27975.37486 33232.85362 30115.17797 38123.34658 30975.6434 0.927337292 0.899075734 0.936502545 1.056846666 0.903141042 1.072870487 0.972221225 1.230752372 1 14.91884663 2.489285662 0.680189644 1.078554615 0.912683469 0.337979669 0.082012497 0.774578922 0.729141804 0.059402101 0.047772071 308.5216618 -2.489285662 -0.165871146 LLLWSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLLWSQR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PQ28;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ; 132.53 0.0078173 141923000 399300 272930 164601 176906 524120 172069 426160 255230 437020 FALSE TRUE 380425.8803 300741.8773 172148.1187 159123.0728 615526.3621 166110.2074 361141.465 232880.7081 504790.8296 0.753630728 0.595775239 0.341028617 0.31522576 1.219369145 0.329067403 0.715427943 0.461341004 1 18.94532618 LLMHGK ddPTM_SK-BR-3_Trastuzumab_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 ;; 88.626 0.051089 7452500000 12436400 10522800 9815900 11684400 10792100 10916900 13777900 12281100 10890500 FALSE TRUE 11848556.02 11595085.28 10265968.72 10509861.91 12674238.82 10538845.02 11675828.31 11205701.78 12579343.12 0.941905782 0.921756023 0.816097361 0.835485749 1.007543773 0.837789773 0.928174722 0.890801823 1 23.58455325 -1.348662644 2.710718858 1.001689769 0.90066647 0.237332602 0.057519237 8680750.204 9808550.751 117380.4874 0.013584579 0.044806122 1.348662644 -0.101023299 LLNEVMVEHFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLNEVMVEHFFR 12 0 Q9H871 Q9H871 RMND5A Protein RMD5 homolog A 0 117.7 0.00070489 19198000 74796 58276 52087 57146 74043 53447 79871 63591 70941 FALSE TRUE 71260.54131 64214.39065 54475.24047 51401.57551 86956.07576 51596.11699 67685.21202 58022.63492 81942.16796 0.869644325 0.783655012 0.664801064 0.62729089 1.061188371 0.629665022 0.826011975 0.708092504 1 16.32231844 LLNIWQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLNIWQER 8 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 118.32 0.0044398 552060000 855420 668680 630470 717790 1009500 647450 952620 784030 952800 FALSE TRUE 814985.9919 736819.2522 659377.6731 645636.3855 1185556.48 625028.6442 807280.3229 715376.1768 1100555.358 0.740522488 0.669497674 0.599131764 0.586645988 1.077234754 0.567921132 0.733520869 0.650013806 1 20.06980028 LLNNGDKWEAEIAANIQADYLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLNNGDKWEAEIAANIQADYLYR 23 1 O00217;Q08E91 O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" 0 ; 105.32 0.0014147 24404300 48910 37264 43153 40654 35148 35909 39346 44134 39378 FALSE TRUE 46598.12123 41061.24397 45131.60773 36567.38268 41277.80007 34665.46233 33343.04506 40269.39299 45484.53913 1.024482651 0.902751677 0.99224063 0.803951923 0.90751277 0.762137267 0.733063272 0.885342443 1 15.47308861 3.237229052 24.99999177 0.825427256 0.965403241 0.308054357 0.082957337 34.46796025 647136.178 0.022473581 0.02829396 1726.748357 -3.237229052 0.139975985 LLNTWTNRYPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLNTWTNRYPDAK 13 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 186.68 6.94E-06 465290000 832430 655010 822680 930770 862360 1010210 1239970 965410 1035480 FALSE TRUE 793082.6836 721756.2637 860400.6917 837207.2313 1012755.311 975226.1744 1050789.803 880873.5824 1196056.95 0.663081038 0.603446403 0.719364318 0.699972716 0.846745058 0.815367675 0.878544958 0.736481304 1 20.18985465 2.847977334 0.199066578 1.03900526 0.454822384 0.727402158 0.060356264 2.692377127 0.244140217 0.182439809 0.463840371 704.6562925 -2.847977334 -0.584182876 LLPAPS(ph)FSLDDMDVDKDPGGMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLPAPSFSLDDMDVDKDPGGMLR 23 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 LLPAPS(0.941)FS(0.059)LDDMDVDKDPGGMLR;LLPAPS(0.853)FS(0.147)LDDMDVDKDPGGMLR;LLPAPS(0.948)FS(0.052)LDDMDVDKDPGGMLR;LLPAPS(0.964)FS(0.036)LDDMDVDKDPGGMLR 98.299 0.0017946 182008000 280159 238049 217635 360700 240817 325198 340988 268842 223838 TRUE FALSE 266916.4393 262306.4637 227613.78 324441.7507 282815.4086 313936.3117 288964.0179 245300.7693 258549.6538 1.032360459 1.014530323 0.880348423 1.254852775 1.093853364 1.214220584 1.117634519 0.948756905 1 17.98008185 3.245551895 24.99999606 1.118055682 0.992144995 0.268669212 0.097617857 204.438351 731042.8211 0.025478519 0.033766816 1760.158975 -3.245551895 -0.125910687 LLPDGAADGSFYLHS(ph)PEGPSKPSLASPYLPEGTSKPLSDRPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLPDGAADGSFYLHSPEGPSKPSLASPYLPEGTSKPLSDRPTK 43 3 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 LLPDGAADGSFY(0.002)LHS(0.854)PEGPS(0.094)KPS(0.017)LAS(0.032)PY(0.001)LPEGTSKPLSDRPTK;LLPDGAADGSFYLHS(1)PEGPSKPSLASPYLPEGTSKPLSDRPTK 279.84 3.27E-81 805850000 1042280 861920 850720 1136610 587070 1008220 1062440 1028970 474700 TRUE FALSE 993013.49 949750.6279 889726.3535 1022355.803 689454.8221 973305.0886 900345.265 938867.9319 548314.0516 1.811030535 1.732128924 1.622658312 1.864544234 1.257408633 1.775086897 1.642024789 1.712281364 1 19.06464292 -2.470820327 0.32553382 4.09E-16 1.725042318 0.619912554 0.166300155 32.49854182 1.258561243 23.48667069 0.134121957 0.003382047 2.470820327 1.725042318 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEET(0.006)LES(0.994)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK 380.68 2.09E-113 3355990000 2894055 2479618 2489781 3084331 1636479 3066565 3206778 3620027 1810917 TRUE FALSE 2757258.756 2732293.893 2603939.922 2774288.188 1921880.419 2960369.085 2717525.12 3303038.245 2091744.759 1.318162143 1.306227197 1.244865039 1.326303401 0.918792989 1.415263058 1.299166692 1.579082835 1 20.99627539 LLPEKHEIENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLPEKHEIENLR 12 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 220.69 1.74E-11 147385000 378960 315650 359200 430680 362650 387340 469750 439050 381720 FALSE TRUE 361047.3118 347815.0939 375669.6753 387387.2282 425896.0452 373926.3187 398081.0099 400604.4544 440915.188 0.818858868 0.788848067 0.852022533 0.878598058 0.965936436 0.848068583 0.902851661 0.908574858 1 18.75014165 7.999999894 0.076949595 1.117195136 0.250135986 0.664344991 0.037027674 117.0009437 0.658840804 1.169946071 10.83570601 99999975.63 -7.999999894 -0.86705915 LLPERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLPERK 6 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;H7C1P9;Q9NQZ7;P31689 A0A0A0MTS7;P31689 TTN;ENTPD7;DNAJA1 Titin;Ectonucleoside triphosphate diphosphohydrolase 7;DnaJ homolog subfamily A member 1 0 88.591 0.081983 184730000 180280 145980 195400 165100 175870 173700 234630 219090 201970 FALSE TRUE 171758.5217 160855.528 204359.2833 148503.8343 206541.6723 167684.7254 198832.8842 199905.3181 233290.4761 0.736243179 0.689507479 0.875986396 0.636561924 0.88534121 0.718780845 0.852297477 0.856894467 1 17.83176789 0.520142257 0.288666029 1.056291326 0.705474623 0.51227444 0.076614526 2.434724866 0.451071785 0.269640621 0.099018662 3.312396041 -0.520142257 -0.350816703 LLPGPENHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLPGPENHR 9 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 120.99 0.00062649 177700000 140290 131960 125910 121680 158890 130230 173740 164300 173250 FALSE TRUE 133658.7697 145406.874 131683.098 109448.4952 186600.3657 125720.1024 147232.772 149913.021 200116.7252 0.667904043 0.726610302 0.658031446 0.546923278 0.932457622 0.628233859 0.735734467 0.749127895 1 17.61048222 -5 0.231730715 2.632092261 0.670362401 0.49233053 0.096935825 131.1643416 1.311361295 100.2466428 0.147711085 1.00E-05 5 -1.96172986 LLPLEEHYR ddPTM_SK-BR-3_Trastuzumab_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 ; 160.59 6.52E-05 200102000 141356 98820 76265 95571 166353 90064 155595 128994 138093 FALSE TRUE 134674.382 108889.8703 79761.82569 85964.02151 195364.9105 86945.0611 131856.1251 117698.6015 159507.7572 0.84431243 0.682661911 0.500049823 0.538933172 1.224798806 0.545083591 0.826643966 0.73788638 1 17.28326706 LLPPYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLPPYLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 101.72 0.020588 142705000 209416 179729 181268 214039 214552 181096 231590 206890 200411 FALSE TRUE 199517.3207 198043.5894 189579.3171 192523.3931 251969.8009 174824.6001 196256.6921 188773.6148 231489.7143 0.861884172 0.855517879 0.818953523 0.831671479 1.088470827 0.755215413 0.847798757 0.815473013 1 17.82058857 -2.456885055 2.19614149 2.426207923 0.858519252 0.205778012 0.086810076 2471859.154 283558.813 17744352.52 0.019456933 0.003492327 2.456885055 -1.567688672 LLPQFLLHLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLPQFLLHLDK 11 0 Q5T8U9;Q8N4J0;Q5T8V1 Q5T8U9 C9orf41 UPF0586 protein C9orf41 0 128.67 0.0011709 0 137350 121890 81677 89839 118580 92752 149510 124760 105850 FALSE TRUE 130857.7377 134310.7296 85421.97124 80808.21304 139260.3145 89539.97498 126699.5036 113835.353 122264.6774 1.070282444 1.098524385 0.698664349 0.660928526 1.139006927 0.732345407 1.036272342 0.931056749 1 16.89964814 3.788171782 24.94588897 0.887844416 1.084403587 0.225405023 0.153267497 486.6637579 244706.5265 0.037325985 0.067290219 6140.048218 -3.788171782 0.196559171 LLPQGTVIFEDISIEHFEGTVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLPQGTVIFEDISIEHFEGTVTK 23 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 183.01 3.77E-17 69538000 86696 74721 89378 96891 85973 85174 114212 98360 83851 FALSE TRUE 82598.05189 82335.15485 93476.06971 87151.3326 100966.664 82224.40302 96786.86175 89747.07696 96854.18483 0.852808292 0.850093932 0.96512164 0.89982 1.042460521 0.848950442 0.999304903 0.926620539 1 16.56352676 3.742650068 24.155518 0.952338562 0.8514511 0.380659296 0.054645554 185.1164599 1093435.024 0.012282863 0.021156013 5529.044276 -3.742650068 -0.100887463 LLPQLTYLDGYDRDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLPQLTYLDGYDRDDK 16 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;; 95.157 0.0035094 225915000 310621 359970 290970 338994 219658 352684 324999 363615 227554 FALSE TRUE 295938.5609 396651.3523 304311.2623 304917.6791 257966.2857 340470.4646 275414.4335 331774.943 262841.9121 1.12591846 1.509087151 1.157772974 1.160080128 0.981450346 1.295343128 1.047833016 1.262260422 1 18.00383582 3.50868161 23.94879148 1.129283375 1.320157431 0.253334373 0.135332245 450.420764 341789.0195 0.032556431 0.050368711 3226.128117 -3.50868161 0.190874056 LLPS(ph)PVTCTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLPSPVTCTPK 11 0 H0YCH4;Q9BU19-2;Q9BU19;Q9BU19-5 H0YCH4 ZNF692 Zinc finger protein 692 1 LLPS(0.964)PVT(0.03)CT(0.005)PK;LLPS(1)PVTCTPK 89.301 0.012939 259527000 833900 683000 725240 819840 596420 794580 880820 849890 698400 TRUE FALSE 794483.1996 752598.4765 758492.9714 737428.1256 700435.4592 767063.4954 746434.7316 775469.126 806704.3051 0.984850576 0.932929788 0.940236672 0.914124446 0.868267908 0.950860793 0.925289139 0.96128051 1 19.62168043 -0.760163267 5.218749273 1.000000022 0.935115363 0.309574233 0.030628391 7.96E-09 1.86E-09 0.02967574 0.006994637 0.173714765 0.760163267 -0.064884659 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR 285.76 4.89E-40 1549952000 513383 555853 464978 560281 474916 440044 416174 452227 392760 TRUE FALSE 489116.403 612495.0527 486297.7012 503960.4894 557741.2 424805.1659 352679.0127 412627.6065 453667.2149 1.078139189 1.350097676 1.07192604 1.110859398 1.229406009 0.936380572 0.777395856 0.909538078 1 18.79127488 2.141371996 4.853240804 0.868366447 1.177397975 0.635406027 0.097912707 0.114704045 4.532103943 0.036387968 0.026550615 138.4751983 -2.141371996 0.309031527 LLPYPTLAS(ph)PASD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.996)PAS(0.004)D 104.17 0.0016291 8240900 20595 16593 22759 21793 20529 16801 23882 19456 22961 TRUE FALSE 19621.51517 18283.84556 23802.52266 19602.32624 24109.2511 16219.17716 20238.36228 17752.3295 26521.67461 0.739829421 0.689392575 0.897474349 0.739105902 0.909039548 0.611544233 0.763087647 0.669351757 1 14.69488425 -2.092597131 2.558593692 1.432673743 0.749304671 0.414772303 0.092383932 10742996.09 4633013.52 26973909.03 0.021044843 0.008079842 2.092597131 -0.683369072 LLPYPTLASPAS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.004)PAS(0.996)D;LLPYPTLASPAS(1)D;LLPYPTLASPAS(1)D 215.04 3.13E-11 53475000 142171 139511 143498 159579 161097 136473 159681 147332 172712 TRUE FALSE 135450.8586 153727.3295 150077.5252 143537.8157 189192.2658 131746.9058 135318.7307 134430.829 199495.2949 0.678967685 0.770581229 0.752286039 0.719504767 0.948354526 0.660401068 0.678305375 0.673854635 1 17.6059952 -1.826806022 2.623149682 1.093442671 0.733970983 0.497125726 0.083663253 10140690.88 6804287.197 5975693.425 0.020747909 0.014900265 1.826806022 -0.359471689 LLQAFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLQAFLER 8 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 124.08 0.0030711 170566000 501090 429180 302300 360810 560590 365750 545240 428130 522850 FALSE TRUE 477404.4688 472913.9299 316160.754 324540.6933 658356.7185 353083.9858 462053.624 390640.6675 603930.9077 0.790495175 0.783059658 0.523504841 0.5373805 1.090119267 0.584643013 0.765076962 0.646830064 1 19.20402398 LLQDFFNGK ddPTM_SK-BR-3_Trastuzumab_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 ; 206.78 2.97E-05 1288360000 1404630 1253010 1247780 1455090 1190100 1331640 1624000 1463890 1349000 FALSE TRUE 1338235.924 1380693.144 1304991.947 1308821.589 1397653.063 1285524.973 1376228.973 1335704.031 1558196.03 0.858836692 0.886084367 0.837501779 0.839959519 0.896968697 0.825008502 0.883219407 0.857211805 1 20.57144531 -1.219728865 0.802229124 1.032644364 0.862030524 0.783984483 0.022978119 40.8062445 10.65020006 3.083682612 0.006886719 0.060293589 1.219728865 -0.17061384 LLQDFFNGKELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQDFFNGKELNK 13 1 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 0 150.22 4.03E-05 51684000 155270 61784 210570 90044 283800 148250 432670 207040 498730 FALSE TRUE 147930.6948 68079.85984 220224.8428 80992.60605 333294.6301 143116.0653 366658.245 188910.48 576070.5012 0.256792692 0.118179736 0.382288005 0.140594955 0.578565695 0.248434983 0.636481549 0.327929445 1 19.13588586 -3.403111587 0.132682743 2.519196835 2.68E-14 0.68607942 0.149715809 41.36929837 0.520128773 18.29078436 1.012006902 0.000395265 3.403111587 -2.519196835 LLQDFFNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 252.81 1.62E-14 1608770000 2215610 1799610 1807663 2238140 2326440 1846497 2499890 2152810 2503720 FALSE TRUE 2110882.506 1982992.305 1890546.137 2013157.915 2732170.399 1782552.346 2118485.867 1964298.544 2891984.11 0.729908058 0.685685754 0.653719407 0.69611652 0.944739077 0.61637695 0.732537174 0.679221762 1 21.46362819 -1.629748748 3.80643415 1.011058975 0.71617419 0.506342988 0.087721592 0.007753 0.000754133 0.079987269 0.018317516 0.023455854 1.629748748 -0.294884784 LLQDHPWLLSQNLVVKPDQLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQDHPWLLSQNLVVKPDQLIK 22 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 242.16 6.41E-31 422800000 663970 583500 586600 659930 436670 676020 736890 691840 476080 FALSE TRUE 632585.454 642959.3134 613496.1902 593592.5826 512825.1097 652609.2579 624463.8966 631258.8219 549908.0549 1.150347678 1.169212394 1.115634122 1.079439694 0.93256519 1.186760681 1.135578741 1.147935216 1 19.06883089 0.6108783 0.01195164 2.85E-05 2.165770191 0.148791545 0.073477379 3069.104563 17.19297867 1597.126415 1515.895987 4.082049812 -0.6108783 2.16574167 LLQDLQLGDEEDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQDLQLGDEEDAR 14 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 79.466 0.044222 14451000 32166 29179 34365 36414 29604 27439 40253 35493 34701 FALSE TRUE 30645.57693 32152.37327 35940.66924 32753.59554 34766.92823 26488.78055 34111.66555 32385.04476 40082.25385 0.764567208 0.802159813 0.896672861 0.817159525 0.867389552 0.660860556 0.851041603 0.807964664 1 15.29067601 0.305623876 1.74010929 1.000001818 0.805553543 0.468504832 0.064065264 7.981402539 18.87920252 0.057301682 0.016079604 2.021267885 -0.305623876 -0.194448275 LLQDS(ph)SSPVDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.478)S(0.313)S(0.209)PVDLAK 89.013 0.008019 18744000 75358 69216 71920 82147 60416 76195 86132 95111 79988 TRUE FALSE 71795.97669 76269.18909 75217.60314 73889.42749 70952.53127 73556.34804 72990.98148 86782.57662 92392.13052 0.777078917 0.82549443 0.81411266 0.79973724 0.767949942 0.796132177 0.79001297 0.939285371 1 16.49548236 1.127261321 3.583263662 0.997491286 0.796440688 0.947549402 0.017282719 0.045141884 1.023496945 0.016818833 0.004418831 13.40483031 -1.127261321 -0.201050598 LLQDSS(ph)SPVDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.206)S(0.397)S(0.397)PVDLAK 158.81 4.89E-05 31735000 102170 96121 91023 113360 79928 110270 110420 119460 100140 TRUE FALSE 97340.62658 105915.8392 95196.49458 101964.8374 93867.41789 106451.3223 93573.401 108999.4491 115669.1998 0.841543183 0.915678845 0.823006425 0.881521076 0.8115161 0.92030828 0.808974223 0.942337712 1 16.81964523 1.028345733 5.630051085 0.99976875 0.861176694 0.607684579 0.039381667 0.089762305 7.975245667 0.03325176 0.008378004 10.67445555 -1.028345733 -0.138592055 LLQEALEAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLQEALEAEER 11 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;B3KPU0;H0YBP7;E5RGS7;H7C1D1;A0A087WUQ1 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 0 ;;; 162.26 5.89E-05 130099000 134715 110876 112401 125841 136628 110554 146007 131883 148051 FALSE TRUE 128347.2889 122174.3905 117554.697 113191.2236 160455.8799 106725.4873 123730.9505 120334.6254 171009.9929 0.750525082 0.71442837 0.687414197 0.6618983 0.938283648 0.624089186 0.723530528 0.703670138 1 17.38372111 -1.496000868 2.911672235 1.009359244 0.724678051 0.518145638 0.083193975 13218344.24 14789947.59 992328.3782 0.017854916 0.031915315 1.496000868 -0.284681193 LLQEALEAEERGGT(ph)PAFLPSSLSPQSSLPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQEALEAEERGGTPAFLPSSLSPQSSLPASR 32 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 LLQEALEAEERGGT(1)PAFLPSSLSPQSSLPASR 175.3 1.09E-14 77545000 33790 14200 33242 24222 43017 28834 46906 33686 61217 TRUE FALSE 32192.81367 15646.99614 34766.17858 21787.15854 50519.15118 27835.47135 39749.62821 30736.27526 70710.21971 0.455278088 0.221283376 0.4916712 0.308118948 0.714453319 0.393655563 0.562148278 0.434679391 1 16.10963112 -5 0.169492506 3.214588467 0.300382083 0.648675101 0.129749399 73.37643759 0.691231436 54.48067981 0.421807442 1.00E-05 5 -2.914206384 LLQETELVEPLT(ph)PSGAMPNQAQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.975)PS(0.025)GAMPNQAQMR 92.822 0.030881 22670000 20671 17938 18952 27584 33051 16361 22974 15583 22367 TRUE FALSE 19693.9228 19765.90259 19820.96795 24811.20391 38815.08394 15794.41447 19468.89435 14218.46991 25835.56013 0.762279691 0.765065766 0.767197144 0.960350919 1.502389875 0.611343992 0.753569664 0.550344945 1 14.65707054 -2.394993731 2.147151963 2.200666895 0.82967393 0.038115914 0.261135833 11363298.42 1273788.617 66174553.82 0.061885435 0.004027228 2.394993731 -1.370992965 LLQHGINADDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLQHGINADDKR 12 1 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 187.44 6.80E-06 782490000 1400790 1261130 1200360 1438860 974320 1430070 1481070 1478740 1053350 FALSE TRUE 1334577.433 1389640.581 1255397.693 1294223.059 1144241.1 1380546.317 1255105.57 1349253.686 1216698.138 1.096884585 1.142140797 1.031807031 1.063717465 0.94044781 1.134666253 1.031566935 1.108946947 1 20.21453985 3.734922854 24.96471596 1.046866896 1.119512692 0.245207106 0.054623033 372.1721655 2554092.723 0.013016415 0.021093662 5431.538396 -3.734922854 0.072645796 LLQHHITEQLQDIVDILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQHHITEQLQDIVDILK 18 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 0 59.434 0.043817 9357700 56468 54321 62748 65340 54277 55164 74717 62656 22642 FALSE TRUE 53798.86955 59856.37166 65625.05787 58771.89906 63742.89162 53253.65685 63317.54938 57169.50848 26153.20572 2.057065972 2.288682018 2.509254834 2.247215874 2.437287891 2.036219094 2.421024407 2.185946499 1 14.67470017 0.949649165 22.03179149 0.999999999 2.278147759 0.874623164 0.15188599 1069.511829 467982.4887 0.137426115 0.034356529 8.905312514 -0.949649165 1.278147759 LLQIIDRDGEEEEEEEEPLDESSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLQIIDRDGEEEEEEEEPLDESSVK 25 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 172.49 5.26E-12 21400000 24542 24458 21208 27482 19806 24074 24853 26113 22338 FALSE TRUE 23381.9483 26950.29801 22180.40778 24719.45715 23260.16013 23240.31134 21061.21839 23826.40729 25802.06295 0.906204606 1.044501676 0.859636992 0.95804189 0.901484512 0.900715241 0.816261027 0.923430321 1 14.6551988 3.723630492 24.87787559 0.897306223 0.975353148 0.157423519 0.06008949 940.8985921 1567807.286 0.015248488 0.023728319 5292.12986 -3.723630492 0.078046926 LLQLVEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLQLVEDR 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 199.29 0.00030037 656866000 811280 772530 741390 828750 938720 763860 942850 864470 1030940 FALSE TRUE 772932.4022 851251.6853 775383.4648 745442.4755 1102432.471 737407.3367 799000.9159 788772.424 1190812.91 0.649079629 0.714849225 0.65113794 0.62599462 0.925781423 0.619247012 0.670970989 0.662381485 1 20.18351534 -1.188067366 5.025742166 1.00002582 0.689173497 0.551033423 0.087956557 2.32E-05 3.76E-06 0.077811891 0.018338917 0.064853383 1.188067366 -0.310852323 LLQTCFS(ph)SPADDSMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQT(0.001)CFS(0.823)S(0.177)PADDSMDR;LLQT(0.011)CFS(0.494)S(0.494)PADDSMDR;LLQT(0.036)CFS(0.482)S(0.482)PADDSMDR 198.85 4.16E-11 159382000 480098 356870 421138 492340 493571 417449 515931 436032 513470 TRUE FALSE 457404.719 393235.4587 440447.5939 442849.0478 579649.6261 402992.6365 437216.2502 397850.7265 593096.3052 0.771214919 0.663021259 0.742624073 0.746673085 0.977328001 0.679472512 0.737175812 0.670802909 1 19.17790686 -1.724986091 2.847250292 1.041993235 0.745144577 0.44060047 0.088972367 34448295.43 31299206.25 10315232.55 0.021186302 0.018837094 1.724986091 -0.296848658 LLQTCFSS(ph)PADDSMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFS(0.245)S(0.755)PADDSMDR;LLQTCFS(0.05)S(0.95)PADDSMDR;LLQTCFS(0.105)S(0.895)PADDSMDR 250.26 9.15E-21 285369000 438460 340244 375008 422720 446990 380585 476400 412970 453470 TRUE FALSE 417734.8647 374915.2504 392202.4877 380227.3825 524944.9145 367405.246 403716.4303 376808.1575 523791.8116 0.7975208 0.7157715 0.748775523 0.725913185 1.002201453 0.701433734 0.77075743 0.719385353 1 18.99863398 -1.399264084 2.965925554 1.003788261 0.770654648 0.405570068 0.086441024 18661642.22 22264430.16 599832.0399 0.020136803 0.039878234 1.399264084 -0.233133613 LLRDDEAHLQEDQGEEECFHDCS(ph)ASFEEEPGADKVENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLRDDEAHLQEDQGEEECFHDCSASFEEEPGADKVENK 38 2 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 1 LLRDDEAHLQEDQGEEECFHDCS(0.5)AS(0.5)FEEEPGADKVENK 142.77 2.04E-13 48908000 40417 30925 36035 43172 23616 46742 53198 42897 30490 TRUE FALSE 38506.56851 34076.29266 37687.24039 38832.26854 27734.62292 45123.31282 45081.66805 39140.71127 35218.23348 1.093370243 0.967575295 1.070105927 1.102618295 0.787507498 1.281248614 1.280066136 1.111376336 1 15.10403493 2.201034192 24.99999933 1.204204529 1.014805015 0.288901083 0.121492702 169.3382563 112811.7341 0.041802747 0.030874065 158.8671819 -2.201034192 -0.189399514 LLREELQLLQEQGSYVGEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLREELQLLQEQGSYVGEVVR 21 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;; 248.46 1.49E-30 127576300 133522 87772.6 117985 132969.7 154633 102606 175364 124185 183758 FALSE TRUE 127210.6797 96716.72773 123394.729 119603.3331 181600.9462 99052.72849 148609.001 113310.7031 212254.2521 0.599331596 0.4556645 0.58135339 0.56349087 0.855582135 0.466670173 0.700146167 0.533844208 1 17.69543393 -5 0.216501369 3.02810883 0.535776592 0.539536982 0.116643377 107.9541823 1.078606035 95.39464042 0.20992933 1.00E-05 5 -2.492332238 LLRPNS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLRPNSLR 8 1 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 LLRPNS(1)LR 74.841 0.032651 0 42762 33421 31301 41609 43940 36238 42490 37579 50576 TRUE FALSE 40740.72501 36826.6379 32736.18181 37426.38427 51603.12209 34983.06897 36007.37012 34288.38354 58419.06777 0.697387455 0.630387291 0.560368097 0.640653569 0.883326695 0.598829634 0.616363312 0.586938218 1 15.83415172 -1.361829817 3.397605244 1.002357689 0.651450019 0.596545865 0.089996861 32168785.02 39490520.87 731852.5124 0.021003205 0.043468053 1.361829817 -0.35090767 LLRQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLRQEK 6 1 P53597;A0A494C0D1 P53597 SUCLG1 "Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial" 0 69.093 0.086104 190900000 386120 339400 465880 558570 658660 540120 742300 640340 834910 FALSE TRUE 367868.8728 373985.2459 487241.0588 502421.4824 773530.0955 521415.509 629048.5017 584268.4349 964383.5787 0.381454932 0.387797194 0.505235748 0.520976812 0.802097954 0.540672322 0.652280395 0.60584652 1 19.87924756 0.287093271 0.103756379 1.538977264 4.86E-13 0.770000283 0.089742558 10.99009542 0.446986587 4.076202985 2.281779604 1.936837885 -0.287093271 -1.538977264 LLS(ph)AACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSAACR 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 1 LLS(1)AACR 70.256 0.060337 34167000 72356 65164 63011 74385 67727 68645 88582 72435 81522 TRUE FALSE 68935.87528 71804.28569 65900.11668 66907.67848 79538.56736 66267.80644 75067.18898 66092.2074 94164.0154 0.732083004 0.762544857 0.699843952 0.710544025 0.844681134 0.703748732 0.797196133 0.701883911 1 16.52288822 -1.449108313 3.147916142 1.004654432 0.74758501 0.743862859 0.047157518 29450491.79 36988957.79 1212058.137 0.010105347 0.035554264 1.449108313 -0.257069422 LLS(ph)FQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 93.267 0.048056 68104000 79733 82906 74995 90124 68615 82799 79559 79418 63398 TRUE FALSE 75964.17911 91354.21566 78433.59493 81064.5643 80581.43428 79931.64987 67420.81335 72463.7389 73229.43805 1.037344832 1.247506714 1.071066459 1.106994215 1.100396731 1.091523464 0.920679103 0.989543834 1 16.1601361 1.863270975 4.913909164 0.965471373 1.120079118 0.562338775 0.057729567 0.151314977 5.157661002 0.026241236 0.015223985 72.99127928 -1.863270975 0.154607745 LLS(ph)PGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 1 LLS(1)PGAR;LLS(1)PGAR 89.542 0.018668 420290000 539460 440340 464710 560580 562570 477980 619070 538330 603380 TRUE FALSE 513960.7949 485211.1466 486017.4132 504229.4334 660682.0299 461427.4327 524619.5015 491190.9713 696949.0888 0.737443815 0.6961931 0.697349951 0.723481014 0.947963116 0.662067632 0.752737194 0.704773102 1 19.41069375 -1.746342981 2.652330673 1.055618666 0.738145338 0.522489025 0.078015479 15290619.18 12457361.79 5598580.421 0.018086087 0.017933168 1.746342981 -0.317473328 LLS(ph)PLSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(0.941)PLS(0.059)SAR;LLS(0.995)PLS(0.005)SAR;LLS(1)PLSSAR;LLS(1)PLSSAR;LLS(0.994)PLS(0.006)SAR;LLS(0.999)PLS(0.001)SAR 215.83 6.56E-07 775296000 1500160 1329430 1221960 1436170 1457060 1342590 1664840 1473710 1592920 TRUE FALSE 1429250.41 1464900.428 1277988.075 1291803.463 1711170.803 1296095.772 1410838.081 1344664.14 1839941.898 0.776791056 0.796166678 0.694580669 0.702089269 0.930013499 0.70442212 0.76678404 0.730818805 1 20.81122878 -2.121498138 2.456472803 1.466853469 0.765204368 0.542861243 0.068398776 5146990.173 1075610.563 13474231.23 0.015114589 0.007559653 2.121498138 -0.701649101 LLS(ph)PQQPALQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;LLS(1)PQQPALQR;LLS(1)PQQPALQR 180.61 6.91E-06 1941850000 1384540 1315280 1213272 1425670 1284339 1250870 1451320 1399370 1366862 TRUE FALSE 1319095.538 1449308.527 1268901.721 1282358.943 1508327.315 1207552.058 1229894.479 1276833.744 1578827.978 0.835490349 0.917964812 0.803698528 0.812222079 0.955346204 0.764840803 0.778992072 0.808722522 1 20.59042256 2.196850185 24.99999089 0.813397714 0.864317013 0 0.079419919 354.4222162 212428.1608 0.026913188 0.019876889 157.3439993 -2.196850185 0.050919299 LLS(ph)PRPSLLTPTGDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LLS(0.998)PRPS(0.001)LLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(0.992)PRPS(0.008)LLTPTGDPR;LLS(1)PRPSLLTPTGDPR 130.11 3.13E-05 1458222000 2355070 2211515 2222318 2426650 2247001 2255415 2627720 2467020 2524490 TRUE FALSE 2243750.508 2436870.893 2324213.478 2182718.532 2638877.263 2177309.413 2226813.053 2250994.65 2915975.016 0.769468358 0.835696767 0.797062206 0.748538146 0.904972522 0.746683151 0.763659853 0.771952653 1 21.47554693 -2.165129914 2.413135276 1.51876133 0.792774311 0.653332705 0.047556699 3098875.259 636820.0312 8829871.621 0.010770171 0.006837071 2.165129914 -0.725987019 LLS(ph)SNEDDANILSSPTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLS(0.949)S(0.051)NEDDANILSSPTDR 140.95 1.29E-07 33723000 52956 54146 58690 62372 70332 59853 68781 60857 78221 TRUE FALSE 50452.87483 59663.53896 61380.99455 56102.24806 82597.87853 57780.2756 58287.1952 55528.03846 90351.11318 0.558409001 0.660352007 0.67936069 0.620935881 0.914187724 0.639508176 0.645118728 0.614580568 1 16.46325476 -2.276027455 2.317037657 2.468122824 0.663382658 0.554700442 0.093852173 6403291.696 1210536.5 49053211.03 0.022230162 0.0052963 2.276027455 -1.804740166 LLS(ph)WSDNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 1 LLS(0.975)WS(0.025)DNWR;LLS(0.959)WS(0.041)DNWR;LLS(0.764)WS(0.236)DNWR;LLS(0.73)WS(0.27)DNWR 138.99 0.00012698 93643000 130381 132120 124496 149254 136519 124857 149555 139725 135376 TRUE FALSE 124218.1485 145583.1782 130204.2647 134250.7044 160327.8704 120533.1708 126737.638 127489.9383 156369.4187 0.794389015 0.93102078 0.832670901 0.858548337 1.025314743 0.770823169 0.810501433 0.815312478 1 17.25459887 -0.030101559 7.788843714 0.999999999 0.855461257 0.274064991 0.074248168 3014107.493 386977.5239 0.068902492 0.017014258 0.933036085 0.030101559 -0.144538742 LLSAACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LLSAACR 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 ;;;;; 179.23 0.0016381 903315000 1363856 881911 435665 583881 1712010 699544 1560800 973094 1547660 FALSE TRUE 1299389.23 971778.7335 455640.6712 525188.1726 2010584.002 675318.6159 1322671.294 887884.7307 1787663.208 0.726864671 0.543602804 0.2548806 0.293784741 1.124699548 0.377766132 0.739888413 0.496673381 1 20.76964353 LLSAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSAER 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;P15924;P15924-3;P15924-2;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;P15924;A0A075B730;P58107;REV__Q15911-2 PLEC;DSP;EPPK1 Plectin;Desmoplakin;Epiplakin 0 96.666 0.097591 251290000 412470 372020 330080 343720 464540 343530 399000 384550 443910 FALSE TRUE 392973.3605 409929.261 345214.4945 309168.6126 545555.6289 331633.47 338125.2219 350876.7634 512749.2956 0.766404486 0.799473085 0.673261763 0.60296253 1.063981235 0.646775086 0.659435761 0.68430472 1 18.96789408 LLSDATVEKDESHAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LLSDATVEKDESHAGK 16 1 Q14320 Q14320 FAM50A Protein FAM50A 0 ;;;; 228.76 2.29E-15 1304462000 2863950 2440380 2349240 2860900 1809430 2824720 3054870 3015900 1778860 FALSE TRUE 2728576.759 2689057.496 2456954.978 2573316.897 2124994.019 2726899.238 2588793.475 2751811.808 2054716.524 1.327957763 1.308724325 1.195763479 1.252395095 1.034203013 1.327141339 1.259927316 1.339265916 1 20.97050794 -1.512256115 3.258892522 0.993362644 1.25947542 0.442981587 0.09001092 19325157.26 26175814.59 1155024.131 0.021158033 0.030742833 1.512256115 0.266112777 LLSDFLDSEVSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSDFLDSEVSELR 14 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 93.058 0.010964 6381100 27901 20432 23564 29028 19885 28094 34052 30702 19916 FALSE TRUE 26582.17502 22514.04403 24644.43271 26110.05029 23352.9377 27121.09774 28856.74199 28013.57012 23004.47156 1.155522088 0.978681208 1.071288799 1.134998916 1.015147757 1.178948956 1.254397082 1.217744561 1 14.4896267 2.153513881 7.190560107 1.192753158 1.069299766 0.190120051 0.084697704 0.249021113 17.78778452 0.029205678 0.021552043 142.4012762 -2.153513881 -0.123453392 LLSFS(ph)PEEFPTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSFSPEEFPTLK 13 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LLSFS(1)PEEFPTLK;LLS(0.167)FS(0.833)PEEFPTLK 200.19 1.17E-07 67511700 317289 276505 306453 339481 267626 335259 362641 359130 294127 TRUE FALSE 302291.3778 304681.1739 320504.1732 305355.7249 314299.8897 323648.8968 307313.4551 327682.6733 339738.713 0.889776073 0.89681029 0.943384315 0.89879579 0.925122389 0.952640616 0.904558248 0.964513789 1 18.3740661 -4.999999998 0.079805069 1.287534635 0.830707484 0.688175066 0.019649425 134.5354182 0.760458618 6.742946539 0.633832607 1.00E-05 4.999999998 -0.456827151 LLSGPSQES(ph)PQTLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLSGPSQESPQTLGK 15 0 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8;E7EVL6 Q9BWE0 REPIN1 Replication initiator 1 1 LLSGPS(0.049)QES(0.951)PQT(0.001)LGK;LLSGPSQES(1)PQTLGK;LLSGPS(0.002)QES(0.998)PQTLGK 270.94 2.31E-33 263045000 486238 457168 472513 528158 403092 478267 572060 566360 532390 TRUE FALSE 463254.4934 503753.939 494178.1884 475066.5544 473391.1172 461704.4939 484781.7404 516766.5159 614950.3221 0.75332019 0.819178267 0.803606683 0.772528345 0.769803836 0.750799662 0.788326671 0.840338638 1 19.23011034 0.823169512 2.22153954 0.999834282 0.780549096 0.918161802 0.020748946 0.179100641 1.583496663 0.02054816 0.00560081 6.655328729 -0.823169512 -0.219285186 LLSHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSHGK 6 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 132.8 0.014739 1395630000 5167400 4770700 4470300 5234400 4308100 5184800 5727100 5552600 4748400 FALSE TRUE 4923147.243 5256839.754 4675267.677 4708228.167 5059431.276 5005249.076 4853325.71 5066384.908 5484757.621 0.897605251 0.958445225 0.852410991 0.858420461 0.922453028 0.912574342 0.884875148 0.923720838 1 22.38699644 0.911038996 6.113277627 0.999998185 0.901966686 0.521106976 0.030525733 0.87024753 59.06244788 0.030061815 0.007556491 8.147774406 -0.911038996 -0.098031499 LLSISGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSISGKR 8 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 161.86 0.00055327 241610000 288190 99390 236530 178120 388740 232300 528240 320790 580660 FALSE TRUE 274567.8298 109517.954 247375.1345 160215.0392 456536.1329 224255.3928 447647.2862 292699.927 670705.7872 0.409371494 0.163287623 0.36882809 0.23887529 0.680680175 0.334357325 0.667427201 0.436405847 1 19.35532052 0.127194653 0.246107403 1.225137571 0.213043778 0.651273039 0.145272946 3.419727646 0.375901348 0.984610387 0.267509288 1.340277272 -0.127194653 -1.012093793 LLSLLEKDEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSLLEKDEFK 11 1 P35270 P35270 SPR Sepiapterin reductase 0 ; 186.91 3.49E-06 397700000 1775340 1516770 1548580 1859840 1034500 1743560 1934750 2064540 1212360 FALSE TRUE 1691423.197 1671330.587 1619583.925 1672885.35 1214916.472 1683180.08 1639568.353 1883757.933 1400366.597 1.207843146 1.19349504 1.156542814 1.194605294 0.867570303 1.201956747 1.170813669 1.345189136 1 20.41737312 3.492844756 2.149718097 1.134051047 1.200806111 0.051795988 0.126026372 1.098204754 10.12805328 0.0360517 0.058933225 3110.604211 -3.492844756 0.066755064 LLSPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 86.086 0.047307 90434000 67418 61020 59902 71884 80002 61621 82562 67150 92306 FALSE TRUE 64231.28475 67238.00737 62648.56595 64658.08375 93954.32347 59487.04932 69965.65054 61269.99002 106620.343 0.60242992 0.630630192 0.587585485 0.606432899 0.881204475 0.557933389 0.656212957 0.57465572 1 16.7021232 -2.156002135 2.402743914 1.859997096 0.637240578 0.610235521 0.091137902 6073849.319 1216962.805 28540382.64 0.020233351 0.00698229 2.156002135 -1.222756518 LLSSNEDDANILS(ph)SPTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLSSNEDDANILS(0.524)S(0.476)PTDR 141.22 1.27E-07 75735000 81640 68793 84237 86675 80666 78803 99297 83132 94997 TRUE FALSE 77781.03899 75803.08491 88099.34977 77962.26433 94734.12486 76074.03235 84147.41894 75852.52137 109728.6496 0.708848959 0.690823091 0.802883751 0.710500536 0.863349045 0.693292341 0.766868263 0.691273625 1 16.74358073 -1.793883166 2.80333283 1.068945645 0.739098014 0.674798409 0.056496556 13955070.9 9662144.475 6523870.697 0.012942163 0.016073736 1.793883166 -0.32984763 LLSSS(ph)LTADCSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLSSSLTADCSLR 13 0 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSS(0.009)S(0.99)LTADCSLR;LLSS(0.061)S(0.939)LTADCSLR;LLSS(0.044)S(0.95)LT(0.006)ADCSLR;LLSS(0.019)S(0.978)LT(0.003)ADCSLR 310.81 1.46E-50 199174000 563050 472336 499117 566919 597630 539993 661840 593020 721160 TRUE FALSE 536435.7424 520467.5754 522002.0081 509931.225 701856.4828 521292.907 560864.1525 541092.025 832993.8096 0.643985269 0.624815658 0.626657728 0.612166884 0.842571067 0.62580646 0.673311309 0.649575085 1 19.66794625 -5 0.309356316 4.001387503 0.643379279 0.718387617 0.066415296 150.7530324 1.367223782 294.7875901 0.058873767 1.00E-05 5 -3.358008223 LLSSSLTADCSLRS(ph)PSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSSSLTADCSLRSPSGR 18 1 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSSSLTADCSLRS(0.999)PSGR;LLSSSLTADCS(0.008)LRS(0.908)PS(0.084)GR 220.28 4.16E-19 292470000 312131 236695 299842 322047 318310 299898 349632 346011 327320 TRUE FALSE 297377.1862 260814.4896 313590.0523 289674.2237 373823.1632 289512.4571 296289.217 315712.4425 378079.1139 0.786547512 0.689841041 0.829429717 0.766173568 0.988743227 0.765745704 0.783669888 0.835043331 1 18.52832863 -5 0.132514453 1.674139805 0.714019801 0.418270928 0.074530265 136.6133301 1.133910858 24.53620244 0.52263925 1.00E-05 5 -0.960120004 LLSVHDFDFEGDS(ph)DDSTQPQGHSLHLSSVPEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.999)DDS(0.001)TQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.926)DDS(0.036)T(0.036)QPQGHS(0.002)LHLS(0.001)SVPEAR;LLSVHDFDFEGDS(0.983)DDS(0.007)T(0.009)QPQGHS(0.001)LHLSSVPEAR 228.95 2.54E-36 249438000 58754 39848.7 45350.7 53489 92162 44418.9 73960 73367 50021 TRUE FALSE 55976.81486 43909.32783 47430.07445 48112.1841 108235.0236 42880.66236 62676.04363 66942.59654 57778.00121 0.968825741 0.759966197 0.82090196 0.832707658 1.873291242 0.74216244 1.084773483 1.158617383 1 15.81823268 LLSVKGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSVKGSPK 9 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 LLS(0.104)VKGS(0.896)PK;LLS(0.003)VKGS(0.997)PK 56.02 0.075504 436630000 1612600 1126840 1437020 1502110 1135770 1651290 1921230 1847280 1189270 TRUE FALSE 1536375.594 1241666.277 1502908.788 1351115.049 1333847.928 1594105.413 1628111.078 1685522.37 1373695.918 1.118424809 0.903887288 1.094062208 0.98356196 0.970992132 1.16044999 1.18520486 1.226998165 1 20.38963125 2.228840713 24.90455345 1.161514059 1.010860039 0.36006715 0.083803963 169.1164178 433310.1421 0.028356146 0.021203458 169.3716478 -2.228840713 -0.150654021 LLSWSDNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 154.28 0.00017699 260730000 387600 334810 320160 367810 421260 327220 420180 361530 398600 FALSE TRUE 369278.9161 368927.5196 334839.6527 330837.04 494727.6106 315888.2894 356073.8239 329872.5166 460412.8522 0.802060399 0.801297179 0.727259569 0.71856604 1.074530409 0.686097896 0.773379418 0.71647113 1 18.81256858 -1.098306008 4.69498011 1.00001235 0.788609719 0.273366483 0.108886844 1.28E-05 2.47E-06 0.096246632 0.022684224 0.079743261 1.098306008 -0.211402631 LLT(ph)PTHSFLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLTPTHSFLAR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LLT(0.999)PT(0.001)HSFLAR;LLT(0.985)PT(0.015)HSFLAR 177.16 2.98E-05 290590000 382180 379080 409430 425350 371790 398960 463480 433180 403300 TRUE FALSE 364115.1088 417708.683 428202.7705 382593.0099 436630.0583 385143.9152 392767.6136 395248.4628 465841.7042 0.781628406 0.896675156 0.91920231 0.821294028 0.937292763 0.826769934 0.843135361 0.848460881 1 18.82948028 -2.24243333 2.26320094 1.500916669 0.858401143 0.468059565 0.047127425 4141462.801 723503.268 10616952.61 0.011163303 0.005722248 2.24243333 -0.642515526 LLTDDGNKWLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLTDDGNKWLYK 12 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 162.31 5.75E-05 530160000 2027500 1616260 2087300 2349400 1777210 2346900 2857500 2571500 2175400 FALSE TRUE 1931664.093 1780958.732 2183004.77 2113233.848 2087154.861 2265626.265 2421535.893 2346325.828 2512749.922 0.768745062 0.708768794 0.868771202 0.841004443 0.830625779 0.901652108 0.96369952 0.933768143 1 21.26083567 2.658230873 0.455447824 1.000731021 0.715181496 0.817433878 0.037512332 0.425127386 0.182971668 0.0354134 0.047509466 455.2299985 -2.658230873 -0.285549525 LLTQGFTNWNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLTQGFTNWNKR 12 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 71.933 0.069351 224050000 151720 115440 100720 118940 250660 156490 255460 180800 237910 FALSE TRUE 144548.4963 127203.4672 105338.1116 106983.9252 294375.0246 151070.7121 216484.8852 164968.1935 274803.8677 0.526006047 0.462888198 0.383321066 0.389310115 1.071218637 0.549740123 0.787779615 0.600312488 1 18.06804278 2.773452692 24.98696062 0.767845202 0.45047629 0.54617452 0.161958748 472.383034 338282.7698 0.044380364 0.04707076 593.5436895 -2.773452692 -0.317368911 LLTSHDCEILESEVTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLTSHDCEILESEVTGR 17 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 122.31 5.74E-05 56224000 67521 63639 64339 66105 74113 66266 68203 71327 67486 FALSE TRUE 64329.41614 70123.88645 67289.00679 59459.99981 87038.28373 63971.1918 57797.37972 65081.22975 77951.38421 0.825250466 0.899584878 0.8632176 0.762783117 1.116571368 0.820654982 0.741454181 0.834895113 1 16.25028702 -0.774750815 6.388055174 1.000000002 0.854713353 0.15886959 0.102390864 2.84E-09 6.67E-10 0.095378411 0.022480907 0.167976754 0.774750815 -0.14528665 LLTSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLTSLR 6 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 119.22 0.049314 142399000 644700 472350 725250 626440 747860 680020 940090 807980 920800 FALSE TRUE 614226.3087 520483.002 758503.4299 563469.061 878286.5472 656470.7369 796662.0046 737228.9878 1063592.961 0.577501291 0.489362962 0.713151983 0.529778855 0.825773185 0.617219896 0.74902903 0.693149555 1 20.0205147 -5 0.082782001 2.244573504 0.280753534 0.659954864 0.08745249 121.8428765 0.710587918 27.14578859 2.342767179 1.00E-05 5 -1.963819969 LLVDSQGLSGCS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LLVDSQGLSGCSPR 14 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 LLVDSQGLSGCS(1)PR;LLVDSQGLSGCS(1)PR;LLVDSQGLSGCS(1)PR;LLVDS(0.006)QGLS(0.27)GCS(0.724)PR 247.99 7.23E-18 814684000 956181 780426 840000 922804 945747 858636 1017459 902260 1045960 TRUE FALSE 910984.2191 859952.2967 878514.8309 830041.9887 1110684.977 828901.22 862226.9426 823253.3312 1208162.135 0.754024806 0.711785506 0.72714978 0.68702864 0.919317818 0.686084422 0.713668239 0.681409645 1 20.20438265 -1.05963208 4.377822523 1.000017089 0.734211283 0.59219962 0.069091092 39698889881 8527234282 8503780.63 0.014934054 0.087170175 1.05963208 -0.265805806 LLVDVDESTLSPEEQKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 267.55 2.48E-31 348629000 751650 623780 688460 818030 574620 802400 830440 864950 653490 FALSE TRUE 716120.9941 687343.8912 720026.572 735800.0702 674833.5461 774612.6868 703741.1259 789210.3926 754829.8916 0.948718383 0.910594425 0.953892499 0.974789258 0.894020697 1.026208283 0.932317511 1.04554735 1 19.52579203 1.718138138 0.894153136 1.011860135 0.936424816 0.322756385 0.039761321 0.612791107 0.928987873 0.031344876 0.013196786 52.25623758 -1.718138138 -0.075435319 LLVGNDDVHIIARS(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLVGNDDVHIIARSDDELLDDFFHDQSTATSQAGTLSSIPTALTR 45 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LLVGNDDVHIIARS(0.999)DDELLDDFFHDQSTATSQAGTLSSIPTALTR 65.452 0.00084213 19738000 11553 6740.8 9281.6 8558.4 10281 8634.1 13067 10036 9505.2 TRUE FALSE 11006.91259 7427.695184 9707.170541 7698.093372 12074.00314 8335.098952 11073.38916 9157.194636 10979.21787 1.002522467 0.676523161 0.884140442 0.701151345 1.099714323 0.759170558 1.008577231 0.834047994 1 13.42248766 2.75572603 24.99935947 0.931373865 0.817320408 0.184050704 0.129193473 1422.775512 2072099.022 0.035480751 0.037547459 569.8047042 -2.75572603 -0.114053457 LLVHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLVHLK 6 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 72.054 0.086609 128300000 363380 312630 277930 335170 354410 305770 419290 362560 368040 FALSE TRUE 346203.7475 344487.3524 290673.3654 301478.0748 416218.9918 295181.1082 355319.6097 330812.3243 425113.7635 0.814379061 0.810341565 0.683754304 0.709170346 0.979076726 0.694357919 0.835822409 0.778173639 1 18.69748944 -4.999998467 0.390821433 4.175444646 0.786416685 0.377643613 0.085549979 702.8693493 5.066891882 1898.710445 0.050223459 1.00E-05 4.999998467 -3.389027961 LLVLDVDYTLFDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLVLDVDYTLFDHR 14 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 155.42 5.85E-06 25213000 49746 45944 47643 48756 54357 40880 58369 52422 47556 FALSE TRUE 47394.60517 50625.74583 49827.47868 43854.95425 63836.84359 39464.31535 49463.73703 47831.65177 54930.7416 0.862806578 0.921628661 0.907096413 0.798368145 1.162133292 0.718437694 0.90047459 0.870762899 1 15.74532615 4.699356437 3.82612244 0.901369716 0.860485843 0.01113866 0.116991675 1.64195967 42.9614253 0.025007498 0.172640829 50044.50949 -4.699356437 -0.040883873 LLVQTSVQAKPGHVS(ph)PLQLTNIQVPQQALPTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLVQTSVQAKPGHVSPLQLTNIQVPQQALPTQR 33 1 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 LLVQT(0.021)S(0.021)VQAKPGHVS(0.959)PLQLTNIQVPQQALPTQR;LLVQT(0.099)S(0.08)VQAKPGHVS(0.821)PLQLT(0.001)NIQVPQQALPTQR 169.01 1.59E-14 205803000 432376 327166 417060 436282 464270 411573 571330 478100 300274 TRUE FALSE 411938.4434 360504.5874 436182.6135 392426.1045 545238.541 397320.1238 484163.1153 436235.0294 346838.9583 1.187693693 1.039400502 1.257594059 1.13143606 1.572022196 1.145546411 1.3959306 1.257745184 1 18.40390643 3.285143189 2.046502163 1.292933366 1.121566994 0.0727512 0.161497507 0.499900281 4.295351242 0.044384051 0.063048786 1928.160531 -3.285143189 -0.171366372 LLVSMCQGNRDENQSINHQMAQEDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LLVSMCQGNRDENQSINHQMAQEDAQR 27 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;;;; 347.35 2.60E-110 2350445000 684140 484544 647843 653773 846772 654107 855177 703244 798428 FALSE TRUE 651802.058 533919.5845 677547.2424 588054.496 994448.7687 631455.1106 724704.0422 641664.2272 922244.1364 0.706756522 0.57893519 0.734672323 0.637634302 1.078292319 0.684694091 0.785804988 0.695763954 1 19.81478919 LLVVDPETDEHFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LLVVDPETDEHFKR 14 1 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 ; 82.069 0.0076237 295410000 765400 704370 712880 824000 631200 749270 869610 864920 628080 FALSE TRUE 729221.0589 776146.1038 745566.2531 741169.9545 741281.0802 723322.592 736935.023 789183.0196 725479.4386 1.005157445 1.069838871 1.027687641 1.021627789 1.021780964 0.997027005 1.015790364 1.087808941 1 19.4685752 -1.647447915 2.641225347 0.996533304 1.029613927 0.106598815 0.027858109 12416422.22 13808200.95 300776.2995 0.006432292 0.022519155 1.647447915 0.033080623 LLVVDRETDEFFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLVVDRETDEFFKK 14 2 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 152.68 3.71E-06 270950000 741400 470680 772670 673500 632060 755700 1043700 936230 786050 FALSE TRUE 706355.4913 518642.8271 808097.6838 605798.5004 742291.0639 729529.9195 884464.3961 854248.7379 907946.6194 0.777970286 0.571226123 0.890027747 0.66721819 0.817549235 0.803494285 0.974137 0.940857887 1 19.79224795 2.008768351 0.892184382 1.002513059 0.704473832 0.596719812 0.085334192 0.348482148 0.512299662 0.065235935 0.032007005 102.0395068 -2.008768351 -0.298039227 LLWAGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLWAGDDR 8 0 A0A087X091 A0A087X091 WDR13 0 81.297 0.054034 37167000 76922 72311 69055 85980 73684 61375 88638 92307 212860 FALSE TRUE 73286.0495 79679.57311 72221.24005 77337.12705 86534.46627 59249.56836 75114.64515 84224.10973 245869.2417 0.298069205 0.324072961 0.29373841 0.314545758 0.3519532 0.240979994 0.305506474 0.342556512 1 17.90753174 0.562241537 2.784029189 0.999996446 0.304564159 0.983961384 0.027769876 0.805942892 4.989625665 0.025074674 0.006604705 3.64956865 -0.562241537 -0.695432287 LLWHGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLWHGSR 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 94.662 0.014036 358560000 326390 344590 472930 518800 701070 426510 581610 559540 766600 FALSE TRUE 310962.1915 379704.1128 494614.3083 466649.2383 823336.386 411739.8518 492874.7125 510543.7113 885480.4127 0.351179074 0.42881142 0.558583003 0.527001198 0.929818858 0.464990355 0.556618425 0.576572563 1 19.75610087 -5 0.070920431 2.478276682 3.88E-10 0.536809515 0.141255105 241.2969722 1.230193844 59.21739237 7.191943826 1.00E-05 5 -2.478276682 LLYDLADQLHAAVGASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LLYDLADQLHAAVGASR 17 0 H0YL12;P13804-2;P13804;H0YK49;H0YNX6 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;; 245.66 1.35E-20 317145500 582762 447564 507073 491549 648730 419883 579223 538190 584129 FALSE TRUE 555215.9952 493171.2804 530322.7986 442137.5606 761868.3066 405342.3464 490851.8932 491063.2305 674712.742 0.822892411 0.730935181 0.7859979 0.655297482 1.129174327 0.600762845 0.727497589 0.727810815 1 19.36391388 -1.968094611 2.761940347 1.1888376 0.76861261 0.203922194 0.141044508 69138231.41 34062937.38 83505209.41 0.030625828 0.010762307 1.968094611 -0.42022499 LLYNNVSNFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LLYNNVSNFGR 11 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 221.68 0.00038638 0 102960 94495 98742 106980 107590 97504 115020 99741 114950 FALSE TRUE 98093.28485 104124.1479 103269.4184 96226.16715 126353.6619 94127.41203 97471.58651 91007.14928 132775.8589 0.738788554 0.784209937 0.77777255 0.724726377 0.95163129 0.708919624 0.73410624 0.685419398 1 17.01863334 -2.17072685 2.402429483 1.607213506 0.763880669 0.508980191 0.073092514 6736205.212 865811.076 22453850.2 0.016955974 0.006749524 2.17072685 -0.843332838 LMALSSAIVTMPHFEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMALSSAIVTMPHFEFR 17 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 105.28 0.00080951 31933000 37515 42013 39859 39651 43161 37089 50963 43891 37516 FALSE TRUE 35741.7403 46294.17246 41686.57458 35665.20615 50688.26473 35804.59863 43187.65835 40047.67136 43333.78967 0.824800706 1.068315806 0.961987744 0.823034551 1.169716868 0.826251267 0.996627774 0.924167299 1 15.40320479 4.727444522 4.540189932 0.968656609 0.817036689 0.165712708 0.103089035 0.306903483 14.63756927 0.021696917 0.142486372 53388.10693 -4.727444522 -0.15161992 LMCKPIFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMCKPIFSK 9 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 85.958 0.01319 177620000 733510 649030 615970 725130 609460 671490 866480 733350 722220 FALSE TRUE 698838.436 715166.8949 644212.8338 652238.5547 715749.631 648236.1329 734282.562 669133.9863 834218.189 0.837716613 0.85728998 0.77223542 0.78185607 0.857988522 0.777058258 0.88020445 0.802109083 1 19.67006524 -1.471784026 0.566495269 1.088646576 0.823354948 0.686663091 0.037877732 29.29231541 3.916284878 3.813858725 0.015146958 0.033745508 1.471784026 -0.265291628 LMCPQEIVDYIADKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMCPQEIVDYIADKK 15 1 O14561;H3BNK3 O14561 NDUFAB1 "Acyl carrier protein, mitochondrial;Acyl carrier protein" 0 ; 155.22 3.75E-06 154093000 497800 562400 410600 522010 344290 442830 422910 555990 342170 FALSE TRUE 474269.9805 619709.1994 429426.4161 469536.563 404334.067 427494.6861 358387.3122 507304.5681 395231.976 1.19997877 1.567963214 1.086517393 1.188002468 1.023029743 1.081629807 0.906777118 1.283561551 1 18.59234015 3.652009981 8.095104408 1.068621566 1.383416897 0.466811549 0.133966845 0.21934579 18.56312472 0.033810972 0.052484614 4487.557034 -3.652009981 0.314795331 LMDEVAGIVAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMDEVAGIVAAR 12 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 ; 103.88 0.0051146 23494000 60023 54230 53889 68144 62174 63933 65902 66725 64446 FALSE TRUE 57185.83174 59756.09865 56359.86395 61294.03565 73017.12591 61718.98418 55847.43953 60882.20527 74439.95654 0.768214201 0.802742256 0.757118443 0.823402357 0.980886198 0.829110965 0.750234714 0.817869973 1 16.18378959 -2.551138511 1.985373409 3.341888347 0.811501449 0.440974678 0.064846067 2280053.585 106564.176 24117155.84 0.016221791 0.002811004 2.551138511 -2.530386898 LMDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMDLLDR 7 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 88.942 0.042427 15970000 52986 46147 41204 50599 55978 44065 60143 50720 56293 FALSE TRUE 50481.45679 50849.43176 43093.24416 45512.69239 65740.54548 42539.018 50967.08075 46278.68792 65022.63094 0.77636749 0.782026673 0.662742241 0.699951567 1.011040995 0.654218653 0.783836028 0.711732012 1 15.98865431 -0.921368748 4.052638607 1.000009761 0.762755968 0.359425173 0.100541528 27343118.5 49262433.92 3803.86563 0.021965628 0.119848127 0.921368748 -0.237253794 LMEDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 LMEDLDR 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;;;;;;;;; 257.98 2.23E-12 1.57075E+11 131556450 126797960 95195550 141025610 115248030 109657950 118217580 122120740 105858690 FALSE TRUE 125338037.3 139718816.3 99560360.13 126849447.8 135347249.9 105860467.7 100181317 111427200.6 122274715 1.025052787 1.142663193 0.814235062 1.037413563 1.106911187 0.865759268 0.819313437 0.911285711 1 26.86555086 2.223383863 24.99902869 0.876445555 1.032207779 0.279606528 0.097313485 252.7050736 416251.1105 0.035528869 0.026338664 167.2568305 -2.223383863 0.155762224 LMEDLDRNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 LMEDLDRNK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;;;;;; 182.65 4.20E-05 19572030000 16039510 7776589 14147150 11923160 14893460 15087650 22458930 17007760 17050440 FALSE TRUE 15281354.15 8569032.26 14795810.82 10724621.3 17490874.71 14565160.9 19032407.74 15518470.37 19694535.15 0.775918499 0.435096954 0.75126479 0.54454808 0.888108024 0.739553424 0.966380145 0.787958195 1 24.23129203 2.730588505 24.69646048 0.870626673 0.618270978 0.511751987 0.120993091 383.2784578 1187339.077 0.035468977 0.034002871 537.7600128 -2.730588505 -0.252355695 LMEEDELPSWIIKDDAEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 232.2 4.26E-26 80369000 153220 152982 145077 174475 131269 160988 169528 158009 140598 FALSE TRUE 145977.5943 168571.0397 151728.924 156936.4415 154162.272 155412.9452 143663.39 144172.8943 162401.2198 0.898870061 1.037991217 0.934284386 0.96635014 0.949267944 0.956969076 0.884620141 0.88775746 1 17.30920294 1.850997108 7.799519958 0.91257227 0.961525491 0.079608167 0.046826264 0.436535504 27.11884893 0.018586964 0.011553305 70.95730432 -1.850997108 0.048953221 LMELHGEGSSSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 205.31 7.09E-08 3574150000 8448600 6972210 7742990 8766740 7367540 8282480 10188880 9179140 7819730 FALSE TRUE 8049251.422 7682686.126 8098013.75 7885490.639 8652436.643 7995655.641 8634379.224 8375365.84 9032373.791 0.891155704 0.850572209 0.896554321 0.873025278 0.957936069 0.885221961 0.95593688 0.927260766 1 23.10667376 1.560784524 0.331656648 1.006434601 0.858756429 0.648609314 0.02694984 0.708294705 0.262016653 0.038406012 0.034092796 36.37345234 -1.560784524 -0.147678172 LMELYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMELYER 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 86.794 0.046098 48682000 56863 53536 44763 55439 66757 42810 67248 54661 67214 FALSE TRUE 54175.19868 58991.37927 46815.42783 49866.16639 78399.39966 41327.47897 56988.08251 49874.59306 77637.20384 0.697799457 0.759833899 0.603002498 0.6422973 1.009817404 0.532315397 0.73403059 0.642405839 1 16.24446054 -1.091927873 4.796825112 1.000012941 0.706340959 0.351207406 0.126908604 1.56E-05 2.96E-06 0.109334422 0.025769235 0.080923028 1.091927873 -0.293671982 LMENMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMENMR 6 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 128.75 0.038361 521440000 525660 417040 411630 477470 562260 422990 582850 504230 606250 FALSE TRUE 500813.0936 459536.8501 430503.6427 429473.8085 660317.966 408341.7502 493925.5277 460076.9481 700264.1537 0.715177395 0.656233577 0.614773211 0.613302575 0.942955544 0.583125308 0.705341727 0.657004854 1 19.41753971 -1.345173961 2.997306981 1.003425965 0.685329768 0.493580461 0.099957317 13894961.55 17342536.38 418430.209 0.022018585 0.045167499 1.345173961 -0.318096197 LMFEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LMFEELR 7 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;;; 168.74 0.0024144 535825000 1333306 1047017 1028449 1217985 1422594 998551 1434592 1218933 1420810 FALSE TRUE 1270283.268 1153709.223 1075604.404 1095550.834 1670693.943 963970.9285 1215718.642 1112196.765 1641141.958 0.774024003 0.702991729 0.655399978 0.667553973 1.018006964 0.587378151 0.740776041 0.677696868 1 20.64626861 -1.039753655 4.72006224 1.000007987 0.727846515 0.357438789 0.114620349 8.68E-06 1.77E-06 0.099954488 0.023558808 0.091252831 1.039753655 -0.272161472 LMFNSPGFVEYVVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMFNSPGFVEYVVDR 15 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 134.99 7.39E-05 77331000 89292 77078 89307 104747 110785 87828 110629 86375 108235 FALSE TRUE 85071.34412 84932.33583 93401.81429 94217.63255 130105.8689 84786.49434 93750.51421 78811.5471 125019.531 0.680464432 0.679352539 0.747097782 0.753623308 1.040684346 0.678185989 0.749886945 0.630393879 1 16.93179397 -2.332714874 2.227812011 2.422154377 0.741984887 0.336867705 0.112386164 4709037.321 632416.6047 33716088.22 0.028098211 0.004648203 2.332714874 -1.68016949 LMHNAS(ph)DS(ph)EVDQDDVVEWK ddPTM_SK-BR-3_Trastuzumab_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 211.5 6.67E-17 850458000 842105 911526 781561 948700 571110 889950 833229 912670 508329 TRUE FALSE 802300.3655 1004411.536 817396.3449 853334.8736 670711.4032 859130.8083 706104.6127 832751.7764 587158.0651 1.366412919 1.710632273 1.392123167 1.453330754 1.142301269 1.46320192 1.202580114 1.418275292 1 19.16338941 0.332180021 0.154879099 0.720763726 1.684380199 0.452598697 0.145407421 8.942247752 0.602982131 2.331028055 1.056471539 2.148720963 -0.332180021 0.963616473 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LMHNAS(0.959)DS(0.041)EVDQDDVVEWK;LMHNAS(0.954)DS(0.046)EVDQDDVVEWK;LMHNAS(0.847)DS(0.153)EVDQDDVVEWK;LMHNAS(0.849)DS(0.151)EVDQDDVVEWK;LMHNAS(0.554)DS(0.446)EVDQDDVVEWK;LMHNAS(0.857)DS(0.143)EVDQDDVVEWK 242.43 1.34E-24 1687659000 1637850 1848250 1496430 1968760 1143538 1729200 1644970 1769210 1047037 TRUE FALSE 1560432.076 2036588.776 1565042.796 1770856.504 1342970.665 1669317.37 1393999.615 1614288.593 1209406.15 1.29024652 1.683957681 1.294058902 1.464236397 1.110438098 1.380278552 1.152631491 1.334777893 1 20.20586739 1.699010003 0.305102619 0.986613023 1.523470246 0.388595459 0.149686205 1.313413305 0.425990825 0.242614615 0.24922672 50.00460527 -1.699010003 0.536857223 LMHQAALLGQALQDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMHQAALLGQALQDSR 16 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225;E9PIZ5 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 178.14 2.84E-09 293640000 374280 395850 298020 418460 351500 319530 348350 342790 286930 FALSE TRUE 356588.5262 436187.565 311684.5118 376395.6058 412801.4887 308464.596 295202.8096 312773.4904 331425.639 1.075923176 1.316094815 0.940435727 1.135686445 1.245532754 0.930720378 0.890706013 0.943721467 1 18.33832569 2.222010811 24.67361259 0.927683373 1.150785066 0.488673653 0.101787924 158.5971111 236445.9461 0.036832612 0.027282164 166.7288717 -2.222010811 0.223101693 LMIEMDGTENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LMIEMDGTENK 11 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 237.44 3.25E-15 419640000 1809574 1482959 1351897 1635097 1266445 1718984 1881560 1853710 1326390 FALSE TRUE 1724039.023 1634074.208 1413882.815 1470733.943 1487312.607 1659455.153 1594493.465 1691389.325 1532079.787 1.125293237 1.066572526 0.922851947 0.959959106 0.970780125 1.083138859 1.040737877 1.103982534 1 20.54706 -0.135222743 7.621458396 1.000000007 1.037511023 0.023923776 0.065553268 0 0 0.067196976 0.015838479 0.732448775 0.135222743 0.037511016 LMIWDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 132.96 0.0077193 1852690000 3340580 2596030 2025860 2310080 3813470 2059230 3746780 2839340 3634650 FALSE TRUE 3182677.404 2860568.408 2118747.685 2077866.37 4478537.961 1987918.349 3175139.897 2590712.337 4198292.959 0.75808845 0.681364649 0.504668851 0.494931247 1.066752131 0.473506344 0.756293076 0.617087079 1 22.00137141 -1.646223771 2.473833409 1.043362806 0.674602514 0.262790286 0.173965903 11126304.56 9000116.042 3066761.942 0.039406605 0.022582719 1.646223771 -0.368760292 LMKPPS(ph)PEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.956)PEHQS(0.042)LDT(0.002)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.597)PEHQS(0.202)LDT(0.202)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.996)PEHQS(0.004)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.695)PEHQS(0.303)LDT(0.002)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.91)PEHQS(0.07)LDT(0.02)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 200.77 2.02E-35 530014000 360852 264622 298960 349650 309504 325792 440377 378221 318878 TRUE FALSE 343795.2411 291587.2827 312667.6117 314502.5177 363481.3996 314509.7413 373189.4006 345101.9642 368327.9716 0.933394332 0.791651205 0.848883701 0.853865419 0.986841694 0.853885031 1.013198642 0.936942048 1 18.49063144 2.325548921 0.954652432 0.980970165 0.853244946 0.415129431 0.056932945 0.504194665 0.891561859 0.037900797 0.023218453 211.6162046 -2.325548921 -0.127725219 LMKPPSPEHQS(ph)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.34)PEHQS(0.536)LDT(0.124)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 86.891 0.00023237 119210000 77756 61521 82478 84821 65040 81335 113540 110620 90060 TRUE FALSE 74080.62798 67790.05984 86259.69788 76294.63193 76382.95541 78518.34856 96217.38769 100933.5264 104026.0448 0.71213539 0.651664301 0.829212511 0.733418559 0.734267611 0.754795097 0.924935557 0.97027169 1 16.66658525 1.681537126 2.06201753 0.988710362 0.722548888 0.862167532 0.043685575 0.103581647 0.932073722 0.032834802 0.012994769 48.03271396 -1.681537126 -0.266161474 LMLDGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMLDGDR 7 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;U3KQI3 P13797 PLS3 Plastin-3 0 99.139 0.025003 87162000 294530 305580 241260 332950 367700 247300 281720 276290 366980 FALSE TRUE 280608.1506 336718.9494 252322.0096 299481.2334 431826.7636 238735.939 238738.4399 252096.5829 423889.3841 0.661984379 0.794355702 0.595254373 0.706507982 1.01872512 0.563203392 0.563209292 0.594722568 1 18.69332831 LMLSTSEYSQS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMLSTSEYSQSPK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LMLS(0.003)T(0.006)S(0.001)EYS(0.023)QS(0.967)PK 97.69 0.0038422 90417000 90816 78493 77543 92204 55585 105160 98542 100370 70607 TRUE FALSE 86523.30766 86491.52594 81098.42325 82935.47874 65279.0064 101518.2828 83507.60805 91581.07071 81556.37295 1.060901859 1.060512169 0.994384869 1.016909847 0.800415762 1.244762109 1.023924986 1.122917405 1 16.31551 2.213345671 24.99991009 1.096928916 1.005181963 0.231524483 0.097527452 392.5827838 389232.4095 0.034461759 0.025461714 163.4352271 -2.213345671 -0.091746953 LMNESLMLVTALNPHIGYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMNESLMLVTALNPHIGYDK 20 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 275.02 1.69E-44 544090000 1633150 1243630 1473860 1518760 1323840 1277550 1698280 1582670 1301180 FALSE TRUE 1555954.236 1370357.311 1541437.939 1366091.359 1554717.277 1233308.123 1439176.195 1444083.025 1502960.349 1.035259671 0.911772098 1.025601201 0.908933732 1.034436656 0.820585935 0.957560987 0.960825763 1 20.51937552 LMQLVDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 2128831000 3067422 2382537 2326508 2550864 3300317 2511316 3393522 2921998 3038719 FALSE TRUE 2922431.041 2625320.229 2433180.693 2294446.304 3875891.24 2424348.497 2875777.893 2666132.365 3509948.023 0.832613766 0.747965557 0.693224138 0.653698086 1.104258871 0.690707806 0.819322074 0.759593119 1 21.74301824 LMS(ph)VEEELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LMSVEEELKK 10 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 LMS(1)VEEELKK;LMS(1)VEEELKK 154.07 9.28E-06 106249000 227138 209250 172881 236810 92156 208339 179884 200044 97862 TRUE FALSE 216401.6369 230572.8129 180807.7649 213005.4089 108227.9772 201124.1682 152439.392 182527.0869 113037.9392 1.914415978 2.039782525 1.599531681 1.884370951 0.957448252 1.779262518 1.348568393 1.614741814 1 16.78644754 8 0.096454223 0.670395082 4.66008768 0.469185686 0.269773889 101.236532 0.695353652 3.439263903 53.42915399 100000000 -8 3.989692598 LMSELYHPDDHVL ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LMSELYHPDDHVL 13 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ;;;;; 160.18 4.22E-05 309281000 577940 490890 495598 561548 653807 499681 642405 536003 27261.2 FALSE TRUE 550621.9216 540912.2491 518321.6585 505100.1282 767830.7338 482376.9217 544394.3187 489067.7358 31488.72767 17.48631851 17.1779646 16.46054626 16.04066489 24.38430482 15.31903501 17.28854606 15.53151785 1 14.94254784 0.343142688 1.180226916 0.973779921 17.78400601 0.817748402 2.465717025 1.289287569 1.95940686 2.219489882 0.663176414 2.203650357 -0.343142688 16.81022609 LMSNLDSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LMSNLDSNR 9 0 P26447 P26447 S100A4 Protein S100-A4 0 ;;; 176.78 0.00012302 3947840000 3848440 3199720 3648980 4442610 3183980 3854550 3975370 4076460 3277270 FALSE TRUE 3666531.868 3525775.106 3816289.342 3996030.402 3739265.104 3721065.967 3368854.294 3719503.552 3785492.294 0.968574649 0.931391437 1.008135547 1.055617101 0.987788328 0.982980727 0.889938225 0.982567989 1 21.8520495 -0.310518032 7.53124833 0.999999587 0.969532312 0.011132778 0.043939015 0 0 0.045409051 0.010703016 0.489194954 0.310518032 -0.030467274 LMSSLPNFCGIFNHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMSSLPNFCGIFNHLER 17 0 Q96PU8-5;Q96PU8-9;Q96PU8-8;Q96PU8-6;Q96PU8-3;Q96PU8;H0YFB7 Q96PU8-5 QKI Protein quaking 0 85.576 0.0050023 49438000 45018 38229 40132 36231 46591 41084 52772 41142 40467 FALSE TRUE 42890.08836 42124.57856 41972.0919 32588.99105 54716.45565 39661.25078 44720.66218 37539.38837 46742.41568 0.917583906 0.901206708 0.897944432 0.697203826 1.170595376 0.848506655 0.956746919 0.803111859 1 15.51244468 2.769434163 24.99995024 0.944528505 0.871030557 0.153952744 0.114294658 1655.033067 1340165.056 0.032043923 0.03398457 588.0769577 -2.769434163 -0.073497948 LMT(ph)PKPVSIATNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LMTPKPVSIATNR 13 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 LMT(0.996)PKPVS(0.003)IAT(0.001)NR 81.373 0.024646 386860000 510040 459140 484370 527560 318060 544120 569790 582850 362780 TRUE FALSE 485931.42 505926.888 506578.8436 474528.6665 373529.5633 525276.988 482858.0706 531812.5641 419038.0696 1.159635497 1.207353042 1.208908881 1.13242376 0.891397681 1.253530469 1.1523012 1.269127086 1 18.67672179 3.1872576 7.823730908 1.124709351 1.19057943 0.091070304 0.110462691 0.664105056 87.67069966 0.030833409 0.037097398 1539.067259 -3.1872576 0.065870079 LMVESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LMVESHR 7 0 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ;;; 131.04 0.003505 767930000 1009447 864113 780615 892164 1115560 815272 1131140 918952 1054930 FALSE TRUE 961732.4408 952167.0971 816406.9699 802481.9797 1310113.311 787038.9262 958563.8182 838483.6912 1218523.157 0.789260701 0.781410753 0.669997091 0.658569331 1.075164886 0.645895748 0.786660322 0.688114696 1 20.21670224 LMYEHNLQRTACNMTYGSFGGVK ddPTM_SK-BR-3_Trastuzumab_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 5879160000 3871490 3402220 3824240 4041180 3432780 3862460 4823390 4216440 420184 FALSE TRUE 3688492.34 3748910.086 3999585.187 3634952.909 4031455.745 3728702.042 4087493.268 3847226.161 485343.9887 7.599748685 7.724233066 8.240722621 7.489436344 8.306388539 7.682596526 8.421847932 7.926802949 1 18.8886481 -0.783438582 11.58039077 1 7.921183014 0.979618373 0.313869012 0 0 0.292567702 0.068958869 0.16464988 0.783438582 6.921183014 LNAS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNASPAAR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 LNAS(1)PAAR;LNAS(1)PAAR 91.313 0.013191 410890000 1266370 1323580 1060480 1524360 1092530 1149180 1197310 1229950 996750 TRUE FALSE 1206511.2 1458454.307 1109104.057 1371128.437 1283066.886 1109383.608 1014638.369 1122249.058 1151320.899 1.047936505 1.266766119 0.96333182 1.190917699 1.114430292 0.963574629 0.881281987 0.974749141 1 20.13485857 2.21863219 4.393540821 0.935578249 1.12850838 0.464557801 0.085322334 0.148252378 6.692582853 0.030197376 0.022820258 165.4368263 -2.21863219 0.192930131 LNATNIELATVQPGQNFHMFTKEELEEVIKDI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNATNIELATVQPGQNFHMFTKEELEEVIKDI 32 2 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 305.23 1.97E-90 493520000 1698980 743760 1651270 1326560 1247980 1723790 2448470 1869890 1331350 FALSE TRUE 1618672.582 819549.9896 1726982.363 1193211.669 1465627.317 1664094.72 2074910.932 1706152.519 1537808.958 1.05258366 0.532933551 1.123014893 0.775916711 0.953062023 1.082120579 1.349264433 1.109469749 1 20.55244486 2.246384637 2.678303742 1.194448368 0.850513592 0.311028969 0.181247407 0.249409488 3.676681638 0.071642778 0.051535319 176.3537248 -2.246384637 -0.343934776 LNCQVIGASVDSHFCHLAWVNTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LNCQVIGASVDSHFCHLAWVNTPK 24 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 240.49 8.77E-38 2990960000 2762634 2257218 2349774 2792103 2283255 2521351 3108060 2689082 147245.5 FALSE TRUE 2632049.766 2487231.08 2457513.462 2511435.502 2681453.949 2434035.983 2633868.364 2453611.724 170079.5801 15.47540136 14.62392533 14.44919761 14.76623766 15.76587823 14.31115941 15.48609399 14.42625695 1 17.37585041 0.834825822 8.419622376 1.000000058 14.97226982 0.988405924 0.473930576 2.751696706 140.3507964 0.416133309 0.104174809 6.836374136 -0.834825822 13.97226976 LNDPFQPFPGNDS(ph)PKEKDPEIFCDPFTSATTTTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNK 35 2 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LNDPFQPFPGNDS(1)PKEKDPEIFCDPFTSATTTTNK;LNDPFQPFPGNDS(1)PKEKDPEIFCDPFTSATTTTNK 243.74 7.75E-48 434420000 1066790 954910 859550 1127420 382660 1082950 916710 1156410 286700 TRUE FALSE 1016364.951 1052216.415 898961.2177 1014089.6 449395.7828 1045447.17 776849.053 1055148.61 331159.9717 3.069105682 3.177365939 2.714582964 3.06223483 1.357035334 3.156924928 2.345842249 3.186220256 1 18.33716878 LNDS(ph)PTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LNDSPTLK 8 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 LNDS(0.999)PT(0.001)LK;LNDS(0.997)PT(0.003)LK;LNDS(0.993)PT(0.007)LK;LNDS(0.989)PT(0.011)LK 176.48 0.00027278 796210000 2618900 2421730 2440040 2843690 1617050 2890880 2973090 2973130 1794670 TRUE FALSE 2495109.787 2668507.04 2551918.248 2557836.879 1899063.008 2790768.101 2519490.516 2712786.976 2072978.258 1.20363529 1.287281731 1.231039563 1.233894697 0.916103679 1.346260189 1.215396499 1.308642271 1 20.98327355 -1.992260672 2.977214859 0.790978386 1.220411028 0.257668719 0.11609324 19586248.53 21333631.82 28119799.92 0.025897045 0.010179802 1.992260672 0.429432642 LNDYIFSFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNDYIFSFDK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 229.53 3.67E-09 141967000 676980 600510 482170 566910 527160 552290 811940 638490 578610 FALSE TRUE 644980.497 661702.6517 504277.9714 509923.1297 619096.5371 533164.0588 688063.6407 582580.4308 668337.8837 0.96505153 0.99007204 0.754525493 0.762972057 0.926322676 0.797746278 1.029514647 0.871685483 1 19.35021813 1.730219802 25 0.964685764 0.882084232 0.206963709 0.089549956 1.530175409 4560.644891 0.04416254 0.024490359 53.73036644 -1.730219802 -0.082601531 LNEAQPSTIATS(ph)MRDSLIDSLT ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LNEAQPSTIATSMRDSLIDSLT 22 1 P56537;P56537-2 P56537 EIF6 Eukaryotic translation initiation factor 6 1 LNEAQPS(0.235)T(0.235)IAT(0.162)S(0.3)MRDS(0.068)LIDSLT;LNEAQPS(0.014)T(0.011)IAT(0.091)S(0.515)MRDS(0.368)LIDSLT;LNEAQPS(0.006)T(0.005)IAT(0.041)S(0.601)MRDS(0.348)LIDSLT 113.93 0.00014807 123280000 177314 154680 165828 191734 188473 157944 213706 196678 212358 TRUE FALSE 168932.7186 170442.0679 173431.3778 172460.534 221342.6315 152474.3597 181101.2247 179455.8317 245289.3941 0.688707799 0.694861139 0.70704801 0.703090057 0.902373429 0.621610079 0.738316573 0.731608606 1 17.90412533 -5 0.319093345 3.637943517 0.707402269 0.602203938 0.070785122 209.0559528 1.855184746 372.2565006 0.058162277 1.00E-05 5 -2.930541248 LNECIS(ph)PVANEMNHLPAHSHDLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNECISPVANEMNHLPAHSHDLQR 24 0 P23497;P23497-2;P23497-3;P23497-4;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 LNECIS(1)PVANEMNHLPAHSHDLQR 63.453 0.052862 74878000 125700 107500 104820 152610 82226 145890 171620 153720 102070 TRUE FALSE 119758.4101 118454.3722 109626.1007 137269.3529 96566.18837 140837.7927 145436.217 140259.4619 117898.4943 1.015775569 1.004714886 0.929834612 1.164301153 0.8190621 1.194568205 1.233571454 1.189662877 1 16.84718577 2.188038695 24.99998968 1.181044754 0.997313048 0.370600124 0.105620355 92.26253273 45654.03387 0.034670267 0.025605723 154.1837822 -2.188038695 -0.183731706 LNEDKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNEDKPK 7 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 80.067 0.028198 666640000 1729970 1498400 1473000 1953180 933810 1897210 1936770 2007420 1017500 FALSE TRUE 1648197.747 1651088.664 1540538.507 1756842.636 1096666.168 1831509.142 1641280.165 1831639.663 1175288.703 1.402376915 1.404836666 1.310774538 1.494817938 0.933103641 1.558348291 1.396491058 1.558459345 1 20.16458376 3.768784202 20.27778126 1.346640629 1.403607008 0.014740011 0.212548258 423.6312224 284213.6408 0.049617886 0.089397248 5871.975051 -3.768784202 0.056966379 LNEELKVDEETQEVLENLKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNEELKVDEETQEVLENLKDR 21 2 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 109.75 0.00016217 33029000 75102 65149 60922 74492 40209 74874 76748 82301 46386 FALSE TRUE 71552.0773 71787.75717 63715.33396 67003.92263 47221.43687 72281.09461 65038.68303 75094.28813 53579.30397 1.335442456 1.339841167 1.189178082 1.250556048 0.881337258 1.349048779 1.213876967 1.401554006 1 15.70938822 3.739273047 23.16469038 1.19410816 1.337641832 0.149093595 0.151347702 40.15448366 1305525.908 0.036752737 0.061594943 5486.217832 -3.739273047 0.143533672 LNEHFLNTTDFLDTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNEHFLNTTDFLDTIK 16 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 294.38 1.26E-45 1151790000 3599800 2759500 2892900 3054300 2429900 2768500 3226000 3222600 2347400 FALSE TRUE 3429644.588 3040696.187 3025542.326 2747275.961 2853673.791 2672626.151 2733814.45 2940412.06 2711422.803 1.264887418 1.121439336 1.115850439 1.013223005 1.052463595 0.985691404 1.008258265 1.084453541 1 21.37061867 4.373090623 0.696762734 1.015589163 1.347764872 0.847233454 0.03250854 0.629470898 0.320010957 0.013081036 0.152557122 23609.70838 -4.373090623 0.332175709 LNENHSGELWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNENHSGELWK 11 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 101.6 0.0026553 0 122800 111770 114760 129570 100450 124750 144570 127940 110470 FALSE TRUE 116995.4874 123159.4901 120021.8595 116545.3774 117968.4482 120429.8762 122513.1913 116736.8953 127601.1234 0.916884462 0.965191268 0.940601903 0.913356986 0.92450948 0.943799498 0.960126275 0.914857897 1 16.96128151 -1.73438375 2.506028837 1.013425189 0.937828036 0.549459113 0.018353891 4294153.282 3023731.403 357425.441 0.004406341 0.018433859 1.73438375 -0.075597152 LNEQASEEILKVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNEQASEEILKVEQK 15 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 161.19 1.52E-06 108620000 226360 191040 192420 230560 115230 241860 229870 244590 138210 FALSE TRUE 215660.4114 210507.1932 201242.6473 207383.6708 135326.0755 233484.3276 194799.1096 223172.4029 159642.9009 1.350892587 1.318612929 1.260579996 1.299047246 0.847679883 1.462541248 1.220217802 1.397947555 1 17.28448887 -1.795185514 2.664695756 0.922729442 1.271717922 0.209279953 0.164704012 17916778.48 11859031.74 8927064.559 0.036266581 0.016025607 1.795185514 0.348988481 LNFAVASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNFAVASR 8 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 115.49 0.0057067 265460000 468010 392290 325830 368880 481260 322160 465980 434060 465660 FALSE TRUE 445888.0948 432264.797 340769.6278 331799.4816 565191.5916 311003.5184 394886.1927 396051.4053 537872.1745 0.828985242 0.803657109 0.633551323 0.616874226 1.050791653 0.578210834 0.734163638 0.736329976 1 19.03690383 -1.546290865 7.681806506 1.000081591 0.750571566 0.259842627 0.133686142 0.000172379 1.02E-05 0.119444354 0.028144157 0.028425567 1.546290865 -0.249510025 LNFDMTAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.015)AS(0.985)PK;LNFDMT(0.001)AS(0.999)PK;LNFDMTAS(1)PK 171.95 4.05E-06 149795000 556720 578280 470890 648890 370790 582320 560630 675910 419850 TRUE FALSE 530404.9489 637207.3894 492480.7723 583662.3444 435455.6586 562154.1124 475095.5968 616723.7372 484958.1937 1.093712728 1.313942929 1.015511808 1.203531257 0.897924119 1.159180564 0.979662996 1.271704954 1 18.88750086 3.723537966 24.96415328 1.071997339 1.203827839 0.158152241 0.123034436 1112.147852 1848130.667 0.028950393 0.045055344 5291.002486 -3.723537966 0.1318305 LNFGDDIPSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNFGDDIPSALR 12 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 107.06 0.0043162 34947000 87274 73896 71385 79635 85086 69383 94466 79417 91545 FALSE TRUE 83148.73098 81426.08641 74658.07286 71629.9385 99924.97146 66980.24931 80053.47671 72462.82646 105741.3311 0.786340877 0.770049758 0.706044383 0.677407195 0.944994455 0.633434899 0.757068933 0.68528385 1 16.69017987 -1.761294393 2.798310744 1.054074201 0.748221522 0.471504262 0.084759871 27415659.82 24173700.55 10269514.44 0.018822896 0.017326291 1.761294393 -0.305852679 LNFHPDQEDQFFSLVHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNFHPDQEDQFFSLVHEK 18 0 Q969Z0;Q969Z0-2;H7C4R5 Q969Z0 TBRG4 Protein TBRG4 0 246.68 1.51E-24 45264000 126240 115450 109400 115010 95454 99267 115800 131290 44056 FALSE TRUE 120272.8854 127214.4863 114416.0982 103448.9763 112101.1474 95829.3589 98132.58319 119793.5516 50887.97947 2.363483216 2.499892658 2.248391455 2.032876474 2.202900342 1.883143326 1.928404 2.354063825 1 15.63503729 -1.396629738 0.202293422 3.92E-14 2.517923261 0.79099247 0.192812095 10.12995466 0.385718104 6.104002413 0.520974407 0.040120863 1.396629738 2.517923261 LNFSHGTHEYHAETIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LNFSHGTHEYHAETIK 16 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 183.36 6.94E-10 7656770000 3218960 2740810 3136960 3443620 3015420 3327710 4167410 3332120 596947 FALSE TRUE 3066806.14 3020101.655 3280792.719 3097460.775 3541308.293 3212470.568 3531595.065 3040341.908 689518.492 4.447750388 4.38001546 4.758092433 4.49220842 5.135914895 4.659005677 5.121827922 4.409369645 1 19.39522972 0.953131444 22.99673269 1 4.694372292 0.953947273 0.254624353 995.5408003 488477.101 0.262914429 0.065728607 8.977004519 -0.953131444 3.694372292 LNGPGENVS(ph)EDEAQSSNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LNGPGENVSEDEAQSSNQR 19 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;A0A3B3IT29;A0A3B3ISF8;G3V0E9;Q659C4-3 A0A3B3ISF0 LARP1B La-related protein 1B 1 LNGPGENVS(1)EDEAQSSNQR;LNGPGENVS(1)EDEAQSSNQR;LNGPGENVS(1)EDEAQSSNQR;LNGPGENVS(1)EDEAQSSNQR 412.57 8.00E-148 496514000 548572 498872 522184 557219 515337 553796 624645 600444 566268 TRUE FALSE 522642.0887 549707.624 546126.6529 501206.2875 605211.6096 534617.9057 529343.9329 547865.9402 654081.9493 0.7990468 0.840426226 0.834951421 0.766274452 0.925284072 0.817356153 0.809292984 0.837610548 1 19.31911188 0.940566738 19.7855498 1 0.826783986 0.638833796 0.040525245 902.0067811 300282.9252 0.035330404 0.008832601 8.721009058 -0.940566738 -0.173216015 LNGTDPEDVIR ddPTM_SK-BR-3_Trastuzumab_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 ; 123.51 0.00085702 187003000 273910 243100 227100 276320 244870 237890 271880 283400 267450 FALSE TRUE 260962.8171 267872.1664 237512.7596 248543.7886 287575.2505 229651.8097 230399.7126 258583.9936 308924.7801 0.844745498 0.867111296 0.768836866 0.804544681 0.930890848 0.743390704 0.745811691 0.837045165 1 18.23689607 3.787020442 24.98360894 0.815638802 0.855928412 0 0.081914285 1322.434314 681779.8966 0.019619176 0.035368951 6123.79215 -3.787020442 0.040289609 LNHS(ph)PPQSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 115.04 0.00075814 1499440000 770740 756400 696090 791920 654621 653270 715960 614120 682553 TRUE FALSE 734308.6477 833478.02 728006.415 712314.6971 768786.6951 630647.0961 606727.1525 560344.3971 788399.8332 0.931391176 1.057176809 0.923397475 0.903494226 0.975122854 0.799907698 0.769567835 0.710736321 1 19.58856795 2.235951231 24.72127402 0.797464891 0.965134198 0.382912977 0.084707456 47.93980102 454171.339 0.028456568 0.021988269 172.167523 -2.235951231 0.167669308 LNHVAAGLVS(ph)PSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNHVAAGLVSPSLK 14 0 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.984)PS(0.016)LK 239.86 2.35E-17 116110000 202920 220530 191170 235260 153480 215910 221470 238320 162150 TRUE FALSE 193328.3737 243002.2577 199935.3336 211611.2178 180246.8634 208432.9826 187680.6839 217451.4374 187295.3939 1.032211043 1.297427837 1.067486656 1.129826065 0.962366771 1.11285696 1.002057125 1.161007929 1 17.51495589 3.320558064 2.366981752 1.052729946 1.163130943 0.155666146 0.089783307 0.406202597 4.640224373 0.02482507 0.035298597 2091.982582 -3.320558064 0.110400998 LNHVAAGLVS(ph)PSLKSDTSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNHVAAGLVSPSLKSDTSSK 20 1 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.986)PS(0.01)LKS(0.003)DTSSK 140.41 1.22E-07 219490000 179050 107170 188760 164720 153760 194700 267920 245770 190790 TRUE FALSE 170586.6613 118090.7448 197414.8327 148162.0327 180575.6953 187957.4902 227043.8833 224249.0759 220376.7388 0.774068363 0.535858483 0.895806126 0.672312484 0.819395442 0.852891695 1.030253395 1.017571442 1 17.74961243 2.159143659 1.094381258 1.036509461 0.693932153 0.649105192 0.093000775 0.27531164 0.62114939 0.06298912 0.033170411 144.2592462 -2.159143659 -0.342577309 LNIHQKT(ph)HTGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LNIHQKTHTGEK 12 1 Q9GZX5 Q9GZX5 ZNF350 Zinc finger protein 350 1 LNIHQKT(0.991)HT(0.009)GEK;LNIHQKT(0.997)HT(0.003)GEK;LNIHQKT(0.999)HT(0.001)GEK;LNIHQKT(0.998)HT(0.002)GEK;LNIHQKT(1)HTGEK 128.85 0.00035874 3063680000 4936530 5909990 4056520 5546760 1723981 5175110 3498310 4689610 1076785 TRUE FALSE 4703190.01 6512224.7 4242515.454 4989189.147 2024642.741 4995894.643 2964578.559 4278962.887 1243767.318 3.781406651 5.235886652 3.411020206 4.011352504 1.627830793 4.016743783 2.383547561 3.440324267 1 20.24628518 3.144313668 1.796134954 2.697697662 4.443241248 0.373465083 0.983249804 0.326917199 2.170486339 0.289446538 0.37896538 1394.163369 -3.144313668 1.745543585 LNIPWNHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNIPWNHIR 9 0 Q9NRN7;E9PLW6;E9PNF3;Q9NRN7-2 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 118.26 0.001979 0 58823 37556 15113 17380 57016 23077 60350 39734 47498 FALSE TRUE 56042.55337 41382.9991 15805.946 15632.92938 66959.57235 22277.8377 51142.4991 36254.68032 54863.74725 1.021486066 0.754286777 0.288094539 0.28494097 1.220470269 0.40605753 0.932172913 0.660813053 1 15.74356554 1.622547526 25 0.847374042 0.69154667 0.080079937 0.310458266 2.904108163 4933.630664 0.142501972 0.078592429 41.93218818 -1.622547526 -0.155827372 LNKHEENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNKHEENLK 9 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 155.84 4.35E-05 240753000 1126990 920400 756140 971180 736900 1013300 1275620 1241120 785960 FALSE TRUE 1073719.416 1014189.806 790809.7669 873555.1413 865415.1267 978209.1669 1081000.741 1132440.953 907842.6627 1.18271531 1.117142703 0.871086808 0.962231868 0.953265541 1.077509581 1.19073578 1.247397814 1 19.79208276 1.908628579 4.926519687 1.162990991 1.035241271 0.218691105 0.106499427 0.371005307 14.44847618 0.052528389 0.031049027 81.0267798 -1.908628579 -0.12774972 LNKPFLFDTKPLIVQYEVNFQNGIECGGAYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNKPFLFDTKPLIVQYEVNFQNGIECGGAYVK 32 2 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 261.57 1.24E-59 241460000 246474 177374 207921 328635 250983 258418 350170 262915 254988 FALSE TRUE 234823.6625 195448.6123 217454.3835 295599.9854 294754.3557 249468.9199 296745.1352 239892.7688 294530.2367 0.797282021 0.663594388 0.7383092 1.00363205 1.000760937 0.847006143 1.007520105 0.814492839 1 18.16805622 3.25011163 24.45092994 0.945923023 0.727350186 0.647155656 0.073929291 90.21408267 190961.6839 0.01878947 0.025216181 1778.736552 -3.25011163 -0.218572837 LNKSELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LNKSELK 7 1 P26447 P26447 S100A4 Protein S100-A4 0 ;; 115.49 0.005169 8437500000 7583480 4443230 5838620 5569140 4566520 6564720 8478170 7007750 5269160 FALSE TRUE 7225023.929 4896000.189 6106326.502 5009319.467 5362919.642 6337382.1 7184669.454 6394114.26 6086274.422 1.187101243 0.804433032 1.00329464 0.823051857 0.881149825 1.041258028 1.180470836 1.050579356 1 22.53712795 2.040027879 6.404370036 1.100602259 0.942260761 0.230172962 0.115306952 0.231688761 25.3534803 0.043059628 0.031215778 109.6548584 -2.040027879 -0.158341499 LNKSELKELLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNKSELKELLTR 12 2 P26447 P26447 S100A4 Protein S100-A4 0 67.964 0.030342 167520000 282560 112010 478180 205630 341360 357590 605250 420090 584750 FALSE TRUE 269203.9488 123423.9463 500105.026 184959.6817 400893.0759 345206.5686 512907.9963 383304.6926 675430.0435 0.398566737 0.182733871 0.740424609 0.27383988 0.593537524 0.511091522 0.759379896 0.56749725 1 19.36544683 1.293511803 0.185179878 1.208567311 0.117062396 0.565193604 0.158459721 2.160222745 0.388801953 0.995753539 0.825934686 19.65675403 -1.293511803 -1.091504916 LNLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNLKPR 6 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 74.832 0.072311 407720000 787870 653540 505370 613920 642840 555970 900890 759930 651210 FALSE TRUE 750628.9465 720136.469 528541.7144 552207.5952 754951.0925 536716.6195 763442.6845 693386.5006 752196.3209 0.99791627 0.957378345 0.702664583 0.734126956 1.003662304 0.713532631 1.014951368 0.921815863 1 19.52074972 1.618937165 25 0.976287452 0.870162553 0.20474423 0.114440985 1.492574785 3362.075722 0.054963374 0.030116569 41.58504399 -1.618937165 -0.106124899 LNLTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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(0.019)S(0.981)PK;LNLT(0.093)S(0.907)PK;LNLT(0.002)S(0.998)PK;LNLT(0.225)S(0.775)PK 109.79 0.0072894 1462390000 5485890 5280970 5073090 5791660 3204410 5744260 5927880 6222370 3650550 TRUE FALSE 5226582.852 5819106.847 5305696.194 5209471.333 3763258.089 5545334.836 5023473.033 5677506.296 4216658.65 1.239508171 1.380027963 1.258270265 1.235450096 0.892473971 1.315101671 1.191339743 1.346446741 1 22.00766881 -5 0.1203691 0.319413117 1.342106784 0.195273996 0.136238322 245.5551864 1.914379313 41.9806135 1.252887909 1.00E-05 5 1.022693667 LNLVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LNLVQR 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;Q9BYZ2;A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8 P00338;A0A5F9ZHM4 LDHA;LDHAL6B;LDHB L-lactate dehydrogenase A chain;L-lactate dehydrogenase A-like 6B;L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;;;; 124.94 0.042201 3534540000 3470470 2789880 2130826 2421800 3667840 2457863 3736530 2961310 3642250 FALSE TRUE 3306427.761 3074171.944 2228526.48 2178356.063 4307510.135 2372746.588 3166453.722 2702001.998 4207071.528 0.785921451 0.730715397 0.529709672 0.517784413 1.023873758 0.563990075 0.752650318 0.64225245 1 22.00438492 -1.64543163 2.837995218 1.029553596 0.700101679 0.293785825 0.149085313 24892243.11 23345645.5 5369507.238 0.032691548 0.022623947 1.64543163 -0.329451917 LNLWISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNLWISR 7 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ; 98.997 0.025247 96349000 163262 117604 65532 78785 198579 78714 180965 120013 185357 FALSE TRUE 155544.9288 129587.9813 68536.70702 70865.38212 233211.1147 75988.11444 153355.4656 109504.0255 214101.2169 0.726501844 0.605265039 0.32011358 0.330990095 1.089256372 0.35491678 0.716275544 0.511459146 1 17.70793347 -1.965937119 2.641503014 1.331984962 0.591571057 0.24154772 0.232295427 35320259.34 14382152.02 71688813.44 0.051484887 0.010815905 1.965937119 -0.740413905 LNNDDNVDGLLVQLPLPEHIDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LNNDDNVDGLLVQLPLPEHIDER 23 0 P13995-2;P13995 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 ;;;;;;; 205.38 1.56E-24 212979400 231704.9 240095.8 195073.1 231874.6 192611.3 190112.2 202443.9 212680.2 170085.5 FALSE TRUE 220752.6686 264561.835 204017.3946 208566.1247 226202.6497 183528.5668 171557.3649 194056.7942 196461.4907 1.123643457 1.34663457 1.038459975 1.061613266 1.151384167 0.934170693 0.873236604 0.98775996 1 17.58388703 2.851455807 0.878701386 0.929924062 1.222756496 0.493508422 0.093245893 0.400140816 0.673311623 0.053512122 0.05646773 710.3228844 -2.851455807 0.292832434 LNNMNKYDYVLTGYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNNMNKYDYVLTGYTR 16 1 O00764;F2Z2Y4 O00764 PDXK Pyridoxal kinase 0 171.29 4.54E-09 387730000 351930 276710 295190 338480 329570 317850 381390 344340 383700 FALSE TRUE 335294.9664 304907.0636 308724.7535 304455.3473 387046.9037 306842.7748 323201.9508 314187.7641 443202.2363 0.756528146 0.68796373 0.696577608 0.68694452 0.873296369 0.692331287 0.729242599 0.708903833 1 18.75760564 -1.332552522 3.194107033 1.001997392 0.72752038 0.70095662 0.055626221 11620118.11 15130720.09 218550.4212 0.012338532 0.046499414 1.332552522 -0.274477012 LNPEDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 115.71 0.0038652 2228000000 4213300 3357300 3824400 4499800 2545800 4818800 5335400 5183300 3223500 FALSE TRUE 4014145.659 3699412.687 3999752.523 4047471.555 2989786.714 4651923.748 4521386.739 4729422.774 3723383.917 1.078090723 0.993561977 1.074225117 1.087041155 0.802975675 1.249380631 1.214321929 1.270194769 1 21.82818295 2.184119761 24.99998673 1.204442273 1.018443934 0.384657962 0.108861818 82.69612691 37974.56304 0.036588623 0.027022507 152.7987357 -2.184119761 -0.185998339 LNPNFLVDFGKEPLGPALAHELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNPNFLVDFGKEPLGPALAHELR 23 1 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 214.17 3.79E-28 4030200000 2812300 2076590 2442500 2632500 2247700 2484900 3374500 2754600 2181070 FALSE TRUE 2679368.152 2288196.882 2554491.041 2367876.099 2639698.168 2398847.29 2859658.048 2513392.621 2519299.196 1.063537097 0.908267222 1.013968902 0.939894754 1.04779066 0.952188328 1.135100607 0.997655469 1 21.26459104 1.763183511 25 1.057698164 0.985787272 0.151255764 0.060418336 19.54815365 19861.43241 0.025139245 0.013941461 57.96735856 -1.763183511 -0.071910892 LNPTWNHPDQDTEAGFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNPTWNHPDQDTEAGFKR 18 1 F8VR84;Q9HB07 F8VR84 C12orf10 "UPF0160 protein MYG1, mitochondrial" 0 ; 223.5 3.32E-19 386690000 567930 441560 507850 563600 444680 547990 695770 591480 451890 FALSE TRUE 541085.0744 486555.466 531135.4248 506945.8572 522232.0512 529012.9689 589617.5078 539686.8756 521966.7933 1.03662739 0.932157893 1.017565546 0.97122243 1.000508189 1.013499279 1.129607315 1.033948677 1 18.9935985 1.963348651 9.835193697 1.069651439 0.98941846 0.28941575 0.042784643 0.49640485 130.2343744 0.016295876 0.010481972 91.90701296 -1.963348651 -0.080232978 LNQPGT(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.965)PT(0.035)R;LNQPGT(0.944)PT(0.056)R;LNQPGT(0.906)PT(0.094)R;LNQPGT(0.946)PT(0.054)R;LNQPGT(0.512)PT(0.488)R 145.95 0.0010727 17182380000 4904510 3940430 4087080 4699960 4807770 4198760 5223990 4230810 4848220 TRUE FALSE 4672683.532 4341964.297 4274476.661 4227511.091 5646243.566 4053355.888 4426974.38 3860337.847 5600057.196 0.834399251 0.775342848 0.763291608 0.754904985 1.008247482 0.723806159 0.790523065 0.689339004 1 22.41701013 -1.156583585 4.942145922 1.000013947 0.794523645 0.365960936 0.085804494 1.20E-05 2.06E-06 0.075901458 0.017888931 0.069729478 1.156583585 -0.205490301 LNQPGTPT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.276)PT(0.724)R;LNQPGT(0.473)PT(0.527)R 103.69 0.037807 8589900000 2472680 2055120 2297930 2513210 2483040 2141790 2640140 2364470 2740960 TRUE FALSE 2355801.317 2264539.064 2403292.363 2260577.356 2916081.39 2067619.275 2237338.154 2157424.472 3166014.078 0.744090601 0.715265002 0.759090865 0.714013678 0.921057619 0.653066987 0.70667347 0.681432369 1 21.59423624 -1.075581193 4.665444762 1.000010825 0.734958175 0.56959005 0.071876814 8.96E-06 1.77E-06 0.06464112 0.015235317 0.08402699 1.075581193 -0.26505265 LNQS(ph)PSLAPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNQSPSLAPVKR 12 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LNQS(0.936)PS(0.064)LAPVKR;LNQS(0.972)PS(0.028)LAPVKR 157.54 4.54E-05 732440000 1218960 1118360 1205450 1314580 1025500 1228120 1652790 1402690 1379180 TRUE FALSE 1161342.177 1232322.155 1260721.075 1182435.921 1204346.875 1185589.896 1400626.53 1279863.027 1593056.191 0.729002645 0.773558499 0.791385189 0.7422437 0.755997737 0.744223527 0.879207236 0.803401057 1 20.60336572 0.649645115 0.553660037 1.0068023 0.750691376 0.818960901 0.034868632 0.560973793 0.342718423 0.042561108 0.015700522 4.463187322 -0.649645115 -0.256110924 LNQSS(ph)PDNVTDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LNQSSPDNVTDTK 13 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 LNQS(0.003)S(0.997)PDNVTDTK;LNQS(0.017)S(0.983)PDNVTDTK;LNQS(0.046)S(0.954)PDNVTDTK 190.44 4.63E-06 301942000 909250 884100 903160 1070760 695720 1002290 1145690 1123160 862190 TRUE FALSE 866271.5545 974190.7951 944570.7793 963125.1705 817053.3477 967580.446 970893.9485 1024810.156 995894.0217 0.869843111 0.978207293 0.948465157 0.967096046 0.820421983 0.97156969 0.974896854 1.029035353 1 19.9256327 1.722362641 2.456122126 1.008836725 0.924235826 0.378229407 0.048556326 0.284400087 3.634498782 0.029890482 0.012977685 52.7670288 -1.722362641 -0.084600899 LNRPLTLSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNRPLTLSEK 10 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 61.932 0.093937 0 590470 481570 395040 416810 420330 492920 539310 533750 447800 FALSE TRUE 562559.6533 530642.5305 413152.9747 374911.4669 493635.4189 475850.0568 457028.3544 487012.0204 517242.537 1.087612896 1.025906596 0.79876063 0.724827214 0.954359674 0.919974717 0.883586174 0.941554465 1 18.9804814 3.895774726 5.401901934 0.882617373 1.065195717 0.442264961 0.079159864 0.175042261 7.405089554 0.020121821 0.037175612 7866.376443 -3.895774726 0.182578345 LNS(ph)KWNILCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNSKWNILCEK 11 1 Q9Y234 Q9Y234 LIPT1 "Lipoyltransferase 1, mitochondrial" 1 LNS(1)KWNILCEK 82.645 0.04833 212710000 523930 422010 478180 544110 405870 542020 604050 560620 418290 TRUE FALSE 499164.8672 465013.2988 500105.026 489415.0291 476653.5995 523249.7115 511891.0784 511529.1408 483156.2769 1.033133359 0.962449048 1.035079228 1.012953888 0.986541254 1.082982332 1.0594731 1.058723989 1 18.88213038 2.244331984 24.99994404 1.056693728 1.004187149 0.34739057 0.02951389 124.7088952 540204.8325 0.009575163 0.007812157 175.5221717 -2.244331984 -0.05250658 LNS(ph)SENGEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;LNS(0.928)S(0.072)ENGEDR 215.93 8.35E-09 769810000 547352 454547 496295 564529 446029 466462 526063 467126 452524 TRUE FALSE 521479.7557 500865.8561 519050.6167 507781.4724 523816.3164 450308.304 445802.4275 426221.971 522699.1107 0.997667195 0.958229784 0.993019896 0.971460372 1.002137378 0.861505778 0.852885376 0.815425093 1 18.99562118 2.234358652 24.99250724 0.868029627 0.981911272 0.504189432 0.049335711 70.09382806 416900.1464 0.015871566 0.01214207 171.5373324 -2.234358652 0.113881645 LNS(ph)VQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Trastuzumab_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 1 LNS(0.969)VQS(0.015)S(0.015)ERPLFLVHPIEGSTTVFHSLASR;LNS(0.923)VQS(0.066)S(0.011)ERPLFLVHPIEGSTTVFHSLASR 296.81 2.92E-81 10718900000 1837590 1384260 1830900 1816260 1431310 1865890 2259670 1875400 627020 TRUE FALSE 1750730.762 1525317.668 1914848.576 1633686.094 1680930.011 1801273.761 1914915.84 1711180.034 724255.0592 2.417284823 2.106050415 2.643887056 2.255677849 2.320908897 2.48707101 2.643979929 2.362675983 1 19.46613833 -0.615434981 9.989547361 1 2.400732192 0.878868192 0.163883521 0 0 0.164696765 0.0388194 0.242418086 0.615434981 1.400732192 LNSGDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LNSGDYK 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 127.02 0.0090623 947880000 2290190 2110820 2044620 2393090 1651360 2295360 2512860 2435050 1862290 FALSE TRUE 2181937.257 2325914.958 2138367.849 2152532.047 1939356.661 2215871.108 2129477.055 2221824.113 2151084.422 1.014342922 1.081275534 0.994088297 1.000672974 0.901571617 1.030118151 0.989955128 1.032885595 1 21.03663272 3.655014133 8.379936001 0.991015274 1.047722105 0.255229992 0.039021393 0.379609964 34.95852932 0.009844626 0.01527724 4518.706487 -3.655014133 0.056706831 LNSHMNALHLGSQANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LNSHMNALHLGSQANR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 242.09 3.60E-20 9555092000 2190526 1648469 1940368 2088567 2554110 1864663 2413650 1981501 1227881 FALSE TRUE 2086984.177 1816449.865 2029335.792 1878620.277 2999545.975 1800089.253 2045403.363 1807990.268 1418294.514 1.471474476 1.28072826 1.430828204 1.324562887 2.114896409 1.269192847 1.442157001 1.274763633 1 20.43572571 -0.484749581 7.102612505 1.000002942 1.444178149 0.246687899 0.2474616 0 0 0.221572635 0.052225171 0.327529498 0.484749581 0.444175207 LNSNDEDIHTANER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNSNDEDIHTANER 14 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 200.97 1.17E-07 0 144100 135330 149030 160960 154230 161360 163890 148490 136150 FALSE TRUE 137288.6786 149120.2809 155863.1729 144779.995 181127.6632 155772.0627 138885.5705 135487.4284 157263.4466 0.872985309 0.94821959 0.991096 0.920620768 1.151746747 0.990516653 0.883139556 0.861531597 1 17.26282385 -2.094181978 7.807131004 1.270707125 0.950202373 0.030199154 0.08374503 0.10500464 0.001266732 0.021577532 0.019130923 0.00805041 2.094181978 -0.320504752 LNSVQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Trastuzumab_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 ; 275.21 1.61E-71 15151900000 8758900 6835100 8388000 9471600 10298400 7881700 10989800 9242900 4146900 FALSE TRUE 8344884.155 7531604.461 8772598.097 8519496.773 12094437.7 7608754.753 9313104.168 8433542.676 4789980.073 1.742154253 1.572366554 1.831447723 1.778607978 2.524945306 1.588473154 1.944288708 1.760663416 1 22.19158822 0.946997626 19.39442041 0.999999995 1.831981105 0.502054675 0.26466458 682.2314989 249641.2401 0.245125551 0.061281234 8.851107713 -0.946997626 0.831981109 LNSVQSSERPLFLVHPIEGSTTVFHSLASRLS(ph)IPTYGLQCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNSVQSSERPLFLVHPIEGSTTVFHSLASRLSIPTYGLQCTR 42 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 1 LNSVQSSERPLFLVHPIEGS(0.002)T(0.002)T(0.015)VFHS(0.084)LAS(0.091)RLS(0.803)IPT(0.001)YGLQCT(0.001)R 123.86 4.35E-09 103900000 60999 38809 58101 52989 73863 49869 64367 58240 38069 TRUE FALSE 58115.69816 42763.68122 60764.98832 47662.44505 86744.68381 48142.02403 54546.63197 53140.19685 43972.54609 1.32163596 0.972508645 1.381884692 1.083913698 1.972700958 1.094820025 1.240470176 1.208485784 1 15.42431545 0.790154114 1.321961431 1.002337082 1.278580677 0.105277544 0.270813517 1.920359684 6.046991007 0.242599964 0.072847743 6.168138457 -0.790154114 0.276243595 LNT(ph)SDFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LNTSDFQK 8 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 LNT(0.985)S(0.015)DFQK;LNT(0.921)S(0.079)DFQK;LNT(0.973)S(0.027)DFQK;LNT(0.965)S(0.035)DFQK;LNT(0.913)S(0.087)DFQK 184.27 0.0024472 2178160000 3898450 3789680 3824130 4795790 2570930 5894400 6672440 6934350 3870060 TRUE FALSE 3714177.994 4175852.701 3999470.143 4313708.078 3019299.378 5690275.45 5654436.73 6327141.553 4470209.139 0.830873429 0.934151529 0.89469419 0.964990215 0.675426872 1.272932714 1.264915478 1.415401686 1 22.0919109 2.220296538 24.99924605 1.261321927 0.873831581 0.683587826 0.127266564 122.5999525 167809.5709 0.042286922 0.031290041 166.0720465 -2.220296538 -0.387490346 LNTAEDAKDVIKEIEDFDSLEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LNTAEDAKDVIKEIEDFDSLEALR 24 2 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;; 126.46 5.15E-05 74263000 191758 110093 191122 157251 143460 188776 267711 218181 159873 FALSE TRUE 182693.9794 121311.6019 199885.1327 141443.8307 168479.3786 182238.6398 226866.7701 199075.915 184665.2883 0.989324962 0.656926935 1.082418545 0.765947039 0.912350015 0.986859206 1.228529585 1.078036467 1 17.49455318 2.073771407 3.086829667 1.124877184 0.863473053 0.370945853 0.128320254 0.213292694 4.03278944 0.053166411 0.034133702 118.5144777 -2.073771407 -0.261404131 LNTQEIFDDWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LNTQEIFDDWAR 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 260.6 5.88E-21 457550000 560164 521033 477315 610956 522540 528275 579351 585146 594023 FALSE TRUE 533686.1579 574126.8551 499200.3649 549541.5421 613670.8106 509980.7043 490960.3644 533907.5142 686141.053 0.77780823 0.836747565 0.727547729 0.800916284 0.894379964 0.743259279 0.715538536 0.77813084 1 19.38814566 -0.898754271 5.425300266 1.000000229 0.783761769 0.624571994 0.052557047 1.49E-07 3.03E-08 0.052104916 0.012281234 0.126254169 0.898754271 -0.21623846 LNVDFALIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNVDFALIHK 10 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ; 124.42 0.00043596 268670000 966260 956750 659040 878140 774710 792360 974850 918600 725970 FALSE TRUE 920586.8047 1054243.913 689257.6359 789867.6988 909819.1787 764920.3745 826118.7282 838162.5142 838549.7199 1.097832106 1.257222903 0.821963945 0.94194498 1.084991333 0.912194419 0.985175606 0.999538244 1 19.6775368 3.749289632 24.99992923 0.965215096 1.177527508 0.569723997 0.07725079 447.9015384 1043662.879 0.018780392 0.033431863 5614.222654 -3.749289632 0.212312412 LNVFKNDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LNVFKNDQDTWDYTNPNLSGQGDPGSNPNKR 31 2 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 100.68 0.00012475 221840000 119490 65503 123000 92519 185720 107360 153650 120960 196280 FALSE TRUE 113841.9445 72177.83017 128639.6717 83218.81435 218109.5092 103642.0963 130207.8705 110368.1012 226718.0999 0.502129934 0.318359364 0.567399214 0.367058538 0.962029539 0.457140812 0.574316169 0.486807631 1 17.79054005 -4.999999999 0.15625364 2.736569061 0.3803843 0.425218336 0.172542156 120.3691924 1.094244516 65.04542517 0.721767363 1.00E-05 4.999999999 -2.356184761 LNVTEQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNVTEQEK 8 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ; 82.645 0.049597 50255000 246490 233570 221390 285110 176289 279800 271560 297590 163344 FALSE TRUE 234838.9062 257371.0485 231540.9505 256450.2011 207033.7458 270110.4558 230128.5345 271531.442 188674.5533 1.244677155 1.364100479 1.227197555 1.359219867 1.09730614 1.431621017 1.219711564 1.439152431 1 17.52554033 -1.069498494 4.361070518 0.999975068 1.294751344 0.440106854 0.105534086 0.269347092 18821166.57 1040.036052 0.021436421 0.085212147 1.069498494 0.294776276 LNVTEQEKIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNVTEQEKIDK 11 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ; 174.9 9.54E-06 1146850000 2986400 2102800 2443900 2554100 1706430 3056200 3403900 3636900 2040600 FALSE TRUE 2845238.79 2317077.711 2555955.232 2297357.016 2004030.852 2950363.028 2884572.538 3318433.756 2357045.826 1.207120693 0.983043132 1.084389283 0.974676432 0.850229906 1.25172069 1.223808424 1.407878336 1 21.16854838 2.198074607 24.99917514 1.238257694 1.032764188 0.356719347 0.132563809 158.7768035 98040.09471 0.046743291 0.034522638 157.7882311 -2.198074607 -0.205493506 LNWLSVDFNNWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNWLSVDFNNWK 12 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 237.36 9.79E-16 311500000 957660 1302830 660910 1016790 612420 766170 817050 898540 546590 FALSE TRUE 912393.3097 1435589.858 691213.3772 914580.3374 719225.8541 739637.3408 692394.0163 819859.0741 631352.3856 1.445141145 2.273832951 1.094813915 1.448605182 1.13918292 1.171512705 1.096683931 1.29857603 1 19.26808594 3.720372349 24.96683892 1.185957316 1.859487064 0.601199632 0.230527309 436.8112644 599606.1526 0.057313741 0.088980402 5252.57605 -3.720372349 0.673529748 LNYSDHDVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LNYSDHDVIK 10 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 107.03 0.0023385 961840000 1918230 1492800 1912810 2201400 1763390 1998450 2353800 2282700 1750310 FALSE TRUE 1827559.069 1644918.017 2000514.231 1980111.09 2070924.658 1929243.175 1994684.579 2082814.687 2021739.135 0.903953946 0.813615361 0.98950166 0.979409784 1.024328323 0.95424931 0.986618177 1.030209412 1 20.94716543 3.725419858 24.78327138 0.992100297 0.858784656 0.776822933 0.030302988 252.0860178 475430.515 0.007576673 0.011817367 5313.979299 -3.725419858 -0.133315641 LPAGHEDGVQLSWDLS(ph)PLGEVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPAGHEDGVQLSWDLSPLGEVLGR 24 0 A0A494BZV2;H0Y2S9 A0A494BZV2 MPRIP 1 LPAGHEDGVQLSWDLS(1)PLGEVLGR;LPAGHEDGVQLS(0.001)WDLS(0.999)PLGEVLGR 161.32 1.25E-11 17729200 19189.4 14819.2 15045.8 20509 19254.5 13077.5 18138.5 16654.6 13339.1 TRUE FALSE 18282.35509 16329.29333 15735.66481 18447.39636 22612.4787 12624.6229 15371.13869 15196.23493 15407.6595 1.186575748 1.059816601 1.021288458 1.197287385 1.467612826 0.819373176 0.997629698 0.986277957 1 13.91136011 2.198102885 24.9999999 0.950971768 1.162224981 0.447819325 0.128487236 157.9781895 97618.36785 0.047752447 0.035267973 157.7985051 -2.198102885 0.211253213 LPAYLATS(ph)PIPTEDQFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPAYLATSPIPTEDQFFK 18 0 Q92539;J3KTK1 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 LPAYLAT(0.018)S(0.982)PIPTEDQFFK 90.444 0.0024018 0 40176 43308 27316 43544 22316 33284 30693 33779 23882 TRUE FALSE 38276.9601 47721.13444 28568.46562 39166.87439 26207.90333 32131.36673 26010.21913 30821.13169 27585.49859 1.387575431 1.729935542 1.03563347 1.419835653 0.95006089 1.164791952 0.942894654 1.117294712 1 14.75162244 3.345761199 1.169269546 1.037961791 1.550644095 0.497007836 0.178124484 0.311540272 0.894517857 0.05980719 0.104376527 2216.977058 -3.345761199 0.512682304 LPDAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LPDAYER 7 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 202.2 0.00073074 4753110000 4998440 4545040 4277450 5232240 4786130 4275350 4972480 4571540 4812670 FALSE TRUE 4762173.647 5008184.743 4473575.313 4706285.295 5620829.557 4127293.557 4213836.85 4171231.722 5558994.284 0.856661008 0.900915613 0.804745442 0.846607328 1.011123464 0.742453283 0.75802144 0.750357261 1 22.40639247 2.171287824 24.99999935 0.787055432 0.878536524 0.102517076 0.091011691 83.05233005 30862.65898 0.030605196 0.022603441 148.3500932 -2.171287824 0.091481092 LPDLS(ph)PVENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 187.58 1.27E-06 678670000 1955190 2303400 1435370 2291700 1007020 1855820 1529460 1791060 849150 TRUE FALSE 1862772.044 2538119.079 1501183.134 2061333.962 1182643.969 1791552.488 1296112.787 1634225.291 980831.8451 1.899175738 2.587720914 1.530520386 2.101618103 1.205756089 1.826564357 1.321442399 1.666162553 1 19.90364629 2.667017484 0.312716394 1.043783788 2.447841547 0.448967168 0.341931588 1.65403106 0.344167232 0.414332382 0.825647872 464.5339763 -2.667017484 1.404057759 LPDLS(ph)PVENKEHKPGPIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPDLSPVENKEHKPGPIGK 19 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 LPDLS(1)PVENKEHKPGPIGK 77.689 0.0053191 214520000 484640 389440 465830 516020 638830 457130 555070 537240 514480 TRUE FALSE 461732.0277 429124.3788 487188.7663 464148.6892 750241.7497 441299.4735 470383.8769 490196.4175 594262.9308 0.776982719 0.722111975 0.819820219 0.781049373 1.262474421 0.742599699 0.791541677 0.824881365 1 19.18074187 2.96242696 24.99934769 0.900038419 0.767369387 0.198090307 0.14470314 1024.280615 681508.523 0.043618606 0.046275318 917.1216802 -2.96242696 -0.132669032 LPDNVTFEEGALIEPLSVGIHACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPDNVTFEEGALIEPLSVGIHACR 24 0 Q00796;A0A6I8PIS1 Q00796 SORD Sorbitol dehydrogenase 0 ; 186.55 2.10E-17 112659000 110525 104137 100309 114938 118978 99818 129385 115538 130776 FALSE TRUE 105300.7023 114748.6787 104908.2669 103384.2139 139727.7255 96361.27763 109644.9419 105420.8802 151056.0742 0.697096776 0.759642929 0.694498831 0.684409511 0.925005673 0.637917265 0.725855895 0.697892361 1 17.20472467 -1.251786945 3.558290149 1.000588774 0.728208603 0.554965894 0.076606494 22858016.11 32273137.59 143276.2781 0.016646086 0.056003227 1.251786945 -0.272380171 LPDS(ph)DDDEDEETAIQR ddPTM_SK-BR-3_Trastuzumab_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 463.62 9.78E-206 12683750000 940220 869812 813822 1008694 881019 922093 958929 882211 810102 TRUE FALSE 895777.6639 958446.8317 851136.5437 907298.1627 1034668.435 890160.6882 812626.7691 804959.9279 935728.4807 0.957305118 1.024278785 0.909597775 0.969616915 1.105735751 0.951302335 0.868442915 0.860249468 1 19.83573044 1.99579991 24.96709683 0.898678149 0.992637597 0.26848569 0.062470754 193.0557227 1147606.413 0.022450412 0.016191853 99.03755508 -1.99579991 0.093959448 LPDSSNKIEEDRCS(ph)NSADITGPSFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPDSSNKIEEDRCSNSADITGPSFIR 26 2 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LPDSSNKIEEDRCS(1)NSADITGPSFIR;LPDSSNKIEEDRCS(1)NSADITGPSFIR 152.19 5.47E-08 176169000 171023 120378 154404 169741 124708 155582 192195 195034 141600 TRUE FALSE 162939.0817 132644.6551 161483.5761 152678.3122 146457.0357 150194.1563 162872.1228 177955.789 163558.6048 0.996212226 0.810991603 0.987313241 0.933477712 0.895440725 0.918289542 0.995802838 1.088024621 1 17.31944814 1.587689216 3.390355836 1.044198725 0.917908232 0.45613173 0.055034496 0.160092425 4.275123807 0.033160462 0.013714503 38.69806203 -1.587689216 -0.126290493 LPDSSNKIEEDRCSNS(ph)ADITGPSFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPDSSNKIEEDRCSNSADITGPSFIR 26 2 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LPDS(0.001)S(0.001)NKIEEDRCS(0.429)NS(0.567)ADIT(0.002)GPSFIR 55.049 0.04985 105000000 75874 66242 87531 92756 70109 91455 99511 111720 89630 TRUE FALSE 72287.58639 72992.13511 91544.38293 83431.99066 82335.9874 88287.89042 84328.76931 101937.2045 103529.3626 0.6982327 0.705038003 0.884235937 0.805877565 0.795291165 0.852781164 0.814539636 0.984621193 1 16.65968047 6.959118561 0.091826935 1.150164257 1.30E-13 0.712872748 0.053797538 60.62123801 0.496353915 0.977988386 8.820960418 9101617.107 -6.959118561 -1.150164257 LPEADDIQYPSMLLLTADHDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPEADDIQYPSMLLLTADHDDR 22 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 297.48 1.34E-55 445940000 275890 284290 242379 300940 236418 253360 261850 280160 198520 FALSE TRUE 262849.2265 313259.4742 253492.3169 270688.9395 277649.2243 244586.0797 221899.9733 255627.7052 229305.4677 1.146284165 1.366123003 1.105478729 1.180473114 1.210826881 1.066638673 0.967704676 1.114791146 1 17.80691123 2.17564708 3.805006355 1.02244629 1.214885158 0.531893631 0.076721984 0.16003729 4.662574076 0.029970193 0.021742314 149.8466646 -2.17564708 0.192438868 LPEDPLLSGLLDSPALK ddPTM_SK-BR-3_Trastuzumab_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 ; 159.08 7.58E-09 104379000 242010 250520 210149 282900 190277 227372 263490 274570 200667 FALSE TRUE 230570.6669 276048.2728 219784.5395 254462.3545 223461.2486 219498.0506 223289.7612 250527.1952 231785.4135 0.994759176 1.190964818 0.948224205 1.097835928 0.964086761 0.946988196 0.963346907 1.080858331 1 17.82243025 3.71850181 24.9448442 0.995953587 1.092862018 0.232809085 0.069608374 912.8288638 1135180.835 0.017586212 0.027282457 5230.001461 -3.71850181 0.096908431 LPEEWSQWLGGSSWPGYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 214.45 9.99E-19 90765000 48812 39445 39472 52786 37036 40470 52645 42625 41058 FALSE TRUE 46504.7535 43464.49035 41281.83024 47479.85099 43495.06667 39068.51375 44613.03836 38892.52903 47425.06494 0.980594408 0.916487735 0.87046439 1.001155213 0.917132464 0.823794628 0.940705899 0.820083833 1 15.53336213 2.475108278 24.99606719 0.891146391 0.940275469 0.106385437 0.062059831 130.3026145 1617986.781 0.01920373 0.016169057 298.6127024 -2.475108278 0.049129078 LPEEWSQWLGGSSWPGYVRPLPPAAIES(ph)PAVAAPAYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 LPEEWSQWLGGSSWPGYVRPLPPAAIES(1)PAVAAPAYSR;LPEEWSQWLGGSSWPGYVRPLPPAAIES(1)PAVAAPAYSR 220.25 1.58E-39 189196000 82154 56782 66694 78057 83981 61962 99855 84311 79626 TRUE FALSE 78270.74323 62568.15036 69751.98587 70210.56206 98627.25981 59816.2404 84620.28579 76928.28188 91973.99341 0.851009512 0.680280893 0.758388141 0.763374074 1.072338562 0.65036037 0.920045794 0.836413415 1 16.48893836 0.45228721 0.243630172 1.061042766 0.740230668 0.223304412 0.117522614 6.576461056 0.894858086 0.647787194 0.242756309 2.833265086 -0.45228721 -0.320812097 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 277.49 1.03E-76 63697000 40239 25861 29418 34524 44295 34398 44724 37525 42906 FALSE TRUE 38336.98222 28496.2653 30766.8444 31053.58193 52020.03398 33206.78863 37900.53239 34239.11207 49559.64335 0.773552423 0.574989313 0.620804395 0.626590101 1.049645043 0.670036877 0.764745866 0.690866797 1 15.59687818 LPEHCIEYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPEHCIEYVR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 140.3 3.95E-05 372100000 450010 373950 411480 459610 473520 385180 485500 451340 458160 FALSE TRUE 428738.9191 412055.9301 430346.765 413409.1296 556101.7381 371841.12 411428.0582 411818.2769 529209.1128 0.810150295 0.778625916 0.813188501 0.781182938 1.050816633 0.70263552 0.777439481 0.778176843 1 19.01347838 -1.58576909 2.764204634 1.013752692 0.807654632 0.299647172 0.090381253 23563765.22 23695846.06 2376670.727 0.020202383 0.02595559 1.58576909 -0.20609806 LPESENLQEFWDNLIGGVDMVTDDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 110.31 0.0022892 1463030000 120828 136765 128775 111218 151859 122632 138300 105083 100240 FALSE TRUE 115116.6999 150701.509 134679.4611 100038.1553 178343.1615 118385.2231 117199.7949 95881.37544 115784.7072 0.994230608 1.301566611 1.163188683 0.864001453 1.540299801 1.022459925 1.012221715 0.828100513 1 16.82108519 1.774555351 2.866485374 0.93009672 1.163773393 0.226587905 0.185321668 0.34667754 5.608305654 0.098679398 0.047102042 59.50525917 -1.774555351 0.233676673 LPETNLFETEETRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPETNLFETEETRK 14 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ; 201.3 2.89E-08 316360000 367420 321250 333560 398740 284580 387820 391880 424100 355070 FALSE TRUE 350052.7848 353985.7402 348854.0559 358657.8976 334210.6619 374389.6962 332091.5086 386963.5557 410132.4422 0.85351157 0.863101047 0.850588786 0.874492873 0.814884724 0.912850723 0.809717727 0.943508769 1 18.64573034 1.042866128 5.031319355 0.999512409 0.855278138 0.752543209 0.028993717 0.067611051 3.799616634 0.023580723 0.005966073 11.03738337 -1.042866128 -0.144234271 LPFPIIDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LPFPIIDDR 9 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 174.27 0.00012749 1382335000 925837 948760 728361 969352 882814 750822 903064 857782 846900 FALSE TRUE 882074.5198 1045439.723 761757.0723 871910.8953 1036776.482 724820.8459 765285.0009 782670.0607 978232.9266 0.901701932 1.068702243 0.77870725 0.891312152 1.059846233 0.74094914 0.78231368 0.800085582 1 19.8998185 2.225527284 24.99989328 0.80687886 0.944560896 0.18941796 0.107068873 291.9772861 560052.6817 0.037654809 0.027979007 168.084352 -2.225527284 0.137682036 LPFTPLSYIQGLSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPFTPLSYIQGLSHR 15 0 J3KS45;Q9UM00-1;Q9UM00;J3QQY2;Q9UM00-2 J3KS45 TMCO1 Transmembrane and coiled-coil domain-containing protein 1 0 ; 165.34 1.43E-06 75041000 151786 132758 143094 170581 199698 139591 187207 160165 183043 FALSE TRUE 144611.3766 146286.1911 149655.0014 153433.8738 234525.268 134756.9287 158645.1339 146140.1035 211428.3736 0.683973367 0.691894795 0.707828372 0.725701434 1.10924217 0.637364448 0.750349308 0.691203839 1 17.68980947 -5 0.23617684 2.376567543 0.718291737 0.252526192 0.132376768 237.7654268 2.374195893 157.7282404 0.206844457 1.00E-05 5 -1.658275805 LPHLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPHLLK 6 0 Q5XPI4;Q5XPI4-2;C9JI97 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 0 84.566 0.055705 148540000 513150 540690 487700 599660 517470 532570 667950 589880 583840 FALSE TRUE 488894.4165 595786.9257 510061.5274 539381.0375 607716.6042 514126.9674 566041.9598 538226.98 674378.9254 0.724955063 0.883460178 0.756342626 0.79981894 0.901150053 0.762371047 0.839352979 0.798107651 1 19.36319993 -4.999999982 0.309922176 2.673904439 0.80179071 0.549458117 0.054744515 216.4828583 1.960964277 236.5967864 0.046581518 1.00E-05 4.999999982 -1.872113728 LPHLPGLEDLGIQATPLELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPHLPGLEDLGIQATPLELK 20 0 Q16795;F5H0J3 Q16795 NDUFA9 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial" 0 133.47 1.07E-05 20774000 77385 75375 80897 79572 71349 66909 86494 78991 62194 FALSE TRUE 73727.16441 83055.79819 84606.20747 71573.27138 83792.24301 64591.92455 73297.75173 72074.12928 71838.72788 1.026287166 1.156142385 1.177724188 0.996304827 1.166393747 0.899124003 1.020309712 1.003276804 1 16.13247418 2.244684297 24.99992199 0.983461987 1.102890335 0.467288686 0.065687736 129.1735016 527352.0332 0.021617011 0.017657072 175.6646184 -2.244684297 0.119428348 LPHSS(ph)SSENIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHS(0.013)S(0.664)S(0.322)S(0.001)ENIK 131.69 0.00012757 163920000 151590 110330 128710 149420 172090 128060 179410 153100 197980 TRUE FALSE 144424.6411 121572.7524 134611.4808 134400.0177 202102.4415 123625.2501 152037.7094 139693.7524 228681.7273 0.631553045 0.531624253 0.588641176 0.587716471 0.883771712 0.540599599 0.664844154 0.610865389 1 17.80298157 -5 0.2540588 3.327995353 0.592144481 0.581396196 0.098564452 128.6395135 1.270509832 155.8796108 0.128263924 1.00E-05 5 -2.735850872 LPHSSS(ph)SENIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHSS(0.001)S(0.993)S(0.006)ENIK;LPHS(0.007)S(0.334)S(0.656)S(0.003)ENIK 132.04 0.00012293 156140000 248570 188988 222823 240472 278460 216305 306760 286050 336640 TRUE FALSE 236820.5887 208246.0921 233039.655 216299.2977 327023.3358 208814.3036 259958.128 261001.9456 388844.4119 0.609036883 0.535551202 0.59931337 0.556261813 0.841013336 0.537012484 0.668540218 0.671224628 1 18.56883348 -5 0.197101986 2.72209021 0.554485715 0.668495957 0.084868434 76.93546601 0.758815392 51.98410159 0.191546229 1.00E-05 5 -2.167604495 LPIGDVATQYFADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPIGDVATQYFADR 14 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 98.407 0.0060254 121680000 105730 73964 98676 135280 117100 100790 134370 95524 125790 FALSE TRUE 100732.3524 81501.01569 103200.3922 121681.3974 137522.2029 97299.61703 113869.3886 87159.41216 145296.8708 0.693286455 0.560927536 0.710272642 0.837467433 0.946491154 0.669660788 0.78370159 0.599871227 1 17.14864411 -5 0.109042816 1.783754347 0.571849267 0.316164457 0.116665971 202.3626743 1.470508444 36.7169492 1.504433498 1.00E-05 5 -1.21190508 LPIGDVATQYFADRDMFCAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LPIGDVATQYFADRDMFCAGR 21 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 247.35 2.01E-30 1700630000 484645 305029 470605 475639 549372 434010 592630 532520 599503 FALSE TRUE 461736.7913 336111.8019 492182.7047 427826.8641 645182.3029 418980.1249 502213.4091 485889.7257 692470.8634 0.666795985 0.485380425 0.710763053 0.61782652 0.931710397 0.605050908 0.725248434 0.701675336 1 19.40139384 -4.999999999 0.116309663 2.083434286 0.493469267 0.480636416 0.108781286 125.8268333 0.957903749 32.16764393 1.075212153 1.00E-05 4.999999999 -1.589965019 LPLDINPVVHPHGHIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPLDINPVVHPHGHIFK 17 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 108.89 0.00022019 153211000 291298 283899 267034 334312 230562 281065 296855 271631 18041.1 FALSE TRUE 277528.9208 312828.6309 279277.773 300706.3226 270771.9398 271331.6486 251564.3176 247845.5496 20838.82165 13.31787975 15.01181958 13.40180255 14.43010203 12.99363008 13.02048903 12.07190703 11.89345318 1 14.34698608 -0.110938292 0.536390431 1.58E-14 14.08953971 0.977941617 0.589197552 0.616049925 0.1960241 2.114206197 0.246141186 0.774571847 0.110938292 14.08953971 LPLETAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPLETAYR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 109.36 0.013182 0 84898 77311 86090 75736 91084 69082 91701 78587 87195 FALSE TRUE 80885.03979 85189.0788 90037.31165 68122.87339 106969.0208 66689.67302 77710.32825 71705.50566 100716.7553 0.803094178 0.845828269 0.893965571 0.676380739 1.06207771 0.66215073 0.771572992 0.711952102 1 16.61994418 LPLLPHEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LPLLPHEVR 9 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;; 99.802 0.0050904 324747000 327707 276345 281328 328254 359632 298663 371990 319991 388455 FALSE TRUE 312216.9396 304504.8697 294227.1671 295257.2843 422351.7069 288320.2254 315236.0934 291970.8917 448694.6174 0.695833931 0.678646139 0.655740354 0.658036163 0.94128989 0.642575628 0.702562681 0.650711821 1 18.77537435 -1.224024418 3.962489084 1.000249376 0.702198129 0.534955406 0.086970294 12043649.33 3720348.21 25880.54788 0.018927936 0.059700172 1.224024418 -0.298051247 LPLLPPES(ph)PGPLR ddPTM_SK-BR-3_Trastuzumab_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 101.32 0.0020944 401232000 481530 400473 396618 552114 543962 406792 474069 424697 453321 TRUE FALSE 458769.0312 441281.654 414803.3276 496614.4518 638828.8006 392704.691 401741.0672 387508.2792 523619.7054 0.876149286 0.842752191 0.792184334 0.948425826 1.220024369 0.749980734 0.767238251 0.740056715 1 18.99815987 -0.922475284 4.296465346 1.000003064 0.863741431 0.08088308 0.140386834 17784928.08 4139704.622 529.6591649 0.03292356 0.119543156 0.922475284 -0.136261633 LPLPS(ph)PALEYTLGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR 100.54 0.0022202 204550000 139828 134831 109697 134057 112103 111340 107025 119791 108414 TRUE FALSE 133218.6076 148570.4322 114726.716 120581.3357 131653.7277 107484.2679 90696.3706 109301.465 125226.2894 1.063823005 1.186415671 0.916155198 0.962907519 1.051326589 0.858320313 0.724259826 0.872831619 1 16.93417794 3.002918249 0.825162982 0.83608508 1.120990817 0.378374706 0.100908166 0.491236663 0.744442731 0.057416763 0.073364444 1006.742143 -3.002918249 0.284905737 LPLQFEWRVSEQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPLQFEWRVSEQHR 14 1 Q6ZU64 Q6ZU64 CCDC108 Coiled-coil domain-containing protein 108 0 62.891 0.047375 228850000 468350 757580 495970 597690 294560 604420 407940 317220 30906 FALSE TRUE 446212.0237 834778.2633 518710.7151 537609.0657 345931.1707 583488.7838 345701.2607 289442.5351 35698.74463 12.49937577 23.38396691 14.53022285 15.05960703 9.690289513 16.34479839 9.683849228 8.107919146 1 15.12358572 1.175582962 0.424870182 0.268506077 17.93402101 0.661354717 3.419423648 0.619850797 0.317013709 4.298735839 2.517173454 14.98245432 -1.175582962 17.66551494 LPLQLDDAVRPEAEGEEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LPLQLDDAVRPEAEGEEEGR 20 1 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;;; 232.82 4.28E-27 2181034000 880032 857503 842231 986868 845197 863873 911806 902472 858439 FALSE TRUE 838434.6314 944883.5306 880848.1244 887666.1537 992599.0892 833956.8614 772693.2482 823446.7674 991561.3358 0.845570114 0.952924944 0.888344566 0.89522062 1.001046585 0.841054236 0.77926924 0.830454696 1 19.91934249 2.048358616 24.99999574 0.836576833 0.913537655 0.076367081 0.070575205 160.2572626 82847.61949 0.024063337 0.017771946 111.7785872 -2.048358616 0.076960822 LPLVPES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 182.28 4.88E-05 410803000 202753 216360 221935 250322 226507 202696 224513 218749 216233 TRUE FALSE 193169.2675 238407.33 232110.9393 225159.157 266009.7491 195676.5867 190259.4184 199594.1779 249765.3093 0.773403112 0.954525393 0.929316165 0.901482907 1.065038815 0.783441813 0.761752779 0.799126902 1 17.93021358 LPLVPES(ph)PRR ddPTM_SK-BR-3_Trastuzumab_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 113.24 0.0009276 2338220000 1619350 1469270 1420500 1602580 1594450 1474210 1650400 1580190 1707070 TRUE FALSE 1542806.535 1618990.283 1485631.33 1441485.614 1872521.575 1423157.738 1398601.168 1441820.186 1971793.697 0.782438111 0.821074885 0.753441566 0.731052957 0.9496539 0.72175793 0.709304006 0.731222637 1 20.91107718 3.756209954 23.86360738 0.781765485 0.801756483 0 0.100741353 3843.740253 5197079.183 0.024032505 0.043183746 5704.399775 -3.756209954 0.019990998 LPNGEPSPDPGGKGT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPNGEPSPDPGGKGTPR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LPNGEPS(0.001)PDPGGKGT(0.999)PR 78.975 0.023478 139310000 176140 186520 152750 211360 108540 158860 157450 184250 115810 TRUE FALSE 167814.2113 205526.6001 159753.7386 190113.6912 127469.3416 153358.6384 133428.1107 168116.0932 133769.2233 1.254505387 1.536426653 1.194248831 1.421206512 0.95290485 1.146441869 0.997449992 1.256762124 1 17.0293867 2.745763808 24.92706181 1.070775792 1.362872326 0.558317128 0.123961017 356.7677316 1234615.335 0.034703741 0.036118228 556.8828045 -2.745763808 0.292096534 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 LPNGLGGPNGFPKPT(0.003)PEEGPPELNRQS(0.983)PNS(0.008)S(0.002)S(0.002)AAAS(0.001)VAS(0.001)R;LPNGLGGPNGFPKPTPEEGPPELNRQS(0.996)PNS(0.001)S(0.001)S(0.001)AAAS(0.001)VAS(0.001)R 94.336 0.00010718 474184000 132395 108379 126649 132058 98357 125477 150899 143137 129250 TRUE FALSE 126136.9507 119422.9433 132455.9819 118783.2789 115510.4297 121131.7 127876.5861 130603.1655 149293.4299 0.844892845 0.799920957 0.887219096 0.795636345 0.773714086 0.811366583 0.856545303 0.874808527 1 17.18779115 0.808720244 1.273830368 0.99930357 0.819714312 0.761312419 0.031469345 0.336402037 1.007407361 0.028936123 0.008777854 6.437544499 -0.808720244 -0.179589258 LPNNS(ph)SRPS(ph)TPTINVLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPNNSSRPSTPTINVLESK 19 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 2 LPNNS(0.534)S(0.451)RPS(0.407)T(0.352)PT(0.255)INVLESK 92.886 0.0010497 144550000 342570 346240 307430 392100 268650 357280 382760 376010 318370 TRUE FALSE 326377.395 381522.2496 321525.9696 352685.3631 315502.4749 344907.304 324362.9321 343084.571 367741.1936 0.887519268 1.037474877 0.874326769 0.959058624 0.857947057 0.937907719 0.882041332 0.932951154 1 18.48833127 4.783341499 22.68440508 0.931570171 0.887518769 0.064370174 0.055624146 7993.274165 5437766.203 0.012627923 1.678386779 60721.36119 -4.783341499 -0.044051403 LPNTYPNSS(ph)SPGPGGLGGSVHYATMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPNTYPNSSSPGPGGLGGSVHYATMAR 27 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 LPNTY(0.001)PNS(0.12)S(0.599)S(0.28)PGPGGLGGSVHYATMAR;LPNTYPNS(0.001)S(0.795)S(0.204)PGPGGLGGSVHYATMAR 291.51 1.06E-70 431400000 312051 267010 285766 340140 390278 275283 362140 345893 410230 TRUE FALSE 297300.9677 294218.6226 298868.6538 305948.481 458342.3596 265749.8807 306888.8918 315604.7752 473846.3732 0.627420583 0.620915637 0.63072901 0.645670197 0.967280506 0.560835527 0.647654829 0.66604873 1 18.85405987 -2.317602208 2.007930364 2.457181198 0.664481171 0.471787094 0.109280448 6151538.987 744460.3151 40650335.27 0.025213412 0.0048128 2.317602208 -1.792700027 LPNTYPNSSS(ph)PGPGGLGGSVHYATMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LPNTYPNSSSPGPGGLGGSVHYATMAR 27 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 LPNTYPNS(0.046)S(0.382)S(0.572)PGPGGLGGSVHYATMAR;LPNTYPNSS(0.231)S(0.769)PGPGGLGGSVHYATMAR;LPNTYPNSS(0.001)S(0.998)PGPGGLGGSVHYATMAR;LPNTYPNS(0.031)S(0.158)S(0.811)PGPGGLGGSVHYATMAR 235.78 3.33E-45 1556220000 570620 439939 514370 626880 686280 542361 720910 631500 717680 TRUE FALSE 543647.9235 484769.2843 537954.3733 563864.8314 805967.0147 523578.9026 610921.9391 576202.5122 828974.149 0.655808054 0.584782149 0.648939866 0.680195917 0.972246258 0.631598589 0.736961388 0.695078988 1 19.66096759 -5 0.119886177 1.980897848 0.543461664 0.479201834 0.101500593 130.6977391 1.016137171 31.2619541 0.945642363 1.00E-05 5 -1.437436185 LPPEEASPYVVDHGESGPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPPEEASPYVVDHGESGPLR 20 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 155.28 3.17E-08 56868000 35229 36537 32190 41993 26535 38897 37915 34626 30967 FALSE TRUE 33563.79499 40260.16184 33665.94334 37771.78386 31162.6956 37549.98714 32130.37039 31593.96388 35769.2042 0.938343352 1.125553748 0.941199115 1.055986139 0.871215793 1.049785366 0.898269087 0.883272764 1 15.1264304 2.754335042 24.98484894 0.940443318 1.020988563 0.19511761 0.075053737 1177.025292 1864268.982 0.021136702 0.022347581 567.982614 -2.754335042 0.080545245 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(1)GSGAAS(1)PTGSAVDIR;LPS(0.999)GS(0.001)GAAS(0.996)PT(0.004)GSAVDIR;LPS(1)GSGAAS(0.954)PT(0.045)GS(0.001)AVDIR;LPS(1)GSGAAS(0.979)PT(0.02)GS(0.001)AVDIR 342.98 1.51E-75 1214940000 1795150 1603780 1584030 1950620 1748430 1514480 1714010 1548490 1500290 TRUE FALSE 1710296.817 1767207.005 1656659.342 1754539.972 2053355.638 1462033.178 1452506.295 1412896.007 1732947.311 0.986929497 1.019769611 0.955977907 1.012460079 1.184892135 0.843668569 0.838171066 0.815313886 1 20.72479636 2.18606252 24.99996239 0.857765463 1.02189573 0.494606374 0.078063184 74.84885657 35642.9937 0.027092805 0.020009382 153.4837918 -2.18606252 0.164130267 LPS(ph)GSGAASPTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPS(0.997)GS(0.003)GAASPTGSAVDIR 214.94 1.03E-18 265230000 62943 50951 56765 66998 76965 48749 62947 59677 84465 TRUE FALSE 59967.80913 56142.96483 59367.7314 60263.23375 90387.67163 47060.80991 53343.27905 54451.36551 97563.40081 0.614654764 0.575451085 0.60850412 0.617682791 0.926450604 0.482361311 0.546755019 0.558112623 1 16.57405243 -1.060473482 4.193241609 1.00003981 0.610795745 0.512429988 0.117533418 7002724.02 2656490.832 2766.722484 0.026530281 0.087001455 1.060473482 -0.389244066 LPS(ph)PDVRQDDGEDTLFSEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSPDVRQDDGEDTLFSEPK 20 1 Q9H425;Q9H425-3;Q9H425-2;E5RFY9 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 LPS(1)PDVRQDDGEDTLFSEPK 81.922 0.002736 22532000 28360 22000 28428 28602 23551 29300 30168 31239 23920 TRUE FALSE 27019.479 24241.82501 29731.45192 25726.87262 27658.28694 28285.33365 25565.31753 28503.54755 27629.39143 0.977925231 0.877392652 1.076080593 0.931141487 1.001045825 1.023740741 0.925294268 1.031638631 1 14.75391617 3.760905449 24.99141263 0.990302271 0.927658953 0.240239191 0.050742993 1076.407036 1203895.361 0.01192381 0.021475854 5766.409088 -3.760905449 -0.062643318 LPS(ph)PTPENKDLFFVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPSPTPENKDLFFVTR 16 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 LPS(0.973)PT(0.027)PENKDLFFVTR;LPS(0.801)PT(0.199)PENKDLFFVTR 97.57 0.0018341 387670000 623190 429780 538770 592890 513860 542900 707460 592450 533770 TRUE FALSE 593733.0437 473575.0706 563473.1374 533291.5708 603477.0213 524099.2369 599523.9836 540571.9372 616544.3255 0.963001392 0.768111961 0.913921537 0.864968744 0.978805572 0.850059299 0.972393969 0.876777086 1 19.23384509 0.834561423 0.329135747 1.010640273 0.866209216 0.187741784 0.064717569 2.915157753 0.840262276 0.145646515 0.070565606 6.832213406 -0.834561423 -0.144431057 LPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Trastuzumab_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 109.59 0.00019559 332898000 370940 370909 293097 435336 224427 396267 372384 348420 204127 TRUE FALSE 353406.4013 408705.0488 306535.7874 391575.1982 263566.9977 382544.1744 315569.9815 317910.4977 235781.9726 1.498869474 1.733402449 1.300081529 1.660751218 1.117842025 1.622448783 1.33839741 1.348324022 1 17.84709389 -3.036153769 0.117767648 6.92E-12 1.772831611 0.440891619 0.175257492 70.61405134 0.878941962 19.61338782 1.791862153 0.000920124 3.036153769 1.772831611 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 39 2 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 382.9 9.94E-180 1036510000 707580 488820 565150 766380 596010 636720 804680 701400 582430 FALSE TRUE 674134.0957 538631.3137 591062.6865 689342.0264 699953.9553 614670.2267 681911.287 639981.6976 672750.2698 1.002056968 0.800640799 0.878576662 1.024662579 1.040436529 0.913667752 1.013617263 0.951291625 1 19.35971154 3.247071998 24.99501523 0.989818572 0.889275667 0.365776268 0.060018361 186.982744 549100.965 0.016272639 0.021683246 1766.330622 -3.247071998 -0.100542905 LPSGS(ph)GAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPSGS(1)GAAS(0.997)PT(0.003)GSAVDIR;LPSGS(1)GAAS(0.998)PT(0.002)GSAVDIR;LPS(0.031)GS(0.969)GAAS(0.867)PT(0.123)GS(0.009)AVDIR 284.84 2.05E-39 1155470000 962600 920330 884260 1027690 985160 886580 1010110 950530 1019860 TRUE FALSE 917099.8057 1014112.673 924804.1957 924384.6487 1156971.592 855877.5123 855999.1676 867296.5541 1178014.68 0.778513054 0.860865905 0.785053201 0.784697054 0.98213682 0.726542315 0.726645586 0.736235778 1 20.16792609 -1.37811411 8.587891073 1.00000092 0.798333541 0.409092445 0.076447796 1.34E-06 9.66E-08 0.07336785 0.017292889 0.041868354 1.37811411 -0.20166738 LPSGSGAAS(ph)PTGS(ph)AVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPSGSGAAS(0.991)PT(0.157)GS(0.853)AVDIR 123.55 4.93E-05 111290000 95967 83067 97176 132930 113540 120110 131330 95895 103110 TRUE FALSE 91430.8301 91531.62174 101631.6157 119567.6238 133341.3401 115950.5606 111293.1965 87497.92543 119099.7722 0.767682662 0.768528941 0.853331739 1.003928233 1.119576785 0.973558206 0.934453479 0.734660729 1 16.86181113 3.462987799 3.55544981 0.963773336 0.770689428 0.418768506 0.094941876 0.210407038 5.691381562 0.027051412 0.039923049 2903.941072 -3.462987799 -0.193083908 LPSGSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.93)PT(0.07)GSAVDIR;LPSGSGAAS(0.546)PT(0.454)GSAVDIR;LPSGSGAAS(0.987)PT(0.013)GSAVDIR;LPSGSGAAS(0.711)PT(0.287)GS(0.003)AVDIR;LPSGSGAAS(0.994)PT(0.006)GSAVDIR;LPS(0.005)GS(0.024)GAAS(0.818)PT(0.122)GS(0.031)AVDIR;LPSGSGAAS(0.998)PT(0.002)GSAVDIR;LPSGSGAAS(0.999)PT(0.001)GSAVDIR 452.38 4.42E-191 36971360000 3318281 3017060 2913152 3524410 3125244 2871775 3304712 3215220 3247416 TRUE FALSE 3161432.433 3324501.844 3046722.901 3170129.611 3670285.564 2772324.712 2800517.489 2933678.292 3751008.688 0.842821944 0.886295426 0.812240961 0.845140567 0.978479622 0.739087787 0.74660384 0.782103838 1 21.83884717 2.203357501 24.9999966 0.788531451 0.86803878 0.052272623 0.08548361 297.7707287 211464.4071 0.028760217 0.021241652 159.7193377 -2.203357501 0.079507329 LPSRPGAQGVEPQNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSRPGAQGVEPQNLR 16 1 A0A0U1RRM1;Q8WXI9 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 65.511 0.052123 144450000 36949 32109 39365 35787 39081 34725 46056 43759 65803 FALSE TRUE 35202.494 35380.9436 41169.92419 32189.62277 45896.71403 33522.46454 39029.31132 39927.22998 76007.39316 0.463145656 0.465493449 0.541656837 0.42350647 0.603845391 0.441042156 0.513493618 0.525307188 1 16.21385213 -5 0.353826431 7.013826998 0.477530385 0.904972101 0.051365828 111.171386 0.900691648 507.8680376 0.033347883 1.00E-05 5 -6.536296614 LPSS(ph)PLGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.217)S(0.783)PLGCR 62.201 0.08829 307480000 99803 92321 102080 98407 119780 100680 110640 103000 128810 TRUE FALSE 95085.50998 101728.6149 106760.469 88514.9414 140669.5941 97193.42636 93759.83596 93980.77396 148785.1969 0.639079102 0.683728065 0.717547654 0.594917661 0.945454232 0.653246616 0.630169116 0.631654062 1 17.18287147 -1.362529284 3.086774218 1.003399743 0.684165115 0.502950588 0.097760125 22649935.91 28746132.71 691140.4756 0.021706963 0.0433981 1.362529284 -0.319234628 LPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPS(0.047)S(0.953)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.09)S(0.91)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.005)S(0.995)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK 370.76 4.18E-97 14454544000 11640650 14068250 9930060 14635360 7550500 11688440 10701720 11405220 6939880 TRUE FALSE 11090419.54 15501820.67 10385363.07 13164185.81 8867304.809 11283666.39 9068976.063 10406518.47 8016081.146 1.383521367 1.933840288 1.295566111 1.642222124 1.106189502 1.407628763 1.131347837 1.298205231 1 22.93446568 2.870580976 1.207085479 1.189181797 1.631330298 0.407571418 0.209354911 0.391701918 1.192083692 0.084547798 0.08972459 742.3025897 -2.870580976 0.442148501 LPSVEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 71.882 0.0040731 57599000 87826 97740 82659 93027 50669 99901 89385 107410 59926 FALSE TRUE 83674.63903 107699.8171 86448.99691 83675.74922 59505.65756 96441.40332 75747.67658 98004.61098 69219.01802 1.208838863 1.555928128 1.248919724 1.208854902 0.859672085 1.393278987 1.094318856 1.415862487 1 16.07888085 3.495744332 5.246577971 1.167519369 1.38657476 0.194399955 0.183541314 0.251056026 20.5693626 0.045850901 0.068079909 3131.441707 -3.495744332 0.219055391 LPTEEEWEFAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPTEEEWEFAAR 12 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 130.94 0.00048286 36697000 42023 39264 31560 39828 36390 37283 38150 36742 39947 FALSE TRUE 40036.65607 43265.04624 33007.05722 35824.41377 42736.40448 35991.88036 32329.51683 33524.6757 46141.77674 0.867687785 0.937654536 0.715339971 0.776398663 0.926197635 0.780028055 0.700656089 0.726557971 1 15.49378594 3.750700325 24.83823511 0.788454374 0.902671165 0.140953958 0.096190899 1003.339718 2052858.889 0.023418255 0.041829273 5632.488645 -3.750700325 0.114216791 LPVDSVFNKFEDEDSDDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPVDSVFNKFEDEDSDDVPR 20 1 P49756 P49756 RBM25 RNA-binding protein 25 0 166.29 1.41E-11 73012000 158410 154290 134690 178880 115920 166470 172830 171160 137630 FALSE TRUE 150922.2732 170012.3264 140865.6697 160898.6426 136136.4113 160705.1022 146461.6093 156172.323 158972.9575 0.949358153 1.069441804 0.886098315 1.012113287 0.856349491 1.010895845 0.92129889 0.982382951 1 17.27842185 3.740712832 24.99976289 0.949825774 1.009399974 0.133595179 0.059637371 306.6981843 3562536.026 0.013559777 0.022976033 5504.436067 -3.740712832 0.059574199 LPVWVVEDHQEVLPFIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LPVWVVEDHQEVLPFIYR 18 0 Q49AR2;E5RFG1;B4DR92;E5RHP8 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 132.47 1.47E-05 47773000 37177 26071 39417 38063 36821 30692 49512 34960 36554 FALSE TRUE 35419.71689 28727.66454 41224.30844 34236.83493 43242.57074 29629.12834 41958.03505 31898.71707 42222.60763 0.838880374 0.680385844 0.976356288 0.810865005 1.024156801 0.701736108 0.993733865 0.755489034 1 15.36572806 7.999999976 0.036984272 1.395309793 7.15E-07 0.109841571 0.121343437 1508.749625 4.259532479 46.06728624 137.1820505 99999994.42 -7.999999976 -1.395309078 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR 249.61 1.03E-47 2434160000 960061 877256 1010518 1291900 1042916 1207360 1313430 1056232 1124043 TRUE FALSE 914680.8192 966649.3838 1056851.25 1162035.758 1224800.22 1165548.82 1113042.131 963742.7266 1298353.848 0.704492709 0.744519212 0.813993236 0.895006981 0.943348551 0.897712763 0.857271793 0.742280487 1 20.30825219 3.608291589 2.151413644 0.883459425 0.718112278 0.51761366 0.065675704 0.233874835 2.121934086 0.018175115 0.032493818 4057.80889 -3.608291589 -0.165347146 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;; 271.54 2.19E-73 2151396000 1003629 898732 961984 1070233 1034132 914854 1094363 1003630 1178824 FALSE TRUE 956189.4462 990313.8126 1006091.918 962651.1455 1214484.293 883172.3766 927397.825 915746.8366 1361630.005 0.702238819 0.727300227 0.738887887 0.70698438 0.891934144 0.648614068 0.681093852 0.672537204 1 20.3769033 -1.650086073 4.494809308 1.007496387 0.719683672 0.637220568 0.066102182 0.004821494 0.000375346 0.062144479 0.014352206 0.022382775 1.650086073 -0.287812715 LQAEAPHIVVGTPGR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 181.51 5.85E-07 1359180000 1968960 1527470 1654920 1860220 1882940 1652010 1957440 1787160 1934760 FALSE TRUE 1875891.163 1683120.93 1730799.719 1673227.151 2211324.14 1594800.479 1658796.577 1630666.796 2234792.699 0.839402761 0.753144097 0.774478867 0.74871694 0.989498552 0.713623451 0.742259708 0.729672509 1 21.09170958 -1.743076395 2.728840156 1.042835657 0.784705757 0.414806138 0.07972926 15143671.56 13163205.87 4408988.517 0.019169998 0.018068563 1.743076395 -0.2581299 LQAEEAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQAEEAERR 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 96.009 0.01228 46527000 70740 68623 73387 77537 86036 68015 85034 102400 92571 FALSE TRUE 67396.26039 75615.76172 76751.86654 69742.83345 101040.6512 65659.6235 72060.50154 93433.31314 106926.4379 0.630304925 0.707175542 0.717800649 0.652250602 0.944954804 0.614063507 0.673925953 0.873809275 1 16.70625908 -5 0.173402805 2.157679419 0.647248698 0.475905566 0.098436083 115.7678374 1.100118011 45.90633535 0.319734428 1.00E-05 5 -1.510430721 LQAFGFCEYKEPESTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQAFGFCEYKEPESTLR 17 1 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 161.99 2.64E-09 151450000 84618 74902 77633 89826 73072 82446 96081 100440 76294 FALSE TRUE 80618.27484 82534.59896 81192.54984 80796.51982 85815.73366 79590.87435 81422.0788 91644.94113 88125.28386 0.914814356 0.936559808 0.921330931 0.916836988 0.973792423 0.903155949 0.923935507 1.039939245 1 16.42726838 1.24495737 24.99996188 1.019969635 0.926974477 0.772577237 0.020924251 55.46484711 216775.6786 0.013317648 0.004596642 17.57751066 -1.24495737 -0.092995158 LQAITASSANLRHS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQAITASSANLRHSPR 16 1 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 LQAITAS(0.003)S(0.148)ANLRHS(0.849)PR 110.77 0.00052465 71303000 69583 59936 60770 65961 70818 63387 103880 65053 95860 TRUE FALSE 66293.94949 66043.54654 63556.36461 59330.47496 83168.63678 61191.8923 88031.19811 59356.61445 110725.4792 0.598723527 0.596462052 0.573999454 0.535833987 0.75112465 0.552645089 0.795040118 0.536070061 1 16.75662772 -5 0.207637705 2.797702251 0.566994514 0.645558716 0.088667011 81.78239273 0.813753884 61.06283617 0.16995442 1.00E-05 5 -2.230707737 LQAKES(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR 116.71 0.00076858 11623640000 9965750 7342260 8751170 9329810 7807360 9977350 12458640 10776460 9703610 TRUE FALSE 9494688.748 8090444.641 9152419.801 8391959.773 9168961.112 9631831.868 10557845.65 9832816.033 11208396.28 0.847105019 0.721820003 0.816568184 0.748720831 0.818043981 0.859340768 0.941958634 0.87727234 1 23.41807653 2.020689844 1.470139591 0.943707531 0.781083663 0.702996498 0.044712532 0.208912095 0.843544809 0.027345047 0.013271305 104.8793155 -2.020689844 -0.162623868 LQAKES(ph)PQRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LQAKESPQRK 10 2 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQRK;LQAKES(1)PQRK;LQAKES(1)PQRK;LQAKES(1)PQRK;LQAKES(1)PQRK 134.99 8.14E-05 3148190000 3519440 2573330 3511810 3691780 2384080 4043240 4955760 4513440 3101030 TRUE FALSE 3353083.046 2835555.253 3672829.962 3320675.26 2799862.797 3903221.585 4199667.793 4118219.266 3581921.895 0.936112831 0.79162956 1.02537969 0.927065234 0.78166495 1.089700362 1.172462135 1.149723357 1 21.77230245 2.12360835 6.497653344 1.127190856 0.890801571 0.609882721 0.083166838 0.12493729 6.640895479 0.029696598 0.021856003 132.9255144 -2.12360835 -0.236389285 LQALAEEPSQPHT(ph)RSPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQALAEEPSQPHTRSPAK 18 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 LQALAEEPS(0.001)QPHT(0.5)RS(0.5)PAK 177.93 1.34E-13 344600000 294580 179030 300480 254150 215480 276450 359290 304350 265600 TRUE FALSE 280655.7872 197273.3605 314257.3052 228602.3591 253059.6438 266876.4672 304473.7117 277699.5005 306787.8915 0.914820288 0.643028509 1.024347159 0.74514792 0.824868421 0.869905477 0.992456743 0.905184032 1 18.22688202 1.948642068 3.374384406 0.962632996 0.818183918 0.263244789 0.10204768 0.302687961 6.480912437 0.046511704 0.026540662 88.84685679 -1.948642068 -0.144449078 LQALAEEPSQPHTRS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQALAEEPSQPHTRSPAK 18 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 LQALAEEPS(0.001)QPHT(0.372)RS(0.627)PAK 163.95 1.92E-11 383690000 262900 167270 278960 236060 215670 261370 345120 274830 257810 TRUE FALSE 250473.238 184315.0032 291750.5919 212330.8003 253282.7797 252318.6914 292465.6054 250764.4282 297789.8581 0.841107349 0.618943185 0.979719705 0.713022269 0.850541994 0.847304515 0.982120772 0.842085187 1 18.18393509 2.135138086 0.529460698 0.983360145 0.747334764 0.286708493 0.101118497 0.919046951 0.540032468 0.088528992 0.069404045 136.501708 -2.135138086 -0.236025381 LQALKDTANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQALKDTANR 10 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ; 141.71 3.38E-05 5835700000 5987800 2703200 5682000 4215000 6543300 4925100 8879700 5865400 8652600 FALSE TRUE 5704768.561 2978659.153 5942525.32 3791300.192 7684449.448 4754542.552 7524938.678 5351794.482 9994401.017 0.570796444 0.298032783 0.594585439 0.379342412 0.768875437 0.47572061 0.752915424 0.535479262 1 23.25268868 -0.544005051 0.202801641 1.308276856 0.373090793 0.539422518 0.138012662 9.168979704 0.52023924 2.101407861 0.377683226 0.285755731 0.544005051 -0.935186063 LQALVNSLCAGQS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LQALVNSLCAGQSP 14 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 1 LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P 300.29 8.35E-44 765218000 2042821 1454346 1705824 1861478 1992918 1607200 1933722 1606829 1819677 TRUE FALSE 1946260.9 1602545.511 1784037.718 1674358.695 2340482.268 1551542.261 1638697.194 1466126.534 2101863.216 0.925969343 0.762440438 0.848788686 0.796606878 1.113527394 0.738174706 0.779640265 0.697536606 1 21.00323735 -0.892272032 4.361328405 1.000002354 0.831738851 0.16673058 0.117421437 12170198.82 5581175.385 267.9772257 0.02586644 0.128152761 0.892272032 -0.168263503 LQASVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQASVR 6 0 P49327;A0A0U1RQF0;H7BZY1 P49327 FASN;SLC20A1 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 ; 119.57 0.048628 1005940000 756650 726060 544320 633000 811950 645190 848430 725720 833360 FALSE TRUE 720884.654 800046.3395 569277.6104 569369.6374 953553.8229 622846.9085 718986.421 662172.1095 962593.2126 0.748898543 0.831136485 0.591399984 0.591495587 0.990609336 0.647051008 0.746926543 0.687904403 1 19.87656673 -1.43420083 2.948754082 1.005651888 0.736357499 0.338858796 0.11842346 25837776.81 31034484.47 1221082.433 0.026680657 0.036795878 1.43420083 -0.26929439 LQAVTDDHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LQAVTDDHIR 10 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;;;; 207.29 1.35E-07 8089810000 8175500 6174870 6523950 7483280 8093010 6475900 8477230 7463280 7797840 FALSE TRUE 7789060.317 6804096.273 6823079.561 6731046.477 9504428.382 6251637.959 7183872.868 6809755.638 9007089.201 0.864769977 0.755415664 0.757523258 0.747305409 1.055216416 0.694079721 0.797579852 0.756043988 1 23.10262952 -1.100375298 4.046940055 1.000038839 0.802075114 0.278291457 0.099428888 20389987436 37496406121 12116175.39 0.021895249 0.079364211 1.100375298 -0.197963725 LQAYHTQTTPLIEYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 183.58 1.96E-09 692330000 468680 334020 390240 458590 445120 369710 454110 398780 368500 FALSE TRUE 446526.4252 368057.0177 408132.89 412491.6619 522748.7871 356906.85 384827.1792 363860.7091 425645.098 1.049058071 0.864703998 0.958857254 0.969097645 1.228132991 0.838508071 0.904103398 0.854845295 1 18.69929149 LQCPQVDLFYLHAPDHGTPVEETLHACQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQCPQVDLFYLHAPDHGTPVEETLHACQR 29 0 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 262.26 1.16E-58 464870000 117854 102499 112595 127318 150116 98933 132411 120120 12614.6 FALSE TRUE 112283.275 112943.7646 117757.5921 114519.7528 176296.1829 95506.9254 112209.2701 109601.656 14570.80774 7.706043273 7.751372926 8.081747712 7.859533581 12.09927315 6.55467611 7.700964287 7.522002757 1 13.83079324 0.148060078 0.897901212 0.918684184 8.279502717 0.715370735 1.430936169 2.26111978 1.937736416 1.802815204 0.430914464 1.406242044 -0.148060078 7.360818533 LQCSLDAHEICLQDIQLDPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQCSLDAHEICLQDIQLDPER 21 0 Q06546 Q06546 GABPA GA-binding protein alpha chain 0 83.064 0.003371 59476000 33128 37907 34887 37740 36594 40040 45529 34536 40771 FALSE TRUE 31562.10509 41769.7664 36486.60346 33946.3035 42975.98201 38653.40476 38582.71485 31511.84475 47093.55845 0.670200047 0.886952861 0.774768454 0.720826895 0.912566037 0.82077902 0.819277968 0.669132803 1 15.52324212 -2.411203773 2.354012866 2.932359682 0.792008217 0.403544275 0.081934707 6979832.99 548850.5441 72960993.51 0.019720813 0.003879683 2.411203773 -2.140351465 LQDAEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LQDAEIAR 8 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;; 221.16 1.31E-05 34349020000 24966000 22238900 19045460 24552600 22284200 21487390 25111400 23276400 22159200 FALSE TRUE 23785906.66 24505069.19 19918713.18 22084526 26170557.42 20743276.3 21280194.73 21238195.02 25595535.56 0.929299041 0.957396228 0.778210447 0.862827267 1.022465709 0.810425562 0.831402597 0.829761697 1 24.60938886 LQDAVLGAAHPVPPGLPLFLPYYICVADEDDYRDFVNLDHAHSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQDAVLGAAHPVPPGLPLFLPYYICVADEDDYRDFVNLDHAHSLLR 46 1 Q9BRP1 Q9BRP1 PDCD2L Programmed cell death protein 2-like 0 66.599 0.00033258 129730000 21835 13895 20389 18048 18717 16551 28490 18672 6084.4 FALSE TRUE 20802.90282 15310.9163 21323.85582 16233.78075 21981.23887 15977.83472 24143.32725 17036.98069 7027.937677 2.960029496 2.178578838 3.034155509 2.309892531 3.127694052 2.273474162 3.435335991 2.424179251 1 12.77888568 0.972914888 23.93146435 0.99999998 2.744345596 0.646793406 0.406269546 981.2813224 867027.4295 0.354729362 0.08868234 9.395391634 -0.972914888 1.744345616 LQDAYYIFQEMADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQDAYYIFQEMADK 14 0 O14579;M0QXB4;O14579-2 O14579 COPE Coatomer subunit epsilon 0 138.42 3.61E-05 39124000 75418 66908 62330 78840 57974 59507 72532 77727 64484 FALSE TRUE 71853.1406 73726.00127 65187.89215 70914.85341 68084.64724 57446.25767 61465.91126 70920.81182 74483.84938 0.964680816 0.989825336 0.875194995 0.952083626 0.914086044 0.771257906 0.825224687 0.952163622 1 16.18464001 3.342876602 1.100177079 0.869999508 0.977773585 0.087907745 0.069996076 0.672159165 1.717459037 0.026337258 0.04686493 2202.300623 -3.342876602 0.107774078 LQDFNVGDYIEAVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQDFNVGDYIEAVLDR 16 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 142.45 3.51E-06 82312000 41707 44970 39329 46167 57173 47406 47756 47334 55212 FALSE TRUE 39735.59277 49552.49413 41132.27355 41526.20545 67143.9531 45764.31833 40469.9451 43189.18403 63773.99498 0.623068898 0.777001569 0.644969373 0.651146372 1.052842199 0.717601561 0.634583816 0.677222496 1 15.96068064 -2.221906942 2.284273966 1.899421402 0.720118644 0.324015976 0.126018738 12600986.29 2343581.861 58542299.76 0.029768857 0.005999196 2.221906942 -1.179302758 LQDLQGEKDALHSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LQDLQGEKDALHSEK 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;;; 234.77 6.96E-18 882590000 2128040 1514220 1904970 1969920 1381550 2081250 2514200 2411340 1362370 FALSE TRUE 2027451.767 1668520.74 1992314.759 1771899.899 1622491.883 2009175.791 2130612.614 2200190.286 1573639.382 1.288383978 1.060294219 1.266055478 1.125988533 1.03104428 1.276770151 1.353939561 1.398154057 1 20.58567354 2.032269344 24.34646705 1.296357115 1.157200251 0.101549299 0.132012123 208.9237507 157626.9888 0.044740457 0.033042721 107.7133031 -2.032269344 -0.139156864 LQDLTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQDLTLR 7 0 A0A494C039;Q9Y4L1;A0A087X054;A0A1W2PS94;A0A2R8Y358;Q9BXT5 A0A494C039;A0A1W2PS94 HYOU1;TEX15 Hypoxia up-regulated protein 1;Testis-expressed sequence 15 protein 0 ; 106.38 0.019969 43473000 237560 189744 195614 210127 238510 194573 259760 223150 242420 FALSE TRUE 226331.0096 209079.1293 204583.0954 189004.6347 280106.0685 187834.8882 220128.8412 203609.803 280013.2555 0.808286769 0.746675828 0.730619324 0.674984598 1.000331459 0.67080713 0.786137216 0.727143444 1 18.0951356 -1.035521366 8.54208058 1.000000001 0.768584651 0.381284767 0.092826651 2.29E-09 2.08E-10 0.079424431 0.018720518 0.092146456 1.035521366 -0.23141535 LQDPFSLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQDPFSLYR 9 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 76.679 0.080842 44857000 355420 219030 193040 183430 337680 179770 313570 251400 321590 FALSE TRUE 338620.001 241349.406 201891.0749 164991.2679 396571.2851 173544.5198 265729.1374 229386.0832 371460.5347 0.911590786 0.64973095 0.543506123 0.444169037 1.067600049 0.467195041 0.71536304 0.617524775 1 18.50284942 -1.233920309 6.294989959 1.00000478 0.682413589 0.219054588 0.191378029 1.18E-05 1.43E-06 0.169729339 0.040004987 0.058355217 1.233920309 -0.317591191 LQDQGLILYHQHQHSCCES(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQDQGLILYHQHQHSCCESPTR 22 0 Q9NP87 Q9NP87 POLM DNA-directed DNA/RNA polymerase mu 1 LQDQGLILYHQHQHS(0.309)CCES(0.604)PT(0.088)R 155.8 2.76E-08 373570000 88337 62222 91940 106650 103400 87485 124930 81149 20691 TRUE FALSE 84161.48508 68562.49254 96155.53994 95929.33938 121432.9273 84455.37251 105869.634 74043.16336 23899.65461 3.52145194 2.868764996 4.023302492 4.013837897 5.080949046 3.533748663 4.429755817 3.098085081 1 14.54470215 3.730218434 24.32652267 3.846493716 3.195108467 0 1.100342971 1090.095548 3178814.382 0.255288745 0.403046438 5373.019716 -3.730218434 -0.651385249 LQDYEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQDYEEK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 150.05 0.0045942 665920000 1354960 1126520 1209230 1419280 941550 1248170 1370230 1431360 1041680 FALSE TRUE 1290913.726 1241313.669 1264674.392 1276611.278 1105756.022 1204945.56 1161176.247 1306022.53 1203218.414 1.072883951 1.03166113 1.051076327 1.060997125 0.918998586 1.001435438 0.965058574 1.085440943 1 20.19846712 2.843770033 22.39034761 0.990353152 1.052317307 0.331829039 0.042052536 14.94620034 3170.622573 0.011769761 0.012483716 697.8627755 -2.843770033 0.061964155 LQEAANYIES(ph)PDRETILDPNLQATL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQEAANYIESPDRETILDPNLQATL 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 LQEAANY(0.163)IES(0.652)PDRET(0.185)ILDPNLQATL 61.612 0.040126 47683000 51354 47624 49118 58095 55125 56183 68874 58123 60276 TRUE FALSE 48926.59819 52476.93974 51370.10888 52255.18023 64738.78255 54237.36862 58366.00634 53033.44199 69623.29423 0.702733169 0.753726757 0.737829335 0.750541623 0.929843715 0.779011812 0.838311473 0.761719803 1 16.08728246 -5 0.074812155 1.720961782 0.53854806 0.627501976 0.056754786 170.7648008 0.912624128 20.92289826 2.27078111 1.00E-05 5 -1.182413722 LQEAANYIESPDRET(ph)ILDPNLQATL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQEAANYIESPDRETILDPNLQATL 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 LQEAANY(0.145)IES(0.131)PDRET(0.723)ILDPNLQATL 65.425 0.075403 56709000 51696 43791 44514 53426 52801 47458 55414 51599 54991 TRUE FALSE 49252.43253 48253.35269 46555.01093 48055.51698 62009.47768 45814.51756 46959.57655 47080.71802 63518.72342 0.775400227 0.759671323 0.732933668 0.756556719 0.976239357 0.721275792 0.739302902 0.741210079 1 15.9548943 -1.477068472 3.207566232 1.004754436 0.77315237 0.482000164 0.073167503 31655868.15 39261310.33 1339160.842 0.016911078 0.033337385 1.477068472 -0.231602066 LQEALRR ddPTM_SK-BR-3_Trastuzumab_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 93.992 0.023295 81154000 143840 101570 106020 116820 159150 125520 153110 137870 160440 FALSE TRUE 137040.9683 111920.0985 110881.1219 105077.0317 186905.7096 121173.2109 129750.2574 125797.3719 185320.2158 0.739482024 0.603928168 0.598321783 0.567002532 1.008555428 0.653858568 0.700140872 0.678810843 1 17.49966074 LQEDKEQMAQQLAEETQGFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 130.05 1.41E-05 311780000 123129 105527 111505 134021 114734 118775 146542 143211 112322 FALSE TRUE 117308.9362 116280.3213 116617.6145 120548.9545 134743.5733 114661.792 124184.3265 130670.6856 129740.3221 0.904182557 0.896254298 0.898854054 0.929155659 1.038563579 0.883779153 0.95717603 1.007170967 1 16.9852674 2.788291553 0.308673671 1.00398389 0.869053953 0.385852736 0.042082314 2.508647899 0.480924784 0.054446056 0.119741523 614.174177 -2.788291553 -0.134929938 LQEDPNYS(ph)PQRFPNAQR ddPTM_SK-BR-3_Trastuzumab_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 LQEDPNY(0.001)S(0.999)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNY(0.011)S(0.989)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR 163.95 1.61E-09 868460000 1153120 1134930 1195440 1333040 1287630 1246910 1450940 1286780 1510920 TRUE FALSE 1098614.303 1250580.657 1250252.106 1199040.287 1512192.264 1203729.194 1229572.455 1174102.722 1745225.757 0.629496957 0.716572428 0.716384171 0.687040219 0.866473726 0.689726925 0.7045349 0.6727512 1 20.73498224 -2.268952719 2.337703559 2.237907586 0.708985513 0.690474058 0.060935754 4187809.398 590917.4328 27489305.2 0.014891897 0.005383284 2.268952719 -1.528922073 LQEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LQEEER 6 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;;; 225.99 8.29E-06 4371520000 5993040 5790570 5525120 6329420 5848780 5769700 6459200 5886630 6082310 FALSE TRUE 5709760.876 6380635.666 5778452.217 5693174.676 6868805.38 5569893.842 5473730.409 5371165.47 7025523.571 0.812716777 0.908207851 0.822494176 0.810355929 0.977693023 0.792808363 0.779120638 0.764521735 1 22.74417431 LQEEERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LQEEERER 8 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;;; 144.77 0.00052903 3195587000 2297723 1496833 2151170 2014512 2629115 2084496 2770159 2272495 2984258 FALSE TRUE 2189114.187 1649361.984 2249803.272 1812009.426 3087631.824 2012309.381 2347520.367 2073503.291 3447041.489 0.635070449 0.478486258 0.652676586 0.525670907 0.895733873 0.583778695 0.681024692 0.601531283 1 21.71692723 -4.999999998 0.183938672 2.559127423 0.54971767 0.522745008 0.110693022 99.85862587 0.967827 56.97560108 0.298714138 1.00E-05 4.999999998 -2.009409753 LQEENRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQEENRK 7 1 H0Y626;O95361;K7ENN8;B3KP96;O95361-2;Q309B1 H0Y626 TRIM16;TRIM16L Tripartite motif-containing protein 16;Tripartite motif-containing protein 16-like protein 0 87.616 0.030803 52810000 67568 57349 53063 63612 50242 60809 72806 65774 66687 FALSE TRUE 64374.19455 63192.9283 55495.99104 57217.60091 59004.18889 58703.16908 61698.10753 60014.47987 77028.47937 0.8357194 0.820383952 0.720460685 0.742810989 0.766004851 0.762096949 0.800977872 0.779120662 1 16.23310432 -1.321629839 4.943780642 1.000096077 0.783060649 0.801381947 0.034595586 4.09E-05 5.61E-06 0.037414026 0.008814677 0.047683724 1.321629839 -0.217035428 LQEGYDHSYYFIATFITDHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LQEGYDHSYYFIATFITDHIR 21 0 P10768;X6RA14 P10768 ESD S-formylglutathione hydrolase 0 ;; 270.68 7.02E-45 1075298000 733477 769240 676795 873342 825009 740241 1000344 782983 472267 FALSE TRUE 698806.9958 847626.4306 707826.7202 785552.0029 968890.3084 714606.2686 847723.1502 714420.8577 545503.7544 1.281030589 1.553841607 1.297565259 1.440048756 1.776138662 1.30999331 1.554018911 1.30965342 1 19.0572296 0.938331455 5.134134035 1.000077282 1.457764304 0.490525304 0.148719788 0.271513081 19.69398571 0.130165413 0.032878749 8.67623796 -0.938331455 0.457687022 LQEIEELER ddPTM_SK-BR-3_Trastuzumab_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 ; 150.61 0.00019736 45377000 84914 80663 72944 89405 81445 73643 85817 83099 82712 FALSE TRUE 80900.2835 88882.65141 76288.55455 80417.83954 95648.98221 71092.72444 72724.04051 75822.41102 95538.55453 0.846781531 0.930332805 0.798510663 0.841731801 1.001155844 0.744126021 0.761200971 0.793631549 1 16.54379543 LQEKEDLQELNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LQEKEDLQELNDR 13 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;;;; 263.83 3.08E-24 44582660000 41575420 30670440 32582240 38537180 29017540 38517450 44517820 39839700 32629930 FALSE TRUE 39610232.29 33795792.71 34076167.93 34663349.45 34078189.79 37183581.05 37725808.93 36351124.66 37690012.89 1.050947698 0.896677664 0.904116643 0.919695877 0.904170287 0.986563235 1.000949749 0.964476313 1 25.16767895 2.144997317 9.061397863 0.989755001 0.938343843 0.255057958 0.044691746 0.450987813 39.49496945 0.017568291 0.012972375 139.6359733 -2.144997317 -0.051411158 LQEKEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LQEKEELR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;;;;;;; 136.63 0.00071367 4239420000 6735220 4973150 5796760 6469710 5000870 6227870 7153680 6532300 5731970 FALSE TRUE 6416859.499 5479919.639 6062547.18 5819362.459 5873020.145 6012197.3 6062254.73 5960297.182 6620854.633 0.969189003 0.827675571 0.915674413 0.878944303 0.887048647 0.908069673 0.915630242 0.900230788 1 22.65858602 -0.236529551 0.590266293 1.009417805 0.894703314 0.439192928 0.035317691 5.993778389 2.019797609 0.161107435 0.01362693 0.580056702 0.236529551 -0.114714491 LQEKLS(ph)PPYSSPQEFAQDVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LQEKLSPPYSSPQEFAQDVGR 21 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LQEKLS(0.991)PPY(0.003)S(0.004)S(0.002)PQEFAQDVGR;LQEKLS(0.992)PPYS(0.007)S(0.001)PQEFAQDVGR;LQEKLS(0.998)PPYS(0.001)S(0.001)PQEFAQDVGR 134.97 4.46E-06 447374000 343005 255439 273612 331215 228357 314517 340874 336529 244412 TRUE FALSE 326791.8334 281468.5245 286157.3808 297920.6389 268182.3885 303625.1974 288867.4107 307060.7367 282314.1647 1.157546713 0.997004613 1.01361326 1.055280522 0.949943085 1.075486941 1.023212601 1.087656147 1 18.10694199 4.615179918 2.993096726 1.026699863 1.163214129 0.511466106 0.040433348 0.224935777 3.324196749 0.008944412 0.062909804 41226.82771 -4.615179918 0.136514265 LQELESCSGLGS(ph)TSDDTDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 LQELESCSGLGS(0.989)T(0.01)SDDTDVR;LQELESCSGLGS(0.924)T(0.06)S(0.016)DDTDVR;LQELESCSGLGS(0.487)T(0.487)S(0.026)DDTDVR 257.37 3.38E-36 242379000 250714 234067 234573 286743 257690 234509 262032 238465 267247 TRUE FALSE 238863.2461 257918.6934 245328.4041 257919.0489 302631.0544 226387.8945 222054.2059 217583.7404 308690.2999 0.773795763 0.835525747 0.794739596 0.835526899 0.980371118 0.733381952 0.719342998 0.704860958 1 18.23580062 -1.695530851 8.594640565 1.000490301 0.797107553 0.396256213 0.078672526 0.000755863 2.68E-05 0.077899787 0.018318616 0.020159008 1.695530851 -0.203382749 LQELPDAVPHGEMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQELPDAVPHGEMPR 15 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 74.12 0.035747 213760000 120452 113482 114404 133485 126399 116734 144582 133649 136769 FALSE TRUE 114758.4727 125045.9448 119649.5366 120066.8342 148442.9456 112691.4723 122523.3605 121945.985 157978.438 0.72641858 0.79153805 0.757378906 0.760020391 0.939640545 0.713334514 0.775570148 0.771915374 1 17.26936814 -2.436117458 2.018627846 2.687075779 0.777801867 0.559976685 0.061418089 2402517.243 177977.8498 18544007.7 0.01382966 0.003663385 2.436117458 -1.909273912 LQELSAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQELSAEER 9 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 98.048 0.011443 0 158570 148070 147650 183490 142650 162150 191730 165930 169960 FALSE TRUE 151074.7104 163158.5013 154419.8985 165045.2366 167528.1148 156534.7048 162478.0671 151400.2895 196316.5288 0.769546565 0.831099156 0.786586333 0.840709835 0.853357157 0.797358765 0.82763315 0.771205005 1 17.58282212 -1.487450266 3.18533837 1.004393328 0.811407023 0.811938712 0.02877394 7454672.734 10449953.99 293730.4844 0.006451403 0.032549906 1.487450266 -0.192986304 LQELSSKADEASELACPT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQELSSKADEASELACPTPK 20 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 LQELSSKADEASELACPT(1)PK 164.05 3.03E-11 184720000 467600 167230 393250 321190 265550 343220 590160 422760 328950 TRUE FALSE 445497.4747 184270.9271 411280.9015 288903.371 311861.8359 331334.2053 500120.253 385740.8932 379961.886 1.172479375 0.484972135 1.082426729 0.760348292 0.820771365 0.872019583 1.316237948 1.015209439 1 18.53549518 1.851800284 8.227273896 1.138553088 0.846406107 0.240175794 0.201901044 0.333982335 21.96680522 0.079709729 0.049822592 71.08865286 -1.851800284 -0.29214698 LQEVFGHAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQEVFGHAIK 10 0 P54136;P54136-2;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 112.13 0.0016622 251700000 876560 728280 645950 754980 798490 731680 1014600 855420 755530 FALSE TRUE 835126.746 802492.56 675567.4464 679087.976 937746.4032 706341.7381 859804.1356 780514.8899 872693.7337 0.956952839 0.919558064 0.774117448 0.778151544 1.074542382 0.809381013 0.985230101 0.894374349 1 19.73511591 2.758813534 24.987896 0.942651711 0.874057628 0.208504112 0.088641985 1761.072286 2172794.726 0.026634815 0.02821741 573.8700165 -2.758813534 -0.068594083 LQEVPHEGPMCDLLWSDPDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 134.47 6.22E-06 251760000 173122 181822 183616 181428 162367 173114 186433 189009 177262 FALSE TRUE 164938.8662 200349.8685 192034.9752 163190.5127 190683.7534 167119.0188 157989.2218 172458.37 204750.8856 0.805558743 0.978505504 0.9378957 0.797019814 0.931296355 0.816206573 0.771616793 0.842283878 1 17.64351017 3.247811251 24.99968513 0.843632654 0.908036702 0.049859305 0.079308033 398.9503219 1078149.938 0.021073614 0.028156207 1769.339819 -3.247811251 0.064404048 LQFHDVAGDIFHQQCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LQFHDVAGDIFHQQCK 16 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 263.04 3.70E-27 5796776000 12495970 10254370 9618680 11470670 9897040 10831550 13408160 11854170 2039261 FALSE TRUE 11905310.26 11299301.96 10059705.99 10317616.46 11623080.64 10456450.71 11362498.93 10816156.03 2355499.181 5.054262111 4.796988279 4.270732112 4.380225025 4.934444782 4.439165504 4.823817825 4.591874249 1 21.1676014 0.919954604 19.47695819 1 4.690999078 0.955376737 0.248713435 817.5773807 198937.0059 0.244235506 0.061058876 8.316768329 -0.919954604 3.690999078 LQFHDVAGDIFHQQCKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQFHDVAGDIFHQQCKR 17 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 188.27 1.71E-10 298710000 263210 117670 263010 195090 282880 236370 464020 276910 118440 FALSE TRUE 250768.5849 129660.7068 275069.2687 175479.1826 332214.1824 228184.4476 393225.2267 252662.2924 136807.0703 1.833008955 0.9477632 2.010636351 1.282676269 2.428340741 1.667928764 2.874304858 1.84685113 1 17.06178327 2.744465547 24.96659149 2.118885102 1.485677669 0.097276772 0.569841318 665.4841132 2813731.113 0.159961385 0.165525034 555.2205688 -2.744465547 -0.633207433 LQFIADHCPTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 118.76 0.00022838 0 185010 172010 196790 162950 181100 175600 231990 201270 204720 FALSE TRUE 176264.944 189538.0146 205813.0162 146569.9564 212683.7827 169518.928 196595.6647 183645.7318 236466.932 0.745410542 0.80154131 0.870367008 0.619832782 0.899422938 0.716882173 0.831387556 0.776623311 1 17.85127892 -4.999999999 0.339718176 3.338279224 0.776093086 0.428605197 0.078999157 342.7043158 2.888018453 580.9984615 0.054164148 1.00E-05 4.999999999 -2.562186138 LQGDANNLHGFEVDSR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 197.49 4.32E-11 1465140000 1881400 2220550 1942530 2148890 1869960 1867050 1963760 1919020 1727790 FALSE TRUE 1792469.951 2446826.57 2031596.922 1932879.495 2196080.432 1802393.59 1664152.345 1750980.435 1995726.849 0.898153949 1.226032796 1.017973438 0.96850904 1.100391285 0.903126393 0.833857773 0.877364774 1 20.92848284 2.165584882 6.461549292 0.882097578 1.049514001 0.335839131 0.09468864 0.202643032 14.11973591 0.034467262 0.025446348 146.4147674 -2.165584882 0.167416424 LQGEGLS(ph)VAGIVCHVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQGEGLSVAGIVCHVGK 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 1 LQGEGLS(1)VAGIVCHVGK 62.611 0.038934 37022000 59411 38642 45909 46642 56228 42305 64322 62563 53267 TRUE FALSE 56602.75977 42579.66373 48013.97306 41953.45755 66034.1454 40839.96724 54508.49755 57084.65205 61527.37431 0.919960593 0.69204422 0.780367659 0.681866535 1.073248227 0.663769057 0.8859227 0.927792754 1 15.90894081 1.26168966 2.274357114 0.988834001 0.802252416 0.229319483 0.12320173 0.40257467 3.504121476 0.101939181 0.029595349 18.26794352 -1.26168966 -0.186581585 LQGEGLSVAGIVCHVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQGEGLSVAGIVCHVGK 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 223.29 3.09E-15 4267800000 2220400 1747000 1803360 1805150 1652970 1597640 2017570 1859690 1661350 FALSE TRUE 2115446.092 1925021.286 1886045.84 1623692.892 1941247.445 1542313.326 1709752.641 1696845.685 1918983.673 1.102378369 1.003146256 0.982835793 0.846121265 1.011601856 0.803713626 0.89096779 0.884241856 1 20.87191101 3.970882709 0.937709193 0.89403139 1.114328272 0.477363074 0.065263305 0.573897028 0.805890594 0.021034587 0.100954248 9351.530807 -3.970882709 0.220296882 LQGPPT(ph)PAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQGPPTPAGK 10 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 LQGPPT(1)PAGK 110.51 0.020976 95540000 260560 282880 243450 285890 180790 244630 259150 276530 235440 TRUE FALSE 248243.8452 311705.7936 254612.4233 257151.794 212319.7188 236158.4018 219611.9079 252315.5672 271950.8327 0.9128262 1.146184369 0.936244323 0.945581933 0.780728327 0.868386389 0.807542693 0.927798473 1 18.05298632 3.244730148 2.304094074 0.861698913 1.027537536 0.283684175 0.086066489 0.263344562 2.865244539 0.02439705 0.033165871 1756.831653 -3.244730148 0.165838624 LQHAAELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQHAAELIK 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 87.298 0.01424 0 306280 247710 165880 226070 273570 197540 353500 284640 268120 FALSE TRUE 291802.7514 272951.9306 173485.7621 203345.0141 321280.5214 190699.1403 299567.0825 259715.4126 309698.6802 0.94221503 0.881346767 0.560175981 0.656589863 1.037397128 0.615757032 0.967285628 0.838606779 1 18.24050571 1.05019361 1.068608166 0.992048693 0.805293101 0.142217785 0.155818565 1.11929415 2.706122209 0.142838037 0.046626024 11.22518765 -1.05019361 -0.186755591 LQHLAPEELHTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQHLAPEELHTDR 13 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 198.23 7.37E-08 577070000 235550 234550 210086 257170 243160 202542 228040 223588 88405 FALSE TRUE 224416.0183 258450.9117 219718.6509 231318.783 285567.027 195527.9198 193248.3098 204009.4494 102114.3959 2.197692268 2.530993886 2.151691238 2.265290618 2.796540336 1.914792895 1.892468815 1.997851994 1 16.63982674 0.745076555 0.603912287 0.983837475 2.376381082 0.74946257 0.236290052 0.554914366 0.422681015 0.252035337 0.097430436 5.560022577 -0.745076555 1.392543607 LQHYAK ddPTM_SK-BR-3_Trastuzumab_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 769020000 4252400 3495200 3157200 4110800 3746200 3685200 4799500 4230700 3869300 FALSE TRUE 4051397.479 3851364.854 3301960.743 3697574.574 4399536.094 3557580.6 4067248.126 3860237.48 4469331.282 0.906488516 0.861731792 0.738804205 0.82732166 0.984383528 0.795998411 0.910035052 0.863717016 1 22.09162756 -0.290689259 0.486170847 1.021068453 0.854540609 0.310867103 0.066154576 8.342087316 1.994553989 0.379090493 0.032354812 0.512048079 0.290689259 -0.166527845 LQINS(ph)PPFDQPMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQINSPPFDQPMSR 14 0 Q00537;Q00537-2;F5H6Z0;F8VQZ9 Q00537 CDK17 Cyclin-dependent kinase 17 1 LQINS(1)PPFDQPMSR;LQINS(0.999)PPFDQPMS(0.001)R 91.076 0.0052039 0 146317 127625 130401 154213 148968 139745 161304 152561 172979 TRUE FALSE 139400.8854 140630.1326 136380.0148 138711.2163 174947.972 134905.5956 136694.1122 139201.9501 199803.6999 0.697689209 0.703841484 0.682570017 0.694237476 0.875599261 0.675190678 0.684142047 0.696693556 1 17.60822377 -1.174369982 4.103024814 1.000117923 0.711453943 0.704043395 0.058310113 8084400.208 2313926.001 8508.254029 0.013079551 0.066931417 1.174369982 -0.288663981 LQIS(ph)TPDIKDNIVAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQISTPDIKDNIVAQLK 17 1 O14896;O14896-2 O14896 IRF6 Interferon regulatory factor 6 1 LQIS(0.852)T(0.148)PDIKDNIVAQLK;LQIS(0.852)T(0.148)PDIKDNIVAQLK 272.1 7.64E-36 629590000 1105380 831020 917200 1062220 728250 1188030 1288780 1206700 733150 TRUE FALSE 1053130.878 915701.8828 959254.5272 955443.6275 855256.5694 1146888.223 1092152.941 1101034.951 846843.1576 1.243596135 1.081312253 1.132741664 1.128241539 1.00993503 1.354310078 1.289675581 1.300163957 1 19.69173527 2.231328835 24.99926428 1.266699474 1.126345093 0.193414435 0.110465502 205.7138278 711117.9973 0.036984473 0.027870216 170.3447822 -2.231328835 -0.140354381 LQISHEAAACITGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQISHEAAACITGLR 15 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 135.09 3.11E-05 648210000 684030 618360 609050 658700 552380 584820 608460 594740 556080 FALSE TRUE 651697.2575 681371.587 636975.5449 592486.2246 648714.8971 564567.5368 515628.2519 542661.4127 642314.0463 1.014608448 1.060807546 0.991688643 0.922424518 1.009965298 0.878958727 0.802766582 0.844853722 1 19.29291932 2.638222973 1.070742179 0.858385447 1.030117267 0.415409287 0.063849575 0.368070928 0.872153827 0.033718292 0.028069806 434.7333654 -2.638222973 0.171731821 LQKEEEIEFLYNENTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQKEEEIEFLYNENTVR 17 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 240.13 2.38E-20 470110000 748950 681550 715120 748770 576180 722350 828490 904880 657170 FALSE TRUE 713548.6178 751000.7199 747908.9594 673502.217 676665.6096 697334.8384 702088.6342 825643.9101 759080.5672 0.940016974 0.989355745 0.985282711 0.887260518 0.891427918 0.918657213 0.924919784 1.087689431 1 19.53389349 1.249178774 24.99903138 1.04384472 0.937131252 0.573077448 0.03939164 142.1802337 334749.4108 0.0281807 0.010053611 17.74919962 -1.249178774 -0.106713467 LQLEETDHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 192.3 6.98E-07 2133060000 2902940 2654130 2516003 3097020 2091453 2839920 3229240 3083940 2206160 FALSE TRUE 2765723.779 2924588.864 2631364.226 2785701.666 2456201.741 2741572.858 2736560.129 2813893.865 2548280.025 1.085329615 1.147671698 1.032604031 1.093169368 0.963866497 1.075852273 1.07388517 1.104232595 1 21.28109239 3.732754842 24.98342545 1.053321423 1.116500657 0.274764412 0.045127167 536.5400419 2308837.52 0.011179484 0.01784869 5404.491543 -3.732754842 0.063179235 LQLHESQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQLHESQK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 74.92 0.03973 668340000 1370000 1239810 1318050 1380070 1119620 1394180 1679060 1512280 1272600 FALSE TRUE 1305242.815 1366148.049 1378483.896 1241342.742 1314881.374 1345899.197 1422888.559 1379856.746 1469948.308 0.887951507 0.929385095 0.937777123 0.84448054 0.89450858 0.915609882 0.967985439 0.938711068 1 20.48733399 1.818276901 3.285093769 0.966083638 0.901411788 0.550091452 0.028901129 0.199608892 3.854018596 0.015180579 0.007792978 65.8077286 -1.818276901 -0.06467185 LQLIKDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQLIKDYR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 59.8 0.087855 284170000 744620 287470 582940 465410 905990 534730 1157800 699730 1209400 FALSE TRUE 709423.2883 316763.5198 609668.3756 418626.1026 1063994.369 516212.166 981156.3455 638457.9317 1396947.575 0.507838161 0.22675405 0.436428959 0.299672021 0.76165662 0.36952866 0.702357313 0.457037861 1 20.41384645 -0.603631926 0.221659531 1.331996954 0.302983777 0.557347276 0.155177307 8.538272241 0.528070307 2.232136532 0.335766453 0.249096758 0.603631926 -1.029013177 LQLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQLKPR 6 1 Q15056;K7EJP0;Q15056-2 Q15056;Q15056-2 EIF4H;TNNI3 Eukaryotic translation initiation factor 4H 0 ; 123.34 0.017175 2437900000 4362900 3379400 2805300 3260900 3556000 3268700 4514900 3749000 3848300 FALSE TRUE 4156674.363 3723764.702 2933925.78 2933108.137 4176165.274 3155504.099 3826069.083 3420717.685 4445074.71 0.935119123 0.83772826 0.6600397 0.659855757 0.939503956 0.709887753 0.860743482 0.769552349 1 22.08377624 -1.413298931 7.176259763 1.00001202 0.80491122 0.283500162 0.100869583 1.91E-05 1.56E-06 0.095950281 0.022614306 0.038610113 1.413298931 -0.1951008 LQLLEDDKENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;;;; 182.07 5.42E-06 3699701000 5669420 6518500 5153840 6377000 3751750 5964550 5292250 5979770 3809420 FALSE TRUE 5401437.752 7182742.561 5390148.662 5735971.844 4406054.012 5757996.138 4484820.064 5456149.638 4400165.398 1.227553345 1.632380129 1.224987739 1.303580963 1.001338271 1.308586296 1.019238974 1.239987397 1 22.06912632 3.231055363 1.920014383 1.126661717 1.422255476 0.371186744 0.149953266 0.288327948 2.188279617 0.043478301 0.060060546 1702.37551 -3.231055363 0.295593759 LQLLEEKTDEDEKTILNLENSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQLLEEKTDEDEKTILNLENSNK 23 2 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 104.66 0.00090873 57137000 77484 59526 75979 84564 50207 85296 89823 91330 43481 FALSE TRUE 73821.48488 65591.76708 79462.7123 76063.46606 58963.0849 82342.17813 76118.85164 83332.66103 50223.81141 1.469850312 1.305989435 1.582172083 1.514490118 1.174006577 1.639504765 1.515592893 1.659226146 1 15.6160839 3.752963084 24.60826074 1.468912077 1.387919894 0 0.211523204 2746.10102 4692008.436 0.04884636 0.087529023 5661.911598 -3.752963084 -0.080992183 LQLLEPFDKWDGKDLEDLQILIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQLLEPFDKWDGKDLEDLQILIK 23 2 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 171.39 3.50E-12 411870000 1093610 737170 885080 901110 550100 839250 1062670 1036610 535280 FALSE TRUE 1041917.223 812288.4611 925661.7935 810528.7108 646037.2658 810186.5621 900540.1742 945838.933 618288.4886 1.685163547 1.313769342 1.497135739 1.310923179 1.044879984 1.310369798 1.456504837 1.529769599 1 19.23792062 5.374650176 0.843505223 1.314669899 2.466258312 0.321139543 0.173189136 7.42142934 1.907608445 0.055363437 10.2326045 236946.4333 -5.374650176 1.151588413 LQLLSNLFHGMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQLLSNLFHGMDK 13 0 Q7L2H7;J3KNJ2;E9PN86 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ; 209.79 3.50E-08 175663000 713910 828520 642680 828600 531640 765950 758760 824130 474230 FALSE TRUE 680164.8891 912947.1299 672147.5137 745307.5538 624357.8477 739424.9594 642997.2264 751964.8082 547771.1664 1.241695312 1.666657878 1.227058953 1.360618447 1.139815102 1.349879302 1.173842776 1.372771797 1 19.0632138 -2.668418509 0.097425334 0.294169291 1.627474663 0.314726616 0.146810046 104.1630352 1.189653482 18.92411534 3.009502595 0.002145762 2.668418509 1.333305372 LQLNGNLQLELAQVLAQERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 427.52 5.44E-174 994661000 1243417 1243150 1083599 1399170 881726 1222493 1287907 1359470 1044633 FALSE TRUE 1184643.143 1369828.398 1133283.086 1258522.773 1035498.735 1180157.761 1091413.133 1240427.6 1206629.35 0.981778822 1.135252012 0.939213923 1.043006929 0.858174662 0.97806154 0.904513994 1.028010465 1 20.20255115 3.71523275 24.70064836 0.957019357 1.058515429 0.253870263 0.066118451 678.8497022 718798.5756 0.016070736 0.024913267 5190.781521 -3.71523275 0.101496073 LQLQGLDLS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 LQLQGLDLS(0.945)S(0.055)R;LQLQGLDLS(0.972)S(0.028)R;LQLQGLDLS(0.974)S(0.026)R;LQLQGLDLS(0.97)S(0.03)R;LQLQGLDLS(0.987)S(0.013)R 160.38 2.89E-05 156006000 284923 377138 337050 404534 334913 339204 368000 388637 439414 TRUE FALSE 271455.2545 415568.791 352504.0759 363869.4738 393321.7212 327457.2804 311854.8412 354605.884 507556.0789 0.534828102 0.818764287 0.694512568 0.716904967 0.774932539 0.64516473 0.614424404 0.698653604 1 18.95320771 0.938146597 22.08796158 1 0.685686937 0.607736267 0.079025735 5421.179021 1935915.805 0.074918718 0.01872968 8.672545706 -0.938146597 -0.314313063 LQLS(ph)PWESSVVNR ddPTM_SK-BR-3_Trastuzumab_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(0.596)PWES(0.389)S(0.015)VVNR;LQLS(0.973)PWES(0.026)S(0.001)VVNR 152.11 4.73E-05 216951000 284490 320030 296840 364610 300540 296210 338450 323570 368690 TRUE FALSE 271042.7215 352641.4208 310450.4076 327958.7101 352954.0808 285952.1734 286813.2364 295236.4954 425864.5622 0.636452867 0.828060027 0.728988592 0.770100964 0.828794204 0.671462711 0.673484628 0.693263825 1 18.70003516 -1.083372422 4.456851292 1.000017714 0.729658296 0.634185323 0.064722402 8860892.859 2153908.109 1918.969502 0.015211976 0.08253299 1.083372422 -0.270359417 LQLWDTAGQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 201.84 9.78E-08 1368667000 1630569 1454792 1302054 1768941 1784001 1545455 1795146 1601729 1774010 FALSE TRUE 1553495.235 1603036.959 1361754.464 1591123.69 2095130.21 1491935.506 1521263.508 1461473.117 2049114.41 0.758130062 0.782307201 0.664557556 0.776493339 1.022456432 0.728087948 0.742400473 0.713221824 1 20.96656911 -1.552633518 2.641604603 1.014914306 0.773271849 0.360759936 0.094770882 14993947.22 14272963.56 1579889.815 0.024637432 0.028013443 1.552633518 -0.241642456 LQMEAPHIIVGTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LQMEAPHIIVGTPGR 15 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;; 211.57 1.31E-09 4618246000 4625882 4192739 4197790 4816510 4820840 4216128 5075330 4702340 4834110 FALSE TRUE 4407225.725 4619983.871 4390262.824 4332345.264 5661592.97 4070122.43 4300995.194 4290578.181 5583759.09 0.789293674 0.827396705 0.786255774 0.77588327 1.013939333 0.728921568 0.770268761 0.768403169 1 22.41280527 -2.374466675 2.3089685 2.416291921 0.806583245 0.379180814 0.07738229 2527237.761 468444.0256 18706658.2 0.018529486 0.004222147 2.374466675 -1.609708676 LQPERGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK 136.06 0.00053506 15190590000 7484460 5718200 6359410 7099160 4324710 7198020 7886970 7703340 4904530 TRUE FALSE 7130684.409 6300891.081 6650995.239 6385538.949 5078938.055 6948750.763 6683667.872 7028794.712 5665099.464 1.258704186 1.11222956 1.174029738 1.127171551 0.896531135 1.226589367 1.179797092 1.240718677 1 22.43366986 LQPFHS(ph)TELEDDAIYSVHVPAGLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.941)T(0.059)ELEDDAIYSVHVPAGLYR;LQPFHS(0.908)T(0.092)ELEDDAIYSVHVPAGLYR;LQPFHS(0.712)T(0.288)ELEDDAIYSVHVPAGLYR;LQPFHS(0.913)T(0.087)ELEDDAIYSVHVPAGLYR 255.83 1.18E-44 327637000 96180 67575 80166 106875 125736 80535 116414 80164 76339 TRUE FALSE 91633.76201 74460.96933 83841.69039 96131.72195 147664.3186 77746.05276 98652.90621 73144.41518 88177.26223 1.039199445 0.844446374 0.950831181 1.090209874 1.674630339 0.881701822 1.118802101 0.829515607 1 16.42811906 3.226637194 5.646718546 1.118163827 0.935744683 0.086688469 0.231499081 0.356670119 36.30282619 0.064070824 0.080811315 1685.14468 -3.226637194 -0.182419144 LQPQEIS(ph)PPPTANLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(1)PPPTANLDR;LQPQEIS(0.982)PPPT(0.018)ANLDR 199.36 4.02E-11 169393000 164580 139168 150805 155779 160180 154672 194203 170807 167392 TRUE FALSE 156800.6296 153349.3774 157719.5584 140119.799 188115.3413 149315.6699 164573.7656 155850.2336 193350.2964 0.810966585 0.793116847 0.815719248 0.724693996 0.972925021 0.772254673 0.851168933 0.806051175 1 17.56085745 -4.999999993 0.235515072 2.016004719 0.797863583 0.448201942 0.06363282 141.4960883 1.413218894 68.6829313 0.091644988 1.00E-05 4.999999993 -1.218141137 LQPS(ph)SSPENSLDPFPPR ddPTM_SK-BR-3_Trastuzumab_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(0.381)S(0.307)S(0.307)PENS(0.006)LDPFPPR 62.165 0.050342 0 53663 42738 54870 57479 80294 45696 59062 42548 83522 TRUE FALSE 51126.45634 47093.05079 57385.84377 51701.10172 94297.24818 44113.53606 50051.00715 38822.27156 96474.16519 0.529949715 0.488141573 0.594831203 0.535906184 0.977435234 0.457257505 0.518802179 0.402411065 1 16.55785503 -2.190253899 2.426641821 2.276475846 0.559155346 0.436095191 0.156079612 7232443.275 1228098.176 51010097.98 0.03611136 0.006452769 2.190253899 -1.7173205 LQPSSS(ph)PENSLDPFPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.002)S(0.003)S(0.995)PENSLDPFPPR;LQPS(0.093)S(0.392)S(0.515)PENSLDPFPPR;LQPSS(0.001)S(0.999)PENSLDPFPPR;LQPS(0.033)S(0.218)S(0.749)PENSLDPFPPR;LQPSS(0.064)S(0.936)PENSLDPFPPR;LQPS(0.005)S(0.015)S(0.979)PENSLDPFPPR;LQPSS(0.023)S(0.977)PENSLDPFPPR;LQPS(0.005)S(0.025)S(0.97)PENSLDPFPPR 268.6 5.52E-28 1618938000 1074352 889865 980037 1086532 1099858 1018628 1223189 1095197 1168988 TRUE FALSE 1023569.51 980543.2552 1024972.666 977311.7391 1291672.887 983352.6569 1036569.053 999295.7447 1350268.689 0.758048764 0.726183806 0.759087931 0.723790566 0.956604339 0.72826443 0.767676138 0.740071775 1 20.36481509 -1.787729793 2.708465028 1.061872266 0.767358389 0.528970362 0.068179176 27209087.07 21023806.51 11139330.92 0.015308294 0.016303101 1.787729793 -0.294513877 LQPTPPIPAPAPKPAAPPRPLDRES(ph)PGVENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQPTPPIPAPAPKPAAPPRPLDRESPGVENK 31 3 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 LQPTPPIPAPAPKPAAPPRPLDRES(1)PGVENK 88.573 0.0004306 114040000 104040 86342 110030 113570 82482 115280 135810 126710 102380 TRUE FALSE 99122.23539 95140.34796 115074.9843 102153.7278 96866.83469 111287.8247 115089.6902 115614.6007 118256.5675 0.838196453 0.804524856 0.973095928 0.863831329 0.819124356 0.941070987 0.973220284 0.977659026 1 16.85156078 2.078042885 4.46675577 0.975945421 0.855858891 0.609779351 0.045758314 0.149216558 5.610982486 0.018776829 0.013305425 119.685871 -2.078042885 -0.120086531 LQPTWNDLGDKYNSMEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQPTWNDLGDKYNSMEDAK 19 1 Q8NBS9 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 228.63 9.05E-20 216600000 330910 285020 286040 333070 204120 340130 352780 386150 223610 FALSE TRUE 315268.5401 314063.862 299155.2169 299589.1708 239718.4634 328351.2128 298956.9318 352336.6589 258286.2968 1.220616595 1.215952476 1.158231082 1.159911209 0.928111427 1.271268422 1.157463387 1.364132218 1 17.97861158 -1.881184398 2.760984274 0.914389072 1.182304608 0.215623234 0.110497907 25501869.7 19594924.44 14331311.93 0.024789912 0.013146665 1.881184398 0.267915536 LQQEFEDKLEVEQQNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQQEFEDKLEVEQQNKR 17 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 163.35 1.53E-09 105920000 259420 217990 205590 257310 146800 246120 279620 270820 160280 FALSE TRUE 247157.7307 240203.4288 215016.5049 231444.7099 172401.8735 237596.8027 236958.8334 247105.5651 185135.4038 1.335010623 1.297447295 1.161401334 1.250137495 0.931220447 1.283367729 1.279921768 1.334728853 1 17.49822129 3.851718668 4.540441628 1.193557241 1.321366345 0.163188034 0.127509423 0.407154079 13.46012765 0.031949114 0.059550214 7107.529447 -3.851718668 0.127809104 LQQELDDLLVDLDHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;;;;;; 314.68 8.89E-58 13861432400 4383842.3 3788816 3982136.8 4834601.2 4365256 3975019.1 4780741.9 4578258.6 4318263.4 FALSE TRUE 4176626.762 4174900.658 4164721.711 4348617.902 5126555.264 3837363.192 4051351.919 4177362.006 4987917.633 0.837348783 0.837002726 0.834962006 0.871830335 1.027794691 0.769331708 0.812233123 0.837496188 1 22.25000621 3.237306065 23.74435772 0.871292423 0.836689017 0.06068582 0.078943426 68.76069904 1301445.024 0.0221492 0.027921032 1727.05459 -3.237306065 -0.034603407 LQQELEFLEVQEEYIKDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LQQELEFLEVQEEYIKDEQK 20 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;; 223.46 5.89E-25 174271000 247853.1 212361.9 219721 257847.5 131782.4 258766.7 258765.3 267010.6 151396.3 FALSE TRUE 236137.5752 234001.819 229795.4252 231928.1794 154765.2088 249805.5443 219285.9009 243629.7364 174874.065 1.350329308 1.338116198 1.314062352 1.326258296 0.8850095 1.428488234 1.25396468 1.393172489 1 17.41595682 -2.080490599 2.624257255 0.53074491 1.288505127 0.263916526 0.150153349 46083865.65 40890677.66 127124489.9 0.033513315 0.008308247 2.080490599 0.757760217 LQQGAGLESPQGQPEPGAAS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLESPQGQPEPGAAS(1)PQR 212.78 1.59E-25 618590000 1415060 1266980 1228060 1450100 747230 1591710 1487830 1524750 830090 TRUE FALSE 1348172.918 1396086.702 1284367.766 1304333.193 877546.6754 1536588.684 1260834.208 1391234.807 958816.1177 1.406080784 1.456052601 1.339535018 1.360358017 0.915239804 1.602589543 1.314990627 1.450992303 1 19.87089464 -1.85098015 2.619787653 0.852754783 1.361786923 0.286877099 0.17603121 8628368.597 5781224.15 7948172.177 0.040409787 0.014093532 1.85098015 0.509032139 LQQGAGLESPQGQPEPGAAS(ph)PQRQQDLHLESPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQQGAGLESPQGQPEPGAASPQRQQDLHLESPQR 34 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LQQGAGLESPQGQPEPGAAS(0.994)PQRQQDLHLES(0.006)PQR 189.42 2.00E-20 269540000 136930 66859 135490 96196 164910 132880 195620 125000 192990 TRUE FALSE 130457.5903 73672.00811 141702.3505 86526.19532 193670.2518 128278.3323 165774.5762 114054.3373 222917.9035 0.585227064 0.330489418 0.635670569 0.388152741 0.868796309 0.575451008 0.743657524 0.511642787 1 17.76615297 -5 0.098153159 2.415644404 0.259575926 0.446178296 0.151695343 150.3064795 1.00789403 43.41194393 2.418175236 1.00E-05 5 -2.156068478 LQQHIQELEAHLEAEEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQQHIQELEAHLEAEEGAR 19 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 191.79 5.13E-15 139231000 113846 98712 101894 115160 131398 99935 126598 104263 55032 FALSE TRUE 108464.7252 108770.865 106565.9407 103583.898 154313.7696 96474.22589 107283.15 95133.17899 63566.0815 1.70633021 1.711146298 1.676459177 1.629546695 2.427611801 1.517699748 1.68774207 1.496602854 1 15.95596954 0.844587623 1.228812071 1.002951427 1.775732371 0.509776488 0.242280404 0.533527161 1.541204157 0.214779102 0.065911671 6.991777874 -0.844587623 0.772780944 LQQLFNHTMFILEQEEYQR ddPTM_SK-BR-3_Trastuzumab_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 ; 186.45 2.05E-14 593880000 378100 458940 350430 464640 352000 392780 390770 399850 318710 FALSE TRUE 360227.9623 505706.5078 366497.5621 417933.5044 413388.6886 379177.9301 331150.8595 364837.0143 368133.9191 0.978524237 1.373702562 0.995554995 1.135275732 1.122930182 1.029999982 0.899539114 0.991044279 1 18.48987116 2.108228858 3.052117247 0.953722882 1.138775542 0.295212426 0.109748876 0.270569819 4.994979328 0.046543595 0.030767485 128.3006505 -2.108228858 0.18505266 LQQLGEAHQAETEVLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQQLGEAHQAETEVLRR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 254.53 3.15E-27 461810000 269963 220343 264570 256345 316596 226120 319777 275568 337466 FALSE TRUE 257202.384 242796.2022 276700.7962 230576.7136 371810.2422 218289.4077 270989.1455 251437.805 389798.5037 0.6598342 0.622876178 0.709855973 0.59152796 0.95385241 0.560005761 0.695203145 0.645045588 1 18.57236903 -1.681665038 2.63639381 1.046871441 0.67600426 0.468330591 0.107159556 15432260.83 12885132.23 4837066.99 0.023122988 0.020813013 1.681665038 -0.370867181 LQQLSVS(ph)ATHLADKVEEAVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQQLSVSATHLADKVEEAVLDR 22 1 Q2KHM9-2;Q2KHM9 Q2KHM9-2 KIAA0753 Uncharacterized protein KIAA0753 1 LQQLS(0.031)VS(0.965)AT(0.004)HLADKVEEAVLDR 119.42 4.04E-05 8766900 10472 12317 12644 11018 10892 12111 13715 12640 11653 TRUE FALSE 9977.009314 13572.1163 13223.73991 9910.449707 12791.56135 11691.59303 11622.52486 11533.17459 13460.08772 0.741229145 1.00832302 0.982440841 0.736284184 0.950332688 0.868611949 0.863480617 0.856842454 1 13.71640019 -2.325509512 2.187646627 1.621251905 0.879464977 0.157356307 0.089892287 4755514.405 539622.9025 14672150.47 0.020314218 0.004725965 2.325509512 -0.741786928 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LQQQAALS(0.68)PT(0.272)T(0.048)APAVSSVSK;LQQQAALS(0.858)PT(0.073)T(0.069)APAVSSVSK 330.05 8.79E-80 178344000 410270 395330 421910 494140 375430 450730 512530 520230 508160 TRUE FALSE 390877.3502 435614.5765 441254.9908 444468.1084 440904.8731 435121.1071 434334.1352 474675.9033 586962.8575 0.665932001 0.742150156 0.751759647 0.757233789 0.751163157 0.74130944 0.739968687 0.808698365 1 19.16290969 -5 0.200615258 2.202252335 0.69683741 0.921285002 0.024474982 37.72954151 0.373404381 18.13661872 0.060849242 1.00E-05 5 -1.505414926 LQQQHSEQPPLQPS(ph)PVMTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LQQQHSEQPPLQPSPVMTR 19 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;Q5JTV8-2;H0YDU3 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(0.998)PVMT(0.002)R;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR 174.4 2.94E-12 1889260000 882210 836602 825150 1150720 1242390 931740 1145930 922780 994950 TRUE FALSE 840509.6817 921852.6949 862983.9437 1035047.439 1459062.423 899473.6102 971097.3321 841976.4912 1149241.764 0.731360196 0.802139918 0.750915926 0.900635072 1.269587016 0.782667005 0.844989594 0.732636524 1 20.1322509 3.211176 7.317764803 0.916254267 0.765789334 0.211044684 0.14583458 0.303753023 58.5203397 0.042069996 0.051410351 1626.20765 -3.211176 -0.150464934 LQQTVPADAS(ph)PDSKCPICLDRFDNVSYLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQQTVPADASPDSKCPICLDRFDNVSYLDR 30 2 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 LQQTVPADAS(1)PDSKCPICLDRFDNVSYLDR 177.1 4.56E-18 95891000 206990 118140 209990 194710 176970 207910 280240 240060 240600 TRUE FALSE 197205.9929 130178.6003 219618.2492 175137.3809 207833.512 200710.0246 237484.241 219039.0738 277911.0192 0.709601201 0.468418275 0.79024664 0.630192287 0.747841926 0.722209667 0.854533375 0.788162608 1 18.08426351 1.562107419 0.377626159 1.010752385 0.584257561 0.611815978 0.086228391 0.657049819 0.284438471 0.105691756 0.085863058 36.48441768 -1.562107419 -0.426494824 LQQWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 167.64 0.015345 12901530000 5772640 4451440 3359600 3949570 6082320 3770040 6058030 4603440 5891160 FALSE TRUE 5499778.747 4905046.797 3513640.983 3552551.72 7143074.682 3639482.569 5133766.26 4200338.389 6804731.005 0.808228678 0.720828905 0.516352664 0.522070853 1.04972183 0.534845913 0.754440735 0.617267367 1 22.6981067 -1.517782496 3.457047891 1.006501271 0.697964749 0.263612227 0.162153877 16961363.95 14933984.83 769983.2526 0.034797182 0.03035411 1.517782496 -0.308536522 LQS(ph)IGTENTEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQSIGTENTEENR 13 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 LQS(1)IGTENTEENR;LQS(0.995)IGT(0.005)ENTEENR 334.4 6.45E-43 230500000 386910 319770 307900 389580 309440 332890 370630 338750 280720 TRUE FALSE 368621.5311 352354.9265 322017.5196 350418.6782 363406.238 321361.9358 314083.5864 309087.2542 324252.6239 1.136834381 1.086667927 0.993106904 1.080696508 1.120750339 0.991085074 0.968638535 0.95322977 1 18.30675872 2.140141172 5.78587152 0.973057964 1.084391866 0.64464779 0.03896407 0.135142184 6.638569957 0.015490298 0.011383074 138.0833046 -2.140141172 0.111333901 LQS(ph)IGTENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 LQS(0.999)IGT(0.001)ENTEENRR;LQS(1)IGTENTEENRR;LQS(1)IGTENTEENRR 204.23 8.53E-09 1104010000 431223 359944 388623 427366 368821 395131 442051 421655 394180 TRUE FALSE 410839.9434 396622.7028 406441.749 384406.3577 433143.2656 381447.5144 374608.0011 384732.6529 455307.4212 0.902335267 0.871109682 0.892675432 0.8442787 0.951320461 0.837780138 0.822758391 0.844995348 1 18.79648145 LQSEPESIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQSEPESIRK 10 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 88.338 0.019662 451240000 291670 228190 283260 295480 268300 280140 359740 294530 314190 FALSE TRUE 277883.3371 251442.8204 296247.7512 265777.789 315091.4351 270438.6816 304855.0559 268739.3918 362912.9805 0.765702392 0.692846037 0.816305195 0.732345778 0.868228617 0.745188781 0.840022463 0.740506419 1 18.46926413 -5 0.182586308 1.939070455 0.726768518 0.630165463 0.053748421 76.79341776 0.742618503 26.17464984 0.142312413 1.00E-05 5 -1.212301937 LQSEVAELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LQSEVAELK 9 0 P53990-2;P53990;P53990-4;P53990-5;J3KR23;H3BQF7;H3BMU1;H3BUI0;P53990-3;F5GXM3 P53990-2 IST1 IST1 homolog 0 ;; 103.74 0.0078483 359424000 654730 685120 532240 748110 450428 659860 661580 687080 477807 FALSE TRUE 623782.2104 754934.5069 556643.7305 672908.5615 528982.5006 637008.8827 560643.8202 626915.6328 551902.8693 1.130239115 1.36787567 1.008590028 1.21925179 0.958470285 1.154204695 1.015837843 1.135916604 1 19.07405486 3.72758613 24.92135723 1.074055286 1.249057397 0.365524959 0.097802187 585.4184715 1329394.695 0.023029779 0.036059684 5340.551781 -3.72758613 0.175002111 LQSFDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQSFDSPER 9 0 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 LQS(0.001)FDS(0.999)PER 71.219 0.052657 97544000 187300 179480 167820 208630 190970 201730 238400 226060 221370 TRUE FALSE 178446.7002 197769.2161 175514.713 187658.116 224275.1075 194744.0395 202027.7015 206264.988 255698.929 0.697878168 0.773445618 0.686411608 0.733902628 0.877106167 0.761614608 0.790099913 0.806671302 1 17.96408659 -5 0.142604529 1.845302757 0.678432068 0.757271926 0.045087561 65.44328608 0.567244794 15.61622683 0.251835121 1.00E-05 5 -1.166870689 LQSGICHLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQSGICHLFR 10 0 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 136.48 0.00011669 150730000 282330 261150 157510 163390 274020 219920 288230 236440 199440 FALSE TRUE 268984.8204 287761.4819 164731.9893 146965.7268 321809.0012 212304.1153 244255.2198 215736.0602 230368.1366 1.167630317 1.249137516 0.715081485 0.637960305 1.396933647 0.921586285 1.060282135 0.93648394 1 17.81358166 3.782761665 24.99975128 0.964344555 1.208384035 0.213103543 0.203358928 663.6091633 375329.7763 0.050753256 0.091496179 6064.034519 -3.782761665 0.24403948 LQSIGTENTEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LQSIGTENTEENR 13 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;; 327.3 5.82E-62 1645844000 845397 781344 670843 865297 729271 700419 807169 800154 708194 FALSE TRUE 805436.7592 860963.8419 701601.8151 778315.7016 856455.6315 676163.3144 684020.5444 730088.2739 818017.1086 0.984620921 1.052501021 0.857685992 0.951466288 1.046989877 0.826588231 0.836193445 0.892509785 1 19.64177149 2.231793992 24.99999644 0.869260861 0.982531342 0.261300612 0.071611679 167.8831979 620256.241 0.025577355 0.01931388 170.5273301 -2.231793992 0.113270481 LQSIGTENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;; 270.97 9.69E-33 1.3269E+11 13174100 11817050 12313960 13285740 13016000 12756170 14409710 12941570 14399170 FALSE TRUE 12551386.4 13021220.83 12878567.25 11950232.17 15285986.28 12314420.63 12211244.09 11808337.52 16632119.74 0.754647429 0.782896049 0.774319055 0.718503255 0.919064227 0.740399951 0.734196499 0.709971892 1 23.98746871 -2.297347029 2.402376515 2.206174332 0.767165438 0.609593649 0.058661954 1904891.514 461957.3984 12625631.06 0.013566956 0.005042582 2.297347029 -1.439008894 LQTLS(ph)PSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQTLSPSHK 9 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 LQTLS(1)PSHK;LQTLS(0.999)PS(0.001)HK 128.68 0.00026453 1279060000 651270 720600 654190 793530 545850 715390 774290 733730 548900 TRUE FALSE 620485.7578 794029.9593 684185.2586 713762.8568 641046.0672 690615.8649 656157.8397 669480.7115 634020.6086 0.978652349 1.252372476 1.079121482 1.125772328 1.011080805 1.089264064 1.034915633 1.055928944 1 19.27417021 2.750890548 24.24348165 1.044152973 1.116738867 0.194750357 0.070129485 804.1130418 1581070.227 0.020553865 0.021650483 563.4956244 -2.750890548 0.072585894 LQTMKEELDFQK ddPTM_SK-BR-3_Trastuzumab_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 ; 194.85 9.10E-07 5945800000 12283700 9674800 10216200 13159300 8905900 13785600 16835300 15236900 10670100 FALSE TRUE 11703073.84 10660673.12 10684622.88 11836502.16 10459086.14 13308201.22 14266765.78 13902676.26 12324764.61 0.949557595 0.864979856 0.866923078 0.960383629 0.848623602 1.07979354 1.157569027 1.128027731 1 23.55505676 2.158244947 5.667373952 1.113223285 0.899946221 0.755149105 0.054267008 0.084149265 4.487576106 0.018710894 0.013776625 143.9610307 -2.158244947 -0.213277064 LQTTDNLLPMS(ph)PEEFDEVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQTTDNLLPMSPEEFDEVSR 20 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta 1 LQTTDNLLPMS(0.999)PEEFDEVS(0.001)R 77.391 0.006494 16710000 25815 21212 23301 27365 28058 24952 26015 26609 25438 TRUE FALSE 24594.77611 23373.52692 24369.3739 24614.21821 32951.30632 24087.90598 22045.93395 24278.9749 29382.79512 0.83704685 0.795483439 0.829375619 0.837708533 1.121449004 0.819796275 0.750300775 0.826299023 1 14.84268402 -2.542127662 2.184776906 3.375896219 0.844636168 0.175294502 0.099572559 2860033.593 351938.5378 33640041.18 0.024743429 0.002869937 2.542127662 -2.53126005 LQVEEVHQLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LQVEEVHQLSR 11 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ; 157.52 3.06E-05 341940000 500860 489220 486520 526170 541390 411540 486380 489070 434600 FALSE TRUE 477185.3404 539072.0742 508827.4232 473278.3919 635808.2446 397288.2666 412173.798 446244.4381 501995.5484 0.950576837 1.073858276 1.013609433 0.942794002 1.26656152 0.791417908 0.821070624 0.888941027 1 18.93731505 2.185746366 24.99999357 0.853762261 1.037335949 0.396745506 0.104608063 86.93304385 41149.71541 0.035624388 0.026310378 153.3721007 -2.185746366 0.183573688 LQVEHPVTEMITGTDLVEWQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQVEHPVTEMITGTDLVEWQLR 22 0 G5E9X5;F5GYT8;E9PG35;E9PHF7;Q96RQ3 G5E9X5 MCCC1 "Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial" 0 181.83 4.83E-17 60862000 135200 102930 105190 105910 134430 94305 136610 111480 115280 FALSE TRUE 128809.3639 113418.684 110013.0655 95263.72558 157874.5494 91039.1942 115767.6355 101718.2202 133157.0336 0.967349305 0.851766376 0.82619042 0.71542391 1.185626813 0.683697975 0.869406837 0.763896712 1 17.02276911 LQVVDQPLPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 174.98 2.41E-05 428709000 1186420 1016810 1121190 1248810 1360880 1117540 1283560 1179800 1469720 FALSE TRUE 1130340.278 1120424.095 1172597.671 1123277.246 1598217.041 1078839.31 1087729.348 1076490.457 1697636.671 0.665831681 0.659990511 0.690723575 0.661671172 0.94143645 0.635494819 0.640731534 0.634111218 1 20.6950963 -1.475286427 3.09102987 1.007438131 0.687514167 0.533054209 0.090755393 16157847.78 20449485.37 1041683.933 0.021694992 0.033474459 1.475286427 -0.319923964 LQWVTIT(ph)S(ph)PQAIMMS(ph)ICLQS(ph)MVDELMVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQWVTITSPQAIMMSICLQSMVDELMVK 28 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 4 LQWVT(0.65)IT(0.697)S(0.697)PQAIMMS(0.979)ICLQS(0.978)MVDELMVK 44.674 0.051948 47202000 22065 20980 17864 26642 17909 19884 25492 24112 14491 TRUE FALSE 21022.03118 23117.88585 18683.08207 23963.89554 21032.32393 19195.41209 21602.72721 22000.62545 16738.19027 1.255932143 1.381146078 1.116194867 1.431689756 1.256547069 1.146803315 1.290625023 1.314396903 1 14.03085593 -3.659479294 0.326746379 4.54E-15 1.290517135 0.44447283 0.095184996 114.3468542 2.288825738 77.78707442 0.074663775 0.000219039 3.659479294 1.290517135 LQYLIDLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LQYLIDLGR 9 0 Q9P015;E5RIZ4;E5RHF4 Q9P015 MRPL15 "39S ribosomal protein L15, mitochondrial" 0 76.572 0.081545 16400000 77543 55861 57714 62698 77174 55635 90005 69611 68905 FALSE TRUE 73877.69607 61553.29941 60360.24399 56395.47792 90633.12117 53708.346 76273.08419 63515.49181 79590.43548 0.928223292 0.773375583 0.758385648 0.708571043 1.138743878 0.674809048 0.958319724 0.798029203 1 16.28030745 LRAELDEVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRAELDEVNK 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 135.8 0.00012285 412310000 569180 462670 471920 585980 422580 498710 612640 587140 504450 FALSE TRUE 542275.9894 509816.599 493557.9988 527076.1771 496277.8182 481439.5477 519170.5161 535726.909 582677.5296 0.930662265 0.874954968 0.847051712 0.904576117 0.851719507 0.826253842 0.891008302 0.919422634 1 19.15233815 0.912511551 2.234674002 0.999552139 0.875967805 0.647829657 0.029534012 0.266050244 2.828843373 0.028847214 0.007889317 8.175447827 -0.912511551 -0.123584334 LRAETEQGEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 240.44 3.01E-16 3042301000 1049507 775370 966726 975544 1279971 1038232 1367320 1044751 1367354 FALSE TRUE 999898.884 854381.0845 1011051.343 877480.4637 1503197.537 1002277.766 1158710.221 953267.0639 1579396.275 0.633089301 0.540954223 0.640150518 0.555579672 0.951754516 0.634595498 0.733641227 0.603564209 1 20.59094176 2.837794103 24.21343951 0.753262928 0.591027289 0.347258004 0.12697431 39.17759627 9552.035899 0.034616498 0.036716344 688.3258876 -2.837794103 -0.162235639 LRAPDLEYLFEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRAPDLEYLFEKPR 14 2 F5GYJ5;Q9NX18 F5GYJ5 SDHAF2 "Succinate dehydrogenase assembly factor 2, mitochondrial" 0 ; 204.82 7.37E-09 186069000 324140 270390 290510 281400 277470 252030 325020 307140 299180 FALSE TRUE 308818.5446 297943.0484 303830.1709 253113.1374 325860.6801 243302.1379 275432.2296 280245.1933 345575.3064 0.893636029 0.862165331 0.879201046 0.732439884 0.942951288 0.704049547 0.797025205 0.8109526 1 18.39864061 3.372007147 20.80812134 0.815222602 0.877107885 0.039385189 0.088519792 7.068311328 1370.730444 0.021655813 0.02932208 2355.08804 -3.372007147 0.061885282 LRAPIICVLGHVDTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRAPIICVLGHVDTGK 16 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 135.45 1.37E-05 86770000 256800 223770 228200 265730 216240 263540 302210 271500 237120 FALSE TRUE 244661.5729 246572.4174 238663.1957 239018.3155 253952.1875 254413.5437 256102.314 247726.0207 273891.3586 0.893279635 0.900256287 0.871379064 0.872675636 0.927200438 0.928884887 0.935050727 0.904468188 1 18.06324422 0.057034404 0.278231854 1.030026353 0.880921156 0.752053628 0.018529365 2.932700462 0.369399232 0.125416811 0.028599247 1.140340121 -0.057034404 -0.149105197 LRDADPILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LRDADPILR 9 1 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;;;; 128.03 0.00039095 2272280000 2687370 1919720 2099010 1984970 2236210 1680480 2347290 2098990 2197600 FALSE TRUE 2560343.346 2115341.651 2195251.685 1785437.044 2626204.316 1622284.556 1989167.8 1915191.308 2538392.584 1.008647505 0.833339044 0.86481961 0.703373093 1.03459344 0.639099155 0.783632844 0.754489798 1 21.27548378 5.035108608 0.835395014 0.802828414 1.233910411 0.16532526 0.122444041 5.149772521 1.984420055 0.036941609 2.294701123 108419.8017 -5.035108608 0.431081997 LRDADVQFLASVLPPDTDPAFFEHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRDADVQFLASVLPPDTDPAFFEHLR 26 1 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31;H0YDA6 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 193.92 1.32E-18 69712000 75839 47044 80070 62569 114770 66876 115810 90836 128730 FALSE TRUE 72254.24077 51837.83708 83741.2887 56279.44525 134785.8517 64560.06735 98141.0575 82881.91829 148692.7909 0.485929683 0.348623741 0.563183246 0.37849478 0.906472001 0.434184246 0.66002566 0.557403743 1 17.18197518 -4.999999969 0.112450941 2.547013177 0.263894484 0.506998801 0.150406759 118.9404154 0.883955984 42.05143655 1.565878373 1.00E-05 4.999999969 -2.283118692 LRDDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LRDDFEK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;; 170.24 0.0021903 1650380000 2826360 2688810 2540420 3294650 2183280 2964560 3223100 3260730 2403240 FALSE TRUE 2692763.564 2962802.796 2656900.77 2963465.523 2564043.341 2861896.544 2731356.899 2975203.195 2775922.185 0.970042885 1.067321992 0.957123649 1.067560733 0.923672628 1.030971458 0.983945772 1.07178912 1 21.4045357 1.257792724 24.99564484 1.035894632 1.003584439 0.081403792 0.048918924 547.3975239 711446.6435 0.028591869 0.010408925 18.104758 -1.257792724 -0.032310193 LRDDFEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRDDFEKK 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 112.11 0.0017462 216520000 596930 498170 536050 599620 374010 621390 684440 687270 402730 FALSE TRUE 568714.3019 548934.0894 560628.4227 539345.0584 439237.2256 599871.1085 580016.1074 627088.9954 465183.3115 1.222559554 1.180038225 1.205177419 1.159424779 0.944223954 1.289537035 1.246854934 1.34804706 1 18.82743982 LRDDTELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRDDTELRK 9 2 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 63.624 0.042096 344857000 286178 264879 278001 307476 219916 273721 315951 326159 262451 FALSE TRUE 272650.9331 291870.4712 290747.6208 276567.9283 258269.2808 264241.9731 267746.8721 297598.7889 303150.5607 0.899391156 0.962790472 0.959086535 0.912312112 0.85195053 0.871652596 0.883214174 0.981686421 1 18.20967497 1.140446007 5.701424904 0.997503255 0.908397019 0.509790646 0.034751717 0.199926024 9.091968508 0.03739283 0.009460167 13.81802606 -1.140446007 -0.089106236 LRDFLLDIEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRDFLLDIEDR 11 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ; 171.29 1.34E-05 54207000 102072 90260 72188 87879 109740 80998 116095 87145 109279 FALSE TRUE 97247.25885 99457.59662 75497.8912 79045.23596 128878.6213 78193.01895 98382.57552 79514.12182 126225.4292 0.770425258 0.787936292 0.598119505 0.626222754 1.021019473 0.619471207 0.779419616 0.629937425 1 16.94564306 LRDFVLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRDFVLVK 8 1 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 113.66 0.0025593 152410000 135030 110090 86988 98781 116150 93906 146780 117780 113720 FALSE TRUE 128647.3995 121308.2962 90976.48584 88851.34621 136406.5232 90654.01167 124386.0152 107466.5588 131355.1168 0.979386282 0.923514052 0.692599482 0.676420899 1.038456107 0.690144502 0.946944575 0.818137591 1 17.00311287 -0.426887588 7.521796276 0.999999999 0.856560554 0.119255137 0.128810088 0 0 0.118757767 0.027991474 0.374207435 0.426887588 -0.143439445 LRDLEDSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 230.93 8.43E-10 17813170000 8745630 5653360 7287410 7411950 9277140 7127200 9948060 8190170 9988000 FALSE TRUE 8332241.402 6229443.811 7621544.957 6666886.704 10895070.28 6880383.277 8430300.738 7472995.296 11536888.03 0.722226079 0.539958765 0.660623986 0.577875653 0.944368208 0.596381213 0.730725714 0.647747926 1 23.45975079 -5 0.22205214 2.683209773 0.631206354 0.447579924 0.112201303 133.5515584 1.33588814 100.6273365 0.191256726 1.00E-05 5 -2.052003419 LRDPDSHIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRDPDSHIVK 10 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 ; 84.658 0.0088751 180564000 317790 314090 240750 301570 279310 280250 354760 333800 267520 FALSE TRUE 302768.6965 346096.1281 251788.6256 271255.6107 328021.5756 270544.8722 300634.8464 304570.7024 309005.6353 0.9798161 1.120031768 0.814835061 0.877833863 1.061539137 0.875533781 0.972910562 0.985647728 1 18.23727362 3.757928474 24.99800258 0.940378854 1.049923925 0.250390168 0.078209345 1002.707216 1294185.355 0.018935382 0.034076699 5727.01702 -3.757928474 0.109545072 LRDPSGDFSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRDPSGDFSVR 11 1 Q96E14;A0A3B3ISX4 Q96E14 RMI2 RecQ-mediated genome instability protein 2 0 86.463 0.010643 0 46870 48969 54562 50204 82473 49420 71998 48789 74917 FALSE TRUE 44654.54799 53958.99677 57063.72167 45157.39854 96856.26509 47708.57301 61013.38277 44516.77651 86534.74574 0.516030267 0.623552959 0.659431321 0.521841234 1.119276012 0.551322739 0.705073809 0.514438173 1 16.4009919 LRDQELILFADLLCQYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRDQELILFADLLCQYHR 18 1 Q14676;Q14676-3;Q14676-2;Q14676-4;A2AB05 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 ; 197.84 1.08E-15 201426000 369080 310450 338260 365810 415390 324290 470820 387870 363080 FALSE TRUE 351634.3198 342085.208 353769.5556 329038.0838 487833.8845 313059.756 398987.7618 353906.0466 419384.592 0.83845312 0.815683777 0.843544475 0.784573611 1.163213656 0.746474148 0.951364855 0.843869931 1 18.67791433 LRDTEEMLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LRDTEEMLSK 10 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ;;;;; 192.6 6.07E-07 1899745000 3861010 3074920 3245830 3735110 2978470 3571260 4202430 3934820 3326230 FALSE TRUE 3678507.709 3388257.844 3394654.516 3359649.647 3497914.225 3447586.371 3561272.121 3590266.301 3842044.76 0.957434892 0.881889217 0.88355413 0.87444313 0.910430368 0.897331131 0.926921039 0.934467588 1 21.8734429 0.83518191 1.053886527 0.99955977 0.901546358 0.640122004 0.023233845 0.488490191 1.054170024 0.022581758 0.00725088 6.841981732 -0.83518191 -0.098013412 LRDYIWNTLNSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRDYIWNTLNSGR 13 1 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 166.64 3.03E-05 346230000 866310 998980 888850 915260 5293000 514340 1207500 700630 6001800 FALSE TRUE 825361.2432 1100777.198 929604.6517 823256.3259 6216097.524 496528.2768 1023273.698 639279.1229 6932528.491 0.119056307 0.158784374 0.13409316 0.118752678 0.896656614 0.07162297 0.147604687 0.092214424 1 22.72495021 -1.958616914 4.061637327 1.536528296 0.209910278 0.504935957 0.243448479 0.072206891 0.000735699 0.014390264 0.052647391 0.010999757 1.958616914 -1.326618018 LRDYQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRDYQVR 7 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 182.68 0.00059623 189670000 240310 213952 194050 218580 265420 203203 256260 214430 277760 FALSE TRUE 228951.0225 235753.952 202947.3844 196607.9231 311709.164 196166.0292 217162.8305 195653.3724 320833.6022 0.713612979 0.734816897 0.632562746 0.612803403 0.971560216 0.611426072 0.676870593 0.609828182 1 18.29146572 -1.160695899 4.748888726 1.000031148 0.698565607 0.442657806 0.10735014 3.25E-05 5.74E-06 0.095432993 0.022491451 0.069072329 1.160695899 -0.301465541 LREAEETQSTLQAECDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LREAEETQSTLQAECDQYR 19 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 102.59 0.00035503 141320000 39091 30000 34329 38217 39933 32834 43964 36035 50892 FALSE TRUE 37243.2459 33057.03411 35903.01861 34375.35455 46897.30256 31696.95035 37256.48435 32879.58437 58784.07144 0.633560163 0.562346794 0.610761006 0.584773285 0.797789289 0.53920985 0.633785368 0.559328123 1 15.84313766 -1.185486546 4.025917795 1.000200684 0.614039559 0.738235499 0.0720086 263454.918 34848072.14 13759.46141 0.015225014 0.065239925 1.185486546 -0.386161125 LREAIAELER ddPTM_SK-BR-3_Trastuzumab_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 ; 196.67 3.00E-07 225480000 285160 210450 249520 248360 302360 247050 337390 269520 342680 FALSE TRUE 271681.0519 231895.0943 260960.7388 223394.3809 355091.4883 238494.5966 285914.9589 245919.4 395821.0642 0.686373406 0.585858397 0.65928967 0.564382245 0.89710104 0.602531341 0.722333864 0.62128932 1 18.59448886 -5 0.279278605 3.428941289 0.643618755 0.544563404 0.094944291 160.9748601 1.542677042 226.6139207 0.09730307 1.00E-05 5 -2.785322534 LRECLPLIIFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRECLPLIIFLR 12 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 256.52 3.27E-21 864060000 585360 499640 469080 513790 595370 452460 671180 554710 575180 FALSE TRUE 557691.1929 550553.884 490587.782 462142.8531 699202.3395 436791.1967 568779.1639 506136.6517 664375.9768 0.839421069 0.828678193 0.738418906 0.695604401 1.05241966 0.657445802 0.856110371 0.761822627 1 19.34164038 -1.799593038 2.302975175 1.066500709 0.807431311 0.244064463 0.108375633 11667286.99 6911638.62 4328079.726 0.023899326 0.01586379 1.799593038 -0.259069398 LREDGIQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LREDGIQKR 9 2 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 91.658 0.005964 78594000 37506 29331 34324 37266 34766 35790 49274 44097 42129 FALSE TRUE 35733.16571 32319.86225 35897.78935 33519.95088 40829.17939 34550.58333 41756.34632 40235.63291 48662.15015 0.734311279 0.664168397 0.73769427 0.688830041 0.839033607 0.710009385 0.858086751 0.826836315 1 15.57051245 1.013900945 0.409818524 1.016231043 0.689328669 0.776827846 0.047375349 0.509822757 0.232921413 0.061516802 0.032710132 10.32525878 -1.013900945 -0.326902374 LREDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LREDLER 7 1 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ;;;;;;;; 215.39 3.63E-05 13229190000 7750690 6997160 6815250 7870990 7546290 7222900 8225360 7553990 8401780 FALSE TRUE 7384330.244 7710178.559 7127735.954 7079783.131 8862360.587 6972769.162 6970430.263 6892522.589 9704685.132 0.76090364 0.794480032 0.734463391 0.729522188 0.913204341 0.718495146 0.718254139 0.710226297 1 23.21024997 -1.276142928 3.39937174 1.000818273 0.760957302 0.614031731 0.059808269 51313752.64 81245829.51 444411.5819 0.013960487 0.052948916 1.276142928 -0.239860971 LREEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LREEGK 6 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 88.029 0.047213 180890000 267530 261160 233070 295650 191880 257130 335070 302910 249530 FALSE TRUE 254884.3871 287772.5009 243756.49 265930.7003 225343.8112 248225.5236 283948.9175 276385.5946 288225.838 0.884321784 0.998427146 0.845713527 0.922646985 0.781830709 0.861218846 0.985161218 0.958920257 1 18.13684015 1.687779585 6.996700627 0.97879826 0.892308056 0.398418983 0.056324825 0.15942578 15.93132886 0.029632698 0.015271238 48.72811198 -1.687779585 -0.086490203 LREEIEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LREEIEELKR 10 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 224.42 2.24E-09 583150000 874730 743910 772580 905220 656690 871160 964520 926640 687050 FALSE TRUE 833383.2464 819715.2748 808003.5572 814225.5658 771216.5281 840991.5108 817364.7594 845498.4892 793594.205 1.050137767 1.032914895 1.018157078 1.025997368 0.971802116 1.059724864 1.029953034 1.065404061 1 19.59804197 LREETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LREETER 7 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ; 145.16 0.0021028 478500000 270040 286820 267700 331680 288110 263910 310930 283510 324490 FALSE TRUE 257275.7444 316047.2841 279974.3098 298338.8962 338356.2928 254770.7305 263491.9179 258684.3614 374810.2519 0.686415975 0.843219422 0.746976126 0.795973148 0.902740229 0.679732556 0.703000829 0.690174188 1 18.51580089 LRENELTYYCCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRENELTYYCCK 12 1 E9PNW4;A0A2U3TZL5;P13987;P13987-2;H0YET2 E9PNW4 CD59 CD59 glycoprotein 0 108.17 0.0015822 95084000 156060 113340 97978 130610 158420 93159 170520 133380 152210 FALSE TRUE 148683.3531 124889.4749 102470.3882 117480.8347 186048.3978 89932.88047 144504.0422 121700.5401 175813.9494 0.845685758 0.710350204 0.582834232 0.668211112 1.058211811 0.511523009 0.821914545 0.692212083 1 17.42369002 -1.414771801 3.312991341 1.002992618 0.739627178 0.231906788 0.150678808 198940034.8 261802909.9 5605714.394 0.032639737 0.038479392 1.414771801 -0.26336544 LRENVFQEHQTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LRENVFQEHQTLK 13 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 111.12 0.00060387 704700000 1125230 923010 1083500 1310980 1091020 1250190 1533640 1338670 1177760 FALSE TRUE 1072042.608 1017065.768 1133179.547 1179197.8 1281293.543 1206895.607 1299655.051 1221448.958 1360401.006 0.788034266 0.747622035 0.832974646 0.866801623 0.941849894 0.887161654 0.955347023 0.897859494 1 20.37560055 3.210478884 1.436784707 0.933887332 0.766267149 0.80390331 0.033866432 0.140994414 0.607892011 0.010531957 0.015094651 1623.599405 -3.210478884 -0.167620183 LREQGTES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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" 1 LREQGT(0.003)ES(0.997)R;LREQGT(0.001)ES(0.999)R;LREQGTES(1)R;LREQGTES(1)R;LREQGT(0.001)ES(0.999)R;LREQGT(0.001)ES(0.999)R 136.93 0.00010832 2190418000 1001378 901656 1003156 1258449 1430520 1152001 1278711 1124066 1351652 TRUE FALSE 954044.8465 993535.7715 1049151.695 1131947.316 1680002.235 1112106.917 1083620.152 1025636.822 1561259.289 0.611073928 0.636368205 0.671990682 0.725021989 1.076055878 0.712314043 0.694068025 0.656929204 1 20.57427872 3.183730056 3.507776967 0.798123147 0.631851691 0.278371186 0.133061688 0.331870233 8.305889929 0.038964682 0.049213804 1526.616864 -3.183730056 -0.166271456 LREQGTESR ddPTM_SK-BR-3_Trastuzumab_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" 0 157.78 6.18E-05 104260000 118610 83813 113730 141760 135890 105960 141380 119480 161320 FALSE TRUE 113003.5404 92353.63999 118944.633 127510.0155 159589.173 102290.5786 119809.8844 109017.6978 186336.6817 0.606448174 0.495627802 0.638331819 0.684299057 0.856456021 0.548955674 0.642975303 0.585057632 1 17.50755218 -5 0.28914363 3.88572704 0.602126201 0.579622984 0.097092961 181.5451937 1.712284535 316.1837612 0.105492885 1.00E-05 5 -3.283600839 LREQLQLLEEQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 227.63 5.28E-12 836770000 1477220 1247150 1232520 1442070 1465410 1355470 1604470 1500790 1450020 FALSE TRUE 1407394.738 1374236.003 1289032.261 1297110.384 1720977.04 1308529.734 1359678.633 1369372.871 1674881.696 0.840295014 0.820497356 0.769625857 0.774448958 1.027521552 0.781266962 0.811805775 0.817593789 1 20.67562776 -1.522190282 2.96045768 1.006581146 0.829007198 0.343646691 0.073647668 34632305.63 41478559.28 1854306.08 0.016716142 0.030047595 1.522190282 -0.177573948 LRETFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRETFER 7 1 Q9Y2W2;F5H5G4 Q9Y2W2 WBP11 WW domain-binding protein 11 0 118.32 0.0045891 84358000 61694 48529 48838 59660 63940 55734 68038 61477 72020 FALSE TRUE 58777.84689 53474.16027 51077.27061 53662.86345 75091.11576 53803.9176 57657.5535 56093.74797 83188.49377 0.706562221 0.64280717 0.613994415 0.645075551 0.902662284 0.646771148 0.693095293 0.674296954 1 16.34409638 -5 0.357101999 4.766696335 0.678908541 0.594062702 0.080227811 323.0772286 2.592573114 934.4895897 0.056582298 1.00E-05 5 -4.087787794 LREVIEIEDAS(ph)PTKCPITTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LREVIEIEDASPTKCPITTK 20 2 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LREVIEIEDAS(0.999)PT(0.001)KCPITTK 178.95 3.13E-17 72712000 131680 103910 137440 141230 88467 155740 164130 179880 111610 TRUE FALSE 125455.7474 114498.5471 143741.7599 127033.2921 103895.6168 150346.6847 139088.954 164128.7536 128917.9088 0.973144449 0.888150826 1.114986749 0.985381265 0.805905229 1.166220319 1.078895519 1.273126094 1 16.97609317 2.211674378 24.97866933 1.131076841 0.955173346 0.420542299 0.102667722 204.3708052 189869.5131 0.035788587 0.02643856 162.807489 -2.211674378 -0.175903494 LREVVETPLLHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LREVVETPLLHPER 14 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 164.63 2.46E-06 216520000 235270 180930 181646 199574 252980 195627 263330 220800 267670 FALSE TRUE 224149.2534 199366.9727 189974.6488 179512.4424 297099.6319 188852.3879 223154.1721 201465.5815 309178.8965 0.724982384 0.644827234 0.614448951 0.580610269 0.960931148 0.610819141 0.721763919 0.651614919 1 18.23808232 -5 0.399632305 6.006044889 0.682337644 0.452424676 0.107288853 655.1433578 4.5814413 2861.763682 0.06108212 1.00E-05 5 -5.323707246 LREYEAALNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LREYEAALNSK 11 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 184.34 4.51E-06 353470000 580840 451660 456050 533420 432650 525130 609600 529450 538970 FALSE TRUE 553384.8443 497684.6675 476960.3436 479799.6082 508104.023 506944.6164 516594.3239 483088.5512 622550.7149 0.888899219 0.799428313 0.766138938 0.770699634 0.81616487 0.814302521 0.829802796 0.775982646 1 19.24783184 -1.64276696 2.94936244 1.016669404 0.811369566 0.740611771 0.035710112 13932190.39 14289833.71 1772083.461 0.009137673 0.022763186 1.64276696 -0.205299837 LRGDVAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRGDVAIK 8 1 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 76.221 0.033162 268190000 406720 389450 380510 419030 314300 380430 413480 396180 376570 FALSE TRUE 387495.1516 429135.3978 397956.7599 376908.3083 369113.8205 367255.6137 350396.0319 361488.3789 434966.5523 0.890861951 0.986594016 0.914913475 0.866522509 0.848602768 0.8443307 0.805570061 0.83107167 1 18.73054494 3.258801244 2.958936634 0.849119672 0.94017824 0.195158528 0.05748469 0.267516417 4.808814549 0.015480098 0.020699536 1814.684977 -3.258801244 0.091058568 LRGTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLTPT(0.078)S(0.078)HT(0.329)ANT(0.258)S(0.258)PRPVSGMER 101.78 8.10E-06 90254000 29378 24575 40040 34580 31282 37587 42896 39505 42249 TRUE FALSE 27989.36016 27079.22044 41875.8736 31103.9527 36737.5709 36285.35277 36351.42736 36045.73277 48800.75914 0.57354354 0.554893426 0.858098815 0.637366165 0.752807365 0.743540744 0.744894711 0.738630575 1 15.57461597 -4.863975679 0.048078546 2.321343885 7.38E-11 0.650780739 0.077277548 326.7569574 1.190531203 57.10921408 13.93439405 1.37E-05 4.863975679 -2.321343885 LRGTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLTPT(0.027)S(0.027)HT(0.105)ANT(0.417)S(0.417)PRPVS(0.007)GMER 87.372 0.0080917 126970000 61789 38501 62580 50592 63212 57935 83399 61512 80251 TRUE FALSE 58868.35642 42424.29567 65449.3549 45506.39604 74236.15279 55928.69642 70674.95082 56125.68318 92695.91521 0.635069585 0.457671685 0.706065146 0.490921266 0.800856787 0.603356645 0.762438676 0.605481731 1 16.50021815 -5 0.13672937 2.310563597 0.481165027 0.563905392 0.103887018 88.01324799 0.744536971 31.27605459 0.59297141 1.00E-05 5 -1.82939857 LRGWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRGWLK 6 1 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ; 130.01 0.014545 1422520000 1256190 720280 776330 812600 1126960 917240 1706800 1292600 1771240 FALSE TRUE 1196812.388 793677.3509 811925.4984 730915.9042 1323501.467 885475.7488 1446396.312 1179413.091 2045914.853 0.584976636 0.387932738 0.396852047 0.357256268 0.646899584 0.432801858 0.706967991 0.576472227 1 20.96431467 0.683027824 0.541131626 1.013709159 0.445554901 0.717810735 0.102774109 0.703984316 0.423721241 0.122377715 0.046480494 4.819786754 -0.683027824 -0.568154258 LRGYDYGPHFQGILEASLEGDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LRGYDYGPHFQGILEASLEGDSGR 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 ;;;;; 251.32 2.28E-39 2843955000 1256091 872440 1207880 1060691 1347822 1191698 1585829 1405265 1555185 FALSE TRUE 1196718.068 961342.6279 1263262.493 954068.3255 1582881.73 1150429.199 1343881.66 1282212.547 1796355.147 0.666192356 0.535162899 0.703236492 0.53111342 0.881163022 0.64042414 0.748115796 0.713785661 1 20.77664117 -4.999999936 0.128261125 2.153351062 0.519813927 0.571012392 0.093686946 92.43371461 0.751601433 27.17270417 0.651169333 1.00E-05 4.999999936 -1.633537135 LRIDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRIDYER 7 1 P15924 P15924 DSP Desmoplakin 0 ; 104.44 0.0074343 276488000 130916 121306 130183 140894 142189 138861 171935 145291 162299 FALSE TRUE 124727.8601 133667.2193 136152.0193 126731.0674 166986.7166 134052.2088 145703.1579 132568.5498 187467.5 0.665330578 0.713015426 0.72626999 0.676016202 0.890750218 0.715069059 0.777218227 0.707154839 1 17.51628098 -5 0.174519963 2.051306278 0.672601101 0.649697647 0.062093581 77.63636978 0.739495825 28.34010094 0.19151661 1.00E-05 5 -1.378705177 LRIEEEIR ddPTM_SK-BR-3_Trastuzumab_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 764990000 1400870 1240900 1233960 1426750 1468190 1281480 1503000 1392050 1644640 FALSE TRUE 1334653.651 1367349.121 1290538.287 1283330.379 1724241.871 1237102.026 1273689.746 1270154.722 1899682.372 0.70256674 0.719777759 0.679344245 0.675549975 0.907647456 0.651215195 0.670475109 0.66861426 1 20.85732679 -0.944330526 4.340459504 1.000007245 0.708488645 0.609565617 0.073087726 6234180.644 4309329.36 395.5286572 0.016177838 0.113676181 0.944330526 -0.2915186 LRLCDDGPQLPT(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRLCDDGPQLPTSPR 15 1 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LRLCDDGPQLPT(0.56)S(0.44)PR 60.564 0.095466 0 110580 68920 107600 95742 133220 90243 131150 105390 159620 TRUE FALSE 105353.1025 75943.02636 112533.5664 86117.83226 156453.5258 87117.86228 111140.6588 96161.49289 184373.0544 0.571412688 0.411898727 0.610357988 0.467084697 0.848570451 0.472508646 0.602803154 0.521559364 1 17.4922683 -5 0.271986164 4.073765158 0.524506447 0.561996488 0.120209511 147.8742471 1.431861228 255.6688157 0.13238538 1.00E-05 5 -3.54925871 LRLECADLLETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRLECADLLETR 12 1 Q6PI48;A0A3B3ITK9;A0A3B3IS01;A0A3B3IT01;A0A3B3ISK7 Q6PI48 DARS2 "Aspartate--tRNA ligase, mitochondrial" 0 117.2 0.00069218 80954000 117010 75585 119040 89625 142350 87250 116670 117920 145410 FALSE TRUE 111479.1692 83287.19743 124498.1017 80615.72472 167175.7949 84228.51062 98869.84871 107594.2997 167959.4401 0.663726725 0.495876846 0.741239085 0.479971383 0.995334319 0.501481254 0.588653121 0.640596918 1 17.35775336 -1.335323561 2.222054535 1.012409411 0.62711431 0.358434469 0.151389814 319549.7532 289861.493 25842.16188 0.035176912 0.046203666 1.335323561 -0.385295101 LRLEGPGDEDADGAGS(ph)PSDWASPLEDPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRLEGPGDEDADGAGSPSDWASPLEDPLR 29 1 O60347 O60347 TBC1D12 TBC1 domain family member 12 1 LRLEGPGDEDADGAGS(0.979)PS(0.021)DWASPLEDPLR 102.4 0.00036336 15544000 16523 12964 13756 17332 16814 12578 17704 18702 18074 TRUE FALSE 15741.99054 14285.04634 14386.72621 15589.75443 19746.35628 12142.42071 15002.92964 17064.35373 20876.82361 0.754041459 0.684253822 0.689124288 0.746749349 0.945850607 0.581622039 0.718640437 0.817382666 1 14.3496146 0.916807217 3.354582452 0.999658581 0.727358357 0.470251039 0.090411834 0.296333283 7.812156212 0.081639994 0.021178048 8.25671354 -0.916807217 -0.272300224 LRLPLDKEPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 150.68 1.90E-05 378080000 716530 594000 456800 566690 592500 541160 777370 648570 684030 FALSE TRUE 682661.0469 654529.2753 477744.7318 509725.2446 695831.8124 522419.4935 658767.9291 591777.7725 790105.8789 0.864012109 0.828407044 0.604659128 0.645135365 0.88068173 0.661201881 0.833771709 0.748985406 1 19.59168647 -1.166511551 4.15610224 1.000079509 0.767236577 0.380945249 0.096217722 16609892427 52818474.39 12709666.67 0.022964963 0.068153545 1.166511551 -0.232842932 LRLPLEAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRLPLEAALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 215.87 7.28E-09 295700000 507400 286850 117502 135400 611540 197785 584110 355710 571190 FALSE TRUE 483416.2076 316080.3411 122889.5829 121789.3348 718192.3824 190935.6559 494993.2916 324562.1467 659767.228 0.732707214 0.479078572 0.18626203 0.184594399 1.088554193 0.289398515 0.750254439 0.491934326 1 19.33159759 -0.144918953 0.454567324 1.068732566 0.495626564 0.228399577 0.27794136 8.037806289 1.914242753 1.251188087 0.147711818 0.716277067 0.144918953 -0.573106001 LRLS(ph)PS(ph)PTSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.881)PS(0.431)PT(0.379)S(0.309)QR;LRLS(0.992)PS(0.728)PT(0.155)S(0.125)QR;LRLS(0.994)PS(0.467)PT(0.298)S(0.24)QR;LRLS(0.999)PS(0.705)PT(0.161)S(0.134)QR;LRLS(0.895)PS(0.653)PT(0.436)S(0.016)QR 147.52 0.00042159 42001360000 3167340 2728630 2808510 3013090 2978240 2659770 3194420 2834860 3381850 TRUE FALSE 3017626.115 3006680.499 2937282.961 2710208.469 3497644.113 2567661.498 2707052.559 2586624.63 3906290.026 0.77250437 0.769702321 0.751936733 0.693806259 0.895387718 0.657314608 0.692998354 0.66216912 1 21.89736764 -0.953150574 4.467394641 1.000005068 0.738921463 0.586011219 0.06945924 7432582.375 3327479.95 376.1794233 0.015668541 0.111390826 0.953150574 -0.261083605 LRLS(ph)PSPT(ph)SQR ddPTM_SK-BR-3_Trastuzumab_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(0.963)PS(0.135)PT(0.532)S(0.371)QR 82.483 0.043114 20095000000 1026800 870700 876330 959310 902590 843440 957480 853760 1018100 TRUE FALSE 978265.1989 959425.3199 916510.5973 862878.3362 1060001.41 814231.4613 811398.8407 779000.2483 1175981.748 0.831871073 0.815850519 0.779357842 0.73375147 0.901375733 0.692384438 0.689975709 0.662425458 1 20.16543424 2.209450081 24.99787664 0.728963451 0.809592045 0.016724319 0.103479407 410.1010834 352160.5922 0.034270204 0.025314242 161.9757805 -2.209450081 0.080628594 LRLS(ph)PSPTS(ph)QR ddPTM_SK-BR-3_Trastuzumab_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(0.691)PS(0.311)PT(0.155)S(0.843)QR 159.75 0.00033828 15993000000 2203800 1795000 1948300 2079800 2092000 1836000 2298300 2027500 2220000 TRUE FALSE 2099630.742 1977912.541 2037631.482 1870734.553 2456844.138 1772418.86 1947652.124 1849961.352 2564266.262 0.818803715 0.771336647 0.794625547 0.7295399 0.958108046 0.691199228 0.759535838 0.721438869 1 21.29011464 -2.109157605 2.303016527 1.391315254 0.780647016 0.472423868 0.07287323 5831802.417 1786719.343 11927254.55 0.015968989 0.007777543 2.109157605 -0.610668238 LRLS(ph)PSPTSQR ddPTM_SK-BR-3_Trastuzumab_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(0.81)PS(0.19)PTSQR;LRLS(0.988)PS(0.012)PTSQR;LRLS(0.986)PS(0.014)PTSQR;LRLS(0.996)PS(0.004)PTSQR;LRLS(0.993)PS(0.007)PTSQR;LRLS(0.874)PS(0.125)PTSQR;LRLS(0.997)PS(0.003)PTSQR 203.97 9.15E-08 69950100000 3255750 2503080 2532900 2820670 3031010 2735040 3114290 2775890 3213490 TRUE FALSE 3101857.15 2758146.698 2649035.97 2537130.893 3559617.184 2640324.879 2639147.863 2532818.356 3711821.617 0.835669779 0.743070918 0.713675452 0.683527161 0.95899468 0.711328601 0.711011502 0.682365323 1 21.82369595 4.610849641 3.141324969 0.760544647 0.837794473 0.011821294 0.113618709 1.033634181 17.10476213 0.025086531 0.165270727 40817.80444 -4.610849641 0.077249826 LRLSPS(ph)PT(ph)SQR ddPTM_SK-BR-3_Trastuzumab_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 2 LRLS(0.666)PS(0.559)PT(0.546)S(0.229)QR;LRLS(0.549)PS(0.614)PT(0.805)S(0.033)QR 135.02 0.0032258 1645130000 1880980 1655520 1697000 1859810 1828210 1648870 1966630 1745300 2155830 TRUE FALSE 1792069.803 1824219.37 1774809.129 1672858.365 2147049.245 1591769.218 1666584.474 1592472.28 2490145.106 0.719664809 0.73257553 0.712733216 0.67179152 0.862218527 0.639227495 0.669272032 0.639509832 1 21.24779838 -1.401374432 3.190180727 1.003589174 0.707133324 0.676573941 0.063904254 14002251.08 18673040.09 463292.9963 0.014683052 0.039684925 1.401374432 -0.29645585 LRLSPS(ph)PTSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.263)PS(0.737)PTSQR;LRLS(0.05)PS(0.95)PTSQR;LRLS(0.077)PS(0.834)PT(0.008)S(0.081)QR;LRLS(0.25)PS(0.647)PT(0.089)S(0.013)QR;LRLS(0.219)PS(0.755)PT(0.025)SQR 210.86 2.98E-08 25258130000 5511750 4331420 4484730 4958150 5352150 4425560 5459180 4805080 5453330 TRUE FALSE 5251220.501 4772796.622 4690359.307 4459747.342 6285563.265 4272301.748 4626281.826 4384321.722 6299004.565 0.833658786 0.757706487 0.744619131 0.708008273 0.997866123 0.678250302 0.734446495 0.69603406 1 22.58669243 4.635496696 3.260515595 0.775183065 0.835917039 0.000298836 0.117010562 1.328172445 23.21979758 0.025665336 0.174134663 43201.28808 -4.635496696 0.060733974 LRLSPSPTSQR ddPTM_SK-BR-3_Trastuzumab_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 0 ; 178.32 6.92E-06 361470000 147457 128222 112676 127994 146203 122003 160444 144207 162765 FALSE TRUE 140486.9998 141287.9676 117842.3061 115127.7999 171700.7569 117778.0055 135965.321 131579.4706 188005.7649 0.747248362 0.751508698 0.626801556 0.612363137 0.913273893 0.626459543 0.723197616 0.69986934 1 17.52041738 -1.421751164 2.735746275 1.0074356 0.715314195 0.518442029 0.087016682 6865040.128 7463941.364 396408.6765 0.020201853 0.037865948 1.421751164 -0.292121405 LRNPSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LRNPSDR 7 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;; 107.9 0.0067258 138720000 240722 160324 200961 274998 474360 203398 308022 199984 451900 FALSE TRUE 229343.5481 176661.1979 210175.2606 247354.6786 557088.2338 196354.2763 261027.5867 182472.3408 521978.344 0.439373684 0.338445454 0.402651304 0.473879197 1.067263116 0.376173223 0.500073594 0.349578374 1 18.99363043 2.990323037 24.77208946 0.611742535 0.394501538 0.202855658 0.235739492 746.6412596 1911337.042 0.066248343 0.075040096 977.9643812 -2.990323037 -0.217240997 LRNPSDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRNPSDRK 8 2 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 95.358 0.0054595 63937000 46314 42763 39995 51208 64058 50374 71857 49942 64341 FALSE TRUE 44124.82901 47120.59832 41828.81031 46060.47455 75229.69492 48629.53575 60893.89491 45568.81372 74318.67367 0.593724657 0.634034436 0.56283042 0.619769868 1.012258309 0.654338047 0.819361971 0.613154292 1 16.18143713 2.959175026 24.97942178 0.797963949 0.602745014 0.41538573 0.126769736 486.9484551 297947.2485 0.034180843 0.036258344 910.2800536 -2.959175026 -0.195218935 LRPGFMEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRPGFMEDR 9 1 Q5BKZ1 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ; 144.77 9.01E-05 720150000 620020 520760 491280 621520 542050 531320 663430 652870 570380 FALSE TRUE 590712.8834 573826.0361 513805.6739 559043.6288 636583.3484 512920.2552 562211.5688 595701.2417 658831.6173 0.896606762 0.870975255 0.779874038 0.848537948 0.966230721 0.778530116 0.85334637 0.904178285 1 19.32955027 0.915123571 3.354557045 0.999823854 0.857575773 0.42069399 0.053667771 0.346693542 9.082607494 0.049056885 0.012725217 8.224766385 -0.915123571 -0.14224808 LRPKS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LRPKSPPPK 9 2 Q9HCE5 Q9HCE5 METTL14 N6-adenosine-methyltransferase subunit METTL14 1 LRPKS(1)PPPK;LRPKS(1)PPPK;LRPKS(1)PPPK 76.655 0.018167 3518390000 9091320 6962620 7962020 8757180 5353000 8868360 10395540 9877670 6285750 TRUE FALSE 8661591.321 7672118.894 8327086.493 7876891.629 6286561.505 8561246.47 8809509.446 9012728.85 7260512.007 1.192972522 1.056691165 1.146900726 1.084894787 0.865856499 1.179151892 1.213345483 1.241335162 1 22.79163986 2.071527878 24.99999948 1.18055033 1.078115462 0.131542176 0.105856917 73.67516342 25748.93911 0.037768419 0.027893822 117.9038206 -2.071527878 -0.102434868 LRPLFEACGEVVQIRPIFSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRPLFEACGEVVQIRPIFSNR 21 2 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 124.66 1.37E-05 266820000 204820 148250 147820 189220 188680 175280 241970 179250 189620 FALSE TRUE 195138.5645 163356.8435 154597.6932 170199.2461 221585.7323 169210.0096 205053.0324 163553.9197 219025.3012 0.890940743 0.745835493 0.705843993 0.777075731 1.011690116 0.772559192 0.936207056 0.746735281 1 17.74073801 LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVK 36 2 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;U3KQA9;U3KQV3;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 ; 253.11 3.70E-62 133708000 185770 108318 163342 176833 141427 183083 257770 195142 170355 FALSE TRUE 176989.0203 119355.7273 170831.3923 159057.4109 166091.824 176742.7898 218442.4522 178054.332 196772.7833 0.899458844 0.60656624 0.868165756 0.80833034 0.844079253 0.8982075 1.110125336 0.904872762 1 17.58617116 2.176848391 2.090680805 1.015775302 0.782120816 0.481379669 0.092963854 0.234748788 2.044309244 0.044456477 0.027789848 150.2617321 -2.176848391 -0.233654486 LRPLWK ddPTM_SK-BR-3_Trastuzumab_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 ; 106.84 0.028979 1174540000 2190790 2261310 1830270 2213880 1716260 1963730 2338900 2182910 1843800 FALSE TRUE 2087235.698 2491740.06 1914189.69 1991336.576 2015575.201 1895725.538 1982057.848 1991762.828 2129727.087 0.980048435 1.169980921 0.898795767 0.935019603 0.946400697 0.89012604 0.930662835 0.935219747 1 21.02223714 3.721967687 24.969017 0.928920784 1.075014684 0.543980105 0.053631917 462.6593636 696209.3837 0.013160915 0.020452211 5271.906349 -3.721967687 0.146093899 LRPLYDIPYMFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LRPLYDIPYMFEAR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 200.63 1.73E-08 3483360000 1994640 1775540 1598320 1866160 1963420 1549410 2124680 1842320 1917940 FALSE TRUE 1900357.32 1956469.545 1671604.553 1678570.051 2305839.826 1495753.543 1800521.044 1680996.694 2215364.34 0.85780803 0.883136697 0.754550628 0.757694805 1.040840003 0.675172709 0.812742632 0.758790175 1 21.07911255 LRPPGAEKPSWLEEQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRPPGAEKPSWLEEQ 15 2 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 103.16 0.0059374 376500000 406550 348100 330380 377850 308340 332040 382860 388450 329640 FALSE TRUE 387333.1872 383571.7858 345528.2498 339867.8001 362114.3984 320541.3715 324447.6753 354435.2587 380758.8876 1.017266306 1.00738761 0.907472579 0.892606348 0.951033345 0.841848692 0.85210795 0.930865359 1 18.53851819 3.731691641 4.186501121 0.897827662 1.014073612 0.432555693 0.046697866 0.147740327 6.404297997 0.011901643 0.020463599 5391.276941 -3.731691641 0.116245951 LRPSGDDVELIGEEEDVSVYDIADHPDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LRPSGDDVELIGEEEDVSVYDIADHPDFR 29 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ;;;;;; 257.04 3.31E-58 303804900 175232 155156.7 157841 181032 182696 165402 199618 175081 170109 FALSE TRUE 166949.1306 170967.3441 165078.166 162834.3194 214558.1246 159674.0873 169162.6079 159749.9795 196488.6349 0.849663039 0.870113145 0.840141039 0.828721312 1.091962009 0.812637776 0.860928205 0.813024018 1 17.58408634 -2.597984163 2.187504203 3.629841071 0.870648298 0.201002856 0.080890361 3768982.946 288228.8 50084097.73 0.019610719 0.002523573 2.597984163 -2.759192773 LRPT(ph)RTSSESIYSRPGSSIPGSPGHTIYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRPTRTSSESIYSRPGSSIPGSPGHTIYAK 30 3 O14639-3;F8W8M4;O14639-2;O14639;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 LRPT(0.41)RT(0.272)S(0.272)S(0.027)ES(0.016)IYS(0.003)RPGSSIPGSPGHTIYAK;LRPT(0.187)RT(0.187)S(0.187)S(0.101)ES(0.101)IY(0.089)S(0.101)RPGS(0.023)S(0.023)IPGSPGHTIYAK 149.29 1.45E-08 1302910000 402370 219570 377230 361830 549110 364380 637390 482560 709760 TRUE FALSE 383350.7675 241944.4326 394526.3686 325458.161 644874.6101 351761.4292 540144.449 440304.4882 819825.9558 0.467600184 0.295116824 0.481231859 0.396984456 0.786599406 0.429068422 0.658852583 0.537070686 1 19.64495814 -4.999999997 0.111056005 2.701350498 0.196567847 0.647857123 0.12255157 90.22923151 0.664529848 34.51976383 1.336690766 1.00E-05 4.999999997 -2.504782651 LRPTVTNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LRPTVTNDR 9 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 ;; 138.22 0.0013897 239474000 277743 240833 254958 310939 301258 268627 338905 305775 352457 FALSE TRUE 264614.6388 265374.1565 266648.0765 279682.821 353797.2998 259324.3796 287198.8178 278999.72 407114.2315 0.649976391 0.651842004 0.65497115 0.686988563 0.869036925 0.636981858 0.705450204 0.685310653 1 18.63507413 -5 0.25749091 2.968880936 0.662698958 0.683495839 0.065870193 109.7207021 1.080260812 114.1934936 0.085962588 1.00E-05 5 -2.306181979 LRQDLQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 110.88 0.0030464 905480000 1312440 1015230 1235140 1568850 1308430 1287320 1638730 1357590 1406690 FALSE TRUE 1250403.562 1118683.091 1291772.391 1411146.217 1536619.778 1242739.786 1388711.641 1238712.223 1624832.301 0.769558533 0.688491416 0.795018901 0.8684873 0.945709768 0.764841876 0.854679982 0.76236312 1 20.63185939 -5 0.041268284 1.839831479 0.313079394 0.424194336 0.070666019 726.5904249 2.236519885 75.81750928 21.96329316 1.00E-05 5 -1.526752085 LRQLLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRQLLSPK 8 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LRQLLS(1)PK 99.343 0.0041669 112020000 197390 96198 110340 81704 145310 134160 260240 225730 203810 TRUE FALSE 188059.7659 106000.6856 115399.1981 73490.95869 170652.018 129514.0056 220535.6084 205963.8845 235415.8139 0.798840837 0.45027003 0.49019306 0.312175115 0.724896154 0.550149981 0.936791818 0.874894006 1 17.84485171 1.730447229 4.957400477 0.931858678 0.554840787 0.630168228 0.137991548 0.112933762 6.648020521 0.071236944 0.036092782 53.75851073 -1.730447229 -0.377017891 LRQPFFQK ddPTM_SK-BR-3_Trastuzumab_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 ; 172.15 0.00026017 4024200000 3508900 2258620 1353600 1687680 2830900 1921080 3561500 2528240 2835100 FALSE TRUE 3343041.251 2488775.946 1415663.899 1518031.2 3324608.064 1854552.518 3018127.764 2306853.903 3274752.828 1.020853001 0.759988945 0.432296412 0.463555963 1.015224122 0.566318319 0.921635287 0.704436036 1 21.64295459 0.303816587 0.73197517 1.003185561 0.738353516 0.134688954 0.208594577 5.791813087 4.211142904 0.270338773 0.07407234 2.012873987 -0.303816587 -0.264832045 LRQYAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LRQYAEK 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;H0YE58;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 118.74 0.0045033 1043400000 1135040 902520 790890 1049030 976960 930190 1437420 1173590 1197520 FALSE TRUE 1081388.909 994487.8141 827153.0888 943579.5114 1147341.515 897977.2871 1218115.179 1070824.238 1383225.286 0.781787985 0.718963009 0.597988699 0.682158952 0.829468292 0.649190914 0.880633973 0.774150277 1 20.39960472 0.880432968 0.661829721 0.998722254 0.709708743 0.570834267 0.076681107 0.651333075 0.633607952 0.074338253 0.029312148 7.593342122 -0.880432968 -0.289013511 LRRES(ph)PESEGPIYEGLIL ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LRRESPESEGPIYEGLIL 18 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 LRRES(0.965)PES(0.035)EGPIYEGLIL;LRRES(0.953)PES(0.047)EGPIYEGLIL;LRRES(0.983)PES(0.017)EGPIYEGLIL;LRRES(0.875)PES(0.125)EGPIYEGLIL 90.714 0.0020906 152418000 210274 179375 189916 207911 204793 193180 236646 204775 243402 TRUE FALSE 200334.7647 197653.5164 198623.8365 187011.3913 240508.8344 186490.1282 200541.3064 186843.8154 281147.539 0.712560976 0.703024174 0.706475458 0.665171717 0.855454169 0.663317662 0.713295614 0.664575675 1 18.10096789 -1.091186205 4.447518289 1.00002625 0.710864935 0.730498908 0.055263898 1.28E-05 2.62E-06 0.047670859 0.01123511 0.081061343 1.091186205 -0.289161315 LRRPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LRRPSPPEPWDEEDGASCSTFFGSEER 27 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(0.75)PPEPWDEEDGAS(0.171)CS(0.057)T(0.019)FFGS(0.002)EER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER 261.94 2.16E-53 980757000 342272 239380 318202 312658 364226 294607 397939 345844 435592 TRUE FALSE 326093.4809 263773.0942 332791.8764 281229.0238 427746.8991 284404.6857 337226.0969 315560.0659 503141.3827 0.648115007 0.524252433 0.661428155 0.558946319 0.85015249 0.565257988 0.670241225 0.627179709 1 18.94060433 -5 0.259234498 3.361494092 0.601993365 0.618605545 0.089175011 118.9666019 1.169283754 149.5569924 0.107613477 1.00E-05 5 -2.759500727 LRRPS(ph)VNGEPGSVPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRRPSVNGEPGSVPPPR 17 2 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 LRRPS(0.999)VNGEPGS(0.001)VPPPR 87.388 0.0035874 99119000 47862 38150 61723 47752 44252 56273 62230 49756 41670 TRUE FALSE 45599.65811 42037.52837 64553.0606 42951.87824 51969.53479 54324.2519 52735.67057 45399.10087 48131.97078 0.947388137 0.873380576 1.341168034 0.892377302 1.079730041 1.128652142 1.09564744 0.943221317 1 15.55470788 LRRPSPPEPWDEEDGAS(ph)CSTFFGSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRRPSPPEPWDEEDGASCSTFFGSEER 27 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 LRRPS(0.157)PPEPWDEEDGAS(0.541)CS(0.187)T(0.049)FFGS(0.066)EER 77.493 0.011455 192220000 61398 45708 71286 60453 70006 59825 70148 66818 74927 TRUE FALSE 58495.83822 50365.69717 74554.53361 54376.14959 82215.02424 57753.24525 59445.63424 60967.0617 86546.29649 0.675890715 0.581950924 0.861441063 0.628289734 0.949954274 0.667310418 0.686865142 0.70444449 1 16.40118446 -5 0.256747381 2.814131711 0.684477519 0.383180777 0.109934764 192.334195 1.894976408 184.1074316 0.141288476 1.00E-05 5 -2.129654192 LRRY(ph)CVFS(ph)HEELICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;LRRY(1)CVFS(1)HEELICK 91.401 0.0092588 166206000 313413 296155 345686 369721 587880 247191 353742 212707 409020 TRUE FALSE 298598.5886 326333.5312 361536.045 332555.9427 690406.0859 238630.7137 299772.161 194081.2474 472448.7326 0.632023261 0.690727922 0.765238681 0.703898476 1.46133546 0.505093351 0.634507282 0.410798535 1 18.84979826 -1.389282526 4.990988864 1.00024813 0.72281889 0.086231815 0.280752535 0.000735673 9.00E-05 0.257990898 0.060755151 0.040805384 1.389282526 -0.27742924 LRS(ph)GSASPMDLLS(ph)Y(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRSGSASPMDLLSYFK 16 1 P11678 P11678 EPX Eosinophil peroxidase;Eosinophil peroxidase light chain;Eosinophil peroxidase heavy chain 3 LRS(0.971)GS(0.06)AS(0.058)PMDLLS(0.956)Y(0.954)FK 43.408 0.066383 0 3932.4 4664.7 3936.3 5827.3 4454.7 3862.2 4739.8 4696.5 4763 TRUE FALSE 3746.523245 5140.038233 4116.783249 5241.528733 5231.59827 3728.451046 4016.656458 4285.249562 5501.621714 0.680985251 0.934276928 0.748285408 0.952724307 0.9509193 0.677700365 0.730085903 0.778906618 1 12.42564123 -1.355464489 8.520472342 1.000000625 0.806115218 0.247563478 0.105882957 1.24E-06 9.41E-08 0.101485692 0.02392033 0.044109843 1.355464489 -0.193885407 LRS(ph)PFLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;LRS(1)PFLQK 99.752 0.0039912 3267340000 4322380 4263140 4440820 4888160 3547030 4345660 5387030 4498750 3991220 TRUE FALSE 4118069.664 4697558.813 4644435.99 4396792.87 4165630.909 4195168.705 4565139.634 4104815.601 4610158.013 0.893259982 1.018958309 1.007435315 0.953718475 0.903576601 0.909983713 0.99023496 0.890385013 1 22.13638477 3.004477361 24.8966904 0.939019943 0.972719345 0.097832001 0.04768329 293.8884481 1634163.565 0.013489976 0.01606785 1010.36283 -3.004477361 0.033699402 LRS(ph)PPEALVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR;LRS(1)PPEALVQGR 164.41 3.47E-05 11519820000 3110390 2688350 2724720 3225920 2978430 2798780 3323990 3019870 3206340 TRUE FALSE 2963368.029 2962295.921 2849651.107 2901644.393 3497867.249 2701857.547 2816854.276 2755434.173 3703562.831 0.800139802 0.799850321 0.769435065 0.783473786 0.94446008 0.729529286 0.760579584 0.743995525 1 21.82048238 -1.018556609 4.835275243 1.000002672 0.791314798 0.553866647 0.058827086 2.26E-06 4.60E-07 0.054251778 0.012787037 0.095817181 1.018556609 -0.208687874 LRS(ph)PRGSPDGS(ph)LQTGKPSAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LRSPRGSPDGSLQTGKPSAPK 21 3 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 2 LRS(1)PRGS(0.249)PDGS(0.749)LQT(0.003)GKPSAPK;LRS(1)PRGS(0.336)PDGS(0.662)LQT(0.003)GKPSAPK;LRS(0.994)PRGS(0.156)PDGS(0.505)LQT(0.341)GKPS(0.004)APK;LRS(1)PRGS(0.045)PDGS(0.618)LQT(0.336)GKPS(0.001)APK;LRS(0.933)PRGS(0.361)PDGS(0.669)LQT(0.038)GKPSAPK 159.56 3.21E-11 3408360000 2090140 1333695 1932010 1888830 1463010 2045840 2619040 1967330 1872170 TRUE FALSE 1991343.224 1469600.037 2020594.57 1698961.22 1718158.481 1974992.048 2219457.346 1795060.156 2162496.562 0.920853822 0.679584912 0.934380477 0.785648056 0.794525416 0.913292572 1.026340289 0.830086941 1 21.04426641 2.102315353 4.679290704 0.958341672 0.816159705 0.321629513 0.086938867 0.214525507 7.999192158 0.031441431 0.022650957 126.5655041 -2.102315353 -0.142181966 LRS(ph)PS(ph)NDSAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(1)NDSAHR 81.526 0.012195 301770000 167160 161110 199240 221470 188800 175960 214510 177890 207130 TRUE FALSE 159258.6781 177527.2922 208375.3511 199207.4148 221726.6602 169866.4611 181782.5598 162313.0085 239250.6625 0.665656163 0.742013795 0.870949944 0.832630567 0.926754634 0.709993691 0.759799609 0.678422399 1 17.86816339 -2.350839247 2.383457626 2.579429178 0.76974558 0.42193807 0.083307653 4095944.616 653479.659 35440765.42 0.020738186 0.004458212 2.350839247 -1.809683597 LRS(ph)PSNDSAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 LRS(0.997)PS(0.003)NDSAHR;LRS(0.993)PS(0.007)NDSAHR;LRS(0.999)PS(0.001)NDSAHR;LRS(0.999)PS(0.001)NDSAHR;LRS(0.993)PS(0.007)NDSAHR;LRS(1)PSNDSAHR 119.63 0.00033927 2585564000 885209 737916 725578 841215 961500 779120 1071256 859335 1112434 TRUE FALSE 843366.9249 813110.4793 758846.469 756654.47 1129185.296 752138.879 907816.2222 784087.0718 1284944.583 0.656344979 0.632798091 0.590567468 0.588861559 0.878781319 0.585347328 0.706502237 0.610210808 1 20.29327471 -5 0.359366115 5.204952291 0.647079446 0.600103841 0.087846342 313.109809 2.495787582 1018.364769 0.058304798 1.00E-05 5 -4.557872845 LRS(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(1)YEDMIGEEVPSDQYYWAPLAQHER 222.25 1.44E-34 63752000 72608 54443 54998 83299 82504 68819 64125 52126 52260 TRUE FALSE 69175.96374 59990.8036 57519.7127 74925.62626 96892.67148 66435.78077 54341.55351 47561.5711 60364.21389 1.145976387 0.993814045 0.95287769 1.241225909 1.605134321 1.100582224 0.900227966 0.787910055 1 15.8814059 1.760649761 4.349512393 0.881394262 1.16334958 0.341287528 0.18231712 0.250013108 9.991004449 0.099847914 0.051582983 57.63015145 -1.760649761 0.281955318 LRTACER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LRTACER 7 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;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 ;;; 132.76 0.0030441 664734000 232647 160910 225998 118812 265086 199947 374753 352595 682730 FALSE TRUE 221650.2374 177306.9119 236360.2318 106868.792 311316.9145 193022.7853 317577.547 321719.9126 788604.2815 0.28106649 0.224836355 0.299719691 0.135516373 0.394769496 0.244765074 0.402708373 0.407961154 1 19.58894202 0.009790584 0.523269561 1.066707633 0.243139725 0.920990531 0.06652992 0.905721348 0.303301645 0.181026036 0.026986509 1.022799682 -0.009790584 -0.823567908 LRTS(ph)TSDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRTSTSDLSR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 LRT(0.067)S(0.861)T(0.067)S(0.006)DLSR 78.191 0.018618 235470000 97912 84605 83852 95888 120530 89205 103100 78291 141330 TRUE FALSE 93283.8938 93226.34569 87696.69714 86249.15606 141550.3938 86115.80848 87370.20144 71435.42499 163246.7346 0.57142885 0.571076328 0.537203377 0.528336179 0.867094795 0.527519333 0.535203364 0.437591754 1 17.31669461 -1.064203626 4.537982031 1.00001928 0.573454733 0.59335397 0.111363304 14180157.21 3325393.497 3408.487783 0.024686563 0.086257402 1.064203626 -0.426564547 LRVDFADTEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LRVDFADTEHR 11 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 118.48 0.0004292 69313000 81431 63506 66731 82662 92390 70123 90064 72761 75702 FALSE TRUE 77581.91801 69977.3336 69790.68236 74352.65871 108502.7867 67694.62293 76323.08266 66389.66111 87441.47953 0.887243885 0.800276184 0.7981416 0.850313365 1.240861744 0.774170603 0.872847567 0.759246772 1 16.41603019 5.123526985 17.51868737 0.877300714 2.340977373 0 0.143275718 3837.758684 552592.3292 0.031358585 3438.945126 132900.6133 -5.123526985 1.463676658 LRVEFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 162.5 0.0011578 2552590000 1627940 946683 502844 711009 1646650 794512 1787520 1176770 1794540 FALSE TRUE 1550990.502 1043151.074 525899.8948 639537.0245 1933825.239 766997.8502 1514800.994 1073725.78 2072828.098 0.748248494 0.503250161 0.253711292 0.308533556 0.932940479 0.370024823 0.730789493 0.518000398 1 20.98316905 -0.317147877 0.492355486 1.068283429 0.527688315 0.318370504 0.210245293 8.494151624 2.033664369 1.256317933 0.100581433 0.481783723 0.317147877 -0.540595114 LS(ph)CSELSLYQPLQNSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSCSELSLYQPLQNSSK 17 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 LS(0.5)CS(0.5)ELSLYQPLQNSSK 103.5 0.00093988 59256000 94920 70022 91388 101080 77000 81433 106470 108710 91855 TRUE FALSE 90433.31971 77157.32141 95578.2302 90919.24636 90428.77562 78612.95479 90226.04604 99190.77609 106099.4043 0.852345217 0.727217292 0.900836634 0.856925135 0.852302388 0.740936816 0.850391637 0.934885325 1 16.69505703 1.149006046 2.644051483 0.996341621 0.817409307 0.56931563 0.05306222 0.177970467 2.261480389 0.048587966 0.013378849 14.09308419 -1.149006046 -0.178932314 LS(ph)CSLEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.826)CS(0.174)LEDLR 90.827 0.011713 134680000 418400 517570 368810 487840 349590 436810 430060 457850 343700 TRUE FALSE 398623.0612 570310.9714 385720.3033 438801.3964 410558.3853 421683.1602 364446.4484 417758.2268 396999.2406 1.004090236 1.436554313 0.971589524 1.105295304 1.034154082 1.062176239 0.918002885 1.052289738 1 18.59877672 3.696175551 24.99996512 1.017624752 1.220322614 0.346537319 0.11402382 433.3977074 255630.8123 0.028898887 0.044770329 4967.930956 -3.696175551 0.202697861 LS(ph)GSRQDLIPSYSLGSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.585)GS(0.415)RQDLIPSYSLGSNK 213.14 6.96E-17 452540000 754560 579910 684330 666170 501300 623680 731750 661240 575590 TRUE FALSE 718893.4442 639003.4883 715707.2074 599205.326 588726.5613 602081.8052 620108.098 603338.3201 664849.5575 1.081287392 0.961124936 1.076494974 0.901264533 0.885503427 0.905591045 0.932704386 0.907480968 1 19.3426684 3.228319752 24.99988138 0.916967442 1.028762252 0.598290198 0.044981677 129.2900519 315620.8001 0.011898016 0.014372545 1691.685987 -3.228319752 0.11179481 LS(ph)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSLCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR 34 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 LS(1)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(1)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(0.893)LCEDS(0.107)PMVTLTVDNVHLEHGVVYEYVSTAGVR 311.69 3.85E-104 151631000 54655 74703 56672 67927 43605 64288 58523 66152 19457.3 TRUE FALSE 52071.56647 82315.32063 59270.46726 61098.84891 51209.69819 62061.69044 49594.2415 60359.38019 22474.63871 2.316903383 3.662587047 2.637215575 2.718568681 2.278554902 2.761409927 2.206675807 2.685666318 1 14.4560103 -0.945076939 0.263346723 1.92E-14 3.003313376 0.634471333 0.399701171 8.681687326 0.567037504 7.223313378 0.572189256 0.113480976 0.945076939 3.003313376 LS(ph)LFSDLPEDTELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSLFSDLPEDTELQR 15 0 Q9BST9 Q9BST9 RTKN Rhotekin 1 LS(1)LFSDLPEDTELQR;LS(1)LFSDLPEDTELQR 135.37 3.09E-05 21026300 48845 54900 42906 52021 37992 48225 49021 46544 34746 TRUE FALSE 46536.19365 60494.37242 44873.28254 46791.75025 44617.79277 46554.95616 41541.94612 42468.36061 40134.23222 1.159513739 1.507301101 1.118080004 1.165881285 1.111714123 1.159981232 1.035075142 1.058158043 1 15.29254568 3.602015588 7.996793098 1.096459266 1.332954886 0.51800036 0.096700358 0.195495196 11.84994735 0.024557462 0.038094629 3999.59105 -3.602015588 0.236495621 LS(ph)PANQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPANQR 7 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LS(1)PANQR 109.29 0.0074071 56881000 120920 136090 120290 155450 88069 121050 122430 128970 98263 TRUE FALSE 115204.3512 149957.7257 125805.4155 139823.8707 103428.2057 116858.0081 103751.0549 117676.7031 113501.1242 1.015006257 1.321200356 1.108406779 1.231916174 0.911252699 1.029575777 0.914097157 1.036788877 1 16.79234706 2.739128933 24.9998527 0.972486114 1.173978284 0.53557936 0.088136743 36.02362424 1584679.462 0.025716751 0.025799641 548.4397609 -2.739128933 0.201492171 LS(ph)PENNQVLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 199.38 2.37E-05 137367000 1051490 1195260 962170 1280170 739966 1149310 1158390 1236380 825687 TRUE FALSE 1001788.152 1317058.353 1006286.446 1151484.879 869015.8361 1109509.107 981656.3302 1128116.013 953730.3229 1.050389326 1.38095468 1.055105853 1.207348505 0.911175639 1.163336302 1.029280821 1.182845911 1 19.86322186 3.63193732 19.66515051 1.080148283 1.216237524 0.187914097 0.118547037 7.664222862 1402.22962 0.028506225 0.044161631 4284.866744 -3.63193732 0.136089241 LS(ph)PEVAPPAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 LS(1)PEVAPPAHR;LS(1)PEVAPPAHR 111.79 0.0010387 152418000 266070 290500 236310 296510 213360 252970 277990 283970 212380 TRUE FALSE 253493.3984 320102.2803 247145.0472 266704.2515 250569.9164 244209.5855 235577.5199 259104.0814 245314.8057 1.033339173 1.304863273 1.007460787 1.087191826 1.021421906 0.995494686 0.960306979 1.056210532 1 17.90427478 3.696790136 24.85377189 1.014880092 1.169101272 0.426425263 0.072627778 351.1026588 208908.8164 0.018685078 0.028947061 4974.966215 -3.696790136 0.15422118 LS(ph)PGESAYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSPGESAYQK 10 0 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK 257.54 3.50E-17 525582000 1526560 1456140 1246800 1646740 941010 1445960 1450300 1508290 929540 TRUE FALSE 1454402.534 1604522.321 1303967.013 1481206.567 1105121.846 1395886.043 1229030.098 1376216.132 1073688.316 1.354585416 1.494402331 1.214474437 1.379549861 1.029276215 1.300084971 1.144680519 1.281765026 1 20.03414382 8 0.085674495 0.806164132 2.565196706 0.453089949 0.114103942 125.5013115 0.777582356 2.21907448 26.00467168 100000000 -8 1.759032574 LS(ph)PGSYPTVIQQQNATSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSPGSYPTVIQQQNATSQR 19 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 LS(0.981)PGS(0.019)Y(0.001)PTVIQQQNATSQR;LS(0.989)PGS(0.011)YPTVIQQQNATSQR;LS(0.935)PGS(0.065)YPTVIQQQNATSQR;LS(1)PGSYPTVIQQQNATSQR 370.25 5.94E-108 318701000 150058 133157 137263 167395 124441 151671 172842 157960 137621 TRUE FALSE 142965.0557 146725.8497 143556.6443 150568.1366 146143.471 146418.5952 146471.7784 144128.185 158962.5618 0.899363058 0.923021421 0.903084617 0.947192439 0.919357799 0.921088548 0.921423112 0.90668006 1 17.2783275 -1.487499242 3.033252384 1.002286449 0.917951361 0.790407494 0.013325859 3639043.683 4821086.699 71020.15635 0.002998933 0.032546235 1.487499242 -0.084335088 LS(ph)PHKVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 144.1 6.06E-05 3286070000 4212570 5501170 3752070 5018480 2498060 4552860 4058160 4604100 1960400 TRUE FALSE 4013450.165 6061745.477 3924106.121 4514012.856 2933720.873 4395193.317 3439013.159 4200940.596 2264408.82 1.772405287 2.676966025 1.732949495 1.993461965 1.295579159 1.940989312 1.518724503 1.855204131 1 21.11070302 0.720891281 0.142438502 0.380637723 2.627024104 0.415373056 0.340917858 8.017896721 0.658558251 5.736054516 3.476788947 5.258856029 -0.720891281 2.246386381 LS(ph)PIPEEVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPIPEEVPK 10 0 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LS(1)PIPEEVPK 131.43 0.00026252 103760000 269840 280980 221650 309870 150790 272070 246160 253020 142440 TRUE FALSE 257085.198 309612.1814 231812.8717 278721.2789 177087.7283 262648.1477 208603.771 230864.2275 164528.8677 1.562553742 1.881810686 1.408949535 1.694056993 1.076332261 1.596365132 1.267885532 1.403183713 1 17.32798121 2.106121864 0.187677988 0.859604341 1.969444628 0.466115812 0.197339257 3.020383734 0.436951276 0.850523796 1.26605878 127.6797029 -2.106121864 1.109840287 LS(ph)PSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(0.975)PS(0.025)FR 155.03 0.010416 749840000 1075800 823990 958020 1047900 978940 983960 1073300 941170 856050 TRUE FALSE 1024949.066 907955.5178 1001946.165 942563.1011 1149666.826 949885.2185 909548.3725 858756.1653 988801.8619 1.03655657 0.918238075 1.013293161 0.953237587 1.162686753 0.960642627 0.919848968 0.868481542 1 19.91532193 2.004820613 24.99991062 0.925464802 1.007071822 0.241856303 0.070512211 192.1164034 996318.2485 0.025493489 0.018761741 101.1161704 -2.004820613 0.08160702 LS(ph)PSWNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSPSWNPK 8 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 LS(0.994)PS(0.006)WNPK;LS(0.988)PS(0.012)WNPK 112.71 0.0031348 69227000 387610 395010 354060 500350 275910 388890 362450 395310 264803 TRUE FALSE 369288.4435 435261.9681 370294.0012 450053.8674 324028.6166 375422.6418 307151.5956 360694.5607 305867.2968 1.20734857 1.423041864 1.210636132 1.471402376 1.059376468 1.227403667 1.004198876 1.179251801 1 18.22254634 2.720276712 24.94542174 1.097905272 1.323985877 0.5456998 0.106057664 568.9513366 776240.849 0.030454635 0.028764529 525.1419494 -2.720276712 0.226080605 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(0.991)PT(0.008)PS(0.001)MQDGLDLPSETDLR 78.516 0.0042228 0 22011 25204 19982 24158 18290 21271 21916 19664 21718 TRUE FALSE 20970.58365 27772.31625 20898.19446 21729.59194 21479.77021 20534.37994 18572.31169 17942.11591 25085.91652 0.835950468 1.107087964 0.833064817 0.866206819 0.856248174 0.818562077 0.740348142 0.715226645 1 14.61459003 3.563432223 10.99132724 0.817651511 0.971578361 0.24022681 0.100179972 0.724611786 89.74247145 0.025363653 0.039295372 3659.58824 -3.563432223 0.15392685 LS(ph)SGFDDIDLPSAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.996)S(0.004)GFDDIDLPSAVK;LS(0.879)S(0.121)GFDDIDLPSAVK;LS(0.999)S(0.001)GFDDIDLPSAVK;LS(0.896)S(0.104)GFDDIDLPSAVK;LS(0.899)S(0.101)GFDDIDLPSAVK;LS(0.5)S(0.5)GFDDIDLPSAVK 408.76 5.17E-133 826432000 2825827 3255024 2543617 3472653 1658285 3067637 2942557 3059757 1625366 TRUE FALSE 2692255.758 3586714.646 2660244.355 3123575.323 1947489.379 2961403.961 2493615.886 2791828.456 1877419.458 1.434019311 1.910449277 1.416968565 1.66375996 1.037322464 1.57738003 1.328214574 1.487056312 1 20.84031959 -2.29313173 0.098624127 2.86E-09 1.966911432 0.352092172 0.217986712 86.29179461 1.107162411 23.82642948 4.381775918 0.005091764 2.29313173 1.966911429 LS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Trastuzumab_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 LS(0.951)S(0.049)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 233.66 5.67E-47 124860000 162540 137940 146210 180270 138610 147810 191620 183960 43593 TRUE FALSE 154857.0563 151996.2428 152913.8731 162148.9171 162783.5401 142691.3026 162384.8497 167851.4872 50353.1798 3.075417619 3.018602667 3.036826547 3.220231925 3.23283536 2.83380917 3.224917479 3.333483364 1 15.61979527 -0.5961632 6.278019713 0.999999997 3.109386581 0.95656355 0.142086251 7.78E-09 1.24E-09 0.130607326 0.030784442 0.253417615 0.5961632 2.109386584 LS(ph)SLRAS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.799)S(0.201)LRAS(0.776)T(0.195)S(0.029)K 115.8 0.00066842 862040000 3379500 3632500 2701700 3846000 1916100 3552400 3215900 3496100 1891300 TRUE FALSE 3219757.733 4002655.88 2825575.617 3459392.773 2250267.233 3429379.497 2725255.391 3189962.95 2184593.145 1.473847769 1.832220288 1.293410457 1.583540982 1.030062389 1.569802371 1.247488759 1.460209173 1 21.05893319 2.508336099 0.053624364 5.12E-15 2.831273263 0.338199011 0.20803528 65.69210079 1.677638257 38.55399787 48.63164871 322.3562532 -2.508336099 2.831273263 LS(ph)SPVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.629)S(0.371)PVLHR;LS(0.614)S(0.386)PVLHR 128.27 0.00073477 856390000 389815 355150 345753 400723 381020 347125 444690 381690 344377 TRUE FALSE 371389.2175 391340.1888 361606.117 360441.5627 447469.7674 335103.9742 376844.3732 348267.2001 397781.2263 0.93365195 0.983807588 0.909057776 0.906130151 1.124914244 0.842432855 0.947365909 0.875524477 1 18.60161566 -0.971822887 4.98029113 1.000000429 0.943320771 0.056058559 0.076053362 3.24E-07 6.70E-08 0.06586109 0.01552349 0.106703119 0.971822887 -0.056679659 LS(ph)STS(ph)SEETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.352)S(0.352)T(0.352)S(0.471)S(0.471)EET(0.001)QLFHIPR 54.898 0.073602 16284000 30835 29822 25886 38382 34122 31453 34005 27134 25865 TRUE FALSE 29377.49066 32860.8957 27072.8987 34523.76844 40072.866 30363.77472 28816.91271 24758.00311 29876.0121 0.983313655 1.099909037 0.906175115 1.155568164 1.341305723 1.016326229 0.964550175 0.828691695 1 14.86669997 1.732642175 3.210736 0.91529157 1.085921952 0.273785733 0.120817527 0.299727723 6.608480757 0.069490233 0.032818324 54.03089663 -1.732642175 0.170630382 LS(ph)STSSEETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.568)S(0.423)T(0.006)S(0.001)S(0.001)EETQLFHIPR;LS(0.517)S(0.43)T(0.016)S(0.015)S(0.021)EETQLFHIPR 165.3 4.56E-09 63784000 38276 29332 37188 45316 43546 35380 43458 35074 38072 TRUE FALSE 36466.76934 32320.96415 38893.10658 40760.74959 51140.40861 34154.78173 36827.68394 32002.73462 43976.01132 0.829242313 0.73496807 0.884416422 0.926886008 1.162916033 0.776668477 0.837449392 0.727731635 1 15.42442914 3.651430628 6.560985632 0.896683929 0.782462767 0.143310133 0.121767095 0.457544411 28.78406559 0.032516667 0.050688007 4481.574578 -3.651430628 -0.114221162 LS(ph)TGSFPEDLLESDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.333)T(0.333)GS(0.333)FPEDLLESDSSR;LS(0.385)T(0.308)GS(0.308)FPEDLLESDSSR 88.974 0.0035923 0 41969 40263 38563 44259 35508 41581 37474 41031 34598 TRUE FALSE 39985.20854 44365.84548 40331.15169 39810.00123 41700.58396 40141.03954 31756.65304 37438.10812 39963.28114 1.000548689 1.110165237 1.009205214 0.996164481 1.043472477 1.004448043 0.794645788 0.93681267 1 15.28638742 1.931855311 8.207166199 0.889953946 1.03602512 0.449801422 0.06010521 0.23686271 26.36914489 0.023670351 0.014893156 85.47818875 -1.931855311 0.146071173 LS(ph)TPQKGPSTHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSTPQKGPSTHPK 13 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 LS(0.5)T(0.5)PQKGPSTHPK 92.264 0.0037158 149880000 406830 369890 403220 463890 270740 465910 484120 551700 355810 TRUE FALSE 387599.9522 407582.2115 421708.0358 417258.8959 317956.9703 449775.4199 410258.6025 503390.2233 410987.1976 0.943094954 0.991715104 1.026085577 1.015260082 0.773642031 1.094378177 0.998227207 1.224831883 1 18.64873393 1.72454069 2.147396378 1.098380319 0.964492647 0.238166572 0.098412734 0.387915426 3.71233525 0.060691262 0.025357434 53.03232774 -1.72454069 -0.133887673 LS(ph)TPQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 98.044 0.0070758 255300000 250240 238050 223840 277930 152690 213220 261540 284330 169680 TRUE FALSE 238411.6511 262307.5656 234103.2854 249991.9484 179319.0877 205836.1379 221637.2695 259432.5579 195993.1078 1.21642875 1.338350969 1.194446519 1.275513977 0.914925477 1.050221308 1.130842161 1.323682046 1 17.5804434 2.808765139 24.9999692 1.092301389 1.262032349 0.374249345 0.110266741 172.0437733 61264.46538 0.032585064 0.034561677 643.8210017 -2.808765139 0.169730961 LS(ph)VPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LS(0.778)VPT(0.346)S(0.876)DEEDEVPAPKPR 161.19 4.63E-10 106250000 229310 188870 209980 220310 157570 216970 241750 223390 185270 TRUE FALSE 218470.9707 208116.0677 219607.7907 198164.0202 185050.1581 209456.2745 204866.5975 203828.7873 214000.7254 1.020888926 0.972501693 1.026201151 0.925996956 0.864717434 0.97876432 0.957317304 0.95246774 1 17.70725616 3.234251038 24.99861703 0.943815836 1.001289876 0.351510116 0.038068259 119.9502676 695796.9168 0.010612204 0.013113464 1714.948324 -3.234251038 0.05747404 LS(ph)VS(ph)SHILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSVSSHILER 10 0 A0A0C4DGQ4;Q86W25 A0A0C4DGQ4 NLRP13 "NACHT, LRR and PYD domains-containing protein 13" 2 LS(0.667)VS(0.667)S(0.667)HILER 46.606 0.08769 0 13273 12607 13788 18614 11738 8194.2 16895 8918.5 21053 TRUE FALSE 12645.61159 13891.66763 14420.19344 16742.88536 13785.10348 7910.432799 14317.35745 8137.54886 24317.79172 0.5200148 0.571255309 0.59298943 0.688503527 0.566873162 0.325294044 0.588760592 0.334633545 1 14.5697246 -1.570014528 3.35368783 1.016935004 0.531304928 0.634571617 0.113493146 34665649.25 47681601.58 5297484.557 0.02569176 0.026914448 1.570014528 -0.485630076 LS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.98)YS(0.02)DKNLIDSMDQSAFAGFSFVNPK;LS(0.977)YS(0.023)DKNLIDSMDQSAFAGFSFVNPK;LS(0.988)YS(0.012)DKNLIDSMDQSAFAGFSFVNPK 197.36 3.96E-25 1354400000 278922 298107 256684 315183 142431 302281 282545 330845 176053 TRUE FALSE 265737.9098 328484.4422 268453.2153 283500.206 167270.9213 291812.9332 239437.571 301874.4579 203354.4001 1.306772363 1.615329897 1.32012494 1.394118868 0.822558652 1.434996897 1.177439833 1.484474679 1 17.63363668 2.971548899 24.95294606 1.203559129 1.431278854 0.224077984 0.20588258 976.7491526 856655.267 0.057417014 0.061018369 936.5886674 -2.971548899 0.227719724 LSAEKVEIATLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSAEKVEIATLTR 13 1 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type 0 ; 150.34 3.58E-05 1536710000 2107850 1733220 1993830 2027770 1790200 2027550 2450500 2166500 1967740 FALSE TRUE 2008216.108 1909837.089 2085249.078 1823934.707 2102410.313 1957335.435 2076631.218 1976789.775 2272887.069 0.883552964 0.840269239 0.917445088 0.802474849 0.924995501 0.861167042 0.913653497 0.86972635 1 21.11609457 -4.99999117 0.216140024 1.625569752 0.859071878 0.524784954 0.037090311 104.313253 1.04211454 28.2830788 0.062838903 1.00E-05 4.99999117 -0.766497874 LSAFRPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSAFRPAPR 9 1 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3;J3QR88;J3QLK9;J3QL23;J3QL32;J3QL24;J3KSA9 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 118.67 0.0018248 0 209620 94916 63715 75098 232200 81920 210390 126090 221300 FALSE TRUE 199711.678 104588.0483 66636.39577 67549.00636 272695.6065 79083.08986 178291.1414 115048.8912 255618.0738 0.781289347 0.409157486 0.26068734 0.264257552 1.066808784 0.309379883 0.697490357 0.450081207 1 17.96363032 -3.90005153 0.348919111 3.210740019 0.519103583 0.247037849 0.256861388 263.9186054 4.576552334 425.5802929 0.183674773 0.000125878 3.90005153 -2.691636436 LSAIYGGTYMLNKPIEEIIVQNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSAIYGGTYMLNKPIEEIIVQNGK 24 1 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 303.07 2.11E-62 267340000 521770 449930 435730 534460 351760 528760 588720 569530 430810 FALSE TRUE 497106.9661 495778.3785 455708.6515 480735.0654 413106.8326 510448.9086 498899.9514 519658.9339 497617.8145 0.998973412 0.996303517 0.915780421 0.96607286 0.830168898 1.025785038 1.002576549 1.044293268 1 18.92467861 LSAKPAPPKPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 99.481 0.0015979 1788330000 1889060 2264140 1592250 2513800 1078560 2135370 1907920 2342410 1125200 FALSE TRUE 1799767.878 2494858.44 1665256.237 2261108.048 1266660.523 2061421.601 1616831.763 2137296.163 1299690.269 1.384766756 1.919579225 1.281271605 1.739728381 0.974586448 1.586086816 1.244013132 1.644465772 1 20.30973642 2.773238709 24.99088289 1.324256402 1.599198919 0.212182124 0.273737639 924.5910922 666308.2006 0.074588101 0.079109717 593.2513139 -2.773238709 0.274942517 LSAKPAPPKPEPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSAKPAPPKPEPKPK 15 3 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 72.433 0.017855 1323000000 461080 343080 421520 481080 314190 478390 548930 551290 347520 FALSE TRUE 439285.6622 378040.242 440847.1089 432720.9244 368984.6365 461823.2343 465180.6467 503016.125 401411.6267 1.094352114 0.941777011 1.098242003 1.077997984 0.919217611 1.150497902 1.158861916 1.253117976 1 18.61472288 2.133227834 11.31781351 1.154830615 1.026632496 0.303709125 0.084815893 0.40896612 41.16648699 0.02889959 0.021343261 135.9026213 -2.133227834 -0.128198119 LSAKPPAKVEAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSAKPPAKVEAKPK 14 3 P05114;A6NEL0;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 97.836 0.0012339 559830000 667890 400390 558470 458570 373100 581040 671070 595280 432670 FALSE TRUE 636320.1633 441190.1962 584076.4019 412473.6724 438168.5219 560918.4391 568685.9465 543154.1274 499766.2538 1.273235555 0.882793091 1.168699162 0.825333182 0.876746916 1.122361574 1.137903854 1.086816333 1 18.93089396 -0.050678609 7.838722608 0.99999999 1.047655573 0.010261618 0.143996078 0 0 0.13438698 0.031675315 0.889859398 0.050678609 0.047655583 LSALGNVTTCNDYVALVHPDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSALGNVTTCNDYVALVHPDLDR 23 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;;; 247.54 1.08E-37 640373000 404368.2 514264 373232.9 468433 333003.5 379946.5 373901 411336 342948.2 FALSE TRUE 385254.5166 566668.0863 390345.9976 421345.2249 391079.205 366788.8574 316855.5353 375317.2392 396130.8553 0.972543571 1.430507315 0.985396599 1.063651617 0.987247521 0.925928522 0.799875927 0.947457726 1 18.59561755 2.987775659 1.274910221 0.89622312 1.186200379 0.332478893 0.132695708 0.384451393 1.307834555 0.052320655 0.062077234 972.2448672 -2.987775659 0.289977258 LSALGNVTTCNDYVALVHPDLDRETEEILADVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSALGNVTTCNDYVALVHPDLDRETEEILADVLK 34 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 314.98 1.08E-104 203490000 363330 304780 317380 402990 331090 369330 444320 362810 311030 FALSE TRUE 346156.111 335837.4285 331932.1869 362480.6796 388831.9912 356540.0095 376530.8235 331040.433 359262.9439 0.963517437 0.934795626 0.923925477 1.008956492 1.082304751 0.992420776 1.048064739 0.921443301 1 18.45468061 3.191033726 7.559528947 1.016212008 0.942780332 0.357659228 0.042273507 0.20520141 27.39670221 0.011303486 0.013628309 1552.507568 -3.191033726 -0.073431676 LSASSS(ph)ISSADLFEEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LSASS(0.015)S(0.985)ISSADLFEEPR;LSASS(0.063)S(0.937)ISSADLFEEPR;LSASS(0.019)S(0.981)ISSADLFEEPR;LS(0.004)AS(0.023)S(0.136)S(0.835)ISSADLFEEPR 328.56 6.47E-72 156139000 163860 141296 171530 232904 191077 233529 249824 165276 184557 TRUE FALSE 156114.6625 155694.223 179394.8202 209492.0474 224400.7683 225441.8322 211708.7605 150803.5573 213177.157 0.732323598 0.730351344 0.841529283 0.982713394 1.052649221 1.057532783 0.993111849 0.707409553 1 17.70169333 3.454865484 2.722647149 0.977661911 0.731819496 0.495364481 0.097928737 0.197128723 2.954895785 0.027647226 0.041998659 2850.135346 -3.454865484 -0.245842415 LSASTASELS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 LSASTASELS(1)PK;LSASTASELS(1)PK 230.69 5.46E-12 168520000 599860 514840 507620 603690 339580 632080 618610 663590 377080 TRUE FALSE 571505.8066 567302.7813 530894.8791 543005.9343 398802.6445 610190.9111 524229.6829 605482.5417 435555.6405 1.312130422 1.302480621 1.218891066 1.246697055 0.915618138 1.400948247 1.203588323 1.390138217 1 18.7324975 -2.186938534 2.296755681 0.328487185 1.249854956 0.251232587 0.134981426 10404134.09 2403629.732 36262221.1 0.030817804 0.006502217 2.186938534 0.921367771 LSCS(ph)LEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.297)CS(0.703)LEDLR;LS(0.051)CS(0.949)LEDLR 82.803 0.018272 250090000 650350 724760 578480 769660 544410 606620 639420 670110 574450 TRUE FALSE 619609.2444 798613.868 605003.8802 692292.3145 639354.9316 585612.5973 541864.7352 611431.6159 663532.7721 0.933803529 1.203578635 0.91179201 1.043343063 0.96356195 0.882567707 0.816635979 0.921479152 1 19.3398082 2.487163528 2.360786894 0.881184869 1.038621363 0.246736192 0.090926776 0.303154555 3.413068831 0.033673642 0.028387972 307.0177804 -2.487163528 0.157436494 LSCS(ph)LEDLRSESVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSCSLEDLRSESVDK 15 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.013)CS(0.987)LEDLRSESVDK 146.18 2.38E-06 199220000 410940 317900 362980 380330 298190 383680 488980 454920 372720 TRUE FALSE 391515.6806 350294.3714 379622.992 342098.5058 350194.2416 370393.0654 414377.1203 415084.7931 430519.514 0.909402868 0.813655038 0.881778827 0.794617885 0.813422459 0.860339783 0.96250485 0.964148615 1 18.71571911 1.729582845 3.272673554 0.977685556 0.843600241 0.762054037 0.034476275 0.105391891 2.433860769 0.019456351 0.009201306 53.65162065 -1.729582845 -0.134085314 LSDDNTIGKEEIQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSDDNTIGKEEIQQR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 160.65 7.06E-09 0 141030 108310 116970 146320 98401 127210 144020 134710 108480 FALSE TRUE 134363.7914 119346.9121 122333.1902 131611.6356 115562.1032 122804.6858 122047.1039 122914.0783 125302.5244 1.07231512 0.952470134 0.976302679 1.050351031 0.922264765 0.980065537 0.974019514 0.980938564 1 16.93505595 4.633665179 3.126242214 0.978806762 1.076732023 0.442616497 0.032579044 0.248641093 3.972808436 0.007305513 0.051768233 43019.48219 -4.633665179 0.097925261 LSDETLLEISKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSDETLLEISKR 12 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 136.53 0.00017366 129790000 74444 64165 72194 81326 59727 71636 93361 84921 84881 FALSE TRUE 70925.17965 70703.48645 75504.16631 73150.95597 70143.36989 69155.22736 79117.06476 77484.86705 98043.91197 0.72340218 0.721141018 0.770105607 0.746104011 0.715428102 0.705349531 0.806955406 0.790307786 1 16.58114043 0.550231208 0.813796414 1.001636359 0.730017591 0.913050039 0.02538513 0.387802883 0.41787732 0.025276642 0.008401036 3.550023339 -0.550231208 -0.271618768 LSDFLITGGGKGS(ph)GFSLDVIDGPISQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSDFLITGGGKGSGFSLDVIDGPISQR 27 1 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LSDFLITGGGKGS(0.92)GFS(0.08)LDVIDGPISQR;LSDFLIT(0.007)GGGKGS(0.991)GFS(0.002)LDVIDGPISQR;LSDFLIT(0.116)GGGKGS(0.76)GFS(0.124)LDVIDGPISQR 260.92 2.81E-53 692311000 1266288 1111040 1133890 1380280 1021464 1232897 1374233 1440644 1168966 TRUE FALSE 1206433.076 1224256.239 1185879.978 1241531.632 1199606.998 1190201.468 1164568.516 1314493.574 1350243.277 0.893493118 0.906693083 0.878271344 0.919487364 0.888437675 0.881471871 0.862487921 0.97352351 1 20.36478793 1.117904075 5.170272573 0.998055292 0.890837184 0.868757554 0.015758891 0.069206829 2.619693928 0.015817015 0.004009696 13.11910099 -1.117904075 -0.107218107 LSDGFNGADLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSDGFNGADLR 11 0 A0A087X2I1;P62333;H0YJC0 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 112.89 0.0034077 63405000 138580 114830 105600 130270 138060 111130 151830 140700 152380 FALSE TRUE 132029.598 126531.3076 110441.8645 117175.0121 162137.6203 107281.5402 128665.545 128379.5621 176010.3122 0.75012422 0.718885763 0.627473829 0.665728108 0.921182505 0.609518493 0.731011401 0.729386594 1 17.42530043 0.508694271 2.643682512 0.999997217 0.717689041 0.518706942 0.085094475 7.660750168 40.14167296 0.074760963 0.019804489 3.226222169 -0.508694271 -0.282308175 LSDGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSDGIR 6 0 P37837 P37837 TALDO1 Transaldolase 0 ; 101.33 0.085259 464560000 1504330 1355400 1258700 1519100 1477860 1321490 1594030 1461740 1524730 FALSE TRUE 1433223.302 1493516.801 1316412.64 1366397.182 1735598.316 1275726.47 1350831.447 1333742.296 1761177.341 0.813787044 0.848021812 0.747461717 0.77584304 0.985476179 0.724360029 0.767004785 0.757301531 1 20.74810876 -1.772471641 2.505476767 1.052743337 0.803951134 0.415233723 0.07367149 11502431.72 8144966.93 3725675.002 0.017071612 0.016886061 1.772471641 -0.248792203 LSDIS(ph)PIGRDPSESSFSSATLTPSSTCPSLVDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSDISPIGRDPSESSFSSATLTPSSTCPSLVDSR 34 1 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 LS(0.003)DIS(0.96)PIGRDPS(0.007)ES(0.007)S(0.007)FS(0.007)S(0.007)AT(0.002)LTPSSTCPSLVDSR;LSDIS(0.999)PIGRDPS(0.001)ESSFSSATLTPSSTCPSLVDSR;LS(0.03)DIS(0.948)PIGRDPS(0.007)ES(0.007)S(0.007)FSSATLTPSSTCPSLVDSR 239.12 3.07E-47 469824000 71514 51676 65160 67432 69788 64236 72387 67874 80476 TRUE FALSE 68133.67495 56941.84315 68147.65045 60653.60725 81959.0051 62011.49121 61343.03367 61930.59274 92955.80707 0.732968462 0.612568972 0.733118808 0.652499388 0.881698602 0.667107233 0.6599161 0.666236943 1 16.50425737 -1.3197664 4.721481203 1.000186985 0.695548757 0.617632072 0.073891955 0.000136545 1.97E-05 0.067170193 0.015822515 0.047888761 1.3197664 -0.304638228 LSDLDSETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 151.97 0.00018979 573750000 1091790 955030 895830 1176000 1020670 1041330 1244870 1207960 1098160 FALSE TRUE 1040183.25 1052348.643 936904.6916 1057786.246 1198674.525 1005268.481 1054942.218 1102184.619 1268457.044 0.820038215 0.829628916 0.738617595 0.833915701 0.944986297 0.792512829 0.831673585 0.868917575 1 20.27464323 -5 0.21776002 1.863778868 0.807243665 0.545600891 0.049985169 117.9889542 1.179284737 44.55358466 0.094838322 1.00E-05 5 -1.056535203 LSDPPTSPSS(ph)PSQMMPHVQTHF ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPTSPS(0.023)S(0.954)PS(0.023)QMMPHVQTHF;LSDPPT(0.005)S(0.018)PS(0.194)S(0.73)PS(0.053)QMMPHVQTHF 160.92 1.16E-11 179728000 164319 137797 161858 171884 180756 155291 201312 158444 33191 TRUE FALSE 156551.9665 151838.671 169279.3494 154605.8938 212279.7892 149913.2337 170598.1571 144569.8034 38338.09076 4.083457559 3.96051728 4.415435042 4.032696743 5.537046445 3.910294716 4.449834451 3.770918179 1 15.22649087 0.75013006 2.834840397 1.000123272 4.303930161 0.833075497 0.466415615 0.566764451 5.919793863 0.419864007 0.110533491 5.625097577 -0.75013006 3.303806889 LSDQFHDILIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LSDQFHDILIR 11 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;;; 225.79 5.22E-12 3596421000 4877130 4011052 4246296 4906970 4920952 4303522 5405681 4819285 4672270 FALSE TRUE 4646597.73 4419782.759 4440992.872 4413712.053 5779164.471 4154489.954 4580945.081 4397282.857 5396821.769 0.860987805 0.818960297 0.822890409 0.81783543 1.070845901 0.769803068 0.848822747 0.814791195 1 22.36367861 -2.385840135 2.261486432 2.110121583 0.851166675 0.244225107 0.081139041 4024248.497 632985.3392 22756609.2 0.019086365 0.004113011 2.385840135 -1.258954908 LSDVDANTAIKHEEQS(ph)NEDIPIAEQSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSDVDANTAIKHEEQSNEDIPIAEQSSK 28 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LSDVDANTAIKHEEQS(1)NEDIPIAEQSSK 243.58 1.24E-45 95082000 160370 144240 161720 175500 100090 184880 206900 204970 105720 TRUE FALSE 152789.6279 158938.22 169135.022 157858.4066 117545.6643 178477.5592 175333.605 187021.7402 122114.5177 1.251199537 1.301550569 1.385052533 1.29270794 0.962585502 1.461558893 1.435812943 1.531527486 1 16.8978752 LSEAVWQPEEHYSSS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.006)S(0.159)S(0.835)PEK;LSEAVWQPEEHYS(0.021)S(0.154)S(0.824)PEK;LSEAVWQPEEHYSS(0.01)S(0.99)PEK 191.4 1.46E-14 154601000 348425 268080 316036 396785 271870 360785 432701 414273 307268 TRUE FALSE 331955.6408 295397.6568 330526.5632 356899.418 319284.0419 348290.925 366684.5154 377997.0599 354917.5521 0.935303534 0.832299375 0.931277028 1.005584018 0.899600597 0.981329108 1.033154075 1.065027801 1 18.4371244 2.445765001 0.747322135 1.041243037 0.889612254 0.528221514 0.046750697 0.47351429 0.530035746 0.03576856 0.026229075 279.103319 -2.445765001 -0.151630782 LSEDYGVLKTDEGIAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSEDYGVLKTDEGIAYR 17 1 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;; 176.21 1.03E-09 335856000 373800 139191 447800 249143 450780 335130 678660 445600 684440 FALSE TRUE 356131.2148 153374.7211 468332.0729 224098.6723 529395.8893 323524.3641 575117.9526 406580.9017 790579.4596 0.45046859 0.194002917 0.592390894 0.283461289 0.66963021 0.409224348 0.727463819 0.514282147 1 19.59255095 0.309140399 0.218264776 1.227365581 0.246429235 0.597018938 0.146229007 3.731087012 0.390632572 1.061590879 0.374364085 2.037700721 -0.309140399 -0.980936345 LSEEAECPNPST(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSEEAECPNPSTPSK 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 LSEEAECPNPS(0.016)T(0.944)PS(0.04)K;LSEEAECPNPST(0.996)PS(0.004)K;LSEEAECPNPS(0.001)T(0.985)PS(0.015)K;LSEEAECPNPS(0.006)T(0.923)PS(0.071)K;LSEEAECPNPS(0.003)T(0.982)PS(0.015)K 297.56 4.45E-43 723280000 1880090 1422750 1694300 2024910 1435280 1658900 2012820 1755400 1380290 TRUE FALSE 1791221.872 1567729.843 1771985.331 1821362.2 1685592.378 1601451.877 1705727.341 1601687.87 1594338.324 1.12348919 0.983310643 1.111423657 1.14239379 1.057236317 1.004461759 1.069865358 1.004609778 1 20.60452638 1.560257804 0.898133546 1.002263081 1.075297385 0.273603561 0.048375979 0.871303747 1.387896422 0.044487651 0.017577305 36.32936479 -1.560257804 0.073034304 LSEFGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSEFGIR 7 0 Q9UBT2;Q9UBT2-2;U3KQ93;K7ESK7 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ; 132.53 0.0078173 50666000 165867 139810 113399 130430 176040 119753 180381 148777 168713 FALSE TRUE 158026.7956 154056.798 118598.4563 117318.9286 206741.3203 115605.9236 152860.5655 135749.2972 194876.1504 0.810908853 0.790536952 0.608583739 0.602017889 1.060885695 0.593227665 0.784398528 0.696592666 1 17.57219801 -1.536977923 2.897278891 1.011405003 0.748811379 0.252695693 0.138403256 50252595.83 53032138.46 4481825.791 0.03077288 0.029041703 1.536977923 -0.262593624 LSEGFSIHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSEGFSIHTR 10 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 238.73 3.25E-12 1620880000 2014260 1595970 1809380 2069800 2495150 1663030 2414810 2169810 2570350 FALSE TRUE 1919049.922 1758601.157 1892341.863 1861739.772 2930303.37 1605438.854 2046386.383 1979809.934 2968946.75 0.646373978 0.59233166 0.637378175 0.627070786 0.986984145 0.540743566 0.689263417 0.666839152 1 21.50151979 -4.999999999 0.25259508 3.040776519 0.637383049 0.427522097 0.118780152 173.1999869 1.712735863 182.8907286 0.156317627 1.00E-05 4.999999999 -2.403393471 LSEGS(ph)QPAEEEEDQETPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LSEGS(1)QPAEEEEDQETPSR;LSEGS(1)QPAEEEEDQETPSR 274.75 2.14E-39 364270000 375620 262460 335330 366320 351590 349590 399620 363880 368540 TRUE FALSE 357865.187 289204.9724 350705.2122 329496.8176 412907.1847 337483.6106 338650.6295 332016.7382 425691.301 0.840668311 0.679377219 0.82384867 0.774027604 0.969968575 0.79278954 0.795531007 0.7799472 1 18.69944808 -5 0.246663996 2.168863456 0.78210862 0.398345846 0.072910419 178.9319697 1.777253615 105.463414 0.105173713 1.00E-05 5 -1.386754837 LSEGSQPAEEEEDQET(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LSEGSQPAEEEEDQET(0.996)PS(0.004)R;LSEGSQPAEEEEDQET(0.998)PS(0.002)R 372.81 5.01E-107 154278000 156341 150438 171300 178758 177425 172941 193818 162672 201035 TRUE FALSE 148951.0708 165767.8032 179154.2744 160788.9062 208367.8638 166952.0098 164247.5044 148427.5773 232210.4811 0.641448526 0.713868739 0.771516745 0.692427428 0.897323251 0.718968451 0.707321666 0.639194134 1 17.82507357 -2.095002748 2.553035192 1.486642886 0.72163151 0.588804451 0.072805953 9183509.013 3729424.313 25889023.62 0.017087406 0.00803521 2.095002748 -0.765011376 LSEHATAPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSEHATAPTR 10 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 87.298 0.01475 0 101550 97946 99585 107270 163060 87746 139100 106710 215540 FALSE TRUE 96749.93275 107926.8088 104151.0708 96487.0158 191497.6124 84707.33402 117877.7403 97365.90669 248964.8424 0.388608817 0.433502207 0.41833646 0.387552776 0.76917532 0.340238136 0.473471431 0.391082957 1 17.9255825 -2.169486004 2.331209068 2.369421643 0.44868691 0.679155323 0.118745732 6768878.014 1476172.867 48973488.85 0.028527103 0.006768836 2.169486004 -1.920734733 LSELEPGTGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSELEPGTGDLR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 143.28 0.00014441 292575000 561857 467713 482822 582407 605984 493439 614783 574782 637022 FALSE TRUE 535299.1331 515373.4864 504959.8663 523862.3419 711667.4177 476351.0837 520986.5621 524451.041 735808.1183 0.72749827 0.700418321 0.68626569 0.711955099 0.967191582 0.647384925 0.708046771 0.712755171 1 19.48897007 -1.281351857 4.316502439 1.000214176 0.729094602 0.48613368 0.086300243 0.000167392 2.79E-05 0.078634992 0.01851989 0.05231764 1.281351857 -0.271119574 LSELLR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 167.64 0.015345 10582300000 9101150 7810710 7283410 8442380 8308390 7246930 9308450 8482390 8720950 FALSE TRUE 8670956.676 8606630.229 7617361.553 7593735.923 9757370.585 6995966.997 7888274.991 7739626.964 10073350.39 0.8607818 0.854395995 0.756189476 0.753844117 0.968632105 0.694502497 0.783083551 0.768326988 1 23.26404027 3.892188295 10.26809149 0.80369379 0.858385076 0.01274044 0.096659072 1.223211352 108.3771545 0.022353638 0.040343753 7801.682914 -3.892188295 0.054691286 LSELSNSQQSVQTLSLWLIHHR ddPTM_SK-BR-3_Trastuzumab_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 ; 229.46 1.62E-26 377660000 392060 430280 352290 455050 373600 352500 395300 377060 196849 FALSE TRUE 373528.1008 474126.0212 368442.845 409307.5095 438755.7217 340292.8366 334989.7248 344042.6275 227375.3376 1.642781952 2.08521305 1.620416924 1.800140305 1.929653965 1.496612783 1.473289621 1.513104417 1 17.79471625 1.127359594 0.545552043 0.998783204 1.855319444 0.711897361 0.157793939 0.428741831 0.324290202 0.159546085 0.077154363 13.40786394 -1.127359594 0.85653624 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 422.5 3.71E-208 1420860000 1455240 1252220 1217890 1468040 1151810 1133320 1388970 1350080 1016620 FALSE TRUE 1386453.689 1379822.642 1273731.461 1320469.83 1352685.299 1094072.844 1177057.116 1231859.838 1174272.237 1.180691875 1.175044932 1.084698608 1.124500595 1.151935008 0.931702896 1.002371579 1.049041099 1 20.16333548 2.252490362 24.98150891 0.994366227 1.147560524 0.783282617 0.038539256 102.2694836 183409.1408 0.013911588 0.0115836 178.8505837 -2.252490362 0.153194297 LSETSIKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSETSIKDR 9 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 179.1 4.58E-05 1680440000 3198160 2187040 2744040 2912600 2403410 2846740 3582830 3111130 2725110 FALSE TRUE 3046989.315 2409901.862 2869856.948 2619819.914 2822563.943 2748156.68 3036203.48 2838702.964 3147706.141 0.968003104 0.765605731 0.911729628 0.832294947 0.896705034 0.873066467 0.964576534 0.901832267 1 21.58586943 1.426658305 0.766923652 0.989772921 0.864123308 0.312481929 0.056842383 0.635393874 0.806267055 0.049358251 0.02048099 26.70904165 -1.426658305 -0.125649613 LSETWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSETWLR 7 0 Q9UJA5;Q9UJA5-4 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 98.418 0.026236 26707000 47557 48573 40295 46205 52112 45040 55005 46274 53876 FALSE TRUE 45309.07486 53522.64392 42142.56561 41560.38562 61200.3163 43480.25351 46612.97701 42222.00325 62230.81492 0.728081014 0.860066576 0.677197714 0.667842542 0.983440702 0.698693301 0.749033691 0.678474214 1 15.92534152 -1.600343564 3.088214623 1.013874581 0.761498782 0.378228528 0.098297576 53559550.05 66731194.55 6147070.043 0.02189555 0.025099001 1.600343564 -0.252375799 LSEVLQAVTDHDIPQQLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSEVLQAVTDHDIPQQLVER 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;; 160.67 2.37E-11 291519000 405295 456045 413328 448816 388340 412889 466322 423390 371990 FALSE TRUE 386137.5086 502516.504 432279.4976 403700.163 456066.373 398590.5504 395176.0143 386315.7271 429676.3093 0.898670697 1.169523413 1.006058487 0.939544849 1.061418475 0.927653077 0.919706313 0.899085471 1 18.71289071 2.222886801 24.52008518 0.928744734 1.021689211 0.203729369 0.075717906 263.4466677 412131.985 0.027608178 0.020463322 167.06551 -2.222886801 0.092944477 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 LSFASET(0.001)PLEKEPHS(0.998)PADQPEQQAESTLTSAETR;LSFASETPLEKEPHS(1)PADQPEQQAESTLTSAETR;LS(0.018)FAS(0.017)ET(0.017)PLEKEPHS(0.946)PADQPEQQAES(0.001)TLTSAETR;LSFASET(0.002)PLEKEPHS(0.998)PADQPEQQAESTLTSAETR;LS(0.023)FAS(0.023)ET(0.022)PLEKEPHS(0.932)PADQPEQQAESTLTSAETR 338.44 7.53E-118 851889000 300456 252973 292078 297675 273168 299222 349298 339110 272010 TRUE FALSE 286254.0403 278751.2363 305470.0652 267752.1435 320808.4127 288859.8671 296006.1748 309415.7307 314191.9216 0.911080205 0.88720052 0.972240355 0.852192959 1.021058756 0.919373947 0.942118987 0.984798492 1 18.26128656 2.20602279 0.230907764 1.013443641 0.873122941 0.295189284 0.044141312 3.336242192 0.579798523 0.10454028 0.170237375 160.7025582 -2.20602279 -0.1403207 LSFDKDAMVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LSFDKDAMVAR 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;;;; 194.39 4.85E-07 6577820000 15946180 13404690 12744180 14264720 12622360 13859040 16888800 15189140 13366520 FALSE TRUE 15192435.67 14770643.15 13328513.26 12830803.24 14823695.59 13379097.97 14312103.38 13859098.38 15439331.65 0.984008635 0.956689284 0.863283046 0.831046546 0.960125472 0.8665594 0.926989827 0.897648855 1 23.88010697 3.916172878 5.727073259 0.901866051 0.974128766 0.23027138 0.048920614 0.247322084 13.10889191 0.011396224 0.021030518 8244.662424 -3.916172878 0.072262715 LSFFFDFR ddPTM_SK-BR-3_Trastuzumab_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 ; 153.78 0.0010134 514040000 1346190 1849830 785980 934440 1150990 764720 1202630 1258890 968840 FALSE TRUE 1282558.267 2038329.78 822017.9604 840508.3159 1351722.292 738237.5547 1019146.706 1148654.918 1119082.759 1.146079909 1.82142899 0.734546175 0.751068953 1.207884118 0.659680929 0.910698246 1.026425355 1 20.0938853 3.727466978 24.99866173 0.888312735 1.48375446 0.537864676 0.225333577 438.5230781 988178.1968 0.055850418 0.087426981 5339.086757 -3.727466978 0.595441724 LSFLS(ph)WGTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSFLSWGTNK 10 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 LSFLS(0.999)WGT(0.001)NK;LSFLS(1)WGTNK 113.22 0.0015907 109584000 385530 332160 358270 404880 369350 390470 467360 418120 339630 TRUE FALSE 367306.7609 366007.4816 374697.0339 364180.6932 433764.5231 376947.926 396055.6483 381507.1962 392298.0858 0.936295063 0.932983093 0.955133475 0.92832646 1.10570135 0.960871183 1.009578335 0.972493137 1 18.58159077 LSFQHDPETSVLVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSFQHDPETSVLVLR 15 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 174.62 9.03E-07 1320360000 1717610 1362750 1549340 1802050 1929850 1545270 2052470 1888590 2038670 FALSE TRUE 1636421.979 1501615.774 1620378.772 1620904.51 2266415.229 1491756.912 1739328.005 1723215.048 2354816.532 0.694925468 0.637678458 0.688112534 0.688335795 0.962459367 0.633491778 0.738625698 0.731783145 1 21.16718323 -5 0.187929374 2.205492673 0.661076999 0.489747736 0.090632125 112.7948689 1.099901094 50.91039319 0.239788855 1.00E-05 5 -1.544415674 LSFS(ph)PENILIQNQDIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LS(0.021)FS(0.979)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR 223.93 3.02E-15 187628000 125132 108703 113657 136666 126303 120408 137107 121342 139235 TRUE FALSE 119217.2583 119779.9593 118868.2859 122928.074 148330.2032 116238.2408 116188.809 110716.6512 160826.8527 0.741277071 0.744775871 0.739107207 0.76435043 0.922297494 0.722753936 0.722446576 0.688421426 1 17.29514878 -1.987993948 2.841879528 1.226758027 0.754699285 0.601434478 0.062501151 11124236.73 5634863.021 16505858.23 0.015302416 0.010280306 1.987993948 -0.472058742 LSGEHS(ph)ES(ph)STPRPR ddPTM_SK-BR-3_Trastuzumab_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 2 LS(0.007)GEHS(0.988)ES(0.525)S(0.302)T(0.179)PRPR;LS(0.03)GEHS(0.946)ES(0.538)S(0.296)T(0.189)PRPR 71.601 0.011303 0 314400 275500 305170 323040 291650 291480 333050 284910 289230 TRUE FALSE 299538.9351 303573.7632 319162.3464 290567.4055 342513.6677 281385.9745 282237.1056 259961.77 334082.3112 0.8966022 0.908679547 0.955340452 0.86974795 1.025237363 0.842265409 0.844813078 0.778136888 1 18.34984407 LSGEHS(ph)ESSTPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.821)ES(0.143)S(0.03)T(0.007)PRPR;LSGEHS(0.42)ES(0.42)S(0.092)T(0.068)PRPR;LSGEHS(0.865)ES(0.134)STPRPR;LSGEHS(0.971)ES(0.024)S(0.004)T(0.001)PRPR;LS(0.001)GEHS(0.962)ES(0.034)S(0.001)T(0.001)PRPR 135.15 2.09E-05 2407176000 912476 731441 907352 941843 966874 876194 1076367 924141 943216 TRUE FALSE 869345.0678 805975.6695 948954.9867 847167.1523 1135496.519 845851.1821 912147.4453 843218.3149 1089485.12 0.797941203 0.739776666 0.871012343 0.777584876 1.042232242 0.776376994 0.837227997 0.773960378 1 20.05521506 -5 0.167904321 1.639737533 0.781062526 0.26583111 0.086269966 173.5323846 1.628590165 37.49964689 0.303103507 1.00E-05 5 -0.858675007 LSGEHSES(ph)STPRPR ddPTM_SK-BR-3_Trastuzumab_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(0.117)ES(0.766)S(0.11)T(0.007)PRPR 140.68 5.98E-06 238770000 107600 83962 96331 108820 105230 101230 123020 98785 111190 TRUE FALSE 102513.9612 92517.82326 100747.8716 97881.20686 123582.0787 97724.37972 104251.0396 90134.86171 128432.7773 0.798191578 0.720359905 0.784440497 0.762120145 0.962231615 0.760899061 0.811716773 0.701805751 1 16.97065391 -1.599102958 3.076596662 1.012417339 0.787283101 0.474015174 0.070273629 17715382.04 21765771.93 1804710.487 0.01596424 0.025170801 1.599102958 -0.225134238 LSGFS(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK 158.76 0.0014778 2203399000 3470790 4000810 2980481 4805910 2524764 3905850 4038820 3858930 2244962 TRUE FALSE 3306732.635 4408497.088 3117139.002 4322810.796 2965082.042 3770589.435 3422623.831 3521021.632 2593099.241 1.275204814 1.700088071 1.202090129 1.667044102 1.143451047 1.454086051 1.31989697 1.357842992 1 21.30624599 -1.345071849 0.252900502 0.677435861 1.476825462 0.326369833 0.178859928 20.45942777 1.043534998 4.55753606 0.25088777 0.04517812 1.345071849 0.799389601 LSGFS(ph)FKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FKK;LSGFS(1)FKK;LS(0.001)GFS(0.999)FKK 129.88 0.0011354 8290248000 5355250 4575230 4492490 5538860 3017088 5616490 6115610 5130340 3092675 TRUE FALSE 5102117.946 5041451.139 4698475.11 4982083.27 3543267.192 5421989.543 5182561.374 4681100.232 3572271.244 1.42825603 1.411273331 1.315262697 1.394654249 0.991880781 1.51779895 1.450774877 1.310398879 1 21.7684102 -2.21755194 1.472612126 0.235736023 1.365465127 0.374233333 0.14239726 125561.7808 19237.02167 318026.7679 0.037800899 0.006059657 2.21755194 1.129729104 LSGINEIPRPFS(ph)PPVT(ph)SNTSPPPAAPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LS(0.001)GINEIPRPFS(0.97)PPVT(0.641)S(0.143)NT(0.125)S(0.121)PPPAAPLAR;LSGINEIPRPFS(0.913)PPVT(0.441)S(0.399)NT(0.123)S(0.123)PPPAAPLAR 85.239 0.0046716 504420000 270459 245642 253899 310115 296715 272318 310297 283997 310231 TRUE FALSE 257674.9391 270673.1991 265540.5203 278941.651 348462.0021 262887.5594 262955.4937 259128.7171 358340.039 0.719079397 0.755352932 0.741029445 0.77842725 0.972433901 0.733625972 0.733815552 0.723136376 1 18.45096973 -2.465260243 2.251551445 3.603162253 0.766716347 0.487187434 0.074230672 4206411.895 254556.0619 56480729.23 0.01807035 0.003425625 2.465260243 -2.836445906 LSGINEIPRPFS(ph)PPVTS(ph)NTSPPPAAPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LS(0.003)GINEIPRPFS(0.997)PPVT(0.032)S(0.466)NT(0.293)S(0.209)PPPAAPLAR 87.712 0.0010398 480000000 102740 83748 108900 113410 104230 98581 126330 105280 103110 TRUE FALSE 97883.68381 92282.01641 113893.1727 102009.8113 122407.679 95167.11525 107056.0383 96061.12508 119099.7722 0.821862897 0.774829496 0.956283716 0.856507191 1.02777425 0.799053714 0.898876936 0.806560108 1 16.86181113 -1.067554929 0.018966842 1.894601653 9.31E-22 0.180673318 0.079427254 2225.820393 7.91097455 441.8118216 351.3252356 0.085594345 1.067554929 -1.894601653 LSGINEIPRPFS(ph)PPVTSNT(ph)SPPPAAPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LSGINEIPRPFS(1)PPVT(0.258)S(0.175)NT(0.473)S(0.094)PPPAAPLAR 90.303 0.0036805 120600000 52622 56451 57844 58957 58414 56494 67308 65078 65795 TRUE FALSE 50134.66235 62203.42108 60496.20462 53030.53035 68601.38311 54537.59861 57038.9284 59379.42532 75998.15257 0.659682646 0.818485963 0.796022042 0.697787098 0.90267172 0.717617426 0.75053046 0.781327221 1 16.21367673 -5 0.397835591 4.754663993 0.758914958 0.546267843 0.067351633 535.2269244 3.766414695 1744.555946 0.038899442 1.00E-05 5 -3.995749035 LSGINEIPRPFS(ph)PPVTSNTSPPPAAPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.371)PPVT(0.312)S(0.225)NT(0.085)S(0.007)PPPAAPLAR;LSGINEIPRPFS(0.905)PPVT(0.024)S(0.017)NT(0.023)S(0.031)PPPAAPLAR;LSGINEIPRPFS(0.988)PPVT(0.001)S(0.008)NT(0.002)SPPPAAPLAR;LSGINEIPRPFS(0.914)PPVT(0.036)S(0.007)NT(0.03)S(0.013)PPPAAPLAR 126.72 1.22E-05 1300115000 616200 475884 560489 587149 556980 520904 656644 548358 587302 TRUE FALSE 587073.4472 524377.1206 586187.975 528127.667 654117.1357 502864.9639 556460.8977 500340.8665 678377.7946 0.865407818 0.772986859 0.864102539 0.778515558 0.964237245 0.741275684 0.82028171 0.7375549 1 19.37172942 -2.282568522 2.410963028 1.873204214 0.818120454 0.413700762 0.068074105 8551700.206 1426224.636 40735573.59 0.014595004 0.005217128 2.282568522 -1.05508376 LSGLS(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSGLSFK 7 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FK;LSGLS(1)FK;LSGLS(1)FK;LSGLS(1)FK 111.61 0.0068612 1916480000 4851730 5201750 4819820 6605970 3292320 6103840 5456100 4880010 2906880 TRUE FALSE 4622398.338 5731814.239 5040813.514 5941925.345 3866499.566 5892462.49 4623671.737 4452690.454 3357664.104 1.376670862 1.707083872 1.501285822 1.769660443 1.15154448 1.754929114 1.377050114 1.326127425 1 21.67902648 0.927782595 1.193939844 1.001110428 1.545546745 0.451616502 0.188101999 0.462324929 1.332225266 0.155754137 0.048470368 8.468034045 -0.927782595 0.544436317 LSGLS(ph)FKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LSGLSFKR 8 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR 157.75 0.00022784 17907420000 20272050 15257070 16677930 21708130 15394960 21247790 24632640 18464270 14652780 TRUE FALSE 19313830.37 16811782.78 17442629.59 19525987.53 18079836.15 20511973.7 20874478.36 16847440.63 16925058.29 1.14113819 0.993307231 1.030580178 1.153673281 1.068228885 1.21192928 1.233347502 0.995414039 1 24.01265747 3.236716367 24.99241432 1.134421392 1.054091058 0.037102764 0.088042118 89.33601306 1210646.686 0.024374166 0.030576872 1724.711136 -3.236716367 -0.080330334 LSGS(ph)RQDLIPSYSLGSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.158)GS(0.842)RQDLIPSYSLGSNK;LS(0.05)GS(0.95)RQDLIPSYSLGSNK;LS(0.021)GS(0.712)RQDLIPS(0.252)YS(0.015)LGSNK 275.75 2.69E-39 929693000 2086870 1581030 1855444 1905300 1537339 1724425 2117340 1941901 1713787 TRUE FALSE 1988227.791 1742138.754 1940517.943 1713775.624 1805450.435 1664707.73 1794300.895 1771857.854 1979552.335 1.004382534 0.880067035 0.980281202 0.865738982 0.912049862 0.840951613 0.906417508 0.895080076 1 20.91674278 7.999977397 0.847081986 0.901233336 37.44029916 0.245430073 0.049145416 770.1125786 2.159289864 0.013975156 54214.71672 99994795.65 -7.999977397 36.53906583 LSIFDANES(ph)GFESYEALPQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSIFDANESGFESYEALPQHK 21 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.002)IFDANES(0.983)GFES(0.013)Y(0.002)EALPQHK 56.719 0.055504 23339000 26879 32254 36251 34035 25809 33372 42030 38602 36129 TRUE FALSE 25608.48294 35540.71927 37913.14421 30613.73714 30310.08143 32216.31927 35617.55157 35221.80424 41731.7008 0.6136458 0.851647994 0.908497461 0.733584698 0.726308318 0.771986731 0.853489095 0.844005961 1 15.3488561 -5 0.100947203 1.690328378 0.640553411 0.488646362 0.076650886 172.3196149 1.181129263 24.94652022 1.284005407 1.00E-05 5 -1.049774968 LSIPTYGLQCTR ddPTM_SK-BR-3_Trastuzumab_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 ; 171.92 8.64E-05 1646590000 440670 335290 353620 412430 421560 353120 463880 375630 453410 FALSE TRUE 419840.4024 369456.4322 369833.8268 370971.7528 495079.9305 340891.3659 393106.5863 342737.8459 523722.5071 0.801646667 0.705443106 0.706163706 0.708336472 0.945309632 0.650900737 0.750600902 0.654426421 1 18.99844308 -1.030760375 4.186995967 1.000021548 0.741688021 0.480858493 0.084774966 8504269.999 4187185.786 1641.038803 0.018001222 0.093162176 1.030760375 -0.258333527 LSIVPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSIVPVRR 8 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 176.09 0.00042067 2586800000 3334500 2786300 1812290 1828480 3698600 2184730 3569600 2765600 3348100 FALSE TRUE 3176884.793 3070227.138 1895385.289 1644677.717 4343634.669 2109072.252 3024991.96 2523429.403 3867306.248 0.821472257 0.793892943 0.490104783 0.425277341 1.123168012 0.545359513 0.782196125 0.652503122 1 21.88289758 2.782300992 24.99993783 0.782401773 0.672609613 0.149800413 0.20217829 1411.358136 806663.198 0.060514252 0.064184741 605.7605573 -2.782300992 -0.10979216 LSIYEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSIYEAR 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 132.96 0.0077193 487634000 970209 866139 790791 910060 1000439 832510 1006830 928827 1067287 FALSE TRUE 924349.1433 954399.5488 827049.5495 818579.0398 1174915.245 803679.97 853219.5918 847493.9839 1232796.417 0.749798694 0.774174499 0.670872772 0.6640018 0.95304888 0.651916212 0.692100967 0.68745656 1 20.23350314 -1.981775855 2.45089178 1.241891783 0.731896727 0.482355085 0.087753016 8845423.222 3975892.335 12115099.82 0.020821927 0.010428555 1.981775855 -0.509995057 LSKDDIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSKDDIDR 8 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 70.1 0.047611 195840000 491750 284490 376370 415370 362300 418410 486580 408940 416440 FALSE TRUE 468505.9521 313479.8544 393626.9368 373616.2184 425485.0053 403920.3568 412343.2843 373131.0457 481019.3883 0.973985589 0.651699 0.818318235 0.776717587 0.884548556 0.839717414 0.857227992 0.775708952 1 18.87573552 2.740005389 24.79908077 0.859680824 0.799085981 0.099223449 0.094837127 296.7372999 5093453.893 0.028012767 0.028277585 549.5476935 -2.740005389 -0.060594844 LSKEDIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 LSKEDIER 8 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;; 137.05 0.00069763 53277100000 47180510 36894250 38449830 45531300 33851380 44853580 54081870 46336320 41645730 FALSE TRUE 44950380.8 40653816.02 40212792.74 40954407.22 39755049.95 43300289.28 45830687.45 42278866.18 48103937.11 0.934442865 0.845124505 0.835956372 0.85137329 0.826440669 0.900140235 0.95274296 0.878906566 1 25.51965164 1.999308547 5.922261024 0.936101798 0.862230581 0.468639719 0.041148366 0.151922452 21.0923959 0.016292512 0.011033829 99.84091364 -1.999308547 -0.073871218 LSKEEIER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 121.5 0.0013046 15342280000 26615090 20120350 22486700 24476840 18855120 23274440 27879420 25022080 21428480 FALSE TRUE 25357047.44 22170636.54 23517737.44 22016381.54 22143446.96 22468440.31 23625902.44 22831014.02 24751499.24 1.024465112 0.895729036 0.950154058 0.889496888 0.894630533 0.907760782 0.954524096 0.922409338 1 24.56101258 -1.06864073 6.980787581 1.000000021 0.93155166 0.229759239 0.040237232 1.33E-08 1.76E-09 0.038258031 0.009017502 0.085380613 1.06864073 -0.068448361 LSKVS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSKVSFR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 LS(0.013)KVS(0.987)FR 63.283 0.048669 149010000 202990 154100 209050 268390 146240 288690 351600 248380 191740 TRUE FALSE 193395.065 169802.9652 218635.1493 241410.9273 171744.2097 278692.5929 297956.9624 226630.5305 221474.0599 0.873217681 0.766694597 0.987181746 1.090018973 0.775459707 1.258353204 1.345335713 1.023282503 1 17.75677821 2.231568068 24.99842146 1.205245058 0.890974448 0.440835007 0.139706393 123.5907731 441834.1528 0.050959032 0.038449063 170.4386429 -2.231568068 -0.31427061 LSLCGEESFGTGSDHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLCGEESFGTGSDHIR 17 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 230.38 8.07E-16 353770000 146820 137540 149480 168890 183360 161220 208300 157010 179070 FALSE TRUE 139880.1096 151555.4824 156333.8059 151912.8563 215337.9259 155636.911 176520.0093 143261.372 206839.261 0.67627446 0.732721059 0.755822686 0.734448845 1.041088258 0.752453428 0.85341636 0.692621755 1 17.65815053 2.962241019 24.98495683 0.852824892 0.720964785 0.316236202 0.103383827 668.6098305 442416.3013 0.028691234 0.030438583 916.7291022 -2.962241019 -0.131860107 LSLDDLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLDDLLQR 9 0 F8VPD4;P27708;H7BZB3 F8VPD4;H7BZB3 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 128.12 0.00099163 16047000 50064 42486 42418 48333 58015 44114 60330 48314 59622 FALSE TRUE 47697.57394 46815.3717 44362.90726 43474.47501 68132.79763 42586.32112 51125.55046 44083.37003 68867.87525 0.692595405 0.679785336 0.644174183 0.631273651 0.989326263 0.61837716 0.742371538 0.640115146 1 16.07154355 -1.997948158 2.760445235 1.290967745 0.705190876 0.427234567 0.107433531 47607860.9 18673175.99 88075979.23 0.023386071 0.010047357 1.997948158 -0.585776869 LSLDELHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSLDELHR 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ;;;; 194.29 0.00016614 399001000 896302 727563 636350 1150767 1173450 724587 952371 828826 915486 FALSE TRUE 853935.5808 801702.4969 665527.2769 1035089.715 1378099.308 699494.3705 807069.3125 756249.6016 1057454.893 0.80753854 0.758143446 0.62936706 0.978849993 1.303222783 0.661488613 0.763218666 0.715160151 1 20.01216469 3.232139761 24.94573319 0.884969213 0.748189611 0.154259783 0.185089727 353.8501645 1374745.985 0.055105057 0.067376888 1706.631514 -3.232139761 -0.136779602 LSLDELHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLDELHRK 9 1 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 157.34 4.46E-05 185380000 246170 138950 175290 271610 266100 205270 335240 254040 261090 FALSE TRUE 234534.032 153109.163 183327.2199 244307.2468 312507.7557 198161.4484 284092.9809 231794.9108 301578.5037 0.777688161 0.507692561 0.607892199 0.810095029 1.036240156 0.657080813 0.942019996 0.768605547 1 18.20217407 3.154130439 4.692899642 0.868775668 0.625666195 0.44642003 0.126311019 0.17651046 6.932437733 0.033876355 0.041348751 1426.035836 -3.154130439 -0.243109473 LSLDGNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSLDGNPK 8 0 B8ZZZ7;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F8VT91 B8ZZZ7 SPATS2L SPATS2-like protein 0 ; 74.127 0.041781 256010000 375360 316260 323550 399340 858250 202275 400960 238721 958630 FALSE TRUE 357617.4767 348487.2536 338385.0875 359197.5845 1007928.528 195270.166 339786.1879 217817.3237 1107289.444 0.322966573 0.314721011 0.305597682 0.324393578 0.910266537 0.176349704 0.306863024 0.196712183 1 20.07860096 -1.341877501 5.041313884 1.000310875 0.353767971 0.495583258 0.2037676 0.00066927 8.74E-05 0.185462002 0.043693373 0.045511641 1.341877501 -0.646542904 LSLEEETLWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSLEEETLWLR 11 0 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ; 154.85 7.40E-05 22495200 33948 27389 28709 29468 30884 28041 33890 34273 31723 FALSE TRUE 32343.34532 30179.97024 30025.33605 26505.82065 36270.15982 27069.93314 28719.45807 31271.87443 36642.44082 0.882674423 0.823634277 0.819414192 0.723363948 0.989840169 0.738759005 0.783775792 0.85343317 1 15.16122799 -1.411033876 6.460380107 1.000027504 0.824475914 0.343563629 0.075147835 2.71E-05 2.47E-06 0.06629352 0.015623087 0.038812009 1.411033876 -0.17555159 LSLEGDHST(ph)PPSAYGSVK ddPTM_SK-BR-3_Trastuzumab_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 1 LSLEGDHS(0.051)T(0.949)PPSAYGSVK;LSLEGDHS(0.201)T(0.799)PPSAYGSVK 118.32 0.00039041 448720000 357960 321220 295510 461640 334170 346860 399580 340100 269780 TRUE FALSE 341039.9402 353952.6832 309059.4258 415235.0701 392449.1422 334848.1512 338616.7322 310319.041 311616.1046 1.094423347 1.135861331 0.991795422 1.332521215 1.259399423 1.074553421 1.086647087 0.995837624 1 18.24941027 1.557529824 1.884794867 0.999517536 1.150205174 0.310632836 0.093286981 0.424653429 3.069032254 0.076452973 0.026412868 36.10188044 -1.557529824 0.150687638 LSLFPAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLFPASPR 9 0 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 LSLFPAS(1)PR 63.624 0.07851 33391000 50132 47301 48304 50606 129210 48404 57016 51462 72064 TRUE FALSE 47762.35971 52121.02568 50518.78618 45518.98873 151744.1831 46727.75734 48317.16203 46955.71446 83239.31707 0.57379567 0.626158737 0.606910147 0.546844813 1.822986882 0.561366419 0.580460817 0.564104994 1 16.34497751 LSLFSDGDS(ph)SESEDTLSSSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLFSDGDSSESEDTLSSSER 21 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 LSLFSDGDS(0.615)S(0.373)ES(0.013)EDTLSSSER 113.23 3.11E-05 0 120860 94596 97321 114290 75567 106740 125170 115590 81752 TRUE FALSE 115147.1873 104235.4399 101783.2641 102801.3521 88745.86087 103043.567 106073.0176 105468.3268 94429.68263 1.219396106 1.103841896 1.077873623 1.088655063 0.93980895 1.091220093 1.123301642 1.116898033 1 16.5269528 4.439624069 1.328805727 1.067727939 1.243140301 0.442763352 0.055253361 0.752042142 1.727464145 0.015891545 0.154700945 27518.45636 -4.439624069 0.175412361 LSLFSDGDSS(ph)ESEDTLSSSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSLFSDGDSSESEDTLSSSER 21 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 LSLFSDGDS(0.207)S(0.769)ES(0.024)EDTLSSSER;LSLFSDGDS(0.487)S(0.513)ESEDTLSSSER 300.5 4.57E-55 92581000 186216 152742 180797 192249 156357 159283 196432 178630 195801 TRUE FALSE 177413.9387 168306.5835 189086.7213 172923.7653 183625.6113 153766.9898 166462.6907 162988.2102 226164.8191 0.784445341 0.744176677 0.836057182 0.764591796 0.811910588 0.679889076 0.736023805 0.720661201 1 17.787015 -0.931085771 9.29256654 1 0.758531669 0.741369133 0.044596035 0 0 0.042264059 0.009961734 0.117196389 0.931085771 -0.24146833 LSLLSS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLLSSTSK 9 0 Q92754;Q92754-2;C9JXZ2;H7C5E5;C1K3N0;P05549-2;Q7Z6R9;A0A6E1XE14;P05549-5;P05549-6;P05549;Q92481;Q92481-2;Q6VUC0 Q92754;A0A6E1XE14 TFAP2C;TFAP2A;TFAP2D;TFAP2B;TFAP2E Transcription factor AP-2 gamma;Transcription factor AP-2-alpha;Transcription factor AP-2-delta;Transcription factor AP-2-beta;Transcription factor AP-2-epsilon 1 LSLLS(0.266)S(0.627)T(0.075)S(0.032)K 74.077 0.044175 122190000 741240 540210 621680 765490 775490 716210 886990 764970 718180 TRUE FALSE 706203.0542 595258.0132 650184.6429 688541.4909 910735.2105 691407.4681 751663.3848 697985.1714 829551.6864 0.851306875 0.717565913 0.783778339 0.830016384 1.097864335 0.833471234 0.906107958 0.841400461 1 19.66197235 2.987800711 24.61050877 0.923994474 0.782941197 0.424617584 0.081848246 454.0660991 916023.1108 0.02297367 0.025579702 972.3009531 -2.987800711 -0.141053277 LSLMPWFHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 94.692 0.0079306 51174000 187650 144710 137520 176780 197300 162840 231930 188920 180380 FALSE TRUE 178780.1564 159456.1135 143825.428 159009.7385 231709.0575 157200.81 196544.8188 172377.1633 208352.4091 0.858066183 0.765319269 0.690298848 0.763176866 1.112101648 0.754494803 0.943328755 0.82733463 1 17.66866626 LSLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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(0.001)LS(0.999)PK 81.215 0.065524 51289000 243450 236110 214650 272280 164270 253080 258980 266090 160930 TRUE FALSE 231942.601 260169.8774 224491.9148 244909.8971 192918.636 244315.7761 219467.8445 242789.749 185886.2025 1.247766633 1.399619089 1.207684658 1.317525959 1.037831928 1.314329804 1.180656991 1.306120335 1 17.50406016 -4.999999999 0.142430841 0.126019766 1.345387934 0.381035552 0.09883445 129.7482205 1.123852867 32.30518458 0.523463755 1.00E-05 4.999999999 1.219368168 LSLS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LSLSPLR 7 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 LS(0.003)LS(0.997)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR 180.34 0.00072154 2589055000 2665533 2119304 1354577 1752281 2578400 1748673 2549720 2187534 2437350 TRUE FALSE 2539538.538 2335263.487 1416685.695 1576138.385 3028072.144 1688116.016 2160713.385 1995981.926 2815321.79 0.902042014 0.829483683 0.503205602 0.559843067 1.075568752 0.59961743 0.767483629 0.70897115 1 21.4248684 -1.070181155 4.234039079 1.000027582 0.752442603 0.183658488 0.169118964 21819050.57 5514909.114 5751.598368 0.038091446 0.085078308 1.070181155 -0.24758498 LSLSPALQDALHTFPQLQVEQSGEGS(ph)PEEGAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLSPALQDALHTFPQLQVEQSGEGSPEEGAVR 33 0 Q9ULL5;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 LSLSPALQDALHTFPQLQVEQS(0.09)GEGS(0.91)PEEGAVR 131.99 3.57E-08 58999000 42398 39634 37972 47004 51566 38996 43403 43072 51528 TRUE FALSE 40393.93056 43672.74966 39713.05376 42279.06862 60559.09407 37645.55874 36781.0752 39300.38734 59518.69907 0.678676302 0.733765192 0.667236589 0.71034934 1.017480137 0.632499691 0.61797512 0.660303198 1 15.86105537 -2.287032131 2.368659846 2.382132152 0.71117384 0.386141985 0.112932929 3441161.471 780519.3385 25450611.88 0.028347823 0.005163782 2.287032131 -1.670958311 LSLT(ph)RSPVSPLAAQGIPLPAQLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 LS(0.087)LT(0.58)RS(0.329)PVS(0.004)PLAAQGIPLPAQLTK 171.15 1.14E-11 292970000 1012200 475880 1019400 837330 1001800 934160 1428500 1087000 1406700 TRUE FALSE 964355.312 524372.713 1066140.498 753159.9976 1176513.603 901809.805 1210556.089 991816.5175 1624843.852 0.593506454 0.322721911 0.656149511 0.463527616 0.724077949 0.555013212 0.745029184 0.610407281 1 20.63186965 -0.147952076 0.202308513 1.245942034 0.398561674 0.61170708 0.111689113 6.023090441 0.423378533 1.312850018 0.332519124 0.711291999 0.147952076 -0.84738036 LSLTRS(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 2 LSLT(0.001)RS(0.999)PVS(1)PLAAQGIPLPAQLTK;LS(0.004)LT(0.091)RS(0.947)PVS(0.958)PLAAQGIPLPAQLTK 205.44 5.54E-25 436550000 1063160 549060 1118530 915170 1144940 1086710 1606170 1172430 1490450 TRUE FALSE 1012906.534 605009.8382 1169815.707 823175.3729 1344617.173 1049076.96 1361119.267 1069765.814 1721581.374 0.588358209 0.351426803 0.679500676 0.47815072 0.781036083 0.60936821 0.790621511 0.621385564 1 20.71530294 0.864370524 0.184470077 1.178400649 0.351915697 0.575938456 0.115879186 3.120046489 0.400095834 0.907500301 0.548332099 7.317631303 -0.864370524 -0.826484952 LSLTRS(ph)PVSPLAAQGIPLPAQLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 LS(0.001)LT(0.049)RS(0.895)PVS(0.055)PLAAQGIPLPAQLTK 226.74 3.01E-33 335180000 695390 340480 671040 572860 703320 636930 1000100 751680 934010 TRUE FALSE 662520.2928 375175.2991 701807.8477 515275.0244 825978.7853 614872.9544 847516.3769 685858.9143 1078851.501 0.614097763 0.347754347 0.650513854 0.477614411 0.76560934 0.569932891 0.785572784 0.635730602 1 20.04106487 0.799948488 0.259865294 1.0953238 0.437750233 0.588941866 0.113733965 1.830720991 0.357750946 0.415966339 0.210023617 6.30882511 -0.799948488 -0.657573567 LSMEDS(ph)KSPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSMEDSKSPPPK 12 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.519)KS(0.481)PPPK 80.967 0.028692 737300000 934000 1016700 780430 1082500 406770 1023700 849470 1018900 442380 TRUE FALSE 889851.671 1120302.886 816213.4875 973685.0434 477710.5592 988249.0123 719867.7499 929679.7145 510982.031 1.74145394 2.19245065 1.597342838 1.905517189 0.934887198 1.934019109 1.40879269 1.819398057 1 18.96291303 -0.394498438 0.090030662 2.27E-12 2.572745383 0.308216609 0.335111566 52.76949131 1.234915242 24.50091254 11.18558453 0.403182397 0.394498438 2.572745383 LSMEDS(ph)KSPPPKATEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LS(0.019)MEDS(0.929)KS(0.052)PPPKATEEK;LS(0.022)MEDS(0.574)KS(0.404)PPPKATEEK 90.968 0.0019158 1666910000 2962500 2253600 2698300 2883500 1233370 3367700 3594300 3585700 1382510 TRUE FALSE 2822468.496 2483244.402 2822019.724 2593645.102 1448469.338 3251075.705 3045923.521 3271717.099 1596902.59 1.767464411 1.555038121 1.767183385 1.624172394 0.907049276 2.035863505 1.90739469 2.0487894 1 20.60684488 LSMEDSKS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LSMEDSKSPPPK 12 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.003)KS(0.997)PPPK;LSMEDS(0.002)KS(0.998)PPPK;LSMEDS(0.003)KS(0.997)PPPK;LSMEDS(0.006)KS(0.994)PPPK;LSMEDS(0.001)KS(0.999)PPPK;LSMEDS(0.001)KS(0.999)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.057)KS(0.943)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.118)KS(0.882)PPPK 174.59 1.82E-05 7312050000 9813290 10836150 8033790 11458820 4266640 10678350 9100370 10741530 4451440 TRUE FALSE 9349435.23 11940366 8402147.218 10306957.64 5010740.665 10308556.06 7711941.417 9800944.689 5141746.58 1.818338396 2.322239305 1.634103721 2.004563524 0.974521126 2.004874394 1.49986805 1.906150864 1 22.29382708 -0.800674734 0.10365014 8.82E-11 2.535142536 0.322441416 0.356490114 48.8693826 1.108004806 21.38610792 7.252044256 0.158243276 0.800674734 2.535142536 LSMEDSKS(ph)PPPKATEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.019)KS(0.981)PPPKATEEK;LS(0.004)MEDS(0.124)KS(0.871)PPPKAT(0.001)EEK;LS(0.003)MEDS(0.07)KS(0.927)PPPKAT(0.001)EEK 88.09 0.0038845 2175770000 2838240 2136710 2660290 2916110 1272580 3226810 3298240 3431950 1397260 TRUE FALSE 2704082.02 2354443.178 2782266.928 2622977.083 1494517.549 3115064.761 2795032.912 3131430.264 1613939.945 1.675453928 1.458817093 1.723897433 1.625201168 0.926005676 1.93009955 1.731807259 1.940239644 1 20.62215547 LSMPQSAAVST(ph)TPPHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.046)T(0.6)T(0.354)PPHNR 94.922 0.0076429 118970000 96727 100190 95161 108850 95077 89305 104330 107340 112900 TRUE FALSE 92154.9064 110399.4749 99524.22598 97908.1912 111658.3987 86212.34546 88412.54235 97940.74055 130407.9554 0.706666293 0.846570093 0.763176032 0.750783884 0.856223827 0.661097287 0.677968933 0.75103348 1 16.99267236 -1.196222354 6.083646107 1.000003203 0.751398732 0.605335797 0.063010037 2.83E-06 3.74E-07 0.063160921 0.01488698 0.063646957 1.196222354 -0.248604471 LSMPQSAAVST(ph)TPPHNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.03)T(0.485)T(0.485)PPHNRR 75.239 0.0078204 81171000 80197 65356 73766 75424 78114 78734 93512 86892 103530 TRUE FALSE 76406.24675 72015.8507 77148.24406 67842.23622 91737.05687 76007.42184 79245.02693 79283.27584 119584.9036 0.638928865 0.602215234 0.645133639 0.567314386 0.767129078 0.635593788 0.662667482 0.662987329 1 16.86767575 -5 0.272280116 3.48852809 0.618995969 0.83735275 0.049169268 74.29636225 0.719127193 104.0111962 0.053451428 1.00E-05 5 -2.869532122 LSMPQSAAVSTT(ph)PPHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.042)T(0.205)T(0.753)PPHNR;LSMPQSAAVS(0.002)T(0.181)T(0.817)PPHNR;LSMPQSAAVS(0.005)T(0.248)T(0.747)PPHNR;LSMPQSAAVS(0.002)T(0.194)T(0.804)PPHNR 130.83 0.00011959 882500000 450201 450281 420738 539330 463620 428104 489460 478067 464035 TRUE FALSE 428920.8909 496165.1458 440029.2535 485115.5237 544475.1812 413278.6511 414783.8875 436204.9191 535995.1778 0.800232742 0.92568957 0.820957486 0.905074418 1.015821044 0.771049196 0.773857498 0.813822469 1 19.0318605 -1.615128182 8.638447302 1.000069837 0.852503277 0.265727977 0.076620369 0.00010471 4.67E-06 0.075378536 0.017758517 0.02425894 1.615128182 -0.14756656 LSMPQSAAVSTT(ph)PPHNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.009)T(0.262)T(0.729)PPHNRR 94.281 0.0015189 251060000 109560 65184 103110 89688 111870 104720 120080 113740 141470 TRUE FALSE 104381.3159 71826.32371 107837.6955 80672.39184 131380.0926 101093.5201 101759.5906 103780.3226 163408.4451 0.638775529 0.439550867 0.659927309 0.493685573 0.803998181 0.61865542 0.622731527 0.635097669 1 17.31812302 -5 0.194325097 2.759614687 0.533651725 0.628428928 0.094581741 82.78081314 0.813966594 56.34323977 0.223598763 1.00E-05 5 -2.225962962 LSMWDRPDDLIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSMWDRPDDLIGR 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ;;;; 231.69 1.82E-12 640438000 792233 683378 689185 768579 796791 685142 851665 812213 823596 FALSE TRUE 754785.7161 753014.9951 720784.8139 691319.9787 935751.0981 661415.3607 721727.8623 741091.3239 951315.0613 0.793412978 0.791551638 0.75767203 0.726699289 0.983639528 0.695264259 0.758663341 0.779017756 1 19.85956369 -2.245101074 2.084158003 1.700059688 0.784078014 0.43712621 0.076388471 3858308.947 643619.1945 12708988.71 0.018202927 0.005687206 2.245101074 -0.915981674 LSNHISSLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSNHISSLFR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 170.52 4.30E-06 1180480000 1133920 691870 424810 582530 2425900 558910 1606260 876860 2428600 FALSE TRUE 1080321.849 762372.3396 444287.9587 523972.9777 2848976.192 539554.8066 1361195.536 800077.4899 2805214.884 0.385111977 0.271769676 0.158379296 0.186785326 1.015599984 0.19233992 0.485237528 0.285210767 1 21.41967986 -5 0.234016925 4.448862774 0.302501927 0.384778853 0.248992735 168.5831152 1.684524235 276.0763164 0.383120302 1.00E-05 5 -4.146360847 LSNRPAFMPSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSNRPAFMPSEGK 13 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 163.99 3.45E-05 1990590000 1983680 1239840 1092490 1692730 1610560 1380190 2378850 1655150 2014620 FALSE TRUE 1889915.378 1366181.106 1142581.747 1522573.564 1891441.154 1332393.674 2015912.742 1510216.291 2327036.98 0.812155283 0.587090415 0.491002832 0.654297107 0.812810957 0.572570907 0.86630026 0.648986803 1 21.15006271 0.251020076 0.470741616 1.026352197 0.651067387 0.423858351 0.118126477 2.808118668 0.951091877 0.277385433 0.062945611 1.782461165 -0.251020076 -0.375284809 LSNSDS(ph)QDIQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSNSDSQDIQGR 12 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LSNSDS(1)QDIQGR 184.87 1.44E-05 166530000 78657 46333 68559 102920 72317 99638 106130 63187 70446 TRUE FALSE 74939.03949 51054.38538 71702.49796 92574.28606 84929.0619 96187.51108 89937.91929 57654.0113 81370.40589 0.920961849 0.627431863 0.881186436 1.137689865 1.043734033 1.182094522 1.105290287 0.708537836 1 16.31221657 3.437345966 5.62712855 1.049100338 0.770513946 0.347791133 0.145483894 0.162259092 12.92980066 0.038605807 0.053411255 2737.448556 -3.437345966 -0.278586392 LSPDAIPGKWTSQDSLLGMEFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSPDAIPGKWTSQDSLLGMEFSGR 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 ; 222.21 7.88E-33 812590000 763590 245436 881020 533680 1069340 684320 1444190 824670 1620370 FALSE TRUE 727496.614 270446.2074 921415.6384 480033.4725 1255832.557 660621.8268 1223852.291 752457.5229 1871648.704 0.388692928 0.144496244 0.492301593 0.256476267 0.670976639 0.352962511 0.653889957 0.402029249 1 20.83587825 -4.999999547 0.112322252 2.990557634 0.068236748 0.620771611 0.149460851 90.62961711 0.67299526 40.96108568 1.530788075 1.00E-05 4.999999547 -2.922320886 LSPFFTLDLS(ph)PTEDK ddPTM_SK-BR-3_Trastuzumab_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(0.985)PT(0.015)EDK;LSPFFTLDLS(0.995)PT(0.005)EDK 270.17 1.01E-26 111865000 497128 544287 364152 581208 271947 479056 434843 515905 264397 TRUE FALSE 473629.7447 599750.4641 380848.7294 522783.8676 319374.4707 462466.1706 368499.7139 470729.6232 305398.3364 1.550858954 1.963830161 1.247055678 1.711809808 1.045763623 1.514304813 1.206619912 1.541362762 1 18.22033268 4.523366099 0.133515959 0.844181954 2.524695332 0.319611971 0.247997666 27.64278836 0.665208531 1.633562307 8.642007032 33370.7601 -4.523366099 1.680513378 LSPFFTLDLS(ph)PTEDKSSKPSSFTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPFFTLDLSPTEDKSSKPSSFTEK 25 2 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.966)PT(0.034)EDKSSKPSSFTEK 150.14 9.19E-08 297040000 1206900 1033600 1098100 1148500 563120 1239100 1313200 1335800 632020 TRUE FALSE 1149852.229 1138925.015 1148448.971 1033050.598 661327.9497 1196189.656 1112847.221 1218830.27 730030.4337 1.575074375 1.560106213 1.573152184 1.415078811 0.905890932 1.638547657 1.524384697 1.669560904 1 19.47759708 3.213167397 6.390228569 1.391704774 1.568607277 0.131253779 0.24622183 0.397084858 53.56289273 0.068998929 0.085096864 1633.681524 -3.213167397 0.176902503 LSPFFTLDLSPT(ph)EDKSSKPSSFTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPFFTLDLSPTEDKSSKPSSFTEK 25 2 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.187)PT(0.812)EDKS(0.001)SKPSSFTEK 137.5 0.00090652 331980000 911180 720970 821200 836770 438280 968850 982850 1013400 496790 TRUE FALSE 868110.3272 794437.6627 858852.8323 752656.2898 514715.8932 935298.4816 832898.1812 924661.3236 573829.6559 1.512836289 1.384448598 1.496703461 1.311637142 0.896983779 1.62992357 1.451472876 1.611386435 1 19.130263 3.236869196 24.99797149 1.348852848 1.454355962 0.069830391 0.234716093 167.1729059 2470707.005 0.065015308 0.081609694 1725.318169 -3.236869196 0.105503113 LSPLEACAHSFFDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSPLEACAHSFFDELR 16 0 P49840;A8MT37 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 ; 134.88 2.59E-05 71165000 58741 48088 55193 59486 81001 48997 66555 58618 81521 FALSE TRUE 55964.42934 52988.22187 57723.65364 53506.35426 95127.54875 47300.2216 56400.81238 53485.09717 94162.86033 0.594336548 0.562729527 0.613019331 0.568232041 1.010244893 0.502323543 0.598970891 0.568006292 1 16.52287052 -1.9615306 2.385536827 1.306415413 0.621468321 0.412139949 0.139761263 11575766.52 5112754.264 19622330.23 0.032663168 0.010926206 1.9615306 -0.684947092 LSPPYSS(ph)PQEFAQDVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSPPYSSPQEFAQDVGR 17 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LSPPYS(0.006)S(0.994)PQEFAQDVGR;LSPPYS(0.027)S(0.972)PQEFAQDVGR;LSPPYS(0.075)S(0.925)PQEFAQDVGR;LSPPYS(0.012)S(0.988)PQEFAQDVGR 207.43 6.39E-12 322489000 172362 142841 141582 182972 161386 158289 180551 173004 184791 TRUE FALSE 164214.7898 157396.6603 148073.6747 164579.3069 189531.6673 152807.4122 153004.6289 157854.8526 213447.4445 0.769345308 0.737402411 0.69372428 0.771053068 0.887954727 0.715901812 0.716825771 0.73954904 1 17.70352136 -1.754649617 2.496239292 1.060568609 0.75180045 0.678659155 0.053185897 19789497.68 14183265.21 7376088.604 0.013504005 0.017593425 1.754649617 -0.308768159 LSPQDPRPLS(ph)PGALQLAGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSPQDPRPLSPGALQLAGEK 20 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 LSPQDPRPLS(1)PGALQLAGEK;LSPQDPRPLS(1)PGALQLAGEK 150.48 5.26E-08 285330000 1104100 949930 1047130 1185320 845380 1137110 1259720 1307410 1050660 TRUE FALSE 1051911.381 1046728.947 1095141.946 1066169.382 992814.0043 1097731.596 1067526.578 1192926.249 1213590.987 0.866775868 0.862505538 0.90239789 0.878524473 0.81807958 0.904531764 0.879642803 0.982972239 1 20.21085085 1.220109835 2.959325551 1.002512341 0.870923901 0.80892714 0.023944025 0.097124097 1.468664705 0.020537802 0.005785616 16.60006679 -1.220109835 -0.131588439 LSPS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LSPS(0.988)PS(0.012)SR;LSPS(0.755)PS(0.227)S(0.018)R;LS(0.006)PS(0.777)PS(0.216)S(0.002)R;LS(0.003)PS(0.997)PSSR;LS(0.015)PS(0.96)PS(0.024)SR 185.27 0.00022409 4882400000 5466700 5303800 5232150 6032040 5458640 5389390 6158930 5673550 5725640 TRUE FALSE 5208299.925 5844263.25 5472049.253 5425687.879 6410625.088 5202754.073 5219272.112 5176743.885 6613543.009 0.787520383 0.883681144 0.82740057 0.820390504 0.969317819 0.786681823 0.789179432 0.782748956 1 22.65699193 4.722096468 4.332435716 0.845684216 0.784180732 0.058444549 0.076124842 0.627011224 25.11296699 0.016875629 0.112677125 52734.69863 -4.722096468 -0.061503484 LSPS(ph)PTSQR ddPTM_SK-BR-3_Trastuzumab_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 LSPS(0.999)PT(0.001)SQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LS(0.018)PS(0.98)PT(0.002)SQR;LSPS(1)PTSQR 255.13 6.33E-15 97092700000 20237490 16880980 17605970 20835540 18969560 18615640 22158370 19433700 21185550 TRUE FALSE 19280903.95 18601171.05 18413221.14 18741111.93 22277845.26 17970975.72 18777703.69 17731982.2 24470896.89 0.787911618 0.760134422 0.752453873 0.765853087 0.910381232 0.734381572 0.767348405 0.724615133 1 24.54456364 -1.857309518 2.471613482 1.09969826 0.775391556 0.655647694 0.051157299 9345765.954 5616087.051 5487060.678 0.011738534 0.013889624 1.857309518 -0.324306704 LSPS(ph)PTTEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LS(0.001)PS(0.978)PT(0.017)T(0.005)EDPR 94.191 0.009113 335500000 239700 238650 201050 288900 194560 222600 216580 246170 221080 TRUE FALSE 228369.856 262968.7063 210268.3414 259859.2231 228491.2024 214891.3062 183536.7432 224614.0498 255363.9573 0.894291655 1.029780041 0.823406496 1.017603369 0.894766845 0.841509931 0.718726108 0.879583995 1 17.96219539 2.359098591 3.520131257 0.823670167 0.94506565 0.092744426 0.091634921 0.294713542 7.112502976 0.031126426 0.025233851 228.6117724 -2.359098591 0.121395483 LSPSPS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LS(0.036)PS(0.25)PS(0.707)S(0.008)R 114.39 0.0027951 115770000 170860 175760 166340 201890 180220 166120 195160 175860 199530 TRUE FALSE 162783.7864 193670.1438 173966.8535 181595.6336 211650.3109 160367.2227 165384.7576 160460.7661 230472.0933 0.706305844 0.840319281 0.754828279 0.787928946 0.91833379 0.695820567 0.71759125 0.696226445 1 17.81423255 -2.206509578 2.421996695 1.739590317 0.766234243 0.522107624 0.070742377 11977954.82 2479237.601 48555819.46 0.01791184 0.006215705 2.206509578 -0.973356074 LSPT(ph)SLVHPVMSTLPELSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.261)PT(0.369)S(0.369)LVHPVMSTLPELSCK 195.09 4.99E-18 162700000 692880 822430 548160 832430 460080 643900 604020 709630 379380 TRUE FALSE 660128.9356 906236.552 573293.6782 748752.5549 540317.8063 621601.5815 511865.6554 647491.0352 438212.3128 1.506413481 2.068030782 1.308255522 1.70865248 1.23300462 1.418494103 1.168076844 1.477573807 1 18.7412705 2.95071481 0.983463878 1.242138842 1.758289378 0.391369216 0.232603859 0.458669869 0.963651612 0.105712779 0.122952148 892.7190647 -2.95071481 0.516150536 LSQELEYLTEDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSQELEYLTEDVKR 14 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;;; 274.38 7.86E-33 321338000 436196 365472 414605 493827 368784 475002 538049 540672 431987 FALSE TRUE 415577.8795 402714.0123 433615.0494 444186.5718 433099.8128 458552.5616 455959.7431 493327.8934 498977.3377 0.832859227 0.807078763 0.869007501 0.890193879 0.867974916 0.918984745 0.91378848 0.988677954 1 18.92861477 2.069266424 0.409610159 1.009056536 0.807299728 0.879570152 0.021211563 0.337155583 0.137319013 0.022469445 0.022771612 117.2914685 -2.069266424 -0.201756808 LSQIGVENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSQIGVENTEENRR 14 1 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 194.67 1.88E-07 256030000 172000 147360 141490 180640 164010 153150 195250 160500 178380 FALSE TRUE 163869.9009 162376.1515 147977.4565 162481.724 192613.2921 147846.3771 165461.0265 146445.7691 206042.2594 0.795321801 0.788072078 0.718189836 0.788584461 0.934824209 0.717553659 0.803044128 0.710755986 1 17.65258074 -1.002364664 4.569516705 1.000004527 0.784706601 0.529885288 0.064475059 3.56E-06 7.77E-07 0.056906158 0.01341254 0.099456996 1.002364664 -0.215297926 LSQSSQDSS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LSQSSQDSSPVR 12 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 LSQSSQDSS(1)PVR;LSQSSQDS(0.004)S(0.996)PVR;LSQSSQDS(0.036)S(0.964)PVR;LSQSSQDS(0.017)S(0.983)PVR;LSQS(0.001)S(0.002)QDS(0.182)S(0.815)PVR;LSQSSQDS(0.167)S(0.832)PVR 200.81 1.63E-07 1624360000 2324394 2106798 2060131 2326927 2137439 2155891 2400470 2301888 2591660 TRUE FALSE 2214524.502 2321483.111 2154590.044 2093019.877 2510207.685 2081231.954 2034234.214 2100322.484 2993561.396 0.739762513 0.775492066 0.719741391 0.69917386 0.838535561 0.695236101 0.679536493 0.701613298 1 21.51343143 -2.171152487 2.499644179 1.717716008 0.732011701 0.766641215 0.046615436 10370403.72 1525590.252 42440296.21 0.011331639 0.006742912 2.171152487 -0.985704306 LSQYLDSSQVKPLFQFFVPDALNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSQYLDSSQVKPLFQFFVPDALNDR 25 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 149.04 1.83E-07 32029000 53373 52654 44063 59962 43399 52288 56619 60603 42459 FALSE TRUE 50850.16407 58019.50246 46083.33213 53934.50584 50967.77186 50477.25345 47980.73167 55296.28004 49043.32487 1.036841695 1.18302547 0.939645349 1.099731839 1.039239733 1.029237997 0.978333582 1.127498598 1 15.58176917 3.74596804 24.99357898 1.029604762 1.109933574 0.20999744 0.064011028 757.4801188 2555826.35 0.015123913 0.026582142 5571.447469 -3.74596804 0.080328812 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR 30 2 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 94.15 0.00050776 77086000 77702 62456 78385 71924 73524 76212 100690 86507 69520 FALSE TRUE 74029.18045 68820.33741 81979.02978 64694.06287 86346.56232 73572.75933 85327.8912 78931.98848 80300.80654 0.921898342 0.857031708 1.020899208 0.805646489 1.075288855 0.91621445 1.062603165 0.982953869 1 16.29312686 2.728396256 24.98870215 1.007889475 0.902901012 0.370327665 0.0686954 692.764868 1703133.721 0.019478029 0.018559651 535.0523254 -2.728396256 -0.104988463 LSS(ph)AGPRS(ph)PYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 2 LS(0.034)S(0.966)AGPRS(0.905)PY(0.095)CK 101.78 0.0014093 187560000 450380 444090 453710 548590 329890 534180 571720 545200 413420 TRUE FALSE 429091.43 489343.2759 474513.0523 493444.6909 387422.7116 515681.2127 484493.6136 497459.3977 477531.0621 0.898562343 1.024736011 0.993679972 1.033324803 0.811303687 1.079890406 1.014580311 1.041732019 1 18.86523505 LSS(ph)ATANALYSSNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSSATANALYSSNLR 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LS(0.017)S(0.983)ATANALYSSNLR;LS(0.005)S(0.995)ATANALYSSNLR 331.84 7.09E-69 461283000 511858 414970 405087 596350 498503 435875 475699 391310 389541 TRUE FALSE 487663.4867 457255.9148 423660.6396 536403.765 585441.7654 420780.5395 403122.3807 357044.8219 449949.0288 1.083819401 1.016239364 0.94157474 1.1921434 1.301129079 0.935173792 0.895928994 0.793522819 1 18.77940205 2.022564191 24.99935818 0.892578148 1.091295706 0.463243127 0.107325393 216.9144741 240323.2512 0.040883684 0.030192702 105.3329363 -2.022564191 0.198717558 LSS(ph)GFDDIDLPSAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.145)S(0.855)GFDDIDLPSAVK;LS(0.348)S(0.652)GFDDIDLPSAVK;LSS(1)GFDDIDLPSAVK;LS(0.017)S(0.983)GFDDIDLPSAVK 393.38 1.30E-114 568236000 794050 709782 652541 937407 485634 813802 882249 736388 514063 TRUE FALSE 756516.8302 782109.5928 682460.6503 843177.0674 570328.4158 785619.8327 747645.7114 671905.9629 593781.2646 1.274066521 1.317167852 1.149346891 1.42001292 0.960502545 1.323079524 1.259126476 1.131571511 1 19.17957205 -4.999999998 0.150063722 0.114420343 1.319446474 0.288967272 0.122755336 160.047377 1.425935408 42.02457215 0.552279699 1.00E-05 4.999999998 1.205026131 LSS(ph)LRAS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.363)S(0.637)LRAS(0.954)T(0.039)S(0.007)K;LS(0.446)S(0.554)LRAS(0.914)T(0.068)S(0.018)K;LS(0.432)S(0.568)LRAS(0.736)T(0.224)S(0.04)K;LS(0.185)S(0.815)LRAS(0.955)T(0.038)S(0.007)K;LS(0.427)S(0.573)LRAS(0.956)T(0.037)S(0.007)K 109.07 0.0011761 3763120000 10427100 10353610 8246560 11750680 5493950 10510920 9905860 10397680 5648280 TRUE FALSE 9934231.648 11408654.63 8624672.933 10569479.32 6452093.141 10146924.2 8394539.123 9487204.018 6524186.415 1.522677467 1.748670854 1.321953786 1.620045573 0.988949844 1.555278093 1.286679839 1.454158942 1 22.63736657 2.726163175 0.051409202 2.81E-17 2.867191944 0.364661854 0.198619825 82.73209151 1.70818513 40.68705218 53.50237405 532.308223 -2.726163175 2.867191944 LSS(ph)LRAS(ph)TSKSESSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSLRASTSKSESSQK 16 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.035)S(0.965)LRAS(0.969)T(0.028)S(0.001)KS(0.001)ESSQK 133.74 0.00015761 584780000 1842300 1032300 1656200 1541400 974160 1899400 2225600 2038800 1280300 TRUE FALSE 1755218.13 1137492.544 1732138.408 1386455.544 1144053.196 1833623.302 1886043.844 1860271.864 1478842.385 1.186886546 0.769177672 1.171279932 0.937527594 0.773614015 1.239904482 1.275351493 1.257924362 1 20.49603687 2.208405065 24.94726795 1.223419626 0.96843501 0.330690212 0.156899387 197.2410355 163173.5735 0.054633019 0.040354197 161.5864965 -2.208405065 -0.254984616 LSS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.001)S(0.999)PVK;LS(0.019)S(0.981)PVK;LS(0.016)S(0.984)PVK;LS(0.012)S(0.988)PVK 125.5 0.018774 982080000 5736880 7467300 5877980 7896600 3267520 7227000 6003950 7210100 3662130 TRUE FALSE 5465709.052 8228226.36 6147491.197 7102818.765 3837374.453 6976727.178 5087937.157 6578745.421 4230034.417 1.292119286 1.94519135 1.453295787 1.67913971 0.907173341 1.649331067 1.202812237 1.555246311 1 22.01223797 LSS(ph)PVKRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSPVKRPR 9 2 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.072)S(0.928)PVKRPR 59.265 0.081443 572980000 552340 493580 558780 557070 455030 645810 708330 649460 555590 TRUE FALSE 526231.9828 543876.3632 584400.6157 501072.2652 534387.0879 623445.4378 600261.2491 592589.8394 641748.0596 0.819997778 0.847492026 0.910638695 0.780792801 0.832705421 0.971480051 0.935353431 0.923399503 1 19.2916475 2.243079087 24.99952463 0.951058761 0.838581045 0.710315767 0.037734488 62.06650733 343399.7075 0.01267932 0.010274123 175.0165372 -2.243079087 -0.112477716 LSS(ph)PVLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.109)S(0.891)PVLHR;LS(0.049)S(0.951)PVLHR;LS(0.004)S(0.996)PVLHR;LS(0.202)S(0.798)PVLHR;LS(0.002)S(0.998)PVLHR;LS(0.026)S(0.974)PVLHR;LS(0.242)S(0.758)PVLHR;LS(0.212)S(0.788)PVLHR 153.97 0.0002786 7325870000 2659500 2420550 2382100 2642390 2314070 2418076 2800760 2574940 2266352 TRUE FALSE 2533790.706 2667206.797 2491321.641 2376771.937 2717643.075 2334337.422 2373452.623 2349464.603 2617806.293 0.96790611 1.018870955 0.95168296 0.90792506 1.038137574 0.891715108 0.906657085 0.89749368 1 21.31992692 2.214400154 24.99999336 0.914292698 0.97752735 0.233724883 0.046168635 269.9013889 279278.2785 0.016025742 0.011841741 163.8325361 -2.214400154 0.063234653 LSS(ph)SASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSSASR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.127)S(0.436)S(0.436)ASR;LS(0.123)S(0.518)S(0.359)ASR 76.064 0.043817 168058000 512330 509050 452060 589750 490370 505790 552950 574220 637550 TRUE FALSE 488113.1762 560922.7737 472787.3981 530467.2095 575890.3727 488274.3655 468587.3219 523938.2527 736417.9978 0.662820813 0.761690745 0.642009565 0.72033439 0.782015614 0.663039696 0.636306178 0.71146856 1 19.49016536 0.944417867 22.75039661 1 0.695779943 0.795518721 0.048270483 3444.035146 1409684.451 0.04649938 0.011624845 8.798686965 -0.944417867 -0.304220057 LSS(ph)SLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LS(0.084)S(0.7)S(0.217)LGR 98.523 0.011748 113080000 444850 409900 438410 485120 434090 418640 517540 507090 494070 TRUE FALSE 423822.8221 451669.276 458511.5321 436354.8159 509795.1586 404142.3918 438579.7677 462686.5113 570687.8522 0.742652609 0.791447153 0.803436643 0.764612063 0.893299475 0.708167153 0.768510782 0.81075234 1 19.12234233 0.8114284 4.15018245 0.99999235 0.780070657 0.67075975 0.047666044 1.02575916 22.0128293 0.042334908 0.010793814 6.477812893 -0.8114284 -0.219921693 LSS(ph)T(ph)SSEETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.46)S(0.535)T(0.422)S(0.313)S(0.27)EETQLFHIPR;LS(0.138)S(0.714)T(0.455)S(0.369)S(0.323)EET(0.001)QLFHIPR 86.479 0.012058 47505000 67338 52446 48526 71017 66888 57818 73922 62304 57438 TRUE FALSE 64155.06619 57790.30703 50750.9651 63878.23624 78553.24602 55815.74816 62643.84123 56848.33147 66345.19169 0.966988934 0.871054941 0.764953176 0.962816364 1.184008125 0.841293042 0.94421072 0.856856843 1 16.01770429 5.722765143 2.80973671 0.924999474 5.605716347 0.010798619 0.112888468 1638.880805 128.3352423 0.02690369 48194.87093 528159.5575 -5.722765143 4.680716873 LSS(ph)TDDGYIDLQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LSSTDDGYIDLQFK 14 0 Q96A57;Q96A57-2;Q5JWB9;A0A087WTT2 Q96A57 TMEM230 Transmembrane protein 230 1 LS(0.021)S(0.959)T(0.021)DDGYIDLQFK;LSS(0.999)T(0.001)DDGYIDLQFK;LS(0.006)S(0.965)T(0.028)DDGYIDLQFK;LS(0.018)S(0.974)T(0.009)DDGYIDLQFK;LS(0.002)S(0.997)T(0.001)DDGYIDLQFK 302.13 6.30E-44 460936000 1344150 1104454 1193720 1824356 1214087 1602914 1698111 1405364 1131027 TRUE FALSE 1280614.693 1216999.118 1248453.243 1640968.269 1425823.388 1547404.686 1439032.979 1282302.878 1306420.891 0.980246644 0.931552095 0.955628658 1.256079324 1.091396654 1.18446107 1.101507936 0.981538865 1 20.31718834 3.335972612 14.30792428 1.112117359 0.953887504 0.425614904 0.079802574 0.645320542 91.70035308 0.020336987 0.027536152 2167.567408 -3.335972612 -0.158229854 LSS(ph)TSS(ph)EETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.084)S(0.796)T(0.126)S(0.129)S(0.863)EET(0.002)QLFHIPR 92.063 0.0025875 31883000 42780 35691 35161 53530 48155 41540 54186 41403 39530 TRUE FALSE 40757.87418 39327.95348 36773.16663 48149.0627 56553.21675 40101.45938 45918.93051 37777.53383 45660.11051 0.892636346 0.861319717 0.805367447 1.054510429 1.238569424 0.878260235 1.005668405 0.827364047 1 15.47864673 3.23748827 24.99985733 1.003784023 0.86051445 0.285223793 0.109883343 37.02005302 863064.6538 0.030595635 0.038589562 1727.779314 -3.23748827 -0.143269572 LSS(ph)TSSEETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.349)S(0.593)T(0.023)S(0.03)S(0.005)EETQLFHIPR 149.36 5.43E-07 38464000 37141 27015 34905 46189 32709 32943 37257 34296 26209 TRUE FALSE 35385.41854 29767.85921 36505.42878 41545.99397 38413.43924 31802.17565 31572.76038 31292.86043 30273.35786 1.168863352 0.983302194 1.205859916 1.372361604 1.268885976 1.050500437 1.042922312 1.03367656 1 14.88576108 2.11508883 8.023126737 1.034502164 1.175418036 0.40895134 0.098147802 0.334640919 22.15860275 0.042499238 0.031355488 130.3433355 -2.11508883 0.140915872 LSSAGPRS(ph)PYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSSAGPRS(1)PYCK;LSSAGPRS(0.998)PY(0.002)CK;LSSAGPRS(1)PYCK;LSSAGPRS(1)PYCK;LS(0.002)S(0.004)AGPRS(0.992)PY(0.001)CK;LSS(0.001)AGPRS(0.998)PY(0.001)CK;LSSAGPRS(1)PYCK;LSS(0.001)AGPRS(0.997)PY(0.002)CK 149.3 0.00017666 12431665000 13956880 12796143 13411137 15163640 10556836 14120880 15947450 15078120 12521630 TRUE FALSE 13297165.94 14100084.52 14026050.9 13639362.1 12397944.86 13631870.38 13514373.61 13757799.88 14463420.43 0.919365236 0.974878978 0.969760297 0.943024658 0.857193146 0.942506681 0.934382961 0.951213439 1 23.78590544 0.811756874 2.70473014 0.99998603 0.936623601 0.29037943 0.032066932 1.161882993 13.94374325 0.030907188 0.008191816 6.482714184 -0.811756874 -0.063362429 LSSAGPRS(ph)PYCKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSSAGPRSPYCKR 13 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSS(0.004)AGPRS(0.993)PY(0.002)CKR;LSSAGPRS(1)PYCKR;LSSAGPRS(1)PYCKR 181.51 6.25E-06 3105680000 1412380 1048780 1559910 1345310 1321440 1493440 1974000 1675320 1863750 TRUE FALSE 1345619.596 1155651.874 1631433.416 1210076.883 1551898.718 1441721.798 1672830.045 1528620.099 2152770.831 0.625064023 0.536820667 0.757829581 0.562102043 0.720884311 0.66970519 0.777059044 0.710070983 1 21.03776332 -4.514471311 0.118876543 2.03639953 0.477376499 0.743077275 0.065785981 57.27687512 0.496030882 14.46453453 0.584779729 3.06E-05 4.514471311 -1.559023032 LSSAHNGGSAFGAAGYGGAQPTPPMPT(ph)RPVSFHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.036)PPMPT(0.482)RPVS(0.482)FHER 98.009 0.00016494 140630000 35286 29676 34179 36788 44689 33768 42308 34951 39861 TRUE FALSE 33618.10071 32700.01814 35746.14096 33090.00035 52482.74745 32598.60569 35853.13756 31890.50515 46042.4403 0.730154625 0.710214705 0.776373727 0.718684764 1.139877624 0.708012118 0.778697596 0.692632818 1 15.49067668 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVS(ph)FHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.001)PPMPT(0.117)RPVS(0.883)FHER 276.96 4.62E-74 179520000 132660 121970 116870 139950 127690 111930 144820 111390 127320 TRUE FALSE 126389.4247 134398.8817 122228.6051 125881.9601 149959.0956 108053.836 122725.0492 101636.1011 147064.1353 0.859417046 0.913879386 0.831124494 0.855966411 1.019685019 0.734739546 0.834500192 0.691100525 1 17.16608593 2.2083696 24.9999032 0.802474412 0.890353848 0.14680081 0.094258475 333.1079793 275830.6241 0.031103322 0.022974184 161.5733018 -2.2083696 0.087879435 LSSANGHEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSANGHEER 10 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;F8WF24;F2Z2Z5;A8MYG5;H0Y6I9;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 99.215 0.0055253 0 120120 75475 104540 96666 123320 108010 119990 112060 119180 FALSE TRUE 114442.1657 83165.98831 109333.2624 86948.95003 144826.969 104269.5866 101683.3217 102247.4323 137661.8257 0.831328257 0.604132539 0.794216275 0.631612646 1.052048876 0.757432833 0.738645744 0.742743544 1 17.07076902 LSSCDSFTSTINELNHCLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSCDSFTSTINELNHCLSLR 21 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 322.15 4.36E-67 380700000 908500 975080 914080 949310 730890 898770 861240 953920 767090 FALSE TRUE 865557.0055 1074441.761 955991.4721 853883.5552 858356.9846 867645.3695 729842.0202 870389.7078 886046.3994 0.976875484 1.212624713 1.078940643 0.963700722 0.968749475 0.979232431 0.823706321 0.982329716 1 19.75702272 3.212628684 3.368152065 0.935460429 1.102554989 0.420800174 0.074425684 0.190872764 4.501407916 0.022019437 0.028367733 1631.656307 -3.212628684 0.16709456 LSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LS(0.002)S(0.002)ERPS(0.498)S(0.498)DGEGVVENGITTCNGK 138.52 3.64E-06 95140000 29938 30309 29628 38321 25445 32002 35447 33879 31361 TRUE FALSE 28522.89007 33397.52156 30986.47311 34468.90027 29882.59994 30893.76272 30038.90912 30912.37516 36224.30371 0.787396503 0.921964486 0.855405624 0.951540727 0.824932349 0.852846281 0.829247385 0.853360092 1 15.14467034 -1.240965893 6.266714038 1.000002454 0.859862039 0.4697503 0.046882413 1.51E-06 1.83E-07 0.042750153 0.010076131 0.057416155 1.240965893 -0.140140416 LSSERPSS(ph)DGEGVVENGITTCNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LSSERPS(0.145)S(0.855)DGEGVVENGITTCNGK 147.23 1.10E-07 129740000 106630 80760 95114 112850 88756 104540 109850 107990 110020 TRUE FALSE 101589.8112 88989.53582 99475.07098 101506.1036 104235.0183 100919.7536 93090.36497 98533.82311 127081.3397 0.799407777 0.700256513 0.782766937 0.798749083 0.820222847 0.794135109 0.732525839 0.77536028 1 16.95539268 -2.314876729 2.029438804 2.000086642 0.770392048 0.799039906 0.035313736 2696547.947 348446.0019 12349636.42 0.009228886 0.004843098 2.314876729 -1.229694594 LSSESHHGGS(ph)PIHWVLPAGMSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LSSESHHGGSPIHWVLPAGMSAK 23 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LSSES(0.008)HHGGS(0.992)PIHWVLPAGMSAK;LS(0.05)S(0.05)ES(0.298)HHGGS(0.602)PIHWVLPAGMSAK;LSSESHHGGS(1)PIHWVLPAGMSAK;LS(0.001)S(0.001)ES(0.004)HHGGS(0.995)PIHWVLPAGMSAK;LSSES(0.011)HHGGS(0.988)PIHWVLPAGMSAK;LSSESHHGGS(1)PIHWVLPAGMSAK;LS(0.024)S(0.024)ES(0.205)HHGGS(0.747)PIHWVLPAGMSAK;LS(0.083)S(0.083)ES(0.074)HHGGS(0.76)PIHWVLPAGMSAK 258.05 2.08E-43 6542810000 6398350 4882670 5751740 6860220 7256770 5837940 8985420 7574380 2082925 TRUE FALSE 6095912.676 5380219.624 6015462.968 6170617.652 8522348.39 5635770.674 7614529.15 6911127.133 2405934.371 2.533698653 2.236228756 2.500260623 2.56474895 3.54221981 2.342445722 3.164894788 2.872533522 1 21.19816586 3.143116022 3.89103999 2.75729932 2.396478877 0 0.676777358 0.660438801 18.90474798 0.175464296 0.215904809 1390.324006 -3.143116022 -0.360820443 LSSEVEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSSEVEALRR 10 1 P15924 P15924 DSP Desmoplakin 0 ;; 139.43 6.59E-05 550610000 197368 197401 206855 204342 324528 201209 248252 224177 323435 FALSE TRUE 188038.8058 217516.3863 216339.5064 183801.1539 381125.5805 194241.0819 210376.5979 204546.8734 373591.6479 0.503327114 0.582230324 0.579080147 0.491984109 1.020166223 0.519928866 0.563119114 0.547514578 1 18.51110268 -2.33574035 2.125432696 3.089749277 0.595953273 0.403465248 0.152396765 5385103.186 606683.1533 54105881.12 0.035127725 0.004615935 2.33574035 -2.493796004 LSSGNEENKKEEDNDEIKIGTSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSGNEENKKEEDNDEIKIGTSCK 24 3 Q9UHD1-2;Q9UHD1;E9PPQ5 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 89.829 0.0043825 67196000 55689 38975 52471 52540 30082 59005 66669 68405 30182 FALSE TRUE 53056.69133 42946.59681 54876.84725 47258.57938 35328.29128 56961.64205 56497.41959 62415.09556 34862.47041 1.52188559 1.231886218 1.574095198 1.355571732 1.013361671 1.633895745 1.620579922 1.790323371 1 15.08938718 LSSGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_SK-BR-3_Trastuzumab_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 320.66 7.02E-105 158840000 28559 24042 34954 34723 26898 29354 42021 30331 20119 TRUE FALSE 27209.07267 26491.90713 36556.67547 31232.57807 31589.00268 28337.46362 35609.92468 27675.05685 23238.95177 1.17083907 1.139978576 1.573077643 1.343975339 1.359312718 1.219395087 1.53233782 1.190890928 1 14.50425737 LSSLFFSTPS(ph)PPEDPDCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSSLFFSTPSPPEDPDCPR 19 0 Q5JX66;Q5JX65;Q8IXH6 Q5JX66 TP53INP2 Tumor protein p53-inducible nuclear protein 2 1 LSSLFFST(0.003)PS(0.996)PPEDPDCPR;LSSLFFST(0.003)PS(0.997)PPEDPDCPR;LSSLFFS(0.001)T(0.027)PS(0.972)PPEDPDCPR 222.3 2.59E-19 111253000 169763 174494 184978 190439 200450 175655 205880 207327 232256 TRUE FALSE 161738.6394 192275.137 193459.4243 171295.7099 235408.4165 169572.0233 174469.2248 189172.3488 268273.0743 0.602888083 0.716714257 0.721128741 0.638512495 0.877495504 0.632087375 0.650341915 0.705148473 1 18.03334274 0.941006365 20.902841 1 0.687932207 0.61688204 0.076063677 1934.811604 685551.5503 0.068573256 0.017143314 8.729841626 -0.941006365 -0.312067794 LSSLRAS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 LSSLRAS(0.621)T(0.28)S(0.099)K;LSSLRAS(0.96)T(0.015)S(0.025)K 105.08 0.0015727 638780000 1122700 899520 932030 992910 657290 1015520 1089290 1086060 776610 TRUE FALSE 1069632.196 991182.1107 974764.4974 893100.8004 771921.1679 980352.2878 923098.8043 990958.8288 897042.7124 1.19239829 1.104944165 1.086642234 0.995605658 0.86051774 1.092871359 1.029046657 1.104695256 1 19.77481715 3.848065735 1.527325799 1.017029417 1.174882345 0.418807304 0.067826027 0.391123749 1.740687006 0.020148975 0.054636084 7047.997394 -3.848065735 0.157852929 LSSPAAFLPACNS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_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(0.972)PS(0.028)K;LSSPAAFLPACNS(0.997)PS(0.003)K 306.2 1.52E-46 257930000 613300 687550 537200 746900 355670 619190 565900 658940 362820 TRUE FALSE 584310.5244 757612.1267 561831.1514 671820.193 417698.7354 597747.295 479561.5615 601239.7203 419084.2726 1.394255434 1.807779906 1.340616168 1.603067061 0.996693894 1.426317651 1.144308181 1.434651118 1 18.67688086 2.759527053 24.72676909 1.222564404 1.554979053 0.427302955 0.191826573 624.5796163 736596.9129 0.052716888 0.055860496 574.8136236 -2.759527053 0.332414649 LSSS(ph)LGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LSS(0.001)S(0.999)LGR;LSS(0.001)S(0.998)LGR;LSS(0.003)S(0.997)LGR;LSS(0.003)S(0.997)LGR;LSS(0.073)S(0.927)LGR;LS(0.02)S(0.176)S(0.804)LGR;LS(0.003)S(0.169)S(0.828)LGR;LSS(0.003)S(0.997)LGR;LS(0.004)S(0.248)S(0.748)LGR;LS(0.033)S(0.271)S(0.695)LGR 154.12 0.0017834 10705950000 13441890 12009470 11795940 13874900 13232520 13299660 15391500 13881270 15277740 TRUE FALSE 12806518.5 13233248.65 12336795.52 12480168.69 15540267.3 12839089.44 13043243.99 12665752.41 17646933.89 0.725707853 0.749889399 0.699090028 0.707214566 0.880621381 0.727553552 0.739122392 0.717731051 1 24.0729142 -2.169929223 2.3999011 1.65592554 0.743553801 0.714555255 0.050975122 2713231.685 524415.378 9723605.351 0.011562144 0.006761932 2.169929223 -0.912371739 LSSS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSSPGK 7 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 LS(0.057)S(0.26)S(0.683)PGK 71.708 0.056207 63335000 451490 401590 373210 469860 280990 469750 502460 517570 357580 TRUE FALSE 430148.9625 442512.4776 390322.0477 422628.7801 329994.567 453482.4397 425800.4987 472248.827 413031.6801 1.041443025 1.071376601 0.945017214 1.023235748 0.798957036 1.097936215 1.030914865 1.143371924 1 18.65589292 -0.605582855 7.619493456 1.000002241 1.020699312 0.003778414 0.093702132 0 0 0.085142974 0.020068391 0.24798028 0.605582855 0.020697071 LSSS(ph)PGLFGAFSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.028)S(0.972)PGLFGAFSVR;LSS(0.004)S(0.996)PGLFGAFSVR;LSS(0.03)S(0.97)PGLFGAFSVR;LS(0.023)S(0.136)S(0.841)PGLFGAFSVR 232.22 2.61E-13 350731000 691267 592990 537497 642352 678748 600660 771421 659066 761570 TRUE FALSE 658592.1789 653416.3552 562141.7691 577781.5566 797121.4363 579858.9936 653726.5583 601354.6871 879670.386 0.74868063 0.742796808 0.639036823 0.656815969 0.906159226 0.659177577 0.743149444 0.683613654 1 19.74660352 -1.335777899 4.763451529 1.000188272 0.725352613 0.5675762 0.07610316 0.000138858 1.94E-05 0.067242915 0.015838518 0.046155356 1.335777899 -0.274835659 LSSS(ph)SATLLNSPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.033)S(0.935)S(0.033)ATLLNSPDR;LSS(0.003)S(0.964)S(0.032)ATLLNSPDR;LSS(0.005)S(0.987)S(0.007)ATLLNSPDR;LSS(0.011)S(0.856)S(0.133)ATLLNSPDR;LSS(0.087)S(0.79)S(0.123)ATLLNSPDR;LSS(0.011)S(0.84)S(0.149)ATLLNSPDR;LSS(0.015)S(0.985)S(0.001)ATLLNSPDR;LS(0.002)S(0.084)S(0.902)S(0.012)AT(0.001)LLNSPDR 360.06 2.01E-82 2627481000 5196460 4664350 4832050 4986820 6032320 4728940 5928750 5179370 6931030 TRUE FALSE 4950833.634 5139652.568 5053604.272 4485535.379 7084354.698 4565175.622 5024210.299 4725836.905 8005858.734 0.618401323 0.641986418 0.631238252 0.560281605 0.884896291 0.57022935 0.627566694 0.590297314 1 22.93262473 -1.170729372 4.468690375 1.000067114 0.639948071 0.606872475 0.090902787 5.79E-05 1.07E-05 0.079411318 0.018713753 0.067494849 1.170729372 -0.360119043 LSSSS(ph)ATLLNSPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.002)S(0.01)S(0.986)AT(0.002)LLNSPDR 82.529 0.01097 36978000 69528 53369 72497 56731 127210 60809 99485 69424 169180 TRUE FALSE 66241.54923 58807.36178 75821.05916 51028.2921 149395.3837 58703.16908 84306.73608 63344.86652 195415.5703 0.338977847 0.300934883 0.387999068 0.261127054 0.764500922 0.300401698 0.431422818 0.324154654 1 17.5761859 -5 0.313779405 6.577042942 0.356049322 0.640260173 0.143285904 183.0244407 1.643941591 676.0878762 0.120761035 1.00E-05 5 -6.22099362 LSSSSATLLNS(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSSSSATLLNS(1)PDR;LSSSSAT(0.001)LLNS(0.999)PDR 240.78 2.17E-17 252910000 283040 212517 272180 263646 377570 227186 314920 261180 470040 TRUE FALSE 269661.2601 234172.7239 284659.7222 237143.8032 443418.0885 219318.4919 266873.1701 238309.6946 542931.4026 0.496676484 0.431311806 0.524301451 0.436784098 0.816711073 0.40395249 0.491541231 0.438931499 1 19.0504104 -1.980018614 2.638510391 1.44231392 0.500569367 0.639634005 0.1167165 12799377.02 7132357.805 34539084.46 0.025941089 0.010470837 1.980018614 -0.941744553 LSSTS(ph)SEETQLFHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.095)S(0.077)T(0.077)S(0.369)S(0.369)EET(0.012)QLFHIPR 94.45 0.0026333 33418000 36999 35830 28753 37251 24210 33721 33757 40636 22166 TRUE FALSE 35250.13059 39481.11774 30071.35349 33506.45871 28432.21633 32553.23331 28606.74966 37077.69642 25603.39007 1.376775907 1.542026959 1.174506712 1.308672743 1.110486395 1.271442306 1.1173032 1.448155745 1 14.64404723 8 0.118276022 0.966543755 2.560494464 0.318204088 0.137258406 90.97923368 0.741462053 0.899381142 23.86429077 99999999.99 -8 1.593950709 LSSTWEGIQAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSTWEGIQAGK 12 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 133.89 0.0005287 0 69313 70541 59519 75057 61556 73218 73287 76652 73965 FALSE TRUE 66036.71186 77729.2081 62248.00502 67512.12776 72291.34691 70682.4423 62105.72214 69939.94452 85435.11444 0.772945788 0.909803991 0.728599773 0.79021522 0.846154973 0.827323083 0.726934382 0.818632303 1 16.38254153 -1.705665651 6.176572155 1.002973492 0.804456184 0.566218392 0.054283558 0.002238542 0.000106674 0.052934063 0.012311748 0.019694019 1.705665651 -0.198517307 LSSWDQAET(ph)PGHT(ph)PSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LSSWDQAET(1)PGHT(1)PSLR;LSSWDQAET(1)PGHT(0.999)PS(0.001)LR 201.15 1.99E-11 198058000 241040 260180 209862 268060 257690 261690 240728 237370 196722 TRUE FALSE 229646.5169 286692.6378 219484.3803 241114.0995 302631.0544 252627.6097 204000.5223 216584.6244 227228.643 1.010640709 1.261692338 0.965918633 1.061107862 1.331834976 1.111777135 0.89777644 0.953157232 1 17.79378518 1.785603732 7.404360834 0.944011106 1.130982434 0.353036404 0.110400525 0.229621867 28.47206049 0.048804618 0.028024216 61.03848301 -1.785603732 0.186971328 LSSWDQAET(ph)PGHTPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LSSWDQAET(1)PGHTPSLR 206.34 2.60E-11 130740000 129520 160660 113400 148450 116470 126830 135590 130440 93822 TRUE FALSE 123397.8463 177031.4367 118599.5022 133527.524 136782.3311 122437.8453 114903.2552 119017.9821 108371.4366 1.138656552 1.633561778 1.094379718 1.232128393 1.262162203 1.12979812 1.060272511 1.098241251 1 16.72562503 2.420673323 0.664248691 1.021142736 1.356704535 0.328011676 0.144608466 0.746906372 0.662156763 0.115960368 0.089521751 263.4349076 -2.420673323 0.335561799 LST(ph)PQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.086)T(0.914)PQKK;LS(0.082)T(0.918)PQKK;LS(0.087)T(0.913)PQKK;LS(0.019)T(0.981)PQKK;LS(0.21)T(0.79)PQKK 106.2 0.0045449 3617540000 3528760 3676680 3233970 4055610 1919750 4069830 4205880 4457390 2304900 TRUE FALSE 3361962.508 4051337.872 3382250.723 3647932.378 2254553.792 3928890.767 3564195.76 4067077.301 2662332.12 1.262788546 1.521725198 1.270409014 1.370201843 0.846834163 1.475732775 1.338749487 1.527637093 1 21.34425912 3.618720139 18.86026394 1.279453782 1.392988585 0.055975992 0.213629261 9.358480233 1431.490619 0.053370115 0.082680576 4156.426828 -3.618720139 0.113534803 LSTDHIPILYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSTDHIPILYR 11 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 104.22 0.002629 649200000 998840 911570 894890 1114660 1202060 906700 1190640 1093200 1168380 FALSE TRUE 951626.8127 1004460.019 935921.5917 1002612.259 1411698.883 875300.7516 1008986 997473.6126 1349566.403 0.705135228 0.74428351 0.693497993 0.742914359 1.046038846 0.64857924 0.747637166 0.739106731 1 20.36406453 -2.712042272 1.914424152 6.661004505 0.754697558 0.334774094 0.106917877 2899688.234 85520.60499 71616242.5 0.024558555 0.001940697 2.712042272 -5.906306948 LSTGS(ph)FPEDLLESDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.338)T(0.291)GS(0.372)FPEDLLESDSSR;LST(0.003)GS(0.997)FPEDLLESDSSR;LS(0.002)T(0.148)GS(0.85)FPEDLLESDSSR 155.57 1.00E-07 23792200 64839 55113 57186 65065 55826 60945 67271 65571 58986 TRUE FALSE 61774.18897 60729.07736 59808.03466 58524.54258 65562.03672 58834.45937 57007.57343 59829.25563 68133.24762 0.906667319 0.891328088 0.877809832 0.858971862 0.962262024 0.863520549 0.836707121 0.878121295 1 16.05607136 LSTTPS(ph)PTSS(ph)LHEDGVEDFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.008)T(0.01)T(0.082)PS(0.894)PT(0.164)S(0.177)S(0.665)LHEDGVEDFRR;LST(0.002)T(0.01)PS(0.882)PT(0.267)S(0.238)S(0.6)LHEDGVEDFRR 135.58 2.23E-05 201690000 361670 291640 345790 365070 387040 320110 427560 380260 410310 TRUE FALSE 344574.5759 321358.4476 361644.8135 328372.47 454539.6535 309024.5104 362327.8693 346962.4185 473938.7792 0.727044485 0.678058985 0.763062297 0.692858412 0.959068288 0.652034659 0.764503529 0.732082779 1 18.85434119 -5 0.283007315 2.918891673 0.725019101 0.472355216 0.08393284 194.0489249 1.848939652 219.1733548 0.085537601 1.00E-05 5 -2.193872572 LSTTPS(ph)PTSSLHEDGVEDFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LS(0.051)T(0.047)T(0.077)PS(0.802)PT(0.017)S(0.005)S(0.002)LHEDGVEDFRR 60.472 0.026587 34835000 18690 16695 14830 17381 18674 15121 16710 16096 22307 TRUE FALSE 17806.56074 18396.23948 15509.97017 15633.82886 21930.73969 14597.35598 14160.5826 14686.54891 25766.25563 0.691080652 0.71396635 0.601948936 0.606755948 0.851141897 0.566529968 0.549578596 0.569991586 1 14.65319528 -0.902948642 4.425907091 1.000004602 0.646128622 0.604891839 0.090437111 5531541.459 1874796.249 254.8570966 0.021659293 0.125040689 0.902948642 -0.35387598 LSVDEAVDVGLVNEELRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSVDEAVDVGLVNEELRER 19 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 209.7 1.92E-16 116604000 128261 75214 110101 111265 149519 105424 144595 126796 160689 FALSE TRUE 122198.3567 82878.39211 115149.2398 100080.4308 175595.0663 101773.1404 122534.3771 115693.0701 185607.8294 0.658368546 0.446524225 0.620389992 0.539203713 0.946054198 0.548323531 0.660178924 0.623319988 1 17.50189804 -4.999999998 0.186650626 2.603313762 0.546847954 0.451775081 0.128675223 117.7803151 1.146360362 70.13877155 0.341888452 1.00E-05 4.999999998 -2.056465808 LSVDYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 88.942 0.042427 439910000 759500 815690 625920 823500 586790 719700 796600 795600 587730 FALSE TRUE 723599.9402 898809.7384 654619.0511 740720.2155 689125.9902 694776.6085 675064.0394 725933.0463 678872.1667 1.065885414 1.323974943 0.9642744 1.091104116 1.015104204 1.023427742 0.994390509 1.069322152 1 19.37278041 3.723479919 24.99998019 1.023084443 1.194930188 0.507073138 0.07067011 524.1171702 868853.7269 0.017453358 0.027161378 5290.295356 -3.723479919 0.171845745 LSVDYGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSVDYGKK 8 1 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 ; 94.85 0.016142 11162200000 19008700 13618600 13123400 13514900 13114900 15417000 20878500 17703600 13769200 FALSE TRUE 18110196.42 15006350.82 13725120.87 12156356.58 15402134.41 14883105.42 17693101.37 16153378.93 15904457.21 1.138686859 0.943531151 0.862973234 0.764336463 0.968416225 0.935782041 1.112461817 1.015651067 1 23.9229278 1.756848201 25 1.052093337 0.944033413 0.207224673 0.09724007 13.04564493 17852.08111 0.0488828 0.027108242 57.12789232 -1.756848201 -0.108059925 LSVEEFFMDLHNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSVEEFFMDLHNFR 14 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 254.89 2.88E-24 215170000 429200 533670 323580 465490 383030 340280 410760 422920 296830 FALSE TRUE 408912.5666 588051.5797 338416.4631 418698.0608 449830.3107 328496.0183 348091.0179 385886.8828 342860.8804 1.192648651 1.715131744 0.987037257 1.221189365 1.311990771 0.958102942 1.015254401 1.125491139 1 18.38726378 3.114417591 0.880265236 1.033836888 1.425925322 0.279348075 0.190594007 0.61464049 1.054182568 0.0939879 0.135458016 1301.420344 -3.114417591 0.392088434 LSVHDMKPLDS(ph)PGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 161.47 8.61E-07 1921860000 1894850 1415160 1760350 1989630 1633820 1839700 2400880 2167400 1994920 TRUE FALSE 1805284.196 1559366.413 1841063.789 1789628.612 1918757.691 1775990.728 2034581.661 1977610.966 2304282.005 0.783447595 0.676725509 0.798975032 0.776653469 0.832692217 0.770734972 0.882956885 0.858233047 1 21.13588586 1.146184752 0.347412132 1.020831059 0.721063523 0.778408962 0.039880872 0.588657263 0.220758667 0.066645016 0.042126459 14.00182845 -1.146184752 -0.299767536 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LSVPT(1)S(1)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR 186.13 1.14E-13 2058350000 3156670 2759380 2919760 3270160 2449240 3064670 3486570 3223740 2651930 TRUE FALSE 3007460.465 3040563.959 3053633.884 2941437.304 2876386.681 2958539.709 2954629.711 2941452.235 3063177.76 0.981810623 0.992617536 0.996884322 0.96025681 0.93902049 0.965840033 0.964563582 0.960261684 1 21.54659766 3.23184017 24.98784433 0.962228055 0.989672236 0.371119563 0.015326298 135.2699873 502957.6025 0.004004291 0.004891558 1705.454628 -3.23184017 0.027444181 LSVPT(ph)SDEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.5)S(0.5)DEEDEVPAPKPR;LSVPT(0.5)S(0.5)DEEDEVPAPKPR 271.43 3.75E-38 310470000 403070 384290 398860 433260 294370 423900 451910 420590 332240 TRUE FALSE 384017.6799 423449.5879 417148.1255 389707.8817 345708.0348 409220.2367 382962.8296 383760.9099 383762.0824 1.000666031 1.103416954 1.086996722 1.015493452 0.90083948 1.066338379 0.997917322 0.999996945 1 18.54985265 3.074969642 6.44924011 0.995493013 1.062530925 0.316394089 0.047310105 0.251355284 17.14702109 0.013300758 0.015935816 1188.419151 -3.074969642 0.067037912 LSVPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.002)S(0.998)DEEDEVPAPKPR;LSVPT(0.001)S(0.999)DEEDEVPAPKPR 268.93 3.57E-31 300010000 558770 540230 554910 635010 408240 610640 685080 603590 512250 TRUE FALSE 532358.0495 595280.0512 580353.1724 571177.5884 479436.9267 589493.3837 580558.4636 550736.4598 591687.1138 0.89972899 1.00607236 0.980844705 0.965337211 0.81028793 0.996292415 0.981191664 0.930790019 1 19.17447495 0.10185402 0.671028381 1.001509596 0.948662098 0.071038171 0.057754052 11.83348779 6.32732506 0.113041129 0.021051439 1.264311303 -0.10185402 -0.052847498 LSYLEEAVMHLDHSDPITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LSYLEEAVMHLDHSDPITR 19 0 Q6P2E9;Q6P2E9-2;I3L0V0;I3L3M2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 147.92 5.82E-08 41579000 42669 42074 36576 52289 56950 35606 42623 38269 23375.3 FALSE TRUE 40652.12093 46361.38843 38253.04578 47032.81038 66882.06197 34372.95529 36120.07852 34917.96348 27000.22214 1.505621721 1.717074333 1.416767817 1.741941608 2.477093026 1.273061944 1.33776968 1.293247267 1 14.72068366 2.064732383 24.99999999 1.262212013 1.735285146 0.454437773 0.294445017 61.11325592 23601.6229 0.108137917 0.079865135 116.0733138 -2.064732383 0.473073133 LSYLPATVEPAS(ph)PTPAHSLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LSYLPATVEPASPTPAHSLPR 21 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4 M0R344 SPHK2 Sphingosine kinase 2 1 LSYLPATVEPAS(0.786)PT(0.214)PAHSLPR 131.04 8.93E-06 82982000 33921 32150 33201 41442 34099 28908 46828 39756 34325 TRUE FALSE 32317.62155 35426.12155 34723.29869 37276.17143 40045.8548 27906.90871 39683.52854 36274.75388 39647.94569 0.815114655 0.893517203 0.875790614 0.940179139 1.010036059 0.703867709 1.00089747 0.914921397 1 15.2749585 7.999999044 0.038030396 1.287660464 0.279684036 0.181322551 0.085358805 1401.701657 4.066060208 30.40779738 93.35619441 99999779.93 -7.999999044 -1.007976428 LSYSGRPGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LSYSGRPGSR 10 1 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 LSYSGRPGS(1)R;LSYSGRPGS(1)R;LSYS(0.003)GRPGS(0.997)R 121.71 0.00030753 799310000 665950 542120 562990 676570 611660 576380 671430 634670 621740 TRUE FALSE 634471.8633 597362.6443 588803.6484 608559.8982 718333.3103 556419.8161 568991.0218 579094.9302 718156.2638 0.883473271 0.831800368 0.819882354 0.847392036 1.000246529 0.774789338 0.792294171 0.806363405 1 19.45393827 LT(ph)ELT(ph)QLY(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTELTQLYK 9 0 Q9BWW8 Q9BWW8 APOL6 Apolipoprotein L6 3 LT(1)ELT(1)QLY(1)K;LT(1)ELT(1)QLY(1)K 47.288 0.090497 460170000 383710 290690 419290 397650 1094440 285910 500470 239920 1095450 TRUE FALSE 365572.7887 320311.6415 438514.8612 357677.4665 1285309.989 276008.865 424114.1097 218911.3329 1265326.791 0.28891571 0.253145388 0.346562536 0.282675961 1.015792915 0.218132475 0.335181483 0.173007743 1 20.2710786 -1.392291305 3.111680673 1.00824349 0.3579915 0.413830709 0.237713592 57538770.92 73641740.24 4251938.661 0.054645032 0.040523663 1.392291305 -0.650251989 LT(ph)QTSSTEQLNVLETETEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.352)QT(0.233)S(0.155)S(0.104)T(0.155)EQLNVLETETEVLNK 161.58 6.33E-11 95390000 44687 47495 45965 49969 37709 48990 46801 51629 35822 TRUE FALSE 42574.73407 52334.7945 48072.54072 44946.02119 44285.43766 47293.46402 39660.64789 47108.09106 41377.09281 1.028944548 1.264825316 1.16181533 1.086253725 1.070288767 1.142986634 0.958517025 1.138506547 1 15.33654466 2.578377452 1.111536094 1.039765863 1.15380374 0.201154626 0.078938118 0.671071496 1.695692028 0.042411151 0.033337734 378.771638 -2.578377452 0.114037877 LT(ph)T(ph)T(ph)S(ph)LNKHLQELMDGLT(ph)AK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTTTSLNKHLQELMDGLTAK 20 1 Q969P6-2;Q969P6 Q969P6-2 TOP1MT "DNA topoisomerase I, mitochondrial" 5 LT(1)T(1)T(1)S(1)LNKHLQELMDGLT(1)AK 46.307 0.052232 368700000 19885 40823 52407 31139 314730 15832 20396 8138.3 138310 TRUE FALSE 18945.07546 44982.91011 54809.91279 28008.84856 369618.8124 15283.73387 17284.2156 7425.667308 159758.4084 0.11858578 0.281568342 0.343079988 0.175320028 2.313611008 0.09566779 0.108189708 0.046480604 1 17.28553234 LTADFREDPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LTADFREDPDPR 12 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 74.326 0.033567 1180770000 2905190 2002070 2439320 2721990 3251120 2510570 3504810 2928290 3702680 FALSE TRUE 2767867.426 2206083.209 2551165.235 2448370.394 3818114.299 2423628.331 2970086.864 2671873.404 4276872.704 0.647170869 0.515816898 0.596502494 0.572467446 0.892735081 0.566682363 0.69445295 0.62472596 1 22.02812484 -5 0.193571483 2.612833378 0.567786118 0.561044036 0.10128141 96.7745424 0.950718909 60.19644573 0.243754043 1.00E-05 5 -2.04504726 LTAEDLFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 173.75 7.72E-06 148175000 319560 343965 289668 356000 304322 283474 305209 338418 326202 FALSE TRUE 304455.0321 379015.4246 302949.5643 320214.2036 357395.6604 273657.2243 258643.7615 308784.3259 376787.7402 0.808027968 1.005912306 0.804032435 0.849853033 0.948533146 0.72629015 0.686444207 0.819517975 1 18.5233925 2.233511817 24.99996534 0.76971518 0.888034319 0.063593093 0.103709907 176.5251757 874084.3529 0.035344324 0.026910664 171.203176 -2.233511817 0.118319139 LTAIIEEAEEAPGARPQLQDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;;;;;;; 296.68 9.70E-62 9683382000 3242394 3031535 2833258 3555331 3060730 2997520 3156796 3183684 2898924 FALSE TRUE 3089132.461 3340451.863 2963165.682 3197942.373 3594520.343 2893715.131 2675168.792 2904903.751 3348474.328 0.922549244 0.997604143 0.884930088 0.955044614 1.073480036 0.864189134 0.798921697 0.867530543 1 21.67507248 2.047456272 24.99841224 0.857745145 0.963182596 0.22685137 0.070697725 122.7589827 64664.84271 0.024448982 0.018056766 111.5465833 -2.047456272 0.105437451 LTALDYHNPAGFNCKDETEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTALDYHNPAGFNCKDETEFR 21 1 Q9Y224;G3V4C6;G3V4E7 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 174.63 1.65E-12 386930000 822720 712740 687600 917230 586240 763540 840390 867940 606410 FALSE TRUE 783831.6561 785369.0163 719127.1401 825028.2978 688480.0704 737098.4183 712173.0707 791938.5724 700448.9657 1.119041778 1.121236599 1.026666003 1.177856401 0.982912538 1.052322802 1.016737986 1.130615664 1 19.41792041 2.731406601 24.99818824 1.037116455 1.109047873 0.326938584 0.053202075 645.7280769 2256354.647 0.015405691 0.014791367 538.7739642 -2.731406601 0.071931418 LTAT(ph)PT(ph)PLGGMTGFHMQTEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LT(0.004)AT(0.996)PT(1)PLGGMTGFHMQTEDR 136.71 7.63E-06 10420000 21173 18206 23705 25429 23330 25010 27245 25496 24925 TRUE FALSE 20172.19425 20061.2121 24791.8977 22872.82861 27398.74461 24143.89743 23088.27486 23263.43508 28790.2417 0.700660816 0.696805963 0.861121555 0.794464626 0.951667753 0.838613919 0.801947934 0.808031948 1 14.81329228 7.841844213 0.129509369 0.993114515 4.89E-29 0.539393226 0.064669358 61.87524935 0.56381437 0.355501894 11.14775316 69477504.75 -7.841844213 -0.993114515 LTAT(ph)PTPLGGMTGFHMQTEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LT(0.022)AT(0.857)PT(0.121)PLGGMTGFHMQTEDR 149.99 2.78E-07 49441000 45545 39577 44697 45002 39758 42437 47743 45395 40553 TRUE FALSE 43392.17811 43609.9413 46746.40166 40478.31346 46691.78261 40967.39605 40458.92849 41419.97315 46841.75212 0.926356854 0.931005766 0.997964413 0.864150285 0.99679838 0.874591453 0.863736446 0.884253284 1 15.51550742 2.192755633 24.99997047 0.89031285 0.93893997 0.075955816 0.053403854 211.1420387 115238.1589 0.017655782 0.013039703 155.8675229 -2.192755633 0.048627119 LTDCVVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTDCVVMR 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 89.752 0.031832 329930000 253080 231240 208910 227340 471630 191346 252430 214719 441050 FALSE TRUE 241117.41 254803.6189 218488.7301 204487.3513 553882.1227 184719.64 213917.1673 195917.0661 509445.7814 0.473293565 0.500158463 0.428875335 0.401391784 1.087224868 0.3625894 0.419901735 0.384569022 1 18.95856909 -1.989048583 2.544603786 1.465473149 0.503672373 0.351135797 0.210457752 15612276.84 7122658.026 42661917.22 0.048134443 0.010255372 1.989048583 -0.961800777 LTDCVVMRDPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LTDCVVMRDPASK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 186.56 7.02E-06 4453110000 4727530 4063770 3787200 5057360 3384200 4399270 4734300 4647570 3811980 FALSE TRUE 4504069.026 4477872.783 3960846.866 4548984.564 3974403.409 4246922.177 4011995.584 4240604.132 4403122.39 1.022926148 1.016976679 0.899554115 1.033126986 0.902632963 0.964525126 0.91117058 0.963090225 1 22.07009552 3.838877724 8.788420984 0.949376799 1.020495287 0.295641181 0.042338221 0.327781219 26.32998179 0.0095948 0.01733753 6900.454942 -3.838877724 0.071118488 LTDCVVMRDPASKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTDCVVMRDPASKR 14 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 69.92 0.025678 12131280000 14262400 8693980 12657200 11930800 12714800 12699500 17689700 14455100 16063900 FALSE TRUE 13588244.62 9579906.446 13237545.14 10731493.32 14932257.09 12259713.13 14990811.37 13189334.81 18555007.57 0.732322235 0.516297631 0.713421705 0.578361031 0.804756184 0.660722615 0.807911897 0.710823467 1 24.14530525 0.294027401 0.313915732 1.069363878 0.611961583 0.599577176 0.083959723 2.366101669 0.42380744 0.323508161 0.088812372 1.968010456 -0.294027401 -0.457402296 LTDDHVQFLIYQILR ddPTM_SK-BR-3_Trastuzumab_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 ; 189.1 2.72E-07 133018000 232942 236011 176239 195605 252783 187623 257590 223528 215202 FALSE TRUE 221931.2933 260060.7892 184319.7325 175942.4138 296868.2752 181125.5685 218289.9145 203954.7033 248574.4271 0.892816272 1.046208946 0.74150722 0.70780577 1.194283252 0.72865729 0.878167224 0.82049753 1 17.92331836 3.75347884 24.87180644 0.861663374 0.969512597 0.074482654 0.148811948 1745.605547 2910281.959 0.035351979 0.063395023 5668.639513 -3.75347884 0.107849224 LTDIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LTDIFR 6 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;; 159.87 0.020901 497520000 1419522 1376312 1228078 1419563 1306847 1288300 1389950 1389685 1300205 FALSE TRUE 1352424.008 1516559.758 1284386.591 1276865.83 1534760.703 1243685.848 1177887.599 1267996.814 1501834.151 0.900514885 1.009805082 0.855212002 0.850204285 1.021924227 0.828111311 0.784299384 0.844298829 1 20.51829407 2.187214356 24.99999428 0.838923559 0.929493237 0.100683176 0.079381586 145.614559 70897.27835 0.027831733 0.020555119 153.8914018 -2.187214356 0.090569678 LTDIHGNVLQYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTDIHGNVLQYHK 13 0 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 138.42 2.85E-05 1181860000 2497300 1800160 1540350 1767720 2273500 1845300 2799400 2139540 1305960 FALSE TRUE 2379257.578 1983598.351 1610976.571 1590025.427 2669997.68 1781396.798 2372300.115 1952190.535 1508481.607 1.577253291 1.314963564 1.067945783 1.054056887 1.769990213 1.180920463 1.572641061 1.29414275 1 20.52466567 0.975068814 23.46043367 0.999999988 1.37064206 0.195299679 0.229471937 1708.601802 1607810.491 0.208980169 0.052245042 9.442104737 -0.975068814 0.370642071 LTEAKPVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTEAKPVDK 9 1 B4DLN1;P52815 B4DLN1 MRPL12 "39S ribosomal protein L12, mitochondrial" 0 72.652 0.042084 145400000 362740 323150 266040 333460 203370 273940 316210 339610 209660 FALSE TRUE 345593.9991 356079.3524 278238.1971 299939.9673 238837.6636 264453.3891 267966.3569 309871.948 242173.002 1.427054198 1.470351152 1.148923269 1.238535942 0.986227456 1.092001945 1.10650797 1.279547866 1 17.88567851 3.702179837 4.735845982 1.120083807 1.450306952 0.691419539 0.090879107 0.093952927 5.223737069 0.022855125 0.037395506 5037.091464 -3.702179837 0.330223145 LTEDKADVQSIIGLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LTEDKADVQSIIGLQR 16 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 274.47 2.84E-35 1244612000 1655560 1242170 1462110 1671010 1188370 1545190 1831420 1766240 1397070 FALSE TRUE 1577304.96 1368748.535 1529149.19 1503036.9 1395621.352 1491679.683 1552003.243 1611578.662 1613720.48 0.977433811 0.848194314 0.947592355 0.931410934 0.864847022 0.924373026 0.961754691 0.998672745 1 20.62195927 1.563842201 2.34712723 0.998806179 0.912021616 0.47232968 0.03701226 0.226919006 2.701608645 0.026792324 0.009664491 36.63044552 -1.563842201 -0.086784562 LTEDLEYHELLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;;; 267.23 1.60E-24 1335404000 2629470 2319390 2408370 2724220 2637340 2392280 2891690 2674970 2308610 FALSE TRUE 2505180.164 2555738.478 2518796.147 2450376.23 3097291.261 2309434.744 2450509.581 2440735.446 2666617.448 0.939459901 0.958419619 0.944565989 0.918908046 1.161505661 0.866054014 0.918958054 0.915292686 1 21.34657944 -3.062723916 10.67320092 0.999685494 0.953819116 0 0.079722033 0 0 0 0.016360632 0.000865518 3.062723916 -0.045866378 LTEEELLDREFDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTEEELLDREFDLLR 15 1 H0Y9P1;Q9NSY1;Q9NSY1-2;Q9NSY1-3 H0Y9P1 BMP2K BMP-2-inducible protein kinase 0 71.344 0.040124 12143000 27480 21958 16508 23809 23443 20063 28565 22666 23406 FALSE TRUE 26181.07486 24195.54516 17264.90813 21415.67409 27531.45178 19368.21328 24206.88462 20681.24488 27035.68294 0.968389625 0.894948547 0.638597078 0.792126248 1.018337574 0.716394453 0.895367972 0.764961067 1 14.72257718 4.758430246 0.001113382 1.647799879 0.055859163 0.005424028 0.125217697 18517788.73 3081.818514 2184836.111 2221733.361 57336.37688 -4.758430246 -1.591940715 LTEEETVCLDLDKVEAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTEEETVCLDLDKVEAYR 18 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 200.48 1.38E-15 248061000 184088 170717 166818 207178 132208 191122 181706 210491 134546 FALSE TRUE 175386.5251 188113.2564 174466.7703 186352.0738 155265.0333 184503.3972 153983.4124 192059.2922 155410.7065 1.128535665 1.210426621 1.122617445 1.199094181 0.999062657 1.187198755 0.990815986 1.235817637 1 17.24572637 2.763693004 24.86478494 1.083140161 1.166277245 0.193870624 0.083666269 1067.753434 1056382.872 0.022249755 0.023592931 580.3540293 -2.763693004 0.083137084 LTEGCS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 1 LTEGCS(1)FR;LTEGCS(1)FR;LTEGCS(1)FR;LTEGCS(1)FR;LTEGCS(1)FR 128.52 0.0011853 1279132000 2482140 2069560 2143910 3146360 2320280 2478120 3097140 2249790 3031170 TRUE FALSE 2364814.161 2280450.517 2242210.394 2830081.915 2724936.097 2392302.083 2624614.41 2052786.461 3501228.363 0.675424142 0.6513287 0.640406784 0.808311147 0.778280025 0.683275078 0.749626742 0.586304647 1 21.73942973 -1.575385282 2.895504142 1.017749904 0.698602322 0.671584434 0.066660411 14919213.92 15247864.18 2031767.008 0.016284475 0.026583657 1.575385282 -0.319147582 LTEGCSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;; 181.33 0.00054531 1660090000 1050640 927395 927930 1063030 1090030 956860 1199000 1055440 1209340 FALSE TRUE 1000978.329 1021897.605 970476.5083 956172.2048 1280130.887 923723.6983 1016070.529 963020.0784 1396878.271 0.716582361 0.731558094 0.694746657 0.684506463 0.91642265 0.661277162 0.727386595 0.689408733 1 20.41377487 -1.235180453 5.067972561 1.000036212 0.727765643 0.596430956 0.070383583 2.61E-05 3.94E-06 0.061715549 0.014544562 0.05818614 1.235180453 -0.272270569 LTELMFEHYNIPAFFLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTELMFEHYNIPAFFLCK 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 159.81 4.21E-11 36108000 199260 222960 153510 213580 175230 169690 233660 208610 170870 FALSE TRUE 189841.3747 245679.8775 160548.5853 192110.5326 205790.0565 163813.5928 198010.8755 190343.0025 197367.6469 0.961866738 1.244782928 0.813449356 0.97336385 1.042673709 0.829992125 1.003259038 0.964408329 1 17.59052599 3.737036065 24.99994503 0.948100486 1.103324827 0.303060499 0.098705862 142.2592535 2332816.01 0.024003122 0.039485319 5458.031841 -3.737036065 0.155224341 LTEVPVEPVLTVHPES(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTEVPVEPVLTVHPESK 17 0 Q9H307 Q9H307 PNN Pinin 1 LTEVPVEPVLTVHPES(1)K 121.44 3.88E-05 22204000 34610 28275 33336 37084 24946 30130 33285 32620 29470 TRUE FALSE 32974.05389 31156.25465 34864.48857 33356.24587 29296.5745 29086.59055 28206.76193 29763.61987 34040.05709 0.96868386 0.915282091 1.024219451 0.979911572 0.860649981 0.85448125 0.82863439 0.874370445 1 15.05494584 2.735536692 24.59191528 0.867095332 0.9650958 0.381677846 0.053339452 186.2282313 1514484.292 0.015766414 0.015453409 543.9220844 -2.735536692 0.098000468 LTEVSISSDAFFPFRDNVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTEVSISSDAFFPFRDNVDR 20 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 148.51 9.99E-08 366810000 534130 357890 540420 499310 565750 510290 757510 632980 574560 FALSE TRUE 508882.7334 394359.3979 565198.7915 449118.4102 664416.6209 492618.5293 641937.9369 577552.9156 663659.8304 0.766782484 0.594219177 0.851639297 0.676729839 1.001140329 0.742275646 0.967269537 0.870254442 1 19.34008443 2.628177609 0.547971755 0.964573744 0.670613831 0.42160349 0.104492323 0.746740957 0.468870093 0.080585632 0.087118078 424.7932521 -2.628177609 -0.293959912 LTEYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LTEYSR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 144.9 0.026088 1286400000 2487680 2300860 2148390 2610070 2331590 2265020 2651230 2670700 2619600 FALSE TRUE 2370092.297 2535320.25 2246895.807 2347700.805 2738218.558 2186581.789 2246736.17 2436839.35 3025834.189 0.783285583 0.837891336 0.742570698 0.775885478 0.904946665 0.722637677 0.742517941 0.805344641 1 21.5289015 -2.128810654 2.001716992 1.382803601 0.788587179 0.611667069 0.052736139 2326035.798 533149.6196 4043543.155 0.01307743 0.007433432 2.128810654 -0.594216422 LTFNHDGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTFNHDGSSR 10 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;;; 140.78 3.87E-05 885650000 890820 750520 864930 895780 815760 804630 980470 933910 1004150 FALSE TRUE 848712.704 826998.8413 904587.896 805734.4925 958028.2857 776765.4613 830881.2939 852131.8894 1159868.454 0.731731863 0.713010893 0.779905595 0.694677478 0.825980121 0.669701343 0.716358214 0.734679771 1 20.14552976 0.906742812 19.02063304 1 0.73021422 0.787467887 0.043531924 2603.961575 531103.8702 0.037301604 0.009325401 8.067571287 -0.906742812 -0.26978578 LTFSCLGGSDNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTFSCLGGSDNFK 13 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 250.72 1.38E-17 137807000 270534 241495 208555 270780 232822 261501 265180 280330 268230 FALSE TRUE 257746.394 266103.6151 218117.453 243560.68 273426.0831 252445.1548 224721.9206 255782.8191 309825.7385 0.831907624 0.858881565 0.70400043 0.786121518 0.882515715 0.814797234 0.725317147 0.825569949 1 18.24109747 -1.785134209 5.50678654 1.012868652 0.803775552 0.558922598 0.054819941 0.009206022 0.000359204 0.056418938 0.012811072 0.016400829 1.785134209 -0.209093101 LTGDAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTGDAFR 7 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 ; 92.467 0.043988 223510000 533380 438740 387720 448130 568800 413310 590680 496600 586740 FALSE TRUE 508168.1845 483448.1048 405497.3455 403083.121 667998.5399 398996.9711 500560.9174 453115.0714 677728.6425 0.749810695 0.713335802 0.598318147 0.594755918 0.98564307 0.588726735 0.738586045 0.668578902 1 19.37034822 -1.861591438 2.6298852 1.126608996 0.70725464 0.391467152 0.115661178 53315529.25 35738799.82 42319289.61 0.025780532 0.013753352 1.861591438 -0.419354356 LTGIKHELQANCYEEVKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTGIKHELQANCYEEVKDR 19 2 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 214.27 2.60E-19 13432770000 2231990 1526030 2054230 2048940 1473030 2206300 2763170 2519850 1813000 FALSE TRUE 2126488.256 1681534.192 2148418.477 1842976.658 1729925.966 2129895.278 2341597.667 2299198.575 2094150.78 1.015441809 0.802967106 1.02591394 0.880059199 0.826075172 1.017068731 1.11816097 1.097914533 1 20.99793389 2.035123535 6.311043784 1.081275845 0.909274876 0.492775337 0.076191791 0.130719282 14.97933967 0.027388035 0.019761268 108.4235281 -2.035123535 -0.172000969 LTGMAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 154.09 0.0039591 11878840000 12645840 8187461 4386507 5212705 13169240 6036908 12846900 8908693 11945970 FALSE TRUE 12048096.2 9021772.584 4587632.685 4688713.99 15465951.29 5827848.362 10886869.46 8128600.613 13798490.02 0.873145988 0.653823177 0.33247353 0.339799064 1.120843749 0.422354066 0.788989914 0.589093488 1 23.71800706 -1.788596172 0.52879091 1.272760334 0.64697676 0.17319028 0.245820638 124.8836812 12.16781076 43.15500881 0.103732691 0.01627061 1.788596172 -0.625783574 LTGS(ph)T(ph)SSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.887)T(0.417)S(0.358)S(0.337)LNK;LT(0.001)GS(0.952)T(0.701)S(0.195)S(0.151)LNK 104.04 0.014506 1012260000 3094600 3161500 2759400 3439800 1759760 3320600 3230700 3480900 1980000 TRUE FALSE 2948324.391 3483660.444 2885921.219 3094024.769 2066661.587 3205606.789 2737797.379 3176093.943 2287048.288 1.289139546 1.523212458 1.261854083 1.35284628 0.903637058 1.40163494 1.197087702 1.388730601 1 21.1250554 -4.999999906 0.066151796 0.029231814 1.678358499 0.220593088 0.164871773 458.6104981 2.196756675 70.77032322 9.870069665 1.00E-05 4.999999906 1.649126685 LTGS(ph)TSS(ph)LNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.933)T(0.076)S(0.416)S(0.575)LNK 122.97 0.00069367 471620000 1555900 1549400 1322600 1686100 829310 1673000 1590200 1623200 888730 TRUE FALSE 1482355.69 1707285.622 1383242.518 1516610.025 973941.4014 1615063.591 1347585.784 1481064.003 1026549.709 1.444017447 1.663130003 1.347467644 1.477385859 0.948752303 1.573293115 1.312733102 1.442759166 1 19.96937206 -3.860342138 0.095129744 2.61E-12 1.739513045 0.31341916 0.188562682 167.7314553 1.399082832 37.76080328 3.747616969 0.00013793 3.860342138 1.739513045 LTGS(ph)TSSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.983)T(0.016)S(0.001)SLNK;LTGS(0.928)T(0.066)S(0.006)SLNK;LTGS(0.988)T(0.011)S(0.001)SLNK;LT(0.002)GS(0.482)T(0.106)S(0.143)S(0.267)LNK 212.12 4.86E-08 1480239000 2490846 2260570 2254357 2653311 1773851 2468090 2784355 2609281 2157865 TRUE FALSE 2373108.646 2490924.653 2357721.498 2386595.137 2083210.053 2382619.424 2359550.507 2380798.523 2492495.683 0.952101407 0.999369696 0.945928017 0.957512245 0.835792843 0.955917172 0.946661823 0.955186618 1 21.24915958 0.68525612 2.073437991 0.999985151 0.945999156 0.158177073 0.041181147 3.294176031 18.69969112 0.039935748 0.010957801 4.844579867 -0.68525612 -0.053985995 LTGSTSS(ph)LNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.005)T(0.109)S(0.209)S(0.678)LNK;LTGST(0.008)S(0.232)S(0.759)LNK;LTGST(0.001)S(0.058)S(0.941)LNK;LTGST(0.001)S(0.059)S(0.94)LNK;LTGST(0.02)S(0.045)S(0.935)LNK 197.3 3.33E-07 1317260000 4019420 3493410 3415620 4200710 2546290 4141370 4322790 4181150 2771940 TRUE FALSE 3829429.982 3849392.451 3572229.556 3778446.65 2990362.17 3997953.318 3663268.992 3815026.34 3201798.298 1.196024742 1.202259509 1.115694751 1.180101399 0.93396332 1.248658706 1.144128596 1.191526132 1 21.610451 -2.418931562 1.929170216 2.23E-05 1.155526923 0.237300057 0.085117148 1787058.908 149546.6633 7798311.017 0.020244007 0.003811259 2.418931562 1.155504603 LTGVFAPRPSTGPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 193.77 4.76E-08 3368300000 3572900 2472600 2524300 3235900 3209400 2869300 4146100 3837700 3440700 FALSE TRUE 3404016.098 2724560.751 2640041.652 2910621.184 3769118.344 2769935.422 3513536.297 3501650.643 3974266.183 0.85651437 0.685550646 0.664284054 0.732366945 0.948380951 0.696967766 0.884071709 0.881081055 1 21.92225707 1.20867672 0.635886016 1.000841801 0.746973372 0.455542685 0.086291014 0.639632816 0.626128963 0.081849795 0.036436022 16.16876019 -1.20867672 -0.253868429 LTHDVELNLDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTHDVELNLDYER 13 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 179.46 1.37E-05 169107000 133820 134548 112051 142954 148791 121607 146891 136310 119368 FALSE TRUE 127494.5938 148258.5942 117188.6492 128583.9923 174740.1033 117395.7191 124480.0801 124373.9738 137878.9798 0.924684778 1.075280615 0.84993847 0.932585899 1.26734404 0.851440294 0.902821302 0.902051741 1 17.073043 LTHVNTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTHVNTGR 8 0 Q99470;K7ELI9 Q99470 SDF2 Stromal cell-derived factor 2 0 ; 110.76 0.0033646 303570000 318980 259450 265080 314780 318850 268940 360880 309630 323300 FALSE TRUE 303902.4476 285888.25 277234.1802 283137.7164 374457.339 259626.5404 305821.128 282517.1557 373435.7128 0.813801244 0.765562157 0.742387968 0.758196677 1.002735749 0.695237578 0.818939157 0.756534916 1 18.51050038 -1.473924539 3.27186658 1.003915444 0.793833332 0.383645071 0.081987391 21307941 26239459.97 748598.6466 0.018414106 0.033579596 1.473924539 -0.210082112 LTIAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTIAEER 7 0 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 ;;;; 182.26 0.0015351 1761020000 3734320 3343820 3271180 3717910 3773430 3430870 3989680 3555100 4018710 FALSE TRUE 3557806.094 3684559.06 3421166.839 3344178.623 4431514.997 3312058.112 3380981.04 3243796.597 4641911.022 0.766452885 0.793759088 0.737016893 0.720431436 0.954674697 0.713511762 0.728359726 0.698806285 1 22.14628744 -1.054861897 4.466940357 1.000013073 0.765458648 0.507607472 0.07299798 9.62E-06 2.04E-06 0.066482968 0.015669246 0.088132909 1.054861897 -0.234554425 LTIFGNSAVSQPASSSNHSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTIFGNSAVSQPASSSNHSSR 21 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 LTIFGNSAVSQPAS(0.002)S(0.014)S(0.023)NHS(0.12)S(0.842)R 157.66 2.27E-09 86376000 57479 46883 58585 65479 91818 49074 89326 70771 98555 TRUE FALSE 54762.08158 51660.431 61271.1802 58896.92652 107831.0301 47374.55507 75697.67812 64573.91606 113838.4061 0.481051022 0.45380494 0.538229428 0.517373078 0.947228917 0.41615617 0.664957291 0.56724192 1 16.79662784 -5 0.130609763 2.436912686 0.384298225 0.478858118 0.144776399 117.8697912 0.969541611 44.48423473 0.998842397 1.00E-05 5 -2.052614461 LTIQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTIQNR 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 114.94 0.057818 112740000 183350 150740 157330 180230 185480 174130 188650 184790 216840 FALSE TRUE 174683.4089 166100.5774 164543.7361 162112.938 217827.6533 168099.8344 159867.9777 168608.808 250466.4397 0.697432395 0.663165003 0.656949236 0.64724415 0.869687985 0.671147139 0.638281032 0.673179242 1 17.93425778 -1.229192148 5.192976535 1.000031155 0.686442306 0.684776847 0.066145706 2.30E-05 3.42E-06 0.061811131 0.014567578 0.058994001 1.229192148 -0.313588849 LTISPDYAYGATGHPGIIPPHATLVFDVELLK ddPTM_SK-BR-3_Trastuzumab_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 0 200.52 4.52E-27 74078000 83476 53561 51902 90160 72482 65259 106610 79770 64209 FALSE TRUE 79530.25491 59018.92679 54281.75804 81096.94551 85122.83785 62999.06447 90344.68647 72784.91591 74166.20379 1.072324736 0.795765777 0.73189344 1.093448786 1.14773082 0.84943089 1.218138207 0.981375778 1 16.17847431 3.211842135 24.9979173 1.060799873 0.880849822 0.294963411 0.130873121 258.1372258 241513.5191 0.036496292 0.043632627 1628.703895 -3.211842135 -0.179950052 LTISPDYAYGATGHPGIIPPHATLVFDVELLKLE ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 34 1 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ; 243.55 1.96E-47 501150000 716490 357170 495690 662340 637410 549180 1103070 709230 624450 FALSE TRUE 682622.9376 393566.0291 518417.8768 595760.3248 748574.1022 530161.7589 934776.4122 647126.0613 721286.5168 0.946396365 0.545644511 0.718740563 0.82596903 1.037831825 0.735022417 1.295984869 0.897183084 1 19.46021293 2.659015153 1.291954175 1.046790023 0.726401228 0.309425663 0.170313359 0.43860094 1.494191957 0.077132633 0.067294924 456.052828 -2.659015153 -0.320388794 LTKEEIVDKYDLFVGSQATDFGEALVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTKEEIVDKYDLFVGSQATDFGEALVR 27 2 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 220.67 1.53E-34 1027300000 208960 154890 197200 221490 165230 208200 251310 230400 179190 FALSE TRUE 199082.8749 170673.4671 206241.8151 199225.4044 194046.0597 200989.9818 212968.0439 210224.9546 206977.87 0.961855849 0.824597659 0.996443799 0.962544471 0.937520807 0.971069911 1.028941132 1.015688076 1 17.659117 2.683428435 0.705131109 1.018503128 0.901919408 0.360727068 0.045675601 0.642790269 0.679875979 0.03336986 0.031523253 482.423478 -2.683428435 -0.11658372 LTKEEIVDKYDLFVGSQATDFGEALVRHDEF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTKEEIVDKYDLFVGSQATDFGEALVRHDEF 31 3 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 264.48 3.56E-59 223310000 791550 205220 897020 464950 913360 735590 1541000 879700 1115000 FALSE TRUE 754135.0002 226132.1513 938149.2543 418212.3427 1072649.695 710116.3339 1305892.148 802668.8044 1287908.505 0.585550136 0.175580913 0.728428495 0.324722091 0.832861721 0.551371725 1.013963447 0.623234338 1 20.29659868 2.438022644 0.789048233 0.899004051 0.402349741 0.396244357 0.207206686 0.543660796 0.675652199 0.139183917 0.098910716 274.1717118 -2.438022644 -0.496654311 LTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAK 40 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 225.61 1.58E-40 40909000 52772 44937 49365 61035 40309 54022 63149 61306 47056 FALSE TRUE 50277.57214 49516.13139 51628.43408 54899.64584 47338.87684 52151.20459 53514.46024 55937.72164 54353.20415 0.925015791 0.911006668 0.949869191 1.010053532 0.870949148 0.959487217 0.984568639 1.029152237 1 15.73007746 1.679634878 2.529740902 1.012442883 0.933215632 0.455072849 0.03578365 0.215323002 3.06576054 0.02260352 0.009467433 47.82278656 -1.679634878 -0.079227252 LTLDDIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTLDDIER 8 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 0 100.02 0.014895 28685000 84763 72070 65724 85488 87167 75807 86421 84572 97972 FALSE TRUE 80756.42097 79414.01494 68737.51041 76894.58382 102368.8972 73181.78458 73235.88922 77166.42734 113164.9974 0.713616603 0.701754224 0.607409641 0.679490881 0.904598591 0.646682157 0.647160261 0.681893069 1 16.78806827 -1.090316444 4.972003471 1.000009115 0.696103754 0.587412645 0.079576142 7.78E-06 1.42E-06 0.074505777 0.017560653 0.081223847 1.090316444 -0.303905361 LTLDKLDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 103.34 0.0040839 0 21066800 15065300 15276000 17910600 12257700 19462200 22647800 20820100 13444100 FALSE TRUE 20071014.11 16600471.2 15976419.71 16110192.46 14395439 18788219.13 19192462.15 18996981.67 15528942.37 1.292490734 1.069002048 1.0288157 1.037430115 0.927007047 1.209884015 1.235915602 1.223327463 1 23.88845624 LTLEDLEDSWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;; 242.59 6.19E-16 153463000 313127 296501 293499 340356 340274 313578 340903 319219 346518 FALSE TRUE 298326.1073 326714.789 306956.2195 306142.7682 399617.6779 302718.7152 288891.9862 291266.4921 400254.2417 0.745341526 0.816268149 0.766903102 0.764870766 0.998409601 0.75631607 0.721771205 0.727703699 1 18.61055717 -2.265063821 2.362230447 1.904316179 0.786147929 0.414270745 0.079512768 6641666.11 1040754.556 32166921.42 0.020407306 0.005431705 2.265063821 -1.11816825 LTLNS(ph)PIFDKPLSR ddPTM_SK-BR-3_Trastuzumab_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(0.002)LNS(0.998)PIFDKPLSR;LTLNS(1)PIFDKPLSR 161.35 2.79E-06 966570000 1625420 1500200 1448510 1764550 1444880 1654400 2000470 1835430 1781070 TRUE FALSE 1548589.618 1653072.086 1514925.616 1587174.082 1696866.615 1597107.713 1695261.56 1674710.019 2057269.239 0.752740375 0.803527343 0.736376935 0.771495559 0.824815042 0.776324111 0.824034856 0.814045137 1 20.97229918 -4.477323515 0.213023116 1.821989753 0.756034271 0.89724519 0.023378364 32.09948466 0.392297361 11.26310828 0.045165121 3.33E-05 4.477323515 -1.065955481 LTLT(ph)SDESTLIEDGGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTLTSDESTLIEDGGAR 17 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 1 LTLT(0.98)S(0.017)DES(0.001)T(0.001)LIEDGGAR 147.92 4.27E-06 25889000 32960 33917 25805 30526 31139 29362 34941 27139 31661 TRUE FALSE 31402.04612 37373.18086 26988.18477 27457.46848 36569.63174 28345.18658 29610.10871 24762.56529 36570.82618 0.858663842 1.021939747 0.737970333 0.750802521 0.999967339 0.775076462 0.809664747 0.677112548 1 15.1584056 3.737275364 24.99995348 0.814974165 0.940301793 0.161438398 0.111783515 167.4350162 3256860.179 0.027020337 0.044548566 5461.040081 -3.737275364 0.125327628 LTLYDIAHT(ph)PGVAADLSHIETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTLYDIAHTPGVAADLSHIETK 22 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 1 LTLYDIAHT(1)PGVAADLSHIETK;LTLYDIAHT(1)PGVAADLSHIETK 220.76 1.85E-25 62976000 164720 133167 138850 139426 122647 128945 154769 145575 74071 TRUE FALSE 156934.012 146736.8687 145216.4098 125410.6336 144036.598 124479.6023 131156.1465 132827.6813 85557.55238 1.834250837 1.715066229 1.697295046 1.465804363 1.683505359 1.454922434 1.532958142 1.552495105 1 16.38460759 -2.240921966 0.123760515 4.23E-16 2.010115745 0.857646173 0.085896383 20.33069475 0.333995405 6.753192849 0.856329468 0.005742196 2.240921966 2.010115745 LTLYDIAHTPGVAADLSHIETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTLYDIAHTPGVAADLSHIETK 22 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ; 226.29 3.12E-26 4078590000 1757040 1247160 1356300 1448430 1296820 1297850 1648900 1606250 504510 FALSE TRUE 1673988.201 1374247.022 1418487.697 1302831.065 1522984.997 1252905.129 1397330.021 1465598.235 582746.8341 2.872582232 2.358223059 2.434140545 2.235672488 2.613459067 2.149999032 2.39783374 2.514982749 1 19.15250974 -1.584149643 0.386735726 1.56E-18 2.517994899 0.836118964 0.200977193 10.68569543 0.814618789 10.66949788 0.12937679 0.026052557 1.584149643 2.517994899 LTNENLDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTNENLDLK 9 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 0 93.429 0.021881 49548000 145500 141390 120980 162680 102910 133480 149050 159860 119100 FALSE TRUE 138622.5034 155797.8017 126527.0527 146327.0973 120857.4714 128857.5541 126309.685 145861.8109 137569.4197 1.007654925 1.132503154 0.919732401 1.063660061 0.87851989 0.936672949 0.918152343 1.060277867 1 17.06980028 3.731605921 24.98916746 0.960523721 1.070079041 0.279126587 0.067241415 536.152882 1926472.925 0.016551375 0.026251733 5390.212929 -3.731605921 0.10955532 LTNSMMMHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTNSMMMHGR 10 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;; 178.54 2.20E-06 1785830000 1537687 1008043 620022 680607 1869932 872741 1757483 1133961 1687553 FALSE TRUE 1465003.583 1110763.728 648450.622 612191.0913 2196047.549 842517.7603 1489346.69 1034665.363 1949250.1 0.751572916 0.569841565 0.332666712 0.314064927 1.126611484 0.432226609 0.764061364 0.530801749 1 20.89448778 2.792878014 24.99999772 0.728870031 0.524987701 0.243699476 0.234522114 579.4353868 266688.3638 0.068260941 0.072401629 620.6946667 -2.792878014 -0.203882329 LTPEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 ;; 95.741 0.02195 1147560000 1015020 868130 973760 943320 1025040 979930 1140670 987080 1036390 FALSE TRUE 967042.0162 956593.434 1018407.859 848495.6814 1203806.651 945994.7784 966639.8417 900646.0424 1197108.068 0.807815135 0.799086949 0.850723411 0.708787873 1.005595638 0.7902334 0.80747918 0.752351493 1 20.19112197 -1.301218957 3.453548905 1.00070643 0.815229592 0.360640032 0.077303856 29765578.39 48381983.52 224049.6752 0.016560371 0.04997825 1.301218957 -0.185476838 LTPEFSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTPEFSQR 8 0 O43813;E9PHS0;F8WDS9 O43813 LANCL1 LanC-like protein 1 0 121.74 0.0077178 0 132850 116840 111640 108830 166630 108950 167450 122560 142770 FALSE TRUE 126570.4438 128746.1288 116758.8044 97890.20164 195690.2192 105177.0342 141902.4271 111827.9967 164910.0424 0.767512044 0.780705207 0.708015126 0.593597577 1.186648286 0.637784289 0.860483843 0.678115141 1 17.33131973 LTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 297.5 2.25E-71 19347160000 3389798 4054053 3205854 3822182 3241774 3261753 3417649 3846333 2681621 FALSE TRUE 3229568.966 4467165.61 3352845.577 3437969.004 3807138.359 3148797.676 2896223.876 3509527.692 3097473.089 1.042646336 1.442196746 1.082445426 1.109926997 1.229111037 1.016569825 0.935027938 1.133029276 1 21.56266032 2.23024351 23.56826106 1.007123871 1.196510677 0.302599037 0.118694872 96.7765219 274231.953 0.043321773 0.032580589 169.9196128 -2.23024351 0.189386806 LTPHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTPHEK 6 0 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 123.99 0.01855 464730000 2111900 1691860 1839200 2152300 1627240 1926500 2282800 2070900 1770880 FALSE TRUE 2012074.672 1864262.457 1923529.139 1935946.715 1911030.141 1859784.822 1934516.934 1889561.017 2045499.026 0.98365956 0.911397382 0.940371574 0.946442257 0.934261086 0.909208363 0.945743268 0.923765298 1 20.96402142 -1.117617382 4.931514912 1.0000028 0.937091757 0.471952173 0.020989123 6.06E-07 1.09E-07 0.01907003 0.004494649 0.076275071 1.117617382 -0.062911043 LTPIHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LTPIHDR 7 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;;; 159.2 0.0013924 1561680000 2916760 2905350 2339610 3265390 2574400 2468580 2651490 2668040 2311570 FALSE TRUE 2778890.535 3201408.468 2446883.433 2937146.793 3023374.545 2383092.456 2246956.503 2434412.273 2670036.47 1.040768756 1.199013011 0.916423225 1.100039953 1.13233455 0.8925318 0.841545248 0.911752443 1 21.34842802 2.229651408 24.98804526 0.891972625 1.084580829 0.496907104 0.081931546 134.141644 376229.9645 0.029016696 0.021748692 169.6881084 -2.229651408 0.192608204 LTPLSHEVISR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 262.54 9.55E-21 1874120000 1909290 1794450 1719420 1966710 2090490 1687400 2221980 1994880 2094030 FALSE TRUE 1819041.646 1977306.495 1798257.108 1769012.574 2455070.794 1628964.915 1882976.142 1820197.732 2418761.478 0.752054993 0.817487178 0.743461943 0.731371237 1.015011533 0.673470671 0.778487734 0.752532959 1 21.20583708 -1.448933066 2.751641901 1.006584567 0.783179895 0.363979769 0.090154607 8703632.874 9338930.499 442308.1209 0.020356606 0.035568613 1.448933066 -0.223404672 LTPS(ph)PDIIVLSDNEASSPR ddPTM_SK-BR-3_Trastuzumab_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 267.38 1.29E-31 203989000 109662 108770 118560 124273 206635 85653 132917 97585 220610 TRUE FALSE 104478.4946 119853.7867 123996.0933 111780.8419 242672.0786 82686.81513 112638.0705 89039.94007 254821.0721 0.41000728 0.47034488 0.486600626 0.438664044 0.952323435 0.324489707 0.442028085 0.349421417 1 17.95912506 -2.254294366 2.350382379 3.05477885 0.481168902 0.464564914 0.17398649 15293906.42 2089956.589 167600927.6 0.044197409 0.005568082 2.254294366 -2.573609948 LTPSGYEWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTPSGYEWGR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 113.74 0.0033689 117640000 221190 159622 177868 198133 214049 196163 241240 189601 212962 FALSE TRUE 210734.7871 175887.6633 186023.4237 178216.2944 251379.0778 189369.8261 204434.4073 172998.5313 245987.0593 0.856690542 0.715028115 0.756232561 0.724494593 1.021919928 0.769836538 0.831077895 0.703283058 1 17.9082229 LTPSPDIIVLS(ph)DNEAS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPSPDIIVLS(1)DNEAS(0.55)S(0.45)PR 95.5 0.0017875 0 79663 66843 69776 74764 75734 73412 74329 72220 84414 TRUE FALSE 75897.48787 73654.37769 72975.29862 67248.58068 88941.98562 70869.72403 62988.7459 65896.03394 97504.49199 0.778399911 0.755394712 0.74843012 0.689697257 0.912183468 0.726835478 0.646008657 0.675825622 1 16.57318106 2.041324438 24.99986113 0.722563825 0.773018566 0 0.111688777 489.1453213 295914.1918 0.037568831 0.027746398 109.9827153 -2.041324438 0.050454741 LTPSPDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR 297.29 1.01E-49 127522000 197419 192755 194038 207807 208041 201054 226461 201257 265456 TRUE FALSE 188087.3951 212396.9536 202934.8342 186917.8456 244323.2845 194091.4496 191910.2152 183633.8701 306621.5607 0.613418687 0.692700647 0.661841371 0.609604377 0.796823563 0.633000005 0.625886238 0.598894186 1 18.22609962 -1.144077214 4.821852121 1.000025736 0.655109207 0.780886322 0.057593512 0.502421447 34665470.22 1758.263539 0.012625166 0.071766668 1.144077214 -0.344916529 LTPSPDIIVLSDNEAS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.5)S(0.5)PR 116.82 0.00011641 44013000 51027 55062 52043 62450 52089 48931 57872 54359 65308 TRUE FALSE 48615.05484 60672.8804 54429.22303 56172.40735 61173.30511 47236.5072 49042.56351 49599.03778 75435.63109 0.644457455 0.804300031 0.721532017 0.744640252 0.810933828 0.626182966 0.650124653 0.657501463 1 16.2029585 -1.112193401 5.030969061 1.000009941 0.708959033 0.666578722 0.065014264 7.43E-06 1.31E-06 0.064566219 0.015217884 0.077233657 1.112193401 -0.291050908 LTPTHGEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTPTHGEMR 9 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 70.1 0.04048 140330000 65278 43242 39640 46285 60447 40695 62477 57058 53113 FALSE TRUE 62192.43831 47648.40896 41457.53321 41632.34386 70988.93766 39285.72195 52944.98618 52061.69904 61349.49278 1.013740057 0.776671604 0.67576 0.678609423 1.157123465 0.64035936 0.863006095 0.848608467 1 15.9047638 LTPVRPAAAS(ph)PIVSGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR 211.27 1.59E-12 5548320000 3012285 2425333 2477106 2817602 2881400 2590364 3128359 2688602 3130970 TRUE FALSE 2869900.258 2672477.19 2590683.76 2534371.294 3383915.248 2500659.045 2651070.378 2453173.756 3616504.837 0.793556317 0.738966851 0.716350144 0.70077918 0.935686637 0.691457404 0.733047652 0.678327243 1 21.78616465 -1.115487573 4.770337062 1.000015099 0.74975413 0.534741455 0.073710907 1.09E-05 2.03E-06 0.065892463 0.015530066 0.076650047 1.115487573 -0.250260969 LTPVS(ph)PESSSTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 LTPVSPESSSTEEK 14 0 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 LTPVS(0.999)PES(0.001)SSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.99)PES(0.002)S(0.004)S(0.004)TEEK;LTPVS(0.994)PES(0.006)SSTEEK;LTPVS(0.813)PES(0.173)S(0.014)STEEK;LTPVS(1)PESSSTEEK;LTPVS(0.928)PES(0.054)S(0.013)S(0.005)T(0.001)EEK;LTPVS(0.999)PES(0.001)SSTEEK;LTPVS(0.999)PES(0.001)SSTEEK 370.65 4.23E-97 3877114000 8268650 7476591 6940101 8600420 5068731 8064990 8219680 8093780 5386599 TRUE FALSE 7877807.301 8238464.123 7258311.496 7735889.442 5952716.082 7785697.374 6965616.851 7385045.715 6221925.262 1.266136601 1.324102071 1.166570023 1.243327285 0.956732174 1.251332513 1.119527567 1.186938995 1 22.56892963 7.999999997 0.104454313 0.935353919 2.058340622 0.385170511 0.091361795 106.705772 0.784341118 0.905415294 17.21579755 99999999.31 -7.999999997 1.122986703 LTPYEVDELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LTPYEVDELRR 11 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;; 225.58 8.61E-12 5059208000 3429580 2830620 3004840 3436250 3386420 2980340 3736550 3293280 3719300 FALSE TRUE 3267470.55 3119063.396 3142614.886 3090831.622 3977010.576 2877130.078 3166470.671 3004902.944 4296070.048 0.760571991 0.726027127 0.731509228 0.719455592 0.925732246 0.669712096 0.73706216 0.699453899 1 22.03458609 -1.699076741 3.578009051 1.02134417 0.745325528 0.577422985 0.068232846 0.011149816 0.000937739 0.063406133 0.014216346 0.019995085 1.699076741 -0.276018642 LTQEPESIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTQEPESIRK 10 1 P09497-2;P09497;H0Y9Q6 P09497-2 CLTB Clathrin light chain B 0 ;;; 109.39 0.0032472 1263730000 1721820 1383100 1520000 1717190 1374410 1631920 1945860 1834640 1554510 FALSE TRUE 1640432.981 1524039.462 1589693.503 1544574.799 1614106.669 1575406.201 1648983.319 1673989.196 1795575.471 0.913597344 0.84877494 0.885339285 0.860211572 0.898935575 0.877382336 0.918359236 0.932285622 1 20.77601486 0.994831182 0.894042964 0.999637787 0.8773961 0.810419183 0.018566008 0.238778384 0.414808233 0.016204404 0.005643172 9.881689012 -0.994831182 -0.122241687 LTQT(ph)SSTEQLNVLETETEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.078)QT(0.274)S(0.274)S(0.187)T(0.187)EQLNVLETETEVLNK 117.31 0.00049713 49917000 25952 29357 26480 32494 25265 25783 28275 27189 26545 TRUE FALSE 24725.30039 32348.51168 27694.13419 29227.64139 29671.208 24890.12825 23961.12944 24808.18702 30661.46303 0.806396628 1.055021792 0.903222856 0.953237012 0.967703595 0.811772361 0.781473781 0.809099912 1 14.90413892 2.234657814 24.99809981 0.826186326 0.94050292 0.176833312 0.085700402 119.9550699 768322.056 0.02904845 0.022260072 171.6555358 -2.234657814 0.114316594 LTQTSST(ph)EQLNVLETETEVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.037)QT(0.078)S(0.078)S(0.29)T(0.516)EQLNVLETETEVLNK 133.24 3.45E-05 83676000 45398 46069 41226 50058 31258 42644 43878 44302 35103 TRUE FALSE 43252.12651 50763.48348 43116.25288 45026.07474 36709.3853 41167.22759 37183.60523 40422.68202 40546.59396 1.066726506 1.251978983 1.063375457 1.110477363 0.905362984 1.015306677 0.917058663 0.996943962 1 15.30729311 2.980467771 2.131077417 0.96214764 1.149745366 0.573964131 0.064669907 0.184677452 1.681750933 0.019799364 0.022903352 956.0217459 -2.980467771 0.187597726 LTQYHGGS(ph)LPNVSQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTQYHGGSLPNVSQLR 16 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LTQYHGGS(1)LPNVSQLR;LTQYHGGS(0.999)LPNVS(0.001)QLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR 224.57 4.95E-15 832820000 957475 748979 778316 928485 932551 782404 974274 882880 960871 TRUE FALSE 912217.0543 825300.8116 814002.5585 835151.9238 1095187.599 755309.1533 825630.6075 805570.3468 1109877.967 0.821907526 0.743595995 0.73341627 0.752471847 0.986763979 0.680533514 0.743893141 0.725818847 1 20.08196963 -2.222009345 2.383481046 1.771028205 0.772027544 0.421325885 0.083386187 8321811.013 1578195.801 34627827.48 0.020395499 0.005997782 2.222009345 -0.999000661 LTQYIDGQGRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTQYIDGQGRPR 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;H0Y6G2;H7C394 Q13555-8 CAMK2G;CAMK2B Calcium/calmodulin-dependent protein kinase type II subunit gamma 0 98.531 0.0039276 126540000 145290 115900 126360 145990 163520 135690 186580 165420 176690 FALSE TRUE 138422.4296 127710.3418 132153.731 131314.8078 192037.8362 130991.0213 158113.7942 150934.9479 204090.1828 0.67824149 0.625754458 0.647526153 0.643415602 0.940945976 0.641829114 0.774725134 0.739550261 1 17.63884726 -4.999999997 0.125322478 2.003234056 0.568222191 0.553673271 0.08723607 104.0198286 0.833172544 26.14257033 0.679734849 1.00E-05 4.999999997 -1.435011865 LTRPAAS(ph)PAVGEK ddPTM_SK-BR-3_Trastuzumab_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 142.4 4.42E-06 0 87738 71450 76205 92030 64903 77829 94168 93245 77536 TRUE FALSE 83590.79862 78730.83623 79699.07463 82778.96955 76222.06265 75133.76221 79800.94209 85079.97348 89559.88688 0.933350873 0.879085928 0.889897 0.924286223 0.851073682 0.838922031 0.891034422 0.949978572 1 16.45056509 1.058152684 3.074448198 0.998877224 0.886922861 0.647798101 0.028375637 0.145891031 2.889592799 0.027819691 0.007353823 11.43280205 -1.058152684 -0.111954363 LTRPGSSYFNLNPFEVLQIDPEVTDEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTRPGSSYFNLNPFEVLQIDPEVTDEEIK 29 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 110.75 0.00030882 51978000 100330 93176 79438 104680 58921 100840 101530 105630 59675 FALSE TRUE 95587.59973 102670.7403 83080.31087 94157.36752 69196.80374 97347.88551 86039.73377 96380.47722 68929.09422 1.386752587 1.489512397 1.205301068 1.366003262 1.003883839 1.412290218 1.248235375 1.398255386 1 16.07282544 -5 0.083185714 0.071264174 1.59807805 0.317655735 0.139150201 264.7794438 1.550574436 46.07108421 3.930346607 1.00E-05 5 1.526813877 LTS(ph)PGALLFQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTSPGALLFQ 10 0 O60566-3;O60566;O60566-2 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 LT(0.202)S(0.798)PGALLFQ 79.906 0.026854 7030800 31579 36630 32016 38506 37566 34674 37730 33445 42830 TRUE FALSE 30086.32325 40362.63864 33483.96527 34635.30372 44117.49851 33473.23069 31973.59554 30516.3785 49471.85765 0.608150263 0.81587069 0.676828542 0.700101136 0.891769596 0.676611558 0.646298665 0.61684319 1 15.59432045 -1.581590668 2.711347871 1.021438571 0.707241576 0.528181093 0.087857216 17568370.17 17106584.01 2709629.753 0.020508093 0.026206519 1.581590668 -0.314196995 LTSNPLASHDYILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTSNPLASHDYILK 14 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 120.7 0.00079154 0 177810 135880 115650 141290 173950 117470 210690 135110 154110 FALSE TRUE 169405.2737 149726.3265 120952.6669 127087.2608 204286.8249 113401.9844 178545.3709 123279.0521 178008.5917 0.951669085 0.841118538 0.679476568 0.713938915 1.147623398 0.637059051 1.003015468 0.692545517 1 17.44158735 LTSS(ph)CPDLPSQTDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTSSCPDLPSQTDKK 15 1 P56962 P56962 STX17 Syntaxin-17 1 LTS(0.002)S(0.998)CPDLPSQTDKK 240.59 4.64E-18 313410000 467010 399230 432610 501800 255440 482010 551530 550390 359840 TRUE FALSE 444935.3628 439911.9909 452445.5964 451358.1106 299988.6551 465317.8728 467383.969 502194.9338 415642.1494 1.070477004 1.058391194 1.088545993 1.085929594 0.721747435 1.119515606 1.124486459 1.208238709 1 18.66498244 2.053898644 24.99999994 1.124064062 1.016964343 0.166357968 0.117421555 164.9801263 76522.33913 0.042540436 0.031418189 113.2136113 -2.053898644 -0.107099719 LTSTATKDPEGFVGHPVNAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTSTATKDPEGFVGHPVNAFK 21 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 167.22 7.44E-12 777210000 853920 527560 699660 821560 672630 788710 1165640 911200 813130 FALSE TRUE 813556.8939 581318.9638 731740.1031 738975.2279 789936.459 761396.7749 987800.2096 831410.4974 939226.0475 0.866199246 0.618934031 0.779088383 0.786791667 0.841050417 0.810664032 1.051717222 0.885208092 1 19.84111289 2.137887168 1.260093355 0.986628743 0.74875757 0.555913223 0.079696654 0.30158534 0.906462455 0.0513063 0.026789833 137.3685037 -2.137887168 -0.237871174 LTTPTYGDLNHLVSATMS(ph)GVTTCLR ddPTM_SK-BR-3_Trastuzumab_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 LTTPTYGDLNHLVSAT(0.163)MS(0.834)GVT(0.002)T(0.001)CLR 143.82 2.04E-07 75562000 121450 119070 93439 125440 128760 111990 135200 127370 130130 TRUE FALSE 115709.2992 131203.3684 97723.27057 112830.5329 151215.7032 108111.7582 114572.7569 116216.8076 150309.8958 0.769804933 0.872885765 0.650145289 0.750652725 1.006026266 0.719259086 0.762243605 0.773181346 1 17.19758047 -0.859820856 6.209483458 1.000000017 0.790616281 0.329591211 0.094946103 2.19E-08 3.93E-09 0.086295797 0.020340113 0.138095378 0.859820856 -0.209383736 LTTPTYGDLNHLVSATMSGVTTCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 328.28 8.82E-88 5424420000 4814280 4469050 4559000 4955360 5373230 4525550 5383200 4939260 5139950 FALSE TRUE 4586718.525 4924451.276 4768034.659 4457237.798 6310319.611 4368829.069 4561893.971 4506752.21 5937027.195 0.772561482 0.829447317 0.803101368 0.750752464 1.062875308 0.735861387 0.768380171 0.759092398 1 22.50130929 -2.245390421 2.331543042 1.713586288 0.808920897 0.287900403 0.093759588 6815558.445 1307083.732 25620435.85 0.021086758 0.005683418 2.245390421 -0.904665392 LTTTGQVTS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.027)S(0.973)PVK;LTTTGQVT(0.138)S(0.862)PVK;LTTTGQVT(0.35)S(0.65)PVK;LTTTGQVT(0.012)S(0.988)PVK 225.36 1.88E-11 962760000 3857890 4922090 3408240 5012120 2406410 4411480 4093600 4655780 2691210 TRUE FALSE 3675535.185 5423656.567 3564511.175 4508292.175 2826087.142 4258709.341 3469046.136 4248095.221 3108549.102 1.18239573 1.744754993 1.146680029 1.45028823 0.909133827 1.369999058 1.115969548 1.366584565 1 21.56780994 2.802117002 24.99948865 1.173885826 1.406560925 0.212130244 0.214308462 306.7769498 120667.8807 0.060023157 0.063664159 634.0405028 -2.802117002 0.232675099 LTTTGQVTS(ph)PVKGASFVTSTNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.101)S(0.899)PVKGASFVTSTNPR;LTTTGQVT(0.026)S(0.974)PVKGASFVTSTNPR 249.09 4.04E-38 1457580000 1257890 1081680 1280250 1349380 991750 1392170 1664680 1518120 1363510 TRUE FALSE 1198432.033 1191904.422 1338950.729 1213737.759 1164710.886 1343958.804 1410702.492 1385185.365 1574956.167 0.760930404 0.756785774 0.850151107 0.770648596 0.739519556 0.853330926 0.89570905 0.879507248 1 20.58688025 1.379032182 0.675982724 0.995617332 0.768045575 0.790408804 0.036850123 0.277935763 0.290833257 0.035085992 0.015688032 23.9349311 -1.379032182 -0.227571757 LTVAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTVASPK 7 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 LT(0.001)VAS(0.999)PK;LT(0.001)VAS(0.999)PK 78.098 0.038033 319658000 953810 924070 868690 1025220 936790 984520 1051730 1070730 1011510 TRUE FALSE 908725.2916 1018233.784 908520.2958 922162.9378 1100165.879 950425.8255 891269.2722 976971.2049 1168369.805 0.777771976 0.871499571 0.777596521 0.789273169 0.941624711 0.813463188 0.762831484 0.836183202 1 20.15606555 0.956751231 22.61033142 1.000000001 0.818946343 0.531238195 0.052995178 2294.362399 1199487.961 0.049379614 0.012344904 9.052139359 -0.956751231 -0.181053658 LTVDEAVR ddPTM_SK-BR-3_Trastuzumab_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 ; 117.04 0.0050165 102553000 234140 200991 185408 226810 265060 204251 263280 215394 272790 FALSE TRUE 223072.6662 221472.2114 193909.1402 204010.6279 311286.3801 197177.7367 223111.8005 196532.9595 315092.88 0.707958448 0.702879137 0.615403116 0.647461878 0.987919435 0.625776554 0.708082647 0.623730246 1 18.26541763 -1.095631185 4.266277433 1.000038366 0.703940127 0.430188017 0.107626125 97149.04357 56523048.1 4868.38294 0.023275078 0.080235916 1.095631185 -0.296098239 LTVEDLEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LTVEDLEKER 10 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;;; 158.56 7.25E-06 1150870000 2928440 1853980 2617350 2575140 2172920 2698970 3443100 2987820 2529920 FALSE TRUE 2790018.445 2042902.67 2737358.086 2316282.035 2551876.56 2605503.992 2917791.858 2726190.641 2922247.073 0.954751044 0.699086223 0.936730543 0.792637302 0.873258317 0.891609754 0.998475415 0.932909016 1 21.47864673 2.015072342 2.143162391 0.977129434 0.839325913 0.371419336 0.073694389 0.306044928 2.636885331 0.038055956 0.020463456 103.5314609 -2.015072342 -0.137803521 LTVENS(ph)PKQEAGISEGQGTAGEEEEKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTVENSPKQEAGISEGQGTAGEEEEKKK 28 3 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LT(0.011)VENS(0.989)PKQEAGISEGQGTAGEEEEKKK 148.94 4.91E-08 91407000 103730 88524 112320 121340 35380 145570 124830 152170 36600 TRUE FALSE 98826.88847 97544.69624 117469.9831 109142.6727 41550.2608 140528.8744 105784.8908 138845.1881 42275.74107 2.33767371 2.307344443 2.778661713 2.581685617 0.982839324 3.324101975 2.502259881 3.284275676 1 15.36754242 3.894458405 16.0910721 2.437614033 2.322189211 0 0.804679521 22.27339722 3337.268774 0.188309843 0.339493134 7842.570032 -3.894458405 -0.115424821 LTWASHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTWASHEK 8 0 P06702 P06702 S100A9 Protein S100-A9 0 ; 138.98 0.00068231 1399710000 3224300 1909320 1839580 2183070 2704100 2190500 3692300 2749000 2560800 FALSE TRUE 3071893.729 2103881.879 1923926.563 1963623.656 3175694.184 2114642.436 3128971.821 2508282.987 2957915.785 1.038533194 0.71127173 0.650433177 0.663853807 1.073625625 0.714909615 1.057829921 0.847989993 1 21.49614955 2.74394267 24.9368632 0.933333593 0.780755033 0.249586249 0.14777813 712.7857752 3302577.124 0.04511852 0.046620051 554.5525037 -2.74394267 -0.15257856 LTWFVNEGLVDGWDDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTWFVNEGLVDGWDDPR 17 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 108.59 0.0015075 52482000 131585 193210 116035 162425 108608 126699 114058 140044 94891 FALSE TRUE 125365.2378 212898.3187 121355.3195 146097.7304 127549.2008 122311.3819 96656.35728 127781.0049 109606.2116 1.143778587 1.942392821 1.107193814 1.332932944 1.163704127 1.115916516 0.881851091 1.165819008 1 16.74197004 2.950588183 1.121271208 1.015586618 1.508785398 0.331917035 0.232952162 0.443541828 1.186576383 0.100921561 0.116155655 892.4588144 -2.950588183 0.49319878 LTWFVNEGLVDGWDDPRFPTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTWFVNEGLVDGWDDPRFPTVR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 212.06 2.32E-23 622340000 101455 93633 79764 109158 100273 91502 104349 95049 103629 FALSE TRUE 96659.42321 103174.3092 83421.2583 98185.23045 117760.5795 88333.2628 88428.64355 86726.00567 119699.2561 0.807518997 0.861946119 0.696923783 0.820266004 0.983803771 0.737959998 0.738756835 0.724532537 1 16.86905466 -1.744482109 8.625264419 1.001255674 0.799189614 0.372367403 0.08297759 0.001990421 5.90E-05 0.079814179 0.018707096 0.018010173 1.744482109 -0.202066059 LTWHS(ph)CPEDEAQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 1 LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ 280.91 4.98E-28 6178800000 5230540 4181810 4711980 5071140 5142550 4711060 5695650 4971180 4628650 TRUE FALSE 4983302.74 4607941.193 4928028.944 4561379.373 6039409.092 4547914.811 4826673.985 4535877.125 5346437.402 0.932079133 0.861871345 0.921740698 0.853162401 1.129613729 0.850643984 0.902783222 0.84839245 1 22.35014644 2.323868281 0.006654102 1.835566484 5.79E-05 0.033327461 0.085789141 19113.65443 70.10767179 9553.552573 9779.85994 210.7988713 -2.323868281 -1.835508628 LTWHSCPEDEAQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;;; 236.32 1.05E-15 5936580000 4615634 3830283 4229583 4491097 4652658 4220521 5161630 4499694 4509444 FALSE TRUE 4397462.128 4220593.192 4423513.564 4039643.397 5464080.082 4074363.299 4374128.544 4105676.939 5208745.544 0.844245911 0.810289763 0.849247391 0.775550152 1.049020352 0.782215845 0.839766217 0.788227588 1 22.31250453 -2.328041674 2.239793846 1.86255284 0.841155777 0.287225941 0.078043262 6228292.125 1103981.08 27008365.72 0.017319589 0.00469849 2.328041674 -1.021397063 LTYEIEDEKRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LTYEIEDEKRR 11 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 181.31 3.53E-06 215940000 190820 158900 187950 169910 142350 168940 214270 221100 195430 FALSE TRUE 181800.3168 175092.0907 196567.6934 152830.324 167175.7949 163089.5654 181579.1762 201739.3119 225736.2863 0.805365942 0.775648849 0.870784652 0.677030381 0.740580071 0.722478287 0.8043863 0.893694652 1 17.78427882 1.068517332 2.16209634 0.99798792 0.769038194 0.698834003 0.051152244 0.161028743 1.526367688 0.047090604 0.013131358 11.70893329 -1.068517332 -0.228949726 LTYHQLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTYHQLLER 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 105.98 0.0031373 606890000 3687800 2982100 3230400 2811400 3564000 3753300 4613800 4188800 4115400 FALSE TRUE 3513485.003 3285979.38 3378517.035 2528792.731 4185560.472 3623322.28 3909880.072 3822006.466 4753595.213 0.739121622 0.691261926 0.710728803 0.531974772 0.880504183 0.76222777 0.822510099 0.804024385 1 22.18058763 1.035826398 0.497071199 1.002754266 0.688120193 0.564521818 0.081237422 0.720158974 0.456164172 0.089148068 0.04378781 10.8599143 -1.035826398 -0.314634074 LTYIDKWFLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LTYIDKWFLYK 11 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 157.03 2.81E-05 533120000 3116000 2475000 2262100 2577400 2541700 2288800 3079500 2870900 2563700 FALSE TRUE 2968712.855 2727205.314 2365819.523 2318314.855 2984971.675 2209538.282 2609665.716 2619508.776 2961265.502 1.002514922 0.920959405 0.798921785 0.78287977 1.00800542 0.746146632 0.881267051 0.884590988 1 21.49778242 4.128413087 2.82932784 0.862246449 0.986709169 0.179195239 0.08551649 0.343047716 5.384860141 0.019890048 0.053496635 13440.42764 -4.128413087 0.124462721 LVAIVDVIDQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVAIVDVIDQNR 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 162.36 0.00014632 98697000 205404 184681 190852 219520 209602 209230 250360 208394 200059 FALSE TRUE 195694.96 203500.2039 199602.753 197453.4325 246156.5224 201984.3126 212162.9838 190145.9166 231083.128 0.846859577 0.880636357 0.863770344 0.854469274 1.065229316 0.874076418 0.918124078 0.822846386 1 17.8180524 LVALLNTLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVALLNTLDR 10 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;A6PVN9;Q5T948;Q5T949;A6PVN6;A6PVN8;C9IZ76;A6PVN7 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 85.716 0.03416 0 97667 120420 71541 87136 88903 75339 119020 94310 78471 FALSE TRUE 93050.47447 132690.9349 74821.22561 78376.92373 104407.6551 72729.99154 100861.313 86051.71643 90639.88191 1.026595275 1.463935435 0.825477969 0.864706817 1.151895312 0.802406071 1.112769687 0.94938028 1 16.46785836 3.728593563 24.99778476 0.966232458 1.245265363 0.378414738 0.152737878 599.4368083 1503412.925 0.037850581 0.059398725 5352.954631 -3.728593563 0.279032904 LVASMEEARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 168.74 7.77E-06 235090000 133692 96193 122036 114892 169024 107564 167183 142140 182445 FALSE TRUE 127372.6441 105995.1761 127631.4713 103342.8379 198501.7321 103839.0317 141676.1628 129693.4681 210737.6388 0.604413359 0.502972211 0.605641555 0.490386238 0.941937725 0.492740795 0.672286942 0.615426218 1 17.68508848 -5 0.20132014 2.791545708 0.545740074 0.472304361 0.129189436 115.2134717 1.140968462 83.01826725 0.273347202 1.00E-05 5 -2.245805634 LVDLDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVDLDWR 7 0 Q9P000;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 ;;; 105.12 0.018609 94383000 602120 543120 499100 555950 663480 460245 665620 591500 697600 FALSE TRUE 573658.9809 598464.5455 521984.2287 500064.8498 779190.7019 444306.6002 564067.4441 539705.1243 805780.2452 0.711929815 0.742714343 0.647799734 0.620597058 0.967001495 0.551399222 0.7000264 0.669791953 1 19.62002691 -1.278276553 3.551749517 1.000809687 0.702731829 0.429431252 0.10815587 33344838 45970431.54 282931.3339 0.023388472 0.052689424 1.278276553 -0.298077858 LVDMMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 126.67 0.0091423 123592000 189202 171194 163764 182016 229220 160940 212660 191880 236990 FALSE TRUE 180258.7964 188638.8632 171272.7414 163719.4059 269195.8954 155366.6074 180214.8112 175077.97 273741.1988 0.658500793 0.689113893 0.625673965 0.598080985 0.983395618 0.567567498 0.658340111 0.639574791 1 18.06245306 -1.254264837 4.929383499 1.000068237 0.676373287 0.441397036 0.113999313 7.77E-05 1.18E-05 0.100338425 0.023645022 0.055684608 1.254264837 -0.323694951 LVDPERDMSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVDPERDMSLR 11 1 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 ; 92.925 0.0087846 551300000 1318720 851720 1249870 1102070 1554020 1220800 1666220 1362660 1866910 FALSE TRUE 1256386.719 938511.2363 1307177.776 991287.8298 1825040.596 1178523.39 1412007.537 1243338.266 2156420.868 0.582625933 0.4352171 0.606179339 0.459691262 0.846328573 0.546518264 0.654792187 0.576574956 1 21.04020735 -4.999999999 0.171083656 2.651683026 0.481323642 0.588531779 0.109806873 84.7555096 0.801338424 47.44471736 0.351842636 1.00E-05 4.999999999 -2.170359385 LVDQNIFSFYLSR ddPTM_SK-BR-3_Trastuzumab_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 0 155.02 0.00010814 240140000 259720 203710 116290 138310 264060 137190 233120 199380 240530 FALSE TRUE 247443.5503 224468.2806 121622.0115 124406.816 310111.9804 132439.0759 197553.2625 181921.2302 277830.1639 0.890628817 0.807933442 0.437756685 0.447780091 1.116192626 0.476690774 0.711057646 0.654792941 1 18.08384372 -1.771028346 8.202056759 1.003925601 0.703554631 0.169587297 0.212428334 0.014628175 0.000408366 0.197308327 0.046150482 0.016942272 1.771028346 -0.30037097 LVDQNIFSFYLSRDPDAQPGGELMLGGTDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVDQNIFSFYLSRDPDAQPGGELMLGGTDSK 31 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;F8WD96 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 264.56 7.31E-59 232600000 217870 108129 214733 168507 233973 192927 336447 223572 297739 FALSE TRUE 207571.7169 119147.468 224578.7204 151568.3562 274777.8171 186245.8896 285115.8309 203994.8505 343910.8435 0.603562583 0.34644871 0.653014363 0.440719911 0.798979801 0.541552827 0.829039957 0.59316202 1 18.39167508 0.930338382 0.255071562 1.090361971 0.422034113 0.508957601 0.134108728 1.908870998 0.401100586 0.462035053 0.26457506 8.518014639 -0.930338382 -0.668327858 LVDQSGPPHEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 84.734 0.01207 233610000 139970 123100 118950 148330 113490 133910 154700 148670 124980 FALSE TRUE 133353.8955 135644.03 124403.9752 133419.5866 133282.6201 129272.6631 131097.6737 135651.6667 144361.2601 0.923751257 0.93961517 0.861754567 0.924206304 0.923257528 0.89548029 0.90812226 0.93966807 1 17.13932412 0.89887502 3.298774347 0.999937883 0.912948185 0.641005288 0.021142047 0.272515425 6.465577944 0.020010893 0.005197279 7.922732987 -0.89887502 -0.086989698 LVDVS(ph)PDRGS(ph)PPSRVPQALNFSPEESDSTFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVDVSPDRGSPPSRVPQALNFSPEESDSTFSK 32 2 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 2 LVDVS(0.988)PDRGS(0.961)PPS(0.041)RVPQALNFS(0.009)PEES(0.001)DSTFSK 48.931 0.044354 23384000 13516 8837.8 11407 11530 8597.5 12194 16023 13025 15221 TRUE FALSE 12877.12547 9738.381868 11930.02223 10370.98249 10096.90128 11771.71872 13578.39707 11884.46195 17581.39494 0.732429111 0.553902685 0.678559481 0.589883939 0.574294663 0.669555445 0.772316253 0.67596809 1 14.10176192 0.459884173 0.616889383 1.008486276 0.627015207 0.749221725 0.064044749 0.899203299 0.567271251 0.081926588 0.025563905 2.883262431 -0.459884173 -0.381471069 LVEALCAEHQINLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LVEALCAEHQINLIK 15 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;; 232.17 9.56E-14 1644490000 2821680 2463437 2584192 2957766 2503025 2825209 3097892 3100803 2497833 FALSE TRUE 2688304.778 2714464.031 2702679.759 2660445.742 2939551.768 2727371.304 2625251.679 2829280.251 2885184.184 0.931761928 0.940828681 0.936744272 0.922106033 1.018843713 0.94530232 0.909907829 0.98062379 1 21.46023199 LVEALDLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVEALDLFER 10 0 G3V325;C9JGL8;O75127 G3V325 ATP5J2-PTCD1;PTCD1 "Pentatricopeptide repeat-containing protein 1, mitochondrial" 0 84.213 0.035071 3274900 13326 8386.7 11618 8066.4 10798 7243.9 10465 9855.7 10459 FALSE TRUE 12696.10639 9241.314265 12150.69679 7255.550147 12681.16778 6993.041927 8868.372047 8992.68266 12080.9283 1.050921425 0.764950675 1.005775093 0.60057886 1.04968488 0.578849717 0.734080348 0.74437017 1 13.5604437 3.258768484 24.99924102 0.767084126 0.918688295 0.154874889 0.16585785 412.2092695 509942.6858 0.041436975 0.056037579 1814.548097 -3.258768484 0.151604169 LVEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVEALR 6 0 O75688;O75688-3 O75688 PPM1B Protein phosphatase 1B 0 ; 109.7 0.068236 333590000 329220 270930 270540 326930 374690 294140 364350 313600 399470 FALSE TRUE 313658.4231 298538.075 282944.5266 294066.3753 440035.8174 283953.858 308761.7158 286139.5215 461417.7674 0.679771013 0.647001689 0.61320683 0.637310472 0.953660324 0.615394287 0.669158705 0.62013113 1 18.81571403 -1.259827536 3.413024655 1.00095254 0.67798934 0.503203354 0.10008504 29761436.36 42868012.41 294120.9652 0.023080172 0.054975915 1.259827536 -0.322963199 LVEDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVEDEER 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 103.75 0.019324 83455000 399670 376730 370140 451910 293240 414330 423080 438580 268240 FALSE TRUE 380778.3912 415119.2153 387111.2851 406483.1482 344380.9632 399981.6482 358531.3756 400175.6101 309837.2892 1.228962441 1.339797467 1.249401859 1.311924556 1.111489724 1.290940962 1.157160187 1.291566974 1 18.24115126 -4.929408747 0.181263786 1.79E-10 1.300695581 0.551270388 0.069909664 88.04713795 0.86952815 31.6988982 0.189315216 1.18E-05 4.929408747 1.300695581 LVEDEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVEDEERR 8 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 151.97 0.00074486 605050000 1004223 870526 966129 1081540 1111452 955521 1228940 1028277 1242630 FALSE TRUE 956755.369 959233.5891 1010426.97 972821.5444 1305288.877 922431.0682 1041442.632 938235.6146 1435330.714 0.666574859 0.668301444 0.703968055 0.677768221 0.909399391 0.642660997 0.725576776 0.653672081 1 20.45295176 -1.951517534 2.551026808 1.222492144 0.70419135 0.594889819 0.076235874 14963264.27 7009311.617 19729341.53 0.018886513 0.011181047 1.951517534 -0.518300794 LVEDKPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVEDKPGSR 9 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;;; 133.81 0.00024314 1164670000 2148480 1753180 1779310 2116490 1607190 1903490 2199970 2027760 1758080 FALSE TRUE 2046925.608 1931831.035 1860893.123 1903736.404 1887483.427 1837571.664 1864324.171 1850198.585 2030714.067 1.007983173 0.951306275 0.916373779 0.937471422 0.929467845 0.904889415 0.918063356 0.911107385 1 20.95355569 4.32705928 1.521638401 0.925474973 1.012843883 0.429308444 0.027054416 0.401815656 1.457957175 0.006575338 0.04197431 21235.34299 -4.32705928 0.087368911 LVEGILHAPDAGWGNLVYVVNYPK ddPTM_SK-BR-3_Trastuzumab_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 ; 290.98 8.29E-62 380420000 499800 433780 447150 498340 438710 452520 543700 479920 397410 FALSE TRUE 476175.4445 477982.6752 467652.2698 448245.9164 515220.8851 436849.1189 460748.5793 437895.6606 459038.3131 1.037332682 1.041269675 1.018765224 0.976489116 1.122391901 0.951661564 1.003725759 0.953941421 1 18.80825505 LVEKLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVEKLEK 7 1 G3V379 G3V379 FERMT2 0 107.47 0.018132 0 447940 285320 407680 340480 331860 352990 476570 420280 408600 FALSE TRUE 426766.7639 314394.4324 426372.5313 306254.3035 389736.2789 340765.8678 403860.4937 383478.0552 471963.6012 0.904236604 0.666141269 0.903401301 0.648893904 0.825776136 0.722017264 0.855702628 0.812516165 1 18.84831607 0.548584178 0.922051672 1.000106261 0.778936221 0.359127859 0.088574503 1.483990835 1.952917772 0.075838906 0.024570322 3.536585627 -0.548584178 -0.22117004 LVEKPSPLTLAPHDFANIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVEKPSPLTLAPHDFANIK 19 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 199.41 4.18E-16 626690000 962220 842170 854400 1037790 691100 1032150 1110930 1092200 795950 FALSE TRUE 916737.7675 927988.0805 893575.0851 933469.3775 811627.6212 996406.3867 941437.2249 996561.1779 919381.8609 0.997124053 1.009360876 0.971930297 1.015322813 0.882797079 1.083778601 1.02398934 1.083946965 1 19.81030468 LVELIHPSQDEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVELIHPSQDEDR 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 ; 95.264 0.0047758 39703000 64039 58321 61105 68288 97004 51274 71057 59745 98026 FALSE TRUE 61012.00338 64263.97621 63906.72469 61423.5605 113921.4669 49498.36852 60215.9496 54513.41107 113227.3714 0.538845004 0.567565734 0.564410565 0.542479788 1.006130103 0.437159036 0.531814426 0.481450822 1 16.78886323 -1.768498659 2.669445843 1.10115025 0.58022913 0.414410467 0.15545992 25485407.15 19208375.13 16881430.04 0.035300099 0.017041246 1.768498659 -0.52092112 LVELNEDVRPHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVELNEDVRPHIR 13 1 Q05D32-2;Q05D32 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 0 71.548 0.025217 317290000 80379 111540 83961 112780 236650 93873 113780 95321 205730 FALSE TRUE 76579.64397 122906.0528 87810.6949 101443.1401 277921.6851 90622.15447 96420.77129 86974.18791 237633.5577 0.322259384 0.517208319 0.369521442 0.426888951 1.169538881 0.381352513 0.40575402 0.366001287 1 17.85837906 2.954526698 24.99971295 0.607539006 0.413718784 0.167484465 0.26689902 980.395326 538988.5203 0.079337892 0.08415378 900.5891233 -2.954526698 -0.193820222 LVEPHS(ph)PSPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 LVEPHS(0.999)PS(0.001)PSSK;LVEPHS(0.987)PS(0.013)PSSK;LVEPHS(0.996)PS(0.004)PSSK;LVEPHS(1)PSPSSK 187.37 6.81E-06 870420000 2328150 2221380 2308240 2647580 1992540 2487680 2856240 2811320 2143900 TRUE FALSE 2218102.963 2447741.147 2414075.087 2381440.228 2340038.345 2401531.018 2420468.13 2565145.917 2476365.062 0.895709198 0.988441157 0.974846207 0.961667673 0.944948861 0.96978069 0.97742783 1.035851279 1 21.23979258 4.588787191 2.583641425 0.977921043 0.890663427 0.539892442 0.024595036 0.274907829 2.952203941 0.005940562 0.045104948 38796.02148 -4.588787191 -0.087257616 LVEPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVEPLR 6 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 96.666 0.097591 21954000 46584 40267 36383 49755 60970 40369 52872 47589 58572 FALSE TRUE 44382.06664 44370.25308 38051.19654 44753.53287 71603.1487 38971.01141 44805.40534 43421.85487 67655.04662 0.656005263 0.655830648 0.562429537 0.661495854 1.058356357 0.576025195 0.662262574 0.641812504 1 16.04590993 -2.051865284 2.592305369 1.435232913 0.68067034 0.341017001 0.137848563 19334384.95 9696739.255 49733840.05 0.032900713 0.008874312 2.051865284 -0.754562573 LVEQANS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK 165.09 6.48E-05 1216865000 2453020 2127060 2012420 2563700 1453950 2395980 2426860 2550960 1649290 TRUE FALSE 2337070.606 2343809.832 2104691.448 2305992.005 1707518.42 2313006.612 2056597.935 2327584.419 1905053.47 1.226774284 1.230311836 1.104793897 1.210460516 0.896309971 1.21414262 1.079548667 1.221794798 1 20.86140006 3.656636734 1.741501677 1.102352725 1.234210029 0.201171929 0.101503083 0.511968024 3.0436627 0.027194782 0.055023466 4535.620752 -3.656636734 0.131857304 LVEQLKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVEQLKEER 9 1 O95232;J3KPP4 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 190.86 3.34E-05 793860000 2261720 1961880 1968880 2336480 1725860 2148520 2427250 2311160 2033710 FALSE TRUE 2154812.978 2161797.802 2059155.095 2101612.591 2026849.438 2074116.214 2056928.433 2108782.578 2349087.36 0.917297932 0.920271353 0.876576636 0.894650675 0.862824207 0.882945543 0.875628752 0.897702918 1 21.16366894 -1.302777147 7.548370298 1.000000587 0.892406824 0.782838709 0.018030309 2.06E-07 1.90E-08 0.020154791 0.004750504 0.049799256 1.302777147 -0.107593763 LVES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVESPK 6 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PK;LVES(1)PK 95.815 0.045018 259370000 1007620 1109900 856260 1288670 627720 1102080 1011370 1180200 679420 TRUE FALSE 959991.7995 1223000.072 895520.368 1159130.443 737194.1693 1063914.693 857066.9314 1076855.431 784780.9836 1.223260782 1.55839667 1.141108649 1.47701138 0.939362936 1.35568358 1.092109709 1.372173197 1 19.58193056 2.761972538 24.9947783 1.168988169 1.359008471 0.231850586 0.177301546 1110.381126 1185451.12 0.047946316 0.050826918 578.0594929 -2.761972538 0.190020303 LVES(ph)PKEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LVESPKEGK 9 1 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PKEGK;LVES(1)PKEGK;LVES(1)PKEGK 90.731 0.006802 1270260000 4923620 3972680 4540040 4934450 2387020 5525900 5542730 5770670 2718080 TRUE FALSE 4690890.24 4377500.609 4748205.325 4438429.711 2803315.532 5334536.697 4697084.739 5265359.543 3139585.964 1.4941111 1.394292323 1.512366719 1.413699055 0.892893383 1.699121081 1.496084131 1.677087235 1 21.58214288 3.014487498 23.90733039 1.394552118 1.456217236 0.025466665 0.257908976 980.9673689 1618775.73 0.071645081 0.085590736 1033.921337 -3.014487498 0.061665118 LVEVDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 117.04 0.0050165 80109000 166610 149040 156040 177330 223440 153070 190450 163740 210560 FALSE TRUE 158734.6755 164227.3454 163194.5883 159504.4515 262407.8653 147769.1475 161393.3546 149402.0576 243212.5694 0.652658191 0.675242015 0.6709957 0.655823224 1.078923947 0.607572001 0.663589695 0.614285922 1 17.89185826 -1.739846634 2.695714904 1.059828343 0.699010822 0.320810644 0.136011253 33573200.95 27651904.35 13466649.29 0.030748073 0.018203436 1.739846634 -0.360817521 LVEVNGENVEKETHQQVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVEVNGENVEKETHQQVVSR 20 1 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 352.41 2.20E-95 1034230000 947680 641230 985620 889360 962780 1005880 1277110 1096880 1140070 FALSE TRUE 902885.0445 706572.066 1030811.652 799959.8431 1130688.527 971046.1234 1082263.414 1000831.372 1316866.233 0.685631556 0.536555687 0.782776281 0.607472364 0.85862064 0.737391619 0.821847646 0.760009899 1 20.32867737 1.147437005 0.161492665 1.151004169 0.483152718 0.598799648 0.081943448 2.907952298 0.402703212 0.789604665 0.604960534 14.04225983 -1.147437005 -0.667851451 LVFGFLNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVFGFLNGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 170.17 0.00013473 237490000 407970 388890 321530 363300 413110 313570 413860 392530 369330 FALSE TRUE 388686.0666 428518.3331 336272.4685 326780.3938 485156.2532 302710.9923 350718.0559 358157.9923 426603.8101 0.911117194 1.004487824 0.788254724 0.766004396 1.137252509 0.709583424 0.822116558 0.839556478 1 18.70253733 LVFVHSAEGNEFWSALLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVFVHSAEGNEFWSALLEK 19 0 P07384;E9PRM1;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 230.07 6.56E-20 409016200 932634 912913 832876 1011993 741937 874322 1008372 1023189 681787 FALSE TRUE 888550.2391 1005939.873 871064.1884 910265.541 871330.5779 844044.0099 854526.3314 933593.1469 787515.0459 1.128296207 1.27735956 1.106092122 1.155870667 1.106430388 1.07178144 1.08509207 1.185492457 1 19.58694796 3.232238392 1.493223328 1.09349471 1.197963799 0.286418999 0.062062893 0.421766847 1.958126167 0.019807672 0.028705884 1707.019144 -3.232238392 0.104469089 LVGATATSS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGATAT(0.002)S(0.031)S(0.967)PPPK;LVGATAT(0.049)S(0.013)S(0.937)PPPK 138.31 5.31E-05 247671000 878540 776650 773780 881660 632240 833220 845010 809510 695320 TRUE FALSE 837013.1553 855791.518 809258.5784 793033.8618 742502.4558 804365.3825 716088.2048 738625.0129 803146.6744 1.042167243 1.065548231 1.007609947 0.987408511 0.924491727 1.001517417 0.891603275 0.919663913 1 19.61530396 3.223728969 1.426193996 0.939544945 1.055089735 0.585371559 0.035499577 0.228079813 0.969236436 0.01163414 0.016903429 1673.897919 -3.223728969 0.11554479 LVGDVDFEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVGDVDFEGVR 11 0 P13995-2;P13995;B9A062 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 86.898 0.032865 21575000 36646 34918 35970 40217 46987 32130 40838 37059 40912 FALSE TRUE 34913.81621 38476.1839 37619.26008 36174.31075 55181.51792 31017.33004 34607.41306 33813.9175 47256.42401 0.738816297 0.814200073 0.796066585 0.765489804 1.167704055 0.656362192 0.732332456 0.715541182 1 15.52822284 -1.505269537 7.758310325 1.000029732 0.795122378 0.172747635 0.138548247 6.72E-05 4.28E-06 0.126456531 0.029801774 0.031241398 1.505269537 -0.204907354 LVGIISS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LVGIISSR 8 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 LVGIIS(0.003)S(0.997)R;LVGIIS(0.003)S(0.997)R;LVGIIS(0.004)S(0.996)R;LVGIIS(0.017)S(0.983)R;LVGIIS(0.002)S(0.998)R 123.5 0.0014106 442315000 1523600 1569150 1347840 1673870 1387120 1422210 1443460 1459160 1313550 TRUE FALSE 1451582.447 1729048.169 1409639.797 1505609.407 1629033.289 1372958.511 1223233.666 1331388.215 1517248.625 0.956720226 1.139594487 0.929076338 0.992328734 1.073675904 0.904900152 0.806218339 0.877501678 1 20.53302608 2.111757837 5.571215251 0.869098636 1.023497611 0.37043634 0.075783366 0.170685234 7.712475445 0.027286186 0.019962966 129.3474398 -2.111757837 0.154398975 LVGLNLS(ph)PPMSPVQLPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.978)PPMS(0.022)PVQLPLR 175.39 3.63E-12 143660000 259100 206450 213670 272490 263250 215490 289480 247300 258950 TRUE FALSE 246852.8565 227487.4897 223466.9808 245098.7875 309160.7167 208027.5273 245314.5093 225645.101 299106.6435 0.82530048 0.760556459 0.747114736 0.81943612 1.033613674 0.695496178 0.820157341 0.754396821 1 18.19030043 -2.175858696 2.242952992 1.482620472 0.805396884 0.311938108 0.090049787 5452534.507 1192878.396 13361774.72 0.020496861 0.006670238 2.175858696 -0.677223587 LVGLNLSPPMS(ph)PVQLPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.175)PPMS(0.825)PVQLPLR 245.66 3.31E-24 172700000 213740 175140 176750 206320 208960 178210 233720 190260 213760 TRUE FALSE 203636.9338 192986.9651 184854.1623 185580.3216 245402.5578 172038.543 198061.7214 173599.8258 246908.8091 0.824745519 0.781612312 0.748673824 0.751614826 0.993899565 0.696769563 0.802165472 0.70309288 1 17.91361878 -1.333585925 4.69118766 1.000156875 0.790189058 0.390333987 0.083289019 0.000122707 1.74E-05 0.072412849 0.01705517 0.0463889 1.333585925 -0.209967817 LVGS(ph)PPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVGSPPWK 8 0 Q86UA6-6;Q86UA6-5;Q86UA6-7;Q86UA6-3;Q86UA6-4;Q86UA6-9;Q86UA6-2;Q86UA6;Q86UA6-8 Q86UA6-6 RPAIN RPA-interacting protein 1 LVGS(1)PPWK;LVGS(1)PPWK 70.908 0.052566 129241000 1173770 1139270 1142720 1263950 856690 1293820 1330540 1272530 837880 TRUE FALSE 1118288.218 1255362.908 1195114.842 1136895.345 1006096.465 1249014.689 1127541.686 1161100.527 967814.1511 1.155478267 1.297111544 1.234859855 1.174704196 1.039555439 1.290552207 1.16503947 1.199714352 1 19.88437051 -4.668241755 0.250165189 1.45E-10 1.218142971 0.407246641 0.073431783 149.1362828 1.725239988 76.00944742 0.101161312 2.15E-05 4.668241755 1.21814297 LVGYLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 139.27 0.0076042 1740290000 2456890 1849710 1272610 1414170 2633820 1396660 2668110 1862480 2389530 FALSE TRUE 2340757.679 2038197.552 1330960.427 1272014.945 3093157.374 1348293.314 2261040.816 1699391.378 2760086.108 0.848074149 0.738454335 0.482216994 0.460860602 1.12067423 0.48849683 0.819192129 0.615702305 1 21.39628185 LVHLWSSDSHQPLWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVHLWSSDSHQPLWSR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ; 202.82 1.70E-11 285530000 255700 172115 182161 212970 280130 188865 277850 220480 122432 FALSE TRUE 243613.5677 189653.7142 190513.262 191561.851 328984.5833 182324.5577 235458.8794 201173.6024 141418.1293 1.722647365 1.341084875 1.347162935 1.354577747 2.32632538 1.28925873 1.664983695 1.422544644 1 17.10960755 0.911851178 5.370530041 1.000026072 1.563979033 0.262910926 0.304168367 0.902325373 52.88421528 0.269727407 0.068024963 8.163025972 -0.911851178 0.563952961 LVHSGSGCRS(ph)PSLGSDLTFATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVHSGSGCRSPSLGSDLTFATR 22 1 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 LVHS(0.034)GS(0.095)GCRS(0.868)PS(0.003)LGSDLTFATR 129.22 9.35E-06 78872000 28511 30403 23553 32714 37115 33649 39366 30861 33819 TRUE FALSE 27163.34153 33501.10027 24632.92835 29425.52657 43587.84425 32483.72669 33359.99369 28158.64724 39063.4778 0.695364137 0.8576067 0.630587181 0.753274624 1.115820882 0.831562588 0.853994462 0.720843325 1 15.25353278 2.953827029 24.99908039 0.890904489 0.743629943 0.336977856 0.117564536 540.829843 292817.1845 0.034121985 0.036193073 899.1393996 -2.953827029 -0.147274546 LVHSYPYDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVHSYPYDWR 10 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ;;; 150.61 2.13E-05 1504550000 1877160 1337550 1264180 1254570 1768280 1197970 1771000 1503370 1684850 FALSE TRUE 1788430.367 1473847.866 1322143.903 1128458.24 2076667.472 1156483.999 1500801.423 1371726.953 1946127.933 0.918968551 0.757323216 0.679371526 0.579847923 1.067076546 0.594248702 0.771173055 0.704849321 1 20.89217512 -0.627292902 4.864858979 1.000000037 0.763169028 0.213709897 0.145026979 24842853.5 86171365.41 27.40544536 0.032007996 0.235888679 0.627292902 -0.23683101 LVIASTLYEDGTLDDGEYNPTDDRPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVIASTLYEDGTLDDGEYNPTDDRPSR 27 1 C9JLU1;P52434;P52434-3;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ; 156.23 2.09E-08 88647000 15564 16104.9 18310.9 20599.8 15404.9 16108.5 19074.5 20305 18224.1 FALSE TRUE 14828.32056 17746.00762 19150.47288 18529.06897 18091.50968 15550.65861 16164.3347 18526.98656 21050.20035 0.704426576 0.843032718 0.909752523 0.880232428 0.859445962 0.738741596 0.767894577 0.880133502 1 14.36154634 0.955512486 5.34614393 0.999944786 0.811563821 0.464206146 0.063556589 0.237028857 22.57050717 0.065222199 0.016453187 9.026356584 -0.955512486 -0.188380966 LVIEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LVIEEAER 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;; 143.89 0.0013825 638383000 1316350 1298730 1162091 1479120 1245350 1262656 1381040 1329530 1290410 FALSE TRUE 1254128.744 1431072.064 1215374.022 1330436.047 1462538.646 1218929.906 1170336.983 1213109.305 1490520.192 0.841403391 0.960115851 0.815402588 0.892598473 0.981226993 0.817788254 0.785186936 0.813883174 1 20.50738449 LVIGDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ;;;;; 160.03 0.0013616 3079720000 5128450 4300510 4562860 5302380 3848810 4727200 5547340 5366100 4063260 FALSE TRUE 4886038.332 4738736.858 4772071.644 4769374.689 4520041.245 4563495.879 4700991.399 4896215.837 4693369.609 1.041051257 1.009666243 1.01676877 1.016194139 0.963069526 0.972328254 1.001623949 1.043219743 1 22.16219265 4.270579467 0.858475788 0.996902099 1.047533893 0.241304859 0.022241638 1.757140128 1.583364252 0.00818761 0.073527567 18645.73325 -4.270579467 0.050631794 LVIGS(ph)LPAHLSPHMFGGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVIGSLPAHLSPHMFGGFK 19 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 LVIGS(1)LPAHLSPHMFGGFK 145.9 2.02E-07 30169000 53869 37476 55484 61531 84454 57285 94366 78914 38553 TRUE FALSE 51322.71913 41294.84701 58027.99628 55345.78698 99182.75086 55301.20609 79968.73355 72003.87181 44531.60234 1.152501065 0.927315543 1.303074519 1.242842927 2.227244151 1.24184182 1.795774896 1.616916258 1 15.4425419 LVIIEGDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 237.08 8.52E-12 218122000 370024 385463 302655 386293 348003 305382 372826 359223 359566 FALSE TRUE 352533.6988 424742.1179 316532.0311 347462.0937 408694.613 294806.5448 315944.5463 327767.5298 415325.6589 0.848812712 1.022672471 0.762129727 0.836601559 0.984034105 0.709820206 0.760715211 0.78918199 1 18.66388348 2.235704678 24.9999947 0.788275037 0.896687535 0.089836185 0.105014698 117.2120666 1026019.138 0.035860853 0.027655895 172.0698095 -2.235704678 0.108412499 LVIIEGDLERTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVIIEGDLERTEER 14 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 ;;; 234.9 2.91E-17 192496000 246744 121163 286997 203265 338151 229838 361193 273197 441493 FALSE TRUE 235080.9001 133509.6475 300156.0963 182832.416 397124.4273 221878.6524 306086.3741 249274.4224 509957.4796 0.460981375 0.26180545 0.588590438 0.358524825 0.778740274 0.435092456 0.600219403 0.488814131 1 18.96001743 -4.999999998 0.138449769 2.782888847 0.290964431 0.586166969 0.136188722 86.89800983 0.740547103 42.70682566 0.772171073 1.00E-05 4.999999998 -2.491924416 LVIIESDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 126.07 0.00091287 49439000 106099 111293 88298 107773 95779 89994 104479 107235 99620 FALSE TRUE 101083.9105 122633.8832 92346.55064 96939.45328 112482.8273 86877.48521 88538.80966 97844.93491 115068.5608 0.878466801 1.065746216 0.802535028 0.842449515 0.977528757 0.755006273 0.769443965 0.850318577 1 16.81213419 3.722884537 24.83998271 0.841074764 0.972106516 0.200812954 0.091606119 849.8933317 1346723.171 0.023370973 0.036341655 5283.047767 -3.722884537 0.131031751 LVIIESDLERAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 205.62 1.09E-08 47267500 77165.3 41201.7 76305.4 60747.9 85265.2 62979.5 80601.1 70928.1 106005.1 FALSE TRUE 73517.8492 45400.20007 79804.07807 54641.40568 100135.4239 60798.50412 68303.92185 64717.25955 122443.8295 0.600421022 0.370783895 0.651760717 0.446256915 0.817807025 0.496542001 0.557838824 0.528546516 1 16.90176055 -5 0.343730059 5.980841965 0.533786204 0.5621211 0.121484254 282.6746693 2.356364834 1035.089789 0.087323615 1.00E-05 5 -5.44705576 LVILEGELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVILEGELER 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 104.2 0.0063123 35318000 22872 22701 17611 24463 20315 18652 22277 18857 19562 FALSE TRUE 21790.88589 25014.25771 18418.48177 22003.93276 23857.92957 18006.07656 18878.2345 17205.78111 22595.57505 0.964387312 1.107042315 0.815136668 0.973816011 1.055867333 0.796885077 0.835483694 0.761466839 1 14.46375265 2.232078614 24.99931529 0.833475596 0.990345601 0.318798368 0.096502746 154.6617169 596482.2531 0.033646493 0.025438708 170.6391246 -2.232078614 0.156870005 LVILEGELERAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 LVILEGELERAEER 14 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;;;;; 198.23 2.04E-08 300619600 383783.6 219526.5 367817 299261.1 459049.4 325694.2 467650 390683.8 554829 FALSE TRUE 365642.9098 241896.4999 384681.7733 269178.8057 539107.47 314415.3282 396301.4035 356473.4553 640869.0476 0.570542315 0.377450746 0.600250199 0.420021542 0.84121315 0.49060776 0.618381251 0.55623447 1 19.28967007 -5 0.188069754 2.928499634 0.463940911 0.560162655 0.123989465 91.76666339 0.895028502 66.16276476 0.310456402 1.00E-05 5 -2.464558723 LVINGNPITIFQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 346.79 1.99E-81 1854430000 498970 577350 440260 593970 475670 448590 447530 462140 476400 FALSE TRUE 475384.677 636182.6214 460446.3565 534263.0071 558626.6974 433055.2158 379251.079 421672.5716 550277.6789 0.863899619 1.156111988 0.836752742 0.970897108 1.015172374 0.786975799 0.68919946 0.766290525 1 19.06980028 2.228847296 21.81361209 0.774562773 0.978740294 0.285352758 0.117629235 39.45024327 88591.83361 0.04064267 0.030499259 169.3742153 -2.228847296 0.20417752 LVINGNPITIFQERDPS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)K;LVINGNPITIFQERDPS(1)K;LVINGNPITIFQERDPS(1)K 205.43 5.83E-16 822545000 1271599 1482081 1054212 1536385 767953 1372742 1393658 1514827 794004 TRUE FALSE 1211493.035 1633106.739 1102548.663 1381944.661 901883.7601 1325203.6 1181029.876 1382180.717 917134.0851 1.320955196 1.780663008 1.202167361 1.506807656 0.983371761 1.444939864 1.287739596 1.507065041 1 19.80677315 -4.187044476 0.096112434 5.91E-09 1.68699141 0.210794237 0.214711549 216.761609 1.697054715 47.67627117 4.011482526 6.50E-05 4.187044476 1.686991404 LVINGNPITIFQERDPS(ph)KIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)KIK;LVINGNPITIFQERDPS(1)KIK 198.09 8.30E-22 8038800000 6568600 4797600 5324600 6717400 3460700 6264500 7243300 6583600 3607700 TRUE FALSE 6258115.296 5286480.894 5568738.177 6042154.19 4064244.984 6047558.794 6138201.553 6007105.082 4167163.69 1.501768531 1.268604088 1.336337756 1.449944048 0.975302457 1.451240998 1.472992666 1.441533265 1 21.99063434 4.649939478 3.252873257 1.326834289 1.510743815 0.091714247 0.182331905 0.727012103 12.53901919 0.041445091 0.29458224 44662.13482 -4.649939478 0.183909526 LVINGNPITIFQERDPS(ph)KIKWGDAGAEYVVESTGVFTTMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEK 41 3 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPIT(0.141)IFQERDPS(0.667)KIKWGDAGAEY(0.13)VVES(0.031)T(0.031)GVFTTMEK 76.274 0.0010853 84176000 139100 42226 136310 83706 124170 135170 294180 144960 166290 TRUE FALSE 132525.0187 46528.87741 142559.9483 75291.71385 145825.2087 130489.029 249297.438 132266.5339 192077.4039 0.68995632 0.242240245 0.742200516 0.391986316 0.759200227 0.67935648 1.297900914 0.688610587 1 17.55132828 2.208914571 1.908193093 1.014764553 0.508806981 0.435770195 0.217383531 0.255447226 1.856559214 0.100458777 0.062859855 161.7761779 -2.208914571 -0.505957572 LVINGNPITIFQERDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 294.39 2.61E-49 24761000000 11387900 8241300 9648500 11411200 9750100 10973400 14635000 12257900 11433500 FALSE TRUE 10849616.54 9081097.84 10090893.27 10264124.5 11450514.35 10593388.41 12402161.96 11184533.29 13206548.79 0.821533068 0.687620815 0.764082535 0.777199605 0.867033056 0.802131471 0.939091822 0.846892968 1 23.65475017 1.750602203 0.520631328 0.987680082 0.743350972 0.66921095 0.050929021 0.443353759 0.276896573 0.047589069 0.03108022 56.31216223 -1.750602203 -0.24432911 LVIPSELGYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVIPSELGYGER 12 0 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 115.82 0.0021121 40015000 53150 48176 48774 54050 57953 47752 55341 53713 59295 FALSE TRUE 50637.70483 53085.18917 51010.33614 48616.79131 68059.98485 46098.33627 46897.71404 49009.60497 68490.16576 0.739342711 0.77507754 0.744783365 0.709836088 0.993719085 0.673065042 0.684736466 0.715571417 1 16.06360923 -1.389088708 2.983526502 1.003709946 0.752280289 0.422970705 0.090075443 13000062.05 15590824.36 414408.3891 0.021458016 0.040823599 1.389088708 -0.251429657 LVKPGNQNTQVTEAWNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVKPGNQNTQVTEAWNK 17 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 289.1 5.59E-46 1576600000 2088800 1717900 1868050 2173500 1685040 2092390 2373100 2142400 1861110 FALSE TRUE 1990066.564 1892955.963 1953701.94 1955015.651 1978910.442 2019930.01 2011040.01 1954800.098 2149721.434 0.925732298 0.880558724 0.908816328 0.909427436 0.920542732 0.939624073 0.935488654 0.909327166 1 21.03571829 -4.999999999 0.160383738 1.324566169 0.891800623 0.740870195 0.015819749 63.97336898 0.58868364 6.565427136 0.065096712 1.00E-05 4.999999999 -0.432765546 LVLEVAQHLGESTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LVLEVAQHLGESTVR 15 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ;;;; 237.05 1.00E-17 1131638000 1530295 1153194 1307895 1368657 1935950 1110916 1711925 1346717 1877185 FALSE TRUE 1457960.988 1270705.78 1367863.279 1231076.998 2273579.067 1072444.7 1450739.4 1228791.32 2168289.262 0.672401516 0.58604071 0.630849077 0.567764191 1.048558929 0.494604073 0.66907097 0.566710052 1 21.0481258 -1.396222616 3.091146889 1.004711614 0.652018873 0.344382169 0.149780354 52051888.64 65411475.19 2183931.686 0.03314028 0.040158491 1.396222616 -0.352692741 LVLPSLISSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVLPSLISSR 10 0 Q13228;Q13228-4;Q13228-2;A6PVX1;F2Z2W8;F8WCR4 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 117.81 0.0021127 59827000 187886 164240 143414 155265 197542 150805 200722 156178 167354 FALSE TRUE 179005.0011 180976.2427 149989.6738 139657.4672 231993.2623 145582.585 170098.1724 142502.2264 193306.4036 0.926016923 0.936214421 0.775916736 0.722466843 1.200132318 0.753118274 0.879940702 0.737183165 1 17.5605299 LVLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVLTSR 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 ; 127.66 0.039465 724740000 815820 613960 596630 634890 826080 605370 811210 648330 843810 FALSE TRUE 777257.8054 676523.222 623986.0756 571069.651 970148.0905 584405.8851 687445.0156 591558.7882 974663.7452 0.797462519 0.694109353 0.640206511 0.585914531 0.995366961 0.599597439 0.705315058 0.60693628 1 19.89454506 -1.330249068 3.203506263 1.002094054 0.706559746 0.371913902 0.121176306 32359372.2 43595843.38 641942.1174 0.027382854 0.046746697 1.330249068 -0.295534308 LYPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYPLRK 6 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 154.74 0.015979 1206400000 719110 624360 645110 991140 1009800 1055800 1434800 1243300 1338400 FALSE TRUE 685119.0954 687982.9938 674688.9316 891508.7242 1185908.8 1019237.381 1215894.908 1134430.061 1545952.236 0.44316964 0.445022154 0.436422883 0.576672877 0.767105718 0.659294225 0.786502247 0.733806669 1 20.56006432 2.268778647 0.313982409 1.009911759 0.319181444 0.88212174 0.062447678 0.53383572 0.136632579 0.087791787 0.131927555 185.6857803 -2.268778647 -0.690730315 down LVNACLAEELPHIHAFEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVNACLAEELPHIHAFEQK 19 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;; 263.92 1.55E-31 1487264000 2591630 2611810 2503880 3157370 2059740 2768570 3100220 2543110 66675.7 FALSE TRUE 2469128.786 2877956.408 2618685.375 2839985.169 2418958.004 2672693.727 2627224.5 2320421.807 77015.42702 32.06018432 37.36857042 34.00208862 36.87553622 31.40874624 34.70335529 34.11296413 30.1293117 1 16.23285984 0.461712075 1.504426741 0.993124581 34.60195264 0.970140499 1.824703421 0.428021165 1.047662676 1.593773132 0.460259861 2.895423366 -0.461712075 33.60882806 LVNHFVEEFK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 190.86 8.55E-07 3911242000 8567640 7284710 7246050 8682620 5816430 7886690 8609250 8618690 5644080 FALSE TRUE 8162664.637 8027030.231 7578288.56 7809826.542 6830813.55 7613571.948 7295750.793 7863991.813 6519335.1 1.252070113 1.231265169 1.162432739 1.197948322 1.047777641 1.167844854 1.119094306 1.206256726 1 22.6362934 7.999999991 0.047021805 0.68527469 2.019550865 0.5696425 0.052083492 362.1533373 1.289134005 9.007171739 35.89916378 99999997.88 -7.999999991 1.334276175 LVNHFVEEFKR ddPTM_SK-BR-3_Trastuzumab_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 ; 197.07 3.79E-08 2766800000 4730800 4054400 3818400 4478300 3568800 4130700 5085400 4699800 3567400 FALSE TRUE 4507184.46 4467547.969 3993477.417 4028132.776 4191197.59 3987652.823 4309528.83 4288260.597 4120614.172 1.093813755 1.084194681 0.969146164 0.977556405 1.017129344 0.967732638 1.045846238 1.040684815 1 21.97442795 3.783874298 10.07928724 1.004442161 1.089131794 0.638260617 0.027019958 0.387639976 84.54801977 0.007074147 0.012735194 6079.590078 -3.783874298 0.084689632 LVNNGEKLEFLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVNNGEKLEFLHK 13 1 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 68.034 0.03096 284850000 176490 124680 146190 159060 139570 153530 238730 170780 177970 FALSE TRUE 168147.6675 137385.0337 152892.9561 143070.9866 163910.9638 148213.2176 202307.3539 155825.5978 205568.6787 0.817963459 0.668316957 0.743756087 0.695976583 0.797353784 0.720991245 0.984135109 0.758022082 1 17.64926094 1.751575969 25 0.906322993 0.738885982 0.52740833 0.077215535 2.856720544 5495.583774 0.031582113 0.017514035 56.43856575 -1.751575969 -0.167437011 LVPGWTKPITIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVPGWTKPITIGR 13 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 167.22 7.92E-07 0 2529800 1914820 1998890 1991330 2074130 1743570 2086880 1966460 2113470 FALSE TRUE 2410221.368 2109942.335 2090541.084 1791157.725 2435857.615 1683189.734 1768488.128 1794266.338 2441216.133 0.987303555 0.864299685 0.856352314 0.73371534 0.99780498 0.689488207 0.72442915 0.734988727 1 21.2191686 4.63798373 0.640320506 0.786090205 1.100671231 0.164662966 0.110394514 4.004822752 1.352528886 0.046435975 0.908595159 43449.39463 -4.63798373 0.314581027 LVPLLDTGDIIIDGGNSEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVPLLDTGDIIIDGGNSEYR 20 0 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 87.498 0.0054778 15488000 11358 11096 12914 12291 12857 8749.3 13097 13892 14118 FALSE TRUE 10821.12985 12226.69502 13506.11967 11055.48533 15099.25673 8446.309547 11098.81211 12675.54283 16307.34734 0.663573886 0.749766027 0.828222972 0.677945045 0.925917405 0.517945033 0.680601932 0.777290296 1 13.9932345 0.892454424 5.262191474 0.999985019 0.71724896 0.401287701 0.106679007 0.909048312 43.39076298 0.09566397 0.024141006 7.806465134 -0.892454424 -0.282736059 LVPLLDTGDIIIDGGNSEYRDTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LVPLLDTGDIIIDGGNSEYRDTTR 24 1 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;;;; 250.83 9.55E-39 963760000 198163.3 127665.7 198925.8 176874 248235.3 186056 268896 223787.2 291035.3 FALSE TRUE 188796.5135 140674.98 208046.7447 159094.2895 291527.4577 179612.8341 227870.9766 204191.2064 336167.5679 0.561614301 0.41846684 0.618878097 0.473258888 0.867208754 0.534295545 0.677849377 0.607409 1 18.35882102 -5 0.127198819 2.402724815 0.398838277 0.572379 0.11500405 95.09466616 0.769104586 33.95903038 0.838140151 1.00E-05 5 -2.003886539 LVPLLDTGDIIIDGGNSEYRDTTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LVPLLDTGDIIIDGGNSEYRDTTRR 25 2 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 179.03 1.58E-17 106272000 81454 48289.3 97617 72357 126038 83389 141741 91210 181386 FALSE TRUE 77603.83085 53210.03457 102092.836 65083.53689 148018.9873 80501.21802 120115.8072 83223.16887 209514.4145 0.370398529 0.253968371 0.487283113 0.310639901 0.706485936 0.384227587 0.573305696 0.397219299 1 17.67668998 -5 0.150678589 3.060220996 0.248251727 0.674386158 0.125493613 69.90692978 0.624146246 43.0549876 0.556376801 1.00E-05 5 -2.811969269 LVPS(ph)QEETKLSVEESEAAGDGVDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVPSQEETKLSVEESEAAGDGVDTK 25 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 LVPS(0.827)QEET(0.173)KLSVEESEAAGDGVDTK;LVPS(0.943)QEET(0.055)KLS(0.002)VEESEAAGDGVDTK 175.28 1.20E-12 132869000 294580 222270 261710 290940 153702 284530 300610 323030 173794 TRUE FALSE 280655.7872 244919.5657 273709.6624 261694.1585 180507.5801 274676.6548 254746.4234 294743.7807 200745.0859 1.398070523 1.220052609 1.363468805 1.303614269 0.899188039 1.368285821 1.26900453 1.468249045 1 17.61500515 7.999924714 0.749228561 1.242698805 29.11959449 0.080297865 0.17094103 1056.413085 4.548120034 0.055349837 49702.11566 99982666.22 -7.999924714 27.87689568 LVPVS(ph)PLPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;LVPVS(1)PLPPK 107.85 0.0023389 385505000 1253938 1296640 1332513 1462371 1095177 1413585 1602607 1469291 1335867 TRUE FALSE 1194666.836 1428769.09 1393610.039 1315370.689 1286175.522 1364632.197 1358099.868 1340632.091 1543026.432 0.774236145 0.92595244 0.903166667 0.85246154 0.833540823 0.884386793 0.88015334 0.868832875 1 20.55733134 -5 0.241204026 1.765873054 0.853340651 0.530488929 0.04040491 143.576805 1.430620199 53.97406041 0.062062946 1.00E-05 5 -0.912532403 LVQAEYWHDPIKEDVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LVQAEYWHDPIKEDVYR 17 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;;;;; 292.13 3.08E-46 4018450000 6322500 5172490 4998190 6074060 4838580 5453580 6611930 6205720 4303070 FALSE TRUE 6023647.955 5699572.612 5227361.955 5463483.949 5682426.82 5264721.157 5603158.642 5662314.258 4970368.119 1.211911837 1.146710359 1.051705192 1.099211129 1.143260757 1.059221577 1.127312607 1.139214264 1 22.24492127 LVQAFQFTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 275.33 1.76E-23 2975200000 2945300 2478800 2119930 2598800 2130900 2449400 2883600 2668600 2129400 FALSE TRUE 2806081.506 2731392.538 2217130.887 2337563.687 2502528.285 2364576.664 2443653.859 2434923.237 2459616.477 1.140861404 1.1104953 0.901413252 0.950377308 1.017446545 0.961359906 0.993510119 0.989960533 1 21.23000195 3.846942593 6.302324861 0.974700533 1.128953655 0.793133898 0.032409355 0.089067 4.469996295 0.008110563 0.014774574 7029.793902 -3.846942593 0.154253123 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSK 39 3 P32119 P32119 PRDX2 Peroxiredoxin-2 0 118.81 1.06E-06 1086400000 1280600 936390 1135300 1207500 665500 1279900 1454200 1535100 628100 FALSE TRUE 1220068.576 1031809.206 1187354.628 1086119.806 781562.9893 1235576.742 1232335.082 1400678.506 725502.5401 1.681687532 1.422199301 1.6365961 1.497058585 1.077271196 1.703063289 1.69859513 1.930632118 1 19.46862114 LVQSPNSYFMDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVQSPNSYFMDVK 13 0 P42677;H0YMV8;Q71UM5;C9JLI6 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 113.24 0.0019484 42993000 152740 134530 118260 163400 100480 151270 134860 150610 111060 FALSE TRUE 145520.2829 148238.7599 123682.338 146974.7216 118003.6802 146031.482 114284.6301 137421.79 128282.6176 1.134372572 1.155563885 0.964139494 1.145710341 0.919872719 1.138357517 0.890881651 1.071242484 1 16.96896617 3.684340958 0.797612334 0.999737282 1.166972883 0.210447652 0.087716993 0.995192004 1.157168766 0.034608271 0.114394913 4834.381928 -3.684340958 0.167235601 LVREDENDAS(ph)DDEDDDEKRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVREDENDASDDEDDDEKRR 20 3 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 LVREDENDAS(1)DDEDDDEKRR;LVREDENDAS(1)DDEDDDEKRR;LVREDENDAS(1)DDEDDDEKRR;LVREDENDAS(1)DDEDDDEKRR 233.83 9.30E-29 2257180000 1104850 849850 988520 1123970 693890 1101120 1256630 1257140 926420 TRUE FALSE 1052625.93 936450.6812 1033844.62 1010986.4 814904.1963 1062987.938 1064908.014 1147058.157 1070084.482 0.983684884 0.875118457 0.966133644 0.944772508 0.76153258 0.99336824 0.995162561 1.071932335 1 20.02929327 2.023379483 24.99986225 1.014937046 0.910510754 0.419712329 0.064058954 228.901861 244765.4931 0.022892816 0.016906536 105.5308614 -2.023379483 -0.104426292 LVRLS(ph)SDSFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.526)S(0.473)DSFAR;LVRLS(0.756)S(0.244)DSFAR 206.55 1.58E-08 172391000 87690 95722 103802 122747 130590 93279 111480 99590 147192 TRUE FALSE 83545.06748 105476.1806 108561.4244 110408.2384 153364.8547 90048.72484 94471.67853 90869.37164 170017.7836 0.491390169 0.620383223 0.638529818 0.649392293 0.902051841 0.529642976 0.555657629 0.534469805 1 17.37532613 -1.814803204 2.70288445 1.122964877 0.610612937 0.529301655 0.11397044 30560576.89 20875866.25 24481617.78 0.027265275 0.015317814 1.814803204 -0.51235194 LVRPPVQVYGIEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVRPPVQVYGIEGR 14 1 A0A494C0K9;H7C0C1;P48047;H7C086 A0A494C0K9 ATP5O "ATP synthase subunit O, mitochondrial" 0 ; 162.32 4.06E-06 2574200000 5043100 4127900 4005900 4643000 3938700 4148000 5132100 4929800 4368500 FALSE TRUE 4804722.657 4548537.703 4189574.477 4176276.819 4625608.033 4004353.72 4349103.888 4498120.577 5045944.669 0.952194876 0.901424411 0.830285457 0.827650141 0.916698128 0.793578603 0.861900828 0.891432799 1 22.26669296 0.851383699 5.093522175 0.999997458 0.872585233 0.436513074 0.046286305 1.96778799 66.66011176 0.047235613 0.011932321 7.102049567 -0.851383699 -0.127412225 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.991)PET(0.009)EASEESLQFNLEKPATGER;LVS(0.967)PET(0.033)EASEESLQFNLEKPATGER;LVS(0.971)PET(0.026)EAS(0.002)EESLQFNLEKPATGER;LVS(0.995)PET(0.005)EASEESLQFNLEKPATGER 209.96 1.24E-25 320482000 241021 222934 198608 265617 193371 234147 254140 242419 198366 TRUE FALSE 229628.415 245651.2281 207714.3733 238916.6745 227094.8412 226038.4307 215366.2754 221191.5072 229127.5862 1.002185808 1.072115463 0.906544588 1.042723308 0.991128327 0.98651775 0.939940402 0.965363931 1 17.80579164 3.36934364 0.681634266 0.967284452 1.033908698 0.083138991 0.044981143 1.394296329 1.345641357 0.025124563 0.055504254 2340.688598 -3.36934364 0.066624247 LVS(ph)PGSANETSSILVESVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(1)PGSANETSSILVESVTR;LVS(0.991)PGS(0.009)ANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(0.445)PGS(0.445)ANET(0.076)S(0.015)S(0.02)ILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(0.918)PGS(0.081)ANETSS(0.001)ILVESVTR;LVS(0.584)PGS(0.416)ANETSSILVESVTR 380.65 6.70E-113 3857723000 671754 576525 561092.5 691118 605119.4 549394.5 610582 614201.6 567078.3 TRUE FALSE 640001.5197 635273.553 586819.1461 621645.5056 710652.0318 530368.8307 517426.5018 560418.8518 655017.9065 0.977074845 0.969856773 0.895882601 0.949051162 1.084935274 0.80970127 0.789942529 0.855577911 1 19.32117482 2.21134541 24.98624629 0.838955099 0.969957133 0.33971827 0.073533503 194.3473934 178428.8961 0.02544511 0.018796986 162.6842128 -2.21134541 0.131002034 LVS(ph)SPELGHDEFSTQALAR ddPTM_SK-BR-3_Trastuzumab_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 137.12 2.89E-06 46154000 18192 18582 14458 25162 27742 17587 19666 18228 21997 TRUE FALSE 17332.10021 20475.52693 15120.9136 22632.66796 32580.19602 16977.95778 16665.59051 16631.85969 25408.18241 0.682146402 0.805863505 0.595119846 0.890762967 1.282271809 0.668208276 0.655914313 0.654586755 1 14.63300555 -1.888747373 5.373223014 1.056829148 0.774909938 0.108913407 0.197975458 0.112109037 0.002321219 0.159447925 0.044796233 0.012919706 1.888747373 -0.281919211 LVSDSLSEHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVSDSLSEHEK 11 0 Q96KR1;H0Y8W1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 179.19 7.21E-06 112780000 252920 217990 240930 294660 232420 260440 306930 307590 250740 FALSE TRUE 240964.9728 240203.4288 251976.8788 265040.217 272953.9744 251420.8975 260102.1913 280655.789 289623.4786 0.831993918 0.829364491 0.870015373 0.915119928 0.942444224 0.868095704 0.898070117 0.969036731 1 18.14381904 8 0.076041974 1.111955999 0.332323625 0.740649248 0.028540214 108.4846064 0.604398344 0.989569668 8.940570041 99999999.98 -8 -0.779632374 LVSFHDDS(ph)DEDLLHI ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVS(0.019)FHDDS(0.981)DEDLLHI;LVS(0.003)FHDDS(0.997)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI 341.29 1.27E-69 1846593800 1317304.7 1168193.4 1268493.6 1478373.4 1576072.3 1320753.6 1668705.3 1464577.7 1149258.3 TRUE FALSE 1255038.317 1287233.636 1326655.286 1329764.497 1850938.81 1275015.572 1414113.659 1336331.512 1327479.408 0.945429594 0.969682564 0.999379183 1.001721375 1.394325817 0.960478607 1.065262218 1.006668356 1 20.34025805 2.981546244 24.98360807 1.089006269 0.971530044 0.169035792 0.118539743 1243.186682 1683090.381 0.034067379 0.036761119 958.3987621 -2.981546244 -0.117476225 LVSGWVKPIIIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVSGWVKPIIIGR 13 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 156.08 1.23E-06 0 268960 225010 221350 256890 261820 228500 312850 252260 286580 FALSE TRUE 256246.7938 247938.7748 231499.1164 231066.9291 307481.3251 220586.9877 265118.9866 230170.7771 331021.3628 0.774109537 0.749011401 0.699347965 0.698042348 0.928886651 0.666382936 0.800912015 0.695335114 1 18.3365648 -1.265860455 3.662315257 1.000497149 0.754429683 0.520658994 0.074885409 5352627.24 5586151.928 17952.25547 0.015430005 0.054217507 1.265860455 -0.246067466 LVSKDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVSKDGK 7 1 P19338;H7BY16 P19338 NCL Nucleolin 0 68.214 0.057509 398850000 754240 362110 852460 534650 766210 834650 1382300 1004900 1151000 FALSE TRUE 718588.57 399009.4207 891546.1342 480905.9662 899836.7814 805745.8612 1171404.747 916905.6287 1329491.202 0.540498929 0.300121896 0.670591978 0.361721812 0.676827933 0.606055806 0.881092516 0.689666564 1 20.3424428 1.872062616 0.570893283 0.971077971 0.423826079 0.632849985 0.127159948 0.427416322 0.295033742 0.108021615 0.067876715 74.48393554 -1.872062616 -0.547251891 LVTSIGDVVNHDPVVGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LVTSIGDVVNHDPVVGDR 18 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 275.04 4.68E-39 1817450000 1607174 1807533 1610861 1797300 1653731 1581456 1604084 1770340 1433710 FALSE TRUE 1531206.07 1991722.668 1684720.57 1616631.989 1942141.163 1526689.782 1359351.525 1615319.644 1656042.424 0.924617659 1.202700268 1.017317277 0.976202038 1.172760513 0.921890502 0.820843418 0.975409579 1 20.6593082 2.102443239 8.565702915 0.902123088 1.060298815 0.296157376 0.095356459 0.253755808 19.10306585 0.033809781 0.024951341 126.602779 -2.102443239 0.158175727 LVVADTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVVADTR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 89.673 0.041178 65321000 164580 168420 147650 190260 215200 154450 192100 172890 229920 FALSE TRUE 156800.6296 185582.1895 154419.8985 171134.7033 252730.8119 149101.3578 162791.6168 157750.8351 265574.8193 0.590419792 0.698794373 0.581455346 0.64439356 0.951636953 0.561428821 0.612978359 0.593997712 1 18.01875884 -1.483408664 3.265197424 1.007090064 0.653739234 0.482560273 0.112470432 47828934.27 59658078.79 3063785.947 0.025708974 0.032854233 1.483408664 -0.35335083 LVVLDEELEGISPDELKDELPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LVVLDEELEGISPDELKDELPER 23 1 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;;; 249.2 5.81E-38 186252000 176130 139261 120877.3 191415 115007.2 156455 196568 169162 128513.3 FALSE TRUE 167804.684 153451.8542 126419.6438 172173.6005 135064.4193 151036.9241 166577.9414 154349.2785 148442.4862 1.130435688 1.033746188 0.851640571 1.1598674 0.909877103 1.017477731 1.122171594 1.03979179 1 17.17954454 -0.48915622 7.81599858 1 1.039171244 0.008243988 0.095551599 0 0 0.085994345 0.020269062 0.324222971 0.48915622 0.039171244 LVVLDEELEGISPDELKDELPERQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LVVLDEELEGISPDELKDELPERQPR 26 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 255.41 7.51E-53 64529000 147271 93713 143330 138781 126354 146576 195148 177149 138454 FALSE TRUE 140309.7917 103262.4612 149901.8223 124830.4702 148390.0976 141500.0364 165374.5885 161636.8944 159924.7392 0.877348885 0.645694104 0.937327289 0.780557598 0.927874564 0.884791416 1.034077587 1.010706006 1 17.2870336 2.368883476 0.87085409 1.025447581 0.780617353 0.523676537 0.080382383 0.404230055 0.600372757 0.054924513 0.035560384 233.82098 -2.368883476 -0.244830228 LVWGSFGS(ph)GLLES(ph)S(ph)GVIVGGGDNGMLILY(ph)NVTHILSSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVWGSFGSGLLESSGVIVGGGDNGMLILYNVTHILSSGK 39 0 E9PKR7;Q9NQW1-2;Q9NQW1-4;Q9NQW1-5;Q9NQW1 E9PKR7 SEC31B Protein transport protein Sec31B 4 LVWGS(0.634)FGS(0.682)GLLES(0.71)S(0.703)GVIVGGGDNGMLILY(0.797)NVT(0.471)HILS(0.003)S(0.001)GK 44.439 0.023498 162310000 43184 26761 39227 36375 55798 25322 49333 29529 15597 TRUE FALSE 41142.7779 29487.97632 41025.59675 32718.51589 65529.15353 24445.09279 41806.34479 26943.28422 18015.7031 2.283717581 1.636792978 2.277213191 1.816110962 3.637335338 1.356876979 2.320550275 1.495544418 1 14.13696734 1.038768274 3.365120098 1.001057244 2.148617057 0.309794012 0.604906758 0.248255397 6.220992096 0.519514003 0.135501884 10.9337282 -1.038768274 1.147559813 LWACNFCFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWACNFCFQR 10 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 95.909 0.016519 49835000 103390 68890 61876 71908 97182 68674 107020 86969 109420 FALSE TRUE 98502.9596 75909.96932 64713.0758 64679.67122 114130.51 66295.80216 90692.13344 79353.53331 126388.2948 0.77936774 0.600609174 0.512017952 0.51175365 0.903014874 0.524540681 0.717567506 0.627855083 1 16.94750333 -2.740376256 0.476474301 1.799650024 0.645036414 0.437648706 0.125675904 149.0352789 6.385243743 122.1989798 0.0581972 0.001818125 2.740376256 -1.15461361 LWDEESAQLLPHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWDEESAQLLPHWK 14 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 170.18 1.68E-07 0 135170 120490 118460 127720 114320 123860 146890 139290 101400 FALSE TRUE 128780.782 132768.068 123891.5082 114881.3429 134257.3718 119570.6971 124479.2327 127093.0292 117124.5941 1.099519558 1.133562673 1.057775347 0.980847309 1.146278225 1.020884623 1.06279329 1.085109666 1 16.83768452 8 0.091022341 0.970968053 1.372566382 0.197595369 0.048342607 213.7486652 1.396420805 0.794192159 10.71791023 100000000 -8 0.401598329 LWDFQGFECIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LWDFQGFECIR 11 0 P43034;I3L3N5;P43034-2 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 133.89 0.00035409 151043000 296250 305570 267220 285140 326100 232920 329310 281400 329720 FALSE TRUE 282246.8496 336707.9304 279472.3013 256477.1855 382971.7368 224853.922 279067.7113 256759.1242 380851.2936 0.741094633 0.884092915 0.73380951 0.67343131 1.005567641 0.59039821 0.73274718 0.674171595 1 18.53886827 3.691658152 24.97380164 0.754878478 0.812594051 0.001070962 0.139159612 1493.280787 795115.9488 0.033596603 0.052047829 4916.523869 -3.691658152 0.057715573 LWDMFDSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LWDMFDSWR 9 0 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 ; 125.31 0.0011749 89650000 319440 280900 258000 291480 328580 259420 376100 268010 302600 FALSE TRUE 304340.7043 309524.0294 269829.5552 262179.8766 385884.248 250436.2204 318719.0374 244541.6236 349525.6625 0.870724919 0.885554517 0.771987823 0.750101937 1.104022649 0.716503099 0.911861622 0.699638538 1 18.41503886 LWDVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LWDVDR 6 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ;;;;; 143.09 0.026623 455492000 1374753 1045390 1092459 1360290 1521060 1083012 1572420 1256733 1603060 FALSE TRUE 1309771.15 1151916.43 1142549.326 1223551.065 1786332.382 1045507.023 1332518.45 1146686.796 1851654.358 0.707351858 0.622101217 0.617042442 0.660788046 0.964722371 0.564634009 0.71963671 0.619276914 1 20.82038339 -1.607808379 2.894932594 1.023185104 0.683229547 0.450561016 0.109504666 23769777.26 23259792.9 4160865.505 0.024379717 0.024671277 1.607808379 -0.339955557 LWEISTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWEISTGR 8 0 Q05048;A0A0A0MSZ9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 94.874 0.023381 52150000 90278 89069 78049 84561 101480 80660 96657 92198 98544 FALSE TRUE 86010.73785 98145.23236 81627.62385 76060.76762 119178.0799 77866.72397 81910.19942 84124.65435 113825.7002 0.755635482 0.862241411 0.717128238 0.66822139 1.047022594 0.684087371 0.719610767 0.739065555 1 16.79646681 -1.861395793 2.340222229 1.106148743 0.775960102 0.292971655 0.110241304 9598824.117 5214850.706 5667331.32 0.02838793 0.013759549 1.861395793 -0.330188641 LWFTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWFTYR 6 0 Q9Y4P1;H0Y2Y0;F2Z2K8;C9JIK8;Q9Y4P1-6;Q9Y4P1-2;G5E979;Q8WYN0-2;Q8WYN0 Q9Y4P1 ATG4B;ATG4A Cysteine protease ATG4B;Cysteine protease ATG4A 0 106.76 0.074087 26638000 79634 55633 63009 58495 81477 66349 109830 77650 76767 FALSE TRUE 75869.85864 61302.06595 65898.02497 52614.97147 95686.563 64051.31749 93073.41633 70850.55435 88671.63429 0.85562716 0.691337951 0.743169171 0.59336869 1.079111305 0.72234281 1.049641377 0.799021637 1 16.43618505 2.74124022 24.99377772 0.925442722 0.732163686 0.411523823 0.123883981 235.3672647 2195375.055 0.034613723 0.035213182 551.1124478 -2.74124022 -0.193279037 LWLFGYDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWLFGYDEQR 10 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 128.12 0.00078632 87213000 919080 759010 751190 853090 434640 946260 959640 930320 384660 FALSE TRUE 875636.9098 836353.9819 785632.8045 767335.7724 510441.0784 913490.7789 813229.293 848856.2489 444311.1082 1.970774292 1.88236118 1.768204283 1.727023606 1.148837085 2.055971057 1.830315016 1.910499722 1 18.76121069 3.6756113 2.025480932 1.676610707 1.942667382 0.12013636 0.326996855 0.756790915 6.073046916 0.088880157 0.171843527 4738.177219 -3.6756113 0.266056675 LWPSGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 LWPSGDR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;;;;;; 196.94 0.0010086 6652722000 3280840 2803550 2898690 3319010 3797470 2798780 3637330 3028780 3887510 FALSE TRUE 3125761.195 3089234.932 3031597.804 2985376.809 4459747.566 2701857.547 3082388.504 2763563.967 4490365.196 0.696104005 0.687969641 0.675133908 0.664840537 0.993181483 0.601701071 0.686444948 0.615443031 1 22.09840135 -2.258065991 2.268647065 2.147646192 0.701955352 0.42834815 0.107968763 5268880.327 721188.1089 31121826.15 0.024247547 0.005519936 2.258065991 -1.44569084 LWSLDSDEPVADIEGHTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LWSLDSDEPVADIEGHTVR 19 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 ;; 222.3 2.47E-19 92919000 94646 83875 87521 93057 104728 81707 115399 94793 100585 FALSE TRUE 90172.27115 92421.95786 91533.92442 83702.73356 122992.53 78877.4661 97792.7631 86492.42239 116183.2081 0.776121374 0.795484643 0.787841255 0.720437445 1.058608486 0.678905906 0.841711679 0.744448564 1 16.82604205 -1.525516678 2.734342067 1.010002836 0.801080554 0.274731114 0.10189222 16500656.16 16660582.96 1224260.652 0.021393234 0.02981833 1.525516678 -0.208922282 LWSVPDCNLLHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWSVPDCNLLHTLR 14 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 165.33 3.98E-06 80960000 139360 118050 94478 115110 154140 100340 164810 127510 138290 FALSE TRUE 132772.729 130079.4292 98809.90975 103538.9241 181021.9672 96865.20064 139665.2076 116344.5484 159735.3069 0.831204644 0.814343627 0.618585281 0.648190598 1.133262086 0.606410709 0.874354019 0.728358374 1 17.28532371 LWSWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LWSWGR 6 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 195.75 0.00058755 809110000 1040930 927090 754390 804730 1012930 714880 1074430 931290 962620 FALSE TRUE 991727.3018 1021561.525 788979.5277 723837.0115 1189584.671 690123.5263 910505.9702 849741.3105 1111898.193 0.891922757 0.918754551 0.709578928 0.650992165 1.069868337 0.620671506 0.818875303 0.764225822 1 20.08459327 3.764159879 24.27327398 0.792372771 0.905338682 0.075689628 0.140748827 1070.481254 1015027.595 0.032363391 0.058313471 5809.782563 -3.764159879 0.11296591 LWTFLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWTFLEDR 8 0 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 75.854 0.066121 0 64382 61422 51517 54711 48236 57604 58810 54590 45732 FALSE TRUE 61338.79045 67680.97163 53879.10541 49211.34634 56648.34313 55609.15904 49837.45438 49809.8102 52823.88499 1.16119423 1.281256985 1.019976199 0.931611644 1.072400168 1.05272755 0.943464389 0.942941062 1 15.68890279 3.668254597 5.950673981 0.992102793 1.220736229 0.752856412 0.054044032 0.092850384 6.062229964 0.014303094 0.02244756 4658.59115 -3.668254597 0.228633436 LWTLSANDMEDDS(ph)MDLIDSDELLDPEDLKKPDPASLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWTLSANDMEDDSMDLIDSDELLDPEDLKKPDPASLR 37 2 Q6FI81-3;Q6FI81 Q6FI81-3 CIAPIN1 Anamorsin 1 LWTLS(0.001)ANDMEDDS(0.915)MDLIDS(0.084)DELLDPEDLKKPDPASLR 60.194 0.014759 30297000 27042 22385 27052 33333 20675 33203 38037 29576 25340 TRUE FALSE 25763.77825 24666.05695 28292.36096 29982.30351 24280.71345 32053.17178 32233.75705 26986.16865 29269.59778 0.880223174 0.842719368 0.966612564 1.024349693 0.829554052 1.095101204 1.101270926 0.921986317 1 14.8371153 3.29256432 0.762847731 1.031376753 0.848830363 0.264615213 0.082114608 0.763529421 0.960533829 0.043894917 0.08357929 1961.391642 -3.29256432 -0.18254639 LWTLVSEQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LWTLVSEQTR 10 0 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 145.25 7.16E-05 302720000 183840 183170 102740 151370 190550 146000 185110 193290 181010 FALSE TRUE 175150.2475 201835.2312 107450.7306 136154 223781.8597 140943.9834 156868.0697 176364.5029 209080.1063 0.837718378 0.965348807 0.513921351 0.651204949 1.070316366 0.674114749 0.750277358 0.843525986 1 17.67369627 0.92621468 6.504979706 0.999995168 0.791820845 0.160160933 0.157185087 1.680984426 146.3032193 0.147932646 0.037141684 8.437517367 -0.92621468 -0.208174323 LWTPPEDYRL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LWTPPEDYRL 10 1 H0YAX3;Q9BYD1 H0YAX3 MRPL13 "39S ribosomal protein L13, mitochondrial" 0 ; 118.26 0.017387 93904000 217330 165113 182054 178731 226540 149200 216170 192646 220770 FALSE TRUE 207057.2416 181938.2024 190401.356 160764.6203 266048.5043 144033.1666 183189.2963 175776.895 255005.8841 0.811970447 0.713466684 0.746654755 0.630434944 1.043303394 0.564822914 0.718372821 0.689305251 1 17.96017101 LWVDEAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LWVDEAVR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 176.29 0.00060758 728650000 1448520 1067750 808680 981150 1585580 898810 1511390 1196410 1580990 FALSE TRUE 1380051.33 1176554.939 845758.7779 882522.9379 1862104.65 867683.9843 1280799.697 1091645.998 1826161.855 0.755711399 0.64427747 0.463134621 0.483266549 1.019682152 0.475140789 0.701361543 0.597781623 1 20.80038321 -1.297017922 3.015222126 1.002642888 0.647153388 0.315314329 0.165414305 28253707.03 36815707.35 685018.4833 0.038930949 0.050464047 1.297017922 -0.3554895 LYANMFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LYANMFER 8 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 164.53 0.00076672 1134753000 1853596 1306730 960653 1006273 2404270 962832 2110674 1383484 2398970 FALSE TRUE 1765980.191 1439887.273 1004699.89 905120.5262 2823573.927 929488.8864 1788651.916 1262338.807 2770990.015 0.637310196 0.519629181 0.362577954 0.326641569 1.018976579 0.335435668 0.645492011 0.455555162 1 21.40197008 -1.881178912 2.45543622 1.233135772 0.543428956 0.334976076 0.204567132 15699549.52 8770760.905 21257102.39 0.044109699 0.013146831 1.881178912 -0.689706816 LYAVHQEGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LYAVHQEGNK 10 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 136.36 0.00011973 3160840000 10110940 8524540 6915460 8722120 7303290 8616650 10033480 9829860 7046870 FALSE TRUE 9633015.904 9393200.318 7232540.681 7845355.927 8576981.464 8318253.25 8502688.348 8969105.347 8139662.609 1.18346624 1.154003645 0.888555341 0.963842889 1.053726902 1.021940792 1.044599605 1.101901366 1 22.95653757 3.901510238 8.920477706 1.01490798 1.172445361 0.574462018 0.05669477 0.222965721 18.47835359 0.0146566 0.026492253 7970.952809 -3.901510238 0.157537381 LYAYEPADTALLLDNMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYAYEPADTALLLDNMKK 18 1 O95994 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 128.64 3.67E-05 149733000 254550 180271 240200 241710 219320 242480 314020 290840 282230 FALSE TRUE 242517.926 198640.8199 251213.4076 217412.8516 257569.3386 234082.8568 266110.4816 265372.5078 325996.787 0.74392735 0.609333674 0.77060087 0.666917161 0.790097783 0.71805265 0.816297866 0.81403412 1 18.31449822 0.750252927 0.408388727 1.023152905 0.677950099 0.76201254 0.05069902 0.706719253 0.274254783 0.080271493 0.03392697 5.6266892 -0.750252927 -0.345202805 LYDAYELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYDAYELK 8 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 134.15 0.002068 272790000 1079400 846720 718090 887990 771690 841660 1143630 972010 879960 FALSE TRUE 1028378.901 933001.7306 751015.1368 798727.5581 906272.4917 812513.1032 969148.2393 886895.6515 1016419.703 1.011766004 0.9179296 0.738882899 0.785824553 0.891632157 0.7993874 0.953492181 0.872568339 1 19.95506482 0.543675402 1.031525055 0.999257823 0.875468641 0.196624352 0.08115326 3.108055312 4.861200362 0.084251158 0.026558846 3.496837104 -0.543675402 -0.123789182 LYDDIDFDIEEFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYDDIDFDIEEFAK 14 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;;; 227.37 4.78E-12 253101000 819260 960950 686485 975540 468208 789870 725886 908140 440862 FALSE TRUE 780535.2034 1058871.898 717961.0163 877476.8658 549863.327 762516.6038 615138.7589 828618.4472 509228.6273 1.532779505 2.079364436 1.409899165 1.723149129 1.079796574 1.497395399 1.207981496 1.627203191 1 18.957954 3.130285532 1.620780367 1.311024995 1.779321633 0.340142424 0.258251216 0.350533035 1.903039608 0.079761926 0.104657769 1349.850064 -3.130285532 0.468296638 LYDIDVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LYDIDVAK 8 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ;; 133.55 0.002128 156549000 608699 557812 558109 659317 496350 611847 670032 633062 557175 FALSE TRUE 579927.0046 614653.677 583698.8497 593041.2025 582913.2828 590658.585 567806.3124 577627.7352 643578.8533 0.901097048 0.955055738 0.906957783 0.921474035 0.90573716 0.917771897 0.882263781 0.897524417 1 19.2957574 LYDKIDPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYDKIDPEK 9 1 O14561;I3L505 O14561 NDUFAB1 "Acyl carrier protein, mitochondrial;Acyl carrier protein" 0 70.17 0.04849 103800000 248900 232140 185700 247420 120670 199260 206050 233240 132950 FALSE TRUE 237134.9903 255795.3299 194214.5287 222548.8715 141714.8098 192359.5762 174613.2881 212816.2691 153567.207 1.544177269 1.665689798 1.26468751 1.44919528 0.922819478 1.252608418 1.137048017 1.385818452 1 17.22851065 3.422165863 1.50895749 1.166880582 1.607472362 0.530525291 0.158994404 0.254910746 1.185656841 0.046396482 0.079678961 2643.418121 -3.422165863 0.44059178 LYDLNHNEIGELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 208.47 8.00E-09 432962000 420130 365328 378577 472758 466014 410425 469998 427165 444247 FALSE TRUE 400271.2875 402555.3385 395935.1299 425235.4677 547286.6941 396211.8793 398291.173 389760.1681 513138.5559 0.780045239 0.784496378 0.771594973 0.828695218 1.066547598 0.772134299 0.776186409 0.75956126 1 18.9689889 -2.523026379 2.201481042 3.639121694 0.813801916 0.28531027 0.090661223 5218239.738 256665.4254 69745979.76 0.021957248 0.00299898 2.523026379 -2.825319778 LYEEGSNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LYEEGSNKR 9 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 158.08 0.00010757 4338580000 3772880 3502990 3269590 3783020 2746840 3460240 3714940 3635480 3032720 FALSE TRUE 3594543.44 3859948.664 3419503.936 3402743.642 3225888.026 3340411.021 3148157.673 3317138.098 3503018.729 1.026127383 1.1018921 0.976159193 0.971374665 0.920888033 0.953580691 0.898698499 0.946937015 1 21.74016727 3.513098883 2.841559807 0.939609967 1.063666143 0.648898055 0.033811078 0.127709886 2.056229747 0.009014684 0.014166268 3259.10898 -3.513098883 0.124056176 LYEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LYEIAR 6 0 Q7Z5M8-2;Q7Z5M8 Q7Z5M8-2 ABHD12B Abhydrolase domain-containing protein 12B 0 ;;;; 130.84 0.036268 1468961000 963410 1516560 2542210 1392210 992010 1870770 1082570 1727960 1077810 FALSE TRUE 917871.5186 1671099.188 2658772.843 1252262.406 1165016.23 1805984.766 917404.0637 1576650.662 1244951.27 0.737275057 1.342300882 2.135644107 1.005872628 0.935792635 1.450646952 0.736899577 1.266435643 1 20.24765784 LYELDGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LYELDGLR 8 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 ;; 122.18 0.0032608 171429000 572430 475310 367030 437700 592870 394710 608120 487630 573770 FALSE TRUE 545372.3683 523744.6294 383858.6885 393701.5644 696266.3403 381041.0937 515340.1251 444930.5321 662747.3212 0.822896375 0.790262914 0.57919312 0.594044747 1.050575865 0.574941734 0.777581604 0.671342634 1 19.33809941 -1.298124016 4.004723727 1.000399288 0.739702189 0.253111058 0.143895502 4597561206 805776450.4 17583330 0.03086614 0.050335685 1.298124016 -0.260697099 LYENFISEFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 LYENFISEFEHR 12 0 Q9UNM6;J3KNQ3;A0A087WUL9;E9PQG3;E9PPD2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;;; 194.12 1.93E-06 345577800 515008 770469 481442 683075 477851 498366 473680 563769 363922 FALSE TRUE 490664.5925 848980.6671 503516.5919 614411.0032 561188.0631 481107.4605 401411.4163 514402.3976 420357.1651 1.167256403 2.019665031 1.197830402 1.461640372 1.335026757 1.144520661 0.954929402 1.223726964 1 18.68125614 2.516012234 1.128040137 1.036983463 1.543782045 0.353886244 0.240868711 0.456269924 1.176431647 0.132666172 0.098075798 328.1045354 -2.516012234 0.506798582 LYEWTTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYEWTTEK 8 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 103.56 0.01661 0 109340 96349 89336 105300 85314 93984 117900 117910 98201 FALSE TRUE 104171.7149 106167.0726 93432.14397 94715.04394 100192.7346 90729.31051 99912.18962 107585.1753 113429.5095 0.918382838 0.935974008 0.823702265 0.835012373 0.883303957 0.799873956 0.880830659 0.948476069 1 16.79143649 1.086035483 3.16219336 0.99810937 0.872831281 0.548077999 0.041369055 0.200767853 3.920702572 0.043778777 0.011577905 12.19089197 -1.086035483 -0.125278089 LYFHSDTCLPLRPQEMEVDS(ph)EDEKDPEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYFHSDTCLPLRPQEMEVDSEDEKDPEWLR 30 2 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR 257.87 1.62E-58 199110000 170599 147025 129322 163179 113638 173451 180337 182711 123407 TRUE FALSE 162535.1234 162007.0147 135251.5416 146775.9369 133456.4312 167444.3484 152823.2785 166711.8562 142544.3273 1.140242663 1.13653779 0.948838471 1.029686272 0.936245123 1.174682652 1.07211056 1.169543955 1 17.1210511 -0.776061809 8.010695061 1.000000006 1.079745314 0.072454562 0.084495438 0 0 0.08083252 0.019052408 0.167470452 0.776061809 0.079745308 LYFLQCETCHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LYFLQCETCHSR 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;; 211.22 3.45E-08 1863334000 1702230 1522250 1320440 1640040 2024100 1458660 1935210 1580280 1660010 FALSE TRUE 1621768.961 1677369.006 1380983.48 1475180.063 2377102.399 1408146.238 1639958.172 1441902.306 1917435.873 0.845800887 0.874797968 0.720224076 0.769350404 1.239729804 0.734390265 0.855287103 0.751995061 1 20.8707469 LYGADGLVFGALTEDGHIDKELCMSLMAICRPLPVTFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYGADGLVFGALTEDGHIDKELCMSLMAICRPLPVTFHR 39 2 Q9NTM9;A0A0B4J226;Q5TCZ7 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 0 140.3 1.47E-13 97575000 276830 212910 238540 261490 267290 240100 344680 270730 136440 FALSE TRUE 263744.7945 234605.7711 249477.2949 235204.5284 313905.2914 231785.2768 292092.7355 247023.446 157598.4184 1.673524375 1.488630238 1.582993646 1.492429498 1.991804833 1.470733521 1.853398902 1.567423382 1 17.26589353 0.963408879 23.53753285 0.999999997 1.645521571 0.600295318 0.165469674 1975.468215 1270737.567 0.14618997 0.036547493 9.191975934 -0.963408879 0.645521574 LYGDADYLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 LYGDADYLEER 11 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;; 218.94 2.38E-11 356442000 560920 497570 503490 589050 516360 486830 578610 541610 546520 FALSE TRUE 534406.4232 548272.9487 526575.5145 529837.5749 606413.0205 469970.955 490332.4176 494183.7571 631271.5304 0.846555559 0.868521583 0.834150582 0.839318026 0.960621526 0.744483051 0.776737733 0.782838657 1 19.26790116 2.213505397 24.99998543 0.801876056 0.864529466 0.031794905 0.077940593 433.4711139 432512.6832 0.025894314 0.01913201 163.4953467 -2.213505397 0.062653411 MNGMLLNDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MNGMLLNDRK 10 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8;H0YEQ8 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 88.187 0.019828 330110000 255070 187780 240770 311140 383080 313740 561140 454690 434260 FALSE TRUE 243013.3466 206914.9955 251809.5427 279863.6161 449889.0307 302875.1051 475527.787 414874.9331 501602.8229 0.484473642 0.412507638 0.50200982 0.557938678 0.896902908 0.603814595 0.948016569 0.827098481 1 18.93618594 2.576981735 0.627358853 0.953035871 0.409832686 0.758727208 0.104027188 0.335382579 0.274333993 0.077175385 0.071010389 377.556312 -2.576981735 -0.543203185 down LYGS(ph)VCDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYGSVCDLR 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LYGS(1)VCDLR;LYGS(1)VCDLR;LYGS(1)VCDLR;LYGS(1)VCDLR 143.24 0.00010743 645870000 1208240 859720 1093040 1366540 1457220 1168100 1436460 1211890 1478630 TRUE FALSE 1151128.89 947326.4454 1143156.965 1229172.803 1711358.707 1127648.404 1217301.645 1105770.487 1707928.389 0.673991309 0.554664031 0.66932371 0.719686382 1.002008467 0.660243375 0.712735764 0.647433753 1 20.70381606 -5 0.132351832 1.953002512 0.579563861 0.37939169 0.11625359 153.2579495 1.271097277 39.31729941 0.84126393 1.00E-05 5 -1.373438651 LYHDPNVNGGTELEPVEGNPYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYHDPNVNGGTELEPVEGNPYRR 23 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 57.227 0.05416 78059000 97520 94340 101410 120460 58357 110410 118760 97398 67176 FALSE TRUE 92910.42287 103953.3533 106059.7488 108351.1319 68534.44232 106586.474 100640.9808 88869.31478 77593.31099 1.197402478 1.33972055 1.366867162 1.396397841 0.883251938 1.373655443 1.297031658 1.145321854 1 16.24364467 LYHRYLMNEEQAVS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYHRYLMNEEQAVSK 15 1 F6UZG9;Q8NFZ0;Q8NFZ0-2 F6UZG9 FBXO18 F-box only protein 18 1 LYHRYLMNEEQAVS(1)K 55.864 0.081769 107230000 143350 132170 170350 169970 215890 127060 208610 137990 293340 TRUE FALSE 136574.1296 145638.2733 178160.716 152884.2927 253541.1476 122659.8803 176782.7131 125906.8641 338829.669 0.403076065 0.429827393 0.52581203 0.451212827 0.748284967 0.362010448 0.521745081 0.371593386 1 18.37020068 -2.161554239 2.342440449 2.254263042 0.475250249 0.687409933 0.110897539 7170240.181 1573653.099 47779054.3 0.024802107 0.006893595 2.161554239 -1.779012793 LYHS(ph)LGPVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYHSLGPVTR 10 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 LYHS(1)LGPVTR 151.66 1.25E-05 443040000 223930 139950 194450 207900 230720 207280 236400 190620 234290 TRUE FALSE 213345.2727 154211.0641 203365.7248 187001.497 270957.495 200101.8416 200332.8382 173928.3023 270622.4966 0.788350102 0.569838303 0.751473833 0.691004995 1.001237881 0.739413183 0.740266758 0.642697131 1 18.04592225 2.907456075 24.99999481 0.801143838 0.691035404 0.183001311 0.124728798 106.0190567 28634.51992 0.035960109 0.038141468 808.0831943 -2.907456075 -0.110108434 LYKDDQLLDDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 215.51 3.76E-11 2220530000 6025590 6209920 4869550 6849390 2814700 6264400 5471430 6477300 2942740 FALSE TRUE 5740772.302 6842717.908 5092823.684 6160876.304 3305582.789 6047462.257 4636662.864 5910113.274 3399085.09 1.688916915 2.0131058 1.498292496 1.812510173 0.972491921 1.779144122 1.364091437 1.738736489 1 21.69671505 -0.111135278 0.07678276 8.00E-14 2.57109276 0.327195276 0.281935894 58.53403103 1.338046772 28.5262208 16.03086693 0.774220599 0.111135278 2.57109276 LYKEELEQTYHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYKEELEQTYHAK 13 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 173.06 1.34E-05 261930000 927500 793490 814200 967210 652530 913380 1075120 1028430 713820 FALSE TRUE 883658.9131 874347.5331 851531.8754 869984.2132 766331.0254 881749.4216 911090.6981 938375.2171 824515.5599 1.071731033 1.060437881 1.032766289 1.055145901 0.929431854 1.069415138 1.105001218 1.138092794 1 19.65318719 2.00741764 24.99456665 1.091325668 1.035836413 0.164168256 0.051974813 275.9009423 929673.5535 0.018713732 0.013793682 101.7226439 -2.00741764 -0.055489254 LYNNHEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 LYNNHEIR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 172.94 0.00028066 2343305000 1794320 1201741 1316010 1731570 2280320 1389650 2056610 1621370 2226690 FALSE TRUE 1709506.05 1324199.774 1376350.36 1557509.294 2678007.086 1341526.072 1742836.372 1479394.247 2571993.713 0.664661831 0.514853426 0.535129753 0.605564969 1.041218364 0.52158995 0.677620775 0.575193571 1 21.29445569 2.977197089 24.95625207 0.7285044 0.572407047 0.214729542 0.167868927 1285.404835 1406790.352 0.047512886 0.050743808 948.8489668 -2.977197089 -0.156097353 LYNSEESRPYT(ph)NK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYNSEESRPYTNK 13 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 LYNSEESRPYT(1)NK 235.95 1.71E-16 645570000 307670 260680 273120 393230 249660 443460 387050 349220 290220 TRUE FALSE 293127.0488 287243.5884 285642.8222 353701.7733 293200.625 428102.869 327998.4138 318640.4455 335225.8354 0.874416641 0.856865904 0.852090716 1.055114899 0.874636123 1.277058102 0.978440142 0.950524726 1 18.35477381 3.241863124 24.9971504 1.029256627 0.862110741 0.3511591 0.103224704 85.28735238 645546.6664 0.027042369 0.035168207 1745.27201 -3.241863124 -0.167145886 LYNSEESRPYTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYNSEESRPYTNK 13 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 117.2 0.00047873 140960000 78481 78480 76887 96798 75934 77826 101190 101140 92686 FALSE TRUE 74771.35866 86477.20122 80412.345 87067.68114 89176.86556 75130.86611 85751.60702 92283.64542 107059.2715 0.698410867 0.807750697 0.751101179 0.813266146 0.832967237 0.70176889 0.800973197 0.861986488 1 16.70805022 -5 0.188929607 1.96795662 0.736781972 0.709745201 0.046487649 74.13105316 0.723903182 26.86447749 0.123182733 1.00E-05 5 -1.231174648 ELLHSQNTWLNTELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 ELLHSQNTWLNTELK 15 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 70.26 0.047217 129660000 64232 55674 72076 111550 134070 172930 240340 196430 181300 FALSE TRUE 61195.88066 61347.2439 75380.75589 100336.7821 157451.7656 166941.3907 203671.7189 179229.5479 209415.078 0.292222896 0.292945687 0.359958588 0.479128738 0.751864512 0.797179421 0.97257428 0.855857895 1 17.6760058 2.714005541 1.092959286 0.944536376 0.280808832 0.973200351 0.04465051 0.06006422 0.149522189 0.02057747 0.01855076 517.6134362 -2.714005541 -0.663727544 down LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LYPPGDEEEAELADSSGLYHEGS(0.002)PS(0.006)PGS(0.993)PWK;LYPPGDEEEAELADSSGLYHEGSPSPGS(1)PWK;LYPPGDEEEAELADSSGLYHEGSPS(0.001)PGS(0.999)PWK;LYPPGDEEEAELADSSGLYHEGSPSPGS(1)PWK 316.65 5.69E-93 230082000 173379 154204 150312 168479 125640 164202 194544 178221 145984 TRUE FALSE 165183.7183 169917.5629 157203.9539 151543.1708 147551.5762 158515.6436 164862.7398 162615.0244 168622.4531 0.979606898 1.00768053 0.932283637 0.898712882 0.875041096 0.940062492 0.977703364 0.964373495 1 17.36343713 -4.361824307 8.775010107 0.999770392 0.954448389 0 0.042545476 0 0 0 0.010261247 4.35E-05 4.361824307 -0.045322003 LYPPSAEYPDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYPPSAEYPDLRK 13 1 P12532;F8WCN3;C9JSQ1;C9J8F6;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 127.79 0.00027708 640370000 987840 705880 766850 918940 820910 765940 1014270 945390 844120 FALSE TRUE 941146.7609 777809.9745 802010.831 826566.4053 964076.4441 739415.3057 859524.4832 862606.6398 975021.8184 0.965257129 0.797735968 0.822556804 0.847741445 0.988774226 0.758357702 0.881543845 0.884704961 1 19.89507498 0.724309464 2.391174985 0.999926817 0.863681033 0.264774213 0.069630869 1.884948382 14.44282088 0.061722421 0.01659706 5.300409996 -0.724309464 -0.136245784 LYQAGEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 LYQAGEGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 206.75 0.00016028 950630000 1459700 1247140 1290290 1535570 1553270 1325990 1591450 1453810 1591490 FALSE TRUE 1390702.874 1374224.984 1349451.073 1381211.586 1824159.796 1280070.634 1348645.074 1326506.689 1838290.141 0.756519791 0.747556087 0.734079481 0.751356685 0.992313322 0.696337648 0.733641031 0.721598109 1 20.80993306 -2.326781918 2.196133108 2.230705726 0.764229798 0.442948966 0.082190019 2696983.807 312066.2818 16531086.27 0.020088161 0.004712139 2.326781918 -1.466475928 LYQHAVEYFLHAIKYEAHSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYQHAVEYFLHAIKYEAHSDK 21 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 216.44 2.08E-25 17528000 112550 59550 110320 97405 112890 103570 165230 116820 49119 FALSE TRUE 107229.9846 65618.2127 115378.2811 87613.66434 132577.9803 99983.34493 140021.1288 106590.6215 56736.12365 1.889977278 1.156550862 2.033594713 1.544230707 2.336747238 1.762251957 2.467936119 1.878708213 1 15.79197997 2.766184965 24.41739307 2.008341663 1.619792316 0.023076795 0.45676761 986.4748745 871951.4079 0.125406854 0.132984607 583.6936455 -2.766184965 -0.388549347 LYQPEYQEVSTEEQREEISGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYQPEYQEVSTEEQREEISGK 21 1 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 238.05 6.43E-30 540719000 357811 286101 303284 352862 254858 332971 329361 355880 267882 FALSE TRUE 340897.9831 315255.0172 317189.8714 317391.6414 299305.1545 321440.1308 279110.9303 324717.2606 309423.7724 1.101718787 1.018845497 1.025098585 1.025750668 0.967298512 1.038834632 0.90203454 1.049425705 1 18.23922451 6.012868341 0.423378669 0.979645909 1.420318072 0.360008788 0.041963378 13.0348792 0.788179671 0.026477233 3.627774501 1030073.8 -6.012868341 0.440672164 LYQSLEFPSSCLLHPITSIEYQWIQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYQSLEFPSSCLLHPITSIEYQWIQGR 27 0 Q70J99;Q70J99-3;K7EM66 Q70J99 UNC13D Protein unc-13 homolog D 0 ; 161.49 1.30E-11 89127000 154672 146936 147867 176345 150397 149964 181112 184394 152021 FALSE TRUE 147360.9611 161908.9455 154646.8482 158618.4656 176626.1892 144770.7091 153480.038 168247.4838 175595.6403 0.839206263 0.922055611 0.880698678 0.90331665 1.005868875 0.824455031 0.874053808 0.958152968 1 17.4218975 -4.999999999 0.2166599 1.517184682 0.882535671 0.289973502 0.051977187 201.4312428 2.012662075 45.37097717 0.099427524 1.00E-05 4.999999999 -0.634649011 LYQTDPSGTYHAWK ddPTM_SK-BR-3_Trastuzumab_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 ; 235.22 3.13E-17 3508400000 6683300 5422000 4101800 4836500 6092800 4744300 7240800 5910100 5634700 FALSE TRUE 6367393.654 5974507.964 4289871.587 4350325.831 7155382.391 4580003.701 6136082.974 5392580.313 6508500.498 0.978319608 0.917954599 0.65911827 0.668406776 1.099390312 0.703695683 0.942779827 0.828544196 1 22.63389377 -1.408344862 3.550714705 1.001112158 0.859570535 0.094931219 0.142957511 2043997.503 63681298.15 115201.0547 0.031697692 0.039053066 1.408344862 -0.141541622 LYRPGSVAYVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYRPGSVAYVSR 12 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 192.35 3.83E-06 2207690000 1639040 1194610 544210 701710 1771940 816960 1722390 1260060 1714800 FALSE TRUE 1561565.827 1316342.117 569162.5668 631172.7776 2080965.775 788668.4704 1459607.772 1149722.466 1980722.426 0.78838196 0.664576773 0.287350998 0.318657864 1.050609489 0.398172132 0.736906773 0.580456126 1 20.91759529 -0.915510067 0.58744374 1.090356434 0.607430161 0.225343454 0.230895392 35.06986101 7.280673169 5.948944181 0.089631236 0.121475846 0.915510067 -0.482926272 LYSESLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYSESLAR 8 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 153.73 0.0010153 300100000 732970 667340 526010 629180 799430 568070 733410 670710 847100 FALSE TRUE 698323.9607 735342.7047 550128.0788 565933.631 938850.3389 548397.5935 621514.8345 611979.0767 978463.9416 0.713694119 0.751527648 0.562236435 0.578389869 0.959514499 0.560467862 0.635194419 0.625448778 1 19.90015916 -1.908756989 2.366136181 1.196495151 0.676950571 0.426176949 0.119066735 14094240.3 7051679.753 15380073.34 0.028477837 0.01233795 1.908756989 -0.51954458 LYSGS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 LYSGSPTR 8 0 Q6PJI9-4;Q6PJI9-3;Q6PJI9;H3BMH3 Q6PJI9-4 WDR59 WD repeat-containing protein 59 1 LYS(0.079)GS(0.92)PT(0.001)R;LY(0.001)S(0.261)GS(0.737)PT(0.002)R;LYS(0.229)GS(0.573)PT(0.198)R;LYSGS(0.991)PT(0.009)R 132.39 0.0010115 979790000 1833540 1686670 1614580 1943530 2136820 1713920 2000530 1858660 2144530 TRUE FALSE 1746872.198 1858543.591 1688610.09 1748162.672 2509480.731 1654566.521 1695312.406 1695905.877 2477092.76 0.705210651 0.750292287 0.681690293 0.705731614 1.013074994 0.667946937 0.684396012 0.684635596 1 21.24021646 -2.281662299 2.35431412 2.220925972 0.73482335 0.401845806 0.100964137 3883659.939 575223.7795 25455996.35 0.024531231 0.005228026 2.281662299 -1.486102622 LYSLALHPNAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYSLALHPNAFK 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 78.692 0.025044 112060000 302530 271160 172650 211370 309780 245900 360670 276600 272300 FALSE TRUE 288230.0065 298791.5123 180566.1733 190122.686 363805.5339 237384.4213 305643.1673 252379.4377 314526.8933 0.916392247 0.94997127 0.574088185 0.604471955 1.156675444 0.754734894 0.971755274 0.802409724 1 18.26282385 2.749709206 24.99698672 0.923234261 0.799530992 0.211449035 0.16017144 1648.964934 3697252.373 0.05012625 0.052724047 561.9649193 -2.749709206 -0.12370327 LYSSEESRPYT(ph)NK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYSSEESRPYTNK 13 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;Q9BVE2;A0A087X209;A0A2R8Y644;A0A2R8YEB7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 LYSSEESRPYT(1)NK;LYSSEESRPYT(1)NK 133.45 0.00017309 439280000 222082 221440 224245 303332 205673 322410 288196 238940 189042 TRUE FALSE 211584.624 244004.9878 234526.8551 272840.4911 241542.3061 311244.8609 244226.4071 218017.1469 218357.6679 0.968981882 1.11745555 1.074049093 1.249511839 1.106177349 1.425390113 1.118469571 0.998440536 1 17.73633367 4.422639094 1.066976734 1.164919037 0.930298326 0.136039903 0.125579075 1.727864201 2.306995624 0.036659073 0.407760681 26463.00104 -4.422639094 -0.234620711 LYTDFDEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 127.68 0.0010205 112063000 159737 196615 109334 173948 138548 136010 137827 152059 127607 FALSE TRUE 152186.5486 216650.292 114347.072 156462.4166 162710.7273 131299.9396 116798.9598 138743.9078 147395.6418 1.03250372 1.469855481 0.775783263 1.061513181 1.103904602 0.890799334 0.792418 0.941302647 1 17.16933434 3.731491062 24.99937071 0.929993265 1.251179604 0.441547017 0.14623181 431.7714163 1526831.289 0.03843102 0.060977563 5388.787551 -3.731491062 0.321186339 LYTDFDEIRQEIENETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 225.54 3.65E-19 191321000 227512 200957 209205 232768 239564 206862 245614 230204 251467 FALSE TRUE 216757.9586 221434.7468 218797.2562 209369.7184 281343.8858 199698.3171 208141.0733 210046.1174 290463.218 0.74624925 0.762350387 0.753270096 0.720813189 0.968604175 0.687516714 0.716583238 0.723141879 1 18.14799596 -1.294319609 3.63735651 1.000653702 0.757793252 0.487744536 0.077331204 19410164.51 23981085.11 129878.12 0.017524803 0.050778561 1.294319609 -0.24286045 LYTLQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 143.85 0.0055686 1586450000 2779660 2757400 2511520 2928360 2190260 2639280 2845630 2863300 2419570 FALSE TRUE 2648270.981 3038382.195 2626675.676 2633995.689 2572240.651 2547881.072 2411476.88 2612574.273 2794784.558 0.947576074 1.087161508 0.939849073 0.942468242 0.920371713 0.911655628 0.862848935 0.934803459 1 21.41430564 3.552033576 7.016460017 0.918349941 1.017472082 0.355449972 0.047611118 0.217642387 17.49537609 0.012251097 0.018974096 3564.786921 -3.552033576 0.099122141 LYTLVLTDPDAPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYTLVLTDPDAPSR 14 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 145.91 1.97E-05 16482000 39298 18748 29058 37682 51421 31614 45851 35716 51051 FALSE TRUE 37440.46142 20658.44251 30390.33804 33894.13377 60388.80612 30519.19925 38855.58784 32588.5177 58967.72835 0.634931385 0.350334719 0.515372372 0.574791241 1.024099246 0.517557656 0.658929705 0.552650045 1 15.847638 2.990075509 24.14882212 0.714113055 0.494559055 0.289592816 0.17842227 406.2194037 988440.3426 0.049492664 0.055963907 977.4071439 -2.990075509 -0.219554001 LYTLVLTDPDAPSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYTLVLTDPDAPSRK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 137.46 2.66E-05 308400000 264080 120140 177730 208920 224760 192160 279140 239990 207950 FALSE TRUE 251597.4618 132382.4026 185879.0963 187918.9647 263958.0728 185505.451 236552.0662 218975.2033 240197.8239 1.047459372 0.551139059 0.773858369 0.782350821 1.098919501 0.772302796 0.984821854 0.911645242 1 17.87386356 2.936233123 22.28889882 0.940242995 0.776369653 0.242576779 0.142977431 97.08395093 33933.81869 0.041569595 0.044091359 863.4419075 -2.936233123 -0.163873342 LYTLVLTDPDAPSRKDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYTLVLTDPDAPSRKDPK 18 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 141.55 6.70E-08 391430000 923380 495620 801540 645700 851060 788830 1555490 933810 1217490 FALSE TRUE 879733.6574 546124.2415 838291.4018 580793.0093 999484.5945 761512.6193 1318171.432 852040.646 1406292.131 0.625569637 0.388343381 0.596100471 0.412995989 0.710723307 0.541503861 0.937338269 0.605877418 1 20.42346489 1.637050002 0.613207045 0.960459726 0.49196735 0.522931566 0.136304501 0.488209009 0.401823475 0.116516111 0.061710759 43.35607928 -1.637050002 -0.468492377 LYTWVEWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYTWVEWVK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 138.1 0.00034 107600000 355000 354860 364920 370780 353380 332930 448650 387050 335950 FALSE TRUE 338219.8535 391020.6374 381651.943 333508.49 415009.3601 321400.5506 380200.2025 353157.8501 388047.4102 0.871594152 1.007662021 0.983518851 0.859452946 1.069481072 0.82825073 0.979777709 0.91008944 1 18.5658734 LYVELHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYVELHR 7 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 119.89 0.0046808 125590000 187640 176870 150480 179700 182600 150720 181870 173160 163140 FALSE TRUE 178770.6291 194893.2541 157379.6568 161636.2146 214445.3822 145500.5286 154122.3912 157997.1924 188438.918 0.948692717 1.034251609 0.835175974 0.857764502 1.138010048 0.772136298 0.817890449 0.838453087 1 17.52373743 2.185695228 24.99999997 0.836873869 0.960673942 0.196728987 0.102474783 129.7288139 61347.69749 0.035920442 0.02652903 153.3540424 -2.185695228 0.123800073 LYVGSLHFNITEDMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 LYVGSLHFNITEDMLR 16 0 Q86U06-3;Q86U06-5;Q86U06-2;Q86U06;Q86U06-4;G3V546;G3V5Z6;H0YJJ3;G3XAP0;Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q86U06-3;Q14498-2;Q14498-3 RBM23;RBM39 Probable RNA-binding protein 23;RNA-binding protein 39 0 ; 206.43 2.00E-11 217250000 424260 299100 316630 322440 510830 296330 497500 390260 463180 FALSE TRUE 404206.0706 329578.63 331147.7987 290027.7186 599918.5903 286068.0178 421597.2378 356086.7655 535007.5888 0.755514649 0.616026084 0.618959068 0.542100196 1.121327254 0.534698991 0.788021042 0.665573298 1 19.02919983 LYVYNTDTDNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LYVYNTDTDNCR 12 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 125.74 0.00069764 90293000 88192 88286 73184 100400 85056 89399 102850 86318 91022 FALSE TRUE 84023.33894 97282.44377 76539.55879 90307.60125 99889.73947 86303.09021 87158.34353 78759.53832 105137.2269 0.799177812 0.925290182 0.727996743 0.858949812 0.950089159 0.82086139 0.828996028 0.74911181 1 16.68191406 -2.267726672 2.48095549 1.744106641 0.838790635 0.366280311 0.068783132 7179194.094 1549106.817 30150589.13 0.015865053 0.005398503 2.267726672 -0.905316006 MADKDGDLIATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MADKDGDLIATK 12 1 O43852;O43852-3;O43852-15;O43852-6;O43852-10;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ;;;;; 148.41 5.78E-05 2106560000 8339000 7733580 6581680 9020880 4362510 8226180 8013170 8535560 4652190 FALSE TRUE 7944831.996 8521640.594 6883456.538 8114084.004 5123330.363 7941305.324 6790613.745 7788141.117 5373627.865 1.478485708 1.585826337 1.280970084 1.509982494 0.953421132 1.477829415 1.263692596 1.449326472 1 22.35746498 4.356052004 0.039532464 9.79E-12 2.954648878 0.324012437 0.176210381 357.4084815 2.505085448 71.79281627 119.1029573 22701.36672 -4.356052004 2.954648878 MADKDGDLIATKEEFTAFLHPEEYDYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MADKDGDLIATKEEFTAFLHPEEYDYMK 28 2 O43852;O43852-3;O43852-15;O43852-6;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 102.6 0.00066764 44260000 106040 69799 106900 105230 72524 113650 139590 132790 61065 FALSE TRUE 101027.6994 76911.59745 111801.4707 94652.08048 85172.16264 109714.272 118292.9818 121162.2036 70534.64832 1.432313079 1.090408746 1.585057463 1.341923193 1.207522326 1.55546635 1.677090403 1.717768593 1 16.1060445 2.219109521 23.53554953 1.558674194 1.319750376 0.062371868 0.235750143 190.1426532 230066.8899 0.080076125 0.059251207 165.6187571 -2.219109521 -0.238923819 MAEDELFNRYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAEDELFNRYER 12 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 88.552 0.0063711 0 73930 54802 69853 73042 87298 70581 87540 71931 95476 FALSE TRUE 70435.47542 60386.3861 73055.82914 65699.67939 102522.7436 68136.76227 74184.16522 65632.34031 110281.9305 0.63868555 0.547563738 0.662446049 0.595742921 0.929642264 0.617841581 0.672677427 0.595132313 1 16.7508369 -5 0.252879928 3.11701572 0.622044008 0.504936924 0.104972825 150.9580975 1.492437254 165.7388776 0.140613956 1.00E-05 5 -2.494971712 MAGNEALS(ph)PTSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.95)PT(0.05)SPFR;MAGNEALS(0.972)PT(0.027)SPFR;MAGNEALS(1)PTSPFR;MAGNEALS(0.993)PT(0.007)SPFR;MAGNEALS(0.996)PT(0.004)SPFR 194.77 1.10E-07 517050000 1134560 858217 973688 1119070 1177030 964616 1182170 1025240 1094930 TRUE FALSE 1080931.597 945670.288 1018332.558 1006578.958 1382303.659 931211.106 1001808.254 935464.5505 1264726.152 0.854676402 0.747727313 0.80518028 0.795886885 1.092966771 0.736294655 0.792114761 0.73965779 1 20.27039361 -2.210152605 2.313022527 1.559474772 0.817355893 0.229045709 0.103309954 6867954.278 1203100.673 20166027.67 0.023516236 0.006163784 2.210152605 -0.742118879 MAGNEALSPT(ph)SPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.31)PT(0.645)S(0.045)PFR;MAGNEALS(0.035)PT(0.964)S(0.001)PFR 140.49 0.00010359 389170000 682430 523956 595773 710042 708295 629262 730204 629440 1287170 TRUE FALSE 650172.8863 577347.7121 623089.7813 638667.2292 831821.4237 607470.4992 618797.9687 574322.8967 1486777.75 0.437303347 0.388321464 0.419087373 0.429564694 0.559479333 0.408581914 0.416200719 0.386286987 1 20.50375757 -1.717841807 2.892043956 1.087237976 0.428765406 0.931295151 0.048601217 26995050.71 24843102.6 17092922.91 0.012118306 0.019149533 1.717841807 -0.658472569 MAGNEALSPTS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALSPTS(1)PFR 193.31 7.59E-08 0 236620 219860 239200 295300 262270 214630 270760 224060 229580 TRUE FALSE 225435.4415 242263.984 250167.5566 265615.883 308009.805 207197.3093 229450.5892 204440.1186 265182.0939 0.850115625 0.913575952 0.943380275 1.001635816 1.161503028 0.781339744 0.865256722 0.770942395 1 18.01662384 -0.630497501 6.289985668 1.000001147 0.909607731 0.0579664 0.112676437 1.61E-09 0 0.107973703 0.025449645 0.234154495 0.630497501 -0.090393416 MAGTAFDFENMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAGTAFDFENMKR 13 1 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 100.02 0.004157 301940000 271640 208000 209910 244320 224500 220930 273890 249630 253580 FALSE TRUE 258800.1155 229195.4365 219534.5811 219760.4894 263652.7289 213279.1387 232103.0502 227771.0738 292903.8913 0.883566669 0.782493655 0.749510634 0.750281905 0.900133924 0.728153995 0.792420507 0.777630754 1 18.16006783 -1.455918903 6.842668171 1.000038478 0.796677754 0.571058406 0.055685407 3.10E-05 2.47E-06 0.051176635 0.012060171 0.035001052 1.455918903 -0.203360724 MAKPEEVLVVENDQGEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MAKPEEVLVVENDQGEVVR 19 1 O14980 O14980 XPO1 Exportin-1 0 ; 156.92 1.02E-08 186220000 269640 244980 212840 296870 200402 288300 312400 301890 256860 FALSE TRUE 256894.6516 269943.7405 222598.9245 267028.0636 235352.0454 278316.0987 264737.6424 275454.9112 296692.5369 0.865861522 0.90984338 0.750268028 0.900016112 0.793252327 0.938062351 0.892296264 0.92841874 1 18.17860911 1.153002157 0.839349596 0.996980862 0.855893925 0.451245196 0.052809691 0.534499484 0.844518958 0.046199017 0.017032294 14.22335851 -1.153002157 -0.141086937 MALIQLGSVEEAIQALIELHNHDLGENHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MALIQLGSVEEAIQALIELHNHDLGENHHLR 31 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 206.56 2.13E-26 125780000 98179 143800 102570 140190 116500 112980 121560 85375 10526 FALSE TRUE 93538.27324 158453.3835 107272.936 126097.8349 136817.5631 109067.4743 103013.7894 77899.1124 12158.31832 7.693356168 13.03250822 8.823007683 10.37132205 11.25300058 8.970605259 8.472700474 6.407063078 1 13.56965608 0.876043517 0.945523636 0.999616548 10.32815837 0.803166612 1.427749788 0.281091416 0.512370769 1.262275561 0.42304555 7.516982119 -0.876043517 9.328541824 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;;;;; 261.6 4.41E-59 3543522000 1716828.2 2028573.2 1618045.5 2204403.1 1951246 1797275.9 2115529.6 1323707.9 121597.04 FALSE TRUE 1635677.133 2235287.115 1692234.487 1982812.312 2291542.685 1735035.785 1792766.705 1207797.019 140453.6879 11.64566881 15.91476271 12.04834499 14.1171965 16.31529025 12.35308101 12.76411272 8.599254577 1 17.09973498 0.889699694 1.407879197 1.000617481 13.90569009 0.879576929 1.511135335 0.161714391 0.629718868 1.317924777 0.39210417 7.757105421 -0.889699694 12.90507261 MALLQEFASRPLGAAPQAEHQGLPVPGS(ph)PGGQK ddPTM_SK-BR-3_Trastuzumab_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 165.61 2.28E-14 241840000 645480 515480 545300 637560 501100 637300 723010 632540 465680 TRUE FALSE 614969.4396 568007.9981 570302.5444 573471.2575 588491.6813 615230.1412 612701.5455 577151.4443 537895.276 1.143288419 1.055982499 1.060248286 1.066139234 1.094063673 1.143773089 1.139072182 1.072981062 1 19.03696579 0.981658487 23.04241591 0.999999997 1.100558794 0.473570478 0.033359078 432.8639072 543807.9694 0.034831886 0.008707972 9.586464913 -0.981658487 0.100558797 MALLVQELSSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MALLVQELSSHR 12 0 Q9HD15;R4GMW4 Q9HD15 SRA1 Steroid receptor RNA activator 1 0 ; 153.74 7.09E-05 108071000 149968 144572 133550 166324 179406 134512 186031 155793 170069 FALSE TRUE 142879.3098 159304.0512 139673.3996 149604.7955 210694.3496 129853.8157 157648.5543 142150.939 196442.4319 0.727334255 0.81094522 0.711014409 0.761570675 1.072550098 0.661027327 0.80251783 0.723626447 1 17.58374706 -2.494297815 2.165602482 3.534849782 0.784506491 0.270280394 0.111625281 3061886.552 248164.8029 38243131.24 0.026397519 0.003204071 2.494297815 -2.750343291 MALPPQEDAT(ph)ASPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.63)AS(0.37)PPR 91.076 0.064474 63214000 49514 35998 39088 47243 37974 35611 48258 44568 48664 TRUE FALSE 47173.57135 39666.23713 40880.22346 42494.04388 44596.65358 34377.78214 40895.35578 40665.38965 56210.56458 0.839229631 0.705672278 0.727269398 0.755979667 0.793385619 0.611589341 0.727538606 0.723447451 1 15.77855368 -1.098132147 6.648255813 1.000000268 0.735018813 0.666933242 0.058738491 2.27E-07 3.09E-08 0.055503336 0.013082249 0.079775191 1.098132147 -0.264981454 MALPPQEDATAS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDATAS(1)PPR;MALPPQEDAT(0.014)AS(0.986)PPR;MALPPQEDAT(0.008)AS(0.992)PPR;MALPPQEDAT(0.033)AS(0.967)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.007)AS(0.993)PPR;MALPPQEDAT(0.062)AS(0.938)PPR 214.63 2.57E-12 4594674000 2811213 2849799 2429743 3133090 2504276 2560763 2765819 2697542 2552661 TRUE FALSE 2678332.533 3140196.758 2541149.12 2818145.841 2941020.942 2472083.135 2343842.514 2461330.922 2948514.631 0.908366709 1.065009726 0.861840431 0.955784927 0.997458487 0.838416438 0.794923142 0.834769784 1 21.49155692 2.229955032 24.79579962 0.843631694 0.963398583 0.234973613 0.075876175 173.0128279 498508.2057 0.026137992 0.01961212 169.806782 -2.229955032 0.119766889 MALPPQEDATAS(ph)PPRQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.306)AS(0.694)PPRQK;MALPPQEDAT(0.172)AS(0.828)PPRQK;MALPPQEDAT(0.033)AS(0.967)PPRQK;MALPPQEDAT(0.035)AS(0.965)PPRQK;MALPPQEDATAS(1)PPRQK;MALPPQEDAT(0.005)AS(0.995)PPRQK;MALPPQEDAT(0.174)AS(0.826)PPRQK;MALPPQEDAT(0.201)AS(0.799)PPRQK;MALPPQEDAT(0.079)AS(0.921)PPRQK;MALPPQEDAT(0.06)AS(0.94)PPRQK;MALPPQEDAT(0.071)AS(0.929)PPRQK 192.94 9.60E-11 4580180000 3884440 2300593 3812800 3370240 3524660 3687380 5229440 4080410 4746390 TRUE FALSE 3700830.219 2535026.042 3987620.651 3031457.072 4139359.588 3559685.106 4431592.883 3723107.669 5482435.92 0.675033922 0.462390455 0.727344689 0.552939809 0.755021974 0.649288958 0.808325523 0.679097343 1 22.38638561 0.331199621 0.252306657 1.112228559 0.541354612 0.614434985 0.089557015 2.891920911 0.379577237 0.492578648 0.160744439 2.143875797 -0.331199621 -0.570873947 MANSS(ph)PVLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.003)S(0.997)PVLSK;MANS(0.227)S(0.773)PVLSK;MANS(0.004)S(0.996)PVLSK;MANS(0.004)S(0.996)PVLSK 179.67 2.18E-06 375710000 1450240 1356570 1240790 1578790 1082840 1377420 1508640 1569150 1217320 TRUE FALSE 1381690.029 1494806.025 1297681.449 1420087.03 1271686.953 1329719.6 1278469.26 1431746.907 1406095.768 0.982642904 1.063089769 0.922896916 1.009950433 0.904409914 0.945682101 0.909233417 1.018242811 1 20.42326343 3.73280159 24.90299929 0.9514313 1.022866337 0.248411956 0.045119562 441.4774481 1909022.461 0.010947322 0.017508463 5405.073324 -3.73280159 0.071435036 MAPALSGANLTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MAPALSGANLTS(1)PR;MAPALSGANLT(0.011)S(0.989)PR;MAPALSGANLT(0.01)S(0.99)PR;MAPALSGANLT(0.009)S(0.991)PR;MAPALSGANLT(0.17)S(0.83)PR;MAPALSGANLT(0.076)S(0.924)PR;MAPALS(0.003)GANLT(0.178)S(0.82)PR;MAPALSGANLT(0.096)S(0.904)PR 178.6 2.06E-06 1129270000 2089120 2153170 1906800 2431080 2056510 2061620 2233280 2211660 2215920 TRUE FALSE 1990371.438 2372580.471 1994228.666 2186703.22 2415164.693 1990225.582 1892552.119 2017995.326 2559553.556 0.777624454 0.926950899 0.779131447 0.854329934 0.943588262 0.77756747 0.739407118 0.788416918 1 21.28746076 MAPPVDDLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MAPPVDDLSPK 11 0 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 MAPPVDDLS(1)PK;MAPPVDDLS(1)PK 105.95 0.0093698 177914000 406340 408060 377080 453930 252880 446320 431390 469120 301000 TRUE FALSE 387133.1135 449641.7779 394369.491 408300.094 296982.1919 430863.8265 365573.5325 428041.3658 347677.5427 1.113483231 1.293272423 1.134296705 1.1743643 0.854188596 1.239262747 1.051472953 1.231144705 1 18.40739036 2.968965486 24.89993441 1.082216828 1.189912718 0.156326578 0.11839784 1086.954478 872097.0339 0.032894708 0.034925632 931.0338818 -2.968965486 0.10769589 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPT(0.125)PIPT(0.42)RS(0.42)PS(0.031)DS(0.003)S(0.001)TASTPVAEQIER;MAPT(0.01)PIPT(0.538)RS(0.416)PS(0.015)DS(0.009)S(0.009)T(0.003)ASTPVAEQIER 78.642 0.021819 475650000 111910 121743 127857 140114 132668 125205 146456 123250 150066 TRUE FALSE 106620.2361 134148.7501 133719.3699 126029.4745 155805.2572 120869.1195 124111.4474 112457.5766 173337.4688 0.615102071 0.773916632 0.771439498 0.727075775 0.898855038 0.697305206 0.716010498 0.648778232 1 17.40322402 -2.374085171 2.297575039 2.943645995 0.731409923 0.547098774 0.07689938 4167692.687 455823.436 42232292.96 0.019234747 0.004225857 2.374085171 -2.212236072 MAPTPIPTRS(ph)PSDSSTASTPVAEQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.165)RS(0.806)PS(0.028)DSSTASTPVAEQIER;MAPTPIPT(0.317)RS(0.487)PS(0.196)DSSTASTPVAEQIER;MAPTPIPT(0.023)RS(0.743)PS(0.234)DSSTASTPVAEQIER;MAPTPIPT(0.171)RS(0.805)PS(0.024)DSSTASTPVAEQIER;MAPTPIPT(0.236)RS(0.71)PS(0.032)DS(0.007)S(0.013)T(0.001)ASTPVAEQIER;MAPTPIPT(0.225)RS(0.732)PS(0.042)DS(0.002)STASTPVAEQIER 291.6 9.92E-71 3220500000 994494 919471 943134 1052690 1075954 948082 1173482 1024465 1250798 TRUE FALSE 947486.2395 1013166.14 986377.6268 946871.6012 1263600.037 915249.6826 994445.7684 934757.4136 1444765.366 0.655806307 0.701266908 0.682725133 0.655380883 0.874605709 0.633493648 0.688309529 0.646996001 1 20.46240378 -1.19889391 4.484118478 1.000078738 0.692080325 0.669019313 0.068010862 4.88E-05 8.72E-06 0.060014679 0.014141989 0.063256636 1.19889391 -0.307998412 MAPTPIPTRSPS(ph)DSSTASTPVAEQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.002)RS(0.132)PS(0.792)DS(0.074)STASTPVAEQIER 220.14 1.72E-34 390250000 117270 105860 109240 118370 118230 103960 121770 118650 141450 TRUE FALSE 111726.8795 116647.2544 114248.7621 106471.2227 138849.2746 100359.8391 103191.75 108260.377 163385.3436 0.683824369 0.713939524 0.699259551 0.651657122 0.849826989 0.614252398 0.631585109 0.66260764 1 17.31791905 -1.51714119 3.275662564 1.008198431 0.686983623 0.696514093 0.064641093 31748309.6 42235127.98 2346370.194 0.015002818 0.030398966 1.51714119 -0.321214807 MAQALEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAQALEELR 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 110.87 0.0051568 16597000 35408 25397 25256 25078 35670 24221 37101 37117 43176 FALSE TRUE 33734.33401 27984.98317 26414.01258 22557.11179 41890.83671 23382.2207 31440.56104 33866.83871 49871.51357 0.676424909 0.561141645 0.529641286 0.452304536 0.839975243 0.468849229 0.630431258 0.67908183 1 15.60592837 0.717144578 1.81129308 0.999764534 0.591854811 0.571968971 0.110078114 0.740836588 3.657592896 0.094826451 0.026628532 5.213682475 -0.717144578 -0.407909723 MAQDLKDIIEHLNTSGAPADTSDPLQQICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAQDLKDIIEHLNTSGAPADTSDPLQQICK 30 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 86.19 0.00078545 47679000 85417 57489 85950 85635 72662 95966 129370 115220 79473 FALSE TRUE 81379.50769 63347.19446 89890.89252 77026.8071 85334.22979 92642.67336 109632.2305 105130.726 91797.26695 0.886513405 0.690077129 0.979232776 0.839096954 0.929594449 1.009209494 1.194286433 1.145248976 1 16.48616358 2.259336522 1.652795152 1.133357102 0.830585577 0.627236882 0.08807181 0.203700186 1.110145336 0.044881386 0.028173283 181.6922996 -2.259336522 -0.302771524 MAQFDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAQFDAK 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 83.206 0.052228 107100000 171620 142050 144600 159090 137080 154610 187580 168660 162980 FALSE TRUE 163507.8627 156525.0565 151230.053 143097.9709 160986.7086 149255.8169 158961.2259 153891.2363 188254.106 0.868548719 0.831456268 0.803329373 0.760132004 0.855156427 0.792842292 0.844397125 0.817465497 1 17.52232181 -1.213295339 4.070993598 1.000110258 0.82417565 0.75913311 0.031541251 3.09E-05 5.97E-06 0.02988271 0.007039016 0.061193411 1.213295339 -0.175934607 MASCLEVLDLFLNQPHMVLSSFVLAEK ddPTM_SK-BR-3_Trastuzumab_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 0 236.94 4.79E-45 890670000 242220 228460 238630 305680 223550 217820 327070 243350 193440 FALSE TRUE 230770.7406 251740.3337 249571.4215 274952.4656 262537.0492 210276.8388 277169.4644 222040.9839 223437.6872 1.032819232 1.126669081 1.116962069 1.230555458 1.174990005 0.94109835 1.240477682 0.993749025 1 17.76951302 -0.550068844 7.321891701 0.999999926 1.112582158 0.105819176 0.096768603 0 0 0.084403751 0.019894155 0.28179362 0.550068844 0.112582232 MASNIFGT(ph)PEENQASWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.999)PEENQAS(0.001)WAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK 322.71 1.01E-60 592738000 1952130 1911290 1945990 2320390 1764902 2163740 2518290 2323820 2171630 TRUE FALSE 1859856.684 2106052.624 2035215.566 2087139.989 2072700.35 2088809.141 2134078.609 2120334.001 2508395.289 0.741452789 0.83960157 0.81136158 0.832061836 0.826305311 0.832727262 0.850774445 0.845295002 1 21.25833328 -5 0.137668407 1.618803784 0.753134105 0.878751766 0.022186153 43.95399101 0.373333764 7.452686817 0.137684528 1.00E-05 5 -0.865669679 MATEVAADALGEEWKGYVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MATEVAADALGEEWKGYVVR 20 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ; 184.83 3.53E-17 336170000 665440 391560 676150 555970 632070 641590 949010 731270 825110 FALSE TRUE 633985.97 431460.4092 707152.1463 500082.8393 742302.8079 619371.5774 804221.0947 667236.1221 953063.8447 0.66520829 0.452708821 0.741977728 0.524710744 0.778859477 0.649874172 0.843827094 0.700095934 1 19.86221334 1.181940066 0.320749059 1.03460113 0.538538402 0.571788885 0.100883085 0.966262627 0.327985864 0.182257717 0.122229044 15.20337703 -1.181940066 -0.496062728 MAVTFIGNSTAIQELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAVTFIGNSTAIQELFK 17 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 321.85 2.82E-58 44770000 116070 116390 104420 134190 80961 112470 137490 120560 93053 FALSE TRUE 110583.6011 128250.2733 109207.7603 120700.9663 95080.57277 108575.1357 116513.3753 110003.1273 107483.184 1.028845602 1.19321245 1.01604508 1.122975351 0.884608822 1.010159279 1.084014922 1.023445 1 16.71375144 FPSLSESLMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 FPSLSESLMNR 11 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 71.223 0.090338 0 8507.2 11620 11985 60154 84128 119010 167260 126420 143870 FALSE TRUE 8105.081516 12804.09121 12534.5241 54107.20563 98799.89656 114888.6539 141741.4151 115349.9946 166180.6248 0.048772723 0.077049242 0.075427109 0.325592744 0.594533187 0.691348068 0.852935866 0.694124208 1 17.34239266 2.723150965 1.094546863 0.843113726 0.038408165 0.94902494 0.077072839 0.086227131 0.215480034 0.035663776 0.032458475 528.6289762 -2.723150965 -0.804705561 down MAYLLIEEDIRDLAASDDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MAYLLIEEDIRDLAASDDYR 20 1 H7C1M5;Q9H147 H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 0 66.893 0.020954 20354000 28241 19650 24963 26738 32216 22005 33674 30341 31655 FALSE TRUE 26906.1039 21652.35734 26107.57824 24050.24544 37834.4602 21242.96133 28536.41283 27684.18119 36563.89573 0.735865349 0.592178621 0.714026165 0.657759382 1.034749155 0.580981892 0.780453293 0.757145283 1 15.15813217 -4.99999999 0.150298535 2.005068758 0.63419746 0.331776257 0.123928951 145.9073412 1.301004825 43.67029279 0.57022924 1.00E-05 4.99999999 -1.370871298 MCDLVSDFDGFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MCDLVSDFDGFSER 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 208.74 1.77E-08 235794000 405446 390287 384625 437593 429091 386736 458630 436528 475761 FALSE TRUE 386281.3711 430057.689 402260.4367 393605.3203 503924.3345 373343.2353 388657.5702 398303.2941 549539.586 0.70291819 0.78257818 0.731995377 0.716245618 0.916993693 0.679374598 0.707242172 0.724794545 1 19.06786388 -1.447532686 3.819931427 1.001983612 0.744233335 0.591006568 0.066591089 0.00106199 0.000153593 0.060868483 0.014240829 0.035683489 1.447532686 -0.257750277 MCEDLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MCEDLWR 7 0 Q14376;Q14376-2;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 121.29 0.010358 310370000 1018150 889890 802140 931940 1111010 760280 1132920 945720 1049710 FALSE TRUE 970024.0673 980570.8027 838918.9124 838259.6206 1304769.792 733951.313 960072.2465 862907.7432 1212493.666 0.800024029 0.808722413 0.691895501 0.691351753 1.07610442 0.605323833 0.791816299 0.711680207 1 20.20954578 -1.147254387 3.91742589 1.000089783 0.775106912 0.248452477 0.124462343 12672934.11 7433605.995 10236.42707 0.026045397 0.07124356 1.147254387 -0.224982871 MCHNVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MCHNVNR 7 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;;; 121.87 0.0043958 539537000 256558 235790 212193 245989 275449 219631 293282 239084 187778 FALSE TRUE 244431.0118 259817.2691 221922.2589 221261.7184 323487.2184 212025.1234 248536.4444 218148.5375 216897.6532 1.126941708 1.197879577 1.023165791 1.020120389 1.491427932 0.97753535 1.14586968 1.005767164 1 17.72665492 1.357828461 1.569599055 0.996797567 1.150996327 0.132278762 0.142600483 0.725550825 3.284105179 0.119695907 0.037278669 22.79441556 -1.357828461 0.154198759 MCHPSIEGFTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MCHPSIEGFTPR 12 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 103.75 0.0022122 265940000 204150 123900 176780 158310 237660 148900 207910 178760 214430 FALSE TRUE 194500.2341 136525.5509 184885.5379 142396.378 279107.8288 143743.5557 176189.511 163106.8267 247682.7092 0.785279823 0.551211472 0.746461222 0.574914488 1.126876517 0.580353615 0.711351679 0.658531341 1 17.91813363 MCINTEWGAFGDDGSLEDIRTEFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIRTEFDR 25 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 201.15 5.76E-25 217540000 97572 78635 76408 105814 90159 78525 83022 78317 77471 FALSE TRUE 92959.96493 86647.9959 79911.38238 95177.37569 105882.7011 75805.65956 70355.4691 71459.1483 89484.80701 1.038835172 0.968298405 0.893016201 1.063614918 1.1832478 0.847134414 0.786228092 0.798561797 1 16.44935514 2.082355999 12.97007095 0.832557294 1.017253077 0.439407573 0.093891445 0.60614478 93.21377791 0.033940937 0.025066742 120.8804307 -2.082355999 0.184695782 MCINTEWGAFGDDGSLEDIRTEFDREIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MCINTEWGAFGDDGSLEDIRTEFDREIDR 29 2 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 260.97 2.18E-58 295808000 167950 80140 150602 128629 178350 114352 178227 135556 203695 FALSE TRUE 160011.3363 88306.35711 157507.2507 115698.9685 209454.1835 110391.9616 151035.1978 123685.998 235282.9803 0.68008037 0.375319783 0.669437502 0.491743892 0.890222418 0.469188045 0.641929976 0.525690375 1 17.84403744 -5 0.391142199 7.288577558 0.576405386 0.439467762 0.143131572 589.47641 4.244846164 3157.204385 0.082863713 1.00E-05 5 -6.712172172 MCIVLRPS(ph)RVHNSEENTMRALTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.427)RVHNS(0.224)EENT(0.349)MRALTLK 67.251 0.036372 375160000 231993 245338 226023 260845 340910 170708 235030 177948 255820 TRUE FALSE 221027.1507 270338.2211 236386.3781 234624.365 400364.5961 164796.3392 199171.8569 162365.9298 295491.2591 0.747998947 0.914877218 0.799977566 0.79401457 1.354911808 0.557702924 0.674036374 0.549477945 1 18.17275593 MCIVLRPSRVHNS(ph)EENTMRALTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.072)RVHNS(0.461)EENT(0.461)MRALT(0.006)LK 54.223 0.059019 42712000 14301 22175 17700 19736 36032 13502 22511 15615 7816.7 TRUE FALSE 13625.02007 24434.65771 18511.56251 17752.09978 42315.96939 13034.42235 19076.53351 14247.66782 9028.873914 1.509049767 2.706279647 2.0502626 1.966147712 4.686738324 1.443637654 2.112836406 1.578011605 1 13.14033035 1.237560141 1.390536853 1.05773078 2.413743357 0.220166213 0.899571718 0.602591229 2.238573341 0.788226745 0.244310777 17.28065266 -1.237560141 1.356012577 MCSFLEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MCSFLEWR 8 0 A0A2R8YGH5;H7C1E4;P61966;P61966-2;F6SFB5;A0A5F9ZI43;H7BZG6;H0Y673;A0A5F9ZHX2;A6NH01;A0A5F9ZHW1;P56377;P56377-2 A0A2R8YGH5 AP1S1;AP1S2 AP-1 complex subunit sigma-1A;AP-1 complex subunit sigma-2 0 ; 87.696 0.035224 94149000 367140 323630 261440 305820 431040 245650 405990 321700 391160 FALSE TRUE 349786.0198 356608.2649 273427.2826 275078.3926 506213.2395 237143.0789 344048.769 293530.2426 451819.095 0.774172725 0.789272231 0.605169825 0.608824186 1.120389211 0.524862896 0.76147461 0.649663208 1 18.78538572 -1.160945972 4.898033773 1.000020621 0.734528136 0.214466612 0.162576517 3.27E-05 5.61E-06 0.140759079 0.033174658 0.069032568 1.160945972 -0.265492484 MCTLIDKFDEHDGPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MCTLIDKFDEHDGPVR 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 228.9 2.21E-15 1472973000 2357860 2386070 2103630 2530090 1741040 2438370 2493830 2653190 1537331 FALSE TRUE 2246408.631 2629213.246 2200083.516 2275760.546 2044676.825 2353928.635 2113350.431 2420862.618 1775732.44 1.26506031 1.480635926 1.238972419 1.28158978 1.151455466 1.325609975 1.190128864 1.363303707 1 20.75998279 -5 0.142505255 1.14E-09 1.39373892 0.461726082 0.0942883 112.1218635 0.971462361 31.92913761 0.516313244 1.00E-05 5 1.393738919 MDADGFLPITLIASFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MDADGFLPITLIASFHR 17 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 ; 157.8 1.21E-08 105089000 265997 262995 225771 283062 306547 215940 310932 276365 258711 FALSE TRUE 253423.849 289794.4895 236122.8237 254608.07 360008.6997 208461.9437 263493.6127 252165.0155 298830.5806 0.848051925 0.969761826 0.790156159 0.852014775 1.204725096 0.697592406 0.881749158 0.843839392 1 18.18896827 -0.834129707 7.244749317 1 0.887964419 0.068093276 0.132374525 8.65E-10 0 0.11608743 0.02736207 0.146511021 0.834129707 -0.112035582 MDDPTVNWSNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDDPTVNWSNER 12 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 101.35 0.0063296 102320000 85196 82998 71154 82209 76771 80171 88687 89269 73295 FALSE TRUE 81168.95392 91455.59056 74416.48128 73945.19513 90159.83809 77394.65817 75156.1693 81452.13312 84661.21426 0.958750174 1.080253707 0.878991424 0.873424694 1.064948559 0.914169007 0.887728459 0.962095026 1 16.36941356 3.736063301 24.99989308 0.933577671 1.019501939 0.195740207 0.065779025 285.9970034 2863035.613 0.016647235 0.027155936 5445.820226 -3.736063301 0.085924269 MDEFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MDEFSR 6 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ; 153.88 0.023438 329760000 648580 578230 566790 651740 627390 600880 693650 615360 662000 FALSE TRUE 617922.9088 637152.2944 592777.8821 586225.857 736806.6174 580071.3749 587820.9527 561475.8162 764659.579 0.808101966 0.833249608 0.775218017 0.766649465 0.963574691 0.758600809 0.768735486 0.734282067 1 19.54445809 -2.384443496 2.40730879 2.659982594 0.802954756 0.489344664 0.063844088 2576018.583 680354.5936 23946041.88 0.014979236 0.004126259 2.384443496 -1.857027838 MDELQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 MDELQLFR 8 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;;;; 215.09 1.99E-05 1694326700 2742080 2136295 2234989 2433842 2562311 2189994 3100888 2479868 2595849 FALSE TRUE 2612467.313 2353985.889 2337465.456 2189187.578 3009177.227 2114153.959 2627790.584 2262717.611 2998400.005 0.871287123 0.785080671 0.779570922 0.730118588 1.003594324 0.705094035 0.876397605 0.754641678 1 21.51576143 -2.008691829 2.32474424 1.192689633 0.816030276 0.313961035 0.086680256 7436517.718 2819073.253 7660408.334 0.018236693 0.009801853 2.008691829 -0.376659357 MDIDAPDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;;; 254.05 9.24E-31 1384421000 2650400 2299680 2371510 2782460 2025130 2412390 2783640 2555690 290042.4 FALSE TRUE 2525120.845 2534020.007 2480246.079 2502761.834 2378312.031 2328848.329 2358944.593 2331900.235 335020.6941 7.537208565 7.563771586 7.403262315 7.470469374 7.099000369 6.95135665 7.041190693 6.960466253 1 18.35389069 -0.646869832 0.577042672 3.64E-12 7.44779227 0.993206059 0.163128482 1.031623368 0.250859603 2.290090412 0.071456492 0.225491496 0.646869832 7.44779227 MDIDAPDVEVQGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MDIDAPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;; 274.81 4.76E-39 1152129000 2366050 1952225 1989467 2392930 1769016 2021730 2472720 2350680 1721508 FALSE TRUE 2254211.506 2151158.947 2080686.03 2152388.13 2077531.83 1951716.983 2095461.149 2144841.997 1988470.668 1.133640813 1.08181578 1.046375017 1.082433935 1.044788773 0.981516607 1.053805411 1.078638992 1 20.92322785 8 0.316453085 1.025265781 2.117966265 0.541575277 0.029263803 39.31834836 0.562499233 0.026711386 24.76731212 100000000 -8 1.092700484 MDIDVPDVEVQGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MDIDVPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;; 234.49 9.09E-24 919123000 2035705 1785207 1772024 2074438 1611646 1792882 2167732 2086180 1573680 FALSE TRUE 1939481.259 1967121.623 1853273.053 1865911.551 1892716.552 1730794.047 1837004.67 1903503.02 1817718.257 1.06698673 1.082192807 1.019560125 1.026513071 1.041259582 0.952179492 1.010610232 1.047193652 1 20.79369717 3.548993155 1.502281843 1.007860793 1.076725035 0.446945906 0.027048948 0.314188138 1.416944485 0.008334047 0.016227671 3539.91762 -3.548993155 0.068864242 MDKEETKDWILPSDYDHAEAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;;;; 214.31 1.73E-32 5013350000 6068312 4639846 5244259 5900254 3856101 5764635 6601329 6184506 3353787 FALSE TRUE 5781474.918 5112651.582 5484713.462 5307149.258 4528603.794 5565004.244 5594175.019 5642957.869 3873875.159 1.492426751 1.319777064 1.415820912 1.369984587 1.169011289 1.436547131 1.444077258 1.456670036 1 21.88534603 -1.301407607 3.53266822 0.998680124 1.3882489 0.641397792 0.091184383 2078873.608 1027983.543 20168.2549 0.020848703 0.049956545 1.301407607 0.389568776 MDMMSLNSQLLDAIQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MDMMSLNSQLLDAIQQK 17 0 H0YHW1;H0YHP2;Q6ZP65-2;Q6ZP65 H0YHW1 CCDC64 Bicaudal D-related protein 1 0 ;;;;;;; 71.692 0.022737 6624900000 3013030 3473060 3859800 3492220 11701710 2647820 5074050 3407160 6148310 FALSE TRUE 2870610.043 3826968.763 4036775.648 3141175.411 13742484.52 2556125.329 4299910.481 3108811.008 7101758.514 0.404211159 0.538876217 0.568419165 0.442309522 1.935081923 0.359928506 0.605471233 0.437752284 1 22.75974487 MDMT(ph)SPEQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDMTSPEQSR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 MDMT(0.5)S(0.5)PEQSR 89.548 0.0023649 0 21280 21381 22507 22453 23315 21525 25971 21552 22322 TRUE FALSE 20274.13657 23559.74821 23538.96821 20195.98178 27381.12862 20779.58385 22008.64696 19664.79263 25783.58176 0.786319634 0.913750015 0.912944076 0.78328845 1.06195985 0.805923089 0.853591528 0.762686612 1 14.65416507 -2.553513277 2.255658759 3.434199254 0.862675972 0.198010931 0.088370098 7170441.831 907764.428 88192693.62 0.020787361 0.002795675 2.553513277 -2.571523282 MDPKELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDPKELGK 8 1 A0A3B3IU97;A0A2R8Y5X9;Q76EJ3 A0A3B3IU97 SLC35D2 UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose transporter 0 59.8 0.087855 510500000 841200 664710 691410 809580 1762600 361960 641790 317880 1729300 FALSE TRUE 801438.1431 732444.7047 723111.8324 728199.4803 2069996.882 349425.2344 543873.1482 290044.742 1997471.012 0.40122642 0.366686025 0.36201368 0.364560725 1.036308847 0.17493382 0.272280872 0.145205983 1 20.92974314 -1.048574673 6.905462413 1.000000164 0.388281839 0.37956281 0.244922919 5.91E-07 8.14E-08 0.22583336 0.053229419 0.089418077 1.048574673 -0.611718325 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 38 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 MDRDPLGGLADMFGQMPGS(0.003)GIGT(0.079)GPGVIQDRFS(0.74)PT(0.179)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.997)PT(0.003)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.995)PT(0.005)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.993)PT(0.007)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(1)PTMGR 329.07 1.93E-129 1594583000 576977 454682 514687 582638 563328 492038 664353 581338 621438 TRUE FALSE 549704.4407 501014.6127 538285.908 524070.1213 661572.2248 474998.6007 562993.7482 530432.9629 717807.4312 0.765810462 0.697979139 0.749902947 0.73009849 0.921656974 0.661735418 0.784324212 0.738962763 1 19.45323733 -1.61055829 2.535859399 1.025342864 0.753667818 0.558726273 0.068024781 11366154.59 9841931.645 1905960.39 0.015386418 0.024515554 1.61055829 -0.271675045 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 2 MDRT(1)PPPPT(0.006)LS(0.994)PAAITVGR;MDRT(1)PPPPT(0.01)LS(0.99)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.014)LS(0.986)PAAITVGR;MDRT(1)PPPPT(0.213)LS(0.787)PAAITVGR;MDRT(1)PPPPT(0.044)LS(0.956)PAAIT(0.001)VGR;MDRT(1)PPPPTLS(1)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.013)LS(0.986)PAAIT(0.001)VGR;MDRT(1)PPPPT(0.027)LS(0.973)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR 173.05 1.64E-11 2774470000 2515001 2310489 2338942 2644069 2382989 2362870 2807772 2570443 2552152 TRUE FALSE 2396121.887 2545930.456 2446184.804 2378282.161 2798581.527 2281043.219 2379394.813 2345361.384 2947926.698 0.812815966 0.863634248 0.829798382 0.806764348 0.949338913 0.773778813 0.807141784 0.795596914 1 21.49126922 -1.179622087 4.968450386 1.00001423 0.830487975 0.549675502 0.048394406 7.12E-06 1.18E-06 0.043726128 0.010305482 0.066126862 1.179622087 -0.169526255 MDRT(ph)PPPPTLSPAAITVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR 137.62 5.68E-06 3689080000 1325372 1129893 1224277 1391636 1043390 1232308 1438057 1330737 1266281 TRUE FALSE 1262724.292 1245030.381 1280411.311 1251746.105 1225356.886 1189632.865 1218654.993 1214210.614 1462649.39 0.86331304 0.851215876 0.875405494 0.855807355 0.837765287 0.813341101 0.833183264 0.830144682 1 20.48015255 -0.969606314 5.076778507 1.000000908 0.845354165 0.882913523 0.017736087 2.01E-07 4.08E-08 0.018922162 0.00445997 0.107249107 0.969606314 -0.154646743 MDS(ph)DEDEKEGEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MDSDEDEKEGEEEK 14 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK 213.99 1.58E-10 1252520000 3769570 3900580 2744040 4352310 1104874 4309780 3217450 4511910 940404 TRUE FALSE 3591389.897 4298053.537 2869856.948 3914807.53 1297563.676 4160531.238 2726568.91 4116823.241 1086237.049 3.306267171 3.956828336 2.642017182 3.604008473 1.194549271 3.83022402 2.510104872 3.789986029 1 20.05090755 3.729589104 24.25549884 2.751224022 3.631547756 0.139904459 0.985574309 726.3411394 1963747.09 0.228287542 0.359697877 5365.239381 -3.729589104 0.880323734 MDS(ph)DEDEKEGEEEKVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MDSDEDEKEGEEEKVAK 17 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK 189.48 3.13E-10 1778047000 2964130 2334230 2497990 2880680 916839 3208660 2862860 3492660 759956 TRUE FALSE 2824021.449 2572090.691 2612525.312 2591108.573 1076735.431 3097543.3 2426078.127 3186824.175 877806.0952 3.21713584 2.930135374 2.976198647 2.951800617 1.226621047 3.528732959 2.763797313 3.630442067 1 19.74354276 2.97403191 24.98205395 2.591489819 3.032693317 0.091271496 0.845312025 2209.082519 2125203.243 0.236337928 0.251543045 941.9588052 -2.97403191 0.441203498 MDS(ph)FDEDLARPSGLLAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER 229.99 4.08E-20 145887000 111169 80676 96458 131349 109748 120414 137715 101828 110306 TRUE FALSE 105914.2617 88896.97612 100880.6947 118145.549 128888.0165 116244.033 116704.0474 92911.4005 127411.6911 0.831275849 0.697714435 0.791769529 0.927274004 1.011587048 0.912349816 0.915960273 0.729221939 1 16.95913814 3.304512888 4.85587897 0.916417788 0.76220397 0.403431638 0.081917055 0.184829875 8.407637357 0.02207064 0.029773229 2016.103801 -3.304512888 -0.154213818 MDSFDEDLARPSGLLAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 107.15 0.00031483 572800000 394732 304982 349731 378123 396005 346212 450164 371496 452630 FALSE TRUE 376073.8006 336060.0125 365766.5123 340113.3577 465068.1466 334222.5916 381483.214 338965.8408 522821.5487 0.7193158 0.642781487 0.699601065 0.650534314 0.889535154 0.639267055 0.729662377 0.648339461 1 18.99595908 -2.137057845 2.472437117 1.651869997 0.701300368 0.615313907 0.073951054 3581413.088 1028458.564 13113193.29 0.016163456 0.007293604 2.137057845 -0.950569629 MDSTEPPYSQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MDSTEPPYSQKR 12 1 P68104;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 69.721 0.07891 96195000 104450 73323 95106 93012 76783 97334 115650 98825 98493 FALSE TRUE 99512.8555 80794.69706 99466.70417 83662.25705 90173.93089 93963.29917 98005.46844 90171.3591 113766.7914 0.874709168 0.710178217 0.874303502 0.735383815 0.79262085 0.825929061 0.86145937 0.792598244 1 16.79571997 -0.704911433 0.415656263 1.058903561 0.794161724 0.537282758 0.055528158 7.926986241 1.131223088 0.662369187 0.031598465 0.197282502 0.704911433 -0.264741837 MDYEDDRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 MDYEDDRLR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;;;;;; 127.4 0.00040726 4910590000 4547920 3973561 3867371 4415975 4280010 3973283 4926910 4383453 4510070 FALSE TRUE 4332948.835 4378471.383 4044693.786 3972072.803 5026442.389 3835687.213 4175219.391 3999614.617 5209468.621 0.831744876 0.840483301 0.776411968 0.762471778 0.964866622 0.736291452 0.801467423 0.767758654 1 22.31270479 -1.896426964 2.512189575 1.103116003 0.812257888 0.469851664 0.063330654 7852653.934 4681708.445 4798590.333 0.013973939 0.012693256 1.896426964 -0.290858116 MDYVEINIDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MDYVEINIDHK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ;; 166.11 2.08E-05 336597000 805660 664510 700800 854330 547440 768330 866130 868320 586420 FALSE TRUE 767578.0485 732224.3245 732932.3732 768451.1253 642913.3627 741722.5394 733985.9609 792285.2975 677359.0186 1.133192336 1.080998856 1.082044164 1.134481278 0.949147121 1.09502128 1.083599599 1.16966819 1 19.36956118 4.919780209 0.912993739 1.074391154 1.183327999 0.08510647 0.061821556 7.369323556 3.877471611 0.018447024 0.862465236 83134.29332 -4.919780209 0.108936845 MEALASTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEALASTEK 9 0 G3V5P0 G3V5P0 KTN1 0 56.258 0.093387 86083000 42124 46804 34375 41553 118690 38016 46065 60187 126510 FALSE TRUE 40132.882 51573.38081 35951.12775 37376.01349 139389.4984 36699.49639 39036.93821 54916.70721 146128.5247 0.274640985 0.352931646 0.246024025 0.255774932 0.953882883 0.251145329 0.267141123 0.375811002 1 17.1568783 -1.199114017 3.048501153 1.002301251 0.362232917 0.463764528 0.211925987 9804573.462 13505345.59 216272.9626 0.050374065 0.063224584 1.199114017 -0.640068334 MEANKENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 MEANKENR 8 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 ;;;;;;;;;;; 137.14 0.00069414 3431070000 5020970 4064550 4167780 4652380 4034300 4580810 5843190 5061650 4876670 FALSE TRUE 4783638.699 4478732.266 4358876.835 4184713.923 4737880.643 4422175.401 4951704.048 4618425.093 5632919.077 0.849229082 0.7950997 0.773822023 0.742903256 0.841105753 0.785059281 0.879065362 0.819899066 1 22.42545132 0.339646498 0.615487671 1.006135707 0.799092089 0.726460043 0.037331267 1.21594939 0.690739898 0.054954587 0.0148564 2.185981577 -0.339646498 -0.207043618 MECCDVPAETLYDVLHDIEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 MECCDVPAETLYDVLHDIEYR 21 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;;;;;;;;;;;;;;;; 257.72 1.72E-36 2941566100 1847180 1883412.9 1740912.7 2051185 1894121.5 1757767.4 1989608.3 1896026.7 1707778 FALSE TRUE 1759867.462 2075334.816 1820735.269 1844995.987 2224455.69 1696895.474 1686057.012 1730000.551 1972611.49 0.892151075 1.052074788 0.923007535 0.935306317 1.127670452 0.860227918 0.854733444 0.877010278 1 20.91167541 MECCDVPAETLYDVLHDIEYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MECCDVPAETLYDVLHDIEYRK 22 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 113.17 0.00017473 9754900 14655 7308.4 15456 13554 15545 12277 20410 17239 18456 FALSE TRUE 13962.28719 8053.134269 16164.67289 12191.52617 18256.04308 11851.84441 17296.07964 15729.46177 21318.06222 0.654951048 0.377761083 0.758261831 0.571887165 0.856365034 0.555953177 0.811334514 0.737846696 1 14.37978868 0.986839312 0.192216568 1.144850792 0.430022298 0.471501629 0.126992857 3.186606475 0.477716512 0.851002423 0.556620648 9.701509478 -0.986839312 -0.714828494 MEDETQKELETMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEDETQKELETMR 13 1 A0A0A0MSW4;P48739;P48739-3 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 93.478 0.0051031 77923000 75249 61030 71415 79536 58131 64668 80683 75689 52886 FALSE TRUE 71692.1289 67249.02639 74689.44839 71540.89017 68269.028 62428.53094 68373.32651 69061.26991 61087.29078 1.173601382 1.100867718 1.222667554 1.171125602 1.117565162 1.021956125 1.11927253 1.130534175 1 15.89858464 2.483681419 7.640061351 1.078941685 1.158442001 0.466210167 0.04899129 0.136662362 58.86181875 0.015880972 0.014016033 304.5659994 -2.483681419 0.079500316 MEDGEFWMSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MEDGEFWMSFR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;; 244.61 1.60E-15 247565500 256296 314821 232498 296438 245641 221915 271616 291384 229662 FALSE TRUE 244181.396 346901.6178 243158.2633 266639.489 288480.7126 214230.0279 230175.9906 265868.8722 265276.81 0.92047773 1.307696733 0.916620881 1.005136819 1.087470528 0.807571638 0.867682292 1.002231866 1 18.01713904 2.860025005 1.175345667 0.911744565 1.091513581 0.114611012 0.129080513 0.653331404 1.890967801 0.057278866 0.060113575 724.4776707 -2.860025005 0.179769015 MEDSVGCLETAEEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEDSVGCLETAEEVKR 16 1 P35579 P35579 MYH9 Myosin-9 0 ; 130.29 5.32E-05 348150000 266610 244360 238980 298580 210710 292140 269780 311440 229370 FALSE TRUE 254007.8737 269260.5618 249937.4694 268566.1711 247457.7573 282023.1185 228620.1062 284168.6626 264939.5281 0.958739058 1.016309509 0.943375536 1.013688569 0.934015996 1.064481093 0.862914295 1.072579334 1 18.01530358 MEEADALIESLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEEADALIESLCR 13 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 100.55 0.0054635 25342000 71018 55486 60709 70360 69996 56945 75704 66767 73241 FALSE TRUE 67661.11988 61140.08648 63492.5677 63287.27912 82203.28024 54972.98037 64153.9644 60920.52753 84598.84022 0.799787795 0.722705965 0.750513453 0.748086841 0.9716833 0.649807731 0.758331488 0.72011067 1 16.36835026 -1.08148118 4.254884636 1.000024304 0.763099977 0.443152174 0.082713993 10241417.73 2603102.715 2775.336707 0.017704483 0.082893184 1.08148118 -0.236924327 MEEEGTEDNGLEDDS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEEEGTEDNGLEDDSR 16 0 Q14151;K7ERX3 Q14151 SAFB2 Scaffold attachment factor B2 1 MEEEGTEDNGLEDDS(1)R;MEEEGTEDNGLEDDS(1)R 140.28 6.71E-06 160864000 250340 336390 238210 306950 210112 307320 223120 279480 197734 TRUE FALSE 238506.9243 370668.5234 249132.1641 276094.8028 246755.4663 296677.4313 189078.9461 255007.2496 228397.5788 1.044262052 1.622909163 1.090782859 1.208834193 1.080376892 1.298951735 0.827850046 1.116505923 1 17.80118783 2.477655056 0.836178402 0.984244511 1.305393892 0.204658289 0.187030492 0.760467467 1.070572646 0.128114663 0.092521114 300.3689639 -2.477655056 0.321149381 MEEEQHHWDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEEEQHHWDDRR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 88.101 0.0041387 53607000 24274 20218 25943 18177 43775 27977 30971 20679 31956 FALSE TRUE 23126.61613 22278.23719 27132.51221 16349.81343 51409.34614 27008.14947 26245.80513 18868.23713 36911.57327 0.626541057 0.603556966 0.735067888 0.44294545 1.392770386 0.731698681 0.71104542 0.511174016 1 15.17178561 MEEFKDQLPADECNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEEFKDQLPADECNK 15 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 205.42 4.02E-09 524520000 838960 764330 548320 859580 324520 642450 604090 797760 301200 FALSE TRUE 799304.0235 842216.096 573461.0144 773173.3853 381116.1853 620201.7954 511924.9756 727903.9052 347908.5577 2.297454333 2.420797297 1.648309597 2.222346557 1.095449298 1.782657488 1.471435423 2.092227653 1 18.40834864 8 0.128221332 0.911351246 6.088677115 0.448895037 0.363775011 64.28694109 0.559310544 1.804934599 60.0764322 99999999.99 -8 5.177325869 MEEIGR ddPTM_SK-BR-3_Trastuzumab_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 ; 196.81 0.00055501 508310000 822480 472700 471410 754930 892610 534750 935340 668940 965560 FALSE TRUE 783603.0004 520868.6674 493024.6148 679043.0021 1048280.901 516231.4734 792636.7043 610364.0673 1115294.113 0.70259763 0.467023596 0.442057937 0.608846576 0.939914314 0.462865774 0.71069747 0.547267362 1 20.08899278 -4.999999998 0.254602219 3.444007675 0.57418027 0.394562713 0.150539538 190.171671 1.877339286 242.4486247 0.196703166 1.00E-05 4.999999998 -2.869827406 MEELHNQEMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEELHNQEMQK 11 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 138.24 6.18E-05 200240000 299170 271210 266240 311760 241320 319280 328780 308830 251720 FALSE TRUE 285028.827 298846.6073 278447.3673 280421.2925 283406.1316 308223.2535 278618.5725 281787.208 290755.452 0.980304325 1.027828043 0.957668602 0.964457556 0.974723362 1.060077297 0.958257431 0.969155371 1 18.14944672 3.742579858 24.99333637 0.983767666 1.004066181 0.066717437 0.032000057 977.4848521 6078383.545 0.00808968 0.013850956 5528.150504 -3.742579858 0.020298516 MEELHNQEVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEELHNQEVQK 11 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 132.32 0.0001849 417330000 580280 515240 587460 563760 742520 561890 713730 562380 367010 FALSE TRUE 552851.3144 567743.5418 614395.6221 507089.7737 872015.2529 542431.6084 604837.3799 513135.0258 423924.0364 1.304128256 1.339257728 1.449305935 1.196180755 2.05700828 1.279549075 1.426758872 1.21044098 1 18.69344624 1.007362075 2.110860023 1.00004488 1.42790901 0.278041194 0.234758416 0.420539531 4.013636757 0.207070792 0.057566586 10.17096302 -1.007362075 0.42786413 MEELHNQEVQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEELHNQEVQKR 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 131.06 0.00013336 176960000 401950 320770 367710 412910 321590 385620 450960 438350 356470 FALSE TRUE 382950.6201 353456.8277 384569.8672 371403.5023 377675.1942 372265.8827 382157.7696 399965.7502 411749.547 0.930057174 0.858426755 0.933989776 0.902013141 0.917244954 0.904107571 0.928131609 0.971381154 1 18.65140754 1.209363089 1.64124118 1.000379139 0.904237785 0.712034631 0.020631481 0.174643547 0.86984808 0.01824646 0.005435402 16.19433388 -1.209363089 -0.096141353 MEEMIFNLADTHLFFNDLEES(ph)RASRESMMLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEEMIFNLADTHLFFNDLEESRASRESMMLVK 32 2 E5RHZ7 E5RHZ7 EYA1 1 MEEMIFNLADT(0.233)HLFFNDLEES(0.256)RAS(0.256)RES(0.256)MMLVK 49.464 0.05251 1032500000 387190 222640 419630 329510 349420 334020 461860 359160 102090 TRUE FALSE 368888.296 245327.2691 438870.4506 296387.0288 410358.7374 322452.8036 391394.7744 327710.0464 117921.5958 3.128250543 2.080426977 3.721713971 2.513424507 3.479928631 2.734467775 3.319110225 2.779050302 1 16.84746843 4.785675647 21.17888964 2.820363484 3.12825887 0.009275923 0.778940365 7064.066882 4192597.753 0.160251239 21.48205402 61048.59136 -4.785675647 0.307895387 MEGGGAEVHAQLPSLEGDLRGPDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEGGGAEVHAQLPSLEGDLRGPDVK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 97.713 0.011037 37141000 66992 58790 60500 68754 52872 68466 75320 78621 53571 FALSE TRUE 63825.42093 64780.76784 63273.98484 61842.7173 62092.86006 66095.00525 63828.55065 71736.52844 61878.51708 1.031463324 1.046902397 1.022551733 0.999421451 1.003463932 1.06814139 1.031513903 1.15931234 1 15.917151 1.402430079 25 1.084909366 1.030858847 0.194182587 0.042427659 53.71092668 17976.33084 0.024687115 0.009021305 25.25980999 -1.402430079 -0.054050518 MEGMDDDPEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEGMDDDPEDR 11 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 96.342 0.0070256 131270000 259450 224610 221410 258930 234390 235260 258990 255860 251000 FALSE TRUE 247186.3127 247498.0144 231561.8675 232901.8645 275267.5418 227112.8872 219476.3188 233455.542 289923.7981 0.852590627 0.853665743 0.798699069 0.803320962 0.949447902 0.783353725 0.757013809 0.805230697 1 18.14531423 MEIATKDPLNPIKQDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEIATKDPLNPIKQDVK 17 2 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 96.143 0.011498 316630000 815260 663460 750130 795700 458160 847700 933710 990790 545380 FALSE TRUE 776724.2755 731067.3283 784524.2025 715714.7243 538062.9589 818343.9364 791255.3907 904031.1751 629954.745 1.232984245 1.160507694 1.245365971 1.13613673 0.854129544 1.299051945 1.256051164 1.435073205 1 19.26488867 MEITIRNS(ph)PYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;MEIT(0.001)IRNS(0.995)PY(0.004)R;MEITIRNS(1)PYR;MEITIRNS(1)PYR;MEITIRNS(1)PYR 183.06 3.34E-06 4140960000 4992240 4039610 3700700 4281580 5309890 4086730 5178490 4607780 5435450 TRUE FALSE 4756266.709 4451250.852 3870380.755 3851187.444 6235933.135 3945205.515 4388416.241 4204298.356 6278351.826 0.757566132 0.708983978 0.616464458 0.613407396 0.993243658 0.628382357 0.69897584 0.669650009 1 22.58195445 -1.395542259 5.419109448 1.00015292 0.711534287 0.40546473 0.110039899 0.000187468 2.09E-05 0.098245774 0.023144567 0.040221452 1.395542259 -0.288618633 MEITIRNS(ph)PYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 MEIT(0.032)IRNS(0.965)PY(0.003)RR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR 259.68 1.44E-21 2508882000 1954000 1458705 1825877 1883659 1822007 1775709 2115645 2016294 2062800 TRUE FALSE 1861638.292 1607348.698 1909595.266 1694310.019 2139764.444 1714215.752 1792864.499 1839736.608 2382688.489 0.781318373 0.674594562 0.801445626 0.711091704 0.898046242 0.719446021 0.752454426 0.772126368 1 21.18415892 -5 0.33364684 3.507967585 0.748710557 0.599880521 0.060463701 237.5436882 2.03403123 423.2249091 0.04591006 1.00E-05 5 -2.759257028 MEIVDHALHALTDEVIIPHSGWER ddPTM_SK-BR-3_Trastuzumab_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 ; 354.56 1.61E-102 189100000 168812 174332 151604 189666 150546 150023 175711 137190 11296.2 FALSE TRUE 160832.5913 192096.629 158555.1934 170600.4133 176801.1747 144827.6659 148903.0598 125176.9163 13047.957 12.32626619 14.72235301 12.15172562 13.0748755 13.55010403 11.0996431 11.41198272 9.59360276 1 13.67153631 0.277882422 0.540087422 0.272162215 13.43938854 0.95268206 0.826432213 0.468690854 0.203962951 1.477356335 0.352713691 1.896192487 -0.277882422 13.16722632 MEIVELEDHPFFVGVQYHPEFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MEIVELEDHPFFVGVQYHPEFLSR 24 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;; 155.91 2.07E-08 346045000 241450 209412 188461 233012 197380 188615 245561 216554 106635 FALSE TRUE 230037.137 230751.3209 197102.1233 209589.1911 231803.0095 182083.2153 208096.1594 197591.3837 123171.4112 1.867617938 1.873416231 1.600226232 1.701605828 1.881954646 1.478291216 1.689484251 1.604198424 1 16.91030791 -2.287753033 0.192790226 1.33E-19 1.915395408 0.814076611 0.112187131 15.42977866 0.392383906 7.077852672 0.311281053 0.005155217 2.287753033 1.915395408 MEKGEHSIVYLKPSYAFGSVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEKGEHSIVYLKPSYAFGSVGK 22 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 216.44 8.07E-26 469660000 1482000 1014500 1338400 1288500 1099200 1317200 1803500 1552200 1248900 FALSE TRUE 1411948.797 1117878.703 1399766.964 1158977.532 1290900.132 1271585.034 1528342.951 1416281.139 1442573.034 0.978771102 0.774920006 0.970326584 0.803409952 0.894859464 0.881470126 1.059456205 0.981774306 1 20.46021293 1.754621873 19.11906278 1.01540368 0.879314012 0.466362286 0.065310988 0.799227517 957.014027 0.027342155 0.015144435 56.8357864 -1.754621873 -0.136089667 MELGAPEEMGQVPPLDS(ph)RPSSPALYFTHDASLVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.333)RPS(0.333)S(0.333)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.278)RPS(0.278)S(0.278)PALY(0.052)FT(0.057)HDAS(0.057)LVHK 156.17 9.35E-12 108612000 189037 202014 175250 197019 145562 190805 206259 214621 22064.1 TRUE FALSE 180101.5956 222599.4563 183285.3858 177214.2758 170947.9667 184197.375 174790.4013 195827.6475 25485.68794 7.06677395 8.734292627 7.191698583 6.953482136 6.707606525 7.227482948 6.858374855 7.683828191 1 14.63739968 -0.825780892 0.657159997 4.96E-24 7.43540652 0.916889545 0.594360217 6.483681164 1.689477886 15.48195097 0.231746601 0.149354774 0.825780892 7.43540652 MELGAPEEMGQVPPLDSRPS(ph)S(ph)PALYFTHDASLVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 2 MELGAPEEMGQVPPLDS(0.598)RPS(0.677)S(0.654)PALY(0.025)FT(0.019)HDAS(0.025)LVHK 79.769 0.0025517 44783000 26504 22060 25959 25663 26103 28810 27400 26465 9894.9 TRUE FALSE 25251.20845 24307.93908 27149.24583 23083.30648 30655.35494 27812.30248 23219.62676 24147.5843 11429.35056 2.209330121 2.126799678 2.37539707 2.01965163 2.682160704 2.433410572 2.031578842 2.112769591 1 13.48045581 0.454414272 1.177101642 0.999705936 2.270276113 0.807982463 0.193721586 0.94854397 1.634664997 0.181023854 0.05491358 2.847175721 -0.454414272 1.270570177 MELGAPEEMGQVPPLDSRPSSPALYFTHDAS(ph)LVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.172)RPS(0.147)S(0.147)PALY(0.159)FT(0.172)HDAS(0.203)LVHK 88.942 0.0003333 171120000 304330 318440 278440 333410 271080 317300 366440 344140 35204 TRUE FALSE 289944.924 350889.398 291206.7494 299894.9934 318356.2662 306311.8214 310532.8479 314005.2772 40663.25652 7.13039114 8.629151427 7.161422235 7.375085495 7.829089291 7.532889582 7.636694019 7.722088786 1 15.31143814 -1.419178263 6.199152102 0.998328041 7.665426081 0.960576217 0.421865464 0.009229617 0.000864755 0.38673176 0.091183048 0.038090944 1.419178263 6.66709804 MELLAHLLGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MELLAHLLGEK 11 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 132.32 0.0001849 261490000 1852410 1486430 1471820 1560890 1466550 1479120 2052620 1767150 1337830 FALSE TRUE 1764850.25 1637898.907 1539304.403 1403986.372 1722315.856 1427897.704 1739455.12 1612408.978 1545293.844 1.142080684 1.059927155 0.996124076 0.908556245 1.114555567 0.924029892 1.125646832 1.043431956 1 20.55944977 4.251216297 2.247294601 1.022052994 1.134787167 0.241113473 0.069777941 0.436892257 4.194081356 0.017224896 0.064561485 17832.66689 -4.251216297 0.112734174 MELLQAEGATAVTGVPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MELLQAEGATAVTGVPSPR 19 0 Q09013-5;M0R1F3;Q09013-2;Q09013-7;Q09013-11;Q09013-15;Q09013;Q09013-16;Q09013-6;Q09013-1 Q09013-5 DMPK Myotonin-protein kinase 1 MELLQAEGATAVT(0.005)GVPS(0.995)PR 67.866 0.020295 0 12907 12526 11821 12441 32067 14069 15630 14710 29458 TRUE FALSE 12296.91169 13802.41364 12363.00454 11190.40704 37659.47465 13581.787 13245.35644 13421.91442 34026.19619 0.361395427 0.405640806 0.363337838 0.328876228 1.106778861 0.399156783 0.389269384 0.394458268 1 15.05435826 -2.608776839 2.006840776 9.999971211 0.45992652 0.347313437 0.228655099 16085133.67 636667.5081 660943711.4 0.055076038 0.002461632 2.608776839 -9.540044691 MELSLNIPVNHGPQEESCGSSQLHENSGS(ph)PETSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MELSLNIPVNHGPQEESCGSSQLHENSGSPETSR 34 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 MELSLNIPVNHGPQEESCGSSQLHENS(0.113)GS(0.883)PET(0.002)S(0.002)R 150.69 2.18E-10 42861000 27419 22364 27220 27362 29355 29203 32519 29321 21159 TRUE FALSE 26122.95821 24642.91703 28468.06392 24611.51978 34474.50271 28191.69279 27557.6293 26753.4978 24440.22965 1.068850767 1.008293186 1.164803454 1.007008532 1.410563779 1.153495413 1.127551978 1.094650017 1 14.57697022 MEQEAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEQEAERR 8 1 P49756 P49756 RBM25 RNA-binding protein 25 0 78.516 0.044738 0 64845 51021 58451 63869 70772 52804 87719 63356 86574 FALSE TRUE 61779.90536 56220.09791 61131.03617 57448.76678 83114.61439 50975.38424 74335.85548 57808.21277 99999.45376 0.617802428 0.56220405 0.611313701 0.574490806 0.831150684 0.509756627 0.743362615 0.578085285 1 16.60963259 -5 0.239714896 3.120009451 0.590362368 0.604115734 0.094096172 104.4084582 1.041082264 107.8694055 0.128955498 1.00E-05 5 -2.529647084 MEQELKEPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEQELKEPGR 10 1 C9JVE2;Q96GG9 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 ; 125.97 0.00036021 258800000 463770 368600 403330 482700 375980 452710 518950 517520 407420 FALSE TRUE 441848.5112 406160.7591 421823.0794 434178.0789 441550.793 437032.5392 439774.6463 472203.2053 470600.6128 0.938903391 0.863068912 0.896350468 0.922604151 0.938270756 0.92866972 0.934496544 1.003405419 1 18.84414367 1.493991488 0.746844704 1.006272513 0.901566466 0.68855177 0.023367603 0.344800889 0.40873966 0.021847464 0.00941552 31.18828456 -1.493991488 -0.104706047 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_SK-BR-3_Trastuzumab_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 199.87 4.43E-22 1471230000 794150 677990 714670 756020 753380 730880 809990 717630 781800 TRUE FALSE 756612.1034 747077.9518 747438.3264 680023.4333 884769.2335 705569.4423 686411.149 654790.5128 903037.5511 0.837852316 0.827294447 0.827693517 0.75304004 0.979770146 0.781329017 0.760113628 0.725097768 1 19.78442646 -1.499479697 8.270784006 1.000013559 0.812970609 0.417835028 0.069897927 1.66E-05 1.01E-06 0.064440562 0.015187686 0.031660685 1.499479697 -0.18704295 MEREDS(ph)S(ph)EEEEEEIDDEEIERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEREDSSEEEEEEIDDEEIERR 22 2 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 MEREDS(1)S(1)EEEEEEIDDEEIERR 45.126 0.096424 223610000 103460 85396 93991 114530 99859 100710 116910 129390 106890 TRUE FALSE 98569.65084 94097.94949 98300.58032 103017.2268 117274.378 97222.38745 99073.2323 118059.9257 123465.9553 0.798354904 0.762136812 0.796175594 0.834377595 0.949851947 0.78744288 0.802433611 0.956214411 1 16.91375376 -5 0.098786781 1.607314005 0.692506498 0.545799371 0.056522149 146.113341 0.98474465 18.02443338 0.986166721 1.00E-05 5 -0.914807507 MES(ph)EGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_SK-BR-3_Trastuzumab_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 78.093 0.001084 78760000 45655 56556 41583 58396 21767 54907 44795 46644 34919 TRUE FALSE 43496.97863 62319.1207 43489.62168 52525.92313 25563.15791 53005.55682 37960.70003 42559.60408 40334.06018 1.078418053 1.545074322 1.078235652 1.302272147 0.633785882 1.314163677 0.94115742 1.05517778 1 15.29971102 MES(ph)HS(ph)EDEDLAGAVGGLGWNSR ddPTM_SK-BR-3_Trastuzumab_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 192.75 5.08E-18 42964000 48573 49548 57944 55762 55284 42081 55908 55072 53197 TRUE FALSE 46277.05055 54596.99753 60600.78971 50156.69782 64925.5121 40623.72442 47378.20778 50249.60372 61446.51907 0.753127293 0.88852873 0.986236334 0.816265894 1.056618228 0.661123283 0.771047872 0.817777874 1 15.90704366 2.221013696 24.99914806 0.786287826 0.885303361 0.096169192 0.117542597 465.5286123 663235.8842 0.04097537 0.03033071 166.3465109 -2.221013696 0.099015535 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.109)EGGADDS(0.891)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.009)EGGADDS(0.991)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.005)EGGADDS(0.995)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 246.97 1.64E-50 6598441000 2562647 2971551 2100755 3005793 1142580 2920421 2214781 2737684 1089240 TRUE FALSE 2441515.755 3274355.425 2197076.695 2703644.977 1341845.59 2819286.088 1876875.481 2497957.876 1258153.776 1.940554328 2.602508125 1.746270397 2.148898671 1.066519543 2.240812007 1.491769541 1.985415394 1 20.26287683 0.01153337 0.11060302 1.03E-12 2.858826855 0.350371247 0.406566673 25.42629598 0.932307348 15.94174196 7.534432415 1.026912334 -0.01153337 2.858826855 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 MES(0.001)EGGADDS(0.999)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK 268.23 1.76E-59 1214680000 825040 673282 764530 909550 614098 818580 865380 867630 722265 TRUE FALSE 786041.9943 741890.2013 799584.4567 818120.306 721196.4968 790232.3693 733350.3872 791655.7176 834270.1674 0.942191181 0.889268525 0.958423887 0.980641929 0.864463965 0.947213984 0.879032256 0.948920084 1 19.67015513 0.9891642 23.90411263 1.000000004 0.920786661 0.308526235 0.036613355 320.1499223 706263.7165 0.032475029 0.008118757 9.753583357 -0.9891642 -0.079213343 MESLSSHRIDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MESLSSHRIDEDGENTQIEDTEPMSPVLNSK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MESLSSHRIDEDGENTQIEDTEPMS(1)PVLNSK 216.53 6.24E-35 260190000 32767 7920 42362 30165 43418 28475 73236 37197 75698 TRUE FALSE 31218.16885 8727.057004 44304.3396 27132.75689 50990.08545 27488.90361 62062.50313 33939.83349 87436.85923 0.357036713 0.099809818 0.50670095 0.310312574 0.583164651 0.314385762 0.709797947 0.388163914 1 16.41595396 -2.684324605 0.118155543 2.184993824 5.72E-13 0.627384227 0.152075497 42.60149288 0.586165904 14.67964896 1.604962011 0.002068595 2.684324605 -2.184993824 MESMNRPYTSLVPPLS(ph)PQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MESMNRPYTSLVPPLSPQPK 20 1 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 MESMNRPYTSLVPPLS(0.999)PQPK 76.668 0.0066438 161900000 248930 184050 220330 239580 174710 202810 220150 197880 162090 TRUE FALSE 237163.5722 202804.9042 230432.3484 215496.9632 205179.3687 195786.6388 186562.0742 180552.5782 187226.0894 1.266722886 1.083208569 1.230770504 1.150998581 1.095890906 1.045723059 0.996453405 0.964355869 1 17.51442196 2.326690229 1.178691562 0.979762947 1.183917293 0.769283935 0.047867759 0.220906379 0.602377858 0.028767023 0.017727337 212.1730545 -2.326690229 0.204154346 MESSFGS(ph)PSKQESSESLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MESSFGSPSKQESSESLPK 19 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MESSFGS(0.998)PS(0.002)KQESSESLPK;MESSFGS(0.881)PS(0.119)KQESSESLPK 223.91 1.27E-19 278980000 277200 265355 236834 310990 128614 300650 260864 334680 143102 TRUE FALSE 264097.3054 292394.9762 247693.0732 279728.6944 151044.2409 290238.4151 221064.4057 305373.6449 165293.5273 1.597747411 1.768943896 1.498504371 1.692314871 0.913794045 1.755897039 1.337405096 1.847462813 1 17.33467071 -3.199571608 0.202190139 5.30E-26 1.651098746 0.2539257 0.27680675 82.33596922 1.569192453 36.81949659 0.618876205 0.00063158 3.199571608 1.651098746 METEADAPS(ph)PAPSLGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 METEADAPSPAPSLGER 17 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 METEADAPS(1)PAPSLGER;METEADAPS(1)PAPSLGER 230.82 6.96E-16 216560000 681000 630630 655200 743220 674290 643800 771100 714150 792500 TRUE FALSE 648810.4796 694891.914 685241.5681 668510.1136 791885.9625 621505.0446 653454.5328 651615.2401 915396.8525 0.708775082 0.759115472 0.748573219 0.730295403 0.865073941 0.678946014 0.71384835 0.711839066 1 19.80403781 -1.090967054 4.58475339 1.000017764 0.73864663 0.729439832 0.04984553 8.55E-06 1.69E-06 0.04557291 0.010740908 0.081102258 1.090967054 -0.261371134 METVSNASSSS(ph)NPSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 METVSNASSS(0.002)S(0.998)NPS(0.002)S(0.998)PGR;METVSNASSS(0.004)S(0.996)NPSS(1)PGR;METVSNASS(0.001)S(0.008)S(0.991)NPSS(1)PGR;METVSNASSS(0.02)S(0.98)NPS(0.002)S(0.998)PGR;METVSNASS(0.001)S(0.031)S(0.968)NPS(0.231)S(0.769)PGR;METVSNASSS(0.015)S(0.984)NPS(0.059)S(0.941)PGR 385.76 2.59E-126 714943000 1524562 1466808 1548971 1680187 1571768 1609005 1760721 1609540 1732427 TRUE FALSE 1452498.976 1616277.403 1619992.852 1511291.411 1845883.842 1553284.753 1492090.674 1468600.145 2001082.931 0.725856462 0.807701359 0.809558078 0.755236771 0.92244245 0.776222079 0.745641598 0.733902689 1 20.93234953 -2.323690719 2.406244905 2.298987634 0.783893775 0.590279349 0.056403252 7043385.888 939116.3124 49918941.33 0.013235717 0.004745798 2.323690719 -1.51509386 METVSNASSSSNPS(ph)SPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPS(0.5)S(0.5)PGR 79.805 0.037735 41587000 58172 52789 57651 70133 64287 61049 69182 57937 65355 TRUE FALSE 55422.32485 58168.25912 60294.35537 63083.0976 75498.63245 58934.85782 58627.01529 52863.72914 75489.91961 0.73416855 0.770543397 0.798707373 0.835649288 1.000115417 0.780698378 0.776620449 0.70027534 1 16.20399639 -2.425765332 2.335184573 2.996481055 0.797704796 0.383213224 0.079869141 8250390.169 870865.8024 87186445.76 0.021907768 0.003751757 2.425765332 -2.198776259 METVSNASSSSNPSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.045)S(0.955)PGR;METVSNASSSSNPS(0.182)S(0.818)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.005)S(0.995)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSS(0.001)NPS(0.228)S(0.771)PGR;METVSNASSSSNPS(0.053)S(0.947)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.055)S(0.944)PGR 421.75 4.46E-168 11862244000 9866713 8738101 9829655 10820432 10569901 10159549 11751994 10123480 11680825 TRUE FALSE 9400333.03 9628523.426 10280354.4 9732741.618 12413288.39 9807721.271 9959011.475 9237014.423 13492227.68 0.696722087 0.713634816 0.761946407 0.72135913 0.920032531 0.726916377 0.738129515 0.684617443 1 23.68562523 -2.341522248 2.399154224 2.692881692 0.743429444 0.597124559 0.065699272 8387044.438 487673.4733 78517416.12 0.016372328 0.004554889 2.341522248 -1.949452248 METWS(ph)VEQVCSWLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 METWSVEQVCSWLVEK 16 0 E9PPN0;E9PRU9;E9PS85;E9PR28;E9PR45;Q8N6K7-2;Q8N6K7 E9PPN0 SAMD3 Sterile alpha motif domain-containing protein 3 1 MET(0.109)WS(0.445)VEQVCS(0.445)WLVEK 65.47 0.095718 16425000 21151 19136 18292 22765 17635 25587 22609 22570 20643 TRUE FALSE 20151.23415 21085.98016 19130.70629 20476.61895 20710.53842 24700.91577 19159.58181 20593.65115 23844.21101 0.84512061 0.88432283 0.802320793 0.858766891 0.868577216 1.035929256 0.803531801 0.863675092 1 14.54135143 2.461490306 24.99970639 0.908794299 0.852223369 0.214720175 0.06766882 474.3222853 758613.6945 0.022344485 0.01869979 289.3945221 -2.461490306 -0.05657093 MEVDRS(ph)PGLPMSDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK 179.58 4.02E-07 2247444000 4168964 3119175 3456221 4183791 3004057 3530487 3953656 3654426 2804660 TRUE FALSE 3971905.334 3437022.479 3614692.152 3763228.38 3527963.59 3408225.35 3350453.163 3334425.086 3239592.349 1.226050968 1.060942893 1.115786112 1.161636396 1.089014669 1.052053772 1.034220606 1.029273047 1 21.62738085 8 0.14925268 0.969718143 1.782314517 0.701044319 0.037040569 40.1572496 0.393550763 0.13612984 7.063549576 100000000 -8 0.812596374 MEVGPFSTGQES(ph)PTAENAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 MEVGPFSTGQES(0.999)PTAENAR 156.67 3.34E-10 0 23786 22614 18277 23889 17913 17964 24459 18905 20024 TRUE FALSE 22661.68292 24918.39231 19115.01853 21487.63233 21037.02153 17341.90218 20727.33033 17249.57798 23129.21965 0.979785884 1.077355513 0.826444593 0.929025391 0.909543073 0.74978328 0.896153465 0.745791611 1 14.49742897 3.735514023 24.99883784 0.860532739 1.028570702 0.411302331 0.081080279 203.9486898 1673505.124 0.019213786 0.031236532 5438.936928 -3.735514023 0.168037963 MEWWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MEWWSR 6 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 128.82 0.0383 805090000 1586040 1170990 1332080 1265060 1508410 1263590 1919530 1426520 1520010 FALSE TRUE 1511071.032 1290315.212 1393157.186 1137893.765 1771476.226 1219831.561 1626670.444 1301606.346 1755725.388 0.860653405 0.734918582 0.793493786 0.648104637 1.008971129 0.694773551 0.926494801 0.741349619 1 20.74363578 -2.988807849 0.251931079 1.386063531 0.780918052 0.242376717 0.108702875 77.41778984 1.898981971 15.9627664 0.139559671 0.001026106 2.988807849 -0.60514548 MFADYLAHESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MFADYLAHESR 11 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;; 211.46 9.25E-09 693230000 1469030 1199350 1015640 1247230 2238400 917300 1626200 1286050 2049390 FALSE TRUE 1399591.863 1321565.129 1062208.099 1121856.071 2628776.251 885533.671 1378093.323 1173436.644 2367198.934 0.591243872 0.558282242 0.448719406 0.473917107 1.110500775 0.374085024 0.582162024 0.495706815 1 21.17474952 -1.434102546 5.099068929 1.000549137 0.578079337 0.304044027 0.200010322 0.00113789 0.000126283 0.176486956 0.04154605 0.036804206 1.434102546 -0.422469799 MFDYTDDPEGPVMPGSHSVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MFDYTDDPEGPVMPGSHSVER 21 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 139.2 3.81E-07 65300000 57019 47285 51800 54602 58698 56320 71602 60859 64666 FALSE TRUE 54323.82487 52103.39526 54175.08124 49113.30322 68934.91262 54369.62428 60677.79984 55529.86333 74694.07301 0.727284277 0.697557291 0.725292905 0.657526109 0.922896688 0.727897437 0.812350932 0.743430651 1 16.18870615 -4.999999999 0.148789797 1.906185894 0.668067922 0.579550504 0.068854435 88.20806974 0.782403635 23.54403735 0.320398013 1.00E-05 4.999999999 -1.238117972 MFEELGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MFEELGQR 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 155.82 0.00093732 161364000 461747 394133 327111 441614 478741 351239 474735 428361 473244 FALSE TRUE 439921.1344 434295.6008 342109.3629 397222.1217 562233.2788 339075.5054 402305.4566 390851.44 546632.2625 0.804784431 0.794493173 0.625849198 0.726671565 1.028540241 0.620299109 0.735970934 0.715017145 1 19.06021109 -1.044039037 4.852867482 1.000005547 0.758315632 0.311524545 0.113754517 6.39E-06 1.26E-06 0.103082197 0.024296149 0.090356825 1.044039037 -0.241689915 MFEFYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MFEFYER 7 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;;; 170.73 0.0022429 301790000 607069 518130 488506 485566 543103 392907 526016 496586 537784 FALSE TRUE 578374.0515 570928.0361 510904.4833 436755.9832 637819.9912 379300.5321 445762.5983 453102.2973 621180.7961 0.931088107 0.919101234 0.822473081 0.703106062 1.026786397 0.610612135 0.717605246 0.729420967 1 19.2446537 3.648487937 3.356263611 0.776327557 0.926857891 0.122739086 0.129786112 0.371540243 7.971803279 0.033177403 0.055107914 4451.310985 -3.648487937 0.150530334 MFEIDYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MFEIDYSR 8 0 P16278-3;P16278;E7EQ29;P16278-2;F8WF40;C9JF15;C9JWX1 P16278-3 GLB1 Beta-galactosidase 0 ;;; 127.56 0.002724 278954000 594474 458402 484168 542738 597382 496887 671793 568599 548418 FALSE TRUE 566374.3922 505113.685 506367.5817 488180.9451 701565.2317 479679.6786 569298.6395 518809.4572 633463.8625 0.894091085 0.797383584 0.799363013 0.770653188 1.107506321 0.757232901 0.898707366 0.819004032 1 19.27290279 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 336.14 1.99E-117 294390000 731140 754080 638930 858610 370680 843330 853420 957810 412590 FALSE TRUE 696580.4612 830921.6093 668225.5725 772300.8915 435326.4746 814125.2706 723215.1049 873939.0787 476572.35 1.461646823 1.743537176 1.40214927 1.620532311 0.913453067 1.708293128 1.517534756 1.833801476 1 18.86233573 3.714593604 24.65950124 1.456828998 1.60259205 0.050483966 0.29486297 2061.288484 2120845.439 0.072128647 0.111814219 5183.147926 -3.714593604 0.145763052 MFGIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MFGIDR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;;;;; 166.22 0.016361 7107217000 10078663 7773933 6661868 7524238 10023829 6147954 9878685 7156610 8528684 FALSE TRUE 9602264.574 8566105.611 6967321.237 6767887.301 11771981.6 5935048.811 8371510.169 6529939.289 9851268.756 0.974723643 0.869543388 0.707251158 0.687006666 1.194971114 0.602465424 0.84979005 0.662852618 1 23.23187811 MFGIDRDAIAQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MFGIDRDAIAQAVR 14 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 232.13 2.58E-13 1727472000 1936802 715291 1280007 1617269 2568290 1668295 3196630 1747678 3229280 FALSE TRUE 1845253.208 788179.9661 1338696.587 1454698.048 3016198.963 1610521.526 2708925.383 1594642.049 3730060.25 0.494697963 0.211304889 0.358894092 0.389993177 0.808619368 0.431768234 0.726241723 0.42751107 1 21.8307675 -0.512511694 0.15970198 1.449048847 0.187460778 0.531447633 0.162656453 13.54557775 0.577567658 3.772308248 0.938883973 0.307247463 0.512511694 -1.261588069 MFLQYYLNEQGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MFLQYYLNEQGDR 13 0 Q9NPE3;H0YM60 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 113.38 0.0019229 100680000 126170 92614 114330 131730 131830 133210 153760 184320 172910 FALSE TRUE 120206.1941 102051.4719 119572.1436 118488.2501 154821.1103 128596.9043 130301.088 168179.9637 199723.9997 0.601861541 0.510962488 0.598686907 0.59325995 0.775175294 0.643873067 0.652405761 0.842061865 1 17.60764818 0.578732177 0.300284671 1.080953829 0.528760634 0.808848324 0.063110822 1.259527768 0.259520295 0.223040466 0.085649755 3.790811394 -0.578732177 -0.552193195 MFLYADNEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MFLYADNEDR 10 0 A0A087WY55;Q9NP79;Q5TGM0;Q9NP79-2 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;;; 109.66 0.0046266 222125000 682190 722560 540880 730540 570008 571720 667430 645120 589910 FALSE TRUE 649944.2307 796189.6855 565679.883 657104.7313 669417.2147 551921.193 565601.2953 588629.8728 681390.23 0.953850235 1.168478282 0.830184905 0.964358898 0.982428549 0.809992819 0.83006957 0.86386603 1 19.37812174 3.728268333 24.93614072 0.887678956 1.061164262 0.392282063 0.084151009 553.7042322 1341514.313 0.021942458 0.03440208 5348.947471 -3.728268333 0.173485306 MFMSELSGNIIDICPVGALTSKPYAFTARPWETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MFMSELSGNIIDICPVGALTSKPYAFTARPWETR 34 2 P28331-4;P28331;P28331-2;B4DJ81;P28331-3;P28331-5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 225.78 9.94E-37 75620000 90762 81098 72806 67697 88037 72586 95725 78815 104020 FALSE TRUE 86471.86013 89361.9784 76144.22711 60891.96894 103390.6249 70072.32862 81120.39314 71913.54078 120150.8903 0.719693877 0.74374795 0.633738351 0.50679582 0.860506523 0.583202741 0.675154324 0.598526907 1 16.87448781 -1.079057493 5.640112662 1.000002096 0.672179492 0.538619692 0.097197752 2.36E-06 3.85E-07 0.086600264 0.020411748 0.083357083 1.079057493 -0.327822604 MFVGGLSWDTSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MFVGGLSWDTSKK 13 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 133.15 0.00017728 1132710000 1657130 1218240 1252320 1446280 1108420 1395370 1819640 1561580 1355500 FALSE TRUE 1578800.749 1342380.041 1309740.111 1300897.187 1301728.097 1347047.987 1542020.498 1424839.777 1565704.017 1.008364756 0.857365138 0.836518331 0.830870441 0.831401135 0.86034651 0.984873566 0.910031373 1 20.57838008 1.74714725 11.08715281 0.9597591 0.875469055 0.381439477 0.056171482 0.128996917 90.66547974 0.028370378 0.015492723 55.86595795 -1.74714725 -0.084290045 MFVLDEADEMLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 329.49 5.11E-62 971629000 1355595 1211397 1245640 1459054 1457420 1159221 1497416 1352724 1484116 FALSE TRUE 1291518.711 1334839.732 1302753.826 1312387.12 1711593.587 1119076.886 1268957.687 1234272.315 1714265.129 0.753394961 0.77866586 0.759948857 0.765568346 0.998441581 0.652802689 0.740234206 0.72000083 1 20.70915882 MFVSSSGLPPS(ph)PVPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 MFVSSSGLPPS(1)PVPSPR 115.38 0.00033296 31338000 66784 54710 63657 70531 65519 55345 70971 66390 78421 TRUE FALSE 63627.25267 60285.0112 66575.73642 63441.08988 76945.49286 53428.38877 60143.07048 60576.53964 90582.12816 0.702426118 0.665528757 0.73497651 0.700370936 0.849455565 0.589833666 0.663961774 0.668747146 1 16.46693881 -0.968472469 5.080041203 1.000001764 0.693244386 0.675366052 0.065995045 0.003675606 42503150.21 178.0970641 0.01469291 0.107529476 0.968472469 -0.306757378 MGAGLGHGMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;; 177.57 7.92E-06 4452123000 3315529 2878182 2921825 3301256 3722168 3026049 3768302 3245800 3550047 FALSE TRUE 3158810.515 3171472.018 3055793.566 2969407.475 4371312.921 2921256.164 3193378.32 2961580.545 4100570.158 0.770334464 0.773422206 0.745211873 0.724145024 1.066025639 0.712402435 0.778764464 0.722236282 1 21.96739309 -1.716699598 2.593707013 1.039435316 0.785818334 0.301398199 0.102113423 19148546.35 14891200 4893495.115 0.022577271 0.019199963 1.716699598 -0.253616982 MGANSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 133.68 0.0037317 110600000 316090 238895 226715 278270 273649 244145 314100 261998 285290 FALSE TRUE 301149.0521 263238.6721 237110.107 250297.7709 321373.299 235690.1974 266178.2762 239056.0662 329531.3161 0.913870814 0.798827484 0.719537402 0.759556857 0.975243575 0.715228526 0.807748044 0.725442635 1 18.33005605 4.520178391 2.773333454 0.801915745 0.913905993 0.08126396 0.100749838 0.629040479 8.676536707 0.022473525 0.127338053 33126.71651 -4.520178391 0.111990248 MGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHT(0.037)LGDS(0.482)DNES(0.482);MGAPESGLAEYLFDKHTLGDS(0.593)DNES(0.407);MGAPESGLAEYLFDKHTLGDS(0.824)DNES(0.176) 140.55 5.91E-07 447760000 658680 315293 522850 506370 553150 524300 794930 607900 653620 TRUE FALSE 627545.5018 347421.7152 546823.1897 455468.7256 649619.1849 506143.3595 673648.8286 554669.0533 754980.0514 0.831208057 0.460173371 0.724288263 0.603285775 0.860445496 0.670406269 0.89227368 0.73468041 1 19.526079 1.324786262 0.461528775 0.994537217 0.638382881 0.383638906 0.121120289 0.860464062 0.504005649 0.128192724 0.077139489 21.12449142 -1.324786262 -0.356154337 MGAPESGLAEYLFDKHTLGDSDNES(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHTLGDS(0.38)DNES(0.62) 210.11 1.19E-25 81519000 81374 48289 76813 69481 82584 73658 114110 83543 93733 TRUE FALSE 77527.61229 53209.704 80334.95203 62496.63787 96986.62345 71107.20499 96700.42373 76227.53203 108268.6349 0.716067145 0.491460006 0.741996536 0.577236777 0.895796123 0.656766431 0.893152701 0.704059233 1 16.72425583 1.473667394 0.294294574 1.025726515 0.567216716 0.441354419 0.114810439 1.225127306 0.396743893 0.212353381 0.186460079 29.76236195 -1.473667394 -0.458509799 MGESDDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ; 162.59 1.56E-05 1419190000 2051650 1991190 1797100 2118330 1755790 1966680 2164370 2027020 1697910 FALSE TRUE 1954672.57 2194094.525 1879498.813 1905391.444 2061999.22 1898573.378 1834155.605 1849523.383 1961213.211 0.996665003 1.118743496 0.958334771 0.971537125 1.051389624 0.968060672 0.935214792 0.943050645 1 20.90331495 3.048121386 0.781240826 0.957338216 1.051442875 0.197453446 0.049427654 0.785520384 1.070975343 0.028780281 0.039506213 1117.175458 -3.048121386 0.094104659 MGFTELPLTGSTFHDQIAMLSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGFTELPLTGSTFHDQIAMLSHR 23 0 A0A3B3IRQ9;P55265-3;P55265-2 A0A3B3IRQ9 ADAR Double-stranded RNA-specific adenosine deaminase 0 67.866 0.015241 31302000 76386 66182 73202 75563 86216 64483 94331 80548 49387 FALSE TRUE 72775.38516 72926.02104 76558.38411 67967.26368 101252.0431 62249.93754 79939.07344 73494.79011 57045.68373 1.275738678 1.278379297 1.342053931 1.191453222 1.774929083 1.091229581 1.401316773 1.28834971 1 15.79983011 -0.407215372 8.349720255 1.000000002 1.326820425 0.252605747 0.178526794 0 0 0.150714689 0.035523793 0.391547655 0.407215372 0.326820422 MGGAGGEGS(ph)DDDTS(ph)LT ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGGAGGEGSDDDTSLT 16 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 2 MGGAGGEGS(1)DDDTS(0.999)LT(0.001) 217.2 1.23E-12 0 114610 101850 117160 123700 99079 103950 137930 127000 106860 TRUE FALSE 109192.6124 112228.6308 122531.9019 111265.441 116358.3462 100350.1854 116886.2452 115879.2067 123431.303 0.884642791 0.909239618 0.992713346 0.901436169 0.94269722 0.813004343 0.946974085 0.938815389 1 16.91334879 0.95402217 1.944024135 0.998620121 0.910048645 0.267802587 0.046141921 0.49186648 3.935787859 0.041007773 0.011506049 8.995434998 -0.95402217 -0.088571476 MGGAGGEGS(ph)DDDTSLT ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 MGGAGGEGSDDDTSLT 16 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT 272.59 3.69E-35 9348390000 7507690 6443860 6859840 7675830 6550050 6922360 8209580 7364230 7350420 TRUE FALSE 7152816.373 7100496.66 7174370.449 6904240.985 7692376.646 6682636.937 6957057.792 6719378.981 8490285.593 0.842470644 0.836308341 0.845009319 0.81319302 0.906020953 0.787092126 0.819413872 0.791419665 1 23.01738165 -1.191825038 4.854891691 1.00002017 0.830834619 0.720951549 0.033212898 6.67E-06 1.11E-06 0.029571334 0.0069692 0.064294669 1.191825038 -0.169185551 MGGEEKPIGAGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGGEEKPIGAGEEK 14 1 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RJ97;D6RHV7;D6RCS6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 162.87 3.99E-06 125230000 179310 166610 154520 181510 102600 197920 209150 201120 116700 FALSE TRUE 170834.3717 183587.7484 161604.8948 163264.27 120493.4075 191065.9808 177240.3262 183508.8666 134797.24 1.267343246 1.361954803 1.198873915 1.211184072 0.893886311 1.41743244 1.314866137 1.361369614 1 17.04043143 3.728269059 24.20296042 1.219662376 1.314649026 0.072406964 0.159031451 1270.8613 2988721.729 0.041440413 0.065057739 5348.956412 -3.728269059 0.09498665 MGGTESS(ph)IS(ph)EPGS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGGTESSISEPGSPSR 16 0 Q8TDW4-8 Q8TDW4-8 3 MGGTES(0.504)S(0.601)IS(0.872)EPGS(0.614)PS(0.409)R 51.004 0.060738 356170000 0 5861.6 0 5201.3 7363.8 0 8318.3 5471.1 5359.6 TRUE FALSE 0 6458.903704 0 4678.455442 8648.044389 0 7049.190559 4992.02148 6190.739395 0 1.043317008 0 0.755718363 1.396932392 0 1.138666985 0.806369185 1 12.59589601 4.336801689 0.392785886 0.902062633 3.33E-27 0.189826142 0.461661725 8.258049248 1.279719035 0.375772526 3.421475554 21717.0929 -4.336801689 -0.902062633 MGIGGLDKEFSDIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGIGGLDKEFSDIFR 15 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 163.23 1.41E-06 220150000 939210 761590 804010 947350 738090 830860 1018720 966320 790540 FALSE TRUE 894815.4046 839196.8869 840874.6538 852120.5782 866812.6623 802087.1099 863295.5539 881703.898 913132.9057 0.97993994 0.919030386 0.92086776 0.933183519 0.949273273 0.878390325 0.945421579 0.965581125 1 19.80046533 1.0482489 2.558669185 0.998954903 0.93199055 0.439694833 0.025569047 0.243065906 3.381485502 0.023612155 0.006399655 11.1750352 -1.0482489 -0.066964353 MGLAMGGGGGAS(ph)FDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 160.8 1.77E-06 831873000 1135344 590540 759429 1517720 1299773 1525330 1485414 759742 1175544 TRUE FALSE 1081678.539 650716.6974 794249.5708 1365155.902 1526453 1472507.44 1258786.813 693214.9628 1357841.36 0.796616285 0.479228809 0.584935468 1.00538689 1.124176244 1.084447332 0.927049986 0.510527211 1 20.3728835 3.240552062 24.99979796 0.955601619 0.615232856 0.406264366 0.182783987 48.57195283 609745.6811 0.05111657 0.065888192 1740.011273 -3.240552062 -0.340368763 MGLGHEQGFGAPCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGLGHEQGFGAPCLK 15 0 Q9UGI8-2;Q9UGI8;F8WDI4 Q9UGI8-2 TES Testin 0 ; 158.81 1.80E-06 471960000 1252160 1175980 1011350 1358600 1020510 1173300 1347990 1320200 1072920 FALSE TRUE 1192972.878 1295813.699 1057721.398 1222030.947 1198486.621 1132668.327 1142329.368 1204596.289 1239302.954 0.962616021 1.045598814 0.853480898 0.986063128 0.967065089 0.913955965 0.921751509 0.971995012 1 20.24109747 3.771204464 24.99971855 0.941206722 1.004107408 0.216866708 0.0463625 790.7820907 605603.944 0.01084928 0.019557288 5904.790096 -3.771204464 0.062900686 MGLS(ph)MER ddPTM_SK-BR-3_Trastuzumab_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 128.57 0.0039279 1288010000 1424640 738740 957040 1880210 1607970 1653980 1795820 890920 1403900 TRUE FALSE 1357300.091 814018.4459 1000921.231 1691207.719 1888399.459 1596702.258 1521834.677 812906.3217 1621609.642 0.837007906 0.50198175 0.617239319 1.042919131 1.164521603 0.984640333 0.93847165 0.501295935 1 20.62899514 3.246085625 24.9965961 0.949236695 0.646331939 0.339685925 0.18790124 181.4436085 602716.2792 0.051645985 0.068594288 1762.323471 -3.246085625 -0.302904756 MGLSMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGLSMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 125.08 0.0095001 152050000 367690 322320 344330 366390 327140 413570 485090 441910 264090 FALSE TRUE 350310.0224 355164.7744 360117.8711 329559.7811 384193.1124 399247.9672 411080.6112 403214.0177 305043.7284 1.148392803 1.164307741 1.180545075 1.080368978 1.259468977 1.30882208 1.347612073 1.32182366 1 18.21865654 2.59416124 6.138451617 1.282842359 1.149912028 0.16437279 0.101345879 0.279034453 13.08181723 0.029361511 0.027569153 392.7907392 -2.59416124 -0.132930331 MGLVMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGLVMDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 121.29 0.010358 66759000 163060 133430 136360 153080 201090 130840 187250 139910 194220 FALSE TRUE 155352.477 147026.6687 142612.2409 137692.1076 236160.0323 126308.978 158681.5734 127658.7387 224338.6457 0.692490928 0.655378249 0.63570073 0.613769006 1.052694384 0.563028174 0.707330531 0.569044795 1 17.77531864 -2.295635091 2.409100103 2.613413477 0.687068327 0.336686171 0.138425101 15412730.09 2228792.657 135646399.8 0.032166636 0.005062499 2.295635091 -1.92634515 MGPLGLDHMASSIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;; 171.26 1.09E-06 1945830000 3046560 2536700 2645460 2796580 4455850 2375450 3415510 2699120 4309520 FALSE TRUE 2902555.147 2795192.614 2766756.958 2515462.465 5232948.829 2293187.571 2894411.219 2462770.744 4977818.352 0.583097844 0.561529653 0.55581718 0.505334323 1.051253473 0.460681248 0.5814618 0.494749019 1 22.24708215 -2.109079948 2.394539497 1.735531922 0.596934432 0.366044672 0.16572338 13345431.76 4056977.13 53377238.79 0.036906304 0.007778933 2.109079948 -1.13859749 MGPLINRPHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MGPLINRPHLER 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 122.33 0.00048485 898861000 334613 300864 292191 353383 362655 307280 364714 329156 359814 FALSE TRUE 318796.5066 331522.3837 305588.2464 317860.2695 425901.9172 296638.8166 309070.1809 300333.3557 415612.1174 0.767052964 0.797672565 0.735272706 0.764800294 1.02475818 0.713739576 0.743650553 0.722628968 1 18.66487819 -2.236335814 2.313595668 1.764118112 0.783067166 0.367684714 0.089141007 8108544.409 1256307.171 32507059.59 0.020775974 0.005803155 2.236335814 -0.981050946 MGPPVGGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 MGPPVGGHR 9 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;;;; 119.29 0.00085104 589222000 906589 777622 745316 887646 897951 753225 957630 876698 860320 FALSE TRUE 863736.3347 856862.5659 779489.4758 798418.1377 1054553.37 727140.6294 811525.9554 799929.6755 993734.0317 0.869182605 0.862265494 0.78440453 0.803452546 1.061202833 0.731725599 0.816643015 0.804973615 1 19.92250025 3.974639274 23.78507722 0.844918855 0.866588757 0 0.100788528 3032.923119 2844497.351 0.024108593 0.043544057 9432.770626 -3.974639274 0.021669902 MGPSGGEGMEPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGPSGGEGMEPERR 14 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 73.415 0.0086291 360350000 222216 170200 223035 200489 401118 220696 302920 248977 630080 FALSE TRUE 211712.2901 187543.5735 233261.3754 180335.4648 471072.8522 213053.2422 256703.9905 227175.254 727789.5884 0.290897663 0.257689278 0.320506612 0.247785167 0.647265171 0.292740162 0.352717316 0.312144138 1 19.47316189 -5 0.314982107 7.088886767 0.304104191 0.767732551 0.113889214 139.9107122 1.253312716 566.6321131 0.098187803 1.00E-05 5 -6.784782576 MGPSGGEGMEPERRDS(ph)QDGSSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.999)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.99)QDGS(0.01)SYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.91)QDGS(0.045)S(0.045)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.998)QDGS(0.001)S(0.001)YR 392.53 1.93E-137 17425347000 3122331 2540725 3145666 3400205 3218409 3139739 4019548 3439016 3835839 TRUE FALSE 2974744.601 2799627.766 3289897.898 3058409.933 3779698.511 3031009.051 3406292.129 3137877.528 4430681.321 0.671396651 0.63187297 0.74252641 0.690279826 0.853073881 0.684095477 0.768796463 0.708215577 1 22.07909713 -5 0.153707972 2.032540907 0.628352648 0.703745629 0.058318576 68.18830402 0.614942286 21.50566928 0.255811434 1.00E-05 5 -1.404188259 MGPSGGEGMEPERRDSQDGS(ph)SYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.36)QDGS(0.488)S(0.15)Y(0.002)R;MGPSGGEGMEPERRDS(0.002)QDGS(0.895)S(0.103)YR;MGPSGGEGMEPERRDS(0.239)QDGS(0.38)S(0.38)YR 120.6 5.10E-05 2256660000 535874 446830 565977 564986 575491 586227 762214 621233 739494 TRUE FALSE 510544.298 492362.485 591927.6053 508192.5339 675856.4482 565925.812 645924.2553 566834.5452 854170.9527 0.597707399 0.57642148 0.692984939 0.594954127 0.791242603 0.662543968 0.756200212 0.663607845 1 19.70416531 -5 0.120130535 2.121301056 0.493704848 0.771007597 0.059872555 61.87970651 0.481768186 16.79825508 0.504679812 1.00E-05 5 -1.627596208 MGQAPSQSLLPPAQDQPRS(ph)PVPSAFSDQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 MGQAPSQSLLPPAQDQPRSPVPSAFSDQSR 30 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MGQAPSQSLLPPAQDQPRS(0.987)PVPS(0.011)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.997)PVPS(0.001)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.994)PVPS(0.006)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.998)PVPS(0.002)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.995)PVPS(0.005)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.997)PVPS(0.003)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.99)PVPS(0.009)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.995)PVPS(0.004)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.997)PVPS(0.003)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.953)PVPS(0.046)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.99)PVPS(0.009)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.994)PVPS(0.006)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.888)PVPS(0.105)AFS(0.007)DQSR 244.51 5.30E-46 13062221000 4178642 3207233 4275326 4186844 4276223 4013611 4933779 4228835 5021723 TRUE FALSE 3981125.874 3534053.689 4471353.926 3765974.487 5021994.937 3874618.645 4181040.398 3858535.789 5800466.155 0.68634585 0.609270633 0.770861135 0.649253764 0.865791611 0.66798401 0.720811101 0.665211327 1 22.46773742 -5 0.29747601 3.441562195 0.683397569 0.61407769 0.072819083 167.2623881 1.55387962 254.5170065 0.068685674 1.00E-05 5 -2.758164626 MGS(ph)PAPLLPGDLLGGGSDSI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI 103.39 0.0011183 22106000 68127 66695 64886 68226 46541 69135 66694 65944 50029 TRUE FALSE 64906.77172 73491.29633 67861.08728 61367.79286 54657.73566 66740.83761 56518.60538 60169.59377 57787.24181 1.123202453 1.27175643 1.174326463 1.061960927 0.945844341 1.154940702 0.978046427 1.041226262 1 15.81846339 3.224200361 3.729989829 1.027958099 1.200776728 0.579871456 0.064695775 0.137820049 4.124969025 0.017435766 0.022467734 1675.715785 -3.224200361 0.172818628 MGSCDGEGLLT(ph)SPDQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGSCDGEGLLTSPDQPR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MGSCDGEGLLT(0.974)S(0.026)PDQPR;MGSCDGEGLLT(0.717)S(0.283)PDQPR 277.34 9.74E-35 334760000 529590 498230 484640 574340 532740 496640 606580 512450 561250 TRUE FALSE 504557.3302 549000.2034 506861.2234 516606.252 625649.6873 479441.2323 514035.0804 467577.1613 648285.7835 0.778294609 0.846849055 0.781848432 0.796880427 0.965083152 0.739552285 0.792914319 0.721251604 1 19.30627041 4.723682808 4.373795933 0.819500347 0.775939499 0.019410026 0.09018791 1.002501645 41.6377955 0.019331865 0.128985702 52927.67393 -4.723682808 -0.043560848 MGSCDGEGLLTS(ph)PDQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGSCDGEGLLTSPDQPR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MGSCDGEGLLT(0.172)S(0.828)PDQPR;MGSCDGEGLLT(0.027)S(0.973)PDQPR 257.72 4.06E-27 293640000 644540 607590 601360 667730 677460 618690 712450 671130 684330 TRUE FALSE 614073.8716 669504.1118 628932.9508 600608.5118 795608.8095 597264.6102 603752.6675 612362.2993 790452.4013 0.776863819 0.846988523 0.795662016 0.759828815 1.006523363 0.755598451 0.763806482 0.774698512 1 19.59231906 -2.449240058 2.186046117 2.828779196 0.809431421 0.390170052 0.074649133 4416826.148 334116.9985 40112097.33 0.017779264 0.003554348 2.449240058 -2.019347774 MGSGIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGSGIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 89.123 0.067852 0 164420 144550 163340 182850 179690 148460 187100 176180 191980 FALSE TRUE 156648.1924 159279.8093 170829.3006 164469.5706 211027.8791 143318.793 158554.4587 160752.7452 221751.2779 0.706413933 0.718281359 0.770364447 0.741684883 0.951642223 0.646304248 0.715010349 0.724923647 1 17.75858289 -1.442866151 3.188022904 1.004304189 0.742006139 0.500121139 0.079415008 82741647.53 107246441.5 3217611.825 0.01825948 0.036068979 1.442866151 -0.26229805 MGSKS(ph)PGNTSQPPAFFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGSKSPGNTSQPPAFFSK 18 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 MGS(0.113)KS(0.878)PGNT(0.009)SQPPAFFSK;MGS(0.091)KS(0.909)PGNTSQPPAFFSK 208.65 3.69E-16 1225540000 1914580 1080280 1891340 1704520 1482760 1902540 2661100 2266500 1962560 TRUE FALSE 1824081.598 1190361.76 1978059.81 1533178.411 1741352.875 1836654.563 2255100.321 2068033.245 2266903.781 0.804657707 0.525104669 0.872582165 0.67633149 0.768163558 0.810204023 0.994793135 0.912272176 1 21.11229173 2.021524186 1.588223475 0.977387094 0.704393699 0.569493171 0.094026476 0.253349971 1.195983836 0.057132045 0.028263501 105.0809973 -2.021524186 -0.272993396 MGVMSS(ph)PTENSFTLDADF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.001)S(0.798)PT(0.201)ENSFTLDADF 192.15 1.26E-14 20627000 35345 27796 30163 32592 37103 34105 37610 33837 37539 TRUE FALSE 33674.3119 30628.444 31546.00339 29315.79024 43573.75145 32923.9353 31871.90374 30874.0529 43360.3564 0.776615201 0.706369748 0.727530999 0.676096616 1.004921432 0.75930961 0.735047089 0.712034113 1 15.40408899 MGVMSSPT(ph)ENSFTLDADF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.065)S(0.256)PT(0.679)ENSFTLDADF 196.38 7.49E-16 22357000 35908 38700 37497 40165 39747 35667 43350 37677 43259 TRUE FALSE 34210.7 42643.574 39216.27454 36127.53789 46678.86422 34431.84285 36736.16132 34377.80214 49967.38478 0.684660607 0.853428175 0.784837444 0.723022388 0.934186658 0.689086351 0.735202802 0.688004831 1 15.60869909 -2.471407551 2.348537571 4.014707282 0.76446046 0.466997263 0.080003696 2545004.177 461871.517 41236336.4 0.018148714 0.003377477 2.471407551 -3.250246821 MGYAEEAPYDAIHVGAAAPVVPQALIDQLKPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MGYAEEAPYDAIHVGAAAPVVPQALIDQLKPGGR 34 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 199.59 2.37E-27 297950000 524640 411530 462490 588850 443320 504210 576790 537500 483090 FALSE TRUE 499841.3069 453465.3749 483695.624 529657.6793 520634.8676 486749.0813 488790.092 490433.6505 558005.1299 0.895764716 0.812654491 0.866830067 0.949198584 0.933028819 0.872302162 0.875959854 0.878905272 1 19.08991886 -5 0.239489134 1.666260798 0.869254148 0.466392836 0.037739884 162.1124873 1.616628542 52.7000047 0.063374619 1.00E-05 5 -0.797006649 MHAPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MHAPGK 6 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;;; 87.758 0.052076 1491014000 5370410 5300430 4945980 5914120 4701470 5518410 6407130 5689980 3502150 FALSE TRUE 5116561.362 5840549.843 5172758.075 5319621.422 5521404.879 5327306.078 5429604.643 5191735.187 4045245.535 1.264833325 1.443806017 1.278725365 1.31503054 1.364912174 1.316930216 1.342218809 1.283416579 1 21.94779584 0.653846345 2.054619408 1.000004729 1.337685147 0.815329403 0.049258268 0.700208115 3.659818065 0.043950836 0.012068735 4.506572324 -0.653846345 0.337680418 MHDLNTDQENLVGTHDAPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MHDLNTDQENLVGTHDAPIR 20 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ;; 301.27 4.96E-55 675830000 162833 153474 146820 184361 205331 182471 183549 159957 84008 FALSE TRUE 155136.2068 169113.1751 153551.8422 165828.682 241140.6614 176151.9835 155545.2289 145950.3171 97035.53159 1.598756705 1.7427964 1.582429031 1.708948045 2.485075904 1.815334864 1.602971885 1.504091488 1 16.5662255 0.946212087 1.505066018 1.008613024 1.797189688 0.504402391 0.255549077 0.409676648 1.882086019 0.24604029 0.072399444 8.835112554 -0.946212087 0.788576665 MHEDINEEWISDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MHEDINEEWISDK 13 0 P28331-4;P28331;P28331-2;B4DJ81;P28331-3;P28331-5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 106.32 0.0010491 64819000 207520 216950 188770 227080 150830 211570 199020 206150 93573 FALSE TRUE 197710.9409 239057.4517 197425.2912 204253.487 177134.7042 204243.2778 168655.8437 188098.4131 108083.8229 1.829237119 2.211778277 1.826594266 1.889769268 1.638864165 1.889674813 1.560417083 1.740301259 1 16.72179108 -1.458429798 0.18117695 0.096906277 2.144323455 0.781892238 0.145398462 11.03932099 0.360377725 5.011844452 0.507411165 0.034799275 1.458429798 2.047417178 MHEGDEGPGHHHKPGLGEGT(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 MHEGDEGPGHHHKPGLGEGTP 21 1 P06702 P06702 S100A9 Protein S100-A9 1 MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P 197.33 5.08E-22 8830590000 3869642 5860782 5691580 8646730 5220355 7654305 9855020 4271061 431983.4 TRUE FALSE 3686731.692 6458002.349 5952544.573 7777544.273 6130783.259 7389234.499 8351455.699 3897064.257 498973.1794 7.388636992 12.94258412 11.92958824 15.58709885 12.2867992 14.80888113 16.73728377 7.810167795 1 18.92860274 0.980416425 5.974831532 1.003683136 12.9720791 0.710620876 2.521433854 0.091016993 15.40160865 2.653859024 0.667488182 9.559087237 -0.980416425 11.96839597 MHIAQDINQDNLQLFLNSYNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MHIAQDINQDNLQLFLNSYNGR 22 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 295.69 1.58E-55 741580000 368490 346730 377470 420940 372570 387540 430730 412310 262070 FALSE TRUE 351072.208 382062.1812 394777.3729 378626.3115 437546.09 374119.3926 365014.2276 376205.9506 302710.4771 1.159762329 1.26213729 1.304141755 1.25078694 1.445427638 1.235898394 1.205819604 1.242791311 1 18.20757908 0.386148368 0.976699741 0.999397454 1.266709537 0.562318078 0.073748165 1.897579657 2.309713169 0.074965777 0.023065766 2.433035065 -0.386148368 0.267312082 MHLAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MHLAGK 6 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ; 100.78 0.037275 801020000 4712100 4621100 4409500 5432000 4384500 4884800 5881900 4868400 2313400 FALSE TRUE 4489368.371 5091995.344 4611679.937 4885965.04 5149155.412 4715638.151 4984508.126 4442097.087 2672150.257 1.680058358 1.905579722 1.72583107 1.828476908 1.92697076 1.7647354 1.865354732 1.662368003 1 21.3495697 0.813960223 3.384368122 1.000065256 1.814657028 0.91697586 0.076470479 0.264724524 4.457571721 0.06733262 0.017422982 6.515687149 -0.813960223 0.814591772 MIDLS(ph)AFSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MIDLSAFSRK 10 1 Q8N1W2 Q8N1W2 ZNF710 Zinc finger protein 710 1 MIDLS(0.5)AFS(0.5)RK;MIDLS(0.5)AFS(0.5)RK 66.071 0.071047 77209000 149502 194900 154226 180272 370870 107312 134610 114028 282530 TRUE FALSE 142435.3367 214760.5316 161297.4147 162150.7161 435549.6106 103595.7585 114072.7722 104043.1038 326343.3094 0.436458578 0.658081613 0.494256845 0.496871581 1.33463625 0.317444101 0.349548371 0.318814882 1 18.31603094 MIEAVQNHIGSLNWGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MIEAVQNHIGSLNWGYR 17 0 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 ;; 231.77 3.60E-16 564707000 746782 692860 678250 736708 876177 683322 857371 808462 751593 FALSE TRUE 711483.0948 763463.2217 709348.4334 662652.7122 1028981.991 659658.3878 726563.3073 737668.7814 868146.2038 0.819542943 0.879417797 0.81708407 0.763296216 1.185263481 0.759847114 0.836913534 0.849705704 1 19.7275785 -2.611488043 1.960664211 3.192599719 0.861340273 0.112430193 0.120001946 4713898.195 169087.3711 46198185.88 0.026671761 0.002446313 2.611488043 -2.331259446 MIFDVESMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MIFDVESMKK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 128.01 0.00054646 536880000 1716540 1358520 1429370 1623680 1286020 1648790 2001040 1925790 1451760 FALSE TRUE 1635402.556 1496954.733 1494908.028 1460464.602 1510301.481 1591691.989 1695744.596 1757157.618 1676891.526 0.975258405 0.892696223 0.891475689 0.870935644 0.900655443 0.949191981 1.011242868 1.047866001 1 20.67735794 1.841428713 2.455939349 1.025479 0.908708325 0.755471305 0.029416672 0.146142605 1.635489353 0.018342671 0.008855603 69.41106585 -1.841428713 -0.116770675 MIIEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MIIEEAKR 8 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 134.48 0.0014028 1069630000 979260 897450 742480 833520 886130 881390 1150550 931770 1131440 FALSE TRUE 932972.3205 988901.1753 776523.4424 749732.986 1040670.791 850867.2433 975012.4662 850179.2792 1306897.937 0.713883077 0.756678198 0.594172981 0.573673709 0.796290791 0.651058678 0.746050965 0.650532268 1 20.31771505 -1.620862734 2.582459571 1.032201212 0.69307432 0.657772049 0.071142852 16712529.07 14782605.13 3616041.507 0.018497475 0.023940723 1.620862734 -0.339126892 MIKPFFHSLSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MIKPFFHSLSEK 12 1 P10599 P10599 TXN Thioredoxin 0 ;;; 136.27 6.79E-05 6447000000 16888100 12843600 11744100 14833500 13543900 13657300 20105400 15712400 15632800 FALSE TRUE 16089832.98 14152377.44 12282578.6 13342408.4 15905951.87 13184344.28 17037951.97 14336538.96 18057054.78 0.891055223 0.783758903 0.680209411 0.738902803 0.880871884 0.73014921 0.943562069 0.793957771 1 24.10605926 0.780384799 0.648059961 0.99782343 0.789724046 0.383375948 0.079466953 1.134438287 1.001093808 0.081582958 0.031329125 6.030937097 -0.780384799 -0.208099384 MIMFLDELGNVPELPDTTEHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MIMFLDELGNVPELPDTTEHSR 22 0 E9PGC0;P20936-2;P20936-4;P20936 E9PGC0 RASA1 Ras GTPase-activating protein 1 0 61.276 0.01877 0 15679 14565 11330 11674 10445 12894 12862 16687 9102.3 FALSE TRUE 14937.88474 16049.19006 11849.49171 10500.50734 12266.60469 12447.47755 10899.66567 15225.79782 10513.8382 1.420783206 1.526482504 1.12703767 0.998732066 1.166710431 1.183913744 1.03669711 1.448167409 1 13.36000182 3.733518451 24.56361233 1.13141657 1.473632864 0.533250603 0.130718242 199.7882215 973297.5994 0.031387084 0.050327804 5414.002493 -3.733518451 0.342216294 MIMQDKLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MIMQDKLEK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;P34932;A0A087WYC1;O95757;E9PDE8 Q92598-2;P34932;O95757 HSPH1;HSPA4;HSPA4L Heat shock protein 105 kDa;Heat shock 70 kDa protein 4;Heat shock 70 kDa protein 4L 0 88.681 0.011509 666470000 772700 553430 598060 733370 732350 817440 1315300 1097100 887870 FALSE TRUE 736176.0023 609825.1462 625481.6426 659650.2543 860071.6081 789131.8478 1114626.828 1001032.108 1025556.345 0.717830869 0.594628612 0.609894957 0.643212104 0.838639059 0.769467082 1.086850892 0.976086894 1 19.96797533 2.169427997 1.292325017 1.031978017 0.640562823 0.834244331 0.069889888 0.15343846 0.489326111 0.042693515 0.023019833 147.7161559 -2.169427997 -0.391415194 MINLSVPDTIDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MINLSVPDTIDER 13 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;U3KQI3;P13796;Q5TBN3 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 208.72 1.02E-07 42303000 79967 47581 50057 67148 79013 57101 88701 61940 91096 FALSE TRUE 76187.11839 52429.558 52352.16296 60398.15547 92792.84218 55123.57805 75168.03334 56516.20524 105222.7024 0.724055899 0.4982723 0.497536765 0.574003082 0.881870928 0.523875331 0.714370869 0.537110376 1 16.68308648 -5 0.324228103 4.696221817 0.604011945 0.477017668 0.124197669 288.7468023 2.531359444 733.8096273 0.100775689 1.00E-05 5 -4.092209872 MINTDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MINTDLSR 8 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;; 137.42 0.0017419 515407000 1231830 987110 836340 912980 1250950 1009430 1461510 1266270 1321880 FALSE TRUE 1173603.837 1087697.631 874687.0163 821205.5159 1469115.284 974473.186 1238529.807 1155388.686 1526870.399 0.768633564 0.712370632 0.572862646 0.537835769 0.962174186 0.638216044 0.811155818 0.756703835 1 20.54214618 0.395369918 0.505354324 1.016734531 0.691029087 0.387520491 0.117229751 2.385366789 1.020109927 0.203111825 0.056827117 2.485249059 -0.395369918 -0.325705444 MIPCDFLIPVQTQHPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MIPCDFLIPVQTQHPIR 17 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 171.09 1.77E-09 1416160000 1411250 1565600 1222680 1564320 1401400 1344810 1450770 1421780 1303500 FALSE TRUE 1344543.009 1725136.42 1278741.087 1407071.582 1645803.716 1298238.892 1229428.391 1297281.406 1505640.123 0.893004237 1.14578271 0.849300618 0.934533798 1.093092361 0.862250463 0.816548638 0.86161453 1 20.52194555 2.197190062 24.37743913 0.863838138 0.988833289 0.180734748 0.098819649 147.4282696 86870.41593 0.035160602 0.025968151 157.4671844 -2.197190062 0.124995151 MIPCDFLIPVQTQHPIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MIPCDFLIPVQTQHPIRK 18 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 162.59 2.29E-11 3290030000 5907090 4506120 5428880 5592460 5689230 5693200 7141730 6097320 6345970 FALSE TRUE 5627873.562 4965298.751 5677799.518 5030295.296 6681429.911 5496043.056 6052127.922 5563406.337 7330070.617 0.767778901 0.677387574 0.774590016 0.686254684 0.911509624 0.749794012 0.825657519 0.758984003 1 22.80539567 -4.999999999 0.14812483 1.848782876 0.688115244 0.57607414 0.063902872 86.68428064 0.767075832 21.56864809 0.298913869 1.00E-05 4.999999999 -1.160667632 MISDAIPELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MISDAIPELK 10 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 94.309 0.019057 12832000 88735 66390 74244 76853 73617 67320 85674 79109 80076 FALSE TRUE 84540.67241 73155.21648 77648.16084 69127.59043 86455.78149 64988.69152 72602.85779 72181.79658 92493.77711 0.914014705 0.790920414 0.839496053 0.747375581 0.93471998 0.702627718 0.784948567 0.780396248 1 16.49706869 4.608527333 2.668327429 0.809343102 0.92111664 0.078084515 0.088242356 0.690268704 7.829963344 0.019153078 0.15007757 40600.12151 -4.608527333 0.111773538 MISTPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIS(0.018)T(0.008)PS(0.974)PK;MIS(0.074)T(0.041)PS(0.885)PK;MIST(0.001)PS(0.999)PK;MIS(0.002)T(0.005)PS(0.993)PK 99.788 0.0068864 552090000 1849560 1864960 1657280 1984870 1161450 1995200 1989050 2129590 1276020 TRUE FALSE 1762134.964 2055001.544 1733267.927 1785347.097 1364006.512 1926105.724 1685583.891 1943111.81 1473898.665 1.195560459 1.394262437 1.175974963 1.211309257 0.925441175 1.306810142 1.143622646 1.318348308 1 20.49120591 -5 0.096167202 0.401574161 1.356900207 0.170832374 0.128990393 314.4069514 2.074443369 39.40546807 2.3220634 1.00E-05 5 0.955326046 MIYASSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 164.89 0.0027471 1154090000 3027900 2155400 1242290 1467750 2678400 1674490 3226400 2219300 2687800 FALSE TRUE 2884777.168 2375037.71 1299250.225 1320208.981 3145512.112 1616501.991 2734153.423 2024966.327 3104610.297 0.929191393 0.76500349 0.4184906 0.425241449 1.013174541 0.520677907 0.880675242 0.65224493 1 21.56598076 -0.402503776 0.656364849 1.02548686 0.709757097 0.169640507 0.205189276 20.0851918 7.048428882 1.475023812 0.075363105 0.395818624 0.402503776 -0.315729763 MKAENSHNAGQVDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKAENSHNAGQVDTR 15 1 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 71.692 0.05778 5299400 11216 8302.3 13212 11519 13513 12170 17370 13664 15292 FALSE TRUE 10685.84191 9148.313809 13817.78327 10361.08824 15869.66292 11748.54985 14719.88748 12467.50772 17663.40526 0.604970658 0.517924697 0.782283091 0.586584981 0.898448668 0.665135045 0.833355022 0.705838288 1 14.10847588 3.31448888 0.083672648 1.334478236 2.66E-16 0.539641879 0.101293738 30.05970917 0.719435275 3.916167887 7.565850498 2062.950845 -3.31448888 -1.334478236 MKDTDSEEEIREAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;;;;;;;; 251.28 1.25E-19 4579744000 7701060 6069420 3814580 8868680 5265650 5785740 6665300 6165550 4617430 FALSE TRUE 7337046.156 6687900.798 3989482.266 7977183.437 6183977.693 5585378.373 5648386.068 5625661.756 5333477.462 1.375658978 1.253947513 0.748007711 1.495681475 1.159464484 1.047230145 1.059043768 1.054783075 1 22.34664506 8 0.340104142 1.052927296 4.783483022 0.193128045 0.187131791 88.29900456 1.253117353 0.151705215 209.1660258 100000000 -8 3.730555725 MKEDCFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKEDCFR 7 1 P53634 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 106.36 0.0070411 525330000 614980 486860 473830 628220 619730 535120 733150 626430 676500 FALSE TRUE 585911.1142 536471.5875 495555.5742 565070.1321 727810.7158 516588.6602 621294.5023 571576.4683 781408.1649 0.749814425 0.68654464 0.634182744 0.723143368 0.931409151 0.661099645 0.795095995 0.731469793 1 19.5757168 -5 0.20792505 2.254104363 0.697991447 0.514244281 0.080782012 114.7214667 1.141710354 59.86665154 0.165358543 1.00E-05 5 -1.556112916 MKEGENNKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKEGENNKPR 10 2 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 90.827 0.0059425 37014000 71844 51662 67189 66320 42791 70542 77231 68661 67784 FALSE TRUE 68448.0765 56926.41653 70269.68211 59653.3876 50253.73685 68099.11285 65447.99251 62648.67885 78295.59653 0.874226387 0.727070475 0.897492135 0.76189965 0.641846273 0.869769385 0.835908983 0.80015584 1 16.25664355 0.056438152 0.724095453 1.006215579 0.794120258 0.398532009 0.076744558 4.37915565 2.533855986 0.148576303 0.025866661 1.138775598 -0.056438152 -0.212095321 MKEIAEAYLGK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 139.89 3.54E-05 7195370000 12685060 10150580 11005690 12118570 8985790 12292000 15349700 13183090 11303300 FALSE TRUE 12085462.35 11184935.64 11510311.77 10900388.32 10552908.93 11866324.96 13007821.35 12028708.75 13056158.03 0.925652272 0.856678941 0.881600218 0.834884833 0.808270619 0.908868055 0.996297786 0.921305389 1 23.63822709 1.968586327 5.920803335 0.968295165 0.865587841 0.653633008 0.036810297 0.123674936 13.17554099 0.01569895 0.009960983 93.02214019 -1.968586327 -0.102707324 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_SK-BR-3_Trastuzumab_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 ; 212.68 3.39E-26 629780000 997780 701670 910230 960650 874350 882050 1121490 991540 1071000 FALSE TRUE 950616.9168 773170.9707 951964.9458 864083.6369 1026836.363 851504.3873 950386.1029 904715.5011 1237085.21 0.768432853 0.624994111 0.769522534 0.698483524 0.830044976 0.688315065 0.768246274 0.731328363 1 20.23851345 -4.999999969 0.262712964 2.778268517 0.708709614 0.687499493 0.056067821 104.0630148 1.01906209 99.95535325 0.065735098 1.00E-05 4.999999969 -2.069558903 MKELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKELER 6 1 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 75.311 0.07116 98917000 284700 242860 246930 273120 235740 253660 345600 303150 278550 FALSE TRUE 271242.7952 267607.7101 258251.9847 245665.4587 276852.9814 244875.6906 292872.3726 276604.5789 321746.1114 0.843033639 0.831735647 0.802657672 0.763538237 0.860470326 0.761083606 0.910259246 0.859698281 1 18.29556319 0.86881712 0.907424882 0.997797691 0.81614906 0.666297737 0.040531174 0.421718135 0.711118531 0.035519576 0.012089764 7.392938956 -0.86881712 -0.181648631 MKETAEAYLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKETAEAYLGK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 137.84 6.39E-05 1488640000 2606600 2240030 2138790 2757600 1702710 2349270 2658300 2457200 1856030 FALSE TRUE 2483391.184 2468291.604 2236855.637 2480400.809 1999662.085 2267914.191 2252727.512 2242034.542 2143853.653 1.158377196 1.151334001 1.043380752 1.156982337 0.932741879 1.057868007 1.050784184 1.045796451 1 21.031775 3.506519123 1.039272347 1.030832484 1.164928298 0.451336614 0.053768423 0.451225434 0.991181845 0.018703041 0.041805099 3210.10415 -3.506519123 0.134095813 MKETAEAYLGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKETAEAYLGKK 12 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 110.98 0.00080471 667460000 1094720 739930 1045820 1082630 769700 1064150 1417700 1227800 912130 FALSE TRUE 1042974.755 815329.7082 1093771.881 973801.9755 903935.4363 1027298.219 1201403.827 1120287.323 1053578.462 0.989935532 0.773867099 1.038149432 0.924280451 0.85796689 0.975056207 1.140307885 1.063316462 1 20.00686633 1.96157302 5.662493205 1.078938733 0.910049895 0.435666814 0.07785596 0.15839241 13.54766657 0.032036778 0.020037812 91.53201428 -1.96157302 -0.168888838 MKETAENYLGHTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MKETAENYLGHTAK 14 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 112.72 0.00077604 550050000 1082670 757300 966160 852730 744650 845450 1067230 1034390 894700 FALSE TRUE 1031494.335 834469.731 1010459.392 767011.9603 874516.7242 816171.8545 904404.4625 943813.328 1033445.507 0.998111974 0.807463699 0.977757787 0.742189071 0.846214647 0.789757998 0.875135125 0.913268597 1 19.97903089 0.936081982 2.551748553 0.999465755 0.862142682 0.243273345 0.078063346 0.480048941 7.083721082 0.069787939 0.018733721 8.63141469 -0.936081982 -0.137323073 MKETAVFINISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKETAVFINISR 12 1 U3KQ56;Q9UBQ7;Q9UBQ7-2 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 92.265 0.007143 177420000 223510 171220 184220 201850 219870 185900 252730 238850 226550 FALSE TRUE 212945.1253 188667.5127 192666.6692 181559.6545 258215.2584 179462.2364 214171.3968 217935.0278 261682.2169 0.813754667 0.720979495 0.736261988 0.69381732 0.986751264 0.685802186 0.818440776 0.832823225 1 17.99745636 -0.606324294 0.347399787 1.079850017 0.756062387 0.404315324 0.085416504 9.13588183 1.061237415 0.88464841 0.066633656 0.247557282 0.606324294 -0.32378763 MKETIMNQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKETIMNQEK 10 1 P20290-2;D6RDG3 P20290-2 BTF3 Transcription factor BTF3 0 ; 132.5 0.00020241 613700000 878470 715180 715390 888350 707690 851810 1111900 1041420 793410 FALSE TRUE 836946.4641 788057.6551 748191.3391 799051.3702 831110.9119 822311.6061 942259.2336 950227.7439 916447.9706 0.913250387 0.859904414 0.816403509 0.87190042 0.906882811 0.897281278 1.028164461 1.036859456 1 19.80569345 1.802921827 3.122155423 1.027058263 0.873900089 0.853537711 0.028198499 0.088668881 1.603510298 0.016178382 0.008096758 63.52165826 -1.802921827 -0.153158174 MKETQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKETQK 6 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 79.469 0.061166 1986000000 1285300 1344800 1033100 1349000 1163000 1262400 1524600 1472400 1410900 FALSE TRUE 1224546.416 1481836.649 1080468.657 1213395.957 1365826.832 1218682.771 1291994.269 1343468.85 1629695.166 0.751395992 0.909272286 0.662988195 0.74455394 0.838087306 0.747797991 0.792782783 0.824368188 1 20.6361707 0.713771026 2.15280188 0.999944453 0.785056087 0.535570141 0.064414756 1.079346947 6.917483397 0.059826693 0.016331527 5.173340046 -0.713771026 -0.214888366 MKEYGEQIDPSTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKEYGEQIDPSTHR 14 1 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 106.14 0.0012898 165880000 161110 117620 129490 138960 136430 129280 172000 161940 140410 FALSE TRUE 153494.6496 129605.6117 135427.2446 124991.4768 160223.3488 124803.0012 145758.241 147759.6751 162184.0657 0.946422504 0.799126666 0.835021887 0.770676677 0.987910546 0.769514568 0.898721094 0.911061604 1 17.30727256 0.967647857 1.602083493 0.998787578 0.853843235 0.300573516 0.070796018 0.497599143 2.617745943 0.060498637 0.017602485 9.282134494 -0.967647857 -0.144944343 MKFNPFVTSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKFNPFVTSDR 11 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3KSS0;E5RHH1;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 189.24 2.55E-06 2684600000 4238000 2940200 3849900 3508800 4266100 3870800 5547500 4216200 5173200 FALSE TRUE 4037678.139 3239809.723 4026421.723 3156088.758 5010106.489 3736753.225 4701126.988 3847007.177 5975433.435 0.675713014 0.542188238 0.673829232 0.528177377 0.838450724 0.625352665 0.786742425 0.643803871 1 22.51061193 -5 0.15242074 2.263652979 0.555332958 0.58324448 0.091576078 82.82371727 0.743801996 31.44244772 0.387403625 1.00E-05 5 -1.708320021 MKGDYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 107.66 0.006773 13571530000 11335940 9164930 7148026 9145820 9703979 9041984 12514820 10235980 11150260 FALSE TRUE 10800112.58 10098846.79 7475770.062 8226464.798 11396349.87 8728857.827 10605454.36 9339663.327 12879385.37 0.838558073 0.784109373 0.580444629 0.638731163 0.884851997 0.677738694 0.823444136 0.725163745 1 23.61856041 -0.953148823 0.585151403 1.061586731 0.747093632 0.42059683 0.094075701 24.40598533 4.909111683 2.762921967 0.038075481 0.111391276 0.953148823 -0.314493099 MKGDYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 98.392 0.010302 18419860000 14282480 12771980 9254640 10881040 13111190 10950490 14902040 12986370 13411800 FALSE TRUE 13607375.48 14073459.28 9678974.398 9787257.187 15397777.38 10571271.79 12628460.1 11849214.6 15491633.45 0.878369316 0.908455479 0.624787207 0.631776967 0.9939415 0.682385871 0.815179377 0.764878322 1 23.88498593 -0.282623455 8.414861737 0.999999782 0.797041159 0.233641465 0.119856451 0 0 0.112906051 0.026612211 0.521646797 0.282623455 -0.202958623 MKGYPHWPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKGYPHWPAR 10 1 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 ; 119.68 0.00039669 1841700000 5220900 2718700 2088500 2600000 4890000 2831900 5877500 4013300 4814800 FALSE TRUE 4974118.404 2995738.621 2184259.791 2338643.06 5742814.452 2733830.593 4980779.427 3661874.176 5561454.593 0.894391624 0.538660987 0.39274973 0.420509243 1.032610148 0.491567547 0.895589336 0.658438204 1 22.40703084 0.938454724 0.589667668 0.992971245 0.622187836 0.212468613 0.213378308 1.486078482 1.214910136 0.218407976 0.093235287 8.678700955 -0.938454724 -0.370783409 MKLDYILGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MKLDYILGLK 10 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;; 124.42 0.0025645 0 4370760 3966400 3127790 3575670 3279310 3875980 4939220 4460280 3407060 FALSE TRUE 4164162.837 4370580.669 3271202.265 3216236.858 3851220.626 3741753.841 4185651.274 4069714.238 3935409.464 1.058126956 1.110578381 0.831222849 0.817255965 0.97860735 0.950791493 1.063587236 1.034127268 1 21.90808232 1.742051476 16.79148789 1.036464318 0.973647321 0.11622642 0.090214508 0.258243973 1030.465606 0.048225122 0.026666462 55.21428795 -1.742051476 -0.062816997 MKLPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKLPGR 6 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 106.84 0.028984 873250000 2168000 1963580 1873660 2363200 1773330 2037300 2436400 2320300 1943570 FALSE TRUE 2065522.937 2163671.034 1959569.164 2125646.646 2082598.191 1966747.79 2064682.432 2117122.231 2244968.909 0.920067502 0.963786637 0.872871404 0.946849035 0.927673511 0.876069055 0.919693108 0.943051916 1 21.09826403 -1.202379241 5.666892547 1.000002347 0.922289214 0.427300227 0.028626717 8.08E-07 1.14E-07 0.026386455 0.006219159 0.062751016 1.202379241 -0.077713132 MKPILLQGHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKPILLQGHER 11 1 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 111.12 0.0010229 592570000 772580 514810 373870 439460 814400 492830 927450 697700 771140 FALSE TRUE 736061.6745 567269.7243 391012.3093 395284.6459 956431.1022 475763.1735 785950.4687 636605.6893 890724.4528 0.826362937 0.636863311 0.438982345 0.443778819 1.07376765 0.534130586 0.882372171 0.714705527 1 19.76461967 2.755911865 24.99926422 0.812336367 0.613347816 0.313061833 0.182721602 1246.481795 1795899.375 0.054055396 0.057212284 570.0485761 -2.755911865 -0.198988551 MKS(ph)LEQDALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKSLEQDALR 10 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MKS(1)LEQDALR;MKS(1)LEQDALR 155.37 7.77E-06 330600000 1578420 1156100 1095980 1551120 1289840 1340030 1667290 1377730 1123190 TRUE FALSE 1503811.215 1273907.904 1146231.767 1395198.471 1514787.688 1293624.425 1412914.289 1257088.657 1297368.569 1.159124131 0.981916731 0.883505115 1.075406407 1.167584697 0.997114048 1.0890616 0.968952607 1 20.30715696 1.220876412 0.00585766 1.82E-08 2.063021876 0.039809807 0.086619091 17694.87551 87.34669166 15447.6038 15307.08719 16.62939357 -1.220876412 2.063021858 MKTPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MKTPADTGFAFPDWAYKPESSPGSR 25 2 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 MKTPADTGFAFPDWAY(0.016)KPES(0.485)S(0.485)PGS(0.014)R 72.533 0.018586 45261000 167110 125210 170760 173670 144700 159300 212540 174120 158390 TRUE FALSE 159211.0415 137969.0414 178589.5149 156212.3616 169935.6342 153783.4011 180113.1194 158873.1297 182952.3123 0.870232464 0.754125704 0.976153363 0.853841964 0.928852071 0.840565496 0.984481241 0.86838547 1 17.48110812 4.651694311 0.101345313 1.082195446 0.582200817 0.270143811 0.065271928 55.92410482 0.942111937 1.085670328 4.31289642 44842.96403 -4.651694311 -0.499994628 MKVVEVLAGHGHLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MKVVEVLAGHGHLYSR 16 1 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 ; 144.5 8.45E-07 538810000 1093360 425970 1278820 849860 1517130 1039390 2024460 1233790 553910 FALSE TRUE 1041679.04 469376.8273 1337455.162 764430.4582 1781716.992 1003395.664 1715591.445 1125752.807 639807.5338 1.628113119 0.733621914 2.090402334 1.194781896 2.784770259 1.56827735 2.681418012 1.759517898 1 19.28727845 2.772377189 24.96043897 2.079884234 1.36045837 0.145481867 0.615906178 805.0168307 594191.7068 0.168410821 0.178618321 592.0756348 -2.772377189 -0.719425863 MKYNTEGRVS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MKYNTEGRVSPSPSQESLSSSK 22 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 MKYNT(0.014)EGRVS(0.977)PS(0.009)PSQESLSSSK;MKYNT(0.016)EGRVS(0.925)PS(0.058)PS(0.001)QESLSSSK;MKYNTEGRVS(0.994)PS(0.006)PSQESLSSSK;MKYNTEGRVS(0.992)PS(0.007)PSQESLSSSK 206.48 8.18E-23 987780000 1580970 1233460 1473140 1483840 979190 1703520 1921360 1800230 1246370 TRUE FALSE 1506240.681 1359150.976 1540684.926 1334681.584 1149960.426 1644526.675 1628221.244 1642592.318 1439650.694 1.046254267 0.944083854 1.070179685 0.927087098 0.798777391 1.142309507 1.130983544 1.140965878 1 20.45728738 2.172540121 24.99999797 1.11724286 0.967321145 0.425558118 0.083334829 52.26855901 19791.78381 0.029925466 0.022101427 148.7784814 -2.172540121 -0.149921715 MLAEDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MLAEDELR 8 0 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;;; 159.04 0.00084097 2727070000 4724810 4800140 3830840 5132220 4386950 4269460 4512160 4614440 4278930 FALSE TRUE 4501477.595 5289279.723 4006487.803 4616319.495 5152032.691 4121607.53 3823747.12 4210375.171 4942484.611 0.910772203 1.070166149 0.810622211 0.934007864 1.042397316 0.833914085 0.773648766 0.85187421 1 22.23680504 2.21033297 24.7743798 0.837813483 0.958207735 0.161908311 0.091210574 239.1572799 209898.0224 0.032307617 0.023865758 162.3054002 -2.21033297 0.120394252 MLAEDELRDAVLLVFANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLAEDELRDAVLLVFANK 18 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 76.713 0.015507 111290000 122000 99461 118310 121110 137670 114320 153780 128860 147900 FALSE TRUE 116233.3018 109596.189 123734.6305 108935.7927 161679.6044 110361.0697 130318.0366 117576.3353 170835.5766 0.680381125 0.641530243 0.724290765 0.637664559 0.946404769 0.646007535 0.762827271 0.688242681 1 17.38224892 -5 0.18732418 2.208915157 0.657201851 0.494381255 0.090474305 106.4921854 1.037528039 48.08358935 0.230182109 1.00E-05 5 -1.551713306 MLAES(ph)DES(ph)GDEESVSQTDKTELQNTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 2 MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.997)GDEES(0.003)VS(0.001)QTDKTELQNTLR;MLAES(0.997)DES(0.821)GDEES(0.116)VS(0.029)QT(0.029)DKT(0.008)ELQNT(0.001)LR;MLAES(0.999)DES(0.973)GDEES(0.018)VS(0.006)QT(0.003)DKT(0.001)ELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(0.996)DES(0.982)GDEES(0.013)VS(0.004)QT(0.004)DKT(0.001)ELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR 242.11 2.03E-45 3710851000 3041615 2547764 2768201 3154320 2390582 2980787 3523276 3302112 2898789 TRUE FALSE 2897843.887 2807384.048 2895125.754 2837241.761 2807498.744 2877561.599 2985735.537 3012961.568 3348318.393 0.865462464 0.838445966 0.864650674 0.847363192 0.83848022 0.859405009 0.891711954 0.899843209 1 21.67500529 0.784425224 0.842716498 0.999991854 0.850050728 0.945798524 0.011055239 0.180415679 0.252193287 0.010363733 0.003592262 6.087307269 -0.784425224 -0.149941127 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAESDES(0.999)GDEES(0.001)VSQTDKTELQNTLR;MLAES(0.005)DES(0.983)GDEES(0.012)VSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAES(0.008)DES(0.992)GDEESVSQTDKTELQNTLR 233.63 3.55E-45 788282000 1327530 905350 1065650 1223270 995220 1135340 1360320 1217700 1077050 TRUE FALSE 1264780.288 997606.1943 1114511.107 1100304.576 1168786.053 1096022.891 1152778.2 1111071.733 1244073.413 1.016644415 0.801886917 0.895856382 0.884437015 0.939483185 0.880995349 0.926615896 0.893091775 1 20.24664019 -1.405037194 0.539737072 1.046989925 0.901485441 0.232698682 0.053855816 59.3828184 7.802690859 3.97794223 0.022310299 0.039351637 1.405037194 -0.145504484 MLAMPIDLDTLSPEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLAMPIDLDTLSPEERR 17 1 Q7Z7F7;Q7Z7F7-2;X6R631 Q7Z7F7 MRPL55 "39S ribosomal protein L55, mitochondrial" 0 75.574 0.034856 4554200 9925.6 10065 10703 9483.3 11445 11083 15404 10370 6383.9 FALSE TRUE 9456.436559 11090.63494 11193.74314 8530.020667 13441.00438 10699.19293 13053.83689 9461.947825 7373.882608 1.282422987 1.504042786 1.518025677 1.156788238 1.82278524 1.45095786 1.770279998 1.283170391 1 12.84820873 2.753734084 24.98211336 1.532428765 1.387713314 0 0.255615615 2153.985822 3546392.393 0.069747046 0.073692349 567.1972071 -2.753734084 -0.144715451 MLDAEDIVGTARPDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLDAEDIVGTARPDEK 16 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4 P12814-3 ACTN1 Alpha-actinin-1 0 ; 142.1 1.41E-06 167733000 244213 170838 159876 229844 189978 198433 282650 216227 207111 FALSE TRUE 232669.5355 188246.5864 167206.4727 206739.6444 223110.1031 191561.2155 239526.5513 197293.0176 239228.7161 0.972581968 0.78688959 0.698939807 0.864192426 0.932622583 0.800745072 1.001244981 0.824704579 1 17.86803105 1.404760723 0.660483901 0.981173675 0.838409511 0.188270568 0.090754794 1.097607557 1.097517782 0.085513667 0.039227006 25.39573125 -1.404760723 -0.142764164 MLDAEDIVNTARPDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MLDAEDIVNTARPDEK 16 1 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;; 254.59 1.26E-26 977000000 2808270 1953650 1229420 1677313 2336780 1523683 2863980 1814719 1774634 FALSE TRUE 2675528.643 2152729.156 1285790.123 1508706.311 2744313.692 1470917.476 2427027.25 1655812.584 2049835.177 1.305240866 1.050196221 0.627265127 0.736013474 1.338797247 0.717578414 1.184010928 0.807778402 1 20.96707648 4.240771742 2.914381813 0.932394343 1.267528538 0.231609982 0.219364308 0.347670757 5.906118599 0.052756228 0.162559584 17408.91649 -4.240771742 0.335134195 MLDEMKDNLLLDMYLAPHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLDEMKDNLLLDMYLAPHVR 20 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 176.42 2.91E-13 41338000 238260 243590 209040 249940 185420 222950 256960 267930 164150 FALSE TRUE 226997.922 268412.0979 218624.6908 224815.5563 217757.1893 215229.1856 217756.0326 244468.6288 189605.5436 1.197211419 1.415634231 1.153050099 1.185701388 1.148474803 1.13514184 1.148468702 1.289353803 1 17.53264162 3.70706361 24.13134002 1.15725507 1.306422827 0.35480096 0.086604891 385.7078809 295508.8072 0.020834221 0.032280462 5094.054769 -3.70706361 0.149167757 MLDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MLDEQK 6 0 H3BV99 H3BV99 SNAP23 Synaptosomal-associated protein 0 ;;; 95.445 0.032873 4206020000 1315000 1709320 1294540 1457010 12468200 970700 1685170 1061570 10312400 FALSE TRUE 1252842.556 1883501.651 1353895.939 1310548.587 14642650.13 937084.4156 1428066.366 968613.3031 11911594.32 0.10517841 0.158123388 0.113662026 0.110022937 1.229277101 0.07866994 0.119888768 0.081316848 1 23.50586319 -2.271689289 2.256546122 4.129613867 0.237328724 0.311777762 0.350000557 49502196.03 7154505.047 790939235.3 0.083736149 0.005349469 2.271689289 -3.892285143 MLDHEYTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 147.2 9.30E-05 133080000 290290 254990 239880 306590 260140 227040 263890 245520 212440 FALSE TRUE 276568.567 280973.7709 250878.7353 275770.9907 305508.3336 219177.5479 223628.7338 224020.9672 245384.1102 1.127084255 1.145036533 1.022391935 1.123833937 1.245020851 0.893201877 0.911341544 0.91293999 1 17.90468231 2.222528248 24.99999274 0.919814586 1.128436664 0.738316229 0.059993488 114.5056369 178552.6318 0.021392023 0.015849051 166.927638 -2.222528248 0.208622078 MLDLLEDFLEHEGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLDLLEDFLEHEGYK 15 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 79.337 0.015355 4179500 7465.7 13787 6529.5 9179.1 5181.9 7736.5 6178.4 9662 6086.2 FALSE TRUE 7112.811157 15191.91097 6828.884034 8256.399429 6085.621719 7468.583065 5235.771606 8815.944059 7030.016812 1.011777261 2.16100635 0.971389431 1.174449457 0.86566247 1.062384809 0.744773696 1.254043098 1 12.77931242 3.680214712 24.95439695 0.988989334 1.586392655 0.377526652 0.306536489 209.8243003 89741.15942 0.076520579 0.118545205 4788.66782 -3.680214712 0.597403321 MLDMGFEPQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 170.5 3.64E-05 189129000 323959 283463 282948 324935 354995 277398 340403 319028 367048 FALSE TRUE 308646.1001 312348.202 295921.4457 292271.9165 416906.0156 267791.6377 288468.2704 291092.217 423967.9292 0.72799398 0.736726013 0.697980732 0.689372701 0.983343283 0.631631827 0.680401159 0.68659018 1 18.69359561 -1.400256162 2.907467943 1.00488305 0.727428693 0.445854223 0.094839569 11396890.91 13560630.83 467169.9058 0.022953074 0.039787242 1.400256162 -0.277454357 MLDSGADYLHLDVMDGHFVPNITFGHPVVESLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLDSGADYLHLDVMDGHFVPNITFGHPVVESLRK 34 1 Q96AT9-4;Q96AT9;C9J9T0;C9IZU8 Q96AT9-4 RPE Ribulose-phosphate 3-epimerase 0 172.36 2.88E-15 56666000 166450 123740 179300 168350 193960 159000 240900 181210 100910 FALSE TRUE 158582.2384 136349.2467 187521.0824 151427.1382 227786.5626 153493.7901 204146.2806 165342.2917 116558.6074 1.360536488 1.169791315 1.608813682 1.2991502 1.954266335 1.316880782 1.751447491 1.418533521 1 16.83069602 3.736991469 24.99999751 1.525178173 1.2651639 0.079509248 0.267116887 221.5180899 3529294.047 0.061074661 0.100525626 5457.471412 -3.736991469 -0.260014274 MLEDRDLFVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLEDRDLFVMR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 163.78 2.15E-05 182320000 290190 180152 243660 223430 362510 218831 374880 269110 402540 FALSE TRUE 276473.2938 198509.6936 254832.052 200970.3919 425731.6292 211252.8276 317685.1709 245545.3018 464963.8473 0.594612453 0.42693576 0.548068529 0.432227996 0.915623078 0.45434248 0.683247037 0.528095471 1 18.82675902 -4.999999999 0.193770523 2.900881169 0.49190029 0.465787297 0.144141674 112.5510957 1.105970574 82.58371382 0.332631149 1.00E-05 4.999999999 -2.408980879 MLEQLDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 92.439 0.027398 196834000 535908 579159 412566 581565 605499 453952 525509 494169 538655 FALSE TRUE 510576.6909 638175.9605 431482.5592 523104.9813 711097.8339 438231.5284 445332.9504 450896.9426 622186.8663 0.820616311 1.025698219 0.693493519 0.840752207 1.142900746 0.704340693 0.715754341 0.724696979 1 19.24698842 MLEVHFVGDDDVLNHILDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLEVHFVGDDDVLNHILDR 19 0 Q13416;C9JK08;B8ZZ80 Q13416 ORC2 Origin recognition complex subunit 2 0 ; 209.53 1.27E-16 31431000 29895 29866 30207 29398 34173 28224 31495 31913 30373 FALSE TRUE 28481.9226 32909.37935 31592.02083 26442.85719 40132.76038 27246.5958 26689.8593 29118.52854 35083.08972 0.811841911 0.93804108 0.900491407 0.753720878 1.143934605 0.776630451 0.760761367 0.829987574 1 15.09848819 -1.080520385 6.388683385 1.000000184 0.86247308 0.120045688 0.115246885 2.85E-07 4.10E-08 0.10530738 0.024821154 0.083076772 1.080520385 -0.137527104 MLFKDDYPSSPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLFKDDYPSSPPK 13 1 P63279;H3BQQ9;B0QYN7;H3BPC4 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ; 161.76 3.79E-05 469190000 1944950 1582800 1753260 2025300 1383780 1969580 2329100 2133300 1581230 FALSE TRUE 1853016.068 1744089.119 1833648.705 1821712.996 1625110.794 1901372.951 1973753.018 1946496.943 1826439.073 1.014551263 0.954912291 1.003947371 0.997412409 0.889770055 1.041027308 1.08065637 1.065733301 1 20.8006022 2.022980023 24.99966312 1.058529268 0.975324009 0.454491088 0.040206786 175.128271 190518.9111 0.013902912 0.010267238 105.4338397 -2.022980023 -0.083205259 MLGEDS(ph)DEEEEMDTSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER 322.84 1.13E-58 1940650000 2268680 2090110 2094540 2413990 2108700 2186440 2453670 2328700 2147750 TRUE FALSE 2161443.992 2303094.585 2190576.731 2171331.139 2476456.612 2110723.035 2079317.577 2124786.683 2480812.101 0.871264693 0.92836317 0.883007919 0.87525014 0.99824433 0.850819388 0.838160043 0.856488358 1 21.24238104 MLISAVS(ph)PEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLISAVSPEIR 11 0 A0AVK6;E9PMT9 A0AVK6 E2F8 Transcription factor E2F8 1 MLIS(0.008)AVS(0.992)PEIR 111.79 0.00085715 0 55900 51083 55539 59192 53724 52178 70377 60132 66188 TRUE FALSE 53257.71778 56288.41578 58085.51809 53241.9077 63093.44859 50371.06278 59639.69609 54866.5233 76452.097 0.696615526 0.736257316 0.759763569 0.696408729 0.825267731 0.658857831 0.780092351 0.717658841 1 16.22226845 -4.999999993 0.397007271 5.204236859 0.728752776 0.758320959 0.047154885 306.0924613 2.160202718 1114.468525 0.025356028 1.00E-05 4.999999993 -4.475484083 MLKHDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MLKHDD 6 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ;;; 113.08 0.024116 2690910000 5153800 3560010 4460180 3840650 3736250 3875320 4998550 4548130 3614700 FALSE TRUE 4910190.088 3922779.066 4664683.665 3454580.565 4387850.817 3741116.697 4235929.393 4149871.626 4175249.215 1.176023235 0.939531718 1.117222811 0.827395058 1.0509195 0.89602237 1.014533307 0.993921898 1 21.99343088 4.634587683 2.509109989 0.979580478 1.197139104 0.367911363 0.080294937 0.37958099 3.56668192 0.017280643 0.160237824 43110.95896 -4.634587683 0.217558626 MLLS(ph)WDGGESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLLSWDGGESR 11 0 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 MLLS(1)WDGGESR 178.1 8.07E-06 14445000 38940 34008 37357 49358 40307 42601 49591 42412 48884 TRUE FALSE 37099.38337 37473.45386 39069.8554 44396.44007 47336.52804 41125.71669 42024.98215 38698.18044 56464.68106 0.657036977 0.663661835 0.691934403 0.786269208 0.838338713 0.728344089 0.744270248 0.685351971 1 15.78506112 -5 0.166523314 2.035008372 0.652376372 0.700128725 0.056421125 77.69813961 0.726729161 26.74583956 0.224433179 1.00E-05 5 -1.382632 MLLYTEVTR ddPTM_SK-BR-3_Trastuzumab_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 ; 145.16 0.00022763 282190000 420810 406850 360080 406940 411090 385390 443250 415070 429670 FALSE TRUE 400919.1453 448308.4776 376590.0242 366033.6181 482783.9658 372043.8477 375624.0717 378724.2704 496301.0291 0.807814455 0.903299512 0.758793559 0.737523391 0.972764386 0.74963344 0.756847255 0.763093865 1 18.92085592 MLMRRDQVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 58.978 0.061994 1703150000 5692960 4788020 5809670 4530710 4441840 6272160 7048550 6155820 3066790 FALSE TRUE 5423865.063 5275924.682 6076049.116 4075274.423 5216495.49 6054953.526 5973164.242 5616783.767 3542372.13 1.531139266 1.489376183 1.715248679 1.150436564 1.472599517 1.709293463 1.686204617 1.585599581 1 21.75628435 MLPDKDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 MLPDKDCR 8 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;;;;;;;; 109.71 0.0032514 68535630000 103705880 77826680 67837520 77325040 82860110 78755530 110474870 88774490 90781720 FALSE TRUE 98803908.58 85757307.17 70947937.39 69552180.07 97310886.95 76028206.25 93619899.57 81000925.03 104859685.5 0.94224876 0.817829147 0.6765988 0.663288086 0.928010479 0.725047056 0.89281118 0.772469655 1 26.64388488 -0.714317311 5.499485881 1.000000016 0.810566399 0.283682481 0.09795319 1.80E-08 4.53E-09 0.092789296 0.021870645 0.193055727 0.714317311 -0.189433618 MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 33 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;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 287.23 8.52E-75 26948594000 11571912 10422595 10238175 11729612 7041455 11969701 11980606 12864808 7212762 TRUE FALSE 11024930.65 11484669.28 10707605.45 10550529.12 8269482.523 11555187.25 10152744.52 11738297.21 8331280.293 1.323317697 1.378499927 1.285229289 1.266375484 0.99258244 1.38696417 1.218629569 1.408942779 1 22.99010679 -2.248511263 2.197624181 0.000166325 1.284304633 0.359863513 0.118418187 1967297.582 341923.1738 9782766.454 0.027334545 0.005642723 2.248511263 1.284138308 MLPHAPGVQMQAIPEDAVHEDS(ph)GDEDGEDPDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 29 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 308.73 1.84E-104 28001710000 9740558 8537329 8927695 10098162 6400550 10185364 10672986 10789263 5340551 TRUE FALSE 9280141.127 9407292.531 9337038.646 9083075.571 7516803.894 9832642.291 9044625.963 9844497.934 6168736.373 1.504382837 1.524995066 1.513606366 1.472436982 1.218532198 1.59394756 1.466204003 1.595869452 1 22.55654356 -1.095964462 4.437910498 0.999952677 1.486518921 0.680972642 0.10459424 4.54E-05 9.25E-06 0.093945184 0.022140944 0.080174367 1.095964462 0.486566244 MLPPGEWMCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLPPGEWMCHR 11 0 K7ENU0;K7ERZ4;K7EMX6 K7ENU0 PHF12 0 46.606 0.097822 41425000 29790 19356 23312 20001 80456 11368 19689 26499 108810 FALSE TRUE 28381.88574 21328.39841 24380.87826 17990.46148 94487.50093 10974.32331 16685.08144 24178.60708 125683.6991 0.225819943 0.169699003 0.193986002 0.14314077 0.751788033 0.087316998 0.132754538 0.192376635 1 16.93943802 -1.834477366 2.708169696 1.275054762 0.227865535 0.620289385 0.187458997 88797786.39 60381925.56 158636099.7 0.042547647 0.014639378 1.834477366 -1.047189227 MLQEDELRDAVLLVFANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MLQEDELRDAVLLVFANK 18 1 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ;;; 256.49 1.24E-30 576369000 1117520 860330 1056180 1135160 1041890 1057270 1441730 1197600 1211640 FALSE TRUE 1064697.044 947998.6051 1104606.898 1021051.56 1223595.286 1020656.475 1221767.609 1092731.795 1399534.943 0.760750598 0.677366871 0.789267108 0.729564892 0.874287057 0.729282595 0.87298114 0.780782074 1 20.41651608 -4.999999998 0.111518588 1.772583528 0.638375648 0.642138291 0.055636583 87.39184469 0.645583104 15.2089274 0.581335794 1.00E-05 4.999999998 -1.13420788 MLQHIDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 161.86 0.00034506 4201420000 4111140 2757790 2003790 2596731 4829690 2272853 4836310 3049390 4228870 FALSE TRUE 3916814.56 3038811.936 2095665.754 2335702.666 5671986.407 2194143.531 4098442.085 2782369.246 4884661.562 0.801859967 0.622113098 0.429029878 0.478170829 1.16118309 0.449190492 0.839043203 0.569613516 1 22.21982718 MLRPVS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLRPVSR 7 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 MLRPVS(1)R;MLRPVS(1)R 70.908 0.033764 1094420000 381910 313440 390170 467220 399290 437340 514930 419810 486400 TRUE FALSE 363857.8712 345379.8924 408059.6804 420254.1579 468926.0496 422194.8061 436367.9712 383049.2108 561828.4278 0.647631649 0.614742643 0.726306574 0.748011559 0.834642795 0.751465724 0.77669258 0.681790369 1 19.0997701 -4.999999998 0.071696825 1.911936718 0.393632791 0.695559711 0.059387204 161.6177443 0.831967966 24.52183156 2.912010874 1.00E-05 4.999999998 -1.518303927 MLSCAGADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 88.921 0.028981 114260000 190310 126550 134060 180290 215050 150440 202180 137620 168630 FALSE TRUE 181314.4235 139445.5889 140206.7836 162166.9067 252554.6519 145230.2251 171333.7277 125569.2632 194780.2792 0.930866432 0.715912255 0.719820221 0.832563273 1.29661305 0.745610519 0.87962564 0.644671338 1 17.57148809 4.762572985 22.01490882 0.848735466 0.930866899 0.015660637 0.185959703 1266.721829 2217602.37 0.042112441 0.644339691 57885.92596 -4.762572985 0.082131433 MLSELKDEYDDLAESEQFGVVMGTVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MLSELKDEYDDLAESEQFGVVMGTVPR 27 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 193.34 2.33E-18 121830000 192860 170790 173370 198320 130890 196790 214520 209260 168590 FALSE TRUE 183743.89 188193.6952 181319.186 178384.4968 153717.1746 189975.113 181791.0341 190936.085 194734.0762 0.943563107 0.966413783 0.931111748 0.916041508 0.789369676 0.975561734 0.933534786 0.980496525 1 17.57114584 1.254170067 1.673787196 0.999294866 0.923051437 0.247831017 0.050517403 0.555998439 2.819362617 0.047071418 0.014100736 17.9543657 -1.254170067 -0.076243429 MLVLVLGDLHIPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 98.531 0.0014694 76691000 70859 72230 71079 79928 72238 65590 86524 77689 35849 FALSE TRUE 67509.6355 79590.31912 74338.04246 71893.48559 84836.28433 63318.60185 73323.17468 70886.1393 41408.27983 1.630341463 1.922087067 1.795245849 1.736210388 2.048775865 1.529129008 1.770737036 1.711883218 1 15.33763165 -0.593528805 0.536835465 0.859847791 1.799884741 0.750481997 0.14008825 5.12916963 1.159724812 1.43127516 0.056778158 0.254959498 0.593528805 0.94003695 MLWGSDPYPHAEPQQAT(ph)TPK ddPTM_SK-BR-3_Trastuzumab_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(0.633)T(0.367)PK 184.76 1.43E-16 282060000 190040 166270 178010 223190 144740 208390 224490 226170 129660 TRUE FALSE 181057.1858 183213.102 186171.9346 200754.5172 169982.6102 201173.402 190239.9275 206365.3558 149767.0106 1.208925685 1.223320819 1.243077056 1.340445512 1.134980324 1.343242422 1.270239198 1.377909294 1 17.19236035 3.662282183 3.868002423 1.262182708 1.215631328 0 0.111206976 0.891171443 25.5442889 0.026435882 0.043252353 4594.964742 -3.662282183 -0.046551379 MLWGSDPYPHAEPQQATT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MLWGSDPYPHAEPQQATTPK 20 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 MLWGSDPYPHAEPQQAT(0.047)T(0.953)PK;MLWGSDPYPHAEPQQAT(0.095)T(0.905)PK;MLWGSDPYPHAEPQQAT(0.075)T(0.925)PK 189.62 7.81E-17 641750000 654940 585550 578070 700830 443731 681240 705740 717160 415271 TRUE FALSE 623982.2842 645218.2107 604575.0813 630381.2369 521117.5459 657648.488 598066.4012 654361.6685 479669.1058 1.300859857 1.34513189 1.260400293 1.314200205 1.086410485 1.371046165 1.246831188 1.364193901 1 18.87168 -1.5124356 2.76882645 0.987210183 1.287194322 0.54851721 0.081577605 7333650.59 7632033.31 709538.749 0.017972721 0.03073013 1.5124356 0.299984138 MMDS(ph)EAHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MMDSEAHEK 9 0 Q9H1U9 Q9H1U9 SLC25A51 Solute carrier family 25 member 51 1 MMDS(1)EAHEK 47.823 0.095334 76445000 6380.3 6606.9 9214.5 7783.9 9684.4 5822.9 6748.1 7397.7 9604.5 TRUE FALSE 6078.715864 7280.150621 9636.993939 7001.447584 11373.35629 5621.251513 5718.553408 6749.91817 11093.91681 0.547932346 0.656229062 0.868673716 0.631106912 1.025188533 0.506696743 0.515467486 0.60843418 1 13.43748119 4.25821968 3.046591204 0.701949039 0.563921309 0.073340242 0.185274698 0.719801246 13.46892805 0.046131569 0.142663717 18122.56559 -4.25821968 -0.13802773 MMLDDIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MMLDDIVSR 9 0 A0A087WTP3;Q92945;M0R0I5;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 130.96 0.002683 19657000 145657 124328 132169 149215 159762 119950 147565 134925 161748 FALSE TRUE 138772.0823 136997.1645 138229.0794 134215.6247 187624.4422 115796.1014 125051.249 123110.2517 186831.0537 0.742767755 0.733267633 0.73986137 0.718379638 1.004246556 0.619790442 0.669327965 0.658938914 1 17.51137474 -2.285254898 2.250268934 2.167975679 0.733627009 0.391744365 0.103420084 9585681.337 1748469.971 56680560.8 0.025382141 0.005184956 2.285254898 -1.43434867 MMNGGHYTYSENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MMNGGHYTYSENR 13 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;; 186.13 8.07E-06 1789548000 1304483 1329226 881647 1287002 1268950 1014634 1224428 1172359 1031566 FALSE TRUE 1242822.674 1464675.641 922071.387 1157630.114 1490254.478 979496.9702 1037619.02 1069701.031 1191535.987 1.043042499 1.229233239 0.773851061 0.971544399 1.250700352 0.822045646 0.870824744 0.897749663 1 20.18439109 2.206196347 24.9999938 0.882853156 1.060195447 0.234735347 0.138564033 258.0484919 199329.7673 0.051372156 0.037943635 160.7667925 -2.206196347 0.177342291 MMNGGHYTYSENRVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 MMNGGHYTYSENRVEK 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;;;;;; 216.99 8.82E-15 2271905000 3890330 2938025 3581626 3941169 3538292 3578216 4810380 4179230 3931800 FALSE TRUE 3706441.811 3237413.088 3745847.095 3544995.204 4155369.005 3454301.483 4076468.182 3813274.466 4541523.463 0.816123013 0.712847377 0.824799679 0.780574015 0.914972484 0.760604126 0.897599278 0.839646541 1 22.1147449 -0.21449531 0.192638576 1.118676504 0.731889765 0.56746043 0.054288594 7.49514842 0.474992993 0.724874332 0.182845782 0.610245646 0.21449531 -0.386786738 MNDFHIS(ph)DDEEKNPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MNDFHISDDEEKNPSK 16 1 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;A8MSM7 E7ETZ8 MAP9 Microtubule-associated protein 9 1 MNDFHIS(1)DDEEKNPSK;MNDFHIS(0.774)DDEEKNPS(0.226)K 79.942 0.010263 257920000 255416 239102 237622 264664 150977 274499 301164 331182 279231 TRUE FALSE 243342.9919 263466.7656 248517.2037 238059.4719 177307.341 264993.0308 255215.9005 302181.9484 322532.7174 0.754475372 0.816868341 0.770517812 0.738094026 0.549734435 0.821600466 0.791286858 0.936903241 1 18.29908599 1.231950454 1.791358421 1.00100937 0.745209268 0.615190496 0.074246851 0.232088937 1.332330675 0.069016577 0.020357935 17.05887765 -1.231950454 -0.255800102 MNDIVKEFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MNDIVKEFEDR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 192.15 1.39E-06 174160000 362270 202200 389520 323650 340160 376620 538120 415730 435240 FALSE TRUE 345146.215 222804.4099 407379.8773 291116.0871 399483.7963 363577.555 456019.9107 379326.4773 502734.7963 0.68653735 0.44318478 0.810327593 0.579064925 0.794621338 0.723199503 0.907078472 0.754526005 1 18.93943802 2.037140337 0.400917303 0.989956246 0.551252543 0.520939044 0.108369467 0.769074287 0.307362697 0.110906603 0.112952256 108.9282024 -2.037140337 -0.438703703 MNGFIDQIDGIVHFETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MNGFIDQIDGIVHFETR 17 0 D6RFN0;Q9BT78;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;;; 208.59 5.04E-12 207946000 457056 371930.3 403666.2 445991 451762.3 407368.8 498876.7 432728.5 421664.7 FALSE TRUE 435451.8687 409830.4204 422174.6946 401159.1374 530549.5021 393261.5163 422763.8969 394836.4985 487054.3081 0.89405198 0.84144707 0.866791829 0.823643546 1.089302555 0.807428473 0.868001555 0.810662162 1 18.89372312 -2.323386855 2.269737798 1.681060305 0.874369924 0.190400429 0.080882853 4351709.211 822390.9472 15137880.68 0.018782036 0.00474912 2.323386855 -0.806690381 IRDSAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 IRDSAGQK 8 1 P52209-2;P52209;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 118.67 0.00168 806810000 1005070 800330 1037740 1415530 1401700 1538860 1953660 1779360 1742830 FALSE TRUE 957562.333 881884.5369 1085321.405 1273238.235 1646156.036 1485568.892 1655593.286 1623549.805 2013099.175 0.475665752 0.43807307 0.539129626 0.632476656 0.817722274 0.73795117 0.822410195 0.806492708 1 20.94098682 2.801248852 0.401455119 0.965526887 0.351415272 0.903442232 0.054896316 0.402626968 0.129625897 0.056245408 0.097145757 632.7743292 -2.801248852 -0.614111615 down MNGVMFPGNS(ph)PSYTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.835)PS(0.139)Y(0.001)T(0.025)ER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.986)PS(0.014)YTER;MNGVMFPGNS(0.943)PS(0.057)YTER;MNGVMFPGNS(0.941)PS(0.059)YTER;MNGVMFPGNS(0.989)PS(0.011)YTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.954)PS(0.045)YT(0.001)ER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.954)PS(0.046)YTER;MNGVMFPGNS(0.956)PS(0.043)YTER;MNGVMFPGNS(0.971)PS(0.026)Y(0.003)T(0.001)ER;MNGVMFPGNS(0.994)PS(0.006)YTER 396.21 9.35E-122 2403846000 3220665 2959216 3083702 3532054 3285484 3107327 3588283 3331452 3587270 TRUE FALSE 3068430.548 3260763.475 3225092.787 3177005.221 3858471.369 2999719.487 3040824.525 3039732.402 4143565.51 0.74052903 0.786946283 0.778337588 0.766732229 0.931195937 0.723946437 0.733866646 0.733603075 1 21.9824413 -1.922288844 2.53211465 1.144356167 0.772895016 0.586878943 0.059474377 10233770.41 5410189.7 8752540.186 0.014385095 0.011959449 1.922288844 -0.371461151 MNLSEEVDLEDYVARPDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MNLSEEVDLEDYVARPDK 18 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 257.47 1.15E-30 384020000 369580 319724 248918 347816 278285 295029 392960 361059 272389 FALSE TRUE 352110.6858 352304.2391 260331.1365 312852.8749 326817.8159 284812.0718 333006.7348 329442.7599 314629.6949 1.119127315 1.119742493 0.827420745 0.994352662 1.038737987 0.905229469 1.058408472 1.04708095 1 18.26329531 3.895700455 24.94877094 0.985635134 1.11950108 0.402652499 0.069658803 27.54092345 6576.488309 0.016984614 0.030619473 7865.031299 -3.895700455 0.133865946 MNS(ph)DQDVALKLAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MNSDQDVALKLAQER 15 1 Q92738 Q92738 USP6NL USP6 N-terminal-like protein 1 MNS(1)DQDVALKLAQER;MNS(1)DQDVALKLAQER;MNS(1)DQDVALKLAQER 70.783 0.027576 1705320000 2702420 1943490 2401530 2651970 1753330 2631760 3087410 2994050 2156840 TRUE FALSE 2574681.962 2141533.841 2511642.526 2385388.937 2059110.197 2540621.491 2616368.9 2731875.11 2491311.732 1.033464391 0.859600914 1.008160679 0.957483123 0.826516478 1.01979269 1.050197319 1.09656093 1 21.24847412 2.017538451 24.96071242 1.049621448 0.938056699 0.398420737 0.064684746 220.0641994 313193.8645 0.022817269 0.016848368 104.1210289 -2.017538451 -0.111564748 MNS(ph)LTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MNSLTFK 7 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 MNS(0.999)LT(0.001)FK;MNS(0.993)LT(0.007)FK;MNS(0.989)LT(0.011)FK;MNS(1)LTFK;MNS(0.995)LT(0.005)FK;MNS(0.987)LT(0.013)FK 141.25 0.0026954 789479000 3528600 3429180 2892430 3849730 1957390 3552470 3395500 3429430 1837870 TRUE FALSE 3361810.071 3778617.341 3025050.777 3462747.826 2298758.196 3429447.073 2877454.112 3129130.929 2122877.493 1.583610021 1.779950729 1.424976611 1.631157633 1.082850143 1.615471022 1.355449913 1.474004477 1 21.01758969 -1.831045534 0.08468215 7.26E-11 2.110760298 0.478726726 0.175732814 76.99140644 0.969257279 21.72582231 5.990826259 0.014755518 1.831045534 2.110760298 MPCQLHQVIVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPCQLHQVIVAR 12 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 223.14 2.31E-11 761020000 309360 314190 301150 364120 333060 327930 386900 337640 313790 FALSE TRUE 294737.1659 346206.3182 314958.0254 327517.9658 391145.5585 316573.7019 327871.2991 308074.4517 362450.9506 0.813178074 0.955181157 0.868967304 0.903620104 1.079168251 0.873424946 0.904594949 0.849975565 1 18.46742625 4.638314869 2.992448156 0.924296004 0.806280391 0.21492757 0.068919744 0.484958976 6.985803078 0.015908429 0.120577145 43482.53643 -4.638314869 -0.118015613 MPDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPDLHLK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 70.268 0.057489 132040000 459940 365140 313930 374680 364680 338600 449040 425630 347700 FALSE TRUE 438199.5477 402348.1811 328324.001 337016.4546 428280.0765 326874.1971 380530.7008 388359.5808 401619.5402 1.091081244 1.001814257 0.817500067 0.83914357 1.066382568 0.813890173 0.947490505 0.966983779 1 18.61546994 4.004584386 4.397594558 0.916484089 1.062547313 0.307979724 0.081928524 0.196906619 9.767061628 0.019479225 0.041033046 10106.1185 -4.004584386 0.146063224 MPDMHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPDMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 92.925 0.015312 154040000 619870 499870 374750 489450 646180 410150 578270 527830 477020 FALSE TRUE 590569.9736 550807.3213 391932.6582 440249.5561 758873.5874 395946.4027 490044.2908 481610.407 550993.8253 1.071826845 0.999661513 0.711319511 0.799009963 1.377281473 0.718604065 0.889382545 0.87407587 1 19.07167663 3.986431343 24.23419535 0.903487686 1.044764901 0.076184393 0.187858603 1083.144436 1934550.529 0.045745005 0.084349257 9692.400311 -3.986431343 0.141277215 MPEFYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MPEFYNR 7 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;; 153.15 0.0041078 2240980000 1178240 977440 963850 1067830 1181920 986170 1263070 1058310 1200140 FALSE TRUE 1122546.93 1077042.247 1008043.476 960489.6997 1388046.474 952018.6856 1070365.474 965638.7659 1386251.582 0.809771433 0.77694573 0.727172101 0.692868244 1.001294781 0.686757511 0.772129307 0.696582625 1 20.40275768 -1.064470177 4.138802774 1.000029744 0.772853887 0.383334418 0.091457237 16113402.44 45659046.59 7085.910283 0.019946298 0.086204477 1.064470177 -0.227175858 MPEMHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MPEMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 92.925 0.015312 895380000 2380700 2012220 1452320 1825480 2046750 1606510 2398600 2099550 1820240 FALSE TRUE 2268169.029 2217267.506 1518910.309 1641979.282 2403702.552 1550876.156 2032649.517 1915702.272 2102513.523 1.07878927 1.054579427 0.72242594 0.780960153 1.143251887 0.737629575 0.966771198 0.911148609 1 21.00368365 3.957535226 24.20388353 0.893255364 1.06971065 0.240987032 0.127240865 371.2459662 211601.1597 0.030117508 0.054297349 9068.49516 -3.957535226 0.176455286 MPETVPQEEMPGPPLNSES(ph)GEEAPTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPETVPQEEMPGPPLNSESGEEAPTGR 27 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 MPETVPQEEMPGPPLNS(0.168)ES(0.823)GEEAPT(0.008)GR 70.666 0.013387 40983000 37842 35560 34858 44883 39339 40686 43389 40088 44942 TRUE FALSE 36053.28366 39183.60443 36456.27378 40371.27557 46199.70914 39277.03362 36769.21116 36577.6822 51911.37583 0.694516049 0.754817298 0.70227909 0.77769612 0.889972735 0.75661708 0.708307391 0.704617853 1 15.6637631 -2.234471267 2.404283745 1.926262569 0.747099913 0.654985194 0.057331843 3490593.524 483037.2724 17779382.29 0.014062753 0.005828123 2.234471267 -1.179162655 MPFGELMFESSSSCGWVHGVCFSASGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MPFGELMFESSSSCGWVHGVCFSASGSR 28 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 162.82 8.35E-12 50553000 19847.2 16490.8 15305.5 17281.8 15109.5 17504.7 19569.9 19240.4 17648.4 FALSE TRUE 18909.06219 18171.23127 16007.27231 15544.60063 17744.59202 16898.50785 16584.15233 17555.60858 20385.22374 0.927586689 0.89139229 0.785238981 0.762542557 0.870463442 0.828958665 0.813537911 0.861192833 1 14.31523617 -0.46008821 7.744423737 0.999998589 0.84576717 0.504638682 0.048916245 0 0 0.052568108 0.012390422 0.346666432 0.46008821 -0.154231419 MPFLSISS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPFLSISSPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MPFLS(0.002)IS(0.323)S(0.675)PK 100.93 0.0038572 176700000 542200 565210 499280 680360 411420 573140 656330 682080 466600 TRUE FALSE 516571.2805 622805.5416 522172.4819 611968.9202 483171.5177 553292.0181 556194.8042 622353.4593 538957.9449 0.958463059 1.155573542 0.968855709 1.135466925 0.896492059 1.026595903 1.031981826 1.154734734 1 19.03981318 -1.302461843 3.815562864 0.999909839 1.041355587 0.02145539 0.087035163 5.95E-05 1.09E-05 0.07512967 0.017669719 0.049835424 1.302461843 0.041445747 MPGGPKPGGGPGLS(ph)TPGGHPKPPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.64)T(0.36)PGGHPKPPHR 110.4 0.0013538 849400000 1041100 1165000 1217900 1395000 1008700 1256300 1507300 1398000 395290 TRUE FALSE 991889.2663 1283714.824 1273741.92 1254771.95 1184616.961 1212794.016 1277333.702 1275583.709 456589.5543 2.172387118 2.811529113 2.789686947 2.748139851 2.594489842 2.656201844 2.797553491 2.793720742 1 18.80053833 -1.019101426 7.972583641 0.999999975 2.666138654 0.883926242 0.190232805 8.78E-08 1.12E-08 0.187581352 0.044213348 0.095697055 1.019101426 1.666138679 MPGGPKPGGGPGLST(ph)PGGHPKPPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.221)T(0.779)PGGHPKPPHR 135.78 3.67E-05 797180000 1411700 1515000 1550800 1732400 1196500 1611200 1842400 1746900 475000 TRUE FALSE 1344971.739 1669380.222 1621905.714 1558255.861 1405169.221 1555403.74 1561308.042 1593932.175 548660.574 2.451373039 3.042646586 2.956118574 2.840109048 2.561090203 2.834910715 2.845672016 2.90513343 1 19.06555438 -1.032722888 4.834700395 0.999961933 2.80738085 0.912458961 0.17566519 6.99E-05 1.40E-05 0.1648872 0.038863474 0.09274214 1.032722888 1.807418918 MPLDLS(ph)PLATPIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.999)PLAT(0.001)PIIR;MPLDLS(1)PLATPIIR 107.35 0.00093244 152629000 593484 530867 501861 622256 476908 537495 764976 597360 553870 TRUE FALSE 565431.1875 584962.9508 524871.8233 559705.6447 560080.6042 518881.4134 648264.8615 545051.9916 639761.3308 0.883815824 0.914345589 0.820418175 0.874866325 0.875452418 0.811054667 1.013291723 0.851961451 1 19.28717427 1.739498095 24.99999999 0.952127506 0.870048233 0.405881752 0.051869159 0.146046274 3869.85478 0.02184078 0.012111812 54.89061474 -1.739498095 -0.082079273 MPLLELGGET(ph)TPPLSTERS(ph)PEAVGSECPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.5)T(0.5)PPLS(0.009)T(0.039)ERS(0.953)PEAVGSECPSR 98.342 0.0013801 61063000 44020 41471 41838 44435 47590 45682 54238 40476 58648 TRUE FALSE 41939.26184 45696.94205 43756.31368 39968.30938 55889.68093 44100.02089 45962.99695 36931.70686 67742.83231 0.619095193 0.674564976 0.645917984 0.590000566 0.825027225 0.65099169 0.678492401 0.545175122 1 16.04778069 -2.214028543 2.525263994 2.187728864 0.657870698 0.690870235 0.072759602 4849821.015 1325458.726 32876117.96 0.015900612 0.006109019 2.214028543 -1.529858167 MPLLELGGETT(ph)PPLSTERS(ph)PEAVGSECPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.47)T(0.53)PPLS(0.043)T(0.039)ERS(0.918)PEAVGSECPSR 117.77 0.00017485 64218000 49509 44628 41939 53799 50876 44175 51595 46656 60377 TRUE FALSE 47168.80769 49175.64394 43861.94463 48391.02231 59748.75829 42645.20867 43723.23514 42570.5533 69739.9568 0.676352694 0.705128684 0.628935644 0.693878008 0.856736382 0.611488889 0.626946691 0.610418407 1 16.08969785 -1.021217269 4.680745309 1.000007141 0.676719382 0.665086816 0.072202804 6.26E-06 1.31E-06 0.068561267 0.016159622 0.095231962 1.021217269 -0.32328776 MPLLELGGETTPPLS(ph)TERSPEAVGSECPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.004)T(0.003)PPLS(0.331)T(0.331)ERS(0.331)PEAVGSECPSR;MPLLELGGET(0.004)T(0.004)PPLS(0.331)T(0.331)ERS(0.315)PEAVGS(0.013)ECPS(0.003)R;MPLLELGGET(0.008)T(0.008)PPLS(0.354)T(0.354)ERS(0.276)PEAVGSECPSR 72.879 0.0032363 158085000 128927.2 108837.7 130967.1 130838.7 143730.5 111444.4 148536.7 138210.5 174922.8 TRUE FALSE 122833.0668 119928.3854 136972.0711 117686.5453 168797.0537 107585.0525 125874.6984 126108.0559 202048.9344 0.607937216 0.593561088 0.677915335 0.582465558 0.835426597 0.532470279 0.622991152 0.624146107 1 17.62434522 -1.769286674 2.299729014 1.10905144 0.62998022 0.670755351 0.080392754 3477135.908 2174679.369 2133922.775 0.018340841 0.017010353 1.769286674 -0.479071221 MPLLELGGETTPPLSTERS(ph)PEAVGSECPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.001)T(0.001)PPLS(0.051)T(0.051)ERS(0.87)PEAVGS(0.019)ECPS(0.005)R;MPLLELGGETTPPLS(0.018)T(0.018)ERS(0.963)PEAVGSECPSR;MPLLELGGETTPPLS(0.046)T(0.046)ERS(0.906)PEAVGSECPSR;MPLLELGGETTPPLS(0.001)T(0.001)ERS(0.999)PEAVGSECPSR;MPLLELGGETTPPLSTERS(0.999)PEAVGSECPSR;MPLLELGGET(0.005)T(0.001)PPLS(0.041)T(0.041)ERS(0.911)PEAVGSECPSR 224.54 5.31E-35 602016000 148339.1 120107.7 155031.6 158489.8 168021.9 149920.2 173480.9 159439 214038 TRUE FALSE 141327.4047 132346.8112 162139.9522 142558.1042 197324.8662 144728.4259 147013.2025 145477.6759 247229.9199 0.571643613 0.535318748 0.655826577 0.576621569 0.798143146 0.585400125 0.59464163 0.588430704 1 17.91549382 -2.489328048 2.073938845 5.063820883 0.607294909 0.737726714 0.072392576 2418358.197 168153.2167 46181536.93 0.017322817 0.003240947 2.489328048 -4.456525975 MPLPS(ph)PTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPLPSPTESR 10 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 MPLPS(0.991)PT(0.009)ESR 68.536 0.062605 49641000 62814 66187 58899 66121 62717 59518 67701 62929 66795 TRUE FALSE 59844.90671 72931.53055 61599.57741 59474.39146 73654.82494 57456.87674 57371.96904 57418.60315 77153.22746 0.775663037 0.945281655 0.798405711 0.770860707 0.954656433 0.744711254 0.743610746 0.744215181 1 16.23543889 MPPSHQLDHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MPPSHQLDHSK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 101.35 0.001937 27471000 82277 75681 67299 91325 70785 81105 86901 71045 46187 FALSE TRUE 78387.92927 83392.97994 70384.72572 82144.83749 83129.88159 78296.31351 73642.6564 64823.92317 53349.44407 1.469329824 1.563146184 1.319315073 1.539750581 1.55821458 1.467612547 1.380382827 1.215081512 1 15.70318562 1.10631664 1.420555865 1.002224659 1.493998613 0.846957262 0.069101182 0.136163086 0.549354104 0.061523395 0.018606573 12.77369789 -1.10631664 0.491773954 MPQDGS(ph)DDEDEEWPTLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MPQDGSDDEDEEWPTLEK 18 0 Q13895;F8WBL2 Q13895 BYSL Bystin 1 MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK 161.64 1.26E-10 317840000 521318 442748 471268 511757 380898 522206 584701 543722 396037 TRUE FALSE 496676.3313 487864.5246 492876.1039 460314.2141 447326.4906 504121.8753 495494.1237 496110.8192 457452.3953 1.085744301 1.066481517 1.077436929 1.006255993 0.977864572 1.102020408 1.083159972 1.084508081 1 18.80326209 -0.766609667 7.832963295 1.000000002 1.062328789 0.191632584 0.038835026 0 0 0.038446276 0.009061874 0.171155292 0.766609667 0.062328787 MPSARPPS(ph)PPLSSWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MPSARPPSPPLSSWER 16 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 MPSARPPS(0.997)PPLS(0.001)S(0.002)WER;MPS(0.002)ARPPS(0.998)PPLSSWER;MPSARPPS(0.97)PPLS(0.027)S(0.003)WER;MPSARPPS(0.932)PPLS(0.03)S(0.038)WER;MPSARPPS(0.963)PPLS(0.016)S(0.021)WER;MPSARPPS(0.999)PPLSSWER 127.5 3.99E-05 1630263000 1123230 1080466 998177 1154129 1133351 1019784 1179047 1123818 1174323 TRUE FALSE 1070137.144 1190566.714 1043944.403 1038113.76 1331007.056 984468.6244 999161.7255 1025410.538 1356431.013 0.788935916 0.877720063 0.769625873 0.765327355 0.981256726 0.725778617 0.736610794 0.755962174 1 20.37138424 MPSGEFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MPSGEFAR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 120.92 0.0033858 462760000 768360 728060 608030 779040 582100 715800 814970 791600 648670 FALSE TRUE 732041.1455 802250.1417 635908.7769 700729.4191 683618.0557 691011.6665 690631.3585 722283.3075 749262.4307 0.977015683 1.070719829 0.848713016 0.935225617 0.912388007 0.922255859 0.921748282 0.963992425 1 19.51511159 3.749196639 24.9971746 0.924936066 1.023867755 0.439230927 0.044272969 515.9001639 1212484.355 0.010222065 0.01819355 5613.020634 -3.749196639 0.09893169 MPTQSEEEKLSPS(ph)PTTEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MPTQSEEEKLSPSPTTEDPR 20 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 MPTQSEEEKLS(0.152)PS(0.848)PTTEDPR;MPTQSEEEKLS(0.13)PS(0.866)PT(0.005)TEDPR 141.5 1.15E-07 847660000 2182400 2030100 2089200 2386600 1451810 2380600 2488700 2506400 1629270 TRUE FALSE 2079242.277 2236969.498 2184991.887 2146694.434 1705005.204 2298159.225 2109003.107 2286926.329 1881928.87 1.104846368 1.188657836 1.161038507 1.140688401 0.905988123 1.221172203 1.120660371 1.215203382 1 20.84378067 -1.09298084 4.157804681 0.999977459 1.13309878 0.179747202 0.088791451 1.71E-05 3.73E-06 0.079232904 0.018672213 0.080727064 1.09298084 0.133121321 MPVWYIMDEFGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MPVWYIMDEFGSR 13 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 188.28 1.45E-05 196332000 250312 210337 261781 229981 218649 220209 267961 279876 256918 FALSE TRUE 238480.2478 231770.5794 273783.9178 206862.8729 256781.3164 212583.1071 227078.628 255368.5737 296759.5313 0.803614451 0.781004669 0.922578347 0.697072381 0.865284142 0.716348035 0.765194051 0.860523578 1 18.17893484 0.929447978 4.150182014 0.999877597 0.791483323 0.504852831 0.06515067 0.240891657 10.66326774 0.055711977 0.014215001 8.500568635 -0.929447978 -0.208394274 MQAQWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MQAQWER 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 133.9 0.0075065 327540000 426930 324830 268660 289750 429430 295950 451340 331300 448910 FALSE TRUE 406749.865 357930.5463 280978.3267 260623.7795 504322.456 285701.1773 382479.7936 302289.6157 518524.6701 0.784436862 0.690286436 0.541880344 0.502625612 0.972610341 0.550988591 0.737630851 0.5829802 1 18.9840531 -1.274827494 4.217375553 1.000264358 0.678270196 0.352673531 0.139964107 6059391203 1041905836 17040605.18 0.029917452 0.053109536 1.274827494 -0.321994162 MQAS(ph)IEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK 133.23 0.0034533 6545380000 11024570 12420090 11610980 13421880 8154690 12748840 13534290 14067730 10145070 TRUE FALSE 10503460.42 13685711.29 12143354.92 12072687.12 9576865.354 12307344.47 11469385.49 12835884.98 11718315.64 0.896328512 1.167890652 1.036271363 1.030240821 0.817256135 1.050265657 0.978757173 1.095369452 1 23.48226188 -1.837352739 6.153278557 0.998836826 1.011653556 0.000214152 0.097771385 0.001619922 4.28E-05 0.098294078 0.021066434 0.014542774 1.837352739 0.012816729 SFVKPPSLANLDKVNSNS(ph)LDLPSSSDTTHASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFVKPPSLANLDKVNSNSLDLPSSSDTTHASK 32 2 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 SFVKPPSLANLDKVNS(0.006)NS(0.994)LDLPSSSDTTHASK 183.05 6.83E-20 161640000 204140 133760 162210 241210 546220 574460 492860 616630 403820 TRUE FALSE 194490.7068 147390.2961 169647.4889 216963.1125 641480.5951 554566.3062 417665.155 562634.6082 466442.3432 0.416966233 0.315988242 0.363705164 0.465144547 1.375262354 1.18892788 0.895427186 1.206225413 1 18.83133924 2.832274385 5.823774391 1.110639995 0.370624623 0.88913418 0.130367474 0.071629613 3.609481652 0.040337803 0.042845417 679.6328851 -2.832274385 -0.740015372 down MQASIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;; 131.06 0.0081485 240980000 754320 650370 580180 664020 636240 657820 853110 732160 683950 FALSE TRUE 718664.7885 716643.4424 606781.8269 597271.448 747200.0546 635039.5285 722952.4011 668048.189 790013.4729 0.90968675 0.907128128 0.768065163 0.756026914 0.945806724 0.803833796 0.915114015 0.845616198 1 19.59151773 -1.173086924 5.624137122 1.000003068 0.86272293 0.321933572 0.064918639 2.43E-06 3.58E-07 0.061195236 0.014423533 0.067129448 1.173086924 -0.137280139 MQES(ph)PKLPQQSYNFDPDTCDESVDPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MQESPKLPQQSYNFDPDTCDESVDPFK 27 1 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 MQES(0.942)PKLPQQS(0.039)Y(0.018)NFDPDTCDESVDPFK;MQES(1)PKLPQQSYNFDPDTCDESVDPFK;MQES(1)PKLPQQSYNFDPDTCDESVDPFK 181.93 9.87E-18 163873000 556230 428040 487090 556800 255309 515980 510400 500050 212131 TRUE FALSE 529938.1102 471657.7626 509423.5583 500829.4061 299834.8088 498111.4832 432529.1059 456262.9711 245027.1921 2.162772653 1.924920082 2.07904908 2.043974801 1.223679732 2.032882469 1.765229003 1.862091171 1 17.90258234 -1.917626339 0.182774886 9.42E-15 2.164015723 0.580690576 0.247501376 24.60725177 0.678968216 11.96690251 0.82167307 0.012088535 1.917626339 2.164015723 MQFS(ph)FEEYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;MQFS(1)FEEYEK 145.52 3.18E-05 68677000 319963 235844 266917 319929 249520 317642 340547 287816 260664 TRUE FALSE 304838.9831 259876.7717 279155.4085 287769.1291 293036.209 306641.9779 288590.3006 262613.3052 301086.4418 1.012463335 0.863130104 0.927160342 0.955769138 0.973262719 1.018451631 0.9584965 0.872218967 1 18.19981822 3.117824997 4.32760872 0.966007228 0.930320644 0.064096899 0.051742082 0.551205006 18.18547363 0.015009842 0.018229232 1311.671242 -3.117824997 -0.035686584 MQFS(ph)FEGPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;MQFS(1)FEGPEK;MQFS(1)FEGPEK 146.79 2.94E-05 396713000 926770 763870 778910 1089810 831160 1070700 1126430 921120 837130 TRUE FALSE 882963.4188 841709.2214 814623.7939 980260.2283 976114.0408 1033621.391 954572.4152 840461.8496 966947.8449 0.913144823 0.870480477 0.842469217 1.013767426 1.009479514 1.068952577 0.987201554 0.869190468 1 19.88307855 3.232515166 24.99900918 0.996667597 0.879715327 0.520439989 0.052305615 109.4120864 452438.3505 0.014849166 0.018186889 1708.107367 -3.232515166 -0.116952271 MQHLIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 MQHLIAR 7 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;; 153.15 0.0017657 13872760000 10195660 9012820 6876622 7961230 10259140 8138090 11275960 9280020 9438560 FALSE TRUE 9713731.358 9931236.605 7191921.921 7160952.035 12048330.77 7856265.903 9555605.205 8467412.252 10902243.68 0.890984612 0.910935115 0.659673562 0.656832873 1.105123966 0.720610008 0.876480611 0.776666941 1 23.37812174 MQHLIAREAEAAIYHLQLFEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQHLIAREAEAAIYHLQLFEELRR 24 2 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 185.28 7.72E-18 59612000 15207 6690.2 10207 6384.5 15703 7130.1 47347 5084.4 3007.7 FALSE TRUE 14488.19525 7371.938986 10675.00105 5742.71793 18441.59823 6883.182849 40123.34556 4639.182982 3474.118755 4.170322395 2.121959411 3.072721976 1.652999893 5.308280899 1.981274486 11.54921532 1.335355326 1 11.76243135 5.072689673 18.38825924 3.995034222 7.976356534 0 3.139954228 4455.795562 1163390.398 0.732271081 23064.45568 118219.6511 -5.072689673 3.981322311 MQHNLEQQIQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MQHNLEQQIQAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 125.89 0.00023543 1071980000 2209520 1587810 1760190 2300840 1615810 2103090 2635670 2372790 1686830 FALSE TRUE 2105080.368 1749609.644 1840896.453 2069555.192 1897606.752 2030259.466 2233550.134 2165015.929 1948414.981 1.080406581 0.897965608 0.944817439 1.062173722 0.973923302 1.042005674 1.146342107 1.111167769 1 20.89386955 2.002422335 4.900735461 1.101038718 0.988969585 0.303737324 0.063768751 0.18269607 12.38134543 0.025700229 0.017015933 100.5593217 -2.002422335 -0.112069132 MQMLEDEDDLAYAETEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQMLEDEDDLAYAETEKK 18 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 191.59 3.49E-14 59258000 109650 92862 100300 119940 63488 111520 127220 130570 69863 FALSE TRUE 104467.0618 102324.7434 104898.8542 107883.4033 74560.2871 107658.0344 107810.2524 119136.5986 80696.99723 1.294559468 1.268011783 1.299910255 1.336894891 0.923953674 1.334102112 1.335988403 1.476344879 1 16.30022737 MQNGFGSPEPSLPGT(ph)PHSPAPPSGGTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 MQNGFGSPEPS(0.002)LPGT(0.566)PHS(0.432)PAPPSGGTWK 95.316 0.0062879 220940000 246090 197070 229870 246610 194270 244000 285330 267250 237200 TRUE FALSE 234457.8134 217151.657 240409.7669 221820.2943 228150.6265 235550.2188 241797.6681 243848.1732 273983.7646 0.855736156 0.792571258 0.877459901 0.80961109 0.832715861 0.859723273 0.882525534 0.890009573 1 18.06373088 0.757446754 0.602869451 1.002971996 0.827820843 0.819764552 0.023997533 0.420817622 0.322321582 0.024372857 0.009488614 5.720668129 -0.757446754 -0.175151153 MQNGFGSPEPSLPGTPHS(ph)PAPPSGGTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 MQNGFGSPEPSLPGT(0.022)PHS(0.978)PAPPSGGTWK;MQNGFGSPEPSLPGT(0.006)PHS(0.994)PAPPSGGTWK;MQNGFGSPEPSLPGT(0.01)PHS(0.989)PAPPSGGTWK 205.03 1.90E-25 688660000 705950 570080 629500 696530 574590 637760 746000 713410 592590 TRUE FALSE 672581.1426 628171.8001 658363.1977 626513.4811 674798.3141 615674.2113 632183.9988 650940.0384 684485.8307 0.982607838 0.917727982 0.961836123 0.91530526 0.985847017 0.899469622 0.923589606 0.950991254 1 19.38466115 0.970488546 21.59861659 1.000000001 0.939697292 0.291477789 0.028706532 666.3381189 487676.6645 0.025415668 0.006353917 9.343047271 -0.970488546 -0.060302709 MQPLHIQIKS(ph)PQESTGDPGNSSSVSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQPLHIQIKSPQESTGDPGNSSSVSEGK 28 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 MQPLHIQIKS(1)PQESTGDPGNSSSVSEGK 199.29 2.91E-25 73994000 163790 118340 182360 166710 105810 185650 214200 207540 133110 TRUE FALSE 156047.9713 130398.9805 190721.3864 149951.9941 124263.2305 179220.8939 181519.8559 189366.6974 153752.019 1.014932827 0.848112314 1.240448013 0.975284715 0.80820552 1.165649044 1.180601446 1.231637143 1 17.23024583 2.191599006 24.87356516 1.161999799 0.975040183 0.291898877 0.127988693 129.723909 68708.35731 0.045735424 0.033777946 155.4529635 -2.191599006 -0.186959616 MQQNIQELEEQLEEEESAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 242.91 4.59E-24 43472000 53638 45714 47163 64434 56727 53925 62163 58717 62423 FALSE TRUE 51102.63804 50372.30857 49325.4702 57956.9719 66620.17084 52057.56373 52678.89265 53575.4282 72103.24003 0.708742603 0.698613662 0.684095058 0.803805375 0.923955301 0.72198647 0.730603682 0.743037736 1 16.13777647 -5 0.230289527 2.344001213 0.717860902 0.55821687 0.069272189 129.2346025 1.292414322 81.16778121 0.124209821 1.00E-05 5 -1.626140312 MQQQLDEYQELLDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 161.63 3.82E-06 21629000 25346 19487 21122 23137 19828 25260 28011 23973 19574 FALSE TRUE 24147.94481 21472.74745 22090.46459 20811.2248 23285.99692 24385.23987 23737.40749 21873.79703 22609.43595 1.068047202 0.94972504 0.977046249 0.920466342 1.029923832 1.078542601 1.049889415 0.96746319 1 14.46463738 2.515967475 24.85990447 1.035009205 0.982928012 0.173779942 0.047362028 773.7732991 495180.2103 0.015269053 0.014393186 328.0707225 -2.515967475 -0.052081193 MQRPS(ph)LPDLSRPNTTSSTGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MQRPSLPDLSRPNTTSSTGMK 21 2 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 MQRPS(1)LPDLSRPNTTSSTGMK;MQRPS(1)LPDLSRPNTTSSTGMK;MQRPS(1)LPDLSRPNTTSSTGMK 166.22 7.14E-12 715140000 689720 570170 572450 689390 509780 695140 835430 735490 690890 TRUE FALSE 657118.3025 628270.9712 598697.3987 620091.2074 598685.4706 671067.1275 707969.8098 671086.5965 798029.6926 0.823425881 0.787277688 0.750219452 0.777027739 0.750204505 0.840904961 0.887147203 0.840929357 1 19.6060829 1.031107414 0.695006009 0.995344859 0.781636715 0.798660682 0.033375293 0.333373178 0.374914828 0.034113141 0.013648496 10.74255075 -1.031107414 -0.213708145 MQS(ph)LQLDCVAVPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MQSLQLDCVAVPSSR 15 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 1 MQS(1)LQLDCVAVPSSR;MQS(1)LQLDCVAVPSSR 94.01 0.004863 60804000 65815 62324 67429 75276 71346 60197 77976 68472 82416 TRUE FALSE 62704.05538 68674.88646 70520.68635 67709.11346 83788.71981 58112.3628 66079.32907 62476.22869 95196.65236 0.658679206 0.721400225 0.740789561 0.711255194 0.880164562 0.610445445 0.694135008 0.656285984 1 16.53862322 -1.373464006 3.962007279 1.000962051 0.707895546 0.621830981 0.071277208 430.2608004 35324532.48 49023.34006 0.015657234 0.042319058 1.373464006 -0.293066505 MQS(ph)LSLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.967)LS(0.033)LNK;MQS(1)LSLNK;MQS(1)LSLNK 131.83 0.0010368 674870000 922220 735560 832710 1112730 775260 1040890 1289380 1011850 755400 TRUE FALSE 878628.4883 810514.4003 870890.5772 1000876.266 910465.0985 1004843.718 1092661.4 923247.0498 872543.574 1.006973766 0.928909942 0.998105542 1.147078835 1.043460895 1.151625831 1.252271442 1.058109964 1 19.73486765 3.312423821 4.585844569 1.130137233 0.967567095 0.395317975 0.073501743 0.168309991 6.646296942 0.020659467 0.027950342 2053.164853 -3.312423821 -0.162570138 MQSLDKDIVALMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MQSLDKDIVALMVR 14 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 128.06 6.92E-05 224680000 395800 358450 356960 391450 351650 353920 464310 403240 391730 FALSE TRUE 377091.3184 394976.4625 373326.9691 352100.7023 412977.6487 341663.6617 393470.9819 367930.1679 452477.4877 0.833392442 0.872919589 0.825073024 0.778161813 0.912703195 0.755095382 0.869592394 0.813145798 1 18.78748649 -1.724903903 2.601605897 1.031600881 0.835787684 0.567963266 0.045829052 8021560.492 6291862.461 1644278.33 0.010414489 0.018840659 1.724903903 -0.195813197 MQSLS(ph)LNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.007)LS(0.993)LNK 88.596 0.015213 106570000 177810 134530 135470 221400 117480 200170 227530 177200 125870 TRUE FALSE 169405.2737 148238.7599 141681.4335 199144.4514 137968.4748 193238.0627 192816.1196 161683.4286 145389.2767 1.165184101 1.019598992 0.974497134 1.369732733 0.948959083 1.329108082 1.326205921 1.112072584 1 17.14956134 3.259412486 24.99983988 1.205289675 1.061929018 0.130090911 0.14667795 399.1359137 478531.3231 0.038133975 0.051579441 1817.240831 -3.259412486 -0.143360657 MRDAGDPS(ph)PPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 109.1 0.00098956 633040000 898160 777250 812900 919900 664130 891470 1037540 971820 779640 TRUE FALSE 855705.7568 856452.6587 850172.2691 827429.9043 779954.0617 860598.1704 879244.2173 886722.2889 900542.5894 0.950211314 0.951040705 0.944066698 0.918812629 0.866093476 0.955644053 0.976349401 0.984653363 1 19.78043498 1.789398047 3.099283113 0.987028359 0.931181425 0.53742391 0.025321775 0.221501883 4.050241165 0.015026073 0.007420578 61.57409643 -1.789398047 -0.055846934 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 286.06 4.96E-78 1998910000 1195130 787300 1119860 1089600 1120010 1121670 1698130 1377350 626510 FALSE TRUE 1138638.573 867526.7651 1171206.689 980071.3379 1315339.389 1082826.287 1439049.08 1256741.932 723665.971 1.57343114 1.198794471 1.618435488 1.354314528 1.817605694 1.496306763 1.988554302 1.736632621 1 19.46496441 2.747465224 24.48927493 1.685174671 1.422033774 0.045173574 0.285438655 817.7437967 2248941.34 0.07885371 0.082467691 559.0687589 -2.747465224 -0.263140897 MREDYDS(ph)VEQDGDEPGPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR;MREDYDS(1)VEQDGDEPGPQR 207.11 5.05E-16 1047790000 608940 535460 573180 639990 729370 600660 714800 639940 765340 TRUE FALSE 580156.613 590023.9828 599460.87 575656.9893 856571.8971 579858.9936 605744.1318 583903.4611 884025.0184 0.656267188 0.667429055 0.678103965 0.65117726 0.968945312 0.655930524 0.685211526 0.660505584 1 19.75372767 -2.234237681 2.211988051 1.99103045 0.699463437 0.488839612 0.095403432 4171996.893 812176.5176 20630223.07 0.022467356 0.005831259 2.234237681 -1.291567013 MREDYDSVEQDGDEPGPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 242.79 1.82E-24 2135120000 671655 592202 607720 720422 722468 644064 747032 680328 801161 FALSE TRUE 639907.1992 652548.0571 635584.5631 648003.8118 848466.1905 621759.9022 633058.5482 620754.8737 925400.9561 0.691491829 0.7051517 0.686820733 0.700241131 0.916863317 0.671881629 0.684091089 0.670795583 1 19.81971906 -1.375603607 3.71015035 1.001370283 0.713956254 0.603030603 0.072420787 1479153.971 34140391 85161.80304 0.01630896 0.042111081 1.375603607 -0.28741403 MREEFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MREEFDK 7 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;; 153.04 0.0016173 902147000 1346930 1327650 1199220 1507900 907040 1349150 1280370 1314640 954260 FALSE TRUE 1283263.288 1462939.044 1254205.423 1356323.027 1065227.489 1302428.597 1085026.041 1199523.152 1102241.767 1.164230323 1.327239711 1.137867808 1.230513185 0.966419093 1.181617896 0.984381171 1.088257756 1 20.07200927 2.755256949 24.56789653 1.049744864 1.22375561 0.542757738 0.07763053 455.945601 670902.6878 0.021596119 0.02284497 569.1895903 -2.755256949 0.174010746 MREESGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 137.05 0.00069763 524622000 229583 182115 212418 231347 278012 228920 280164 239377 312841 FALSE TRUE 218731.0666 200672.7255 222157.5754 208091.56 326497.2048 220992.443 237419.8362 218415.8809 361354.7845 0.605308345 0.555334353 0.61479074 0.575864964 0.90353641 0.611566395 0.657026962 0.604436112 1 18.46305647 -5 0.215328683 2.77676128 0.586972113 0.570938443 0.097523465 107.1133587 1.069797923 82.54056005 0.187364136 1.00E-05 5 -2.189789167 MREHLELFWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MREHLELFWSR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 72.265 0.028101 200940000 169940 103670 133290 157300 184280 197220 210900 203910 183110 FALSE TRUE 161907.273 114234.0909 139401.4783 141487.9051 216418.3737 190390.2219 178723.3316 186054.5594 211505.7636 0.765498161 0.540099187 0.659090684 0.668955317 1.023226838 0.900165644 0.845004545 0.879666616 1 17.69033745 2.806300004 7.604281117 0.911255112 0.649563573 0.7573884 0.075821081 0.145701214 14.68434227 0.022858613 0.024238743 640.1769068 -2.806300004 -0.261691539 MREIVHLQAGQCGNQIGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MREIVHLQAGQCGNQIGAK 19 1 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0R2T4;P04350;M0QYM7;M0R042 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ; 99.092 0.00051172 1914550000 1853200 866860 2195300 1325300 1904980 1896340 2980200 2131000 2630000 FALSE TRUE 1765602.909 955194.0195 2295956.676 1192078.326 2237207.909 1830669.27 2525515.755 1944398.343 3037846.968 0.581202058 0.31443125 0.755784179 0.392408946 0.73644523 0.602620636 0.831350552 0.640058029 1 21.53461776 1.481896365 0.310669931 1.034174478 0.41639175 0.50288901 0.141028917 1.005164668 0.347006955 0.233137321 0.201684202 30.33167301 -1.481896365 -0.617782728 MRIPNYQLS(ph)PTKLPSINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MRIPNYQLSPTKLPSINK 18 2 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 MRIPNYQLS(0.99)PT(0.009)KLPS(0.001)INK 60.032 0.037016 355690000 185430 136450 185000 167240 168460 188050 247650 239950 237630 TRUE FALSE 176665.0914 150354.4101 193482.433 150428.7175 197839.3707 181537.7813 209866.4441 218938.7059 274480.4468 0.643634523 0.547778218 0.704904248 0.548048938 0.720777647 0.661386935 0.764595244 0.797647732 1 18.06634385 1.025965822 0.529744258 1.009177951 0.599661803 0.834875513 0.053192419 0.312551654 0.219693529 0.051528788 0.024275762 10.61612006 -1.025965822 -0.409516148 MRKET(ph)PPPLVPPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MRKETPPPLVPPAAR 15 2 Q9BQA1;Q9BQA1-2 Q9BQA1 WDR77 Methylosome protein 50 1 MRKET(1)PPPLVPPAAR;MRKET(1)PPPLVPPAAR 108.49 0.051218 752120000 325350 263733 303580 329360 280525 313740 394630 350450 346550 TRUE FALSE 309971.3503 290607.6925 317499.4433 296252.1071 329448.4712 302875.1051 334421.9456 319762.7401 400291.2041 0.77436463 0.725990703 0.793171172 0.740091474 0.82302201 0.756636923 0.83544665 0.798825297 1 18.61069039 -3.351145197 0.206182741 1.499301618 0.736629909 0.852656211 0.029508579 20.29972853 0.371530313 4.352935987 0.059056633 0.000445507 3.351145197 -0.762671709 MRPFEGFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MRPFEGFQR 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 175.93 0.00088147 390590000 509870 445300 381420 487050 564410 424150 639820 516410 601370 FALSE TRUE 485769.4556 490676.5763 398908.4843 438090.8087 662842.9253 409461.5791 542203.7079 471190.4027 694627.3882 0.699323787 0.70638818 0.57427693 0.630684618 0.954242428 0.589469385 0.780567707 0.67833548 1 19.40587977 -5 0.257078517 2.883656771 0.67872261 0.435759788 0.107276304 175.2709776 1.726319404 174.017505 0.132404033 1.00E-05 5 -2.204934162 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR 32 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 220.78 5.82E-36 138180000 54574 43561 49366 54802 52028 49893 57918 54658 55243 FALSE TRUE 51994.39518 47999.91542 51629.47993 49293.19884 61101.66673 48165.1929 49081.54536 49871.85576 63809.8023 0.81483398 0.752234198 0.809115184 0.772501984 0.957559255 0.754824356 0.76918504 0.781570448 1 15.96149044 -1.357964902 3.009789684 1.002349345 0.797672761 0.524973153 0.059249172 13714386.3 17500066.48 285804.9967 0.013335878 0.043856614 1.357964902 -0.204676584 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK 41 2 A0A2R8Y5Y7;P32969;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;; 316 3.65E-114 625914000 525854 416006 481649 545072 345466 540844 637586 591669 424066 FALSE TRUE 500997.9236 458397.4844 503733.0831 490280.327 405715.161 522114.4367 540310.5456 539859.3257 489827.9895 1.022803789 0.935833587 1.028387707 1.000923462 0.828280886 1.065913847 1.103061804 1.102140624 1 18.90191569 2.032525522 24.99998122 1.081011206 0.967720898 0.398603353 0.063045672 166.2976531 127820.1591 0.021964683 0.016221881 107.7768589 -2.032525522 -0.113290307 MRS(ph)PQPARPGSAAVPGAAFAPIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MRSPQPARPGSAAVPGAAFAPIPR 24 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 MRS(1)PQPARPGSAAVPGAAFAPIPR;MRS(1)PQPARPGSAAVPGAAFAPIPR;MRS(1)PQPARPGSAAVPGAAFAPIPR;MRS(1)PQPARPGSAAVPGAAFAPIPR 143.19 1.30E-07 2074800000 1216800 1084130 1108340 1243530 1142100 1120340 1323740 1242410 1278990 TRUE FALSE 1159284.275 1194604.08 1159158.485 1118528.002 1341281.878 1081542.345 1121779.151 1133617.994 1477329.237 0.784716261 0.808624137 0.784631114 0.757128454 0.907909926 0.732092967 0.759329148 0.767342828 1 20.49455995 -2.124506373 2.428062077 1.426466071 0.787410034 0.665268711 0.047320917 4257802.994 1054347.102 10031118.76 0.010703466 0.00750747 2.124506373 -0.639056037 MRVSS(ph)GER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MRVSSGER 8 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 MRVS(0.021)S(0.979)GER;MRVS(0.012)S(0.988)GER 120.06 0.0038436 240190000 222082 170102 182323 196657 245976 203767 301121 217297 333937 TRUE FALSE 211584.624 187435.5872 190682.6899 176888.6647 288874.1365 196710.4977 255179.461 198269.3227 385722.2444 0.54854141 0.485934088 0.494352329 0.458590779 0.748917494 0.509979656 0.66156273 0.514020971 1 18.55720282 -5 0.216599937 3.241354695 0.492612943 0.724517686 0.087166457 72.49152366 0.724308561 70.69240934 0.155163782 1.00E-05 5 -2.748741752 MS(ph)ADMSEIEAR ddPTM_SK-BR-3_Trastuzumab_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(0.995)ADMS(0.005)EIEAR 139.77 4.08E-05 74920000 121370 112660 119600 115020 126830 111920 132040 111660 132480 TRUE FALSE 115633.0806 124140.1821 125083.7783 103457.9711 148949.1118 108044.1823 111894.8729 101882.4585 153024.3218 0.755651646 0.811244779 0.817411094 0.676088414 0.973368874 0.706058887 0.731222799 0.665792583 1 17.22340145 MS(ph)FVLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSFVLSR 7 0 F8VV96;Q8N9I9 F8VV96 DTX3 Probable E3 ubiquitin-protein ligase DTX3 1 MS(1)FVLSR 85.89 0.021482 154140000 30891 27390 33233 23590 35460 32901 40014 32377 38838 TRUE FALSE 29430.84365 30181.07214 34756.76592 21218.68838 41644.21277 31761.63012 33909.12939 29541.89824 44860.79868 0.656048143 0.672771619 0.774769218 0.472989537 0.928298514 0.708004116 0.755874402 0.65852368 1 15.45316769 -4.999999999 0.19837604 2.328954605 0.6538592 0.402583637 0.113749198 130.6481102 1.290261204 68.82007347 0.24510302 1.00E-05 4.999999999 -1.675095405 MS(ph)GFIYQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK 162.26 6.70E-05 8112308000 13990630 12268430 11597710 14323760 8348680 13811710 13915670 14847840 9519740 TRUE FALSE 13329320.65 13518596.97 12129476.48 12883908.43 9804687.149 13333407.02 11792578.96 13547684.42 10996012.66 1.212195826 1.229409003 1.10307953 1.171689123 0.891658409 1.212567449 1.072441377 1.232054276 1 23.39047714 3.734998582 22.68009653 1.100529703 1.22080243 0.208056433 0.099773006 110.6232783 704369.0279 0.023597154 0.038318994 5432.485576 -3.734998582 0.120272727 MS(ph)GFIYQGKLPTTGMTITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(1)GFIYQGKLPTTGMTITK;MS(1)GFIYQGKLPTTGMTITK 179.47 2.16E-14 1063250000 1481563 622140 1432230 1141052 1333728 1442020 2457080 1653870 1837290 TRUE FALSE 1411532.453 685536.7733 1497899.162 1026351.285 1566329.741 1392082.486 2082207.319 1509048.375 2122207.55 0.665124603 0.323030032 0.705821239 0.483624368 0.738066237 0.655959633 0.981151593 0.711074831 1 21.01713433 2.194978994 0.857170687 0.928661747 0.511307326 0.525883684 0.138206175 0.409556213 0.568177511 0.099245923 0.056088956 156.6675292 -2.194978994 -0.417354421 MS(ph)PMGTASGSNSPTSDSASVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 MS(1)PMGTASGSNSPTSDSASVQR;MS(0.748)PMGT(0.252)ASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(0.98)PMGT(0.015)AS(0.004)GSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR 491.77 9.67E-251 949669000 563697 517078 551074 638034 502892 567166 642526 557142 528939 TRUE FALSE 537052.1599 569768.8361 576341.288 573897.6101 590596.2056 547524.8992 544496.8579 508355.6929 610964.1587 0.879024002 0.932573258 0.943330766 0.939331059 0.966662606 0.896165334 0.891209165 0.832054852 1 19.22072822 -0.137973526 7.673274622 0.999999999 0.911622674 0.350522147 0.038428622 0 0 0.037075388 0.008738753 0.72782417 0.137973526 -0.088377326 MS(ph)SHTETSSFLQTLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSSHTETSSFLQTLTGR 17 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 MS(0.997)S(0.003)HTETSSFLQTLTGR;MS(0.991)S(0.009)HTETSSFLQTLTGR 325.06 2.36E-59 94386000 101184 94713 85469 99829 83893 91241 90204 98379 77600 TRUE FALSE 96401.23285 104364.3624 89387.83819 89793.99926 98523.91264 88081.30129 76441.72309 89764.41322 89633.81167 1.075500763 1.164341451 0.997255796 1.001787133 1.099182449 0.982679411 0.852822408 1.001457057 1 16.45175543 2.838777896 0.764504445 0.93772638 1.114212023 0.342017654 0.066844096 0.57878108 0.742391452 0.044493984 0.047963809 689.8868963 -2.838777896 0.176485643 MS(ph)SPLADAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.506)S(0.494)PLADAK 68.626 0.057929 0 51824 47021 46164 62693 47040 52814 60385 60077 61483 TRUE FALSE 49374.38223 51812.49336 48280.66506 56390.98053 55243.76111 50985.03794 51172.1592 54816.33939 71017.46963 0.695242769 0.729573915 0.679842091 0.794043787 0.777889742 0.71792248 0.720557343 0.771871198 1 16.11588634 -5 0.291471431 3.114239545 0.716561454 0.858780128 0.034040016 88.67732633 0.832976099 114.0349237 0.035854595 1.00E-05 5 -2.397678091 MSADMS(ph)EIEAR ddPTM_SK-BR-3_Trastuzumab_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(0.382)ADMS(0.618)EIEAR 132.86 0.0011553 0 38613 37813 39324 47474 42849 40203 43635 47826 48984 TRUE FALSE 36787.84001 41666.18769 41127.0443 42701.82333 50321.85203 38810.76003 36977.67934 43638.1019 56580.18854 0.650189421 0.736409488 0.726880651 0.754713344 0.889389967 0.685942572 0.653544647 0.771261161 1 15.78800936 -2.351846634 1.294506328 1.781071665 0.726337635 0.597493247 0.068505953 32889.33747 3515.062228 74349.74396 0.019853402 0.004447883 2.351846634 -1.05473403 MSAEINEIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSAEINEIIR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 171.33 9.43E-06 56960000 105840 94548 98879 104042 120885 89151 111676 105330 129690 FALSE TRUE 100837.153 104182.5487 103412.7 93583.50049 141967.3057 86063.67852 94637.77513 96106.74681 149801.6628 0.673137741 0.695469908 0.690330788 0.624716033 0.947701801 0.574517511 0.631753836 0.641559947 1 17.19269411 -1.033057311 4.261149338 1.000023243 0.682615483 0.495283423 0.099941832 27935192.03 52788088.96 9200.822489 0.022385911 0.092670752 1.033057311 -0.31740776 MSATFIGNSTAIQELFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSATFIGNSTAIQELFKR 18 1 P68371;Q13885;Q9BVA1 P68371;Q13885;Q9BVA1 TUBB4B;TUBB2A;TUBB2B Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 ; 249.47 1.82E-24 262420000 372460 207506 368210 285090 359550 349700 520040 424300 476720 FALSE TRUE 354854.5539 228651.0973 385092.7927 256432.2116 422255.4062 337589.8013 440698.3468 387146.0426 550647.3029 0.644431657 0.415240565 0.699345644 0.465692305 0.766834604 0.613078098 0.800327804 0.703074437 1 19.07076902 1.108259688 0.371297232 1.025706876 0.51867127 0.60449309 0.104201387 0.789095284 0.321762286 0.150418426 0.089757774 12.83097588 -1.108259688 -0.507035606 MSCFSRPS(ph)MS(ph)PTPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MS(0.004)CFS(0.006)RPS(0.99)MS(0.5)PT(0.5)PLDR;MS(0.007)CFS(0.009)RPS(0.984)MS(0.947)PT(0.052)PLDR;MS(0.013)CFS(0.014)RPS(0.973)MS(0.86)PT(0.14)PLDR;MSCFS(0.005)RPS(0.995)MS(0.559)PT(0.441)PLDR;MS(0.006)CFS(0.009)RPS(0.986)MS(0.636)PT(0.363)PLDR;MSCFS(0.014)RPS(0.986)MS(0.982)PT(0.018)PLDR;MS(0.006)CFS(0.008)RPS(0.936)MS(0.836)PT(0.213)PLDR;MS(0.084)CFS(0.143)RPS(0.745)MS(0.605)PT(0.424)PLDR;MS(0.009)CFS(0.014)RPS(0.977)MS(0.5)PT(0.5)PLDR 187 1.69E-08 4523250000 2162350 1652886 1954647 2102685 2211610 2009505 2481300 2172216 2531800 TRUE FALSE 2060140.001 1821316.963 2044269.498 1891319.109 2597314.084 1939915.338 2102732.113 1982005.251 2924418.613 0.70446139 0.622796256 0.699034498 0.646733371 0.888147159 0.66335077 0.719025691 0.677743344 1 21.47971841 -5 0.279593781 3.189572319 0.678998293 0.622494697 0.072394558 142.7149783 1.367036531 181.3749507 0.077251938 1.00E-05 5 -2.510574026 MSCFSRPS(ph)MSPT(ph)PLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFS(0.001)RPS(0.998)MS(0.248)PT(0.753)PLDR 113.88 0.00097154 104170000 185460 137540 166780 179550 188750 173320 218990 192860 206130 TRUE FALSE 176693.6733 151555.4824 174427.028 161501.2929 221667.9402 167317.8849 185579.0535 175972.156 238095.5876 0.742112339 0.636532091 0.732592442 0.678304434 0.931003982 0.702734085 0.77943088 0.73908197 1 17.86118136 -5 0.162973402 1.997024501 0.667419853 0.541508577 0.075796852 95.1727248 0.8820472 30.63539695 0.28308992 1.00E-05 5 -1.329604648 MSCFSRPSMS(ph)PTPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPSMS(0.991)PT(0.009)PLDR;MSCFSRPS(0.011)MS(0.805)PT(0.184)PLDR;MSCFSRPS(0.005)MS(0.498)PT(0.498)PLDR;MSCFSRPS(0.054)MS(0.805)PT(0.141)PLDR;MSCFSRPSMS(0.968)PT(0.031)PLDR;MSCFSRPSMS(0.979)PT(0.02)PLDR;MS(0.006)CFS(0.002)RPS(0.083)MS(0.894)PT(0.015)PLDR;MSCFS(0.001)RPS(0.011)MS(0.982)PT(0.006)PLDR;MSCFSRPS(0.077)MS(0.912)PT(0.011)PLDR;MSCFSRPS(0.175)MS(0.814)PT(0.01)PLDR;MS(0.001)CFS(0.003)RPS(0.269)MS(0.72)PT(0.007)PLDR;MS(0.023)CFS(0.023)RPS(0.252)MS(0.686)PT(0.015)PLDR;MSCFSRPS(0.001)MS(0.734)PT(0.265)PLDR;MSCFSRPS(0.069)MS(0.93)PT(0.002)PLDR;MSCFSRPS(0.274)MS(0.722)PT(0.004)PLDR;MSCFSRPS(0.008)MS(0.991)PT(0.001)PLDR 221.99 6.09E-15 14816350000 5915889 4214855 5240466 5283619 5792068 5127507 6565174 5794873 6735451 TRUE FALSE 5636256.651 4644353.516 5480746.55 4752499.58 6802202.825 4949940.147 5563536.129 5287443.2 7779950.341 0.724459207 0.596964417 0.704470634 0.610865028 0.87432471 0.636243154 0.715112036 0.679624286 1 22.89132952 -5 0.304531413 3.667506129 0.672720107 0.605744276 0.077685476 176.3733724 1.615833094 300.9934175 0.067916758 1.00E-05 5 -2.994786022 MSCFSRPSMSPT(ph)PLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPSMS(0.18)PT(0.82)PLDR;MSCFSRPS(0.012)MS(0.159)PT(0.828)PLDR;MSCFSRPS(0.008)MS(0.112)PT(0.88)PLDR 184.66 2.89E-09 5871800000 1558950 1031970 1252660 1252840 1346280 1208130 1543540 1396670 1546830 TRUE FALSE 1485261.523 1137128.916 1310095.7 1126902.143 1581070.806 1166292.155 1308044.624 1274370.171 1786704.496 0.83128549 0.636439276 0.733246993 0.630715457 0.884908953 0.652761639 0.732099027 0.713251785 1 20.76886962 -1.612305664 2.597328548 1.027126956 0.724285444 0.528611333 0.081034953 9167478.91 8104209.829 1683779.047 0.017410921 0.024417114 1.612305664 -0.302841512 MSDT(ph)GSPGMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MSDT(0.743)GS(0.256)PGMQR;MSDT(0.954)GS(0.046)PGMQR;MSDT(0.684)GS(0.316)PGMQR;MS(0.004)DT(0.498)GS(0.498)PGMQR;MS(0.013)DT(0.532)GS(0.455)PGMQR;MS(0.008)DT(0.496)GS(0.496)PGMQR;MS(0.002)DT(0.802)GS(0.196)PGMQR;MS(0.001)DT(0.728)GS(0.271)PGMQR 185.9 4.77E-05 972372000 1680054 1388682 1443491 1683399 1558534 1507966 1768217 1527322 1622727 TRUE FALSE 1600641.177 1530190.275 1509676.49 1514180.534 1830341.836 1455744.759 1498443.021 1393581.589 1874371.215 0.853961672 0.816375253 0.805430897 0.80783386 0.976509787 0.776657658 0.799437704 0.743492846 1 20.83797527 2.520132412 0.00927528 1.668188769 3.21E-06 0.110702325 0.078362441 8569.211718 36.90111117 3248.818959 3384.781925 331.2320954 -2.520132412 -1.668185558 MSDTGS(ph)PGMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MSDT(0.182)GS(0.818)PGMQR;MSDT(0.263)GS(0.737)PGMQR;MS(0.012)DT(0.378)GS(0.61)PGMQR 173.72 1.24E-05 616664000 854980 720550 802930 882950 845080 806990 945670 842010 836250 TRUE FALSE 814566.7898 793974.8642 839745.1347 794194.1885 992461.6844 779043.734 801390.6731 768279.1406 965931.379 0.843296747 0.82197854 0.869363138 0.822205599 1.027466035 0.806520785 0.829655906 0.795376522 1 19.88156118 -2.095956686 2.151966604 1.241125353 0.850085403 0.334104271 0.065622825 9019974.46 2332058.335 10653819.34 0.015001008 0.00801758 2.095956686 -0.39103995 MSES(ph)PTPCS(ph)GSSFEETEALVNTAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 2 MS(0.08)ES(0.453)PT(0.453)PCS(0.254)GS(0.254)S(0.254)FEET(0.254)EALVNTAAK 85.248 0.0092734 27509000 24746 20446 22425 31126 22702 25173 33198 30687 23254 TRUE FALSE 23576.30562 22529.47065 23453.20843 27997.15534 26661.22161 24301.2527 28133.03538 27999.8836 26860.11156 0.877744144 0.838770554 0.873161244 1.042332058 0.992595342 0.904733871 1.047390861 1.04243363 1 14.71317768 3.293223191 7.141009039 1.002474147 0.85895962 0.717803886 0.041859568 0.110591919 11.703018 0.011541607 0.015570815 1964.369539 -3.293223191 -0.143514527 MSES(ph)PTPCSGSSFEETEALVNTAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.162)ES(0.757)PT(0.082)PCSGSSFEETEALVNTAAK;MS(0.023)ES(0.835)PT(0.141)PCSGSSFEETEALVNTAAK;MS(0.061)ES(0.467)PT(0.467)PCS(0.001)GS(0.001)S(0.002)FEETEALVNTAAK;MS(0.028)ES(0.969)PT(0.003)PCSGSSFEETEALVNTAAK;MS(0.032)ES(0.84)PT(0.126)PCS(0.001)GS(0.001)SFEETEALVNTAAK;MS(0.117)ES(0.723)PT(0.16)PCSGSSFEETEALVNTAAK;MS(0.053)ES(0.555)PT(0.384)PCS(0.004)GS(0.004)SFEETEALVNTAAK 287.05 4.48E-54 2684110000 1179805 1065236 1102921 1199779 864411 1139438 1306685 1327954 1098579 TRUE FALSE 1124037.956 1173784.759 1153491.019 1079174.935 1015164.005 1099978.976 1107326.204 1211671.308 1268941.021 0.88580788 0.925011281 0.909018623 0.850453187 0.800008817 0.866847993 0.872638039 0.954868105 1 20.27519358 1.092139502 3.362247458 0.99880961 0.876160911 0.636337239 0.033684755 0.160852991 3.447494579 0.035732873 0.009384572 12.36344504 -1.092139502 -0.122648699 MSESPT(ph)PCSGSSFEETEALVNTAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.031)ES(0.404)PT(0.56)PCS(0.003)GS(0.001)SFEETEALVNTAAK;MS(0.044)ES(0.408)PT(0.546)PCS(0.001)GS(0.001)SFEETEALVNTAAK;MS(0.069)ES(0.388)PT(0.541)PCS(0.001)GS(0.001)SFEETEALVNTAAK;MS(0.047)ES(0.406)PT(0.533)PCS(0.007)GS(0.007)S(0.001)FEETEALVNTAAK 223.51 3.42E-33 1032330000 417506 366099 404304 418530 324031 394703 475112 458259 366893 TRUE FALSE 397771.3188 403404.9043 422841.7383 376458.5692 380541.9038 381034.3361 402624.9384 418131.4126 423788.8926 0.93860723 0.951900607 0.997765033 0.888316272 0.897951576 0.899113551 0.950060149 0.98665024 1 18.69298625 1.272887522 3.176828514 0.997626244 0.931869586 0.408447895 0.03159443 0.266914399 4.576085807 0.028618589 0.008430139 18.74508968 -1.272887522 -0.065756659 MSIPEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSIPEALRR 9 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 129.63 0.00061575 661420000 832700 566020 585440 526070 1295370 540560 860090 629770 1161910 FALSE TRUE 793339.9213 623698.0815 612283.0031 473188.4441 1521282.118 521840.2717 728867.4739 574624.0002 1342093.069 0.591121391 0.46472044 0.45621501 0.352574985 1.133514622 0.388825696 0.54308266 0.428155106 1 20.35605329 MSLKDWFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSLKDWFAK 9 1 O00267;O00267-2;M0QYL9 O00267 SUPT5H Transcription elongation factor SPT5 0 98.943 0.0051732 64533000 148200 102080 135280 156610 168000 170880 266900 208330 213140 FALSE TRUE 141194.8797 112482.0681 141482.7218 140867.2653 197299.1468 164962.3828 226179.503 190087.5208 246192.6626 0.57351376 0.456886354 0.574682934 0.572183036 0.801401409 0.670054018 0.918709358 0.772108798 1 17.90942824 2.240963128 0.569481199 0.962408876 0.489739342 0.788603543 0.078324984 0.319448749 0.210294594 0.064148568 0.049743577 174.1658999 -2.240963128 -0.472669534 MSLQTDEDEHSIEMHLPYTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSLQTDEDEHSIEMHLPYTAK 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 154.84 1.73E-08 89642000 159120 140540 147260 155320 124460 140430 162850 131720 5777.9 FALSE TRUE 151598.7129 154861.1858 154012.0167 139706.9385 146165.7846 135566.8739 138004.2416 120185.8985 6673.907223 22.71513641 23.20397641 23.07673924 20.93330546 21.90108129 20.3129695 20.67817801 18.00832623 1 12.70431592 0.005162104 0.582558504 9.51E-14 22.69601738 0.989239049 0.682601648 0.386407442 0.153161179 1.921616064 0.282202536 1.011957106 -0.005162104 22.69601738 MSPNETLFLES(ph)TNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MSPNETLFLESTNK 14 0 Q9HB90;Q9NQL2 Q9HB90 RRAGC;RRAGD Ras-related GTP-binding protein C;Ras-related GTP-binding protein D 1 MSPNETLFLES(0.987)T(0.013)NK;MSPNETLFLES(0.971)T(0.029)NK;MSPNETLFLES(0.95)T(0.05)NK 302.62 5.75E-44 114928000 285722 268814 245241 320429 176750 308062 274636 304068 193043 TRUE FALSE 272216.4873 296206.4522 256485.5424 288218.8681 207575.144 297393.7357 232735.2342 277442.194 222979.1225 1.220816031 1.328404421 1.150267072 1.292582305 0.930917396 1.333729061 1.043753476 1.244251887 1 17.76654911 3.778576048 0.02641819 6.61E-07 2.454212811 0.210352855 0.124753848 774.9010882 4.521932073 182.5663832 238.982772 6005.871663 -3.778576048 2.45421215 MSQPGS(ph)PSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 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(0.972)PS(0.026)PK;MSQPGS(0.992)PS(0.008)PK;MSQPGS(0.975)PS(0.025)PK;MSQPGS(0.998)PS(0.002)PK;MS(0.01)QPGS(0.979)PS(0.011)PK;MSQPGS(0.983)PS(0.017)PK;MS(0.021)QPGS(0.602)PS(0.377)PK;MSQPGS(0.98)PS(0.019)PK;MSQPGS(0.98)PS(0.02)PK;MSQPGS(0.969)PS(0.031)PK;MSQPGS(0.717)PS(0.283)PK;MSQPGS(0.984)PS(0.016)PK;MSQPGS(0.993)PS(0.007)PK;MSQPGS(0.934)PS(0.066)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.986)PS(0.014)PK;MSQPGS(0.964)PS(0.036)PK;MSQPGS(0.987)PS(0.013)PK;MS(0.004)QPGS(0.995)PS(0.001)PK 222.48 5.12E-09 22721160000 28475430 25053320 25733670 30024530 18714730 30109930 32513330 30574680 21270330 TRUE FALSE 27129452.86 27606281.79 26913584.22 27006407.2 21978572.99 29067215.57 27552824.36 27897398.93 24568824.14 1.104222681 1.123630567 1.095436398 1.099214478 0.894571627 1.183093477 1.121454743 1.135479613 1 24.55032548 -1.660568359 2.666412374 0.987840539 1.097726317 0.133295794 0.075475104 18459285.28 17403983.05 1543110.399 0.017068169 0.021849004 1.660568359 0.109885777 MSS(ph)HTETSSFLQTLTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSSHTETSSFLQTLTGR 17 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 MS(0.376)S(0.54)HT(0.082)ET(0.001)SSFLQTLTGR;MS(0.384)S(0.468)HT(0.148)ETSSFLQTLTGR 114.02 0.00024724 95528000 75928 64125 64062 75592 54312 62160 66685 63984 48935 TRUE FALSE 72339.03391 70659.4104 66999.30607 67993.34854 63783.9956 60007.38361 56510.9785 58381.22176 56523.58987 1.27980254 1.250087097 1.185333526 1.202919855 1.128449126 1.061634333 0.999776883 1.032864719 1 15.78656548 2.595723826 0.767116172 0.991874961 1.270284095 0.961078061 0.020067275 0.107692699 0.131826155 0.014463976 0.012043106 394.2065411 -2.595723826 0.278409134 MSS(ph)PEDDSDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.05)S(0.95)PEDDSDTKR 117.48 0.00044664 299580000 243490 233170 250260 288130 204070 301030 289980 299040 205740 TRUE FALSE 231980.7103 256930.2881 261734.6685 259166.625 239659.7434 290605.2556 245738.2252 272854.4723 237645.1084 0.976164466 1.081151175 1.101367793 1.09056158 1.008477494 1.222853934 1.034055474 1.14815943 1 17.85844918 4.507115931 1.931325875 1.090228217 0.966377508 0.212928237 0.065905195 0.640012302 3.593381385 0.01498352 0.120495812 32145.18513 -4.507115931 -0.123850709 MSS(ph)PLADAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.011)S(0.989)PLADAK;MS(0.008)S(0.992)PLADAK 155.26 7.73E-05 144720000 338280 373590 365940 446130 276010 385650 467000 452750 354360 TRUE FALSE 322290.1748 411659.2457 382718.711 401284.1648 324146.0566 372294.8438 395750.573 413104.8098 409312.339 0.787394232 1.00573378 0.935028521 0.980386191 0.791928378 0.909561741 0.96686695 1.009265469 1 18.64284263 1.592456299 3.180296151 1.001411221 0.905012904 0.282578528 0.0695204 0.292112059 6.884383513 0.044713276 0.018213743 39.12517552 -1.592456299 -0.096398318 MSSCVPRPPS(ph)HGGPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(1)HGGPTR 95.5 0.0022536 76054000 74906 56895 61596 65605 64640 62559 66540 52845 60373 TRUE FALSE 71365.34183 62692.66518 64420.23753 59010.26076 75913.19553 60392.56614 56388.10091 48217.61165 69735.3365 1.023374166 0.899008571 0.923781841 0.846203141 1.08859008 0.866025306 0.808601546 0.691437284 1 16.08960227 2.0099563 24.97046387 0.818388171 0.950468668 0.24946191 0.098781199 240.8859812 604140.9689 0.033686694 0.024851737 102.3190031 -2.0099563 0.132080497 MSSPEDDSDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 105.65 0.0032178 414960000 970520 991210 477870 1286000 559480 735250 703390 751840 507730 FALSE TRUE 924645.443 1092215.426 499780.8122 1156728.837 657053.1349 709788.1081 596074.9369 686004.9038 586466.1753 1.576638998 1.862367297 0.852190345 1.972370932 1.120359814 1.210279703 1.01638417 1.169726291 1 19.16168838 2.758921677 0.568633741 0.994419885 1.709950588 0.307792587 0.312832064 0.909601555 0.624446579 0.235964091 0.278324744 574.012932 -2.758921677 0.715530703 MSSYAFFVQTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 289.96 1.83E-27 935368000 1162010 752669 549265 610144 1147188 685057 1189047 945496 1066819 FALSE TRUE 1107084.09 829366.8268 574449.3435 548811.1659 1347257.224 661333.3043 1007636.042 862703.3579 1232255.842 0.898420646 0.673047592 0.46617701 0.445371121 1.093325897 0.536685063 0.817716587 0.700100846 1 20.23287039 2.765694521 24.97933679 0.794044824 0.651733949 0.200486535 0.19605335 1693.608711 1559124.907 0.058934778 0.062496409 583.0348579 -2.765694521 -0.142310874 MSVQPTVS(ph)LGGFEITPPVVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 MSVQPT(0.001)VS(0.999)LGGFEITPPVVLR;MSVQPTVS(1)LGGFEITPPVVLR 229.51 1.33E-25 74392000 59863 51194 50520 64795 50286 56444 67052 54580 57719 TRUE FALSE 57033.39463 56410.7268 52836.39197 58281.6835 59055.86248 54489.33013 56821.98591 49800.68585 66669.76773 0.855461127 0.846121544 0.792509015 0.874184589 0.885796733 0.817301934 0.852290143 0.746975541 1 16.02474508 -1.408684587 3.306606891 1.001790605 0.838066038 0.619979737 0.040765786 290895711.2 406612214.7 4969465.481 0.008963946 0.039022529 1.408684587 -0.163724567 MSVQPTVSLGGFEITPPVVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 181.58 1.16E-16 22064000 24323 22229 24145 29562 26305 23330 27494 30305 28976 FALSE TRUE 23173.29999 24494.16037 25252.07213 26590.3716 30892.58367 22522.07625 23299.28534 27651.33354 33469.45009 0.692371698 0.731836355 0.754481238 0.79446694 0.923008403 0.67291444 0.696135887 0.826166354 1 15.03055723 -5 0.34526067 3.773549631 0.743614335 0.51171894 0.07357442 351.0620143 2.914122389 719.3615002 0.058421183 1.00E-05 5 -3.029935296 MSWFVDLAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MSWFVDLAGK 10 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 87.323 0.030138 757430000 1109700 1028970 980830 1153600 714550 1068840 1142270 1179990 825810 FALSE TRUE 1057246.68 1133823.213 1025802.026 1037637.936 839167.2938 1031825.803 967995.7323 1076663.82 953872.3971 1.108373283 1.188652923 1.07540802 1.087816294 0.879747958 1.081723096 1.014806315 1.128729402 1 19.86343676 3.35354981 2.356108335 1.025895175 1.146506316 0.32312548 0.068921757 0.290702465 3.28125939 0.019148107 0.027835932 2257.094851 -3.35354981 0.120611141 MSYLTAMGADYLS(ph)CDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 MSYLTAMGADYLSCDSR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.995)CDS(0.005)R;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.999)CDS(0.001)R;MSYLTAMGADYLS(0.981)CDS(0.019)R;MSYLTAMGADYLS(0.999)CDS(0.001)R;MSYLTAMGADYLS(0.996)CDS(0.004)R;MSYLTAMGADYLS(0.996)CDS(0.004)R;MSYLTAMGADYLS(0.987)CDS(0.013)R;MSYLTAMGADYLS(0.985)CDS(0.015)R 271.82 1.35E-35 895414000 1591375 1287089 1614307 1639714 1724837 1545495 2041587 1769667 2075250 TRUE FALSE 1516153.858 1418244.832 1688324.573 1474886.833 2025648.027 1491974.121 1730105.407 1614705.576 2397069.171 0.632503173 0.591657867 0.704328683 0.615287557 0.845051971 0.622415965 0.721758649 0.673616596 1 21.19284011 -4.999999999 0.186521834 2.392632104 0.606477913 0.68252677 0.070388257 71.63845249 0.697125129 37.01912607 0.181073136 1.00E-05 4.999999999 -1.786154191 MTDFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTDFDR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 116.11 0.05549 538140000 1395200 1290100 1196700 1461700 1464100 1385800 1641400 1481800 1402700 FALSE TRUE 1329251.661 1421562.657 1251569.879 1314767.139 1719438.576 1337809.399 1390974.284 1352045.736 1620223.552 0.820412504 0.877386738 0.772467403 0.811472674 1.061235392 0.825694329 0.858507631 0.834480979 1 20.62776145 MTDQEAIQDLWQWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;;;;;;;; 360.32 4.15E-82 16288338000 10332537 8750307 8927239 10360384 10203160 8720007 11190128 9987155 10679360 FALSE TRUE 9844138.453 9641973.232 9336561.738 9318938.517 11982587.87 8418030.971 9482868.453 9112626.763 12335460.61 0.798035742 0.781646794 0.75688797 0.755459307 0.971393631 0.682425346 0.768748631 0.738734211 1 23.55630825 -1.131724475 3.970990498 1.000069552 0.781396035 0.46158783 0.074105461 7724381.046 4402869.488 4818.350394 0.015880294 0.073837252 1.131724475 -0.218673516 MTEEEVEMLVAGHEDS(ph)NGCINYEELVR ddPTM_SK-BR-3_Trastuzumab_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 202.3 2.72E-25 181958000 136896 105938 117630 129084 144159 125434 153146 133353 139530 TRUE FALSE 130425.1974 116733.2026 123023.4519 116108.2311 169300.284 121090.1891 129780.765 121675.9044 161167.5998 0.809251969 0.72429696 0.763326202 0.720419186 1.050461037 0.751330846 0.805253445 0.754965046 1 17.29820222 MTEEEVEMLVAGHEDSNGCINYEELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;; 352.84 2.90E-110 551330000 637474 499201 554748 606485 626964 532489 689305 621464 573458 FALSE TRUE 607341.8674 550070.1494 580183.7445 545519.9756 736306.3231 514048.7724 584138.8623 567045.3176 662386.9378 0.916898919 0.830436287 0.875898529 0.823566928 1.111595475 0.776055117 0.881869537 0.856063556 1 19.3373147 -1.349470812 3.411052612 1.000716966 0.881168811 0.141725448 0.089425502 5337982.103 3183783.364 26667.1705 0.018763589 0.044722821 1.349470812 -0.119548155 MTESWFSSLSRDPLELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTESWFSSLSRDPLELFR 18 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 144.68 8.80E-08 69292000 161300 106140 135620 140570 174560 138810 213180 166160 196070 FALSE TRUE 153675.6687 116955.7867 141838.3111 126439.6365 205003.2087 134002.9749 180655.4757 151610.1495 226475.5342 0.678553068 0.516416871 0.626285359 0.558292696 0.905189205 0.591688525 0.797682082 0.669432794 1 17.78899568 -1.694219688 0.166400517 1.41341824 0.526223899 0.513875501 0.107456581 24.58026847 0.665367227 4.544497634 0.455310228 0.020219961 1.694219688 -0.88719434 MTGLVDEAIDTKS(ph)LLDASEEAIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTGLVDEAIDTKSLLDASEEAIKK 24 2 P18206;P18206-2 P18206 VCL Vinculin 1 MTGLVDEAIDT(0.361)KS(0.639)LLDASEEAIKK 103.42 0.0016876 101540000 267360 66077 147340 238060 165520 169820 458630 229950 219710 TRUE FALSE 254722.4227 72810.32142 154095.6847 214129.7565 194386.6356 163939.0908 388657.5702 209814.359 253781.5047 1.003707591 0.286901607 0.607198247 0.843756352 0.765960608 0.645985179 1.531465308 0.82675197 1 17.95322741 1.766978764 25 1.169473565 0.674829112 0.380831384 0.253445926 17.99371724 15838.67416 0.110861599 0.061486744 58.47614898 -1.766978764 -0.494644453 MTGSAPPPS(ph)PTPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 MTGSAPPPS(0.998)PT(0.002)PNK 114.7 0.0011028 0 142680 147920 122920 174630 92428 133730 145070 141460 96773 TRUE FALSE 135935.7992 162993.2162 128556.0036 157075.8606 108547.4139 129098.8966 122936.9071 129073.0125 111780.0626 1.216100582 1.458160001 1.150079903 1.405222514 0.971080275 1.1549367 1.099810684 1.154705137 1 16.77030336 2.742863887 24.99564805 1.090196119 1.313636116 0.550028008 0.1034452 265.2691729 1540824.48 0.029128185 0.029904857 553.1767099 -2.742863887 0.223439997 MTGSEFDFEEMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 MTGSEFDFEEMKR 13 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;;;;;;;; 236.28 1.67E-16 7415060000 8304200 7085590 7625100 8974040 6382170 8537350 9662690 9014900 7164580 FALSE TRUE 7911676.923 7807619.677 7974718.377 8071952.45 7495218.427 8241699.429 8188469.173 8225507.565 8275626.475 0.956021511 0.943447569 0.963639236 0.975388688 0.90569801 0.995900365 0.989468193 0.993943793 1 22.9804371 2.148843084 25 0.993540877 0.950629641 0.613565611 0.018091867 13.13587345 3656.707999 0.006186933 0.004569352 140.8779695 -2.148843084 -0.042911236 MTNGFSGADLTEICQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MTNGFSGADLTEICQR 16 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 121.79 0.0002253 74874000 84504 69654 69460 83125 77135 76792 86215 81526 86510 FALSE TRUE 80509.66339 76751.82179 72644.80971 74769.11707 90587.31958 74132.67378 73061.3183 74387.15124 99925.52897 0.805696645 0.768090223 0.726989494 0.748248399 0.906548312 0.741879223 0.731157684 0.744425894 1 16.60856568 -0.964133111 4.26598398 1.000008398 0.771035301 0.647993282 0.052895595 4618364.231 3247807.118 328.2335027 0.012121335 0.108609269 0.964133111 -0.228973097 MTNYDVEHTIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTNYDVEHTIKK 12 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 125.61 0.00014421 126050000 201700 108380 130270 235930 171910 154340 212270 156080 156170 FALSE TRUE 192166.0407 119424.0452 136243.0084 212213.8682 201891.0496 148995.1671 179884.3129 142412.8078 180388.046 1.065292546 0.662039685 0.755277367 1.176429774 1.119204149 0.825970292 0.997207503 0.789480295 1 17.46074421 4.762163965 23.40303764 0.91213973 1.06529298 0.076973785 0.162380622 1303.372399 2507433.857 0.03913493 0.620832715 57831.43446 -4.762163965 0.15315325 MTPHEK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 117.7 0.022498 529750000 1686290 1490100 1488670 1819170 1396290 1604040 1845840 1712120 1464050 FALSE TRUE 1606582.414 1641942.884 1556926.992 1636303.575 1639802.534 1548491.693 1564223.207 1562197.696 1691087.397 0.950029204 0.970939105 0.920666191 0.967604382 0.96967344 0.915678099 0.924980702 0.923782945 1 20.68951979 3.761861306 24.87993539 0.941938613 0.960484154 0.029394954 0.027440884 1907.698156 2036987.557 0.006680606 0.012029639 5779.114589 -3.761861306 0.018545541 MTSERAPS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MTSERAPSPSSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MTSERAPS(0.992)PS(0.008)SR;MTSERAPS(0.982)PS(0.017)S(0.001)R;MTSERAPS(0.968)PS(0.026)S(0.006)R;MT(0.002)S(0.006)ERAPS(0.791)PS(0.17)S(0.032)R;MTSERAPS(0.488)PS(0.488)S(0.023)R 146.27 3.91E-05 2059810000 1345649 632933 1469986 1001534 1956180 1181950 2271070 1362414 2799210 TRUE FALSE 1282042.839 697429.5923 1537386.312 900857.8995 2297337.173 1141018.775 1924576.56 1243113.808 3233297.19 0.396512527 0.215702285 0.475485618 0.27861896 0.710524594 0.352896349 0.595236518 0.384472486 1 21.62457469 -5 0.151703379 3.119690767 0.237729826 0.633312307 0.139642706 75.04026789 0.67229892 47.77342882 0.600280135 1.00E-05 5 -2.881960941 MTSERAPSPS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MTSERAPSPSSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MTS(0.001)ERAPS(0.178)PS(0.792)S(0.029)R 74.141 0.056587 365530000 178810 55843 202310 107550 255160 153820 298530 177800 387650 TRUE FALSE 170358.0057 61533.46519 211586.1136 96738.86967 299659.8232 148493.1748 252983.7656 162230.8894 447764.7822 0.380463164 0.137423638 0.472538534 0.216048411 0.669234909 0.3316321 0.564992549 0.36231275 1 18.77238154 -5 0.150328181 3.254456757 0.185071724 0.631183031 0.149098332 75.07707322 0.669504199 50.32441446 0.656583245 1.00E-05 5 -3.069385033 MTSSDKDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 94.409 0.0079723 3005180000 12745040 10185090 10035120 11996310 10359810 11663420 14871080 12621770 11865060 FALSE TRUE 12142607.22 11222962.25 10495240.18 10790418.13 12166557.58 11259512.84 12602223.62 11516540.91 13705032.91 0.88599621 0.818893492 0.765794599 0.787332522 0.88774377 0.821560438 0.919532533 0.840314721 1 23.70820246 0.574141854 0.540969994 1.004278338 0.825212519 0.569348423 0.044979701 1.235019293 0.683927039 0.061901301 0.02139018 3.750954998 -0.574141854 -0.179065818 MVDPEKPQLGMIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVDPEKPQLGMIDR 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 101.75 0.0011511 231290000 808500 720910 691840 837950 695270 749100 852210 836800 736730 FALSE TRUE 770283.8073 794371.5486 723561.5483 753717.674 816524.8679 723158.4792 722189.7126 763525.3558 850978.3257 0.905174414 0.933480354 0.850270244 0.885707252 0.959513119 0.84979659 0.848658175 0.897232436 1 19.69876286 MVEGFFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MVEGFFDR 8 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;; 150.4 0.0011395 572755100 840059 628973 645811 648119 830943 518137 744787 651190 821126 FALSE TRUE 800351.0759 693066.0638 675422.0731 582968.8468 975859.1961 500193.7858 631156.0642 594168.3514 948462.0263 0.843840927 0.730726212 0.712123474 0.614646481 1.02888589 0.52737355 0.665452118 0.626454549 1 19.85523049 4.47540165 1.929695307 0.716350287 0.85213604 0.025892605 0.161568555 1.391238828 8.059711643 0.03831945 0.280402503 29881.44875 -4.47540165 0.135785753 MVEKDQDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 MVEKDQDGGR 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;;;;;;; 161.19 7.50E-06 6105960000 8169590 6208823 7654680 7713390 7107220 8028590 9943080 8611330 8593430 FALSE TRUE 7783429.671 6841509.123 8005654.65 6938025.383 8346716.918 7750557.915 8426080.529 7857276.294 9926055.235 0.784141281 0.689247537 0.806529327 0.698971063 0.84088963 0.780829618 0.848885114 0.791580956 1 23.24278905 -0.711486598 0.2366708 1.136438727 0.71972692 0.704695664 0.046914739 6.251611787 0.399058245 0.67998035 0.083349923 0.194318165 0.711486598 -0.416711807 MVEKDQDGGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVEKDQDGGRK 11 2 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 71.085 0.02812 292120000 766070 461750 768950 659020 586510 773540 992040 866080 736270 FALSE TRUE 729859.3893 508802.85 804207.1181 592774.0575 688797.1583 746752.1158 840686.0779 790241.4438 850446.9913 0.858206798 0.598276971 0.945628742 0.697014704 0.809923682 0.878070148 0.988522608 0.929207172 1 19.69786179 2.101405808 2.000246431 0.972376817 0.763063388 0.466419717 0.093037894 0.265624637 2.052332476 0.046648011 0.026644952 126.3007148 -2.101405808 -0.209313428 MVEPENAVTITPLRPEDDYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 196.55 1.28E-22 219489000 273497 229310 224570 334536 326110 224124 276238 226951 236873 TRUE FALSE 260569.3388 252676.9497 234866.7566 300907.8057 382983.4807 216362.5297 234092.8196 207077.9673 273606.0551 0.952352238 0.923506425 0.85841213 1.099784892 1.399762446 0.790781219 0.855583476 0.756847166 1 18.06174063 MVIENDLSGLIDFTRLPS(ph)PTPENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 MVIENDLSGLIDFTRLPSPTPENK 24 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 MVIENDLSGLIDFTRLPS(0.972)PT(0.028)PENK;MVIENDLSGLIDFTRLPS(0.973)PT(0.027)PENK;MVIENDLS(0.001)GLIDFT(0.023)RLPS(0.841)PT(0.136)PENK 264.42 1.86E-44 382433000 593799 496052 515942 625880 455498 587624 610032 599789 431469 TRUE FALSE 565731.2981 546600.2628 539598.451 562965.3533 534936.707 567274.4335 516960.4144 547268.2955 498379.0089 1.135142709 1.09675619 1.082707019 1.129592826 1.073353206 1.138239018 1.037283684 1.098096601 1 18.92688378 -5 0.125833125 0.658506327 1.144380082 0.574506262 0.028527319 96.2287454 0.772826294 8.227455216 0.210908939 1.00E-05 5 0.485873755 MVIENDLSGLIDFTRLPS(ph)PTPENKDLFFVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVIENDLSGLIDFTRLPSPTPENKDLFFVTR 31 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 MVIENDLSGLIDFT(0.001)RLPS(0.969)PT(0.031)PENKDLFFVTR 226.59 1.67E-35 219790000 279260 134240 264050 222430 296280 244900 413120 273710 337840 TRUE FALSE 266059.9332 147919.2086 276156.9537 200070.9138 347951.1382 236419.0516 350090.9565 249742.5014 390230.5018 0.681801992 0.379055989 0.707676495 0.512699322 0.89165541 0.605844624 0.897138883 0.639987136 1 18.57396702 1.732429367 0.314082356 1.008820738 0.490036823 0.394648569 0.145907286 1.229809664 0.407718349 0.216143908 0.223956442 54.00442756 -1.732429367 -0.518783915 MVINHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVINHLEK 8 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 97.635 0.0080918 1141890000 3442880 3128900 2664150 3497470 2613690 3160520 3676640 3269000 2770660 FALSE TRUE 3280141.886 3447738.467 2786303.913 3145897.671 3069516.708 3051070.4 3115701.042 2982749.03 3200319.802 1.024941908 1.077310607 0.870632963 0.982994783 0.959128118 0.953364222 0.97355928 0.932015928 1 21.60978465 3.762623339 24.99836567 0.954659736 1.051126266 0.550691751 0.036790609 482.5121994 501272.1309 0.008427468 0.015183821 5789.263795 -3.762623339 0.096466531 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.637)S(0.363)PQGEAMVTDVLEDQK 290.02 1.10E-61 77560000 219200 253890 185910 268690 141520 241140 197220 235850 131810 TRUE FALSE 208838.8504 279761.6796 194434.1574 241680.7707 166201.0432 232789.2613 167130.4668 215197.7237 152250.4216 1.371679948 1.837510049 1.277068105 1.587389829 1.091629445 1.528989272 1.097734016 1.413445831 1 17.2160867 2.039302715 0.326091518 1.006055407 1.6463109 0.316487333 0.211396126 1.482655734 0.449182893 0.270364687 0.337401203 109.4719149 -2.039302715 0.640255493 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.558)S(0.442)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.509)S(0.489)PQGEAMVT(0.002)DVLEDQKEGR;MVIQGPS(0.604)S(0.396)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.538)S(0.461)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.499)S(0.499)PQGEAMVT(0.001)DVLEDQKEGR 151.37 1.81E-07 647542000 631074 476414 595412 598740 466296 610576 720132 668917 564839 TRUE FALSE 601244.3827 524961.1282 622712.2291 538553.5177 547617.8748 589431.6 610262.6373 610343.0813 652431.3473 0.92154429 0.804622786 0.954448666 0.825456226 0.839349423 0.903438503 0.935366824 0.935490123 1 19.31546658 1.416179638 1.085892067 0.990630542 0.867246317 0.459095809 0.045363343 0.381320566 0.88952808 0.038512694 0.01341401 26.07231759 -1.416179638 -0.123384225 MVIQGPSS(ph)PQGEAMVTDVLEDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.112)S(0.888)PQGEAMVTDVLEDQK 246.2 9.23E-38 74711000 166620 194440 142520 200670 95325 172940 146700 173410 100140 TRUE FALSE 158744.2028 214253.6571 149054.683 180498.2704 111949.6498 166951.0444 124318.2207 158225.3011 115669.1998 1.372398211 1.852296528 1.288628981 1.560469604 0.967843212 1.443349178 1.074773759 1.367912127 1 16.81964523 3.076886744 1.686091877 1.192402087 1.58746417 0.34628803 0.217067612 0.337482373 1.968928341 0.067087593 0.084092439 1193.676775 -3.076886744 0.395062083 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 19 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.185)S(0.81)PQGEAMVT(0.004)DVLEDQKEGR;MVIQGPS(0.163)S(0.836)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.212)S(0.788)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.054)S(0.946)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.412)S(0.587)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.145)S(0.855)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.049)S(0.951)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.008)S(0.992)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.192)S(0.808)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.094)S(0.898)PQGEAMVT(0.008)DVLEDQKEGR;MVIQGPS(0.256)S(0.744)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.113)S(0.887)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.002)S(0.998)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.18)S(0.82)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.008)S(0.992)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.224)S(0.776)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.179)S(0.821)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.172)S(0.828)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.295)S(0.704)PQGEAMVT(0.001)DVLEDQKEGR 290.67 1.90E-70 7300542000 3716000 2861457 3562681 3586153 2816827 3705261 4311409 4056145 3355928 TRUE FALSE 3540352.044 3153042.722 3726033.448 3225666.087 3308080.737 3576946.882 3653624.373 3700967.441 3876348.175 0.913321478 0.813405447 0.961222594 0.832140443 0.853401343 0.922762023 0.94254288 0.954756197 1 21.88626673 1.642069186 1.223367214 0.986910493 0.871968106 0.495016586 0.042738806 0.341739119 0.971803222 0.034181636 0.012619167 43.86005643 -1.642069186 -0.114942387 MVIQLRPGRS(ph)PEPDGPAPAFLR ddPTM_SK-BR-3_Trastuzumab_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 127.53 9.41E-06 621150000 343390 264940 282430 330610 342650 271930 348880 329290 350010 TRUE FALSE 327158.6352 291937.6872 295379.6949 297376.4547 402408.0515 262512.9959 295651.9484 300455.6219 404287.7632 0.809222205 0.722103694 0.730617451 0.735556407 0.99535056 0.649322141 0.731290866 0.743172684 1 18.62502301 -1.298839048 5.537487212 1.000031304 0.76106662 0.399192694 0.090674984 3.26E-05 4.12E-06 0.081558034 0.019220898 0.05025288 1.298839048 -0.238964685 MVMISLEGEDGLDEIYSFSESLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVMISLEGEDGLDEIYSFSESLRK 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 174.7 4.14E-12 74377000 87758 82461 87448 89315 81151 95317 102330 96511 85544 FALSE TRUE 83609.85326 90863.86965 91457.5773 80336.88651 95303.70871 92016.14839 86717.67908 88059.9852 98809.72662 0.846170272 0.919584263 0.925592858 0.813046339 0.964517482 0.931245855 0.877622903 0.89120766 1 16.59236544 -5 0.252561363 1.634250297 0.886665946 0.363717447 0.043434879 204.0574719 2.017935121 67.01171566 0.057325523 1.00E-05 5 -0.747584351 MVNHFIAEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 146.11 2.92E-05 8564200000 19071400 16345500 14912400 17918700 14833900 17444600 20991200 19035300 15058500 FALSE TRUE 18169932.72 18011125.03 15596148.29 16117478.23 17420927.46 16840489.13 17788606.91 17368468.22 17393695.27 1.044627518 1.035497331 0.896655256 0.926627607 1.001565636 0.968195019 1.022704298 0.998549644 1 24.05206113 1.733080535 24.99968876 1.008194469 0.986157646 0.064767994 0.045139787 2.383813576 10787.17058 0.023641662 0.013110375 54.08546093 -1.733080535 -0.022036823 MVNHFIAEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVNHFIAEFKR 11 1 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 192.3 9.43E-07 1600110000 3142000 1991140 2074730 1944210 3137600 2234500 4079700 2917700 3199600 FALSE TRUE 2993483.887 2194039.43 2169858.423 1748774.317 3684796.447 2157118.705 3457266.836 2662210.72 3695777.627 0.809974027 0.593661105 0.587118231 0.473181694 0.997028723 0.58367113 0.935463977 0.720338448 1 21.81744652 1.388890564 0.605794413 0.978463686 0.651331002 0.289100047 0.158335932 0.861564152 0.754295708 0.143228502 0.070105864 24.48446193 -1.388890564 -0.327132684 MVPTSDKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MVPTSDKGR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 166.19 5.56E-05 2625600000 6257702 5105922 5081929 6455380 4605298 6133917 7343140 7095537 5240091 FALSE TRUE 5961912.828 5626221.257 5314940.471 5806472.938 5408460.513 5921497.916 6222809.127 6474214.164 6052697.55 0.985000949 0.929539467 0.878111029 0.959319855 0.893561998 0.978323775 1.028105085 1.069641116 1 22.52914683 1.878675372 2.939216776 1.03697582 0.933333908 0.647285994 0.034589387 0.161397597 2.459903513 0.01802932 0.009408394 75.62673855 -1.878675372 -0.103641912 MVQFEENGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVQFEENGRK 10 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 128.01 0.00054646 1141410000 1107640 999050 1182870 1178640 929100 1420480 1515950 1378340 995550 FALSE TRUE 1055284.052 1100854.331 1237105.76 1060160.868 1091134.746 1371288.421 1284663.985 1257645.243 1149934.809 0.917690328 0.957318903 1.075805123 0.921931278 0.948866611 1.192492314 1.117162447 1.093666556 1 20.13312065 2.254406979 24.99963022 1.114222588 0.962268628 0.5283052 0.063520023 160.3811045 253021.0583 0.020871472 0.017408832 179.6416269 -2.254406979 -0.151953959 MVSDINNGWQHLEQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MVSDINNGWQHLEQAEK 17 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 297.7 3.30E-46 926798000 1741100 1157201 962431 1552110 1384526 1201954 1926320 1477360 1325380 FALSE TRUE 1658801.654 1275121.098 1006559.413 1396088.954 1625986.896 1160330.032 1632424.505 1347994.526 1530913.161 1.083537392 0.832915367 0.657489555 0.911932165 1.062102631 0.757933279 1.066307708 0.880516649 1 20.54596102 2.999012384 24.99993875 0.953864247 0.872316869 0.09200051 0.134401457 106.2492762 2689661.768 0.038749055 0.04578041 997.728513 -2.999012384 -0.081547378 MVSQS(ph)QPGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 2 MVS(0.145)QS(0.855)QPGS(1)R 70.889 0.076943 217060000 262960 243240 245700 277000 304340 249260 303210 274800 318390 TRUE FALSE 250530.4019 268026.4325 256965.588 249155.4337 357416.7996 240628.0637 256949.7457 250737.0552 367764.2951 0.681225462 0.728799495 0.698723589 0.677486741 0.971863785 0.654299688 0.698680511 0.68178738 1 18.48842189 -1.774817078 2.433470352 1.078618413 0.722324282 0.479562589 0.090306897 12575523.05 8424223.147 5883485.035 0.021280392 0.016795113 1.774817078 -0.356294131 MVSQS(ph)QPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 MVS(0.419)QS(0.581)QPGSR 67.952 0.064441 102830000 120970 120390 188620 135370 263670 110940 205940 129910 295290 TRUE FALSE 115251.9878 132657.8779 197268.4136 121762.3504 309653.9645 107098.12 174520.0707 118534.3917 341082.0651 0.33790105 0.388932434 0.578360558 0.356988429 0.907857657 0.313995167 0.511665926 0.347524552 1 18.37975937 -2.319799927 2.167603813 3.649920533 0.462934461 0.471836329 0.176852485 9952549.668 1230604.762 129240547.9 0.03978355 0.004788506 2.319799927 -3.186986072 MVVNEGSDGGQSVYHVHLHVLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVVNEGSDGGQSVYHVHLHVLGGR 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 164.98 5.16E-12 593160000 249030 254890 255800 287820 350500 252230 342810 254300 219300 FALSE TRUE 237258.8454 280863.5808 267528.683 258887.7868 411627.089 243495.2119 290508.0384 232032.1439 253307.924 0.936642019 1.108783241 1.056140206 1.022027984 1.625006761 0.961261725 1.146857287 0.916008233 1 17.95053268 1.240515584 24.97292624 0.958004087 1.113598284 0.110976625 0.192180993 114.463848 1462338.609 0.136809672 0.044236511 17.39865128 -1.240515584 0.155594197 MVVPGLDGAQIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MVVPGLDGAQIPR 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 ;;; 132.32 0.00027964 312879000 651849 607069 606826 702322 735600 629606 739809 673646 761362 FALSE TRUE 621037.3896 668930.0213 634649.5723 631723.2582 863888.4071 607802.5863 626937.5495 614657.985 879430.1305 0.706181615 0.760640326 0.721660028 0.718332516 0.982327506 0.69113232 0.712890687 0.698927594 1 19.74620944 -2.075903645 2.203144054 1.371011309 0.747550194 0.461663703 0.085163566 7876696.152 2273263.578 14677794.09 0.019747658 0.008396463 2.075903645 -0.623461115 MVVPGLDGAQIPRDPSQQELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MVVPGLDGAQIPRDPSQQELPR 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 ; 155.16 1.93E-08 271100000 241000 84042 291700 156173 350400 188236 465030 229520 648800 FALSE TRUE 229608.4076 92605.97535 305074.7335 140474.1933 411509.6491 181717.3401 394081.1326 209422.012 749412.5904 0.306384508 0.123571417 0.407085146 0.187445734 0.549109602 0.2424797 0.525853365 0.279448217 1 19.51540069 -5 0.184067408 3.862949123 0.185164401 0.718937026 0.133158261 61.90996048 0.600154608 64.71257371 0.338105788 1.00E-05 5 -3.677784722 MWDPHNDPNAQGDAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 MWDPHNDPNAQGDAFK 16 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 172.91 4.41E-09 520410000 2055280 1715690 1797770 2064400 1465780 1972480 2176760 2099540 1359970 FALSE TRUE 1958130.988 1890520.762 1880199.533 1856882.59 1721411.568 1904172.523 1844655.283 1915693.147 1570867.202 1.24652866 1.203488595 1.196918193 1.182074836 1.095835196 1.212179184 1.174291042 1.21951311 1 20.58312979 -4.9204444 0.2350307 3.31E-16 1.213043332 0.687421303 0.040186029 92.24698104 0.954088561 44.10432965 0.064921509 1.20E-05 4.9204444 1.213043332 MWSAGRGGAAWPVLLGLLLALLVPGGGAAKTGAELVTCGSVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MWSAGRGGAAWPVLLGLLLALLVPGGGAAKTGAELVTCGSVLK 43 2 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 6.4483 0.095821 20952000 53483 36515 75145 48050 59766 55195 112540 69803 65928 FALSE TRUE 50954.96458 40235.92001 78590.47258 43219.92271 70189.17148 53283.58331 95369.95606 63690.67927 76151.77753 0.669123771 0.528364817 1.032024138 0.567549755 0.921701026 0.699702424 1.252366775 0.836364972 1 16.21659009 2.561793262 0.679164781 1.047219364 0.62617356 0.286976325 0.190720152 0.727042587 0.693688009 0.138447608 0.118868055 364.5803541 -2.561793262 -0.421045804 MWSESS(ph)LDEPYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MWSESSLDEPYEK 13 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 MWSES(0.027)S(0.973)LDEPYEK 145 4.36E-05 31429000 114200 69357 81121 141460 115250 121920 133870 75407 88533 TRUE FALSE 108801.9923 76424.55715 84840.47809 127240.172 135349.5635 117697.8798 113445.6728 68803.96332 102262.2455 1.063950746 0.74733893 0.82963637 1.244253649 1.323553604 1.150941672 1.109360275 0.67281882 1 16.64191408 3.253106449 24.99609881 1.10573414 0.878049701 0.198524184 0.188936693 336.3281559 577955.3225 0.051733636 0.069741596 1791.044799 -3.253106449 -0.227684439 MWVFEETVNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 MWVFEETVNGR 11 0 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 120.99 0.002063 0 64928 46720 61156 55627 67125 52721 82132 70646 85419 FALSE TRUE 61858.98211 51480.82112 63960.06309 50035.26828 78831.57875 50895.25855 69601.25494 64459.86172 98665.34226 0.626957559 0.521772083 0.648252584 0.507121013 0.798979428 0.515837247 0.705427593 0.653318179 1 16.59025578 -5 0.209182111 2.86432812 0.559711839 0.657915689 0.087484143 77.17010351 0.768573192 60.1372386 0.160654423 1.00E-05 5 -2.304616281 MYEEHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 MYEEHLK 7 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;;; 117.02 0.0053251 2127660000 3280370 3166150 2582710 3436380 2320400 2937450 3208400 3164260 2126800 FALSE TRUE 3125313.411 3488784.285 2701129.808 3090948.554 2725077.025 2835725.37 2718899.654 2887180.62 2456613.282 1.272204068 1.420160149 1.099533992 1.258215356 1.109282053 1.154323064 1.106767465 1.175268668 1 21.22823934 3.756026793 0.243277402 1.007355189 1.515909747 0.512905332 0.08130823 4.250181302 0.329571978 0.127694369 0.645910171 5701.994482 -3.756026793 0.508554558 MYEEHLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 MYEEHLKR 8 1 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;;;;; 161.02 0.00016703 3751646000 3639582 2711869 3214785 3257568 3023444 3302037 4416851 3629918 3181474 FALSE TRUE 3467546.172 2988211.534 3362186.072 2930111.076 3550731.676 3187686.631 3742979.259 3312063.137 3674840.739 0.94359087 0.813154024 0.914920213 0.79734369 0.966227363 0.867435314 1.018541897 0.901280728 1 21.8092503 2.110725558 1.441750125 0.971483005 0.87289401 0.280578794 0.061966343 0.469145102 1.85117548 0.035192678 0.018395993 129.0403575 -2.110725558 -0.098588995 MYFPDVEFDIKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MYFPDVEFDIKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MYFPDVEFDIKS(1)PK;MYFPDVEFDIKS(1)PK 187.31 5.83E-07 543790000 1461130 1566850 1553570 1963850 830280 1774120 1687850 1939640 851880 TRUE FALSE 1392065.281 1726513.796 1624802.721 1766440.067 975080.5691 1712681.78 1430337.483 1769794.839 983985.1996 1.414721767 1.754613583 1.651247114 1.795189671 0.990950443 1.740556444 1.453616867 1.798599044 1 19.90827709 MYMDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 MYMDRR 6 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 103.28 0.055827 269340000 538230 224150 95344 87777 755360 151985 655110 282900 672130 FALSE TRUE 512788.9346 246991.1398 99715.61671 78953.48919 887094.5448 146721.7213 555160.9376 258127.7763 776360.4876 0.660503648 0.318139761 0.12843984 0.101696944 1.142632268 0.18898659 0.715081391 0.332484433 1 19.56636717 -2.008251618 0.28513792 1.598241448 0.398882455 0.226283545 0.319673435 48.29873782 2.072388571 19.39634068 0.346330896 0.009811793 2.008251618 -1.199358993 MYPIDFEKDDDSNFHMDFIVAASNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 MYPIDFEKDDDSNFHMDFIVAASNLR 26 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 196.49 4.13E-25 645966000 1131565 1069427 1029250 1270802 824875 1107844 1296090 1274996 755377 FALSE TRUE 1078078.165 1178402.827 1076442.131 1143058.569 968732.9388 1069479.084 1098347.666 1163350.591 872517.0072 1.235595588 1.350578633 1.233720514 1.310070244 1.11027399 1.225740101 1.258826656 1.333327123 1 19.73482373 -1.622885179 3.004277858 0.98092754 1.259362977 0.589502707 0.067447885 10461395.1 13113164.59 1593642.631 0.015774772 0.023829494 1.622885179 0.278435437 MYPPRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;MYPPRS(1)PK;MYPPRS(1)PK;MYPPRS(1)PK 62.303 0.048749 2016440000 2129560 1988690 1897440 2240990 1552990 2158580 2255290 2013640 1422640 TRUE FALSE 2028899.919 2191339.772 1984439.501 2015721.428 1823830.964 2083827.833 1911204.089 1837315.007 1643255.745 1.234682991 1.333535439 1.207626693 1.226663247 1.109888689 1.268109264 1.163059429 1.118094376 1 20.6481256 0.228153737 0.183369082 0.869042347 1.336378234 0.674066928 0.053321655 4.983265739 0.388823446 0.634576614 0.237511284 1.69103944 -0.228153737 0.467335887 MYSYPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 100.74 0.022265 424540000 487140 290110 225566 270390 529460 266480 526720 369460 556300 FALSE TRUE 464113.8576 319672.5388 235908.4242 243209.8835 621797.6564 257251.7308 446359.1901 337108.1238 642568.1628 0.722279572 0.497492029 0.367133695 0.378496629 0.967675793 0.400349326 0.69464878 0.524626247 1 19.29348998 -3.665483234 0.337238097 2.620261656 0.555028632 0.346488631 0.185882361 158.1996953 3.173089143 179.9358768 0.140516928 0.000216031 3.665483234 -2.065233024 NAADKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NAADKER 7 1 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 76.899 0.036032 96917000 296640 229010 212402 254813 184689 222828 297140 309230 242590 FALSE TRUE 282618.4151 252346.3794 222140.8418 229198.7131 216898.7031 215111.4105 251805.8356 282152.1819 280209.6182 1.00859641 0.900562875 0.792766655 0.817954482 0.774058737 0.767680324 0.898633806 1.006932537 1 18.09614695 -0.38329882 7.541990816 0.999999312 0.87231455 0.178584261 0.086967957 0 0 0.089120452 0.021005892 0.413714917 0.38329882 -0.127684762 NAAEELKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NAAEELKPR 9 1 P78406 P78406 RAE1 mRNA export factor 0 ;; 120.09 0.00065789 795130000 1027660 836840 930060 1008040 619600 950460 1062270 1013990 659100 FALSE TRUE 979084.5484 922114.9474 972704.171 906709.904 727658.0438 917545.3319 900201.2016 925199.6601 761309.8618 1.286052628 1.211221598 1.277671839 1.190986679 0.955797475 1.205219291 1.182437332 1.215273447 1 19.53812424 7.999999973 0.021415574 1.37E-11 2.722804168 0.370486717 0.085872453 3006.418118 4.960550826 228.833908 431.4099586 99999993.75 -7.999999973 2.722804168 NACDHLSGFNVCNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NACDHLSGFNVCNR 14 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 ; 183.06 1.45E-06 371490000 391160 277440 365510 417520 451010 320330 554510 445800 571310 FALSE TRUE 372670.642 305711.4514 382268.995 375550.0964 529666.0012 309236.8918 469909.3152 406763.3887 659905.837 0.564733059 0.463265263 0.579278093 0.569096491 0.802638758 0.468607602 0.712085405 0.616396107 1 19.33190065 -5 0.154324407 2.523713992 0.465609162 0.653650481 0.095454367 73.79173758 0.66679007 34.28460662 0.401007537 1.00E-05 5 -2.05810483 NADDDRGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NADDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 101.97 0.0033377 700904000 1493260 1203450 1380260 1513740 1235590 1410860 1648140 1612680 1314570 FALSE TRUE 1422676.559 1326082.923 1443546.286 1361575.979 1451076.505 1362001.564 1396685.973 1471465.19 1518426.802 0.936941154 0.873326868 0.950685463 0.896701756 0.955644686 0.896982036 0.919824368 0.969072192 1 20.53414593 1.106036294 2.981134912 0.999101831 0.915576918 0.553171404 0.025385649 0.155205453 2.625919563 0.021592658 0.005781129 12.76545485 -1.106036294 -0.083524912 NADGFIDLEEYIGDMYSHDGNTDEPEWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NADGFIDLEEYIGDMYSHDGNTDEPEWVK 29 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;; 287.53 4.19E-72 139471000 154563 198462 124755 186781 85758 158453 136919 160725 63685 FALSE TRUE 147257.1133 218685.5034 130475.1401 168005.419 100714.168 152965.7329 116029.4919 146651.0669 73560.94454 2.001838261 2.972847953 1.773701262 2.28389426 1.369125542 2.079442207 1.57732466 1.993599564 1 16.16665238 1.588314606 0.159768565 0.526328 2.993249917 0.433681479 0.401461131 3.249206683 0.539211077 3.438306673 3.529633169 38.75382788 -1.588314606 2.466921916 NADGTICYDSTHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NADGTICYDSTHYK 14 0 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;;; 215 6.67E-12 5570140000 4790660 3997360 3829840 4907870 2957280 4119030 4778080 4709580 2750600 FALSE TRUE 4564214.996 4404695.529 4005441.952 4414521.583 3473028.696 3976386.958 4049096.141 4297184.208 3177149 1.436575683 1.386367315 1.260703213 1.389460042 1.093127422 1.251558224 1.274443264 1.352528386 1 21.59930132 -0.815789316 0.041146198 3.41E-12 2.226878354 0.551669321 0.091202246 201.0473852 1.72038123 57.43290687 36.73019708 0.152830729 0.815789316 2.226878354 NADGTICYDSTHYKETWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NADGTICYDSTHYKETWK 18 1 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 173.77 4.50E-12 343950000 325950 134829 346774 248574 260724 304766 495090 361190 328520 FALSE TRUE 310542.9895 148568.2284 362673.9309 223586.8693 306194.1831 294211.877 419554.9275 329562.2888 379465.2038 0.818370134 0.391520031 0.955750164 0.589215736 0.806909777 0.775332953 1.105647958 0.86849146 1 18.53360807 2.120237909 1.736760009 0.998908509 0.670586373 0.366501798 0.16209351 0.329552547 1.913726665 0.086528406 0.048066684 131.8979086 -2.120237909 -0.328322136 NADGYKLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NADGYKLDK 9 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 118.9 0.00083325 1116370000 2500570 1938180 2234080 2529800 1388240 2648070 2887710 2889650 1654630 FALSE TRUE 2382373.012 2135682.746 2336514.778 2275499.698 1630348.616 2556366.672 2447136.803 2636616.927 1911221.57 1.246518483 1.117443827 1.222524282 1.190599632 0.853040088 1.337556415 1.280404555 1.379545401 1 20.86606361 NADHSMNYQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NADHSMNYQYR 11 0 Q12906;K7ELV3;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;; 184.03 5.08E-06 948620000 253861 183609 176823 188827 209834 165482 250856 224135 211697 FALSE TRUE 241861.4936 202318.9658 184930.5095 169845.7512 246428.9832 159751.3168 212583.3099 204508.5512 244525.8896 0.989103829 0.827392822 0.756281921 0.6945921 1.00778279 0.653310441 0.869369335 0.836347233 1 17.8996277 0.450040118 2.174198044 0.999988269 0.831799126 0.185761803 0.112306256 13.87555398 52.51313094 0.101066854 0.027453506 2.818643294 -0.450040118 -0.168189142 NADNDWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NADNDWFR 8 0 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 110.41 0.0079835 401300000 1481430 1578590 1379570 1648190 1187570 1442980 1473060 1608900 1204280 FALSE TRUE 1411405.74 1739450.116 1442824.649 1482510.81 1394681.832 1393009.241 1248317.642 1468016.187 1391033.592 1.014645331 1.25047312 1.037232068 1.065762048 1.002622683 1.001420274 0.897402945 1.05534201 1 20.40772583 2.990475129 1.430939923 0.973815946 1.126758011 0.329928007 0.072465205 0.358618321 1.514619304 0.026677613 0.031553341 978.3069268 -2.990475129 0.152942065 NADSELMPPPPERGDPPRLS(ph)PDPVAGSAVSQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NADSELMPPPPERGDPPRLSPDPVAGSAVSQELR 34 2 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 NADSELMPPPPERGDPPRLS(0.997)PDPVAGS(0.001)AVS(0.001)QELR;NADSELMPPPPERGDPPRLS(0.957)PDPVAGS(0.036)AVS(0.007)QELR;NADSELMPPPPERGDPPRLS(1)PDPVAGSAVSQELR;NADSELMPPPPERGDPPRLS(0.978)PDPVAGS(0.017)AVS(0.005)QELR 135.63 1.05E-08 309159000 399748 273247 391785 395525 357446 369526 507280 431505 430574 TRUE FALSE 380852.7043 301091.18 409748.7298 355766.0756 419784.4692 356729.222 429885.1192 393720.1346 497345.2169 0.765771322 0.605396754 0.823871862 0.715330244 0.84405048 0.71726682 0.864359613 0.791643553 1 18.92388808 -0.423532133 0.175760445 1.185864655 0.641613841 0.571981325 0.068684639 9.706811771 0.48779732 1.232811322 0.29243603 0.377109842 0.423532133 -0.544250814 NAEAVLQS(ph)PGLSGK ddPTM_SK-BR-3_Trastuzumab_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(0.984)PGLS(0.016)GK;NAEAVLQS(0.89)PGLS(0.11)GK;NAEAVLQS(1)PGLSGK 252.88 3.41E-24 2153544000 3427790 3416080 3405260 3951200 2226980 3851490 4186510 4145670 2661030 TRUE FALSE 3265765.16 3764182.436 3561394.539 3554017.869 2615364.607 3718111.936 3547781.009 3782653.157 3073688.942 1.062490454 1.22464651 1.158671097 1.156271157 0.85088786 1.209657843 1.154242045 1.230655811 1 21.55153974 -2.473103399 1.848178455 9.39E-05 1.133539196 0.121267363 0.110575755 1780125.693 111138.4625 7459250.552 0.025738192 0.003364315 2.473103399 1.13344531 NAEPADRDSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NAEPADRDSPR 11 1 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ;; 172.11 1.25E-05 1060970000 1437960 1230170 1331930 1495070 1162240 1291020 1486030 1365830 1257380 FALSE TRUE 1369990.481 1355525.722 1393000.308 1344782.723 1364934.288 1246311.654 1259308.831 1246230.684 1452368.069 0.943280502 0.933321071 0.959123474 0.925924187 0.939799158 0.858123833 0.867072788 0.858068083 1 20.46997569 2.253823995 24.83646631 0.881895575 0.939814427 0.185210414 0.042059709 237.1986721 385967.6336 0.012781556 0.010655414 179.4006429 -2.253823995 0.057918852 NAEQYKDQADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NAEQYKDQADK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 174.72 9.73E-06 4257980000 4272400 3666340 3603110 4697630 1962160 4477020 4475410 4735780 2107550 FALSE TRUE 4070452.119 4039944.214 3768316.157 4225415.307 2304360.083 4321979.675 3792604.008 4321089.997 2434378.09 1.672070635 1.659538521 1.547958459 1.735726806 0.946590873 1.775393762 1.557935484 1.775028298 1 21.21512182 -1.601657203 2.933405888 0.96027679 1.586713635 0.368982743 0.239894448 99510441.08 101547450.5 30456063.45 0.052627478 0.025023197 1.601657203 0.626436844 NAEQYKDQADKASTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NAEQYKDQADKASTR 15 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 161.24 9.35E-07 377810000 1045200 345790 1240500 823550 820520 1210730 1943330 1428920 1218130 FALSE TRUE 995795.4674 381026.3941 1297378.152 740765.1894 963618.4282 1168802.117 1646839.317 1303796.19 1407031.379 0.707727974 0.270801632 0.922067675 0.526473823 0.684859231 0.830686603 1.170435387 0.926629078 1 20.42422307 2.131021278 2.357910713 1.047166088 0.58262249 0.53283615 0.173941794 0.201986216 2.22323703 0.080546937 0.050109154 135.2138809 -2.131021278 -0.464543598 NAFACFDEEATGTIQEDYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NAFACFDEEATGTIQEDYLR 20 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;; 220.61 1.96E-24 63025000 97179 69699 77075 93048 74636 79054 96861 89579 85178 FALSE TRUE 92585.54126 76801.40734 80608.96499 83694.63826 87652.49477 76316.34016 82083.07548 81734.98787 98386.96921 0.94103459 0.78060548 0.819305297 0.850667918 0.890895364 0.775675283 0.834288078 0.830750134 1 16.58617963 -1.272952429 6.598257293 1.000002568 0.838990382 0.516983772 0.048463763 1.74E-06 1.92E-07 0.044678457 0.010530645 0.053339332 1.272952429 -0.161012186 NAFMMLIHADQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NAFMMLIHADQDR 13 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 145.29 4.17E-05 908840000 1419120 1224400 1196240 1474260 997890 1218430 1531280 1408750 877660 FALSE TRUE 1352041.01 1349167.752 1251088.787 1326064.584 1171921.7 1176235.464 1297655.112 1285392.382 1013763.03 1.333685457 1.330851207 1.234103779 1.308061691 1.156011479 1.160266678 1.280037912 1.267941662 1 19.95128903 -5 0.11315629 0.180003603 1.40624217 0.676364691 0.05820506 96.94789019 0.723763237 18.53713152 0.67676371 1.00E-05 5 1.226238568 NAHVTDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NAHVTDPR 8 0 R4GN43;A0A2Y9D025;P56556 R4GN43 NDUFA6 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 0 ; 81.548 0.022576 106032000 340720 303980 307720 305420 256760 275510 318280 300800 214380 FALSE TRUE 324614.8408 334955.9076 321829.2664 274718.6013 301538.8627 265969.0196 269720.5404 274460.3574 247624.9555 1.310913273 1.352674277 1.299664106 1.109414036 1.217724046 1.07408003 1.089230041 1.108371153 1 17.91779719 2.993355044 0.735761273 1.059201996 1.355255263 0.796925098 0.052958414 0.268288474 0.324080989 0.031129311 0.040794088 984.815883 -2.993355044 0.296053267 NAINTEMYHEIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NAINTEMYHEIMR 13 0 A0A0C4DGA2;O75521-2;O75521;F1LLU7 A0A0C4DGA2 ECI2 "Enoyl-CoA delta isomerase 2, mitochondrial" 0 167.55 3.17E-05 162450000 88961 73331 68070 84419 75575 73127 98307 75543 66438 FALSE TRUE 84755.98983 80803.51227 71191.07683 75933.04173 88755.25607 70594.59365 83308.46162 68928.05444 76740.86572 1.104444015 1.052939806 0.92768144 0.989473353 1.15655792 0.919908747 1.085581467 0.898192297 1 16.22770742 3.991819235 20.63785122 1.005451953 1.085130151 0.165508429 0.078018761 78.78522134 198766.6783 0.018048658 0.034608458 9813.393988 -3.991819235 0.079678197 NAIS(ph)LPQLNQAAYDSLVVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NAISLPQLNQAAYDSLVVGK 20 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 NAIS(1)LPQLNQAAYDSLVVGK 126.22 1.53E-05 55750000 103230 74941 84075 98963 84952 88515 117220 98385 74883 TRUE FALSE 98350.52248 82577.5731 87929.92191 89015.05122 99767.6019 85449.70336 99335.93611 89769.88783 86495.47319 1.137059766 0.954703987 1.01658409 1.029129594 1.153443044 0.987909543 1.148452427 1.037856486 1 16.40033701 NAKPLSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NAKPLSFK 8 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 82.287 0.018845 477310000 629320 485950 630720 810900 542390 787920 967530 904260 662390 FALSE TRUE 599573.2908 535468.8575 659639.1359 729386.7914 636982.6443 760634.1328 819915.5286 825078.2006 765110.0582 0.783643195 0.699858604 0.862149345 0.953309636 0.832537277 0.994149959 1.071630832 1.078378453 1 19.54530776 2.816254381 0.702819432 1.065259923 0.732779857 0.750521319 0.062102738 0.311180879 0.335842516 0.04351046 0.047366417 655.0197293 -2.816254381 -0.332480066 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(0.997)PT(0.003)PDENSDQNSR;NALFPEVFS(0.999)PT(0.001)PDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR 212.32 6.52E-23 230347000 359302 342777 356492 401012 292139 362136 386380 386000 314002 TRUE FALSE 342318.5065 377706.366 372837.5108 360701.5119 343087.9491 349595.1395 327430.6346 352199.7937 362695.8265 0.943817054 1.041386028 1.027961955 0.994501413 0.945938508 0.963879687 0.902769237 0.97106106 1 18.46840062 2.78966656 4.263936396 0.947199988 1.004361857 0.268839996 0.03532626 0.236526069 9.226140595 0.010976157 0.011442644 616.1217784 -2.78966656 0.05716187 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK 232.02 8.69E-34 8480860000 4907130 4608480 4738970 5427220 3112980 5415020 5954940 5699090 3342520 TRUE FALSE 4675179.69 5078089.351 4956256.462 4881665.535 3655882.726 5227496.5 5046404.533 5200047.467 3860860.93 1.210916367 1.315273832 1.283717946 1.26439818 0.94690868 1.353971716 1.30706716 1.346862153 1 21.88049116 2.967890692 24.9939532 1.21871811 1.271593597 0.053196449 0.137426609 2790.718319 2172302.404 0.040722925 0.043225168 928.7326037 -2.967890692 0.052875487 NAMS(ph)LPQLNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 NAMSLPQLNEK 11 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK 215.61 1.33E-11 2234819000 8050735 6943776 7006883 8443478 4943399 8017281 8866276 8962138 5680691 TRUE FALSE 7670192.712 7651354.669 7328155.516 7594723.55 5805526.22 7739640.549 7513562.756 8177365.685 6561623.547 1.168947389 1.166076446 1.116820473 1.15744579 0.88476978 1.17953133 1.145076779 1.246241212 1 22.6456214 1.133969513 0.01017991 5.80E-07 2.214288088 0.077365377 0.099074137 3772.754225 29.62087718 3251.111651 3186.8699 13.61349115 -1.133969513 2.214287508 NAPAAVDEGSIS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR 324.78 1.14E-56 3628347000 4135560 3676110 3738200 4388780 3096572 4045710 4476490 4160040 3366630 TRUE FALSE 3940080.275 4050709.788 3909600.168 3947611.496 3636613.176 3905606.048 3793519.234 3795764.844 3888709.786 1.013210163 1.041659062 1.00537206 1.015146852 0.935172172 1.004344953 0.975521302 0.976098771 1 21.89086014 2.970003577 24.20828075 0.978452556 1.022040028 0.49396924 0.020447024 336.2038648 271329.6649 0.005663949 0.006015614 933.2619877 -2.970003577 0.043587472 NAPWTLTPEFLAEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NAPWTLTPEFLAEHR 15 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ;; 183.6 4.99E-07 224894000 332983 269411 273939 315443 242219 279111 331679 320840 225818 FALSE TRUE 317243.5535 296864.2872 286499.3741 283734.0703 284461.9169 269445.3161 281075.2768 292745.5487 260836.7021 1.216253506 1.138123143 1.09838597 1.087784303 1.090574734 1.033003845 1.077590978 1.122332656 1 17.99278736 8 0.306443639 1.048141356 2.632382782 0.72724901 0.03042993 24.89446139 0.356044404 0.027779516 21.77598814 100000000 -8 1.584241427 NAQAIEDMVGYAQETQHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NAQAIEDMVGYAQETQHEK 19 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 249.14 5.58E-25 72046000 140260 127040 118780 161430 90485 153390 155500 144600 84099 FALSE TRUE 133630.1878 139985.5204 124226.1805 145202.7497 106265.5554 148078.0658 131775.619 131938.0574 97140.6434 1.375636223 1.441060256 1.278828059 1.494768252 1.093935058 1.524367769 1.356544639 1.358216837 1 16.56778742 0.523416896 2.765684603 1.000003159 1.373189918 0.477914731 0.11990653 8.078693389 45.79361511 0.099888681 0.026326228 3.337466353 -0.523416896 0.373186759 NAS(ph)ASFQELEDKK ddPTM_SK-BR-3_Trastuzumab_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(0.999)AS(0.001)FQELEDKK;NAS(0.94)AS(0.06)FQELEDKK 151.41 2.74E-05 184830000 229740 270060 189452 277440 93695 240050 194675 270700 91831 TRUE FALSE 218880.6455 297579.421 198138.5616 249551.2041 110035.3783 231737.0083 164973.7533 246996.0729 106071.6825 2.063516298 2.80545584 1.8679685 2.352665653 1.037368087 2.184720775 1.555304389 2.328576932 1 16.69468003 3.151799279 1.930525074 1.704871478 2.390633191 0.249378354 0.499305827 0.402168351 3.078097153 0.144513655 0.188624243 1418.401818 -3.151799279 0.685761713 NAS(ph)VPNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NASVPNLR 8 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019;E9PPQ0;C9JF50;E9PLU1;E9PRK5;Q9H019-2;E9PNJ0;E9PRW1;E9PSD6 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 NAS(1)VPNLR;NAS(1)VPNLR 136.49 0.00082741 317630000 530060 378420 438620 515540 418680 449830 507130 440660 480430 TRUE FALSE 505005.1143 416981.4282 458731.1609 463716.9397 491697.6594 434252.2743 429758.0044 402073.4743 554932.6307 0.91002959 0.751409099 0.826642975 0.835627451 0.886049283 0.782531519 0.774432752 0.72454466 1 19.08195311 NASEMIDKLTLTFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NASEMIDKLTLTFNR 15 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 210.09 1.88E-09 187659000 592310 487600 544550 549660 465270 510260 640460 667290 482570 FALSE TRUE 564312.6801 537286.9944 569518.1561 494407.1325 546412.9407 492589.5683 542746.0641 608858.5501 557404.491 1.012393494 0.963908621 1.02173227 0.886980892 0.980280837 0.883720128 0.973702352 1.092310091 1 19.0883651 1.359453098 7.651198985 1.044971121 0.960551861 0.340486969 0.049931576 0.245453854 14.9874586 0.0314738 0.0114648 22.87984603 -1.359453098 -0.084419259 NASS(ph)PEKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NASSPEKAK 9 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 NAS(0.019)S(0.981)PEKAK;NAS(0.03)S(0.97)PEKAK;NAS(0.023)S(0.977)PEKAK;NAS(0.008)S(0.992)PEKAK 130.56 0.00021659 923276000 2957810 2426830 2723060 3049000 1103287 3149840 3281980 3820120 1615756 TRUE FALSE 2818000.183 2674126.736 2847914.994 2742508.727 1295699.903 3040760.251 2781253.673 3485610.041 1866319.188 1.509924026 1.432834615 1.525952802 1.469474645 0.694254183 1.629281995 1.490234731 1.867638753 1 20.83176431 NASYYGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NASYYGNR 8 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9;A0A6I8PR93 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 109.11 0.0085645 95818000 108491 82826 77665 89669 91535 78503 110773 100087 98332 FALSE TRUE 103362.8454 91266.06357 81226.01707 80655.30176 107498.675 75784.42143 93872.54436 91322.85169 113580.8243 0.910037817 0.803534083 0.715138471 0.710113721 0.946450914 0.667229014 0.82648233 0.804034063 1 16.79335976 0.372608942 2.208424209 0.999997429 0.79986418 0.350928628 0.086385279 15.71373784 53.52039624 0.078143851 0.02117164 2.35835371 -0.372608942 -0.200133249 NAT(ph)SPQVQRPSFMDYFDKQDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NATSPQVQRPSFMDYFDKQDFK 22 2 A0A087WZ06;Q13188;Q13188-2 A0A087WZ06 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 1 NAT(0.5)S(0.5)PQVQRPSFMDYFDKQDFK 95.794 0.074463 196120000 143840 102610 121700 139240 82022 143460 169030 140640 90377 TRUE FALSE 137040.9683 113066.0757 127280.0654 125243.3307 96326.61083 138491.9442 143241.3691 128324.816 104392.2036 1.312750987 1.083089271 1.219248766 1.199738356 0.922737595 1.326650262 1.372146235 1.229256703 1 16.67165444 NATS(ph)PQVQRPSFMDYFDKQDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NATSPQVQRPSFMDYFDKQDFK 22 2 A0A087WZ06;Q13188;Q13188-2 A0A087WZ06 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 1 NAT(0.416)S(0.584)PQVQRPSFMDYFDKQDFK 156.69 5.20E-09 219100000 599930 460180 536790 634030 337350 588480 658400 636310 333590 TRUE FALSE 571572.4978 507072.8652 561402.3525 570296.0998 396183.7332 568100.79 557948.9877 580591.3231 385321.4335 1.48336544 1.315973681 1.456971514 1.480052887 1.02819023 1.47435554 1.448009218 1.506771419 1 18.55570291 -2.177801358 2.255996414 0.000153558 1.397013691 0.438736902 0.141881949 1488830.595 326187.7115 7625733.769 0.032681884 0.006640467 2.177801358 1.396860133 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK 40 2 H0YGK0;H0YFX0;H0YF95;A0A0A0MSU7;C9JFF1;Q53EL9-4;Q53EL9-2;Q53EL9-3;Q53EL9 H0YGK0 SEZ6 Seizure protein 6 homolog 0 ;;; 22.801 0.090307 23367200000 23131900 28572100 16246240 26515200 2809840 28286100 14883470 27825000 1196407 FALSE TRUE 22038500.93 31483629.47 16991146.17 23849841.72 3299875.206 27306545.26 12612723.3 25388495.49 1381939.687 15.94751286 22.78220227 12.29514307 17.25823633 2.387857616 19.75957816 9.126826167 18.37163787 1 20.39826322 1.045873123 0.192424602 8.51E-17 21.65062517 0.319396314 5.95389937 4.654025927 0.733456566 38.67953682 26.458382 11.11406988 -1.045873123 21.65062517 NAVEEYVYDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NAVEEYVYDFR 11 0 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;;;;; 209.97 3.34E-08 599935000 798560 681405 691211 795348 647967 666280 857809 803655 727325 FALSE TRUE 760813.6514 750840.9442 722903.7081 715398.108 760972.2396 643206.5565 726934.4823 733282.7078 840114.8463 0.905606721 0.893736074 0.860482006 0.851547989 0.905795491 0.765617414 0.865279891 0.872836269 1 19.68022704 0.722167447 4.487655974 0.999999608 0.86579883 0.532602876 0.03976733 6.997740477 112.4490542 0.0384513 0.009762261 5.274331796 -0.722167447 -0.134200778 NAVEEYVYEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NAVEEYVYEFR 11 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;; 220.82 2.06E-11 942047000 1011465 878625 906152 1049273 817962 817894 1095768 1037824 924801 FALSE TRUE 963655.054 968157.8864 947699.9655 943798.0846 960614.3138 789570.1257 928588.4664 946946.6287 1068214.416 0.902117627 0.906332916 0.887181404 0.883528691 0.899271064 0.739149476 0.869290334 0.886476174 1 20.02676983 NAVEEYVYEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NAVEEYVYEMR 11 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 138.99 0.00064603 113660000 387800 202979 252101 193394 234047 206577 261573 400283 334573 FALSE TRUE 369469.4625 223662.7909 263660.0802 173953.6677 274864.7227 199423.1867 221665.2347 365232.0985 386456.8721 0.956043195 0.578752267 0.682249688 0.4501244 0.711242942 0.516029604 0.573583369 0.945078545 1 18.5599479 1.194885444 7.198179346 0.980189359 0.641651376 0.509062792 0.136507015 0.196624731 24.99017013 0.128745211 0.033161637 15.66337856 -1.194885444 -0.338537982 NCCFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NCCFEHR 7 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 117.72 0.005167 79354000 88916 106390 80133 101600 77029 100050 83797 112240 93316 FALSE TRUE 84713.11689 117231.262 83807.17731 91386.97497 90462.83321 96585.24341 71012.22861 102411.6706 107786.9687 0.78593097 1.087619991 0.777526062 0.847848085 0.839274305 0.896075329 0.658820166 0.950130353 1 16.71782324 3.683156426 24.99990442 0.830281105 0.936777287 0.055745983 0.118122753 517.3742078 233453.3087 0.02933261 0.045441905 4821.214192 -3.683156426 0.106496182 NCEEVGLFNELAS(ph)PFENEFKK ddPTM_SK-BR-3_Trastuzumab_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 119.14 4.04E-05 17249000 21147 19329 19650 21831 12067 20072 20566 24488 15190 TRUE FALSE 20147.42322 21298.64708 20550.97194 19636.5064 14171.48098 19376.90161 17428.27898 22343.7009 17545.58762 1.148290023 1.213903321 1.171290035 1.119170633 0.807694862 1.104374617 0.993314066 1.273465522 1 14.09882065 2.99222916 24.26811164 1.030162995 1.176825096 0.244865933 0.114834609 314.3984694 981863.5825 0.031317532 0.035897048 982.2661087 -2.99222916 0.146662101 NCEQCKPFYYQHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NCEQCKPFYYQHPER 15 1 P07942;G3XAI2;E7EPA6 P07942 LAMB1 Laminin subunit beta-1 0 124.29 5.86E-05 73889000 151720 142420 142380 155330 113530 167740 156870 155220 106450 FALSE TRUE 144548.4963 156932.7599 148908.2638 139715.9333 133329.5961 161931.1217 132936.6004 141628.1139 122957.7223 1.175595103 1.276314793 1.211052555 1.136292464 1.084353171 1.316965854 1.081156985 1.151843994 1 16.90780282 -1.308056392 0.185832474 0.814984139 1.249463971 0.411731016 0.071940498 22.55850805 0.806672182 2.213414819 0.240894432 0.049197565 1.308056392 0.434479832 NCGSFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NCGSFTR 7 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 116.9 0.01854 143180000 287610 248860 250960 301810 190884 236460 275860 270650 189724 FALSE TRUE 274015.2453 274219.1169 262466.7642 271471.4854 224174.1092 228271.3309 233772.4905 246950.4512 219145.4289 1.250380839 1.251311142 1.197683043 1.238773205 1.022946772 1.041643132 1.066745912 1.126879317 1 17.74152906 2.744625094 24.82016878 1.05577638 1.237045723 0.865865221 0.035743267 144.647803 592002.2745 0.010615535 0.010996404 555.4245778 -2.744625094 0.181269342 NCLTNFHGMDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NCLTNFHGMDLTR 13 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;;;; 236.4 1.03E-16 6114980000 5755530 4275880 4461620 4948190 4721800 4770940 6822930 5300000 5347670 FALSE TRUE 5483477.503 4711597.033 4666189.69 4450788.54 5545280.425 4605721.152 5781966.717 4835903.903 6176959.351 0.887730871 0.762769636 0.755418552 0.72054684 0.897736266 0.745629182 0.936053872 0.782893917 1 22.55846541 0.366729992 0.515619188 1.00930013 0.79617415 0.398768432 0.072843237 2.295731695 0.992783897 0.124880875 0.033687431 2.326644298 -0.366729992 -0.21312598 NCPAVTLTS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NCPAVTLTSPAK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 NCPAVTLT(0.005)S(0.995)PAK 106.11 0.0020534 119070000 619510 550720 536030 673770 387780 626980 650980 683450 489260 TRUE FALSE 590226.9901 606838.9941 560607.5057 606041.3595 455408.7092 605267.5254 551661.0449 623603.4948 565131.942 1.044405644 1.073800557 0.991994018 1.072389144 0.805844928 1.071019846 0.976163271 1.103465312 1 19.10822821 3.598156679 2.209469521 0.997282701 1.058991648 0.062775367 0.082010946 0.736455411 7.046771226 0.021777602 0.03831647 3964.21024 -3.598156679 0.061708947 NCPHIVVGTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 138.24 7.80E-05 452130000 359100 293950 296940 328170 260260 332430 330630 316060 235870 FALSE TRUE 342126.0547 323903.8392 310554.9927 295181.7281 305649.2616 320917.8657 280186.3211 288384.1109 272447.5149 1.255750322 1.188866925 1.139870895 1.083444377 1.121864744 1.177907113 1.028404759 1.058494187 1 18.05561881 8 0.152596643 0.974052769 2.04532732 0.772297513 0.037221428 28.57947973 0.284859739 0.122800515 6.810394072 100000000 -8 1.071274551 NCPS(ph)PVLIDCPHPNCNKK ddPTM_SK-BR-3_Trastuzumab_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 239.57 3.00E-24 3178060000 3620260 3036590 3382590 3856000 2034350 3845210 4209070 3975730 2217300 TRUE FALSE 3449137.484 3346021.973 3537685.097 3468387.554 2389139.996 3712049.414 3566899.067 3627594.005 2561147.56 1.346715644 1.306454195 1.381289057 1.354231833 0.932839651 1.4493696 1.392695651 1.416393988 1 21.28835895 NCQHANAERPTVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NCQHANAERPTVAR 14 1 Q9Y5J1;F6VJE8 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ;;; 152.11 4.06E-06 173219000 67039 64484 59839 71676 79083 58318 70623 63958.5 84954 FALSE TRUE 63870.19933 71054.99291 62582.67734 64470.9923 92875.05016 56298.43304 59848.16427 58357.95467 98128.23244 0.650885049 0.724103463 0.637764238 0.657007578 0.946466148 0.573723093 0.609897506 0.594711157 1 16.58238065 -1.132903582 4.579295744 1.000034816 0.674564487 0.486950104 0.105058292 3.58E-05 6.77E-06 0.097402176 0.02295546 0.073637056 1.132903582 -0.325470328 NCS(ph)ASTSQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NCSASTSQGR 10 0 F5GYV5;F8WCT1;Q66PJ3-2;A0A0C4DH18;Q66PJ3-5;A0A0A0MTG7;Q66PJ3-6;Q66PJ3 F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCS(0.526)AS(0.028)T(0.223)S(0.223)QGR;NCS(0.719)AS(0.087)T(0.173)S(0.022)QGR 87.719 0.013305 60666000 142780 139139 133245 152155 114736 141464 160285 163448 157024 TRUE FALSE 136031.0724 153317.4223 139354.415 136860.0903 134745.9221 136565.0662 135830.5794 149135.6266 181374.48 0.750001171 0.84530868 0.768324271 0.754571924 0.742915553 0.752945322 0.748895762 0.822252539 1 17.46861195 0.868488006 4.012218912 0.999968892 0.770478181 0.860318954 0.029527013 0.291893746 8.223366721 0.031048892 0.007934777 7.387338614 -0.868488006 -0.229490711 NCSASTS(ph)QER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NCSASTSQER 10 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F8WEP2 H7BZV4 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCS(0.007)AS(0.073)T(0.017)S(0.903)QER;NCSAST(0.005)S(0.995)QER;NCSAS(0.003)T(0.017)S(0.98)QER;NCSAS(0.004)T(0.005)S(0.991)QER;NCSAS(0.02)T(0.01)S(0.97)QER;NCSAST(0.004)S(0.996)QER 172.41 3.91E-06 1356460000 2428190 2077390 2321100 2634370 2030910 2387940 2843930 2523650 2410480 TRUE FALSE 2313414.271 2289078.403 2427524.731 2369558.123 2385100.061 2305245.039 2410036.246 2302665.827 2784284.927 0.830882733 0.822142296 0.871866491 0.851047283 0.856629305 0.827948683 0.865585351 0.827022337 1 21.40887543 -5 0.410481525 3.706204901 0.840827847 0.883890229 0.017684036 259.5227309 1.746035723 631.5859402 0.010361629 1.00E-05 5 -2.865377053 NCSETQYESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NCSETQYESK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 172.8 8.39E-06 253570000 216596 199385 196328 234212 159364 209084 222385 219394 180112 FALSE TRUE 206357.9363 219702.5582 205329.833 210668.5648 187157.0311 201843.3687 188456.0839 200182.6983 208042.8491 0.991901126 1.056044748 0.98695934 1.012621033 0.899608095 0.970200944 0.905852255 0.962218597 1 17.66652117 2.794948192 10.58847374 0.940769955 1.015698321 0.452287281 0.034604644 0.543418061 100.705802 0.009523356 0.010098565 623.6604329 -2.794948192 0.074928367 NCVAIAADRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NCVAIAADRR 10 1 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ;;; 208.84 1.70E-07 1625220000 1449500 1184000 896890 1024920 1022500 1058610 1372410 1218100 1012330 FALSE TRUE 1380985.008 1304650.946 938013.2936 921893.0944 1200823.676 1021950.07 1163023.648 1111436.706 1169316.966 1.181018533 1.115737635 0.802189073 0.788403077 1.026944542 0.873971814 0.994617954 0.950500795 1 20.15723462 3.880845236 5.871784683 0.920586873 1.156764591 0.585946457 0.0806138 0.140976726 6.205067841 0.020466502 0.037500671 7600.553781 -3.880845236 0.236177718 NCVLLSRPEISTDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NCVLLSRPEISTDER 15 1 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 ; 98.439 0.00267 642700000 504260 471860 475340 573470 375210 483460 552270 503470 424820 FALSE TRUE 480424.6291 519943.0705 497134.8092 515823.7061 440646.5052 466717.659 468011.0684 459383.4977 490698.9159 0.979061933 1.059596941 1.013115768 1.051202049 0.897997715 0.951128368 0.953764219 0.936182011 1 18.90447856 2.748591306 24.98388084 0.946017779 1.025497809 0.585667626 0.032550716 436.0490216 1086086.327 0.009150327 0.009601612 560.520248 -2.748591306 0.07948003 NCVVLSDIHIDIMDYIQPATCTDAEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NCVVLSDIHIDIMDYIQPATCTDAEFR 27 0 P53618 P53618 COPB1 Coatomer subunit beta 0 170.44 5.39E-12 61554000 38539 37748 36408 42562 30989 38599 39657 42373 27825 FALSE TRUE 36717.33785 41594.56412 38077.34281 38283.5869 36393.47179 37262.30695 33606.5963 38662.59549 32139.95889 1.142420187 1.294169798 1.184735268 1.191152329 1.132343446 1.15937631 1.045632834 1.202944771 1 14.97208046 1.464772971 0.354522776 0.999368834 1.232815923 0.466636115 0.059797367 0.95253366 0.386729799 0.084367119 0.067201843 29.15902316 -1.464772971 0.233447089 NCWQNYLDFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NCWQNYLDFHR 11 0 P14854;A0A494C160 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;; 221.09 8.66E-12 2938900000 4497510 3375260 2694830 2975160 2744270 2488060 3902610 3022260 2427120 FALSE TRUE 4284921.616 3719202.831 2818390.621 2676091.264 3222869.819 2401897.858 3307195.168 2757614.892 2803505.374 1.528415696 1.326625897 1.005309513 0.954551858 1.149585747 0.856748084 1.179664287 0.983631035 1 21.4188004 3.924226387 2.509251471 1.02668129 1.478534939 0.77093967 0.095153154 0.112929569 1.397630069 0.023666637 0.053406447 8398.9769 -3.924226387 0.451853649 NDAPTPGT(ph)STTPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 NDAPT(0.007)PGT(0.248)S(0.248)T(0.248)T(0.248)PGLR 83.692 0.096315 39992000 70216 61403 61612 64906 57031 61419 65539 69130 57847 TRUE FALSE 66897.02883 67660.03551 64436.97114 58381.52557 66977.18834 59292.04463 55539.82184 63076.61072 66817.61732 1.001188482 1.012607726 0.964370981 0.873744499 1.002388158 0.88737143 0.83121524 0.944011673 1 16.02794092 3.464630478 4.402997921 0.910388145 1.00519811 0.275073237 0.05366328 0.201873196 9.621467167 0.014774113 0.021372751 2914.945761 -3.464630478 0.094809965 NDEELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 137.88 0.0066061 10376610000 9824830 10106330 7508800 10667420 4623786 9713360 8623680 9146970 4517037 FALSE TRUE 9360429.757 11136176.52 7853085.907 9595110.675 5430172.814 9376983.908 7307979.231 8346012.816 5217516.028 1.794039483 2.134382809 1.505138818 1.839018917 1.040758243 1.797212286 1.400662536 1.599614217 1 22.3149317 8 0.056085105 6.54E-11 4.852760948 0.434736574 0.26657455 306.7912212 1.290938021 23.98825465 124.0096896 100000000 -8 4.852760948 NDEELNKLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 163.99 2.13E-05 34977812000 43239010 24786800 39517270 33688830 23165950 42375010 52689790 45764150 25753730 FALSE TRUE 41195187.69 27312603.1 41329175.92 30302364.8 27206084.35 40907552.78 44650994.82 41756798.41 29747486.92 1.384829172 0.918148252 1.389333359 1.018652933 0.914567487 1.375159955 1.50100057 1.403708439 1 24.82626446 2.162611955 14.940825 1.377254041 1.127678383 0.153045719 0.209266624 1.942240324 379.3200833 0.072525842 0.053564579 145.4159199 -2.162611955 -0.249575658 NDEELNKLLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NDEELNKLLGR 11 1 Q7L7L0;P04908 Q7L7L0 HIST3H2A;HIST1H2AB Histone H2A type 3;Histone H2A type 1-B/E 0 ;;;;; 186.46 3.66E-06 7313490000 14088500 6492410 13608810 10715780 9853840 13681450 18999200 15055700 12324050 FALSE TRUE 13422564.53 7153993.96 14232787.4 9638609.436 11572346.58 13207657.96 16100523.1 13737343.09 14235200.73 0.942913611 0.502556592 0.999830467 0.67709684 0.81293877 0.92781677 1.131035902 0.9650263 1 23.7629595 2.131662711 2.876707309 1.044225159 0.764262968 0.380356252 0.14208251 0.231708886 3.82739296 0.058605858 0.038875658 135.4137332 -2.131662711 -0.279962191 NDEWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NDEWAR 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 163.84 0.018062 230244000 305740 255210 279880 304910 252840 300190 331890 293900 272910 FALSE TRUE 291288.2761 281216.1891 292712.7748 274259.8675 296935.2159 289794.345 281254.0849 268164.5579 315231.489 0.924045618 0.89209422 0.928564516 0.870026876 0.941959247 0.919306463 0.892214435 0.850690896 1 18.26605213 -1.902564409 9.047643171 1.012656786 0.90364242 0.549058454 0.02778643 0.006832801 7.36E-05 0.025913381 0.005771945 0.012515137 1.902564409 -0.109014365 NDFQLIGIQDGYLSLLQDSGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDFQLIGIQDGYLSLLQDSGEVR 23 0 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 90.534 0.0054887 8856000 16691 16512 13237 12992 10721 12692 15187 15000 11670 FALSE TRUE 15902.04951 18194.59157 13843.92954 11686.01948 12590.73901 12252.47286 12869.94422 13686.52048 13479.724 1.179701418 1.349774786 1.027018769 0.866933142 0.934050208 0.908955766 0.954763185 1.015341299 1 13.71850334 3.589332558 4.600785829 0.942227054 1.262565293 0.829032374 0.058762876 0.071900748 2.414640095 0.015053928 0.023635896 3884.477037 -3.589332558 0.320338239 NDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGK 35 2 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 53.408 0.031418 177690000 18480 7738.9 14793 12070 12204 13141 19347 14264 14024 FALSE TRUE 17606.48702 8527.502708 15471.27368 10856.70067 14332.37374 12685.92387 16395.25982 13014.96854 16198.7703 1.086902691 0.526429016 0.955089393 0.670217583 0.88478159 0.783141167 1.012129904 0.803454108 1 13.98359668 1.753660097 25 0.935653749 0.807033137 0.109339116 0.160480609 10.49321263 17395.69221 0.068114032 0.037772763 56.71005868 -1.753660097 -0.128620612 NDGSVNGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDGSVNGKR 9 1 K7EP07;Q99426-2;Q99426;A0A494C0X0 K7EP07 TBCB Tubulin-folding cofactor B 0 72.006 0.076923 49919000 46576 32167 47586 40996 33659 39880 50870 49900 45991 FALSE TRUE 44374.44478 35444.85387 49767.86517 36875.00419 39529.11894 38498.9456 43108.84721 45530.49146 53123.04939 0.835314337 0.667221748 0.936841272 0.694143213 0.744104855 0.724712644 0.811490449 0.857076015 1 15.69705034 0.939811559 1.589731908 0.998684206 0.764369445 0.481744611 0.076047776 0.355477468 1.826693156 0.065021717 0.018910351 8.705857595 -0.939811559 -0.234314761 NDHQEDFWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NDHQEDFWK 9 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 185.08 4.33E-05 2222460000 6362020 6197190 6080150 7395340 4059170 6844380 7828250 6054010 2270620 FALSE TRUE 6061299.923 6828690.707 6358930.892 6651946.373 4767087.963 6607357.404 6633906.687 5523888.79 2622736.153 2.311059737 2.603651419 2.424540831 2.536262127 1.817601041 2.519261191 2.529383933 2.106154973 1 21.32264125 0.860089831 4.013792506 1.000155158 2.404376967 0.794509108 0.221250139 0.352491491 9.449364943 0.202779628 0.051817639 7.245858204 -0.860089831 1.404221809 NDHSAYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 96.711 0.0056784 29980000 51296 41685 46470 52972 33221 52066 62076 50240 28554 FALSE TRUE 48871.33974 45932.74889 48600.69547 47647.15392 39014.73188 50262.94136 52605.1661 45840.71926 32982.00849 1.481757539 1.392660757 1.473551724 1.444640763 1.182909522 1.523950289 1.594965513 1.389870459 1 15.00939164 0.964870472 23.79847153 0.999999998 1.446738746 0.625218291 0.106673301 2100.127113 1422731.309 0.103992717 0.025998179 9.222963113 -0.964870472 0.446738748 NDIASHPPVEGSYAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NDIASHPPVEGSYAPR 16 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 188.27 1.21E-09 6270650000 4456300 3820040 3981190 4629260 3248800 4306380 4856410 4482400 3140380 FALSE TRUE 4245659.531 4209306.419 4163731.499 4163917.99 3815389.691 4157248.981 4115475.46 4089897.293 3627374.092 1.170449869 1.160427988 1.147863825 1.147915237 1.051832426 1.146076714 1.134560527 1.127509099 1 21.79049411 -5 0.156428465 0.49671902 1.178502625 0.682517675 0.030124588 77.68081989 0.706553868 12.16387885 0.13433252 1.00E-05 5 0.681783604 NDIHTLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDIHTLLK 8 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;H0YAH9 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 108.98 0.006548 0 415480 421150 483720 517890 326580 397370 398780 454280 427210 FALSE TRUE 395841.0838 464065.6638 505899.0405 465830.7133 383535.4486 383608.9773 337938.7869 414500.8349 493459.5449 0.802175351 0.940433048 1.025208744 0.944009936 0.777237876 0.777386883 0.68483585 0.839989497 1 18.91257229 2.734517083 24.41779488 0.784251119 0.921463326 0.210062149 0.097465083 299.4383501 1808217.983 0.030101102 0.02936699 542.6465955 -2.734517083 0.137212207 NDITAWQECVNNSMAQLEHQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDITAWQECVNNSMAQLEHQAVR 23 0 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 150.53 8.30E-08 24554000 31146 29854 31322 33462 29589 33297 34335 35472 28788 FALSE TRUE 29673.79031 32896.15654 32758.14468 30098.33619 34749.31223 32143.91654 29096.56514 32365.88363 33252.29601 0.8923832 0.989289778 0.985139332 0.905150615 1.045019935 0.966667581 0.875024243 0.973342822 1 15.02116634 4.677374888 3.56281272 0.959955741 0.888682172 0.179288687 0.048065643 0.47507508 10.09309726 0.011619211 0.080628038 47574.5718 -4.677374888 -0.071273569 NDKS(ph)EEEQSSSSVK ddPTM_SK-BR-3_Trastuzumab_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 1 NDKS(0.998)EEEQS(0.001)SSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(0.976)EEEQS(0.021)S(0.003)SSVK 305.85 1.22E-44 4980831000 5810150 5876404 5352965 7238400 2283359 6478004 5343976 6718040 2173448 TRUE FALSE 5535515.724 6475216.249 5598403.74 6510782.28 2681576.087 6253669.097 4528654.312 6129772.803 2510495.215 2.204949721 2.57925855 2.229999765 2.593425488 1.068146265 2.491010164 1.803888844 2.441658827 1 21.25954054 NDKS(ph)EEEQSSSSVKK ddPTM_SK-BR-3_Trastuzumab_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 184.78 2.35E-07 535360000 526160 511490 512520 677140 189778 597040 552450 694500 195290 TRUE FALSE 501289.4595 563611.4125 536019.549 609072.6007 222875.2231 576364.3551 468163.6061 633685.8982 225574.5758 2.222278188 2.498559115 2.376240971 2.700094186 0.988033436 2.555094487 2.075427181 2.809207979 1 17.78324495 NDKSEEEQS(ph)SS(ph)SVKKDETNVK ddPTM_SK-BR-3_Trastuzumab_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(0.021)EEEQS(0.945)S(0.04)S(0.573)S(0.419)VKKDET(0.002)NVK 75.226 0.0059824 118210000 123440 121310 121920 141620 44255 143500 130960 141380 45214 TRUE FALSE 117605.2358 133671.6269 127510.1526 127384.0885 51973.05799 138530.559 110979.6468 129000.0177 52225.5562 2.25187139 2.559506047 2.441527901 2.439114062 0.995165237 2.652543488 2.125006507 2.470055411 1 15.67246833 NDKSEEEQS(ph)SSS(ph)VKKDETNVK ddPTM_SK-BR-3_Trastuzumab_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(0.964)S(0.036)S(0.294)S(0.706)VKKDETNVK 177.12 9.45E-17 155210000 303960 275410 274270 343920 86350 363770 282470 349530 69083 TRUE FALSE 289592.4132 303474.5921 286845.5508 309348.5082 101409.4127 351172.5537 239374.0136 318923.3002 79796.03881 3.629157756 3.803128534 3.594734213 3.876740159 1.270857729 4.400877022 2.999823264 3.996730978 1 16.28402951 NDKSEEEQSS(ph)SSVKKDETNVK ddPTM_SK-BR-3_Trastuzumab_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 1 NDKSEEEQS(0.046)S(0.354)S(0.354)S(0.246)VKKDETNVK 169.36 6.85E-12 896290000 496880 480630 463450 480800 114190 590070 433520 580780 104930 TRUE FALSE 473393.4671 529606.7434 484699.6409 432469.0705 134104.6998 569635.7279 367378.5619 529923.8243 121202.0085 3.905821966 4.36962019 3.999105683 3.568167524 1.106456085 4.699886867 3.031126022 4.372236326 1 16.88705408 3.083024095 4.731383321 3.057964776 4.112641312 0.176445234 1.184829002 0.378980624 15.29234983 0.317081999 0.38122271 1210.665301 -3.083024095 1.054676536 NDKSEEEQSSS(ph)SVKKDETNVK ddPTM_SK-BR-3_Trastuzumab_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 1 NDKSEEEQS(0.012)S(0.071)S(0.575)S(0.341)VKKDETNVK 99.711 0.00056843 557790000 517930 423610 462430 526580 139230 564250 435880 591160 103800 TRUE FALSE 493448.4753 466776.3406 483632.8729 473647.178 163511.6679 544709.881 369378.5005 539394.8965 119896.7739 4.11561095 3.893151797 4.033743839 3.950458071 1.363770372 4.543157113 3.080804334 4.498827442 1 16.87143331 2.951412333 24.9999467 3.114532664 4.001404428 0.175961931 1.131400412 743.2095453 382405.2958 0.308111352 0.326807445 894.1540189 -2.951412333 0.886871764 NDKSEEEQSSSSVK ddPTM_SK-BR-3_Trastuzumab_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 0 ;;;;; 228.51 1.49E-12 2500472000 2893331 2296299 2485044 3146647 1224085 2824791 2637444 2904159 1297676 FALSE TRUE 2756568.978 2530294.479 2598985.725 2830340.065 1437565.036 2726967.779 2235053.478 2649855.442 1498912.966 1.839045388 1.688086323 1.733913699 1.888261779 0.95907172 1.819296944 1.491116247 1.767851437 1 20.51548519 -2.749061667 0.16652195 4.29E-15 1.849558467 0.371609338 0.266837719 57.34880246 1.077312031 22.68634097 1.037366541 0.001782126 2.749061667 1.849558467 NDKSEEEQSSSSVKK ddPTM_SK-BR-3_Trastuzumab_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 0 128.9 3.89E-05 158880000 176430 126280 154110 186510 69162 167040 162970 171700 75599 FALSE TRUE 168090.5036 139148.0756 161176.0959 167761.6605 81223.8309 161255.3629 138105.9334 156665.0378 87322.50681 1.924939053 1.593496117 1.84575663 1.921173207 0.930159175 1.84666438 1.581561712 1.794096888 1 16.41406593 -2.659333539 0.227151932 1.03E-20 1.78253504 0.348544849 0.291828818 53.23675848 1.374445421 27.62188695 0.513252699 0.002191122 2.659333539 1.78253504 NDLAVVDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NDLAVVDVR 9 0 P19338 P19338 NCL Nucleolin 0 ;;;;; 130.98 0.00080473 1281042000 4070460 3479440 3685670 4263930 3333090 3923180 4492460 4072380 3311920 FALSE TRUE 3878057.423 3833998.892 3854661.615 3835311.655 3914379.841 3787319.293 3807052.717 3715780.818 3825515.639 1.013734563 1.002217545 1.007618836 1.002560705 1.02322934 0.990015373 0.995173743 0.971315025 1 21.86722279 2.152523543 10.83879142 0.989399497 1.008737715 0.545990416 0.009368176 0.319867014 38.13135529 0.003201668 0.002364598 142.0769229 -2.152523543 0.019338219 NDLGHPFCNNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDLGHPFCNNLR 12 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 71.176 0.045293 304190000 184710 164450 154550 163990 120070 164620 191120 186490 136090 FALSE TRUE 175979.1244 181207.642 161636.2704 147505.4136 141010.17 158919.1681 161961.1338 170159.947 157194.1421 1.119501795 1.152763325 1.028258866 0.93836457 0.897044687 1.010973857 1.030325505 1.082482748 1 17.26218793 3.632966525 4.278244525 0.993360343 1.135897008 0.571474754 0.050312197 0.156478047 4.847051212 0.014472773 0.023085649 4295.033198 -3.632966525 0.142536665 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 41 0 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ;; 327.46 2.24E-133 1094180000 706630 710340 606070 884710 409925 667860 705290 693160 57534 FALSE TRUE 673229.0003 782724.4536 633858.909 795777.27 481415.7902 644731.8407 597685.057 632463.2357 66456.07888 10.13043519 11.77807157 9.538012469 11.97448425 7.244119701 9.701623262 8.993685259 9.517011031 1 16.02011355 -0.249429981 0.440641158 1.26E-16 10.6533539 0.825680296 1.289391902 2.307465251 0.486002072 6.886076387 0.690016036 0.563079892 0.249429981 10.6533539 NDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NDQDTWDYTNPNLSGQGDPGSNPNKR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 211.49 1.68E-25 1059700000 464510 479750 430400 536320 272580 482320 530050 533170 332400 FALSE TRUE 442553.5329 528637.0704 450134.2657 482408.0947 320117.8657 465617.1375 449181.1375 486482.8083 383946.8943 1.152642564 1.37684945 1.172386787 1.256444841 0.83375558 1.212712342 1.169904339 1.267057542 1 18.55054725 -4.999999977 0.029554428 9.95E-06 1.878796086 0.118356053 0.140984945 2857.97119 6.358326978 313.1500821 128.6134737 1.00E-05 4.999999977 1.878786132 NDQWHWDNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NDQWHWDNIR 10 0 O75116;E9PF63;C9JFJ0;D6REE7 O75116 ROCK2 Rho-associated protein kinase 2 0 ; 130.01 0.00028807 144211000 279480 225030 202404 239700 228141 217556 316430 247310 209990 FALSE TRUE 266269.5343 247960.8128 211684.4236 215604.9006 267928.7182 210021.9812 268152.7919 225654.2253 242554.1767 1.097773445 1.022290427 0.872730482 0.888893787 1.104613913 0.865876581 1.105537721 0.930325045 1 17.8879475 4.15863311 3.229669078 0.974206302 1.082413111 0.18360532 0.086314676 0.377617008 7.640028578 0.020727192 0.054164115 14408.97572 -4.15863311 0.108206809 NDRGDQVPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NDRGDQVPNR 10 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;; 136.49 0.0001061 697930000 234901 189623 216373 211564 196761 230194 234394 224856 213801 FALSE TRUE 223797.6953 208945.7993 226293.9161 190297.1848 231076.0561 222222.3241 198632.8904 205166.4166 246956.1671 0.906224363 0.846084557 0.916332314 0.770570693 0.935696641 0.89984521 0.804324479 0.830780697 1 17.91389547 NDS(ph)PTQIPVSSDVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NDSPTQIPVSSDVCR 15 0 Q8TC07-2;Q8TC07-3;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 NDS(0.996)PT(0.004)QIPVSSDVCR;NDS(1)PTQIPVSSDVCR;NDS(0.997)PT(0.003)QIPVSSDVCR;NDS(1)PTQIPVSSDVCR;NDS(0.992)PT(0.008)QIPVSSDVCR;NDS(1)PTQIPVSSDVCR 314.56 2.99E-56 1483095000 1250820 1015124 1110283 1229852 849449 1142474 1354620 1211580 945357 TRUE FALSE 1191696.217 1118566.29 1161190.574 1106224.94 997592.6367 1102909.839 1147947.84 1105487.632 1091958.135 1.091338742 1.024367376 1.0634021 1.013065341 0.913581395 1.010029417 1.051274589 1.012390124 1 20.05848612 4.397449728 0.857931619 1.006315835 1.109620111 0.338662881 0.038240312 1.917739283 1.539081039 0.014362832 0.16938683 24971.79308 -4.397449728 0.103304276 NDS(ph)WGSFDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NDS(1)WGSFDLR;NDS(1)WGSFDLR;NDS(1)WGSFDLR;NDS(1)WGSFDLR;NDS(0.998)WGS(0.002)FDLR;NDS(0.994)WGS(0.006)FDLR;NDS(1)WGSFDLR;NDS(1)WGSFDLR;NDS(0.984)WGS(0.016)FDLR;NDS(0.944)WGS(0.056)FDLR 243.26 2.21E-12 6413899000 7954530 6618310 6759950 7526560 6042730 7424640 8571560 7581880 5720340 TRUE FALSE 7578535.131 7292723.313 7069900.394 6769975.889 7096580.199 7167522.855 7263811.095 6917970.393 6607421.112 1.14697323 1.103717046 1.069993917 1.024601849 1.074031771 1.084768586 1.099341327 1.047000074 1 22.65565586 4.04514659 1.929262804 1.064247583 1.140725031 0.494809891 0.029592189 0.293398485 2.108298842 0.007963078 0.024033795 11095.49265 -4.04514659 0.076477448 NDSWGSFDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ;;; 176.65 5.65E-06 272992000 649901 511062 511126 597830 477071 513689 681060 598160 517366 FALSE TRUE 619181.4677 563139.7988 534561.6327 537734.9926 560272.0314 495899.8211 577151.7885 545781.9394 597596.4769 1.036119675 0.94234123 0.894519384 0.89982959 0.937542394 0.82982387 0.965788472 0.913295109 1 19.18881212 4.378595998 1.922071355 0.916139043 1.038139214 0.386127287 0.045133681 0.359249431 2.241603678 0.01064169 0.060400475 23910.90413 -4.378595998 0.122000171 NDTFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDTFLR 6 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494C007 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 126.2 0.040927 61862000 92001 76584 71820 87522 75785 80436 102600 86292 76974 FALSE TRUE 87652.29506 84387.99667 75113.01804 78724.12228 89001.88001 77650.48115 86946.48562 78735.81502 88910.73479 0.985846032 0.949131698 0.844813826 0.885428767 1.001025132 0.873353272 0.977907626 0.885560278 1 16.44007 -1.504283432 4.562750134 1.000377838 0.930954271 0.156534479 0.05305061 0.000194559 2.11E-05 0.049011985 0.011489536 0.031312415 1.504283432 -0.069423568 NDTKEDVFVHQTAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 192.4 8.15E-08 1181420000 1866140 1569050 1604920 2013100 1017050 1777950 2062250 2132230 1032850 FALSE TRUE 1777931.261 1728937.979 1678507.169 1810739.363 1194423.198 1716379.146 1747615.887 1945520.638 1193019.103 1.490278954 1.449212317 1.406940732 1.517779019 1.001176926 1.438685384 1.464868318 1.630753969 1 20.18618571 NDTKEDVFVHQTAIKK ddPTM_SK-BR-3_Trastuzumab_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 0 150.39 4.47E-07 868390000 1407800 958010 1394400 1300400 747710 1552400 2065200 1858700 982070 FALSE TRUE 1341256.084 1055632.308 1458334.619 1169681.321 878110.3873 1498639.999 1750115.81 1695942.374 1134364.4 1.182385558 0.930593651 1.285596251 1.031133665 0.774099035 1.321127496 1.542816233 1.49505959 1 20.11345273 2.021992856 21.49476343 1.412696661 1.049163214 0.341359736 0.19936738 40.43964214 39522.92048 0.068317101 0.05044507 105.194457 -2.021992856 -0.363533447 NDTSGEYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NDTSGEYKK 9 1 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;; 88.187 0.020771 1179820000 1966780 1331290 1446280 3301620 1470490 2262650 2314670 1902510 1094670 FALSE TRUE 1873814.207 1466949.965 1512593.369 2969734.885 1726942.99 2184293.863 1961524.58 1735916.139 1264425.833 1.481948691 1.160170827 1.196268954 2.348682547 1.36579224 1.727498606 1.551316438 1.372888859 1 20.27005098 0.892877268 3.511576458 1.000320037 1.522805266 0.212867243 0.331590621 0.777077742 20.22628003 0.309651251 0.079949972 7.814069466 -0.892877268 0.522485229 NDYDKS(ph)PIKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NDYDKSPIKPK 11 2 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 NDY(0.003)DKS(0.997)PIKPK;NDY(0.044)DKS(0.956)PIKPK 93.424 0.0048317 897180000 2706500 2398000 2315500 3009700 945120 3131000 2956500 3373300 950580 TRUE FALSE 2578569.109 2642358.926 2421667.965 2707159.238 1109948.629 3022572.685 2505431.625 3077915.969 1097991.092 2.34844265 2.406539494 2.205544275 2.465556651 1.010890377 2.752820773 2.28183238 2.803224901 1 20.06643492 NDYEARPQYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NDYEARPQYYK 11 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 113.77 0.0012289 272000000 275100 285260 215990 287810 156610 271950 279110 302920 163230 FALSE TRUE 262096.5682 314328.3183 225893.3551 258878.792 183922.7344 262532.3033 236526.6433 276394.7189 188542.8747 1.390116537 1.667145039 1.198100726 1.373049989 0.975495545 1.392427604 1.254497915 1.465951547 1 17.5245331 3.727553909 24.93514278 1.252000059 1.528630791 0.333290978 0.170421307 663.454528 1503022.821 0.040787619 0.063863907 5340.155572 -3.727553909 0.276630732 NECDPALALLSDYVLHNSNTMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NECDPALALLSDYVLHNSNTMR 22 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 62.735 0.028407 22287000 63585 56266 53248 63225 31649 68783 63634 70141 30875 FALSE TRUE 60579.46306 61999.56937 55689.47347 56869.50288 37168.57558 66401.02746 53925.46458 63999.0822 35662.93731 1.698667234 1.738487462 1.561550384 1.594638781 1.042218571 1.861905734 1.512087019 1.794554432 1 15.12213791 -1.683258649 2.708816307 0.916092916 1.605461379 0.412685812 0.225070288 40863965.37 34626755.46 23518582.83 0.052587581 0.020736781 1.683258649 0.689368463 NEDEDS(ph)PNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEDEDSPNKLYTLVTYVPVTTFK 23 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 NEDEDS(0.91)PNKLY(0.043)T(0.046)LVTYVPVTTFK 61.911 0.029785 53154000 169310 175460 150460 202720 67262 176560 162320 186610 73238 TRUE FALSE 161307.0518 193339.5735 157358.7398 182342.2005 78992.4715 170445.6829 137555.1028 170269.4391 84595.37499 1.906806984 2.285462692 1.860134078 2.155462996 0.933768206 2.014834534 1.626035735 2.01275116 1 16.36829117 NEDEEEEEEEKDEAEDLLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;; 269.01 2.95E-37 1244300000 2053430 2063040 1679680 2344090 891660 2203670 1986730 2316920 841002 FALSE TRUE 1956368.433 2273266.121 1756694.989 2108457.62 1047165.222 2127356.355 1683617.85 2114038.202 971420.2949 2.01392584 2.340146828 1.808377896 2.170489572 1.077973383 2.189944318 1.733150788 2.176234338 1 19.8897361 3.257547101 1.905643526 1.73918152 2.154281867 0.159735494 0.423779314 0.577641444 4.317403202 0.120770907 0.170264998 1809.45214 -3.257547101 0.415100347 NEDVQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 116.73 0.031323 0 427680 391220 364800 437540 291690 378100 399000 388990 319130 FALSE TRUE 407464.414 431085.7628 381526.4408 393557.6479 342560.6436 365006.3022 338125.2219 354927.9734 368619.0505 1.105380781 1.169461432 1.035015527 1.06765412 0.92930803 0.990199236 0.917275495 0.962858466 1 18.49177111 3.160731474 1.330482252 0.952582517 1.135517511 0.742396974 0.039840365 0.164307051 0.611458991 0.0132455 0.018409369 1447.87635 -3.160731474 0.182934994 NEEDAAELVALAQAVNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 285.58 2.69E-39 122824000 272490 232267 243444 284657 217487 246109 293338 287275 253040 FALSE TRUE 259609.9377 255935.2714 254606.1482 256042.7375 255416.6639 237586.1836 248583.9006 262119.6781 292280.1509 0.88822295 0.875650538 0.871103109 0.87601822 0.873876188 0.812871428 0.850498742 0.896809713 1 18.15699233 -1.559523629 4.937294105 1.000890667 0.86680838 0.764194403 0.023010303 0.000237104 2.12E-05 0.023416351 0.005483184 0.027572514 1.559523629 -0.134082287 NEEDEGHS(ph)NS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.999)NS(0.552)S(0.449)PR 72.583 0.038399 0 56000 64174 48692 68364 39379 62123 48444 48851 23689 TRUE FALSE 53352.99098 70713.40356 50924.57636 61491.92084 46246.68513 59971.66493 41052.97806 44573.34746 27362.56913 1.949853127 2.584311554 1.861103616 2.247300703 1.690144113 2.191741011 1.500333462 1.628989853 1 14.73991607 1.250747265 0.475258753 0.970869118 2.24972576 0.663702672 0.255212789 0.487192043 0.298517832 0.261372317 0.148009124 17.81341826 -1.250747265 1.278856643 NEEDEGHS(ph)NSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(1)NS(0.017)S(0.983)PR 186.17 1.17E-05 38374000 123900 152600 109140 159170 96810 138980 107760 117240 53724 TRUE FALSE 118043.4925 168150.1135 114144.177 143169.9292 113693.6333 134167.0878 91319.23285 106973.8441 62055.24354 1.902232363 2.709684209 1.839396165 2.30713669 1.832135801 2.162058838 1.471579639 1.72384859 1 15.9212655 1.284660046 0.516966656 0.992906765 2.277661452 0.624892309 0.282906575 0.479035228 0.333817238 0.273560456 0.14719294 19.2601669 -1.284660046 1.284754687 NEEDEGHSNS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.674)S(0.326)PR;NEEDEGHS(0.002)NS(0.499)S(0.499)PR;NEEDEGHS(0.043)NS(0.479)S(0.479)PR;NEEDEGHS(0.004)NS(0.498)S(0.498)PR;NEEDEGHS(0.006)NS(0.497)S(0.497)PR 185.33 5.64E-06 885437000 781527 957082 672480 941180 544082 809120 699675 749962 335561 TRUE FALSE 744585.7675 1054609.744 703313.8732 846570.7983 638969.7285 781099.9715 592926.7283 684291.3515 387598.0861 1.921025398 2.720884808 1.814544237 2.184145972 1.648536852 2.015231756 1.529746275 1.765466281 1 18.56420192 1.301352631 0.308439643 0.89361206 2.387925407 0.598929395 0.28134317 0.928228609 0.311215492 0.533371048 0.40067941 20.01486343 -1.301352631 1.494313346 NEEDEGHSNS(ph)SPRHS(ph)EAATAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEEDEGHSNSSPRHSEAATAQR 22 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.004)NS(0.538)S(0.458)PRHS(0.999)EAAT(0.001)AQR 102.72 0.00080552 56159000 36061 51200 32891 48926 36639 40618 36006 35756 23754 TRUE FALSE 34356.468 56417.33821 34399.08488 44007.86553 43028.83 39211.38848 30512.6234 32625.01509 27437.649 1.252165154 2.056201616 1.253718381 1.603922607 1.568240413 1.429108903 1.112071351 1.189060152 1 14.74386925 1.862235662 2.073692412 1.088787036 1.581623674 0.445127205 0.226204428 0.27243367 2.193388389 0.135040224 0.063047468 72.81748281 -1.862235662 0.492836638 NEEDEGHSNSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.041)S(0.959)PR;NEEDEGHSNS(0.016)S(0.984)PR;NEEDEGHSNS(0.029)S(0.971)PR;NEEDEGHSNS(0.253)S(0.747)PR;NEEDEGHSNS(0.023)S(0.977)PR;NEEDEGHSNS(0.026)S(0.974)PR 249.86 1.24E-17 14963860000 12130480 13643020 10250320 15068550 8284960 11984110 10857950 11316690 5125798 TRUE FALSE 11557096.25 15033259.25 10720307.31 13553830.73 9729854.401 11569097.27 9201370.308 10325740.63 5920680.575 1.9519878 2.539109999 1.810654565 2.289235258 1.643367562 1.954014766 1.554106862 1.744012449 1 22.49733159 1.149206261 0.332096269 0.903725807 2.298576373 0.661930035 0.24141781 0.796073555 0.280007312 0.419539515 0.270347562 14.09958276 -1.149206261 1.394850566 NEEDEGHSNSSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 223.06 1.64E-11 1105400000 1670550 1795610 1380200 1980130 1087240 1487380 1419770 1509510 805640 FALSE TRUE 1591586.412 1978584.7 1443483.535 1781083.57 1276854.312 1435871.658 1203158.011 1377329.302 930574.5366 1.710326631 2.126196906 1.551174547 1.913961215 1.372113959 1.542994786 1.29291955 1.480084881 1 19.82776219 2.049419049 0.399052327 1.025873484 1.975129856 0.642846723 0.1884774 0.623642898 0.24659887 0.192877639 0.198919451 112.0518546 -2.049419049 0.949256372 NEEPS(ph)EEEIDAPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK 218.83 1.40E-12 8486380000 7555230 8312240 7341710 8764150 3630540 9229700 8654520 8934800 3493930 TRUE FALSE 7198109.251 9159266.706 7678334.665 7883160.991 4263705.027 8910073.175 7334114.023 8152421.546 4035750.82 1.783586146 2.269532267 1.902578977 1.953331943 1.056483717 2.207785756 1.817286138 2.020050769 1 21.94440567 2.973305148 24.9451491 1.708476464 2.006173458 0.146936391 0.396498016 1496.688987 1398590.253 0.111575014 0.118690173 940.38382 -2.973305148 0.297696995 NEEPVRS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEEPVRSPER 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PER 81.185 0.013182 93897000 162970 182340 145670 206100 123350 180640 183030 168240 119330 TRUE FALSE 155266.7311 200920.6533 152349.1136 185382.4364 144862.2009 174384.3915 155105.4119 153508.0137 137835.0869 1.126467393 1.457688733 1.105299942 1.344958244 1.050982041 1.265166913 1.125297015 1.113707816 1 17.07258366 1.403023655 0.449183107 0.995382977 1.278147577 0.28768467 0.118141974 1.052449159 0.588506021 0.123284179 0.079015877 25.29435764 -1.403023655 0.2827646 NEEPVRS(ph)PERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 91.812 0.0082395 8442550000 5706500 5130990 5056750 5941460 4659600 5403720 5780180 5704870 5169500 TRUE FALSE 5436765.054 5653843.714 5288606.989 5344213.153 5472232.765 5216587.821 4898307.381 5205321.339 5971159.658 0.91050405 0.946858573 0.885691774 0.89500423 0.916443887 0.873630604 0.820327652 0.871743788 1 22.50957971 2.220109578 7.264698771 0.870159523 0.913935395 0 0.049002732 0.289200848 67.19782725 0.016654016 0.012649138 166.0005694 -2.220109578 0.043775872 NEEQKAEQEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEEQKAEQEEGK 12 1 Q9H307 Q9H307 PNN Pinin 0 155.98 0.00028218 0 144090 132260 133230 149870 72855 184750 156270 160820 68593 FALSE TRUE 137279.1513 145737.4444 139338.7273 134804.7829 85560.88893 178352.0612 132428.1414 146737.7482 79230.05212 1.732665164 1.839421286 1.758660048 1.701434989 1.079904489 2.251065807 1.671438272 1.852046595 1 16.27376013 3.190835191 4.766003421 1.648264921 1.784910888 0.04202545 0.358447323 0.851455643 41.65516287 0.096325153 0.119194261 1551.79801 -3.190835191 0.136645966 NEES(ph)EKEDA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NEESEKEDA 9 1 Q9BYD6 Q9BYD6 MRPL1 "39S ribosomal protein L1, mitochondrial" 1 NEES(1)EKEDA;NEES(1)EKEDA 88.338 0.033809 210112000 681180 670860 605880 682680 272340 592160 529290 685760 236260 TRUE FALSE 648981.9714 739221.3967 633660.1973 614055.7094 319836.0098 571653.3507 448537.0894 625711.219 272897.9942 2.378111915 2.708782815 2.321967222 2.250129069 1.17199839 2.094751017 1.643607132 2.292839201 1 18.05800227 2.951277855 6.126399596 1.711126396 2.483954403 0.493532721 0.391005434 0.168569565 15.39298649 0.106858434 0.115428681 893.8771889 -2.951277855 0.772828007 NEGGTWSVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NEGGTWSVEK 10 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 152.64 4.11E-05 131950000 424360 313610 399670 341820 428910 364340 578580 381120 533050 FALSE TRUE 404301.3438 345567.2155 417995.2648 307459.6042 503711.7682 351722.8144 490306.9946 347747.1124 615712.6716 0.656639635 0.561247529 0.6788804 0.499355655 0.818095504 0.571245048 0.796324353 0.564787974 1 19.23189773 -5 0.21276714 2.736684966 0.595883012 0.534702761 0.103526162 101.6901663 1.014614312 75.35441197 0.183053236 1.00E-05 5 -2.140801954 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK 33 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 187.69 3.81E-20 24791000 7353.3 9141.7 6506.2 10394 6228.2 9687.5 12227 9843.8 4710.7 FALSE TRUE 7005.724082 10073.24962 6804.515706 9349.175373 7314.396108 9352.019446 10361.54659 8981.824687 5441.211297 1.287530239 1.851288082 1.250551639 1.718215828 1.344258789 1.718738519 1.904272049 1.650703161 1 12.40971214 4.736775543 5.062978411 1.605005015 1.27338505 0.055368079 0.286306736 0.348070587 25.65999682 0.062199032 0.395461095 54547.58695 -4.736775543 -0.331619966 NEGS(ph)ESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGS(0.96)ES(0.04)APEGQAQQR 108.77 0.0020822 0 18154 22418 14288 23472 11289 18391 13765 19120 12219 TRUE FALSE 17295.8964 24702.41969 14943.11893 21112.54997 13257.79803 17754.11506 11664.89644 17445.75144 14113.86011 1.225454713 1.750224211 1.058754927 1.495873545 0.939345999 1.257920577 0.826485196 1.236072293 1 13.784825 2.900439705 1.223185034 1.026028552 1.450087635 0.293485627 0.22813456 0.438317646 1.370621728 0.089759437 0.098076293 795.1328667 -2.900439705 0.424059083 NEGSES(ph)APEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGSES(1)APEGQAQQR;NEGSES(1)APEGQAQQR 237.34 1.03E-17 735370000 334005 442550 309114 468150 236513 406064 347742 351383 234665 TRUE FALSE 318217.2456 487646.3481 323287.1827 421090.6726 277760.7923 392001.9019 294687.5712 320614.0417 271055.6497 1.1739923 1.799063582 1.192696714 1.553521106 1.024737144 1.446204506 1.087184759 1.18283475 1 18.04822955 2.031498447 0.581573684 1.028034176 1.468061052 0.262547201 0.218096627 0.925607636 0.638620916 0.184698622 0.123654611 107.5222755 -2.031498447 0.440026877 NEHFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NEHFQK 6 0 P15924 P15924 DSP Desmoplakin 0 ; 69.344 0.093749 280530000 496360 432290 454880 532780 329160 516650 557140 519660 310840 FALSE TRUE 472898.0465 476340.8425 475736.6979 479223.9422 386565.3998 498758.281 472138.0604 474155.8155 359043.4796 1.317105235 1.326694034 1.325011384 1.33472398 1.076653446 1.389130591 1.314988538 1.320608345 1 18.45379904 -0.974663555 4.529532289 0.999993109 1.303794313 0.566561857 0.082591136 5.30E-06 1.20E-06 0.073764495 0.017386064 0.106007464 0.974663555 0.303801204 NEHRPAS(ph)ALVNPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEHRPASALVNPLAR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 NEHRPAS(1)ALVNPLAR 91.547 0.003383 280620000 234150 204900 241940 260360 206000 227410 277670 271960 246970 TRUE FALSE 223082.1935 225779.543 253033.1883 234188.1181 241926.3348 219534.7347 235306.3417 248145.7406 285268.8463 0.782006856 0.79146232 0.886999024 0.820938288 0.848064336 0.769571362 0.824858181 0.869866247 1 18.12196268 -4.99999998 0.246021859 2.083285711 0.801438474 0.717632679 0.035386142 95.88335196 0.952766028 52.04917572 0.05278169 1.00E-05 4.99999998 -1.281847237 NEKAPVDFGYVGIDSILEQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEKAPVDFGYVGIDSILEQMR 21 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2;K7ENQ5;K7ER14;K7EN52;K7EKN4;K7EIR4;K7EJL9;K7EQ08 Q9UHD8 9-Sep Septin-9 0 181.26 4.65E-17 98071000 304400 174410 244630 239400 226880 284340 390300 305060 289200 FALSE TRUE 290011.6153 192182.5773 255846.5275 215335.0572 266447.8002 274493.2345 330752.5666 278347.3292 334047.659 0.868174368 0.575314845 0.76589828 0.644623758 0.797634089 0.821718779 0.990135862 0.833256338 1 18.34969442 2.157261176 1.917940669 0.938389092 0.712023968 0.534865999 0.090115226 0.242579956 1.753053049 0.044071642 0.026230566 143.6352968 -2.157261176 -0.226365124 NEKDNALLSAIEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NEKDNALLSAIEESR 15 1 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;; 185.25 3.93E-07 259551000 456103 388310 406474 526670 312918 478610 491500 493540 332582 FALSE TRUE 434543.9151 427879.2305 425111.235 473728.131 367490.8001 462035.6157 416512.648 450323.0212 384157.118 1.131161951 1.1138131 1.106607727 1.233162445 0.956615882 1.20272564 1.084224731 1.172236567 1 18.55133696 -1.462853355 5.462081943 0.999857166 1.122678991 0.215216574 0.07493297 0.000110007 1.08E-05 0.06123713 0.014416991 0.034446622 1.462853355 0.122821825 NELDS(ph)PHEEKQDKENHTESTVNSLPH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NELDSPHEEKQDKENHTESTVNSLPH 26 2 Q8TBZ6 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 1 NELDS(1)PHEEKQDKENHTESTVNSLPH 82.554 0.007358 63568000 101370 89103 82466 106280 41052 97072 91209 108240 18475 TRUE FALSE 96578.441 98182.697 86247.14767 95596.53248 48211.4558 93710.3723 77293.39188 98761.93178 21340.00864 4.525698307 4.600874285 4.041570419 4.479685743 2.259205074 4.391299641 3.621994404 4.628017422 1 14.38127314 2.87570937 21.58332734 3.454032195 4.435709269 0.231734934 1.050272383 9.296518125 1576.509303 0.2845435 0.30180434 751.1200764 -2.87570937 0.981677073 NELESYAYSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NELESYAYSLK 11 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 140.24 9.00E-05 98100000 268690 216830 234090 253470 204390 242900 279300 256480 200230 FALSE TRUE 255989.5562 238925.2235 244823.258 227990.714 240035.5513 234488.3121 236687.6553 234021.2515 231280.6458 1.106835184 1.033053253 1.058554888 0.985775153 1.037854034 1.013869152 1.023378565 1.011849698 1 17.81928502 8 0.481883614 1.013142534 3.749878294 0.713079058 0.018102542 45.51732854 0.506733027 0.008731754 124.9115557 99999999.94 -8 2.73673576 NELMYQLEQDHDLQAILQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;;;;; 330.64 8.05E-80 1488994000 1254266 1229807 1095833 1483976 932682 1217327 1304306 1304775 822689 FALSE TRUE 1194979.332 1355125.731 1146078.027 1334803.913 1095341.446 1175170.661 1105310.164 1190521.984 950267.4084 1.257519011 1.426046731 1.206058439 1.404661363 1.15266654 1.236673646 1.163156975 1.252828386 1 19.85797402 0.654083649 0.248106051 0.925719547 1.373293386 0.539437837 0.082835788 2.525603278 0.411495238 0.370730159 0.166388814 4.509035444 -0.654083649 0.447573839 NENLAANFLLQQNFDED ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NENLAANFLLQQNFDED 17 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;; 187.16 1.12E-09 289870000 556169 529134 426746 595223 383210 499786 527958 565970 377192 FALSE TRUE 529879.9936 583053.3562 446312.7262 535390.0532 450041.7027 482478.2855 447408.3105 516410.6664 435685.0089 1.216199738 1.338245164 1.024393121 1.228846626 1.032952003 1.107401622 1.026907746 1.185284451 1 18.73292595 3.739175517 24.99999689 1.088751042 1.277222455 0.503686038 0.078667859 36.63068385 1489266.365 0.01843377 0.030900289 5484.985922 -3.739175517 0.188471412 NENLAANFLLSQNFDDE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725;K7EQ16;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 108.58 0.0015092 13554000 41344 34939 31994 41813 25404 37221 35683 36806 25951 FALSE TRUE 39389.75106 38499.32382 33460.95655 37609.8778 29834.44956 35932.02744 30238.90299 33583.07152 29975.34854 1.314071495 1.284366177 1.116282485 1.254693594 0.995299505 1.198719254 1.008792373 1.120356331 1 14.87148891 4.214692101 0.319095471 1.012978087 1.511868323 0.579800318 0.076799506 2.926202416 0.312421747 0.073298831 0.553584907 16394.27066 -4.214692101 0.498890236 NENTEGS(ph)PQEDGVELEGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NENTEGSPQEDGVELEGLK 19 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK 398.44 1.46E-127 513920000 1610620 1828930 1479560 2068220 920070 1856690 1701240 1968940 951180 TRUE FALSE 1534489.185 2015300.046 1547399.289 1860318.596 1080529.917 1792392.36 1441684.593 1796529.176 1098684.136 1.396660909 1.834285196 1.408411424 1.693224226 0.983476398 1.631399144 1.312192053 1.63516439 1 20.06734525 NENTFLDLTVQQIEHLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NENTFLDLTVQQIEHLNK 18 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;; 288.82 6.72E-41 383183000 755007 672596 678237 757859 485958 743527 844187 800907 519390 FALSE TRUE 719319.3154 741134.2971 709334.8373 681677.5735 570708.9213 717778.4736 715390.7686 730775.3372 599934.3485 1.198996719 1.235359 1.182354101 1.136253617 0.951285624 1.196428368 1.192448424 1.218092178 1 19.19444511 NEQDAYAINSYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEQDAYAINSYTR 13 0 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 217.09 6.14E-11 95202000 95561 79029 77503 79912 81653 66339 91858 92435 87417 FALSE TRUE 91044.02091 87082.14495 81056.58921 71879.09394 95893.25735 64041.6638 77843.37501 84340.90137 100973.1819 0.901665365 0.862428452 0.802753639 0.711863215 0.949690359 0.634244287 0.770931187 0.835280218 1 16.62361264 3.850104806 2.910048568 0.79408632 0.889246953 0.043267627 0.106126218 0.522425236 8.549196153 0.02568742 0.05169076 7081.166504 -3.850104806 0.095160633 NEQESAVHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEQESAVHPR 10 0 Q9UJU6-2;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 62.338 0.085735 57065000 45327 49806 62365 53520 124450 46777 61087 51997 99230 FALSE TRUE 43184.48254 54881.28802 65224.49694 48140.06792 146154.0406 45157.10076 51767.05621 47443.86703 114618.0816 0.376768499 0.478818763 0.569059402 0.420004132 1.275139477 0.393978857 0.451648252 0.413930039 1 16.80647513 3.726776703 1.497600308 0.626808249 0.401738456 0.101205866 0.284890333 1.081036671 4.702063105 0.084427798 0.199666142 5330.607461 -3.726776703 -0.225069793 NESEDNKFS(ph)DDS(ph)DDDFVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;NESEDNKFS(1)DDS(1)DDDFVQPR 199.46 8.28E-22 548180000 1085270 924000 972080 1112230 539400 1125750 1150780 1091210 631440 TRUE FALSE 1033971.438 1018156.651 1016650.83 1000426.527 633471.1892 1086764.995 975207.3755 995657.8675 729360.4903 1.417641141 1.395958054 1.393893477 1.371648918 0.86852962 1.490024494 1.337071844 1.36511078 1 19.47627252 -4.07975174 0.213859814 6.81E-17 1.386739377 0.26790575 0.169809195 133.0696327 1.896538486 58.57388725 0.339003266 8.32E-05 4.07975174 1.386739377 NESSFASHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NESSFASHK 9 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YB83 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 123.51 0.00055561 186040000 339510 331240 260790 326490 212880 264950 287140 304730 159430 FALSE TRUE 323462.0351 364993.7326 272747.4795 293670.6049 250006.2046 255774.7151 243331.5193 278046.2257 184153.5901 1.756479659 1.982007151 1.481086952 1.59470475 1.357596148 1.388920601 1.321350939 1.509860468 1 17.49055 4.989953063 0.143762174 0.853846937 2.944657194 0.712150788 0.1409055 13.67285164 0.305552663 0.718169027 5.485793636 97713.16104 -4.989953063 2.090810257 NEYLQADEANKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NEYLQADEANKR 12 1 Q9UBS8;Q9UBS8-2;E7EP22 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 68.809 0.082847 117000000 129580 110490 105240 136960 80394 119660 133760 134790 98002 FALSE TRUE 123455.0102 121749.0566 110065.3581 123192.5206 94414.68815 115516.1442 113352.4553 122987.073 113199.6496 1.090595338 1.07552503 0.972311827 1.088276518 0.834054597 1.020463796 1.001349878 1.086461605 1 16.78850997 3.809176934 6.166794067 0.998725476 1.084279682 0.194147921 0.070003468 0.324549019 22.43204767 0.016732764 0.03038209 6444.31757 -3.809176934 0.085554206 NFAADHFNQEILPVFLNANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFAADHFNQEILPVFLNANR 20 0 Q6PI48;A0A3B3ITK9;A0A3B3ITS3 Q6PI48 DARS2 "Aspartate--tRNA ligase, mitochondrial" 0 ; 185.87 3.48E-17 199230000 548710 431870 476490 473790 404920 401860 487550 486360 401440 FALSE TRUE 522773.5657 475878.044 498337.5378 426163.7291 475537.9198 387943.4874 413165.293 443771.74 463693.2649 1.127412463 1.026277671 1.074713772 0.919063875 1.02554416 0.836638176 0.891031473 0.957037278 1 18.82281125 3.340820304 0.951017202 0.914292635 1.100715851 0.509551143 0.060814395 0.387081397 0.746667075 0.02440577 0.045763396 2191.897817 -3.340820304 0.186423216 NFAFLEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFAFLEFR 8 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 90.657 0.03034 124054000 396140 382320 248640 359980 270850 284130 352240 341050 219050 FALSE TRUE 377415.2473 421278.8427 260040.3899 323794.1265 318086.1542 274290.5069 298499.3187 311185.854 253019.1552 1.491646934 1.665007704 1.027749815 1.279721791 1.257162344 1.084070123 1.179749882 1.229890495 1 17.94888709 3.742823255 24.99998619 1.164899897 1.578327337 0.750915241 0.102036666 147.7578366 866583.2106 0.024168978 0.041707629 5531.249586 -3.742823255 0.41342744 NFDEALVDYFCDEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFDEALVDYFCDEFK 15 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 218.31 4.55E-12 44679000 94315 78913 76501 92853 57990 79198 97751 97206 53542 FALSE TRUE 89856.91686 86954.32442 80008.64652 83519.24003 68103.43764 76455.3534 82837.28963 88694.12732 61845.01991 1.452936987 1.406003661 1.293695865 1.350460234 1.101195177 1.236241067 1.33943347 1.434135318 1 15.91636981 -5 0.083534736 0.092280042 1.602071277 0.46661096 0.105983445 220.2470513 1.294365689 38.04298548 3.213177231 1.00E-05 5 1.509791235 NFDEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NFDEILR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 200.66 0.00081247 6362410000 8438870 7481470 7254900 8909130 6744290 7589670 8682000 8275900 6541850 FALSE TRUE 8039981.339 8243840.299 7587544.341 8013567.326 7920492.041 7326837.825 7357401.444 7551218.323 7556326.687 1.064006583 1.090985163 1.004131327 1.060510968 1.048193437 0.969629574 0.973674346 0.999323962 1 22.84925365 2.297596054 5.624061234 0.981942458 1.058408104 0.671925244 0.02343883 0.107803855 6.841109022 0.008465441 0.00695345 198.424847 -2.297596054 0.076465646 NFDFEGSLS(ph)PVIAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.051)LS(0.949)PVIAPK;NFDFEGS(0.145)LS(0.855)PVIAPK;NFDFEGS(0.001)LS(0.999)PVIAPK;NFDFEGS(0.079)LS(0.921)PVIAPK 278.79 1.30E-33 300595000 431496 417907 437340 505389 309532 462643 506867 472263 337779 TRUE FALSE 411100.0392 460492.1984 457392.4716 454586.3375 363514.2828 446621.5569 429535.1299 430909.1481 390160.0422 1.053670276 1.180264888 1.172320131 1.165127867 0.931705566 1.144713729 1.100920349 1.104442028 1 18.57370651 NFDKLNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFDKLNVR 8 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 75.378 0.035152 314970000 1150380 735890 979330 1158420 1012970 1105910 1517550 1211300 1219120 FALSE TRUE 1096003.817 810878.0276 1024233.249 1041973.421 1189631.647 1067612.059 1286019.876 1105232.15 1408174.903 0.778315119 0.575836159 0.727348035 0.739946024 0.844803898 0.758153023 0.913252944 0.784868519 1 20.42539511 1.787421181 0.396865667 0.992199875 0.657798344 0.592436075 0.072400148 0.677537529 0.291877192 0.081476774 0.072451282 61.29445396 -1.787421181 -0.334401532 NFDLRPGVIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFDLRPGVIVR 11 1 P31153;P31153-2;Q00266 P31153 MAT2A;MAT1A S-adenosylmethionine synthase isoform type-2;S-adenosylmethionine synthase isoform type-1 0 ; 91.313 0.0098808 842620000 2757000 2398700 2291800 2513800 2073200 2422500 2950400 2735800 2387300 FALSE TRUE 2626682.074 2643130.257 2396881.297 2261108.048 2434765.424 2338608.218 2500262.292 2496238.849 2757510.291 0.952555674 0.958520541 0.869219348 0.819981726 0.882957874 0.84808685 0.906710049 0.905250964 1 21.39493484 -0.44617064 7.785736014 0.999998589 0.897821844 0.379011402 0.042669284 0 0 0.047033832 0.011085981 0.357955764 0.44617064 -0.102176744 NFDRENVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFDRENVR 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 169.44 0.00027453 251000000 440020 289730 365190 354980 401210 384750 500610 426750 447830 FALSE TRUE 419221.1266 319253.8164 381934.3227 319296.736 471180.897 371426.011 424232.7502 389381.5077 517277.1892 0.81043807 0.617181316 0.738355239 0.617264288 0.910886671 0.718040576 0.820126538 0.752752133 1 18.98057805 -0.451155206 0.295633725 1.101874952 0.698663854 0.470178868 0.086547879 7.118911928 0.715361101 0.81349893 0.095775334 0.353870854 0.451155206 -0.403211098 NFEATLGWLQEHACSR ddPTM_SK-BR-3_Trastuzumab_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 ; 241.79 6.41E-20 1328800000 1207010 1041060 1067340 1202100 928340 1125330 1254830 1199460 871130 FALSE TRUE 1149957.029 1147145.198 1116278.595 1081262.624 1090242.202 1086359.54 1063382.637 1094428.924 1006220.391 1.142848067 1.140053618 1.109377831 1.074578327 1.083502393 1.079643733 1.056808872 1.087663233 1 19.9405149 8 0.081642785 0.924614565 1.545359411 0.86317618 0.015165266 56.74070203 0.336875774 0.377147337 3.967232016 99999999.95 -8 0.620744846 NFEDVAFDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFEDVAFDEK 10 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 174.98 6.84E-06 381980000 1427880 1237760 1228690 1552700 813280 1327550 1446800 1483270 906920 FALSE TRUE 1360386.942 1363889.151 1285026.652 1396619.646 955115.7745 1281576.611 1226064.088 1353387.015 1047560.522 1.298623721 1.301966925 1.226684879 1.333211416 0.911752357 1.223391474 1.170399287 1.291941599 1 19.99860217 7.999999998 0.034264874 0.369561812 2.49079716 0.283455593 0.116799295 1252.728571 3.283078979 60.7153612 166.9894039 99999999.5 -7.999999998 2.121235348 NFEDVAFDEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 182.02 9.57E-06 11224400000 19438940 16741090 17411010 21005330 9600100 21360440 21950420 22103350 10424340 FALSE TRUE 18520099.83 18447026.1 18209322.03 18893834.32 11274354.4 20620722.61 18601480.28 20167863.5 12040893.41 1.53810014 1.532031344 1.512289945 1.569138907 0.936338693 1.712557525 1.544858812 1.674947432 1 23.5214391 NFEES(ph)PERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFEESPERK 9 1 Q6MZP7-3;Q6MZP7;Q6MZP7-4;Q6MZP7-2 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 NFEES(1)PERK 75.088 0.024042 225280000 211130 177840 179630 209550 123960 204450 214290 210030 143610 TRUE FALSE 201150.3033 195962.0982 187866.2132 188485.6359 145578.5848 197369.8452 181596.1248 191638.6598 165880.3053 1.21262318 1.18134638 1.132540797 1.136274951 0.87761223 1.189832903 1.094741925 1.155282777 1 17.33978308 3.504472715 1.891984919 1.079661063 1.2001457 0.257775979 0.086900824 0.45454121 3.249904346 0.024887101 0.04254583 3195.013625 -3.504472715 0.120484637 NFEHLNSDFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ;;; 191.23 1.92E-06 1373040000 1623620 1412480 1239950 1661150 1803020 1356330 1592300 1431350 1512200 FALSE TRUE 1546874.7 1556413.318 1296802.934 1494168.046 2117466.117 1309359.952 1349365.39 1306013.406 1746704.253 0.88559623 0.891057153 0.742428452 0.855421313 1.212263675 0.749617429 0.772520814 0.747701509 1 20.73620393 NFEWVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NFEWVAER 8 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 172.25 0.00066227 1066920000 1425434 1675346 1148661 1268688 1107620 1194423 1335275 1434708 987621 FALSE TRUE 1358056.56 1846065.662 1201328.243 1141157.072 1300788.577 1153059.832 1131554.275 1309077.362 1140776.221 1.190467101 1.618253982 1.053079667 1.000333853 1.14026621 1.010767766 0.991916078 1.147532126 1 20.12158438 3.711557751 23.2039469 1.044931778 1.404360472 0.622096744 0.115069243 153.3442352 131770.7814 0.028749044 0.044557806 5147.042456 -3.711557751 0.359428694 NFFLTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFFLTNR 7 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 166.61 0.0025983 696200000 1182350 879620 829640 937110 917230 923750 1314870 1034930 961130 FALSE TRUE 1126462.659 969254.278 867679.8146 842909.9224 1077194.622 891760.3059 1114262.432 944306.0427 1110177.132 1.014669305 0.873062731 0.781568805 0.759257148 0.970290768 0.80325948 1.003679864 0.850590429 1 20.08235845 1.730827768 24.99999999 0.947005104 0.875613494 0.161748318 0.088970282 1.586401471 5098.221851 0.041202415 0.022848875 53.8056359 -1.730827768 -0.071391611 NFGDQPDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFGDQPDIR 9 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 81.163 0.043928 0 315270 249140 293270 306010 266350 293690 367390 307180 302670 FALSE TRUE 300367.8119 274527.6492 306716.7196 275249.2934 312801.3557 283519.4417 311337.9079 280281.6907 349606.5178 0.859159646 0.785247515 0.877319798 0.787311676 0.894724039 0.810967265 0.890538054 0.801706137 1 18.41537256 -5 0.293953622 2.29052364 0.829497973 0.585454138 0.042161124 160.5294934 1.501171121 127.2772022 0.037566727 1.00E-05 5 -1.461025667 NFGEDMDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 245.5 3.58E-12 4069230000 5349210 5860780 4378430 6329520 3829930 5195450 4869110 5183440 3619680 FALSE TRUE 5096363.444 6458000.145 4579185.346 5693264.624 4497868.579 5015530.264 4126237.842 4729550.514 4181001.488 1.21893366 1.544606039 1.095236479 1.36169878 1.075787366 1.19960021 0.986901788 1.13120039 1 21.99541713 2.713063295 0.832542941 1.037770585 1.362219912 0.417538436 0.129208104 0.491213467 0.726354578 0.076277658 0.06983609 516.4916385 -2.713063295 0.324449327 NFGEDMDDERLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 227.06 1.26E-11 2939540000 3715840 2911500 3320020 3690740 2123820 3776690 4007760 4083710 2345490 FALSE TRUE 3540199.607 3208185.16 3472246.201 3319739.803 2494213.536 3645902.278 3396302.604 3726118.703 2709216.61 1.306724458 1.184174476 1.28164215 1.225350454 0.920640131 1.345740412 1.253610579 1.375349128 1 21.36944432 2.998570585 24.89801145 1.199232437 1.249411775 0.050088001 0.141941044 247.3062687 4307861.824 0.039674723 0.046794599 996.7140601 -2.998570585 0.050179338 NFGEEVDDESLKELFSQFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFGEEVDDESLKELFSQFGK 20 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 240.31 9.75E-30 126650000 145490 126520 131020 160900 86514 142580 159550 170300 93027 FALSE TRUE 138612.976 139412.5318 137027.3966 144726.0263 101602.0142 137642.4188 135207.7172 155387.6292 107453.152 1.289985202 1.297426173 1.275229195 1.346875578 0.945547081 1.280952827 1.258294565 1.44609652 1 16.71334828 -2.279736797 2.06365654 4.82E-05 1.264674667 0.306762933 0.126334538 1147974.763 190434.6761 5342051.172 0.029040592 0.005251256 2.279736797 1.264626487 NFGIWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFGIWLR 7 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 124.89 0.0095448 479950000 1145860 916890 429380 537700 797210 531640 1074470 785120 619670 FALSE TRUE 1091697.469 1010322.133 449067.4977 483649.3744 936243.1716 513229.1735 910539.8675 716370.7306 715765.2588 1.525217179 1.411527203 0.627394935 0.675709485 1.308031034 0.717035602 1.272120791 1.000845908 1 19.449127 3.884026016 7.033926549 0.963890062 1.482579249 0.475063095 0.229885412 0.195137515 10.59288819 0.057342697 0.104184705 7656.424701 -3.884026016 0.518689187 NFGSYVTHETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFGSYVTHETK 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 127.17 0.00029214 192988000 1390280 1635360 1452620 1943710 780800 1672290 1416640 1610740 712260 FALSE TRUE 1324564.22 1802005.043 1519224.064 1748324.578 916971.2728 1614378.178 1200505.55 1469695.067 822713.6431 1.609994232 2.190318659 1.846601277 2.125070603 1.114569183 1.962260127 1.45920219 1.786399288 1 19.65003084 2.760951375 24.99150128 1.53103816 1.941861111 0.344438487 0.320810978 942.745633 1052246.45 0.08716889 0.092395248 576.7018902 -2.760951375 0.410822951 NFHIFYQLLEGGEEETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFHIFYQLLEGGEEETLR 18 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 178.06 9.07E-14 99607000 221767 247540 220050 264140 194005 241840 281940 242610 151155 FALSE TRUE 211284.5134 272764.6074 230139.5102 237588.1454 227839.4106 233465.0202 238924.8748 221365.7822 174595.3454 1.210138294 1.562267349 1.318130845 1.360793123 1.304956957 1.337177802 1.368449281 1.267879059 1 17.41365557 -0.062724591 0.58898288 0.972885152 1.371283099 0.601469379 0.088758218 3.166235807 1.211755927 0.277393683 0.035162154 0.865516614 0.062724591 0.398397947 NFIVWLEDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFIVWLEDQK 10 0 Q9Y224;G3V4C6;G3V4E7 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 103.31 0.0093951 0 265950 225560 245170 263500 236630 265700 307330 307010 240690 FALSE TRUE 253379.0706 248544.8204 256411.287 237012.4794 277898.1971 256498.7424 260441.164 280126.5768 278014.9759 0.911386409 0.893997957 0.922293075 0.85251695 0.999579955 0.922607646 0.936788254 1.007595278 1 18.08480307 1.678192489 0.613787721 1.004738078 0.899527163 0.495103117 0.035853405 0.589718525 0.479567216 0.031453966 0.016919047 47.66421987 -1.678192489 -0.105210914 NFKEHHQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFKEHHQLQR 10 1 Q13268;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 131.82 0.00014423 159380000 595780 273780 520960 415480 458360 414350 656240 528950 138340 FALSE TRUE 567618.6601 301678.4933 544846.5313 373715.161 538297.8389 400000.9556 556118.5353 482632.3339 159793.0607 3.552210952 1.88793238 3.409700828 2.338744621 3.368718495 2.503243595 3.48024209 3.02035853 1 17.28584523 NFLEGDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFLEGDWK 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 93.551 0.025564 28631000 239488 197308 204545 238860 149094 213001 253370 243765 172462 FALSE TRUE 228167.8769 217413.9095 213923.5906 214849.339 175095.9464 205624.722 214713.753 222419.6443 199206.5261 1.145383544 1.091399533 1.073878425 1.078525604 0.878966918 1.032218803 1.077844974 1.1165279 1 17.60390539 3.729805333 1.396814112 1.031653943 1.132400958 0.266866351 0.063334926 0.613135982 2.310497938 0.020195266 0.050085976 5367.911324 -3.729805333 0.100747015 NFLIEPFVPHSQAEEFYVCIYATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NFLIEPFVPHSQAEEFYVCIYATR 24 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;; 261.03 4.84E-44 1161537000 2199460 2031459 2071621 2355461 1742026 2120764 2451960 2283286 1403867 FALSE TRUE 2095495.885 2238466.982 2166606.872 2118685.585 2045834.783 2047321.411 2077868.469 2083349.373 1621571.524 1.292262384 1.380430618 1.336115515 1.306563142 1.261637092 1.262553874 1.281391809 1.284771804 1 20.62896123 -4.117694111 0.217827818 1.81E-14 1.349254979 0.907724563 0.030663518 27.66083437 0.391685585 12.18268991 0.062183949 7.63E-05 4.117694111 1.349254979 NFLNAIATDIIHLHSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFLNAIATDIIHLHSQR 17 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 90.367 0.002209 10161000 20394 28129 20416 26198 17286 17677 21787 21765 4076.7 FALSE TRUE 19430.01604 30995.37708 21352.09379 23564.52727 20300.67293 17064.84106 18462.993 19859.14122 4708.893815 4.126237881 6.582305377 4.534418195 5.00425964 4.311134148 3.623959624 3.920876904 4.217368664 1 12.20117248 0.112235187 0.283151371 1.07E-10 5.518836646 0.72375711 0.723971735 2.659450724 0.357000047 4.249399917 1.015639697 1.294896887 -0.112235187 5.518836645 NFMPALEETPFHSCTAGPNPTLGRPLS(ph)PKPSSPGSVLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFMPALEETPFHSCTAGPNPTLGRPLSPKPSSPGSVLAR 39 2 F8VWK5;F8VUY0;F8VVS9;Q15583-4;Q15583-2;Q15583-3;Q15583 F8VWK5 TGIF1 Homeobox protein TGIF1 1 NFMPALEETPFHSCTAGPNPT(0.002)LGRPLS(0.998)PKPSSPGSVLAR 170.45 1.07E-18 176040000 86819 81518 68344 95449 45842 80878 65677 87041 46039 TRUE FALSE 82715.23793 89824.77688 71477.64 85854.28518 53836.83029 78077.17458 55656.76741 79419.22861 53178.49299 1.555426513 1.689118511 1.34410804 1.614455024 1.012379766 1.468209613 1.046602946 1.493446394 1 15.69855527 3.032890143 1.339656368 1.213359181 1.6050304 0.3726027 0.202744641 0.375229996 1.405372804 0.068712659 0.084722212 1078.673832 -3.032890143 0.391671219 NFNETFLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFNETFLKR 9 1 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 96.015 0.012273 152290000 318320 231990 283130 287320 264180 297140 455300 388370 341640 FALSE TRUE 303273.6444 255630.0448 296111.7906 258438.0477 310252.9084 286849.9673 385835.6228 354362.2639 394619.7863 0.768521131 0.647788209 0.750372386 0.654903927 0.786207177 0.72690214 0.977740185 0.897984025 1 18.59010377 1.759339306 5.757813842 0.952661625 0.71755455 0.82633171 0.050923815 0.061848336 5.065571842 0.022970568 0.012263321 57.45651833 -1.759339306 -0.235107075 NFPNAIEHTLQWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 278.82 3.41E-33 5740900000 2812800 2343310 2081950 2460200 2084960 2327100 2826200 2480900 2035500 FALSE TRUE 2679844.518 2582095.953 2177409.467 2212896.022 2448576.364 2246511.943 2395011.283 2263659.244 2351154.944 1.139799197 1.098224496 0.926102073 0.941195317 1.041435559 0.955492937 1.018653105 0.962786077 1 21.16493819 3.868582672 5.242999078 0.981060635 1.124387867 0.7335208 0.035583224 0.099291104 3.806486527 0.008835945 0.016301086 7388.949058 -3.868582672 0.143327232 NFQKPGTWRGS(ph)LDESSLGFGYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFQKPGTWRGSLDESSLGFGYPK 23 2 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 NFQKPGT(0.229)WRGS(0.766)LDES(0.004)S(0.002)LGFGYPK 63.095 0.021146 225750000 378700 322740 327540 291200 382560 376300 544270 441220 343860 TRUE FALSE 360799.6015 355627.5729 342558.033 261928.0228 449278.3429 363268.6366 461231.6153 402584.4377 397184.0526 0.908393978 0.895372235 0.862466735 0.659462587 1.131159068 0.914610328 1.161254114 1.013596682 1 18.59944817 2.716062052 24.98777957 1.052050633 0.852358751 0.540944718 0.096357324 618.5412669 686975.1513 0.029509505 0.027840065 520.0702991 -2.716062052 -0.199691882 NFQLLVITHDEDFVELLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NFQLLVITHDEDFVELLGR 19 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 197.09 8.04E-16 31471300 77956 87261 75642.5 99551 59109.7 68891 83299 85385 45577.1 FALSE TRUE 74271.17437 96152.99511 79110.78345 89543.94435 69418.41297 66505.2874 70590.20766 77908.23675 52644.96389 1.410793529 1.826442417 1.502722722 1.700902379 1.318614504 1.263279191 1.340872943 1.479880144 1 15.68400791 2.726285712 22.84635516 1.303057777 1.618123332 0.506185563 0.16087147 190.9684805 355433.6784 0.047155961 0.044829185 532.4584353 -2.726285712 0.315065555 NFRNPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFRNPLAK 8 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 148.38 0.0004762 9594200000 2359810 981510 1399740 1357360 1648720 1688610 3084530 2078410 1877490 FALSE TRUE 2248266.458 1081526.985 1463919.464 1220915.594 1936256.246 1630133.012 2613928.297 1896413.402 2168641.56 1.036716486 0.49871173 0.675039845 0.562986349 0.892842912 0.751683931 1.2053298 0.874470653 1 21.04836019 1.762259851 25 1.04232432 0.729014488 0.389837033 0.170648801 12.37644294 13065.32147 0.075982562 0.0421379 57.84420424 -1.762259851 -0.313309831 NFS(ph)AAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFSAAK 6 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;H0Y6G2;E9PF82;E9PBG7;Q13557;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5;H0Y9J2 Q13555-8;E9PF82;Q13557 CAMK2G;CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit gamma;Calcium/calmodulin-dependent protein kinase type II subunit delta 1 NFS(1)AAK 74.173 0.084992 123690000 410320 290430 190900 558580 224650 319350 368270 274730 176100 TRUE FALSE 390924.9868 320025.1472 199652.9538 502430.4772 263828.8889 308290.8294 312083.6478 250673.1848 203408.6886 1.921869658 1.573311098 0.981536016 2.470054159 1.297038444 1.515622718 1.534269012 1.232362228 1 17.63402178 1.101984078 0.738890817 0.990237723 1.676834726 0.245256623 0.383887899 0.925546947 1.17122639 0.338501686 0.132722805 12.64689982 -1.101984078 0.686597003 NFSDNQLQEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NFSDNQLQEGK 11 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 305.74 5.31E-36 1237070000 1965960 1661530 1624910 1909490 1206522 1871690 2108310 2030660 1333749 FALSE TRUE 1873032.967 1830841.796 1699413.731 1717544.437 1416939.055 1806872.906 1786648.588 1852844.645 1540579.983 1.215797289 1.188410739 1.103099968 1.114868722 0.919743908 1.172852384 1.159724654 1.202692924 1 20.55504215 3.803418627 3.390006976 1.103805859 1.206654988 0.216360063 0.083398215 0.376305694 8.591994134 0.022060826 0.041630583 6359.436376 -3.803418627 0.102849128 NFSGKDDIQALDIFLANLPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFSGKDDIQALDIFLANLPEAK 22 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 73.783 0.0034269 0 94631 95733 97901 98405 58983 109760 114000 115580 65285 FALSE TRUE 90157.98017 105488.3015 102389.8577 88513.14244 69269.61653 105958.9837 96607.20625 105459.2025 75409.06437 1.19558545 1.398880923 1.357792442 1.173773248 0.91858475 1.405122641 1.281108671 1.39849504 1 16.20245033 3.239345031 24.9999398 1.216376973 1.317470725 0.103513451 0.16104033 56.64115553 1805154.588 0.044766303 0.057235067 1735.181988 -3.239345031 0.101093753 NFTKPQDGDVIAPLIT(ph)PQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NFTKPQDGDVIAPLITPQKK 20 2 Q9Y3Z3-4;Q9Y3Z3;Q9Y3Z3-3 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 NFTKPQDGDVIAPLIT(1)PQKK 132.84 0.00056379 981020000 438860 477260 430880 520350 207310 551120 524100 630000 242630 TRUE FALSE 418115.9575 525893.3366 450636.2742 468043.4294 243464.7984 532034.5762 444138.9192 574833.8602 280255.8212 1.491908199 1.876476051 1.607946169 1.670057833 0.86872343 1.898389029 1.584762512 2.051104086 1 18.09638481 2.945737445 24.99965214 1.527860668 1.676269893 0.047997339 0.366083084 1209.962662 557448.932 0.104218891 0.110541421 882.5461907 -2.945737445 0.148409226 NFTKYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NFTKYPK 7 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 72.547 0.046793 713680000 1395140 805310 1233600 1369690 1541650 1305150 2308010 1687960 1822840 FALSE TRUE 1329194.497 887372.0046 1290161.78 1232006.159 1810513.272 1259952.328 1955880.685 1540153.274 2105516.717 0.631291353 0.421450942 0.612753045 0.585132452 0.859890238 0.598405284 0.928931444 0.731484705 1 21.0057429 2.117290796 0.461348009 0.973940084 0.497350704 0.587463901 0.113666954 0.606635492 0.289483692 0.104475057 0.094853953 131.0058822 -2.117290796 -0.47658938 NFWNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NFWNGR 6 0 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ;; 122.51 0.044642 1974460000 1343970 1323750 1007910 1258120 984300 1133390 1348120 1268450 916300 FALSE TRUE 1280443.202 1458641.63 1054123.67 1131651.387 1155961.608 1094140.42 1142439.534 1157377.794 1058395.124 1.209796958 1.378163596 0.995964216 1.069214475 1.092183422 1.033773111 1.079407405 1.093521471 1 20.01344689 3.735263141 24.99998254 1.057798781 1.29398028 0.784388729 0.052673831 104.03012 788710.7414 0.012896033 0.020937952 5435.79589 -3.735263141 0.2361815 NFWSHETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NFWSHETR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 170.5 0.00029484 865640000 949120 898180 859960 1192180 812590 1092860 1096700 1017150 716660 FALSE TRUE 904256.9786 989705.5631 899390.0166 1072339.801 954305.4387 1055013.984 929378.2727 928082.9537 827795.9726 1.09236697 1.195591179 1.086487548 1.295415582 1.152826868 1.274485524 1.122714175 1.121149395 1 19.6589157 0.900366462 1.70436661 1.00148988 1.175891679 0.402082877 0.06826844 0.46759982 2.722775732 0.059305605 0.016974723 7.949987804 -0.900366462 0.174401799 NFYES(ph)DDDQKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NFYESDDDQKEK 12 1 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFY(0.002)ES(0.998)DDDQKEK 203.59 7.46E-08 1968610000 2955610 3493380 2503930 3825750 1170930 3513830 2727990 3675290 1070110 TRUE FALSE 2815904.173 3849359.394 2618737.667 3441178.342 1375139.821 3392145.186 2311785.023 3353462.124 1236057.193 2.278134206 3.114224337 2.11862176 2.783996048 1.112521191 2.744327046 1.870289688 2.713031518 1 20.23731407 NFYNEHEEITNLTPQQLIDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NFYNEHEEITNLTPQQLIDLR 21 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 226.51 2.40E-25 501960000 473180 404393 444680 504200 391799 453156 501910 478390 357526 FALSE TRUE 450813.7192 445601.1065 465069.0178 453516.8581 460128.6216 437463.0941 425334.4113 436499.6355 412969.3061 1.091639772 1.079017496 1.126158799 1.098185389 1.114195691 1.059311401 1.029941947 1.056978398 1 18.65567503 2.035983682 3.768517096 1.034010388 1.098624692 0.757929229 0.018819354 0.115234451 3.462805904 0.007819257 0.005117938 108.6384805 -2.035983682 0.064614305 NFYQEHPDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NFYQEHPDLAR 11 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;;;; 205.09 3.10E-08 9264570000 6391300 5803245 5860432 6435120 5111930 6147630 7530980 6472540 5081300 FALSE TRUE 6089195.915 6394602.263 6129138.604 5788249.512 6003448.974 5934736.032 6381990.685 5905770.085 5869282.052 1.037468614 1.089503317 1.044273993 0.98619379 1.022859171 1.011151957 1.087354574 1.006216779 1 22.48475261 3.478726766 24.99206941 1.026240422 1.064053084 0.261046151 0.029854688 86.06506222 1339745.633 0.00841039 0.011547362 3011.111002 -3.478726766 0.037812661 NFYVEHPEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 151.13 3.36E-05 4006410000 5927820 4687280 4991830 5690690 4526810 5074240 6010920 5390070 3919480 FALSE TRUE 5647623.696 5164919.161 5220710.343 5118651.03 5316284.231 4898517.796 5093843.756 4918086.896 4527292.94 1.247461512 1.140840504 1.153163803 1.130620681 1.174274407 1.081997092 1.125141188 1.086319565 1 22.11021723 8 0.049120743 0.718873044 1.900091933 0.817896077 0.027526075 191.8248602 0.711909474 4.083671159 17.2915306 99999999.96 -8 1.181218888 NGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NGAAGPHSPDPLLDEQAFGDLTDLPVVPK 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NGAAGPHS(0.999)PDPLLDEQAFGDLT(0.001)DLPVVPK;NGAAGPHS(0.989)PDPLLDEQAFGDLT(0.011)DLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 162.81 3.76E-12 147564000 235723 194620 216307 268078 148420.4 220458 231063 195579 113260.5 TRUE FALSE 224580.8409 214451.9993 226224.8899 241130.2901 174304.8708 212823.4842 195810.0956 178453.0659 130824.3599 1.7166592 1.639235991 1.729226041 1.843160481 1.33235791 1.626787888 1.49674033 1.364066035 1 16.99727167 0.71424678 0.422403793 0.948854927 1.722471139 0.768521733 0.118117638 0.768035744 0.307819854 0.191536255 0.077619716 5.179010368 -0.71424678 0.773616212 NGALDQQKDELDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGALDQQKDELDVR 14 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 92.457 0.0045154 232600000 537570 495570 478870 590490 277570 550610 563970 576700 312910 FALSE TRUE 512160.1315 546069.1464 500826.6632 531132.8233 325978.1201 531542.2376 477926.0185 526201.0907 361434.4847 1.417020658 1.510838532 1.385663749 1.469513414 0.901900992 1.470646162 1.322303318 1.455868527 1 18.46337464 -4.420607622 0.144263349 9.74E-15 1.499648484 0.293269314 0.175121972 140.7930345 1.435505745 42.33460966 0.953358119 3.80E-05 4.420607622 1.499648484 NGDECAYHHPIS(ph)PCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 89.483 0.010668 157620000 74972 77299 82105 92377 53397 85030 86401 87133 18339 TRUE FALSE 71428.22214 85175.85598 85869.59546 83091.08846 62709.41989 82085.38978 73218.94059 79503.1726 21182.91846 3.371972671 4.020968884 4.053718832 3.922551495 2.960376778 3.875074624 3.456508636 3.753173707 1 14.37061375 2.751920243 23.98917578 3.25496026 3.831567072 0.167813916 0.826621991 991.8588242 1781026.055 0.224072503 0.236246347 564.8332346 -2.751920243 0.576606812 NGDLDEVKDYVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NGDLDEVKDYVAK 13 1 P58546;C9JL85 P58546 MTPN Myotrophin 0 ;;;; 174.83 1.76E-05 2479260000 3914590 3408400 3207090 4144970 1727010 3968350 3941810 4334580 1721500 FALSE TRUE 3729555.089 3755719.835 3354138.249 3728309.741 2028199.997 3830925.044 3340414.488 3955021.196 1988461.428 1.875598408 1.888756695 1.686800761 1.874972121 1.019984581 1.926577499 1.679899062 1.988985625 1 20.92322115 3.348748882 1.915195326 1.609835301 1.87474108 0.118564879 0.338600989 0.747700152 5.606813399 0.096736387 0.145772218 2232.281101 -3.348748882 0.264905779 NGDLDEVKDYVAKGEDVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGDLDEVKDYVAKGEDVNR 19 2 P58546 P58546 MTPN Myotrophin 0 ; 172.3 4.84E-12 312620000 579520 406350 649510 441730 354340 611900 793430 677110 406310 FALSE TRUE 552127.2381 447757.527 679290.676 397326.4612 416136.7838 590709.7496 672377.6812 617818.6588 469318.4797 1.1764447 0.954059016 1.4473981 0.84660306 0.886683141 1.258654358 1.432668242 1.316416646 1 18.84020774 2.057321086 10.13249526 1.309722173 1.065865006 0.160537358 0.200436011 0.556825676 94.85919258 0.070329191 0.051909363 114.1093119 -2.057321086 -0.243857167 NGEELHGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGEELHGGKR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 83.862 0.0099412 43724000 65341 64360 55167 76589 41902 62005 65131 68228 46509 FALSE TRUE 62252.46042 70918.35717 57696.46152 68890.12821 49209.69553 59857.7513 55194.06974 62253.59462 53721.37818 1.158802371 1.320114256 1.073994441 1.282359659 0.916016997 1.114225906 1.02741351 1.158823484 1 15.7132087 2.753125725 24.99939156 1.049406234 1.214319674 0.44520517 0.091582607 685.626184 1176800.334 0.025265253 0.026682817 566.4032346 -2.753125725 0.16491344 NGEFELMHVDEFIDELLHSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 125.04 1.37E-05 51370000 13632 10876 13100 14642 12418 14051 14904 17268 7884.7 FALSE TRUE 12987.64238 11984.27676 13700.64796 13170.15834 14583.69527 13564.41035 12630.12107 15755.92238 9107.419007 1.426050824 1.315880685 1.504339259 1.446091185 1.601298376 1.489380288 1.386794773 1.730009607 1 13.15282654 -1.07839784 5.139941629 0.99999148 1.465335136 0.63133632 0.11597743 1.09E-05 1.95E-06 0.107843352 0.025418456 0.083483791 1.07839784 0.465343656 NGHDGDTHQEDDGEKS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGHDGDTHQEDDGEKSD 17 1 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 NGHDGDTHQEDDGEKS(1)D 175.86 7.13E-10 96299000 130050 211670 154950 234410 86314 216670 170010 132400 9535.6 TRUE FALSE 123902.7942 233239.4136 162054.6108 210846.6615 101367.1343 209166.6636 144071.8521 120806.3541 11014.33215 11.24923351 21.17599238 14.71306736 19.14293655 9.203202965 18.9904082 13.08039835 10.96810524 1 13.4270944 0.735583962 1.036892695 0.972163691 16.02007208 0.61510323 3.631157361 0.559001549 1.076892979 3.111301946 0.996312469 5.439812893 -0.735583962 15.04790839 NGIHDLDNISFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGIHDLDNISFPK 13 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 116.96 0.00054403 120260000 523820 573030 456490 636700 270460 511000 484280 529450 233260 FALSE TRUE 499060.0667 631422.4085 477420.518 572697.7063 317628.1384 493303.9419 410394.1916 483088.5512 269432.7695 1.852261949 2.343524916 1.771946742 2.125568124 1.178877161 1.830898086 1.523178463 1.792983653 1 18.0395658 -0.104508616 0.109973009 4.99E-06 2.684335908 0.489841221 0.285763887 21.14864198 0.720250621 11.95104111 5.358608954 0.786124595 0.104508616 2.684330918 NGIS(ph)FTIWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NGISFTIWDR 10 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NGIS(0.903)FT(0.097)IWDR;NGIS(0.997)FT(0.003)IWDR;NGIS(0.835)FT(0.165)IWDR;NGIS(0.606)FT(0.394)IWDR 147.7 2.77E-05 130980000 248558 268066 228065 278110 178653 252155 240845 259551 172009 TRUE FALSE 236809.1559 295382.2302 238522.0058 250153.8544 209810.0266 243422.8091 204099.6718 236823.3385 198683.2772 1.191892741 1.486699003 1.200513748 1.259058427 1.056002446 1.225180159 1.027261452 1.191964124 1 17.60011092 3.070066991 1.615605926 1.103783596 1.332179283 0.424579539 0.105512718 0.300907524 1.615171594 0.034032226 0.042599492 1175.078801 -3.070066991 0.228395686 NGIS(ph)PTNPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGISPTNPTK 10 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q9UJF2;Q9UJF2-2 Q5VWQ8;Q9UJF2 DAB2IP;RASAL2 Disabled homolog 2-interacting protein;Ras GTPase-activating protein nGAP 1 NGIS(0.786)PT(0.214)NPTK 101.72 0.0032938 172510000 356650 272560 322390 358410 242230 342180 399400 377830 251460 TRUE FALSE 339791.8613 300334.1739 337171.9004 322381.9459 284474.8353 330330.2208 338464.1945 344745.2022 290455.1325 1.169860069 1.03401228 1.160839877 1.109919949 0.979410599 1.137284846 1.165289081 1.18691379 1 18.1479558 2.051442787 24.99990351 1.139648785 1.091305891 0.020253453 0.074198323 242.4509888 117823.902 0.025657504 0.018949318 112.5752154 -2.051442787 -0.048342893 NGLEGSSEET(ph)SFHDESLQDDREEIENNSYHMHPAGIILTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.223)S(0.223)EET(0.276)S(0.276)FHDESLQDDREEIENNSYHMHPAGIILTK 110.57 4.18E-06 29356000 18480 16765 16802 19463 14152 19172 23214 21194 7101.2 TRUE FALSE 17606.48702 18473.37256 17572.38832 17506.54226 16620.10432 18508.06883 19672.27795 19338.141 8202.417828 2.146499653 2.252186239 2.1423425 2.134314861 2.026244538 2.256416245 2.398351115 2.357614719 1 13.00183352 -0.588539973 5.948681559 0.999999995 2.218746436 0.922997963 0.11021308 2.80E-08 23827295.23 0.376438805 0.028136358 0.257905158 0.588539973 1.218746441 NGLHRPVS(ph)TDFAQYNSYGDVSGGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGLHRPVSTDFAQYNSYGDVSGGVR 25 1 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 NGLHRPVS(0.499)T(0.499)DFAQYNS(0.002)YGDVSGGVR;NGLHRPVS(0.5)T(0.5)DFAQYNSYGDVSGGVR 141.09 2.28E-07 180143000 90028 69009 80865 86463 66562 84276 100785 85030 69138 TRUE FALSE 85772.55486 76041.09556 84572.74024 77771.57497 78170.39173 81357.50099 85408.39721 77584.32243 79859.56793 1.074042311 0.952185161 1.059018254 0.973854192 0.978848167 1.018757089 1.069482335 0.971509419 1 16.28517765 2.007173182 24.95318432 1.027068063 1.006206753 0 0.044375474 598.133307 2080706.42 0.015652255 0.011538293 101.6654019 -2.007173182 -0.020861311 NGMVEDWDSFQAILDHTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGMVEDWDSFQAILDHTYK 19 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 ; 178.43 3.80E-14 191774000 445580 431050 404080 503370 300830 489530 530790 492150 296330 FALSE TRUE 424518.3165 474974.4851 422607.4677 452770.2913 353294.6568 472577.4534 449808.2369 449054.7369 342283.343 1.240254091 1.38766462 1.234671439 1.322793821 1.032170171 1.380661557 1.314140013 1.311938621 1 18.38483156 -1.757644942 2.519355564 0.930123772 1.285065637 0.428392236 0.100642267 9567578.932 6910690.375 4147685.3 0.025801269 0.0174725 1.757644942 0.354941865 NGMVLKPHFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGMVLKPHFHK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 87.298 0.0089216 554650000 2257800 1618600 1341600 1678700 1599600 1614100 2422700 1892300 919960 FALSE TRUE 2151078.269 1783537.18 1403113.687 1509953.887 1878569.734 1558203.312 2053072.619 1726600.18 1062622.698 2.024310484 1.678429402 1.320425104 1.420968975 1.767861478 1.466374956 1.932080523 1.624847825 1 20.019198 4.325622796 2.460118925 1.567486483 1.999280379 0.263465837 0.257515359 0.406052844 4.623604266 0.062701266 0.250919474 21165.22043 -4.325622796 0.431793895 NGNYCVLQMDQSYKPDENEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGNYCVLQMDQSYKPDENEVR 21 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 102.39 0.00042211 136480000 58730 49641 53356 60078 29252 53891 56665 55164 34396 FALSE TRUE 55953.94929 54699.47434 55802.42538 54038.8453 34353.53954 52024.74116 48019.71353 50333.54772 39729.95601 1.408356689 1.376781649 1.404542843 1.360153666 0.864676002 1.309458816 1.208652572 1.266891605 1 15.27793958 7.999999998 0.1022882 0.896551527 2.522912531 0.376206854 0.14260057 125.6213248 0.907169283 1.593929778 28.71186826 99999999.44 -7.999999998 1.626361004 NGPLNES(ph)QEDEEDSEHGTSLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(1)QEDEEDSEHGTSLNR 271.7 1.60E-45 216080000 78086 40070 50650 91544 70908 64959 78839 50516 47191 TRUE FALSE 74395.02953 44153.17856 52972.3526 82341.8232 83274.33275 62709.45354 66810.66257 46092.55124 54509.13926 1.364817543 0.810014232 0.971806807 1.510605823 1.527713222 1.150439255 1.225678179 0.845593085 1 15.73421052 1.245215834 24.75731842 0.92279651 1.200537682 0.232926876 0.223622461 211.5867537 787125.1056 0.165684054 0.057374745 17.58797477 -1.245215834 0.277741171 NGPLNESQEDEEDS(ph)EHGTSLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(0.003)QEDEEDS(0.997)EHGTSLNR 264.32 1.15E-37 202030000 41638 22306 25261 43989 38850 33908 38043 28755 28688 TRUE FALSE 39669.85426 24579.00676 26419.24184 39567.14215 45625.4277 32733.75746 32238.84164 26237.05976 33136.78852 1.197154463 0.74174378 0.797278282 1.194054823 1.376881398 0.987837353 0.972901813 0.791780403 1 15.01614617 3.242947144 24.99881474 1.057329965 0.916290729 0.108370918 0.191509371 270.0952345 1539261.111 0.055631362 0.072795571 1749.633736 -3.242947144 -0.141039236 NGS(ph)EADIDEGLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 NGS(1)EADIDEGLYSR 230.29 2.53E-09 0 167170 155210 145510 177870 112500 175000 181440 154060 107190 TRUE FALSE 159268.2054 171026.0755 152181.7774 159990.1697 132119.9644 168939.7061 153757.9956 140569.6897 123812.4777 1.286366353 1.381331499 1.229131184 1.292197463 1.06709733 1.364480456 1.241861874 1.135343483 1 16.91779719 -4.999999999 0.117566879 0.098873249 1.404833057 0.508593174 0.086169811 120.9181869 0.927492297 25.70063943 0.829400099 1.00E-05 4.999999999 1.305959808 NGS(ph)GTLDLEEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 1 NGS(0.955)GT(0.045)LDLEEFLR;NGS(0.998)GT(0.002)LDLEEFLR;NGS(0.5)GT(0.5)LDLEEFLR 132.64 0.00012213 67959200 158668 128048 135373 153533 97285 144272 162104 149641 111820 TRUE FALSE 151168.0781 141096.2368 141579.986 138099.5711 114251.4732 139275.8245 137372.0576 136537.6407 129160.4745 1.170389615 1.092410332 1.096155666 1.069209227 0.88456994 1.078316141 1.063576594 1.057116283 1 16.97880512 3.803694181 1.153357727 1.029354773 1.157993068 0.406260537 0.057013336 0.572194008 1.40679235 0.018919123 0.05938038 6363.472637 -3.803694181 0.128638295 NGS(ph)PPPGAPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR 164.3 6.05E-05 1299127000 1155160 988140 1092512 1196901 755488 1110530 1164201 1081593 760655 TRUE FALSE 1100557.876 1088832.589 1142604.756 1076586.238 887244.868 1072072.068 986580.7554 986882.983 878613.4925 1.252607529 1.239262314 1.300463475 1.225324044 1.009823859 1.22018621 1.122883684 1.123227667 1 19.74486913 1.90558265 0.230675144 0.9656987 1.32936035 0.571170299 0.066581738 1.755289318 0.375216966 0.192577561 0.250407363 80.46048579 -1.90558265 0.363661649 NGSGTLDLEEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 174.89 4.47E-05 154354000 323320 276660 273660 328020 258360 290890 345940 309780 246690 FALSE TRUE 308037.3044 304851.9685 286207.5817 295046.8064 303417.9022 280816.4064 293160.4994 282654.021 284945.4253 1.081039655 1.069860898 1.004429467 1.035450231 1.064828122 0.98550944 1.028830342 0.991958445 1 18.12032611 6.975980966 0.234861613 0.994868032 1.353781429 0.525443164 0.023429999 21.14329876 0.425216155 0.03138326 2.662278015 9461956.915 -6.975980966 0.358913397 NGSLDS(ph)PGKQDTEEDEEEDEKDKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGS(0.278)LDS(0.361)PGKQDT(0.361)EEDEEEDEKDKGK 68.552 0.029824 186750000 110980 114130 103710 133040 35692 155360 114700 143850 33952 TRUE FALSE 105734.1953 125759.9768 108465.2061 119666.5664 41916.6735 149979.8442 97200.40839 131253.7314 39217.10276 2.696124596 3.206763578 2.765762855 3.051387227 1.068836568 3.824347892 2.478520889 3.346849262 1 15.25919534 NGVAAEVS(ph)PAKEENPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGVAAEVSPAKEENPRR 17 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR 157.01 2.17E-08 514920000 644880 526380 605810 648970 311540 650220 701670 697160 381390 TRUE FALSE 614397.8004 580018.7204 633586.9877 583734.3026 365872.4774 627702.7184 594617.3544 636112.9745 440534.0133 1.394665978 1.316626419 1.438224901 1.325060688 0.830520383 1.424867773 1.349764914 1.443958821 1 18.74889389 -2.239965175 2.078592348 3.63E-05 1.317105587 0.236006332 0.178352118 4280172.038 601196.2516 20157053.28 0.041544947 0.005754861 2.239965175 1.317069272 NGVMPSHFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NGVMPSHFSR 10 0 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;; 130.56 0.00020732 606294000 670068 481937 533006 608677 673888 512462 864810 665969 784080 FALSE TRUE 638395.2136 531046.9282 557444.8523 547491.6315 791413.8538 494715.3124 732867.3512 607653.2238 905671.1219 0.704886352 0.58635736 0.615504722 0.604514838 0.87384243 0.546241677 0.8091981 0.670942475 1 19.78862773 -2.051575364 0.238041462 1.388685377 0.619816566 0.526906929 0.098466005 23.34250757 0.810543306 5.113765421 0.153584201 0.008880239 2.051575364 -0.768868811 NGYGFINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 114.72 0.0060528 874220000 1453140 1088470 876360 914000 1185610 927630 1605990 1156470 1199310 FALSE TRUE 1384452.952 1199386.33 916541.9728 822122.9835 1392380.009 895505.9405 1360966.729 1055203.356 1385292.87 0.99939369 0.86579983 0.661623252 0.593465109 1.005115986 0.646437992 0.982439713 0.761718608 1 20.40175958 -0.425323756 8.556529116 1 0.828614723 0.123269658 0.151367087 0 0 0.139845388 0.032961874 0.375557331 0.425323756 -0.171385277 NGYGFVEFDDLRDADDAVYELNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGYGFVEFDDLRDADDAVYELNGK 24 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ; 200.98 1.34E-24 206613000 357010 208574 310370 320420 242850 315780 428570 355830 277190 FALSE TRUE 340134.8448 229827.9277 324600.7715 288210.7728 285202.9631 304844.4594 363183.7753 324671.6388 320175.2095 1.062339728 0.717819247 1.013822313 0.900165798 0.890771536 0.952117623 1.134328219 1.014043652 1 18.28850208 1.937608168 6.187490073 1.060813194 0.907693516 0.280012099 0.095973593 0.247602948 18.92075067 0.039454778 0.024319973 86.61800321 -1.937608168 -0.153119678 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_SK-BR-3_Trastuzumab_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 168.22 6.51E-12 82516000 134876 129747 104310 142921 70804 117329 123143 135765 74014 TRUE FALSE 128500.6788 142968.3668 109092.7167 128554.3095 83152.19518 113265.8673 104355.2737 123876.6969 85491.71311 1.503077598 1.672306726 1.276061886 1.503704919 0.972634565 1.324875397 1.220647825 1.448990696 1 16.38349696 3.404434241 1.559689611 1.230049926 1.583689505 0.388589766 0.173422748 0.335006277 1.666630396 0.050331644 0.08405528 2537.664716 -3.404434241 0.353639579 NGYGFVEFEDSRDADDAVYELNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 333.54 5.91E-87 324058000 397930 343130 362160 437330 235340 415890 434230 464500 282512 FALSE TRUE 379120.6375 378095.3371 378765.3942 393368.7575 276383.2215 401487.625 367980.2383 423825.9175 326322.5181 1.161797352 1.158655367 1.160708726 1.205460046 0.846963376 1.230339933 1.127658123 1.298794579 1 18.31593902 NHAAPFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 98.033 0.0097117 0 229280 232990 229660 282150 184070 259880 314380 218760 86778 FALSE TRUE 218442.3888 256731.9459 240190.1382 253787.746 216171.7497 250880.2904 266415.557 199604.2147 100235.089 2.179300591 2.561298128 2.396268018 2.531925181 2.156647455 2.502918817 2.657907122 1.991360676 1 16.61302811 0.923656911 4.559474882 1.00037397 2.429335852 0.890663811 0.158310842 0.113297717 5.781139917 0.149964779 0.038065145 8.387970816 -0.923656911 1.428961882 NHAVVCQGCHNAIDPEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NHAVVCQGCHNAIDPEVQR 19 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;;; 211.16 8.22E-17 1817040000 342862 362837 378441 461835 294839 407923 480056 331374 107810 FALSE TRUE 326655.5927 399810.5028 395792.8942 415410.4684 346258.8283 393796.5242 406814.6404 302357.1358 124528.6242 2.623136607 3.210591183 3.178328652 3.335863309 2.780556121 3.162297237 3.266836384 2.42801314 1 16.92611787 0.907576824 3.572465825 1.00109442 3.07418206 0.898831708 0.221204903 0.113891245 3.291721099 0.212377143 0.054767447 8.083079016 -0.907576824 2.07308764 NHDEESLECLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 173.59 3.26E-05 1785390000 2591130 2471950 2308870 2877440 2452030 2471450 3036030 2299100 1915460 FALSE TRUE 2468652.42 2723844.515 2414733.973 2588194.264 2879663.256 2385863.067 2572827.863 2097778.616 2212499.754 1.115775229 1.231116302 1.091405307 1.169805447 1.301542859 1.078356308 1.16286018 0.948148632 1 21.07724586 1.243838144 24.88642302 0.974074275 1.165689477 0.586378322 0.066451903 72.00195751 339542.0793 0.043922092 0.014980763 17.53226977 -1.243838144 0.191615202 NHET(ph)DGGSAHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.581)DGGS(0.419)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.5)DGGS(0.5)AHGDDDDDGPHFEPVVPLPDKIEVK 190 2.56E-20 342369000 153740 307247 279825 418468 121521 410214 403534 192881 26779.6 TRUE FALSE 146473.0149 338555.8186 292655.253 376402.8016 142714.2239 396008.1863 341967.4769 175991.3171 30932.4436 4.735255216 10.94500722 9.461110052 12.16854402 4.613739082 12.80235702 11.05530107 5.689538124 1 14.91683319 0.980944063 4.53824681 1.011514114 9.403574332 0.494950813 2.772932454 0.142508215 9.66650816 2.537015727 0.644433933 9.570707939 -0.980944063 8.392060219 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.009)DGGS(0.991)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.032)DGGS(0.968)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.037)DGGS(0.963)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.002)DGGS(0.998)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.008)DGGS(0.992)AHGDDDDDGPHFEPVVPLPDKIEVK 252.79 1.63E-59 1118275000 507973 1011228 910594 1414054 450875 1310959 1349213 676114 134289.4 TRUE FALSE 483962.123 1114273.283 952345.6356 1271910.605 529507.4572 1265560.161 1143365.777 616909.8739 155114.3143 3.120035215 7.183561929 6.139637337 8.199827406 3.41365953 8.158886992 7.371117115 3.977130522 1 17.2429723 4.654496548 3.318657085 6.128252369 2.968287802 0.077901273 2.343246886 0.497310038 8.949461431 0.498797325 3.509035796 45133.24374 -4.654496548 -3.159964566 NHKPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NHKPSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 NHKPS(1)R;NHKPS(1)R 66.457 0.061384 871490000 550370 1066100 585100 1004720 308720 765590 609710 670430 132245 TRUE FALSE 524355.1008 1174736.802 611927.4137 903723.6368 362560.6703 739077.4263 516687.5414 611723.595 152752.8792 3.432701915 7.690439672 4.005995939 5.916246172 2.373511204 4.838386224 3.382506072 4.004661636 1 17.22084005 2.747964941 24.93092724 3.417279981 5.393270595 0.319487269 1.513543183 776.3943325 2058226.2 0.424942249 0.445186753 559.7124161 -2.747964941 1.975990614 NHLS(ph)PQQGGATPQVPSPCCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NHLSPQQGGATPQVPSPCCR 20 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR 217.7 6.70E-25 754970000 272864 292671 346894 383480 269663 360788 428575 252143 146363 TRUE FALSE 259966.2595 322494.5076 362799.433 344931.8618 316692.1418 348293.8211 363188.0124 230064.0222 169060.2265 1.537713895 1.907571723 2.145977445 2.040289836 1.873250429 2.060175999 2.148275913 1.360840613 1 17.36717776 1.056195092 4.472444443 1.006082618 1.944810764 0.780267734 0.17700384 0.091259212 3.620738035 0.189803578 0.048332842 11.38138441 -1.056195092 0.938728146 NHPGLLLMDTTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NHPGLLLMDTTFR 13 0 P11498;A0A494C016 P11498 PC "Pyruvate carboxylase, mitochondrial" 0 71.279 0.0427 59032000 253170 241050 238440 271040 213920 236730 281140 238850 217740 FALSE TRUE 241203.1558 265613.2691 249372.7098 243794.5443 251227.5803 228531.9807 238246.9295 217935.0278 251506.0071 0.959035367 1.056091153 0.991517907 0.969338852 0.998892961 0.908654164 0.947281269 0.866520169 1 17.94023333 2.248262543 24.63363229 0.92784979 0.998719546 0.3701203 0.041492283 154.254552 391659.2179 0.013418846 0.011093727 177.1179363 -2.248262543 0.070869756 NHPWLELSDVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NHPWLELSDVHR 12 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 168.82 2.63E-05 51716000 70433 58762 71705 79117 67331 65631 74691 61736 19006 FALSE TRUE 67103.77167 64749.91461 74992.74518 71164.00885 79073.50508 63358.18201 63295.51616 56330.06856 21953.35341 3.056652458 2.949431615 3.416004096 3.24160084 3.601887311 2.886036626 2.883182126 2.565898134 1 14.42215371 0.645259397 0.97191076 0.997941232 3.186414356 0.917657742 0.205081516 0.319221095 0.504376902 0.203879023 0.066058522 4.418342688 -0.645259397 2.188473125 NHS(ph)GS(ph)RT(ph)PPVALNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 NHS(1)GS(1)RT(1)PPVALNSSR;NHS(1)GS(1)RT(1)PPVALNSSR 68.228 0.041502 945100000 820670 838840 964130 1232570 803060 968480 1320480 568860 259010 TRUE FALSE 781878.5555 924318.7497 1008336.314 1108669.722 943113.4097 934941.2948 1119016.524 519047.6027 299175.948 2.613440555 3.089548996 3.370378939 3.705744828 3.152370423 3.125055009 3.740329165 1.734924235 1 18.19063467 1.07875421 4.612784936 1.019918435 3.226785022 0.857459335 0.326735063 0.071409802 2.597342092 0.342156495 0.087054206 11.98820636 -1.07875421 2.206866587 NHSDSSTSESEVSSVS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 NHSDSSTSESEVSS(0.001)VS(0.999)PLK;NHSDSSTSESEVSS(0.014)VS(0.986)PLK 213.39 2.41E-17 1253090000 1061610 1811770 1212010 1874830 713130 1554320 1415590 1336520 335340 TRUE FALSE 1011429.799 1996391.423 1267581.857 1686368.526 837499.6462 1500493.509 1199615.746 1219487.223 387342.8145 2.611200625 5.154068561 3.272506446 4.353684806 2.162166471 3.873812686 3.097038854 3.148340895 1 18.56325145 2.749172562 24.94523026 2.910966254 3.896194141 0.237432953 1.003453886 1106.182295 2600273.449 0.28039937 0.294622818 561.2709467 -2.749172562 0.985227887 NHSGNDERDEEDEERESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NHSGNDERDEEDEERESK 18 2 A0A0D9SGE8;Q8IWS0-3;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 105.79 0.00028097 50766000 60560 57495 63763 89447 51854 66354 85844 48202 40408 FALSE TRUE 57697.44882 63353.80587 66686.59662 80455.61762 60897.32118 64056.14434 72746.92117 43981.17735 46674.26626 1.236172594 1.35736051 1.428765827 1.723768236 1.304730123 1.37240817 1.558608779 0.942300348 1 15.51033972 1.229577555 24.99969105 0.971149809 1.416989348 0.658196166 0.136142368 136.0227738 378534.9522 0.126393631 0.033437043 16.96592548 -1.229577555 0.445839538 NHSGS(ph)RTPPVALNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.02)GS(0.49)RT(0.49)PPVALNSSR;NHS(0.056)GS(0.627)RT(0.316)PPVALNSSR;NHS(0.151)GS(0.669)RT(0.18)PPVALNSSR;NHS(0.073)GS(0.612)RT(0.315)PPVALNSSR;NHS(0.03)GS(0.485)RT(0.485)PPVALNSSR;NHS(0.083)GS(0.459)RT(0.459)PPVALNSSR 177.67 1.76E-09 1115390000 373808 353668 525880 518070 435024 485142 687815 369971 207155 TRUE FALSE 356138.8367 389707.1713 549992.1182 465992.6193 510892.0479 468341.4109 582876.1892 337574.3779 239279.5394 1.488379815 1.628669013 2.298533838 1.947482098 2.135126343 1.957298196 2.435963353 1.410795 1 17.86833751 3.919065168 7.421588495 1.986810268 1.540314604 0.056006384 0.425800969 0.410429028 33.07935217 0.096689767 0.175692645 8299.752993 -3.919065168 -0.446495664 NHSGSRT(ph)PPVALNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.005)GS(0.201)RT(0.793)PPVALNSSR 128.26 9.05E-05 108870000 50136 36776 47740 50843 56600 52290 75267 42324 34771 TRUE FALSE 47766.17064 40523.51621 49928.92622 45732.16504 66471.02208 50479.18419 63783.63678 38617.88619 40163.10909 1.189304606 1.008973586 1.243153913 1.138660977 1.655026804 1.256854495 1.588115019 0.961526313 1 15.29358333 2.939899782 24.99744656 1.351691364 1.131975858 0.060652413 0.226959334 385.5326043 160353.8508 0.062172103 0.065943589 870.7626284 -2.939899782 -0.219715506 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_SK-BR-3_Trastuzumab_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 460.27 3.78E-236 2883000000 476850 594960 640500 740780 520750 623470 792430 448010 199150 TRUE FALSE 454310.2455 655587.1004 669867.5585 666315.387 611568.6351 601879.0776 671530.2495 408779.8693 230033.1649 1.974977155 2.849967746 2.912047743 2.896605745 2.658610707 2.61648827 2.919275792 1.777047538 1 17.81148235 1.024799616 3.848883856 1.006452896 2.676871867 0.805429892 0.279881465 0.081945947 2.901081771 0.278951975 0.071723703 10.58765097 -1.024799616 1.670418971 NHVQPYIPSILEALMVPTSQGFTEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NHVQPYIPSILEALMVPTSQGFTEVR 26 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 68.689 0.032868 44674000 100310 99374 103770 120050 100970 115380 135120 101950 55056 FALSE TRUE 95568.5451 109500.3236 108527.9571 107982.3459 118579.136 111384.3617 114504.9624 93022.71753 63593.80329 1.502796501 1.721870967 1.706580697 1.698001068 1.8646335 1.751497094 1.800567924 1.462763866 1 15.95659857 0.934557386 3.826328321 1.000527008 1.714345885 0.860376524 0.092873848 0.11087163 4.210759514 0.096349534 0.024722029 8.601167119 -0.934557386 0.713818877 NICFTVWDVGGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NICFTVWDVGGQDR 14 0 P18085;C9JPM4;C9JAK5 P18085 ARF4 ADP-ribosylation factor 4 0 ;; 206.69 2.44E-08 89213000 287998 295019 255270 258822 216690 260913 290631 280572 222570 FALSE TRUE 274384.9053 325081.7715 266974.382 232804.7208 254480.6674 251877.5174 246289.9031 256003.6283 257085.0189 1.067292472 1.264491307 1.038467287 0.905555376 0.989869688 0.979744049 0.95800955 0.995793646 1 17.97188602 3.519328043 6.487925695 0.970013429 1.164761917 0.687812857 0.053581586 0.099075617 11.35988394 0.013415159 0.020478498 3306.191792 -3.519328043 0.194748488 NIDDGTSDRPYSHALVAGIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;;;; 212.06 6.94E-23 7254170000 3379379 3627810 2788921 3659470 2555673 3429079 3205437 3461053 2401412 FALSE TRUE 3219642.452 3997487.963 2916795.786 3291613.123 3001381.562 3310329.134 2716388.714 3157984.851 2773810.708 1.160728972 1.441153844 1.051548247 1.186675469 1.082042676 1.193422869 0.979298517 1.13850049 1 21.40343791 3.720529016 24.97592366 1.092367821 1.300941417 0.452195569 0.096403481 591.4086655 819171.7614 0.02387563 0.037065806 5254.4712 -3.720529016 0.208573596 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;; 350.71 3.92E-102 8670880000 3664300 2068376 3188156 3334430 3647500 3341390 4940520 3534850 4361250 FALSE TRUE 3491095.801 2279145.866 3334336.106 2999246.761 4283622.845 3225676.826 4186752.935 3225319.795 5037570.376 0.693011817 0.452429583 0.661893702 0.595375655 0.850335087 0.640323923 0.831105597 0.640253049 1 22.26429666 -0.016591925 0.177204169 1.214211115 0.49015437 0.511491741 0.106812931 8.295720746 0.529296043 1.518286114 0.485316423 0.962516261 0.016591925 -0.724056745 NIDEHANEDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIDEHANEDVER 12 0 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 152.16 6.96E-05 526360000 909140 664350 659970 918370 981170 776220 1075020 815360 788910 FALSE TRUE 866166.7539 732048.0203 690230.2773 826053.7028 1152285.737 749339.3068 911005.9549 743962.7559 911250.1336 0.950525791 0.80334476 0.75745424 0.906505988 1.264510912 0.822320106 0.99973204 0.816419914 1 19.7974876 2.996944316 24.96063516 0.980638798 0.844313762 0.201450025 0.130749746 194.586475 1589520.448 0.035864303 0.042091273 992.9887223 -2.996944316 -0.136325036 NIDLATPLHHTWTYQALVHDVLDFHLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIDLATPLHHTWTYQALVHDVLDFHLNR 28 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ; 252.28 5.93E-54 538210000 152329 112915 126770 156550 155604 134349 186241 156488 32063 FALSE TRUE 145128.7101 124421.1669 132582.5299 140813.2966 182741.2883 129696.4604 157826.5149 142785.0811 37035.16628 3.918673105 3.359541197 3.579909129 3.802151055 4.934264016 3.501981318 4.261531154 3.855391927 1 15.17660819 0.90380747 20.72388139 1.000000004 3.884371617 0.808981181 0.44307347 10952.02882 2359528.753 0.416857618 0.104214405 8.013227451 -0.90380747 2.884371613 NIDPKPCTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NIDPKPCTPR 10 1 K7EQ55;K7EK33;Q96EP5;Q96EP5-2 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ;;; 110.84 0.0016717 1526600000 4316540 3635370 3646220 4320040 2662870 4268070 4717190 4538700 2944980 FALSE TRUE 4112505.709 4005818.336 3813402.794 3885781.372 3127273.685 4120265.666 3997496.028 4141267.367 3401672.458 1.208965813 1.177602602 1.121037619 1.14231497 0.919334158 1.211247031 1.175156068 1.217420965 1 21.6978128 3.880392599 2.411881783 1.121559122 1.201145436 0.115364884 0.092098843 0.674005012 7.668969522 0.024559616 0.053926398 7592.636336 -3.880392599 0.079586314 NIEDVIAQGIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIEDVIAQGIGK 12 0 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 174.84 0.00031473 0 376413 322244 288466 348884 288163 341011 416045 394750 338424 FALSE TRUE 358620.7035 355081.03 301692.4514 313813.5175 338418.536 329201.7036 352569.6941 360183.5973 390905.0655 0.917411247 0.908356175 0.771779335 0.802787032 0.865730751 0.842152565 0.901931761 0.921409388 1 18.57645875 1.035587176 1.354035369 0.998169603 0.858999498 0.538476123 0.044198248 0.409201469 1.533571401 0.046599785 0.014151115 10.85393398 -1.035587176 -0.139170105 NIEDYIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;;; 189.7 0.00019031 1301244000 1553871 1301030 1245396 1393119 1359268 1351957 1604415 1518377 1238752 FALSE TRUE 1480422.597 1433606.436 1302498.638 1253080.031 1596323.909 1305138.39 1359632.025 1385419.86 1430851.333 1.034644594 1.001925499 0.910296275 0.87575837 1.115646239 0.912141156 0.95022592 0.968248642 1 20.44844235 3.965482281 9.124101411 0.958694369 1.022461363 0.12210728 0.06501258 0.689822395 177.3316495 0.015671859 0.028701778 9235.965063 -3.965482281 0.063766994 NIETIINTFHQYSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIETIINTFHQYSVK 15 0 P06702 P06702 S100A9 Protein S100-A9 0 196.22 9.04E-09 275300000 984210 652730 787890 923160 787260 834690 1130500 937610 854080 FALSE TRUE 937688.3438 719243.9291 824015.5358 830362.2029 924557.8947 805784.476 958021.4619 855507.8978 986526.3644 0.950494967 0.729067114 0.835269655 0.841703002 0.937185186 0.816789601 0.971105787 0.867192129 1 19.91199808 1.396856895 0.536462901 0.992669015 0.832782626 0.290448728 0.069493361 0.91067753 0.659989128 0.06749898 0.036834121 24.93772863 -1.396856895 -0.159886389 NIGLGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIGLGFK 7 0 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 ; 107.66 0.017281 69815000 627470 569800 545260 604160 447060 623640 640100 643810 480120 FALSE TRUE 597810.7366 627863.2678 570260.7103 543428.689 525027.1225 602043.1904 542440.9888 587434.5833 554574.5575 1.077962789 1.132153034 1.028285021 0.979901948 0.946720536 1.085594682 0.978120942 1.059252675 1 19.08102191 3.614321294 4.945551184 1.007497498 1.104500792 0.470826573 0.04177847 0.162762041 5.861586952 0.010387533 0.01632002 4114.54005 -3.614321294 0.097003293 NIGNGIIS(ph)SPLTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIGNGIISSPLTGK 14 0 Q9P275;A0A075B784;E9PEW0;K7EMM6 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 NIGNGIIS(0.668)S(0.332)PLTGK 153.09 6.80E-06 61550000 275630 276120 292100 331030 186740 283700 342770 322230 224040 TRUE FALSE 262601.5161 304256.9419 305493.0739 297754.2355 219307.3969 273875.3979 290474.1411 294013.833 258782.979 1.014755751 1.175722388 1.180499101 1.150594358 0.847456806 1.058320756 1.122462313 1.136140538 1 17.9813832 NIGNGIISS(ph)PLTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIGNGIISSPLTGK 14 0 Q9P275;A0A075B784;E9PEW0;K7EMM6 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 NIGNGIIS(0.185)S(0.815)PLTGK 235.35 3.25E-17 90358000 446570 428910 426650 516800 267890 494650 515330 513860 377080 TRUE FALSE 425461.5211 472616.4166 446212.3245 464850.2821 314609.9312 477520.1465 436706.9438 468863.6943 435555.6405 0.97682473 1.0850885 1.024466872 1.067258093 0.722318579 1.096347061 1.002643298 1.076472557 1 18.7324975 -0.27168605 6.585428818 1.000004791 1.009120734 0 0.107946346 0 0 0.095594658 0.022531877 0.534950933 0.27168605 0.009115942 NIGRDT(ph)PTSAGPNSFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 NIGRDT(0.93)PT(0.07)SAGPNSFNK;NIGRDT(0.999)PT(0.001)SAGPNSFNK;NIGRDT(0.999)PT(0.001)SAGPNSFNK;NIGRDT(0.992)PT(0.008)SAGPNSFNK 250.42 4.34E-21 2418450000 2216070 1747310 1995910 2294000 1531050 2064180 2299040 2334800 1787580 TRUE FALSE 2111320.763 1925362.876 2087424.448 2063402.762 1798064.635 1992696.929 1948279.223 2130352.534 2064788.777 1.022535955 0.932474497 1.010962705 0.999328738 0.870822554 0.965085122 0.943573137 1.031753252 1 20.97756277 1.236114837 24.9964553 1.015876638 0.963154528 0.19595993 0.04406826 106.3097268 1086395.223 0.034457104 0.010183866 17.22323934 -1.236114837 -0.05272211 NIHESCMSQIGWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NIHESCMSQIGWNR 14 0 P11413;P11413-3;P11413-2;E9PD92 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 263.98 1.18E-24 1943170000 1322610 874930 1109220 1314670 1521650 1045960 1763120 1411680 1693640 FALSE TRUE 1260092.846 964086.3617 1160078.834 1182516.874 1787025.278 1009738.143 1494123.662 1288065.815 1956281.041 0.644126697 0.492815879 0.593002135 0.604471877 0.913480855 0.516151883 0.763757165 0.658425752 1 20.89968221 -5 0.131333604 2.242397526 0.488112322 0.501126386 0.115424163 108.5243228 0.895768856 35.23530436 0.77546929 1.00E-05 5 -1.754285204 NIHLNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NIHLNLDR 8 0 Q9Y5S9;Q9Y5S9-2;A0A0J9YW13 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;;; 133.57 0.0009136 911393000 1307873 1065617 671887 805160 969123 799649 1275914 1018493 774906 FALSE TRUE 1246052.435 1174204.584 702693.6835 724223.7871 1138137.744 771956.9546 1081249.886 929308.3535 895074.4648 1.392121532 1.311851282 0.785067289 0.809121269 1.27155649 0.86244998 1.207999924 1.038246973 1 19.77164819 3.887865436 7.017496628 1.012683856 1.362108012 0.469136021 0.157376338 0.197958993 10.93640313 0.039241235 0.071313024 7724.412107 -3.887865436 0.349424156 NIHLWTPTDGGSWHVDQRPFVGHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIHLWTPTDGGSWHVDQRPFVGHTR 25 1 Q9BQ67;M0QX71 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ; 138.54 2.82E-06 283500000 105476 87403 112426 92774 83147 91807 111300 91668 46027 FALSE TRUE 100490.3585 96309.46507 117580.8433 83448.18126 97647.81047 88627.70057 94319.14084 83641.06396 53164.63209 1.89017312 1.811532616 2.211636547 1.569618334 1.836706221 1.667042488 1.774095618 1.573246361 1 15.69817919 -0.758202177 0.291037386 0.595069669 1.931841368 0.747446128 0.155219386 5.41747026 0.447401219 2.076665314 0.171136006 0.174500961 0.758202177 1.336771699 NIHPWVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIHPWVK 7 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 80.18 0.030613 1027920000 4268000 2957500 3943000 3349600 3036600 3557800 4662400 3892300 3170000 FALSE TRUE 4066260.098 3258872.612 4123790.45 3012891.844 3566182.079 3434592.494 3951065.249 3551469.578 3661587.41 1.110518374 0.890016337 1.126230235 0.822837613 0.97394427 0.938006419 1.079058017 0.969926204 1 21.80403781 1.751669103 25 1.023452392 0.976875108 0.035827211 0.093965652 13.11682779 25053.71 0.039837952 0.022092957 56.45067029 -1.751669103 -0.046577284 NIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR 324.6 4.02E-83 1341367000 502362.3 452407.2 492769.9 533798.7 482431.5 492179.2 597377 592561 483507 TRUE FALSE 478616.6297 498508.008 515363.8873 480140.2405 566567.4009 475134.9109 506236.1671 540673.2175 558486.7961 0.856988264 0.892604823 0.922786162 0.859716369 1.014468748 0.850754063 0.906442499 0.96810385 1 19.09116365 -4.999999988 0.059604381 1.367014252 0.747169135 0.362133339 0.046852497 434.6339786 1.893048539 23.27987984 3.92946143 1.00E-05 4.999999988 -0.619845117 NIIGSS(ph)PVADFSAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 NIIGS(0.001)S(0.999)PVADFSAIK;NIIGS(0.001)S(0.999)PVADFSAIK;NIIGS(0.007)S(0.993)PVADFSAIK;NIIGS(0.04)S(0.96)PVADFSAIK;NIIGS(0.022)S(0.978)PVADFSAIK;NIIGSS(1)PVADFSAIK 266.29 2.85E-25 991922000 4018520 3553480 3125820 4230370 2268086 3702890 3717510 3870250 2144646 TRUE FALSE 3828572.524 3915583.652 3269141.939 3805125.17 2663639.48 3574657.991 3150335.573 3531350.393 2477226.748 1.545507502 1.580631912 1.31967812 1.53604234 1.075250573 1.44300799 1.271718697 1.425525699 1 21.2402945 8 0.038950237 7.63E-10 3.620468568 0.505999935 0.137643675 573.5877796 1.702901841 44.04340443 138.8939355 100000000 -8 3.620468568 NIIHGS(ph)DSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 NIIHGS(0.921)DS(0.079)VK 168 3.27E-06 288370000 299400 244570 237780 267740 189100 232980 346920 238150 176110 TRUE FALSE 285247.9554 269491.9611 248682.4482 240826.2665 222078.9801 224911.8442 293990.9824 217296.3235 203420.2394 1.402259462 1.32480407 1.222505927 1.183885474 1.091725095 1.105651261 1.445239585 1.068213882 1 17.6341037 8 0.286665598 1.145242033 3.359616514 0.34856703 0.118855252 66.06438742 0.93772645 0.131268058 73.86373295 100000000 -8 2.214374481 NIIHGSDSVESAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;;;; 222.45 3.89E-12 5024600000 9778540 7952850 8181040 10891440 6700110 8586690 11097070 11026540 6917180 FALSE TRUE 9316327.793 8763254.457 8556148.776 9796611.759 7868607.063 8289330.772 9404008.16 10060997.7 7989860.946 1.166018765 1.096796867 1.070875805 1.226130445 0.984824031 1.037481231 1.176992719 1.259220626 1 22.92973896 1.627199827 15.030984 1.163553088 1.102218105 0.045146713 0.090982598 0.307199881 210.3544973 0.039703661 0.02161558 42.38379374 -1.627199827 -0.061334983 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 38 1 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;; 217.21 1.95E-39 1760993000 2727952 1254688 2751484 2261002 3457906 2251367 4521400 2912481 1394612 FALSE TRUE 2599007.115 1382542.134 2877642.263 2033721.783 4060963.712 2173401.596 3831577.389 2657448.724 1610881.306 1.613406962 0.858252019 1.786377588 1.262490151 2.520957749 1.349200334 2.37855972 1.649686239 1 20.61941877 3.705045692 21.92950622 1.792133635 1.235829732 0.113991128 0.503843222 197.6493412 129325.6229 0.120658924 0.186954478 5070.440517 -3.705045692 -0.556303903 NIIHGSDSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 191.53 7.82E-07 9088910000 18631530 12418920 14589740 17669030 15697020 15505150 24705600 20248680 18579080 FALSE TRUE 17750854.5 13684422.07 15258694.01 15892905.54 18434575.32 14968202.77 20936306.97 18475598.23 21460228.84 0.827151222 0.637664312 0.711021962 0.74057484 0.859011125 0.697485702 0.97558638 0.860922704 1 24.35516212 1.713896459 0.838187141 0.985932058 0.723887237 0.5615713 0.078265115 0.383855312 0.517763226 0.064971313 0.028211372 51.74834434 -1.713896459 -0.26204482 NIIIALIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIIIALIDR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 91.867 0.024341 15398000 118720 130360 114900 118780 96416 117460 129180 116820 56349 FALSE TRUE 113108.3409 143643.8322 120168.2787 106840.0087 113230.9199 113392.3307 109471.2184 106590.6215 65087.31513 1.737793926 2.206940506 1.846262646 1.641487416 1.739677227 1.74215714 1.681913261 1.637655836 1 15.99008878 -1.928659717 0.187428014 6.44E-21 2.047939458 0.771178209 0.140851653 15.45313426 0.436299742 7.262403172 0.465482845 0.01178529 1.928659717 2.047939458 NIILEEGKEILVGDVGQTVDDPYATFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NIILEEGKEILVGDVGQTVDDPYATFVK 28 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;; 342.12 1.33E-96 625499000 1156376 897896 1111208 1178596 737395 1188810 1398930 1350010 847590 FALSE TRUE 1101716.398 989392.6232 1162157.986 1060121.291 865996.4545 1147641.212 1185497.535 1231795.968 979029.9283 1.12531432 1.010584656 1.18705052 1.082828278 0.884545436 1.172222808 1.210889985 1.258180094 1 19.90099344 2.040872791 24.99998859 1.182731452 1.061666588 0.184430661 0.102240149 195.0199306 119283.8609 0.035415406 0.026155983 109.8683978 -2.040872791 -0.121064864 NIIS(ph)PPWDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIISPPWDFR 10 0 Q5T8C6;Q13042-4;Q13042-3;Q13042-2;Q13042 Q5T8C6 CDC16 Cell division cycle protein 16 homolog 1 NIIS(1)PPWDFR;NIIS(1)PPWDFR 93.011 0.0095212 47137000 72538 73417 62463 82458 58648 62390 74427 70616 58364 TRUE FALSE 69109.2725 80898.27577 65326.99033 74169.16518 68876.19263 60229.41866 63071.7942 64432.48868 67414.79104 1.025135159 1.20000781 0.969030525 1.100191279 1.021677759 0.893415491 0.935577983 0.955761899 1 16.04077754 2.455276227 4.352702947 0.939009185 1.082308345 0.46620937 0.063712065 0.154159615 6.973529651 0.021424434 0.018336995 285.2832195 -2.455276227 0.14329916 NILFVITKPDVYK ddPTM_SK-BR-3_Trastuzumab_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 573180000 1732990 1589760 1503320 1929910 1012770 1822520 1969120 1986240 1119120 FALSE TRUE 1651074.997 1751758.351 1572248.709 1735911.78 1189396.767 1759405.675 1668694.579 1812314.296 1292667.414 1.277262024 1.355150082 1.216282465 1.342891266 0.920110428 1.361066007 1.29089243 1.401995808 1 20.30191971 3.729677186 24.04721428 1.23582873 1.316206051 0.055467027 0.155098121 1173.301167 3176095.572 0.038187986 0.060234955 5366.327647 -3.729677186 0.080377321 NILGGTVFREPIICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NILGGTVFREPIICK 15 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 193.77 7.23E-08 624380000 1105640 705880 1117360 999350 958960 993620 1434000 1241620 1165730 FALSE TRUE 1053378.588 777809.9745 1168592.061 898893.4394 1126202.32 959210.6903 1215216.963 1132897.171 1346505.455 0.782305474 0.577650816 0.867870276 0.667575045 0.836388977 0.712370445 0.902496873 0.841360996 1 20.36078864 1.375846788 0.455845173 1.00649654 0.693203987 0.485411487 0.087235921 0.686177961 0.393084209 0.089694879 0.055978574 23.76001926 -1.375846788 -0.313292553 NILPFDHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NILPFDHTR 9 0 Q06124;Q06124-1;Q06124-3 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 91.549 0.0092401 144580000 326380 283810 256730 343580 273170 284510 330490 318230 251340 FALSE TRUE 310952.6642 312730.5617 268501.3244 309042.6856 320810.7615 274657.3474 280067.6806 290364.0942 290316.5235 1.071081523 1.07720552 0.924857191 1.064502571 1.1050379 0.946061712 0.964697693 1.000163858 1 18.14726716 2.224877567 24.99991511 0.972681772 1.049599709 0.330471138 0.049837147 262.0155433 478718.3792 0.018600381 0.013809918 167.833081 -2.224877567 0.076917938 NINDAWVCTNDMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NINDAWVCTNDMFR 14 0 P61970 P61970 NUTF2 Nuclear transport factor 2 0 ;; 174.9 5.74E-06 336539000 567870 477070 448420 509820 489220 499940 623460 587920 486240 FALSE TRUE 541027.9105 525683.9754 468980.5005 458571.925 574539.8131 482626.9524 528339.7264 536438.608 561643.6158 0.963293974 0.935974274 0.835014389 0.81648204 1.022961531 0.859311739 0.940702808 0.955122773 1 19.09929545 1.078115971 1.722024501 0.998829278 0.911366356 0.199988073 0.061209846 0.606430757 3.579132858 0.056123895 0.016268279 11.97060145 -1.078115971 -0.087462922 NINMDNDLEVLTS(ph)SPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLTS(0.5)S(0.5)PT(0.001)R;NINMDNDLEVLT(0.018)S(0.487)S(0.487)PT(0.008)R;NINMDNDLEVLT(0.001)S(0.497)S(0.497)PT(0.004)R 248.06 8.47E-21 190720000 471920 415310 438780 530300 410780 483500 531360 475560 486990 TRUE FALSE 449613.2769 457630.5612 458898.497 476993.2365 482419.9019 466756.2738 450291.2729 433917.4453 562509.922 0.799298393 0.813551092 0.81580516 0.847973019 0.857620254 0.829774295 0.800503698 0.771395185 1 19.10151902 -1.066605092 4.351050526 1.00001552 0.817064791 0.845235749 0.024610648 3.92E-06 8.40E-07 0.024612439 0.005800704 0.085781751 1.066605092 -0.18295073 NINMDNDLEVLTSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLTS(0.005)S(0.995)PTR;NINMDNDLEVLTS(0.001)S(0.992)PT(0.007)R;NINMDNDLEVLTSS(1)PTR;NINMDNDLEVLTS(0.063)S(0.934)PT(0.002)R 404.84 3.05E-140 557561000 1053870 986570 989620 1089540 928990 1013340 1196840 1096070 1037720 TRUE FALSE 1004055.654 1087102.605 1034995.056 980017.3692 1091005.562 978247.7817 1014240.077 1000092.3 1198644.318 0.837659378 0.906943443 0.863471374 0.817604818 0.910199586 0.816128494 0.846155996 0.834352848 1 20.19297219 -1.582872384 6.282190463 1.000344485 0.85623765 0.663954766 0.032595622 0.000148864 9.88E-06 0.029873898 0.007024687 0.02612929 1.582872384 -0.144106835 NINPSTANS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NINPSTANSPK 11 0 P46937-6;P46937-7;P46937;P46937-9;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 NINPS(0.002)T(0.002)ANS(0.995)PK;NINPS(0.007)T(0.007)ANS(0.986)PK;NINPSTANS(1)PK;NINPSTANS(1)PK 166.03 2.19E-05 152329000 974610 850400 889370 1051700 655210 1024660 1134190 1124480 840340 TRUE FALSE 928542.1168 937056.7268 930148.4942 945981.1179 769478.4166 989175.7673 961148.4847 1026014.57 970655.6353 0.956613327 0.965385346 0.958268268 0.974579535 0.792740894 1.019080023 0.990205434 1.057032518 1 19.88860003 NINTFVET(ph)PVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NINTFVET(1)PVQK;NINTFVET(1)PVQK 194.23 2.00E-05 115795000 450930 622210 465080 617610 277640 527440 498290 560330 351830 TRUE FALSE 429615.4326 685613.9064 486404.378 555526.6694 326060.3281 509174.6205 422266.7088 511264.5347 406389.9995 1.057150602 1.687083607 1.196890619 1.366979183 0.802333543 1.252921138 1.039067667 1.25806377 1 18.63250537 2.84455666 24.52182449 1.08511022 1.349823631 0.278642786 0.202891806 32.29231309 7454.370236 0.057463406 0.060949151 699.1279428 -2.84455666 0.264713411 NIPS(ph)PGQLDPDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIPSPGQLDPDTR 13 0 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 NIPS(1)PGQLDPDTR 83.729 0.010563 64665000 24514 32779 27806 27387 23655 25370 33510 24632 25733 TRUE FALSE 23355.2718 36119.21737 29080.9326 24634.00673 27780.42451 24491.43054 28397.43405 22475.0915 29723.54221 0.78574995 1.215172038 0.97838045 0.828770897 0.934626981 0.823974154 0.955385258 0.756137722 1 14.85931843 3.409864274 7.075773875 0.885194416 1.016034959 0.148911921 0.123320003 0.338293549 29.2390669 0.032191729 0.043749133 2569.592605 -3.409864274 0.130840542 NIPS(ph)PGQLDPDTRIPVINLEDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NIPSPGQLDPDTRIPVINLEDGTR 24 1 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 NIPS(1)PGQLDPDTRIPVINLEDGTR;NIPS(0.998)PGQLDPDT(0.002)RIPVINLEDGTR;NIPS(1)PGQLDPDTRIPVINLEDGTR;NIPS(0.998)PGQLDPDT(0.002)RIPVINLEDGTR 97.408 0.0035882 272590000 154130 110766 142798 140394 142889 130884 170707 150595 171308 TRUE FALSE 146844.5804 122053.1813 149345.4295 126281.3284 167808.7964 126351.4543 144662.5119 137408.1034 197873.5697 0.742113161 0.616824074 0.754751783 0.638191996 0.848060691 0.638546393 0.731085572 0.694423736 1 17.5942194 -4.99999973 0.40581672 5.965146984 0.698576668 0.641352143 0.068423046 450.196527 3.080132905 1984.375853 0.036450263 1.00E-05 4.99999973 -5.266570315 NIQVSHQEFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIQVSHQEFSK 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 188.29 3.22E-06 930710000 3369700 2809600 2882000 3354400 2277200 3106700 3675500 3554300 2310000 FALSE TRUE 3210420.959 3095901.434 3014142.551 3017209.339 2674342.959 2999114.2 3114734.97 3243066.649 2668223.002 1.203205638 1.160285865 1.129644167 1.130793542 1.002293645 1.124011823 1.167344321 1.215440631 1 21.34744782 -2.388169824 2.174771183 6.15E-05 1.143151048 0.370565081 0.057978466 2260640.008 209698.2947 11213584.51 0.015418261 0.004091007 2.388169824 1.143089592 NIRDDEGFIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 216.03 1.13E-11 484306000 384110 359060 358450 391070 312162 347710 384780 389560 317238 FALSE TRUE 365953.8815 395648.6222 374885.2871 351758.9006 366602.954 335668.7155 326074.744 355448.0612 366433.6488 0.998690712 1.079727868 1.02306458 0.959952509 1.000462035 0.916042281 0.889860266 0.970020254 1 18.48319246 2.966092315 1.362512667 0.934378292 1.040458114 0.418246831 0.040718675 0.307009011 1.179889397 0.015742159 0.018261208 924.8947508 -2.966092315 0.106079822 NISFNDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NISFNDKK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 129.85 0.0017205 3258700000 3795300 2906300 3104700 3718900 1905010 3569800 3744700 3508700 1971710 FALSE TRUE 3615903.691 3202455.274 3247053.566 3345069.107 2237243.141 3446176.931 3173377.239 3201459.627 2277472.717 1.58768255 1.406144298 1.425726658 1.468763635 0.982335869 1.513158382 1.393376621 1.405707126 1 21.11900234 -4.248288954 0.134690724 6.73E-20 1.563436631 0.403521881 0.156307981 116.8763532 1.188076977 33.58744911 1.066428132 5.65E-05 4.248288954 1.563436631 NISFTVWDVGGQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NISFTVWDVGGQDK 14 0 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 204.13 3.27E-08 184013000 694310 634070 629190 747560 555490 672930 702260 728660 484060 FALSE TRUE 661491.3423 698682.4539 658038.9839 672413.8485 652367.2801 649626.2654 595117.3391 664854.6675 559125.5526 1.183081938 1.249598504 1.176907371 1.202616918 1.166763488 1.161861164 1.064371564 1.189097269 1 19.09281275 0.970502938 0.303912743 0.976325183 1.234315646 0.676211758 0.040712201 1.055355714 0.294967085 0.098855107 0.055805213 9.343356896 -0.970502938 0.257990463 NISFTVWDVGGQDKIRPLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NISFTVWDVGGQDKIRPLWR 20 2 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 127.17 1.24E-05 389260000 253830 150298 260200 196002 299970 228520 401560 255370 348520 FALSE TRUE 241831.9589 165613.5371 272130.4274 176299.5066 352284.673 220606.2951 340294.6468 233008.449 402566.7016 0.600725192 0.411394028 0.675988417 0.437938622 0.875096404 0.547999361 0.845312455 0.57880706 1 18.61886832 -0.097191039 0.151436258 1.312498768 0.366293251 0.441327215 0.143147646 12.50321477 0.623654765 2.779756482 0.966352726 0.799482498 0.097191039 -0.946205517 NISHDTFGTTYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NISHDTFGTTYGR 13 0 Q9H7B2 Q9H7B2 RPF2 Ribosome production factor 2 homolog 0 ; 140.33 3.93E-05 200631000 553380 465780 480350 547390 302650 553880 597610 497990 334190 FALSE TRUE 527222.8241 513243.5115 502374.5226 492365.3172 355432.0642 534698.9967 506433.6186 454383.3556 386014.4784 1.365811009 1.329596531 1.301439585 1.275509974 0.920773919 1.385178605 1.311954984 1.1771148 1 18.55829543 -5 0.095221189 0.186800379 1.465847258 0.326797067 0.127595047 247.9433148 1.623067999 41.19174507 2.493346678 1.00E-05 5 1.279046879 NIVQS(ph)TEHLHEDNGDVEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NIVQSTEHLHEDNGDVEVR 19 0 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NIVQS(0.971)T(0.029)EHLHEDNGDVEVR;NIVQS(0.984)T(0.016)EHLHEDNGDVEVR 154.14 6.48E-08 202445000 125946 157800 132996 153917 132957 137695 144520 142539 67633 TRUE FALSE 119992.7822 173879.9994 139093.9982 138444.9707 156144.6587 132926.5876 122470.8197 130057.5295 78121.18022 1.535982711 2.225772818 1.78049023 1.772182273 1.998749357 1.701543515 1.567703142 1.664817776 1 16.25342612 0.619169596 0.566186829 0.977989539 1.886480041 0.651497432 0.187996026 0.873588816 0.541985847 0.227714355 0.08180841 4.160730592 -0.619169596 0.908490502 NIYAFMGT(ph)PVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NIYAFMGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK 205.27 1.16E-06 205840000 867614 957213 854976 1065723 602276 977368 983657 1016888 700738 TRUE FALSE 826603.6057 1054754.093 894177.4953 958594.4993 707312.7437 943521.5011 833582.0585 927843.8959 809404.8702 1.021248619 1.303122988 1.104734513 1.184320153 0.873867665 1.16569783 1.029870327 1.146328531 1 19.626502 NIYSEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 253.21 1.36E-12 7647741000 8445930 6543090 6588880 7816270 6693700 6714220 8352550 7648530 6848820 FALSE TRUE 8046707.627 7209838.31 6890986.665 7030563.69 7861079.161 6481704.878 7078215.092 6978784.166 7910900.027 1.017167149 0.911380284 0.871074927 0.888718561 0.993702251 0.819338489 0.894742073 0.882173222 1 22.91541041 4.467683591 2.136125717 0.899354125 1.021188365 0.275866289 0.054503715 0.430859048 3.248184396 0.012696101 0.081219773 29355.10184 -4.467683591 0.12183424 NIYSEELRETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NIYSEELRETK 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 64.827 0.061211 90774000 54203 36994 53084 53042 76482 58903 89602 57443 113810 FALSE TRUE 51640.93161 40763.73066 55517.95391 47710.11739 89820.43658 56863.17434 75931.56925 52412.9864 131459.0735 0.392828964 0.310086855 0.422321202 0.362927534 0.683257794 0.4325542 0.577606149 0.39870193 1 17.0042542 -4.999999999 0.162207783 3.103833997 0.294215287 0.743001504 0.103629084 60.43591333 0.558953849 40.85892067 0.3855037 1.00E-05 4.999999999 -2.80961871 NKAGT(ph)PVSELTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKAGTPVSELTK 12 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 NKAGT(0.989)PVS(0.011)ELTK 127.3 0.00044014 291640000 495670 371840 474480 473580 278080 492030 596930 622780 392220 TRUE FALSE 472240.6614 409730.9187 496235.3773 425974.8387 326577.064 474990.8777 505857.3651 568246.0816 453043.4744 1.04237383 0.904396469 1.095337215 0.940251571 0.720851491 1.048444365 1.116575767 1.254285987 1 18.78928997 2.005446929 24.9997791 1.123057635 0.946352226 0.354549261 0.113759413 156.873406 719998.0381 0.041229384 0.030355006 101.2620999 -2.005446929 -0.176705409 NKAPGEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKAPGEYR 8 1 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2;A0A096LP52 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 ; 87.639 0.013845 294310000 358740 303640 322810 345200 213850 345030 385650 381040 276630 FALSE TRUE 341783.0712 334581.2612 337611.1578 310499.8402 251145.3723 333081.5246 326812.0096 347674.1176 319528.3676 1.0696486 1.047109725 1.056592128 0.971744207 0.785987717 1.042416131 1.022794978 1.088085293 1 18.28558449 3.244694132 24.24941047 0.983622013 1.057191293 0.159155028 0.078619806 189.9438016 750950.5109 0.022390444 0.029550238 1756.685967 -3.244694132 0.073569281 NKAS(ph)PQSEFMPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NKASPQSEFMPSK 13 1 Q9NQW6;Q9NQW6-2;H7C1K5 Q9NQW6 ANLN Actin-binding protein anillin 1 NKAS(0.999)PQS(0.001)EFMPSK;NKAS(0.817)PQS(0.183)EFMPSK;NKAS(1)PQSEFMPSK;NKAS(0.998)PQS(0.002)EFMPSK;NKAS(0.98)PQS(0.02)EFMPSK;NKAS(0.954)PQS(0.046)EFMPSK;NKAS(0.982)PQS(0.018)EFMPSK 198.51 7.59E-08 3500910000 8230390 5639400 6141000 7674240 3992250 7642670 8096370 7931510 4149930 TRUE FALSE 7841355.776 6214061.271 6422570.924 6902810.815 4688497.136 7378002.422 6861120.056 7236984.937 4793479.949 1.635837817 1.296356997 1.339855594 1.440041658 0.978098831 1.539174566 1.431344269 1.509755963 1 22.19264197 4.594648683 2.716884112 1.341902919 1.651244981 0.200857011 0.193455028 0.539649582 6.51080668 0.044036715 0.322559372 39323.18472 -4.594648683 0.309342062 NKDEMSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKDEMSTK 8 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 121.83 0.0012918 179890000 413380 343370 332520 420350 202300 382190 409770 450330 241950 FALSE TRUE 393840.3466 378359.7934 347766.3709 378095.6194 237581.0559 368954.6645 347252.0606 410896.7179 279470.3703 1.40923829 1.353845823 1.244376535 1.352900556 0.850111787 1.32019242 1.242536231 1.470269343 1 18.09233581 3.705335801 1.546882441 1.211187862 1.398730134 0.152047465 0.174358249 0.737782609 3.438171477 0.049882331 0.112928128 5073.8287 -3.705335801 0.187542272 NKDEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKDEVK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 91.626 0.043483 350570000 586950 532780 551770 683410 289530 507920 590030 884580 389680 FALSE TRUE 559206.0367 587070.8877 577069.2003 614712.3284 340023.9403 490330.603 500010.0869 807121.4857 450109.5842 1.242377537 1.304284353 1.282063792 1.365694822 0.755424795 1.089358281 1.110863009 1.793166629 1 18.77991676 NKDQEVNFQEYVTFLGALALIYNEALKG ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NKDQEVNFQEYVTFLGALALIYNEALKG 28 2 P06703 P06703 S100A6 Protein S100-A6 0 ;;; 248.53 3.12E-45 4954760000 1636250 1613010 1234800 1828450 768280 1580170 1980980 1633890 710003 FALSE TRUE 1558907.705 1777377.553 1291416.801 1644650.732 902267.7888 1525448.317 1678745.118 1490817.93 820106.639 1.900859755 2.167251755 1.574693753 2.005410826 1.100183495 1.860060929 2.046983938 1.817834241 1 19.64545199 3.737852251 24.99718757 1.701101812 2.034055756 0.159208585 0.358273771 114.4001854 4037038.195 0.088272945 0.146161895 5468.298966 -3.737852251 0.332953944 NKDQGTYEDYVEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 290.62 6.10E-44 17546180000 12243320 9785380 10314190 11597240 7787450 11416550 12360800 11758760 8653260 FALSE TRUE 11664602.53 10782521.35 10787105.81 10431463.4 9145578.814 11021192.01 10474932.94 10729100.64 9995163.366 1.1670247 1.078773898 1.079232567 1.043651116 0.915000434 1.102652514 1.048000173 1.073429242 1 23.25279872 4.300220113 1.057440767 1.036051348 1.184392727 0.412048886 0.050538298 0.919227009 1.348759825 0.015565164 0.130392375 19962.73828 -4.300220113 0.148341379 NKDQSEQETSDADQHVTSNAS(ph)DSESSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKDQSEQETSDADQHVTSNASDSESSYR 28 1 A0A590UJD9;A0A0C4DFT3;A0A590UJ08;Q12959-4;Q12959-2 A0A590UJD9;A0A590UJ08 DLG1 Disks large homolog 1 1 NKDQSEQETSDADQHVTS(0.442)NAS(0.556)DS(0.001)ESSYR 204.51 1.89E-25 108950000 91288 104890 85750 113150 59911 95761 99167 110310 58077 TRUE FALSE 86972.99716 115578.4103 89681.72232 101775.947 70359.45943 92444.77256 84037.25282 100650.6716 67083.28454 1.296492826 1.722909232 1.336871367 1.517158078 1.048837425 1.378059724 1.252730146 1.500383774 1 16.03366571 2.778936287 24.99094103 1.263274793 1.484382229 0.277618251 0.182524201 656.5320744 406366.1362 0.050794976 0.053875687 601.0855492 -2.778936287 0.221107437 NKDSGSDTAS(ph)AIIPSTTPSVDS(ph)DDESVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 2 NKDS(0.101)GS(0.151)DT(0.151)AS(0.592)AIIPS(0.003)T(0.003)T(0.002)PS(0.043)VDS(0.927)DDES(0.027)VVK;NKDS(0.012)GS(0.012)DT(0.112)AS(0.863)AIIPS(0.001)T(0.001)T(0.001)PS(0.097)VDS(0.901)DDESVVK 150.63 2.05E-08 162631000 368690 286088 326640 393180 195899 402010 396110 401040 192839 TRUE FALSE 351262.7544 315240.6925 341616.7671 353656.7994 230063.7236 388088.2929 335676.1444 365922.8116 222743.4872 1.576983277 1.415263343 1.533677915 1.587731268 1.032863975 1.742310394 1.507007673 1.64279915 1 17.76502372 -1.849134178 2.800848523 0.810486504 1.501414597 0.414989957 0.188330531 113919414 70888556.17 143896038 0.040877456 0.014153564 1.849134178 0.690928093 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPS(0.022)T(0.016)T(0.011)PS(0.204)VDS(0.746)DDES(0.001)VVK;NKDSGSDTASAIIPS(0.001)T(0.001)T(0.001)PS(0.361)VDS(0.636)DDESVVK;NKDSGSDTASAIIPS(0.01)T(0.004)T(0.015)PS(0.256)VDS(0.714)DDESVVK;NKDSGSDTASAIIPSTTPS(0.005)VDS(0.986)DDES(0.008)VVK 180.97 6.47E-18 740390000 1883022 1423204 1522862 2060142 829423 1895768 1906384 1927216 931888 TRUE FALSE 1794015.282 1568230.106 1592686.729 1853052.612 974074.1086 1830117.079 1615530.108 1758458.75 1076400.432 1.666680196 1.456920733 1.479641481 1.721527192 0.904936564 1.70021957 1.500863489 1.633647385 1 20.03778344 -1.820601593 2.622199013 0.827953475 1.508500716 0.318620343 0.233490473 12372504.24 8533139.589 13459200 0.050287253 0.015114661 1.820601593 0.680547241 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKDSGSDTASAIIPSTTPSVDSDDESVVKDK 31 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTTPS(0.002)VDS(0.992)DDES(0.007)VVKDK;NKDSGSDTASAIIPSTTPS(0.018)VDS(0.963)DDES(0.019)VVKDK 210.79 1.36E-26 648900000 1181400 901300 1088230 1312210 497740 1403330 1439680 1447030 559840 TRUE FALSE 1125557.563 993143.4947 1138126.422 1180304.158 584545.6984 1354732.33 1220030.374 1320320.382 646657.1279 1.740578608 1.535811563 1.760015274 1.825239539 0.903949981 2.094977805 1.886672739 2.041762667 1 19.30264144 NKEDQYDHLDAADMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKEDQYDHLDAADMTK 16 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 188.47 1.58E-09 132340000 343870 284880 270730 340430 153390 335420 330310 351760 150350 FALSE TRUE 327615.9466 313909.5959 283143.2383 306209.3296 180141.1674 323804.3213 279915.1429 320958.0296 173665.5101 1.886476747 1.807552897 1.630394188 1.763213256 1.037288102 1.864528662 1.611806183 1.848139158 1 17.40595174 -2.630311493 0.255750636 3.59E-36 1.767226083 0.406077448 0.25179875 47.86062975 1.389580686 27.87719686 0.345972172 0.002342548 2.630311493 1.767226083 NKEEAAEYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NKEEAAEYAK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 148.18 2.33E-05 5538290000 9821420 8427720 8224790 10061190 4999890 10191970 10903130 10699070 5809340 FALSE TRUE 9357180.941 9286514.25 8601904.757 9049820.066 5871869.233 9839019.523 9239657.269 9762202.711 6710222.777 1.39446651 1.383935312 1.281910458 1.348661642 0.875063232 1.466273155 1.376952387 1.454825426 1 22.67792923 3.742411816 3.135850148 1.278493628 1.392533223 0.069034712 0.18897301 0.765253171 15.51776178 0.049282787 0.089421604 5526.0119 -3.742411816 0.114039595 NKEES(ph)S(ph)DDEDKES(ph)EEEPPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKEESSDDEDKESEEEPPKK 20 3 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 3 NKEES(1)S(1)DDEDKES(1)EEEPPKK 97.839 0.0017252 177170000 469650 590750 348180 569680 133280 621220 362630 619630 106500 TRUE FALSE 447450.5753 650948.0966 364144.3974 512414.6841 156523.9898 599706.9956 307304.1333 565371.9123 123015.4761 3.637351897 5.291595151 2.960151105 4.165448937 1.272392668 4.875053244 2.498093274 4.595941343 1 16.9084803 3.719807066 24.33204108 3.157572857 4.464473583 0.158251642 1.336896571 872.5524752 1132104.704 0.309214243 0.480019293 5245.74368 -3.719807066 1.306900726 NKEFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 99.375 0.035449 759015000 1206820 998130 1095600 1177030 784440 1163770 1340400 1219820 908120 FALSE TRUE 1149776.01 1099840.582 1145834.344 1058712.708 921246.0876 1123468.353 1135897.362 1113006.094 1048946.612 1.096124433 1.048519124 1.092366695 1.009310385 0.878258319 1.071044361 1.082893399 1.061070298 1 20.00050982 3.235863417 24.98857229 1.022717663 1.07491693 0.19608269 0.058159707 141.4572922 1310558.133 0.0176018 0.021965201 1721.327144 -3.235863417 0.052199267 NKEIFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKEIFLR 7 1 P14625;Q96GW1;A0A1W2PRR1;F8W026 P14625 HSP90B1 Endoplasmin 0 ; 131.06 0.0031944 3784600000 4680700 3409600 4164100 4474300 3486900 4369200 5644900 4837000 3724500 FALSE TRUE 4459452.587 3757042.116 4355028.104 4024534.863 4095014.256 4217893.508 4783666.829 4413446.637 4302076.438 1.03658144 0.87330901 1.012308397 0.935486601 0.951869246 0.980432024 1.111943709 1.025887546 1 22.03660173 1.92365584 7.073436201 1.056228968 0.958361779 0.351181047 0.051663584 0.235536911 18.79515652 0.020500322 0.012731117 83.87950134 -1.92365584 -0.097867189 NKESKDPADETEAD ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NKESKDPADETEAD 14 2 P16949 P16949 STMN1 Stathmin 0 ;; 109.84 0.0029575 1180580000 1711430 1366470 1564400 1769980 805010 1784460 1937870 1976730 939640 FALSE TRUE 1630534.096 1505714.847 1636129.287 1592058.248 945403.4891 1722663.703 1642212.34 1803637.042 1085354.572 1.502305456 1.387302256 1.50746063 1.46685543 0.871054965 1.587189797 1.513065299 1.661795222 1 20.049735 NKFDVDAADEKFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKFDVDAADEKFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 174.83 1.09E-05 91517000 370080 305280 351770 401450 247320 419210 453570 489860 281130 FALSE TRUE 352587.0518 336388.3791 367899.0024 361095.4833 290452.5297 404692.6526 384369.5661 446965.2615 324726.2046 1.085797964 1.035913869 1.132951383 1.111999827 0.894453622 1.246258069 1.18367277 1.376437304 1 18.30886429 2.193760056 24.99999978 1.214386995 1.059437595 0.305144498 0.110963644 144.0442842 80379.94195 0.03703314 0.02735089 156.2284257 -2.193760056 -0.1549494 NKFEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NKFEEAER 8 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;;;; 123.63 0.0012217 6289930000 13052010 10568990 11061380 12870670 8060110 12224560 14091000 13294150 8580740 FALSE TRUE 12435067.35 11645982.1 11568555.21 11576885.8 9465790.632 11801220.42 11941159.15 12130043.75 9911397.335 1.25462303 1.175009104 1.1671972 1.168037705 0.955040981 1.190671711 1.204790682 1.223847994 1 23.24065704 NKGNECFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NKGNECFQK 9 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 155.5 6.67E-05 1810079000 2633810 2123080 2013700 2729120 1582975 2427400 2588270 2571060 1527734 FALSE TRUE 2509315.021 2339424.266 2106030.137 2454783.673 1859045.339 2343338.529 2193381.875 2345924.356 1764647.186 1.421992476 1.325717846 1.193456773 1.39109035 1.053494066 1.327936002 1.242957738 1.329401353 1 20.75094834 -5 0.09884459 0.160142214 1.478639398 0.432788549 0.104060003 171.3370926 1.155272711 30.48136305 1.664993916 1.00E-05 5 1.318497185 NKHEAMITDLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NKHEAMITDLEER 13 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 227.42 5.48E-12 5451580000 5293870 4671730 4740190 5641920 3669750 5390520 5792490 5317850 3066845 FALSE TRUE 5043639.257 5147784.598 4957532.4 5074783.483 4309753.238 5203844.941 4908739.264 4852190.862 3542435.659 1.423777237 1.453176598 1.399469991 1.432568992 1.216607344 1.469001964 1.385696096 1.369732955 1 21.75631022 -3.195104834 0.316876479 3.80E-13 1.422215814 0.767326304 0.068494752 39.0635789 1.005159881 25.95687032 0.05873984 0.000638109 3.195104834 1.422215814 NKKDELQSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKKDELQSER 10 2 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 88.734 0.0067451 122710000 188230 121900 149050 194350 110780 175150 211690 204730 117100 FALSE TRUE 179332.7409 134321.7486 155884.0899 174813.5688 130099.9969 169084.5116 179392.8025 186802.7559 135259.2699 1.325844366 0.993068709 1.152483597 1.292433183 0.961856418 1.250077068 1.326288414 1.381071744 1 17.04536795 2.024374167 24.99080405 1.276076543 1.144366814 0.069518382 0.149401873 397.1322088 407177.3567 0.051159945 0.037782729 105.7728403 -2.024374167 -0.131709728 NKKS(ph)PEIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 114.56 0.00084417 43859180000 20714760 16459760 18371810 21715640 8727008 21545580 21626600 21082980 7366770 TRUE FALSE 19735614.35 18137028.26 19214175.66 19532742.61 10248995.43 20799451.16 18327064.97 19236842.5 8509171.067 2.319334538 2.131468284 2.258054928 2.295492999 1.204464612 2.444356918 2.153801448 2.260718741 1 23.02058717 NKKS(ph)PEIHRR ddPTM_SK-BR-3_Trastuzumab_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 154.1 1.08E-05 7483300000 9217400 5635650 8152000 7201050 4521950 9082500 10462500 9540400 5005220 TRUE FALSE 8781711.769 6209929.142 8525777.263 6477186.773 5310576.648 8767970.748 8866253.468 8704991.999 5781403.954 1.518958343 1.074121302 1.474689769 1.120348418 0.91856177 1.516581581 1.533581382 1.505688249 1 22.46298845 NKLDFLRPYTVPNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKLDFLRPYTVPNKK 15 3 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 114.63 0.00025903 507520000 756650 521110 654210 709880 475320 750830 882110 759350 550550 FALSE TRUE 720884.654 574211.7015 684206.1756 638521.5137 558215.6575 724828.5688 747527.9184 692857.2884 635926.4822 1.133597474 0.902952963 1.075920244 1.00408071 0.877799043 1.139799315 1.175494242 1.089524195 1 19.27850046 2.19011217 24.99877112 1.12307797 1.001777122 0.240494441 0.086485116 132.3996109 68315.56603 0.030418033 0.022465252 154.9216701 -2.19011217 -0.121300848 NKLDLETLTDILQHQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKLDLETLTDILQHQIR 17 1 P18440;F5H5R8 P18440 NAT1 Arylamine N-acetyltransferase 1 0 65.716 0.025628 20690000 73903 61862 65528 69100 66821 67257 95081 81318 72415 FALSE TRUE 70409.75165 68165.80813 68532.52362 62153.93672 78474.56124 64927.87323 80574.64717 74197.36483 83644.74836 0.841771337 0.814944267 0.819328469 0.743070401 0.938188742 0.776233709 0.963295948 0.887053477 1 16.35198734 1.445510931 0.776968971 0.991680192 0.815722273 0.492717596 0.058927695 0.438325841 0.564765574 0.048228749 0.019954661 27.89400861 -1.445510931 -0.175957919 NKLEGDS(ph)DVDS(ph)ELEDRVDGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKLEGDSDVDSELEDRVDGVK 21 2 Q92614;Q92614-2 Q92614 MYO18A Unconventional myosin-XVIIIa 2 NKLEGDS(1)DVDS(1)ELEDRVDGVK;NKLEGDS(1)DVDS(1)ELEDRVDGVK 97.771 0.0005805 128979000 175829 140498 138461 163213 74681 169005 168496 180958 75234 TRUE FALSE 167517.9116 154814.9059 144809.5738 146806.5192 87705.34276 163152.3145 142788.8406 165112.3582 86900.90448 1.927688931 1.78151087 1.66637591 1.68935548 1.009256961 1.877452432 1.643122605 1.900007361 1 16.40708357 3.765727888 1.517820572 1.561572331 1.897121091 0.166738061 0.308738685 0.755675198 3.359085118 0.086847265 0.213304359 5830.796549 -3.765727888 0.335548761 NKNSDGGS(ph)DPETQKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKNSDGGSDPETQKEK 16 2 O75554-2;O75554 O75554-2 WBP4 WW domain-binding protein 4 1 NKNS(0.001)DGGS(0.999)DPETQKEK;NKNSDGGS(1)DPETQKEK 100.28 0.0010996 164696000 250870 145047 247090 218750 101356 278060 317200 295300 122489 TRUE FALSE 239011.8723 159827.4542 258419.3209 196760.8344 119032.4543 268430.7125 268805.3142 269441.9665 141483.9685 1.689321234 1.12965063 1.826491889 1.390693493 0.841314076 1.897251789 1.899899452 1.904399271 1 17.11027907 NKPEWFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKPEWFFK 8 1 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 131.5 0.00091405 663850000 2436200 2551100 2550200 3197500 1424080 2928800 2750600 3175300 1949930 FALSE TRUE 2321045.654 2811059.99 2667129.192 2876081.225 1672439.101 2827374.922 2330945.452 2897253.899 2252315.186 1.030515475 1.248075762 1.184172273 1.276944383 0.742542213 1.255319389 1.034910863 1.286344787 1 21.1029773 -2.114729492 3.451899538 0.678106366 1.129323577 0.058879691 0.165901441 981266.9831 34033867.55 383529.9447 0.034628767 0.007678396 2.114729492 0.451217211 NKPGPNIES(ph)GNEDDDASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK 328.87 1.99E-75 60931530000 19046250 16648310 16581210 19306020 7912160 19935490 19732480 20567590 8274330 TRUE FALSE 18145971.51 18344791.72 17341474.88 17365342.19 9292038.199 19245118.98 16721927.76 18766582.78 9557470.837 1.898616466 1.919419063 1.81444183 1.816939072 0.972227732 2.013620477 1.749618497 1.963551143 1 23.18819746 2.979722857 24.93791575 1.61403489 1.880269056 0.158535716 0.34886658 1563.379091 1922729.549 0.098999587 0.106252626 954.383357 -2.979722857 0.266234166 NKPLFFADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKPLFFADK 9 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 104.79 0.0029205 366300000 532540 332810 252210 484100 391580 349960 517040 440370 308970 FALSE TRUE 507367.8896 366723.7174 263774.078 435437.3483 459871.428 337840.7974 438156.0519 401808.8683 356883.4896 1.421662544 1.027572662 0.739104177 1.220110655 1.2885758 0.946641712 1.227728558 1.12588248 1 18.44509363 4.580488349 3.083063823 1.083047448 1.425636067 0.315710706 0.160402891 0.349108559 5.782166513 0.038732637 0.238311205 38061.71465 -4.580488349 0.342588619 NKPLS(ph)PIKLTPTSVLDYFGTGSVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKPLSPIKLTPTSVLDYFGTGSVQR 25 2 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(1)PIKLTPTSVLDYFGTGSVQR;NKPLS(1)PIKLTPTSVLDYFGTGSVQR 281.69 1.35E-53 555660000 829400 697530 787820 768220 384410 893060 943320 921660 449650 TRUE FALSE 790195.9057 768609.1 823942.3263 690997.0661 451450.9823 862133.1083 799399.2087 840954.5644 519379.4255 1.521423196 1.479860507 1.5863977 1.330428261 0.869212295 1.659929265 1.539143003 1.619152633 1 18.98642934 3.23267432 24.97075034 1.375479998 1.517533726 0.101692568 0.252228264 420.9655009 1785813.95 0.071995578 0.088209045 1708.733447 -3.23267432 0.142053729 NKPRS(ph)PVVELSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKPRSPVVELSK 12 2 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 NKPRS(1)PVVELSK;NKPRS(1)PVVELSK 162.79 3.22E-05 807600000 1817280 1588440 1643470 2041790 781630 1874800 2001360 2103890 905410 TRUE FALSE 1731380.776 1750303.842 1718824.725 1836545.39 917946.0245 1809875.206 1696015.775 1919662.238 1045816.359 1.655530401 1.673624463 1.643524421 1.75608784 0.877731561 1.730586055 1.621714712 1.835563407 1 19.99619811 -1.97148588 2.660695937 0.495280059 1.601181457 0.336484396 0.264464351 32190244.98 13863031.98 99999014.05 0.061301733 0.010678595 1.97148588 1.105901398 NKPSAPTPAVNRHS(ph)TGSYIAGYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKPSAPTPAVNRHSTGSYIAGYLK 24 2 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 NKPSAPTPAVNRHS(0.999)T(0.001)GSYIAGYLK 198.02 9.40E-25 339900000 234980 191570 207450 231040 155460 192070 255930 226730 148270 TRUE FALSE 223872.9611 211091.2008 216961.7877 207815.4203 182572.1748 185418.5677 216883.178 206876.3192 171262.9543 1.307188481 1.23255611 1.266834316 1.213428911 1.066034248 1.082654264 1.266375317 1.207945525 1 17.38585359 7.999996406 0.022471289 3.26E-06 2.779978358 0.505239716 0.070590374 2226.157645 3.852386696 170.1872566 330.9933508 99999172.37 -7.999996406 2.779975101 NKPSDLGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NKPSDLGTK 9 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 115.57 0.001326 1427570000 2829640 2212810 2278650 2955370 1443190 2601770 2759320 2936490 1492070 FALSE TRUE 2695888.525 2438297.855 2383128.356 2658290.593 1694881.879 2511670.053 2338335.056 2679355.368 1723452.595 1.564237121 1.414775122 1.382764088 1.542421648 0.983422395 1.457347919 1.356773643 1.554644077 1 20.71687019 -3.693616729 0.222103576 3.27E-33 1.461741214 0.346362684 0.169858123 91.66639492 1.546791831 42.78076115 0.304559473 0.000202481 3.693616729 1.461741214 NKPYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKPYPK 6 1 P27635;X1WI28;A0A087WV22;Q96L21;A6QRI9 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 106.75 0.029053 2819900000 3012300 2110220 1825000 2662400 1410000 2391920 2958800 2821900 1702210 FALSE TRUE 2869914.549 2325253.817 1908678.055 2394770.494 1655903.554 2309087.211 2507380.718 2574799.476 1966180.033 1.459639759 1.182625079 0.97075447 1.21798129 0.842193251 1.174402736 1.275254898 1.309544107 1 20.906964 4.403816547 2.308675086 1.127597937 1.454888324 0.352305981 0.144942667 0.375271013 3.566068491 0.037018736 0.185056701 25340.57975 -4.403816547 0.327290387 NKQDDDLNCEPLS(ph)PHNITPEPVSK ddPTM_SK-BR-3_Trastuzumab_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 220.78 5.92E-33 1218238000 1909440 1670100 1760300 2042000 1035837 2067690 2100650 2208700 1060327 TRUE FALSE 1819184.555 1840285.089 1841011.496 1836734.28 1216486.645 1996085.377 1780157.261 2015294.519 1224757.096 1.485343144 1.502571485 1.503164589 1.499672292 0.993247273 1.629780618 1.45347781 1.645464661 1 20.22406422 -1.715849642 2.819795265 0.926733362 1.463639333 0.400240697 0.178538112 72282284.45 69139616.27 37700161.15 0.039662762 0.019237576 1.715849642 0.536905971 NKQEMAFYSLPEFEEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKQEMAFYSLPEFEEWK 17 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 161.86 2.66E-09 202260000 1187420 1058940 1100070 1284240 736970 1323150 1437890 1413990 777090 FALSE TRUE 1131293.01 1166847.19 1150509.298 1155145.755 865497.3347 1277328.984 1218513.472 1290173.54 897597.1484 1.260357179 1.299967577 1.281765767 1.286931178 0.964238062 1.423053745 1.357528234 1.437363679 1 19.77570857 NKQGLETDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKQGLETDNK 10 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 51.445 0.094074 506840000 1023800 757550 845270 1002900 1057300 621720 1021300 957360 1737300 FALSE TRUE 975407.003 834745.2063 884026.4656 902086.5866 1241692.785 600189.6805 865481.9275 873528.4831 2006711.611 0.486072337 0.415976666 0.440534883 0.449534742 0.618769921 0.299091149 0.431293626 0.435303448 1 20.93640187 -1.38693085 3.820881742 1.002526569 0.444042092 0.833233718 0.077728986 17397020.72 12636521.87 341676.2902 0.016821829 0.041026942 1.38693085 -0.558484476 NKS(ph)EDEDEDEGDATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NKSEDEDEDEGDATR 15 1 Q9BZI1 Q9BZI1 IRX2 Iroquois-class homeodomain protein IRX-2 1 NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR 205.63 2.61E-09 1284950000 1006950 839760 895600 1066760 479324 1040720 1052180 1043330 504348 TRUE FALSE 959353.4691 925332.4987 936664.1459 959527.2581 562917.9538 1004679.605 891650.6164 951970.4942 582559.712 1.646789933 1.58839082 1.607842298 1.647088253 0.9662837 1.724595067 1.530573773 1.634116597 1 19.15204641 -1.961043874 2.636664125 0.567373923 1.54806486 0.394615161 0.211369837 6162807.555 3307140.008 16293097.9 0.047027396 0.010938459 1.961043874 0.980690937 NKS(ph)NEDQSMGNWQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK 293.09 3.47E-44 4475250000 6240120 5720240 4855030 6625100 2869920 6021170 5670660 6139620 2771170 TRUE FALSE 5945161.894 6303138.959 5077637.928 5959132.361 3370433.139 5812655.373 4805496.668 5602002.325 3200908.89 1.857335556 1.969171624 1.586311295 1.861700087 1.052961285 1.815939026 1.5012913 1.75012864 1 21.61005018 -0.871897255 0.088705627 5.06E-13 2.469291467 0.435359005 0.251642783 55.48024586 1.031047685 21.83052032 8.329944013 0.134308267 0.871897255 2.469291467 NKS(ph)NEDQSMGNWQIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NKSNEDQSMGNWQIKR 16 2 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)NEDQSMGNWQIKR;NKS(1)NEDQSMGNWQIKR;NKS(1)NEDQSMGNWQIKR;NKS(1)NEDQSMGNWQIKR;NKS(1)NEDQSMGNWQIKR 147.9 5.13E-07 2023545000 1609150 1126948 1662672 1380610 938536 1671692 1947271 1748421 924444 TRUE FALSE 1533088.669 1241785.282 1738907.156 1241828.46 1102216.381 1613800.887 1650179.045 1595319.988 1067802.054 1.435742386 1.162935843 1.62849205 1.162976279 1.032229126 1.511329633 1.545397893 1.494022213 1 20.0262128 NKS(ph)TESLQANVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NKSTESLQANVQR 13 1 P26373;J3QSB4 P26373 RPL13 60S ribosomal protein L13 1 NKS(0.921)T(0.079)ESLQANVQR;NKS(0.85)T(0.149)ESLQANVQR;NKS(0.975)T(0.024)ES(0.001)LQANVQR 219.97 1.31E-11 917950000 535990 461004 482720 578230 357637 588270 587510 603720 367392 TRUE FALSE 510654.8149 507980.8317 504853.1895 520105.2218 420008.7796 567898.0624 497874.5591 550855.0763 424365.275 1.203337891 1.197036755 1.18966659 1.225607401 0.989734091 1.338229341 1.173221723 1.298068218 1 18.69494708 NKTEDLEATSEHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKTEDLEATSEHFK 14 1 C9JXZ5;Q9BV40 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ; 206.06 6.83E-09 623820000 1555330 1239740 1359050 1810950 953670 1704890 1974720 1788540 937670 FALSE TRUE 1481812.633 1366070.915 1421363.787 1628909.865 1119989.746 1645849.232 1673440.196 1631925.956 1083079.075 1.368148151 1.261284561 1.312336117 1.503962087 1.034079387 1.519602096 1.545076657 1.506746824 1 20.04670715 NKWFFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NKWFFQK 7 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 105.12 0.0072951 376590000 1422100 772540 1133000 1065300 1039000 1292200 1887400 1476200 1185600 FALSE TRUE 1354880.151 851262.7043 1184949.171 958214.0201 1220201.271 1247450.79 1599442.466 1346936.102 1369456.793 0.989355895 0.621606106 0.865269483 0.699703726 0.891011149 0.910909199 1.167939342 0.983555019 1 20.38517232 2.131947618 2.342780929 1.064180173 0.794509339 0.475943629 0.112068155 0.219333751 2.382929585 0.050663848 0.031479098 135.5025967 -2.131947618 -0.269670834 NKYNTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NKYNTPK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ; 121.62 0.0040315 2912200000 2659100 2139800 2319400 2869900 1545140 2951900 3230700 3137900 1879670 FALSE TRUE 2533409.613 2357848.053 2425746.784 2581412.2 1814611.927 2849674.963 2737797.379 2863128.841 2171159.624 1.166846318 1.085985584 1.11725861 1.188955511 0.835780063 1.312512876 1.260983923 1.318709509 1 21.05003437 NLADEIESYMNLKS(ph)PLGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLADEIESYMNLKSPLGSK 19 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 NLADEIESYMNLKS(1)PLGSK 214.05 3.65E-18 134540000 464500 388940 442800 498150 273030 524020 560690 575250 332930 TRUE FALSE 442544.0056 428573.4282 463102.818 448075.0156 320646.3456 505873.056 475146.4427 524878.0604 384559.084 1.150782868 1.114454049 1.204243606 1.165165599 0.833802552 1.315462505 1.235561614 1.364882751 1 18.55284575 NLDDGIDDER ddPTM_SK-BR-3_Trastuzumab_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 2448630000 3012460 3007340 2721480 3399880 2385750 2906410 3147650 3031290 2361370 FALSE TRUE 2870066.986 3313791.365 2846262.55 3058117.603 2801824.045 2805760.293 2667418.182 2765854.178 2727559.199 1.052247367 1.214929218 1.043519991 1.121192018 1.027227583 1.028670723 0.97795061 1.014040017 1 21.37917908 2.660948493 1.253967333 0.995554042 1.124353096 0.500414617 0.048385748 0.314354351 1.011507721 0.02206911 0.019192855 458.0875546 -2.660948493 0.128799054 NLDDGIDDERLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 236.28 4.13E-16 7195640000 11063700 8149880 10176280 10660680 9353850 10386160 12674320 11200490 10321890 FALSE TRUE 10540740.83 8980362.038 10642872.5 9589048.192 10985158.48 10026484.67 10740619.7 10219715.72 11922555.98 0.884100762 0.753224564 0.892667019 0.804277892 0.921376129 0.840967716 0.900865529 0.857174899 1 23.50719022 -2.149833053 0.182376453 1.202238669 0.807566119 0.474983017 0.048366033 29.5148321 0.745741096 2.63563021 0.150685671 0.00708218 2.149833053 -0.394672549 NLDFGIDMDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLDFGIDMDSR 11 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 183.33 1.25E-05 194934000 395920 341620 334500 403090 357330 341940 404530 387270 374340 FALSE TRUE 377205.6462 376431.4664 349837.1559 362570.6274 419648.2389 330098.5321 342811.5188 353358.5858 432390.7353 0.872372175 0.870581711 0.809076438 0.83852543 0.970530135 0.763426468 0.792828085 0.81722053 1 18.72197609 NLDIERPTYTNLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 290.38 1.69E-43 1.40679E+11 34141147 30181920 29215668 35387688 27437682 31274793 36343143 34667807 29140793 FALSE TRUE 32527362.64 33257491.96 30555235.28 31830450.37 32222805.05 30191739.08 30798329.05 31632110.03 33659798.35 0.966356432 0.988047867 0.907766439 0.945651844 0.957308321 0.896967319 0.914988519 0.939759345 1 25.0045232 3.748833858 24.92480841 0.931661838 0.977202152 0.219484708 0.029584335 736.9897451 1788068.85 0.007008546 0.012458487 5608.333852 -3.748833858 0.045540314 NLDKDMYGDDLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLDKDMYGDDLEAR 14 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 76.574 0.028419 129500000 190730 161690 174780 191250 120240 182680 198360 193080 142800 FALSE TRUE 181714.5709 178166.3948 182793.8359 172025.1866 141209.8179 176353.7458 168096.5389 176172.8916 164944.6947 1.101669691 1.080158384 1.108212885 1.042926461 0.856104031 1.069168949 1.019108491 1.068072495 1 17.33162285 3.006246926 16.26190499 1.004396475 1.091570153 0.348311646 0.05867589 2.548192492 6624.640567 0.016386716 0.019401043 1014.488028 -3.006246926 0.087173678 NLDKEYLPIGGLAEFCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLDKEYLPIGGLAEFCK 17 1 P00505 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 228.01 1.43E-15 1695330000 4078100 2745900 3177800 3202800 2352440 2865200 3679700 3441900 2372080 FALSE TRUE 3885336.295 3025710.332 3323505.273 2880848.459 2762704.791 2765977.406 3118294.183 3140508.989 2739930.051 1.418042148 1.104302035 1.212989095 1.051431389 1.008312161 1.009506576 1.138092624 1.146200425 1 21.38570763 5.489140643 0.718509198 1.069850591 2.210882037 0.725781503 0.065895102 3.772583296 0.675259751 0.024215223 4.472232593 308418.6582 -5.489140643 1.141031446 NLDQEQLSQVLDAMFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLDQEQLSQVLDAMFER 17 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 134.9 3.59E-05 31348000 56738 51771 51905 51048 39216 48991 57470 52683 46497 FALSE TRUE 54056.10718 57046.52376 54284.89559 45916.55806 46055.25798 47294.42939 48701.89599 48069.79723 53707.51729 1.006490523 1.062170188 1.010750419 0.854937267 0.857519772 0.88059236 0.906798498 0.895029219 1 15.71283641 3.327324995 5.65078992 0.892519524 1.034123491 0.665203466 0.042529097 0.099791074 5.000856598 0.010779377 0.014612485 2124.833943 -3.327324995 0.141603967 NLDSLEEDLDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NLDSLEEDLDFLR 13 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;;;;;; 180.2 3.05E-05 143489000 223349 238833 176663 259566 176557 182853 209846 214579 174032 FALSE TRUE 212791.7354 263170.3542 184763.1733 233473.9325 207348.4849 176520.7548 177830.1386 195789.3252 201019.9937 1.058560054 1.30917502 0.919128341 1.161446323 1.031481899 0.878125362 0.884639062 0.973979362 1 17.61697948 2.464919134 3.75548744 0.919414655 1.127355254 0.391008954 0.10282184 0.192466985 5.991717293 0.035335189 0.030413629 291.6883836 -2.464919134 0.207940599 NLDSLEEDLDFLRDQFTTTEVNMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLDSLEEDLDFLRDQFTTTEVNMAR 25 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;; 119.69 0.00039309 878580000 619580 483719 575300 576749 591186 556998 663761 612194 721248 FALSE TRUE 590293.6813 533010.516 601678.074 518773.0948 694288.6512 537709.0196 562492.0686 558587.0479 833095.4562 0.708554676 0.63979525 0.722219848 0.622705467 0.833384273 0.645435065 0.675183215 0.670495852 1 19.66812228 -1.267108751 5.30456764 1.000040567 0.686784341 0.729880604 0.059296715 2.52E-05 3.48E-06 0.050787833 0.01196926 0.054061893 1.267108751 -0.313256226 NLDSTTVAIHDEEIY(ph)CK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLDSTTVAIHDEEIYCK 17 0 F8VQR7;F8VW96;Q16527 F8VQR7 CSRP2 Cysteine and glycine-rich protein 2 1 NLDSTTVAIHDEEIY(0.999)CK 66.022 0.046286 0 215260 183210 186820 251820 167790 235720 268890 237290 132990 TRUE FALSE 205085.0864 201879.3073 195385.8818 226506.5752 197052.5229 227556.9573 227865.892 216511.6296 153613.41 1.335072807 1.314203671 1.271932456 1.474523449 1.282782036 1.481361278 1.483372396 1.40945787 1 17.22894464 -0.855513329 4.921510914 0.99999912 1.381405149 0.689742205 0.080429426 8.25E-07 1.92E-07 0.081867907 0.019296406 0.139471885 0.855513329 0.381406029 NLDSTTVAVHGEEIYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLDSTTVAVHGEEIYCK 17 0 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 267.36 9.05E-28 1955080000 3837600 2766000 3153600 3590800 2497700 3278400 3930800 3730300 2781600 FALSE TRUE 3656204.253 3047858.545 3298195.679 3229845.962 2933298.089 3164868.186 3331084.266 3403655.156 3212956.322 1.137956414 0.948614995 1.026529884 1.005256729 0.912959218 0.985033057 1.036766122 1.059353074 1 21.61546994 -0.320298276 6.44136516 1.000000001 1.013149361 0.005020963 0.061013608 0 0 0.057587933 0.013573606 0.478301479 0.320298276 0.013149361 NLEAQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NLEAQHK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;; 117.18 0.0052897 575711000 1634070 1435480 1331800 1674560 1007260 1498710 1656190 1639340 952590 FALSE TRUE 1556830.75 1581757.044 1392864.347 1506230.047 1182925.825 1446809.297 1403507.797 1495790.699 1100312.792 1.414898346 1.437552172 1.265880355 1.368910784 1.075081407 1.314907277 1.275553468 1.359423166 1 20.06948227 -4.62067048 0.064084008 2.80E-12 1.755581857 0.516449493 0.09808307 256.8944501 1.279652389 41.68243844 6.897354493 2.40E-05 4.62067048 1.755581857 NLEELEEKST(ph)TPPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 NLEELEEKS(0.078)T(0.461)T(0.461)PPPAEPVSLPQEPPKPR 118.82 0.0074475 686380000 501780 225970 529210 372930 330690 531070 786440 575420 464610 TRUE FALSE 478061.8538 248996.5999 553474.802 335442.3679 388362.2313 512678.9127 666454.134 525033.1743 536659.3459 0.890810637 0.463975149 1.031333575 0.625056417 0.723666203 0.955315353 1.241856942 0.978336031 1 19.03364708 2.09136059 3.859546083 1.100587618 0.729287423 0.450189224 0.165101977 0.169581258 4.83750486 0.062891385 0.043643025 123.4129091 -2.09136059 -0.371300195 NLEELEEKSTT(ph)PPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 NLEELEEKS(0.02)T(0.114)T(0.866)PPPAEPVSLPQEPPKPR 119.89 0.0044496 260750000 511960 222970 575750 392080 381270 556760 800960 621400 460600 TRUE FALSE 487760.6654 245690.8965 602148.707 352667.3735 447763.3673 537479.2616 678758.8414 566986.9218 532027.4956 0.916795973 0.461801126 1.131799976 0.662874337 0.841616967 1.010247151 1.275796546 1.065709811 1 19.02114128 2.171723245 2.965435055 1.143884405 0.770498514 0.371536514 0.184713338 0.221295088 3.941210707 0.073899301 0.051150774 148.4989029 -2.171723245 -0.373385891 NLEQILNGGES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 363.25 2.99E-77 302253000 891869 934449 709609 1043973 396633.8 895574 774708 878547 394639 TRUE FALSE 849712.1199 1029670.415 742145.2745 939030.8506 465806.6091 864560.0478 656512.0661 801616.7672 455837.6006 1.864067639 2.258853623 1.628091394 2.060011832 1.02186965 1.896640485 1.440232366 1.758557798 1 18.79816041 2.067292469 0.079662044 1.74E-10 3.268842088 0.40366012 0.317158376 17.80104716 1.030698733 18.37526957 22.07254885 116.7595652 -2.067292469 3.268842088 NLEQILNGGES(ph)PKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLEQILNGGESPKQK 15 1 Q13033-2;Q13033;G3V340 Q13033-2 STRN3 Striatin-3 1 NLEQILNGGES(1)PKQK;NLEQILNGGES(1)PKQK;NLEQILNGGES(1)PKQK 231.76 9.19E-14 440410000 546189 350208 477264 488882 251565 517394 545726 557301 270977 TRUE FALSE 520371.7284 385894.5934 499147.0265 439738.6525 295437.8564 499476.516 462465.4758 508500.77 312998.7292 1.662536234 1.23289508 1.594725409 1.404921527 0.943894747 1.595778096 1.477531481 1.624609695 1 18.25579727 3.009509136 24.83003005 1.36808771 1.46836718 0.072011215 0.24814148 784.0098594 2047171.032 0.068878256 0.082231827 1022.137063 -3.009509136 0.100279469 NLETFCEETRR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 236.61 2.37E-15 2207890000 1785990 1545610 1636450 1692980 1505290 1629970 1945140 1766960 1686990 FALSE TRUE 1701569.792 1703109.416 1711482.851 1522798.434 1767812.099 1573523.73 1648373.168 1612235.615 1948599.793 0.873226918 0.874017036 0.878314191 0.781483422 0.907221742 0.807515086 0.845926995 0.8273816 1 20.89400639 -1.012230334 7.511955009 1.000000006 0.851302094 0.621805202 0.036887754 3.12E-09 4.53E-10 0.03260418 0.007684879 0.097223145 1.012230334 -0.148697911 NLETQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLETQHK 7 0 P17676-3;P17676-2;P17676 P17676-3 CEBPB CCAAT/enhancer-binding protein beta 0 96.253 0.0249 0 108050 66913 79101 99608 63400 90258 109950 91771 72966 FALSE TRUE 102942.6906 73731.51077 82727.85909 89595.2146 74456.93993 87132.34283 93175.10813 83735.04473 84281.19462 1.221419453 0.874827547 0.981569607 1.063051076 0.883434795 1.033828996 1.105526666 0.993519908 1 16.36292314 NLETVLSQSVQSIPLYLMPRPNS(ph)VAATSSAHLEDLAYLDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLETVLSQSVQSIPLYLMPRPNSVAATSSAHLEDLAYLDEQR 42 1 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4;J3KRP9 Q9HCD6 TANC2 Protein TANC2 1 NLETVLS(0.013)QS(0.013)VQS(0.002)IPLY(0.063)LMPRPNS(0.226)VAAT(0.226)S(0.226)S(0.226)AHLEDLAY(0.004)LDEQR 58.446 0.01759 20848000 4452.5 2944 4702.7 4523.8 4200.2 2897.1 7032.4 4976.2 4003.6 TRUE FALSE 4242.039149 3243.996947 4918.323447 4069.059029 4932.71355 2796.772701 5959.478221 4540.457548 4624.45784 0.917305184 0.701486976 1.063545959 0.879899692 1.066657697 0.604778505 1.288686896 0.981835645 1 12.17506852 1.725771125 24.99999991 1.104743892 0.871159015 0.284578143 0.162309147 0.988236994 1923.39845 0.068013094 0.037716719 53.18279094 -1.725771125 -0.233584877 NLFASFPTEESSINYTFKT(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLFASFPTEESSINYTFKTPEK 22 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NLFASFPTEESSINYT(0.014)FKT(0.986)PEK 195.86 3.55E-22 119880000 294200 367000 283550 402440 140010 410660 341270 403920 149200 TRUE FALSE 280293.749 404397.7172 296551.048 361985.9666 164427.6997 396438.7412 289202.9936 368550.6235 172337.174 1.626426514 2.346549545 1.720760769 2.100452028 0.954104653 2.300366961 1.678123106 2.138543966 1 17.39487441 NLGLEELGIELDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NLGLEELGIELDPR 14 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;; 172.57 6.60E-06 254025000 561636 457574 509337 495131 451938 423315 529444 496103 473832 FALSE TRUE 535088.5793 504201.3108 532690.6053 445359.4912 530755.8441 408655.4954 448667.5939 452661.5913 547311.4466 0.977667437 0.921232899 0.973286067 0.813722231 0.969751039 0.746659873 0.819766509 0.827063995 1 19.0620025 3.157554926 1.205043222 0.840612378 0.958485439 0.167185225 0.079990112 0.567353791 1.751019009 0.028370727 0.04007366 1437.324822 -3.157554926 0.117873061 NLGQNLWGPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLGQNLWGPHR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 171.85 1.40E-05 465470000 521190 409430 256790 289250 413890 310320 479240 399460 366250 FALSE TRUE 496554.3816 451151.3825 268564.0755 260174.0405 486072.285 299573.5406 406123.1362 364481.1647 423046.1795 1.173759286 1.066435308 0.634833946 0.615001513 1.148981621 0.708134372 0.959997173 0.861563542 1 18.69045563 3.939344071 8.331917956 0.846476108 1.133888948 0.327110927 0.165768529 0.330166969 42.55970334 0.040103806 0.072781709 8696.491388 -3.939344071 0.287412841 NLGS(ph)INTELQDVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.972)INT(0.028)ELQDVQR;NLGS(1)INTELQDVQR;NLGS(0.924)INT(0.076)ELQDVQR;NLGS(0.926)INT(0.074)ELQDVQR 314.72 8.03E-56 306998000 411015 334903 365204 468737 421327 440594 522555 449985 482103 TRUE FALSE 391587.1355 369029.9965 381948.9646 421618.6662 494806.2954 425336.1193 442829.6374 410581.9279 556865.071 0.703199313 0.662691944 0.685891403 0.757128949 0.88855689 0.76380463 0.795218915 0.737309537 1 19.08696828 -5 0.092048875 1.818280555 0.541594497 0.687387168 0.05636463 115.9906564 0.738825627 18.59471888 1.231702911 1.00E-05 5 -1.276686058 NLGSINT(ph)ELQDVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.247)INT(0.753)ELQDVQR 303.59 4.96E-43 127500000 109920 89952 90914 128510 109680 115340 127900 118120 111310 TRUE FALSE 104724.2994 99118.21107 95082.49683 115591.9306 128808.1573 111345.7469 108386.506 107776.7866 128571.3863 0.814522597 0.770919673 0.739530774 0.899048645 1.001841553 0.86602276 0.843006435 0.838264171 1 16.97221008 3.226621041 24.99311102 0.897861045 0.779765956 0.522463621 0.059372058 188.8620089 395344.1412 0.017217368 0.020731476 1685.082007 -3.226621041 -0.118095089 NLHSEISGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLHSEISGK 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 134.68 0.00024221 104530000 358970 364060 307310 422250 200110 356430 352910 358960 198050 FALSE TRUE 342002.1995 401158.1279 321400.4675 379804.6278 235009.1206 344086.7397 299067.0979 327527.5594 228762.5825 1.495009349 1.753600276 1.404952086 1.660256776 1.027305769 1.504121592 1.307325239 1.431735714 1 17.80349157 -1.153836781 0.074057923 1.18E-10 2.19585984 0.427556022 0.182061348 82.72214431 1.13785593 25.40179764 10.26649323 0.070171897 1.153836781 2.19585984 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR 35 0 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 169.65 2.51E-15 44308000 16942 14866 14109 22375 18492 15384 19509 16583 7263.2 FALSE TRUE 16141.18524 16380.8623 14755.91161 20125.82249 21716.99895 14851.24822 16532.54374 15130.90461 8389.539961 1.923965475 1.952534034 1.758846334 2.398918485 2.588580428 1.770210082 1.970613862 1.803544018 1 13.03437599 0.610033408 1.110402925 1.000489637 2.057066201 0.624970069 0.257154412 0.90556259 1.715486743 0.248463821 0.077296778 4.074116164 -0.610033408 1.056576563 NLIQHNNS(ph)TQTDIFYTDRLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLIQHNNSTQTDIFYTDRLEDR 22 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLIQHNNS(0.993)T(0.005)QT(0.001)DIFYTDRLEDR;NLIQHNNS(0.934)T(0.049)QT(0.017)DIFYTDRLEDR 135.3 3.78E-06 150548000 106425 93568 115477 130362 111787 123712 137074 119490 105324 TRUE FALSE 101394.5012 103102.6856 120771.7347 117257.7641 131282.6174 119427.8224 116160.8438 109026.8221 121657.108 0.833444941 0.847485916 0.992722387 0.963838168 1.079119992 0.981675665 0.954821676 0.896181275 1 16.89246109 3.749113763 11.13470405 0.98106776 0.84041218 0.626084952 0.045214084 0.282928894 291.3485633 0.011715072 0.020291207 5611.949609 -3.749113763 -0.140655579 NLIYDNADNKLALVEENGIFELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLIYDNADNKLALVEENGIFELLR 24 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 163.68 1.50E-11 163434000 168121 89420 130723 135332 127952 142293 192910 154402 160579 FALSE TRUE 160174.2535 98531.99966 136716.7789 121728.1702 150266.7883 137365.3577 163478.0365 140881.7423 185480.7712 0.863562581 0.531224876 0.737094082 0.656284581 0.810147528 0.740590827 0.881374578 0.759549043 1 17.5009101 1.141766567 0.500036314 0.996478249 0.687140868 0.442350728 0.095565688 0.78898575 0.51840258 0.101521385 0.052486544 13.86010648 -1.141766567 -0.309337381 NLKPIKPMQFLGDEETVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLKPIKPMQFLGDEETVR 18 2 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;; 222.79 3.09E-19 2116900000 2830370 2482470 2152630 2884310 1580520 2535050 2783580 2964400 1689640 FALSE TRUE 2696584.019 2735436.515 2251330.215 2594373.679 1856162.188 2447260.583 2358893.747 2704821.421 1951660.742 1.381686869 1.401594271 1.153545884 1.329315912 0.951068056 1.253937496 1.208659731 1.385907583 1 20.89627086 3.743944912 24.5839071 1.193470903 1.391640589 0.298145943 0.132226635 386.8023831 1766076.035 0.031014313 0.053931434 5545.55366 -3.743944912 0.198169685 NLKPIKPMQFLGDEETVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLKPIKPMQFLGDEETVRK 19 3 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 247.61 3.97E-25 2114800000 3184800 2361300 2679500 3110700 1621270 3116300 3400700 3366700 1779610 FALSE TRUE 3034260.816 2601919.155 2802357.725 2798006.526 1904018.975 3008381.75 2881860.757 3071893.9 2055582.83 1.476107297 1.265781713 1.363291075 1.361174303 0.926267211 1.463517649 1.401967712 1.494415042 1 20.97111608 4.625614664 2.88015878 1.306055693 1.486539396 0.083320357 0.187247096 0.888486934 11.8643245 0.043129651 0.327904023 42229.37602 -4.625614664 0.180483703 NLKT(ph)LQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLKTLQK 7 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 NLKT(1)LQK;NLKT(1)LQK 104.22 0.013257 832600000 2227000 1021520 2057780 2517900 1716110 2953500 3424300 2338400 1651540 TRUE FALSE 2121734.123 1125614.049 2152131.248 2264795.908 2015399.041 2851219.554 2901860.143 2133637.299 1907652.388 1.112222613 0.59005197 1.128156923 1.187216247 1.056481282 1.494622171 1.521168197 1.118462311 1 20.86336688 3.188491671 1.460772188 1.318736706 0.859831815 0.270632255 0.221128681 0.36725856 1.634734533 0.076405356 0.107018548 1543.446822 -3.188491671 -0.458904891 NLLALIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLLALIHR 8 0 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 94.302 0.010456 53439000 94619 77457 53483 70034 73550 62153 97253 85783 60101 FALSE TRUE 90146.54739 85349.95636 55935.24845 62994.04926 86377.09671 60000.62603 82415.26868 78271.38576 69421.15613 1.298545752 1.22945167 0.805737783 0.907418614 1.244247453 0.864298859 1.187177991 1.127486059 1 16.08308777 3.972146952 23.80046348 1.030726711 1.272635541 0.349604412 0.139271552 373.6748382 319306.1879 0.034356678 0.062008664 9378.793027 -3.972146952 0.24190883 NLLEDDS(ph)DEEEDFFLR ddPTM_SK-BR-3_Trastuzumab_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 275.23 3.09E-35 260291000 462709 399596 402256 531084 425792 456086 530987 442748 410349 TRUE FALSE 440837.6626 440315.2867 420699.8355 477698.4273 500049.99 440291.6275 449975.1809 403978.638 473983.8271 0.930068997 0.9289669 0.88758268 1.007836977 1.054993781 0.928916985 0.949347119 0.852304688 1 18.85447831 4.978389502 0.004917328 1.869202832 0.000138722 0.032823688 0.058257983 127767.4684 90.97333664 16629.78589 17968.16309 95145.77376 -4.978389502 -1.86906411 NLLHVTDTGVGMTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NLLHVTDTGVGMTR 14 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;;;; 173.03 2.76E-06 5121640000 5091380 4144804 4237220 4906090 3647960 4777390 5730050 5230780 3728770 FALSE TRUE 4850720.558 4567164.24 4431500.728 4412920.512 4284163.069 4611947.786 4855825.633 4772745.173 4307008.608 1.126238882 1.060402859 1.028904544 1.024590595 0.99469573 1.070800689 1.127424177 1.10813458 1 22.03825478 -0.317851193 7.605773226 1.000000008 1.070283741 0.187033954 0.044020502 0 0 0.046294177 0.010911642 0.481004132 0.317851193 0.070283733 NLLIFENLIDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLLIFENLIDLKR 13 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 180.78 2.02E-05 66080000 157572 134377 152947 189572 127481 176716 220124 203823 148892 FALSE TRUE 150123.8838 148070.1691 159959.7712 170515.8624 149713.646 170596.2806 186540.0409 185975.1776 171981.4109 0.872907619 0.860966126 0.930099191 0.991478448 0.870522257 0.991946046 1.084652347 1.081367902 1 17.39189311 2.029119012 3.788100015 1.061193135 0.901581149 0.711547387 0.043837021 0.116552019 3.579209358 0.019721681 0.012814503 106.9347879 -2.029119012 -0.159611986 NLLPAYRPNLS(ph)PPAEAGLALPPTGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLLPAYRPNLSPPAEAGLALPPTGYR 26 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 NLLPAYRPNLS(1)PPAEAGLALPPTGYR;NLLPAYRPNLS(1)PPAEAGLALPPTGYR 135.2 2.02E-05 397840000 276346 243172 256516 289935 233220 291245 304043 292334 256948 TRUE FALSE 263283.6722 267951.5033 268277.5123 260790.183 273893.4942 281159.1126 257655.6562 266735.6852 296794.1835 0.887091752 0.902819254 0.903917688 0.878690343 0.922839831 0.947320157 0.868129062 0.898722751 1 18.17910329 -1.376398487 3.050779163 1.001247436 0.900221792 0.662438615 0.02215709 3811249.719 4803336.868 41977.80345 0.005174322 0.042034077 1.376398487 -0.101025643 NLLQQS(ph)WEDMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NLLQQSWEDMKR 12 1 Q8TDM6-4;Q8TDM6;Q8TDM6-2;R4GMQ2 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLLQQS(1)WEDMKR;NLLQQS(1)WEDMKR;NLLQQS(1)WEDMKR;NLLQQS(1)WEDMKR 160.8 3.75E-05 751118000 850257 642079 670157 805355 490279 715997 811176 760171 492551 TRUE FALSE 810067.0367 707507.5801 700884.3613 724399.1853 575783.5024 691201.8444 687416.2029 693606.3973 568933.2935 1.423834826 1.243568601 1.231927133 1.273258559 1.012040443 1.214908412 1.208254484 1.219134836 1 19.11789998 8 0.299903713 1.127096393 3.643647387 0.538302474 0.083000606 41.22337247 0.588728805 0.079216977 55.64636014 100000000 -8 2.516550994 NLLSVAYK ddPTM_SK-BR-3_Trastuzumab_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 ; 133.23 0.0021592 1007540000 1590930 1260050 907550 1081050 1131910 1062820 1719660 1361510 1159620 FALSE TRUE 1515729.892 1388450.528 949162.0652 972380.8001 1329314.746 1026014.277 1457294.283 1242288.967 1339447.947 1.13160791 1.036584162 0.708621837 0.725956393 0.992434793 0.765997872 1.087981274 0.927463415 1 20.35320709 3.982908971 22.71983064 0.891354039 1.095974123 0.312753924 0.124596591 253.1826918 336568.8423 0.032063856 0.058552962 9614.107447 -3.982908971 0.204620083 NLNIINTHAYNQPEDLVYS(ph)QPEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NLNIINTHAYNQPEDLVYSQPEMR 24 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR 232.53 1.85E-34 1330710000 477164 387367 451452 468025 386563 448921 558069 514959 505240 TRUE FALSE 454609.4034 426840.1377 472151.5207 420978.2378 453979.4648 433374.7532 472925.3244 469866.46 583590.0388 0.778987599 0.731404084 0.809046573 0.721359533 0.77790818 0.742601354 0.81037251 0.805131049 1 19.15459573 0.356699634 0.763151778 1.003584595 0.758380269 0.876004619 0.027594711 0.642215145 0.522541984 0.02818177 0.00830222 2.273524475 -0.356699634 -0.245204327 NLNNSNLFS(ph)PVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;NLNNS(0.001)NLFS(0.999)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR 330.25 2.19E-62 2680560000 2608300 2301426 2284007 2795240 2211045 2319170 2559902 2208829 2003701 TRUE FALSE 2485010.828 2535943.926 2388730.98 2514257.165 2596650.548 2238856.561 2169341.934 2015412.223 2314424.718 1.073705621 1.095712428 1.032105716 1.086342168 1.121942109 0.967349054 0.937313673 0.87080483 1 21.14222221 2.113422768 4.898096099 0.934416918 1.080687872 0.768417816 0.037899529 0.090568134 3.516056456 0.013646762 0.009903902 129.8442637 -2.113422768 0.146270955 NLNNYEVEY(ph)LCDY(ph)KVVKDMEY(ph)YLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLNNYEVEYLCDYKVVKDMEYYLVK 25 2 Q9H5I1-3;Q9H5I1 Q9H5I1-3 SUV39H2 Histone-lysine N-methyltransferase SUV39H2 3 NLNNY(0.001)EVEY(0.75)LCDY(0.75)KVVKDMEY(0.75)Y(0.75)LVK 50.215 0.042188 636640000 280080 461130 266970 399250 63155 375780 211690 249070 12085 TRUE FALSE 266841.1735 508119.6713 279210.8386 359116.6315 74169.212 362766.6444 179392.8025 227260.1104 13959.08008 19.11595692 36.40065595 20.00209448 25.72638236 5.313330935 25.98786183 12.85133415 16.28045037 1 13.76891625 1.41892822 0.290530312 4.13E-11 29.70819705 0.450685459 7.60146087 1.355032585 0.430931306 15.42712847 13.02024833 26.23784851 -1.41892822 29.70819705 NLPFDFTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLPFDFTWK 9 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 141.02 0.00025059 505770000 1078820 819630 1027440 1039650 712810 1034740 1327470 1150850 708570 FALSE TRUE 1027826.317 903151.2288 1074549.14 935142.4068 837123.8383 998906.6943 1124940.071 1050075.473 818451.4167 1.255818361 1.103487892 1.312905224 1.142575341 1.022814331 1.220483799 1.374473851 1.283002817 1 19.64253726 2.001007066 24.999962 1.269945038 1.168070109 0 0.124080688 66.31018562 1646087.009 0.043066985 0.031553378 100.2321545 -2.001007066 -0.101874929 NLPIMSTAS(ph)VEIDDALYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLPIMSTASVEIDDALYSR 19 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NLPIMST(0.001)AS(0.999)VEIDDALYSR;NLPIMS(0.001)T(0.024)AS(0.975)VEIDDALYSR 186.01 2.25E-14 98426000 33578 27790 33281 43633 42825 41074 46269 33259 47554 TRUE FALSE 31990.83449 30621.83259 34806.96677 39246.92794 50293.66644 39651.59708 39209.81426 30346.66564 54928.43145 0.582409394 0.557486019 0.633678513 0.714510262 0.915621748 0.721877469 0.713834589 0.552476465 1 15.74526547 3.310291379 2.800969323 0.758483449 0.572693908 0.338579739 0.120242444 0.294511877 4.68778506 0.033225171 0.045990162 2043.108255 -3.310291379 -0.185789541 NLPIYSEEIVEMYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLPIYSEEIVEMYK 14 0 P35579;Q5BKV1 P35579 MYH9 Myosin-9 0 182.02 2.16E-07 0 24298 24089 23096 25799 21453 24744 27203 24130 23030 FALSE TRUE 23149.48169 26543.69649 24154.97445 23205.63551 25194.39641 23887.10908 23052.68273 22017.04928 26601.37478 0.87023629 0.997831755 0.908034816 0.872347226 0.94710881 0.897965209 0.866597419 0.827665843 1 14.69921319 2.015417289 14.25660102 0.883018597 0.922756404 0.008188077 0.056532933 3.727951072 3442.686139 0.019696562 0.014480725 103.6137254 -2.015417289 0.039737807 NLPLGWDGKPIPYWLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLPLGWDGKPIPYWLYK 17 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 141.97 5.51E-07 221590000 836890 697230 685530 830320 553670 721890 905130 861250 616690 FALSE TRUE 797331.8683 768278.5297 716962.2286 746854.6561 650229.8727 696890.7683 767035.7946 785834.3842 712323.1356 1.119340126 1.078553386 1.006512624 1.048477326 0.912829923 0.978335159 1.076808763 1.1031993 1 19.44217232 3.946830634 2.454084548 1.018909535 1.11005326 0.299409208 0.052756732 0.35826803 4.256808534 0.014809674 0.03453723 8847.705001 -3.946830634 0.091143726 NLPT(ph)PTSAPTPGLAQGVHAPSTCSYMEATASSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLPTPTSAPTPGLAQGVHAPSTCSYMEATASSR 33 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 NLPT(0.993)PT(0.005)S(0.001)APTPGLAQGVHAPSTCSYMEATASSR 164.77 1.50E-13 167180000 6049.9 3079.4 2981.1 6827.2 6311.1 4300.5 9846.3 7554.6 28489 TRUE FALSE 5763.933217 3393.194361 3117.786384 6140.916885 7411.753842 4151.572607 8344.066095 6893.079175 32906.92862 0.175158651 0.103114891 0.094745591 0.186614708 0.225233838 0.126161048 0.25356563 0.20947197 1 15.00610376 -5 0.302772232 8.076480053 0.125555446 0.97375652 0.042986169 37.10903247 0.341188265 166.7955911 0.039351539 1.00E-05 5 -7.950924607 NLQEEIDALESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLQEEIDALESR 12 0 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 ;; 315.49 4.52E-46 154829000 347440 314482 332807 366230 307664 314155 368290 352560 344350 FALSE TRUE 331017.1998 346528.0733 348066.5301 329415.8646 361320.5042 303275.7336 312100.5964 321687.9774 397750.0393 0.832224179 0.871220714 0.875088613 0.828198195 0.908410983 0.762478199 0.784665155 0.808769191 1 18.60150255 2.242000275 24.99973509 0.815045692 0.860310236 0 0.06864154 203.5746894 1479610.45 0.021559752 0.017357253 174.5823259 -2.242000275 0.045264544 NLQLLMDRVDEMSQDIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLQLLMDRVDEMSQDIVK 18 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 209.66 4.55E-16 152854000 485730 357290 439760 480180 328770 463120 605510 531990 356080 FALSE TRUE 462770.5055 393698.2572 459923.431 431911.3941 386107.3839 447082.0383 513128.3285 485406.1353 411299.0678 1.12514358 0.957206782 1.118221428 1.050115179 0.938750934 1.086999882 1.247579605 1.180178059 1 18.64982828 1.991232525 24.58976632 1.169393502 1.036846191 0.220079457 0.085298867 350.6474436 983446.7891 0.030348435 0.021277277 98.00145543 -1.991232525 -0.132547311 NLQLLTQASSEGS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLQLLTQASSEGSP 14 0 B8ZZB7;H0YEJ0 B8ZZB7 SAMD12 1 NLQLLTQASSEGS(1)P;NLQLLTQASSEGS(1)P 249.82 3.56E-18 105329000 292100 253170 281210 314130 236950 280370 338860 308800 276260 TRUE FALSE 278293.0119 278968.3108 294103.7567 282553.0556 278274.005 270660.7166 287160.6834 281759.8349 319100.9899 0.87211579 0.874232045 0.921663567 0.885465933 0.872056226 0.848197672 0.899905336 0.882980135 1 18.28365356 0.070294401 1.241414248 1.000310318 0.880641725 0.789147687 0.019158448 4.447254671 5.426867709 0.021921535 0.005403738 1.17569427 -0.070294401 -0.119668593 NLQMWEEMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLQMWEEMKK 10 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 98.156 0.0089293 189040000 343790 281250 453520 542830 409360 562330 681260 598470 457990 FALSE TRUE 327539.728 309909.6948 474314.3406 488263.6971 480752.2544 542856.3711 577321.2748 546064.7941 529012.7501 0.619152805 0.585826513 0.896602852 0.922971511 0.908772528 1.026168785 1.091318262 1.032233711 1 19.01294297 3.494133611 1.026518217 1.036394018 0.566141943 0.881871879 0.058211587 0.155252513 0.333989586 0.022624997 0.050072291 3119.849263 -3.494133611 -0.470252075 NLQS(ph)PTQFQTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLQSPTQFQTPR 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 NLQS(0.999)PT(0.001)QFQTPR;NLQS(0.978)PT(0.022)QFQTPR 229.17 9.26E-12 189419000 292930 234960 278590 302880 254880 289250 351420 313140 312470 TRUE FALSE 279083.7794 258902.6911 291363.6271 272433.927 299330.9913 279233.2 297804.4247 285719.8015 360926.2517 0.773243227 0.717328512 0.807266376 0.754818819 0.829341146 0.773657218 0.825111566 0.791629315 1 18.46134455 -5 0.182061943 1.921296038 0.735047553 0.841972288 0.030017832 43.98854478 0.425006105 14.61477116 0.080590002 1.00E-05 5 -1.186248485 NLRDIDEVSSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLRDIDEVSSLLR 13 1 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 99.069 0.0027632 115230000 31579 36503 40605 29491 324460 21619 41207 21142 183260 FALSE TRUE 30086.32325 40222.6972 42466.77941 26526.50865 381045.7213 20870.32861 34920.11533 19290.6944 211679.0248 0.142131811 0.190017397 0.200618741 0.125314772 1.800110906 0.098594221 0.164967291 0.091131818 1 17.69151879 NLS(ph)FEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;NLS(1)FEIK;NLS(1)FEIK 136.96 0.0030729 3404349000 6114109 4616179 4812606 6886569 3804907 6737821 6919059 5470204 3501390 TRUE FALSE 5825107.185 5086572.888 5033268.745 6194318 4468481.576 6504488.569 5863429.472 4991203.938 4044367.679 1.440301092 1.257692992 1.244513147 1.531591213 1.104865317 1.608283194 1.449776563 1.23411231 1 21.94748273 0.956694789 4.894204589 1.000206983 1.375067684 0.406692935 0.146333023 0.218559047 17.05866736 0.13043853 0.033010798 9.05096299 -0.956694789 0.3748607 NLS(ph)FNELYPSGTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLSFNELYPSGTLK 14 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 NLS(1)FNELYPSGTLK 264.52 1.13E-24 48487000 170550 180920 171410 197220 134560 189440 224520 196400 158040 TRUE FALSE 162488.4395 199355.9537 179269.318 177395.0709 158027.2214 182879.6453 190265.3504 179202.1748 182548.036 0.890113326 1.092073944 0.982039149 0.971772005 0.865674728 1.001816559 1.042275527 0.981671338 1 17.47791662 2.015213481 24.99926151 1.015021226 0.970115442 0.107064026 0.061830993 568.04373 933424.5159 0.023498216 0.017348397 103.5651125 -2.015213481 -0.044905784 NLS(ph)GSTLYPVSNIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLSGSTLYPVSNIPR 15 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 NLS(0.97)GS(0.03)TLYPVSNIPR;NLS(0.995)GS(0.001)T(0.004)LYPVSNIPR 229.69 4.50E-13 154084000 238260 205109 228620 249030 201389 213840 276680 234540 223960 TRUE FALSE 226997.922 226009.8403 239102.4531 223997.0313 236511.1778 206434.6672 234467.3844 214002.4342 258690.573 0.877488187 0.873668637 0.924279731 0.865887878 0.91426284 0.797998415 0.906362307 0.827252543 1 17.98086796 -1.47318634 5.862119081 1.000101904 0.875136604 0.51756225 0.038380205 4.41E-05 3.97E-06 0.032092442 0.007558107 0.033636722 1.47318634 -0.1249653 NLS(ph)LVR ddPTM_SK-BR-3_Trastuzumab_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 82.279 0.062583 220853000 432527 375326 413032 511935 347142 418746 475833 415062 331956 TRUE FALSE 412082.3059 413572.1461 431969.9257 460474.3212 407683.4549 404244.721 403235.9366 378716.9709 383434.0411 1.074714975 1.078600494 1.126582096 1.200921858 1.063242725 1.054274472 1.051643551 0.987697831 1 18.5486189 1.743562967 1.27232011 0.99672204 1.106412021 0.578931124 0.039134817 0.358733437 1.094371248 0.03399435 0.013254725 55.40678709 -1.743562967 0.109689982 NLS(ph)NEELTK ddPTM_SK-BR-3_Trastuzumab_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 156.46 7.43E-05 1212880000 2941220 2492260 2501700 2965550 1605230 2918110 3006400 3051830 1810450 TRUE FALSE 2802194.36 2746224.127 2616405.42 2667447.28 1885181.604 2817055.119 2547718.464 2784595.586 2091205.34 1.339990056 1.313225476 1.251147063 1.27555493 0.901480868 1.347096369 1.218301434 1.331574444 1 20.9959033 -5 0.083364038 0.327266879 1.453953819 0.241973311 0.131594356 345.2827111 2.025679203 44.42216305 3.770369868 1.00E-05 5 1.12668694 NLS(ph)PGAVESDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;NLS(1)PGAVESDVR;NLS(1)PGAVESDVR;NLS(1)PGAVESDVR 166.04 5.56E-05 830866000 935450 883770 866520 1046160 933980 881060 1040540 946560 936170 TRUE FALSE 891233.1324 973827.1678 906250.7991 940998.0092 1096865.816 850548.6713 881786.5122 863674.1884 1081346.462 0.824188328 0.900569061 0.83807626 0.870209542 1.014351879 0.786564437 0.815452348 0.798702561 1 20.0443974 -0.693817171 8.417454022 0.999999995 0.856542854 0.324553995 0.065275069 0 0 0.06136913 0.014464843 0.202387101 0.693817171 -0.143457141 NLS(ph)SDEATNPISR ddPTM_SK-BR-3_Trastuzumab_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(0.921)S(0.079)DEATNPISR 242.93 6.17E-17 518930000 564460 491450 519590 623500 485310 541930 662940 590560 518680 TRUE FALSE 537779.0945 541529.3137 543413.7154 560824.5954 569947.9103 523162.8282 561796.3273 538847.4356 599114.2453 0.897623615 0.903883221 0.907028534 0.936089569 0.951317574 0.873227155 0.937711516 0.899406816 1 19.19247161 -5 0.305654701 1.746144367 0.908771611 0.575207481 0.023213706 197.9637381 1.809445699 94.94386687 0.020822776 1.00E-05 5 -0.837372756 NLSDIGWPVFEIPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLSDIGWPVFEIPSPR 16 0 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(1)PR 118.48 0.00028208 23536000 80371 82266 72550 91992 64707 81218 96255 87153 73155 TRUE FALSE 76572.02211 90648.99893 75876.48926 82744.78939 75991.88031 78405.4003 81569.53191 79521.42129 84499.50378 0.906183098 1.072775518 0.897951892 0.979234027 0.899317474 0.927880009 0.965325573 0.941087435 1 16.36665525 4.771296715 23.49452836 0.960987249 0.906182867 0.099603815 0.051250027 3281.777746 3620220.285 0.011810304 0.485499684 59060.44498 -4.771296715 -0.054804382 NLSFDIPTGSLRDS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NLSFDIPTGSLRDSR 15 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 NLSFDIPT(0.005)GS(0.002)LRDS(0.993)R;NLSFDIPTGSLRDS(1)R;NLSFDIPT(0.001)GS(0.002)LRDS(0.997)R;NLSFDIPTGSLRDS(1)R;NLSFDIPT(0.004)GS(0.002)LRDS(0.994)R 134.29 2.18E-05 594272000 860049 710890 783863 860963 684154 796845 895223 869216 747620 TRUE FALSE 819396.1882 783330.4992 819803.8939 774417.3635 803470.241 769250.0578 758640.2895 793102.839 863557.0913 0.948861629 0.907097524 0.949333752 0.896776104 0.930419366 0.890792358 0.878506236 0.918413903 1 19.71993203 7.999971651 0.634227792 0.911851277 3.85383785 0.000273723 0.035437772 491.702415 3.352299028 0.012897047 2023.631928 99993472.68 -7.999971651 2.941986573 NLSS(ph)DEATNPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NLS(0.207)S(0.793)DEATNPISR;NLS(0.261)S(0.739)DEATNPISR;NLS(0.097)S(0.903)DEATNPISR 295.71 1.17E-40 726760000 856930 744660 776360 914170 725960 877720 971120 935490 745630 TRUE FALSE 816424.6172 820541.7006 811956.8739 822275.8948 852567.1942 847324.3363 822957.8082 853573.5363 861258.4922 0.947943764 0.952724075 0.942756305 0.954737634 0.989908607 0.983821169 0.955529397 0.991077062 1 19.71608678 2.865897416 5.284611389 0.979097244 0.948897039 0.656453201 0.012179968 0.159619089 6.218388205 0.003699333 0.003943364 734.3403909 -2.865897416 -0.030200205 NLSS(ph)TTDDEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.009)S(0.413)T(0.413)T(0.164)DDEAPR;NLS(0.415)S(0.514)T(0.054)T(0.017)DDEAPR 219.26 3.39E-11 395100000 686770 570650 625980 723140 547140 590880 660110 642290 543220 TRUE FALSE 654307.7431 628799.8838 654681.8022 650448.5933 642561.0428 570417.6774 559398.0957 586047.6826 627459.7832 1.042788336 1.002135755 1.043384484 1.036637902 1.024067295 0.909090419 0.891528207 0.934000391 1 19.25916347 2.243647322 24.75948982 0.920515905 1.028138548 0.695581237 0.031059792 50.55685684 246086.0535 0.010058673 0.008173646 175.2456806 -2.243647322 0.107622642 NLSST(ph)TDDEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.36)S(0.118)T(0.506)T(0.016)DDEAPR;NLS(0.007)S(0.034)T(0.557)T(0.402)DDEAPR;NLS(0.04)S(0.164)T(0.718)T(0.079)DDEAPR 268.21 6.10E-21 2652060000 2171500 1768850 1860740 2197980 1771720 1925810 2069020 1865060 1516880 TRUE FALSE 2068857.498 1949097.826 1946056.77 1977034.875 2080707.407 1859118.717 1753352.999 1701745.459 1752110.003 1.180780599 1.112428913 1.110693259 1.128373716 1.18754382 1.061074198 1.000709428 0.971254919 1 20.74066192 1.944469913 2.874904005 0.990424288 1.140632583 0.864498145 0.027657469 0.092358599 1.40026103 0.014170677 0.007761066 87.99741472 -1.944469913 0.150208295 NLSSTT(ph)DDEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.141)S(0.231)T(0.231)T(0.396)DDEAPR 222.81 2.67E-10 1115300000 552930 468440 494050 596160 452980 500060 559970 494960 428850 TRUE FALSE 526794.0947 516174.5686 516702.6812 536232.8642 531979.5686 482742.7968 474536.2919 451618.6785 495353.8677 1.063470236 1.042031974 1.043098106 1.082524835 1.073938457 0.974541289 0.957974335 0.9117092 1 18.91809999 2.153269249 4.673609313 0.955406842 1.058777175 0.806395597 0.024394202 0.08468165 3.300546144 0.008972899 0.006553043 142.3210859 -2.153269249 0.103370332 NLSTVMDEIHTVLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLSTVMDEIHTVLKK 15 1 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 131.24 3.56E-05 44958000 161742 126925 140599 161892 117094 156418 188411 158721 116895 FALSE TRUE 154096.7762 139858.8018 147045.6032 145618.3086 137515.1565 151001.2054 159665.4415 144822.5478 135022.4796 1.141267563 1.035818645 1.089045348 1.078474555 1.0184612 1.118341227 1.182510068 1.072581012 1 17.04284009 2.106240874 21.15361901 1.11687024 1.074309105 0 0.057008916 7.377133108 1437.377523 0.019967111 0.014746702 127.714696 -2.106240874 -0.042561135 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 NLTANDPSQEYVAS(1)EGEEDPEVEFLK 230.88 3.10E-35 117730000 174200 139220 145010 177140 102380 172440 183650 174180 125780 TRUE FALSE 165965.9112 153406.6763 151658.8519 159333.5507 120235.0396 166468.3596 155630.8195 158927.8758 145285.32 1.142344672 1.055899359 1.04386907 1.096694082 0.827578723 1.145803028 1.071208155 1.093901819 1 17.14852941 4.533063558 1.539370841 1.044025189 1.159719968 0.122313618 0.085078689 1.550299786 4.677021816 0.021809812 0.242535366 34124.2848 -4.533063558 0.11569478 NLTEQNSYSNIPHEGKHT(ph)PLYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLTEQNSYSNIPHEGKHTPLYER 23 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52;Q5T035 Q9NZB2 FAM120A;C9orf129 Constitutive coactivator of PPAR-gamma-like protein 1;Putative uncharacterized protein C9orf129 1 NLTEQNSYSNIPHEGKHT(0.984)PLY(0.016)ER 114.68 0.00094769 179430000 70994 61529 63684 76186 51474 74812 87442 79756 30778 TRUE FALSE 67638.25432 67798.87505 66603.97439 68527.63854 60451.0493 72221.24168 74101.11692 72772.14183 35550.89505 1.902575286 1.907093337 1.87348235 1.927592496 1.700408646 2.031488703 2.084367125 2.046984801 1 15.11759826 -1.273528517 5.251893164 0.999856755 1.936334533 0.880897046 0.107957824 0.000190253 2.63E-05 0.109829506 0.025883182 0.053268625 1.273528517 0.936477778 NLTEQNSYSNIPHEGKHTPLY(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLTEQNSYSNIPHEGKHTPLYER 23 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52;Q5T035 Q9NZB2 FAM120A;C9orf129 Constitutive coactivator of PPAR-gamma-like protein 1;Putative uncharacterized protein C9orf129 1 NLTEQNSY(0.002)S(0.013)NIPHEGKHT(0.461)PLY(0.524)ER 77.287 0.0055648 129830000 76066 56268 61332 69831 40468 66823 69598 64091 16432 TRUE FALSE 72470.51093 62001.77317 64144.13287 62811.45521 47525.60639 64508.90275 58979.54685 58478.85227 18980.19064 3.818218284 3.26665703 3.379530485 3.30931635 2.503958327 3.398748937 3.107426473 3.081046623 1 14.21220686 -1.018841497 0.345908258 4.64E-17 3.457306073 0.844813026 0.305183752 5.488610263 0.498706353 6.091726509 0.250014041 0.095754348 1.018841497 3.457306073 NLVDFLTGEEVVCHVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NLVDFLTGEEVVCHVAR 17 0 Q9H9J2 Q9H9J2 MRPL44 "39S ribosomal protein L44, mitochondrial" 0 226.74 1.98E-15 29983000 54838 37080 47942 45155 47346 37776 50809 47376 48766 FALSE TRUE 52245.91642 40858.49416 50140.18812 40615.93361 55603.12741 36467.80765 43057.15388 43227.50628 56328.38222 0.927523823 0.725362465 0.890140745 0.721056278 0.987124523 0.647414433 0.764395358 0.767419631 1 15.78157442 2.222447273 24.99819416 0.769456079 0.836179852 0.024972367 0.11909296 658.2071879 1021134.336 0.03941498 0.0292009 166.8965168 -2.222447273 0.066723774 NLVLTGFSHIDLIDLDTIDVSNLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLVLTGFSHIDLIDLDTIDVSNLNR 25 0 Q9UBT2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ; 189.51 1.02E-17 129584000 64417 52990 55604 62251 51767 56858 68626 62042 45429 FALSE TRUE 61372.13607 58389.74124 58153.4984 55993.41121 60795.14841 54888.9932 58155.8433 56609.27357 52473.8973 1.169574574 1.112738795 1.108236693 1.067071708 1.158578866 1.04602471 1.10828138 1.078808255 1 15.67931232 -5 0.03049801 0.36750198 1.532677887 0.599767487 0.03179467 889.0034364 2.039700942 61.20265735 24.43708164 1.00E-05 5 1.165175907 NLVTEDVMR ddPTM_SK-BR-3_Trastuzumab_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 ; 177.36 0.00012146 189623000 511550 432240 333660 405050 407390 375590 514430 457820 428130 FALSE TRUE 487370.0453 476285.7474 348958.641 364333.6045 478438.687 362583.2241 435944.2553 417730.8537 494522.2138 0.985537215 0.963123059 0.70564806 0.736738602 0.967476634 0.733199064 0.881546356 0.844716055 1 18.9156758 3.906297554 10.38281781 0.831407682 0.977142916 0.253321557 0.096680186 0.531115466 56.00950234 0.022527127 0.040656582 8059.304296 -3.906297554 0.145735234 NLVYDQS(ph)PNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NLVYDQSPNR 10 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 NLVYDQS(1)PNR;NLVYDQS(1)PNR;NLVYDQS(1)PNR 122.34 0.0026441 319630000 657780 577430 613750 692120 608000 592490 750080 648390 648510 TRUE FALSE 626688.043 636270.7735 641891.0446 622546.7827 714035.0075 571971.9227 635641.5198 591613.5343 749077.6187 0.836612959 0.849405666 0.856908588 0.831084479 0.953218985 0.763568299 0.848565628 0.789789362 1 19.51475569 -1.085235625 4.758315872 1.000007007 0.842135649 0.50799537 0.049122902 3.24E-06 6.23E-07 0.042175157 0.009940339 0.082179667 1.085235625 -0.157871358 NLYSDDIPHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NLYSDDIPHALR 12 0 P60228;H0YBR5;E5RIT4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 127.02 0.0002772 673600000 1268720 1103570 1008910 1326750 1096550 1139810 1355310 1278430 1125300 FALSE TRUE 1208750.12 1216025.038 1055169.521 1193382.569 1287787.973 1100338.094 1148532.568 1166483.892 1299805.777 0.929946721 0.935543648 0.811790146 0.918123762 0.990754154 0.846540394 0.883618605 0.89742938 1 20.30986463 -0.833294126 7.692302347 0.999998474 0.902980277 0.283872306 0.049021456 0 0 0.046115482 0.010869523 0.146793178 0.833294126 -0.097018197 NMACVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMACVQR 7 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 115.78 0.013037 87077000 183810 144020 148980 181430 145300 150640 211860 183460 167910 FALSE TRUE 175121.6656 158695.8017 155810.8804 163192.3117 170640.274 145423.299 179536.8659 167395.2698 193948.6252 0.90292811 0.818236281 0.803361613 0.841420307 0.879822034 0.749803196 0.925692903 0.863090778 1 17.56531502 0.711338374 0.987774474 0.998894497 0.840220058 0.50096662 0.049045916 0.790546577 1.368742452 0.043230602 0.014030349 5.144443169 -0.711338374 -0.158674439 NMAPGAVCS(ph)PGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NMAPGAVCSPGESK 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NMAPGAVCS(1)PGESK;NMAPGAVCS(1)PGESK;NMAPGAVCS(1)PGESK;NMAPGAVCS(0.993)PGES(0.007)K 250.41 2.39E-18 553090000 1354770 1334500 1363240 1655670 825960 1540210 1545790 1594030 921540 TRUE FALSE 1290732.707 1470487.067 1425745.902 1489238.906 970007.1625 1486872.142 1309951.345 1454448.283 1064447.717 1.212584411 1.38145542 1.339423139 1.399071916 0.911277414 1.396848449 1.230639443 1.366387714 1 20.02167366 NMAPSQQS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMAPSQQSPVR 11 0 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 NMAPS(0.017)QQS(0.983)PVR 83.204 0.065997 25029000 72290 70412 68327 73555 64123 69954 86920 73985 67132 TRUE FALSE 68872.99496 77587.06285 71459.86053 66161.11165 75306.0309 67531.47544 73658.7576 67506.48118 77542.4877 0.888196871 1.000574848 0.921557493 0.853224002 0.971158305 0.870896427 0.949914812 0.870574097 1 16.2426994 -1.451497035 5.480494536 1.000077151 0.921763342 0.227190032 0.047697886 4.11E-05 4.12E-06 0.042263453 0.009951787 0.035359244 1.451497035 -0.078313808 NMDPLNDNIATLLHQSSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMDPLNDNIATLLHQSSDK 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 136.46 5.77E-06 67532000 98844 97551 85409 130240 100080 95420 109200 110530 87071 FALSE TRUE 94171.84001 107491.5578 89325.08713 117148.0278 117533.9203 92115.58147 92539.5344 100851.4072 100573.526 0.9363482 1.068785814 0.88815706 1.164799848 1.168636768 0.915902874 0.920118227 1.002762966 1 16.61789107 -0.791776939 5.810320743 0.999999423 1.00475924 0 0.099948832 7.14E-10 1.23E-10 0.09579869 0.022579966 0.161518793 0.791776939 0.004759817 NMDPLNDNIATLLHQSSDKFVSELWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NMDPLNDNIATLLHQSSDKFVSELWK 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 313.19 4.89E-82 991567000 761350 610780 744060 823520 789850 718800 1054890 918480 753660 FALSE TRUE 725362.4944 673019.1764 778175.887 740738.205 927599.5899 693907.7758 893947.1561 838053.022 870533.7436 0.833238803 0.773110958 0.893906632 0.850901198 1.06555271 0.797106121 1.026895468 0.962688728 1 19.7315407 3.198685078 1.529154034 0.962414954 0.80572985 0.405730726 0.077022422 0.329897519 1.604195184 0.023834515 0.033389891 1580.101837 -3.198685078 -0.156685104 NMDPLNDNVAALLHQSTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NMDPLNDNVAALLHQSTDR 19 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 173.36 6.57E-12 93743000 82140 63234 67266 87988 85066 71880 96936 88326 94428 FALSE TRUE 78257.40499 69677.61649 70350.21264 79143.27907 99901.48347 69390.77758 82146.63285 80591.70719 109071.412 0.717487778 0.638825658 0.644992225 0.725609742 0.915927296 0.636195831 0.753145406 0.738889373 1 16.73491349 -5 0.192649921 2.248034435 0.664311118 0.562302407 0.078931398 100.0862423 0.98215314 47.90191151 0.198811913 1.00E-05 5 -1.583723317 NMFHPMDFEDDPLVLNEIREDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMFHPMDFEDDPLVLNEIREDLR 23 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 65.784 0.017349 14420000 8100.5 6330.4 8892 8351.2 8431.4 7166.9 11625 9164.4 9958.3 FALSE TRUE 7717.605419 6975.474957 9299.706995 7511.72151 9901.833491 6918.708456 9851.392742 8361.916552 11502.5823 0.670945464 0.606426868 0.808488629 0.653046534 0.8608357 0.601491758 0.856450533 0.726959941 1 13.48967016 -5 0.110325898 1.937416371 0.550190678 0.508193672 0.090007019 115.9933146 0.850172069 24.40002793 0.964384661 1.00E-05 5 -1.387225693 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 NMGGPYGGGNYGPGGS(0.002)GGS(0.998)GGYGGR;NMGGPYGGGNYGPGGS(0.168)GGS(0.832)GGYGGR;NMGGPYGGGNYGPGGS(0.132)GGS(0.868)GGYGGR;NMGGPYGGGNYGPGGS(0.006)GGS(0.994)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGS(0.008)GGS(0.992)GGYGGR;NMGGPYGGGNYGPGGS(0.001)GGS(0.999)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR 457.3 1.80E-206 3130580000 2012850 1805420 1897820 2119680 1664920 2005740 2309800 2101750 1915990 TRUE FALSE 1917706.57 1989394.351 1984836.924 1906605.739 1955281.521 1936280.721 1957397.588 1917709.628 2213111.944 0.866520365 0.898912663 0.896853379 0.861504428 0.883498698 0.87491314 0.884454848 0.866521747 1 21.077645 -2.181101379 2.415800187 1.327499005 0.880407773 0.901818567 0.012525667 3256462.983 1013614.981 5796165.423 0.002876601 0.0065902 2.181101379 -0.447091231 NMGGPYGGGNYGPGGSGGSGGYGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 486.22 2.01E-257 356235000 120254 88864 103242 113306 90701 99158 124380 113787 88899 FALSE TRUE 114569.8317 97919.34263 107975.7478 101916.2656 106519.2257 95724.1336 105403.5466 103823.2071 102685.0029 1.115740649 0.95358952 1.051524028 0.992513636 1.037339657 0.932211432 1.026474594 1.011084425 1 16.64786597 4.67543518 3.471390313 1.001635932 1.122457109 0.499663049 0.036114748 0.194280804 3.881290611 0.007742756 0.055185285 47362.56122 -4.67543518 0.120821177 NMLAFSSPAAGGVCEPLKS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR 190.15 1.14E-17 2171280000 2074060 2255340 1824790 2470040 1021290 2245860 2019910 2336960 1084470 TRUE FALSE 1976023.294 2485161.71 1908458.426 2221746.886 1199402.653 2168085.305 1711735.631 2132323.393 1252644.069 1.577481859 1.983932844 1.523544057 1.773645796 0.957496772 1.730807145 1.366498013 1.702258005 1 20.25654511 -2.107586428 0.103258024 2.51E-10 2.07831072 0.31009995 0.272747011 84.75456227 1.203689621 25.80981445 4.800002093 0.007805731 2.107586428 2.07831072 NMMAACDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMMAACDPR 9 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 74.301 0.096497 449020000 900130 643010 552620 624840 811710 645290 957340 737130 758320 FALSE TRUE 857582.6388 708533.45 577958.1736 562029.8961 953271.967 622943.4455 811280.2002 672582.9894 875916.3926 0.97906906 0.808905343 0.65983258 0.64164788 1.088313879 0.711190532 0.926207349 0.767862087 1 19.74043364 2.763834069 24.99617344 0.881279291 0.795169554 0.15285574 0.140104264 2092.530572 2069569.336 0.042140052 0.044680592 580.5425678 -2.763834069 -0.086109737 NMPGLSAATLASLGGTS(ph)SR ddPTM_SK-BR-3_Trastuzumab_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(0.117)S(0.442)S(0.442)R;NMPGLSAATLASLGGT(0.039)S(0.481)S(0.481)R;NMPGLSAATLASLGGT(0.108)S(0.446)S(0.446)R 244.22 1.76E-24 404112000 672142 533599 585117 630906 499016 568922 672986 700370 616115 TRUE FALSE 640371.1797 587973.3448 611945.1932 567486.1302 586044.2324 549220.0885 570309.6255 639041.8899 711658.9675 0.899828723 0.826200992 0.859885452 0.797413025 0.823490266 0.771746178 0.801380509 0.897960848 1 19.44082653 -1.246110551 4.553534853 1.000061989 0.832051047 0.608268712 0.041629758 2.64E-05 4.37E-06 0.040647799 0.009577247 0.056740015 1.246110551 -0.168010942 NMPGLSAATLASLGGTSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.013)S(0.1)S(0.888)R;NMPGLSAATLASLGGTS(0.097)S(0.902)R;NMPGLSAATLASLGGT(0.001)S(0.118)S(0.881)R;NMPGLSAATLASLGGT(0.037)S(0.111)S(0.853)R;NMPGLSAATLASLGGT(0.005)S(0.104)S(0.891)R;NMPGLSAATLASLGGT(0.016)S(0.265)S(0.72)R;NMPGLSAATLASLGGT(0.086)S(0.24)S(0.673)R 335.03 2.15E-75 3695880000 3409295 2979128 3193788 3535410 2716863 2999989 3629857 3535430 3011916 TRUE FALSE 3248144.382 3282704.53 3340226.339 3180023.87 3190683.047 2896098.629 3076055.648 3225849.007 3478988.551 0.933646183 0.943580148 0.960114209 0.914065633 0.917129505 0.832454199 0.884181021 0.927237604 1 21.7302365 2.929666747 2.614036412 0.896581841 0.943205726 0.050397082 0.043188073 0.441078442 5.945967413 0.01298711 0.01447866 850.4851742 -2.929666747 0.046623885 NMQNVEHVPLSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NMQNVEHVPLSLDR 14 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;;;;; 140.93 7.44E-06 5489880000 6451560 5441419 5742659 6473695 5378629 5646440 6768370 6125540 5402276 FALSE TRUE 6146607.545 5995905.782 6005965.595 5822946.879 6316660.195 5450902.367 5735730.847 5589155.244 6240033.371 0.985027992 0.960877198 0.962489339 0.933159574 1.012279874 0.873537374 0.91918272 0.895693166 1 22.57312231 2.236701712 24.99998447 0.914283239 0.968629017 0.279014939 0.037870225 51.85852581 697418.3023 0.012079607 0.009378637 172.4652934 -2.236701712 0.054345778 NMSVIAHVDHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;;;; 198.33 1.07E-07 6948680000 9250150 7800540 8286600 9932740 5891310 9014080 10872990 9667610 367310.3 FALSE TRUE 8812913.742 8595423.894 8666548.807 8934282.104 6918752.599 8701920.149 9214115.679 8821062.817 424270.9054 20.77190217 20.25928195 20.42692227 21.05796554 16.30739349 20.51029198 21.71752897 20.79110942 1 18.69462622 -0.650673829 7.475617695 0.999969752 20.29723276 0.945222372 1.454787201 0 0 1.376726747 0.324497606 0.223525035 0.650673829 19.29726301 NMTVEQLLTGS(ph)PTSPTVEPEKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGS(0.983)PT(0.016)S(0.001)PTVEPEKPTR 155.14 2.94E-08 92181000 102910 84780 103490 115330 64453 99265 112800 121970 73635 TRUE FALSE 98045.64825 93419.17839 108235.1189 103736.8093 75693.58279 95827.42816 95590.28829 111289.6602 85053.93972 1.152746699 1.09835216 1.2725468 1.219659073 0.889947991 1.126666542 1.123878431 1.308459791 1 16.37609044 4.76243827 20.61724821 1.131628907 1.152746892 0.003226188 0.122838736 1458.523773 2416667.189 0.02742998 0.388872105 57867.97302 -4.76243827 0.021117985 NMTVEQLLTGSPTS(ph)PTVEPEKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGSPT(0.003)S(0.994)PT(0.003)VEPEKPTR;NMTVEQLLTGSPT(0.138)S(0.859)PT(0.003)VEPEKPTR;NMTVEQLLTGSPT(0.047)S(0.952)PT(0.001)VEPEKPTR;NMTVEQLLTGSPT(0.005)S(0.983)PT(0.012)VEPEKPTR;NMTVEQLLTGSPT(0.001)S(0.998)PT(0.001)VEPEKPTR;NMTVEQLLTGSPT(0.267)S(0.705)PT(0.028)VEPEKPTR 288.61 9.51E-54 2289580000 2468280 1833380 2139460 2375520 1573830 2147010 2561880 2243580 1538990 TRUE FALSE 2351609.296 2020203.506 2237556.357 2136728.216 1848305.454 2072658.505 2171018.154 2047120.241 1777648.709 1.322876271 1.13644698 1.258716835 1.201996888 1.039747305 1.165955059 1.221286378 1.151588742 1 20.76153882 -4.999999691 0.032211054 0.051547668 1.821305015 0.49661478 0.067778012 1198.524868 2.900831411 128.3088347 48.67429236 1.00E-05 4.999999691 1.769757347 NMVDLVNTHHLHSS(ph)SDDEDDRLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.034)S(0.483)S(0.483)DDEDDRLK;NMVDLVNTHHLHS(0.085)S(0.458)S(0.458)DDEDDRLK 189.24 9.45E-18 648070000 873600 911670 647360 916560 496160 853300 788350 1025100 206548 TRUE FALSE 832306.6593 1004570.209 677042.0963 824425.6474 582690.1469 823750.007 668072.7285 935336.8096 238578.4089 3.488608475 4.210650134 2.837817971 3.45557526 2.442342329 3.452743317 2.800222918 3.920458745 1 17.86410396 -1.072140757 0.329746084 6.45E-32 3.565292585 0.614015108 0.559541986 10.19969689 0.84261763 11.51513379 0.486154667 0.084695287 1.072140757 3.565292585 NMVDLVNTHHLHSSS(ph)DDEDDRLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHSS(0.051)S(0.948)DDEDDRLK 242.63 1.19E-37 177100000 129130 141930 98145 144530 95317 127840 119990 149670 52373 TRUE FALSE 123026.2808 156392.8284 102645.0453 130001.5698 111940.2546 123412.8687 101683.3217 136564.1013 60494.73736 2.033669145 2.585230306 1.696759914 2.148973208 1.850413102 2.040059584 1.680862273 2.25745424 1 15.88452202 -1.696414197 0.211371171 4.94E-15 2.291292084 0.57020251 0.275937973 18.33452877 0.648060853 10.5068085 0.618689121 0.020118046 1.696414197 2.291292084 NMVDYHLIMDMIPAISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NMVDYHLIMDMIPAISR 17 0 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 126.88 4.21E-05 33304000 83923 89404 91889 96174 76465 81802 95871 88348 62051 FALSE TRUE 79956.12611 98514.36924 96102.20154 86506.4068 89800.47179 78969.17623 81244.11816 80611.78076 71673.55217 1.115559697 1.374487049 1.340832129 1.206950182 1.252909463 1.101789626 1.133529952 1.124707487 1 16.12915324 1.847005902 0.79507818 1.036722043 1.272685707 0.54300366 0.07724711 0.479070292 0.572821922 0.068190263 0.032383557 70.30818749 -1.847005902 0.235963664 NNASTDYDLSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NNASTDYDLSDK 12 0 P39023;G5E9G0;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 190.68 6.38E-05 139930000 573480 522860 478060 609740 339300 576190 592630 619790 409680 FALSE TRUE 546372.7369 576140.0284 499979.5239 548447.7768 398473.8126 556236.3958 502213.4091 565517.9019 473211.082 1.154606808 1.217511699 1.056567656 1.158991827 0.842063569 1.175450907 1.061288351 1.195064789 1 18.85212433 3.733663555 24.35365473 1.072528225 1.186059256 0.182433784 0.102099154 409.3256228 2035626.744 0.024541922 0.039402537 5415.811688 -3.733663555 0.113531031 NNCPDKTSAAAGSS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NNCPDKTSAAAGSSSR 16 1 A0A087X2H1;Q9ULT8;H0YJP0 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 NNCPDKTS(0.001)AAAGS(0.103)S(0.448)S(0.448)R;NNCPDKTSAAAGS(0.114)S(0.443)S(0.443)R;NNCPDKTSAAAGS(0.082)S(0.459)S(0.459)R 62.617 0.04567 272449000 212530 123398 207545 189167 153945 193733 249346 210067 187396 TRUE FALSE 202484.1281 135972.3965 217061.1435 170151.5738 180792.9593 187023.9776 211303.6881 191672.4198 216456.4146 0.935449885 0.628174484 1.002793768 0.786077761 0.835239554 0.864026035 0.976195085 0.885501223 1 17.72371703 1.830354879 0.776582333 0.983157843 0.812317474 0.196281674 0.101923207 0.839139055 0.964778977 0.085257381 0.04074866 67.66356549 -1.830354879 -0.170840369 NNDLCYWVPELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NNDLCYWVPELVR 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 162.32 2.17E-06 68722000 233369 175311 186664 187712 191265 189237 267057 216652 225011 FALSE TRUE 222338.1099 193175.3902 195222.729 168842.8331 224621.5554 182683.6752 226312.5498 197680.8023 259904.5567 0.855460607 0.743255111 0.751132383 0.649633986 0.864246315 0.702887543 0.870752528 0.760589983 1 17.9876224 -0.083338553 0.600445088 1.015710205 0.768024857 0.493873703 0.071698012 4.140907875 1.607859311 0.22212893 0.026833752 0.825394265 0.083338553 -0.247685347 NNEDISIIPPLFTVSVDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNEDISIIPPLFTVSVDHR 19 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 85.737 0.0029887 44188000 99627 84464 93003 118120 97905 86139 118420 104140 94554 FALSE TRUE 94917.82915 93070.97763 97267.27954 106246.3532 114979.601 83155.98483 100352.8541 95020.94952 109216.9514 0.869075981 0.852166046 0.890587755 0.972800942 1.052763326 0.761383501 0.918839546 0.87002016 1 16.73683727 NNLNPVWRPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NNLNPVWRPFK 11 1 O75131;A0A087WYQ3;H0YB26 O75131 CPNE3 Copine-3 0 ; 190.86 1.90E-06 1623890000 3613300 2344900 2092950 3561700 2692700 2435680 3265600 2611800 2077850 FALSE TRUE 3442506.47 2583847.976 2188913.828 3203671.149 3162306.027 2351331.791 2767372.743 2383096.946 2400072.366 1.434334447 1.076570862 0.912019929 1.334822731 1.317587783 0.979692039 1.153037209 0.992927122 1 21.19464648 4.557725365 2.814563481 1.107894713 1.440417738 0.357966619 0.141036751 0.338640321 4.660434202 0.033901419 0.212564737 36118.13903 -4.557725365 0.332523025 NNMTAS(ph)MFDLSMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNMTASMFDLSMK 13 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2;Q7L804;Q7L804-2 Q6WKZ4 RAB11FIP1;RAB11FIP2 Rab11 family-interacting protein 1;Rab11 family-interacting protein 2 1 NNMT(0.003)AS(0.997)MFDLSMK 114.01 0.00081451 71178000 152870 93906 120430 149590 156220 144440 196040 133520 250050 TRUE FALSE 145644.1381 103475.1282 125951.8346 134552.929 183464.7185 139438.0066 166130.4975 121828.281 288826.4769 0.504261727 0.358260535 0.436081331 0.465860784 0.635207411 0.482774322 0.575191372 0.421804407 1 18.13984348 -5 0.239841192 3.950610733 0.430158816 0.806213431 0.078980677 69.01479438 0.688123613 99.3029546 0.118323384 1.00E-05 5 -3.520451917 NNMTAS(ph)MFDLSMKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NNMTASMFDLSMKDK 15 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2;Q7L804;Q7L804-2 Q6WKZ4 RAB11FIP1;RAB11FIP2 Rab11 family-interacting protein 1;Rab11 family-interacting protein 2 1 NNMTAS(1)MFDLSMKDK;NNMTAS(1)MFDLSMKDK 221.25 9.46E-13 808870000 848950 458270 675250 883940 441990 865160 1096310 919930 515770 TRUE FALSE 808821.816 504968.234 706210.8804 795084.6718 519072.9161 835199.2923 929047.7744 839376.0523 595752.9774 1.357646284 0.847613446 1.185408898 1.334587827 0.871288832 1.401922145 1.559451332 1.408933038 1 19.18435473 2.142860573 12.0752671 1.408672155 1.116778609 0.177392074 0.219252695 0.596686246 71.53335343 0.07601786 0.056143086 138.9506468 -2.142860573 -0.291893545 NNQITNNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NNQITNNQR 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;;; 182.98 0.0001246 316127000 402492 343599 360299 429256 378488 365810 423231 375619 381173 FALSE TRUE 383467.0008 378612.1287 376819.0655 386106.3713 444496.1874 353141.908 358659.3378 342727.8091 440283.3621 0.870955012 0.859928313 0.855855792 0.876949721 1.009568441 0.802078703 0.814610246 0.778425529 1 18.7480728 -0.372146026 7.493141247 0.99999986 0.858578551 0.337917906 0.062225227 0 0 0.05947683 0.014018823 0.424476815 0.372146026 -0.141421309 NNRPAFFS(ph)PSLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNRPAFFSPSLKR 13 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 NNRPAFFS(0.99)PS(0.01)LKR 118.47 0.00022177 247240000 820280 614870 696040 765080 437280 694040 817130 818710 549790 TRUE FALSE 781506.99 677525.952 727954.1225 688172.7048 513541.4936 670005.2208 692461.8109 747019.4121 635048.6253 1.230625434 1.066888306 1.146296667 1.083653562 0.808664838 1.055045542 1.090407543 1.176318446 1 19.27650754 4.815805543 0.840103808 1.043566198 1.354856561 0.256290589 0.098272942 3.783761498 1.89053481 0.033863054 1.128512883 65434.31245 -4.815805543 0.311290364 NNRPSEGPLQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NNRPSEGPLQTR 12 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 169.79 3.91E-05 1086570000 630533 520571 491333 710346 429542 574095 668744 661057 465064 FALSE TRUE 600728.9547 573617.7767 513861.104 638940.6705 504453.9888 554213.9462 566714.8205 603171.3446 537183.7499 1.118293237 1.067824142 0.956583486 1.189426655 0.939071573 1.031702739 1.054973872 1.122839894 1 19.03505614 4.239276572 3.122654896 1.044368135 1.110214081 0.093104065 0.07343269 0.530173488 10.50960325 0.016784222 0.049711122 17349.08488 -4.239276572 0.065845946 NNRQPYAVSELAGHQTSAESWGTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NNRQPYAVSELAGHQTSAESWGTGR 25 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;; 247.39 3.23E-39 799950000 394664 183392 412814 325702 392355 335309 602236 435562 485837 FALSE TRUE 376009.0149 202079.8533 431741.9302 292961.8162 460781.5878 323697.1653 510353.8374 397421.8822 561178.1206 0.670035058 0.360099309 0.769349186 0.522047823 0.821096851 0.576817152 0.909432885 0.708192047 1 19.09809924 1.734690507 0.374938168 1.004339931 0.504535336 0.437820903 0.140610523 0.902681951 0.369054264 0.160649674 0.14613256 54.28633308 -1.734690507 -0.499804595 NNS(ph)FTAPSTVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 112.42 0.0013378 39303000 84615 78308 72772 104180 55036 94738 93791 87308 65639 TRUE FALSE 80615.41664 86287.67423 76108.66818 93707.62847 64634.26097 91457.1993 79481.46036 79662.84867 75817.96088 1.06327598 1.138090147 1.00383428 1.235955536 0.852492737 1.20627353 1.048319678 1.050712097 1 16.21025204 NNS(ph)NTCNIENELEDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NNSNTCNIENELEDSR 16 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NNS(0.974)NT(0.026)CNIENELEDSR;NNS(0.999)NT(0.001)CNIENELEDSR 247.3 2.95E-20 210751000 137631 129155 133407 157015 108681 137391 147125 141605 112063 TRUE FALSE 131125.4554 142316.0413 139523.8429 141231.5539 127634.932 132633.1152 124678.3791 129205.3155 129441.1577 1.013012072 1.099465146 1.077893967 1.091086919 0.986045971 1.024659525 0.963205068 0.998177997 1 16.98193689 2.731368482 24.78803648 0.992292643 1.069260437 0.657792267 0.027190483 299.3499459 1031720.862 0.008673168 0.008344116 538.726677 -2.731368482 0.076967794 NNS(ph)NTCNIENELEDSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NNSNTCNIENELEDSRK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NNS(0.539)NT(0.461)CNIENELEDSRK;NNS(0.712)NT(0.288)CNIENELEDSRK;NNS(0.638)NT(0.362)CNIENELEDSRK 241.71 1.38E-20 2230770000 866580 800980 836670 879640 472590 940850 949380 1014190 565280 TRUE FALSE 825618.4808 882600.7726 875032.1471 791216.916 555009.5464 908268.1286 804534.6444 925382.147 652940.7353 1.264461591 1.351731826 1.34014023 1.211774474 0.850015195 1.391042218 1.232171009 1.417252894 1 19.31659252 -1.377930537 4.098863616 0.999269289 1.259133548 0.205170956 0.159134543 0.001013857 0.000153869 0.147011642 0.034555215 0.041886055 1.377930537 0.259864259 NNSDKDQSLGNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNSDKDQSLGNWR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 140.31 3.58E-05 361520000 484940 379370 421920 486450 396130 431600 530670 461190 445100 FALSE TRUE 462017.8473 418028.2343 441265.4493 437551.1218 465214.9466 416653.5838 449706.5451 420805.7587 514123.8347 0.898650901 0.81308861 0.858286311 0.851061733 0.90486944 0.810414837 0.87470472 0.818491053 1 18.97175637 -0.971108178 5.153227443 1.000000728 0.853940889 0.658405416 0.03311785 2.44E-07 4.87E-08 0.028198807 0.006646489 0.106878862 0.971108178 -0.14605984 NNSQIASGQNQPQAAAGSHQLS(ph)MGQPHNAAGPSPHTLRR ddPTM_SK-BR-3_Trastuzumab_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(0.057)HQLS(0.378)MGQPHNAAGPS(0.283)PHT(0.283)LRR 159.62 2.49E-18 156170000 23297 12840 23434 19418 23233 21278 33935 31153 11599 TRUE FALSE 22195.79698 14148.4106 24508.47208 17466.06575 27284.82784 20541.13752 28757.59249 28425.07817 13397.71368 1.656685425 1.056031718 1.829302571 1.303660174 2.036528657 1.533182304 2.146455222 2.121636486 1 13.70969921 2.743834864 24.80991323 1.84329553 1.435989342 0.113733062 0.391481096 589.8002719 2774407.331 0.109419143 0.11293805 554.4148629 -2.743834864 -0.407306188 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.254)HQLS(0.254)MGQPHNAAGPS(0.38)PHT(0.113)LR;NNSQIASGQNQPQAAAGS(0.14)HQLS(0.14)MGQPHNAAGPS(0.581)PHT(0.14)LR;NNSQIASGQNQPQAAAGS(0.042)HQLS(0.042)MGQPHNAAGPS(0.885)PHT(0.031)LR;NNSQIASGQNQPQAAAGS(0.003)HQLS(0.144)MGQPHNAAGPS(0.748)PHT(0.105)LR;NNSQIASGQNQPQAAAGSHQLS(0.02)MGQPHNAAGPS(0.826)PHT(0.153)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(1)PHTLR 293.43 5.19E-92 1859210000 328002 306895 309295 379086 259814 284163 328951 349608 116034.9 TRUE FALSE 312497.9955 338167.9494 323476.4817 340979.5551 305125.4793 274322.3641 278763.4834 318994.4701 134028.9997 2.331570006 2.523095377 2.41348128 2.544072969 2.276563133 2.046738875 2.079874386 2.38004067 1 17.03218566 -1.456244158 0.288409235 6.94E-13 2.485756261 0.886199673 0.15074734 6.53212533 0.3713036 5.030343593 0.175395553 0.034974849 1.456244158 2.485756261 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.042)HQLS(0.042)MGQPHNAAGPS(0.78)PHT(0.136)LRR;NNSQIASGQNQPQAAAGS(0.021)HQLS(0.021)MGQPHNAAGPS(0.832)PHT(0.126)LRR;NNSQIASGQNQPQAAAGSHQLS(0.028)MGQPHNAAGPS(0.82)PHT(0.152)LRR 249.47 2.42E-51 393338000 61938 34775.6 59402.3 46928.2 52311.2 43694 81560 69736 26597.4 TRUE FALSE 59010.31349 38319.27318 62125.95421 42210.88818 61434.25672 42180.86582 69116.52405 63629.54615 30721.98895 1.920784282 1.247291418 2.022198312 1.373963393 1.999683576 1.372986166 2.249741192 2.071140194 1 14.906984 1.749010362 24.99999736 1.90236109 1.645768016 0 0.423356454 7.022301655 16833.11536 0.171823783 0.09528518 56.10613621 -1.749010362 -0.256593073 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHT(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.242)HQLS(0.242)MGQPHNAAGPS(0.242)PHT(0.275)LR 45.192 0.034058 214710000 14863 15302 15621 15886 13674 14746 16740 16810 6946.2 TRUE FALSE 14160.45545 16861.2912 16337.2383 14289.1091 16058.74127 14235.34232 14186.00555 15338.02728 8023.38122 1.764898745 2.101519389 2.036203672 1.780933587 2.00149299 1.774232326 1.768083201 1.911666274 1 12.96999463 -2.070079022 0.330198992 2.71E-11 1.9549449 0.844100108 0.120815519 13.49261653 0.655368624 10.29125596 0.100323512 0.008509832 2.070079022 1.9549449 NNTAAET(ph)EDDES(ph)DGEDRGGGTSGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 2 NNT(0.002)AAET(0.998)EDDES(1)DGEDRGGGTSGVR 149 4.62E-07 295740000 181110 146560 152820 175060 132310 178770 176920 155320 136760 TRUE FALSE 172549.2892 161494.6306 159826.9482 157462.6362 155384.8221 172579.1501 149927.6046 141719.3574 157968.0423 1.092305043 1.022324695 1.011767607 0.99680058 0.983647197 1.092494074 0.949100859 0.897139417 1 17.2692732 7.999999949 0.285097027 0.968722475 1.937306489 0.353616675 0.047131837 55.73136844 0.790252626 0.049362271 27.05573158 99999988.29 -7.999999949 0.968584013 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(1)DGEDRGGGTSGVR 248.9 2.09E-39 365690000 165597 121350 142330 168249 120852 150364 152195 139071 130664 TRUE FALSE 157769.558 133715.703 148855.9713 151336.2909 141928.5505 145156.857 128974.8575 126893.206 150926.7058 1.045338909 0.885964497 0.986279867 1.002713801 0.940380629 0.961770524 0.854552922 0.840760456 1 17.20348858 1.754694699 25 0.884862656 0.967126578 0.237933767 0.058880365 6.85578172 10635.68177 0.025096027 0.013916986 56.84531784 -1.754694699 0.082263922 NNVVPSKPGASAISHTVS(ph)TPELANMQLQGSHNYSTAHMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NNVVPSKPGASAISHTVSTPELANMQLQGSHNYSTAHMLK 40 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 NNVVPSKPGASAIS(0.001)HT(0.153)VS(0.652)T(0.194)PELANMQLQGSHNYSTAHMLK 112.3 2.23E-06 143820000 180890 134630 168320 175460 132920 182640 212880 200730 81142 TRUE FALSE 172339.6882 148348.9501 176037.6385 157822.4274 156101.2059 176315.131 180401.2462 183153.0171 93725.08694 1.838778643 1.582809415 1.878233931 1.683886701 1.665522124 1.881194638 1.924791452 1.954151477 1 16.51614764 2.259485478 24.9697174 1.788070707 1.724354509 0 0.286338686 1573.581336 1877755.5 0.087577553 0.073202136 181.7546282 -2.259485478 -0.063716198 NPDDITNEEYGEFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NPDDITNEEYGEFYK 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;; 369.69 3.62E-97 2912370000 2861398 2448425 2496071 2957556 2067564 2660446 3031039 2961708 2352778 FALSE TRUE 2726145.387 2697922.291 2610518.324 2660256.852 2428146.507 2568314.088 2568598.332 2702365.147 2717634.796 1.003131617 0.992746448 0.96058467 0.978886808 0.893477855 0.945054903 0.945159495 0.994381272 1 21.37392016 3.687322371 1.661019093 0.951823828 1.001575259 0.197300266 0.030370291 0.44883678 2.4196351 0.008572119 0.018309585 4867.683938 -3.687322371 0.049751431 NPDDITNEEYGEFYKS(ph)LTNDWEDHLAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPDDITNEEYGEFYKSLTNDWEDHLAVK 28 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 NPDDIT(0.001)NEEYGEFY(0.001)KS(0.972)LT(0.026)NDWEDHLAVK 79.616 0.0037891 17396000 19458 17530 15980 23269 16879 16464 20845 21410 14359 TRUE FALSE 18538.2589 19316.32693 16712.69881 20929.95591 19822.69226 15893.84755 17664.71241 19535.2269 16585.72038 1.117724071 1.164635993 1.007655888 1.261926249 1.195166191 0.95828503 1.065055481 1.177834091 1 14.01765406 2.257667788 24.9990667 1.053236025 1.147284697 0.255023457 0.084077084 347.9474882 455239.845 0.027817967 0.023241672 180.9955045 -2.257667788 0.094048672 NPDDITQEEYGEFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 393.1 2.99E-114 3299692000 2811565 2469220 2509544 2913861 1984721 2628585 2961460 2970803 2253694 FALSE TRUE 2678667.894 2720836.325 2624609.075 2620954.156 2330855.714 2537556.442 2509634.886 2710663.74 2603185.355 1.028996222 1.045195003 1.008229809 1.006825792 0.895385997 0.974788997 0.964063078 1.041287258 1 21.31184661 3.230834083 2.536369253 0.971506563 1.034800184 0.281948945 0.037297067 0.288245508 3.79714529 0.010760859 0.01434945 1701.508343 -3.230834083 0.063293621 NPDELAEALDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NPDELAEALDER 12 0 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ;;; 120.86 0.00089941 239119000 257866 238336 230491 266458 243939 249884 261715 264185 270329 FALSE TRUE 245677.1852 262622.7094 241059.2403 239673.1356 286481.8844 241230.4544 221785.57 241051.5609 312250.2407 0.786795823 0.841064874 0.77200658 0.767567497 0.917475304 0.772554903 0.710281502 0.771981986 1 18.25234316 NPDTQWITKPVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPDTQWITKPVHK 13 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 207.41 3.25E-08 2074100000 4382200 3813000 3830100 4800800 2875600 4348700 4705400 5049700 3210400 FALSE TRUE 4175062.091 4201549.035 4005713.873 4318214.463 3377103.73 4198103.429 3987504.809 4607521.498 3708252.436 1.125884001 1.133026704 1.08021607 1.164487731 0.910699524 1.132097532 1.075305654 1.242504813 1 21.82230803 NPDVDTSFLPDRDREEEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPDVDTSFLPDRDREEEENR 20 2 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 186.63 1.81E-17 314470000 143630 152120 103100 151610 100720 115620 109690 123630 109200 FALSE TRUE 136840.8945 167621.2009 107827.237 136369.8748 118285.5361 111616.0504 92954.7759 112804.3018 126134.1783 1.084883546 1.328911824 0.854861374 1.08114927 0.937775452 0.884899334 0.736951532 0.894319869 1 16.94459973 3.244598805 0.981736215 0.852173315 1.199673499 0.400946668 0.125397898 0.40614873 0.847217313 0.052251384 0.085849496 1756.300419 -3.244598805 0.347500184 NPDVDTSFLPDRDREEEENRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPDVDTSFLPDRDREEEENRLR 22 3 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ; 299.42 4.76E-56 675710000 267200 195833 210051 260850 202046 223828 241610 236880 228692 FALSE TRUE 254569.9855 215788.6053 219682.0461 234628.8624 237282.7584 216076.7802 204747.957 216137.5314 264156.3874 0.96370937 0.81689717 0.831636321 0.888219531 0.898266216 0.817988096 0.775101292 0.818218077 1 18.01103277 2.229959546 24.93412921 0.827190683 0.877006906 0 0.071885891 423.336914 1227225.261 0.024859912 0.018647274 169.8085471 -2.229959546 0.049816223 NPEAALS(ph)PTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPEAALSPTFR 11 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 NPEAALS(0.981)PT(0.019)FR;NPEAALS(0.966)PT(0.034)FR;NPEAALS(0.967)PT(0.033)FR 185.95 4.45E-06 437861000 427301 379910 378440 477626 365443 404989 473960 421624 425310 TRUE FALSE 407103.3286 418623.2609 395791.8483 429614.127 429176.1435 390964.1294 401648.6971 384704.3674 491264.9026 0.828683927 0.852133459 0.805658711 0.874506045 0.873614503 0.795831592 0.817580688 0.78308946 1 18.90614165 -0.954024331 8.26888272 1 0.830515049 0.753643199 0.030733158 4.33E-10 2.62E-11 0.029081943 0.00685468 0.111166945 0.954024331 -0.169484952 NPEDKSPQLSLSPRPAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPEDKSPQLSLSPRPASPK 19 2 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 NPEDKSPQLSLS(0.001)PRPAS(0.999)PK;NPEDKSPQLS(0.001)LS(0.001)PRPAS(0.998)PK;NPEDKSPQLSLSPRPAS(1)PK 196.2 4.42E-16 1384130000 1935800 1305750 1930000 1821210 1004660 2104460 2467240 2503740 1244820 TRUE FALSE 1844298.57 1438807.41 2018492.409 1638138.511 1179872.386 2031582.023 2090817.224 2284499.252 1437860.328 1.282668792 1.000658674 1.403816748 1.139289039 0.820575102 1.412920284 1.454117054 1.588818613 1 20.45549211 2.107278996 21.7753502 1.407978352 1.136845978 0.216886623 0.214070211 4.815936011 956.2828905 0.073388298 0.054200876 128.0203458 -2.107278996 -0.271132374 NPEHFVVCNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPEHFVVCNR 10 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 98.353 0.0054345 135720000 143310 126150 124180 145580 117710 138060 141290 151550 117560 FALSE TRUE 136536.0203 139004.8284 129873.7758 130946.0218 138238.5867 133278.9476 119733.6155 138279.4786 135790.6044 1.005489451 1.023670445 0.956426819 0.964323139 1.018027627 0.981503457 0.881751842 1.018328766 1 17.05102413 3.739019333 24.99739391 0.966156557 1.01457995 0.126339095 0.039694546 63.89238905 3481687.926 0.010598019 0.017716892 5483.013719 -3.739019333 0.048423393 NPEISHMLNNPDIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPEISHMLNNPDIMR 15 0 Q9UMX0;Q9UMX0-2 Q9UMX0 UBQLN1 Ubiquilin-1 0 ;; 243.9 5.30E-18 613335000 515367 428701 390760 516593 418030 427403 542498 495778 398543 FALSE TRUE 491006.6233 472386.1193 408676.7325 464664.0902 490934.2996 412601.9269 459729.9664 452365.05 460347.013 1.066601084 1.026152242 0.887757976 1.009377876 1.066443978 0.896284575 0.998659606 0.982660987 1 18.81236226 3.988074419 24.25587217 0.976941533 1.051432793 0.244148558 0.052480909 539.7196357 1097761.788 0.012555918 0.023335023 9729.139239 -3.988074419 0.07449126 NPEVGLKPVWYSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPEVGLKPVWYSPK 14 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 105.28 0.00092028 387830000 857560 776810 772040 936420 520500 893650 930870 933070 629650 FALSE TRUE 817024.8383 855967.8222 807438.7977 842289.2825 611275.0352 862702.6764 788848.6849 851365.4443 727292.9062 1.123377983 1.176923101 1.110197543 1.15811563 0.840479853 1.186183268 1.084636847 1.170595007 1 19.47217698 NPFDTFFGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPFDTFFGQR 10 0 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 145.25 7.16E-05 224190000 72822 73140 56208 68922 61502 57556 66590 67260 52300 FALSE TRUE 69379.84838 80593.04915 58785.1924 61993.82962 72227.92933 55562.82129 56430.47249 61370.35783 60410.41689 1.148474915 1.334091922 0.97309695 1.026210922 1.195620442 0.919755634 0.934118243 1.015890321 1 15.88250972 3.729371174 24.9158031 1.005032222 1.24128342 0.553505858 0.08657895 401.2478464 1087923.94 0.023289103 0.036629163 5362.547766 -3.729371174 0.236251197 NPFRGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPFRGSPK 8 1 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 NPFRGS(1)PK;NPFRGS(1)PK 61.344 0.052423 475150000 414770 278820 366360 340790 233760 379630 396120 408540 251600 TRUE FALSE 395164.6441 307232.075 383157.9684 306533.1417 274527.67 366483.3179 335684.6188 372766.0718 290616.843 1.359744466 1.057172295 1.318430014 1.054767296 0.944637851 1.261053262 1.155076269 1.282671947 1 18.14875879 4.670749176 3.365525126 1.143364434 1.373107887 0.240977571 0.124538616 0.38607617 7.167465526 0.028022413 0.204503898 46854.26997 -4.670749176 0.229743452 NPGFEIIHGLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPGFEIIHGLLDR 13 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ;; 191.06 3.89E-06 235190000 530435 504325 439540 531554 413753 464824 498761 501043 373366 FALSE TRUE 505362.3888 555716.2909 459693.3438 478121.182 485911.3922 448727.0283 422665.8491 457169.0187 431265.6924 1.171812174 1.288570597 1.065916793 1.108646457 1.126710055 1.040488581 0.98005906 1.060063499 1 18.71821743 3.059586995 0.697218392 1.005844252 1.2355214 0.617514988 0.055246122 0.421785482 0.456124045 0.035192304 0.051136817 1147.062271 -3.059586995 0.229677148 NPHLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPHLNK 6 0 P48163;E9PND9;E9PKA0;E9PNN2;E9PMB9;Q16798-2;Q16798 P48163 ME1;ME3 "NADP-dependent malic enzyme;Malic enzyme;NADP-dependent malic enzyme, mitochondrial" 0 80.555 0.064204 76805000 285350 218360 222050 276500 259650 234630 278800 250330 252640 FALSE TRUE 271862.071 240611.1323 232231.2121 248705.6947 304932.8778 226504.7043 236263.9395 228409.7781 291818.1209 0.931614768 0.824524301 0.795808058 0.852262683 1.044941544 0.776184507 0.809627376 0.782712799 1 18.15470995 -0.458010294 5.306116948 0.999999997 0.851977446 0.24502258 0.081528245 2445688.344 691377.997 0.083915227 0.018552591 0.348329059 0.458010294 -0.148022552 NPHNDRFVLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPHNDRFVLSK 11 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 107.53 0.0013128 405730000 832640 388190 832980 605450 676530 732060 1243300 872860 947380 FALSE TRUE 793282.7573 427747.0023 871172.9569 544589.0157 794516.6178 706708.5786 1053611.75 796427.7511 1094294.852 0.72492597 0.390888252 0.79610441 0.497662047 0.72605351 0.645811846 0.962822541 0.727799962 1 20.06157009 1.876974041 0.849010975 0.947048582 0.581327276 0.437575102 0.138401836 0.471404973 0.63307686 0.108394253 0.050428983 75.33105341 -1.876974041 -0.365721307 NPHPSSAFLNLIGFVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPHPSSAFLNLIGFVSR 17 0 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 105.91 0.00077887 41934000 172010 153780 166180 175890 171640 165230 220600 172670 150160 FALSE TRUE 163879.4282 169450.3568 173799.5174 158209.203 201573.9617 159508.0437 186943.4184 157550.0994 173446.0459 0.944843841 0.976962928 1.002037933 0.912152262 1.162170983 0.919640704 1.077818854 0.908352212 1 17.40412743 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR ddPTM_SK-BR-3_Trastuzumab_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 ; 325.19 4.16E-105 279000000 253414 220393 223298 276782 214928 255145 272502 259534 208910 FALSE TRUE 241435.6224 242851.2973 233536.4342 248959.3475 252411.3752 246309.2647 230926.8151 236807.8271 241306.6958 1.000534285 1.006400989 0.967799229 1.031713383 1.046018944 1.020731165 0.956984696 0.981356221 1 17.88050842 1.748108825 25 0.976085103 1.010976855 0.308546754 0.022881153 2.800137705 7347.461495 0.010741204 0.005956588 55.98978821 -1.748108825 0.034891752 NPLPNIDHELQELLIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NPLPNIDHELQELLIDR 17 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 0 ;;; 230.29 8.36E-16 74714000 76327 88826 73667 97533 64997 78838 77990 85129 57806.4 FALSE TRUE 72719.17398 97877.47039 77044.70482 87728.79754 76332.45622 76107.82029 66091.19312 77674.65346 66770.72128 1.089087741 1.465874091 1.15386959 1.313881232 1.143202511 1.139838223 0.989822962 1.163304095 1 16.026928 2.376535882 1.703811953 1.053538385 1.267971101 0.375433014 0.11099353 0.338582755 1.996673936 0.049642744 0.035376531 237.9774911 -2.376535882 0.214432716 NPLPNIDHELQELLIDRGEDVPS(ph)EEEEEEENGFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDR 36 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR;NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR;NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR 266.75 8.24E-63 118256000 64385 57106 79678 71164 67766 67573 83378 76219 72035 TRUE FALSE 61341.64865 62925.16632 83331.31511 64010.45952 79584.36894 65232.93007 70657.15476 69544.8603 83205.8199 0.737227861 0.756259194 1.00150825 0.769302671 0.95647599 0.783994799 0.849185247 0.835817259 1 16.34439682 4.407669436 0.031195306 1.577097956 1.63E-16 0.28800496 0.08399998 687.4266901 3.725444784 76.21483109 114.5779358 25566.39153 -4.407669436 -1.577097956 NPPGFAFVEFEDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 115.14 0.0010166 552979000 671298 765433 546612 749341 506153 615387 610863 657679 453492 FALSE TRUE 639567.0739 843431.4929 571674.7009 674015.819 594425.9229 594075.9939 517664.6301 600089.1402 523817.2232 1.22097374 1.610163728 1.091362933 1.286738559 1.134796445 1.134128409 0.988254313 1.145607883 1 18.99870397 3.006461314 0.940303879 1.050307761 1.397092416 0.429441493 0.133340958 0.429465436 0.833345639 0.063631695 0.079388921 1014.988949 -3.006461314 0.346784656 NPPGFAFVEFEDPRDAADAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NPPGFAFVEFEDPRDAADAVR 21 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;; 166.61 1.20E-11 3929620000 604447 368027 585049 536097 579684 572288 806955 605957 673792 FALSE TRUE 575875.9882 405529.3697 611874.0753 482207.511 680780.7061 552469.5231 683839.194 552896.1927 778280.2221 0.739933988 0.5210583 0.786187363 0.619580836 0.874724407 0.709859389 0.87865421 0.71040761 1 19.56993017 1.04436764 0.217991708 1.079895878 0.576065155 0.448800398 0.101348344 2.4882738 0.459769279 0.477623088 0.315767052 11.07560963 -1.04436764 -0.503830723 NPPGFAFVEFEDPRDAEDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NPPGFAFVEFEDPRDAEDAVR 21 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;;;;; 186.9 2.80E-17 2768516000 730631.1 551153 636029.7 715412 666680.4 675362.5 801637 727000 746030.8 FALSE TRUE 696095.6159 607316.1173 665192.2909 643497.4266 782949.2507 651974.5273 679332.5526 663340.0259 861721.4463 0.807796555 0.704770805 0.771934241 0.74675805 0.908587403 0.756595452 0.78834356 0.769784748 1 19.71686206 -5 0.294871571 2.780964461 0.765879671 0.624640693 0.052918664 163.2568924 1.524101227 179.2990452 0.05169961 1.00E-05 5 -2.01508479 NPPPNSDPNLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPPPNSDPNLRR 12 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 74.76 0.057142 76262000 24113 16130 23311 21099 20006 17873 23468 18027 17342 FALSE TRUE 22973.22628 17773.66534 24379.83241 18978.08843 23495.04007 17254.05353 19887.52558 16448.46031 20031.30879 1.146865965 0.887294261 1.217086345 0.947421291 1.172915874 0.861354278 0.992822076 0.821137574 1 14.28996907 2.22347245 24.99956778 0.924191013 1.056130636 0.314729584 0.112114834 316.1800421 523874.7983 0.037688421 0.027942819 167.2909508 -2.22347245 0.131939623 NPPS(ph)PRPSQLPVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NPPSPRPSQLPVLDR 15 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR 102.48 0.00093747 521310000 661880 734120 566460 796860 472968 617740 553370 649590 447187 TRUE FALSE 630594.2441 808927.6626 592432.7513 716758.1189 555453.4695 596347.5089 468943.2432 592708.4559 516534.476 1.220817338 1.566067126 1.146937482 1.387628807 1.075346362 1.154516371 0.907864363 1.14747124 1 18.97850512 2.64122864 1.262664236 1.015537441 1.367023733 0.496847904 0.132496176 0.306591512 0.998568554 0.059419368 0.050752117 437.7525052 -2.64122864 0.351486292 NPPS(ph)PRPSQLPVLDRDSTSVLESCGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPPSPRPSQLPVLDRDSTSVLESCGLGR 28 2 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NPPS(0.998)PRPS(0.002)QLPVLDRDSTSVLESCGLGR;NPPS(0.999)PRPS(0.001)QLPVLDRDSTSVLESCGLGR 105.24 0.00049881 315520000 171502 101990 156316 152295 156466 155980 196679 156999 171441 TRUE FALSE 163395.4403 112382.897 163483.2432 136986.0173 183753.6209 150578.3735 166672.0063 143251.3353 198027.1947 0.82511617 0.567512443 0.825559558 0.691753562 0.927921143 0.760392398 0.84166221 0.723392237 1 17.59533904 2.762421978 24.776306 0.833602682 0.717119682 0.240382132 0.105726748 986.0081465 1023814.337 0.029356266 0.031120758 578.6580212 -2.762421978 -0.116483 NPQMPQYSSPQPGSALS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPQMPQYSSPQPGSALSPR 19 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 NPQMPQYSSPQPGSALS(1)PR;NPQMPQYSSPQPGS(0.045)ALS(0.955)PR 286.81 3.33E-40 193566000 97376 86904 84166 103276 74022 96336 102674 94627 89479 TRUE FALSE 92773.22946 95759.6164 88025.09435 92894.50027 86931.41336 92999.86016 87009.19556 86340.95823 103354.9463 0.897617702 0.926512178 0.851677617 0.898791046 0.84109582 0.899810444 0.841848394 0.835382933 1 16.65724791 3.744902266 24.69030348 0.873078549 0.91206494 0.044486575 0.049192823 858.8285147 3343716.077 0.011043472 0.019325749 5557.791704 -3.744902266 0.038986391 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK 39 0 Q01081-2 Q01081-2 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 260.22 6.95E-63 68681200 30609.9 28459.9 27812.2 30331.2 19309.5 34660.7 35441.4 30522.2 12442.4 FALSE TRUE 29163.03069 31359.99617 29087.41688 27282.25015 22677.07069 33460.39127 30034.1635 27849.51436 14371.90385 2.029169622 2.182034928 2.023908398 1.898304528 1.577875202 2.328180847 2.089783221 1.937774888 1 13.81096357 0.802550631 4.988513934 1.000004624 2.034201324 0.728532589 0.193864666 2.009215173 50.47624005 0.183455646 0.04637528 6.346738881 -0.802550631 1.034196701 NPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPQTHLKDPDMVWDFWSLRPESLHQVSFLFSDR 33 2 P04040 P04040 CAT Catalase 0 203.52 1.44E-27 151460000 139680 112910 123680 143850 106890 127510 161480 134220 61838 FALSE TRUE 133077.6032 124415.6574 129350.8503 129389.9247 125531.5822 123094.2967 136843.2602 122466.9853 71427.52122 1.863113838 1.741844813 1.810938531 1.81148558 1.75746799 1.723345493 1.915833812 1.714563003 1 16.12419244 0.961101261 23.36118376 0.999999999 1.802732665 0.951749318 0.056411435 610.8829868 366874.8764 0.051719821 0.012929955 9.143264027 -0.961101261 0.802732665 NPS(ph)PTTRPVSR ddPTM_SK-BR-3_Trastuzumab_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(0.978)PT(0.022)TRPVSR 61.732 0.051749 356900000 74722 114810 98893 87624 82667 107240 130190 117700 75296 TRUE FALSE 71190.03914 126509.2695 103427.3419 78815.86905 97084.09863 103526.2519 110327.1244 107393.564 86972.51912 0.818534864 1.454588999 1.189195655 0.906215778 1.116261776 1.190332912 1.268528559 1.234798821 1 16.408272 2.205428532 5.602083448 1.204444926 1.115806438 0.024399094 0.182379061 0.660056506 54.52963482 0.068230822 0.05122312 160.4828144 -2.205428532 -0.088638488 NPSDSAVHS(ph)PFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 176.17 1.10E-05 682220000 1692170 2061440 1468780 2320610 1163710 1657830 1595020 1821700 918480 TRUE FALSE 1612184.478 2271503.08 1536125.016 2087337.874 1366660.656 1600418.931 1351670.404 1662182.291 1060913.187 1.519619604 2.141082896 1.447927157 1.967491684 1.28819273 1.508529586 1.274063157 1.566746752 1 20.01687518 2.728818554 24.72022125 1.35336381 1.785487728 0.438427273 0.247030581 516.521005 1310655.384 0.071369845 0.068080068 535.5728516 -2.728818554 0.432123918 NPSDSAVHS(ph)PFTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NPSDSAVHSPFTKR 14 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTKR;NPSDSAVHS(1)PFTKR;NPSDSAVHS(0.999)PFT(0.001)KR;NPSDSAVHS(0.998)PFT(0.002)KR;NPSDSAVHS(0.998)PFT(0.002)KR 203.56 7.00E-09 1637067000 1220863 1022521 1182981 1352806 945218 1170096 1340868 1313207 880163 TRUE FALSE 1163155.226 1126717.052 1237221.849 1216819.371 1110063.72 1129575.282 1136293.96 1198215.633 1016654.183 1.144101156 1.10825989 1.216954467 1.196886209 1.091879361 1.111071298 1.117679914 1.178587226 1 19.9553976 2.72048074 24.63430256 1.10880334 1.157141204 0.269185996 0.052488132 1218.308908 1659974.694 0.016319343 0.015418951 525.3887146 -2.72048074 0.048337864 NPSPIRT(ph)MT(ph)DILSRGPK ddPTM_SK-BR-3_Trastuzumab_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 197190000 369200 295040 330610 378030 473760 262220 454610 299720 634930 TRUE FALSE 351748.6477 325104.9114 345768.7955 340029.7062 556383.594 253139.2556 385250.895 273474.9279 733391.7016 0.479619072 0.443289596 0.471465378 0.46363997 0.758644518 0.345162422 0.525300319 0.372890677 1 19.48422442 -1.470711524 3.220806695 1.010172247 0.48316353 0.682008676 0.111050641 53064680.3 66613918.3 4841431.538 0.023638245 0.033828947 1.470711524 -0.527008717 NPSTVEAFDLAQSNSEHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPSTVEAFDLAQSNSEHSR 19 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 107.91 0.00028529 129890000 43621 33829 43382 42309 40746 34893 48237 52902 47950 FALSE TRUE 41559.12178 37276.21356 45371.10761 38056.01894 47852.0895 33684.64666 40877.55972 48269.62043 55385.84111 0.750356426 0.67302785 0.819182425 0.687107358 0.86397694 0.608181549 0.738050717 0.871515526 1 15.75722959 1.038169895 3.008650933 0.997842631 0.728728732 0.604626449 0.071872229 0.136909966 2.729217438 0.060989166 0.016130452 10.9186739 -1.038169895 -0.269113899 NPTDAYQLNYDMHNPFDICAASYRPIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPTDAYQLNYDMHNPFDICAASYRPIYR 28 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 86.449 0.0021945 188850000 43851 41325 45198 57151 42966 42943 55725 50327 53641 FALSE TRUE 41778.25013 45536.06448 47270.37301 51406.0729 50459.2568 41455.87314 47223.12779 45920.10108 61959.37232 0.674284593 0.734934244 0.762925305 0.829673881 0.81439264 0.669081554 0.762162785 0.741132445 1 15.91903491 -2.332151301 1.883735125 2.075305203 0.745420921 0.705182926 0.051054214 1893654.176 223050.5143 8648844.373 0.012901627 0.004654239 2.332151301 -1.329884281 NPVAS(ph)PT(ph)QPS(ph)GT(ph)EKGGHVLKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPVASPTQPSGTEKGGHVLKDK 22 2 O43435 O43435 TBX1 T-box transcription factor TBX1 4 NPVAS(1)PT(1)QPS(1)GT(1)EKGGHVLKDK 49.588 0.083743 1807800000 702830 554620 725730 704880 1267400 431550 731000 432640 1530000 TRUE FALSE 669608.6188 611136.4086 759005.4383 634024.1232 1488434.159 416605.3153 619472.5243 394755.748 1767264.586 0.378895511 0.345809232 0.429480364 0.358760159 0.842224855 0.235734546 0.350526191 0.223371051 1 20.75308662 -1.332330758 3.751762946 1.001896829 0.393055753 0.553364955 0.170632872 113997473.4 165499963.7 2346647.806 0.038496569 0.046523164 1.332330758 -0.608841075 NPVTIFSLATNEMWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NPVTIFSLATNEMWR 15 0 A0A0G2JLD8;E7EUY5;Q04837;C9K0U8 A0A0G2JLD8 SSBP1 "Single-stranded DNA-binding protein, mitochondrial" 0 ; 179.65 1.54E-06 104341000 88493 93321 87363 99344 77233 86967 99292 91214 68834 FALSE TRUE 84310.11127 102830.516 91368.67996 89357.75238 90702.41075 83955.31098 84143.18178 83226.8186 79508.42516 1.060392167 1.293328547 1.149169786 1.12387778 1.14078993 1.055929743 1.058292648 1.046767288 1 16.27882012 2.257227796 0.939089157 1.023590481 1.176687194 0.486439476 0.058523043 0.464560097 0.782500865 0.042559152 0.024647941 180.8122272 -2.257227796 0.153096713 NPVWYQALTHGLNEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 200.48 1.24E-11 182070000 79874 88099 78713 98313 71860 90869 93688 94305 73561 FALSE TRUE 76098.51432 97076.38826 82322.06891 88430.39046 84392.36125 87722.18375 79394.1749 86047.15426 84968.46418 0.895608919 1.142499034 0.968854383 1.040743661 0.993219803 1.032408725 0.934395786 1.012695182 1 16.37463987 1.764655013 25 0.975908746 1.016982203 0.038683953 0.06483006 44.15066307 42326.49046 0.028118062 0.015594048 58.16410009 -1.764655013 0.041073458 NPWGEVEWTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NPWGEVEWTGR 11 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 189.66 6.07E-06 1854220000 702095 681160 590831 698390 563720 622045 661926 676101 572023 FALSE TRUE 668908.3608 750570.9784 617921.1858 628186.5103 662032.5895 600503.4257 560937.0316 616898.0122 660729.4054 1.012378676 1.135973323 0.935210664 0.950747016 1.001972342 0.908849252 0.84896635 0.933662112 1 19.33370003 3.719532774 23.00535494 0.929870441 1.074175979 0.520105212 0.052936805 188.1389275 227466.8435 0.014625179 0.022713844 5242.431621 -3.719532774 0.144305538 NPWS(ph)MDENLMHISYEAGILENPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPWSMDENLMHISYEAGILENPK 23 0 P00966 P00966 ASS1 Argininosuccinate synthase 1 NPWS(0.998)MDENLMHIS(0.001)Y(0.001)EAGILENPK 74.838 0.011542 7037900 19926 14421 16597 20309 18529 20274 25741 23215 19003 TRUE FALSE 18984.13747 15890.5163 17357.98887 18267.50074 21760.45173 19571.9063 21813.73768 21182.17153 21949.88819 0.864885384 0.723945205 0.790800788 0.832236619 0.991369594 0.891663143 0.993797212 0.96502412 1 14.42192597 2.86625816 3.638173896 0.963869257 0.790165274 0.76835904 0.045362551 0.109269192 2.609371336 0.013757323 0.014751547 734.9506198 -2.86625816 -0.173703983 NPWSMDENLMHISYEAGILENPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPWSMDENLMHISYEAGILENPK 23 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 236.59 3.98E-37 108130000 219550 177020 179640 223470 194170 204920 263910 251380 196230 FALSE TRUE 209172.3066 195058.5393 187876.6717 201006.371 228033.1865 197823.569 223645.6825 229367.8346 226660.3462 0.922844733 0.860576376 0.828890782 0.886817542 1.006056817 0.872775377 0.986699642 1.011945135 1 17.79017249 2.012797646 0.801818539 1.009224566 0.877298009 0.523244667 0.046514142 0.503633934 0.604518417 0.038783493 0.020020759 102.9906137 -2.012797646 -0.131926557 NPYLLS(ph)EEEDDDVDGDVNVEKNETEPPKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NPYLLSEEEDDDVDGDVNVEKNETEPPKGK 30 2 O60524-4;O60524-3;O60524;G3V5V3;O60524-5 O60524-4 NEMF Nuclear export mediator factor NEMF 1 NPYLLS(1)EEEDDDVDGDVNVEKNETEPPKGK 129.61 5.19E-06 108260000 40009 26348 34155 33007 18196 42099 50725 43723 16908 TRUE FALSE 38117.85386 29032.89116 35721.04053 29689.07365 21369.37664 40641.10107 42985.96962 39894.38233 19530.00629 1.951758402 1.48657869 1.829033745 1.520177373 1.094181759 2.080956886 2.201021802 2.042722452 1 14.25340479 NPYYGGESASITPLEDLYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NPYYGGESASITPLEDLYKR 20 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 285.61 6.59E-45 1279360000 1138158 935327 998687 1115050 738751 1110740 1208240 1240180 773952 FALSE TRUE 1084359.527 1030637.885 1044477.787 1002963.056 867588.9405 1072274.795 1023900.797 1131583.265 893972.5234 1.2129674 1.15287423 1.168355581 1.121917094 0.970487255 1.199449387 1.145338106 1.265791996 1 19.76987096 -2.408101252 1.995595788 4.46E-05 1.153316113 0.285987838 0.07676786 1737992.334 117843.6969 7888176.256 0.017941789 0.003907498 2.408101252 1.153271558 NQAAIQGRPPYAAS(ph)AEEVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQAAIQGRPPYAASAEEVAK 20 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 NQAAIQGRPPYAAS(1)AEEVAK 184.59 2.39E-17 101270000 110540 92146 97502 111750 89245 99807 123890 109330 109450 TRUE FALSE 105314.9933 101535.7822 101972.5631 100516.6777 104809.2997 96350.65856 104988.3051 99756.48561 126422.947 0.833037006 0.803143611 0.806598529 0.795082539 0.829036992 0.762129509 0.830452917 0.789069453 1 16.94789883 -1.747490217 2.762557872 1.038616004 0.807533364 0.887965857 0.021642912 8567294.594 7006857.596 2261479.262 0.004640489 0.017885858 1.747490217 -0.23108264 NQALNTDNYGHDLASVQALQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQALNTDNYGHDLASVQALQR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 267.57 3.75E-37 558250000 324520 257280 274640 344390 253780 302750 324050 323730 240070 FALSE TRUE 309180.5827 283497.1245 287232.5157 309771.2629 298039.1517 292265.6916 274610.2209 295382.485 277298.8295 1.114972549 1.022352402 1.035823037 1.11710267 1.074794121 1.053973766 0.990304292 1.065213602 1 18.081082 1.949927534 6.872429226 1.018274028 1.069805446 0.333467803 0.035007847 0.292144424 32.93863252 0.014588004 0.009139323 89.11022375 -1.949927534 0.051531418 NQDECVIALHDCNGDVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 161.22 3.86E-11 350410000 232675 218160 232278 244570 201165 224599 245882 233891 212136 FALSE TRUE 221676.9139 240390.752 242928.1761 219985.3589 236248.1123 216821.0803 208368.185 213410.2641 245032.9674 0.904681995 0.981054731 0.991410171 0.897778618 0.964148273 0.884864933 0.850367961 0.870945107 1 17.90261634 2.229466938 24.81578468 0.884777579 0.94813356 0.140141641 0.049764303 222.1211956 606142.4543 0.016982994 0.012723314 169.6160473 -2.229466938 0.063355981 NQDHYAVLGLGHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQDHYAVLGLGHVR 14 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9;C9IZ83 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 102.5 0.00067654 65353000 51835 38167 31215 44798 37504 35620 50266 45662 20889 FALSE TRUE 49384.86228 42056.26069 32646.23863 40294.81993 44044.68573 34386.47047 42596.9985 41663.59321 24128.35943 2.04675591 1.743021974 1.353023554 1.670019051 1.825432261 1.425147473 1.765432856 1.726747868 1 14.5584422 -2.583398894 0.231272981 3.92E-20 1.812048771 0.551169595 0.195714908 35.95912954 0.973019979 19.16327565 0.361540576 0.002609763 2.583398894 1.812048771 NQDNLQGWNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQDNLQGWNK 10 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 249.69 3.64E-08 0 292490 247140 241060 274460 200525 249340 321580 288960 227324 FALSE TRUE 278664.5774 272323.847 252112.8394 246870.7594 235496.4965 240705.2933 272517.0648 263657.1305 262576.2449 1.061271089 1.03712294 0.960150982 0.940186952 0.896869009 0.916706282 1.037858794 1.004116464 1 18.00237688 3.80795872 3.982289997 0.964243563 1.052389051 0.413309139 0.041924148 0.22403833 6.977683773 0.012065608 0.022401622 6426.266316 -3.80795872 0.088145487 NQESLGS(ph)PHICDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NQESLGSPHICDLGK 15 0 A4D1E1;A0A087WUA7 A4D1E1 ZNF804B Zinc finger protein 804B 1 NQES(0.004)LGS(0.996)PHICDLGK;NQES(0.005)LGS(0.995)PHICDLGK;NQES(0.013)LGS(0.987)PHICDLGK;NQES(0.013)LGS(0.987)PHICDLGK 92.866 0.0053259 403306000 1528350 1344080 1363500 1568960 793070 1577280 1576550 1686210 805170 TRUE FALSE 1456107.924 1481043.28 1426017.824 1411245.16 931381.1569 1522658.398 1336018.342 1538556.513 930031.6514 1.565654161 1.592465458 1.533300315 1.517416271 1.001451032 1.637211374 1.436529972 1.65430554 1 19.82692029 -2.054127713 2.57716021 0.317261731 1.495083796 0.410651472 0.185315432 2223458.836 1668442.668 8946154.886 0.043749115 0.008828203 2.054127713 1.177822065 NQGGSSWEAPYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQGGSSWEAPYSR 13 0 Q5BKZ1 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 131.17 1.83E-05 0 46489 40738 40016 48605 35653 42666 49015 45125 34751 FALSE TRUE 44291.5571 44889.24852 41850.77318 43719.13306 41870.87191 41188.46572 41536.86153 41173.61578 40140.0076 1.103426724 1.118316891 1.042619962 1.089166038 1.043120677 1.026120028 1.034799543 1.025750074 1 15.29275327 3.168988347 0.400929166 1.004701367 1.135397464 0.770902026 0.018137506 0.715594875 0.205981496 0.016480222 0.039404527 1475.666937 -3.168988347 0.130696097 NQGGYDRYS(ph)GGNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRY(0.001)S(0.998)GGNYR 52.731 0.093409 92934000 43205 42763 37740 43825 32112 42062 44911 46241 35746 TRUE FALSE 41162.78527 47120.59832 39470.41633 39419.62774 37712.32263 40605.38239 38059.0021 42191.8929 41289.30711 0.996935724 1.141230057 0.955947655 0.954717589 0.913367777 0.983435791 0.921764126 1.021860037 1 15.33348059 3.711843144 24.20691991 0.957727994 1.069082886 0.452285928 0.047427867 330.7053823 299629.971 0.011581437 0.017948824 5150.425904 -3.711843144 0.111354892 NQGGYDRYS(ph)GGNYRDNYDN ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQGGYDRYSGGNYRDNYDN 19 2 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYRDNYDN 142.94 1.18E-07 311080000 139900 119950 157330 161980 143660 135410 188850 177240 162360 TRUE FALSE 133287.2043 132173.0414 164543.7361 145697.4627 168714.2585 130720.7177 160037.464 161719.926 187537.9596 0.710721203 0.704780204 0.877388964 0.776895851 0.899627248 0.697036046 0.853360378 0.862331692 1 17.51682312 -5 0.041462895 1.994543838 0.223185925 0.550281711 0.065984612 545.3902279 1.686380244 66.19794447 19.06618042 1.00E-05 5 -1.771357913 NQGGYGGSSSS(ph)SSYGSGR ddPTM_SK-BR-3_Trastuzumab_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 NQGGYGGS(0.018)S(0.011)S(0.011)S(0.478)S(0.478)S(0.004)YGSGR 84.365 0.00402 509000000 416350 406840 454030 519980 399860 515160 561320 516890 463630 TRUE FALSE 396669.9606 448297.4585 474847.7246 467710.6225 469595.4574 497319.88 475680.3247 471628.3714 535527.3725 0.74070903 0.837113996 0.88669179 0.87336455 0.876884136 0.928654455 0.888246519 0.880680233 1 19.03060079 7.74725801 0.211423855 0.958107215 1.04E-33 0.80112488 0.029041823 18.80833731 0.258204531 0.046821307 5.945220364 55880207.47 -7.74725801 -0.958107215 NQGGYGGSSSSS(ph)SYGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 NQGGYGGSSS(0.003)S(0.031)S(0.934)S(0.031)YGSGR;NQGGYGGSSS(0.001)S(0.211)S(0.786)S(0.003)YGSGR;NQGGYGGSSSS(0.025)S(0.89)S(0.085)YGSGR;NQGGYGGSSS(0.014)S(0.085)S(0.898)S(0.002)YGSGR;NQGGYGGSSSS(0.105)S(0.889)S(0.005)YGSGR 320.76 1.44E-61 591023000 1467262 1103201 1321585 1565104 1214239 1506890 1627301 1488766 1307548 TRUE FALSE 1397907.433 1215618.436 1382180.979 1407776.772 1426001.897 1454706.021 1379026.345 1358401.757 1510315.866 0.925572898 0.804876956 0.915160206 0.932107518 0.944174612 0.963179991 0.913071481 0.89941567 1 20.52641887 3.50342379 14.34222091 0.936449473 0.864352963 0.382825239 0.039489844 3.500586823 1907.340553 0.009876157 0.015076061 3187.306221 -3.50342379 -0.07209651 NQGGYGGSSSSSSYGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 438.82 3.61E-190 370141000 98867.5 80177.2 87051.7 103908 69156.6 89095.1 100152.5 92850.4 70010.5 FALSE TRUE 94194.22921 88347.34783 91043.10655 93462.97043 81217.48914 86009.71435 84872.3967 84719.92675 80867.37078 1.164798958 1.09249685 1.125832405 1.155756265 1.004329538 1.063589845 1.049525858 1.047640426 1 16.30327009 2.742454413 24.99976517 1.039692022 1.130531907 0.76849373 0.027560443 168.9360998 1084640.351 0.008135307 0.008352596 552.6553936 -2.742454413 0.090839885 NQGIEGS(ph)PGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQGIEGSPGGR 11 0 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 NQGIEGS(1)PGGR 124.45 0.0009711 0 399990 337780 359450 413380 328660 355070 404120 373680 349460 TRUE FALSE 381083.2654 372200.166 375931.138 371826.257 385978.1999 342773.8369 342464.0718 340958.5982 403652.472 0.94408753 0.92208073 0.93132376 0.921154416 0.956214136 0.849180572 0.848413166 0.844683538 1 18.6227542 2.237097479 24.99968823 0.86946107 0.933248963 0.183657207 0.046461746 43.12433897 736816.1156 0.014796902 0.011521211 172.6225306 -2.237097479 0.063787893 NQIGDKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NQIGDKEK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 126.31 0.0011167 2971230000 6701520 4509870 5006560 6117300 3200280 6247600 7331640 6586990 3394740 FALSE TRUE 6384752.431 4969430.88 5236115.728 5502377.382 3758407.819 6031244.045 6213063.663 6010198.236 3921178.941 1.628273671 1.267330809 1.335342204 1.403245673 0.958489239 1.538120075 1.584488685 1.53275286 1 21.90285605 4.653601467 3.317689475 1.360564363 1.641594597 0.1467271 0.214612016 0.572356566 10.29559443 0.051102797 0.3586217 45040.31998 -4.653601467 0.281030233 NQIHVKS(ph)PPREGSQGELTPANSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NQIHVKSPPREGSQGELTPANSQSR 25 2 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 NQIHVKS(0.941)PPREGS(0.059)QGELTPANSQSR;NQIHVKS(0.825)PPREGS(0.175)QGELTPANSQSR;NQIHVKS(0.975)PPREGS(0.023)QGELT(0.001)PANSQSR 110.7 0.0014473 366110000 204758 89197 224078 163712 147381 193421 279982 209239 162176 TRUE FALSE 195079.4951 98286.27571 234352.1979 147255.3587 173084.1997 186722.7823 237265.6037 190916.9239 187325.4258 1.041393576 0.524681982 1.251043188 0.786093816 0.923976011 0.996782906 1.266595833 1.019172507 1 17.51518721 2.091666445 3.332210987 1.125955258 0.875353266 0.143609051 0.197428387 0.333797319 7.309798455 0.080396533 0.053735111 123.4998542 -2.091666445 -0.250601991 NQKDPGVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NQKDPGVLDR 10 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;; 176.95 2.17E-06 36651230000 36876700 23320600 31233000 33118600 23596900 34405000 43786200 36364500 27539200 FALSE TRUE 35133611.47 25696995.65 32665063.94 29789455.41 27712191.89 33213546.22 37105811 33180231.6 31809838.49 1.104488836 0.807831692 1.026885564 0.936485591 0.871183043 1.0441281 1.166488507 1.043080794 1 24.92296971 2.040000125 7.799153998 1.092613325 0.947622876 0.276234875 0.089998054 0.226843931 37.71834146 0.031972816 0.023436786 109.6478511 -2.040000125 -0.144990449 NQKPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NQKPEVR 7 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;; 133.12 0.0030123 2168050000 5976300 4800500 5292300 6361900 3605260 5890400 6655500 6231400 4093840 FALSE TRUE 5693812.143 5289676.408 5534957.19 5722389.725 4234016.203 5686413.971 5640081.238 5685745.581 4728691.799 1.204098805 1.118634209 1.170504957 1.210142248 0.895388489 1.202534276 1.192736063 1.202392929 1 22.17300968 5.843159297 0.950322018 1.132940418 1.66545387 0.049509601 0.102759528 52.06101322 7.415015129 0.029707174 46.34286773 696882.08 -5.843159297 0.532513452 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.962)PT(0.038)EPAGQK;NQKPSQVNGAPGS(0.951)PT(0.049)EPAGQK;NQKPSQVNGAPGS(0.999)PT(0.001)EPAGQK 208.96 1.72E-22 2170525000 2661280 2415590 2550200 3168930 1311300 2995750 3032630 2854670 1477430 TRUE FALSE 2535486.569 2661741.367 2667129.192 2850383.136 1539990.305 2892006.426 2569946.595 2604699.961 1706542.299 1.48574493 1.559727743 1.562884902 1.670268084 0.902403829 1.694658508 1.505937824 1.526302608 1 20.70264474 -1.091991697 4.198406422 0.999926079 1.494912431 0.329102896 0.219019728 13536154.66 3520712.596 9418.671176 0.046482437 0.080911137 1.091991697 0.494986352 NQKPSQVNGAPGSPT(ph)EPAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.294)PT(0.706)EPAGQK 209.67 3.97E-22 1231800000 1395200 1336600 1479800 1735900 685810 1638200 1675800 1614600 792350 TRUE FALSE 1329251.661 1472801.06 1547650.294 1561404.034 805415.0469 1581468.723 1420125.932 1473217.064 915223.5912 1.452379149 1.609225411 1.691007868 1.706035606 0.88001998 1.727958871 1.551671029 1.60967995 1 19.80376471 NQLS(ph)QNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQLSQNR 7 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 NQLS(1)QNR;NQLS(1)QNR 64.803 0.046574 367700000 14007.3 15418.5 15169.2 16332.3 15170.7 11752.4 15258.2 19635.3 16363.3 TRUE FALSE 13345.20269 16989.66268 15864.72282 14690.54617 17816.46528 11345.41144 12930.28135 17915.92904 18900.83699 0.706064112 0.898884144 0.839366152 0.777243155 0.942628376 0.600259737 0.684111575 0.947890776 1 14.2061625 1.09288194 6.104922241 0.99793922 0.779914583 0.399135246 0.100711273 0.203595593 10.05228838 0.098467419 0.024772183 12.38459875 -1.09288194 -0.218024637 NQLTSNPENTVFDAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NQLTSNPENTVFDAKR 16 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 305.32 3.65E-46 905670000 610857 346298 586293 590920 481527 652290 852920 754940 614330 FALSE TRUE 581983.0002 381586.1599 613175.114 531519.5989 565505.1563 629701.0337 722791.389 688833.4514 709597.1588 0.82015971 0.537750406 0.864117206 0.749044148 0.796938304 0.887406363 1.018593973 0.970738739 1 19.43664071 2.259352142 1.009346203 1.01596924 0.706862802 0.624347368 0.086314773 0.310779002 0.606413534 0.059439144 0.034181236 181.6988347 -2.259352142 -0.309106437 NQMPS(ph)PTSTGTPSPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQMPSPTSTGTPSPGPR 17 0 Q9Y572;H0YJN5 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 NQMPS(0.988)PT(0.006)S(0.006)T(0.001)GTPSPGPR;NQMPS(0.938)PT(0.018)S(0.018)T(0.025)GT(0.001)PSPGPR 164.01 2.78E-09 154483000 160019 120001 144220 151707 126183 137367 167610 153929 136333 TRUE FALSE 152455.219 132229.2383 150832.6297 136457.1241 148189.2752 132609.9463 142038.0161 140450.1607 157474.8253 0.968124389 0.839684934 0.957820587 0.866532945 0.941034701 0.842102514 0.901972844 0.891889611 1 17.26476169 -1.277985432 6.802609854 1.000001237 0.899062924 0.326189633 0.044561987 7.27E-07 7.73E-08 0.037537257 0.008847508 0.052724755 1.277985432 -0.100938313 NQMPSPT(ph)STGTPSPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQMPSPTSTGTPSPGPR 17 0 Q9Y572;H0YJN5 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 NQMPS(0.117)PT(0.435)S(0.435)T(0.012)GTPSPGPR 291.59 5.94E-45 89672000 116240 86441 107280 118280 87799 112250 121930 112650 88399 TRUE FALSE 110745.5656 95249.43618 112198.8941 106390.2697 103111.1178 108362.7544 103327.3391 102785.7688 102107.4654 1.084598125 0.932835183 1.098831448 1.041944085 1.009829373 1.061261818 1.011946959 1.006643034 1 16.63972883 1.540463893 8.289135073 1.005373691 1.031368529 0.08869767 0.045453182 0.368449557 42.83704873 0.023777903 0.011045984 34.71074161 -1.540463893 0.025994838 NQNYLVPS(ph)PVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQNYLVPSPVLR 12 0 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 NQNYLVPS(1)PVLR 80.312 0.021693 37278000 101040 86550 85889 102790 99177 90686 119230 104530 109490 TRUE FALSE 96264.03944 95369.5434 89827.09561 92457.35391 116473.4374 87545.52108 101039.2737 95376.79905 126469.15 0.761166177 0.754093337 0.710268833 0.731066461 0.920963234 0.692228271 0.798924273 0.754150708 1 16.94842598 -5 0.326134178 3.315984148 0.755562823 0.582433959 0.062468348 231.4551355 2.019709651 370.9873978 0.048569861 1.00E-05 5 -2.560421326 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 NQPTVYIAAS(0.996)PPNT(0.004)DELMSR;NQPTVYIAAS(0.995)PPNT(0.005)DELMSR 162.43 5.25E-11 56155000 132409 106976 130369 143609 110079 130343 153872 141299 117656 TRUE FALSE 126150.289 117876.976 136346.5476 129173.1505 129276.7427 125829.1892 130396.0003 128926.1105 135901.4916 0.928248009 0.86737073 1.003274843 0.950491043 0.951253303 0.92588527 0.959489104 0.948673256 1 17.05220176 7.999999976 0.075413081 1.047899561 0.675027917 0.25954703 0.033064183 252.8308897 1.398089095 1.114091148 9.893738343 99999994.57 -7.999999976 -0.372871644 NQQFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NQQFHK 6 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 141.59 0.011634 2009820000 4915610 3922410 4049520 4814290 2846480 4414590 5207590 4619590 3009910 FALSE TRUE 4683258.857 4322108.038 4235194.498 4330348.423 3342905.211 4261711.641 4413076.502 4215074.21 3476671.47 1.34705246 1.243174132 1.218175066 1.245544326 0.961524619 1.22580223 1.269339522 1.212387839 1 21.72927531 7.999982274 0.0221182 9.02E-07 2.800708793 0.368769902 0.094650387 3014.007019 5.134652478 233.4148021 449.2601838 99995918.55 -7.999982274 2.800707891 NQRPS(ph)SMVSETSTAGTASTLEAKPGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQRPSSMVSETSTAGTASTLEAKPGPK 27 2 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;E9PIK1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 NQRPS(0.483)S(0.483)MVS(0.033)ETSTAGTASTLEAKPGPK 93.6 0.0049126 50272000 79958 60430 63163 71300 46220 77580 90388 88240 53147 TRUE FALSE 76178.5438 66587.8857 66059.08603 64132.78854 54280.75337 74893.38515 76597.65051 80513.23781 61388.76532 1.240919953 1.084691724 1.076077775 1.044699111 0.884213147 1.2199852 1.247747045 1.311530496 1 15.90568703 NQS(ph)PTEAEKPASSSLPSSPPPQLLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQS(0.967)PT(0.033)EAEKPASSSLPSSPPPQLLTR;NQS(0.972)PT(0.028)EAEKPASSSLPSSPPPQLLTR;NQS(0.871)PT(0.129)EAEKPASSSLPSSPPPQLLTR 218.93 2.03E-34 813850000 382474 298611 303124 390157 212740 338900 359551 364667 226395 TRUE FALSE 364395.212 329039.8004 317022.5352 350937.6771 249841.7886 327163.808 304694.8913 332734.8243 261503.1803 1.393463787 1.258263093 1.212308527 1.342001564 0.95540631 1.251089213 1.165167058 1.272393031 1 17.99646897 8 0.138043843 1.022751961 2.220809598 0.382452785 0.107924243 75.96058677 0.700706043 0.435097399 17.92175069 100000000 -8 1.198057637 NQSFCPTVNLDKLWTLVSEQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQSFCPTVNLDKLWTLVSEQTR 22 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 294.08 1.63E-55 1740130000 1308450 862810 1269830 1231670 998910 1181430 1599840 1303620 1148130 FALSE TRUE 1246602.162 950731.3199 1328052.962 1107860.192 1173119.588 1140516.783 1355755.025 1189468.122 1326176.137 0.939997431 0.716896718 1.001415215 0.835379375 0.884588069 0.860004001 1.022303891 0.896915643 1 20.33884097 1.754405474 25 0.972114448 0.864111857 0.256873055 0.079229821 6.85818382 10833.89668 0.034126137 0.018924821 56.80747349 -1.754405474 -0.108002591 NQSLGQS(ph)APSLTAGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQSLGQSAPSLTAGLK 16 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 NQSLGQS(0.999)APS(0.001)LTAGLK;NQSLGQS(0.999)APS(0.001)LTAGLK 200.48 3.72E-11 186749000 296347 250660 272359 321142 190263 313576 353346 347095 238843 TRUE FALSE 282339.2646 276202.539 284846.9295 288860.196 223444.807 302716.7845 299436.5781 316701.5217 275881.5526 1.023407553 1.001163493 1.032497196 1.04704426 0.809930221 1.097270846 1.085380937 1.147961938 1 18.07368947 NQSPTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQSPTEAEKPAS(0.002)S(0.003)S(0.012)LPS(0.518)S(0.441)PPPQLLT(0.024)R;NQSPTEAEKPASSSLPS(0.522)S(0.478)PPPQLLTR 177.78 1.53E-17 216170000 608080 560580 555280 630220 352985 615340 649080 644970 398353 TRUE FALSE 579337.2635 617703.7393 580740.1372 566869.0883 414545.4722 594030.6215 550050.9248 588493.0076 460127.5487 1.259079716 1.342461978 1.262128596 1.231982501 0.900935998 1.291012944 1.195431411 1.27897799 1 18.81167431 -4.99999985 0.042962423 0.108808646 1.735266272 0.244607546 0.120322323 1019.779881 3.262678276 115.926001 31.93656908 1.00E-05 4.99999985 1.626457626 NQTAEKEEFEHQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 225.31 1.70E-12 7100320000 12971410 9934860 7894690 15553660 5623160 12062000 13662040 12729140 5065590 FALSE TRUE 12358277.16 10947233.53 8256669.345 13990176.55 6603837.324 11644289.92 11577644.88 11614509.02 5851135.826 2.112115925 1.870958709 1.411122488 2.391018934 1.128641946 1.990090516 1.978700413 1.985000753 1 22.48028528 -1.816197172 2.542511636 0.703586193 1.869520205 0.366696412 0.354281438 27137886.44 18621346.69 49432714.13 0.077052302 0.015268727 1.816197172 1.165934012 NQTYS(ph)FSPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQT(0.02)YS(0.751)FS(0.227)PS(0.001)K 73.466 0.047102 133920000 223570 231250 191560 252490 144390 235720 274220 296620 151330 TRUE FALSE 213002.2892 254814.6379 200343.2155 227109.2255 169571.5703 227556.9573 232382.7026 270646.3803 174797.4835 1.218566108 1.457770631 1.146144735 1.299270567 0.970103041 1.301831998 1.329439635 1.548342544 1 17.41532489 3.730215343 24.91793559 1.243504555 1.338168372 0.058118011 0.176053711 1797.948641 5368443.788 0.044514773 0.070138484 5372.981469 -3.730215343 0.094663818 NQTYSFS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQTYSFS(1)PSK;NQT(0.002)YS(0.031)FS(0.966)PS(0.001)K 177.41 2.44E-06 223053000 594740 579380 493830 666850 309180 616800 627230 689660 381540 TRUE FALSE 566627.8189 638419.4807 516472.594 599816.9711 363100.8941 595440.0613 531534.5436 629269.7143 440707.2746 1.285723771 1.448624785 1.17191756 1.361032608 0.823904925 1.35110105 1.206094327 1.427863234 1 18.74946119 3.727233137 24.65490373 1.202021766 1.367174279 0.137209842 0.181502929 1046.625423 2278039.513 0.043978407 0.068811578 5336.212758 -3.727233137 0.165152514 NQVAMNPTNTVFDAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQVAMNPTNTVFDAKR 16 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 203.06 4.61E-11 970100000 811210 600410 725770 796600 499350 841910 968980 975140 671880 FALSE TRUE 772865.711 661592.4616 759047.2724 716524.2546 586436.4819 812754.4456 821144.3045 889751.5721 776071.7189 0.995868928 0.852488817 0.978063308 0.923270668 0.755647278 1.047267187 1.058077861 1.146481118 1 19.56583046 2.032314498 24.96403215 1.069147743 0.907061151 0.538786272 0.074520378 136.9542301 105801.1823 0.026153028 0.019315145 107.7245027 -2.032314498 -0.162086592 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 341.57 1.35E-106 498720000 523570 508560 469410 621150 219912 614470 597000 656210 177385 TRUE FALSE 498821.8837 560382.8422 490932.9128 558710.8219 258264.5832 593190.7498 505916.6853 598748.7736 204892.9598 2.434548674 2.735002914 2.396045785 2.726842456 1.260485394 2.895125095 2.469175543 2.92225157 1 17.64451089 NQVIIPLVLS(ph)PDRDEDLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQVIIPLVLSPDRDEDLMR 19 1 Q96G25-2;Q96G25 Q96G25-2 MED8 Mediator of RNA polymerase II transcription subunit 8 1 NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR 91.729 0.0012294 26249000 27804 29578 25621 29114 26342 28290 32453 27231 26480 TRUE FALSE 26489.76002 32592.03183 26795.74819 26187.40541 30936.03646 27310.31021 27501.69881 24846.50928 30586.38316 0.866063826 1.065573254 0.876067891 0.856178557 1.011431665 0.89289113 0.899148444 0.812338914 1 14.9006019 2.09487293 24.29949504 0.893356714 0.941307467 0.036952825 0.078524475 33.09055787 8449.671902 0.027970331 0.020657461 124.4150534 -2.09487293 0.047950752 NQYDNDVTVWSPQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;; 340.29 5.75E-69 689390000 502960 424923 418758 499588 430329 450932 546780 473762 444627 FALSE TRUE 479186.0776 468223.1368 437958.4685 449368.4651 505378.2414 435316.1118 463358.6687 432276.8877 513577.4843 0.933035603 0.911689377 0.852760259 0.874976958 0.984035042 0.847615258 0.902217646 0.841697506 1 18.97022243 NQYREDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NQYREDWK 8 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 117.89 0.0018168 510330000 535290 372830 513500 447790 363110 440760 537050 456630 352550 FALSE TRUE 509987.9025 410821.8009 537044.4829 402777.2985 426436.269 425496.3707 455113.1589 416645.0565 407221.6534 1.252359491 1.008840756 1.318801391 0.989086153 1.047184661 1.044876585 1.117605498 1.023140722 1 18.63545475 8 0.27707593 1.03517249 2.354796832 0.294661027 0.093970615 73.72397595 1.038908094 0.097935848 46.93529689 100000000 -8 1.319624342 NRAEASLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRAEASLER 9 1 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0QZS6;M0R286;A0A590UKA0 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 104.82 0.0037686 0 120990 90095 102190 99190 135930 87728 148010 113960 144860 FALSE TRUE 115271.0425 99275.78293 106875.5126 89219.23275 159636.149 84689.95736 125428.3561 103981.0583 167324.149 0.688908584 0.593314136 0.63873334 0.533211932 0.954053255 0.506143064 0.749612993 0.621434855 1 17.35228615 -5 0.300637168 3.840086871 0.642052541 0.416642834 0.12571072 244.1790806 2.254596107 437.1550617 0.108874781 1.00E-05 5 -3.198034329 NRAEVSQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NRAEVSQPR 9 1 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 174.98 4.95E-05 216105000 249786 168786 200878 227904 213708 194187 285152 233365 230147 FALSE TRUE 237979.1108 185985.4853 210088.455 204994.6569 250978.6075 187462.2555 241646.8252 212930.3235 265837.0213 0.895206806 0.699622213 0.790290434 0.771129077 0.944107056 0.705177385 0.90900366 0.8009807 1 18.02018251 -0.460133255 0.36752511 1.055351172 0.792131109 0.338490506 0.081625297 8.543783238 1.181155199 0.664510628 0.057437679 0.346630477 0.460133255 -0.263220063 NRDEAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NRDEAIK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 119.17 0.0044152 2094870000 2828420 2321330 2695670 3035800 3205480 2301709 3144140 2752280 3866160 FALSE TRUE 2694726.192 2557876.166 2819269.136 2730635.616 3764514.697 2222000.24 2664443.697 2511275.772 4465704.347 0.603426914 0.572782246 0.631315671 0.61146807 0.842983414 0.497569939 0.59664579 0.562347074 1 22.09045631 -1.1146606 4.809195253 1.000021474 0.611237624 0.649310602 0.088927352 1.91E-05 3.51E-06 0.080291939 0.018923947 0.076796142 1.1146606 -0.38878385 NRDVITLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRDVITLR 8 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 147.2 0.0004935 174810000 59808 48645 61645 56884 50080 51079 58278 61768 58957 FALSE TRUE 56980.99437 53601.9808 64471.48423 51165.91225 58813.93614 49310.12142 49386.62075 56359.26647 68099.75045 0.836728387 0.787109798 0.946721299 0.751337735 0.86364393 0.724086668 0.725210011 0.827598722 1 16.05536189 NRDYPLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRDYPLASK 9 1 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 ; 101.95 0.0033407 382180000 795030 502450 667890 781970 680300 802850 1095460 909930 838980 FALSE TRUE 757450.5075 553650.2262 698513.4171 703364.89 798944.1046 775047.1032 928327.4575 830251.7054 969084.7335 0.781614323 0.571312505 0.72079705 0.725803292 0.824431628 0.799772276 0.957942505 0.856737989 1 19.88626329 2.247514315 0.805302272 0.960493067 0.673075746 0.707997968 0.065692775 0.313022327 0.388031919 0.049563687 0.029871151 176.8130497 -2.247514315 -0.28741732 NREEEWDPEYT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NREEEWDPEY(0.005)T(0.995)PK;NREEEWDPEY(0.001)T(0.999)PK;NREEEWDPEY(0.002)T(0.998)PK;NREEEWDPEYT(1)PK 122.31 0.00038245 2238750000 3284490 3034140 2802130 3241420 1876890 3187420 3369040 3531580 1850970 TRUE FALSE 3129238.667 3343322.316 2930610.432 2915586.303 2204219.022 3077038.846 2855031.071 3222336.133 2138008.974 1.463622793 1.563755043 1.370719425 1.363692266 1.030968087 1.439207638 1.335369077 1.507166795 1 21.02783648 -4.611171778 0.104244918 6.91E-17 1.623804402 0.380063459 0.14747449 169.6544652 1.296402714 38.98672797 2.197683052 2.45E-05 4.611171778 1.623804402 NREEEWDPEYTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 112.72 0.00080099 1050410000 1461230 1192660 1284680 1525310 944970 1412890 1552830 1524070 1023480 FALSE TRUE 1392160.554 1314193.41 1343583.849 1371982.941 1109772.469 1363961.265 1315917.264 1390614.351 1182196.051 1.177605485 1.111654373 1.136515257 1.160537577 0.938738095 1.153752175 1.113112552 1.176297578 1 20.17303788 NREELDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NREELDK 7 1 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 111.95 0.0058957 6239440000 4267760 6060050 3586480 5496110 2328420 4735160 3740760 4668570 1941010 FALSE TRUE 4066031.443 6677575.985 3750923.656 4943630.581 2734495.711 4571180.222 3170038.358 4259765.261 2242011.917 1.813563706 2.978385589 1.673016823 2.204997459 1.219661541 2.038874185 1.413925739 1.899974406 1 21.09636252 3.200015952 1.617847272 1.582787122 2.355292312 0.298616757 0.463915512 0.386532906 2.097068292 0.141359997 0.196221331 1584.951406 -3.200015952 0.77250519 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 38 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;; 345.59 2.66E-145 4932721000 1314253 1479355 1174483 1564972 805735 1366113 1271524 1392518 831178.1 FALSE TRUE 1252130.865 1630102.956 1228334.207 1407658.041 946254.9289 1318804.164 1077529.661 1270581.742 960072.9547 1.304203872 1.697894882 1.279417571 1.466199037 0.985607317 1.373649948 1.122341438 1.323422075 1 19.87278451 2.768706706 24.02002732 1.18229949 1.456925414 0.402874955 0.165002248 398.1710139 317256.7092 0.045894476 0.048671406 587.0927351 -2.768706706 0.274625925 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;; 218.71 2.09E-39 4591640000 1393416.6 1097049 1370820.6 1385186 1055855.8 1366872 1678119 1517209 1169304.3 FALSE TRUE 1327552.559 1208839.54 1433674.08 1245944.472 1239996.717 1319536.88 1422091.126 1384354.137 1350634.039 0.982910634 0.895016345 1.061482266 0.922488576 0.918084901 0.976975881 1.052906328 1.024966125 1 20.36520539 1.921957359 5.300397907 1.029339867 0.952918027 0.316374983 0.046717421 0.23508941 11.39146361 0.019764715 0.011879335 83.55209795 -1.921957359 -0.07642184 NREELGFRPEYSASQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NREELGFRPEYSASQLK 17 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;; 233.79 2.28E-20 3143410000 1504220 1296360 1388740 1588720 1048450 1460120 1675090 1649370 1229390 FALSE TRUE 1433118.502 1428460.558 1452415.103 1429018.847 1231299.348 1409555.678 1419524.255 1504942.419 1420037.522 1.009211714 1.005931558 1.02280051 1.00632471 0.867089305 0.992618615 0.999638554 1.059790601 1 20.43749762 1.444089857 4.971098146 1.030660595 0.987020946 0.141035476 0.045640709 0.3989995 19.07912399 0.030422961 0.011660096 27.8028846 -1.444089857 -0.043639649 NREILDESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NREILDESLR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 99.589 0.0041881 210900000 169620 122130 136290 156010 218290 133740 191560 160130 246930 FALSE TRUE 161602.3988 134575.1859 142539.0313 140327.5784 256359.7069 129108.5503 162334.0038 146108.1683 285222.6433 0.566583343 0.471825043 0.499746548 0.491993121 0.898805593 0.452658838 0.569148374 0.51226006 1 18.12172899 -2.155308629 2.210153426 1.984019652 0.55361413 0.545139242 0.126867 11112468.33 2595574.121 54734314.14 0.028546251 0.006993448 2.155308629 -1.430405522 NRENS(ph)PSSQSAGLSSINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRENSPSSQSAGLSSINK 18 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 NRENS(0.985)PS(0.014)S(0.002)QSAGLSSINK 179.17 5.15E-14 369240000 222510 244360 200820 271220 141220 245790 236760 224900 152540 TRUE FALSE 211992.3933 269260.5618 210027.7956 243956.4503 165848.7233 237278.2307 200637.9136 205206.5637 176195.1241 1.20316833 1.528195307 1.192018205 1.384581165 0.941278733 1.346678756 1.138725686 1.164655178 1 17.42681448 1.930067371 0.319172601 0.996125986 1.390603793 0.273846761 0.148743837 1.731222657 0.537945095 0.206532668 0.243213634 85.12700824 -1.930067371 0.394477807 NREPVQLETLSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NREPVQLETLSIR 13 1 P62314;J3QLI9 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 ;; 214.58 2.79E-11 3233640000 1933920 1601970 1527450 1925020 1525360 1710850 2179570 1927190 1633410 FALSE TRUE 1842507.434 1765212.564 1597485.093 1731513.332 1791382.301 1651602.836 1847036.566 1758435.027 1886710.88 0.976571161 0.935603108 0.846703705 0.917741743 0.949473668 0.875387349 0.978971704 0.932010858 1 20.84744193 0.879423293 0.985958365 0.998134209 0.924105397 0.261270535 0.040265438 1.035938728 2.040313296 0.038107339 0.012575036 7.575709157 -0.879423293 -0.074028812 NRGNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NRGNRGSGGGGGGGGQGSTNYGK 23 2 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 NRGNRGS(0.965)GGGGGGGGQGS(0.034)T(0.001)NYGK;NRGNRGS(0.985)GGGGGGGGQGS(0.015)TNYGK;NRGNRGS(0.948)GGGGGGGGQGS(0.052)T(0.001)NYGK 79.467 0.0064278 66919000 70713 23883.6 90861 55299 63194 68121 137578 86140 107368 TRUE FALSE 67370.53663 26317.36599 95027.06672 49740.23946 74215.01359 65761.95269 116587.9493 78597.12494 124018.0811 0.543231568 0.21220588 0.766235584 0.401072481 0.598420915 0.530261008 0.940088319 0.633755371 1 16.92019095 1.80579608 0.497125758 0.987640851 0.39853479 0.48044355 0.169357146 0.640755703 0.368958678 0.158099399 0.111405459 63.94345223 -1.80579608 -0.589106061 NRGPS(ph)PEPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRGPSPEPLK 10 1 Q92674-2;Q92674 Q92674-2 CENPI Centromere protein I 1 NRGPS(1)PEPLK 50.675 0.097852 95470000 170600 147510 138810 192240 98326 170840 186700 184670 130560 TRUE FALSE 162536.0761 162541.4367 145174.5758 172915.67 115474.0233 164923.768 158215.486 168499.3158 150806.578 1.077778425 1.077813971 0.962654134 1.146605621 0.765709459 1.093611235 1.049128547 1.11732073 1 17.20233983 -3.076545027 9.743535364 1.001291825 1.036817699 0 0.108333394 0 0 0 0.021613866 0.000838407 3.076545027 0.035525874 NRHS(ph)PDHPGMGSSQASSSSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(0.999)PDHPGMGS(0.001)S(0.001)QASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(0.995)PDHPGMGS(0.004)S(0.001)QASSSSSLR 234.8 1.15E-30 1945349000 506458 426177 439522 556206 449442 436193 588956 475501 84920.1 TRUE FALSE 482518.734 469604.9208 459674.5184 500295.1162 527824.5425 421087.527 499099.9453 433863.6117 98089.0754 4.91918934 4.7875354 4.686296783 5.100416271 5.381073686 4.292909535 5.088231725 4.423159357 1 16.58180485 0.754842571 3.552188229 1.000039721 4.879513417 0.947160347 0.286694409 0.458522383 6.440470823 0.249639166 0.064309011 5.686467627 -0.754842571 3.879473695 NRLEEVSPNLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRLEEVSPNLVR 12 1 P28331-4;P28331;P28331-2;B4DJ81;P28331-3;P28331-5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 106.32 0.0017642 111330000 130120 89934 97562 111470 78645 114390 120810 128340 88473 FALSE TRUE 123969.4855 99098.37685 102035.3142 100264.8238 92360.6631 110428.6456 102378.2157 117101.8692 102192.941 1.213092453 0.969718416 0.998457557 0.98113258 0.903787113 1.08058976 1.001812989 1.145890001 1 16.64093602 4.603812248 2.872633887 1.008680946 1.222278405 0.48910076 0.064851145 0.251005456 3.420665142 0.015054935 0.106888791 40161.71481 -4.603812248 0.213597459 NRLENDGATALAEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NRLENDGATALAEAFR 16 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 265.37 3.97E-27 815020000 692702 526296 600942 649619 608677 610128 802320 680679 685202 FALSE TRUE 659959.3493 579926.1607 628495.7851 584318.0639 714830.0761 588999.1144 679911.3484 621075.1383 791459.6266 0.833850934 0.732729935 0.794097088 0.738279053 0.903179457 0.744193506 0.859060052 0.784721188 1 19.59415623 -4.999999921 0.238583533 2.157734916 0.776589823 0.573274709 0.054646157 110.3923779 1.101296431 61.86104675 0.076173473 1.00E-05 4.999999921 -1.381145093 NRNEQESAVHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NRNEQESAVHPR 12 1 Q9UJU6-2;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;;;;;;; 173.19 2.03E-05 1332778300 1170143.2 862628.9 1045225.6 1155523.8 1009439.2 1049528.8 1306609.4 1212691.3 1061770.2 FALSE TRUE 1114832.85 950531.7656 1093150.228 1039368.352 1185485.077 1013183.354 1107262.139 1106501.621 1226424.1 0.90901088 0.775043287 0.891331333 0.847478741 0.966619196 0.826128054 0.902837883 0.902217774 1 20.22602652 -1.177981624 0.220798102 1.105013382 0.838997567 0.385473321 0.050761885 18.23201503 0.84942111 1.223964044 0.107102016 0.066377116 1.177981624 -0.266015815 NRPDYVS(ph)EEEEDDEDFETAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NRPDYVSEEEEDDEDFETAVK 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NRPDYVS(1)EEEEDDEDFETAVK 285.77 1.31E-45 182580000 159880 140260 138350 158380 90456 172500 178000 183580 113280 TRUE FALSE 152322.7893 154552.6535 144693.4843 142459.3415 106231.4978 166526.2817 150842.8308 167504.762 130846.8838 1.164130049 1.181171832 1.105822929 1.088748446 0.811876406 1.272680532 1.152819436 1.280158587 1 16.99752004 -0.219079279 7.460490618 1.000010764 1.134486595 0.09318639 0.129401679 0 0 0.119493049 0.028164782 0.60383839 0.219079279 0.134475831 NRPEDYQGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NRPEDYQGGR 10 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;;;; 212.82 3.07E-08 8028224000 4139274 3292776 3425216 3961766 3091181 3544373 4119811 3662332 3184731 FALSE TRUE 3943618.721 3628313.618 3582265.542 3563521.755 3630281.988 3421630.474 3491258.166 3341638.795 3678602.818 1.072042543 0.986329266 0.973811449 0.968716094 0.986864352 0.930144037 0.949071791 0.908398911 1 21.81072649 5.873334783 0.504693006 0.947318105 1.41955683 0.658704715 0.025740607 6.351338737 0.514585562 0.012661634 2.27652727 747024.3924 -5.873334783 0.472238726 NRPLLDFVSMEELNDMDDYDS(ph)EDDNDWRPTVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVK 33 2 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 NRPLLDFVSMEELNDMDDY(0.326)DS(0.674)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDY(0.01)DS(0.99)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK 245.47 3.41E-47 341565000 155115 122536 107191 153006 105394 125031 171667 172345 123772 TRUE FALSE 147783.0214 135022.5577 112105.8134 137625.5462 123774.6802 120701.1451 145476.0463 157253.5581 142965.9296 1.033693984 0.944438707 0.784143563 0.962645761 0.865763476 0.844265102 1.017557446 1.099937297 1 17.12531185 1.575539567 5.832686124 1.052297595 0.916249341 0.430032571 0.072292645 0.142206863 10.04743457 0.041493127 0.019213503 37.63046344 -1.575539567 -0.136048253 NRPLSDEELDAMFPEGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRPLSDEELDAMFPEGYK 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 93.776 0.0019029 354950000 440680 357740 381580 455880 272280 455970 432380 457190 277110 FALSE TRUE 419849.9297 394194.1127 399075.8204 410054.0763 319765.5458 440179.6446 366412.4898 417156.0199 320082.8035 1.311691616 1.231537928 1.246789318 1.281087493 0.999008826 1.37520554 1.144742816 1.303275325 1 18.28808564 -4.63039139 0.227669727 7.82E-13 1.262766143 0.328658413 0.10438675 146.6380386 1.712408447 67.76685104 0.163171574 2.34E-05 4.63039139 1.262766143 NRPT(ph)SISWDGLDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.879)S(0.119)IS(0.002)WDGLDSGK;NRPT(0.891)S(0.109)ISWDGLDSGK 190.67 3.35E-07 577074000 998640 517510 678730 842320 508460 796580 996510 857910 526890 TRUE FALSE 951436.2663 570244.8574 709850.4419 757648.3933 597135.263 768994.2349 844474.0973 782786.8523 608597.4102 1.563326183 0.936982064 1.166371118 1.244909 0.98116629 1.263551606 1.387574254 1.286214564 1 19.21512867 2.026527272 24.99508839 1.282136009 1.177994198 0 0.194552502 662.5209149 624251.7191 0.069903849 0.051626253 106.2985332 -2.026527272 -0.104141811 NRPTS(ph)ISWDGLDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.155)S(0.465)IS(0.379)WDGLDSGK;NRPT(0.241)S(0.715)IS(0.044)WDGLDSGK 175.91 2.93E-11 139320000 895180 475020 605700 764100 474670 707420 889100 764100 496590 TRUE FALSE 852866.6155 523425.0781 633471.9441 687291.2163 557452.2977 682921.868 753451.4656 697191.3533 573598.641 1.486870007 0.912528449 1.104381878 1.198209283 0.971850799 1.190591852 1.313551692 1.215468977 1 19.12968208 2.010853345 24.8560946 1.221402457 1.133245029 0 0.170754438 649.1556447 1486674.468 0.061896474 0.045675022 102.5305637 -2.010853345 -0.088157428 NRPTSISWDGLDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;;;; 203.9 4.72E-09 4874650000 11061750 4299270 7049400 9402470 6262970 8149880 11641490 9233190 6407710 FALSE TRUE 10538883 4737370.501 7372621.963 8457315.852 7355229.985 7867647.612 9865366.89 8424682.935 7401384.941 1.423906888 0.640065412 0.996113838 1.142666666 0.993764011 1.062996679 1.332908229 1.138257637 1 22.81936382 1.974468212 20.32134047 1.195022345 1.023045812 0.051265664 0.206431037 148.3161563 118045.7254 0.082362659 0.053555474 94.29055923 -1.974468212 -0.171976533 NRS(ph)AEEGELAESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.965)AEEGELAES(0.035)K;NRS(1)AEEGELAESK;NRS(0.999)AEEGELAES(0.001)K 239.13 5.12E-17 2349630000 3841050 3305460 3484380 3960550 2285930 3888790 4259600 4126490 2308180 TRUE FALSE 3659491.179 3642290.132 3644142.27 3562427.989 2684595.468 3754120.227 3609719.787 3765152.66 2666120.766 1.372590179 1.366138466 1.366833159 1.33618403 1.006929432 1.408083338 1.353922085 1.412221347 1 21.3463107 -2.019652945 2.968165362 0.62131583 1.331088297 0.438258206 0.116602717 20743490.38 22219929.71 53425716.35 0.027055167 0.00955756 2.019652945 0.709772468 NRS(ph)PADAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRSPADAGR 9 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NRS(1)PADAGR;NRS(1)PADAGR 74.76 0.024333 55113000 43696 27396 32864 36869 38843 35274 46157 33921 43663 TRUE FALSE 41630.57668 30187.68355 34370.84691 33162.85807 45617.2069 34052.45254 39114.90192 30950.69741 50434.03504 0.825446083 0.59855777 0.681501032 0.657549174 0.904492509 0.675187946 0.775565586 0.613686717 1 15.62211003 NRSAEEGELAES(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.058)AEEGELAES(0.942)K;NRS(0.002)AEEGELAES(0.998)K;NRS(0.016)AEEGELAES(0.984)K 223.03 4.33E-11 1186830000 2274520 1891280 2143380 2329230 1706470 2205690 2654200 2090600 1862230 TRUE FALSE 2167007.947 2084003.582 2241656.093 2095091.375 2004077.828 2129306.402 2249253.042 1907535.981 2151015.117 1.007435015 0.968846553 1.042138698 0.974001232 0.931689327 0.989907688 1.045670495 0.886807334 1 21.03658623 NRT(ph)PSDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.997)PS(0.003)DVK;NRT(1)PSDVK;NRT(0.998)PS(0.002)DVK 107.11 0.0076052 603800000 511050 379227 364740 481540 252853 477230 472240 455370 270137 TRUE FALSE 486893.6793 417870.6624 381463.6898 433134.6843 296950.4831 460703.4054 400191.1147 415495.3887 312028.4663 1.560414295 1.33920686 1.22252849 1.388125543 0.95167754 1.476478768 1.282546812 1.331594497 1 18.25131813 8 0.030311771 7.59E-10 3.209710327 0.328318146 0.155616546 1594.935158 3.707272814 124.5076429 304.9837658 100000000 -8 3.209710326 NRTPS(ph)DVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.002)PS(0.998)DVK 78.342 0.018698 101070000 127780 99950 110310 113920 130580 132200 122060 122310 120970 TRUE FALSE 121740.0926 110135.0186 115367.8226 102468.5452 153353.1107 127621.8809 103437.5052 111599.888 139729.4098 0.871256043 0.788202132 0.825651685 0.733335561 1.097500597 0.913350175 0.740270108 0.798685747 1 17.09227618 5.254302544 6.059615792 0.848473042 1.66338915 0 0.115845142 14016.49544 8967.673661 0.02664983 150757.1073 179598.4334 -5.254302544 0.814916108 NRTPSDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 140.11 0.00059716 679190000 1198850 825664 990840 1050780 690188 1145830 1286590 1217730 804190 FALSE TRUE 1142182.736 909800.1003 1036270.994 945153.598 810556.5687 1106149.62 1090297.066 1111099.106 928899.678 1.229608281 0.979438493 1.115589787 1.017498036 0.872598611 1.190817099 1.17375115 1.196145431 1 19.82516327 NRVPS(ph)AGDVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 1 NRVPS(1)AGDVEK;NRVPS(1)AGDVEK 128.71 0.00015758 465400000 824040 725030 765190 943270 510460 888170 951700 970180 628300 TRUE FALSE 785089.2623 798911.3813 800274.7184 848450.7075 599484.0624 857412.4502 806500.6858 885225.896 725733.5551 1.081787189 1.10083291 1.102711474 1.169093949 0.826038783 1.181442479 1.111290335 1.219767075 1 19.46908045 NS(ph)FTPLSSSNTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSFTPLSSSNTIR 13 0 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NS(0.993)FT(0.007)PLSSSNTIR;NS(0.967)FT(0.033)PLSSSNTIR;NS(0.991)FT(0.009)PLSSSNTIR;NS(0.721)FT(0.279)PLSSSNTIR 252.01 1.00E-23 433480000 879070 737070 742880 965610 680800 898460 1050490 895390 777840 TRUE FALSE 837518.1032 812178.271 776941.7828 868545.0483 799531.3045 867346.1049 890218.4569 816984.9048 898463.4545 0.932167134 0.903963614 0.864745003 0.966700475 0.889887397 0.965366037 0.990823224 0.909313451 1 19.7771003 2.217155583 20.37247426 0.968303859 0.912730142 0.373455875 0.035264204 28.9185731 27521.78879 0.012058887 0.00892642 164.8752938 -2.217155583 -0.055573717 NS(ph)IEVAGLSHGLEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSIEVAGLSHGLEGLR 16 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 NS(1)IEVAGLSHGLEGLR;NS(1)IEVAGLSHGLEGLR;NS(1)IEVAGLSHGLEGLR;NS(1)IEVAGLSHGLEGLR 146.39 7.27E-07 238766000 334026 293452 294001 360089 327819 310176 335774 330045 290989 TRUE FALSE 318237.253 323355.0924 307481.2367 323892.1696 384990.5298 299434.5273 284545.5094 301144.5101 336114.088 0.946813193 0.962039688 0.914812106 0.96363759 1.145416225 0.890871695 0.846574183 0.895959202 1 18.35859149 -0.886053997 4.781111751 1.000000214 0.943186834 0.043155991 0.079435504 2.33E-07 5.43E-08 0.078861296 0.018587698 0.130000793 0.886053997 -0.05681338 NS(ph)PEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 108.47 0.004438 702658000 939154 1212285 751076 1204293 405108 964653 792921 1075371 464865 TRUE FALSE 894762.0516 1335818.22 785513.5775 1083235.18 475758.7069 931246.8247 671946.3385 981205.8143 536953.89 1.666366644 2.487770821 1.46290695 2.017370951 0.886032704 1.734314328 1.251404173 1.827355817 1 19.03443868 3.183466636 1.709126771 1.393891551 2.036278341 0.275165726 0.405934043 0.385208979 2.325209188 0.121012055 0.164292384 1525.691181 -3.183466636 0.642386791 NS(ph)PEDLGLSLTGDSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;NS(0.998)PEDLGLS(0.002)LTGDSCK;NS(1)PEDLGLSLTGDSCK 404.17 9.14E-140 2881553000 3995034 3533497 3284339 4150828 1745532 3972752 3680072 3902625 1815697 TRUE FALSE 3806196.66 3893564.362 3434929.192 3733578.883 2049952.228 3835174.602 3118609.427 3560890.466 2097266.017 1.81483733 1.856495232 1.63781283 1.780212359 0.977440254 1.828654339 1.486988013 1.697872581 1 21.00007843 -1.862590768 0.099534513 3.38E-13 2.203028299 0.404391121 0.251622486 73.26007378 1.080076767 23.57104386 5.179165016 0.013721741 1.862590768 2.203028299 NS(ph)PGLGSLVSPHGPHMPPAASIPPPPGLGGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.325)PGLGS(0.325)LVS(0.325)PHGPHMPPAAS(0.024)IPPPPGLGGVK 78.311 0.002415 103900000 256780 220330 248430 278270 176210 264550 307500 288110 22325 TRUE FALSE 244642.5183 242781.8775 259820.7612 250297.7709 206940.9682 255388.5672 260585.2274 262881.561 25787.04698 9.487031163 9.414877077 10.07563066 9.706337105 8.02499675 9.903753903 10.10527602 10.1943259 1 14.65435895 -0.427722798 10.20799646 0.999968439 9.607810131 0.950091277 0.620459356 0 0 0.59183712 0.139497347 0.373488473 0.427722798 8.607841692 NS(ph)PGSQVASNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(0.993)PGS(0.007)QVASNPR;NS(0.994)PGS(0.006)QVASNPR;NS(1)PGSQVASNPR;NS(1)PGSQVASNPR;NS(1)PGSQVASNPR;NS(1)PGSQVASNPR 297.67 2.55E-36 2476063000 1478246 1448888 1458227 1644285 1111106 1492568 1504745 1440453 1179837 TRUE FALSE 1408372.241 1596531.334 1525088.15 1478998.348 1304882.535 1440879.996 1275168.514 1314319.299 1362800.096 1.033440081 1.171508088 1.11908427 1.085264341 0.957501058 1.057293729 0.935697405 0.964425599 1 20.37814252 2.841094194 4.321548504 0.981723175 1.110018984 0.626772099 0.045895688 0.142222546 4.531668891 0.013962717 0.014846282 693.5762193 -2.841094194 0.128295809 NS(ph)PPFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSPPFLK 7 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 NS(1)PPFLK;NS(1)PPFLK 68.657 0.064885 140458000 726700 741070 657540 816340 412580 738620 739440 765450 442910 TRUE FALSE 692350.3312 816585.8755 687688.8594 734279.9523 484533.8214 713041.4042 626624.8473 698423.1401 511594.2207 1.353319297 1.596159304 1.344207639 1.435278044 0.947105737 1.393763603 1.224847392 1.36518966 1 18.96464044 0.878562362 0.046652833 2.10E-11 2.420995236 0.339253302 0.158884771 73.30596415 2.063605597 56.5779326 48.95370085 7.560706194 -0.878562362 2.420995236 NS(ph)PQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPQALR 7 0 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALR;NS(1)PQALR;NS(1)PQALR 99.973 0.010631 457950000 1212960 1330690 1015700 1352340 922170 1057100 1100520 1136770 854620 TRUE FALSE 1155625.785 1466288.824 1062270.85 1216400.214 1082996.156 1020492.362 932615.4616 1037228.392 987150.1048 1.170668755 1.485375747 1.076098604 1.232234295 1.097093695 1.033776279 0.94475547 1.050730165 1 19.91290995 2.844087361 0.995580368 0.987048765 1.309148655 0.533847139 0.103905783 0.338489463 0.719300157 0.051669809 0.053363523 698.3728726 -2.844087361 0.32209989 NS(ph)PQALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPQALRR 8 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALRR;NS(1)PQALRR;NS(1)PQALRR 114.71 0.0015949 836450000 510090 423820 399833 515200 331611 441870 511170 445620 436450 TRUE FALSE 485979.0566 467007.7398 418165.7385 463411.1172 389443.8534 426567.9311 433181.6282 406599.1504 504132.4369 0.96399085 0.926359237 0.829475963 0.919224956 0.772503066 0.8461426 0.859261568 0.806532412 1 18.94344326 3.895197121 3.732282933 0.854226116 0.951788167 0.233744818 0.06273281 0.25337203 6.394114338 0.014395378 0.028116927 7855.921236 -3.895197121 0.097562051 NS(ph)PVT(ph)KTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.966)PVT(0.551)KT(0.477)PPRDLPT(0.006)IPGVTSPSSDEPPMEASQSHLR;NS(0.994)PVT(0.849)KT(0.156)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.995)PVT(0.502)KT(0.502)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.998)PVT(0.548)KT(0.451)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;NS(0.992)PVT(0.503)KT(0.503)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.998)PVT(0.541)KT(0.449)PPRDLPT(0.013)IPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.5)KT(0.5)PPRDLPTIPGVTSPSSDEPPMEASQSHLR 216.11 1.23E-38 2479396000 462976 306103 396153 457909 268467 502739 553546 557049 299183 TRUE FALSE 441092.042 337295.2437 414317.0069 411879.1173 315287.5598 485329.0224 469092.3911 508270.8365 345578.7716 1.276386394 0.976029986 1.198907575 1.191853063 0.912346434 1.404394778 1.357410899 1.47078142 1 18.39865507 2.213304525 24.99981886 1.342391912 1.115372354 0.255739343 0.162335366 250.7842123 248237.9118 0.054488189 0.040257761 163.4197437 -2.213304525 -0.227019558 NS(ph)PVTKT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPVTKTPPR 10 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(1)PVT(0.035)KT(0.965)PPR;NS(1)PVT(0.072)KT(0.928)PPR;NS(1)PVT(0.194)KT(0.806)PPR 137.46 0.00020787 1293520000 3791760 4039420 3037610 4663600 1571860 4209280 3449120 4012180 1515650 TRUE FALSE 3612531.019 4451041.49 3176887.423 4194806.068 1845991.886 4063511.578 2922893.397 3660852.249 1750689.261 2.063490706 2.542450902 1.814649518 2.396088307 1.054437202 2.321092422 1.669567216 2.091091966 1 20.7394916 -1.27232719 0.154637949 5.85E-13 2.490498218 0.36746261 0.417690655 29.44285986 0.863140018 14.73218933 2.275826993 0.053416178 1.27232719 2.490498218 NS(ph)PVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.995)PVT(0.211)KT(0.794)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.145)KT(0.854)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR 244.1 1.31E-48 945950000 495078 335290 460980 456089 278350 481801 622088 572539 276641 TRUE FALSE 471676.6441 369456.4322 482116.389 410242.0672 326894.1519 465116.1106 527177.0502 522404.4499 319541.0734 1.476106464 1.156209523 1.508777522 1.283847685 1.023011372 1.455575353 1.649794327 1.634858531 1 18.28564186 2.017983473 24.90431243 1.513484035 1.293162939 0.051994585 0.228220405 369.5240424 511731.154 0.077727566 0.057394668 104.2277766 -2.017983473 -0.220321095 NS(ph)PVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(0.444)PVT(0.322)KT(0.234)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.381)PVT(0.319)KT(0.267)PPRDLPT(0.034)IPGVTSPSSDEPPMEASQSHLR;NS(0.383)PVT(0.3)KT(0.3)PPRDLPT(0.017)IPGVTSPSSDEPPMEASQSHLR;NS(0.544)PVT(0.267)KT(0.188)PPRDLPTIPGVTSPSSDEPPMEASQSHLR 192.79 5.42E-24 2581770000 961370 467097 893310 803649 679379 863190 1289380 917450 677792 TRUE FALSE 915927.9454 514694.7153 934269.1471 722864.6757 797862.4825 833297.5139 1092661.4 837113.2143 782900.5217 1.169916126 0.657420325 1.19334337 0.923316125 1.019110935 1.064372153 1.39565803 1.069245953 1 19.57846948 1.97886915 8.176901312 1.206927341 0.97472758 0.121205243 0.179072079 0.294109717 96.12992187 0.068924589 0.045413017 95.25091351 -1.97886915 -0.232199761 NS(ph)QKHSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_SK-BR-3_Trastuzumab_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 2 NS(0.246)QKHS(0.246)PT(0.246)S(0.246)EPT(0.016)PPGDALPPVS(0.333)S(0.333)PHT(0.333)HR;NS(0.249)QKHS(0.249)PT(0.249)S(0.249)EPT(0.004)PPGDALPPVS(0.333)S(0.333)PHT(0.333)HR;NS(0.249)QKHS(0.249)PT(0.249)S(0.249)EPT(0.003)PPGDALPPVS(0.333)S(0.333)PHT(0.333)HR 66.793 0.0069324 485392000 339544 290823 346090 396607 243775 336391 411253 330453 48331 TRUE FALSE 323494.428 320458.1943 361958.5688 356739.3109 286289.2828 324741.6953 348508.8017 301516.7835 55825.92464 5.79469897 5.740311449 6.483700381 6.390208728 5.128249727 5.817041051 6.24277706 5.401017277 1 15.76864762 0.805392668 4.737331946 1.000027821 5.924635025 0.941453098 0.384312709 0.660044685 15.92098148 0.364485293 0.092323872 6.388408334 -0.805392668 4.924607205 NS(ph)QKHSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_SK-BR-3_Trastuzumab_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(0.252)QKHS(0.252)PT(0.246)S(0.246)EPT(0.003)PPGDALPPVS(0.288)S(0.288)PHT(0.425)HR 58.722 0.076144 400680000 234210 205210 226610 260290 160170 212920 295470 227170 23142 TRUE FALSE 223139.3575 226121.1323 237000.2926 234125.1547 188103.5973 205546.527 250390.6248 207277.7905 26730.74317 8.347667555 8.459216075 8.866206643 8.75864742 7.036975969 7.689517861 9.367140422 7.754284615 1 14.70621233 0.953981837 22.40871992 0.999999978 8.382863114 0.928760434 0.636207948 756.0437943 368159.0765 0.608565251 0.152141313 8.994599637 -0.953981837 7.382863135 NS(ph)QKHSPTSEPTPPGDALPPVSSPHTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.475)QKHS(0.475)PT(0.036)S(0.014)EPT(0.001)PPGDALPPVSSPHTHR;NS(0.525)QKHS(0.382)PT(0.077)S(0.016)EPTPPGDALPPVSSPHTHR;NS(0.24)QKHS(0.24)PT(0.24)S(0.24)EPT(0.039)PPGDALPPVSSPHTHR;NS(0.495)QKHS(0.495)PT(0.008)S(0.002)EPTPPGDALPPVSSPHTHR;NS(0.427)QKHS(0.427)PT(0.115)S(0.031)EPTPPGDALPPVSSPHTHR 123.35 2.19E-05 6307500000 2280360 1831316 2253350 2538420 1795720 2245978 3208210 2610183 87563 TRUE FALSE 2172571.902 2017929.182 2356668.326 2283253.199 2108892.999 2168199.219 2718738.642 2381621.539 101141.8228 21.48045033 19.95148126 23.30063134 22.57476813 20.85085023 21.43721715 26.8804592 23.54734641 1 16.62602016 -0.488803212 7.558986623 0.999850516 22.47133833 0.927086899 1.895125087 0 0 2.0783057 0.489861351 0.324486615 0.488803212 21.47148782 NS(ph)RFAQDFLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSRFAQDFLIR 11 1 A0A087WVD4;Q9HBK9-2;Q9HBK9 A0A087WVD4 AS3MT Arsenite methyltransferase 1 NS(1)RFAQDFLIR 60.255 0.057415 172560000 38674 34636 52326 42221 43060 47590 62598 40287 30569 TRUE FALSE 36845.95666 38165.44778 54725.19886 37976.86487 50569.65037 45941.94637 53047.52541 36759.25671 35309.4844 1.043514435 1.080883746 1.5498725 1.075542889 1.4321832 1.301121983 1.502359106 1.041059005 1 15.10776813 3.959023424 23.98581388 1.305445765 1.057527777 0.155333705 0.191731741 362.0477906 211926.3088 0.043532692 0.078484565 9099.623517 -3.959023424 -0.247917988 NS(ph)SEASSGDFLDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.991)S(0.009)EASSGDFLDLK;NS(0.773)S(0.225)EAS(0.002)SGDFLDLK;NS(0.792)S(0.208)EASSGDFLDLK 273.44 5.47E-33 147847000 342180 484549 293677 457394 163398 378444 303354 383274 156995 TRUE FALSE 326005.8295 533925.094 307142.3809 411415.8861 191894.5595 365338.3894 257071.7758 349712.4967 181340.9828 1.797750429 2.944315652 1.693728446 2.268741902 1.058197416 2.014648778 1.417615433 1.928480211 1 17.46834548 3.113240138 1.762775322 1.555676733 2.321872884 0.2952919 0.479706343 0.374572243 2.391494284 0.145673897 0.18681123 1297.896731 -3.113240138 0.766196151 NS(ph)TELAPPLPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSTELAPPLPVR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 NS(0.996)T(0.004)ELAPPLPVR;NS(0.98)T(0.02)ELAPPLPVR 124.62 0.00033542 113416000 225840 301520 191172 300800 172121 239030 192764 223940 144558 TRUE FALSE 215164.9908 332245.2308 199937.4253 270563.0125 202138.8479 230752.3312 163354.3114 204330.6264 166975.3163 1.288603582 1.989786503 1.197407076 1.620377302 1.210591196 1.381954748 0.978314131 1.223717558 1 17.34927532 2.412792284 0.838926225 1.047104054 1.596949108 0.383201619 0.234014592 0.539396795 0.751843945 0.159221907 0.108280248 258.6975314 -2.412792284 0.549845055 NS(ph)WDSPAFSNDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.998)WDS(0.002)PAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(0.998)WDS(0.002)PAFSNDVIR 335.67 1.41E-68 767600000 938865 963934 812074 1103201 686910 909469 1013783 964742 687223 TRUE FALSE 894486.7121 1062159.971 849308.3962 992305.1395 806706.8865 877973.8605 859111.7839 880264.0761 793794.033 1.126849882 1.338080064 1.069935476 1.25007886 1.01626726 1.106047443 1.082285515 1.108932594 1 19.59840519 2.741536904 24.98158575 1.072521299 1.205150461 0.413472875 0.078224678 247.8472949 2080321.677 0.022613514 0.02307169 551.4890624 -2.741536904 0.132629162 NSASAT(ph)TPLSGNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASAT(0.562)T(0.242)PLS(0.179)GNS(0.008)S(0.008)R 88.507 0.075551 48377000 96363 79042 93152 96081 79799 90840 106620 93666 115120 TRUE FALSE 91808.11196 87096.46966 97423.11134 86422.75534 93715.92033 87694.18802 90353.16079 85464.10849 132972.2216 0.690430759 0.654997477 0.732657619 0.649930897 0.70477818 0.659492539 0.679488992 0.642721521 1 17.02076537 -1.055130966 4.588131089 1.000014938 0.676796552 0.932187226 0.027394385 3.60E-06 7.41E-07 0.022797213 0.005373107 0.088078322 1.055130966 -0.323218386 NSASATTPLS(ph)GNSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASAT(0.002)T(0.055)PLS(0.943)GNSSR;NSASATT(0.016)PLS(0.981)GNS(0.001)S(0.002)R;NSASATT(0.012)PLS(0.987)GNSSR 168.42 1.32E-06 480493000 461470 369079 432500 456710 378028 420720 519470 432080 455670 TRUE FALSE 439657.2276 406688.5697 452330.5528 410800.6431 443955.9635 406150.3609 440215.3108 394244.7846 526332.9764 0.835321455 0.77268305 0.859399987 0.780495735 0.843488786 0.771660487 0.836381778 0.749040631 1 19.00561626 -1.077064635 4.401338533 1.000016693 0.807387152 0.731963801 0.03687503 4195987.535 1026812.569 673.4305942 0.007251115 0.083740464 1.077064635 -0.192629541 NSASATTPLSGNS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASATTPLS(0.002)GNS(0.643)S(0.355)R;NSASATTPLS(0.034)GNS(0.607)S(0.359)R;NSASATT(0.004)PLS(0.14)GNS(0.428)S(0.428)R 112.16 0.00082414 441751000 1126030 906760 1028530 1100840 776190 1130750 1324850 1193470 1001170 TRUE FALSE 1072804.793 999159.8749 1075689.118 990181.4717 911557.2902 1091591.844 1122719.8 1088963.44 1156426.33 0.927689698 0.864006508 0.930183869 0.856242586 0.788253662 0.943935481 0.970852851 0.941662613 1 20.14124193 2.019864505 24.99133067 0.965048501 0.877714295 0.543264844 0.041773113 189.7941206 238777.0912 0.015335516 0.01132468 104.6801906 -2.019864505 -0.087334207 NSASATTPLSGNSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASATTPLS(0.04)GNS(0.289)S(0.67)R 82.149 0.012469 253400000 420490 372210 383630 434430 300890 416040 462400 476380 360460 TRUE FALSE 400614.271 410138.6222 401219.815 390760.271 353365.1207 401632.4305 391852.3874 434665.6418 416358.2958 0.962186355 0.985061728 0.963640737 0.938519239 0.848704407 0.964631747 0.94114226 1.043970172 1 18.66746604 1.246190503 24.99960834 1.021985092 0.946898203 0.422751001 0.038001498 160.1554962 524767.5052 0.027198538 0.00951317 17.62749106 -1.246190503 -0.07508689 NSATCHS(ph)EDS(ph)DLEID ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 2 NSATCHS(1)EDS(1)DLEID;NSAT(0.014)CHS(0.987)EDS(1)DLEID 152.94 4.01E-06 421470000 595270 472310 550390 597850 497260 552010 654600 568100 452970 TRUE FALSE 567132.7668 520438.926 575625.9259 537752.9822 583981.9866 532893.7553 554728.7474 518354.1523 523214.2741 1.083939783 0.99469558 1.100172442 1.027787292 1.116143071 1.018500033 1.060232442 0.99071103 1 18.99704237 1.23743939 24.99952354 0.995355486 1.05370562 0.320991091 0.037194424 34.4778166 768569.957 0.0264952 0.008047158 17.27584862 -1.23743939 0.058350134 NSATCHSEDS(ph)DLEID ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 1 NSATCHS(0.019)EDS(0.981)DLEID;NSATCHS(0.066)EDS(0.934)DLEID;NSATCHS(0.008)EDS(0.992)DLEID 197.73 8.69E-09 1390750000 1603230 1270160 1503220 1656300 1329470 1434080 1782860 1509260 1211570 TRUE FALSE 1527448.495 1399590.748 1572144.124 1489805.577 1561329.147 1384417.45 1510851.963 1377101.193 1399454.088 1.091460241 1.000097653 1.123398143 1.064561953 1.115670146 0.989255355 1.07960095 0.984027419 1 20.41643273 1.233725809 24.99958166 0.992013669 1.061945672 0.330871171 0.043574985 148.3367946 766967.1581 0.03414823 0.009608286 17.12875547 -1.233725809 0.069932003 NSATFKS(ph)FEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 NSATFKSFEDR 11 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6 O43399 TPD52L2 Tumor protein D54 1 NSAT(0.003)FKS(0.997)FEDR;NS(0.012)AT(0.266)FKS(0.722)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSAT(0.001)FKS(0.999)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NS(0.002)AT(0.201)FKS(0.797)FEDR;NSAT(0.004)FKS(0.996)FEDR 179.79 4.21E-06 38604620000 37212890 22482340 32072850 42902200 26529040 47053830 50272520 32884620 22929690 TRUE FALSE 35453910.44 24773316.01 33543421.9 38589589.35 31155696.18 45424344.07 42602523.76 30005068.34 26485509.22 1.338615397 0.935353585 1.266482046 1.457007643 1.176329891 1.715064026 1.608521981 1.132886217 1 24.65869991 3.462827523 5.757422569 1.408392352 1.13061764 0.081614651 0.239128705 0.24022019 27.36440482 0.063449249 0.089595322 2902.869572 -3.462827523 -0.277774713 NSATFKS(ph)FEDRVGTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSATFKSFEDRVGTIK 16 2 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6 O43399 TPD52L2 Tumor protein D54 1 NSAT(0.008)FKS(0.992)FEDRVGTIK;NSAT(0.005)FKS(0.995)FEDRVGTIK;NS(0.002)AT(0.075)FKS(0.923)FEDRVGTIK 208.72 7.37E-12 1522110000 1986860 416444 2142790 1410207 2115090 2408700 4855720 2071320 2469050 TRUE FALSE 1892945.065 458880.1171 2241039.041 1268450.313 2483961.026 2325286.115 4114890.733 1889944.24 2851937.664 0.663739986 0.160901174 0.78579524 0.444767896 0.870973113 0.815335533 1.442840348 0.66268778 1 21.44351102 2.526536047 1.550228687 1.076048879 0.468772536 0.415568817 0.256975587 0.296144788 1.43986858 0.110175268 0.088244571 336.1522686 -2.526536047 -0.607276343 NSDDAPWS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 108.17 0.0022939 84237000 208630 197100 177120 218550 122690 219360 230290 222570 130560 TRUE FALSE 198768.4734 217184.7141 185241.1272 196580.9388 144087.0972 211763.5082 195155.0309 203080.5909 150806.578 1.318035831 1.440154116 1.228335857 1.303530266 0.955443052 1.404206043 1.294075056 1.346629528 1 17.20233983 -2.251980432 2.097809888 0.000158965 1.296015823 0.315887628 0.131722875 1432914.698 231854.8829 6796496.617 0.031136632 0.005597828 2.251980432 1.295856858 NSDLLTS(ph)PDVGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NSDLLTSPDVGLLK 14 0 P05412 P05412 JUN Transcription factor AP-1 1 NSDLLT(0.24)S(0.76)PDVGLLK;NSDLLT(0.01)S(0.99)PDVGLLK;NSDLLT(0.023)S(0.977)PDVGLLK;NSDLLT(0.065)S(0.935)PDVGLLK;NSDLLT(0.09)S(0.91)PDVGLLK 287.03 6.99E-34 1035725000 3899000 2959690 3065380 3934450 2291320 3673620 4036950 3760320 2319990 TRUE FALSE 3714701.997 3261285.776 3205930.705 3538951.611 2690925.483 3546401.618 3421039.134 3431046.446 2679762.2 1.386205834 1.217005664 1.196348954 1.320621513 1.004165773 1.323401613 1.276620416 1.280354819 1 21.35367355 -1.768476705 2.68777876 0.9394486 1.253760893 0.36967779 0.102759931 50549698.05 38720606.48 20193041.18 0.023103929 0.017042107 1.768476705 0.314312293 NSDLLTVLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSDLLTVLSR 10 0 A0A2R8YCY2;A0A0C4DFX2;A0A286YFA9;A0A2R8Y5V8;Q5TBA9 A0A2R8YCY2 FRY Protein furry homolog 1 NSDLLTVLS(1)R 92.856 0.0096316 20612000 43233 41929 41135 49728 39718 45788 49138 47809 40048 TRUE FALSE 41189.46177 46201.61277 43021.08044 44729.24696 46644.80662 44202.35008 41641.09562 43622.59051 46258.4393 0.890420481 0.998771542 0.930015822 0.966942414 1.008352364 0.955552127 0.900183756 0.943019072 1 15.49742897 3.522280724 0.003677084 1.895474251 2.25E-07 0.093668645 0.03870107 122096.9542 111.1033878 28161.42144 29112.19625 3328.74651 -3.522280724 -1.895474025 NSEGWEQNGLYEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSEGWEQNGLYEFFR 15 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 169.17 2.82E-06 71405000 273360 354130 260548 402300 197114 327390 312950 353190 211560 FALSE TRUE 260438.8145 390216.2496 272494.3835 361860.0397 231490.6192 316052.4022 265203.7298 322262.8112 244367.6443 1.065766359 1.596840902 1.115100096 1.480801768 0.947304705 1.293347993 1.08526532 1.318762196 1 17.89869375 2.746155186 24.99833077 1.143734773 1.322926818 0.188035773 0.19001718 960.3228602 3161004.505 0.052707939 0.054933213 557.384883 -2.746155186 0.179192045 NSGTEHWWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSGTEHWWK 9 0 Q96P70 Q96P70 IPO9 Importin-9 0 91.867 0.010463 121250000 629370 620130 575220 728690 433090 655240 745030 727060 429040 FALSE TRUE 599620.9274 683321.952 601594.406 655440.6968 508620.7589 632548.8745 631361.9901 663394.772 495573.332 1.209953984 1.378851338 1.213936197 1.322590734 1.026327944 1.276398131 1.274003158 1.338640983 1 18.91873903 -1.196454999 3.644007076 0.99970259 1.259473038 0.407477402 0.096541611 11236044.7 21988097.63 40856.43731 0.021807411 0.063612872 1.196454999 0.259770448 NSGVPDDIFKLDDLSVLDLSHNQLTECPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSGVPDDIFKLDDLSVLDLSHNQLTECPR 29 1 Q13045-3;Q13045;Q13045-2;J3KS54;K7EP37;K7EP27 Q13045-3 FLII Protein flightless-1 homolog 0 217.67 1.47E-34 48012000 83548 62503 73195 77080 47892 83357 91140 78805 53547 FALSE TRUE 79598.85162 68872.12676 76551.06315 69331.77196 56244.34964 80470.32619 77234.9191 71904.41643 61850.79528 1.286949525 1.113520472 1.237673061 1.120951988 0.909355318 1.301039475 1.248729604 1.162546352 1 15.91650453 4.646081225 3.068096544 1.154008127 1.295244665 0.123909784 0.117420613 0.700062923 10.60910735 0.02814698 0.212372644 44267.1156 -4.646081225 0.141236537 NSHLINVLMWELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSHLINVLMWELEK 14 0 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 138.57 1.46E-05 54116000 162800 170610 151780 202760 89925 180420 169430 159920 59822 FALSE TRUE 155104.7666 187995.353 158739.2631 182378.1796 105607.8915 174172.0102 143580.3417 145916.557 69098.89023 2.244678114 2.720671089 2.297276593 2.639379286 1.528358721 2.5206195 2.077896493 2.11170623 1 16.07637492 -1.34538515 0.253451464 2.56E-15 2.523826588 0.62797668 0.317837879 11.86481675 0.606703311 8.35720078 0.45758225 0.04514554 1.34538515 2.523826588 NSILQGSVHTGFSLLVQGHVEELWGLATHPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSILQGSVHTGFSLLVQGHVEELWGLATHPSR 32 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 73.975 0.00088211 3052300 1175.8 1131.7 1536 1906.4 1882.4 1839 2585.3 1517.6 924.93 FALSE TRUE 1120.222264 1247.021517 1606.427119 1714.76505 2210.689964 1775.314969 2190.865003 1384.710899 1068.363421 1.048540452 1.167225958 1.503633584 1.605039088 2.069230303 1.661714483 2.050673919 1.296104745 1 10.06118677 3.620149063 1.868088251 1.717629919 1.076312561 0.259701982 0.323149128 0.31422803 2.155221224 0.086432212 0.163981905 4170.124901 -3.620149063 -0.641317359 NSKYEYDPDIS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR 146.78 4.97E-06 1237080000 2888410 2055480 2712570 2737200 1978710 2805930 3435070 3071050 2378710 TRUE FALSE 2751880.584 2264935.749 2836944.018 2462051.456 2323796.398 2708759.941 2910986.982 2802132.581 2747588.198 1.001562238 0.824335958 1.032521547 0.896077315 0.845758618 0.98586824 1.059469896 1.019851732 1 21.38973436 2.00793104 22.83361709 1.030453519 0.918213499 0.373775089 0.063637707 59.05378041 170014.747 0.022448369 0.016536188 101.8429662 -2.00793104 -0.11224002 NSLDASRPAGLS(ph)PTLTPGER ddPTM_SK-BR-3_Trastuzumab_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 NSLDAS(0.003)RPAGLS(0.935)PT(0.062)LTPGER;NSLDAS(0.051)RPAGLS(0.764)PT(0.179)LT(0.006)PGER 102.46 0.00018145 275650000 316450 276790 290230 337910 250460 298050 320390 333640 289210 TRUE FALSE 301492.0356 304995.2157 303537.3326 303942.6448 294140.1447 287728.4538 271508.6211 304424.7129 334059.2097 0.902510773 0.912997477 0.908633331 0.909846626 0.880503025 0.861309748 0.812755982 0.911289688 1 18.34974431 2.663307319 4.034451177 0.872648446 0.908683145 0 0.048874891 0.511690901 15.99363194 0.014959994 0.014202346 460.5823792 -2.663307319 0.036034699 NSLESYAFNMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 209.85 3.43E-08 290220000 610340 509830 479330 635420 497110 551410 716610 590750 553770 FALSE TRUE 581490.4378 561782.2566 501307.7546 571546.3744 583805.8266 532314.5334 607277.9831 539020.7982 639645.8233 0.909081896 0.878270812 0.783727082 0.893535694 0.912701694 0.832202 0.949397246 0.842686341 1 19.28691377 -1.841197863 0.362836806 1.110781057 0.872949122 0.401373205 0.047220165 34.94796292 2.13164956 3.355532706 0.032959591 0.014414585 1.841197863 -0.237831936 NSLFTGDTLGAGQFSFQRPLLVLVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSLFTGDTLGAGQFSFQRPLLVLVDR 26 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3;H0YJY1 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 224.53 1.83E-34 84654000 77526 55369 66106 71786 66845 69248 81665 75505 72734 FALSE TRUE 73861.49962 61011.16405 69137.02549 64569.9349 78502.74684 66849.9244 69205.50437 68893.38192 84013.21725 0.879165232 0.726209114 0.822930341 0.768568768 0.934409482 0.79570723 0.823745437 0.820030278 1 16.3583287 -5 0.303635186 2.558900716 0.807875648 0.494099179 0.056604822 223.075078 2.047424522 221.6849485 0.051169965 1.00E-05 5 -1.751025068 NSLLAGGDDDTMSVIS(ph)GIS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 2 NSLLAGGDDDTMSVIS(0.996)GIS(0.547)S(0.457)R;NSLLAGGDDDTMSVIS(0.993)GIS(0.547)S(0.46)R 115.88 0.00020943 92674000 353170 293720 317130 324510 257420 338610 374900 345600 310050 TRUE FALSE 336476.354 323650.4019 331670.7242 291889.6383 302313.9665 326883.8508 317702.1195 315337.4319 358130.9705 0.939534365 0.903720785 0.926115727 0.815036013 0.844143599 0.912749462 0.887111548 0.880508691 1 18.45012776 -1.010041427 7.103718452 1.00000001 0.891366391 0.470762629 0.037013284 6.25E-09 8.50E-10 0.036826337 0.00868005 0.097714401 1.010041427 -0.108633619 NSLLAGGDDDTMSVIS(ph)GISSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.955)GIS(0.022)S(0.022)R 193.02 9.19E-18 57608000 42679 35052 37060 44046 32328 35476 40293 41972 36586 TRUE FALSE 40661.64825 38623.83865 38759.23766 39618.4124 37965.99296 34247.45722 34145.56282 38296.70917 42259.57002 0.962187931 0.913966674 0.917170658 0.93750155 0.898399888 0.810407139 0.807995983 0.906225718 1 15.36699047 2.464770669 7.040632711 0.85656428 0.930738254 0.091940547 0.056798419 0.181800494 45.80119186 0.017990803 0.015409848 291.5886863 -2.464770669 0.074173973 NSLLAGGDDDTMSVISGISS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.009)GIS(0.176)S(0.815)R 118.32 8.96E-05 18767000 16145 20847 20211 19758 16695 19051 19400 18371 22340 TRUE FALSE 15381.85785 22971.333 21137.69434 17771.8883 19606.60271 18391.25909 16440.17369 16762.33785 25804.3731 0.596095002 0.890210853 0.819151632 0.688716142 0.759817053 0.712718694 0.637108045 0.649592911 1 14.65532796 -1.037918754 4.644316507 1.000009402 0.72368296 0.504251874 0.087405575 11815897.63 2640634.079 1132.939436 0.020990528 0.091639191 1.037918754 -0.276326442 NSLTSKDPDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSLTSKDPDIK 11 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ; 88.552 0.011759 449230000 793790 669700 730400 847250 403940 824940 954770 935600 441860 FALSE TRUE 756269.1198 737943.1914 763889.5625 762082.8203 474387.0081 796372.121 809102.3009 853673.9041 510381.3921 1.481772517 1.445866175 1.496703395 1.493163411 0.929475517 1.560347092 1.585289577 1.672619569 1 18.96121621 NSMFHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 58.917 0.080913 7651100 11195 6904.5 5388.7 10294 12513 8348.1 13615 9181.5 11776 FALSE TRUE 10665.83454 7608.0764 5635.777225 9259.227563 14695.26324 8059.003204 11537.78169 8377.519186 13602.16194 0.78412789 0.559328468 0.41432952 0.680717345 1.080362321 0.592479581 0.848231461 0.615896151 1 13.73154835 2.991727462 24.94577261 0.809064314 0.600915348 0.292175996 0.171893562 516.8397288 1558532.76 0.047389987 0.054185915 981.1320478 -2.991727462 -0.208148967 NSMPTVSFLDQDQS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSMPTVSFLDQDQSPPR 17 0 A7KAX9;A7KAX9-2 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 NSMPTVSFLDQDQS(1)PPR 149 3.58E-07 50806000 44014 44581 39788 53143 27685 38571 45858 47671 30793 TRUE FALSE 41933.54545 49123.85458 41612.31916 47800.96467 32513.25523 37235.2766 38861.51986 43496.67452 35568.22117 1.178960996 1.381116428 1.169929723 1.343923398 0.914109679 1.046869238 1.092591043 1.222908346 1 15.1183012 2.751944325 24.96378036 1.06284535 1.271832927 0.530808865 0.099432528 589.2639237 1099115.571 0.028710948 0.03030146 564.8645568 -2.751944325 0.208987578 NSNILEDLETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSNILEDLETLR 12 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 160.52 0.0001578 103910000 235444 198102 200050 246563 173777 213005 243035 220489 177458 FALSE TRUE 224315.0287 218288.819 209222.4904 221778.0188 204083.6538 205628.5834 205955.5471 201181.8143 204977.2803 1.094340936 1.064941533 1.020710637 1.081963906 0.995640363 1.003177441 1.004772562 0.981483479 1 17.64510448 3.418523467 0.49910191 0.988036369 1.105914748 0.706598096 0.021270989 0.694793047 0.314225234 0.015557753 0.042020044 2621.340681 -3.418523467 0.11787838 NSNLVGAAHEELQQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 303.07 4.40E-46 15922050000 8418610 6330640 7087890 8099710 6058150 7396810 8714500 7744610 5639253 FALSE TRUE 8020678.989 6975739.413 7412876.767 7285511.762 7114689.442 7140656.615 7384942.972 7066450.892 6513759.554 1.231344038 1.070923689 1.138033528 1.118480303 1.092255461 1.096241971 1.133745099 1.084849822 1 22.63505904 -2.583536302 0.017895438 1.07E-08 2.01512483 0.595437369 0.037236065 1935.491426 4.151294435 276.4733772 196.5832349 0.002608938 2.583536302 2.015124819 NSNPVIAELSQAINSGTLLSKPS(ph)PPLPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 NSNPVIAELSQAINSGTLLS(0.003)KPS(0.997)PPLPPKR 104.35 0.00018087 115630000 158350 151430 146990 174440 100320 173060 189400 163630 84900 TRUE FALSE 150865.1093 166860.8892 153729.6369 156904.9598 117815.7762 167066.8888 160503.5514 149301.6897 98065.85839 1.538406045 1.701518672 1.567616288 1.599995782 1.201394432 1.703619298 1.636691445 1.522463497 1 16.58146333 0.946921026 18.71165364 0.999999998 1.575521328 0.609896792 0.140647776 343.1713018 120977.631 0.129506643 0.032376583 8.849546713 -0.946921026 0.57552133 NSNS(ph)PPS(ph)PSSMNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 NSNS(1)PPS(0.976)PS(0.019)S(0.005)MNQR;NSNS(1)PPS(0.799)PS(0.174)S(0.027)MNQR;NS(0.02)NS(0.98)PPS(0.984)PS(0.013)S(0.003)MNQR;NS(0.007)NS(0.993)PPS(0.998)PS(0.001)SMNQR 182.09 1.41E-07 145722000 331586 258996 285900 313976 242416 313176 345212 305338 297328 TRUE FALSE 315912.5869 285387.9869 299008.7978 282414.536 284693.2736 302330.6366 292543.5691 278600.986 343436.1077 0.919858395 0.830978399 0.870638792 0.822320454 0.828955568 0.880311155 0.851813664 0.811216351 1 18.3896822 -1.657751793 6.995654361 1.000587992 0.854245723 0.676011613 0.03216414 0.000282205 1.38E-05 0.029795454 0.006995264 0.021991163 1.657751793 -0.146342269 NSNSPPS(ph)PSSMNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(0.99)PS(0.01)SMNQR;NSNSPPS(1)PSSMNQR;NSNS(0.002)PPS(0.978)PS(0.017)S(0.002)MNQR;NSNS(0.001)PPS(0.997)PS(0.002)SMNQR;NSNSPPS(0.998)PS(0.002)SMNQR;NSNS(0.008)PPS(0.902)PS(0.074)S(0.016)MNQR;NS(0.001)NS(0.136)PPS(0.836)PS(0.023)S(0.004)MNQR;NSNSPPS(0.999)PS(0.001)SMNQR;NSNSPPS(0.993)PS(0.007)SMNQR 379.68 1.03E-97 2019201000 1812372 1564042 1656942 1836860 1290743 1700071 1893895 1761850 1450850 TRUE FALSE 1726704.767 1723419.658 1732914.43 1652215.343 1515848.171 1641197.115 1604946.534 1607573.074 1675840.408 1.030351553 1.028391277 1.034056955 0.985902557 0.904530147 0.979327809 0.957696524 0.959263821 1 20.67645334 3.090056358 4.299297917 0.958013626 1.0299718 0.641892503 0.023989917 0.11586871 3.944684015 0.006406345 0.007726435 1230.428431 -3.090056358 0.071958174 NSPEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 ;; 91.9 0.025758 471591000 740946 561257 578177 718272 404189 655980 797054 705442 478867 FALSE TRUE 705922.951 618449.7264 604686.9873 646069.9339 474679.4336 633263.2481 675448.7734 643669.7587 553127.2486 1.276239695 1.118096655 1.093214968 1.16803129 0.858174018 1.144878054 1.22114536 1.163692008 1 19.07725189 4.520265128 1.84268638 1.104811373 1.294913942 0.230668764 0.102539488 0.838051643 4.104106117 0.026983708 0.238279739 33133.33323 -4.520265128 0.190102569 NSPGLGS(ph)LVSPHGPHMPPAASIPPPPGLGGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.283)PGLGS(0.356)LVS(0.356)PHGPHMPPAAS(0.004)IPPPPGLGGVK 128.08 1.83E-07 103790000 202990 168210 187850 227650 136290 202590 245800 225520 11767 TRUE FALSE 193395.065 185350.7902 196463.1083 204766.1895 160058.9328 195574.2575 208298.6956 205772.2732 13591.76626 14.22883982 13.63699071 14.4545679 15.06545842 11.77616873 14.38917163 15.32535886 15.13947998 1 13.73044533 -1.344748051 7.852661942 0.999905382 14.23916971 0.94450915 1.009461657 0.001648943 0.000137593 0.962877725 0.226951503 0.045211816 1.344748051 13.23926433 NSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 43 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 NS(0.027)PMAQT(0.973)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 143.61 8.87E-14 101420000 312670 270480 287790 325590 192330 319580 376830 390480 183750 TRUE FALSE 297890.7088 298042.2195 300985.4562 292861.0746 225872.2911 308512.8645 319337.6625 356287.5011 212245.0115 1.403522781 1.404236629 1.418103794 1.379825479 1.064205417 1.453569449 1.504570874 1.678661367 1 17.69537112 2.056328333 24.99997831 1.457633722 1.347714411 0.006369959 0.198090163 232.508739 103192.0381 0.067704008 0.050002719 113.8487674 -2.056328333 -0.109919311 NSPTFKS(ph)FEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 NSPTFKSFEEK 11 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPT(0.014)FKS(0.986)FEEK;NSPT(0.002)FKS(0.998)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPT(0.008)FKS(0.992)FEEK 214.82 8.04E-12 17637780000 15444400 10754270 11402890 22336620 7382180 22562830 18879540 12926110 5390957 TRUE FALSE 14714373.82 11850142.34 11925723.79 20091300.52 8669629.855 21781473.54 15999119.43 11794231.28 6226959.078 2.363011164 1.903038416 1.915176194 3.226502739 1.392273459 3.497931055 2.569331069 1.894059546 1 22.57009637 NSPTFKS(ph)FEEKVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPTFKSFEEKVENLK 16 2 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEKVENLK;NS(0.001)PT(0.007)FKS(0.992)FEEKVENLK;NS(0.039)PT(0.131)FKS(0.83)FEEKVENLK 157.97 1.21E-08 4635646000 384579 189012 445229 483695 216276 576704 577242 355935 176714 TRUE FALSE 366400.7128 208272.5377 465643.19 435073.0596 253994.4659 556732.5959 489173.1311 324767.4445 204117.9046 1.795044455 1.020354085 2.28124618 2.131479159 1.244351721 2.727504954 2.396522403 1.591077692 1 17.63904321 2.255832069 24.99986851 2.107169874 1.658241194 0 0.593457577 518.1028435 749935.6041 0.197711223 0.165049328 180.2320693 -2.255832069 -0.44892868 NSPTFKS(ph)FEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NSPTFKSFEER 11 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 NSPTFKS(1)FEER;NSPTFKS(1)FEER;NSPTFKS(1)FEER;NS(0.019)PT(0.134)FKS(0.847)FEER;NSPT(0.001)FKS(0.999)FEER;NSPT(0.003)FKS(0.997)FEER;NSPTFKS(1)FEER 188.19 1.97E-06 2161331000 4240090 2657330 3301760 5788500 3493200 5620920 6011370 3534700 2669020 TRUE FALSE 4039669.349 2928114.948 3453148.962 5206628.983 4102412.974 5426266.131 5094225.1 3225182.929 3082917.99 1.310339542 0.949786844 1.120091087 1.688863927 1.330691568 1.760107193 1.652403702 1.046146196 1 21.55586508 3.263073989 24.05441462 1.478931737 1.115049046 0.172953737 0.270257738 178.1537637 174816.3272 0.069416824 0.093937439 1832.626611 -3.263073989 -0.363882691 NSPVTKT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPVTKTPPR 10 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(0.004)PVT(0.11)KT(0.887)PPR;NSPVTKT(1)PPR;NS(0.008)PVT(0.083)KT(0.909)PPR 99.941 0.0070359 1198280000 1248010 1050010 1136410 1319730 601640 1202070 1175530 1208760 561970 TRUE FALSE 1189019.041 1157007.213 1188515.523 1187068.233 706565.8255 1160442.014 996181.3084 1102914.566 649117.4375 1.831747188 1.782431261 1.830971491 1.828741865 1.088502303 1.787722756 1.534670386 1.699098657 1 19.30811999 -2.387076092 0.14791132 6.75E-14 1.968783152 0.511211556 0.216567111 41.9189223 0.78850255 15.69408164 1.252100637 0.004101322 2.387076092 1.968783152 NSPVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(0.004)PVT(0.058)KT(0.935)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;NS(0.166)PVT(0.166)KT(0.668)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.176)PVT(0.176)KT(0.648)PPRDLPTIPGVTSPSSDEPPMEASQSHLR 233.25 1.67E-49 1070370000 849137 392699 807293 713003 602530 760380 1033060 845360 588870 TRUE FALSE 808999.9768 432715.4746 844308.1826 641330.5838 707611.0412 734047.8499 875447.7236 771335.7969 680188.9521 1.189375356 0.636169513 1.241284764 0.942871215 1.040315399 1.079182259 1.287065485 1.134002242 1 19.37557605 2.201291298 2.536576578 1.172250243 0.977647034 0.078911122 0.176483292 0.455474344 5.960611822 0.074555005 0.050789892 158.9612606 -2.201291298 -0.194603209 NSPVTKTPPRDLPT(ph)IPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(0.237)PVT(0.237)KT(0.237)PPRDLPT(0.265)IPGVT(0.009)S(0.01)PS(0.002)S(0.002)DEPPMEASQSHLR 52.106 0.059762 422940000 74678 34877 66842 52400 49511 69218 94992 67378 47885 TRUE FALSE 71148.11894 38431.00595 69906.77182 47132.65245 58145.70272 66820.9633 80499.22575 61478.02513 55310.76124 1.286334112 0.69481969 1.263890973 0.852142538 1.051254791 1.20810059 1.455398985 1.111502061 1 15.75527258 2.232510101 4.134487019 1.259209439 1.007446504 0.0992967 0.209276979 0.287498167 11.25121799 0.073731302 0.056176742 170.8087446 -2.232510101 -0.251762936 NSQDDYDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSQDDYDEER 10 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ;; 130.23 0.0006563 352380000 420416 367035 364612 431009 273010 409353 411900 423860 252710 FALSE TRUE 400543.7689 404436.2838 381329.8209 387683.1565 320622.8576 395177.003 349057.0899 386744.5714 291898.9761 1.372199979 1.385535123 1.306376014 1.328141543 1.098403502 1.353814283 1.195814712 1.324926098 1 18.15510962 -4.999999999 0.088951482 0.047399773 1.549716686 0.585190173 0.082009117 136.8770892 0.847765267 24.97105242 1.80661894 1.00E-05 4.999999999 1.502316912 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NS(0.004)QEDS(0.996)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NS(0.026)QEDS(0.974)EDS(1)EDKDVK;NS(0.005)QEDS(0.995)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NS(0.019)QEDS(0.982)EDS(0.999)EDKDVK;NSQEDS(1)EDS(1)EDKDVK 235.57 1.32E-16 15826660000 11311080 9852660 9454570 11198300 3228485 12588170 10752020 13331180 2974561 TRUE FALSE 10776427.66 10856657.26 9888071.386 10072625.61 3791531.762 12152238.52 9111601.875 12163831.21 3435840.728 3.136474743 3.159825532 2.877919022 2.931633451 1.103523726 3.536903913 2.651927897 3.540277961 1 21.71223173 2.980819253 24.85793773 2.523411744 3.06779006 0.11699804 0.847467084 1740.803358 2256055.814 0.23562539 0.253560896 956.7957845 -2.980819253 0.544378315 NSQEDS(ph)EDSEDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(1)EDSEDKDVK;NSQEDS(0.839)EDS(0.161)EDKDVK;NSQEDS(0.964)EDS(0.036)EDKDVK;NSQEDS(0.929)EDS(0.071)EDKDVK;NSQEDS(1)EDSEDKDVK;NSQEDS(0.935)EDS(0.065)EDKDVK;NSQEDS(0.998)EDS(0.002)EDKDVK;NSQEDS(0.943)EDS(0.057)EDKDVK;NSQEDS(0.999)EDS(0.001)EDKDVK 351.22 5.98E-82 7484100000 6793160 5959940 5763480 7124600 2156011 7526040 6564200 7443010 1826458 TRUE FALSE 6472060.79 6567264.662 6027741.259 6408421.672 2532018.636 7265411.348 5562710.73 6791260.587 2109695.778 3.067769702 3.112896527 2.85716136 3.037604634 1.200181875 3.443819446 2.636735963 3.219071041 1 21.00860354 2.903061063 23.57386171 2.474741108 3.03129109 0.156649284 0.771516576 62.79376186 15260.17616 0.214036308 0.227019909 799.9467214 -2.903061063 0.556549982 NSQEDSEDSEDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 157.91 9.46E-09 416550000 605662 503985 476605 592749 216495 587824 532940 606649 193437 FALSE TRUE 577033.5576 555341.6445 498457.8107 533164.7444 254251.6595 567467.5075 451630.2149 553527.5975 223434.222 2.582565698 2.485481586 2.23089286 2.38622687 1.137926219 2.539751979 2.021311735 2.477362655 1 17.76949065 -1.586648776 0.199761865 3.61E-29 2.554854237 0.437706431 0.429886366 25.607126 0.887832598 15.59382648 1.155833521 0.025903069 1.586648776 2.554854237 NSQKHS(ph)PTSEPTPPGDALPPVSSPHTHR ddPTM_SK-BR-3_Trastuzumab_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(0.035)QKHS(0.56)PT(0.202)S(0.202)EPT(0.001)PPGDALPPVSSPHTHR;NS(0.051)QKHS(0.929)PT(0.015)S(0.004)EPTPPGDALPPVSSPHTHR;NS(0.169)QKHS(0.629)PT(0.169)S(0.032)EPTPPGDALPPVSSPHTHR 135.2 5.69E-06 5257310000 1703870 1413810 1671930 1906850 1278240 1716370 2473200 2137850 66753 TRUE FALSE 1623331.442 1557878.846 1748589.644 1715169.815 1501164.651 1656931.677 2095867.917 1950648.521 77104.71431 21.05359518 20.20471589 22.67811586 22.24468154 19.46916819 21.48936925 27.18209821 25.29869332 1 16.23453145 -0.44975212 7.066362944 1.000046373 22.39344209 0.896097431 2.295631566 0 0 2.499218178 0.589071444 0.355015962 0.44975212 21.39339572 NSQKHSPT(ph)SEPTPPGDALPPVSSPHTHR ddPTM_SK-BR-3_Trastuzumab_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 1 NS(0.103)QKHS(0.103)PT(0.645)S(0.149)EPTPPGDALPPVSSPHTHR 128.89 1.58E-05 770140000 658030 501020 629790 708550 492290 642280 873770 764120 27782 TRUE FALSE 626926.226 552074.5076 658666.4944 637325.2078 578145.2201 620037.6826 740460.3386 697209.6019 32090.29067 19.5363212 17.20378644 20.52541378 19.86037504 18.01620391 19.3216599 23.07427958 21.72649694 1 14.96984924 -0.67782309 7.830792356 0.999872858 19.82077205 0.926649966 1.671668894 0 0 1.811340828 0.426937128 0.209979506 0.67782309 18.82089919 NSQKHSPTS(ph)EPTPPGDALPPVS(ph)SPHTHR ddPTM_SK-BR-3_Trastuzumab_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 2 NS(0.176)QKHS(0.22)PT(0.274)S(0.306)EPT(0.023)PPGDALPPVS(0.461)S(0.42)PHT(0.119)HR;NS(0.156)QKHS(0.214)PT(0.297)S(0.322)EPT(0.011)PPGDALPPVS(0.473)S(0.436)PHT(0.091)HR 61.84 0.015095 617228000 289367 244561 279709 327519 198108 297956 334704 306147 38984 TRUE FALSE 275689.1954 269482.0439 292533.9343 294596.1679 232657.9725 287637.709 283638.7575 279339.1457 45029.43962 6.122421192 5.984574675 6.496503994 6.542301445 5.166796977 6.387770122 6.298962633 6.20347817 1 15.4585809 -0.71095777 6.956849947 0.999999994 6.148379395 0.945830678 0.387354888 2.08E-08 8.97E-09 0.349134926 0.082291891 0.194554925 0.71095777 5.1483794 NSQPNRYT(ph)NR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NSQPNRYTNR 10 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR 157.22 1.54E-05 1005204000 986159 720354 870679 979091 725100 980237 1072757 900487 769023 TRUE FALSE 939545.2184 793758.8916 910600.4934 880670.9125 851557.2104 946291.1469 909088.2171 821635.5845 888279.1592 1.057713905 0.893591709 1.025128738 0.991434847 0.95865945 1.065308284 1.023426259 0.924974515 1 19.76065362 NSRPEANEALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ;;;; 162.13 5.54E-05 2178690000 1718880 1418850 1468560 1587010 1243790 1553340 1791840 1566780 1417500 FALSE TRUE 1637631.949 1563432.428 1535894.929 1427480.74 1460706.582 1499547.446 1518461.899 1429584.437 1637318.66 1.000191342 0.954873639 0.938054983 0.871840512 0.89213335 0.915855589 0.927407679 0.873125355 1 20.6429037 3.948384605 1.645868475 0.910726155 0.992971115 0.357869739 0.036592111 0.353309544 1.820362084 0.009483187 0.027927841 8879.420134 -3.948384605 0.08224496 NSS(ph)PAPPQPAPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NSSPAPPQPAPGK 13 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 NS(0.011)S(0.989)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NS(0.008)S(0.992)PAPPQPAPGK;NS(0.002)S(0.998)PAPPQPAPGK;NS(0.121)S(0.879)PAPPQPAPGK;NS(0.147)S(0.853)PAPPQPAPGK;NS(0.006)S(0.994)PAPPQPAPGK;NS(0.118)S(0.882)PAPPQPAPGK 215.61 3.03E-11 655864000 2114210 2407170 1693766 2603610 954173 2088190 1785449 2119240 962972 TRUE FALSE 2014275.483 2652463.36 1771426.846 2341890.176 1120580.469 2015875.457 1513045.963 1933668.111 1112304.78 1.810902479 2.384655185 1.592573258 2.105439282 1.007440128 1.81234091 1.360280016 1.738433698 1 20.08512072 2.761554044 24.97318835 1.43748306 2.002725284 0.436411751 0.329109879 700.9432097 761294.0818 0.090445043 0.09587163 577.502733 -2.761554044 0.565242224 NSSETRVFLSPYPDSAFRFVHISWVSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSSETRVFLSPYPDSAFRFVHISWVSFK 28 2 Q8TDX9-2;Q8TDX9 Q8TDX9-2 PKD1L1 Polycystic kidney disease protein 1-like 1 0 48.489 0.059379 123280000 109680 77919 95432 106690 97056 84691 130410 100020 112600 FALSE TRUE 104495.6438 85859.03469 99807.6516 95965.3185 113982.5357 81758.12943 110513.5594 91261.71856 130061.4329 0.803432973 0.660142156 0.767388528 0.73784608 0.876374596 0.628611631 0.849702766 0.701681632 1 16.9888337 -5 0.344542387 3.750498783 0.744567536 0.489579309 0.078424398 320.4765137 2.665524077 649.6605617 0.053711662 1.00E-05 5 -3.005931247 NSSLGSPSNLCGS(ph)PPGSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(0.996)PPGS(0.004)IR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPS(0.001)NLCGS(0.999)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR 450.44 2.61E-191 957880000 916572 733071 844323 888785 610355 831931 923452 900869 688632 TRUE FALSE 873247.458 807771.7683 883036.0447 799442.6432 716800.7188 803121.0209 782562.437 821984.1346 795421.5335 1.097842366 1.015526654 1.110148528 1.005055319 0.901158302 1.009679757 0.983833608 1.03339437 1 19.60136009 3.059067118 7.92574095 0.983281276 1.064666739 0.481032849 0.041927618 0.210066915 24.67197956 0.011420281 0.013657753 1145.689988 -3.059067118 0.081385463 NSSNKPAVTTKS(ph)PAVKPAAAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSSNKPAVTTKSPAVKPAAAPK 22 3 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 NS(0.001)S(0.001)NKPAVT(0.028)T(0.028)KS(0.942)PAVKPAAAPK 77.522 0.0069238 341220000 1325000 1295400 1505600 1615200 530250 1617400 1629700 1731600 624280 TRUE FALSE 1262369.876 1427402.733 1574633.249 1452837.027 622725.4321 1561389.032 1381059.334 1579971.924 721090.154 1.750640844 1.979506619 2.183684301 2.014778623 0.863588871 2.165317365 1.915238096 2.191087918 1 19.45982012 -1.852121122 2.708701502 0.649578 1.881373683 0.339293577 0.387225084 25978251.52 13668931.07 58387629.78 0.089550209 0.014056554 1.852121122 1.231795683 NSSQSGGKPGS(ph)SPITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.698)S(0.302)PITK 108.71 0.0006232 271610000 359310 313720 275340 361150 167950 335850 347810 370740 181540 TRUE FALSE 342326.1284 345688.4247 287964.6113 324846.5159 197240.4268 324219.4303 294745.1965 338276.0402 209692.296 1.632516477 1.648550906 1.373272251 1.549158086 0.940618375 1.546167582 1.405608132 1.613202042 1 17.67791433 3.134674419 0.042837399 3.45E-15 2.965681088 0.309856684 0.210048678 201.8618216 2.650944767 77.50698345 105.5453278 1363.560522 -3.134674419 2.965681088 NSSQSGGKPGSS(ph)PITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.2)S(0.8)PITK;NSSQSGGKPGS(0.179)S(0.821)PITK;NSSQSGGKPGS(0.207)S(0.793)PITK;NSSQSGGKPGS(0.112)S(0.886)PIT(0.002)K 191.22 4.42E-10 5684940000 4610550 3772310 3975480 4424500 2015530 4712620 4773140 4673640 2333870 TRUE FALSE 4392618.439 4156712.678 4157759.69 3979740.854 2367037.794 4549420.788 4044909.828 4264391.305 2695794.64 1.629433627 1.541924825 1.542313212 1.476277456 0.87804826 1.687599167 1.500451766 1.581868011 1 21.36227917 -2.079515112 2.436190823 0.23713915 1.488265495 0.313417125 0.22283067 6359975.262 2156911.483 26932339.75 0.05181354 0.00832693 2.079515112 1.251126345 NSSS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSSS(1)PVSPASVPGQR;NSS(0.001)S(0.999)PVSPASVPGQR;NSS(0.019)S(0.981)PVSPASVPGQR;NSS(0.006)S(0.994)PVSPASVPGQR 321.19 1.32E-56 1110730000 1826190 1456460 1447910 1760590 1368810 1686000 1883470 1794400 1554780 TRUE FALSE 1739869.618 1604874.93 1514298.106 1583612.148 1607530.031 1627613.397 1596112.059 1637272.823 1795887.342 0.968807774 0.893638979 0.843203285 0.881799271 0.895117413 0.906300389 0.888759569 0.911679026 1 20.77626542 0.863121904 6.134961084 0.999999729 0.898925996 0.522718257 0.030699902 2.64375096 118.245804 0.031330605 0.007874636 7.296622941 -0.863121904 -0.101073733 NSSTETDQQPHS(ph)PDSSSSVHSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(1)PDSSSSVHSIR 116.28 0.00082068 246630000 42964 35886 46922 40802 45371 41325 49883 45487 27084 TRUE FALSE 40933.17687 39542.8242 49073.42011 36700.50544 53283.68804 39893.90489 42272.43219 41503.91714 31284.04839 1.308436055 1.263993192 1.568640334 1.173137983 1.703222274 1.275215547 1.351245582 1.326679866 1 14.9331396 0.351606686 1.191047117 0.999573314 1.369742422 0.368931388 0.153956527 3.483119235 5.41139476 0.133981482 0.040048954 2.247018699 -0.351606686 0.370169107 NSSYFVEWIPNNVK ddPTM_SK-BR-3_Trastuzumab_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 ; 324.11 3.55E-56 313430000 1762610 1455210 1575100 1780620 985860 1659140 1978030 1780450 1095730 FALSE TRUE 1679294.918 1603497.553 1647319.893 1601628.695 1157793.672 1601683.566 1676245.194 1624544.359 1265650.212 1.326823875 1.266935792 1.30156016 1.265459192 0.914781715 1.265502546 1.324414264 1.283565035 1 20.27144731 -2.317941351 1.894704639 4.82E-05 1.249796527 0.290138347 0.119415957 1443430.085 171412.8297 6172890.45 0.029531408 0.004809043 2.317941351 1.24974832 NSSYVHGGLDSNGKPADAVYGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSSYVHGGLDSNGKPADAVYGQK 23 1 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 245.09 1.04E-37 165290000 303160 224860 277340 310680 165710 284630 344840 346270 189780 FALSE TRUE 288830.2276 247773.4896 290056.3133 279449.8561 194609.7715 274773.1917 292228.3246 315948.7631 219210.1131 1.317595358 1.130301363 1.323188557 1.274803667 0.887777342 1.253469504 1.333096911 1.441305598 1 17.74195483 2.00743094 24.99477504 1.294679562 1.190263896 0.02732656 0.165305775 455.9866263 1533752.249 0.057999952 0.042756641 101.7257593 -2.00743094 -0.104415666 NST(ph)PSEPGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.077)T(0.893)PS(0.029)EPGSGR;NS(0.009)T(0.959)PS(0.032)EPGSGR;NS(0.043)T(0.905)PS(0.052)EPGSGR;NS(0.053)T(0.946)PSEPGSGR;NS(0.014)T(0.986)PS(0.001)EPGSGR;NS(0.037)T(0.962)PS(0.001)EPGSGR 172.09 0.00015394 2007160000 2463040 2244400 2267410 2717790 1718030 2435300 2561130 2459880 1796130 TRUE FALSE 2346616.98 2473106.912 2371372.991 2444592.586 2017653.888 2350964.95 2170382.58 2244479.867 2074664.667 1.13108254 1.192051396 1.143015076 1.178307331 0.972520485 1.133178285 1.046136571 1.081851878 1 20.98444674 2.764945758 24.98547648 1.056453909 1.161927975 0.596364426 0.046373898 494.6936466 468450.5618 0.012520543 0.013275916 582.0305194 -2.764945758 0.105474066 NSTFSEIFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 148.28 4.07E-05 4040700000 7854100 5653800 5522500 5977900 4052500 6165000 8132200 6471700 3771700 FALSE TRUE 7482852.258 6229928.648 5775712.087 5376990.135 4759254.717 5951504.504 6891483.532 5905003.639 4356595.973 1.717591511 1.429999175 1.325739665 1.234218222 1.092425083 1.366090531 1.581850503 1.355416861 1 22.05476989 4.324405301 1.609159866 1.315428892 1.732047904 0.41649195 0.16066922 0.5388371 2.256255787 0.045972377 0.275441676 21105.96926 -4.324405301 0.416619012 NSTPS(ph)EPGS(ph)GRGPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSTPSEPGSGRGPPQEEEEEEDEEEEATKEDAEAPGIR 38 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 NS(0.136)T(0.122)PS(0.743)EPGS(1)GRGPPQEEEEEEDEEEEATKEDAEAPGIR 114.37 4.02E-06 36692000 29046 20521 27365 25281 14311 30748 37284 28629 21180 TRUE FALSE 27673.05314 22612.11323 28619.71232 22739.70585 16806.83387 29683.18905 31595.64103 26122.09299 24464.48623 1.131152025 0.924283184 1.169847266 0.929498606 0.686989038 1.213317491 1.29149007 1.067755633 1 14.57840136 NSTPS(ph)EPGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.005)T(0.229)PS(0.753)EPGS(0.014)GR;NS(0.003)T(0.07)PS(0.911)EPGS(0.017)GR;NSTPS(1)EPGSGR 122.52 0.00040812 1229150000 353570 327725 337307 409146 246588 347651 361463 351211 265256 TRUE FALSE 336857.4468 361120.5501 352772.8596 368017.8668 289592.8691 335611.7587 306315.1806 320457.103 306390.5457 1.099438124 1.178628241 1.15138298 1.201139761 0.945175604 1.095372437 0.999754023 1.045910546 1 18.22501226 2.746676282 24.99999809 1.022282307 1.154328405 0.700540546 0.045525746 327.9518344 1010243.562 0.012688478 0.013248821 558.0540721 -2.746676282 0.132046098 NSTWSGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NSTWSGESK 9 0 P19338 P19338 NCL Nucleolin 0 ; 123.96 0.0012636 426830000 364110 339800 324980 388090 258210 389140 396380 359960 293930 FALSE TRUE 346899.2419 374426.0063 339880.6544 349078.4559 303241.7422 375663.9842 335904.951 328439.9941 339511.1632 1.02176093 1.102838572 1.001088304 1.028179611 0.893171639 1.106484926 0.989378222 0.967390854 1 18.37309949 3.705554687 21.13383266 1.000446268 1.062299709 0.185840948 0.055800984 139.0906706 89059.82802 0.013682603 0.021201703 5076.386572 -3.705554687 0.061853441 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.742)S(0.258)PVIMAR;NSVLS(0.003)DPGLDS(0.995)PRT(0.597)S(0.404)PVIMAR;NS(0.001)VLS(0.023)DPGLDS(0.976)PRT(0.606)S(0.394)PVIMAR 141.38 3.58E-07 417010000 126143 100229 121070 113468 94154 105098 125928 121714 250701 TRUE FALSE 120180.4704 110442.4491 126621.1793 102061.9811 110574.4278 101458.4299 106715.3708 111056.0769 289578.4307 0.415018723 0.381390454 0.437260396 0.352450218 0.381846215 0.350365977 0.36851975 0.383509492 1 18.14359462 -1.045279438 4.213335461 1.000057868 0.383436046 0.982026245 0.026199004 1446002.988 717473.2894 728.8519839 0.006054878 0.090099123 1.045279438 -0.616621822 NSVLSDPGLDS(ph)PRTS(ph)PVIMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLS(0.001)DPGLDS(0.998)PRT(0.383)S(0.617)PVIMAR 89.055 0.0013464 192240000 59014 46735 48051 44659 63303 56487 59272 62104 138350 TRUE FALSE 56224.52517 51497.34963 50254.18588 40169.79247 74343.02316 54530.84103 50228.9678 56665.84453 159804.6114 0.351832933 0.322251962 0.314472689 0.251368168 0.465212002 0.341234465 0.314314883 0.354594552 1 17.28594951 -3.956600408 0.578092366 10 0.334430817 0.938692402 0.053066847 350.2411223 4.235355155 4025.189469 0.020371035 0.000110509 3.956600408 -9.665569183 NSWGEPWGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NSWGEPWGER 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;;; 233.14 1.08E-11 1048520000 1446090 1052780 1177670 1332310 1095940 1161950 1466980 1283500 1091870 FALSE TRUE 1377736.192 1160059.479 1231667.334 1198383.668 1287071.589 1121711.38 1243165.258 1171109.936 1261191.623 1.092408296 0.91981223 0.976590164 0.950199514 1.020520249 0.889405987 0.985706879 0.928574147 1 20.26635606 4.637342343 3.123815246 0.958612148 1.099157648 0.529357698 0.039426878 0.199228429 3.167600309 0.008336516 0.059810184 43385.2738 -4.637342343 0.1405455 NSYATTENKT(ph)LPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSYATTENKTLPR 13 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;B4DWA1;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 NSYATTENKT(1)LPR 120.9 0.00040893 302020000 228970 166260 194340 244520 123950 217580 257880 250500 151260 TRUE FALSE 218147.0419 183202.083 203250.6812 219940.385 145566.8408 210045.15 218535.6697 228564.892 174716.6283 1.248576303 1.048566956 1.163316184 1.258840599 0.833159627 1.202204691 1.250800636 1.308203428 1 17.41465739 2.03050609 24.99997601 1.217277326 1.114906456 0.059028683 0.141935501 433.7043169 355422.2615 0.049177575 0.036319657 107.276869 -2.03050609 -0.10237087 NSYNNSQAPS(ph)PGLGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NSYNNSQAPSPGLGSK 16 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 NSYNNSQAPS(1)PGLGSK 191.64 6.96E-10 115950000 202250 150210 185760 199780 125590 203090 212720 201140 120620 TRUE FALSE 192690.0433 165516.5698 194277.2797 179697.7348 147492.8562 196056.9424 180265.6571 183527.1153 139325.1336 1.383024286 1.187987878 1.394416605 1.289772565 1.058623469 1.407190055 1.293848802 1.317257774 1 17.08809601 -1.986271144 2.604537022 0.733579133 1.28929434 0.43513021 0.104355359 10596798.22 5277230.42 16974213.54 0.023378667 0.010321168 1.986271144 0.555715207 NSYVAGQYDDAASYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NSYVAGQYDDAASYQR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 361.49 1.38E-87 995220000 633670 506880 539960 604950 440100 532500 642240 602340 509480 FALSE TRUE 603717.6749 558531.6483 564717.7001 544139.2767 516853.3007 514059.3915 544254.4925 549595.9164 588487.5563 1.025880103 0.949096786 0.959608566 0.924640242 0.878273967 0.873526357 0.924836025 0.933912553 1 19.16665238 4.362572967 0.907190472 0.915491933 1.048944054 0.416594361 0.036153489 1.057927758 1.002863446 0.011682705 0.124349073 23044.80127 -4.362572967 0.133452121 NT(ph)PSQHSHSIQHS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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)PSQHSHSIQHS(1)PER;NT(1)PSQHS(0.001)HS(0.004)IQHS(0.995)PER;NT(0.996)PS(0.004)QHSHSIQHS(1)PER;NT(0.989)PS(0.011)QHS(0.004)HS(0.237)IQHS(0.759)PER;NT(0.987)PS(0.013)QHS(0.005)HS(0.016)IQHS(0.979)PER 239.89 1.63E-19 660525000 601920 561265 582800 648180 565945 621882 720272 595329 112608.2 TRUE FALSE 573468.4345 618458.5416 609521.9565 583023.7149 664645.6288 600346.0704 610381.2777 543198.8367 130070.9045 4.408890955 4.754780047 4.686074558 4.482353045 5.10987166 4.615529296 4.692681118 4.176174823 1 16.98893876 0.629908043 2.128006758 1.000133237 4.677772135 0.974298147 0.186268573 0.303858071 1.580894771 0.167179514 0.045641543 4.264892048 -0.629908043 3.677638898 NT(ph)RTPRT(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTRTPRTPRTPQLK 14 3 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 3 NT(0.71)RT(0.375)PRT(0.915)PRT(1)PQLK 95.227 0.0065237 418080000 551640 412770 574350 612520 430190 613370 722730 637620 469570 TRUE FALSE 525565.0704 454831.7323 600684.5156 550948.3259 505214.9998 592128.8431 612464.2647 581786.6126 542388.5174 0.968982664 0.838571831 1.107480148 1.015781692 0.931463303 1.091706082 1.129198434 1.072638144 1 19.04896711 3.364311351 0.798912565 1.076060285 0.903424376 0.240451896 0.077516979 0.743337575 1.006593476 0.03867289 0.079920876 2313.722934 -3.364311351 -0.172635909 NT(ph)S(ph)FPLDADKILLRGCVIRNTDFCHGLVIFAGADTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTSFPLDADKILLRGCVIRNTDFCHGLVIFAGADTK 36 3 O43520;A0A2R8Y5C5;A0A3B3IRQ1 O43520 ATP8B1 Phospholipid-transporting ATPase IC 2 NT(0.826)S(0.837)FPLDADKILLRGCVIRNT(0.336)DFCHGLVIFAGADTK 64.72 0.0040412 308410000 50239 37176 50958 46713 20395 60149 61529 66794 21339 TRUE FALSE 47864.30203 40964.27667 53294.4747 42017.32049 23951.88154 58066.02505 52141.62099 60945.16326 24648.14314 1.941902957 1.661961976 2.162210533 1.704685025 0.971751966 2.355797138 2.115438096 2.472606676 1 14.58919135 NTAELQPESGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTAELQPESGKR 12 1 O15355 O15355 PPM1G Protein phosphatase 1G 0 66.708 0.091925 136050000 259210 213050 258910 290260 147990 274050 278460 235620 156700 FALSE TRUE 246957.657 234760.0372 270781.2796 261082.5133 173799.4091 264559.5798 235975.8127 214987.8637 181000.2357 1.364405168 1.297015091 1.496027221 1.442442947 0.96021648 1.461653234 1.303732074 1.187776706 1 17.46563205 -0.691288545 0.292142279 0.84427964 1.374039821 0.35173624 0.147779242 12.60960156 1.08622967 1.908934854 0.169874943 0.203568912 0.691288545 0.529760181 NTDDDRPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NTDDDRPPRR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 173.28 1.95E-06 768608000 1183890 997934 1108309 1265003 979564 1162212 1342318 1217246 1107400 FALSE TRUE 1127929.866 1099624.609 1159126.064 1137842.495 1150399.651 1121964.307 1137522.736 1110657.487 1279129.936 0.881794596 0.859666073 0.906183204 0.889544106 0.899361057 0.877130833 0.889294124 0.868291372 1 20.28673139 -1.880338707 2.698233974 1.055594958 0.883066762 0.876744389 0.01367629 53911506.33 41050728.09 19250982.93 0.003294574 0.01317229 1.880338707 -0.172528196 NTDEMVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NTDEMVELR 9 0 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;; 162.31 0.00014859 1368080000 2130710 2006550 1843240 2263420 1815670 1952710 2250060 1988520 1894850 FALSE TRUE 2029995.561 2211019.726 1927754.377 2035896.721 2132322.273 1885087.163 1906772.022 1814394.647 2188693.66 0.927491863 1.010200635 0.880778527 0.930188065 0.974244277 0.861284152 0.871191824 0.828985198 1 21.06163861 2.234073335 24.99959439 0.87807179 0.948421016 0.175843807 0.055211397 141.7694774 789818.3192 0.018600287 0.014209594 171.424675 -2.234073335 0.070349227 NTDKNGEELHGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NTDKNGEELHGGKR 14 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 239.61 1.37E-17 927320000 1113170 806018 1000825 1108620 565609 1138460 1376580 1279270 663851 FALSE TRUE 1060552.66 888152.1506 1046713.816 997179.4114 664251.0305 1099034.845 1166557.438 1167250.337 766797.6226 1.383093308 1.158261482 1.365045724 1.300446665 0.866266419 1.433278889 1.521336796 1.522240422 1 19.54848634 NTDVAQS(ph)PEAPKQEAPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;NTDVAQS(1)PEAPKQEAPAK 293.07 1.91E-49 3354370000 4920200 4674310 4852500 5515450 2416720 5651220 6128680 6095530 2988050 TRUE FALSE 4687631.897 5150627.503 5074991.925 4961026.487 2838195.203 5455516.834 5193637.305 5561773.079 3451421.533 1.358174263 1.492320614 1.470406288 1.437386433 0.822326446 1.580657935 1.504782089 1.611444162 1 21.71875925 2.946532627 24.99998194 1.347514568 1.441491648 0.053491048 0.248483869 1403.406897 656196.2328 0.07417156 0.078671498 884.1635905 -2.946532627 0.093977081 NTDVAQS(ph)PEAPKQEAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTDVAQSPEAPKQEAPAKK 19 2 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPKQEAPAKK 99.11 0.00044285 155830000 318570 286130 320260 316950 124310 344180 328440 362640 138160 TRUE FALSE 303511.8274 315286.9723 334944.2378 285089.5838 145989.6246 332260.9603 278330.4458 330885.3191 159585.1472 1.901880174 1.975666144 2.098843431 1.786441839 0.914807093 2.08202935 1.744087409 2.073409243 1 17.28396686 3.003099438 24.80781902 1.631375577 1.97157592 0.194322699 0.386488939 160.5746525 1285207.847 0.104969949 0.124839372 1007.162247 -3.003099438 0.340200342 NTEDLTEEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NTEDLTEEWLR 11 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;; 289.22 4.91E-35 443727000 597239 410685 446030 580750 512880 452124 659500 531307 605160 FALSE TRUE 569008.6961 452534.2684 466480.9167 522371.9066 602326.1096 436466.8325 558881.1625 484782.9424 699005.1221 0.814026504 0.647397643 0.667349783 0.747307695 0.861690552 0.624411494 0.799538007 0.693532747 1 19.4149435 -1.601900292 2.624024652 1.024181279 0.731883872 0.547812278 0.076547631 12582720.23 11594922.75 2096319.727 0.018287828 0.025009195 1.601900292 -0.292297407 NTEESS(ph)SPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEES(0.106)S(0.612)S(0.282)PVRK;NTEES(0.07)S(0.465)S(0.465)PVRK;NTEES(0.056)S(0.472)S(0.472)PVRK 68.83 0.034401 1131064000 226985 203153 209987 238594 168562 223300 249674 247133 189875 TRUE FALSE 216255.8689 223854.5217 219615.1117 214610.0778 197959.1594 215567.065 211581.6457 225492.7244 219319.8453 0.986029644 1.020676088 1.001346282 0.978525576 0.902604866 0.982889007 0.964717285 1.028145557 1 17.74267684 1.237707374 24.9999739 1.014072782 0.979635623 0.194361736 0.031199636 43.95135291 1287394.112 0.026129472 0.007988185 17.28651209 -1.237707374 -0.034437158 NTEESSS(ph)PVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEESS(0.009)S(0.991)PVRK;NTEESS(0.017)S(0.983)PVRK 170.35 9.69E-06 1345460000 934280 695860 805240 940750 556900 890690 967570 927000 692080 TRUE FALSE 890118.436 766768.9251 842161.0505 846184.0227 654023.1837 859845.182 819949.4259 845826.9657 799404.2317 1.113477263 0.959175464 1.053485855 1.058518318 0.818138256 1.075607493 1.025700632 1.058071664 1 19.60856568 -0.223306423 6.624943689 0.999999663 1.019411417 0.005917456 0.081901176 0 0 0.072748138 0.017146901 0.597989526 0.223306423 0.019411754 NTENCDFLFS(ph)PPEVTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 147.06 4.34E-07 27141000 38185 40076 39423 41177 36468 35161 44495 39279 45924 TRUE FALSE 36380.07073 44159.78996 41230.58354 37037.80973 42828.00765 33943.36575 37706.47054 35839.52253 53045.65937 0.685825592 0.832486399 0.777265926 0.698225079 0.80738006 0.6398896 0.710830462 0.675635348 1 15.69494708 -1.110321015 4.989224678 1.000009737 0.732541872 0.663041812 0.060776584 6.47E-06 1.15E-06 0.057839751 0.013632464 0.077567356 1.110321015 -0.267467865 NTETSKS(ph)PEKDVPMVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTETSKSPEKDVPMVEK 17 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NT(0.021)ET(0.142)S(0.106)KS(0.732)PEKDVPMVEK 108.4 0.00034293 454730000 588600 667690 533360 798590 197960 741680 626340 754870 169790 TRUE FALSE 560778.0445 735728.3701 557815.0836 718314.216 232484.1613 715995.4356 530780.3295 688769.581 196120.166 2.859359422 3.751416211 2.844251536 3.662622924 1.185416911 3.650799661 2.706403631 3.51197735 1 17.58137836 NTFGSTS(ph)LCFDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTFGSTSLCFDSR 13 0 Q8NEV8-2;Q8NEV8;E9PPH6;F5GXG5;A0A087WZJ0 Q8NEV8-2 EXPH5 Exophilin-5 1 NTFGS(0.009)T(0.207)S(0.784)LCFDSR 149.86 4.61E-05 98426000 247120 162770 219830 234520 213990 223670 290120 231540 254690 TRUE FALSE 235439.1273 179356.4481 229909.4229 210945.604 251309.7882 215924.2518 245856.8656 211265.1301 294186.0244 0.800306975 0.609670185 0.78151035 0.717048352 0.85425468 0.73397182 0.835719052 0.718134488 1 18.16636919 -5 0.170252137 1.97775454 0.692785914 0.5383639 0.070263361 92.34714013 0.871469632 30.41074371 0.230655499 1.00E-05 5 -1.284968626 NTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK 250.24 8.74E-32 2025037000 4375970 3891170 4141840 4653520 2684979 4662550 5153140 4776190 2831231 TRUE FALSE 4169126.57 4287684.647 4331747.461 4185739.328 3153238.488 4501084.724 4366933.849 4357961.483 3270283.844 1.274851594 1.31110474 1.324578437 1.279931507 0.96420942 1.376359038 1.335337866 1.332594262 1 21.64098443 2.986445573 24.93221514 1.233626311 1.301195756 0.085236423 0.137039408 2147.842208 3950780.084 0.040008077 0.044204629 969.2717905 -2.986445573 0.067569444 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFT(0.003)AWS(0.997)DEESDYEIDDRDVNK 310.29 2.15E-67 1848490000 867310 773994 837481 905816 520803 878828 949550 967147 579928 TRUE FALSE 826313.9751 852864.8686 875880.3322 814761.6547 611630.8783 848393.966 804678.7078 882458.4815 669860.2724 1.233561698 1.273198163 1.307556767 1.216315832 0.913072328 1.266523783 1.201263519 1.317376948 1 19.35350067 -2.313687651 2.115061739 2.09E-05 1.217033739 0.262222486 0.113911192 2801602.663 275565.8542 13467918.42 0.027148217 0.004856377 2.313687651 1.217012885 NTGKEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTGKEEQR 8 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 80.239 0.02368 40797000 133850 124570 132820 150140 123350 119870 156010 194090 166870 FALSE TRUE 127523.1758 137263.8246 138909.9284 135047.642 144862.2009 115718.8718 132207.8092 177094.4507 192747.3473 0.661607942 0.712143781 0.720683995 0.700645917 0.751565212 0.600365574 0.68591247 0.918790599 1 17.55635148 1.153662285 3.944508068 0.992882621 0.68871419 0.886221496 0.040544621 0.063602182 1.719411738 0.037294752 0.009789119 14.24499448 -1.153662285 -0.304168431 NTGVSPASRPSPGT(ph)PTSPSNLTSGLK ddPTM_SK-BR-3_Trastuzumab_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 NTGVSPASRPS(0.009)PGT(0.522)PT(0.23)S(0.23)PS(0.008)NLTSGLK 178.89 3.84E-17 345360000 387300 331120 344290 404680 212760 376070 386650 404180 238190 TRUE FALSE 368993.0966 364861.5045 360076.037 364000.7976 249865.2766 363046.6016 327659.4412 368787.8565 275127.2887 1.341172293 1.326155272 1.308761624 1.323026877 0.908180638 1.319558679 1.19093763 1.340426311 1 18.06973972 -4.325595828 0.042792649 6.10E-10 1.874123599 0.283940013 0.130684579 813.9686994 2.909286315 111.6709115 35.28778923 4.73E-05 4.325595828 1.874123598 NTKDEFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NTKDEFEER 9 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 81.017 0.020497 307800000 764760 628360 667740 790570 585340 697610 806600 793600 621150 FALSE TRUE 728611.3104 692390.5984 698356.5395 711100.4016 687423.1107 673451.5908 683538.3558 724108.1769 717474.7696 1.015521857 0.965038253 0.973353446 0.991115551 0.958114682 0.938641496 0.952700199 1.009245492 1 19.45256857 4.588462829 2.3077885 0.969165803 1.019826604 0.23983709 0.022160088 0.52221978 4.213949813 0.005466144 0.04712388 38767.05665 -4.588462829 0.050660801 NTLQLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;; 134.08 0.0032089 2517100000 4559190 3535780 2599020 3209570 4013670 2916820 4792560 3671790 3674510 FALSE TRUE 4343686.124 3896080.002 2718187.638 2886937.926 4713652.777 2815809.792 4061366.951 3350268.602 4244334.244 1.023408119 0.917948441 0.640427328 0.680186281 1.1105753 0.663427909 0.956891403 0.789350793 1 22.01710684 3.994791582 23.37471051 0.830681609 0.983860858 0.133374625 0.153850456 237.7657495 1067087.499 0.035851536 0.070471668 9880.788008 -3.994791582 0.153179249 NTPENLHEMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NTPENLHEMAK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;;;; 150.69 2.56E-05 622229000 1235697 1109524 1017119 1264870 723947 1162518 1251230 1270840 760060 FALSE TRUE 1177288.052 1222585.757 1063754.912 1137722.865 850203.1276 1122259.71 1060331.883 1159558.512 877926.223 1.340987455 1.39258371 1.211667774 1.295920813 0.968422067 1.27830754 1.20776878 1.320792661 1 19.74374018 8 0.041953707 0.479515995 2.524295909 0.347133841 0.112834093 722.9998132 2.306420197 29.88711069 102.8566719 100000000 -8 2.044779913 NTPS(ph)QHSHSIQHS(ph)PER ddPTM_SK-BR-3_Trastuzumab_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(0.137)PS(0.842)QHS(0.019)HS(0.002)IQHS(1)PER;NT(0.27)PS(0.371)QHS(0.151)HS(0.208)IQHS(1)PER 99.11 0.001185 130081000 37911 46627 39743 50247 62721 39956 45870 37480 27910.2 TRUE FALSE 36119.02216 51378.34431 41565.25586 45196.0761 73659.52254 38572.3137 38871.68904 34198.05251 32238.37127 1.120373665 1.593701614 1.289310043 1.401934227 2.284840072 1.19647216 1.205758464 1.060787228 1 14.97649124 2.028095046 24.99974599 1.134060718 1.511036921 0.317933636 0.306914864 286.7099314 255121.1856 0.113119502 0.083542758 106.6829572 -2.028095046 0.376976202 NTPSQHS(ph)HSIQHS(ph)PER ddPTM_SK-BR-3_Trastuzumab_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(0.261)PS(0.261)QHS(0.366)HS(0.115)IQHS(0.997)PER 61.616 0.039587 129220000 41212 56002 64590 59459 78411 55153 53320 41717 13437 TRUE FALSE 39263.99043 61708.66747 67551.51539 53482.06836 92085.85357 53243.03778 45185.05471 38064.03832 15520.74133 2.529775453 3.975884022 4.352338199 3.445844964 5.933083452 3.430444245 2.911269104 2.452462644 1 13.92190985 1.164642668 1.353030287 1.092289817 3.895940256 0.552033093 0.871984191 0.317193979 1.149777526 0.815436142 0.251439234 14.60974607 -1.164642668 2.803650439 NTPSQHSHSIQHS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 NTPSQHSHS(0.004)IQHS(0.996)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.003)IQHS(0.997)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHS(0.002)IQHS(0.998)PER 277.17 4.24E-35 26277543000 2874325.2 1826387.8 2754074.2 2886673.5 3233077.7 2452835.9 4296291.4 3039149.4 225633.63 TRUE FALSE 2738461.544 2012498.793 2880351.226 2596499.595 3796925.427 2367893.578 3640813.24 2773025.367 260623.741 10.50733726 7.721855215 11.05176073 9.962636504 14.56860919 9.085486875 13.96961469 10.63995688 1 17.99160898 0.926812965 22.18243623 0.999999976 10.86933404 0.701465407 2.037741996 10237.95911 3103052.372 1.979897712 0.494974428 8.449148914 -0.926812965 9.869334069 NTPVFRDDVCFFLSQSGETADTLMGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTPVFRDDVCFFLSQSGETADTLMGLR 27 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 195.63 6.02E-25 71878000 37570 28186 31211 29966 30610 29064 39566 41792 39243 FALSE TRUE 35794.14056 31058.18544 32642.05522 26953.76075 35948.37431 28057.50639 33529.48002 38132.47093 45328.60401 0.78965901 0.685178512 0.720120461 0.594630286 0.79306158 0.618980156 0.73969805 0.841245208 1 15.46813411 1.001333149 2.204966979 0.99838584 0.704091259 0.704815042 0.062903447 0.155705874 1.645441777 0.054119498 0.014931884 10.03074405 -1.001333149 -0.294294581 NTRT(ph)PRT(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NTRTPRTPRTPQLK 14 3 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 3 NT(0.423)RT(0.588)PRT(0.989)PRT(1)PQLK;NT(0.428)RT(0.632)PRT(0.94)PRT(1)PQLK;NT(0.381)RT(0.625)PRT(0.994)PRT(1)PQLK 105.91 0.0016472 1029940000 1502550 1107440 1500020 1582500 1035680 1520000 1946510 1624870 1292370 TRUE FALSE 1431527.439 1220289.395 1568797.401 1423424.093 1216302.264 1467362.019 1649534.149 1482587.769 1492784.139 0.958964797 0.817458709 1.050920464 0.953536453 0.814787773 0.982969996 1.105005142 0.993169561 1 20.50957413 2.001796894 24.95011644 1.044291006 0.9149802 0.326567753 0.074320066 54.76610411 760426.2012 0.026897459 0.019730006 100.4146072 -2.001796894 -0.129310806 NTSLPPLWS(ph)PEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;NTSLPPLWS(1)PEAER 225.34 2.95E-12 1179331000 1244860 1048292 1139301 1279870 979621 1193407 1349020 1211920 1077205 TRUE FALSE 1186017.935 1155114.147 1191539.078 1151215.036 1150466.592 1152079.016 1143202.223 1105797.86 1244252.45 0.953197187 0.928359954 0.957634504 0.925226256 0.924624735 0.925920633 0.918786395 0.88872468 1 20.2468478 3.201528623 23.93495259 0.925469057 0.943503512 0.041380266 0.028816709 252.9824507 163509.0975 0.007338758 0.008771778 1590.481502 -3.201528623 0.018034455 NTVDLVTTCHIHSS(ph)SDDEIDFK ddPTM_SK-BR-3_Trastuzumab_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 NT(0.002)VDLVT(0.001)T(0.004)CHIHS(0.096)S(0.449)S(0.449)DDEIDFK;NT(0.006)VDLVT(0.003)T(0.003)CHIHS(0.084)S(0.452)S(0.452)DDEIDFK 170.1 1.26E-11 125319000 329520 358680 251070 352220 189271 340350 296020 403480 76471 TRUE FALSE 313944.2426 395229.8998 262581.8078 316814.1764 222279.8025 328563.5942 250856.7122 368149.1522 88329.73212 3.554230666 4.47448317 2.972745434 3.586721807 2.516477715 3.719739506 2.840003091 4.16789617 1 16.43061152 3.724620413 24.54430375 3.084367944 4.014356922 0.186376616 0.881462504 861.4346723 1516715.309 0.20185246 0.314506069 5304.206374 -3.724620413 0.929988978 NTVDLVTTCHIHSSS(ph)DDEIDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTVDLVTTCHIHSSSDDEIDFK 22 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;E9PQP7;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 NTVDLVT(0.001)T(0.001)CHIHS(0.04)S(0.139)S(0.819)DDEIDFK 169.7 1.34E-11 240920000 356410 422880 288400 416830 196330 410850 336090 489070 51585 TRUE FALSE 339563.2056 465971.9528 301623.4253 374929.4565 230569.8898 396622.1615 284813.2978 446244.4381 59584.53834 5.698847639 7.82035014 5.062108958 6.29239509 3.869626186 6.656461098 4.77998665 7.48926568 1 15.86265039 3.714824012 24.11370742 5.25177718 6.759599043 0.124064835 1.842681505 891.849137 906017.7881 0.423728637 0.656908883 5185.898494 -3.714824012 1.507821863 NTVELLTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NTVELLTDR 9 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 66.299 0.064123 4096170000 1381770 1545380 1417990 1421760 7588460 533991 1476760 619752 5284860 FALSE TRUE 1316456.471 1702855.979 1483006.244 1278841.984 8911885.021 515498.7578 1251453.139 565483.2294 6104409.097 0.215656659 0.278955088 0.24294018 0.209494803 1.459909531 0.084446955 0.205008072 0.092635212 1 22.54142022 NTVELLVEDKGNQVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTVELLVEDKGNQVYR 16 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 248.97 1.57E-20 113320000 206190 112260 120870 182360 126930 154400 258370 188950 201860 FALSE TRUE 196443.8073 123699.4216 126412.0091 164028.8263 149066.5518 149053.0893 218950.9112 172404.5363 233163.4178 0.842515559 0.530526713 0.542160559 0.703492974 0.639322211 0.639264472 0.939044869 0.739415033 1 17.83098193 1.757305727 10.50357841 0.87771183 0.648170243 0.530848605 0.107472257 0.12745667 58.93161965 0.048375353 0.026473506 57.18810783 -1.757305727 -0.229541587 NTVGNVPLEWYDDFPHVGYDLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTVGNVPLEWYDDFPHVGYDLDGR 24 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 148.87 1.54E-07 32331000 26952 47579 20286 34818 17210 26447 20730 27509 16265 FALSE TRUE 25678.03237 52427.35419 21216.13317 31318.02849 20211.41855 25531.13376 17567.25777 25100.16613 18787.29313 1.366776587 2.790575195 1.129281 1.666979286 1.075802587 1.358957546 0.93506061 1.336018231 1 14.1974696 3.706692549 24.99976682 1.216352501 2.078676044 0.45262037 0.395051531 479.7641474 376363.9655 0.098800304 0.153075294 5089.704268 -3.706692549 0.862323542 NTVGNVPLEWYDDFPHVGYDLDGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTVGNVPLEWYDDFPHVGYDLDGRR 25 1 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 89.829 0.0091665 21540000 24749 18933 22659 21992 20458 25014 27325 21250 16721 FALSE TRUE 23579.16382 20862.29423 23697.93756 19781.32238 24025.86872 24147.75891 23156.06939 19389.23735 19314.00728 1.220832294 1.080163941 1.226981911 1.024195657 1.24396084 1.250271813 1.198926202 1.003895104 1 14.23735991 1.233205112 24.87826411 1.001947404 1.174596561 0.502756142 0.072692343 107.7868627 500679.9781 0.059934318 0.016700189 17.10823126 -1.233205112 0.172649158 NTVLQQHLETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NTVLQQHLETLR 12 0 Q9NP66;H0YKL0 Q9NP66 HMG20A High mobility group protein 20A 0 91.812 0.0080872 94525000 72548 57910 62244 60676 79620 58730 75469 59188 92248 FALSE TRUE 69118.79982 63811.09484 65097.94897 54576.7332 93505.70279 56696.16537 63954.81797 54005.18494 106553.3487 0.648677875 0.598865222 0.61094231 0.512201014 0.877548232 0.532091821 0.600214059 0.50683705 1 16.70121641 -1.033246338 8.821966548 1 0.61265135 0.574626737 0.105194374 1.97E-09 2.31E-10 0.091186642 0.021492897 0.092630426 1.033246338 -0.38734865 NVADHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVADHKK 7 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 89.296 0.01167 256720000 223950 203810 199570 234810 176020 223350 250900 301180 209870 FALSE TRUE 213364.3273 224578.4707 208720.4819 211206.4527 206717.8323 215615.3335 212620.5969 274807.0825 242415.5677 0.880159345 0.926419342 0.861002797 0.871257794 0.852741572 0.889445078 0.877091347 1.13361978 1 17.88712282 1.250555962 24.99951782 1.066809879 0.882772955 0.814013206 0.037154631 70.19873407 146303.139 0.022666019 0.008137231 17.80557332 -1.250555962 -0.184036924 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 137.9 1.52E-06 985428000 674715 602695 713113 702552 429463 724081 775358 761056 466782 TRUE FALSE 642822.5591 664110.3057 745809.9364 631930.1382 504361.2112 699005.8934 657062.8967 694413.902 539168.1686 1.19224872 1.231731294 1.383260326 1.172046451 0.935443226 1.296452451 1.218660401 1.287935643 1 19.0403758 -1.186661013 4.245633584 0.999924509 1.214308515 0.252884804 0.1159858 7.94E-05 1.52E-05 0.107553485 0.025341687 0.065063735 1.186661013 0.214384006 NVALLSQLYHS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR 188.84 5.07E-07 929330000 1454490 1392500 1571480 1587780 1317960 1606690 1824590 1732930 1548620 TRUE FALSE 1385739.14 1534397.333 1643533.912 1428173.338 1547811.807 1551049.922 1546215.285 1581185.462 1788772.08 0.774687371 0.857793651 0.91880566 0.7984099 0.865292914 0.867103159 0.86440039 0.883950214 1 20.77053814 -5 0.130789475 1.50264275 0.788485509 0.653208282 0.036140528 88.78918423 0.730969396 11.67776343 0.260908844 1.00E-05 5 -0.714157241 NVALLSQLYHS(ph)PARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PARR;NVALLSQLYHS(1)PARR 150.65 1.48E-06 431040000 1686740 1151430 1308890 1374360 1293600 1360810 2101820 1635210 1374380 TRUE FALSE 1607011.143 1268762.026 1368903.901 1236206.722 1519203.43 1313684.808 1781148.756 1492022.344 1587511.831 1.01228294 0.799214218 0.862295244 0.778707092 0.956971407 0.827511822 1.121975107 0.93984959 1 20.59833591 1.749526973 25 1.028223611 0.874274009 0.418703073 0.081906736 2.597413018 5932.319846 0.035267428 0.019557859 56.17291649 -1.749526973 -0.153949602 NVASVCLQIGYPTVASVPHSIINGYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVASVCLQIGYPTVASVPHSIINGYKR 27 1 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VZS0;F8W1K8 F8VWS0 RPLP0 60S acidic ribosomal protein P0 0 110.68 0.00089541 75529000 62731 44943 55080 65244 53681 60187 79145 76140 59416 FALSE TRUE 59765.82995 49522.7428 57605.47248 58685.54916 63042.9494 58102.7091 67069.97665 69472.77796 68629.92983 0.870842067 0.721591045 0.83936371 0.855101401 0.918592654 0.846608896 0.977270075 1.012281058 1 16.06655026 2.085327691 0.71429331 1.016882182 0.799290641 0.697126433 0.048454986 0.357047046 0.347523175 0.041021947 0.023743836 121.7104005 -2.085327691 -0.217591541 NVATETQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NVATETQLK 9 0 Q5T3J3 Q5T3J3 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1 0 ;;; 83.998 0.01579 3521590000 2468810 2472790 2597500 2483880 8981800 2428690 4390860 2934340 12733600 FALSE TRUE 2352114.244 2724770.112 2716597.944 2234195.663 10548223.08 2344583.856 3720953.663 2677393.634 14708261.65 0.159917895 0.185254395 0.184698777 0.151900729 0.717163138 0.159405912 0.252983918 0.182033315 1 23.81012341 -4.831729993 0.376949134 10 0.224849496 0.655989656 0.170257445 301.6017776 2.593559287 2206.820734 0.109704436 1.47E-05 4.831729993 -9.775150504 NVCSEAAQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVCSEAAQKR 10 1 Q96AT9-4;Q96AT9;C9J6A7;Q96AT9-5;Q96AT9-3;Q96AT9-2 Q96AT9-4 RPE Ribulose-phosphate 3-epimerase 0 87.001 0.021124 59874000 74997 46196 57941 60039 58821 67309 79127 71575 69777 FALSE TRUE 71452.04044 50903.42492 60597.65216 54003.76565 69079.36378 64978.07245 67054.72288 65307.51356 80597.66079 0.886527472 0.63157447 0.751853733 0.670041353 0.857088942 0.806202957 0.831968598 0.810290434 1 16.29845035 0.660112611 0.476728342 1.009668532 0.741993961 0.484429114 0.075405383 1.339511299 0.636151441 0.11006243 0.041578251 4.572067264 -0.660112611 -0.267674571 NVDAAVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVDAAVSPR 9 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 NVDAAVS(1)PR 105.66 0.00346 0 337260 282020 300190 355440 297960 327780 365610 322820 312240 TRUE FALSE 321318.3882 310758.1586 313954.0084 319710.4959 349924.1297 316428.8964 309829.4796 294552.1694 360660.5845 0.890916285 0.861636042 0.870497143 0.886458098 0.970231139 0.87735924 0.859061103 0.816701858 1 18.46028224 -2.580265474 2.281071717 3.542342801 0.879338929 0.496454628 0.038262537 4493507.011 466247.6663 58758800.61 0.009489442 0.002628661 2.580265474 -2.663003872 NVDLLSDMVQEHDEPILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 295.65 2.59E-49 1570231000 3813285 3456920 3431645 4102979 2635835 3811520 4295822 4186962 2540615 FALSE TRUE 3633038.575 3809184.078 3588989.318 3690539.756 3095523.789 3679526.107 3640415.456 3820329.411 2934600.599 1.238001034 1.298024706 1.222990726 1.257595244 1.054836488 1.253842212 1.240514794 1.30182261 1 21.48473273 -2.282238256 2.222675802 9.90E-05 1.235845348 0.53555893 0.068290332 2794705.071 576612.9429 13939278.38 0.016209888 0.005221097 2.282238256 1.235746388 NVELVEGEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVELVEGEEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 133.07 0.000394 87685000 79101 72346 74329 93947 64361 76962 99544 71522 68404 FALSE TRUE 75362.05249 79718.13965 77737.05817 84503.26907 75585.53802 74296.78664 84356.73455 65259.15452 79011.74296 0.953808253 1.008940401 0.983867148 1.069502658 0.956636763 0.940325879 1.067648066 0.825942475 1 16.26977947 1.245362657 24.99993644 0.912971234 0.996831014 0.254155725 0.060016969 182.7687793 671759.012 0.037625069 0.013053045 17.5939218 -1.245362657 0.08385978 NVFEVGPGDS(ph)PTFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 NVFEVGPGDS(0.951)PT(0.049)FPR 89.039 0.0057157 0 262560 231960 247170 283090 182130 257100 319100 303820 207420 TRUE FALSE 250149.3091 255596.9877 258502.989 254633.2554 213893.4143 248196.5625 270415.4343 277215.9101 239585.6342 1.044091437 1.066829355 1.078958635 1.062806859 0.892763938 1.035940921 1.128679669 1.157063991 1 17.87018188 1.762664978 12.34037762 1.10700482 1.033353326 0.172134239 0.065304113 0.481244314 243.0299163 0.029683663 0.016367132 57.89818873 -1.762664978 -0.073651494 NVFIIGATNRPDIIDPAILRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVFIIGATNRPDIIDPAILRPGR 23 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 264.52 3.30E-44 1472460000 1970800 1661610 1606440 2033440 1362230 1776950 1925500 1919570 1335620 FALSE TRUE 1877644.19 1830929.948 1680096.863 1829034.748 1599802.481 1715413.776 1631729.611 1751482.275 1542741.128 1.217083123 1.186803097 1.08903356 1.185574634 1.036986991 1.111925873 1.057682058 1.135305362 1 20.55706457 8 0.152307331 0.997724233 1.859198609 0.592176231 0.044766631 37.96203889 0.377832982 0.131614527 7.257594462 100000000 -8 0.861474376 NVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEK 36 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 165.8 5.43E-18 77193000 162310 60784 164240 104950 131690 143490 276380 177920 197220 FALSE TRUE 154637.928 66977.95871 171770.5665 94400.22661 154656.6943 138520.9053 234213.1549 162340.3816 227803.8703 0.67882046 0.294015894 0.754028306 0.414392549 0.678902839 0.608070904 1.0281351 0.712632236 1 17.79743273 1.870092979 4.966594203 0.906810241 0.547083479 0.513338786 0.15678304 0.166133452 5.749977021 0.066588338 0.038823941 74.14689661 -1.870092979 -0.359726762 NVGESVAAALS(ph)PLGIEVDIDVEHGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVGESVAAALSPLGIEVDIDVEHGGKR 27 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 NVGESVAAALS(1)PLGIEVDIDVEHGGKR;NVGESVAAALS(1)PLGIEVDIDVEHGGKR;NVGESVAAALS(1)PLGIEVDIDVEHGGKR 164.84 4.78E-12 201649000 233180 150770 204625 206202 163978 210415 252932 208372 156266 TRUE FALSE 222158.0435 166133.6344 214007.2587 185474.1832 192575.7113 203128.2758 214342.578 190125.843 180498.9332 1.230799759 0.920413387 1.18564279 1.027563875 1.066907753 1.12537106 1.187500525 1.053334996 1 17.46163078 2.235980713 24.89930775 1.116432615 1.078637683 0 0.097212741 269.6830392 2602731.411 0.033095781 0.025609482 172.1792107 -2.235980713 -0.037794932 NVGIFLKNEDEEEEEEEKDEAEDLLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVGIFLKNEDEEEEEEEKDEAEDLLGR 27 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 117.08 0.0003117 19330000 41855 19635 42192 36115 21669 45888 55047 47397 19452 FALSE TRUE 39876.5971 21635.82882 44126.54493 32484.65159 25448.06674 44298.88705 46648.56914 43246.66741 22468.51681 1.774776565 0.962939788 1.963927806 1.445785312 1.132609996 1.971598189 2.076174833 1.924767343 1 14.45561727 2.220734043 24.9972644 1.863847026 1.440372864 0.075472553 0.410319928 373.0765942 523142.3939 0.14066735 0.104108351 166.2394308 -2.220734043 -0.423474162 NVHS(ph)EDFENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 NVHS(1)EDFENR;NVHS(1)EDFENR;NVHS(1)EDFENR 154.6 0.0014565 58475000 303906 365196 320183 392166 326532 342817 371594 335922 369846 TRUE FALSE 289540.9657 402409.8876 334863.7073 352744.7286 383479.0774 330945.1613 314900.5105 306506.8888 427199.8288 0.677764704 0.941971088 0.783857307 0.825713647 0.897657376 0.774684677 0.737126959 0.71747896 1 18.70455154 NVICDKCEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVICDKCEGR 10 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 84.479 0.013583 444630000 1399500 1065780 1202190 1319680 735030 1347010 1475990 1377680 909430 FALSE TRUE 1333348.409 1174384.194 1257311.601 1187023.259 863218.9993 1300362.706 1250800.617 1257043.036 1050459.76 1.269299843 1.117971615 1.196915531 1.130003552 0.821753514 1.237898638 1.190717308 1.196659866 1 20.00258947 4.883804404 1.075128708 1.117687406 1.38408619 0.141474657 0.121873288 4.829101725 3.745126165 0.035624408 1.577726073 76525.18787 -4.883804404 0.266398785 NVIGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVIGAR 6 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 110.54 0.066582 375061000 279630 252730 250730 290460 242090 288000 288650 291010 239590 FALSE TRUE 266412.4441 278483.4743 262226.2185 261262.409 284310.4194 278026.4878 244611.1411 265527.6217 276744.3935 0.962666093 1.006284069 0.947539407 0.944056736 1.0273394 1.004632774 0.883888334 0.959468838 1 18.07819456 1.764782993 25 0.935824294 0.982333712 0.124437498 0.038778428 23.61073485 22524.65227 0.01681999 0.009328127 58.18124272 -1.764782993 0.046509418 NVIGLQMGTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVIGLQMGTNR 11 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 208.6 4.42E-08 186830000 409000 389580 317650 375740 291980 413190 464140 484050 338890 FALSE TRUE 389667.3806 429278.6449 332214.5667 337969.9013 342901.2196 398881.1267 393326.9185 441664.0159 391443.3304 0.995463073 1.096655918 0.848691345 0.863394201 0.875991984 1.019000953 1.004811905 1.128296184 1 18.57844394 -0.37878464 7.80766772 0.999998068 0.983511648 0.002880442 0.09415437 0 0 0.093715649 0.02208899 0.418037614 0.37878464 -0.016486421 NVIIWGNHSSTQYPDVNHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVIIWGNHSSTQYPDVNHAK 20 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51;C9JF79 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ; 284.88 2.89E-45 1539710000 629370 433780 587320 664330 617950 562090 897470 700960 346962 FALSE TRUE 599620.9274 477982.6752 614249.2029 597550.2863 725720.2843 542624.6824 760544.4683 639580.2264 400767.0949 1.496183032 1.192669461 1.532683723 1.491016338 1.810828018 1.353965156 1.897721839 1.595890068 1 18.61240454 3.55679512 5.705255598 1.586668325 1.344251129 0.044808446 0.258391371 0.389369591 21.34014454 0.062148702 0.096408505 3604.085791 -3.55679512 -0.242417197 NVIKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVIKEK 6 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 69.998 0.083928 307330000 532490 256210 580380 365590 472610 512560 893090 664530 685300 FALSE TRUE 507320.253 282318.0903 606990.9971 328840.1986 555033.0344 494809.9187 756832.7178 606340.2303 791572.824 0.640901554 0.356654602 0.766816367 0.415426337 0.701177475 0.625097153 0.956112558 0.765994248 1 19.59436256 1.951946863 1.08004356 0.940964937 0.531860517 0.549848755 0.136370422 0.329359146 0.706286429 0.096972959 0.04378399 89.52552219 -1.951946863 -0.40910442 NVKDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVKDLR 6 1 A0A0A0MSQ3 A0A0A0MSQ3 UHRF2 0 69.344 0.0855 291950000 554640 430570 568050 488290 555790 550660 750340 645220 635700 FALSE TRUE 528423.2664 474445.5725 594095.6544 439206.1615 652719.6 531590.5061 635861.8521 588721.1163 734281.1093 0.719647094 0.646136155 0.809084759 0.598144438 0.888923318 0.723960482 0.865965152 0.801765303 1 19.48597296 1.009122053 0.293034703 1.040996378 0.658063271 0.550922812 0.079486641 1.325761146 0.360020517 0.186894978 0.110486232 10.21226446 -1.009122053 -0.382933107 NVKFPDEDEILEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVKFPDEDEILEK 13 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 79.633 0.018221 1039800000 1729800 826530 1628800 1172200 1154900 1971500 3095400 2432700 2102200 FALSE TRUE 1648035.782 910754.3467 1703482.091 1054368.229 1356314.194 1903226.461 2623139.879 2219679.891 2428198.439 0.678707208 0.375074101 0.701541548 0.434218313 0.558568102 0.783801863 1.080282335 0.914126233 1 21.2114549 2.049672938 2.964295449 1.000562072 0.538188296 0.791232318 0.105350969 0.101601212 1.762614688 0.045078809 0.027846661 112.1173794 -2.049672938 -0.462373776 NVKGPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVKGPVR 7 1 P62857 P62857 RPS28 40S ribosomal protein S28 0 68.422 0.056996 195710000 568870 279890 336740 284510 522270 344570 813650 523640 682120 FALSE TRUE 541980.6425 308411.1092 352179.8621 255910.5143 613353.7226 332637.4545 689512.7488 477787.3056 787899.6858 0.687880262 0.391434487 0.446985661 0.324800884 0.778466769 0.422182494 0.875127584 0.606406265 1 19.58765243 1.270463905 0.660195625 0.977987451 0.486120437 0.462080532 0.163562417 0.556316271 0.575122056 0.145450366 0.064131951 18.64077244 -1.270463905 -0.491867014 NVKLPDAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NVKLPDAYER 10 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 105.17 0.0023572 1822750000 4468260 2149403 4319660 3611830 4009120 4298680 6662730 4908520 5065560 FALSE TRUE 4257054.205 2368429.609 4517720.684 3248761.986 4708309.259 4149815.634 5646208.169 4478703.967 5851101.174 0.727564621 0.404783568 0.772114607 0.555239414 0.804687719 0.709236691 0.964982146 0.765446338 1 22.48027673 2.207925852 0.731490455 0.947029852 0.578903461 0.490897552 0.123920753 0.489653872 0.502390023 0.094139226 0.058054325 161.4082956 -2.207925852 -0.368126392 NVLFSHLDDNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 155.98 7.28E-05 48159000 45189 42803 42621 51769 39902 41709 51009 44576 38653 FALSE TRUE 43053.00553 47164.67436 44575.21501 46565.08177 46860.89617 40264.60687 43226.64021 40672.68913 44647.10983 0.964295465 1.056388074 0.998389709 1.042958479 1.049584091 0.901841284 0.968184511 0.910981456 1 15.44627917 2.244895106 24.99999856 0.943885975 1.02154322 0.506282402 0.037803786 114.3930179 451469.6681 0.012171563 0.009951351 175.7499079 -2.244895106 0.077657245 NVLGHMQQGGAPSPFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVLGHMQQGGAPSPFDR 17 0 Q01813;Q01813-2;B1APP6;H0Y757 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 120.24 6.14E-05 127010000 62270 46100 58987 65079 53214 64711 72975 63538 41545 FALSE TRUE 59326.62051 50797.64241 61691.6123 58537.13528 62494.50475 62470.04184 61841.32347 57974.27588 47987.58642 1.236290986 1.058557977 1.285574393 1.219839122 1.302305646 1.301795871 1.288694183 1.208109851 1 15.55037363 3.71818304 24.70195789 1.250597357 1.147424464 0.076025515 0.0996185 1005.179429 1218491.461 0.023530296 0.03650991 5226.164074 -3.71818304 -0.103172893 NVMEEGKDFQPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NVMEEGKDFQPSR 13 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;; 134.02 9.16E-05 2458100000 2391970 1837690 2027430 2318590 1453430 2304490 2594980 2488550 1686730 FALSE TRUE 2278906.319 2024952.7 2120389.671 2085520.928 1706907.732 2224684.933 2199068.141 2270639.369 1948299.474 1.169689952 1.039343657 1.088328411 1.070431397 0.876101315 1.141859844 1.128711561 1.165446791 1 20.89378402 -0.144233802 7.301562081 0.999959443 1.085182763 0.090229597 0.084809985 0 0 0.079722182 0.018790698 0.717407972 0.144233802 0.08522332 NVMLLPVGSADDGAHSQNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVMLLPVGSADDGAHSQNEK 20 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 280.69 1.00E-44 829850000 774450 640070 639770 782140 464110 730940 835280 838880 507180 FALSE TRUE 737843.2833 705293.8607 669104.0873 703517.8012 545050.6371 705627.3645 707842.695 765423.22 585830.8841 1.259481709 1.203920585 1.142145465 1.200888892 0.930389045 1.204489868 1.208271387 1.306560034 1 19.16012473 4.068053556 1.79405784 1.150764594 1.253892604 0.112501709 0.107824005 0.861771901 5.264020046 0.0288308 0.09503097 11696.43618 -4.068053556 0.10312801 NVMSAFGLTDDQVS(ph)GPPS(ph)APAEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVMSAFGLTDDQVSGPPSAPAEDR 24 0 Q92734-2;Q92734;Q92734-4;Q92734-3 Q92734-2 TFG Protein TFG 2 NVMSAFGLTDDQVS(1)GPPS(1)APAEDR 71.44 0.00093336 0 18069 18550 14521 19011 17790 19833 17347 20180 15747 TRUE FALSE 17214.91418 20440.26609 15186.80221 17099.97816 20892.57037 19146.17824 14700.39655 18412.93222 18188.96434 0.946448289 1.123772949 0.834945956 0.940129292 1.148639911 1.052626081 0.808204155 1.012313394 1 14.15077578 1.774547499 25 0.920022651 1.012600728 0.071450955 0.105974197 80.29129177 55802.46364 0.047369015 0.026288233 59.50418329 -1.774547499 0.092578077 NVMVEPHRHEGVFICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVMVEPHRHEGVFICR 16 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 81.656 0.0073135 89187000 78283 59331 75136 82058 61444 79454 92889 63283 26310 FALSE TRUE 74582.71773 65376.89635 78581.05992 73809.37394 72159.81415 76702.48806 78717.07703 57741.60504 30390.02043 2.454184521 2.151262008 2.585752126 2.428737227 2.374457573 2.523936706 2.590227842 1.900018632 1 14.89131002 0.942036795 3.730677903 1.001343137 2.426708114 0.929893792 0.127316306 0.070074025 2.57913525 0.131897707 0.03391439 8.750579098 -0.942036795 1.425364977 NVNANLLAEAGTS(ph)QDGGDAGTSHDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVNANLLAEAGTSQDGGDAGTSHDFK 26 0 Q96DT7-3;Q96DT7-2;Q96DT7;Q96DT7-4 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 NVNANLLAEAGT(0.373)S(0.627)QDGGDAGTSHDFK 102.24 0.0024809 91776000 37377 25479 30111 31752 20592 30328 35703 31857 24238 TRUE FALSE 35610.26328 28075.33907 31491.61913 28560.22864 24183.23828 29277.73376 30255.85162 29067.4322 27996.70525 1.271944787 1.002808681 1.124833042 1.020128204 0.863788723 1.045756402 1.080693294 1.038244748 1 14.77296944 4.957959744 1.183853768 1.022436515 1.502087132 0.567150555 0.068037858 1.776683568 1.510476251 0.019551551 1.185817895 90773.6386 -4.957959744 0.479650617 NVNIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVNIFK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 110.54 0.066582 1783100000 3623500 3297700 3100500 3640400 2370900 3325600 3595800 3545500 2441800 FALSE TRUE 3452224.336 3633739.379 3242660.992 3274460.076 2784384.209 3210433.638 3047194.669 3235037.224 2820461.873 1.223992556 1.288349052 1.149691482 1.160965907 0.987208597 1.138265214 1.080388534 1.146988461 1 21.4275 3.384388479 1.903629107 1.083421646 1.255256419 0.592978962 0.058378923 0.196642821 1.450748186 0.016215505 0.025144508 2423.19564 -3.384388479 0.171834773 NVPHEDICEDS(ph)DIDGDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 1 NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR 314.87 1.80E-61 2020580000 880700 872830 854870 1073680 733919 887410 901420 864250 652473 TRUE FALSE 839071.0564 961772.3693 894066.6351 965751.6465 861914.2412 856678.7692 763891.8233 788571.6883 753655.1805 1.113335486 1.276143778 1.18630729 1.281423749 1.143645348 1.136698574 1.013582661 1.046329553 1 19.52354507 2.004069789 1.664810231 1.01542291 1.210215047 0.722481385 0.051296987 0.185711044 0.961264672 0.030659834 0.015129349 100.9415081 -2.004069789 0.194792137 NVPHEDICEDSDIDGDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ;; 228.01 2.66E-19 1193740000 422790 370443 375335 438270 348522 416060 426440 404310 324479 FALSE TRUE 402805.5546 408191.5629 392544.481 394214.2669 409304.1265 401651.7379 361378.7459 368906.473 374797.5461 1.074728367 1.089098814 1.047350723 1.051805891 1.092067253 1.07164986 0.964197204 0.984281986 1 18.51575198 1.75986479 7.80079792 0.981435815 1.072706477 0.866440029 0.016320104 0.048875916 9.621306853 0.007758191 0.004216495 57.52608115 -1.75986479 0.091270663 NVPNLHVMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVPNLHVMK 9 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 ; 120.12 0.0007167 759370000 1585120 1117380 597950 787770 1018010 834400 1596800 1227100 793500 FALSE TRUE 1510194.519 1231242.292 625366.599 708581.8629 1195550.622 805504.5188 1353178.833 1119648.619 916551.9274 1.647691172 1.343341556 0.682303512 0.773095164 1.304400314 0.878842207 1.476379889 1.221587763 1 19.80585709 3.986891272 6.817334715 1.07553579 1.537300619 0.387501754 0.24435071 0.14976663 37.230809 0.064662692 0.125738967 9702.670253 -3.986891272 0.461764829 NVPNWHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 134.44 0.0031745 1193680000 2184050 2241380 1856420 2209920 1664900 2064470 2178580 2150660 1458297 FALSE TRUE 2080814.285 2469779.17 1941538.693 1987774.643 1955258.033 1992976.886 1846197.609 1962336.809 1684442.251 1.235313519 1.466229649 1.152630013 1.180078831 1.16077475 1.183167238 1.096029031 1.164977195 1 20.68383954 2.874188977 0.328457761 1.020054516 1.405910609 0.503001931 0.083332204 1.583229251 0.328644924 0.099812293 0.222364135 748.4951265 -2.874188977 0.385856094 NVPQEESLEDS(ph)DVDADFK ddPTM_SK-BR-3_Trastuzumab_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;NVPQEESLEDS(1)DVDADFK 399.82 1.77E-127 1046927000 1279189 1347287 1130646 1445270 645879 1353833 1250088 1412946 702682 TRUE FALSE 1218724.271 1484577.077 1182487.237 1299988.714 758520.0931 1306949.424 1059364.116 1289220.958 811650.3358 1.501538553 1.829084535 1.456892439 1.601661031 0.934540478 1.610237027 1.305197657 1.588394535 1 19.63049881 -1.550243359 0.073993616 1.50E-10 2.18785671 0.302908359 0.232499678 127.6674696 1.528469476 36.34794705 12.8736134 0.028168041 1.550243359 2.18785671 NVQRPESVSDHMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVQRPESVSDHMYR 14 1 Q7Z4H3-2;Q7Z4H3;V9GYS5;V9GZ04;Q7Z4H3-3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ; 144.55 5.30E-06 182588000 405740 317120 336810 415170 302190 362450 405880 407230 384520 FALSE TRUE 386561.4743 349434.8885 352253.0717 373436.3228 354891.8403 349898.2656 343955.5515 371570.7823 444149.3977 0.870341098 0.786750788 0.793095912 0.840789889 0.799037086 0.787794079 0.77441409 0.836589635 1 18.76068551 0.962907406 20.08726311 1.000000001 0.807201212 0.817419327 0.028382915 173.4976841 93957.2906 0.028031385 0.007007846 9.181368243 -0.962907406 -0.192798789 NVS(ph)ES(ph)PNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 108.32 0.0017577 232017000 898400 998640 751390 1031270 497240 945580 846510 902250 511330 TRUE FALSE 855934.4125 1100402.551 785841.9747 927604.7803 583958.4986 912834.3275 717359.3523 823244.2069 590624.4449 1.449202484 1.863117182 1.330527345 1.570549252 0.988713731 1.545541055 1.214577823 1.393853935 1 19.17188154 2.66411386 0.190990701 0.920841536 1.903496305 0.344317156 0.214060648 5.466026772 0.527848748 0.743521093 1.642145189 461.4385346 -2.66411386 0.982654769 NVS(ph)ES(ph)PNRKNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 154.69 0.00035271 1645880000 2776800 1945200 2464200 2576100 1405200 2763000 3338800 2781900 1517410 TRUE FALSE 2645546.167 2143418.092 2577186.007 2317145.534 1650266.435 2667316.617 2829404.739 2538302.088 1752722.193 1.509392748 1.222908057 1.470390469 1.322026698 0.941544782 1.521813684 1.614291615 1.448205596 1 20.74116592 KLEEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 KLEEYK 6 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 89.55 0.080234 3581900000 3554100 2802300 3365900 6269400 4956100 7094600 9198100 7706700 5938300 FALSE TRUE 3386104.737 3087857.556 3520229.844 5639188.001 5820442.271 6848912.223 7794760.91 7031860.492 6859181.235 0.493660194 0.450178739 0.513214292 0.822137192 0.848562251 0.998502881 1.136398156 1.025174908 1 22.70960494 2.921788043 1.140106804 1.065936867 0.453233361 0.939370375 0.06052178 0.092923277 0.25570358 0.026755364 0.02987653 835.1953015 -2.921788043 -0.612703506 down NVSES(ph)PNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.018)ES(0.982)PNR;NVS(0.026)ES(0.974)PNR 129.39 0.0011463 686280000 636480 557150 502340 637060 460290 538230 595670 538290 473660 TRUE FALSE 606394.8518 613924.2184 525372.7859 573021.5185 540564.4303 519590.9601 504789.6013 491154.4739 547112.7737 1.108354403 1.122116404 0.960264156 1.047355401 0.98803109 0.949696269 0.92264269 0.897720722 1 19.06147871 3.430200237 0.697709958 0.932817321 1.138983831 0.653949935 0.043667009 0.435477152 0.431442258 0.023069798 0.055064347 2692.776054 -3.430200237 0.20616651 NVSES(ph)PNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVSES(1)PNRK;NVS(0.005)ES(0.995)PNRK;NVS(0.001)ES(0.999)PNRK;NVSES(1)PNRK;NVSES(1)PNRK;NVS(0.001)ES(0.999)PNRK;NVS(0.001)ES(0.999)PNRK 130.36 0.00022257 2778230000 3224081 3054310 2583872 3454027 1987395 2869814 2917800 3080054 2120604 TRUE FALSE 3071685.081 3365547.661 2702345.087 3106821.644 2333996.059 2770431.622 2472636.021 2810348.143 2449456.438 1.254027234 1.373997761 1.103242762 1.268371871 0.952862857 1.131039352 1.009463154 1.147335425 1 21.2240302 3.239761553 1.259811198 1.054584064 1.308942592 0.51150002 0.092412159 0.287744168 0.963623469 0.030271343 0.046043415 1736.846963 -3.239761553 0.254358528 NVSES(ph)PNRKNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.018)ES(0.982)PNRKNEK;NVS(0.015)ES(0.985)PNRKNEK;NVS(0.016)ES(0.984)PNRKNEK;NVS(0.001)ES(0.999)PNRKNEK;NVS(0.001)ES(0.999)PNRKNEK;NVS(0.003)ES(0.997)PNRKNEK 203.53 6.47E-08 1075465000 1924190 993591 1951300 1545846 1183830 1918910 2666170 2186340 1619290 TRUE FALSE 1833237.352 1094839.053 2040769.035 1390454.623 1390289.577 1852457.666 2259396.799 1994892.479 1870401.223 0.980130535 0.585349838 1.091086239 0.74339912 0.743310879 0.990406573 1.207974402 1.066558584 1 20.83491635 2.03810386 4.992799959 1.112207367 0.818737218 0.40750596 0.14541997 0.157268873 9.445630432 0.0540313 0.037897449 109.1701382 -2.03810386 -0.293470149 NVSKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NVSKPR 6 1 Q9Y3U8;J3QSB5;J3KTD3 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;; 141.98 0.010564 3376830000 5355930 4248910 4479670 5313300 3460750 4947180 5923610 5414920 3938360 FALSE TRUE 5102765.803 4681878.76 4685067.3 4779196.989 4064303.704 4775857.916 5019854.5 4940760.899 4549100.754 1.12170868 1.029187748 1.029888664 1.050580598 0.893430136 1.04984659 1.103482814 1.086096168 1 22.11714996 -0.816471665 7.4004811 1.000001933 1.04808392 0.04926211 0.061958624 0 0 0.060368375 0.014228963 0.152590795 0.816471665 0.048081987 NVSS(ph)FPDDATSPLQENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVS(0.047)S(0.953)FPDDATSPLQENR;NVS(0.023)S(0.977)FPDDATSPLQENR;NVS(0.097)S(0.903)FPDDATSPLQENR 197.05 1.62E-11 104403000 229372 228540 227561 256342 201480 241438 265783 244910 194315 TRUE FALSE 218530.0401 251828.4858 237994.8969 230574.0151 236618.0482 233076.9415 225232.9219 223464.3821 224448.3778 0.973631631 1.121988443 1.060354721 1.027291965 1.054220354 1.038443422 1.003495432 0.995615937 1 17.77602414 1.784632683 2.519733258 0.997333277 1.050647328 0.269506284 0.03604571 0.35170249 4.370578274 0.021687624 0.010062443 60.90215813 -1.784632683 0.053314051 NVSSFPDDAT(ph)SPLQENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDAT(0.5)S(0.5)PLQENR 388.47 8.76E-121 786020000 420010 385960 429050 474090 362410 424100 474610 448860 436970 TRUE FALSE 400156.9597 425289.7628 448722.3669 426433.5725 425614.1893 409413.3107 402199.5277 409555.4388 504733.0759 0.792809068 0.842603315 0.88902905 0.844869482 0.843246083 0.81114817 0.796855897 0.81142976 1 18.94516111 -1.930349742 2.417159505 1.116954199 0.827650198 0.782319896 0.028339819 3480539.482 1741803.532 2298221.407 0.007763784 0.011739518 1.930349742 -0.289304001 NVSSFPDDATS(ph)PLQENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDATS(1)PLQENR;NVSSFPDDAT(0.037)S(0.963)PLQENR;NVSSFPDDAT(0.053)S(0.947)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDAT(0.003)S(0.997)PLQENR;NVSSFPDDAT(0.003)S(0.997)PLQENR 412.96 1.42E-140 3158020000 2212110 2226511 2395760 2532940 2026840 2409600 2781510 2527490 2599060 TRUE FALSE 2107547.944 2453395.002 2505607.966 2278324.059 2380320.254 2326154.948 2357139.564 2306169.577 3002108.951 0.702022471 0.817223839 0.834615934 0.758907853 0.792882701 0.774840283 0.785161232 0.768183172 1 21.5175449 -1.119817962 3.690582438 1.000123904 0.779688858 0.79385612 0.035354852 10302234.07 17233475.93 15206.30648 0.008315315 0.075889561 1.119817962 -0.220435046 NVTELNEPLSNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;; 333.32 3.90E-68 1407611000 896524 751170 773526 916473 937390 820115 960437 884617 989838 FALSE TRUE 854147.0873 827715.077 808992.9322 824347.3929 1100870.519 791714.2119 813904.696 807155.2458 1143337.022 0.747065013 0.723946712 0.707571711 0.721001225 0.962857406 0.692459176 0.7118677 0.70596441 1 20.1248193 -1.097089464 4.419585618 1.000026138 0.744276627 0.507776173 0.078380018 1.92E-05 3.92E-06 0.072211674 0.017018716 0.079966951 1.097089464 -0.255749511 NVTFHGVLLDAFFNESSADWR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 273.27 1.04E-44 829236000 1074865 1715336 957069 1465909 785812 1080851 955556 1181156 595764 FALSE TRUE 1024058.262 1890130.689 1000951.56 1318553.042 922857.364 1043420.859 809768.3822 1077727.719 688152.0384 1.48812792 2.746676001 1.454550019 1.916078088 1.341066091 1.516265012 1.176728887 1.566118617 1 19.39236782 2.935863586 1.222810694 1.298490732 2.06655091 0.353833078 0.384448327 0.42182598 1.3223906 0.153889301 0.174007057 862.7075241 -2.935863586 0.768060178 NVTGHYISPFHDIPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVTGHYISPFHDIPLK 16 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967;D6RGV9;D6RAD3;A0A0C4DGB9 Q9H2U2-2;A0A0C4DGB9 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 108.56 0.0006019 161550000 478950 415110 400120 491770 611580 342020 479540 451700 388750 FALSE TRUE 456310.9827 457410.1809 418465.8978 442336.3453 718239.3584 330175.7616 406377.3656 412146.7534 449035.3645 1.016202773 1.018650683 0.931921917 0.98508131 1.599516241 0.735300129 0.905000803 0.917849207 1 18.77646955 NVTGILWNLSSSDHLKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVTGILWNLSSSDHLKDR 18 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 189.64 1.90E-14 174935000 572110 322400 552020 508910 507130 518210 860970 682850 558380 FALSE TRUE 545067.4941 355252.9265 577330.663 457753.3999 595573.3114 500264.2578 729613.2137 623056.034 644970.7186 0.845104248 0.550804736 0.895126936 0.709727414 0.923411396 0.775638712 1.131234632 0.966022202 1 19.29887414 2.241278392 1.032410141 1.042052427 0.725807519 0.459400091 0.118764918 0.390871916 0.795666862 0.077807341 0.0439934 174.2923767 -2.241278392 -0.316244908 NVVFIDMGHSAYQVLVCAFNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVVFIDMGHSAYQVLVCAFNK 21 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 207.07 3.87E-22 162174000 557300 516880 520630 585150 358250 554790 572650 606700 312960 FALSE TRUE 530957.5335 569550.6596 544501.4005 526329.6103 420728.6866 535577.4832 485281.7251 553574.1317 361492.2384 1.468793731 1.575554325 1.506260281 1.455991455 1.163866445 1.481573949 1.342440234 1.531358278 1 18.46360515 -3.594603885 0.184116735 2.33E-14 1.544046541 0.577400058 0.117163936 52.39216102 0.811165633 20.37998218 0.344419304 0.000254329 3.594603885 1.544046541 NVVGAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 124.94 0.042201 846441000 826681 699648 693790 834938 677929 764653 875430 809602 810910 FALSE TRUE 787605.4275 770942.9266 725600.9578 751008.446 796159.603 738172.8749 741867.0751 738708.9569 936661.7812 0.840864273 0.823075033 0.774666985 0.801792558 0.849996892 0.78808903 0.792033037 0.788661363 1 19.83716867 -0.735492431 6.147175989 1.000000003 0.808810104 0.862388703 0.024173247 1.08E-09 2.35E-10 0.024268812 0.005720214 0.1838686 0.735492431 -0.191189899 NVVHELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVVHELR 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 85.064 0.021085 92943000 102860 92711 78251 95789 87071 88465 103450 95213 84039 FALSE TRUE 97998.01165 102158.3563 81838.88575 86160.10773 102256.1548 85401.43487 87666.80251 86875.64496 97071.33891 1.009546306 1.052404937 0.843079808 0.887595749 1.053412428 0.879780127 0.903117269 0.894967 1 16.56675777 3.757462135 24.75019642 0.919397255 1.030975634 0.341833228 0.062041552 695.4836501 910683.2533 0.015084956 0.027137611 5720.870735 -3.757462135 0.11157838 NVVHQLS(ph)VTLEDLYNGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 NVVHQLS(0.989)VT(0.011)LEDLYNGATR;NVVHQLS(1)VTLEDLYNGATR;NVVHQLS(0.974)VT(0.026)LEDLYNGATR;NVVHQLS(0.995)VT(0.005)LEDLYNGATR 155.05 1.92E-08 56765400 83845 66413.1 62521.6 85836 58036.1 68354.7 71951.3 73746.2 61037.8 TRUE FALSE 79881.81301 73180.6704 65388.2772 77207.6022 68157.57747 65987.5596 60973.80771 67288.59177 70503.23029 1.133023447 1.037976134 0.927450798 1.095093117 0.966729853 0.935950868 0.864837079 0.95440438 1 16.10540174 4.683090515 0.449985999 0.925172709 1.274869051 0.465714663 0.058783003 3.607290327 0.591159507 0.041414696 0.67563629 48204.82553 -4.683090515 0.349696341 NVVHQLSVTLEDLYNGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 245.03 1.49E-24 131950000 142340 122410 126560 141520 105490 128790 149790 136370 109200 FALSE TRUE 135611.8703 134883.7182 132362.9012 127294.1407 123887.4226 124329.97 126936.7844 124428.7199 126134.1783 1.075139761 1.069366923 1.049381722 1.009196258 0.982187574 0.985696119 1.006363114 0.986479014 1 16.94459973 3.297418607 2.139522525 0.992965469 1.072290969 0.954998781 0.007329671 0.055144883 0.516917763 0.002311305 0.003287064 1983.437898 -3.297418607 0.0793255 NVYS(ph)SSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVYSSSR 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 NVYS(0.493)S(0.493)S(0.014)R;NVYS(0.498)S(0.498)S(0.003)R 103.19 0.0088439 163189000 265980 277650 274060 317930 338490 289250 307000 319520 364170 TRUE FALSE 253407.6525 305942.8507 286625.9221 285971.0724 397522.5488 279233.2 260161.5116 291541.1349 420643.6237 0.60242837 0.727320785 0.681398471 0.679841691 0.945034054 0.663823684 0.618484382 0.693083452 1 18.68223895 -2.090944811 2.371737165 1.499037892 0.696369011 0.499323127 0.093838182 12139864.47 3111908.637 32759114.68 0.022245419 0.008110641 2.090944811 -0.802668881 NWASGHDLQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NWASGHDLQGK 11 0 M0R0N0;M0R1K9;O95182 M0R0N0 NDUFA7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 0 89.301 0.012335 190830000 480950 404360 375860 442510 307480 359750 462250 464320 284320 FALSE TRUE 458216.4467 445564.7437 393093.5528 398028.0541 361104.4146 347291.7673 391725.2727 423661.6793 328410.8935 1.395253494 1.356729489 1.196956497 1.211981886 1.09955066 1.057491618 1.192790131 1.290035403 1 18.32514246 3.669008784 1.546523496 1.142493697 1.394941782 0.591392113 0.08012233 0.252281202 1.181265466 0.023432031 0.05097342 4666.688188 -3.669008784 0.252448085 NWDDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NWDDMK 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 107.67 0.072273 986690000 1424660 1265850 1262620 1524670 901830 1382620 1595700 1525090 950700 FALSE TRUE 1357319.145 1394841.554 1320512.376 1371407.275 1059108.866 1334739.523 1352246.658 1391545.035 1098129.7 1.23602808 1.270197458 1.202510391 1.248857284 0.964466097 1.21546619 1.231408874 1.267195518 1 20.06661703 -2.360880969 1.886320086 4.83E-05 1.208572074 0.346718982 0.088068606 2511959.977 252345.5868 10701083.68 0.022194361 0.004356313 2.360880969 1.208523777 NWQDYGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NWQDYGVR 8 0 Q8WU39 Q8WU39 MZB1 Marginal zone B- and B1-cell-specific protein 0 102.46 0.017261 0 239970 183280 154750 171540 187030 168460 226580 182790 180340 FALSE TRUE 228627.0937 201956.4404 161845.4406 154296.4733 219647.9728 162626.188 192011.0596 166783.9386 208306.2062 1.097552963 0.969517155 0.776959283 0.740719521 1.054447569 0.780707358 0.92177311 0.80066716 1 17.6683463 4.091364874 2.864247821 0.865480107 1.07029847 0.339400015 0.102306046 0.247753513 4.014802663 0.024195159 0.062139123 12341.41266 -4.091364874 0.204818364 NWQWWR ddPTM_SK-BR-3_Trastuzumab_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 ; 142.53 0.026789 1903520000 2871800 2422800 1606320 2100950 2091800 1744920 2881200 2297700 1870720 FALSE TRUE 2736055.705 2669686.074 1679971.361 1889758.514 2456609.258 1684492.983 2441620.023 2096501.207 2160821.703 1.266210767 1.23549577 0.777468756 0.874555504 1.136886608 0.779561303 1.129949787 0.970233316 1 21.0431486 3.835937874 8.128684679 0.96220539 1.253567362 0.504025199 0.122760109 0.221275429 16.65032362 0.029606108 0.053552366 6853.901743 -3.835937874 0.291361973 NWRDPDQTDGLGLSYLSSHIANVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 NWRDPDQTDGLGLSYLSSHIANVER 25 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;; 298.31 2.62E-63 927505000 485639 343418 415405 465079 459196 394272 549589 458398 497220 FALSE TRUE 462683.8069 378412.6846 434451.7301 418328.3753 539279.637 380618.2618 465739.1042 418258.241 574326.3382 0.805611333 0.658880952 0.756454478 0.72838097 0.938977723 0.662721238 0.810931126 0.728258854 1 19.1315112 -5 0.311219311 3.158372997 0.746806837 0.45585766 0.081201806 254.114972 2.295386935 359.8127872 0.068557198 1.00E-05 5 -2.41156616 NWTEDMEGGISS(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_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(0.026)S(0.974)PVKK;NWTEDMEGGIS(0.248)S(0.752)PVKK;NWTEDMEGGIS(0.065)S(0.935)PVKK 221.99 6.16E-15 1125630000 1149810 1110410 1056980 1245690 596334 1349600 1286630 1396570 687472 TRUE FALSE 1095460.76 1223562.041 1105443.578 1120470.875 700334.4608 1302863.014 1090330.963 1274278.927 794081.6466 1.379531645 1.540851683 1.392103171 1.411027291 0.881942636 1.640716693 1.373071607 1.604720286 1 19.59892783 3.32779045 3.1767346 1.340654629 1.458918441 0.052476712 0.237039077 0.847320221 17.07065945 0.064500073 0.089121997 2127.112453 -3.32779045 0.118263811 NY(ph)KEKMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYKEKMK 7 2 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 NY(1)KEKMK 43.704 0.095638 736850000 182280 133400 156410 205530 127690 194770 312070 344550 6507700 TRUE FALSE 173663.9856 146993.6117 163581.5532 184869.7339 149959.0956 188025.0661 264457.9899 314379.3754 7516880.879 0.023103198 0.019555134 0.021761892 0.024593942 0.019949644 0.025013708 0.035181879 0.041823115 1 22.84170271 -2.548827406 0.598198306 3.085259897 0.020841776 0.999952252 0.002114873 1.767472856 0.101500739 4.811528111 0.00081171 0.002826003 2.548827406 -3.06441812 NYADHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYADHVR 7 0 Q6P587;Q6P587-2;Q6P587-3 Q6P587 FAHD1 "Acylpyruvase FAHD1, mitochondrial" 0 81.548 0.026903 67582000 178140 128120 137750 152060 244460 123420 180080 120590 245460 FALSE TRUE 169719.6752 141175.5737 144065.9738 136774.6399 287093.7466 119145.9345 152605.4886 110030.5003 283524.6832 0.598606348 0.497930452 0.508124979 0.482408228 1.012588193 0.420231259 0.538244102 0.388080851 1 18.11311481 -1.184740984 4.553198933 1.000086207 0.55579794 0.395311956 0.172663059 0.000139147 2.49E-05 0.153956322 0.036280842 0.06535202 1.184740984 -0.444288267 NYAES(ph)DHS(ph)EDEDNDNNSATAEESTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYAESDHSEDEDNDNNSATAEESTKK 26 1 Q9P2R6;A0A590UJ84;A0A590UK57;H7BYW9 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 NYAES(1)DHS(1)EDEDNDNNSATAEESTKK 164.14 1.44E-11 95250000 106730 84424 94954 108040 58132 105360 121100 105890 57840 TRUE FALSE 101685.0844 93026.90158 99307.73482 97179.61394 68270.20239 101711.3568 102623.9708 96617.71024 66809.53179 1.522014624 1.392419601 1.486430636 1.454577084 1.021863207 1.522407867 1.536067805 1.446166552 1 16.02776633 -1.944241259 2.38902 0.684180273 1.429271738 0.441878566 0.149150823 5429251.581 2328710.129 9526953.337 0.03525433 0.011369955 1.944241259 0.745091465 NYAGAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYAGAYR 7 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ; 159.19 0.0032398 858820000 1185970 808730 687630 712180 954130 714420 1174040 923000 834200 FALSE TRUE 1129911.548 891140.5064 719158.5157 640590.3133 1120529.97 689679.4563 994918.6353 842177.2269 963563.4755 1.172638417 0.924838404 0.746353026 0.664813818 1.16290208 0.715759235 1.032540835 0.87402361 1 19.87802018 4.418078497 2.441897179 0.885066617 1.166614976 0.253999354 0.15261554 0.401430614 4.310785184 0.035940202 0.175759421 26186.56276 -4.418078497 0.281548359 NYDPQKDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYDPQKDKR 9 2 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 48.64 0.097323 177060000 916230 357660 800260 616330 644580 831240 1372000 959470 801300 FALSE TRUE 872921.6237 394105.9606 836952.7126 554375.3374 756994.5479 802453.9504 1162676.201 875453.7203 925561.5115 0.943126538 0.425802019 0.904264819 0.598961096 0.817876001 0.866991486 1.256184691 0.945862279 1 19.81996935 2.080324674 2.749667296 1.090795475 0.711531889 0.42988923 0.169071315 0.209860722 3.123247084 0.073288548 0.045619489 120.316357 -2.080324674 -0.379263586 NYDYYASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ;; 100.02 0.014895 606900000 515113 374941 353194 389221 481184 385280 556654 426832 468378 FALSE TRUE 490764.6293 413147.9142 369388.2943 350095.7656 565102.3373 371937.657 471726.2086 389456.3273 541011.6681 0.907123928 0.763658048 0.682773249 0.647113152 1.044528927 0.687485463 0.871933521 0.71986678 1 19.04530018 NYEYCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYEYCR 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 98.503 0.092734 57674000 157170 144830 112700 143250 122750 117320 149950 149090 142320 FALSE TRUE 149740.8856 159588.3417 117867.4065 128850.2378 144157.5611 113257.179 127072.3735 136034.8892 164390.2587 0.910886611 0.970789528 0.716997512 0.783807014 0.876922771 0.688953104 0.772992113 0.827511863 1 17.32676529 3.749973748 24.81514859 0.793392032 0.940838079 0.263153559 0.088112447 645.4358843 1403343.089 0.02023377 0.036063808 5623.073344 -3.749973748 0.147446047 NYGYNPS(ph)PVKPEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 NYGYNPS(1)PVKPEGLR 102.37 0.00094293 375330000 351060 311790 329990 406590 180240 360980 405790 401170 221860 TRUE FALSE 334466.0895 343561.7555 345120.3679 365718.8007 211673.7989 348479.1721 343879.2827 366041.4281 256264.9157 1.30515755 1.340650766 1.346732802 1.427112251 0.825996014 1.359839567 1.341889824 1.428371211 1 17.96727645 -2.257625299 2.03679986 4.47E-05 1.298717854 0.227260547 0.172067845 3162708.477 532933.4412 14519164.1 0.04101644 0.00552554 2.257625299 1.298673177 NYILDQTNVYGS(ph)AQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYILDQTNVYGSAQR 15 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 NYILDQTNVYGS(1)AQR;NYILDQTNVYGS(1)AQR 259.14 1.00E-16 37869000 201162 168041 165139 219360 175925 185894 212910 201798 175529 TRUE FALSE 191653.4709 185164.5689 172710.7865 197309.516 206606.2643 179456.4442 180426.6691 184127.4973 202749.1408 0.945273899 0.913269315 0.851844727 0.973170664 1.019024117 0.885115682 0.889901029 0.908154267 1 17.62933628 4.68979337 3.834662415 0.923821665 0.946359591 0 0.053218063 1.469872168 37.86337476 0.012580811 0.08322737 48954.58457 -4.68979337 0.022537926 NYISQYSEIAIQMMMHMQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYISQYSEIAIQMMMHMQPK 20 0 P07602 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 ; 211.49 2.66E-22 263160000 463710 310480 338630 343340 296130 393220 531420 476020 256030 FALSE TRUE 441791.3473 342118.265 354156.5205 308826.8109 347774.9782 379602.6928 450342.1188 434337.1653 295733.8248 1.493881695 1.156845231 1.197551618 1.044272873 1.17597295 1.283595791 1.522795437 1.468675981 1 18.17393974 1.988246278 21.88757476 1.392233104 1.223552665 0.046959059 0.179302859 196.3816229 365697.0543 0.068043843 0.046659663 97.32990009 -1.988246278 -0.168680439 NYIVEDGDIIFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYIVEDGDIIFFK 13 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 183.08 2.48E-05 46564000 176115 138920 163672 180290 113698 173704 183493 192187 119031 FALSE TRUE 167790.393 153076.1059 171176.5231 162166.9067 133526.8952 167688.5869 155497.7728 175358.0874 137489.7196 1.220385011 1.113364013 1.245013254 1.179483871 0.971177304 1.219644548 1.130977453 1.275426905 1 17.06896422 -2.333738606 2.285207454 0.051121155 1.163885111 0.2758586 0.085854931 2450101.307 462088.2724 12376517.14 0.018834501 0.004637259 2.333738606 1.112763956 NYLLSLPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYLLSLPHK 9 0 P28482 P28482 MAPK1 Mitogen-activated protein kinase 1 0 64.297 0.070435 154310000 390530 295180 215480 258760 322040 250040 442560 340020 300430 FALSE TRUE 372070.4209 325259.1776 225359.9711 232748.9532 378203.674 241381.0521 375039.3438 310246.0462 347019.15 1.07218988 0.937294606 0.649416527 0.670709248 1.089863986 0.695584241 1.080745382 0.894031486 1 18.40465575 -1.257931962 6.609646656 1.000001252 0.899472201 0.037846774 0.168928374 3.02E-06 3.39E-07 0.15841525 0.037338367 0.055216394 1.257931962 -0.100529051 NYLPAINGIVFLVDCADHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYLPAINGIVFLVDCADHER 20 0 Q9Y6B6;D6RD69;D6RDB2;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 170.38 9.38E-12 152945000 333600 279670 309380 348170 303150 287800 373340 326540 275060 FALSE TRUE 317831.3891 308168.691 323565.379 313171.2901 356019.264 277833.4138 316380.1261 297946.4265 317714.9 1.000366647 0.969953537 1.018414242 0.985699097 1.120562064 0.874473982 0.995798831 0.937779206 1 18.27737322 -0.359148141 6.232375139 0.999999998 0.987378338 0.003716586 0.061873207 0 0 0.053482822 0.012606022 0.437372889 0.359148141 -0.012621659 NYLPAINGIVFLVDCADHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYLPAINGIVFLVDCADHSR 20 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 180.83 5.32E-17 842970000 727780 613090 656260 703570 540560 669430 761470 657700 497410 FALSE TRUE 693379.2817 675564.568 686350.1701 632845.8069 634833.4929 646247.4712 645293.7661 600108.3013 574545.8024 1.206830298 1.175823695 1.194596092 1.101471465 1.104931043 1.124797133 1.123137204 1.044491664 1 19.13206238 7.999999988 0.056210155 0.760944736 1.871203675 0.844148938 0.025286251 137.6811303 0.58055932 2.458052909 12.75252799 99999997.2 -7.999999988 1.110258939 NYQFDFLRPQHSLFNYFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYQFDFLRPQHSLFNYFTK 19 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 159.26 2.03E-11 177608000 401160 391480 253902 304486 292502 289067 423350 359680 235464 FALSE TRUE 382197.9618 431372.2571 265543.6578 273878.4888 343514.2562 279056.5373 358760.1821 328184.5124 271978.5545 1.405250361 1.586052466 0.976340426 1.006985603 1.263019641 1.026024047 1.319075259 1.206655845 1 18.05313337 3.745175849 24.99922093 1.134655073 1.495651427 0.609387096 0.126188941 329.3112505 1244476.471 0.032143859 0.05630839 5561.293921 -3.745175849 0.360996355 NYQQNYQNS(ph)ES(ph)GEKNEGSESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 2 NYQQNY(0.013)QNS(0.987)ES(0.936)GEKNEGS(0.064)ES(0.001)APEGQAQQR 208.58 7.95E-26 722400000 276200 261060 251350 311600 150910 317400 338650 363270 190840 TRUE FALSE 263144.5734 287662.3108 262874.6461 280277.376 177228.6562 306408.3584 286982.7228 331460.153 220434.4925 1.193754073 1.30497867 1.19252955 1.271476949 0.803996934 1.390020023 1.301895722 1.503667367 1 17.74999046 NYQQNYQNS(ph)ESGEKNEGS(ph)ESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 2 NYQQNYQNS(0.946)ES(0.054)GEKNEGS(0.63)ES(0.37)APEGQAQQR;NYQQNY(0.021)QNS(0.858)ES(0.122)GEKNEGS(0.867)ES(0.132)APEGQAQQR;NYQQNYQNS(0.993)ES(0.007)GEKNEGS(0.916)ES(0.084)APEGQAQQR 276.97 1.93E-71 923160000 1192130 1079740 1101070 1287110 695960 1317920 1346430 1452090 752260 TRUE FALSE 1135780.377 1189766.734 1151555.149 1157727.257 817335.2037 1272280.1 1141007.375 1324937.302 868916.6388 1.307122371 1.369253022 1.325276899 1.332380122 0.940637073 1.464214222 1.313137905 1.524815204 1 19.72885825 2.954159062 24.99892274 1.274029918 1.336539608 0.042340164 0.179164214 1936.265999 1055923.964 0.051182849 0.054289278 899.8270871 -2.954159062 0.06250969 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.994)ES(0.006)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.989)ES(0.011)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.99)ES(0.01)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.951)ES(0.049)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.996)ES(0.004)GEKNEGSESAPEGQAQQR 381.28 1.09E-137 8593120000 2822525 2717523 2745959 3075871 1695723 3142193 3415039 3307347 1824748 TRUE FALSE 2689109.837 2994441.683 2871863.936 2766678.603 1991456.554 3033378.069 2894012.079 3017738.163 2107720.6 1.275837906 1.420701436 1.362544891 1.312640111 0.944838967 1.439174655 1.373052993 1.431754362 1 21.00725221 2.999844078 24.99835381 1.270766839 1.354138639 0.073934269 0.168297543 19.28122229 3092066.128 0.047514907 0.056220158 999.6410409 -2.999844078 0.083371801 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNSESGEKNEGS(0.886)ES(0.114)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.694)ES(0.306)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.999)ESAPEGQAQQR;NYQQNYQNSESGEKNEGS(1)ESAPEGQAQQR;NYQQNYQNSESGEKNEGS(0.63)ES(0.37)APEGQAQQR 495.42 4.43E-301 9866080000 1475568 1323424 1327643 1443055 795053 1568342 1587119 1566990 903119 TRUE FALSE 1405820.825 1458282.41 1388516.745 1297996.37 933709.9915 1514029.923 1344974.847 1429776.048 1043170.082 1.347642967 1.397933506 1.331054992 1.244280671 0.895069757 1.451373989 1.289315012 1.370606839 1 19.99254297 -2.269545337 1.94855457 4.24E-05 1.298379857 0.264726011 0.151912767 4035403.953 556319.7565 17760527.74 0.036284497 0.005375943 2.269545337 1.298337475 NYQQNYQNSESGEKNEGSESAPEGQAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 412.52 5.83E-175 458330000 198249 175917 191661 219028 126199 213829 220596 207433 136646 FALSE TRUE 188878.1627 193843.1423 200448.8464 197010.8893 148208.0656 206424.0481 186940.0287 189269.0668 157836.3638 1.196670768 1.228127268 1.269978867 1.248197086 0.938998226 1.307835806 1.18439138 1.19914741 1 17.2680701 -4.254035453 0.302705233 1.70E-09 1.210529822 0.282064874 0.098775843 216.1266784 3.060568891 135.5506245 0.090184798 5.57E-05 4.254035453 1.21052982 NYS(ph)SPPPCHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.621)S(0.379)PPPCHLSR 113.59 0.00074057 155600000 154460 125710 147900 173160 194080 144580 225190 193110 242390 TRUE FALSE 147158.9819 138519.9919 154681.3613 155753.6278 227927.4906 139573.1583 190833.1296 176200.2647 279978.6032 0.525607958 0.494752064 0.552475652 0.556305468 0.814088962 0.49851366 0.681598977 0.629334751 1 18.09495705 -4.999999999 0.142663514 2.4653195 0.439300219 0.702592244 0.087296188 69.43614624 0.60199357 28.78318693 0.463420008 1.00E-05 4.999999999 -2.02601928 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYSEVIEVDESDVEEDIFPTTSK 23 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 1 NYSEVIEVDES(1)DVEEDIFPTTSK 139.36 1.33E-07 38243000 161100 131340 132260 158810 109400 151340 176790 173520 127720 TRUE FALSE 153485.1223 144723.6953 138324.2518 142846.1171 128479.3254 146099.0579 149817.4385 158325.6689 147526.1653 1.040392543 0.981003573 0.937625211 0.968276487 0.870891785 0.990326411 1.015531301 1.073203988 1 17.17061133 1.698890585 3.230254599 1.037072127 0.967309101 0.317287678 0.045738055 0.279502586 6.603784901 0.028206934 0.012887596 49.9908573 -1.698890585 -0.069763026 NYSS(ph)PPPCHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.209)S(0.791)PPPCHLSR 73.208 0.025647 135080000 168410 135840 151170 178650 215750 148790 252510 205690 251520 TRUE FALSE 160449.5931 149682.2504 158101.294 160691.7626 253376.7317 143637.365 213984.9618 187678.6932 290524.437 0.552275721 0.515213976 0.544192756 0.553109281 0.872135695 0.494407171 0.736547204 0.645999679 1 18.14829999 -5 0.122179015 2.331939034 0.415275738 0.60531935 0.105000186 92.7604702 0.730531379 30.23442121 0.857958161 1.00E-05 5 -1.916663297 NYSVGSRPLKPLS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYSVGSRPLKPLS(1)PLR;NYSVGS(0.001)RPLKPLS(0.999)PLR 174.2 2.06E-09 4831800000 7072700 5635300 5513400 6275600 3730200 6218600 7410000 7120600 4005800 TRUE FALSE 6738387.488 6209543.477 5766194.843 5644764.765 4380745.699 6003248.323 6279468.406 6497082.515 4626999.005 1.4563192 1.342023949 1.246206199 1.21996239 0.946779045 1.297438862 1.357136321 1.404167692 1 22.14164536 4.008190523 1.798378818 1.226075613 1.440368392 0.245905832 0.142938936 0.553407057 3.430136514 0.040394548 0.121480259 10190.38338 -4.008190523 0.214292779 NYTEEEDRFLICMLHK ddPTM_SK-BR-3_Trastuzumab_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 ; 139.04 1.99E-06 78081000 160625 149873 138455 184565 110045 144382 160732 159923 102353 FALSE TRUE 153032.5746 165145.2291 144803.2987 166012.1755 129236.8132 139382.0151 136209.3814 145919.2943 118225.3805 1.294413889 1.396867816 1.224807212 1.404200814 1.093139329 1.178951715 1.152116244 1.234246773 1 16.85118026 2.734771271 24.998465 1.14578224 1.33139487 0.6098681 0.078390753 211.5978888 1395913.91 0.022139296 0.021620929 542.9642945 -2.734771271 0.18561263 NYVPPKGDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYVPPKGDKK 10 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 85.813 0.0078652 714690000 1954920 1543950 1752510 2179560 1108210 2194250 2464640 2536600 1234330 FALSE TRUE 1862514.806 1701280.26 1832864.317 1960466.488 1301481.473 2118262.572 2088613.902 2314481.857 1425743.592 1.306346257 1.193258219 1.285549749 1.37504843 0.912843993 1.485724771 1.464929538 1.623350699 1 20.44328312 NYVPSYDPSS(ph)PQTSQSWYLG ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NYVPSYDPSSPQTSQSWYLG 20 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;Q5VW31 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 NYVPSYDPS(0.013)S(0.986)PQT(0.001)SQSWYLG;NYVPSYDPS(0.053)S(0.762)PQT(0.173)S(0.012)QSWYLG 190.11 2.04E-17 70002000 201504 203217 198431 228146 176835 216366 241112 237438 213416 TRUE FALSE 191979.3053 223925.0433 207529.2576 205212.3306 207674.968 208873.1912 204325.9361 216646.67 246511.4633 0.778784494 0.908375782 0.841864532 0.832465671 0.842455621 0.847316341 0.828869917 0.878850286 1 17.91129521 0.86152781 3.714457777 0.99997585 0.842540934 0.721642472 0.031151636 0.376011118 9.102848443 0.028394218 0.007294969 7.26988951 -0.86152781 -0.157434917 NYVPSYDPSSPQTSQS(ph)WYLG ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 NYVPSYDPSSPQTSQSWYLG 20 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;Q5VW31 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 NYVPSYDPS(0.098)S(0.112)PQT(0.167)S(0.167)QS(0.252)WY(0.204)LG 70.622 0.019296 33049000 53210 55207 49436 63102 43001 54928 62075 61078 58328 TRUE FALSE 50694.86875 60832.65607 51702.6895 56758.86707 50500.36079 53025.82959 52604.31866 55729.68653 67373.20834 0.752448488 0.902920576 0.767407264 0.842454567 0.749561466 0.787046229 0.780789871 0.827178754 1 16.03988738 0.880249593 7.032157732 0.999999776 0.802336519 0.653791236 0.045849121 2.272719027 133.4604716 0.042189598 0.010580037 7.590136624 -0.880249593 -0.197663258 NYYEQWGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 236.21 3.05E-08 26487060000 10171370 8151730 8284900 9874490 6480770 9490800 10480910 9383680 7114550 FALSE TRUE 9690589.498 8982400.555 8664770.86 8881887.505 7611014.236 9162131.216 8881854.684 8561995.233 8217838.078 1.179213974 1.093036936 1.054385689 1.080805854 0.926157727 1.114907732 1.080801861 1.041879282 1 22.97032747 4.310370322 1.248126285 1.047506665 1.193035184 0.419477288 0.051393979 0.704139805 1.56163204 0.014631634 0.108935086 20434.79674 -4.310370322 0.145528519 NYYGYQGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 NYYGYQGYR 9 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 151.27 0.0001937 1659030000 1101390 738290 655216 773461 820020 761734 1130960 887940 854640 FALSE TRUE 1049329.477 813522.5904 685258.3017 695711.2308 963031.2284 735354.9606 958411.2805 810187.2663 987173.2063 1.062963896 0.824093062 0.694162177 0.704750926 0.975544334 0.744909764 0.970864357 0.820714401 1 19.91294371 -0.16239855 7.753967209 0.999999964 0.85864446 0.126402867 0.122161564 0 0 0.116371431 0.027429009 0.688020614 0.16239855 -0.141355504 PAGAT(ph)LERPK ddPTM_SK-BR-3_Trastuzumab_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 91.62 0.016207 150940000 276170 284490 173010 363940 192040 268640 273540 363500 189200 TRUE FALSE 263115.9914 313479.8544 180942.6796 327356.0598 225531.7152 259336.9294 231806.4491 331670.013 218540.1697 1.203970839 1.4344267 0.827960735 1.497921687 1.031992038 1.18667854 1.060704077 1.517661551 1 17.73753896 PAGGPKPPS(ph)GK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PAGGPKPPSGK 11 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 1 PAGGPKPPS(1)GK 60.937 0.0548 80120000 393130 586910 356950 515220 317460 451060 302230 412950 293150 TRUE FALSE 374547.524 646716.7963 373316.5106 463429.1067 372824.9235 435439.6791 256119.2627 376789.9088 338610.2048 1.106131826 1.909915257 1.102496337 1.368621206 1.101044559 1.285961477 0.756383768 1.112754145 1 18.36926593 2.63156092 0.959345847 0.956803643 1.467279585 0.295282007 0.252147373 0.545179663 1.043076857 0.144767764 0.119342629 428.1154686 -2.63156092 0.510475942 PAQPQEHPFASSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 PAQPQEHPFASSR 13 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 132.86 0.00011395 1436160000 512529 457714 490627 588781 416009 514280 569642 558071 418542 FALSE TRUE 488302.7699 504355.577 513122.7332 529595.6153 488560.8379 496470.3546 482732.6507 509203.3447 483447.3557 1.010043315 1.043248186 1.061382852 1.095456639 1.010577123 1.026937781 0.998521649 1.053275685 1 18.88299927 PAS(ph)LGTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PASLGTGK 8 0 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 PAS(0.945)LGT(0.055)GK 66.321 0.06502 51601000 208620 263580 221880 270610 117290 227210 209780 268520 120810 TRUE FALSE 198758.946 290439.1017 232053.4175 243407.7687 137745.3389 219341.6607 177774.2081 245006.9653 139544.5978 1.424339954 2.081335331 1.662933723 1.744300908 0.987106209 1.571839141 1.273959802 1.75576102 1 17.09036675 2.851861141 12.4975747 1.350523552 1.750305116 0.34487046 0.278382871 0.756414108 79.60568462 0.077266663 0.081964199 710.9861503 -2.851861141 0.399781564 PAS(ph)PSLQLLPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 PASPSLQLLPWR 12 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 PAS(0.976)PS(0.024)LQLLPWR;PAS(0.82)PS(0.18)LQLLPWR;PAS(0.999)PS(0.001)LQLLPWR;PAS(0.999)PS(0.001)LQLLPWR 190.03 7.51E-06 406331000 706080 728030 497820 627400 561860 593922 634570 711505 507134 TRUE FALSE 672704.9977 802217.0847 520645.5394 564332.56 659848.2061 573354.3322 537754.6918 649201.8503 585777.7506 1.148396294 1.369490534 0.888810712 0.963390227 1.126448052 0.978791584 0.918018295 1.108273316 1 19.15999387 3.737662606 24.99994926 0.992471843 1.258943417 0.591570989 0.090172363 46.64526441 1298580.312 0.02272262 0.037544415 5465.911636 -3.737662606 0.266471574 PAT(ph)PHLLHHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PATPHLLHHR 10 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 PAT(1)PHLLHHR 109.72 0.0036977 30030000 38432 43461 23099 39174 26715 30450 36822 32336 6039.9 TRUE FALSE 36615.39552 47889.72531 24158.112 35236.15509 31374.08754 29395.50886 31204.12762 29504.48842 6976.536844 5.248362668 6.864397964 3.46276563 5.050665664 4.497086196 4.213481491 4.47272455 4.229102357 1 12.76829534 0.14812617 0.238715647 1.93E-13 6.080809207 0.68999006 0.823725423 3.662573695 0.390507566 6.324820145 1.797816251 1.406456065 -0.14812617 6.080809207 PAVEASTGGEATQETGKEEAGKEEPPPLT(ph)PPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PAVEASTGGEATQETGKEEAGKEEPPPLTPPAR 33 2 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR 166.28 1.69E-12 79138000 104360 130200 93557 140440 40298 107780 79416 95351 24268 TRUE FALSE 99427.10962 143467.528 97846.68099 126322.7044 47325.95844 104047.5516 67299.63063 87001.56095 28031.3575 3.546995883 5.118108463 3.490615144 4.506478304 1.688322032 3.71182707 2.400869477 3.103722714 1 14.77475399 2.751818727 24.77339012 2.571340997 4.21808484 0.505515 0.865051143 554.2843586 1035705.016 0.235560244 0.248479689 564.7012216 -2.751818727 1.646743843 PCIQAQYGTPAPS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 PCIQAQYGTPAPSPGPR 17 0 P22736;F8VVX9;P22736-3 P22736 NR4A1 Nuclear receptor subfamily 4 group A member 1 1 PCIQAQYGT(0.004)PAPS(0.996)PGPR;PCIQAQYGTPAPS(1)PGPR;PCIQAQYGTPAPS(1)PGPR;PCIQAQYGTPAPS(1)PGPR 355.02 8.09E-88 611730000 648030 702850 662720 702110 470904 623110 619460 615040 445372 TRUE FALSE 617398.9062 774471.2141 693106.3675 631532.5689 553029.5085 601531.5445 524949.9998 561183.8371 514438.0151 1.200142462 1.505470419 1.347307833 1.227616448 1.075016799 1.169298393 1.020433919 1.090867744 1 18.97263773 2.964411634 2.224737399 1.072996905 1.363886019 0.695559203 0.084984183 0.162105219 1.602499013 0.027555309 0.031510545 921.3224071 -2.964411634 0.290889114 PCS(ph)LCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PCSLCEK 7 0 A0A087WTR9;A0A087WZ58;O15151-4;O15151-5;O15151 A0A087WTR9 MDM4 Protein Mdm4 1 PCS(1)LCEK 72.021 0.055318 369490000 239930 288120 335760 237040 1416600 239480 396980 313870 1080000 TRUE FALSE 228588.9844 317479.7556 351154.9281 213212.2889 1663654.591 231186.7476 336413.41 286385.8789 1247480.884 0.183240471 0.25449669 0.28149123 0.170914273 1.33361129 0.185322878 0.2696742 0.229571357 1 20.25058628 -2.566097955 2.015739254 9.999981376 0.349809006 0.247649735 0.347898714 14721146.18 651828.1289 607333352.2 0.083234453 0.002715827 2.566097955 -9.65017237 PCSEETPAIS(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(1)PSKR;PCSEETPAIS(0.972)PS(0.028)KR;PCSEETPAIS(0.967)PS(0.033)KR;PCSEETPAIS(0.997)PS(0.003)KR;PCSEETPAIS(0.964)PS(0.035)KR;PCSEETPAIS(0.988)PS(0.012)KR;PCSEETPAIS(0.965)PS(0.035)KR;PCSEETPAIS(0.84)PS(0.16)KR;PCSEETPAIS(0.96)PS(0.04)KR 274.68 5.08E-33 7542620000 3920370 4001410 3802860 4305280 1843486 4675470 4195010 4752120 2044389 TRUE FALSE 3735061.88 4409158.228 3977224.893 3872505.075 2164989.375 4513557.302 3554984.178 4335999.18 2361422.405 1.581700026 1.86716202 1.684249664 1.639903588 0.916815801 1.91137227 1.505441877 1.836181096 1 21.1712247 -1.751729694 2.601144053 0.858945423 1.624027705 0.324238578 0.280192774 37078769.23 28544804.23 33627998.71 0.062589471 0.01771211 1.751729694 0.765082282 PDMGY(ph)NT(ph)LANFRIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PDMGYNTLANFRIEK 15 1 F5H3U7;F8WAG2;Q8TDX7-2;Q8TDX7 F5H3U7 NEK7 Serine/threonine-protein kinase Nek7 2 PDMGY(1)NT(1)LANFRIEK 72.819 0.066619 777310000 1466600 1297500 1404400 1568700 1739100 1294500 1641600 1310600 2109400 TRUE FALSE 1397276.725 1429716.725 1468793.129 1411011.296 2042398.489 1249671.14 1391143.77 1195836.916 2436514.979 0.57347348 0.586787579 0.602825405 0.579110454 0.838245817 0.512892862 0.570956379 0.490798098 1 21.21638766 -1.092858268 4.994847219 1.000007585 0.594152551 0.651614254 0.093207186 1.16E-05 2.11E-06 0.084346744 0.019880133 0.080749851 1.092858268 -0.405855034 PEDIDEEDDDVPDLVENFDEAS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PEDIDEEDDDVPDLVENFDEASK 23 0 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 1 PEDIDEEDDDVPDLVENFDEAS(1)K 40.756 0.093484 4016200000 60243 121460 118640 124970 413480 69614 79587 63470 269360 TRUE FALSE 57395.43278 133836.9121 124079.7614 112407.7782 485590.7811 67203.24972 67444.54143 57912.23032 311130.9731 0.184473542 0.430162612 0.398802344 0.36128765 1.56072787 0.215996656 0.216772187 0.186134571 1 18.2471625 4.240391522 1.21582765 0.529778734 0.169367385 0.073728139 0.426583179 2.271504018 4.994482717 0.127551051 0.830705049 17393.68185 -4.240391522 -0.360411349 PEEQLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PEEQLRK 7 1 A0A590UK20;Q9BXX2 A0A590UK20 ANKRD30B Ankyrin repeat domain-containing protein 30B 0 79.469 0.052177 637390000 534130 623480 416780 623710 395070 522770 475980 519370 365800 FALSE TRUE 508882.7334 687013.3208 435889.7753 561013.4858 463970.0829 504666.3438 403360.509 473891.2094 422526.3958 1.20438093 1.625965449 1.031627325 1.327759618 1.098085439 1.194401933 0.954639788 1.121565929 1 18.68868195 2.890760884 0.792701779 1.028682626 1.391518477 0.342975359 0.156716106 0.580538125 0.805792121 0.090790737 0.102672074 777.6082936 -2.890760884 0.362835851 PEINTNHLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PEINTNHLDK 10 0 Q13907 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 64.86 0.070699 111400000 525970 417380 485640 520970 356470 562200 638160 610480 392160 FALSE TRUE 501108.4405 459911.4965 507907.0744 468601.1058 418638.2551 542730.873 540796.9714 557023.1348 452974.1699 1.106262727 1.01531506 1.121271605 1.034498514 0.924198956 1.198149716 1.193880374 1.229701762 1 18.78906926 2.20320619 24.99927621 1.174926619 1.046312667 0.317253987 0.08146116 176.9410907 125114.8398 0.027799209 0.020531821 159.6637004 -2.20320619 -0.128613952 PFLELDTNLPANRVPAGLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PFLELDTNLPANRVPAGLEK 20 1 P30046;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 167.16 1.29E-11 167020000 337620 293480 298420 335370 232600 307900 368200 362230 252130 FALSE TRUE 321661.3717 323385.9457 312102.8522 301657.9704 273165.3664 297237.3458 312024.3275 330511.2209 291229.0327 1.10449624 1.110417951 1.071674926 1.03581009 0.937974363 1.020630886 1.071405294 1.134884176 1 18.15179466 3.469438118 3.009887589 1.034304367 1.106957822 0.277639094 0.049649406 0.336398654 6.226315144 0.01467234 0.022193105 2947.393476 -3.469438118 0.072653455 PFRLDLLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PFRLDLLEDR 10 1 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 124.42 0.0003976 44351000 102110 66156 82755 72011 93581 88568 116390 96904 105540 FALSE TRUE 97283.46266 72897.37161 86549.39861 64772.31747 109901.4968 85500.86795 98632.56785 88418.57204 121906.6042 0.798016345 0.597977215 0.709964806 0.531327387 0.901522092 0.701363708 0.809083056 0.725297638 1 16.89541676 0.04868823 0.366654007 1.053562477 0.677169686 0.439773035 0.101864458 3.877989346 0.748771122 0.417560269 0.076586064 1.118634554 -0.04868823 -0.376392791 PFVPNVHAAEFVPSFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 119.23 0.00013002 223670000 450450 505190 359590 493560 344110 385510 404230 461430 291760 FALSE TRUE 429158.1212 556669.4354 376077.5572 443946.4111 404122.6751 372159.692 342557.2893 421024.743 337004.6507 1.273448661 1.651815292 1.115941743 1.317330221 1.199160529 1.10431619 1.016476445 1.249314341 1 18.36240898 3.080327983 0.98199549 1.085116251 1.444711216 0.410566912 0.143362283 0.428810691 0.903834531 0.063804138 0.08609981 1203.172739 -3.080327983 0.359594965 PGADGGSLEAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PGADGGSLEAVR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 0 ;; 81.594 0.040072 119625200 11409.4 6280.05 8668.2 9793.5 10748.4 9354.8 10412.5 9329 13556.9 FALSE TRUE 10870.10027 6919.994235 9065.645544 8809.038774 12622.91756 9030.84093 8823.881886 8512.103304 15659.23481 0.694165481 0.441911391 0.578932857 0.562545928 0.806100535 0.576710231 0.56349381 0.543583605 1 13.9347261 -1.299069984 5.207346583 1.000091804 0.589938218 0.634612263 0.096261163 9.89E-05 1.33E-05 0.089811645 0.021164096 0.050226165 1.299069984 -0.410153586 PGDRFDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PGDRFDRDR 9 2 Q5JVS0 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 0 84.213 0.062155 698270000 499410 431420 513180 509520 506880 432960 536270 464280 632330 FALSE TRUE 475803.879 475382.1885 536709.8106 458302.0816 595279.7115 417966.4866 454452.1622 423625.1819 730388.5069 0.651439439 0.650862088 0.734827842 0.627477127 0.815017906 0.572252278 0.62220607 0.579999792 1 19.47830454 -1.13430693 4.50761332 1.000040867 0.65580359 0.69342918 0.071721463 1.546933804 40228741.87 3457.169123 0.015672696 0.073399495 1.13430693 -0.344237277 PGHLQEGFGCVVTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PGHLQEGFGCVVTNR 15 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 218.63 1.91E-12 880400000 891350 1046100 884820 1095700 661300 878460 802420 899880 547070 FALSE TRUE 849217.652 1152698.779 925389.8722 985558.1543 776630.5106 848038.7099 679996.0915 821081.7366 631906.8216 1.343896953 1.824159417 1.46444039 1.559657406 1.229026945 1.342031263 1.076101837 1.299371535 1 19.26935231 2.569550431 1.226721154 1.146018597 1.585201693 0.576462571 0.152885014 0.296003551 0.906920075 0.073977025 0.05854996 371.1508255 -2.569550431 0.439183096 PGHLQEGFGCVVTNRFDQLFDDES(ph)DPFEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PGHLQEGFGCVVTNRFDQLFDDESDPFEVLK 31 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 PGHLQEGFGCVVTNRFDQLFDDES(1)DPFEVLK 122.06 4.91E-06 70421000 58744 34369 66267 56573 36540 60034 89545 69983 55478 TRUE FALSE 55967.28754 37871.24017 69305.4075 50886.17456 42912.56443 57955.00753 75883.26564 63854.91752 64081.2449 0.873380154 0.590987897 1.08152405 0.794088421 0.66965872 0.904398902 1.184172776 0.996468118 1 15.96761455 1.971875795 6.701893781 1.073198402 0.791309252 0.422417413 0.137242632 0.163384345 26.44416859 0.055262917 0.035563618 93.72939096 -1.971875795 -0.281889151 PGHLQEGFGCVVTNRFDQLFDDESDPFEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PGHLQEGFGCVVTNRFDQLFDDESDPFEVLK 31 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 258.25 1.01E-58 273390000 457010 237100 447070 376440 339020 447930 616180 470740 333170 FALSE TRUE 435408.043 261260.7596 467568.6017 338599.536 398144.9807 432418.0718 522170.4241 429519.5101 384836.302 1.131411046 0.678888032 1.214980498 0.879853419 1.034582701 1.123641584 1.35686374 1.116109649 1 18.55388537 2.252939821 2.922862691 1.203733029 0.958126878 0.163942397 0.168707067 0.304865234 5.379259727 0.064234582 0.047378597 179.0357754 -2.252939821 -0.245606151 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPSGTNVGS(0.001)S(0.037)GRS(0.961)PS(0.001)K;PGPTPSGTNVGSS(0.007)GRS(0.985)PS(0.008)K;PGPTPSGTNVGSS(0.001)GRS(0.998)PSK;PGPTPSGTNVGS(0.001)S(0.07)GRS(0.929)PS(0.001)K;PGPTPSGTNVGS(0.001)S(0.015)GRS(0.98)PS(0.004)K;PGPTPSGTNVGS(0.001)S(0.013)GRS(0.985)PS(0.001)K 223.6 1.31E-19 6908930000 1721690 1320054 1557580 2320210 1227440 2126190 2108900 2003720 1091169 TRUE FALSE 1640309.126 1454569.003 1628996.584 2086978.083 1441505.147 2052559.507 1787148.572 1828263.654 1260381.916 1.301438164 1.154070037 1.292462676 1.655829917 1.143705039 1.628521864 1.417942094 1.450563224 1 20.26542953 3.466171081 24.99346976 1.415388426 1.227006099 0.081311521 0.200471935 344.6077797 786555.0041 0.048231035 0.065359915 2925.304513 -3.466171081 -0.188382326 PGPYDRPGTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PGPYDRPGTAR 11 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 96.113 0.0066159 50046000 35122 53892 30999 41021 35755 41099 35903 40549 37288 FALSE TRUE 33461.85267 59383.65607 32420.33481 36897.49115 41990.66068 39675.73132 30425.33795 36998.3146 43070.4326 0.776910067 1.378756899 0.75272833 0.856677979 0.974930089 0.921182559 0.706408924 0.859018876 1 15.39441019 3.688806885 24.99974605 0.853547859 1.077835281 0.210488589 0.167902266 445.5703306 223885.4517 0.042786359 0.066284425 4884.351222 -3.688806885 0.224287422 PGSGAAAS(ph)GGRGDLPYGPGRRS(ph)SGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 PGSGAAASGGRGDLPYGPGRRSSGGGGR 28 3 P54826 P54826 GAS1 Growth arrest-specific protein 1 2 PGS(0.001)GAAAS(0.996)GGRGDLPY(0.013)GPGRRS(0.522)S(0.468)GGGGR;PGS(0.018)GAAAS(0.967)GGRGDLPY(0.042)GPGRRS(0.512)S(0.461)GGGGR;PGS(0.014)GAAAS(0.783)GGRGDLPY(0.227)GPGRRS(0.506)S(0.47)GGGGR;PGS(0.024)GAAAS(0.973)GGRGDLPY(0.015)GPGRRS(0.518)S(0.471)GGGGR 102.53 0.0016017 1430860000 758340 679738 713730 825060 881660 685140 877180 758610 999230 TRUE FALSE 722494.7711 749004.075 746455.2265 742123.4013 1035421.225 661413.43 743350.0805 692182.0868 1154185.485 0.625978043 0.648946018 0.646737666 0.642984521 0.897101236 0.573056444 0.64404733 0.599714774 1 20.13844366 -1.702102049 4.704025607 1.01357063 0.658083851 0.596955696 0.08783441 0.011859878 0.000751066 0.080685365 0.018687762 0.019856283 1.702102049 -0.355486779 PGWLSS(ph)PTLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PGWLSSPTLGR 11 0 Q5XPI4;Q5XPI4-2;C9JS59;C9J266 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 1 PGWLS(0.001)S(0.998)PT(0.001)LGR;PGWLS(0.001)S(0.999)PTLGR;PGWLSS(0.999)PT(0.001)LGR 234.24 1.80E-15 459940000 1312950 1378960 1065820 1485570 808030 1262970 1105950 1326190 756690 TRUE FALSE 1250889.456 1519477.592 1114688.901 1336237.681 948950.1762 1219233.032 937217.0153 1210061.773 874033.6206 1.43116858 1.738465839 1.2753387 1.528817256 1.085713586 1.394949809 1.072289433 1.384456781 1 19.73732925 3.054834712 1.148387434 1.189035578 1.569782686 0.401998994 0.175090234 0.391074377 1.100822126 0.065563513 0.083913814 1134.578925 -3.054834712 0.380747108 PIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 PIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR;PIS(1)PGLSYASHTVGFTPPTSLTR 258.87 7.47E-44 354750000 238340 228690 201909 265030 143387 224030 200939 210138 161272 TRUE FALSE 227074.1405 251993.771 211166.7274 238388.6809 168393.6474 216271.7849 170282.0651 191737.2027 186281.2381 1.218985566 1.352759803 1.133590959 1.279724589 0.90397535 1.160996068 0.914112805 1.029288857 1 17.50712285 2.749080202 24.9651122 1.002883075 1.254723582 0.656018438 0.087910737 380.3600076 902670.9782 0.024608845 0.02585111 561.1515959 -2.749080202 0.251840507 PIS(ph)PSPSAILER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.983)PS(0.017)PSAILER 130.65 0.00022305 34038000 34035 31640 25221 41029 19743 29545 24756 33254 23237 TRUE FALSE 32426.233 34864.15197 26377.4078 36904.68697 23186.17295 28521.84924 20979.01752 30342.10347 26840.47528 1.208109494 1.298939441 0.982747419 1.374963989 0.863851057 1.062643226 0.781618705 1.130460737 1 14.7121226 2.728609287 24.98235704 0.94798515 1.216114767 0.442328031 0.137648159 542.9994823 1363172.702 0.039895841 0.038032189 535.3148446 -2.728609287 0.268129617 PKEGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PKEGDDR 7 1 F8WE91;Q9Y6K1;A0A0C4DG02;Q9UBC3-7;Q9Y6K1-2;Q9UBC3-8;Q9UBC3-4;Q9UBC3-3;Q9UBC3-5;Q9UBC3-2;Q9UBC3-6;Q9UBC3 F8WE91;Q9UBC3-4 DNMT3A;DNMT3B DNA (cytosine-5)-methyltransferase 3A;DNA (cytosine-5)-methyltransferase 3B 0 100.07 0.082098 362240000 720950 975190 566030 767610 675230 605400 705700 585990 585480 FALSE TRUE 686872.1223 1074562.97 591983.0354 690448.3844 792989.8982 584434.8462 598032.5039 534677.6091 676273.2482 1.015672473 1.588947918 0.875360717 1.020960664 1.172588004 0.864199268 0.884306019 0.790623628 1 19.36724676 3.109038571 0.925497356 0.88953854 1.274148415 0.258979653 0.195353789 0.604368634 1.139876646 0.092612581 0.130969697 1285.400815 -3.109038571 0.384609876 PKHEFSVDMTCGGCAEAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 PKHEFSVDMTCGGCAEAVSR 20 1 O00244 O00244 ATOX1 Copper transport protein ATOX1 0 ;;; 184.26 2.45E-17 932850000 829270 766840 834520 944360 725410 865620 941040 979040 713758 FALSE TRUE 790072.0506 844981.8678 872783.5675 849431.1386 851921.2743 835643.3624 797467.0646 893310.0674 824443.9453 0.958308997 1.024911242 1.058633 1.030307935 1.033328317 1.013584207 0.967278696 1.083530387 1 19.65306188 4.525187374 2.672521213 1.023109212 0.957566393 0.311893187 0.0313464 0.397253758 4.978351656 0.007815429 0.046637944 33510.99897 -4.525187374 -0.065542819 PKPINVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PKPINVR 7 1 P15311;E9PNP4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3 P15311;A0A2R8Y5S7 EZR;RDX Ezrin;Radixin 0 ; 110.61 0.0061693 2417500000 3404100 3193000 3176600 3763600 4865200 3135200 3527300 3576600 5130200 FALSE TRUE 3243194.939 3518370.33 3322250.252 3385275.778 5713689.34 3026627.238 2989145.602 3263413.943 5925765.215 0.547303989 0.593741095 0.560644935 0.571280781 0.964211226 0.510757198 0.504432001 0.550716038 1 22.49857004 -1.63832066 2.702163183 1.042665106 0.594679048 0.473375861 0.132340161 18545173.6 16836217.72 5525578.318 0.032317369 0.022997432 1.63832066 -0.447986058 PLELELCPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PLELELCPGR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 164.57 1.42E-05 148547000 210677 201087 192168 214396 190771 194402 221863 217960 181751 FALSE TRUE 200718.7157 221577.9939 200979.0929 192844.5068 224041.402 187669.81 188013.7246 198874.2669 209936.0168 0.956094713 1.055454882 0.957334982 0.918587052 1.067188972 0.893938129 0.895576316 0.947308946 1 17.67959017 2.209557083 24.99930732 0.921169993 0.991748154 0.200117832 0.053595082 258.9731984 223217.7645 0.018901138 0.013961699 162.0156931 -2.209557083 0.070578161 PLENLEEEGLPKNPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PLENLEEEGLPKNPDLR 17 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 177.64 9.27E-10 194293000 497020 379890 429800 484450 270980 531050 499530 545800 287190 FALSE TRUE 473526.8496 418601.2229 449506.7551 435752.1656 318238.8262 512659.6053 423317.524 498006.8585 331725.9584 1.427463958 1.261888653 1.355054507 1.313590795 0.959342548 1.545431077 1.276106115 1.501259838 1 18.33963239 4.62636878 2.784453089 1.292482344 1.437038394 0.055067386 0.185538877 1.113070549 13.69845876 0.040946439 0.324846641 42302.76747 -4.62636878 0.14455605 PLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PLFLVHPIEGSTTVFHSLASR 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 0 103.2 0.00025656 80293000 346370 339950 297890 346320 819110 195420 412210 231850 894590 FALSE TRUE 329997.7765 374591.2915 311548.5512 311507.2556 961962.5247 188652.5564 349319.7937 211547.9849 1033318.448 0.319357287 0.362512923 0.301502941 0.301462977 0.930944886 0.18256962 0.338056283 0.204726805 1 19.9788535 -0.976915649 4.142585619 1.000035413 0.366737791 0.476756865 0.208192459 70953279.19 146560378.5 37375.16601 0.045763633 0.10545917 0.976915649 -0.633297622 PLKPLS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PLKPLSPLR 9 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 PLKPLS(1)PLR;PLKPLS(1)PLR 55.452 0.077758 433500000 1483310 1591970 756300 1145410 861130 1160180 1245330 1399010 638800 TRUE FALSE 1413196.876 1754193.553 790977.1031 1030271.211 1011310.799 1120002.676 1055332.036 1276505.268 737861.8415 1.915259465 2.377401099 1.071985375 1.396292846 1.370596421 1.517902963 1.430256963 1.730005803 1 19.49299118 3.742633912 24.99627251 1.391173352 2.146330302 0.659038782 0.234409474 178.7316039 1096804.111 0.055956109 0.096424852 5528.838599 -3.742633912 0.75515695 PLPKGT(ph)MMETLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PLPKGTMMETLSR 13 1 K7ENC0;P21217;Q11128 K7ENC0 FUT5;FUT3 "Galactoside 3(4)-L-fucosyltransferase;Alpha-(1,3)-fucosyltransferase 5" 1 PLPKGT(0.5)MMET(0.5)LSR 66.059 0.030709 440020000 718630 726430 651260 777940 454270 782590 830350 887250 525840 TRUE FALSE 684661.7841 800454.0429 681120.9152 699739.9932 533494.5442 755488.7121 703664.8571 809557.6864 607384.5816 1.127229444 1.317870205 1.121399745 1.152054258 0.878347196 1.243839134 1.158516167 1.332858474 1 19.21225076 3.679578806 24.97902411 1.132826706 1.222550453 0.083433815 0.130839772 595.6914988 252277.169 0.033101816 0.051281126 4781.66125 -3.679578806 0.089723747 PLTS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PLTSPLR 7 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 PLT(0.033)S(0.967)PLR;PLT(0.223)S(0.777)PLR;PLT(0.08)S(0.92)PLR 116.37 0.0057384 326236000 1183160 1351670 895680 1289450 753460 1076210 981780 1098160 605980 TRUE FALSE 1127234.372 1489406.71 936747.8139 1159832.036 884863.1854 1038940.578 831991.4294 1001999.289 699952.2835 1.610444595 2.12786892 1.33830239 1.657015862 1.264176439 1.484302005 1.18864021 1.431525137 1 19.41689705 2.807924804 0.41005426 1.089190631 1.947182082 0.492662223 0.218526184 1.021094411 0.343368197 0.204631287 0.347515526 642.5764487 -2.807924804 0.857991451 PMMS(ph)NLKEIHLVS(ph)NEDPT(ph)VAAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PMMSNLKEIHLVSNEDPTVAAFK 23 1 Q8IXQ6-3;Q8IXQ6-2;Q8IXQ6 Q8IXQ6-3 PARP9 Poly [ADP-ribose] polymerase 9 3 PMMS(1)NLKEIHLVS(1)NEDPT(1)VAAFK 43.992 0.054798 581920000 81493 108160 224170 145380 688220 36136 82398 26394 599030 TRUE FALSE 77640.98739 119181.627 234448.4162 130766.1262 808245.3501 34884.60126 69826.67176 24082.80144 691924.513 0.112210199 0.172246574 0.338835251 0.188989006 1.168112034 0.050416773 0.100916604 0.034805533 1 19.40025513 -1.161461401 3.730839209 1.000521044 0.25735025 0.323366272 0.330979601 174626634.9 298170526.6 1146729.533 0.079552045 0.068950687 1.161461401 -0.743170793 PMPTEGTPPPLSGTPIPVPAYFRHAEPGFSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PMPTEGTPPPLSGTPIPVPAYFRHAEPGFSLK 32 1 I3L136;A6NHV6;Q99640-3 I3L136 PKMYT1 0 62.683 0.0083413 52772000 101450 89228 102180 108700 66974 106610 126000 108590 74167 FALSE TRUE 96654.65955 98320.43464 106865.0541 97773.26948 78654.2444 102918.069 106776.3859 99081.28393 85668.43957 1.128241159 1.147685602 1.247426177 1.141298592 0.91812393 1.201353375 1.246391161 1.156566927 1 16.38647619 4.509319375 3.685991455 1.146600191 1.129324926 0 0.103787482 3.188727798 91.46403934 0.02522139 0.109727685 32308.69193 -4.509319375 -0.017275266 PNKVQLIAMDLPMVS(ph)GDRIHCLDILFAFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PNKVQLIAMDLPMVSGDRIHCLDILFAFTK 30 2 A0A1B0GWA6;A0A2R8YDP4;A0A1W2PRD1;Q9NY46-4;Q9NY46-2;Q15858-4;Q15858-3;Q15858-2;Q15858;Q9NY46-3;Q9NY46;Q99250-2;Q99250 A0A1B0GWA6 SCN3A;SCN9A;SCN2A Sodium channel protein type 3 subunit alpha;Sodium channel protein type 9 subunit alpha;Sodium channel protein type 2 subunit alpha 1 PNKVQLIAMDLPMVS(1)GDRIHCLDILFAFTK;PNKVQLIAMDLPMVS(1)GDRIHCLDILFAFTK 80.132 0.0023277 230750000 390050 147719 502700 259980 474510 382140 744620 459440 683000 TRUE FALSE 371613.1095 162771.734 525749.2922 233846.3165 557264.3938 368906.396 631014.5431 419208.998 788916.1517 0.471042593 0.206323237 0.666419734 0.296414665 0.706367074 0.467611666 0.799849948 0.531373324 1 19.58951245 1.165042103 0.233593267 1.123026062 0.25001497 0.522078576 0.162042597 1.718881243 0.378323542 0.590539599 0.424573677 14.62318932 -1.165042103 -0.873011092 PQYQTWEEFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PQYQTWEEFSR 11 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ;; 188.49 7.28E-06 328860000 388690 312107 323495 378660 269815 361010 383647 353731 283957 FALSE TRUE 370317.394 343911.0581 338327.5657 340596.3774 316870.6506 348508.1332 325114.604 322756.4384 327991.6013 1.129045355 1.048536172 1.031512894 1.038430179 0.966093794 1.062552004 0.991228442 0.984038729 1 18.32329935 7.999999841 0.3832675 0.997289604 3.019488017 0.697208181 0.025840961 32.52992631 0.442436702 0.017268465 48.98881184 99999963.36 -7.999999841 2.022198413 PRPAT(ph)STPDLASHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PRPATSTPDLASHR 14 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 PRPAT(0.59)S(0.397)T(0.013)PDLASHR 104.89 0.0016673 233150000 125620 111400 105910 135480 96150 127770 133900 118030 87203 TRUE FALSE 119682.1916 122751.7867 110766.0783 121861.293 112918.5296 123345.2929 113471.0958 107694.6675 100725.9959 1.188195664 1.21867037 1.099677172 1.209829617 1.121046544 1.224562654 1.126532379 1.06918444 1 16.62007654 1.173032691 1.825394435 1.002583512 1.179082074 0.681858006 0.040898753 0.168319733 1.032828294 0.034705153 0.010092036 14.89473193 -1.173032691 0.176498562 PRPATS(ph)TPDLASHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PRPATSTPDLASHR 14 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 PRPAT(0.041)S(0.932)T(0.027)PDLASHR 102.55 0.00070708 285300000 122930 108160 99320 125710 92913 103250 97216 108660 77258 TRUE FALSE 117119.3425 119181.627 103873.9202 113073.392 109116.9978 99674.42661 82383.91371 99145.15436 89238.77606 1.31242659 1.335536324 1.163999831 1.267088109 1.222753186 1.116940763 0.923185159 1.111009796 1 16.44538311 2.1624523 2.367264854 1.003756517 1.277274117 0.757274704 0.06473535 0.131069109 1.470782623 0.030241408 0.019431913 145.362472 -2.1624523 0.273517599 PRPPGRPVS(ph)GHGMDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PRPPGRPVSGHGMDSR 16 2 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 PRPPGRPVS(0.997)GHGMDS(0.003)R;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR 102.33 0.00079603 486020000 267399 371161 236644 382952 179321 304233 219470 305414 132025 TRUE FALSE 254759.5792 408982.7279 247494.3615 344456.9374 210594.5256 293697.3349 185985.8207 278670.3311 152498.7627 1.670568172 2.681875712 1.622927013 2.258752342 1.380958913 1.925899789 1.219589047 1.827361259 1 17.21843801 1.849045609 0.439423299 1.063478948 2.187838021 0.36288269 0.391370616 0.903527878 0.434580851 0.383014276 0.316349065 70.63917347 -1.849045609 1.124359073 PRPS(ph)ITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PRPSITK 7 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 PRPS(1)ITK 130.41 0.0021594 265810000 359950 366630 311710 405520 155600 347170 306070 366560 168510 TRUE FALSE 342935.8769 403990.0138 326002.2118 364756.3592 182736.5907 335147.4158 259373.4001 334462.0631 194641.6702 1.761883139 2.075557682 1.674883963 1.873989053 0.938835916 1.721868784 1.332568714 1.718347684 1 17.57046108 2.798299724 24.97417219 1.391615768 1.865792955 0.451833098 0.272639739 215.0805913 89914.79116 0.074019529 0.078509549 628.4919562 -2.798299724 0.474177188 PS(ph)AGVGGS(ph)SSS(ph)LGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PSAGVGGSSSSLGSGSR 17 0 A0A3B3ISQ9;Q8NHY2-5;Q8NHY2-2;Q8NHY2-4;Q8NHY2 A0A3B3ISQ9 RFWD2 E3 ubiquitin-protein ligase RFWD2 3 PS(0.879)AGVGGS(0.369)S(0.378)S(0.377)S(0.997)LGSGSR 68.576 0.024475 173190000 184990 241080 252990 253230 454410 184050 269290 243320 461230 TRUE FALSE 176245.8893 265646.3261 264589.8417 227774.8393 533658.9601 177676.3024 228204.8646 222013.6109 532755.1928 0.330819655 0.49862738 0.496644322 0.427541284 1.001696403 0.33350459 0.428348457 0.416727258 1 19.02311322 -2.090370043 2.39950763 1.848677817 0.484896096 0.413472936 0.190088363 13750931.13 4215401.273 63738392.5 0.046007723 0.008121382 2.090370043 -1.363781721 PS(ph)Y(ph)AT(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PSYATLR 7 0 Q15596;H0YBB6 Q15596 NCOA2 Nuclear receptor coactivator 2 3 PS(1)Y(1)AT(1)LR 57.047 0.075458 335570000 17616 8823.7 14344 23078 16286 19457 19053 13616 26721 TRUE FALSE 16783.32659 9722.845062 15001.68659 20758.15559 19126.27324 18783.19921 16146.11492 12423.71086 30864.75621 0.543769939 0.315014478 0.486045847 0.672552067 0.619680036 0.608564639 0.523124654 0.402520946 1 14.91367278 -5 0.307190338 5.183226538 0.491211532 0.648250312 0.108675325 191.4052233 1.743903879 517.9337893 0.109261648 1.00E-05 5 -4.692015006 PSATSHSGSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 PSATSHSGSGSK 12 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;; 121.68 0.00037197 64884000 146381 127092 122009 154381 94187 140325 166716 172584 124057 FALSE TRUE 139461.8602 140042.8193 127603.2333 138862.3286 110613.183 135465.5101 141280.4123 157471.63 143295.126 0.973249155 0.977303438 0.890492489 0.969065261 0.771925648 0.945360208 0.98594011 1.098932214 1 17.12863001 1.545634558 3.266831145 1.04865302 0.926935679 0.40041836 0.064508787 0.221178452 5.252289476 0.043285751 0.016876328 35.12647408 -1.545634558 -0.121717341 PSMS(ph)PTPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 PSMSPTPLDR 10 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 PS(0.003)MS(0.982)PT(0.015)PLDR;PSMS(0.999)PT(0.001)PLDR;PS(0.022)MS(0.918)PT(0.06)PLDR;PSMS(0.999)PT(0.001)PLDR;PSMS(0.5)PT(0.5)PLDR;PSMS(0.973)PT(0.027)PLDR;PS(0.003)MS(0.981)PT(0.016)PLDR 200.76 2.67E-07 1202810000 2117090 2516470 1767100 2475860 1233222 2075720 1721090 1995040 1169498 TRUE FALSE 2017019.351 2772901.154 1848123.283 2226981.849 1448295.526 2003837.296 1458506.111 1820343.721 1350857.777 1.493139682 2.052696591 1.368110925 1.6485687 1.07213028 1.483381397 1.079688873 1.347546538 1 20.36544436 3.049131061 1.331574421 1.204947083 1.749197118 0.46096676 0.229179819 0.31743549 1.176957456 0.08004869 0.100232384 1119.775759 -3.049131061 0.544250036 PSQMEHAMETMMFTFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PSQMEHAMETMMFTFHK 17 0 P60903 P60903 S100A10 Protein S100-A10 0 113.88 0.00022584 61980000 125770 112450 102270 147040 104270 122100 141190 128150 31154 FALSE TRUE 119825.1014 123908.7828 106959.1807 132259.2598 122454.655 117871.6464 119648.8724 116928.5066 35985.20321 3.329843677 3.443325917 2.972310036 3.675378991 3.402916868 3.275558726 3.324946414 3.249349627 1 15.13511618 -0.449250177 0.895147133 0.903459898 3.360088569 0.948098447 0.171796004 3.905643263 2.06575465 1.495047944 0.049089024 0.355426515 0.449250177 2.456628671 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;PSTQPRPDS(1)WGEDNWEGLETDSR 324.4 2.87E-74 4365530000 2145480 2237710 1883390 2439870 1477240 2136880 2068220 2232360 1254370 TRUE FALSE 2044067.412 2465735.193 1969745.294 2194609.632 1734870.188 2062879.31 1752675.054 2036882.724 1448891.293 1.410780382 1.701808276 1.359484527 1.514682049 1.197377744 1.423764032 1.209666358 1.405821633 1 20.46651793 1.034720613 0.187147608 0.832905069 1.681877472 0.534961075 0.130208495 2.822306652 0.425604143 0.916020836 0.625925177 10.83229836 -1.034720613 0.848972402 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK 31 2 O75821;K7ENA8;K7ER90;K7EL20;K7EL60;K7ENH0 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 153.99 3.29E-09 64100000 68015 55389 56777 67020 28386 74920 68197 77306 19967 FALSE TRUE 64800.06574 61033.20207 59380.28161 60283.02227 33336.50941 72325.50161 57792.29513 70536.67682 23063.38038 2.809651693 2.646325086 2.574656474 2.613798206 1.445430325 3.1359454 2.50580332 3.058384142 1 14.49331636 2.976806503 24.90636219 2.373217283 2.677414793 0.075481031 0.653564045 2432.92448 2612601.419 0.180961171 0.193121158 947.9959954 -2.976806503 0.30419751 PTHGDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PTHGDIIR 8 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 106.42 0.0041983 62475000 108080 110230 77892 107540 83941 79167 82811 98368 60693 FALSE TRUE 102971.2726 121462.5623 81463.42525 96729.87489 98580.28382 76425.42694 70176.66102 89754.37644 70104.96046 1.468815786 1.732581568 1.162020843 1.379786455 1.406181291 1.090157193 1.00102276 1.280285672 1 16.09722891 2.928219605 0.617895804 1.046077192 1.612330913 0.524494801 0.158008132 0.56422198 0.470101934 0.115314278 0.152764763 847.6559301 -2.928219605 0.56625372 PTSS(ph)PAKGPPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 PTS(0.01)S(0.99)PAKGPPQK;PT(0.003)S(0.175)S(0.822)PAKGPPQK 142.85 3.74E-05 866550000 1352200 1790860 1153800 1752390 520720 1628490 1150640 1511820 508820 TRUE FALSE 1288284.186 1973350.67 1206702.871 1576236.428 611533.4031 1572094.983 975088.735 1379437.026 587725.2069 2.191983891 3.357607683 2.053175289 2.681927556 1.040509061 2.674880989 1.659089526 2.347078209 1 19.16478225 3.122184044 1.96879299 1.862568763 2.717810574 0.245716373 0.637427424 0.406834591 3.229249168 0.185551716 0.236809977 1324.902879 -3.122184044 0.855241811 PTTLSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PTTLSEER 8 0 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 0 ; 77.282 0.030599 154220000 129721 122839 132991 138456 268360 105218 145173 103198 277130 FALSE TRUE 123589.3454 135356.4338 139088.7689 124538.1398 315161.899 101574.2743 123024.1926 94161.43603 320105.905 0.386088927 0.422848912 0.434508601 0.389052929 0.984555093 0.317314591 0.384323409 0.294157135 1 18.28818977 -1.393022689 2.990747192 1.008432138 0.447893621 0.439468125 0.194599576 40693201.43 49456178.88 2950865.49 0.045596846 0.040455476 1.393022689 -0.560538517 PTTQQS(ph)PQDEQEKLLDEAIQAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PTTQQSPQDEQEKLLDEAIQAVK 23 1 Q96QK1;I3L4S0;A0A1W2PP10;A0A3B3ITD4 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 PTTQQS(1)PQDEQEKLLDEAIQAVK 202.85 1.22E-24 55932000 171010 131050 152200 171510 70724 185630 189550 192130 73994 TRUE FALSE 162926.6962 144404.144 159178.5205 154269.489 83058.24321 179201.5866 160630.6662 175306.0787 85468.61161 1.906275218 1.68955762 1.862420806 1.804984146 0.971798203 2.096694718 1.879411203 2.05111649 1 16.38310707 5.26115186 0.975104555 1.712749719 2.259283973 0.024595647 0.391331638 24.63746145 9.228026441 0.110898329 18.03733855 182453.3574 -5.26115186 0.546534254 PTVEELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PTVEELYR 8 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-3;E9PQK6 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 169.06 0.00070539 119197000 315240 286950 250490 321760 226920 284500 302760 324580 249650 FALSE TRUE 300339.2299 316190.5312 261975.2143 289416.0735 266494.7762 274647.6937 256568.4014 296158.0545 288364.447 1.041526558 1.096496238 0.908486525 1.003646866 0.924159615 0.952432578 0.889736596 1.027026936 1 18.13753378 3.742648239 24.95210202 0.949894776 1.069011403 0.498419269 0.045780172 215.7267575 1316855.853 0.010877344 0.018749862 5529.020998 -3.742648239 0.119116627 PTWGNHTPIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PTWGNHTPIFR 11 0 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 110.08 0.0018429 214520000 289300 324940 222470 280500 174050 218580 203320 252500 147830 FALSE TRUE 275625.3623 358051.7554 232670.4696 252303.6071 204404.2649 211010.5198 172299.7998 230389.7614 170754.7214 1.614159539 2.09687763 1.362600505 1.477579097 1.19706362 1.235752183 1.009048525 1.349243872 1 17.38156594 3.266106592 1.34710862 1.147541185 1.846844086 0.657426365 0.186635948 0.209969199 0.798069869 0.061807387 0.094793822 1845.46831 -3.266106592 0.6993029 PVS(ph)SAASVYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.496)S(0.496)AAS(0.009)VYAGAGGSGSR 188.71 3.82E-14 40664000 218470 189040 179560 235680 179660 196150 236740 202020 214210 TRUE FALSE 208143.3561 208303.3909 187793.0036 211988.9986 210992.6471 189357.2763 200620.965 184330.0578 247428.5928 0.841225962 0.841872754 0.758978587 0.856768396 0.852741572 0.765300704 0.810823692 0.744982848 1 17.9166527 -1.829446468 6.967849048 1.012115566 0.813045905 0.683372894 0.040760687 0.007529703 0.000184306 0.038736434 0.008897856 0.014809948 1.829446468 -0.199069661 PVSS(ph)AASVYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(1)AASVYAGAGGSGSR;PVSS(0.994)AAS(0.006)VYAGAGGSGSR 361.35 4.45E-91 454290000 559580 610270 521610 716680 418550 613410 518190 581240 385120 TRUE FALSE 533129.7624 672457.2068 545526.3344 644637.9648 491544.9875 592167.4579 439130.5983 530343.5443 444842.4427 1.198468741 1.511675016 1.226336073 1.449137724 1.104986711 1.33118471 0.987159848 1.192205359 1 18.76293492 2.097921168 0.962215483 1.045088995 1.350965099 0.407515626 0.132580801 0.472361638 0.812256596 0.092444745 0.047086851 125.2913727 -2.097921168 0.305876105 PVSSAAS(ph)VYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.002)AAS(0.998)VYAGAGGSGSR;PVSSAAS(1)VYAGAGGSGSR 221.13 6.72E-19 1931690000 138241 65534 136510 140375 139418 160553 198224 108591 131838 TRUE FALSE 131706.6219 72211.98911 142769.1185 126264.2383 163732.4551 154993.0094 167981.2882 99082.19636 152282.7637 0.864882004 0.474196733 0.937526448 0.829143333 1.075187047 1.017797455 1.103087993 0.650646166 1 17.21639313 3.611963176 7.330215758 0.964828281 0.670284089 0.335522773 0.15949212 0.237587518 13.08377215 0.040405785 0.062741793 4092.259597 -3.611963176 -0.294544191 PVSSAASVYAGAGGS(ph)GSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSSAASVYAGAGGS(0.948)GS(0.052)R;PVSSAASVYAGAGGS(0.936)GS(0.064)R;PVSSAASVYAGAGGS(0.962)GS(0.038)R;PVSSAASVYAGAGGS(1)GSR;PVSSAASVYAGAGGS(0.933)GS(0.067)R;PVSSAASVYAGAGGS(0.997)GS(0.003)R 306.01 3.89E-50 6939830000 1312280 1408240 1290440 1538050 1010104 1423830 1351160 1444000 953650 TRUE FALSE 1250251.125 1551741.257 1349607.95 1383442.292 1186265.818 1374522.41 1145015.726 1317555.705 1101537.171 1.135005842 1.408705305 1.225204183 1.255919753 1.076918554 1.247822085 1.039470801 1.19610644 1 20.07108675 1.945192574 0.525749808 1.028122738 1.279242414 0.360664186 0.095963642 0.815396537 0.489774905 0.086927992 0.061793117 88.14396329 -1.945192574 0.251119676 PWIS(ph)LPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;PWIS(1)LPR;PWIS(1)LPR 70.919 0.035893 1544270000 1144534 999189 1081667 1098909 4042940 645833 1285417 693824 3540720 TRUE FALSE 1090434.146 1101007.495 1131262.502 988444.5795 4748027.456 623467.6413 1089303.028 633069.0924 4089796.774 0.266623064 0.269208363 0.276606043 0.2416855 1.160944594 0.152444651 0.266346493 0.154792311 1 21.96359773 -1.871578782 2.438354705 1.320358217 0.341127596 0.327741234 0.293028121 32908770.92 18309719.09 60928390.91 0.071485559 0.013440679 1.871578782 -0.979230621 PWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 38 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;PWLHPEQSPLPSLALS(0.008)ELS(0.003)VQHADS(0.989)LENIDESAVAESR 246.95 3.76E-50 141177000 24516 29124 19013.3 28858 19527.7 26244 21359 28088 10939.6 TRUE FALSE 23357.17727 32091.76871 19885.07861 25957.13901 22933.3247 25335.1637 18100.29227 25628.46582 12636.0573 1.848454523 2.539697942 1.573677465 2.05421188 1.814911421 2.004989619 1.432431956 2.02820114 1 13.62525876 -1.4278192 0.170494844 1.35E-11 2.299645967 0.490580137 0.29464012 21.37344689 0.658740546 10.45716751 1.218193663 0.037340558 1.4278192 2.299645967 PYQYPALTPEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PYQYPALTPEQK 12 0 P04075;J3KPS3;H3BQN4;H3BUH7;H3BR04;H3BMQ8 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 140.49 0.00013892 135125000 580780 578410 454830 616660 329300 559430 575780 653970 334380 FALSE TRUE 553327.6804 637350.6366 475684.4054 554672.1652 386729.8157 540056.7988 487934.1861 596704.9199 386233.9426 1.432623132 1.650167337 1.231596587 1.436104143 1.001283867 1.398263434 1.263312548 1.544931333 1 18.55911543 3.730493831 24.81123905 1.281520774 1.541395236 0.283190747 0.17987137 578.7971778 1780223.719 0.042502543 0.067124366 5376.427961 -3.730493831 0.259874462 PYQYPALTPEQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 PYQYPALTPEQKK 13 1 P04075;J3KPS3;H3BQN4;H3BUH7;H3BR04;H3BMQ8 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 178.84 2.29E-05 1107000000 1103450 513370 1113180 786980 744980 1136350 1631410 1488220 1085880 FALSE TRUE 1051292.105 565682.9867 1164220.404 707871.2752 874904.2761 1096997.915 1382508.442 1357903.567 1254272.724 0.838168673 0.451004774 0.928203557 0.564367909 0.697539107 0.874608762 1.102239102 1.082622256 1 20.25841965 2.018849792 2.684944363 1.069212296 0.678992386 0.609510795 0.133334755 0.166005897 2.294566898 0.061799173 0.035785198 104.4358947 -2.018849792 -0.39021991 QAAPPIELDAVWEDIRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QAAPPIELDAVWEDIRER 18 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 242.26 4.53E-24 353011000 201435 130448 191703 188116 221762 178516 255202 208585 260878 FALSE TRUE 191913.5668 143740.7995 200492.7722 169206.2223 260437.2226 172333.9462 216266.2478 190320.1916 301333.6279 0.636880683 0.477015461 0.66535147 0.561524525 0.864281974 0.57190413 0.717697023 0.631592939 1 18.20100216 -4.999999997 0.155080935 2.351129948 0.524153707 0.567815724 0.100209401 87.96980837 0.79680693 36.50819218 0.41828425 1.00E-05 4.999999997 -1.826976241 QAAS(ph)PLEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAASPLEPK 9 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 QAAS(1)PLEPK 93.011 0.010163 209970000 343590 269800 337000 350520 265870 340350 395110 357600 295870 TRUE FALSE 327349.1816 297292.9267 352451.7833 315285.0637 312237.6438 328563.5942 334828.7128 326286.6482 341752.0085 0.957855912 0.869908353 1.031308594 0.922555115 0.913638065 0.961409402 0.979741756 0.954746834 1 18.38259029 1.447049622 0.346231884 1.004375852 0.923787877 0.141552877 0.04202047 2.054279235 0.810512906 0.062809902 0.050114569 27.99301144 -1.447049622 -0.080587975 QACTAQT(ph)PEPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QACTAQTPEPLRR 13 1 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 QACTAQT(1)PEPLRR;QACTAQT(1)PEPLRR 111.3 0.00058055 330210000 214181 213473 233850 248880 338280 234936 260540 240590 387890 TRUE FALSE 204057.0886 235226.1414 244572.2538 223862.1096 397275.9249 226800.1074 220789.8379 219522.6642 448042.0001 0.455441875 0.525009132 0.545869034 0.499645367 0.88669349 0.506202783 0.49278826 0.489960013 1 18.77327445 -1.855218061 2.593649986 1.191702476 0.544839546 0.571792418 0.122250555 47147082.63 30494500.66 55927580.39 0.029172006 0.013956674 1.855218061 -0.646862929 QADFEAHNILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QADFEAHNILR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;; 237.49 1.39E-15 1907180000 2834720 2357590 2157880 2428280 2930460 2352100 3138120 2608420 2720800 FALSE TRUE 2700728.403 2597831.101 2256820.932 2184184.681 3441531.296 2270646.187 2659342.158 2380012.917 3142727.768 0.859358049 0.826616651 0.718108948 0.694996462 1.095077764 0.722508074 0.846189156 0.757308011 1 21.58358588 QADLYISEGLHPR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 201.08 1.05E-07 2686730000 3357610 2787160 2903750 3526870 3729860 2996130 3953160 3424390 3728800 FALSE TRUE 3198902.429 3071174.773 3036889.81 3172342.327 4380346.403 2892373.267 3350032.837 3124532.258 4307043.26 0.742714256 0.713058724 0.705098516 0.736547589 1.017019365 0.671544977 0.777803387 0.72544715 1 22.03826638 -5 0.303118964 3.032840045 0.745936603 0.377026572 0.095644777 291.6384464 2.67951258 377.6294144 0.088313377 1.00E-05 5 -2.286903441 QADNPHVALYQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QADNPHVALYQAR 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;; 150.12 4.41E-05 1667920000 2159479 1744045 1593094 1830746 2193545 1741106 2338853 1974585 2144522 FALSE TRUE 2057404.707 1921765.168 1666138.936 1646715.934 2576098.553 1680811.063 1982018.019 1801679.869 2477083.519 0.830575429 0.775817672 0.672621219 0.664780142 1.039972425 0.678544365 0.800141781 0.727339169 1 21.24021108 QADVFPDRDHFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QADVFPDRDHFGR 13 1 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;A0A0G2JM88 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ;;; 151.54 2.69E-05 2473040000 1173620 896100 929780 848010 1120250 827530 1035770 918120 1046040 FALSE TRUE 1118145.308 987413.6088 972411.3327 762766.4237 1315621.245 798872.4286 877744.2633 837724.5455 1208254.541 0.925421979 0.817223172 0.804806686 0.631296137 1.088860998 0.661178917 0.726456416 0.69333449 1 20.20449299 QAEATRAS(ph)PPRS(ph)PAEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAEATRASPPRSPAEPK 17 2 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 2 QAEAT(0.233)RAS(0.771)PPRS(0.997)PAEPK 51.029 0.083017 250020000 184430 136070 165490 175480 121020 166130 195000 186670 129890 TRUE FALSE 175712.3594 149935.6877 173077.8802 157840.417 142125.8497 160376.8764 165249.1686 170324.1852 150032.6778 1.17116059 0.99935354 1.15360122 1.052040258 0.947299293 1.068946304 1.101421177 1.135247252 1 17.19491724 4.708753225 3.966299727 1.061812027 1.177916585 0.23767771 0.063588116 0.32642832 9.627643829 0.014728761 0.101540061 51139.11706 -4.708753225 0.116104558 QAEEECAHRGS(ph)PLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 95.5 0.0024528 581490000 444842 391731 399924 449514 341784 470974 509881 519541 371350 TRUE FALSE 423815.2003 431648.8343 418260.911 404327.9987 401391.0214 454664.0523 432089.2888 474047.2358 428937.0614 0.988059178 1.006322076 0.975110217 0.9426278 0.935780695 1.059978475 1.007348928 1.105167351 1 18.71040645 2.227560108 24.99795023 1.040417564 0.975296475 0.516825754 0.03505002 197.5231623 448855.5788 0.01285374 0.009584865 168.8729571 -2.227560108 -0.065121089 QAEEYLSFAFEHCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAEEYLSFAFEHCHR 15 0 Q5JVF3-3;Q5JVF3-2;Q5JVF3;Q5JVF3-4 Q5JVF3-3 PCID2 PCI domain-containing protein 2 0 121.99 6.46E-05 49158000 63812 62562 65758 76658 68897 68658 74764 62893 7474.5 FALSE TRUE 60795.73322 68937.13893 68773.06934 68952.1922 80912.61499 66280.35624 63357.37866 57385.7555 8633.607286 7.041753373 7.984743416 7.96573982 7.986486983 9.37182018 7.677017735 7.338459646 6.646787792 1 13.07574776 0.510891005 1.173996513 0.995911118 7.959035048 0.933481217 0.577992606 0.445472106 0.818525598 0.566642898 0.172736836 3.242582283 -0.510891005 6.963123929 QAEVANQETKEDLPAENGETKTEES(ph)PASDEAGEKEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAEVANQETKEDLPAENGETKTEESPASDEAGEKEAK 37 3 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 QAEVANQETKEDLPAENGET(0.097)KT(0.097)EES(0.403)PAS(0.403)DEAGEKEAK 79.063 0.0014698 104430000 63504 39858 52390 52967 16357 67033 59294 67315 15626 TRUE FALSE 60502.29177 43919.57551 54792.13332 47642.65653 19209.65562 64711.6304 50247.61129 61420.54174 18049.20027 3.35207604 2.433325291 3.035709754 2.639599307 1.064294004 3.585290729 2.783924525 3.402950868 1 14.13964729 4.629596925 2.658080035 2.59671401 3.417371122 0.076801613 0.868382017 1.01975441 11.15460764 0.195779362 1.661289801 42618.37881 -4.629596925 0.820657113 QAFEELRDDLVELSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QAFEELRDDLVELSK 15 1 Q15397 Q15397 KIAA0020 Pumilio domain-containing protein KIAA0020 0 ;;; 143.14 4.07E-06 89624000 266427 248441 221981 289597 184332 261549 273291 273531 220209 FALSE TRUE 253833.5237 273757.4204 232159.0484 260486.1594 216479.4424 252491.4925 231595.4386 249579.1756 254357.887 0.997938482 1.076268653 0.912725967 1.024093109 0.851082091 0.992662329 0.910510153 0.981212647 1 17.9565003 3.737176624 24.99954906 0.948357806 1.037103568 0.288021078 0.054444194 117.1886325 2116828.997 0.012503965 0.020559545 5459.798615 -3.737176624 0.088745762 QAFPNTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QAFPNTNR 8 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 158.07 0.00085402 260630000 233375 207677 195558 233084 212790 223135 238507 224386 213451 FALSE TRUE 222343.8263 228839.5224 204524.5277 209653.9535 249900.5086 215407.779 202118.3767 204737.5723 246551.8909 0.90181351 0.928159673 0.829539481 0.850344131 1.013581797 0.87368131 0.819780274 0.830403578 1 17.91153179 2.013544542 24.99065924 0.859210316 0.905232012 0 0.069302373 555.1524741 1024292.143 0.024215368 0.017875688 103.1678886 -2.013544542 0.046021696 QAGDFHQVIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAGDFHQVIIR 11 0 Q9H3G5;H7C0X5;H7C218 Q9H3G5 CPVL Probable serine carboxypeptidase CPVL 0 ; 138.45 5.73E-05 257760000 558400 447710 421060 489580 541240 447010 548700 505320 520830 FALSE TRUE 532005.5386 493332.158 440366.0175 440366.4883 635632.0846 431529.9316 464985.7374 461071.5019 601597.6564 0.884321162 0.820036702 0.731994237 0.73199502 1.056573406 0.717306537 0.772918133 0.766411732 1 19.19843942 QAGEVTFADAHRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QAGEVTFADAHRPK 14 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;; 105.46 0.00059991 1220492000 1174490 1127470 1023460 1292610 820670 1259930 1404590 1324770 995250 FALSE TRUE 1118974.185 1242360.475 1070386.653 1162674.387 963794.5882 1216298.308 1190293.998 1208766.116 1149588.287 0.973369508 1.080700359 0.931104349 1.011383293 0.838382401 1.058029489 1.035408948 1.051477411 1 20.13268584 QAGEVTYADAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 148.52 6.65E-05 1423650000 2066920 1835110 1757530 2236990 1339220 1936830 2087340 2141810 1515690 FALSE TRUE 1969220.788 2022109.795 1838114.489 2012123.515 1572779.544 1869757.091 1768877.946 1954261.762 1750735.464 1.124796309 1.155005903 1.049909896 1.149301854 0.898353621 1.067983787 1.010362778 1.116251885 1 20.73952968 2.813948713 24.99999997 1.022591473 1.122309118 0.399861927 0.061439524 122.3559839 40574.64149 0.017087355 0.018123876 651.551446 -2.813948713 0.099717645 QAGEVTYADAHKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAGEVTYADAHKER 14 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 144.68 5.28E-06 174260000 200560 73939 224050 156970 247140 191100 352200 276090 325660 FALSE TRUE 191079.9263 81473.46816 234322.9141 141191.0774 290241.1378 184482.1591 298465.4214 251914.096 376161.6896 0.507972852 0.216591616 0.622931363 0.375346776 0.771586118 0.490433141 0.793449811 0.669696311 1 18.5209934 1.711963184 0.334415036 1.024228343 0.318065999 0.593322722 0.142586862 0.778808422 0.279765492 0.190274908 0.186798341 51.518497 -1.711963184 -0.706162345 QAGPASVPLRTEEEFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 163.56 1.52E-09 729200000 1223010 920740 1135550 1165140 751420 1195800 1357430 1322080 908140 FALSE TRUE 1165200.741 1014564.453 1187616.091 1048017.914 882467.4101 1154389.146 1150329.123 1206311.666 1048969.713 1.110804942 0.967200902 1.132173862 0.999092634 0.841270629 1.100498071 1.096627584 1.14999666 1 20.00054159 QAHDLS(ph)PAAESSSTFSFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 198.99 9.67E-22 548100000 306538 255023 274112 308869 446817 251358 359098 277408 455676 TRUE FALSE 292048.5562 281010.1336 286680.3063 277820.9013 524741.7433 242653.4094 304311.0048 253116.6849 526339.9068 0.554866831 0.533894789 0.544667624 0.527835526 0.996963629 0.461020353 0.578164416 0.480899665 1 19.00563526 -1.860505191 2.399532758 1.193377844 0.582021242 0.42833238 0.150718194 10337712.54 5833799.096 11407697.06 0.035663281 0.013787795 1.860505191 -0.611356602 QAHDLSPAAES(ph)SSTFSFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAHDLSPAAESSSTFSFSGR 20 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 QAHDLS(0.319)PAAES(0.558)S(0.114)S(0.006)T(0.003)FSFSGR 242.16 9.72E-28 0 45900 34869 44259 43902 76322 35911 45941 35240 40282 TRUE FALSE 43730.39797 38422.19074 46288.31893 39488.88755 89632.53264 34667.39307 38931.85669 32154.19878 46528.72683 0.939858039 0.825773524 0.99483313 0.848699078 1.926391259 0.745075041 0.836727315 0.691061221 1 15.50583409 QAHLCVLASNCDEPMYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAHLCVLASNCDEPMYVK 18 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 237.21 7.65E-24 357980000 120030 93820 116980 124490 99579 112340 147980 132770 127420 FALSE TRUE 114356.4198 103380.3647 122343.6487 111976.0287 116945.5461 108449.6376 125402.9332 121143.9549 147179.6428 0.776985306 0.7024094 0.831253877 0.760811934 0.794576912 0.736852159 0.852039934 0.823102656 1 17.16721861 0.074835015 0.377533679 1.041588748 0.74800823 0.770480089 0.038838352 1.792985494 0.369755571 0.149884909 0.028027142 1.188050811 -0.074835015 -0.293580519 QAHLTNQYMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QAHLTNQYMQR 11 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;; 146.16 2.72E-05 190478000 226973 165618 163751 190856 245155 180250 285007 221724 296995 FALSE TRUE 216244.4361 182494.6625 171259.1453 171670.7923 287909.9544 174007.8973 241523.9476 202308.6711 343051.4678 0.630355665 0.531974586 0.49922289 0.500422847 0.839261689 0.507235542 0.704045808 0.589732708 1 18.38806551 -5 0.220114417 3.060965962 0.547565559 0.596488443 0.10468369 99.52943069 0.995294936 90.74668968 0.181522495 1.00E-05 5 -2.513400403 QAHLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QAHLYR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 116 0.055721 415141000 471067 414227 369180 466776 476939 433912 540888 463605 491052 FALSE TRUE 448800.5965 456437.2022 386107.2682 419854.7897 560117.0106 418885.5186 458365.6015 423009.2885 567201.8362 0.791253779 0.804717427 0.680722881 0.74022114 0.987509163 0.738512275 0.808117274 0.74578265 1 19.11350268 QAHTMDPQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 24 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 ;;;;;;;;;;;;;;;;;;;;;;; 171.62 3.97E-06 27079060000 5856127 5223475 5318581 6260355 5487196 5624173 6661665 6360099 5839383 FALSE TRUE 5579319.482 5755753.041 5562443.2 5631052.222 6444161.245 5429406.479 5645305.654 5803175.015 6744924.692 0.82718781 0.853345783 0.824685738 0.834857686 0.955408924 0.804961764 0.836970895 0.860376547 1 22.6853709 0.831802387 6.066367368 0.999999825 0.847080463 0.578765943 0.040411101 3.650678367 131.5606983 0.036242919 0.009111331 6.788946518 -0.831802387 -0.152919362 QAHVDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAHVDVK 7 0 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;A0A0U1RQL1 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 73.931 0.047556 118610000 349050 266270 276920 287310 219090 269040 299800 291050 211720 FALSE TRUE 332551.0983 293403.2157 289617.0559 258429.0529 257299.2266 259723.0773 254060.0038 265564.119 244552.4563 1.359835445 1.19975575 1.184273756 1.056742823 1.052122847 1.062034221 1.038877334 1.085918838 1 17.89978443 4.169914365 0.670143393 1.038325657 1.437822843 0.927665911 0.028623862 0.364535938 0.201012599 0.012527008 0.099647067 14788.16762 -4.169914365 0.399497185 QALDYVELSPLT(ph)QASPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 QALDYVELSPLT(0.5)QAS(0.5)PQR 140.16 1.44E-06 27743000 40315 29071 34115 41656 30957 32320 39791 39534 35950 TRUE FALSE 38409.38985 32033.36795 35679.20649 37468.65974 36355.891 31200.7503 33720.15214 36072.19338 41524.94239 0.924971538 0.771424741 0.859223504 0.902316959 0.87551936 0.751373717 0.81204573 0.868687379 1 15.34169055 0.914910843 7.538583242 0.999999558 0.838722133 0.453394133 0.053880956 1.87887131 166.3756858 0.051524409 0.01291058 8.220738669 -0.914910843 -0.161277425 QALDYVELSPLTQAS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 QALDYVELSPLT(0.007)QAS(0.993)PQR;QALDYVELSPLTQAS(1)PQR;QALDYVELS(0.001)PLT(0.172)QAS(0.828)PQR 322.94 8.89E-62 131964000 118009 109048 103408 128271 124611 119056 133447 127608 143442 TRUE FALSE 112430.9484 120160.1152 108149.3591 115376.9554 146343.1189 114933.0609 113087.2092 116433.967 165686.2528 0.678577411 0.725226826 0.652735862 0.696358047 0.883254443 0.69367892 0.682538275 0.702737645 1 17.33809438 -1.907302629 2.275114107 1.176732281 0.712704714 0.670367438 0.062931624 4673335.251 2201789.323 4410481.251 0.014817066 0.012379337 1.907302629 -0.464027567 QALTEFNTAIQEIVVTHWHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QALTEFNTAIQEIVVTHWHR 20 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 250.22 7.54E-31 667264000 469883 268419 322419 420533 446496 384047 537101 444526 155542 FALSE TRUE 447672.5618 295771.2013 337202.2301 378260.2239 524364.761 370747.3561 455156.3779 405600.9469 179662.659 2.491739599 1.646258621 1.876863184 2.105391438 2.918607373 2.063574914 2.533394421 2.257569543 1 17.45493107 2.990808929 24.72364017 2.288614278 1.996818312 0 0.532412776 1086.947386 2923860.626 0.140586745 0.159726341 979.0591472 -2.990808929 -0.291795966 QALYLMFDTSQES(ph)PVKSS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QALYLMFDTSQESPVKSSPVR 21 1 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 2 QALYLMFDT(0.001)S(0.003)QES(0.996)PVKS(0.289)S(0.711)PVR 119.35 3.47E-05 34081000 106860 95262 89233 111690 74114 113470 123910 119310 77409 TRUE FALSE 101808.9396 104969.3061 93324.42131 100462.709 87039.45813 109540.5054 105005.2537 108862.5839 89413.19237 1.138634433 1.173980073 1.043743309 1.123578147 0.97345208 1.225104512 1.174382112 1.217522616 1 16.44820009 QALYLMFDTSQESPVKSS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QALYLMFDTSQESPVKSSPVR 21 1 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 QALYLMFDTSQESPVKS(0.035)S(0.965)PVR;QALYLMFDTSQESPVKS(0.215)S(0.785)PVR 243.97 2.40E-30 959590000 1213790 831540 985810 1090230 843850 1248140 1318040 1369550 987500 TRUE FALSE 1156416.552 916274.8714 1031010.364 980638.0091 991017.1728 1204916.599 1116948.791 1249624.942 1140636.457 1.013834465 0.803301408 0.903890418 0.859728797 0.868828247 1.056354627 0.97923294 1.095550589 1 20.12140762 2.241123375 24.99992634 1.026405305 0.888633733 0.577804334 0.060569397 48.795542 476009.888 0.02070705 0.016586047 174.2301759 -2.241123375 -0.137771572 QAPAPTVIRDPPSITPAVKS(ph)PLPGPSEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAPAPTVIRDPPSITPAVKSPLPGPSEEK 29 2 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 QAPAPT(0.002)VIRDPPS(0.022)IT(0.022)PAVKS(0.953)PLPGPS(0.001)EEK 52.155 0.040707 99824000 77797 82191 88253 92512 49007 108190 109680 104280 64084 TRUE FALSE 74119.68999 90566.35634 92299.48734 83212.518 57553.80528 104443.3532 92946.30159 95148.69038 74021.81942 1.001322185 1.22350892 1.246922706 1.124162019 0.777524867 1.410980627 1.255660862 1.2854141 1 16.17566298 QAQAQES(ph)EEEEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 370.04 4.44E-97 4337510000 1327360 1151880 1164050 1360890 1249020 1253860 1419360 1240280 1400270 TRUE FALSE 1264618.323 1269257.882 1217422.844 1224090.752 1466848.693 1210438.514 1202810.564 1131674.508 1617416.72 0.781875387 0.784743886 0.752695844 0.756818411 0.906908328 0.748377644 0.743661512 0.699680233 1 20.62526 -1.795372813 3.820632627 1.03745938 0.773344694 0.64306851 0.053408644 0.017194468 0.000920909 0.052176767 0.011696824 0.016018697 1.795372813 -0.264114686 QAQEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 171.75 0.00066903 181943000 221355 188162 192886 212834 205855 207217 240900 216992 249400 FALSE TRUE 210891.9878 207335.9217 201730.0139 191439.522 241756.0468 200041.0233 204146.2806 197991.0301 288075.6782 0.732071479 0.719727271 0.700267427 0.664545939 0.839210197 0.694404417 0.708655038 0.687288255 1 18.13608834 -1.118732998 4.122950507 1.000064018 0.718863962 0.782112623 0.046731141 60067.20072 23485152.46 3153.404315 0.010008758 0.076079386 1.118732998 -0.281200056 QAQEYEALLNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QAQEYEALLNIK 12 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 293.8 7.82E-36 1235464000 2003584 1727022 1766240 2045257 1508768 1936862 2257672 2120295 1850657 FALSE TRUE 1908878.555 1903007.505 1847223.851 1839663.881 1771896.662 1869787.983 1913222.671 1934630.729 2137647.436 0.892981005 0.890234504 0.864138688 0.860602104 0.828900328 0.874694279 0.8950132 0.905027975 1 21.0275925 0.719513763 1.204039188 0.999663306 0.871920907 0.829582788 0.018389823 0.422984434 1.040615215 0.019518866 0.005979698 5.242202139 -0.719513763 -0.127742399 QAQQERDELADEIANSSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 313.93 1.18E-61 4639940000 4426110 3206550 3923060 4272050 3264850 4387070 4945160 4670100 4149740 FALSE TRUE 4216896.552 3533301.091 4102936.181 3842615.418 3834238.806 4235144.666 4190685.018 4261161.286 4793260.485 0.879755349 0.737139386 0.855980223 0.801670477 0.799922896 0.883562385 0.874286935 0.888990135 1 22.19257591 1.018593111 0.602676336 1.000188458 0.808508371 0.654657445 0.040936773 0.481452728 0.421185964 0.039705563 0.017256466 10.43741882 -1.018593111 -0.191680087 QAQT(ph)QTSPEHLVLQQK ddPTM_SK-BR-3_Trastuzumab_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(0.546)QT(0.16)S(0.294)PEHLVLQQK;QAQT(0.539)QT(0.165)S(0.296)PEHLVLQQK 187.47 4.91E-09 299430000 414900 408990 402080 499920 336350 452200 542270 499100 402650 TRUE FALSE 395288.4993 450666.546 420515.7657 449667.0918 395009.3335 436540.2006 459536.752 455396.1581 465090.9055 0.849916639 0.968985935 0.904158221 0.966836991 0.8493164 0.938612636 0.988057918 0.979155156 1 18.8271532 1.847772391 3.828875534 0.987398229 0.912271847 0.454896759 0.040140799 0.217450832 5.208975041 0.018813065 0.010242171 70.43238433 -1.847772391 -0.075126383 QAQYLGMSCDGPFKPDHYRY ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAQYLGMSCDGPFKPDHYRY 20 2 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 142.31 8.69E-07 108740000 112510 72895 85285 104320 90559 100210 108230 108010 98415 FALSE TRUE 107191.8753 80323.08337 89195.40161 93833.5554 106352.4609 96739.70257 91717.52572 98552.0718 113676.6956 0.942953828 0.706592349 0.784641049 0.825442321 0.935569603 0.851007342 0.806827866 0.866950533 1 16.794577 2.982866282 23.90357825 0.871782938 0.8073956 0.172086198 0.077629885 844.4425294 1178100.44 0.022947222 0.024898757 961.3162474 -2.982866282 -0.064387338 QAREEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAREEEAR 8 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 94.85 0.0099105 110010000 71050 78468 75982 85474 114353 67131 88740 69801 138210 FALSE TRUE 67691.60731 86463.97841 79465.84986 76881.99113 134296.127 64806.23664 75201.08318 63688.8544 159642.9009 0.4240189 0.541608665 0.497772525 0.481587284 0.841228305 0.405944995 0.47105811 0.398945735 1 17.28448887 -1.083582331 4.599536682 1.000028146 0.507403007 0.599798322 0.126358891 1.468555112 72924385.12 4619.279079 0.027842783 0.082493109 1.083582331 -0.492625139 QAS(ph)ASERLPSVEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QASASERLPSVEEAEVPKPLPPASKDEDEDIQSILR 36 3 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QAS(0.58)AS(0.119)ERLPS(0.302)VEEAEVPKPLPPASKDEDEDIQSILR 110.28 1.23E-05 171970000 45809 27204 41404 56162 25085 44122 50978 38293 21253 TRUE FALSE 43643.69935 29976.11853 43302.41435 50516.48906 29459.81606 42594.04408 43200.36982 34939.86192 24548.80669 1.777833843 1.221082511 1.763931538 2.057798152 1.200050838 1.735075949 1.759774736 1.42328148 1 14.58336528 0.941376594 5.437153057 1.000098905 1.62488166 0.3853151 0.259106898 0.372797517 30.96345992 0.237517383 0.059883123 8.737286845 -0.941376594 0.624782756 QAS(ph)DTGSNDAHNKK ddPTM_SK-BR-3_Trastuzumab_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 1 QAS(0.999)DT(0.001)GSNDAHNKK;QAS(1)DTGSNDAHNKK;QAS(0.998)DT(0.002)GSNDAHNKK;QAS(0.992)DT(0.008)GSNDAHNKK;QAS(1)DTGSNDAHNKK;QAS(0.997)DT(0.003)GSNDAHNKK 256.68 1.20E-24 674050000 1278339 862932 1071813 1959260 819013 1841365 2011389 1081734 760547 TRUE FALSE 1217914.449 950865.7519 1120956.686 1762311.462 961848.6079 1777598.068 1704514.666 987011.6363 878488.7444 1.386374563 1.082388087 1.276005747 2.006071761 1.094890076 2.023472787 1.940280598 1.123533617 1 19.74466428 3.443673039 24.74581717 1.617817936 1.225183693 0.078607514 0.389461406 257.969465 190851.3938 0.099857343 0.135208266 2777.62133 -3.443673039 -0.392634244 QAS(ph)ESSSRPH ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.983)ES(0.017)SSRPH;QAS(0.975)ES(0.025)SSRPH;QAS(0.989)ES(0.011)SSRPH;QAS(0.996)ES(0.004)SSRPH;QAS(0.969)ES(0.026)S(0.005)SRPH 142.39 2.17E-05 2309383000 1750280 1466210 1592780 1948430 1951420 1726740 2051260 1885060 1908350 TRUE FALSE 1667547.733 1615618.466 1665810.538 1752570.115 2291747.03 1666942.561 1738302.613 1719994.153 2204287.171 0.756502036 0.732943732 0.755713938 0.795073408 1.039677162 0.756227493 0.788600794 0.780294952 1 21.07188076 -5 0.135614445 1.649612306 0.7195313 0.342969216 0.086959084 166.7171391 1.403432407 29.8232967 0.58309882 1.00E-05 5 -0.930081007 QAS(ph)FLEAEGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QASFLEAEGGAK 12 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 QAS(1)FLEAEGGAK;QAS(1)FLEAEGGAK 186.85 1.18E-05 175747000 380540 285380 316260 418120 271590 387070 404730 351160 301730 TRUE FALSE 362552.6284 314460.5465 330760.8338 376089.7832 318955.21 373665.6688 342981.0051 320410.5688 348520.7474 1.04026125 0.902272099 0.949042019 1.079102998 0.915168501 1.07214756 0.984104986 0.919344318 1 18.41088502 4.754719395 23.89707581 0.979159319 1.040261337 0.093558683 0.061088006 383.0737352 1939493.411 0.013530329 0.108194557 56848.55038 -4.754719395 0.061102018 QAS(ph)LDGLQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR 195.94 6.52E-08 948890000 892988 714755 786975 923433 888084 801586 1011128 852932 911623 TRUE FALSE 850778.227 787589.3471 823058.5822 830607.7604 1042965.568 773826.8758 856861.853 778244.7524 1052992.839 0.807962026 0.747953184 0.781637397 0.788806656 0.990477361 0.734883322 0.813739487 0.739078865 1 20.00606419 -1.45268501 2.823511749 1.005717968 0.799194266 0.425729323 0.072777603 11216663.36 12254037.25 505431.9736 0.016172966 0.035262654 1.45268501 -0.206523702 QAS(ph)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK ddPTM_SK-BR-3_Trastuzumab_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(0.913)PQNLGT(0.087)PGLLHPQTSPLLHSLVGQHILSVQQFTK 304.9 3.99E-93 428034000 193264 200890 220039 262061 221769 229935 313760 280479 63826 TRUE FALSE 184128.7937 221360.9194 230128.0058 235718.1304 260445.4434 221972.2933 265890.1494 255918.7718 73723.8101 2.497548533 3.002570256 3.121488234 3.19731346 3.532718168 3.010863017 3.606570917 3.471317767 1 16.16984301 4.40756347 1.469372953 3.158637583 2.428829779 0.004313153 0.754478697 1.635975174 5.040989563 0.180809737 1.464975884 25560.15421 -4.40756347 -0.729807804 QAS(ph)PTEVVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(0.962)PT(0.038)EVVER;QAS(0.982)PT(0.018)EVVER;QAS(0.979)PT(0.021)EVVER;QAS(0.966)PT(0.034)EVVER;QAS(0.956)PT(0.044)EVVER 193.46 5.98E-07 2047620000 1602370 1351480 1464180 1691930 1600560 1474570 1775050 1508530 1677820 TRUE FALSE 1526629.146 1489197.349 1531314.101 1521853.982 1879697.157 1423505.271 1504233.521 1376435.116 1938007.756 0.787731185 0.768416609 0.790148593 0.78526723 0.969912092 0.734519904 0.776175181 0.710231995 1 20.88614291 -2.100102521 2.462688414 1.370705304 0.789874063 0.479112112 0.068714068 4843521.609 1221496.123 10095416.92 0.015688498 0.007941407 2.100102521 -0.580831241 QAS(ph)VHDS(ph)GEEGEA ddPTM_SK-BR-3_Trastuzumab_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 179.94 1.95E-05 2551900000 3075900 2618010 3006390 3428760 3321480 3040750 3436930 2776730 3054420 TRUE FALSE 2930508.303 2884788.195 3144235.955 3084094.531 3900745.06 2935448.065 2912563.205 2533584.801 3528083.854 0.830623201 0.817664295 0.891202161 0.874155677 1.105627083 0.832023327 0.825536843 0.718119213 1 21.75045342 -0.421407842 14.48027438 1 0.860609908 0.164228172 0.097892928 0 0 0.092815719 0.021876875 0.378958941 0.421407842 -0.139390092 QAS(ph)VHDSGEEGEA ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;QAS(1)VHDSGEEGEA 204.17 8.39E-08 4562112000 3233118 2358599 2761443 3026203 3258595 2597094 3450662 2850116 3283387 TRUE FALSE 3080294.92 2598942.92 2888057.893 2722003.325 3826892.936 2507155.984 2924200.136 2600544.734 3792557.887 0.812194569 0.685274424 0.761506608 0.717722288 1.00905327 0.661072569 0.771036388 0.685696781 1 21.85473977 -1.237446849 3.662110265 1.000383333 0.761065697 0.363244102 0.098609034 22095711.5 36885609.76 95944.87621 0.022232171 0.057883282 1.237446849 -0.239317636 QASASERLPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QASASERLPSVEEAEVPKPLPPASKDEDEDIQSILR 36 3 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QASASERLPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;QAS(0.002)AS(0.001)ERLPS(0.996)VEEAEVPKPLPPAS(0.001)KDEDEDIQSILR 147.41 1.96E-12 112215000 81133 47540 69762 89085 48017 76943 86701 73054 50459 TRUE FALSE 77298.00388 52384.38005 72960.6567 80130.00655 56391.1496 74278.44462 73473.17008 66657.00448 58283.92401 1.326231979 0.898779225 1.251814423 1.374821752 0.967524932 1.274424224 1.260607815 1.143660205 1 15.83081039 QASDTGSNDAHNKK ddPTM_SK-BR-3_Trastuzumab_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 0 ;;; 267.07 3.93E-25 384631000 506777 417550 404250 462828 348892 477071 613811 567283 417910 FALSE TRUE 482822.6555 460098.8197 422785.2624 416303.6501 409738.6543 460549.9116 520162.8585 517608.6932 482717.3484 1.000218155 0.953143328 0.87584435 0.862417006 0.848816923 0.954077812 1.077572331 1.072281108 1 18.88081915 1.85975344 4.517477301 1.055451532 0.917961033 0.629528048 0.049153389 0.169478955 5.154387771 0.026486961 0.015074474 72.40247968 -1.85975344 -0.137490499 QASEGPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QASEGPLK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 114.28 0.0062496 1355620000 2581600 2060530 1617080 2046160 1998740 2082800 2784930 2451420 2366130 FALSE TRUE 2459572.884 2270500.35 1691224.718 1840476.109 2347319.623 2010672.114 2360037.78 2236760.669 2733057.356 0.899934602 0.830754739 0.618803229 0.673412911 0.858862189 0.735686029 0.863515643 0.818409707 1 21.38208431 0.628976879 0.900371047 0.999407851 0.782170734 0.391178895 0.086522899 1.457602536 1.996544969 0.088906146 0.029399937 4.255757552 -0.628976879 -0.217237117 QATENAKEEVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QATENAKEEVRR 12 2 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 267.23 4.51E-22 2725210000 1530370 1014050 1464990 1407290 1468170 1471540 1939660 1611120 1658230 FALSE TRUE 1458032.443 1117382.848 1532161.241 1265826.536 1724218.383 1420580.201 1643729.243 1470041.792 1915379.839 0.761223656 0.583374026 0.799925534 0.66087494 0.900196581 0.741670227 0.858174034 0.767493612 1 20.86919909 0.560892649 0.185724637 1.121907332 0.610285602 0.498702875 0.083064953 4.796232452 0.484305104 0.753471647 0.360865516 3.638250931 -0.560892649 -0.511621729 QATVGDINTERPGMLDFTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QATVGDINTERPGMLDFTGK 20 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;; 260.24 2.29E-36 295800000 674790 545320 425120 754540 482330 588730 718620 707980 577250 FALSE TRUE 642894.014 600888.728 444612.1725 678692.2057 566448.1993 568342.1325 608981.3206 645985.518 666766.9818 0.964195936 0.901197486 0.666817921 1.017885145 0.849544466 0.852384938 0.913334549 0.968832494 1 19.34682314 1.244406986 2.448917773 0.997231268 0.88169794 0.195723143 0.090668583 0.47615247 4.802739351 0.07833624 0.022503946 17.55524868 -1.244406986 -0.115533327 QATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 QATVSWDSGGSDEAPPKPS(0.011)RPGYPS(0.989)PR;QATVSWDSGGSDEAPPKPS(0.003)RPGYPS(0.997)PR 240.48 1.89E-45 412065000 259992 201633 215524 251636 168473 236724 261130 260884 214720 TRUE FALSE 247702.6934 222179.6319 225405.9886 226341.0712 197854.6379 228526.1885 221289.8225 238039.6139 248017.681 0.998729979 0.895821746 0.908830321 0.912600547 0.797744085 0.921410875 0.89223406 0.959768727 1 17.92008345 1.040090597 3.88656294 0.999574074 0.906596571 0.315730213 0.048279553 0.243078939 8.11625436 0.046357428 0.011918591 10.96706953 -1.040090597 -0.092977503 QAVDFLSNEGHIYSTVDDDHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAVDFLSNEGHIYSTVDDDHFK 22 0 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ; 329.79 5.88E-81 354050000 328790 273040 293760 317450 241020 317490 356390 367040 111996 FALSE TRUE 313248.7483 300863.0864 307229.1866 285539.3229 283053.8117 306495.2417 302016.1599 334900.0318 129363.7677 2.421456594 2.325713697 2.374924541 2.207258864 2.188045515 2.369251044 2.334627117 2.588824041 1 16.98107408 -1.366093552 3.920249598 0.995604643 2.344750883 0.936033274 0.111001358 0.004073582 0.0006587 0.102536504 0.024128252 0.043043388 1.366093552 1.34914624 QAVEQQIQSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAVEQQIQSHR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 123.26 0.00037375 706620000 597090 518490 524430 647040 495930 573890 699300 654010 559910 FALSE TRUE 568866.739 571324.7205 548475.6342 581998.3099 582420.035 554016.0454 592608.9415 596741.4173 646737.9832 0.879593829 0.883394412 0.84806467 0.899898143 0.900550223 0.856631371 0.916304527 0.922694248 1 19.30282182 0.849409317 0.961484205 0.999927333 0.87839013 0.818728431 0.017977294 0.280059859 0.517308039 0.015741472 0.005227154 7.069835628 -0.849409317 -0.121537203 QAVRVS(ph)PCHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.957)PCHS(0.043)R 58.83 0.062885 105780000 76901 50659 69217 62204 85962 68597 84858 76117 96241 TRUE FALSE 73266.04213 55821.20969 72390.66791 55951.13574 100953.7456 66221.46869 71911.35358 69451.79196 111165.5627 0.659071392 0.502144804 0.651196883 0.503313565 0.908138664 0.595701286 0.646885167 0.624759955 1 16.76235041 -5 0.235537373 3.058641382 0.58937523 0.511599273 0.111653815 127.918678 1.277602826 125.8826545 0.167869663 1.00E-05 5 -2.469266152 QAVRVSPCHS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.246)PCHS(0.754)R;QAVRVS(0.406)PCHS(0.594)R 65.773 0.039079 245850000 172632 125022 156223 166197 185778 150533 196443 169160 197758 TRUE FALSE 164472.0275 137761.8839 163385.9791 149490.5618 218177.6244 145320.0045 166472.0124 154347.4536 228425.3006 0.72002544 0.603093806 0.715270938 0.654439598 0.955137736 0.636181737 0.728780971 0.675702093 1 17.80136293 -5 0.280506724 3.144147596 0.68666541 0.465920985 0.096186194 195.9940101 1.874778522 244.9276353 0.101908676 1.00E-05 5 -2.457482186 QAWRKGPDGPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAWRKGPDGPQK 12 2 Q9BYZ6-2;E5RI44 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 ; 68.536 0.029475 2683100000 5208600 4415100 4341200 5058200 2991100 4871300 4936100 4771400 1989040 FALSE TRUE 4962399.8 4865003.71 4540248.314 4549740.126 3512746.893 4702605.66 4183007.287 4353590.921 2297490.165 2.159922108 2.117529722 1.976177476 1.980308859 1.528949698 2.04684474 1.820685612 1.894933431 1 21.13162725 -1.850688059 0.205933304 2.46E-15 2.183710913 0.783789968 0.1600276 13.52677972 0.436199108 7.297964704 0.397321561 0.014103014 1.850688059 2.183710913 QAYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QAYSPR 6 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAYS(1)PR;QAYS(1)PR;QAYS(1)PR;QAY(0.001)S(0.999)PR;QAYS(1)PR;QAYS(1)PR 95.311 0.045619 7799496000 5675010 4821680 5051760 5799340 5544440 5069420 6057000 5422700 5898390 TRUE FALSE 5406763.524 5313014.674 5283388.193 5216379.325 6511388.581 4893864.714 5132893.406 4947859.64 6813082.196 0.793585541 0.779825418 0.775476949 0.765641625 0.955718483 0.718304076 0.753387858 0.72622926 1 22.69987618 -1.218474199 3.540792154 1.000368933 0.783025494 0.519048047 0.065486951 13677744.73 22976227.25 56501.93505 0.014735424 0.060468027 1.218474199 -0.217343439 QAYS(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QAYSPRR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAYS(1)PRR 65.157 0.0437 11488000 27231 17286 29711 24932 44411 23793 36114 24981 39966 TRUE FALSE 25943.8446 19047.46305 31073.27874 22425.78799 52156.26434 22969.04244 30604.14602 22793.53121 46163.72316 0.561996365 0.412606734 0.673110326 0.485788114 1.129810612 0.497556108 0.662947958 0.493754179 1 15.49447196 3.318370904 2.004389378 0.705181997 0.496965488 0.150969963 0.215357297 0.583975131 4.804714664 0.061577719 0.089892094 2081.473588 -3.318370904 -0.208216508 QAYVDKLEELMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QAYVDKLEELMK 12 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 160.31 5.63E-05 288370000 679710 494780 503770 582060 404220 601110 714940 713920 442010 FALSE TRUE 647581.4554 545198.6445 526868.3528 523550.223 474715.84 580293.41 605862.7722 651405.3801 510554.6533 1.268388117 1.067855598 1.031952895 1.025453827 0.929804159 1.136594106 1.186675644 1.275877863 1 18.96170588 -0.157522826 7.551376922 0.999999992 1.115748356 0.099946853 0.108755242 0 0 0.108435019 0.025558379 0.695788384 0.157522826 0.115748364 QCEGITS(ph)PEGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QCEGITSPEGSK 12 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 QCEGITS(1)PEGSK;QCEGIT(0.063)S(0.937)PEGSK;QCEGIT(0.06)S(0.94)PEGSK;QCEGIT(0.03)S(0.97)PEGSK 262.39 2.16E-21 1035930000 3622750 2772250 3109150 3812190 2466000 3797190 4043100 3690120 2500040 TRUE FALSE 3451509.787 3054745.427 3251707.603 3428981.419 2896069.619 3665692.358 3426250.838 3366993.53 2887733.435 1.195231438 1.057834975 1.12604147 1.187430037 1.002886757 1.269401225 1.186484458 1.165964105 1 21.46150614 2.225256768 24.99994408 1.176175741 1.117532401 0.029537887 0.086693645 533.3986536 1002330.831 0.029069976 0.021595184 167.9796871 -2.225256768 -0.058643339 QCVENADLPEGEKKPIDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QCVENADLPEGEKKPIDQR 19 2 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 190.23 6.91E-15 887630000 1841600 1428550 1588170 1897150 1084748 1988030 2200260 2179570 1314730 FALSE TRUE 1754551.218 1574120.869 1660989.165 1706444.878 1273927.708 1919184.023 1864569.926 1988715.296 1518611.614 1.155365336 1.036552635 1.093755079 1.123687493 0.838876574 1.263775415 1.22781224 1.309561496 1 20.53432152 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 54.311 0.035419 25227000 19426 12932 13579 20605 12630 14674 19754 18214 12671 FALSE TRUE 18507.77148 14249.7855 14201.61058 18533.74625 14832.668 14165.8357 16740.16449 16619.0856 14635.95397 1.26454152 0.973615081 0.970323534 1.266316244 1.013440466 0.967879219 1.143769961 1.135497258 1 13.83722916 4.683229944 3.635412233 1.064957542 1.27566756 0.303109534 0.097447935 0.303651967 6.806198405 0.022488849 0.155328486 48220.30397 -4.683229944 0.210710018 QDAQDLYEAGEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDAQDLYEAGEKK 13 1 P09525;Q6P452;P09525-2 P09525 ANXA4 Annexin A4;Annexin 0 92.551 0.0096545 253390000 179370 123030 119090 217710 112720 157120 163310 153210 77688 FALSE TRUE 170891.5356 135566.8969 124550.3943 195825.3772 132378.3323 151678.895 138394.0601 139794.1202 89735.45826 1.904392521 1.51073945 1.387973012 2.182251932 1.475206511 1.690289412 1.542244981 1.557847064 1 16.45339055 -0.043934436 0.496599093 0.925183728 1.704641107 0.471921554 0.226062328 3.878014531 1.146102452 0.768918617 0.104772876 0.903785905 0.043934436 0.779457379 QDAQSLHGDIPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDAQSLHGDIPQK 13 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 147.35 4.27E-05 361220000 381040 400150 352340 376790 309940 387580 461920 437870 299390 FALSE TRUE 363028.9943 440925.7399 368495.1375 338914.3533 363993.4379 374158.0074 391445.6203 399527.7815 345817.8721 1.049769325 1.275022998 1.065575747 0.980037125 1.052558202 1.081951043 1.131941556 1.155312706 1 18.3996529 1.467551413 0.01066493 5.95E-07 2.171059712 0.049987939 0.082254705 2293.703443 24.58075444 2505.355937 2494.011843 29.34616893 -1.467551413 2.171059118 QDATVWIPS(ph)PSRQPVYYDELDAASSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDATVWIPSPSRQPVYYDELDAASSSLR 28 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDAT(0.006)VWIPS(0.766)PS(0.195)RQPVY(0.015)Y(0.018)DELDAASSSLR 51.607 0.053254 31965000 35584 31749 31395 34006 41355 35247 44694 39258 44736 TRUE FALSE 33902.01484 34984.2592 32834.4918 30587.65227 48567.29891 34026.38755 37875.10944 35820.3614 51673.4304 0.656082141 0.677026064 0.635423109 0.591941585 0.939889195 0.65848904 0.73297068 0.693206569 1 15.65713504 -5 0.193174941 2.330779359 0.641874345 0.529184587 0.09139639 104.9087655 1.030138235 53.74236057 0.219940343 1.00E-05 5 -1.688905014 QDAVDYLTWTFLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDAVDYLTWTFLYR 14 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 117.07 0.00075529 58823000 67071 49408 46873 50870 47923 56480 76137 57100 56491 FALSE TRUE 63900.68675 54442.73137 49022.17341 45756.45095 56280.75603 54524.08344 64520.9023 52100.02129 65251.33576 0.979300822 0.834354282 0.751282297 0.701233935 0.862522665 0.835601031 0.988805847 0.798451414 1 15.99371982 1.768503536 25 0.926276337 0.833445667 0.221045353 0.089467412 42.30778309 35343.01711 0.042532616 0.023591485 58.68181474 -1.768503536 -0.09283067 QDDILKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QDDILKR 7 1 Q13155 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ;;;; 109.21 0.01135 2673629000 4012970 3337140 3459760 4191810 2787540 3724740 4268020 4157290 3255670 FALSE TRUE 3823284.861 3677198.36 3618393.418 3770441.295 3273686.093 3595751.32 3616855.161 3793255.648 3760542.676 1.016684343 0.977837157 0.962199802 1.002632232 0.870535552 0.956178836 0.96179075 1.008699003 1 21.84250944 1.238380952 24.9999957 1.004349518 0.966336815 0.157615496 0.038501333 9.787185111 1360047.587 0.030320618 0.009429695 17.31334374 -1.238380952 -0.038012703 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_SK-BR-3_Trastuzumab_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 211.3 1.73E-22 974090000 1693230 1419090 1515460 1686640 1191460 1639510 1763360 1656760 1350620 TRUE FALSE 1613194.374 1563696.884 1584945.34 1517095.743 1399250.247 1582733.358 1494327.046 1511685.311 1560067.252 1.034054379 1.002326587 1.015946805 0.972455348 0.89691662 1.014528929 0.957860659 0.968987273 1 20.57317679 3.214549161 5.311900987 0.965342968 1.016838159 0.349372998 0.031435892 0.178232932 13.65793975 0.008417809 0.010516096 1638.88757 -3.214549161 0.051495191 QDDS(ph)PSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDDSPSGASYGQDYDLSPSR 20 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 QDDS(0.962)PS(0.038)GASYGQDYDLS(0.868)PS(0.132)R;QDDS(0.994)PS(0.006)GASYGQDYDLS(0.712)PS(0.288)R 238.1 1.87E-29 714343000 298270 335960 271913 344950 235542 302250 300970 294860 275364 TRUE FALSE 284171.3682 370194.706 284380.48 310274.9706 276620.4502 291783.0067 255051.4988 269040.4952 318066.0428 0.893435105 1.163892576 0.894092552 0.97550486 0.86969501 0.917366105 0.801882202 0.845863623 1 18.27896683 3.081856327 1.444986197 0.869468177 1.019634876 0.195809939 0.090462642 0.441754849 1.916445715 0.031259222 0.039957188 1207.414334 -3.081856327 0.150166699 QDDSPSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QDDSPSGASYGQDYDLSPSR 20 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 QDDSPSGASYGQDYDLS(0.716)PS(0.284)R;QDDSPSGASYGQDYDLS(0.999)PS(0.001)R;QDDSPSGASYGQDYDLS(0.994)PS(0.006)R 373.08 3.30E-112 718590000 415740 407020 395230 458960 387650 427820 459720 431330 449500 TRUE FALSE 396088.7941 448495.8007 413351.6864 412824.4688 455256.0373 413004.4861 389581.2707 393560.4586 519206.1643 0.762873828 0.863810624 0.796122456 0.795107025 0.876830956 0.795453742 0.750340226 0.75800421 1 18.98594799 -0.93123506 4.34655095 1.000004193 0.801386121 0.694476321 0.041715889 4675442.673 2151334.444 186.4813118 0.009949021 0.117156109 0.93123506 -0.198618072 QDEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QDEFKR 6 1 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ;; 85.849 0.086981 1115540000 2241840 2022250 1710980 2316780 1400690 2045460 2043370 2209210 1442810 FALSE TRUE 2135872.666 2228319.574 1789430.125 2083892.873 1644969.893 1974625.207 1731616.377 2015759.861 1666553.606 1.28161054 1.337082447 1.073730913 1.250420548 0.987048893 1.184855501 1.039040311 1.209537967 1 20.66843629 3.739953166 24.99210392 1.109471377 1.309346502 0.476574063 0.088387087 85.05639107 1526495.929 0.020043844 0.033816997 5494.816151 -3.739953166 0.199875125 QDEHGYISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;; 148.19 9.06E-05 82060543700 47155409 31440167 35254520 41890010 38609007 37054649 44312642 38052939 33682102 FALSE TRUE 44926466.27 34643955.76 36870974.61 37679146.61 45342405.6 35771437.21 37551934.61 34720821.93 38905350.35 1.154763185 0.890467646 0.947709615 0.968482388 1.165454242 0.919447759 0.965212606 0.892443369 1 25.21346524 4.676950579 3.54071035 0.970094836 1.165061222 0.359217661 0.077928213 0.274331902 5.743039331 0.018180291 0.1269815 47528.11381 -4.676950579 0.194966386 QDENDDDDDWNPCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDENDDDDDWNPCK 14 0 Q14974;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 ; 283.35 4.42E-33 296850000 477660 415760 438320 520930 287860 503600 511690 536800 305720 FALSE TRUE 455081.9584 458126.4167 458417.4056 468565.1267 338062.6929 486160.2057 433622.2927 489794.9462 353129.4962 1.288711261 1.297332626 1.298156655 1.326893199 0.95733349 1.376719337 1.2279413 1.387012276 1 18.42983781 -2.253461119 2.252265803 0.000114265 1.268528792 0.333028599 0.120071559 4722828.483 903990.0382 23982597.62 0.026943592 0.005578775 2.253461119 1.268414527 QDGPMPKPHSVSLNDTETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QDGPMPKPHSVSLNDTETR 19 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;;; 148.44 5.74E-08 333068000 222535 155534 190589 245137 230893 218294 283181 228468 217151 FALSE TRUE 212016.2116 171383.0914 199327.6942 220495.363 271160.6661 210734.424 239976.5375 208462.1307 250825.668 0.845273186 0.68327573 0.794686189 0.879078145 1.081072237 0.840162914 0.95674633 0.83110366 1 17.93632547 3.190534554 3.492142126 0.935497259 0.762246236 0.463168532 0.081689256 0.18235433 4.557409549 0.022266323 0.028238493 1550.724163 -3.190534554 -0.173251023 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK 38 2 O43809;H3BND3 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 159.8 6.21E-18 105440000 142800 110370 110480 151940 86554 136500 148410 141930 84958 FALSE TRUE 136050.127 121616.8285 115545.6173 136666.7025 101648.9902 131772.9708 125767.3288 129501.8568 98132.85273 1.38638716 1.23930799 1.177440725 1.392670229 1.035830381 1.342801795 1.281602697 1.319658536 1 16.58244858 -1.402171563 3.334692025 0.997225825 1.273387433 0.394641992 0.105843026 3185452.244 2049303.934 60037.97761 0.022222567 0.039612152 1.402171563 0.276161609 QDHAQQLATAAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDHAQQLATAAEER 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 132.25 5.15E-05 625860000 442080 460330 450470 531170 499340 477260 533700 461210 442440 FALSE TRUE 421183.7545 507238.1504 471124.4951 477775.7824 586424.7379 460732.3665 452274.2629 420824.0074 511051.3355 0.824151558 0.992538548 0.921873132 0.934888042 1.147486949 0.901538328 0.884987929 0.823447623 1 18.96310869 -0.459715528 10.23053687 1 0.930213348 0.055227279 0.092315449 0 0 0.086582001 0.020407573 0.346964045 0.459715528 -0.069786652 QDHPSSMGVYGQESGGFSGPGENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDHPSSMGVYGQESGGFSGPGENR 24 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;Q01844-4 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 265.52 2.50E-44 399050000 294780 205642 282150 315250 371740 249260 393020 328810 381590 FALSE TRUE 280846.3336 226597.1536 295086.8566 283560.4711 436571.3383 240628.0637 333057.5807 300017.6533 440765.0283 0.637179258 0.514099665 0.669487908 0.643337045 0.990485429 0.545932749 0.755635224 0.680674813 1 18.74965023 -4.999999999 0.100178126 2.044883961 0.444069888 0.411743896 0.125807855 170.1783909 1.159541635 37.27078841 1.960493971 1.00E-05 4.999999999 -1.600814073 QDHQLDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDHQLDKK 8 1 O75146;H0YH66 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 110.87 0.0021697 27913000 112950 92317 89533 114860 74753 112740 127370 121770 80296 FALSE TRUE 107611.0773 101724.2073 93638.17661 103314.0546 87789.89953 108835.7855 107937.3672 111107.1733 92747.89358 1.160253599 1.09678186 1.009598957 1.113923461 0.946543324 1.1734583 1.163771629 1.197948212 1 16.5010269 QDIAFAYQR ddPTM_SK-BR-3_Trastuzumab_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 ; 111.65 0.0048624 167960000 320260 293040 184286 244750 344860 218020 287450 262010 317220 FALSE TRUE 305121.9445 322901.1092 192735.6954 220147.265 405003.4748 210469.9127 243594.2231 239067.0154 366412.8575 0.832727177 0.881249396 0.526006911 0.600817522 1.105320041 0.574406461 0.664808066 0.652452583 1 18.4831106 QDLPALEEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDLPALEEKPR 11 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 107.17 0.0020372 210450000 215780 226480 184170 230010 170500 213270 205900 243880 172620 FALSE TRUE 205580.507 249558.5695 192614.3767 206888.9578 200235.146 205884.4064 174486.1734 222524.5743 199389.028 1.031052256 1.25161636 0.966022948 1.037614556 1.004243554 1.032576409 0.875104188 1.116032194 1 17.6052265 3.71679325 24.97559266 0.995125561 1.141334322 0.331381865 0.079937169 695.035021 797474.2128 0.020140881 0.031233996 5209.466507 -3.71679325 0.146208761 QDLPDAMKPHEIQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDLPDAMKPHEIQEK 15 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ; 207.53 2.01E-09 334260000 1157750 1195740 990990 1323030 601570 1301980 1143340 1291810 571830 FALSE TRUE 1103025.452 1317587.265 1036427.872 1190036.511 706483.6175 1256892.106 968902.4841 1178692.268 660506.4759 1.669969171 1.994813546 1.569141121 1.801703018 1.069608919 1.9029217 1.466908379 1.784527951 1 19.33321318 -2.648370056 0.186334022 1.02E-13 1.837123604 0.374385316 0.261675738 48.0975169 1.039042555 20.97045511 0.749387809 0.002247139 2.648370056 1.837123604 QDLPNAMNAAEITDKLGLHSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QDLPNAMNAAEITDKLGLHSLR 22 1 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;; 313.65 1.69E-67 3115590000 5141470 3873950 4443220 5079240 3912560 4795610 5667100 5212630 4181890 FALSE TRUE 4898442.903 4268709.909 4646946.032 4568665.145 4594909.225 4629536.823 4802479.812 4756184.483 4830396.143 1.014087201 0.883718391 0.962021725 0.945815832 0.951248943 0.95841763 0.994220695 0.984636527 1 22.20371008 1.841261167 2.798979829 0.993040887 0.94817388 0.267725587 0.031351719 0.341219637 4.8392938 0.016964307 0.008497317 69.38429299 -1.841261167 -0.044867008 QDLPSLDEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QDLPSLDEKPR 11 1 Q92598-2;Q92598;Q92598-4;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 150.69 3.08E-05 859790000 1011120 1133130 951900 1173830 782750 1073170 1009160 1161960 781880 FALSE TRUE 963326.3614 1248597.235 995545.5566 1055834.378 919261.3522 1036005.854 855194.1075 1060212.622 903129.9571 1.066653092 1.382522222 1.10232813 1.169083552 1.017861654 1.147128213 0.946922534 1.173931408 1 19.78457408 3.077753413 1.686976083 1.051789366 1.21801134 0.238482376 0.105809762 0.407307886 2.378937027 0.03406579 0.042726543 1196.061231 -3.077753413 0.166221973 QDPSVLHTEEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QDPSVLHTEEMR 12 0 P50502;Q3KNR6;Q8NFI4;F8WAQ7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ;;; 164.68 6.49E-05 1711920000 2741580 2474470 2432000 2781900 2917750 2526580 3060220 2776560 2971540 FALSE TRUE 2611990.947 2726621.306 2543509.606 2502258.127 3426604.676 2439083.901 2593327.234 2533429.687 3432351.247 0.76099174 0.794388776 0.741040011 0.729021579 0.998325763 0.710616055 0.755554152 0.738103272 1 21.71076577 -0.986396388 4.173552128 1.000012583 0.778124185 0.42292721 0.081309779 4435455.919 1594129.795 507.9009214 0.017590675 0.103181922 0.986396388 -0.221888397 QDS(ph)DEDDGPQRVEEVDQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDSDEDDGPQRVEEVDQGR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 QDS(1)DEDDGPQRVEEVDQGR 118.85 4.31E-05 144120000 127520 130170 110280 132700 83888 127420 118540 123220 77269 TRUE FALSE 121492.3823 143434.471 115336.4471 119360.7439 98518.04064 123007.4135 100454.5459 112430.2036 89251.48188 1.361236584 1.607082235 1.292263665 1.337353077 1.103825265 1.378211441 1.125522442 1.259701253 1 16.4455885 2.60693004 0.261330118 0.988920012 1.601230902 0.518476278 0.117954138 2.038288743 0.324314334 0.198995094 0.423160562 404.510724 -2.60693004 0.61231089 QDS(ph)LEPVLRDPCYLINEGICNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QDSLEPVLRDPCYLINEGICNR 22 1 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;E7EWD5 D6RD37 TSC22D3 1 QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR 152.2 2.60E-08 377845000 158609.4 117997 138508 166986 131144 171315 186698 141280.2 138705.4 TRUE FALSE 151112.248 130021.0285 144858.7288 150200.25 154015.4721 165382.3186 158213.7912 128908.9567 160215.125 0.94318341 0.811540286 0.904151395 0.937491076 0.961304197 1.032251597 0.987508459 0.804599171 1 17.28965083 3.212651264 2.632095608 0.964005878 0.875582787 0.185856771 0.067443194 0.370832543 5.25785708 0.019809518 0.026036554 1631.741144 -3.212651264 -0.088423091 QDSGEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDSGEWR 7 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 93.195 0.03516 336310000 649410 526980 503720 626990 599880 537390 623880 588060 633080 FALSE TRUE 618713.6763 580679.8611 526816.0602 563963.774 704498.8821 518780.0496 528695.6477 536566.3489 731254.8131 0.846098604 0.794086891 0.720427477 0.771227435 0.963410933 0.709438133 0.722997836 0.733761118 1 19.48001469 QDTVSEPVTPASLAALQSDVQPVGHDYVEEVRNDEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDTVSEPVTPASLAALQSDVQPVGHDYVEEVRNDEGK 37 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 181.32 2.77E-23 43476000 29005 20495 30121 30899 26095 30122 37226 31310 25203 FALSE TRUE 27633.99113 22583.4638 31502.07764 27792.97382 30645.95974 29078.86759 31546.49 28568.33042 29111.35252 0.949251366 0.775761407 1.082123464 0.954712557 1.052715078 0.998884115 1.083649067 0.981346724 1 14.82929425 3.731980691 24.99753006 1.025968059 0.862506385 0.561977355 0.058425278 294.206137 1117706.88 0.014180101 0.02254176 5394.866359 -3.731980691 -0.163461674 QDVEALWENMAVIDCFASDHAPHTLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QDVEALWENMAVIDCFASDHAPHTLEEK 28 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 247.85 5.54E-46 28734000 63358 45101 54744 60130 46639 63140 74831 67505 9994.7 FALSE TRUE 60363.1929 49696.84318 57254.06655 54085.61816 54772.82683 60953.44597 63414.15658 61593.90433 11544.62703 5.22868281 4.304759525 4.959369099 4.68491689 4.744443167 5.279810756 5.492958449 5.335287504 1 13.49493394 3.612978746 15.98353156 4.791076682 4.744574484 0 1.327888746 59.83372822 7388.254967 0.309213105 0.479031683 4101.840288 -3.612978746 -0.046502197 QDWEHAANDVSFATIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDWEHAANDVSFATIR 16 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1;E9PH66 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 136.34 1.80E-05 154686000 165146 176356 149551 198593 170852 176662 185349 180259 157522 FALSE TRUE 157339.8759 194326.8769 156408.0613 178630.0543 200648.5347 170544.1506 157070.6059 164474.5663 181949.7072 0.86474377 1.068025224 0.859622495 0.981755107 1.102769209 0.937314785 0.863263856 0.903956202 1 17.4731802 -0.772533063 4.602119099 1.000000104 0.949616494 0.036462302 0.084000359 10522365.11 2286423.662 11.81101673 0.019350976 0.168836732 0.772533063 -0.05038361 QDYINLDESEAAAFDDEWRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QDYINLDESEAAAFDDEWRR 20 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ; 98.816 0.0011959 44802000 28490 25700 24921.4 30349 27566 30585 28681 31314 27704 FALSE TRUE 27143.33416 28318.85922 26064.07084 27298.26086 32373.50167 29525.83378 24305.18669 28571.98015 32000.19483 0.848224028 0.884958963 0.814497255 0.853065458 1.011665768 0.922676688 0.75953246 0.892868944 1 14.96579307 -2.502570086 2.012853143 2.347889683 0.86877411 0.261525252 0.066428578 2160772.681 140840.8926 13308069.74 0.016295354 0.003143619 2.502570086 -1.479115574 QEAKPQQAAGMLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 177.09 4.65E-07 878090000 1666330 2145760 1368490 2167880 711170 1879850 1451240 1934120 695500 TRUE FALSE 1587565.883 2364415.384 1431236.62 1949960.584 835197.8228 1814750.323 1229826.684 1764758.199 803354.5879 1.976170806 2.943177794 1.781575212 2.427272606 1.039637833 2.258965531 1.530864083 2.196736318 1 19.61567739 3.142326175 1.788026929 1.696736169 2.408603073 0.2345598 0.528901379 0.434671608 2.860049756 0.156708918 0.204987694 1387.797737 -3.142326175 0.711866904 QEALEWLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEALEWLIR 9 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 122.96 0.0035454 0 96661 76033 94166 92575 92840 78287 111260 87726 88777 FALSE TRUE 92092.02609 83780.84914 98483.60424 83269.18512 109031.2666 75575.90156 94285.24357 80044.24638 102544.0837 0.898072543 0.817022748 0.960402596 0.81203305 1.063262381 0.737008892 0.919460588 0.780583759 1 16.64588473 2.519913251 0.007578444 1.762656273 1.95E-06 0.034922705 0.100790852 17591.63727 61.88378628 7073.888943 7314.939965 331.0649859 -2.519913251 -1.762654326 QEALKNDLVEALKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEALKNDLVEALKR 14 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 123.97 5.61E-05 645050000 1279470 1006720 1077180 1337010 813760 1290000 1448250 1524990 961400 FALSE TRUE 1218991.989 1109305.913 1126569.768 1202611.215 955679.4864 1245326.977 1227292.864 1391453.791 1110489.002 1.097707394 0.998934623 1.014480798 1.082956439 0.860593383 1.121422161 1.105182367 1.25300997 1 20.08276367 2.051812295 24.99993445 1.126640766 1.018153629 0.275784766 0.08705287 123.2138299 59451.26542 0.02969081 0.021928115 112.6710379 -2.051812295 -0.108487138 QEARPEPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 130.01 0.00034047 903050000 1823940 1357320 1240050 1576690 1710270 1486590 1902370 1654530 1928560 FALSE TRUE 1737725.971 1495632.451 1296907.519 1418198.126 2008540.547 1435109.016 1612128.517 1509650.582 2227631.235 0.780077934 0.671400377 0.582191297 0.63663954 0.901648583 0.644230963 0.723696315 0.677693219 1 21.087079 -1.775706368 2.490624003 1.081911352 0.703421062 0.529888485 0.088146757 11663426.68 7933857.452 5816087.541 0.020342127 0.016760757 1.775706368 -0.37849029 QECLDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QECLDSR 7 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;; 101.54 0.034855 398820000 1272380 1087790 1079100 1360790 1355050 1110730 1588490 1219570 1601520 FALSE TRUE 1212237.119 1198637.038 1128577.802 1224000.804 1591370.291 1072265.142 1346136.676 1112777.985 1849875.542 0.655307393 0.647955503 0.610083098 0.661666569 0.860258031 0.579641774 0.727690401 0.601542082 1 20.81899678 -2.168029897 2.330686377 1.814021295 0.669655893 0.633235453 0.079392661 3481164.25 615348.4224 15025485.2 0.017531941 0.006791569 2.168029897 -1.144365403 QEDEWDKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEDEWDKPR 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 138.71 0.00011753 565800000 1318940 1293670 1025500 1433440 735380 1213170 1196760 1254030 750380 FALSE TRUE 1256596.32 1425496.444 1072520.189 1289347.888 863630.0392 1171157.619 1014172.282 1144220.485 866745.098 1.449787628 1.644654752 1.237411313 1.487574479 0.996406027 1.351213432 1.170092896 1.320134937 1 19.72524825 4.146503447 0.200332967 0.990006022 1.944954366 0.429363129 0.155668717 8.793763871 0.419074449 0.338970908 2.144087137 14012.10706 -4.146503447 0.954948343 QEDKDDLDVTELTNEDLLDQLVK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 241.2 2.52E-37 319089000 322226 308103 289530 388880 198385 397022 389756 399929 196066 FALSE TRUE 306995.0156 339499.046 302805.2369 349789.0436 232983.2812 383273.0286 330291.5638 364909.0966 226470.9139 1.355560457 1.499084541 1.337060162 1.544520828 1.028755866 1.692371978 1.458428185 1.611284603 1 17.78896625 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QEEAEEQGAGSPGQPAHLAR 20 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR 329.57 5.57E-80 8750300000 3166234 3635573 2964784 3935008 2847760 3209466 3131314 3477149 2566314 TRUE FALSE 3016572.394 4006042.022 3100722.279 3539453.52 3344408.442 3098321.388 2653574.539 3172671.4 2964284.868 1.01763917 1.351436249 1.046027091 1.194032854 1.128234495 1.045217152 0.895182028 1.070299091 1 21.49925267 2.171862007 2.993253001 0.975840497 1.16349196 0.348571782 0.09915203 0.235757629 4.278015915 0.039679436 0.027529921 148.5463574 -2.171862007 0.187651463 QEEDSYEIFICHANVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEEDSYEIFICHANVIR 17 0 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 125.18 4.78E-05 62112000 33070 36062 28407 35728 31203 31635 33873 33911 24767 FALSE TRUE 31506.84664 39736.7588 29709.48905 32136.55356 36644.79332 30539.47202 28705.05173 30941.57307 28607.73987 1.101339945 1.389021257 1.038512276 1.123351712 1.280939826 1.067524808 1.003401592 1.081580482 1 14.8041179 2.087680019 6.421151301 1.030352035 1.196423825 0.36057982 0.09883607 0.216681596 12.9872144 0.036859938 0.027059935 122.3714255 -2.087680019 0.16607179 QEEEMMAKEEELVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEEEMMAKEEELVK 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 160.48 4.33E-06 79509000 211122 80110 232390 175406 166864 237240 316500 282270 227640 FALSE TRUE 201142.6815 88273.30008 243045.3114 157773.8556 195965.0288 229024.3193 268212.1121 257552.9424 262941.2486 0.764971957 0.335714919 0.924333145 0.600034633 0.745280666 0.871009477 1.020045784 0.979507566 1 18.00438096 2.287631328 0.990677886 1.027998711 0.604145266 0.503939061 0.148617578 0.390119721 0.737379765 0.100365835 0.059240237 193.9238961 -2.287631328 -0.423853444 QEEKHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEEKHLK 7 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 56.411 0.073163 266480000 1471400 953750 686500 1164500 768450 953320 1158800 1047000 552850 FALSE TRUE 1401849.838 1050938.209 717976.704 1047442.248 902467.4367 920306.2894 982003.7772 955319.1295 638583.1544 2.195250263 1.645734314 1.12432766 1.640259754 1.413234017 1.441169068 1.537785283 1.495998012 1 19.28451497 4.297301841 2.14916534 1.422360771 2.167338546 0.622060222 0.19739095 0.194886252 1.661636302 0.045921509 0.195178958 19829.04692 -4.297301841 0.744977775 QEESES(ph)PVERPLKENPPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.034)ES(0.966)PVERPLKENPPNK;QEES(0.039)ES(0.961)PVERPLKENPPNK 113.24 9.44E-05 192639000 250414 271930 209904 282420 157334 263820 264300 262550 172634 TRUE FALSE 238577.4265 299639.9762 219528.306 254030.605 184772.9998 254683.8472 223976.1808 239559.7301 199405.199 1.196445367 1.502668825 1.100915659 1.273941734 0.926620774 1.277217688 1.12322137 1.201371535 1 17.6053435 3.717289245 24.93651205 1.139781096 1.349557112 0.326557019 0.130948898 740.4879573 868076.8478 0.031257938 0.04847413 5215.419478 -3.717289245 0.209776016 QEFAQHANAFHQWIQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEFAQHANAFHQWIQETR 18 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 173.56 4.64E-12 167400000 148700 118190 128580 158390 153820 131010 169390 144460 39981 FALSE TRUE 141671.2457 130233.6954 134475.5202 142468.3363 180646.1593 126473.0908 143546.4444 131810.3166 46181.04929 3.06773553 2.820067915 2.911919982 3.084995653 3.911694561 2.738636146 3.108340903 2.854207919 1 15.49501333 0.399974754 1.545698239 0.999602661 3.075479577 0.808129179 0.317673248 1.779547068 4.137906863 0.292496125 0.083919844 2.511740418 -0.399974754 2.075876915 QEFEFWYPVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEFEFWYPVDLR 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 191.29 1.29E-05 213832000 186099 205342 154938 229260 165495 163452 185095 201270 179276 FALSE TRUE 177302.4691 226266.5833 162042.0606 206214.3492 194357.2756 157791.6163 156855.3582 183645.7318 207077.2065 0.856214318 1.09266774 0.782520024 0.995833162 0.938573969 0.761994132 0.757472833 0.886846674 1 17.65980924 2.263081347 20.5651985 0.820973128 0.943919253 0.092649154 0.106714762 42.19374804 35386.42614 0.03432104 0.028682019 183.2657663 -2.263081347 0.122946125 QEFEKQDELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEFEKQDELKR 11 2 Q86VP6;Q86VP6-2;A0A0C4DGH5;O75155-2;O75155 Q86VP6 CAND1;CAND2 Cullin-associated NEDD8-dissociated protein 1;Cullin-associated NEDD8-dissociated protein 2 0 ; 122.39 0.00022032 798390000 1165870 691220 1155540 1116790 849150 1358260 1580670 1512880 1028850 FALSE TRUE 1110761.636 761656.1039 1208522.652 1004528.147 997241.4911 1311223.116 1339509.761 1380404.207 1188398.803 0.934670779 0.640909518 1.016933582 0.845278659 0.839147169 1.103352773 1.12715509 1.161566473 1 20.18058763 2.234755046 7.817901702 1.111005657 0.83993861 0.57556441 0.102801682 0.078988005 34.45623877 0.036071194 0.028087933 171.6939715 -2.234755046 -0.271067047 QEIQHLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEIQHLFR 8 0 P04844-2;P04844;H0Y5M1 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 95.099 0.0098907 91012000 59154 42940 46799 69383 85858 55323 67727 50737 55483 FALSE TRUE 56357.90765 47315.63482 48944.78044 62408.48902 100831.608 53407.15064 57394.00226 46294.19931 64087.02027 0.879396599 0.73830293 0.763723765 0.973808561 1.573354598 0.833353625 0.895563595 0.722364671 1 15.96774457 3.19422159 6.789379577 1.003679094 0.794188548 0.157107702 0.225157929 0.370909671 42.37750872 0.065748976 0.079708896 1563.94541 -3.19422159 -0.209490546 QEKPAEKPAET(ph)PVATS(ph)PTATDSTSGDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 2 QEKPAEKPAET(1)PVAT(0.25)S(0.744)PT(0.006)ATDSTSGDSSR 116.53 0.00029806 111610000 157180 126180 136200 152950 84718 138010 151740 149880 78235 TRUE FALSE 149750.4129 139037.8855 142444.9047 137575.1754 99492.79238 133230.6791 128589.2761 136755.7126 90367.28423 1.657130832 1.538586521 1.576288432 1.522400242 1.100982432 1.474324256 1.422962715 1.513332107 1 16.46351295 -3.097332698 0.091814131 6.18E-12 1.900218886 0.568801803 0.137562862 95.79149243 0.924668405 23.30992302 3.431732009 0.000799222 3.097332698 1.900218886 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.444)S(0.444)PT(0.086)AT(0.021)DS(0.004)T(0.001)SGDSSR;QEKPAEKPAETPVAT(0.517)S(0.393)PT(0.085)AT(0.004)DSTSGDSSR 134.42 1.26E-05 2011870000 466500 373850 395340 468890 255000 454580 465360 415720 265700 TRUE FALSE 444449.4695 411945.74 413466.73 421756.2864 299471.9193 438837.7806 394360.7851 379317.3529 306903.399 1.448173826 1.34226516 1.347221085 1.374231396 0.975785606 1.429888955 1.284967147 1.235950316 1 18.2274251 -4.921427973 0.076686806 2.00E-11 1.645538075 0.435576701 0.122734142 249.4640898 1.382395048 43.50546935 4.597661081 1.20E-05 4.921427973 1.645538075 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAET(0.001)PVAT(0.227)S(0.758)PT(0.013)AT(0.001)DSTSGDSSR;QEKPAEKPAETPVAT(0.009)S(0.99)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.116)S(0.859)PT(0.024)AT(0.001)DSTSGDSSR;QEKPAEKPAET(0.021)PVAT(0.401)S(0.457)PT(0.108)AT(0.008)DS(0.001)T(0.001)S(0.001)GDS(0.001)S(0.001)R;QEKPAEKPAETPVAT(0.039)S(0.811)PT(0.122)AT(0.003)DS(0.011)T(0.011)S(0.002)GDSSR;QEKPAEKPAETPVAT(0.141)S(0.856)PT(0.003)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.008)S(0.991)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.005)S(0.978)PT(0.016)AT(0.001)DSTSGDSSR 174.9 4.03E-13 45206900000 9360976 7014307 7503002 8866869 5127268 8760145 8921265 8316120 5280574 TRUE FALSE 8918501.216 7729072.858 7847022.063 7975554.482 6021461.916 8456778.982 7560162.174 7587916.446 6099458.446 1.462179191 1.267173623 1.286511275 1.307584034 0.987212548 1.386480301 1.239480888 1.244031173 1 22.54024972 7.999999986 0.027969969 1.77E-08 3.045170884 0.427570331 0.112718208 1542.088442 3.312128109 118.4978086 270.9683434 99999996.77 -7.999999986 3.045170866 QEKPAEKPAETPVATSPTATDSTSGDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;; 237.97 1.44E-45 1745040000 545032 485604 520532 627540 324792 587460 678720 680910 414728 FALSE TRUE 519269.4175 535087.5997 544398.9071 564458.487 381435.622 567116.1129 575168.7985 621285.9107 479041.9001 1.083974945 1.116995402 1.136432757 1.178307131 0.796246888 1.183854925 1.200664907 1.296934382 1 18.86979232 2.052566176 24.99995784 1.189193265 1.072902149 0.145020036 0.125293054 164.189341 78085.96778 0.043658534 0.032243959 112.8667907 -2.052566176 -0.116291116 QELASGLPS(ph)PAATQELPVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QELASGLPSPAATQELPVER 20 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QELASGLPS(1)PAATQELPVER;QELASGLPS(1)PAATQELPVER;QELASGLPS(1)PAATQELPVER 378.1 1.56E-112 360420000 805910 715900 622250 871450 738010 642260 713200 666550 654580 TRUE FALSE 767816.2315 788851.0239 650780.778 783850.1904 866718.7103 620018.3752 604388.2412 608183.3484 756088.9233 1.015510488 1.043331015 0.860719894 1.036716934 1.146318487 0.820033671 0.799361322 0.804380715 1 19.52819639 2.21262837 24.99755864 0.834267557 1.016647345 0.447063536 0.089458634 178.3030824 171875.3023 0.031536585 0.023299118 163.1655126 -2.21262837 0.182379789 QELGS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QELGSPEER 9 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER;QELGS(1)PEER 169.98 6.09E-05 6106420000 4339300 3513040 3792430 4348500 4081690 4096500 4561560 4051410 4323440 TRUE FALSE 4134189.889 3871022.77 3966316.667 3911380.518 4793535.444 3954637.178 3865610.243 3696647.063 4993896.994 0.827848451 0.775150704 0.794232775 0.783232118 0.959878718 0.791894022 0.774066876 0.740232942 1 22.25173463 -1.081469891 4.601653104 1.000011567 0.805030852 0.516962206 0.058985143 0.104712684 34926960.29 854.4167739 0.013329099 0.082895338 1.081469891 -0.194980715 QELS(ph)FAARSFYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QELSFAARSFYYK 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 1 QELS(0.27)FAARS(0.27)FY(0.23)Y(0.23)K;QELS(0.273)FAARS(0.273)FY(0.227)Y(0.227)K 56.122 0.075216 1346040000 784930 879680 769010 837780 581360 937440 866470 977310 617280 TRUE FALSE 747827.9145 969320.3921 804269.8692 753564.7627 682748.9999 904976.2177 734274.0877 891731.5554 713004.6298 1.048840194 1.359486813 1.128000907 1.056886213 0.957566012 1.269243116 1.029830743 1.250667272 1 19.44355192 -4.999999989 0.115621676 0.57964662 1.211848885 0.068330665 0.126540073 376.6779971 2.855627691 38.03575377 1.296043343 1.00E-05 4.999999989 0.632202265 QELSFAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 208.72 0.00021402 1814430000 6510460 6047300 5383590 6326680 5608140 5469820 7144260 6499660 5505500 FALSE TRUE 6202723.458 6663526.745 5630432.927 5690710.106 6586197.84 5280398.762 6054271.924 5930515.314 6359264.822 0.975383733 1.047845456 0.885390542 0.894869182 1.035685417 0.830347361 0.952039598 0.932578762 1 22.60042856 3.74158196 24.99828601 0.928804124 1.011614594 0.226615154 0.060001858 317.4412802 2626465.858 0.014089816 0.0240706 5515.462801 -3.74158196 0.082810471 QELSHALYQHDAACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QELSHALYQHDAACR 15 0 Q9UMS4;F5GY56;F5H2I0 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;; 215.15 1.38E-12 1444640000 873940 754127 732052 870766 896944 808543 1002429 893571 183909 FALSE TRUE 832630.5882 830973.3987 765617.3083 783234.9473 1053370.75 780542.9532 849490.0452 815325.1861 212428.6684 3.919577307 3.911776149 3.604114802 3.687049178 4.958703349 3.674376716 3.998942569 3.838112775 1 17.69661895 0.253443312 1.846089676 0.999794917 3.958465031 0.85750469 0.378119659 4.923960976 11.66014136 0.337753032 0.093813442 1.792434572 -0.253443312 2.958670114 QELVDAFVEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QELVDAFVEHR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;;;; 203.39 3.68E-08 610607000 751963 839890 734863 862437 738268 784142 792062 862083 614195 FALSE TRUE 716419.1992 925475.7459 768557.1954 775743.1942 867021.7055 756986.9659 671218.3947 786594.4423 709441.2237 1.009835875 1.30451363 1.083327511 1.093456608 1.22211915 1.067018578 0.946122628 1.108752094 1 19.43632364 2.014536618 10.79977051 1.010852228 1.147499381 0.295896105 0.088257067 0.377656728 271.9812065 0.031652908 0.023096745 103.4038284 -2.014536618 0.136647153 QEMQEVQSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 QEMQEVQSSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;; 290.68 9.72E-32 4061390000 2368906 1789148 1922787 2249743 2177249 2006848 2481700 2224675 2443406 FALSE TRUE 2256932.508 1971464.215 2010948.686 2023594.559 2556960.536 1937350.351 2103071.085 2029870.663 2822316.923 0.799673662 0.698526873 0.712516964 0.716997635 0.905979238 0.686439689 0.745157664 0.719221377 1 21.42844857 -1.081987771 4.550631588 1.000015767 0.746569855 0.604253828 0.064065227 0.225659852 35930055.97 1278.924009 0.013865644 0.082796548 1.081987771 -0.253445912 QENKRPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QENKRPSPR 9 2 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR 89.663 0.0094148 499106000 549010 445870 519510 577770 388866 597660 669700 635380 519970 TRUE FALSE 523059.3853 491304.6599 543330.0474 519691.4619 456684.1073 576962.8843 567524.9651 579742.7588 600604.292 0.870888524 0.818017231 0.904638969 0.865280966 0.760374365 0.960637298 0.944923259 0.965265761 1 19.19605526 2.203879223 24.70116339 0.961079134 0.84651587 0.702483332 0.039931264 90.13375133 64195.47804 0.014062618 0.010386447 159.9113254 -2.203879223 -0.114563264 QENLPDEIYHVYSFALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QENLPDEIYHVYSFALR 17 0 Q9BV86;S4R338 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 ; 154.26 1.44E-07 91394000 171819 110685 137332 165909 153885 142495 181733 170847 167399 FALSE TRUE 163697.4564 121963.9273 143628.808 149231.5121 180722.4953 137560.3624 154006.2931 155886.731 193358.382 0.846601294 0.630766177 0.742811388 0.771787137 0.934650432 0.711426942 0.796481081 0.806206224 1 17.56091778 -5 0.19937644 2.049082232 0.733771316 0.439184363 0.079222457 127.598941 1.261377174 53.14038239 0.184275599 1.00E-05 5 -1.315310916 QEPCAQHNGSEPAS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEPCAQHNGSEPASPKR 17 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 QEPCAQHNGS(0.004)EPAS(0.996)PKR 92.01 0.0016055 89233000 88307 80441 80700 91477 100590 83828 104840 100700 110330 TRUE FALSE 84132.90312 88638.02935 84400.17482 82281.55817 118132.8642 80925.01534 88844.73248 91882.17416 127439.4129 0.660179619 0.695530741 0.662276865 0.645652364 0.926972759 0.635007754 0.697152713 0.720987111 1 16.959452 -5 0.296604148 3.424179283 0.685195109 0.561447656 0.082311701 188.6623572 1.755586339 283.9288942 0.078339875 1.00E-05 5 -2.738984173 QEPES(ph)EEEEEEKQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEPESEEEEEEKQEK 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK 229.98 2.36E-13 1243970000 965340 993080 705680 1036540 372890 1083530 881740 1025790 340705 TRUE FALSE 919710.2913 1094275.981 738036.126 932345.0299 437921.8979 1046007.084 747214.3687 935966.3895 393539.7913 2.337019818 2.780598062 1.875378659 2.369125182 1.112776669 2.657944908 1.898700932 2.378327199 1 18.58614999 -1.524422324 0.188474819 6.98E-23 2.55065637 0.358938673 0.479617532 28.96819201 0.963613902 16.85333853 1.492778711 0.029893563 1.524422324 2.55065637 QEPES(ph)EEEEEEKQEKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEPESEEEEEEKQEKEEK 18 2 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEKEEK;QEPES(1)EEEEEEKQEKEEK 171.72 6.56E-12 694910000 973670 851230 789360 951960 325660 1000590 853510 1035890 301330 TRUE FALSE 927646.5487 937971.3048 825552.9368 856267.1722 382455.0009 965939.3174 723291.3737 945181.98 348058.7174 2.665201307 2.694865141 2.371878351 2.460122759 1.098823221 2.775219436 2.078072858 2.715581977 1 18.40897118 3.255161969 2.357750819 2.06642182 2.655601587 0.185433988 0.588169717 0.490913314 5.589264887 0.163058738 0.222513798 1799.541926 -3.255161969 0.589179767 QEPGGSHGS(ph)ETEDTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEPGGSHGSETEDTGR 16 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 QEPGGS(0.003)HGS(0.986)ET(0.012)EDTGR;QEPGGS(0.001)HGS(0.933)ET(0.065)EDT(0.001)GR 197.41 1.43E-12 32770000 50043 48612 43347 54477 43461 49045 49591 42485 41445 TRUE FALSE 47677.56657 53565.61807 45334.50283 49000.86846 51040.58464 47346.55935 42024.98215 38764.78817 47872.07893 0.995936831 1.118932356 0.946992565 1.023579288 1.066186925 0.98902242 0.877859978 0.809757776 1 15.54689684 1.860324492 3.494581291 0.883301684 1.03484152 0.473988125 0.063899354 0.177418576 3.641017906 0.030304572 0.016280107 72.49774395 -1.860324492 0.151539836 QEPLGS(ph)DSEGVNCLAYDEAIMAQQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.713)DS(0.287)EGVNCLAYDEAIMAQQDR;QEPLGS(0.5)DS(0.5)EGVNCLAYDEAIMAQQDR 199.76 3.61E-25 172536000 66872 61328 65618 70107 70211 66982 80237 72066 86860 TRUE FALSE 63711.09309 67577.39292 68626.65021 63059.71117 82455.77617 64662.39654 67995.372 65755.51899 100329.8052 0.635016613 0.673552518 0.6840106 0.628524206 0.821847267 0.644498376 0.677718569 0.655393668 1 16.61439073 -2.0540308 2.641920358 1.449638695 0.676327841 0.775893704 0.054454593 6171249.274 2004104.122 16783813.4 0.012030212 0.008830173 2.0540308 -0.773310854 QEPLLIGSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEPLLIGSTK 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 ; 134.13 0.0068034 0 406060 351500 387110 439160 313860 429490 479130 443980 374910 FALSE TRUE 386866.3485 387318.2496 404859.3764 395014.8025 368597.0846 414616.6536 406029.9187 405102.7575 433049.128 0.893354411 0.894397944 0.934904033 0.912170876 0.851166902 0.957435604 0.937607057 0.935466051 1 18.72417118 0.99169864 0.507083054 1.00203761 0.896716051 0.560984545 0.026677072 0.735346254 0.473933516 0.029910477 0.014183987 9.810669385 -0.99169864 -0.10532156 QEPQGQEIQSENLIMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEPQGQEIQSENLIMEK 17 0 Q4VCS5 Q4VCS5 AMOT Angiomotin 0 62.165 0.044855 518610000 681630 523070 624590 633730 981460 485780 852560 603930 1001300 FALSE TRUE 649410.7008 576371.4277 653228.0693 570026.2564 1152626.313 468957.3168 722486.3137 551046.6876 1156576.49 0.561493949 0.49834268 0.564794525 0.492856513 0.996584595 0.405470214 0.624676638 0.476446385 1 20.14142925 -1.541774846 2.69459558 1.024727857 0.575115135 0.406440231 0.160402385 13832472.79 13663885.1 2480532.376 0.036088677 0.028722693 1.541774846 -0.449612723 QEPQS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEPQSPSR 8 0 Q8WUQ7-2;Q8WUQ7;K7ENY9 Q8WUQ7-2 CACTIN Cactin 1 QEPQS(0.977)PS(0.023)R 76.619 0.037062 74777000 130420 114320 115550 132750 133180 124180 129970 116650 124180 TRUE FALSE 124255.3051 125969.338 120848.0818 119405.7178 156406.5498 119879.6155 110140.6894 106435.5076 143437.2002 0.866269733 0.878219442 0.842515621 0.832459903 1.090418313 0.835763772 0.767866978 0.742035591 1 17.13005971 -1.047674398 4.630501218 1.000004685 0.857570911 0.190180127 0.092764891 5.27E-06 1.08E-06 0.089212987 0.021026884 0.08960363 1.047674398 -0.142433773 QEPS(ph)PKPNNK ddPTM_SK-BR-3_Trastuzumab_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 1 QEPS(1)PKPNNK;QEPS(1)PKPNNK 70.412 0.032739 744730000 2470900 2760800 2290500 2909200 1230030 2942000 2501400 2840000 1201580 TRUE FALSE 2354105.454 3042128.659 2395521.691 2616761.689 1444546.843 2840117.802 2119765.489 2591314.544 1387914.89 1.696145399 2.191869748 1.725986016 1.885390602 1.040803621 2.04631986 1.527302218 1.8670558 1 20.40448767 -2.30704907 0.186850065 1.14E-12 1.967322773 0.353124703 0.313555567 42.85330931 1.04841958 19.64268078 0.925942308 0.004931181 2.30704907 1.967322773 QEQEEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QEQEEEGR 8 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 ;; 187.78 0.00046632 688070000 665980 591000 647160 720790 641430 640300 741530 692440 790420 FALSE TRUE 634500.4452 651223.5719 676832.9261 648334.8198 753295.1889 618126.2504 628395.9794 631806.2827 912994.2967 0.694966494 0.713283286 0.741333137 0.710119244 0.825082031 0.677031886 0.68828029 0.692015585 1 19.80024632 -1.304467585 3.40397308 1.001216793 0.715802824 0.816622803 0.042022553 14542456.07 19021624.39 175957.3763 0.009827238 0.049605795 1.304467585 -0.285413969 QEQHEAQAQVAELELQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEQHEAQAQVAELELQLR 18 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 142.98 1.09E-07 50305000 34300 33006 32039 35533 33919 29284 33444 38939 41163 FALSE TRUE 32678.70698 36369.34892 33508.01984 31961.15533 39834.46286 28269.88774 28341.50356 35529.29473 47546.34781 0.687302148 0.764924134 0.704744347 0.672210523 0.83780279 0.594575378 0.59608161 0.747256022 1 15.53704691 0.971063691 23.29281254 1.000000003 0.693717061 0.6419843 0.071350607 917.4990436 738559.0525 0.070932892 0.017733223 9.355428642 -0.971063691 -0.306282941 QEQINTEPLEDTVLS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 QEQINTEPLEDTVLS(0.999)PT(0.001)K;QEQINTEPLEDTVLS(0.997)PT(0.003)K 235.85 8.78E-24 277420000 890980 911810 820290 1028700 605270 1033840 1032330 1112300 746790 TRUE FALSE 848865.1412 1004724.476 857901.1079 925293.1216 710828.8964 998037.8616 874829.0985 1014901.115 862598.3791 0.984079221 1.164765086 0.99455451 1.072681266 0.824055451 1.157013375 1.014178927 1.176562743 1 19.71832948 -0.811001962 7.384263213 1.000000002 1.049677335 0.020182055 0.105883748 0 7.41E-19 0.091329624 0.021526599 0.154524746 0.811001962 0.049677333 QEQLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 104.22 0.0086015 1503600000 3577490 3349460 3091260 4123600 2205220 3688340 3831990 3919270 2447910 TRUE FALSE 3408389.138 3690773.782 3232997.329 3709087.894 2589809.67 3560611.861 3247349.546 3576077.941 2827519.381 1.205434403 1.305304504 1.143404127 1.311781599 0.915929945 1.259270541 1.148480031 1.264740382 1 21.43110548 -5 0.129695936 0.383022501 1.277638259 0.202774894 0.115716798 212.1077695 1.736982582 34.59975027 0.796818438 1.00E-05 5 0.894615758 QEQLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEQLSPR 7 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QEQLS(1)PR 104.05 0.018963 0 427140 403010 434690 504490 481830 477350 504970 512100 532720 TRUE FALSE 406949.9387 444077.1772 454620.9665 453777.7067 565860.9994 460819.2498 427927.5521 467257.8092 615331.4968 0.661350737 0.721687707 0.738822844 0.737452429 0.919603502 0.748895924 0.695442301 0.759359486 1 19.23100432 -5 0.22016841 2.288681913 0.708537405 0.590331844 0.06653721 115.1891613 1.151903376 66.05009442 0.131933275 1.00E-05 5 -1.580144508 QEQSYFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QEQSYFVR 8 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ;;; 166.52 0.00073982 423377000 380085 286620 292103 324437 363178 321804 423261 333917 400325 FALSE TRUE 362119.1353 315826.9039 305496.2115 291823.9764 426516.1282 310659.8468 358684.7607 304677.4573 462405.3564 0.783120546 0.683008749 0.660667545 0.631099905 0.922385786 0.671834447 0.775693352 0.658896903 1 18.81879858 -1.77320406 2.382011413 1.078971521 0.726014642 0.504153706 0.086190704 7421551.468 4822662.413 3413559.752 0.020968812 0.016857608 1.77320406 -0.352956878 QERLS(ph)PEVAPPAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;QERLS(1)PEVAPPAHR 148.19 4.74E-06 3743620000 4083740 3368160 3521660 4249570 4195760 3915050 4577040 3977570 3986500 TRUE FALSE 3890709.703 3711379.333 3683131.594 3822395.15 4927499.216 3779470.837 3878728.485 3629272.884 4604706.06 0.844942034 0.805997014 0.799862477 0.830106222 1.070100708 0.820784386 0.842340083 0.788166028 1 22.13467763 -2.394831216 2.306780694 2.232480941 0.848663004 0.255242677 0.080326983 5600225.491 542215.5271 36720463.26 0.020501179 0.004028736 2.394831216 -1.383817937 QES(ph)DEESRPQNANYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QESDEESRPQNANYPR 16 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 QES(1)DEESRPQNANYPR 67.928 0.030534 80341000 99756 113550 101520 129490 75292 124360 118890 133010 96529 TRUE FALSE 95040.73158 125120.8741 106174.7924 116473.4192 88422.90096 120053.382 100751.1469 121362.9393 111498.2243 0.852396818 1.122178177 0.952255456 1.044621292 0.793043131 1.076729094 0.903612121 1.088474189 1 16.76666121 1.227312218 24.99922659 1.044237064 0.970820875 0.094062567 0.102185463 620.3268865 1378613.96 0.084489574 0.021882588 16.87765939 -1.227312218 -0.073416189 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 QES(1)DPEDDDVKKPALQSSVVATSK;QES(0.996)DPEDDDVKKPALQS(0.002)S(0.002)VVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK 268.3 5.49E-45 10104125000 4328590 3876710 3837550 4588330 1580574 4981760 4420690 4670740 1567931 TRUE FALSE 4123986.129 4271751.156 4013505.463 4127102.351 1856225.605 4809240.402 3746232.549 4261745.244 1811077.732 2.277089524 2.358679079 2.216086805 2.278810169 1.024928733 2.655457752 2.068510083 2.353154241 1 20.78841704 2.944300714 24.999961 1.938217824 2.292548838 0.143014294 0.519443047 668.4068015 300005.8886 0.145435396 0.154258163 879.6313808 -2.944300714 0.354331013 QES(ph)FEAEKDHITPSLLHNGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QESFEAEKDHITPSLLHNGFR 21 1 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 QES(1)FEAEKDHITPSLLHNGFR 142.4 8.87E-08 51851000 66567 57959 58460 69930 48256 67560 77887 70054 26423 TRUE FALSE 63420.50983 63865.08799 61140.44882 62900.50354 56671.83112 65220.38026 66003.90766 63919.70038 30520.54389 2.077961325 2.092527847 2.003255546 2.060923415 1.85684211 2.136933748 2.162605879 2.094317212 1 14.89749305 -0.890308245 5.206741444 0.99999822 2.067292884 0.939966816 0.084226038 1.76E-06 3.74E-07 0.082304938 0.019399428 0.128733553 0.890308245 1.067294664 QES(ph)LQSVKNTTEQEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QESLQSVKNTTEQEILK 17 1 A0A494BZZ1;A0A499FIV7;Q9NPP4 A0A494BZZ1 NLRC4 NLR family CARD domain-containing protein 4 1 QES(0.488)LQS(0.488)VKNT(0.012)T(0.012)EQEILK 50.305 0.097314 1390600000 2004100 1809000 1753000 1941200 1545300 2083100 2170100 2328900 1605800 TRUE FALSE 1909370.165 1993339.157 1833376.784 1746066.888 1814799.831 2010961.725 1839011.388 2124969.17 1854819.263 1.02941036 1.074681074 0.988439586 0.94136767 0.97842408 1.084182036 0.991477404 1.145647564 1 20.82284718 1.281583748 24.99970479 1.072825775 1.017766596 0.16648537 0.05510426 228.7889322 132943.4987 0.035609106 0.013002452 19.12422074 -1.281583748 -0.055059179 QESCSPHHPQVLAQQGSGSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGSGS(0.003)S(0.997)PK;QESCSPHHPQVLAQQGSGS(0.011)S(0.989)PK;QESCSPHHPQVLAQQGSGS(0.003)S(0.997)PK;QESCSPHHPQVLAQQGS(0.001)GS(0.043)S(0.956)PK 166.23 1.99E-11 489732000 339408 265985 296152 399228 260390 347297 413284 422330 75185 TRUE FALSE 323364.8565 293089.1739 309730.8621 359096.843 305801.9336 335270.0178 350229.9353 385348.5463 86844.30581 3.723500965 3.374880727 3.566507432 4.134949777 3.521266371 3.860587228 4.03284858 4.437234459 1 16.40614364 -0.562073988 9.771109133 1 3.795074905 0.887986714 0.315807991 0 1.39E-17 0.312934171 0.073759292 0.274110714 0.562073988 2.795074905 QESDKNGES(ph)ASPERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.5)AS(0.5)PERDR 57.496 0.092796 37234000 65871 62565 58111 70049 42815 68206 71134 72287 44189 TRUE FALSE 62757.40837 68940.44463 60775.44683 63007.54144 50281.92244 65844.00912 60281.20183 65957.16706 51041.60443 1.229534398 1.350671582 1.190704084 1.23443497 0.985116416 1.290006649 1.181020904 1.292223624 1 15.63938606 -5 0.160765451 0.210126333 1.282433247 0.302088949 0.099531154 158.3129654 1.458362261 40.38090981 0.396239728 1.00E-05 5 1.072306914 QESDKNGESAS(ph)PERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.012)AS(0.988)PERDR;QESDKNGES(0.082)AS(0.918)PERDR;QESDKNGES(0.054)AS(0.946)PERDR;QESDKNGES(0.033)AS(0.967)PERDR;QESDKNGESAS(1)PERDR;QESDKNGES(0.004)AS(0.996)PERDR;QESDKNGES(0.06)AS(0.94)PERDR;QESDKNGESAS(1)PERDR 201.61 1.70E-11 2396225000 2043056 1990632 1881958 2347878 1279498 2218154 2121795 2204619 1415199 TRUE FALSE 1946484.792 2193479.664 1968247.636 2111864.843 1502642.046 2141338.771 1798076.203 2011570.873 1634660.833 1.190757589 1.341856133 1.204070958 1.291928454 0.919237811 1.309959062 1.099968976 1.230573849 1 20.6405599 -4.999997708 0.076521492 0.299306499 1.42932295 0.229640473 0.119042165 343.8654488 1.874344497 41.06577233 4.242598828 1.00E-05 4.999997708 1.130016451 QET(ph)VECLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QETVECLR 8 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;H0Y6G2 Q13555-8 CAMK2G Calcium/calmodulin-dependent protein kinase type II subunit gamma 1 QET(1)VECLR;QET(1)VECLR;QET(1)VECLR;QET(1)VECLR 160.91 0.0039195 2013890000 2240300 2309080 1808420 3012100 1816310 2688510 2324080 2348030 1584800 TRUE FALSE 2134405.459 2544377.877 1891337.846 2709317.985 2133073.889 2595406.225 1969498.911 2142424.046 1830562.69 1.165983263 1.389943044 1.033200259 1.480046545 1.165255853 1.417818815 1.075898095 1.170363658 1 20.80385575 1.6369136 9.364826408 1.091881138 1.274002807 0.299949176 0.138703785 0.128670465 23.63909584 0.059119262 0.030980419 43.34246427 -1.6369136 0.182121669 QETHCQS(ph)TPLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QETHCQSTPLKK 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 QETHCQS(0.598)T(0.402)PLKK;QETHCQS(0.674)T(0.326)PLKK;QETHCQS(0.671)T(0.329)PLKK 192.96 1.60E-06 1273820000 2566480 2313930 2673510 3120180 1763700 2919840 3200520 3204490 2009400 TRUE FALSE 2445167.577 2549722.098 2796093.078 2806533.578 2071288.722 2818725.209 2712221.892 2923887.868 2321007.489 1.053494049 1.09854109 1.204689382 1.209187644 0.892409323 1.214440376 1.168553701 1.259749432 1 21.14631975 QEVPSWLENMAYEHHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 182.7 4.24E-10 266830000 727930 601540 639380 748160 577960 670270 803970 735310 221003 FALSE TRUE 693522.1915 662837.6099 668696.2054 672953.5354 678756.041 647058.3818 681309.6106 670922.3583 255275.0165 2.716764848 2.596562793 2.619512926 2.636190351 2.65892076 2.534750132 2.66892397 2.628233532 1 17.96169282 0.879750622 20.77979381 1 2.63339376 0.991564739 0.047319653 8047.238649 1390611.536 0.042445229 0.010611307 7.581421149 -0.879750622 1.63339376 QEWISHIEECVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QEWISHIEECVR 12 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 0 119.87 0.00047122 90120000 52200 60136 42588 59566 68537 49458 56243 52151 61956 FALSE TRUE 49732.60945 66263.92677 44540.70193 53578.31251 80489.8311 47745.25706 47662.09738 47584.38197 71563.82005 0.694940676 0.925941722 0.622391341 0.748678766 1.124727985 0.667170325 0.666008289 0.66492233 1 16.12694278 -1.141340568 5.682083059 1.000003056 0.768711809 0.189586178 0.152880813 5.70E-06 8.62E-07 0.142639654 0.033620045 0.072220324 1.141340568 -0.231291247 QEYDESGPSIVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 254.1 8.44E-24 78841509200 20003827.2 21341942.8 15811815.3 22253064.3 17909166.2 18136940.3 19524858.6 20843214.5 15525506.6 FALSE TRUE 19058285.93 23516711.04 16536802.67 20016144 21032519.12 17508853.51 16545982.82 19018072.14 17933122.87 1.062742171 1.311356154 0.922137365 1.116154958 1.172830815 0.97634158 0.922649275 1.06049974 1 24.0961234 2.228425989 24.62728436 0.976661786 1.129704977 0.270030872 0.101707566 194.4339348 472472.9938 0.03714355 0.027757339 169.2099858 -2.228425989 0.153043191 QEYDESGPSIVHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 200.44 1.25E-08 3729780000 4725120 2665450 4503110 3810700 5105760 4432040 6958540 5502410 6434120 FALSE TRUE 4501772.942 2937062.385 4709582.048 3427641.196 5996202.927 4278557.343 5896886.921 5020589.81 7431890.469 0.605737256 0.395197211 0.633699066 0.461207173 0.806820681 0.575702422 0.793457189 0.675546798 1 22.82529781 1.123450852 0.30717148 1.04882415 0.463402788 0.61172639 0.109037233 1.005875092 0.312642218 0.2222342 0.143660943 13.28773174 -1.123450852 -0.585421363 QEYVDYSESAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QEYVDYSESAKK 12 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 135.37 0.00014089 316950000 511830 366970 469870 555280 350130 559370 588210 569410 385630 FALSE TRUE 487636.8102 404364.6602 491414.0043 499462.1994 411192.5611 539998.8766 498467.7613 519549.4418 445431.5309 1.094751441 0.907804303 1.103231294 1.121299605 0.923133035 1.21230501 1.119067077 1.166395744 1 18.76484416 2.229820074 24.9999783 1.135508817 1.026732074 0.216277065 0.088054927 247.1920277 707020.3952 0.030441878 0.02282125 169.7540225 -2.229820074 -0.108776744 QFAPIHAEAPEFMEMSVEQEILVTGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFAPIHAEAPEFMEMSVEQEILVTGIK 27 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 81.297 0.01107 18590000 10317 9180 9069 9518.6 7223.5 7471.7 10272 10190 10504 FALSE TRUE 9829.335856 10115.45244 9484.82262 8561.772244 8483.276113 7212.953156 8704.817742 9297.709579 12132.90667 0.810138586 0.833720452 0.78174364 0.705665384 0.699195695 0.594495066 0.717455262 0.766321693 1 13.5666376 0.879816933 7.997016096 0.99999994 0.740772532 0.605161912 0.066693109 6.06239419 403.6914275 0.07517031 0.018825327 7.582578819 -0.879816933 -0.259227408 QFCQEGQPHVLEALS(ph)PPQTSGLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 2 QFCQEGQPHVLEALS(1)PPQTSGLS(0.991)PS(0.008)R;QFCQEGQPHVLEALS(0.998)PPQT(0.002)S(0.001)GLS(0.853)PS(0.145)R;QFCQEGQPHVLEALS(1)PPQT(0.016)S(0.464)GLS(0.499)PS(0.021)R;QFCQEGQPHVLEALS(1)PPQT(0.006)S(0.018)GLS(0.944)PS(0.031)R 181.08 1.09E-17 745410000 349632 240969 297599 345645 355445 321925 426332 359436 374963 TRUE FALSE 333105.5883 265524.0151 311244.2085 310900.1079 417434.4955 310776.6565 361287.2233 327961.8783 433110.347 0.769100971 0.613063199 0.718625659 0.717831172 0.963806333 0.717546137 0.834168996 0.75722476 1 18.72437511 -4.999999998 0.094456397 1.821154302 0.561188635 0.459286902 0.086517736 163.2311694 1.061648603 26.49783165 1.639120321 1.00E-05 4.999999998 -1.259965667 QFCQEGQPHVLEALSPPQTSGLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALSPPQT(0.015)S(0.062)GLS(0.874)PS(0.049)R;QFCQEGQPHVLEALSPPQTSGLS(0.988)PS(0.012)R;QFCQEGQPHVLEALSPPQTSGLS(0.99)PS(0.01)R;QFCQEGQPHVLEALSPPQTSGLS(0.998)PS(0.002)R;QFCQEGQPHVLEALSPPQTSGLS(0.943)PS(0.057)R 282.82 3.80E-61 1419063000 986576 718609 809436 951250 958589 879175 1113461 910803 1006946 TRUE FALSE 939942.5077 791836.0741 846549.4412 855628.5427 1125766.618 848728.9493 943582.0743 831048.2608 1163098.043 0.808136952 0.680799077 0.727840139 0.735646103 0.967903458 0.729714021 0.811266153 0.714512647 1 20.14954128 -5 0.26269139 2.493004691 0.752303942 0.428003631 0.081349232 187.446333 1.835656699 151.4199643 0.099635956 1.00E-05 5 -1.740700749 QFCTGEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QFCTGEFR 8 0 C9JQD4;O43447;A6NM32 C9JQD4 PPIH Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H 0 ; 121.09 0.0033688 148080000 299310 258010 242130 319420 301440 267260 274430 301880 287750 FALSE TRUE 285162.2095 284301.5123 253231.9 287311.2947 354011.0406 258004.7192 232560.6632 275445.7868 332372.8004 0.857958922 0.855369368 0.761891165 0.86442481 1.065102319 0.776251002 0.699698239 0.828725415 1 18.3424428 -0.442024406 9.219747294 0.999999993 0.833759168 0.218635345 0.095441974 0 0 0.095410938 0.022488574 0.361389553 0.442024406 -0.166240824 QFDNYGEEFTMHDTIGCYLDIDKGHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFDNYGEEFTMHDTIGCYLDIDKGHVK 27 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 151.9 5.01E-08 11460000 29406 21372 20940 24934 18407 27752 35992 34488 11891 FALSE TRUE 28016.03666 23549.8311 21900.11971 22427.58695 21617.17497 26790.94128 30500.75936 31468.04789 13734.99555 2.039755787 1.714586001 1.594475923 1.632879084 1.573875644 1.950560609 2.220660302 2.291085408 1 13.74556882 2.091311104 7.574726715 2.000545282 1.733369857 0 0.377585362 0.519941426 37.24006788 0.129407534 0.095375188 123.3988475 -2.091311104 -0.267175424 QFDTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFDTDR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 116.11 0.05549 223730000 388630 354730 313760 427610 405840 333700 486550 413670 444240 FALSE TRUE 370260.2301 390877.3903 328146.2064 384625.8304 476618.3675 322143.8853 412317.8614 377446.8618 513130.4703 0.721571319 0.761750496 0.639498578 0.749567318 0.928844407 0.627801123 0.80353416 0.735576785 1 18.96896617 -5 0.295709224 3.048222962 0.732901792 0.479808392 0.083407296 217.0911959 2.02352395 275.0249578 0.077629647 1.00E-05 5 -2.31532117 QFEDEKANWEAQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFEDEKANWEAQQR 14 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 164.65 3.73E-06 118980000 105500 45064 100920 72800 100570 97092 158000 127380 151110 FALSE TRUE 100513.2241 49656.07283 105547.2818 65482.00569 118109.3762 93729.67969 133894.1981 116225.9319 174543.367 0.5758639 0.28449132 0.604705201 0.375161811 0.676676394 0.536999379 0.767111351 0.665885699 1 17.41322601 1.282431699 0.451393552 1.007734845 0.42431879 0.663434455 0.114728689 0.504706628 0.28633864 0.121099877 0.072509353 19.16159685 -1.282431699 -0.583416055 QFEDELHPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;;; 128.31 0.00026842 680557000 3422770 2712700 2946700 3512180 2347420 3406860 3792290 3554840 2139400 FALSE TRUE 3260982.445 2989127.214 3081809.11 3159128.994 2756809.305 3288879.584 3213706.51 3243559.364 2471167.225 1.319612211 1.209601351 1.247106662 1.278395473 1.115589943 1.330901264 1.300481197 1.312561663 1 21.23676121 -1.873815794 2.711295109 0.88001558 1.26387291 0.628250582 0.063888518 11022499.49 8097422.375 8535925.342 0.015504266 0.013371626 1.873815794 0.383857329 QFEEIWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 185.47 0.00049462 436734000 798250 647793 591265 733670 755190 657316 795540 747340 815240 FALSE TRUE 760518.3045 713803.8432 618375.0851 659920.0977 886894.8969 634552.9821 674165.7619 681898.9477 941663.2555 0.807632983 0.758024526 0.656683885 0.700802642 0.941838701 0.673864015 0.715930836 0.724143099 1 19.84485171 -1.645149604 2.82421081 1.025074269 0.747945831 0.490661835 0.080890495 31683845.18 28640116.79 5753640.021 0.018998146 0.022638643 1.645149604 -0.277128438 QFEGHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QFEGHTK 7 0 H0Y8P4;Q8TED0-3;Q8TED0 H0Y8P4 UTP15 U3 small nucleolar RNA-associated protein 15 homolog 0 ; 93.429 0.014942 97639000 180729 156623 159893 195517 177734 165993 218825 199693 212750 FALSE TRUE 172186.2983 172583.0618 167224.2522 175863.2597 208730.7533 160244.6208 185439.2273 182206.8223 245742.1834 0.700678638 0.702293189 0.680486557 0.715641317 0.849389187 0.652084305 0.754608853 0.74145521 1 17.906786 -5 0.260644527 2.8094957 0.69938518 0.744981304 0.051206869 92.25903688 0.905472874 89.36225048 0.061996661 1.00E-05 5 -2.11011052 QFFDER ddPTM_SK-BR-3_Trastuzumab_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 ;; 134.66 0.032419 771360000 2124090 1880430 1823910 2154740 2220920 1855760 2422210 2066220 2468350 FALSE TRUE 2023688.475 2072047.955 1907538.078 1938141.441 2608247.745 1791494.566 2052657.378 1885290.823 2851129.111 0.709784929 0.726746448 0.669046544 0.679780314 0.914812218 0.628345647 0.719945431 0.661243581 1 21.44310194 -1.09374732 4.459078145 1.000025252 0.714859602 0.57489905 0.077361129 33633844459 6835735991 9328723.57 0.016382332 0.080584716 1.09374732 -0.28516565 QFGFIVLTTSAGIMDHEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFGFIVLTTSAGIMDHEEAR 20 0 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 186.06 3.42E-17 195230000 352340 325400 320740 339350 323380 360110 393290 382790 300460 FALSE TRUE 335685.5865 358558.6299 335446.2463 305237.8933 379777.3696 347639.3004 333286.3872 349270.8783 347053.8023 0.96724365 1.033149983 0.966554016 0.879511739 1.094289609 1.001687053 0.960330603 1.006388278 1 18.40479981 3.673494406 24.99986066 0.984747802 1.000198702 0.008681559 0.054935272 1153.138235 443058.6182 0.014089149 0.021826818 4715.13798 -3.673494406 0.0154509 QFHDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QFHDSK 6 0 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;;; 116.54 0.023486 1684480000 6541920 4146030 5804170 6614330 6814510 5680420 9386040 7859920 9344400 FALSE TRUE 6232696.406 4568515.171 6070296.936 5949444.982 8002958.386 5483705.631 7954027.212 7171663.737 10793481.83 0.57745003 0.42326612 0.562403961 0.551207208 0.741462163 0.508057151 0.736928763 0.664443953 1 23.363657 -0.260553347 0.226861999 1.217653912 0.452090364 0.743514418 0.081326732 4.334368588 0.333670933 0.873544049 0.176505002 0.548841134 0.260553347 -0.765563548 QFLEVWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFLEVWEK 8 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 105.78 0.010053 92224000 286770 219650 140750 208170 235420 198580 287850 278820 258330 FALSE TRUE 273214.9504 242032.5847 147203.5267 187244.3561 276477.1735 191703.1248 243933.1958 254405.0427 298390.497 0.915628859 0.811126987 0.493325117 0.627514475 0.92656159 0.642457205 0.81749653 0.852590968 1 18.18684206 0.969496372 1.618456284 0.998220807 0.751892466 0.283928682 0.132235727 0.611629437 3.28823099 0.127922588 0.037150412 9.321726835 -0.969496372 -0.246328341 QFLIS(ph)PPAS(ph)PPVGWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 2 QFLIS(1)PPAS(1)PPVGWK 100.77 0.002964 63257000 241830 209090 183240 250530 162150 230990 240520 239940 176070 TRUE FALSE 230399.1752 230396.5087 191641.7352 225346.2484 190428.9087 222990.7584 203824.2565 218929.5816 203374.0364 1.132883918 1.132870807 0.942311706 1.108038432 0.936348179 1.096456374 1.002213754 1.07648737 1 17.63377598 3.778392026 23.11983988 1.026160508 1.132877522 0.379497487 0.058245642 182.1034144 105699.3157 0.012680835 0.022859985 6003.327363 -3.778392026 0.106717015 QFLPFLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QFLPFLQR 8 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 143 0.0014154 271980000 474840 314850 174188 194736 521680 231430 501620 335150 456350 FALSE TRUE 452395.2542 346933.573 182174.6921 175160.7673 612660.8268 223415.5211 425088.6561 305802.4893 527118.4273 0.858242154 0.658170071 0.345604863 0.332298698 1.162283076 0.423843124 0.806438618 0.580140009 1 19.0077676 2.793521622 24.99985913 0.753892215 0.589975099 0.172607456 0.252095172 771.7819275 351055.2525 0.074979782 0.079528046 621.6151943 -2.793521622 -0.163917116 QFTPCQLLADHANS(ph)PNKK ddPTM_SK-BR-3_Trastuzumab_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" 1 QFTPCQLLADHANS(1)PNKK 116.65 7.26E-05 291530000 226020 159110 194100 190120 94620 196470 180930 212820 116310 TRUE FALSE 215336.4825 175323.4899 202999.677 171008.7764 111121.698 189666.1946 153325.8055 194184.3526 134346.7608 1.602840897 1.305007198 1.511012814 1.272890953 0.827125994 1.411766041 1.141269091 1.44539661 1 17.03560201 3.08227673 5.496542712 1.178582857 1.452860933 0.345633059 0.191755487 0.232519602 11.75478932 0.051548674 0.061879722 1208.583691 -3.08227673 0.274278076 QFTPCQLLADHANSPNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 270.95 3.93E-39 810750000 1681750 1342070 1360750 1430340 1068110 1395510 1597310 1592370 1165610 FALSE TRUE 1602257.01 1478828.459 1423141.733 1286559.506 1254388.046 1347183.139 1353611.023 1452933.641 1346366.846 1.190059764 1.098384488 1.057023751 0.955578719 0.931683701 1.000606293 1.005380537 1.079151381 1 20.36064013 3.889375274 1.533997031 0.994957141 1.175410682 0.709749997 0.040460712 0.213155095 0.951466525 0.012241256 0.03496713 7751.312995 -3.889375274 0.180453541 QFWFQGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QFWFQGNR 8 0 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3;A0A1B0GUY7 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 0 77.058 0.063193 0 113930 89433 92828 88569 111120 77107 122700 117380 137950 FALSE TRUE 108544.7547 98546.32438 97084.25562 79665.87585 130499.2928 74436.76526 103979.8615 107101.5849 159342.5814 0.681203691 0.618455679 0.609280048 0.499966017 0.818985682 0.467149236 0.652555397 0.672146666 1 17.28177233 0.656639314 2.167537817 0.999904817 0.621078888 0.605132855 0.095511513 1.220631716 6.906670977 0.080103949 0.021818841 4.535647695 -0.656639314 -0.378825929 QFYINVER ddPTM_SK-BR-3_Trastuzumab_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 80.165 0.060845 75486000 58349 60089 56204 66340 50818 53677 61768 63381 50636 FALSE TRUE 55590.95841 66212.13742 58781.00899 59671.37716 59680.64311 51818.15203 52344.15715 57831.02364 58488.37227 0.950461711 1.132056422 1.005003332 1.020226326 1.02038475 0.885956473 0.894949802 0.988761037 1 15.83586222 2.327350108 6.609972595 0.928101089 1.0330935 0.328682652 0.057125631 0.196268331 12.09709898 0.01932186 0.016067262 212.4956814 -2.327350108 0.104992411 QFYPDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QFYPDLIR 8 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ;; 119.29 0.0040072 819940000 1784800 1252940 661670 749370 1735970 861970 1713100 1290610 1499490 FALSE TRUE 1700436.041 1380616.01 692008.224 674041.9039 2038722.618 832119.7628 1451735.132 1177597.346 1732023.251 0.981762826 0.797111707 0.399537491 0.389164466 1.17707578 0.480432213 0.838173004 0.679896962 1 20.72402687 -1.233796984 4.111387757 1.00018889 0.732393964 0.108039183 0.251693137 0.000414024 7.72E-05 0.230932272 0.054392946 0.058371791 1.233796984 -0.267794926 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;QGAIYHGLATLLNQPS(1)PMMQR;QGAIYHGLATLLNQPS(1)PMMQR;QGAIYHGLATLLNQPS(1)PMMQR;QGAIYHGLATLLNQPS(1)PMMQR 240.24 3.81E-30 4175460000 3017430 1937470 2579880 2949580 2761570 2675590 3265010 2953440 2834440 TRUE FALSE 2874802.064 2134900.396 2698170.05 2653082.615 3243186.934 2582933.647 2766872.758 2694821.136 3273990.479 0.878072823 0.652078987 0.824122754 0.810351353 0.990591437 0.788925217 0.845107149 0.82309987 1 21.6426187 -4.999999994 0.125981105 1.608748154 0.735360481 0.302359115 0.082960868 170.4623317 1.370060273 26.23426802 0.66975157 1.00E-05 4.999999994 -0.873387673 QGANINEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QGANINEIR 9 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;; 121.73 0.0014089 496879000 600908 526506 556974 618040 614575 556602 648670 597567 689030 FALSE TRUE 572504.2697 580157.56 582511.8088 555913.445 721756.6854 537326.7332 549703.4779 545240.8656 795881.2533 0.719333779 0.7289499 0.73190794 0.698487925 0.90686479 0.6751343 0.690685295 0.685078161 1 19.60219367 -1.34690792 3.195219676 1.002215665 0.728097746 0.625096419 0.065812825 19690859.65 25363061.17 407385.8425 0.015416858 0.044987523 1.34690792 -0.274117919 QGDETPSTNNGS(ph)DDEKTGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;Q9Y3P9-3;Q9Y3P9-4;C9JGR5;B5MCD9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 QGDETPSTNNGS(1)DDEKTGLK;QGDETPSTNNGS(1)DDEKTGLK 136.87 2.79E-06 899000000 900060 737010 805570 940750 430370 944190 939340 996290 422590 TRUE FALSE 857515.9475 812112.1569 842506.1813 846184.0227 505426.3917 911492.4635 796026.4308 909049.5659 488123.0989 1.756761664 1.663744573 1.726011703 1.733546363 1.035448625 1.867341385 1.630790333 1.86233671 1 18.8968855 -1.353127412 3.595128794 0.996901596 1.658491548 0.439021706 0.234283246 8510478.477 9615358.853 174636.7507 0.050271159 0.044347852 1.353127412 0.661589951 QGDTGDWIGTFLGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 162.79 1.58E-06 883500000 1906430 1647150 1552860 2003020 1561160 1821280 2226040 2099770 1559140 FALSE TRUE 1816316.832 1814996.458 1624060.167 1801672.624 1833425.81 1758208.617 1886416.714 1915903.007 1800923.468 1.008547484 1.007814318 0.901792994 1.000415984 1.018047597 0.976281695 1.047471893 1.063844767 1 20.78030544 1.715818713 7.219690437 1.041257846 0.988469015 0.307104225 0.036104701 0.1508106 19.63519988 0.017510307 0.009152133 51.97789809 -1.715818713 -0.052788831 QGEEIHNEVEFEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGEEIHNEVEFEWLR 15 0 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3;A0A1B0GUY7 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 0 114.29 0.00061772 31340000 35111 36029 30153 38527 32650 31843 39350 33344 29977 FALSE TRUE 33451.37261 39700.39606 31535.54488 34654.19276 38344.14966 30740.26893 33346.43479 30424.22259 34625.68006 0.96608565 1.146559317 0.910755971 1.000823455 1.107390515 0.887788164 0.963055014 0.878660651 1 15.07955479 2.226603281 24.99697421 0.931431651 1.030830616 0.284110535 0.073903861 270.9024648 566321.4742 0.026055589 0.019394269 168.5013099 -2.226603281 0.099398965 QGFDFLCMPVFHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 135.37 3.33E-05 336730000 741810 548780 539760 586750 814360 577470 920360 715410 776470 FALSE TRUE 706746.1114 604701.3059 564508.5299 527768.7752 956384.1262 557472.0691 779942.1784 652764.9078 896881.0019 0.788004328 0.674226909 0.629412964 0.588449052 1.066344503 0.621567485 0.869616122 0.727816629 1 19.77455706 2.801495391 24.99997456 0.8312501 0.681576832 0.312337243 0.134436326 303.5139041 120565.9189 0.037209901 0.039467055 633.1336432 -2.801495391 -0.149673268 QGFGELLQAVPLADSFR ddPTM_SK-BR-3_Trastuzumab_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 ; 211.7 3.01E-17 45828000 219180 183886 179063 200358 206560 204488 258730 211799 232790 FALSE TRUE 208819.7958 202624.1925 187273.2157 180217.6332 242583.9986 197406.5293 219255.9866 193252.7567 268889.8843 0.776599671 0.753558257 0.696468059 0.670228386 0.902168556 0.734153796 0.815411808 0.718705939 1 18.03665596 -5 0.300101996 2.985775075 0.748863313 0.571698475 0.065418413 191.0573768 1.765958632 238.6643863 0.060252698 1.00E-05 5 -2.236911763 QGGDVLQNEEGETTSHLMGMFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGGDVLQNEEGETTSHLMGMFYR 23 0 P39748;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ; 310.47 3.69E-73 309500000 193706 215143 165920 210656 172656 188156 190110 207516 147488 FALSE TRUE 184549.9013 237066.3163 173527.5961 189480.4587 202767.1517 181640.1105 161105.2279 189344.7989 170359.6858 1.083295619 1.391563475 1.018595423 1.112237662 1.190229665 1.066215341 0.945676949 1.111441349 1 17.37822445 2.615681872 0.748655961 1.00476665 1.213512792 0.226016588 0.10784942 0.780778045 0.915415006 0.077050721 0.066096962 412.7450484 -2.615681872 0.208746141 QGGLGPMNIPLVSDPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGGLGPMNIPLVSDPKR 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 208.2 8.65E-12 947270000 1376530 990830 1140890 1278020 957390 1301560 1414970 1420760 1123780 FALSE TRUE 1311464.155 1091796.703 1193200.935 1149551.002 1124358.513 1256486.651 1199090.339 1296350.722 1298050.063 1.010334033 0.841105235 0.919225667 0.885598356 0.866190407 0.967980116 0.923762783 0.998690851 1 20.3079146 1.387018026 1.358800262 1.003943196 0.90834919 0.336817002 0.04810976 0.453149005 1.588915971 0.041942465 0.013566171 24.37912004 -1.387018026 -0.095594006 QGGS(ph)PDEPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QGGSPDEPDSK 11 0 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 QGGS(1)PDEPDSK;QGGS(1)PDEPDSK;QGGS(1)PDEPDSK;QGGS(1)PDEPDSK;QGGS(1)PDEPDSK;QGGS(1)PDEPDSK 167.09 2.06E-05 514030000 1555700 1380672 1389321 1703185 955089 1575159 1607766 1609482 1023327 TRUE FALSE 1482165.144 1521364.046 1453022.742 1531977.608 1121656.219 1520610.849 1362471.768 1468547.224 1182019.325 1.253926322 1.28708898 1.229271562 1.296068157 0.948932218 1.286451767 1.152664546 1.242405427 1 20.17282219 -4.99999999 0.0932942 0.331060092 1.379293232 0.320187368 0.100585074 224.492138 1.445601679 29.9455177 1.914564254 1.00E-05 4.99999999 1.048233139 QGHEPPTFTGWFLGWDSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGHEPPTFTGWFLGWDSSK 19 0 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ; 183.26 2.75E-14 134037000 718600 659950 538670 844630 487890 639670 716660 679960 383620 FALSE TRUE 684633.2021 727199.6553 563368.5523 759726.1877 572977.8615 617518.0675 607320.3546 620419.0977 443109.8303 1.54506435 1.641127336 1.271397098 1.714532461 1.293083164 1.393600469 1.370586507 1.400147447 1 18.75730481 -3.16653845 0.119189822 1.80E-12 1.749516418 0.585111957 0.130051567 55.30187174 0.672270203 15.31556679 1.269736402 0.000681493 3.16653845 1.749516418 QGHEPPTFTGWFLGWDSSKW ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGHEPPTFTGWFLGWDSSKW 20 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 128.38 3.18E-05 132330000 320000 202730 284390 282670 273430 287520 387470 317100 235390 FALSE TRUE 304874.2342 223388.4175 297429.5628 254255.4746 321116.1054 277563.1103 328354.3351 289333.0429 271893.079 1.12130193 0.821603913 1.093921051 0.935130366 1.181038174 1.020853901 1.207659777 1.064142729 1 18.0526799 2.744848049 24.91973458 1.109528558 0.984289357 0.183218189 0.103461027 634.1485157 2513398.263 0.029278802 0.030384981 555.7097915 -2.744848049 -0.125239201 QGIAVMTPTVPGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 QGIAVMTPT(0.007)VPGS(0.993)PK 106.36 0.0013036 32050000 96976 85662 94860 105080 60023 99236 107170 105630 69399 TRUE FALSE 92392.13667 94391.05519 99209.42483 94517.15876 70490.9922 95799.43244 90819.24819 96380.47722 80161.04248 1.152581526 1.17751781 1.23762643 1.179090938 0.879367209 1.195087158 1.132959919 1.202335626 1 16.29061365 -5 0.197980636 0.381586627 1.168582482 0.164512498 0.099167538 263.2141193 2.598434017 64.96421117 0.23382489 1.00E-05 5 0.786995855 QGIETPEDQNDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGIETPEDQNDLRK 14 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 142.1 1.52E-05 264060000 217640 203930 215840 284210 177600 237930 265310 288100 206260 FALSE TRUE 207352.5885 224710.6988 225736.4775 255640.6708 208573.3838 229690.4244 224832.0867 262872.4367 238245.7474 0.870330702 0.943188709 0.947494257 1.073012524 0.875454803 0.964090344 0.943698216 1.103366753 1 17.86209094 7.266376734 0.379110621 0.992423385 1.12E-18 0.265760467 0.063940255 52.072258 1.216006097 0.045492585 34.75940988 18466165.94 -7.266376734 -0.992423385 QGLYELSASNFELHVAQGDHFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QGLYELSASNFELHVAQGDHFIK 23 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 336.87 5.20E-87 286559000 503412 325151 381248 474705 397858 412993 528379 516299 117584 FALSE TRUE 479616.7124 358284.2566 398728.5979 426986.7515 467244.3092 398690.9489 447765.0792 471089.1225 135818.3262 3.531310729 2.637966957 2.935749608 3.143808082 3.440215488 2.935472407 3.296794268 3.468523989 1 17.05131863 -1.046189503 11.07856831 0.999999916 3.147528177 0.855629063 0.280427823 0 0 0.263732205 0.062162277 0.089910517 1.046189503 2.147528261 QGMEYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGMEYYR 7 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 83.313 0.052046 161340000 294290 234200 185450 233260 451930 196630 306900 220750 520380 FALSE TRUE 280379.4949 258065.2463 193953.0659 209812.2616 530746.4489 189820.6538 260076.7684 201419.9597 601077.8727 0.466461182 0.429337459 0.322675438 0.349060032 0.882991161 0.315800435 0.432683984 0.335097945 1 19.19719239 -1.534632129 3.049934412 1.021206837 0.442594302 0.530085886 0.165178129 106647576 122423329.3 18679195.09 0.038090554 0.029198993 1.534632129 -0.578612535 QGMSMRES(ph)PVSAPLEGLICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGMSMRESPVSAPLEGLICR 20 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 QGMS(0.084)MRES(0.91)PVS(0.006)APLEGLICR;QGMS(0.469)MRES(0.53)PVSAPLEGLICR 102.69 0.00017939 89851000 51309 49710 52065 59380 61848 49411 65981 62204 67456 TRUE FALSE 48883.72525 54775.50552 54452.23175 53411.00959 72634.27162 47699.88468 55914.38663 56757.088 77916.73196 0.627384183 0.703000551 0.698851587 0.685488319 0.932203774 0.61219052 0.717617195 0.728432604 1 16.24964555 -5 0.243739582 2.693572259 0.679786168 0.533014132 0.085230924 134.523007 1.338577298 113.2391851 0.121871943 1.00E-05 5 -2.013786091 QGPPCS(ph)DS(ph)EEEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGPPCSDSEEEVER 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 QGPPCS(1)DS(1)EEEVER;QGPPCS(1)DS(1)EEEVER 176.21 3.31E-06 705260000 834990 647000 770420 827200 821930 789360 938730 825810 918810 TRUE FALSE 795521.6775 712930.0356 805744.519 744048.2844 965274.3318 762024.2653 795509.4975 753497.6985 1061294.362 0.749576843 0.671755227 0.759209271 0.701076262 0.909525544 0.718014052 0.749565366 0.709979931 1 20.01739343 -2.17527712 2.318567451 1.655646716 0.742813121 0.609656994 0.063803005 4677444.917 877884.9287 16146791.99 0.014845399 0.006679176 2.17527712 -0.912833595 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK 32 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 85.44 0.00011073 144750000 258320 239670 209420 264840 198770 256220 294260 249520 33835 FALSE TRUE 246109.7255 264092.6455 219022.1141 238217.78 233435.4251 247347.0372 249365.2325 227670.706 39081.95899 6.297271986 6.757405521 5.604174401 6.095338774 5.972971444 6.328931392 6.38057147 5.825468115 1 15.25421516 0.69217642 3.423524235 1.000033351 6.244264388 0.967406365 0.298233174 0.725567459 7.894587271 0.295936748 0.076442323 4.922394538 -0.69217642 5.244231037 QGPSPVS(ph)PNALDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QGPSPVSPNALDR 13 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QGPS(0.003)PVS(0.997)PNALDR;QGPS(0.046)PVS(0.954)PNALDR;QGPS(0.28)PVS(0.72)PNALDR;QGPS(0.052)PVS(0.948)PNALDR 130.87 0.00014376 1878940000 1452190 1215220 1195610 1558180 1194490 1316590 1502020 1260470 1212830 TRUE FALSE 1383547.857 1339052.3 1250429.901 1401548.786 1402808.678 1270996.158 1272859.263 1150096.565 1400909.482 0.98760689 0.955844983 0.892584365 1.000456349 1.001355688 0.907265012 0.908594937 0.820964223 1 20.41793231 2.148175399 7.958418967 0.901941625 0.96579734 0.230029517 0.052313509 0.325335562 25.09492356 0.018212958 0.013444114 140.6615499 -2.148175399 0.063855714 QGPVSQSATQQPVTADKQQGHEPVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QGPVSQSATQQPVTADKQQGHEPVSPR 27 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVT(0.001)ADKQQGHEPVS(0.999)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR 307.4 2.06E-72 5039920000 3793680 2582970 3574790 3479870 2977260 3740360 4733110 4203910 3524540 TRUE FALSE 3614360.265 2846177.58 3738697.657 3130066.856 3496493.201 3610830.395 4010987.14 3835793.354 4071107.662 0.887807586 0.699116264 0.918349002 0.768848951 0.858855499 0.886940532 0.985232392 0.942198947 1 21.95698994 2.054800962 1.563589411 0.979911001 0.811132049 0.544945477 0.062135939 0.267793989 1.232162715 0.036428327 0.018478231 113.4490757 -2.054800962 -0.168778953 QGQDVAPPPNPVPQRT(ph)SPTGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGQDVAPPPNPVPQRTSPTGPK 22 1 Q9UPY8-2 Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 QGQDVAPPPNPVPQRT(0.475)S(0.475)PT(0.05)GPK 71.06 0.027164 177040000 80423 57459 70865 79450 55193 87355 96986 93043 77058 TRUE FALSE 76621.56417 63314.13743 74114.23035 71463.53505 64818.64173 84329.87445 82189.00443 84895.66167 89007.76108 0.860841383 0.711332772 0.83267155 0.802891053 0.728235841 0.947444059 0.923391437 0.953800665 1 16.44164352 2.225534545 24.99586788 0.94686499 0.786325526 0.755703314 0.047604965 110.8205648 212653.3775 0.016712558 0.01241897 168.0871623 -2.225534545 -0.160539465 QGQEHIGSSCSFAEQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGQEHIGSSCSFAEQALR 18 0 O75382;O75382-2;O75382-4;A0A1W2PPI7;E9PMK8 O75382 TRIM3 Tripartite motif-containing protein 3 0 129.11 2.19E-05 172480000 170580 127300 164820 174600 162560 164330 222080 186880 184810 FALSE TRUE 162517.0215 140272.0147 172377.16 157048.8763 190910.4125 158639.2109 188197.6172 170515.7965 213469.3909 0.761312996 0.657105987 0.807502937 0.735697402 0.894322187 0.743147344 0.881614064 0.798783356 1 17.70366969 -2.846319724 0.086280064 1.54464832 0.533370796 0.597799157 0.061340211 76.17305133 0.736650438 9.549808698 1.732127248 0.001424558 2.846319724 -1.011277524 QGQQQAGGDGKTEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QGQQQAGGDGKTEQK 15 1 Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 236.43 9.52E-18 292608000 537366 381228 528453 557435 325489 594620 681827 660710 428185 FALSE TRUE 511965.7741 420075.5666 552683.0928 501400.5747 382254.1785 574028.1603 577801.7685 602854.7298 494585.7429 1.035140583 0.849348313 1.117466689 1.013778868 0.772877472 1.160624156 1.168253992 1.218908427 1 18.91586113 2.181461019 24.9997105 1.15316551 0.959790736 0.39286386 0.109875337 74.93962621 32809.89471 0.038297293 0.028284438 151.8661624 -2.181461019 -0.193374774 QGQTS(ph)PIKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGQTSPIKPK 10 1 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 QGQT(0.237)S(0.763)PIKPK;QGQT(0.074)S(0.926)PIKPK 93.649 0.0052335 1027690000 1974970 1509180 1597240 2036300 1080870 1988940 2068700 2044090 1261010 TRUE FALSE 1881617.082 1662967.158 1670475.034 1831607.255 1269373.386 1920062.509 1753081.821 1865098.643 1456560.99 1.291821691 1.141707878 1.1468624 1.257487512 0.8714866 1.318216348 1.203575979 1.280480979 1 20.47413468 4.59847453 2.842750666 1.164219789 1.297392647 0.090447908 0.13378503 0.811480783 10.86268626 0.030229143 0.213395258 39671.12621 -4.59847453 0.133172858 QGRPVVICDKEDTETIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGRPVVICDKEDTETIK 17 2 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 121.77 3.33E-05 307710000 642730 596540 581980 786330 376980 737480 752500 789380 402060 FALSE TRUE 612349.4267 657328.1042 608664.3587 707286.6145 442725.1926 711940.8827 637692.3044 720257.7024 464409.4114 1.318555162 1.41540651 1.310620207 1.522980795 0.953307969 1.533002702 1.373125283 1.550911081 1 18.82503768 -1.393401925 3.615893331 0.997627842 1.370452367 0.317614489 0.171452474 8816303.676 7031935.546 150893.4588 0.035353287 0.040420164 1.393401925 0.372824525 QGS(ph)FSEDVISHK ddPTM_SK-BR-3_Trastuzumab_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(0.994)FS(0.006)EDVISHK;QGS(0.942)FS(0.058)EDVISHK 94.569 0.0042098 233866000 310060 367870 294113 293550 301020 383077 284220 265133 264840 TRUE FALSE 295404.0783 405356.3712 307598.372 264041.7963 353517.7927 369810.9474 240857.0189 241916.549 305910.0346 0.965656712 1.325083604 1.005519065 0.863135453 1.155626664 1.208887927 0.787345924 0.790809459 1 18.22274791 1.709735575 8.613693132 0.844848237 1.09604895 0.363834729 0.141009563 0.114359184 19.43551398 0.0675832 0.036003875 51.25492179 -1.709735575 0.251200713 QGS(ph)GSSQPMEVQEGYGFGSGDDPYSSAEPHVSGVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGSGSSQPMEVQEGYGFGSGDDPYSSAEPHVSGVKR 36 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 QGS(0.333)GS(0.333)S(0.333)QPMEVQEGYGFGSGDDPYSSAEPHVSGVKR 89.577 0.00032472 78064000 46001 21788 41682 35946 52998 37770 65201 53898 70643 TRUE FALSE 43826.6239 24008.22197 43593.16093 32332.63979 62240.83442 36462.01543 55253.38995 49178.40539 81597.95565 0.537104435 0.294225778 0.534243298 0.396243258 0.762774434 0.446849619 0.677141842 0.602691636 1 16.31624539 -0.283919787 0.226222451 1.254803173 0.363830921 0.640654992 0.119347622 5.53521813 0.418800289 1.293831868 0.256534803 0.520092048 0.283919787 -0.890972252 QGS(ph)LYHEMAIEPLDDIAAVTDILTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QGSLYHEMAIEPLDDIAAVTDILTQR 26 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 QGS(0.539)LY(0.461)HEMAIEPLDDIAAVTDILTQR;QGS(1)LYHEMAIEPLDDIAAVTDILTQR;QGS(1)LYHEMAIEPLDDIAAVTDILTQR 216.94 2.47E-34 916030000 112256 99308 109667 149919 110636 158158 128406 91298 80727 TRUE FALSE 106949.8813 109427.5981 114695.3404 134848.8573 129930.8834 152680.9488 108815.3064 83303.46312 93245.73086 1.146968128 1.173540033 1.230033154 1.446166554 1.393424473 1.637404173 1.166973601 0.893375625 1 16.50875005 1.434638451 5.79043404 0.963648772 1.313068279 0.546686566 0.145385422 0.171793937 11.19928709 0.104518678 0.040416846 27.20435608 -1.434638451 0.349419507 QGS(ph)PTPALPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGSPTPALPEKR 12 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 QGS(0.983)PT(0.017)PALPEKR 74.12 0.022885 115470000 269810 247230 270550 297050 169710 275520 304160 314620 225970 TRUE FALSE 257056.616 272423.0181 282954.9851 267189.9696 199307.3703 265978.6733 257754.8057 287070.2049 261012.2735 0.984844937 1.043717272 1.084067739 1.023668221 0.763593863 1.019027457 0.987519867 1.099834123 1 17.99375812 -0.709040128 4.317406484 1.000000003 0.999675911 0 0.0919818 0 2.95E-10 0.085337006 0.020114072 0.195415889 0.709040128 -0.000324092 QGS(ph)SLNLFEDVQITEPEAEPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QGSSLNLFEDVQITEPEAEPESK 23 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK;QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK;QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK;QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK 164.58 9.10E-12 160363000 573150 490730 513800 655270 342182 618860 595600 565880 317431 TRUE FALSE 546058.3354 540735.9449 537358.2382 589401.0147 401858.4325 597428.723 504730.2811 516328.5473 366656.5783 1.489290982 1.474774972 1.465562791 1.607501541 1.096007698 1.629395894 1.376575005 1.40820751 1 18.4840699 -3.151249564 0.274806158 6.00E-15 1.487687479 0.492671146 0.143687467 54.33792424 1.316010628 31.32670512 0.153374936 0.000705912 3.151249564 1.487687479 QGSGPAPTTHKGT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QGSGPAPTTHKGTPK 15 1 A0A2R8Y7K2;A0A2R8Y481;A0A2R8YGN6;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0;A0A2R8Y5N9;A0A2R8YFW8;A0A2R8YCL5 A0A2R8Y7K2 SPAST Spastin 1 QGSGPAPTTHKGT(1)PK 110.77 0.0013122 62106000 67678 61843 65081 84099 42470 74309 83452 86936 52365 TRUE FALSE 64478.99506 68144.87201 68065.02822 75645.20874 49876.75455 71735.6607 70719.8647 79323.42296 60485.49676 1.066024064 1.1266316 1.125311552 1.250633835 0.824606843 1.185997711 1.169203668 1.311445342 1 15.88430163 QGSGRES(ph)PSLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.989)PS(0.011)LASR;QGSGRES(0.992)PS(0.008)LASR;QGSGRES(0.995)PS(0.004)LASR;QGSGRES(0.999)PS(0.001)LASR;QGSGRES(1)PSLASR;QGSGRES(0.944)PS(0.055)LASR;QGS(0.001)GRES(0.99)PS(0.009)LASR;QGSGRES(0.97)PS(0.03)LASR;QGSGRES(0.986)PS(0.014)LASR;QGS(0.014)GRES(0.93)PS(0.056)LASR 199.01 7.34E-08 12506671000 5642519 4894155 5169822 5718048 5483995 5420438 6225121 5712633 6243573 TRUE FALSE 5375808.309 5392874.959 5406863.452 5143258.951 6440401.992 5232726.873 5275364.459 5212404.57 7211794.413 0.745418963 0.747785454 0.749725123 0.713173263 0.893037381 0.725579041 0.731491243 0.722761115 1 22.78192684 -1.174162939 4.288681642 1.000071058 0.752615041 0.697243292 0.051018476 3.22E-05 6.19E-06 0.045840184 0.010801538 0.066963333 1.174162939 -0.247456017 QGSGRESPS(ph)LASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.201)PS(0.783)LAS(0.015)R 227.34 2.44E-11 1054000000 625790 542320 540010 615620 586800 595730 682620 601440 668630 TRUE FALSE 596210.1469 597583.0246 564769.9926 553736.708 689137.7342 575099.7207 578473.7818 548774.7252 772317.7255 0.771975221 0.773752828 0.731266387 0.716980447 0.892298223 0.744641359 0.749010106 0.710555652 1 19.55883496 -1.487304108 3.530965553 1.003667792 0.762963388 0.684600907 0.050904286 5838897.491 2462207.347 163494.0417 0.011481692 0.032560862 1.487304108 -0.240704404 QGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.015)IT(0.557)S(0.428)PQANEQS(0.011)VT(0.989)PQRR;QGS(0.025)IT(0.537)S(0.439)PQANEQS(0.008)VT(0.992)PQRR 140.71 1.07E-07 1639390000 788090 861000 692620 946750 662790 818760 817910 787510 684680 TRUE FALSE 750838.5475 948736.8789 724377.3121 851580.8913 778380.3662 790406.1359 693122.8076 718551.4495 790856.6775 0.949399011 1.199631875 0.915940059 1.07678283 0.984224308 0.999430312 0.876420251 0.908573538 1 19.59305674 2.227583412 1.618247329 0.918778276 1.047021728 0.199049946 0.083509711 0.457036636 2.364906438 0.043213502 0.026096086 168.8820188 -2.227583412 0.128243452 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.01)IT(0.473)S(0.516)PQANEQS(0.005)VT(0.995)PQRR;QGSIT(0.219)S(0.781)PQANEQS(0.002)VT(0.998)PQRR 190.39 1.03E-14 1621760000 1078530 1059250 953280 1211720 931710 959410 961240 1030890 784480 TRUE FALSE 1027550.024 1167188.779 996988.8309 1089915.603 1094199.929 926185.3911 814585.1836 940619.8065 906133.1518 1.133994515 1.288098528 1.100267471 1.20282058 1.207548722 1.022129462 0.898968526 1.038059147 1 19.78936354 2.148517489 4.294673942 0.966542664 1.192598732 0.724760843 0.060321924 0.097672071 3.301331626 0.022179295 0.016071314 140.7723915 -2.148517489 0.226056068 QGSITSPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_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;QGSITSPQANEQS(0.015)VT(0.985)PQRR;QGSITSPQANEQS(0.001)VT(0.999)PQRR;QGSITSPQANEQS(0.008)VT(0.992)PQRR;QGSITSPQANEQSVT(1)PQRR 349.21 6.18E-91 5235380000 366922 358831 285367 373614 284304 332919 344521 306511 295342 TRUE FALSE 349578.3242 395396.2869 298451.3592 336057.6109 333886.5276 321389.9316 291957.9939 279671.2719 341142.129 1.024729268 1.159036816 0.874859286 0.985095602 0.978731441 0.9420998 0.855825092 0.819808661 1 18.3800134 3.399841358 0.879771662 0.897854484 1.093885443 0.335009131 0.07899801 0.57116054 0.929692014 0.034434169 0.071996237 2510.969038 -3.399841358 0.196030958 QGTEIDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QGTEIDGR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 93.098 0.026311 503250000 4162790 3362470 3438790 3902470 3778750 3707030 4432130 3860710 4018730 FALSE TRUE 3966023.167 3705109.516 3596461.923 3510186.301 4437762.804 3578654.622 3755927.167 3522645.765 4641934.124 0.854390231 0.79818227 0.774776597 0.75619046 0.956015895 0.770940415 0.809129787 0.758874571 1 22.14629462 -1.022158296 4.191696296 1.000014552 0.811251278 0.503227726 0.059370255 16250642.12 30529812.05 3310.886253 0.013161336 0.095025837 1.022158296 -0.188763274 QGTTPPIWHLTDK ddPTM_SK-BR-3_Trastuzumab_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 ; 141.85 4.00E-05 456250000 1197680 942480 997910 1220600 890720 1151660 1313100 1223920 966440 FALSE TRUE 1141068.04 1038519.784 1043665.161 1097902.969 1046061.286 1111777.725 1112762.478 1116747.076 1116310.579 1.022177932 0.930314379 0.934923649 0.983510315 0.937070118 0.995939433 0.996821583 1.000391018 1 20.09030704 2.135486088 9.336055216 0.998087159 0.962651796 0.316346364 0.026789847 0.375424943 31.09727166 0.010010612 0.007391709 136.6111314 -2.135486088 -0.035435363 QGVLTHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 QGVLTHGR 8 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;;;; 147.51 0.00053616 4252220000 7125840 5766030 5373350 6478030 7352400 6191810 8481170 7128040 7987570 FALSE TRUE 6789015.665 6353595.012 5619723.412 5826846.117 8634656.232 5977386.067 7187211.749 6503871.029 9226241.561 0.735837624 0.688643905 0.609102133 0.631551437 0.935880139 0.647867935 0.778996702 0.704931796 1 23.13731163 -5 0.232230791 2.55649742 0.685118311 0.493001376 0.09136097 134.4448406 1.344013627 98.31576608 0.142977877 1.00E-05 5 -1.871379108 QGYACPYYHNS(ph)KDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGYACPYYHNSKDR 14 1 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPY(0.003)Y(0.017)HNS(0.98)KDR;QGYACPYYHNS(1)KDR 111.33 0.00039745 124988000 348280 289910 306130 350480 216188 332610 370300 382470 217100 TRUE FALSE 331817.4946 319452.1586 320166.3633 315249.0845 253891.1188 321091.6323 313803.934 348978.8992 250766.7592 1.32321164 1.273901531 1.276749615 1.257140641 1.012459225 1.280439374 1.251377714 1.391647363 1 17.9359866 -1.96404949 3.029504779 0.799740139 1.257343389 0.415192181 0.096358282 0.075948876 0.00090127 0.054367109 0.021159576 0.010863018 1.96404949 0.45760325 QGYACPYYHNS(ph)KDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QGYACPYYHNSKDRR 15 2 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDRR;QGYACPYYHNS(1)KDRR 150.68 1.64E-06 188246000 349020 277820 298820 322920 225130 327270 377120 361250 242430 TRUE FALSE 332522.5163 306130.1739 312521.1926 290459.4681 264392.6007 315936.5578 319583.4177 329617.0349 280024.8062 1.187475212 1.093225197 1.116048241 1.037263348 0.94417564 1.128244894 1.14126824 1.177099412 1 18.09519511 4.5507797 1.48608411 1.083210531 1.208134536 0.192584229 0.069595509 1.426491724 3.839242893 0.019535248 0.237786085 35545.09666 -4.5507797 0.124924005 QGYGEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QGYGEGFR 8 0 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ;; 127.46 0.0027343 901050000 1635650 1445590 1404290 1768800 1621320 1444080 1720160 1551840 1744520 FALSE TRUE 1558336.066 1592897.264 1468678.086 1590996.863 1904077.695 1394071.148 1457717.999 1415952.663 2015051.252 0.773348104 0.790499628 0.728853961 0.789556525 0.944927675 0.691829127 0.72341485 0.702688163 1 20.9423851 -2.229812321 2.299218766 1.781798897 0.768421337 0.510109259 0.071407509 3461768.194 620553.0252 14094645.33 0.016901969 0.005890982 2.229812321 -1.01337756 QGYVIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QGYVIYR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 138.07 0.0065628 2744420000 4025120 3017700 3038330 3842090 3843280 3546220 4272950 3855520 4213500 FALSE TRUE 3834860.555 3325207.061 3177640.436 3455875.814 4513546.815 3423413.512 3621032.999 3517910.229 4866908.06 0.787945962 0.683227836 0.65290743 0.710076248 0.927395126 0.703406243 0.744010973 0.722822413 1 22.21457409 -2.133461372 2.141069533 1.502757624 0.739624093 0.539044738 0.075114457 6201869.646 1510039.319 15138743.81 0.017533893 0.007354254 2.133461372 -0.763133531 QHAHTVLS(ph)SPPRGTVSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHAHTVLSSPPRGTVSLR 18 1 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 QHAHT(0.001)VLS(0.495)S(0.495)PPRGT(0.005)VS(0.005)LR;QHAHT(0.001)VLS(0.496)S(0.496)PPRGT(0.004)VS(0.004)LR 88.872 0.0018096 189907000 92633 70618 90433 73551 101877 80601 113679 92079 38782 TRUE FALSE 88254.42167 77814.05449 94579.4425 66157.51374 119644.3165 77809.76716 96335.18069 84016.07462 44796.11449 1.97013564 1.737071516 2.111331386 1.476858306 2.67086371 1.736975808 2.15052537 1.875521473 1 15.45108598 0.953469747 21.22919717 0.999999996 1.965562462 0.483169597 0.315563402 1270.248429 579546.3437 0.264531558 0.06613289 8.984000081 -0.953469747 0.965562466 QHEAEEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHEAEEGVR 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 0 157.38 6.87E-05 64348000 55467 47895 48231 63610 50427 49430 60710 44435 34007 FALSE TRUE 52845.18484 52775.55495 50442.43906 57215.80195 59221.45283 47718.22671 51447.57448 40544.03584 39280.63188 1.345324205 1.343551578 1.28415549 1.456590671 1.507650208 1.21480293 1.309744065 1.032163535 1 15.26153052 1.29048945 1.699251228 0.984588722 1.366207986 0.744007393 0.081968398 0.168226855 0.870278648 0.072238879 0.021780191 19.52043315 -1.29048945 0.381619263 QHEAPSNRPLNELLTPQGPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR 155.56 1.10E-08 769035000 553440 574853 602636 697160 662674 582304 689050 542651 362496 TRUE FALSE 527279.988 633431.1743 630267.4567 627080.1523 778244.1358 562138.6665 583922.7672 495133.6017 418710.0283 1.259296297 1.512815866 1.505259999 1.497647799 1.858670878 1.342548849 1.394575548 1.182521478 1 18.67559195 1.174976555 1.51723563 1.004629453 1.493910977 0.559239946 0.152343846 0.28714984 1.266887424 0.142081861 0.042734197 14.96154885 -1.174976555 0.489281524 QHFIQEEQILEIDCTMLTPEPVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHFIQEEQILEIDCTMLTPEPVLK 24 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 81.922 0.015327 106396000 108650 107410 96130 123186 87113 119668 138401 136908 78272 FALSE TRUE 103514.3298 118355.2011 100537.6556 110803.1092 102305.4796 115523.8672 117285.3855 124919.6097 90410.022 1.144943089 1.309093821 1.112018926 1.225562242 1.131572334 1.277777226 1.297260889 1.381700911 1 16.46419508 2.202862131 24.99767752 1.268018484 1.19655995 0.022237824 0.112174391 425.7679987 298139.5262 0.037530211 0.027718754 159.5372609 -2.202862131 -0.071458534 QHFISFDTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ;;; 190.53 8.91E-07 3532620000 1093230 851700 758920 839760 1004280 815870 1095780 879880 698940 FALSE TRUE 1041555.184 938489.1983 793717.2327 755345.7294 1179426.114 787616.2173 928598.6356 802833.0427 807328.0455 1.29012635 1.162463268 0.983140914 0.935611903 1.460900709 0.975583868 1.150212285 0.994432247 1 19.62279548 4.17922542 2.742460206 1.085737469 1.269090536 0.168287667 0.151941703 0.446620776 6.61593786 0.03646246 0.10623301 15108.64165 -4.17922542 0.183353067 QHFPATPLLDYALEVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QHFPATPLLDYALEVEK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 166.76 2.31E-09 487659000 974819 827048 834211 1051149 697717 988165 1131381 996446 557210 FALSE TRUE 928741.2378 911325.1315 872460.3995 945485.5055 819398.6239 953944.5983 958768.0492 909191.9057 643619.281 1.442997849 1.415938208 1.355553547 1.469013644 1.273110747 1.482156651 1.489650913 1.412623787 1 19.29584802 0.926451463 21.83413084 1 1.422845256 0.805054808 0.064562449 5824.708372 1729165.994 0.059410652 0.014852663 8.442118871 -0.926451463 0.422845256 QHGCTANDANTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHGCTANDANTK 12 0 Q8N6H7;G5E9L0;Q8N6H7-2;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48;H0YDX1 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 111.12 0.00037334 0 12113 9487.1 11445 11344 7599.5 10647 12726 12176 7033.5 FALSE TRUE 11540.4425 10453.84628 11969.76457 10203.67957 8924.850394 10278.29172 10784.41497 11109.80489 8124.219258 1.420498651 1.28675088 1.473343369 1.255958172 1.098548686 1.265142089 1.327440167 1.367492006 1 12.98801346 -4.524596225 0.182735703 3.07E-16 1.375212754 0.481382683 0.101597554 103.6451825 1.173638964 38.52094951 0.309808739 2.99E-05 4.524596225 1.375212754 QHGDVVSAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QHGDVVSAIR 10 0 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 181.4 1.89E-06 2013779000 612873 540932 575554 592623 1104811 465261 662283 503817 1022331 FALSE TRUE 583903.7079 596053.5858 601943.7202 533051.4101 1297489.689 449148.8949 561239.5647 459700.1126 1180868.87 0.494469558 0.504758488 0.509746455 0.451406099 1.098758483 0.38035459 0.475276789 0.389289721 1 20.17141734 -2.147837232 2.475881097 2.081926824 0.534278611 0.33478241 0.204602327 7796890.942 2442531.819 47283022.26 0.046055158 0.007114801 2.147837232 -1.547648213 QHHPPYHQQHHQGPPPGGPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 QHHPPYHQQHHQGPPPGGPGGR 22 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;;; 145.05 3.33E-08 638571000 108712 154213.1 162147.8 189591.8 157583.8 179687.8 197455.2 98868.9 8756.17 FALSE TRUE 103573.3992 169927.5902 169582.437 170533.6721 185066.3648 173465.1664 167329.7827 90211.41498 10114.03212 10.24056459 16.80117169 16.76704552 16.86109654 18.29798072 17.15094082 16.54431988 8.919431329 1 13.30407065 0.995199135 3.028466894 1.046185277 15.98563916 0.838512258 2.18555588 0.097274189 2.151904791 2.252014144 0.59289707 9.890064741 -0.995199135 14.93945388 QHIAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHIAEK 6 0 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 68.422 0.096181 67208000 336470 329890 339950 397040 253750 362480 411810 396700 218340 FALSE TRUE 320565.7299 363506.1661 355537.0438 357128.7849 298003.9197 349927.2267 348980.8211 361962.845 252199.0521 1.271082216 1.441346282 1.40974774 1.416059188 1.181621886 1.387504131 1.383751518 1.435226826 1 17.94420333 -1.172728551 4.260519088 0.999890726 1.366480179 0.669638572 0.080742981 4.877417397 21765056.33 4540.124409 0.017942424 0.067184865 1.172728551 0.366589453 QHIPYREDK ddPTM_SK-BR-3_Trastuzumab_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 ; 60.563 0.057022 274600000 904500 864390 866380 1090970 674020 1073000 1092420 968370 351660 FALSE TRUE 861746.0775 952472.3237 906104.38 981303.6229 791568.8746 1035841.741 925751.2653 883574.3891 406193.6368 2.121515454 2.344872587 2.230720272 2.415851786 1.9487476 2.550118089 2.279088547 2.175254138 1 18.63180811 0.677398575 3.292492832 1.000016276 2.273393813 0.858943846 0.160685937 1.426950755 14.21864891 0.136979757 0.035498928 4.757716663 -0.677398575 1.273377537 QHIVNDMNPGNLHLFINAYNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHIVNDMNPGNLHLFINAYNSR 22 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ; 161.68 9.88E-12 400340000 146744 91896 113979 151737 138501 143802 185902 171229 94412 FALSE TRUE 139807.7019 101260.3069 119205.0499 136484.1085 162655.5305 138822.1007 157539.2356 156235.281 109052.9308 1.282016916 0.928542738 1.093093501 1.251540032 1.491528283 1.272979091 1.444612579 1.4326555 1 16.73466902 3.09042055 3.790250623 1.359450356 1.090552139 0.282160918 0.160076535 0.220452747 6.12224312 0.043464116 0.052560252 1231.46068 -3.09042055 -0.268898217 QHLASIYEKEEDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHLASIYEKEEDWR 14 1 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 126.88 4.98E-05 100870000 106280 113180 118090 147470 92913 113680 134540 114920 49756 FALSE TRUE 101256.355 124713.1707 123504.5433 132646.0354 109116.9978 109743.2331 114013.452 104856.9956 57471.90636 1.761840896 2.16998493 2.148955048 2.308015234 1.898614553 1.909510925 1.983811904 1.824491342 1 15.81056928 0.193293199 0.711715009 0.971521062 2.053575175 0.819008406 0.151561717 1.316618365 0.832486241 0.240875671 0.055074462 1.560605736 -0.193293199 1.082054114 QHLEITGGQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHLEITGGQVR 11 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;C9J165;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 ; 100.19 0.0042163 516590000 1193570 948430 905430 1027060 1159850 1090660 1414190 1264750 1153030 FALSE TRUE 1137152.312 1045076.095 946944.8611 923817.9775 1362127.473 1052890.171 1198429.342 1154001.785 1331836.004 0.853823075 0.784688274 0.711007105 0.693642442 1.022744144 0.79055542 0.899832516 0.866474387 1 20.34498502 2.751670651 24.98961447 0.898568551 0.772344491 0.482577683 0.078282834 793.4797953 1512485.85 0.023107503 0.024381265 564.508715 -2.751670651 -0.12622406 QHLLTNLVEVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHLLTNLVEVDGR 13 0 Q8NFV4;Q8NFV4-4;Q8NFV4-6 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 149.32 1.78E-06 134190000 270080 246540 269540 277940 257500 242210 291200 259640 182603 FALSE TRUE 257313.8536 271662.7063 281898.6756 250000.9431 302407.9185 233822.207 246772.0917 236904.5452 210920.1406 1.219958667 1.287988456 1.336518527 1.185287201 1.433755532 1.108581695 1.169978794 1.123195464 1 17.68633734 1.423407492 0.936566272 1.016020712 1.27925795 0.555464179 0.082056293 0.356178293 0.637686037 0.068258445 0.025320497 26.50986351 -1.423407492 0.263237239 QHLVEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHLVEVR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 72.485 0.051478 93502000 164180 107880 112660 125340 144150 123400 174390 133810 109700 FALSE TRUE 156419.5368 118873.0946 117825.5724 112740.5851 169289.7144 119126.6271 147783.6026 122092.887 126711.7157 1.234452046 0.938138151 0.929871179 0.889740814 1.336022588 0.940139011 1.166297858 0.963548527 1 16.9511904 0.587630006 0.004982847 7.95E-08 2.078469709 0.014660241 0.149347559 84633.14893 193.7218313 40847.25246 39948.01182 3.869278641 -0.587630006 2.07846963 QHLYVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QHLYVDK 7 0 P53597;A0A494C0D1;H7C233 P53597 SUCLG1 "Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial" 0 ;; 98.392 0.011296 689980000 2863330 2371240 2290880 2642470 2214140 2243430 2622060 2518920 1495520 FALSE TRUE 2727986.065 2612872.052 2395919.114 2376843.895 2600285.315 2165739.457 2222016.59 2298350.011 1727437.604 1.579209611 1.512571016 1.386978672 1.375936179 1.505284654 1.253729485 1.286307873 1.330496689 1 20.72020217 0.369379629 0.058399296 2.86E-15 2.411829262 0.84959887 0.063409783 23.51804259 0.545322971 12.83202031 9.362334454 2.340882574 -0.369379629 2.411829262 QHMDITGEENPLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QHMDITGEENPLNK 14 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 246.5 9.73E-18 1212910000 1638410 1421068 1523668 1870580 1324983 1798743 1989660 1850050 997880 FALSE TRUE 1560965.606 1565876.445 1593529.685 1682545.745 1556059.616 1736452.079 1686100.824 1688049.814 1152626.134 1.354268796 1.358529361 1.38252087 1.459749779 1.350012437 1.506518053 1.46283411 1.464525022 1 20.13649321 -0.53484144 6.907092343 1 1.414170733 0.849996719 0.055087164 0 0 0.058044319 0.013681177 0.291849235 0.53484144 0.414170733 QHPQPYIFPDSPGGTSYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHPQPYIFPDSPGGTSYER 19 0 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 64.723 0.029615 201273000 112984 89337 116733 120420 150048 97222 138173 117011 192182 FALSE TRUE 107643.4702 98440.54187 122085.3235 108315.1528 176216.3237 93855.17776 117092.1711 106764.8965 221984.603 0.484914128 0.443456621 0.549972033 0.487939935 0.79382228 0.422800395 0.527478796 0.480956314 1 17.76010009 -2.082081261 2.434528668 1.763190309 0.518301427 0.678941351 0.102822596 8176038.487 2251020.478 34657303.49 0.024662092 0.008277873 2.082081261 -1.244888882 QHQETSACDS(ph)PHGEDGPGDFAHTGVPGHVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QHQETSACDSPHGEDGPGDFAHTGVPGHVPR 31 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QHQETSACDS(1)PHGEDGPGDFAHTGVPGHVPR;QHQETSACDS(1)PHGEDGPGDFAHTGVPGHVPR;QHQETSACDS(1)PHGEDGPGDFAHTGVPGHVPR;QHQET(0.006)S(0.025)ACDS(0.969)PHGEDGPGDFAHTGVPGHVPR;QHQETSACDS(1)PHGEDGPGDFAHTGVPGHVPR 299.7 7.35E-82 3341360000 689269 628011 737210 795877 1050847 617096 827128 616737 688552 TRUE FALSE 656688.6204 692006.0349 771011.8077 715873.9319 1234114.384 595725.8108 700934.4324 562732.2388 795329.1275 0.825681592 0.870087629 0.969424834 0.900097717 1.551702737 0.749030546 0.88131367 0.707546372 1 19.60119248 -2.68502355 2.086100573 2.960297482 0.927064945 0.008012103 0.232903608 12496426.4 974853.6708 115658939.3 0.0559787 0.002065268 2.68502355 -2.033232537 QHSITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 104.21 0.034027 188022000 794280 704670 712070 837540 621050 743500 919320 821050 583140 FALSE TRUE 756735.9585 776476.6741 744719.1138 753348.888 729360.9234 717752.4086 779060.8495 749154.5093 673570.3729 1.12346978 1.152777357 1.105629261 1.118441247 1.082828094 1.065593793 1.15661389 1.112214164 1 19.36146916 -1.873159195 2.303712763 0.939707775 1.118188848 0.626575798 0.027710534 5854369.036 3119162.274 1927568.323 0.007030438 0.013391857 1.873159195 0.178481072 QHSLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHSLLK 6 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 104.11 0.03411 238690000 768480 800880 584570 891470 689390 788420 977890 953170 586060 FALSE TRUE 732155.4734 882490.5825 611373.1127 801857.7419 809619.3977 761116.8177 828694.9203 869705.3817 676943.1916 1.081561174 1.303640532 0.903137989 1.184527375 1.195993117 1.124343707 1.224172029 1.284753865 1 19.36867524 QHTFVETESVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QHTFVETESVR 11 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 154.28 3.21E-05 337260000 117840 90139 96703 116370 120270 92324 118410 99475 71160 FALSE TRUE 112269.9367 99324.26658 101136.9282 104672.2665 141245.0499 89126.79673 100344.3798 90764.44165 82195.12937 1.36589525 1.208396013 1.230449164 1.273460694 1.718411432 1.084331851 1.220806884 1.104255719 1 16.32676529 1.489556284 1.445807707 1.034318692 1.320897085 0.332085045 0.160549839 0.469963809 1.877043479 0.135946104 0.045256728 30.87139707 -1.489556284 0.286578393 QHVIDGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QHVIDGEK 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;; 123.86 0.0013295 4250934000 8956770 7868250 7957330 10164630 6487670 9297630 10404970 9343350 4676610 FALSE TRUE 8533401.233 8670033.62 8322181.451 9142862.081 7619117.594 8975650.742 8817500.726 8525196.742 5401834.794 1.579722735 1.605016434 1.540621246 1.692547519 1.410468458 1.661592974 1.632315882 1.578203901 1 22.36501809 0.922575079 20.84909008 1 1.592246199 0.853912164 0.076378523 2963.936249 798134.7057 0.06520774 0.016301935 8.367102297 -0.922575079 0.592246199 QHYIDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 127.56 0.0038425 16228530000 35379590 31562330 30190940 37011680 24721440 35752990 39323590 35657120 19414240 FALSE TRUE 33707266.9 34778567.31 31575224.46 33291195.61 29032851.31 34514854.99 33324054.12 32534793.54 22424901.19 1.503117745 1.550890549 1.40804297 1.484563759 1.2946702 1.539130751 1.486029028 1.450833307 1 24.41859829 0.72213456 4.608619459 1.000000409 1.474260432 0.800443008 0.072876592 3.946014732 65.17710558 0.068218541 0.017298793 5.273932419 -0.72213456 0.474260023 QIANS(ph)QDGYVWQVTDMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 197.1 1.97E-15 152663000 139973 109338 117632 132843 138404 115722 142583 140470 217897 TRUE FALSE 133356.7537 120479.6665 123025.5436 119489.3693 162541.6138 111714.5181 120829.3446 128169.7021 251687.3539 0.529850831 0.478687803 0.488803039 0.474753171 0.645807631 0.443862262 0.480077138 0.509241724 1 17.9412732 -1.308764183 2.41964008 1.0105521 0.503454509 0.890058224 0.054512199 231554.7331 235088.0109 17563.20785 0.013064102 0.049117451 1.308764183 -0.507097592 QIAQEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIAQEIIK 8 0 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5 A8MY87 KSR1 Kinase suppressor of Ras 1 0 79.906 0.026824 645270000 743100 560960 591700 558570 1907900 291990 827260 335490 1805600 FALSE TRUE 707975.1357 618122.4618 618830.0303 502421.4824 2240637.156 281878.3131 701046.2933 306112.7171 2085603.226 0.339458209 0.296375866 0.296715129 0.240899839 1.074335294 0.135154333 0.336135984 0.146774187 1 20.99203329 -1.175697373 3.977133744 1.000316117 0.356128118 0.367685134 0.264477555 153174714 263209128.5 644266.8017 0.058829863 0.066727158 1.175697373 -0.644187999 QIAQSKEDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK 284.47 1.84E-74 3255690000 4240180 2744540 3387770 3599550 2090880 4175010 4825900 4742600 1171850 TRUE FALSE 4039755.095 3024211.746 3543102.605 3237716.395 2455528.81 4030428.357 4089620.321 4327312.802 1353574.513 2.984508836 2.234241054 2.617589628 2.391975 1.81410686 2.977618386 3.021348498 3.196952041 1 20.36834288 4.713457742 4.098547494 2.515412129 3.012536867 0.050106746 0.652131717 0.714867034 23.47238253 0.144590731 0.980691654 51696.0954 -4.713457742 0.497124738 QIATLHAQVADMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 ; 138.55 4.78E-05 898680000 1627300 1341350 1324070 1758260 1148020 1491980 1683180 1794990 1239050 FALSE TRUE 1550380.754 1478035.09 1384779.919 1581516.364 1348234.325 1440312.358 1426379.977 1637811.16 1431195.546 1.083276676 1.032727564 0.967568634 1.105031642 0.942033622 1.006370068 0.996635283 1.144365747 1 20.44878937 -1.783523101 8.211574842 0.999483373 1.030959471 0.026805666 0.062179739 0.000543991 1.43E-05 0.055689298 0.012911787 0.016461784 1.783523101 0.031476098 QICLVMLETLS(ph)QSPQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLET(0.158)LS(0.421)QS(0.421)PQGR;QICLVMLETLS(0.5)QS(0.5)PQGR 151.48 2.60E-07 91637000 63733 46280 51145 68313 57631 59546 67861 53346 63419 TRUE FALSE 60720.4674 50995.98462 53490.04884 61446.04745 67681.82815 57483.90709 57507.5581 48674.74144 73253.69462 0.828906552 0.696155803 0.730202744 0.838811582 0.9239374 0.784723656 0.785046521 0.664468075 1 16.1606139 -1.573197996 3.016535097 1.011266871 0.781546973 0.461745907 0.074128183 27995277.26 33134230.85 2556745.424 0.017614693 0.026717881 1.573197996 -0.229719898 QICLVMLETLSQS(ph)PQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.001)QS(0.999)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.004)QS(0.996)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR 481 1.82E-231 5359051000 3701687 2379504 3090525 3478635 3567330 3237320 3931525 3708264 4203184 TRUE FALSE 3526715.592 2621978.163 3232228.628 3128956.001 4189471.223 3125210.797 3331698.654 3383548.745 4854992.308 0.72641013 0.54005815 0.665753604 0.644482175 0.86292026 0.643710762 0.686241799 0.696921546 1 22.21103758 -5 0.233131272 2.787168958 0.639129508 0.61058597 0.079850978 107.4526344 1.073947456 90.68078645 0.128796571 1.00E-05 5 -2.148039449 QICVVMLETLSQS(ph)PPKGVTIPYRPKPSSSPVIFAGGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QICVVMLETLSQSPPKGVTIPYRPKPSSSPVIFAGGQDR 39 3 Q15366;Q15366-2 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 QICVVMLET(0.036)LS(0.089)QS(0.546)PPKGVT(0.149)IPY(0.043)RPKPS(0.046)S(0.046)S(0.046)PVIFAGGQDR 43.041 0.062579 90768000 61164 38266 61110 59486 49559 74034 89566 84244 65950 TRUE FALSE 58272.89894 42165.3489 63911.95395 53506.35426 58202.07391 71470.18402 75901.06171 76867.14875 76177.18917 0.764965202 0.553516733 0.838990709 0.702393392 0.764035462 0.938209782 0.996375195 1.009057299 1 16.21707144 2.241913717 1.619129458 1.010113451 0.695088016 0.770707038 0.071503757 0.164314235 0.85425414 0.037853772 0.0231952 174.5475337 -2.241913717 -0.315025435 QIDNPDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;; 172.94 0.00065293 593394000 2540390 2111230 2033890 2663280 1774240 2407980 2673170 2652590 1915920 FALSE TRUE 2420310.799 2326366.737 2127145.868 2395562.034 2083666.894 2324591.049 2265328.82 2420315.157 2213031.088 1.093663262 1.051212859 0.961191137 1.082480064 0.941544339 1.05041048 1.02363172 1.093665231 1 21.07759229 4.15125624 3.222974522 1.022947172 1.084931852 0.182005424 0.047801676 0.34681348 6.962476483 0.010899363 0.028290645 14166.29366 -4.15125624 0.061984679 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QIDS(0.003)S(0.997)PVGGETDETTVSQNYR;QIDS(0.003)S(0.997)PVGGETDETTVSQNYR;QIDS(0.001)S(0.999)PVGGETDETTVSQNYR;QIDS(0.026)S(0.974)PVGGETDETTVSQNYR;QIDS(0.01)S(0.99)PVGGETDETTVSQNYR 407.2 1.40E-151 2026630000 1543169 1389353 1462950 1642691 1685709 1482724 1780100 1553920 1805268 TRUE FALSE 1470226.46 1530929.65 1530027.705 1477564.58 1979696.116 1431376.896 1508513.051 1417850.527 2085219.741 0.705070276 0.734181449 0.733748906 0.708589388 0.949394482 0.686439356 0.723431215 0.679952572 1 20.99176799 -2.123507356 2.446943842 1.523420446 0.739029935 0.531657393 0.076654891 10256472.13 2578927.505 29871908.95 0.018903698 0.00752476 2.123507356 -0.784390511 QIEEQIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIEEQIKR 8 1 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;Q9NRL3-2;M0R0P4 F5GYK2 STRN4 Striatin-4 0 74.162 0.06685 64855000 75656 58837 64976 64558 78175 54232 80371 68605 120100 FALSE TRUE 72079.89082 64832.55719 67955.21387 58068.50719 91808.69525 52353.93224 68108.92784 62597.5825 138724.4946 0.519590221 0.467347583 0.489857354 0.41858871 0.661805945 0.377395012 0.490965406 0.451236695 1 17.08186302 -1.462662735 3.129931675 1.010709714 0.484315055 0.825376134 0.07450296 40686996.59 50954753.71 3822156.918 0.015444456 0.034461745 1.462662735 -0.526394659 QIEETLAHFHLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QIEETLAHFHLTK 13 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 261.35 2.70E-24 888292000 1432549 1164428 1195744 1553998 1356596 1253774 1429684 1154339 41274 FALSE TRUE 1364835.248 1283084.537 1250570.045 1397787.169 1593185.913 1210355.492 1211559.448 1053258.958 47674.56112 28.62816596 26.91340008 26.23139082 29.31935052 33.41794608 25.38786857 25.4131222 22.09268282 1 15.54093204 0.506096336 0.965499584 0.917820584 28.37484616 0.940164959 2.138391918 0.371993493 0.504053819 2.080877202 0.662073938 3.206980621 -0.506096336 27.45702558 QIEHCEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIEHCEGR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 134.51 0.00087357 51036000 82866 75730 78333 90888 93323 79613 95431 91461 86830 FALSE TRUE 78949.0884 83446.9731 81924.64553 81751.76556 109598.5017 76855.98185 80871.24824 83452.18997 100295.1529 0.787167536 0.832014017 0.816835541 0.815111829 1.092759704 0.766298067 0.806332568 0.832066032 1 16.61389236 -2.584791541 2.083211206 3.660411881 0.839058845 0.224459855 0.091035915 4451259.452 193044.5751 56277621.3 0.021063043 0.002601408 2.584791541 -2.821353037 QIEIQFAQGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 158.05 7.05E-05 101338000 100696 85831 85260 106565 111970 96544 109382 104570 119978 FALSE TRUE 95936.29964 94577.27648 89169.25533 95852.88374 131497.5325 93200.65707 92693.76696 95413.29644 138583.5755 0.692263129 0.682456605 0.643433069 0.691661212 0.94886809 0.672523109 0.66886546 0.68848921 1 17.08039676 -1.556392561 2.846526916 1.015977596 0.707291288 0.526759647 0.085999366 28394285.14 30388249.79 3470706.079 0.020632108 0.027772018 1.556392561 -0.308686308 QIESTETSCHGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QIESTETSCHGCR 13 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 ;;;;; 261.27 4.71E-24 2345780000 1149259 845523 987221 1159786 1563560 921458 1460040 1166803 1687320 FALSE TRUE 1094935.805 931682.755 1032486.059 1043202.108 1836244.369 889547.6784 1237284.083 1064631.544 1948980.968 0.561799126 0.47803584 0.529756871 0.535255154 0.942156131 0.456416811 0.634836411 0.546250354 1 20.89428857 -5 0.229882355 3.23987689 0.531871454 0.476251889 0.136090716 136.223029 1.362388653 142.1276053 0.219833596 1.00E-05 5 -2.708005436 QIEYEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIEYEYK 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 107.66 0.017277 153177000 433530 345560 360670 424410 319840 401700 462390 420650 373260 FALSE TRUE 413037.8961 380772.9569 377207.0763 381747.5005 375619.9947 387789.0283 391843.9131 383815.656 431143.2545 0.958006166 0.883170392 0.874899636 0.885430762 0.871218536 0.899443571 0.90884853 0.890227673 1 18.71780778 -1.497297565 3.920556113 1.001089538 0.898113748 0.637430322 0.024523697 338336615.1 43382269.28 3382493.105 0.005933596 0.031820166 1.497297565 -0.102975791 QIEYYFSVDNLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIEYYFSVDNLER 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 ; 124.51 0.00049064 56319000 101213 81691 89176 98210 92457 92227 111971 105148 93882 FALSE TRUE 96428.86207 90015.40577 93264.80781 88337.74421 108581.4715 89033.15586 94887.76746 95940.6837 108440.7411 0.88923094 0.830088442 0.860053213 0.814617674 1.001297764 0.8210305 0.875019541 0.884729141 1 16.72654735 -4.999999964 0.266754395 1.885894046 0.859047696 0.375495777 0.052378279 206.5515191 2.013327037 100.5582654 0.059580111 1.00E-05 4.999999964 -1.02684635 QIFDEYENETFLCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QIFDEYENETFLCHR 15 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ;; 240.2 7.85E-18 242967000 343592 393086 305795 360005 280897 308716 305929 352982 260668 FALSE TRUE 327351.0871 433141.9103 319816.0032 323816.6134 329885.3479 298025.0875 259253.9123 322073.0248 301091.0621 1.087216222 1.438574454 1.062190292 1.075477336 1.095633147 0.989817118 0.861048184 1.069686435 1 18.19984036 3.113294705 1.211323058 0.969731959 1.253327349 0.404427595 0.11260375 0.357881895 1.114856247 0.044141976 0.05953362 1298.059815 -3.113294705 0.28359539 QIFLGGVDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIFLGGVDKR 10 1 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 139.78 6.49E-05 697190000 1771060 1019960 1328290 1659670 2029050 1362320 2450600 1593510 2182700 FALSE TRUE 1687345.504 1123895.084 1389193.41 1492836.818 2382915.678 1315142.517 2076715.962 1453973.817 2521181.968 0.669267639 0.445781026 0.551008784 0.592117839 0.945158147 0.521637285 0.823707288 0.576703243 1 21.26566882 2.975405031 23.67916304 0.749030938 0.551073534 0.307847466 0.154016226 453.4855277 436600.0932 0.041354351 0.044097971 944.9417348 -2.975405031 -0.197957404 QIFVWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIFVWK 6 0 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ; 120.96 0.046203 107554000 508820 402430 396410 528000 406850 440780 510080 475600 417610 FALSE TRUE 484769.087 443438.0745 414585.7906 474924.4369 477804.5112 425515.6781 432257.9277 433953.9427 482370.8259 1.00497182 0.919288752 0.859475259 0.984562936 0.990533601 0.882133942 0.896111258 0.899627256 1 18.87978313 2.225338081 24.99979589 0.908211612 0.949470242 0.06834193 0.051997233 490.3976393 927186.8008 0.018866772 0.014016839 168.0111408 -2.225338081 0.04125863 QIGLDQIWDDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QIGLDQIWDDLR 12 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJ59;A0A590UJ97 A0A590UJ56 CUL1 Cullin-1 0 ;;; 222.49 5.74E-11 164474000 181681 152054 144653 184403 192434 164501 198082 181358 198429 FALSE TRUE 173093.2992 167548.4755 151285.4831 165866.4601 225994.4287 158804.2891 167860.9529 165477.3321 229200.3559 0.755205194 0.731013156 0.660057802 0.723674531 0.986012556 0.692862315 0.732376493 0.721976768 1 17.80624976 -1.975408018 2.831061143 1.214074893 0.748693497 0.444230875 0.08772097 20199239.83 10464888.12 28275947.93 0.020809118 0.01058259 1.975408018 -0.465381396 QIGVEHVVVYVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIGVEHVVVYVNK 13 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 95.651 0.0045986 615890000 1343500 1006900 994860 1129400 1072400 972980 1250600 1135300 1169000 FALSE TRUE 1279995.418 1109504.255 1040475.315 1015870.566 1259426.22 939285.4586 1059798.001 1035887.113 1350282.55 0.947946352 0.821683029 0.77056118 0.752339254 0.932713098 0.695621416 0.784871286 0.767163224 1 20.3648299 4.43463572 2.050710111 0.79980262 0.951930724 0.159424475 0.090160758 0.562209427 3.937414302 0.020708045 0.126523951 27204.18502 -4.43463572 0.152128104 QIHKFEELNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIHKFEELNR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 122.51 0.00029238 109810000 202490 149750 195010 205570 223600 185330 261640 218290 230430 FALSE TRUE 192918.699 165009.6953 203951.4014 184905.713 262595.7692 178911.9756 221722.0127 199175.3704 266163.9075 0.724811643 0.619955188 0.766262426 0.694706186 0.986594207 0.672187215 0.833028094 0.748318479 1 18.02195543 -5 0.082100813 1.828879673 0.504816178 0.416436723 0.096147231 209.9805203 1.216040532 31.30242067 2.754770153 1.00E-05 5 -1.324063495 QIILEKEETEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIILEKEETEELKR 14 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 106.19 0.00053785 437650000 316810 239800 280390 312620 181700 341750 355330 363010 195460 FALSE TRUE 301835.0192 264235.8926 293246.1588 281194.8437 213388.4225 329915.1118 301117.8824 331222.92 225770.9385 1.336908201 1.170371591 1.298865836 1.245487331 0.945154518 1.461282457 1.33373181 1.46707509 1 17.78450027 QILEDAAALIIHHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QILEDAAALIIHHVK 15 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 111.74 0.00047342 10075000 63388 56150 52626 65351 46480 60326 63912 62700 20566 FALSE TRUE 60391.77486 61871.74884 55038.95415 58781.79332 54586.09728 58236.89549 54161.05058 57209.65561 23755.27024 2.542247436 2.604548305 2.316915513 2.474473779 2.297852086 2.451535802 2.279959353 2.408293192 1 14.53596 -1.552885142 0.375778416 2.00E-13 2.511127021 0.95353949 0.098921774 4.938870285 0.369983427 4.769181206 0.06695388 0.027997217 1.552885142 2.511127021 QILIACS(ph)PVSSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.999)PVS(0.001)SVR;QILIACS(0.998)PVS(0.001)S(0.001)VR;QILIACS(0.991)PVS(0.009)S(0.001)VR;QILIACS(0.759)PVS(0.218)S(0.023)VR;QILIACS(0.533)PVS(0.466)SVR;QILIACS(0.878)PVS(0.12)S(0.002)VR 219.59 2.33E-11 907734000 1584883 1282639 1449073 1663229 1631289 1483507 1771581 1692208 2005682 TRUE FALSE 1509968.722 1413341.372 1515514.43 1496038.061 1915785.285 1432132.781 1501293.781 1544029.297 2316712.921 0.651772046 0.610063232 0.65416583 0.645758932 0.826941166 0.618174469 0.648027543 0.666474159 1 21.14364785 -5 0.435832381 7.983208775 0.655404842 0.752681717 0.060236767 540.7936676 3.307869857 3632.025859 0.032347504 1.00E-05 5 -7.327803933 QILIACSPVS(ph)SVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.04)PVS(0.95)S(0.01)VR;QILIACS(0.099)PVS(0.895)S(0.006)VR 221.62 1.97E-11 524260000 507620 393830 449010 521700 496960 498380 553790 514110 609700 TRUE FALSE 483625.8086 433961.7247 469597.5526 469257.7248 583629.6667 481120.9756 469299.1644 469091.8029 704249.1621 0.68672543 0.616204815 0.66680598 0.666323441 0.828726107 0.683168687 0.666382283 0.66608784 1 19.42572642 -5 0.420916698 6.921261011 0.675708066 0.762116775 0.055120918 460.5535719 2.981799444 2522.665808 0.032162805 1.00E-05 5 -6.245552945 QINIHNLSAFYDSELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QINIHNLSAFYDSELFR 17 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 165.8 2.42E-09 51750000 80627 43682 60415 79470 83536 66738 92539 86732 87045 FALSE TRUE 76815.9215 48133.24546 63185.08751 71481.52462 98104.65195 64426.84633 78420.47595 79137.28628 100543.494 0.764006883 0.478730582 0.628435366 0.710951268 0.975743412 0.64078583 0.779965693 0.787095048 1 16.61746021 0.655172242 0.210753427 1.110498882 0.562525178 0.404963476 0.119977593 4.782729576 0.61748351 0.849555138 0.411537467 4.520351872 -0.655172242 -0.547973704 QINWTVLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QINWTVLYR 9 0 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 211.48 1.18E-05 773760000 782440 476490 394420 498770 812930 483740 872900 682880 795690 FALSE TRUE 745455.6118 525044.8727 412504.5471 448632.692 954704.7346 466987.9625 739723.0731 623083.407 919081.5414 0.811087568 0.571271263 0.448822578 0.488131544 1.038759557 0.508102863 0.80485032 0.677941378 1 19.80983334 2.794236941 24.99973148 0.770182281 0.596819504 0.27216878 0.177521756 486.4321393 218416.3049 0.051413897 0.054532652 622.6398911 -2.794236941 -0.173362777 QIQEERDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIQEERDER 9 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 69.672 0.049776 239060000 117760 89255 114400 116850 149360 114090 140010 121300 166240 FALSE TRUE 112193.7182 98350.18597 119645.3532 105104.016 175408.3367 110139.0347 118648.903 110678.3289 192019.6502 0.584282484 0.512188132 0.623089111 0.547360731 0.913491596 0.573582103 0.617899798 0.576390639 1 17.55089443 -5 0.252216306 3.359727332 0.577649994 0.534558192 0.110876063 142.4438244 1.409034469 173.7488215 0.149972243 1.00E-05 5 -2.782077339 QIQELVEAIVLPMNHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIQELVEAIVLPMNHK 16 0 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 140.84 1.66E-06 84761000 344520 278566 312455 357250 289378 321685 396030 347680 294338 FALSE TRUE 328235.2224 306952.1921 326781.3708 321338.5513 339845.4316 310544.9678 335608.3499 317235.296 339982.4338 0.965447593 0.902847211 0.961171338 0.945162218 0.999597032 0.913414744 0.987134383 0.933093197 1 18.37510068 -4.999999938 0.121698849 1.165674463 0.925738195 0.187730649 0.030342848 214.7727231 1.686944184 8.7236861 0.250883208 1.00E-05 4.999999938 -0.239936268 QIS(ph)LPDLSQEEPQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QISLPDLSQEEPQLK 15 0 H0YBZ4;Q15390-2;Q15390 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 QIS(0.999)LPDLS(0.001)QEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(0.999)LPDLS(0.001)QEEPQLK;QIS(1)LPDLSQEEPQLK 243.95 5.52E-18 244925000 440034 361429 379979 459110 319782 388481 448356 408628 351406 TRUE FALSE 419234.4649 398259.026 397401.413 412959.3905 375551.8796 375027.8056 379951.0576 372846.366 405900.2477 1.032850971 0.981174632 0.979061765 1.017391324 0.925231954 0.923940815 0.936070031 0.91856649 1 18.6307657 2.735318872 24.99856157 0.935417452 1.001095761 0.549478551 0.027582265 188.7817703 1455775.917 0.007996615 0.007824634 543.649348 -2.735318872 0.065678308 QIS(ph)QDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QISQDVK 7 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4;E9PJF6;E9PIJ1 A0A5F9UK94 AMPD2 AMP deaminase 2 1 QIS(1)QDVK;QIS(1)QDVK;QIS(1)QDVK 89.171 0.018953 418080000 1565910 1548140 1284830 1715160 1050800 1719080 1567560 1488540 1081520 TRUE FALSE 1491892.538 1705897.226 1343740.726 1542748.858 1234059.187 1659547.829 1328399.932 1358195.546 1249236.598 1.19424338 1.365551753 1.075649504 1.234953299 0.987850652 1.328449576 1.063369368 1.087220426 1 20.25261531 2.49942605 0.194218229 0.953191584 1.36912791 0.267953857 0.111639991 5.658412167 0.628470053 0.385450037 0.762546002 315.810125 -2.49942605 0.415936326 QIS(ph)QDVKLEPDILLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QISQDVKLEPDILLR 15 1 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4;E9PJF6;E9PIJ1 A0A5F9UK94 AMPD2 AMP deaminase 2 1 QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR;QIS(1)QDVKLEPDILLR 275.23 1.02E-33 2008969000 2954508 1453952 2572707 2601738 2331749 3033928 3735947 2855988 2872358 TRUE FALSE 2814854.262 1602111.362 2690668.161 2340206.353 2738405.287 2928862.313 3165959.67 2605902.55 3317788.609 0.848412782 0.482885304 0.810982398 0.705351253 0.825370634 0.882775444 0.954237911 0.78543357 1 21.66179054 2.630075777 1.341998453 0.914392281 0.680506203 0.406037109 0.109737025 0.373141671 1.36625367 0.04900392 0.041881774 426.653956 -2.630075777 -0.233886078 QIT(ph)MEELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 177.16 0.00058621 466020000 540350 464230 442240 582840 580440 497260 572750 410460 611240 TRUE FALSE 514808.7264 511535.5648 462517.1414 524251.8159 681668.5522 480039.7615 485366.4682 374517.9464 706027.9774 0.729161935 0.724525913 0.65509747 0.742536886 0.965497932 0.679916061 0.687460673 0.530457657 1 19.42936583 3.022492763 24.34164363 0.751827897 0.709743238 0.038770598 0.137090921 931.3483462 1007894.125 0.037900494 0.045296483 1053.156138 -3.022492763 -0.042084658 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.333)QEEDDS(0.667)DEEVAPENFFSLPEK;QIT(0.098)QEEDDS(0.902)DEEVAPENFFSLPEK 114.71 0.0007714 417720000 203293 197520 182859 222488 138852 195159 201464 207764 149720 TRUE FALSE 193683.7428 217647.5126 191243.266 200123.0835 163067.7448 188400.5949 170726.9667 189571.0827 172937.8129 1.119961791 1.258530502 1.105849917 1.157196799 0.942927068 1.089412383 0.987215946 1.096180642 1 17.39989382 2.85000796 6.786052694 1.025222252 1.170717919 0.560357314 0.060160715 0.165099907 8.895247202 0.016929342 0.017990221 707.9587594 -2.85000796 0.145495666 QITT(ph)SPITVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.013)T(0.687)S(0.3)PITVR;QIT(0.016)T(0.914)S(0.07)PITVR 177.83 2.55E-05 404360000 848920 746790 760900 934160 821930 804790 864710 816960 824510 TRUE FALSE 808793.234 822888.75 795788.0176 840256.462 965274.3318 776919.9205 732782.608 745422.6514 952370.7998 0.849241949 0.864042398 0.835586326 0.88227869 1.013548853 0.815774613 0.769429941 0.782702128 1 19.86116386 -0.485604542 7.388868606 0.999999122 0.850196567 0.326387133 0.066985013 0 0 0.067287539 0.015859825 0.32688535 0.485604542 -0.149802555 QITTS(ph)PITVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.003)T(0.425)S(0.571)PIT(0.001)VR;QIT(0.014)T(0.048)S(0.938)PITVR 168.76 5.08E-06 440100000 936710 874480 789500 1045890 928290 900340 978420 924990 922950 TRUE FALSE 892433.5747 963590.5062 825699.3559 940755.1501 1090183.482 869161 829144.0591 843992.9719 1066076.372 0.837119739 0.9038663 0.774521767 0.8824463 1.02261293 0.81528962 0.777752965 0.791681529 1 20.02387936 -0.636006238 7.306472549 0.999999999 0.851350268 0.286177716 0.074115686 0 0 0.072176513 0.017012167 0.231203158 0.636006238 -0.14864973 QITVNDLPVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 ;;;;; 200.68 1.07E-07 2126890000 3446570 2621240 2845670 3393970 3479170 3053380 3649250 3388660 3741370 FALSE TRUE 3283657.467 2888347.336 2976146.784 3052801.687 4085936.146 2947640.685 3092489.889 3091930.966 4321562.551 0.759831063 0.668357174 0.688673772 0.706411547 0.945476572 0.682077524 0.715595309 0.715465975 1 22.04312161 -1.50820262 3.051463936 1.008483121 0.731196303 0.526100919 0.078888584 39951629.69 50180535.67 2864114.293 0.018509292 0.031031115 1.50820262 -0.277286818 QIVWNGPVGVFEWEAFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QIVWNGPVGVFEWEAFAR 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 280.97 6.28E-39 235830000 107449 42082 68944 84918 103767 65407 120631 108957 126891 FALSE TRUE 102370.0987 46370.20364 72105.15059 76381.88131 121863.9319 63141.93919 102226.5254 99416.14746 146568.6082 0.698444912 0.316371999 0.491954938 0.521133974 0.831446334 0.430801247 0.697465349 0.678290861 1 17.16121662 0.362240675 0.384967078 1.059901482 0.49611517 0.496675187 0.141495685 2.321727898 0.61070617 0.383750685 0.105161786 2.302717571 -0.362240675 -0.563786312 QIYVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 116 0.055721 345570000 194750 182700 170940 214720 216070 188090 235400 197680 253870 FALSE TRUE 185544.5535 201317.3377 178777.7681 193135.9377 253752.5396 181576.3961 199485.4066 180370.0912 293238.863 0.63274203 0.686530208 0.609666012 0.658630086 0.865344167 0.619209863 0.680282977 0.615096135 1 18.16171679 -2.162402495 2.357168186 1.792036492 0.671965043 0.661305586 0.074005585 3765274.966 944542.9033 15915965.82 0.016951016 0.006880144 2.162402495 -1.12007145 QIYYSDKYDDEEFEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QIYYSDKYDDEEFEYR 16 1 P61024;Q5T179 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;; 199.49 3.46E-11 870460000 793050 664680 716700 856440 680320 851290 966090 968770 841930 FALSE TRUE 755564.0982 732411.6477 749561.4039 770349.0241 798967.5926 821809.6138 818695.227 883939.363 972492.2044 0.776935892 0.753128554 0.770763406 0.792139022 0.821567092 0.84505522 0.84185274 0.908942364 1 19.89132716 1.164215952 0.432779054 1.010626975 0.755362575 0.967640897 0.013280817 0.169920704 0.089182487 0.017077757 0.00981832 14.59539833 -1.164215952 -0.255264399 QIYYSDKYFDEHYEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QIYYSDKYFDEHYEYR 16 1 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 139.08 1.86E-06 113720000 162060 114960 152280 158150 169130 169230 222100 194730 181130 FALSE TRUE 154399.745 126674.5547 159262.1886 142252.4615 198626.2185 163369.5227 188214.5659 177678.4089 209218.7153 0.737982473 0.605464738 0.761223433 0.679922259 0.949371179 0.780855204 0.899606737 0.849247203 1 17.67465239 2.749680568 24.85841487 0.880974479 0.689297838 0.660464263 0.070618077 385.1920221 861088.2378 0.019544221 0.020549543 561.9278639 -2.749680568 -0.19167664 QKAEADKNDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 65.395 0.038862 375020000 136480 129480 113970 154690 71289 147520 144500 198630 79687 FALSE TRUE 130028.8609 142674.1592 119195.6372 139140.2673 83721.77903 142411.3454 122453.8711 181236.9042 92044.45298 1.412674601 1.550057115 1.294979039 1.511663797 0.909579842 1.547201823 1.33037752 1.969014952 1 16.49004316 3.742403434 24.74864707 1.375247736 1.481365849 0.025211806 0.293690672 1308.767202 8428746.651 0.069127066 0.118975528 5525.905249 -3.742403434 0.106118113 QKAHEEANAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKAHEEANAAR 11 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 150.46 2.04E-05 14810000 25258 25011 27348 27908 28667 29324 38438 33289 26965 FALSE TRUE 24064.1044 27559.64934 28601.93285 25102.63482 33666.51572 28308.50253 32573.57714 30374.03868 31146.59448 0.772607882 0.884836683 0.918300486 0.805951188 1.080905193 0.908879542 1.045815046 0.975196139 1 14.92678681 3.807027044 0.447442245 1.01864176 0.725317542 0.529385308 0.067003023 1.570810318 0.444171554 0.049356248 0.227264902 6412.495073 -3.807027044 -0.293324218 QKDEEDKAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKDEEDKAR 9 2 O00170 O00170 AIP AH receptor-interacting protein 0 ; 94.297 0.0049594 132618000 282359 267745 247228 314360 164131 298813 319097 317667 177703 FALSE TRUE 269012.4497 295028.5199 258563.6483 282759.9356 192755.3944 288465.0309 270412.892 289850.3934 205260.2737 1.310591888 1.437338627 1.259686756 1.377567761 0.939077937 1.405362205 1.317414652 1.412111502 1 17.64709491 -1.863659445 2.751559931 0.867815432 1.313571279 0.316505058 0.141704744 35825839.07 22651946.4 30936054.92 0.031982008 0.013688018 1.863659445 0.445755847 QKDFLDGVYAFEYYPS(ph)TPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKDFLDGVYAFEYYPSTPGR 20 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 QKDFLDGVYAFEY(0.001)Y(0.004)PS(0.497)T(0.497)PGR;QKDFLDGVYAFEYY(0.001)PS(0.5)T(0.5)PGR 99.135 0.00042419 74138000 172345 104084 119754 155841 148381 137416 183711 171784 172108 TRUE FALSE 164198.5934 114690.2779 125244.8394 140175.5666 174258.5994 132657.2495 155682.5129 156741.6823 198797.6296 0.825958507 0.576919746 0.630011734 0.705116891 0.876562763 0.667297944 0.783120569 0.788448447 1 17.60094103 0.226230497 0.411760572 1.036659079 0.686386956 0.517213102 0.086313762 2.62728747 0.698126553 0.25805471 0.057742076 1.683567358 -0.226230497 -0.350272123 QKDFLDGVYAFEYYPST(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QKDFLDGVYAFEYYPSTPGR 20 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 QKDFLDGVYAFEYYPS(0.045)T(0.955)PGR;QKDFLDGVYAFEYYPS(0.076)T(0.924)PGR;QKDFLDGVYAFEYYPS(0.002)T(0.998)PGR;QKDFLDGVYAFEYYPS(0.022)T(0.978)PGR 300.25 1.33E-54 679038000 1869230 1051910 1282580 1582800 1528460 1453210 2021030 1743830 1780470 TRUE FALSE 1780875.202 1159100.825 1341387.562 1423693.937 1795022.94 1402884.973 1712684.755 1591131.001 2056576.194 0.865941757 0.563607042 0.652243066 0.692264133 0.872821024 0.682145878 0.832784489 0.773679577 1 20.97181309 0.575922628 0.454917775 1.016849268 0.69622269 0.449888048 0.094743342 1.682275021 0.691799986 0.16023513 0.055669102 3.76636693 -0.575922628 -0.320626578 QKDFLDGVYAFEYYPSTPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKDFLDGVYAFEYYPSTPGR 20 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 ; 168.84 1.06E-11 829630000 2239800 1354530 1731620 1977830 1878920 1843300 2616040 2295730 2286580 FALSE TRUE 2133929.093 1492558.147 1811016.49 1779014.771 2206603.053 1779466.059 2216915.051 2094703.711 2641171.148 0.807948055 0.565112241 0.685686912 0.673570424 0.835463864 0.673741291 0.839368192 0.793096544 1 21.33274636 0.908333432 0.489426789 1.008425473 0.676940363 0.584933323 0.077808636 0.763912664 0.445808916 0.091564981 0.041967707 8.097173261 -0.908333432 -0.33148511 QKDYDFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKDYDFEER 9 1 Q96NC0 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 ; 79.82 0.023585 478450000 1379600 1251870 1200930 1411190 1040250 1248000 1447560 1367730 1184080 FALSE TRUE 1314389.042 1379436.976 1255993.828 1269334.5 1221669.271 1204781.447 1226708.136 1247964.31 1367701.079 0.961020695 1.008580747 0.918324806 0.928078891 0.893228271 0.880880673 0.896912457 0.912453993 1 20.38332152 3.65611052 5.777452391 0.910006219 0.984582736 0.367787541 0.034808215 0.169609742 9.266945177 0.008446086 0.013242699 4530.128491 -3.65611052 0.074576516 QKEDVEVVGGS(ph)DGEGAIGLSSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKEDVEVVGGSDGEGAIGLSSDPK 24 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 1 QKEDVEVVGGS(1)DGEGAIGLSSDPK;QKEDVEVVGGS(1)DGEGAIGLSSDPK 220.26 6.19E-33 545730000 459060 439314 449756 490790 259315 532670 499750 534460 311923 TRUE FALSE 437361.1436 484080.5961 470377.7575 441454.8568 304539.4539 514223.5043 423503.959 487659.849 360294.4258 1.213899279 1.343569485 1.305537149 1.225261412 0.845251639 1.427231363 1.175438554 1.35350373 1 18.45881681 -2.057854197 2.410080122 0.671281319 1.238418847 0.181306451 0.157683763 6765027.993 2282354.737 12247119.78 0.035502963 0.008752776 2.057854197 0.567137528 QKEECTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKEECTIR 8 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 109.29 0.0033258 135520000 156680 147620 156090 199990 164700 196660 237420 225930 213600 FALSE TRUE 149274.0469 162662.6458 163246.8809 179886.6252 193423.6279 189849.6149 201197.2185 206146.3715 246723.9971 0.605024435 0.659289926 0.661657896 0.729100644 0.783967632 0.769481757 0.815474866 0.835534338 1 17.91253852 2.547911677 0.121624052 1.193020089 0.303259626 0.980821922 0.015434203 1.558650133 0.09331099 0.236487059 0.398856844 353.1113495 -2.547911677 -0.889760463 QKEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QKEEEAR 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;;;; 107.47 0.0068139 1124645000 1843276 1684889 1421422 2022209 1213326 1703494 1789305 1986167 1564807 FALSE TRUE 1756147.997 1856581.105 1486595.605 1818932.709 1424929.67 1644501.576 1516313.659 1812247.688 1807469.278 0.971606001 1.027171597 0.822473512 1.006342255 0.788356233 0.90983653 0.838915316 1.002643702 1 20.78553969 3.756756898 24.9023319 0.898555544 0.999388806 0.171868037 0.078813178 979.2747342 1340171.6 0.017819204 0.032041346 5711.588337 -3.756756898 0.100833262 QKEELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QKEELQR 7 1 P80303-2;P80303;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;; 95.099 0.012508 367562000 628690 555250 557650 673430 635470 608000 780360 680140 703420 FALSE TRUE 598973.0696 611830.6063 583218.8041 605735.537 746295.7668 586944.8075 661301.7497 620583.336 812502.781 0.737195101 0.753019707 0.717805302 0.745518109 0.918514723 0.722391137 0.81390706 0.763792261 1 19.63201323 -5 0.195128848 2.015961573 0.730310693 0.619877865 0.057161909 87.01968892 0.856435257 34.40068238 0.133617283 1.00E-05 5 -1.28565088 QKEIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKEIEER 7 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 101.64 0.0081244 322130000 825430 681620 692400 777400 612270 775700 822930 778150 756380 FALSE TRUE 786413.5597 751077.8529 724147.2249 699254.275 719049.6941 748837.3145 697376.9144 710011.0608 873675.5473 0.900120831 0.859675946 0.828851428 0.800359215 0.823016847 0.857111449 0.798210407 0.812671321 1 19.73673809 -1.431934803 3.2851061 1.00221019 0.837576181 0.73681343 0.030956913 234772468.4 265702752.7 4693791.977 0.008463138 0.03698837 1.431934803 -0.164634009 QKET(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.664)S(0.336)PR 78.334 0.05758 326930000 431590 439780 409900 512150 292720 419990 469730 570930 449350 TRUE FALSE 411189.596 484594.082 428694.3204 460667.709 343770.2753 405445.641 398064.0613 520936.3425 519032.903 0.7922226 0.933648097 0.825948255 0.887550108 0.662328483 0.781155951 0.766934156 1.003667281 1 18.98546647 1.2301125 24.91156556 1.00183382 0.813522325 0.557412252 0.071958901 158.2081846 466501.0732 0.067314909 0.017921545 16.98683625 -1.2301125 -0.188311495 QKETS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.298)S(0.702)PR 71.614 0.032606 200900000 520450 498170 425000 523230 320760 472170 511030 614680 487790 TRUE FALSE 495849.3599 548934.0894 444486.6704 470633.9263 376700.4424 455818.6345 433062.9878 560855.3606 563433.9819 0.880048729 0.974265144 0.788888645 0.835295601 0.668579558 0.809000964 0.768613541 0.995423383 1 19.10388705 -0.879570332 5.715464258 1.000000063 0.840862186 0.217422202 0.095376239 7.83E-08 1.53E-08 0.094656488 0.022310739 0.13195616 0.879570332 -0.159137877 QKFEECQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKFEECQR 8 1 P49792;J3KNE0;A6NKT7;O14715;Q99666;J3KQ37;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD8;RGPD5;RGPD1;RGPD2 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;RANBP2-like and GRIP domain-containing protein 2 0 ; 72.643 0.041609 126273000 203831 186772 204918 270040 241680 283750 352720 267910 251090 FALSE TRUE 194196.3126 205804.2791 214313.693 242895.0662 283828.9155 273923.6664 298906.0859 244450.3801 290027.7548 0.669578374 0.709602015 0.738942013 0.837489041 0.978626738 0.944473975 1.030612005 0.842851679 1 18.14583144 3.08345477 1.735279302 0.968555295 0.689706407 0.840757705 0.050517831 0.11198907 0.69140167 0.015880635 0.019952039 1211.86647 -3.08345477 -0.278848888 QKFNDS(ph)EGDDT(ph)EETEDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;QKFNDS(1)EGDDT(0.999)EET(0.001)EDYR 184.4 1.34E-13 921410000 743350 661930 604430 773750 473210 757410 797130 857940 536870 TRUE FALSE 708213.3187 729381.4196 632143.7134 695971.18 555737.6742 731180.7018 675513.1782 782814.2254 620125.0576 1.142049188 1.176184401 1.019381019 1.122307785 0.896170325 1.179085884 1.089317662 1.262348966 1 19.24219966 3.766720029 24.47652554 1.085239835 1.159116807 0.094350513 0.099720995 1264.969159 1099522.049 0.023666815 0.042652076 5844.132168 -3.766720029 0.073876971 QKFNDS(ph)EGDDTEETEDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;QKFNDS(1)EGDDTEETEDYR;QKFNDS(1)EGDDTEETEDYR 288.58 9.05E-41 19650400000 18570020 15848980 15086890 19355830 11359890 18622940 20334110 19822880 12853190 TRUE FALSE 17692251.96 17464009.08 15778638.83 17410145.19 13341051.22 17978022.92 17231768.06 18087083.54 14846397.06 1.191686568 1.176312947 1.062792458 1.172684869 0.898605309 1.210935074 1.160670026 1.218281006 1 23.82360952 0.564778912 0.010981206 1.02E-06 2.206955933 0.087601956 0.099338575 5158.919691 25.55870555 2631.220932 2502.130013 3.670953742 -0.564778912 2.206954917 QKFNDS(ph)EGDDTEETEDYRQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKFNDSEGDDTEETEDYRQFR 21 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 QKFNDS(0.999)EGDDT(0.001)EETEDYRQFR 81.553 0.0026746 155990000 83381 68724 82991 82260 81814 91256 112520 89388 106580 TRUE FALSE 79439.74538 75727.05373 86796.21944 73991.06852 96082.3357 88095.78184 95353.00743 81560.71284 123107.8821 0.645285615 0.615127581 0.705041935 0.601026248 0.780472656 0.715598225 0.774548354 0.662514142 1 16.90956361 -4.999999999 0.143791878 2.116690605 0.575901391 0.76876829 0.055357048 56.50931041 0.492078355 17.9886301 0.28077868 1.00E-05 4.999999999 -1.540789213 QKGADFLVTEVENGGSLGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKGADFLVTEVENGGSLGSK 20 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 241.68 8.57E-30 139411000 314950 217573 297290 300750 253715 302170 410760 357700 330300 FALSE TRUE 300062.9377 239743.9361 310921.0406 270518.0386 297962.8157 291705.7771 348091.0179 326377.8917 381521.2371 0.786490786 0.628389491 0.814950808 0.709051063 0.780986186 0.764585949 0.912376518 0.855464546 1 18.54140384 1.517417713 0.657535864 0.993551854 0.716812746 0.691199747 0.057135948 0.329971553 0.315434603 0.049743442 0.023754747 32.9168079 -1.517417713 -0.276739108 QKGYNHGQGS(ph)YSYSNSYNSPGGGGGSDYNYESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKGYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 33 1 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 QKGY(0.084)NHGQGS(0.137)Y(0.084)S(0.137)Y(0.084)S(0.137)NS(0.137)Y(0.084)NS(0.117)PGGGGGSDYNYESK 67.406 0.0027926 56173000 12203 16422 14238 16739 10504 14575 15834 15940 9294.1 TRUE FALSE 11626.18837 18095.42047 14890.82638 15056.36392 12335.89427 14070.2641 13418.23249 14544.2091 10735.38156 1.082978589 1.685587081 1.387079379 1.402499188 1.149087641 1.310644062 1.249907366 1.354792004 1 13.39008585 2.763908154 21.0182035 1.238001591 1.404679683 0.196845604 0.172022037 174.582161 144761.9894 0.049994805 0.052981941 580.6416091 -2.763908154 0.166678092 QKGYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKGYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 33 1 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 QKGYNHGQGSYSYSNS(0.001)YNS(0.999)PGGGGGSDYNYESK 388.53 1.55E-166 344500000 110290 83095 135070 116540 92270 117070 183800 147350 130550 TRUE FALSE 105076.8103 91562.47497 141263.0931 104825.1778 108361.8588 113015.8365 155757.9343 134447.2528 150795.0272 0.696818802 0.607198239 0.936788803 0.695150097 0.718603662 0.749466601 1.032911609 0.891589433 1 17.20222933 1.804024215 6.015234804 0.972165239 0.720796426 0.61464395 0.089601348 0.138073257 8.843825851 0.040724098 0.023559278 63.68310273 -1.804024215 -0.251368813 QKIDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKIDDR 6 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 88.591 0.046631 101390000 466410 452190 427200 546830 413810 498130 561740 527110 463430 FALSE TRUE 444363.7236 498268.6751 446787.5426 491861.6095 485978.333 480879.6332 476036.2459 480953.454 535296.3575 0.83012656 0.930827696 0.834654554 0.918858503 0.907867812 0.898342808 0.88929476 0.898480715 1 19.02997831 -5 0.191817771 1.479561466 0.868896839 0.579145207 0.031060958 96.93338576 0.950222804 17.78407943 0.075473518 1.00E-05 5 -0.610664627 QKIDDRDS(ph)DEEGASDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QKIDDRDSDEEGASDR 16 2 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QKIDDRDS(1)DEEGASDR;QKIDDRDS(0.998)DEEGAS(0.002)DR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(0.999)DEEGAS(0.001)DR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR 232.29 2.88E-16 1774600000 2441859 2018720 2120662 2464091 1530245 2464433 2554332 2449380 1806591 TRUE FALSE 2326437.164 2224429.863 2217896.45 2216395.891 1797119.244 2379089.067 2164621.74 2234899.302 2086747.905 1.114862585 1.0659792 1.062848294 1.062129204 0.861205725 1.140094144 1.037318276 1.070996308 1 20.99282489 4.024257154 1.247700376 1.033329209 1.111845568 0.13030111 0.070547718 1.182991157 3.174211696 0.020581582 0.085898241 10574.43457 -4.024257154 0.078516359 QKIPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QKIPAR 6 1 A0A3B3ISL2;A0A3B3IRU6;Q9GZU2-2;Q9GZU2-4;Q9GZU2 A0A3B3ISL2 PEG3 Paternally-expressed gene 3 protein 0 ;;;; 113.97 0.023422 6146660000 10681290 7681920 8532820 10610050 8894100 9881440 11868940 9646290 10258000 FALSE TRUE 10176406.59 8464716.382 8924058.237 9543507.616 10445228.22 9539243.255 10058115.21 8801609.709 11848758.25 0.858858488 0.714396919 0.753164007 0.805443694 0.881546235 0.805083795 0.848875047 0.742829715 1 23.49823254 -5 0.273555864 2.38822961 0.787581585 0.557794283 0.054494136 162.3130168 1.56834531 127.5792425 0.063447422 1.00E-05 5 -1.600648025 QKLDILDQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKLDILDQER 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 134.99 0.00014231 547910000 1165650 1001150 970410 1205210 890910 1088370 1257130 1207530 976350 FALSE TRUE 1110552.035 1103168.323 1014904.258 1084060.001 1046284.422 1050679.474 1065331.73 1101792.272 1127757.371 0.98474376 0.978196508 0.89993139 0.961252862 0.927756669 0.93165383 0.944646213 0.976976342 1 20.10502529 1.030500087 3.791276995 0.99971875 0.949858033 0.343781202 0.024726571 0.252728698 8.409086997 0.025373246 0.006534304 10.72753864 -1.030500087 -0.049860717 QKLDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QKLDPK 6 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ;;; 83.614 0.05179 8043950000 11590100 7379550 8602030 10773000 6946610 10356200 13950300 12145000 9063310 FALSE TRUE 11042258.94 8131534.535 8996441.584 9690077.573 8158096.585 9997562.197 11821925.52 11081519.42 10468801.83 1.054777722 0.776739752 0.85935733 0.925614768 0.77927701 0.954986288 1.129252967 1.058527958 1 23.319593 1.959998902 5.966978692 1.070298106 0.880978607 0.50138076 0.083342843 0.156934921 15.1295284 0.034708026 0.021755671 91.20085335 -1.959998902 -0.189319499 QKLDSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKLDSQR 7 1 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 114.28 0.0054175 171781000 462060 363560 318110 401930 413080 406930 547680 487760 469000 FALSE TRUE 440219.3395 400607.1773 332695.6582 361527.2328 485121.0212 392837.9121 464121.3572 445049.1486 541730.1247 0.812617426 0.739495847 0.614135421 0.667356708 0.895503128 0.725154268 0.856739059 0.821532952 1 19.04721479 0.944297084 0.60539522 0.999891995 0.732189007 0.535187287 0.076683691 0.73796775 0.633260385 0.079799538 0.033669128 8.796240276 -0.944297084 -0.267702988 QKLEEDAEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKLEEDAEMK 10 1 P05455 P05455 SSB Lupus La protein 0 ; 102.28 0.0027073 770830000 1081900 906750 897440 1089130 547170 1117530 1103440 1175910 617750 FALSE TRUE 1030760.731 999148.8559 938588.5117 979648.5832 642596.2748 1078829.656 935089.9619 1072941.087 713547.515 1.444557944 1.400255533 1.315383337 1.372926908 0.9005655 1.51192406 1.310480301 1.503671534 1 19.44464998 3.720488698 1.841052957 1.28541239 1.433767171 0.096013856 0.193340694 0.869412423 5.748777264 0.052423955 0.110145968 5253.983417 -3.720488698 0.14835478 QKLPDGSEIPLPPILLGR ddPTM_SK-BR-3_Trastuzumab_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 ; 146.78 7.42E-08 404740000 1641170 1249910 1337910 1609320 1243930 1502250 1790480 1728850 1415300 FALSE TRUE 1563595.147 1377277.25 1399254.497 1447548.096 1460870.998 1450226.706 1517309.392 1577462.729 1634777.496 0.956457469 0.842486059 0.85592963 0.88547102 0.893620693 0.887109536 0.928144286 0.964940326 1 20.64066286 1.293745469 1.394964677 0.999171187 0.884824815 0.648081331 0.029606451 0.246242148 0.908944518 0.027551865 0.008633572 19.66733289 -1.293745469 -0.114346373 QKLQLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKLQLEK 7 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;Q7Z406-4;Q7Z406-5;M0QY43 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 103.56 0.019899 0 854010 641580 768350 763390 613040 813320 1064800 958200 884340 FALSE TRUE 813642.6398 706957.7314 803579.6075 686652.5869 719953.9819 785154.5245 902345.2036 874294.9283 1021478.931 0.796533942 0.692092328 0.786682508 0.672214146 0.704815303 0.768644855 0.883371332 0.855910878 1 19.96222802 1.398744653 1.072329299 0.980459956 0.729538586 0.775292506 0.04690223 0.203482571 0.465998645 0.041360912 0.014400069 25.04636198 -1.398744653 -0.25092137 QKLSVDEAVDVGLVNEELRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKLSVDEAVDVGLVNEELRER 21 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 69.259 0.010917 80438000 73055 36079 74958 61442 79860 64386 103870 92458 111960 FALSE TRUE 69601.83493 39755.49112 78394.89844 55265.73343 93787.55872 62156.29668 88022.7238 84361.88737 129322.185 0.53820491 0.307414317 0.606198375 0.427349209 0.72522405 0.480631352 0.680646741 0.652338865 1 16.98061026 -0.055940242 0.227162122 1.222077157 0.376683381 0.677792693 0.106767489 4.181464286 0.364338243 0.956615295 0.234115258 0.879143477 0.055940242 -0.845393776 QKLTAEFEEAQTSACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKLTAEFEEAQTSACR 16 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 148.15 8.75E-07 55585000 102110 106940 117720 126710 55722 164340 192900 202850 122070 FALSE TRUE 97283.46266 117837.3076 123117.5784 113972.8701 65439.89916 158648.8646 163469.5621 185087.3786 140999.9922 0.689953674 0.835725632 0.873174364 0.808318272 0.464112786 1.125169315 1.159358661 1.312676517 1 17.10533556 2.115617425 8.49503199 1.166572483 0.754236544 0.702538339 0.133902844 0.134005863 9.406716631 0.047425282 0.035002263 130.5020774 -2.115617425 -0.412335939 QKLYTLQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 169.93 5.30E-05 6211500000 7603700 4818500 5804900 5622300 6051000 6984000 10013300 8381800 7112600 FALSE TRUE 7244288.17 5309510.628 6071060.407 5057135.722 7106292.484 6742142.329 8485587.178 7647845.157 8215585.682 0.881773796 0.64627293 0.738968668 0.61555389 0.864976979 0.82065267 1.032864546 0.930894699 1 22.969932 2.104754181 1.709769223 0.989601309 0.731500762 0.627955673 0.084279712 0.22495188 1.25862688 0.046659149 0.025414847 127.2782457 -2.104754181 -0.258100546 QKPELLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKPELLNK 8 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 125.56 0.0028378 0 743400 675570 669690 789090 580600 708960 791730 768580 630440 FALSE TRUE 708260.9553 744411.3511 700395.9489 709769.174 681856.4562 684408.5374 670937.0474 701279.0607 728205.4154 0.972611492 1.022254621 0.961810959 0.974682636 0.936351807 0.939856424 0.92135685 0.963023682 1 19.47398594 3.239749821 1.73533454 0.944968074 0.995981538 0.243850691 0.025959744 0.318134319 1.979113169 0.007838134 0.011087443 1736.800042 -3.239749821 0.051013465 QKPQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 QKPQAER 7 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;;;;; 117.4 0.0047788 11050430000 8827460 7265280 7049080 9051220 6723250 7924070 9546100 9026440 8617860 FALSE TRUE 8410203.46 8005620.292 7372287.29 8141374.169 7895782.671 7649657.469 8089667.119 8236037.061 9954273.715 0.844883685 0.804239518 0.740615288 0.817877266 0.7932053 0.768479719 0.812682808 0.82738704 1 23.24688463 0.580939721 1.717417488 0.999959451 0.798607893 0.837679721 0.027834929 0.830000014 2.93512566 0.026826979 0.007578524 3.810129363 -0.580939721 -0.201351557 QKREEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QKREEEER 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 169.09 0.00017045 107634000 169848 119411.8 137445 154644 116376 143339.8 168354 159357.2 151807 FALSE TRUE 161819.6216 131579.9982 143746.9892 139098.8913 136671.9376 138375.9068 142668.5053 145403.0388 175348.4542 0.922846012 0.750391549 0.81977905 0.793271272 0.779430524 0.789148142 0.813628531 0.829223385 1 17.41986519 0.593239449 2.213584176 0.999989557 0.809337981 0.637141444 0.044773012 2.02352049 10.23783763 0.041516768 0.011263105 3.919579244 -0.593239449 -0.190651576 QKRPS(ph)PSRTPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKRPSPSRTPEER 13 3 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2;E9PJG2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 QKRPS(0.962)PS(0.03)RT(0.008)PEER 88.992 0.042297 66780000 37156 18743 36642 36397 36717 39238 55353 39089 54360 TRUE FALSE 35399.70952 20652.93301 38322.07194 32738.30441 43120.43317 37879.17822 46907.88322 35666.15994 62789.87117 0.563780573 0.328921411 0.610322513 0.521394674 0.686741864 0.603268927 0.747061307 0.568024098 1 15.93824423 -2.976583287 0.104424711 1.961360926 0.226621311 0.679014064 0.097293113 51.28508651 0.57798508 12.63059832 1.533737422 0.001055399 2.976583287 -1.734739615 QKS(ph)DAEEDGGT(ph)VSQEEEDRKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.924)VS(0.076)QEEEDRKPK;QKS(1)DAEEDGGT(0.732)VS(0.268)QEEEDRKPK 209.4 1.09E-22 3334750000 1400540 1204200 1217020 2036630 710650 2057630 1817780 1731820 550620 TRUE FALSE 1334339.25 1326909.349 1272821.571 1831904.083 834587.135 1986373.757 1540444.275 1580172.66 636007.3374 2.097993484 2.086311385 2.00126869 2.880319102 1.312228784 3.123193146 2.422054251 2.484519544 1 19.27868388 2.228337488 24.99999419 2.407573396 2.112312342 0 0.644867417 686.660148 1679170.604 0.210159587 0.15696577 169.1755073 -2.228337488 -0.295261054 QKS(ph)DAEEDGGTVS(ph)QEEEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDR;QKS(1)DAEEDGGT(0.148)VS(0.852)QEEEDR;QKS(1)DAEEDGGT(0.003)VS(0.997)QEEEDR 208.53 1.51E-16 1187270000 2323960 2390510 1943370 3613710 1824860 2972840 2531850 2476660 1294080 TRUE FALSE 2214111.016 2634105.687 2032475.437 3250453.005 2143115.006 2869889.805 2145569.782 2259790.521 1494759.317 1.481249182 1.762227307 1.359734248 2.174566144 1.433752566 1.919967832 1.435394821 1.511808955 1 20.51148177 0.765549874 1.145539909 1.003711237 1.671916034 0.414601786 0.247490851 0.741995424 1.754207315 0.203463713 0.063358342 5.828407044 -0.765549874 0.668204797 QKS(ph)DAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.093)VS(0.907)QEEEDRKPK;QKS(1)DAEEDGGT(0.215)VS(0.785)QEEEDRKPK;QKS(1)DAEEDGGT(0.217)VS(0.783)QEEEDRKPK;QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDRKPK;QKS(1)DAEEDGGT(0.015)VS(0.985)QEEEDRKPK;QKS(1)DAEEDGGT(0.05)VS(0.95)QEEEDRKPK;QKS(1)DAEEDGGT(0.004)VS(0.996)QEEEDRKPK 226.85 7.08E-26 5314790000 3422730 2824030 3068690 4915370 1786053 4740210 4216910 4107450 1295818 TRUE FALSE 3260944.336 3111801.868 3209392.472 4421267.669 2097540.078 4576055.339 3573542.931 3747779.903 1496766.837 2.178658863 2.079015776 2.144216716 2.953878693 1.401380646 3.057293377 2.387508088 2.503916983 1 20.51341807 QKS(ph)DAEEDGGTVSQEEEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDR;QKS(1)DAEEDGGTVSQEEEDR;QKS(1)DAEEDGGTVSQEEEDR 266.4 9.94E-32 1370150000 753775 776994 565672 1120099 508577 884124 749004 765733 424942 TRUE FALSE 718145.5496 856170.572 591608.6207 1007504.52 597272.6678 853506.5642 634729.6834 698681.3591 490839.8351 1.463095491 1.744297245 1.205298711 2.052613599 1.216838213 1.738869797 1.293150307 1.42344062 1 18.90489281 0.805654634 0.690302601 0.997956429 1.58435358 0.30961147 0.259013588 1.048270647 1.050214236 0.22448528 0.0848496 6.392262977 -0.805654634 0.586397151 QKS(ph)DAEEDGGTVSQEEEDRKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(0.981)DAEEDGGT(0.019)VSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK 224.84 4.69E-26 8279360000 7431427 5449400 6334360 9927790 3672729 9198036 8553704 8289111 2845246 TRUE FALSE 7080158.173 6004700.055 6624796.672 8929829.688 4313251.775 8879505.707 7248679.355 7563272.497 3286472.218 2.154333797 1.827095943 2.015777476 2.717147474 1.312426057 2.701835013 2.205611024 2.301334682 1 21.64810836 QKS(ph)FSEDVISHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKSFSEDVISHK 12 1 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 QKS(0.995)FS(0.005)EDVISHK;QKS(0.976)FS(0.024)EDVISHK 136.39 6.71E-05 316940000 543810 527080 510240 575350 353860 552470 633420 622180 362520 TRUE FALSE 518105.179 580790.0512 533635.0087 517514.7249 415573.072 533337.8254 536780.1454 567698.6208 418737.7501 1.237302295 1.387001891 1.27438954 1.235892214 0.992442339 1.273679828 1.281900534 1.355737859 1 18.67568746 -1.936306554 2.486717533 0.819363338 1.260240137 0.36758514 0.104813588 7188653.387 3473079.273 7527309.1 0.025651551 0.011579597 1.936306554 0.440876799 QKS(ph)PAQSDSTTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QKSPAQSDSTTQR 13 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 QKS(0.986)PAQS(0.014)DSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR 171.98 1.46E-05 779613000 229886.9 196355.1 193635.1 235458.9 171195.9 205115.4 227200.4 236076.7 182042.3 TRUE FALSE 219020.6018 216363.9079 202513.4609 211790.124 201052.4108 198012.2023 192536.8062 215404.5726 210272.4901 1.041603691 1.028969162 0.963100122 1.007217463 0.956151756 0.941693334 0.915653807 1.024406818 1 17.68190059 3.722930127 1.043617459 0.958899634 1.047276222 0.325306119 0.033959727 0.523043366 1.069785911 0.011681694 0.035024855 5283.602382 -3.722930127 0.088376587 QKS(ph)PEIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 142.97 0.0003688 26088500000 19986560 17990010 16917510 21756420 12976360 19813950 20522610 19575040 12142520 TRUE FALSE 19041834.92 19823212.47 17693194.57 19569423.33 15239433.08 19127787.94 17391508.92 17860945.72 14025519.99 1.357656254 1.413367383 1.261500079 1.395272571 1.086550309 1.363784584 1.239990313 1.273460502 1 23.74155092 -4.999999996 0.111763575 9.15E-14 1.48217057 0.562146563 0.088255221 108.4599279 0.802495774 24.72589012 0.938636158 1.00E-05 4.999999996 1.48217057 QKS(ph)PEIHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR;QKS(1)PEIHRR 144.28 5.21E-05 12443020000 9699960 7026000 8999120 9199860 6620580 9772970 11043050 9803300 7287540 TRUE FALSE 9241462.114 7741957.388 9411738.553 8275072.594 7775207.056 9434529.598 9358229.903 8944871.081 8417654.484 1.097866648 0.919728578 1.118095138 0.983061565 0.92367857 1.120802667 1.111738421 1.062632245 1 23.00498686 2.211696128 24.9970872 1.087519103 1.008334812 0.160319128 0.071253156 319.8189585 297585.7871 0.024964026 0.018442163 162.8156426 -2.211696128 -0.079184292 QKSAS(ph)TLCLPSVGAARPQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKSASTLCLPSVGAARPQVK 20 2 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 QKS(0.026)AS(0.956)T(0.019)LCLPSVGAARPQVK 129.93 8.89E-06 402150000 448410 189950 503320 323760 408060 449520 650580 526730 468130 TRUE FALSE 427214.548 209306.121 526397.7199 291215.0297 479225.5348 433953.0097 551322.0723 480606.7288 540725.2095 0.790076994 0.387084081 0.973503196 0.538563811 0.886264458 0.80253889 1.019597501 0.888818794 1 19.04453609 2.440704275 0.868545144 0.984976424 0.628859561 0.349223514 0.163959859 0.55412803 0.83333324 0.106744047 0.073768383 275.8698729 -2.440704275 -0.356116863 QKSAST(ph)LCLPSVGAARPQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKSASTLCLPSVGAARPQVK 20 2 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 QKSAS(0.366)T(0.634)LCLPSVGAARPQVK 182.03 2.33E-15 466070000 553460 268230 593040 421610 429550 564230 754060 675780 630660 TRUE FALSE 527299.0427 295562.942 620231.4706 379228.9618 504463.384 544690.5736 639014.2977 616605.1207 728459.5318 0.723854956 0.405736941 0.851428863 0.520590294 0.692507081 0.747729352 0.877213174 0.846450755 1 19.4744893 1.783665514 0.75137287 0.983068462 0.596088562 0.523771285 0.120106329 0.439629125 0.481584644 0.09958035 0.047609785 60.7666806 -1.783665514 -0.386979901 QKSDAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.01)VS(0.99)QEEEDRKPK;QKSDAEEDGGT(0.01)VS(0.99)QEEEDRKPK;QKSDAEEDGGT(0.116)VS(0.884)QEEEDRKPK 217.84 6.79E-25 825250000 943170 705880 791730 1240250 523680 1259060 1196050 1180170 447440 TRUE FALSE 898588.2233 777809.9745 828031.6036 1115577.714 615009.6262 1215458.436 1013570.606 1076828.058 516826.71 1.738664442 1.504972478 1.602145531 2.158514048 1.189972605 2.351771712 1.961142073 2.083537939 1 18.97932111 3.368505145 18.69274865 1.859061771 1.608950458 0.020454328 0.422510011 4.646497941 774.515415 0.104865682 0.141988537 2336.173778 -3.368505145 -0.250111314 QKSQT(ph)PPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKSQTPPRR 9 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QKSQT(1)PPRR 116.55 0.061773 69488000 186030 155310 168800 181830 146010 183900 214440 206190 161600 TRUE FALSE 177236.7306 171136.2656 176539.647 163552.1029 171474.0978 177531.4969 181723.2395 188134.9105 186660.1027 0.949515874 0.916833663 0.945781366 0.876202791 0.918643542 0.951095035 0.973551589 1.007901034 1 17.51005407 1.701548111 1.78365659 1.003159784 0.922905496 0.729260493 0.020480501 0.174172573 1.121771573 0.015143939 0.00590029 50.29769825 -1.701548111 -0.080254288 QKT(ph)VDIDDAQILPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;QKT(1)VDIDDAQILPR;QKT(1)VDIDDAQILPR 228.38 2.71E-12 1169580000 1202880 917579 997195 1175340 818972 1209910 1258340 1228390 981740 TRUE FALSE 1146022.246 1011081.343 1042917.377 1057192.59 961800.4575 1168010.513 1066357.122 1120825.659 1133983.225 1.010616578 0.891619312 0.919693831 0.932282389 0.848161098 1.030006871 0.940364106 0.988397037 1 20.11296787 2.219080771 24.99988696 0.981586956 0.925235735 0.352449755 0.045789458 330.5413697 424204.9606 0.016627364 0.012297039 165.6077937 -2.219080771 -0.05635122 QKVDSLLENLEK ddPTM_SK-BR-3_Trastuzumab_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 ; 228.8 8.84E-12 1425880000 3184900 2460600 2588300 3483100 1857600 3114000 3291500 3275000 2207230 FALSE TRUE 3034356.089 2711337.937 2706976.115 3132972.171 2181564.852 3006161.399 2789321.222 2988223.638 2549515.955 1.190169484 1.063471649 1.061760806 1.228849799 0.855678054 1.179110644 1.094059136 1.172074892 1 21.28179194 -4.999952595 0.010421246 1.85E-05 2.013327844 0.066634865 0.106016494 39880.9953 31.55140772 3563.994174 2601.760813 1.00E-05 4.999952595 2.013309387 QKVENLFNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKVENLFNEK 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 117.23 0.00089818 461040000 736830 599090 666460 763520 511390 731480 870660 828730 685260 FALSE TRUE 702001.5062 660137.9521 697017.8502 686769.519 600576.2541 706148.6642 737824.8262 756162.0078 791526.621 0.886895636 0.834006001 0.880599378 0.867651827 0.758756861 0.892135079 0.932154152 0.955321006 1 19.59427835 1.64826734 2.068936206 0.975458747 0.849738252 0.668630425 0.037944814 0.175771319 1.610753552 0.02700955 0.010342301 44.49050547 -1.64826734 -0.125720495 QKWDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QKWDQK 6 1 O15371-2;O15371;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 97.068 0.037842 720610000 692020 594490 650740 718430 437620 710440 792240 798100 610400 FALSE TRUE 659309.5861 655069.2069 680577.0727 646212.0515 513940.7894 685837.2847 671369.2375 728214.133 705057.7145 0.935114349 0.92910012 0.965278528 0.916537807 0.728934354 0.972739211 0.952218838 1.032843295 1 19.42738183 1.619366483 2.304789587 1.010416267 0.906923501 0.305293682 0.067621534 0.353494567 4.158016763 0.048402852 0.01846943 41.62617278 -1.619366483 -0.103492767 QKWLLLTGISAQQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QKWLLLTGISAQQNR 15 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 114.69 0.001481 0 73722 40998 64545 60689 67497 84318 90137 80909 81800 FALSE TRUE 70237.30716 45175.74281 67504.45209 54588.42642 79268.45543 81398.04652 76384.94517 73824.17903 94485.12622 0.74336893 0.478125443 0.714445276 0.57774624 0.838951681 0.861490583 0.808433541 0.781331221 1 16.52779962 2.73074165 24.21637853 0.843552287 0.620923172 0.6042024 0.091844321 251.7509772 779704.1619 0.027040336 0.025948903 537.9496761 -2.73074165 -0.222629114 QKYNVR ddPTM_SK-BR-3_Trastuzumab_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 299081000 480280 337120 326720 449070 388920 411030 492750 470560 485980 FALSE TRUE 457578.1162 371472.9113 341700.4352 403928.6304 456747.5249 396795.928 417571.9375 429355.2718 561343.2964 0.815148447 0.661757099 0.608719187 0.71957505 0.813668797 0.706868561 0.743879797 0.764871113 1 19.09852381 -0.352751442 0.529688182 1.03826463 0.713790108 0.668491523 0.060932496 4.664683642 1.221232886 0.404455054 0.0281676 0.443862605 0.352751442 -0.324474522 QLAEAHAQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 143.24 3.43E-05 199970000 495790 383310 369770 451950 386920 430130 526630 471500 406890 FALSE TRUE 472354.9893 422369.7248 386724.3203 406519.1274 454398.7255 415234.4902 446282.9213 430212.9604 469988.4231 1.005035371 0.898681125 0.822837971 0.864955619 0.966829614 0.883499401 0.94956152 0.915369271 1 18.84226569 0.348837985 0.773009793 1.000890469 0.911963097 0.221270452 0.051704608 4.012457979 3.306996865 0.062335393 0.018283129 2.232739136 -0.348837985 -0.088927372 QLAEDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QLAEDFLR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 165.72 0.00075059 500547000 1500860 1130489 932207 1137865 1674590 1023745 1619470 1298580 1675550 FALSE TRUE 1429917.322 1245687.114 974949.613 1023484.648 1966637.966 988292.454 1372390.108 1184869.451 1935385.736 0.738828077 0.643637643 0.503749508 0.528827215 1.016147804 0.510643659 0.709104176 0.612213591 1 20.8841897 -1.868466391 2.457880383 1.161106702 0.660707624 0.339832362 0.149804799 30782818.82 17879789.92 28946848.3 0.033033548 0.013537348 1.868466391 -0.500399078 QLAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLAEKR 6 1 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2;Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 P16949;E5RGX5;Q9NZL9 STMN1;STMN2;MAT2B Stathmin;Stathmin-2;Methionine adenosyltransferase 2 subunit beta 0 82.386 0.095213 215670000 405330 204950 358480 319040 412940 346900 588850 483050 590920 FALSE TRUE 386170.8542 225834.638 374916.6626 286969.4931 484956.6053 334886.766 499010.1175 440751.5812 682556.8556 0.56577097 0.33086568 0.549282685 0.420433098 0.71049994 0.490635708 0.731089452 0.64573607 1 19.3805897 0.837139819 0.369277958 1.045298499 0.430668102 0.702958384 0.101419424 0.842441223 0.293074026 0.177925302 0.083789594 6.872896736 -0.837139819 -0.614630397 QLAPIWDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLAPIWDK 8 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 146.81 0.0012734 596370000 2440800 2263500 1834090 2385400 1789830 2148600 2390500 2418700 1849740 FALSE TRUE 2325428.221 2494153.223 1918184.841 2145615.06 2101975.785 2074193.443 2025785.32 2206905.806 2136588.232 1.088383895 1.167353253 0.897779372 1.00422488 0.983800132 0.970796999 0.948140259 1.032911149 1 21.02687746 3.747059243 24.99969991 0.974135751 1.12786858 0.706050907 0.040493569 270.9793567 797115.2371 0.009493007 0.016782087 5585.463821 -3.747059243 0.15373283 QLAPIWDKLGETYKDHENIVIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLAPIWDKLGETYKDHENIVIAK 23 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 144.22 9.17E-08 738340000 1632550 731570 1704170 1246720 1262530 1684410 2509250 1958160 1468560 FALSE TRUE 1555382.597 806117.8147 1782307.88 1121397.337 1482714.832 1626078.459 2126417.827 1786693.13 1696296.784 0.916928341 0.475222156 1.050705217 0.661085576 0.874089278 0.958604929 1.253564734 1.053290406 1 20.69395718 2.182753842 2.340090057 1.125995307 0.758918711 0.411494789 0.165886842 0.236606052 2.608985508 0.072197572 0.047139219 152.3189164 -2.182753842 -0.367076596 QLCAEHGISPEGIVEEFATEGTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLCAEHGISPEGIVEEFATEGTDR 24 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 60.464 0.066799 4104800 7440.2 6969.5 6623.3 7279.6 7159.9 6362.8 8016.2 6179.7 6835.4 FALSE TRUE 7088.516491 7679.699974 6926.984856 6547.840778 8408.584293 6142.454641 6793.181462 5638.572707 7895.398922 0.897803463 0.972680424 0.877344505 0.829323615 1.064998029 0.777979011 0.860397496 0.714159318 1 12.94679645 2.181132197 24.99999943 0.828399363 0.924856709 0.180763794 0.094343642 121.5205486 52899.83172 0.03138461 0.023179081 151.7512218 -2.181132197 0.096457345 QLCAEHGISPEGIVEEFATEGTDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLCAEHGISPEGIVEEFATEGTDRK 25 1 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 109.39 0.0020229 33248000 42973 38958 38959 48953 36241 45476 50448 50472 39011 FALSE TRUE 40941.75145 42927.86449 40745.30869 44032.15144 42561.41893 43901.15472 42751.23106 46052.40411 45060.62664 0.90859259 0.952669053 0.904233068 0.977175746 0.944536774 0.974268624 0.948749146 1.022009846 1 15.45957976 2.294140994 0.353033517 1.008097953 0.912076786 0.570449248 0.024040541 1.07425295 0.323981717 0.026701315 0.03669587 196.852527 -2.294140994 -0.096021166 QLDDLKVELSQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLDDLKVELSQLR 13 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 180.11 1.20E-05 3785670000 5923970 4765050 4591800 5772210 4952070 5660440 7356630 6346730 5805290 FALSE TRUE 5643955.678 5250614.012 4802338.572 5191976.484 5815709.44 5464417.543 6234240.98 5790976.675 6705544.724 0.841684891 0.783025724 0.716174266 0.774281091 0.867298583 0.814910312 0.929714324 0.863610178 1 22.6769231 1.470738292 0.685831523 0.987344145 0.784490007 0.680737819 0.045506409 0.375287606 0.390088778 0.042967263 0.019547394 29.56230492 -1.470738292 -0.202854139 QLDMILDEQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLDMILDEQRR 11 1 P49257 P49257 LMAN1 Protein ERGIC-53 0 ; 91.62 0.0095113 85060000 652160 484530 699480 593390 648090 671010 887080 513910 305600 FALSE TRUE 621333.6893 533904.1579 731551.8499 533741.3098 761116.6908 647772.7554 751739.6537 468909.316 352990.8872 1.760197534 1.512515414 2.072438344 1.512054076 2.156193597 1.835097672 2.129629067 1.328389296 1 18.42927141 1.036939473 5.468138553 1.002137729 1.831639635 0.629992413 0.226860567 0.101319194 7.396742905 0.214532502 0.054105451 10.8877834 -1.036939473 0.829501905 QLDWRPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLDWRPER 8 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 67.563 0.0536 295880000 913850 798330 732370 913990 962160 793050 999600 887500 999850 FALSE TRUE 870654.1216 879680.7346 765949.8889 822113.9887 1129960.399 765586.4796 847092.6611 809785.7951 1154901.631 0.753877298 0.761693213 0.663216562 0.71184763 0.97840402 0.662901895 0.733476028 0.70117296 1 20.13933854 -1.188050729 5.008653194 1.000021737 0.746503171 0.44570315 0.089078301 2.00E-05 3.25E-06 0.079920062 0.018835725 0.064855867 1.188050729 -0.253518566 QLEAIDQLHLEYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 199.15 2.10E-08 1474520000 3357660 1865230 1685810 2798860 2675930 2092370 3606250 2680440 2583460 FALSE TRUE 3198950.066 2055299.058 1763106.056 2517513.275 3142611.345 2019910.702 3056050.329 2445726.464 2984089.782 1.07200195 0.68875242 0.590835459 0.843645285 1.05312225 0.676893408 1.024114739 0.819588766 1 21.50885951 2.995141189 24.9922258 0.909677604 0.793719475 0.120839279 0.161161059 505.4695405 2600001.143 0.046152232 0.053785885 988.8745254 -2.995141189 -0.115958129 QLEEAEEEAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QLEEAEEEAQR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 300.43 1.94E-35 2732160000 1713892 1446065 1471060 1762412 1616385 1597769 1740420 1723503 1737266 FALSE TRUE 1632879.722 1593420.668 1538509.556 1585250.997 1898282.032 1542437.859 1474886.964 1572583.94 2006672.339 0.813725136 0.794061211 0.766696947 0.789989958 0.94598505 0.768654568 0.734991426 0.783677489 1 20.93637363 -0.908464413 5.15591209 0.999999975 0.797114212 0.557350332 0.056049058 0.000263238 38611344.02 46.36623956 0.013151136 0.123462648 0.908464413 -0.202885763 QLEEEDGSRDSPLFDFIESCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QLEEEDGSRDSPLFDFIESCLR 22 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;; 135.21 5.82E-06 127416300 105680.3 74682.9 91805.7 104321.2 122695.2 102986.9 132610 111574.6 139735 FALSE TRUE 100685.0017 82293.17242 96015.08215 93834.63478 144093.204 99420.43783 112377.909 101804.5365 161404.3901 0.623805843 0.509857088 0.594872804 0.581363584 0.892746498 0.615971088 0.696250634 0.630742054 1 17.30032029 -5 0.143217892 2.270933471 0.509526871 0.586672373 0.09666428 92.16333656 0.800767687 33.37381666 0.529203557 1.00E-05 5 -1.7614066 QLEEQLR ddPTM_SK-BR-3_Trastuzumab_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 ;; 118.05 0.011849 396809000 1141710 1113590 1087440 1384750 1202820 1201090 1400400 1398150 1458720 FALSE TRUE 1087743.631 1227066.087 1137300.2 1245552.299 1412591.427 1159495.952 1186743.26 1275720.574 1684930.847 0.645571676 0.72825902 0.674983309 0.739230516 0.838367598 0.688156403 0.704327576 0.757135271 1 20.68425795 -5 0.249363392 2.70549672 0.691705011 0.761689972 0.04970832 89.03379082 0.882665889 77.37155344 0.071923964 1.00E-05 5 -2.013791709 QLES(ph)GGFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLESGGFEAR 10 0 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 1 QLES(1)GGFEAR 102.09 0.0031398 112190000 119490 100870 118260 146290 119690 111570 148070 116440 142950 TRUE FALSE 113841.9445 111148.7677 123682.338 131584.6513 140563.8981 107706.3029 125479.202 106243.8963 165117.9559 0.689458296 0.673147672 0.74905444 0.796913034 0.851293836 0.652299154 0.759936745 0.643442415 1 17.33313749 -2.196682083 2.393510101 1.811388008 0.725570785 0.630721375 0.065654486 3448203.01 841844.691 15142548.1 0.015789479 0.006357962 2.196682083 -1.085817223 QLFHGT(ph)PVTIENFLNWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLFHGTPVTIENFLNWK 17 0 Q9H446-2;Q9H446;E5RGS5;E5RGQ3 Q9H446-2 RWDD1 RWD domain-containing protein 1 1 QLFHGT(1)PVTIENFLNWK;QLFHGT(0.999)PVT(0.001)IENFLNWK 132.45 8.67E-05 91298000 269160 151782 230743 245120 258550 234300 341020 287320 278510 TRUE FALSE 256437.3402 167248.7584 241322.7948 220480.0719 303641.0381 226186.1323 288991.1357 262160.7376 321699.9084 0.797132152 0.5198906 0.750148783 0.685359449 0.943864236 0.703096664 0.898325204 0.814923259 1 18.295356 1.881528796 0.400658488 0.990276686 0.643103306 0.429885635 0.104753799 0.931407763 0.392894361 0.112998322 0.105080699 76.1252613 -1.881528796 -0.34717338 QLFHPEQLITGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 164.68 5.66E-05 10323353000 13353110 11892680 10557900 14486870 9517000 12442420 13133590 13298260 8679850 FALSE TRUE 12721934.95 13104557.61 11041990.16 13030622.3 11176761.79 12011535.88 11129819.63 12133793.86 10025876.81 1.268909961 1.307073472 1.101349076 1.299699024 1.114791454 1.198053408 1.110109354 1.210247651 1 23.25722508 6.207800177 0.025954312 1.49E-06 2.66983455 0.51508169 0.068596769 867.6013308 2.406302182 93.31249021 162.4095066 1613615.945 -6.207800177 2.66983306 QLFHPEQLITGKEDAANNYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 197.72 5.38E-22 5723720000 1971130 896982 1837730 1514410 1974900 1749470 2642210 2144830 2274800 FALSE TRUE 1877958.591 988385.4856 1921991.738 1362178.63 2319321.935 1688885.415 2239092.337 1957017.315 2627564.366 0.714714591 0.376160333 0.731472752 0.518418748 0.882688913 0.64275701 0.852155086 0.744802807 1 21.32529467 1.741133154 0.392619263 0.995115875 0.531455785 0.449417859 0.132712853 0.865781627 0.373829841 0.145840495 0.127575049 55.09765996 -1.741133154 -0.46366009 QLGEAHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLGEAHGR 8 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 77.732 0.030064 0 16557 13679 13342 17759 26536 14394 20836 13942 24222 FALSE TRUE 15774.38342 15072.90565 13953.7439 15973.83158 31163.87 13895.53217 17657.08552 12721.16457 27978.22405 0.563809318 0.538737041 0.498735869 0.570938011 1.113861621 0.496655261 0.631101012 0.454680917 1 14.77201677 2.975298178 24.96871265 0.704821555 0.538584298 0.179638488 0.202211818 1451.321076 1467003.019 0.057986338 0.061778329 944.7092722 -2.975298178 -0.166237257 QLHDEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QLHDEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;;;;;; 147.04 0.0021785 848907000 413807 355205 376318 438634 445565 398119 468860 407335 459876 FALSE TRUE 394247.1632 391400.7933 393572.5525 394541.677 523271.3949 384332.0392 397326.7958 371666.588 531191.2214 0.742194425 0.73683596 0.740924429 0.742748865 0.985090442 0.723528597 0.747992022 0.69968511 1 19.01887178 -1.925614272 2.678996398 1.149607456 0.76322036 0.462324531 0.079669329 9948363.509 6304598.581 9336558.341 0.018235703 0.011868224 1.925614272 -0.386387096 QLHLEGASLELS(ph)DDDTESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK 302.53 3.08E-50 228653000 208417 178131 151753 217050 110945 210101 182126 219630 98217 TRUE FALSE 198565.5415 196282.7514 158711.0252 195231.7216 130293.7729 202825.1497 154339.3337 200398.0329 113447.9907 1.750278169 1.730156261 1.398976078 1.720891841 1.14848903 1.787824962 1.360441315 1.766430869 1 16.79167153 -3.077365078 0.169352205 2.24E-19 1.748726011 0.391358704 0.220431926 59.1537023 1.014415557 22.89987626 0.777765509 0.000836826 3.077365078 1.748726011 QLIEFQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLIEFQHR 8 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 92.051 0.012052 81861000 188320 153690 125660 139270 184820 141310 202900 175630 172340 FALSE TRUE 179418.4868 169351.1857 131421.6353 125270.315 217052.5495 136416.3993 171943.8785 160250.9061 199065.607 0.901303291 0.850730512 0.660192573 0.629291603 1.090356856 0.685283617 0.863754825 0.805015535 1 17.60288446 QLIYNYPEQLFGAAGVMAIEHADFAGVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLIYNYPEQLFGAAGVMAIEHADFAGVER 29 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 203.02 2.78E-25 54968000 50092 28002 33865 40054 49824 34684 55306 51469 51391 FALSE TRUE 47724.25043 30855.43564 35417.74375 36027.69582 58513.28983 33482.88438 46868.05394 46962.10151 59360.45381 0.803973814 0.519797839 0.596655542 0.606930936 0.985728479 0.564060452 0.789550129 0.791134476 1 15.8572145 0.619070241 0.420875094 1.026144515 0.642926416 0.363977177 0.134199746 2.02587651 0.752833316 0.240099434 0.088148976 4.159778839 -0.619070241 -0.383218099 QLLDS(ph)DEEQEEDEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR 372.57 1.27E-97 700490000 304730 363770 316860 399320 331760 348790 329600 335960 310440 TRUE FALSE 290326.0168 400838.5766 331388.3444 359179.5949 389618.839 336711.3148 279313.4665 306541.5614 358581.4497 0.809651523 1.117845268 0.924164774 1.001668088 1.086556037 0.939009297 0.778940089 0.854872893 1 18.45194133 1.990795225 24.30362094 0.854775239 0.989328923 0.191066253 0.099718138 376.0163853 992806.2492 0.0365458 0.025538259 97.90282532 -1.990795225 0.134553684 QLLEEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 92.838 0.022811 133028000 189924 156898 201926 195169 208070 202064 231370 204462 165189 FALSE TRUE 180946.6689 172886.0846 211184.5068 175550.2413 244357.3421 195066.473 196070.2571 186558.2234 190805.6665 0.94832964 0.906084645 1.106804168 0.920047316 1.280660825 1.022330608 1.027591375 0.977739429 1 17.54174449 3.748934887 24.73039737 1.050334756 0.927207133 0.213666166 0.096154504 798.9340541 1904510.119 0.022852498 0.040637666 5609.638656 -3.748934887 -0.123127623 QLLEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QLLEELER 8 0 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ;; 85.676 0.038558 133889000 193468 172835 173454 209536 191856 189423 215775 211109 218917 FALSE TRUE 184323.1511 190447.083 181407.0375 188473.0432 225315.6257 182863.234 182854.5608 192623.1768 252865.5303 0.728937435 0.753155572 0.717405165 0.745348893 0.891049189 0.723163943 0.723129644 0.761761307 1 17.94801086 0.934720572 21.32695603 1 0.752118992 0.700052014 0.050298796 3296.195362 1076877.731 0.046966414 0.011741604 8.604399616 -0.934720572 -0.247881008 QLLGHMEDLEGDAQSVLDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QLLGHMEDLEGDAQSVLDAR 20 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ;; 217.82 1.03E-24 90122000 98320 83347 80245 110835 106994 88547 112151 97649 100383 FALSE TRUE 93672.60845 91840.15406 83924.31262 99693.65523 125653.7197 85480.59519 95040.30516 89098.33589 115949.883 0.807871522 0.792067674 0.723798166 0.859799533 1.083689923 0.737220194 0.819667107 0.768421094 1 16.82314184 -2.569823223 2.214175189 4.252103197 0.821995483 0.232493375 0.100395601 4596551.018 385367.1428 75277260.92 0.025375794 0.002692631 2.569823223 -3.430107715 QLLHSCTVIATNILLVDEIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 292.64 9.10E-55 922650900 661599.9 548216.2 556489 679709.4 738310.9 604718.5 801642.1 696061.4 721518.7 FALSE TRUE 630327.3839 604080.0541 582004.5711 611383.7197 867072.0872 583776.9467 679336.8745 635110.5738 833408.135 0.756324971 0.724831003 0.698342801 0.733594615 1.040393117 0.700469461 0.815131082 0.762064284 1 19.66866366 -4.999999984 0.153792736 1.802286775 0.709246541 0.344653652 0.097874927 149.0555931 1.34459381 36.61894811 0.434577051 1.00E-05 4.999999984 -1.093040234 QLLLTADDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QLLLTADDR 9 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;; 223.08 8.36E-07 2000090000 5390840 4055120 3072620 4650620 4719680 3746770 4637890 4616230 4483060 FALSE TRUE 5136025.677 4468341.338 3213502.666 4183130.842 5542790.698 3617018.415 3930294.7 4212008.429 5178270.049 0.991841991 0.862902339 0.620574562 0.807824004 1.070394291 0.698499379 0.758997631 0.81340069 1 22.30403877 4.262256368 3.012649567 0.809460406 0.973293204 0.121978248 0.131879243 0.425634424 7.756774188 0.031967519 0.100108054 18291.79678 -4.262256368 0.163832798 QLLLTADDRVNPCIGGVILFHETLYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLLLTADDRVNPCIGGVILFHETLYQK 27 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 254.11 4.81E-53 3996080000 4745290 1886790 3612580 4023100 4598200 3791730 6284190 5133750 5559530 FALSE TRUE 4520989.546 2079056.046 3778220.366 3618690.345 5400124.624 3660421.439 5325421.398 4684211.634 6421673.518 0.70402046 0.323756111 0.588354477 0.56351204 0.840921702 0.570010517 0.829288718 0.729437836 1 22.61451789 1.57594079 0.414639732 0.998535938 0.495604522 0.51711477 0.129897328 0.743165709 0.360854904 0.146068356 0.110396091 37.66524442 -1.57594079 -0.502931416 QLLNCLHVVTLYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLLNCLHVVTLYNR 14 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 88.507 0.0065184 116060000 148390 82482 103020 115820 123060 120170 149760 143710 152220 FALSE TRUE 141375.8988 90887.00957 107743.5689 104177.5536 144521.625 116008.4828 126911.3615 131125.9905 175825.5002 0.804069368 0.516915973 0.612786932 0.592505373 0.821960551 0.659793276 0.721802932 0.745773454 1 17.4237848 0.170932172 0.461264191 1.034396497 0.642579147 0.572216451 0.089664859 2.363795727 0.727687876 0.244651254 0.049139891 1.482286565 -0.170932172 -0.391817351 QLLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QLLSER 6 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 ;;;; 117.93 0.051873 920227000 851913 753019 967440 805278 1169300 905697 1105340 940924 1300430 FALSE TRUE 811644.7608 829752.4922 1011798.081 724329.9255 1373225.55 874332.4858 936700.082 858531.7064 1502094.043 0.540342174 0.552397166 0.673591701 0.482213433 0.91420744 0.58207573 0.623596163 0.571556562 1 20.51854371 -5 0.245415056 3.257007699 0.575615499 0.506247329 0.117843465 139.6433888 1.388131087 158.0223464 0.16280022 1.00E-05 5 -2.681392199 QLLTLS(ph)SELSQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLT(0.013)LS(0.932)S(0.055)ELSQAR;QLLTLS(0.953)S(0.047)ELSQAR 163.91 3.98E-05 161134000 298780 232230 239490 280190 293760 249830 296110 288280 273360 TRUE FALSE 284657.2615 255894.501 250470.8534 252024.7689 344991.651 241178.3245 250932.9811 263036.6749 315751.2727 0.901523719 0.810430624 0.793253662 0.79817499 1.092605734 0.76382376 0.794717244 0.833050245 1 18.26842902 -1.379939965 2.899874782 1.002466535 0.844823398 0.202805208 0.094186318 25425249.38 30504478.28 526904.4776 0.022609781 0.041692701 1.379939965 -0.157643136 QLLTLSSELS(ph)QAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLTLS(0.009)S(0.005)ELS(0.986)QAR 129.38 0.00016193 17835000 29627 22468 23807 34877 27772 25888 28454 27367 31211 TRUE FALSE 28226.59043 24757.51474 24898.5745 31371.0977 32615.42801 24991.49207 24112.81971 24970.6004 36051.04248 0.782961837 0.686735058 0.690647837 0.870185591 0.904701384 0.693225226 0.668852218 0.692645723 1 15.13775336 -2.176026053 2.429040159 1.686103504 0.743708241 0.481217092 0.081837814 5799512.68 1770574.437 21797647.26 0.020840885 0.006667668 2.176026053 -0.942395263 QLMEQDASSS(ph)PSAQVIGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLMEQDASSSPSAQVIGLK 19 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 QLMEQDASS(0.231)S(0.762)PS(0.007)AQVIGLK 209.23 4.46E-25 0 71520 70916 69892 79974 64363 73141 83912 76094 77739 TRUE FALSE 68139.39134 78142.42102 73096.61733 71934.86158 75587.88682 70608.10883 71109.68325 69430.80596 89794.36708 0.758838149 0.87023745 0.814044574 0.801106616 0.841788737 0.78633116 0.791916972 0.773220061 1 16.45433733 -2.140068187 2.440154067 1.423709227 0.807140802 0.782454875 0.032342456 2741281.657 474489.1423 6480533.794 0.007591076 0.007243222 2.140068187 -0.616568425 QLNENKQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QLNENKQER 9 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;;;;; 181.53 4.32E-05 2404470000 2622903 1952231 2243056 2551551 2260481 2517593 3115900 2781636 2697413 FALSE TRUE 2498923.573 2151165.558 2345902.336 2295064.246 2654708.171 2430408.123 2640512.228 2538061.205 3115714.032 0.80203881 0.690424582 0.752926075 0.736609401 0.852038455 0.780048521 0.847482215 0.814600178 1 21.57113139 0.340472676 0.326294331 1.04349043 0.731860709 0.758094404 0.041207126 1.592380291 0.313921197 0.149266352 0.042416655 2.190144029 -0.340472676 -0.311629721 QLNVNAKPFVPNVHAAEFVPSFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLNVNAKPFVPNVHAAEFVPSFLR 24 1 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 187.62 1.11E-17 797120000 1919610 1214090 1622870 1741470 1771500 1748670 2219100 2114820 2114100 FALSE TRUE 1828873.84 1337807.151 1697280.195 1566414.127 2080449.039 1688113.119 1880535.538 1929635.149 2441943.831 0.748941813 0.547845177 0.695052922 0.641461981 0.85196433 0.691298915 0.770097786 0.79020456 1 21.21959859 0.361537902 0.304589223 1.067148101 0.633137522 0.642298009 0.072980995 2.215151346 0.397174277 0.291570972 0.087864367 2.298994339 -0.361537902 -0.434010578 QLPAHDQDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QLPAHDQDPSK 11 0 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;; 154.36 3.20E-05 1756270000 1501950 1295530 1196000 1544140 1160710 1407310 1565490 1561280 1094480 FALSE TRUE 1430955.8 1427545.98 1250837.783 1388920.114 1363137.457 1358574.502 1326645.748 1424566.046 1264206.369 1.131900484 1.129203282 0.989425314 1.098649831 1.078255489 1.074646146 1.04939018 1.126846124 1 20.26980056 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 QLPALDGSLMGPES(1)PPAQEEEAPVSPHK;QLPALDGSLMGPES(1)PPAQEEEAPVSPHK 261.25 6.24E-54 174046000 255200 241090 185955 279910 178990 226640 255910 248550 160884 TRUE FALSE 243137.2018 265657.3451 194481.2207 251772.915 210205.7993 218791.4 216866.2294 226785.6444 185833.069 1.308363485 1.429548285 1.046537205 1.354833756 1.131153892 1.177354499 1.166994822 1.220372916 1 17.50364773 8 0.078974075 0.817449002 2.288229952 0.39868311 0.102932692 164.8521654 0.950163675 2.707935092 26.50115677 100000000 -8 1.47078095 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHKKPAPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLPALDGSLMGPESPPAQEEEAPVSPHKKPAPQKR 35 3 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 QLPALDGS(0.001)LMGPES(0.874)PPAQEEEAPVS(0.125)PHKKPAPQKR 45.407 0.067238 84760000 74968 39762 67987 60238 61855 70447 99454 78758 68818 TRUE FALSE 71424.41121 43813.79301 71104.2712 54182.7618 72642.49242 68007.40273 84280.4657 71861.532 79489.94397 0.898533923 0.551186613 0.894506495 0.681630394 0.913857638 0.855547247 1.060265758 0.904032994 1 16.27848474 2.386646722 1.403583566 0.988081769 0.742305669 0.408129616 0.11306237 0.349961667 1.384690936 0.055810025 0.037949603 243.582858 -2.386646722 -0.2457761 QLPDKWQHDLFDSGFGGGAGVETGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLPDKWQHDLFDSGFGGGAGVETGGK 26 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 277.59 6.53E-61 932560000 1985930 1680960 1730970 2033370 1487740 2078900 2235100 2279700 1400900 FALSE TRUE 1892059.025 1852251.735 1810336.687 1828971.784 1747201.385 2006907.172 1894094.445 2080077.383 1618144.417 1.169276985 1.144676406 1.118773249 1.130289587 1.079756149 1.240252199 1.170534857 1.28547079 1 20.62590894 2.237076071 24.99996425 1.188231189 1.134089238 0.064997495 0.076345156 84.57769344 1424261.236 0.02437125 0.018965537 172.6140217 -2.237076071 -0.054141951 QLPFRGDDGIFDDNFIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLPFRGDDGIFDDNFIEER 19 1 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ; 105.56 0.000302 50383000 53952 33210 50724 45658 73494 47360 71227 68029 86896 FALSE TRUE 51401.79588 36594.13676 53049.74557 41068.3711 86311.33033 45719.91132 60360.01298 62072.02012 100371.3879 0.512116022 0.364587334 0.528534543 0.409164125 0.859919666 0.455507414 0.601366727 0.618423451 1 16.61498854 -4.999999998 0.138744074 2.663188398 0.351193101 0.592632813 0.12643286 88.62309626 0.756186101 40.51447399 0.726613697 1.00E-05 4.999999998 -2.311995297 QLPS(ph)PEPCEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QLPSPEPCEIQK 12 0 A0A590UK32;A0A590UJW2;A0A590UJD8;Q5VVJ2;Q5VVJ2-2 A0A590UK32 MYSM1 Histone H2A deubiquitinase MYSM1 1 QLPS(1)PEPCEIQK;QLPS(1)PEPCEIQK;QLPS(1)PEPCEIQK;QLPS(1)PEPCEIQK;QLPS(1)PEPCEIQK 178.23 2.33E-05 614460000 1045221 817031 915853 1085238 801099 970969 1177962 1067582 991962 TRUE FALSE 995815.4748 900287.3878 957845.766 976147.8144 940810.412 937344.1001 998242.2621 974098.8605 1145790.401 0.869107888 0.785734797 0.835969446 0.851942741 0.82110167 0.818076412 0.87122589 0.850154496 1 20.12791173 0.00914718 0.608108483 1.01013898 0.828125347 0.81840551 0.024266546 1.661241644 0.706930571 0.062995948 0.009361246 1.021285532 -0.00914718 -0.182013633 QLPTAAPDKTEVTGDHIPTPQDLPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLPTAAPDKTEVTGDHIPTPQDLPQR 26 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 150.94 7.65E-08 114890000 225550 187660 184070 218230 160420 207210 237330 211840 167080 FALSE TRUE 214888.6985 206782.7674 192509.7916 196293.1058 188397.1972 200034.2657 201120.9496 193290.1666 192989.9131 1.11347114 1.071469301 0.997512194 1.017115883 0.976202301 1.036501144 1.042131925 1.001555799 1 17.55816592 3.952392229 2.884875322 1.014115054 1.102286179 0.750374966 0.020177948 0.125275789 2.077999979 0.005584295 0.012297123 8961.737711 -3.952392229 0.088171125 QLQDIATLADQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLQDIATLADQRR 13 1 O95373 O95373 IPO7 Importin-7 0 ; 244.44 7.78E-17 441880000 254060 147606 252256 215926 313110 237301 332040 261390 396070 FALSE TRUE 242051.0873 162647.2192 263822.1871 194220.7082 367716.2849 229083.2069 281381.1997 238501.3059 457490.5128 0.529084387 0.35552042 0.576672477 0.424534942 0.80376811 0.500738705 0.615053628 0.521325141 1 18.8033823 -4.999999998 0.16648348 2.800929134 0.413741074 0.612819813 0.116100167 80.68775735 0.754617022 47.9399886 0.402715345 1.00E-05 4.999999998 -2.38718806 QLQDKLNES(ph)DEQHQENEGTNQLVMGIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLQDKLNESDEQHQENEGTNQLVMGIQK 28 1 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 QLQDKLNES(0.994)DEQHQENEGT(0.006)NQLVMGIQK 86.324 0.002218 48715000 31534 26550 30345 33375 22370 31180 34018 34702 23915 TRUE FALSE 30043.45031 29255.47518 31736.34827 30020.08159 26271.32092 30100.22878 28827.92932 31663.30891 27623.61606 1.087600199 1.059074783 1.148884643 1.08675423 0.951045687 1.089655631 1.043597234 1.146240552 1 14.75361457 2.966110747 24.99930979 1.048644692 1.092171456 0.16407647 0.055233715 1248.719297 921150.338 0.015775496 0.016741405 924.9340058 -2.966110747 0.043526764 QLQEERPELSESELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLQEERPELSESELTR 16 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 160.97 7.84E-09 88585000 57801 48603 52753 69937 64644 64405 72579 57897 82463 FALSE TRUE 55068.86128 53555.70096 55171.77723 62906.79989 75917.89313 62174.6387 61505.74055 52827.23175 95250.94088 0.578145064 0.562259023 0.579225535 0.66043232 0.797030375 0.652745665 0.645723181 0.554611128 1 16.53944572 -5 0.250296424 3.237429608 0.592945096 0.71051862 0.073425343 104.0849709 1.031158063 119.4002277 0.108332898 1.00E-05 5 -2.644484512 QLQGPEKEPPKPEQVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLQGPEKEPPKPEQVESR 18 2 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 105.99 0.00025986 940040000 631180 491820 522620 645520 408430 627890 633290 659870 428010 FALSE TRUE 601345.3723 541937.0172 546582.6439 580631.1032 479660.0627 606146.0119 536669.9793 602088.2846 494383.6048 1.216353792 1.096187276 1.105584082 1.174454609 0.970218385 1.226064145 1.085533529 1.217856496 1 18.91527137 -2.408916387 2.139475861 0.000172606 1.133367043 0.229481819 0.078433252 3292693.415 529352.1949 15744419.81 0.017162627 0.003900171 2.408916387 1.133194437 QLQQKQDDVLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLQQKQDDVLNK 12 1 A0A0C4DH05;Q5JPF3-2;Q5JPF3 A0A0C4DH05 ANKRD36C Ankyrin repeat domain-containing protein 36C 0 57.019 0.069804 31289000 242580 348690 206940 239980 101040 232630 172060 219810 56784 FALSE TRUE 231113.7241 384221.9074 216428.4037 215856.7545 118661.344 224573.9648 145809.0869 200562.2711 65589.77271 3.52362441 5.857954549 3.299727911 3.291012387 1.809144004 3.423917411 2.223046077 3.057828421 1 16.00118326 3.380953307 2.413934332 2.502017292 4.675356366 0.492000183 0.913841199 0.205028477 2.422227043 0.244262947 0.360125473 2404.104311 -3.380953307 2.173339074 QLQTFFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 95.358 0.0097068 162000000 399660 201900 259000 305280 401950 304470 512680 344890 479560 FALSE TRUE 380768.8638 222473.8395 270875.4062 274592.6744 472049.9527 293926.1276 434461.25 314689.6032 553927.7155 0.687398108 0.401629731 0.489008581 0.495719327 0.852186918 0.530621811 0.78432842 0.5681059 1 19.0793382 -0.11955334 0.271521323 1.144904409 0.501039346 0.477699233 0.135205896 5.664084242 0.613812874 1.022383094 0.196200477 0.759358153 0.11955334 -0.643865064 QLRDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLRDELR 7 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 ; 126.28 0.0036185 199840000 355100 294269 266341 329061 325090 301814 376600 327170 359830 FALSE TRUE 338315.1267 324255.3457 278552.9983 295983.1631 381785.5931 291362.1055 319142.7533 298521.2604 415630.5986 0.813980318 0.780152729 0.670193675 0.712130349 0.918569505 0.701012164 0.76785192 0.718236967 1 18.66494234 -1.693810258 2.858041206 1.03152069 0.763523424 0.535775103 0.070071921 23496613 21161019.91 5343524.246 0.016551866 0.020239032 1.693810258 -0.267997266 QLS(ph)EEQPSGNGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QLSEEQPSGNGVK 13 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 QLS(1)EEQPSGNGVK;QLS(0.999)EEQPS(0.001)GNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK 260.14 5.56E-24 1481350000 2715350 2292630 2310350 2885970 1891660 2636170 2888910 2678100 2103570 TRUE FALSE 2587000.787 2526251.604 2416281.833 2595866.813 2221564.905 2544878.772 2448153.721 2443591.366 2429780.892 1.06470538 1.039703461 0.994444331 1.068354279 0.914306682 1.047369654 1.007561517 1.005683835 1 21.21239479 4.07948465 1.082204876 1.00487108 1.069980231 0.202575382 0.039822824 1.048324554 1.933609317 0.011645303 0.060797773 12008.3863 -4.07948465 0.06510915 QLS(ph)ESESSLEMDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.764)ES(0.235)ESS(0.001)LEMDDER;QLS(0.988)ES(0.012)ESSLEMDDER 193.71 3.20E-07 662240000 545870 577930 492910 615410 518040 547550 499020 445510 443300 TRUE FALSE 520067.8069 636821.7241 515510.4111 553547.8176 608386.012 528588.2062 422885.3339 406498.7826 512044.6999 1.015668763 1.243683851 1.006768376 1.0810537 1.188150199 1.032308715 0.825875815 0.793873626 1 18.96591023 1.886391303 4.00219169 0.859093643 1.111743139 0.589574313 0.088459801 0.141391935 3.662178727 0.039962118 0.022485207 76.98237459 -1.886391303 0.252649496 QLS(ph)ESESSLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.783)ES(0.209)ES(0.007)S(0.001)LEMDDERYFNEMSAQGLRPR;QLS(0.73)ES(0.208)ES(0.034)S(0.028)LEMDDERYFNEMSAQGLRPR;QLS(0.994)ES(0.003)ES(0.001)S(0.002)LEMDDERYFNEMSAQGLRPR;QLS(0.864)ES(0.133)ES(0.001)S(0.001)LEMDDERYFNEMSAQGLRPR;QLS(0.599)ES(0.398)ES(0.001)S(0.002)LEMDDERYFNEMSAQGLRPR;QLS(0.983)ES(0.012)ES(0.003)S(0.003)LEMDDERYFNEMSAQGLRPR;QLS(0.688)ES(0.28)ES(0.024)S(0.007)LEMDDERYFNEMSAQGLRPR 256.03 7.96E-54 976470000 124268.1 112290.9 125780.7 118429.7 125735.1 115972.6 144651.4 119253.4 153173.1 TRUE FALSE 118394.1932 123733.4704 131547.8695 106524.9216 147663.2616 111956.4398 122582.1722 108810.9401 176926.402 0.669171994 0.69934995 0.743517463 0.602086067 0.83460275 0.632785376 0.692842735 0.615006799 1 17.43278983 -1.120171488 4.415730944 1.000040657 0.687943734 0.681846861 0.067361023 8157973.652 2069494.79 3201.977828 0.013612473 0.07582781 1.120171488 -0.312096924 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_SK-BR-3_Trastuzumab_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(0.991)LEGS(0.009)GLGVEDLKDNTPSGK;QLS(1)LEGSGLGVEDLKDNTPSGK;QLS(0.999)LEGS(0.001)GLGVEDLKDNTPSGK 238.59 8.90E-31 341154000 607320 522450 569770 740450 382750 725260 713930 726900 436110 TRUE FALSE 578613.1872 575688.249 595894.5181 666018.5592 449501.4788 700144.0643 605006.8663 663248.7825 503739.7115 1.148635246 1.142828798 1.182941318 1.322148213 0.892328853 1.389892535 1.201030716 1.316649784 1 18.94231894 QLS(ph)LGQGSYTVVQPGDSLEQG ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSLGQGSYTVVQPGDSLEQG 21 0 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 QLS(0.967)LGQGS(0.025)Y(0.003)T(0.004)VVQPGDSLEQG;QLS(0.966)LGQGS(0.033)YTVVQPGDSLEQG 108.71 0.00032843 64968000 93275 81899 85150 112674 102692 113996 133086 99302 144547 TRUE FALSE 88866.0756 90244.60121 89054.21172 101347.7955 120601.4523 110048.2899 112781.2864 90606.59045 166962.6105 0.532251355 0.540507847 0.53337817 0.607008929 0.722326106 0.659119366 0.675488279 0.542675933 1 17.34916554 -5 0.157753608 2.459029783 0.48849769 0.793135984 0.064523343 56.92274166 0.519820811 26.04133815 0.27738124 1.00E-05 5 -1.970532093 QLS(ph)LPLTQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 QLS(0.98)LPLT(0.02)QSK;QLS(0.989)LPLT(0.011)QSK;QLS(0.998)LPLT(0.002)QSK;QLS(0.988)LPLT(0.012)QSK;QLS(0.814)LPLT(0.186)QSK 175.21 3.01E-06 1183700000 3490740 2704620 2647960 3572460 3122210 3320050 3974840 3195450 3256660 TRUE FALSE 3325739.638 2980223.853 2769371.585 3213349.534 3666722.435 3205075.836 3368405.155 2915639.458 3761686.2 0.884108738 0.792257433 0.73620484 0.854231151 0.974755001 0.852031686 0.895450863 0.775088432 1 21.84294807 3.002473367 24.99159244 0.891881942 0.810821169 0.27007769 0.070775262 111.9258339 1130903.468 0.019261921 0.022892295 1005.711387 -3.002473367 -0.081060773 QLS(ph)MTLR ddPTM_SK-BR-3_Trastuzumab_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(0.99)MT(0.01)LR 121.6 0.0046385 50705000 89274 73245 79431 98880 99181 74527 97571 81679 95485 TRUE FALSE 85054.19494 80708.74877 83072.98992 88940.39454 116478.135 71946.1113 82684.75194 74526.75375 110292.3261 0.77117056 0.731771208 0.753207343 0.806406009 1.056085578 0.652322005 0.749687261 0.67572021 1 16.75097289 -2.311095833 2.18185039 2.087782381 0.772087927 0.2948331 0.109517919 4258632.726 671606.0305 22769761.2 0.026582892 0.004885445 2.311095833 -1.315694454 QLS(ph)PQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QLSPQSK 7 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 QLS(0.977)PQS(0.023)K;QLS(0.993)PQS(0.007)K;QLS(0.701)PQS(0.299)K;QLS(0.944)PQS(0.056)K;QLS(0.959)PQS(0.041)K;QLS(1)PQSK;QLS(0.999)PQS(0.001)K;QLS(0.976)PQS(0.024)K 131.09 0.0036715 5367110000 13601460 11711750 11939840 14848510 9709710 13258330 14722720 14111270 11098930 TRUE FALSE 12958545.94 12905190.64 12487293.47 13355909.56 11403080.35 12799190.71 12476498.66 12875612.39 12820095.38 1.010799496 1.006637647 0.974040606 1.041794867 0.889469229 0.998369383 0.973198583 1.004330468 1 23.61190366 QLS(ph)SGVSEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.499)S(0.499)GVS(0.003)EIR;QLS(0.966)S(0.025)GVS(0.009)EIR;QLS(0.79)S(0.199)GVS(0.011)EIR;QLS(0.961)S(0.038)GVS(0.001)EIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.965)S(0.035)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.499)S(0.499)GVS(0.003)EIR;QLS(0.967)S(0.033)GVSEIR;QLS(0.5)S(0.5)GVS(0.001)EIR;QLS(0.498)S(0.498)GVS(0.005)EIR;QLS(0.491)S(0.491)GVS(0.017)EIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.595)S(0.401)GVS(0.004)EIR;QLS(0.498)S(0.498)GVS(0.004)EIR;QLS(0.499)S(0.499)GVS(0.002)EIR 218.07 7.29E-09 2.99729E+11 29532844 20251349 22960783 28136883 28533304 25485800 29390302 22817294 25487324 TRUE FALSE 28136884.99 22314984.49 24013557.61 25308510.06 33509503.18 24603220.36 24906271.64 20819290.78 29439768.03 0.955744113 0.757987782 0.815684335 0.859670838 1.138239376 0.835713798 0.846007741 0.707182569 1 24.81126297 -1.780199781 4.280894069 1.015541844 0.86434244 0.117155315 0.116871026 0.018104038 0.000929542 0.118174207 0.025571378 0.016588237 1.780199781 -0.151199404 QLSDAISIIGREDFPQKWPDLLTEMVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLSDAISIIGREDFPQKWPDLLTEMVNR 28 2 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 132.12 1.11E-05 94958000 55184 34275 62783 49160 70282 64496 101030 74073 94342 FALSE TRUE 52575.56168 37767.66147 65661.66265 44218.3434 82539.15855 62262.48735 85616.01796 67586.77543 108972.0755 0.482468205 0.346581097 0.602554942 0.40577683 0.757434032 0.571361856 0.785669334 0.620221053 1 16.73359896 1.512929883 0.229893278 1.096274329 0.293504601 0.684442092 0.108047715 1.075561091 0.263449514 0.34134104 0.327064687 32.57840985 -1.512929883 -0.802769728 QLSES(ph)ESSLEMDDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.192)ES(0.808)ESSLEMDDER;QLS(0.036)ES(0.964)ESSLEMDDER 377.88 5.96E-98 654590000 809000 862640 690280 928830 770360 820800 752140 686920 663680 TRUE FALSE 770760.1733 950543.9967 721930.0208 835462.2437 904710.5401 792375.4902 637387.229 626769.6432 766600.1048 1.005426647 1.239947648 0.941729614 1.08982798 1.180159687 1.033622987 0.831446833 0.817596605 1 19.54811467 1.875207873 4.352997814 0.869659365 1.09762802 0.496227968 0.095274796 0.16570529 4.801612332 0.042544046 0.024211763 75.02532278 -1.875207873 0.227968655 QLSES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.104)ES(0.667)ES(0.114)S(0.114)LEMDDERYFNEMSAQGLRPR 46.31 0.092852 55391000 21527 15507 16949 16749 22141 19102 24536 18586 22576 TRUE FALSE 20509.46137 17087.18093 17726.12841 15065.3587 26002.38339 18440.49295 20792.58257 16958.51131 26076.97078 0.78649708 0.655259427 0.679761793 0.577726563 0.997139722 0.707156253 0.797354215 0.650325203 1 14.67048867 2.768250187 24.99993504 0.80611377 0.684237177 0.278369827 0.120592779 1078.220873 907908.1948 0.033688308 0.035727624 586.4759226 -2.768250187 -0.121876593 QLSES(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSESFK 7 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 QLS(0.009)ES(0.991)FK;QLS(0.011)ES(0.989)FK 107.55 0.0078161 388260000 1162640 1408320 1137080 1540310 737530 1452360 1348980 1519810 922490 TRUE FALSE 1107684.311 1551829.409 1189216.243 1385475.112 866154.9985 1402064.409 1143168.325 1386727.379 1065545.038 1.039547154 1.456371485 1.116063799 1.300250166 0.812875071 1.315819003 1.072848434 1.301425402 1 20.02316014 -4.999999999 0.143423821 0.38747516 1.244434447 0.063213788 0.183031156 341.6610386 2.970924023 60.29961124 0.950765806 1.00E-05 4.999999999 0.856959287 QLSESESSLEMDDERYFNEMS(ph)AQGLRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.001)ES(0.011)ES(0.044)S(0.26)LEMDDERYFNEMS(0.684)AQGLRPR 150.77 4.33E-08 78128000 30967 21856 29799 28134 31846 24690 29143 23649 39226 TRUE FALSE 29503.25128 24083.15125 31165.31363 25305.91687 37399.93232 23834.97911 24696.7001 21578.16819 45308.96774 0.651156995 0.531531669 0.687839851 0.558518945 0.825442163 0.52605434 0.545073113 0.476244975 1 15.467509 -1.130963319 5.010913785 1.000017767 0.597946122 0.608403711 0.10077878 1.86E-05 3.23E-06 0.090862334 0.021415512 0.073966775 1.130963319 -0.402071645 QLSESESSLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 266.31 2.41E-54 142112000 49060 33936 40614 45292 53663 36844 42550 43836 62921 FALSE TRUE 46741.03103 37394.11698 42476.19207 40739.16211 63021.81021 35568.08304 36058.21602 39997.48745 72678.46732 0.643120758 0.514514386 0.584439844 0.560539643 0.8671318 0.489389559 0.496133413 0.550334768 1 16.14924038 -1.328490767 5.542815581 1.000079372 0.581475732 0.584120307 0.10906846 0.00010332 1.25E-05 0.101992887 0.024035421 0.046936341 1.328490767 -0.41860364 QLSILVHPDKNQDDADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLSILVHPDKNQDDADR 17 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;;; 228.01 9.43E-16 1258580000 2990980 2205100 2492740 2961610 2232440 2741170 3113420 3100490 2371380 FALSE TRUE 2849602.303 2429802.197 2607034.595 2663903.336 2621776.829 2646242.596 2638410.597 2828994.659 2739121.499 1.040334393 0.887073537 0.951777639 0.972539311 0.957159743 0.966091718 0.963232408 1.032810943 1 21.38528183 1.251902157 23.33333089 1.016405445 0.960374306 0.262134221 0.037383863 115.3516687 201746.8037 0.024356402 0.008755419 17.86085138 -1.251902157 -0.056031139 QLSMT(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLSMTLR 7 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 QLS(0.358)MT(0.642)LR;QLS(0.052)MT(0.948)LR 108.74 0.08031 100166000 184037 140366 151506 193340 181157 155974 193072 159934 183347 TRUE FALSE 175337.9357 154669.455 158452.7 173905.0959 212750.7234 150572.5813 163615.3204 145929.3311 211779.5164 0.827926793 0.730332459 0.748196533 0.821161078 1.004585935 0.710987464 0.772573869 0.689062538 1 17.69220353 -1.070899862 4.275587531 1.000022685 0.787033066 0.36149169 0.088493396 11424735.51 2861536.377 2413.317382 0.019910214 0.08493763 1.070899862 -0.212989619 QLSSGVSEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 185.27 3.41E-06 2009210000 1852120 1330770 1336940 1757570 1661420 1607840 1897690 1719340 1725470 FALSE TRUE 1764573.958 1466376.976 1398240.021 1580895.724 1951171.122 1552160.098 1608162.537 1568785.475 1993047.075 0.885364917 0.735746282 0.701558954 0.793205411 0.978988979 0.778787474 0.806886379 0.787129162 1 20.92654436 2.977359019 24.931224 0.850648376 0.777546455 0.196232307 0.087583094 1478.40778 1627956.993 0.025792809 0.027550607 949.2028178 -2.977359019 -0.073101921 QLT(ph)QPETHFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR 208.39 7.26E-08 7638520000 5690020 4826660 4236570 8203930 7236550 6746420 6631960 4200410 4415040 TRUE FALSE 5421064.031 5318502.141 4430820.925 7379255.37 8498602.029 6512789.784 5620132.698 3832599.833 5099701.854 1.063015875 1.042904525 0.868839209 1.446997409 1.666489978 1.277092263 1.102051229 0.751534098 1 22.28198147 1.420885525 4.953775593 0.880192625 1.203616704 0.280481485 0.228112042 0.309188096 13.1304985 0.169439903 0.062507392 26.35636569 -1.420885525 0.323424079 QLT(ph)QPETHFGREPAAAISRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QLTQPETHFGREPAAAISRPR 21 2 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR 256.24 9.18E-35 4577960000 1216736 551760 1113557 1260886 2127140 1507333 2164710 964129 1640920 TRUE FALSE 1159223.301 607984.9713 1164614.69 1134139.344 2498112.543 1455133.68 1834443.732 879704.7536 1895385.493 0.611602919 0.320771143 0.614447401 0.598368695 1.317997079 0.767724395 0.9678473 0.464129728 1 20.85405987 2.979039595 23.87159154 0.902033351 0.502424863 0.401182533 0.224652871 383.0730138 436278.5873 0.062945033 0.067501424 952.8830345 -2.979039595 -0.399608487 QLTACPELPHNVQEILGLAPPAEPHS(ph)PS(ph)PTASPLPLSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLTACPELPHNVQEILGLAPPAEPHSPSPTASPLPLSPTR 40 0 Q9HA65-2;Q9HA65 Q9HA65-2 TBC1D17 TBC1 domain family member 17 2 QLTACPELPHNVQEILGLAPPAEPHS(0.855)PS(0.822)PT(0.259)AS(0.062)PLPLS(0.001)PT(0.001)R 80.531 0.00046857 14998000 7945.5 8228.2 8058.6 7770 7798.8 8453.1 8686.3 8451.8 8674.6 TRUE FALSE 7569.931961 9066.662935 8428.094781 6988.944838 9158.908251 8160.367027 7361.0454 7711.715586 10019.81266 0.755496357 0.904873498 0.84114295 0.697512526 0.914079789 0.814423114 0.734649005 0.769646683 1 13.29056791 1.993985598 24.93456503 0.797595353 0.826336949 0 0.095108796 1403.962419 5820568.281 0.033423901 0.023878067 98.62467789 -1.993985598 0.028741597 QLTEMLPSILNQLGADS(ph)LTSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLTEMLPSILNQLGADSLTSLRR 23 1 P20290-2;D6RDG3;H0Y9Y1;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 1 QLTEMLPSILNQLGADS(0.994)LT(0.006)SLRR;QLTEMLPSILNQLGADS(0.954)LT(0.045)S(0.001)LRR;QLTEMLPSILNQLGADS(0.96)LT(0.039)S(0.001)LRR;QLTEMLPSILNQLGADS(0.951)LT(0.039)S(0.01)LRR 265.15 3.21E-44 865694000 596986 417711 479761 504009 627710 533296 673030 606581 729630 TRUE FALSE 568767.6549 460276.2258 501758.5164 453345.0578 737182.4253 514827.8258 570346.9125 553465.552 842777.294 0.674873017 0.546142177 0.595363117 0.537917978 0.874706083 0.610870546 0.67674689 0.656716259 1 19.68479192 -5 0.216596595 2.800780253 0.593062632 0.599401804 0.09211248 98.78616469 0.987033807 77.37167831 0.169839185 1.00E-05 5 -2.20771762 QLTLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLTLRK 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 86.512 0.085772 399240000 544580 290120 429260 384520 535360 408640 659520 545070 729260 FALSE TRUE 518838.7827 319683.5578 448941.9956 345867.3191 628726.6145 394488.6943 558898.1111 497340.7812 842349.9163 0.615942107 0.379513966 0.53296378 0.410598152 0.746396008 0.468319266 0.663498744 0.590420645 1 19.68406013 -0.594341191 0.324082531 1.179334021 0.482243724 0.652781948 0.106160656 5.346052149 0.564810135 1.093340153 0.093404288 0.254483019 0.594341191 -0.697090297 QLTQPETHFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLTQPETHFGR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 158.42 2.99E-05 1626440000 1251710 1179440 1168710 1331200 1325940 1102040 1305290 1265190 1057550 FALSE TRUE 1192544.149 1299626.277 1222296.51 1197385.247 1557183.516 1063876.078 1106144.037 1154403.256 1221549.453 0.976255318 1.06391622 1.000611565 0.980218397 1.27476093 0.870923462 0.905525384 0.945031946 1 20.22028084 QLTSNTVQQHPS(ph)TPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;QLTSNTVQQHPS(0.591)T(0.409)PKR 99.86 0.0010584 69676000 77652 50690 71375 80132 79418 77286 93903 83138 93838 TRUE FALSE 73981.54385 55855.36863 74647.61435 72076.97912 93268.47406 74609.56644 79576.3727 75857.99598 108389.9178 0.68255005 0.515318858 0.688695184 0.664978631 0.860490311 0.688344156 0.734167664 0.699862105 1 16.72587104 -5 0.113671949 2.041618613 0.506024726 0.626812029 0.07799899 99.16954371 0.742768773 23.86579698 0.858813152 1.00E-05 5 -1.535593887 QLVAGNS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 104.24 0.0034527 242580000 977560 1027352 967159 1157500 641490 1159380 1171410 1209890 778729 TRUE FALSE 931352.6761 1132040.337 1011504.197 1041145.901 753365.6529 1119230.38 992689.8901 1103945.618 899490.3161 1.035422683 1.258535324 1.124530391 1.15748428 0.837547264 1.244293974 1.10361376 1.227301281 1 19.77874822 -2.47392686 1.893849391 7.63E-05 1.126602104 0.091092332 0.12236148 1634627.728 112789.4091 7018315.686 0.027879164 0.003357942 2.47392686 1.126525799 QLVALLEELSAEHYLPIFAHHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLVALLEELSAEHYLPIFAHHR 22 0 Q6UWE0;Q6UWE0-2;Q6UWE0-3 Q6UWE0 LRSAM1 E3 ubiquitin-protein ligase LRSAM1 0 ; 109.66 0.00013295 50737000 40589 43980 40592 50591 45575 46165 58929 50613 35457 FALSE TRUE 38670.43841 48461.612 42453.18335 45505.49656 53523.26557 44566.29447 49938.29874 46181.0574 40955.49047 0.944206454 1.183275098 1.036568794 1.111096364 1.306864231 1.088164101 1.21933099 1.127591365 1 15.32176925 4.629899874 2.473957386 1.14535433 0.922583095 0.300872687 0.088910491 0.43965779 4.010645683 0.020275514 0.187819276 42648.1183 -4.629899874 -0.222771235 QLVHELDEAEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QLVHELDEAEYR 12 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 215.51 4.13E-11 1494040000 2003040 2021180 1504130 2319880 1843110 1878840 1845150 1927260 1379230 FALSE TRUE 1908360.269 2227140.54 1573095.848 2086681.255 2164547.8 1813775.3 1563638.479 1758498.897 1593113.944 1.197880588 1.39797944 0.987434611 1.309812937 1.358689884 1.138509462 0.981498206 1.103812382 1 20.60341803 2.005083696 5.89145734 1.033353595 1.256512448 0.439986458 0.114504083 0.13690579 18.30815276 0.043917911 0.030094286 101.1774421 -2.005083696 0.223158853 QLVHFAWEHFRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QLVHFAWEHFRPR 13 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 176.91 1.03E-05 27399000 22479 15712 17210 22214 23311 19023 24617 22446 8489.4 FALSE TRUE 21416.46222 17313.07066 17999.09552 19981.00652 27376.43102 18364.22874 20861.22453 20480.50925 9805.892794 2.184040012 1.765578212 1.835538681 2.037652964 2.791834624 1.872774782 2.127417153 2.088592 1 13.25943327 -0.447277905 9.845407924 0.999989906 2.071328646 0.591548824 0.283806386 0 0 0.265673971 0.062619956 0.357044293 0.447277905 1.07133874 QLWWGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLWWGHR 7 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ; 124.12 0.0041769 748110000 1214930 828560 631940 740530 1242710 755850 1231660 1025320 930630 FALSE TRUE 1157502.667 912991.206 660915.0741 666090.5175 1459438.231 729674.725 1043747.646 935537.5452 1074947.347 1.076799407 0.849335745 0.614834834 0.619649436 1.357683457 0.678800433 0.9709756 0.870310111 1 20.03583457 QLYLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QLYLER 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;; 114.72 0.058261 543870000 454760 391489 379205 436180 499920 403772 520580 479820 547890 FALSE TRUE 433264.396 431382.1742 396591.9243 392334.3577 587105.8897 389789.2744 441155.9599 437804.4171 632853.983 0.684619846 0.681645665 0.626672084 0.619944518 0.927711456 0.615922922 0.697089647 0.69179373 1 19.27151314 -4.999999999 0.393450072 5.763276118 0.684783169 0.541758401 0.088740628 513.1832347 3.666435696 2095.589262 0.051991567 1.00E-05 4.999999999 -5.078492949 QLYQTLTDYDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 105.46 0.004717 75958000 129231 125796 98322 120122 118610 130654 121542 125529 134428 FALSE TRUE 123122.5067 138614.7554 102830.161 108047.1083 139295.5464 126129.4192 102998.5356 114537.0153 155274.4077 0.792934963 0.892708319 0.662247968 0.695846212 0.897092757 0.812300115 0.663332336 0.737642584 1 17.24446054 3.766631839 24.91990568 0.764427122 0.84282163 0.035638089 0.108753256 1638.518012 1454569.528 0.026120625 0.047079054 5842.945554 -3.766631839 0.078394508 QLYVLGHEAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QLYVLGHEAMK 11 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 105.65 0.0018488 490330000 966120 896170 845370 968510 733340 934040 1007910 1105380 705960 FALSE TRUE 920453.4223 987490.7419 884131.0507 871153.5348 861234.2638 901693.9606 854134.818 1008587.067 815436.6713 1.128785907 1.210996239 1.084242446 1.06832764 1.056163273 1.105780488 1.047456961 1.236867439 1 19.63721331 3.719449794 23.65458183 1.084550711 1.169891068 0.231922829 0.063791552 464.2340705 574609.9059 0.015256076 0.023684851 5241.430048 -3.719449794 0.085340357 QMEKDETVSDCSPHIANIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 QMEKDETVSDCSPHIANIGR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;;;;;; 257.5 1.92E-36 3803635000 3276035 2435161 2858010 3307568 2611750 3072822 3813795 3508221 3017183 FALSE TRUE 3121183.318 2683306.674 2989052.585 2975084.981 3067238.373 2966409.404 3231930.528 3201022.571 3485072.33 0.895586382 0.769942894 0.857673042 0.853665204 0.880107522 0.85117585 0.927363975 0.918495305 1 21.73275717 1.299892549 0.599801187 0.999920205 0.834211688 0.679052629 0.033978252 0.39179076 0.344510061 0.032241255 0.015444989 19.94768719 -1.299892549 -0.165708517 QMEQISQFLQAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QMEQISQFLQAAER 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 378.52 3.19E-97 416035000 463854 335366 353810 434149 478514 368676 581685 463446 590562 FALSE TRUE 441928.5407 369540.1767 370032.5385 390507.5177 561966.6901 355908.6577 492938.2699 422864.2114 682143.3388 0.647852901 0.541733908 0.542455694 0.572471349 0.823824933 0.521750543 0.722631508 0.619905212 1 19.3797154 -5 0.215737979 2.897673799 0.570209391 0.637248547 0.090317943 88.58456936 0.884863502 72.74466514 0.163349564 1.00E-05 5 -2.327464408 QMEVIS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QMEVISLR 8 0 C4P092;C4P0A0;C4P093;C4P0B0;C4P0B1;A0A087WYX6;Q9NRI5-7;Q9NRI5-6;Q9NRI5-9;Q9NRI5-3;Q9NRI5-8;Q9NRI5-5;Q9NRI5-2;Q9NRI5 C4P092 DISC1 Disrupted in schizophrenia 1 protein 1 QMEVIS(1)LR 81.972 0.083967 45805000 57015 54662 65941 61734 63257 66501 83715 46138 71004 TRUE FALSE 54320.01394 60232.11995 68964.46007 55528.38103 74289.00077 64198.0537 70942.73922 42097.91213 82014.93768 0.662318542 0.734404264 0.840876821 0.677052042 0.905798418 0.782760501 0.864997782 0.513295667 1 16.32359908 -2.564382034 2.395008347 6.473869132 0.756464571 0.324179669 0.113863742 5676858.545 1569628.019 162047801.1 0.026050371 0.002726578 2.564382034 -5.717404561 QMGFPLIYVEAEQVEDDRLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QMGFPLIYVEAEQVEDDRLLR 21 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;; 148.06 8.54E-08 57664000 35585 21553.3 33473.8 34408.8 44166 27450.2 47316 36437 54229 FALSE TRUE 33902.96757 23749.60577 35008.60684 30949.96205 51868.53642 26499.59269 40097.07518 33246.38312 62638.55636 0.541247588 0.379153147 0.558898686 0.494104013 0.828060853 0.42305561 0.640134089 0.530765475 1 15.93476334 -4.999999999 0.189038251 2.966821892 0.45488789 0.579524361 0.121283564 89.86387425 0.877669853 66.4949249 0.304014821 1.00E-05 4.999999999 -2.511934002 QMLDDFGPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QMLDDFGPHR 10 0 A0A1B0GVZ4;A0A494C085;P06132;A0A494BZY8;A0A494C0Q8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 90.653 0.010647 0 69683 49580 48470 55442 66867 54677 70393 72664 66319 FALSE TRUE 66389.22269 54632.25837 50692.39744 49868.86483 78528.58363 52783.52178 59653.25499 66301.15494 76603.41181 0.866661433 0.713183096 0.661751171 0.651000571 1.025131672 0.689049228 0.778728435 0.865511775 1 16.22512103 0.965161659 2.555355158 0.999248373 0.767270081 0.314623554 0.1106396 0.355046843 5.342672954 0.099367641 0.026719326 9.229149026 -0.965161659 -0.231978292 QMNPHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QMNPHIR 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;;; 170.72 0.00096426 1286853000 1281359 846977 957109 952292 1461980 1009169 1538130 1192709 1473849 FALSE TRUE 1220791.699 933284.9192 1000993.394 856565.7989 1716948.849 974221.2245 1303460.019 1088269.077 1702405.976 0.71709787 0.548215251 0.587987477 0.503150136 1.008542541 0.572261399 0.765657568 0.639253558 1 20.69914369 2.793026058 24.99998577 0.762761656 0.596454528 0.317115968 0.146781286 417.6894746 191721.1989 0.040374054 0.042823131 620.9062873 -2.793026058 -0.166307128 QMQVLHPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QMQVLHPAAR 10 0 P50991 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 150.08 2.22E-05 473460000 471650 328783 295531 330882 453850 324608 451600 393508 445443 FALSE TRUE 449356.0392 362286.3615 309081.3887 297621.1127 533001.2963 313366.7436 382700.1258 359050.3534 514520.0254 0.873349951 0.7041249 0.600717899 0.578444177 1.035919439 0.609046739 0.743800254 0.697835528 1 18.9728677 -1.343776074 3.661007987 1.001057717 0.732692876 0.274801348 0.137591877 50002564.03 85624594.42 576931.5158 0.030804416 0.045313116 1.343776074 -0.268364842 QMS(ph)VKGDGGITHSEEINGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QMSVKGDGGITHSEEINGK 19 1 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 QMS(1)VKGDGGITHSEEINGK;QMS(1)VKGDGGITHSEEINGK;QMS(0.992)VKGDGGIT(0.008)HSEEINGK;QMS(1)VKGDGGITHSEEINGK;QMS(1)VKGDGGITHSEEINGK;QMS(0.999)VKGDGGIT(0.001)HSEEINGK 225.84 2.07E-19 2664310000 1883620 1689310 2133540 2262350 1493340 2326110 2477540 1831490 1080469 TRUE FALSE 1794585.016 1861452.61 2231364.919 2034934.28 1753778.023 2245556.227 2099545.77 1671115.026 1248022.614 1.437942706 1.491521538 1.787920262 1.630526768 1.405245388 1.799291296 1.682297857 1.339010213 1 20.25121265 0.975129811 4.09259657 1.000992123 1.595252813 0.686530305 0.133404059 0.120565228 6.023278553 0.133996619 0.034242607 9.443431 -0.975129811 0.59426069 QMVEHGGFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QMVEHGGFYR 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 88.187 0.012366 147310000 143670 119430 122970 149620 143490 134200 144260 153120 142160 FALSE TRUE 136879.0038 131600.0528 128608.2961 134579.9133 168514.6106 129552.6204 122250.4875 139712.0011 164205.4467 0.833583822 0.801435369 0.783215774 0.819582517 1.026242515 0.788966645 0.744497152 0.850836582 1 17.32514246 -2.312239275 1.839210702 1.657782047 0.824730181 0.327811808 0.075554318 2435796.642 304521.238 6641158.893 0.019700301 0.0048726 2.312239275 -0.833051866 QMVEILHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QMVEILHK 8 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 93.551 0.010989 366920000 836960 737160 730140 856650 714200 849910 1017480 855960 780650 FALSE TRUE 797398.5595 812277.4421 763617.6412 770537.9145 838756.2539 820477.4036 862244.7387 781007.6047 901709.215 0.884318965 0.900819719 0.846855758 0.854530376 0.930184853 0.909913518 0.9562337 0.866141314 1 19.78230274 2.722529614 23.58213867 0.930159714 0.876529296 0.401626109 0.036637805 414.2478138 609370.885 0.010876387 0.010290241 527.8732008 -2.722529614 -0.053630418 QMVIDVLHPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 102.66 0.0028385 630380000 1545500 1146100 1227500 1563500 1147600 1467900 1712200 1612000 1313500 FALSE TRUE 1472447.278 1262888.893 1283782.089 1406334.01 1347741.077 1417066.255 1450972.443 1470844.734 1517190.872 0.970508922 0.832386298 0.846157272 0.926932818 0.888313463 0.934006579 0.956354583 0.969452665 1 20.53297117 1.736933798 1.015050586 0.993479807 0.888271046 0.500861767 0.038609891 0.429196257 0.825845908 0.03348024 0.013537111 54.56746749 -1.736933798 -0.105208761 QNEEFRPFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QNEEFRPFIR 10 1 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 0 ;;; 130.23 0.00025728 1270410000 1257840 1171300 1163090 1443600 1845820 1226590 1367290 1214960 1714310 FALSE TRUE 1198384.396 1290656.802 1216418.827 1298486.585 2167730.424 1184112.881 1158684.798 1108571.661 1980156.439 0.605196828 0.651795371 0.614304407 0.655749495 1.094726851 0.597989561 0.58514811 0.559840445 1 20.91718298 2.982347686 24.69449626 0.731172269 0.628107661 0.113410289 0.174525423 1835.134853 2567244.224 0.052167891 0.056448019 960.1690128 -2.982347686 -0.103064608 QNGDDPLLTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 94.66 0.019399 294580000 253120 241400 214700 239700 236330 222300 250740 237310 254000 FALSE TRUE 241155.5192 265998.9344 224544.2074 215604.9006 277545.8772 214601.6953 212485.0078 216529.8783 293389.0227 0.821965038 0.906642423 0.765346315 0.73487719 0.945999528 0.731457821 0.724243211 0.738029925 1 18.16245537 QNGSNDS(ph)DRYS(ph)DNEEDSKIELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 QNGS(0.453)NDS(0.547)DRY(0.302)S(0.698)DNEEDSKIELK 62.683 0.020302 94277000 109210 99721 114360 154120 67619 132110 138360 109650 73605 TRUE FALSE 104047.8597 109882.6833 119603.5191 138627.5648 79411.73219 127534.9976 117250.6408 100048.4647 85019.28748 1.22381477 1.29244418 1.40678101 1.630542538 0.934043728 1.500071353 1.379106369 1.176773738 1 16.37550255 0.994045849 4.034747101 1.00091892 1.333873679 0.274018015 0.181680596 0.235980202 10.87370567 0.15984757 0.040905918 9.863836147 -0.994045849 0.33295476 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 QNGS(0.002)NDS(0.008)DRY(0.018)S(0.972)DNEEDSKIELK;QNGSNDS(0.012)DRY(0.012)S(0.883)DNEEDS(0.092)KIELK;QNGS(0.003)NDS(0.003)DRY(0.001)S(0.989)DNEEDS(0.004)KIELK 105.17 0.0004155 455972000 357694 303818 341392 496830 279577 507510 463785 440466 250715 TRUE FALSE 340786.5135 334777.3996 357045.1609 446887.7045 328335.1403 489934.8014 393026.0803 401896.462 289594.6017 1.176770946 1.156020857 1.232913731 1.543149292 1.133775072 1.691795353 1.357159553 1.387789895 1 18.14367518 3.460486274 23.07081429 1.38256002 1.171074428 0.133663279 0.191657426 131.8231608 182822.0077 0.046560485 0.063068475 2887.262523 -3.460486274 -0.211485592 QNGSNDSDRYS(ph)DNEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QNGSNDSDRYSDNEEGK 17 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK 309.99 2.63E-58 1856650000 1669890 2076580 1402200 2151470 903150 1923830 1552950 1852310 826450 TRUE FALSE 1590957.609 2288185.863 1466492.257 1935200.148 1060659.074 1857207.285 1316018.956 1690111.917 954611.6451 1.666601929 2.396980882 1.536218696 2.027211964 1.111089603 1.94551082 1.37859093 1.770470668 1 19.86455441 -0.489475681 0.119986957 0.110084491 2.407034749 0.330225105 0.345269988 29.66116495 0.912592145 13.34653778 4.572106746 0.323984564 0.489475681 2.296950258 QNGSNDSDRYS(ph)DNEEGKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 QNGSNDSDRYSDNEEGKKK 19 3 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDS(0.001)DRYS(0.999)DNEEGKKK;QNGSNDS(0.005)DRYS(0.995)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDS(0.001)DRYS(0.999)DNEEGKKK;QNGSNDS(0.002)DRYS(0.998)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDS(0.002)DRYS(0.998)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK 215.79 2.84E-19 2394460000 1838637 1602460 1793912 1977480 776181 2299573 2153550 2325913 842620 TRUE FALSE 1751728.273 1765752.496 1876164.64 1778699.953 911546.7207 2219938.21 1824986.395 2122243.727 973289.2061 1.799802424 1.814211526 1.927653803 1.827514312 0.936563064 2.280861841 1.875071031 2.180486246 1 19.89250903 QNIVLPSDEKGELDLS(ph)LENLDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNIVLPSDEKGELDLSLENLDLSK 24 1 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 QNIVLPS(0.002)DEKGELDLS(0.989)LENLDLS(0.009)K 57.076 0.054442 53406000 85375 67054 62190 82235 55524 84527 89725 95684 59206 TRUE FALSE 81339.49295 73886.87883 65041.47301 73968.58156 65207.36802 81599.8088 76035.80334 87305.40171 68387.3641 1.189393597 1.080417118 0.951074425 1.081611823 0.953500239 1.193200087 1.111839948 1.276630601 1 16.06144216 2.200574439 24.99998271 1.151515128 1.064577704 0.183263454 0.096184889 302.2694883 198932.0047 0.034754026 0.025668046 158.6990911 -2.200574439 -0.086937424 QNLFQEAEEFLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QNLFQEAEEFLYR 13 0 A0A087X1Z3;Q9UL46 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;; 261.22 1.10E-23 737131000 468355 305927 348292 445078 432503 346421 508854 471197 497395 FALSE TRUE 446216.7873 337101.3091 364261.5327 400337.9138 507931.3863 334424.3539 431218.9766 429936.4927 574528.4763 0.776666094 0.586744301 0.634018239 0.696811264 0.884083918 0.582084906 0.750561538 0.7483293 1 19.13201888 -1.421730839 0.338348661 1.206085242 0.676467561 0.520878439 0.089779061 16.72016591 1.181174471 3.055385594 0.072328965 0.03786772 1.421730839 -0.529617681 QNLFQTGSNVS(ph)FSCGGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QNLFQTGSNVSFSCGGETR 19 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 QNLFQT(0.004)GS(0.119)NVS(0.87)FS(0.003)CGGET(0.004)R;QNLFQTGS(0.153)NVS(0.845)FS(0.001)CGGETR 140.2 3.57E-07 36447000 42036 33929 42188 54911 47599 44531 56496 51319 55378 TRUE FALSE 40049.04159 37386.40367 44122.36153 49391.24196 55900.25053 42988.8803 47876.49758 46825.2363 63965.73741 0.62610146 0.584475458 0.689781175 0.772151529 0.873909264 0.672061045 0.748470971 0.732036215 1 15.96501173 -5 0.056698174 2.087808713 0.210043745 0.656905125 0.070621947 273.4153483 1.137049595 42.79439358 7.864644693 1.00E-05 5 -1.877764968 QNLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNLNDR 6 0 K7EMD9 K7EMD9 KRT13 0 97.473 0.095458 100770000 93832 158190 256700 307210 62914 220410 104740 164850 97401 FALSE TRUE 89396.74732 174309.7408 268469.9489 276328.6671 73886.18168 212777.1464 88759.98932 150414.8601 112505.4496 0.794599263 1.549344867 2.386283952 2.456135841 0.656734246 1.891260798 0.788939466 1.336956215 1 16.77963536 2.001199176 1.483835249 1.0579231 1.608979825 0.139312976 0.602876654 0.923887128 3.793008748 0.41573988 0.198904616 100.2765021 -2.001199176 0.551056725 QNNT(ph)FPFFSEGITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNNTFPFFSEGITR 14 0 Q9BYX2-4;Q9BYX2-2;Q9BYX2;Q9BYX2-3 Q9BYX2-4 TBC1D2 TBC1 domain family member 2A 1 QNNT(1)FPFFSEGITR 92.939 0.053206 31946000 68898 57527 66070 76284 65142 66882 69450 67996 67355 TRUE FALSE 65641.32808 63389.0667 69099.37485 68615.78739 76502.74418 64565.85957 58854.12696 62041.90977 77800.0694 0.843718117 0.814768768 0.88816598 0.881950208 0.983324883 0.829894627 0.756479106 0.797453142 1 16.24748382 -0.251296992 7.51393512 0.999999999 0.844680217 0.372461787 0.061125076 8569136.197 1140432.536 0.063145182 0.015314956 0.560664435 0.251296992 -0.155319782 QNPHDGVVT(ph)PAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.983)PS(0.017)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.995)PS(0.005)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.872)PS(0.128)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.997)PS(0.003)LPQPGLQMPGQWGPVQGGPQPSGQHR 220.92 9.86E-44 460660000 113314 96561 107784 112677 110176 100867 120191 115562 93678 TRUE FALSE 107957.8718 106400.6757 112726.003 101350.4939 129390.6595 97373.9505 101853.6555 105442.7786 108205.1058 0.997715135 0.983323984 1.041780812 0.936651678 1.195790703 0.899901625 0.94130175 0.974471379 1 16.72340905 QNRDEVLDNLLAFVCDIRPEIHENYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QNRDEVLDNLLAFVCDIRPEIHENYR 26 2 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ;; 177.6 1.54E-17 687964300 545397 354060.8 458703 506445 570718 479353 677840 559395 596501 FALSE TRUE 519617.1647 390139.9981 479734.9863 455536.1864 670251.0385 462752.8854 574423.0586 510411.4083 689003.3286 0.754157699 0.566238191 0.69627383 0.661152374 0.972783455 0.671626487 0.833701428 0.740796723 1 19.39415143 -1.001769699 0.144488184 1.297906872 0.570183814 0.425026201 0.103457327 25.33289933 0.767103503 3.637803809 0.744311753 0.099593341 1.001769699 -0.727723058 QNS(ph)PAGNKENIKPNETSPSFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;QNS(1)PAGNKENIKPNETSPSFSK 162.07 8.69E-12 343430000 561810 529370 568950 647770 297280 637380 706130 691440 294020 TRUE FALSE 535254.3547 583313.4048 595036.9203 582654.9289 349125.5379 615307.3708 598396.8995 630893.848 339615.12 1.576061616 1.717571953 1.752091957 1.715633064 1.028003517 1.811778495 1.761985449 1.857673027 1 18.37354116 QNSTLVGDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNSTLVGDKR 10 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 96.334 0.010921 54062000 133300 123770 114620 137820 126310 152240 185250 160260 158580 FALSE TRUE 126999.1732 136382.3037 119875.4404 123966.0718 148338.424 146967.8906 156986.7102 146226.7848 183171.7765 0.693333742 0.744559595 0.654442746 0.67677496 0.809832316 0.802350086 0.857046392 0.798304125 1 17.4828377 1.233276984 0.407691136 1.007020788 0.683636573 0.815730751 0.04321585 0.464670476 0.225822523 0.058976808 0.036768903 17.11106276 -1.233276984 -0.323384215 QNVAYEYLCHLEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QNVAYEYLCHLEEAKR 16 1 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 138.66 3.51E-06 507660000 727550 587760 656530 734070 522440 731460 834200 798920 577210 FALSE TRUE 693160.1534 647653.4122 686632.5499 660279.889 613553.3706 706129.3568 706927.4689 728962.3295 666720.7788 1.039655843 0.971401271 1.029865233 0.990339449 0.92025536 1.059108069 1.06030514 1.093354749 1 19.34672316 2.10467029 22.99838119 1.058508093 0.993647518 0.381703168 0.039387223 5.631174423 1219.048279 0.013789616 0.010184307 127.2536622 -2.10467029 -0.064860575 QNVGTLESFS(ph)PGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QNVGTLESFSPGDFR 15 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 QNVGTLES(0.036)FS(0.964)PGDFR 90.259 0.0063808 13271000 22011 20721 20642 24214 19918 21873 22761 24281 28813 TRUE FALSE 20970.58365 22832.49346 21588.45612 21779.96272 23391.69289 21115.53253 19288.39142 22154.82692 33281.17288 0.630103504 0.686048341 0.648668729 0.654422931 0.702850617 0.634458785 0.579558644 0.665686483 1 15.02241866 0.946821978 23.56689178 1 0.647026479 0.918348584 0.032817149 3065.942669 1358734.56 0.034094239 0.00852356 8.847528656 -0.946821978 -0.352973522 QPAIMPGQSYGLEDGSCSYKDFSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPAIMPGQSYGLEDGSCSYKDFSESR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 119.48 0.00034555 179130000 110210 64482 103890 96211 109860 117620 150120 120780 140650 FALSE TRUE 105000.5917 71052.78911 108653.4593 86539.68749 129019.5492 113546.7899 127216.4369 110203.8629 162461.2837 0.646311474 0.437352134 0.668796016 0.532678836 0.794155668 0.698915996 0.783056947 0.678339235 1 17.30973642 1.021727678 0.240510303 1.084907649 0.479200005 0.641787932 0.090694843 1.548414347 0.320803579 0.351940169 0.222284439 10.51302453 -1.021727678 -0.605707644 QPAPFSDEIEVDFSKPYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPAPFSDEIEVDFSKPYVR 19 1 P49585;C9JEJ2;C9J050;C9J2E1;C9JPY0;C9JVS0;F8WAZ5 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 138.82 1.07E-06 55875000 120700 114230 116840 127950 94667 129630 132430 136010 122500 FALSE TRUE 114994.7502 125870.1669 122197.2296 115088.2229 111176.8948 125140.8806 112225.3713 124100.2434 141496.6744 0.812702848 0.889562723 0.863604958 0.813363448 0.785720904 0.884408635 0.793130805 0.877054135 1 17.11040862 0.977923385 22.24749895 1.000000001 0.837375287 0.67995077 0.035644397 236.1830646 238012.3222 0.032845451 0.008211363 9.504371091 -0.977923385 -0.162624714 QPAQELS(ph)PTPGGTAHQALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPAQELSPTPGGTAHQALK 19 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 QPAQELS(0.995)PT(0.005)PGGTAHQALK;QPAQELS(0.843)PT(0.156)PGGT(0.001)AHQALK 209.75 1.34E-16 295840000 346000 341380 368720 394160 270190 370140 433450 424200 341960 TRUE FALSE 329645.2657 376167.0101 385626.1767 354538.2879 317311.0505 357321.959 367319.2416 387054.7992 394989.4103 0.834567351 0.952347076 0.976294976 0.89758935 0.803340652 0.904636807 0.929947062 0.979911838 1 18.59145445 1.331572956 2.143362059 0.997852612 0.896984254 0.384990399 0.049564339 0.35044109 2.743804881 0.045885701 0.013741699 21.45719539 -1.331572956 -0.100868358 QPAQSQNLS(ph)PLSGFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPAQSQNLSPLSGFSR 16 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 QPAQSQNLS(1)PLSGFSR;QPAQSQNLS(0.965)PLS(0.035)GFSR;QPAQSQNLS(0.992)PLS(0.007)GFSR 204.71 2.57E-11 500949000 663690 476290 662150 636410 522220 705490 818020 706240 592490 TRUE FALSE 632318.689 524824.4925 692510.2325 572436.8577 613295.0027 681058.7044 693216.025 644397.8816 684370.3232 0.923942298 0.766872079 1.011894013 0.836443134 0.896144941 0.995161072 1.012925315 0.94159238 1 19.38441768 2.291205111 4.663037629 0.991767523 0.875885068 0.370299599 0.064459154 0.188821327 8.573231514 0.02207721 0.017824766 195.526268 -2.291205111 -0.115882455 QPASAQSTPSTTPHSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 QPASAQSTPSTTPHS(0.33)S(0.67)PK 183.25 4.14E-14 101160000 57195 42964 55454 55693 38659 44795 65978 60708 39731 TRUE FALSE 54491.5057 47342.08045 57996.62075 50094.63383 45401.11736 43243.73792 55911.84433 55392.08569 45892.28056 1.187378466 1.031591367 1.263755473 1.091569938 0.989297477 0.94228784 1.218327868 1.207002245 1 15.48596388 4.736485919 5.03647798 1.099493924 1.191341386 0.067869077 0.107545055 0.513602083 37.05800345 0.025236623 0.160777763 54511.22217 -4.736485919 0.091847462 QPDISCILGTGGKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPDISCILGTGGKSPR 16 1 P57740;P57740-2;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 QPDISCILGT(0.039)GGKS(0.961)PR;QPDISCILGTGGKS(1)PR 150.98 4.16E-07 702240000 1289000 1066620 1165430 1343920 988850 1258150 1445410 1313570 1103860 TRUE FALSE 1228071.525 1175309.791 1218866.118 1208826.608 1161305.127 1214579.95 1224886.158 1198546.847 1275040.971 0.963162402 0.92178198 0.955942708 0.948068835 0.910798283 0.952581115 0.960664156 0.940006537 1 20.28211218 -0.238056452 0.571279171 1.005592869 0.941803039 0.52054823 0.016746843 5.143291596 1.64543302 0.079217432 0.006787083 0.578020909 0.238056452 -0.06378983 QPDKEFS(ph)FMDEEEEDEIRV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 QPDKEFS(1)FMDEEEEDEIRV 130.57 1.36E-05 40902000 62897 53987 55012 75093 61287 68456 73784 62625 51154 TRUE FALSE 59923.98346 59488.33668 57534.35461 67544.50897 71975.4334 66085.35156 62526.89566 57141.223 59086.70106 1.014170404 1.006797394 0.973727651 1.143142327 1.218132543 1.118447136 1.058222824 0.96707418 1 15.85054583 3.246734768 24.99881035 1.093473517 1.002344232 0.237601287 0.071153871 249.8763945 764185.7449 0.020150966 0.02682535 1764.959595 -3.246734768 -0.091129285 QPDKEFSFMDEEEEDEIRV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 0 121.26 0.00014101 48261000 41450 33162 32034 39353 31539 33188 40122 43714 32628 FALSE TRUE 39490.74065 36541.2455 33502.79059 35397.16167 37039.39161 32038.69124 34000.65201 39886.17042 37687.7836 1.047839296 0.969577991 0.888956245 0.939221103 0.982795699 0.85010813 0.902166399 1.05833155 1 15.20180933 4.271963949 2.278014194 0.9351469 1.04165408 0.196627527 0.060123389 0.401373999 3.942628492 0.014861759 0.057230305 18705.26862 -4.271963949 0.106507181 QPEDDSSQAFISTQNGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;QPEDDSSQAFIST(0.001)QNGS(0.999)PR;QPEDDSSQAFISTQNGS(1)PR 416.48 3.80E-148 462040000 236857 234231 226733 274343 236090 227044 263732 249167 236005 TRUE FALSE 225661.239 258099.4052 237128.9323 246765.5204 277264.0213 219181.4093 223494.8396 227348.6166 272603.4501 0.827800378 0.946794346 0.869867686 0.905217892 1.017096523 0.804030211 0.819853306 0.833990239 1 18.0564443 -1.557404296 8.674912845 1.000017616 0.878272117 0.257001521 0.065146945 2.23E-05 1.14E-06 0.063276169 0.01491218 0.027707395 1.557404296 -0.121745499 QPEKEEEEEAGESVEDIFSEVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 128.97 8.34E-06 20769100 28350 25356 25677 28506 19782.9 28840 29559 28188 21193.6 FALSE TRUE 27009.95168 27939.80523 26854.31585 25640.52272 23233.0315 27841.26357 25049.23166 25719.70929 24480.19525 1.1033389 1.14132281 1.096981277 1.04739862 0.949054175 1.137297448 1.023244766 1.05063334 1 14.57932744 3.317335431 3.505150819 1.037592799 1.121726886 0.388594467 0.04758478 0.223226761 5.426290954 0.012719686 0.017372685 2076.516713 -3.317335431 0.084134087 QPEYSPES(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 208.82 1.12E-07 3392970000 1471950 1507160 1215150 1596480 1419330 1414670 1423680 1439970 1403660 TRUE FALSE 1402373.841 1660741.317 1270865.829 1435998.797 1666860.703 1365679.623 1206471.468 1313878.593 1621332.424 0.864951456 1.024306486 0.783840384 0.885690544 1.02808078 0.842319319 0.744123445 0.810369653 1 20.62874849 2.018832183 24.90277393 0.815605549 0.920973451 0.07104751 0.096883057 334.1229635 441826.4029 0.033786041 0.024949198 104.4316604 -2.018832183 0.105367902 QPGS(ph)PMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPGSPMYR 8 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 QPGS(1)PMYR 63.073 0.07932 158020000 109390 63160 108550 93287 117720 116370 175840 124250 208220 TRUE FALSE 104219.3515 69596.07581 113527.1249 83909.61353 138250.3307 112340.0777 149012.3785 113370.0113 240509.6942 0.43332703 0.289369109 0.472027231 0.348882459 0.57482228 0.467091683 0.619569115 0.471373978 1 17.87573552 -5 0.146587097 3.004651955 0.266483365 0.827085157 0.08091403 46.11562286 0.405815864 26.7192281 0.386242418 1.00E-05 5 -2.73816859 QPGTCS(ph)PDLAAPLDENGAVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPGTCSPDLAAPLDENGAVDR 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.014)CS(0.986)PDLAAPLDENGAVDR 138.02 2.44E-06 41426000 45735 51200 41157 53494 45193 43213 43716 38797 49205 TRUE FALSE 43573.19719 56417.33821 43044.08916 48116.68149 53074.64489 41716.52297 37046.3213 35399.729 56835.4601 0.766655132 0.992643292 0.757345662 0.846596146 0.933829775 0.7339876 0.651817039 0.622845825 1 15.7945037 2.135039501 6.849783003 0.7134291 0.86360822 0.126310612 0.12329005 0.284535165 16.59769673 0.04201394 0.03096362 136.4707257 -2.135039501 0.15017912 QPGVDS(ph)LSPVASLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDS(0.701)LS(0.299)PVASLPK 94.461 0.0046808 26320000 76745 81699 62940 91801 51934 71577 77738 78146 61027 TRUE FALSE 73117.41594 90024.22098 65825.86126 82572.98907 60991.27316 69098.27054 65877.64034 71303.12196 70490.75548 1.037262481 1.277106769 0.93382261 1.171401675 0.865237899 0.98024585 0.934557161 1.01152444 1 16.10514645 2.746087394 24.923966 0.954525428 1.116580474 0.362700269 0.095925439 529.4173939 1753099.308 0.027560593 0.028704713 557.2978843 -2.746087394 0.162055045 QPGVDSLS(ph)PVASLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDSLS(1)PVASLPK;QPGVDSLS(1)PVASLPK 252.79 1.24E-24 210790000 355530 369470 320230 416240 258430 372230 371900 374660 276681 TRUE FALSE 338724.8015 407119.4131 334912.8623 374398.7644 303500.1102 359339.5818 315159.8246 341852.7842 319587.2764 1.059881999 1.273891181 1.047954305 1.171507103 0.949662682 1.124386383 0.986146345 1.069669569 1 18.28585045 2.756787271 24.86259283 1.030085573 1.147171985 0.339104165 0.077371272 792.7321204 1081347.296 0.021645904 0.022917805 571.1987794 -2.756787271 0.117086412 QPGYQPPNPHPGPS(ph)SPPAAPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.508)S(0.492)PPAAPASK 153.39 3.31E-08 229210000 228370 175180 178200 238080 181110 212580 251560 238160 185650 TRUE FALSE 217575.4027 193031.0412 186370.6463 214147.7461 212695.5267 205218.3013 213179.9018 217305.4478 214439.6538 1.01462299 0.900164861 0.869105331 0.998638742 0.991866583 0.956997914 0.994125377 1.013364105 1 17.71021219 3.142422595 23.39380678 0.989895025 0.934284822 0.373515463 0.039016487 11.1861159 2710.067481 0.011574815 0.01383456 1388.105884 -3.142422595 -0.055610203 QPGYQPPNPHPGPSS(ph)PPAAPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.139)S(0.861)PPAAPASK;QPGYQPPNPHPGPS(0.033)S(0.967)PPAAPASK 197 1.96E-24 422460000 774940 601470 574430 784490 557760 647170 839840 774010 611800 TRUE FALSE 738310.122 662760.4768 600768.1837 705631.5748 655033.1674 624758.3406 711706.9833 706233.5811 706674.8194 1.044766421 0.937857779 0.850133848 0.998523728 0.926923034 0.884081792 1.007120905 0.999375613 1 19.43068698 1.610311777 25 1.002441157 0.946309941 0.221919411 0.053776219 0.412581052 4158.753745 0.026697024 0.013927075 40.76728387 -1.610311777 -0.056131216 QPGYQPPNPHPGPSS(ph)PPAAPASKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASKR 24 1 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.202)S(0.798)PPAAPASKR 97.057 0.0028747 149010000 61017 27828 54799 45438 66513 47070 90063 65869 83920 TRUE FALSE 58132.84733 30663.70484 57311.58835 40870.48591 78112.84614 45439.9541 76322.23523 60101.16117 96933.885 0.59971647 0.316336283 0.591244108 0.4216326 0.80583633 0.46877265 0.787363833 0.620022206 1 16.56471345 0.842867838 0.308696469 1.066626158 0.428867338 0.534018179 0.137000622 1.506462965 0.394827998 0.334625596 0.166497394 6.964145528 -0.842867838 -0.63775882 QPHVGDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 QPHVGDYR 8 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;;;;; 109.29 0.0036467 4032581000 4409350 3848470 3988200 4561240 4597500 4088710 4862900 4248820 4570600 FALSE TRUE 4200928.764 4240633.468 4171062.915 4102735.489 5399302.544 3947116.947 4120975.292 3876770.796 5279385.305 0.795723085 0.803243791 0.790066016 0.777123709 1.022714243 0.747647069 0.780578619 0.734322383 1 22.33193853 -2.197311859 2.338796813 1.561315151 0.80606265 0.367369607 0.079829406 5342304.548 1134969.563 15879193.36 0.018967259 0.006348749 2.197311859 -0.755252501 QPLLLS(ph)EDEEDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.99)EDEEDT(0.01)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR 223.46 2.15E-12 40925260000 10376770 9460320 9245130 11043070 7342390 11397930 11985020 11844890 8607770 TRUE FALSE 9886280.647 10424337.36 9669028.355 9932999.623 8622900.491 11003216.83 10156485.08 10807688.64 9942619.009 0.99433365 1.048449845 0.97248304 0.99903251 0.86726651 1.106671875 1.021510034 1.087006213 1 23.24519449 QPPGPVPT(ph)PPLPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPPGPVPTPPLPSER 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 QPPGPVPT(1)PPLPSER 122.16 0.0012365 69454000 106620 103150 111930 127050 105010 106080 132480 127010 103450 TRUE FALSE 101580.2839 113661.1023 117062.1012 114278.6926 123323.7108 102406.423 112267.7428 115888.3311 119492.4977 0.850097587 0.951198649 0.979660678 0.956367093 1.032062374 0.857011319 0.939538005 0.969837717 1 16.86656052 4.503398983 2.266169687 0.955647185 0.84597126 0.363717645 0.045485129 0.415042991 3.514676214 0.011208245 0.074560426 31871.2416 -4.503398983 -0.109675926 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGTQQS(0.02)HS(0.196)S(0.784)PGEITSSPQGLDNPALLR;QPPGTQQS(0.019)HS(0.125)S(0.856)PGEITSSPQGLDNPALLR;QPPGTQQS(0.011)HS(0.12)S(0.869)PGEITSSPQGLDNPALLR 240.33 1.36E-45 1355130000 284214 247568 224365 268958 262582 247550 274861 250228 250472 TRUE FALSE 270779.7675 272795.4607 234652.3572 241921.8309 308376.2177 238977.2814 232925.9063 228316.7098 289313.9185 0.935937576 0.942904725 0.811064875 0.83619147 1.065887944 0.826013773 0.805097478 0.789166007 1 18.14227621 QPPGVPNGPS(ph)SPTNESAPELPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.522)S(0.394)PT(0.079)NES(0.004)APELPQR 98.121 0.0019844 583070000 408740 359780 370880 468900 404930 343270 418000 385130 393240 TRUE FALSE 389419.6702 396441.991 387885.2149 421765.2811 475549.6638 331382.4738 354226.4229 351405.9755 454221.6508 0.857334012 0.872794131 0.853955804 0.928545085 1.046955078 0.729561159 0.779853673 0.773644266 1 18.79303695 2.202638334 24.99997614 0.797399484 0.899741477 0.174235135 0.09045789 248.3850689 172861.2521 0.031547835 0.023300405 159.4550707 -2.202638334 0.102341993 QPPGVPNGPSS(ph)PTNESAPELPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.061)S(0.707)PT(0.206)NES(0.025)APELPQR;QPPGVPNGPS(0.2)S(0.799)PT(0.002)NESAPELPQR;QPPGVPNGPS(0.245)S(0.712)PT(0.04)NES(0.003)APELPQR 138.57 2.02E-06 1367210000 1030220 904220 905030 1059680 1015040 890450 995210 956620 1020120 TRUE FALSE 981523.5423 996361.046 946526.5207 953158.9531 1192062.655 859613.4932 843372.4362 872853.2814 1178315 0.832989093 0.845581229 0.803288188 0.808916931 1.011667216 0.729527752 0.715744463 0.740763957 1 20.16829384 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR 38 0 P14866;M0QXS5;P14866-2 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 119.8 3.04E-07 75930000 16730 16761 16489 20318 19514 15280 19543 17965 8843.3 FALSE TRUE 15939.20606 18468.96496 17245.03696 18275.59604 22917.23542 14750.84977 16561.35642 16391.88936 10214.6738 1.560422425 1.808081718 1.688261153 1.789151215 2.243560183 1.444084271 1.621329936 1.604739386 1 13.31835551 0.565534665 0.809368297 0.998234134 1.761700989 0.564232719 0.205597536 1.058217055 1.146263197 0.200108341 0.066917714 3.677347442 -0.565534665 0.763466855 QPPTAAGRPVDAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 QPPTAAGRPVDAS(1)PR;QPPTAAGRPVDAS(1)PR 68.411 0.031922 335370000 302190 368200 306380 405790 312480 304000 333270 341240 342060 TRUE FALSE 287906.0776 405719.9986 320427.8261 364999.2182 366976.4131 293472.4038 282423.5406 311359.2166 395104.9178 0.728682597 1.026866486 0.810994274 0.923803278 0.928807505 0.74277082 0.714806442 0.788041866 1 18.59187628 2.236779436 24.99557505 0.778232772 0.887737486 0.062279582 0.109590011 75.3607752 1057521.835 0.036681183 0.028504566 172.4961618 -2.236779436 0.109504713 QPPTAAGRPVDASPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ; 111.64 0.00075359 209330000 151027 127602 139991 147153 152704 131424 164248 135173 180318 FALSE TRUE 143888.253 140604.7889 146409.7258 132360.9009 179335.5293 126872.7539 139188.951 123336.5355 208280.7945 0.690837834 0.675073231 0.702943957 0.635492587 0.86102768 0.609142836 0.668275495 0.592164706 1 17.66817029 -1.15362723 4.989464881 1.000019126 0.680434377 0.654193549 0.073256943 1.40E-05 2.38E-06 0.063839055 0.01504611 0.070205764 1.15362723 -0.319584749 QPPYQLRPSLFVLS(ph)PIKEPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPPYQLRPSLFVLSPIKEPAK 21 2 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 QPPYQLRPS(0.003)LFVLS(0.997)PIKEPAK;QPPYQLRPS(0.211)LFVLS(0.789)PIKEPAK 103.63 0.00022614 216380000 545810 574020 455320 642940 270690 604550 532500 670090 273690 TRUE FALSE 520010.643 632513.2906 476196.8724 578310.4497 317898.2503 583614.2819 451257.345 611413.3672 316132.4474 1.644913856 2.000785733 1.506320773 1.82932962 1.005585643 1.846106867 1.427431283 1.934041799 1 18.27016959 3.354218049 1.910704661 1.508681096 1.808873061 0.12016964 0.333040068 0.629881601 4.698646018 0.092031804 0.13933093 2260.570465 -3.354218049 0.300191965 QPS(ph)ATRLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPSATRLPK 9 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67;Q6P582 H7BZ50;Q6P582 MZT2B;MZT2A Mitotic-spindle organizing protein 2B;Mitotic-spindle organizing protein 2A 1 QPS(0.993)AT(0.007)RLPK;QPS(0.997)AT(0.003)RLPK;QPS(0.971)AT(0.029)RLPK 101.71 0.0023 2600730000 2335490 1296920 2275790 2096220 2119680 2235730 3170830 2647950 2954160 TRUE FALSE 2225096.016 1429077.622 2380137.223 1885503.983 2489351.521 2158306.11 2687061.647 2416081.46 3412276.045 0.652085584 0.418804811 0.697521886 0.552564903 0.729528177 0.632512165 0.787469012 0.708055687 1 21.70230293 0.877435133 0.304653711 1.058252876 0.516683781 0.673151815 0.08620219 1.126918089 0.296604527 0.215151901 0.111130166 7.541107522 -0.877435133 -0.541569095 QPS(ph)EEEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;QPS(1)EEEIIK;QPS(1)EEEIIK 153.38 8.21E-05 30542477000 11125810 8764260 9080240 13408320 7861000 12865400 12768260 9023600 7229980 TRUE FALSE 10599915.01 9657348.058 9496577.986 12060490.2 9231955.911 12419867.97 10820227.43 8233445.747 8351168.373 1.269273297 1.15640682 1.137155612 1.444168009 1.10546878 1.487201242 1.295654326 0.985903454 1 22.99354662 1.235862138 24.99937186 0.992951554 1.267338357 0.468751259 0.122912996 62.34290597 577504.0585 0.095745038 0.028122003 17.21322072 -1.235862138 0.274386803 QPS(ph)SPYEDKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.5)S(0.5)PYEDKDK 60.549 0.056288 110400000 145700 165480 171500 157820 139640 154530 144110 144280 81106 TRUE FALSE 138813.0497 182342.6001 179363.4446 141955.6338 163993.1718 149178.5874 122123.3727 131646.0783 93683.50425 1.481723499 1.94636827 1.914568056 1.515268188 1.750502109 1.592367712 1.303573919 1.405221542 1 16.51550742 1.409466681 0.728516332 1.025131972 1.757654863 0.687223434 0.158390982 0.336056064 0.393761295 0.145701809 0.062267591 25.67241241 -1.409466681 0.732522891 QPS(ph)SPYEDKDKDKK ddPTM_SK-BR-3_Trastuzumab_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(0.599)S(0.399)PY(0.002)EDKDKDKK 88.565 0.0046354 621240000 696180 704800 559780 747430 175950 737550 563590 736160 108500 TRUE FALSE 663272.9511 776619.9213 585446.4667 672296.9164 206635.6243 712008.4586 477603.9945 671697.9278 125325.6259 5.292396879 6.19681662 4.671402697 5.364401029 1.648789885 5.681267927 3.810904523 5.359621571 1 16.93532191 2.95518129 24.9981136 3.828204921 5.480808182 0.270042081 1.48066336 598.4170661 333773.2914 0.403745107 0.428256735 901.9475638 -2.95518129 1.652603262 QPSLTLELFPNHTDNLNSSQRLS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QPSLTLELFPNHTDNLNSSQRLSPSSR 27 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 QPSLTLELFPNHTDNLNS(0.006)S(0.006)QRLS(0.89)PS(0.072)S(0.026)R;QPSLTLELFPNHT(0.01)DNLNS(0.21)S(0.21)QRLS(0.542)PS(0.014)S(0.014)R 155.49 1.94E-08 169495000 95349 50300 97686 68713 125367 85853 114102 85705 158724 TRUE FALSE 90842.04173 55425.62719 102164.9997 61805.83869 147230.9651 82879.88908 96693.64427 78200.21585 183338.1073 0.495489143 0.302313731 0.557249124 0.337113978 0.80305708 0.452060351 0.527406144 0.426535525 1 17.48414716 -5 0.242042248 3.989411563 0.428120365 0.570653954 0.138364248 117.7150304 1.172424422 173.5373722 0.195224555 1.00E-05 5 -3.561291198 QPSS(ph)PYEDKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.108)S(0.892)PYEDKDK;QPS(0.062)S(0.938)PYEDKDK;QPS(0.026)S(0.974)PYEDKDK 153.79 1.96E-05 902910000 1596410 2205640 1236160 2065490 708270 1733160 1139880 1618540 578810 TRUE FALSE 1520950.863 2430397.224 1292839.159 1857863.021 831792.0638 1673140.235 965970.3707 1476812.057 668568.8986 2.274935113 3.635223278 1.933741102 2.778865461 1.244138137 2.50256965 1.444832945 2.208915282 1 19.35071672 3.106426837 1.391543203 1.749724382 2.891338458 0.33434154 0.633146033 0.399022945 1.613955585 0.209394384 0.274792992 1277.693946 -3.106426837 1.141614076 QPSS(ph)PYEDKDKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPSSPYEDKDKDK 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.181)S(0.819)PYEDKDKDK 100.04 0.001348 167560000 167830 192230 150520 202900 64592 188470 155930 181460 57266 TRUE FALSE 159897.0085 211818.4555 157421.4909 182504.1065 75856.82435 181943.2366 132140.0146 165570.4004 66146.51881 2.41731555 3.202261576 2.37989079 2.759088608 1.146799948 2.750609404 1.997686606 2.503085626 1 16.01337761 2.875699746 19.34798021 2.010896327 2.727892639 0.312707533 0.577534989 3.96344822 600.8028802 0.157656644 0.167220747 751.103432 -2.875699746 0.716996311 QPSS(ph)PYEDKDKDKK ddPTM_SK-BR-3_Trastuzumab_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(0.029)S(0.971)PYEDKDKDKK 165.8 2.16E-05 1418100000 1450800 1532100 1103900 1615900 417250 1887100 1280100 1763500 267940 TRUE FALSE 1382223.559 1688222.732 1154514.907 1453466.662 490018.2679 1821749.254 1084797.234 1609078.591 309490.7668 4.46612212 5.45484038 3.730369468 4.696316718 1.583304966 5.886279817 3.505103709 5.199116626 1 18.23953684 3.725021226 23.23020386 3.833587365 4.96048124 0.105649758 1.510071552 611.9068591 1049879.667 0.351859477 0.549174232 5309.103912 -3.725021226 1.126893874 QPT(ph)PPFFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QPTPPFFGR 9 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 QPT(1)PPFFGR;QPT(1)PPFFGR;QPT(1)PPFFGR 118.77 0.010464 17728430000 2263780 1961400 1950330 2352060 2303640 2071970 2433150 2180830 2404690 TRUE FALSE 2156775.606 2161268.89 2039754.56 2115626.46 2705394.087 2000217.159 2061928.28 1989864.964 2777597.044 0.77648974 0.778107427 0.734359422 0.761675083 0.974005244 0.720125032 0.742342481 0.716397999 1 21.40540589 -2.089176642 2.605001558 1.383987975 0.775108126 0.477973362 0.073752951 12522448.2 3197732.696 28630499.87 0.01744867 0.00814373 2.089176642 -0.608879849 QPTHQGGPAQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QPTHQGGPAQDR 12 0 Q15477 Q15477 SKIV2L Helicase SKI2W 0 76.728 0.030334 10799000 6686.9 6789.8 6015.7 8033.9 7331.9 6755.1 6552.7 7434.5 5983.7 FALSE TRUE 6370.823489 7481.688339 6291.525795 7226.317109 8610.581039 6521.169193 5552.965266 6783.495767 6911.621635 0.921755244 1.082479443 0.910282149 1.045531351 1.245811981 0.943507839 0.803424371 0.981462257 1 12.75480853 2.012333426 24.96957006 0.898206834 1.035569274 0.189652817 0.106159905 285.9961158 579009.2848 0.03841689 0.028354597 102.8805853 -2.012333426 0.13736244 QPYAVSELAGHQTSAESWGTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QPYAVSELAGHQTSAESWGTGR 22 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 337.87 4.82E-81 4340050000 1574082 1323932 1392446 1674667 1699814 1355661 1766020 1633772 1716570 FALSE TRUE 1499678.263 1458842.176 1456291.026 1506326.292 1996261.023 1308714.12 1496581.214 1490710.263 1982766.909 0.75635631 0.735760805 0.734474143 0.759709215 1.006805699 0.660044362 0.754794327 0.751833338 1 20.91908366 -1.7596592 2.552553867 1.056963776 0.766038083 0.395901388 0.089180652 15756811.94 11280428.69 5631390.385 0.02053349 0.017391651 1.7596592 -0.290925693 QQAAYYAQTS(ph)PQGMPQHPPAPQGQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 QQAAYYAQT(0.036)S(0.964)PQGMPQHPPAPQGQ;QQAAYYAQT(0.004)S(0.996)PQGMPQHPPAPQGQ;QQAAYYAQT(0.004)S(0.996)PQGMPQHPPAPQGQ 167.87 3.75E-11 764720000 339456 306521 316257 365541 374625 315478 378221 380995 386804 TRUE FALSE 323410.5876 337755.8384 330757.6963 328796.1242 439959.4814 304552.9178 320516.4399 347633.058 446787.5888 0.723857591 0.755965132 0.74030189 0.735911499 0.98471733 0.681650353 0.717379909 0.778072325 1 18.76922958 -1.663138498 1.856127911 1.056965606 0.759611766 0.445002005 0.082395367 170879.4014 93198.30723 45722.13129 0.020886293 0.021720084 1.663138498 -0.29735384 QQASKS(ph)PYNGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.018)KS(0.982)PYNGVR;QQAS(0.03)KS(0.97)PYNGVR;QQAS(0.001)KS(0.999)PYNGVR;QQAS(0.082)KS(0.918)PYNGVR;QQAS(0.084)KS(0.916)PYNGVR;QQAS(0.018)KS(0.982)PYNGVR 211.78 1.69E-08 2128742000 2963784 1984062 2423481 2856930 2207788 2821172 3159627 2959198 2728515 TRUE FALSE 2823691.804 2186240.173 2534600.001 2569745.969 2592825.528 2723474.106 2677567.871 2700074.935 3151639.171 0.895943873 0.693683526 0.804216429 0.815368077 0.82269111 0.864145278 0.849579449 0.856720833 1 21.58767094 0.476404402 0.418618873 1.017091328 0.790904934 0.571029851 0.050298861 1.627148228 0.537769918 0.108181327 0.033682081 2.995052244 -0.476404402 -0.226186394 QQDLHLES(ph)PQRQPEYS(ph)PESPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEY(0.224)S(0.546)PES(0.23)PR 77.566 0.012952 283450000 91606 94399 97502 84067 76302 102970 104860 100310 78235 TRUE FALSE 87275.96593 104018.3654 101972.5631 75616.42544 89609.04464 99404.12308 88861.68111 91526.32462 90367.28423 0.965791621 1.151062205 1.128423456 0.83676771 0.991609357 1.100001222 0.983339069 1.012825885 1 16.46351295 QQDLHLES(ph)PQRQPEYSPES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEYS(0.016)PES(0.984)PR 136.34 6.77E-06 186760000 273210 260260 241920 277460 239980 260530 281400 264700 233090 TRUE FALSE 260295.9048 286780.7899 253012.2713 249569.1937 281832.436 251507.7808 238467.2617 241521.4647 269236.4067 0.966793117 1.065163487 0.939740187 0.926951881 1.046784272 0.934152197 0.885716997 0.897060942 1 18.03851398 2.045582937 9.968516403 0.913649535 0.992287669 0.231170264 0.052146153 0.451034781 95.31837374 0.018813878 0.013875724 111.0664617 -2.045582937 0.078638134 QQDLHLES(ph)PQRQPEYSPESPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QQDLHLES(1)PQRQPEYSPESPR 131.57 7.84E-06 211010000 97333 83908 92114 107030 90460 79296 101590 89309 96026 TRUE FALSE 92732.26199 92458.3206 96337.51801 96271.14106 106236.1954 76549.95964 86090.57967 81488.6305 110917.2216 0.836049268 0.833579486 0.868553292 0.867954855 0.957797119 0.690153959 0.776169637 0.734679694 1 16.75912386 2.235922983 24.99966868 0.777750801 0.863688503 0.117504825 0.087872602 109.4847781 1037686.848 0.028590858 0.022080798 172.1563248 -2.235922983 0.085937702 QQDS(ph)QPEEVMDVLEMVENVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQDSQPEEVMDVLEMVENVK 20 0 Q9H307 Q9H307 PNN Pinin 1 QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK 94.856 0.0027833 3183600 19502.4 17920.9 17705.8 23171.7 16168.7 22894.5 21661.3 20402.4 16630.7 TRUE FALSE 18580.5602 19747.06008 18517.62844 20842.43669 18988.51616 22101.65772 18356.47085 18615.8577 19209.70402 0.967248646 1.027973157 0.963972606 1.084995202 0.988485619 1.1505465 0.955583221 0.969086128 1 14.22954767 5.183137964 1.026861712 1.020582958 0.883786983 0.062142958 0.060227454 11.66803823 5.346061373 0.016649939 2.175615638 152453.6984 -5.183137964 -0.136795975 QQDTPGS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQDTPGSPDHR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QQDT(0.004)PGS(0.996)PDHR;QQDT(0.007)PGS(0.993)PDHR;QQDT(0.114)PGS(0.886)PDHR 145.62 3.79E-05 458363000 719597 692620 692996 844345 807144 719702 793803 759102 674966 TRUE FALSE 685583.0759 763198.7654 724770.5521 759469.8364 947909.658 694778.5393 672693.7732 692631.0046 779636.28 0.879362715 0.978916432 0.929626507 0.974133523 1.215835746 0.89115727 0.862830259 0.888402736 1 19.5724417 -2.088291018 8.254656678 1.272293449 0.949157712 0.020271865 0.101317435 0.118206804 0.001264329 0.022839716 0.023086754 0.008160354 2.088291018 -0.323135738 QQDVIYELIQTELHHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQDVIYELIQTELHHVR 17 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ; 117.18 0.00013312 65695000 106500 111857 98029 113655 91555 104570 100102 109747 13063.3 FALSE TRUE 101465.9561 123255.3555 102523.7266 102230.1835 107522.163 100948.7147 84829.6014 100136.9709 15089.08985 6.72445834 8.168508288 6.794560021 6.775106021 7.125821644 6.690179177 5.621916382 6.636382439 1 13.88121817 -0.29228369 0.424971537 1.35E-16 7.351398649 0.918839731 0.549540175 1.597993583 0.308675488 3.349134625 0.321661472 0.510171636 0.29228369 7.351398649 QQEEIS(ph)KLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQEEISKLEER 11 1 B4DDJ5;P21757-2;P21757-3;P21757 B4DDJ5 MSR1 Macrophage scavenger receptor types I and II 1 QQEEIS(1)KLEER 77.379 0.01985 377610000 368300 374230 391610 347030 780220 238220 376870 274970 656850 TRUE FALSE 350891.1889 412364.4625 409565.7059 312145.8851 916290.121 229970.3817 319371.5598 250892.1691 758710.9433 0.462483363 0.543506676 0.539817844 0.411416084 1.207693298 0.303106715 0.420939704 0.330682154 1 19.53319082 4.304134953 1.213342815 0.570184358 0.454729778 0.015418605 0.292058483 5.185660754 10.75652885 0.082899668 0.624182205 20143.50095 -4.304134953 -0.11545458 QQEEMMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQEEMMR 7 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 91.318 0.061113 0 145080 129940 128680 151890 133020 121810 157420 124050 166690 FALSE TRUE 138222.3559 143181.0337 134580.1053 136621.7286 156218.6459 117591.6892 133402.6878 113187.5244 192539.4339 0.717891152 0.743645241 0.698974244 0.709577908 0.811359225 0.610740807 0.692859042 0.587866714 1 17.55479443 -1.003432405 4.377554393 1.000011956 0.701489756 0.697447651 0.062724436 19765.28284 34581850.56 1030.642524 0.013874816 0.099212774 1.003432405 -0.298522199 QQEGFKPNYMENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQEGFKPNYMENR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 154.65 4.22E-05 1121970000 795990 647160 662010 817210 695210 700050 896070 782680 747900 FALSE TRUE 758365.1302 713106.3398 692363.8133 735062.4982 816454.4039 675807.093 759358.064 714144.39 863880.5123 0.877858824 0.825468719 0.801457845 0.850884454 0.945101079 0.782292323 0.879008212 0.826670332 1 19.72047225 -1.652142398 4.124444393 1.005546739 0.849076432 0.520963914 0.045625704 0.002173262 0.000183294 0.041256583 0.009405436 0.022277046 1.652142398 -0.156470307 QQEIILWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QQEIILWR 8 0 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;; 170.66 0.0006837 442865000 595290 523930 512326 626980 562990 547280 625540 601280 590830 FALSE TRUE 567151.8215 577319.0627 535816.6539 563954.7792 661175.2778 528327.5564 530102.3842 548628.7356 682452.8989 0.831049033 0.845947118 0.78513353 0.826364398 0.968821847 0.774159737 0.776760396 0.803907107 1 19.38036995 -2.250301494 2.282958008 1.650344554 0.825550812 0.48766908 0.055873912 3282095.154 694737.103 10976427.37 0.014308712 0.005619511 2.250301494 -0.824793742 QQEKEDKDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQEKEDKDEK 10 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 109.24 0.0011504 284220000 781920 688930 651320 854540 283600 854790 754370 977390 335950 FALSE TRUE 744960.1912 759132.7502 681183.6662 768640.0157 333059.7502 825188.408 639277.0015 891804.5501 388047.4102 1.919765914 1.956288665 1.75541351 1.980788933 0.858296542 2.126514406 1.647419838 2.298184517 1 18.5658734 QQELDNLLHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQELDNLLHEK 11 0 Q12788;J3KNP2 Q12788 TBL3 Transducin beta-like protein 3 0 121.04 0.00041988 26693000 109720 117160 91837 128410 85029 122200 115510 123080 91522 FALSE TRUE 104533.753 129098.7372 96047.81729 115501.9828 99858.03068 117968.1834 97886.82801 112302.4627 105714.7643 0.988828322 1.221198742 0.90855632 1.092581378 0.944598716 1.115910196 0.925952289 1.062315784 1 16.68981735 3.732124544 24.98338234 1.006756549 1.105013532 0.176678967 0.087842743 703.9128257 2732429.169 0.020731937 0.033014647 5396.65362 -3.732124544 0.098256983 QQELTHQEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QQELTHQEHR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ;;;; 137.89 4.57E-05 1683114000 555317 555379 507578 559138 594400 521100 621491 569087 45467.4 FALSE TRUE 529068.2659 611972.7515 530850.9534 502932.3859 698063.1718 503054.1763 526671.1335 519254.7254 52518.25218 10.07398845 11.6525727 10.1079326 9.576335181 13.29182033 9.578654191 10.02834465 9.887128833 1 15.68053128 -0.304309304 0.678495435 0.308426953 10.80769074 0.881331748 1.103726898 2.563623685 1.01590541 5.631227148 0.371580014 0.496238775 0.304309304 10.49926379 QQFHDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQFHDAK 7 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 61.357 0.091967 399160000 1488910 1318560 1266960 1474130 1033530 1427000 1651450 1567420 1209090 FALSE TRUE 1418532.175 1452922.763 1325051.369 1325947.652 1213777.305 1377582.632 1399490.972 1430168.395 1396589.502 1.015711612 1.040336306 0.94877655 0.949418315 0.86910098 0.986390511 1.002077539 1.024043495 1 20.4134766 -0.093378224 6.805824131 1.000000001 0.983668709 0.010652603 0.049137785 7686600.691 47932161.2 0.050906346 0.012726587 0.80653232 0.093378224 -0.016331292 QQFTEEEIYKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQFTEEEIYKDR 12 1 B4DGJ5;Q8N7H5-3;Q8N7H5-2;Q8N7H5 B4DGJ5 PAF1 RNA polymerase II-associated factor 1 homolog 0 97.69 0.0043593 249620000 129290 97613 96255 126110 96546 122120 133480 131620 99924 FALSE TRUE 123178.7179 107559.8757 100668.387 113433.1832 113383.5918 117890.9538 113115.1745 120094.655 115419.7036 1.067224348 0.9319022 0.872194121 0.982788724 0.982359063 1.021410991 0.980033486 1.040503929 1 16.81653001 2.558521522 2.783401293 1.005972057 0.964741181 0.159405091 0.050173985 0.634925787 9.663139505 0.018928952 0.016997243 361.8441223 -2.558521522 -0.041230876 QQGDHSLKEHELLEQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQGDHSLKEHELLEQQKR 18 2 Q13435;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 191.35 7.40E-15 574860000 523280 384720 466770 510790 343500 538100 617610 535500 31044 FALSE TRUE 498545.5914 423923.4054 488171.8662 459444.4188 403406.2912 519465.4621 523382.2513 488608.7811 35858.14497 13.90327335 11.82223469 13.61397436 12.81283288 11.25006025 14.48667974 14.59590985 13.6261589 1 15.13001324 -0.4268744 8.557411752 1.000042045 13.26398013 0.928665169 1.068198556 0 0 1.074584478 0.253281998 0.374218798 0.4268744 12.26393808 QQGHEPVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 106.58 0.0015446 1185770000 1534900 1386200 1241490 1598430 1264700 1379470 1453570 1396640 1208500 TRUE FALSE 1462348.319 1527455.356 1298413.545 1437752.78 1485263.28 1331698.608 1231801.2 1274342.798 1395908.008 1.047596482 1.094237835 0.930156957 1.02997674 1.064012293 0.954001697 0.882437233 0.912913165 1 20.41277244 2.096106011 4.76976366 0.918548744 1.037623703 0.458043308 0.05132449 0.159428182 6.1975493 0.019719039 0.014209681 124.7688037 -2.096106011 0.119074959 QQGNEPSQILSLTGDRVPLHCVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQGNEPSQILSLTGDRVPLHCVDR 24 1 Q8NFH3 Q8NFH3 NUP43 Nucleoporin Nup43 0 97.974 0.003377 37970000 32269 29684 29766 37897 30214 32511 36221 34401 30907 FALSE TRUE 30743.70832 32708.83335 31130.80054 34087.52156 35483.31203 31385.13592 30694.82121 31388.66607 35699.89971 0.86117072 0.916216393 0.872013669 0.954835219 0.993933101 0.87913793 0.859801329 0.879236814 1 15.1236324 4.813059902 1.270483687 0.912830725 0.830900691 0.104714871 0.050229102 4.36128361 5.436465748 0.014202852 0.488076172 65021.9368 -4.813059902 -0.081930034 QQHQGILSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQHQGILSR 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 ; 125.75 0.00049291 254750000 169396 128967 126192 159796 146615 123924 161898 150455 164781 FALSE TRUE 161388.9868 142108.8839 131978.028 143733.0025 172184.6096 119632.4808 137197.4866 137280.3626 190334.3959 0.847923393 0.746627446 0.69340083 0.755160421 0.904642636 0.628538422 0.720823401 0.721258824 1 17.53817677 -0.995899932 9.645862406 1.000006216 0.752470145 0.506529389 0.076835382 0 0 0.072348362 0.017052673 0.100948546 0.995899932 -0.247536071 QQITEKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQITEKEEK 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 76.282 0.032716 80147000 124910 90482 145040 123550 96143 120480 165840 163190 103900 FALSE TRUE 119005.7518 99702.21867 151690.2275 111130.5193 112910.3088 116307.7474 140538.0621 148900.2185 120012.2814 0.991613112 0.830766798 1.26395587 0.92599289 0.940822952 0.969132043 1.171030669 1.240708174 1 16.87282252 1.741004363 6.651428241 1.152917453 0.975724107 0.237226163 0.124575461 0.168343112 21.301856 0.058428032 0.030754077 55.08132293 -1.741004363 -0.177193346 QQLS(ph)AEELDAQLDAYNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 1 QQLS(1)AEELDAQLDAYNAR 160.02 4.37E-11 26256000 44863 44766 43920 44197 44851 49124 47627 42923 54660 TRUE FALSE 42742.4149 49327.70629 45933.77544 39754.23359 52673.0002 47422.82356 40360.62642 39164.43457 63136.39364 0.676985371 0.781287993 0.727532455 0.629656388 0.834273185 0.751117079 0.639260878 0.620314724 1 15.94618424 -2.026677817 2.784466412 1.342968448 0.710983577 0.637565292 0.069252019 5474355.467 6759516.383 11925331.17 0.01679292 0.009404207 2.026677817 -0.63198487 QQLSAEELDAQLDAYNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 223.7 1.16E-18 109724000 175759 154987 146850 179720 188432 161972 190371 174957 194295 FALSE TRUE 167451.2204 170780.3515 153583.2178 161654.2042 221294.4811 156362.869 161326.4075 159636.8376 224425.2763 0.746133516 0.760967545 0.684340108 0.720303019 0.986049721 0.69672575 0.718842415 0.711313985 1 17.77587565 -1.285818169 4.870415444 1.000082337 0.752280149 0.449802994 0.085817928 7.26E-05 1.06E-05 0.078635174 0.018528346 0.051782359 1.285818169 -0.247802188 QQLSPS(ph)PGQEAGILPETEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQLSPSPGQEAGILPETEK 19 0 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 QQLS(0.007)PS(0.993)PGQEAGILPETEK;QQLS(0.033)PS(0.967)PGQEAGILPETEK 184.56 2.59E-14 116622000 279400 238740 262210 291380 199373 274120 301080 335760 245232 TRUE FALSE 266193.3157 263067.8774 274232.5879 262089.9288 234143.5881 264627.1557 255144.7163 306359.0744 283261.3261 0.93974465 0.928710887 0.968125764 0.925258426 0.826599209 0.934215621 0.90073968 1.081542188 1 18.11177412 1.245056445 24.9998549 1.040771108 0.919006899 0.60480728 0.041371921 90.10434203 346786.0523 0.027983438 0.00967212 17.58152107 -1.245056445 -0.121764209 QQLVASHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQLVASHLEK 10 0 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VX93 Q13561 DCTN2 Dynactin subunit 2 0 79.82 0.025859 136610000 122580 90821 91802 111710 104940 102590 141270 127840 110320 FALSE TRUE 116785.8863 100075.7632 96011.2125 100480.6986 123241.5028 99037.28258 119716.6669 116645.6519 127427.8622 0.916486272 0.785352288 0.753455413 0.78853005 0.967147221 0.777202732 0.939485799 0.915385771 1 16.95932123 1.338167491 0.798292916 0.997379486 0.825122002 0.406123654 0.06862264 0.565999568 0.790978806 0.061694326 0.024376774 21.78549797 -1.338167491 -0.172257485 QQMLEQHLQDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QQMLEQHLQDVR 12 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;;;; 112.42 0.00023554 1059110000 1883690 1649610 1791780 2060150 1811190 1850190 2202410 2034870 1885610 FALSE TRUE 1794651.707 1817707.134 1873934.885 1853059.808 2127060.963 1786117.456 1866391.904 1856685.995 2178020.768 0.823982826 0.83456832 0.860384305 0.85079988 0.9766027 0.820064474 0.856921078 0.85246478 1 21.05458628 -5 0.247251297 1.843854162 0.843193709 0.499815151 0.044001421 150.0853609 1.49014676 64.04433195 0.062899036 1.00E-05 5 -1.000660453 QQMQDFFLAHKDEEWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQMQDFFLAHKDEEWFR 17 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 148.15 2.24E-07 477300000 563670 349480 432880 497210 410220 446360 601080 573120 434870 FALSE TRUE 537026.4362 385092.4093 452727.9762 447229.5062 481762.2381 430902.4413 509374.2064 522934.5745 502307.4186 1.069119062 0.766646868 0.901296615 0.890350191 0.959098393 0.857846063 1.014068651 1.041064804 1 18.93821106 1.644079526 6.144827933 1.0229546 0.904950509 0.319019911 0.076293163 0.154907305 12.17591392 0.038701536 0.019029993 44.06355437 -1.644079526 -0.118004091 QQNAS(ph)ESKLELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQNASESKLELR 12 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 QQNAS(1)ESKLELR;QQNAS(1)ESKLELR;QQNAS(0.92)ES(0.08)KLELR 191.15 3.47E-06 443400000 786260 816370 485000 997420 477320 742940 831780 934100 588190 TRUE FALSE 749095.048 899559.0311 507237.7297 897157.4466 560564.4569 717211.8015 704876.6843 852305.252 679403.5011 1.10257755 1.324042384 0.746592752 1.320507541 0.825083262 1.055649257 1.037493453 1.254490521 1 19.37390913 3.836836473 19.1195793 1.039596164 1.213302424 0.149080699 0.177432336 10.49710627 2036.058069 0.039991969 0.072097077 6868.09784 -3.836836473 0.17370626 QQNELAELHANLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQNELAELHANLAR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 154.6 6.08E-06 699240000 471690 383800 422940 464390 440360 435600 529940 464610 516320 FALSE TRUE 449394.1485 422909.6563 442332.2173 417708.6349 517158.6446 420515.0628 449087.92 423926.2853 596388.2686 0.753526138 0.709118 0.741684974 0.700397135 0.867150935 0.705102841 0.753012666 0.710822643 1 19.18589235 -2.020518931 2.416154996 1.289357685 0.741840866 0.736539015 0.048378342 8748952.732 3684542.521 14034347.97 0.010677734 0.009538522 2.020518931 -0.547516819 QQPGPSEHIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQPGPSEHIER 11 0 P50552;K7EQD0 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 93.348 0.0093167 368870000 83884 59985 74988 73814 90840 63800 75637 72028 108117 FALSE TRUE 79918.96956 66097.5397 78426.27397 66394.07648 106682.4672 61590.59 64097.18648 65720.84648 124883.2322 0.639949561 0.529274736 0.62799683 0.531649248 0.854257736 0.493185426 0.513256947 0.526258372 1 16.93022026 -1.470814685 3.338832053 1.00709113 0.584778728 0.598529216 0.105600572 38046970.3 43244126.39 2447153.772 0.024005827 0.033820912 1.470814685 -0.422312402 QQPPEPEWIGDGES(ph)TSPSDKVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.325)T(0.325)S(0.325)PS(0.024)DKVVK;QQPPEPEWIGDGES(0.399)T(0.263)S(0.263)PS(0.075)DKVVK 81.534 0.0059455 605092000 124431 116988 127424 125688 80478 149368 156957 142719 86971 TRUE FALSE 118549.3932 128909.2102 133266.5164 113053.6034 94513.33772 144195.3487 133010.3269 130221.7678 100458.0185 1.180088907 1.283214741 1.326589141 1.125381579 0.940824228 1.435379185 1.324038926 1.296280473 1 16.6162332 QQPPEPEWIGDGEST(ph)SPSDKVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.01)T(0.484)S(0.484)PS(0.022)DKVVK 114.06 0.0011422 115940000 132190 117300 137510 162250 87892 143580 144700 161500 80706 TRUE FALSE 125941.6407 129253.0034 143814.9695 145940.3217 103220.337 138607.7886 122623.3574 147358.2038 93221.47429 1.350993874 1.386515332 1.542723612 1.565522567 1.107259221 1.486865442 1.315398178 1.58073239 1 16.50837471 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.054)T(0.162)S(0.782)PS(0.003)DKVVK;QQPPEPEWIGDGES(0.182)T(0.133)S(0.657)PS(0.028)DKVVK 181.92 2.49E-17 844420000 618060 541770 582630 638820 347750 657870 706720 670330 389760 TRUE FALSE 588845.5287 596976.9789 609344.1618 574604.5999 408397.4899 635087.7969 598896.8842 611632.3516 450201.9902 1.30795852 1.326020302 1.3534906 1.27632621 0.907142791 1.410673011 1.330284844 1.358573185 1 18.78021291 3.00142399 24.88109299 1.232260621 1.324137714 0.108046327 0.155694892 128.9531895 2253087.165 0.044077802 0.052303355 1003.28424 -3.00142399 0.091877093 QQPPLGPSSS(ph)LLSLPGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 QQPPLGPS(0.002)S(0.225)S(0.773)LLSLPGLK;QQPPLGPS(0.001)S(0.098)S(0.902)LLSLPGLK 297.55 2.29E-49 292970000 791170 732960 722570 853220 584780 781590 836220 867730 759820 TRUE FALSE 753772.962 807649.4573 755700.5492 767452.7046 686765.4469 754523.3423 708639.2808 791746.9611 877649.005 0.858854688 0.920241979 0.861050995 0.874441491 0.782505811 0.859709677 0.807429025 0.902122553 1 19.74328456 0.984578597 21.10547142 1.000000003 0.855864501 0.619128786 0.036919858 81.95362576 112161.7617 0.037594994 0.009399349 9.651139587 -0.984578597 -0.144135502 QQPTTEGGDGETKPSQGPADGSRPEPQRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQPTTEGGDGETKPSQGPADGSRPEPQRPR 30 3 Q9Y2T7;I3L2D6 Q9Y2T7 YBX2 Y-box-binding protein 2 0 148.04 1.37E-08 68127000 22106 18730 18897 20308 15993 20125 20910 20863 18330 FALSE TRUE 21061.09319 20638.60829 19763.44614 18266.60126 18782.17414 19428.0662 17719.79546 19036.12512 21172.52278 0.994737066 0.97478267 0.933447863 0.862750341 0.887101378 0.917607524 0.836924142 0.899095744 1 14.36990556 3.586512238 2.629419866 0.889482711 0.986587159 0.367821395 0.043382827 0.214704665 2.883949538 0.011050042 0.018474946 3859.332868 -3.586512238 0.097104448 QQQDQVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQQDQVDR 8 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 149.82 0.0011612 135615000 299570 251180 261060 320560 302090 276170 339540 295180 370570 FALSE TRUE 285409.9198 276775.5276 273029.8592 288336.6998 354774.4004 266606.1637 287736.9369 269332.4744 428036.103 0.666789361 0.646617249 0.637866426 0.673627056 0.828842235 0.622859057 0.672225859 0.629228405 1 18.70737296 -1.230158574 3.431202413 1.000748224 0.67118851 0.756730608 0.058396696 12008104.32 19684787.46 97358.36516 0.013245275 0.058862869 1.230158574 -0.329559715 QQQQQQHGS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQQQQQHGSPTR 12 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 QQQQQQHGS(0.992)PT(0.008)R;QQQQQQHGS(0.976)PT(0.024)R 113.59 0.00074057 31824000 24585 25676 28619 31985 30941 27507 34597 31818 34368 TRUE FALSE 23422.91577 28292.41359 29931.20946 28769.80703 36337.1006 26554.42569 29318.59223 29031.84724 39697.61391 0.590033341 0.712698089 0.753980063 0.724723836 0.915347222 0.668917425 0.738547972 0.731324742 1 15.27676467 -5 0.126223581 1.855175369 0.606392254 0.558967656 0.077862197 114.2847458 0.919697363 25.20490192 0.639153249 1.00E-05 5 -1.248783115 QQQQQQQQHSENKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQQQQQQQHSENKR 14 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ; 61.038 0.057236 51384000 12981.3 13206.2 12590.9 13927.8 12134.4 12216.8 14304.8 15764.2 9739.5 FALSE TRUE 12367.69968 14551.92679 13168.20522 12527.75108 14250.63552 11793.72915 12122.34003 14383.80308 11249.85192 1.099365553 1.29352163 1.170522538 1.113592532 1.266739831 1.048345279 1.07755552 1.278577103 1 13.45761839 2.22965906 24.99987941 1.102249663 1.190665336 0.182935259 0.091960266 323.5395283 908648.6746 0.03192102 0.023923721 169.691098 -2.22965906 0.088415673 QQQS(ph)PPKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQQSPPKGK 9 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QQQS(1)PPKGK 68.355 0.035309 181880000 860540 788030 818000 1060000 626250 975980 1027000 1013500 695250 TRUE FALSE 819863.9796 868331.1529 855506.1091 953446.7861 735467.8017 942181.5679 870312.2879 924752.5671 803065.8192 1.020917539 1.081270217 1.065300115 1.187258583 0.91582506 1.173230818 1.083737182 1.151527739 1 19.61515871 QQREDITQSAQHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQREDITQSAQHALR 15 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;; 161.94 9.75E-07 336040000 235906 117832 247236 180796 311371 194633 334888 234568 410459 FALSE TRUE 224755.1909 129839.2148 258572.0151 162622.0426 365674.0038 187892.8104 283794.685 214027.9824 474110.8854 0.474056171 0.273858329 0.545382996 0.343004237 0.771283712 0.396305624 0.598582934 0.451430222 1 18.85486499 -4.999999999 0.172401524 3.089670356 0.349681257 0.590827228 0.136699937 82.45207529 0.78183703 58.86007391 0.421207134 1.00E-05 4.999999999 -2.739989099 QQS(ph)ASYIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQSASYIPK 9 0 O95835 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QQS(0.465)AS(0.465)Y(0.07)IPK 53.569 0.08778 0 52438 25181 42542 41172 42133 38563 62339 45221 48013 TRUE FALSE 49959.35966 27746.97253 44492.59278 37033.31234 49480.98186 37227.55364 52828.04062 41261.20951 55458.61082 0.900840445 0.500318564 0.802266629 0.667764875 0.892214593 0.67126733 0.952566965 0.744000055 1 15.75912386 1.253000029 0.472115288 0.994653733 0.702141576 0.246985668 0.132057344 1.133297717 0.687444317 0.13865136 0.079002769 17.90605975 -1.253000029 -0.292512157 QQS(ph)GSELEELMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QQSGSELEELMNK 13 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QQS(0.968)GS(0.032)ELEELMNK;QQS(0.627)GS(0.373)ELEELMNK;QQS(0.995)GS(0.005)ELEELMNK;QQS(0.997)GS(0.003)ELEELMNK 189.81 5.19E-06 99070000 184058 161093 164918 195665 130288 161297 175130 157375 140460 TRUE FALSE 175357.9431 177508.5598 172479.6534 175996.3825 153010.1859 155711.2444 148410.702 143594.4107 162241.8194 1.080843051 1.094098676 1.063102313 1.084778161 0.943099544 0.959747894 0.914749986 0.885064105 1 17.30778621 2.723825561 5.441701963 0.934435451 1.082418071 0.839312218 0.030418043 0.059170213 6.054438009 0.009121006 0.008946826 529.4507421 -2.723825561 0.14798262 QQS(ph)LGGFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QQSLGGFFK 9 0 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 QQS(1)LGGFFK;QQS(1)LGGFFK;QQS(1)LGGFFK;QQS(1)LGGFFK 111.52 0.002214 1288939000 2952472 2044472 2141084 3999090 3074893 3346416 3813469 2369554 2405370 TRUE FALSE 2812914.5 2252806.021 2239254.819 3597093.875 3611153.366 3230528.775 3231654.265 2162063.29 2778382.495 1.012428816 0.810833651 0.80595628 1.294671948 1.299732262 1.162737233 1.163142322 0.778173378 1 21.4058138 3.249810932 24.9997042 1.138502979 0.881786747 0.329345021 0.159321687 227.8747259 506365.0897 0.043132234 0.057886363 1777.505413 -3.249810932 -0.256716232 QQS(ph)LPLRPIIPLVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQSLPLRPIIPLVAR 15 1 Q9NU19 Q9NU19 TBC1D22B TBC1 domain family member 22B 1 QQS(1)LPLRPIIPLVAR;QQS(1)LPLRPIIPLVAR 111.62 0.00050148 139811000 223380 175023 202180 263140 279960 214347 283410 182126 258960 TRUE FALSE 212821.2701 192858.0427 211450.153 236688.6673 328784.9354 206924.1096 240170.5993 166178.0819 299118.1942 0.71149557 0.644755305 0.706911706 0.791288099 1.099180664 0.691780419 0.802928755 0.555559926 1 18.19035614 3.252757734 4.249564469 0.817660359 0.679248253 0.157603716 0.14906009 0.373827885 15.54506137 0.040709962 0.053253377 1789.607264 -3.252757734 -0.138412106 QQS(ph)PQEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;QQS(1)PQEPK;QQS(1)PQEPK 196.44 0.00015956 16028800000 13508120 12375170 11161900 14821340 7782473 13102870 12989710 12868470 7639272 TRUE FALSE 12869617.94 13636213.89 11673684.16 13331470.74 9139733.827 12649114.33 11007891.17 11741638.55 8823931.286 1.458490272 1.54536719 1.322957283 1.510831206 1.035789325 1.433501 1.24750418 1.33065843 1 23.07299013 -0.276004149 0.054054429 3.92E-13 2.29216579 0.490069348 0.132063424 91.70073319 1.327657887 34.46660369 21.94652502 0.529658384 0.276004149 2.29216579 QQS(ph)PS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQSPSPIR 8 0 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;Q8WZ42-6 A0A0A0MTS7;Q8WZ42-6 TTN Titin 2 QQS(1)PS(1)PIR 46.844 0.09418 496610000 30237 9329.5 21847 11157 24337 17858 32822 20065 21708 TRUE FALSE 28807.75693 10280.18666 22848.70656 10035.47716 28581.36509 17239.57298 27814.40108 18308.00223 25074.36577 1.148892746 0.409987904 0.911237667 0.400228554 1.139863929 0.687537748 1.109276356 0.730148168 1 14.61392559 2.716132731 24.9699257 0.933609751 0.725001449 0.147058726 0.257947903 1513.061366 1684554.154 0.075897061 0.071604161 520.1549441 -2.716132731 -0.208608303 QQSHFAMMHGGTGFAGIDSS(ph)SPEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.112)S(0.488)S(0.399)PEVK;QQSHFAMMHGGTGFAGIDS(0.061)S(0.551)S(0.388)PEVK;QQSHFAMMHGGTGFAGIDS(0.071)S(0.551)S(0.378)PEVK 84.107 0.020854 729230000 224520 161321 198329 243565 174610 238757 300586 310379 98940 TRUE FALSE 213907.3846 177759.7933 207422.5808 219081.3835 205061.9287 230488.7852 254726.0851 283200.5693 114283.1099 1.871732269 1.555433637 1.814988943 1.917005791 1.794332766 2.016822831 2.228904038 2.478061453 1 16.80225268 2.666830706 1.404732946 2.04359342 1.733306209 0 0.394754155 0.924322233 3.697226512 0.159563665 0.142323746 464.3342356 -2.666830706 -0.310287211 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.001)S(0.003)S(0.997)PEVK;QQSHFAMMHGGTGFAGIDS(0.005)S(0.18)S(0.815)PEVK;QQSHFAMMHGGTGFAGIDS(0.006)S(0.504)S(0.49)PEVK;QQSHFAMMHGGTGFAGIDS(0.078)S(0.375)S(0.547)PEVK;QQSHFAMMHGGTGFAGIDS(0.004)S(0.137)S(0.859)PEVK;QQSHFAMMHGGTGFAGIDS(0.002)S(0.053)S(0.946)PEVK;QQSHFAMMHGGTGFAGIDS(0.007)S(0.417)S(0.576)PEVK 127.59 0.00013667 2690900000 1153153 841503 1062140 1235308 830760 1278538 1479360 1491210 388957 TRUE FALSE 1098645.743 927253.1124 1110840.17 1111132.493 975644.281 1234261.908 1253656.462 1360631.747 449274.465 2.445377667 2.063890082 2.472520154 2.473170811 2.171599672 2.747233606 2.790402213 3.028508969 1 18.77723754 2.242577792 24.95700318 2.574861185 2.313990545 0 0.568889015 329.4163971 2046536.726 0.177408841 0.14333212 174.8146369 -2.242577792 -0.26087064 QQSLPSLCSTSDPDTPLGAPSTPGRIS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQSLPSLCSTSDPDTPLGAPSTPGRISLR 29 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 QQSLPSLCSTSDPDTPLGAPSTPGRIS(0.999)LR;QQSLPSLCSTSDPDTPLGAPS(0.002)T(0.002)PGRIS(0.996)LR 118.42 5.95E-05 299560000 140987 78466 104753 120110 122798 96525 123376 106293 109768 TRUE FALSE 134322.8239 86461.77461 109556.0287 108036.3146 144213.9323 93182.31505 104552.7252 96985.42143 126790.2608 1.059409635 0.681927571 0.864072902 0.852086855 1.137421213 0.73493275 0.824611643 0.764928006 1 16.95208441 -1.178940502 5.052643526 1.000009984 0.859452303 0.083890084 0.139241642 1.46E-05 2.38E-06 0.126015216 0.029699962 0.066230723 1.178940502 -0.140557681 QQSNEHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QQSNEHLR 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 199.89 0.00012424 593303000 648600 384561 323312 533769 711270 387956 712750 530555 697140 FALSE TRUE 617941.9634 423748.2031 338136.175 480113.526 835315.2628 374520.9864 604006.8969 484096.7916 805248.9107 0.767392486 0.526232569 0.419915098 0.59622996 1.037337961 0.46509965 0.750087195 0.601176587 1 19.61907528 2.962923615 24.98455699 0.738376974 0.579390308 0.198566277 0.187103286 1051.039405 708260.9898 0.053276273 0.05652325 918.1710918 -2.962923615 -0.158986667 QQSSSSKGDS(ph)PELKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QQSSSSKGDSPELKPR 16 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QQSSSSKGDS(1)PELKPR;QQS(0.001)S(0.003)S(0.002)S(0.004)KGDS(0.991)PELKPR;QQSSSS(0.001)KGDS(0.999)PELKPR;QQS(0.001)S(0.005)S(0.005)S(0.006)KGDS(0.983)PELKPR;QQSSS(0.001)S(0.002)KGDS(0.997)PELKPR 192.11 3.07E-10 2115170000 4681590 3724800 4036660 4611640 2248528 4994110 5061220 5376730 2602400 TRUE FALSE 4460300.519 4104361.355 4221744.854 4148069.186 2640670.571 4821162.718 4289037.933 4905915.017 3005966.901 1.483815579 1.365404707 1.40445487 1.379945063 0.878476264 1.603864207 1.426841371 1.632058895 1 21.51939769 4.584532315 1.345753209 1.353879587 1.51747685 0.033342242 0.235573407 4.421953234 8.824057611 0.062068498 0.917491625 38417.78442 -4.584532315 0.163597264 QQTEKPES(ph)EDEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QQTEKPESEDEWER 14 1 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER;QQT(0.001)EKPES(0.999)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER 213.03 9.70E-10 7213770000 11176520 10439480 8790290 12047090 7192225 11534010 11312540 11898920 8120142 TRUE FALSE 10648228.05 11503274.88 9193333.491 10836093.63 8446546.763 11134584.34 9586604.254 10856987.48 9379372.149 1.135281539 1.22644402 0.980165127 1.155311193 0.900545008 1.187135361 1.022094454 1.157538832 1 23.16105992 3.749318657 24.99230058 1.061544818 1.180862781 0.236947078 0.091786567 861.4052365 2001149.94 0.020457343 0.036410863 5614.597878 -3.749318657 0.119317963 QQTEKPES(ph)EDEWERTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQTEKPESEDEWERTER 17 2 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWERTER;QQT(0.001)EKPES(0.999)EDEWERTER 221.14 1.97E-15 549700000 452920 233676 461670 363610 366550 449990 595270 504090 534470 TRUE FALSE 431511.3692 257487.8501 482838.0262 327059.232 430476.2039 434406.7335 504450.6286 459949.2073 617352.8779 0.69897037 0.417083745 0.78211027 0.5297768 0.697293589 0.703660336 0.817118777 0.745034524 1 19.23573584 1.300084631 0.436066839 1.006779688 0.565667166 0.56779692 0.102927304 0.638918687 0.344634504 0.114387793 0.070984785 19.95651169 -1.300084631 -0.441112522 QQVAFYGQTLGQAQAHS(ph)QEQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQVAFYGQTLGQAQAHSQEQ 20 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QQVAFYGQTLGQAQAHS(1)QEQ 131.33 1.53E-05 63930000 57307 38397 48351 54775 52426 51520 62274 52635 47412 TRUE FALSE 54598.21168 42309.69795 50567.94118 49268.91293 61569.0778 49735.84948 52772.95756 48026.00036 54764.41081 0.996965198 0.772576521 0.923372322 0.899652022 1.12425345 0.908178299 0.963635996 0.876956397 1 15.74095103 2.968060834 24.98649839 0.970716765 0.888339085 0.165993031 0.084070841 1073.453461 839779.5852 0.024345514 0.025844894 929.0965205 -2.968060834 -0.08237768 QQVSWEQEFLVGS(ph)SPGGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QQVSWEQEFLVGSSPGGSGR 20 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 QQVSWEQEFLVGS(0.479)S(0.479)PGGS(0.043)GR;QQVSWEQEFLVGS(0.5)S(0.5)PGGSGR 102.98 0.00030635 48963000 81181 72729 77558 85171 77818 79929 92085 91936 128572 TRUE FALSE 77343.73502 80140.16779 81114.11102 76609.44927 91389.43456 77161.03869 78035.74199 83885.59646 148510.2891 0.520797148 0.53962704 0.546185126 0.515852805 0.61537443 0.519566955 0.525456805 0.564847035 1 17.18020336 0.728397678 4.526889832 0.999999535 0.53938126 0.962130985 0.028503602 1.283804632 21.28861709 0.025435004 0.006455016 5.350540776 -0.728397678 -0.460618275 QQYLQSIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QQYLQSIEER 10 0 P21912;A0A087WWT1;A0A087WXX8 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 97.597 0.013843 102500000 117380 98741 101900 90180 96156 95408 127210 99117 101350 FALSE TRUE 111831.68 108802.8202 106572.2158 81114.93507 112925.576 92103.99704 107801.7781 90437.79003 117066.8404 0.955280587 0.929407677 0.910353568 0.692894203 0.964624787 0.786764183 0.920856647 0.772531229 1 16.83697296 3.464706456 24.99893088 0.852632241 0.938600256 0.136529433 0.091619932 362.1142671 729165.2562 0.022148017 0.030007651 2915.455759 -3.464706456 0.085968015 QRAS(ph)LSSAPVVLVGDHA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRASLSSAPVVLVGDHA 17 1 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 QRAS(0.991)LS(0.009)SAPVVLVGDHA;QRAS(0.738)LS(0.262)SAPVVLVGDHA 193.06 9.17E-11 149973000 127358 89643 99867 115618 127505 104683 121433 130525 147602 TRUE FALSE 121338.0397 98777.72362 104446.0007 103995.859 149741.8316 101057.8015 102906.1656 119095.539 170491.3643 0.711696104 0.579370832 0.612617543 0.609977282 0.878295697 0.5927444 0.603585794 0.698542941 1 17.37933914 0.926895864 10.93430184 0.999999993 0.650694347 0.599445438 0.087746984 7.400966859 1107.480622 0.080530247 0.020139071 8.450761867 -0.926895864 -0.349305646 QRDEKDEHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRDEKDEHGR 10 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 150.09 1.25E-05 246438000 43106 28205.7 40260 48397 42988 44016 53280 31224 44665.3 FALSE TRUE 41068.46481 31079.8929 42105.96082 43532.04161 50485.09359 42491.71488 45151.15745 28489.86103 51591.76661 0.796027496 0.602419629 0.816137217 0.843778852 0.978549426 0.823614264 0.875162074 0.552217203 1 15.65485323 3.56195127 7.029981196 0.845172934 0.699560431 0.17869705 0.128112682 0.381281834 27.19875861 0.031570302 0.048950413 3647.130218 -3.56195127 -0.145612503 QRDELNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QRDELNR 7 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;;;; 161.9 0.0011784 745392000 513613 434381 464374 474789 622279 481924 579937 520974 672674 FALSE TRUE 489335.5314 478644.9178 485666.0072 427062.3077 730804.2606 465234.851 491456.9594 475354.7547 776988.8484 0.629784497 0.616025466 0.625061747 0.549637628 0.940559523 0.598766446 0.632514817 0.611790962 1 19.56753437 -1.498859803 2.67332504 1.016112432 0.647632336 0.517561586 0.106006968 8412885.469 8567654.038 993921.8683 0.024388874 0.031705908 1.498859803 -0.368480097 QREEHYFCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QREEHYFCK 9 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ;;; 137.95 9.02E-05 601540000 1527550 1113120 1100800 1195340 1275210 1148440 1511450 1367400 1255430 FALSE TRUE 1455345.739 1226548.194 1151272.769 1075182.152 1497606.22 1108669.235 1280850.543 1247663.207 1450115.673 1.003606655 0.845827831 0.793917886 0.741445784 1.032749489 0.764538482 0.883274739 0.860388747 1 20.46773655 -0.72052387 6.149226876 1.000000002 0.867918149 0.16918222 0.093404671 2.52E-09 4.10E-10 0.084512439 0.019919773 0.190316363 0.72052387 -0.132081853 QREEKS(ph)PDDLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QREEKSPDDLKK 12 3 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 QREEKS(1)PDDLKK;QREEKS(1)PDDLKK 114.59 0.0057564 1047580000 1145710 989310 959970 1308340 472800 1342260 1218960 1358300 488620 TRUE FALSE 1091554.559 1090121.814 1003985.574 1176823.178 555256.1703 1295777.2 1032985.264 1239360.051 564392.6941 1.934033821 1.931495261 1.778877694 2.085114123 0.983811761 2.295878762 1.830259809 2.195917956 1 19.10633979 QREESYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QREESYSR 8 1 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 207.68 5.60E-05 1574476000 675227 492337 449165 520094 642819 527435 675117 577110 704261 FALSE TRUE 643310.3579 542506.7 469759.6595 467813.163 754926.4301 509169.7937 572115.5023 526575.1889 813474.199 0.790818392 0.66690093 0.577473336 0.575080517 0.928027504 0.625920028 0.703298891 0.647316399 1 19.63373706 -1.741437249 2.604160292 1.065356257 0.691793226 0.46314976 0.105078271 21880101.03 16932265.06 9237030.875 0.025581157 0.018136887 1.741437249 -0.373563031 QREFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 125.31 0.0037039 8229400000 386710 353580 325640 448670 508190 327760 459340 336160 573390 FALSE TRUE 368430.9847 389610.204 340570.9161 403568.8392 596818.1751 316409.589 389259.2466 306724.0483 662308.3927 0.556283128 0.58826101 0.514218029 0.609336743 0.901118243 0.47773755 0.58773111 0.463113637 1 19.33714361 -1.303336409 4.518582115 1.000292802 0.588370965 0.532963264 0.121430494 0.000335438 5.17E-05 0.110108406 0.025934599 0.049735168 1.303336409 -0.411921837 QRELEQLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QRELEQLGR 9 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 ;;; 168.83 5.37E-05 1071130000 709630 595835 736540 753650 730540 813393 994000 798180 547572 FALSE TRUE 676087.1963 656551.2639 770311.0875 677891.6702 857945.9447 785224.9965 842347.0439 728287.1278 632486.6691 1.068935093 1.038047592 1.217908812 1.071788076 1.356464866 1.241488611 1.331802052 1.151466368 1 19.27067555 3.420779649 1.336246651 1.238413585 1.051549166 0.152986289 0.112536867 0.481537772 1.768051091 0.034639304 0.062249005 2634.99411 -3.420779649 -0.186864419 QRESDITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRESDITK 8 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 93.098 0.010314 245840000 309620 244190 265810 281760 225620 290790 350470 348530 298560 FALSE TRUE 294984.8762 269073.2386 277997.6514 253436.9495 264968.0566 280719.8694 296999.3647 318010.8655 344859.16 0.855377819 0.78024095 0.806119378 0.734899863 0.768337012 0.814013087 0.861219301 0.922147075 1 18.39564776 1.235774354 1.352825889 0.996746284 0.792279481 0.842334701 0.030920657 0.15629675 0.554349286 0.030162296 0.009409292 17.20974176 -1.235774354 -0.204466804 QRHDGAFLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRHDGAFLIR 10 1 P62993;J3KT38;J3QRL5 P62993 GRB2 Growth factor receptor-bound protein 2 0 94.297 0.0049271 41826000 59289 36774 40312 42954 62569 40855 68318 48019 60741 FALSE TRUE 56486.52647 40521.31241 42160.34507 38636.18231 73481.01379 39440.18111 57894.83435 43814.2018 70160.40406 0.80510549 0.577552438 0.600913658 0.550683578 1.047328829 0.562143015 0.825178178 0.624486167 1 16.09836944 QRIDEFEAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRIDEFEAL 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 104.44 0.026589 352530000 916510 651290 647520 796430 896380 672900 946130 821600 935080 FALSE TRUE 873188.3886 717657.1915 677209.4325 716371.3433 1052708.388 649597.3043 801780.4916 749656.3484 1080087.431 0.80844232 0.66444361 0.626995013 0.663253106 0.974651087 0.601430297 0.742329249 0.694070061 1 20.04271667 -1.369239404 3.376444624 1.002031466 0.721109097 0.400563591 0.10689081 41509535.47 58949069.16 843828.7994 0.023652576 0.042732726 1.369239404 -0.28092237 QRLEAEAGR ddPTM_SK-BR-3_Trastuzumab_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 ;; 141.95 9.62E-05 934390000 660100 499560 515230 643170 670570 564490 745240 613060 782040 FALSE TRUE 628898.3812 550465.732 538853.8051 578517.3297 787517.1957 544941.5698 631539.9507 559377.2164 903314.7691 0.696211778 0.609384182 0.596529387 0.64043825 0.87180817 0.603268748 0.699136084 0.619249497 1 19.78486927 -2.147691203 2.302802822 1.730037662 0.666393705 0.624878888 0.081081865 5926665.447 1474687.745 22578215.62 0.018294289 0.007117194 2.147691203 -1.063643957 QRPGQQVATCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRPGQQVATCVR 12 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 160.52 6.19E-05 231990000 83683 68244 74505 81661 79709 79143 104379 77783 98247 FALSE TRUE 79727.47043 75198.14119 77921.12795 73452.28113 93610.22436 76402.25807 88454.0665 70971.90817 113482.643 0.702552111 0.662640023 0.686634765 0.647255644 0.824885832 0.673250605 0.77945018 0.625398795 1 16.79211213 -5 0.308480883 3.600208029 0.688588962 0.69305332 0.061918556 151.7244076 1.378606097 256.2464143 0.052321323 1.00E-05 5 -2.911619067 QRPQATAEQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 216.84 1.08E-11 519351000 309679 201184 164148 196871 328195 208222 358369 281750 371803 FALSE TRUE 295041.0874 221684.8783 171674.3482 177081.153 385432.1041 201011.2199 303693.2272 257078.4763 429460.3103 0.687004318 0.5161941 0.399744386 0.412334152 0.897480151 0.468055406 0.707150859 0.59860823 1 18.71216528 -0.416968002 0.399879532 1.103070798 0.548828972 0.445931806 0.148493938 6.968988671 1.127015457 1.136030486 0.094377446 0.38285295 0.416968002 -0.554241826 QRQEELCLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 187.42 1.12E-06 1101280000 1438170 1240580 1303320 1351720 1455810 1376980 1637670 1535080 1644290 FALSE TRUE 1370190.554 1366996.512 1363078.511 1215842.537 1709702.803 1329294.837 1387813.364 1400660.257 1899278.095 0.721427029 0.719745316 0.717682426 0.640160354 0.900185606 0.699894787 0.730705718 0.737469811 1 20.85701973 -4.999999998 0.348768558 4.074940005 0.722727062 0.62566639 0.064944911 263.8628422 2.168925847 606.3828777 0.04513642 1.00E-05 4.999999998 -3.352212943 QRQELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QRQELEK 7 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 110.12 0.0062709 4817620000 2167800 1713710 1822970 2147100 1908700 2038690 2430140 2168140 2182550 FALSE TRUE 2065332.39 1888338.997 1906554.978 1931269.429 2241576.676 1968089.654 2059377.51 1978286.168 2521008.707 0.819248416 0.749041045 0.756266717 0.766070114 0.889158641 0.780675469 0.816886314 0.784720085 1 21.26556967 -5 0.276592419 2.477884138 0.780014953 0.717880797 0.040355698 115.3103084 1.10943883 97.62970146 0.044910116 1.00E-05 5 -1.697869185 QRQEVCQSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRQEVCQSYK 10 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 173.04 3.22E-06 442300000 741300 413670 301800 611530 831330 489970 858570 555140 642520 FALSE TRUE 706260.2181 455823.4433 315637.8285 550057.8426 976313.6888 473002.216 727579.3778 506528.9986 742158.7201 0.951629616 0.614185929 0.425296934 0.741159307 1.315505245 0.637332963 0.980355493 0.682507643 1 19.50136823 2.981566963 24.81979716 0.915532835 0.680350643 0.227633719 0.222618997 1068.540865 1438775.718 0.064085133 0.069144643 958.4444852 -2.981566963 -0.235182192 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GN77;R4GND1;A0A1B0GX65;Q969T4;R4GMM6;R4GNG6 R4GN77 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 QRS(0.997)DDES(0.003)PSTSSGSSDADQRDPAAPEPEEQEER;QRS(1)DDESPSTSSGSSDADQRDPAAPEPEEQEER;QRS(0.999)DDES(0.001)PSTSSGSSDADQRDPAAPEPEEQEER;QRS(0.996)DDES(0.004)PSTSSGSSDADQRDPAAPEPEEQEER 268.76 1.50E-60 514889000 156212.9 124932.2 145184.6 155668.1 159569.7 160075.1 198934.6 169352.6 176965.8 TRUE FALSE 148829.0258 137662.9332 151841.4575 140020.0468 187398.6052 154531.6591 168583.4731 154523.1885 204408.7524 0.728095172 0.673468878 0.742832465 0.685000252 0.916783665 0.755993358 0.824737058 0.755951918 1 17.64109745 -4.999999991 0.101882773 1.802873288 0.58969684 0.616919937 0.063346745 108.2860107 0.747537761 18.29211183 0.916947062 1.00E-05 4.999999991 -1.213176448 QRS(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRSMVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 34 1 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4;R4GNG3;Q14161-9;Q14161-5;F8WAK2;Q14161-11;Q14161-7;Q14161-10;Q14161-8 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 QRS(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR;QRS(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 76.358 0.0015612 130091000 22774.5 13659.1 20262.9 22323.6 22376 20124.4 20977 18722 22024.8 TRUE FALSE 21697.99452 15050.97782 21191.97401 20079.58932 26278.36732 19427.48698 17776.57338 17082.60243 25440.2935 0.85289875 0.591619661 0.833008236 0.789282927 1.032942773 0.763650269 0.698756615 0.671478198 1 14.63482769 QRS(ph)PIALPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRSPIALPVK 10 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVK;QRS(1)PIALPVK 62.466 0.071235 316450000 2237100 2166400 2194100 2305600 1835640 2435800 2754000 2449100 1079120 TRUE FALSE 2131356.717 2387158.623 2294701.655 2073836.708 2155775.035 2351447.635 2333826.719 2234643.821 1246464.418 1.709921828 1.915143816 1.84096844 1.663775297 1.729511892 1.886493991 1.872357273 1.792785889 1 20.24941027 0.923515896 21.5718047 1 1.810513772 0.905287658 0.081434889 4097.776374 1155750.963 0.079743889 0.019935972 8.385247704 -0.923515896 0.810513772 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QRSPIALPVKQEPPQIDAVK 20 2 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVKQEPPQIDAVK;QRS(1)PIALPVKQEPPQIDAVK;QRS(1)PIALPVKQEPPQIDAVK;QRS(1)PIALPVKQEPPQIDAVK 191.22 8.04E-18 1468790000 1536300 1123650 1394860 1436810 1073930 1600530 1837520 1714790 1354770 TRUE FALSE 1463682.144 1238151.212 1458815.711 1292379.129 1261223.052 1545103.245 1557172.576 1564633.897 1564860.812 0.935343343 0.791221304 0.932233525 0.825874812 0.805965005 0.987374233 0.995086952 0.999854993 1 20.57760291 2.220829621 22.78343549 0.994882571 0.857926073 0.679528337 0.046903121 48.15478916 61875.29839 0.016546699 0.012257838 166.27602 -2.220829621 -0.136956498 QRS(ph)PLLNQPVPELSHASLIANQSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QRSPLLNQPVPELSHASLIANQSPFR 26 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR 279.72 5.35E-61 924559000 344635 278353 362791 402612 550081 314360 539931 424204 709103 TRUE FALSE 328344.7866 306717.4872 379425.3262 362140.6768 646014.9522 303473.6344 457554.6094 387058.4489 819067.0716 0.400876556 0.374471759 0.46324085 0.442138 0.788720454 0.370511335 0.558628988 0.472560139 1 19.64362207 -5 0.187503759 3.214097555 0.37628965 0.65687982 0.118655456 78.63442818 0.76631785 65.01645502 0.309745552 1.00E-05 5 -2.837807905 QRS(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QRSPSPAPAPAPAAAAGPPTR 21 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 QRS(1)PS(0.999)PAPAPAPAAAAGPPT(0.001)R;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR 182.19 5.69E-16 2080748000 923463 895026 916027 1045364 908075 985588 1094561 888695 1122569 TRUE FALSE 879812.7341 986230.167 958027.744 940282.0247 1066442.992 951456.8404 927565.6165 810876.1545 1296651.267 0.678526876 0.760597851 0.738847652 0.725161845 0.822459376 0.733780057 0.715354729 0.625361788 1 20.30635909 -2.03384357 2.86879662 1.339911486 0.728184545 0.742396433 0.050876236 3885974.621 7388601.884 8611056.659 0.011874579 0.009250313 2.03384357 -0.611726942 QRS(ph)SPVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.619)S(0.381)PVTK 71.555 0.029335 130830000 224460 197580 191570 230540 146500 216220 226580 244990 202620 TRUE FALSE 213850.2206 217713.6266 200353.674 207365.6812 172049.5536 208732.2472 192011.0596 223537.3768 234041.2748 0.913728661 0.930236031 0.856061283 0.886021841 0.735124836 0.891860837 0.820415372 0.955119464 1 17.83640346 1.058577934 5.390663042 0.999403115 0.8679625 0.443174346 0.054761983 0.173021756 9.470917041 0.054011555 0.013632058 11.44400222 -1.058577934 -0.131440614 QRS(ph)VSPYS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRSVSPYSR 9 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 QRS(0.973)VS(0.052)PYS(0.975)R;QRS(0.984)VS(0.186)PY(0.002)S(0.828)R 103.11 0.063326 103670000 390940 354520 386160 430340 403340 387460 451790 385470 444830 TRUE FALSE 372461.041 390645.9911 403865.818 387081.4056 473682.3683 374042.163 382861.1378 351716.2033 513811.9645 0.724897563 0.760289791 0.786018711 0.753352262 0.921898284 0.727974802 0.745138619 0.684523187 1 18.97088096 -2.095868798 2.486146816 1.410791691 0.762750615 0.587612732 0.062392749 10755772.47 3060702.341 25020399.68 0.01505012 0.008019203 2.095868798 -0.648041076 QRSS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.3)S(0.698)PVT(0.002)K;QRS(0.164)S(0.836)PVTK;QRS(0.211)S(0.789)PVTK;QRS(0.172)S(0.828)PVTK;QRS(0.282)S(0.718)PVTK;QRS(0.159)S(0.841)PVTK;QRS(0.005)S(0.995)PVTK;QRS(0.245)S(0.755)PVTK;QRS(0.336)S(0.664)PVTK 113.42 0.0017274 7579710000 7695470 6714680 6230340 8007810 5122450 7313340 8138370 7841030 6647320 TRUE FALSE 7331720.384 7398913.526 6516007.252 7202849.725 6015803.658 7060077.202 6896712.185 7154427.845 7678152.436 0.954880806 0.963632018 0.848642601 0.938096734 0.783496252 0.919502089 0.898225484 0.931790285 1 22.87232777 0.878875304 3.530331996 0.999976945 0.906897605 0.253872975 0.053085932 0.855642573 20.95163548 0.050991917 0.013156898 7.566156224 -0.878875304 -0.09307934 QRT(ph)LEDEEEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QRTLEDEEEQER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQER;QRT(1)LEDEEEQER;QRT(1)LEDEEEQER 234.3 8.26E-16 1939590000 735992 593331 613698 793100 632794 734401 706166 542631 580569 TRUE FALSE 701203.1168 653792.1035 641836.6603 713376.0812 743153.0733 708968.5092 598427.4071 495115.353 670600.6754 1.045634373 0.974935051 0.957107089 1.063786703 1.108190165 1.057214129 0.892375193 0.738316216 1 19.35509441 1.6315605 4.794298276 0.853754796 1.029087987 0.486690056 0.075795345 0.119140667 6.075197282 0.039765252 0.018582805 42.81150543 -1.6315605 0.175333191 QRT(ph)LEDEEEQERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QRTLEDEEEQERER 14 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER 175.32 6.49E-06 5727380000 1154050 894740 1048860 1250470 1055800 1078210 1308470 922380 1132900 TRUE FALSE 1099500.344 985915.0232 1096951.268 1124770.38 1239931.186 1040871.317 1108838.87 841611.5174 1308584.346 0.840221226 0.753421074 0.838273262 0.859532199 0.947536312 0.795417827 0.847357584 0.643146558 1 20.31957549 -2.345222015 2.32528471 2.151549079 0.818674621 0.351757903 0.078566862 3221745.999 576335.9548 19541141.32 0.017658576 0.00451625 2.345222015 -1.332874457 QRVELLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRVELLER 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 78.098 0.028733 217380000 157730 150050 137390 160530 178470 166880 198120 176650 124740 FALSE TRUE 150274.4155 165340.2656 143689.4674 144393.2194 209595.1115 161100.9038 167893.1553 161181.5895 144084.0421 1.042963629 1.147526563 0.997261496 1.002145812 1.454672623 1.118103722 1.165244623 1.118663713 1 17.13655103 QRVEQFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QRVEQFAR 8 1 P34897-3;P34897-2;P34897 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 ;;;; 195.88 0.00014279 1252024000 1335450 750879 536342 580820 1243640 601593 1203270 857860 1298230 FALSE TRUE 1272325.925 827394.4238 560933.8112 522434.8701 1460530.422 580759.6836 1019689.062 782741.2306 1499552.878 0.848470197 0.551760752 0.374067377 0.348393763 0.973977273 0.387288566 0.679995402 0.52198308 1 20.51610097 -1.382387347 2.918747192 1.006374756 0.59409421 0.288436862 0.204107415 24001947.41 28819132.25 1293322.237 0.046110763 0.041458411 1.382387347 -0.412280546 QRVS(ph)GNTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QRVSGNTSR 9 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 1 QRVS(0.993)GNT(0.006)SR 75.479 0.023102 42671000 13128 9351.9 15338 17098 16079 12767 16405 11683 20848 TRUE FALSE 12507.46546 10304.86924 16041.26247 15379.27656 18883.17251 12324.87559 13902.11595 10659.97458 24081.00136 0.519391419 0.42792528 0.666137684 0.638647718 0.784152296 0.511809098 0.577306389 0.442671566 1 14.55560776 -2.113151215 2.482844429 1.831475559 0.564627787 0.614243558 0.106735401 5741208.485 2075602.291 26862582.13 0.026522154 0.007706351 2.113151215 -1.266847772 QRWDEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QRWDEAFR 8 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;;;; 169.09 0.00027639 2068380000 980824 805659 564232 692807 1109312 694727 1067349 904960 1009479 FALSE TRUE 934462.3933 887756.5681 590102.5953 623164.7241 1302775.662 670668.4298 904505.3068 825716.9049 1166023.848 0.801409332 0.761353698 0.506081069 0.53443566 1.117280461 0.575175569 0.775717674 0.708147528 1 20.15316586 QRYEILTPNSIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QRYEILTPNSIPK 13 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 91.207 0.0060537 787420000 1787300 1367510 1667340 1711620 1274130 1793530 1874140 1884170 1680720 FALSE TRUE 1702817.871 1506860.824 1743789.188 1539564.706 1496337.869 1731419.606 1588205.522 1719182.086 1941357.474 0.877127419 0.776189261 0.898231888 0.793035145 0.770768851 0.891860273 0.818090199 0.885556684 1 20.88863436 0.758530038 1.509695725 1.000248686 0.828895113 0.571782309 0.045835945 0.557481809 2.155148047 0.03935058 0.011454889 5.73495531 -0.758530038 -0.171353573 QS(ph)LGELIGTLNAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSLGELIGTLNAAK 14 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 QS(1)LGELIGTLNAAK;QS(1)LGELIGTLNAAK 135.38 3.49E-05 133871000 392379 415240 363113 452510 283468 394292 425760 454280 236482 TRUE FALSE 373832.0223 457553.4281 379762.0902 407022.8351 332904.7295 380637.5692 360802.4924 414500.8349 273154.4208 1.368573942 1.675072389 1.390283522 1.490083279 1.21874187 1.393488592 1.320873707 1.517459735 1 18.05935725 -3.697212057 0.168647855 1.03E-15 1.546322898 0.51943956 0.124902406 60.1293497 0.844675621 21.3387865 0.458173294 0.000200811 3.697212057 1.546322898 QS(ph)PALQHRPMGQSQANHIPGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.999)PALQHRPMGQS(0.001)QANHIPGDR;QS(0.828)PALQHRPMGQS(0.172)QANHIPGDR 87.489 0.0017071 363560000 161701 138311 149366 166323 183524 130059 168700 145800 165604 TRUE FALSE 154057.7142 152405.0481 156214.5788 149603.896 215530.5275 125555.0242 142961.7166 133032.9791 191285.0225 0.805383046 0.796743238 0.816658705 0.782099372 1.126750671 0.65637666 0.747375381 0.695469919 1 17.54536439 -1.717087586 9.067301611 1.000539683 0.80166886 0.195155685 0.125459033 0.001289525 4.02E-05 0.114445104 0.02690518 0.019182818 1.717087586 -0.198870823 QS(ph)PECENFLDVGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 70.197 0.049724 13443000 19708 20422 18353 19301 13548 18470 16828 18884 11132 TRUE FALSE 18776.4419 22503.02502 19194.5032 17360.82681 15910.76691 17830.37927 14260.57953 17230.41685 12858.29371 1.460259217 1.750078629 1.492772186 1.350165676 1.237393333 1.386683154 1.109056914 1.340023587 1 13.65041159 3.165237235 1.888088832 1.223473499 1.607645058 0.615855527 0.128559928 0.194270055 1.42439523 0.038534659 0.05090837 1462.976111 -3.165237235 0.384171559 QS(ph)PGPALAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSPGPALAR 9 0 P85037 P85037 FOXK1 Forkhead box protein K1 1 QS(1)PGPALAR;QS(1)PGPALAR 107.85 0.0028398 741580000 1282720 1055400 1043090 1245320 1441580 1122170 1263860 1151130 1345880 TRUE FALSE 1222088.368 1162946.46 1090916.708 1120138.068 1692991.096 1083308.972 1071034.945 1050330.955 1554592.197 0.786115079 0.748071721 0.701738186 0.720534987 1.089025855 0.696844468 0.688949132 0.675631176 1 20.56810475 -1.033952517 4.79635913 1.000004153 0.761558769 0.276576419 0.120242676 6.86E-06 1.38E-06 0.111967779 0.026390445 0.092479928 1.033952517 -0.238445384 QS(ph)PSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSPSFK 6 0 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 QS(0.982)PS(0.018)FK;QS(0.89)PS(0.11)FK;QS(0.981)PS(0.019)FK 81.915 0.063588 1992960000 7452500 6836000 6262300 8121700 4651960 7511700 7387700 7327100 4777800 TRUE FALSE 7100235.094 7532596.172 6549432.649 7305291.286 5463260.351 7251567.945 6260570.681 6685500.281 5518716.822 1.28657355 1.364918044 1.186767298 1.323730048 0.989951202 1.313995296 1.134425063 1.211422962 1 22.39590143 7.026866408 0.028305055 2.16E-08 2.843757483 0.396247975 0.100881584 1110.143893 2.850298764 99.73666534 202.9658076 10638157.3 -7.026866408 2.843757461 QS(ph)PSSS(ph)PTRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSPSSSPTRER 11 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 QS(0.791)PS(0.259)S(0.341)S(0.608)PT(0.001)RER;QS(0.999)PS(0.001)S(0.26)S(0.735)PT(0.005)RER;QS(0.999)PS(0.096)S(0.414)S(0.486)PT(0.005)RER 110.97 0.0045001 301683000 491341 388959 532532 474582 454331 472453 539400 474313 515042 TRUE FALSE 468116.2847 428594.3643 556949.1189 426876.1157 533566.1826 456091.8341 457104.6232 432779.6392 594912.0829 0.786866326 0.720433114 0.93618727 0.717544874 0.89688241 0.766654178 0.768356597 0.727468229 1 19.18231695 -2.266647701 2.363221402 1.910736983 0.786602731 0.449276794 0.072962986 5554658.458 857304.2476 27111705.34 0.017151341 0.005411932 2.266647701 -1.124134252 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Trastuzumab_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(0.872)PT(0.128)GGGGGGGSGGTR;QSAGPNS(0.979)PT(0.021)GGGGGGGSGGTR 249.93 9.12E-31 105992000 110126 93610 108893 118829 109651 106239 121026 97864 116153 TRUE FALSE 104920.5622 103148.9654 113885.8518 106884.0832 128774.0997 102559.9168 102561.2609 89294.50935 134165.414 0.782023914 0.768819343 0.848846572 0.79665899 0.959815916 0.764428877 0.764438896 0.665555352 1 17.03365329 -2.122232133 2.645646302 1.433713246 0.794036985 0.432724561 0.074187511 5881680.41 3176178.472 15373052.69 0.017212191 0.007546887 2.122232133 -0.639676261 QSANDFFSYYDSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSANDFFSYYDSHR 14 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 103.88 0.0010904 81631000 58714 58418 50781 57040 62057 61976 69643 68989 58048 FALSE TRUE 55938.70558 64370.86062 53109.35908 51306.23083 72879.72115 59829.75558 59017.68127 62947.95743 67049.78737 0.8342861 0.960045708 0.792088404 0.765196026 1.086949325 0.892318349 0.880206837 0.938824117 1 16.03294514 2.765859412 24.9997062 0.940771756 0.855313709 0.354939715 0.077763968 1152.744871 1055659.122 0.023980234 0.025428795 583.2562641 -2.765859412 -0.085458047 QSAPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSAPSPTR 8 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QS(0.001)APS(0.985)PT(0.014)R 65.241 0.067952 343480000 361710 440650 402630 378480 320190 342600 336620 314790 344350 TRUE FALSE 344612.6851 485552.736 421090.9838 340434.4713 376031.0346 330735.6761 285262.4365 287225.3188 397750.0393 0.866405157 1.22074843 1.058682444 0.855900535 0.945395342 0.831516388 0.717190216 0.72212518 1 18.60150255 2.796729149 1.323224355 0.791078946 1.054105479 0.34066697 0.124445747 0.386921869 1.388671632 0.05250785 0.052275331 626.2231943 -2.796729149 0.263026533 QSDEVGDRDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSDEVGDRDHR 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 86.313 0.0087505 14910000 13129 12346 12018 13361 15866 13959 12544 15414 14946 FALSE TRUE 12508.41819 13604.07144 12569.03719 12017.9269 18633.02538 13475.59633 10630.18241 14064.26845 17263.74935 0.724548181 0.788013725 0.728059527 0.696136549 1.079315101 0.780571825 0.615751666 0.814670566 1 14.0754582 -2.288511238 1.959234783 1.84648115 0.769669051 0.247019 0.120750443 5159005.791 679514.9799 19319451.2 0.030067564 0.005146225 2.288511238 -1.076812098 QSDS(ph)VKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QSDSVKGK 8 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 1 QS(0.046)DS(0.954)VKGK;QS(0.01)DS(0.99)VKGK;QS(0.043)DS(0.957)VKGK;QS(0.007)DS(0.993)VKGK 93.258 0.0067807 695730000 2597340 1969830 1825690 3212720 1638580 2431390 3059830 2543730 1951180 TRUE FALSE 2474568.886 2170557.917 1909399.692 2889771.282 1924347.833 2347190.355 2592996.736 2320987.516 2253759.029 1.097974031 0.963083404 0.847206675 1.282200645 0.853839212 1.041455774 1.150520842 1.029829492 1 21.10390184 1.995684883 24.99384326 1.081628073 1.010117196 0.024156775 0.128675086 533.2610922 3088743.234 0.044936365 0.032411699 99.01132742 -1.995684883 -0.071510877 QSFDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Trastuzumab_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 263.18 1.33E-27 7029110000 6827134 6323850 5930983 7036851 2700102 7600141 6875283 8071976 2894658 TRUE FALSE 6504428.906 6968257.505 6202924.437 6329493.368 3170998.934 7336946.211 5826332.305 7365150.989 3343546.779 1.945367999 2.084091525 1.855192958 1.893047649 0.94839377 2.19436027 1.742560428 2.202795856 1 21.67294787 3.251950533 2.888764102 1.700029843 2.001146543 0.106951553 0.421144365 0.611010569 10.46445804 0.115653546 0.154321933 1786.2841 -3.251950533 0.3011167 QSFTMVADT(ph)PENLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSFTMVADTPENLR 14 0 Q14847;Q14847-2;C9J9W2;F6S2S5 Q14847 LASP1 LIM and SH3 domain protein 1 1 QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR 311.95 1.06E-54 168077000 392270 396480 392280 455990 405110 436800 502510 475020 526730 TRUE FALSE 373728.1745 436881.7628 410266.426 410153.0189 475761.0557 421673.5065 425842.8703 433424.7306 608412.5982 0.614267646 0.718068239 0.6743227 0.674136302 0.781971079 0.693071622 0.699924478 0.712386186 1 19.2146905 -5 0.252493368 2.885262477 0.667039685 0.860303353 0.038989105 63.35569709 0.626563206 61.71142596 0.052884632 1.00E-05 5 -2.218222792 QSGLSSLVNGKS(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSGLSSLVNGKSPIR 15 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 QSGLSSLVNGKS(1)PIR 162.39 9.68E-07 465610000 350830 307410 315400 361470 249840 348750 394520 390430 344470 TRUE FALSE 334246.9612 338735.4285 329861.402 325134.3489 293412.0169 336672.7001 334328.7281 356241.8794 397888.6483 0.840051513 0.851332226 0.829029437 0.817149095 0.737422438 0.84614804 0.840257016 0.895330593 1 18.60200521 0.916798854 1.553330706 0.999639592 0.822861887 0.768945495 0.031623248 0.240837798 1.166206468 0.030771707 0.008977822 8.256554541 -0.916798854 -0.176777705 QSHAASAAPQASS(ph)PPDYTMAWAEYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QSHAASAAPQAS(0.008)S(0.992)PPDYTMAWAEYYR;QSHAASAAPQAS(0.006)S(0.994)PPDYTMAWAEYYR;QSHAASAAPQAS(0.008)S(0.992)PPDYTMAWAEYYR;QSHAASAAPQAS(0.211)S(0.789)PPDYTMAWAEYYR;QSHAASAAPQAS(0.04)S(0.96)PPDYTMAWAEYYR;QSHAASAAPQAS(0.062)S(0.938)PPDYTMAWAEYYR 246.89 1.21E-45 1082178000 662560 564090 600621 700260 712570 641720 801311 702543 714227 TRUE FALSE 631242.1019 621571.4123 628160.0669 629868.5344 836841.9824 619497.0755 679056.2899 641024.6105 824985.6754 0.765155227 0.753432976 0.761419362 0.763490268 1.014371531 0.750918584 0.823112825 0.777013019 1 19.65400954 -5 0.154336026 1.711443664 0.739528744 0.393673735 0.078204242 134.9124793 1.219128592 29.60368974 0.346147518 1.00E-05 5 -0.971914919 QSHSES(ph)PSLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSES(1)PSLQSK;QSHSES(0.999)PS(0.001)LQSK;QSHSES(1)PSLQSK;QSHSES(1)PSLQSK;QSHSES(0.999)PS(0.001)LQSK;QSHS(0.005)ES(0.981)PS(0.014)LQSK;QSHSES(0.97)PS(0.029)LQSK;QSHS(0.005)ES(0.97)PS(0.024)LQSK;QSHSES(0.999)PS(0.001)LQSK;QSHSES(0.964)PS(0.036)LQSK;QSHS(0.01)ES(0.989)PSLQSK 238.83 3.96E-16 15702747000 13639528 10875527 11811612 13965107 9660789 13165567 14611949 13468852 8921424 TRUE FALSE 12994814.54 11983755.57 12353186.09 12561307.91 11345627.54 12709640.11 12382627.81 12289447.92 10304912.87 1.261030996 1.162916729 1.198766671 1.218963039 1.100992089 1.233357358 1.201623727 1.192581448 1 23.29682897 0.79476291 7.833491632 1.000000001 1.197332317 0.677473193 0.042569638 28.22809954 1078.067036 0.037790316 0.009465674 6.233944189 -0.79476291 0.197332316 QSHSGSIS(ph)PYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSGS(0.002)IS(0.998)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(0.999)PY(0.001)PK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.004)IS(0.996)PYPK;QSHSGS(0.001)IS(0.999)PYPK;QSHSGSIS(1)PYPK 148.15 3.86E-05 13090932000 21283490 20464670 17104890 23459230 11715970 20929960 20112240 21460400 10470560 TRUE FALSE 20277461.61 22550043.14 17889166.13 21101063.63 13759231.46 20205150.24 17043748.4 19581213.61 12094280.97 1.676615721 1.86452119 1.479142594 1.744714191 1.137664281 1.670636749 1.409240322 1.619047355 1 23.52782166 -2.162252105 0.104587025 1.52E-11 2.062219995 0.488384056 0.193117323 59.39854167 0.840844416 18.03444098 3.203170907 0.006882527 2.162252105 2.062219995 QSHSS(ph)S(ph)SPHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.101)HS(0.426)S(0.559)S(0.489)S(0.425)PHPK 44.968 0.090653 71620000 328210 327510 256100 306700 257830 290760 338130 294720 310920 TRUE FALSE 312696.1637 360883.6413 267842.4383 275869.9333 302795.4704 280690.9083 286542.0583 268912.7544 359135.8856 0.870690388 1.004866558 0.745796923 0.768149172 0.84312229 0.781572991 0.797865292 0.748777176 1 18.45417029 3.735607297 24.9988808 0.801313296 0.937778474 0.291712678 0.079978865 233.6530039 1977801.06 0.018470352 0.030056465 5440.105188 -3.735607297 0.136465178 QSHSS(ph)SS(ph)PHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QSHS(0.077)S(0.919)S(0.307)S(0.696)PHPK 118.21 0.00039668 182960000 494990 495240 481760 573330 370310 518620 578840 571560 244590 TRUE FALSE 471592.8037 545705.519 503849.1725 515697.7791 434891.9468 500660.0594 490527.3269 521511.1764 282519.768 1.669238252 1.931565791 1.783412099 1.825351135 1.539332804 1.772123993 1.736258423 1.845928092 1 18.10799229 -1.586949879 2.735260686 0.943168403 1.766381497 0.838930614 0.105044581 7751404.424 7599023.802 3185438.288 0.02537613 0.025885116 1.586949879 0.823213094 QSHSSS(ph)SPHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QS(0.001)HS(0.002)S(0.01)S(0.493)S(0.493)PHPK 88.282 0.0084348 124800000 159690 130650 143210 174210 135250 151060 221370 209310 87010 TRUE FALSE 152141.7702 143963.3835 149776.3202 156698.0798 158837.5572 145828.7543 187595.9408 190981.7068 100503.0664 1.513802271 1.432427772 1.490266173 1.559137302 1.580424984 1.450988109 1.866569324 1.90025751 1 16.61687999 1.771428147 25 1.682574669 1.501378997 0 0.250400503 67.32999929 51238.11416 0.101761494 0.056452747 59.07832144 -1.771428147 -0.181195673 QSHSSSS(ph)PHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QS(0.001)HS(0.004)S(0.032)S(0.159)S(0.804)PHPK;QSHS(0.006)S(0.034)S(0.163)S(0.797)PHPK;QSHSS(0.001)S(0.035)S(0.964)PHPK;QSHSS(0.019)S(0.156)S(0.825)PHPK;QSHSS(0.003)S(0.184)S(0.813)PHPK;QSHSS(0.004)S(0.206)S(0.79)PHPK;QSHSSS(0.005)S(0.995)PHPK 141.59 2.45E-05 3832340000 5031640 3560180 4156780 5107600 4710180 4375420 7024320 6143270 2758998 TRUE FALSE 4793804.349 3922966.39 4347372.475 4594174.344 5531633.901 4223898.108 5952630.974 5605332.711 3186849.319 1.504245689 1.230985841 1.364160034 1.44160388 1.735768889 1.325415069 1.867873369 1.758894805 1 21.60369938 2.958141598 5.635299676 1.596092735 1.361523373 0.061582399 0.255179968 0.345556069 28.26764554 0.070622063 0.076966328 908.1165662 -2.958141598 -0.234569362 QSIAIDDCTFHQCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSIAIDDCTFHQCVR 15 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 232.78 1.42E-14 492960000 502450 355330 406630 466850 421580 434220 505680 511390 522820 FALSE TRUE 478700.1843 391538.531 425274.3877 419921.351 495103.4185 419182.8525 428529.2285 466609.9806 603896.2554 0.792686128 0.648353964 0.704217627 0.695353461 0.819848466 0.694130571 0.709607362 0.772665795 1 19.2039412 0.803300433 3.184366175 0.999965602 0.720573256 0.752416397 0.049492642 0.521460774 7.72632964 0.045044309 0.011720637 6.357705887 -0.803300433 -0.279392346 QSIDALKDWFRDEMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSIDALKDWFRDEMQK 16 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 57.788 0.064909 43566000 101840 106820 86579 97553 57586 108670 105250 90068 33897 FALSE TRUE 97026.22503 117705.0794 90548.73279 87746.7871 67628.98017 104906.7307 89192.17945 82181.16844 39153.57364 2.478093722 3.006241028 2.312655637 2.241092676 1.727274777 2.679365404 2.278008651 2.098944255 1 15.25685637 -1.155094771 0.22191003 1.92E-12 2.743069315 0.663213672 0.314978575 11.77493981 0.557817928 8.172174218 0.723871723 0.06996893 1.155094771 2.743069315 QSIRNS(ph)QK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSIRNSQK 8 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QSIRNS(1)QK;QSIRNS(1)QK 87.667 0.0091819 295560000 311100 242960 213049 430000 270790 277910 396430 265600 287390 TRUE FALSE 296394.9195 267717.9002 222817.5074 386775.5831 318015.6903 268285.907 335947.3226 242342.656 331956.9734 0.892871496 0.806483736 0.67122406 1.165137696 0.958002741 0.808194822 1.012020682 0.730042371 1 18.34063673 3.26522312 24.99999985 0.941843063 0.808352412 0.242956739 0.127846041 342.9517668 321565.1364 0.033230656 0.044982068 1841.717948 -3.26522312 -0.133490651 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK 34 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 287.67 4.24E-90 116340000 689430 532780 574230 624240 322040 562280 614090 691150 342180 FALSE TRUE 656842.0102 587070.8877 600559.0135 561490.2092 378203.674 542808.1026 520399.292 630629.242 395243.5268 1.661866585 1.485339665 1.519465779 1.420618356 0.956887712 1.373351025 1.316654813 1.595546035 1 18.59238231 3.056403319 4.337415079 1.274329337 1.552668446 0.358965413 0.18580081 0.235744471 9.207915496 0.052125859 0.0621243 1138.684264 -3.056403319 0.278339108 QSLGES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSLGESPR 8 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 QSLGES(1)PR 99.439 0.0083578 0 175780 158580 161380 184920 188520 188450 203600 170030 208930 TRUE FALSE 167471.2278 174739.4823 168779.4326 166331.4903 221397.8283 181923.9292 172537.0806 155141.2718 241329.7973 0.693951719 0.724069237 0.699372537 0.689228981 0.917407758 0.753839481 0.71494313 0.642859993 1 17.88064653 -1.720759365 2.933545933 1.040891499 0.730312666 0.578244963 0.072608951 28565502.91 27311723.5 8604242.035 0.017434237 0.019021319 1.720759365 -0.310578833 QSLLDMAQTWGEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSLLDMAQTWGEFR 14 0 M0QZP4;B3KSI3;M0QZ10;M0QXF9;O15382-2;O15382 M0QZP4 BCAT2 "Branched-chain-amino-acid aminotransferase;Branched-chain-amino-acid aminotransferase, mitochondrial" 0 112.15 0.0029557 0 54719 52310 45763 60458 50908 50595 63987 56969 57343 FALSE TRUE 52132.54131 57640.44847 47861.27882 54380.64698 59786.33908 48842.88246 54224.60795 51980.49235 66235.45957 0.787079031 0.870235503 0.722592991 0.82102015 0.902633415 0.737412902 0.818664327 0.784783448 1 16.01531616 -1.057019198 4.937755659 1.000004219 0.808809906 0.559416641 0.054162866 2.28E-06 4.36E-07 0.047620768 0.011224075 0.087696205 1.057019198 -0.191194314 QSMAFSILNT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSMAFSILNTPK 12 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 QSMAFSILNT(1)PK;QSMAFSILNT(1)PK;QSMAFSILNT(1)PK 162.14 0.00070951 354124000 1188160 977428 1161080 1243480 927916 1129200 1397100 1349450 974590 TRUE FALSE 1131998.032 1077029.024 1214316.666 1118483.028 1089744.257 1090095.521 1183946.735 1231285.004 1125724.44 1.005572937 0.956743042 1.078697969 0.993567332 0.968038197 0.968350231 1.051719847 1.093771229 1 20.10242229 1.64674569 6.46154077 1.055476952 0.993790832 0.274765893 0.040266594 0.149411361 12.7688926 0.019880455 0.009879668 44.33489559 -1.64674569 -0.061686121 QSMDMS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QSMDMSPIK 9 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QS(0.006)MDMS(0.994)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK 122.97 0.00059885 840850000 2401820 2030960 1472740 1979220 1513620 2115500 2448010 2412780 1573130 TRUE FALSE 2288290.729 2237917.133 1540266.586 1780265.045 1777594.849 2042239.705 2074521.114 2201504.192 1817082.966 1.259320995 1.231598763 0.847658921 0.979737898 0.978268402 1.123911094 1.141676606 1.211559534 1 20.79319286 3.958807426 24.71746292 1.050919938 1.248925273 0.409167661 0.102051535 400.6122017 240386.1566 0.02754421 0.049658369 9095.098903 -3.958807426 0.198005335 QSMDMS(ph)PIKIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSMDMSPIKIVK 12 1 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QS(0.002)MDMS(0.998)PIKIVK 51.695 0.093211 106950000 282740 175590 261650 236210 269760 267600 364710 299160 323840 TRUE FALSE 269375.4405 193482.8206 273646.9113 212465.722 316806.0586 258332.9449 309066.7911 272963.9645 374059.4533 0.720140711 0.51725152 0.73155994 0.567999873 0.846940388 0.690620014 0.826250449 0.729734169 1 18.51290807 0.846032196 0.293890483 1.051097194 0.594123261 0.559452903 0.090842595 1.54490892 0.376159088 0.246821637 0.12502513 7.015073014 -0.846032196 -0.456973933 QSNAS(ph)SDVEVEEKETSVSKEDTDHEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSNASSDVEVEEKETSVSKEDTDHEEK 27 2 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QS(0.019)NAS(0.573)S(0.408)DVEVEEKETSVSKEDTDHEEK 144.36 8.22E-08 223740000 151650 127860 132540 162790 72075 166140 160650 175700 73156 TRUE FALSE 144481.805 140889.0794 138617.0901 146426.0399 84644.85718 160386.5301 136139.892 160314.7766 84500.65885 1.709830515 1.667313383 1.640426146 1.732839032 1.001706476 1.898050646 1.61111042 1.897201498 1 16.36667497 QSNASS(ph)DVEVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNAS(0.018)S(0.982)DVEVEEK;QSNASS(1)DVEVEEK;QSNASS(1)DVEVEEK;QSNAS(0.205)S(0.795)DVEVEEK;QSNAS(0.009)S(0.991)DVEVEEK;QSNAS(0.005)S(0.995)DVEVEEK;QSNAS(0.001)S(0.999)DVEVEEK 423.9 4.57E-146 1766650000 4410510 5665010 4027040 5815240 2664021 5232430 4313400 5159090 2576149 TRUE FALSE 4202033.933 6242280.96 4211683.767 5230681.027 3128625.419 5051229.637 3655311.609 4707332.73 2975645.03 1.412142205 2.097790865 1.415385143 1.757830983 1.051410833 1.697524263 1.228409831 1.581953722 1 21.504771 2.767822539 24.92898809 1.349733672 1.699027247 0.275355887 0.284046227 852.6633345 726404.5017 0.078263136 0.082998929 585.8987058 -2.767822539 0.349293576 QSNNEANLREEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSNNEANLREEVLK 14 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 115.68 0.00036967 135860000 185720 116250 165520 169640 150510 189580 230060 203660 191620 FALSE TRUE 176941.3837 128096.0072 173109.2557 152587.4649 176758.8963 183014.7971 194960.1217 185826.4507 221335.4509 0.799426314 0.578741483 0.782112648 0.689394601 0.798601831 0.826866172 0.880835496 0.839569305 1 17.75587502 1.748927924 0.536991317 0.984881566 0.686279332 0.64558293 0.065915035 0.453335106 0.295983486 0.060955165 0.038510264 56.09548714 -1.748927924 -0.298602234 QSPGHQS(ph)PLASPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSPGHQSPLASPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QS(0.184)PGHQS(0.816)PLASPK 70.091 0.029586 60022000 121180 109010 109960 144280 106750 122440 167850 136200 133740 TRUE FALSE 115452.0616 120118.2429 115001.7748 129776.7003 125367.1662 118199.8721 142241.3997 124273.606 154479.7162 0.747360653 0.77756644 0.744445793 0.840088935 0.811544514 0.76514817 0.920777195 0.804465525 1 17.23705789 -4.999999826 0.09396982 1.685755792 0.639885094 0.719625161 0.042856475 94.58068545 0.612599895 12.6789013 0.795212824 1.00E-05 4.999999826 -1.045870698 QSPGSTS(ph)PKPPHTLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QS(0.002)PGS(0.031)T(0.183)S(0.784)PKPPHTLSR;QSPGS(0.009)T(0.065)S(0.926)PKPPHTLSR;QSPGS(0.004)T(0.028)S(0.968)PKPPHTLSR 162.41 4.88E-09 745790000 924970 822330 693560 966260 490550 835200 846710 912280 520580 TRUE FALSE 881248.5012 906126.3619 725360.412 869129.709 576101.7647 806276.8146 717528.8386 832395.9269 601308.8876 1.465550434 1.506923281 1.206302496 1.445396413 0.958079577 1.340869612 1.193278286 1.384306708 1 19.19774676 8 0.136923558 1.007540926 2.778891744 0.356279505 0.151949479 72.1353056 0.661173369 0.619545677 24.91954146 100000000 -8 1.771350818 QSPS(ph)PS(ph)TRPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.006)PS(0.991)PS(0.637)T(0.365)RPIR 115.79 0.012862 181810000 270700 221590 261990 266890 277360 255150 325570 251450 319680 TRUE FALSE 257904.5475 244170.2729 274002.5006 240061.7101 325731.4962 246314.0915 275898.317 229431.705 369254.3417 0.698446892 0.661252273 0.742042732 0.650125626 0.882133152 0.667058078 0.747176907 0.621337867 1 18.49425536 -1.147161616 4.045318603 1.000100785 0.709227836 0.611962648 0.072898017 7535822.687 4273985.331 6375.937962 0.015246895 0.07125878 1.147161616 -0.29087295 QSQQPMKPIS(ph)PVKDPVS(ph)PASQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.996)PAS(0.004)QK 87.719 0.0014973 126160000 239430 220290 217790 272830 106230 293970 273210 297760 105240 TRUE FALSE 228112.6184 242737.8014 227775.8869 245404.6101 124756.4784 283789.7452 231526.7967 271686.5559 121560.0817 1.876542161 1.996854543 1.873772078 2.018792737 1.026294789 2.334563626 1.904628505 2.234998135 1 16.89131002 QSQQPMKPIS(ph)PVKDPVSPASQK ddPTM_SK-BR-3_Trastuzumab_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 199.64 9.09E-23 1206940000 2806300 2326990 2303450 2935500 1189420 3198100 3097200 3418300 1323400 TRUE FALSE 2673651.761 2564112.927 2409065.461 2640417.963 1396854.471 3087348.995 2624665.256 3118975.53 1528626.113 1.749055402 1.677397046 1.575967753 1.727314443 0.913797337 2.019688771 1.717009302 2.040378287 1 20.54380415 QSS(ph)PSGSEQLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(1)PSGSEQLVR;QSS(0.998)PS(0.001)GSEQLVR;QS(0.011)S(0.989)PSGSEQLVR 278.06 6.72E-28 927110000 1596620 1562780 1413340 1679000 1423100 1352000 1692040 1545080 1534700 TRUE FALSE 1521150.937 1722029.059 1478143.037 1510223.73 1671288.189 1305179.901 1433888.222 1409784.604 1772693.438 0.858101522 0.971419548 0.833840192 0.851937339 0.942795948 0.736269381 0.808875461 0.795278289 1 20.75751163 2.252826023 24.98963424 0.815113746 0.89502376 0.088673664 0.078820024 352.6581489 617773.4125 0.024764996 0.020631703 178.9888685 -2.252826023 0.079910014 QSS(ph)SEQCS(ph)DGEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSSSEQCSDGEGR 13 0 O60343-2;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 2 QS(0.138)S(0.854)S(0.012)EQCS(0.995)DGEGR;QS(0.204)S(0.795)S(0.009)EQCS(0.993)DGEGR 107.98 0.0018312 80125000 231450 189901 233940 251340 238030 220680 279380 226885 286480 TRUE FALSE 220509.8172 209252.1278 244666.3804 226074.8257 279542.3566 213037.7963 236755.4498 207017.7466 330905.8553 0.666382337 0.632361515 0.739383654 0.683199835 0.844779118 0.643801833 0.715476762 0.625609198 1 18.33606129 -1.644868526 2.795132671 1.031336089 0.691794145 0.691396061 0.064261273 17789722.7 16420572.42 4009547.197 0.014623852 0.0226533 1.644868526 -0.339541945 QSS(ph)SEQCSDGEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSSSEQCSDGEGR 13 0 O60343-2;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 QS(0.002)S(0.993)S(0.005)EQCSDGEGR 189.32 5.63E-06 119100000 151260 108450 132030 159940 140090 131900 153450 128290 149700 TRUE FALSE 144110.2396 119501.1783 138083.7061 143862.5273 164521.6516 127332.2699 130038.3842 117056.2475 172914.7114 0.833418038 0.691098966 0.798565402 0.831985469 0.951461274 0.736387719 0.752037713 0.676959447 1 17.39970109 -2.204637839 2.436506756 1.689815841 0.781182308 0.423216954 0.079190354 4438488.503 1557100.919 16738307.03 0.019208313 0.006242552 2.204637839 -0.908633533 QSS(ph)SWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSSSWTR 7 0 Q92934;F5H1R6 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 QS(0.139)S(0.43)S(0.43)WTR 74.267 0.052324 0 173920 135310 149610 159560 178980 161830 182410 153420 191570 TRUE FALSE 165699.1463 149098.2428 156469.7665 143520.7257 210194.0553 156225.7865 154580.0043 139985.7315 221277.6972 0.748828953 0.673806013 0.707119463 0.648600051 0.949910714 0.706016867 0.698579234 0.632624676 1 17.75549852 -1.308139197 3.211966701 1.001640366 0.720184374 0.499895748 0.087797031 13353686.35 18141102.26 214000.1395 0.01986046 0.049188186 1.308139197 -0.281455992 QSS(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.146)S(0.68)T(0.167)PS(0.007)APELGQQPDVNISEWK;QS(0.15)S(0.699)T(0.15)PS(0.001)APELGQQPDVNISEWK 299.66 6.81E-56 298840000 478220 444450 464930 537810 358640 520310 571060 548170 406080 TRUE FALSE 455615.4883 489739.9603 486247.5004 483748.317 421186.7025 502291.5342 483934.3088 500169.3288 469052.8124 0.971352215 1.044104091 1.03665832 1.031330171 0.897951555 1.070863495 1.031726697 1.066339047 1 18.83939084 QSSGASSSS(ph)FSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QSSGASSSSFSSSR 14 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 1 QSSGASS(0.001)S(0.032)S(0.967)FSSSR;QSSGASSS(0.003)S(0.997)FSSSR;QSSGAS(0.053)S(0.176)S(0.176)S(0.592)FS(0.001)SSR;QSSGAS(0.003)S(0.023)S(0.113)S(0.86)FS(0.001)SSR;QSSGASSS(0.049)S(0.95)FSSSR;QSSGAS(0.006)S(0.023)S(0.191)S(0.776)FS(0.003)SSR 242.1 1.90E-17 556435000 915525 695235 808692 1356460 944314 1108322 1348410 856557 896744 TRUE FALSE 872249.9476 766080.2369 845771.3281 1220106.064 1109002.063 1069940.531 1142685.289 781552.3282 1035806.48 0.842097404 0.739597842 0.816534116 1.177928588 1.070665307 1.032954082 1.103184149 0.754535083 1 19.98232306 3.346606512 7.577491884 1.035757038 0.78925591 0.470859608 0.111451484 0.170136511 10.85543861 0.028841412 0.039078295 2221.296397 -3.346606512 -0.246501128 QSSLAEPVS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSSLAEPVSPSK 12 0 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 QSSLAEPVS(0.99)PS(0.01)K 140.96 0.00027414 0 186500 169000 167760 210360 112800 169600 180960 200740 113590 TRUE FALSE 177684.5146 186221.2921 175451.9619 189214.2131 132472.2843 163726.7095 153351.2284 183162.1414 131204.9571 1.354251536 1.419315979 1.337235771 1.442127015 1.009659141 1.247869845 1.168791423 1.396000163 1 17.0014627 2.760853597 24.93517014 1.181152485 1.386804325 0.476674249 0.115769925 666.6530358 745664.3928 0.031635984 0.03353385 576.5720646 -2.760853597 0.205651841 QSSSSRDDNMFQIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSSSSRDDNMFQIGK 15 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;; 172.91 5.93E-09 654598000 305643 147093 306180 252742 283747 300398 423590 350465 380191 FALSE TRUE 291195.8611 162081.9439 320218.6559 227335.894 333232.387 289995.1419 358963.5657 319776.4267 439149.0785 0.663091135 0.369081826 0.729179842 0.517673622 0.758813813 0.660356941 0.817407079 0.728172829 1 18.74435125 1.511887516 0.365225441 1.013082161 0.503076734 0.57963324 0.108967918 0.722322835 0.302742031 0.139264198 0.112299572 32.50031097 -1.511887516 -0.510005427 QSTIVCHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QSTIVCHNR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 123.86 0.00054588 845371000 614690 480474 439489 538909 576670 500282 665190 568516 600210 FALSE TRUE 585634.8219 529434.8469 459640.0054 484736.8435 677241.0654 482957.1089 563703.0484 518733.7251 693287.5014 0.844721448 0.763658433 0.662986141 0.699185897 0.976854572 0.696618802 0.813086991 0.748223102 1 19.40309423 -1.784030788 2.600644161 1.060827997 0.778141573 0.381687783 0.089682484 24616310.02 17753224.52 9508418.941 0.02139927 0.016442552 1.784030788 -0.282686425 QSVDHFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSVDHFAK 8 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;; 107.15 0.0040577 727940000 978930 693660 834290 1033740 909050 863040 1160730 1132380 1022880 FALSE TRUE 932657.919 764344.7426 872543.0217 929826.4912 1067588.032 833152.7084 983639.3202 1033222.804 1181503.006 0.789382603 0.64692577 0.738502583 0.786986141 0.903584694 0.705163427 0.83253222 0.874498667 1 20.17219187 0.59473509 0.28103295 1.05528139 0.701136469 0.590555124 0.065101263 2.244473525 0.421926692 0.256474154 0.102897601 3.933100918 -0.59473509 -0.354144921 QSVDKVT(ph)SPTKV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSVDKVTSPTKV 12 2 Q05682-5;Q05682-4;E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682 Q05682-5 CALD1 Caldesmon 1 QSVDKVT(0.599)S(0.399)PT(0.003)KV 90.754 0.01396 569910000 371040 285680 364070 392260 262860 385760 418130 435200 230200 TRUE FALSE 353501.6745 314791.1168 380762.9696 352829.2796 308702.7008 372401.0345 354336.589 397091.5809 265898.2403 1.329462256 1.18387815 1.43198755 1.326933488 1.160980608 1.400539673 1.332602234 1.493396799 1 18.0205147 QSVDKVTS(ph)PTKV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSVDKVTSPTKV 12 2 Q05682-5;Q05682-4;E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682 Q05682-5 CALD1 Caldesmon 1 QSVDKVT(0.143)S(0.853)PT(0.004)KV 98.507 0.003402 456790000 421380 280700 352280 395630 278320 416800 471310 471320 239160 TRUE FALSE 401462.2025 309303.6491 368432.3865 355860.5208 326858.9199 402366.1115 399403.0033 430048.7222 276247.7113 1.453268882 1.119660495 1.333702946 1.288193553 1.183209513 1.456540977 1.445814705 1.556750353 1 18.07560299 2.227210154 24.98453367 1.408580389 1.273705535 0.036876415 0.170147295 421.504104 927804.646 0.056668569 0.042217218 168.7369341 -2.227210154 -0.134874854 QSVENDIHGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QSVENDIHGLR 11 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 189.24 2.80E-06 472650000 783284 367108 476842 774885 815860 650752 948990 746021 982030 FALSE TRUE 746259.7176 404516.7226 498705.6774 696992.0876 958145.7257 628216.2951 804204.1461 680695.4463 1134318.197 0.65789275 0.356616621 0.439652365 0.614459055 0.844688667 0.553827221 0.708975796 0.600092151 1 20.11339397 -2.395215446 0.150956496 1.664065885 0.408796473 0.519831406 0.127910351 40.12380518 0.768347584 9.746114945 0.737519155 0.004025173 2.395215446 -1.255269412 QSVENDIHGLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QSVENDIHGLRK 12 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 157.56 4.53E-05 994433000 1017460 446971 580456 923790 802900 877180 1377860 974090 1152620 FALSE TRUE 969366.6822 492517.8531 607070.4817 830928.8741 942925.5058 846803.0367 1167642.151 888793.5156 1331362.423 0.728101279 0.369935222 0.455976879 0.624119218 0.708241039 0.636042465 0.877028021 0.667581945 1 20.34447192 1.687159548 0.558658969 0.963880689 0.515767432 0.555256828 0.120851677 0.549518902 0.387260104 0.115631521 0.068290508 48.65859313 -1.687159548 -0.448113257 QSVFKDFYELEPEKFQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QSVFKDFYELEPEKFQNK 18 2 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 58.49 0.046909 91561000 184430 81601 162330 143400 116820 168260 251460 207610 157520 FALSE TRUE 175712.3594 89916.23467 169772.9911 128985.1596 137193.371 162433.114 213095.1586 189430.5678 181947.3971 0.965731647 0.494188079 0.93308832 0.708914563 0.754027665 0.892747666 1.171191026 1.04112821 1 17.47316189 1.981265294 3.76746614 1.083390915 0.757371926 0.503935932 0.134721183 0.163641701 4.883930328 0.058326563 0.035386952 95.77789638 -1.981265294 -0.326018989 QSVSGLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QSVSGLHR 8 0 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 83.647 0.018013 106874000 564170 484060 418590 510730 439790 435180 578690 569870 513170 FALSE TRUE 537502.8022 533386.2643 437782.7655 459390.4501 516489.2368 420109.6075 490400.2121 519969.1617 592749.7827 0.906795444 0.899850628 0.738562507 0.775015805 0.871344456 0.708746962 0.827330902 0.877215272 1 19.1770637 0.893058714 3.134868203 0.999778799 0.824982657 0.439389181 0.064932947 0.470604414 9.862299274 0.066610126 0.017388552 7.817334824 -0.893058714 -0.174796142 QTDDLRGEIAVLEATVQNNQDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 QTDDLRGEIAVLEATVQNNQDER 23 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;;;; 183.86 3.21E-17 150105000 98357 87746 96242 114804 108715 102665 104359 102324 106615 FALSE TRUE 93707.85953 96687.41716 100654.7909 103263.6838 127674.8616 99109.68531 88437.11787 93363.96811 123148.3097 0.760935004 0.785129876 0.817346102 0.838531069 1.036756915 0.804799396 0.718135053 0.758142506 1 16.9100373 -2.507697472 2.229380169 3.584878588 0.809215506 0.311952565 0.08598148 2859928.006 302155.0196 38024836.87 0.021745063 0.003106723 2.507697472 -2.775663082 QTDDLRGEIAVLEATVQNNQDERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QTDDLRGEIAVLEATVQNNQDERR 24 2 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 91.729 0.0050517 38330000 72270 34076 70533 56723 86947 60838 98152 74030 110480 FALSE TRUE 68853.94033 37548.38314 73767.00782 51021.09627 102110.5293 58731.16481 83177.10971 67547.54074 127612.6741 0.53955409 0.2942371 0.57805393 0.399812139 0.80015978 0.460229873 0.651793486 0.529316866 1 16.9614121 -4.999999999 0.140670037 2.695333575 0.344575088 0.569266686 0.131730771 88.51332166 0.761292055 41.84200959 0.711651305 1.00E-05 4.999999999 -2.350758487 QTDFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QTDFEHR 7 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;;;;; 128.69 0.0037335 1637346000 2625068 2441635 2209876 2982060 2561800 2491776 2632084 2568264 2354470 FALSE TRUE 2500986.238 2690440.382 2311201 2682297.663 3008577.109 2405485.172 2230511.244 2343373.189 2719589.183 0.91961913 0.989281911 0.849834606 0.986287812 1.10626161 0.88450314 0.820164773 0.861664403 1 21.37495731 -0.74024297 4.381796211 1.000000203 0.927207967 0.069544161 0.083683228 23658901.89 50997037.91 84.429715 0.021030924 0.18186831 0.74024297 -0.072792235 QTDFEHRIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTDFEHRIPK 10 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 146.16 1.75E-05 116770000 124300 56807 122450 97271 165970 118010 213890 141660 208410 FALSE TRUE 118424.5853 62595.69788 128064.4536 87493.13428 194915.1155 113923.2841 181257.1521 129255.4994 240729.1584 0.491941176 0.260025409 0.531985633 0.363450505 0.809686358 0.473242564 0.75295055 0.536933292 1 17.87705137 0.676065999 0.185211665 1.229466794 0.231632774 0.567465449 0.144031811 3.817242357 0.420758408 1.227712021 0.642712464 4.74314061 -0.676065999 -0.997834021 QTDPST(ph)PQQESSKPLGGIQPSSQTIQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QT(0.002)DPS(0.066)T(0.454)PQQES(0.239)S(0.239)KPLGGIQPSSQTIQPK 149.37 1.06E-07 258640000 236790 214380 228180 267820 148520 247440 269790 254890 185830 TRUE FALSE 225597.406 236225.5657 238642.2787 240898.2248 174421.841 238871.0908 228628.5805 232570.4803 214647.5673 1.051013104 1.10052757 1.111786552 1.122296552 0.812596402 1.112852541 1.065134738 1.08349926 1 17.7116103 QTDVGITHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTDVGITHFR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 143.79 3.34E-05 221090000 208010 140680 159410 213200 213120 184680 215950 177640 189420 FALSE TRUE 198177.7795 155015.4519 166719.1062 191768.7309 250288.0605 178284.4853 183002.8613 162084.8999 218794.2862 0.905772189 0.70849863 0.76199022 0.876479611 1.143942399 0.814849823 0.836415176 0.740809565 1 17.73921554 4.78936536 21.22458689 0.849252546 0.905774084 0.00555567 0.129461629 9829.81517 5298635.569 0.030433564 5.834262849 61569.46214 -4.78936536 0.056521538 QTELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 138.07 0.01998 1644240000 1816340 1473420 1436060 1873970 1398950 1749750 2118130 1937220 1776960 FALSE TRUE 1730485.208 1623563.173 1501904.771 1685594.975 1642926.437 1689155.719 1794970.366 1767586.747 2052521.881 0.843101954 0.791008948 0.731736302 0.821231184 0.800442837 0.822965998 0.874519479 0.861178028 1 20.96896617 0.851362806 0.666214191 1.000313029 0.795952086 0.806802303 0.030577926 0.402456317 0.389712437 0.031438256 0.012243867 7.101707908 -0.851362806 -0.204360943 QTFTGHESDINAICFFPNGNAFATGSDDATCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTFTGHESDINAICFFPNGNAFATGSDDATCR 32 0 P62873-2;P62873;B3KVK2 P62873-2 GNB1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 0 136.14 6.47E-18 0 80369 62203 75278 84590 72302 72489 90098 80229 87530 FALSE TRUE 76570.11665 68541.55642 78729.57076 76086.85249 84911.44591 69978.68775 76351.89534 73203.72344 101103.7054 0.757342338 0.677933179 0.778701141 0.752562453 0.839845044 0.692147607 0.755183948 0.724045901 1 16.62547635 -1.220147301 4.822326741 1.000044439 0.743862749 0.756774313 0.045000913 2.03E-05 3.29E-06 0.04121224 0.009712136 0.060235525 1.220147301 -0.25618169 QTGIET(ph)PNKSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QTGIETPNKSGK 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 QTGIET(1)PNKSGK;QTGIET(1)PNKSGK 107.98 0.0028384 537830000 812770 688100 840500 827430 449220 922480 980710 932380 564300 TRUE FALSE 774351.9729 758218.1723 879037.7564 744255.1644 527563.8258 890534.2863 831084.6775 850735.8643 651808.762 1.188004854 1.163252501 1.348612979 1.141830561 0.809384372 1.366250867 1.275043734 1.305192434 1 19.31408922 QTGIVLNRPVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTGIVLNRPVLR 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 69.795 0.044699 524170000 992440 810310 810060 887560 856800 881750 1081700 1017500 994580 FALSE TRUE 945529.328 892881.5102 847202.0523 798340.7825 1006225.649 851214.7764 916666.7982 928402.3059 1148814.387 0.823047952 0.777219994 0.737457732 0.694925822 0.875881831 0.740950659 0.797924198 0.808139519 1 20.13171429 0.250470202 1.007401888 1.001196057 0.777118519 0.666162197 0.049092953 2.151446886 2.38573889 0.04912386 0.014038263 1.780205759 -0.250470202 -0.224077538 QTNPSAMEVEEDDPVPEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QTNPSAMEVEEDDPVPEIRR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 137.99 4.18E-06 170390000 25815 13566 28701 20467 47567 21659 36099 26444 43517 FALSE TRUE 24594.77611 14948.39082 30016.96924 18409.61828 55862.66974 20908.9434 30591.43455 24128.42317 50265.39411 0.489298384 0.297389309 0.597169679 0.366248362 1.111354456 0.415970943 0.608598323 0.480020571 1 15.61727788 QTPS(ph)PDVVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.017)PS(0.983)PDVVLR;QT(0.084)PS(0.916)PDVVLR;QT(0.013)PS(0.987)PDVVLR;QT(0.001)PS(0.999)PDVVLR;QT(0.034)PS(0.966)PDVVLR;QT(0.428)PS(0.572)PDVVLR 170 4.68E-06 1237370000 1671700 1459120 1504340 1746960 1703400 1591250 1873610 1702990 1831680 TRUE FALSE 1592682.054 1607805.987 1573315.477 1571352.262 2000472.421 1536144.614 1587756.383 1553867.167 2115727.579 0.752782196 0.759930533 0.743628571 0.742700656 0.945524575 0.726059739 0.750454075 0.734436315 1 21.01272245 -1.490048155 2.981057062 1.007001093 0.768027349 0.565872235 0.063454654 14551009.61 16131112.04 831753.1554 0.014295256 0.032355778 1.490048155 -0.238973744 QTS(ph)IETDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 QT(0.016)S(0.984)IETDR;QT(0.011)S(0.987)IET(0.002)DR 158.06 0.00038516 463400000 1362550 1321880 1299150 1651540 1428970 1369370 1454220 1315940 1344410 TRUE FALSE 1298144.962 1456581.075 1358717.313 1485524.061 1678181.916 1321948.374 1232352.03 1200709.317 1552894.237 0.835951948 0.937978286 0.87495805 0.956616379 1.080680111 0.851280366 0.793584007 0.773207401 1 20.56652814 -1.109480822 5.803581858 1.00000076 0.888103986 0.136241166 0.088600752 9.00E-07 1.38E-07 0.088641444 0.020892847 0.077717564 1.109480822 -0.111896773 QTSDGNWLMVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QTSDGNWLMVHR 12 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ;;; 133.71 0.00012011 694600000 677700 508983 451104 675759 1129240 418183 607838 459547 841840 FALSE TRUE 645666.4641 560848.9464 471787.5646 607830.4215 1326179.098 403701.2179 515101.1494 419306.6285 972388.2477 0.664000687 0.576774707 0.485184355 0.625090259 1.363837029 0.415164641 0.529727864 0.43121318 1 19.89117293 2.987750474 24.92970736 0.707791061 0.58415491 0.065162299 0.283987365 2257.700414 4594787.576 0.084290691 0.093845957 972.1884884 -2.987750474 -0.123636151 QVAEQGGDLS(ph)PAANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 QVAEQGGDLSPAANR 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR 306.29 5.94E-45 5609820000 4908220 4009210 4375010 5018810 5171220 4582930 5459910 4780900 5492160 TRUE FALSE 4676218.168 4417753.057 4575608.536 4514309.684 6073079.131 4424221.985 4626900.451 4362259.051 6343856.123 0.737125508 0.696382921 0.721266127 0.711603415 0.957316656 0.697402636 0.729351417 0.687635244 1 22.59692862 -1.681550886 2.792647946 1.033531497 0.739925562 0.517713373 0.078150353 15793271.65 14938735.17 3774017.951 0.019302183 0.020818485 1.681550886 -0.293605935 QVDFLNWEVTDHNLHELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVDFLNWEVTDHNLHELR 18 0 Q9NV31 Q9NV31 IMP3 U3 small nucleolar ribonucleoprotein protein IMP3 0 103.9 0.00030199 28333000 30075 31120 27863 34480 32902 30022 32140 30934 5913.1 FALSE TRUE 28653.41435 34291.16338 29140.54611 31014.00489 38640.09838 28982.33061 27236.45271 28225.25497 6830.073348 4.195183989 5.020614221 4.266505589 4.540801147 5.6573475 4.24334105 3.987724775 4.132496612 1 12.73768536 0.241129923 0.734188037 0.922566621 4.675629338 0.858155752 0.455175666 0.988022046 0.683052568 0.616472763 0.154902261 1.742328029 -0.241129923 3.753062717 QVDLES(ph)NPQNRSPESRPSVVYPSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVDLESNPQNRSPESRPSVVYPSTK 25 2 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QVDLES(0.616)NPQNRS(0.358)PES(0.023)RPS(0.003)VVYPSTK 55.846 0.053662 452150000 149630 115140 122380 175180 134590 198020 212040 157420 156930 TRUE FALSE 142557.2864 126872.8969 127991.2441 157570.5736 158062.4534 191162.5177 179689.4036 143635.4703 181265.9029 0.786453956 0.699926985 0.706096635 0.869278618 0.8719922 1.054597223 0.991302836 0.792402035 1 17.46774805 2.916634236 1.93800548 0.960830579 0.732568711 0.612757592 0.075963449 0.200802524 1.503616557 0.025544487 0.028400352 825.3425508 -2.916634236 -0.228261868 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK 40 1 P30049 P30049 ATP5D "ATP synthase subunit delta, mitochondrial" 0 291.26 4.02E-93 221440000 192930 142560 165870 167590 157580 139110 181330 191850 74751 FALSE TRUE 183810.5813 157087.0261 173475.3036 150743.5348 185061.9021 134292.5858 153664.7781 175050.5969 86343.0033 2.128841646 1.819337063 2.009141412 1.745868559 2.143334086 1.555338368 1.779701565 2.02738601 1 16.39779166 -2.110968968 0.286233819 1.40E-17 1.979089715 0.697346238 0.185660396 18.58190723 0.762155779 12.57297144 0.194314686 0.007745171 2.110968968 1.979089715 QVEDEKNSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QVEDEKNSFR 10 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 119.76 0.00059202 1335770000 2228860 1405760 2021910 2062620 2098770 1822060 2535360 2120730 2887280 FALSE TRUE 2123506.205 1549008.542 2114616.573 1855281.519 2464794.824 1758961.605 2148544.267 1935027.639 3335024.636 0.636728791 0.464466896 0.634063254 0.556302193 0.739063453 0.527420873 0.6442364 0.580213896 1 21.66926599 -5 0.30388925 4.479128947 0.571673858 0.737926394 0.075061308 130.2545382 1.194884146 289.1882722 0.066323224 1.00E-05 5 -3.907455089 QVEDLQATFSSIHSFQDLSSSILAQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVEDLQATFSSIHSFQDLSSSILAQSR 27 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 315.57 3.68E-82 301830000 111033 96527 94102 114869 125629 92108 130095 115081 145470 FALSE TRUE 105784.6901 106363.211 98416.66978 103322.1499 147538.6578 88918.27686 110246.6184 105003.8976 168028.7446 0.629563057 0.633006045 0.585713296 0.614907587 0.878056062 0.529184914 0.65611761 0.624916277 1 17.35834853 -1.717025085 2.363354946 1.0766724 0.642369075 0.606620946 0.090103835 4091759.319 2852179.793 1849769.238 0.021050326 0.019185579 1.717025085 -0.434303325 QVEEKPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVEEKPQR 8 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 92.062 0.010984 98001000 152130 134420 123730 146300 192100 123420 158080 123430 254350 FALSE TRUE 144939.1164 148117.5508 129403.1429 131593.646 225602.1792 119145.9345 133961.9927 112621.8149 293793.299 0.49333704 0.504155647 0.440456414 0.447912347 0.76789423 0.405543404 0.455973615 0.383336908 1 18.16444196 -1.047579814 4.330972551 1.000035944 0.488874499 0.697547855 0.106088208 56487381.56 114881755 31049.20545 0.023966324 0.089623146 1.047579814 -0.511161445 QVEELFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QVEELFER 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 203.02 0.00023032 401933000 563590 511472 482148 585842 666340 497698 619799 572216 678260 FALSE TRUE 536950.2176 563591.5783 504254.9627 526952.0491 782549.485 480462.5935 525237.2792 522109.7335 783441.0967 0.685374076 0.719379645 0.643641194 0.672612212 0.998861929 0.613272134 0.670423445 0.666431383 1 19.57946528 -1.153397339 3.406192799 1.000380758 0.706943257 0.423108911 0.106859911 30380631.65 49167281.79 127974.075 0.024938622 0.070242937 1.153397339 -0.293437501 QVELALWDTAGQEDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 204.17 2.10E-11 289123000 467268 389281 390406 511688 542579 459012 532087 467437 536332 FALSE TRUE 445181.1677 428949.1765 408306.5013 460252.1501 637204.6058 443116.2993 450907.3557 426505.7382 619503.6274 0.718609461 0.692407853 0.659086538 0.742936974 1.028572841 0.71527636 0.727852648 0.688463666 1 19.2407532 -2.59155933 2.068617107 5.297516409 0.743255662 0.373110439 0.103121097 3120800.112 165815.9763 63043573.77 0.024912389 0.002561183 2.59155933 -4.554260747 QVEPPAKKPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QVEPPAKKPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 39 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 QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;QVEPPAKKPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 338.52 6.33E-130 4903340000 1962106 825488 1961436 1431317 1102162 2052454 2958810 2450833 1541186 TRUE FALSE 1869361.138 909606.1657 2051369.781 1287438.296 1294378.704 1981377.003 2507389.192 2236225.07 1780185.254 1.050093598 0.510961521 1.152335004 0.723204674 0.727103374 1.113017311 1.408499024 1.256175482 1 20.76359595 2.076880352 4.67492746 1.266330424 0.819904931 0.440420242 0.202703587 0.156463811 6.37275182 0.073963932 0.052764275 119.3659208 -2.076880352 -0.446425492 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR 37 1 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 173.6 1.64E-18 178597000 153278 118114 125888 156744 114763 141657 168571 179108 127860 FALSE TRUE 146032.8527 130149.9509 131660.0893 140987.7953 134777.6309 136751.3826 142852.3979 163424.354 147687.8758 0.988793778 0.88125007 0.891475273 0.954633511 0.91258426 0.925948605 0.967258803 1.106552269 1 17.17219187 1.442788597 4.189729299 1.052496588 0.925885629 0.63059404 0.039637608 0.121693404 3.957127605 0.025772301 0.009483629 27.71970452 -1.442788597 -0.12661096 QVGYEDQWLQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QVGYEDQWLQLLR 13 0 O60568 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ;; 156.69 0.00011004 67817000 71280 57010 72523 72892 73693 65087 84599 74229 79414 FALSE TRUE 67910.73566 62819.38381 75848.25129 65564.75767 86545.03587 62833.02087 71691.86878 67729.11525 91729.11753 0.740340009 0.684835802 0.826872135 0.714764945 0.943484885 0.684984469 0.781560651 0.738360044 1 16.48509214 -5 0.305917602 3.064797383 0.747535172 0.473541696 0.077230525 235.2267824 2.148865412 312.5640621 0.068095382 1.00E-05 5 -2.317262211 QVHPDTGISS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.014)S(0.986)K 168.5 1.16E-05 112530000 189220 175280 144640 187720 122050 188850 221420 204160 125870 TRUE FALSE 180275.9456 193141.2313 151271.8871 168850.029 143335.4814 182310.0771 187638.3123 186282.6681 145389.2767 1.239953521 1.328442067 1.040461102 1.16136508 0.985873818 1.253944453 1.290592515 1.281268277 1 17.14956134 3.767304253 24.85324932 1.165198151 1.284197801 0.190591303 0.113533513 1170.483946 1012057.286 0.029624151 0.053394037 5851.999131 -3.767304253 0.11899965 QVHPDTGISSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 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 ;;;;;;;;;;;;;;;;; 193.28 1.02E-06 1.39191E+11 57649676 47511982 52283167 58284546 47070147 53590522 64933111 56878053 51795764 FALSE TRUE 54924690.07 52353506.98 54680401.92 52425672.7 55279165.73 51734668.79 55026372.34 51897509.15 59827986.55 0.918043431 0.875067172 0.913960256 0.876273392 0.923968345 0.864723548 0.919743009 0.867445357 1 25.83431718 -1.860687089 2.663530954 1.044324797 0.895822409 0.672754964 0.023027724 6554733.134 4681714.466 1847813.852 0.004586831 0.013782021 1.860687089 -0.148502388 QVHQCIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 QVHQCIER 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ;;;;; 149.72 0.00050068 1011379000 613117 501962 485803 607589 631866 472891 622402 542846 591141 FALSE TRUE 584136.1745 553112.4985 508077.5481 546512.9994 742063.2303 456514.6661 527443.1437 495311.5264 682812.1272 0.85548594 0.810050783 0.744095671 0.800385608 1.086775118 0.668580196 0.7724572 0.725399428 1 19.38112916 -0.526277921 7.364902056 1 0.808224549 0.227082233 0.111375843 0 0 0.10136942 0.023893001 0.297661098 0.526277921 -0.191775451 QVITLLNELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVITLLNELKR 11 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 211.67 0.0011068 0 323593 249395 260654 298252 248042 289142 361980 312885 350800 FALSE TRUE 308297.4002 274808.634 272605.2437 268271.1423 291300.4463 279128.94 306753.3028 285487.1307 405200.2724 0.760851908 0.678204465 0.672766684 0.662070489 0.718904863 0.688866615 0.757041206 0.704558092 1 18.62827562 -0.693385401 0.567526129 1.054406667 0.69911162 0.88989311 0.03262873 4.385490198 1.007267672 0.480108681 0.013703801 0.202588411 0.693385401 -0.355295046 QVKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVKEER 6 1 Q5VX52-4;Q5VX52 Q5VX52-4 SPATA1 Spermatogenesis-associated protein 1 0 67.055 0.091002 443210000 296380 193200 205170 272750 175010 248360 290300 261490 235330 FALSE TRUE 282370.7048 212887.2997 214577.2474 245332.6518 205531.6886 239759.2309 246009.4033 238592.5494 271823.7745 1.038800617 0.783181309 0.789398381 0.902543025 0.75612109 0.882039223 0.905032695 0.877747172 1 18.05231212 0.56225674 0.9621972 0.999555414 0.862210865 0.22024691 0.079889516 2.352325128 3.360444582 0.07630194 0.02452858 3.649696411 -0.56225674 -0.13734455 QVLGQMVIDEELLGDGHSYSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVLGQMVIDEELLGDGHSYSPR 22 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 262.98 2.18E-37 281010000 365320 312630 307310 368400 359180 326300 381660 397160 320120 FALSE TRUE 348052.0476 344487.3524 321400.4675 331367.7321 421820.8783 315000.1492 323430.7573 362382.5649 369762.5747 0.941285223 0.931644726 0.869207674 0.896163524 1.14078846 0.851898409 0.874698467 0.98004122 1 18.49623968 2.096786212 0.005099801 1.874866942 1.60E-07 0.033141677 0.083226418 33873.98464 119.039415 21739.52512 22015.32598 124.9643723 -2.096786212 -1.874866783 QVLIRPCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVLIRPCSK 9 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 111.06 0.0019942 938120000 1675320 1063500 1523610 1553240 1580980 1665480 2178240 1997390 2094760 FALSE TRUE 1596130.944 1171871.859 1593469.026 1397105.364 1856702.411 1607804.01 1845909.482 1822487.943 2419604.682 0.659666001 0.484323686 0.658565855 0.577410589 0.767357753 0.66449037 0.762897136 0.753217233 1 21.20633993 0.865996368 0.320712981 1.04965261 0.549423114 0.771203102 0.065232698 0.856265109 0.242159952 0.149970535 0.075479126 7.345077259 -0.865996368 -0.500229496 QVLLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVLLGR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 98.03 0.093984 103180000 140480 121480 103790 137610 116670 115830 146350 138610 117980 FALSE TRUE 133839.7888 133858.9501 108548.8742 123777.1814 137017.2111 111818.7781 124021.6196 126472.5736 136275.7358 0.982124866 0.982265473 0.796538529 0.908284814 1.005440992 0.820533291 0.910078517 0.928063773 1 17.05616918 QVNELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVNELVR 7 0 M0R1K3;Q15102;M0R389 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 77.046 0.090984 24935000 67057 51710 54168 56678 75051 50479 74346 68266 91590 FALSE TRUE 63887.3485 56979.30779 56651.65638 50980.61976 88139.87064 48730.89957 63003.15224 62288.26714 105793.3094 0.603888364 0.538590844 0.535493754 0.481888883 0.833132748 0.460623643 0.595530592 0.588773217 1 16.69088887 -4.967702943 0.445552178 9.99999983 0.571219835 0.629945139 0.101291645 730.64441 4.436336531 6475.972265 0.048828195 1.08E-05 4.967702943 -9.428779995 QVQDESQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVQDESQR 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 0 121.53 0.0033248 47537000 110610 88675 101920 117770 141130 103700 132170 111770 150610 FALSE TRUE 105381.6845 97711.08332 106593.1328 105931.5359 165743.0273 100108.843 112005.039 101982.8263 173965.8296 0.605760825 0.561668251 0.612724539 0.608921511 0.952733233 0.575451186 0.643833558 0.58622332 1 17.40844443 -2.56982108 2.119050959 6.829268751 0.638489315 0.497436132 0.112543358 3306369.713 157911.4418 93046194.25 0.026598591 0.002692644 2.56982108 -6.190779436 QVQEFLKDGDDVIIIGVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVQEFLKDGDDVIIIGVFK 19 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 229.61 6.96E-20 137373000 880740 669780 713990 901660 469800 893300 902480 974670 564430 FALSE TRUE 839109.1657 738031.3435 746727.1477 811023.4238 551732.9713 862364.797 764790.1008 889322.7277 651958.9217 1.287058337 1.132021235 1.145359198 1.243979332 0.846269532 1.322728731 1.173064859 1.364077855 1 19.31442154 4.616930473 3.013305117 1.161295856 1.292466389 0.07066744 0.149311206 0.864757928 12.94985577 0.033251958 0.233391056 41393.34024 -4.616930473 0.131170533 QVQPEGPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 182.29 0.00010817 2910920000 2561343 2408229 2102975 2474758 2533007 2348854 2724664 2525183 2598247 FALSE TRUE 2440273.392 2653630.273 2199398.484 2225990.624 2974762.619 2267512.597 2308966.465 2304064.59 3001169.875 0.813107386 0.884198624 0.732847048 0.74170764 0.991201013 0.755542902 0.769355472 0.76772215 1 21.51709355 3.835997405 18.80111315 0.810028004 0.848647504 0 0.099151682 25.72106022 4947.933519 0.023483453 0.04233583 6854.841302 -3.835997405 0.0386195 QVS(ph)ASELHTSGILGPETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.996)AS(0.004)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.982)AS(0.018)ELHTSGILGPETLR;QVS(0.994)AS(0.006)ELHTSGILGPETLR 364.36 8.77E-108 66230640000 8066290 5374600 7050740 9072050 15937210 6955650 11947530 7955730 17638380 TRUE FALSE 7685012.458 5922277.85 7374023.403 8160110.298 18716654.38 6714774.096 10124714.87 7259084.105 20373649.89 0.37720352 0.290683205 0.361939242 0.400522751 0.918669678 0.329581304 0.496951451 0.356297676 1 24.28020112 -5 0.198511872 3.496016998 0.340840351 0.48464266 0.179506518 119.1333063 1.176701259 118.313476 0.419849552 1.00E-05 5 -3.155176646 QVS(ph)DLGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVSDLGSK 8 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QVS(1)DLGSK 97.779 0.0087889 0 210080 223650 189120 306270 153820 276310 245760 205470 152640 TRUE FALSE 200149.9347 246440.1893 197791.3391 275483.1577 180646.1593 266741.3154 208264.7983 187477.9575 176310.6316 1.135211943 1.397761366 1.121834442 1.562487498 1.024590279 1.51290545 1.181237889 1.063338925 1 17.42775995 1.32705299 3.356891549 1.021462125 1.289148458 0.281016047 0.170549826 0.278924867 5.145410483 0.120429145 0.037621954 21.23503545 -1.32705299 0.267686333 QVSASELHTSGILGPETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 202.95 5.28E-16 757800000 409820 288680 387920 428610 783170 317590 608960 470110 914510 FALSE TRUE 390448.6208 318096.8202 405706.5157 385525.3085 919754.6 306591.7787 516051.9677 428944.6762 1056327.54 0.369628364 0.301134646 0.384072648 0.364967582 0.870709666 0.290243099 0.488534047 0.406071659 1 20.01062582 -5 0.209595056 3.725632742 0.342136985 0.541587683 0.164074308 108.7163928 1.083009546 124.7193786 0.329552344 1.00E-05 5 -3.383495757 QVSDLGSKGEHPEGDPGEVPAPS(ph)PQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVSDLGSKGEHPEGDPGEVPAPSPQER 27 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QVSDLGSKGEHPEGDPGEVPAPS(1)PQER;QVSDLGSKGEHPEGDPGEVPAPS(1)PQER 108.99 0.00096476 223820000 457300 236499 430810 377390 443460 388650 593990 470300 522270 TRUE FALSE 435684.3353 260598.517 450563.0646 339454.0402 520799.2836 375190.953 503365.9161 429118.0388 603260.9642 0.722215361 0.431983059 0.746879197 0.562698501 0.863306785 0.621938059 0.834408235 0.711330691 1 19.20242271 0.871693042 0.269259346 1.06660251 0.552302256 0.450735147 0.118507281 2.097887138 0.456358686 0.381989442 0.203787232 7.442057849 -0.871693042 -0.514300255 QVSDVQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVSDVQKR 8 1 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 107.21 0.0064904 458510000 842930 678890 744180 801410 683180 812640 1003880 882150 803990 FALSE TRUE 803086.3694 748069.6628 778301.3891 720850.7442 802326.3757 784498.073 850719.6685 804904.2694 928668.663 0.86477169 0.805529133 0.838082968 0.77621952 0.863953321 0.844755621 0.916063718 0.866729224 1 19.82480443 0.929318895 0.58699687 0.999625023 0.823710212 0.730670148 0.031606067 0.459466349 0.371132474 0.031698366 0.013512423 8.498042423 -0.929318895 -0.175914811 QVTEEVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVTEEVRK 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 79.128 0.043623 0 289490 243070 276370 306280 537960 264460 371310 287770 725400 FALSE TRUE 275806.3814 267839.1093 289041.8379 275492.1525 631780.0537 255301.6839 314659.8399 262571.3332 837891.3272 0.329167247 0.319658529 0.344963396 0.328792223 0.754011926 0.304695461 0.375537769 0.313371585 1 19.67640362 -1.489537282 2.846290098 1.021863379 0.379209987 0.678116306 0.133392707 19081418.11 20916938.33 3273787.878 0.032132411 0.032393861 1.489537282 -0.642653392 QVVESAYEVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVVESAYEVIK 11 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 192.3 3.38E-06 180174000 375850 305950 327220 345090 270930 329190 376080 348670 313600 FALSE TRUE 358084.3154 337126.6528 342223.3607 310400.8976 318180.1062 317790.0678 318702.0888 318138.6064 362231.4864 0.988551048 0.93069395 0.944764256 0.856913077 0.878388871 0.877312105 0.87982989 0.878274304 1 18.46655243 3.884980138 1.221432326 0.88803767 0.980820326 0.294835906 0.041975374 0.503476387 1.36327094 0.011773203 0.039887469 7673.263961 -3.884980138 0.092782656 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(ph)PDDDDIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLTPDDDDIVR 39 1 P41743 P41743 PRKCI Protein kinase C iota type 1 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR;QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR 236.43 6.26E-50 185149000 91601 73538 83018 95317 79770 88208 113771 95789 97035 TRUE FALSE 87271.20227 81031.60581 86824.45742 85735.55407 93681.86274 85153.33484 96413.1444 87401.20735 112082.6922 0.778632281 0.7229627 0.77464643 0.764931252 0.835828092 0.759736701 0.860196543 0.779792184 1 16.77420399 -5 0.161675713 1.838062536 0.723392726 0.797450992 0.035037062 49.94694261 0.461271896 13.34003915 0.127697945 1.00E-05 5 -1.114669811 QVVS(ph)VVQDEEVGLPFEASPESPPPASPDGVTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVS(0.625)VVQDEEVGLPFEAS(0.327)PES(0.039)PPPAS(0.007)PDGVT(0.001)EIR;QVVS(0.999)VVQDEEVGLPFEAS(0.001)PESPPPASPDGVTEIR 62.663 0.0091833 55494000 27151 23088.4 24184 27334 26254 29116 33345 28556 33915 TRUE FALSE 25867.62604 25441.13421 25292.86032 24586.33439 30832.68929 28107.70562 28257.60783 26055.48526 39174.36499 0.660320239 0.649433225 0.645648253 0.627612838 0.787062899 0.717502521 0.721329059 0.665115702 1 15.25762227 -5 0.21382205 2.555594018 0.639544706 0.830482773 0.045210352 56.31433348 0.562125138 37.60450827 0.08883332 1.00E-05 5 -1.916049313 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEAS(0.004)PES(0.965)PPPAS(0.031)PDGVTEIR 173.83 4.12E-15 43055000 69560 55792 58219 69944 72050 56203 67762 58134 69129 TRUE FALSE 66272.03665 61477.26823 60888.39874 62913.09624 84615.49719 54256.67602 57423.66237 53043.47877 79849.17226 0.82996523 0.769917414 0.762542642 0.787899166 1.059691601 0.679489524 0.71915163 0.664295913 1 16.28498983 -1.375133233 6.92088487 1.00001024 0.783771912 0.276767265 0.109671364 1.67E-05 1.51E-06 0.102636258 0.024190453 0.042156716 1.375133233 -0.216238328 QVVSVVQDEEVGLPFEASPESPPPAS(ph)PDGVTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEAS(0.003)PES(0.198)PPPAS(0.759)PDGVT(0.04)EIR;QVVSVVQDEEVGLPFEAS(0.003)PES(0.219)PPPAS(0.777)PDGVTEIR 161.66 2.13E-14 224801000 58809 44951.4 55286 65752 69162 53285 61107 48581 59002 TRUE FALSE 56029.21512 49531.99877 57820.91779 59142.48404 81223.8309 51439.72709 51784.00484 44326.9901 68151.72882 0.822124634 0.726790055 0.848414542 0.867806071 1.191808811 0.754782424 0.759834061 0.650416224 1 16.05646263 -1.381032296 7.807910104 1.0000026 0.823064948 0.12325802 0.143895941 6.44E-06 5.11E-07 0.137786696 0.032476159 0.041587968 1.381032296 -0.176937652 QWADDWLVHLISPNVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QWADDWLVHLISPNVYR 17 0 Q9H7Z7;A6NHH0;X6RJ95 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 123.59 5.31E-05 192679000 622930 356830 276690 321460 592310 314550 611240 456210 441000 FALSE TRUE 593485.3334 393191.3827 289376.5102 289146.2301 695608.6765 303657.0546 517984.1118 416261.8339 509388.0277 1.165094783 0.771889721 0.568086595 0.567634523 1.3655772 0.596121303 1.016875316 0.817180246 1 18.95840553 QWGWTQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 130.28 0.0024537 595670000 199680 185250 156890 177240 379820 154350 214150 189900 270380 FALSE TRUE 190241.5221 204127.1856 164083.5617 159423.4985 446060.4877 149004.8208 181477.4844 173271.3493 312309.1495 0.609144889 0.653606165 0.525388263 0.510466948 1.428265834 0.477106806 0.58108283 0.55480715 1 18.25261531 QWIQISDAVYHMVYEQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QWIQISDAVYHMVYEQAK 18 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 176.46 8.03E-13 65322000 141360 108290 121880 134780 103220 142530 159240 171210 94929 FALSE TRUE 134678.1929 119324.8741 127468.3186 121231.6583 121221.5353 137594.1504 134945.0134 156217.9448 109650.1045 1.228254123 1.088233109 1.162500657 1.105622825 1.105530504 1.254847417 1.230687504 1.424694901 1 16.74254766 2.230553058 24.97843718 1.24534516 1.139079758 0.134987319 0.108523746 280.2632582 874233.3783 0.035795193 0.026905857 170.0407679 -2.230553058 -0.106265402 QWLQEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 179.17 0.00057169 1825228000 2216473 1861357 1490045 2190651 2738443 1795445 2323369 1995465 2301640 FALSE TRUE 2111704.714 2051031.394 1558365.037 1970442.6 3216026.592 1733268.289 1968896.387 1820731.506 2658566.576 0.794301987 0.77148017 0.586167392 0.741167296 1.20968443 0.651955947 0.7405857 0.684854584 1 21.34221716 4.753696752 16.77109695 0.783654636 0.794302287 0 0.182032425 109.642968 492990.1906 0.040774128 0.276675162 56714.84533 -4.753696752 0.010647651 QWLQEIDRYASENVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QWLQEIDRYASENVNK 16 1 Q9H0U4;E9PLD0;P62820;E7END7;P62820-2 Q9H0U4;P62820 RAB1B;RAB1A Ras-related protein Rab-1B;Ras-related protein Rab-1A 0 161.75 7.59E-09 102170000 180700 122100 180660 189540 174000 187410 219550 196060 206610 FALSE TRUE 172158.6691 134542.1288 188943.4397 170487.0791 204345.5449 180919.9447 186053.6152 178891.947 238650.0236 0.721385511 0.563763317 0.791717666 0.714381153 0.856256127 0.758097326 0.779608618 0.749599536 1 17.86453695 -5 0.084222688 1.885665898 0.48107325 0.601650449 0.069601461 145.0616782 0.85843464 23.48947967 1.945265967 1.00E-05 5 -1.404592648 QWQS(ph)LIEESAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QWQSLIEESAR 11 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 QWQS(1)LIEESAR;QWQS(1)LIEESAR;QWQS(1)LIEESAR 175.01 1.08E-05 47623000 95300 69162 80385 108172 112282 95692 136245 80947 119198 TRUE FALSE 90795.35787 76209.68643 84070.73176 97298.34505 131863.9453 92378.16205 115458.3229 73858.85155 137682.6171 0.659454039 0.553517126 0.610612535 0.706685761 0.957738515 0.670950074 0.838583152 0.536442821 1 17.0709869 3.083525907 4.174293037 0.788072235 0.604560522 0.300432404 0.133207768 0.252110653 8.333266878 0.035333584 0.042549526 1212.064991 -3.083525907 -0.183511713 QWTEILHFTEHSGLTTGVAFGHHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QWTEILHFTEHSGLTTGVAFGHHAK 25 0 Q9UMS4;H0YGZ5 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 145.25 8.76E-08 127657000 89053 105185 94792 111180 82335 106054 105853 107048 10826.3 FALSE TRUE 84843.64118 115903.4711 99138.30696 100003.9752 96694.19793 102381.3234 89703.18073 97674.30962 12505.18731 6.784675756 9.268431428 7.92777465 7.99699938 7.732327036 8.187108345 7.173277656 7.810703446 1 13.61023905 -0.664484048 0.622513161 1.39E-10 8.032618044 0.918334596 0.643204191 3.823137411 1.029092212 8.95203203 0.235520481 0.216528941 0.664484048 8.032618044 QWTSLS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 QWTSLSLR 8 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QWT(0.001)S(0.005)LS(0.994)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(1)LR;QWTSLS(0.999)LR;QWTS(0.001)LS(0.999)LR 157.14 0.00040041 5823805000 3746085 2524288 3237581 3756184 3781470 3971220 4845700 3295248 4304980 TRUE FALSE 3569014.986 2781515.817 3386027.291 3378605.248 4440957.171 3833695.656 4106399.468 3006698.616 4972574.312 0.717739899 0.559371393 0.680940511 0.679447915 0.893090157 0.770967997 0.825809573 0.604656346 1 22.2455615 2.905631233 5.644520602 0.80552385 0.646160915 0.355588467 0.106152765 0.240770871 11.52361255 0.029477349 0.031510786 804.6948714 -2.905631233 -0.159362935 QWYESHYALPLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QWYESHYALPLGR 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 164.2 3.74E-05 3722900000 3886400 3330800 2846100 3980300 3945700 3427800 4868000 4250400 4273000 FALSE TRUE 3702697.574 3670212.307 2976596.5 3580192.682 4633828.831 3309094.426 4125297.193 3878212.443 4935635.017 0.750196796 0.743615015 0.603082783 0.725376303 0.9388516 0.670449581 0.835818933 0.785757543 1 22.23480428 -0.550716477 0.282252849 1.111256131 0.710153038 0.478649599 0.085147522 8.581816068 0.761722689 0.964609609 0.107529108 0.281373714 0.550716477 -0.401103093 QY(ph)T(ph)FKMNEDT(ph)QEEPGKSEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYTFKMNEDTQEEPGKSEEEK 21 2 A0A087WZU3;A0A5F9ZI30;A0A5F9ZHS1;A0A5F9ZGX3;A0A5F9ZHE4;D6RHE1;A0A5F9ZHR8;A0A5F9ZHD2;A0A5F9ZGY3;I6L894;A0A5F9ZI40;A0A5F9ZHN5;A0A5F9ZH19;A0A5F9ZHT8;A0A5F9ZI46;A0A5F9ZI65;A0A5F9ZGZ5;A0A5F9ZHT4;A0A5F9ZHF7;A0A5F9ZGY4;A0A5F9ZH30;Q01484 A0A087WZU3 ANK2 Ankyrin-2 3 QY(0.891)T(0.9)FKMNEDT(0.704)QEEPGKS(0.506)EEEK 62.7 0.041212 66840000 113450 158670 74775 112700 45505 114500 88291 99264 21751 TRUE FALSE 108087.4433 174838.6534 78203.50771 101371.1819 53441.05759 110534.8363 74820.58637 90571.91793 25124.03399 4.302153204 6.959019935 3.112697099 4.034829037 2.12708905 4.399565624 2.978048286 3.60499106 1 14.61678051 3.718702641 24.75250281 3.191463188 5.630586523 0.464792102 1.147867951 506.2950273 631084.9738 0.270516607 0.41972828 5232.42053 -3.718702641 2.439123334 QYDISDPQRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 QYDISDPQRPR 11 1 Q13228;Q13228-4;Q13228-2;Q13228-3;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;;;;;;;; 172.13 1.25E-05 18551360000 16949630 13517800 13526130 16302020 15900110 14410490 17269320 15642830 16940670 FALSE TRUE 16148454.58 14895279.19 14146316.44 14663309.98 18673084.15 13911451.12 14634568.06 14273060.88 19567742.58 0.825258944 0.761216023 0.722940645 0.749361349 0.954278914 0.710937966 0.747892507 0.729417858 1 24.22197399 -1.223978082 4.489052825 1.000073881 0.775022158 0.498855464 0.070821249 4.96E-05 8.57E-06 0.064923507 0.015297603 0.059706542 1.223978082 -0.225051723 QYDPPAESQQSES(ph)PPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.329)ES(0.67)PPRR;QYDPPAESQQS(0.088)ES(0.912)PPRR;QYDPPAESQQS(0.016)ES(0.984)PPRR;QYDPPAES(0.003)QQS(0.11)ES(0.887)PPRR 145.55 2.88E-07 2829270000 1244900 1157660 1115500 1303650 1210070 1177840 1249450 1184610 1139870 TRUE FALSE 1186056.044 1275626.87 1166646.778 1172604.625 1421105.825 1137051.105 1058823.455 1080879.268 1316635.218 0.900823575 0.968853675 0.886082008 0.890607064 1.07934666 0.863603745 0.804188921 0.820940572 1 20.32842426 2.028508636 24.9999542 0.848438723 0.941874455 0.156035406 0.076549052 265.3554574 232695.9121 0.026169454 0.019327161 106.7846027 -2.028508636 0.093435732 QYDPPAESQQSES(ph)PPRRDS(ph)LASLFPSEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QYDPPAESQQSESPPRRDSLASLFPSEEEER 31 2 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 2 QY(0.012)DPPAES(0.141)QQS(0.155)ES(0.692)PPRRDS(0.999)LASLFPSEEEER;QYDPPAES(0.075)QQS(0.068)ES(0.856)PPRRDS(0.993)LAS(0.007)LFPSEEEER 84.48 0.00039279 316750000 175454 136180 165796 175817 164023 178389 216483 207302 190951 TRUE FALSE 167160.6371 150056.8968 173397.9106 158143.5411 192628.5593 172211.3442 183454.5424 189149.5379 220562.7058 0.757882601 0.68033667 0.786161513 0.717000367 0.873350545 0.78078179 0.831756854 0.857577156 1 17.75082935 0.713916762 0.25067575 1.063086091 0.688283552 0.768775526 0.043142553 1.458197552 0.252719169 0.183105434 0.086506984 5.17507636 -0.713916762 -0.374802539 QYEMGECTR ddPTM_SK-BR-3_Trastuzumab_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 ; 92.445 0.02343 636570000 503270 418610 407340 498900 391440 457070 549070 522690 450390 FALSE TRUE 479481.4245 461266.8349 426016.9419 448749.6242 459707.0121 441241.5513 465299.2871 476920.4926 520234.1809 0.921664593 0.886652304 0.818894562 0.86259158 0.883653995 0.848159478 0.894403529 0.916741941 1 18.98880167 0.866497587 1.645136311 0.999631511 0.874474839 0.692891245 0.027015886 0.343222677 1.798728056 0.027281307 0.007846142 7.353559098 -0.866497587 -0.125156672 QYESLPATHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYESLPATHIR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 76.326 0.035659 233570000 383660 285850 242230 317960 395730 278130 361440 340090 483430 FALSE TRUE 365525.1521 314978.44 253336.4851 285998.0567 464745.1867 268498.2884 306295.6897 310309.9167 558397.8554 0.654596268 0.564075304 0.45368456 0.512176137 0.832283259 0.48083689 0.548525906 0.555714736 1 19.09093388 -1.09845169 3.958962049 1.000096836 0.574939214 0.612988871 0.10606791 24755637.3 53067990.74 38322.76681 0.024222387 0.079716516 1.09845169 -0.425157622 QYMEGFNDELEAFKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QYMEGFNDELEAFKER 16 1 Q16543;K7EKQ2;K7EQA9;K7EL68 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 257.02 1.07E-26 560130000 423300 320412 413654 416702 356147 425156 546900 525895 452161 FALSE TRUE 403291.4479 353062.3471 432620.4451 374814.3233 418258.924 410432.7411 463460.3605 479844.8459 522279.8186 0.772175056 0.676002278 0.828330772 0.717650405 0.800833019 0.785848364 0.887379416 0.918750503 1 18.99446343 1.49894284 0.771616533 1.00109745 0.738205896 0.813620393 0.041154853 0.21225683 0.265257727 0.034677051 0.014646886 31.54589404 -1.49894284 -0.262891554 QYNEEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYNEEGR 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 133.79 0.0075314 187070000 136790 124230 112390 153680 147070 138960 150220 154360 142850 FALSE TRUE 130324.2078 136889.1782 117543.1927 138231.7944 172718.9614 134147.7804 127301.18 140843.4201 165002.4484 0.789831963 0.829619073 0.712372415 0.83775602 1.046766052 0.813004787 0.771510855 0.853583819 1 17.33212791 -5 0.2268252 1.895585754 0.806773437 0.285323866 0.08541857 222.4763246 2.225701375 91.60876811 0.153549631 1.00E-05 5 -1.088812317 QYNEEGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYNEEGRK 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 71.692 0.0771 156360000 99471 75915 89588 110670 90051 116410 129050 126320 110160 FALSE TRUE 94769.20296 83650.82481 93695.69841 99545.24134 105755.8659 112378.6925 109361.0523 115258.7511 127243.0502 0.744788834 0.657409774 0.736352188 0.782323602 0.831132747 0.883181379 0.859465819 0.905815689 1 16.95722734 2.217096634 0.443141645 0.988552213 0.674644079 0.889802212 0.032431091 0.322139534 0.141420283 0.034006946 0.034408563 164.8529161 -2.217096634 -0.313908135 QYNGVPLDGRPMNIQLVTSQIDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYNGVPLDGRPMNIQLVTSQIDAQR 25 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 261.82 3.78E-45 155180000 169740 140830 152850 178610 165030 150360 173600 162910 183670 FALSE TRUE 161716.7266 155180.7371 159858.3237 160655.7835 193811.1797 145152.9955 147114.1316 148644.7368 212152.6055 0.76226604 0.731458078 0.753506295 0.757265191 0.913546073 0.684191434 0.693435422 0.700650065 1 17.69474287 -1.659431383 2.606975645 1.032730594 0.747001536 0.598819131 0.064396551 10439583.56 8765976.239 2277425.751 0.016358148 0.021906279 1.659431383 -0.285729057 QYPEFPWTDVQAEIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 QYPEFPWTDVQAEIFR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;; 166.09 1.58E-08 82887000 80331 54299 72349 72924 78761 66418 95144 82862 101581 FALSE TRUE 76533.91283 59832.12983 75666.27321 65593.54097 92496.89346 64117.92801 80628.03536 75606.164 117333.6627 0.652275835 0.509931493 0.6448812 0.559034291 0.788323584 0.54645808 0.687168827 0.644368907 1 16.84025745 -4.999999997 0.23212601 3.074235577 0.580614647 0.7003572 0.076981084 81.12908389 0.811047263 79.00445676 0.115210114 1.00E-05 4.999999997 -2.49362093 QYPWGVAEVENGEHCDFTILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 QYPWGVAEVENGEHCDFTILR 21 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 356.07 1.37E-95 718238000 554935 407794 446017 509508 540166 469121 595778 554812 474474 FALSE TRUE 528704.3223 449348.6722 466467.3206 458291.2878 634370.7794 452875.2221 504881.1239 506229.72 548053.0046 0.9646956 0.819900025 0.851135413 0.836217088 1.157498954 0.826334713 0.921226815 0.923687519 1 19.0639559 QYQDFLEDLEEDEAIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 QYQDFLEDLEEDEAIRK 17 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;;;;;; 229.93 1.53E-15 292262600 336432.3 357931.6 293102.3 399333.6 233552.9 359369.8 336322.8 385745.3 249201.5 FALSE TRUE 320529.8119 394405.237 306541.3304 359191.8278 274284.4518 346924.7337 285010.5799 351967.3966 287846.3959 1.113544642 1.370193418 1.064947607 1.24785939 0.952884788 1.205242583 0.990148162 1.222761173 1 18.13493962 3.178092031 1.613634706 1.081580087 1.229318086 0.152724695 0.122030083 0.525683307 2.836247891 0.037022492 0.050507518 1506.926364 -3.178092031 0.147737999 QYTS(ph)PEEIDAQLQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 QYTS(1)PEEIDAQLQAEK;QYTS(1)PEEIDAQLQAEK 298.15 9.49E-46 116499000 406820 358900 364810 441550 317190 443310 439820 434730 349130 TRUE FALSE 387590.4248 395472.318 381536.8993 397164.5551 372507.8356 427958.0635 372717.3812 396662.7366 403271.2973 0.961115823 0.980660713 0.946104773 0.984856988 0.923715221 1.061216274 0.924234836 0.983612618 1 18.6213912 QYVETHWCAQSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 QYVETHWCAQSEK 13 0 Q96P70 Q96P70 IPO9 Importin-9 0 ; 177.93 1.50E-05 446900000 424560 420650 371541 446730 322628 417410 447350 507100 329737 FALSE TRUE 404491.8902 463514.7132 388576.5224 401823.8517 378894.2211 402954.987 379098.5414 462695.6357 380870.9299 1.062018281 1.216986325 1.020231506 1.055013182 0.99481003 1.057983047 0.995346485 1.214835787 1 18.53894265 3.716358085 24.93912066 1.043839385 1.139502316 0.20768758 0.073640932 914.3660958 1027067.611 0.017890207 0.027739942 5204.249206 -3.716358085 0.095662931 QYYTLLNQAPDMLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 QYYTLLNQAPDMLHR 15 0 Q13283;E5RH42;E5RJU8;Q13283-2;E5RIF8;E5RI46;E5RH00 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 93.181 0.0049557 865730000 250890 160430 185510 254650 214360 196520 255530 214660 218090 FALSE TRUE 239030.9269 176777.9994 194015.817 229052.0982 251744.3161 189714.4631 216544.2054 195863.2324 251910.2834 0.948873241 0.701749833 0.770178233 0.909260611 0.999341165 0.75310329 0.859608439 0.777511858 1 17.94255049 -0.978403936 4.025157964 1.000012082 0.836648112 0.225377973 0.093068604 20159705.17 48288522.17 3773.555078 0.021678364 0.10509839 0.978403936 -0.163363969 RAAAAADLANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAAAAADLANR 11 1 O76031 O76031 CLPX "ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial" 0 103.13 0.004451 35232000 95375 67972 89893 86690 67105 80893 105250 96629 85832 FALSE TRUE 90866.81277 74898.42408 94014.68297 77975.7565 78808.09075 78091.65513 89192.17945 88167.6525 99142.38819 0.916528383 0.755463182 0.948279386 0.786502705 0.794898047 0.787671717 0.899637189 0.889303295 1 16.59721439 0.981434489 1.332821408 0.99689532 0.832843699 0.408318818 0.062097695 0.443087647 1.607085023 0.054045658 0.016398355 9.58152173 -0.981434489 -0.164051621 RAAATQPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RAAATQPDAK 10 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 150.09 3.56E-05 1229080000 1947350 1621660 1759320 1921950 1484870 1940860 2253450 2068200 1687170 FALSE TRUE 1855302.625 1786908.998 1839986.562 1728751.935 1743830.858 1873647.532 1909644.815 1887097.444 1948807.707 0.952019339 0.916924226 0.944160143 0.887081844 0.894819356 0.961432739 0.979904179 0.96833435 1 20.89416031 2.062614184 5.738819618 0.978276951 0.921530681 0.664411119 0.02094816 0.130987484 8.420300373 0.008183012 0.005941244 115.5085637 -2.062614184 -0.05674627 RAAATQPDAKDTPDEPWAFPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAAATQPDAKDTPDEPWAFPAR 22 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 55.302 0.053359 98912000 78077 37484 89187 59665 82301 78103 140140 94967 133500 FALSE TRUE 74386.45494 41303.66222 93276.31217 53667.36084 96654.26834 75398.27353 118759.0692 86651.18603 154202.4982 0.482394616 0.267853392 0.604894948 0.348031721 0.626800924 0.488956239 0.770150098 0.561931143 1 17.23446661 0.954817656 0.301777098 1.075517211 0.339559655 0.662880673 0.119967498 1.061569884 0.29052712 0.282437328 0.157439612 9.011926813 -0.954817656 -0.735957556 RAADEDWDS(ph)ELEDDLLGEDLLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 205.89 5.66E-25 190248000 199084.3 165713.9 167987.7 194343 141384.5 181255.1 202016 195349.3 154067.8 TRUE FALSE 189673.9797 182600.3348 175690.1022 174807.2724 166041.912 174978.1904 171194.7489 178243.4797 177959.8476 1.065824579 1.026076035 0.987245745 0.982284908 0.933030199 0.983245338 0.961985253 1.001593798 1 17.44119224 3.927143821 1.455400041 0.972506778 1.062415309 0.68903819 0.019776448 0.206140243 0.814493097 0.005430865 0.017030079 8455.588146 -3.927143821 0.089908531 RAAEDDEDDDVDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;; 287.42 8.63E-34 10382440000 7482140 6533580 6639760 8143430 5079780 7659010 8560910 8544610 5609890 FALSE TRUE 7128474.07 7199359.23 6944199.564 7324836.945 5965692.024 7393776.563 7254785.948 7796398.651 6479843.09 1.100099797 1.11103913 1.071661685 1.130403444 0.920653778 1.141042532 1.119592843 1.203177074 1 22.62752745 RAAEDDEDDDVDTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;; 236.81 5.73E-18 11019680000 7758073 6790800 6472621 7924018 3736617 7918534 8255694 8229436 4001540 FALSE TRUE 7391364.264 7482790.24 6769397.075 7127480.656 4388281.822 7644313.182 6996136.254 7508822.957 4622078.386 1.599142993 1.618923267 1.464578596 1.542051013 0.949417438 1.653869221 1.513634272 1.62455552 1 22.1401103 -1.929919936 2.546725783 0.665341943 1.504847482 0.370538582 0.202766384 29758124.85 12064822.59 59055346.89 0.047322917 0.011751142 1.929919936 0.839505539 RAAEEAEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 160.72 1.17E-05 588270000 377360 204390 293560 307450 283020 330470 409050 365370 351200 FALSE TRUE 359522.9407 225217.5734 307020.0164 276544.5419 332378.5984 319025.741 346641.9098 333376.2659 405662.3023 0.886261648 0.555184872 0.756836449 0.681711217 0.819348006 0.786431816 0.85450856 0.82180736 1 18.62991972 1.207016882 0.546471581 0.995801305 0.712160306 0.4673294 0.086724233 0.678364405 0.517555178 0.08671786 0.043248312 16.10708244 -1.207016882 -0.283640999 RAAPTRGS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAAPTRGSPTK 11 2 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 RAAPT(0.089)RGS(0.89)PT(0.021)K 45.825 0.097179 35997000 42761 35461 42682 38771 39157 38363 51833 46427 54436 TRUE FALSE 40739.77227 39074.51622 44639.01192 34873.66542 45985.9684 37034.47969 43924.92387 42361.60575 62877.65686 0.647921286 0.621437219 0.709934405 0.554627306 0.731356267 0.588992681 0.69857762 0.673714764 1 15.94025984 -0.734255873 0.5327625 1.076118932 0.640242164 0.809535176 0.053156011 4.969429671 1.009470453 0.692194637 0.020026653 0.184392871 0.734255873 -0.435876769 RAASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAASSDQLRDNS(1)PPPAFKPEPPK;RAASSDQLRDNS(1)PPPAFKPEPPK;RAASSDQLRDNS(1)PPPAFKPEPPK 160.41 1.35E-11 1141150000 2006210 1353480 1954970 1742460 1110740 1867450 2261310 2354920 1477410 TRUE FALSE 1911380.429 1491401.151 2044607.308 1567304.61 1304452.704 1802779.738 1916305.628 2148710.721 1706519.197 1.120046251 0.873943377 1.198115621 0.918421904 0.764393806 1.056407535 1.122932359 1.259118986 1 20.70262521 1.867523139 3.843514464 1.1398269 0.97793732 0.202375351 0.135196651 0.348457616 8.328002602 0.063735856 0.035159919 73.70944468 -1.867523139 -0.16188958 RAAVAASSS(ph)S ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAAVAASSSS 10 1 P61927 P61927 RPL37 60S ribosomal protein L37 1 RAAVAASS(0.02)S(0.75)S(0.231);RAAVAASS(0.041)S(0.74)S(0.218) 93.442 0.0050218 294770000 736650 634030 665770 746080 733170 644880 798050 771030 971160 TRUE FALSE 701830.0144 698638.3778 696296.213 671082.6209 861034.6159 622547.6439 676292.8153 703514.5257 1121762.533 0.625649363 0.622804165 0.620716232 0.598239468 0.767572985 0.554972756 0.602884118 0.627151028 1 20.09733587 0.885240619 19.57386077 1 0.625046416 0.823323268 0.054219782 11504.38922 1962245.11 0.048143798 0.012035949 7.677867608 -0.885240619 -0.374953584 RADAGEKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RADAGEKPK 9 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ;; 119.53 0.00045698 550840000 949240 822510 873280 1027270 620640 1013180 1159930 1114540 809980 FALSE TRUE 904371.3064 906324.7041 913320.7518 924006.8679 728879.4195 978093.3226 982961.3749 1016944.969 935587.5616 0.966634598 0.968722481 0.976200186 0.98762201 0.779060613 1.045432157 1.05063536 1.086958625 1 19.83551316 2.051521229 24.99999997 1.050628734 0.944269565 0.429698782 0.062516013 94.74514472 45973.36899 0.022137651 0.016349735 112.5955507 -2.051521229 -0.106359169 RADAGSHTEGS(ph)PSQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RADAGSHTEGSPSQPR 16 1 Q86V15;Q86V15-2 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 RADAGS(0.004)HT(0.137)EGS(0.812)PS(0.047)QPR;RADAGS(0.01)HT(0.402)EGS(0.533)PS(0.054)QPR;RADAGS(0.015)HT(0.036)EGS(0.934)PS(0.015)QPR 79.293 0.011488 289836000 96489 96344 97836 112079 108444 93518 123783 102230 111267 TRUE FALSE 91928.15619 106161.5631 102321.8774 100812.606 127356.5993 90279.44821 104897.6299 93278.19924 128521.7181 0.715273322 0.826020417 0.796144643 0.784401325 0.99093446 0.702445077 0.816186023 0.725777718 1 16.97165265 -2.509013115 2.25347736 3.866472358 0.795715833 0.385891056 0.081402763 3738965.932 406668.1601 54593788.33 0.017921979 0.003097326 2.509013115 -3.070756525 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RADDFPVRDDPSDVTDEDEGPAEPPPPPKLPLPAFR 36 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR 69.873 0.0031098 117339000 143390 103655 99575 127617 112828 117669 173177 145346 167698 TRUE FALSE 136612.2389 114217.5623 104140.6122 114788.6967 132505.1675 113594.093 146755.668 132618.7337 193703.7494 0.705263782 0.589650757 0.537628273 0.592599251 0.684060933 0.586432082 0.757629465 0.684647221 1 17.56349235 0.460992527 0.623667404 1.009328722 0.613392904 0.797873826 0.058789567 0.792628223 0.509713076 0.074515889 0.023318403 2.890630143 -0.460992527 -0.395935818 RADDNATIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RADDNATIR 9 1 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 112.13 0.0032281 504930000 214470 227520 198191 207372 284460 206114 248090 231980 278840 FALSE TRUE 204332.4281 250704.5467 207278.2534 186526.5726 334069.7339 198976.2205 210239.314 211666.6014 322081.0831 0.634413006 0.778389542 0.643559229 0.579129239 1.037222462 0.617783009 0.652752754 0.657184208 1 18.2970644 -1.079313036 4.045804587 1.000052816 0.700660064 0.343569231 0.130294072 53696868.06 64758773.43 35628.86376 0.028924064 0.083308049 1.079313036 -0.299392752 RADLNQGIGEPQS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(1)PSR;RADLNQGIGEPQS(0.986)PS(0.014)R 204.17 1.59E-11 614370000 393980 372793 416530 434680 426640 383556 449150 430574 534690 TRUE FALSE 375357.3462 410781.0305 435628.3125 390985.1406 501045.8809 370273.3595 380623.9183 392870.6579 617606.9944 0.607760841 0.665117193 0.705348735 0.633064625 0.811269765 0.59952909 0.616288225 0.636117566 1 19.23632957 -0.993025728 4.249653314 1.000017142 0.656223853 0.74855785 0.062030465 3515807.676 1240974.651 569.6902059 0.013886805 0.101618849 0.993025728 -0.343793289 RADLNQGIGEPQS(ph)PSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RADLNQGIGEPQSPSRR 17 2 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.965)PS(0.035)RR;RADLNQGIGEPQS(0.5)PS(0.5)RR 174.55 1.06E-09 589030000 170386 154679 191855 174855 197091 180631 224110 193023 229912 TRUE FALSE 162332.1915 170440.966 200651.7415 157278.2432 231463.608 174375.7032 189917.9034 176120.8828 265565.5787 0.611269699 0.641803681 0.755563814 0.592238813 0.871587384 0.656620124 0.715145029 0.663191682 1 18.01870864 -5 0.211776619 2.509700222 0.64025242 0.598491746 0.080175061 94.72899999 0.944731533 60.90567691 0.151888307 1.00E-05 5 -1.869447802 RADS(ph)GEEENTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RADSGEEENTK 11 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(1)GEEENTK;RADS(1)GEEENTK;RADS(1)GEEENTK;RADS(1)GEEENTK 201.37 2.67E-08 798723000 1062860 1072870 961320 1298610 728975 1136580 1107550 1148450 785360 TRUE FALSE 1012620.714 1182196.673 1005397.473 1168071.256 856108.0092 1097219.95 938572.9059 1047885.63 907149.6177 1.116266484 1.303199218 1.108303915 1.287628008 0.943734079 1.209524789 1.034639587 1.155140904 1 19.79098099 2.754304189 24.99954081 1.079444669 1.205368185 0.325244525 0.096081717 933.934205 1483011.453 0.025809529 0.027289669 567.9422653 -2.754304189 0.125923515 RADS(ph)GEEENTKNGGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RADSGEEENTKNGGEK 16 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(1)GEEENTKNGGEK;RADS(1)GEEENTKNGGEK 102.45 0.0011939 220821000 267680 179114 261070 235390 148349 261010 342170 304010 191707 TRUE FALSE 255027.2969 197365.9202 273040.3177 211728.15 174221.0186 251971.1583 289965.6821 277389.2727 221435.9425 1.151697841 0.891300292 1.23304426 0.956159816 0.78677841 1.137896384 1.309478845 1.252684048 1 17.75652989 2.007756853 24.95188805 1.222252557 1.006171539 0.245649893 0.146973073 197.3380294 634785.0723 0.051711527 0.038120997 101.8021273 -2.007756853 -0.216081018 RAEATAASTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAEATAASTSR 11 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ; 123.95 0.00057615 93468000 25061.6 19162.8 19711.1 21101.8 20310.1 23930.3 26557.5 25373.6 27039.5 FALSE TRUE 23876.98784 21115.51111 20614.87343 18980.60697 23852.17501 23101.58771 22505.66561 23151.75307 31232.64756 0.764488114 0.676071763 0.660042457 0.607716875 0.763693663 0.739661525 0.720581423 0.741267708 1 14.93076725 -0.343685776 0.533219288 1.039681135 0.694663809 0.799379463 0.046523509 3.304784877 0.879842775 0.302403641 0.021364408 0.453225382 0.343685776 -0.345017326 RAEDGSVIDYELIDQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RAEDGSVIDYELIDQDAR 18 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;;;; 224.12 7.66E-19 2989140000 2399190 1898310 1688940 2551800 2760190 1796720 2067080 1815250 2234900 FALSE TRUE 2285785.043 2091749.947 1766379.57 2295288.216 3241566.262 1734499.136 1751708.981 1656297.087 2581476.878 0.885456331 0.810291955 0.684251556 0.889137623 1.255702226 0.671901868 0.678568534 0.641608337 1 21.29976525 RAEDYGEHHLAVLTNLGDIQVVSLPLLKPQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAEDYGEHHLAVLTNLGDIQVVSLPLLKPQVR 32 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 125.52 4.31E-08 54005000 134850 108470 127720 141290 137460 126670 158850 153340 44080 FALSE TRUE 128475.9077 119523.2163 133576.0883 127087.2608 161432.9805 122283.3861 134614.515 139912.7367 50915.70127 2.52330626 2.347472653 2.623475372 2.496032807 3.170593284 2.401683235 2.643870391 2.747929091 1 15.635823 -0.610277342 8.378110752 0.999999431 2.595956168 0.83159885 0.228790389 0 0 0.211950151 0.04995713 0.245314183 0.610277342 1.595956737 RAEGAIAGFRDPFSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAEGAIAGFRDPFSGK 16 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 99.011 0.0014281 171710000 352090 289440 291960 328540 368710 297310 470590 359990 372450 FALSE TRUE 335447.4035 318934.2651 305346.6548 295514.535 433012.9073 287014.0802 398792.8525 328467.3672 430207.6438 0.779733713 0.741349601 0.709765759 0.6869114 1.00652072 0.667152442 0.926977608 0.763508905 1 18.71467363 -0.184917666 0.235487854 1.099638801 0.720884604 0.322674974 0.103300087 9.51737752 0.806818195 0.968459323 0.201858495 0.653254385 0.184917666 -0.378754196 RAEILAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAEILAK 7 1 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 84.743 0.034187 944330000 1029920 839080 776710 773360 848900 753680 1085020 895390 815350 FALSE TRUE 981237.7227 924583.206 812322.9218 695620.3835 996947.8912 727579.8726 919480.2712 816984.9048 941790.3138 1.041885554 0.981729364 0.862530555 0.738614927 1.058566728 0.772549751 0.97631103 0.867480683 1 19.84504636 3.927215108 3.801113645 0.893642474 1.022361349 0.201996687 0.097901823 0.298190805 8.325791371 0.022878182 0.045417995 8456.976192 -3.927215108 0.128718875 RAELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Trastuzumab_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(0.149)WS(0.425)S(0.425)QEHLEWEPACQTPQPSAR 119.99 0.00010992 59205000 22676 12512 21663 17768 17764 18727 26951 20928 24922 TRUE FALSE 21604.15042 13786.98702 22656.26998 15981.92688 20862.03598 18078.47929 22839.12996 19095.43337 28786.77648 0.750488699 0.47893473 0.787037409 0.555182929 0.724708999 0.628013328 0.793389631 0.663340454 1 14.81311863 -0.534263378 0.335785923 1.118902825 0.624768396 0.519802778 0.099376707 6.356795475 0.733254426 0.923757329 0.081306422 0.292237956 0.534263378 -0.494134429 RAELYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAELYEK 7 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 101.25 0.014744 289080000 456910 413390 402760 438950 434250 410940 485200 465440 511660 FALSE TRUE 435312.7698 455514.911 421226.9444 394825.912 509983.0625 396709.0448 411173.8287 424683.6061 591005.6196 0.736562827 0.770745482 0.712729169 0.668057797 0.862907298 0.671244116 0.695718983 0.718577949 1 19.17281232 -2.292367655 2.186259629 2.175897551 0.73013474 0.696979522 0.056037406 2450281.951 362277.8777 14224572.57 0.013524542 0.00510073 2.292367655 -1.445762811 RAEPPKPEVVDSTESIPVS(ph)DEDS(ph)DAMVDDPNDEDFVPFRPR ddPTM_SK-BR-3_Trastuzumab_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 137.36 7.17E-10 32826000 60140 54070 58650 59732 45610 61902 66717 56521 48726 TRUE FALSE 57297.30139 59579.79447 61339.16051 53727.62588 53564.36956 59758.31822 56538.09631 51571.7216 56282.17922 1.018036298 1.058590753 1.089850488 0.954611684 0.951711009 1.061762694 1.004547036 0.91630641 1 15.78039057 3.235115185 24.99999212 0.987388143 1.050805533 0.399602433 0.042221345 102.6131175 744559.0985 0.012115679 0.015033768 1718.364078 -3.235115185 0.06341739 RAETFGGFDSHQMNASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAETFGGFDSHQMNASK 17 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 0 79.82 0.030962 62059000 121310 116550 118790 111730 90835 124620 131830 129260 100790 FALSE TRUE 115575.9167 128426.5775 124236.639 100498.6881 106676.5952 120304.3782 111716.9123 117941.3091 116419.9984 0.992749684 1.103131586 1.067141734 0.86324248 0.916308166 1.033365227 0.95960242 1.013067435 1 16.82897938 3.322076706 25 0.964626224 1.055998689 0.372611079 0.055083601 26.95396235 8065.526348 0.01502479 0.020343657 2099.310638 -3.322076706 0.091372465 RAEVLGHKT(ph)PEPAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RAEVLGHKTPEPAPR 15 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 1 RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR 181.32 2.83E-05 1873590000 1702170 1406420 1581380 1812180 1210610 1860500 2064060 2084710 1361280 TRUE FALSE 1621711.797 1549735.797 1653887.837 1630016.223 1421740.001 1796070.418 1749149.738 1902161.741 1572380.35 1.031373737 0.985598553 1.051837004 1.036655173 0.904195986 1.142262061 1.112421519 1.209733854 1 20.58451881 2.207530259 24.99912301 1.124674155 1.00622798 0.43112934 0.064732525 168.4699654 135724.2236 0.021659765 0.015998511 161.2613381 -2.207530259 -0.118446176 RAFS(ph)TEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAFSTEK 7 1 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 RAFS(0.951)T(0.049)EK 65.627 0.042921 268090000 141390 113550 117770 155700 117220 132160 174650 129680 118470 TRUE FALSE 134706.7749 125120.8741 123169.871 140048.7402 137663.1309 127583.2661 148003.9348 118324.5317 136841.7225 0.984398416 0.914347406 0.900090036 1.023435964 1.006002616 0.93234186 1.081570241 0.864681689 1 17.06214864 3.235346723 24.9993124 0.992388095 0.936310474 0.130043132 0.060719714 142.400295 1107664.259 0.01599373 0.019874394 1719.280442 -3.235346723 -0.05607762 RAFS(ph)WLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAFSWLR 7 1 Q9P206-2 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 RAFS(1)WLR 77.379 0.021766 0 18127 14879 13011 16679 19095 13608 22438 15742 20065 TRUE FALSE 17270.17263 16395.18702 13607.56722 15002.39523 22425.16195 13136.75155 19014.671 14363.54703 23176.57772 0.745156288 0.707403276 0.587125821 0.647308477 0.967578657 0.566811533 0.820426174 0.619744088 1 14.50037993 -2.095501998 2.473660576 1.492899483 0.713902251 0.371941365 0.119129506 10106441.08 3704317.012 27982761.91 0.025675593 0.008025979 2.095501998 -0.778997232 RAGAES(ph)PTMSVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.856)PT(0.14)MS(0.003)VDGR;RAGAES(0.995)PT(0.005)MS(0.001)VDGR;RAGAES(0.784)PT(0.207)MS(0.009)VDGR;RAGAES(0.774)PT(0.166)MS(0.059)VDGR;RAGAES(0.891)PT(0.106)MS(0.002)VDGR 101.04 0.0016378 1561780000 1034513 813650 896677 993816 989383 896633 1060677 976340 982957 TRUE FALSE 985613.6207 896561.86 937790.5274 893915.7276 1161931.082 865582.3744 898851.243 890846.4937 1135388.951 0.868084562 0.789651739 0.825964112 0.787321144 1.023377126 0.762366389 0.791668126 0.784617899 1 20.11475518 -1.136377265 4.329655139 1.000027813 0.826768331 0.339279243 0.07487227 2.13E-05 4.24E-06 0.067496155 0.015906098 0.073050423 1.136377265 -0.173259482 RAGAESPT(ph)MSVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.134)PT(0.864)MS(0.002)VDGR 122.16 0.00021349 267340000 131490 97582 114170 118500 133450 102590 142430 116350 143870 TRUE FALSE 125274.7283 107525.7167 119404.8074 106588.1549 156723.6377 99037.28258 120699.6876 106161.7772 166180.6248 0.753846776 0.647041235 0.718524242 0.641399411 0.94309212 0.595961669 0.726316246 0.638833663 1 17.34239266 -1.036643394 4.451978437 1.000013306 0.707128118 0.476117112 0.09621302 0.259232425 50262947.81 1679.234666 0.019826626 0.091908696 1.036643394 -0.292885188 RAGDLLEDS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK 228.33 3.55E-12 5057530000 10692150 11503040 8126500 12276540 5134570 11258370 9489120 11012580 4775130 TRUE FALSE 10186753.26 12675212.85 8499108.063 11042478.88 6030037.382 10868489.82 8041380.464 10048260.11 5515632.772 1.846887507 2.29805235 1.540912605 2.002033009 1.093263027 1.970488296 1.457925282 1.821778303 1 22.39509498 0.076541187 0.092784373 7.18E-17 2.747461431 0.375321277 0.321855742 32.31892072 1.012445097 19.02104433 10.32551764 1.192727374 -0.076541187 2.747461431 RAGDLLEDS(ph)PKRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK 142.78 3.72E-05 70666141000 16726540 12719760 14282760 15364420 8382514 17350610 18388890 17702340 9553176 TRUE FALSE 15935909.6 14015918.01 14937638.67 13819959.31 9844421.788 16749754.03 15583327.1 16152229.26 11034633.74 1.444172047 1.270175189 1.353704982 1.252416676 0.892138517 1.517925689 1.412219695 1.463775748 1 23.39553541 RAGDLLEDSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RAGDLLEDSPK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 111.94 0.0025548 463430000 799640 671490 692050 828370 576670 790880 926960 863870 720320 FALSE TRUE 761842.6019 739915.5944 723781.177 745100.6738 677241.0654 763491.6273 785535.2272 788224.9631 832023.5467 0.91565029 0.88929646 0.86990468 0.89552835 0.813968629 0.917632236 0.944126197 0.947358961 1 19.66626483 1.676982195 2.004706146 0.971606392 0.882350428 0.637884031 0.02989812 0.204283855 1.727796163 0.021458558 0.008392764 47.53157387 -1.676982195 -0.089255964 RAGELTEDEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 199.3 2.78E-07 4772560000 3083270 2729380 2957610 3322620 3541150 2923470 3648380 3203490 3839770 FALSE TRUE 2937529.938 3007506.925 3093219.344 2988623.925 4158725.439 2822229.501 3091752.624 2922975.433 4435221.921 0.662318592 0.678096154 0.697421549 0.673838644 0.93765893 0.636322049 0.697090851 0.659037019 1 22.08057486 -1.769188877 2.463477395 1.080292174 0.702511284 0.544155154 0.084757435 10024675.7 6777234.62 4856528.053 0.019356132 0.017014184 1.769188877 -0.37778089 RAGQTPTTPGTSEGAPGRPQLLAPLSFQNPVYQMAAGLPLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAGQTPTTPGTSEGAPGRPQLLAPLSFQNPVYQMAAGLPLSPR 43 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 RAGQTPTTPGTSEGAPGRPQLLAPLSFQNPVYQMAAGLPLS(1)PR 205.29 5.55E-36 78669000 132290 98302 113180 112070 146310 109250 150420 134850 143020 TRUE FALSE 126036.9139 108319.0856 118369.415 100804.5107 171826.4177 105466.6451 127470.6663 123041.8191 165198.8112 0.762940804 0.655689256 0.716527039 0.610201187 1.040118972 0.638422543 0.771619756 0.74481056 1 17.33384378 -4.99999985 0.218355316 2.324061784 0.702886901 0.324655084 0.117922215 169.6818388 1.696199609 98.68741315 0.206791504 1.00E-05 4.99999985 -1.621174883 RAGS(ph)SASSPPSASSSPHPSAAVPAADPADSASGSSNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAGSSASSPPSASSSPHPSAAVPAADPADSASGSSNKR 38 2 G4U4J3;Q8NDF8-4;Q8NDF8-2;Q8NDF8;Q8NDF8-3;Q8NDF8-5 G4U4J3 PAPD5 Non-canonical poly(A) RNA polymerase PAPD5 1 RAGS(0.263)S(0.263)AS(0.263)S(0.209)PPSASSSPHPSAAVPAADPADSASGSSNKR 117.32 1.88E-06 172020000 69313 43422 72543 72166 86187 61004 118910 85938 119560 TRUE FALSE 66036.71186 47846.75117 75869.1683 64911.73657 101217.9855 58891.41618 100768.0956 78412.81313 138100.7542 0.478177779 0.346462635 0.549375481 0.470031731 0.73292855 0.426438049 0.729670856 0.567794243 1 17.07536167 -5 0.10427031 2.596912012 0.21251655 0.683719956 0.106562271 86.22641531 0.605907028 29.33583122 1.374759408 1.00E-05 5 -2.384395462 RAHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 108.96 0.00068867 262610000 87789 87853 82593 103310 113130 64193 99273 78976 115510 TRUE FALSE 83639.38795 96805.32058 86379.97075 92925.08252 132859.8362 61969.98031 84127.08058 72060.44276 133422.7009 0.626875242 0.725553597 0.647415846 0.696471305 0.995781343 0.464463543 0.630530487 0.540091321 1 17.02564463 4.702925567 3.849884688 0.690940449 0.622881821 0.010224235 0.172972354 1.502487347 40.27258434 0.03822336 0.266090031 50457.48125 -4.702925567 -0.068058629 RAHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RAHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 34 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.991)PT(0.009)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.99)PT(0.01)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.991)PT(0.009)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.863)PT(0.13)PGIYMGRPT(0.005)HS(0.001)GGGGGGGGGGGGGGGGR;RAHT(0.992)PT(0.008)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 222.92 2.25E-36 936418000 84512.8 62783.3 78251.6 74426 77675.9 72335.3 85750.7 85815.1 74172.4 TRUE FALSE 80518.04743 69180.98965 81839.51326 66944.55708 91222.55237 69830.31042 72667.8558 78300.67491 85674.67697 0.939811509 0.807484686 0.955235738 0.78138091 1.064755136 0.815063597 0.848183598 0.913930203 1 16.38658123 0.97760893 19.37332784 1.000000005 0.882240502 0.148339438 0.083923256 148.3306296 128342.0986 0.070871553 0.017717888 9.497491868 -0.97760893 -0.117759503 RALANSLACQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RALANSLACQGK 12 1 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 167.3 7.95E-05 1498880000 2589300 2041270 2055640 2309400 2160100 2267390 3172700 2721600 2558600 FALSE TRUE 2466908.92 2249277.734 2149893.127 2077254.724 2536820.756 2188869.716 2688646.344 2483282.276 2955374.62 0.834719532 0.761080412 0.727451983 0.702873575 0.858375361 0.740640358 0.909748066 0.840259728 1 21.49490959 1.131061387 0.767009807 0.993852913 0.768229807 0.621730676 0.055996844 0.399775043 0.540446159 0.050569924 0.019516507 13.5226369 -1.131061387 -0.225623106 RALDDTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RALDDTAR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 74.92 0.063705 84559000 81043 64454 79631 73367 104500 71045 92909 79560 93535 FALSE TRUE 77212.258 71021.93588 83282.16012 65992.00977 122724.7669 68584.69384 78734.02566 72593.30463 108039.9301 0.714664087 0.657367473 0.770846113 0.610811297 1.135920458 0.634808758 0.728749321 0.671911807 1 16.72120509 -2.085937507 2.512739981 1.435320136 0.735231467 0.231323349 0.148294897 11374525.34 4402523.79 28292835.1 0.03440718 0.008204696 2.085937507 -0.700088669 RALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDR 39 1 P34897-3;P34897-2;P34897;G3V540;G3V5L0;G3V4W5;G3V241;G3V3Y8;G3V4T0;G3V4X0;G3V2W0;G3V2E4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 218.16 1.15E-39 94043000 54996 34707 54973 38899 56621 51583 70102 54729 72335 FALSE TRUE 52396.44807 38243.68276 57493.56643 34988.79862 66495.68447 49796.66778 59406.65239 49936.63862 83552.34236 0.627109266 0.457721252 0.688114358 0.418765024 0.795856616 0.595993677 0.711011214 0.597668925 1 16.35039265 -5 0.169269439 2.564445555 0.508961937 0.566650294 0.108694994 84.47254832 0.79534611 44.16174434 0.343987192 1.00E-05 5 -2.055483618 RALS(ph)SDSILSPAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.968)S(0.029)DS(0.003)ILSPAPDAR;RALS(0.894)S(0.093)DS(0.01)ILS(0.002)PAPDAR;RALS(0.43)S(0.43)DS(0.14)ILSPAPDAR;RALS(0.956)S(0.024)DS(0.02)ILSPAPDAR;RALS(0.964)S(0.035)DSILSPAPDAR;RALS(0.421)S(0.366)DS(0.188)ILS(0.024)PAPDAR 295.65 1.21E-45 2021763000 1284316 959161 1099301 1253082 1494309 1191487 1549994 1162159 1612492 TRUE FALSE 1223608.928 1056900.596 1149705.038 1127119.817 1754916.016 1150225.506 1313513.948 1060394.197 1862549.024 0.656953944 0.567448471 0.617275048 0.605149074 0.942211987 0.617554487 0.705223825 0.569324181 1 20.82884697 -5 0.263942487 3.228161905 0.632100507 0.475926641 0.109998809 173.0094722 1.691917754 209.8199885 0.133673255 1.00E-05 5 -2.596061398 RALSSDS(ph)ILSPAPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.084)S(0.084)DS(0.823)ILS(0.009)PAPDAR;RALS(0.341)S(0.012)DS(0.616)ILS(0.031)PAPDAR 260.09 9.54E-27 361374000 185175 137846 158005 168796 194555 157211 223719 168952 204851 TRUE FALSE 176422.1447 151892.6641 165249.6855 151828.3054 228485.3304 151766.7437 189586.5577 154157.6672 236618.2468 0.745598224 0.641931322 0.69838099 0.641659329 0.965628532 0.641399155 0.801233887 0.651503716 1 17.85220181 -5 0.254362351 2.712032904 0.699413499 0.413359714 0.101823408 173.6598202 1.7146991 155.0627877 0.126590745 1.00E-05 5 -2.012619405 RALVEFESNPEETREPGS(ph)PPSVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RALVEFESNPEETREPGSPPSVQR 24 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RALVEFESNPEETREPGS(1)PPSVQR;RALVEFESNPEETREPGS(1)PPSVQR;RALVEFESNPEET(0.004)REPGS(0.99)PPS(0.006)VQR;RALVEFESNPEETREPGS(1)PPSVQR 220.33 5.30E-33 1326230000 361184 273135 353698 334423 400272 325313 447584 369737 530792 TRUE FALSE 344111.5481 300967.767 369915.4032 300806.1647 470079.3101 314047.3292 379296.8404 337360.8682 613104.5125 0.561260831 0.490891456 0.603348036 0.490627876 0.766719704 0.512224789 0.618649566 0.55025018 1 19.2257735 -5 0.287819761 4.301577638 0.544493061 0.730915149 0.081014262 114.0573681 1.078198411 225.8461898 0.077941283 1.00E-05 5 -3.757084576 RAMS(ph)LNTLNVDAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAMSLNTLNVDAPR 14 1 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 RAMS(1)LNTLNVDAPR 103.17 0.00069294 50887000 47860 42208 52611 47061 59943 49799 68407 58818 49975 TRUE FALSE 45597.75265 46509.04319 55023.26639 42330.33887 70397.04022 48074.44814 57970.25577 53667.58411 57724.86776 0.789915238 0.805702031 0.953198656 0.733312011 1.219527094 0.832820412 1.004250993 0.929713418 1 15.81690534 2.79004741 24.99962208 0.984378512 0.822028848 0.387756567 0.109679402 355.5768997 172651.1279 0.029903318 0.031717268 616.6623162 -2.79004741 -0.162349664 RAPAPPPPQPPPPS(ph)PLIPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 79.445 0.0046301 120010000 27277 31460 22515 33897 25823 21488 32426 29515 27020 TRUE FALSE 25987.67027 34665.80977 23547.33502 30489.60916 30326.52302 20743.86517 27478.81816 26930.51013 31210.1236 0.83266797 1.110723245 0.754477468 0.976914079 0.971688655 0.664651811 0.880445669 0.862877394 1 14.92972645 RAPEEELPPLDPEEIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAPEEELPPLDPEEIRK 17 2 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 86.455 0.0026915 38545000 63385 54400 56960 67426 63390 61880 71287 69222 69791 FALSE TRUE 60388.91667 59943.42185 59571.67234 60648.21038 74445.19593 59737.08008 60410.85887 63160.55471 80613.83184 0.749113586 0.743587304 0.738975818 0.752330078 0.923479188 0.741027671 0.749385775 0.783495255 1 16.29873978 -5 0.31675088 3.141086177 0.758183763 0.629552603 0.054923824 204.9325563 1.828433279 293.7421061 0.04868208 1.00E-05 5 -2.382902414 RAPFDLFENK ddPTM_SK-BR-3_Trastuzumab_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 ; 190.26 1.48E-06 3417600000 7371300 7375200 4839600 5515700 5133900 5891200 7380900 6815800 4952100 FALSE TRUE 7022873.258 8126741.265 5061500.447 4961251.357 6029250.535 5687186.267 6254808.145 6218972.419 5720046.376 1.227765091 1.420747443 0.884870526 0.867344604 1.054056233 0.994255272 1.093489062 1.087224126 1 22.44759541 3.740958952 24.99996387 1.003470224 1.324256275 0.706414849 0.08755393 108.1905458 1127760.366 0.023651925 0.040227385 5507.556387 -3.740958952 0.320786051 RAPFDLFENKK ddPTM_SK-BR-3_Trastuzumab_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 ; 177.83 4.39E-06 2411600000 8817500 8834900 7861300 8930800 5118500 8917900 9016900 9885800 5438700 FALSE TRUE 8400714.25 9735186.354 8221748.381 8033059.017 6011164.779 8609070.887 7641206.298 9020146.944 6282105.819 1.337244945 1.549669273 1.308756748 1.278720742 0.956870984 1.370411632 1.216344729 1.435847661 1 22.58281681 3.442971057 3.13263869 1.219645231 1.443089958 0.275697938 0.154255602 0.292739927 5.89894745 0.040630339 0.060013389 2773.135287 -3.442971057 0.223444727 RAPFDLFENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RAPFDLFENR 10 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 218.55 1.08E-08 10273048000 6811050 6081520 3843344 4308017 6741270 4502602 6617000 5678610 7246720 FALSE TRUE 6489105.165 6701233.802 4019565.124 3874966.946 7916945.354 4346675.764 5607455.12 5181360.804 8370504.326 0.775234671 0.800577067 0.480205847 0.46293112 0.945814618 0.519284812 0.669906484 0.619002225 1 22.99688312 -1.641987617 6.107987259 1.002147873 0.669825447 0.329428316 0.152163456 0.004319543 0.000253184 0.142993146 0.033516595 0.022804071 1.641987617 -0.332322426 RAPFDLFENRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAPFDLFENRK 11 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 173.04 7.12E-06 3108600000 3933500 2958100 3095500 3284700 3146500 3296900 4494400 4123500 3697500 FALSE TRUE 3747571.25 3259533.753 3237431.737 2954515.715 3695248.604 3182727.526 3808696.735 3762424.48 4270889.416 0.877468575 0.763197881 0.758022843 0.691779961 0.86521758 0.74521422 0.891780696 0.880946359 1 22.02610511 1.162956606 1.067717918 0.994778435 0.785220599 0.588824107 0.058434904 0.331362404 0.79524853 0.052285145 0.017340284 14.55313661 -1.162956606 -0.209557836 RAPS(ph)PDGFSPYSPEETNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAPSPDGFSPYSPEETNR 18 1 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 RAPS(1)PDGFSPYSPEETNR 170.65 9.32E-12 222570000 86623 67895 82221 98703 104280 80821 95892 87229 103480 TRUE FALSE 82528.50246 74813.57769 85990.91418 88781.18692 122466.399 78022.1485 81261.91422 79590.76633 119527.1499 0.690458214 0.625912839 0.719425789 0.742770048 1.02459064 0.652756705 0.679861557 0.665880232 1 16.86697883 -2.441721444 2.257455235 3.80734215 0.717477735 0.372338638 0.111724918 5644844.614 369467.5803 81751167.57 0.02703831 0.003616417 2.441721444 -3.089864415 RAPS(ph)PGAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RAPSPGAYK 9 1 P54259 P54259 ATN1 Atrophin-1 1 RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK 125.54 0.00030544 3660580000 5803000 4859500 4850410 5572600 4434140 5411700 6222400 5879300 5108400 TRUE FALSE 5528703.69 5354688.575 5072806.096 5012431.661 5207452.612 5224291.472 5273058.598 5364477.324 5900584.582 0.936975585 0.90748442 0.859712462 0.84948052 0.882531644 0.885385405 0.893650201 0.909143365 1 22.49242646 0.654241061 1.900229515 0.999981588 0.890449446 0.680265944 0.023971663 1.14509976 5.363428108 0.026202246 0.00728603 4.510670062 -0.654241061 -0.109532143 RAPS(ph)PLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RAPSPLPK 8 1 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK 80.834 0.014959 1500000000 2852950 2279820 2322520 2773760 1914430 2702000 3038710 2653820 2312350 TRUE FALSE 2718096.708 2512136.25 2429009.839 2494936.375 2248305.986 2608429.062 2575098.98 2421437.452 2670937.428 1.017656452 0.940544778 0.909422218 0.934105138 0.841766626 0.976596844 0.964118048 0.906587113 1 21.34891475 -0.483761035 7.364955095 0.999999999 0.94138398 0.146596447 0.046885147 0 0 0.04537748 0.010695575 0.328275873 0.483761035 -0.05861602 RAPS(ph)SPVAKPGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RAPSSPVAKPGPVK 14 2 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 RAPS(0.5)S(0.5)PVAKPGPVK;RAPS(0.5)S(0.5)PVAKPGPVK;RAPS(0.5)S(0.5)PVAKPGPVK 88.133 0.0034787 1077410000 1077060 904230 1003400 1081500 766710 1020640 1176540 1193420 1025430 TRUE FALSE 1026149.508 996372.065 1049406.882 972785.5653 900423.9813 985294.9809 997037.2144 1088917.818 1184448.447 0.866352192 0.841211846 0.885987807 0.821298358 0.760205295 0.831859743 0.841773415 0.919345895 1 20.17578398 1.021802248 2.48188455 0.999407955 0.835933582 0.741655955 0.03245021 0.143036305 1.936029188 0.031919456 0.008663929 10.51482982 -1.021802248 -0.163474373 RAPS(ph)TSPSFEGTQETYTVAHEENVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAPSTSPSFEGTQETYTVAHEENVR 25 1 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 RAPS(0.309)T(0.309)S(0.309)PS(0.073)FEGTQETYTVAHEENVR;RAPS(0.318)T(0.318)S(0.318)PS(0.044)FEGT(0.001)QETYTVAHEENVR 224.27 4.01E-34 257246000 54942 56711 52262 69884 58269 51250 60024 64297 58973 TRUE FALSE 52345.00054 62489.91538 54658.26439 62859.12755 68431.09515 49475.19965 50866.23638 58666.81382 68118.23165 0.768443327 0.917374304 0.802402867 0.922794471 1.004592948 0.726313623 0.74673454 0.861249806 1 16.05575336 0.966062777 23.0283776 1.000000003 0.838303671 0.244024784 0.087011491 2759.947983 1872788.423 0.085390629 0.021347657 9.248318488 -0.966062777 -0.161696332 RAPS(ph)VANVGSHCDLSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RAPSVANVGSHCDLSLK 17 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 RAPS(1)VANVGSHCDLSLK;RAPS(1)VANVGSHCDLSLK;RAPS(1)VANVGSHCDLSLK 224.68 1.24E-15 663390000 686680 609190 522720 750900 466280 600500 692060 708070 499840 TRUE FALSE 654221.9973 671267.1536 546687.229 675418.1054 547599.0844 579704.5344 586473.5364 646067.6371 577352.6344 1.133141097 1.162664052 0.946886178 1.169853682 0.948465551 1.004073594 1.015797801 1.119017388 1 19.13909323 3.761785343 24.65085601 1.029854101 1.147902598 0.336478043 0.06931974 634.5530232 673515.3151 0.016016394 0.028846954 5778.103845 -3.761785343 0.118048496 RAPS(ph)WR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RAPS(1)WR;RAPS(1)WR;RAPS(1)WR 68.95 0.058059 2153820000 1531900 1315050 1231880 1588440 1765630 1328370 1673800 1515570 1686940 TRUE FALSE 1459490.123 1449055.09 1288362.916 1428766.993 2073555.313 1282368.214 1418431.069 1382858.656 1948542.04 0.749016492 0.743661189 0.661193287 0.733249252 1.06415734 0.658116781 0.727944812 0.7096889 1 20.89396363 -1.635396199 2.59973953 1.027749602 0.753770492 0.311117921 0.114122859 18168119.82 15942897.83 3390701.63 0.02830406 0.023152815 1.635396199 -0.27397911 RAPSS(ph)PVAKPGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAPSSPVAKPGPVK 14 2 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 RAPS(0.17)S(0.83)PVAKPGPVK 72.187 0.02052 193830000 388560 341710 343390 392450 292160 381610 479640 425850 361840 TRUE FALSE 370193.5389 376530.6375 359134.7712 353000.1804 343112.6115 368394.75 406462.1088 388560.3164 417952.2992 0.885731553 0.900893806 0.859272151 0.844594422 0.820937251 0.881427739 0.972508369 0.929676227 1 18.67297877 1.789006627 4.85083636 0.963303662 0.867609261 0.751653511 0.027629095 0.114783825 5.176355437 0.014365078 0.007836898 61.51862601 -1.789006627 -0.095694401 RAPSTS(ph)PSFEGTQETYTVAHEENVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAPSTSPSFEGTQETYTVAHEENVR 25 1 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 RAPS(0.121)T(0.121)S(0.704)PS(0.054)FEGTQETYTVAHEENVR 207.23 1.58E-25 154860000 9921.9 11095 14338 10859 11294 12628 17169 12645 14771 TRUE FALSE 9452.91145 12225.59311 14995.41148 9767.432689 13263.67002 12190.68919 14549.55372 11537.73676 17061.61124 0.554045648 0.716555602 0.878897735 0.572480087 0.777398444 0.714509844 0.852765516 0.676239577 1 14.05846628 -5 0.065094872 1.958511584 0.34049945 0.469250535 0.099580125 289.3614697 1.366003453 43.25709991 6.221208991 1.00E-05 5 -1.618012134 RAQQQAEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RAQQQAEAER 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 ;;; 199.03 4.59E-07 222702000 134033 88921.7 90958.2 111988 140551 105310 139455 124995 157068 FALSE TRUE 127697.5257 97982.92233 95128.72344 100730.7535 165063.0499 101663.0883 118178.5785 114049.7752 181425.3032 0.703857309 0.54007308 0.524340992 0.555218879 0.909812727 0.560357825 0.651389726 0.628632132 1 17.46901616 -5 0.308490387 4.250881788 0.612375196 0.512392131 0.11228153 234.5621238 2.131247686 495.0707458 0.101061201 1.00E-05 5 -3.638506592 RAQS(ph)TDSLGTSGSLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 RAQS(0.762)T(0.215)DS(0.023)LGTSGSLQSK 124.66 3.03E-05 186480000 129870 75602 106580 116740 97161 116410 138420 126210 117340 TRUE FALSE 123731.3025 83305.92975 111466.7984 105005.0734 114105.8476 112378.6925 117301.4867 115158.3833 135536.4879 0.912900315 0.614638398 0.822411737 0.774736567 0.841882872 0.829139771 0.865460575 0.849648571 1 17.04832177 0.944528099 0.449833362 1.006412517 0.765366119 0.413721718 0.075223435 1.117335355 0.575591681 0.097791793 0.047532917 8.800920514 -0.944528099 -0.241046399 RAS(ph)AAAAAGGGATGHPGGGQGAENPAGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASAAAAAGGGATGHPGGGQGAENPAGLK 29 1 Q07617 Q07617 SPAG1 Sperm-associated antigen 1 1 RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK 197.1 2.01E-25 307660000 143876 111911 119356 139113 117428 144546 158619 173680 130174 TRUE FALSE 137075.2666 123314.8581 124828.5907 125129.0969 137907.406 139540.3358 134418.7583 158471.6585 150360.7191 0.911642798 0.820126818 0.830194159 0.832192728 0.917177085 0.928037167 0.893975229 1.053943207 1 17.19806819 1.600651194 0.967327396 1.020422191 0.854591922 0.66930726 0.042843198 0.307089716 0.553984805 0.037519309 0.014547127 39.87045522 -1.600651194 -0.165830269 RAS(ph)AGPAPGPVVTAEGLHPSLPS(ph)PTGNSTPLGSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 2 RAS(1)AGPAPGPVVTAEGLHPSLPS(0.977)PT(0.023)GNSTPLGSSK;RAS(0.997)AGPAPGPVVT(0.003)AEGLHPS(0.003)LPS(0.996)PT(0.001)GNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPS(0.993)PT(0.006)GNSTPLGSSK 208.28 7.57E-28 376026000 376868 288484 357905 405700 378515 408610 518300 447700 448090 TRUE FALSE 359054.1965 317880.8476 374315.2983 364918.2652 444527.8962 394459.7332 439223.8158 408497.0146 517577.5087 0.693720632 0.61417052 0.723206268 0.705050469 0.858862467 0.762126883 0.848614572 0.789248002 1 18.9814154 1.656459686 0.186062892 1.087673709 0.536287658 0.778223238 0.050489434 1.270083404 0.243405338 0.276368303 0.29831104 45.33772105 -1.656459686 -0.551386051 RAS(ph)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RAS(0.793)AGPAPGPVVT(0.194)AEGLHPS(0.013)LPSPTGNSTPLGSSK;RAS(0.995)AGPAPGPVVT(0.004)AEGLHPSLPSPTGNSTPLGSSK 86.195 0.00037619 540520000 336390 274751 313150 352330 316140 314400 440660 374340 381580 TRUE FALSE 320489.5114 302748.4393 327508.2372 316913.119 371274.7159 303512.2492 373429.2237 341560.8051 440753.4776 0.727140063 0.686888373 0.743064443 0.719025794 0.842363668 0.688621337 0.847251906 0.774947499 1 18.74961243 -4.999999999 0.138957665 1.898417943 0.654505307 0.741197416 0.048477253 59.65006623 0.509427182 14.69913717 0.262076949 1.00E-05 4.999999999 -1.243912636 RAS(ph)AILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASAILR 7 1 P46779 P46779 RPL28 60S ribosomal protein L28 1 RAS(1)AILR 88.056 0.011569 203860000 50300 37049 32875 40677 60410 34189 65609 33964 54678 TRUE FALSE 47922.41868 40824.33522 34382.35127 36588.07068 70945.48487 33005.02636 55599.14206 30989.93211 63157.18498 0.758780156 0.646392572 0.544393346 0.579317629 1.123316134 0.522585457 0.880329642 0.490679439 1 15.94665925 RAS(ph)APHGPLDMAPFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASAPHGPLDMAPFAR 16 1 Q8N4B1-2;Q8N4B1;Q8N4B1-4 Q8N4B1-2 FAM109A Sesquipedalian-1 1 RAS(1)APHGPLDMAPFAR 112.47 0.00045098 197990000 157740 118470 135780 156740 122260 129110 151340 149400 138440 TRUE FALSE 150283.9428 130542.2277 142005.6473 140984.1974 143582.1053 124638.8883 128250.3035 136317.744 159908.5681 0.939811697 0.816355429 0.888042767 0.881655055 0.897901263 0.779438461 0.802022712 0.852473045 1 17.28688772 2.283166993 24.99911748 0.835469448 0.880440289 0 0.066343881 296.1592014 165977.6647 0.020939211 0.017518926 191.9406641 -2.283166993 0.044970841 RAS(ph)CTSSTSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RASCTSSTSGSK 12 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.998)CT(0.001)SSTSGSK;RAS(0.807)CT(0.035)S(0.014)S(0.056)T(0.056)S(0.034)GSK;RAS(0.982)CT(0.004)S(0.004)S(0.004)T(0.005)S(0.001)GSK;RAS(0.972)CT(0.028)SSTSGSK;RAS(0.948)CT(0.048)S(0.004)STSGSK;RAS(0.934)CT(0.064)S(0.002)STSGSK;RAS(0.971)CT(0.013)S(0.013)S(0.002)T(0.001)SGSK 132.51 0.00011003 425318000 1040530 1068431 917364 1195096 664669 951755 1013822 1088734 890850 TRUE FALSE 991346.209 1177305.334 959426.0468 1074962.68 780587.0632 918795.4857 859144.8338 993398.6792 1028998.468 0.963408829 1.144127392 0.932388217 1.044668882 0.75858914 0.892902676 0.834933054 0.965403458 1 19.9728094 2.767621473 24.57898814 0.876787302 1.030298249 0.356843295 0.085790863 503.2737511 425656.1418 0.024015843 0.025468666 585.6275144 -2.767621473 0.153510947 RAS(ph)DDGKLTDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASDDGKLTDPSK 13 2 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 RAS(0.995)DDGKLT(0.005)DPSK 57.148 0.091961 492990000 291910 214580 249310 307030 185390 326080 363550 361860 204020 TRUE FALSE 278111.9928 236445.946 260741.1101 276166.7611 217721.9573 314787.7678 308083.7704 330173.6201 235658.3796 1.180148965 1.003341983 1.106436828 1.171894509 0.923888035 1.335780074 1.307332126 1.401068872 1 17.84633746 2.217470337 24.99998777 1.290626026 1.082081158 0.325133155 0.128444123 226.0027737 267897.4035 0.042585012 0.031481901 164.9948303 -2.217470337 -0.208544868 RAS(ph)DGGANIQLHAQQLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASDGGANIQLHAQQLLK 18 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2;H7C3X8 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RAS(1)DGGANIQLHAQQLLK;RAS(1)DGGANIQLHAQQLLK 262.05 3.82E-31 689150000 627880 533270 549580 627310 493610 602010 729240 663700 583130 TRUE FALSE 598201.3567 587610.8193 574778.7866 564251.607 579695.4277 581162.2427 617981.0446 605582.9095 673558.8222 0.888120439 0.872397183 0.853346089 0.837716898 0.860645587 0.862823296 0.917486379 0.899079471 1 19.36144442 0.815215621 0.845425813 0.998968858 0.864088187 0.849938567 0.017747675 0.334316592 0.480425379 0.018298463 0.006364612 6.534549026 -0.815215621 -0.134880671 RAS(ph)DTSLTQGIVAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASDTSLTQGIVAFR 15 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 RAS(0.994)DT(0.006)SLTQGIVAFR;RAS(0.999)DT(0.001)SLTQGIVAFR 240.68 4.60E-18 280250000 134165 135226 130301 135958 177995 114828 154130 149336 288680 TRUE FALSE 127823.2863 149005.6831 136275.4297 122291.2435 209037.2716 110851.4776 130614.6377 136259.3482 333447.02 0.383339117 0.446864642 0.408686902 0.366748647 0.626898005 0.33244105 0.391710316 0.408638674 1 18.34709803 -1.697721044 2.55209536 1.098337628 0.418986803 0.840877097 0.079198185 5238315.969 4175906.106 3312921.99 0.018211137 0.0200576 1.697721044 -0.679350825 RAS(ph)EELDGLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASEELDGLFR 11 1 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 RAS(1)EELDGLFR;RAS(1)EELDGLFR 153.32 3.45E-05 121263000 216026 194749 200902 231690 226955 198186 235550 230162 254740 TRUE FALSE 205814.8791 214594.1445 210113.5554 208400.081 266535.8801 191322.7691 199612.5213 210007.7951 294243.7782 0.699470624 0.729307331 0.714079858 0.708256543 0.90583353 0.650218572 0.678391647 0.713720427 1 18.16665238 -1.636253302 2.879309334 1.024946578 0.721782659 0.616807682 0.068101768 20255677.69 19355616.87 3753933.747 0.016202232 0.023107167 1.636253302 -0.303163919 RAS(ph)FAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK;RAS(1)FAEK 147.62 0.0013101 33680030000 30465350 25839610 25834370 30699620 20947600 30205550 32770740 31513530 23812960 TRUE FALSE 29025313.28 28472695.64 27018901.42 27613635.87 24600854.81 29159524.23 27770961.74 28754038.25 27505752.22 1.05524521 1.035154226 0.982300037 1.003922222 0.894389458 1.060124588 1.009641966 1.045382727 1 24.71323002 -4.723391002 8.748484318 1.000123756 1.012349107 0 0.048053365 0 0 0 0.010347324 1.89E-05 4.723391002 0.01222535 RAS(ph)FAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RASFAK 6 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0;K7ENT7;Q96J92-2;Q96J92-3;Q96J92;Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;A6PVV2;Q9Y3S1-3 F5GWT4;Q9Y3S1 WNK1;WNK4;WNK2 Serine/threonine-protein kinase WNK1;Serine/threonine-protein kinase WNK4;Serine/threonine-protein kinase WNK2 1 RAS(1)FAK;RAS(1)FAK;RAS(1)FAK 102.51 0.021729 3460060000 3397460 2772450 2903690 3461980 2539200 3338550 3714090 3280220 2726500 TRUE FALSE 3236868.799 3054965.807 3036827.059 3113975.193 2982035.676 3222935.176 3147437.357 2992986.547 3149311.695 1.027801981 0.970042378 0.964282787 0.988779611 0.946884896 1.023377642 0.999404842 0.950362123 1 21.58660512 RAS(ph)GQAFELILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR 192.12 1.43E-06 2800840500 1120068 1081280 1229515 1312605 1280938 1198561 1427912 1263652 1451506 TRUE FALSE 1067124.605 1191463.661 1285889.479 1180659.452 1504333.182 1157054.532 1210057.799 1152999.932 1676598.137 0.636482042 0.710643555 0.766963442 0.704199429 0.897253282 0.690120373 0.721733952 0.687702024 1 20.6771055 -2.62950787 2.159483109 7.318276943 0.72383668 0.608721595 0.068775545 2495449.109 102280.2823 78658345.23 0.016332115 0.002346887 2.62950787 -6.594440263 RAS(ph)GQAFELILSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR 203.82 8.89E-09 9414405000 2852376 2299074 2316316 2543838 3139770 2331498 3157939 2668827 3037370 TRUE FALSE 2717549.839 2533352.254 2422521.38 2288126.571 3687344.894 2250757.64 2676137.406 2435130.36 3508389.827 0.774586056 0.722084027 0.690493788 0.652187096 1.051007749 0.64153579 0.762782227 0.694087738 1 21.74237763 -1.404172421 3.039768695 1.003881006 0.74846293 0.318637346 0.115535568 21939423.95 27538613.93 743248.7015 0.024810388 0.039430073 1.404172421 -0.255418077 RAS(ph)HTLLPSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RASHTLLPSHR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RAS(0.832)HT(0.168)LLPSHR;RAS(0.835)HT(0.165)LLPSHR;RAS(0.699)HT(0.301)LLPSHR;RAS(0.891)HT(0.109)LLPSHR;RAS(0.648)HT(0.352)LLPSHR 104.55 0.0012155 1285607000 766844 643020 639573 716879 825431 647625 857947 760334 356973 TRUE FALSE 730596.8039 708544.4691 668898.0547 644816.9609 969385.9051 625197.5839 727051.4279 693755.1242 412330.5497 1.771871632 1.718389456 1.622237438 1.563835038 2.350992197 1.516253366 1.763273249 1.682521765 1 18.65344183 0.189349445 1.12932 0.997539939 1.75802482 0.518287483 0.227999819 4.125538429 5.019958834 0.219813093 0.061078117 1.546498291 -0.189349445 0.76048488 RAS(ph)ISEPSDTDPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 RAS(0.916)IS(0.084)EPSDTDPEPR 142.98 2.75E-06 243910000 141950 145970 146610 164100 163750 145200 176620 155080 205850 TRUE FALSE 135240.3048 160844.509 153332.2135 147604.3562 192307.9482 140171.6876 149673.3752 141500.3731 237772.1667 0.568781059 0.676464833 0.644870321 0.620780633 0.808790831 0.589521009 0.62948232 0.59510907 1 17.85922032 -1.20933483 4.993090942 1.000040402 0.641688499 0.740736406 0.066612829 2.79E-05 4.41E-06 0.059980334 0.01413591 0.061754011 1.20933483 -0.358351903 RAS(ph)KLTY ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASKLTY 7 2 Q6AI12 Q6AI12 ANKRD40 Ankyrin repeat domain-containing protein 40 1 RAS(1)KLTY 76.85 0.031219 137180000 54251 48742 51157 61269 59512 57664 75142 61532 61314 TRUE FALSE 51686.66275 53708.86522 53502.59905 55110.12372 69890.87396 55667.08122 63677.70782 56143.93188 70822.26197 0.729808132 0.758361336 0.755448888 0.778146902 0.986848937 0.78601106 0.899119938 0.792744122 1 16.1119153 7.478609206 0.063567967 1.228159547 2.05E-11 0.521964489 0.0671878 197.2051269 1.025733189 4.100525366 22.55093649 30102960.33 -7.478609206 -1.228159547 RAS(ph)LSDLTDLEDIEGLTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.897)LS(0.103)DLTDLEDIEGLTVR;RAS(0.841)LS(0.158)DLT(0.001)DLEDIEGLTVR;RAS(0.985)LS(0.015)DLTDLEDIEGLTVR 250.71 1.24E-25 57740000 40489 30812.6 36072 42371 44371 38394 52013 39670 46470 TRUE FALSE 38575.16521 33952.43897 37725.93688 38111.78658 52109.28835 37064.40615 44077.46157 36196.2845 53676.33026 0.718662491 0.632540243 0.702841209 0.710029661 0.970805718 0.690516769 0.821171294 0.674343501 1 15.71199842 -4.999999997 0.118062931 1.828099874 0.606829875 0.422826552 0.095070366 140.6634769 1.082112598 28.09213648 0.894105616 1.00E-05 4.999999997 -1.221269999 RAS(ph)LSEIGFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RASLSEIGFGK 11 1 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 RAS(0.986)LS(0.014)EIGFGK;RAS(0.997)LS(0.003)EIGFGK;RAS(0.999)LS(0.001)EIGFGK;RAS(0.998)LS(0.002)EIGFGK 186.08 2.56E-06 1097150000 5068500 3966090 4162110 5204940 3912660 4716780 5642490 4794850 4447960 TRUE FALSE 4828922.05 4370239.08 4352946.86 4681729.542 4595026.665 4553436.726 4781624.519 4374987.515 5137726.92 0.939894651 0.850617238 0.847251504 0.911245307 0.89436958 0.886274572 0.930688726 0.851541466 1 22.29269878 -4.999999359 0.430726077 3.163315398 0.889353914 0.52543422 0.032824539 858.7061286 5.357021491 1763.275991 0.017753597 1.00E-05 4.999999359 -2.273961484 RAS(ph)LTLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RASLTLEEK 9 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 RAS(1)LTLEEK;RAS(0.991)LT(0.009)LEEK;RAS(1)LTLEEK;RAS(0.999)LT(0.001)LEEK;RAS(0.999)LT(0.001)LEEK;RAS(0.999)LT(0.001)LEEK 156.52 4.33E-05 937800000 1727890 1364215 1464720 1753520 1329220 1629270 1861480 1793210 1445090 TRUE FALSE 1646216.064 1503230.059 1531878.861 1577252.838 1561035.547 1572847.971 1577477.038 1636187.026 1669187.177 0.986238145 0.900576089 0.917739414 0.944922691 0.935207009 0.942283761 0.945057007 0.980229808 1 20.67071431 1.156265184 1.949389998 1.000357035 0.936508095 0.505419846 0.02166151 0.256155703 1.797516851 0.020013569 0.005745666 14.33062672 -1.156265184 -0.063848941 RAS(ph)MQPIQIAEGTGITTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RASMQPIQIAEGTGITTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR 158.91 2.72E-11 811890000 345643 322238 316680 370355 361396 349147 398684 391879 399287 TRUE FALSE 329305.1404 355074.4186 331200.0912 333126.2118 424423.348 337055.9518 337857.4335 357563.9973 461206.3887 0.714008193 0.76988183 0.718116876 0.722293142 0.92024603 0.73081371 0.732551504 0.775279801 1 18.81505297 -5 0.363387479 4.055763375 0.750712092 0.611734501 0.060174841 332.9722251 2.622187514 797.0191713 0.041319097 1.00E-05 5 -3.305051284 RAS(ph)PS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RASPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPK;RAS(1)PS(1)PPPK;RAS(1)PS(1)PPPK 88.803 0.0083792 299035000 857010 709660 738620 894500 619260 803030 900340 799070 692180 TRUE FALSE 816500.8357 781975.1608 772486.4576 804583.1606 727258.7479 775220.8697 762976.5971 729099.1947 799519.7392 1.021239121 0.978056103 0.9661881 1.006333079 0.909619503 0.969608168 0.954293634 0.911921443 1 19.60877413 4.576789168 0.578376369 0.951114928 1.056689564 0.303892824 0.030683881 3.417559406 0.987874072 0.014376051 0.23607389 37738.89394 -4.576789168 0.105574636 RAS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 63.185 0.043027 2239860000 196313 140972 155706 180417 133417 174603 205730 167075 172271 TRUE FALSE 187033.6735 155337.2071 162845.2741 162281.1404 156684.8826 168556.4543 174342.11 152445.0273 198985.9068 0.939934272 0.780644265 0.818375918 0.815540874 0.787416984 0.847077348 0.876153054 0.766109669 1 17.60230673 -1.963632259 7.097949364 1.092016349 0.833274748 0.525836056 0.050909321 0.033973854 0.000174072 0.022590779 0.011152088 0.010873459 1.963632259 -0.258741601 RAS(ph)PSKPASAPASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.999)PS(0.001)KPASAPASR;RAS(0.996)PS(0.004)KPASAPASR;RAS(0.987)PS(0.013)KPASAPASR;RAS(0.939)PS(0.06)KPAS(0.002)APASR 156.06 4.47E-06 1742710000 909040 921120 874140 1031190 714551 934190 1107960 1129260 918090 TRUE FALSE 866071.4807 1014983.175 914220.1836 927532.8221 839168.4682 901838.7661 938920.3529 1030376.008 1060462.708 0.816692067 0.957113501 0.862095552 0.874649165 0.79132294 0.850420066 0.885387431 0.971628705 1 20.01626246 1.217814553 2.914680075 0.998898504 0.86506678 0.595008241 0.042942959 0.187567852 2.747451773 0.040007821 0.011260026 16.51256547 -1.217814553 -0.133831724 RAS(ph)QEANLLTLAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RASQEANLLTLAQK 14 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RAS(1)QEANLLTLAQK;RAS(0.999)QEANLLT(0.001)LAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK 278.95 3.57E-33 1818720000 2683862 2575803 2234571 2782800 1913753 2511887 2876980 2748470 2206900 TRUE FALSE 2557001.162 2838280.254 2337028.291 2503067.657 2247510.917 2424899.723 2438043.862 2507799.396 2549134.781 1.003085903 1.113428868 0.916792752 0.98192833 0.881675984 0.951263833 0.956420147 0.983784543 1 21.28157622 3.731383049 24.99975702 0.949890276 1.058257386 0.508212627 0.042904538 352.4098365 1227457.36 0.010482547 0.016595101 5387.447477 -3.731383049 0.108367111 RAS(ph)SASVPAVGASAEGTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSASVPAVGASAEGTRR 19 2 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 RAS(0.845)S(0.076)AS(0.076)VPAVGAS(0.002)AEGT(0.001)RR 76.959 0.0069867 0 116730 100250 102380 114320 93788 115270 107830 129370 104200 TRUE FALSE 111212.4042 110465.589 107074.2243 102828.3364 110144.5975 111278.171 91378.55307 118041.677 120358.8038 0.924007224 0.917802317 0.889625195 0.854348275 0.915135362 0.924553647 0.759217857 0.980748173 1 16.87698215 3.739079488 4.380955473 0.88538606 0.921489392 0 0.067940973 0.660613956 33.09742554 0.017062454 0.029463678 5483.773243 -3.739079488 0.036103332 RAS(ph)SDLSIASSEEDKLSQNACILESVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSDLSIASSEEDKLSQNACILESVSEK 29 2 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RAS(0.439)S(0.439)DLS(0.092)IAS(0.015)S(0.015)EEDKLSQNACILESVSEK 98.967 0.0004519 74953000 133590 105680 106250 133780 64863 117120 122640 129190 72306 TRUE FALSE 127275.4654 116448.9121 111121.6676 120332.1802 76175.08666 113064.105 103929.0156 117877.4387 83518.84519 1.523913138 1.394283073 1.330498133 1.440778784 0.912070641 1.353755608 1.244378024 1.411387316 1 16.34981414 8 0.126651611 1.014494756 2.638614552 0.351675657 0.155987358 92.4348869 0.796295565 0.831174068 26.71270548 100000000 -8 1.624119795 RAS(ph)SLNFLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.832)S(0.168)LNFLNK 140.08 2.45E-05 326100000 1195800 981490 984510 1140900 1108100 1101500 1403400 1223700 1244500 TRUE FALSE 1139276.904 1081504.947 1029650.757 1026214.564 1301352.289 1063354.779 1189285.555 1116546.341 1437490.704 0.79254558 0.752356133 0.71628342 0.713893009 0.905294403 0.739729847 0.827334432 0.776732912 1 20.4551212 -5 0.227448817 2.192533121 0.751524529 0.62103185 0.055325028 100.0645735 1.001030109 54.73977236 0.090259312 1.00E-05 5 -1.441008591 RAS(ph)SLNVLNVGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RASSLNVLNVGGK 13 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 RAS(0.5)S(0.5)LNVLNVGGK;RAS(0.5)S(0.5)LNVLNVGGK;RAS(0.5)S(0.5)LNVLNVGGK;RAS(0.5)S(0.5)LNVLNVGGK;RAS(0.5)S(0.5)LNVLNVGGK 188.47 3.73E-06 1542456000 3998035 3047920 3640624 3981360 3419047 3880123 4837900 4162160 4121090 TRUE FALSE 3809055.809 3358506.513 3807550.211 3581146.129 4015327.714 3745753.368 4099789.501 3797699.205 4760167.59 0.800193635 0.705543754 0.799877345 0.752315136 0.843526544 0.786895271 0.861269992 0.797807878 1 22.18258094 -1.90055933 0.191518556 1.256240515 0.729389764 0.751383615 0.038838599 14.20120849 0.414855327 1.745721162 0.108753133 0.012573051 1.90055933 -0.526850751 RAS(ph)SPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSPFR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 RAS(0.5)S(0.5)PFR 72.607 0.031328 266620000 203040 217100 182380 242340 217920 198370 222280 232180 194760 TRUE FALSE 193442.7016 239222.7368 190742.3034 217979.5228 255925.179 191500.3972 188367.1035 211849.0883 224962.3861 0.859889091 1.063389934 0.847885314 0.968959863 1.137635422 0.851255183 0.837327105 0.941708932 1 17.77932428 RAS(ph)YASTDQPSWMELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASYASTDQPSWMELAR 17 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 RAS(0.995)YAS(0.001)T(0.003)DQPSWMELAR;RAS(1)YASTDQPSWMELAR 208.46 3.16E-12 172356000 101824 80358 84596 95872 91302 80888 109114 100244 109526 TRUE FALSE 97010.98132 88546.57156 88474.81028 86234.76442 107225.0399 78086.82828 92466.65528 91466.10393 126510.7327 0.766820168 0.699913515 0.69934628 0.68163991 0.847556864 0.617234812 0.73089969 0.722990864 1 16.94890026 -1.871950826 1.586564441 1.175465424 0.719838492 0.687756412 0.059118577 40527.10876 13378.37449 26672.01321 0.014428993 0.01342917 1.871950826 -0.455626932 RASEDT(ph)TSGSPPKK ddPTM_SK-BR-3_Trastuzumab_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(0.327)T(0.327)S(0.327)GS(0.019)PPKK 87.85 0.0109 65512000 58995 56403 62671 66277 31890 68068 72116 72325 39734 TRUE FALSE 56206.42327 62150.52982 65544.52734 59614.71004 37451.6059 65710.78809 61113.3797 65991.83958 45895.74579 1.224654318 1.354167554 1.428117709 1.298915815 0.816014758 1.431740284 1.331569597 1.437863977 1 15.48607281 -2.20028304 2.535837779 0.060713915 1.291681279 0.202078128 0.181322307 55398597.34 42649794.02 285388334.4 0.043744439 0.006305463 2.20028304 1.230967364 RASEDTTSGS(ph)PPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDT(0.004)T(0.019)S(0.123)GS(0.854)PPKK;RASEDTT(0.002)S(0.277)GS(0.721)PPKK;RASEDTT(0.001)S(0.013)GS(0.985)PPKK;RASEDTTS(0.002)GS(0.997)PPKK;RASEDTT(0.001)S(0.004)GS(0.996)PPKK 218.14 4.33E-12 2872270000 2938510 2757010 2725400 3230030 1579540 3437910 3414510 3431830 1826270 TRUE FALSE 2799612.456 3037952.453 2850362.286 2905341.248 1855011.276 3318854.315 2893563.788 3131320.772 2109478.624 1.327158485 1.440143749 1.351216482 1.377279302 0.879369553 1.573305497 1.371696188 1.484405073 1 21.00845504 2.931774515 24.99999985 1.29860922 1.378691219 0.05163226 0.207481225 726.4488801 266192.208 0.060004091 0.063643979 854.6228779 -2.931774515 0.080081999 RASGQAFELILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR 203.56 9.11E-09 453194000 352815 307409 382396 391260 425121 339187 438705 355652 430334 TRUE FALSE 336138.1342 338734.3266 399929.2348 351929.8015 499261.9678 327440.8691 371772.4949 324509.2255 497067.9989 0.676241751 0.681464764 0.804576508 0.708011383 1.00441382 0.658744618 0.747930858 0.652846746 1 18.9230837 -2.465126223 2.299338526 4.072974613 0.738180972 0.37901428 0.103783337 4750249.923 421365.2009 76710226.82 0.023610124 0.003426682 2.465126223 -3.334793642 RASHT(ph)LLPSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASHTLLPSHR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RAS(0.056)HT(0.944)LLPSHR 106.32 0.0017888 206110000 161200 114880 123440 131040 167870 119110 172010 136150 66324 TRUE FALSE 153580.3955 126586.4026 129099.8461 117867.6102 197146.4749 114985.1908 145766.7153 124227.9842 76609.18718 2.004725557 1.652365823 1.685174466 1.538557118 2.573405124 1.500932134 1.902731522 1.621580763 1 16.22522979 0.834627584 2.90330303 0.99999374 1.826722956 0.426278854 0.304817739 0.659210608 9.618762463 0.262728546 0.069077511 6.833254309 -0.834627584 0.826729216 RASS(ph)LNFLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.079)S(0.921)LNFLNK 128.09 0.00020746 406150000 818980 690620 632020 748920 725790 742910 972720 819800 838320 TRUE FALSE 780268.4385 760994.9632 660998.7422 673637.1387 852367.5462 717182.8404 824313.6988 748013.966 968322.3841 0.805794074 0.785890088 0.682622599 0.695674447 0.880251825 0.740644699 0.851280227 0.772484431 1 19.88512792 -0.414184053 0.435197025 1.047268002 0.763954688 0.581999456 0.060273565 5.488986555 1.013893178 0.453572998 0.034202653 0.385315027 0.414184053 -0.283313314 RASS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RAS(0.129)S(0.616)LS(0.254)R 68.557 0.065809 73220000 134820 114420 132140 140710 140620 125170 143090 138930 161870 TRUE FALSE 128447.3258 126079.5281 138198.7497 126565.5635 165144.0835 120835.3315 121258.9925 126764.5527 186971.9729 0.686987059 0.674323141 0.739141528 0.676922651 0.883255821 0.646275106 0.648541012 0.677986924 1 17.5124625 -1.095424278 4.055661657 1.000058919 0.699648013 0.646089568 0.068734151 7480905.251 4044914.656 3957.256307 0.015488921 0.080274151 1.095424278 -0.300410906 RASS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RASSPFR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 RAS(0.44)S(0.56)PFR;RAS(0.112)S(0.888)PFR 81.263 0.016951 717290000 299280 302950 269740 275420 346390 290880 323410 272440 344880 TRUE FALSE 285133.6275 333820.9494 282107.8458 247734.2583 406800.3063 280806.7527 274067.8647 248583.7093 398362.229 0.715764716 0.837983436 0.708169162 0.621881896 1.021181921 0.704903056 0.687986573 0.624014254 1 18.60372134 2.638114804 0.014261765 1.518337209 4.62E-06 0.090281393 0.135479437 4945.889295 29.82544785 1529.948413 1642.151519 434.6251004 -2.638114804 -1.518332585 RASSDLS(ph)IASSEEDKLSQNACILESVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSDLSIASSEEDKLSQNACILESVSEK 29 2 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RAS(0.178)S(0.178)DLS(0.214)IAS(0.214)S(0.214)EEDKLS(0.003)QNACILESVSEK 82.077 0.0014122 86140000 148270 109590 109870 128510 64728 113520 123790 130480 63150 TRUE FALSE 141261.5709 120757.3456 114907.6482 115591.9306 76016.54271 109588.7739 104903.5619 119054.4795 72942.97947 1.936602699 1.655503332 1.57530785 1.58468891 1.042136519 1.502389602 1.438158445 1.632158164 1 16.15448151 8 0.214928863 1.220836271 4.953463148 0.522813899 0.193559237 39.25044282 0.495476166 0.298003252 50.48163531 100000000 -8 3.732626877 RASSLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RAS(0.083)S(0.083)LS(0.834)R 109.88 0.0073402 118420000 267600 227370 239170 266520 276590 253320 300560 268990 338180 TRUE FALSE 254951.0783 250539.2615 250136.1811 239728.9032 324827.2084 244547.4649 254704.0518 245435.8096 390623.2272 0.652677723 0.64138342 0.64035153 0.613708778 0.831561427 0.626044351 0.652045332 0.628318524 1 18.57541821 -1.527237212 3.027707221 1.012590932 0.659516126 0.747283699 0.061994805 15566012.43 18260822.94 1618472.268 0.014267189 0.029700433 1.527237212 -0.353074806 RAT(ph)SLPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 3 RAT(0.518)S(0.465)LPS(0.017)IPNPFPELCS(0.994)PPS(0.659)QS(0.347)PILGGPSSAR;RAT(0.522)S(0.476)LPS(0.002)IPNPFPELCS(0.996)PPS(0.592)QS(0.413)PILGGPSSAR 103.54 1.01E-05 165734000 112133 80384 113830 117469 135602 126393 159048 135224 167154 TRUE FALSE 106832.6953 88575.22099 119049.2181 105660.7929 159250.9459 122015.9787 134782.3065 123383.0697 193075.3886 0.553321146 0.458759771 0.616594476 0.547251484 0.824812251 0.631960291 0.698081239 0.639040898 1 17.55880475 -5 0.086528152 2.293617423 0.260337358 0.707645752 0.082948973 111.0150534 0.672006242 26.69394881 2.069587276 1.00E-05 5 -2.033280065 RAT(ph)SLPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.53)S(0.436)LPS(0.034)IPNPFPELCSPPSQSPILGGPSSAR 61.526 0.011527 82542000 28212 28826 23744 36265 37525 23770 41472 30710 33303 TRUE FALSE 26878.47467 31763.40217 24832.68589 32619.5733 44069.34812 22946.83894 35144.68471 28020.8696 38467.45915 0.69873278 0.825721347 0.645550458 0.84797837 1.145626696 0.596525984 0.913621162 0.728430476 1 15.23135092 -4.80424561 0.026678824 2.097669582 1.11E-06 0.147330845 0.154337365 3462.107847 7.184110664 414.7231698 190.1537814 1.57E-05 4.80424561 -2.097668468 RATS(ph)LPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.11)S(0.89)LPSIPNPFPELCS(0.995)PPS(0.004)QS(0.001)PILGGPSSAR;RAT(0.18)S(0.819)LPS(0.001)IPNPFPELCS(0.988)PPS(0.01)QS(0.002)PILGGPSSAR 199.1 3.02E-26 454610000 206427 135536 193417 193312 244320 192070 246330 220036 275090 TRUE FALSE 196669.6048 149347.2725 202285.3608 173879.9105 286929.3306 185418.5677 208747.8343 200768.4814 317749.5522 0.618945341 0.470015682 0.63661887 0.547223149 0.903004673 0.583536834 0.656957131 0.631845049 1 18.27753057 -5 0.163531001 2.429189262 0.522098791 0.540903194 0.108562367 96.87064585 0.899118584 44.9233743 0.408875637 1.00E-05 5 -1.907090471 RATS(ph)LPSIPNPFPELCSPPS(ph)QSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.128)S(0.872)LPSIPNPFPELCS(0.002)PPS(0.772)QS(0.226)PILGGPSSAR 210.07 8.24E-27 689230000 116900 77450 114030 103410 126810 105120 136330 127090 147300 TRUE FALSE 111374.3687 85342.24305 119258.3883 93015.03033 148925.6239 101479.668 115530.3546 115961.3259 170142.5317 0.654594519 0.501592648 0.700932254 0.546688881 0.875299212 0.596439156 0.679021015 0.681554016 1 17.3763843 -4.999999999 0.180334322 2.469452139 0.569264678 0.561854531 0.097860063 90.49079766 0.871661621 47.5501904 0.274688674 1.00E-05 4.999999999 -1.900187461 RATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.257)S(0.702)LPS(0.042)IPNPFPELCS(0.02)PPS(0.446)QS(0.534)PILGGPSSAR;RAT(0.035)S(0.964)LPS(0.001)IPNPFPELCS(0.001)PPS(0.384)QS(0.615)PILGGPSSAR 242.21 2.82E-46 913370000 276380 191519 263500 275370 337090 295310 360030 325750 381550 TRUE FALSE 263316.0651 211035.0038 275581.7356 247689.2844 395878.3893 285083.3407 305100.8111 297225.6031 440718.8253 0.59746952 0.478842726 0.625300577 0.562012036 0.898256136 0.646859912 0.692279961 0.674410953 1 18.749499 -4.999999988 0.089196683 2.202043296 0.323975191 0.606574999 0.09698261 136.1442959 0.845142502 31.13245399 2.236692903 1.00E-05 4.999999988 -1.878068104 RATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.122)S(0.877)LPS(0.001)IPNPFPELCSPPSQSPILGGPSSAR;RAT(0.293)S(0.637)LPS(0.069)IPNPFPELCSPPSQSPILGGPSSAR;RAT(0.17)S(0.829)LPS(0.002)IPNPFPELCSPPSQSPILGGPSSAR 258.8 1.78E-59 2628362000 656040 450305 623869 636032 723155 610149 804756 637115 831308 TRUE FALSE 625030.2893 496191.5915 652474.0107 572096.855 849273.003 589019.3871 681975.6918 581325.833 960222.9989 0.650922015 0.516746206 0.679502586 0.595795826 0.884453928 0.61341937 0.710226367 0.605407112 1 19.87300997 -5 0.190034623 2.48172989 0.587494727 0.545577462 0.097333089 98.12642496 0.959676007 55.14354796 0.245471943 1.00E-05 5 -1.894235163 RATVVESSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RATVVESSEK 10 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 170.4 6.95E-06 876370000 1042600 841700 864670 1028460 802580 1035280 1152020 1178530 956200 FALSE TRUE 993318.3642 927470.1869 904315.9748 925077.2469 942549.6979 999427.994 976258.1907 1075331.665 1104482.612 0.899351744 0.839732719 0.818768865 0.837566148 0.853385728 0.904883411 0.883905441 0.973606695 1 20.07493928 1.289306866 1.155503606 1.003630932 0.852530981 0.81115046 0.025556578 0.18865515 0.504752621 0.024125197 0.007963433 19.46735128 -1.289306866 -0.151099951 RAVS(ph)PSNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.999)PS(0.001)NPK;RAVS(0.991)PS(0.009)NPK;RAVS(0.996)PS(0.004)NPK;RAVS(1)PSNPK;RAVS(1)PSNPK;RAVS(0.977)PS(0.023)NPK;RAVS(0.998)PS(0.002)NPK;RAVS(0.999)PS(0.001)NPK 127.52 0.00027142 6123560000 4419640 3966770 3982250 4468650 3360190 4559830 5175350 4955480 4257270 TRUE FALSE 4210732.376 4370988.373 4164840.101 4019452.812 3946206.072 4401921.944 4385755.306 4521551.901 4917465.688 0.856280988 0.888870131 0.846948482 0.817382991 0.80248777 0.895160683 0.891873087 0.919488246 1 22.22948356 1.062201852 1.037084731 0.997682305 0.851367107 0.764927253 0.027039675 0.277427682 0.636130995 0.027420871 0.009063085 11.53989486 -1.062201852 -0.146315198 RAVSEGCAS(ph)EDEVEGEA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RAVSEGCASEDEVEGEA 17 1 Q9BYX2-4;Q9BYX2-2;Q9BYX2;Q9BYX2-6;Q9BYX2-5 Q9BYX2-4 TBC1D2 TBC1 domain family member 2A 1 RAVSEGCAS(1)EDEVEGEA;RAVSEGCAS(1)EDEVEGEA 275.5 1.07E-35 883520000 849800 622770 767820 743050 763530 714130 896060 820810 928950 TRUE FALSE 809631.6381 686230.971 803025.3065 668357.2023 896689.3903 689399.499 759349.5897 748935.525 1073006.822 0.754544726 0.639540176 0.748387886 0.622882529 0.835679114 0.642493119 0.707683842 0.697978345 1 20.03322782 -1.078371279 4.525786589 1.000020016 0.703199389 0.677727016 0.063652822 1.10E-05 2.24E-06 0.052617813 0.012401302 0.083488897 1.078371279 -0.296820627 RCDELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RCDELTR 7 1 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 115.49 0.0090878 154973000 77403 58466 63557 64621 86927 58377 95059 68816 90882 FALSE TRUE 73744.31359 64423.75187 66471.15132 58125.17431 102087.0413 56355.38985 80556.00367 62790.10622 104975.5164 0.702490601 0.613702643 0.633206233 0.553702199 0.972484297 0.536843178 0.76737897 0.598140484 1 16.67969336 -5 0.344488592 4.620415156 0.662773929 0.393482664 0.126758496 394.2463518 3.279577152 1052.020046 0.087093695 1.00E-05 5 -3.957641227 RCDIIIISGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCDIIIISGR 10 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 119.55 0.0047003 0 67785 76981 97333 113710 94411 90399 98825 99636 97437 FALSE TRUE 64580.93739 84825.45142 101795.8143 102279.6548 110876.2485 87268.45996 83747.4312 90911.34364 112547.0323 0.573812886 0.753688922 0.904473554 0.908772561 0.985154795 0.775395478 0.744110524 0.807763135 1 16.78016849 4.209502995 2.024059052 0.856853416 0.587979013 0.551104075 0.08562729 0.276624515 2.131655014 0.024155755 0.091538486 16199.55165 -4.209502995 -0.268874403 RCEAFGWHAIIVDGHSVEELCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCEAFGWHAIIVDGHSVEELCK 22 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 83.602 0.0013904 65406000 142440 105470 125140 105240 120730 99681 141790 118050 95295 FALSE TRUE 135707.1435 116217.5129 130877.7928 94661.07526 141785.2738 96229.02198 120157.3313 107712.9162 110072.8619 1.232884665 1.055823487 1.189010538 0.859985592 1.288103819 0.874230217 1.09161631 0.978560149 1 16.7480993 8 0.358179581 1.012557147 3.667516522 0.205309268 0.127542848 91.40377964 1.279493432 0.088490955 165.1465896 100000000 -8 2.654959375 RCEPIAMTVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCEPIAMTVPR 11 1 P31146;H3BRY3 P31146 CORO1A Coronin-1A;Coronin 0 68.563 0.020308 0 96537 93149 94490 104920 90793 99029 113700 101840 106390 FALSE TRUE 91973.88733 102640.989 98822.45996 94373.24227 106627.2705 95599.6009 96352.97676 92922.34971 122888.4178 0.74843414 0.835237289 0.804164149 0.767958803 0.867675509 0.777938251 0.78406882 0.756152218 1 16.90698942 -1.002642864 4.352508851 1.000008931 0.794287377 0.76416725 0.03618161 7961.641258 19459029.87 419.9710797 0.007851925 0.099393306 1.002642864 -0.205721553 RCGAQDKEHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RCGAQDKEHPR 11 2 Q96GX9 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 0 ;; 138.45 3.44E-05 93095000 174017 107350 140428 136474 144825 149181 199998 168826 154467 FALSE TRUE 165791.5613 118289.087 146866.7627 122755.3742 170082.4341 144014.8246 169484.6319 154042.7004 178420.9535 0.929215757 0.662977553 0.823147505 0.688009855 0.95326491 0.807163182 0.949914394 0.863366648 1 17.44492553 2.727029731 24.97925053 0.905925455 0.77669798 0.374998195 0.088699536 797.3165876 1727216.673 0.026334154 0.02502923 533.3714082 -2.727029731 -0.129227474 RCLYASVLTAQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RCLYASVLTAQPR 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 257.02 1.11E-23 1062490000 402940 285920 309650 295190 461050 267420 515300 435230 615300 FALSE TRUE 383893.8248 315055.5731 323847.7588 265516.9404 541456.974 258159.1783 436681.5209 397118.9539 710717.5815 0.54014961 0.443292218 0.455663075 0.373589942 0.761845476 0.36323736 0.614423411 0.558757746 1 19.43891686 -1.010120039 0.372941544 1.224778145 0.473185017 0.65175741 0.113871195 8.371101399 0.848741588 2.08581662 0.073389289 0.097696715 1.010120039 -0.751593128 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 38 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 342.94 2.08E-130 1325200000 519680 373365 461962 490377 635049 486266 709354 522163 360758 FALSE TRUE 495115.7563 411411.318 483143.4146 441083.3723 745801.3445 469426.4865 601129.0191 476439.6396 416702.5081 1.188175609 0.987302236 1.15944446 1.058509041 1.789769272 1.126526664 1.442585555 1.143356784 1 18.66865826 RCPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RCPSQSSSRPAAMISQPPTPPTGQPVREDAK 31 3 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RCPS(0.995)QS(0.004)S(0.001)SRPAAMISQPPTPPTGQPVREDAK;RCPS(0.25)QS(0.25)S(0.25)S(0.25)RPAAMISQPPTPPTGQPVREDAK;RCPS(0.95)QS(0.023)S(0.023)S(0.004)RPAAMISQPPTPPTGQPVREDAK 212.41 7.52E-26 404949000 227789 168080 216857 213452 185671 217792 264945 245467 217305 TRUE FALSE 217021.8654 185207.5431 226800.108 191995.3994 218051.9636 210249.8084 224522.7742 223972.6082 251003.5496 0.864616719 0.737868223 0.903573309 0.764911093 0.868720638 0.837636794 0.894500395 0.892308529 1 17.93734824 1.001059719 0.522451526 1.003825418 0.809619613 0.558602687 0.048632129 0.643278474 0.437780941 0.04915353 0.023053007 10.02443072 -1.001059719 -0.194205805 RCPT(ph)PEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCPTPEIQK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQK 75.683 0.022014 325070000 540520 540480 472430 672970 444040 552120 570130 583840 480280 TRUE FALSE 514970.6908 595555.5265 494091.3828 605321.777 521480.4354 532999.946 483146.1973 532715.8745 554759.3695 0.928277591 1.073538473 0.890640898 1.091142954 0.940011948 0.960776826 0.870911289 0.960264763 1 19.0815026 2.514713472 24.97206763 0.933394571 0.997488313 0.10253379 0.067142925 890.3530927 591450.0063 0.019660039 0.018531407 327.1248012 -2.514713472 0.064093743 RCPT(ph)PEIQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCPTPEIQKK 10 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQKK 119.39 0.033326 917010000 2148700 1679700 1746900 2112700 1518000 2077900 2628600 2623100 1759800 TRUE FALSE 2047135.209 1850863.34 1826997.093 1900327.382 1782738.719 2005941.802 2227558.792 2393407.458 2032700.796 1.007101101 0.910543914 0.898802763 0.934878063 0.877029577 0.986835744 1.095861622 1.177451921 1 20.95496644 1.842905417 3.241223641 1.103045605 0.930318271 0.653004726 0.054531027 0.138195554 2.527128447 0.027128885 0.014136824 69.64748162 -1.842905417 -0.172727335 RCQYVTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 207.29 0.0001035 1964590000 2789370 3420590 2447270 2930850 2315870 2847440 3104070 3089630 2508230 FALSE TRUE 2657522.008 3769152.01 2559479.75 2636235.39 2719756.995 2748832.439 2630487.111 2819085.618 2897193.498 0.9172746 1.300966612 0.883434176 0.909927277 0.938755729 0.948791456 0.907943192 0.973040158 1 21.46622461 3.699492444 24.99955513 0.93182322 1.10912085 0.352934185 0.096427236 459.1763775 293824.964 0.024013107 0.037201528 5006.018425 -3.699492444 0.17729763 RCS(ph)QVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RCSQVK 6 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 RCS(1)QVK;RCS(1)QVK 101.43 0.022377 155978000 172150 155231 125854 180856 107857 147820 173213 219004 169451 TRUE FALSE 164012.8107 171049.2154 131624.5304 162676.0113 126667.2267 142700.9563 146786.1756 199826.8487 195728.5956 0.837960392 0.873910196 0.672484927 0.831130529 0.64715749 0.729075667 0.749947523 1.020938448 1 17.57849502 1.236929179 24.999923 1.010469358 0.771623716 0.671950428 0.071665814 28.09384297 430440.1742 0.061096626 0.018349429 17.25556479 -1.236929179 -0.238845642 RCS(ph)SSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.332)S(0.332)S(0.332)LGVPLT(0.005)EVVEPLDFEDVLLSRPPDAEPGPLR 49.626 0.036564 19469000 2632.8 1201.1 3141.5 3713.4 1927 1000.7 4039.1 3486.6 3121.3 TRUE FALSE 2508.352762 1323.493456 3285.540882 3340.121977 2263.06819 966.0455081 3422.861112 3181.29482 3605.335263 0.695733567 0.367093033 0.911299683 0.926438662 0.627699791 0.26794887 0.949387744 0.882385295 1 11.81591771 1.607144996 25 0.93695544 0.62728162 0.337998295 0.20514943 0.097091983 2977.39626 0.104220723 0.052674127 40.47109885 -1.607144996 -0.30967382 RCS(ph)VTSMESTVSSGTQTTVQDDPEQFEVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RCSVTSMESTVSSGTQTTVQDDPEQFEVIK 30 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 RCS(0.998)VT(0.002)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.999)VT(0.001)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.996)VT(0.003)S(0.001)MESTVSSGTQTTVQDDPEQFEVIK 267.29 5.08E-59 475120000 444540 394640 475800 533930 372280 522390 586650 529300 480180 TRUE FALSE 423527.4752 434854.2647 497615.9006 480258.342 437205.5141 504299.5033 497145.7679 482951.686 554643.862 0.763602564 0.784024298 0.897180939 0.865885976 0.788263504 0.909231198 0.896333309 0.870741965 1 19.08120219 7.999999999 0.063705055 1.191691938 0.114932593 0.688634264 0.039434305 157.1616557 0.744827846 2.412010551 15.47264168 99999999.82 -7.999999999 -1.076759345 RCVPDPDTGLYMLQLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RCVPDPDTGLYMLQLAGR 18 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 145.48 1.46E-07 108140000 75007 41051 80566 69271 143650 49296 89655 73037 166070 FALSE TRUE 71461.56776 45234.14357 84260.03079 62307.74747 168702.5145 47588.86716 75976.48312 66641.49309 191823.2874 0.372538542 0.235811534 0.439258611 0.324818474 0.879468373 0.248087017 0.396075389 0.347410859 1 17.54941835 -1.507665718 3.095463019 1.018121346 0.394132847 0.518001626 0.179950439 148303523.4 174809646.2 22755211.36 0.040761691 0.031069501 1.507665718 -0.623988499 RDDASMDR ddPTM_SK-BR-3_Trastuzumab_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 80497000 88774 77022 77760 90497 69874 81788 90800 84356 82791 FALSE TRUE 84577.82895 84870.62937 81325.37292 81400.06963 82060.00348 78955.66105 76946.79234 76969.34144 95629.80544 0.884429583 0.887491394 0.85041868 0.851199783 0.858100705 0.825638625 0.804631903 0.804867699 1 16.54517272 3.654477559 2.743209443 0.842894832 0.886735814 0.003895337 0.055997319 0.600289718 8.802027151 0.014016795 0.024342236 4513.127045 -3.654477559 0.043840982 RDDAYWPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDDAYWPEAK 10 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 101.71 0.005043 197950000 763280 607120 625320 739970 547850 712980 798360 746690 649010 FALSE TRUE 727201.2671 668986.2182 653991.5405 665586.8097 643394.8665 688289.3238 676555.5191 681305.8651 749655.1561 0.970047709 0.892391939 0.872389838 0.887857309 0.85825444 0.918141252 0.902488983 0.908825691 1 19.51586758 0.203961302 1.340791506 1.000104475 0.901880284 0.522116404 0.029756807 6.485707157 9.958290536 0.030772871 0.00877683 1.599415507 -0.203961302 -0.098224191 RDDDYRGGGDRYEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDDDYRGGGDRYEDR 15 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 117.4 0.00016336 772550000 72809.6 42281.8 89768 73159.6 113518 74593 123166 87354.7 140647 FALSE TRUE 69368.0345 46590.36349 93883.95159 65805.45801 133315.5033 72009.82571 104374.7646 79705.45937 162457.8184 0.42699105 0.286784372 0.577897404 0.40506181 0.820616112 0.443252448 0.642473016 0.49062249 1 17.30970565 -4.999999995 0.09640983 2.598821685 0.13257567 0.57441719 0.138064624 123.9491446 0.81945168 40.20714776 2.353060699 1.00E-05 4.999999995 -2.466246015 RDDGLSAAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDDGLSAAAR 10 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 ;;;;; 226.93 4.49E-09 2824660000 1273092 988013 812646 958118 1235410 895996 1254860 1150817 1319200 FALSE TRUE 1212915.464 1088692.648 849906.6229 861806.1583 1450865.113 864967.4339 1063408.06 1050045.363 1523774.798 0.795993913 0.714470832 0.557763932 0.56557318 0.952151928 0.567647814 0.697877443 0.689107973 1 20.53921827 -1.902011495 2.27394325 1.182406268 0.695244873 0.395043352 0.119518758 14162354.15 6827074.084 13808767.42 0.027167701 0.01253108 1.902011495 -0.487161395 RDDGTGQLLLPLSDAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 209.7 1.86E-11 1316760000 1443880 1357230 1319840 1479860 1552650 1368110 1588070 1469770 1660930 FALSE TRUE 1375630.654 1495533.28 1380355.969 1331101.661 1823431.668 1320732.008 1345780.755 1341069.147 1918498.542 0.717035027 0.779533186 0.719498055 0.693824693 0.950447253 0.688419605 0.701476037 0.699020155 1 20.87154624 -1.113822503 3.916905239 1.000084948 0.743625587 0.516640627 0.077922905 6287976.419 5370117.486 3964.809035 0.017130005 0.076944485 1.113822503 -0.256459361 RDDGYEAAASSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDDGYEAAASSK 12 1 O43290;E9PQI8 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 81.632 0.027458 69221000 122030 103910 104300 128090 111840 119930 153040 129970 134330 FALSE TRUE 116261.8837 114498.5471 109082.2582 115214.1498 131344.8606 115776.794 129690.9372 118589.1378 155161.2103 0.74929735 0.737932805 0.703025311 0.7425448 0.846505775 0.746170991 0.835846388 0.764296292 1 17.24340841 -5 0.170241694 1.938465198 0.708163268 0.788154681 0.039454759 54.51432838 0.514433304 17.1869375 0.13039413 1.00E-05 5 -1.23030193 RDDMESLGYVLMYFNR ddPTM_SK-BR-3_Trastuzumab_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 ; 200.69 5.60E-11 144327000 217980 212354 189622 192735 220010 193058 265020 208360 230510 FALSE TRUE 207676.5174 233993.114 198316.3563 173360.9116 258379.6743 186372.3531 224586.3316 190114.8938 266256.3135 0.779987203 0.878826537 0.744832502 0.651105355 0.97041708 0.69997346 0.843496737 0.714029618 1 18.02245621 -2.029281528 2.77620219 1.248889133 0.79359768 0.33849076 0.093679653 118747099 95658421.21 187325524.2 0.020046572 0.009347995 2.029281528 -0.455291453 RDDNSAANNSANEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDDNSAANNSANEKER 16 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8;H0YEI7 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 142.35 8.53E-07 45264000 14887 10468 15871 14010 14934 15721 22791 18259 22605 FALSE TRUE 14183.32101 11534.7011 16598.70105 12601.68818 17538.48487 15176.57783 19313.81436 16660.14516 26110.46795 0.543204398 0.441765392 0.635710592 0.482629733 0.6717032 0.581244957 0.739696217 0.638063829 1 14.67234069 -0.590930423 0.196825486 1.298787389 0.426860289 0.802859246 0.069003676 5.33766569 0.284450826 1.120548313 0.201469242 0.256489492 0.590930423 -0.8719271 RDDSNESDVVESLDEIYHTGTFAQIHEMQDLGDKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDDSNESDVVESLDEIYHTGTFAQIHEMQDLGDKLR 36 2 K7EKE6;K7EJE8;P36776-2;P36776;K7EQF8 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 138.7 3.01E-10 24385000 13671 13062 11177 13030 11262 11188 13125 12297 4237 FALSE TRUE 13024.79892 14393.03265 11689.47651 11720.19964 13226.08923 10800.55675 11122.54019 11220.20949 4894.05232 2.661352611 2.940923331 2.388506649 2.394784297 2.70248219 2.206873987 2.27266475 2.292621483 1 12.25681381 -0.966290773 0.235924205 1.38E-15 2.861254607 0.887780163 0.173593326 4.619333436 0.258522982 3.451396409 0.328285503 0.108071014 0.966290773 2.861254607 RDDVTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDDVTLLR 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 112.11 0.0086665 0 28802 32758 37361 40704 28453 33971 31141 36124 29604 FALSE TRUE 27440.58654 36096.07744 39074.03881 36612.35659 33415.19419 32794.57575 26389.86851 32960.79105 34194.83712 0.802477475 1.055600216 1.142688256 1.070698376 0.977199981 0.959050503 0.771750086 0.963911334 1 15.0614909 1.979071683 11.75582749 0.88122772 1.002830171 0.130170328 0.105766008 1.582324636 883.3906623 0.044262318 0.029310697 95.29534418 -1.979071683 0.12160245 RDEFEFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDEFEFLEK 9 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 137.78 0.00024868 129330000 408480 373070 374390 436800 310450 429890 470000 475840 336610 FALSE TRUE 389171.9599 411086.2571 391556.1518 392892.0341 364592.3817 415002.8015 398292.8679 434172.927 388809.7596 1.000931562 1.05729408 1.007063589 1.010499414 0.937714069 1.067367244 1.024390098 1.116671885 1 18.56870491 RDEFLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDEFLGR 7 1 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 123.98 0.0067194 102370000 39393 33743 38487 43369 42954 39219 37651 40537 38688 FALSE TRUE 37530.97096 37181.45006 40251.66702 39009.46572 50445.164 37860.8362 31906.64844 36987.36538 44687.53745 0.839853192 0.832031752 0.90073585 0.872938362 1.128841885 0.847234785 0.713994332 0.827688602 1 15.44758493 -3.193497979 8.772264178 0.998073588 0.869054982 0 0.112600157 0 0 0 0.025239749 0.000640475 3.193497979 -0.129018606 RDELLAQHAAGALGLPDLVAVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 159.7 1.39E-11 2061740000 540440 550660 416460 635560 402000 503950 489650 560240 368100 FALSE TRUE 514894.4722 606772.88 435555.1029 571672.3013 472108.6727 486498.0851 414944.8995 511182.4156 425183.068 1.210994771 1.427086179 1.02439428 1.344532142 1.110365648 1.144208511 0.975920564 1.202264281 1 18.69772462 2.674201889 0.751337137 1.043513886 1.297975322 0.294078168 0.122192906 0.673682413 0.806959725 0.079489479 0.072215948 472.2825391 -2.674201889 0.254461436 RDEQDDDDKGDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDEQDDDDKGDSK 13 2 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;;;; 183.41 5.84E-06 2211550000 4656990 4892550 3900070 5313580 1934840 5105370 4199160 5011720 1728640 FALSE TRUE 4436863.312 5391106.407 4078892.067 4779448.843 2272275.483 4928569.757 3558501.019 4572867.228 1996708.663 2.222088478 2.699996504 2.042807819 2.393663599 1.13801053 2.46834696 1.782183393 2.290202529 1 20.92919242 -1.196488607 0.164609902 6.40E-14 2.626992204 0.409194192 0.427960325 24.72392288 0.803316049 13.6215341 2.001844951 0.063607949 1.196488607 2.626992204 RDGFVMGEGAAVLVLEEYEHAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDGFVMGEGAAVLVLEEYEHAVQR 24 1 Q9NWU1 Q9NWU1 OXSM "3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial" 0 ;;;;; 227.51 2.82E-33 134757000 184125 123486.7 144651.1 164708 185028 132483.4 188486 149405.2 166010 FALSE TRUE 175421.7762 136070.1351 151283.496 148151.2389 217296.8246 127895.4666 159728.9989 136322.4886 191753.9829 0.914827288 0.709607869 0.788945782 0.772611013 1.133206316 0.666976845 0.832989211 0.710923896 1 17.54889702 -2.35583607 2.270942366 2.19196653 0.814623455 0.159621091 0.132446609 4899428.805 761192.1199 29980601.26 0.028999756 0.004407212 2.35583607 -1.377343075 RDHHSTHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RDHHSTHYR 9 1 P05060 P05060 CHGB Secretogranin-1;PE-11;GAWK peptide;CCB peptide 0 ;;;; 92.838 0.015722 2828850000 2199610 1834530 1791260 1490420 2482260 2036080 2765920 2240730 2250630 FALSE TRUE 2095638.795 2021470.693 1873391.043 1340600.15 2915165.358 1965570.039 2343928.104 2044519.802 2599646.206 0.806124614 0.777594539 0.720633076 0.515685614 1.121370036 0.756091361 0.901633499 0.786460788 1 21.30988386 2.74157814 24.99744934 0.893604874 0.729209982 0.383991407 0.128051361 335.9231838 2782826.624 0.037455006 0.038166776 551.5414291 -2.74157814 -0.164394893 RDHRPPCAQEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDHRPPCAQEAPR 13 2 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ; 63.727 0.040157 43769000 56977 51658 46864 57341 51834 54013 62290 53419 42709 FALSE TRUE 54283.81013 56922.00893 49012.76075 51576.97374 60873.83319 52142.51627 52786.51647 48741.34917 49332.09359 1.100375155 1.153853502 0.993526874 1.045505471 1.23396006 1.056969459 1.070023845 0.98802515 1 15.59023889 1.44307006 2.083611819 0.992660031 1.103695386 0.295087 0.064464763 0.380284645 3.072850979 0.053767514 0.017123119 27.73767531 -1.44307006 0.111035355 RDINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 35 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RDINVSVGSQQPDT(0.001)KDS(0.999)PVCPHFTTNGNENSSIEK 202.03 7.27E-28 85736000 26189 29337 29908 31214 19839 34767 39732 39684 21537 TRUE FALSE 24951.09787 32326.47365 31279.31138 28076.30942 23298.91532 33563.01007 33670.15367 36209.05858 24876.84796 1.002984699 1.299460193 1.257366344 1.128612011 0.936570234 1.349166507 1.353473467 1.455532414 1 14.60251608 RDLEIERPILGQNDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDLEIERPILGQNDNK 16 2 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 120.63 5.80E-05 173120000 54998 54631 45260 64637 61704 57681 73373 61516 67506 FALSE TRUE 52398.35354 60197.96101 47335.21577 58139.56596 72465.15806 55683.49251 62178.60126 56129.33292 77974.48571 0.671993577 0.772021264 0.607060314 0.745622949 0.929344482 0.714124524 0.797422397 0.719842297 1 16.25071451 -5 0.159446247 1.933362405 0.676326014 0.505565831 0.08164932 109.6754502 1.00653877 32.44849371 0.330048187 1.00E-05 5 -1.257036391 RDNEVDGQDYHFVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDNEVDGQDYHFVVSR 16 1 Q92796-2;Q5JUW8;Q92796-3;Q92796 Q92796-2 DLG3 Disks large homolog 3 0 ; 87.49 0.0041883 248940000 237673 193698 205902 239500 258860 225776 276020 240734 243370 FALSE TRUE 226438.6683 213436.0464 215342.8104 215425.005 304005.102 217957.3205 233908.0795 219654.0547 281110.5766 0.805514581 0.759260107 0.766043074 0.766335467 1.081443131 0.775343721 0.832085659 0.781379546 1 18.10077821 RDNYVPEVSALDQEIIEVDPDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RDNYVPEVSALDQEIIEVDPDTK 23 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 158.77 3.35E-11 342094000 346155 386376 306462 433260 231635 364646 364534 394830 234566 FALSE TRUE 329792.9392 425748.1537 320513.5858 389707.8817 272032.0707 352018.2176 308917.6432 360256.5921 270941.2973 1.217211782 1.571366779 1.182963207 1.438348032 1.004025866 1.299241648 1.140164479 1.32964814 1 18.04762078 2.757608218 24.97139636 1.173250767 1.364508697 0.294371078 0.150177351 974.6866565 1277812.368 0.041385451 0.043829067 572.2795382 -2.757608218 0.19125793 RDPEVGKDELSKPSSDAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDPEVGKDELSKPSSDAESR 20 3 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 113.99 5.73E-05 415890000 389970 378050 348230 428490 226380 392110 446050 476000 263460 FALSE TRUE 371536.8909 416573.7248 364196.6899 385417.3711 265860.6003 378531.1324 377996.8802 434318.9166 304316.0312 1.220891615 1.368885244 1.196771292 1.266503672 0.87363324 1.243875095 1.242119512 1.427196966 1 18.21521081 -2.05844934 2.681940682 0.666158326 1.232669125 0.199781611 0.144564367 15249268.72 6555386.406 31627031.86 0.035130006 0.008740789 2.05844934 0.566510799 RDPHLACVAYER ddPTM_SK-BR-3_Trastuzumab_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 ;; 89.507 0.0060919 920590000 434789 342709 372789 427192 490930 366001 510560 457081 452440 FALSE TRUE 414237.3856 377631.4367 389881.7444 384249.8485 576548.0366 353326.2936 432664.6949 417056.5645 522602.0845 0.79264396 0.722598413 0.746039398 0.735262755 1.103225673 0.676090479 0.827904648 0.798038463 1 18.99535335 -5 0.159651614 1.752635736 0.738689532 0.235812361 0.115350573 188.6345121 1.732201934 45.09118078 0.456084314 1.00E-05 5 -1.013946204 RDPSEEIEILLR ddPTM_SK-BR-3_Trastuzumab_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 ;; 138.42 0.00011983 50941000 36974.7 31712.2 32675.2 39181 36959.9 33826.2 38294.1 36246.2 45183.5 FALSE TRUE 35226.97921 34943.70923 34173.39024 35242.45144 43405.69486 32654.79021 32451.63173 33072.29057 52190.32641 0.674971429 0.669543795 0.654783991 0.675267887 0.831680847 0.625686645 0.621793998 0.633686218 1 15.6714948 -0.929397564 5.619702688 1.000000316 0.67154351 0.747781068 0.059596336 2.33E-07 4.43E-08 0.05695727 0.013424944 0.117652846 0.929397564 -0.328456806 RDPSSNDINGGMEPTPSTVS(ph)TPS(ph)PSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 2 RDPSSNDINGGMEPTPS(0.002)T(0.014)VS(0.539)T(0.479)PS(0.925)PS(0.041)ADLLGLR 115.41 7.04E-06 85415000 40111 34254 39144 48502 40976 40709 48459 42691 43475 TRUE FALSE 38215.03252 37744.52154 40938.79112 43626.48681 48122.20143 39299.23712 41065.68954 38952.74972 50216.88096 0.760999723 0.751630146 0.815239623 0.86876138 0.958287343 0.782590164 0.817766631 0.775690345 1 15.6158848 -5 0.154446495 1.631948883 0.759623635 0.447063006 0.062171704 131.8189147 1.191592081 25.98462163 0.302915463 1.00E-05 5 -0.872325248 RDPSSNDINGGMEPTPSTVS(ph)TPSPSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPT(0.002)PS(0.027)T(0.023)VS(0.521)T(0.086)PS(0.323)PS(0.018)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.001)VS(0.492)T(0.087)PS(0.345)PS(0.073)ADLLGLR;RDPSSNDINGGMEPTPS(0.002)T(0.007)VS(0.501)T(0.101)PS(0.37)PS(0.019)ADLLGLR 81.204 0.0003072 216516000 107376 90033 103775 119680 97712 93673 110188 103776 115999 TRUE FALSE 102300.5493 99207.46506 108533.1864 107649.539 114752.9419 90429.08052 93376.79686 94688.82329 133987.5325 0.763507973 0.740423107 0.810024518 0.803429521 0.856444922 0.674906679 0.696906609 0.706698762 1 17.03173924 -1.091137645 4.168058927 1.00003677 0.753606584 0.651693162 0.055898499 6731802.549 3524578.066 2296.501334 0.013804425 0.081070407 1.091137645 -0.246430186 RDPSSNDINGGMEPTPSTVST(ph)PS(ph)PSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 2 RDPSSNDINGGMEPTPST(0.001)VS(0.474)T(0.541)PS(0.982)PS(0.003)ADLLGLR 158.6 7.28E-14 72804000 50941 42740 54621 57118 57756 59435 56900 49099 60845 TRUE FALSE 48533.11989 47095.25459 57125.42688 51376.39012 67828.62811 57376.75105 48218.85996 44799.63127 70280.53185 0.690562786 0.670103845 0.812820071 0.731018801 0.965112618 0.816396085 0.686091279 0.637440129 1 16.10083749 -2.320550907 2.329242022 2.41552606 0.746356883 0.401242613 0.095355761 6043127.092 746282.4849 45256180.64 0.02396611 0.004780233 2.320550907 -1.669169176 RDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPS(0.001)T(0.001)VS(0.081)T(0.017)PS(0.702)PS(0.198)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.085)T(0.043)PS(0.871)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.001)T(0.014)PS(0.978)PS(0.008)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.001)T(0.018)PS(0.977)PS(0.004)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.102)T(0.25)PS(0.621)PS(0.027)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.189)T(0.189)PS(0.614)PS(0.008)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.006)T(0.066)PS(0.909)PS(0.018)ADLLGLR;RDPSSNDINGGMEPTPST(0.005)VS(0.088)T(0.056)PS(0.85)PSADLLGLR;RDPSSNDINGGMEPTPSTVS(0.385)T(0.046)PS(0.565)PS(0.004)ADLLGLR 240.06 6.07E-47 4960198000 1020710 948944 998516 1157670 1043932 1030291 1142610 1030442 1110026 TRUE FALSE 972463.0612 1045642.472 1044298.946 1041298.812 1225993.41 994611.7643 968283.859 940211.0358 1282163.163 0.758455 0.81552996 0.814482101 0.8121422 0.956191416 0.775729481 0.755195506 0.733300615 1 20.29014843 4.538346427 1.589213722 0.821696383 0.747807049 0.058083431 0.08456954 2.312384078 7.52919558 0.021589656 0.236508447 34541.91622 -4.538346427 -0.073889334 RDPTEEIEILLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDPTEEIEILLR 12 1 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 116.51 0.0013369 13994000 13549 15843 14161 15437 15279 14113 16849 15785 15147 FALSE TRUE 12908.56562 17457.41971 14810.29586 13885.24343 17943.65276 13624.26327 14278.3756 14402.78172 17495.9194 0.73780436 0.997799505 0.846500005 0.793627538 1.025590731 0.778710907 0.816097472 0.823208052 1 14.09473086 -2.532358201 2.106309962 2.909849278 0.855584757 0.203555026 0.091553026 3417981.297 268423.005 31153802.69 0.021548681 0.002935228 2.532358201 -2.054264521 RDQALTEEHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RDQALTEEHAR 11 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 ;;;; 177.83 5.07E-06 1015538000 576628 349406 367439 491671 609312 425568 631839 530620 571997 FALSE TRUE 549371.9372 385010.8686 384286.4416 442247.297 715575.8199 410830.4735 535440.356 484156.0998 660699.3734 0.831500618 0.582732305 0.58163585 0.669362368 1.083058118 0.621811508 0.810414506 0.732793339 1 19.33363445 2.935667674 24.9999888 0.822770379 0.665609469 0.273053856 0.14500311 301.8555624 117302.678 0.041452935 0.043967512 862.318441 -2.935667674 -0.15716091 RDRS(ph)PIRGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDRSPIRGSPR 11 3 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 RDRS(1)PIRGS(1)PR;RDRS(1)PIRGS(1)PR 72.175 0.067492 345280000 239170 179833 199465 221880 202702 212200 252750 210029 235880 TRUE FALSE 227864.9081 198158.1872 208610.6675 199576.2009 238053.1646 204851.4608 214188.3454 191637.7473 272459.0657 0.836327129 0.72729526 0.76565875 0.732499762 0.873720843 0.751861423 0.786130367 0.703363446 1 18.05567997 -1.272675021 3.615049423 1.000528903 0.773614122 0.663358713 0.051010224 10327383.94 20008493.76 62698.3458 0.011244737 0.053373413 1.272675021 -0.226914781 RDS(ph)ASYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(1)ASYR;RDS(0.5)AS(0.5)YR;RDS(0.999)AS(0.001)YR;RDS(1)ASYR 149.23 0.0012437 1782491000 604273 828975 751896 817877 538767 779115 684848 691401 642363 TRUE FALSE 575710.2128 913448.495 786371.1753 735662.4501 632727.7942 752134.0522 580361.8595 630858.2631 741977.3733 0.775913436 1.231100203 1.059831746 0.991489062 0.852758881 1.013688664 0.782182692 0.85023922 1 19.50101567 2.889058135 4.273262953 0.887730257 1.031424012 0.162581822 0.128415461 0.361129701 11.04940668 0.039316132 0.04226893 774.5654744 -2.889058135 0.143693755 RDS(ph)DGVDGFEAEGK ddPTM_SK-BR-3_Trastuzumab_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 211.7 3.68E-09 969820000 2176625 2174581 1875009 2431340 1342985 2260933 2155701 2251923 1290108 TRUE FALSE 2073740.25 2396173.276 1960980.017 2186937.084 1577201.159 2182636.323 1826809.22 2054732.684 1490171.36 1.391611935 1.607985055 1.315942629 1.467574229 1.058402544 1.464688144 1.225905469 1.378856647 1 20.50704681 -3.451508892 0.080472358 4.62E-13 1.79996878 0.424743286 0.141632204 144.3945872 1.129572808 29.75490196 4.83292523 0.000353583 3.451508892 1.79996878 RDS(ph)DGVDGFEAEGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSDGVDGFEAEGKK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK 190.37 1.15E-07 750960000 2035800 1788310 1800020 2101120 1096550 2129660 2184370 2131140 1039250 TRUE FALSE 1939571.769 1970540.822 1882552.697 1889911.426 1287787.973 2055909.34 1851104.238 1944526.084 1200411.582 1.615755627 1.641554323 1.568256026 1.574386197 1.072788693 1.712670363 1.542057962 1.619882807 1 20.19509771 -2.05729565 2.367164523 0.246939858 1.551050326 0.489843665 0.174130334 2855437.396 974894.8935 11628500.49 0.04016281 0.00876404 2.05729565 1.304110468 RDS(ph)DTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)DTYR;RDS(0.907)DT(0.093)YR;RDS(0.831)DT(0.168)YR;RDS(0.824)DT(0.176)Y(0.001)R;RDS(0.992)DT(0.008)YR 105.52 0.0048435 627337000 708619 565150 636146 737051 740511 682148 825597 690741 862666 TRUE FALSE 675123.9842 622739.4275 665313.9233 662961.2332 869655.8839 658525.0437 699637.0145 630256.0562 996443.8374 0.677533403 0.624961894 0.667688332 0.665327245 0.872759559 0.660875223 0.702133917 0.632505348 1 19.92642897 -2.359593045 2.305272361 3.11843091 0.685936943 0.666977426 0.069277549 3343129.647 282590.4596 37269864.99 0.017878505 0.004369251 2.359593045 -2.432493967 RDS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.758)FDDRGPS(0.242)LNPVLDYDHGSR;RDS(0.974)FDDRGPS(0.026)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.998)FDDRGPS(0.002)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR 271.44 1.20E-45 23566520000 7678033 5932750 7054949 8256586 8835353 6964605 10178928 8006709 9397149 TRUE FALSE 7315107.596 6537303.97 7378425.39 7426618.289 10376235.77 6723418.983 8625945.585 7305599.114 10854410.87 0.673929491 0.602271652 0.679762861 0.684202798 0.955946471 0.619418139 0.794694957 0.673053489 1 23.37177809 -5 0.126458466 1.957675121 0.576293698 0.46202252 0.099691389 122.7824559 0.98928039 30.01956341 0.756295885 1.00E-05 5 -1.381381424 RDS(ph)FDNCSLGESSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSFDNCSLGESSK 14 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RDS(1)FDNCSLGESSK 76.155 0.017305 146270000 140640 124500 123890 211330 123480 215910 205670 144920 161700 TRUE FALSE 133992.2259 137186.6915 129570.479 190086.7069 145014.8729 208432.9826 174291.2641 132230.0365 186775.6102 0.717396805 0.734500032 0.693722692 1.017727672 0.776412256 1.115953964 0.933158585 0.707962011 1 17.51094655 3.249325536 24.99912558 0.928949235 0.71965369 0.421362216 0.115911441 189.2890408 439578.9831 0.029846206 0.04001505 1775.519868 -3.249325536 -0.209295545 RDS(ph)FIGTPYWMAPEVVMCETMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(0.999)FIGT(0.001)PYWMAPEVVMCETMK;RDS(0.998)FIGT(0.002)PYWMAPEVVMCETMK;RDS(0.981)FIGT(0.017)PY(0.002)WMAPEVVMCETMK;RDS(0.997)FIGT(0.003)PYWMAPEVVMCETMK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETMK 219.73 6.58E-26 668885000 768802 736034 626887 850487 496902 767660 791026 827847 455952 TRUE FALSE 732462.2531 811036.7014 655630.389 764994.4309 583561.5515 741075.7417 670340.4555 755356.328 526658.7075 1.390772131 1.539966376 1.24488664 1.452543023 1.108045007 1.407127104 1.272817569 1.434242551 1 19.00650882 -4.412512769 0.142366979 1.09E-13 1.492679053 0.437470705 0.124175446 96.90297794 0.9813158 28.54580571 0.677371253 3.87E-05 4.412512769 1.492679053 RDS(ph)FIGTPYWMAPEVVMCETSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RDS(0.996)FIGT(0.004)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.439)FIGT(0.263)PY(0.297)WMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.996)FIGT(0.002)PY(0.002)WMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.828)FIGT(0.147)PY(0.025)WMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK 305.75 1.12E-56 4616607000 3845341.9 3059162.4 3259314.9 3907137 2566846.4 3768344.8 4091089 3970607 2811739.1 TRUE FALSE 3663580.209 3370894.527 3408757.712 3514384.166 3014503.599 3637846.075 3466918.235 3622919.602 3247769.239 1.128029715 1.037910725 1.049568938 1.082091709 0.928176658 1.120106081 1.067476775 1.115510165 1 21.6310177 -0.774998487 7.397892687 1.000000838 1.065697013 0.116178094 0.057293646 0 0 0.050995464 0.012019746 0.167880987 0.774998487 0.065696175 RDS(ph)FSGVKDSNNNSDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSFSGVKDSNNNSDGK 17 2 Q14865;Q14865-2;Q14865-3 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 RDS(0.988)FS(0.012)GVKDSNNNSDGK 70.98 0.016429 45983000 38351 31920 38419 37647 31523 38643 49563 44605 40934 TRUE FALSE 36538.22423 35172.68429 40180.54915 33862.65204 37020.60122 37304.78322 42001.25406 40699.14973 47281.83566 0.772775078 0.743894221 0.849809416 0.716187338 0.782977241 0.788987625 0.888316908 0.8607777 1 15.52899843 1.168980148 0.737737189 0.996503891 0.76471812 0.774463222 0.038997648 0.265874512 0.335742142 0.034293271 0.013662513 14.75639078 -1.168980148 -0.231785771 RDS(ph)GDNSAPSGQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER 234.38 2.01E-17 735369000 378972 467971 398581 476560 333407 414176 381491 410919 322865 TRUE FALSE 361058.7446 515657.7769 416856.3331 428655.2834 391553.0752 399832.9813 323287.5414 374936.7539 372933.2552 0.968159153 1.38270795 1.117777316 1.149415552 1.049928023 1.072130135 0.866877751 1.005372272 1 18.50855793 2.395374041 1.392378092 0.95016556 1.174521789 0.348137407 0.110130245 0.3959195 1.542368984 0.057239737 0.039181348 248.5272652 -2.395374041 0.224356229 RDS(ph)IVAELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR 174.68 1.86E-06 2880620000 2542352 2489345 2415878 2449109 1970789 2665135 2862358 2862747 2157665 TRUE FALSE 2422180.059 2743012.086 2526648.396 2202919.91 2314493.978 2572840.707 2425652.716 2612069.696 2492264.668 0.971879147 1.100610268 1.013796178 0.883902877 0.928671022 1.03233045 0.973272521 1.048070748 1 21.24902585 3.470250426 24.97636017 0.975282914 1.039737805 0.163908052 0.055778032 248.7440513 904211.3015 0.015180515 0.020599115 2952.911462 -3.470250426 0.064454891 RDS(ph)IVAELDREMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDSIVAELDREMSR 14 2 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDREMSR;RDS(1)IVAELDREMSR 234.38 1.71E-17 75165000 23411 14094.3 24028.6 20730.8 26640 21255 31632 20386.1 28058 TRUE FALSE 22304.40843 15530.52519 25130.33508 18646.9006 31286.00757 20518.93402 26805.95744 18600.98501 32409.09134 0.688214557 0.479202735 0.775410048 0.575360179 0.965346644 0.63312278 0.82711228 0.573943429 1 14.98411095 3.229447356 1.636814396 0.773033473 0.595709085 0.17394491 0.155005507 0.547833281 3.040446946 0.0457353 0.064882685 1696.083996 -3.229447356 -0.177324389 RDS(ph)LASLFPSEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSLASLFPSEEEER 15 1 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 RDS(1)LASLFPSEEEER 103.4 0.00090372 72060000 57197 64965 49037 60323 45187 56392 50455 57580 46104 TRUE FALSE 54493.41116 71585.00736 51285.39495 54259.21743 53067.59849 54439.1309 42757.16308 52537.98995 53253.57285 1.023281786 1.344229195 0.963041392 1.018884077 0.996507758 1.022262507 0.802897548 0.986562725 1 15.7005907 3.675000756 12.81921982 0.958659267 1.183725002 0.44534671 0.098531857 1.196162404 240.3892529 0.026108627 0.040453146 4731.520823 -3.675000756 0.225065735 RDS(ph)LDKSGLFPEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSLDKSGLFPEWK 14 2 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 RDS(0.999)LDKS(0.001)GLFPEWK;RDS(1)LDKSGLFPEWK;RDS(1)LDKSGLFPEWK;RDS(0.996)LDKS(0.004)GLFPEWK 235.26 2.46E-17 2305480000 3031290 2295600 2514020 2812560 1445790 2717540 3051340 3112140 1599840 TRUE FALSE 2888006.929 2529524.25 2629290.304 2529836.125 1697935.318 2623430.908 2585802.041 2839624.523 1847935.016 1.562829268 1.368838313 1.422826171 1.369007082 0.918828478 1.419655391 1.399292734 1.536647392 1 20.81748259 4.418865008 0.943033558 1.304016375 1.621291388 0.171999309 0.191659228 2.488100805 2.456444318 0.06123116 0.727038749 26234.02981 -4.418865008 0.317275013 RDS(ph)LEEGELR ddPTM_SK-BR-3_Trastuzumab_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 241.41 1.58E-12 845500000 918010 1142570 792320 1102650 781450 1026870 838060 874970 537330 TRUE FALSE 874617.4866 1258999.182 828648.6557 991809.5271 917734.6326 991309.2344 710198.555 798352.9883 620656.3921 1.409181469 2.028496279 1.335116606 1.598000987 1.478651705 1.597194917 1.144270105 1.286304304 1 19.24343526 1.649280021 0.636357259 1.003255783 1.667049187 0.496912076 0.199689953 0.512608341 0.444868539 0.178314709 0.091830697 44.59436883 -1.649280021 0.663793404 RDS(ph)LGAYASQDANEQGQDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RDSLGAYASQDANEQGQDLGK 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.999)LGAY(0.001)ASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK 301.85 2.17E-55 543140000 541760 764670 434483 733800 316252 580450 469121 571370 274460 TRUE FALSE 516152.0785 842590.7424 454404.4753 660037.0299 371406.2487 560348.871 397547.9755 521337.8138 317021.8551 1.628127747 2.65783172 1.433353783 2.081992201 1.171547774 1.767540193 1.254008104 1.644485405 1 18.27422278 3.028245066 1.28000451 1.394015169 2.090647543 0.306651377 0.399035746 0.448636933 1.542477136 0.144224922 0.177739976 1067.198155 -3.028245066 0.696632374 RDS(ph)LGAYASQDANEQGQDLGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDSLGAYASQDANEQGQDLGKR 22 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.983)LGAYAS(0.017)QDANEQGQDLGKR;RDS(0.973)LGAYAS(0.027)QDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR 257.19 2.04E-37 2816040000 1752110 1838910 1557700 2047810 1107074 1794340 1767480 1961400 1182930 TRUE FALSE 1669291.233 2026297.02 1629122.086 1841960.248 1300147.355 1732201.556 1497818.464 1789649.418 1366372.743 1.221695355 1.482975294 1.192296973 1.348065715 0.951531975 1.267737201 1.096200485 1.309781264 1 20.38191967 2.788274035 24.99948346 1.139880858 1.323317495 0.326095675 0.13155476 406.8856639 204610.5806 0.036159926 0.038353331 614.149404 -2.788274035 0.183436637 RDS(ph)LGTYSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(0.677)LGT(0.266)YS(0.029)S(0.029)R;RDS(0.814)LGT(0.088)YS(0.01)S(0.088)R 137.73 5.12E-05 1572230000 818629 848357 646516 937555 802400 689813 795193 759556 700023 TRUE FALSE 779934.0295 934805.5428 676159.3981 843310.1902 942338.306 665924.6028 673871.7031 693045.25 808578.9916 0.9645737 1.156109115 0.836231717 1.042953377 1.165425167 0.823573961 0.833402438 0.857115084 1 19.62502919 2.217737431 24.99995814 0.859826203 1.035115436 0.34541377 0.104286435 232.800494 279494.4848 0.036767786 0.027182942 165.0963345 -2.217737431 0.175289234 RDS(ph)LTGSSDLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.952)LT(0.038)GS(0.005)S(0.005)DLYK;RDS(0.999)LT(0.001)GSSDLYK;RDS(0.974)LT(0.026)GSSDLYK;RDS(0.98)LT(0.02)GSSDLYK;RDS(0.98)LT(0.014)GS(0.005)S(0.001)DLYK;RDS(0.999)LTGSSDLYK 220.99 2.99E-11 1466996000 3379758 3430472 2771442 3712520 2145661 3339630 3371110 3518570 2215627 TRUE FALSE 3220003.537 3780040.997 2898515.357 3339330.436 2519863.599 3223977.776 2856785.255 3210465.358 2559215.119 1.258199638 1.477031363 1.132579804 1.304826004 0.984623598 1.259752551 1.116273983 1.254472644 1 21.28726999 3.723736927 24.72376618 1.158744188 1.367615502 0.372877115 0.11674102 582.6707844 971810.2924 0.027395213 0.042633536 5293.426981 -3.723736927 0.208871314 RDS(ph)LTGSSDLYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RDSLTGSSDLYKR 13 2 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(1)LTGSSDLYKR;RDS(0.726)LT(0.192)GS(0.058)S(0.024)DLYKR;RDS(1)LTGSSDLYKR;RDS(0.947)LT(0.033)GS(0.016)S(0.004)DLYKR;RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR 182.49 5.82E-06 4518940000 3212080 2160760 2952020 3036690 2470580 3222070 3962590 3610280 2925010 TRUE FALSE 3060251.344 2380943.901 3087373.037 2731436.152 2901448.37 3110488.908 3358024.118 3294144.744 3378605.612 0.905773475 0.704711995 0.913800956 0.808450724 0.858770956 0.920642793 0.993908287 0.975001265 1 21.68799652 2.111924131 1.623562183 0.993772491 0.82281156 0.591736251 0.057652714 0.242519801 1.222423916 0.032700744 0.017657233 129.3969771 -2.111924131 -0.170960931 RDS(ph)PPPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;RDS(1)PPPPAR 123.26 0.00034475 4576287000 1692851 1559074 1519967 1855617 1569030 1826686 2040394 1897408 1757002 TRUE FALSE 1612833.288 1717945.413 1589658.99 1669086.854 1842668.335 1763427.406 1729094.421 1731260.897 2029468.897 0.794707074 0.846499996 0.783288176 0.822425442 0.907955938 0.868910782 0.851993555 0.853061064 1 20.9526708 -5 0.138255883 1.554989994 0.779651742 0.757956489 0.03015848 68.70112299 0.584992314 10.48736948 0.190635587 1.00E-05 5 -0.775338252 RDS(ph)QDGSSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RDS(1)QDGSSYR;RDS(0.737)QDGS(0.131)S(0.131)YR;RDS(0.532)QDGS(0.054)S(0.414)YR;RDS(0.996)QDGS(0.003)S(0.001)YR 188.68 1.16E-06 1358844000 1662968 1946906 1447767 2100641 1346109 1878178 1703187 1775935 1383630 TRUE FALSE 1584362.798 2145297.935 1514148.549 1889480.576 1580869.983 1813136.225 1443334.542 1620424.717 1598196.274 0.99134432 1.34232445 0.947410887 1.182258154 0.989158847 1.134489083 0.903102182 1.013908456 1 20.60801317 2.414207677 0.930197658 0.972333471 1.139977094 0.144998231 0.120485832 0.817749362 1.401415708 0.077180428 0.051414182 259.5420183 -2.414207677 0.167643623 RDS(ph)SDDWEIPDGQITVGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.791)S(0.209)DDWEIPDGQITVGQR;RDS(0.796)S(0.204)DDWEIPDGQITVGQR;RDS(0.668)S(0.332)DDWEIPDGQITVGQR;RDS(0.753)S(0.201)DDWEIPDGQIT(0.047)VGQR;RDS(0.83)S(0.17)DDWEIPDGQITVGQR 235.73 2.21E-24 3083590000 1826410 1798734 1835460 2090750 1861173 1913410 2204350 2046570 2046560 TRUE FALSE 1740079.219 1982027.04 1919617.657 1880583.838 2185760.982 1847148.132 1868035.922 1867361.481 2363930.072 0.736095894 0.838445715 0.812045026 0.79553277 0.924630135 0.781388652 0.790224696 0.789939391 1 21.17275593 -2.572002316 2.1952614 4.46760662 0.807563565 0.60547483 0.048565096 1179919.932 124466.6046 20601120.77 0.012655427 0.002679154 2.572002316 -3.660043055 RDS(ph)SDTTPLLNGSSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.323)S(0.323)DT(0.323)T(0.029)PLLNGSSQDR;RDS(0.912)S(0.087)DT(0.001)TPLLNGSSQDR;RDS(0.737)S(0.118)DT(0.118)T(0.018)PLLNGS(0.006)S(0.003)QDR;RDS(0.747)S(0.02)DT(0.165)T(0.068)PLLNGSSQDR 280.32 6.88E-36 822220000 891185 824546 812306 1125492 859265 948313 1072512 946594 934356 TRUE FALSE 849060.4512 908568.1748 849551.0336 1012355.406 1009120.544 915472.683 908880.5964 863705.2111 1079251.156 0.78671257 0.841850546 0.787167128 0.938016512 0.935019192 0.848248045 0.842140025 0.800281942 1 20.04159921 RDS(ph)SES(ph)QLASTESDKPTTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 2 RDS(0.956)S(0.112)ES(0.93)QLAS(0.001)TESDKPTTGR;RDS(0.609)S(0.395)ES(0.922)QLAS(0.046)T(0.027)ESDKPTTGR 114.98 0.00057143 700510000 2213700 1940950 2170100 2338600 1643920 2311800 2507200 2425000 1757130 TRUE FALSE 2109062.788 2138735.012 2269601.232 2103519.485 1930619.128 2231741.786 2124680.592 2212654.144 2029616.746 1.039143371 1.05376299 1.118241282 1.036412164 0.951223491 1.099587787 1.046838324 1.090183232 1 20.9527759 -0.40081317 6.221286555 0.999999412 1.053280779 0.1231744 0.045543436 0 0 0.041207531 0.009712708 0.397362455 0.40081317 0.053281367 RDS(ph)SESQLASTESDKPTTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.824)S(0.175)ESQLASTESDKPTTGR;RDS(0.999)S(0.001)ESQLASTESDKPTTGR;RDS(0.698)S(0.302)ESQLASTESDKPTTGR;RDS(0.827)S(0.173)ESQLASTESDKPTTGR 285.95 1.93E-45 1183390000 1303630 1244350 1280490 1381790 901370 1381050 1539320 1373750 964230 TRUE FALSE 1242009.993 1371150.68 1339201.733 1242889.844 1058568.643 1333223.892 1304468.462 1253457.167 1113757.864 1.115152614 1.231103029 1.202417309 1.115942598 0.950447738 1.197050037 1.171231652 1.125430588 1 20.08700419 -5 0.218194567 0.279294398 1.1647143 0.239464047 0.077361825 228.3064324 2.282142869 72.44721999 0.152453112 1.00E-05 5 0.885419902 RDS(ph)SGGTKDGDRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSSGGTKDGDRPK 14 3 Q9Y478;F5H4Y8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 RDS(0.952)S(0.036)GGT(0.012)KDGDRPK 125.45 0.00050376 68449000 200430 84195 219720 176500 144420 227530 348580 259340 239900 TRUE FALSE 190956.0711 92774.56622 229794.3793 158757.8847 169606.8023 219650.579 295397.7189 236630.8148 277102.4668 0.689117182 0.334802383 0.829275834 0.572921225 0.61207251 0.792669158 1.066023418 0.85394698 1 18.08006003 2.066211204 2.918241411 0.97620827 0.584546223 0.609647447 0.132986737 0.160730621 2.702356841 0.059442311 0.037185401 116.46923 -2.066211204 -0.391662047 RDS(ph)SSHEETPGSHPLYGHGECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.295)S(0.295)S(0.295)HEET(0.084)PGS(0.032)HPLYGHGECK;RDS(0.308)S(0.308)S(0.308)HEET(0.059)PGS(0.016)HPLYGHGECK 94.031 0.00069135 184226000 193090 153599 161318 192425 156758 181802 223413 187178 33891 TRUE FALSE 183963.0184 169250.9127 168714.5899 173082.0734 184096.5456 175506.1512 189327.2436 170787.702 39146.64319 4.699330604 4.323510241 4.309809887 4.421377143 4.702741553 4.483300147 4.8363596 4.362767484 1 15.25660098 0.94510925 23.3499626 0.999999998 4.53855957 0.977233183 0.168933209 1482.621204 630692.5547 0.167673992 0.041918498 8.812705361 -0.94510925 3.538559571 RDSAS(ph)YR ddPTM_SK-BR-3_Trastuzumab_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(0.308)AS(0.675)Y(0.017)R 92.732 0.01637 118990000 305920 302350 300000 370550 312860 317040 356690 336500 366310 TRUE FALSE 291459.7679 333159.8087 313755.2967 333301.61 367422.6849 306060.8253 302270.3894 307034.2761 423115.4839 0.688842122 0.787396872 0.741535842 0.787732009 0.868374472 0.723350567 0.714392172 0.725651241 1 18.69069196 -1.549742041 2.768030856 1.01398015 0.753343036 0.698779346 0.050616015 11339492.08 11387803.33 1176027.427 0.0121733 0.028200575 1.549742041 -0.260637114 RDSASYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 111.95 0.010365 45427000 21276 16391 13632 14374 19289 16672 20102 20025 22091 FALSE TRUE 20270.32564 18061.26154 14257.04068 12929.09821 22652.99549 16094.64446 17035.0707 18271.50484 25516.75945 0.79439263 0.707819563 0.558732417 0.506690445 0.887769293 0.630747979 0.667603217 0.716058984 1 14.6391575 0.791053498 4.502927345 0.999997433 0.683841036 0.462547927 0.107759513 2.953191581 62.94836394 0.100718216 0.025568919 6.180925339 -0.791053498 -0.316156397 RDSFIGT(ph)PYWMAPEVVMCETMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(0.189)FIGT(0.809)PY(0.002)WMAPEVVMCETMK;RDS(0.334)FIGT(0.452)PY(0.214)WMAPEVVMCETMK 143.12 5.33E-08 134829000 135946 130380 116911 154848 90634 141976 141703 141258 90008 TRUE FALSE 129520.102 143665.8702 122271.485 139282.3848 106440.5409 137059.3355 120083.6048 128888.7007 103965.9809 1.245793103 1.381854612 1.176072056 1.339691922 1.023801631 1.318309454 1.155027863 1.23971995 1 16.66575201 -5 0.102977094 0.207802423 1.403696064 0.372545852 0.099911051 164.4873678 1.144881139 27.6993993 1.346285113 1.00E-05 5 1.195893641 RDSGDNSAPS(ph)GQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(0.268)GDNS(0.213)APS(0.519)GQER 76.759 0.028139 9573800 14509 17179 14175 17380 12370 15774 14567 13687 13875 TRUE FALSE 13823.18832 18929.55963 14824.93777 15632.92938 14527.32408 15227.74242 12344.53661 12488.49372 16026.66414 0.862511887 1.181129115 0.925017062 0.97543252 0.906447153 0.950150468 0.77024991 0.77923226 1 13.96818655 2.488611885 1.220652944 0.837875402 1.010037546 0.194607015 0.105245501 0.540104501 1.625369373 0.055160897 0.040205033 308.0433832 -2.488611885 0.172162145 RDSHLTLLNQLLQGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSHLTLLNQLLQGLR 16 1 E9PKV2;Q9NRX2 E9PKV2 MRPL17 "39S ribosomal protein L17, mitochondrial" 0 111.43 0.00053044 9631900 41374 30128 28426 26016 60165 24341 53420 38874 42982 FALSE TRUE 39418.33302 33198.07745 29729.36022 23400.82225 70657.75695 23498.06507 45269.79787 35469.98648 49647.42904 0.793965242 0.668676669 0.598809662 0.471340061 1.423190653 0.473298729 0.911825622 0.714437528 1 15.59943139 RDSIVAELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 138.89 8.44E-05 80059000 70250 72697 59091 63376 73165 60491 72795 65374 67735 FALSE TRUE 66929.42172 80104.90695 61800.3808 57005.32407 85924.95284 58396.1815 61688.78578 59649.50599 78238.99786 0.855448351 1.023848837 0.789892285 0.728604988 1.098236879 0.746382023 0.78846595 0.762401202 1 16.25560027 3.724392192 24.8815662 0.833058837 0.939648601 0.085193969 0.124559656 1386.474204 2434826.263 0.031028203 0.048317821 5301.419752 -3.724392192 0.106589764 RDSQDGS(ph)SYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RDS(0.203)QDGS(0.399)S(0.399)YR 122.46 0.00051691 104550000 174510 220120 159300 233960 150160 198510 197930 193860 148080 TRUE FALSE 166261.2581 242550.4783 166604.0626 210441.8963 176347.8565 191635.5489 167732.1433 176884.5907 171043.4901 0.972040842 1.418063196 0.974045036 1.230341454 1.031011799 1.120390778 0.980640322 1.034149798 1 17.38400367 2.345617991 0.995949089 1.002931809 1.17011637 0.143226242 0.131625184 0.848139932 1.642174271 0.08433806 0.052420213 221.6246134 -2.345617991 0.16718456 RDSS(ph)DDWEIPDGQITVGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.285)S(0.715)DDWEIPDGQITVGQR 199.1 4.35E-16 261000000 208030 175380 196990 195420 183810 204310 223010 189660 202960 TRUE FALSE 198196.8342 193251.4214 206022.1863 175776.0103 215866.4058 197234.6935 188985.7286 173052.3649 234434.0002 0.845427003 0.824331885 0.878806769 0.749788896 0.920798202 0.841322902 0.806136177 0.738170934 1 17.8388223 -1.235648637 3.602983357 1.000302105 0.827914351 0.506046745 0.054107425 1842008527 3565465684 6537034.16 0.011809366 0.058123447 1.235648637 -0.172387754 RDSS(ph)ESQLASTESDKPTTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.044)S(0.956)ESQLASTESDKPTTGR;RDS(0.397)S(0.594)ES(0.009)QLASTESDKPTTGR 299.3 4.83E-55 782330000 669940 571080 620020 701160 456390 667960 725290 666060 494600 TRUE FALSE 638273.2639 629273.7013 648448.5303 630678.0647 535984.2715 644828.3777 614633.6896 607736.2554 571300.0419 1.117229506 1.101476729 1.135040229 1.103934918 0.938183498 1.128703536 1.075850944 1.063777719 1 19.12388911 2.973123094 24.99809527 1.05221741 1.11494401 0.332811952 0.050401888 953.5263511 886871.9049 0.014516768 0.015441172 939.9896984 -2.973123094 0.0627266 RDSS(ph)SHEETPGSHPLYGHGECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.252)S(0.374)S(0.374)HEETPGSHPLYGHGECK 175.39 5.80E-13 113920000 200770 143030 166670 202170 160320 190110 216520 182760 26613 TRUE FALSE 191280 157604.9196 174311.9844 181847.4875 188279.7572 183526.443 183485.8973 166756.5655 30740.00812 6.222509742 5.127029212 5.670524994 5.915661661 6.124909158 5.970279589 5.968960601 5.424740452 1 14.90782993 0.715757384 3.65366117 1.000031484 5.823277008 0.962169786 0.300421482 0.758488832 9.569234698 0.299675005 0.077021894 5.197055849 -0.715757384 4.823245523 RDSSDT(ph)TPLLNGSSQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.079)S(0.176)DT(0.709)T(0.034)PLLNGS(0.002)S(0.001)QDR 158.74 6.38E-09 135670000 141940 147170 128020 185670 148440 164150 173450 171580 165510 TRUE FALSE 135230.7775 162166.7903 133889.8436 167006.0989 174327.889 158465.4443 146987.0169 156555.5456 191176.4455 0.707361083 0.848257168 0.700346966 0.873570478 0.911869078 0.828896279 0.768855266 0.818906038 1 17.54454526 -5 0.175077705 1.750215875 0.76240253 0.480568862 0.065144802 123.7304566 1.17990122 32.49732751 0.216326222 1.00E-05 5 -0.987813345 RDTDS(ph)DTQDANDSSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 RDT(0.005)DS(0.985)DT(0.01)QDANDSSCK;RDT(0.015)DS(0.972)DT(0.012)QDANDSSCK 126.02 0.00024764 130780000 304440 281400 283090 333060 205102 298450 373680 357080 246750 TRUE FALSE 290049.7245 310074.9799 296069.9565 299580.176 240871.7239 288114.6017 316668.2529 325812.1822 285014.7298 1.017665735 1.087926158 1.038788265 1.051104188 0.845120265 1.010876181 1.111059253 1.143141558 1 18.12067696 -1.056443619 5.043365177 0.9999993 1.040142497 0.021597662 0.079887878 6.30E-07 1.18E-07 0.077565723 0.018282098 0.087812508 1.056443619 0.040143196 RDTDSDTQDANDSSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 ; 213.99 7.79E-13 266380000 250267 210952 210680 248212 182370 248422 265417 253937 215802 FALSE TRUE 238437.3749 232448.2486 220339.8864 223261.2582 214175.2703 239819.0838 224922.7619 231700.9301 249267.472 0.956552305 0.932525398 0.883949617 0.895669445 0.859218688 0.962095383 0.90233499 0.92952734 1 17.92733511 0.958408012 17.47987641 1.000000001 0.916325351 0.423809683 0.0314595 128.317729 53929.58258 0.03047775 0.007619437 9.086738115 -0.958408012 -0.08367465 RDTQKS(ph)YSQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDTQKSYSQQK 11 2 A0A1B0GVN3 A0A1B0GVN3 1 RDT(0.046)QKS(0.345)Y(0.265)S(0.345)QQK 52.391 0.075472 354940000 920580 864270 725030 785170 319640 826910 644690 681470 226660 TRUE FALSE 877066.0078 952340.0956 758273.3427 706243.2199 375385.1148 798273.8994 546330.7 621796.8741 261809.2752 3.350018853 3.63753383 2.896281433 2.697548509 1.433811367 3.049066534 2.086750745 2.37499941 1 17.99815668 6.169466796 0.095565525 2.67E-12 8.282059071 0.643753711 0.490863175 53.08273533 0.543589661 8.362562062 58.6353343 1477293.53 -6.169466796 8.282059071 RDVEQLEQLIESHDVVFLLMDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDVEQLEQLIESHDVVFLLMDTR 23 1 O95352-3;O95352-2;O95352 O95352-3 ATG7 Ubiquitin-like modifier-activating enzyme ATG7 0 120.52 5.28E-05 38079000 31992 25881 23702 30435 26753 24255 39494 28327 23193 FALSE TRUE 30479.80156 28518.30332 24788.76014 27375.61598 31418.71473 23415.04327 33468.46494 25846.53771 26789.65199 1.137745335 1.064526831 0.925311018 1.021872774 1.172792941 0.874033126 1.249305701 0.964795576 1 14.70938822 RDVQEIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 213.53 2.27E-05 1122230000 604341 408895 378214 432141 877793 402342 637699 514592 890633 FALSE TRUE 575774.9986 450561.8654 395555.486 388701.3657 1030879.821 388408.7957 540406.3054 469531.5965 1028747.817 0.559685269 0.437971151 0.384501896 0.37783931 1.002072427 0.377554916 0.525304935 0.456410783 1 19.97245794 -2.038555765 2.610610383 1.615003997 0.512258733 0.407654376 0.183639164 15990905.69 8018315.062 58688318.14 0.040708284 0.009150488 2.038555765 -1.102745264 RDVTQLDPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RDVTQLDPNK 10 1 Q9UNN5;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 110.08 0.0031009 197500000 663310 518700 544050 621980 469570 596370 693410 663090 489040 FALSE TRUE 631956.6509 571556.1197 568995.2306 559457.3887 551462.8593 575717.5574 587617.5692 605026.3243 564877.8255 1.118749263 1.011822546 1.007289019 0.990404232 0.976251562 1.019189516 1.040256039 1.071074659 1 19.10757934 4.547297174 2.339478171 1.014927583 1.124813726 0.60394242 0.026412514 0.274351397 2.408952648 0.007067064 0.052110974 35261.20695 -4.547297174 0.109886143 RDVYLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 RDVY(0.002)LS(0.998)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR 126.12 0.00075513 856376000 1225670 1059200 986003 1069370 1185400 996990 1261080 1117310 1266790 TRUE FALSE 1167735.008 1167133.684 1031212.213 961874.8959 1392133.385 962463.9863 1068679.085 1019472.413 1463237.323 0.798048949 0.797637995 0.704747068 0.657360826 0.951406421 0.65776342 0.730352532 0.696723899 1 20.48073235 -1.673928464 7.387756869 1.000964469 0.752699333 0.452172115 0.086663388 0.001281252 5.66E-05 0.078094075 0.018340379 0.021187101 1.673928464 -0.248265136 RDYDDMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDY(0.002)DDMS(0.998)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR 145.08 4.51E-05 18969120000 11557700 9875170 9835480 12558000 12166600 10941630 13194780 11167610 12383990 TRUE FALSE 11011390.43 10881461.05 10286446.49 11295645.98 14288451.19 10562718.61 11181673.97 10189714.87 14304435.92 0.769788511 0.760705358 0.719108852 0.789660357 0.998882533 0.738422589 0.781692758 0.7123465 1 23.76995927 -2.234476386 2.402461024 1.79246269 0.783417583 0.415718353 0.080539813 3230007.102 892534.9683 13889691.44 0.019271429 0.005828055 2.234476386 -1.009045107 RDYDDMSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;; 149.33 0.00014091 2320962000 1077261 925017 960054 1000936 1002746 1009432 1274189 1040944 985286 FALSE TRUE 1026341.007 1019277.284 1004073.426 900320.0116 1177624.585 974475.1167 1079788.066 949793.425 1138079.121 0.901818677 0.895611971 0.882252743 0.791087364 1.034747553 0.856245492 0.948781193 0.834558343 1 20.11816943 2.755318997 24.99364498 0.926628846 0.876946584 0.191872557 0.066132433 1675.195195 2498403.658 0.018223332 0.019280785 569.2709175 -2.755318997 -0.049682261 RDYEVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 126.31 0.0019634 244340000 505870 401480 434200 481590 563290 414990 515120 436420 524150 FALSE TRUE 481958.5276 442391.2684 454108.4995 433179.6582 661527.5977 400618.7922 436528.9832 398204.7512 605432.505 0.796056577 0.730702869 0.750056358 0.715487944 1.092652925 0.661706778 0.721020063 0.657719478 1 19.20760661 -2.297731717 2.293620137 2.135951785 0.76427051 0.263611117 0.123061405 4463651.702 717707.5897 26331375.17 0.029138602 0.005038117 2.297731717 -1.371681275 RDYYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RDYYDR 6 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;; 116.88 0.037191 635590000 711260 669210 773050 753440 657830 732350 769810 720260 764000 FALSE TRUE 677640.1494 737403.2598 808495.1072 677702.7798 772555.3437 706988.5359 652361.346 657190.2161 882477.218 0.767884015 0.835606002 0.916165416 0.767954986 0.87543942 0.801140836 0.739238739 0.744710688 1 19.75119951 2.019591481 24.11450629 0.791804674 0.828851514 0 0.085369466 562.8337476 692769.1875 0.028913428 0.021350606 104.614403 -2.019591481 0.03704684 REALEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 98.997 0.063014 425760000 733330 456500 452570 680000 571070 560020 913290 644110 727170 FALSE TRUE 698666.9442 503017.869 473320.7822 611645.1081 670664.4272 540626.367 773950.8368 587708.3138 839935.8097 0.831809927 0.598876561 0.563520184 0.728204585 0.798471049 0.643652004 0.921440457 0.699706224 1 19.67991955 0.893533873 0.503073257 1.001341481 0.678795874 0.42211334 0.105310461 1.068757987 0.64882484 0.12418586 0.05576111 7.825892414 -0.893533873 -0.322545607 RECPSDECGAGVFMASHFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RECPSDECGAGVFMASHFDR 20 1 P62979 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 171.47 5.05E-12 760140000 353770 272904 316852 344000 329310 317042 409290 384690 355030 FALSE TRUE 337047.9932 300713.2279 331379.9776 309420.4664 386741.5597 306062.756 346845.2934 351004.5042 410086.2392 0.821895399 0.733292657 0.808073878 0.754525358 0.943073731 0.746337543 0.845786228 0.855928511 1 18.64556781 -1.900357255 0.215412075 1.223463688 0.764611563 0.532283938 0.058135099 21.81010061 0.724215929 2.575686508 0.119254372 0.012578902 1.900357255 -0.458852126 REDEGEPGDEGQLEDEGS(ph)QEKQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REDEGEPGDEGQLEDEGSQEKQGR 24 2 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEKQGR;REDEGEPGDEGQLEDEGS(1)QEKQGR 229.95 1.24E-33 708130000 724490 575250 671440 736670 410600 696890 776170 736470 468650 TRUE FALSE 690244.7935 633868.629 702226.1881 662618.532 482208.51 672756.5246 657751.0112 671980.7825 541325.8485 1.275100377 1.170955776 1.297233801 1.224065937 0.890791584 1.242794015 1.215074087 1.241360974 1 19.04613775 -4.619474805 0.266178853 3.68E-36 1.210637148 0.219411965 0.113815271 265.7995425 3.138160896 145.9264374 0.1395341 2.40E-05 4.619474805 1.210637148 REDIVDTMVFKPSDVMLVHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REDIVDTMVFKPSDVMLVHFR 21 2 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 ; 191.4 8.74E-18 141411000 271890 237930 239360 266880 225420 251070 310110 291030 220120 FALSE TRUE 259038.2985 262175.3375 250334.8928 240052.7154 264733.1766 242375.3829 262797.0239 265545.8704 254255.0854 1.018812655 1.031150811 0.984581655 0.944141255 1.041210941 0.953276441 1.03359594 1.044407312 1 17.9559171 1.604850729 25 1.029254531 1.000264003 0.148651281 0.032800191 0.583689347 4794.217259 0.016220436 0.008011376 40.25786408 -1.604850729 -0.028990528 REDLVEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 REDLVEEIK 9 1 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ;; 187.16 6.55E-05 545070000 849280 764550 757202 844230 564242 859692 885070 912200 616083 FALSE TRUE 809136.2175 842458.5142 791920.4607 759366.3965 662645.6262 829920.6505 750036.3161 832322.9321 711622.0051 1.137030912 1.18385675 1.112838635 1.067092348 0.931176413 1.166238037 1.053981342 1.16961382 1 19.4407516 3.462559259 3.618538453 1.067711296 1.159870747 0.240427535 0.070460086 0.298008414 8.40955435 0.018498239 0.027238642 2901.07702 -3.462559259 0.092159451 REDLVEEIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REDLVEEIKR 10 2 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 80.014 0.014217 612690000 1218600 1114200 1083800 1228200 1203700 1154700 1376300 1240900 1135100 FALSE TRUE 1160999.193 1227738.247 1133493.302 1104739.003 1413624.899 1114712.449 1166320.158 1132240.218 1311125.511 0.885498134 0.936400243 0.864519295 0.84258829 1.078176641 0.850195073 0.889556452 0.863563563 1 20.32237437 4.752165738 21.163698 0.909668071 0.885498087 0.010375517 0.074442262 106.0866924 1035449.33 0.016128019 0.104336164 56515.26102 -4.752165738 -0.024169984 REDS(ph)MEDRGEEDDSLAIKPPQQMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(0.999)MEDRGEEDDS(0.001)LAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR 205.44 2.34E-24 1196190000 591869 550317 531168 646117 431650 603540 673460 628854 481484 TRUE FALSE 563892.5253 606394.928 555522.5782 581168.0916 506929.6233 582639.2585 570711.3081 573788.21 556150.0796 1.013921504 1.090344046 0.998871705 1.044984282 0.911497889 1.047629551 1.026182192 1.031714695 1 19.08511473 3.712324007 24.95991929 1.010616265 1.052132787 0.151962831 0.042470751 1218.114925 1158840.459 0.010689092 0.016565083 5156.131765 -3.712324007 0.041516522 REDS(ph)PGPEVQPMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 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;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK 242.22 1.10E-17 18621499000 24155098 20922684 20666295 24455218 17383244 23427027 24814440 24678505 18935454 TRUE FALSE 23013334.39 23054729.29 21613865.07 21996933.02 20414876.25 22615743.18 21028541.43 22517524.27 21871867.5 1.052188817 1.054081426 0.988203914 1.0057181 0.933385147 1.034010616 0.96144243 1.029519966 1 24.38257307 3.7392721 24.43427333 0.990406374 1.053135126 0.413471711 0.029542177 34.50081621 1184826.175 0.006768744 0.011336734 5486.205861 -3.7392721 0.062728752 REDS(ph)PGPEVQPMDKQFLVCSICLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REDSPGPEVQPMDKQFLVCSICLDR 25 2 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5 O75382 TRIM3 Tripartite motif-containing protein 3 1 REDS(1)PGPEVQPMDKQFLVCSICLDR;REDS(1)PGPEVQPMDKQFLVCSICLDR 228.72 2.15E-34 244910000 169406 36441 244880 97198 304110 149600 455320 213590 590820 TRUE FALSE 161398.5141 40154.37933 256107.9902 87427.47238 357146.6877 144419.3145 385852.5715 194886.9273 682441.3481 0.236501664 0.058839312 0.375282053 0.12810987 0.523336824 0.211621577 0.565400342 0.285573153 1 19.38034553 -5 0.135589972 3.501130165 0.005975201 0.712992701 0.145477646 63.82954209 0.537261765 42.89909682 0.839321548 1.00E-05 5 -3.495154964 REEAAVDAQQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 113.99 0.001774 170620000 287370 291600 286490 346220 235700 268930 343790 336850 298440 FALSE TRUE 273786.5896 321314.3715 299625.8499 311417.3078 276806.0054 259616.8867 291338.5214 307353.6282 344720.551 0.79422764 0.932101004 0.869184761 0.903390607 0.802986664 0.753122742 0.845144046 0.891602277 1 18.39506778 0.893601894 3.238122555 0.999834913 0.845964404 0.476930536 0.052090057 0.416616781 9.325542785 0.051587617 0.013421692 7.827118224 -0.893601894 -0.153870509 REEAAVDAQQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REEAAVDAQQQKR 13 2 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 0 103.85 0.00088743 58327000 50589 26522 50637 48404 71721 42524 73700 52791 91260 FALSE TRUE 48197.75823 29224.62195 52958.75654 43538.33796 84229.11969 41051.38322 62455.71141 48168.34018 105412.1347 0.457231593 0.277241534 0.502397155 0.413029658 0.799045764 0.389436978 0.592490718 0.456952516 1 16.68568143 -5 0.157321299 2.929150944 0.326611151 0.594846699 0.134920174 84.74897271 0.772931074 51.02712676 0.549963685 1.00E-05 5 -2.602539793 REEALGLYQWIYHTHEDAQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REEALGLYQWIYHTHEDAQEAR 22 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 115.5 7.87E-05 25619000 19598 22089 23295 26936 29363 26271 23863 26762 13065 FALSE TRUE 18671.64138 24339.89421 24363.09879 24228.3421 34483.8979 25361.22868 20222.26108 24418.57741 15091.05347 1.237265603 1.612869125 1.614406763 1.605477189 2.28505571 1.680547268 1.340016528 1.618083022 1 13.8814059 0.496367601 1.048421155 1.002195617 1.623388841 0.340208073 0.273096881 2.328808252 3.545810404 0.273692648 0.085458612 3.13593896 -0.496367601 0.621193224 REEDEENDNDNES(ph)DHDEADS ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 REEDEENDNDNESDHDEADS 20 1 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS 356.24 1.50E-95 2453980000 1669510 1589947 1590230 1776160 1485382 1571845 1745339 1651416 1475995 TRUE FALSE 1590595.571 1751964.407 1663143.618 1597617.022 1744432.151 1517411.614 1479055.48 1506809.26 1704884.766 0.932963683 1.027614559 0.975516734 0.937082115 1.023196515 0.89003764 0.867539853 0.883818831 1 20.7012428 2.221552515 24.97796744 0.8955755 0.979567759 0.325520789 0.047216653 213.0223832 312840.978 0.01609736 0.011919172 166.5530211 -2.221552515 0.083992259 REEDEPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 REEDEPEER 9 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 220.82 7.09E-07 679730000 577312 462711 467968 578321 553196 511361 574856 548450 554719 FALSE TRUE 550023.6059 509861.777 489424.7957 520187.0743 649673.2073 493652.4403 487151.1592 500424.8105 640741.9894 0.858416672 0.795736483 0.763840678 0.811851077 1.013938868 0.770438723 0.760292235 0.781008298 1 19.28938401 -1.081389093 4.272865875 1.000018763 0.817128644 0.364368995 0.074891815 9998218.038 2530377.878 2021.143308 0.017276545 0.082910762 1.081389093 -0.182890119 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.933)GDET(0.035)PGS(0.032)EVPGDK;REEDEPEERS(1)GDETPGSEVPGDK;REEDEPEERS(0.997)GDET(0.003)PGSEVPGDK;REEDEPEERS(0.959)GDET(0.041)PGSEVPGDK;REEDEPEERS(0.926)GDET(0.074)PGSEVPGDK;REEDEPEERS(1)GDETPGSEVPGDK 277.75 6.51E-52 5030060000 3551870 3102510 2953820 3661730 2127548 3452880 3477350 3626070 2300204 TRUE FALSE 3383980.144 3418659.296 3089255.569 3293645.944 2498591.698 3333305.9 2946816.392 3308552.088 2656907.889 1.273653542 1.28670599 1.162725882 1.239653794 0.940413369 1.254580904 1.109115 1.245264129 1 21.34131678 8 0.111269799 0.976361293 1.95545316 0.295767627 0.099831725 118.0313362 0.914716169 0.790963648 17.77176881 100000000 -8 0.979091867 REEDEPEERS(ph)GDETPGSEVPGDKAAEEQGDDQDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REEDEPEERSGDETPGSEVPGDKAAEEQGDDQDSEK 36 3 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.999)GDET(0.001)PGSEVPGDKAAEEQGDDQDSEK 181.26 3.35E-22 214290000 185860 83405 176920 149140 102200 173170 248640 203400 125490 TRUE FALSE 177074.7661 91904.06432 185031.957 134148.1639 120023.6476 167173.0795 210705.4014 185589.2177 144950.3483 1.221623599 0.634038244 1.276519575 0.925476658 0.828032834 1.153312713 1.453638462 1.280364069 1 17.14519927 2.017512837 7.238450743 1.29758183 0.965290263 0.242753396 0.212390808 0.162759768 40.32659658 0.076007473 0.054479576 104.1148881 -2.017512837 -0.332291567 REEEEFNTGPLSVLTQSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REEEEFNTGPLSVLTQSVK 19 1 P62316;P62316-2;K7ERG4 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 ; 220.28 4.71E-19 200749000 426280 329420 331770 403760 358930 381090 484640 403540 404420 FALSE TRUE 406130.5892 362988.2725 346981.9827 363173.2777 421527.2784 367892.7577 410699.267 368203.8983 467135.3881 0.869406599 0.77705154 0.742786763 0.777447581 0.9023664 0.787550605 0.8791868 0.788216666 1 18.83348122 -2.70311218 0.29990405 1.317751958 0.803780907 0.551607104 0.052110244 42.47714478 1.362269665 8.715391864 0.051310885 0.001981015 2.70311218 -0.513971051 REEEEREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REEEEREK 8 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ; 52.579 0.079879 42196000 65208 49374 53791 58149 56925 56431.5 70679 67238 61939 FALSE TRUE 62125.74707 54405.26673 56257.37056 52303.75204 66852.70198 54477.26301 59895.62044 61350.28427 71544.18378 0.868354963 0.760442902 0.786330455 0.73106924 0.934425392 0.761449221 0.837183643 0.857516028 1 16.12654687 0.375888305 0.724234776 1.003853584 0.803311003 0.511274626 0.058406752 1.671438125 1.274052639 0.064710918 0.01917545 2.376229075 -0.375888305 -0.200542581 REEGDPS(ph)PHSGGVCKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REEGDPSPHSGGVCKPK 17 2 O75376;O75376-2;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 REEGDPS(1)PHSGGVCKPK 85.808 0.0025803 40497000 70505 56948 59311 74977 45007 72833 84607 76682 45036 TRUE FALSE 67172.36838 62751.06594 62030.46802 67440.16951 52856.20655 70310.77495 71698.64824 69967.31756 52019.95287 1.291280839 1.206288404 1.192436067 1.296428885 1.016075633 1.351611662 1.378291296 1.345009246 1 15.66677747 REEQT(ph)DT(ph)S(ph)DGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 3 REEQT(1)DT(1)S(1)DGESVTHHIR 68.445 0.010936 153660000 81312 64811 71204 91992 78017 78078 94358 87960 96541 TRUE FALSE 77468.5429 71415.31458 74468.77383 82744.78939 91623.1401 75374.13928 79961.9541 80257.75609 111512.0852 0.69470984 0.640426681 0.667808997 0.742025308 0.821643142 0.675927987 0.717069849 0.719722494 1 16.76684055 -5 0.239399848 2.680091117 0.674348722 0.785767674 0.047914586 78.66642962 0.784513964 64.32370709 0.077533453 1.00E-05 5 -2.005742395 REEQT(ph)DT(ph)SDGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.555)S(0.445)DGESVTHHIR;REEQT(1)DT(0.778)S(0.222)DGESVTHHIR 171.29 6.02E-12 1981270000 378550 336110 370090 389660 457580 331950 440480 399230 283250 TRUE FALSE 360656.6917 370359.9911 387058.9926 350490.6365 537381.8071 320454.4883 373276.686 364271.3047 327174.9634 1.102335851 1.131993681 1.183033655 1.071263623 1.642490616 0.979459079 1.140908467 1.113383802 1 18.31970283 REEQT(ph)DTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.302)S(0.698)DGESVTHHIR;REEQT(1)DT(0.202)S(0.798)DGESVTHHIR 189.09 3.73E-14 1817940000 758820 547950 613760 708600 849340 620050 824620 820090 549220 TRUE FALSE 722952.0824 603786.728 641901.5031 637370.1817 997464.6271 598577.513 698809.0738 748278.572 634390.2326 1.139601534 0.951759181 1.011840142 1.004697344 1.572320278 0.943547807 1.101544504 1.179524106 1 19.27501103 5.153355154 10.31200329 1.092432419 2.939110211 0.005369082 0.183379463 944890.3431 979599.1048 0.04089005 39750553.42 142349.2402 -5.153355154 1.846677792 REEQTDT(ph)SDGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.142)DT(0.551)S(0.307)DGESVTHHIR;REEQT(0.088)DT(0.456)S(0.456)DGESVTHHIR;REEQT(0.073)DT(0.54)S(0.386)DGESVTHHIR 226.51 2.65E-19 2273620000 585072 514548 493862 658350 614891 597355 644383 618547 277336 TRUE FALSE 557416.8061 566981.0262 516506.0612 592171.4072 722127.7957 576668.4466 546070.5384 564383.7456 320343.8504 1.74005777 1.769913877 1.61234892 1.848549321 2.254227121 1.800154571 1.704638743 1.761806087 1 18.28926177 0.251498637 1.136853344 0.998124777 1.817677323 0.700187003 0.167598099 2.574028583 3.367334601 0.172601942 0.050105484 1.78442639 -0.251498637 0.819552545 REEQTDTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQTDT(0.183)S(0.817)DGESVTHHIR;REEQT(0.004)DT(0.247)S(0.749)DGESVTHHIR;REEQTDT(0.02)S(0.98)DGESVTHHIR;REEQT(0.024)DT(0.364)S(0.612)DGESVTHHIR;REEQT(0.001)DT(0.144)S(0.854)DGESVTHHIR 207.17 3.63E-16 3919020000 1114648 898596 1005998 1200749 1178459 1044460 1323647 1124010 420718 TRUE FALSE 1061960.798 990163.954 1052124.003 1080047.429 1383981.876 1008290.088 1121700.34 1025585.726 485960.7987 2.18528079 2.037538741 2.165038839 2.222499082 2.847929051 2.074838322 2.308211573 2.110428924 1 18.89048041 0.755852397 3.755580804 1.000009844 2.243611377 0.755556303 0.223770087 1.397977007 21.0107404 0.21039501 0.053975645 5.699705248 -0.755852397 1.243601532 REERPENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REERPENK 8 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 49.097 0.09227 11784000 23806 22104 24420 31742 21629 23700 28915 26839 28296 FALSE TRUE 22680.73756 24356.42273 25539.68115 28551.23385 25401.09075 22879.26306 24503.48569 24488.83488 32683.99916 0.693940097 0.745209379 0.781412367 0.873553867 0.777172054 0.700014186 0.749708919 0.749260663 1 14.9962969 -1.101291897 4.108685744 1.000047278 0.755298744 0.69989311 0.049593237 10529617696 19642725783 6967395.985 0.012590733 0.079196886 1.101291897 -0.244748534 REES(ph)KPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REESKPR 7 2 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 REES(1)KPR;REES(1)KPR 67.207 0.051812 550420000 692320 537600 524320 752970 452240 614510 717780 610200 496700 TRUE FALSE 659595.4056 592382.0512 548360.5906 677280.0251 531110.5128 593229.3646 608269.4781 556767.6531 573725.6992 1.149670316 1.032517895 0.955788788 1.180494487 0.925722019 1.033994756 1.060209572 0.970442241 1 19.13000162 4.48079872 2.39282005 1.024424729 1.151397789 0.252483734 0.069744328 0.447662029 4.420114301 0.015884511 0.093280334 30255.10886 -4.48079872 0.12697306 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.963)PS(0.037)AQDTQSIASDGTPQGEK 247.53 1.52E-46 244610000 386370 392250 355600 431750 271180 418800 407460 426160 300280 TRUE FALSE 368107.0558 432220.721 371904.6117 388349.6697 318473.7061 404296.851 345294.4935 388843.1712 346845.8888 1.061298599 1.2461463 1.072247427 1.119660582 0.918199455 1.165638297 0.995527134 1.121083408 1 18.40393526 3.313658165 2.374370847 1.047647523 1.151674796 0.176807377 0.08461588 0.396473055 4.559724148 0.022921262 0.03243317 2059.008622 -3.313658165 0.104027273 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REESPMDVDQPSPSAQDTQSIASDGTPQGEKEK 33 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.957)PS(0.043)AQDTQSIASDGTPQGEKEK;REES(0.004)PMDVDQPS(0.924)PS(0.07)AQDT(0.002)QS(0.001)IASDGTPQGEKEK 120.47 1.24E-07 235920000 94940 82021 88747 93041 58723 118792 102828 110336 63347 TRUE FALSE 90452.37435 90379.03315 92816.13773 83688.34191 68964.27261 114678.2033 87139.70003 100674.3949 73170.52923 1.23618587 1.235183538 1.268490726 1.143743838 0.942514334 1.567273115 1.190912529 1.375887205 1 16.15897507 2.247229637 24.99997718 1.297366908 1.184932431 0.101470982 0.167123261 432.938808 1248523.073 0.053160194 0.043826994 176.6971876 -2.247229637 -0.112434476 REFQLDLDEIENDNGTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REFQLDLDEIENDNGTVR 18 1 Q14008;Q14008-3;Q14008-2;H0YEK7;H0YCF6 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 129.46 3.39E-05 67296000 76831 55120 69235 72602 78271 71606 86383 76248 90345 FALSE TRUE 73199.35089 60736.79067 72409.49323 65303.90903 91921.43762 69126.26627 73203.68682 69571.3209 104355.2412 0.701443934 0.582019551 0.693875002 0.625784659 0.880851183 0.66241298 0.701485484 0.666677784 1 16.67114354 -5 0.252530836 2.93909778 0.656138382 0.608395951 0.077932987 120.3727088 1.190402324 120.695464 0.103331363 1.00E-05 5 -2.282959397 REGDVAACYANPSLAQEELGWTAALGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 REGDVAACYANPSLAQEELGWTAALGLDR 29 1 Q14376;Q14376-2;Q5QPP4;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ;; 221.5 2.94E-34 114040000 71177 62483 66987 74242 70971.5 67296 84158 75134 77370 FALSE TRUE 67812.60427 68850.08874 70058.42021 66779.05311 83348.90713 64965.52265 71318.15143 68554.86865 89368.14445 0.75880063 0.770409738 0.783930568 0.747235534 0.932646724 0.726942727 0.798026544 0.767106323 1 16.44747305 -1.940959345 2.281453041 1.158202047 0.784261664 0.593216078 0.055775891 6697965.521 2992270.998 5630946.203 0.012770053 0.011456202 1.940959345 -0.373940383 REGGDGEEQDVGDAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 REGGDGEEQDVGDAGR 16 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;; 156.67 2.25E-07 1730090000 1138070 960230 1118930 1159040 1128750 1048590 1294920 1162480 1191350 FALSE TRUE 1084275.687 1058078.529 1170234.047 1042531.097 1325603.643 1012277.065 1097356.171 1060687.089 1376098.473 0.787934663 0.768897393 0.850399931 0.757599196 0.963305801 0.735613828 0.797440149 0.770793013 1 20.39215228 -1.635683068 2.899265701 1.017429214 0.801301096 0.479161374 0.064165763 18891704.77 19314623.19 2482681.827 0.014348545 0.023137527 1.635683068 -0.216128118 REGS(ph)YDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 REGSYDR 7 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(0.995)Y(0.005)DR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR 113.93 0.0036873 1738052600 809098 710727 748707 863346 844459 792948 931718 875707 977392 TRUE FALSE 770853.541 783150.8893 783035.9565 776560.8198 991732.3822 765488.0119 789567.3069 799025.4527 1128960.96 0.682799112 0.693691737 0.693589933 0.68785445 0.878447013 0.678046486 0.699375209 0.707752953 1 20.10656417 -2.29210036 2.139681744 2.214061373 0.712131748 0.698170328 0.058819971 2549986.765 339700.2919 14978900.45 0.013608103 0.00510387 2.29210036 -1.501929626 REGT(ph)PPPPPPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REGTPPPPPPSR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 REGT(1)PPPPPPSR;REGT(1)PPPPPPSR 54.281 0.079455 710220000 384570 358350 333540 431350 395540 343080 458780 382420 437790 TRUE FALSE 366392.1382 394866.2724 348833.1389 387989.8785 464522.0508 331199.0536 388784.6849 348933.2775 505680.2373 0.72455301 0.780861587 0.689829487 0.767263282 0.918608276 0.654957479 0.768835039 0.690027515 1 18.94786587 -1.047778777 4.492616748 1.000012126 0.75157563 0.54296481 0.072240038 8.57E-06 1.82E-06 0.063216336 0.014899448 0.089582097 1.047778777 -0.248436496 REPAEQPGDGER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 137.81 0.00013732 589572000 627810 502052 542230 667630 584760 588080 650680 582270 585910 FALSE TRUE 598134.6655 553211.6696 567091.7818 600518.564 686741.9589 567714.6421 551406.8154 531283.352 676769.9304 0.883807981 0.817429446 0.837938798 0.887330446 1.014734739 0.838859141 0.814762581 0.78502801 1 19.36830594 -2.273014306 2.386147331 1.635695351 0.858188248 0.327707553 0.062977587 20062548.61 876727.9924 69887481.03 0.015634852 0.005333173 2.273014306 -0.777507104 REPAPNAPGDIAAAFPAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REPAPNAPGDIAAAFPAER 19 1 O95359-3;E9PBC6;E7EMZ9;O95359;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 82.593 0.0067926 171060000 163730 129950 133390 143420 133920 165020 164360 169310 167670 FALSE TRUE 155990.8074 143192.0527 139506.0634 129003.1491 157275.6056 159305.316 139283.8633 154484.3188 193671.4073 0.805440563 0.739355668 0.720323487 0.666092899 0.812074471 0.822554647 0.719176182 0.797661983 1 17.56325145 -0.747690913 0.569314336 1.048003858 0.752148872 0.707537442 0.048921529 8.757772292 1.947179437 0.823760505 0.020408591 0.178775947 0.747690913 -0.295854987 REPLPSR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 128.12 0.0060745 1318163000 1193107 1285458 897886 1235598 1081575 993191 1114056 1063830 999319 FALSE TRUE 1136711.197 1416447.632 939054.9612 1111393.342 1270201.338 958796.5466 944086.2962 970675.4055 1154288.287 0.984772357 1.227117738 0.813535901 0.96283862 1.100419498 0.830638721 0.817894721 0.840929789 1 20.13857216 3.097398826 0.763621018 0.865352162 1.09021429 0.160472636 0.124221067 0.8541019 1.111173415 0.071425628 0.105105836 1251.40771 -3.097398826 0.224862128 REPWLLPSQHNDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 REPWLLPSQHNDIIR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 227.89 4.35E-13 1653170000 859520 663240 724960 823320 1059090 731890 1011220 912500 1038100 FALSE TRUE 818892.193 730824.91 758200.1331 740558.3094 1243794.961 706544.4658 856939.8167 832596.6625 1199083.246 0.682931895 0.609486383 0.63231651 0.61760375 1.037288249 0.589237209 0.714662489 0.694361017 1 20.19350039 -5 0.197494379 2.373211885 0.638778534 0.366084843 0.126600444 148.152797 1.461828704 80.31681347 0.292859775 1.00E-05 5 -1.734433351 REPYGHLGPAELLEAS(ph)PAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REPYGHLGPAELLEASPAAR 20 1 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 REPYGHLGPAELLEAS(1)PAAR 120.11 1.93E-05 26087000 20516 18237 22284 24190 27191 21630 25978 23086 28313 TRUE FALSE 19546.24934 20095.37103 23305.74344 21758.37524 31933.10179 20880.94768 22014.57898 21064.46745 32703.63544 0.597678181 0.614469027 0.712634639 0.665319771 0.976438899 0.638490107 0.673153877 0.644101708 1 14.9971634 -5 0.207010277 2.44011675 0.636999091 0.439994595 0.108071837 138.8896959 1.381428493 83.47655202 0.236242562 1.00E-05 5 -1.803117659 REQAEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REQAEEER 8 1 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 151.83 0.0012864 0 87608 62024 77380 86464 105979 53920 82995 80228 109811 FALSE TRUE 83466.94346 68344.31612 80927.94954 77772.47445 124461.704 52052.73688 70332.58844 73202.811 126839.929 0.658049434 0.538823355 0.638032126 0.613154509 0.981250187 0.410381315 0.5544988 0.577127499 1 16.95264945 -0.966269308 4.00605962 1.000027043 0.613354901 0.401061721 0.145098909 36492620.67 73249878.07 14261.98552 0.033360938 0.108076356 0.966269308 -0.386672143 REQEEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 REQEEELR 8 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 105.52 0.0070092 232536000 177325 142194 164257 166846 165071 149214 202816 186580 181911 FALSE TRUE 168943.1987 156683.7303 171788.3459 150074.3231 193859.3301 144046.6818 171872.6942 170242.0661 210120.8288 0.804028804 0.745683953 0.817569333 0.714228684 0.922608821 0.685542136 0.817970761 0.81021033 1 17.68085965 0.521582679 1.502036744 0.99994798 0.782974148 0.513958221 0.064756765 1.667786833 4.44595999 0.052781889 0.01526901 3.323400485 -0.521582679 -0.216973832 REQGGSGLGSGSS(ph)GGGGSTSGLGSGYIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 REQGGSGLGSGSSGGGGSTSGLGSGYIGR 29 1 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 REQGGSGLGS(0.015)GS(0.095)S(0.882)GGGGS(0.005)T(0.001)S(0.001)GLGSGYIGR 64.53 0.0064391 140840000 32266 36743 32230 31087 39149 32715 42786 34069 38226 TRUE FALSE 30740.85013 40487.15347 33707.77738 27962.0757 45976.5732 31582.07135 36258.20988 31085.73775 44153.89285 0.696220608 0.916955468 0.763415754 0.633286759 1.041280173 0.715272636 0.821178101 0.704031643 1 15.43025302 -1.485842178 2.938525375 1.006322723 0.793946331 0.239030942 0.119077464 31996166.2 35660147.93 1643595.05 0.025762656 0.032670654 1.485842178 -0.212376391 REQS(ph)PLLHLDLFNFDCPEAEGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 REQSPLLHLDLFNFDCPEAEGSR 23 1 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(1)PLLHLDLFNFDCPEAEGSR 178.63 2.40E-17 149946000 79539.8 66070.3 68712.8 82436.1 76362.1 68182.8 86700.3 75097.4 70620.1 TRUE FALSE 75780.11129 72802.93869 71863.34985 74149.46661 89679.62606 65821.61254 73472.57687 68521.47354 81571.50443 0.929002252 0.892504548 0.880985956 0.90901188 1.099398947 0.806919193 0.900713765 0.840017283 1 16.31577764 -0.341885716 6.78543785 0.999999998 0.907298323 0.12605922 0.076691233 0 0 0.068474063 0.016139491 0.455107806 0.341885716 -0.092701675 REREEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 REREEIEK 8 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;; 134.25 0.00049764 245841000 356608 260538 340224 340461 305126 366427 430290 386139 382750 FALSE TRUE 339751.8466 287087.1184 355823.6069 306237.2134 358339.8778 353737.5411 364641.3577 352326.6221 442104.9152 0.768486924 0.649364231 0.804839744 0.692679957 0.810531314 0.800121258 0.824784673 0.796929892 1 18.75402925 -0.249869593 0.227710358 1.122184099 0.686310431 0.727033385 0.047902289 4.404608393 0.342945421 0.506635377 0.102972524 0.562510207 0.249869593 -0.435873667 RES(ph)AAS(ph)GLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RES(1)AAS(1)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AAS(1)GLGGLLEEEGAGAGAAQEEVLEPGR 155.38 1.34E-08 169919000 54680 60043 52865 63944 52069 62804 62652 56755 58969 TRUE FALSE 52095.38477 66161.44996 55288.91254 57516.22763 61149.81711 60629.08173 53093.28672 51785.23132 68113.61135 0.764830755 0.971339629 0.811716064 0.844416065 0.897762076 0.890116976 0.779481306 0.760277282 1 16.0556555 1.756487304 25 0.823356939 0.866850827 0 0.08397941 22.48109161 31383.98324 0.035316795 0.019585031 57.08043889 -1.756487304 0.043493887 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(0.999)AAS(0.001)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.989)AAS(0.011)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.999)AAS(0.001)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.998)AAS(0.002)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.998)AAS(0.002)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.988)AAS(0.012)GLGGLLEEEGAGAGAAQEEVLEPGR 330.34 7.20E-106 2222683000 509016 598597 517557 584070 512966 506367 514337 628788 492480 TRUE FALSE 484955.8225 659594.7148 541287.5004 525358.1739 602427.108 488831.3838 435865.4442 573727.9893 568851.2832 0.852517761 1.159520483 0.951544835 0.923542215 1.059023906 0.859330722 0.766220376 1.008572902 1 19.11769201 2.22376437 24.87185571 0.874827702 0.995324167 0.085598631 0.107534306 332.4524518 558834.5506 0.038557941 0.028596513 167.403437 -2.22376437 0.120496464 RES(ph)CGSSVLTDFEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.999)CGS(0.001)SVLTDFEGK;RES(0.999)CGS(0.001)SVLTDFEGK;RES(0.996)CGS(0.004)SVLTDFEGK;RES(0.984)CGS(0.016)SVLTDFEGK;RES(0.995)CGS(0.005)SVLTDFEGK;RES(0.97)CGS(0.029)S(0.001)VLTDFEGK 238.63 5.47E-18 2183410000 3132710 3559090 2590390 3765530 1995000 3225660 3024210 3394780 2089810 TRUE FALSE 2984633.007 3921765.317 2709161.944 3387011.77 2342927.368 3113954.585 2562811.221 3097515.066 2413887.062 1.236442688 1.624668105 1.122323404 1.403135973 0.970603557 1.290016685 1.06169475 1.283206292 1 21.20292675 3.253912391 1.53427093 1.141015876 1.413000573 0.253959307 0.170731279 0.421253982 2.059938722 0.051712299 0.075913821 1794.371618 -3.253912391 0.271984697 RES(ph)CGSSVLTDFEGKDVATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.999)CGS(0.001)SVLTDFEGKDVATK;RES(1)CGSSVLTDFEGKDVATK;RES(0.931)CGS(0.031)S(0.031)VLT(0.007)DFEGKDVATK;RES(0.95)CGS(0.043)S(0.007)VLTDFEGKDVATK;RES(1)CGSSVLTDFEGKDVATK;RES(1)CGSSVLTDFEGKDVATK;RES(0.997)CGS(0.003)SVLTDFEGKDVATK;RES(1)CGSSVLTDFEGKDVATK;RES(0.954)CGS(0.045)S(0.001)VLTDFEGKDVATK 277.59 7.19E-45 4124980000 5171468 3829058 5027888 5147159 3432238 5571769 6600456 6456616 4478935 TRUE FALSE 4927022.957 4219243.363 5258421.638 4629756.798 4030819.221 5378817.242 5593435.212 5891240.474 5173505.365 0.952356789 0.815548273 1.016413682 0.894897458 0.779127291 1.039685255 1.081169307 1.138732843 1 22.30271069 2.082388111 7.275338344 1.076945526 0.89293774 0.586516621 0.072675256 0.14621999 10.90086215 0.025797996 0.01899407 120.8893691 -2.082388111 -0.184007785 RES(ph)EDDPES(ph)EPDDHEK ddPTM_SK-BR-3_Trastuzumab_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 167.28 2.23E-08 1225630000 2685200 2600800 2382600 3030200 1677500 2946300 2956100 2697800 1399610 TRUE FALSE 2558275.918 2865824.477 2491844.567 2725598.539 1970055.469 2844268.892 2505092.652 2461566.33 1616654.371 1.582450748 1.772688417 1.541358878 1.685950064 1.21860028 1.759354964 1.549553633 1.522629929 1 20.62457984 -2.706563264 0.277266264 3.52E-18 1.649829722 0.590426309 0.153077219 34.36973663 1.03260463 20.69311599 0.169770033 0.001965336 2.706563264 1.649829722 RES(ph)EDDPES(ph)EPDDHEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RESEDDPESEPDDHEKR 17 2 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 2 RES(1)EDDPES(1)EPDDHEKR;RES(1)EDDPES(1)EPDDHEKR;RES(1)EDDPES(1)EPDDHEKR;RES(1)EDDPES(1)EPDDHEKR 155.05 6.17E-08 620168000 666721 608509 619000 732370 409549 670331 681646 636069 396527 TRUE FALSE 635206.4196 670516.7589 647381.7623 658750.7762 480974.2159 647117.2694 577648.3834 580371.4263 458018.382 1.386857918 1.463951634 1.413440569 1.438262747 1.050119897 1.412863096 1.261190394 1.267135663 1 18.80504597 -4.147173384 0.098084844 1.31E-12 1.624579798 0.549368476 0.108281709 107.767965 0.866409616 23.25687633 1.897214711 7.13E-05 4.147173384 1.624579798 RES(ph)FLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RESFLYR 7 1 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12;P27815 Q08499-10;P27815 PDE4D;PDE4A "cAMP-specific 3,5-cyclic phosphodiesterase 4D;cAMP-specific 3,5-cyclic phosphodiesterase 4A" 1 RES(1)FLYR;RES(1)FLYR;RES(1)FLYR 147.73 0.0013056 364849000 135607 100118 112397 156570 122478 144297 163569 116518 156146 TRUE FALSE 129197.1259 110320.138 117550.5136 140831.2861 143838.1244 139299.9587 138613.5449 106315.0662 180360.3242 0.716327864 0.611665224 0.651753728 0.780832962 0.797504246 0.772342583 0.768536792 0.589459277 1 17.46052248 -5 0.218853818 2.415339629 0.675306599 0.562093222 0.076990551 114.3602023 1.143316103 71.61411194 0.148098815 1.00E-05 5 -1.740033029 RES(ph)LSTSSDLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RESLSTSSDLYK 12 1 Q8TB72-3;Q8TB72;Q8TB72-4 Q8TB72-3 PUM2 Pumilio homolog 2 1 RES(0.93)LS(0.049)T(0.015)S(0.004)S(0.002)DLYK 64.476 0.038798 135720000 109810 110000 91153 127660 89325 104260 116760 130290 97706 TRUE FALSE 104619.4989 121209.1251 95332.45521 114827.3743 104903.2517 100649.4501 98946.11756 118881.1169 112857.7475 0.927003252 1.073999152 0.844713432 1.017452296 0.929517504 0.891825792 0.876733054 1.053371342 1 16.78414593 RES(ph)LSTSSDLYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RESLSTSSDLYKR 13 2 Q8TB72-3;Q8TB72;Q8TB72-4 Q8TB72-3 PUM2 Pumilio homolog 2 1 RES(1)LSTSSDLYKR;RES(0.999)LS(0.001)TSSDLYKR 134.82 4.75E-05 413090000 618890 421650 550590 573370 535110 584080 794860 753390 722390 TRUE FALSE 589636.2962 464616.6144 575835.0961 515733.7583 628433.0146 563853.1631 673589.5084 687419.1776 834414.5517 0.706646708 0.556817488 0.690106728 0.618078576 0.753142444 0.67574704 0.807260021 0.82383412 1 19.67040479 1.18621531 0.578015594 1.003519764 0.631700469 0.826072245 0.051150574 0.273295979 0.228490586 0.047212753 0.022392397 15.35377988 -1.18621531 -0.371819296 RES(ph)PPAGQK ddPTM_SK-BR-3_Trastuzumab_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 87.641 0.008161 500254000 714690 666550 658090 775440 557720 714460 723190 736230 571410 TRUE FALSE 680908.0201 734472.2028 688264.0774 697491.298 654986.1914 689718.0711 612854.0832 671761.7982 660021.3444 1.031645455 1.112800683 1.042790636 1.056770821 0.992371227 1.044993585 0.928536764 1.017787991 1 19.33215316 2.666179716 1.230464296 0.982203142 1.070795079 0.423788944 0.036250043 0.345530786 1.072644528 0.01657787 0.01444702 463.6387393 -2.666179716 0.088591937 RES(ph)PS(ph)PAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RES(1)PS(1)PAPKPR 78.932 0.015301 779180000 479890 439460 428620 465800 355410 389550 529250 465770 438490 TRUE FALSE 457206.5508 484241.4736 448272.651 418976.899 417393.3915 376059.7858 448503.1922 424984.7096 506488.7897 0.902698263 0.956075403 0.885059374 0.827218504 0.824092063 0.742483928 0.885514549 0.839080189 1 18.95017081 3.470901247 4.243062942 0.841602248 0.928939404 0.171521647 0.065695217 0.252458787 10.90271781 0.016505916 0.024104524 2957.339927 -3.470901247 0.087337156 RES(ph)PSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.737)PS(0.263)EER;RES(0.902)PS(0.098)EER 121.61 0.0015105 141793000 296310 318650 232080 331140 282100 292910 281780 262830 257300 TRUE FALSE 282304.0135 351120.7973 242721.0976 297853.1781 331298.1507 282766.4533 238789.2858 239815.2119 297200.7699 0.949876454 1.181426271 0.816690676 1.002195177 1.11472844 0.951432439 0.803461195 0.806913158 1 18.18107833 1.972693457 6.360201543 0.854311298 1.021961097 0.256079872 0.109472007 0.20975436 29.55040421 0.043975298 0.028252982 93.90602495 -1.972693457 0.167649799 RES(ph)PSEERLEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RESPSEERLEPK 12 2 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.996)PS(0.004)EERLEPK;RES(0.995)PS(0.005)EERLEPK;RES(0.997)PS(0.003)EERLEPK;RES(0.987)PS(0.013)EERLEPK;RES(0.955)PS(0.045)EERLEPK 129.11 0.00018905 1869740000 1687370 1373770 1523020 1849200 1376730 1715340 1909590 1834400 1600880 TRUE FALSE 1607611.364 1513758.725 1592851.973 1663314.903 1616831.276 1655937.346 1618246.973 1673770.211 1849136.294 0.869385004 0.818630152 0.861403228 0.899509089 0.874371068 0.895519357 0.875136667 0.905163246 1 20.81842013 -4.999999998 0.140807942 1.46497123 0.822388894 0.823447227 0.019427191 53.42508883 0.459760142 6.911809363 0.117110993 1.00E-05 4.999999998 -0.642582336 RES(ph)PSPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RESPSPAPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.994)PS(0.006)PAPK;RES(1)PSPAPK;RES(0.997)PS(0.003)PAPK 110.98 0.0013472 916229000 816970 1019320 684890 1076980 546680 833750 781990 834090 502010 TRUE FALSE 778353.4472 1123189.867 716292.8839 968719.9243 642020.8189 804877.0284 662683.0633 761052.6578 579859.1469 1.342314683 1.937004655 1.235287721 1.670612475 1.10720133 1.388056104 1.142834543 1.312478491 1 19.14534297 2.824844557 1.196382944 1.190635126 1.604888374 0.339408667 0.224684042 0.453198727 1.351215763 0.093483268 0.094838893 668.1047458 -2.824844557 0.414253248 RES(ph)PSPAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.992)PS(0.008)PAPKPR;RES(0.996)PS(0.004)PAPKPR;RES(0.75)PS(0.25)PAPKPR;RES(0.852)PS(0.148)PAPKPR;RES(0.992)PS(0.008)PAPKPR;RES(0.999)PS(0.001)PAPKPR;RES(0.877)PS(0.123)PAPKPR;RES(0.998)PS(0.002)PAPKPR;RES(0.994)PS(0.006)PAPKPR;RES(0.981)PS(0.019)PAPKPR;RES(0.999)PS(0.001)PAPKPR 160.48 2.16E-05 35076750000 8739240 7481170 8089220 9276620 6756240 8494480 9490630 8818000 7440420 TRUE FALSE 8326153.445 8243509.728 8460118.738 8344116.533 7934526.117 8200314.028 8042660.086 8045849.173 8594242.333 0.968805989 0.959189817 0.984393785 0.97089612 0.92323742 0.954163696 0.935819561 0.936190633 1 23.03493903 2.784867979 24.93232656 0.945501566 0.969412918 0.176804548 0.021220392 542.2752321 291965.122 0.005701443 0.006047282 609.3516319 -2.784867979 0.023911352 RES(ph)QEEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RESQEEPR 8 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;H0YD62;H0YF37 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 RES(1)QEEPR;RES(1)QEEPR;RES(1)QEEPR;RES(1)QEEPR 193.28 0.00010502 2219150000 2153590 1978960 1927770 2404190 2017940 2143410 2453640 2138490 2276330 TRUE FALSE 2051794.069 2180618.274 2016160.161 2162516.254 2369868.097 2069183.174 2079292.154 1951232.479 2629331.631 0.780348148 0.829343187 0.76679569 0.82245854 0.901319586 0.786961656 0.790806352 0.742102083 1 21.32626469 -1.211532202 4.994959257 1.000022547 0.80436566 0.674669562 0.043080214 1.04E-05 1.63E-06 0.039935518 0.009411808 0.061442347 1.211532202 -0.195656887 RES(ph)VNLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RESVNLGK 8 1 P46013 P46013 MKI67 Antigen KI-67 1 RES(1)VNLGK;RES(1)VNLGK 111.27 0.0020008 258940000 355470 353130 370700 418420 314460 387070 471010 401390 418130 TRUE FALSE 338667.6376 389114.3485 387696.9617 376359.6267 369301.7244 373665.6688 399148.7738 366242.1637 482971.4649 0.70121666 0.805667367 0.802732645 0.779258515 0.764645018 0.773680633 0.826443802 0.758310149 1 18.88157843 -5 0.252274343 2.364791648 0.75851773 0.815228954 0.033478074 75.21428055 0.743973742 52.98689507 0.045667008 1.00E-05 5 -1.606273919 RESCGSS(ph)VLTDFEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.236)CGS(0.321)S(0.442)VLT(0.001)DFEGK 73.809 0.022461 147010000 246600 214740 204520 278870 157870 238040 239650 242750 161460 TRUE FALSE 234943.7067 236622.2501 213897.4443 250837.4578 185402.478 229796.6151 203086.991 221493.5231 186498.3922 1.259762639 1.26876295 1.146913074 1.344984559 0.994123734 1.232164055 1.088947678 1.18764307 1 17.50880367 7.99999842 0.037206836 0.423696302 2.380243584 0.381589226 0.090629132 766.2844047 2.176048564 32.69253127 97.98827696 99999636.29 -7.99999842 1.956547282 RESPS(ph)PAPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.256)PS(0.744)PAPKPR 157.67 2.40E-05 4659800000 918650 837700 831490 986360 700960 893050 1059400 943880 811780 TRUE FALSE 875227.2351 923062.5824 869614.639 887209.2188 823207.2021 862123.4546 897769.0728 861228.8634 937666.6964 0.933409748 0.984425048 0.927424043 0.946188259 0.877931578 0.919434867 0.957450101 0.918480806 1 19.83871567 -1.164106723 4.262379132 1.000017186 0.937184706 0.354268221 0.027906086 4.64E-06 9.09E-07 0.027495631 0.00647901 0.06853198 1.164106723 -0.06283248 RESSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RESSLK 6 1 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 97.033 0.066594 35536000 114960 87294 110190 116900 129480 101530 134950 119650 162360 FALSE TRUE 109526.0686 96189.35785 115242.3205 105148.9899 152061.271 98013.99064 114360.899 109172.8117 187537.9596 0.584020797 0.51290607 0.614501303 0.560681102 0.810829292 0.522635475 0.60980134 0.582137141 1 17.51682312 -5 0.35231256 5.750144939 0.581338945 0.697371663 0.082596719 238.6656694 1.942098629 857.257076 0.05844094 1.00E-05 5 -5.168805994 RET(ph)DDEGEDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RETDDEGEDD 10 1 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RET(1)DDEGEDD;RET(1)DDEGEDD;RET(1)DDEGEDD 172.51 7.15E-06 531734000 988944 907220 894100 1057550 765531 924187 939553 981946 913153 TRUE FALSE 942198.577 999666.7494 935095.3694 951243.0648 899039.364 892182.1725 796206.9338 895961.6026 1054760.104 0.893282343 0.947766934 0.886547914 0.901857267 0.852363832 0.845862646 0.754870165 0.849445859 1 20.00848348 2.746743898 1.893029311 0.833423153 0.91535564 0.042417911 0.063747295 0.459576952 3.25965451 0.021951556 0.021697761 558.1409635 -2.746743898 0.081932487 RET(ph)PS(ph)PRPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RETPSPRPMR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RET(1)PS(1)PRPMR;RET(1)PS(1)PRPMR 69.314 0.040551 616310000 667710 573770 608570 696480 607710 630990 676080 623380 712410 TRUE FALSE 636148.6716 632237.8153 636473.5365 626468.5072 713694.4316 609138.6581 572931.5789 568793.5425 822886.9043 0.773069383 0.768316778 0.77346417 0.76130572 0.867305614 0.740245901 0.696245834 0.691217152 1 19.65033464 -1.61495703 3.100021949 1.015419946 0.758823881 0.709919862 0.048435131 24879847.02 27633967.18 3116726.607 0.012145091 0.024268502 1.61495703 -0.256596065 RFDAMPFTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RFDAMPFTLR 10 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 162.93 1.06E-05 1935760000 2352642 1473066 837602 980373 2705560 1085905 2582160 1696313 2269640 FALSE TRUE 2241437.275 1623173.1 876006.8802 881824.0435 3177408.807 1048299.838 2188204.067 1547774.841 2621604.179 0.854986917 0.619152621 0.334149177 0.33636811 1.212009361 0.399869609 0.834681332 0.590392269 1 21.32201845 RFDDAVVQSDMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 25 RFDDAVVQSDMK 12 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;;;;;;;;;;;;;;; 203.25 2.04E-07 40950480000 22393030 20984350 18265790 22590460 15821230 21434120 22839230 23084670 17789860 FALSE TRUE 21334555.85 23122679.12 19103294.54 20319624.04 18580447.5 20691851.05 19354685.99 21063253.92 20548620.63 1.03824759 1.125266729 0.929663109 0.988855866 0.904218723 1.006970318 0.941897091 1.025044663 1 24.29253822 3.736758892 24.99998802 0.967239311 1.081757161 0.538703416 0.042521255 94.49676117 1311202.048 0.009928659 0.016277063 5454.549556 -3.736758892 0.11451785 RFDDAVVQSDMKHWPFMVVNDAGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFDDAVVQSDMKHWPFMVVNDAGRPK 26 3 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 219.93 1.87E-34 1286500000 1801730 740690 1965230 1336970 1940740 1832780 3294010 2244580 2579450 FALSE TRUE 1716565.794 816167.1531 2055337.739 1202575.236 2279204.442 1769310.369 2791448.276 2048032.676 2979457.932 0.57613359 0.273931424 0.689836133 0.403622156 0.764972855 0.593836332 0.936898033 0.687384324 1 21.50661845 2.134683998 0.571116805 0.956761723 0.426355427 0.543081996 0.147940737 0.525487806 0.348751016 0.121651529 0.088007067 136.3590597 -2.134683998 -0.530406297 RFDDPGLMLMGFKPLVLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFDDPGLMLMGFKPLVLLK 19 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 138.08 1.47E-06 35801000 60890 50731 56827 60272 49567 53348 73063 66031 64320 FALSE TRUE 58011.85037 55900.54658 59432.57416 54213.34405 58211.46911 51500.54538 61915.89746 60248.97559 74294.4171 0.780837277 0.752419209 0.799960165 0.729709528 0.783524138 0.693195362 0.833385601 0.810948897 1 16.18096618 0.660758553 1.091639332 0.999462812 0.761594234 0.807299934 0.035978356 0.419406932 0.817594337 0.030241591 0.00948438 4.578872522 -0.660758553 -0.237868578 RFDEATQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RFDEATQLR 9 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;; 195.36 5.03E-05 753850000 324306 289338 547499 304731 415997 299553 390141 347890 435880 FALSE TRUE 308976.6981 318821.8711 572602.3707 274098.8609 488546.7451 289179.4045 330617.825 317426.9073 503474.0442 0.613689428 0.633243908 1.137302662 0.544415078 0.970351403 0.574368049 0.656673028 0.630473231 1 18.94155788 3.959135417 24.99992641 0.761760618 0.621021358 0.095997261 0.197762074 1100.971745 673547.3266 0.046676009 0.084150284 9101.970352 -3.959135417 -0.14073926 RFDEILEASDGIMVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 36 RFDEILEASDGIMVAR 16 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 358.31 2.23E-87 11660006900 5957964.8 4807873.3 5534304.3 6009360.3 6622180.8 5249076.8 6700939.9 5937556.9 7144608.4 FALSE TRUE 5676343.611 5297801.055 5788057.626 5405287.986 7777087.035 5067299.954 5678588.447 5417632.941 8252557.781 0.6878284 0.641958675 0.701365295 0.654983355 0.942385045 0.614027807 0.688100417 0.65647925 1 22.9764099 -1.274559258 3.288019746 1.00123777 0.694526222 0.522383998 0.090567025 21025155.48 29308589.99 261773.4373 0.021627331 0.053142348 1.274559258 -0.306711548 RFDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFDSEK 6 1 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 152.63 0.021467 0 520090 418420 392690 485160 384420 477850 570090 457260 437740 FALSE TRUE 495506.3764 461057.4737 410695.2249 436390.7951 451462.7263 461301.9347 483112.3001 417219.8903 505622.4835 0.979992766 0.911861099 0.812256651 0.863076325 0.89288499 0.912344585 0.955480256 0.825160874 1 18.94770109 2.004449455 12.19566271 0.924927394 0.898176318 0.062182093 0.059671449 1.001092758 2616.59874 0.023125041 0.016689235 101.0297911 -2.004449455 -0.026751076 RFDVSGYPTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFDVSGYPTLK 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 177.1 1.30E-05 1064230000 2290050 1787870 1943970 2159640 1921000 2081780 2668100 2344700 2173070 FALSE TRUE 2181803.875 1970055.986 2033102.947 1942548.884 2256021.792 2009687.437 2261032.342 2139385.638 2510058.597 0.869224279 0.78486454 0.809982265 0.773905791 0.89879248 0.800653594 0.900788669 0.852324978 1 21.25928961 0.509944362 0.505114799 1.008401479 0.815332313 0.62932481 0.041453219 1.137258489 0.532195975 0.06060794 0.019531416 3.235522036 -0.509944362 -0.193069166 RFEDLGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFEDLGSR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 146.88 0.00087574 206486000 166621 132379 128616 170201 287440 115212 161305 134683 225569 FALSE TRUE 158745.1555 145868.5706 134513.1708 153092.0721 337569.445 111222.1796 136694.9597 122889.4425 260549.0885 0.609271583 0.559850627 0.516268054 0.587574775 1.295607853 0.426876103 0.524641865 0.471655623 1 17.99119568 2.971281415 24.99604169 0.699572227 0.566131547 0.088801884 0.259660458 2305.250575 2006441.778 0.078080535 0.082964971 936.0119956 -2.971281415 -0.13344068 RFEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFEEGK 6 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 107.67 0.049812 220760000 369010 338480 300600 395540 284490 355050 399610 402090 306570 FALSE TRUE 351567.6286 372971.4968 314382.8073 355779.5677 334104.9659 342754.5295 338642.1552 366880.868 354111.3099 0.992816718 1.053260617 0.887807869 1.004711112 0.943502669 0.967928784 0.956315559 1.036060859 1 18.4338434 3.794611927 24.99963059 0.968456355 1.023038657 0.207570265 0.042138761 360.1935842 160649.602 0.009612818 0.017329752 6231.777335 -3.794611927 0.054582302 RFEELGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RFEELGVK 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;;;; 148.14 0.00084335 3830050000 5711240 2931910 3778210 5056560 4898350 4391600 7021940 5449420 5656060 FALSE TRUE 5441281.004 3230674.962 3951444.666 4548264.982 5752620.689 4239517.791 5950614.086 4972239.896 6533172.898 0.832869586 0.494503209 0.604827811 0.696180103 0.880524789 0.64892172 0.910830645 0.761075816 1 22.63935239 1.532844224 0.508117737 0.985457219 0.64149259 0.413885957 0.117265244 0.762873155 0.492925552 0.116874992 0.071013866 34.10705521 -1.532844224 -0.343964629 RFEIACYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFEIACYK 8 1 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 122.28 0.0022402 852930000 1308050 1025460 707430 751750 1035850 708010 1210930 981660 1152320 FALSE TRUE 1246221.069 1129955.54 739866.3652 676182.6618 1216501.912 683491.4362 1026180.388 895700.6463 1331015.9 0.936293149 0.84894218 0.55586591 0.508019973 0.913964973 0.513511098 0.770975304 0.672945114 1 20.34409638 3.931826231 6.419230812 0.689540821 0.904439653 0.190805971 0.162121773 0.278900602 21.26985828 0.037129333 0.068163992 8547.246544 -3.931826231 0.214898832 RFEKPLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RFEKPLEEK 9 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;; 195.51 1.75E-05 2200970000 3580430 3320600 2866830 4043390 1810970 3620440 3931760 4228420 2493420 FALSE TRUE 3411190.17 3658972.915 2998276.991 3636940.755 2126802.595 3495063.255 3331897.8 3858157.129 2880086.839 1.184405318 1.2704384 1.04103701 1.262788575 0.738450857 1.213527039 1.156874076 1.3395975 1 21.45768088 3.748260575 24.48019836 1.114251551 1.227421857 0.081731124 0.165950846 1275.975171 3220221.181 0.039964537 0.070854554 5600.935544 -3.748260575 0.113170306 RFES(ph)IPDMLELDHLTVSGDVTFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 1 RFES(1)IPDMLELDHLTVSGDVTFGK 112.33 0.00069628 24482000 32407 29227 31112 40999 29728 36265 43860 39957 40682 TRUE FALSE 30875.18533 32205.26453 32538.51597 36877.70263 34912.55379 35009.13396 37168.35146 36458.15325 46990.75679 0.657048055 0.685353179 0.69244503 0.78478631 0.742966408 0.74502171 0.790971544 0.775857972 1 15.52008938 -5 0.10936112 1.900758048 0.566001606 0.93181441 0.02470233 37.22302964 0.271070781 7.462067819 0.30302783 1.00E-05 5 -1.334756442 RFESIPDMLELDHLTVSGDVTFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 188.72 1.03E-17 100670000 197670 158010 168300 202800 177450 183440 234160 206490 180190 FALSE TRUE 188326.5308 174111.3986 176016.7215 182414.1587 208397.2238 177087.4268 198434.5914 188408.6409 208132.9449 0.904837679 0.836539351 0.845693706 0.87643097 1.00126976 0.850838039 0.953403083 0.905232187 1 17.66714582 2.974664083 24.37040369 0.933484745 0.862664385 0.390863958 0.046896601 550.7097274 529723.2754 0.012788468 0.013620814 943.330949 -2.974664083 -0.07082036 RFFES(ph)IIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFFESIIK 8 1 Q8NHU0;Q5HYN5;Q5DJT8;P0DMV2;P0DMV1;P0DMV0;P0DMU9;P0DMU8;P0DMU7 Q8NHU0 CT45A3;CT45A1;CT45A2;CT45A9;CT45A8;CT45A7;CT45A10;CT45A5;CT45A6 Cancer/testis antigen family 45 member A3;Cancer/testis antigen family 45 member A1;Cancer/testis antigen family 45 member A2;Cancer/testis antigen family 45 member A9;Cancer/testis antigen family 45 member A8;Cancer/testis antigen family 45 member A7;Cancer/testis antigen family 45 member A10;Cancer/testis antigen family 45 member A5;Cancer/testis antigen family 45 member A6 1 RFFES(1)IIK 66.682 0.06467 132500000 179570 109700 146890 128590 182670 168360 254600 198680 241030 TRUE FALSE 171082.082 120878.5547 153625.0518 115663.8889 214527.5902 162529.651 215756.094 181282.5259 278407.7014 0.614501974 0.4341782 0.551798858 0.415447878 0.770551925 0.583782885 0.774964532 0.651140486 1 18.08683959 0.993983687 0.402184629 1.020814852 0.493789517 0.659407679 0.100935485 0.734236521 0.322284683 0.141410802 0.074566535 9.862424397 -0.993983687 -0.527025336 RFFPYYVYNIIGGLDEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFFPYYVYNIIGGLDEEGK 19 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 192.69 1.11E-14 128240000 551700 600920 466060 534030 336800 521350 490360 605730 323600 FALSE TRUE 525622.2344 662154.4312 487429.312 480348.2898 395537.8134 503295.5188 415546.5759 552689.07 373782.2353 1.406225831 1.771497863 1.304046223 1.285101978 1.058203885 1.346493951 1.111734418 1.478639213 1 18.51183848 3.567092763 5.22327085 1.219057368 1.587485274 0.46645316 0.163583899 0.161611781 7.113978328 0.039518758 0.061510317 3690.564185 -3.567092763 0.368427905 RFGFPEGSVELYAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFGFPEGSVELYAEK 15 1 P23396;E9PPU1;F2Z2S8;H0YCJ7;H0YF32 P23396 RPS3 40S ribosomal protein S3 0 ; 126.63 0.0001333 553270000 706720 674260 632080 702910 630990 616670 829760 774690 671710 FALSE TRUE 673314.7462 742967.8606 661061.4932 632252.1514 741034.4562 595314.5633 703164.8724 706854.0367 775875.3562 0.867813033 0.957586621 0.852020222 0.814888817 0.95509472 0.767281186 0.90628587 0.911040712 1 19.56546538 0.857663161 2.177971107 0.999520572 0.878138107 0.321859313 0.057707024 0.652843139 5.999252599 0.051474491 0.014094137 7.205484043 -0.857663161 -0.121382465 RFNDGSDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RFNDGSDEK 9 1 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 95.483 0.012851 662260000 1149470 1198810 1068940 1120870 809120 1105980 1132280 1318490 890090 FALSE TRUE 1095136.831 1320970.102 1117951.956 1008198.018 950230.2718 1067679.635 959529.8903 1203036.026 1028120.611 1.065183228 1.284839626 1.087374326 0.980622319 0.924240076 1.038477027 0.933285336 1.170131221 1 19.97157809 3.461589798 4.948797643 0.999426876 1.177427599 0.394415146 0.085232141 0.146388625 9.878008802 0.022009904 0.031412566 2894.608265 -3.461589798 0.178000723 RFPEEPHVPLEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFPEEPHVPLEQR 13 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 115.25 0.00044079 172542000 129670 127478 111173 135765 139464 130288 141584 127046 133636 FALSE TRUE 123540.7561 140468.1531 116270.392 122117.6443 163786.4774 125776.0939 119982.7604 115921.1787 154359.5884 0.800343907 0.91000601 0.753243729 0.791124449 1.061070965 0.814825274 0.777293861 0.750981393 1 17.23593558 -1.337549921 3.369985147 1.000954115 0.835507953 0.243495391 0.092714517 26502576.9 39400590.85 255022.6649 0.021581948 0.045967415 1.337549921 -0.165446162 RFPELESLVPNALDYIR ddPTM_SK-BR-3_Trastuzumab_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 82.482 0.011355 77498000 72776 51514 74079 72597 64833 57603 82594 68243 73706 FALSE TRUE 69336.02271 56763.33517 77475.59542 65299.41163 76139.85467 55608.19367 69992.76836 62267.28114 85135.95004 0.814415328 0.666737555 0.910022093 0.76700162 0.89433259 0.653169356 0.82212941 0.73138646 1 16.37748084 -1.201595908 4.844649987 1.000030067 0.778140567 0.39411094 0.084644785 2.44E-05 4.03E-06 0.072863272 0.017171713 0.062864301 1.201595908 -0.2218895 RFPGYDSESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RFPGYDSESK 10 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;; 218.43 1.09E-08 9350100000 17884840 15438610 15407810 18617880 12975740 18033380 19150340 18855700 13944520 FALSE TRUE 17039459.06 17011821.91 16114273.33 16746375.33 15238704.95 17408879.53 16228603.91 17204594.95 16106964.94 1.057893844 1.056177993 1.000453741 1.039697757 0.946094128 1.080829293 1.007551949 1.068146296 1 23.94118133 3.768186379 20.69495805 1.021316751 1.05703604 0.13981155 0.037729542 144.9231144 101232.0298 0.008624667 0.015539693 5863.897613 -3.768186379 0.035719289 RFQILGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFQILGK 7 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 138.37 0.0044776 238230000 308190 252220 231670 278920 234090 259560 309200 288800 289090 FALSE TRUE 293622.4695 277921.5048 242292.2987 250882.4317 274915.2219 250571.3721 262025.8612 263511.141 333920.6007 0.879318224 0.83229817 0.725598535 0.751323611 0.823295182 0.750392074 0.784695106 0.789143109 1 18.34914558 -1.512684934 5.312743332 1.000525933 0.795868505 0.678031898 0.044973445 0.000308289 2.83E-05 0.047917381 0.011265679 0.030712493 1.512684934 -0.204657427 RFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGR 45 3 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 89.119 2.59E-05 36979000 25058 12064 23603 22553 27065 24134 41141 27561 32067 FALSE TRUE 23873.558 13293.33532 24685.2209 20285.92959 31785.12743 23298.23353 34864.18484 25147.61273 37039.78658 0.644538217 0.35889341 0.666451488 0.54767944 0.858134735 0.629005609 0.941263113 0.678935141 1 15.17678817 2.357917689 0.516766491 0.937662485 0.483535604 0.493581271 0.13468583 0.664661872 0.369553759 0.113500327 0.105531314 227.9909924 -2.357917689 -0.454126881 RFS(ph)ADEQFFSVGQAASSSAHSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RFSADEQFFSVGQAASSSAHSSK 23 1 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 1 RFS(1)ADEQFFSVGQAASSSAHSSK;RFS(0.969)ADEQFFS(0.031)VGQAASSSAHSSK;RFS(1)ADEQFFSVGQAASSSAHSSK 259.27 5.26E-44 438310000 353053 351841 440837 398870 368181 433513 531640 389502 416530 TRUE FALSE 336364.8844 387693.9979 461049.8125 358774.8298 432391.6498 418500.3361 450528.5538 355395.14 481123.3451 0.699124014 0.80580999 0.958277783 0.745702393 0.898712678 0.869840012 0.936409672 0.738677812 1 18.87604728 6.065427512 0.515488903 0.886889025 1.89E-13 0.30643821 0.084403306 15.91637886 1.117116122 0.039519753 11.48818816 1162592.487 -6.065427512 -0.886889025 RFS(ph)DFLGLHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFSDFLGLHSK 11 1 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 1 RFS(1)DFLGLHSK;RFS(1)DFLGLHSK 155.1 1.94E-05 2117500000 2171000 2202300 1729700 2014510 1629550 2006540 2289500 2244700 1454080 TRUE FALSE 2068381.133 2426716.874 1809008.456 1812007.627 1913743.004 1937053.017 1940194.725 2048142.168 1679571.3 1.231493496 1.444843023 1.077065592 1.078851268 1.139423497 1.153302046 1.155172588 1.219443419 1 20.67966161 8 0.161530067 1.031711734 2.212676713 0.262395703 0.102798137 70.3950564 0.732302882 0.300992174 19.84722765 100000000 -8 1.180964978 RFS(ph)DFLGLYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RFSDFLGLYEK 11 1 Q13596-2;Q13596;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 1 RFS(1)DFLGLYEK;RFS(1)DFLGLYEK;RFS(1)DFLGLYEK;RFS(1)DFLGLYEK 150.92 2.06E-05 274995000 1641670 1140343 1012848 1216380 1302254 1174222 1734181 1479987 1385856 TRUE FALSE 1564071.513 1256545.248 1059288.083 1094107.171 1529366.685 1133558.398 1469599.838 1350391.492 1600767.471 0.977076022 0.784964257 0.661737637 0.683489134 0.955395904 0.708134328 0.918059534 0.843590039 1 20.61033232 0.860445111 0.909242427 0.997070661 0.805660891 0.240096415 0.108885522 1.177430669 1.982345542 0.103080217 0.035021225 7.251788188 -0.860445111 -0.19140977 RFS(ph)DGAASIQAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSDGAASIQAFK 13 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RFS(0.838)DGAAS(0.162)IQAFK 176.18 1.80E-05 88643000 313310 310020 306770 332240 267650 302540 382950 356900 336700 TRUE FALSE 298500.4572 341611.3905 320835.7079 298842.604 314328.0753 292062.9639 324523.9441 325647.944 388913.7164 0.767523604 0.878373213 0.824953439 0.768403354 0.808220595 0.750971107 0.83443687 0.837326971 1 18.56909059 0.617895966 1.624274889 0.999869139 0.807016148 0.733838088 0.036785483 0.865644433 3.010888909 0.034782676 0.009934785 4.148546538 -0.617895966 -0.192852991 RFS(ph)DQAAGPAIPTSNSYSK ddPTM_SK-BR-3_Trastuzumab_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 110.94 0.00013835 244610000 232620 206090 226550 269580 193850 222460 292350 267320 233890 TRUE FALSE 221624.5136 227090.8053 236937.5416 242481.3062 227657.3786 214756.1544 247746.6381 243912.0436 270160.4667 0.820343984 0.840577484 0.877025216 0.897545482 0.842674657 0.794920726 0.917035128 0.902841362 1 18.04345705 1.02005436 1.207347267 0.997332772 0.847212434 0.676647237 0.032979795 0.283391772 0.854892446 0.030966169 0.009684316 10.47259623 -1.02005436 -0.150120338 RFS(ph)DQAGPAIPTSNSYSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 251.37 7.42E-26 3206880000 4481730 3876210 4184600 4698720 3617150 4406950 5221950 4769410 4258120 TRUE FALSE 4269887.505 4271200.206 4376468.049 4226395.739 4247979.815 4254336.216 4425245.62 4351775.176 4918447.502 0.868137253 0.868404147 0.889806803 0.859294673 0.863683065 0.864975425 0.899724073 0.884786342 1 22.22977157 0.026226602 0.635187043 1.00663876 0.868902079 0.927772089 0.011122103 0.992963083 0.45856889 0.026865199 0.004175089 1.062249662 -0.026226602 -0.137736681 RFS(ph)EGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RFS(1)EGVLQS(0.999)PS(0.001)QDQEK;RFS(1)EGVLQS(1)PSQDQEK 215.39 5.65E-14 393800000 676920 600510 630450 703900 479600 703530 787800 823850 607070 TRUE FALSE 644923.3331 661702.6517 659356.7561 633142.6347 563242.0882 679166.5797 667606.6411 751709.3265 701211.3151 0.919727505 0.943656552 0.940311062 0.902927008 0.803241585 0.968561923 0.952076252 1.072015397 1 19.41948975 1.524437632 2.320891329 1.032991336 0.912621262 0.521863947 0.047399755 0.221724874 2.468766698 0.036141161 0.012485096 33.45319733 -1.524437632 -0.120370074 RFS(ph)EGVLQSPSQDQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK 308.39 8.35E-58 10255510000 7634140 7342750 6896480 8010540 5132390 8076450 8866110 9585590 6883730 TRUE FALSE 7273289.332 8090984.573 7212690.43 7205305.3 6027477.191 7796760.511 7513422.082 8746224.923 7951223.691 0.914738362 1.01757728 0.907117031 0.906188227 0.758056549 0.980573659 0.94493909 1.099984765 1 22.92274548 1.420265545 3.298038979 1.04843997 0.920955761 0.364740744 0.071446113 0.27885072 5.32464216 0.055136584 0.018631503 26.31876733 -1.420265545 -0.127484209 RFS(ph)FCCSPEPEAEAEAAAGPGPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RFSFCCSPEPEAEAEAAAGPGPCER 25 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 1 RFS(0.973)FCCS(0.027)PEPEAEAEAAAGPGPCER;RFS(1)FCCSPEPEAEAEAAAGPGPCER;RFS(0.949)FCCS(0.051)PEPEAEAEAAAGPGPCER;RFS(0.997)FCCS(0.003)PEPEAEAEAAAGPGPCER;RFS(1)FCCSPEPEAEAEAAAGPGPCER;RFS(0.987)FCCS(0.013)PEPEAEAEAAAGPGPCER;RFS(0.993)FCCS(0.007)PEPEAEAEAAAGPGPCER 296.77 3.11E-63 8397350000 1865810 1436070 1615860 1829120 1936650 1586750 2045020 1746290 2239030 TRUE FALSE 1777616.859 1582407.166 1689948.779 1645253.382 2274401.147 1531800.45 1733014.64 1593375.59 2586247.337 0.687334438 0.611854537 0.653436644 0.636154694 0.879421359 0.592286912 0.670088516 0.616095594 1 21.30242882 -1.743251214 4.241951849 1.027188212 0.666192081 0.627922235 0.080220566 0.019129566 0.001157838 0.072034908 0.016808649 0.018061291 1.743251214 -0.360996131 RFS(ph)FSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RFS(0.999)FS(0.001)QR;RFS(0.997)FS(0.003)QR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(0.998)FS(0.002)QR;RFS(0.994)FS(0.006)QR;RFS(0.638)FS(0.362)QR;RFS(1)FSQR;RFS(1)FSQR 162.64 0.00077462 30590210000 7756950 6134978 6820798 7473610 7367020 6756086 7592480 6581690 7560860 TRUE FALSE 7390294.346 6760139.233 7133538.335 6722348.524 8651825.956 6522121.048 6434107.731 6005362.332 8733359.553 0.846214369 0.77405942 0.816814914 0.769732253 0.99066412 0.746805511 0.736727681 0.687634844 1 23.05810531 -1.476050225 7.729322102 1.000018181 0.796105697 0.382400295 0.081442898 2.46E-05 1.67E-06 0.075954936 0.017901156 0.033415639 1.476050225 -0.203912484 RFS(ph)IPESGQGGTEMDGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RFSIPESGQGGTEMDGFR 18 1 Q9Y572 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR 214.71 4.25E-19 718626000 358539 436071 351579 438000 354954 381934 390624 409108 369017 TRUE FALSE 341591.572 480507.1307 367699.2449 393971.4079 416857.8652 368707.5298 331027.1345 373284.3347 426242.2717 0.801402382 1.127309895 0.862653165 0.924289856 0.977983398 0.865018686 0.776617329 0.875756253 1 18.70131415 2.156282499 6.360111432 0.850413338 0.947678428 0.044287352 0.100504131 0.36474998 22.60634306 0.03599169 0.02653854 143.3119809 -2.156282499 0.09726509 RFS(ph)IPESGQGGTEMDGFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFSIPESGQGGTEMDGFRR 19 2 Q9Y572 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 RFS(1)IPESGQGGTEMDGFRR;RFS(1)IPESGQGGTEMDGFRR 162.82 1.40E-11 763830000 92436 77864 75281 88656 111566 96836 116812 96418 121518 TRUE FALSE 88066.73347 85798.43012 78732.70831 79744.13044 131023.0751 93482.54504 98990.184 87975.12878 140362.3908 0.627424006 0.61126367 0.560924532 0.568130323 0.933462834 0.666008498 0.705247206 0.626771376 1 17.0987969 2.810870656 24.99999505 0.753148369 0.597377085 0.389876188 0.116708585 170.8330799 59061.9164 0.032538055 0.034511818 646.9499089 -2.810870656 -0.155771284 RFS(ph)LFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFSLFGK 7 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RFS(1)LFGK;RFS(1)LFGK 133.23 0.0020165 395270000 906540 745140 772200 1053240 766890 849750 1154980 890190 674580 TRUE FALSE 863689.6508 821070.6132 807606.1338 947366.3142 900635.3732 820322.9444 978766.5883 812240.2444 779190.4211 1.108444903 1.05374834 1.036468252 1.215834138 1.155860427 1.052788795 1.256132727 1.042415592 1 19.57161642 3.265160319 24.99979221 1.138385083 1.069579954 0.062910913 0.080769277 408.1323318 383581.4775 0.020355561 0.027553343 1841.451643 -3.265160319 -0.068805128 RFS(ph)LSVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RFSLSVPR 8 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6R9X1 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)LSVPR;RFS(1)LSVPR;RFS(1)LSVPR 143.5 0.00036776 155300000 180199 137900 147606 179356 175751 150987 196788 167586 92329 TRUE FALSE 171681.3504 151952.1668 154373.8811 161326.7941 206401.9188 145758.2823 166764.3763 152911.2814 106646.9098 1.609810831 1.424815469 1.447523247 1.512718882 1.935376461 1.366737045 1.563705659 1.433808835 1 16.70248264 0.582485105 1.435223286 0.999888801 1.547124467 0.555324809 0.154270204 1.253543444 3.426214692 0.13816874 0.040404158 3.823711395 -0.582485105 0.547235665 RFS(ph)PSQVPIQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RFSPSQVPIQTR 12 1 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 RFS(0.977)PS(0.023)QVPIQTR;RFS(0.91)PS(0.09)QVPIQTR;RFS(0.986)PS(0.014)QVPIQTR;RFS(0.983)PS(0.017)QVPIQTR;RFS(1)PSQVPIQTR 168.67 2.81E-05 2627860000 1115085 967516 994438 1093138 1287325 1038109 1235323 1082460 1310941 TRUE FALSE 1062377.142 1066106.98 1040033.966 983253.6914 1511834.072 1002159.025 1046851.788 987674.0639 1514235.035 0.701593291 0.704056475 0.68683787 0.649340207 0.998414406 0.661825279 0.691340356 0.652259419 1 20.53015772 -1.38964953 3.081536328 1.003710179 0.716889977 0.431480207 0.101643608 17816221.34 22242001.96 587139.7542 0.025351067 0.040770916 1.38964953 -0.286820201 RFS(ph)VSPSSPSSQQTPPPVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSVSPSSPSSQQTPPPVTPR 21 1 A0A096LNH6;Q14185 A0A096LNH6 DOCK1 Dedicator of cytokinesis protein 1 1 RFS(0.987)VS(0.013)PSSPSSQQTPPPVTPR 188.86 1.45E-17 77597000 36192 30061 37007 36066 35852 32660 42164 43877 49089 TRUE FALSE 34481.27589 33124.25008 38703.80755 32440.57716 42104.57745 31528.97601 35731.10741 40034.89727 56701.47141 0.608119596 0.584186781 0.682589121 0.572129371 0.74256587 0.556052166 0.630161908 0.706064521 1 15.79109855 0.77937849 2.300203454 0.999849404 0.620734395 0.822150949 0.05456528 0.323358574 2.713464644 0.046475173 0.012583233 6.016978918 -0.77937849 -0.379115009 RFSDIQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 156.62 0.00062547 934550000 368370 300555 274365 316661 432157 325861 423605 410274 448907 FALSE TRUE 350957.8801 331181.8962 286944.9066 284829.6347 507525.044 314576.3519 358976.2772 374348.2336 518521.2049 0.676843834 0.638704634 0.553390881 0.54931145 0.978793228 0.606679821 0.692307805 0.721953567 1 18.98404346 -5 0.202406413 2.529051666 0.619787993 0.446043245 0.117399527 130.1615744 1.290197266 80.32305755 0.256929997 1.00E-05 5 -1.909263673 RFSEGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFSEGVLQS(0.999)PS(0.001)QDQEK 141.79 9.62E-07 188460000 209360 167230 190660 207240 148950 199840 233630 222740 187250 TRUE FALSE 199463.9677 184270.9271 199401.9496 186407.8415 174926.8328 192919.4907 197985.4526 203235.7048 216287.7737 0.92221564 0.851971075 0.921928902 0.861851034 0.808768937 0.891957448 0.91537977 0.939654153 1 17.72259259 1.147092886 1.364301958 0.996992558 0.876199317 0.596779721 0.033408539 0.278024585 1.02850578 0.030695113 0.009422087 14.03113768 -1.147092886 -0.120793241 RFSFS(ph)QR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RFS(0.416)FS(0.584)QR 91.085 0.017651 543230000 790680 608910 719390 783840 822700 717220 830660 734280 791660 TRUE FALSE 753306.1234 670958.6213 752374.7431 705046.914 966178.6195 692382.4916 703927.5609 669982.5505 914426.5896 0.823801639 0.733747934 0.822783099 0.771026261 1.056595062 0.757176683 0.769802157 0.732680522 1 19.80250783 -2.409844974 2.238777852 2.617099817 0.804510056 0.291451214 0.093681456 3642275.581 489377.5186 29764510.78 0.021696631 0.00389184 2.409844974 -1.812589761 RFSFSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 113.94 0.025216 0 77547 61536 70768 74650 89690 67394 82643 75605 99975 FALSE TRUE 73881.50699 67806.58836 74012.7828 67146.04017 105331.9076 65060.12888 70034.29251 68984.62539 115478.6124 0.639785199 0.587178759 0.640921996 0.581458668 0.912133471 0.563395485 0.606469813 0.597380103 1 16.81726615 -1.660382513 4.210970891 1.013492244 0.636751641 0.561715643 0.099568381 0.011943592 0.000963258 0.091296193 0.021104718 0.021858356 1.660382513 -0.376740604 RFSPS(ph)QVPIQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RFSPSQVPIQTR 12 1 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 RFS(0.184)PS(0.671)QVPIQT(0.145)R 79.337 0.024688 91024000 230580 220150 223490 264240 293800 186750 258910 210440 290510 TRUE FALSE 219680.9404 242583.5353 233737.2376 237678.0932 345038.627 180282.8007 219408.5243 192012.758 335560.8071 0.654668053 0.722919752 0.696557025 0.708301113 1.028244717 0.537258216 0.65385623 0.572214496 1 18.3562147 4.640121185 1.597690731 0.721841399 0.637064531 0.016128273 0.160963577 4.989581646 14.29713819 0.040242272 0.62390285 43663.76537 -4.640121185 -0.084776868 RFVEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 169.06 0.001645 1090100000 846270 773190 690500 870880 929430 791510 1014190 948950 952360 FALSE TRUE 806268.4942 851978.94 722160.108 783337.4878 1091522.298 764099.8102 859456.6886 865854.9073 1100047.125 0.732939959 0.774493129 0.656481065 0.712094482 0.992250489 0.694606434 0.781290791 0.787107105 1 20.0691339 -5 0.213737004 2.158444287 0.73167125 0.423555878 0.088227259 143.9838146 1.43718573 71.55576052 0.169417582 1.00E-05 5 -1.426773037 RFVNVVPTFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RFVNVVPTFGK 11 1 P62861;E9PR30 P62861 FAU 40S ribosomal protein S30 0 ; 111.63 0.0026207 352700000 1788190 1627880 1451030 1876280 1571680 1622570 1998570 1867310 1641770 FALSE TRUE 1703665.803 1793762.823 1517561.161 1687672.77 1845780.494 1566379.994 1693651.44 1703798.437 1896367.307 0.898383871 0.945894193 0.800246427 0.889950361 0.97332436 0.825989769 0.893103058 0.898453813 1 20.854807 0.696519472 4.021243158 0.999999463 0.892553347 0.32223658 0.049845978 9.171325522 120.431342 0.045342882 0.011579262 4.971866653 -0.696519472 -0.107446116 RGAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.101)S(0.511)S(0.365)PES(0.023)QHGGTQSPGGGQPLLQPTK 158.37 1.89E-14 383070000 191750 170740 182640 221870 187200 180340 257990 239010 200350 TRUE FALSE 182686.3575 188138.6001 191014.2247 199567.2061 219847.6207 174094.7806 218628.8872 218081.0173 231419.2548 0.789417275 0.812977297 0.825403335 0.86236215 0.949997099 0.752291683 0.944730755 0.94236332 1 17.82014938 2.059887362 0.176684957 1.059865403 0.707130841 0.550241135 0.054526911 3.064418444 0.428566609 0.292933109 0.417445276 114.7855876 -2.059887362 -0.352734563 RGAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.024)S(0.152)S(0.817)PES(0.006)QHGGT(0.001)QSPGGGQPLLQPTK 108.92 5.89E-06 417880000 155900 144600 129860 193460 151490 169270 203410 187390 159790 TRUE FALSE 148530.916 159334.9044 135814.2094 174013.0333 177909.808 163408.1375 172376.0686 170981.1382 184569.4171 0.804742835 0.863279014 0.735843519 0.942805347 0.963918133 0.885347855 0.933936246 0.926378491 1 17.49380399 3.214608653 24.99990013 0.935633621 0.815065626 0.704029875 0.042581843 126.2915438 131816.6392 0.011369615 0.013595933 1639.112089 -3.214608653 -0.120567995 RGAAGDWGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAAGDWGER 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 72.817 0.075123 147900000 137450 134260 191640 152100 266220 144540 161060 132030 295760 FALSE TRUE 130953.0109 147941.2466 200426.8836 136810.619 312648.6837 139534.5436 136487.3389 120468.7533 341624.9503 0.383323908 0.433051645 0.586686902 0.40047022 0.915181059 0.408443656 0.399523919 0.352634529 1 18.38205382 -1.684354984 2.877420031 1.064442555 0.478265658 0.488447443 0.165535885 63904252.53 60399448.17 30114045.96 0.042098521 0.020684499 1.684354984 -0.586176896 RGADDDRPSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RGADDDRPSWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;;; 104.17 0.0014822 1594606000 457935 399909 455255 522906 425559 475896 474897 466628 483985 FALSE TRUE 436289.3201 440660.1818 476128.8921 470342.4954 499776.3549 459415.6022 402442.7406 425767.5786 559038.9219 0.78042745 0.788245978 0.851691847 0.841341232 0.893992055 0.821795378 0.719883222 0.761606324 1 19.09258921 -2.360885714 2.402485305 2.447618293 0.803388043 0.601171503 0.049212531 2536928.837 589936.4704 20079824.97 0.01353518 0.004356265 2.360885714 -1.64423025 RGAEDDRGPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGAEDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 145.09 2.05E-05 1122100000 358071 299672 320102 373299 600770 342453 477745 378568 593180 FALSE TRUE 341145.6935 330208.9175 334778.9933 335774.2753 705544.0978 330593.7667 404856.2259 345418.579 685167.3249 0.497901288 0.481939091 0.488609105 0.490061716 1.029739849 0.482500777 0.590886651 0.504137554 1 19.38609683 -5 0.193389821 2.852896688 0.489157805 0.391443028 0.167223691 142.1963344 1.396640846 102.1037662 0.415463733 1.00E-05 5 -2.363738883 RGAEGPEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAEGPEAER 10 1 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 133.05 0.0003326 85204000 76774 63023 72904 88787 100150 78677 97085 82639 92656 FALSE TRUE 73145.04517 69445.11535 76246.72051 79861.96208 117616.1283 75952.39576 82272.90016 75402.69106 107024.6193 0.683441302 0.648870473 0.712422254 0.746201786 1.098963296 0.709672188 0.768728735 0.704535943 1 16.70758318 3.101253212 4.016041385 0.831599294 0.675098118 0.281224368 0.124095117 0.303307409 9.108858049 0.035453645 0.042969736 1262.563447 -3.101253212 -0.156501176 RGAEVHLVPWNHDFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAEVHLVPWNHDFTK 16 1 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 98.035 0.0011675 320780000 340090 242980 275610 273610 345250 232550 311790 260110 172160 FALSE TRUE 324014.6197 267739.9382 288246.9911 246106.203 405461.4907 224496.7352 264220.7091 237333.3895 198857.6935 1.629379351 1.346389639 1.449513901 1.237599605 2.038952999 1.128931605 1.328692415 1.193483567 1 17.60137685 1.442968015 1.190913375 1.040896311 1.491526488 0.325883016 0.239687611 0.502199308 1.379534264 0.198833471 0.067778489 27.73115861 -1.442968015 0.450630177 RGAGAELKDTQS(ph)PSTCSEGLLGWSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGAGAELKDTQSPSTCSEGLLGWSQK 26 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RGAGAELKDT(0.045)QS(0.794)PS(0.07)T(0.07)CS(0.021)EGLLGWSQK;RGAGAELKDT(0.115)QS(0.877)PS(0.008)TCSEGLLGWSQK;RGAGAELKDT(0.379)QS(0.62)PS(0.001)T(0.001)CSEGLLGWSQK 283.77 2.61E-61 821470000 1333450 789990 1293940 1229650 918430 1360710 1788420 1481630 1170970 TRUE FALSE 1270420.461 870490.8791 1353268.429 1106043.246 1078603.901 1313588.272 1515563.682 1351890.623 1352558.047 0.939272413 0.643588555 1.000525214 0.817741795 0.797454796 0.971188094 1.120516554 0.999506546 1 20.36725908 2.078120602 4.273233767 1.052346048 0.82901325 0.465881045 0.098736555 0.16292074 5.685732912 0.037745255 0.026532605 119.7072908 -2.078120602 -0.223332798 RGAPS(ph)SPATGVLPSPQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGAPSSPATGVLPSPQGK 18 1 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 RGAPS(0.496)S(0.496)PAT(0.001)GVLPS(0.006)PQGK 109.85 0.00021475 85745000 88843 71995 80564 99451 85619 96483 116110 97639 98625 TRUE FALSE 84643.56746 79331.37235 84257.93909 89453.99654 100550.9265 93141.76952 98395.28699 89089.21154 113919.2613 0.743013662 0.696382433 0.739628559 0.785240314 0.882650795 0.817612127 0.863728275 0.782038178 1 16.79765217 -4.999998559 0.039230611 2.106620685 0.139484444 0.741618935 0.044190415 393.6126869 1.153852823 51.50397053 15.85075921 1.00E-05 4.999998559 -1.967136241 RGAQPGRHS(ph)VTGYGDCAVGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGAQPGRHSVTGYGDCAVGAR 21 2 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 RGAQPGRHS(0.999)VT(0.001)GYGDCAVGAR;RGAQPGRHS(1)VTGYGDCAVGAR;RGAQPGRHS(0.999)VT(0.001)GYGDCAVGAR;RGAQPGRHS(1)VTGYGDCAVGAR 253.7 1.19E-36 765700000 137912 78955 121678 122682 151753 132454 170914 133577 169075 TRUE FALSE 131393.1731 87000.60426 127257.0567 110349.7723 178218.6752 127867.0848 144837.9302 121880.2897 195294.2875 0.672795783 0.445484634 0.651616892 0.565043523 0.912564712 0.654740527 0.741639359 0.624085278 1 17.57529022 2.777045338 24.52491071 0.757516627 0.574360209 0.376598258 0.126408034 463.4566592 295343.1 0.034851854 0.036965271 598.4740686 -2.777045338 -0.183156418 RGAS(ph)GSIFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGASGSIFSK 10 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 RGAS(0.94)GS(0.06)IFSK;RGAS(0.998)GS(0.002)IFSK;RGAS(0.999)GS(0.001)IFSK 125.95 0.00024233 611995000 1696830 1330110 1457980 1684000 2194610 1297580 1789970 1456410 2155010 TRUE FALSE 1616624.209 1465649.721 1524829.825 1514721.121 2577349.289 1252644.479 1516877.201 1328879.019 2489197.945 0.649455867 0.588804006 0.612578774 0.608517745 1.035413554 0.503232168 0.60938392 0.533858315 1 21.24724953 -2.127732856 2.503486284 1.752777559 0.639552081 0.371700035 0.145958464 7348392.555 2680144.972 31351528.06 0.033537948 0.007451902 2.127732856 -1.113225478 RGAS(ph)S(ph)SPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGASSSPQR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RGAS(0.843)S(0.923)S(0.233)PQR 52.79 0.097473 197520000 265150 287360 291410 319270 285510 254840 306940 311750 331950 TRUE FALSE 252616.885 316642.3107 304771.4367 287176.373 335302.8536 246014.8269 260110.6657 284451.5173 383427.1106 0.658839393 0.825821393 0.79486147 0.74897253 0.874489164 0.641620845 0.678383605 0.741865949 1 18.54859282 -0.818937679 4.183571518 1.000002865 0.743511652 0.542962838 0.073327368 18387100.24 41095191.82 848.2478167 0.017751984 0.151726808 0.818937679 -0.256491214 RGAS(ph)SS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGASSSPQR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RGAS(0.81)S(0.204)S(0.986)PQR 86.996 0.0091966 201940000 426880 465480 449920 491940 422390 434630 466700 454740 516380 TRUE FALSE 406702.2284 512912.9412 470549.277 442489.2566 496054.6823 419578.6541 395496.3435 414920.5549 596457.5731 0.681862796 0.859931979 0.788906535 0.741862081 0.831668009 0.703450963 0.663075399 0.695641356 1 19.18605999 2.220202212 24.97295214 0.728279799 0.781226576 0 0.105401779 745.0150118 1013438.014 0.035530094 0.026291482 166.035981 -2.220202212 0.052946777 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGAYGGGYGGYDDYNGYNDGYGFGSDR 27 1 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 275.6 1.13E-60 1234670000 372555 284688 344054 379402 417800 340599 439160 373102 412411 FALSE TRUE 354945.0635 313698.0309 359829.2162 341263.7901 490664.1877 328803.9712 372158.0763 340431.2109 476365.5916 0.745110625 0.658523698 0.755363575 0.716390512 1.030016014 0.690234511 0.781244663 0.714642739 1 18.86170968 -5 0.187038559 1.99956176 0.710449437 0.339073813 0.102582762 152.003754 1.480313239 56.90119086 0.274489175 1.00E-05 5 -1.289112323 RGDDSFGDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;;; 191.79 9.44E-07 5478842000 3034209 2110636 1818640 1950805 2680290 2122537 3490399 2630235 2855435 FALSE TRUE 2890787.954 2325712.208 1902026.443 1754706.375 3147731.727 2049033.011 2957874.527 2399917.68 3298241.276 0.876463458 0.705137076 0.576678988 0.532012739 0.954366726 0.621250188 0.896803563 0.727635573 1 21.65326551 1.686904964 9.280937088 0.857870247 0.720527562 0.220579203 0.143043618 0.210685431 30.17628509 0.066134458 0.035395793 48.6300778 -1.686904964 -0.137342686 RGDDWNDREWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RGDDWNDREWDR 12 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;; 190.1 3.98E-06 2257672000 669536 547042 619333 645429 697260 593194 768353 596971 801673 FALSE TRUE 637888.3602 602786.2017 647730.0307 580549.2507 818861.9232 572651.543 651126.6381 544697.0545 925992.3545 0.688870008 0.650962396 0.699498249 0.626948212 0.884307434 0.618419299 0.703166322 0.588230618 1 19.82064076 -1.256053573 4.781304008 1.000087752 0.683559263 0.604649945 0.080667116 6.67E-05 1.04E-05 0.069075158 0.016276673 0.05545573 1.256053573 -0.316528489 RGDESQFLLQAPGSTELEELTVQVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGDESQFLLQAPGSTELEELTVQVAR 26 1 Q9NX33;C9JX57;D3DSE6;C9J818;A0A669KBI0;A0A669KAZ0;A0A669KAW7;A0A5F9ZHZ7;A0A669KAW9;A0A669KAY3;P57076 Q9NX33 C21orf59 UPF0769 protein C21orf59 0 105.17 0.00523 24217000 16918 14515 19478 13840 24982 14415 20951 17687 24785 FALSE TRUE 16118.31967 15994.095 20371.08557 12448.77691 29338.85289 13915.80494 17754.54016 16138.23252 28628.53122 0.563015949 0.558676758 0.711565865 0.434838127 1.02481167 0.486081693 0.62016944 0.563711508 1 14.80516603 -1.795379488 2.64585502 1.110591538 0.615039916 0.352534519 0.161547131 18922909.4 14082947.99 13488458.94 0.035163105 0.016018451 1.795379488 -0.495551622 RGDIIGVQGNPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGDIIGVQGNPGK 13 1 Q15046;Q15046-2;H3BVA8;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 ; 162.48 1.61E-06 330170000 1029890 851190 977340 1083860 844790 977830 1183740 1120050 1072420 FALSE TRUE 981209.1407 937927.2287 1022152.006 974908.3336 992121.1085 943967.5019 1003138.722 1021972.484 1238725.416 0.792111898 0.757171215 0.825164312 0.787025374 0.800920927 0.762047415 0.809815241 0.825019387 1 20.240425 0.50705584 1.206782647 1.00012992 0.786245355 0.917694055 0.019608336 0.468601325 0.892954717 0.017655095 0.005347234 3.214073763 -0.50705584 -0.213884564 RGDLIIEFEVIFPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGDLIIEFEVIFPER 15 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 120.29 0.00023316 49153200 72290 64800 70635.3 72562.1 75038 70358 101834 75044.3 76526.9 FALSE TRUE 68872.99496 71403.19367 73873.99837 65268.01985 88124.60344 67921.48482 86297.35299 68473.02326 88394.30081 0.779156511 0.807780513 0.835732595 0.73837362 0.996948928 0.768392127 0.976277341 0.774631652 1 16.43166573 -4.999989579 0.036318477 1.86245517 0.309929802 0.301178133 0.084410234 1041.800874 2.834188818 103.4615713 34.72308339 1.00E-05 4.999989579 -1.552525368 RGDLPFVVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGDLPFVVPR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 199.68 4.40E-07 6974170000 2355576 1782085 1856578 2224938 2299846 1908721 2666580 2229353 2367020 FALSE TRUE 2244232.591 1963681.488 1941703.938 2001283.005 2700938.414 1842621.513 2259744.246 2034139.033 2734085.373 0.820834862 0.718222447 0.710184092 0.731975316 0.9878764 0.673944395 0.826508297 0.743992508 1 21.38262686 -5 0.346639173 3.524035288 0.768677762 0.381890903 0.088802475 425.7246703 3.520381527 797.5664535 0.062591245 1.00E-05 5 -2.755357525 RGDPFTDLCFLNS(ph)PIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGDPFTDLCFLNSPIFK 17 1 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 RGDPFTDLCFLNS(1)PIFK;RGDPFTDLCFLNS(1)PIFK 101.05 0.00072402 264850000 1252910 1128630 1256280 1376200 1019340 1268120 1554540 1521580 1132820 TRUE FALSE 1193687.427 1243638.68 1313881.681 1237861.761 1197112.573 1224204.686 1317366.372 1388342.389 1308491.94 0.912261964 0.950436638 1.004119048 0.946021694 0.914879593 0.93558443 1.006782183 1.061024792 1 20.31947361 1.616624352 4.015289346 1.031375683 0.943576709 0.62672071 0.028956652 0.110655996 4.11336163 0.017124826 0.00762872 41.36417357 -1.616624352 -0.087798974 RGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(0.989)ES(0.063)EEDEQDS(0.948)EEVR;RGDS(0.999)ES(0.443)EEDEQDS(0.558)EEVR 232.7 4.00E-17 762220000 1069890 931650 994010 1086930 912040 1026390 1152500 991410 894470 TRUE FALSE 1019318.42 1026586.194 1039586.342 977669.7314 1071099.487 990845.8569 976664.9579 904596.8846 1033179.839 0.98658373 0.993618105 1.006200762 0.94627256 1.036701885 0.959025544 0.945300054 0.875546396 1 19.97865997 1.894887002 3.129489409 0.93383543 0.991796279 0.294183173 0.037221818 0.27279014 4.67719115 0.017024836 0.009130459 78.50313528 -1.894887002 0.057960849 RGDS(ph)QECSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.848)QECS(0.152)PR 128.68 0.00034248 27032000 47477 44517 47357 54878 46532 47495 60256 49098 59168 TRUE FALSE 45232.8563 49053.33291 49528.36529 49361.55918 54647.16607 45850.23624 51062.84052 44798.71884 68343.47125 0.661846047 0.717747168 0.72469783 0.722257127 0.799595997 0.670879535 0.747150234 0.655493758 1 16.06051591 -1.311826826 4.655377885 1.000179047 0.713796737 0.815536642 0.04297284 7.35E-05 1.09E-05 0.038278188 0.009016649 0.048772293 1.311826826 -0.28638231 RGDTVATLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 599600000 252256 192165 218685 228020 354426 185759 255496 206857 225603 FALSE TRUE 240332.3588 211746.832 228711.9236 205098.9964 416237.7822 179326.1193 216515.3927 188743.5045 260588.361 0.922268201 0.812572101 0.87767513 0.787061232 1.597299974 0.688158591 0.830871309 0.724297523 1 17.99141312 -2.617410156 1.99844001 2.727502035 0.899286651 0.013011524 0.255649223 9993440.823 606209.9216 78148331.53 0.058302081 0.002413181 2.617410156 -1.828215384 RGDTWHDRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGDTWHDRDR 10 2 Q9UBU9;Q9UBU9-2;E9PIN3;E9PMV7;E9PLA7 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 ;; 117.52 0.00053249 107299000 48449 29686.8 29036.5 30815.3 57457 25960.8 53270 37301.9 53888 FALSE TRUE 46158.91179 32711.91867 30367.85225 27717.6875 67477.48261 25061.77099 45142.68313 34035.54789 62244.67582 0.741572049 0.525537618 0.487878712 0.445302142 1.084068344 0.402633168 0.725245694 0.546802557 1 15.92566282 -2.004136361 2.305549817 1.386950787 0.621421966 0.268007272 0.197410877 10084814.79 3763175.849 20703402.19 0.043463289 0.009905209 2.004136361 -0.765528821 RGEAGWEGGYPEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGEAGWEGGYPEIVK 15 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 79.317 0.015868 0 232360 179370 219820 233650 203420 248630 304820 256940 147730 FALSE TRUE 221376.8033 197648.0069 229898.9644 210163.0581 238896.3836 240019.8808 258314.1106 234440.9715 170639.2139 1.297338392 1.158280107 1.347280963 1.231622282 1.400008698 1.406592748 1.513802746 1.373898567 1 17.3805897 3.615022409 5.723833132 1.360937433 1.22822312 0.029047877 0.14296217 0.415688942 17.68078164 0.035880039 0.056019384 4121.187831 -3.615022409 -0.132714314 RGEAHLAVNDFELAR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 200.77 4.38E-09 6070900000 2932320 2348630 2467080 2829800 2918610 2566540 3273500 2740050 2973640 FALSE TRUE 2793715.045 2587958.067 2580198.058 2545343.128 3427614.66 2477660.076 2774067.453 2500116.696 3434776.904 0.813361427 0.753457398 0.751198151 0.741050496 0.997914786 0.721345271 0.807641233 0.727883285 1 21.71178497 -1.060855064 4.248510748 1.000020233 0.789442656 0.40550639 0.080201217 9695854.123 2421059.518 1931.017514 0.01705107 0.086925047 1.060855064 -0.210577577 RGEDVETSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGEDVETSKK 10 2 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 139.86 2.27E-05 1639890000 2683490 2166290 2144550 2692840 1466610 2640750 2989920 2894000 1826970 FALSE TRUE 2556646.746 2387037.414 2242879.739 2422150.607 1722386.32 2549300.165 2533752.79 2640586.018 2110287.177 1.211516032 1.131143401 1.062831525 1.14778246 0.816185749 1.208034714 1.200667292 1.251292263 1 21.00900791 -0.260636626 7.404609176 0.999999925 1.131815072 0.097309323 0.122842769 0 0 0.11521722 0.027156959 0.5487359 0.260636626 0.131815147 RGEEGHDPKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGEEGHDPKEPEQLR 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 196.64 5.30E-09 1172870000 602440 582530 597970 626290 455270 616280 735450 730460 450690 FALSE TRUE 573963.8551 641890.4693 625387.516 563334.1393 534668.9439 594938.0691 623243.595 666497.05 520580.7034 1.102545391 1.233027781 1.201326734 1.082126432 1.027062548 1.142835424 1.197208408 1.280295343 1 18.98976231 4.760327174 22.44180655 1.154288981 1.102545176 0.014057902 0.089108112 896.8041909 1948527.231 0.020501289 0.256379762 57587.36054 -4.760327174 -0.051743805 RGEEGHDPKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGEEGHDPKEPEQLRK 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 116.06 0.00027403 158460000 196130 139900 188690 180130 125940 193700 205240 211720 112720 FALSE TRUE 186859.3236 154155.9691 197341.6231 162022.9902 147903.8961 186992.1204 173926.8685 193180.6744 130200.0419 1.435170994 1.183993237 1.515680181 1.244415807 1.135974259 1.436190939 1.335843414 1.48372206 1 16.99037039 4.749844799 10.9628678 1.309108902 1.43539874 0.063192594 0.161723039 0.205530168 1066.692711 0.034125865 0.196619736 56214.04008 -4.749844799 0.126289838 RGEFCIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGEFCIAK 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 113.62 0.0045108 3260730000 3930230 2886300 1823720 2165940 3241680 2434510 4497470 3277190 3425210 FALSE TRUE 3744455.817 3180417.251 1907339.366 1948215.596 3807027.966 2350202.308 3811298.35 2990221.87 3956374.073 0.946436244 0.803871725 0.482092778 0.492424518 0.962251773 0.594029347 0.963331141 0.755798571 1 21.91574741 1.698590755 11.04475141 0.89313025 0.734117547 0.203431204 0.176023028 0.233941556 49.45990961 0.084681721 0.046065648 49.95635636 -1.698590755 -0.159012703 RGEGDAPFSEPGT(ph)TSTQRPSSPETATK ddPTM_SK-BR-3_Trastuzumab_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(0.018)EPGT(0.47)T(0.11)S(0.184)T(0.145)QRPS(0.063)S(0.01)PETATK 151.37 1.36E-07 1208100000 1026000 1037600 803160 1189000 631250 1019500 988660 1038300 687500 TRUE FALSE 977503.0133 1143332.62 839985.6804 1069479.461 741339.8001 984194.4594 837821.759 947380.9476 794113.9887 1.230935391 1.43975882 1.057764619 1.346758118 0.933543308 1.239361695 1.055039668 1.193003726 1 19.59898658 3.374283248 1.357758694 1.106863211 1.325198529 0.249327361 0.136554117 0.473758689 1.807500287 0.041267677 0.070277459 2367.463261 -3.374283248 0.218335318 RGEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFSEPGT(0.013)T(0.074)S(0.081)T(0.086)QRPS(0.81)S(0.93)PET(0.006)ATK 85.619 0.0045353 156460000 75552 92076 78206 89077 47184 76770 78267 93452 61610 TRUE FALSE 71980.80669 101458.6491 81791.82246 80122.81072 55412.87466 74111.43565 66325.93168 85268.84746 71164.16414 1.011475474 1.425698599 1.149340029 1.125887049 0.778662622 1.041415108 0.932013078 1.198199241 1 16.11886331 3.057304121 3.483810492 0.983309541 1.217969127 0.293419783 0.144324898 0.245965997 6.120678295 0.041313958 0.049279943 1141.048543 -3.057304121 0.234659586 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTT(0.001)S(0.029)T(0.105)QRPS(0.431)S(0.431)PET(0.003)ATK;RGEGDAPFSEPGTTS(0.004)T(0.015)QRPS(0.696)S(0.284)PET(0.001)ATK;RGEGDAPFSEPGTTSTQRPS(0.496)S(0.496)PET(0.007)AT(0.001)K;RGEGDAPFSEPGT(0.092)T(0.092)S(0.092)T(0.092)QRPS(0.284)S(0.284)PET(0.027)AT(0.038)K;RGEGDAPFSEPGTTS(0.009)T(0.041)QRPS(0.588)S(0.361)PETATK;RGEGDAPFSEPGTTSTQRPS(0.617)S(0.382)PETATK;RGEGDAPFSEPGT(0.016)T(0.083)S(0.083)T(0.083)QRPS(0.362)S(0.362)PET(0.011)ATK;RGEGDAPFSEPGTTST(0.001)QRPS(0.489)S(0.489)PET(0.02)AT(0.001)K 247.36 7.23E-46 6767470000 2441064 2267012 2071956 2597979 1461037 2349110 2326715 2347771 1500895 TRUE FALSE 2325679.742 2498023.1 2166957.232 2336825.215 1715841.39 2267759.732 1971731.894 2142187.725 1733646.131 1.341496226 1.440907147 1.249942069 1.347925146 0.989729887 1.308086864 1.137332388 1.235654547 1 20.72537802 6.706515795 0.097697447 0.844380089 2.235281165 0.470345696 0.107543162 74.63533449 0.686679853 1.514743084 13.912136 5087633.226 -6.706515795 1.390901076 RGEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTTSTQRPS(0.084)S(0.916)PET(0.001)ATK;RGEGDAPFSEPGTTSTQRPS(0.189)S(0.811)PETATK;RGEGDAPFSEPGTTSTQRPS(0.327)S(0.673)PETATK;RGEGDAPFSEPGTTSTQRPS(0.354)S(0.646)PETATK 283.27 1.58E-61 5405630000 3235940 3129980 2754150 3671910 1971800 3266010 3210700 3341480 2041530 TRUE FALSE 3082983.529 3448928.52 2880430.502 3302802.631 2315681.296 3152907.255 2720848.746 3048882.297 2358120.046 1.307390408 1.462575464 1.22149443 1.400608352 0.982003143 1.337042726 1.153821135 1.292929214 1 21.16920573 0.549722365 0.039884176 1.88E-13 2.30355436 0.348629101 0.127333416 125.5044987 2.252555979 70.42649489 58.5811611 3.545866373 -0.549722365 2.30355436 RGEIIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGEIIAK 7 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 106.38 0.01237 1857370000 4224740 3388610 3748470 4336710 3215280 3962400 4396020 4241170 3541280 FALSE TRUE 4025044.913 3733913.212 3920341.057 3900775.672 3776023.814 3825181.094 3725326.411 3869790.671 4090443.616 0.984011831 0.912838206 0.958414643 0.953631449 0.92313308 0.935150672 0.910738971 0.946056476 1 21.96382588 0.963961127 23.3211858 1.000000001 0.938267763 0.419849735 0.022054808 2494.833116 1614439.601 0.020844266 0.005211066 9.203671865 -0.963961127 -0.061732238 RGEVPAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGEVPAELR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 121.61 0.00097667 191700000 101450 104890 78661 108480 93420 93896 105410 91915 87386 FALSE TRUE 96654.65955 115578.4103 82267.68466 97575.3843 109712.4184 90644.35798 89327.76851 83866.43533 100937.3746 0.957570572 1.145050688 0.815036898 0.966692315 1.086935527 0.898025715 0.884982088 0.830875934 1 16.62310094 2.132267741 10.00767837 0.89235872 1.002020253 0.177535868 0.095034024 0.458235088 39.9872167 0.034612808 0.025560155 135.6025139 -2.132267741 0.109661533 RGFCFITYTDEEPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGFCFITYTDEEPVKK 16 2 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 221.49 5.91E-15 313060000 785620 740870 727270 785670 516530 857030 911430 931290 582610 FALSE TRUE 748485.2995 816365.4953 760616.0489 706692.9589 606612.6685 827350.8362 772374.6139 849741.3105 672958.1832 1.112231515 1.213099886 1.130257522 1.050129082 0.901412129 1.229423844 1.147730473 1.262695561 1 19.36015733 -0.294747656 7.335475366 0.999997682 1.133332317 0.139385111 0.102036514 0 0 0.09652531 0.022751234 0.507285377 0.294747656 0.133334635 RGFEVVYMTEPIDEYCVQQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGFEVVYMTEPIDEYCVQQLK 21 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 194.25 6.98E-18 96122000 57906 50824 59504 63951 54940 61945 79960 69359 66482 FALSE TRUE 55168.89814 56003.02338 62232.31726 57522.52398 64521.51861 59799.82912 67760.63343 63285.55826 76791.68902 0.718422773 0.729284954 0.81040433 0.749072259 0.840214865 0.778727879 0.882395404 0.824119889 1 16.22866256 -4.999999975 0.055880956 1.888477439 0.3895664 0.841364143 0.03301601 137.2258953 0.563028507 16.97071294 3.194452023 1.00E-05 4.999999975 -1.498911039 RGFGFVTFDDHDPVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGFGFVTFDDHDPVDK 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 108.56 0.00067567 1286290000 3508830 3032150 2913660 3731060 2285590 3371160 3536250 3683330 1950790 FALSE TRUE 3342974.56 3341129.532 3047254.193 3356006.76 2684196.172 3254415.884 2996730.115 3360798.099 2253308.55 1.483584909 1.482766101 1.352346616 1.489368493 1.191224421 1.444283289 1.329924441 1.49149485 1 21.10361345 -3.55425778 0.228610319 5.79E-14 1.464634258 0.622581814 0.098306601 46.93171532 0.851244355 22.38800786 0.161414784 0.000279089 3.55425778 1.464634258 RGFS(ph)DSGGGPPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGFSDSGGGPPAK 13 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 1 RGFS(0.996)DS(0.004)GGGPPAK 94.569 0.0031206 179100000 156610 129580 137390 144180 98454 148420 163870 139950 134010 TRUE FALSE 149207.3557 142784.3493 143689.4674 129686.7525 115624.3464 143280.1782 138868.6218 127695.2361 154791.5864 0.963924197 0.922429653 0.928276987 0.837815255 0.746967901 0.925632856 0.897132881 0.824949463 1 17.23996753 3.351520694 5.970557527 0.867258172 0.940197429 0.178811757 0.066633878 0.320749255 15.59706562 0.017620401 0.023926908 2246.573822 -3.351520694 0.072939257 RGFVFITFKEEEPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGFVFITFKEEEPVKK 16 3 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 152.68 2.30E-07 741780000 1050790 757420 850060 914280 665820 939220 1112880 1060720 719860 FALSE TRUE 1001121.239 834601.9591 889036.0918 822374.8374 781938.7972 906694.5759 943089.7166 967837.7336 831492.2123 1.204005551 1.003739959 1.069205554 0.989034925 0.940404234 1.090442655 1.134213529 1.163976907 1 19.66534323 -0.80155005 7.883064654 1.000000006 1.07428176 0.077030687 0.080910514 0 0 0.07955733 0.018751842 0.15792466 0.80155005 0.074281754 RGGADVNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 135.86 0.00033513 643870000 843360 630700 674860 784810 893240 769540 903000 810780 939680 FALSE TRUE 803496.0442 694969.047 705802.9985 705919.4078 1049020.773 742890.6368 765230.7653 739783.805 1085400.775 0.740275908 0.640287959 0.650269481 0.650376731 0.966482425 0.684439014 0.705021392 0.681576632 1 20.04979641 -5 0.377122414 4.978110383 0.704312161 0.469668842 0.094721185 513.9142557 3.87671211 1670.757501 0.06178507 1.00E-05 5 -4.273798222 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 285.64 7.46E-74 800460000 251951 203401 203419 255478 250966 209323 261955 238520 281875 FALSE TRUE 240041.7755 224127.7931 212745.9624 229796.8661 294734.3909 202074.092 221988.9536 217633.9243 325586.7354 0.737259076 0.688381217 0.65342331 0.705793084 0.905240782 0.62064596 0.681812032 0.66843609 1 18.3126824 -1.013368477 4.771871413 1.000004209 0.706183129 0.588930944 0.076757713 4.44E-06 9.19E-07 0.070264757 0.016561238 0.096968689 1.013368477 -0.29382108 RGGFNT(ph)FRDRENY(ph)DR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGGFNTFRDRENYDR 15 3 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 2 RGGFNT(1)FRDRENY(1)DR 40.496 0.082842 67934000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 RGGGS(ph)GGGEES(ph)EGEEVDED ddPTM_SK-BR-3_Trastuzumab_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 234 2.67E-24 2090700000 1392300 1132690 1295970 1375770 1087350 1307290 1493450 1315500 1153690 TRUE FALSE 1326488.738 1248112.399 1355391.506 1237474.986 1276983.496 1262018.22 1265596.773 1200307.846 1332598.353 0.995415262 0.936600586 1.017104294 0.928618126 0.958265852 0.947035704 0.9497211 0.900727397 1 20.34581058 3.19326854 24.99999954 0.945737586 0.974857104 0.203258791 0.031813611 210.8945891 116407.3792 0.008275277 0.009890885 1560.517129 -3.19326854 0.029119518 RGGGSGGGEES(ph)EGEEVDED ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGS(0.001)GGGEES(0.999)EGEEVDED 315.06 1.24E-61 16262370000 7013003 5619955 6129891 6674592 5646757 6646637 7622512 6935348 6015982 TRUE FALSE 6681512.247 6192634.804 6410952.566 6003649.331 6631549.633 6416462.294 6459557.797 6328052.163 6948909.763 0.961519501 0.891166387 0.922583943 0.863969966 0.954329508 0.923376834 0.929578598 0.910653956 1 22.72835522 -4.999992251 0.438879947 2.682915415 0.918805572 0.445941666 0.028080513 1053.47139 6.367828602 1718.276042 0.014225887 1.00E-05 4.999992251 -1.764109843 RGGIPAS(ph)PIDPFQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGGIPASPIDPFQSR 15 1 Q96LD4;Q96LD4-2 Q96LD4 TRIM47 Tripartite motif-containing protein 47 1 RGGIPAS(1)PIDPFQSR;RGGIPAS(1)PIDPFQSR;RGGIPAS(1)PIDPFQSR;RGGIPAS(1)PIDPFQSR 126.04 5.31E-05 1367630000 531583 354976 483336 489412 561900 447576 574791 478532 535007 TRUE FALSE 506456.1251 391148.458 505497.4337 440215.3759 659895.1821 432076.3309 487096.0762 436629.2012 617973.1531 0.819543895 0.632953804 0.817992547 0.712353561 1.067837945 0.699183013 0.788215594 0.706550437 1 19.23718464 -2.587206065 2.167390126 5.222201299 0.774703866 0.254849356 0.117531856 4136731.538 236872.7358 86475005.91 0.028333136 0.002586985 2.587206065 -4.447497433 RGGPNYQEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGGPNYQEGLR 11 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 189.56 4.26E-06 5091800000 2555740 1883670 2128470 2337390 2594970 2135040 2852090 2553380 3068230 FALSE TRUE 2434935.235 2075618.115 2226062.455 2102431.116 3047531.946 2061103.029 2416951.288 2329792.511 3544035.438 0.687051605 0.585665169 0.628115179 0.593230839 0.859904479 0.581569532 0.681977178 0.65738409 1 21.7569616 -5 0.323666528 4.343758675 0.641277767 0.639391553 0.080435378 199.852213 1.754420076 458.4398855 0.063851833 1.00E-05 5 -3.702480908 RGGPPFAFVEFEDPRDAEDAVYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGGPPFAFVEFEDPRDAEDAVYGR 24 2 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 87.659 0.0062837 48218000 45318 21365 39959 37864 69451 35777 70221 46522 86099 FALSE TRUE 43175.90795 23542.11779 41791.15967 34057.83878 81563.23241 34538.03352 59507.49675 42448.28705 99450.79319 0.434143425 0.236721267 0.420219471 0.342459197 0.82013657 0.347287663 0.598361208 0.426827034 1 16.60169526 -4.999999994 0.142591419 2.957644892 0.246975925 0.5660981 0.154310946 91.28677148 0.791208512 50.59683735 0.816244579 1.00E-05 4.999999994 -2.710668967 RGGS(ph)DTNLNFDVPDGILDFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGGSDTNLNFDVPDGILDFHK 21 1 G3V207;Q9ULS5;F8VQF2 G3V207 TMCC3 Transmembrane and coiled-coil domains protein 3 1 RGGS(0.992)DT(0.008)NLNFDVPDGILDFHK;RGGS(0.998)DT(0.002)NLNFDVPDGILDFHK 246.63 1.21E-30 67410000 81335 59020 71031 97888 74745 73061 97543 85002 73113 TRUE FALSE 77490.45574 65034.2051 74287.84161 88048.11226 87780.50433 70530.87925 82661.02385 77558.77426 84450.99063 0.917579002 0.770082205 0.879656249 1.042594191 1.039425395 0.835169354 0.978804668 0.918387975 1 16.36582673 3.457996054 17.17040857 0.962692895 0.840670344 0.378914825 0.069158682 6.218251297 5581.610095 0.01850168 0.025081938 2870.754496 -3.457996054 -0.122022551 RGHDDLGDHYLDCGDLSNALK ddPTM_SK-BR-3_Trastuzumab_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 43.116 0.078286 33744000 32999 28397 33064 37406 30097 32674 43383 31341 12690 FALSE TRUE 31439.20267 31290.68658 34580.0171 33645.87781 35345.90727 31542.49119 36764.12657 28596.61589 14657.90039 2.144863987 2.134731834 2.359138498 2.295409091 2.411389512 2.151910598 2.508144113 1.950935341 1 13.83939084 0.917744767 5.702539109 1.000056291 2.272550468 0.91719425 0.121582536 0.185501011 12.4805942 0.121549271 0.030602982 8.274557279 -0.917744767 1.272494177 RGHHDDS(ph)DEEASPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGHHDDSDEEASPEK 15 1 Q5VT06;H0Y6Q4 Q5VT06 CEP350 Centrosome-associated protein 350 1 RGHHDDS(1)DEEASPEK 131.71 2.44E-05 125100000 73669 76850 75341 86562 56919 80952 89200 74285 18568 TRUE FALSE 70186.81237 84681.10237 78795.45937 77860.6233 66845.65558 78148.61194 75590.90173 67780.21159 21447.43061 3.272504462 3.948309889 3.673888067 3.630300744 3.116720916 3.643728397 3.524473542 3.160295181 1 14.3885172 0.55861656 1.614841509 0.999808728 3.571742558 0.925073232 0.225766205 0.521243629 1.628956864 0.210215607 0.060025951 3.619233139 -0.55861656 2.57193383 RGILTLK ddPTM_SK-BR-3_Trastuzumab_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 ; 155.38 0.0025898 10949600000 10242300 7743800 6234000 7203600 8021200 7163700 11821800 8526900 10074700 FALSE TRUE 9758166.777 8532902.024 6519835.066 6479480.442 9420094.74 6915619.273 10018167.29 7780239.432 11637033.02 0.83854422 0.733254087 0.560266097 0.556798321 0.809492825 0.594276845 0.860886729 0.668575866 1 23.47221994 -0.080734015 0.662772513 1.014959228 0.70353621 0.409611236 0.111300921 5.750793947 2.606740962 0.34152847 0.041471422 0.830359168 0.080734015 -0.311423018 RGKNENESEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGKNENESEKR 11 3 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 212.09 3.12E-09 71833000 111179 60953 107195 88175 87850 111150 144443 128913 109212 FALSE TRUE 105923.789 67164.18 112109.9968 79311.48148 103171.0122 107300.8476 122405.5675 117624.6943 126148.0392 0.839678442 0.532423496 0.888717712 0.628717513 0.817856646 0.850594653 0.9703327 0.93243379 1 16.94475826 2.14590149 1.34419943 0.975261704 0.710248713 0.515169546 0.101768539 0.314101752 1.081097748 0.060715249 0.032277172 139.9269895 -2.14590149 -0.265012991 RGLDDDRGPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGLDDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 102.4 0.0016162 700823000 195508 102996 175724 136885 284427 159299 254533 194343 330981 FALSE TRUE 186266.7243 113491.4095 183781.1192 123125.0597 334030.9787 153782.4357 215699.316 177325.2966 382307.8431 0.487216592 0.296858701 0.480715012 0.322057373 0.873722537 0.402247661 0.56420322 0.463828561 1 18.54437527 -4.999999999 0.178848677 3.130772324 0.365081105 0.519938961 0.156836169 99.28222448 0.953756593 75.10064557 0.451561476 1.00E-05 4.999999999 -2.765691219 RGLDEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGLDEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 84.368 0.034629 189685000 455990 400330 414210 503520 476790 418480 492570 471610 467760 FALSE TRUE 434436.2564 441124.0821 433201.9382 452905.213 559942.025 403987.9327 417419.3998 430313.3282 540297.8318 0.80406811 0.816446145 0.801783595 0.838251028 1.036358083 0.747713407 0.772572783 0.796437266 1 19.04339537 -2.394408769 2.103954723 2.196481605 0.82299335 0.323778522 0.078544203 2432414.92 243449.7155 13861503.36 0.018955333 0.004032657 2.394408769 -1.373488255 RGLEVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGLEVNK 7 1 P31146;H3BRY3 P31146 CORO1A Coronin-1A;Coronin 0 ;;; 134.81 0.0050319 926740000 1993130 1737390 1688060 2164540 1853140 2075480 2448890 2351830 2116890 FALSE TRUE 1898918.695 1914432.016 1765459.221 1946956.327 2176327.029 2003605.607 2075266.854 2145891.297 2445166.49 0.776600981 0.782945466 0.722020046 0.796246937 0.890052697 0.819414799 0.848722106 0.877605393 1 21.22150127 0.68679259 0.282714528 1.042208916 0.746735674 0.806359417 0.033733166 1.285706172 0.261649311 0.126172446 0.055386463 4.861749632 -0.68679259 -0.295473243 RGLEVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGLEVSK 7 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 111.95 0.010365 761850000 1617660 1385250 1307550 1630370 1226720 1606760 1817660 1715450 1480620 FALSE TRUE 1541196.418 1526408.55 1367502.461 1466482.11 1440659.58 1551117.498 1540342.583 1565236.104 1710226.988 0.901164833 0.892518105 0.799602901 0.857478054 0.842379164 0.906965864 0.900665581 0.915221263 1 20.70575639 0.902953919 0.849694337 0.998798083 0.866548634 0.664308919 0.030390611 0.496776976 0.759531963 0.030940129 0.010879521 7.997493935 -0.902953919 -0.132249449 RGLKPSCTIIPLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGLKPSCTIIPLMK 14 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 ; 105.78 0.00055101 1512690000 3699200 2533500 3146600 3570300 2984000 3522500 4741400 3951800 3790600 FALSE TRUE 3524346.147 2791666.53 3290874.722 3211406.661 3504408.655 3400514.942 4018012.348 3605759.442 4378426.888 0.804934338 0.637595785 0.751611208 0.733461296 0.800380763 0.776652215 0.917684011 0.823528526 1 22.06198119 1.536145203 0.568343167 0.989517067 0.714589004 0.692173989 0.05482571 0.380799603 0.28917536 0.05070138 0.027698412 34.36728328 -1.536145203 -0.274928063 RGLLEDVQEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGLLEDVQEGR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 112.02 0.002536 209274000 224150 207410 204250 233200 195362 223760 252180 233480 200084 FALSE TRUE 213554.8737 228545.3148 213615.0645 209758.2929 229433.0709 216011.1351 213705.3094 213035.2534 231112.0048 0.924031938 0.988894173 0.924292378 0.907604489 0.99273541 0.934659951 0.924682859 0.92178359 1 17.81823268 RGLLYDS(ph)DEEDEERPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RGLLYDS(1)DEEDEERPAR;RGLLYDS(1)DEEDEERPAR 257.37 2.15E-27 4493070000 1259503 936403 1209345 1236720 1109648 1125091 1409250 1320790 1347560 TRUE FALSE 1199968.789 1031823.53 1264794.664 1112402.556 1303170.26 1086128.817 1194243.03 1205134.626 1556532.722 0.770924229 0.662898708 0.812571844 0.71466699 0.837226382 0.697787333 0.767245695 0.774243039 1 20.56990448 -5 0.287636909 2.937695562 0.733629049 0.691497975 0.051614698 124.4838732 1.177126926 144.4751264 0.050093009 1.00E-05 5 -2.204066514 RGNDPLT(ph)SSPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.713)S(0.143)S(0.143)PGR 50.155 0.096591 77161000 62373 60047 59938 60372 45382 57275 58491 66576 46668 TRUE FALSE 59424.7519 66165.85757 62686.21659 54303.29186 53296.60643 55291.55239 49567.12369 60746.2525 53905.03509 1.102397054 1.227452268 1.162900951 1.007388118 0.988712953 1.02572148 0.919526786 1.126912401 1 15.71813242 3.238816496 6.070580141 1.000858325 1.169815424 0.596690702 0.058822135 0.087886051 12.28880557 0.015735742 0.020127771 1733.071561 -3.238816496 0.168957099 RGNDPLTS(ph)SPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.324)S(0.57)S(0.106)PGR 92.856 0.0012348 0 45240 41820 43869 44080 40696 47965 47870 50897 49692 TRUE FALSE 43101.59486 46081.50555 45880.43704 39648.99465 47793.36952 46303.96002 40566.55231 46440.18886 57397.98157 0.750925271 0.802841917 0.799338858 0.690773326 0.83266638 0.806717567 0.706759213 0.809090975 1 15.80871238 0.97036283 23.34187524 1.000000001 0.770273166 0.722036665 0.044541158 759.5330838 598200.167 0.040202834 0.010050709 9.340343111 -0.97036283 -0.229726835 RGNDPLTSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.013)S(0.036)S(0.952)PGR;RGNDPLTS(0.001)S(0.999)PGR;RGNDPLT(0.019)S(0.104)S(0.877)PGR;RGNDPLT(0.078)S(0.399)S(0.524)PGR;RGNDPLT(0.025)S(0.21)S(0.765)PGR;RGNDPLT(0.032)S(0.127)S(0.841)PGR 228.38 1.13E-11 3810220000 1742908 1687854 1756799 1932260 1795960 1839968 2101320 1926360 2003770 TRUE FALSE 1660524.193 1859848.242 1837349.972 1738025.554 2109174.855 1776249.447 1780725.041 1757677.706 2314504.418 0.717442654 0.803562191 0.793841635 0.750927732 0.911285733 0.767442669 0.769376384 0.759418601 1 21.14227189 -1.538003 3.059266644 1.008365172 0.783225687 0.639852965 0.05088538 68593573.22 70751934.2 4672977.307 0.011611884 0.028973236 1.538003 -0.225139484 RGNGLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGNGLIK 7 1 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 143.02 0.0039283 1232300000 2250300 1961450 1842010 2232000 1794220 2127860 2385400 2223100 1950930 FALSE TRUE 2143932.779 2161323.985 1926467.98 2007635.119 2107131.4 2054171.675 2021463.419 2028433.579 2253470.26 0.951391645 0.959109167 0.854889463 0.890908194 0.935060665 0.911559256 0.89704464 0.900137718 1 21.10371698 -1.150360631 5.171456666 1.000003397 0.915867273 0.442400477 0.030662585 1.31E-06 2.15E-07 0.032429687 0.007643442 0.070735816 1.150360631 -0.084136123 RGNVAGDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 156.16 0.00011479 8229874000 8378480 8249170 6047680 9043170 4578940 7329640 7539310 8140820 5609190 FALSE TRUE 7982445.855 9089769.802 6324972.11 8134133.371 5377505.686 7075812.729 6389049.791 7427966.644 6479034.537 1.232042492 1.402951281 0.976221391 1.255454547 0.829985649 1.092109123 0.986111396 1.146461961 1 22.62734742 3.73587656 24.99966493 1.040304403 1.317496892 0.482272582 0.119140258 160.4642918 1494587.533 0.028019899 0.045645831 5443.479102 -3.73587656 0.277192489 RGNVCGDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGNVCGDSK 9 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 148.56 0.00014387 1426420000 1904720 1412550 1368440 1677620 1286380 1668340 1998630 1845500 1467930 FALSE TRUE 1814687.66 1556490.451 1431184.328 1508982.45 1510724.265 1610564.967 1693702.286 1683898.236 1695569.087 1.070252857 0.917975247 0.844073142 0.889956335 0.890983609 0.949866909 0.998899012 0.993116853 1 20.69333814 1.837165624 3.812988939 0.996958841 0.92980274 0.249542388 0.058142801 0.419048876 10.1114313 0.032826834 0.017727172 68.7330513 -1.837165624 -0.067156101 RGPAEESSSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGPAEESSSWR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 101.53 0.0051518 493095000 155917 124669 131794 159554 157627 135227 170584 145431 203365 FALSE TRUE 148547.1124 137372.9128 137836.8853 143515.3288 185117.0989 130544.0551 144558.2778 132696.2907 234901.8056 0.632379611 0.584809949 0.586785125 0.610958815 0.788061626 0.555738832 0.615398751 0.56490111 1 17.84169828 -1.227086542 4.560328122 1.000114556 0.616505589 0.774167917 0.064943557 7.05E-05 1.20E-05 0.058640663 0.01381763 0.059280718 1.227086542 -0.383608967 RGPCIIYNEDNGIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGPCIIYNEDNGIIK 15 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 198.87 1.24E-08 1121860000 901640 660200 761130 891980 715480 812560 1015280 926250 749670 FALSE TRUE 859021.2641 727475.1306 796028.5634 802316.4757 840259.4855 784420.8435 860380.3891 845142.6396 865924.9948 0.992027334 0.84011333 0.919281194 0.926542692 0.970360586 0.9058762 0.993596898 0.975999821 1 19.72388254 1.806225006 0.850081173 1.000172362 0.915031952 0.311824079 0.041659489 0.650736316 0.88396791 0.035461295 0.015922616 64.00663653 -1.806225006 -0.085140411 RGPEEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGPEEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 93.143 0.024294 11842000 29755 26360 27191 31762 26882 26818 29637 31898 28225 FALSE TRUE 28348.54012 29046.11397 28437.73425 28569.22342 31570.21229 25889.28594 25115.33133 29104.84202 32601.98885 0.869534072 0.890930738 0.872269921 0.876303085 0.968352343 0.794101429 0.770361939 0.892732102 1 14.99267236 2.210915643 24.99999077 0.835324453 0.89057299 0 0.069413568 431.7306955 390421.2957 0.023897758 0.017653882 162.5233041 -2.210915643 0.055248537 RGPFELEAFYSDPQGVPYPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGPFELEAFYSDPQGVPYPEAK 22 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 119.06 0.00012596 61449000 205740 175460 180640 217190 148470 182390 226210 209310 184760 FALSE TRUE 196015.0779 193339.5735 188922.5227 195357.6486 174363.121 176073.7886 191697.5099 190981.7068 213411.6372 0.918483549 0.905946724 0.885249395 0.91540298 0.81702724 0.825043052 0.898252375 0.894898279 1 17.70327932 -1.389796385 7.567125761 1.00000279 0.884349811 0.527755032 0.034882053 1.72E-06 1.38E-07 0.035312307 0.00832299 0.040757132 1.389796385 -0.11565298 RGPGLYYVDSEGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGPGLYYVDSEGNR 14 1 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 189.07 1.22E-06 5187400000 2609010 2521130 2710180 2700790 2986930 2467600 3081670 2766530 3195730 FALSE TRUE 2485687.268 2778036.013 2834444.434 2429301.458 3507849.646 2382146.393 2611504.643 2524277.967 3691307.487 0.673389382 0.752588622 0.767870042 0.658114087 0.950300038 0.645339464 0.707474154 0.683843862 1 21.81570049 -1.673494467 2.852871172 1.03173588 0.728730064 0.485733554 0.087346187 22526315.34 22672732 5239690.684 0.018743449 0.021208284 1.673494467 -0.303005815 RGPLSQNGSFGPSPVSGGECS(ph)PPLTVEPPVRPLS(ph)ATLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGPLSQNGSFGPSPVSGGECSPPLTVEPPVRPLSATLNR 39 2 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 2 RGPLS(0.011)QNGS(0.013)FGPS(0.25)PVS(0.147)GGECS(0.568)PPLT(0.103)VEPPVRPLS(0.481)AT(0.427)LNR 44.439 0.038178 44953000 12975 10058 12249 10685 8700 9281.2 13887 10696 12707 TRUE FALSE 12361.69746 11082.92163 12810.62877 9610.9235 10217.27725 8959.789717 11768.2831 9759.401537 14677.53666 0.84221881 0.75509412 0.872805094 0.654804939 0.696116622 0.610442333 0.801788704 0.664920944 1 13.84132224 -1.226562042 4.881767377 1.000042884 0.744115461 0.487717423 0.084362022 3.81E-05 6.04E-06 0.079095991 0.018639984 0.059352355 1.226562042 -0.255927423 RGPNYTSGYGTNSELSNPS(ph)ETESER ddPTM_SK-BR-3_Trastuzumab_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(0.993)ET(0.007)ESER;RGPNYTSGYGTNSELSNPS(0.983)ET(0.017)ESER 257.92 3.71E-45 737320000 303470 318300 265260 365230 271430 305930 285620 279660 254740 TRUE FALSE 289125.5745 350735.1319 277422.4334 328516.3865 318767.3061 295335.5674 242043.4232 255171.4878 294243.7782 0.982605567 1.191988269 0.942831944 1.116476918 1.083344253 1.003710492 0.822594873 0.867211159 1 18.16665238 1.945674725 4.576211161 0.88164261 1.069243996 0.46505869 0.080877239 0.157322175 6.731392912 0.033827255 0.020287596 88.24187449 -1.945674725 0.187601386 RGPNYTSGYGTNSELSNPSETESER ddPTM_SK-BR-3_Trastuzumab_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 0 ; 277.2 6.69E-53 222630000 84989 96823 73538 103129 73679 84634 84118 87733 75430 FALSE TRUE 80971.7384 106689.3738 76909.79004 92762.27699 86528.59427 81703.10336 71284.25417 80050.63342 87127.29916 0.929349804 1.224522909 0.882728958 1.064675227 0.993128389 0.937744015 0.818162101 0.918777859 1 16.4108372 2.263437539 2.605189819 0.890262721 1.03924506 0.184414002 0.100293149 0.327952924 4.572127523 0.040077792 0.029047644 183.4161354 -2.263437539 0.148982339 RGPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGPPEK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 81.784 0.097755 32183000 80438 81527 72411 94292 56971 73809 74882 75798 65038 FALSE TRUE 76635.85515 89834.69399 75731.11597 84813.58902 66906.72436 71252.97582 63457.3756 69160.72529 75123.76087 1.020128043 1.195822639 1.008084727 1.128984865 0.890620006 0.948474557 0.844704457 0.920623841 1 16.19698167 2.735330012 24.99500029 0.908207858 1.094159422 0.611312323 0.065812107 160.0144039 1238018.392 0.019319782 0.018921065 543.6632933 -2.735330012 0.185951564 RGPPEKEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGPPEKEWR 9 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 110.47 0.001283 774350000 1443910 894200 1131630 1026090 1639660 1123390 1479160 1683800 1074340 FALSE TRUE 1375659.236 985319.9966 1183516.355 922945.4838 1925616.185 1084486.723 1253486.975 1536357.546 1240943.16 1.108559425 0.794008967 0.953723259 0.743745172 1.551736007 0.873921351 1.010108291 1.238056339 1 20.24300561 RGPPPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 133.6 0.0014631 205469000 154202 129107 121793 141605 142587 127012 156005 145699 162933 FALSE TRUE 146913.1771 142263.1501 127377.3295 127370.5964 167454.1277 122613.5426 132203.572 132940.8232 188199.8175 0.780623377 0.755915452 0.676819623 0.676783846 0.889767747 0.651507234 0.702463869 0.706381254 1 17.5219057 -1.704611366 7.383634513 1.001771072 0.731293668 0.607148015 0.068239846 0.001898029 7.59E-05 0.063034852 0.014773558 0.019741886 1.704611366 -0.270477404 RGPRT(ph)PPITTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGPRTPPITTK 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RGPRT(1)PPITTK;RGPRT(1)PPITTK 137.46 0.003717 234481000 404950 371960 339580 429180 294080 381280 415910 432460 316220 TRUE FALSE 385808.816 409863.1469 355150.0789 386038.011 345367.4589 368076.178 352455.2908 394591.5098 365257.7826 1.056264464 1.12212023 0.972327205 1.056891953 0.945544422 1.007716182 0.964949435 1.080309657 1 18.47855549 3.736645524 24.97296509 1.000369261 1.089192348 0.399421181 0.043275055 131.3719364 1713098.329 0.010252433 0.016831426 5453.125893 -3.736645524 0.088823088 RGQAALDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RGQAALDR 8 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;;; 131.11 0.0016344 2197572000 2525548 1931416 1591886 1807622 2687304 1813776 2849633 2148812 2611376 FALSE TRUE 2406170.351 2128229.486 1664875.548 1625916.402 3155968.967 1750964.482 2414869.149 1960650.63 3016334.853 0.797713274 0.705568045 0.551953158 0.539037103 1.046292643 0.580494066 0.800597171 0.650010932 1 21.52436517 RGQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.995)PS(0.005)AHMVSHSHSPSVVS;RGQPAS(0.892)PS(0.107)AHMVSHSHSPSVVS;RGQPAS(0.97)PS(0.029)AHMVSHSHSPSVVS;RGQPAS(0.969)PS(0.031)AHMVSHSHSPSVVS 138.54 6.23E-07 510836000 186944 139545 180123 195874 262590 172388 255493 211773 29862.8 TRUE FALSE 178107.5276 153764.7941 188381.8177 176184.3734 308385.6129 166418.1603 216512.8504 193229.0334 34493.77051 5.163469374 4.45775547 5.461328668 5.107715706 8.940327727 4.824585944 6.276868177 5.601853048 1 15.07404822 3.432895192 2.740152771 5.731940511 4.825030199 0 1.957547145 0.963153266 14.64589308 0.504367866 0.754089717 2709.537662 -3.432895192 -0.906910312 RGQS(ph)SPPPAPPICLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.5)S(0.5)PPPAPPICLR;RGQS(0.612)S(0.388)PPPAPPICLR;RGQS(0.593)S(0.407)PPPAPPICLR 104.88 0.00083233 2341120000 902230 720770 839130 1014020 879130 864730 987080 961520 998340 TRUE FALSE 859583.3759 794217.2824 877604.9405 912088.7831 1032449.994 834784.1833 836482.817 877324.2115 1153157.468 0.745417169 0.688732722 0.761045186 0.790949032 0.895324378 0.7239117 0.725384728 0.760801743 1 20.1371581 -1.899965364 2.35917287 1.142311562 0.754955008 0.647251395 0.055161232 11085641.79 5616428.764 8754041.838 0.013903357 0.012590258 1.899965364 -0.387356554 RGQSS(ph)PPPAPPICLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.316)S(0.684)PPPAPPICLR 91.622 0.0034038 788680000 267910 259260 257950 291680 175360 265800 259480 299940 223090 TRUE FALSE 255246.4252 285678.8888 269777.2626 262359.7722 205942.7285 256595.2794 219891.5603 273675.6635 257685.6578 0.990534077 1.108633252 1.046923857 1.018138823 0.799201361 0.995768571 0.853332553 1.06205237 1 17.97525272 2.981707594 24.01046421 0.92876944 1.050644038 0.275326649 0.079439301 452.0501126 593358.143 0.021511726 0.023237647 958.7548948 -2.981707594 0.121874598 RGQTCVVHYTGMLEDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGQTCVVHYTGMLEDGK 17 1 P62942;Q5W0X3;A0A087WZM5 P62942 FKBP1A Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 159.88 2.05E-09 247770000 271830 155080 181270 258360 217470 216550 404820 284920 281960 FALSE TRUE 258981.1346 170882.8283 189581.4088 232389.1619 255396.6991 209050.8192 343057.274 259970.8943 325684.9167 0.795189219 0.524687572 0.582100672 0.713539836 0.784183381 0.641880568 1.053340994 0.798228229 1 18.31311738 1.749088147 25 0.945581155 0.668038729 0.613082431 0.103619403 1.769998892 4211.436554 0.046290914 0.025670679 56.1161861 -1.749088147 -0.277542427 RGRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(0.997)PQPPAEEDEDDFDDT(0.003)LVAIDTYNCDLHFK;RGRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(0.825)PQPPAEEDEDDFDDT(0.175)LVAIDTYNCDLHFK;RGRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK;RGRS(0.85)PQPPAEEDEDDFDDT(0.15)LVAIDTYNCDLHFK;RGRS(0.998)PQPPAEEDEDDFDDT(0.002)LVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 319.35 8.98E-105 2032363000 787075 420634.1 711783.2 669118 771245 689173.8 1041666 826973 817885 TRUE FALSE 749871.5246 463497.193 744419.1638 601856.9874 905749.8838 665307.5385 882740.7202 754558.8601 944718.4286 0.793751346 0.490619405 0.787979933 0.637075523 0.958751154 0.704238976 0.934395576 0.798712968 1 19.84952488 2.75030491 24.87094844 0.865591302 0.665312183 0.416309563 0.117777876 641.5680457 1358651.197 0.032823088 0.034548635 562.7362726 -2.75030491 -0.200279119 RGRS(ph)PS(ph)PKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGRSPSPKPR 10 3 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGRS(1)PS(1)PKPR;RGRS(1)PS(1)PKPR;RGRS(1)PS(1)PKPR 84.169 0.021684 570010000 724220 491950 591940 673840 416698 644900 745630 499880 531390 TRUE FALSE 689987.5559 542080.2643 619081.0345 606104.323 489369.9993 622566.9513 631870.4491 456107.8572 613795.2472 1.124133103 0.883161391 1.008611646 0.987469886 0.797285416 1.014290929 1.02944826 0.743094475 1 19.22739795 4.649772731 3.190304379 0.942473361 1.134276584 0.266294789 0.098308263 0.385449177 6.367367128 0.022238044 0.161815958 44644.99009 -4.649772731 0.191803223 RGS(ph)ASGSEPAGDSDR ddPTM_SK-BR-3_Trastuzumab_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(1)ASGSEPAGDSDR;RGS(0.991)AS(0.009)GSEPAGDSDR;RGS(0.331)AS(0.331)GS(0.331)EPAGDS(0.007)DR;RGS(0.665)AS(0.159)GS(0.176)EPAGDSDR;RGS(0.987)AS(0.013)GSEPAGDSDR 199.97 4.38E-09 567681700 442074.4 377243 397137.6 436269.8 367434.1 402108.8 478330.7 427828.3 358705 TRUE FALSE 421178.4192 415684.4906 415346.7518 392415.1308 431514.4907 388183.6714 405352.5666 390365.386 414331.1394 1.016526105 1.003266352 1.002451209 0.947105089 1.041472508 0.936892342 0.978329959 0.942157972 1 18.66042473 3.532260392 0.634622981 0.968291125 1.020938681 0.182061312 0.031148081 1.513496278 1.152445457 0.016807013 0.048103015 3406.123508 -3.532260392 0.052647557 RGS(ph)DPASGEVEASQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(1)DPASGEVEASQLR;RGS(1)DPASGEVEASQLR 133.38 2.08E-05 238830000 143003 134541 149677 204533 180067 154197 161486 147947 194625 TRUE FALSE 136243.5316 148250.8809 156539.8385 183972.9543 211470.6278 148857.1192 136848.3448 134991.9764 224806.451 0.60604814 0.659460083 0.696331612 0.818361544 0.940678645 0.662156796 0.608738514 0.600480884 1 17.77832391 -2.07565809 2.659888013 1.48844646 0.692713846 0.439213455 0.106664709 13758267.25 3171912.634 41123926.82 0.027600012 0.008401211 2.07565809 -0.795732614 RGS(ph)FDATGSGFSMTFSSSSYSSSGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSFDATGSGFSMTFSSSSYSSSGYGR 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 1 RGS(0.992)FDAT(0.006)GS(0.002)GFSMTFSSSSYSSSGYGR;RGS(1)FDATGSGFSMTFSSSSYSSSGYGR 264.97 1.62E-53 522770000 185166 143946 177349 183443 161506 171720 201250 163499 178890 TRUE FALSE 176413.5701 158614.2611 185480.6271 165002.9611 189672.5953 165773.2933 170545.6163 149182.1608 206631.3476 0.853759956 0.767619545 0.897640311 0.798537894 0.917927495 0.802265945 0.825361777 0.721972549 1 17.65669961 -1.494563408 3.025274477 1.005201004 0.823515112 0.482366489 0.057577967 15604171.38 17962686.94 675975.8456 0.012375335 0.032021125 1.494563408 -0.181685892 RGS(ph)FSSENYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(1)FSSENYWR;RGS(1)FSSENYWR;RGS(1)FSSENYWR;RGS(0.985)FS(0.015)SENYWR;RGS(0.98)FS(0.01)S(0.01)ENYWR;RGS(0.989)FS(0.011)SENYWR 238.01 8.22E-16 2007319000 967823 829992 858156 1050854 880932 975466 1158138 1101251 1028834 TRUE FALSE 922075.9248 914569.1284 897503.3014 945220.1594 1034566.262 941685.3678 981442.7774 1004819.624 1188380.322 0.775909789 0.769592959 0.755232382 0.795385233 0.870568321 0.792410771 0.825865894 0.845537077 1 20.18056519 -5 0.150875305 1.744709489 0.735562219 0.867854401 0.025820619 44.09659914 0.393968666 9.762610724 0.125479611 1.00E-05 5 -1.00914727 RGS(ph)GDTSISIDTEASIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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(1)GDTSISIDTEASIR;RGS(0.96)GDT(0.039)S(0.001)ISIDTEASIR;RGS(0.936)GDT(0.06)S(0.004)ISIDTEASIR;RGS(0.985)GDT(0.015)SISIDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.995)GDT(0.005)SISIDTEASIR;RGS(0.971)GDT(0.027)S(0.002)ISIDTEASIR;RGS(0.974)GDT(0.024)S(0.002)ISIDTEASIR;RGS(0.943)GDT(0.045)S(0.011)IS(0.001)IDTEASIR;RGS(0.995)GDT(0.005)SISIDTEASIR;RGS(0.988)GDT(0.011)S(0.001)ISIDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.991)GDT(0.009)SISIDTEASIR;RGS(0.918)GDT(0.064)S(0.018)IS(0.001)IDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.963)GDT(0.036)SISIDTEASIR;RGS(0.961)GDT(0.038)S(0.001)ISIDTEASIR 257.66 2.38E-27 2520229400 2009750.7 1704605.7 1770874 2031297.5 1464848.8 1880051.9 2150639.4 2079504.3 1507720.5 TRUE FALSE 1914753.767 1878306.959 1852070.325 1827107.616 1720317.967 1814945.231 1822519.86 1897411.879 1741530.095 1.099466368 1.078538329 1.063473052 1.049139272 0.987819833 1.042155537 1.046504947 1.089508522 1 20.73192397 3.579292703 1.691396344 1.036861533 1.092494936 0.399301185 0.027632281 0.359167518 2.035450161 0.008190711 0.015584088 3795.707196 -3.579292703 0.055633403 RGS(ph)GDTSSLIDPDTSLSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(1)GDTSSLIDPDTSLSELR;RGS(0.995)GDT(0.005)SSLIDPDTSLSELR;RGS(0.981)GDT(0.019)SSLIDPDTSLSELR;RGS(1)GDTSSLIDPDTSLSELR;RGS(0.999)GDT(0.001)SSLIDPDTSLSELR;RGS(0.999)GDT(0.001)SSLIDPDTSLSELR;RGS(0.851)GDT(0.145)S(0.003)SLIDPDTSLSELR 247.04 2.65E-30 4842770000 3708350 3677050 3288760 4046120 2682980 3485480 3639440 3754180 2801380 TRUE FALSE 3533063.645 4051745.575 3439552.899 3639396.33 3150890.863 3364776.954 3084176.585 3425444.097 3235803.703 1.091865876 1.252160498 1.062967106 1.124727167 0.973758346 1.039858181 0.953140817 1.058606891 1 21.62569266 3.054056057 1.52337145 0.999825197 1.164857757 0.52880035 0.058323248 0.241712464 1.157029473 0.019392527 0.02408992 1132.546539 -3.054056057 0.16503256 RGS(ph)GDTSSLIDPDTSLSELRDIYDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGSGDTSSLIDPDTSLSELRDIYDLK 26 2 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.909)GDT(0.087)S(0.003)SLIDPDTSLSELRDIYDLK;RGS(0.998)GDT(0.001)S(0.001)SLIDPDTSLSELRDIYDLK;RGS(0.94)GDT(0.02)S(0.02)S(0.02)LIDPDTSLSELRDIYDLK;RGS(0.968)GDT(0.026)S(0.005)S(0.001)LIDPDTSLSELRDIYDLK;RGS(0.847)GDT(0.005)S(0.006)S(0.008)LIDPDT(0.09)S(0.019)LS(0.025)ELRDIYDLK;RGS(0.829)GDT(0.137)S(0.029)S(0.006)LIDPDTSLSELRDIYDLK 233.08 3.87E-45 348729000 614333 390154 514362 527330 374884 572680 651775 620652 400972 TRUE FALSE 585294.6966 429911.1362 537946.0065 474321.7865 440263.6509 552847.948 552334.7531 566304.4206 463152.6899 1.26371866 0.928227657 1.161487385 1.024115366 0.950579929 1.193662393 1.192554346 1.222716467 1 18.82112837 2.18574227 24.99999008 1.171787099 1.067367704 0.115962364 0.113184625 170.0582078 80490.72931 0.03965968 0.029290649 153.3706542 -2.18574227 -0.104419395 RGS(ph)GDTSSLIDPDTSLSELRDIYDLKDQIQDVEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSGDTSSLIDPDTSLSELRDIYDLKDQIQDVEGR 35 3 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.895)GDT(0.028)S(0.034)S(0.043)LIDPDTSLSELRDIYDLKDQIQDVEGR 144.29 6.30E-10 58203000 45685 14399 52235 32643 43599 46356 82919 58903 60652 TRUE FALSE 43525.56059 15866.27447 54630.02642 29361.66362 51202.6518 44750.6801 70268.18364 53745.14106 70057.60239 0.621282475 0.2264747 0.779787269 0.419107458 0.730865032 0.638769792 1.00300583 0.767156443 1 16.09625399 2.21870693 0.786667774 0.965482359 0.459040926 0.51038011 0.165796261 0.443842819 0.523307688 0.122956469 0.073345467 165.4652997 -2.21870693 -0.506441432 RGS(ph)GVFCANCLTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;RGS(1)GVFCANCLTTK;RGS(1)GVFCANCLTTK 197.84 1.40E-08 4314670000 3717170 3333170 3154120 3877070 2439530 3803320 4168660 4059220 2746700 TRUE FALSE 3541466.741 3672823.812 3298739.522 3487339.558 2864983.26 3671610.075 3532654.354 3703773.178 3172644.208 1.116250833 1.15765386 1.039744549 1.099190243 0.903026962 1.157271296 1.113473218 1.167408929 1 21.59725431 3.747529655 24.14674884 1.075467414 1.136952348 0.112543084 0.077971934 908.598828 2446150.221 0.019433789 0.03430794 5591.517074 -3.747529655 0.061484934 RGS(ph)IGENQIKDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSIGENQIKDEK 13 2 Q05682-5;Q05682-4;C9J813;E9PGZ1 Q05682-5 CALD1 Caldesmon 1 RGS(1)IGENQIKDEK 128.94 0.00012556 425410000 293310 249640 247860 303460 130810 309590 298530 337410 148690 TRUE FALSE 279445.8176 275078.5998 259224.6262 272955.6243 153623.2226 298868.8207 252983.7656 307864.5917 171748.0858 1.627068018 1.601639975 1.509330511 1.58927899 0.894468325 1.740158088 1.472993218 1.792535796 1 17.38993449 RGS(ph)IS(ph)S(ph)MSSVSSVLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSISSMSSVSSVLDEK 17 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 3 RGS(0.366)IS(0.433)S(0.456)MS(0.473)S(0.465)VS(0.42)S(0.387)VLDEK 61.767 0.024974 172820000 224700 229560 238490 232510 233730 226030 271060 207070 285380 TRUE FALSE 214078.8763 252952.425 249425.0024 209137.6531 274492.438 218202.5244 229704.8186 188937.8531 329635.2729 0.649441652 0.767370624 0.756669637 0.634451681 0.832715612 0.661951382 0.696845385 0.573172438 1 18.3305111 -1.644063384 2.986889123 1.025745276 0.702159108 0.620423691 0.074472087 17828592.54 17421417.5 3521663.343 0.017940242 0.022695336 1.644063384 -0.323586169 RGS(ph)KGHMNYEGPGMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGSKGHMNYEGPGMAR 16 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR 235.92 5.35E-20 1005839000 361397 208992 330645 336861 315912 342845 465164 364508 386723 TRUE FALSE 344314.48 230288.5224 345805.4003 302999.0923 371006.9528 330972.1917 394194.6885 332589.7471 446694.0277 0.770806097 0.515539739 0.774143774 0.678314626 0.830561704 0.740937132 0.882471365 0.744558303 1 18.76892744 1.411990605 0.304998321 1.021087717 0.621276658 0.500999008 0.089315318 1.081232113 0.364444175 0.164918704 0.136068113 25.82204332 -1.411990605 -0.399811059 RGS(ph)LEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RGS(1)LEK;RGS(1)LEK 105.1 0.020375 5845890000 8042570 6672140 6718290 8205790 4516780 7751100 8389040 8397040 5383620 TRUE FALSE 7662413.655 7352038.652 7026330.242 7380928.399 5304505.002 7482677.463 7109137.873 7661750.662 6218484.294 1.232199567 1.182287886 1.129910427 1.186933672 0.853022176 1.20329603 1.143226796 1.232092951 1 22.56813155 3.833314916 1.491851001 1.109168116 1.224164917 0.139533603 0.109757413 0.847982095 3.598821215 0.031465005 0.085075033 6812.631776 -3.833314916 0.114996801 RGS(ph)LLGSMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGSLLGSMK 9 1 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 RGS(1)LLGSMK;RGS(1)LLGSMK;RGS(1)LLGSMK 93.348 0.0040598 370150000 1237870 1011350 1008910 1302050 946950 1214070 1405940 1222260 948920 TRUE FALSE 1179358.338 1114407.715 1055169.521 1171165.46 1112097.78 1172026.451 1191438.031 1115232.435 1096073.667 1.075984556 1.016727021 0.962681208 1.068509805 1.014619558 1.069295328 1.087005433 1.017479453 1 20.06391333 2.237439131 24.99994845 1.055250134 1.029495802 0 0.039744603 78.40323774 1747668.095 0.013946274 0.010886523 172.7583831 -2.237439131 -0.025754332 RGS(ph)LPAGASWQNTDLFEMIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(0.979)LPAGAS(0.021)WQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(0.997)LPAGAS(0.003)WQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(0.998)LPAGAS(0.002)WQNTDLFEMIEK;RGS(0.999)LPAGAS(0.001)WQNTDLFEMIEK 322.6 2.39E-67 2568021000 3082490 2419052 2650191 2899788 1880608 2908850 3200724 3106738 2051092 TRUE FALSE 2936786.807 2665556.149 2771704.879 2608295.801 2208585.44 2808115.795 2712394.768 2834695.551 2369164.872 1.239587351 1.125103694 1.169907975 1.100934693 0.932221082 1.185276647 1.144873791 1.196495687 1 21.17594717 4.679220107 1.025891311 1.108226313 1.298733514 0.213055369 0.082346219 2.748055022 2.502599719 0.024675008 0.563833172 47777.13543 -4.679220107 0.190507201 RGS(ph)LPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 RGS(1)LPDQK;RGS(1)LPDQK 124.12 0.00080744 433710000 732280 734030 714310 839470 533850 865400 842690 906560 591360 TRUE FALSE 697666.5756 808828.4915 747061.82 755084.8807 626953.271 835430.981 714122.1634 827176.8004 683065.0886 1.021376421 1.18411628 1.093690532 1.105436207 0.917852898 1.223062041 1.045467226 1.210978008 1 19.38166353 -0.472538097 7.031231466 0.999999812 1.099063372 0.103897002 0.092465656 0 0 0.078537513 0.018511469 0.336869663 0.472538097 0.099063559 RGS(ph)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGSLQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER 36 2 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 RGS(1)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER;RGS(0.979)LQAYT(0.021)FEEQPTLPVLLPTSSGLPPGWEEKQDER;RGS(0.999)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER 169.79 4.11E-18 329369000 268896 197822 240693 230162 163438 243167 296653 279971 187785 TRUE FALSE 256185.819 217980.2867 251729.0121 207025.6785 191941.5355 234746.0658 251393.1364 255455.255 216905.7387 1.181092859 1.004953986 1.160545653 0.954449982 0.884907594 1.082249217 1.158997166 1.177724741 1 17.7267087 -0.872436011 7.866744346 1.000000004 1.075349478 0.052450489 0.100998136 0 0 0.098151446 0.023134518 0.134141757 0.872436011 0.075349474 RGS(ph)LSNAGDPEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RGSLSNAGDPEIVK 14 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 RGS(0.998)LS(0.002)NAGDPEIVK;RGS(0.987)LS(0.013)NAGDPEIVK;RGS(0.998)LS(0.002)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.999)LS(0.001)NAGDPEIVK;RGS(0.999)LS(0.001)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.992)LS(0.008)NAGDPEIVK;RGS(0.979)LS(0.021)NAGDPEIVK;RGS(0.542)LS(0.458)NAGDPEIVK;RGS(0.669)LS(0.331)NAGDPEIVK 235.56 1.88E-17 15454410000 25563920 27352220 23107320 29740890 15356460 29708080 26282280 29367310 15807840 TRUE FALSE 24355564.16 30139442.31 24166813.48 26751279.23 18034621.76 28679281.74 22272435.48 26795752.65 18259239.09 1.333876184 1.650640652 1.323538914 1.46508182 0.987698429 1.570672337 1.219789903 1.467517486 1 24.12212331 -4.137297512 0.142217186 3.83E-10 1.530330191 0.275417255 0.187333896 122.2057562 1.332014093 36.33324769 1.033275684 7.29E-05 4.137297512 1.530330191 RGS(ph)LTLTISGESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.926)LT(0.066)LT(0.008)ISGESPK;RGS(1)LTLTISGESPK;RGS(0.999)LT(0.001)LTISGESPK;RGS(0.988)LT(0.012)LTISGESPK;RGS(0.981)LT(0.019)LTISGESPK 265.1 1.03E-24 1520329000 3071500 2614880 2797690 3151120 1929480 3214950 3474980 3304670 2077060 TRUE FALSE 2926316.282 2881339.245 2925966.854 2834363.431 2265980.701 3103615.475 2944807.979 3015295.576 2399159.857 1.219725428 1.200978433 1.219579782 1.181398323 0.944489253 1.293625961 1.227432999 1.256813116 1 21.19409786 3.011405667 21.76648212 1.165099717 1.210263562 0.061380693 0.108015023 190.1475122 362861.6934 0.030457602 0.036351665 1026.610417 -3.011405667 0.045163845 RGS(ph)MFYDEDGDLAHEFYEETIVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RGSMFYDEDGDLAHEFYEETIVTK 24 1 O75896 O75896 TUSC2 Tumor suppressor candidate 2 1 RGS(0.533)MFY(0.456)DEDGDLAHEFY(0.008)EET(0.002)IVTK;RGS(0.261)MFY(0.239)DEDGDLAHEFY(0.239)EET(0.261)IVTK;RGS(0.547)MFY(0.453)DEDGDLAHEFYEETIVTK;RGS(0.505)MFY(0.43)DEDGDLAHEFY(0.065)EETIVTK;RGS(0.901)MFY(0.099)DEDGDLAHEFY(0.001)EETIVTK;RGS(0.539)MFY(0.46)DEDGDLAHEFY(0.001)EETIVTK;RGS(0.48)MFY(0.434)DEDGDLAHEFY(0.07)EET(0.016)IVTK;RGS(0.34)MFY(0.301)DEDGDLAHEFY(0.301)EET(0.057)IVTK;RGS(0.458)MFY(0.415)DEDGDLAHEFY(0.081)EET(0.046)IVTK 146.39 8.37E-08 403521000 485286.8 436316.4 409348 493607.2 347735.3 490543.5 548340 503886.2 310660.1 TRUE FALSE 462348.2547 480777.5372 428117.0107 443988.8665 408380.2262 473555.8556 464680.662 459763.2531 358835.6817 1.288467893 1.339826449 1.193072575 1.237304118 1.138070284 1.319701133 1.294967824 1.281264034 1 18.45296383 -1.952550961 2.564120198 0.797234334 1.268329343 0.649498255 0.060209764 9344707.623 4264144.982 11280383.07 0.01562943 0.011154473 1.952550961 0.471095008 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(0.999)MNNELLS(0.001)PEFGPVRDPLADGVEGLGR 174.92 6.80E-13 190349000 86805.2 77898.6 73965.2 87028.3 73847.3 83978.9 92019.7 84540.8 71393.1 TRUE FALSE 82702.09023 85836.5559 77356.57758 78280.04994 86726.24574 81070.68964 77980.40471 77137.95937 82464.37732 1.002882613 1.040892549 0.938060531 0.949258971 1.051681327 0.983099518 0.945625338 0.935409469 1 16.33148342 1.992027092 24.20167403 0.956818077 0.999952963 0.151767906 0.038310565 387.269349 1175552.26 0.014905772 0.010508229 98.18091875 -1.992027092 0.043134886 RGS(ph)PAPANPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;RGS(1)PAPANPGR 72.175 0.028797 346500500 137751.6 119576.9 147548 150523.5 168430 131175 155093.1 145057.2 150010 TRUE FALSE 131240.3549 131761.9221 154313.2217 135392.5918 197804.1387 126632.3769 131430.7991 132355.2226 173272.7847 0.757420475 0.760430568 0.890579684 0.781384059 1.141576498 0.730826697 0.758519576 0.763854652 1 17.40268555 -2.478632989 2.140578918 2.953260635 0.815444127 0.171012882 0.121391468 6459449.997 238762.6318 61956945.33 0.028975211 0.003321751 2.478632989 -2.137816508 RGS(ph)PTT(ph)GFIEQKGSPTSAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSPTTGFIEQKGSPTSAYPER 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 RGS(0.751)PT(0.252)T(0.607)GFIEQKGS(0.334)PT(0.04)S(0.015)AYPER 71.524 0.01798 459350000 278580 169610 306110 244100 218750 298840 431540 315850 271690 TRUE FALSE 265412.0755 186893.4518 320145.4463 219562.6042 256899.9307 288491.0959 365700.6472 288192.4996 313822.2976 0.845740018 0.59553911 1.020148819 0.699639911 0.818615926 0.919281702 1.165311229 0.91833022 1 18.25958834 2.099494014 3.222948104 1.045793609 0.777757085 0.415383395 0.123921781 0.197714625 4.054730894 0.050232169 0.033480538 125.7459523 -2.099494014 -0.268036523 RGS(ph)PTTGFIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.945)PT(0.047)T(0.009)GFIEQK;RGS(0.968)PT(0.03)T(0.001)GFIEQK;RGS(0.928)PT(0.039)T(0.033)GFIEQK;RGS(0.966)PT(0.017)T(0.017)GFIEQK;RGS(0.94)PT(0.06)TGFIEQK;RGS(0.961)PT(0.038)T(0.001)GFIEQK;RGS(0.631)PT(0.369)TGFIEQK;RGS(0.891)PT(0.109)TGFIEQK;RGS(0.978)PT(0.022)TGFIEQK;RGS(0.885)PT(0.095)T(0.019)GFIEQK;RGS(0.783)PT(0.192)T(0.024)GFIEQK 225.09 1.96E-11 7761230000 12190310 11229070 10893610 13317520 8192040 12392060 12703210 13360530 8473160 TRUE FALSE 11614098.21 12373325 11393092.79 11978817.59 9620729.182 11962919.85 10765102 12190611.16 9787134.378 1.186669944 1.264243907 1.164088726 1.22393513 0.982997557 1.22231078 1.099923797 1.245575129 1 23.22245508 -4.999999998 0.097377533 0.473807976 1.295586577 0.28546362 0.083179482 220.9281694 1.472208662 24.12388107 1.373617466 1.00E-05 4.999999998 0.821778601 RGS(ph)PVPPVPER ddPTM_SK-BR-3_Trastuzumab_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 98.694 0.0032647 3878700000 2837560 2575420 2470470 2974980 2307220 2665220 2998380 2858840 2365900 TRUE FALSE 2703434.162 2837858.226 2583743.493 2675929.358 2709598.438 2572922.763 2540922.062 2608504.814 2732791.689 0.989257313 1.038446596 0.945459364 0.979192585 0.991512982 0.941499776 0.929789882 0.95452018 1 21.38194406 3.731448441 24.99905667 0.958975162 1.013851955 0.404115735 0.02521018 439.3879018 1544434.592 0.006754892 0.01070476 5388.258721 -3.731448441 0.054876792 RGS(ph)PVPPVPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR 115.73 0.00047918 1449420000 447801 325070 380222 374712 386432 364431 446588 439080 436873 TRUE FALSE 426634.3342 358195.0026 397655.5548 337045.2379 453825.6185 351810.6631 378452.7984 400631.8275 504621.0336 0.845454917 0.709829711 0.788028101 0.667917537 0.899339481 0.697177961 0.749974284 0.793926136 1 18.94484082 0.810276271 4.340249404 0.999994835 0.763396933 0.531745605 0.068621336 1.519885815 34.12874737 0.058141075 0.014787503 6.460650844 -0.810276271 -0.236597902 RGS(ph)QNSSEHRPPASSTSEDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(0.77)QNS(0.115)S(0.115)EHRPPASSTSEDVK;RGS(0.999)QNSSEHRPPASSTSEDVK 194.19 2.38E-18 105384000 84098 65691 77896 92077 53129 82829 97614 90255 56365 TRUE FALSE 80122.85421 72384.98758 81467.60865 82821.24503 62394.68078 79960.61096 82721.1915 82351.79373 65105.79633 1.230656235 1.111805579 1.251311147 1.272102481 0.958358308 1.228164241 1.270565697 1.264891889 1 15.99049837 RGS(ph)RPEMTPVSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSRPEMTPVSLR 13 2 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 RGS(0.948)RPEMT(0.05)PVS(0.002)LR;RGS(0.972)RPEMT(0.025)PVS(0.002)LR 86.005 0.0094816 389960000 192638 148521 139420 166563 127690 145748 199276 157079 165000 TRUE FALSE 183532.3835 163655.4588 145812.5449 149819.7708 149959.0956 140700.7102 168872.7862 143324.33 190587.3573 0.962982992 0.858690005 0.765069347 0.786095011 0.78682604 0.738247868 0.886064997 0.752013838 1 17.54009289 4.25641406 2.164545413 0.80936648 0.955243651 0.2518079 0.077674535 0.369087152 3.253043424 0.017971826 0.070141334 18047.37571 -4.25641406 0.145877171 RGS(ph)RSS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.998)RS(0.025)S(0.977)PEPK 107.13 0.011436 4669200000 1544800 1256900 1337100 1497400 780490 1556600 1613400 1403400 813480 TRUE FALSE 1471780.365 1384979.539 1398407.358 1346878.507 916607.2089 1502694.552 1367246.198 1280510.856 939630.3237 1.566339792 1.473962157 1.488252691 1.433413198 0.975497689 1.599240163 1.455089479 1.362781536 1 19.84173375 -3.674828519 0.18777717 1.26E-13 1.523990431 0.3943737 0.16804881 83.03353064 1.268814365 32.84909366 0.481284563 0.000211432 3.674828519 1.523990431 RGS(ph)RSSPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGS(0.382)RS(0.382)S(0.235)PEPK 77.593 0.016976 25829000 78681 29984 67656 53839 56280 65273 106240 77457 81253 TRUE FALSE 74961.90506 33039.40369 70758.09452 48427.00143 66095.21418 63012.57964 90031.13677 70674.45445 93853.30026 0.798713576 0.352032412 0.753922284 0.515986133 0.704239638 0.671394394 0.95927513 0.753031106 1 16.51811986 1.981240587 1.625068008 0.908280351 0.595413324 0.439050743 0.142025487 0.318690488 1.568159541 0.08505965 0.040901048 95.77244765 -1.981240587 -0.312867027 RGS(ph)S(ph)PGSLEIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 RGS(0.999)S(0.994)PGS(0.007)LEIPK;RGS(0.995)S(0.998)PGS(0.008)LEIPK 120.66 0.0013649 110748000 597640 537370 518920 659040 338260 612850 607710 586800 346650 TRUE FALSE 569390.7416 592128.6139 542712.9953 592792.0471 397252.4369 591626.8508 514992.6781 535416.6812 400406.7116 1.422030963 1.478817904 1.355404342 1.480474802 0.992122323 1.47756477 1.286173941 1.337182084 1 18.61110663 -4.383948581 0.117213414 1.63E-14 1.558451869 0.416391596 0.139133749 120.4895822 1.064579431 29.84552405 1.349755535 4.13E-05 4.383948581 1.558451869 RGS(ph)S(ph)PGSLEIPKDLPDILNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSSPGSLEIPKDLPDILNK 20 2 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 2 RGS(0.999)S(0.997)PGS(0.004)LEIPKDLPDILNK 169.6 5.65E-12 18151000 57634 30329 58473 43625 31696 54409 75747 57840 39076 TRUE FALSE 54909.75504 33419.55958 61154.04489 39239.73212 37223.77236 52524.80269 64190.40396 52775.22297 45135.70651 1.216548035 0.740423983 1.354892825 0.869372281 0.82470787 1.163708442 1.422164599 1.169256605 1 15.46198157 2.011577147 22.47220642 1.256269829 0.995203346 0.149506841 0.207886529 83.35481383 161796.3684 0.072305412 0.053331521 102.7015853 -2.011577147 -0.261066483 RGS(ph)SDPTVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGSSDPTVQR 10 1 H7BXG1;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3;Q2KHT3-2 H7BXG1;Q2KHT3 CLEC16A Protein CLEC16A 1 RGS(0.957)S(0.042)DPTVQR;RGS(0.943)S(0.057)DPTVQR;RGS(0.95)S(0.049)DPT(0.002)VQR;RGS(0.748)S(0.241)DPT(0.01)VQR 105.4 0.0020276 163395000 721130 586270 636180 748720 610892 718700 818850 768960 739460 TRUE FALSE 687043.614 646011.5795 665349.4823 673457.2431 717431.3714 693811.2388 693919.3933 701625.7859 854131.6802 0.80437669 0.756337219 0.778977642 0.788470044 0.839954059 0.812300088 0.812426713 0.821449201 1 19.70409898 -4.999999971 0.214563393 2.004234223 0.770874437 0.917657519 0.019072838 38.64965745 0.385908349 16.69256499 0.038666626 1.00E-05 4.999999971 -1.233359786 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.282)S(0.282)GS(0.282)VDET(0.153)LFALPAASEPVIR;RGS(0.32)S(0.32)GS(0.32)VDET(0.04)LFALPAASEPVIR;RGS(0.634)S(0.148)GS(0.214)VDET(0.004)LFALPAASEPVIR;RGS(0.315)S(0.315)GS(0.315)VDET(0.054)LFALPAASEPVIR 131.95 1.76E-05 147767000 144094 153238 121424 203386 119676 148873 136175 144924 109725 TRUE FALSE 137282.9622 168853.1264 126991.4105 182941.2529 140547.4565 143717.4907 115399.0027 132233.6863 126740.5926 1.083180687 1.332273449 1.001978986 1.443430626 1.108937978 1.133949966 0.910513359 1.043341234 1 16.95151914 2.041261078 2.439263754 0.97939539 1.207644296 0.34923293 0.128784642 0.281838156 3.209739392 0.058946065 0.033882921 109.9666709 -2.041261078 0.228248905 RGS(ph)SPGSLEIPK ddPTM_SK-BR-3_Trastuzumab_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(0.988)S(0.012)PGSLEIPK;RGS(0.978)S(0.022)PGSLEIPK;RGS(0.957)S(0.043)PGSLEIPK;RGS(0.779)S(0.221)PGSLEIPK 164.82 3.45E-05 2641070000 6185200 5816000 5390900 6858500 3408600 6440400 6157600 6815900 3398190 TRUE FALSE 5892837.854 6408657.012 5638078.097 6169070.55 4003058.761 6217367.333 5218145.028 6219063.663 3925163.95 1.501297253 1.632710657 1.436393019 1.57167207 1.019844983 1.583976469 1.329408171 1.584408637 1 21.90432148 -3.627396381 0.166300339 1.23E-15 1.58993009 0.374095705 0.181209876 78.59499647 1.11643605 28.0923014 0.668016593 0.000235832 3.627396381 1.58993009 RGS(ph)SSSSPEHSASSDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RGSSSSSPEHSASSDSTK 18 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 RGS(0.2)S(0.2)S(0.2)S(0.2)S(0.2)PEHSASSDSTK;RGS(0.2)S(0.2)S(0.2)S(0.2)S(0.2)PEHSASSDSTK;RGS(0.198)S(0.198)S(0.198)S(0.198)S(0.198)PEHS(0.011)ASSDSTK;RGS(0.2)S(0.2)S(0.2)S(0.2)S(0.2)PEHSASSDSTK;RGS(0.2)S(0.2)S(0.2)S(0.2)S(0.2)PEHS(0.001)ASSDSTK 148.29 3.31E-08 207239000 391765 314821 323093 401434 288942 347595 421254 387357 319363 TRUE FALSE 373247.0449 346901.6178 337907.1336 361081.0916 339333.3933 335557.698 356983.9654 353437.9676 368888.183 1.011816214 0.940397752 0.916015067 0.978836158 0.919881441 0.909646103 0.967729469 0.958116806 1 18.49282405 0.737558061 1.7571382 0.999812809 0.950101552 0.207795747 0.031131119 1.682293639 8.210461156 0.029818047 0.008423948 5.464596015 -0.737558061 -0.049711256 RGS(ph)TAGGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSTAGGCR 9 1 P07384;P17655;P17655-2 P07384;P17655 CAPN1;CAPN2 Calpain-1 catalytic subunit;Calpain-2 catalytic subunit 1 RGS(0.973)T(0.027)AGGCR 64.121 0.043849 9826600 5183.1 4619.6 4575 5489.9 6057.3 3733.7 5326.2 3348.3 6814.8 TRUE FALSE 4938.105135 5090.342492 4784.768275 4938.044822 7113.691202 3604.401033 4513.590368 3055.105102 7871.604379 0.627331469 0.646671536 0.607851722 0.627323806 0.90371554 0.45789916 0.573401577 0.388117206 1 12.942442 RGS(ph)WREEEDREVAAAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSWREEEDREVAAAVR 17 3 Q86UK7-2 Q86UK7-2 ZNF598 Zinc finger protein 598 1 RGS(1)WREEEDREVAAAVR 108.5 0.0036076 249690000 188130 175250 183430 200130 152150 200750 234160 207260 199490 TRUE FALSE 179237.4677 193108.1742 191840.4469 180012.5522 178684.9118 193797.9772 198434.5914 189111.2156 230425.8903 0.77785299 0.838048945 0.832547274 0.781216694 0.775455013 0.841042545 0.861164477 0.820702983 1 17.8139433 -0.882427663 0.363478042 1.077418336 0.801846033 0.822940125 0.027288354 5.379257986 0.566700722 0.47232502 0.021539251 0.131090837 0.882427663 -0.275572303 RGSCVTQVGLLESVYEMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSCVTQVGLLESVYEMFR 19 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 164.94 3.65E-11 89146000 128061 77426 128596 104280 153440 117432 193488 118368 171413 FALSE TRUE 122007.8103 85315.79743 134492.2538 93797.57628 180199.8874 113365.3004 163967.8519 108003.0704 197994.8526 0.616217082 0.430899068 0.679271466 0.473737449 0.910124102 0.572566907 0.828141994 0.545484234 1 17.5951034 -4.999999853 0.086885305 2.243014227 0.293571783 0.402618134 0.144632818 187.7569907 1.140456575 43.45545882 3.334906738 1.00E-05 4.999999853 -1.949442444 RGSGDT(ph)SISIDTEASIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.006)GDT(0.949)S(0.043)IS(0.002)IDTEASIR 204.6 1.67E-11 167250000 64730 54812 60414 69315 51194 62712 70484 70651 62562 TRUE FALSE 61670.34118 60397.40512 63184.04166 62347.32451 60122.21739 60540.26772 59730.37127 64464.4239 72263.79544 0.853405787 0.835790658 0.874352659 0.862774009 0.831982558 0.837767617 0.826560118 0.892070829 1 16.14098541 0.911840655 4.030856284 0.9999441 0.845543788 0.917393602 0.014607963 0.10798648 4.035310486 0.014594638 0.003730042 8.162828177 -0.911840655 -0.154400312 RGSGDT(ph)SSLIDPDTSLSELRDIYDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSGDTSSLIDPDTSLSELRDIYDLK 26 2 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.005)GDT(0.329)S(0.329)S(0.329)LIDPDT(0.003)S(0.003)LS(0.003)ELRDIYDLK;RGS(0.442)GDT(0.516)S(0.039)S(0.003)LIDPDTSLSELRDIYDLK 118.9 0.00079563 65862000 163981 100255 135830 151486 105004 148472 176012 161853 108401 TRUE FALSE 156229.9431 110471.0985 142057.9399 136258.3395 123316.6644 143330.3774 149158.1367 147680.2933 125211.2734 1.247730646 0.882277573 1.134545923 1.088227407 0.984868702 1.144708248 1.191251655 1.179448856 1 16.93400494 2.097153046 11.83707053 1.150597314 1.062663525 0.057898706 0.107407188 0.903638289 103.7278364 0.037854916 0.027956779 125.0699702 -2.097153046 -0.087933789 RGSLT(ph)LTISGESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.248)LT(0.62)LT(0.133)ISGESPK 98.439 0.0015103 54521000 194680 164200 164710 186840 116250 176210 209040 191770 133700 TRUE FALSE 185477.8622 180932.1667 172262.1164 168058.4882 136523.9632 170107.8035 177147.1087 174977.6022 154433.5132 1.201020805 1.17158616 1.115445171 1.088225507 0.884030677 1.101495395 1.147076856 1.133028697 1 17.23662634 3.600745967 2.154741441 1.067327834 1.190604059 0.328992501 0.074919378 0.390586001 3.556825792 0.022715286 0.040345651 3987.915683 -3.600745967 0.123276225 RGSMNNELLS(ph)PEFGPVRDPLADGVEGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(0.449)MNNELLS(0.551)PEFGPVRDPLADGVEGLGR;RGSMNNELLS(1)PEFGPVRDPLADGVEGLGR 128.62 1.34E-05 104869000 84459 79047 81533 89580 62221 84813 83933 79405 71284 TRUE FALSE 80466.79045 87101.97917 85271.3687 80575.24821 73072.3227 81875.90454 71127.47931 72451.87725 82338.35865 0.97726979 1.057854208 1.03562143 0.97858701 0.887463922 0.994383491 0.863843784 0.879928607 1 16.32927707 2.975060958 3.953579167 0.91850101 1.023582294 0.458224885 0.04876456 0.171864295 5.949367 0.014118099 0.015890119 944.1933958 -2.975060958 0.105081283 RGSPT(ph)TGFIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.279)PT(0.72)T(0.001)GFIEQK 196.8 3.91E-07 849280000 1181800 1152700 1076100 1298700 713640 1228000 1244900 1262400 750120 TRUE FALSE 1125938.656 1270161.441 1125440.249 1168152.209 838098.5901 1185474.052 1054967.641 1151857.564 866444.7785 1.29949269 1.465946211 1.298917458 1.348213109 0.967284483 1.36820497 1.217582086 1.329406781 1 19.72474828 -4.999999972 0.090901317 0.076636569 1.530153012 0.337175933 0.128627371 222.1271858 1.400489427 40.04430307 2.740568992 1.00E-05 4.999999972 1.453516443 RGSPTTGFIEQKGS(ph)PTSAYPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSPTTGFIEQKGSPTSAYPER 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGSPTTGFIEQKGS(0.641)PT(0.18)S(0.18)AYPER 75.103 0.0064495 50636000 27529 18084 31622 19839 35720 27860 47182 34773 54109 TRUE FALSE 26227.75873 19926.78016 33071.89998 17844.74603 41949.55669 26895.20121 39983.51934 31728.09178 62499.94737 0.419644493 0.318828751 0.529150845 0.285516177 0.671193472 0.430323582 0.639736848 0.507649896 1 15.93156735 -5 0.136184645 2.893753765 0.255231904 0.719864593 0.108719589 62.62782663 0.528532096 31.94367031 0.614801959 1.00E-05 5 -2.638521861 RGSQNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSQNSSEHRPPASSTSEDVKASPSSANK 29 3 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGSQNSSEHRPPASSTSEDVKAS(0.993)PS(0.006)S(0.001)ANK 88.242 0.0012718 19801000 13108 9460.6 12559 13240 8067.7 11265 14075 15254 7523.5 TRUE FALSE 12488.41082 10424.6459 13134.84257 11909.09005 9474.704326 10874.89023 11927.60024 13918.27889 8690.205955 1.437067301 1.199585597 1.511453542 1.37040366 1.090273852 1.251396144 1.372533667 1.601605182 1 13.08517465 RGSS(ph)PGSLEIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.335)S(0.665)PGSLEIPK 104.41 0.002268 199110000 207740 198700 199210 227300 140140 211740 226600 245860 170160 TRUE FALSE 197920.5419 218947.7559 208343.9755 204451.3722 164580.3716 204407.3907 192028.0082 224331.195 196547.5437 1.006985578 1.113968416 1.06001821 1.040213316 0.837356542 1.039989546 0.977005383 1.141358425 1 17.58451881 2.9869715 24.85721026 0.993359872 1.062439054 0.115762139 0.077790832 1059.83904 2022080.795 0.021912052 0.024252108 970.4462801 -2.9869715 0.069079181 RGSS(ph)SSSPEHSASSDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGSSSSSPEHSASSDSTK 18 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 RGS(0.043)S(0.383)S(0.222)S(0.222)S(0.13)PEHSASSDSTK;RGS(0.286)S(0.475)S(0.073)S(0.121)S(0.044)PEHSASSDSTK 186.06 3.06E-14 535170000 655630 514470 566880 729850 478790 637140 774740 718130 513360 TRUE FALSE 624639.6692 566895.0779 592872.0087 656484.0914 562290.8244 615075.682 656539.1839 655246.7302 592969.2469 1.05340989 0.956027789 0.999836015 1.107113218 0.948263046 1.037280913 1.107206128 1.105026498 1 19.17759776 1.991448277 24.52058407 1.080052892 1.010889426 0.187958525 0.053635077 403.7187334 1157594.422 0.019398106 0.013609841 98.05015322 -1.991448277 -0.069163466 RGSSGS(ph)VDETLFALPAASEPVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.167)S(0.258)GS(0.401)VDET(0.173)LFALPAASEPVIR 187.29 1.52E-17 76095000 76696 79776 65907 110890 63091 80274 74430 75133 51722 TRUE FALSE 73070.73208 87905.2651 68928.90114 99743.12652 74094.05042 77494.09125 63074.3365 68553.95621 59742.7836 1.223088843 1.471395536 1.153761124 1.669542671 1.240217579 1.297128901 1.055764943 1.147485137 1 15.86647684 1.890433634 1.921742635 1.062701923 1.364055699 0.437979887 0.147429389 0.291747454 2.009334492 0.084377061 0.039419164 77.70225702 -1.890433634 0.301353775 RGSSS(ph)SSPEHSASSDSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGSSSSSPEHSASSDSTK 18 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 RGS(0.15)S(0.15)S(0.229)S(0.229)S(0.229)PEHS(0.012)ASSDSTK 99.603 0.00061596 88968000 129360 101620 107060 134880 90118 120370 140390 129550 91677 TRUE FALSE 123245.4092 111975.1935 111968.8069 121321.6061 105834.5507 116201.5567 118970.9271 118205.9152 105893.8009 1.163858584 1.057429165 1.057368854 1.145691297 0.999440475 1.097340502 1.123492839 1.116268508 1 16.69225861 4.635824907 3.205276565 1.081636328 1.167389972 0.232380566 0.049373107 0.41873277 7.054536686 0.011139036 0.077165081 43233.94911 -4.635824907 0.085753643 RGT(ph)GQSDDSDIWDDTALIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.494)GQS(0.494)DDS(0.011)DIWDDTALIK 100.64 0.00035408 153660000 25556 20006 24001 27218 17380 23215 30249 25417 24076 TRUE FALSE 24348.01853 22044.63414 25101.46959 24481.99493 20411.0665 22411.05873 25633.95949 23191.35274 27809.58312 0.875526196 0.792699195 0.902619413 0.880343831 0.733958018 0.805875393 0.921767125 0.833933851 1 14.7632945 0.353242414 0.80560102 1.00122065 0.837287334 0.431577323 0.056142606 2.250884522 1.98546507 0.062104481 0.018467805 2.25549783 -0.353242414 -0.163933316 RGT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Trastuzumab_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(0.499)S(0.499)PRPPEGGLGY(0.002)SQLGDDDLK 176.54 1.17E-11 114420000 143440 161160 120590 177070 91995 144920 129140 163530 94435 TRUE FALSE 136659.8755 177582.3872 126119.1708 159270.5872 108038.8989 139901.3841 109437.3212 149210.4463 109079.4975 1.252846581 1.62800885 1.156213346 1.460133122 0.990460181 1.282563518 1.003280394 1.367905516 1 16.73502043 2.748424446 24.98806671 1.131370836 1.390974381 0.331667377 0.172397953 701.7259556 1777683.043 0.04786502 0.050219745 560.3049327 -2.748424446 0.259603545 RGTGGVDTAATGGVFDISNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RGTGGVDTAATGGVFDISNLDR 22 1 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ;;; 213.14 2.01E-23 1478990000 1151570 814994 1052110 1095630 1149490 972092 1269320 1080333 1176340 FALSE TRUE 1097137.568 898042.8152 1100350.284 985495.1908 1349960.692 938428.2103 1075661.921 985733.3153 1358760.799 0.807454534 0.660927822 0.80981898 0.725289684 0.993523432 0.690650047 0.791649216 0.725464935 1 20.37386007 -1.735913096 2.612673961 1.046731481 0.770993296 0.371270144 0.091599542 24354654.7 18830081.49 7385411.022 0.020025063 0.018369059 1.735913096 -0.275738186 RGTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 RGT(0.341)GQS(0.668)DDS(0.991)DIWDDTALIK;RGT(0.462)GQS(0.556)DDS(0.982)DIWDDTALIK 166.69 6.80E-11 123639000 111473 87051 95968 108131 69577 106856 117802 114390 80245 TRUE FALSE 106203.8922 95921.59587 100368.2277 97261.46644 81711.20677 103155.5499 99829.14132 104373.4052 92688.98477 1.145809208 1.034875893 1.082849575 1.049331446 0.881563294 1.112921349 1.077033496 1.126060507 1 16.50011028 4.611568184 2.407021879 1.048886835 1.155446333 0.170021327 0.068866978 0.757541795 6.605286207 0.016797463 0.150013903 40885.39366 -4.611568184 0.106559499 RGTLVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RGTLVAER 8 1 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ;;;; 106.88 0.0065907 1154770000 1565130 991607 550417 669286 1606280 739566 1700790 1108567 1547980 FALSE TRUE 1491149.407 1092652.881 575654.1639 602008.0997 1886414.723 713954.644 1441303.248 1011494.997 1788032.832 0.833960865 0.61109218 0.321948319 0.336687386 1.055022419 0.39929616 0.806083212 0.565702698 1 20.7699418 -0.605505294 0.515279542 1.073065563 0.612872026 0.209248105 0.233640182 18.15080141 3.824305181 2.522167975 0.103468835 0.24802457 0.605505294 -0.460193537 RGVMLAVDAVIAELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RGVMLAVDAVIAELKK 16 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 181.72 1.27E-09 524600000 1404920 1029506 1163564 1139050 862005 1122650 1361707 1317020 924280 FALSE TRUE 1338512.216 1134413.832 1216914.56 1024550.53 1012338.399 1083772.349 1153953.588 1201694.747 1067612.622 1.253743341 1.062570645 1.139846547 0.959665059 0.948226331 1.015136321 1.080872935 1.125590614 1 20.02595684 4.70992484 0.992380473 1.03295202 1.364269254 0.548599315 0.061982429 1.417617721 1.15232437 0.019805896 0.498473169 51277.26341 -4.70992484 0.331317234 RGVTIKPTVDDD ddPTM_SK-BR-3_Trastuzumab_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 ;; 122.46 0.0014228 1669170000 2195650 2189250 2096310 2371350 1672790 2248930 2383610 2434750 1776160 FALSE TRUE 2091865.976 2412337.064 2192427.887 2132977.393 1964524.046 2171048.99 2019946.516 2221550.383 2051597.821 1.019627704 1.175833313 1.06864409 1.039666435 0.957558068 1.058223482 0.984572364 1.082839121 1 20.96831651 3.273117058 3.239536281 1.015801928 1.100185856 0.287822369 0.051287859 0.249450483 5.38648129 0.013974929 0.018725776 1875.499955 -3.273117058 0.084383928 RGWDCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGWDCVR 7 1 H3BTQ8;H3BSM2;H3BVD9;O43278-2;O43278 H3BTQ8 SPINT1 Kunitz-type protease inhibitor 1 0 98.523 0.017959 56167000 103410 99982 70428 88944 104620 77993 122600 94004 106020 FALSE TRUE 98522.01424 110170.2795 73657.19346 80003.18014 122865.6949 75292.08285 103895.1183 85772.51141 122461.0401 0.804517209 0.89963534 0.601474505 0.653294959 1.003304355 0.614824787 0.848393237 0.700406524 1 16.90196332 -1.955296019 6.574887395 1.113130714 0.777410758 0.240683376 0.129298185 0.075574281 0.000513845 0.044125481 0.027039341 0.01108419 1.955296019 -0.335719957 RGWVTFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RGWVTFDR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 99.855 0.014105 0 272840 230490 181310 242990 352900 211870 363880 269110 342560 FALSE TRUE 259943.3939 253977.193 189623.2428 218564.1835 414445.6483 204532.8888 308363.4229 245545.3018 395682.4552 0.656949507 0.641871252 0.479230859 0.552372693 1.047419826 0.516911695 0.779320434 0.62056151 1 18.59398357 RGYFDEEMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RGYFDEEMNR 10 1 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 ;;;;; 196.44 5.35E-07 1402620000 1174755 945670 808489 906253 1346769 894789 1274413 1068977 1333397 FALSE TRUE 1119226.659 1042034.848 845559.0204 815154.7267 1581645.087 863802.2326 1079977.891 975371.7069 1540173.397 0.726688736 0.676569827 0.549002484 0.529261659 1.026926637 0.560847392 0.701205392 0.633286946 1 20.55466135 -1.658214081 2.790205498 1.035861971 0.677609152 0.34314109 0.141080669 56594842.34 50713133.73 14473135.53 0.03097525 0.021967767 1.658214081 -0.358252819 RHEDGEFWMSFSDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RHEDGEFWMSFSDFLR 16 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;; 198.15 2.69E-11 535853000 876523 766101 737381 827463 1073544 755761 1173899 854728 586100 FALSE TRUE 835091.4949 844167.5629 771190.6482 744284.8472 1260769.734 729588.8071 994799.1474 779883.4851 676989.3946 1.233537041 1.246943556 1.139147311 1.099403998 1.862318293 1.077696066 1.469445689 1.151987744 1 19.36877371 0.99930998 24.67322881 0.999999979 1.298129319 0.164672101 0.227988424 27.92140597 998444.6013 0.198325422 0.049581355 9.984124327 -0.99930998 0.29812934 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 334.18 9.51E-130 13170891000 3602316.8 3416635.5 3806999 3905569 4167640.5 3701220.9 4714062 3747503.4 2249328.8 FALSE TRUE 3432042.424 3764794.542 3981553.67 3512973.784 4894475.684 3573046.692 3994845.262 3419352.136 2598143.222 1.320959674 1.449032721 1.532461196 1.352109366 1.88383598 1.375230842 1.537577 1.316075306 1 21.30904953 -0.479933274 7.308130079 0.999999996 1.471279419 0.441900844 0.166315491 0 0 0.146963401 0.034639606 0.331182001 0.479933274 0.471279422 RHEHPPNPPVS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 82.482 0.0049797 189538000 428203 486887 365550 533434 238170 443609 464095 475622 132400 TRUE FALSE 407962.6928 536501.3388 382310.8291 479812.2009 279706.7726 428246.7091 393288.7841 433974.0162 152931.9158 2.667609901 3.508105787 2.499876021 3.137423594 1.828962719 2.800244193 2.571659304 2.837694238 1 17.22252999 2.765462582 24.85081274 2.374733012 2.988803329 0.250922369 0.601471101 1035.975708 956985.5527 0.165051558 0.17502073 582.7235658 -2.765462582 0.614070317 RHEHPPNPPVS(ph)PGKTVNDVNSNNNMSYR ddPTM_SK-BR-3_Trastuzumab_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(0.994)PGKT(0.006)VNDVNSNNNMSYR 184.78 5.02E-18 181420000 41100 32170 48721 48206 34882 51438 62853 49558 6903.1 TRUE FALSE 39157.28445 35448.15957 50954.90604 43360.24129 40965.40976 49656.68916 53263.62048 45218.4388 7973.597492 4.91086796 4.445692125 6.390453756 5.437977191 5.137632016 6.227639307 6.679998649 5.671020997 1 12.96101506 2.368934357 20.58163349 5.557224 5.179623017 0 1.654522993 19.50359468 3621.868757 0.518679546 0.433957665 233.8483755 -2.368934357 -0.377600982 RHGAPAAPS(ph)PPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHGAPAAPSPPPR 13 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RHGAPAAPS(1)PPPR 54.7 0.06364 31751000 26220 22238 24991 26077 38906 23544 33676 24013 36613 TRUE FALSE 24980.63256 24504.07748 26136.86207 23455.69042 45691.19408 22728.66538 28538.1077 21910.29442 42290.75705 0.59068776 0.579419221 0.618027765 0.554629239 1.080406152 0.53743813 0.674807208 0.51808707 1 15.36805477 RHNS(ph)SDGFDSAIGRPNGGNFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHNSSDGFDSAIGRPNGGNFGR 22 2 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 RHNS(0.974)S(0.026)DGFDSAIGRPNGGNFGR;RHNS(0.953)S(0.047)DGFDSAIGRPNGGNFGR 184 2.12E-17 850440000 137261 96074 105349 119284 100245 106070 125571 93195 69899 TRUE FALSE 130772.9446 105864.0498 110179.3559 107293.3457 117727.6963 102396.7693 106412.8377 85034.35174 80738.57993 1.619708257 1.311195341 1.364643222 1.328898103 1.458134344 1.268250809 1.317992437 1.053205937 1 16.30097059 7.999998222 0.040213078 1.15E-07 3.51531565 0.727513073 0.092816762 389.7257136 1.193362365 28.47693447 93.16771958 99999590.61 -7.999998222 3.515315535 RHNS(ph)WSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RHNSWSSSSR 10 1 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(1)WSSSSR;RHNS(0.987)WS(0.007)S(0.002)S(0.002)S(0.002)R;RHNS(1)WSSSSR 156.08 7.09E-06 981443000 245427.6 187530.9 213115.7 256267.1 286522.2 204776.2 292317.7 235988.6 218574.2 TRUE FALSE 233826.7237 206640.5119 222887.2656 230506.6442 336491.581 197684.7488 247719.2661 215324.1871 252469.5706 0.926158044 0.818476902 0.882828236 0.91300763 1.332800544 0.783004258 0.981184645 0.85287184 1 17.94574999 2.989010799 24.96275722 0.986142985 0.874123226 0.12050083 0.143486166 1102.67868 2504820.849 0.040305036 0.045276751 975.013882 -2.989010799 -0.112019759 RHPHTEHVQQTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHPHTEHVQQTFR 13 1 C9J5A3;D3YTC6;Q68DG0;Q8N241;Q9UBY9;Q9UBY9-2 C9J5A3 HSPB7;DKFZp779D0968 Heat shock protein beta-7 0 116.51 0.00023572 47677000 4977.2 3705.8 4680.5 5667.5 11372 3628.9 5374.6 5657.5 5059.7 FALSE TRUE 4741.93762 4083.425233 4895.105555 5097.792132 13355.2732 3503.230283 4554.606059 5162.099308 5844.332435 0.811373698 0.698698317 0.837581642 0.872262519 2.285166586 0.599423514 0.779320155 0.883265859 1 12.51282253 2.985786081 24.96435746 1.082319584 0.779477826 0.102242908 0.450820956 1690.865296 2969726.375 0.135432212 0.148952624 967.8010323 -2.985786081 -0.302841758 RHPKGEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(1)DDDETENGPKPK;RHPKGEEGS(0.996)DDDET(0.004)ENGPKPK;RHPKGEEGS(1)DDDETENGPKPK 236.94 5.44E-30 731770000 920580 703330 1002030 904210 462680 1130950 1251750 1111580 373657 TRUE FALSE 877066.0078 775000.1266 1047974.067 813317.0929 543371.2455 1091784.918 1060772.548 1014244.162 431601.8192 2.032118422 1.79563684 2.428103914 1.884415349 1.258964215 2.529611483 2.45775736 2.3499534 1 18.71934142 RHPKGEEGSDDDET(ph)ENGPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(0.322)DDDET(0.678)ENGPKPK 235.68 4.39E-30 286070000 530830 387400 573890 524050 245020 658970 681170 613890 207710 TRUE FALSE 505738.7179 426876.5004 600203.4242 471371.4984 287751.4104 636149.7037 577245.006 560134.5372 239920.606 2.107941983 1.779240673 2.501675176 1.964697849 1.199360969 2.651500904 2.405983445 2.334666232 1 17.87219755 5.042744245 13.52349699 2.050856627 2.323223049 0 0.545814066 4507576.975 49180021.81 0.120933117 29197185.31 110342.8622 -5.042744245 0.272366421 RHS(ph)ALQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSALQR 7 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 RHS(1)ALQR 68.657 0.036564 0 12653 11093 12887 12236 22338 11347 14818 9361 22613 TRUE FALSE 12054.91777 12223.38931 13477.8817 11006.01403 26233.74013 10954.05054 12557.24195 8541.301214 26119.70855 0.461525738 0.467975716 0.516004291 0.421368179 1.004365729 0.419378743 0.480757353 0.327005992 1 14.67285118 -1.876343909 2.803889035 1.219990949 0.510967321 0.414253783 0.18224861 37060043.01 21214462.89 53958664.81 0.041546853 0.013294013 1.876343909 -0.709023628 RHS(ph)ASNLHALAHPAPSPGSCSPK ddPTM_SK-BR-3_Trastuzumab_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 107.94 0.00049035 348760000 358930 304680 358810 408650 334060 390510 496910 354730 9202.6 TRUE FALSE 341964.0902 335727.2384 375261.7934 367571.7256 392319.9582 376986.5408 421097.2531 323667.9607 10629.69221 32.17064836 31.58390966 35.30316646 34.57971486 36.9079321 35.46542397 39.61518781 30.44941983 1 13.3758122 0.959446691 20.31823796 0.999999973 34.86610153 0.957256697 2.245820173 132.3564735 66314.34902 2.552575108 0.638143777 9.108496394 -0.959446691 33.86610156 RHS(ph)DENDGGQPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RHS(1)DENDGGQPHK 212.59 5.98E-09 2393961000 2787055 3266335 2828522 3639977 2188309.8 3172484 3158339 2652288 567378.1 TRUE FALSE 2655316.434 3599178.25 2958212.531 3274079.596 2569950.336 3062620.084 2676476.379 2420039.602 655364.198 4.051665382 5.491874993 4.513845188 4.995816992 3.921407889 4.673157449 4.083952689 3.692663727 1 19.32193734 0.195506608 0.543427458 0.758597161 4.77288238 0.869042673 0.435341587 0.934374136 0.384554906 0.878400669 0.183722593 1.568579765 -0.195506608 4.014285219 RHS(ph)DENDGGQPHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR 169.28 1.75E-06 308920000 194411.9 184948.7 213918.3 228361 163018.1 213042 232878.9 180388.9 56442.59 TRUE FALSE 185222.4348 203795.1828 223726.6656 205405.7184 191448.405 205664.3021 197348.9467 164593.0916 65195.41859 2.84103452 3.125912636 3.431631708 3.150615839 2.936531572 3.154582125 3.027037037 2.524611317 1 15.99248297 0.777941255 1.818936204 1.000598362 3.100729902 0.948735451 0.153591874 0.166335396 0.929588185 0.151008069 0.042462083 5.997099505 -0.777941255 2.10013154 RHS(ph)EVETDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RHSEVETDSK 10 1 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RHS(0.997)EVET(0.003)DSK;RHS(1)EVETDSK;RHS(1)EVETDSK 143.64 2.06E-05 326297000 602730 589160 536795 738648 563166 592718 652800 567898 568685 TRUE FALSE 574240.1474 649196.0738 561407.5817 664397.6997 661381.9721 572192.027 553203.3705 518169.8405 656873.7654 0.874201677 0.98831177 0.85466586 1.011454156 1.006863125 0.871083696 0.842176077 0.788842344 1 19.32525662 2.09173648 8.607992222 0.858783534 0.944708651 0.176555261 0.073343353 0.35918357 30.01807694 0.025314063 0.018679857 123.5197717 -2.09173648 0.085925117 RHS(ph)EVETDSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHSEVETDSKK 11 2 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RHS(1)EVETDSKK;RHS(1)EVETDSKK 126.71 0.00015753 109737000 158467 140762 144975 170761 104281 172858 173903 156697 81450 TRUE FALSE 150976.579 155105.8078 151622.2471 153595.7799 122467.5734 166871.8841 147370.9034 142975.78 94080.85001 1.60475356 1.648643776 1.611616467 1.632593454 1.301726902 1.773707233 1.566428273 1.519711822 1 16.52161347 0.648710565 2.21613321 1.000089233 1.597624453 0.712615027 0.117085192 1.080546848 6.184485943 0.101755737 0.027622315 4.453593402 -0.648710565 0.59753522 RHS(ph)HS(ph)HS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 3 RHS(1)HS(1)HS(1)PMSTR 92.439 0.0036364 114640000 70724 57372 73214 73655 64526 71274 109470 57627 39888 TRUE FALSE 67381.01668 63218.27203 76570.93432 66251.05946 75779.31397 68805.76351 92768.34095 52580.87438 46073.62732 1.4624639 1.372114064 1.661925461 1.437938867 1.644743824 1.493387161 2.0134803 1.141235831 1 15.49165356 1.020314309 23.85610055 0.999999902 1.572325387 0.59550551 0.177743686 81.32015912 95497.73113 0.181038467 0.045259635 10.47886653 -1.020314309 0.572325485 RHS(ph)HSHS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.945)HS(0.055)HS(1)PMSTR;RHS(0.996)HS(0.006)HS(0.997)PMSTR 96.773 0.0039413 172180000 31497 33823 38506 40360 39896 37744 47027 24845 6731.9 TRUE FALSE 30008.19923 37269.60215 40271.53819 36302.93612 46853.84977 36436.91582 39852.16744 22669.44009 7775.84867 3.859154223 4.792994789 5.179053746 4.668678322 6.025560907 4.685908556 5.125121274 2.91536539 1 12.92478443 1.012632212 3.184177973 1.01235722 4.866653583 0.850446831 0.545967332 0.081723233 1.963838324 0.532194943 0.139424144 10.29513894 -1.012632212 3.854296363 RHS(ph)HTIGGLPESDDQSELPSPPALPMSLSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSHTIGGLPESDDQSELPSPPALPMSLSAK 31 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6;H7BZD9 Q8NEY1-5 NAV1 Neuron navigator 1 1 RHS(0.249)HT(0.249)IGGLPES(0.249)DDQS(0.249)ELPS(0.002)PPALPMSLSAK 50.857 0.0361 51935000 34386 30201 31330 38715 31336 38199 42340 30110 6108.8 TRUE FALSE 32760.64193 33278.51624 32766.51149 34823.29465 36800.98848 36876.15905 35880.25537 27473.40878 7056.121505 4.642868168 4.71626179 4.643700008 4.9351892 5.215469781 5.226123024 5.084982642 3.893556646 1 12.78465969 0.85833544 3.103311134 1.001455106 4.904528669 0.969852456 0.217569771 0.110795875 1.983030497 0.248065906 0.064774888 7.216646625 -0.85833544 3.903073563 RHS(ph)LAMPGETVLNGNQEWVVQADLPLTAAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHSLAMPGETVLNGNQEWVVQADLPLTAAIR 31 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 RHS(0.997)LAMPGET(0.003)VLNGNQEWVVQADLPLTAAIR;RHS(0.824)LAMPGET(0.176)VLNGNQEWVVQADLPLTAAIR 59.971 0.013985 47884000 38243 43459 40177 45638 31764 41260 40160 43674 27251 TRUE FALSE 36435.32918 47887.52151 42019.15519 41050.38153 37303.63154 39831.15585 34032.85441 39849.67303 31476.9459 1.157524281 1.521352219 1.33491843 1.304141185 1.185109625 1.26540726 1.081199381 1.265995537 1 14.94200795 1.748521335 0.53852203 1.032985896 1.354699394 0.418806288 0.109601616 0.715204567 0.468922145 0.103850719 0.06540537 56.04299481 -1.748521335 0.321713498 RHS(ph)LSSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSLSSTK 8 1 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 RHS(1)LSSTK 79.82 0.016567 62714000 48204 46860 43702 59518 52719 57174 64844 58900 43247 TRUE FALSE 45925.49245 51635.08728 45705.77993 53535.13756 61913.17691 55194.05004 54950.85686 53742.40375 49953.52388 0.919364419 1.033662558 0.91496608 1.071698919 1.239415603 1.104908038 1.100039649 1.0758481 1 15.60829883 3.080197488 6.0011352 1.11368418 0.968507388 0.50289218 0.066719043 0.155189528 9.047514392 0.018085127 0.021688713 1202.811268 -3.080197488 -0.145176792 RHS(ph)PESPSIAVVESELVAEYITTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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)IAVVES(0.001)ELVAEYITTER;RHS(0.25)PES(0.25)PS(0.25)IAVVES(0.25)ELVAEYITTER;RHS(0.336)PES(0.336)PS(0.328)IAVVESELVAEYITTER;RHS(0.322)PES(0.322)PS(0.322)IAVVES(0.035)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER 148.28 1.02E-07 42853000 46885.3 38483 37095.9 47205.4 48559.2 40856.3 48858.7 42104.2 32705.6 TRUE FALSE 44669.12479 42404.46145 38796.78371 42460.22351 57027.90911 39441.43609 41404.40796 38417.33304 37777.41741 1.182429288 1.122481746 1.026983483 1.123957814 1.5095767 1.044047973 1.096009489 1.016939105 1 15.20523646 RHS(ph)PPIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 153.74 0.0002672 967080000 1331940 1157030 1234050 1460150 1067230 1371600 1595680 1345890 916580 TRUE FALSE 1268981.836 1274932.672 1290632.413 1313372.948 1253354.574 1324101.148 1352229.709 1228036.737 1058718.545 1.198601688 1.20422248 1.219051484 1.240530785 1.183841144 1.250663979 1.277232476 1.159927482 1 20.01388768 0.94125523 6.772921029 1.000005754 1.223802467 0.874864146 0.026873571 0.22232477 25.15701873 0.02849596 0.007149942 8.734845546 -0.94125523 0.223796713 RHS(ph)SDINHLVTQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.91)S(0.09)DINHLVTQGR;RHS(0.949)S(0.051)DINHLVTQGR;RHS(0.847)S(0.153)DINHLVTQGR 148.2 3.68E-06 3071060000 1487280 1200700 1476880 1688580 2382400 1362860 2195210 1481170 526920 TRUE FALSE 1416979.222 1323052.695 1544596.409 1518840.73 2797889.806 1315663.816 1860290.397 1351470.903 608632.0625 2.328137654 2.173813666 2.537816366 2.495499044 4.597013497 2.161673526 3.056510676 2.220505599 1 19.21521081 3.380301977 2.835711405 2.776525311 2.263503417 0 0.901993311 0.777868379 12.61227248 0.238793554 0.343640856 2400.501473 -3.380301977 -0.513021894 RHS(ph)SDINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RHSSDINHLVTQGRESPEGSYTDDANQEVR 30 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 2 RHS(0.917)S(0.083)DINHLVTQGRES(1)PEGSYTDDANQEVR;RHS(0.79)S(0.21)DINHLVT(0.396)QGRES(0.604)PEGSYTDDANQEVR;RHS(0.886)S(0.114)DINHLVTQGRES(1)PEGSYTDDANQEVR;RHS(0.74)S(0.26)DINHLVT(0.002)QGRES(0.998)PEGSYTDDANQEVR 259.91 1.53E-58 2463810000 552279 481705 577021 582982 652941 569665 830412 640363 369574 TRUE FALSE 526173.8662 530791.2872 603477.9836 524379.5418 766813.7037 549937.3582 703717.3978 584289.4209 426885.6484 1.232587388 1.243403917 1.413675971 1.228384097 1.796297689 1.288254502 1.648491582 1.368725848 1 18.70349014 3.43895145 1.503230652 1.455228089 1.235150958 0.035046987 0.221692613 0.707671637 3.258363768 0.063641717 0.111204008 2747.586984 -3.43895145 -0.220077132 RHS(ph)TFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHSTFK 6 1 Q9H329-2;Q9H329 Q9H329-2 EPB41L4B Band 4.1-like protein 4B 1 RHS(0.978)T(0.022)FK;RHS(0.985)T(0.015)FK 78.149 0.04321 124385000 185518 150515 141518 186819 156517 158641 201000 166370 141771 TRUE FALSE 176748.9318 165852.6496 148006.7403 168039.5992 183813.5152 153147.2224 170333.7584 151801.7608 163756.1226 1.079342433 1.01280274 0.903824162 1.026157658 1.122483314 0.935215245 1.040167266 0.926998993 1 17.32118932 4.373058642 2.844719413 0.998370927 1.074064092 0.14637007 0.06333302 0.499224382 7.573365503 0.015027836 0.058494371 23607.96986 -4.373058642 0.075693165 RHS(ph)VSEMTSCPEPQGFSDPPGQGPTGTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.368)VS(0.368)EMT(0.111)S(0.153)CPEPQGFSDPPGQGPTGTFR;RHS(0.25)VS(0.25)EMT(0.25)S(0.25)CPEPQGFSDPPGQGPTGTFR;RHS(0.845)VS(0.12)EMT(0.018)S(0.018)CPEPQGFSDPPGQGPTGTFR 148.02 2.09E-08 400901000 105482 89971 99740 109426 109487 105090 127520 99162 95712 TRUE FALSE 100496.0749 99139.14719 104313.1777 98426.29058 128581.4981 101450.7069 108064.4819 90478.84959 110554.5281 0.909018171 0.896744338 0.943545049 0.890296329 1.163059535 0.917653113 0.97747676 0.81840926 1 16.75439859 RHS(ph)VTDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RHSVTDKR 8 2 Q17R89-3;Q17R89 Q17R89-3 ARHGAP44 Rho GTPase-activating protein 44 1 RHS(0.991)VT(0.009)DKR;RHS(0.994)VT(0.006)DKR;RHS(0.8)VT(0.2)DKR 87.568 0.0079477 56018000 72155 69486 68423 83703 53893 69385 82605 74588 51065 TRUE FALSE 68744.37615 76566.7024 71560.26223 75289.01541 63291.92214 66982.18005 70002.09011 68056.6793 58983.8994 1.165476967 1.298094958 1.213216877 1.276433335 1.073037266 1.135601083 1.186799971 1.153817906 1 15.84803358 2.744330654 24.99929579 1.128787235 1.238784562 0.501282777 0.062089112 432.1378252 1872283.824 0.018037961 0.018655154 555.0481436 -2.744330654 0.109997327 RHS(ph)VTLPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RHSVTLPSSK 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 RHS(0.999)VT(0.001)LPSSK;RHS(0.992)VT(0.008)LPSSK;RHS(1)VTLPSSK;RHS(0.998)VT(0.002)LPSSK 152.07 1.14E-05 2386810000 4000590 3041470 3422550 4188090 3352250 3929900 4790550 3767030 2690930 TRUE FALSE 3811490.039 3351399.251 3579477.303 3767095.236 3936881.339 3793806.578 4059663.613 3437168.883 3108225.681 1.226259104 1.078235493 1.151614352 1.211976099 1.266600866 1.220569858 1.306103234 1.105829896 1 21.56765983 3.247233194 6.330888156 1.213605327 1.146461454 0 0.094096101 0.3395986 54.53545557 0.024365972 0.031548705 1766.986349 -3.247233194 -0.067143872 RHS(ph)VVAGGGGGEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RHSVVAGGGGGEGR 14 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR 171.47 1.84E-06 1977970000 982608 901612 989442 1117502 959652 1009258 1222887 1030041 847030 TRUE FALSE 936162.0672 993487.2878 1034808.894 1005168.576 1127015.005 974307.1424 1036313.128 939845.1494 978383.0864 0.956846127 1.015437922 1.05767251 1.027377302 1.151915871 0.995834 1.059209979 0.960610586 1 19.90003994 4.285508213 1.898408029 1.041458396 0.958143484 0.182398153 0.051069284 0.545698278 3.509863899 0.01249085 0.058145004 19297.8183 -4.285508213 -0.083314913 RHS(ph)WGPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;RHS(1)WGPGK 158.3 0.00022405 1000450000 1840890 1665630 1747670 2029940 1726660 1814120 2165520 1695720 1607360 TRUE FALSE 1753874.778 1835359.591 1827802.398 1825886.575 2027788.957 1751296.57 1835130.151 1547233.767 1856621.18 0.944659469 0.988548235 0.984477834 0.983445947 1.092193162 0.943270813 0.988424656 0.833359968 1 20.82424805 -0.829200701 4.180189997 1.000000305 0.974338576 0.017530366 0.063418195 7302744.571 1747024.868 21.47430463 0.013558307 0.148183312 0.829200701 -0.02566173 RHSHS(ph)HS(ph)PMSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.426)HS(0.584)HS(0.988)PMS(0.001)T(0.001)R 60.918 0.090281 50364000 6605.3 5409.4 10556 9756.7 10385 7122.3 11709 5771.1 2464.2 TRUE FALSE 6293.080559 5960.62401 11040.00304 8775.937979 12196.14071 6875.652965 9922.576999 5265.751889 2846.335551 2.210941208 2.094139607 3.878672365 3.083240828 4.284856966 2.415615743 3.486088278 1.850010934 1 11.47489003 3.791110706 24.97487105 3.027008168 2.152539502 0.063500314 0.965869753 580.2167508 275750.7568 0.218519571 0.393941446 6181.739587 -3.791110706 -0.874468666 RHSLS(ph)STK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSLSSTK 8 1 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 RHS(0.001)LS(0.932)S(0.054)T(0.014)K 53.08 0.085046 60982000 73739 63418 53994 70843 61883 69200 86799 75785 55040 TRUE FALSE 70253.50361 69880.3663 56469.67831 63721.72705 72675.37561 66803.58665 73556.21838 69148.86364 63575.32209 1.105043613 1.099174397 0.888232673 1.002302858 1.143138142 1.05077858 1.156993248 1.087668318 1 15.95617925 2.743433912 24.92541581 1.099132547 1.037783541 0.134067805 0.074160672 852.9113732 4362383.58 0.023793094 0.024456735 553.9032487 -2.743433912 -0.061349006 RHSPESPSIAVVES(ph)ELVAEYITTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.226)PES(0.226)PS(0.226)IAVVES(0.323)ELVAEYITTER 76.02 0.014207 7253500 10199 8099.3 8744.5 12879 11776 9102.1 10268 9272.4 7841.2 TRUE FALSE 9716.913482 8924.627878 9145.443974 11584.37845 13829.73067 8786.891995 8701.428015 8460.4595 9057.173249 1.072841737 0.985365702 1.009745946 1.279028029 1.526936749 0.970158321 0.960722267 0.934117 1 13.14484514 2.052803016 24.99993098 0.961788633 1.146225123 0.301226266 0.15444969 147.6532549 69906.59577 0.062851118 0.04641862 112.9283587 -2.052803016 0.18443649 RHSS(ph)DINHLVTQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.386)S(0.614)DINHLVTQGR;RHS(0.29)S(0.71)DINHLVTQGR;RHS(0.396)S(0.604)DINHLVTQGR;RHS(0.415)S(0.585)DINHLVTQGR;RHS(0.416)S(0.584)DINHLVTQGR 113.54 0.00024897 3694610000 1637690 1334010 1491300 1873770 2407310 1409740 2129990 1665180 564896 TRUE FALSE 1560279.639 1469947.136 1559677.58 1685415.08 2827144.102 1360920.35 1805020.906 1519368.012 652497.1866 2.391243474 2.252802259 2.390320774 2.583022754 4.332806577 2.085710679 2.766327492 2.328543391 1 19.31561216 3.231154831 5.085659454 2.668832796 2.328143527 0 0.818879786 0.696041541 50.12806897 0.215787257 0.274938183 1702.765456 -3.231154831 -0.34068927 RHSS(ph)DINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RHSSDINHLVTQGRESPEGSYTDDANQEVR 30 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 2 RHS(0.455)S(0.545)DINHLVT(0.034)QGRES(0.801)PEGS(0.145)Y(0.02)TDDANQEVR;RHS(0.458)S(0.542)DINHLVT(0.23)QGRES(0.715)PEGS(0.027)Y(0.028)TDDANQEVR 188.2 6.08E-18 841780000 76388 70708 73716 108760 105556 73689 119154 95466 35257 TRUE FALSE 72777.29063 77913.22559 77095.95152 97827.23817 123964.933 71137.13145 100974.8689 87106.49094 40724.47549 1.787065143 1.913179351 1.893110975 2.402173066 3.043990904 1.746790612 2.479463951 2.138922353 1 15.3136085 3.307530585 7.806428813 2.240371099 1.861113867 0.030861332 0.530250039 0.536098625 52.61322555 0.131115457 0.177382078 2030.161487 -3.307530585 -0.379257232 RHT(ph)MDKDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 79.693 0.035193 71812000 128996 114319 102372 120240 94543 139789 170594 146873 71860 TRUE FALSE 122898.6147 125968.2361 107065.8575 108153.2468 111031.2693 134948.0719 144566.7521 134012.0215 83003.68179 1.480640522 1.517622271 1.289892872 1.302993366 1.337666798 1.625808265 1.741690838 1.61453105 1 16.34088771 2.234518793 24.98941175 1.579515849 1.40424916 0 0.213947255 200.9534443 1242420.49 0.072670304 0.05563551 171.6005963 -2.234518793 -0.175266689 RHT(ph)PLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 103.7 0.0048738 678513000 1189470 1139460 1124870 1445180 918150 1182300 1377570 1169250 580166 TRUE FALSE 1133246.11 1255572.269 1176446.402 1299907.761 1078275.069 1141356.655 1167396.396 1066864.271 670135.1802 1.691070912 1.873610439 1.755535953 1.939769466 1.609041133 1.70317376 1.742031205 1.592013526 1 19.35409262 -0.178458686 0.512613921 0.907279348 1.795967983 0.875832793 0.089859384 1.691826921 0.476601186 0.385686878 0.039828011 0.663042419 0.178458686 0.888688635 RHT(ph)VGVADPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHTVGVADPR 10 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2;H7C3X8 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RHT(1)VGVADPR 50.222 0.09641 244840000 294250 246110 301230 308810 364110 296040 390440 294950 252360 TRUE FALSE 280341.3856 271188.8888 315041.6935 277767.8321 427610.6687 285788.0606 330871.2071 269122.6144 291494.6999 0.961737506 0.930339004 1.080780177 0.952908688 1.466958641 0.980422837 1.135084813 0.923250455 1 18.15311013 3.53063205 1.940388611 1.099022877 0.945429932 0.097577047 0.154137381 0.607883006 4.547933934 0.042587058 0.073804043 3393.376517 -3.53063205 -0.153592946 RHVTLPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RHVTLPSSPR 10 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 RHVT(0.001)LPS(0.603)S(0.396)PR 71.548 0.031026 240740000 109730 108500 119110 136250 124710 115540 144560 115640 114090 TRUE FALSE 104543.2804 119556.2734 124571.3113 122553.8911 146459.3845 111538.8208 122504.717 105513.9486 131782.4945 0.793301726 0.907224239 0.945279658 0.929970946 1.111372076 0.846385715 0.9295978 0.80066741 1 17.00779922 4.412840567 1.745095294 0.935569256 0.78508409 0.228281392 0.082667843 0.704757821 3.358433476 0.02087573 0.143281024 25872.62935 -4.412840567 -0.150485166 RIACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIACDEEFSDSEDEGEGGR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 RIACDEEFS(1)DS(1)EDEGEGGR 80.975 0.0015674 0 102010 93427 78892 96124 82846 96734 95899 93022 80676 TRUE FALSE 97188.18946 102947.3175 82509.27623 86461.4329 97294.31617 93384.07732 81267.84624 84876.50054 93186.82204 1.042939198 1.104741156 0.885417857 0.927828968 1.044078058 1.002116772 0.872095909 0.910820851 1 16.50783833 3.746617196 24.92418504 0.945476815 1.073840183 0.460767275 0.056092318 471.7581945 1459447.626 0.014877938 0.026247665 5579.781549 -3.746617196 0.128363368 RIDFIPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 RIDFIPVS(1)PAPS(0.979)PT(0.021)R;RIDFIPVS(1)PAPS(0.976)PT(0.024)R;RIDFIPVS(1)PAPS(0.989)PT(0.011)R;RIDFIPVS(1)PAPS(0.967)PT(0.033)R;RIDFIPVS(1)PAPS(0.98)PT(0.02)R;RIDFIPVS(1)PAPS(0.892)PT(0.108)R 106.03 0.0024139 439633000 490648 409240 435222 457172 495905 424393 509189 461056 567733 TRUE FALSE 467456.0414 450942.0213 455177.3592 411216.202 582390.675 409696.164 431502.8662 420683.4924 655774.1341 0.712830862 0.687648381 0.694106912 0.627069872 0.888096442 0.624751942 0.658005316 0.641506687 1 19.32283947 -1.05779079 4.844596537 1.000006588 0.691168626 0.621857864 0.075540116 6.28E-06 1.22E-06 0.06693546 0.01577641 0.087540538 1.05779079 -0.308837962 RIDFTPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.887)PT(0.113)R;RIDFT(0.013)PVS(0.987)PAPS(0.993)PT(0.007)R;RIDFT(0.001)PVS(0.999)PAPS(0.994)PT(0.006)R;RIDFT(0.003)PVS(0.997)PAPS(0.993)PT(0.007)R 124.68 6.36E-05 1198760000 1198000 1133850 1124580 1272020 1181670 1105730 1195200 1234660 1238840 TRUE FALSE 1141372.914 1249390.604 1176143.105 1144154.133 1387752.874 1067438.293 1012850.289 1126546.625 1430952.98 0.79763132 0.87311786 0.821929946 0.799574933 0.969810255 0.74596322 0.707815213 0.78727019 1 20.44854484 RIDIS(ph)PSTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.999)PS(0.001)TFR;RIDIS(0.796)PS(0.192)T(0.012)FR;RIDIS(0.936)PS(0.06)T(0.004)FR;RIDIS(0.996)PS(0.003)T(0.001)FR;RIDIS(0.926)PS(0.064)T(0.01)FR;RIDIS(0.675)PS(0.24)T(0.085)FR;RIDIS(0.792)PS(0.196)T(0.012)FR;RIDIS(0.929)PS(0.052)T(0.019)FR;RIDIS(0.967)PS(0.028)T(0.005)FR 151.16 1.24E-05 19851610000 1092988 852547 957342 1066646 1989310 933957 1184940 895961 2041800 TRUE FALSE 1041324.623 939422.5086 1001237.078 959424.7176 2336245.034 901613.8349 1004155.64 817505.9051 2358431.916 0.44153262 0.398325049 0.424535078 0.406806197 0.990592528 0.382293773 0.425772579 0.346631124 1 21.16939652 -1.951603642 2.620103493 1.39433597 0.471869809 0.441111146 0.184905334 47811299.19 24372089.75 114824443.6 0.046201678 0.01117883 1.951603642 -0.922466161 RIDIS(ph)PSTFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.994)PS(0.005)T(0.001)FRK;RIDIS(0.885)PS(0.015)T(0.1)FRK;RIDIS(0.927)PS(0.027)T(0.047)FRK 126.71 0.00015753 2282920000 930245 524380 946342 776778 946081 887186 1275550 994529 1211018 TRUE FALSE 886274.1624 577814.9182 989732.7168 698694.7997 1111077.227 856462.5264 1080941.42 907442.7684 1398816.486 0.633588588 0.413074141 0.70755008 0.499489966 0.794298064 0.612276546 0.772754275 0.648721814 1 20.41577527 -1.065830642 0.155168582 1.398407713 0.43150989 0.573177365 0.105841771 16.67194815 0.533854063 3.29194415 0.582211737 0.085934857 1.065830642 -0.966897822 RIDIS(ph)PSTLR ddPTM_SK-BR-3_Trastuzumab_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(0.957)PS(0.032)T(0.011)LR;RIDIS(0.875)PS(0.108)T(0.017)LR;RIDIS(0.995)PS(0.005)TLR;RIDIS(0.927)PS(0.048)T(0.025)LR;RIDIS(0.981)PS(0.018)T(0.001)LR;RIDIS(0.999)PS(0.001)TLR;RIDIS(0.498)PS(0.498)T(0.003)LR;RIDIS(0.998)PS(0.002)TLR;RIDIS(0.686)PS(0.234)T(0.08)LR 132.93 0.00012898 19303030000 1129343 938993 919856 1171692 1153490 947221 1180565 1052777 1129008 TRUE FALSE 1075961.195 1034677.454 962032.3075 1053911.294 1354658.291 914418.4993 1000448.127 960590.2648 1304088.794 0.825067433 0.793410279 0.737704604 0.808159152 1.038777648 0.701193433 0.767162582 0.736598818 1 20.31461067 -2.214299035 2.326448396 1.629655117 0.800247932 0.315111892 0.092190075 7809989.553 1124053.111 26021362.32 0.021283418 0.006105215 2.214299035 -0.829407184 RIDIS(ph)PSTLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.997)PS(0.002)TLRK;RIDIS(0.997)PS(0.002)TLRK;RIDIS(0.997)PS(0.003)TLRK;RIDIS(0.996)PS(0.004)T(0.001)LRK;RIDIS(0.998)PS(0.002)TLRK;RIDIS(0.964)PS(0.025)T(0.011)LRK 119.32 0.00031443 5716760000 3344420 2457398 3203460 3351910 3138470 3208440 4409180 3734590 3848630 TRUE FALSE 3186335.895 2707809.65 3350341.81 3014969.639 3685818.174 3097330.918 3736478.611 3407569.501 4445455.884 0.71676246 0.609118552 0.753655395 0.678213825 0.829120403 0.696740897 0.840516408 0.766528696 1 22.08389995 -0.527226442 0.180654365 1.208394389 0.60891178 0.707436446 0.058139517 7.458235178 0.367940978 1.041628766 0.220704194 0.2970117 0.527226442 -0.59948261 RIDISPS(ph)TFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.323)PS(0.67)T(0.008)FR 85.081 0.008871 3972600000 97549 70506 87200 104940 437120 71534 137960 76422 425320 TRUE FALSE 92938.05209 77690.64156 91198.20625 94391.23183 513353.5896 69056.75964 116911.6682 69730.08454 491276.4534 0.189176687 0.158140373 0.185635207 0.192134655 1.044938315 0.140565987 0.237975314 0.141936549 1 18.90617557 -1.704124543 2.791572471 1.1079998 0.276466088 0.404434044 0.271943744 95906764.94 85003880.69 72843561.73 0.062809483 0.019764028 1.704124543 -0.831533712 RIDISPS(ph)TFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.347)PS(0.632)T(0.021)FRK 118.52 0.00037001 1571000000 948520 517270 839860 839500 936960 803280 1265200 986090 1249100 TRUE FALSE 903685.3394 569980.4011 878368.4117 755111.8651 1100365.527 775462.2122 1072170.503 899742.732 1442804.048 0.62633962 0.395050459 0.608792589 0.523364116 0.762657638 0.537468836 0.743115813 0.623607019 1 20.46044395 -1.289884095 0.194391322 1.385272864 0.462736205 0.644309741 0.097476229 12.8030707 0.486582862 2.748229395 0.278691265 0.051299828 1.289884095 -0.922536659 RIDISPS(ph)TLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.291)PS(0.58)T(0.129)LR;RIDIS(0.152)PS(0.8)T(0.048)LR 122.97 0.00050261 2707910000 755500 630800 669520 751670 760470 692320 828110 704690 702570 TRUE FALSE 719789.0123 695079.2372 700218.1542 676110.7035 893095.7272 668344.7848 701766.6102 642983.6078 811520.9674 0.886962927 0.856514206 0.862846658 0.833140154 1.100520828 0.823570569 0.864754749 0.792319156 1 19.63026884 -2.523508862 2.224749279 2.786425922 0.877752963 0.175054913 0.083518166 2158681.361 479721.772 19141160.89 0.019652166 0.00299565 2.523508862 -1.908672959 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.973)PS(0.027)LEEPSDLEELEQFAK;RIDT(0.955)PS(0.043)LEEPS(0.003)DLEELEQFAK;RIDT(0.996)PS(0.004)LEEPSDLEELEQFAK;RIDT(0.996)PS(0.004)LEEPSDLEELEQFAK;RIDT(0.972)PS(0.028)LEEPSDLEELEQFAK;RIDT(0.999)PS(0.001)LEEPSDLEELEQFAK 262.97 5.89E-37 282726000 431771 344842 374444 420560 341590 399846 460933 456103 405447 TRUE FALSE 411362.0405 379981.7919 391612.6278 378284.5098 401163.1878 385999.2328 390609.2052 416164.2034 468321.65 0.878375024 0.811369263 0.836204407 0.807745082 0.856597571 0.824218211 0.834061815 0.888629008 1 18.83714021 0.883836391 2.518244242 0.999863002 0.834940836 0.865683589 0.020581227 0.145933488 1.907309791 0.018510492 0.004965053 7.653082429 -0.883836391 -0.164922165 RIEGLIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIEGLIER 8 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 0 74.267 0.066414 72292000 99070 116700 84364 105520 94035 88787 100610 88356 60486 FALSE TRUE 94387.15744 128591.8627 88232.17285 94912.92913 110434.6742 85712.28393 85260.09667 80619.08024 69865.85996 1.350976822 1.840553637 1.262879651 1.358502267 1.580667214 1.226812122 1.220339902 1.153912373 1 16.09230003 1.828258227 0.562060612 0.998043762 1.557531318 0.497916914 0.165633105 0.598827618 0.408337656 0.154119683 0.096358199 67.33769203 -1.828258227 0.559487556 RIENAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RIENAK 6 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;; 114.72 0.040155 2017360000 2922660 2476110 2358050 2852000 2199360 2520360 3032410 3056500 2857600 FALSE TRUE 2784511.654 2728428.424 2466168.925 2565311.542 2582927.688 2433079.301 2569760.16 2788856.656 3300742.013 0.843601724 0.826610627 0.747155917 0.77719238 0.782529406 0.737131012 0.778540143 0.844918096 1 21.65435895 0.873431957 3.33455171 0.999902056 0.788691653 0.818755715 0.031906452 0.264484045 5.720037286 0.035421246 0.009185434 7.47191559 -0.873431957 -0.211210403 RIEQHYFEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 ;;; 149.96 1.46E-05 895032000 957916 755797 743586 921676 1011687 650239 859591 775366 886646 FALSE TRUE 912637.2091 832813.5736 777680.1536 829027.3774 1188124.892 627721.0604 728444.6055 707470.8426 1024142.533 0.891123237 0.813181317 0.759347579 0.809484374 1.160116736 0.612923534 0.711272681 0.690793341 1 19.96598508 RIESLIDRDYMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIESLIDRDYMER 13 2 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 194.48 5.55E-07 134670000 57549 50998 55982 57756 67991 52530 63775 53548 89717 FALSE TRUE 54828.77282 56194.75418 58548.83007 51950.25715 79848.60887 50710.87293 54044.95244 48859.05324 103629.8541 0.529082794 0.542264144 0.564980338 0.501305899 0.77051743 0.489346177 0.52151914 0.471476619 1 16.66108016 -1.661651168 3.308559428 1.034324411 0.548084901 0.743669374 0.08324644 6719069.438 3636864.514 1659748.893 0.018062871 0.021794596 1.661651168 -0.48623951 RIILLAEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIILLAEGR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 185.29 6.90E-05 532660000 512090 381050 152089 179035 609500 245610 568890 434810 573730 FALSE TRUE 487884.5206 419879.4282 159062.4311 161038.0617 715796.607 237104.4641 482095.3821 396735.7313 662701.1182 0.736205972 0.633587928 0.240021371 0.24300255 1.080119812 0.357784916 0.727470301 0.598664648 1 19.33799883 0.040899576 0.594794173 1.025431597 0.563819143 0.225058838 0.251897236 6.3725809 2.684730343 0.626143372 0.099270552 1.098751742 -0.040899576 -0.461612454 RIPHS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIPHSPAR 8 1 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 RIPHS(1)PAR;RIPHS(1)PAR 81.625 0.013706 919600000 186447 117980 93915 119784 217240 128888 202423 149587 238720 TRUE FALSE 177634.0198 130002.2961 98221.09564 107743.0847 255126.5872 124424.5762 171539.6536 136488.3693 275739.4784 0.644209603 0.471467839 0.356209768 0.390742325 0.925245049 0.451239616 0.622107703 0.494990308 1 18.07294631 -5 0.302146603 4.83245433 0.522437056 0.436991599 0.162268032 258.400105 2.378768834 627.7967909 0.150481839 1.00E-05 5 -4.310017274 RIPLAEWESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RIPLAEWESR 10 1 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 138.99 8.02E-05 66255000 54237 45096 42904 63682 76570 37343 68339 45925 78928 FALSE TRUE 51673.3245 49691.33367 44871.19084 57280.56437 89923.78376 36049.80255 57912.63042 41903.56354 91167.75113 0.566793892 0.545053849 0.49218271 0.628298534 0.986355182 0.395422747 0.635231534 0.459631427 1 16.47623597 -1.552944007 3.168649764 1.015762867 0.588436343 0.397951959 0.159017239 39190402.79 43254531.26 5204031.14 0.035227837 0.027993422 1.552944007 -0.427326524 RIPSIVSS(ph)PLNSPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 RIPSIVS(0.169)S(0.831)PLNSPLDR;RIPSIVS(0.174)S(0.826)PLNSPLDR 124.45 5.05E-05 373050000 256100 180277 225840 252560 279550 224000 299400 243983 293010 TRUE FALSE 243994.6605 198647.4313 236194.9874 227172.189 328303.4315 216242.8238 253721.0311 222618.5551 338448.4943 0.720921099 0.586935485 0.697875722 0.671216427 0.970024796 0.638923876 0.749659211 0.65776199 1 18.36857677 -5 0.218152789 2.450348673 0.668609379 0.425434532 0.103488407 141.2430079 1.411846175 90.16758092 0.189952608 1.00E-05 5 -1.781739294 RIQLVEEELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 247.13 7.07E-16 2920320000 3508350 3136100 2947530 3427130 3611750 3001830 3451720 3300290 3476920 FALSE TRUE 3342517.248 3455672.155 3082677.166 3082628.381 4241638.056 2897875.874 2925096.719 3011299.112 4016102.996 0.832278767 0.860454067 0.76757921 0.767567063 1.056157688 0.721564133 0.728342057 0.749806246 1 21.93736484 RIQLVEEELDRAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIQLVEEELDRAQER 15 2 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 ; 240.5 4.30E-18 220620000 99804 55577 133678 76493 177360 103761 180061 137251 236180 FALSE TRUE 95086.46271 61240.35949 139807.2685 68803.77831 208291.5278 100167.7306 152589.3874 125232.5748 272805.5882 0.348550275 0.224483523 0.512479489 0.252208097 0.763516353 0.367176242 0.559333804 0.459054287 1 18.05751367 -4.999999999 0.122478526 2.927790626 0.144851295 0.622334482 0.145234951 86.79065406 0.684643567 41.190308 1.159146248 1.00E-05 4.999999999 -2.782939331 RIQTYLQSTKPIIDLYEEMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIQTYLQSTKPIIDLYEEMGK 21 2 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 ; 112.93 0.00011985 60648000 153039 124249 143626 144139 110142 146671 180391 176103 134048 FALSE TRUE 145805.1498 136910.1144 150211.3942 129649.8739 129350.7299 141591.7465 152869.0398 160682.4877 154835.4792 0.941677905 0.884229603 0.970135494 0.837339572 0.83540756 0.914465775 0.987299814 1.037762718 1 17.24037656 1.679726865 3.114368319 1.017072034 0.89635133 0.618247051 0.04182947 0.14357224 3.208907975 0.025373909 0.011264413 47.8329168 -1.679726865 -0.120720703 RIS(ph)EMEEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 128.9 0.00019445 79989000 230993 184221 187259 222111 228517 202528 240175 217805 252840 TRUE FALSE 220074.4187 202993.3293 195845.0104 199783.9803 268370.2924 195514.4046 203531.8926 198732.8395 292049.1359 0.753552713 0.695065674 0.670589248 0.684076601 0.918921714 0.669457227 0.696909758 0.68047741 1 18.15585159 -1.126354617 4.710856046 1.000021457 0.719986147 0.581711087 0.074311122 1.58E-05 2.92E-06 0.067712175 0.015958691 0.074755884 1.126354617 -0.28003531 RIS(ph)FSASHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RISFSASHR 9 1 E9PKY8;E9PJM0;Q03393 E9PKY8 PTS 6-pyruvoyl tetrahydrobiopterin synthase 1 RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR;RIS(0.999)FS(0.001)ASHR 171.62 3.48E-05 2001301000 1471299 1017726 1017776 1208629 1657373 1034760 1563333 1217324 1502035 TRUE FALSE 1401753.612 1121433.436 1064442.036 1087135.317 1946418.326 998926.0017 1324817.838 1110728.657 1734962.916 0.807944423 0.646373145 0.613524373 0.626604354 1.121878922 0.575762163 0.763600089 0.640203111 1 20.7264734 RIS(ph)HEGSPVKPVAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RISHEGSPVKPVAIR 15 2 Q96II8-3;Q96II8;Q96II8-2 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 RIS(1)HEGSPVKPVAIR;RIS(1)HEGSPVKPVAIR 102.33 0.00081404 370920000 412270 338290 329050 413910 318052 409110 474750 442300 368425 TRUE FALSE 392782.8141 372762.1356 344137.268 372302.9804 373520.1681 394942.4181 402318.1681 403569.8672 425558.4673 0.922982021 0.875936362 0.80867212 0.874857414 0.877717627 0.928056773 0.945388704 0.948330014 1 18.69899783 1.740371827 1.091213304 0.98309831 0.87320909 0.683276849 0.029669344 0.314629597 0.698849477 0.026960433 0.010712598 55.00115724 -1.740371827 -0.10988922 RIS(ph)HSLYSGIEGLDESPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RISHSLYSGIEGLDESPSR 19 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 RIS(0.968)HS(0.032)LYSGIEGLDESPSR;RIS(0.904)HS(0.096)LYSGIEGLDESPSR;RIS(0.968)HS(0.032)LYSGIEGLDESPSR 313.45 8.21E-62 854000000 299303 253092 296953 306059 373108 271677 343219 308221 334447 TRUE FALSE 285155.5404 278882.3625 310568.5888 275293.3678 438177.9171 262268.7574 290854.6379 281231.5353 386311.3326 0.73814956 0.721910902 0.803933415 0.712620481 1.1342611 0.678905161 0.752902163 0.727991937 1 18.55940447 -2.525510538 2.129805399 3.922704643 0.777930113 0.216211232 0.128910007 5976191.938 396349.2727 84391710.34 0.030446798 0.002981875 2.525510538 -3.14477453 RIS(ph)LDQQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;RIS(1)LDQQ;RIS(1)LDQQ;RIS(1)LDQQ;RIS(1)LDQQ 101.48 0.0095624 2064510000 3273400 2913880 3052500 3533170 3771360 3187110 3882400 3540750 4366670 TRUE FALSE 3118672.869 3210807.685 3192460.144 3178009.039 4429083.99 3076739.582 3290068.575 3230703.159 5043830.882 0.618314321 0.636581154 0.632943534 0.630078429 0.878119052 0.610000544 0.652295577 0.640525671 1 22.26608847 -2.178918898 2.28205203 1.872719856 0.659161877 0.650234439 0.077792601 4442442.615 958378.4001 20031733.75 0.018710424 0.006623402 2.178918898 -1.213557979 RIS(ph)LSDMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(0.998)LS(0.002)DMPR;RIS(1)LSDMPR;RIS(0.999)LS(0.001)DMPR;RIS(1)LSDMPR 179.6 3.04E-05 2631757000 1348201 1399387.4 1247479 1560566.3 1454719.5 1347577 1441541 1393957 1408335 TRUE FALSE 1284474.211 1541986.567 1304677.146 1403695.211 1708422.12 1300910.071 1221607.445 1271894.735 1626732.399 0.789603878 0.947904258 0.802023213 0.862892515 1.050217062 0.799707482 0.750957838 0.781870906 1 20.63354551 -1.2207968 6.789677043 1.000000773 0.849181683 0.219745617 0.089906837 1.06E-06 1.21E-07 0.087542142 0.020633775 0.060145508 1.2207968 -0.150819089 RIS(ph)MEDLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RISMEDLNK 9 1 Q00537;Q00537-2;F5H6Z0;F8VQZ9;F8VZY6 Q00537 CDK17 Cyclin-dependent kinase 17 1 RIS(1)MEDLNK 117.2 0.00072899 156230000 342210 259850 286040 351920 276970 342440 375250 350390 280700 TRUE FALSE 326034.4115 286329.0104 299155.2169 316544.333 325273.4803 330581.2169 317998.7206 319707.9941 324229.5224 1.005566702 0.883105919 0.922664953 0.976297071 1.003219811 1.019590118 0.980782744 0.986054545 1 18.30665593 3.072711121 4.294975663 0.996744872 0.9356214 0.4392803 0.031259544 0.197227646 7.079866393 0.009378788 0.011250154 1182.254894 -3.072711121 -0.061123473 RIS(ph)QSQPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RISQSQPVR 9 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(1)QSQPVR 198.52 1.61E-05 3523672000 1734797 1412653 1630487 1826103 1938793 1614394 2061166 1640653 1991638 TRUE FALSE 1652796.584 1556603.947 1705246.442 1642539.657 2276917.885 1558487.131 1746697.271 1496988.726 2300491.049 0.718453821 0.676639862 0.741253239 0.713995239 0.989752986 0.677458463 0.759271492 0.650725734 1 21.13351041 -2.483374389 2.302876503 4.385592649 0.739134657 0.427643309 0.094165877 2467502.418 465550.3977 43166019.94 0.022412572 0.003285683 2.483374389 -3.646457992 RIS(ph)QVSSGETEYNPTEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.985)QVS(0.013)S(0.002)GETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR;RIS(0.882)QVS(0.091)S(0.027)GETEYNPTEAR 311.89 2.15E-61 2890040000 648756 572341 605344 704499 747299 705321 815306 680250 775867 TRUE FALSE 618090.5896 630663.1986 633099.6212 633681.4221 877627.709 680895.5569 690916.0956 620683.7038 896184.4918 0.689691236 0.703720277 0.706438939 0.707088136 0.979293569 0.759771635 0.77095297 0.692584741 1 19.77343624 -5 0.133065398 1.796373375 0.652553959 0.452149847 0.085801404 131.4631693 1.093960678 28.26873085 0.593038885 1.00E-05 5 -1.143819416 RIS(ph)SSSVQPCSEEVSTPQDSLAQCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RISSSSVQPCSEEVSTPQDSLAQCK 25 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 RIS(0.323)S(0.323)S(0.265)S(0.089)VQPCSEEVSTPQDSLAQCK;RIS(0.743)S(0.13)S(0.051)S(0.076)VQPCSEEVSTPQDSLAQCK;RIS(0.818)S(0.159)S(0.022)S(0.001)VQPCSEEVSTPQDSLAQCK;RIS(0.726)S(0.272)S(0.003)SVQPCSEEVSTPQDSLAQCK 273.73 3.31E-53 2244100000 1825090 1552400 1768590 1970730 1522490 1868250 2274590 2160340 2062870 TRUE FALSE 1738821.613 1710591.325 1849681.601 1772628.476 1788011.774 1803552.034 1927559.52 1971169.177 2382769.344 0.729748189 0.717900509 0.776273879 0.743936244 0.750392302 0.756914235 0.808957663 0.827259752 1 21.18420787 0.423399545 0.470201779 1.019910675 0.728465018 0.964851567 0.01526287 0.366175544 0.141622752 0.029356256 0.008489009 2.650937844 -0.423399545 -0.291445657 RIS(ph)TSDILSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RISTSDILSEK 11 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 RIS(0.913)T(0.043)S(0.043)DILSEK 137.39 4.86E-05 107550000 234060 204800 295840 261640 193180 261550 285480 271760 243230 TRUE FALSE 222996.4477 225669.3528 309404.5566 235339.4501 226870.5308 252492.4579 241924.7828 247963.2537 280948.8662 0.793726099 0.803239949 1.101284233 0.83765937 0.807515382 0.898713212 0.861098983 0.882592114 1 18.09994805 RISAVSVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RISAVSVAER 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 181.66 6.11E-06 1150060000 971520 659960 509810 610500 1121150 665710 1124680 835280 1102430 FALSE TRUE 925598.175 727210.6743 533185.2928 549131.3801 1316678.205 642656.2958 953089.4098 762138.4551 1273389.214 0.726877662 0.571082797 0.41871353 0.431236086 1.033995098 0.504681749 0.74846669 0.598511788 1 20.28024202 2.798729744 24.99999932 0.738068328 0.557191604 0.287779681 0.180819745 392.8886197 163242.478 0.051930696 0.055080812 629.1145711 -2.798729744 -0.180876725 RISEQFTAMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RISEQFTAMFR 11 1 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 0 225.19 9.06E-12 283860000 265610 135610 173200 151670 383710 162920 382930 231010 425320 FALSE TRUE 253055.1417 149428.8132 181141.3913 136423.8434 450628.9025 157278.0395 324506.9955 210781.5397 491276.4534 0.515097233 0.304164411 0.368715802 0.277692616 0.917261349 0.32014162 0.660538467 0.429048733 1 18.90617557 -5 0.166932343 3.077174965 0.33595151 0.438409233 0.190728761 114.0822813 1.068119946 78.10704399 0.648189428 1.00E-05 5 -2.741223455 RISQVSS(ph)GETEYNPTEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.02)QVS(0.076)S(0.902)GET(0.002)EYNPTEAR 329.59 7.80E-75 208760000 102820 98819 102540 122520 125770 110960 120410 99535 130900 TRUE FALSE 97959.90237 108888.7684 107241.5604 110204.0568 147704.2482 107117.4274 102039.243 90819.18773 151199.3035 0.647885937 0.72016713 0.709272847 0.728866167 0.976884449 0.708451857 0.674865827 0.600658771 1 17.20609197 -2.18195499 2.353079895 1.750275886 0.720063834 0.440937992 0.098767791 8977021.954 1716718.84 35968681.42 0.025375922 0.00657726 2.18195499 -1.030212052 RISTS(ph)DILSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RISTSDILSEK 11 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 RIS(0.252)T(0.287)S(0.461)DILSEK 70.47 0.031653 79469000 108630 94876 271110 119780 103930 123440 127810 117570 145080 TRUE FALSE 103495.2752 104543.9723 283540.6617 107739.4868 122055.3591 119165.2418 108310.2371 107274.9475 167578.2654 0.617593665 0.623851619 1.691989477 0.642920408 0.728348386 0.711102013 0.646326281 0.640148335 1 17.35447552 RITEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RITEAEK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 103.87 0.013274 165945000 216660 187392 173582 220400 212150 170966 205730 205601 226830 FALSE TRUE 206418.9112 206487.4578 181540.9064 198244.9733 249148.8928 165045.4046 174342.11 187597.4865 262005.6379 0.787841486 0.788103109 0.692889313 0.756643921 0.95092951 0.629930737 0.665413582 0.716005533 1 17.99923833 RITEAEKNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RITEAEKNER 10 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 127.56 0.00019848 1142590000 1032210 663129 795390 899000 887011 856848 1231930 1013350 1091540 FALSE TRUE 983419.4789 730702.599 831859.4182 808630.812 1041705.438 827175.1389 1043976.453 924615.7019 1260810.448 0.77998995 0.579549924 0.659781507 0.641357956 0.826218913 0.656066215 0.828020147 0.733350285 1 20.26591996 0.406572319 0.40790237 1.031685196 0.663553344 0.604993213 0.076448496 1.643550993 0.49279033 0.175953087 0.050377957 2.550188713 -0.406572319 -0.368131852 RIVDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RIVDGK 6 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 110.9 0.045388 17808080000 29058030 25745310 27108390 32319180 25423450 29879530 35377340 31004510 29536230 FALSE TRUE 27684514.51 28368786.36 28351336.5 29070394.62 29857291.63 28844794.38 29979877.03 28289590.74 34116557.7 0.811468576 0.831525461 0.831013983 0.852090498 0.875155457 0.845477866 0.878748592 0.829204136 1 25.02396875 -5 0.183729152 1.647579544 0.812964864 0.863164127 0.019645832 43.12332047 0.417807661 10.2039928 0.053800137 1.00E-05 5 -0.83461468 RIVNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RIVNAK 6 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 122.5 0.030777 1054570000 1107030 1082770 1015050 1200660 939380 1145430 1242500 1330990 1117960 FALSE TRUE 1054702.886 1193105.494 1061591.047 1079967.376 1103207.575 1105763.472 1052933.805 1214441.46 1291327.527 0.816758618 0.923937165 0.822092788 0.83632336 0.854320497 0.856299776 0.815388647 0.94045967 1 20.30042354 1.047066682 4.529579096 0.999256655 0.850404455 0.73946407 0.031516749 0.089065154 3.870554172 0.030024323 0.00763727 11.14465636 -1.047066682 -0.148852201 RKAEDS(ph)DS(ph)EPEPEDNVR ddPTM_SK-BR-3_Trastuzumab_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 158.37 1.65E-08 1245870000 1841770 1295040 1666780 1673620 1195360 1776930 2252000 1769120 1551550 TRUE FALSE 1754713.182 1427006.048 1743203.512 1505384.538 1403830.406 1715394.469 1908416.039 1614206.474 1792156.45 0.979107143 0.796250823 0.972684897 0.839985001 0.783319116 0.957167812 1.064871339 0.900706227 1 20.77326516 2.011555864 24.6050036 0.999555238 0.875590165 0.336860763 0.074726966 177.5890096 378124.6835 0.026241251 0.019364459 102.6965524 -2.011555864 -0.123965073 RKAS(ph)PEPPDSAEGALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RKAS(1)PEPPDSAEGALK;RKAS(1)PEPPDSAEGALK;RKAS(1)PEPPDSAEGALK;RKAS(0.997)PEPPDS(0.003)AEGALK 189.11 5.58E-10 1278400000 2964890 2448440 2550040 3012140 1641130 3072160 3350230 3309400 1942780 TRUE FALSE 2824745.526 2697938.82 2666961.856 2709353.965 1927342.552 2965770.329 2839090.882 3019611.392 2244056.4 1.258767616 1.202259809 1.188455805 1.207346644 0.858865469 1.321611315 1.265160217 1.345604055 1 21.09767751 RKAS(ph)VHSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKASVHSSGR 10 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 RKAS(1)VHSSGR 65.563 0.035791 7498500 5881.6 2325.1 5309.6 5336.1 8827.8 4948.9 10171 7576.2 10878 TRUE FALSE 5603.588424 2562.030333 5553.050412 4799.70509 10367.36553 4777.518352 8619.227147 6912.787764 12564.90468 0.445971423 0.203903682 0.441949267 0.381992957 0.825104988 0.380227186 0.685976326 0.550166351 1 13.61711211 -0.210733184 0.142768978 1.482891331 0.104363899 0.588856719 0.150507468 11.84010898 0.515630233 3.650120136 1.244968196 0.615554932 0.210733184 -1.378527432 RKDDEDSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKDDEDSFR 9 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 111.61 0.0011797 173480000 50954 39485 36550 50359 44522 38427 56080 48828 36447 FALSE TRUE 48545.5054 43508.56639 38225.85365 45296.81764 52286.6227 37096.26335 47523.96602 44552.36147 42099.01461 1.153126881 1.033481823 0.907998774 1.075959095 1.241991604 0.881167022 1.128861719 1.058275636 1 15.36149884 -2.722710616 1.674188243 0.000313999 1.061642862 0.030178207 0.106771171 1600660.086 42543.32472 6107354.204 0.024248476 0.001893605 2.722710616 1.061328863 RKDDSYFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RKDDSYFDR 9 2 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ;; 153.97 4.32E-05 1163070000 584650 488120 429430 546020 531560 472050 687200 535570 569070 FALSE TRUE 557014.7532 537859.9829 449119.7903 491133.0322 624263.8957 455702.7901 582355.0187 488672.6516 657318.4692 0.847404689 0.818263913 0.683260567 0.747176681 0.949713001 0.6932755 0.885955661 0.743433624 1 19.326233 -1.564745856 2.647613149 1.013878628 0.802500128 0.365515733 0.08406281 12417418.14 11835292.49 1217365.332 0.019051352 0.027242951 1.564745856 -0.211378499 RKDGVFLYFEDNAGVIVNNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKDGVFLYFEDNAGVIVNNK 20 2 J3KTJ3;P62829;J3KT29 J3KTJ3 RPL23 60S ribosomal protein L23 0 206.8 4.11E-22 40327000 117550 128500 103190 133380 85116 126750 111650 128760 80299 FALSE TRUE 111993.6445 141594.2961 107921.3636 119972.389 99960.20345 122360.6157 94615.74191 117485.0918 92751.35881 1.207460957 1.526600773 1.163555607 1.293483896 1.077722254 1.319232594 1.020100871 1.266667069 1 16.5010808 2.342202087 0.375398698 1.026790037 1.384041933 0.277005227 0.133587287 1.463261963 0.477021776 0.14021991 0.186397373 219.8882823 -2.342202087 0.357251896 RKDGVFLYFEDNAGVIVNNKGEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKDGVFLYFEDNAGVIVNNKGEMK 24 3 J3KTJ3;P62829;J3KT29 J3KTJ3 RPL23 60S ribosomal protein L23 0 193.19 2.34E-18 154340000 473550 309230 465180 416860 348220 472730 651840 528540 439280 FALSE TRUE 451166.23 340740.8886 486508.9631 374956.4408 408949.4577 456359.2416 552389.8361 482258.2356 507401.2989 0.889170428 0.671541223 0.958824828 0.738974145 0.805968488 0.899404953 1.088664608 0.950447381 1 18.95276769 1.99989404 3.881610187 1.019456097 0.805060186 0.540164989 0.08385837 0.146546019 4.855816563 0.034534049 0.021665878 99.97560467 -1.99989404 -0.214395911 RKDNPIEDELVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKDNPIEDELVFR 13 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ; 192.18 1.65E-06 168571000 105675 91242 96002 110567 100007 104743 132053 118896 111888 FALSE TRUE 100679.9522 100539.6635 100403.7867 99452.5951 117448.1891 101115.7236 111905.8895 108484.8359 129239.0196 0.779021324 0.777935827 0.776884465 0.769524524 0.908767255 0.78239315 0.865883151 0.839412402 1 16.97968219 -4.999999996 0.123323524 1.659224857 0.716685791 0.737349971 0.038365272 68.17576589 0.540284063 11.04578566 0.30361737 1.00E-05 4.999999996 -0.942539067 RKDPELWGSVLLESNPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKDPELWGSVLLESNPYR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 184.01 3.40E-14 800140000 1226110 866310 1173800 1210870 1308690 1212210 1589020 1339940 1531960 FALSE TRUE 1168154.21 954587.9739 1227619.891 1089151.047 1536925.122 1170230.864 1346585.815 1222607.75 1769528.533 0.660149971 0.539458933 0.693755353 0.615503524 0.86855063 0.661323535 0.760985647 0.69092288 1 20.75493359 -4.999999999 0.111884597 2.061257436 0.49404885 0.629482506 0.079677738 94.66987546 0.701013073 22.84762394 0.864395696 1.00E-05 4.999999999 -1.567208587 RKDREDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER 161.21 3.95E-05 1830387400 955792 695572.5 808495 893414 691092.2 854354 968438 936978 720565.8 TRUE FALSE 910613.6064 766452.1286 845565.2955 803606.3273 811618.4609 824767.5068 820684.9965 854931.2391 832307.4641 1.094083191 0.920876192 1.015929007 0.965516185 0.975142596 0.990940899 0.986035848 1.027181992 1 19.66675705 1.252412923 24.81641365 1.013591002 0.991200611 0.036845479 0.044039838 686.8695838 1230541.331 0.028031541 0.010113301 17.88186958 -1.252412923 -0.02239039 RKDS(ph)AQDDQAK ddPTM_SK-BR-3_Trastuzumab_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 199.33 2.64E-08 3781380000 3807061 3198964 3121038 3939717 1788247 4030219 4085610 4320530 2409661 TRUE FALSE 3627108.771 3524942.069 3264140.679 3543689.162 2100116.711 3890651.505 3462275.157 3942201.489 2783338.921 1.303150236 1.26644371 1.1727428 1.273179179 0.754531435 1.397836058 1.243928697 1.416356973 1 21.40838516 -0.997025898 0.014579693 6.09E-05 2.296113551 0.053605135 0.191126618 9490.238428 26.60499012 2278.622593 1919.481765 0.100687163 0.997025898 2.296052628 RKDS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.772)PS(0.228)R;RKDS(0.5)PS(0.5)R 84.244 0.01708 250779000 232828 235394 195037 257134 167264 205992 253533 261320 216992 TRUE FALSE 221822.6819 259380.9162 203979.6394 231286.4018 196434.7886 198858.4454 214851.8844 238437.4355 250642.0111 0.885017962 1.034866083 0.813828609 0.922775878 0.78372651 0.793396305 0.857206194 0.951306744 1 17.93526873 3.72873729 24.93513551 0.861782041 0.959942025 0.155769019 0.078284458 829.9247788 2106648.182 0.019232488 0.030187715 5354.726454 -3.72873729 0.098159984 RKDSPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.07)PS(0.93)R;RKDS(0.229)PS(0.771)R;RKDS(0.087)PS(0.913)R;RKDS(0.299)PS(0.701)R 79.986 0.024524 1071100000 724330 726691 591797 794190 481737 674209 761620 904760 727349 TRUE FALSE 690092.3564 800741.6391 618931.4778 714356.5123 565751.7803 650860.9733 645420.8809 825534.418 840142.5681 0.821399108 0.953102092 0.736698153 0.850280107 0.673399732 0.774703006 0.768227805 0.982612296 1 19.68027464 1.229238072 24.25771216 0.991306445 0.806572147 0.543507275 0.07367769 130.8164934 340372.8343 0.071037067 0.018779625 16.95266857 -1.229238072 -0.184734298 RKEDEVEEWQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RKEDEVEEWQHR 12 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;; 208.95 3.66E-08 9943940000 7029348 6211726 6022062 7211464 5120452 6382706 7059935 6894730 4890446 FALSE TRUE 6697084.651 6844707.942 6298179.499 6486553.938 6013457.208 6161671.291 5982812.251 6290990.89 5648831.389 1.185569933 1.211703354 1.114952645 1.148300151 1.064548894 1.090786902 1.059123886 1.113680062 1 22.42952101 4.013159609 0.215805378 0.996172341 1.342106323 0.741383667 0.031569074 3.844313848 0.217559656 0.060398413 0.360804558 10307.64871 -4.013159609 0.345933983 RKEDQDRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKEDQDRSPR 10 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 RKEDQDRS(1)PR;RKEDQDRS(1)PR 87.18 0.072127 74153000 81976 74909 73386 83334 62044 75358 92392 83048 76819 TRUE FALSE 78101.15694 82542.31226 76750.82069 74957.108 72864.45396 72748.33356 78295.9035 75775.87685 88731.69818 0.880194548 0.930246056 0.864976353 0.844761337 0.821177273 0.819868605 0.882389328 0.853988805 1 16.43716196 -1.162028694 3.716371599 1.000101474 0.866961816 0.6398835 0.03231289 17627728.27 39595166.87 23184.09872 0.008839141 0.06886068 1.162028694 -0.133139658 RKEEEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKEEEEEAR 9 2 B1AK53;A0A0J9YY76;H0Y7L4;A0A2R8YG57;A0A0J9YWQ8;A0A0A0MSQ4;B1AK53-2;A0A1B0GUS9 B1AK53;A0A1B0GUS9 ESPN Espin 0 58.63 0.060505 19540000 26126 21854 24817 27980 23485 22387 30959 29584 30667 FALSE TRUE 24891.07576 24080.94745 25954.884 25167.39724 27580.77656 21611.73258 26235.63595 26993.46813 35422.68173 0.702687502 0.679817176 0.73271934 0.710488196 0.7786191 0.610110006 0.740645108 0.762039089 1 15.11238582 0.690283135 1.723983521 0.999771107 0.703794348 0.817730302 0.043170573 0.444206259 1.924863585 0.037231115 0.010538645 4.900982305 -0.690283135 -0.295976759 RKEEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKEEWER 7 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 ; 113.71 0.0034136 107063000 233300 211412 231315 274490 198002 255550 276550 261960 244200 FALSE TRUE 222272.3714 232955.1232 241921.0216 246897.7437 232533.4861 246700.2394 234357.2183 239021.3937 282069.2888 0.788006281 0.825879074 0.85766523 0.875308846 0.824384275 0.874608648 0.830849822 0.847385388 1 18.10569007 -5 0.209458606 1.76913924 0.814322469 0.806712623 0.024805102 63.35591387 0.631090074 20.49234231 0.054344361 1.00E-05 5 -0.954816771 RKEPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RKEPEPK 7 2 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ;; 81.548 0.015131 530920000 579870 506156 487565 636590 431423 582436 687590 616680 486484 FALSE TRUE 552460.6943 557733.8719 509920.3375 572598.7638 506663.0346 562266.0953 582685.517 562680.23 561925.4541 0.983156556 0.992540679 0.907451929 1.018994174 0.901655248 1.000606203 1.036944514 1.001343196 1 19.10001923 2.012618161 24.99702597 1.01734449 0.9660016 0.298392314 0.036993061 256.3304469 507796.962 0.012651655 0.009337705 102.9480586 -2.012618161 -0.051342889 RKEQEEEEQKER ddPTM_SK-BR-3_Trastuzumab_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 ;;; 141.58 2.66E-05 524204000 404194 379067 352279 381448 277589 403213 418759 454329 319026 FALSE TRUE 385088.5507 417694.3583 368431.3406 343104.1223 326000.4337 389249.6327 354869.6235 414545.5442 368498.9227 1.045019475 1.133502251 0.999816602 0.931085822 0.884671334 1.056311454 0.963014005 1.124957276 1 18.49130088 3.640644281 6.493926468 0.987279309 1.088866333 0.246585645 0.068422554 0.274022003 15.33544588 0.017393791 0.027099586 4371.638896 -3.640644281 0.101587025 RKEQEEK ddPTM_SK-BR-3_Trastuzumab_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 79.713 0.01793 14345000 32144 23732 35174 39726 33810 35164 43927 51079 38129 FALSE TRUE 30624.61682 26150.31778 36786.76269 35732.66701 39706.4533 33946.26186 37225.12938 46606.25197 44041.85058 0.695352634 0.593760649 0.835268323 0.811334368 0.901561873 0.770772831 0.845221735 1.058226468 1 15.42658747 3.100025731 0.296538457 1.023072968 0.53321749 0.643999767 0.08053569 1.822614515 0.278974882 0.108004219 0.309064572 1259.000002 -3.100025731 -0.489855478 RKES(ph)IDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKESIDVK 8 2 A0A2R8Y4E6;O95263-3;O95263-6;O95263-4;O95263;O95263-2 A0A2R8Y4E6 PDE8B "High affinity cAMP-specific and IBMX-insensitive 3,5-cyclic phosphodiesterase 8B" 1 RKES(1)IDVK;RKES(1)IDVK 72.29 0.036649 324130000 430140 404800 390990 486410 287740 483580 548950 548680 326170 TRUE FALSE 409808.1347 446049.5802 408917.2782 437515.1427 337921.7649 466833.5033 465197.5953 500634.6705 376750.7778 1.087743301 1.183938048 1.085378724 1.161285307 0.896937139 1.239104286 1.234762137 1.328821863 1 18.52325096 RKGS(ph)GS(ph)EQEGEDEEGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RKGS(1)GS(1)EQEGEDEEGGER 141.36 5.93E-07 3218930000 2742610 2277240 2549720 2747980 1679970 2702530 3137190 2756420 1953710 TRUE FALSE 2612972.261 2509293.345 2666627.184 2471747.83 1972956.236 2608940.708 2658554.047 2515053.252 2256681.369 1.157882675 1.111939585 1.181658705 1.095302094 0.874273286 1.156096179 1.178081267 1.114491965 1 21.1057713 -2.547860986 1.723847046 5.32E-05 1.113648477 0.128109527 0.088302617 1507916.183 90917.89668 5871748.728 0.023945767 0.002832298 2.547860986 1.113595235 RKHDNEGSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 75.045 0.022027 43012000 37011 28412 28667 41105 24108 37833 39616 46472 30120 FALSE TRUE 35261.56338 31307.2151 29981.41031 36973.04731 28312.42757 36522.83372 33571.8516 42402.66532 34790.85577 1.013529636 0.899869072 0.86176122 1.062723135 0.81378934 1.049782563 0.964961938 1.218787649 1 15.08642055 1.365273777 7.349603065 1.109028675 0.951255984 0.325546257 0.094051345 0.230461324 13.58906605 0.056140735 0.020440415 23.18855986 -1.365273777 -0.157772691 RKHS(ph)PS(ph)PPPPTPTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKHSPSPPPPTPTESR 16 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR 134.86 1.40E-05 206215000 325600 283960 286310 320160 273100 307700 366200 284340 317080 TRUE FALSE 310209.5333 312895.8468 299437.5967 287976.9085 320728.5535 297044.2718 310329.4643 259441.6822 366251.147 0.846985834 0.854320456 0.817574495 0.786282612 0.875706619 0.811039841 0.84731329 0.708370975 1 18.48247375 -1.223054567 4.994006396 1.000023014 0.825392281 0.593464168 0.046911082 1.08E-05 1.69E-06 0.040980262 0.009657868 0.059833641 1.223054567 -0.174630733 RKLDLFANVVHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKLDLFANVVHVK 13 2 A0A087X2E5;A0A087WZN1;O43837-2;O43837 A0A087X2E5 IDH3B "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial" 0 ; 120.14 0.00017636 83563000 186522 152452 145921 140712 133107 138045 169180 170959 132146 FALSE TRUE 177705.4747 167987.0321 152611.6222 126567.3624 156320.8187 133264.467 143368.4838 155988.9236 152638.5268 1.164224252 1.100554596 0.999823737 0.829196698 1.024124262 0.873072283 0.939268 1.021949877 1 17.21975963 3.72700825 2.7393759 0.941530101 1.141514153 0.589320065 0.062957817 0.150269874 2.249974617 0.015700299 0.028925278 5333.45027 -3.72700825 0.199984051 RKLEEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RKLEEQAR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;; 131.44 0.00056525 444020000 576220 500610 467520 468810 537130 517770 687220 592610 598750 FALSE TRUE 548983.2226 551622.7281 488956.2544 421684.3281 630805.3019 499839.4951 582371.9673 540717.9268 691601.092 0.793785939 0.797602454 0.706991733 0.609721895 0.912094138 0.72272803 0.842063401 0.781834981 1 19.39958062 0.045789953 0.542173488 1.017829203 0.759204614 0.463558317 0.079266291 3.511504882 1.280173771 0.212777788 0.033894027 1.111194167 -0.045789953 -0.258624589 RKLESTESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 1364270000 1583450 1167088 1253860 1447050 1412890 1365120 1821110 1605560 1688090 FALSE TRUE 1508603.457 1286015.594 1311350.721 1301589.785 1659297.569 1317845.552 1543266.223 1464968.655 1949870.376 0.773694229 0.659539019 0.672532255 0.667526314 0.850978398 0.675863159 0.791471188 0.75131592 1 20.89494679 -0.658321726 0.364537339 1.096099336 0.701199535 0.674736615 0.060267843 5.597267638 0.676555074 0.673999425 0.043414356 0.21962323 0.658321726 -0.394899801 RKLS(ph)GDQPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RKLSGDQPAAR 11 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR 166.64 1.59E-05 2419840000 2094070 1251578 1990470 1897160 1833120 1966650 2634000 2140640 2224130 TRUE FALSE 1995087.461 1379115.221 2081735.018 1706453.872 2152815.548 1898544.417 2232134.923 1953194.213 2569036.721 0.776589702 0.536821918 0.810317346 0.664238801 0.83798551 0.73901023 0.868860653 0.760282715 1 21.29279608 1.035084529 0.276319272 1.043963537 0.638019315 0.489529689 0.087543473 1.603788756 0.406963964 0.242592399 0.14927804 10.84137906 -1.035084529 -0.405944222 RKLS(ph)SIGIQVDCIQPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKLSSIGIQVDCIQPVPK 18 2 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 RKLS(0.916)S(0.084)IGIQVDCIQPVPK 164.04 2.49E-11 368280000 602600 469250 612530 710800 434490 663230 780810 729240 565460 TRUE FALSE 574116.2922 517067.1085 640615.1064 639349.0336 510264.9184 640262.1788 661683.0939 665383.8797 653148.6488 0.878997902 0.791653032 0.980810582 0.978872167 0.781238573 0.980270234 1.01306662 1.018732689 1 19.31705184 2.056292906 9.942372595 1.008230584 0.878538571 0.466276847 0.064761163 0.350047364 59.36556095 0.024717671 0.018241443 113.8394808 -2.056292906 -0.129692012 RKLTATEGPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKLTATEGPGSPR 13 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 RKLTATEGPGS(1)PR 92.236 0.0048558 95240000 105660 71615 103660 89354 99331 104850 134330 114290 130520 TRUE FALSE 100665.6612 78912.64992 108412.9135 80371.96616 116654.295 101219.0182 113835.4914 104282.1617 150760.375 0.667719626 0.523430974 0.719107481 0.533110681 0.773772916 0.671390067 0.755075671 0.691708028 1 17.20189776 -1.58273656 0.195809924 1.361181919 0.55927108 0.683178176 0.074969517 13.56419165 0.460389574 2.554107776 0.198501544 0.026137464 1.58273656 -0.801910839 RKNAT(ph)RET(ph)TSTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKNATRETTSTLK 13 3 P78413-2;P78413;D6RAS8;P78412 P78413-2;P78412 IRX4;IRX6 Iroquois-class homeodomain protein IRX-4;Iroquois-class homeodomain protein IRX-6 2 RKNAT(0.99)RET(0.252)T(0.252)S(0.252)T(0.252)LK 62.89 0.036354 56653000 95060 71161 99342 90440 200010 63036 117440 83682 248850 TRUE FALSE 90566.70219 78412.3868 103896.929 81348.79938 234891.6807 60853.04751 99522.37107 76354.36045 287440.3871 0.315079948 0.272795301 0.36145557 0.283011028 0.817183984 0.211706671 0.346236561 0.265635464 1 18.13290326 -1.121151554 4.00570818 1.000173607 0.353129483 0.587676181 0.168634048 62634029.38 122420567.9 160828.5628 0.039050438 0.075656883 1.121151554 -0.647044124 RKNS(ph)TGSGHSAQELPTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKNSTGSGHSAQELPTIR 18 2 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 RKNS(0.925)T(0.059)GS(0.015)GHSAQELPTIR;RKNS(0.65)T(0.156)GS(0.156)GHS(0.038)AQELPTIR 196.62 1.01E-15 742000000 407200 212880 334490 337980 420510 339500 545230 421420 505330 TRUE FALSE 387952.463 234572.714 349826.6974 304005.6083 493846.8109 327743.0299 462045.1497 384518.2307 583693.9955 0.664650426 0.401876181 0.599332356 0.520830453 0.846071426 0.561498032 0.791587978 0.658766809 1 19.1548527 0.662320224 0.278115818 1.082285911 0.495964805 0.542533859 0.116218142 2.147019523 0.418143012 0.414894131 0.178884163 4.595367244 -0.662320224 -0.586321106 RKPEEES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 96.64 0.0056947 673000000 1190820 1442270 914150 1397220 802760 1349670 1092720 1244740 757740 TRUE FALSE 1134532.299 1589238.953 956064.6817 1256768.791 942761.0898 1302930.589 926005.4948 1135743.967 875246.4492 1.296243246 1.815761668 1.092337687 1.435902759 1.077137863 1.488644245 1.057994003 1.29762762 1 19.73932978 2.568765412 0.316346167 1.015379857 1.59897925 0.226770505 0.219210875 2.382233584 0.530416363 0.269495327 0.495862099 370.480549 -2.568765412 0.583599394 RKPEEESPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 110.53 0.0012775 112236000 133996 126962 112558 144102 110123 135575 147750 166794 146334 FALSE TRUE 127662.2746 139899.5721 117718.8956 129616.5932 129328.4163 130880.0038 125208.0239 152188.6331 169026.7293 0.755278619 0.827677212 0.696451361 0.766840805 0.765135886 0.774315425 0.740758721 0.90038205 1 17.36689188 1.048953646 3.594982741 0.998701033 0.764946357 0.860219367 0.032965182 0.06860007 1.886527956 0.030879665 0.008002997 11.19318407 -1.048953646 -0.233754676 RKPNAGGS(ph)PAPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR 156.17 2.45E-05 1534690000 1621150 1339530 1401750 1580500 1409280 1488280 1745160 1548780 1598540 TRUE FALSE 1544521.452 1476029.63 1466021.624 1421625.137 1655057.986 1436740.49 1478903.79 1413160.613 1846433.419 0.836489113 0.799394993 0.793974811 0.769930355 0.896354003 0.778116598 0.800951594 0.765346098 1 20.81630981 -1.022595757 4.649556795 1.000005259 0.806184693 0.721380824 0.038066338 1.99E-06 4.18E-07 0.033590662 0.007917169 0.094930167 1.022595757 -0.193820566 RKPQEESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKPQEESER 9 2 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 163.66 3.53E-05 39425000 51575 49402 50333 53522 44315 58247 63301 54771 61562 FALSE TRUE 49137.15196 54436.11997 52640.81784 48141.86687 52043.52197 56229.89178 53643.26985 49974.96088 71108.72054 0.69101443 0.765533672 0.740286387 0.677017762 0.731886632 0.790759436 0.754383843 0.702796514 1 16.11773888 -5 0.363036826 4.33657159 0.72739227 0.851605287 0.035091438 180.4820163 1.422828533 471.158584 0.024638259 1.00E-05 5 -3.60917932 RKPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK 192.18 1.14E-07 6376700000 6605940 6167080 5345820 7093860 3397630 6593950 6259430 6707060 3677610 TRUE FALSE 6293690.308 6795512.463 5590931.135 6380771.715 3990175.596 6365599.858 5304438.991 6119754.27 4247914.976 1.481595169 1.599728926 1.316158908 1.502094969 0.939325674 1.498523368 1.248715904 1.440648955 1 22.01832346 7.999999995 0.036847892 1.19E-12 3.514926626 0.332862385 0.179354415 914.5222479 2.572638847 70.49491016 209.0899679 99999998.77 -7.999999995 3.514926626 RKPS(ph)SEEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKPSSEEGKR 10 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 RKPS(0.915)S(0.085)EEGKR;RKPS(0.966)S(0.034)EEGKR 120.29 0.0032039 331990000 333460 286770 304060 350230 184702 360880 377270 393920 245530 TRUE FALSE 317698.0067 315992.189 318001.4518 315024.215 216913.9703 348382.6351 319710.5325 359426.2765 283605.5384 1.120210869 1.114196115 1.121280824 1.110783015 0.764843915 1.228405612 1.127307084 1.26734576 1 18.11352618 -0.216030533 7.433248883 0.999999684 1.105664265 0.060101129 0.132659858 0 0 0.11970057 0.028213695 0.608092248 0.216030533 0.105664581 RKPS(ph)VPDSASPADDSFVDPGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(1)VPDSASPADDSFVDPGER;RKPS(0.998)VPDS(0.002)ASPADDSFVDPGER;RKPS(1)VPDSASPADDSFVDPGER;RKPS(1)VPDSASPADDSFVDPGER;RKPS(0.948)VPDS(0.041)AS(0.011)PADDSFVDPGER;RKPS(0.999)VPDS(0.001)ASPADDSFVDPGER;RKPS(0.929)VPDS(0.037)AS(0.034)PADDSFVDPGER 242.94 5.10E-31 3227510000 3411700 2875490 3040160 3504070 2770910 3301030 3856220 3645970 3216160 TRUE FALSE 3250435.702 3168505.7 3179554.343 3151834.226 3254155.827 3186714.503 3267882.815 3326709.538 3714905.667 0.874971263 0.852916866 0.855891005 0.848429142 0.875972668 0.857818418 0.879667778 0.895503099 1 21.82489415 0.504082167 0.887175646 1.000794389 0.85993668 0.958958369 0.008916821 0.281214629 0.333008229 0.008356535 0.00269873 3.192141743 -0.504082167 -0.140857709 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.976)PT(0.02)S(0.004)EGASEANLVDLQK 397.65 1.15E-167 1578400000 1344900 999350 1155500 1301600 834070 1269600 1485800 1392400 893310 TRUE FALSE 1281329.242 1101184.901 1208480.818 1170760.695 979531.5439 1225633.434 1259113.921 1270474.074 1031839.952 1.241790686 1.06720514 1.171190178 1.134634002 0.949305696 1.187813508 1.220260873 1.231270481 1 19.97678778 RKPVLPALTINPTIAEGPSPT(ph)SEGASEANLVDLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.004)PT(0.961)S(0.035)EGASEANLVDLQK 384.47 4.82E-165 1762200000 226900 186180 202480 227610 151580 216760 255120 245620 183400 TRUE FALSE 216174.8867 205151.9537 211763.9083 204730.2104 178015.504 209253.5468 216196.7584 224112.2107 211840.7353 1.02045948 0.968425423 0.999637336 0.966434572 0.840327068 0.987787106 1.020562726 1.057927836 1 17.69262051 1.772432936 3.910826895 1.030039096 0.964698756 0.269382148 0.049214548 0.303721236 9.199113092 0.026359897 0.013532326 59.21516401 -1.772432936 -0.065340341 RKPYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKPYHK 6 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 69.093 0.053101 284540000 622800 446340 501200 572260 673730 450910 688980 537240 851700 FALSE TRUE 593361.4783 491822.5534 524180.5158 514735.3376 791228.2987 435294.8736 583863.447 490196.4175 983777.2861 0.603146146 0.499932821 0.532824373 0.523223442 0.804275835 0.442472986 0.59349149 0.498279869 1 19.90797222 -1.743948728 2.889767785 1.079838059 0.561299819 0.664684431 0.097719931 20115757.44 18468953.34 11550542.92 0.021001611 0.018032306 1.743948728 -0.518538241 RKQEEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKQEEADR 8 2 Q05682-5;Q05682-4;C9J813;E9PGZ1;E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682 Q05682-5 CALD1 Caldesmon 0 ; 69.598 0.030093 18468300 34840 25968 28472 31956 25954 29768 31464 30239 30831 FALSE TRUE 33193.18225 28614.16872 29777.46936 28743.72217 30480.36938 28737.1267 26663.58892 27591.11285 35612.11402 0.932075592 0.80349537 0.836161239 0.807133274 0.855898905 0.806948071 0.748722441 0.774767621 1 15.12008046 4.592480841 2.377227055 0.815914797 0.942217857 0.156341487 0.06875844 0.573998759 4.971902193 0.015562904 0.131553432 39127.38653 -4.592480841 0.126303059 RKQEEADRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKQEEADRK 9 3 Q05682-5;Q05682-4;C9J813;E9PGZ1;E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682 Q05682-5 CALD1 Caldesmon 0 47.261 0.079762 18959000 12886 9528.4 8794.4 13099 11422 11389 9920.4 15091 7854.4 FALSE TRUE 12276.90432 10499.35479 9197.631939 11782.26363 13413.99318 10994.59607 8406.860779 13769.55204 9072.420237 1.353211601 1.157282679 1.013801356 1.298690242 1.478546279 1.211870238 0.92663926 1.517737459 1 13.14727175 -2.323084988 2.025643144 5.52E-05 1.22158472 0.135843441 0.186011523 2116095.268 315513.5373 9649508.241 0.045972548 0.004752422 2.323084988 1.221529484 RKQEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 196.88 8.35E-05 465280000 621104.8 482575.5 545585.7 576336.6 471745.2 586066.5 702363.3 625219.8 587665.7 FALSE TRUE 591746.407 531750.4921 570601.344 518402.15 554017.4135 565770.8702 595204.8788 570472.2398 678797.8954 0.871756396 0.783370862 0.840605647 0.763706183 0.816174324 0.833489429 0.876851391 0.840415452 1 19.37262257 0.370738041 0.625388999 1.005012699 0.815710801 0.738366893 0.032847423 1.078988099 0.645887459 0.044868227 0.012691401 2.348215989 -0.370738041 -0.189301898 RKQEELQQLEQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 221.86 1.04E-11 1138080000 1161190 982330 1026680 1198770 917650 1135640 1244590 1227010 1088790 FALSE TRUE 1106302.85 1082430.544 1073754.294 1078267.362 1077687.869 1096312.502 1054704.937 1119566.5 1257633.992 0.879669965 0.860688046 0.853789179 0.857377718 0.856916938 0.871726201 0.838642199 0.890216475 1 20.26228069 0.90037263 5.679869629 0.999996573 0.860490741 0.943286415 0.010760465 0.214861164 12.04531714 0.010479643 0.00263872 7.9501007 -0.90037263 -0.139505832 RKQEELQQLEQQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKQEELQQLEQQRR 14 3 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 ; 139.86 4.43E-06 195082000 109698 83423 106595 102211 99134 117053 137732 123868 126410 FALSE TRUE 104512.7929 91923.89854 111482.4862 91936.55609 116422.9382 112999.4253 116718.4538 113021.4613 146013.0172 0.71577723 0.629559613 0.763510599 0.6296463 0.797346295 0.773899666 0.799370193 0.774050584 1 17.15573747 -0.0772706 0.233445662 1.12425374 0.641282014 0.766295272 0.050110971 3.35380429 0.299737061 0.440192943 0.102769507 0.837007598 0.0772706 -0.482971726 RKQQDTPGS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RKQQDTPGSPDHR 13 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RKQQDT(0.005)PGS(0.995)PDHR;RKQQDT(0.002)PGS(0.998)PDHR;RKQQDT(0.012)PGS(0.988)PDHR;RKQQDT(0.002)PGS(0.998)PDHR;RKQQDT(0.076)PGS(0.924)PDHR;RKQQDT(0.004)PGS(0.996)PDHR 123.97 0.00011336 261941000 390872 266211.1 432289 354179 394490 382889 537344 432458 413200 TRUE FALSE 372396.2552 293338.3137 452109.8782 318576.254 463288.9311 369629.4579 455362.3038 394589.6849 477276.9457 0.780251924 0.614608178 0.947269468 0.667487204 0.970692038 0.774454876 0.954084013 0.826752033 1 18.86446712 2.698267937 0.287744652 0.99873453 0.643371554 0.299816197 0.110073958 2.556564589 0.452674847 0.145159475 0.314178295 499.1923677 -2.698267937 -0.355362976 RKQQDTPGSPDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKQQDTPGSPDHR 13 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 71.241 0.025708 3121800 3390 1728 4506.7 2480.9 4533 3479.4 5996.7 4078.6 7604 FALSE TRUE 3229.761418 1904.085165 4713.336653 2231.515219 5323.553765 3358.907506 5081.793278 3721.456162 8783.189484 0.367720795 0.21678744 0.536631558 0.254066615 0.606107129 0.382424575 0.578581765 0.423702138 1 13.10052921 -5 0.148576884 3.14286363 0.218331485 0.713333589 0.119003616 61.84574529 0.548157829 38.92222204 0.532770411 1.00E-05 5 -2.924532145 RKREPEDEGEDDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKREPEDEGEDDD 13 3 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 105.65 0.0017559 350130000 610150 387030 621770 515690 533280 540370 746200 637580 722510 FALSE TRUE 581309.4187 426468.797 650278.7695 463851.8615 626283.8632 521656.8514 632353.4851 581750.1152 834553.1607 0.696551695 0.511014537 0.779193945 0.555808645 0.750442144 0.625073244 0.757715044 0.697079758 1 19.67064443 -1.870253825 0.235304112 1.368892568 0.602818243 0.614564214 0.08372912 16.75655015 0.620820296 3.553173957 0.133532442 0.013481747 1.870253825 -0.766074326 RKRET(ph)DDEGEDD ddPTM_SK-BR-3_Trastuzumab_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 97.902 0.010923 11752240000 6587570 5266890 6062910 6329890 3890514 6457860 7252350 5606810 4857010 TRUE FALSE 6276188.621 5803592.079 6340900.421 5693597.431 4569018.41 6234222.689 6145870.809 5115847.993 5610210.305 1.118708262 1.034469612 1.13024291 1.014863458 0.814411254 1.111227984 1.095479577 0.911881679 1 22.41962342 3.117354838 7.56185804 1.001966807 1.084716223 0.226768213 0.088039229 0.429434304 26.70566519 0.025861241 0.030990621 1310.25202 -3.117354838 0.082749416 RKRS(ph)PS(ph)PSPTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKRSPSPSPTPEAK 14 3 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 RKRS(0.999)PS(0.986)PS(0.015)PTPEAK 152.71 9.46E-06 58750000 114860 37130 100500 78372 88057 108020 179960 84950 122980 TRUE FALSE 109430.7954 40913.58921 105108.0244 70493.89766 103414.1129 104279.2403 152503.7968 77511.32765 142051.1103 0.770362127 0.2880202 0.73993103 0.49625728 0.728006368 0.734096623 1.073583983 0.54565802 1 17.11605058 2.360593793 1.929622034 0.87911284 0.556492492 0.294543108 0.192443933 0.349420514 2.658018961 0.080282104 0.058456362 229.4002005 -2.360593793 -0.322620349 RKS(ph)CLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSCLVK 7 2 Q5JR89;Q5JR91;Q99661-2;Q99661 Q5JR89 KIF2C Kinesin-like protein;Kinesin-like protein KIF2C 1 RKS(1)CLVK 61.593 0.071309 306390000 514120 423770 499450 561180 428600 548030 708280 615610 509420 TRUE FALSE 489818.5665 466952.6448 522350.2765 504769.1202 503347.7043 529051.5837 600218.8775 561703.9248 588418.2518 0.832432653 0.793572673 0.887719364 0.857840692 0.855425036 0.899108044 1.020054826 0.954599765 1 19.16648247 1.990206736 2.616635401 0.992655153 0.838892156 0.835984306 0.029329389 0.105971608 1.363755311 0.015742892 0.008784583 97.77025232 -1.990206736 -0.153762997 RKS(ph)ELPQDPHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSELPQDPHTK 12 2 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 1 RKS(1)ELPQDPHTK 75.462 0.017608 103150000 252830 244230 232860 283210 182120 265210 288160 299690 169000 TRUE FALSE 240879.227 269117.3147 243536.8613 254741.1927 213881.6703 256025.7112 244195.8996 273447.5548 195207.6569 1.23396403 1.37862069 1.247578426 1.304975413 1.0956623 1.31155568 1.250954514 1.400803428 1 17.57465012 -1.401507373 3.02787949 0.995716199 1.278307487 0.51810094 0.084263268 20678962.84 25586939.55 769509.6039 0.018726673 0.039672779 1.401507373 0.282591289 RKS(ph)ELPQDVYTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;RKS(1)ELPQDVYTIK 144.5 3.26E-05 526650000 515180 424470 465880 636200 388900 598680 660060 650190 489270 TRUE FALSE 490828.4624 467723.9756 487241.0588 572247.9673 456724.0369 577947.5615 559355.7242 593255.9167 565143.4928 0.868502369 0.827619855 0.862154594 1.012571099 0.80815588 1.022656315 0.989758763 1.049743869 1 19.1082577 2.410525939 0.730343796 1.032210451 0.848829924 0.499901103 0.062971315 0.50193321 0.532830907 0.045636656 0.032874095 257.3510466 -2.410525939 -0.183380527 RKS(ph)FDASDTLALPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSFDASDTLALPR 14 2 Q5JXC2 Q5JXC2 MIIP Migration and invasion-inhibitory protein 1 RKS(0.995)FDAS(0.005)DTLALPR 77.08 0.020216 82967000 72465 62228 63994 81430 61251 87514 88289 75287 68598 TRUE FALSE 69039.72306 68569.10395 66928.1882 73244.50169 71933.15501 84483.36824 74818.89151 68694.47116 79235.82749 0.871319519 0.865380045 0.84467078 0.924386152 0.907836231 1.066226869 0.944255823 0.866962248 1 16.27386529 2.868622267 2.030943616 0.964638127 0.864073977 0.409719833 0.05271219 0.305183453 2.490722513 0.017647581 0.019009417 738.9622745 -2.868622267 -0.10056415 RKS(ph)GDSIQQHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSGDSIQQHVK 12 2 A0A2R8Y4E6;O95263-3;O95263-6;O95263-4;O95263 A0A2R8Y4E6 PDE8B "High affinity cAMP-specific and IBMX-insensitive 3,5-cyclic phosphodiesterase 8B" 1 RKS(0.707)GDS(0.293)IQQHVK 59.709 0.050672 62159000 172800 156940 154040 178310 107410 163490 187980 181100 128880 TRUE FALSE 164632.0865 172932.3644 161102.8864 160385.94 126142.27 157828.3003 159300.1985 165241.9239 148866.0522 1.105907519 1.161664207 1.0822003 1.07738425 0.847354169 1.060203438 1.070090838 1.110004071 1 17.18365527 3.300139644 2.716099115 1.025951134 1.131309827 0.279303772 0.071916977 0.338184237 5.077064051 0.021358287 0.029482846 1995.903977 -3.300139644 0.105358693 RKS(ph)HEAEVLK ddPTM_SK-BR-3_Trastuzumab_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 166.86 2.83E-06 10767710000 8385060 6923650 6540110 8570340 5509290 8426680 9748660 8526820 5482700 TRUE FALSE 7988714.831 7629177.807 6839980.513 7708833.141 6470108.432 8134861.959 8261322.871 7780166.437 6332929.114 1.261456537 1.20468391 1.080065857 1.217261871 1.021661275 1.284533872 1.304502659 1.228525742 1 22.5944415 RKS(ph)LPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKSLPAR 7 2 Q8NCE2;Q8NCE2-2;C9JSR1;Q8NCE2-3 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 RKS(1)LPAR;RKS(1)LPAR 67.704 0.05075 747020000 980170 820770 1005580 1010050 852760 1043900 1216470 1059920 966850 TRUE FALSE 933839.3066 904407.3961 1051686.838 908517.855 1001481.074 1007749.481 1030875.159 967107.7858 1116784.16 0.836186024 0.809831862 0.941710024 0.813512483 0.896754368 0.902367277 0.923074661 0.865975558 1 20.09091895 -4.9999998 0.038190726 1.662235124 0.477528446 0.533135645 0.040595774 598.9312929 1.710717632 46.54592694 14.77468338 1.00E-05 4.9999998 -1.184706678 RKS(ph)LSDS(ph)ESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.998)LS(0.044)DS(0.45)ES(0.45)DDS(0.057)K;RKS(0.997)LS(0.01)DS(0.651)ES(0.09)DDS(0.252)K;RKS(0.999)LS(0.055)DS(0.924)ES(0.021)DDS(0.001)K;RKS(0.991)LS(0.149)DS(0.832)ES(0.029)DDSK 127.01 0.00089496 3675340000 12862800 12247100 11655000 14223400 5558570 14384100 13922800 12702900 5954180 TRUE FALSE 12254800.94 13495093.41 12189393.28 12793636.81 6527982.848 13885975.01 11798621.15 11590566.73 6877523.825 1.781862375 1.96220235 1.772352025 1.860209741 0.949176334 2.019036991 1.715533301 1.685281946 1 22.7134578 -2.430609222 0.250831545 1.45E-13 1.835038824 0.377974901 0.29135006 43.55168439 1.35515362 25.10016237 0.420023354 0.003710144 2.430609222 1.835038824 RKS(ph)LSDSES(ph)DDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.99)LS(0.052)DS(0.084)ES(0.869)DDS(0.004)K 124.69 0.0010273 3876200000 9003400 8790300 8437000 9969500 3921400 10698000 9993300 8957900 4322200 TRUE FALSE 8577827.125 9686041.564 8823844.795 8967346.919 4605290.918 10327525.58 8468638.545 8173498.787 4992464.701 1.718154787 1.940132208 1.767432586 1.796176329 0.922448368 2.068622653 1.696284111 1.637167066 1 22.2513208 -2.435873277 0.294243154 7.42E-15 1.77527991 0.34636644 0.300471243 50.64536122 1.823937061 33.47166641 0.305518828 0.003665445 2.435873277 1.77527991 RKS(ph)LSDSESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 RKS(0.998)LS(0.002)DSESDDSK;RKS(0.994)LS(0.002)DS(0.002)ES(0.002)DDSK;RKS(0.987)LS(0.013)DSESDDSK;RKS(0.918)LS(0.02)DS(0.063)ESDDSK;RKS(0.766)LS(0.173)DS(0.056)ES(0.005)DDSK;RKS(0.984)LS(0.005)DS(0.009)ES(0.001)DDSK;RKS(0.799)LS(0.04)DS(0.08)ES(0.08)DDS(0.001)K;RKS(0.744)LS(0.249)DS(0.006)ES(0.001)DDSK;RKS(0.996)LS(0.003)DSESDDSK;RKS(0.999)LS(0.001)DSESDDSK 237.3 5.06E-17 9531420000 7294280 6215400 6849160 7564900 3784530 7862730 7768920 7500630 3728900 TRUE FALSE 6949493.84 6848756.326 7163200.761 6804461.88 4444550.834 7590441.689 6583628.568 6843835.074 4307158.767 1.613475197 1.590086806 1.663091877 1.579802893 1.031898538 1.762285093 1.528531666 1.588944231 1 22.03830507 -1.740061686 2.624462498 0.885637447 1.550308609 0.440450578 0.192876553 21326926.19 16394679.37 15864183.16 0.042942537 0.018194424 1.740061686 0.664671162 RKS(ph)LVGTPYWMAPELISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(0.997)LVGT(0.003)PYWMAPELISR;RKS(0.997)LVGT(0.003)PYWMAPELISR;RKS(0.994)LVGT(0.006)PYWMAPELISR;RKS(0.992)LVGT(0.008)PYWMAPELISR 208.46 3.29E-16 4680810000 5511590 3799410 5089130 5167710 4980950 5158140 7060370 5433320 5869230 TRUE FALSE 5251068.064 4186574.199 5322471.644 4648241.973 5849626.103 4979512.318 5983180.884 4957549.697 6779400.213 0.774562336 0.61754345 0.785094769 0.685642067 0.862853043 0.734506322 0.882553131 0.731266711 1 22.69272621 -0.962574859 0.171621686 1.226114782 0.648750028 0.523963687 0.07461333 15.21463194 0.573804344 1.914901825 0.312700662 0.108999659 0.962574859 -0.577364754 RKS(ph)NTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSNTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK 41 2 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 RKS(0.26)NT(0.26)QGPAY(0.218)S(0.26)HLT(0.001)EFAPPPTPMVDHLVASNPFEDDFGAPK 238.21 8.70E-55 122100000 117890 106310 117890 140560 86779 134240 157090 146310 84808 TRUE FALSE 112317.5733 117143.1099 123295.3731 126430.6418 101913.2301 129591.2351 133123.0353 133498.3208 97959.5915 1.146570454 1.195830935 1.258635027 1.290640761 1.040359893 1.322905018 1.358958661 1.362789684 1 16.57989914 RKS(ph)PENTEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.996)PENT(0.004)EGK;RKS(0.985)PENT(0.015)EGK;RKS(0.993)PENT(0.007)EGK;RKS(1)PENTEGK;RKS(0.994)PENT(0.006)EGK;RKS(1)PENTEGK;RKS(1)PENTEGK;RKS(1)PENTEGK 204.94 9.28E-08 7727820000 6865480 6739010 5472950 7263440 3275347 6931230 6376740 6833050 3332310 TRUE FALSE 6540962.366 7425722.781 5723890.171 6533305.212 3846566.48 6691199.767 5403851.196 6234711.918 3849067.616 1.699362812 1.929226379 1.487084859 1.697373459 0.999350197 1.738394966 1.403937716 1.619797972 1 21.87607758 1.612650344 0.063078841 1.01E-10 2.898801775 0.389585565 0.239191756 22.01110966 1.415215405 31.26768952 31.77484158 40.98739755 -1.612650344 2.898801775 RKS(ph)PENTEGKDGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RKSPENTEGKDGSK 14 3 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.998)PENT(0.002)EGKDGSK;RKS(1)PENTEGKDGSK;RKS(0.999)PENT(0.001)EGKDGSK;RKS(1)PENTEGKDGSK;RKS(1)PENTEGKDGSK;RKS(0.992)PENT(0.008)EGKDGSK 130.01 0.00035679 3126460000 3602627 1958397 3433346 2945664 1778840 3880760 4731544 4148720 2211091 TRUE FALSE 3432337.961 2157959.881 3590768.31 2649560.258 2089069.133 3746368.308 4009660.062 3785436.083 2553975.7 1.343919585 0.84494143 1.405952418 1.03742579 0.817967506 1.466877038 1.569967977 1.482173884 1 21.28431337 2.207576036 24.97511875 1.443958509 1.091666397 0.247797865 0.239466321 214.1745926 172634.1729 0.082626022 0.061029697 161.2783367 -2.207576036 -0.352292112 RKS(ph)PPKEYIDEEGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR 145.52 2.24E-05 4280690000 3093960 2530190 2542080 3154190 1670434 3096760 3351340 3410880 1995680 TRUE FALSE 2947714.642 2788019.238 2658636.882 2837124.829 1961757.161 2989518.425 2840031.531 3112205.265 2305159.862 1.278746299 1.209468933 1.153341652 1.230771399 0.851028683 1.296881173 1.232032354 1.350103876 1 21.13643537 -2.24429957 2.422584128 0.212785282 1.201487968 0.178428204 0.135051167 1728082.815 1356408.411 7619856.695 0.031757263 0.005697711 2.24429957 0.988702686 RKS(ph)QEALHEQSSYILSSAETPARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RKSQEALHEQSSYILSSAETPARPR 25 3 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 RKS(0.999)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR 170.44 6.10E-12 731110000 202958 185544 183859 235379 148497 236441 262487 253588 175176 TRUE FALSE 193364.5776 204451.1445 192289.117 211718.2557 174394.8298 228252.9889 222439.7872 231382.4904 202341.3994 0.955635269 1.010426661 0.950320189 1.046341759 0.861884075 1.128058764 1.099329094 1.143525206 1 17.626432 2.210834812 24.99999991 1.101792291 0.973319783 0.520834452 0.060339883 152.8487991 137820.8461 0.019723391 0.014569829 162.493058 -2.210834812 -0.128472508 RKS(ph)QVNGEAGSYEMTNQHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(0.999)QVNGEAGS(0.001)YEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK 301.34 3.66E-55 3361410000 1534856 1360790 1539882 1687262 1078815 1614890 1792558 1732488 1162697 TRUE FALSE 1462306.399 1499456.048 1610487.113 1517655.218 1266959.994 1558965.954 1519070.355 1580782.166 1343002.113 1.088834027 1.116495673 1.199169456 1.130046784 0.943379003 1.160806777 1.131100495 1.177051139 1 20.35703014 4.539989299 3.459072248 1.113736156 1.089710837 0 0.078923909 1.903151053 44.24914974 0.018277459 0.09114263 34672.83066 -4.539989299 -0.024025319 RKS(ph)SVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSSVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR 39 3 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3;E9PQ33;F8W961;E9PQX3;U5GXS1 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 1 RKS(0.978)S(0.021)VTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR 241.27 2.08E-50 142000000 145910 114750 125520 151270 125650 140070 178380 166300 110210 TRUE FALSE 139013.1235 126443.1555 131275.2162 136064.0522 147563.3202 135219.3408 151164.8548 151737.8904 127300.8039 1.092005071 0.99326282 1.031220637 1.068838908 1.159170372 1.062203353 1.187461903 1.191963332 1 16.957882 2.931637288 4.047384279 1.131113239 1.037471971 0.25877584 0.062053097 0.249270031 7.923680067 0.01784775 0.019524792 854.352881 -2.931637288 -0.093641267 RKS(ph)TDSVPISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RKSTDSVPISK 11 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RKS(0.86)T(0.14)DSVPISK;RKS(0.493)T(0.478)DS(0.029)VPISK;RKS(0.496)T(0.496)DS(0.008)VPISK;RKS(0.909)T(0.068)DS(0.023)VPISK;RKS(0.854)T(0.143)DS(0.003)VPISK;RKS(0.903)T(0.097)DSVPISK;RKS(0.957)T(0.039)DS(0.004)VPISK 198.74 2.75E-08 19196700000 35246850 30885980 30842400 36233750 21036100 37134630 40858890 39151110 27337670 TRUE FALSE 33580801.25 34033296.48 32256554.55 32591464.61 24704789.18 35848648.45 34625115.91 35722831.26 31577056.24 1.063455725 1.077785599 1.021518735 1.032124855 0.782365176 1.135275188 1.09652767 1.131290738 1 24.91237335 -0.508719226 7.685317615 1.000007517 1.04615389 0.01654725 0.099675315 0 0 0.09366951 0.022078115 0.309942244 0.508719226 0.046146373 RKS(ph)TITALLFGEDDLEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSTITALLFGEDDLEALK 19 2 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 1 RKS(0.798)T(0.187)IT(0.015)ALLFGEDDLEALK 106.93 0.00023972 65262000 131700 97157 146850 146320 81533 143550 152960 130600 118740 TRUE FALSE 125474.802 107057.4088 153583.2178 131611.6356 95752.32939 138578.8275 129623.1427 119163.9716 137153.5928 0.914848816 0.780565836 1.119789972 0.959593059 0.698139418 1.010391523 0.945094766 0.868835947 1 17.06543289 -4.999999996 0.108745027 1.27742792 0.856771313 0.034217509 0.11718019 562.6306584 4.080208652 35.32871965 1.459712123 1.00E-05 4.999999996 -0.420656608 RKS(ph)VEEESKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSVEEESKK 10 3 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RKS(1)VEEESKK 133.16 0.0011303 110460000 259930 224700 217390 263710 120690 275900 293050 331040 135960 TRUE FALSE 247643.624 247597.1855 227357.5465 237201.3698 141738.2978 266345.5138 248339.8403 302052.3826 157043.9824 1.576906165 1.576610461 1.447731667 1.510413619 0.902538866 1.695993121 1.581339421 1.923361711 1 17.26080914 3.7448276 21.96496318 1.465170233 1.576758355 0.029653335 0.300370592 437.9928121 1535072.256 0.073773727 0.12842231 5556.836259 -3.7448276 0.111588122 RKSPENT(ph)EGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.095)PENT(0.905)EGK 118.52 0.0013086 889410000 1225900 1317300 986230 1440700 603330 1245100 1206000 1358100 650590 TRUE FALSE 1167954.136 1451534.368 1031449.621 1295878.099 708550.561 1201981.875 1022002.55 1239177.564 751480.1744 1.554204856 1.931567082 1.372557329 1.724434181 0.942873259 1.599485809 1.359986045 1.648982377 1 19.51937552 -0.037824978 0.065893511 1.66E-10 2.508060964 0.281350862 0.260984431 83.7120639 1.695890809 39.56146231 24.58153887 0.916589804 0.037824978 2.508060964 RKT(ph)DTVVESSVSGDHSGTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RKTDTVVESSVSGDHSGTLR 20 2 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 RKT(0.854)DT(0.146)VVESSVSGDHSGTLR;RKT(0.983)DT(0.017)VVESSVSGDHSGTLR;RKT(0.93)DT(0.07)VVESSVSGDHSGTLR;RKT(0.998)DT(0.002)VVESSVSGDHSGTLR 294.38 6.99E-53 1316860000 387286 350287 385813 422619 421028 371427 512033 454066 537857 TRUE FALSE 368979.7583 385981.6435 403502.9077 380136.5352 494455.1499 358564.3899 433912.9617 414305.5739 621265.1166 0.593916749 0.621283303 0.649485859 0.611874907 0.795884296 0.577151976 0.698434453 0.666874033 1 19.24484953 -5 0.228698942 2.885910285 0.607297265 0.778020806 0.059253101 66.61220854 0.666302282 58.06139293 0.092641321 1.00E-05 5 -2.278613021 RKT(ph)PEASAIGLHQDPELGDAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKTPEASAIGLHQDPELGDAALR 23 2 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 RKT(1)PEASAIGLHQDPELGDAALR 138.08 0.00023906 176700000 87636 74449 86169 100450 74752 88648 110490 101070 84263 TRUE FALSE 83493.61996 82035.43774 90119.93388 90352.57516 87788.72513 85578.09753 93632.72121 92219.77499 97330.07568 0.857839875 0.842858049 0.925920721 0.928310951 0.901969145 0.879256457 0.96201221 0.947495153 1 16.57059806 7.999999641 0.085253537 1.080857732 0.422073054 0.701804014 0.026184982 86.74191059 0.535109308 0.578199677 6.700180869 99999917.23 -7.999999641 -0.658784678 RKT(ph)SDANETEDHLESLICK ddPTM_SK-BR-3_Trastuzumab_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 226.14 7.49E-18 329574000 447000 293268 459370 439150 340640 448460 547860 414090 268624 TRUE FALSE 425871.1959 323152.3426 480432.5689 395005.8077 400047.5081 432929.7178 464273.8949 377830.0844 310280.838 1.372534632 1.041483402 1.548379758 1.273058982 1.289307811 1.395283449 1.496302182 1.217703571 1 18.24321508 3.747235696 24.97920115 1.348313644 1.207009044 0.043337423 0.172064926 1257.864658 3621911.673 0.040314092 0.071226503 5587.733642 -3.747235696 -0.141304599 RKT(ph)SDFNTFLAQEGCTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKTSDFNTFLAQEGCTK 17 2 Q9UHD1-2;Q9UHD1;E9PHZ2 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 1 RKT(0.474)S(0.474)DFNT(0.053)FLAQEGCTK 142.01 2.87E-05 56817000 86369 78505 87032 93033 55540 91964 98268 104890 74236 TRUE FALSE 82286.50854 86504.74875 91022.50329 83681.14609 65226.15842 88779.26362 83275.41178 95705.27554 85748.13974 0.959630247 1.00882362 1.061509947 0.975894595 0.760671411 1.03534915 0.971162897 1.116120721 1 16.38781775 1.26791484 23.91703534 1.058060281 0.971021852 0.163152299 0.084916904 206.1652178 167978.4746 0.054581561 0.01992238 18.53168204 -1.26791484 -0.08703843 RKT(ph)SQSEEEEAPR ddPTM_SK-BR-3_Trastuzumab_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(0.858)S(0.14)QS(0.002)EEEEAPR 124.18 0.00034543 395050000 112110 75520 105960 109350 78340 96328 123870 98126 97764 TRUE FALSE 106810.7825 83215.57386 110818.3708 98357.93025 92002.4712 92992.13721 104971.3565 89533.56724 112924.7418 0.945858107 0.736911792 0.981347126 0.871004252 0.814723768 0.823487712 0.929569152 0.7928605 1 16.78500209 -1.810903004 2.762358806 1.041577227 0.861554678 0.252731891 0.074587405 24248367.64 13968970.06 6658811.339 0.016554686 0.015455996 1.810903004 -0.180022549 RKTS(ph)DANETEDHLESLICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.42)S(0.552)DANET(0.028)EDHLESLICK 96.903 0.00062717 126140000 156540 94273 158380 160530 114350 152310 170580 131840 91199 TRUE FALSE 149140.6644 103879.5259 165641.8797 144393.2194 134292.6038 147035.4665 144554.8881 120295.3907 105341.6751 1.415780262 0.986119935 1.572424963 1.370713151 1.274828824 1.395795788 1.372247858 1.141954412 1 16.68471678 1.034520673 4.077934593 1.001627174 1.32183694 0.37879718 0.1481371 0.205616647 7.836696761 0.140608424 0.036001536 10.82731253 -1.034520673 0.320209767 RKVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 34 2 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 RKVDEGAGDSAAVASGGAQTLALAGS(0.999)PAPS(0.001)GHPK 136.18 8.95E-09 83293000 40917 34412 45372 43393 24306 49091 52697 44425 32658 TRUE FALSE 38982.9345 37918.62192 47452.35108 39031.0532 28544.9587 47390.96636 44657.1048 40534.91149 37722.43585 1.033415092 1.00520078 1.257934436 1.034690691 0.756710378 1.256307163 1.183834071 1.074557106 1 15.20313522 RKVDWLTEK ddPTM_SK-BR-3_Trastuzumab_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 ; 167.12 3.39E-05 3461900000 2509700 2523800 1751150 1819890 1511950 2139000 2337000 2334900 1569430 FALSE TRUE 2391071.455 2780978.089 1831441.96 1636951.2 1775633.601 2064925.894 1980447.728 2130443.778 1812809.189 1.318986835 1.534071046 1.010278396 0.902991451 0.979492829 1.139075147 1.092474454 1.17521678 1 20.78979565 3.731997127 24.99962291 1.04695654 1.426528946 0.743539651 0.093669956 229.9352792 875798.803 0.025635701 0.040766936 5395.070534 -3.731997127 0.379572406 RKVMDS(ph)DEDDDY ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY;RKVMDS(1)DEDDDY 142.32 4.06E-05 7449260000 10944820 8113010 9997860 9838270 7515680 10652340 13018130 11066140 9079880 TRUE FALSE 10427480.05 8939734.943 10456271.77 8849308.408 8826412.212 10283446.79 11031975.17 10097130.12 10487941.42 0.994235154 0.852382235 0.996980375 0.843760282 0.841577185 0.980501929 1.051872311 0.962737082 1 23.3222282 2.038812866 9.373337364 1.0120375 0.908016008 0.384770928 0.058831032 0.311378207 71.42475148 0.02105099 0.015498801 109.348509 -2.038812866 -0.104021492 RKVMDSDEDDDY(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(0.005)DEDDDY(0.995);RKVMDS(0.039)DEDDDY(0.961) 55.567 0.052258 389090000 988400 724670 933760 915660 721110 952930 1118250 1121800 924930 TRUE FALSE 941680.2908 798514.6969 976573.8196 823616.1172 846871.3557 919929.7952 947640.4244 1023569.245 1068363.421 0.881423187 0.747418605 0.914083916 0.770913812 0.792680973 0.861064482 0.887001938 0.958072155 1 20.02697106 1.37548232 1.367137315 0.998642507 0.81948618 0.62183586 0.049319128 0.237112446 0.840504866 0.041293243 0.013289177 23.74008777 -1.37548232 -0.179156327 RKVTGTEGSSSTLVDYTSTSS(ph)TGGSPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKVTGTEGSSSTLVDYTSTSSTGGSPVRK 29 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKVTGTEGSSSTLVDYTS(0.005)T(0.021)S(0.071)S(0.416)T(0.416)GGS(0.071)PVRK 116.35 0.00090112 200160000 95724 66802 92017 81439 75247 88128 105680 96484 89701 TRUE FALSE 91199.31623 73609.19975 96236.07047 73252.597 88370.05298 85076.10526 89556.57505 88035.34947 103611.373 0.880205653 0.710435521 0.928817636 0.706993788 0.85289916 0.821107788 0.864350819 0.849668786 1 16.66082284 0.379788331 0.543508694 1.009092591 0.805090922 0.39986764 0.068545943 2.012651803 0.961200151 0.101533586 0.028105825 2.397664049 -0.379788331 -0.204001669 RKVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RKVTGTEGSSSTLVDYTSTSSTGGSPVR 28 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKVTGTEGSSSTLVDYTSTSSTGGS(1)PVR;RKVTGTEGSSSTLVDYTS(0.001)T(0.001)S(0.025)S(0.149)T(0.116)GGS(0.707)PVR;RKVTGTEGSSSTLVDYTST(0.002)SST(0.004)GGS(0.993)PVR;RKVTGTEGSSSTLVDYTSTSS(0.002)T(0.005)GGS(0.992)PVR;RKVTGTEGSSSTLVDYTSTSS(0.001)T(0.004)GGS(0.995)PVR 140.34 6.98E-08 943824000 455240 300944 420614 381305 393699 420607 529309 441232 522533 TRUE FALSE 433721.7074 331610.5357 439899.5679 342975.497 462359.981 406041.2741 448553.1906 402595.387 603564.7489 0.718600131 0.549419986 0.728835752 0.568249716 0.766048683 0.67273855 0.743173274 0.667029325 1 19.20314902 -5 0.213266662 2.621593747 0.626747793 0.681437458 0.069844536 75.92306518 0.75768524 52.59446348 0.126084765 1.00E-05 5 -1.994845954 RKVTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKVTGTEGSSSTLVDYTSTSSTGGSPVRK 29 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKVTGTEGSSSTLVDYTSTSS(0.001)T(0.001)GGS(0.998)PVRK 232.4 4.31E-35 269690000 208020 176070 224400 203840 187450 238650 262230 250450 230770 TRUE FALSE 198187.3069 194011.7332 234688.962 183349.6159 220141.2207 230385.4907 222221.9973 228519.2703 266556.633 0.743509192 0.727844327 0.880446903 0.687844883 0.825870353 0.864302224 0.833676487 0.857301008 1 18.02408256 -4.999999498 0.075996905 1.747377214 0.55640433 0.653201201 0.052398515 146.3250266 0.792823899 18.30665762 1.920108665 1.00E-05 4.999999498 -1.190972884 RKYNWSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RKYNWSAK 8 2 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 115.7 0.0013575 542660000 506970 184990 173350 193580 443170 257510 654570 441740 573800 FALSE TRUE 483006.5328 203840.6913 181298.269 174120.9706 520458.7077 248592.3641 554703.3245 403058.9038 662781.9734 0.728756291 0.307553162 0.27354134 0.262712291 0.785263825 0.375074118 0.836931822 0.608131965 1 19.33817484 1.350084004 0.722400821 0.969609588 0.430174607 0.436351774 0.196745821 0.568613009 0.669476937 0.178992343 0.075663493 22.39154209 -1.350084004 -0.53943498 RLAAAEETAVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEET(0.009)AVS(0.991)PR;RLAAAEETAVS(1)PR 170.23 1.66E-05 4612890000 2771120 2531690 2506150 2928710 3057220 2654350 3127020 2761430 3371370 TRUE FALSE 2640134.649 2789672.089 2621059.456 2634310.507 3590398.2 2562429.194 2649935.667 2519624.55 3894184.841 0.677968498 0.716368689 0.67307012 0.676472898 0.921989671 0.65801427 0.680485333 0.64702233 1 21.89288993 -1.369669456 3.055854407 1.003480383 0.706082941 0.578001978 0.078833529 15622326.55 19768221.07 482811.419 0.017796782 0.042690431 1.369669456 -0.297397442 RLAEDEAFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 148.28 4.07E-05 440630000 164434 133614 155988 153439 212148 147042 195674 154607 216511 FALSE TRUE 156661.5307 147229.4185 163140.2041 138015.0202 249146.544 141949.8987 165820.3375 141068.7915 250086.4201 0.626429578 0.588714167 0.652335317 0.55186931 0.996241795 0.567603385 0.663052146 0.564080174 1 17.93206719 -2.089040502 2.587073088 1.596829414 0.64887392 0.421628636 0.128324746 9763845.706 2325692.497 34527165.29 0.028752611 0.008146283 2.089040502 -0.947955493 RLAPEYEAAATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLAPEYEAAATR 12 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 222.81 3.84E-11 1284480000 723190 534720 622470 624750 807560 587450 826230 671530 826420 FALSE TRUE 689006.2419 589208.5759 651010.8652 561948.9431 948398.2083 567106.4592 700173.4387 612727.2732 954576.9928 0.721792215 0.617245733 0.68198885 0.588688966 0.993527202 0.5940919 0.733490796 0.641883554 1 19.86450204 -2.204675569 2.284910783 1.896842414 0.694514418 0.401649927 0.116358137 5993359.277 1145809.59 27806347.11 0.02516136 0.00624201 2.204675569 -1.202327995 RLAS(ph)TSDIEEKENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLASTSDIEEKENR 14 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 RLAS(0.985)T(0.015)SDIEEKENR;RLAS(0.602)T(0.199)S(0.199)DIEEKENR 149.34 3.92E-06 261930000 314930 154088 266230 279740 295580 252410 334170 245130 277740 TRUE FALSE 300043.883 169789.7424 278436.9088 251620.0037 347129.0584 243668.9784 283186.229 223665.1177 320810.5007 0.935268273 0.529252447 0.867917067 0.784325959 1.082037707 0.759541779 0.882721197 0.697187646 1 18.29136184 3.590155214 19.28024316 0.862896521 0.726629485 0.127243595 0.14683742 7.340241976 1234.344568 0.035930525 0.055663338 3891.842118 -3.590155214 -0.136267036 RLAVPTEVSTEVPEMDTS(ph)T ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.08)S(0.46)T(0.46) 89.866 0.016679 45667000 48531 51987 44032 58388 53378 54345 60142 59704 63157 TRUE FALSE 46237.03581 57284.5344 46050.91075 52518.72731 62687.1063 52463.01902 50966.23332 54476.00125 72951.065 0.633808921 0.785246033 0.631257553 0.719917212 0.859303511 0.719153573 0.698635905 0.746747169 1 16.15464142 -5 0.285608747 3.09524746 0.705984136 0.644003249 0.065232787 151.4700551 1.437171706 188.7028529 0.068906227 1.00E-05 5 -2.389263324 RLDECEEAFQGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDECEEAFQGTK 13 1 K7ESG5;K9J957;P61289;P61289-2;B3KQ25;P61289-3;K7ENH2;K7EMD0;K7EPX6;K7EKR3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 159.41 7.31E-05 388810000 605740 554040 584030 610330 600670 561360 696920 656980 754750 FALSE TRUE 577107.8707 610497.3059 610808.3532 548978.4688 705426.6578 541919.9624 590592.0542 599451.3483 871792.7753 0.661978267 0.700278006 0.700634796 0.629712111 0.809167818 0.621615569 0.677445456 0.687607612 1 19.73362572 0.882652594 17.32829667 1 0.684718998 0.788056102 0.051165038 2569.788924 379475.6564 0.043399415 0.010849564 7.632250108 -0.882652594 -0.315281002 RLDEEEEDNEGGEWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 242.9 9.12E-20 813700000 514640 394060 468830 539610 494110 535890 614460 536590 547890 FALSE TRUE 490313.9871 434215.162 490326.3192 485367.3776 580282.6276 517331.9949 520712.8417 489603.335 632853.983 0.774766376 0.686122192 0.774785863 0.766950024 0.916929723 0.817458701 0.822800924 0.773643444 1 19.27151314 -4.999999999 0.097894492 1.67990757 0.63437409 0.606553573 0.054740937 123.5448074 0.826720327 17.25664159 0.968313189 1.00E-05 4.999999999 -1.045533481 RLDEELEDAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLDEELEDAEK 11 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;; 173.19 2.00E-05 890620000 1264490 1155440 1043960 1346430 871770 1250300 1236820 1341490 932360 FALSE TRUE 1204720.064 1273180.65 1091826.599 1211084.298 1023806.412 1207001.797 1048120.393 1224022.024 1076945.627 1.118645207 1.18221442 1.013817756 1.12455473 0.950657476 1.120763915 0.973234272 1.13656808 1 20.03851398 3.738089913 24.99841734 1.044162786 1.150429816 0.301443929 0.066278144 40.98103353 2176498.656 0.015031471 0.024924256 5471.292247 -3.738089913 0.10626703 RLDEVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLDEVSR 7 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 167.9 0.0017141 625800000 1004780 968830 1104600 1343360 814270 1026930 994300 1076570 1005190 FALSE TRUE 957286.0407 1067554.878 1155247.003 1208322.901 956278.4302 991367.1566 842601.2734 982299.8235 1161069.731 0.82448626 0.919458022 0.994985031 1.04069796 0.823618431 0.853839464 0.72571117 0.846029999 1 20.14702319 2.602068691 22.34183078 0.824572259 0.93028555 0.187358862 0.087910512 9.769309026 1707.875086 0.028380449 0.026757317 400.0080127 -2.602068691 0.10571329 RLDEYTQEEIDAFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDEYTQEEIDAFPR 15 1 H0YAX3;Q9BYD1;E5RJI7 H0YAX3 MRPL13 "39S ribosomal protein L13, mitochondrial" 0 ; 233.78 1.97E-17 176951000 131858 101221 117214 117181 131385 98457 114408 124495 148322 FALSE TRUE 125625.3337 111535.535 122588.3778 105401.7433 154298.5024 95047.4094 96952.95835 113593.5578 171323.0182 0.733265938 0.651024808 0.715539448 0.615222311 0.900629139 0.554784817 0.565907368 0.663037337 1 17.38635947 -0.52435676 13.36525454 1 0.669338232 0.518947142 0.098229228 0 0 0.09197172 0.021677942 0.298980759 0.52435676 -0.330661768 RLDGESSELQEQMVEQQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDGESSELQEQMVEQQQR 19 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 197.1 1.29E-15 258720000 135270 93812 110414 113076 139689 109129 121081 121144 146655 FALSE TRUE 128876.0552 103371.5495 115476.5911 101709.3856 164050.7174 105349.8354 102607.8696 110535.9891 169397.5084 0.760790737 0.610230637 0.681690021 0.600418428 0.968436425 0.621909002 0.605722425 0.652524291 1 17.37005313 -0.973989628 4.835555767 1.000003475 0.682087603 0.439228221 0.110730082 3.90E-06 8.27E-07 0.100720477 0.023739784 0.106172091 0.973989628 -0.317915872 RLDIDEKPLVVQLNWNKDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 103.17 0.0001267 122420000 94046 64856 64434 84259 63050 76885 87145 86380 64067 FALSE TRUE 89600.63196 71464.90014 67388.36263 75789.12524 74045.90004 74222.45317 73849.42972 78816.10927 74002.18315 1.21078363 0.965713403 0.910626684 1.024147154 1.000590751 1.002976534 0.997935825 1.065051137 1 16.17528021 4.577462393 2.839946251 0.99492836 1.217075678 0.740409428 0.039795991 0.150039961 2.05880423 0.009739656 0.064384166 37797.44056 -4.577462393 0.222147317 RLDINEGAARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLDINEGAARPR 12 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;; 161.23 3.68E-05 2102400000 709950 621920 658730 710060 787820 684120 839290 730140 804490 FALSE TRUE 676392.0705 685294.3551 688933.4221 638683.4198 925215.5586 660428.7529 711240.8959 666205.0709 929246.2004 0.727893286 0.7374734 0.74138955 0.687313458 0.995662461 0.710714504 0.765395538 0.716930638 1 19.82570136 -2.577184836 2.192109984 5.441254637 0.758901425 0.432250921 0.086302866 2686711.9 166397.169 60298980.24 0.019337331 0.002647373 2.577184836 -4.682353212 RLDLDACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLDLDACK 8 1 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 122.33 0.0022369 119170000 712290 405220 218060 254740 613510 318050 756400 520510 628210 FALSE TRUE 678621.4633 446512.3787 228058.2667 229133.0512 720505.9498 307035.8488 640997.2878 474931.385 725629.5983 0.935217451 0.615344771 0.314290193 0.315771368 0.99293903 0.423130271 0.883367064 0.654509389 1 19.46887378 0.824389812 0.77251008 0.993191469 0.621124541 0.192589391 0.24036738 1.57424738 1.943408282 0.231076204 0.083629661 6.674055478 -0.824389812 -0.372066928 RLDLPIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLDLPIER 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;;; 154.85 0.0006709 1273550000 932480 787698 800774 919306 1017780 801729 1000154 916172 1013931 FALSE TRUE 888403.5184 867965.3217 837490.28 826895.6143 1195280.51 773964.9237 847562.1382 835947.1227 1171166.241 0.75856312 0.741111971 0.715090865 0.706044612 1.020589962 0.660849755 0.723690718 0.71377324 1 20.15951444 -1.249325085 3.428443058 1.000658187 0.75282866 0.381921171 0.097930606 160906975.2 239382542.8 1110927.656 0.021942137 0.056321591 1.249325085 -0.247829527 RLDQELDFILSQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLDQELDFILSQQK 14 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 154.6 9.74E-06 61830000 163240 137560 136500 144830 128670 132260 165120 153160 146250 FALSE TRUE 155523.9687 151577.5204 142758.66 130271.4132 151110.0073 127679.803 139927.9114 139748.4984 168929.7031 0.920643119 0.897281636 0.845077316 0.771157534 0.894514135 0.755816181 0.828320354 0.827258297 1 17.3660635 3.759667698 3.369728411 0.831496243 0.911911216 0.106506401 0.068238702 0.339429522 8.109804065 0.015980416 0.02910752 5749.998057 -3.759667698 0.080414974 RLDQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDQLER 7 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 127.46 0.014334 228880000 293760 279150 257270 328560 352730 249790 316700 303710 326300 FALSE TRUE 279874.547 307595.7024 269066.084 295532.5246 414246.0003 241139.7097 268381.5984 277115.5423 376900.9375 0.742567925 0.816118167 0.713890726 0.784111938 1.099084558 0.639795993 0.712074637 0.735247687 1 18.52382586 -2.214424929 2.24734921 1.674210897 0.777753695 0.240515292 0.1225811 10030998.69 1953355.076 34352869.75 0.028430351 0.006103446 2.214424929 -0.896457202 RLDQVEQELNELRETEGGTVLTATTSELEAINKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLDQVEQELNELRETEGGTVLTATTSELEAINKR 34 3 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 97.257 8.39E-05 17488000 19723 14457 18284 17589 15944 17592 24145 19683 19601 FALSE TRUE 18790.73288 15930.18474 19122.33949 15820.9203 18724.62855 16982.78463 20461.2368 17959.45217 22640.62297 0.82995653 0.703610707 0.844603062 0.698784672 0.827036808 0.750102356 0.903740008 0.793240195 1 14.46662603 0.560943882 0.497986651 1.009662213 0.765941674 0.539231941 0.061515641 1.215822223 0.577762284 0.084692969 0.028863631 3.638680155 -0.560943882 -0.243720539 RLDS(ph)SGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLDSSGER 8 1 A0A087X2H1;Q9ULT8;G3V4V5;A0A087WVU6 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 RLDS(0.968)S(0.032)GER;RLDS(0.5)S(0.5)GER 106.38 0.0025767 362800000 156988 138032 147988 173459 183572 152669 159428 141553 171585 TRUE FALSE 149567.4884 152097.6177 154773.3962 156022.5718 215586.8987 147382.0342 135104.3305 129157.8689 198193.5255 0.754653756 0.767419709 0.780920546 0.787223354 1.087759543 0.743626886 0.68167883 0.651675521 1 17.59655031 -1.161333144 5.054688128 1.000012728 0.77922172 0.255533846 0.11693066 1.67E-05 2.78E-06 0.113031921 0.026640344 0.068971053 1.161333144 -0.220791008 RLDVFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLDVFEK 7 1 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 135 0.0050026 921760000 1901300 1768100 1665770 2022760 1757490 1858790 2016980 1949790 1824540 FALSE TRUE 1811429.317 1948271.4 1742147.202 1819428.322 2063995.7 1794419.636 1709252.657 1779056.051 2107480.345 0.859523706 0.924455312 0.826649324 0.863319236 0.979366524 0.851452608 0.811040853 0.844162583 1 21.00708775 RLDVTVQSFGWSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 0 174.59 4.04E-06 288910000 173540 180730 158500 180670 186520 157430 174700 181430 191810 FALSE TRUE 165337.1081 199146.5925 165767.3818 162508.7083 219049.0289 151978.1596 148046.3064 165543.0274 221554.9152 0.746257911 0.898858833 0.748199974 0.733491777 0.988689548 0.68596158 0.668214949 0.747187338 1 17.75730481 RLDYITAEIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLDYITAEIKR 11 2 O15212 O15212 PFDN6 Prefoldin subunit 6 0 151.26 1.88E-05 217200000 424810 321030 285370 308940 352140 315620 448810 366350 363910 FALSE TRUE 404730.0732 353743.322 298454.4968 277884.7643 413553.1045 304690.0003 380335.7915 334270.4519 420343.3042 0.962856002 0.841558123 0.710025576 0.661090022 0.983846062 0.724859888 0.904821815 0.795232013 1 18.68120857 -1.203108047 7.035879992 1.000000418 0.830765581 0.210958261 0.106629635 6.68E-07 7.57E-08 0.098550316 0.023228475 0.062645799 1.203108047 -0.169234838 RLEAAYLDLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLEAAYLDLQR 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;; 147.42 5.66E-05 1481930000 2797410 1978760 1704870 2227930 3119760 2054190 3254530 2635800 3119930 FALSE TRUE 2665181.973 2180397.894 1783039.976 2003974.244 3663845.156 1983052.885 2757991.675 2404995.379 3603752.81 0.739557376 0.605035364 0.494773107 0.556079828 1.016674936 0.550274392 0.765311002 0.667358586 1 21.78106863 RLEAEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEAEQAR 8 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 153.24 0.00071218 148350000 74372 55999 55502 58197 106600 42909 87146 55710 105490 FALSE TRUE 70856.58295 61705.36177 58046.8216 52346.92699 125191.0062 41423.05057 73850.27715 50831.73706 121848.8504 0.581512117 0.50640906 0.476383826 0.429605424 1.027428702 0.339954381 0.606081033 0.417170428 1 16.89473311 -1.149982657 4.384622027 1.00007169 0.549845512 0.365111841 0.187275465 23855297.85 6256687.918 19293.34227 0.038934928 0.070797406 1.149982657 -0.450226178 RLEDELGGQFLDLSLHDTVTTLILGGHNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEDELGGQFLDLSLHDTVTTLILGGHNKR 30 2 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 182.09 2.05E-18 58928000 77235 57830 73600 75831 89500 71480 111140 89970 58880 FALSE TRUE 73584.25462 63722.94275 76974.6328 68208.32381 105108.7717 69004.62968 94183.55177 82091.74984 68010.80968 1.081949398 0.936953156 1.131799976 1.002904158 1.545471553 1.014612677 1.384832091 1.207039737 1 16.05347645 RLEDLSESIVNDFAYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEDLSESIVNDFAYMK 17 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 168.69 3.31E-09 98536000 208440 150890 153920 166630 217520 179580 257820 177020 208340 FALSE TRUE 198587.4543 166265.8625 160977.3842 149880.0358 255455.4191 173361.0996 218484.8238 161519.1904 240648.3031 0.825218594 0.690908103 0.668932139 0.622817755 1.061530108 0.720391947 0.907900953 0.671183583 1 17.87656673 2.775826928 24.99992781 0.857409097 0.711984646 0.308385186 0.125198105 756.6832305 507616.0501 0.03471738 0.036822427 596.7974074 -2.775826928 -0.145424451 RLEEALMADMLAHVEELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEEALMADMLAHVEELAR 19 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 119.79 3.43E-05 26477000 60982 72667 58557 70845 74240 60868 65416 65653 56645 FALSE TRUE 58099.50171 80071.84992 61241.89637 63723.526 87187.43249 58760.1259 55435.58775 59904.07527 65429.2173 0.887974885 1.223793486 0.936002277 0.97393074 1.332545858 0.898071662 0.847260445 0.915555431 1 15.99764739 2.075036921 25 0.896094962 1.068776477 0.239197554 0.136005857 47.39920823 15790.35628 0.04778664 0.035292769 118.8603271 -2.075036921 0.172681515 RLEELEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLEELEAK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 104.05 0.0074646 547320000 399220 349910 338180 416750 336880 373530 440030 430170 353700 FALSE TRUE 380349.6618 385566.2268 353685.8875 374857.4982 395631.7653 360594.5624 372895.3418 392502.0343 408549.9896 0.930974597 0.943743083 0.865710186 0.917531533 0.96838031 0.882620418 0.9127288 0.960719727 1 18.64015309 1.019451521 3.642068196 0.999579019 0.919010538 0.481301512 0.028729385 0.171828083 5.494099737 0.026757222 0.006912162 10.45806943 -1.019451521 -0.080568481 RLEEMLRPLVEEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEEMLRPLVEEGLR 15 2 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 197.17 4.81E-09 32613000 48771 41879 39926 50478 44603 43443 50928 46410 39874 FALSE TRUE 46465.69148 46146.51771 41756.64659 45403.85554 52381.74908 41938.55802 43157.99824 42346.09437 46057.45627 1.008863607 1.001933703 0.906620773 0.985809014 1.137313115 0.910570436 0.937046935 0.919418869 1 15.49114711 RLEEPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 169.09 0.00048593 206068000 173548 141246 153556 174753 191454 155678 175701 170508 188572 FALSE TRUE 165344.73 155639.128 160596.6945 157186.4964 224843.517 150286.8318 148894.5855 155577.4156 217814.7827 0.759107017 0.714548049 0.737308517 0.721652105 1.032269317 0.689975354 0.683583472 0.714264724 1 17.73274234 -2.267914857 2.193605002 1.961607713 0.751531538 0.365354369 0.100625195 6172410.202 1117585.513 29323542.5 0.025236446 0.005396164 2.267914857 -1.210076174 RLEEQAAQHK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 147.3 1.76E-05 852990000 1123670 936260 885570 1003060 832710 976780 1171510 1125210 899160 FALSE TRUE 1070556.346 1031665.958 926174.2604 902230.5031 977934.3604 942953.8637 992774.6332 1026680.647 1038597.141 1.030771513 0.9933264 0.891755065 0.868701124 0.941591616 0.907911092 0.955880384 0.988526357 1 19.98620473 3.927936164 5.044485266 0.931870431 1.017610251 0.383274272 0.040700611 0.182298879 8.661980825 0.010290259 0.019353417 8471.028912 -3.927936164 0.08573982 RLEESDVLQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLEESDVLQEAR 12 1 O43615;M0QXU7;M0R301;M0R124 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 ; 149.57 0.00010804 464550000 377880 270005 315670 321140 349670 270240 372230 315030 379140 FALSE TRUE 360018.3613 297518.8165 330143.7817 288858.3971 410652.3373 260881.521 315439.477 287444.3031 437935.0948 0.822081549 0.679367377 0.753864638 0.659591799 0.937701368 0.595708186 0.720288191 0.656362796 1 18.74035754 -1.411416107 8.886638028 1.000001601 0.727850097 0.441155961 0.096166955 2.71E-06 1.79E-07 0.08261697 0.019472892 0.038777865 1.411416107 -0.272151503 RLEEWLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 193.1 0.00027645 1460680000 1071390 910613 928039 1114540 1245300 936646 1261720 1083530 1233510 FALSE TRUE 1020747.518 1003405.5 970590.5061 1002504.322 1462479.926 904209.7142 1069221.441 988650.369 1424796.431 0.716416392 0.704244816 0.68121346 0.70361232 1.026448336 0.634623792 0.75043804 0.693888859 1 20.44232438 -1.729765092 2.366125013 1.060381441 0.736598053 0.372514774 0.106477494 6704749.374 4649844.863 2381664.844 0.024891534 0.018630946 1.729765092 -0.323783388 RLEFLYDK ddPTM_SK-BR-3_Trastuzumab_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 92.538 0.018771 396640000 498310 357790 213700 276050 426840 259520 509010 391190 384080 FALSE TRUE 474755.8739 394249.2078 223498.3564 248300.9295 501280.7609 250532.7573 431351.1759 356935.3298 443641.1648 1.070134856 0.888666876 0.503781827 0.559688661 1.129923913 0.564719366 0.972297456 0.804558635 1 18.75903371 -0.531591617 10.04016518 1 0.826633394 0.065973249 0.216261968 0 0 0.201477168 0.047488624 0.294041333 0.531591617 -0.173366606 RLEGEDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEGEDSAR 9 1 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 92.611 0.015968 34998000 32661 22862 27493 27437 39319 25035 36122 25933 50824 FALSE TRUE 31117.17926 25191.66379 28753.58124 24678.98063 46176.22115 24168.03167 30610.92547 23662.16904 58705.52635 0.530055366 0.42911912 0.489793432 0.420385987 0.786573667 0.411682395 0.521431752 0.403065444 1 15.8412087 -1.644833897 3.013511724 1.042658173 0.498379045 0.665479282 0.111627116 42093913.15 43474149.64 13975983.89 0.024931132 0.022655106 1.644833897 -0.544279128 RLEIS(ph)PDS(ph)SPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(1)PDS(0.589)S(0.412)PER;RLEIS(0.999)PDS(0.649)S(0.352)PER;RLEIS(0.999)PDS(0.706)S(0.296)PER 144.29 4.21E-05 683480000 1364560 1111070 1232040 1300720 1403920 1169010 1428310 1292420 1362470 TRUE FALSE 1300059.953 1224289.296 1288530.253 1169969.154 1648763.204 1128526.891 1210395.077 1179248.853 1573754.889 0.826087952 0.777941536 0.818761715 0.743425271 1.047662006 0.717091904 0.76911283 0.749321804 1 20.58577943 -0.945791807 4.196891718 1.000007178 0.803957903 0.304491898 0.092006411 35006274.8 103245630.8 4333.595645 0.020368907 0.113294335 0.945791807 -0.196049275 RLEIS(ph)PDSS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(1)PDS(0.082)S(0.918)PER;RLEIS(0.999)PDS(0.14)S(0.861)PER;RLEIS(1)PDS(0.443)S(0.557)PER 156.57 4.08E-05 661140000 864460 699900 759310 849630 891080 740830 884390 796180 877650 TRUE FALSE 823598.689 771220.6057 794125.1146 764223.5782 1046484.07 715174.8713 749460.0626 726462.2584 1013751.48 0.812426621 0.760759043 0.783352854 0.75385693 1.032288575 0.705473566 0.739293681 0.71660784 1 19.95127259 -2.215286624 2.359192466 1.689317162 0.785979183 0.342819408 0.092204876 4891272.929 896775.0206 18065360.86 0.021141674 0.006091347 2.215286624 -0.903337978 RLELQLQEVQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLELQLQEVQGR 12 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 152.16 0.00011155 101400000 81063 66602 68989 82067 109930 62636 87060 66172 115230 FALSE TRUE 77231.31264 73388.81952 72152.21389 73817.46924 129101.7572 60466.89961 73777.39803 60377.62888 133099.2799 0.580253422 0.551384046 0.542093195 0.554604573 0.969965858 0.454299224 0.55430351 0.453628516 1 17.02214324 -1.980997303 2.727011396 1.37147541 0.581392424 0.452541191 0.144284919 45615205.99 28020133.7 106859969 0.034718332 0.010447267 1.980997303 -0.790082986 RLEPPFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLEPPFRPK 9 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 0 71.614 0.027606 197230000 203860 167880 152170 211070 187000 178850 275520 216700 229680 FALSE TRUE 194223.9418 184987.1629 159147.145 189852.8426 219612.7408 172656.3797 233484.3637 197724.5992 265297.6014 0.732098371 0.697281701 0.599881583 0.71562216 0.827797687 0.650802641 0.880084714 0.74529358 1 18.01725211 0.624245052 0.421244586 1.020841199 0.685136717 0.608943119 0.072529245 1.21652122 0.454496207 0.126549705 0.046717629 4.209640917 -0.624245052 -0.335704482 RLES(ph)SGAGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLESSGAGGR 10 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 RLES(0.803)S(0.197)GAGGR 89.46 0.0048794 0 145030 119500 146620 145770 164350 134430 158610 132500 174590 TRUE FALSE 138174.7193 131677.1859 153342.672 131116.9227 193012.588 129774.6554 134411.1314 120897.5976 201664.5255 0.685171172 0.652951656 0.760384959 0.650173462 0.957097375 0.64351752 0.666508555 0.599498584 1 17.6215978 -2.044207623 2.583546029 1.391176692 0.699286406 0.469730947 0.099498703 17880371.56 4941501.613 41420098.22 0.023243976 0.009032176 2.044207623 -0.691890286 RLFDANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLFDANK 7 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 ; 174.69 0.0013099 1379800000 5606800 4355100 2023600 2499190 4707100 2930500 5816200 4241200 4218200 FALSE TRUE 5341777.676 4798889.641 2116384.062 2247966.673 5528016.75 2829016.05 4928831.868 3869818.044 4872336.912 1.096348174 0.984925658 0.434367348 0.461373405 1.134571941 0.580628167 1.011595043 0.794242704 1 22.21618247 -1.487138862 8.37935802 1.000008302 0.835329811 0.044719914 0.25348683 3.89E-05 2.38E-06 0.242900347 0.057249276 0.032573253 1.487138862 -0.164678491 RLFDANKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLFDANKDR 9 2 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 ;;; 115.57 0.00081775 1790541000 3923830 2691082 2601019 2173701 3921260 2886249 5110910 3557600 4409700 FALSE TRUE 3738358.332 2965306.315 2720278.294 1955196.446 4605126.502 2786297.473 4331146.811 3246077.684 5093533.754 0.733941996 0.58217074 0.534065037 0.383858543 0.904112297 0.547026408 0.850322589 0.63729384 1 22.28023548 0.694480358 0.504708048 1.008651823 0.601323971 0.375831964 0.149508518 1.499512859 0.806177166 0.190036002 0.07357426 4.948577298 -0.694480358 -0.407327852 RLFDDEAS(ph)VDEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RLFDDEASVDEPR 13 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR 153.56 5.76E-07 683324000 1070341 923421 1045322 1092009 1151034 927947 1216239 1102431 1245934 TRUE FALSE 1019748.102 1017518.65 1093251.048 982238.1806 1351773.965 895811.9627 1030679.403 1005896.297 1439147.081 0.708578098 0.70702895 0.759652062 0.682514104 0.939288265 0.622460327 0.716173778 0.698953088 1 20.45678261 -1.892139492 2.374359098 1.151743943 0.726326897 0.517249084 0.08213186 9606677.604 4979293.026 8157569.396 0.017917313 0.012819188 1.892139492 -0.425417046 RLGDS(ph)SGPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLGDSSGPALK 11 1 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 RLGDS(0.954)S(0.046)GPALK 72.898 0.027585 174530000 82368 56653 69664 99488 69008 105250 118230 82444 104480 TRUE FALSE 78474.62788 62426.00511 72858.16331 89487.27723 81042.97335 101605.1661 100191.8421 75224.7663 120682.2248 0.650258379 0.517275889 0.603719093 0.741511663 0.671540266 0.84192321 0.83021209 0.623329297 1 16.88085367 2.827508049 1.05727582 0.816544847 0.578088383 0.468092685 0.102292856 0.40870366 0.969228722 0.047208429 0.04782965 672.2147681 -2.827508049 -0.238456464 RLGDSS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RLGDS(0.021)S(0.973)LS(0.006)R;RLGDS(0.024)S(0.933)LS(0.043)R;RLGDS(0.01)S(0.986)LS(0.004)R;RLGDS(0.079)S(0.7)LS(0.222)R;RLGDS(0.095)S(0.904)LS(0.001)R 153.25 8.32E-05 1039960000 2011843 1568325 1891894 2146437 2548025 2009260 2755288 2369789 2985685 TRUE FALSE 1916747.168 1728139.101 1978639.211 1930673.075 2992399.753 1939678.822 2334918.211 2162277.712 3448689.781 0.555789964 0.501100189 0.573736502 0.559827992 0.867691774 0.562439345 0.677045011 0.626985275 1 21.71761693 -5 0.133431384 2.331062095 0.44953536 0.642672097 0.094135268 84.43756553 0.703827511 29.96541313 0.622303302 1.00E-05 5 -1.881526735 RLGDSSLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RLGDS(0.041)S(0.317)LS(0.642)R 87.667 0.014094 78483000 167070 127770 163700 177100 222070 169850 219720 195520 241890 TRUE FALSE 159172.9322 140789.9083 171205.8069 159297.5715 260798.9377 163968.0519 186197.6786 178399.2323 279401.0658 0.569693361 0.503898966 0.612760035 0.570139456 0.933421413 0.586855499 0.666417209 0.638505912 1 18.091978 -5 0.121687387 2.206057995 0.447846325 0.540480728 0.109959237 113.4082709 0.890714886 33.75156102 0.970966203 1.00E-05 5 -1.75821167 RLGDSSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 107.51 0.0052658 0 317095 252075 241138 273462 271622 252078 350300 312233 272355 FALSE TRUE 302106.5478 277761.7291 252194.4158 245973.0802 318992.7908 243348.4757 296855.3013 284892.2233 314590.4224 0.960317054 0.882931295 0.801659548 0.781883563 1.013993968 0.773540637 0.943624726 0.905597256 1 18.26311522 0.843302312 1.178507712 0.998738472 0.878307075 0.19935154 0.077963302 1.130521046 3.015842435 0.069250212 0.021497707 6.971116045 -0.843302312 -0.120431396 RLGGLRPES(ph)PESLTSVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLGGLRPESPESLTSVSR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RLGGLRPES(0.999)PES(0.001)LTSVSR;RLGGLRPES(0.992)PES(0.005)LT(0.001)S(0.001)VS(0.001)R;RLGGLRPES(0.934)PES(0.066)LTSVSR;RLGGLRPES(0.989)PES(0.011)LTSVSR;RLGGLRPES(0.99)PES(0.008)LT(0.001)SVSR 219.78 5.63E-19 3310400000 709268 400569 715740 604013 1329810 665711 943384 697610 1262980 TRUE FALSE 675742.3073 441387.4365 748557.387 543296.4657 1561728.443 642657.2611 799453.4444 636523.5701 1458836.488 0.463206338 0.302561281 0.513119457 0.372417656 1.070530149 0.440527274 0.548007574 0.436322765 1 20.47638676 RLGSLVDEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLGSLVDEFK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 119.55 0.0010864 127000000 394730 294080 363820 380220 302410 357810 439370 424960 336570 FALSE TRUE 376071.8952 324047.0863 380501.5069 341999.5632 355150.2083 345418.95 372336.0369 387748.2495 388763.5566 0.967353778 0.83353257 0.97874788 0.879710964 0.91353781 0.888506508 0.957744188 0.997388369 1 18.56853346 1.500198108 3.041219305 0.997579428 0.907452201 0.440642567 0.041394258 0.20009425 3.801409144 0.027679528 0.009989071 31.63720497 -1.500198108 -0.090127228 RLGYDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLGYDTR 7 1 A0A2R8Y891;P08237;P08237-3 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 82.529 0.03887 280330000 375660 336760 351630 386230 391090 360770 421500 401050 400250 FALSE TRUE 357903.2963 371076.2269 367752.5833 347405.4266 459295.9722 348276.4444 357192.4336 365931.9359 462318.7258 0.774148388 0.802641568 0.795452494 0.751441391 0.993461754 0.753325412 0.772610785 0.791514415 1 18.81852827 -1.392345196 2.976817701 1.003061707 0.801718911 0.43920864 0.069431618 12868212.35 15447570.2 338028.78 0.015661509 0.040518635 1.392345196 -0.201342796 RLHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLHPPSPVPQGVCPAHREPLAAFCGDELR 29 2 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHREPLAAFCGDELR 106.19 0.00022863 223590000 23960 9219.8 25286 20039 33542 26019 27415 20639 20017 TRUE FALSE 22827.45828 10159.3081 26445.38811 18024.64165 39391.71418 25117.95551 23232.33824 18831.73975 23121.13413 0.987298381 0.439394886 1.143775559 0.779574287 1.703710292 1.08636347 1.00480963 0.814481662 1 14.49692455 3.715349854 24.76422838 1.085499968 0.713346599 0.221675778 0.282162799 855.7375206 913010.9346 0.071703224 0.11115976 5192.181362 -3.715349854 -0.372153369 RLIELYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLIELYK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 139.88 0.0042686 1493490000 2559300 2173500 1725420 1986360 2143340 1905940 2639100 2375600 2161380 FALSE TRUE 2438326.961 2394982.121 1804532.214 1786687.319 2517137.817 1839936.82 2236456.825 2167579.87 2496555.772 0.976676343 0.959314488 0.722808693 0.715660887 1.008244176 0.736990073 0.895816889 0.868228098 1 21.25150771 3.955389208 23.11974612 0.842653558 0.970165701 0.181160255 0.104006219 236.7153789 122678.7495 0.024424766 0.044034036 9023.794744 -3.955389208 0.127512143 RLKEDILENEDEQNS(ph)PPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLKEDILENEDEQNSPPKK 19 3 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RLKEDILENEDEQNS(1)PPKK 147.26 7.65E-08 237810000 357090 315920 297400 360310 139880 420170 374770 462470 189160 TRUE FALSE 340211.0634 348112.6072 311036.0842 324090.9543 164275.0277 405619.4075 317591.9534 421973.6751 218493.9667 1.557073033 1.593236703 1.423545413 1.483294752 0.751851551 1.856432988 1.45355022 1.931282962 1 17.73723392 3.737211663 22.98241515 1.436674804 1.57515487 0.03279529 0.347016879 161.775587 2756305.444 0.084652469 0.139645333 5460.239131 -3.737211663 0.138480066 RLKPGYLEATVDWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLKPGYLEATVDWFR 15 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 155.98 1.24E-06 232410000 278610 144840 264710 192100 314360 246420 423850 302620 465560 FALSE TRUE 265440.6575 159599.3607 276847.2153 172789.743 369184.2845 237886.4136 359183.898 276120.9885 537756.667 0.493607376 0.296787321 0.51481875 0.321315855 0.686526652 0.442368134 0.667930162 0.513468276 1 19.03659398 -1.177792331 0.211211273 1.43625272 0.340317792 0.685223167 0.113569722 9.939305932 0.438484158 2.672701665 0.255082969 0.066406053 1.177792331 -1.095934929 RLLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 119.56 0.033528 3328010000 6724060 5057570 4283290 5468790 5240810 5245580 7346070 6157580 5678540 FALSE TRUE 6406227.01 5572942.133 4479683.083 4919056.839 6154805.605 5063924.249 6225292.102 5618389.652 6559138.981 0.976687188 0.84964538 0.68296816 0.749954659 0.938355724 0.772041005 0.949102027 0.856574265 1 22.64507501 0.899734702 0.850135086 0.995645495 0.839287479 0.231928338 0.091667196 1.225199096 1.871841342 0.089802 0.031554918 7.938431512 -0.899734702 -0.156358016 RLLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 RLLEDGEDFNLGDALDS(0.304)S(0.304)NS(0.304)MQT(0.088)IQK;RLLEDGEDFNLGDALDS(0.392)S(0.353)NS(0.25)MQT(0.005)IQK;RLLEDGEDFNLGDALDS(0.675)S(0.292)NS(0.033)MQTIQK 137.36 9.85E-06 177135000 166595 117868 169906 164759 169863 171726 218177 174478 172524 TRUE FALSE 158720.3845 129878.8832 177696.3582 148197.1123 199487.0534 165779.0856 184890.0916 159199.7814 199278.1408 0.796476643 0.651746763 0.891700201 0.743669686 1.001048347 0.831897994 0.92779916 0.79888231 1 17.60442394 3.277405772 1.435629545 0.898345328 0.731387631 0.331339378 0.090203723 0.382572909 1.642697074 0.027590535 0.042047549 1894.11251 -3.277405772 -0.166957697 RLLEDGEDFNLGDALDSSNS(ph)MQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 RLLEDGEDFNLGDALDS(0.037)S(0.382)NS(0.578)MQT(0.003)IQK 141.21 1.85E-07 75589000 166320 127560 180820 169170 168610 187880 211950 186470 174720 TRUE FALSE 158458.3832 140558.509 189110.7759 152164.7102 198015.5306 181373.6685 179613.1348 170141.6983 201814.6853 0.785167754 0.696473147 0.937051611 0.753982348 0.981175034 0.898713928 0.889990411 0.843059057 1 17.62267163 3.738474537 24.99999993 0.893081596 0.740820447 0.455673601 0.072227164 5.883766798 1708951.281 0.016973097 0.028263232 5476.139926 -3.738474537 -0.152261149 RLLEDGEDFNLGDALDSSNSMQTIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;; 382.95 1.50E-144 7359873000 3191193 2301140 3171663 2999625 2929362 3170874 4222546 3441819 3811697 FALSE TRUE 3040351.631 2535628.782 3317086.886 2698096.996 3440241.805 3061065.838 3578319.055 3140435.082 4402795.503 0.690550272 0.575913367 0.753404714 0.612814516 0.781376696 0.695255057 0.812737964 0.713282068 1 22.06998841 -2.767056809 0.148740022 1.552235922 0.571489921 0.703086615 0.063694966 28.45945947 0.477717628 5.370583333 0.328402586 0.001709792 2.767056809 -0.980746001 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 34 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 RLLGPAPEDDGGHNDHSQPQAS(0.002)QDQDS(0.006)HT(0.035)LS(0.957)PQV;RLLGPAPEDDGGHNDHSQPQASQDQDS(0.002)HT(0.007)LS(0.991)PQV;RLLGPAPEDDGGHNDHS(0.001)QPQAS(0.006)QDQDS(0.063)HT(0.063)LS(0.868)PQV 98.139 6.00E-05 335840000 144133 125361 152581 149584 156742 159719 179802 159142 53285 TRUE FALSE 137320.1187 138135.4284 159576.9898 134547.5321 184077.7552 154187.891 152369.9026 145206.6828 61548.16566 2.231100103 2.244346796 2.592717233 2.186052674 2.990791898 2.505158185 2.475620532 2.359236563 1 15.90942824 3.946732611 24.07870753 2.403193963 2.236066783 0 0.517997562 974.3389162 440434.5067 0.115085387 0.207473769 8845.708234 -3.946732611 -0.16712718 RLNHS(ph)PPQSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RLNHSPPQSSSR 12 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 RLNHS(0.995)PPQS(0.002)S(0.002)S(0.002)R;RLNHS(0.917)PPQS(0.083)S(0.001)SR;RLNHS(1)PPQSSSR;RLNHS(1)PPQSSSR;RLNHS(0.973)PPQS(0.025)S(0.002)SR;RLNHS(0.997)PPQS(0.002)SS(0.001)R;RLNHS(0.987)PPQS(0.005)S(0.007)S(0.002)R 128.64 0.00015214 3188024000 884712 757153.1 848137 839597 866821 878185.8 1024949 945277 890054 TRUE FALSE 842893.4171 834307.8617 887024.9204 755199.1144 1017994.308 847774.0055 868574.2056 862503.5347 1028079.029 0.819872202 0.811521137 0.86279838 0.734573018 0.990190715 0.824619491 0.844851594 0.838946726 1 19.97151974 -5 0.204531177 1.74863659 0.813417543 0.396529293 0.062446248 136.6958334 1.357245936 41.9146392 0.126701338 1.00E-05 5 -0.935219047 RLNKHEENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLNKHEENLK 10 2 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 109.66 0.0011944 1392980000 1928510 1323540 1477680 1493230 1543250 1698480 2331210 2204940 1681840 FALSE TRUE 1837353.154 1458410.231 1545433.09 1343127.683 1812392.311 1639661.212 1975541.099 2011863.764 1942651.158 0.945796752 0.750731919 0.795527845 0.691389022 0.932947897 0.844032757 1.016930441 1.035627913 1 20.88959543 1.878207556 1.606723916 1.030351056 0.81264198 0.582588099 0.075913501 0.26057295 1.26262429 0.051553775 0.022726422 75.54531845 -1.878207556 -0.217709076 RLNLEEWILEQLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLNLEEWILEQLTR 14 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ; 168.45 5.59E-06 129697000 110955 107785 101638 125065 122614 93191 124594 106842 116642 FALSE TRUE 105710.377 118768.414 106298.2028 112493.2286 143997.8428 89963.7723 105584.897 97486.34807 134730.2456 0.784607618 0.881527481 0.788970601 0.834951559 1.068786315 0.667732564 0.783676275 0.723566914 1 17.03971423 -0.175484126 7.566669032 1 0.818576491 0.226504567 0.106387684 0 0 0.097005849 0.022864498 0.667599303 0.175484126 -0.181423509 RLNPDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLNPDGK 7 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 74.184 0.075153 150320000 221020 189020 284870 316280 181510 304620 320960 286380 237180 FALSE TRUE 210572.8226 208281.3529 297931.5713 284486.9335 213165.2865 294070.933 271991.6572 261303.049 273960.6631 0.768624299 0.76026007 1.087497628 1.038422562 0.778087205 1.073405684 0.992812815 0.953797695 1 18.06360923 3.75468977 24.64404347 0.98772004 0.764442145 0.546456156 0.085099103 445.2458471 680297.2367 0.020768223 0.037288657 5684.467268 -3.75468977 -0.223277895 RLNSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLNSSPR 7 1 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 RLNS(0.342)S(0.658)PR 64.42 0.045027 39586000 24303 27161 25150 28964 150900 18299 26504 20270 105020 TRUE FALSE 23154.24535 29928.73678 26303.15238 26052.48369 177216.9122 17665.30104 22460.32802 18495.05134 121305.9652 0.190874746 0.246721064 0.216833132 0.214766715 1.460908471 0.145625988 0.185154357 0.152466132 1 16.88829097 RLNVTPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLNVTPLAR 9 1 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 109.02 0.0040355 276770000 266230 177090 146700 151710 375610 145650 263100 184750 340840 FALSE TRUE 253645.8355 195135.6723 153426.3401 136459.8226 441116.2651 140606.104 222959.2628 168572.3106 393695.7264 0.644268704 0.495650979 0.389707914 0.346612405 1.120449717 0.357144095 0.566323808 0.428179173 1 18.58672153 -1.423736541 3.035098013 1.00805914 0.545244344 0.288675024 0.225167366 35545988.35 43438566.2 2480054.141 0.053253064 0.037693239 1.423736541 -0.462814796 RLNVWDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLNVWDLSK 9 1 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 ; 153.1 0.00012649 592120000 3259800 1637030 450790 606880 3101600 1072770 3660200 1967710 2861900 FALSE TRUE 3105715.714 1803845.218 471459.1674 545875.2694 3642518.058 1035619.706 3101769.266 1795406.881 3305708.835 0.939500685 0.545675771 0.142619689 0.16513108 1.101887141 0.313282191 0.938306856 0.543123115 1 21.65652823 0.941697289 0.684292451 0.983190003 0.555423762 0.143173076 0.326391158 1.714562327 1.821311914 0.316973 0.12506025 8.743741081 -0.941697289 -0.427766241 RLPDAHSDYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RLPDAHSDYAR 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;;;; 184.43 3.19E-06 1512793000 586819 436324 376366 492334 628733 448829 647868 474172 585455 FALSE TRUE 559081.2288 480785.9117 393622.7534 442843.6509 738383.8361 433285.9392 549023.8377 432650.9859 676244.3713 0.826744373 0.710964752 0.582071763 0.65485743 1.091889068 0.640723912 0.811871952 0.639784972 1 19.36718516 RLPDLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLPDLIK 7 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 107.01 0.012145 145310000 339980 303980 219920 252330 319720 262880 396350 329260 322540 FALSE TRUE 323909.8192 334955.9076 230003.5495 226965.309 375479.0668 253776.3997 335879.528 300428.2489 372557.8559 0.869421525 0.899070848 0.617363306 0.609208222 1.007840959 0.681173127 0.901549981 0.806393542 1 18.50710496 0.379636638 0.774739036 1.001851885 0.799058603 0.196816961 0.129516699 3.885087929 3.304819902 0.143536853 0.04332502 2.396826724 -0.379636638 -0.202793282 RLPEESGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLPEESGGR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 108.43 0.0041888 115690000 87565 71468 84837 93859 100760 83134 95699 87435 112180 FALSE TRUE 83425.97599 78750.67045 88726.86037 84424.115 118332.5121 80255.04873 81098.35992 79778.72788 129576.3015 0.643836682 0.607755196 0.684746048 0.65153978 0.913226499 0.619365176 0.625873397 0.615689188 1 16.98344236 -1.689449037 2.832365583 1.044172317 0.665007734 0.572672218 0.089415801 18103674.92 17184723.9 5759720.145 0.021124325 0.020443298 1.689449037 -0.379164584 RLPEYPQVDDLLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLPEYPQVDDLLLR 14 1 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 ; 174.62 4.03E-06 288930000 188483 155135 155398 184658 174395 171458 212450 200797 216826 FALSE TRUE 179573.7821 170943.4329 162523.152 166095.827 204809.4328 165520.3665 180036.8506 183214.1502 250450.2687 0.717003751 0.682544418 0.648923848 0.663188855 0.817764875 0.660891152 0.718852695 0.731539044 1 17.93416463 -4.999999973 0.307759318 3.610791457 0.688387962 0.799790393 0.046788164 118.2321814 1.075931061 199.7761286 0.041542165 1.00E-05 4.999999973 -2.922403495 RLPIFSRLS(ph)ISDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLPIFSRLSISDD 13 2 P47974;Q07352 P47974;Q07352 ZFP36L2;ZFP36L1 "Zinc finger protein 36, C3H1 type-like 2;Zinc finger protein 36, C3H1 type-like 1" 1 RLPIFS(0.001)RLS(0.995)IS(0.004)DD;RLPIFS(0.003)RLS(0.997)ISDD 130.08 0.00011515 351000000 238749 119550 226419 194163 364650 196411 332070 231505 348670 TRUE FALSE 227463.8079 131732.2809 236800.5351 174645.3664 428244.8445 189609.2378 281406.6226 211233.1949 402739.9628 0.564790756 0.327090165 0.587973772 0.433643002 1.063328411 0.470798171 0.698730319 0.524490278 1 18.61948911 RLPLNFLSGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLPLNFLSGEK 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 122.33 0.00063034 226430000 830150 720020 667200 760520 683980 743120 968310 847480 762610 FALSE TRUE 790910.4547 793390.8566 697791.78 684071.0847 803265.8954 717385.5681 820576.5253 773270.1584 880871.6639 0.897872513 0.900688363 0.792160548 0.776584278 0.911898893 0.814404183 0.931550598 0.877846558 1 19.74857232 0.73395449 0.853516657 0.998725865 0.857538728 0.437738911 0.050923196 1.009522334 1.386909548 0.049774354 0.017032994 5.419440961 -0.73395449 -0.141187137 RLPQDHADSCVVS(ph)S(ph)DDEELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLPQDHADSCVVSSDDEELSR 21 1 D6RA71;P78317 D6RA71 RNF4 E3 ubiquitin-protein ligase RNF4 2 RLPQDHADSCVVS(0.999)S(0.999)DDEELS(0.002)R 142.32 5.16E-07 113050000 146420 132370 150080 155950 150580 141030 156690 143020 134790 TRUE FALSE 139499.0168 145858.6535 156961.3164 140273.6097 176841.1043 136146.0957 132784.0627 130496.4106 155692.5448 0.895990344 0.936837751 1.008149213 0.900965489 1.135835403 0.874454817 0.852860764 0.838167369 1 17.24834034 -0.657553224 5.319359201 0.999999994 0.928362824 0.05908502 0.086937403 10960079.22 2060413.396 0.707969284 0.019927419 0.220012206 0.657553224 -0.07163717 RLPSS(ph)PASPSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLPSSPASPSPK 12 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 RLPS(0.143)S(0.713)PAS(0.143)PSPK;RLPS(0.095)S(0.905)PASPSPK 150.22 7.20E-05 436941000 837600 714220 749900 879170 713540 820960 997840 1008790 903000 TRUE FALSE 798008.308 786999.83 784283.6568 790794.1613 837981.1501 792529.9493 845601.1814 920454.9997 1043032.628 0.765084702 0.754530404 0.751926292 0.758168191 0.803408376 0.759832366 0.810714026 0.882479584 1 19.99235286 0.998858716 1.186313042 1.000499173 0.762106312 0.966005861 0.014421867 0.077706569 0.226191708 0.012896299 0.004045869 9.973755461 -0.998858716 -0.238392861 RLPSSPASPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLPSSPASPSPK 12 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 RLPSSPAS(0.241)PS(0.759)PK;RLPSSPAS(0.224)PS(0.776)PK 122.46 0.00021931 934800000 1763890 1875280 1714250 2091700 1259010 1824410 2018740 2203800 1434150 TRUE FALSE 1680514.415 2066373.164 1792850.058 1881438.342 1478580.945 1761230.224 1710744.136 2010823.589 1656550.657 1.014466058 1.247395095 1.082279042 1.1357566 0.892566091 1.063191286 1.032714652 1.213861816 1 20.65975089 RLPTEEEWEFAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLPTEEEWEFAAR 13 1 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ;;; 222.56 2.77E-11 587270000 442082 381815 421279 443296 586981 367759 496978 429793 604344 FALSE TRUE 421185.66 420722.3826 440595.0589 398735.0439 689350.3006 355023.4136 421154.8785 392158.0464 698062.581 0.603363755 0.602700093 0.631168424 0.571202432 0.987519342 0.508583934 0.603319659 0.561780644 1 19.41299685 -1.830004431 2.684629934 1.129310835 0.630133552 0.438103619 0.13031295 28144645.36 18943213.63 23455031.51 0.029325938 0.014790933 1.830004431 -0.499177283 RLQAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLQAEEK 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 85.161 0.033695 185770000 257850 173570 198090 216310 171650 216580 256510 228000 201830 FALSE TRUE 245661.9415 191256.9803 207172.6224 194566.1078 201585.7057 209079.7803 217374.6884 208035.1113 233128.7656 1.053760744 0.820392026 0.888661774 0.834586446 0.864696835 0.89684248 0.93242328 0.892361398 1 17.8307675 0.124852611 0.873678732 1.001217744 0.896973617 0.199544623 0.063944754 7.731446587 6.242907545 0.09079524 0.020437404 1.333068944 -0.124852611 -0.104244127 RLQGQLQGGS(ph)R ddPTM_SK-BR-3_Trastuzumab_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 66.285 0.038666 41155000 39582 35810 32627 43524 55145 36681 49751 39438 45583 TRUE FALSE 37711.0373 39459.07971 34122.98022 39148.88483 64762.27054 35410.72777 42160.57121 35984.59965 52651.77883 0.716234819 0.749434883 0.648087889 0.743543441 1.230011065 0.672545706 0.800743529 0.683445089 1 15.68419465 2.976896764 24.92396315 0.857223385 0.713354827 0.19955023 0.160699986 1343.549609 1449433.813 0.046661079 0.049807375 948.193041 -2.976896764 -0.143868558 RLQLS(ph)PWESSVVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLQLSPWESSVVNR 14 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RLQLS(1)PWESSVVNR 121.34 7.05E-05 63935000 63284 42606 61221 51087 67195 44621 82814 57078 81268 TRUE FALSE 60292.69074 46947.59984 64028.04341 45951.6377 78913.78673 43075.76358 70179.20332 52079.94773 93870.62638 0.642295605 0.500130889 0.682088166 0.489520945 0.84066539 0.458884374 0.747616225 0.554805584 1 16.51838617 -5 0.270104933 3.661878223 0.585135797 0.49395755 0.121555733 156.3968892 1.518116067 232.1476452 0.1261689 1.00E-05 5 -3.076742426 RLQSIGTENTEENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RLQSIGTENTEENR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;; 310.9 1.63E-55 4054340000 1808088 1950296 1548921 2048428 1622532 1589630 1614495 1680785 1617360 FALSE TRUE 1722623.264 2149033.38 1619940.56 1842516.126 1905501.067 1534580.715 1368174.136 1533606.555 1868171.928 0.922090327 1.150340259 0.867126058 0.986266894 1.01998164 0.821434415 0.732359862 0.820912964 1 20.8331958 2.232265287 22.41726793 0.811838271 0.999364104 0.323614074 0.099300134 35.82482014 127565.6242 0.034466319 0.026160331 170.7124862 -2.232265287 0.187525833 RLQSIGTENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RLQSIGTENTEENRR 15 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;; 312.04 1.94E-56 32814280000 4640655 2483550 4620876 3746618 5247240 4280110 5929450 4561029 6487450 FALSE TRUE 4421300.435 2736626.569 4832747.735 3370000.841 6162356.995 4131888.717 5024803.501 4161641.121 7493490.613 0.590018813 0.365200507 0.644926108 0.449723769 0.822361342 0.551397063 0.670555788 0.555367496 1 22.83720648 -5 0.147774922 2.533033245 0.431364626 0.548942441 0.120907963 91.17617348 0.805814717 40.95772272 0.57309235 1.00E-05 5 -2.101668619 RLQTQVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLQTQVFK 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 144.5 0.00093712 827770000 1187100 1062700 759080 943960 1024500 1007800 1293600 1166200 1008800 FALSE TRUE 1130988.136 1170990.338 793884.5688 849071.3474 1203172.476 972899.6333 1096237.561 1064081.346 1165239.552 0.970605687 1.004935283 0.681305889 0.728666776 1.032553756 0.834935299 0.940783 0.913186773 1 20.15219515 0.779088564 0.993221689 0.99892728 0.890917948 0.096556189 0.112827155 2.540732055 4.717115249 0.111159747 0.036236554 6.012963455 -0.779088564 -0.108009332 RLREEFSFIPSAALDLLDHMLTLDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLREEFSFIPSAALDLLDHMLTLDPSK 27 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ;;; 56.95 0.039705 2571572000 1687255 1374410 1789307 1674900 1849603 1713758 2423961 1686150 1904622 FALSE TRUE 1607501.8 1514463.942 1871348.496 1506535.87 2172173.178 1654410.131 2054141.23 1538501.767 2199981.052 0.730688929 0.68839863 0.850620279 0.68479493 0.987359948 0.752011082 0.933708601 0.699325008 1 21.06905967 5.527793667 0.052067026 1.373253987 1.74E-09 0.305109026 0.102744761 274.5684219 1.79264734 14.457304 37.07148079 337127.1017 -5.527793667 -1.373253985 RLS(ph)AEGGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;RLS(1)AEGGDK;RLS(1)AEGGDK 142.39 6.40E-05 617760000 1188130 1068450 1059270 1363710 857740 1257410 1349240 1312480 1026450 TRUE FALSE 1131969.45 1177326.27 1107838.577 1226627.28 1007329.584 1213865.576 1143388.658 1197552.293 1185626.624 0.954743616 0.992999184 0.934390773 1.034581423 0.849617885 1.023817745 0.964374985 1.010058537 1 20.17721832 RLS(ph)APLPSSCGDPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RLSAPLPSSCGDPEK 15 1 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK 186.13 2.42E-07 3088490000 4843870 4883860 4146760 5453670 3463910 5086870 5297900 5797260 4109580 TRUE FALSE 4614909.865 5381530.886 4336893.048 4905456.73 4068014.807 4910710.416 4489608.052 5289621.181 4746872.678 0.972200052 1.133700281 0.913631635 1.033408112 0.856988397 1.03451488 0.945803344 1.114338121 1 22.17854592 3.731970383 24.99446795 0.980874259 1.052950166 0.106665254 0.080246795 897.9232649 3405507.973 0.019095449 0.030353009 5394.738317 -3.731970383 0.072075907 RLS(ph)AQAHPAGK ddPTM_SK-BR-3_Trastuzumab_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 108.71 0.001241 830680000 1887440 1660160 1719340 1921220 1535380 1853410 2304180 2148140 1799120 TRUE FALSE 1798224.452 1829332.191 1798173.44 1728095.316 1803149.786 1789225.947 1952635.022 1960037.474 2078118.341 0.865313787 0.880282973 0.86528924 0.831567328 0.86768388 0.860983666 0.939616856 0.943178949 1 20.98684638 1.430268989 1.352299705 0.990626589 0.861896109 0.889643361 0.016882486 0.122199518 0.425424727 0.015185266 0.004990565 26.93202378 -1.430268989 -0.12873048 RLS(ph)CSELSLYQPLQNSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSCSELSLYQPLQNSSK 18 1 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 RLS(0.69)CS(0.279)ELS(0.031)LYQPLQNSSK;RLS(0.958)CS(0.042)ELSLYQPLQNSSK 270.34 3.83E-39 229430000 410140 361130 375730 424500 356640 380800 490560 447200 429980 TRUE FALSE 390753.495 397929.5576 392957.5921 381828.4535 418837.9031 367612.8005 415716.0622 408040.7972 496659.1024 0.786763986 0.801212654 0.791201833 0.76879383 0.843310635 0.740171274 0.837024954 0.821571165 1 18.92189643 0.302708846 0.876556847 1.001874836 0.791534391 0.835028476 0.028562292 0.923767089 0.882658286 0.02718803 0.007880693 2.007746356 -0.302708846 -0.210340445 RLS(ph)DEHEPEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSDEHEPEQR 11 1 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 RLS(1)DEHEPEQR;RLS(1)DEHEPEQR 131.86 0.00011916 534420000 376770 371410 359910 395250 395510 376530 416280 368200 359950 TRUE FALSE 358960.8288 409257.1013 376412.2295 355518.7191 464486.8188 363490.6717 352768.8405 335958.456 415769.2076 0.863365594 0.984337209 0.905339363 0.855086698 1.117174649 0.874260684 0.848472744 0.808040735 1 18.66542339 -0.852483903 4.308856412 1.000000971 0.909948596 0.099270471 0.087632738 4999806.586 1740549.261 46.07027206 0.019688563 0.140448174 0.852483903 -0.090052375 RLS(ph)EDYGVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 1 RLS(0.998)EDY(0.002)GVLK 91.812 0.0060602 132590000 273380 222250 219490 272760 243450 234250 299580 262600 264040 TRUE FALSE 260457.8692 244897.5277 229553.8336 245341.6466 285907.6029 226137.8638 253873.5688 239605.3519 304985.9747 0.853999498 0.802979638 0.752670131 0.804435833 0.937445085 0.741469715 0.832410635 0.785627444 1 18.21838337 -1.035436921 4.481492324 1.000006365 0.814939835 0.530653704 0.055001408 4.41E-06 9.50E-07 0.048573915 0.011448437 0.092164374 1.035436921 -0.18506653 RLS(ph)EQLAHTPTAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLSEQLAHTPTAFK 14 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK 229.6 7.50E-13 4467940000 4029660 3845670 3407040 4125800 3225260 3943130 4246110 4367830 3331440 TRUE FALSE 3839185.958 4237548.145 3563256.154 3711066.745 3787744.323 3806578.419 3598287.934 3985359.65 3848062.701 0.997693192 1.101215982 0.925987031 0.964398721 0.984325001 0.989219437 0.935090775 1.035679499 1 21.87570088 3.736015617 24.99998124 0.972091586 1.049454586 0.365759281 0.039690022 188.0914025 1847660.343 0.009674841 0.01579681 5445.222338 -3.736015617 0.077363001 RLS(ph)EQLAHTPTAFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSEQLAHTPTAFKR 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFKR 203.81 2.72E-09 1036300000 456120 361340 427280 452760 404900 449750 614670 527010 559200 TRUE FALSE 434560.1115 398160.9568 446871.2106 407247.7046 475514.4318 434175.0447 520890.8023 480862.2105 645917.88 0.672779195 0.616426591 0.691839047 0.630494552 0.736184036 0.672183041 0.806435026 0.744463384 1 19.30099123 0.45000865 0.371410585 1.043202483 0.633537191 0.872525601 0.039447217 0.768482725 0.203398034 0.095026846 0.029336991 2.818439067 -0.45000865 -0.409665291 RLS(ph)ESLHVVDENKNESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSESLHVVDENKNESK 17 2 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 RLS(0.971)ES(0.029)LHVVDENKNESK 93.006 0.0016533 182310000 149680 134790 163120 179630 120150 153180 193080 180970 117900 TRUE FALSE 142604.923 148525.2542 170599.2133 161573.2511 141104.122 147875.3382 163622.0998 165123.3074 136183.3299 1.047154033 1.090627277 1.252717301 1.186439275 1.036133586 1.085854916 1.201484058 1.21250749 1 17.05519059 3.986888746 24.33565997 1.14727928 1.06345647 0.120637964 0.080226646 828.8822047 1538485.637 0.019784986 0.03658496 9702.613817 -3.986888746 -0.08382281 RLS(ph)ESQLSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(0.51)ES(0.251)QLS(0.239)FR 120.49 0.00058566 158550000 256140 199740 209060 231700 284820 197870 297130 231610 302820 TRUE FALSE 244032.7698 220093.7331 218645.6078 208409.0758 334492.5178 191017.7123 251797.3613 211329.0006 349779.779 0.697675465 0.629235154 0.625095048 0.5958294 0.956294611 0.546108505 0.719873979 0.604177295 1 18.41608736 -2.127917988 2.435771226 1.67166852 0.672277542 0.456382648 0.112573728 8129713.046 1613966.607 30326701.37 0.024236184 0.007448726 2.127917988 -0.999390978 RLS(ph)EVIYEPFQLLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSEVIYEPFQLLSK 15 1 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 RLS(1)EVIYEPFQLLSK;RLS(1)EVIYEPFQLLSK 289.22 4.43E-44 801790000 917370 801680 903380 1116810 860510 978780 1122740 940250 1058790 TRUE FALSE 874007.7382 883372.1034 944800.8666 1004546.137 1010582.672 944884.6032 951445.3925 857916.7254 1222981.746 0.714653135 0.72231013 0.772538813 0.821390949 0.826326865 0.772607283 0.777971867 0.701495937 1 20.22197144 -2.076573764 2.667943057 1.380248444 0.762450522 0.760742873 0.041648409 11695376.23 5831052.352 26943434.97 0.010980127 0.008383517 2.076573764 -0.617797922 RLS(ph)FAVPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSFAVPFR 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 RLS(1)FAVPFR;RLS(1)FAVPFR 151.7 5.04E-05 196464000 344890 324640 340840 383760 394640 379360 420710 365160 439820 TRUE FALSE 328587.7332 357721.1851 356467.8511 345183.7157 463465.0911 366222.6681 356522.9626 333184.6546 508025.0393 0.646794366 0.704140854 0.701673783 0.679462013 0.91228789 0.720875232 0.701782265 0.655842978 1 18.95454008 -2.289542298 2.404377063 2.42089687 0.713993933 0.595766092 0.073677685 3598226.516 677287.6034 27850557.73 0.017494244 0.005134022 2.289542298 -1.706902937 RLS(ph)FLVSYIASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSFLVSYIASK 12 1 P47897;A0A1B0GVU9;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 1 RLS(1)FLVSYIASK;RLS(1)FLVSYIASK;RLS(0.994)FLVS(0.006)YIASK 168.1 3.99E-05 189879800 615702 554006 385374 429846 504497 476744 680006 514413 491885 TRUE FALSE 586598.9867 610459.8413 403043.7791 386637.0634 592481.1171 460234.2357 576258.5955 469368.2706 568164.0136 1.032446569 1.074442989 0.70937928 0.680502556 1.042799443 0.810037638 1.014246911 0.826114043 1 19.11594793 3.776762449 24.98291845 0.873969787 1.053444851 0.279667965 0.122856604 658.6286213 430722.3364 0.030598696 0.055161111 5980.843639 -3.776762449 0.179475064 RLS(ph)GEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLSGEER 7 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 RLS(1)GEER;RLS(1)GEER;RLS(1)GEER;RLS(1)GEER;RLS(1)GEER 152.54 0.0011068 2704910000 2259920 2037660 2106800 2489640 2808480 2090060 2662390 2157410 2769800 TRUE FALSE 2153098.06 2245299.871 2203398.864 2239376.657 3298278.023 2017680.698 2256193.507 1968495.743 3199326.438 0.672984799 0.701803931 0.68870711 0.699952537 1.03092888 0.630657964 0.705208909 0.61528443 1 21.60933677 -1.981263 2.801480639 1.250607795 0.717126801 0.370843139 0.115348964 56958217.48 21998824.38 92316826.51 0.026220899 0.010440878 1.981263 -0.533480995 RLS(ph)GGSHSYGGESPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSGGSHSYGGESPR 15 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 RLS(0.79)GGS(0.21)HSYGGESPR 130.02 6.54E-05 0 65241 52174 57307 69205 65871 63678 66628 62023 78743 TRUE FALSE 62157.18723 57490.58992 59934.58263 62248.38192 77358.88154 61472.81489 56462.67489 56591.93732 90954.06228 0.683390996 0.632083807 0.658954434 0.684393642 0.850526954 0.675866623 0.620782332 0.622203516 1 16.47285045 -1.92931318 2.730553209 1.208250712 0.675201975 0.702936544 0.065645793 23319589.82 16472261.92 31089208.8 0.015919814 0.011767571 1.92931318 -0.533048737 RLS(ph)GLSSVGHNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSGLSSVGHNWR 13 1 Q14D93;A0A0G2JR24;Q8WYQ4 Q14D93 C22orf15 Uncharacterized protein C22orf15 1 RLS(0.982)GLS(0.009)S(0.009)VGHNWR 47.545 0.089159 58220000 103480 92672 84421 93732 68260 95355 99265 90894 73985 TRUE FALSE 98588.70548 102115.3822 88291.78635 84309.88128 80164.52239 92052.83244 84120.30112 82934.8395 85458.21594 1.153648065 1.194915913 1.033157379 0.986562618 0.938055183 1.07716773 0.984344223 0.970472395 1 16.38293158 3.639643257 3.973426435 0.995746195 1.174439095 0.803306173 0.036533478 0.083287198 2.346810076 0.009471892 0.015271303 4361.574117 -3.639643257 0.1786929 RLS(ph)IIGPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLSIIGPTSR 10 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR 196.74 2.01E-07 2249480000 601504 539551 531634 628014 642724 554234 659908 607163 689994 TRUE FALSE 573072.098 594531.8603 556009.9448 564884.8396 754814.8621 535040.7376 559226.9146 553996.5889 796994.7455 0.71904125 0.745967102 0.697633137 0.708768587 0.947076334 0.671322792 0.701669513 0.695106953 1 19.60421069 -1.946614684 2.818090179 1.187565972 0.73473269 0.533679083 0.077600799 8162158.49 5652169.225 10013971.78 0.01767693 0.011307987 1.946614684 -0.452833282 RLS(ph)LGAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSLGAQK 8 1 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 RLS(1)LGAQK;RLS(1)LGAQK;RLS(1)LGAQK 158.02 0.00022517 609170000 1311220 637100 694440 1112150 1331060 842270 1786970 930490 1235160 TRUE FALSE 1249241.229 702021.2143 726280.7609 1000354.569 1563196.443 813101.9787 1514334.907 849011.3628 1426702.304 0.875614503 0.492058653 0.509062583 0.701165594 1.095671071 0.569917057 1.061423187 0.595086557 1 20.4442529 2.985642249 24.63725066 0.863578204 0.629240005 0.234925866 0.201082351 748.8747285 1285038.101 0.054928909 0.06037353 967.4805632 -2.985642249 -0.2343382 RLS(ph)LGQGDSTEAATEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER 194.04 5.93E-11 1851367000 830935 860135 781053 928433 795903 814110 884014 898677 873668 TRUE FALSE 791658.3493 947783.7344 816865.0526 835105.1509 934708.2312 785917.1666 749141.4283 819984.0777 1009151.971 0.784478822 0.93918831 0.809456926 0.827531605 0.926231388 0.778789705 0.742347485 0.812547665 1 19.94471202 2.201607851 24.99997445 0.803308434 0.858371629 0 0.083686287 405.0280897 274014.7278 0.028563194 0.021095941 159.0771682 -2.201607851 0.055063195 RLS(ph)LGQGDSTEAATEERGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RLSLGQGDSTEAATEERGPR 20 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR 308.35 1.74E-66 1983160000 739813 695818 742133 764786 789876 777202 940502 866045 963576 TRUE FALSE 704843.5057 766722.6453 776160.5321 687908.2583 927630.1243 750287.2999 797011.1464 790209.5086 1113002.445 0.633281184 0.688877773 0.697357437 0.618065361 0.833448416 0.674111098 0.716091101 0.70998003 1 20.08602533 -5 0.224748265 2.602174545 0.656385952 0.756509888 0.055036433 70.46000565 0.704919354 51.19104115 0.090623892 1.00E-05 5 -1.945788593 RLS(ph)LPADIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR;RLS(1)LPADIR 138.02 9.08E-05 2667751000 4380720 4079418 3673044 4585930 4376228 3951290 4246750 4128977 4030065 TRUE FALSE 4173652.047 4495115.332 3841456.701 4124943.604 5139440.778 3814455.837 3598830.291 3767421.885 4655026.897 0.896590318 0.965647553 0.825227606 0.886126696 1.104062531 0.819427239 0.773106229 0.809323333 1 22.15035807 RLS(ph)LPADIRLPEGYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSLPADIRLPEGYLEK 17 2 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RLS(1)LPADIRLPEGYLEK;RLS(1)LPADIRLPEGYLEK 197.37 7.91E-12 400590000 934420 590520 899270 889230 865360 856160 1276210 1045610 1182250 TRUE FALSE 890251.8184 650694.6594 940502.419 799842.911 1016278.51 826510.9645 1081500.725 954050.8453 1365587.292 0.651918646 0.476494372 0.688716441 0.585713499 0.744206186 0.605242132 0.791967479 0.698637759 1 20.38109011 0.141580456 0.252765329 1.129448688 0.537660679 0.706950108 0.075375456 2.842259198 0.328072514 0.482029066 0.130021591 1.38541682 -0.141580456 -0.59178801 RLS(ph)LPGLLSQVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.323)QVS(0.677)PR;RLS(1)LPGLLS(0.016)QVS(0.984)PR;RLS(1)LPGLLS(0.077)QVS(0.923)PR;RLS(1)LPGLLS(0.162)QVS(0.838)PR;RLS(1)LPGLLS(0.229)QVS(0.771)PR;RLS(1)LPGLLS(0.111)QVS(0.889)PR 138.35 5.58E-05 693012000 585382 476251 492835 562205 634665 522305 647025 572610 680887 TRUE FALSE 557712.153 524781.5184 515431.9722 505691.0853 745350.3751 504217.4469 548309.4528 522469.2328 786475.4785 0.70912847 0.667257318 0.655369412 0.642983919 0.947709618 0.641110194 0.69717298 0.664317257 1 19.58504226 -1.453492515 3.13367996 1.005784109 0.701273252 0.5194157 0.089725898 16524035.26 21242568.29 844380.3395 0.020190541 0.035197149 1.453492515 -0.304510857 RLS(ph)LPGLLSQVSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 RLS(1)LPGLLSQVSPR 146.67 5.05E-06 39417000 33762 29438 33548 32617 35755 32999 39582 34771 44416 TRUE FALSE 32166.13717 32437.76567 35086.20898 29338.27719 41990.66068 31856.23636 33543.03893 31726.26691 51303.80643 0.626973697 0.632268206 0.683890951 0.57185381 0.818470667 0.620933193 0.653811895 0.618399864 1 15.64677825 -1.819174167 2.475117829 1.12417249 0.651963992 0.736239697 0.065206308 7561052.512 4783859.242 5598300.739 0.014087547 0.015164421 1.819174167 -0.472208498 RLS(ph)LPMDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSLPMDIR 9 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44;D6RGH0 Q07002 CDK18 Cyclin-dependent kinase 18 1 RLS(1)LPMDIR 55.04 0.062754 0 48213 37244 36916 44715 56203 39172 54468 47177 54308 TRUE FALSE 45934.06704 41039.20594 38608.63511 40220.16325 66004.78541 37815.46382 46157.90623 43045.93178 62729.80727 0.732252641 0.654221776 0.615475111 0.641165101 1.052207687 0.602830862 0.735820948 0.686211765 1 15.93686351 -5 0.302755492 3.425331553 0.6972098 0.326913599 0.128004522 322.1608841 2.962115322 496.810434 0.117260539 1.00E-05 5 -2.728121753 RLS(ph)LPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 41 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 2 RLS(0.979)LPNT(0.021)AWGSPSPEAAGYPGAGAEDEQQQLAANRHS(1)LVEK 174.86 3.22E-20 148030000 71432 65939 66212 80234 65795 80097 85372 75445 67211 TRUE FALSE 68055.55092 72658.25907 69247.88569 72168.72589 77269.62717 77323.22081 72346.93344 68838.63584 77633.73861 0.876623387 0.93591086 0.891981849 0.929605184 0.995309881 0.996000221 0.931900675 0.886710302 1 16.24439614 2.990207997 8.865556668 0.958943899 0.905951025 0.357545799 0.036943424 0.197283795 137.2221799 0.010895089 0.012258652 977.705361 -2.990207997 -0.052992874 RLS(ph)LQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSLQPR 7 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 RLS(1)LQPR;RLS(1)LQPR;RLS(1)LQPR;RLS(1)LQPR 153.24 0.0010775 420087000 307215 247977 268900 351800 320910 292918 382294 315549 367006 TRUE FALSE 292693.5558 273246.1382 281229.331 316436.3956 376876.6024 282774.1762 323968.029 287917.8567 423919.4161 0.690446214 0.644570944 0.663402808 0.746454122 0.889028877 0.667047003 0.764220785 0.679180632 1 18.69343052 -5 0.194027864 2.234665029 0.665324145 0.602692234 0.07159034 93.55118161 0.919549692 44.79806689 0.179200359 1.00E-05 5 -1.569340884 RLS(ph)LTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSLTLR 7 1 Q00537;Q00537-2;F8VQZ9;F8VZY6;F8VUX2;F8W1S5 Q00537 CDK17 Cyclin-dependent kinase 17 1 RLS(0.993)LT(0.007)LR 135.63 0.0018732 267720000 109080 96888 107980 112690 108180 106580 123190 102840 122550 TRUE FALSE 103924.0046 106760.9974 112930.9898 101362.1871 127046.5577 102889.1079 104395.103 93834.78441 141554.4281 0.734162866 0.754204575 0.797791996 0.71606511 0.897510304 0.72685192 0.737490903 0.662888372 1 17.11099735 -1.181038008 3.655488482 1.000247109 0.754366948 0.616268719 0.061156652 10070076.31 15984399.91 28406.33613 0.013718516 0.065911621 1.181038008 -0.24588016 RLS(ph)LTMGGVQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSLTMGGVQAR 12 1 O75815;O75815-3 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 RLS(1)LTMGGVQAR 144.41 3.86E-05 76052000 97231 91849 103040 104010 126350 97979 117940 101560 124860 TRUE FALSE 92635.08332 101208.5175 107764.4859 93554.71719 148385.4 94585.96266 99946.08688 92666.868 144222.6511 0.642306064 0.701751887 0.74720916 0.648682551 1.02886335 0.655832922 0.692998542 0.64252645 1 17.13793824 -2.163499751 2.371656521 1.691262985 0.716982815 0.370001261 0.114753327 5815055.125 1490045.473 21584529.09 0.027443885 0.006862783 2.163499751 -0.97428017 RLS(ph)MEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSMEIEK 8 1 A0A5K1VW66;P35240-4;P35240-6;P35240-5;P35240-3;P35240;P35240-2;P35240-8 A0A5K1VW66 NF2 Merlin 1 RLS(1)MEIEK;RLS(1)MEIEK 107.97 0.0023896 728560000 970460 816680 887580 977450 729720 980630 1070430 969050 579130 TRUE FALSE 924588.2791 899900.6205 928276.4209 879194.869 856982.937 946670.5372 907116.2437 884194.8447 668938.5226 1.382172274 1.345266553 1.387685698 1.314313407 1.281108664 1.415183167 1.356053229 1.3217879 1 19.3515141 0.673243271 2.941465833 1.000009202 1.35547262 0.896895162 0.037498865 0.961929271 8.32733066 0.034469335 0.00903081 4.712412189 -0.673243271 0.355463418 RLS(ph)MENEELLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;RLS(1)MENEELLWK 206.81 5.25E-08 106564000 257450 227540 245560 271530 214970 256140 286150 261540 219821 TRUE FALSE 245280.8487 250726.5847 256819.1689 244235.2885 252460.6999 247269.8076 242492.562 238638.1711 253909.718 0.966015994 0.987463523 1.011458604 0.961898152 0.994293176 0.973849325 0.955034584 0.939854421 1 17.95395609 1.964127321 5.401224831 0.960766541 0.983336821 0.148657057 0.020272806 0.294431546 22.68905103 0.008076004 0.005047787 92.07194563 -1.964127321 0.02257028 RLS(ph)MSEVKDDNSATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSMSEVKDDNSATK 15 2 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 RLS(0.989)MS(0.011)EVKDDNSATK;RLS(0.999)MS(0.001)EVKDDNSATK;RLS(0.973)MS(0.027)EVKDDNSATK;RLS(0.998)MS(0.002)EVKDDNSATK 262.91 2.61E-25 581260000 763840 654750 661850 801720 518347 787740 829250 884640 591860 TRUE FALSE 727734.797 721469.7694 692196.4772 721129.5824 608746.5527 760460.3663 702732.6823 807176.2318 683642.626 1.064495936 1.055331751 1.012512168 1.054834141 0.890445577 1.112365346 1.027924029 1.180699098 1 19.38288283 RLS(ph)PGSDIYVTVSSMALAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSPGSDIYVTVSSMALAR 19 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 RLS(0.999)PGS(0.001)DIYVTVSSMALAR;RLS(0.773)PGS(0.227)DIYVTVSSMALAR 141.36 1.02E-07 123955000 398670 366820 362210 443350 338300 405440 473470 406750 297870 TRUE FALSE 379825.6592 404199.375 378817.6868 398783.6157 397299.4129 391399.5111 401233.4556 371132.8137 344062.1583 1.103944883 1.174785908 1.10101526 1.159045266 1.154731502 1.137583723 1.166165607 1.078679549 1 18.3923097 0.983185377 3.992568955 1.000240076 1.143260687 0.785706051 0.024347415 0.077491111 3.571159316 0.021315069 0.005457332 9.620228268 -0.983185377 0.14302061 RLS(ph)PPECLNASLLGGVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSPPECLNASLLGGVLR 18 1 Q92754;Q92754-2;C9JXZ2;H7C5E5;C1K3N0;P05549-2;H7C4N4;A0A6E1XE14;P05549-5;P05549-6;P05549;Q92481;Q92481-2;Q6VUC0 Q92754;A0A6E1XE14 TFAP2C;TFAP2A;TFAP2B;TFAP2E Transcription factor AP-2 gamma;Transcription factor AP-2-alpha;Transcription factor AP-2-beta;Transcription factor AP-2-epsilon 1 RLS(1)PPECLNASLLGGVLR;RLS(1)PPECLNASLLGGVLR 163.61 2.00E-11 265120000 629380 521490 574530 661720 685920 581060 778530 668150 734650 TRUE FALSE 599630.4547 574630.4239 600872.7688 595202.6484 805544.2308 560937.7465 659750.9498 609643.2439 848575.7699 0.706631601 0.677170436 0.7080956 0.701413674 0.949289691 0.661034367 0.777480307 0.718431124 1 19.69468396 -5 0.196183344 2.172275118 0.688513136 0.512300703 0.080873805 108.2274428 1.066403277 49.74016007 0.187830195 1.00E-05 5 -1.483761982 RLS(ph)PPFPLEPAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSPPFPLEPAQK 13 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 RLS(1)PPFPLEPAQK;RLS(1)PPFPLEPAQK;RLS(1)PPFPLEPAQK 151.57 2.74E-05 493650000 1144420 973200 979300 1184300 950400 1123830 1255900 1261500 1117460 TRUE FALSE 1090325.535 1072370.186 1024201.874 1065251.914 1116149.459 1084911.485 1064289.389 1151036.372 1290749.99 0.844722482 0.830811695 0.793493614 0.82529686 0.864729396 0.840527983 0.82455115 0.891757801 1 20.29977816 0.913215723 2.786030133 0.999872518 0.832269531 0.897039018 0.018187619 0.109916382 1.908164584 0.017666806 0.00468011 8.188714374 -0.913215723 -0.167602987 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 RLS(0.987)PPS(0.008)S(0.003)S(0.001)AASSYSFSDLNSTR;RLS(0.958)PPS(0.033)S(0.008)S(0.001)AASSYSFSDLNSTR;RLS(0.999)PPS(0.001)SSAASSYSFSDLNSTR;RLS(0.954)PPS(0.032)S(0.006)S(0.008)AASSYSFSDLNSTR;RLS(0.938)PPS(0.045)S(0.014)S(0.004)AASSYSFSDLNSTR 196.63 1.29E-22 1361490000 555808 534703 565118 728820 783024 603324 675510 537351 726140 TRUE FALSE 529536.0573 589189.8436 591029.2193 655557.6289 919583.1377 582430.7386 572448.5429 490297.6978 838746.0826 0.63134251 0.702465091 0.704658098 0.781592478 1.096378459 0.694406508 0.682505176 0.584560343 1 19.6778746 3.361790728 3.428381691 0.788990804 0.671223066 0.133548288 0.150435157 0.555967653 12.7573453 0.0433192 0.060452685 2300.333097 -3.361790728 -0.117767738 RLS(ph)PSAS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.979)PS(0.022)AS(0.999)PPR;RLS(0.997)PS(0.009)AS(0.995)PPR;RLS(0.932)PS(0.076)AS(0.991)PPR 89.624 0.029189 3121360000 1002610 900830 950690 1144130 1050490 953240 1141430 975440 1175850 TRUE FALSE 955218.6123 992625.6012 994280.0769 1029119.879 1233695.123 920229.0598 967283.8897 890025.3025 1358194.813 0.703300148 0.730841844 0.732059987 0.757711537 0.908334439 0.677538341 0.712183466 0.655300178 1 20.373259 -2.271964231 2.421231526 2.211529245 0.734050217 0.599724565 0.06812406 3825109.915 583777.5231 25651590.05 0.016085317 0.005346084 2.271964231 -1.477479028 RLS(ph)QIGVENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSQIGVENTEENRR 15 2 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 1 RLS(1)QIGVENTEENRR 102.47 0.0008083 60200000 19557 17933 16290 21254 28780 16174 24054 17654 24548 TRUE FALSE 18632.57937 19760.39309 17036.91261 19117.50754 33799.22289 15613.89032 20384.12052 16108.12217 28354.77847 0.65712308 0.696898165 0.600848024 0.674225248 1.192011531 0.550661693 0.718895425 0.568091977 1 14.79130426 2.966461342 24.99736435 0.778922444 0.659038587 0.123401044 0.18988205 1605.196168 1196400.901 0.054967455 0.058335467 925.6809829 -2.966461342 -0.119883857 RLS(ph)QPAGGLLDSITNIFGR ddPTM_SK-BR-3_Trastuzumab_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 187.51 1.12E-14 258810000 162615 134515 143844 148488 164191 142680 189462 156348 156241 TRUE FALSE 154928.5112 148222.2314 150439.3897 133561.7041 192825.8584 137738.9558 160556.0922 142657.3403 180470.0563 0.858472117 0.821312047 0.833597511 0.740076813 1.068464555 0.763223322 0.889655024 0.79047651 1 17.46139996 RLS(ph)QPESAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(0.998)QPES(0.002)AEK;RLS(1)QPESAEK;RLS(0.995)QPES(0.005)AEK;RLS(0.999)QPES(0.001)AEK;RLS(1)QPESAEK;RLS(1)QPESAEK;RLS(1)QPESAEK 198.52 3.13E-07 5434087000 10027100 8813258 9174110 10692720 7890270 9885670 10713150 10279270 8323218 TRUE FALSE 9553138.855 9711339.01 9594752.018 9617867.471 9266330.59 9543326.769 9078662.207 9379162.625 9613940.138 0.993675716 1.010131005 0.998004136 1.000408504 0.963843175 0.992655106 0.944322731 0.97557947 1 23.19669639 2.748453267 23.9861697 0.971055052 1.001244818 0.37238382 0.015772437 331.8538677 804626.6645 0.004483431 0.004703446 560.3421171 -2.748453267 0.030189766 RLS(ph)QRPTPEELEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSQRPTPEELEQR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RLS(0.993)QRPT(0.007)PEELEQR;RLS(1)QRPTPEELEQR;RLS(0.998)QRPT(0.002)PEELEQR;RLS(0.996)QRPT(0.004)PEELEQR 175.8 1.83E-06 1673280000 367838 330585 342424 375478 384311 307655 402052 369769 407091 TRUE FALSE 350451.0267 364271.9873 358124.4791 337734.2381 451334.7167 297000.8302 340711.5832 337390.0661 470220.5931 0.745290682 0.774683186 0.761609518 0.718246378 0.959836135 0.631620211 0.724578183 0.717514441 1 18.8429782 -1.04223211 4.561566436 1.000008781 0.753148193 0.466628883 0.082590148 0.119184462 46173507.45 1074.888369 0.017775944 0.090733547 1.04223211 -0.246860589 RLS(ph)QRPTTEELEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RLSQRPTTEELEQR 14 2 J3KP75;O75167-5;O75167-2;O75167;O75167-4 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 RLS(0.999)QRPTT(0.001)EELEQR;RLS(1)QRPTTEELEQR;RLS(0.953)QRPT(0.047)TEELEQR;RLS(0.942)QRPT(0.058)TEELEQR;RLS(0.992)QRPT(0.007)T(0.001)EELEQR 256.13 1.38E-24 1808410000 728938 666291 729011 807869 783471 675113 791356 691577 783188 TRUE FALSE 694482.5454 734186.8104 762436.8754 726660.4733 920108.0943 651733.6675 670620.1079 631018.8516 904640.7951 0.767688733 0.811578269 0.842806205 0.803258572 1.017097725 0.720433647 0.741310929 0.697535259 1 19.78698553 -0.303089272 7.482250215 1 0.799231405 0.334937711 0.088464729 0 0 0.083455649 0.019670685 0.497634783 0.303089272 -0.200768595 RLS(ph)QSDEDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RLSQSDEDVIR 11 1 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 RLS(0.905)QS(0.095)DEDVIR;RLS(0.706)QS(0.294)DEDVIR;RLS(0.999)QS(0.001)DEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR 217.39 6.97E-12 2373710000 2288590 2046077 2086338 2328410 2416370 2145469 2519930 2350030 2654070 TRUE FALSE 2180412.886 2254574.572 2181998.661 2094353.803 2837784.163 2071170.871 2135468.397 2144248.915 3065649.62 0.711240082 0.735431263 0.711757354 0.683168027 0.925671396 0.675605867 0.696579408 0.69944357 1 21.54776139 -1.074575593 3.814939542 1.000073197 0.72835886 0.583848287 0.071664369 21566815.85 42891803.67 22472.21461 0.016129147 0.084221778 1.074575593 -0.271714337 RLS(ph)S(ph)LRAS(ph)TSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.869)T(0.119)S(0.013)K;RLS(1)S(1)LRAS(0.855)T(0.13)S(0.015)K;RLS(1)S(1)LRAS(0.812)T(0.157)S(0.032)K 109.42 0.0012752 1224710000 3342880 3078960 2814260 3827940 2075290 3423860 3511800 2734370 1998590 TRUE FALSE 3184868.687 3392709.524 2943296.605 3443148.199 2437219.919 3305290.87 2976010.411 2494934.067 2308521.13 1.379614267 1.469646295 1.274970615 1.491495206 1.055749453 1.431778478 1.289141508 1.080749938 1 21.13853751 1.013573965 0.330589117 0.949128237 1.439462867 0.491200703 0.126242864 1.365456408 0.445162651 0.245040202 0.14041662 10.31748781 -1.013573965 0.49033463 RLS(ph)SASTGKPPLSVEDDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 RLS(0.5)S(0.5)AS(0.001)TGKPPLSVEDDFEK;RLS(0.828)S(0.172)ASTGKPPLSVEDDFEK 302.83 2.81E-55 414510000 604560 628850 536780 694960 365060 686890 631500 699990 387780 TRUE FALSE 575983.6469 692930.5299 561391.8939 625101.3005 428726.3484 663102.8271 535153.0767 638695.1647 447914.9419 1.285921931 1.547013652 1.253344869 1.39558037 0.957160184 1.480421315 1.194764958 1.425929579 1 18.77286527 -4.708067958 0.149705651 1.87E-13 1.425279803 0.240284807 0.168590217 159.3068067 1.536759519 48.41320904 0.783680361 1.96E-05 4.708067958 1.425279803 RLS(ph)SSSATLLNSPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSSSATLLNSPDR 15 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 RLS(0.56)S(0.288)S(0.15)S(0.003)ATLLNSPDR 212.79 4.28E-10 234500000 64976 58862 54629 59391 64474 66617 83320 70116 87068 TRUE FALSE 61904.71325 64860.10472 57133.79369 53420.90384 75718.24519 64310.03659 70608.00372 63976.27133 100570.0608 0.615538191 0.644924585 0.568099425 0.531180984 0.752890518 0.639455083 0.702077767 0.63613635 1 16.61784136 -5 0.232940677 3.004931044 0.597678261 0.79957271 0.058128015 68.27194341 0.682384171 64.49493547 0.092062987 1.00E-05 5 -2.407252783 RLS(ph)STSLASGHSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.919)S(0.075)T(0.006)SLASGHSVR;RLS(0.894)S(0.096)T(0.011)SLASGHSVR;RLS(0.783)S(0.21)T(0.006)SLASGHSVR;RLS(0.936)S(0.022)T(0.042)SLASGHSVR 214.24 4.26E-12 4214620000 992689 663424 753619 853517 1154892 736659 1045072 878681 1089850 TRUE FALSE 945766.5583 731027.6599 788173.1766 767719.8496 1356304.799 711148.3141 885627.0723 801739.0335 1258858.372 0.751289088 0.580706834 0.626101549 0.609854029 1.077408571 0.564915268 0.703516052 0.636877866 1 20.26368455 RLS(ph)TIFEECDEELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSTIFEECDEELER 15 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RLS(0.985)T(0.015)IFEECDEELER;RLS(0.977)T(0.023)IFEECDEELER;RLS(0.934)T(0.066)IFEECDEELER 264.03 2.60E-25 531000000 103552 90069 91945 97096 106096 93581 107855 103362 106849 TRUE FALSE 98657.30218 99247.1335 96160.7692 87335.72561 124599.1088 90340.26651 91399.73886 94311.07532 123418.5972 0.799371443 0.804150555 0.779143268 0.707638294 1.009565103 0.731982607 0.740566988 0.764156111 1 16.91320028 -1.135193743 5.031998849 1.000009311 0.790740436 0.383120443 0.082902623 8.01E-06 1.38E-06 0.074233982 0.017496339 0.073249769 1.135193743 -0.209268874 RLS(ph)TSPDVIQGHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.947)T(0.05)S(0.003)PDVIQGHQPR;RLS(0.825)T(0.135)S(0.041)PDVIQGHQPR;RLS(0.968)T(0.027)S(0.006)PDVIQGHQPR;RLS(0.936)T(0.04)S(0.024)PDVIQGHQPR;RLS(0.915)T(0.03)S(0.056)PDVIQGHQPR;RLS(0.979)T(0.02)SPDVIQGHQPR;RLS(0.923)T(0.061)S(0.016)PDVIQGHQPR 195.46 5.77E-09 2369833000 964405 774635 872126 1250829 1412744 990830 1242825 904655 1174194 TRUE FALSE 918819.4869 853571.1872 912113.8398 1125093.293 1659126.106 956517.3087 1053209.22 825438.6123 1356282.009 0.677454601 0.629346391 0.672510462 0.829542297 1.223289917 0.705249574 0.776541467 0.608603968 1 20.37122576 3.240097823 5.385643036 0.848706155 0.65415416 0.239177298 0.165991397 0.2536016 22.44136436 0.046971626 0.060347903 1738.192306 -3.240097823 -0.194551995 RLS(ph)YNTASNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 1 RLS(0.998)Y(0.001)NT(0.001)ASNK;RLS(0.99)Y(0.007)NT(0.003)ASNK 87.083 0.008035 587390000 1003780 632560 672320 866760 847090 899730 1256070 923890 913890 TRUE FALSE 956333.3087 697018.5832 703146.537 779631.6381 994822.2278 868572.1245 1064433.452 842989.2938 1055611.394 0.905952052 0.660298465 0.666103588 0.738559325 0.94241331 0.822814276 1.008357298 0.798579192 1 20.0096474 2.743364661 24.30606468 0.915089274 0.742869066 0.456277059 0.093136766 248.9835492 1259732.54 0.027898946 0.028720966 553.8149316 -2.743364661 -0.172220209 RLS(ph)YQGQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSYQGQSR 9 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 RLS(1)YQGQSR;RLS(1)YQGQSR 130.1 0.00022707 322790000 141288 131322 132023 153137 152312 122421 141012 118689 131967 TRUE FALSE 134609.5962 144703.8611 138076.3851 137743.3778 178875.1646 118181.5301 119498.0295 108295.962 152431.7684 0.883080986 0.949302515 0.905824203 0.903639571 1.173476937 0.775307742 0.783944389 0.710455328 1 17.21780408 RLSEDYGVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 195.8 5.53E-07 2086820000 5777800 3582730 3075200 3099770 5190220 3434610 6411500 4602270 5513690 FALSE TRUE 5504694.844 3947814.26 3216200.962 2788175.23 6095392.725 3315668.594 5433307.92 4199270.841 6368724.885 0.864332334 0.619875145 0.504999198 0.437791753 0.957082122 0.520617338 0.853123352 0.659358179 1 22.60257312 0.290950705 0.593330105 1.011926643 0.660874655 0.268915105 0.169107251 3.489716711 1.792584326 0.270244766 0.067358355 1.954117641 -0.290950705 -0.351051988 RLSELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLSELLR 7 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 164.53 0.0019148 7908650000 4501043 3538450 2521282 2701178 4859939 2766574 4705123 3692345 4752023 FALSE TRUE 4288287.618 3899022.078 2636885.274 2429650.456 5707510.823 2670766.849 3987270.071 3369023.697 5488942.457 0.78125935 0.710341219 0.480399511 0.442644548 1.039819759 0.486572208 0.726418632 0.613783752 1 22.38809678 -1.284993514 3.102955452 1.001981878 0.667945221 0.268682319 0.175787355 48538457.35 65072078.45 911006.6803 0.040437704 0.051880779 1.284993514 -0.334036657 RLSKPPFQTNPS(ph)PEMVSK ddPTM_SK-BR-3_Trastuzumab_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 RLS(0.029)KPPFQT(0.029)NPS(0.942)PEMVSK 55.127 0.057695 104300000 267760 214530 246470 261790 194940 246230 305620 279120 219330 TRUE FALSE 255103.5154 236390.8509 257770.8933 235474.3718 228937.4743 237702.9934 258992.0559 254678.7731 253342.5762 1.006950822 0.933087736 1.017479561 0.929470188 0.903667586 0.938267057 1.022299764 1.005274269 1 17.95073003 1.725500128 8.876205558 1.009622458 0.955811312 0.349926228 0.034869471 0.124037903 29.8410759 0.016789945 0.008994408 53.14961568 -1.725500128 -0.053811146 RLSPS(ph)AS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.317)PS(0.691)AS(0.992)PPR;RLS(0.391)PS(0.688)AS(0.921)PPR;RLS(0.373)PS(0.678)AS(0.949)PPR 116.98 0.00068054 1522530000 805810 701730 743410 846220 839150 792170 924870 776310 924170 TRUE FALSE 767720.9583 773237.0848 777496.0838 761156.3579 985497.4943 764736.9543 783764.0951 708332.1809 1067485.564 0.719186268 0.724353669 0.728343418 0.713036676 0.923195149 0.71639091 0.734215171 0.663552 1 20.02578513 -2.14147528 2.503474338 1.586925726 0.740359801 0.5907528 0.067934552 6926821.124 1669282.936 23153577.93 0.015420472 0.007219793 2.14147528 -0.846565924 RLSQIGVENTEENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSQIGVENTEENRR 15 2 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 91.592 0.0031321 58419000 34461 31846 34458 47754 39192 35994 53848 53008 51896 FALSE TRUE 32832.09683 35091.14361 36037.93338 42953.67719 46027.07239 34747.51875 45632.49861 48366.33851 59943.76663 0.547714945 0.585401045 0.601195677 0.716566202 0.767837508 0.579668591 0.761255109 0.806861851 1 15.87132212 -4.999999999 0.066845086 2.308713894 0.169655626 0.819268618 0.058448864 127.1811927 0.614957168 25.66877744 3.508531179 1.00E-05 4.999999999 -2.139058268 RLSQPESAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 96.64 0.0093892 0 79932 69755 72176 86940 73303 87878 103160 87675 85460 FALSE TRUE 76153.77277 76863.1138 75485.34099 78200.62602 86087.01999 84834.76283 87421.04734 79997.71221 98712.70033 0.771468844 0.778654758 0.764697356 0.792204304 0.872096698 0.859410821 0.88561094 0.810409521 1 16.59094809 -4.999999998 0.071395251 1.673629184 0.581487393 0.803820671 0.031770379 118.6612681 0.608560038 12.90498471 1.545918065 1.00E-05 4.999999998 -1.092141791 RLSS(ph)AS(ph)TGKPPLSVEDDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.363)S(0.639)AS(0.889)T(0.109)GKPPLSVEDDFEK 96.533 0.00057406 49333000 46491 39897 40984 51035 25549 48422 46212 50309 33050 TRUE FALSE 44293.46257 43962.54966 42863.15694 45904.86484 30004.73751 46745.134 39161.51066 45903.67726 38175.2252 1.160267224 1.15159896 1.122800369 1.202477905 0.78597408 1.224488755 1.025835747 1.202446797 1 15.22034905 RLSS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSLR 6 1 P62753;A2A3R5;Q9Y253-2;Q9Y253 P62753 RPS6;POLH 40S ribosomal protein S6;DNA polymerase eta 1 RLS(0.001)S(0.999)LR 72.968 0.089191 1083700000 2007700 1745800 1731900 2073300 1954300 1763600 2043200 2107100 2420500 TRUE FALSE 1912800 1923699.005 1811309.328 1864887.945 2295129.301 1702526.09 1731472.314 1922591.154 2795858.778 0.684154727 0.688052995 0.64785437 0.667017934 0.820903158 0.608945668 0.619298917 0.687656747 1 21.41486006 0.937873838 22.03509281 1 0.674301467 0.755651272 0.05756871 3763.344257 1334796.382 0.054434308 0.013608577 8.667100605 -0.937873838 -0.325698534 RLSS(ph)LRAST(ph)SK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 RLS(0.441)S(0.559)LRAS(0.181)T(0.703)S(0.116)K 69.379 0.060326 830530000 2256400 1991700 1908000 2441100 1423400 2228900 2152500 2199600 1639100 TRUE FALSE 2149744.444 2194656.494 1995483.687 2195715.99 1671640.509 2151712.634 1824096.592 2006991.363 1893283.257 1.135458435 1.159180216 1.053980528 1.159739824 0.882932072 1.136498 0.963456781 1.060058687 1 20.85245884 2.784029277 24.9999645 1.013456796 1.129306415 0.4107984 0.070363474 391.9811454 215521.7735 0.018860003 0.020003981 608.1759986 -2.784029277 0.11584962 RLSS(ph)TSLASGHSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.246)S(0.709)T(0.044)SLASGHSVR 166.3 2.34E-06 1092700000 189380 119780 140070 157080 199680 144070 193480 161940 222350 TRUE FALSE 180428.3827 131985.7182 146492.348 141290.02 234504.1288 139080.8198 163961.0725 147759.6751 256830.9024 0.702518198 0.513901236 0.570384431 0.550128581 0.913068196 0.541526812 0.638400874 0.575318911 1 17.97045928 -1.989625595 2.466599968 1.356042702 0.622343204 0.509937594 0.115288913 14934325.04 6757139.039 30257189.84 0.026056452 0.010241756 1.989625595 -0.733699498 RLSSS(ph)SATLLNSPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSSSSATLLNSPDR 15 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 RLS(0.248)S(0.248)S(0.502)S(0.002)ATLLNSPDR 172.57 6.24E-07 239370000 157340 111750 135420 138600 167470 131530 164590 153970 191070 TRUE FALSE 149902.85 123137.452 141629.1409 124667.6647 196676.715 126975.0831 139478.7726 140487.5706 220700.1597 0.679214959 0.557940022 0.641726499 0.564873468 0.891148947 0.57532846 0.631983107 0.636554005 1 17.75172815 -1.849199956 2.300122129 1.161096656 0.641923816 0.576435931 0.09490139 5436124.669 2959965.639 4803861.328 0.022845471 0.014151421 1.849199956 -0.51917284 RLST(ph)SPDVIQGHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.209)T(0.672)S(0.12)PDVIQGHQPR 191.64 9.80E-08 268390000 55394 54316 49346 86228 69314 69284 73098 60364 67399 TRUE FALSE 52775.6354 59850.86215 51608.56291 77560.19762 81402.33965 66884.67771 61945.55756 55078.20815 77850.89269 0.677906618 0.768788386 0.662915493 0.996266002 1.045618577 0.859138224 0.795694891 0.707483322 1 16.24842596 3.250469492 24.99985292 0.888007561 0.713643545 0.439243831 0.104317343 240.1646272 504165.6379 0.030166834 0.040529071 1780.20285 -3.250469492 -0.174364016 RLSYNTASNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 0 ; 132.03 0.000376 744510000 1624180 1084840 534970 648950 1501440 895640 1974240 1303490 1558950 FALSE TRUE 1547408.23 1195386.429 559498.9037 583716.3131 1763290.661 864623.7622 1673033.429 1189349.505 1800704.004 0.859335142 0.663843934 0.310711201 0.324160057 0.979222935 0.480158738 0.929099633 0.660491398 1 20.78012962 1.715110243 10.6755251 0.843616591 0.62226318 0.224050634 0.225324539 0.194101908 56.67548065 0.10602446 0.057590206 51.89317501 -1.715110243 -0.221353411 RLT(ph)ADMISHPLGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLTADMISHPLGDFR 15 1 Q00587-2;Q00587;B0QYC6;B0QYC7;B0QYC8 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RLT(1)ADMISHPLGDFR 126.4 6.44E-05 22061000 14467 15233 12611 18942 19626 12922 19584 17148 20411 TRUE FALSE 13783.17358 16785.26002 13189.22682 17037.91417 23048.76819 12474.5079 16596.10112 15646.43021 23576.23364 0.584621522 0.711956807 0.559428916 0.722673283 0.977627239 0.529113687 0.703933519 0.663652662 1 14.52504564 -5 0.34449379 4.546657896 0.668988679 0.393137614 0.124193408 421.3537832 3.505025416 1101.656899 0.091191214 1.00E-05 5 -3.877669217 RLT(ph)AIIEEAEEAPGARPQLQDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLTAIIEEAEEAPGARPQLQDAWR 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RLT(1)AIIEEAEEAPGARPQLQDAWR 149.84 6.55E-06 19553000 7394.5 3821.5 4904.3 6458.1 6957.4 6425.6 6608 4461.4 8601 TRUE FALSE 7044.976639 4210.915195 5129.167006 5808.919518 8170.768357 6203.079861 5599.828236 4070.736165 9934.799152 0.709121194 0.423855091 0.516282909 0.584704273 0.822439209 0.62437899 0.563657921 0.40974519 1 13.27827509 2.99038255 24.25714097 0.650676028 0.54616075 0.104410686 0.170048571 836.1051916 2108835.069 0.047391993 0.053694071 978.0984026 -2.99038255 -0.104515278 RLTAEDLFEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 118.76 0.0010851 92169000 75985 60391 66641 71708 83294 67913 83915 75572 81978 FALSE TRUE 72393.33964 66544.91156 69696.55577 64499.7756 97820.44723 65561.15578 71112.22555 68954.51505 94690.72955 0.764524046 0.702760575 0.736044131 0.681162516 1.033051997 0.692371429 0.750994589 0.728207665 1 16.53093557 -1.864638044 2.329216445 1.117313957 0.757527298 0.358905647 0.100223596 9373827.719 4992771.414 6080521.506 0.022694652 0.013657209 1.864638044 -0.359786659 RLTAIIEEAEEAPGARPQLQDAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLTAIIEEAEEAPGARPQLQDAWR 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 197.33 1.06E-24 936851000 318692 103367 340982 218543 516142 290845 520263 293053 646305 FALSE TRUE 303628.0607 113900.2148 356616.362 196574.6424 606157.0014 280772.9647 440887.3241 267391.7257 746530.6785 0.406718799 0.152572718 0.477698201 0.263317568 0.811965293 0.376103719 0.590581656 0.358179152 1 19.50984202 -4.999999997 0.124077168 2.919537961 0.149687718 0.518236554 0.175665236 106.8696389 0.850370473 51.24404392 1.379332609 1.00E-05 4.999999997 -2.769850243 RLTDADAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLTDADAMK 9 1 P25705;P25705-2;P25705-3;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 129.88 0.0006044 829660000 1666080 1444900 1148271 1127100 1192682 1201273 1407830 1458930 1142751 FALSE TRUE 1587327.7 1592136.953 1200920.361 1013801.767 1400685.363 1159672.615 1193039.677 1331178.355 1319962.989 1.202554703 1.206198179 0.909813663 0.768053177 1.061155029 0.878564494 0.90384328 1.008496728 1 20.33206605 3.739957024 24.99879397 0.922940082 1.204376459 0.659480117 0.080873233 59.09755736 1057971.259 0.019428814 0.03280622 5494.864959 -3.739957024 0.281436377 RLTLEDLEDSWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 230.69 5.87E-12 287616000 303979 222198 279558 302356 362191 288462 369846 315644 398204 FALSE TRUE 289610.5151 244840.2288 292376.0108 271962.6004 425356.9957 278472.4886 313419.2 288004.538 459955.4426 0.629649067 0.532312929 0.635661596 0.591280318 0.924778699 0.60543362 0.681412091 0.626157474 1 18.81113458 -5 0.180067851 2.426939692 0.572868723 0.527256323 0.103438877 102.6407482 0.988224277 52.52206708 0.305595908 1.00E-05 5 -1.854070969 RLTVMSLQESGLK ddPTM_SK-BR-3_Trastuzumab_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 0 130.47 0.00022723 166820000 234340 215000 231440 251850 215670 241700 260070 265120 246720 FALSE TRUE 223263.2126 236908.7444 242051.7529 226533.5595 253282.7797 233329.8684 220391.545 241904.6873 284980.0775 0.783434458 0.831316864 0.84936377 0.794910162 0.888773636 0.818758527 0.773357727 0.848847714 1 18.12050154 0.97026298 23.37774628 1.000000001 0.818352711 0.741659581 0.033136775 765.6433736 601911.3477 0.031108089 0.007777022 9.338195881 -0.97026298 -0.181647289 RLVPDSDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RLVPDSDVR 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 94.297 0.014139 689130000 1390470 1040240 1083080 1332410 1444390 1070800 1411970 1129340 1176230 FALSE TRUE 1324745.239 1146241.639 1132740.289 1198473.615 1696291.159 1033717.928 1196548.044 1030449.003 1358633.741 0.975056926 0.843672289 0.833734843 0.882116776 1.248527184 0.760851064 0.880699491 0.758445026 1 20.37372516 RLVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLVSEK 6 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 115.46 0.039143 50354000 176440 152900 154330 188410 204700 179880 204930 186000 197420 FALSE TRUE 168100.0309 168480.6838 161406.1832 169470.6688 240399.6152 173650.7105 173664.1647 169712.854 228034.8853 0.737168046 0.738837321 0.707813556 0.743178697 1.054222975 0.761509408 0.761568409 0.744240749 1 17.79889502 2.964150478 24.99797753 0.840410568 0.730830933 0.279876184 0.101930644 897.21575 625631.2791 0.030031757 0.031864703 920.768553 -2.964150478 -0.109579635 RLYWDDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RLYWDDLKR 9 2 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 115.78 0.00079882 428430000 234450 204200 184290 230420 268080 206780 363930 253130 306140 FALSE TRUE 223368.0131 225008.2122 192739.8788 207257.7438 314833.0671 199619.1568 308405.7945 230964.5953 353614.6277 0.631670739 0.636309119 0.545056295 0.586111907 0.890328178 0.564510462 0.872152254 0.653153397 1 18.43181843 -0.028226644 0.234231576 1.142754614 0.568048727 0.496294634 0.111320105 5.951939559 0.551006221 0.937294817 0.228640543 0.937072852 0.028226644 -0.574705887 RMDAPTSAAVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMDAPTSAAVTR 12 1 A0A499FJT0;Q8NHP1;Q8NHP1-3;O95154 A0A499FJT0;O95154 AKR7L;AKR7A3 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 3 0 76.759 0.031746 30800000 17408 13897 13713 14938 19195 10710 15574 19559 26281 FALSE TRUE 16585.15834 15313.1201 14341.75461 13436.40386 22542.60192 10339.11001 13197.90026 17846.31027 30356.52326 0.546345779 0.504442487 0.472443912 0.442619985 0.742594985 0.340589399 0.434763235 0.587890455 1 14.88971895 0.880575531 5.468456194 0.999989271 0.496718089 0.700322863 0.10260108 0.711364595 32.15604431 0.09292876 0.023422816 7.595835157 -0.880575531 -0.503271182 RMDEISDHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RMDEISDHAK 10 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 84.658 0.0095887 519732000 233000 180329 200566 204559 293980 212505 290522 243141 234088 FALSE TRUE 221986.5518 198704.7301 209762.1495 183996.3407 345250.0189 205145.8986 246197.5331 221850.2851 270389.1715 0.82098906 0.734884201 0.775778661 0.680487091 1.276863334 0.758706044 0.910530299 0.820485095 1 18.04467785 RMDKLEAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMDKLEAEKR 10 3 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 103.21 0.001246 228930000 314940 220480 253140 293630 284400 326100 435520 377070 308800 FALSE TRUE 300053.4104 242947.1627 264746.7194 264113.7545 333999.27 314807.0752 369073.4251 344051.7518 356687.1269 0.841222987 0.681121197 0.742237943 0.740463377 0.936392835 0.88258603 1.034725947 0.964575747 1 18.44429962 2.524833493 1.611388554 0.988620185 0.745816502 0.782803181 0.055393438 0.158078659 0.829974522 0.023747123 0.019169556 334.837039 -2.524833493 -0.242803682 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 184.66 2.37E-17 4532300000 1900150 1667190 1903180 2038500 2268840 1694980 2078010 1814630 2277160 TRUE FALSE 1810333.675 1837078.556 1990442.686 1833586.107 2664524.978 1636282.418 1760971.409 1655731.377 2630290.343 0.688263819 0.698431852 0.756738773 0.697104071 1.013015535 0.622091938 0.669496968 0.629486164 1 21.32679063 -2.165988212 2.372093101 1.696865924 0.718595812 0.385319046 0.110348236 5348980.559 1317155.094 20032649.58 0.025902729 0.006823572 2.165988212 -0.978270112 RMEDEGGFPVPQENGQPES(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RMEDEGGFPVPQENGQPESPRR 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR 111.64 0.00016612 282760000 103106 86312 109415 114016 129942 85805 114184 88510 111228 TRUE FALSE 98232.38372 95107.29093 114431.786 102554.8951 152603.8437 82833.55133 96763.13367 80759.59518 128476.6702 0.764593164 0.740268959 0.890681443 0.798237493 1.1877942 0.644736132 0.753157235 0.628593464 1 16.97114688 -1.716565408 9.516630586 1.000407029 0.797246942 0.137965126 0.156069199 0.001277236 3.80E-05 0.143201249 0.033687913 0.019205897 1.716565408 -0.203160087 RMEEEQHHWDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RMEEEQHHWDDR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;;;; 159.08 2.92E-05 676568000 410857 382469 387772 449793 433015 400946 498643 410101 215371 FALSE TRUE 391436.6039 421443.0259 405551.7298 404578.9531 508532.6789 387061.1395 422565.8521 374190.3824 248769.6347 1.573490287 1.694109598 1.630230033 1.626319681 2.044191123 1.555901869 1.698623116 1.504164215 1 17.92445087 0.768182074 1.892486327 0.999990357 1.687199931 0.718422723 0.135718094 0.434370901 2.555379286 0.120500602 0.033639879 5.863839495 -0.768182074 0.687209574 RMEEEQHHWDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RMEEEQHHWDDRR 13 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;; 105.14 0.00088668 835230000 370014 301960 349073 392820 417773 356619 455830 376770 147666.4 FALSE TRUE 352524.1715 332730.0673 365078.3423 353332.9873 490632.4789 344269.1946 386284.7616 343778.0214 170565.7511 2.066793416 1.950743717 2.140396533 2.071535375 2.876500562 2.018395794 2.264726412 2.015516123 1 17.37996846 0.813836313 4.282957584 1.000017653 2.176130767 0.676901652 0.257880228 1.155355911 26.01753472 0.240947367 0.061325647 6.513828391 -0.813836313 1.176113114 RMEELHNQEMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RMEELHNQEMQK 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;; 142.83 4.00E-05 1435338000 1367826 1160687 1169827 1376036 1296937 1309629 1697900 1443684 1340147 FALSE TRUE 1303171.576 1278962.325 1223464.725 1237714.247 1523122.402 1264276.219 1438854.171 1317267.376 1547970.152 0.841858335 0.826218983 0.790367129 0.799572424 0.983948172 0.816731652 0.929510281 0.850964325 1 20.56194622 2.768221277 24.97534927 0.905129819 0.818155067 0.441010733 0.056074939 672.3426527 566135.7927 0.015155853 0.016073353 586.4368829 -2.768221277 -0.086974752 RMEELHNQEVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 138.89 3.17E-05 651720000 497283 408202 397688 497245 424191 457236 516241 497114 410198 FALSE TRUE 473777.4181 449798.2479 415922.3882 447260.9879 498169.7761 441401.8027 437478.954 453584.0628 473809.4108 0.999932478 0.949323162 0.877826355 0.943968139 1.051413848 0.931602017 0.923322636 0.957313326 1 18.85394733 4.498434239 2.996816651 0.949595929 0.998594545 0.079182879 0.04616514 0.628726039 10.65219593 0.011317959 0.055964192 31508.97233 -4.498434239 0.048998616 RMEELHNQEVQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMEELHNQEVQKR 13 2 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 96.464 0.0025376 189090000 239140 167960 213370 240410 175860 235580 265700 246030 212240 FALSE TRUE 227836.3261 185075.315 223153.2256 216243.5301 206529.9283 227421.8055 225162.5851 224486.3089 245153.0952 0.929363449 0.754937704 0.91026069 0.882075463 0.842452869 0.927672585 0.918457035 0.915698448 1 17.90332345 1.301309733 0.487222691 0.999710932 0.848404629 0.408713056 0.049274251 0.801102402 0.509328601 0.052093818 0.02964794 20.01288651 -1.301309733 -0.151306303 RMGESDDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;;;;; 209.43 2.60E-08 2777180000 4716250 3813428 3883030 4244610 5047230 4151772 5345480 4377420 5199020 FALSE TRUE 4493322.209 4202020.649 4061070.766 3817933.739 5927465.314 4007995.095 4529928.85 3994109.899 6005257.469 0.748231401 0.699723646 0.676252565 0.635765204 0.987045992 0.667414364 0.754327166 0.665102191 1 22.51779467 -2.074130722 2.431193046 1.408777691 0.73008957 0.425970248 0.098777152 8998629.131 3150141.356 20374811.91 0.021599432 0.00843081 2.074130722 -0.678688121 RMGS(ph)S(ph)MS(ph)AATARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMGSSMSAATARR 13 2 Q86UX6 Q86UX6 STK32C Serine/threonine-protein kinase 32C 3 RMGS(0.996)S(0.997)MS(0.916)AAT(0.091)ARR 43.03 0.064294 271560000 404750 299700 268560 393340 568310 253110 423840 320240 498720 TRUE FALSE 385618.2696 330239.7707 280873.7416 353800.7159 667423.0841 244344.7372 359175.4236 292198.0879 576058.9505 0.669407652 0.573274264 0.487578123 0.614174497 1.158602055 0.424166202 0.623504631 0.507236434 1 19.13585693 -1.82773301 2.548359818 1.134508258 0.630217644 0.249148446 0.20060978 18685303 12685454.04 15428173.74 0.048368002 0.014868494 1.82773301 -0.504290614 RMHS(ph)QPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RMHSQPR 7 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 RMHS(1)QPR;RMHS(1)QPR;RMHS(1)QPR 99.815 0.006279 137618700 62027.1 48248.5 56318.6 66717.7 103829.8 59579.5 74058.4 65144.4 94999 TRUE FALSE 59095.20191 53165.077 58900.86352 60011.11004 121937.6842 57516.24698 62759.4309 59440.01098 109730.9597 0.538546296 0.484503891 0.536775252 0.546893148 1.111242302 0.524156966 0.571939141 0.541688609 1 16.7436111 2.970138814 24.99814759 0.706064977 0.518359161 0.235106891 0.191647584 1150.853305 963431.7582 0.056263608 0.059760297 933.5526451 -2.970138814 -0.187705816 RMNSTGGQT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMNSTGGQTPR 11 1 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 RMNSTGGQT(1)PR 83.856 0.0096078 93032000 150390 114170 119520 130670 142030 116570 144380 126190 136840 TRUE FALSE 143281.3627 125804.0528 125000.1102 117534.8033 166799.987 112533.1517 122352.1793 115140.1346 158060.4483 0.906497256 0.795923674 0.790837376 0.743606668 1.055292382 0.711962751 0.774084729 0.728456333 1 17.27011688 RMS(ph)DEFVDSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 203.53 2.22E-08 694653000 2091771 2091350 1739879 2349300 1564946 2111361 2194850 2206358 1575412 TRUE FALSE 1992897.13 2304460.943 1819654.173 2113143.901 1837872.087 2038244.039 1859985.321 2013157.597 1819718.847 1.095167604 1.266382962 0.999964459 1.161247466 1.009975849 1.120087338 1.022127855 1.106301449 1 20.79528414 3.73208479 24.99859193 1.06406874 1.180775284 0.350146635 0.068249534 468.6432602 1809101.036 0.016001822 0.025453591 5396.159648 -3.73208479 0.116706544 RMS(ph)DEFVDSFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RMSDEFVDSFKK 12 2 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK 153.22 3.68E-05 1997474000 3061220 2378050 2803400 2916070 2174900 2970460 3596980 3379780 2713300 TRUE FALSE 2916522.197 2620375.999 2931938.663 2622941.103 2554201.871 2867592.225 3048194.638 3083828.546 3134064.706 0.930587742 0.836095054 0.935506742 0.836913513 0.81498058 0.914975437 0.972601054 0.983970924 1 21.57960354 1.815123106 2.886554677 0.986692778 0.87264374 0.637526561 0.039265258 0.161934283 2.493073802 0.021263678 0.010523913 65.33157167 -1.815123106 -0.114049037 RMS(ph)FQKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMSFQKPK 8 2 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;E5RII8 Q8N573-2 OXR1 Oxidation resistance protein 1 1 RMS(1)FQKPK 107.06 0.0021271 260040000 234120 198590 217480 248390 189620 249650 288020 294760 240280 TRUE FALSE 223053.6116 218826.5468 227451.6731 223421.3653 222689.668 241004.5579 244077.2591 268949.2518 277541.3952 0.803676912 0.788446518 0.819523419 0.805001953 0.8023656 0.868355359 0.879426505 0.969041939 1 18.08234344 1.456815445 1.001564412 1.004038134 0.800165021 0.959072851 0.014806902 0.078128573 0.156028041 0.012235244 0.004449737 28.62961084 -1.456815445 -0.203873113 RMS(ph)GEPIQTVESIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 140.2 4.30E-06 359604000 180156 200344 177565 216409 223506 175837 203561 196502 232313 TRUE FALSE 171640.3829 220759.2814 185706.5309 194655.1562 262485.3756 169747.7206 172504.0308 179295.2432 268338.9135 0.639640299 0.822688288 0.692059636 0.725407857 0.978186027 0.632587046 0.642858796 0.668167135 1 18.03369676 -2.333401185 2.293501481 2.599057563 0.725105882 0.40036339 0.105690713 3586403.362 525385.4128 29793949.2 0.02624893 0.004640864 2.333401185 -1.873951681 RMS(ph)GEPIQTVESIRVPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMSGEPIQTVESIRVPGK 18 2 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 RMS(1)GEPIQTVESIRVPGK 78.324 0.010733 60214000 66436 47634 77807 67745 67733 67438 99455 80034 106410 TRUE FALSE 63295.70194 52487.95876 81374.52791 60935.14389 79545.61375 65102.60515 84281.31313 73025.79867 122911.5193 0.514969649 0.427038564 0.662057782 0.495764304 0.647177858 0.529670494 0.685707195 0.594133073 1 16.90726061 -5 0.150190966 2.610304143 0.420967916 0.792043423 0.071893641 50.90704767 0.453752799 24.31148738 0.318386073 1.00E-05 5 -2.189336227 RMSDEFVDS(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(0.096)DEFVDS(0.904)FK 158.83 3.11E-05 102760000 281860 283470 253400 308150 212030 287770 300580 299480 207300 TRUE FALSE 268537.0364 312355.9153 265018.6406 277174.1766 249007.9649 277804.4527 254721.0005 273255.9436 239447.0253 1.121488296 1.304488602 1.106794458 1.15755949 1.039929248 1.160191706 1.063788536 1.141195817 1 17.86934699 2.182986169 0.239072603 0.988505139 1.24956707 0.33241609 0.067614032 2.633601521 0.486957161 0.157567217 0.25144866 152.4004219 -2.182986169 0.261061931 RNAEQYKDQADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNAEQYKDQADK 12 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 146.59 3.65E-05 123250000 209620 169970 173520 243210 132000 206750 217520 232580 146110 FALSE TRUE 199711.678 187290.1362 181476.0636 218762.0687 155020.7582 199590.1957 184333.329 212214.0622 168767.9926 1.183350439 1.10974915 1.075299059 1.296229607 0.918543593 1.18263062 1.092229197 1.257430743 1 17.36468179 -2.010655862 2.715255631 0.856370547 1.134359075 0.147711835 0.104628435 255060.4378 5439193.53 248197.2097 0.021126474 0.009757625 2.010655862 0.277988529 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNAETPEATTQQETDTDLPEAPPPPLEPAVIAR 33 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.994)PEAT(0.002)T(0.002)QQET(0.002)DTDLPEAPPPPLEPAVIAR 136.82 1.13E-08 52305000 57670 63583 52733 64413 54226 56764 57943 59705 58847 TRUE FALSE 54944.05339 70062.17999 55150.86021 57938.08286 63682.99723 54798.24845 49102.73115 54476.91368 67972.69221 0.808325397 1.030740106 0.811367895 0.852372931 0.936890907 0.806180345 0.722389088 0.801452935 1 16.05266764 2.182434692 9.101040592 0.799610483 0.895026749 0.026556723 0.095838772 0.532089938 80.51616046 0.033556806 0.02481236 152.2070229 -2.182434692 0.095416267 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 48 2 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.945)PEAT(0.027)T(0.027)QQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 123.31 1.35E-10 56349000 16754 8860.4 14901 11721 21333 15021 22852 18143 23766 TRUE FALSE 15962.07162 9763.284833 15584.22559 10542.78281 25053.46845 14500.819 19365.50769 16554.30274 27451.5099 0.58146425 0.355655659 0.567700125 0.384051109 0.912644461 0.528233932 0.705444173 0.603037968 1 14.74459788 -1.712590409 0.143025437 1.588643155 0.338456383 0.487750547 0.146181296 31.34042313 0.713939541 7.321616783 0.969205198 0.019382491 1.712590409 -1.250186772 RNALFPEVFS(ph)PTPDENSDQNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNALFPEVFSPTPDENSDQNSR 22 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RNALFPEVFS(0.989)PT(0.011)PDENSDQNSR;RNALFPEVFS(0.998)PT(0.002)PDENSDQNSR;RNALFPEVFS(0.968)PT(0.032)PDENSDQNSR;RNALFPEVFS(0.967)PT(0.033)PDENSDQNSR;RNALFPEVFS(0.997)PT(0.003)PDENSDQNSR;RNALFPEVFS(0.968)PT(0.032)PDENSDQNSR 310.37 2.17E-67 677223000 458067 403273 475421 501360 506485 434981 574701 528114 584836 TRUE FALSE 436415.0807 444366.9772 497219.5231 450962.3403 594815.8236 419917.4989 487019.8073 481869.5385 675529.38 0.646034197 0.657805553 0.736044261 0.667568804 0.880518067 0.621612488 0.720945412 0.713321364 1 19.36565899 -5 0.245991241 2.769840145 0.671497048 0.631704715 0.071019513 109.009298 1.08321624 96.84985724 0.098291223 1.00E-05 5 -2.098343096 RNDDIS(ph)ELEDLSELEDLKDAK ddPTM_SK-BR-3_Trastuzumab_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 RNDDIS(1)ELEDLSELEDLKDAK 154.69 1.64E-08 6773700 21494 17725 18961 20135 12260 22261 21431 26213 11302 TRUE FALSE 20478.02122 19531.19765 19830.3806 18110.99155 14398.14012 21490.09599 18161.30734 23917.65076 13054.65644 1.568637315 1.496109664 1.519027383 1.387320427 1.10291222 1.646163274 1.391174669 1.832116446 1 13.67227687 3.266316238 10.56716668 1.41497032 1.527037181 0.06254443 0.235966823 1.539105515 570.7200441 0.059728171 0.080206445 1846.359384 -3.266316238 0.112066862 RNDDISELEDLS(ph)ELEDLKDAK ddPTM_SK-BR-3_Trastuzumab_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 RNDDISELEDLS(1)ELEDLKDAK;RNDDISELEDLS(1)ELEDLKDAK 243.04 2.32E-30 40178000 105052 100924 94688 106882 55750 120114 115374 134776 62571 TRUE FALSE 100086.4002 111208.2703 99029.53846 96138.0183 65472.78235 115954.4221 97771.57731 122974.2989 72274.19111 1.384815224 1.538699619 1.370192277 1.330184632 0.905894363 1.604368313 1.352786877 1.701496718 1 16.14119294 3.541186497 6.540694616 1.336457815 1.461555467 0.054380818 0.239393862 0.771442005 64.00980456 0.05993723 0.092593095 3476.854346 -3.541186497 0.125097653 RNDFQLIGIQDGYLSLLQDSGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RNDFQLIGIQDGYLSLLQDSGEVR 24 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;;; 313.03 2.56E-73 4991433000 1986942 1525516 1647305 2004276 1984289 1732454 2145947 2005292 2052210 FALSE TRUE 1893023.189 1680967.815 1722835.564 1802802.369 2330348.373 1672458.684 1818543.372 1829698.002 2370456.246 0.798590226 0.709132606 0.726794923 0.760529696 0.983080104 0.705542946 0.767170192 0.771875881 1 21.17673333 -2.130602528 2.021179881 1.416331046 0.773315882 0.439592303 0.078683626 2732541.476 640901.6252 5214191.857 0.020024942 0.007402825 2.130602528 -0.643015164 RNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGK 36 3 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 260.86 1.59E-62 195330000 149230 49908 167740 110000 177840 150120 257000 183820 239710 FALSE TRUE 142176.1936 54993.68194 175431.0449 98942.59101 208855.2397 144921.3068 217789.9299 167723.7463 276883.0025 0.513488341 0.198617038 0.633592685 0.357344402 0.754308635 0.523402684 0.786577464 0.605756745 1 18.07891697 1.645913505 0.29470658 1.039787594 0.294343145 0.56018723 0.148793265 0.967541172 0.306476094 0.255135656 0.255941999 44.25002346 -1.645913505 -0.745444449 RNDS(ph)IYEASSLYGISAMDGVPFTLHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNDSIYEASSLYGISAMDGVPFTLHPR 27 1 E9PLZ8;Q96EY5;M0QZK6;E9PQA6;Q96EY5-2;Q96EY5-3 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 RNDS(0.396)IY(0.087)EAS(0.243)S(0.243)LY(0.03)GISAMDGVPFTLHPR;RNDS(0.616)IY(0.379)EAS(0.002)S(0.002)LY(0.002)GISAMDGVPFTLHPR;RNDS(1)IYEASSLYGISAMDGVPFTLHPR;RNDS(1)IYEASSLYGISAMDGVPFTLHPR;RNDS(0.996)IY(0.004)EASSLYGISAMDGVPFTLHPR;RNDS(1)IYEASSLYGISAMDGVPFTLHPR 292.86 7.10E-71 878421000 295209 224599 281751 297644 369900 299323 402719 282121 354825 TRUE FALSE 281255.0556 247485.8934 294669.562 267724.2596 434410.4429 288957.3695 341276.8201 257416.9896 409849.4488 0.686239926 0.603845861 0.718970253 0.653225862 1.059926869 0.705032959 0.83268825 0.628076945 1 18.64473453 RNDYVHALVAYFNIEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNDYVHALVAYFNIEFTR 18 1 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 152.18 2.75E-08 29921200 53234 50531 45329.3 44242 57081 46900 70830 47274 36591.9 FALSE TRUE 50717.73432 55680.16635 47407.69324 39794.71011 67035.90833 45275.84124 60023.58262 43134.43794 42266.38497 1.199954393 1.317362873 1.121640596 0.941521498 1.586033638 1.071202121 1.420125773 1.020537668 1 15.3672231 1.118899122 9.182735907 1.001186865 1.240836173 0.215160855 0.179954865 0.385697771 28.23349156 0.153861221 0.038502445 13.14919367 -1.118899122 0.239649308 RNEES(ph)DDDLDFDIDLEDTGGDHQMN ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNEESDDDLDFDIDLEDTGGDHQMN 25 1 Q96MD7-1 Q96MD7-1 1 RNEES(1)DDDLDFDIDLEDTGGDHQMN;RNEES(1)DDDLDFDIDLEDTGGDHQMN;RNEES(1)DDDLDFDIDLEDTGGDHQMN 235.35 1.27E-38 184550000 168301 134156 137945 168395 146152 157668 166165 151368 130760 TRUE FALSE 160345.7453 147826.6489 144269.9147 151467.6147 171640.8625 152207.9176 140813.4774 138113.4155 151037.593 1.06162805 0.978740763 0.955192094 1.002847117 1.136411533 1.007748565 0.932307478 0.914430724 1 17.20454815 1.802696338 5.421972691 0.942918692 1.022966371 0.304409552 0.053349547 0.256906363 13.44165712 0.02525253 0.014311292 63.48868588 -1.802696338 0.080047679 RNEFLGELQK ddPTM_SK-BR-3_Trastuzumab_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 ; 130.1 0.00045799 201879000 581870 474030 412360 498740 452810 460760 616220 549880 481010 FALSE TRUE 554366.1583 522334.1959 431267.1139 448605.7077 531779.9206 444803.7657 522204.3213 501729.5921 555602.5741 0.99777464 0.940121987 0.776215111 0.807421939 0.957122853 0.800579022 0.939888232 0.903036839 1 19.08369376 0.596278051 1.389814325 0.999708445 0.893750302 0.18115846 0.073734482 3.129462731 8.311556255 0.072803169 0.021444201 3.947099283 -0.596278051 -0.105958143 RNEIDAEPPAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNEIDAEPPAKR 12 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ; 172.09 2.06E-05 551930000 607690 546890 503590 616080 493890 578060 672630 655630 623090 FALSE TRUE 578965.698 602618.7128 526680.0996 554150.4679 580024.2596 558041.6373 570007.9398 598219.5615 719715.6149 0.804436761 0.837301151 0.73178918 0.769957545 0.805907566 0.775364082 0.791990514 0.831188804 1 19.45706743 0.745286841 2.382137422 0.999962273 0.791475851 0.85327535 0.02744822 0.465883855 3.759795406 0.027534993 0.007411291 5.562715403 -0.745286841 -0.208486422 RNELVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RNELVIR 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;;;; 153.78 0.0027629 11108520000 3497101 2766490 2750704 3162078 4077763 2858900 3617963 3099542 4063967 FALSE TRUE 3331799.966 3048398.476 2876826.499 2844219.912 4788923.576 2759895.576 3065976.296 2828129.671 4694186.246 0.709771575 0.649398706 0.612848819 0.605902655 1.020181843 0.587939087 0.6531433 0.60247496 1 22.16244365 -1.197971238 4.086739896 1.000144077 0.679067286 0.389005684 0.125946573 17227648.56 5050066.918 25869.3267 0.027424263 0.063391169 1.197971238 -0.321076791 RNES(ph)PGAPPAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RNESPGAPPAGK 12 1 P49796-1;P49796-4;P49796-6;P49796;C9J582;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RNES(1)PGAPPAGK;RNES(1)PGAPPAGK;RNES(1)PGAPPAGK;RNES(1)PGAPPAGK 78.964 0.014891 869760000 2189670 1888950 2027950 2231820 1672210 2151930 2491900 2442990 2171370 TRUE FALSE 2086168.639 2081436.153 2120933.513 2007473.213 1963842.895 2077408.125 2111714.888 2229068.844 2508094.97 0.831774181 0.829887296 0.845635249 0.800397608 0.783001807 0.828281285 0.8419597 0.888749777 1 21.25816055 0.87870153 1.468726934 0.999685203 0.820903691 0.914494466 0.017502181 0.155512807 0.654014506 0.017426904 0.005132823 7.563129386 -0.87870153 -0.178781512 RNFAELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNFAELK 7 1 P18124 P18124 RPL7 60S ribosomal protein L7 0 ; 131.03 0.014645 171320000 812560 607590 556480 601570 1996750 578730 1175880 778560 2220700 FALSE TRUE 774151.8991 669504.1118 581995.1584 541099.0407 2344982.568 558688.435 996477.9095 710385.159 2565074.814 0.301804803 0.261007635 0.226892079 0.210948639 0.914196559 0.217805903 0.388479082 0.276945201 1 21.29056947 -5 0.278687441 5.721521774 0.301355405 0.488178715 0.208329318 188.6223668 1.809233217 515.202579 0.224594859 1.00E-05 5 -5.420166369 RNGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNGAAGPHSPDPLLDEQAFGDLTDLPVVPK 30 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 142.37 1.88E-06 359572000 375310 299802 352640 464680 321538 350576 416620 346350 236862 TRUE FALSE 357569.8401 330352.1646 368808.8928 417969.4836 377614.1254 338435.4652 353056.9672 316021.7579 273593.3492 1.30693908 1.207456854 1.348018487 1.527703377 1.380202137 1.237001799 1.290444261 1.155078363 1 18.06167363 1.021660589 1.272825271 1.000143909 1.330040183 0.634416226 0.084906331 0.345892432 1.152583166 0.086971765 0.026802022 10.51140063 -1.021660589 0.329896274 RNKLDHYAIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNKLDHYAIIK 11 2 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 0 66.289 0.037907 176380000 448090 299650 261210 291850 328960 335840 546380 413070 346850 FALSE TRUE 426909.6737 330184.6757 273186.7369 262512.6835 386330.5198 324209.7766 463019.696 376899.401 400637.7265 1.06557532 0.824147737 0.68187971 0.655237054 0.964288918 0.809234266 1.155706678 0.940748651 1 18.61193876 1.753199719 25 1.042758318 0.842541658 0.339764204 0.129914928 5.819444856 9951.381433 0.062284406 0.034539961 56.64997453 -1.753199719 -0.20021666 RNLADCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNLADCLR 8 1 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ;; 156.35 0.00063239 399060000 361347 174797 89904 85822 396404 145896 372246 208759 389014 FALSE TRUE 344266.8434 192609.013 94026.18733 77195.00951 465536.7321 140843.5849 315453.0359 190478.9553 449340.3043 0.766160614 0.428648423 0.209253847 0.171796317 1.036044903 0.313445252 0.702035924 0.423908012 1 18.77744895 -1.671239924 0.399862513 1.371154148 0.495778117 0.251539862 0.266367192 47.04686077 3.548426762 17.21373391 0.159789742 0.021318668 1.671239924 -0.875376031 RNLDIERPTYTNLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 300.29 1.64E-44 6647700000 1219595 867858 1061142 1106796 1171647 965960 1449667 1140306 1389899 FALSE TRUE 1161947.161 956293.7169 1109796.41 995538.7633 1375981.866 932508.563 1228493.674 1040454.761 1605437.438 0.72375736 0.595659285 0.691273533 0.620104365 0.85707598 0.580843913 0.765208064 0.648081785 1 20.61453502 -5 0.300962634 3.648029329 0.66726257 0.580210234 0.083658685 175.0929794 1.615660095 292.6103889 0.072275989 1.00E-05 5 -2.980766759 RNLELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNLELPR 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 114.5 0.0094467 55925000 35055 30890 26655 31327 36299 29012 38930 39345 44325 FALSE TRUE 33398.01962 34037.72612 27877.15812 28177.95044 42629.53411 28007.30717 32990.5135 35899.74322 51198.69462 0.652321702 0.664816288 0.544489627 0.550364627 0.832629317 0.547031665 0.644362395 0.701184737 1 15.64381941 0.743841556 2.439628165 0.999911054 0.635178613 0.650049527 0.083944803 0.747452356 6.220586353 0.073990154 0.019848697 5.544234053 -0.743841556 -0.36473244 RNMEELKKEVVMDDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNMEELKKEVVMDDHK 16 3 E9PRA5;Q13733 E9PRA5 ATP1A4 Sodium/potassium-transporting ATPase subunit alpha-4 0 47.545 0.087724 709220000 1006800 662270 835870 1033600 1344700 737130 1401900 862750 1962900 FALSE TRUE 959210.5593 729756.0659 874195.4663 929700.5643 1579215.254 711603.0033 1188014.407 787203.0363 2267296.507 0.423063572 0.32186177 0.385567333 0.410048073 0.69651907 0.31385529 0.523978405 0.347198981 1 21.11254164 -5 0.313309932 6.190222755 0.399431834 0.708155614 0.11464978 156.6166376 1.408212403 537.4243807 0.097136652 1.00E-05 5 -5.790790922 RNNGVVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNNGVVDK 8 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 84.213 0.028239 86262000 119540 105160 112960 126820 93074 113230 135270 127810 116210 FALSE TRUE 113889.5811 115875.9236 118139.3277 114071.8127 109306.0761 109308.8167 114632.0771 116618.2788 134231.2533 0.848458003 0.863255916 0.880117892 0.849815597 0.814311671 0.814332088 0.853989472 0.868786337 1 17.03436109 0.673326427 2.259108472 0.999971058 0.847096637 0.853671042 0.019846405 0.738950094 4.597108473 0.020452035 0.005538693 4.713314582 -0.673326427 -0.152874422 RNPDTQWITKPVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNPDTQWITKPVHK 14 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 160.8 2.82E-06 2143100000 3753000 2948200 3059900 3510000 2587100 3297500 4095500 3751200 3042500 FALSE TRUE 3575603.128 3248624.932 3200199.442 3157168.131 3038289.421 3183306.748 3470656.256 3422725.042 3514315.361 1.017439461 0.92439767 0.910618175 0.898373597 0.864546607 0.905811352 0.987576782 0.973937934 1 21.74481223 1.683647142 6.548462283 0.985666675 0.924907339 0.388178914 0.039245276 0.176402524 15.77439899 0.022498397 0.011452794 48.26664835 -1.683647142 -0.060759336 RNPPGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 69.383 0.096025 26345000 48623 46657 42762 54096 36479 44448 54565 50138 50661 FALSE TRUE 46324.68715 51411.40134 44722.68 48658.1673 42840.92605 42908.75461 46240.1071 45747.65092 58517.24914 0.791641573 0.878568321 0.764264907 0.831518365 0.732107655 0.733266776 0.790196186 0.781780613 1 15.83657433 -1.049526462 7.692335038 1.00000001 0.792563969 0.700639019 0.043472713 7.83E-09 9.83E-10 0.044131428 0.010401877 0.089222325 1.049526462 -0.207436041 RNPS(ph)PDHSYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNPSPDHSYKR 11 2 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.999)PDHS(0.001)YKR;RNPS(1)PDHSYKR;RNPS(0.998)PDHS(0.002)YKR;RNPS(0.994)PDHS(0.005)Y(0.001)KR;RNPS(0.992)PDHS(0.008)YKR;RNPS(0.999)PDHS(0.001)YKR 123.76 0.00018955 1169437000 933912 742148 859141 919415 762099 914017 1062770 1000935 819216 TRUE FALSE 889767.8306 817773.725 898533.4647 826993.6574 895008.8243 882364.3621 900624.9174 913287.8251 946255.8333 0.940303668 0.864220538 0.94956716 0.873964131 0.945842332 0.932479707 0.951777401 0.965159519 1 19.85187076 1.484693592 0.644316179 0.998945587 0.904836359 0.530135525 0.027521051 0.468092496 0.438270042 0.02362452 0.011343876 30.52766533 -1.484693592 -0.094109227 RNQKPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNQKPEVR 8 2 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 126.07 0.00069462 1474030000 1271910 1039170 1062280 1211330 973090 1214030 1413790 1280090 1128390 FALSE TRUE 1211789.335 1145062.604 1110986.589 1089564.807 1142796.588 1171987.837 1198090.369 1167998.533 1303374.958 0.929731945 0.8785366 0.852392155 0.83595653 0.876798024 0.899194686 0.919221565 0.896133938 1 20.31382075 0.518047589 0.708035993 1.000918513 0.879777163 0.658508106 0.026580263 1.119942795 0.933363079 0.032248352 0.010688877 3.296458324 -0.518047589 -0.12114135 RNRS(ph)PHHSTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNRSPHHSTVK 11 2 Q8TAD8;A0A1W2PRA0 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RNRS(0.998)PHHS(0.001)T(0.001)VK 50.563 0.074188 7215400 10311 7860.8 10709 9617.5 15371 10114 15606 13453 12450 TRUE FALSE 9823.619464 8661.824457 11200.01824 8650.730628 18051.69753 9763.749644 13225.01808 12274.984 14380.68241 0.68311219 0.602323604 0.778823836 0.601552164 1.255274055 0.678948979 0.919637726 0.853574514 1 13.81184452 RNS(ph)CNVGGGGGGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSCNVGGGGGGFK 14 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFK 72.417 0.023695 158040000 167210 171870 149760 207280 127400 175420 171840 186360 117250 TRUE FALSE 159306.3147 189383.7484 156626.6441 186443.8206 149618.5197 169345.1614 145622.6519 170041.3304 135432.5312 1.176278057 1.398362319 1.156492039 1.376654626 1.104745798 1.250402396 1.075241308 1.255542734 1 17.04721479 1.057485451 0.349828859 0.98554479 1.29479595 0.335796473 0.102826683 1.490423141 0.542410691 0.170573446 0.099783131 11.41525063 -1.057485451 0.309251159 RNS(ph)DNRNPSADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSDNRNPSADR 12 2 Q9ULD2;Q9ULD2-2;H0YC63;Q9ULD2-5 Q9ULD2 MTUS1 Microtubule-associated tumor suppressor 1 1 RNS(0.999)DNRNPS(0.001)ADR 63.681 0.054309 79128000 84599 61787 64037 73364 81043 68943 79984 63112 87588 TRUE FALSE 80600.17293 68083.16555 66973.15979 65989.31134 95176.87354 66555.48662 67780.97179 57585.5787 101170.6997 0.796675057 0.672953392 0.661981779 0.652257141 0.940755316 0.657853379 0.669966423 0.569192255 1 16.626432 4.686839983 3.684204137 0.712656643 0.801402517 0.013185867 0.136551895 0.932695547 21.69157201 0.02957216 0.203536247 48622.80202 -4.686839983 0.088745874 RNS(ph)FSENEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.922)FS(0.078)ENEK;RNS(0.998)FS(0.002)ENEK;RNS(0.993)FS(0.007)ENEK;RNS(0.999)FS(0.001)ENEK;RNS(0.94)FS(0.06)ENEK 225.72 1.61E-07 2148460000 2619880 2256300 2361140 2715350 1785750 2719820 3004430 2846790 2024630 TRUE FALSE 2496043.465 2486219.535 2469400.604 2442397.859 2097184.235 2625631.951 2546049.023 2597509.976 2338599.28 1.06732414 1.063123365 1.055931482 1.044384936 0.896769384 1.122737005 1.088706836 1.110711868 1 21.15721325 RNS(ph)FTPLSSSNTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.999)FT(0.001)PLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(0.934)FT(0.065)PLS(0.001)S(0.001)SNTIR;RNS(1)FTPLSSSNTIR 262.83 1.48E-24 7993280000 2628180 2388060 2197970 2779480 2793350 2594610 3307220 2730930 2958900 TRUE FALSE 2503951.14 2631406.029 2298749.099 2500081.39 3280509.356 2504758.005 2802642.848 2491795.292 3417751.1 0.732631215 0.769923248 0.672591137 0.731498964 0.95984443 0.732867295 0.820025439 0.729074534 1 21.7046159 -4.999999999 0.193919085 2.000486712 0.729638135 0.473070671 0.077111696 119.7062772 1.176487111 46.38453916 0.18608711 1.00E-05 4.999999999 -1.270848577 RNS(ph)GSSLVSSSSASSNLSHLEEDSWILWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.969)GS(0.024)S(0.007)LVSSSSASSNLSHLEEDSWILWGR 210.28 2.96E-26 97758000 24725 22628 21349 23474 27333 23726 29425 25987 28577 TRUE FALSE 23556.29825 24933.81893 22327.87277 21114.34892 32099.86655 22904.36267 24935.67582 23711.44051 33008.57521 0.713641776 0.755373983 0.676426432 0.639662536 0.972470528 0.693891285 0.755430238 0.718341836 1 15.01055325 -5 0.33493504 3.696600446 0.731537527 0.453260664 0.089445912 333.5686888 2.846760378 641.9854562 0.067435446 1.00E-05 5 -2.965062919 RNS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDTWILWGR 30 1 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 RNS(0.507)GS(0.1)S(0.1)LVS(0.048)S(0.048)S(0.048)S(0.048)AS(0.048)S(0.048)NLS(0.001)HLEEDTWILWGR 85.658 0.00081962 37623000 9975 8969.3 10160 12716 7873.8 8706.6 13918 11131 9459.2 TRUE FALSE 9503.501519 9883.281867 10625.84605 11437.76352 9246.988227 8405.088259 11794.55348 10156.31063 10926.08443 0.869799385 0.904558439 0.972520954 1.046830967 0.846322238 0.769268105 1.079485845 0.929547149 1 13.41548886 7.999999996 0.074483534 1.070413179 0.592626278 0.078243276 0.090263707 561.1742625 3.068588277 3.215792473 27.83891973 99999999.1 -7.999999996 -0.477786901 RNS(ph)IEVAGLSHGLEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RNSIEVAGLSHGLEGLR 17 1 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 RNS(1)IEVAGLSHGLEGLR;RNS(1)IEVAGLSHGLEGLR;RNS(1)IEVAGLSHGLEGLR;RNS(1)IEVAGLSHGLEGLR 257.2 2.47E-27 1134160000 408255 311050 344174 397858 413076 343492 446196 374148 405707 TRUE FALSE 388957.5952 342746.3486 359954.7183 357864.558 485116.3236 331596.7859 378120.6052 341385.6176 468621.9695 0.830002903 0.731391977 0.768113195 0.763652968 1.035197569 0.707599745 0.806877675 0.728488291 1 18.83806507 -1.469090708 2.814694287 1.006545365 0.794825339 0.323843349 0.092423835 11645115.61 12557626.33 596825.1886 0.020389143 0.033955435 1.469090708 -0.211720025 RNS(ph)LDGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RNSLDGGGR 9 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR;RNS(1)LDGGGR 145.31 5.97E-05 395643000 311154 266699 274125 315824 309028 299188 317792 306215 331052 TRUE FALSE 296446.3671 293875.9313 286693.9024 284076.7715 362922.3854 288827.0445 269306.9937 279401.1913 382389.8534 0.775246426 0.768524397 0.749742442 0.742898299 0.949089998 0.75532089 0.704273378 0.730671038 1 18.54468472 -1.622810293 2.947326109 1.01778516 0.769965615 0.540087789 0.066106923 29201983.13 30960371.28 4002026.126 0.016285813 0.023833603 1.622810293 -0.247819545 RNS(ph)LEGYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(1)LEGYSR 71.806 0.020117 0 68711 76814 55170 75551 73748 60202 75757 63963 72548 TRUE FALSE 65463.1672 84641.43393 57699.59907 67956.46994 86609.62785 58117.18964 64198.87828 58362.06063 83798.37332 0.781198544 1.010060584 0.688552734 0.810952137 1.033547841 0.693536012 0.766111271 0.696458157 1 16.35463462 2.178950318 24.99993896 0.766454696 0.86659865 0.064606902 0.131362132 154.5157759 64800.83038 0.045258436 0.033425581 150.9907416 -2.178950318 0.100143954 RNS(ph)LIELPDDYSCLLNQASHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSLIELPDDYSCLLNQASHFR 22 1 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR 285.48 2.39E-46 150172000 66116 96957 52688 91638 59359 73086 61866 71500 57279 TRUE FALSE 62990.82771 106837.0285 55103.79692 82426.37414 69711.19081 70555.01349 52427.20545 65239.08095 66161.53478 0.952076277 1.614790662 0.832867573 1.245835279 1.053651356 1.066405332 0.792412172 0.986057551 1 16.01370508 2.52507184 1.017570628 0.908909146 1.223174183 0.148760972 0.21446826 0.715900912 1.50558032 0.124931088 0.092359848 335.020853 -2.52507184 0.314265037 RNS(ph)LILKPKPDPAQQTDSQNSDTEQYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSLILKPKPDPAQQTDSQNSDTEQYFR 28 3 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 RNS(1)LILKPKPDPAQQTDSQNSDTEQYFR;RNS(1)LILKPKPDPAQQTDSQNSDTEQYFR 316.5 4.02E-82 582140000 936950 893930 867730 1084430 623520 1002070 1147700 1118460 710780 TRUE FALSE 892662.2304 985022.4833 907516.2788 975421.0361 732261.6906 967368.0646 972597.286 1020521.713 821004.1322 1.087281044 1.199777741 1.105373582 1.18808298 0.891909872 1.178274294 1.184643594 1.243016537 1 19.64702996 -0.557132639 6.920871028 0.999999766 1.136760031 0.15894737 0.097352094 0 0 0.0883727 0.020829645 0.277247323 0.557132639 0.136760265 RNS(ph)LPQIPMLNLEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNSLPQIPMLNLEAR 15 1 Q14289;Q14289-2;H0YB74 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR 171.47 6.62E-07 191564000 133854 110417 118601 133243 123201 121265 146056 139290 145038 TRUE FALSE 127526.9867 121668.6178 124038.9732 119849.1605 144687.2154 117065.5626 123772.4747 127093.0292 167529.7523 0.761219932 0.726250807 0.740399669 0.715390304 0.863650864 0.698774761 0.738808916 0.758629601 1 17.35405781 0.77880354 5.995453732 0.999999957 0.747263669 0.758303546 0.044307335 6.086781221 164.9763352 0.038745984 0.009742946 6.009018487 -0.77880354 -0.252736288 RNS(ph)LTGEEGQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNSLTGEEGQLAR 13 1 Q9BX95 Q9BX95 SGPP1 Sphingosine-1-phosphate phosphatase 1 1 RNS(0.996)LT(0.004)GEEGQLAR;RNS(0.996)LT(0.004)GEEGQLAR;RNS(1)LTGEEGQLAR 167.95 1.90E-05 488750000 454454 358376 409767 571844 518225 420348 551093 462646 518308 TRUE FALSE 432972.8601 394894.9218 428555.2223 514361.1547 608603.2759 405791.2434 467013.6413 422134.2636 598684.5575 0.723206995 0.659604322 0.715828088 0.8591522 1.01656752 0.677804761 0.780066289 0.705102977 1 19.19143653 -5 0.149182726 1.779243366 0.689943749 0.301613935 0.106800385 175.6180003 1.559879978 41.37739631 0.557053433 1.00E-05 5 -1.089299617 RNS(ph)PAFLSTDLGDEDVGLGPPAPR ddPTM_SK-BR-3_Trastuzumab_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 279.93 2.10E-52 337431000 198012 168849 179670 183108 161521 172177 207622 212997 234745 TRUE FALSE 188652.3652 186054.9051 187908.0472 164701.636 189690.2113 166214.4673 175945.4507 194345.8535 271148.0557 0.695754077 0.686174587 0.693009016 0.60742326 0.699581676 0.613002615 0.648890696 0.716751787 1 18.0487213 0.802690171 3.70466935 0.999981558 0.665270882 0.910936227 0.032825215 0.415690311 7.47738126 0.031268347 0.008031343 6.348778433 -0.802690171 -0.334710676 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(0.999)PMAQT(0.999)PPCHLPNIPGVT(0.002)SPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.995)PMAQT(0.995)PPCHLPNIPGVT(0.005)S(0.005)PGT(0.001)LIEDSK;RNS(0.999)PMAQT(0.999)PPCHLPNIPGVT(0.001)S(0.001)PGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVT(0.001)SPGTLIEDSK 143.12 4.17E-08 277434000 235044 255759 208073 294343 181779 280335 291071 309033 195970 TRUE FALSE 223933.9359 281821.1329 217613.3529 264755.0824 213481.2 270626.9287 246662.7731 281972.4322 226360.0267 0.989282159 1.24501281 0.961359459 1.169619417 0.943104678 1.195559713 1.089692278 1.245681211 1 17.78825969 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 84.17 0.00021371 204093000 89175 74524 79552 91337 74165 102232 129130 120918 73336 TRUE FALSE 84959.87448 82118.08033 83199.53789 82155.63123 87099.35252 98691.68021 109428.8469 110329.7789 84708.57233 1.002966667 0.969418774 0.982185576 0.969862069 1.028223592 1.165073115 1.291827307 1.302462972 1 16.37022035 2.213986379 2.906926814 1.23035223 0.983064923 0.578461579 0.08396763 0.144368533 2.508583505 0.031148569 0.022228495 163.6765185 -2.213986379 -0.247287307 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.814)PMAQT(0.186)PPCHLPNIPGVTSPGTLIEDSK 185.68 1.99E-18 117900000 114120 141500 102070 149600 82635 123990 114810 126690 71634 TRUE FALSE 108725.7738 155919.0109 106750.0105 134561.9238 97046.51784 119696.1952 97293.62587 115596.352 82742.63486 1.314023586 1.884385373 1.290145167 1.626270713 1.172871978 1.446608455 1.175858444 1.397059112 1 16.33634328 1.699435902 0.371844663 1.008103257 1.608572285 0.341208265 0.202422132 1.115311078 0.456630359 0.240760068 0.215856518 50.05366726 -1.699435902 0.600469028 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK 45 3 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.699)PMAQT(0.301)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK 155.64 2.70E-15 257010000 203090 173610 214290 207870 137240 244310 296820 259730 112920 TRUE FALSE 193490.3382 191301.0564 224115.4085 186974.5127 161174.6125 235849.4834 251534.6575 236986.6643 130431.0569 1.4834683 1.466683326 1.718267212 1.433512211 1.235707326 1.808231023 1.928487459 1.816949659 1 16.9929279 2.210312426 24.99876006 1.741881421 1.478712637 0.029170851 0.281641214 355.6586787 314744.6145 0.095134865 0.070275286 162.2977227 -2.210312426 -0.263168784 RNS(ph)RTEEPTVASESVENGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSRTEEPTVASESVENGHR 20 2 Q14686;A0A0D9SFT8;F6M2K2 Q14686 NCOA6 Nuclear receptor coactivator 6 1 RNS(0.482)RT(0.482)EEPT(0.035)VASESVENGHR;RNS(0.493)RT(0.493)EEPT(0.015)VASESVENGHR 288.83 1.19E-46 888460000 255318 190023 274483 238096 278580 241319 314380 252241 308600 TRUE FALSE 243249.6241 209386.5597 287068.3171 214162.1377 327164.2638 232962.0625 266415.557 230153.4408 356456.1119 0.682411147 0.587411894 0.805339865 0.600809274 0.917824812 0.653550479 0.747400727 0.645671187 1 18.44336493 -5 0.225710317 2.548959106 0.664625925 0.447485568 0.100903445 133.4868728 1.335478002 94.47695856 0.163070847 1.00E-05 5 -1.884333181 RNS(ph)SEASSGDFLDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.748)S(0.252)EASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.983)S(0.017)EASSGDFLDLK;RNS(0.944)S(0.056)EASSGDFLDLK;RNS(0.998)S(0.002)EASSGDFLDLK;RNS(0.999)S(0.001)EASSGDFLDLK;RNS(0.825)S(0.009)EAS(0.164)S(0.003)GDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.999)S(0.001)EASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.995)S(0.005)EASSGDFLDLK;RNS(0.963)S(0.029)EAS(0.006)S(0.002)GDFLDLK 310.51 4.05E-56 16478737000 10516950 14246440 9427197 13739700 6063617 12194950 10261710 11994930 5887159 TRUE FALSE 10019834.62 15698168.43 9859443.307 12358559.25 7121109.885 11772635.82 8696097.67 10944590.34 6800109.55 1.473481352 2.30851699 1.449894775 1.817405905 1.047205171 1.731242083 1.278817291 1.60947265 1 22.69712656 3.150822237 1.802085153 1.384827181 1.862544307 0.249014192 0.332116177 0.410577333 2.744804694 0.09944452 0.130770548 1415.214395 -3.150822237 0.477717126 RNS(ph)SIVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RNSSIVGR 8 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 RNS(0.996)S(0.004)IVGR;RNS(0.953)S(0.047)IVGR;RNS(0.952)S(0.048)IVGR;RNS(0.998)S(0.002)IVGR 124.34 0.00088183 849970000 439759 359156 362051 447204 404366 369701 492257 400064 426597 TRUE FALSE 418972.4636 395754.4047 378651.3965 402250.2043 474887.3024 356898.1617 417154.1537 365032.2753 492751.484 0.850271338 0.803152132 0.768442935 0.816334841 0.963746062 0.724296472 0.846581223 0.74080401 1 18.91050069 -1.540589805 3.206136738 1.006166035 0.81673077 0.430923095 0.067044545 24100991.63 26037878.86 1263007.635 0.014464036 0.028801174 1.540589805 -0.189435266 RNS(ph)SS(ph)PVS(ph)PASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 3 RNS(0.939)S(0.061)S(1)PVS(0.976)PAS(0.024)VPGQR 164.2 1.50E-08 0 160460 123360 159410 172390 139160 157150 202060 144410 161070 TRUE FALSE 152875.3738 135930.5242 166719.1062 155061.0297 163429.4599 151707.8561 171232.0359 131764.6948 186047.913 0.821698945 0.730621065 0.896108446 0.833446757 0.878426731 0.815423585 0.920365261 0.7082299 1 17.50531468 -5 0.1805109 1.67461566 0.792376694 0.335813283 0.07019849 142.5202802 1.373273503 34.81615859 0.200172302 1.00E-05 5 -0.882238965 RNS(ph)SS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.997)S(0.096)S(0.907)PVSPASVPGQR;RNS(0.923)S(0.094)S(0.983)PVSPASVPGQR;RNS(0.995)S(0.015)S(0.61)PVS(0.38)PASVPGQR;RNS(0.945)S(0.429)S(0.625)PVSPASVPGQR;RNS(0.997)S(0.056)S(0.919)PVS(0.028)PASVPGQR 214.9 1.11E-14 1011361000 1074703 847968 949928 1066685 927225 934795 1152289 895417 955386 TRUE FALSE 1023903.919 934376.9033 993483.1384 959459.7972 1088932.746 902422.8148 976486.1498 817009.5406 1103542.381 0.927833798 0.846706859 0.900267317 0.869436293 0.986761147 0.817750935 0.884865109 0.740351757 1 20.07371061 RNS(ph)SSPVSPASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.37)S(0.37)S(0.26)PVSPASVPGQR 80.236 0.0098787 367140000 212370 123720 177150 176910 241680 186000 245550 190870 264500 TRUE FALSE 202331.691 136327.2087 185272.5027 159126.6707 283828.9155 179558.7734 208086.8377 174156.4109 305517.3091 0.662259338 0.446217627 0.606422279 0.520843389 0.929010917 0.58772046 0.681096722 0.570037788 1 18.22089459 -4.999999999 0.183560691 2.575654402 0.542701013 0.45648248 0.127509237 115.7932024 1.121573381 66.65749875 0.353044483 1.00E-05 4.999999999 -2.032953389 RNS(ph)SSSSSPSERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.823)S(0.066)S(0.066)S(0.032)S(0.006)S(0.006)PSERPR;RNS(0.648)S(0.111)S(0.111)S(0.108)S(0.018)S(0.003)PSERPR;RNS(0.958)S(0.029)S(0.001)S(0.002)S(0.008)S(0.002)PSERPR;RNS(0.921)S(0.026)S(0.026)S(0.01)S(0.01)S(0.005)PSERPR;RNS(0.614)S(0.149)S(0.149)S(0.05)S(0.029)S(0.008)PSERPR;RNS(0.815)S(0.071)S(0.028)S(0.028)S(0.028)S(0.028)PSERPR 158.76 3.95E-06 3060660000 1281455 1130850 1301838 1414630 1384978 1337220 1576602 1382367 1585204 TRUE FALSE 1220883.162 1246084.901 1361528.56 1272428.705 1626517.725 1290911.736 1336062.409 1261319.617 1831029.34 0.666774221 0.680537921 0.743586424 0.69492535 0.888307844 0.705019689 0.729678318 0.688858223 1 20.80422348 -5 0.263825931 2.819633664 0.699781566 0.645959232 0.063460876 125.5175974 1.227640761 124.2237016 0.079379791 1.00E-05 5 -2.119852098 RNS(ph)TDSRPVSVTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.988)T(0.01)DS(0.001)RPVSVTYR;RNS(0.5)T(0.5)DSRPVSVTYR;RNS(0.994)T(0.006)DSRPVSVTYR 152.01 3.54E-06 1031770000 393625 321177 324294 383146 359955 316183 428034 376386 389060 TRUE FALSE 375019.1263 353905.3014 339163.2007 344631.4362 422731.038 305233.5034 362729.5519 343427.6465 449393.4378 0.834500673 0.787517733 0.754713292 0.766881328 0.940670251 0.679212195 0.807153646 0.764202629 1 18.77761953 -2.002283966 2.503149159 1.210095737 0.792641029 0.492494557 0.066398347 5943498.088 2593555.94 7194583.665 0.014282049 0.009947548 2.002283966 -0.417454708 RNS(ph)TIVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNSTIVLR 8 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 RNS(0.997)T(0.003)IVLR;RNS(0.951)T(0.049)IVLR;RNS(0.997)T(0.003)IVLR;RNS(0.986)T(0.014)IVLR;RNS(0.971)T(0.029)IVLR;RNS(0.996)T(0.004)IVLR 178.53 0.00015259 1847370000 909556 795001 773574 1006196 773144 926083 991908 927645 771839 TRUE FALSE 866563.0904 876012.5057 809043.1331 905051.2664 907980.0688 894012.5135 840574.217 846415.486 891531.8501 0.971993418 0.982592496 0.9074753 1.015164255 1.01844939 1.002782473 0.942842611 0.949394557 1 19.76592681 4.773118875 17.65889482 0.975674807 0.971993142 0.000292073 0.035250302 1414.597042 1078941.28 0.008282016 0.227699544 59308.76416 -4.773118875 -0.003681665 RNS(ph)TTFPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.987)T(0.013)T(0.001)FPSR;RNS(0.963)T(0.037)T(0.001)FPSR 101.39 0.0024595 1325560000 309190 244958 258937 296430 264590 291170 374330 321050 364020 TRUE FALSE 294575.2015 269919.4987 270809.5176 266632.2932 310734.4122 281086.7099 317219.0835 292937.16 420470.3624 0.700584935 0.64194655 0.644063272 0.634128626 0.739016207 0.668505405 0.754438628 0.696689199 1 18.68164459 -1.182723543 0.33638937 1.182196135 0.655348468 0.888238989 0.035720667 4.911232918 0.392213701 0.845957182 0.029011532 0.065656308 1.182723543 -0.526847667 RNS(ph)TTIMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSTTIMSR 9 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RNS(0.955)T(0.041)T(0.004)IMSR;RNS(0.975)T(0.022)T(0.003)IMSR 142.08 6.44E-05 1624040000 321910 261333 315651 312810 330540 317740 412890 313730 343580 TRUE FALSE 306693.9523 287963.1298 330123.9106 281365.7445 388186.0713 306736.5841 349896.0473 286258.138 396860.6316 0.772800141 0.72560266 0.831838394 0.708978725 0.978142049 0.772907564 0.881659755 0.721306462 1 18.59827293 -5 0.119660489 1.628687474 0.702587412 0.350129415 0.083584689 152.9570725 1.187660731 23.5208709 0.715974528 1.00E-05 5 -0.926100062 RNS(ph)VDTATSSSLSTPSEPLSPTSSLGEERN ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSVDTATSSSLSTPSEPLSPTSSLGEERN 30 2 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RNS(0.953)VDT(0.024)AT(0.008)S(0.008)S(0.003)S(0.004)LSTPSEPLSPTSSLGEERN;RNS(0.992)VDT(0.008)ATSSSLSTPSEPLSPTSSLGEERN 156.32 4.22E-09 277690000 122936 115626 114057 135826 108147 122838 127693 131995 133168 TRUE FALSE 117125.0589 127408.4209 119286.6263 122172.5124 127007.8026 118584.0893 108211.0876 120436.8181 153819.0133 0.761447212 0.828300859 0.775499879 0.794261449 0.825696381 0.770932583 0.703496176 0.782977445 1 17.23087432 0.923940679 22.59846428 1 0.778831629 0.796890011 0.034853237 13506.06628 4012876.034 0.037058917 0.009264729 8.393453303 -0.923940679 -0.221168371 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNSVERPAEPVAGAATPSLVEQQK 24 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK 228.41 1.89E-33 2916970000 1207670 1129947 1233620 1373690 906284 1305620 1420540 1306960 979792 TRUE FALSE 1150585.832 1245089.884 1290182.697 1235604.071 1064339.643 1260406.052 1203810.533 1192515.654 1131733.139 1.01665825 1.100162079 1.140006113 1.09178041 0.940451071 1.113695454 1.063687623 1.053707462 1 20.11010238 RNS(ph)YPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RNSYPR 6 1 Q14134-2;Q14134 Q14134-2 TRIM29 Tripartite motif-containing protein 29 1 RNS(1)YPR;RNS(1)YPR;RNS(1)YPR;RNS(1)YPR;RNS(1)YPR;RNS(0.999)Y(0.001)PR 84.498 0.034167 1272491000 638077 445891 492536 612683 559859 553989 689468 621515 649816 TRUE FALSE 607916.3648 491327.7998 515119.2628 551094.9408 657498.2323 534804.222 584276.9937 567091.8517 750586.1465 0.809922176 0.654592151 0.686289329 0.734219441 0.875979707 0.712515445 0.778427628 0.755531999 1 19.51765814 -5 0.24709643 2.52005493 0.723210158 0.618742285 0.061831775 116.8434139 1.160219749 89.45212801 0.088207339 1.00E-05 5 -1.796844772 RNSFS(ph)ENEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.179)FS(0.821)ENEK 218.12 3.31E-07 1026000000 1120900 915930 1050400 1140900 833510 1186600 1248500 1280600 890600 TRUE FALSE 1067917.278 1009264.308 1098561.879 1026214.564 978873.8801 1145507.744 1058018.395 1168463.875 1028709.699 1.038113356 0.9810973 1.067902713 0.9975745 0.951555021 1.113538392 1.028490735 1.135853852 1 19.97240448 2.231259995 24.99927756 1.068688916 1.008805658 0.286599167 0.048739226 212.8713731 728920.8341 0.016252114 0.012238194 170.3177828 -2.231259995 -0.059883258 RNSFTPLSS(ph)SNTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.019)FT(0.013)PLS(0.008)S(0.689)S(0.27)NT(0.002)IR 242.44 1.85E-17 587660000 452190 328040 351690 395170 425190 420490 497510 406650 474130 TRUE FALSE 430815.8749 361467.649 367815.3344 355446.7608 499343.0014 405928.3259 421605.7121 371041.5702 547655.6589 0.786654658 0.660027233 0.671617883 0.649033302 0.911782784 0.741210867 0.769837224 0.677508877 1 19.06290955 2.767355725 24.98322698 0.796523851 0.695944897 0.284085934 0.097144959 1072.553542 930567.8819 0.027273104 0.028922678 585.2692738 -2.767355725 -0.100578954 RNSNSPPS(ph)PSSMNQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNSNSPPSPSSMNQR 15 1 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RNS(0.004)NS(0.008)PPS(0.936)PS(0.026)S(0.026)MNQR;RNSNSPPS(0.888)PS(0.056)S(0.056)MNQR 45.436 0.094284 118468000 75064 33222 67992 59592 91305 65632 103661 70540 107254 TRUE FALSE 71515.87348 36607.35957 71109.50045 53601.69894 107228.5631 63359.14738 87845.61059 64363.14364 123886.4025 0.577269757 0.295491344 0.57398955 0.432668137 0.865539405 0.511429391 0.709081939 0.519533559 1 16.91865832 -4.999999999 0.10904902 2.486939366 0.279231147 0.484664535 0.147089233 126.8554029 0.921858341 41.93195377 1.717811379 1.00E-05 4.999999999 -2.207708219 RNSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.052)PMAQT(0.948)PPCHLPNIPGVTSPGTLIEDSK 225.3 3.62E-35 114970000 129190 153420 116350 160120 91302 135340 130240 139600 81656 TRUE FALSE 123083.4447 169053.6724 121684.7626 144024.4334 107225.0399 130653.1419 110369.496 127375.8839 94318.79544 1.304972611 1.792364625 1.290143306 1.526996106 1.1368364 1.385229119 1.170174995 1.350482513 1 16.52525767 1.909667955 0.353101977 1.013095319 1.572621573 0.371256229 0.173322719 1.18000138 0.419509237 0.211255202 0.226322845 81.22092948 -1.909667955 0.559526255 RNSS(ph)S(ph)PVSPASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.086)S(0.667)S(0.761)PVS(0.487)PASVPGQR 105.39 0.00087592 0 101170 78880 87382 97243 79815 82911 112210 86973 89059 TRUE FALSE 96387.8946 86917.96168 91388.55113 87467.94889 93734.71073 80039.77128 95090.30362 79357.18305 102869.8149 0.936989094 0.844931643 0.888390353 0.850278082 0.911197428 0.778068585 0.92437518 0.771433128 1 16.65046019 -1.110900406 5.254875482 1.000002805 0.868157508 0.365853546 0.056264012 1.59E-06 2.69E-07 0.046839767 0.011040004 0.077463942 1.110900406 -0.131845297 RNSSEASS(ph)GDFLDLK ddPTM_SK-BR-3_Trastuzumab_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(0.1)S(0.118)EAS(0.352)S(0.43)GDFLDLK 66.386 0.035971 436560000 88175 82430 71121 88512 60396 80836 97018 88778 67741 TRUE FALSE 84007.1425 90829.71072 74381.9682 79614.6056 70929.04328 78036.62905 82216.12224 81004.12768 78245.92831 1.073629572 1.160823479 0.950617749 1.017491994 0.906488616 0.99732511 1.050739943 1.035250388 1 16.25572806 3.739349314 24.99940282 0.996944597 1.117226527 0.554622134 0.045853396 49.33747779 1563827.719 0.012173471 0.020451399 5487.181357 -3.739349314 0.120281931 RNSSS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.326)S(0.326)S(0.348)PVSPASVPGQR 92.002 0.0030132 374550000 223980 158770 193340 180220 233960 179740 288180 220440 302290 TRUE FALSE 213392.9093 174948.8435 202204.8302 162103.9432 274762.5499 173515.5587 244212.8482 201137.105 349167.5893 0.611147529 0.501045483 0.579105382 0.464258276 0.786907372 0.496940621 0.699414424 0.576047466 1 18.41356012 -5 0.226673852 3.20158746 0.538161472 0.652083574 0.095063929 86.61276412 0.866499003 87.16061091 0.146676571 1.00E-05 5 -2.663425988 RNT(ph)FVGTPFWMAPEVIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNTFVGTPFWMAPEVIK 17 1 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;C9JDH9;C9J6L2;C9JCC0;C9J232;H7C279;O00506-3;O00506-2;O00506 B4DR80 STK24;STK25 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 25 1 RNT(0.995)FVGT(0.005)PFWMAPEVIK;RNT(0.996)FVGT(0.004)PFWMAPEVIK 183.01 4.19E-10 369360000 687920 608260 762120 797690 682650 840710 1062610 866030 766160 TRUE FALSE 655403.3849 670242.3855 797063.9558 717504.6857 801703.9439 811596.0019 900489.3283 790195.8221 884972.1798 0.740592077 0.757359837 0.900665551 0.810765244 0.90590864 0.917086458 1.017534052 0.892904704 1 19.75527258 3.310607193 0.467675637 0.992853318 0.689670165 0.741753428 0.046441759 0.628033905 0.251851019 0.037108858 0.091537781 2044.594522 -3.310607193 -0.303183153 RNT(ph)LQLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RNTLQLHR 8 1 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 1 RNT(1)LQLHR 89.403 0.019198 0 154040 145740 126260 166220 104720 149100 153290 128320 133040 TRUE FALSE 146758.8345 160591.0717 132049.1459 149511.2498 122983.1348 143936.6296 129902.7951 117083.6205 153671.1637 0.955018697 1.045030621 0.859296843 0.972929769 0.800300667 0.936653476 0.845329677 0.761910157 1 17.22948694 3.469832387 1.515513911 0.86919469 0.9980078 0.221354055 0.079866442 0.443584481 2.064292593 0.023089806 0.041425664 2950.070445 -3.469832387 0.12881311 RNVSSFPDDATS(ph)PLQENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RNVSSFPDDATSPLQENR 18 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 RNVSSFPDDAT(0.071)S(0.929)PLQENR;RNVSSFPDDAT(0.225)S(0.775)PLQENR 185.58 3.21E-14 249830000 218052 223281 246570 271720 249430 238931 268260 268880 315810 TRUE FALSE 207745.1141 246033.5877 257875.4784 244406.1894 292930.513 230656.7596 227332.0101 245335.4418 364784.2019 0.569501401 0.674463385 0.706926114 0.670002122 0.803024121 0.632310167 0.623195876 0.672549525 1 18.47668372 -1.935376728 2.181686019 1.242812025 0.664019937 0.746604081 0.060540688 2762727.529 1184344.312 3412916.565 0.015433781 0.011604416 1.935376728 -0.578792087 RPAEAT(ph)SSPTS(ph)PERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.914)S(0.053)S(0.034)PT(0.266)S(0.733)PERPR;RPAEAT(0.822)S(0.031)S(0.143)PT(0.094)S(0.911)PERPR 132.48 4.29E-05 1156770000 483322 413189 458050 501577 518950 447938 582774 491878 568410 TRUE FALSE 460476.3269 455293.4289 479052.0456 451157.527 609454.7157 432425.7947 493861.1229 448806.5547 656556.1198 0.701351054 0.693456987 0.729643714 0.687157599 0.928259896 0.658627316 0.752199405 0.683576836 1 19.32455881 -1.835223515 2.639549308 1.099994587 0.727760893 0.560553684 0.075317981 23141333.57 15737087.14 14661282.46 0.017649321 0.014614248 1.835223515 -0.372233694 RPAEATSS(ph)PT(ph)SPERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.021)S(0.025)S(0.952)PT(0.634)S(0.368)PERPR;RPAEAT(0.133)S(0.148)S(0.722)PT(0.714)S(0.284)PERPR;RPAEAT(0.31)S(0.362)S(0.406)PT(0.647)S(0.275)PERPR 104.86 0.0014663 7332720000 2675240 1939410 2287180 2412980 2409870 2390410 2503080 2488820 2676050 TRUE FALSE 2548786.707 2137038.084 2392049.465 2170422.666 2830150.565 2307629.502 2121189.174 2270885.727 3091038.167 0.82457303 0.691365803 0.77386604 0.702166246 0.915598712 0.746554839 0.686238428 0.734667644 1 21.55966004 -1.722316019 2.639512999 1.045325276 0.754872083 0.543728537 0.069162426 12432656 10173375.34 3720054.048 0.015878668 0.018953263 1.722316019 -0.290453193 RPAEATSS(ph)PTS(ph)PERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.168)S(0.397)S(0.436)PT(0.262)S(0.738)PERPR 133.3 0.00016931 1112900000 324850 276460 296100 314650 332670 291710 347690 293170 342350 TRUE FALSE 309494.9843 304631.5883 309676.4779 283020.7842 390687.5427 281608.0096 294643.5047 267498.4806 395439.8895 0.782660001 0.770361302 0.783118967 0.715711267 0.987982126 0.712138601 0.745103143 0.67645801 1 18.59309888 -2.259059147 2.403973416 1.954031168 0.772632842 0.42181988 0.083996086 11714800.54 1589982.868 61030886.61 0.020403495 0.005507327 2.259059147 -1.181398326 RPAEATSSPT(ph)SPERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEATSS(0.002)PT(0.499)S(0.499)PERPR;RPAEATSS(0.001)PT(0.722)S(0.277)PERPR;RPAEATSS(0.001)PT(0.859)S(0.14)PERPR;RPAEAT(0.005)S(0.007)S(0.046)PT(0.471)S(0.471)PERPR;RPAEATSSPT(0.87)S(0.13)PERPR;RPAEATSS(0.003)PT(0.859)S(0.138)PERPR;RPAEAT(0.007)S(0.022)S(0.072)PT(0.45)S(0.45)PERPR;RPAEAT(0.107)S(0.016)S(0.107)PT(0.385)S(0.385)PERPR 200.2 5.81E-11 7501231000 1028596.3 922966.1 955530.4 1037225.2 1099870.3 948121.3 1179139.2 1081594.4 1215918.2 TRUE FALSE 979976.5914 1017017.395 999342.414 932961.3523 1291687.332 915287.6216 999239.8587 986884.2604 1404476.584 0.697752175 0.724125561 0.711540815 0.6642769 0.919693035 0.651693045 0.711467795 0.702670498 1 20.42160114 -1.059824074 4.765595635 1.000009216 0.721368342 0.584239312 0.073451647 6.48E-06 1.28E-06 0.064101395 0.015108344 0.087131648 1.059824074 -0.278640874 RPAEDMEEEQAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPAEDMEEEQAFK 13 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;; 240.11 1.25E-16 824620000 1084560 1313620 975900 1389040 760620 1119430 987700 1153920 692815 FALSE TRUE 1033294.998 1447479.371 1020645.98 1249411.06 893271.8872 1080663.858 837008.2246 1052876.647 800253.2118 1.291210061 1.80877671 1.275403791 1.56126966 1.116236554 1.350402401 1.045929229 1.315679377 1 19.61009704 2.748161857 1.364248159 1.152877501 1.526418997 0.3819561 0.188684559 0.377985955 1.432965172 0.075026319 0.071715223 559.9662558 -2.748161857 0.373541496 RPAEDMEEEQAFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RPAEDMEEEQAFKR 14 2 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;; 272.72 3.07E-33 5797452000 4406440 3706800 3912500 4591320 3493710 4322140 4869370 4683780 3666260 FALSE TRUE 4198156.314 4084527.134 4091891.995 4129791.791 4103011.918 4172463.208 4126458.174 4273643.393 4234804.876 0.991345868 0.964513656 0.966252783 0.975202379 0.968878623 0.985278739 0.974415184 1.009171265 1 22.01386407 1.243165946 24.9983943 1.004585639 0.975117781 0.678685516 0.008426913 59.62930844 323690.7921 0.005912554 0.001998948 17.50515441 -1.243165946 -0.029467858 RPAEPGPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPAEPGPAR 9 1 A0A0A0MTR2;Q8N543;H3BR79;H3BR02 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 111.61 0.003363 47677000 37275 35559 30236 32413 46848 29968 42959 34725 49026 FALSE TRUE 35513.08462 39182.50253 31622.35051 29154.78366 55018.27637 28930.20065 36404.81555 31684.29491 56628.70169 0.627121646 0.691919492 0.558415601 0.51484111 0.971561677 0.510875224 0.642868624 0.559509471 1 15.78924583 -1.117301558 4.486552601 1.000035688 0.638323419 0.428431513 0.132562034 4.71E-05 9.26E-06 0.114930981 0.027086528 0.076330559 1.117301558 -0.361712269 RPAERS(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPAERSSPGQTPEEGAQALAEFAALHGPALR 31 2 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 RPAERS(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;RPAERS(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;RPAERS(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;RPAERS(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR 268.45 1.36E-59 292756000 79570 44901.4 94977 69645 137605 69313.3 141557 77899 169470 TRUE FALSE 75808.88379 49476.90371 99331.7894 62644.15228 161603.2684 66912.96304 119959.8798 71077.75059 195750.5421 0.387272919 0.252754875 0.507440686 0.320020326 0.825557195 0.341827728 0.612820166 0.363103723 1 17.57865678 -5 0.144531566 2.922114867 0.256992169 0.519205934 0.166253212 97.89854785 0.85491119 54.24843564 0.829713439 1.00E-05 5 -2.665122698 RPAETNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RPAETNLR 8 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;;;;;;;; 182.29 0.0003677 3669240000 1794008 1477932 1349994 1593508 1968817 1445478 1945716 1650255 2028614 FALSE TRUE 1709208.797 1628534.951 1411892.56 1433325.548 2312178.061 1395420.734 1648861.289 1505749.924 2343201.098 0.729433252 0.695004348 0.602548608 0.611695492 0.986760404 0.595518983 0.70367895 0.642603797 1 21.16004934 -1.773951118 2.575004659 1.079230834 0.697196982 0.41780794 0.11280299 13782584.22 10016352.65 6889513.657 0.024829203 0.016828635 1.773951118 -0.382033852 RPAGGRPS(ph)PSAMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPAGGRPSPSAMGK 14 2 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 RPAGGRPS(0.995)PS(0.005)AMGK;RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.998)PS(0.002)AMGK;RPAGGRPS(0.964)PS(0.036)AMGK;RPAGGRPS(0.991)PS(0.009)AMGK;RPAGGRPS(0.929)PS(0.071)AMGK;RPAGGRPS(0.927)PS(0.073)AMGK;RPAGGRPS(0.992)PS(0.008)AMGK 118.31 0.00022425 1509790000 2097890 1988579 1981418 2394135 1693523 2153554 2366644 2290887 1982746 TRUE FALSE 1998726.897 2191217.461 2072267.975 2153472.001 1988872.875 2078975.885 2005568.991 2090284.79 2290220.123 0.872722616 0.956771552 0.904833537 0.940290402 0.868419963 0.907762474 0.875710143 0.912700386 1 21.12705484 0.953248057 22.64240207 1 0.905072216 0.530269553 0.02823011 3133.915667 1517786.809 0.026261272 0.006565318 8.979415271 -0.953248057 -0.094927784 RPAPAVS(ph)PGSWKPGPPGS(ph)PRPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(0.994)PGS(0.008)WKPGPPGS(0.997)PRPWK;RPAPAVS(0.999)PGS(0.001)WKPGPPGS(1)PRPWK 112.33 0.0012536 1583930000 1346750 1312250 1228150 1402890 904150 1414520 1566400 1500780 1260310 TRUE FALSE 1283091.797 1445969.767 1284461.892 1261868.832 1061833.474 1365534.818 1327416.911 1369363.747 1455752.438 0.881394228 0.99327999 0.882335388 0.866815537 0.729405252 0.938026811 0.911842478 0.940657018 1 20.4733336 -0.610834786 5.829797705 1.000000001 0.898308365 0.189289112 0.068827505 0 1.71E-10 0.066831981 0.015752449 0.244999509 0.610834786 -0.101691636 RPAPAVSPGSWKPGPPGS(ph)PRPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 RPAPAVSPGSWKPGPPGS(1)PRPWK 85.489 0.0050595 275580000 695680 600260 635870 719680 492610 665980 772830 700410 572140 TRUE FALSE 662796.5851 661427.1764 665025.2685 647336.3991 578521.028 642916.9456 654920.5895 639078.3873 660864.5491 1.002923498 1.00085135 1.006295873 0.979529618 0.875400305 0.972842236 0.991005782 0.967033847 1 19.33399508 3.002940608 21.59812633 0.960527753 1.001527506 0.249918026 0.033254523 23.41436285 171953.0006 0.009669815 0.011467444 1006.793974 -3.002940608 0.040999753 RPAS(ph)PS(ph)SPEHLPATPAESPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.993)PS(0.603)S(0.404)PEHLPATPAESPAQR 131.95 3.97E-05 799060000 378520 351200 357630 383670 462090 366260 397440 381690 414350 TRUE FALSE 360628.1098 386987.6793 374027.6892 345102.7627 542678.3497 353576.3244 336803.2285 348267.2001 478605.2818 0.753497973 0.808573775 0.781495114 0.721059244 1.133874552 0.738763941 0.703718161 0.727671034 1 18.86847679 -2.320440182 2.260674979 2.098466799 0.792848582 0.210287041 0.124049531 8143292.587 980659.2146 45839047.55 0.030174978 0.004781452 2.320440182 -1.305618218 RPAS(ph)PSHNGSSGGGYGASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.869)PS(0.115)HNGS(0.016)SGGGYGASK 250.4 1.67E-25 105650000 70871 77294 68768 87076 67319 74128 78103 81048 71466 TRUE FALSE 67521.06828 85170.34648 71921.08082 78322.95505 79059.41229 71560.92877 66186.95289 73951.00746 82548.58228 0.817955517 1.031760257 0.871257614 0.94881042 0.957731921 0.866894704 0.801793938 0.895848304 1 16.33295582 2.220184232 24.12000723 0.866538743 0.928809405 0.002983676 0.074758277 311.4898595 408843.5625 0.026050283 0.019279649 166.0291071 -2.220184232 0.062270662 RPAS(ph)PSS(ph)PEHLPATPAESPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.756)PS(0.279)S(0.958)PEHLPAT(0.006)PAES(0.001)PAQR;RPAS(0.985)PS(0.462)S(0.553)PEHLPATPAESPAQR;RPAS(0.9)PS(0.395)S(0.677)PEHLPAT(0.029)PAESPAQR;RPAS(0.931)PS(0.289)S(0.779)PEHLPATPAESPAQR 127.44 2.14E-05 2758750000 846593 723647 847459 931560 976320 787071 953650 846640 955610 TRUE FALSE 806576.2267 797387.452 886315.8334 837917.819 1146589.899 759814.5339 808153.1775 772503.7133 1103801.118 0.730726046 0.722401381 0.802966965 0.759120285 1.038764937 0.688361808 0.732154701 0.699857701 1 20.07404882 -2.119404528 2.536155206 1.46778388 0.767097204 0.337762851 0.100230622 16237203.68 2449049.221 44115138.02 0.023189297 0.007596184 2.119404528 -0.700686676 RPAS(ph)PSSPEHLPATPAESPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.943)PS(0.046)S(0.01)PEHLPATPAESPAQR;RPAS(0.911)PS(0.038)S(0.051)PEHLPATPAESPAQR;RPAS(0.895)PS(0.058)S(0.047)PEHLPATPAESPAQR;RPAS(0.986)PS(0.006)S(0.008)PEHLPATPAESPAQR 150.11 3.58E-08 839430000 421717 356047 395187 407079 488750 372942 456275 411315 488320 TRUE FALSE 401783.2732 392328.5941 413306.7148 366158.6455 573987.8453 360026.925 386661.8687 375298.0781 564046.1716 0.712323376 0.695561133 0.732753338 0.649164313 1.017625638 0.638293358 0.68551457 0.665367654 1 19.10545374 -1.784975314 2.815540686 1.06910057 0.721441945 0.390375158 0.108104136 25181974.98 21647036.06 12015208.4 0.024445652 0.01640683 1.784975314 -0.347658625 RPAS(ph)VSSSAAVEHEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RPAS(0.973)VS(0.027)SSAAVEHEQR;RPAS(0.946)VS(0.054)SSAAVEHEQR;RPAS(0.956)VS(0.044)SSAAVEHEQR;RPAS(0.989)VS(0.008)S(0.002)SAAVEHEQR;RPAS(0.942)VS(0.058)SSAAVEHEQR;RPAS(0.991)VS(0.009)SSAAVEHEQR 235.35 6.51E-20 5977890000 644542 544146 546419 642439 594219 552163 633062 580400 553984 TRUE FALSE 614075.777 599595.096 571472.8516 577859.8112 697850.6055 533041.4569 536476.7649 529577.0991 639893.0094 0.95965383 0.937023983 0.893075629 0.903056922 1.090573885 0.833016534 0.8383851 0.82760257 1 19.28747118 RPASEATFNVFYYLLACGDGTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPASEATFNVFYYLLACGDGTLR 23 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 129.23 6.30E-05 26397700 30557.8 29108 22880.5 27173.8 29609.1 27033.4 34846.8 28990.2 27367.3 FALSE TRUE 29113.39335 32074.13829 23929.59356 24442.238 34772.91767 26097.22658 29530.28065 26451.6644 31611.28111 0.920981129 1.014642152 0.756995374 0.77321251 1.100016084 0.825566876 0.934169057 0.83677926 1 14.94815188 3.54475846 0.001289784 1.81741458 3.14E-05 0.006316941 0.11039832 6410532.118 1938.825084 1357749.764 1374188.419 3505.568515 -3.54475846 -1.817383192 RPASPS(ph)HNGSSGGGYGASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.107)PS(0.866)HNGS(0.027)SGGGYGASK 240.26 1.58E-24 103760000 57789 58754 54583 67799 45240 58353 67452 66739 60117 TRUE FALSE 55057.4285 64741.0994 57085.68454 60983.71571 53129.84168 56332.22098 57160.95856 60894.97935 69439.63732 0.792881856 0.93233637 0.822090765 0.878226299 0.765122684 0.811240138 0.823174785 0.876948407 1 16.08347179 0.875059809 3.825623667 0.99996316 0.837020893 0.567791429 0.045951405 0.485955705 13.27003377 0.043619656 0.011183874 7.499974892 -0.875059809 -0.162942267 RPASPS(ph)S(ph)PEHLPATPAESPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.295)PS(0.779)S(0.925)PEHLPATPAESPAQR 119.28 0.00025066 395050000 83903 67399 82169 83658 86591 82213 90616 84036 85921 TRUE FALSE 79937.07147 74267.03473 85936.52993 75248.5389 101692.443 79365.9432 76790.86492 76677.36234 99245.18986 0.805450336 0.748318733 0.865901209 0.758208423 1.024658657 0.799695616 0.773748985 0.772605327 1 16.59870956 -2.495944622 2.24356994 3.418568379 0.813452859 0.333125993 0.080381967 2875137.768 429772.4848 35030389.62 0.01956115 0.003191945 2.495944622 -2.60511552 RPASVSSSAAVEHEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 82.707 0.0060012 18646000 76978 93947 62558 85312 30986 82311 56553 72060 25269 FALSE TRUE 73339.4025 103520.3061 65426.34618 76736.27568 36389.94859 79460.54943 47924.80118 65750.04439 29187.58746 2.512691485 3.546723628 2.24158116 2.629072231 1.246761098 2.722408953 1.641958289 2.25267143 1 14.83306735 2.431362913 0.17339537 0.593728596 3.896969013 0.447673961 0.555765016 4.668082116 0.470717534 2.750995652 5.01711916 269.9994707 -2.431362913 3.303240417 RPATADS(ph)PKPSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RPATADSPKPSAK 13 2 Q03111 Q03111 MLLT1 Protein ENL 1 RPATADS(0.984)PKPS(0.015)AK;RPATADS(0.986)PKPS(0.013)AK;RPATADS(1)PKPSAK;RPATADS(1)PKPSAK;RPAT(0.041)ADS(0.959)PKPSAK;RPATADS(0.996)PKPS(0.004)AK;RPATADS(1)PKPSAK;RPAT(0.006)ADS(0.994)PKPSAK;RPAT(0.015)ADS(0.985)PKPSAK 132.84 5.96E-05 4565490000 8828470 7738380 7516330 9084440 4336260 9391460 9176030 9658140 5002760 TRUE FALSE 8411165.719 8526929.72 7860961.165 8171254.832 5092502.371 9066231.385 7776058.094 8812422.061 5778562.47 1.455580997 1.475614353 1.360366217 1.414063597 0.881274953 1.568942351 1.34567345 1.525019779 1 22.46227921 -2.065631465 2.502245226 0.440736544 1.383080945 0.282163456 0.189500586 8932429.955 1572945.596 28696955.88 0.042442931 0.008597428 2.065631465 0.942344401 RPDADLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPDADLK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;; 118.06 0.0081639 3251080000 4619680 3697720 4007960 5822640 4831820 4809740 5934970 4649160 4531800 FALSE TRUE 4401316.882 4074521.872 4191728.93 5237337.165 5674487.878 4643177.498 5029481.323 4242054.904 5234568.399 0.840817532 0.778387359 0.800778328 1.000528939 1.084041213 0.887022032 0.960820633 0.810392487 1 22.31963916 3.247845904 24.85575025 0.956592808 0.805481872 0.483880945 0.073253761 148.886195 398550.1814 0.019739122 0.026363934 1769.481 -3.247845904 -0.151110936 RPDDVPLSLS(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.002)LS(0.985)PS(0.013)KR;RPDDVPLS(0.006)LS(0.988)PS(0.006)KR;RPDDVPLS(0.002)LS(0.997)PSKR;RPDDVPLS(0.227)LS(0.691)PS(0.082)KR;RPDDVPLS(0.001)LS(0.993)PS(0.006)KR;RPDDVPLS(0.003)LS(0.899)PS(0.098)KR 164.2 2.17E-06 2932850000 1956870 2039580 1813930 2294530 1343382 2220360 2265540 2351490 1652450 TRUE FALSE 1864372.633 2247415.521 1897100.485 2063879.485 1577667.395 2143468.376 1919890.264 2145581.07 1908703.506 0.976774353 1.177456589 0.993920993 1.081299153 0.826564938 1.122997034 1.005860919 1.124103907 1 20.86416158 RPDHSGGS(ph)PS(ph)PPTSEPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 RPDHS(0.089)GGS(0.912)PS(0.98)PPT(0.012)S(0.008)EPAR;RPDHS(0.003)GGS(0.997)PS(0.982)PPT(0.008)S(0.01)EPAR;RPDHS(0.013)GGS(0.987)PS(0.965)PPT(0.019)S(0.016)EPAR;RPDHS(0.009)GGS(0.99)PS(0.847)PPT(0.104)S(0.05)EPAR 141.36 4.22E-07 1981050000 929210 795227 862240 884889 945196 842272 1023785 831155 695750 TRUE FALSE 885288.0848 876261.5354 901774.5569 795938.2765 1110037.883 813103.9094 867587.7951 758374.662 803643.3566 1.101593235 1.090361201 1.122107897 0.990412314 1.38125684 1.011772079 1.079568179 0.943670667 1 19.61619587 1.546097922 2.092602007 0.978165135 1.119175815 0.234489508 0.105464682 0.426244726 3.862758461 0.076693646 0.026569988 35.1639717 -1.546097922 0.14101068 RPDHSGGS(ph)PSPPTSEPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RPDHS(0.147)GGS(0.852)PSPPTSEPAR;RPDHS(0.007)GGS(0.992)PS(0.001)PPTSEPAR;RPDHS(0.012)GGS(0.986)PS(0.002)PPTSEPAR;RPDHS(0.062)GGS(0.937)PS(0.002)PPTSEPAR 185.71 3.17E-14 1116750000 373951 350010 388504 425219 451003 386911 452207 397560 438130 TRUE FALSE 356275.0773 385676.4169 406317.2927 382475.1783 529657.7804 373512.1751 383214.5168 362747.5388 506072.9627 0.70399943 0.762096467 0.80288283 0.75577082 1.046603592 0.738059929 0.757231753 0.716789012 1 18.94898587 -2.590024674 2.121656217 4.894718457 0.781944897 0.325978823 0.09684988 3925455.025 182871.649 74014219.45 0.02405542 0.00257025 2.590024674 -4.11277356 RPDLLTMVVDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPDLLTMVVDYR 12 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;; 164.81 9.03E-05 621530000 1059314 796946 590922 669281 1169145 626495 1172271 866198 1128283 FALSE TRUE 1009242.327 878155.7035 618016.3582 602003.6023 1373043.518 604799.3211 993419.5287 790349.1111 1303251.365 0.774403429 0.673819132 0.474211173 0.461924398 1.053552334 0.464069586 0.762262412 0.606444108 1 20.31368394 -1.741155821 2.589985518 1.071279723 0.665938117 0.259538064 0.180745755 27890974.89 21320466.29 12772427.45 0.043148255 0.018148644 1.741155821 -0.405341606 RPDLYGNLGHPLS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPDLYGNLGHPLS 13 1 Q86X76-2;Q86X76-4;Q86X76 Q86X76-2 NIT1 Nitrilase homolog 1 0 88.706 0.012483 120030000 187670 150360 161760 179670 195560 144180 188150 176370 193750 FALSE TRUE 178799.211 165681.8549 169176.856 161609.2302 229665.6021 139187.0104 159444.2619 160926.1078 223795.7605 0.798939223 0.740326155 0.755943078 0.722128203 1.026228565 0.621937655 0.712454345 0.719075766 1 17.77182318 -2.099595747 2.440476315 1.421587065 0.75911939 0.340524368 0.103957524 13140295.73 2820439.423 30866960.71 0.0246958 0.00795068 2.099595747 -0.662467676 RPDPDS(ph)DEDEDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER 189.34 4.47E-07 7050730000 757310 932474 815903 946104 1269370 783558 843626 732710 1161097 TRUE FALSE 721513.4571 1027494.161 853312.9596 850999.8284 1490747.726 756423.19 714915.3594 668550.0281 1341153.993 0.537979577 0.766126907 0.636252782 0.634528051 1.111541057 0.5640092 0.53305986 0.498488639 1 20.35504347 4.685994456 3.60619776 0.693819484 0.528599619 0.062411852 0.200340652 0.814682638 17.97358703 0.046465132 0.327768358 48528.23047 -4.685994456 -0.165219865 RPDPDS(ph)DEDEDYERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPDPDSDEDEDYERER 16 2 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER 245.06 3.36E-20 9717550000 1314011 1002286 1305516 1356846 1422758 1113158 1537928 1266573 1660117 TRUE FALSE 1251900.304 1104420.083 1365375.2 1220453.262 1670886.545 1074609.059 1303288.838 1155665.154 1917559.466 0.652861268 0.575950891 0.712037996 0.636461755 0.871361006 0.560404555 0.679660194 0.602675001 1 20.87083989 -1.754647411 2.641083865 1.077014072 0.657428645 0.596800131 0.087403415 12115591.22 9378430.171 6083801.969 0.019958131 0.017593514 1.754647411 -0.419585427 RPDQQLQGEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RPDQQLQGEGK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;;;;;; 210.15 2.20E-08 6519450000 4557590 4070570 4057627 4607130 3583132 4377610 5073940 4697860 3984050 FALSE TRUE 4342161.753 4485365.711 4243673.211 4144012.539 4208029.086 4226012.268 4299817.264 4286490.473 4601876.126 0.943563372 0.974681975 0.922161548 0.900505017 0.914415984 0.918323778 0.934361801 0.931465853 1 22.13379072 -1.061380127 4.17982597 1.000007167 0.932780093 0.545834058 0.019935829 3067313.222 778880.5759 223.2882191 0.005402298 0.086820018 1.061380127 -0.067227073 RPDS(ph)PTRPTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPDSPTRPTLR 11 2 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RPDS(0.981)PT(0.013)RPT(0.006)LR;RPDS(0.989)PT(0.004)RPT(0.007)LR;RPDS(0.837)PT(0.157)RPT(0.006)LR;RPDS(0.99)PT(0.009)RPTLR;RPDS(0.966)PT(0.032)RPT(0.003)LR;RPDS(0.992)PT(0.007)RPTLR;RPDS(0.952)PT(0.042)RPT(0.005)LR;RPDS(0.972)PT(0.024)RPT(0.004)LR 113.25 0.0011156 5362440000 2831530 2385380 2396880 2688600 2648680 2563500 2842750 2659800 2920390 TRUE FALSE 2697689.188 2628452.934 2506779.319 2418336.82 3110608.953 2474725.352 2409036.277 2426893.812 3373269.166 0.799725446 0.779200474 0.743130535 0.716911904 0.922134819 0.73362819 0.714154773 0.71944861 1 21.68571601 -1.652816646 2.954662774 1.022007013 0.76639064 0.584920631 0.061937466 39556409.26 42807915.27 6676030.144 0.015002066 0.022242487 1.652816646 -0.255616373 RPDSSDDRYVMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPDSSDDRYVMTK 13 2 Q96KR1;H0Y8W1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 99.927 0.0014827 218870000 211725 201992 213520 254150 218230 226770 263130 254150 223035 FALSE TRUE 201717.1788 222575.2144 223310.1032 228602.3591 256289.2429 218916.898 222984.6858 231895.2787 257622.1287 0.782996321 0.863960001 0.866812585 0.887355292 0.994826198 0.849759682 0.865549427 0.900137266 1 17.97489699 8 0.082792669 1.05615529 0.397005732 0.501063104 0.045946675 168.1404378 1.010740796 1.165482601 12.64494763 100000000 -8 -0.659149558 RPDTTESLNSSLSNGTSDADLFDS(ph)HDDRDDDAEAGSVEEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPDTTESLNSSLSNGTSDADLFDSHDDRDDDAEAGSVEEHK 41 2 Q96SU4-7;Q96SU4-2;Q96SU4;Q96SU4-6;Q96SU4-5;Q96SU4-4;Q96SU4-3 Q96SU4-7 OSBPL9 Oxysterol-binding protein-related protein 9 1 RPDTTESLNSSLSNGTSDADLFDS(1)HDDRDDDAEAGSVEEHK 123.84 5.61E-09 76075000 24964 29754 24588 31197 18853 25644 31587 27487 18078 TRUE FALSE 23784.00119 32785.96643 25715.38412 28061.01829 22140.95723 24755.94185 26767.82301 25080.09256 20881.44391 1.139001752 1.570100543 1.231494538 1.343825571 1.060317348 1.185547415 1.281895214 1.201070801 1 14.34993385 2.76829265 24.10316187 1.176086192 1.337392647 0.280057122 0.133784977 610.8749779 495222.6131 0.039330722 0.041709632 586.5332673 -2.76829265 0.161306456 RPDYAPMES(ph)S(ph)DEEDEEFQFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDYAPMES(1)S(1)DEEDEEFQFIK;RPDY(0.004)APMES(0.998)S(0.998)DEEDEEFQFIK;RPDY(0.011)APMES(0.995)S(0.995)DEEDEEFQFIK;RPDYAPMES(1)S(1)DEEDEEFQFIK 161.49 6.94E-11 184422000 334576 320248 300427 362298 266801 333914 345056 330180 291268 TRUE FALSE 318761.2555 352881.6353 314201.8751 325879.1167 313331.0099 322350.4745 292411.3698 301267.6888 336436.3538 0.947463768 1.04888081 0.933911783 0.968620403 0.931323284 0.958132113 0.869143202 0.895467108 1 18.35997408 2.930033433 1.11436506 0.915261688 0.993071602 0.168778533 0.045903709 0.546941821 1.44414306 0.019808314 0.022323724 851.2035637 -2.930033433 0.077809914 RPDYAPMES(ph)S(ph)DEEDEEFQFIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPDYAPMESSDEEDEEFQFIKK 22 2 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDYAPMES(1)S(1)DEEDEEFQFIKK 72.569 0.010601 84641000 70589 61892 72811 76639 65331 76307 93983 79884 81523 TRUE FALSE 67252.39786 68198.86517 76149.45637 68935.10212 76724.70572 73664.46946 79644.16723 72888.93347 94165.17048 0.714196104 0.724247244 0.808679642 0.732065813 0.814788582 0.782289981 0.845792206 0.77405407 1 16.52290592 -5 0.113850598 1.753735352 0.645503182 0.827301208 0.034238556 54.61265965 0.409502881 9.501750401 0.340215376 1.00E-05 5 -1.10823217 RPEDYEAVFVGNIDDHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPEDYEAVFVGNIDDHFR 18 1 Q68CQ4;H7C2R4 Q68CQ4 DIEXF Digestive organ expansion factor homolog 0 163.53 2.14E-11 28601000 43067 40562 36837 51122 44309 41721 43877 39778 37366 FALSE TRUE 41031.30826 44695.31392 38526.01289 45983.11943 52036.47557 40276.19131 37182.75779 36294.82744 43160.52844 0.950667421 1.035559932 0.892621436 1.065397508 1.20564964 0.933171876 0.861499132 0.840926392 1 15.39742491 2.012116441 24.99888542 0.88839848 1.023105958 0.30922609 0.090044124 252.415552 520786.6085 0.033068264 0.024406275 102.8291963 -2.012116441 0.134707478 RPEGACGDGQSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RPEGACGDGQSSR 13 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ;;;; 148.85 6.60E-05 516290300 224950.5 198190.1 220025.6 233734.5 246447.7 209358.8 243624.6 224401.3 283705.5 FALSE TRUE 214317.5357 218385.8965 230113.9914 210239.064 289428.1009 202108.6523 206455.1928 204751.5325 327701.1 0.654003101 0.666417954 0.702206954 0.641557395 0.883207596 0.616746945 0.63001068 0.624811856 1 18.32202099 -1.111716759 4.195448375 1.000058298 0.674757405 0.632750834 0.077222283 101175.2724 40936681.47 5168.671031 0.017144273 0.077318468 1.111716759 -0.325300893 RPEGACGDGQSSRVS(ph)PPAADVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPEGACGDGQSSRVSPPAADVLK 23 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RPEGACGDGQS(0.171)S(0.171)RVS(0.659)PPAADVLK;RPEGACGDGQS(0.003)S(0.003)RVS(0.994)PPAADVLK;RPEGACGDGQSS(0.001)RVS(0.998)PPAADVLK;RPEGACGDGQSSRVS(1)PPAADVLK;RPEGACGDGQS(0.248)S(0.248)RVS(0.503)PPAADVLK;RPEGACGDGQS(0.109)S(0.109)RVS(0.781)PPAADVLK 186.43 1.43E-17 3981360000 2097258 1957874 1806016 2296076 1462823 2001374 2149605 2197174 1564541 TRUE FALSE 1998124.771 2157383.587 1888823.62 2065270.078 1717938.868 1932065.917 1821643.277 2004777.797 1807162.028 1.105669962 1.193796435 1.045187754 1.142825074 0.950628024 1.069116043 1.008013255 1.109351439 1 20.78529443 3.220848989 1.541663727 1.032778644 1.143848177 0.329534774 0.059206633 0.35412946 1.749377941 0.018043536 0.025718627 1662.834355 -3.220848989 0.111069533 RPEGACGDGQSSRVS(ph)PPAADVLKDFSLAGNFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPEGACGDGQSSRVSPPAADVLKDFSLAGNFSR 33 3 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RPEGACGDGQS(0.114)S(0.026)RVS(0.86)PPAADVLKDFSLAGNFSR;RPEGACGDGQS(0.001)S(0.007)RVS(0.992)PPAADVLKDFSLAGNFSR 171.37 1.30E-14 715790000 552540 308569 589380 481780 572130 525480 760330 599200 742310 TRUE FALSE 526422.5292 340012.5319 616403.656 433350.5591 671909.2909 507282.4958 644327.6941 546730.8714 857423.6436 0.613958494 0.396551383 0.718902098 0.505410088 0.783637465 0.591635768 0.751469474 0.637643801 1 19.70964867 -5 0.104717442 2.301236722 0.35875163 0.576634831 0.10689965 106.5525086 0.75117447 29.66719184 1.372878767 1.00E-05 5 -1.942485093 RPEGPGAQAPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.033)S(0.967)PR;RPEGPGAQAPS(0.149)S(0.851)PR;RPEGPGAQAPS(0.026)S(0.974)PR;RPEGPGAQAPS(0.005)S(0.995)PR;RPEGPGAQAPS(0.038)S(0.962)PR;RPEGPGAQAPS(0.136)S(0.864)PR;RPEGPGAQAPS(0.007)S(0.993)PR;RPEGPGAQAPS(0.039)S(0.961)PR 198.04 2.39E-08 13366709000 7257515 6674141 6945057 8061420 7268413 6503661 7098187 6520014 6538142 TRUE FALSE 6914466.649 7354243.556 7263494.733 7251070.746 8536021.926 6278437.589 6015228.206 5949087.009 7552043.669 0.915575565 0.973808399 0.96179194 0.960146824 1.130292978 0.831356102 0.796503366 0.787745314 1 22.84843568 2.110878925 23.12993996 0.83235549 0.977554963 0.389493488 0.081047289 4.308271217 876.9603741 0.027975575 0.020661334 129.0859351 -2.110878925 0.145199473 RPEILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPEILK 6 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;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 85.359 0.087873 163530000 251610 260370 227740 290700 208340 251870 265700 263280 209790 FALSE TRUE 239716.8939 286901.999 238182.1043 261478.2837 244674.43 243147.6787 225162.5851 240225.8075 242323.1617 0.989244661 1.183964409 0.982911013 1.079047838 1.009703027 1.003402551 0.929183094 0.991344805 1 17.88657278 2.510752798 1.379106229 0.966339075 1.072268407 0.266363403 0.058879091 0.436988076 1.683067195 0.027885562 0.021367563 324.1550546 -2.510752798 0.105929331 RPELEDSTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 213.16 4.39E-08 2859060000 1815190 1572100 1629240 1803100 1900200 1606850 1935640 1771570 2097210 FALSE TRUE 1729389.566 1732298.777 1703942.266 1621848.962 2231594.278 1551204.382 1640322.568 1616441.939 2422434.616 0.71390557 0.715106516 0.703400725 0.669511966 0.921219613 0.640349329 0.677138015 0.667279905 1 21.2080263 -1.014427021 4.367362671 1.000013189 0.712343526 0.574627289 0.077464782 67127243677 57725129.93 9633871.726 0.017408477 0.096732626 1.014427021 -0.287669662 RPELLTHSTTEVTQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RPELLTHSTTEVTQPR 16 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;;; 207.39 1.14E-11 1179979000 623462 573504 580186 661651 662482 551449 704198 637242 686094 FALSE TRUE 593992.1868 631944.7096 606788.102 595140.5844 778018.6511 532352.1829 596759.6616 581441.7122 792489.9534 0.749526457 0.797416683 0.765672927 0.750975557 0.98173945 0.671746286 0.753018583 0.733689695 1 19.59603312 -1.081241769 4.266702559 1.000026715 0.774755936 0.438349984 0.079868055 7268211.845 1841866.24 1827.905602 0.017766606 0.082938892 1.081241769 -0.225270779 RPENSLLEETLHFDHAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPENSLLEETLHFDHAVR 18 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ;; 267.55 1.10E-31 159287000 117834 103743 100945 118791 111774 101270 121510 102456 2291.2 FALSE TRUE 112264.2203 114314.5296 105573.4281 106849.903 131267.3502 97762.99451 102971.4178 93484.40949 2646.507594 42.41976127 43.19448389 39.89160217 40.37392646 49.60021672 36.94037936 38.90841577 35.32368836 1 11.36987408 0.1279662 0.729217517 1.57E-11 42.63394142 0.9434969 3.114972055 0.731469904 0.454095606 4.96005911 1.013515568 1.342660462 -0.1279662 42.63394142 RPES(ph)PSEIS(ph)PIKGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPESPSEISPIKGSVR 16 2 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(0.999)PS(0.043)EIS(0.957)PIKGSVR;RPES(0.983)PS(0.022)EIS(0.994)PIKGS(0.001)VR 109.44 0.00052123 657430000 643730 592930 614460 674810 489400 682780 780960 714260 582930 TRUE FALSE 613302.1586 653350.2411 642633.5988 606976.8167 574751.2051 659135.1574 661810.2087 651715.6079 673327.8072 0.910852266 0.970330104 0.954414168 0.901458116 0.853597904 0.978921634 0.982894515 0.967902411 1 19.36094952 2.052868777 24.99993216 0.981501469 0.924710106 0.491565587 0.03211477 95.74022803 45271.96326 0.012580952 0.009291648 112.9454597 -2.052868777 -0.056791363 RPES(ph)PSEISPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 RPES(0.958)PS(0.042)EISPIK;RPES(0.991)PS(0.009)EISPIK;RPES(0.95)PS(0.05)EISPIK;RPES(0.908)PS(0.092)EISPIK;RPES(0.998)PS(0.002)EISPIK;RPES(0.932)PS(0.068)EISPIK 202.34 8.44E-08 2777280000 3567690 3151995 3054603 3782630 2688270 3439672 3659600 3653170 2997746 TRUE FALSE 3399052.364 3473186.874 3194659.569 3402392.846 3157103.437 3320555.296 3101260.807 3333279.068 3462621.139 0.981641429 1.003051369 0.922613084 0.982606156 0.911766927 0.958971589 0.895639656 0.962646196 1 21.72343311 3.744092986 24.8734838 0.941333093 0.992346402 0.228888205 0.032407676 442.5262383 1989586.661 0.007568493 0.013165802 5547.444758 -3.744092986 0.051013308 RPFDPNDR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 111.61 0.0051325 1694940000 657515 694602 854398 686169 708749 633136 675554 598730 869128 FALSE TRUE 626435.569 765382.7335 893572.9934 617193.9885 832354.6012 611210.3416 572485.8299 546302.0271 1003907.931 0.623997031 0.762403314 0.890094565 0.614791426 0.829114479 0.608831072 0.570257304 0.544175427 1 19.93719553 -1.190004084 4.940111896 1.000031728 0.681641339 0.438683038 0.113587931 3.98E-05 6.52E-06 0.110214665 0.025975261 0.064564816 1.190004084 -0.31839039 RPGAPSLS(ph)PAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPGAPSLSPAPR 12 1 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 1 RPGAPS(0.001)LS(0.999)PAPR;RPGAPS(0.189)LS(0.811)PAPR 113.98 0.00067819 497180000 398120 317370 359100 410050 378660 349770 409130 357200 418070 TRUE FALSE 379301.6566 349710.3638 375565.0902 368830.995 444698.1841 337657.3772 346709.7043 325921.6744 482902.1604 0.785462745 0.724184716 0.777725016 0.763779965 0.920886715 0.699225236 0.717970912 0.674922792 1 18.88137139 -1.574434467 2.986435363 1.013013955 0.756725299 0.560364004 0.067350054 14817448.54 15097239.38 1519424.113 0.015597923 0.026641921 1.574434467 -0.256288657 RPGFS(ph)PTSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.839)PT(0.128)S(0.033)HR 64.313 0.044649 153710000 86918 105950 84461 92251 92413 106650 100620 94981 93495 TRUE FALSE 82809.55839 116746.4255 88333.62039 82977.75421 108529.7979 102956.6838 85268.57099 86663.96011 107993.7271 0.766799708 1.081048211 0.817951401 0.768357167 1.004963907 0.953358001 0.789569666 0.802490686 1 16.72058799 1.742186253 25 0.843719782 0.905594656 0.007534613 0.114394359 2.005264505 13899.11644 0.050662288 0.028094798 55.23142556 -1.742186253 0.061874875 RPGHGS(ph)LTNISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPGHGSLTNISR 12 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 RPGHGS(0.993)LT(0.007)NISR 127.94 0.00015975 121990000 59116 59956 58565 60352 61201 60448 65527 58644 61833 TRUE FALSE 56321.70384 66065.58456 61250.26318 54285.3023 71874.43502 58354.6706 55529.65266 53508.82047 71421.74584 0.788579209 0.925006576 0.857585634 0.760066863 1.006338254 0.817043464 0.777489433 0.749195078 1 16.12407578 2.041378495 24.99992553 0.812444241 0.86691421 0.000362594 0.094782204 386.8001994 233694.0548 0.032144753 0.023740457 109.996406 -2.041378495 0.054469969 RPGQSFHVNSEVNSVLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPGQSFHVNSEVNSVLSPR 19 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 RPGQSFHVNSEVNSVLS(1)PR;RPGQSFHVNSEVNSVLS(1)PR;RPGQSFHVNSEVNSVLS(1)PR;RPGQSFHVNSEVNSVLS(1)PR 234.15 1.86E-24 1593820000 707962 667448 660676 763587 828091 713239 884352 855525 848860 TRUE FALSE 674498.0393 735461.71 690968.6481 686829.784 972509.8082 688539.3546 749427.8602 780610.6956 980496.8734 0.687914523 0.750090826 0.70471275 0.70049156 0.991854064 0.702235135 0.764334778 0.796137873 1 19.9031535 -4.999999996 0.149857598 1.862499155 0.680665022 0.468980715 0.084328954 119.0413499 1.059839253 30.60288287 0.404453769 1.00E-05 4.999999996 -1.181834133 RPGRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;RPGRS(1)PK 98.033 0.0091041 5669550000 4377930 4139270 3418540 4708560 2308309 4200370 4054460 4307050 2579822 TRUE FALSE 4170993.925 4561066.319 3575283.44 4235246.603 2710877.359 4054910.134 3435877.662 3929901.869 2979887.62 1.399715176 1.530616889 1.19980479 1.421277291 0.909724696 1.360759415 1.153022563 1.318808751 1 21.50682649 3.455332498 1.586884606 1.185198974 1.463074115 0.314372648 0.160346025 0.388097766 1.981061129 0.045139366 0.078498696 2853.20186 -3.455332498 0.277875141 RPGS(ph)VSSTDQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RPGS(0.983)VS(0.009)S(0.004)T(0.004)DQER;RPGS(0.567)VS(0.144)S(0.144)T(0.144)DQER;RPGS(0.776)VS(0.07)S(0.125)T(0.028)DQER;RPGS(0.964)VS(0.003)S(0.003)T(0.031)DQER;RPGS(0.877)VS(0.051)S(0.051)T(0.02)DQER;RPGS(0.984)VS(0.014)S(0.001)TDQER 135.57 7.68E-05 914235000 758212 552606 660872 761689 776574 652551 789467 695653 773797 TRUE FALSE 722372.8214 608917.1797 691173.6349 685122.5746 912008.2597 629952.9952 669019.3096 634737.9354 893793.4868 0.808209986 0.681272787 0.773303504 0.766533416 1.020379174 0.704808219 0.748516653 0.710161737 1 19.76958201 -2.194235626 2.361024796 1.655801836 0.771903189 0.355217033 0.094377398 8188998.709 1953737.393 28640932.97 0.022412967 0.006393878 2.194235626 -0.883898647 RPGTQGHLGPEKEEEES(ph)DGEPEDSSTS ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPGTQGHLGPEKEEEESDGEPEDSSTS 27 2 Q8IYB7;H7C1Q8 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 RPGTQGHLGPEKEEEES(0.956)DGEPEDS(0.01)S(0.01)T(0.012)S(0.012);RPGTQGHLGPEKEEEES(0.724)DGEPEDS(0.055)S(0.065)T(0.078)S(0.078);RPGTQGHLGPEKEEEES(0.911)DGEPEDS(0.018)S(0.03)T(0.019)S(0.022);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.91)DGEPEDS(0.02)S(0.023)T(0.023)S(0.023) 164.85 5.30E-12 3052632000 2477698 2339279 2353477 2666182 1551541 2710050 2723370 2722880 1414181 TRUE FALSE 2360582.126 2577654.19 2461386.248 2398172.32 1822129.259 2616200.289 2307869.888 2484450.192 1633484.967 1.445120202 1.578009129 1.506831283 1.468132471 1.115485784 1.601606591 1.4128504 1.520950754 1 20.63952175 -1.99234054 2.867733851 0.561830454 1.461005918 0.534089931 0.133814927 25900381.77 24005678.18 75122608.06 0.030253162 0.01017793 1.99234054 0.899175464 RPHS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 119.22 0.0029584 3121520000 3125810 2792530 2574830 3301980 1932699 3084600 3075800 3155080 1990209 TRUE FALSE 2978059.156 3077091.982 2692888.502 2970058.697 2269761.094 2977779.529 2606530.219 2878804.469 2298840.447 1.29546144 1.338540909 1.171411659 1.291981225 0.987350426 1.295339802 1.13384564 1.252285461 1 21.13247491 7.999999974 0.025793725 3.30E-07 2.880218982 0.368201876 0.098737781 1702.278248 3.375752069 128.0154677 274.5805461 99999994.02 -7.999999974 2.880218651 RPHS(ph)PEKAFSSNPVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPHSPEKAFSSNPVVR 16 2 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 RPHS(1)PEKAFSSNPVVR 85.224 0.003768 208380000 271990 100650 317980 196070 323150 281650 457300 291860 366990 TRUE FALSE 259133.5717 110906.3494 332559.6975 176360.6711 379507.2577 271896.3899 387530.4861 266303.1912 423900.9349 0.611306913 0.261632708 0.784522208 0.416042185 0.895273462 0.641414933 0.914200593 0.628220344 1 18.69336762 2.869183647 0.964801043 0.829239956 0.458099678 0.350792508 0.183734256 0.503082918 1.011498168 0.086689057 0.092227481 739.9180934 -2.869183647 -0.371140278 RPHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.656)PT(0.344)PGIYMGR;RPHT(0.992)PT(0.008)PGIYMGR;RPHT(0.998)PT(0.002)PGIYMGR;RPHT(0.901)PT(0.099)PGIYMGR;RPHT(0.909)PT(0.091)PGIYMGR;RPHT(0.897)PT(0.103)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.98)PT(0.02)PGIYMGR;RPHT(0.955)PT(0.045)PGIYMGR;RPHT(0.962)PT(0.038)PGIYMGR;RPHT(0.955)PT(0.045)PGIYMGR;RPHT(0.929)PT(0.071)PGIYMGR;RPHT(0.932)PT(0.068)PGIYMGR;RPHT(0.961)PT(0.039)PGIYMGR;RPHT(0.999)PT(0.001)PGIYMGR;RPHT(0.996)PT(0.004)PGIYMGR 178 8.77E-06 22253310000 2757812 3128747 2088464 3095686 2374823 2366919 2332054 2517547 1936685 TRUE FALSE 2627455.692 3447569.876 2184222.14 2784501.762 2788991.379 2284952.002 1976256.331 2297097.238 2237016.219 1.174535826 1.541146572 0.976399778 1.244739193 1.24674616 1.021428447 0.883434065 1.026857659 1 21.09314429 2.189501271 3.665043942 0.955976219 1.263399305 0.438568274 0.141551888 0.189945938 5.260701209 0.05605939 0.040857231 154.7039031 -2.189501271 0.307423086 RPILQLS(ph)PPGPR ddPTM_SK-BR-3_Trastuzumab_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 142.03 3.74E-05 3718270000 1683200 1347599 1460862 1619360 1782700 1493870 1901700 1589790 1809170 TRUE FALSE 1603638.472 1484920.87 1527843.968 1456578.856 2093602.316 1442136.907 1611560.738 1450579.56 2089726.844 0.76739143 0.710581325 0.731121377 0.697018781 1.001854535 0.690107854 0.771182484 0.694147928 1 20.99488294 -1.623894626 2.913978814 1.019457048 0.756940463 0.409468409 0.091354538 39960005.58 42683905.32 5943649.726 0.020768121 0.023774171 1.623894626 -0.262516585 RPIVACELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPIVACELGR 10 1 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 148.28 4.07E-05 362880000 235773 203904 170181 196694 326560 187786 256688 219777 313080 FALSE TRUE 224628.4775 224682.0494 177983.9672 176921.9454 383511.9606 181282.9237 217525.5312 200532.1608 361630.8474 0.621154083 0.621302223 0.492170313 0.489233556 1.060506766 0.501292755 0.601512655 0.554521723 1 18.46415822 -1.530914633 2.927024522 1.016156146 0.617470235 0.345425302 0.165384639 37668812.32 42147938.89 4850650.323 0.040074436 0.029450005 1.530914633 -0.398685911 RPIVEFSLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPIVEFSLEDR 11 1 Q9NW13;Q9NW13-2 Q9NW13 RBM28 RNA-binding protein 28 0 111.79 0.0025856 41481000 47325 58686 43430 43317 43672 41535 39757 45500 45670 FALSE TRUE 45088.04104 64666.17012 45421.30846 38962.69286 51288.38297 40096.63254 33691.33946 41515.77879 52752.27035 0.854712806 1.225846199 0.8610304 0.738597459 0.972249775 0.760093021 0.63867089 0.78699511 1 15.68694557 3.502355645 16.3693567 0.791603463 1.040811343 0.294596033 0.138301171 9.689071702 6283.904766 0.035820142 0.054759957 3179.476685 -3.502355645 0.249207881 RPKEEDPATGTGDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPKEEDPATGTGDPPR 16 2 P45974-2;P45974;F5H571 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 79.317 0.01051 227552000 708820 519788 702580 701060 644220 703270 854770 753700 781530 FALSE TRUE 675315.4833 572754.9881 734793.9879 630588.1169 756571.764 678915.5836 724359.1376 687702.0324 902725.6809 0.748084936 0.634472908 0.81397262 0.698537917 0.838097088 0.75207297 0.80241335 0.761806213 1 19.78392812 -5 0.143820155 1.890797508 0.662367791 0.669420336 0.055307588 71.40563228 0.621862106 18.12688856 0.282717024 1.00E-05 5 -1.228429717 RPKS(ph)ESQGNATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPKSESQGNATK 12 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 RPKS(0.993)ES(0.007)QGNATK;RPKS(0.977)ES(0.023)QGNATK 88.385 0.0078877 52629000 67289 48462 59208 75498 48745 80512 94582 79151 62375 TRUE FALSE 64108.38232 53400.3329 61922.74536 67908.7976 57246.11257 77723.84925 80151.77878 72220.11883 72047.79643 0.889803512 0.741179266 0.859467582 0.942552041 0.794557438 1.078781768 1.112480641 1.002391779 1 16.13666669 2.233656668 24.99996388 1.064396832 0.840356536 0.71674754 0.062980093 58.94857056 300512.0083 0.022898749 0.017450402 171.2602871 -2.233656668 -0.224040295 RPLDDGVGNQLGALVHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPLDDGVGNQLGALVHQR 18 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 77.357 0.0089005 161310000 223100 203160 216450 211660 179240 228840 276960 235810 123340 FALSE TRUE 212554.5051 223862.235 226374.4466 190383.5347 210499.3993 220915.2134 234704.6653 215161.2263 142466.9373 1.491956725 1.571327631 1.588961277 1.33633486 1.477531582 1.550641978 1.647432519 1.51025375 1 17.12026762 0.939697336 23.12504239 1 1.530825929 0.79805159 0.082453864 6086.569953 2334098.069 0.081725239 0.02043131 8.703568178 -0.939697336 0.530825929 RPLDS(ph)PEAEELPAMK ddPTM_SK-BR-3_Trastuzumab_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 176.46 4.89E-07 376366000 1014930 870130 838410 1092720 838210 947840 1122660 1086370 943460 TRUE FALSE 966956.2703 958797.2363 876851.9278 982877.7096 984393.5586 915016.0631 951377.5979 991241.6836 1089766.958 0.88730555 0.879818597 0.804623338 0.901915499 0.903306483 0.839643794 0.873010134 0.90959051 1 20.05558822 0.871499134 2.587847604 0.999865151 0.870662783 0.663643386 0.029327738 0.294171039 3.93667835 0.026735204 0.007140319 7.438735796 -0.871499134 -0.129202368 RPLEDGDQPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPLEDGDQPDAK 12 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 135.65 0.0001987 257290000 678720 608930 605870 721420 481700 668250 734490 703230 526770 FALSE TRUE 646638.2507 670980.6593 633649.7388 648901.491 565708.3275 645108.3349 622430.0607 641651.4531 608458.8012 1.062747797 1.102754464 1.041401221 1.066467425 0.92973974 1.060233386 1.022961718 1.054552012 1 19.21480006 3.273140196 2.191115242 1.019661357 1.080423979 0.285381432 0.039636602 0.345523535 3.399803773 0.011323935 0.015786188 1875.59988 -3.273140196 0.060762622 RPLEEDFRRS(ph)PTEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.984)PT(0.016)EDFR;RPLEEDFRRS(0.995)PT(0.005)EDFR;RPLEEDFRRS(0.996)PT(0.004)EDFR;RPLEEDFRRS(0.994)PT(0.006)EDFR;RPLEEDFRRS(0.873)PT(0.127)EDFR 175.52 1.93E-08 2376830000 1627140 1110561 1520880 1549700 1885140 1407570 1905380 1682500 2212660 TRUE FALSE 1550228.317 1223728.429 1590613.852 1393921.212 2213907.819 1358825.498 1614679.286 1535171.381 2555788.012 0.606555907 0.478806702 0.622357506 0.545397821 0.866232962 0.531665964 0.631773558 0.600664599 1 21.28533675 -5 0.238207782 3.238552445 0.561168787 0.588697375 0.102256077 113.1931421 1.129414282 122.6918244 0.152570244 1.00E-05 5 -2.677383659 RPLEMEQQQAYRPEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 157.11 5.52E-08 187230000 140800 131930 136550 152210 125360 133440 147230 144950 120060 FALSE TRUE 134144.663 145373.817 142810.9526 136909.5616 147222.7443 128818.9393 124767.3594 132257.4096 138678.2916 0.967308304 1.048280991 1.029800345 0.987245805 1.061613484 0.928904862 0.899689187 0.953699444 1 17.08138244 2.2204243 24.97218375 0.932896814 1.017238749 0.473521125 0.037323558 171.3503255 235933.5133 0.013016626 0.009631657 166.1209095 -2.2204243 0.084341935 RPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_SK-BR-3_Trastuzumab_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 218.55 1.97E-32 448513000 238914 107873.7 191889 238514 427253 202558 418376 241159 475250 TRUE FALSE 227621.0087 118866.1527 200687.3005 214538.1196 501765.7879 195543.3657 354545.0572 220041.8395 548949.3428 0.414648477 0.216533919 0.365584371 0.390815878 0.914047525 0.356213862 0.645861156 0.400841794 1 19.0663135 -4.999999982 0.092831703 2.768645519 0.02178596 0.477739086 0.184435163 161.7789631 1.037586572 56.27098458 3.645292041 1.00E-05 4.999999982 -2.746859559 RPLHSAQAVDVASASNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPLHSAQAVDVASASNFR 18 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 156.22 8.56E-09 729380000 597290 504450 550790 595620 678260 522270 764580 640040 752820 FALSE TRUE 569057.2854 555854.0285 576044.2663 535747.146 796548.3293 504183.6589 647929.2785 583994.7045 869563.4807 0.654417185 0.639233409 0.662452229 0.616110448 0.916032408 0.579812366 0.745120158 0.671595251 1 19.72993183 -5 0.228277243 2.687733861 0.645965069 0.540479456 0.091613239 114.0052888 1.140411428 88.81389707 0.143288497 1.00E-05 5 -2.041768792 RPLLAFACDDKDGKYDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPLLAFACDDKDGKYDSSR 19 3 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 91.637 0.0008957 150690000 132450 102480 126870 140550 125920 153290 178840 165610 128080 FALSE TRUE 126189.351 112922.8285 132687.115 126421.647 147880.4081 147981.5289 151554.6734 151108.3104 147941.9923 0.852965065 0.763291252 0.89688609 0.854535248 0.999583728 1.000267244 1.024419579 1.02140243 1 17.17467208 2.857799161 1.408859861 1.019453854 0.815326419 0.852039034 0.034466274 0.12375793 0.501504781 0.01289009 0.013609412 720.7740804 -2.857799161 -0.204127435 RPLS(ph)ASLGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.574)AS(0.426)LGQLNEVGLPSAAILPDEGAVDLPSR 128.65 6.35E-08 62599000 28192 30742 24929 30365 30756 27131 27139 30428 30178 TRUE FALSE 26859.42003 33874.64475 26072.01931 27312.65251 36119.83666 26191.44667 22998.44711 27763.56301 34857.85011 0.770541498 0.971793861 0.747952591 0.783543805 1.036203798 0.751378716 0.659778128 0.7964795 1 15.08919597 RPLS(ph)GPDVGTPQPAGLASGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPLSGPDVGTPQPAGLASGAK 21 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RPLS(1)GPDVGTPQPAGLASGAK 282.58 2.61E-45 315130000 198930 196490 174630 251140 181920 214390 227330 237250 181150 TRUE FALSE 189526.9731 216512.5544 182636.9582 225894.9301 213646.7904 206965.6205 192646.6333 216475.1323 209241.8168 0.905779619 1.034748014 0.872851139 1.079587883 1.021052071 0.989121695 0.920688972 1.034569168 1 17.67481168 4.708610742 3.945014434 0.987956825 0.900624951 0.172304296 0.059430213 0.396890169 11.52658061 0.013348309 0.092588221 51122.34212 -4.708610742 -0.087331874 RPLS(ph)SSHEASEGQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.705)S(0.176)S(0.088)HEAS(0.031)EGQAK;RPLS(0.331)S(0.331)S(0.331)HEAS(0.006)EGQAK 181.54 3.58E-07 368170000 275231 248979 241821 290370 213568 255299 278559 318678 226571 TRUE FALSE 262221.3761 274350.2432 252908.732 261181.4559 250814.1916 246457.9316 236059.7085 290772.8649 261706.4735 1.001967481 1.048312789 0.966383172 0.997993869 0.958379776 0.941734181 0.902001793 1.111064854 1 17.99759009 3.725765563 23.85887621 0.971409702 1.025140135 0.065586269 0.055772125 705.9540062 1316389.008 0.014134477 0.022084625 5318.210983 -3.725765563 0.053730433 RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.234)AS(0.766)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.214)AS(0.786)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.24)AS(0.76)LGQLNEVGLPSAAILPDEGAVDLPSR 189.94 3.92E-20 504293000 238191 222595 229946 250311 263070 221384 239146 251704 264851 TRUE FALSE 226932.1835 245277.6836 240489.2515 225149.2627 308949.3247 213717.4166 202659.8855 229663.4634 305922.7404 0.741795733 0.801763489 0.786111066 0.735967723 1.009893296 0.698599314 0.662454466 0.750723739 1 18.22280783 -2.416278084 2.276346742 3.046860976 0.76907821 0.368758436 0.093013605 3588583.668 419876.2063 38017942.22 0.022236304 0.003834616 2.416278084 -2.277782765 RPMEEDGEEKS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_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(0.971)PS(0.029)K;RPMEEDGEEKS(0.748)PS(0.252)K;RPMEEDGEEKS(0.967)PS(0.033)K;RPMEEDGEEKS(0.998)PS(0.002)K;RPMEEDGEEKS(0.869)PS(0.131)K;RPMEEDGEEKS(0.975)PS(0.025)K;RPMEEDGEEKS(0.843)PS(0.157)K;RPMEEDGEEKS(0.947)PS(0.053)K;RPMEEDGEEKS(0.998)PS(0.002)K;RPMEEDGEEKS(0.659)PS(0.341)K;RPMEEDGEEKS(0.951)PS(0.049)K;RPMEEDGEEKS(0.725)PS(0.275)K;RPMEEDGEEKS(0.956)PS(0.044)K 219.23 2.66E-12 16425831000 7878480 7943650 6734910 8686500 3505166 9196910 8058940 9251940 3590850 TRUE FALSE 7506079.864 8753116.966 7043712.285 7813316.517 4116465.841 8878418.701 6829400.69 8441791.086 4147700.678 1.809696612 2.11035406 1.698220974 1.883770581 0.992469361 2.140563987 1.646550998 2.035294188 1 21.98388035 3.466108965 2.493247805 1.653352566 1.955397382 0.105351556 0.387961164 0.626073366 7.817505493 0.10220301 0.158797604 2924.886144 -3.466108965 0.302044816 RPMEEDGEEKS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.997)PS(0.003)KK;RPMEEDGEEKS(0.98)PS(0.02)KK;RPMEEDGEEKS(0.962)PS(0.038)KK 134.32 2.56E-05 1156450000 1464150 1547270 1353320 1653090 523379 1822550 1549140 1750640 558081 TRUE FALSE 1394942.531 1704938.572 1415371.061 1486918.253 614656.1319 1759434.637 1312790.241 1597344.681 644625.3512 2.163958536 2.64485188 2.195649082 2.30663943 0.95350909 2.729391007 2.03651662 2.477942696 1 19.2981014 2.967370339 24.93197957 1.951880301 2.361134293 0.136696044 0.57135398 1354.403961 1034886.056 0.1597955 0.169623669 927.6205027 -2.967370339 0.409253992 RPMEEDGEEKSPS(ph)K ddPTM_SK-BR-3_Trastuzumab_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 1 RPMEEDGEEKS(0.45)PS(0.55)K;RPMEEDGEEKS(0.379)PS(0.621)K;RPMEEDGEEKS(0.306)PS(0.694)K 88.551 0.003954 4331690000 1294030 1250020 1050400 1385520 533972 1423630 1301280 1446290 531535 TRUE FALSE 1232863.766 1377398.459 1098561.879 1246244.897 627096.5477 1374329.336 1102745.836 1319645.18 613962.7331 2.008043322 2.243456133 1.78929733 2.029838018 1.021391876 2.238457258 1.796112006 2.149389709 1 19.22779156 3.554610435 2.574189683 1.754260511 2.123665446 0.128962501 0.423458794 0.559552199 7.267863276 0.109582303 0.180042546 3586.001235 -3.554610435 0.369404935 RPMEEDGEEKSPS(ph)KK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.452)PS(0.548)KK 78.917 0.015337 558810000 580690 576550 524810 631440 226050 688940 600470 729200 242590 TRUE FALSE 553241.9345 635301.1005 548873.0576 567966.4515 265473.0484 665081.8351 508857.2731 665347.3823 280209.6182 1.974385954 2.267235167 1.958794495 2.026934176 0.947408765 2.373515368 1.815987889 2.374463041 1 18.09614695 2.974442489 24.98431321 1.780435591 2.083591041 0.107432909 0.479596439 1828.630261 1787619.321 0.133765095 0.142406587 942.8497465 -2.974442489 0.30315545 RPMEEDGEEKSPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 50.653 0.096043 46630000 44997 38372 52071 48004 71437 44723 58752 49608 74318 FALSE TRUE 42870.08099 42282.15043 54458.50686 43178.54672 83895.59018 43174.2313 49788.30335 45264.06053 85842.85588 0.499401849 0.492552933 0.63439766 0.502995226 0.977315926 0.502944955 0.579993557 0.527289779 1 16.38941045 -5 0.273313218 3.888450933 0.552513889 0.430271223 0.14639955 203.9524086 1.971337771 333.6878861 0.166987065 1.00E-05 5 -3.335937044 RPMS(ph)DPSWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 1 RPMS(0.998)DPS(0.002)WNR;RPMS(0.955)DPS(0.045)WNR;RPMS(0.998)DPS(0.002)WNR 82.515 0.010891 354700000 452310 437590 391040 512170 449620 436410 459770 437180 414970 TRUE FALSE 430930.2027 482180.9185 408969.5708 460685.6985 528033.5856 421297.0123 389623.6422 398898.2016 479321.4282 0.899042224 1.005965705 0.853226137 0.9611206 1.101627331 0.878944665 0.812865062 0.832214414 1 18.87063391 2.023119487 24.99763906 0.85715143 0.961410275 0.183537779 0.081805002 287.2273236 310559.4662 0.028612243 0.021130346 105.4677028 -2.023119487 0.104258845 RPNEDS(ph)DEDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPNEDSDEDEEK 12 1 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK 202.33 8.45E-08 573640000 666380 783510 600090 779650 378650 781710 654040 733150 365970 TRUE FALSE 634881.538 863350.5598 627604.7201 701278.1008 444686.4401 754639.1867 554254.1857 668951.4993 422722.7585 1.501886343 2.042356468 1.484672182 1.658955158 1.051957651 1.785187032 1.311152936 1.582482811 1 18.68935226 -1.967975882 0.105898605 1.20E-10 2.057648631 0.329082203 0.258078085 72.34126094 1.100685742 22.39477151 4.274732124 0.01076525 1.967975882 2.057648631 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;RPNEDS(1)DEDEEKGAVVPPVHDIYR 231.93 4.04E-34 16150560000 7479630 6229740 6783570 7440750 4713695 7678160 8165260 8181400 5438310 TRUE FALSE 7126082.713 6864557.589 7094603.394 6692791.673 5535761.916 7412263.394 6919499.622 7464993.244 6281655.34 1.134427524 1.09279437 1.129416214 1.065450317 0.881258461 1.179985687 1.101540796 1.188379948 1 22.58271336 -1.263069183 5.299182222 0.999988018 1.096304267 0.112864515 0.085157828 1.14E-05 1.58E-06 0.077896155 0.018358016 0.054567093 1.263069183 0.096316249 RPNKPLFTALVTQCQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPNKPLFTALVTQCQK 16 2 Q8NCW5-2;Q8NCW5;Q5T3I4;Q5T3I3 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 122.27 5.30E-05 538760000 1447100 1158700 1242700 1333700 1077900 1345900 1572100 1481900 1293900 FALSE TRUE 1378698.451 1276772.847 1299679.024 1199633.942 1265885.419 1299291.146 1332247.271 1352136.98 1494551.404 0.922483126 0.854285001 0.869611457 0.802671584 0.847000254 0.869351929 0.891402777 0.904710923 1 20.51128109 0.788644489 1.116646484 0.999436733 0.862869183 0.683995246 0.029452325 0.495299402 1.142802899 0.029284944 0.00920159 6.146734988 -0.788644489 -0.136567551 RPNKQEESES(ph)PVERPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.173)ES(0.827)PVERPLK;RPNKQEES(0.015)ES(0.985)PVERPLK;RPNKQEES(0.006)ES(0.994)PVERPLK;RPNKQEES(0.032)ES(0.968)PVERPLK 231.37 2.69E-15 686010000 630219 679150 486550 722350 359383 657340 611840 684580 367915 TRUE FALSE 600429.7968 748356.1571 508858.7988 649738.0056 422059.2814 634576.151 518492.5708 624634.546 424969.3792 1.412877789 1.760964893 1.197401092 1.528905464 0.993152218 1.493227941 1.220070424 1.469834244 1 18.69699937 7.999932662 0.038476913 2.18E-08 3.583561033 0.259308431 0.208679844 917.9705236 2.693216635 70.29752892 218.649322 99984496.02 -7.999932662 3.583561011 RPNPDILDHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPNPDILDHER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;; 153.38 2.11E-05 350083000 425650 360822 384200 417460 464250 370674 468640 389650 425980 FALSE TRUE 405530.3681 397590.172 401815.95 375496.1277 545215.053 357837.4664 397140.3608 355530.1803 492038.8028 0.824183714 0.808046377 0.81663468 0.763143324 1.108073286 0.727254567 0.807132199 0.722565331 1 18.90841257 2.667255098 0.012345361 1.662913025 2.66E-06 0.070581129 0.117079775 6034.733317 30.80136575 2007.760272 2138.161342 464.7882043 -2.667255098 -1.662910361 RPNT(ph)SPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.5)S(0.5)PDR;RPNT(0.5)S(0.5)PDR 96.24 0.0053218 736930000 483620 485420 404320 511550 418500 388330 417820 402420 366940 TRUE FALSE 460760.241 534884.8499 422858.4719 460128.0221 491486.2675 374882.0347 354073.8852 367181.9714 423843.1811 1.087100752 1.261987626 0.997676713 1.085609118 1.159594608 0.884482873 0.835388891 0.866315628 1 18.69317105 2.233153551 24.65188845 0.877805345 1.128152587 0.656155003 0.079110944 60.01038041 273595.8291 0.028577304 0.021726098 171.0620023 -2.233153551 0.250347241 RPNTS(ph)PDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.274)S(0.726)PDR 92.112 0.0073557 1173800000 311030 311200 271290 331930 273510 268490 266200 268520 213630 TRUE FALSE 296328.2283 342911.6338 283728.9148 298563.7658 321210.0574 259192.124 225586.3009 245006.9653 246758.6493 1.200882843 1.38966409 1.149823585 1.209942454 1.301717521 1.050387189 0.914198151 0.992901225 1 17.91274113 2.105921423 4.147892378 0.963810293 1.258135111 0.786621723 0.068368194 0.091449994 2.867011992 0.027063578 0.019201264 127.6207882 -2.105921423 0.294324818 RPNTS(ph)PDRGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.406)S(0.594)PDRGSR;RPNT(0.443)S(0.555)PDRGS(0.002)R;RPNT(0.13)S(0.863)PDRGS(0.007)R 84.566 0.0082786 162832700 63198.8 47205.7 69598.8 59015.2 104915 60516.4 79758.7 70751.6 119365 TRUE FALSE 60211.51797 52016.0145 72789.97382 53082.87997 123212.1428 58420.70189 67590.04545 64556.21483 137875.5146 0.436709289 0.377267963 0.527939816 0.385005852 0.893647746 0.423720645 0.490225155 0.468221026 1 17.07300674 -5 0.253981534 4.13547769 0.446592681 0.527125645 0.147997189 144.6633103 1.428864724 236.260748 0.194794791 1.00E-05 5 -3.688885009 RPNTSPDRGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.004)S(0.013)PDRGS(0.983)R;RPNT(0.147)S(0.005)PDRGS(0.848)R 127.32 0.00022764 1547160000 471290 265693 451030 357710 524440 413850 570330 446660 639280 TRUE FALSE 449013.0557 292767.4188 471710.1716 321752.3112 615902.17 399518.2707 483315.6837 407548.0825 738416.2774 0.608075783 0.39648018 0.638813344 0.435732961 0.83408531 0.541047486 0.654530105 0.551921856 1 19.49407483 -4.999999995 0.188277342 2.819636913 0.494262264 0.543418611 0.120449937 94.01834441 0.917261917 64.05312144 0.298888258 1.00E-05 4.999999995 -2.325374649 RPNWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPNWSK 6 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 92.822 0.074269 940810000 1598460 1398720 1361220 1550120 1515500 1382950 1671020 1681330 1568550 FALSE TRUE 1522903.964 1541251.158 1423633.283 1394298.993 1779802.72 1335058.095 1416075.209 1534103.832 1811792.723 0.840550878 0.850677419 0.785759467 0.769568712 0.982343453 0.73687132 0.781587866 0.846732528 1 20.78898648 -2.079099009 1.6296952 1.238750123 0.822565078 0.40431408 0.067009685 232863.7904 52732.85067 206335.017 0.017140081 0.008334911 2.079099009 -0.416185044 RPPDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RPPDEQR 7 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;;;;;; 143.61 0.0038644 2068150000 494953 428689 454189 519794 600981 440132 557450 497080 676314 FALSE TRUE 471557.5526 472372.8965 475014.0149 467543.3196 705791.8961 424890.1185 472400.7642 453553.04 781193.321 0.603637461 0.604681177 0.608062053 0.59849887 0.903479174 0.543898811 0.60471685 0.580590013 1 19.57532009 -1.142406708 4.718077875 1.000033462 0.627824781 0.578469461 0.09897544 3.26E-05 5.93E-06 0.089761983 0.021155203 0.072043249 1.142406708 -0.372208681 RPPEEDFRHS(ph)PEEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPPEEDFRHSPEEDFR 16 2 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR;RPPEEDFRHS(1)PEEDFR 182.22 1.14E-09 1340360000 1077370 955110 995180 1130220 1170010 983860 1166020 1011890 946510 TRUE FALSE 1026444.855 1052436.795 1040809.987 1016608.138 1374059.374 949788.6815 988122.2336 923283.5472 1093289.937 0.938858779 0.962632838 0.951998141 0.929861425 1.256811508 0.868743642 0.90380621 0.844500179 1 20.06024462 RPPEEDFRHS(ph)PEEDFRQS(ph)PQEHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPEEDFRHSPEEDFRQSPQEHFR 24 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 2 RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR 118.86 0.00021492 264960000 76232 64536 64250 73420 90151 67962 73206 69627 53326 TRUE FALSE 72628.66444 71112.29177 67195.92605 66039.68211 105873.3059 65608.4589 62037.08018 63530.09076 61595.52373 1.179122443 1.154504215 1.090922229 1.072150671 1.718847401 1.065149786 1.007168645 1.031407591 1 15.91053789 2.021755918 24.99997631 1.019280876 1.225644465 0.264317344 0.180385486 340.6993653 391499.8731 0.065956538 0.048708836 105.1370816 -2.021755918 0.206363589 RPPES(ph)PPIVEEWNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 196.43 5.47E-09 1543250000 300114 271149 258712 298519 303527 270289 307924 293151 330874 TRUE FALSE 285928.206 298779.3914 270574.2011 268511.303 356462.0127 260928.8242 260944.5384 267481.1443 382184.25 0.748142306 0.781767933 0.707967953 0.702570299 0.932696762 0.682730448 0.682771565 0.699874849 1 18.5439088 -1.881392542 2.583899436 1.127087621 0.742539287 0.543914047 0.074156274 13334486.6 8196075.449 10368060.07 0.017194662 0.013140366 1.881392542 -0.384548334 RPPGGT(ph)SPPNGGLPGPLATSAAPPGPPAAASPCLGPVAAAGSGLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPGGTSPPNGGLPGPLATSAAPPGPPAAASPCLGPVAAAGSGLRR 46 2 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7 Q8WWM7 ATXN2L Ataxin-2-like protein 1 RPPGGT(0.572)S(0.428)PPNGGLPGPLATSAAPPGPPAAASPCLGPVAAAGSGLRR 173.67 6.21E-20 297540000 60499 30477 80646 54497 89833 51536 107380 73499 122040 TRUE FALSE 57639.33217 33582.64095 84343.69887 49018.85802 105499.8468 49751.2954 90997.20883 67063.03792 140965.3399 0.408890102 0.23823332 0.598329341 0.347736955 0.748409835 0.352932823 0.645528957 0.475741327 1 17.10498096 -4.999999998 0.119924454 2.777465987 0.196634453 0.578127156 0.145831981 94.76228389 0.736910571 40.7111063 1.230155915 1.00E-05 4.999999998 -2.580831533 RPPGPTTS(ph)PASTSLSSPGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPGPTTSPASTSLSSPGQR 20 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 RPPGPT(0.142)T(0.142)S(0.715)PASTSLSSPGQR 54.103 0.035955 0 19086 21636 18462 22817 22699 19975 24522 20008 26556 TRUE FALSE 18183.8426 23840.733 19308.50096 20523.39181 26657.69841 19283.26074 20780.71852 18255.99345 30674.16885 0.592806367 0.777225069 0.62947104 0.669077357 0.869060171 0.62864819 0.677466393 0.595158537 1 14.90473663 -1.168559386 3.885875341 1.000166357 0.684396504 0.581380373 0.085295151 5114893098 5656829072 10496008.4 0.018963457 0.067832936 1.168559386 -0.315769853 RPPPPPVPLLPPGTSPPVDPFT(ph)TLASKASPTLDFTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPPPPVPLLPPGTSPPVDPFTTLASKASPTLDFTER 37 2 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 RPPPPPVPLLPPGTSPPVDPFT(0.237)T(0.237)LAS(0.237)KAS(0.237)PT(0.048)LDFT(0.002)ER 95.252 0.017191 73019000 81156 44487 76522 74207 75786 75105 107670 85699 103010 TRUE FALSE 77319.91672 49020.27588 80030.60939 66747.57138 89003.05441 72504.09502 91242.964 78194.74124 118984.2647 0.649833126 0.411989569 0.672615069 0.560978139 0.748023738 0.609358685 0.766848997 0.657185565 1 16.86041127 -0.581929381 0.192588384 1.271927297 0.477663846 0.64920869 0.089787137 8.230145236 0.428451585 1.559269174 0.290914615 0.261860878 0.581929381 -0.794263451 RPPPPPVPLLPPGTSPPVDPFTTLAS(ph)KASPTLDFTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPPPPVPLLPPGTSPPVDPFTTLASKASPTLDFTER 37 2 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 RPPPPPVPLLPPGTSPPVDPFT(0.092)T(0.092)LAS(0.357)KAS(0.357)PT(0.092)LDFT(0.007)ER 52.057 0.02735 61756000 28511 15856 28703 21326 28356 27912 38189 33923 36615 TRUE FALSE 27163.34153 17471.74443 30019.06094 19182.26996 33301.27742 26945.40044 32362.56666 30952.52228 42293.0672 0.642264639 0.413111311 0.709786803 0.453555895 0.787393292 0.637111523 0.765197911 0.731858064 1 15.36813357 1.094491134 0.349940741 1.033272892 0.513557742 0.601930499 0.105258151 0.875277389 0.324455324 0.169931858 0.102591089 12.43057258 -1.094491134 -0.51971515 RPPRS(ph)PGMEPPFSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPPRSPGMEPPFSHR 15 2 G3V470;Q99973-2;Q99973 G3V470 TEP1 Telomerase protein component 1 1 RPPRS(1)PGMEPPFSHR;RPPRS(1)PGMEPPFSHR 97.32 0.0029782 61153000 49120 37404 39251 39588 52478 44041 49857 42053 50857 TRUE FALSE 46798.19495 41215.51012 41050.69717 35608.53903 61630.14658 42515.84913 42250.39896 38370.61638 58743.64382 0.79665121 0.701616506 0.698810876 0.606168374 1.049137278 0.723752331 0.719233541 0.653187543 1 15.84214514 RPPS(ph)AFFLFCSEYRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 1 RPPS(0.999)AFFLFCS(0.001)EYRPK 55.127 0.071719 95233000 145570 121190 140350 146690 114440 129500 155320 142810 123440 TRUE FALSE 138689.1946 133539.3988 146785.1863 131944.4425 134398.2998 125015.3825 131623.0814 130304.7993 142582.4448 0.972694744 0.936576722 1.02947587 0.925390519 0.942600613 0.876793653 0.923136657 0.913890904 1 17.12143684 3.051068273 24.9999374 0.923014162 0.970389338 0.245729785 0.038253335 130.3090743 63790.497 0.010088815 0.012058438 1124.781782 -3.051068273 0.047375176 RPPS(ph)PDVIVLS(ph)DNEQPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_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(0.653)S(0.347)PR 121.19 1.33E-05 719290000 772620 701610 878910 858240 707080 815330 1013300 894500 615500 TRUE FALSE 736099.7838 773104.8567 919208.8929 771968.0847 830394.5281 787094.9177 858702.4745 816172.838 710948.5965 1.035376942 1.087427221 1.292932988 1.08582827 1.168009238 1.107105242 1.207826387 1.148005414 1 19.43938573 3.98706469 24.60519453 1.155126577 1.054895767 0.16812223 0.077127668 694.8558256 1321741.039 0.017284084 0.031964489 9706.545398 -3.98706469 -0.100230811 RPPS(ph)PDVIVLS(ph)DNEQPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.11)S(0.89)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.011)S(0.989)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.015)S(0.985)PR 203.25 4.40E-22 1794930000 1319430 1338460 1390260 1298410 1305640 1449060 1601250 1324650 1249670 TRUE FALSE 1257063.159 1474850.596 1454004.796 1167891.36 1533343.203 1398878.689 1356949.904 1208656.624 1443462.441 0.870866552 1.021745044 1.007303519 0.809090231 1.062267475 0.969113327 0.940065959 0.837331536 1 20.46110214 -1.632254592 0.00348795 1.42407344 0.489023649 0.007198145 0.083162672 917389.4145 499.1273688 68621.55397 65214.59485 0.023320905 1.632254592 -0.935049791 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_SK-BR-3_Trastuzumab_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)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR 203.21 3.80E-21 670070000 455270 416560 438920 498520 461820 437700 498100 451310 508980 TRUE FALSE 433750.2894 459007.9376 459044.9162 448407.8225 542361.2618 422542.3392 422105.6968 411790.9039 587910.0189 0.737783462 0.780745221 0.780808119 0.762715055 0.922524271 0.718719405 0.717976703 0.700431853 1 19.16523584 4.554838136 1.701771764 0.783537032 0.730453044 0.01861879 0.095465656 3.252658726 12.39520305 0.02339103 0.252014562 35878.81871 -4.554838136 -0.053083988 RPPS(ph)PDVIVLSDNEQPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.933)S(0.067)PR 202.05 4.20E-21 131670000 88008 74560 76347 86081 81901 72375 88841 79105 92126 TRUE FALSE 83848.03626 82157.74877 79847.58547 77427.97434 96184.50847 69868.6356 75286.67377 72178.14684 106412.4296 0.787953405 0.7720691 0.750359575 0.727621526 0.90388415 0.656583407 0.707498871 0.678286805 1 16.69930715 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.016)S(0.984)PR 276.03 5.48E-44 164900000 135340 131350 118840 136460 129580 115450 144290 130160 136730 TRUE FALSE 128942.7464 144734.7143 124288.9315 122742.7815 152178.711 111451.9376 122275.9104 118762.5004 157933.3901 0.816437527 0.916428845 0.78697058 0.777180693 0.963562619 0.705689516 0.774224566 0.751978415 1 17.26895669 2.219442239 24.99999266 0.784577457 0.85127522 0.025555742 0.09515619 536.9752075 702166.9399 0.031906816 0.023601556 165.7456881 -2.219442239 0.066697763 RPPS(ph)PDVIVLSDNEQPSSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 RPPS(1)PDVIVLSDNEQPSSPR;RPPS(1)PDVIVLSDNEQPSSPR;RPPS(1)PDVIVLSDNEQPSSPR 219.65 5.55E-25 589020000 281448 243983 247250 280335 297686 262630 294709 271825 300799 TRUE FALSE 268144.5108 268845.1451 258586.6571 252155.1932 349602.3441 253535.0572 249745.7293 248022.562 347445.3727 0.771760202 0.773776732 0.744251262 0.725740542 1.006208088 0.729711998 0.718805743 0.713846209 1 18.40642664 -2.206279016 2.351794972 1.697427262 0.771803754 0.410435365 0.085485432 5376545.258 1430722.208 19852789.99 0.019798313 0.006219006 2.206279016 -0.925623507 RPPS(ph)PEPSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.905)PEPS(0.095)TK;RPPS(0.989)PEPS(0.011)TK;RPPS(0.997)PEPS(0.003)TK;RPPS(0.986)PEPS(0.012)T(0.001)K;RPPS(1)PEPSTK;RPPS(0.963)PEPS(0.03)T(0.007)K;RPPS(0.997)PEPS(0.003)TK;RPPS(0.999)PEPS(0.001)TK;RPPS(0.997)PEPS(0.003)T(0.001)K;RPPS(0.993)PEPS(0.006)T(0.002)K;RPPS(0.991)PEPS(0.004)T(0.006)K;RPPS(0.998)PEPS(0.001)T(0.001)K 105.19 0.0015814 25910060000 12299640 10722830 11089410 12797910 9790280 11929490 13149230 12881040 10892830 TRUE FALSE 11718260.39 11815498.57 11597870.42 11511439.77 11497701.73 11516368.77 11143073.46 11753107.85 12582034.44 0.931348618 0.939076953 0.921780215 0.914910846 0.913818968 0.915302594 0.88563368 0.934118238 1 23.58486188 0.974353731 24.00321765 1.000000001 0.918153237 0.777222871 0.013824381 855.8745751 801043.551 0.015895396 0.003973849 9.426570745 -0.974353731 -0.081846764 RPPSAFFLFCSEHRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPPSAFFLFCSEHRPK 16 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 123.97 5.11E-05 646810000 636250 488280 528880 612640 560190 560430 734010 640060 544230 FALSE TRUE 606175.7234 538036.2871 553129.6711 551056.2633 657886.9586 541022.1686 622023.2935 584012.9532 628626.4089 0.964286124 0.855891957 0.879902058 0.876603743 1.046546803 0.860641807 0.989495962 0.929030255 1 19.26184336 RPPSAFFLFCSEYRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 230.29 1.35E-15 11350400000 5033200 4123900 4191500 4595900 4241700 5132100 5882200 5391700 4529000 FALSE TRUE 4795290.611 4544130.098 4383684.421 4133911.4 4981451.137 4954374.09 4984762.356 4919574.165 5231334.189 0.91664773 0.868636935 0.83796681 0.790221242 0.952233399 0.947057464 0.952866358 0.940405256 1 22.3187475 2.644597582 10.4247715 0.954654242 0.862119398 0.685613226 0.035106086 0.351333881 37.24706259 0.011799562 0.01112119 441.1614774 -2.644597582 -0.092534844 RPPSGFFLFCSEFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPPSGFFLFCSEFRPK 16 2 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 147.92 5.52E-07 198428000 503240 418400 385700 412920 402490 402800 537720 485830 412650 FALSE TRUE 479452.8425 461035.4357 403384.7265 371412.4971 472684.1286 388850.935 455680.9381 443288.1497 476641.6545 1.005897907 0.967257963 0.846306072 0.779227945 0.991697062 0.815814001 0.956024162 0.93002394 1 18.86254551 -3.250995515 8.743181344 0.99934212 0.92161393 0 0.080716684 0 0 0 0.017462808 0.000561054 3.250995515 -0.07772819 RPPT(ph)PCS(ph)DPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER 92.939 0.0098637 762910000 738580 684690 716470 769880 827540 698620 855300 754380 923190 TRUE FALSE 703668.7871 754460.6894 749320.8582 692490.1997 971862.714 674426.6142 724808.2763 688322.488 1066353.59 0.65988317 0.707514558 0.702694552 0.649400167 0.911388795 0.632460584 0.679707259 0.64549179 1 20.02425447 -1.347842977 5.066332645 1.000150072 0.697760422 0.586869226 0.079478835 0.000123399 1.59E-05 0.070484739 0.016605219 0.044890767 1.347842977 -0.30238965 RPPT(ph)PCSDPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPPTPCSDPER 11 1 Q9BW71;Q9BW71-2;Q9BW71-3 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 RPPT(0.999)PCS(0.001)DPER;RPPT(0.999)PCS(0.001)DPER 57.159 0.067055 397090000 564410 435430 521140 562680 401730 584880 637570 424500 457050 TRUE FALSE 537731.4579 479800.812 545034.7845 506118.3374 471791.5848 564625.4589 540296.9867 387328.5296 527926.9797 1.018571656 0.908839348 1.032405627 0.95869004 0.893668259 1.069514309 1.023431284 0.733678225 1 19.00997887 1.276800074 24.99994668 0.866837463 0.984475186 0.262936016 0.083202842 176.3804309 115312.7407 0.05007416 0.018284963 18.91472687 -1.276800074 0.117637722 RPQS(ph)PGAS(ph)PSQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(1)PGAS(0.596)PS(0.404)QAER;RPQS(1)PGAS(0.89)PS(0.11)QAER 115.39 0.0014773 570640000 310560 345720 300195 383230 355180 319680 315310 314320 301730 TRUE FALSE 295880.4443 380949.2611 313959.2377 344706.9923 417123.2795 308609.4014 267203.6684 286796.4745 348520.7474 0.848960776 1.09304615 0.900833709 0.989057308 1.196839163 0.885483587 0.766679374 0.822896418 1 18.41088502 2.014281194 24.98064108 0.834470891 1.001478559 0.260364097 0.111666806 250.3237388 437864.1134 0.039270266 0.028991006 103.3430308 -2.014281194 0.167007668 RPQS(ph)PSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPQSPSPR 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 RPQS(0.972)PS(0.028)PR;RPQS(0.982)PS(0.018)PR;RPQS(0.954)PS(0.046)PR;RPQS(0.999)PS(0.001)PR 112.75 0.0018261 268444000 166699 176448 173998 184799 230071 179384 174889 177746 201682 TRUE FALSE 158819.4686 194428.2518 181975.9804 166222.6534 270195.3096 173171.8871 148206.471 162181.6179 232957.8145 0.681752054 0.834607125 0.781154222 0.713531133 1.159846516 0.743361572 0.63619446 0.696184493 1 17.8297092 -1.598796262 6.012853942 1.000863338 0.776868905 0.182656319 0.145489526 0.001654285 0.000110381 0.138399063 0.032499892 0.025188583 1.598796262 -0.223994432 RPQT(ph)PPKIDYLLPGPGPAHS(ph)PQPSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPQTPPKIDYLLPGPGPAHSPQPSKR 26 3 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 2 RPQT(0.956)PPKIDY(0.044)LLPGPGPAHS(0.807)PQPS(0.193)KR;RPQT(1)PPKIDYLLPGPGPAHS(0.85)PQPS(0.15)KR 74.397 0.015938 797600000 500630 420980 443180 517400 306280 486020 533350 517260 335880 TRUE FALSE 476966.2121 463878.3406 463500.2414 465389.969 359695.135 469189.0055 451977.6619 471965.9722 387966.555 1.229400333 1.195665798 1.194691232 1.199562084 0.927129234 1.209354259 1.164991302 1.216512006 1 18.56557276 -5 0.115644628 0.522174516 1.250078842 0.254181513 0.087867811 230.2852055 1.746057558 26.77951295 0.911909856 1.00E-05 5 0.727904326 RPQYS(ph)NPPVQGEVMEGADNQGAGEQGRPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR;RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR;RPQYS(1)NPPVQGEVMEGADNQGAGEQGRPVR 240.95 6.86E-46 365710000 129907 102394 115659 137249 136425 130820 144014 128995 138528 TRUE FALSE 123766.5536 112828.065 120962.0796 123452.4698 160217.4768 126289.6706 122042.0193 117699.514 160010.2147 0.773491578 0.705130389 0.755964735 0.77152868 1.001295305 0.789260053 0.762713927 0.735575002 1 17.28780448 -5 0.25668364 2.342890135 0.764310977 0.394513883 0.081042937 205.2010388 2.021867464 145.5462808 0.11188019 1.00E-05 5 -1.578579158 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;;;;;;; 345.09 6.70E-108 5438063000 1390910 1235719 1353540 1487250 1528765 1389369 1579355 1470782 1672131 FALSE TRUE 1325164.441 1361640.171 1415601.148 1337748.804 1795381.132 1341254.803 1338395.388 1341992.531 1931436.535 0.68610302 0.704988306 0.732926566 0.692618566 0.929557404 0.694433795 0.692953335 0.694815753 1 20.88124284 -1.715102803 2.697859924 1.046836169 0.725041604 0.5780507 0.072830537 13019780.43 10799398.79 4119837.744 0.018409119 0.019270687 1.715102803 -0.321794565 RPRPTPGDGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPRPTPGDGEK 11 2 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L410;I3L1N0;Q9BUL5-3 I3L4Q4 PHF23 PHD finger protein 23 0 85.813 0.0084008 18758000 54890 32412 40415 42011 55032 38214 90465 42990 51853 FALSE TRUE 52295.45848 35714.81965 42268.06773 37787.97446 64629.56338 36890.6396 76662.90275 39225.5677 59894.09841 0.873132076 0.596299479 0.705713398 0.630913153 1.079063966 0.615931128 1.279974234 0.654915405 1 15.87012624 2.747607506 24.95580426 0.945193695 0.703280568 0.228754583 0.203091603 833.5863038 2299443.819 0.056581077 0.059228409 559.251949 -2.747607506 -0.241913126 RPRS(ph)PGSNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPRSPGSNSK 10 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPRS(0.996)PGS(0.004)NSK 72.705 0.037161 121280000 24608 7629.2 41714 13461 49553 27985 62687 29905 93615 TRUE FALSE 23444.82861 8406.624154 43626.62816 12107.87471 58195.02751 27015.87243 53122.94682 27286.35966 108132.3361 0.216816074 0.07774385 0.403455892 0.111972747 0.538183393 0.249840828 0.491277159 0.252342275 1 16.72243849 -5 0.155463611 3.647974835 0.073555513 0.716672904 0.142466904 61.25365127 0.555482983 49.89117195 0.565675978 1.00E-05 5 -3.574419323 RPRSPGS(ph)NSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPRSPGSNSK 10 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPRS(0.124)PGS(0.873)NS(0.003)K 90.689 0.0083953 110350000 23085 4323.9 34952 11063 48002 26540 58814 23004 81594 TRUE FALSE 21993.8178 4764.510326 36554.58377 9950.926222 56373.5336 25620.91315 49840.84411 20989.64781 94247.1808 0.233363137 0.050553346 0.387858644 0.105583277 0.598145569 0.271848059 0.52883114 0.222708495 1 16.52416184 -5 0.135443764 3.434918696 0.014219559 0.651362997 0.16419058 75.12215518 0.631902806 49.34888159 0.969417668 1.00E-05 5 -3.420699137 RPS(ph)ANCDPFSVTEALIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPSANCDPFSVTEALIR 17 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 RPS(1)ANCDPFSVTEALIR;RPS(1)ANCDPFSVTEALIR;RPS(1)ANCDPFSVTEALIR 181.82 4.79E-10 214894000 206382 197535 185450 232476 201336 184290 204796 198177 185112 TRUE FALSE 196626.7319 217664.0411 193953.0659 209107.0708 236448.9347 177907.9911 173550.6089 180823.5713 213818.2235 0.919597631 1.017986388 0.907093244 0.977966552 1.10584089 0.832052517 0.811673608 0.845688306 1 17.70602529 2.197691835 24.9999977 0.850960823 0.980166935 0.345248151 0.074817589 137.8454929 84321.19853 0.025825782 0.019073812 157.6492232 -2.197691835 0.129206113 RPS(ph)ASSPNNNTAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.333)AS(0.333)S(0.333)PNNNTAAK;RPS(0.639)AS(0.255)S(0.106)PNNNTAAK 132.13 3.20E-05 315590000 181838 185207 167280 190462 138097 181814 200190 190421 177155 TRUE FALSE 173242.8781 204079.8039 174949.9535 171316.3979 162181.0731 175517.7356 169647.3388 173746.7278 204627.2926 0.846626449 0.997324459 0.854968813 0.837211868 0.792568142 0.857743527 0.829055287 0.849088729 1 17.64263905 3.51685647 24.15186399 0.84754186 0.922670699 0.113939472 0.065129303 480.8952281 292296.2299 0.015423969 0.023889364 3287.429668 -3.51685647 0.075128839 RPS(ph)DSGPPAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPSDSGPPAER 11 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 RPS(0.891)DS(0.109)GPPAER;RPS(0.53)DS(0.47)GPPAER;RPS(0.998)DS(0.002)GPPAER;RPS(1)DSGPPAER;RPS(0.96)DS(0.04)GPPAER;RPS(0.96)DS(0.04)GPPAER 215.37 7.88E-12 7483520000 3025180 2656030 2851260 2994920 3295840 2805910 3426980 2968080 3438100 TRUE FALSE 2882185.737 2926682.477 2981993.091 2693864.952 3870633.452 2708740.633 2904131.26 2708179.18 3971262.989 0.725760481 0.736965163 0.750892877 0.678339601 0.974660571 0.682085432 0.731286563 0.681944054 1 21.92116647 -1.545944303 2.922671612 1.012017846 0.744540507 0.467213024 0.085493893 36780159.19 41854999.74 3503698.391 0.018702667 0.028448259 1.545944303 -0.267477339 RPS(ph)EGPQPLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSEGPQPLVR 11 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 RPS(1)EGPQPLVR 92.269 0.0023742 0 104300 100980 98051 105080 114440 108610 126480 117220 121810 TRUE FALSE 99369.9457 111269.9768 102546.7353 94517.15876 134398.2998 104848.8085 107183.153 106955.5954 140699.6727 0.706255699 0.790833231 0.728834214 0.671765307 0.955214019 0.745195824 0.761786797 0.760169468 1 17.10225945 -5 0.270406723 2.61541966 0.747191423 0.498327 0.074590053 173.9895303 1.688227471 157.0631577 0.084700817 1.00E-05 5 -1.868228236 RPS(ph)GPAELGTWHALHSVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSGPAELGTWHALHSVTPR 20 1 A0A5E8;Q99501;Q99501-4 A0A5E8 GAS2L1 GAS2-like protein 1 1 RPS(1)GPAELGTWHALHSVTPR;RPS(1)GPAELGTWHALHSVTPR 195.39 1.15E-19 480810000 133200 119453 129015 143242 137958 128023 159364 153957 48403 TRUE FALSE 126903.9 131625.3965 134930.4654 128843.042 162017.8315 123589.5314 135050.0949 140475.7089 55909.09003 2.269825889 2.354275422 2.413390475 2.304509731 2.897879959 2.210544499 2.41553019 2.512573695 1 15.77079524 -0.787767008 6.405266498 0.999999976 2.408569167 0.847798283 0.189312598 6.03E-08 1.18E-08 0.168710528 0.039765452 0.163017036 0.787767008 1.408569191 RPS(ph)GPDGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSGPDGAAR 10 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 RPS(1)GPDGAAR 63.401 0.083496 41916000 90777 90975 83765 102420 86082 88151 92221 84571 80286 TRUE FALSE 86486.15111 100245.4559 87605.7081 92124.54701 101094.6735 85098.30877 78150.9927 77165.5149 92736.34284 0.932602564 1.080972711 0.944675037 0.993402847 1.090130045 0.917637101 0.842722392 0.83209573 1 16.50084721 2.038760321 8.530293559 0.875575048 1.007688357 0.398050784 0.067028423 0.211635793 42.29643898 0.023123448 0.016990557 109.3352798 -2.038760321 0.132113309 RPS(ph)ILPEGSSDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSILPEGSSDSR 13 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 RPS(1)ILPEGSSDSR 71.685 0.025478 133690000 88933 80133 81185 95802 102120 73101 92625 77877 93389 TRUE FALSE 84729.31334 88298.6438 84907.41255 86171.80095 119929.6957 70569.49404 78493.35508 71057.67703 107871.2892 0.785466773 0.818555563 0.787117807 0.798839076 1.111785134 0.654200896 0.727657523 0.658726503 1 16.71895141 -1.190263789 6.353437112 1.000001483 0.793106534 0.209537801 0.126476672 2.54E-06 3.24E-07 0.117268216 0.027640185 0.064526218 1.190263789 -0.206894949 RPS(ph)LGELLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSLGELLLR 10 1 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 RPS(1)LGELLLR;RPS(1)LGELLLR;RPS(1)LGELLLR;RPS(1)LGELLLR 182.33 1.10E-06 270049000 232783 221098 190324 227706 236942 202460 264835 232695 261238 TRUE FALSE 221779.8089 243628.1376 199050.5437 204816.5603 278264.6098 195448.7594 224429.5567 212318.9922 301749.4548 0.734979982 0.80738551 0.659655023 0.678763646 0.922171044 0.647718683 0.743761267 0.703626763 1 18.20299164 -1.142323294 5.018003849 1.000012864 0.741052032 0.514198296 0.080184175 1.05E-05 1.79E-06 0.070585613 0.016636363 0.072057088 1.142323294 -0.258960832 RPS(ph)LPV ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSLPV 6 1 Q15053 Q15053 KIAA0040 Uncharacterized protein KIAA0040 1 RPS(1)LPV;RPS(1)LPV 71.501 0.093286 304970000 362550 275730 264380 406040 481170 283320 424810 376250 433410 TRUE FALSE 345412.98 303827.2005 276502.0845 365224.0878 565085.8957 273508.5574 359997.4323 343303.5554 500621.0092 0.689969006 0.606900619 0.55231818 0.729542071 1.128769838 0.546338552 0.719101727 0.68575539 1 18.93335931 3.012135845 21.54343302 0.785773435 0.62687863 0.221849229 0.1650778 75.15366241 133406.201 0.045900122 0.054787831 1028.337907 -3.012135845 -0.158894805 RPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_SK-BR-3_Trastuzumab_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 222.99 6.00E-34 400873000 94554 107995 83698 108285 82207 101545 94273 84951 76148 TRUE FALSE 90084.61981 118999.8133 87535.63609 97399.98607 96543.87477 98028.47119 79889.92241 77512.24009 87956.64293 1.024193475 1.352937189 0.995213473 1.107363615 1.097630282 1.114509012 0.908287535 0.881255099 1 16.42450492 1.764789089 4.849359367 0.920804834 1.131359992 0.429243578 0.099498196 0.162550828 8.29793424 0.04940577 0.026088565 58.18205941 -1.764789089 0.210555158 RPS(ph)PPPQPS(ph)SVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSPPPQPSSVK 12 1 H0YAU4;H3BLZ3;Q8IX03-2 H0YAU4 WWC1 Protein KIBRA 2 RPS(0.965)PPPQPS(0.989)S(0.046)VK 54.871 0.087825 144250000 539460 464320 489930 555890 342950 529820 568400 570300 408720 TRUE FALSE 513960.7949 511634.7359 512393.7751 500010.8811 402760.3714 511472.2006 481680.1406 520361.5086 472102.2101 1.088664242 1.083737218 1.085345004 1.059115739 0.853121131 1.083392938 1.020287832 1.102222141 1 18.84873971 2.989454473 24.94550673 1.013255904 1.084140034 0.215172257 0.065595215 756.6586087 1789888.237 0.018470267 0.020807768 976.0104627 -2.989454473 0.07088413 RPS(ph)PQPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RPS(0.999)PQPS(0.001)PR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR 122.18 0.00036328 1277844000 643533 585372 545096 608028 577255 585270 691910 626457 675695 TRUE FALSE 613114.4704 645022.0723 570089.1908 546907.8703 677928.0892 565001.9531 586346.4217 571601.104 780478.3296 0.785562452 0.826444563 0.730435643 0.700734216 0.868605909 0.723917541 0.751265473 0.732372806 1 19.57399905 -0.946061599 5.450529366 1.000000417 0.768674727 0.677674882 0.050893187 2.49E-07 4.81E-08 0.047543983 0.011206204 0.113223976 0.946061599 -0.23132569 RPS(ph)PTSGDSRPAAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.879)PT(0.06)S(0.06)GDSRPAAGR;RPS(0.541)PT(0.179)S(0.28)GDSRPAAGR;RPS(0.868)PT(0.068)S(0.064)GDSRPAAGR;RPS(0.907)PT(0.046)S(0.046)GDSRPAAGR 90.422 0.0047411 525720000 148786 152605 159034 168709 182627 147098 185694 155396 197249 TRUE FALSE 141753.1806 168155.623 166325.8662 151750.0508 214477.091 142003.9594 157362.9698 141788.7024 227837.3675 0.622168269 0.738051114 0.730020137 0.666045489 0.941360468 0.623268961 0.690681127 0.622324178 1 17.79764486 -2.248145167 2.278069731 2.086469946 0.704424484 0.493887043 0.094091651 4225579.156 755322.0969 23632370.37 0.022236599 0.005647482 2.248145167 -1.382045462 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RPSQEQSASASSGQPQAPLNR 21 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 RPS(1)QEQSASASSGQPQAPLNR;RPS(0.959)QEQS(0.039)AS(0.001)ASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.999)QEQS(0.001)ASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR 353.58 1.11E-95 7719620000 1103461 995667 1014764 1223383 1174717 1076659 1214167 1183270 1253418 TRUE FALSE 1051302.585 1097126.599 1061291.933 1100406.217 1379587.273 1039374.029 1028923.524 1079656.606 1447791.662 0.726142174 0.757793147 0.733041888 0.760058402 0.952890743 0.717903036 0.710684798 0.745726498 1 20.46542258 -1.368853916 3.069346328 1.002770845 0.759387317 0.533662654 0.069542464 18784171.7 24189855.15 466784.5836 0.016235864 0.042770673 1.368853916 -0.243383528 RPS(ph)QGPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR 138.45 8.35E-05 10608838000 2077364 1858865 1911973 2006520 1790964 1935676 2196007 1950440 1655076 TRUE FALSE 1979171.121 2048285.457 1999638.853 1804820.797 2103307.555 1868643.055 1860965.8 1779649.134 1911736.733 1.035273888 1.071426531 1.045980243 0.944073923 1.100207742 0.977458361 0.973442508 0.930907014 1 20.86645243 2.064775183 12.40210491 0.967734447 1.039351202 0.394643356 0.042557998 0.744969488 140.7884494 0.014923565 0.011021094 116.0847534 -2.064775183 0.071616755 RPS(ph)QGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RPS(0.914)QGPPARS(0.489)PS(0.489)QDFS(0.108)FIEDTEILDSAMYR;RPS(0.499)QGPPARS(0.499)PS(0.499)QDFS(0.499)FIEDT(0.005)EILDSAMYR;RPS(0.457)QGPPARS(0.732)PS(0.454)QDFS(0.356)FIEDT(0.001)EILDSAMYR 118.43 3.38E-05 36022600 30219.3 23119.5 34896.9 32647.6 35896.3 28308.4 42643.9 32125.1 42911.7 TRUE FALSE 28790.89358 25475.40333 36496.95738 29365.80122 42156.60335 27328.07301 36137.78985 29312.05594 49566.22727 0.580857071 0.513966964 0.73632712 0.592455848 0.850510633 0.551344625 0.729080905 0.591371536 1 15.59706983 -5 0.16728864 2.367868814 0.548491886 0.537893866 0.102956884 93.96457801 0.88053354 42.81757373 0.351914054 1.00E-05 5 -1.819376928 RPS(ph)QGPPARSPSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.492)QGPPARS(0.492)PS(0.015)QDFSFIEDTEILDSAMYR;RPS(0.642)QGPPARS(0.358)PSQDFSFIEDTEILDSAMYR 358.06 8.81E-121 71235000 60821.2 35380.3 69930 59635.1 67552 55402.5 71552 59944.1 82945 TRUE FALSE 57946.30241 38985.59279 73136.35967 53640.46645 79333.04741 53483.89753 60635.42826 54695.07682 95807.68698 0.604818927 0.406915082 0.763366302 0.559876437 0.8280447 0.558242237 0.632886882 0.570884013 1 16.54785379 -5 0.230608736 3.108274796 0.559956018 0.503569911 0.117582641 128.0247012 1.280245974 126.2498357 0.191585753 1.00E-05 5 -2.548318778 RPS(ph)QNAISFFNVGHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 RPS(1)QNAISFFNVGHSK;RPS(1)QNAISFFNVGHSK;RPS(1)QNAISFFNVGHSK;RPS(0.993)QNAIS(0.007)FFNVGHSK 302.59 2.97E-46 3693237000 2001092 1734447 1985765 2140152 1835413 2064914 2578936 2367320 2144638 TRUE FALSE 1906504.347 1911189.121 2076814.289 1925019.855 2155508.446 1993405.51 2185471.948 2160024.911 2477217.508 0.76961524 0.771506384 0.83836574 0.777089557 0.870132897 0.804695391 0.882228525 0.871956098 1 21.24028912 -4.999999755 0.081117914 1.654498022 0.626178765 0.846893267 0.027387674 73.76928686 0.422849011 8.446945316 0.764632972 1.00E-05 4.999999755 -1.028319257 RPS(ph)RHDNSAIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR 194.77 5.73E-07 1181983000 205235.9 154873.6 148612.9 201650.7 212501.4 143540.8 198309.8 156880.6 232168.1 TRUE FALSE 195534.8057 170655.3959 155426.9485 181380.3885 249561.5769 138569.9461 168053.9978 143143.303 268171.5432 0.729140771 0.636366536 0.579580319 0.676359566 0.930604246 0.516721291 0.626666035 0.53377514 1 18.03279663 -1.24828911 4.653060083 1.000109635 0.655092056 0.465189932 0.116698784 0.000125567 2.03E-05 0.106899246 0.025188423 0.056456102 1.24828911 -0.345017578 RPS(ph)SMYS(ph)TGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 2 RPS(0.818)S(0.185)MY(0.095)S(0.881)T(0.021)GGK 54.524 0.086238 39724000 185320 159380 193200 222600 173540 227650 246610 210720 181370 TRUE FALSE 176560.2909 175621.0032 202058.4111 200223.8251 203805.3211 219766.4234 208985.1152 192268.2397 209495.9333 0.842786245 0.838302684 0.964498012 0.955740868 0.972836646 1.049024771 0.99756168 0.917765976 1 17.67656271 3.677366423 2.998375288 0.986347502 0.837899741 0.745479373 0.033771033 0.113084664 2.006509233 0.009367097 0.016223737 4757.364455 -3.677366423 -0.148447761 RPS(ph)SMYSTGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.5)S(0.5)MYSTGGK;RPS(0.542)S(0.458)MYSTGGK;RPS(0.625)S(0.375)MYSTGGK;RPS(0.978)S(0.022)MYSTGGK;RPS(0.975)S(0.024)MYSTGGK;RPS(0.485)S(0.485)MY(0.03)STGGK 124.51 0.00043631 2086091000 1599780 1385519 1387960 1651710 1299555 1449393 1721840 1632170 1468270 TRUE FALSE 1524161.57 1526704.961 1451599.339 1485676.973 1526196.981 1399200.157 1459141.684 1489248.542 1695961.813 0.898700406 0.900200081 0.855915108 0.876008505 0.899900557 0.825018669 0.860362346 0.878114431 1 20.69367226 -1.147824564 3.850007024 1.00006509 0.875025539 0.741188877 0.023343892 3516282.738 1049547.329 1905.510136 0.005855139 0.071150087 1.147824564 -0.125039551 RPS(ph)SPVISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSSPVISK 9 1 Q96T17-5;Q96T17-4;Q96T17;Q96T17-2 Q96T17-5 MAP7D2 MAP7 domain-containing protein 2 1 RPS(0.5)S(0.5)PVISK 72.089 0.02924 128280000 196430 195410 181290 243510 203460 222260 251080 234070 198740 TRUE FALSE 187145.1432 215322.5012 189602.3258 219031.9122 238943.3596 214563.0805 212773.1346 213573.5899 229559.5842 0.815235591 0.937980882 0.82593949 0.954139697 1.040877297 0.934672718 0.926875414 0.930362331 1 17.80850914 7.070703207 0.372896507 0.963069865 9.42E-09 0.439299501 0.051073313 32.75837253 0.871731756 0.039572238 20.20147445 11768014.84 -7.070703207 -0.963069855 RPS(ph)STSVPLGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.649)S(0.33)T(0.017)S(0.004)VPLGDK;RPS(0.723)S(0.19)T(0.069)S(0.018)VPLGDK 91.317 0.0051241 1104770000 1582290 1474090 1363700 1727750 1069800 1461540 1690500 1713190 1264240 TRUE FALSE 1507498.287 1624301.447 1426226.994 1554073.287 1256372.781 1410926.503 1432583.177 1563174.001 1460291.882 1.032326691 1.112312865 0.976672548 1.064221 0.8603573 0.966194855 0.981025228 1.07045312 1 20.47782533 3.482587989 2.012309725 0.979117001 1.070271405 0.19649202 0.062565586 0.409253387 3.317344242 0.017738808 0.029265809 3038.001533 -3.482587989 0.091154403 RPS(ph)T(ph)SSASGQWSPTPEWVLSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.476)T(0.385)S(0.342)S(0.36)AS(0.337)GQWS(0.089)PT(0.011)PEWVLSWK 100.06 0.00079038 150000000 238220 226370 241680 281050 226170 287690 306430 273540 276650 TRUE FALSE 226959.8127 249437.3604 252761.2671 252798.32 265613.9764 277727.2232 259678.4755 249587.3875 319551.4691 0.710244936 0.780585866 0.790987655 0.791103608 0.831208748 0.869115776 0.812634272 0.781055359 1 18.28568879 -5 0.095661383 1.631868565 0.645764433 0.790701479 0.03469649 86.70983457 0.569708739 11.15795979 0.667011398 1.00E-05 5 -0.986104132 RPS(ph)TFGIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSTFGIPR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPS(0.856)T(0.144)FGIPR;RPS(0.587)T(0.413)FGIPR 125.54 0.00030544 383960000 97914 85996 86989 116381 104909 107092 117447 112667 132981 TRUE FALSE 93285.79927 94759.09017 90977.53169 104682.1608 123205.0964 103383.3772 99528.30309 102801.2802 153603.0143 0.607317504 0.616909053 0.592290015 0.68151111 0.802100772 0.673055654 0.647958007 0.669266034 1 17.228847 -5 0.217661508 2.713036601 0.61082427 0.789466526 0.055616737 71.17026658 0.711319506 53.43931278 0.114049284 1.00E-05 5 -2.102212331 RPS(ph)TS(ph)SASGQWSPTPEWVLSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.837)T(0.32)S(0.466)S(0.377)ASGQWSPTPEWVLSWK 213.77 1.74E-23 167470000 184320 175200 200150 230010 195740 221420 252510 211130 224120 TRUE FALSE 175607.5589 193053.0792 209327.0755 206888.9578 229876.994 213752.1699 213984.9618 192642.3379 258875.385 0.678347843 0.745737488 0.808601697 0.799183583 0.887983205 0.825695228 0.826594471 0.744150851 1 17.98189827 2.128350662 0.038551275 1.635357713 2.94E-17 0.643710743 0.052090989 59.32626037 1.534812959 30.59436933 33.83179128 134.3849587 -2.128350662 -1.635357713 RPS(ph)TSSASGQWSPTPEWVLSWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.844)T(0.123)S(0.032)SAS(0.001)GQWSPTPEWVLSWK;RPS(0.684)T(0.155)S(0.064)S(0.095)AS(0.002)GQWSPTPEWVLSWK 298.38 7.50E-56 4980900000 3233320 3005410 2921650 3477780 2871440 3283860 3872250 3461350 3251130 TRUE FALSE 3080487.371 3311664.696 3055610.542 3128186.947 3372218.227 3170139.105 3281467.144 3158255.844 3755298.636 0.820304234 0.881864538 0.813679773 0.833006173 0.897989362 0.844177631 0.873823219 0.841013232 1 21.84049621 -4.999999999 0.295382474 2.190698519 0.84436631 0.757072386 0.026639293 120.2043342 1.121116044 88.41508913 0.025164606 1.00E-05 4.999999999 -1.346332209 RPS(ph)VSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSVSK 6 1 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5;A0FGR8-4 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 RPS(1)VSK;RPS(0.999)VS(0.001)K;RPS(0.996)VS(0.004)K;RPS(1)VSK 106.68 0.019547 2738760000 3021160 2421700 2707660 4044470 3290970 3380320 3736800 3087300 3214090 TRUE FALSE 2878355.754 2668473.983 2831808.889 3637912.192 3864914.126 3263258.671 3166682.529 2816959.645 3712514.662 0.775311619 0.718778032 0.762773793 0.979905138 1.041050199 0.878988763 0.85297509 0.758774012 1 21.82396529 3.31527186 7.404217933 0.910105056 0.746863021 0.482180769 0.080949242 0.207134911 16.94235628 0.023111793 0.031281119 2066.673448 -3.31527186 -0.163242035 RPS(ph)VYLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSVYLPTR 9 1 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 RPS(1)VYLPTR 60.157 0.05976 163470000 52019 42082 38627 48535 52746 39902 55780 46946 60692 TRUE FALSE 49560.16496 46370.20364 40398.08616 43656.16959 61944.8857 38520.18373 47269.73653 42835.15936 70103.80539 0.70695399 0.661450593 0.576260959 0.622736089 0.883616593 0.549473506 0.674282035 0.611024739 1 16.09720514 -1.102518466 3.76056116 1.000139328 0.662449563 0.575512586 0.091560692 136576840.2 253577720.3 242903.2439 0.020152978 0.078973527 1.102518466 -0.337689765 RPS(ph)YLEWQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSYLEWQAR 10 1 E9PIY0;A0A3B3IU03;Q96KS9 E9PIY0 FAM167A Protein FAM167A 1 RPS(1)YLEWQAR;RPS(1)YLEWQAR 153.18 1.02E-05 156755000 130791 117890 116557 136735 268490 96795 149165 130197 245150 TRUE FALSE 124608.7686 129903.125 121901.2537 122990.138 315314.571 93442.96488 126407.1396 118796.2605 283166.6099 0.440054598 0.458751563 0.430493036 0.43433842 1.113530197 0.329992879 0.446405527 0.419527784 1 18.11129163 -1.855037126 2.730042522 1.200272476 0.501805852 0.33261769 0.218293765 44762020.12 27430372.07 58180156.42 0.050264152 0.01396249 1.855037126 -0.698466625 RPS(ph)YRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSYRK 6 2 P16220-1;P16220;P16220-3;H7C3I0;C9J896;E7EWP8;C9J4L5;C9JBT4;A0A0A0MSU8;F8VS03;F8VYN3;Q03060-25;P18846;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;Q03060-1;Q03060-30;Q03060-2;Q03060-13;Q03060-14 P16220-1;Q03060-6 CREB1;CREM;ATF1 Cyclic AMP-responsive element-binding protein 1;cAMP-responsive element modulator;Cyclic AMP-dependent transcription factor ATF-1 1 RPS(1)YRK 63.673 0.087465 104770000 121820 103000 105840 143230 96893 102550 123470 124890 117490 TRUE FALSE 116061.81 113495.8171 110692.8687 128832.2483 113791.1085 98998.66779 104632.3838 113953.9695 135709.7491 0.855220872 0.836312924 0.815658929 0.949321984 0.838488828 0.729488253 0.771001232 0.839688897 1 17.05016484 2.469134538 24.96007896 0.805047466 0.859619724 0 0.079314048 425.1271039 1328593.954 0.024952722 0.020910121 294.5333911 -2.469134538 0.054572259 RPS(ph)YTLGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSYTLGMK 9 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 RPS(0.998)YT(0.002)LGMK;RPS(0.982)Y(0.001)T(0.017)LGMK 141.13 6.58E-05 266910000 691950 533480 532320 560950 684500 570550 765370 659890 692270 TRUE FALSE 659242.8948 587842.2185 556727.3985 504562.2403 803876.5833 550791.7104 648598.7495 602106.5333 799623.696 0.824441419 0.735148572 0.696236744 0.63099961 1.005318611 0.688813642 0.811129976 0.752987357 1 19.6089617 -5 0.321761096 3.221459443 0.758893855 0.34068479 0.101506104 367.0831225 3.237185588 555.5585726 0.081171535 1.00E-05 5 -2.462565589 RPSDSSRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ;;; 100.48 0.0026062 208653000 298238 244349 222795 275022 231541 261603 316582 280511 286154 FALSE TRUE 284140.8808 269248.4409 233010.3711 247376.2661 271921.6771 252543.6225 268281.6015 255947.9698 330529.3008 0.859654137 0.814597799 0.704961317 0.748424619 0.822685542 0.7640582 0.811672674 0.774357883 1 18.33441864 -1.272943515 4.379653713 1.000136017 0.792102185 0.701632345 0.043448885 6.01E-05 9.98E-06 0.043823997 0.010322681 0.053340427 1.272943515 -0.208033832 RPSGVPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPSGVPDR 8 1 P01709;P01706 P01709 Ig lambda chain V-II region MGC;Ig lambda chain V-II region BOH 0 ;;; 86.898 0.025185 447870000 881420 681280 661000 686480 974200 792660 1045590 856770 984980 FALSE TRUE 839757.0234 750703.2066 691307.5038 617473.7262 1144100.172 765209.9854 886066.0419 781746.6768 1137725.668 0.738101501 0.65982796 0.607622315 0.542726374 1.005602848 0.672578643 0.778804651 0.68711351 1 20.1177213 2.766254937 24.96379141 0.799343332 0.65045244 0.365419804 0.121610662 929.2523394 837630.9243 0.034484399 0.0365689 583.7876955 -2.766254937 -0.148890892 RPSNDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSNDCR 7 1 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ; 75.738 0.068396 80168000 144412 108191 103829 163981 173624 110827 156134 133804 176486 FALSE TRUE 137585.931 119215.7859 108589.6624 147497.3183 203903.9706 106989.0332 132312.8907 122087.4124 203854.5475 0.674922059 0.584808077 0.53268207 0.723541957 1.000242443 0.52483025 0.64905538 0.598894721 1 17.63718061 -1.741781164 2.522430276 1.076593904 0.656598595 0.383020377 0.135058416 17894134.03 13038441.18 8558348.562 0.033127939 0.01812253 1.741781164 -0.41999531 RPSPDEPMTNLELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSPDEPMTNLELK 14 1 Q9UHD1-2;Q9UHD1;E9PPQ5 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 ; 145.69 1.36E-05 1054370000 796720 808090 745210 834990 643070 841940 930300 959160 574450 FALSE TRUE 759060.6245 890435.2897 779378.6156 751055.2188 755221.2044 812783.4067 788365.6489 875170.8656 663532.7721 1.143968552 1.341961282 1.174589483 1.131903729 1.138182221 1.224933328 1.188133702 1.318956504 1 19.3398082 -1.866788859 2.721699747 0.908975749 1.209836584 0.450180348 0.072150964 7334452.436 4990832.097 4312791.729 0.01791934 0.01358974 1.866788859 0.300860835 RPSQGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.138)QGPPARS(0.859)PS(0.004)QDFSFIEDTEILDSAMYR 297.29 2.42E-81 52178000 26973 18339 28216 26435 33432 20832 33155 24315 36645 TRUE FALSE 25698.03975 20207.76495 29509.73151 23777.70358 39262.53022 20110.58262 28096.59582 22185.8497 42327.71944 0.60712082 0.477412089 0.697172725 0.561752532 0.927584352 0.475116139 0.66378714 0.524144697 1 15.36931514 -2.176574628 2.370908966 2.01923748 0.611316694 0.454030623 0.131952789 8678807.382 1874414.051 47531424.57 0.031606223 0.006659251 2.176574628 -1.407920786 RPSS(ph)MYS(ph)TGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 2 RPS(0.094)S(0.898)MY(0.012)S(0.578)T(0.418)GGK 94.023 0.0057964 54972000 160510 128960 167370 184950 145830 188660 205720 171000 149380 TRUE FALSE 152923.0104 142101.1706 175044.0801 166358.4746 171262.7058 182126.6569 174333.6357 156026.3335 172545.0875 0.886278553 0.823559643 1.014483128 0.964144949 0.992567846 1.055530816 1.010365686 0.90426413 1 17.39661387 3.735432956 24.99980326 0.995768961 0.854919094 0.651246472 0.041503627 138.1330708 1104117.451 0.010591473 0.017214257 5437.921781 -3.735432956 -0.140849866 RPSS(ph)MYSTGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.423)S(0.577)MYSTGGK;RPS(0.441)S(0.559)MYSTGGK;RPS(0.437)S(0.563)MYSTGGK 126.25 0.00019074 1756510000 2871070 2582880 2456660 3046740 2373780 2611500 3155130 3028670 2653920 TRUE FALSE 2735360.211 2846078.408 2569300.291 2740475.907 2787766.48 2521063.1 2673756.971 2763463.599 3065476.359 0.892311631 0.92842941 0.838140631 0.893980441 0.909407268 0.822405005 0.872215818 0.901479338 1 21.54767985 0.852979956 4.782337043 0.999995869 0.8821693 0.59217275 0.031155806 1.092166696 34.83277293 0.030462681 0.007713758 7.12820131 -0.852979956 -0.117826568 RPSSMYS(ph)TGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPSSMYS(0.97)T(0.03)GGK 79.81 0.016003 169230000 117360 95710 108980 114000 99143 109290 136600 122720 103080 TRUE FALSE 111812.6254 105462.9578 113976.8408 102540.5034 116433.5078 105505.2599 115759.1612 111973.9862 119065.1199 0.939088 0.885758632 0.957264738 0.861213624 0.977897707 0.886113918 0.972234028 0.940443232 1 16.86139131 1.051124758 0.638180108 0.999668853 0.914260015 0.311456303 0.037365781 0.818419585 0.797170323 0.032057264 0.013588175 11.24928081 -1.051124758 -0.085408838 RPSST(ph)SVPLGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.197)S(0.291)T(0.436)S(0.077)VPLGDK 87.18 0.0062666 434170000 662690 545530 546100 703440 487700 677220 709490 745930 518340 TRUE FALSE 631365.957 601120.1272 571139.2252 632728.8748 572754.7256 653767.7016 601244.2698 680612.4148 598721.5199 1.054523574 1.004006215 0.953931346 1.056799954 0.956629596 1.091939541 1.004213561 1.136776268 1 19.1915256 2.226438621 24.99990336 1.053949399 1.009521318 0.203223485 0.051495858 405.5638608 836413.1578 0.017365784 0.012926877 168.4374356 -2.226438621 -0.044428081 RPSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPSSVK 6 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076;H0YBE8;Q8IX03 A0A3B3ITJ4;P14866;M0QYT0;H0YBE8 HNRNPL;WWC1 Heterogeneous nuclear ribonucleoprotein L;Protein KIBRA 0 ; 94.262 0.071645 3459600000 2230560 1834370 1862390 2285000 1615410 1779690 2198400 2189250 2058820 FALSE TRUE 2125125.849 2021294.389 1947782.424 2055307.459 1897136.993 1718058.889 1862993.704 1997547.664 2378091.291 0.89362669 0.84996501 0.819052839 0.864267687 0.797756167 0.722452875 0.783398733 0.839979387 1 21.18137267 4.076716409 0.961084512 0.81043333 0.899706969 0.009383937 0.072985542 1.77723414 2.460572918 0.02326975 0.132766292 11932.08693 -4.076716409 0.089273639 RPSTSQTVST(ph)PAPVPVIESTEAIEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 RPSTSQTVS(0.042)T(0.957)PAPVPVIESTEAIEAK 121.45 8.41E-05 52593000 40217 42734 41301 43823 28239 38965 45117 49836 35698 TRUE FALSE 38316.02211 47088.64318 43194.6917 39417.82878 33163.87266 37615.63228 38233.57302 45472.09564 41233.86352 0.929236769 1.141989597 1.047553831 0.955957687 0.804287298 0.912250977 0.927237221 1.102785229 1 15.33154202 3.192928574 5.225565003 0.93517551 1.046029518 0.167297531 0.090070717 0.268366924 16.48009062 0.02561491 0.031517691 1559.296031 -3.192928574 0.110854007 RPT(ph)SRAPS(ph)PSGLMSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPTSRAPSPSGLMSPSR 17 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 RPT(0.926)S(0.076)RAPS(0.574)PS(0.423)GLMS(0.001)PS(0.001)R 76.21 0.022502 604250000 222770 180480 198700 222310 218050 170530 233250 197200 213600 TRUE FALSE 212240.1036 198871.1172 207810.5915 199962.9764 256077.851 164624.5033 197663.4286 179932.1226 246723.9971 0.860232917 0.806046917 0.842279608 0.810472345 1.037912218 0.667241554 0.80115202 0.72928505 1 17.91253852 RPT(ph)SRAPSPS(ph)GLMSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPTSRAPSPSGLMSPSR 17 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 RPT(0.884)S(0.128)RAPS(0.142)PS(0.816)GLMS(0.019)PS(0.011)R 69.649 0.037865 350990000 197030 136330 204080 186490 202170 177780 200130 187780 203600 TRUE FALSE 187716.7824 150222.182 213437.2699 167743.6709 237428.384 171623.434 169596.4929 171336.9877 235173.2482 0.79820636 0.638772408 0.907574614 0.713277008 1.009589253 0.729774476 0.721155549 0.728556454 1 17.84336443 -1.577180422 3.013946355 1.01213187 0.77170666 0.289702914 0.106984769 92287409.9 107966450.5 9048486.826 0.024196427 0.026474001 1.577180422 -0.240425209 RPTEICADPQFIIGGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPTEICADPQFIIGGATR 18 1 P17655 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 180.08 1.29E-13 1436400000 912217 795414 835844 985614 1044031 853255 1041965 934327 1145209 FALSE TRUE 869098.3102 876467.5909 874168.2742 886538.2082 1226109.676 823706.5654 882994.1022 852512.3747 1322802.163 0.65701307 0.662584032 0.660845816 0.670197126 0.926903289 0.62269823 0.667517885 0.644474585 1 20.33516588 -1.753283605 2.799587969 1.063982203 0.686090795 0.564082609 0.085877262 25777145.66 24175421.37 11509438.96 0.01960872 0.017648849 1.753283605 -0.377891408 RPTELLSNPQFIVDGATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPTELLSNPQFIVDGATR 18 1 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 151.96 7.04E-08 1271290000 533980 508530 486520 603290 559490 488100 576260 515810 594030 FALSE TRUE 508739.8236 560349.7852 508827.4232 542646.143 657064.8789 471196.9746 488340.9533 470642.9419 686149.1385 0.74144205 0.816658877 0.741569718 0.790857428 0.957612335 0.68672676 0.71171255 0.685919307 1 19.38816266 -2.393320407 2.366071038 2.981935679 0.767493578 0.460464058 0.079406223 7239244.522 571082.5252 77761812.76 0.020538564 0.004042775 2.393320407 -2.214442101 RPTETNPVTSNS(ph)DEECNETVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;RPT(0.001)ET(0.001)NPVT(0.008)S(0.211)NS(0.779)DEECNETVK 202.85 3.77E-22 595120000 139906 148581 133701 170238 105984 159451 152090 160752 118509 TRUE FALSE 133292.9206 163721.5728 139831.3231 153125.3528 124467.576 153929.1719 128885.8772 146675.7027 136886.7705 0.973745821 1.196036493 1.021510864 1.118627843 0.909273961 1.124499989 0.941551011 1.071511163 1 17.0626235 2.788421062 24.99948364 1.010062742 1.082604168 0.142143083 0.08271265 643.8909191 322838.622 0.022724077 0.02410251 614.3573554 -2.788421062 0.072541426 RPTETNPVTSNS(ph)DEECNETVKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RPTETNPVTSNSDEECNETVKEK 23 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTSNS(1)DEECNETVKEK;RPTETNPVTS(0.001)NS(0.961)DEECNET(0.037)VKEK;RPTETNPVTS(0.006)NS(0.921)DEECNET(0.073)VKEK;RPTETNPVTS(0.001)NS(0.999)DEECNETVKEK;RPTETNPVT(0.003)S(0.023)NS(0.97)DEECNET(0.004)VKEK 171.05 3.45E-12 1318580000 936557 598032 902811 862073 606046 985296 1133190 1081320 777643 TRUE FALSE 892287.8067 658972.1407 944205.7774 775415.7842 711740.2305 951174.9525 960301.053 986633.8884 898235.9048 0.993378022 0.733629258 1.05117795 0.863265185 0.792375618 1.058936686 1.069096713 1.098412881 1 19.77673487 2.217974251 24.16494882 1.062967933 0.881980251 0.454210346 0.09231571 135.8054498 159411.3586 0.032516901 0.024046506 165.1863858 -2.217974251 -0.180987682 RPTLAWLEDSS(ph)SCSDIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPTLAWLEDSSSCSDIPK 18 1 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 RPTLAWLEDS(0.025)S(0.57)S(0.335)CS(0.069)DIPK 90.475 0.0016531 64651000 76245 71099 64187 87125 58319 84523 72736 84062 62183 TRUE FALSE 72641.04995 78344.06893 67130.03744 78367.02947 68489.81514 81595.94732 61638.78731 76701.08564 71826.02205 1.011347251 1.090747708 0.93462001 1.091067377 0.953551557 1.136022085 0.858167911 1.067873223 1 16.132219 1.740925892 24.99999967 0.96334241 1.035625912 0.108980789 0.079618227 0.655683319 6974.010924 0.031929873 0.017706661 55.07137142 -1.740925892 0.072283502 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK 116.35 3.96E-05 123230000 37343 51159 42991 53797 32709 50498 52356 55117 24554 TRUE FALSE 35577.8704 56372.16026 44962.17987 48389.22335 38413.43924 48749.2416 44368.13062 50290.66329 28361.70892 1.25443324 1.987615077 1.585312789 1.706146251 1.354412012 1.718840065 1.564367322 1.773188754 1 14.79165684 -1.101269514 4.543046007 0.999948508 1.623325214 0.468804199 0.206684185 9.81E-05 1.94E-05 0.182183372 0.042937499 0.079200967 1.101269514 0.623376706 RPTPQDS(ph)PIFLPVDDTSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 RPT(0.043)PQDS(0.957)PIFLPVDDTSFR;RPT(0.01)PQDS(0.99)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPT(0.001)PQDS(0.999)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPT(0.009)PQDS(0.991)PIFLPVDDTSFR 209.17 1.45E-16 6330073000 2133339 1914089 1902912 2268906 2286903 1960451 2314755 2143190 2341695 TRUE FALSE 2032500.293 2109136.845 1990162.397 2040831.258 2685738.159 1892560.09 1961596.611 1955520.922 2704833.101 0.751432794 0.779765984 0.73578011 0.754512823 0.992940436 0.6996957 0.725219094 0.72297286 1 21.36710815 -2.337112052 2.27907435 2.356525447 0.768748543 0.435666626 0.082145753 2498069.962 341386.1112 17578553.59 0.018998324 0.004601378 2.337112052 -1.587776904 RPTPQDSPIFLPVDDT(ph)SFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 RPTPQDSPIFLPVDDT(0.5)S(0.5)FR;RPTPQDSPIFLPVDDT(0.5)S(0.5)FR 156.28 1.03E-08 163997000 150992 177584 145105 188614 189076 162798 152909 171596 175145 TRUE FALSE 143854.9074 195680.0115 151758.2078 169654.1624 222050.7945 157160.2644 129579.9237 156570.1446 202305.5921 0.711077266 0.967249642 0.750143415 0.838603425 1.097600873 0.776845874 0.640515778 0.773928901 1 17.62617667 -0.96157075 5.751428995 1.000000194 0.817908471 0.159903002 0.129979666 3.29E-07 5.93E-08 0.127891349 0.030144248 0.109251963 0.96157075 -0.182091723 RPTPQDSPIFLPVDDTSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 246.1 2.00E-24 36608278000 11552538 10779731 10604846 12485149 12032565 10686645 12345685 12172112 12653583 FALSE TRUE 11006472.42 11878197.84 11091088.68 11230118.1 14131040.53 10316563.8 10462124.01 11106257.34 14615836.03 0.75305117 0.812693699 0.758840525 0.76835277 0.966830806 0.705848354 0.715807429 0.759878349 1 23.80102902 4.686714504 3.584803036 0.793763136 0.750521083 0.006612191 0.099816358 1.515263858 32.97851033 0.022362976 0.15944182 48608.75575 -4.686714504 -0.043242053 RPVDPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPVDPIR 7 1 Q8IYB8 Q8IYB8 SUPV3L1 "ATP-dependent RNA helicase SUPV3L1, mitochondrial" 0 73.26 0.07917 43687000 50024 47381 43335 65437 53935 55930 59428 61662 68064 FALSE TRUE 47659.46466 52209.17777 45321.95261 58859.14844 63341.24692 53993.13008 50361.16713 56262.54839 78619.0175 0.606207838 0.664078227 0.576475693 0.748662987 0.805673346 0.686769331 0.640572329 0.715635354 1 16.26259071 -5 0.221506857 2.65830185 0.633446645 0.723492543 0.06332563 86.4404703 0.864589409 64.05024424 0.123499771 1.00E-05 5 -2.024855205 RPVGASFSFGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RPVGASFSFGGK 12 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 0 80.967 0.020703 0 708980 560970 597140 687360 607560 678830 837260 780990 722660 FALSE TRUE 675467.9205 618133.4808 624519.4597 618265.2669 713518.2716 655321.9469 709520.6097 712602.3753 834726.422 0.809208745 0.740522241 0.748172627 0.740680121 0.854792963 0.785073923 0.850003775 0.853695722 1 19.67094391 0.771099263 0.507538425 1.007827682 0.762140155 0.820722604 0.033024138 0.504714861 0.288944644 0.040833534 0.01679666 5.903359934 -0.771099263 -0.245687527 RPVVGAVS(ph)VPELTNAQLQAQDYPSPNIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPVVGAVSVPELTNAQLQAQDYPSPNIMR 29 1 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 RPVVGAVS(0.999)VPELT(0.001)NAQLQAQDYPSPNIMR;RPVVGAVS(0.995)VPELT(0.005)NAQLQAQDYPSPNIMR;RPVVGAVS(0.756)VPELT(0.244)NAQLQAQDYPSPNIMR 181.08 4.55E-18 382610000 175168 124421 161421 154012 194327 148013 194097 156311 244685 TRUE FALSE 166888.1558 137099.6414 168822.3125 138530.4212 228217.5673 142887.2727 164483.9378 142623.5802 282629.5001 0.590483852 0.485086098 0.597327287 0.490148484 0.807479641 0.505563901 0.581977245 0.504630904 1 18.10855253 -1.837237724 2.677968619 1.15849775 0.567571183 0.672791202 0.094150274 9959209.236 6652520.143 10125930.54 0.020698335 0.014546626 1.837237724 -0.590926568 RPWRPEEAVEDPDEEDEDNT(ph)SEAENGFSLEEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.563)S(0.437)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.5)S(0.5)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.55)S(0.45)EAENGFSLEEVLR 161.96 1.54E-12 422554000 57030 41533 33396.6 55216 55667 40364 61249 51390 63611 TRUE FALSE 54334.30492 45765.25992 34927.86714 49665.58278 65375.30718 38966.18456 51904.34013 46890.01916 73475.469 0.739489052 0.622864482 0.475367733 0.675947816 0.889756922 0.530329171 0.706417269 0.638172438 1 16.16497504 -1.506503638 2.540419956 1.018906782 0.660700422 0.473735516 0.112684902 4566291.385 4333033.412 598438.5505 0.027289745 0.031152748 1.506503638 -0.358206359 RPWRPEEAVEDPDEEDEDNTS(ph)EAENGFSLEEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.042)S(0.958)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.053)S(0.947)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.164)S(0.836)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.095)S(0.905)EAENGFSLEEVLR 312.98 1.10E-104 861924000 383261 268192 233797 372088 344073 314126 432852 364342 432512 TRUE FALSE 365145.0121 295521.0697 244516.8237 334685.0073 404079.2223 303247.7379 366812.4775 332438.283 499583.752 0.730898494 0.59153459 0.489441105 0.669927727 0.808831794 0.607000801 0.734236204 0.665430534 1 18.93036703 -2.216163666 0.289088573 1.426985298 0.628927103 0.610249312 0.086008137 25.94938788 1.022207484 7.280074076 0.094827563 0.006079059 2.216163666 -0.798058195 RPYDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 102 0.013948 889490000 741420 579613 486207 585544 805240 523085 755710 612816 773920 FALSE TRUE 706374.546 638676.2237 508500.0719 526684.0047 945673.6011 504970.4353 640412.5599 559154.5823 893935.561 0.790185084 0.714454432 0.568833028 0.589174464 1.0578767 0.564884604 0.716396783 0.625497638 1 19.76981131 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR 32 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;; 285.93 2.76E-74 1584410000 773025 588270 626721 728314 829579 711524 844880 749526 748552 FALSE TRUE 736485.6402 648215.3818 655456.7778 655102.493 974257.3149 686883.7455 715978.0387 683893.53 864633.6211 0.851789269 0.749699487 0.75807459 0.757664839 1.126786296 0.79442174 0.828071013 0.790963378 1 19.72172941 RPYPDPEDEIPDEMIQCVVCEDWFHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RPYPDPEDEIPDEMIQCVVCEDWFHGR 27 1 E9PCJ7;Q8N806;H0YJA0;H0YJM2 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ;;; 174.86 1.05E-12 81860600 29873.3 26382.2 31900.7 32111.1 37045.8 25382.7 34023.6 31311.5 31032.1 FALSE TRUE 28461.24831 29070.57617 33363.37865 28883.23122 43506.57579 24503.69073 28832.67493 28569.69907 35844.39958 0.794022181 0.811021429 0.930783582 0.805794812 1.213762158 0.68361281 0.804384374 0.797047779 1 15.12946011 -2.556629582 2.074537555 3.170710161 0.848031024 0.0930325 0.14071859 5917573.437 444501.4881 60236167.21 0.031865344 0.002775687 2.556629582 -2.322679137 RPYTVILIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RPYTVILIER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 142.1 0.00014151 338810000 450400 379250 388960 452580 458530 380130 482250 433080 437380 FALSE TRUE 429110.4846 417896.0062 406794.2007 407085.7986 538497.4868 366966.0028 408673.9054 395157.2193 505206.6566 0.849376149 0.827178345 0.805203565 0.80578075 1.06589547 0.726368107 0.808924229 0.782169463 1 18.94651412 -2.430842277 2.254725458 2.565477449 0.832825502 0.257850166 0.088564038 3925277.476 607971.9488 31139628.57 0.021144237 0.003708154 2.430842277 -1.732651947 RQACTAQT(ph)PEPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQACTAQTPEPLRR 14 2 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 RQACTAQT(1)PEPLRR;RQACT(0.004)AQT(0.996)PEPLRR 154.31 0.00029321 407879000 130857 96890 129704 117643 153241 131241 169138 154344 219260 TRUE FALSE 124671.6489 106763.2012 135651.0567 105817.3021 179966.1819 126696.0913 143332.8917 140828.8211 253261.721 0.492264083 0.421552853 0.535616106 0.417817986 0.710593694 0.500257563 0.565947713 0.556060429 1 17.95026951 -5 0.204272882 3.263196553 0.441965686 0.79825874 0.076578778 55.86914435 0.554613741 51.58889564 0.157020207 1.00E-05 5 -2.821230867 RQAQQERDELADEIANSSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQAQQERDELADEIANSSGK 20 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 150.68 4.76E-08 648140000 612350 425367 608040 595920 551160 606890 772760 660980 710290 FALSE TRUE 583405.4291 468712.3809 635919.2354 536016.9894 647282.1295 585873.2471 654861.2693 603101.0871 820438.1455 0.711090083 0.571295208 0.77509711 0.653330166 0.788946897 0.71409801 0.798184815 0.735096351 1 19.64603504 -5 0.124359813 1.996377393 0.573216177 0.699355048 0.06096784 71.18409471 0.56727292 17.58397177 0.469601203 1.00E-05 5 -1.423161216 RQATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQATVSWDSGGSDEAPPKPSRPGYPSPR 28 3 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 RQATVSWDSGGSDEAPPKPS(0.059)RPGYPS(0.941)PR;RQATVSWDSGGS(0.042)DEAPPKPS(0.322)RPGYPS(0.636)PR 193.4 1.13E-17 407900000 173505 133646 172972 179655 155714 162208 218710 201321 187971 TRUE FALSE 165303.7625 147264.6793 180902.9373 161595.7381 182870.4723 156590.6963 185341.7726 183692.266 217120.5827 0.761345426 0.678262178 0.833191101 0.744267246 0.842253047 0.721215347 0.853635203 0.846038011 1 17.72813697 -0.512885322 0.206496916 1.149543379 0.697765208 0.687309006 0.050290932 6.656264216 0.392999907 0.744869938 0.13428446 0.306983249 0.512885322 -0.451778171 RQAVDVSPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RQAVDVSPLR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;; 209.8 1.43E-07 1566930000 1169220 1065991 762075 898272 1260292 858978 1247341 1042639 1238307 FALSE TRUE 1113953.288 1174616.695 797016.8925 807975.992 1480086.526 829231.3765 1057036.221 951340.0018 1430337.325 0.7788046 0.821216558 0.557223026 0.564884925 1.034781446 0.579745324 0.739011842 0.665115833 1 20.447924 -1.270632403 3.347853793 1.000981859 0.725490181 0.273645449 0.144085005 32950954.26 48291099.71 332414.3296 0.032268965 0.053625036 1.270632403 -0.275491678 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;;; 286.37 2.23E-61 318667000 326967 326796 300208 366532 262218 323922 364132 371143 305672 FALSE TRUE 311511.9179 360096.8839 313972.8337 329687.507 307948.7362 312704.4999 308576.9757 338643.7514 353074.0526 0.882284936 1.019890534 0.889254907 0.933763058 0.872193054 0.885662647 0.873972396 0.959129534 1 18.42961128 4.782708054 22.42373011 0.923040821 0.882284392 0.063791485 0.051909928 6808.86358 4667397.797 0.012324385 1.469336058 60632.85999 -4.782708054 -0.040756429 RQDFNPCEYDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQDFNPCEYDLK 12 1 Q9BZE9;Q9BZE9-2;J3QL04;C9JAL9;J3QR50;J3QRW3;J3KRG1 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 ; 114.74 0.0016432 202559000 414950 333290 337780 418730 311430 392900 434720 435950 378330 FALSE TRUE 395336.1359 367252.6299 353267.5471 376638.4649 365743.2934 379293.7745 368395.4798 397775.9069 436999.4842 0.904660418 0.840396026 0.808393511 0.861873935 0.836942163 0.867950165 0.843011246 0.910243424 1 18.73727205 0.941268309 2.99605823 0.99984804 0.852926757 0.78681266 0.024852164 0.134892523 2.917089488 0.023732619 0.006237762 8.735108607 -0.941268309 -0.146921284 RQDLEDSLQAQQYFADANEAESWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQDLEDSLQAQQYFADANEAESWMR 25 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 234.45 3.51E-38 309201000 149226 132143 132717 154947 157592 127808 171033 146513 174570 FALSE TRUE 142172.3827 145608.5219 138802.2057 139371.4332 185075.9949 123381.9769 144938.7746 133683.545 201641.424 0.705075276 0.722116116 0.688361563 0.691184531 0.917847093 0.611888046 0.718794639 0.662976596 1 17.62143252 -1.098355167 4.026280088 1.000055487 0.715095621 0.563883009 0.078829058 16209586.7 38261823.18 15146.59975 0.017172255 0.079734235 1.098355167 -0.284959867 RQDLLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RQDLLSR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;;; 141.52 0.004091 8218540000 3007380 2270684 2234039 2591678 3277580 2261137 3254880 2729300 3485840 FALSE TRUE 2865227.107 2502069.281 2336471.898 2331157.604 3849188.914 2182833.259 2758288.276 2490308.023 4026406.264 0.711609043 0.621415008 0.58028717 0.57896731 0.955986222 0.542129412 0.685049668 0.618493977 1 21.94106132 -1.210600662 3.409658495 1.00066781 0.661398209 0.456881683 0.115902712 32450999.01 47608337.74 235045.0924 0.025773553 0.061574279 1.210600662 -0.339269601 RQDS(ph)SRKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQDSSRKPR 9 3 B1AK53;A0A1B0GUN9 B1AK53 ESPN Espin 1 RQDS(0.709)S(0.291)RKPR 86.911 0.076358 123790000 96084 76364 86397 101930 69035 85688 119850 93599 107640 TRUE FALSE 91542.29974 84145.57842 90358.38791 91683.80275 81074.68214 82720.60307 101564.6813 85402.97536 124332.2615 0.736271493 0.676779924 0.726749332 0.737409596 0.652080813 0.665318897 0.816881155 0.686893123 1 16.92384117 -0.832861028 0.490787314 1.078793933 0.704204209 0.77926636 0.047929971 6.605551888 1.111739761 0.831652456 0.022592734 0.14693964 0.832861028 -0.374589724 RQEAIAQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQEAIAQNR 9 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 137.46 0.00026308 47866000 19875 17711 15897 21585 20183 17356 18389 19506 22852 FALSE TRUE 18935.54814 19515.77104 16625.89317 19415.23479 23702.90881 16754.95737 15583.42031 17797.95123 26395.77145 0.717370514 0.739352175 0.629869569 0.735543374 0.897981287 0.634759147 0.590375634 0.674272819 1 14.68801921 -0.85213825 4.32705256 1.000003161 0.700078977 0.550755361 0.084433571 27331471.6 68564544.1 1466.150595 0.021129004 0.140560001 0.85213825 -0.299924184 RQEELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQEELQR 7 1 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 101.43 0.014534 29859000 51673 59867 63506 59725 36472 54747 45638 51560 45805 FALSE TRUE 49230.5197 65967.51536 66417.81292 53721.32953 42832.70525 52851.09766 38675.0849 47045.13306 52908.20546 0.930489312 1.246829576 1.255340497 1.015368582 0.809566397 0.998920625 0.730984628 0.889184062 1 15.69120386 2.971807257 4.958211554 0.869556929 1.136676082 0.496609526 0.118348711 0.149379722 9.646154003 0.035451374 0.039367203 937.1460017 -2.971807257 0.267119153 RQEENDKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQEENDKLR 9 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 129.85 0.00021242 125920000 265410 212100 224670 265090 221460 252630 335980 305740 255220 FALSE TRUE 252864.5953 233713.2311 234971.3417 238442.6496 260082.5539 243881.3598 284720.0803 278967.7848 294798.2141 0.857754841 0.792790526 0.797058227 0.808833426 0.882239245 0.827282351 0.96581345 0.946300796 1 18.16936826 1.730528351 1.164859644 0.992960965 0.817032929 0.819439187 0.031287367 0.171394729 0.435550624 0.024677195 0.009634061 53.76855329 -1.730528351 -0.175928036 RQELDAFLAQALSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQELDAFLAQALSPK 15 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 107.07 0.0019019 41473000 120470 93805 97789 115730 105570 111390 116770 118040 118020 FALSE TRUE 114775.6218 103363.8361 102272.7224 104096.6005 123981.3746 107532.5364 98954.59187 107703.7918 136321.9388 0.841945345 0.758233319 0.750229371 0.763608568 0.909474848 0.788813138 0.725888971 0.790069396 1 17.05665823 -1.042640743 6.196386646 1.000000248 0.787906512 0.613139761 0.052112258 1.78E-07 2.75E-08 0.050295048 0.011854643 0.090648215 1.042640743 -0.212093736 RQELEAELAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQELEAELAK 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 0 103.43 0.0045138 80311000 116070 112950 102910 104390 104540 109190 128950 125960 113870 FALSE TRUE 110583.6011 124459.7334 107628.5253 93896.51887 122771.7429 105408.7229 109276.3092 114930.2746 131528.378 0.840758495 0.946257646 0.818291284 0.71388791 0.933423986 0.801414299 0.830819256 0.873805914 1 17.00501458 0.865661122 4.948467679 0.999995023 0.846717506 0.366384901 0.065169287 1.498170889 54.08940734 0.061318254 0.01550643 7.339409537 -0.865661122 -0.153277517 RQEQIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQEQIAK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;; 139.88 0.0042686 2802460000 1469080 1149676 1193789 1436890 1220489 1415534 1714035 1571537 1487005 FALSE TRUE 1399639.5 1266829.291 1248525.406 1292451.087 1433341.895 1366513.703 1452527.48 1433924.889 1717602.141 0.814879923 0.737556889 0.726900239 0.752474078 0.834501693 0.795593852 0.845671676 0.834841117 1 20.71196446 0.608826144 0.473799402 1.012005019 0.7594321 0.831080523 0.031829508 0.680212674 0.307638911 0.051275709 0.018408917 4.062806552 -0.608826144 -0.252572918 RQEQIQAMPLADSQAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 102.07 0.0015486 330460000 202159 189819 211790 245460 221910 211000 221210 223380 216920 FALSE TRUE 192603.3447 209161.7719 221500.781 220785.8945 260611.0337 203693.0171 187460.3517 203819.663 250558.8457 0.768695051 0.834781032 0.884026985 0.881173817 1.040119071 0.812954803 0.748168963 0.813460257 1 17.93478995 -2.500594002 2.223910679 3.060064742 0.841306878 0.256712075 0.080629248 3591677.858 338677.7378 37697142.88 0.021081702 0.003157955 2.500594002 -2.218757864 RQEQPSIES(ph)TSPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.583)T(0.208)S(0.208)PIS(0.001)R 95.361 0.0017978 0 135070 104880 131110 139670 142820 123360 155710 131290 137170 TRUE FALSE 128685.5088 115567.3912 137121.5232 125630.1062 167727.7628 119088.0123 131953.5797 119793.5516 158441.623 0.812195093 0.729400451 0.865438769 0.792911003 1.058609219 0.751620755 0.832821434 0.756073747 1 17.27359186 -2.311476737 2.161463974 1.846133832 0.820451295 0.260597705 0.092433219 6465471.641 858838.4876 26716072.3 0.021064862 0.004881162 2.311476737 -1.025682537 RQEQPSIESTS(ph)PISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.099)T(0.027)S(0.874)PISR 214.24 1.53E-12 260040000 190490 162280 212550 226910 195060 218720 230230 195550 206860 TRUE FALSE 181485.9152 178816.5165 222295.6277 204100.5757 229078.4022 211145.6716 195104.185 178426.6053 238938.7923 0.759549814 0.74837792 0.93034549 0.854196063 0.958732569 0.883681003 0.816544619 0.746746075 1 17.86628157 3.754002362 24.56154551 0.87502112 0.753963847 0.358916268 0.071595458 664.8233926 1057460.179 0.017659904 0.03168588 5675.476925 -3.754002362 -0.121057273 RQEQTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RQEQTLR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;;; 175.38 0.0012688 4890920000 2879913 2528504 2046845 2704362 2550689 2414785 2958088 2775781 2604980 FALSE TRUE 2743785.22 2786161.432 2140694.868 2432514.394 2995528.354 2331160.39 2506777.347 2532718.9 3008946.994 0.911875558 0.925958961 0.711443197 0.808427134 0.99554042 0.774742923 0.833107845 0.841729318 1 21.52082726 RQES(ph)SSSLEMPSGVALEEGAHVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQESSSSLEMPSGVALEEGAHVLR 24 1 P48553 P48553 TRAPPC10 Trafficking protein particle complex subunit 10 1 RQES(0.25)S(0.25)S(0.25)S(0.25)LEMPS(0.001)GVALEEGAHVLR;RQES(0.465)S(0.156)S(0.361)S(0.017)LEMPSGVALEEGAHVLR 178.89 1.67E-17 92702000 56289 39779 48555 57863 61856 47327 59860 43459 63436 TRUE FALSE 53628.33052 43832.52532 50781.29478 52046.50131 72643.66682 45688.05412 50727.2576 39653.49957 73273.33089 0.731894263 0.598205715 0.693039257 0.710306201 0.99140664 0.623529101 0.692301783 0.541172335 1 16.16100058 -2.269137783 2.300709741 2.264225667 0.696243661 0.388949958 0.119052599 7652584.343 1163810.641 50376787.16 0.027411689 0.00538099 2.269137783 -1.567982005 RQGSFS(ph)EDVISHK ddPTM_SK-BR-3_Trastuzumab_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(0.362)FS(0.638)EDVISHK 89.877 0.0044395 118820000 199770 155870 159330 186130 154280 178970 193060 192370 168880 TRUE FALSE 190327.268 171753.3302 166635.4381 167419.8588 181186.3832 172772.224 163605.1512 175525.063 195069.0479 0.975691787 0.88047454 0.85423823 0.858259476 0.928832048 0.885697787 0.838703797 0.899809913 1 17.57362535 4.535033475 2.550020541 0.883518779 0.97830787 0.211528015 0.046506291 0.403182356 4.454920789 0.010505483 0.067832405 34279.42076 -4.535033475 0.09478909 RQGSVVS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQGSVVSSR 9 1 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 RQGS(0.113)VVS(0.444)S(0.444)R 87.568 0.014166 60001000 96390 87182 89668 94588 102060 92592 113140 97498 127790 TRUE FALSE 91833.83573 96065.94492 93779.36649 85079.83453 119859.2317 89385.51582 95878.41504 88960.55825 147607.0205 0.622150866 0.650822329 0.635331342 0.576394227 0.812015792 0.605564122 0.649551862 0.602685143 1 17.17140182 -1.884204452 2.483550309 1.183121696 0.644896747 0.754368573 0.063784275 5165749.469 2873345.908 5549694.305 0.013908586 0.013055561 1.884204452 -0.53822495 RQHEAEEGVR ddPTM_SK-BR-3_Trastuzumab_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 ; 140.07 2.59E-05 113316000 55007 51490 49965 57926 63357 51610 59156 54971 69780 FALSE TRUE 52406.92812 56736.88954 52255.94467 52103.16843 74406.44074 49822.73276 50130.66573 50157.44782 80601.12601 0.650200943 0.703921798 0.648327725 0.646432265 0.923143936 0.618139413 0.621959868 0.622292148 1 16.29851237 -1.110617635 4.701026027 1.000021211 0.678206508 0.555176152 0.090209898 1.91E-05 3.62E-06 0.083377306 0.019650925 0.077514396 1.110617635 -0.321814703 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR 32 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 191.99 6.45E-20 143190000 47593 51056 51830 54492 56369 47957 60028 54881 62719 FALSE TRUE 45343.37321 56258.66445 54206.45677 49014.36063 66199.73575 46296.23707 50869.62611 50075.3287 72445.1422 0.62589943 0.776569177 0.74824143 0.676572081 0.913791232 0.639052332 0.702181327 0.691217205 1 16.14460133 -1.243760487 3.396007879 1.000751897 0.720964322 0.534436943 0.081631577 14455813.59 22029585.05 114078.7686 0.018669869 0.05704788 1.243760487 -0.279787575 RQLEEAEEEAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 247.14 2.11E-16 2341170000 1625860 1301044 1576419 1574740 1774440 1530360 1946873 1723499 1450120 FALSE TRUE 1549008.82 1433621.863 1648699.37 1416444.143 2083901.774 1477363.249 1649841.767 1572580.291 1674997.203 0.924782929 0.855895078 0.984299775 0.845639706 1.244122539 0.882009383 0.984981804 0.938855472 1 20.67572726 RQLS(ph)MTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQLSMTLR 8 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RQLS(0.996)MT(0.004)LR 74.944 0.024297 91373000 36021 32458 36282 38090 46828 36505 39256 27378 42470 TRUE FALSE 34318.35872 35765.5071 37945.56559 34261.12083 54994.78837 35240.8227 33266.77621 24980.63718 49056.03069 0.699574716 0.729074623 0.773514796 0.69840793 1.121060705 0.718379009 0.67813836 0.50922663 1 15.58214288 3.893897576 1.866135898 0.773916649 0.705125872 0.027544587 0.169858205 1.805204613 12.19159673 0.046890865 0.118391112 7832.449005 -3.893897576 -0.068790777 RQLS(ph)PQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQLSPQSK 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RQLS(1)PQSK;RQLS(1)PQSK;RQLS(1)PQSK;RQLS(1)PQSK 126.03 0.00075756 1033130000 1255930 1006790 1072730 1234300 959970 1200730 1367790 1272660 1149340 TRUE FALSE 1196564.678 1109383.046 1121915.732 1110225.819 1127388.464 1159148.419 1159108.514 1161219.144 1327573.777 0.901316897 0.835647001 0.845087294 0.836281823 0.849209651 0.873132958 0.8731029 0.874692739 1 20.34036061 0.052503949 0.713798685 1.00481735 0.85579436 0.841064247 0.019217197 1.676100346 0.946015803 0.040957647 0.007021061 1.128506198 -0.052503949 -0.14902299 RQNGDDPLLTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQNGDDPLLTYR 12 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 ;;; 165.51 8.73E-05 1438660000 1823190 1513260 1446010 1594850 1861340 1445220 1907230 1656300 1889120 FALSE TRUE 1737011.422 1667462.914 1512310.989 1434532.648 2185957.107 1395171.669 1616247.035 1511265.591 2182075.081 0.796036505 0.764163859 0.693060932 0.657416722 1.001779052 0.639378398 0.740692678 0.692581848 1 21.05726931 -1.337359713 3.14609907 1.002025457 0.75008196 0.376947889 0.101734673 13340021.63 18541812.75 256690.4993 0.022441036 0.045987551 1.337359713 -0.251943498 RQQEEMMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQQEEMMR 8 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 182.29 0.0003677 480120000 224687 166371 135119 170177 281640 162408 263100 217385 271130 FALSE TRUE 214066.4908 183324.394 141314.3398 153070.4846 330757.9268 156783.7702 222959.2628 198349.617 313175.4557 0.683535338 0.585372802 0.451230571 0.488769097 1.056142558 0.500625983 0.711930832 0.633349815 1 18.25661162 RQQEGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 127.02 0.0062459 1752180000 1560970 1410300 1210440 1673350 1215020 1482340 1659840 1628870 1339210 FALSE TRUE 1487186.042 1554011.173 1265939.871 1505141.679 1426919.103 1431006.194 1406600.923 1486237.508 1546887.847 0.961405214 1.00460494 0.818378575 0.973012802 0.922445093 0.92508723 0.909310216 0.960792025 1 20.56093717 0.99064508 20.75521034 1.000000005 0.935732105 0.170850827 0.048935617 84.73581387 188003.5025 0.046055432 0.011513858 9.786898405 -0.99064508 -0.0642679 RQQEQQVPILEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 166.62 8.25E-05 22131910000 11207520 9424830 10387150 12119500 9106040 11064360 13467320 12247020 11441230 FALSE TRUE 10677762.74 10385230.89 10863411.1 10901224.83 10694130.49 10681198.44 11412632.99 11174606 13215477.51 0.807974039 0.78583849 0.822021837 0.824883159 0.809212568 0.808234014 0.863580826 0.845569598 1 23.65572522 -0.561513109 0.333390478 1.067713217 0.795401674 0.941370644 0.014583805 1.909241598 0.21438699 0.15310982 0.013107768 0.27446495 0.561513109 -0.272311543 RQQPPLGPSSS(ph)LLSLPGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQQPPLGPSSSLLSLPGLK 19 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RQQPPLGPS(0.008)S(0.084)S(0.908)LLSLPGLK 136.64 3.33E-06 215360000 291710 247650 277700 278750 230370 291360 309590 341640 328260 TRUE FALSE 277921.4464 272885.8166 290432.8197 250729.5204 270546.4551 281270.1301 262356.3595 311724.1905 379164.8843 0.732983084 0.71970224 0.765980268 0.661267778 0.713532466 0.741814819 0.691932113 0.822133598 1 18.53246583 0.934899223 3.384204367 0.99975537 0.719041673 0.910072917 0.028398291 0.074795888 2.132988775 0.025260613 0.006550348 8.607939848 -0.934899223 -0.280713698 RQQVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQQVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 140.09 0.0042457 272322000 360119 325065 266496 341416 415594 292486 397137 353151 415901 FALSE TRUE 343096.8886 358189.4931 278715.1052 307096.215 488073.462 282357.1365 336546.4567 322227.2263 480396.803 0.714194779 0.745611734 0.580176853 0.639255326 1.01597983 0.587758151 0.700559318 0.670752229 1 18.87386702 -1.448386569 5.709902658 1.000206715 0.708237137 0.364388036 0.121689541 0.000294172 2.84E-05 0.108239568 0.025494438 0.035613399 1.448386569 -0.291969577 RQS(ph)FASLALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RQSFASLALR 10 1 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;H0YA66;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 RQS(1)FASLALR;RQS(1)FASLALR;RQS(0.957)FAS(0.043)LALR;RQS(1)FASLALR;RQS(1)FASLALR 237.59 2.17E-12 3606380000 1387300 1052033 720703 778656 1605090 862011 1555360 1140330 1545610 TRUE FALSE 1321725.078 1159236.359 753747.9454 700384.0195 1885017.188 832159.3429 1318061.266 1040476.66 1785295.305 0.740339749 0.649324711 0.422197909 0.392307098 1.05585736 0.466118597 0.738287533 0.582803672 1 20.7677313 -4.999984902 0.399277915 6.81259492 0.631085759 0.26456237 0.1929243 1015.226787 7.108428653 5143.295905 0.110733502 1.00E-05 4.999984902 -6.181509161 RQS(ph)FAVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR 165.66 0.00019782 9018700000 2207414 1727212 1872879 2126100 2288655 2200799 2538520 1841761 2675427 TRUE FALSE 2103073.915 1903216.866 1958752.355 1912380.389 2687795.707 2124584.779 2151222.151 1680486.643 3090318.555 0.680536287 0.615864298 0.633835095 0.618829533 0.869747134 0.687497014 0.696116634 0.543790749 1 21.55932413 -1.469626799 3.440341646 1.004931822 0.670590682 0.605114932 0.084197516 32262343.05 45751738.98 1520391.205 0.019423272 0.033913546 1.469626799 -0.334341139 RQS(ph)GLYDSQNPPTVNNCAQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RQSGLYDSQNPPTVNNCAQDR 21 1 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 RQS(1)GLYDSQNPPTVNNCAQDR;RQS(0.999)GLYDSQNPPTVNNCAQDR;RQS(0.999)GLYDSQNPPTVNNCAQDR 222.46 2.40E-25 845070000 313653 287721 258780 318742 287632 263931 299711 303770 288184 TRUE FALSE 298827.2443 317040.097 270645.319 286701.4486 337794.9297 254791.0033 253984.5824 277170.2884 332874.1029 0.897718512 0.952432449 0.813056097 0.861290939 1.014782847 0.765427533 0.763004932 0.832658011 1 18.34461711 2.211623632 24.99996289 0.812392687 0.906587542 0.097716765 0.084943554 315.8709918 293155.0085 0.029364089 0.02169261 162.7884664 -2.211623632 0.094194855 RQS(ph)HLLLQSSIPDQQLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RQSHLLLQSSIPDQQLLK 18 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 RQS(1)HLLLQSSIPDQQLLK;RQS(0.767)HLLLQS(0.116)S(0.116)IPDQQLLK;RQS(0.954)HLLLQS(0.023)S(0.023)IPDQQLLK 194.04 5.70E-15 542990000 980300 822730 830840 994430 720970 918910 1122760 1084600 727570 TRUE FALSE 933963.1618 906567.1224 868934.8358 894468.0071 846706.9397 887087.9163 951462.3411 989626.6742 840397.8397 1.111334558 1.078735665 1.033956532 1.064338775 1.007507278 1.055557112 1.132157052 1.177569274 1 19.68071293 1.751534805 11.95883877 1.115743753 1.062266327 0.125230884 0.051659496 0.220986402 169.8217008 0.02292252 0.012570059 56.43321656 -1.751534805 -0.053477425 RQS(ph)ILFSTEV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RQSILFSTEV 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RQS(1)ILFSTEV;RQS(1)ILFSTEV;RQS(1)ILFSTEV 93.928 0.0089526 170205000 274473 241381 205523 229036 302747 203372 277850 256132 301456 TRUE FALSE 261499.2052 265977.9983 214946.4328 206012.8661 355545.9809 196329.1766 235458.8794 233703.7242 348204.2569 0.750993706 0.763856251 0.617299842 0.591643732 1.021084533 0.563833362 0.676209078 0.671168487 1 18.40957431 -2.085142524 2.343213106 1.460507477 0.709114553 0.340177765 0.128207481 10972719.97 3148206.371 26980908.95 0.028671182 0.008219729 2.085142524 -0.751392925 RQS(ph)KSEHETSDAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSKSEHETSDAKK 14 3 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RQS(0.472)KS(0.472)EHET(0.028)S(0.028)DAKK 98.796 0.001738 19548000 41546 25205 34314 37968 23172 44878 61211 53674 26282 TRUE FALSE 39582.20292 27773.41816 35887.33084 34151.38451 27213.18946 43323.86361 51872.13773 48974.02002 30357.67833 1.303861332 0.914872931 1.182150046 1.12496694 0.896418664 1.427113863 1.708699103 1.61323338 1 14.88977384 2.093524891 6.143905219 1.530874971 1.089087014 0.361095615 0.222279287 0.166857369 9.061949996 0.076162625 0.055853427 124.029471 -2.093524891 -0.441787958 RQS(ph)LATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQSLATK 7 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 RQS(0.995)LAT(0.005)K;RQS(1)LATK 132.32 0.0020706 802256000 744080 727090 678660 804960 511800 768610 870360 892590 693390 TRUE FALSE 708908.813 801181.2976 709777.2323 724043.8915 601057.758 741992.843 737570.5967 814430.0877 800917.3799 0.885121026 1.000329519 0.886205307 0.904018204 0.750461624 0.926428695 0.920907219 1.016871538 1 19.6112939 1.341499297 2.983008998 1.010492014 0.899832704 0.366672736 0.061429141 0.315754896 4.619706664 0.053261185 0.016453593 21.95327397 -1.341499297 -0.110659311 RQS(ph)LTSPDSQSARPANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQSLTSPDSQSARPANR 17 2 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.873)LT(0.095)S(0.032)PDSQSARPANR;RQS(1)LTSPDSQSARPANR;RQS(0.992)LT(0.008)SPDSQSARPANR;RQS(0.939)LT(0.045)S(0.007)PDS(0.008)QSARPANR 198.98 7.15E-12 240059000 93989.9 69988.1 94941.2 84213.3 99004.1 92991.6 116978.5 98112.3 116382 TRUE FALSE 89547.1837 77119.96696 99294.34793 75748.01909 116270.3837 89771.27757 99131.28137 89521.06689 134429.9262 0.666125365 0.573681539 0.738632764 0.563475866 0.864914435 0.667792359 0.737419741 0.665931087 1 17.03649481 -4.999999999 0.171422717 2.259937047 0.603954981 0.583519682 0.084558143 83.97887285 0.794598175 35.961986 0.264252365 1.00E-05 4.999999999 -1.655982066 RQS(ph)LYENQV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSLYENQV 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 RQS(0.991)LY(0.009)ENQV 58.676 0.048174 0 56929 45413 49510 51249 52546 51576 59531 50605 69523 TRUE FALSE 54238.07899 50040.63633 51780.08247 46097.35315 61710.00576 49789.91019 50448.45259 46173.75793 80304.27177 0.675407146 0.623137913 0.644798606 0.574033637 0.768452343 0.620015711 0.628216301 0.574985078 1 16.29318911 -1.185542671 4.490397937 1.000078206 0.639867143 0.810284445 0.054949458 3.94E-05 7.14E-06 0.048027396 0.011317682 0.065231495 1.185542671 -0.360211063 RQS(ph)MKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSMKEK 7 2 Q9H307 Q9H307 PNN Pinin 1 RQS(1)MKEK 66.19 0.053983 170470000 385610 205750 381000 341080 228160 371240 511420 447660 324070 TRUE FALSE 367382.9795 226716.1589 398469.2269 306793.9904 267951.0318 358383.8657 433393.4861 408460.5172 374325.1205 0.981454248 0.605666429 1.064500364 0.819592311 0.715824339 0.957413345 1.15779963 1.091191841 1 18.51393234 1.991841901 5.552912201 1.092226514 0.828297381 0.422224273 0.131034449 0.142902975 15.13861276 0.051519388 0.034038718 98.13906164 -1.991841901 -0.263929133 RQS(ph)MLF ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RQSMLF 6 1 Q00537 Q00537 CDK17 Cyclin-dependent kinase 17 1 RQS(1)MLF;RQS(1)MLF;RQS(1)MLF 115.49 0.025828 138480000 298340 261063 271852 310534 320980 244614 323930 292666 319010 TRUE FALSE 284238.0595 287665.6165 284316.6831 279318.5323 376958.8104 236142.9558 274508.5291 267038.6135 368480.4415 0.771378959 0.780680829 0.771592332 0.758028109 1.023009006 0.640856147 0.74497449 0.724702273 1 18.49122852 -2.229223195 2.31629956 1.763532448 0.775189353 0.346832783 0.096190783 3725604.212 670064.4568 14950440.93 0.021560658 0.005898978 2.229223195 -0.988343095 RQS(ph)NLQEVLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSNLQEVLER 11 1 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 RQS(1)NLQEVLER 153.56 0.00073638 0 42098 35795 41425 41476 41012 41516 49033 43055 50049 TRUE FALSE 40108.11097 39442.5512 43324.37722 37306.75368 48164.47982 40078.29051 41552.1153 39284.87595 57810.34331 0.693787801 0.682274986 0.74942259 0.645330084 0.833146407 0.693271969 0.718766105 0.679547529 1 15.81904002 -2.021751668 2.284003697 1.324324361 0.710715697 0.76069853 0.050770465 5322353.614 1813981.934 9048939.485 0.011118421 0.009511485 2.021751668 -0.613608665 RQS(ph)PEPSPVTLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RQS(1)PEPSPVTLGR 130.38 8.74E-05 1709240000 1487640 1348070 1320320 1596710 1545260 1567530 1637200 1476280 1662480 TRUE FALSE 1417322.205 1485439.866 1380857.978 1436205.677 1814752.855 1513246.043 1387415.071 1347009.097 1920288.908 0.738077588 0.773550198 0.71908866 0.74791125 0.945041576 0.788030404 0.722503299 0.701461687 1 20.87289195 -1.524742781 2.84138982 1.010395638 0.766781807 0.535011537 0.068277076 13427952.04 14474919.17 1079028.71 0.01705243 0.029871513 1.524742781 -0.243613831 RQS(ph)PLPPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK 115.91 0.0014815 34822250000 25368340 18950180 20886210 24329680 19527670 22005620 25977390 23213410 22334580 TRUE FALSE 24169228.84 20881224.89 21843863.39 21884014.34 22933289.47 21243559.86 22014062.05 21180720.76 25798112.6 0.936860352 0.809409014 0.846723314 0.848279666 0.88895222 0.823454033 0.853320644 0.821018231 1 24.62076219 -1.652931137 6.076662868 1.001137082 0.853845501 0.610280236 0.036790396 0.000537066 3.07E-05 0.033756327 0.007897011 0.022236625 1.652931137 -0.147291581 RQS(ph)PLPPQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RQSPLPPQKK 10 2 Q01105;B2REB7 Q01105 SET Protein SET 1 RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK;RQS(1)PLPPQKK 90.759 0.0068104 17803300000 14769550 11969510 12676890 14207380 8992130 13659130 14781710 14317290 10873490 TRUE FALSE 14071422.64 13189216.68 13258137.95 12779227.17 10560354.62 13186110.9 12526488.65 13063592.19 12559695.3 1.120363378 1.050122345 1.05560984 1.017479077 0.840812964 1.049875064 0.997356095 1.040120153 1 23.58229813 3.656880652 1.430573185 0.989720093 1.099109595 0.33212673 0.058783567 0.471371474 1.891109028 0.018018803 0.040404039 4538.16887 -3.656880652 0.109389502 RQS(ph)PS(ph)PSTRPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(0.998)PS(0.585)PS(0.239)T(0.178)RPIR 84.508 0.059996 963210000 409110 304430 351970 376110 392370 349920 434600 350370 431520 TRUE FALSE 389772.1811 335451.7631 368108.1726 338302.7082 460799.2038 337802.1827 368293.788 319689.7454 498437.9177 0.78198742 0.673006108 0.738523615 0.678725868 0.924486656 0.677721679 0.738896009 0.641383278 1 18.9270543 -1.14739143 4.890153658 1.000018143 0.732020659 0.528103289 0.079663153 1.41E-05 2.47E-06 0.069238844 0.016318648 0.071221083 1.14739143 -0.267997484 RQS(ph)PSPS(ph)TRPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(0.989)PS(0.333)PS(0.629)T(0.05)RPIR;RQS(0.995)PS(0.064)PS(0.916)T(0.024)RPIR;RQS(0.999)PS(0.02)PS(0.942)T(0.039)RPIR;RQS(1)PS(0.018)PS(0.941)T(0.041)RPIR 121.32 0.001861 9861530000 4403147 3324460 3814080 4178954 4484076 3859118.2 4393643 3619089 4544809 TRUE FALSE 4195018.968 3663226.254 3988959.341 3758877.604 5266097.435 3725475.969 3723312.066 3302182.381 5249594.768 0.799112913 0.697811244 0.759860431 0.716031955 1.003143608 0.709669248 0.709257044 0.629035674 1 22.32377463 -1.730502595 2.9899635 1.038744129 0.752225233 0.380425613 0.099062585 43401007.23 37510765.64 12464057.33 0.022670219 0.018599334 1.730502595 -0.286518896 RQS(ph)S(ph)GSATNVASTPDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 2 RQS(0.997)S(0.741)GS(0.257)AT(0.004)NVASTPDNR 126.63 9.64E-05 0 112560 77877 88500 106320 99814 93571 110830 99327 111620 TRUE FALSE 107239.5119 85812.75484 92557.81254 95632.51161 117221.53 90330.61281 93920.84797 90629.40131 128929.4595 0.831768878 0.665579109 0.717894986 0.741742903 0.9091912 0.700620426 0.728466933 0.702937883 1 16.97622242 -1.594623455 6.06206974 1.0008821 0.747105808 0.550339726 0.071045564 0.000809683 5.41E-05 0.065759809 0.015448207 0.025431768 1.594623455 -0.253776292 RQS(ph)S(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 2 RQS(0.928)S(0.595)T(0.476)PS(0.001)APELGQQPDVNISEWK 125.62 0.00018638 36906000 28098 26218 31193 35405 23117 34838 35953 32019 30814 TRUE FALSE 26769.86322 28889.64401 32623.2299 31846.02213 27148.59748 33631.55132 30467.70953 29215.24662 35592.47774 0.752121373 0.811678361 0.916576534 0.894740242 0.762762224 0.944906156 0.856015413 0.820826435 1 15.11928475 0.02491402 0.024731824 1.839977522 2.33E-06 0.409931393 0.06067564 483.8064621 3.728056897 150.5737072 126.4807362 1.059044039 -0.02491402 -1.839975195 RQS(ph)SGSATNVASTPDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RQS(0.692)S(0.281)GS(0.027)ATNVASTPDNR;RQS(0.941)S(0.058)GS(0.001)ATNVASTPDNR;RQS(0.498)S(0.498)GS(0.003)ATNVASTPDNR;RQS(0.923)S(0.07)GS(0.007)ATNVASTPDNR 286.22 2.21E-36 1659010000 581664 469438 501320 606209 642022 530203 741020 598234 717330 TRUE FALSE 554169.8955 517274.2659 524306.0179 545271.7196 753990.4335 511841.9372 627963.7892 545849.4595 828569.8728 0.668826992 0.6242977 0.632784313 0.658087794 0.909990163 0.617741429 0.757888755 0.658785067 1 19.66026384 -5 0.191870869 2.346833737 0.63249038 0.559247407 0.086587202 96.91909716 0.95014704 49.93728951 0.211626973 1.00E-05 5 -1.714343357 RQS(ph)SPSCGPVAETSSIGNGDGISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSSPSCGPVAETSSIGNGDGISK 24 1 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 RQS(0.831)S(0.162)PS(0.007)CGPVAETSSIGNGDGISK 143.82 1.46E-07 257090000 49592 41038 50985 48500 41622 54610 61039 60553 58760 TRUE FALSE 47247.88444 45219.81886 53322.71268 43624.68786 48880.86362 52718.84201 51726.37949 55250.65831 67872.2007 0.696130138 0.666249486 0.785634061 0.642747508 0.720189755 0.776736889 0.76211437 0.814039588 1 16.05053317 0.461670593 0.429650942 1.027506569 0.684434681 0.846351465 0.039110897 0.772150637 0.263762939 0.076786693 0.023407129 2.895146819 -0.461670593 -0.343071889 RQS(ph)SSYDDPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.879)S(0.095)S(0.025)Y(0.001)DDPWK 104.21 0.0016116 149020000 494780 465880 339450 646860 291260 474030 477440 540470 334140 TRUE FALSE 471392.73 513353.7017 355014.1183 581836.4038 342055.6518 457614.2222 404597.7592 493143.5816 385956.7246 1.221361619 1.330080988 0.919828819 1.507517208 0.886253898 1.185662 1.04829825 1.277717293 1 18.55807957 3.405137494 0.708682089 1.101016141 1.275073232 0.063546176 0.187597458 2.005196157 2.077355621 0.093295341 0.213612976 2541.777282 -3.405137494 0.174057091 RQS(ph)ST(ph)PSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 2 RQS(0.92)S(0.502)T(0.578)PS(0.001)APELGQQPDVNISEWK 160.99 1.58E-11 25501000 31614 25874 27334 34442 23904 31019 41365 32333 29556 TRUE FALSE 30119.66887 28510.59002 28587.29094 30979.82472 28072.85003 29944.80425 35054.00953 29501.75111 34139.39353 0.882255534 0.83512292 0.837369619 0.907450939 0.822300783 0.877133457 1.026790634 0.864155688 1 15.05914981 1.910462911 7.445847772 0.96401323 0.857020567 0.514652955 0.047689354 0.199470075 14.59929446 0.018060957 0.01124692 81.36973678 -1.910462911 -0.106992663 RQS(ph)VS(ph)PPYKEPSAYQSSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(0.999)VS(0.998)PPYKEPSAYQSSTR 48.489 0.085487 435110000 138730 145450 130850 155120 91271 154500 134660 142980 99315 TRUE FALSE 132172.5078 160271.5204 136849.6019 139527.0429 107188.6335 149149.6263 114115.1438 130459.9132 114716.263 1.152168877 1.39711246 1.192939853 1.216279534 0.934380451 1.300161131 0.994759948 1.137239916 1 16.80771041 2.959362467 12.16030288 1.084340975 1.258253642 0.334543451 0.116335106 1.560010945 465.7085566 0.032159784 0.034243373 910.6730142 -2.959362467 0.173912668 RQS(ph)VSGLHR ddPTM_SK-BR-3_Trastuzumab_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(1)VSGLHR 144.92 6.03E-05 2137120000 341637 330979 304881 395470 390431 326733 415585 338359 368451 TRUE FALSE 325488.4961 364706.1364 318860.0954 355716.6043 458522.0428 315418.1543 352179.8755 308730.4922 425588.4993 0.764796268 0.85694547 0.749221598 0.835822878 1.077383537 0.741134111 0.82751267 0.725420195 1 18.69909964 -2.479382259 2.331442219 3.302700178 0.824390278 0.235282398 0.10062821 9352244.623 1365110.237 112604938.1 0.022746848 0.003316025 2.479382259 -2.478309899 RQSHLLLQS(ph)SIPDQQLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSHLLLQSSIPDQQLLK 18 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 RQS(0.264)HLLLQS(0.368)S(0.368)IPDQQLLK 84.14 0.0018217 152620000 280160 238320 262020 270050 239100 258230 351510 292040 225810 TRUE FALSE 266917.392 262605.0789 274033.8762 242904.0609 280798.9643 249287.4304 297880.6936 266467.4294 260827.4615 1.023348502 1.0068153 1.050632761 0.93128254 1.076569785 0.955756073 1.142060318 1.021623367 1 17.99273625 1.750812177 25 1.068199213 1.009955222 0.122119219 0.055461949 5.196401179 10620.90542 0.022185896 0.012303186 56.33939475 -1.750812177 -0.058243991 RQSPEPS(ph)PVTLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSPEPSPVTLGR 13 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 RQS(0.074)PEPS(0.804)PVT(0.122)LGR 102.63 0.00049612 0 177990 145010 167800 206300 174790 176270 193790 169350 181780 TRUE FALSE 169576.7654 159786.6839 175493.796 185562.3321 205273.3207 170165.7257 164223.7763 154520.8162 209969.514 0.807625651 0.760999446 0.835806078 0.883758449 0.977633928 0.810430631 0.782131526 0.735920245 1 17.67982035 -2.480748455 2.314614213 3.323342538 0.820815022 0.398132939 0.067775786 2234160.727 590194.4712 26669585.84 0.017177226 0.003305609 2.480748455 -2.502527517 RQSS(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 RQS(0.092)S(0.757)T(0.151)PSAPELGQQPDVNISEWK;RQS(0.113)S(0.855)T(0.032)PSAPELGQQPDVNISEWK;RQS(0.075)S(0.801)T(0.124)PSAPELGQQPDVNISEWK;RQS(0.055)S(0.471)T(0.471)PS(0.002)APELGQQPDVNISEWK 273.68 6.90E-52 1268830000 1048224 769540 967910 1076240 885189 1089738 1296060 1139359 1094112 TRUE FALSE 998676.5289 847957.0009 1012289.631 968054.3105 1039565.681 1052000.1 1098322.243 1039590.686 1263781.301 0.790228917 0.670968149 0.80100064 0.765998286 0.822583528 0.832422587 0.869076194 0.822603314 1 20.26931539 0.991173143 0.261293108 1.043469966 0.70317786 0.757524433 0.040654674 1.087103106 0.24720189 0.136591399 0.082047379 9.798805639 -0.991173143 -0.340292106 RQSVS(ph)PPY(ph)KEPSAYQSSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(0.585)VS(0.531)PPY(0.574)KEPS(0.276)AY(0.004)QS(0.011)S(0.01)T(0.009)R 89.511 0.0039133 190400000 565430 672660 522230 662590 391680 625420 569300 588650 406790 TRUE FALSE 538703.2445 741204.8188 546174.7621 595985.1944 459988.868 603761.5486 482442.8291 537104.6854 469872.9156 1.146487117 1.577458062 1.162388263 1.26839657 0.978964424 1.284946479 1.02675173 1.143085008 1 18.84191108 3.240844837 1.944608085 1.10374983 1.354151376 0.306017059 0.145827588 0.331946688 2.583010765 0.042546162 0.059067668 1741.18468 -3.240844837 0.250401546 RQT(ph)IEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RQT(1)IEER;RQT(1)IEER;RQT(1)IEER;RQT(1)IEER 166.66 0.00065354 640620000 565830 451519 491209 523178 609770 503492 595960 478219 733230 TRUE FALSE 539084.3373 497529.2994 513731.4185 470587.1535 716113.6949 486055.9458 505035.3564 436343.6092 846935.5636 0.636511631 0.587446461 0.606576746 0.555635132 0.845535039 0.573899558 0.596309068 0.515202842 1 19.69189269 -1.697195367 2.719315288 1.05776489 0.615168916 0.65358603 0.088168253 11022722 9409584.844 4366656.233 0.02145498 0.020081892 1.697195367 -0.442595974 RQTEPVS(ph)PVLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQTEPVSPVLKR 12 2 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 RQT(0.001)EPVS(0.999)PVLKR 52.008 0.079153 73582000 173690 138720 155640 156350 140820 169490 199680 188390 180860 TRUE FALSE 165480.0179 152855.7257 162776.2479 140633.401 165378.9634 163620.5188 169215.1486 171893.5729 208906.8451 0.792123484 0.731693237 0.779181017 0.673187137 0.791639754 0.783222391 0.810002892 0.822824033 1 17.67250024 0.553698597 0.645168065 1.004705781 0.750668863 0.825564578 0.034717091 0.573876554 0.422195214 0.037628945 0.012791568 3.578480026 -0.553698597 -0.254036918 RQVEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 172.59 0.00045323 1011647000 961632 772207 736958 918861 1009109 807386 1063158 895456 1087252 FALSE TRUE 916177.5611 850895.7712 770748.2533 826495.3466 1185097.29 779426.0204 900953.7209 817045.1255 1255857.487 0.729523509 0.677541664 0.613722704 0.658112369 0.94365587 0.620632539 0.717401242 0.650587454 1 20.26024133 -1.78772277 2.871746333 1.073260466 0.701809636 0.500895334 0.093673122 79296537.68 47625957.98 40115808.84 0.020871865 0.016303364 1.78772277 -0.371450829 RQVLLSAAEAAEVILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQVLLSAAEAAEVILR 16 1 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 104.88 0.0021275 28073900 67961 47391 62240 60658 66640 63557 78993 63677 67771 FALSE TRUE 64748.61822 52220.19678 65093.76556 54560.5426 78261.9949 61356.00515 66941.16704 58101.10431 78280.58055 0.827135131 0.667090055 0.831544236 0.696986944 0.999762576 0.78379599 0.855143978 0.742216063 1 16.25636684 2.777192267 24.99984355 0.858684026 0.753075213 0.274290282 0.095009082 748.0077216 484059.7283 0.026017167 0.027594886 598.6765776 -2.777192267 -0.105608813 RQVS(ph)ASELHTSGILGPETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.942)AS(0.058)ELHTSGILGPETLR;RQVS(0.936)AS(0.064)ELHTSGILGPETLR;RQVS(0.5)AS(0.5)ELHTSGILGPETLR;RQVS(0.509)AS(0.485)ELHT(0.007)SGILGPETLR;RQVS(0.949)AS(0.051)ELHTSGILGPETLR;RQVS(0.946)AS(0.054)ELHTSGILGPETLR;RQVS(0.996)AS(0.004)ELHTSGILGPETLR;RQVS(0.995)AS(0.005)ELHTSGILGPETLR;RQVS(0.965)AS(0.035)ELHTSGILGPETLR;RQVS(0.993)AS(0.007)ELHTSGILGPETLR;RQVS(0.887)AS(0.113)ELHTSGILGPETLR 309.38 1.93E-66 20646258000 1570943 829879 1540888 1497992 3425513 1309145 2919726 1619044 4645500 TRUE FALSE 1496687.638 914444.6136 1611539.239 1347410.998 4022921.383 1263808.98 2474268.174 1477271.924 5365900.414 0.27892572 0.170417739 0.300329696 0.251106225 0.749719725 0.235525985 0.461109596 0.275307369 1 22.35538885 -5 0.185504688 3.786448343 0.202750033 0.621988526 0.1622079 83.39551253 0.810275904 85.83128815 0.431455711 1.00E-05 5 -3.58369831 RQVSAS(ph)ELHTSGILGPETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.247)AS(0.741)ELHT(0.009)S(0.004)GILGPETLR 59.628 0.039837 2213200000 13835 11363 14787 13340 26590 10700 19700 14286 29607 TRUE FALSE 13181.04697 12520.90262 15464.99858 11999.03786 31227.28758 10329.45632 16694.40318 13035.04211 34198.30235 0.385429862 0.366126438 0.452215388 0.350866477 0.913123911 0.30204588 0.488164676 0.381160502 1 15.06163709 -2.138864656 2.28732346 2.144359088 0.449342347 0.500208381 0.171159765 9831725.785 2420721.421 58371277.38 0.043738106 0.007263323 2.138864656 -1.695016741 RQVSASELHTSGILGPETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 122.19 2.01E-05 151640000 55242 28802 57256 47307 123720 45242 99133 54051 168870 FALSE TRUE 52630.82014 31736.95655 59881.24423 42551.61048 145296.7288 43675.2582 84008.44015 49318.0079 195057.4971 0.269822083 0.162705648 0.306992785 0.218149064 0.744891793 0.223909662 0.430685523 0.25283831 1 17.57353992 -5 0.207768278 4.201146849 0.218511647 0.62087879 0.165156038 89.77779693 0.893383421 119.7812421 0.332229822 1.00E-05 5 -3.982635203 RQWTSLS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RQWTSLSLR 9 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RQWTS(0.001)LS(0.999)LR;RQWTSLS(1)LR;RQWTSLS(1)LR;RQWTSLS(1)LR;RQWTSLS(1)LR;RQWTS(0.001)LS(0.999)LR;RQWTS(0.006)LS(0.994)LR;RQWTSLS(1)LR 202.65 1.19E-05 3200260000 2034825 1176325 1579828 1786856 2377601 1897739 2807629 1629682 2692574 TRUE FALSE 1938642.855 1296193.855 1652264.676 1607237.84 2792253.862 1832019.823 2379273.63 1486978.405 3110124.624 0.623332853 0.416765889 0.531253527 0.516776025 0.897794847 0.589050293 0.765009097 0.478108946 1 21.56854096 2.792155313 21.08132222 0.721443644 0.516254723 0.341436913 0.152359265 64.895784 25525.91324 0.041147962 0.0436442 619.6626394 -2.792155313 -0.205188921 RQYHES(ph)EEES(ph)EEEEAA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RQYHESEEESEEEEAA 16 1 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 RQYHES(1)EEES(1)EEEEAA;RQYHES(1)EEES(1)EEEEAA 100.07 0.0014566 614830000 1588210 1402150 1459770 1561150 1529460 1530470 1840830 1493320 1444880 TRUE FALSE 1513138.461 1545030.679 1526701.898 1404220.236 1796197.34 1477469.44 1559977.574 1362556.984 1668944.611 0.906643906 0.925753119 0.914770861 0.841382169 1.076247425 0.885271704 0.934709016 0.816418337 1 20.67050464 RRAS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRASPSPPPKR 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRAS(1)PS(1)PPPKR;RRAS(1)PS(1)PPPKR 74.853 0.056973 178658000 228670 177721 195900 229580 188736 203283 236970 210950 226626 TRUE FALSE 217861.2223 195830.972 204882.2088 206502.1822 221651.4986 196243.2587 200815.8742 192478.0997 261770.0026 0.832261986 0.748103182 0.782680241 0.788868779 0.846741401 0.749678178 0.767146244 0.735294716 1 17.99794026 -1.656551206 3.074201604 1.01924019 0.781161972 0.789100565 0.035524533 9762097.256 12619145.72 1515782.131 0.008227453 0.022052041 1.656551206 -0.238078218 RRAS(ph)QEANLLTLAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRASQEANLLTLAQK 15 2 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RRAS(1)QEANLLTLAQK;RRAS(1)QEANLLTLAQK;RRAS(1)QEANLLTLAQK 250.86 3.99E-19 1401650000 1504980 1149110 1277370 1448740 1258530 1437380 1771300 1651590 1739830 TRUE FALSE 1433842.578 1266205.615 1335938.678 1303109.903 1478017.234 1387603.17 1501055.653 1506968.024 2009633.951 0.713484452 0.630067787 0.664767172 0.648431473 0.735465896 0.690475581 0.746929884 0.749871898 1 20.93850131 0.056616152 0.448663418 1.039712992 0.662403718 0.920951285 0.029087764 0.940507176 0.253828925 0.094998562 0.015968675 1.139242432 -0.056616152 -0.377309274 RRDEDMLYS(ph)PELAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLY(0.013)S(0.987)PELAQR;RRDEDMLY(0.003)S(0.997)PELAQR 210.92 8.56E-10 2074390000 740843 599279 644380 734724 731170 616444 776712 687467 766720 TRUE FALSE 705824.8196 660346.2114 673925.4604 660868.1476 858685.8165 595096.3897 658210.3191 627268.745 885619.0217 0.79698471 0.745632372 0.760965431 0.746221718 0.969588272 0.671955294 0.743220621 0.708282828 1 19.75632668 -1.211706544 5.18356209 1.000019129 0.766727227 0.461351215 0.078822454 1.61E-05 2.45E-06 0.070612894 0.016642255 0.061417687 1.211706544 -0.233291902 RRDS(ph)DGVDGFEAEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RRDSDGVDGFEAEGK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK;RRDS(1)DGVDGFEAEGK 230.77 2.23E-13 4828050000 4494370 3995610 3937630 4660200 3137790 4491500 4744730 4403500 3092870 TRUE FALSE 4281930.037 4402767.202 4118174.23 4191747.842 3685019.583 4335958.229 4020834.296 4017906.196 3572496.483 1.198582016 1.232406308 1.152744096 1.17333855 1.03149705 1.213705388 1.125497062 1.124677439 1 21.76850116 -5 0.065299799 0.412300052 1.391792566 0.54206644 0.050684774 246.1491095 1.165322345 22.33089977 3.192531196 1.00E-05 5 0.979492514 RRDS(ph)DGVDGFEAEGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RRDSDGVDGFEAEGKK 16 3 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK 261.17 4.45E-26 6187050000 5052710 4270170 4632570 5047590 2843081 5163150 5723670 5653450 3145597 TRUE FALSE 4813878.412 4705305.178 4844977.917 4540196.663 3338913.426 4984348.821 4850419.019 5158403.947 3633400.117 1.324896311 1.295014319 1.33345565 1.249572444 0.918950107 1.37181391 1.334953174 1.41971811 1 21.79288882 3.169044515 6.850231653 1.235769726 1.313754125 0.077646734 0.156030302 0.734746702 58.48376929 0.044566798 0.05364606 1475.857801 -3.169044515 0.077984399 RRDS(ph)DYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRDSDYKR 8 3 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3;F8WE23 P52756 RBM5 RNA-binding protein 5 1 RRDS(1)DYKR;RRDS(1)DYKR 106.29 0.023341 30226000 49121 48135 53212 59925 62597 54648 57703 53618 72760 TRUE FALSE 46799.14768 53040.01122 55651.82283 53901.22515 73513.89698 52755.52606 48899.34756 48922.92367 84043.24919 0.556846006 0.631103768 0.662180762 0.641351039 0.874715075 0.627718782 0.58183552 0.582116043 1 16.35884432 -2.086921789 2.615988465 1.607028369 0.64041717 0.617395338 0.087833804 9014974.044 2335246.531 32751211.08 0.021213479 0.008186122 2.086921789 -0.966611198 RRDS(ph)EEFGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;RRDS(1)EEFGVK;RRDS(1)EEFGVK 167.89 4.02E-06 6192060000 5665790 4551120 4679840 5667200 4097840 5340920 6097020 5679850 4838450 TRUE FALSE 5397979.335 5014884.302 4894415.293 5097522.289 4812501.999 5155962.601 5166807.62 5182492.223 5588772.115 0.965861414 0.89731415 0.875758609 0.91210058 0.861101848 0.922557316 0.924497817 0.927304266 1 22.41409992 0.621414025 1.046317735 0.999826844 0.907732536 0.518072474 0.027943373 1.088171132 1.894858293 0.027271849 0.008630066 4.182288854 -0.621414025 -0.092094309 RRDS(ph)GDNSAPSGQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RRDSGDNSAPSGQER 15 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.993)GDNS(0.007)APSGQER;RRDS(0.997)GDNS(0.003)APSGQER;RRDS(1)GDNSAPSGQER;RRDS(1)GDNSAPSGQER;RRDS(0.998)GDNS(0.002)APSGQER;RRDS(0.987)GDNS(0.013)APSGQER;RRDS(0.997)GDNS(0.003)APSGQER;RRDS(0.987)GDNS(0.013)APSGQER 211.4 1.10E-09 3236561000 882755.2 820240.4 820649.2 1050507.9 900445.2 792490.7 922762.2 829130.9 829921.3 TRUE FALSE 841029.1111 903823.8293 858276.7776 944908.8501 1057482.558 765046.5483 781977.8787 756527.8029 958621.2566 0.877332007 0.94283725 0.895324167 0.9856957 1.103128635 0.798069668 0.815731837 0.789183213 1 19.87060141 RRDS(ph)GDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRDSGDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR 44 3 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.329)GDNS(0.329)APS(0.329)GQEREDHGLET(0.014)GDPPLPPPPVLPGPGEELPGAR 94.052 4.83E-05 119100000 57404 28589 53181 44676 80281 50155 82189 56956 81735 TRUE FALSE 54690.62668 31502.2516 55619.40145 40185.0836 94281.98098 48418.11977 69649.55855 51968.6307 94410.04636 0.579288209 0.333674782 0.589125878 0.425644146 0.99864352 0.512849232 0.737734608 0.550456574 1 16.52665277 2.792314135 24.999485 0.722926433 0.473995765 0.375987047 0.174246535 335.7606776 156153.5898 0.047260537 0.05012734 619.8892934 -2.792314135 -0.248930668 RRDS(ph)YYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RRDSYYDR 8 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RRDS(1)YYDR;RRDS(1)YYDR;RRDS(1)YYDR;RRDS(1)YYDR;RRDS(1)YYDR;RRDS(0.999)YYDR 127.87 0.00091192 1629702000 1028063 869243 911233 1064605 1119991 1018518 1112447 1054473 1253434 TRUE FALSE 979468.4994 957819.8499 953013.9344 957588.8828 1315317.076 983246.4663 942722.7787 962137.754 1447810.143 0.676517224 0.661564539 0.658245101 0.66140501 0.908487264 0.67912666 0.651137018 0.664546908 1 20.465441 -1.59679066 2.762849395 1.023700013 0.691541308 0.610154208 0.076537602 10311999.65 10179390.19 1780149.803 0.018745886 0.025305175 1.59679066 -0.332158705 RRDSGDNS(ph)APSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRDSGDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR 44 3 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.278)GDNS(0.323)APS(0.323)GQEREDHGLET(0.076)GDPPLPPPPVLPGPGEELPGAR 85.894 9.58E-05 165520000 39276 21278 37275 33276 53366 33342 59731 40784 57774 TRUE FALSE 37419.50132 23446.25239 38984.09562 29931.03326 62673.0135 32187.35818 50617.93891 37212.73675 66733.29685 0.560732095 0.351342635 0.584177576 0.448517227 0.93915656 0.482328308 0.758510988 0.557633723 1 16.02611916 -4.999999996 0.083160369 2.446459257 0.161500104 0.440997812 0.156336237 190.458759 1.115057561 49.58093039 4.23284707 1.00E-05 4.999999996 -2.284959153 RRDSGIGEETATGLGSHVEVT(ph)PHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_SK-BR-3_Trastuzumab_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(0.04)GIGEET(0.033)AT(0.208)GLGS(0.208)HVEVT(0.254)PHT(0.254)APPGVS(0.002)AGPDAISEVLSTLSLEVNK 117.73 1.51E-08 308090000 70415 82869 74506 88400 116990 79601 83887 78967 60820 TRUE FALSE 67086.6225 91313.44531 77922.1738 79513.86405 137393.019 76844.39741 71088.49746 72052.23085 70251.65497 0.954947218 1.299804899 1.109186308 1.131843287 1.955726438 1.093844657 1.011912068 1.02563037 1 16.10024459 2.015864247 24.9998171 1.023597575 1.268934677 0.195347863 0.261668819 433.9429358 683830.1909 0.097736297 0.072161899 103.7204153 -2.015864247 0.245337102 RRDSLDS(ph)STEASGSDVVLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRDSLDSSTEASGSDVVLGGR 21 2 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RRDS(0.309)LDS(0.493)S(0.163)T(0.035)EASGSDVVLGGR 128.18 1.46E-05 426670000 119440 121050 112820 116700 81128 92477 135610 116750 114930 TRUE FALSE 113794.3079 133385.1326 117992.9086 104969.0943 95276.69751 89274.4983 114920.2039 106526.7511 132752.7574 0.857189787 1.004763556 0.888817008 0.790711216 0.717700328 0.67248696 0.865670937 0.802444734 1 17.0183823 3.347553082 4.042452578 0.792590654 0.933011891 0.225114663 0.094063893 0.250051726 7.487401475 0.024952218 0.034241032 2226.143122 -3.347553082 0.140421237 RRDYYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRDYYDR 7 2 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ; 116.73 0.021418 103581000 74319 53690 52443 54164 73777 59150 89973 71065 99795 FALSE TRUE 70806.08816 59161.07204 54847.56342 48719.33182 86643.68544 57101.62067 76245.96638 64842.17186 115270.6989 0.614259207 0.513235997 0.475815311 0.422651483 0.751654031 0.495369779 0.66145141 0.562520853 1 16.81466631 -1.571606826 0.344944093 1.332171326 0.531736914 0.688189637 0.093565718 13.62253402 0.90872251 3.947403948 0.070332706 0.026815949 1.571606826 -0.800434411 RREDQMDGDGPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RREDQMDGDGPRPR 14 3 Q15527 Q15527 SURF2 Surfeit locus protein 2 0 ; 125.53 3.97E-05 80955000 28324.3 29828.6 28760.7 35913.8 32484.1 27410.2 38438.5 34141.2 33847.9 FALSE TRUE 26985.46647 32868.16825 30079.40654 32303.67659 38149.31676 26460.9779 32574.00085 31151.61553 39096.85946 0.690220822 0.840685638 0.76935608 0.826247352 0.975764225 0.676805714 0.833161571 0.796780508 1 15.2547651 -5 0.227158292 2.040787297 0.776430743 0.366438409 0.082914805 172.5831565 1.726527366 82.69002998 0.137391589 1.00E-05 5 -1.264356554 RREDS(ph)YHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RREDSYHVR 9 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 RREDS(1)YHVR;RREDS(1)YHVR;RREDS(1)YHVR;RREDS(1)YHVR 120.57 0.00033549 350293000 101358 77872 90113 96707 112137 87200.7 106150 94698 125543 TRUE FALSE 96567.00821 85807.24533 94244.77018 86985.82863 131693.6573 84180.91789 89954.86792 86405.74109 145011.5673 0.665926243 0.591726901 0.649912086 0.599854414 0.908159672 0.580511745 0.620328913 0.595854129 1 17.14580846 -1.253674928 4.810101003 1.000090532 0.647871432 0.569413094 0.095183839 8.60E-05 1.33E-05 0.085807135 0.020219758 0.055760296 1.253674928 -0.3522191 RREEEGLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RREEEGLQLR 10 2 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 ; 177.57 1.30E-06 418701000 283854 263532 278163 313263 318310 267112 335420 280181 315120 FALSE TRUE 270436.784 290386.2104 290917.0487 281773.2081 373823.1632 257861.8445 284245.5186 255646.8663 363987.2002 0.742984324 0.797792368 0.799250766 0.774129442 1.027022827 0.708436572 0.780921742 0.702351253 1 18.47352819 -2.115221318 2.462167478 1.400740343 0.791482663 0.345309213 0.090175843 32838687.43 9367268.622 73614546.97 0.020432599 0.007669705 2.115221318 -0.609257679 RREEEMMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RREEEMMIR 9 2 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 103.7 0.0016307 306202000 74630 75498 71917 77213.4 74583 62275.5 81070 86903 90978 FALSE TRUE 71102.3878 83191.33203 75214.46559 69451.76234 87590.25159 60118.88382 68701.28255 79293.31262 105086.4036 0.676608823 0.791646961 0.715739268 0.660901505 0.833506987 0.57209003 0.653759956 0.75455349 1 16.6812165 0.924171203 8.920960117 0.999999861 0.702859073 0.62551549 0.072325795 2.334175646 274.8076602 0.067995108 0.017016092 8.397909742 -0.924171203 -0.297140789 RREEGPPPPS(ph)PDGAS(ph)SDAEPEPPSGR ddPTM_SK-BR-3_Trastuzumab_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(0.891)S(0.109)DAEPEPPSGR 160.63 8.88E-11 400060000 181840 172620 177640 201620 203590 188550 238470 184140 213350 TRUE FALSE 173244.7836 190210.1743 185784.9697 181352.7745 239096.0315 182020.4662 202087.0217 168015.7254 246435.2284 0.703003319 0.771846523 0.753889657 0.735904423 0.970218557 0.738613823 0.820041124 0.681784526 1 17.91084898 -5 0.270127346 2.52026489 0.757789477 0.424244116 0.08136551 199.8934243 1.940272764 169.9874506 0.092332372 1.00E-05 5 -1.762475413 RREEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 RREEGPPPPS(0.025)PDGAS(0.488)S(0.488)DAEPEPPSGR;RREEGPPPPS(0.001)PDGAS(0.5)S(0.5)DAEPEPPSGR;RREEGPPPPS(0.266)PDGAS(0.627)S(0.107)DAEPEPPSGR;RREEGPPPPS(0.005)PDGAS(0.498)S(0.498)DAEPEPPSGR;RREEGPPPPS(0.001)PDGAS(0.499)S(0.499)DAEPEPPSGR 161.15 1.37E-11 2040760000 365555 322827 360249 384216 381788 374446 441606 407510 454041 TRUE FALSE 348275.9396 355723.4383 376766.773 345593.8777 448371.7063 361478.8411 374230.894 371826.2641 524451.3594 0.664076722 0.678277274 0.718401747 0.658962688 0.854934778 0.689251414 0.713566449 0.70898141 1 19.00044945 -5 0.258856912 2.870326348 0.683065137 0.7368418 0.054498309 94.86712254 0.932771086 94.33736559 0.068547081 1.00E-05 5 -2.187261212 RREEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 RREEGPPPPS(0.007)PDGAS(0.158)S(0.835)DAEPEPPSGR;RREEGPPPPSPDGAS(0.137)S(0.862)DAEPEPPSGR;RREEGPPPPS(0.003)PDGAS(0.16)S(0.837)DAEPEPPSGR 177.92 1.31E-17 2259850000 470746 461816 499924 554044 542404 501085 574962 495221 648850 TRUE FALSE 448494.7695 508875.5754 522846.0099 498350.4445 636999.0859 483732.3008 487240.987 451856.8239 749470.3441 0.598415632 0.678980268 0.697620678 0.664936843 0.849932343 0.64543221 0.650113765 0.602901539 1 19.51551187 -1.665408056 3.101943318 1.030027222 0.672352625 0.683896921 0.069746652 29093124.17 28139448.48 6879268.872 0.01639258 0.021606874 1.665408056 -0.357674597 RREPGGYDSSSTLMSSELETTSFFDS(ph)DEDDSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RREPGGYDSSSTLMSSELETTSFFDSDEDDSTSR 34 2 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 RREPGGYDSSSTLMSSELETTS(0.001)FFDS(0.999)DEDDS(0.001)TSR 95.252 0.0001386 71751000 18761 19039 16020 18707 17944 16602 20469 18162 19029 TRUE FALSE 17874.20471 20979.09575 16754.53285 16826.53682 21073.42792 16027.06858 17346.07811 16571.639 21979.92013 0.813206081 0.954466423 0.762265411 0.765541308 0.958758166 0.729168645 0.789178396 0.753944459 1 14.42389852 3.727503316 24.94898321 0.810291063 0.883836256 0.054304306 0.095754167 1415.969589 3194903.632 0.023084648 0.036144118 5339.533511 -3.727503316 0.073545193 RREQEEAAAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RREQEEAAAPR 11 2 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 72.531 0.025895 14403000 19223 15865 28515 21578 47341 19318 19457 17915 23888 FALSE TRUE 18314.36689 17481.66154 29822.44096 19408.93844 55597.25541 18649.01282 16488.4773 16346.26763 27592.42904 0.66374609 0.633567328 1.080819703 0.703415361 2.014946032 0.675874269 0.597572518 0.59241858 1 14.75198485 -1.72938452 2.649830007 1.029615794 0.845061047 0.005850148 0.431481195 92901737.91 75509892.78 18231584.77 0.101454013 0.018647279 1.72938452 -0.184554747 RRES(ph)EKS(ph)LENETLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.855)EKS(0.622)LENET(0.522)LNK 122.16 0.00015879 89660000 140340 154520 121860 160070 92546 159580 145180 147570 91255 TRUE FALSE 133706.4063 170265.7637 127447.4015 143979.4595 108685.9931 154053.7046 123030.1246 134647.9885 105406.3593 1.268485196 1.615327242 1.209105431 1.365946613 1.031114193 1.461521919 1.167198311 1.277418074 1 16.68560238 -4.007686649 0.073628397 9.32E-06 1.723896448 0.293446278 0.155828969 243.8365312 1.556147652 44.06663339 6.900503145 9.82E-05 4.007686649 1.72388713 RRES(ph)EKSLENET(ph)LNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.769)EKS(0.287)LENET(0.943)LNK 121.33 0.00021914 121910000 239880 249780 173890 264310 123740 262650 235210 237400 113680 TRUE FALSE 228541.3478 275232.866 181863.0285 237741.0566 145320.2168 253554.3646 199324.3946 216611.9975 131308.9138 1.740486165 2.096071455 1.385001393 1.810547736 1.106704889 1.930976027 1.517980682 1.649636656 1 17.00260533 -2.258762275 0.129091127 1.86E-12 2.052105334 0.365037602 0.275461767 59.09928799 1.00814881 20.6823947 2.391379148 0.005511093 2.258762275 2.052105334 RRES(ph)QEEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;RRES(1)QEEPR;RRES(1)QEEPR;RRES(1)QEEPR;RRES(1)QEEPR;RRES(1)QEEPR 168.76 4.20E-05 16887535000 12945711 11022402 11697455 13755778 13912491 12534213 15207027 14068358 16390917 TRUE FALSE 12333792.9 12145597.3 12233794.88 12373021.06 16338825.03 12100150.06 12886915.73 12836457.99 18932736.7 0.651453252 0.641513031 0.646171501 0.653525228 0.862993306 0.639112573 0.680668407 0.678003302 1 24.17437963 -5 0.294603544 3.581274161 0.659691685 0.697436994 0.065943327 142.012271 1.326426328 225.8448905 0.065566313 1.00E-05 5 -2.921582476 RRET(ph)PS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRETPSPR 8 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRET(1)PS(1)PR 84.658 0.019087 74762000 67228 73267 53436 79826 64879 66071 55314 61506 51825 TRUE FALSE 64050.26567 80732.9906 55886.09346 71801.73882 76193.87706 63782.9447 46874.83339 56120.20858 59861.75631 1.069969704 1.348657232 0.93358593 1.199459275 1.272830631 1.065504065 0.783051422 0.93749686 1 15.86934699 1.9615183 6.005071654 0.89043015 1.172528201 0.477483307 0.122609144 0.149364767 14.96860825 0.049523837 0.031120615 91.52048229 -1.9615183 0.282098051 RRET(ph)PS(ph)PRPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR;RRET(1)PS(1)PRPMR 82.908 0.009355 7115720000 2785006 2143287 2487665 2803826 2859231 2345900 2923075 2320538 3316822 TRUE FALSE 2653364.286 2361690.382 2601726.901 2521980.084 3357879.981 2264660.895 2477106.223 2117339.391 3831177.816 0.692571427 0.616439773 0.679093226 0.658278003 0.876461533 0.591113491 0.646565193 0.552660172 1 21.86935656 -1.477742256 3.085376832 1.008223088 0.66363685 0.601250099 0.085954536 60106471.08 70443023.76 4211703.154 0.019800289 0.033285704 1.477742256 -0.344586239 RRGDDWNDREWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RRGDDWNDREWDR 13 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;;; 207.97 2.17E-08 4735310000 319238 251136 344755 289801 566835 247994 445011 318916 537594 FALSE TRUE 304148.2524 276727.0439 360562.3578 260669.6529 665690.8445 239405.9056 377116.3988 290990.0244 620961.3319 0.489802242 0.445642957 0.580651869 0.419784034 1.072032686 0.385540763 0.6073106 0.468612149 1 19.24414391 -5 0.248981712 3.650194716 0.511671415 0.325713915 0.196316088 205.4897574 2.037759929 277.7146649 0.260737151 1.00E-05 5 -3.138523301 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(0.855)ES(0.863)EEDEQDS(0.282)EEVR;RRGDS(1)ES(0.999)EEDEQDS(0.001)EEVR;RRGDS(0.997)ES(0.588)EEDEQDS(0.415)EEVR 173.55 3.95E-11 4619100000 1039515 847891 960291 1047817 933244 1004738 1169611 949656 952254 TRUE FALSE 990379.1861 934292.0569 1004321.292 942488.4444 1096001.458 969943.6711 991165.3606 866499.0862 1099924.687 0.900406362 0.849414572 0.913081872 0.856866343 0.996433184 0.881827349 0.901121115 0.787780379 1 20.06897331 RRGDS(ph)ESEEDEQDSEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 RRGDS(0.564)ES(0.43)EEDEQDS(0.005)EEVR 73.981 0.015205 105800000 37478 31990 35889 38143 30432 35248 37111 28102 28873 TRUE FALSE 35706.48921 35249.81737 37534.54615 34308.79317 35739.33116 34027.35292 31449.03536 25641.2399 33350.47738 1.070644021 1.056950909 1.125457538 1.028734695 1.071628773 1.020295828 0.942986063 0.768841765 1 15.02541979 1.701785397 2.532466679 0.879154707 1.067446908 0.612479757 0.060927559 0.141380025 1.975182261 0.034387333 0.014752363 50.32518691 -1.701785397 0.188292202 RRGEEGHDPKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRGEEGHDPKEPEQLR 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 66.022 0.033411 163730000 115130 78043 92403 101100 73336 111090 120940 119850 81955 FALSE TRUE 109688.0331 85995.67043 96639.76895 90937.23592 86125.77518 107242.9254 102488.3818 109355.2986 94664.16283 1.158707052 0.908428996 1.020869631 0.960630012 0.909803379 1.132877767 1.082652386 1.155192159 1 16.53053075 2.219502634 24.99982458 1.098945497 0.995432615 0.279683801 0.080131553 312.436347 409844.1352 0.028854515 0.021343389 165.7687391 -2.219502634 -0.103512883 RRGNDPLTSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRGNDPLTSSPGR 13 2 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RRGNDPLT(0.221)S(0.317)S(0.461)PGR 63.682 0.052925 369400000 344150 195240 341290 271600 347880 321550 438570 387760 524780 TRUE FALSE 327882.7115 215135.178 356938.4841 244298.252 408550.1619 310414.6429 371658.0916 353805.6788 606160.2022 0.540917583 0.354914719 0.588851731 0.403025885 0.673997007 0.512100005 0.613135092 0.583683451 1 19.20933961 -5 0.171259552 2.923455761 0.408501107 0.755158336 0.08637815 55.8047123 0.527825232 36.24729232 0.267527553 1.00E-05 5 -2.514954654 RRGS(ph)GVFCANCLTTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRGSGVFCANCLTTK 15 2 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 RRGS(1)GVFCANCLTTK;RRGS(1)GVFCANCLTTK 104.17 0.00073838 641180000 474100 296940 445860 445930 481890 486500 638600 509430 611130 TRUE FALSE 451690.2326 327198.5236 466303.122 401104.2692 565931.4634 469652.383 541169.8413 464821.6085 705900.9192 0.639877666 0.46351905 0.660578715 0.568216103 0.801715153 0.665323376 0.766637111 0.658479959 1 19.42910617 -4.515971408 0.097902589 2.098431839 0.368263984 0.667269813 0.082820686 87.84471676 0.650742714 20.18706499 1.404331548 3.05E-05 4.515971408 -1.730167855 RRGS(ph)QEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RRGS(1)QEK 96.143 0.010197 757430000 492466 550110 542300 750750 407238 510510 614470 826630 514620 TRUE FALSE 469188.1082 606166.8344 567164.9914 675283.1837 478260.1783 492830.9107 520721.316 754245.895 594424.6413 0.789314701 1.01975388 0.954141117 1.136028248 0.804576636 0.829088965 0.876008967 1.268867141 1 19.1811344 1.254622542 24.99971543 1.134433625 0.916156899 0.356693759 0.122199822 221.6192292 344943.8431 0.078531406 0.02847832 17.97308142 -1.254622542 -0.218276726 RRGS(ph)SGSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RRGSSGSVDETLFALPAASEPVIR 24 2 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RRGS(0.25)S(0.25)GS(0.25)VDET(0.25)LFALPAASEPVIR;RRGS(0.276)S(0.276)GS(0.276)VDET(0.171)LFALPAASEPVIR;RRGS(0.708)S(0.146)GS(0.146)VDETLFALPAASEPVIR;RRGS(0.25)S(0.25)GS(0.25)VDET(0.25)LFALPAASEPVIR 210.68 3.07E-25 205901000 195689 127488.3 189524.4 220133 256848 182594.8 241974 201420 269222 TRUE FALSE 186439.1688 140479.5027 198214.2812 198004.8126 301642.2099 176271.4963 205056.4221 183782.597 310971.5728 0.599537659 0.451743873 0.637403218 0.636729624 0.969999306 0.56684119 0.659405682 0.590994847 1 18.24642318 -5 0.136252473 2.203133371 0.490741756 0.420423872 0.131837998 135.6476445 1.145105751 44.92972003 0.86311986 1.00E-05 5 -1.712391615 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 385.52 2.55E-180 4121992000 801012.55 694805.3 932878.9 803095.93 986486.2 813850.6 1213182.5 864853.3 859017.6 FALSE TRUE 763150.2742 765606.75 975652.3203 722367.2013 1158529.081 785666.7497 1028089.228 789122.1602 992229.6622 0.769126648 0.771602361 0.983292838 0.728024195 1.167601741 0.791819454 1.036140389 0.795301925 1 19.92031456 3.735516237 1.171615233 0.940668256 0.751327045 0.175195873 0.132847594 0.734371999 1.913563472 0.038685913 0.108991495 5438.964657 -3.735516237 -0.189341211 RRHS(ph)DENDGGQPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RRHSDENDGGQPHK 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHK;RRHS(1)DENDGGQPHK;RRHS(1)DENDGGQPHK;RRHS(1)DENDGGQPHK;RRHS(1)DENDGGQPHK 109.72 0.00035684 1133929000 192989.8 204748.3 245719.1 245289.2 211101.2 219468.3 259859.1 189358.4 157938.2 TRUE FALSE 183867.5546 225612.3845 256985.5638 220632.2636 247917.1824 211868.0577 220212.8217 172777.1746 182430.4494 1.007877551 1.236703551 1.408676921 1.209404813 1.358968216 1.161363459 1.207105625 0.947085178 1 17.47698702 1.244693465 22.58926231 0.973542432 1.219560095 0.486101307 0.108191333 36.31573621 133777.9647 0.079200906 0.027100419 17.56683268 -1.244693465 0.246017663 RRHS(ph)DENDGGQPHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RRHSDENDGGQPHKR 15 3 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR 181.32 2.41E-07 4333742000 1216494.3 758661.3 1479920.2 1115054 1404707 1296381.2 1964640 1226857.7 591343.2 TRUE FALSE 1158993.025 835969.749 1547776.005 1002966.653 1649687.456 1251487.194 1664898.085 1119427.536 683045.6833 1.696801625 1.223885561 2.265991928 1.468374192 2.415193444 1.832215948 2.437462275 1.638876525 1 19.38162255 3.743616934 24.98873795 1.957688083 1.4603436 0.092490477 0.461922224 622.9743908 3078781.272 0.105660533 0.183365682 5541.367255 -3.743616934 -0.497344483 RRHS(ph)EVETDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRHSEVETDSK 11 2 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RRHS(0.99)EVET(0.01)DSK;RRHS(0.996)EVET(0.004)DSK;RRHS(0.993)EVET(0.007)DSK 82.171 0.010263 67917000 114653 63114 64195 62113 91088 55455 64338 111672 66798 TRUE FALSE 109233.5799 69545.38835 67138.40425 55869.28323 106973.7184 53534.57944 54522.05645 101893.4077 77156.69268 1.415736939 0.901352636 0.870156585 0.724101582 1.38644769 0.69384233 0.706640663 1.32060362 1 16.23550368 4.547460552 2.393687154 0.91946742 1.441748512 0.258666375 0.241394283 0.452786297 4.212816634 0.057440161 0.41317407 35274.47449 -4.547460552 0.522281092 RRHT(ph)MDKDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;RRHT(1)MDKDSR 117.7 0.00048854 201200500 65799.7 70405.4 68571.4 69375.5 76042.2 71093.3 97418.3 80278.1 71767.4 TRUE FALSE 62689.47858 77579.7903 71715.46652 62401.74294 89303.9356 68631.32119 82555.34913 73248.52398 82896.72185 0.756235918 0.935860774 0.865118245 0.752764905 1.077291521 0.827913573 0.995881951 0.883611829 1 16.33902743 2.75228357 24.99986859 0.949204 0.839728447 0.360004526 0.084721059 955.5173909 1740718.14 0.023616651 0.024926589 565.3059675 -2.75228357 -0.109475553 RRKDS(ph)AQDDQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK 171.26 0.00021506 808454000 947758 693078 869684 914385 515059 1052813 1171042 1099222 716705 TRUE FALSE 902959.3576 763703.4362 909559.8716 822469.2826 604885.1265 1016353.822 992378.0352 1002968.294 827847.951 1.090730921 0.922516551 1.09870402 0.993502831 0.730671769 1.22770591 1.198744327 1.211536845 1 19.65900629 RRKEDEVEEWQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RRKEDEVEEWQHR 13 3 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 222.99 9.91E-12 4466110000 1406603 854045 1295711 1226130 1306257 1231768 1643888 1448714 1338858 FALSE TRUE 1340115.664 941073.1565 1355120.631 1102877.083 1534067.807 1189111.565 1393082.694 1321856.922 1546481.261 0.866557971 0.608525419 0.876260622 0.713152568 0.991973098 0.768914306 0.900808001 0.854751335 1 20.56055792 1.574340368 0.322132177 1.008539077 0.72954934 0.282920101 0.101501512 1.521938585 0.542673205 0.154857362 0.141108485 37.5266994 -1.574340368 -0.278989737 RRLS(ph)EQLAHTPTAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRLSEQLAHTPTAFK 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RRLS(1)EQLAHTPTAFK;RRLS(1)EQLAHTPTAFK 131.67 2.72E-05 726020000 893700 827780 773510 950110 776990 910000 1081650 980820 837240 TRUE FALSE 851456.5721 912131.7231 808976.1986 854603.1377 912496.81 878486.4718 916624.4266 894934.2011 967074.9032 0.88044532 0.943186221 0.836518656 0.883699013 0.943563737 0.908395481 0.947831883 0.925403191 1 19.88326811 0.952914916 0.483455315 1.001937828 0.893159484 0.529151469 0.030915918 0.9350288 0.54636235 0.037723688 0.01789079 8.972529928 -0.952914916 -0.108778344 RRNDLDDPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRNDLDDPER 10 2 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;; 146.16 1.64E-05 319930000 164486 117048 118662 110871 142211 117028 116738 152664 132921 FALSE TRUE 156711.0728 128975.3243 124102.7701 99726.03644 167012.5534 112975.291 98927.47406 139295.9308 153533.7098 1.020694888 0.840045645 0.80830959 0.649538375 1.087790776 0.735833786 0.644337157 0.907266105 1 17.22819592 4.445068227 1.812821469 0.806325477 1.034470107 0.123162068 0.142559459 0.803809035 4.092516255 0.035903088 0.258118307 27865.58898 -4.445068227 0.228144631 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.397)Y(0.205)T(0.397)EEEPEWFSAGPTSQSETIELTGFDDK 221.41 2.31E-36 48517000 57278 58122 49305 70505 40657 57738 59566 64036 35033 TRUE FALSE 54570.58245 64044.69788 51565.68302 63417.70345 47747.56793 55738.51858 50478.1127 58428.66836 40465.73872 1.348562616 1.582689453 1.274304749 1.567195002 1.179950483 1.377424961 1.247428425 1.443904652 1 15.30441331 -3.990694006 0.154089205 4.45E-17 1.509123881 0.457452816 0.129157425 73.60866608 0.886325644 23.44127969 0.558900223 0.000102166 3.990694006 1.509123881 RRNES(ph)PGAPPAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRNESPGAPPAGK 13 2 P49796-1;P49796-4;P49796-6;P49796;C9J582;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RRNES(1)PGAPPAGK;RRNES(1)PGAPPAGK;RRNES(1)PGAPPAGK 118.31 0.0003448 253202000 217032 183101 211533 226094 179485 214090 277171 254981 242484 TRUE FALSE 206773.3275 201759.2001 221231.9973 203366.6016 210787.1272 206676.0096 234883.4734 232653.5119 280087.1803 0.738246311 0.720344287 0.789868344 0.726083219 0.752576848 0.737898855 0.83860844 0.830646771 1 18.09551643 0.850942605 0.70563038 1.001369401 0.736344424 0.909201875 0.025366481 0.225188984 0.241119911 0.023426973 0.008884845 7.094839993 -0.850942605 -0.265024977 RRNS(ph)RDGDPLPSSLSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRNSRDGDPLPSSLSCK 17 3 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 RRNS(1)RDGDPLPSSLSCK 98.76 0.0096615 129200000 114910 64198 132280 99540 174250 109760 169050 115120 103030 TRUE FALSE 109478.432 70739.84919 138345.1688 89534.05009 204639.1448 105958.9837 143258.3177 105039.4825 119007.3662 0.919929879 0.594415719 1.162492485 0.752340405 1.719550238 0.890356514 1.203776894 0.882630091 1 16.86069135 3.72786632 24.82114521 1.101934915 0.757172796 0.199578017 0.273645055 793.0534949 1840654.08 0.06541002 0.102480274 5343.998406 -3.72786632 -0.344762119 RRPEAS(ph)PVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRPEASPVQK 10 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RRPEAS(1)PVQK 81.185 0.026853 0 207980 177060 165400 201700 120310 193970 187350 186310 112480 TRUE FALSE 198149.1976 195102.6153 172983.7536 181424.7328 141292.0259 187252.7703 158766.3166 169995.7087 129922.8239 1.525130009 1.501680839 1.331434681 1.39640386 1.08750735 1.441261547 1.222004816 1.308436067 1 16.98729537 7.999999988 0.067588242 0.624412822 2.9721494 0.621516922 0.104859226 154.5200931 0.773369999 4.858097612 34.74586125 99999997.25 -7.999999988 2.347736577 RRPEAS(ph)PVQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRPEASPVQKK 11 3 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RRPEAS(1)PVQKK;RRPEAS(1)PVQKK 104.55 0.014285 250567000 852520 650610 831660 920280 578030 910110 1042070 1011070 778850 TRUE FALSE 812223.0691 716907.8987 869792.4336 827771.706 678838.249 878592.6625 883083.0826 922535.3508 899630.0802 0.902841164 0.796891872 0.966833427 0.920124531 0.754574868 0.97661548 0.981606887 1.025460766 1 19.77897237 2.031458821 24.47942268 0.995011976 0.868262574 0.527437569 0.060324983 120.5296391 93788.55843 0.02173484 0.016052084 107.5124655 -2.031458821 -0.126749401 RRPENPKPQDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRPENPKPQDGK 12 3 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 176.05 1.14E-05 575656000 882530 868540 720410 984960 478910 965390 881590 934800 537650 FALSE TRUE 840814.5559 957045.2134 753441.5111 885949.9495 562431.7524 931958.3022 747087.254 852943.9563 621026.0161 1.353911969 1.541071048 1.213220528 1.426590717 0.905649261 1.500675138 1.202988659 1.373443196 1 19.24429418 -4.63758354 0.069622383 5.67E-10 1.720696494 0.229955986 0.180661275 378.2869391 2.027201837 64.04501242 9.059960656 2.30E-05 4.63758354 1.720696493 RRPGAALEDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRPGAALEDSR 11 2 Q9H5N1;Q9H5N1-2 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 0 ; 84.658 0.0088851 25044000 21884.7 17099.1 19777.2 22135.8 21082.3 18458.1 21897.1 19859.9 22830.7 FALSE TRUE 20850.2536 18841.51773 20684.00418 19910.66733 24759.04645 17818.89137 18556.29523 18120.86187 26371.16835 0.790645804 0.714474136 0.784341593 0.755016504 0.938868013 0.675695939 0.703658442 0.687146721 1 14.68667387 RRPPS(ph)PEPSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(0.999)PEPS(0.001)TK;RRPPS(0.993)PEPS(0.007)T(0.001)K;RRPPS(0.981)PEPS(0.015)T(0.004)K 105.03 0.0019851 178923000 300146 248870 262974 320796 270037 309334 431430 358946 336350 TRUE FALSE 285958.6934 274230.1359 275031.618 288548.9766 317131.3673 298621.686 365607.4297 327514.7853 388509.4402 0.736040528 0.705851924 0.707914891 0.742707761 0.816277121 0.768634311 0.941051599 0.843003416 1 18.56759013 1.755067161 0.604039216 0.987705452 0.70769399 0.823087688 0.041422935 0.257433935 0.199558697 0.035632289 0.020087216 56.89409074 -1.755067161 -0.280011462 RRPS(ph)PQPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 102.73 0.014307 2427044000 771880 667433 704089 762840 822880 713168 808810 713140 848950 TRUE FALSE 735394.7621 735445.1815 736372.1771 686157.8739 966390.0115 688470.8133 685411.1797 650693.681 980600.8302 0.749943034 0.749994451 0.750939786 0.699732096 0.985508049 0.702090792 0.69897063 0.663566317 1 19.90330646 -2.087591014 2.598115471 1.422801215 0.749690211 0.441012455 0.088420141 8764635.621 2361774.993 22040576.22 0.020064333 0.008173517 2.087591014 -0.673111004 RRPS(ph)PQPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRPSPQPSPR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RRPS(0.999)PQPS(0.001)PR 59.155 0.083823 10329000 3501 3448.4 3388.6 3097.4 4476 3284.5 3469.5 2597.4 3150.7 TRUE FALSE 3335.514668 3799.795881 3543.970662 2786.043467 5256.612983 3170.756941 2940.164053 2369.957886 3639.294464 0.916527833 1.044102344 0.973807065 0.765544941 1.444404413 0.871255946 0.80789397 0.651213555 1 11.82944307 2.014906328 24.99984468 0.808661637 1.018897258 0.213381353 0.188500667 335.4127267 562528.3314 0.065234738 0.048162101 103.4918924 -2.014906328 0.210235621 RRPVVVEPISDEDWYLFCGDTVEILEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRPVVVEPISDEDWYLFCGDTVEILEGK 28 2 Q96A35;X6RIR5;X6RHI2;X6RJ73 Q96A35 MRPL24 "39S ribosomal protein L24, mitochondrial" 0 ; 101.32 0.00070149 73444000 76118 66999 68977 70534 72931 69197 92063 72096 76633 FALSE TRUE 72520.05299 73826.27427 72139.66368 63443.78831 85650.14331 66800.69054 78017.0985 65782.89204 88516.85425 0.819279601 0.834036353 0.814982235 0.716742465 0.967613954 0.754666341 0.881381282 0.743167983 1 16.43366456 -2.061430645 2.519846235 1.25506719 0.821418618 0.389023625 0.072041603 15308725.07 6307268.743 22431016.33 0.014966404 0.008680992 2.061430645 -0.433648572 RRQEIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRQEIEQK 8 2 Q9H307 Q9H307 PNN Pinin 0 69.598 0.030093 27029000 29919 24553 26856 30647 24279 32746 34431 33489 32534 FALSE TRUE 28504.78816 27054.97861 28087.37416 27566.30533 28513.24991 31611.99781 29177.91858 30556.52562 37579.20656 0.758525546 0.719945446 0.747417967 0.733552085 0.758750717 0.841209826 0.776437856 0.813123225 1 15.19764699 -0.807535724 0.278339539 1.127631173 0.723751363 0.900355832 0.025589997 3.438848504 0.259994864 0.391961779 0.032906688 0.15576299 0.807535724 -0.40387981 RRS(ph)AS(ph)PPPATSSSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSASPPPATSSSSSSR 17 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 RRS(1)AS(0.999)PPPAT(0.001)SSSSSSR 101.33 0.0054788 109730000 48308 40785 49278 56163 62007 49839 55499 46195 65839 TRUE FALSE 46024.57658 44941.03787 51537.44504 50517.38854 72821.00117 48113.06293 47031.60824 42149.9209 76048.97586 0.605196534 0.590948627 0.677687562 0.66427441 0.957554002 0.63265892 0.618438417 0.554247055 1 16.2146412 -2.142836915 2.504383892 1.779890641 0.657801553 0.477669438 0.110770348 17854886.38 4998326.455 79041448.52 0.02690892 0.007197192 2.142836915 -1.122089088 RRS(ph)FLESNYFTKPNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSFLESNYFTKPNLK 16 3 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 RRS(0.999)FLES(0.001)NYFTKPNLK 146.97 5.93E-06 250970000 190360 163590 173730 179390 155470 163750 236020 194430 173910 TRUE FALSE 181362.0601 180260.007 181695.6923 161357.3764 182583.9188 158079.2964 200010.8142 177404.6785 200879.0746 0.902841973 0.897355821 0.904502834 0.803256271 0.908924532 0.786937598 0.995677696 0.883141655 1 17.61596776 RRS(ph)FNDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSFNDFR 8 2 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 RRS(1)FNDFR 66.595 0.048257 128730000 116590 78906 136040 123890 157440 120230 186920 124570 226780 TRUE FALSE 111079.0218 86946.61111 142277.5686 111436.3418 184897.4862 116066.405 158401.921 113661.9904 261947.8842 0.424050082 0.331923319 0.543152196 0.42541417 0.705856002 0.443089683 0.60470777 0.433910702 1 17.99892028 -5 0.16583505 2.966106386 0.352116138 0.701214787 0.105225128 66.49381881 0.620860987 43.04100802 0.367980524 1.00E-05 5 -2.613990249 RRS(ph)IQDLTVTGTEPGQVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRSIQDLTVTGTEPGQVSSR 20 2 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RRS(0.497)IQDLT(0.497)VT(0.007)GTEPGQVSSR;RRS(0.989)IQDLT(0.011)VTGTEPGQVSSR;RRS(0.88)IQDLT(0.12)VT(0.001)GTEPGQVSSR 264.85 1.07E-36 318360000 133107 69390 147169 110453 173360 107596 193661 157664 266809 TRUE FALSE 126815.2959 76460.91989 153916.8442 99350.05459 203593.9291 103869.9235 164114.4576 143858.1043 308184.377 0.411491644 0.24810122 0.499431041 0.322372132 0.660623783 0.337038251 0.532520367 0.466792333 1 18.2334342 -5 0.187544608 3.48206139 0.312291711 0.726228245 0.111309487 62.56280408 0.609731037 57.79613144 0.275045476 1.00E-05 5 -3.169769679 RRS(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RRSLEPAENVHGAGGGAFPASQTPSKPASADGHR 34 3 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;RRS(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 169.96 1.06E-14 1824977000 670750 583155 580142 726612 579670 629922 770362 677606 483412 TRUE FALSE 639044.9768 642579.1575 606742.0845 653571.5813 680764.2645 608107.6432 652829.1282 618271.2264 558377.064 1.144468528 1.150797909 1.086617133 1.17048429 1.219183789 1.089062718 1.169154627 1.107264725 1 19.09088016 0.903889192 4.499942677 1.000016854 1.146502214 0.592405672 0.038436746 0.346770941 14.75293829 0.033781789 0.008579293 8.014735446 -0.903889192 0.14648536 RRS(ph)PGLCSDSLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRSPGLCSDSLEK 13 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RRS(0.999)PGLCS(0.001)DSLEK;RRS(0.918)PGLCS(0.082)DSLEK;RRS(0.999)PGLCS(0.001)DSLEK 198.98 9.57E-08 786830000 1060150 824430 991000 1038660 833210 1036510 1270990 1167090 1038970 TRUE FALSE 1010038.811 908440.3543 1036438.33 934251.9235 978521.5602 1000615.399 1077077.132 1064893.412 1200088.161 0.841637176 0.756978015 0.863635159 0.778486076 0.81537473 0.833784909 0.89749834 0.887345986 1 20.19470896 1.146158572 0.710495591 0.997950662 0.80305289 0.775883367 0.032173215 0.273490697 0.323937113 0.028381332 0.011516872 14.00098441 -1.146158572 -0.194897773 RRS(ph)PPADAIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK 113.65 0.0010732 47683134900 16118687 13190534 14202638 15984147 12174596 15692112 17427997 16365228 13444138 TRUE FALSE 15356788.61 14534664.41 14853843 14377390.18 14297841.69 15148690.23 14769035.97 14932201.88 15528986.26 0.988911211 0.935969945 0.956523675 0.92584216 0.920719579 0.975510569 0.951062466 0.96156965 1 23.88846032 0.526852491 0.992381319 1.000052737 0.950133245 0.36213971 0.020612068 1.861786757 2.691393238 0.019753874 0.006270264 3.363972917 -0.526852491 -0.049919492 RRS(ph)PPPGPDGHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK 172.93 1.18E-05 15457630000 1525722 1431687 1349781 1570624 1201271 1495036 1662929 1568922 1281537 TRUE FALSE 1453604.145 1577577.533 1411669.794 1412741.892 1410772.282 1443262.528 1409218.639 1431538.872 1480271.213 0.981985012 1.065735468 0.953656183 0.95438044 0.953049867 0.974998714 0.9520003 0.967078776 1 20.4974301 3.717506853 24.98746997 0.962131611 1.023860243 0.494351046 0.024603879 496.189846 588898.7396 0.006004366 0.009312654 5218.033384 -3.717506853 0.061728632 RRS(ph)PPPGPDGHAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;RRS(1)PPPGPDGHAKK;RRS(1)PPPGPDGHAKK;RRS(1)PPPGPDGHAKK 154.39 4.37E-06 3202720000 1224885 739563 1228215 1012942 951571 1235623 1628326 1427054 1193358 TRUE FALSE 1166987.114 814925.3105 1284529.873 911119.1457 1117524.681 1192833.066 1379894.962 1302093.586 1378417.864 0.846613457 0.591203388 0.931887134 0.660989073 0.810729976 0.865363905 1.00107159 0.944629071 1 20.39458187 2.079466844 1.929910422 0.983541563 0.748938585 0.516033902 0.094329867 0.244547976 1.740531068 0.048349639 0.026717305 120.0789395 -2.079466844 -0.234602979 RRS(ph)PQEGPTWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSPQEGPTWSR 12 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RRS(1)PQEGPTWSR;RRS(0.999)PQEGPTWSR 89.911 0.0072116 401650000 131330 105015 118203 135413 131549 119261 136225 122179 142138 TRUE FALSE 125122.2912 115716.1479 123622.7245 121801.028 154491.104 115130.9617 115441.3743 111480.359 164180.0351 0.762104181 0.704812542 0.752970508 0.741874783 0.940985936 0.701248246 0.703138931 0.679012884 1 17.32491918 -2.344550316 2.351491323 2.643253603 0.745628914 0.537693163 0.073320083 2633340.5 462284.6508 23094461.56 0.017168622 0.004523241 2.344550316 -1.897624688 RRS(ph)PS(ph)LSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(0.995)LS(0.005)SK;RRS(1)PS(0.998)LS(0.002)SK 122.46 0.0028785 3875560000 5675900 4569200 5070800 5920500 4037800 5638700 6391100 4887100 4685000 TRUE FALSE 5407611.456 5034806.675 5303301.196 5325360.092 4741991.042 5443430.405 5416020.314 4459159.616 5411525.872 0.999276652 0.930385772 0.980001079 0.98407736 0.876276147 1.005895663 1.000830531 0.824011512 1 22.36760401 4.704582722 3.896369297 0.954835478 1.002004356 0.057615694 0.059758251 0.734280114 20.4060129 0.01317224 0.091003425 50650.38165 -4.704582722 0.047168878 RRS(ph)PS(ph)PAPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSPSPAPPPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(1)PAPPPR;RRS(1)PS(1)PAPPPR 98.654 0.026365 2479810000 309042 257880 267767 324400 331840 279119 310960 262742 334130 TRUE FALSE 294434.1971 284158.2652 280044.3818 291790.6957 389712.7909 269453.039 263517.3408 239734.9176 385945.1739 0.762891253 0.736265885 0.725606642 0.75604183 1.009762052 0.698164033 0.682784392 0.621163144 1 18.55803639 -2.232434172 2.454914269 1.934636228 0.748839874 0.377556721 0.101247936 12675534.77 2169474.521 66004101.08 0.024522418 0.005855525 2.232434172 -1.185796353 RRS(ph)PS(ph)PKPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.972)PKPT(0.028)K;RRS(1)PS(0.994)PKPT(0.006)K;RRS(1)PS(0.977)PKPT(0.023)K;RRS(1)PS(0.999)PKPT(0.001)K;RRS(1)PS(0.998)PKPT(0.002)K 101.32 0.0048979 3108730000 2231190 1840930 1865060 2302100 1120060 2295260 2420710 1605330 1259750 TRUE FALSE 2125726.07 2028522.86 1950574.846 2070688.534 1315398.109 2215774.571 2051386.23 1464758.795 1455105.596 1.460874095 1.394072613 1.340503982 1.423050354 0.903988077 1.522758607 1.409785129 1.006634019 1 20.47269242 -4.103273362 0.082449535 1.13E-09 1.68876112 0.310896224 0.183497794 248.8712369 1.729154068 48.01219169 5.85379652 7.88E-05 4.103273362 1.688761119 RRS(ph)PS(ph)PYYSR ddPTM_SK-BR-3_Trastuzumab_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(0.845)PS(0.96)PY(0.148)Y(0.014)S(0.033)R 110.9 0.0089731 6707500000 1527400 1321600 1274500 1642900 1474200 1221600 1450300 1210000 1612900 TRUE FALSE 1455202.829 1456272.543 1332937.086 1477752.571 1731300.013 1179295.686 1229030.098 1104045.985 1863020.294 0.781098753 0.781672936 0.71547105 0.793202616 0.929297452 0.633002061 0.659697644 0.592610821 1 20.82921196 2.200651375 24.99999196 0.687262636 0.791733061 0.061082402 0.122666706 296.7006369 195663.3534 0.040881371 0.030193565 158.7272074 -2.200651375 0.104470424 RRS(ph)PSLS(ph)SK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(0.354)LS(0.641)S(0.005)K;RRS(0.994)PS(0.207)LS(0.798)SK 129.04 0.001969 3257900000 6195900 4944000 5164800 6083300 4455700 5786900 6397000 5144400 4776600 TRUE FALSE 5903032.086 5447799.221 5401611.189 5471795.126 5232772.669 5586498.202 5421020.161 4693929.064 5517330.733 1.069907238 0.987397618 0.979026172 0.991746805 0.948424686 1.012536401 0.982543992 0.850760865 1 22.39553903 8 0.456374004 0.960862703 3.613727861 0.363689248 0.044046861 91.93286382 1.090114055 0.024117137 228.1800905 100000000 -8 2.652865158 RRS(ph)PSLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.944)PS(0.056)LSSK;RRS(0.97)PS(0.03)LSSK;RRS(0.737)PS(0.263)LSSK;RRS(0.989)PS(0.011)LSSK;RRS(0.552)PS(0.448)LSSK;RRS(0.997)PS(0.003)LSSK;RRS(0.971)PS(0.029)LSSK;RRS(0.995)PS(0.005)LSSK;RRS(0.5)PS(0.5)LSSK 164.13 4.92E-05 24659680000 6667650 5502418 5210353 6115817 4792616 5648864 7104703 6363196 5557253 TRUE FALSE 6352483.399 6063120.65 5449252.839 5501043.456 5628446.713 5453242.423 6020750.071 5806000.825 6419043.413 0.989630852 0.944552056 0.848919767 0.856988044 0.876835745 0.84954129 0.937951293 0.90449627 1 22.61392689 0.260738607 1.407442508 1.000027351 0.905822082 0.306841228 0.04619105 10.08265729 17.50917138 0.05054607 0.014582107 1.822798265 -0.260738607 -0.094205269 RRS(ph)PSPYYS(ph)R ddPTM_SK-BR-3_Trastuzumab_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(0.839)PS(0.306)PY(0.189)Y(0.122)S(0.543)R 115.1 0.0062352 2118500000 468510 389430 404130 482560 462620 419100 467170 399210 506620 TRUE FALSE 446364.4608 429113.3597 422659.7602 434052.152 543300.7815 404586.4619 395894.6363 364253.0561 585184.0421 0.762776201 0.733296414 0.72226809 0.741736139 0.9284272 0.691383279 0.67653013 0.62245897 1 19.1585309 4.751359248 17.27803356 0.748427586 0.762776269 0 0.11592046 22.13349541 276439.1894 0.025131002 0.153085971 56410.40888 -4.751359248 0.014348682 RRS(ph)QS(ph)IEQESQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(1)QS(0.833)IEQES(0.167)QEK;RRS(1)QS(0.964)IEQES(0.036)QEK;RRS(1)QS(1)IEQESQEK;RRS(0.625)QS(0.876)IEQES(0.5)QEK;RRS(0.999)QS(0.84)IEQES(0.161)QEK 190.37 2.20E-05 3573573000 4679800 3475190 3893350 4244390 2954970 4158890 4900090 4075780 3134450 TRUE FALSE 4458595.128 3829315.812 4071863.949 3817735.853 3470315.832 4014866.596 4152491.274 3718883.096 3620524.497 1.231477686 1.057668803 1.124661344 1.054470383 0.958511905 1.1089185 1.14693086 1.027166947 1 21.78776728 4.684236254 1.64177177 1.068635823 1.281561235 0.456159531 0.05783045 0.843671034 2.419410738 0.015445464 0.277541671 48332.16545 -4.684236254 0.212925411 RRS(ph)QSIEQES(ph)QEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(1)QSIEQES(1)QEK;RRS(0.962)QS(0.038)IEQES(1)QEK;RRS(0.997)QS(0.003)IEQES(1)QEK 266.28 1.03E-23 4440240000 7792600 6090400 6666700 7182600 4980950 7144100 8106000 7038000 5394100 TRUE FALSE 7424259.241 6711018.684 6972374.789 6460591.402 5849626.103 6896698.026 6869280.823 6421715.409 6230589.479 1.191582156 1.077108146 1.119055398 1.036914954 0.938855966 1.106909394 1.102508976 1.030675417 1 22.57093723 4.705842764 0.85678921 1.049828295 1.267128584 0.436703437 0.05266848 2.247839059 1.319831942 0.018386336 0.458333855 50797.54974 -4.705842764 0.217300289 RRS(ph)QSIEQESQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 RRS(0.5)QS(0.5)IEQESQEK;RRS(0.993)QS(0.007)IEQESQEK 123.92 0.00017152 707630000 272550 198347 291420 276040 219340 286760 328800 303940 256630 TRUE FALSE 259667.1016 218558.7848 304781.8953 248291.9348 257592.8266 276829.4293 278635.5212 277325.4023 296426.8697 0.875990432 0.737310977 1.02818579 0.837616155 0.868992837 0.933887773 0.939980648 0.935560945 1 18.1773167 2.685245539 0.268693772 1.008932929 0.778772046 0.271467265 0.070827751 3.217088295 0.511322987 0.112666995 0.250627414 484.4461831 -2.685245539 -0.230160883 RRS(ph)QVIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RRSQVIEK 8 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK 109.72 0.0028066 3694180000 1960020 1463960 1635520 1853180 1492070 1709680 2064520 1885530 1738800 TRUE FALSE 1867373.739 1613139.188 1710510.21 1666894.826 1752286.536 1650473.353 1749539.556 1720422.997 2008444.223 0.929761313 0.803178485 0.851659304 0.829943299 0.872459646 0.821767084 0.871091931 0.856594859 1 20.93764697 -0.040808507 1.134127429 1.000874251 0.852752573 0.640359407 0.034267673 7.183086062 7.089750815 0.054415371 0.00941069 0.910314569 0.040808507 -0.148121678 RRS(ph)S(ph)DEDAAGEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSSDEDAAGEPK 13 2 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 2 RRS(1)S(1)DEDAAGEPK;RRS(1)S(1)DEDAAGEPK 84.499 0.047792 469770000 870400 608570 697130 827690 512410 758570 861090 714440 553270 TRUE FALSE 829257.917 670583.9749 729094.1001 744489.0287 601774.1418 732300.5307 729714.9055 651879.8461 639068.2859 1.297604552 1.049315057 1.140870414 1.16496006 0.941642943 1.145887766 1.141841837 1.020047248 1 19.28561057 4.611647273 2.685547105 1.087882614 1.312004301 0.454626435 0.075002321 0.310709477 3.566420489 0.017331639 0.136272642 40892.84001 -4.611647273 0.224121687 RRS(ph)SLPNGEGLQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSSLPNGEGLQLK 14 2 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 RRS(0.5)S(0.5)LPNGEGLQLK 80.469 0.0084584 102010000 170740 99859 156220 134090 154490 161740 222170 170800 187290 TRUE FALSE 162669.4586 110034.7456 163382.8415 120611.0184 181433.0071 156138.9032 188273.8861 155843.8465 216333.9767 0.75193671 0.508633675 0.75523431 0.55752231 0.838670882 0.721749332 0.870292725 0.720385438 1 17.72290074 1.31390396 0.379143889 1.006315337 0.616194629 0.482201497 0.102263918 0.875318852 0.387576115 0.132673174 0.091303997 20.60174278 -1.31390396 -0.390120708 RRS(ph)SPSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.435)S(0.435)PS(0.129)ARPPDVPGQQPQAAK 114.21 0.0010099 304810000 72339 56857 65570 62816 56886 67545 83281 73493 73117 TRUE FALSE 68919.67883 62650.79294 68576.44936 56501.61634 66806.90039 65205.89971 70574.95389 67057.56331 84455.61093 0.816046182 0.741819191 0.81198216 0.669009622 0.791029745 0.772073033 0.835645532 0.793997729 1 16.36590565 0.239718762 0.631552902 1.008192108 0.76572607 0.715043345 0.04466223 1.416393108 0.771573222 0.069386504 0.016297322 1.736675837 -0.239718762 -0.242466038 RRS(ph)SS(ph)PFLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRSSSPFLSK 10 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RRS(0.996)S(0.45)S(0.553)PFLSK;RRS(0.997)S(0.293)S(0.711)PFLSK;RRS(0.998)S(0.019)S(0.983)PFLSK 157.37 4.57E-05 2833420000 3230700 2833620 2693500 3405600 2227660 2876880 3125950 2710270 2424520 TRUE FALSE 3077991.214 3122369.1 2816999.639 3063262.618 2616163.199 2777252.924 2649028.915 2472944.391 2800502.179 1.099085456 1.114931859 1.005890894 1.093826186 0.934176455 0.991698184 0.945912107 0.883036053 1 21.41725412 2.955976792 0.89726971 0.93981161 1.107947997 0.630874994 0.046336921 0.307543626 0.544877518 0.022447145 0.026617577 903.6011847 -2.955976792 0.168136388 RRSPS(ph)LSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.171)PS(0.828)LSSK 112.95 0.0014801 1450700000 485600 378270 376790 406910 389300 443460 561950 489540 421130 TRUE FALSE 462646.6504 416816.1431 394066.1942 366006.6337 457193.7967 428102.869 476214.2066 446673.2824 486436.6896 0.951093247 0.856876449 0.810107878 0.752423988 0.939883456 0.880079316 0.978984967 0.91825574 1 18.89189252 2.025258916 1.641773648 0.964215044 0.858966371 0.393126684 0.059709148 0.440614619 2.225060381 0.038625469 0.019340177 105.9885416 -2.025258916 -0.105248673 RRSPS(ph)PY(ph)YSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.083)PS(0.976)PY(0.84)Y(0.03)S(0.072)R;RRS(0.049)PS(0.994)PY(0.953)Y(0.004)S(0.001)R;RRS(0.129)PS(0.891)PY(0.414)Y(0.27)S(0.296)R 123.68 0.00074779 15134200000 2449680 2073340 2186320 2326050 2381700 2178700 2509180 1989630 2676540 TRUE FALSE 2333888.481 2284615.703 2286564.935 2092231.035 2797067.726 2103251.073 2126358.507 1815407.45 3091604.153 0.754911808 0.738974199 0.739604691 0.676746094 0.904730227 0.680310599 0.687784853 0.587205657 1 21.55992418 4.443257475 2.086855971 0.736739248 0.755349083 0 0.119757607 6.136802871 44.56032761 0.027938012 0.171409896 27749.64777 -4.443257475 0.018609835 RRSS(ph)DPLGDTASNLGSAVDELMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRSSDPLGDTASNLGSAVDELMR 23 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 RRS(0.417)S(0.582)DPLGDT(0.001)ASNLGSAVDELMR 106.28 0.0011489 79842000 12293 9010.2 13345 13194 14942 11449 16533 11921 18215 TRUE FALSE 11711.93425 9928.349624 13956.88145 11867.71405 17547.88007 11052.51826 14010.5872 10877.13404 21039.68917 0.556659091 0.471886706 0.663359679 0.564063183 0.83403704 0.525317564 0.665912271 0.516981689 1 14.36082577 -5 0.235767545 3.222315356 0.552223305 0.577163618 0.105646743 114.0185875 1.13868694 121.4945197 0.161044253 1.00E-05 5 -2.670092052 RRSS(ph)PSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.204)S(0.66)PS(0.136)ARPPDVPGQQPQAAK;RRS(0.218)S(0.471)PS(0.311)ARPPDVPGQQPQAAK 128.4 0.00010071 478640000 128143 107193 131360 111368 105250 123682 149970 131146 129989 TRUE FALSE 122085.9343 118116.0886 137382.9859 100173.0771 123605.5667 119398.8613 127089.3221 119662.161 150147.0302 0.813109218 0.786669496 0.914989699 0.667166556 0.82323018 0.79521294 0.846432473 0.796966552 1 17.19601641 -0.807866465 0.565011629 1.041986092 0.801515873 0.498307249 0.061268805 13.46722583 2.841337066 1.068735874 0.023110424 0.155644413 0.807866465 -0.240470219 RRT(ph)AS(ph)PPPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRTASPPPPPK 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)AS(1)PPPPPK;RRT(1)AS(1)PPPPPK 99.711 0.0050451 467630000 1074220 950730 958190 1132010 836340 1040840 1180730 1076590 914160 TRUE FALSE 1023443.749 1047610.468 1002123.959 1018218.204 982197.4312 1004795.45 1000587.953 982318.0722 1055923.264 0.969240649 0.992127462 0.949049986 0.964291856 0.930178797 0.951579991 0.947595329 0.930293049 1 20.01007356 3.726176974 24.34519525 0.950376767 0.980684055 0.228642549 0.020385879 539.0509956 1059727.768 0.004750742 0.00742655 5323.251368 -3.726176974 0.030307288 RRT(ph)IHTFPCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRTIHTFPCLK 11 2 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 RRT(0.999)IHT(0.001)FPCLK;RRT(0.986)IHT(0.014)FPCLK 121.18 0.019869 5432800000 6621700 4446000 4894400 5905600 5941100 5812400 7614400 6147000 5658300 TRUE FALSE 6308705.364 4899052.455 5118813.081 5311957.868 6977225.959 5611115.131 6452683.432 5608736.093 6535760.265 0.965259604 0.749576523 0.783200863 0.812752863 1.067546188 0.858525237 0.98728888 0.858161234 1 22.63992364 2.784051706 24.99528356 0.948365347 0.827489916 0.36439981 0.082880757 473.3530054 260085.0098 0.023804094 0.025247971 608.207408 -2.784051706 -0.120875432 RRT(ph)NS(ph)SSSSPVVLK ddPTM_SK-BR-3_Trastuzumab_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(0.917)NS(0.917)S(0.131)S(0.02)S(0.013)S(0.002)PVVLK 74.147 0.037364 212820000 253920 187570 209130 244990 188950 220310 294240 240170 248940 TRUE FALSE 241917.7048 206683.5962 218718.8174 220363.1397 221902.8202 212680.6095 249348.2839 219139.4416 287544.3438 0.841323121 0.7187886 0.760643783 0.766362283 0.771716867 0.739644559 0.867164628 0.762106598 1 18.13342493 -0.276626028 0.512793258 1.029686578 0.767861069 0.709065388 0.044510472 3.444657164 0.904740166 0.238514319 0.020092968 0.528900494 0.276626028 -0.261825509 RRT(ph)PS(ph)PPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRTPSPPPR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)PS(1)PPPR 64.534 0.076279 222990000 117460 107940 119000 135490 130240 112640 131290 113150 139240 TRUE FALSE 111907.8986 118939.2087 124456.2677 121870.2878 152953.8148 108739.2486 111259.2992 103241.9862 160832.6281 0.695803457 0.739521639 0.773824747 0.757746045 0.951012345 0.67610192 0.691770697 0.6419219 1 17.29520059 4.186308865 1.93471746 0.766428291 0.699245926 0.044415621 0.114559269 1.38004719 9.680287054 0.029291725 0.110621683 15357.08771 -4.186308865 -0.067182365 RRT(ph)PT(ph)PPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRTPTPPPR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)PT(1)PPPR 62.14 0.09797 304800000 191940 197910 175380 201860 259240 213660 219100 201840 231820 TRUE FALSE 182867.3766 218077.254 183421.3465 181568.6493 304451.3739 206260.9006 185672.271 184165.8196 267769.4616 0.682928425 0.814421677 0.684997256 0.678078255 1.136990649 0.770292846 0.693403459 0.687777532 1 18.03063191 -2.090869036 2.512203098 1.392718316 0.767911286 0.216194472 0.138455007 11922718 4497456.202 26740376.9 0.032450059 0.008112056 2.090869036 -0.62480703 RRT(ph)SS(ph)KSEAGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRTSSKSEAGAR 12 3 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 RRT(0.959)S(0.047)S(0.974)KS(0.02)EAGAR 109.36 0.0030421 238990000 174850 124460 156100 184000 117410 162210 194650 160330 136930 TRUE FALSE 166585.187 137142.6155 163257.3394 165503.9704 137886.2668 156592.627 164952.5675 146290.6552 158164.4051 1.053240689 0.867088998 1.032200256 1.04640466 0.87179076 0.990062378 1.042918395 0.9249278 1 17.27106543 2.013502003 24.99580065 0.999660713 0.969182618 0.001722741 0.07020989 880.5592377 1630144.604 0.025228066 0.018622176 103.1577837 -2.013502003 -0.030478094 RRTETVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRTETVQK 8 2 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 120.46 0.00084259 39835000 121698 65019 62103 70319 97031 74706 118901 125705 113713 FALSE TRUE 115945.5767 71644.51002 64950.48398 63250.40052 113953.1757 72118.91249 100760.4687 114697.6038 131347.0313 0.882742271 0.545459683 0.494495257 0.481551809 0.867573287 0.549071508 0.767131679 0.87324093 1 17.00302407 1.218554171 1.61041947 0.996862154 0.64032873 0.444430628 0.140485678 0.335555286 1.61137658 0.128430767 0.038454842 16.54071088 -1.218554171 -0.356533424 RRVEHHDHAVVSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RRVEHHDHAVVSGR 14 2 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;;;;; 196.33 1.50E-08 531375000 238266 138925.6 221538.1 210321.3 361812 165735.2 284273.9 195952.7 72205.37 FALSE TRUE 227003.6384 153082.2766 231695.841 189179.4033 424911.8982 159995.7485 240902.6955 178794.0428 83402.61001 2.721780989 1.835461463 2.778040651 2.268267184 5.094707446 1.918354215 2.888431135 2.143746374 1 16.34780491 3.691140964 24.62218396 2.720624161 2.278620296 0.001551289 1.064691301 1254.31992 651292.631 0.258502493 0.400471871 4910.672422 -3.691140964 -0.442003865 RRVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RRVS(1)EVEEEKEPVPQPLPSDDTR 177.44 3.02E-16 4812290000 3976540 3837080 3636200 4507370 2589382 4091180 4082960 4187550 2505997 TRUE FALSE 3788576.835 4228082.814 3802923.367 4054280.604 3040969.401 3949501.411 3460029.463 3820865.922 2894614.216 1.308836533 1.460672303 1.313792818 1.400628996 1.050561206 1.364431014 1.195333542 1.319991418 1 21.46493965 -4.919830611 0.102797022 7.26E-10 1.516937446 0.458698708 0.108258796 140.2024503 0.991265741 29.84230319 1.513424173 1.20E-05 4.919830611 1.516937446 RRVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 34 3 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RRVS(1)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK;RRVS(0.955)GPDPKPGS(0.015)NCS(0.015)PAQS(0.015)VLSEVPSVPTNGMAK 183.77 3.53E-19 714480000 588760 420160 585580 561480 400960 620090 702920 661620 523220 TRUE FALSE 560930.4816 462974.7817 612429.4222 505038.9637 470887.2971 598616.1278 595676.644 603685.0453 604358.2854 0.928142288 0.766060122 1.013354887 0.83566152 0.779152547 0.990498753 0.985634943 0.998886025 1 19.20504456 2.210723362 24.29716029 0.991742708 0.862299811 0.456364885 0.070076211 139.8189614 122036.8481 0.024906026 0.018399081 162.4513639 -2.210723362 -0.129442897 RRVS(ph)QDLEVEKPDASPTSLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRVSQDLEVEKPDASPTSLQLR 22 3 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RRVS(1)QDLEVEKPDASPTSLQLR;RRVS(1)QDLEVEKPDASPTSLQLR 100.95 0.0042994 349570000 181769 92397 163004 144154 168951 157177 239715 204551 226007 TRUE FALSE 173177.1396 101812.3593 170477.8946 129663.366 198416.0009 151733.9211 203142.0741 186639.43 261055.0113 0.663374125 0.390003467 0.653034369 0.496689818 0.760054365 0.581233512 0.77815811 0.714942912 1 17.99399433 1.023397991 0.400964272 1.023294771 0.520159873 0.630763908 0.100740003 0.741540504 0.328534018 0.13780589 0.074477454 10.55353587 -1.023397991 -0.503134898 RRWEEEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RRWEEEGFR 9 2 Q3KQV9 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 175.73 3.02E-05 113220000 85243 56729 71405 53487 100550 77033 116380 97488 136310 FALSE TRUE 81213.73233 62509.7496 74678.98988 48110.38514 118085.8882 74365.32789 98624.09353 88951.4339 157448.2586 0.515812198 0.397017726 0.474308135 0.305563145 0.749998058 0.472315976 0.626390501 0.564956607 1 17.26451828 -0.773827339 0.273793321 1.265646578 0.41740661 0.679487755 0.110348946 6.499611123 0.489146883 1.541172518 0.138606905 0.168334317 0.773827339 -0.848239969 RRYEDDGIS(ph)DDEIEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RRYEDDGISDDEIEGKR 17 3 I3VM54;Q9Y2K7;Q9Y2K7-3 I3VM54 KDM2A Lysine-specific demethylase 2A 1 RRYEDDGIS(1)DDEIEGKR;RRYEDDGIS(1)DDEIEGKR 186.63 2.83E-09 620870000 451290 338310 493910 465770 386440 481570 629410 553330 480730 TRUE FALSE 429958.4161 372784.1736 516556.262 418949.9147 453835.0136 464893.1101 533381.9446 504877.4918 555279.1532 0.774310387 0.671345523 0.930264101 0.754485221 0.817309656 0.837224138 0.960565405 0.90923185 1 19.08285371 2.087655248 0.455475936 1.006881184 0.72645386 0.574233157 0.066213142 0.637896534 0.300793684 0.064486639 0.058405883 122.3644459 -2.087655248 -0.280427324 RRYS(ph)DFEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RRYSDFEWLR 10 2 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RRYS(1)DFEWLR;RRYS(1)DFEWLR;RRYS(1)DFEWLR 115.83 0.00092255 389140000 360810 275654 323520 358020 386490 328473 500910 400150 444160 TRUE FALSE 343755.2264 303743.456 338353.712 322031.1494 453893.7336 317097.8976 424486.9797 365110.7447 513038.0643 0.670038444 0.592048577 0.659509957 0.627694457 0.884717461 0.618078696 0.827398607 0.711664046 1 18.96870634 -4.999989719 0.108764271 2.041798409 0.504143666 0.59792716 0.083802077 100.9276012 0.732026478 23.17015378 0.956832105 1.00E-05 4.999989719 -1.537654743 RS(ph)AS(ph)PERMD ddPTM_SK-BR-3_Trastuzumab_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 91.093 0.0062303 1400260000 1366560 1433410 1207250 1490300 1082210 1347400 1324480 1210770 1061800 TRUE FALSE 1301965.417 1579476.109 1262603.607 1340492.213 1270947.081 1300739.2 1122406.25 1104748.56 1226458.521 1.061564981 1.287834918 1.029471103 1.092978025 1.036274003 1.060565178 0.915160383 0.900763084 1 20.22606701 2.541746517 0.836858068 0.933714231 1.160249181 0.491518956 0.075818462 0.439174313 0.629508852 0.051050474 0.039180626 348.1340617 -2.541746517 0.226534949 RS(ph)ASASHQADIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.333)AS(0.333)AS(0.333)HQADIK 86.497 0.0067855 35248000 44141 32143 44689 56934 53803 59418 63452 51229 50676 TRUE FALSE 42054.54241 35418.40824 46738.03485 51210.88615 63186.22617 57360.33976 53771.23202 46743.11718 58534.57526 0.718456437 0.605085252 0.798468848 0.874882681 1.079468432 0.979939455 0.918623425 0.798555674 1 15.83700143 3.367063628 2.391059952 0.949621306 0.663550596 0.691397364 0.078182456 0.146416469 1.699429723 0.022951755 0.033582762 2328.432366 -3.367063628 -0.28607071 RS(ph)ASPDDDLGSSNWEAADLGNEERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSASPDDDLGSSNWEAADLGNEERK 25 2 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.703)AS(0.297)PDDDLGSSNWEAADLGNEERK 143.48 1.69E-07 127410000 135640 89802 134050 118790 93894 132160 162540 147740 139300 TRUE FALSE 129228.566 98952.9259 140196.3251 106849.0035 110269.0839 127583.2661 137741.5377 134803.1024 160901.9326 0.803151112 0.614989045 0.871315359 0.664062897 0.68531858 0.792925629 0.85605894 0.837796664 1 17.29582213 1.218805459 0.802670242 0.992116605 0.721182556 0.55438138 0.075446263 0.399935709 0.580554345 0.066339025 0.025405769 16.55028432 -1.218805459 -0.270934048 RS(ph)DSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.492)DS(0.372)MT(0.136)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.484)DS(0.484)MT(0.033)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.359)DS(0.32)MT(0.32)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.447)DS(0.447)MT(0.106)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.443)DS(0.443)MT(0.114)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 275.53 9.44E-77 1626888000 452228.6 354428.9 420766.5 458983.3 480075.2 464247 579228.3 476173.7 529464.6 TRUE FALSE 430852.6503 390545.6079 440059.0602 412845.4267 563800.1629 448170.01 490856.3846 434477.4065 611571.266 0.704501134 0.638593782 0.719554833 0.675056939 0.921887921 0.73281731 0.802615185 0.71042809 1 19.2221611 -5 0.106578805 1.85215401 0.570400056 0.570957228 0.074046705 115.3215083 0.823870643 21.58997227 0.948079432 1.00E-05 5 -1.281753953 RS(ph)EEKEAGEI ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSEEKEAGEI 10 2 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 RS(1)EEKEAGEI 95.067 0.0060444 422380000 525240 490280 544420 545210 495490 536890 547640 537160 523610 TRUE FALSE 500412.9461 540240.0894 569382.1955 490404.455 581903.2991 518297.3647 464087.4599 490123.4227 604808.7646 0.827390368 0.893241172 0.941425172 0.810842176 0.962127755 0.856960737 0.767329257 0.810377513 1 19.20611952 1.998715586 24.99993467 0.828073709 0.883789166 0 0.075727557 103.7770111 2019944.726 0.025829343 0.018822301 99.70468967 -1.998715586 0.055715457 RS(ph)FSKEVEER ddPTM_SK-BR-3_Trastuzumab_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(0.636)FS(0.364)KEVEER;RS(0.5)FS(0.5)KEVEER 109 0.0010838 386310000 582830 494790 517250 619670 489900 593590 656760 642370 492010 TRUE FALSE 555280.781 545209.6635 540966.4241 557379.5943 575338.4049 573033.8295 556559.1998 586120.6774 568308.398 0.977076501 0.959355282 0.951888844 0.98076959 1.012370056 1.008314907 0.979326017 1.031342629 1 19.11631451 2.964109365 4.567689885 1.002804885 0.964136213 0.657815163 0.014318895 0.131745162 6.431636489 0.004269313 0.004729621 920.6813897 -2.964109365 -0.038668672 RS(ph)GSPLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.627)GS(0.373)PLEK 59.418 0.051764 0 112270 91468 92619 107580 76280 104830 112290 110770 86771 TRUE FALSE 106963.2196 100788.6932 96865.67276 96765.85401 89583.20785 101199.7108 95158.09815 101070.3916 100227.0035 1.067209593 1.005604175 0.966462823 0.965466896 0.893803114 1.009705042 0.949425752 1.008414779 1 16.61291173 4.192446524 1.609357368 0.966098762 1.066313046 0.44441089 0.034134009 0.348363036 1.587448711 0.008730049 0.039358886 15575.66234 -4.192446524 0.100214284 RS(ph)ISSPNVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.832)IS(0.084)S(0.084)PNVNR;RS(0.58)IS(0.157)S(0.263)PNVNR 74.987 0.042737 153723000 315190 257210 288960 284570 301930 271650 321500 277790 321280 TRUE FALSE 300291.5933 283419.9914 302209.1018 255964.483 354586.4964 262242.6924 272449.2702 253465.2349 371102.4615 0.809187824 0.763724364 0.814354883 0.689740731 0.955494865 0.706658456 0.734161851 0.683006073 1 18.50145804 4.70282622 3.837101255 0.779655404 0.811044917 0 0.108400034 1.973282868 52.41160904 0.023024333 0.160899848 50445.94011 -4.70282622 0.031389513 RS(ph)LSMDSQVPVYSPSIDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSLSMDSQVPVYSPSIDLK 19 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 RS(0.583)LS(0.393)MDS(0.024)QVPVYSPSIDLK;RS(0.622)LS(0.377)MDS(0.001)QVPVYSPSIDLK 173.89 2.38E-12 326570000 595180 480700 583670 607330 519390 636920 739670 658770 617010 TRUE FALSE 567047.0209 529683.8765 610431.8468 546280.0345 609971.4516 614863.3007 626819.7565 601084.6064 712692.7595 0.795640216 0.743214898 0.85651473 0.766501451 0.855868736 0.862732633 0.879509085 0.843399345 1 19.44292074 -0.78304696 0.127214616 1.216799136 0.684674333 0.757756191 0.034702634 13.35193808 0.383658793 1.351344585 0.3706769 0.164798419 0.78304696 -0.532124803 RS(ph)LSVEHLETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSLSVEHLETK 11 1 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 RS(0.5)LS(0.5)VEHLETK 99.705 0.0028025 172130000 225480 181050 207730 210900 174640 217460 264540 246430 229360 TRUE FALSE 214822.0073 199499.2008 217254.626 189699.9313 205097.1607 209929.3057 224179.5644 224851.2828 264927.9774 0.810869465 0.753031835 0.820051654 0.716043406 0.774161954 0.792401421 0.846190601 0.848726076 1 18.01524068 0.83819898 0.823257349 0.999228403 0.774054504 0.83570588 0.030842816 0.296801464 0.41333085 0.027844243 0.009828714 6.88967887 -0.83819898 -0.225173899 RS(ph)NSPDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.705)NS(0.295)PDKFK;RS(0.915)NS(0.085)PDKFK;RS(0.733)NS(0.267)PDKFK 102.73 0.0027856 8856260000 6346610 6031890 4839860 6508070 2553930 6460860 5552040 6265290 2510010 TRUE FALSE 6046618.323 6646546.449 5061772.368 5853866.439 2999334.583 6237118.798 4704974.328 5716667.993 2899249.531 2.085580512 2.292505828 1.745890553 2.019097141 1.03452102 2.151287335 1.622824899 1.971775086 1 21.46724808 -0.09202456 0.094771001 3.94E-12 2.864788902 0.395672137 0.345410743 35.9834259 1.04491224 20.83235466 10.40288776 0.809050145 0.09202456 2.864788902 RS(ph)PERPTGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSPERPTGDLR 11 2 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.999)PERPT(0.001)GDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR;RS(1)PERPTGDLR;RS(0.999)PERPT(0.001)GDLR 88.282 0.010313 2305644000 2992862 2748835 2617847 3079747 2726163 2859648 3170946 2985795 2915527 TRUE FALSE 2851395.345 3028944.412 2737877.874 2770164.98 3201604.964 2760617.673 2687159.949 2724342.961 3367652.037 0.846701296 0.899423212 0.812993102 0.822580525 0.950693519 0.819745521 0.797932779 0.808974007 1 21.68331165 RS(ph)PESCSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.999)PES(0.001)CSKPEK;RS(0.998)PES(0.002)CS(0.001)KPEK 51.841 0.077289 412720000 269129 276258 286295 332932 191290 305982 324557 323975 222810 TRUE FALSE 256407.8055 304409.0043 299421.9089 299465.0428 224650.9154 295385.7666 275039.8688 295606.0315 257362.2368 0.996291487 1.182803693 1.163425966 1.163593566 0.872897742 1.147743236 1.068687746 1.148599092 1 17.97344085 RS(ph)PGGGSEANGLALVSGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSPGGGSEANGLALVSGFK 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.999)PGGGS(0.001)EANGLALVSGFK 194.19 2.24E-15 321280000 562670 550690 535270 608820 453120 551070 599880 595630 485060 TRUE FALSE 536073.7042 606805.9371 559812.659 547620.2569 532143.9845 531986.3077 508357.2884 543473.4796 560280.6275 0.956795002 1.083039297 0.999164761 0.977403519 0.94978116 0.949499736 0.907326193 0.970002268 1 19.09579008 3.10093384 2.202642528 0.945818736 1.021502322 0.305095954 0.038375756 0.278283604 2.751746726 0.01191743 0.014858718 1261.635325 -3.10093384 0.075683586 RS(ph)PLGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 98.997 0.0066472 1818620000 2290000 2118250 1961870 2380640 1712620 2235560 2448290 2404190 1904560 TRUE FALSE 2181756.238 2334102.083 2051823.68 2141333.544 2011300.386 2158141.997 2074758.395 2193666.378 2199909.438 0.991748206 1.060999168 0.932685521 0.973373498 0.914265084 0.981014018 0.94311082 0.997162129 1 21.0690127 3.734389822 24.99531816 0.959298841 1.026373687 0.401010568 0.031895782 260.7909698 1562905.079 0.007506182 0.012103313 5424.876074 -3.734389822 0.067074846 RS(ph)PLSDPPSQDPTPAATPETPPVISAVVHATDEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSPLSDPPSQDPTPAATPETPPVISAVVHATDEEK 35 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y9Y7 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RS(0.991)PLS(0.008)DPPS(0.001)QDPTPAATPETPPVISAVVHATDEEK;RS(0.998)PLS(0.002)DPPSQDPTPAATPETPPVISAVVHATDEEK 210 2.48E-28 83760000 115561 152100 103031 150195 63541 128153 114803 138696 64181 TRUE FALSE 110098.6605 167599.1629 107755.0733 135097.1132 74622.53028 123715.0295 97287.69385 126551.043 74133.86169 1.485133218 2.260763963 1.453520305 1.822340158 1.006591706 1.66880595 1.312324647 1.707061255 1 16.17784504 3.143636866 1.910923549 1.389937499 1.843436688 0.234621304 0.32991461 0.410929879 3.080942435 0.097391937 0.126540842 1391.992405 -3.143636866 0.453499189 RS(ph)PPAPGLQPMR ddPTM_SK-BR-3_Trastuzumab_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 140.22 3.64E-05 682190000 801930 569790 616350 683160 724950 628330 815480 662500 761670 TRUE FALSE 764024.3582 627852.2488 644610.2572 614487.4589 851381.0505 606570.7745 691063.5487 604487.9879 879785.8935 0.868420787 0.713642096 0.732689921 0.698451138 0.967713914 0.689452717 0.785490599 0.687085338 1 19.74679294 -1.553424217 3.171073721 1.008809669 0.769537998 0.399198914 0.089475977 39923121.69 48425727.96 3013204.917 0.019495703 0.027962486 1.553424217 -0.239271671 RS(ph)PPWEP ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 114.89 0.0061463 877240000 1111380 1139850 927090 1239240 883120 1046570 1039450 1114140 917920 TRUE FALSE 1058847.27 1256002.011 969597.9935 1114669.241 1037135.848 1010327.018 880862.8117 1016579.995 1060266.346 0.998661586 1.184609901 0.914485306 1.051310593 0.978184258 0.952899262 0.830793899 0.958796815 1 20.01599529 2.862572617 1.000905584 0.91212094 1.075076718 0.241754495 0.079578097 0.512745512 1.102938727 0.039272125 0.041372782 728.7400154 -2.862572617 0.162955778 RS(ph)PS(ph)PYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.9)PS(0.924)PY(0.088)Y(0.016)S(0.072)R;RS(0.916)PS(0.991)PY(0.09)Y(0.002)S(0.001)R;RS(0.873)PS(0.981)PY(0.122)Y(0.01)S(0.014)R 87.831 0.0088191 416600000 715490 609650 687400 731910 601820 709650 773210 625900 688170 TRUE FALSE 681670.2057 671774.0281 718917.9699 658337.0163 706777.2175 685074.6426 655242.6135 571092.8779 794887.8889 0.857567734 0.845117956 0.904426876 0.828213671 0.889153335 0.861850649 0.824320791 0.718457138 1 19.60039187 1.755796115 7.127608358 0.828890476 0.862784695 0 0.071072867 0.492173452 75.84402299 0.030034552 0.016161242 56.9896664 -1.755796115 0.033894219 RS(ph)PVPAQIAITVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK 120.92 7.20E-05 1301000000 3654890 3210920 3217760 3670020 2513530 3573280 4001180 3834510 3095600 TRUE FALSE 3482130.593 3538116.399 3365297.479 3301102.617 2951888.836 3449536.418 3390726.504 3498739.976 3575649.838 0.973845525 0.989503044 0.941170873 0.923217532 0.825553108 0.96472993 0.948282594 0.978490662 1 21.76977403 1.139195023 1.958275279 0.999520673 0.941508183 0.194975335 0.044299797 0.627913117 4.515224157 0.044525801 0.012737469 13.77828052 -1.139195023 -0.05801249 RS(ph)PVSTRPLPSASQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(0.998)PVS(0.002)TRPLPSASQK 94.281 0.0052471 0 117160 98519 107030 115440 87354 115930 129850 119640 101740 TRUE FALSE 111622.079 108558.1981 111937.4314 103835.7519 102588.5099 111915.315 110038.9976 109163.6873 117517.3196 0.949835134 0.923763395 0.952518588 0.883578287 0.872965026 0.952330392 0.936364087 0.928915735 1 16.84251387 0.234995596 0.859411744 1.000738794 0.923982693 0.432751344 0.027139158 3.338357081 2.90821549 0.033260597 0.008895431 1.717890967 -0.234995596 -0.076756101 RS(ph)QQGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSQQGPR 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 1 RS(1)QQGPR;RS(1)QQGPR;RS(1)QQGPR 114.39 0.0036229 318764000 86925 96331 78371 89288 82052 89036.3 103861 95494 107039 TRUE FALSE 82816.22752 106147.2384 81964.38787 80312.6006 96361.84282 85952.95061 88015.09691 87132.03911 123638.0614 0.669827936 0.858532051 0.662938151 0.649578291 0.779386555 0.695198142 0.711877038 0.704734756 1 16.91576341 -1.640333384 2.759938399 1.028171913 0.722940654 0.672691476 0.062001765 10641068.92 10043066.45 2139449.571 0.015088431 0.022891098 1.640333384 -0.305231259 RS(ph)QSPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.795)QS(0.205)PVK 58.676 0.066226 160860000 317150 261370 211590 272690 197750 261710 325040 363970 288410 TRUE FALSE 302158.948 288003.9002 221291.6108 245278.6831 232237.5374 252646.9171 275449.1782 332098.8573 333135.1498 0.907016111 0.864525705 0.664269774 0.736273801 0.697127089 0.758391653 0.826839132 0.996889273 1 18.34574806 1.290797798 3.49268762 1.006180365 0.784841506 0.619529524 0.072074458 0.188763489 3.934786298 0.070598148 0.021481263 19.53429754 -1.290797798 -0.221338858 RS(ph)S(ph)VKRSDSGDEQLPT(ph)ICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSVKRSDSGDEQLPTICR 19 3 Q01668-3 Q01668-3 3 RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(0.999)ICR 59.003 0.058664 106990000 122040 151650 87446 160710 81862 98870 113330 116960 71160 TRUE FALSE 116271.4111 167103.3074 91455.4856 144555.1255 96138.70688 95446.10711 96039.42705 106718.3624 82195.12937 1.41457787 2.033007414 1.112663078 1.758682377 1.169639949 1.161213661 1.168432093 1.298353846 1 16.32676529 2.859669573 1.086634677 1.144657185 1.668411049 0.363394896 0.255126063 0.452323019 1.132471656 0.113586689 0.119031452 723.8849925 -2.859669573 0.523753864 RS(ph)SAIGIENIQEVQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSSAIGIENIQEVQEK 16 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.5)S(0.5)AIGIENIQEVQEK 236.59 6.01E-20 5591710000 4515170 3785370 3906960 4562150 2930110 4299260 4691520 4670130 3520350 TRUE FALSE 4301746.862 4171103.507 4086097.981 4103554.014 3441120.256 4150375.548 3975742.458 4261188.659 4066267.899 1.057910342 1.025781776 1.004876728 1.009169616 0.846260095 1.020684237 0.977737463 1.047936035 1 21.95527384 3.714991058 1.608923092 0.979355233 1.049267148 0.176458349 0.053237052 0.593665545 2.992002677 0.015336465 0.034324007 5187.893569 -3.714991058 0.069911915 RS(ph)SAIGIENIQEVQEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSAIGIENIQEVQEKR 17 2 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.5)S(0.5)AIGIENIQEVQEKR 72.227 0.015048 370680000 275610 145820 246530 197030 232700 209640 348450 280520 347200 TRUE FALSE 262582.4615 160679.2238 257833.6444 177224.1701 273282.8063 202380.1142 295287.5528 255956.1817 401042.0027 0.654750524 0.400654352 0.642909328 0.441909249 0.681431881 0.504635706 0.736300813 0.638227866 1 18.61339382 0.466239402 0.488554127 1.026816852 0.528882752 0.649000408 0.09977935 1.129037546 0.482131216 0.154294975 0.047144591 2.925764744 -0.466239402 -0.4979341 RS(ph)SDGS(ph)LSHEEDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.732)S(0.345)DGS(0.891)LS(0.032)HEEDLAK 108.96 0.0036318 237410000 639820 525070 558140 694170 458140 681050 737190 637000 426980 TRUE FALSE 609576.9766 578575.23 583731.2711 624390.7128 538039.4709 657465.0677 624718.1261 581220.9031 493193.8777 1.235978393 1.173119246 1.183573636 1.266014728 1.090928933 1.333076296 1.266678591 1.178483613 1 18.91179537 0.966990764 18.77551432 0.999999997 1.221315859 0.534515779 0.064557718 110.8551311 63055.04281 0.05923977 0.014809917 9.268101124 -0.966990764 0.221315861 RS(ph)SDGSLSHEEDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.398)S(0.398)DGS(0.102)LS(0.102)HEEDLAK 119.38 0.00013304 223590000 307280 268890 278450 340210 267290 289820 368660 347150 279560 TRUE FALSE 292755.4834 296290.1967 291217.2079 306011.4444 313905.2914 279783.4607 312414.1461 316751.7056 322912.737 0.906608659 0.917555001 0.901844909 0.947659876 0.972105635 0.866436745 0.967487839 0.980920445 1 18.30078482 1.548883427 6.579156464 0.985169372 0.919848094 0.544483295 0.028104185 0.099121906 8.403678055 0.014715531 0.006789755 35.39023343 -1.548883427 -0.065321279 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.63)S(0.37)DPALIGLSTSVSDSNFSSEEPSR;RS(0.683)S(0.317)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.61)S(0.387)DPALIGLS(0.003)TSVSDSNFSSEEPSR;RS(0.671)S(0.329)DPALIGLSTSVSDSNFSSEEPSR;RS(0.624)S(0.376)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.499)S(0.499)DPALIGLS(0.001)TSVSDSNFSSEEPSR 352.82 3.22E-110 4779667000 1090708 949546 1050549 1118171 1096863 958543 1155180 1057765 1265873 TRUE FALSE 1039152.394 1046305.817 1098717.711 1005770.327 1288155.56 925348.4156 978936.0747 965141.489 1462178.12 0.710687966 0.715580272 0.751425354 0.687857596 0.880984021 0.63285615 0.669505351 0.660071079 1 20.47968764 -1.469979132 3.437470812 1.004336575 0.712175964 0.637357694 0.067879955 39230586.72 64472310.94 1684995.031 0.015526794 0.033886044 1.469979132 -0.292160611 RS(ph)SDPLGDTASNLGSAVDELMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RSSDPLGDTASNLGSAVDELMR 22 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 RS(0.5)S(0.5)DPLGDT(0.001)ASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR 232.37 2.60E-27 269126000 241501 260088 253967 288184 258939 261244 298240 300634 321102 TRUE FALSE 230085.7263 286591.2629 265611.6382 259215.1968 304097.8796 252197.0548 252738.0104 274308.8932 370896.8582 0.620349623 0.772698006 0.716133427 0.698887551 0.819898775 0.679965465 0.681423972 0.739582682 1 18.50065852 -2.692306066 1.086570536 2.616765964 0.7139762 0.729636967 0.054295962 10685.10554 549.6713044 41807.6032 0.015357724 0.002030925 2.692306066 -1.902789764 RS(ph)SDSWEVWGSASTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.499)S(0.499)DS(0.002)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.001)WEVWGSASTNR;RS(0.496)S(0.496)DS(0.007)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.001)WEVWGSASTNR;RS(0.333)S(0.333)DS(0.333)WEVWGSASTNR 238.05 5.43E-20 3166911000 2208806 1994494.6 2116720 2262903.1 2530087.7 2240935.9 2768765.4 2546619.4 3141872.9 TRUE FALSE 2104400.118 2197735.867 2213773.706 2035431.781 2971334.194 2163331.728 2346339.386 2323623.905 3629098.503 0.579868559 0.605587273 0.610006508 0.560864297 0.818752699 0.596107195 0.646535051 0.640275788 1 21.79117979 -5 0.249073667 3.241359019 0.594380521 0.739046327 0.069296766 87.16170982 0.864290039 99.3992934 0.093099783 1.00E-05 5 -2.646978498 RS(ph)SDTEEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.458)S(0.458)DT(0.084)EEES(0.001)R 83.182 0.016717 50524000 75258 72430 74254 88312 83368 84071 90618 85366 95017 TRUE FALSE 71700.70349 79810.69935 77658.61935 79434.70998 97907.3528 81159.60019 76792.55979 77890.90049 109751.7511 0.653298948 0.727192947 0.707584331 0.723767131 0.892080098 0.73948342 0.699693253 0.709700754 1 16.74388443 -5 0.35302004 4.178316933 0.720072878 0.646811818 0.062057884 294.3190553 2.390091109 709.2064144 0.047507581 1.00E-05 5 -3.458244056 RS(ph)SFSEGQTLTVTSGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSFSEGQTLTVTSGAK 17 1 E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622;H7C3H3 E9PEM3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 RS(0.484)S(0.484)FS(0.032)EGQTLTVTSGAK 208.64 3.06E-12 296330000 389080 291470 335540 377820 288130 363390 392220 384720 315300 TRUE FALSE 370688.9595 321171.1244 350924.8409 339840.8158 338379.7808 350805.7132 332379.6354 351031.8773 364195.1137 1.017830678 0.88186555 0.963562738 0.933128433 0.929116751 0.963235639 0.912641666 0.963856636 1 18.47435204 -0.485224545 7.194896074 0.999996809 0.942478829 0.176889006 0.036271337 0 0 0.031849513 0.007507002 0.327171493 0.485224545 -0.057517981 RS(ph)SGFISELPSEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK 219.78 1.08E-12 2539960000 5040320 4377930 4573400 5407970 3813360 5365160 6105270 5922180 4057300 TRUE FALSE 4802074.063 4824046.044 4783094.914 4864350.581 4478408.777 5179363.164 5173798.931 5403602.524 4686485.362 1.024664261 1.029352632 1.0206145 1.037952795 0.955600718 1.105170029 1.103982736 1.153018116 1 22.16007495 2.208296187 24.99993499 1.099932527 1.018204919 0.422654206 0.043880517 167.5746601 138424.0826 0.014547292 0.010745357 161.5459916 -2.208296187 -0.081727608 RS(ph)SGREEDDEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSGREEDDEELLR 14 2 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 RS(0.5)S(0.5)GREEDDEELLR 206.62 5.52E-09 412750000 114520 103090 107540 139250 134840 104860 134750 120550 124060 TRUE FALSE 109106.8666 113594.9882 112470.8154 125252.3254 158356.0533 101228.6719 114191.4126 109994.0029 143298.5912 0.761395249 0.792715317 0.78487035 0.874065295 1.105077531 0.706417775 0.796877427 0.767586073 1 17.1286649 -2.50769295 2.156843281 3.253192973 0.818994027 0.206097259 0.108450999 3362129.483 296410.737 37105452.09 0.025819504 0.003106755 2.50769295 -2.434198946 RS(ph)SITEPEGPNGPNIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSITEPEGPNGPNIQK 17 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 RS(0.481)S(0.481)IT(0.039)EPEGPNGPNIQK;RS(0.499)S(0.499)IT(0.001)EPEGPNGPNIQK 149.53 1.97E-07 1246870000 681360 521530 637270 743280 627680 649240 857040 704740 726300 TRUE FALSE 649153.4631 574674.4999 666489.4598 668564.0823 737147.1933 626756.656 726282.8074 643029.2295 838930.8946 0.773786574 0.68500815 0.794450966 0.796923902 0.878674511 0.747089731 0.865724236 0.766486529 1 19.67819245 -5 0.119636071 1.70746504 0.677229675 0.614720946 0.053588655 92.31400686 0.716686917 15.78806568 0.480915308 1.00E-05 5 -1.030235365 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.419)S(0.419)LDAEIDS(0.049)LT(0.057)S(0.057)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.5)S(0.5)LDAEIDS(0.001)LTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 233.68 3.07E-61 3537840000 803215 713692 729092 866597 547882 801329 786491 822036 527712 TRUE FALSE 765248.6188 786418.0262 762521.5894 779485.0231 643432.4473 773578.7758 666497.3531 750054.17 609546.8818 1.255438493 1.290168238 1.25096463 1.27879421 1.055591402 1.26910464 1.09343083 1.230511044 1 19.21737766 -4.999999981 0.06858028 0.18834399 1.513213562 0.518162376 0.072169279 218.406581 1.080653541 27.87269291 3.622637299 1.00E-05 4.999999981 1.324869572 RS(ph)SLLSLMTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.7)S(0.3)LLSLMTGK;RS(0.735)S(0.265)LLSLMTGK;RS(0.5)S(0.5)LLSLMTGK 202.63 2.41E-08 3757210000 7376630 6114570 5360070 7576200 5687580 6086040 7722260 6909810 6186020 TRUE FALSE 7027951.319 6737651.635 5605834.511 6814625.982 6679492.151 5875278.909 6544087.408 6304750.405 7145316.388 0.983574546 0.942946578 0.784546717 0.953719277 0.934807052 0.822255949 0.915856913 0.882361265 1 22.76856646 3.988288955 24.6665828 0.893560263 0.968339082 0.164514459 0.06188947 741.1623191 1561091.737 0.014180615 0.026397979 9733.946494 -3.988288955 0.074778818 RS(ph)SLPLDHGSPAQENPESEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.429)S(0.429)LPLDHGS(0.143)PAQENPESEK;RS(0.497)S(0.497)LPLDHGS(0.007)PAQENPESEK;RS(0.497)S(0.497)LPLDHGS(0.005)PAQENPESEK;RS(0.333)S(0.333)LPLDHGS(0.333)PAQENPESEK 231.29 5.15E-26 991509000 788543 582303 743570 891426 820225 839457 1212658 1005787 1008068 TRUE FALSE 751270.1351 641640.3377 777663.42 801818.1649 963271.9803 810386.3936 1027644.75 917714.9583 1164394.037 0.645202664 0.551050862 0.667869635 0.688614111 0.827273199 0.695972641 0.882557551 0.788148109 1 20.15114793 2.019706394 0.316424631 1.012698392 0.537819069 0.779578437 0.060911795 0.61942257 0.18223245 0.08360658 0.105338684 104.6420874 -2.019706394 -0.474879323 RS(ph)SLPNGEGLQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSLPNGEGLQLK 13 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 RS(0.5)S(0.5)LPNGEGLQLK 130.01 9.01E-05 471640000 241020 223920 238280 262450 210100 246480 287120 278430 254380 TRUE FALSE 229627.4623 246737.7026 249205.3737 236068.0274 246741.3735 237944.3358 243314.5707 254049.1931 293827.9512 0.781503126 0.839735299 0.848133653 0.803422637 0.839747793 0.809808375 0.828085176 0.864618877 1 18.16461212 0.740777159 1.782946291 0.999947144 0.820408915 0.891271923 0.019584559 0.277484382 1.396625723 0.017915557 0.005048755 5.505251435 -0.740777159 -0.179538229 RS(ph)SLSSHSHQSQIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLSSHSHQSQIYR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 RS(0.5)S(0.5)LSSHSHQSQIYR;RS(0.498)S(0.498)LS(0.001)S(0.002)HSHQSQIYR 218.88 8.83E-13 450850000 55340 31223 47063 42045 136566 36049 97046 67362 25023.1 TRUE FALSE 52724.18787 34404.6592 49220.8851 37818.55672 160383.0672 34800.61409 82239.85033 61463.42617 28903.55455 1.824142003 1.190326233 1.702935361 1.308439647 5.548904613 1.204025409 2.845319602 2.126500603 1 14.81895931 RS(ph)SLYGIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLYGIAK 9 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.672)S(0.328)LYGIAK;RS(0.665)S(0.335)LYGIAK 107.53 0.0016898 1322420000 1709470 1239940 1238020 1487480 1281920 1341840 1757840 1514730 1433790 TRUE FALSE 1628666.741 1366291.296 1294784.442 1337955.684 1505486.442 1295371.744 1489649.223 1382092.211 1656134.83 0.98341434 0.82498796 0.781811008 0.807878477 0.909036157 0.782165631 0.899473398 0.834528799 1 20.6593887 -1.839601518 8.571724492 1.006054803 0.856453818 0.349189572 0.062941962 0.007292873 0.000136468 0.06102596 0.013998334 0.014467666 1.839601518 -0.149600985 RS(ph)SMIETGQGAEGGLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSSMIETGQGAEGGLSLR 18 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RS(0.5)S(0.5)MIETGQGAEGGLSLR;RS(0.622)S(0.378)MIETGQGAEGGLSLR;RS(0.5)S(0.5)MIET(0.001)GQGAEGGLSLR 191.71 1.30E-14 774680000 244042 201374 221916 221854 247881 191027 259217 238300 272873 TRUE FALSE 232506.6183 221894.2395 232091.0681 199552.8144 291111.3679 184411.6871 219668.6858 217433.1887 315188.7512 0.737674227 0.704004311 0.73635581 0.633121625 0.923609636 0.585083339 0.696943292 0.689850726 1 18.26585652 -1.609566997 6.298033218 1.00100212 0.711676683 0.513634339 0.087654366 0.001089501 6.75E-05 0.074969958 0.017613111 0.024571575 1.609566997 -0.289325437 RS(ph)SNPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.679)S(0.321)NPPAR 90.827 0.0079139 318260000 97382 79467 77478 98101 85899 76264 114440 105780 106180 TRUE FALSE 92778.94585 87564.77765 81030.44294 88239.7011 100879.7584 73622.95856 96980.07617 96517.34242 122645.8521 0.756478464 0.713964444 0.660686371 0.719467471 0.822528905 0.600289022 0.790732622 0.786959695 1 16.90413892 0.736974428 1.349827949 0.999297674 0.719170197 0.675812795 0.060707413 0.485129419 1.490535037 0.052021564 0.015504845 5.457257268 -0.736974428 -0.280127478 RS(ph)SPPPPPSGSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RS(0.5)S(0.5)PPPPPSGSSSR 64.275 0.038236 382310000 169900 139510 143430 147990 121570 145780 175950 160490 147870 TRUE FALSE 161869.1637 153726.2276 150006.4074 133113.764 142771.7695 140731.602 149105.596 146436.6448 170800.9244 0.947706602 0.90003159 0.878252901 0.779350372 0.835895766 0.823951056 0.872978858 0.857352765 1 17.38195626 -1.261815203 6.789885654 1.000001298 0.866498347 0.477947573 0.045122828 9.88E-07 1.07E-07 0.048704414 0.011479629 0.054724877 1.261815203 -0.133502951 RS(ph)SPSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.499)S(0.499)PS(0.002)ARPPDVPGQQPQAAK;RS(0.482)S(0.482)PS(0.037)ARPPDVPGQQPQAAK;RS(0.487)S(0.487)PS(0.025)ARPPDVPGQQPQAAK;RS(0.497)S(0.497)PS(0.007)ARPPDVPGQQPQAAK;RS(0.499)S(0.499)PS(0.002)ARPPDVPGQQPQAAK 211.5 2.09E-22 6771000000 1603070 1316830 1412660 1598660 1172502 1499260 1661270 1567530 1379340 TRUE FALSE 1527296.058 1451016.474 1477431.858 1437959.66 1376985.978 1447340.25 1407812.75 1430268.763 1593241.003 0.958609561 0.910732571 0.927312225 0.902537442 0.864267223 0.908425184 0.883615692 0.89771024 1 20.60353308 4.714499517 0.92783705 0.90219627 0.9879516 0.10706244 0.036347663 3.069581825 2.130991215 0.010337935 0.264758297 51820.25162 -4.714499517 0.08575533 RS(ph)SPSSSSTQPQEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSPSSSSTQPQEESR 16 1 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 RS(0.498)S(0.498)PS(0.004)SSSTQPQEESR 134.29 1.78E-05 112740000 63783 59396 60225 64810 70608 61111 76487 66361 83117 TRUE FALSE 60768.104 65448.51993 62986.37582 58295.17567 82922.01284 58994.71075 64817.50337 60550.07904 96006.35986 0.632959151 0.681710254 0.656064618 0.607201187 0.863713747 0.614487528 0.6751376 0.630688208 1 16.55084236 -2.11809998 2.443538321 1.640689485 0.670374743 0.668986922 0.072896546 3395231.169 1088022.331 12062131.39 0.016341274 0.007619036 2.11809998 -0.970314742 RS(ph)SPVPPVPER ddPTM_SK-BR-3_Trastuzumab_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(0.788)S(0.212)PVPPVPER 85.734 0.0091848 1906060000 1314640 1203006 1171623 1410791 1423340 1218439 1452345 1378566 1541987 TRUE FALSE 1252499.573 1325593.679 1225343.073 1268975.608 1671570.045 1176244.152 1230763.096 1257851.453 1781110.469 0.70321274 0.744251242 0.687965792 0.712463169 0.938498804 0.660399325 0.69100885 0.70621754 1 20.76434557 -1.87998812 2.560570254 1.133772259 0.728563345 0.547069373 0.077046196 9049550.594 5718130.212 7347685.137 0.018342114 0.013182928 1.87998812 -0.405208914 RS(ph)SQPSPTAVPASDSPPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.499)S(0.499)QPS(0.001)PT(0.002)AVPASDSPPTK 109.17 0.00015965 151700000 307870 296790 265440 345380 226040 295350 331920 330370 283780 TRUE FALSE 293317.5952 327033.2384 277610.6866 310661.7462 265461.3044 285121.9554 281279.5079 301441.0514 327787.1531 0.894841645 0.997699987 0.846923633 0.94775449 0.809858782 0.869838713 0.858116327 0.919624362 1 18.32239979 5.132658537 15.68599013 0.902268228 0.000616185 0 0.062921953 20698866.43 15152377.89 0.014574708 664393954.7 135724.5895 -5.132658537 -0.901652043 RS(ph)SQPSPTAVPASDSPPTKQEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSQPSPTAVPASDSPPTKQEVK 23 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.5)S(0.5)QPSPTAVPASDSPPTKQEVK;RS(0.609)S(0.391)QPSPTAVPASDSPPTKQEVK 266.69 1.92E-44 871660000 966580 631510 950430 861360 696270 1045730 1284270 1190300 927830 TRUE FALSE 920891.679 695861.587 994008.1556 774774.4563 817699.2676 1009516.108 1088331.024 1086071.022 1071713.138 0.859270682 0.649298364 0.927494607 0.722930819 0.762983338 0.941964853 1.015505909 1.013397134 1 20.03148736 2.121230816 3.543471088 1.005872676 0.776114207 0.66619236 0.074236385 0.130572086 3.170541859 0.028807588 0.020000885 132.1998056 -2.121230816 -0.229758469 RS(ph)SSLKER ddPTM_SK-BR-3_Trastuzumab_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(0.445)S(0.445)S(0.11)LKER 56.359 0.09301 2664900000 413360 276170 333060 376270 260170 379350 428030 369150 281330 TRUE FALSE 393821.292 304312.037 348331.1304 338446.6247 305543.5656 366213.0144 362726.1622 336825.269 324957.2196 1.211917349 0.936467998 1.071929194 1.041511326 0.940257816 1.126957619 1.11622743 1.036521883 1 18.30989028 RS(ph)SSSGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.434)S(0.434)S(0.039)S(0.017)GDQS(0.038)S(0.038)DSLNSPTLLAL 193.27 8.34E-18 86425000 172340 116440 143080 156230 171380 133870 151530 141560 175010 TRUE FALSE 164193.8297 128305.3684 149640.3595 140525.4636 201268.6177 129234.0483 128411.3155 129164.2559 202149.657 0.812238973 0.634704853 0.740245429 0.695155588 0.995641649 0.639298875 0.635228956 0.638953624 1 17.62506423 4.75164318 22.39588707 0.727084431 0.812239165 0.002399851 0.141516904 82.81621354 1127898.616 0.03101094 0.195775439 56447.3008 -4.75164318 0.085154733 RS(ph)STAKPEVEHPEPDHSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSTAKPEVEHPEPDHSKR 19 3 Q9NZI5-3;Q9NZI5;B7Z1S6;F8WFB0 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RS(0.486)S(0.486)T(0.028)AKPEVEHPEPDHSKR 97.5 0.00045027 105010000 149390 95082 135280 150710 109760 151210 177390 166680 31487 TRUE FALSE 142328.6308 104770.9639 141482.7218 135560.3445 128902.1092 145973.5598 150325.8975 152084.6156 36369.84315 3.913369387 2.880709809 3.89011086 3.727273278 3.544203057 4.013587829 4.13325669 4.181613183 1 15.15045508 RS(ph)STSGDT(ph)EEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Trastuzumab_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 2 RS(0.336)S(0.358)T(0.293)S(0.313)GDT(0.701)EEEEEEEVVPFSSDEQK;RS(0.494)S(0.419)T(0.143)S(0.366)GDT(0.578)EEEEEEEVVPFSSDEQK 152.95 9.80E-08 312180000 662690 571560 590270 674140 406410 678900 670750 648320 416610 TRUE FALSE 631365.957 629802.6138 617334.4634 606374.1664 477287.7753 655389.5228 568414.7683 591549.6638 481215.7511 1.312022634 1.308773897 1.282864208 1.260087944 0.991837392 1.361945284 1.181205659 1.229281591 1 18.87632434 -4.999999999 0.092024906 0.223759681 1.44054664 0.413136919 0.096835558 194.2229046 1.236879259 29.66782881 1.96651819 1.00E-05 4.999999999 1.216786959 RS(ph)STSGDTEEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.211)S(0.211)T(0.211)S(0.211)GDT(0.155)EEEEEEEVVPFSSDEQK;RS(0.429)S(0.429)T(0.115)S(0.022)GDT(0.004)EEEEEEEVVPFSSDEQK;RS(0.443)S(0.443)T(0.088)S(0.024)GDT(0.002)EEEEEEEVVPFSSDEQK 158.97 1.48E-11 381340000 655140 620260 634180 705330 442106 717370 771180 738590 475932 TRUE FALSE 624172.8306 683465.1992 663257.7803 634428.8884 519209.1464 692527.297 653522.3273 673915.1441 549737.1038 1.135402406 1.243258267 1.206499935 1.154058702 0.944468079 1.259742688 1.188790647 1.225886227 1 19.06838233 -1.479662118 3.102925361 0.995800017 1.173375496 0.265313513 0.08859949 16627777.6 18314052.65 590488.2987 0.020503318 0.033138884 1.479662118 0.177575479 RS(ph)STSGDTEEEEEEEVVPFSSDEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSTSGDTEEEEEEEVVPFSSDEQKR 26 2 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(0.485)S(0.485)T(0.023)S(0.008)GDTEEEEEEEVVPFSSDEQKR 184.43 8.25E-18 114130000 137730 110260 128010 147030 91737 134690 156740 159750 121460 TRUE FALSE 131219.7759 121495.6194 133879.3851 132250.2651 107735.9038 130025.6515 132826.4343 145761.4431 140295.3965 0.935310631 0.865998617 0.954267841 0.942655771 0.767921874 0.926799131 0.9467626 1.038960984 1 17.09810814 1.504684901 2.576153237 1.017893429 0.896596165 0.452352212 0.054155756 0.231369161 3.132832516 0.040004806 0.01385883 31.96575017 -1.504684901 -0.121297263 RS(ph)STSSEPTPTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.429)S(0.429)T(0.101)S(0.04)S(0.001)EPTPTVK;RS(0.483)S(0.483)T(0.025)S(0.01)SEPTPTVK;RS(0.497)S(0.497)T(0.006)S(0.001)SEPTPTVK;RS(0.485)S(0.485)T(0.022)S(0.003)S(0.006)EPTPTVK;RS(0.48)S(0.48)T(0.033)S(0.006)SEPTPTVK;RS(0.489)S(0.489)T(0.017)S(0.005)SEPTPTVK;RS(0.486)S(0.486)T(0.023)S(0.003)S(0.003)EPTPTVK;RS(0.355)S(0.355)T(0.243)S(0.043)S(0.005)EPTPTVK;RS(0.314)S(0.314)T(0.124)S(0.247)S(0.001)EPTPTVK 169.98 1.69E-05 4154050000 6024930 5053260 5458680 6377080 4929920 6311420 7273210 6755220 6228750 TRUE FALSE 5740143.499 5568192.939 5708965.877 5736043.803 5789696.487 6092853.943 6163548.233 6163697.125 7194672.738 0.797832467 0.773932761 0.793499035 0.797262643 0.804719922 0.846856301 0.856682223 0.856702918 1 22.77849763 0.469663914 0.367369144 1.026549303 0.776098685 0.967722512 0.011591291 0.414019069 0.109201846 0.031530925 0.009996894 2.948926267 -0.469663914 -0.250450619 RS(ph)TGVVNIPAAECLDEYEDDEAGQKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSTGVVNIPAAECLDEYEDDEAGQKER 27 2 Q96IZ0;H0YI16 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 RS(0.5)T(0.5)GVVNIPAAECLDEYEDDEAGQKER 102.58 0.0012649 75818000 83923 54235 64158 64231 52438 65826 79456 80943 70162 TRUE FALSE 79956.12611 59761.60816 67099.70776 57774.37785 61583.1706 63546.42911 67333.52789 73855.20181 81042.36462 0.986596658 0.73741195 0.827958415 0.712891068 0.75988862 0.784113709 0.830843574 0.911315978 1 16.30638865 1.067858921 2.110108425 0.998692237 0.804374911 0.445243119 0.073908155 0.289145599 2.606994852 0.070238625 0.019659 11.69119544 -1.067858921 -0.194317327 RS(ph)TQGVTLTDLQEAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSTQGVTLTDLQEAEK 16 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 RS(0.5)T(0.5)QGVT(0.001)LTDLQEAEK;RS(0.498)T(0.498)QGVT(0.003)LTDLQEAEK 192.94 2.79E-10 182202000 305643 100024 168097 235719 322530 235207 313705 224785 306940 TRUE FALSE 291195.8611 110216.5593 175804.4137 212024.0783 378779.1299 227061.7226 265843.5407 205101.6337 354538.6876 0.821337336 0.310873152 0.495868067 0.598028045 1.068371783 0.640442723 0.749829426 0.578502829 1 18.43558354 2.981345914 24.61665315 0.780653901 0.53458908 0.297941184 0.190362626 786.2665095 1037589.141 0.054836151 0.059126353 957.956776 -2.981345914 -0.24606482 RS(ph)TSPIIGS(ph)PPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.639)T(0.257)S(0.104)PIIGS(1)PPVR 112.91 0.00057689 84655000 124390 103480 103480 119160 136300 115290 152920 127370 154170 TRUE FALSE 118510.3312 114024.7296 108224.6604 107181.8104 160070.6768 111297.4784 129589.2454 116216.8076 178077.8962 0.665497143 0.640308158 0.607737752 0.601881607 0.898880098 0.624993224 0.727711008 0.652617815 1 17.44214893 -5 0.234333561 2.785394185 0.641326142 0.584624842 0.085797173 112.0713699 1.11974336 95.0820876 0.130858197 1.00E-05 5 -2.144068044 RS(ph)TSPIIGSPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.43)T(0.43)S(0.14)PIIGSPPVR 74.993 0.019968 414690000 251460 219970 215470 255010 225780 204890 280750 241920 240100 TRUE FALSE 239573.9841 242385.1931 225349.5126 229375.9103 265155.9605 197794.6079 237916.4312 220736.2023 277333.4817 0.863848038 0.873984604 0.812557904 0.827076157 0.956090692 0.71320133 0.857871288 0.79592338 1 18.08126227 -1.499354575 6.066921233 1.000146258 0.84059764 0.404018564 0.061902218 0.000110199 9.09E-06 0.053935534 0.012701127 0.031669808 1.499354575 -0.159548618 RS(ph)TVLGLPQHVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSTVLGLPQHVQK 13 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 RS(0.635)T(0.365)VLGLPQHVQK 133.86 4.81E-05 227710000 199030 135040 162300 196490 179820 162220 233190 191960 157600 TRUE FALSE 189622.2463 148800.7295 169741.6155 176738.4519 211180.5511 156602.2807 197612.5827 175150.9648 182039.8031 1.041652667 0.81740766 0.932442316 0.970878066 1.160078991 0.860263954 1.085546014 0.962157516 1 17.47389441 3.068748065 4.768366947 1.016219092 0.923437978 0.138354449 0.093438401 0.338336423 14.86834878 0.025353302 0.030366427 1171.515571 -3.068748065 -0.092781114 RS(ph)WGQQAQEYQEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSWGQQAQEYQEQK 14 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(1)WGQQAQEYQEQK;RS(1)WGQQAQEYQEQK 219.06 3.16E-12 775750000 500040 428810 490290 520030 350750 522230 531180 560350 420120 TRUE FALSE 476404.1002 472506.2265 512770.2815 467755.5964 411920.6889 504145.0442 450138.7352 511282.7834 485270.0639 0.981729836 0.973697456 1.056669924 0.963907793 0.848848342 1.038895827 0.927604583 1.053604624 1 18.88842834 1.22774627 24.99873864 1.026802306 0.971180935 0.140849155 0.058085266 471.7855651 1090555.911 0.049460411 0.012853989 16.89453607 -1.22774627 -0.055621371 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 RS(0.536)Y(0.464)DVPPPPMEPDHPFYSNISK;RS(0.537)Y(0.463)DVPPPPMEPDHPFYSNISK;RS(0.536)Y(0.464)DVPPPPMEPDHPFYSNISK 105.79 0.00021732 411380000 252870 223934 228707 294727 213012 259757 297415 286357 235377 TRUE FALSE 240917.3362 246753.1292 239193.4422 265100.482 250161.2254 250761.55 252038.8793 261282.063 271878.063 0.886122748 0.907587491 0.879782059 0.975071247 0.920122876 0.922330942 0.927029112 0.961026646 1 18.05260022 -5 0.041921117 1.396784058 0.697135892 0.632943656 0.023025463 467.7755769 1.461760179 22.56222405 6.410602835 1.00E-05 5 -0.699648166 RS(ph)YSPDGKESPSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.983)YS(0.017)PDGKESPSDKK;RS(0.5)YS(0.5)PDGKESPSDKK 160.13 9.54E-06 428940000 712570 456700 712880 618630 344170 808280 921030 884080 418310 TRUE FALSE 678888.2283 503238.2492 745566.2531 556444.1371 404193.139 780289.0609 780509.9576 806665.2684 483179.3784 1.40504388 1.041514336 1.54304237 1.151630558 0.836528124 1.614905552 1.615362726 1.669494404 1 18.88219936 2.189278301 24.99981724 1.538939579 1.207387912 0.196606927 0.266459172 141.1114783 71581.76416 0.091342515 0.067461041 154.6244973 -2.189278301 -0.331551668 RS(ph)YSSPDITQAIQEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.493)Y(0.001)S(0.493)S(0.013)PDITQAIQEEEKR 83.039 0.0022398 339460000 27833 27927 24089 27737 26302 25602 30690 32222 36816 TRUE FALSE 26517.38925 30772.79305 25193.50448 24948.82406 30889.06047 24715.39632 26007.67684 29400.47086 42525.23725 0.623568285 0.723636011 0.592436541 0.586682772 0.726370092 0.581193614 0.611582169 0.69136524 1 15.37603166 0.832804613 4.604613861 0.999992397 0.639428538 0.828676249 0.051726336 0.707249079 19.13528635 0.048536732 0.012310075 6.804631521 -0.832804613 -0.360563859 RSAPGGGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSAPGGGSK 9 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ;;;; 158.94 0.00010652 493557000 960596 833822 783757 935357 856369 786677 960301 914192 1099667 FALSE TRUE 915190.5308 918789.4098 819693.0337 841333.1373 1005719.482 759434.1782 813789.4453 834140.502 1270197.742 0.72051028 0.723343602 0.645327107 0.662363906 0.791781822 0.597886576 0.640679335 0.656701295 1 20.27662168 -0.806240504 5.949134636 1.000000025 0.681245394 0.775491561 0.054135259 1.81E-08 3.71E-09 0.052860777 0.012459404 0.156228224 0.806240504 -0.318754632 RSAS(ph)ASHQADIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.179)AS(0.73)AS(0.091)HQADIK 154.51 4.38E-05 137600000 141320 121000 148750 207290 171260 175500 203910 181230 166400 TRUE FALSE 134640.0837 133330.0376 155570.3346 186452.8154 201127.6898 169422.391 172799.7844 165360.5404 192204.4621 0.700504464 0.693688565 0.809400224 0.970075373 1.046425705 0.881469603 0.899041482 0.860336636 1 17.5522823 3.481440489 3.181065098 0.93532325 0.698707891 0.768796192 0.056095279 0.112516721 2.346138107 0.016404893 0.02485668 3029.98507 -3.481440489 -0.236615359 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.004)AS(0.996)PDDDLGSSNWEAADLGNEER;RS(0.03)AS(0.97)PDDDLGSSNWEAADLGNEER;RS(0.001)AS(0.999)PDDDLGSSNWEAADLGNEER;RS(0.006)AS(0.994)PDDDLGSSNWEAADLGNEER;RS(0.001)AS(0.999)PDDDLGSSNWEAADLGNEER;RS(0.012)AS(0.988)PDDDLGSSNWEAADLGNEER 386.27 2.00E-137 8716280000 1677010 1470290 1688430 1810070 1727540 1540820 1893510 1720970 2006760 TRUE FALSE 1597741.061 1620114.223 1765846.186 1628118.325 2028822.429 1487461.017 1604620.273 1570272.743 2317958.092 0.689288157 0.698940256 0.761811092 0.702393339 0.875262774 0.641711782 0.692255947 0.677437935 1 21.14442305 -1.558874846 2.988580498 1.013706145 0.714593768 0.661672101 0.063481914 12032407.09 12194815.8 1304167.372 0.014300909 0.027613735 1.558874846 -0.299112376 RSASAS(ph)HQADIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.288)AS(0.288)AS(0.423)HQADIK 91.207 0.005162 134580000 98466 81060 97898 132410 125160 107670 144480 106340 126020 TRUE FALSE 93811.70732 89320.10616 102386.7201 119099.8952 146987.8644 103941.3609 122436.9224 97028.30586 145562.538 0.644476997 0.613620148 0.703386473 0.818204305 1.009791849 0.714066698 0.841129346 0.666574705 1 17.15127959 6.541927594 0.157569231 0.963578492 6.07E-26 0.369162715 0.110918623 41.5626293 0.641413749 0.36632802 8.557995905 3482792.449 -6.541927594 -0.963578492 RSATSTSAS(ph)PTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSATSTSASPTLR 13 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 RS(0.001)AT(0.001)S(0.003)T(0.006)S(0.074)AS(0.849)PT(0.067)LR;RSATS(0.001)T(0.002)S(0.021)AS(0.488)PT(0.488)LR;RSATSTS(0.006)AS(0.497)PT(0.497)LR;RSATSTS(0.007)AS(0.989)PT(0.003)LR 110.37 0.00065182 662980000 299136 239410 264545 277959 305042 236208 320493 286475 340841 TRUE FALSE 284996.4341 263806.1512 276674.6499 250018.0332 358241.2282 228028.0577 271595.9066 261389.7303 393696.8815 0.723898124 0.670074272 0.702760583 0.635052105 0.909941747 0.579197013 0.689860447 0.663936502 1 18.58672576 -1.138164588 4.596170706 1.000033344 0.695093959 0.554147599 0.085446095 27674313409 5189075970 10109297.87 0.017752743 0.072750404 1.138164588 -0.304939385 RSDAEEVDFAGWLCSTIGLNQPS(ph)TPTHAAGV ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.455)T(0.455)PT(0.09)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.459)T(0.459)PT(0.082)HAAGV 163.49 1.02E-12 96661000 61134 47028.2 60159 63316 68916 58059.1 70368 56672 64460.8 TRUE FALSE 58244.31698 51820.42705 62917.34966 56951.35539 80934.92858 56048.49881 59632.0692 51709.49924 74457.05164 0.782253872 0.695977425 0.845015324 0.764888672 1.087001524 0.752762802 0.800892164 0.694487602 1 16.18412087 -2.604441092 2.183200676 5.20414489 0.798626623 0.237786584 0.110659006 5931247.615 428037.9091 123308460 0.026518138 0.002486331 2.604441092 -4.405518268 RSDAEEVDFAGWLCSTIGLNQPST(ph)PTHAAGV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.141)T(0.84)PT(0.019)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.024)T(0.972)PT(0.003)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.178)T(0.821)PT(0.001)HAAGV 266.03 3.50E-59 229971000 154595 138918 155482 165071 174480 130611 165049 140581 156207 TRUE FALSE 147287.6007 153073.9021 162611.0035 148477.7495 204909.2568 126087.9083 139867.7437 128270.9824 180430.7838 0.816310818 0.848380187 0.901237583 0.822906969 1.135666833 0.698815943 0.775187808 0.710915176 1 17.46108598 -1.308818948 6.860402879 1.000002944 0.837556416 0.148217745 0.121511322 5.20E-06 5.23E-07 0.111715769 0.026331182 0.049111257 1.308818948 -0.162446528 RSDLDLGYEPEGSAS(ph)PTPPYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSDLDLGYEPEGSASPTPPYLK 22 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 RSDLDLGYEPEGS(0.003)AS(0.782)PT(0.215)PPYLK;RSDLDLGYEPEGS(0.002)AS(0.712)PT(0.286)PPYLK 184.3 2.42E-17 401310000 495340 357180 443610 455400 382140 443920 542550 508670 446710 TRUE FALSE 471926.2599 393577.0481 463949.9573 409622.3268 448785.095 428546.9391 459774.0329 464128.1582 515983.5053 0.914615012 0.7627706 0.899156567 0.793867096 0.86976636 0.830543873 0.891063432 0.899501929 1 18.97696542 0.87971324 0.910095723 0.999551867 0.840381946 0.528578164 0.045657198 0.515129168 0.878825604 0.038813895 0.013212928 7.580768605 -0.87971324 -0.15916992 RSDS(ph)ASSEPVGIYQGFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.057)DS(0.909)AS(0.033)S(0.001)EPVGIYQGFEK;RS(0.043)DS(0.957)AS(0.001)SEPVGIYQGFEK;RS(0.004)DS(0.898)AS(0.093)S(0.005)EPVGIYQGFEK;RS(0.011)DS(0.702)AS(0.275)S(0.013)EPVGIYQGFEK 275.39 2.80E-39 1706680000 1715590 1475530 1549920 2054140 1433550 1679230 2165470 1705160 1561420 TRUE FALSE 1634497.461 1625888.185 1620985.365 1847653.945 1683560.666 1621077.844 1835087.78 1555847.151 1803557.039 0.906263248 0.90148975 0.898771334 1.024449965 0.933466827 0.898822609 1.017482531 0.862654808 1 20.78241362 8 0.135941001 0.993293711 0.65851614 0.113492033 0.053212155 137.1562771 1.250030117 0.225409313 8.878382401 100000000 -8 -0.33477757 RSDS(ph)IKFQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSDSIKFQHR 10 2 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 RS(0.002)DS(0.998)IKFQHR;RS(0.001)DS(0.999)IKFQHR;RS(0.001)DS(0.999)IKFQHR;RS(0.006)DS(0.994)IKFQHR 157.5 4.73E-06 4261580000 2872790 2017680 2259240 2460890 2399930 2490870 3165650 2700390 2220460 TRUE FALSE 2736998.91 2223283.886 2362828.389 2213516.662 2818477.032 2404610.547 2682671.951 2463929.536 2564797.596 1.067140313 0.866845746 0.921253354 0.863037561 1.09890817 0.93754398 1.045958541 0.960672117 1 21.29041355 2.747964959 24.97557621 1.008358932 0.933939013 0.23721392 0.070240538 1010.099143 2682569.599 0.020606503 0.021573038 559.7124393 -2.747964959 -0.074419919 RSDS(ph)LLSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(0.999)LLSFR;RSDS(0.998)LLS(0.002)FR;RSDS(0.609)LLS(0.391)FR;RS(0.026)DS(0.939)LLS(0.035)FR 198.74 2.74E-05 1448530000 2015951 1787089 1729193 1995923 1902363 1707317 2005618 1939443 1954091 TRUE FALSE 1920660.991 1969195.401 1808478.209 1795289.028 2234134.505 1648192.184 1699624.138 1769615.089 2257121.452 0.850933825 0.872436616 0.801232121 0.795388758 0.989815813 0.730218652 0.753005177 0.78401412 1 21.10605262 RSDS(ph)MTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.033)DS(0.484)MT(0.484)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 110.41 5.24E-06 39138000 5324.5 4093.6 3733.3 5610.4 3409.6 3090.3 5379.8 4717.4 7064.7 TRUE FALSE 5072.821437 4510.742494 3904.475498 5046.431933 4004.23316 2983.282136 4559.012703 4304.319447 8160.257595 0.62164967 0.552769621 0.47847454 0.618415764 0.490699358 0.36558676 0.558684901 0.527473477 1 12.99439898 -0.135083244 2.510624857 1.000009737 0.529826202 0.803125214 0.073627239 333.4928525 730.7628158 0.086663368 0.01894495 0.732684081 0.135083244 -0.470183535 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RS(0.052)DS(0.948)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.063)DS(0.937)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.226)DS(0.774)PEIPFQAAAGPSDGLDASSPGNSFVGLR 230.2 8.67E-37 2443950000 430877 392287 418597 469550 480670 423071 488130 452830 514040 TRUE FALSE 410510.2981 432261.4913 437790.0865 422349.9419 564498.6958 408419.9452 413656.8034 413177.8046 593754.6978 0.691380295 0.728013594 0.737324838 0.71132059 0.950727123 0.687859728 0.69667963 0.695872902 1 19.1795075 -1.892546875 2.622920007 1.138775348 0.73436663 0.529947135 0.077678033 18898124.05 10738433.66 16209417.93 0.018056407 0.012807169 1.892546875 -0.404408718 RSDS(ph)PENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.057)DS(0.943)PENK 75.819 0.013034 0 123240 141760 106780 163100 80994 120630 103270 156940 85385 TRUE FALSE 117414.6894 156205.5052 111675.9686 146704.8781 95119.32796 116452.5529 87514.26482 143197.5016 98626.06971 1.190503584 1.583815574 1.132316931 1.487485799 0.964444069 1.180748185 0.887333999 1.451923432 1 16.58968142 2.736859715 24.9996528 1.080155906 1.35817425 0.282967208 0.197789139 169.6209062 2493048.93 0.056498742 0.05581887 545.5816003 -2.736859715 0.278018344 RSDS(ph)PENKYSDSTGHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 RS(0.002)DS(0.998)PENKYSDSTGHSK;RS(0.001)DS(0.972)PENKYS(0.021)DS(0.003)T(0.003)GHSK;RSDS(0.999)PENKYSDSTGHSK;RS(0.004)DS(0.984)PENKYS(0.012)DSTGHSK;RS(0.003)DS(0.872)PENKYS(0.1)DS(0.024)T(0.002)GHSK;RS(0.001)DS(0.999)PENKYSDSTGHSK 248.97 3.12E-21 2467080000 1101513 621840 1051741 960505 743878 1101265 1458690 1257150 859445 TRUE FALSE 1049446.663 685206.203 1099964.365 863953.2126 873610.0877 1063127.917 1236140.05 1147067.281 992723.3412 1.057139104 0.690228762 1.1080271 0.870285987 0.880013647 1.070920641 1.245200952 1.155475281 1 19.92103219 2.087043761 4.241374173 1.160645158 0.908888003 0.369881022 0.127112042 0.1841933 6.185614692 0.04755926 0.033556802 122.192278 -2.087043761 -0.251757154 RSDS(ph)QQAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSDSQQAVK 9 1 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 RS(0.035)DS(0.965)QQAVK;RS(0.01)DS(0.99)QQAVK;RS(0.028)DS(0.972)QQAVK;RS(0.019)DS(0.981)QQAVK 93.623 0.0056803 617464000 329216 336453 361886 407664 403467 372224 406034 371449 498983 TRUE FALSE 313654.6121 370737.9432 378478.8311 366684.8402 473831.5171 359333.7895 344086.056 338922.9564 576362.7352 0.54419655 0.643237185 0.656667768 0.636204976 0.822106441 0.623450767 0.596995668 0.588037595 1 19.13661754 -1.934751709 2.72620244 1.24166666 0.635928889 0.709121159 0.072667866 9219014.941 6588269.913 14217918.78 0.017702833 0.011621128 1.934751709 -0.605737771 RSDS(ph)VSASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RS(0.006)DS(0.991)VS(0.001)AS(0.002)ER;RS(0.001)DS(0.494)VS(0.494)AS(0.012)ER;RSDS(0.999)VS(0.001)ASER;RS(0.001)DS(0.988)VS(0.011)ASER 171.36 2.48E-06 492622000 222665 173193 197992 241787 262942 245155 286081 188412 260664 TRUE FALSE 212140.0667 190841.5636 207070.129 217482.1114 308799.0015 236665.2209 242434.0892 171913.6464 301086.4418 0.704581931 0.6338431 0.68774312 0.722324493 1.025615766 0.786037456 0.805197629 0.570977708 1 18.19981822 2.986149526 24.30570729 0.825173809 0.674954035 0.267676453 0.124730383 609.0119482 1068736.427 0.035015019 0.038607823 968.6112892 -2.986149526 -0.150219774 RSDSAS(ph)SEPVGIYQGFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.062)DS(0.329)AS(0.432)S(0.177)EPVGIYQGFEK 190.8 1.58E-14 116350000 183190 181170 196230 220870 194200 221550 245120 197490 196670 TRUE FALSE 174530.9717 199631.429 205227.3396 198667.728 228068.4185 213877.6679 207722.4421 180196.7286 227168.5791 0.768288345 0.87878099 0.903414285 0.874538762 1.003961108 0.94149318 0.914397769 0.793229105 1 17.79340378 4.54175223 0.96874698 0.921734483 0.714887149 0.393312188 0.059513265 1.418620879 1.318335082 0.018061093 0.287118398 34813.86415 -4.54175223 -0.206847334 RSDSLLS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RS(0.001)DS(0.439)LLS(0.56)FR 104.94 0.0033665 588710000 589890 565170 480310 630560 568430 526390 590530 584320 553220 TRUE FALSE 562007.0687 622761.4655 502332.6886 567174.9108 667564.012 508160.9823 500433.8027 533153.8431 639010.5321 0.879495784 0.97457152 0.786110186 0.88758304 1.044683896 0.795230997 0.783138583 0.83434281 1 19.28548018 RSDSPENKYS(ph)DSTGHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 RS(0.009)DS(0.31)PENKYS(0.516)DS(0.083)T(0.083)GHSK 73.21 0.01396 141620000 57191 28274 50715 45049 38763 55073 73289 51366 43272 TRUE FALSE 54487.69477 31155.15274 53040.33291 40520.58893 45523.25493 53165.8082 62107.41701 46868.12073 49982.40076 1.090137607 0.623322455 1.061180178 0.810697132 0.910785681 1.063690567 1.242585711 0.937692468 1 15.60913258 2.232155888 4.180643329 1.101511726 0.880235556 0.201239639 0.15097647 0.237338604 9.564557507 0.053856192 0.041056711 170.6694889 -2.232155888 -0.22127617 RSDSVS(ph)ASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RSDS(0.279)VS(0.708)AS(0.013)ER 112.95 0.0016448 237680000 84626 72069 82003 109350 104350 103520 117830 87735 111080 TRUE FALSE 80625.89669 79412.91304 85762.91866 98357.93025 122548.607 99935.07644 99852.8694 80052.45829 128305.7191 0.628388955 0.6189351 0.668426312 0.766590382 0.955129731 0.778882478 0.778241766 0.623919642 1 16.96922595 3.251087021 3.165180641 0.810836537 0.627005749 0.411868302 0.102406717 0.233538614 4.840754048 0.028369243 0.037577116 1782.735943 -3.251087021 -0.183830788 RSEEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSEEVVR 7 1 O14907;A0A087X282 O14907 TAX1BP3 Tax1-binding protein 3 0 75.043 0.071417 28684000 116830 100280 111120 110330 106390 107990 125630 157350 166200 FALSE TRUE 111307.6774 110498.646 116214.9619 99239.41879 124944.3823 104250.2792 106462.8361 143571.5998 191973.4472 0.579807672 0.575593384 0.60536998 0.516943464 0.650842 0.543045305 0.554570633 0.747872177 1 17.55054725 0.955152547 3.033265666 0.999256105 0.574660666 0.933493709 0.036687442 0.057258801 1.294773262 0.031929182 0.008385045 9.018878719 -0.955152547 -0.424595439 RSEKDTAAVVS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSEKDTAAVVSR 12 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RSEKDTAAVVS(1)R 86.772 0.0056996 83318000 60039 46845 53986 64422 57159 57220 68327 58491 58937 TRUE FALSE 57201.07546 51618.55876 56461.3115 57946.17817 67127.5115 55238.45705 57902.46124 53369.21796 68076.64895 0.84024517 0.758241769 0.829378537 0.851190225 0.986057812 0.811415631 0.850548053 0.783957771 1 16.0548724 -5 0.266575959 2.077930836 0.823819562 0.390395798 0.061251642 216.8673198 2.114330344 128.8275296 0.076681432 1.00E-05 5 -1.254111274 RSEKDTAAVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSEKDTAAVVSR 12 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 0 ; 134.61 8.00E-05 73100000 77924 55743 80510 78017 94828 72990 103801 79183 103487 FALSE TRUE 74240.68695 61423.27507 84201.46314 70174.58294 111365.9732 70462.338 87964.25101 72249.31674 119535.2354 0.621077849 0.513850789 0.704407055 0.587061904 0.931658124 0.589469187 0.735885538 0.604418576 1 16.86707642 -5 0.140140079 2.158825469 0.531773784 0.459785727 0.114899507 114.37732 0.98161586 37.25023379 0.64286607 1.00E-05 5 -1.627051685 RSELIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSELIAK 7 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;; 127.02 0.0062459 1505920000 2904240 2531410 2394130 2858290 2258720 2638870 3243980 2950250 2552470 FALSE TRUE 2766962.331 2789363.557 2503903.229 2570969.259 2652640.053 2547485.27 2749051.271 2691910.47 2948294.011 0.938496066 0.946094096 0.84927189 0.872019293 0.899720327 0.864054012 0.932421007 0.913040036 1 21.49144897 0.523572106 1.276313004 0.999871025 0.903362682 0.484724843 0.032105575 1.95067606 4.124770201 0.033472585 0.01001979 3.338659321 -0.523572106 -0.096508343 RSES(ph)SSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSESSSPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.129)ES(0.741)S(0.129)S(0.001)PR 83.862 0.0091811 0 342450 366790 283480 381840 303280 334750 346860 362060 284000 TRUE FALSE 326263.0672 404166.318 296477.8384 343456.7178 356171.936 323157.5236 293940.1365 330356.107 328041.2695 0.994579333 1.232059364 0.903782133 1.046992405 1.085753437 0.985112404 0.896046211 1.007056543 1 18.3235178 2.705664106 0.807984021 0.955743262 1.088424743 0.1013 0.090063847 0.934032276 1.300626175 0.05877335 0.053804188 507.7665711 -2.705664106 0.132681481 RSES(ph)VK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSESVK 6 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 RS(0.001)ES(0.999)VK;RSES(1)VK;RS(0.001)ES(0.999)VK 93.166 0.028132 1202790000 1052250 1006600 926180 1210720 833300 972330 1143680 1364180 1010110 TRUE FALSE 1002512.228 1109173.684 968646.2691 1089016.125 978627.2562 938657.9683 969190.6109 1244725.167 1166752.7 0.859232833 0.950650197 0.830207009 0.933373564 0.83876151 0.804504646 0.830673553 1.066828615 1 20.15406738 1.237794224 24.99982263 1.033414364 0.867741731 0.678700268 0.048429212 12.42404714 405145.3351 0.039610739 0.012125446 17.28996938 -1.237794224 -0.165672633 RSET(ph)PPHWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 RS(0.159)ET(0.841)PPHWR;RS(0.009)ET(0.991)PPHWR;RS(0.022)ET(0.978)PPHWR 87.719 0.0077765 871390000 284644 218792 212907 237910 415290 183306 235109 258582 673200 TRUE FALSE 271189.4422 241087.1535 222668.9965 213994.8348 487716.4445 176958.0673 199238.804 235939.1893 777596.4178 0.348753461 0.310041492 0.286355481 0.275200387 0.627210251 0.227570579 0.256223922 0.303421137 1 19.56866205 -1.23297766 3.430860639 1.001574165 0.325073425 0.782975758 0.110943251 35512760 54888264.06 595089.7267 0.027427563 0.058482017 1.23297766 -0.67650074 RSFS(ph)KEVEER ddPTM_SK-BR-3_Trastuzumab_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(0.18)FS(0.82)KEVEER;RS(0.014)FS(0.986)KEVEER 126.09 0.00020448 526770000 496640 415060 426000 506840 381600 535810 597980 547640 440630 TRUE FALSE 473164.8114 457355.0859 445532.5214 455891.4803 448150.9192 517254.7653 506747.1683 499685.7384 508960.65 0.92966875 0.898605984 0.875377146 0.895730309 0.880521744 1.016296182 0.995650977 0.981776761 1 18.95719459 2.238527278 25 0.998460531 0.89845339 0.905091353 0.016474303 0.270733778 202577.6947 0.006305787 0.004961279 173.1917808 -2.238527278 -0.100007141 RSGKNS(ph)QEDS(ph)EDS(ph)EDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSGKNSQEDSEDSEDKDVK 19 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 RS(0.116)GKNS(0.884)QEDS(1)EDS(1)EDKDVK 99.219 0.0016212 88507000 159230 133170 129670 160930 58897 192540 164980 186950 65761 TRUE FALSE 151703.5135 146740.1744 135615.4978 144753.0107 69168.61815 185872.2915 139809.2709 170579.6669 75958.88002 1.99717944 1.931836993 1.785380429 1.905675948 0.910606082 2.447012008 1.840591527 2.245684334 1 16.21293101 3.842276029 2.410578202 1.78604036 1.980712908 0.030815705 0.477298296 1.338002242 15.21050286 0.120725506 0.255739625 6954.66201 -3.842276029 0.194672547 RSGS(ph)FGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.119)GS(0.881)FGK;RS(0.097)GS(0.903)FGK;RS(0.054)GS(0.946)FGK 73.499 0.029845 434210000 685230 573150 582570 706630 495700 670300 742770 717600 591700 TRUE FALSE 652840.5359 631554.6366 609281.4107 635598.2099 582149.9231 647087.3429 629446.7946 654763.1398 683457.814 0.955202388 0.924057965 0.891468937 0.929974311 0.851771552 0.946784614 0.92097388 0.958015442 1 19.38249277 0.978043753 1.596332807 1.000035561 0.917635179 0.477555985 0.02882696 0.373959635 1.954424125 0.026348711 0.007677818 9.507005681 -0.978043753 -0.082400382 RSIQFVDWCPTGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSIQFVDWCPTGFK 14 1 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ; 172.82 4.49E-06 1441110000 2713400 2523600 2528400 2085240 2070860 2557000 3291300 3566900 3396500 FALSE TRUE 2585142.959 2780757.709 2644329.641 1875627.714 2432017.328 2468450.449 2789151.736 3254563.327 3923211.873 0.658935343 0.708796211 0.674021625 0.478084736 0.619904662 0.629191216 0.710935791 0.829566037 1 21.90360382 1.072561601 1.565491324 0.997836637 0.635310749 0.805287579 0.060647691 0.172358493 0.84650621 0.060535696 0.017859287 11.81847935 -1.072561601 -0.362525888 RSIS(ph)SPNVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RSIS(0.809)S(0.191)PNVNR;RSIS(0.775)S(0.225)PNVNR;RS(0.157)IS(0.62)S(0.223)PNVNR;RS(0.009)IS(0.951)S(0.04)PNVNR 177.36 1.43E-06 1045095000 450074 340454 336146 392281 454112 310448 418125 387394 459925 TRUE FALSE 428799.894 375146.6497 351558.6266 352848.1686 533308.989 299697.1079 354332.3519 353471.7277 531247.82 0.807156054 0.706161297 0.66176013 0.664187513 1.003879863 0.564138047 0.666981282 0.665361276 1 19.01902549 RSLS(ph)GSSPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.055)LS(0.875)GS(0.062)S(0.008)PCPK 84.365 0.0054584 0 65277 52253 52210 61386 43936 59044 67326 68397 56518 TRUE FALSE 62191.48558 57577.64011 54603.88014 55215.36265 51598.42449 56999.29148 57054.18217 62407.79608 65282.52279 0.952651382 0.881976334 0.836424173 0.845790884 0.790386497 0.873117169 0.873957987 0.955964834 1 15.99440919 1.123852173 2.790726415 0.999267258 0.867847154 0.581965379 0.040738709 0.204044128 2.971442378 0.042585797 0.01155916 13.30001631 -1.123852173 -0.131420105 RSLS(ph)VEHLETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSLSVEHLETK 11 1 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 RS(0.197)LS(0.803)VEHLETK 130.27 0.00013946 236180000 418730 347910 372420 430120 322010 392090 465030 466740 378350 TRUE FALSE 398937.4627 383362.4245 389495.8254 386883.5204 378168.442 378511.825 394081.1326 425869.7713 437022.5857 0.912853193 0.877214215 0.891248732 0.885271227 0.865329286 0.866115019 0.901740884 0.974480005 1 18.73734832 1.212944697 2.928887931 0.998823666 0.884226223 0.910565068 0.013472632 0.06976742 1.0356268 0.012802667 0.003591654 16.32844008 -1.212944697 -0.114597443 RSNS(ph)PDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.344)NS(0.656)PDKFK;RS(0.101)NS(0.899)PDKFK;RS(0.148)NS(0.852)PDKFK;RS(0.358)NS(0.642)PDKFK;RS(0.056)NS(0.944)PDKFK;RS(0.463)NS(0.537)PDKFK 129.37 0.00030811 13950520000 17008460 16986110 13450410 18397020 7392320 17283200 15648050 17764630 7483790 TRUE FALSE 16204503.8 18717013.92 14067124.6 16547716.6 8681538.268 16684678.45 13260652.58 16209064.82 8644337.931 1.874580093 2.165233945 1.627322383 1.914283862 1.004303434 1.930127973 1.534027554 1.875107724 1 23.04332404 -0.714788143 0.092915021 1.40E-13 2.568801129 0.365867389 0.310425443 54.19139565 1.131512692 23.39050361 9.128479757 0.192846543 0.714788143 2.568801129 RSNVSSPATPTAS(ph)SSSSTTPTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPT(0.007)AS(0.141)S(0.141)S(0.141)S(0.141)S(0.141)T(0.141)T(0.141)PT(0.008)RK 52.707 0.060775 30803000 15253 11917 14566 15254 9960.9 14521 17759 14412 13411 TRUE FALSE 14532.02092 13131.35585 15233.86551 13720.63894 11698.07781 14018.13413 15049.53838 13150.00888 15490.70939 0.938112036 0.84769235 0.983419489 0.885733416 0.75516734 0.904938165 0.971520284 0.848896493 1 13.91911559 -1.056301484 4.15010263 1.000011998 0.89545189 0.205883262 0.066380351 67496236232 15348103481 8596538.941 0.015096845 0.087841252 1.056301484 -0.104560107 RSNVSSPATPTASSSSS(ph)TTPTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPT(0.019)AS(0.019)S(0.019)S(0.019)S(0.063)S(0.285)T(0.285)T(0.285)PT(0.007)RK 64.27 0.016663 20928000 13246 12573 11293 10809 8037.8 12732 14303 12566 12289 TRUE FALSE 12619.88783 13854.20299 11810.79522 9722.458784 9439.589775 12291.08765 12120.81466 11465.65442 14194.71536 0.889055364 0.976011329 0.832055798 0.6849351 0.665007331 0.865891801 0.853896281 0.80774106 1 13.7930663 3.604801991 5.599665878 0.802471216 0.931486293 0.201241331 0.095664526 0.297168274 12.28708281 0.024969182 0.03897997 4025.334643 -3.604801991 0.129015076 RSPES(ph)CSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.003)PES(0.997)CSKPEK;RS(0.033)PES(0.484)CS(0.484)KPEK;RS(0.041)PES(0.957)CS(0.002)KPEK 158.93 2.30E-05 2636130000 1733280 1525040 1514030 1899570 948730 1880870 1822400 1962760 1064590 TRUE FALSE 1651351.289 1680443.31 1583449.773 1708621.615 1114188.212 1815735 1544359.409 1790890.329 1229681.18 1.342910111 1.366568292 1.287691313 1.389483423 0.906078933 1.476590054 1.255902289 1.456385898 1 20.22985289 -2.27131204 1.873593695 5.76E-05 1.310229229 0.274239686 0.158590375 1530380.37 221512.8826 6464157.646 0.034773767 0.005354118 2.27131204 1.310171638 RSPGPGPSQSPRS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSPGPGPSQSPRSPK 15 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 RSPGPGPS(0.152)QS(0.121)PRS(0.727)PK 65.784 0.031577 39962000 11312 7000.6 11470 10015 9838.7 11647 14742 10542 13228 TRUE FALSE 10777.30418 7713.969099 11995.91085 9008.273173 11554.56616 11243.66147 12492.83714 9618.886593 15279.33068 0.705351851 0.504863024 0.78510709 0.589572499 0.75622201 0.735873953 0.817629869 0.629535861 1 13.89929373 -5 0.119810404 2.055240318 0.527642363 0.519602503 0.093907272 106.7083747 0.829267146 27.10526968 0.821641032 1.00E-05 5 -1.527597954 RSPQQTVPYVVPLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSPQQTVPYVVPLSPK 16 1 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 RSPQQTVPYVVPLS(1)PK;RSPQQTVPYVVPLS(1)PK 92.792 0.0028489 372977000 655690 570880 569530 691060 408440 651340 666600 727250 411850 TRUE FALSE 624696.8332 629053.321 595643.5138 621593.3359 479671.8067 628783.9325 564897.9271 663568.1346 475717.5946 1.313167392 1.322325111 1.252094774 1.30664357 1.0083121 1.321758833 1.18746486 1.394878269 1 18.85974586 -4.435770814 0.2312065 1.07E-25 1.291775412 0.34691667 0.108125633 133.628412 1.697343879 63.17014948 0.171242913 3.67E-05 4.435770814 1.291775412 RSPS(ph)YPPPGCGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSPSYPPPGCGK 12 1 F5H3X8;E9PFI7;Q8N3A8-2;Q8N3A8 F5H3X8 PARP8 Poly [ADP-ribose] polymerase 8 1 RS(0.005)PS(0.995)YPPPGCGK 109.35 0.0009844 328120000 211010 185080 186030 234820 174860 189370 239970 199900 203040 TRUE FALSE 201035.9755 203939.8624 194559.6595 211215.4475 205355.5286 182812.0694 203358.1691 182395.6963 234526.4062 0.857199744 0.869581663 0.829585302 0.900604119 0.87561794 0.779494609 0.867101374 0.777719231 1 17.83939084 -1.10343029 4.833139714 1.000007045 0.848240532 0.596778532 0.0400419 2.77E-06 5.14E-07 0.035347428 0.008331082 0.078807892 1.10343029 -0.151766514 RSPTGSTTS(ph)R ddPTM_SK-BR-3_Trastuzumab_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(0.001)PT(0.001)GS(0.063)T(0.017)T(0.112)S(0.806)R 72.531 0.050535 12321000 27424 28844 25711 31573 32295 26270 31080 28091 34166 TRUE FALSE 26127.72187 31783.23639 26889.87478 28399.22206 37927.23778 25360.26331 26338.17518 25631.20312 39464.28878 0.662059869 0.805367013 0.68137234 0.71961824 0.961052104 0.642612957 0.667392622 0.6494784 1 15.26826013 4.726603304 4.495500376 0.747063637 0.657391137 0.044442808 0.126939085 0.677958617 31.16904043 0.027949645 0.184441354 53284.79555 -4.726603304 -0.0896725 RSPVS(ph)TRPLPSASQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(0.388)PVS(0.595)T(0.017)RPLPSASQK 120.31 0.00011313 379450000 174590 125990 150230 148500 109450 175580 169450 157120 140650 TRUE FALSE 166337.4767 138828.5242 157118.1941 133572.4979 128538.0453 169499.6206 143597.2903 143361.7399 162461.2837 1.02385918 0.854532976 0.967111613 0.82218049 0.791191861 1.043323164 0.883886223 0.882436336 1 17.30973642 -0.113623032 7.651411268 1 0.910335197 0.109299891 0.081891001 0 0 0.073589546 0.017345222 0.769798336 0.113623032 -0.089664803 RSQAGVSSGAPPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSQAGVSSGAPPGR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 95.264 0.0061525 31750000 26618 17737.9 24317 24291 22940 24448 30385 25955.1 29832 FALSE TRUE 25359.81989 19545.41218 25431.9585 21849.22253 26940.72874 23601.35963 25749.21019 23682.33385 34458.1942 0.735959051 0.567221023 0.738052562 0.634079151 0.78183809 0.68492735 0.747259419 0.687277276 1 15.07255948 -4.999999997 0.221609124 2.590895957 0.653247164 0.707897981 0.061235474 75.72120853 0.757383763 53.72543753 0.103312762 1.00E-05 4.999999997 -1.937648794 RSQS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.051)QS(0.949)PVK 69.276 0.036861 151140000 304160 277490 228190 286930 199670 262590 348970 386950 298180 TRUE FALSE 289782.9596 305766.5465 238652.7372 258087.2513 234492.3848 253496.4425 295728.2172 353066.6066 344420.2315 0.841364511 0.887771735 0.692911494 0.749338243 0.680832202 0.736009152 0.85862615 1.025104144 1 18.39381036 1.386466816 3.286603288 1.013607301 0.77894525 0.714555818 0.063624795 0.160675236 2.896738263 0.058634578 0.019182727 24.34819749 -1.386466816 -0.234662051 RSS(ph)AIGIENIQEVQEK ddPTM_SK-BR-3_Trastuzumab_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(0.129)S(0.871)AIGIENIQEVQEK 236.77 5.94E-20 1127500000 1495100 1330400 1360300 1464700 1115600 1415100 1633600 1601500 1180000 TRUE FALSE 1424429.586 1465969.273 1422671.101 1317465.573 1310160.287 1366094.732 1384364.317 1461264.17 1362988.373 1.04507831 1.075555229 1.043788141 0.966600742 0.961240985 1.002279079 1.015683144 1.07210318 1 20.37834182 3.427830507 8.109078278 1.002692426 1.060234212 0.395617332 0.030696998 0.236217633 34.43037022 0.008673056 0.011781702 2678.122924 -3.427830507 0.057541786 RSS(ph)DGS(ph)LSHEEDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.494)S(0.576)DGS(0.911)LS(0.019)HEEDLAK 102.48 0.0054172 286590000 247280 202370 218170 259540 196730 251150 277790 259580 239360 TRUE FALSE 235591.5645 222991.7331 228173.3103 233450.5461 231039.6497 242452.6125 235408.0335 236849.7991 276478.7263 0.852114619 0.806542102 0.825283425 0.844370738 0.835650731 0.876930445 0.851450803 0.856665546 1 18.07680895 -4.999980717 0.21863971 1.810053958 0.820808608 0.906633861 0.016079913 40.50029011 0.404885194 14.39924137 0.029947209 1.00E-05 4.999980717 -0.98924535 RSS(ph)DPALIGLSTSVSDSNFSSEEPSR ddPTM_SK-BR-3_Trastuzumab_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(0.121)S(0.879)DPALIGLSTSVSDSNFSSEEPSR 332.31 3.18E-95 1263800000 187460 170550 184790 184460 207530 168510 210410 185880 226380 TRUE FALSE 178599.1373 187929.2389 193262.8043 165917.7303 243723.1663 162674.4564 178308.0901 169603.3618 261485.8542 0.68301644 0.718697535 0.739094682 0.634518953 0.932070177 0.622115705 0.681903389 0.648613908 1 17.99637338 -1.456910402 5.594162857 1.000268528 0.706828714 0.524652636 0.087494719 0.000263903 2.56E-05 0.076296193 0.017966945 0.034921235 1.456910402 -0.293439815 RSS(ph)DSWEVWGSASTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.001)S(0.519)DS(0.009)WEVWGS(0.183)AS(0.144)T(0.144)NR;RS(0.025)S(0.972)DS(0.003)WEVWGSASTNR 212.61 4.30E-12 389340000 529340 414880 455030 490860 592550 494430 634600 561410 655440 TRUE FALSE 504319.1473 457156.7437 475893.5756 441517.8202 695890.5324 477307.7651 537780.1148 512249.9642 757082.2877 0.666135182 0.603840231 0.62858897 0.583183397 0.919174235 0.630456917 0.710332448 0.676610684 1 19.53009059 -5 0.196908112 2.464897029 0.617011276 0.559173498 0.091548573 99.03964205 0.976630161 56.97269766 0.211017378 1.00E-05 5 -1.847885753 RSS(ph)DTEEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.182)S(0.768)DT(0.05)EEESR 144.8 1.93E-05 278680000 78177 63388 62595 74883 74423 73842 86647 70744 82928 TRUE FALSE 74481.72814 69847.30927 65465.04266 67355.61857 87402.34764 71284.83302 73427.40877 64549.28032 95788.0507 0.777568054 0.729186039 0.683436422 0.703173497 0.912455646 0.744193378 0.766561259 0.673876124 1 16.54755807 -1.963519098 2.849283659 1.195781172 0.75127234 0.581391075 0.066956516 7886559.089 5968848.173 10130343.06 0.015308692 0.010876293 1.963519098 -0.444508831 RSS(ph)GREEDDEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSGREEDDEELLR 14 2 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 RS(0.108)S(0.892)GREEDDEELLR 126.84 6.54E-05 1046000000 516400 457860 485260 522950 437160 492680 543870 499640 505420 TRUE FALSE 491990.7954 504516.4545 507509.651 470382.0725 513400.5656 475618.3681 460892.6426 455888.8728 583797.9523 0.842741557 0.864197027 0.869324137 0.805727513 0.879414811 0.814696876 0.789472866 0.780901802 1 19.15510962 2.210700217 24.97097248 0.824017513 0.851697339 0 0.064582114 756.3609832 677913.1311 0.021315358 0.015745995 162.4427064 -2.210700217 0.027679826 RSS(ph)LDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSLDEK 7 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 RS(0.169)S(0.831)LDEK 89.171 0.011067 132780000 141180 126330 125080 143820 114610 113560 150840 137960 119950 TRUE FALSE 134506.7012 139203.1706 130815.0417 129362.9404 134597.9477 109627.3887 127826.5876 125879.491 138551.2334 0.9708084 1.004705388 0.944163675 0.933683066 0.971466976 0.7912408 0.922594368 0.908541108 1 17.08006003 3.131739084 1.319405759 0.903150864 0.986272568 0.171062808 0.055287133 0.519917882 1.90316657 0.019236882 0.026049281 1354.375486 -3.131739084 0.083121704 RSS(ph)LGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSLGAK 7 1 A0A590UJL1;F8W6W8;Q9UJD0;Q9UJD0-2;D6RA03 A0A590UJL1;D6RA03 RIMS2;RIMS3 Regulating synaptic membrane exocytosis protein 3 1 RS(0.022)S(0.978)LGAK 76.943 0.024126 85518000 103250 94998 86995 96956 104690 96837 124770 106890 140950 TRUE FALSE 98369.57712 104678.4042 90983.8068 87209.79868 122947.9029 93483.51041 105734.0449 97530.14494 162807.8061 0.60420676 0.642956912 0.558841796 0.53566104 0.755172039 0.574195505 0.64944088 0.59905079 1 17.31281035 -4.99999992 0.441439449 9.176149081 0.612215825 0.798822053 0.06071199 482.0989745 2.884919792 3845.210039 0.029941114 1.00E-05 4.99999992 -8.563933255 RSS(ph)LGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLGEK 7 1 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 RS(0.001)S(0.999)LGEK;RS(0.007)S(0.993)LGEK 113.46 0.0037515 1126720000 1529630 1252940 1294920 1608270 1090390 1395570 1598370 1583670 1388100 TRUE FALSE 1457327.421 1380616.01 1354293.363 1446603.644 1280553.671 1347241.061 1354509.3 1444995.459 1603359.459 0.908921211 0.861077036 0.844659852 0.902232894 0.798669109 0.840261399 0.84479453 0.901229884 1 20.61266647 0.906351671 3.792515752 0.999936058 0.858912787 0.676626652 0.031253347 0.249731865 8.055115771 0.030059306 0.007714684 8.060308621 -0.906351671 -0.141023272 RSS(ph)LLNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.046)S(0.954)LLNAK;RS(0.253)S(0.747)LLNAK 115.65 0.0014845 1282330000 1232170 1044360 1039400 1277250 901910 1146710 1297170 1253200 970060 TRUE FALSE 1173927.766 1150781.471 1087057.518 1148858.403 1059202.818 1106999.145 1099262.892 1143463.164 1120491.95 1.047689602 1.027032341 0.970160935 1.02531607 0.945301587 0.987958142 0.981053806 1.020501008 1 20.09570085 3.905139265 4.337835977 0.988394476 1.040632271 0.426102673 0.023212208 0.16931837 5.513082383 0.005476793 0.010439939 8037.838304 -3.905139265 0.052237794 RSS(ph)LLSLMTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RSS(0.999)LLSLMTGK;RS(0.052)S(0.948)LLSLMTGK;RS(0.005)S(0.733)LLS(0.262)LMTGK 194.53 5.00E-07 2677300000 5501070 4959920 3882000 5543300 3897020 4925360 5490900 5045390 4186560 TRUE FALSE 5241045.323 5465341.487 4059993.54 4986076.952 4576659.054 4754793.548 4653162.358 4603588.904 4835790.343 1.083803257 1.130185781 0.83957187 1.031077983 0.94641387 0.983250557 0.962234098 0.951982732 1 22.20532027 3.767351455 24.99987211 0.961597922 1.106994548 0.595363199 0.050618932 391.7726263 340185.5792 0.011311286 0.020387383 5852.635199 -3.767351455 0.145396626 RSS(ph)LLSLMTGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLLSLMTGKK 12 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RSS(1)LLSLMTGKK;RS(0.183)S(0.817)LLSLMTGKK 170.77 3.17E-05 994980000 1108330 594530 888450 966670 915330 994050 1528580 1235240 1211050 TRUE FALSE 1055941.437 655113.2829 929186.3113 869498.495 1074963.262 959625.7992 1295367.047 1127075.837 1398853.449 0.75486209 0.468321598 0.664248504 0.621579405 0.768460244 0.686008817 0.926020555 0.805714021 1 20.4158134 1.844355377 0.724862314 0.972391444 0.606953406 0.641870905 0.090075817 0.367672267 0.374175178 0.075555769 0.038067886 69.88039916 -1.844355377 -0.365438038 RSS(ph)LPLDHGSPAQENPES(ph)EKSSPAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSLPLDHGSPAQENPESEKSSPAVSR 27 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 RS(0.479)S(0.521)LPLDHGS(0.001)PAQENPES(0.392)EKS(0.305)S(0.281)PAVS(0.02)R 57.14 0.037263 84947000 29548 19902 28711 31865 26670 28396 39944 33895 40894 TRUE FALSE 28151.3246 21930.03643 30027.42775 28661.86966 31321.23956 27412.6394 33849.80918 30926.97411 47235.63266 0.595976449 0.464268926 0.635694412 0.606784922 0.663085002 0.580338144 0.71661598 0.654738221 1 15.52758796 -5 0.147600352 2.448728515 0.474093304 0.84551616 0.054171816 44.63764492 0.394259649 18.81207988 0.264486872 1.00E-05 5 -1.974635212 RSS(ph)LPLDHGSPAQENPESEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.128)S(0.872)LPLDHGSPAQENPESEK;RS(0.197)S(0.802)LPLDHGSPAQENPESEK;RS(0.324)S(0.481)LPLDHGS(0.195)PAQENPESEK 213.57 3.72E-23 925820000 640570 508070 620110 728350 689650 645620 881970 791180 800180 TRUE FALSE 610291.5256 559842.9106 648542.6569 655134.8742 809924.7416 623262.0175 747409.278 721900.0849 924267.8276 0.660297272 0.605715025 0.701682605 0.708814972 0.87628793 0.674330534 0.808650107 0.781050755 1 19.81795144 -4.999999894 0.061508039 2.098851491 0.267263271 0.722724722 0.061050201 179.2540539 0.803620913 29.04168802 4.636904988 1.00E-05 4.999999894 -1.83158822 RSS(ph)LS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.491)S(0.65)LS(0.859)PGR;RS(0.079)S(0.943)LS(0.978)PGR 62.089 0.054701 405530000 769240 615740 657710 811010 725990 717030 805350 703610 801910 TRUE FALSE 732879.5497 678484.606 687866.6541 729485.734 852602.4261 692199.0713 682479.0662 641998.1783 926266.1072 0.791219223 0.732494259 0.74262315 0.787555248 0.920472443 0.747300442 0.736806692 0.693103389 1 19.8210672 -2.397921527 2.403700495 3.099007639 0.768007334 0.589168917 0.060630866 5842222.653 543126.7232 67711339.67 0.014660979 0.00400017 2.397921527 -2.331000305 RSS(ph)LYGIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSLYGIAK 9 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.231)S(0.769)LYGIAK;RS(0.189)S(0.811)LYGIAK 139.48 6.82E-05 878720000 2342190 1833430 1775250 2185870 1933070 1982200 2611680 2179060 2042250 TRUE FALSE 2231479.32 2020258.601 1856646.968 1966142.195 2270196.796 1913555.917 2213220.249 1988249.954 2358951.7 0.945962277 0.856422199 0.787064427 0.833481328 0.962375277 0.811189105 0.938221944 0.842853186 1 21.16971445 -1.936699466 0.463236302 1.118278631 0.873315863 0.309567411 0.059423722 73.66960615 5.563145592 9.417341807 0.029181333 0.011569126 1.936699466 -0.244962768 RSS(ph)MIETGQGAEGGLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSMIETGQGAEGGLSLR 18 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RS(0.364)S(0.635)MIET(0.001)GQGAEGGLSLR 164.82 1.27E-11 302390000 88142 75556 80224 78784 92340 90141 86948 89531 96815 TRUE FALSE 83975.70234 83255.2423 83902.34975 70864.48264 108444.0668 87019.39457 73682.48569 81691.19101 111828.5757 0.750932414 0.744489874 0.750276476 0.633688502 0.969734847 0.778149896 0.658887813 0.730503724 1 16.77092936 -1.131432994 4.213771265 1.000049932 0.74870748 0.433165915 0.089052711 2.794727818 47640981.33 5238.711881 0.019854714 0.073886825 1.131432994 -0.251342452 RSS(ph)NPPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.165)S(0.835)NPPAR;RS(0.125)S(0.875)NPPAR;RS(0.126)S(0.874)NPPAR;RS(0.19)S(0.81)NPPAR;RS(0.019)S(0.981)NPPAR;RS(0.174)S(0.826)NPPAR 111.86 0.0019313 838338500 353178.9 322227.7 335982.9 356100.2 366700.2 318261.9 393984.9 364849.1 416143 TRUE FALSE 336484.8333 355063.069 351388.0483 320304.3313 430652.5988 307240.4106 333875.2675 332900.9786 480676.3311 0.70002372 0.738673918 0.731028398 0.666361771 0.895930527 0.639183564 0.694594774 0.692567861 1 18.87470624 -1.491576291 5.81484054 1.000310804 0.718881827 0.620756968 0.068826345 0.000251174 2.20E-05 0.060358019 0.014211058 0.032242129 1.491576291 -0.281428977 RSS(ph)NVSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSNVSYK 8 1 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 RS(0.37)S(0.63)NVSYK;RS(0.19)S(0.81)NVSYK 109.72 0.0021828 251810000 542200 499830 444330 570780 431260 528660 679090 583300 465690 TRUE FALSE 516571.2805 550763.2453 464702.97 513404.11 506471.6075 510352.3716 575482.3482 532223.1597 537906.8268 0.960335982 1.023900828 0.863909783 0.954448028 0.941560103 0.948774669 1.069855074 0.989433733 1 19.03699677 1.759379868 24.99999995 1.025703535 0.955041503 0.360955764 0.043743612 10.85017939 13040.26599 0.020184319 0.01119386 57.4618849 -1.759379868 -0.070662032 RSS(ph)PAAFINPPIGTVTPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSPAAFINPPIGTVTPALK 20 1 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 RS(0.375)S(0.625)PAAFINPPIGTVTPALK 201.21 7.85E-22 264960000 575770 467460 494880 619930 527910 580880 678470 660790 592390 TRUE FALSE 548554.4932 515094.7055 517570.7375 557613.4586 619977.3369 560763.9799 574956.9405 602927.7245 684254.8157 0.801681597 0.752781995 0.756400577 0.814920766 0.906062073 0.819525076 0.840267291 0.881145022 1 19.38417416 -0.21605635 0.18962149 1.120615087 0.732331823 0.767632132 0.035478082 5.775681704 0.358189376 0.557357807 0.142788261 0.608056101 0.21605635 -0.388283265 RSS(ph)PESDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.029)S(0.971)PESDR 79.659 0.011912 0 20168 14844 16034 18014 20022 18886 18440 17366 23811 TRUE FALSE 19214.69861 16356.62048 16769.17476 16203.1985 23513.83046 18231.97308 15626.63933 15845.34098 27503.48827 0.698627695 0.594710762 0.609710834 0.589132489 0.854939935 0.662896754 0.56816936 0.576121139 1 14.74732699 -1.112072806 4.555519039 1.000032276 0.642024066 0.634193122 0.084886024 2.73E-05 5.33E-06 0.080767709 0.019035417 0.077255106 1.112072806 -0.35800821 RSS(ph)PSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.057)S(0.903)PS(0.039)ARPPDVPGQQPQAAK 184.59 3.11E-17 1008100000 227030 195160 207590 230800 167390 215110 236940 229970 210360 TRUE FALSE 216298.7418 215047.0259 217108.2068 207599.5455 196582.763 207660.6868 200790.4513 209832.6077 242981.5544 0.890185851 0.885034366 0.893517236 0.854383972 0.809043976 0.854635601 0.826360881 0.863574225 1 17.89048727 -0.731545416 3.885283003 1.00000105 0.860291218 0.730453887 0.026801923 3434658.803 7746759.367 87.91693159 0.007163237 0.185547276 0.731545416 -0.139709832 RSS(ph)PVPPVPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.171)S(0.829)PVPPVPER;RS(0.184)S(0.816)PVPPVPER 91.355 0.006617 2751800000 2946600 2698300 2775800 3050500 3113400 2801100 3269000 2844600 3379300 TRUE FALSE 2807320.058 2973259.838 2903073.176 2743857.944 3656375.974 2704097.205 2770254.011 2595511.744 3903344.585 0.719208872 0.761721076 0.743739916 0.702950479 0.936728976 0.692764153 0.709712901 0.664945584 1 21.8962794 -1.049012413 4.504655998 1.000012411 0.742104019 0.544183521 0.074356945 9.35E-06 1.97E-06 0.067230008 0.015845441 0.089327995 1.049012413 -0.257908392 RSS(ph)RDMAGGAGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSRDMAGGAGPR 13 2 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.148)S(0.852)RDMAGGAGPR 89.866 0.0057123 70412000 41842 19715 34741 29585 57065 35097 56471 36586 81257 TRUE FALSE 39864.21158 21723.98091 36333.90921 26611.05959 67017.11793 33881.58209 47855.31179 33382.33589 93857.92056 0.424729329 0.231456022 0.387116069 0.283524922 0.714027304 0.36098799 0.509869721 0.35566882 1 16.51819088 -4.999999999 0.211137234 3.887668565 0.317213389 0.666571693 0.131595262 81.59002333 0.813443441 99.77324319 0.253070325 1.00E-05 4.999999999 -3.570455176 RSS(ph)RS(ph)SPELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.446)S(0.575)RS(0.871)S(0.109)PELTR;RS(0.438)S(0.564)RS(0.772)S(0.225)PELT(0.001)R 95.067 0.039521 949910000 610940 527480 581490 625880 616140 596560 684670 549250 608340 TRUE FALSE 582062.077 581230.8117 608151.8917 562965.3533 723594.6209 575900.9776 580211.0167 501154.7582 702678.2602 0.828347922 0.827164927 0.865477027 0.80117087 1.029766626 0.819579899 0.82571363 0.713206579 1 19.42250474 -2.347113981 2.386676191 2.074427417 0.840542822 0.294854616 0.078300751 8820752.875 906439.2291 51698422.62 0.017488487 0.004496618 2.347113981 -1.233884595 RSS(ph)RSS(ph)PELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.437)S(0.575)RS(0.315)S(0.606)PELT(0.068)R 82.464 0.092806 1184600000 1343000 1158700 1167500 1386000 1271500 1205300 1406800 1130300 1313800 TRUE FALSE 1279519.052 1276772.847 1221031.03 1246676.647 1493249.197 1163560.159 1192166.822 1031324.94 1517537.394 0.843154875 0.84134523 0.804613471 0.821512967 0.983994993 0.766742331 0.785593045 0.679604301 1 20.53330064 RSS(ph)SEGLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.035)S(0.961)S(0.004)EGLSK;RS(0.064)S(0.935)S(0.001)EGLSK;RS(0.037)S(0.958)S(0.005)EGLSK;RS(0.028)S(0.964)S(0.008)EGLSK;RS(0.029)S(0.964)S(0.008)EGLSK;RS(0.057)S(0.927)S(0.015)EGLSK;RS(0.012)S(0.976)S(0.012)EGLSK;RS(0.011)S(0.791)S(0.198)EGLSK;RS(0.049)S(0.903)S(0.049)EGLSK 161.25 3.96E-05 3044904000 2753947 2179114 2298720 2813207 2035466 2703461 3187680 2936620 2649490 TRUE FALSE 2623773.383 2401168.194 2404118.586 2530418.088 2390450.626 2609839.468 2701340.87 2679473.985 3060359.377 0.857341593 0.784603342 0.785567409 0.826836909 0.78110128 0.85278856 0.882687468 0.875542266 1 21.54526965 0.976520346 0.715457817 0.99837079 0.8073289 0.823125544 0.027325188 0.298629072 0.347709179 0.026382455 0.010247589 9.473715665 -0.976520346 -0.19104189 RSS(ph)SLKER ddPTM_SK-BR-3_Trastuzumab_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(0.016)S(0.82)S(0.164)LKER 97.813 0.0041562 464380000 331380 264380 301690 300690 238740 337930 400020 331910 285150 TRUE FALSE 315716.3241 291320.6226 315522.7849 270464.0699 280376.1804 326227.3994 338989.6021 302846.2008 329369.6057 0.958547233 0.884479374 0.957959628 0.821156735 0.851250922 0.990459939 1.029207299 0.919472215 1 18.3293479 2.217762294 24.24403044 0.9918334 0.898628675 0.443872193 0.049731148 154.1236621 179656.0835 0.018366102 0.013580749 165.1057863 -2.217762294 -0.093204725 RSS(ph)SSGDQSSDSLNS(ph)PTLLAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 2 RS(0.35)S(0.407)S(0.169)S(0.072)GDQS(0.005)S(0.004)DS(0.046)LNS(0.923)PT(0.023)LLAL 54.626 0.021492 0 27522 21424 25768 26685 26786 25415 30147 23638 31590 TRUE FALSE 26221.0896 23607.12996 26949.48829 24002.5731 31457.46992 24534.87218 25547.52146 21568.13141 36488.81586 0.718606208 0.646968925 0.738568453 0.657806304 0.862112655 0.67239431 0.70014663 0.591088828 1 15.15516671 -1.066139279 4.26660236 1.000030224 0.698851155 0.640756971 0.070956051 8632923.203 2157196.553 2502.645761 0.015107836 0.085873808 1.066139279 -0.301179069 RSS(ph)SSGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.162)S(0.595)S(0.16)S(0.084)GDQSSDSLNSPTLLAL 210.66 2.03E-22 177240000 292250 256440 282510 272830 301020 263130 327980 277990 316580 TRUE FALSE 278435.9217 282571.5275 295463.3629 245404.6101 353517.7927 254017.7421 277940.6272 253647.7219 365673.6095 0.761432913 0.772742468 0.807997502 0.671102873 0.966757741 0.694657026 0.760078442 0.693645139 1 18.48019699 -1.92970804 2.641128871 1.151875522 0.76706598 0.441600776 0.082669062 8159973.474 4292376.49 7636918.305 0.017731768 0.011756877 1.92970804 -0.384809541 RSS(ph)TSGDT(ph)EEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 2 RS(0.402)S(0.493)T(0.105)S(0.113)GDT(0.888)EEEEEEEVVPFSSDEQK 214.41 1.58E-33 413880000 604210 460350 539980 638860 400470 595650 648800 639530 376520 TRUE FALSE 575650.1907 507260.1884 564738.6171 574640.579 470311.8412 575022.4911 549813.644 583529.3628 434908.7986 1.323611278 1.166359913 1.298521941 1.321289845 1.081403372 1.322167988 1.264204462 1.341728116 1 18.73035337 -1.020525001 4.339143089 0.999987012 1.25969837 0.506619427 0.082015209 6970367.699 21596819.36 1591.32832 0.017987942 0.095383883 1.020525001 0.259711358 RSS(ph)TSGDT(ph)EEEEEEEVVPFSSDEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSTSGDTEEEEEEEVVPFSSDEQKR 26 2 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 2 RS(0.436)S(0.526)T(0.035)S(0.005)GDT(0.999)EEEEEEEVVPFSSDEQKR 152.19 1.16E-07 180850000 151830 118950 131240 149310 103200 133020 172710 144240 103160 TRUE FALSE 144653.2968 131071.1402 137257.4838 134301.0751 121198.0473 128413.484 146359.9175 131609.5809 119157.5259 1.213966937 1.099982055 1.15189941 1.127088483 1.01712457 1.077678334 1.228289328 1.104500785 1 16.86251055 -2.5274606 1.663671162 2.59E-05 1.132578561 0.293218092 0.061808453 1130627.477 70877.29543 4245215.171 0.01546748 0.002968516 2.5274606 1.132552702 RSS(ph)TSSEPTPTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.017)S(0.949)T(0.017)S(0.017)SEPTPTVK 188.59 6.34E-06 113490000 364050 305920 329340 380830 284950 386130 430310 422620 387110 TRUE FALSE 346842.078 337093.5958 344440.5648 342548.2449 334645.1898 372758.2213 364658.3063 385613.1524 447141.0417 0.775688308 0.753886502 0.77031749 0.766085447 0.748410811 0.833647969 0.81553307 0.862397133 1 18.77037045 0.792183885 0.619728169 1.003809074 0.760517751 0.944408138 0.017733847 0.208150528 0.171227049 0.0175366 0.00687981 6.19703409 -0.792183885 -0.243291323 RSS(ph)WECTGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RSSWECTGSGR 11 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 RS(0.191)S(0.809)WECTGSGR;RS(0.011)S(0.922)WECT(0.005)GS(0.062)GR;RS(0.05)S(0.95)WECTGSGR;RS(0.113)S(0.887)WECTGSGR;RS(0.178)S(0.603)WECT(0.17)GS(0.048)GR 137.89 4.22E-05 1352884000 932160 754437 855102 955459 1071452 838283 1060968 941971 1138759 TRUE FALSE 888098.6442 831314.988 894309.2725 859414.4461 1258312.89 809253.0495 899097.8456 859487.0255 1315351.93 0.675179489 0.632009555 0.679901137 0.653372247 0.956635909 0.615236904 0.683541663 0.653427426 1 20.32701742 -2.075688513 2.469645829 1.477868302 0.689331095 0.500399287 0.096108964 7298162.5 2378475.997 19639844.52 0.02171857 0.008400623 2.075688513 -0.788537206 RSSDT(ph)EEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.047)S(0.088)DT(0.864)EEESR 143.94 0.0051512 0 61233 54121 53195 59136 62371 53188 62259 59381 68776 TRUE FALSE 58338.63744 59635.99143 55634.04337 53191.53693 73248.48265 51346.08622 52760.24609 54181.28484 79441.43082 0.734360356 0.750691306 0.700315223 0.669569221 0.922043849 0.64633889 0.664140179 0.682028059 1 16.27760399 -1.732423896 2.8503905 1.048204634 0.720862304 0.557351641 0.078087118 41283211.44 36178902.76 14134635.12 0.017980293 0.018517234 1.732423896 -0.32734233 RSSLDAEIDS(ph)LTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.163)S(0.163)LDAEIDS(0.218)LT(0.218)S(0.218)ILADLECS(0.002)S(0.002)PY(0.002)KPRPPQS(0.002)S(0.002)T(0.002)GS(0.002)T(0.002)AS(0.003)PPVSTPVTGHK 48.87 0.0087053 2310700000 32387 31935 40928 33983 19171 31387 32962 29722 22188 TRUE FALSE 30856.13069 35189.21281 42804.58928 30566.96428 22514.41633 30300.06032 27933.04151 27119.38411 25628.80172 1.203963066 1.37303387 1.67017521 1.192680197 0.878481038 1.182265978 1.089908214 1.05816044 1 14.64547841 3.006258869 24.99978989 1.059788872 1.383212512 0.60669991 0.136194006 118.3405585 472682.5307 0.039135131 0.046661678 1014.515925 -3.006258869 0.32342364 RSSS(ph)LKER ddPTM_SK-BR-3_Trastuzumab_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(0.134)S(0.134)S(0.731)LKER 58.889 0.080402 852420000 763120 549380 693700 707780 524850 652980 769860 705340 617190 TRUE FALSE 727048.83 605362.4466 725506.8312 636632.6097 616383.6738 630367.1389 652403.7176 643576.6904 712900.673 1.019845902 0.849153984 1.01768291 0.893017266 0.864613679 0.884228565 0.915139713 0.902757866 1 19.44334156 4.709083031 3.971383434 0.911331337 1.026555019 0.263268072 0.054161867 0.26167501 7.752304343 0.011734615 0.080902802 51177.96715 -4.709083031 0.115223682 RSST(ph)SGDTEEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.17)S(0.17)T(0.22)S(0.22)GDT(0.22)EEEEEEEVVPFSSDEQK 88.79 0.0087314 140610000 183350 153130 170810 186900 118720 174970 186110 181830 123800 TRUE FALSE 174683.4089 168734.1211 178641.8075 168112.4569 139424.7304 168910.745 157715.5014 165908.0013 142998.2717 1.221577064 1.17997315 1.249258507 1.175625795 0.975009899 1.181208297 1.102918934 1.160209835 1 17.12563819 7.999999805 0.038930418 0.588597632 2.050484264 0.426361931 0.067620565 745.2360206 2.211408403 23.1132194 72.84711563 99999955.17 -7.999999805 1.461886632 RST(ph)SPIIGS(ph)PPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.317)T(0.442)S(0.264)PIIGS(0.977)PPVR;RS(0.029)T(0.664)S(0.308)PIIGS(0.999)PPVR;RS(0.295)T(0.355)S(0.35)PIIGS(1)PPVR 168.16 6.80E-05 602700000 488050 393402 455680 484120 503810 449830 599330 526930 644450 TRUE FALSE 464980.8437 433490.1111 476573.3787 435455.3378 591674.3045 434252.2743 507891.201 480789.2158 744388.0146 0.624648483 0.582344292 0.640221725 0.584984349 0.79484663 0.583368171 0.682293631 0.645885219 1 19.5056953 -5 0.253714594 3.25074474 0.606946869 0.771218194 0.061599058 79.08902067 0.781355787 92.43679491 0.076743064 1.00E-05 5 -2.643797871 RST(ph)SPIIGSPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.214)T(0.639)S(0.148)PIIGSPPVR;RS(0.172)T(0.723)S(0.105)PIIGSPPVR 105.89 0.00083067 2355300000 1399810 1079040 1195830 1254800 1232800 1195980 1372500 1225740 1373740 TRUE FALSE 1333643.755 1188995.403 1250659.988 1128665.12 1447799.93 1154562.913 1163099.917 1118407.708 1586772.583 0.840475673 0.749316831 0.788178471 0.711296081 0.91241804 0.72761713 0.732997236 0.704831757 1 20.59766394 RSTAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSTAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 38 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 RSTAPSAAASASASAAAS(0.064)S(0.935)PAGGGAEALELLEHCGVCR;RSTAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR 174.04 7.78E-19 653220000 156629 88039 161914 130840 190279 143207 229822 163911 214452 TRUE FALSE 149225.4576 97010.27419 169337.9171 117687.7146 223463.5974 138247.7057 194758.4329 149558.0839 247708.1209 0.602424567 0.391631384 0.683618754 0.475106404 0.902124632 0.55810728 0.786241615 0.603767383 1 17.91828164 -4.999999875 0.077381554 2.348242731 0.190511203 0.454656379 0.13779225 200.3618773 1.102790867 46.14225722 4.650434938 1.00E-05 4.999999875 -2.157731528 RSTDFTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSTDFTSR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 124.81 0.0020669 154621000 239230 185062 256450 266660 243970 262810 325330 310050 325930 FALSE TRUE 227922.072 203920.0282 268208.4862 239854.8302 286518.2908 253708.8238 275694.9334 282900.3783 376473.5598 0.605413225 0.5416583 0.712423168 0.637109364 0.761058203 0.673908744 0.732308887 0.751448199 1 18.52218902 -4.999999999 0.094214617 2.128861031 0.399184448 0.852157411 0.047048209 64.12096003 0.416182068 14.25270631 0.88772709 1.00E-05 4.999999999 -1.729676583 RSVSDNDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 100.92 0.006948 2204870000 3270830 2643610 2698920 3109270 3260330 2911310 3550500 3076860 3739720 FALSE TRUE 3116224.348 2912996.865 2822668.152 2796720.272 3828930.52 2810490.605 3008806.016 2807433.827 4319656.678 0.721405561 0.674358423 0.653447337 0.647440406 0.886396954 0.650628236 0.69653823 0.649920592 1 22.04248522 -1.117997553 4.370851232 1.000042227 0.697524062 0.640255135 0.071256464 2.70E-05 5.45E-06 0.063514789 0.014968493 0.07620833 1.117997553 -0.302518165 RSYS(ph)PDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.001)YS(0.999)PDGK;RS(0.004)YS(0.996)PDGK;RS(0.136)Y(0.005)S(0.859)PDGK;RS(0.004)YS(0.996)PDGK 120.86 0.00089316 1449102000 986170 1046410 813570 1154640 610890 1018300 965520 1065740 652860 TRUE FALSE 939555.6985 1153040.369 850872.9892 1038573.394 717429.0226 983036.0157 818212.191 972418.1558 754102.1945 1.245926222 1.52902402 1.128325836 1.377231629 0.951368432 1.303584611 1.085014998 1.289504477 1 19.52440052 3.328684461 1.612719297 1.150722376 1.375129487 0.225394616 0.155057791 0.445287762 2.387308363 0.044802213 0.069282178 2131.495701 -3.328684461 0.224407111 RSYS(ph)PDGKESPSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.055)YS(0.944)PDGKESPSDKK 136.68 0.00011806 141720000 320790 185460 302620 307730 164140 338790 416170 408410 203290 TRUE FALSE 305626.8924 204358.5849 316495.4263 276796.3958 192765.964 327057.6174 352675.623 372647.4553 234815.1749 1.301563634 0.870295478 1.347849118 1.178784105 0.820926348 1.392829988 1.501928583 1.586981997 1 17.84116612 2.070336706 13.37657592 1.425897501 1.104544029 0.245016949 0.224092078 1.063810503 200.2092474 0.076700501 0.056646213 117.58088 -2.070336706 -0.321353471 RSYS(ph)SPDITQAIQEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.001)YS(0.5)S(0.5)PDITQAIQEEEKR;RS(0.195)YS(0.588)S(0.216)PDITQAIQEEEKR 238.05 3.76E-24 350936000 552680 460450 519760 543780 398760 559810 596340 610420 467050 TRUE FALSE 526555.9117 507370.3785 543591.5101 489118.2013 468303.6177 540423.6393 505357.3805 556968.3888 539477.7286 0.976047543 0.940484382 1.007625489 0.906651332 0.868068491 1.001753382 0.936752999 1.032421468 1 19.04120388 1.240492764 24.99694295 1.01621075 0.949243871 0.309373917 0.042224264 58.81484461 760996.5097 0.030023671 0.009714613 17.39773712 -1.240492764 -0.066966879 RSYSS(ph)PDITQAIQEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RSYS(0.1)S(0.899)PDITQAIQEEEKR 250.39 3.34E-25 105460000 134110 103070 128620 142720 95707 137450 161450 144630 111230 TRUE FALSE 127770.8861 113572.9502 134517.3542 128373.5144 112398.2705 132690.072 136817.8373 131965.4305 128478.9803 0.994488637 0.883980787 1.046998925 0.99917912 0.874837816 1.032776503 1.064904445 1.027136347 1 16.97117282 2.039147666 24.99352205 1.040629091 0.958048597 0.298990427 0.053503792 164.2468715 104861.4854 0.019281256 0.014240129 109.4328389 -2.039147666 -0.082580494 RT(ph)ASPPPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTASPPPPPK 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.5)AS(0.5)PPPPPK;RT(0.5)AS(0.5)PPPPPK;RT(0.602)AS(0.398)PPPPPK 65.563 0.040197 525710000 751370 643620 726150 763180 577550 714440 834320 771870 692300 TRUE FALSE 715854.2292 709205.6097 759444.6958 686463.6965 678274.5371 689698.7637 707029.1607 704280.9709 799658.3482 0.895200095 0.88688577 0.949711458 0.858446233 0.84820541 0.862491794 0.884164046 0.880727341 1 19.60902422 -1.706410539 5.424768287 1.002974087 0.883585135 0.63870306 0.027599542 0.001006563 5.45E-05 0.027095081 0.006235793 0.019660269 1.706410539 -0.119388952 RT(ph)EARS(ph)SDEENGPPS(ph)SPDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTEARSSDEENGPPSSPDLDR 21 2 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 3 RT(0.603)EARS(0.585)S(0.592)DEENGPPS(0.641)S(0.58)PDLDR 52.853 0.022754 0 93996 78798 101580 109680 89546 91773 115720 85533 108010 TRUE FALSE 89552.99536 86827.60579 106237.5435 98654.75802 105162.794 88594.878 98064.78866 78043.27708 124759.6392 0.717804219 0.695959097 0.851537758 0.790758603 0.842923198 0.710124513 0.786029755 0.625549077 1 16.92879176 -2.230123289 2.515099969 1.937230067 0.752806253 0.559229717 0.0690298 6598591.981 1273399.262 35466260.75 0.015955745 0.005886765 2.230123289 -1.184423814 RT(ph)HS(ph)DASDDEAFTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.806)HS(0.757)DAS(0.437)DDEAFTTSK 78.413 0.018355 339700000 389570 315610 370640 411100 313940 382080 444130 356620 290330 TRUE FALSE 371155.7982 347771.0178 387634.2106 369775.447 368691.0366 368848.4738 376369.8115 325392.4622 335352.8936 1.106761878 1.03703002 1.155899406 1.102645762 1.099412123 1.09988159 1.122309718 0.970298657 1 18.35532052 1.236175975 24.99999886 0.985149274 1.09961499 0.727768925 0.030002471 34.31945605 359757.0534 0.024712663 0.007289252 17.22566411 -1.236175975 0.114465716 RT(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTNSDSALHQSTMTPTQPESFSSGSQDVHQK 31 1 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 RT(0.475)NS(0.262)DS(0.262)ALHQSTMTPTQPESFSSGSQDVHQK 141.9 1.06E-08 71486000 21878 15273 19772 21966 26310 16552 34064 26735 28037 TRUE FALSE 20843.8703 16829.33606 20678.56576 19757.93595 30898.45567 15978.80009 28866.91117 24393.94167 32384.83477 0.64363059 0.519667189 0.638526209 0.610098402 0.954102619 0.493403786 0.891371266 0.753252003 1 14.98303076 1.349986868 0.270557803 1.053263773 0.523941823 0.440707924 0.131825283 1.505923427 0.433877006 0.311760014 0.253624644 22.38653447 -1.349986868 -0.529321949 RT(ph)NSTGGSSGSSVGGGSGK ddPTM_SK-BR-3_Trastuzumab_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(0.578)NS(0.387)T(0.029)GGS(0.003)S(0.003)GSSVGGGSGK 114.01 9.72E-05 23528000 30961 24117 29969 33668 27027 32566 34351 31324 32229 TRUE FALSE 29497.53489 26574.54972 31343.10829 30283.62867 31740.50024 31438.23125 29110.12405 28581.1045 37226.90872 0.792371322 0.713853248 0.84194765 0.813487601 0.852622507 0.84450287 0.78196458 0.767753904 1 15.1840582 -5 0.289442254 2.562913832 0.784634001 0.669012187 0.043182854 155.3239638 1.464216095 146.711796 0.048578067 1.00E-05 5 -1.778279832 RT(ph)PDSTFSETFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.916)PDS(0.083)T(0.001)FSETFK;RT(0.985)PDS(0.012)T(0.004)FSETFK;RT(0.989)PDS(0.011)TFSETFK;RT(0.992)PDS(0.008)TFSETFK;RT(0.889)PDS(0.111)TFSETFK 228.9 5.55E-12 1604164000 2493310 2625380 2104995 2908120 1507477 2470540 2467270 2717460 1583320 TRUE FALSE 2375456.178 2892909.207 2201511.103 2615790.253 1770380.512 2384984.58 2090842.647 2479504.796 1828853.179 1.298877463 1.581815993 1.203765905 1.430289912 0.968027686 1.304087506 1.143253417 1.355770285 1 20.80250783 3.175109834 1.701067246 1.179789105 1.423721302 0.270653466 0.15964674 0.400223946 2.392947401 0.047771492 0.064485646 1496.614107 -3.175109834 0.243932197 RT(ph)PTMPQEEAAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTPTMPQEEAAEK 13 1 Q9NYV4-2 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 RT(0.966)PT(0.034)MPQEEAAEK;RT(0.79)PT(0.21)MPQEEAAEK 142.58 2.37E-05 291443000 631139 572191 506249 679416 365855 623841 594239 661666 425863 TRUE FALSE 601306.3103 630497.9134 529461.0174 611119.8129 429659.9962 602237.2297 503576.9266 603727.0173 491903.659 1.222406663 1.28175081 1.076351045 1.242356713 0.873463712 1.224299146 1.0237308 1.227327763 1 18.90801626 3.601811071 1.841261754 1.089684994 1.253711617 0.210233338 0.118283567 0.440410737 2.94165821 0.030945704 0.058074953 3997.708019 -3.601811071 0.164026623 RT(ph)QSSLTVSEVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTQSSLTVSEVLTR 14 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RT(0.726)QS(0.23)S(0.044)LTVSEVLTR 159.26 2.90E-06 295690000 64155 44393 64152 59239 66345 68833 81962 62167 73890 TRUE FALSE 61122.52029 48916.69717 67093.43265 53284.18317 77915.54699 66449.29595 69457.19156 56723.32791 85348.48382 0.716152386 0.573140787 0.786111594 0.624313178 0.912910734 0.778564457 0.813806976 0.664608501 1 16.3810779 2.751051977 24.95998113 0.817335343 0.668721806 0.366566223 0.102458687 801.8132918 1602166.031 0.028345916 0.029872307 563.705117 -2.751051977 -0.148613537 RT(ph)SEEDTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSEEDTPK 9 1 A0A1B0GW41;Q8WYH8-2;Q8WYH8 A0A1B0GW41 ING5 Inhibitor of growth protein 5 1 RT(0.5)S(0.5)EEDTPK;RT(0.5)S(0.5)EEDTPK 70.806 0.030102 1104020000 2826800 2448870 2763100 2888600 4232800 2515980 3441200 2615400 4785700 TRUE FALSE 2693182.766 2698412.637 2889790.868 2598232.44 4970998.98 2428850.982 2916181.738 2386381.711 5527841.914 0.48720329 0.488149386 0.522770172 0.470026546 0.899265764 0.439385029 0.527544344 0.431702235 1 22.39828493 -1.89847558 2.736321695 1.247436795 0.530749886 0.545292097 0.133929631 9566474.5 5894868.227 15233612.68 0.030496825 0.012633521 1.89847558 -0.716686909 RT(ph)SFSFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.922)S(0.07)FS(0.008)FQK 67.385 0.069058 0 413580 338140 342750 410270 327640 394170 431080 417800 362120 TRUE FALSE 394030.893 372596.8504 358465.4265 369028.8801 384780.3123 380519.7941 365310.8287 381215.2171 418275.7201 0.942036255 0.890792443 0.857007494 0.882262255 0.919920267 0.909734359 0.873373259 0.911396954 1 18.67409473 0.965034049 22.63215471 1.000000001 0.897072071 0.646554036 0.023874021 1037.858227 671768.1688 0.023758942 0.005939735 9.226437609 -0.965034049 -0.10292793 RT(ph)SFSTSDVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.366)S(0.366)FS(0.238)T(0.027)S(0.003)DVSK;RT(0.416)S(0.416)FS(0.164)T(0.003)S(0.001)DVSK 93.51 0.0053889 1243890000 1935560 1697000 1709800 1899370 1556410 1880960 2416530 2181210 2094680 TRUE FALSE 1844069.915 1869926.229 1788196.021 1708441.719 1827847.411 1815821.884 2047843.966 1990211.689 2419512.276 0.762165967 0.772852549 0.739072928 0.706109961 0.755461102 0.750490874 0.846387095 0.822567304 1 21.20628483 0.849217285 0.800120486 0.998620682 0.747779639 0.898219769 0.026386841 0.251341899 0.335211393 0.026342232 0.009432352 7.066710259 -0.849217285 -0.250841044 RT(ph)SNERPGSGQGQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.747)S(0.253)NERPGSGQGQGR;RT(0.962)S(0.038)NERPGSGQGQGR 227.64 3.35E-11 1017290000 201805 178391 202462 214635 220198 193361 232517 206506 213970 TRUE FALSE 192266.0776 196569.2457 211745.083 193059.482 258600.4615 186664.8601 197042.2612 188423.2399 247151.3748 0.777928416 0.795339479 0.856742485 0.781138613 1.046324188 0.755265312 0.797253349 0.762379898 1 17.91503541 -2.423365023 2.144991664 2.468463579 0.818589642 0.304356053 0.084682348 3061956.415 270187.2277 21882786.54 0.019259088 0.00377255 2.423365023 -1.649873937 RT(ph)SPQVLGSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.509)S(0.491)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK;RT(0.672)S(0.328)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK 199.33 1.01E-07 3739220000 5250090 4610780 3961470 4487430 4628030 4517190 6309910 5361220 5429030 TRUE FALSE 5001928.65 5080623.724 4143107.318 4036345.011 5435156.967 4360758.578 5347217.34 4891763.155 6270936.245 0.797636661 0.810185836 0.660684012 0.643659073 0.866721771 0.695391949 0.852698406 0.78006903 1 22.58024942 0.36984066 0.697938202 1.004303158 0.754868238 0.514808219 0.073997599 1.834848322 1.311413593 0.090857434 0.026491717 2.343368889 -0.36984066 -0.24943492 RT(ph)SSEDNLYLAVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 RT(0.333)S(0.333)S(0.333)EDNLYLAVLR;RT(0.333)S(0.333)S(0.333)EDNLYLAVLR;RT(0.333)S(0.333)S(0.333)EDNLYLAVLR 195.46 1.57E-08 153779000 83966.8 64078.3 66723 74295.8 89202 77947.5 97800 88442.1 93636 TRUE FALSE 79997.85577 70607.95162 69782.31555 66827.44503 104758.8006 75248.15853 82878.81378 80697.64086 108156.5927 0.739648447 0.65283077 0.64519706 0.61787676 0.968584512 0.695733442 0.766285362 0.746118557 1 16.72276208 2.779480593 24.99933211 0.804971246 0.669424733 0.401958677 0.100083075 584.9260494 357349.1754 0.028134923 0.029841287 601.8393679 -2.779480593 -0.135546513 RT(ph)SSEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.477)S(0.477)S(0.029)EELRDAT(0.008)S(0.01)LLAAGEGGLLDEVEPLRPDELER;RT(0.297)S(0.297)S(0.297)EELRDAT(0.055)S(0.055)LLAAGEGGLLDEVEPLRPDELER;RT(0.295)S(0.295)S(0.295)EELRDAT(0.057)S(0.057)LLAAGEGGLLDEVEPLRPDELER 169.84 7.23E-15 125183000 20756.6 15747.4 18195.7 19068.4 20322.2 19218.5 23572.6 20160.9 28654.5 TRUE FALSE 19775.47665 17352.07796 19029.99084 17151.6082 23866.38525 18552.95853 19976.16693 18395.50472 33098.09351 0.597480838 0.524262159 0.574957311 0.518205322 0.721080362 0.560544628 0.603544338 0.555787442 1 15.0144605 -4.999999999 0.401733898 7.848248308 0.572176732 0.841027041 0.057005217 264.4957135 1.836022934 1589.807325 0.032244244 1.00E-05 4.999999999 -7.276071577 RT(ph)SSLDTITGPYLTGQWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 RT(0.333)S(0.333)S(0.333)LDTITGPYLTGQWPR;RT(0.333)S(0.333)S(0.333)LDTITGPYLTGQWPR;RT(0.333)S(0.333)S(0.333)LDTITGPYLTGQWPR 275.39 1.14E-39 645768000 121893 90146.5 108925 109652 117598 102346.7 136951 110381.1 122119 TRUE FALSE 116131.3595 99332.53084 113919.319 98629.57263 138107.054 98802.40812 116056.6097 100715.5457 141056.5908 0.82329623 0.7042034 0.807614294 0.699219881 0.979089691 0.700445173 0.822766302 0.714008081 1 17.10591455 -2.056385886 2.466706234 1.302109103 0.780684422 0.387964133 0.086311073 15861730.47 5796360.718 26991598.51 0.019691176 0.008782418 2.056385886 -0.521424681 RT(ph)SSPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSSPPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.657)S(0.334)S(0.009)PPR 64.711 0.042517 73939000 11928 8819 12525 12595 14912 11720 13117 12575 17586 TRUE FALSE 11364.18708 9717.666126 13099.28364 11328.92667 17512.64808 11314.13346 11115.76074 11473.86634 20313.14706 0.55944985 0.478392939 0.644867267 0.557714008 0.862133673 0.55698575 0.54722002 0.564849272 1 14.31012615 -1.903970028 2.360167187 1.244968926 0.58714334 0.601579948 0.102962659 9667337.254 4787533.676 13129907.06 0.024501166 0.012474696 1.903970028 -0.657825586 RT(ph)SSTLDSEGTFNSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.483)S(0.483)S(0.032)T(0.001)LDSEGTFNSYR;RT(0.412)S(0.412)S(0.173)T(0.004)LDSEGTFNSYR;RT(0.483)S(0.483)S(0.032)T(0.002)LDSEGTFNSYR 197.85 2.47E-11 793010000 338670 245231 318802 309527 340922 294628 384880 337101 409681 TRUE FALSE 322661.7403 270220.3177 333419.387 278412.7579 400378.6889 284424.9585 326159.4872 307582.6494 473212.2371 0.681854177 0.571034087 0.704587415 0.588346488 0.84608693 0.601051571 0.689245674 0.64998879 1 18.85212786 -4.999999999 0.326818102 4.346188673 0.648231552 0.640956272 0.0781476 199.8082398 1.740625847 463.8700422 0.059697523 1.00E-05 4.999999999 -3.697957121 RT(ph)SVPSPEQPQPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 RT(0.615)S(0.385)VPSPEQPQPYR 115.57 0.00024134 187600000 55837 53195 51476 53345 52375 56236 51965 62405 68049 TRUE FALSE 53197.69567 58615.63098 53836.22552 47982.65925 61509.18342 54288.53322 44036.78485 56940.48737 78601.69137 0.676800903 0.745729894 0.684924517 0.610453266 0.782542746 0.690678944 0.560252382 0.724418093 1 16.26227274 -2.151711756 2.670540795 1.809678191 0.681465656 0.710402235 0.063285427 11627314.82 3874487.441 56975881.15 0.015847051 0.007051609 2.151711756 -1.128212535 RT(ph)TLCGTLDYLPPEMIEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTTLCGTLDYLPPEMIEGR 19 1 A3KFJ0;O14965 A3KFJ0 AURKA Aurora kinase A 1 RT(0.493)T(0.493)LCGT(0.013)LDYLPPEMIEGR;RT(0.494)T(0.494)LCGT(0.012)LDYLPPEMIEGR 99.387 0.00047139 95911000 91773 93692 97898 110529 117690 107219 125869 121996 163578 TRUE FALSE 87435.07217 103239.3213 102386.7201 99418.41493 138215.0987 103505.9791 106665.3723 111313.3835 188944.8408 0.462754483 0.546399261 0.541886826 0.526176923 0.731510308 0.547810561 0.564531807 0.589131638 1 17.5276056 -5 0.227908551 3.345421318 0.506539109 0.827900215 0.063456968 62.15630078 0.621779509 67.17484363 0.109432477 1.00E-05 5 -2.838882209 RTAADKDRGEEDADGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTAADKDRGEEDADGSK 17 3 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 63.918 0.021818 20444000 38314 28985 29557 36799 33514 44997 42789 42217 29330 FALSE TRUE 36502.97315 31938.60445 30912.21769 33099.89461 39358.83099 43438.74261 36260.75218 38520.25567 33878.3466 1.077472097 0.942743896 0.912447648 0.977022137 1.161769535 1.282197833 1.070322368 1.13701699 1 15.04807585 2.742436385 24.6279495 1.141834606 0.979148928 0.457286611 0.082192092 229.1515915 1456108.727 0.024659112 0.025269091 552.6324529 -2.742436385 -0.162685677 RTAFYNEDDS(ph)EEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RTAFYNEDDSEEEQR 15 1 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 RTAFYNEDDS(1)EEEQR;RTAFYNEDDS(1)EEEQR;RTAFYNEDDS(1)EEEQR;RTAFYNEDDS(1)EEEQR 224.97 6.50E-13 641790000 402071 347794 390568 405824 440580 298149 378705 383454 504720 TRUE FALSE 383065.9007 383234.604 408475.9291 365029.8005 517417.0125 287824.0254 320926.5969 349876.7349 582989.3998 0.657071811 0.657361187 0.700657558 0.626134541 0.887523877 0.493703703 0.550484446 0.600142533 1 19.15311013 -2.167668316 2.363707485 1.890002622 0.642681909 0.534618365 0.103553321 3954003.614 986382.6128 18836170.18 0.025115286 0.006797226 2.167668316 -1.247320713 RTAQEVETYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTAQEVETYR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 172.92 5.72E-06 396450000 178576 153708 149400 182765 199380 134657 168556 157699 202636 FALSE TRUE 170135.0664 169371.02 156250.1378 164393.115 234151.8089 129993.7943 142839.6865 143890.0395 234059.756 0.72688731 0.723622988 0.667565157 0.702355321 1.000393288 0.555387208 0.610270167 0.61475771 1 17.83651737 RTAQEVETYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RTAQEVETYRR 11 2 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 228.12 1.97E-12 1009155000 487803 391888 462562 479809 542713 450518 616454 497855 644558 FALSE TRUE 464745.5189 431821.8327 483770.9252 431577.6877 637361.9754 434916.4487 522402.6203 454260.1769 744512.7627 0.62422774 0.580005951 0.64978191 0.579678025 0.856079314 0.584162516 0.70167047 0.610144244 1 19.50593705 -5 0.24916882 3.130619226 0.613179416 0.635784548 0.083319517 107.2881689 1.063788881 116.425901 0.108777768 1.00E-05 5 -2.517439809 RTAS(ph)PPPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTASPPPPPK 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.245)AS(0.755)PPPPPK 80.96 0.013747 222780000 447220 380040 412440 447110 331320 439200 462730 435780 401200 TRUE FALSE 426080.7969 418766.5081 431350.782 402165.6533 389102.1031 423990.3939 392132.0399 397620.793 463416.047 0.919434706 0.903651289 0.930806744 0.867828501 0.839638821 0.91492385 0.846177085 0.858021201 1 18.82194848 3.233019564 24.97766243 0.87760162 0.915107251 0.056561059 0.046759832 249.2348713 1123490.023 0.011768924 0.014452159 1710.092349 -3.233019564 0.037505631 RTDALTS(ph)S(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 2 RT(0.025)DALT(0.416)S(0.569)S(0.99)PGR 76.868 0.022842 195100000 256950 306530 225080 279320 233560 259840 239540 247010 222480 TRUE FALSE 244804.4827 337765.7555 235400.1406 251242.2229 274292.7901 250841.6756 202993.7735 225380.4949 256981.0621 0.952616822 1.314360493 0.916021355 0.977668241 1.067365773 0.976109576 0.789917249 0.877031533 1 17.97130252 2.637898411 0.880767896 0.876011257 1.105232856 0.198646231 0.123442086 0.678174748 1.100257692 0.07844228 0.065624971 434.4085967 -2.637898411 0.229221598 RTDALTS(ph)SPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.046)S(0.477)S(0.477)PGR;RTDALT(0.126)S(0.558)S(0.315)PGR 127.32 0.00017705 2869100000 1372540 1788890 1343040 1666910 1294020 1654010 1634920 1544520 1469810 TRUE FALSE 1307662.754 1971179.925 1404619.712 1499349.04 1519696.678 1596731.219 1385482.927 1409273.641 1697740.628 0.770237063 1.161060702 0.827346468 0.883143759 0.895128887 0.940503627 0.816074554 0.830087716 1 20.69518464 RTDALTSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.018)S(0.122)S(0.859)PGR;RTDALT(0.138)S(0.202)S(0.66)PGR;RT(0.003)DALT(0.051)S(0.155)S(0.791)PGR;RTDALT(0.01)S(0.093)S(0.896)PGR 172.92 1.36E-05 1952040000 1598150 2076980 1585810 2098320 1538020 1735510 1785870 1818040 1474290 TRUE FALSE 1522608.617 2288626.623 1658520.957 1887392.887 1806250.201 1675408.854 1513402.732 1658842.78 1702915.364 0.894118786 1.343946195 0.973930351 1.108330412 1.060681135 0.9838474 0.88871283 0.974119334 1 20.6995753 2.236907945 2.70258596 0.940737335 1.09671315 0.183077607 0.117908587 0.364207102 5.465098273 0.047820761 0.034199619 172.5472115 -2.236907945 0.155975815 RTDDIPVWDQEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTDDIPVWDQEFLK 14 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 231.58 7.82E-13 595460000 1603270 1618150 1302460 1711920 1172180 1447040 1475980 1556870 1171430 FALSE TRUE 1527486.604 1783041.325 1362179.079 1539834.549 1376607.821 1396928.642 1250792.143 1420542.209 1353089.382 1.128888176 1.317755759 1.006717736 1.138013918 1.01738129 1.032399382 0.924397279 1.049850977 1 20.36782571 3.215205088 1.067143092 0.990192813 1.216459582 0.473400374 0.078062217 0.34406108 0.84297803 0.030439496 0.047136079 1641.364695 -3.215205088 0.226266769 RTDEAAFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RTDEAAFQK 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ;;;;;;;; 221.83 6.50E-07 25891660000 19522550 14022140 11837060 16154600 15133190 15558030 20269350 15847570 15207010 FALSE TRUE 18599757.75 15451012.01 12379800.91 14530708.92 17772413.54 15019251.52 17176888.39 14459872.76 17565235.44 1.058896011 0.879635918 0.704789921 0.827242479 1.011794781 0.85505552 0.977891156 0.823209732 1 24.06621958 2.761757584 24.84972934 0.929509176 0.881843494 0.083269597 0.103604657 2825.589866 3026904.045 0.032931902 0.034913131 577.7734536 -2.761757584 -0.047665683 RTDEEGKDVPDHAVLEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTDEEGKDVPDHAVLEMK 18 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 110.96 0.00019134 93213000 220980 166820 187420 217490 139460 243390 259820 258300 136020 FALSE TRUE 210534.7133 183819.1477 196013.3924 195627.492 163781.7798 234961.3433 220179.6871 235681.8827 157113.2869 1.340018515 1.169978372 1.247592716 1.245136524 1.042443851 1.495489961 1.401407172 1.500076074 1 17.26144567 2.223372177 24.9993909 1.388727295 1.21900957 0.141178636 0.158039699 342.1371305 563136.5029 0.052327174 0.03879127 167.2523302 -2.223372177 -0.169717725 RTDLCDHALHISHDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RTDLCDHALHISHDEL 16 1 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;; 188.25 4.91E-10 900814000 531893 438058 515157 609262 840903 496688 762944 473608 48963 FALSE TRUE 506751.472 482696.6082 538777.458 548017.8262 987556.217 479487.57 646542.8804 432136.3728 56555.93197 8.960182501 8.534853753 9.526453534 9.689838132 17.46158506 8.478112787 11.43191983 7.640867327 1 15.78739073 0.89763791 3.678977115 1.002671105 10.37217207 0.572549967 2.617664959 0.333944392 9.70341538 2.44141418 0.627974829 7.900196799 -0.89763791 9.369500964 RTEARS(ph)S(ph)DEENGPPSS(ph)PDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTEARSSDEENGPPSSPDLDR 21 2 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 3 RT(0.254)EARS(0.868)S(0.869)DEENGPPS(0.21)S(0.799)PDLDR 97.639 0.0003313 0 121860 110590 131770 135160 114540 116000 152860 118230 152040 TRUE FALSE 116099.9193 121859.2467 137811.7848 121573.46 134515.7397 111982.8909 129538.3995 107877.1544 175617.5867 0.661095062 0.693889769 0.784726561 0.692262445 0.765958252 0.637651918 0.737616329 0.614273072 1 17.4220778 -1.20945685 3.823203964 1.000273733 0.700270711 0.758006886 0.053539836 4070664.98 3877543.09 8191.213638 0.011239417 0.061736663 1.20945685 -0.300003022 RTEEENGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 123.79 0.00030809 86765000 197940 125510 163790 172990 100590 158160 209720 210960 162700 FALSE TRUE 188583.7685 138299.6117 171299.9335 155600.7165 118132.8642 152682.8795 177723.3622 192487.224 187930.685 1.003475129 0.735907559 0.911505928 0.827968655 0.628598061 0.812442521 0.945685704 1.024245849 1 17.51984112 1.595045594 3.53050672 1.006005993 0.821104535 0.410531009 0.098087593 0.19907249 5.778657041 0.06147581 0.025938671 39.35913942 -1.595045594 -0.184901459 RTEEGPTLSYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RTEEGPTLSYGR 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 217.12 6.00E-11 2482767000 1188630 998301 968622 1161198 1337776 981190 1255182 1163784 1456905 FALSE TRUE 1132445.816 1100029.007 1013034.277 1044472.171 1571083.711 947211.1443 1063680.933 1061876.903 1682834.387 0.67293955 0.653676331 0.60198097 0.620662484 0.933593777 0.562866526 0.632077013 0.631004995 1 20.68246177 -1.041386071 4.543863944 1.000013926 0.661501183 0.52504791 0.100532744 76625599840 16165682099 12493331.71 0.021940975 0.090910475 1.041386071 -0.338512743 RTEEPDRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTEEPDRDER 10 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ; 100.69 0.0021619 97065000 39820 38194 37138 40183 54855 34145 46013 36269 53537 FALSE TRUE 37937.78752 42086.01202 38840.81403 36143.7285 64421.69463 32962.55009 38992.87176 33093.09409 61839.24453 0.613490475 0.680571251 0.628093282 0.584478817 1.041760699 0.533036106 0.630552201 0.535147128 1 15.91623507 -1.462301449 3.230853826 1.006270483 0.656676445 0.35952708 0.144335317 41857427.1 49763517.72 2342524.221 0.032018971 0.034490425 1.462301449 -0.349594037 RTELFIAAEGIHTGQFVYCGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTELFIAAEGIHTGQFVYCGK 21 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;; 192.94 5.88E-18 525689000 734141 587884 675360 752690 631558 679270 858645 750482 650091 FALSE TRUE 699439.6099 647790.048 706325.924 677028.1712 741701.5152 655746.7096 727642.9352 684765.8175 750903.7921 0.93146368 0.862680486 0.940634381 0.901617728 0.987745065 0.873276599 0.969022853 0.911922173 1 19.51826855 -5 0.115862315 1.267407252 0.877176767 0.29069274 0.038437642 170.8582771 1.297195892 10.67420839 0.361278401 1.00E-05 5 -0.390230485 RTELS(ph)IDISSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTELSIDISSK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 RT(0.024)ELS(0.976)IDISSK 107.34 0.001354 105720000 355900 293800 294710 430020 346500 435230 466280 347970 290590 TRUE FALSE 339077.3123 323738.554 308222.745 386793.5726 406929.4903 420157.876 395140.4222 317499.9021 335653.2131 1.0102013 0.964503069 0.918277356 1.152360703 1.212350946 1.251761817 1.177228183 0.945916469 1 18.35661193 3.228862411 24.97836812 1.147814507 0.970918356 0.360949783 0.095930049 175.9072122 453060.008 0.026627621 0.032202927 1693.801103 -3.228862411 -0.176896151 RTES(ph)FHSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTESFHSYR 9 1 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 RTES(1)FHSYR;RT(0.095)ES(0.903)FHS(0.002)YR 139.77 6.78E-05 432660000 205060 178769 185156 221340 247800 209500 215390 183310 213440 TRUE FALSE 195367.2202 196985.7643 193645.5857 199090.4827 291016.2415 202244.9625 182528.2996 167258.4046 246539.1851 0.792438817 0.799003875 0.785455609 0.807540929 1.180405628 0.820335974 0.740362225 0.678425235 1 17.91145744 -1.415086568 4.336905214 1.000512687 0.823572384 0.145639763 0.132754941 0.000651976 8.79E-05 0.127345463 0.029929435 0.038451513 1.415086568 -0.176940303 RTETVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTETVQK 7 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;; 136.27 0.0048048 417094000 767430 458340 595320 691810 656260 652050 854750 744590 730810 FALSE TRUE 731155.1048 505045.3671 622616.0109 622267.9444 770711.5362 629469.345 724342.1889 679389.7523 844140.2823 0.866153553 0.598295541 0.737574102 0.73716177 0.913013574 0.745692817 0.858082719 0.80483039 1 19.68712325 0.65835563 0.343973873 1.028421322 0.721015542 0.428530439 0.084185019 2.096236498 0.571072028 0.209370836 0.083640711 4.553607881 -0.65835563 -0.307405781 RTGCIGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTGCIGAK 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 92.051 0.019325 284400000 600420 449630 461510 536280 433350 505160 637300 596890 512830 FALSE TRUE 572039.3365 495447.8082 482670.69 482372.1155 508926.1028 487666.1825 540068.1802 544623.1473 592357.0572 0.965700213 0.836400617 0.814830657 0.814326612 0.859154283 0.823263902 0.911727435 0.919416998 1 19.17610753 1.077360312 1.409266705 0.996893721 0.857413674 0.520078869 0.045222163 0.360583649 1.446631653 0.044705844 0.013502056 11.94979107 -1.077360312 -0.139480046 RTGCTFPEKPDFH ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTGCTFPEKPDFH 13 2 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 89.959 0.0040555 643330000 675610 635620 642880 724970 577970 618780 799500 733910 613120 FALSE TRUE 643675.2542 700390.4006 672356.6839 652094.6382 678767.785 597351.4934 677521.5912 669644.9497 708199.5182 0.908889709 0.98897328 0.94938879 0.920778144 0.958441467 0.843479102 0.956681802 0.945559736 1 19.43379634 0.772542892 2.168708667 0.999821456 0.934346628 0.231816652 0.038507691 1.412588338 10.57746222 0.035140635 0.009597135 5.923015817 -0.772542892 -0.065474828 RTGGPAYGPSSDVST(ph)ASETESEKREEPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTGGPAYGPSSDVSTASETESEKREEPNR 29 3 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 RTGGPAYGPSSDVS(0.091)T(0.451)AS(0.451)ET(0.004)ES(0.003)EKREEPNR 127.31 1.97E-05 99201000 52317 48901 50440 64627 41286 63505 60772 65375 52837 TRUE FALSE 49844.07909 53884.0675 52752.72389 58130.57118 48486.26533 61305.80593 51500.11525 59650.41843 61030.69211 0.816705126 0.882901138 0.864363848 0.952480943 0.794457078 1.004507795 0.843839607 0.977383942 1 15.89724733 7.999999209 0.026513448 1.537331979 2.17E-06 0.361577984 0.060914459 1746.757738 3.559247329 69.32868002 151.8860799 99999817.87 -7.999999209 -1.537329807 RTHEHVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTHEHVSEK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ;; 84.17 0.010174 26686300 97416 66036 80695 90113 114517 83735 134130 97704 7358.3 FALSE TRUE 92811.33874 72765.14348 84394.94557 81054.67004 134488.7285 80835.23595 113666.005 89148.5198 8499.387583 10.91976779 8.561221943 9.929532539 9.536530632 15.82334341 9.510712997 13.37343472 10.48881686 1 13.05314318 0.943653784 22.53053316 0.999999989 10.99896202 0.689126139 2.117621701 4109.950646 1643402.507 1.985634988 0.496408747 8.783220468 -0.943653784 9.998962032 RTHS(ph)DAS(ph)DDEAFTTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.007)HS(0.993)DAS(1)DDEAFTTSK 198.83 1.39E-10 504490000 549080 443620 544660 563370 435130 511280 647030 585040 430780 TRUE FALSE 523126.0766 488825.3824 569633.1997 506738.9773 511016.5342 493574.2454 548313.69 533810.7961 497583.1623 1.05133396 0.982399364 1.144799991 1.018400572 1.02699724 0.991943222 1.101953867 1.072807194 1 18.92457814 1.730554456 24.99999675 1.067321008 1.034141057 0.030498516 0.050617636 1.851980375 5749.468243 0.021938361 0.012165928 53.77178535 -1.730554456 -0.033179951 RTHS(ph)EGSLLQEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RTHSEGSLLQEPR 13 1 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RT(0.083)HS(0.917)EGSLLQEPR;RT(0.008)HS(0.991)EGS(0.001)LLQEPR;RT(0.141)HS(0.859)EGSLLQEPR;RT(0.1)HS(0.9)EGSLLQEPR 196.24 8.78E-08 2301150000 1777440 1258010 1616170 1666550 1815660 1585880 2141900 1704680 1869910 TRUE FALSE 1693423.934 1386202.649 1690272.993 1499025.228 2132310.529 1530960.578 1815113.816 1555409.182 2159886.093 0.784033908 0.641794331 0.782575062 0.694029761 0.987232862 0.708815425 0.840374788 0.72013482 1 21.0425238 -5 0.146538811 1.817157633 0.68903981 0.358755207 0.095501941 134.7469969 1.185558758 32.15221611 0.46539573 1.00E-05 5 -1.128117823 RTIAPCQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTIAPCQK 8 1 P38646;H0YBG6 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 110.88 0.005356 739160000 945080 723010 765080 832510 773350 806210 989900 967570 840850 FALSE TRUE 900407.9414 796685.541 800159.6748 748824.5131 908221.9951 778290.7455 838872.5742 882844.4414 971244.7235 0.92706598 0.82027271 0.823849701 0.770994678 0.935111381 0.801333306 0.863708758 0.908982484 1 19.88947533 0.945047102 2.164692333 0.999500459 0.848192567 0.479896673 0.051009172 0.303672105 3.089916641 0.045398755 0.012505352 8.811444335 -0.945047102 -0.151307892 RTIAQDYGVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTIAQDYGVLK 11 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 77.597 0.051601 358800000 522060 429550 378560 379800 391850 429980 526280 476650 400120 FALSE TRUE 497383.2584 473321.6334 395917.3504 341621.7824 460188.5159 415089.6848 445986.3202 434911.9991 462168.5661 1.076194477 1.024132033 0.856651403 0.739171392 0.99571574 0.898134826 0.964986269 0.94102462 1 18.81805961 3.891530229 4.929584432 0.911214032 1.05747293 0.364061064 0.07604683 0.211580419 7.838956392 0.019420242 0.036187779 7789.870338 -3.891530229 0.146258897 RTIQEVLEEQS(ph)EDEDREAK ddPTM_SK-BR-3_Trastuzumab_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 226.14 8.20E-20 509481000 214038 213706 212583 242516 188155 251460 284820 278880 236359 TRUE FALSE 203920.8479 235482.8844 222330.1408 218137.8309 220969.1724 242751.8771 241365.4779 254459.7888 273012.3466 0.746929033 0.862535659 0.81435929 0.799003538 0.809374284 0.889160802 0.884082647 0.932044986 1 18.05860667 1.400710977 0.637546276 1.001215057 0.800745434 0.823415958 0.030489035 0.273156286 0.25841759 0.029025072 0.013675238 25.16001972 -1.400710977 -0.200469623 RTIQEVLEEQS(ph)EDEDREAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTIQEVLEEQSEDEDREAKR 20 3 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDREAKR 103.53 0.0002026 208310000 49238 43081 53051 49318 59731 46262 72393 54705 81573 TRUE FALSE 46910.61732 47471.00288 55483.44082 44360.46094 70148.06749 44659.93534 61348.11826 49914.74019 94222.92422 0.497868408 0.503815852 0.588852886 0.470803271 0.744490452 0.473981631 0.651095461 0.52975155 1 16.52379049 -5 0.229386937 3.385613886 0.504307715 0.728421556 0.085170159 73.69961868 0.73713351 81.57003318 0.127819653 1.00E-05 5 -2.881306172 RTIQFVDWCPTGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTIQFVDWCPTGFK 14 1 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 101.01 0.0024976 199090000 562390 484840 512950 507770 442990 552370 610440 618020 562830 FALSE TRUE 535806.9392 534245.7472 536469.2649 456727.9949 520247.3157 533241.2884 517306.1665 563902.8925 650110.8019 0.824177875 0.821776451 0.825196664 0.702538696 0.800244073 0.820231393 0.795719999 0.867395052 1 19.3103261 0.878194665 2.345151067 0.999938395 0.800542915 0.759322337 0.036127612 0.233682137 2.603429386 0.034360072 0.009310447 7.55430761 -0.878194665 -0.19939548 RTLDS(ph)DEERPRPAPPDWSHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTLDSDEERPRPAPPDWSHMR 21 3 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 RT(0.081)LDS(0.919)DEERPRPAPPDWSHMR;RT(0.224)LDS(0.776)DEERPRPAPPDWSHMR 97.059 0.00084723 199136000 55735 26825 55094 40728 68532 47224 76113 58245 160395 TRUE FALSE 53100.51701 29558.498 57620.1144 36633.94406 80483.9591 45588.62104 64500.56394 53144.75902 185268.2374 0.28661425 0.159544336 0.311009136 0.197734618 0.43441855 0.246068196 0.348146908 0.28685305 1 17.49925604 -5 0.286954142 6.540682681 0.233932745 0.902843868 0.074039309 61.23882771 0.5797448 202.7004878 0.071516919 1.00E-05 5 -6.306749936 RTLEGELHDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 158.06 1.97E-05 1549780000 935120 704880 733830 892630 938870 746960 967050 857610 887320 FALSE TRUE 890918.7308 776708.0734 767476.8314 802901.1365 1102608.631 721092.5879 819508.7614 782513.1219 1024921.054 0.869255956 0.757822342 0.748815559 0.783378518 1.075798596 0.703559152 0.799582327 0.76348624 1 19.96708136 -2.215280063 2.379267435 1.61626732 0.810537839 0.247042409 0.102694583 6533725.766 1162824.174 21788787.46 0.023029052 0.00609144 2.215280063 -0.805729481 RTLS(ph)MDKGF ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTLSMDKGF 9 2 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 RTLS(1)MDKGF;RT(0.001)LS(0.999)MDKGF 171.62 4.47E-05 453980000 660090 378460 427600 657350 589450 746460 943830 469770 602520 TRUE FALSE 628888.8539 417025.5043 447205.883 591271.9291 692249.8934 720609.903 799831.3989 428634.4484 695955.7244 0.903633424 0.599212694 0.642578065 0.84958268 0.994675191 1.035424924 1.149256154 0.615893272 1 19.408636 2.961386573 3.517425624 0.988225725 0.717973633 0.323912626 0.157157306 0.240872895 6.135817434 0.047427192 0.053184331 914.9272707 -2.961386573 -0.270252092 RTNPPGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 81.95 0.034528 271580000 376170 326790 323460 400870 288040 357400 416610 377320 362290 FALSE TRUE 358389.1896 360090.2725 338290.9609 360573.786 338274.0848 345023.1484 353048.4929 344279.8605 418472.0829 0.856423174 0.86048816 0.808395529 0.861643586 0.808355201 0.824483072 0.843660802 0.822706877 1 18.67477186 -1.310102162 3.473527747 1.000648377 0.838251415 0.868660034 0.020048547 6960624.855 9872526.235 46124.94169 0.004743376 0.048966362 1.310102162 -0.162396962 RTNST(ph)GGSSGSSVGGGSGK ddPTM_SK-BR-3_Trastuzumab_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(0.06)NS(0.221)T(0.33)GGS(0.302)S(0.08)GS(0.006)SVGGGSGK 110.06 0.00030916 0 157950 125020 146350 166430 132810 148410 187190 162760 158680 TRUE FALSE 150484.0165 137759.6801 153060.2923 149700.1402 155972.022 143270.5245 158630.7275 148507.8716 183287.284 0.821028133 0.751605224 0.835084076 0.81675137 0.850970229 0.781671927 0.865475903 0.810246452 1 17.48374717 -5 0.21046489 1.901741531 0.787363424 0.765504157 0.032004762 62.93120284 0.627201606 23.91364508 0.061746967 1.00E-05 5 -1.114378106 RTNSTGGS(ph)SGSSVGGGSGK ddPTM_SK-BR-3_Trastuzumab_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(0.188)NS(0.188)T(0.239)GGS(0.305)S(0.072)GS(0.006)S(0.002)VGGGSGK;RT(0.094)NS(0.072)T(0.123)GGS(0.581)S(0.123)GS(0.006)S(0.001)VGGGSGK 81.312 0.0037091 100843000 96515 81498 86378 102735 85466 97228 111967 91531 96042 TRUE FALSE 91952.92722 89802.73886 90338.51674 92407.88262 100371.2433 93860.96998 94884.37773 83516.0604 110935.7028 0.828884884 0.809502591 0.814332216 0.832985957 0.904769527 0.846084422 0.855309655 0.752833022 1 16.75936422 -1.402848025 3.204675255 1.002034488 0.832774245 0.659433401 0.038232877 29621105.8 41517595.84 562225.0827 0.008886117 0.0395505 1.402848025 -0.169260242 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR 196.68 1.06E-21 1530960000 710743 556630 714424 709835 790609 691939 853298 758213 949334 TRUE FALSE 677147.5869 613351.2298 747181.0471 638481.0372 928490.9593 667976.9789 723111.7182 691819.8502 1096551.868 0.617524448 0.559345388 0.681391431 0.582262505 0.846736927 0.609161316 0.659441417 0.630904812 1 20.06454262 -5 0.25247304 3.190841482 0.61093524 0.660137684 0.079072241 107.2938507 1.061112017 121.5359307 0.104207177 1.00E-05 5 -2.579906241 RTPDGTENGDFLALDLGGTNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTPDGTENGDFLALDLGGTNFR 22 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 219.16 1.80E-25 393825000 416433 266951 352304 390506 463307 335533 434621 350374 510087 FALSE TRUE 396749.0374 294153.6104 368457.4869 351251.595 544107.5941 323913.4081 368311.5841 319693.3951 589188.6868 0.673381968 0.499251966 0.625364158 0.596161472 0.923486154 0.549761758 0.625116524 0.542599344 1 19.1683702 -2.019196877 2.853624292 1.425972999 0.624509322 0.502749579 0.115742161 24893808.63 10044859.77 69782666.96 0.026380956 0.009567602 2.019196877 -0.801463677 RTPDS(ph)TFSETFKEGVQEVFFPSDLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTPDSTFSETFKEGVQEVFFPSDLSLR 27 2 Q9NZI5-3;Q9NZI5 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.037)PDS(0.451)T(0.451)FS(0.053)ET(0.007)FKEGVQEVFFPSDLSLR;RT(0.004)PDS(0.717)T(0.144)FS(0.067)ET(0.067)FKEGVQEVFFPSDLSLR 207.7 1.81E-25 160641000 193936 97144 187997 151539 156277 168818 269160 203262 209305 TRUE FALSE 184769.0296 107043.084 196616.8484 136306.0118 183531.6593 162971.7903 228094.6985 185463.3017 241762.9504 0.76425701 0.442760497 0.813262942 0.56380025 0.759138896 0.674097458 0.943464241 0.767128716 1 17.88323365 1.727498702 0.67843738 0.97521731 0.621038909 0.444961259 0.121477942 0.527233694 0.494228062 0.101834779 0.051280093 53.39476782 -1.727498702 -0.354178401 RTPDSTFS(ph)ETFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RTPDS(0.02)T(0.22)FS(0.76)ETFK 225.33 1.90E-11 278460000 618650 648390 490130 713630 358440 638250 583560 637530 344960 TRUE FALSE 589407.6405 714461.6782 512602.9453 641894.5566 420951.8225 616147.2425 494527.2042 581704.4934 398454.635 1.479233993 1.793081609 1.286477557 1.610960195 1.056461101 1.546342264 1.241112942 1.459901435 1 18.60405595 0.642503569 0.059800328 2.01E-15 2.506994568 0.361872298 0.196517517 49.65707323 1.459904691 33.68266137 26.27539279 4.390394736 -0.642503569 2.506994568 RTPS(ph)DDEEDNLFAPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.087)PS(0.913)DDEEDNLFAPPK;RT(0.022)PS(0.978)DDEEDNLFAPPK;RT(0.115)PS(0.885)DDEEDNLFAPPK 229.15 2.11E-15 566909000 973200 949350 885530 1094360 670190 1036320 1031610 1058340 743040 TRUE FALSE 927198.7647 1046089.844 926132.4264 984352.8537 787070.9238 1000431.979 874218.9477 965666.139 858266.8483 1.08031525 1.218839859 1.079072818 1.146907696 0.917046866 1.165642108 1.01858641 1.12513508 1 19.71106675 RTPS(ph)EADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.196)PS(0.804)EADR;RT(0.137)PS(0.863)EADR;RT(0.042)PS(0.958)EADR;RT(0.026)PS(0.974)EADR 98.156 0.0047299 548378000 722937 674638 621862 719790 636358 564696 664177 634889 507565 TRUE FALSE 688765.2007 743384.3792 650374.9878 647435.3417 747338.6337 545140.4359 562844.6002 579294.7534 586275.5879 1.174814737 1.267977713 1.109333224 1.104319121 1.274722416 0.929836492 0.960034175 0.988092913 1 19.16121946 2.230505892 24.99994558 0.964206706 1.189123485 0.774451462 0.05807912 79.98230838 248243.9236 0.021368936 0.016057231 170.0223019 -2.230505892 0.224916779 RTPS(ph)TKPTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.001)PS(0.807)T(0.191)KPTVR;RT(0.069)PS(0.913)T(0.017)KPT(0.001)VR;RT(0.003)PS(0.994)T(0.003)KPTVR 134.04 0.00014264 1459820000 1670110 1288060 1326390 1599600 1336270 1344630 1676660 1553060 1478530 TRUE FALSE 1591167.21 1419314.778 1387206.293 1438805.169 1569315.065 1298065.126 1420854.723 1417065.833 1707812.881 0.931698799 0.831071597 0.812270658 0.842484083 0.918903401 0.760074561 0.831973303 0.82975474 1 20.70371848 -1.750259385 6.947684892 1.002849854 0.84513914 0.494806709 0.049289423 0.002167324 7.79E-05 0.047538492 0.011025254 0.017772176 1.750259385 -0.157710713 RTQAPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RTQAPTK 7 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ;;;;; 166.52 0.0017966 1582223000 2875330 1930138 1312064 1704199 2642160 1902917 3539270 2629420 3156510 FALSE TRUE 2739418.849 2126821.257 1372223.432 1532889.679 3102951.867 1837018.507 2999289.358 2399174.045 3646005.45 0.751347985 0.583329149 0.376363517 0.420429892 0.851055192 0.503844147 0.822623389 0.658028102 1 21.79788529 0.858896733 0.638168091 0.997134711 0.579589031 0.413953224 0.152023766 0.977591962 0.881684961 0.154488467 0.061519677 7.225979631 -0.858896733 -0.41754568 RTQAPTKAS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RTQAPTKASE 10 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E 167.59 4.09E-06 1245520000 1178387 971481 1034676 1256376 922876 1247780 1401338 1257087 1014859 TRUE FALSE 1122686.982 1070476.018 1082116.918 1130082.698 1083825.282 1204569.066 1187538.151 1147009.798 1172238.151 0.957729435 0.913189882 0.923120372 0.964038491 0.924577725 1.027580501 1.013051956 0.978478475 1 20.16083427 2.242874247 24.99999926 1.007410927 0.935916134 0.75186229 0.019453954 49.27588523 285584.0286 0.006677695 0.005404504 174.9340083 -2.242874247 -0.071494793 RTS(ph)DPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSDPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK 35 1 H7C3A2;Q8NHH9-2;Q8NHH9 H7C3A2 ATL2 Atlastin-2 1 RT(0.211)S(0.589)DPS(0.09)AAVNHVS(0.021)S(0.021)T(0.021)T(0.021)S(0.021)LGENY(0.004)EDDDLVNSDEVMK 86.324 0.00033986 74418000 21010 19659 17858 29857 18380 21939 20664 22318 16909 TRUE FALSE 20016.89894 21662.27445 18676.80696 26855.71764 21585.46618 21179.24693 17511.32728 20363.7176 19531.16136 1.024869877 1.109113485 0.956256856 1.375018983 1.105180884 1.084382364 0.896584026 1.042627073 1 14.25349012 1.899614262 6.816761886 0.971780653 1.10873929 0.231048358 0.111902997 0.358553538 20.93018589 0.046466287 0.028642687 79.36230303 -1.899614262 0.136958637 RTS(ph)EEDTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSEEDTPK 9 1 A0A1B0GW41;Q8WYH8-2;Q8WYH8 A0A1B0GW41 ING5 Inhibitor of growth protein 5 1 RT(0.318)S(0.615)EEDT(0.066)PK;RT(0.15)S(0.822)EEDT(0.028)PK 116.81 0.00082856 0 455371 372715 391694 465091 284670 441390 464618 459711 320016 TRUE FALSE 433846.5153 410695.0822 409653.5573 418339.1691 334316.3579 426104.5536 393731.9908 419456.2678 369642.4469 1.173692359 1.111060393 1.108242738 1.131740071 0.90443173 1.152747898 1.065169853 1.134762177 1 18.49577091 3.979530821 0.967775883 1.067405889 1.174020697 0.193910566 0.072402266 1.299610487 1.955053235 0.02364779 0.112636802 9539.614404 -3.979530821 0.106614808 RTS(ph)FSFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.144)S(0.856)FSFQK 135.08 0.00051999 596730000 645030 574750 575370 690320 565160 590920 729990 669950 610690 TRUE FALSE 614540.7102 633317.6784 601751.2836 620927.7221 663723.7251 570456.2922 618616.6183 611285.6264 705392.6862 0.871203689 0.897822859 0.853072757 0.880258237 0.940927994 0.80870741 0.8769819 0.866589119 1 19.42806709 -1.305526833 3.248562146 1.000681641 0.875065075 0.586911476 0.033099577 11427046.6 16965717.3 77970.26216 0.007267848 0.049484954 1.305526833 -0.125616566 RTS(ph)FSTSDVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.177)S(0.75)FS(0.07)T(0.003)S(0.001)DVSK;RT(0.209)S(0.775)FS(0.015)TSDVSK 147.51 2.16E-05 1208700000 2081720 1772690 1678230 2096140 1712330 1938900 2622630 2320910 2145440 TRUE FALSE 1983321.221 1953329.126 1755178.505 1885432.025 2010959.81 1871755.407 2222499.626 2117678.816 2478143.878 0.800325291 0.788222647 0.708263358 0.760824277 0.811478231 0.755305381 0.896840432 0.854542319 1 21.24082852 1.137653536 0.81932721 0.99495956 0.769127847 0.786040053 0.038124006 0.260893512 0.395528157 0.035019075 0.01303975 13.72946252 -1.137653536 -0.225831713 RTS(ph)NERPGSGQGQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.235)S(0.765)NERPGSGQGQGR;RT(0.37)S(0.629)NERPGSGQGQGR;RT(0.444)S(0.556)NERPGSGQGQGR;RT(0.376)S(0.624)NERPGSGQGQGR;RT(0.2)S(0.8)NERPGSGQGQGR 238.72 4.63E-18 2917981000 481819 424563 417564.2 513191 494698.3 405526.4 473415.1 449413.9 477575 TRUE FALSE 459044.3707 467826.4524 436709.9316 461604.0657 580973.5269 391482.9191 401186.9316 410060.8364 551634.8919 0.83215253 0.848072628 0.791664809 0.836792727 1.053184879 0.709677587 0.727268955 0.74335551 1 19.07335419 RTS(ph)SEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.039)S(0.958)S(0.004)EELR;RT(0.054)S(0.936)S(0.01)EELR 142.47 0.00037789 228550000 193101 221241 171213 230630 190944 211574 192462 207952 180228 TRUE FALSE 183973.4984 243785.7094 179063.2854 207446.6342 224244.5731 204247.1393 163098.3871 189742.6205 208176.8378 0.883736637 1.171051074 0.860149896 0.996492388 1.077183108 0.981123268 0.783460777 0.911449239 1 17.66745003 1.941099898 10.50612302 0.876077805 1.00671671 0.153536251 0.102126262 0.955212866 167.6318957 0.039805724 0.025393772 87.3172196 -1.941099898 0.130638905 RTS(ph)SEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.12)S(0.695)S(0.182)EELRDAT(0.001)S(0.002)LLAAGEGGLLDEVEPLRPDELER;RT(0.016)S(0.497)S(0.117)EELRDAT(0.35)S(0.019)LLAAGEGGLLDEVEPLRPDELER 324.34 8.48E-105 129287000 23590.1 13606.4 25882 21047.6 27102 21528.7 29950 26291 39436 TRUE FALSE 22475.04272 14992.90763 27068.7153 18931.85526 31828.58022 20783.15572 25380.57743 23988.82066 45551.53347 0.493398158 0.329141666 0.594243777 0.415614005 0.698737843 0.456255896 0.55718382 0.526630364 1 15.475212 -5 0.20241993 3.322000215 0.417802423 0.719208399 0.097448629 68.40726796 0.67807946 64.21841641 0.205342201 1.00E-05 5 -2.904197791 RTS(ph)SPHKEESPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSSPHKEESPKK 13 3 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.037)S(0.763)S(0.2)PHKEESPKK 73.498 0.026166 88263000 92102 75817 69755 86161 47248 90921 97944 92711 45717 TRUE FALSE 87748.52099 83542.8385 72953.33575 77499.93258 55488.03624 87772.38297 83000.84394 84592.73335 52806.55887 1.661697389 1.582054205 1.381520351 1.467619444 1.050779248 1.662149264 1.571790431 1.601936107 1 15.68842951 3.89010038 3.833597458 1.429026722 1.635233788 0.146165344 0.220287756 0.451712406 11.80273495 0.054765258 0.106091208 7764.265537 -3.89010038 0.206207065 RTS(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSSPPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.045)S(0.477)S(0.477)PPR;RT(0.035)S(0.482)S(0.482)PPR 75.378 0.026725 122640000 51802.8 42972.4 38541.9 56107.5 59444 48520.3 70102 57637.8 63013 TRUE FALSE 49354.18431 47351.33642 40309.08424 50467.4675 69811.01478 46840.02984 59406.65239 52590.72867 72784.73421 0.678084283 0.650566866 0.553812344 0.693379842 0.959143638 0.643541951 0.816196597 0.722551635 1 16.15134827 -4.999999864 0.10114919 1.96898692 0.508800224 0.48514237 0.101290108 150.4882687 1.033089551 30.36657583 1.554083061 1.00E-05 4.999999864 -1.460186696 RTS(ph)VPSPEQPQPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 RT(0.141)S(0.859)VPSPEQPQPYR 123.19 6.39E-05 136150000 48538 56341 49539 53184 60881 54405 61545 49225 57439 TRUE FALSE 46243.70493 62082.21195 51810.41215 47837.84328 71498.62712 52520.94121 52155.1799 44914.59804 66346.34676 0.69700454 0.935729169 0.780908289 0.721032063 1.077657333 0.791617682 0.786104774 0.676971683 1 16.01772941 4.729170962 4.612192934 0.836912089 0.689614063 0.119157723 0.125216287 0.394714386 20.00956271 0.027676453 0.18097618 53600.76172 -4.729170962 -0.147298026 RTSS(ph)EELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.301)S(0.301)S(0.392)EELRDAT(0.003)S(0.003)LLAAGEGGLLDEVEPLRPDELER 171.03 3.21E-14 68561000 3201.8 1713.7 1873.2 4235.8 3753.1 2019.5 3855.7 4018.7 3713.1 TRUE FALSE 3050.457259 1888.327978 1959.088073 3810.009337 4407.639452 1949.564209 3267.44215 3666.801324 4288.908584 0.711243245 0.440281704 0.456780096 0.888340066 1.027683236 0.454559516 0.761835345 0.85494975 1 12.06639485 0.949250669 0.173038889 1.161380194 0.451272062 0.27099936 0.18834423 7.175756243 0.912411 1.867289783 1.226204335 8.89714502 -0.949250669 -0.710108132 RTSS(ph)KSEAGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RTSSKSEAGAR 11 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RT(0.067)S(0.197)S(0.588)KS(0.148)EAGAR;RT(0.125)S(0.125)S(0.686)KS(0.065)EAGAR 68.033 0.045949 99857000 111497 68481 114149 95638 84665 107546 149592 118351 119038 TRUE FALSE 106226.7578 75459.29176 119382.8446 86024.28654 99430.54919 103821.6551 126768.993 107987.559 137497.8051 0.772570571 0.54880361 0.868252729 0.625641162 0.72314281 0.755078636 0.92197103 0.785376603 1 17.06904906 1.528131344 0.631585525 0.98472843 0.678840599 0.470183934 0.096296158 0.528136524 0.472171325 0.085129341 0.042191899 33.73893298 -1.528131344 -0.305887831 RTSS(ph)PPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.155)S(0.155)S(0.69)PPRK 52.49 0.074398 301900000 9177.6 8345 11836 12811 13629 12008 12977 13370 14918 TRUE FALSE 8743.793036 9195.364987 12378.69231 11523.21394 16005.89328 11592.15995 10997.12031 12199.25192 17231.40725 0.507433485 0.533639816 0.71837965 0.66873319 0.928879055 0.672734373 0.638202101 0.707966085 1 14.07275291 0.748991379 0.066738973 1.578035967 5.01E-20 0.563140653 0.101547917 31.91915882 1.154714813 14.89052191 11.6685279 5.610368384 -0.748991379 -1.578035967 RTSSTENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTSSTENK 8 1 Q9Y2K7-5 Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 107.43 0.082104 1221300000 1273500 1116100 906310 1010800 930150 1029900 1339000 1095400 973930 FALSE TRUE 1213304.179 1229831.859 947865.21 909192.4636 1092367.866 994234.3048 1134710.958 999480.9689 1124962.09 1.078528947 1.093220713 0.842575246 0.808198313 0.971026379 0.883793608 1.008665952 0.888457467 1 20.10144495 3.753187466 24.79806973 0.916720419 1.085874854 0.547852693 0.064639221 495.5310366 840110.7909 0.016419677 0.029429506 5664.83763 -3.753187466 0.169154435 RTT(ph)GAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RTTGAK 6 1 I3L2A8;Q6NT04-2;Q6NT04 I3L2A8 TIGD7 Tigger transposable element-derived protein 7 1 RT(0.04)T(0.96)GAK 54.765 0.094295 423540000 954770 1036700 825600 1165100 667440 1026300 936850 932510 411290 TRUE FALSE 909639.9143 1142340.909 863454.5766 1047981.934 783841.3247 990758.9737 793916.3261 850854.4809 475070.7526 1.914746191 2.404570061 1.817528383 2.205949174 1.649946498 2.085497725 1.671153869 1.791005816 1 18.85778287 -0.273690135 0.267894048 0.593232748 2.194967399 0.692508072 0.210068381 3.98790089 0.385613111 1.766695345 0.290137253 0.532488049 0.273690135 1.601734651 RTTS(ph)FFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RTTSFFSR 8 1 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 RT(0.294)T(0.21)S(0.496)FFSR;RT(0.136)T(0.3)S(0.563)FFSR;RT(0.013)T(0.039)S(0.948)FFSR 111.26 0.0020019 606730000 138440 113605 129567 150927 167459 115669 144231 136195 166795 TRUE FALSE 131896.2156 125181.4787 135507.7751 135755.5312 196663.7966 111663.3535 122225.912 124269.0438 192660.7167 0.684603576 0.649750924 0.703349273 0.704635244 1.020777873 0.579585478 0.634410138 0.645014956 1 17.55570291 -2.245842481 2.21135039 2.061900109 0.696361338 0.379649443 0.119156838 4198321.904 731484.373 22272814.61 0.031036684 0.005677505 2.245842481 -1.365538772 RTVQSLEIDLDSMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 233.4 5.57E-17 3364726000 2843255 2257920 2595898 2645179 3042633 2527389 3273822 2945142 3344290 FALSE TRUE 2708859.971 2488004.615 2714922.491 2379280.581 3573267.232 2439864.885 2774340.326 2687249.753 3862905.413 0.701249366 0.644075987 0.702818786 0.615930324 0.925020639 0.631613934 0.718200429 0.695655075 1 21.88125492 -5 0.305700217 3.580924358 0.685436613 0.540754168 0.085549889 204.9936367 1.873520841 340.0272723 0.074487257 1.00E-05 5 -2.895487745 RVAFISLS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVAFISLSPVR 11 1 Q6ZU65;Q6ZU65-2 Q6ZU65 UBN2 Ubinuclein-2 1 RVAFIS(0.001)LS(0.999)PVR;RVAFIS(0.005)LS(0.995)PVR 128.22 0.00049805 259300000 186560 100398 61773 74511 216161 86348 219114 128329 231058 TRUE FALSE 177741.6785 110628.6703 64605.35315 67021.01272 253859.41 83357.74711 185684.135 117091.8324 266889.2946 0.665975302 0.414511457 0.242067983 0.25111915 0.951178691 0.312330801 0.695734669 0.438728098 1 18.02588191 -1.268894543 0.354906144 1.291757643 0.465104643 0.338505618 0.22182147 21.85473535 1.786574919 6.211829019 0.163156955 0.05384005 1.268894543 -0.826652999 RVASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 33 1 Q14764 Q14764 MVP Major vault protein 1 RVASGPS(0.003)PGEGIS(0.997)PQSAQAPQAPGDNHVVPVLR;RVAS(0.039)GPS(0.039)PGEGIS(0.914)PQS(0.008)AQAPQAPGDNHVVPVLR 157.86 2.25E-12 126745000 36585 24518 34537 33555 39499 30329 37294 32538 45131 TRUE FALSE 34855.69955 27016.41207 36120.55561 30181.98765 46387.61309 29278.69913 31604.11535 29688.80023 52129.68498 0.668634379 0.518253891 0.692898022 0.5789789 0.889850248 0.561651181 0.606259473 0.569518121 1 15.66981752 -1.211411651 3.554903757 1.000555374 0.629722658 0.548132653 0.103805727 209613215.5 330163293.8 1348157.907 0.023238122 0.061459405 1.211411651 -0.370832716 RVDAENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 6226051000 2900329 2258860 2181424 2698052 3006180 2388809 2961203 2548337 3152263 FALSE TRUE 2763236.196 2489040.402 2281444.448 2426838.687 3530456.84 2306083.945 2509417.096 2325191.103 3641099.847 0.758901517 0.683595756 0.626581128 0.666512534 0.969612751 0.633348176 0.689192058 0.638595809 1 21.79594287 -1.761110743 2.646624739 1.067983634 0.708425508 0.45466829 0.100399779 22237166.02 16575113.34 9833683.693 0.022639682 0.017333619 1.761110743 -0.359558126 RVDALNDEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVDALNDEIR 10 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 165.78 9.22E-06 114333000 248580 177221 191955 190247 269300 195494 245080 253480 517860 FALSE TRUE 236830.116 195280.0214 200756.3266 171123.0101 316265.8347 188723.9938 207688.5448 231283.9474 598167.0839 0.39592636 0.326464004 0.335619147 0.286078948 0.528724905 0.31550381 0.347208247 0.386654421 1 19.190189 0.692527049 4.433239049 0.999999674 0.360303631 0.901725304 0.065897831 3.1326488 44.97017942 0.057925152 0.014714639 4.926370254 -0.692527049 -0.639696042 RVDAYDRPELSLGSYEFLATVDYCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVDAYDRPELSLGSYEFLATVDYCK 25 2 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ; 70.76 0.02158 176401000 139424 96953 130318 141737 124086 136005 152881 141744 135518 FALSE TRUE 132833.7038 106832.6209 136293.2092 127489.3275 145726.5591 131295.1127 129556.1956 129332.1439 156533.4393 0.848596341 0.682490728 0.870697084 0.814454266 0.930961204 0.838767188 0.82765827 0.826226936 1 17.25611136 -5 0.127606697 1.583613971 0.744631576 0.425193078 0.061896794 132.9975641 1.077882538 19.95977535 0.487081007 1.00E-05 5 -0.838982395 RVDIIPGFEFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RVDIIPGFEFDR 12 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 179.5 3.31E-05 2316820000 1491520 1339567 1360614 1559751 1620480 1341338 1570367 1536703 1640190 FALSE TRUE 1421018.806 1476070.4 1422999.498 1402961.866 1903091.199 1294887.129 1330778.672 1402141.139 1894542.288 0.750059164 0.779117156 0.751104637 0.740528134 1.004512388 0.683482832 0.702427537 0.740094928 1 20.85341791 -2.177600483 2.367073291 1.616694503 0.765802455 0.404670544 0.088012728 5008294.375 1362513.59 16509471.93 0.021676836 0.006643539 2.177600483 -0.850892047 RVEDAYILTCNVSLEYEKTEVNSGFFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVEDAYILTCNVSLEYEKTEVNSGFFYK 28 2 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 340.65 1.22E-96 452597000 414821 375696 416198 445826 405591 436973 574624 463859 495987 FALSE TRUE 395213.2334 413979.8495 435281.09 401010.7235 476325.942 421840.5154 486954.5551 423241.0469 572902.1308 0.689844237 0.722601344 0.759782634 0.699963749 0.831426375 0.736322127 0.849978607 0.738766753 1 19.12792918 -4.999999999 0.124887989 1.832543701 0.638347046 0.760470303 0.045497554 60.85548979 0.486323751 12.67638706 0.33360375 1.00E-05 4.999999999 -1.194196655 RVEEELEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVEEELEKR 9 2 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 70.488 0.029397 31145000 55033 54841 51731 61884 72231 54051 65674 57471 70519 FALSE TRUE 52431.69915 60429.36025 54102.91752 55663.30275 84828.06353 52179.20032 55654.22511 52438.53457 81454.72636 0.643691306 0.741876659 0.66420845 0.683364922 1.041413646 0.640591438 0.683253478 0.643775222 1 16.31371079 -2.376747662 2.277296187 3.043661731 0.716598494 0.357005571 0.11902414 5220935.114 366037.7567 55678558.2 0.028254739 0.004200029 2.376747662 -2.327063237 RVEELQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVEELQNR 8 1 P22736;F5GXF0;P22736-2 P22736 NR4A1 Nuclear receptor subfamily 4 group A member 1 0 80.755 0.03949 67467000 42205 52146 43296 58244 46871 49465 51605 57783 42926 FALSE TRUE 40210.05329 57459.73669 45281.16443 52389.20246 55045.28756 47752.01465 43731.70946 52723.21419 49582.74484 0.810968683 1.158865587 0.913244407 1.056601498 1.110170236 0.963077272 0.881994524 1.063337949 1 15.59755052 -2.297818217 9.179132426 5.469569379 0.991748138 0 0.106976122 0.57720254 0.018727423 0.006110057 0.023081711 0.005037114 2.297818217 -4.477821242 RVEELVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVEELVAK 8 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 89.029 0.022762 116860000 278860 267430 249760 328780 253550 297830 330900 361540 319130 FALSE TRUE 265678.8404 294681.421 261211.743 295730.4098 297769.0397 287516.0724 280415.1276 329881.641 368619.0505 0.720740939 0.799419945 0.708622473 0.802265671 0.807796123 0.779981588 0.760717948 0.894912079 1 18.49177111 1.038913347 2.957345237 0.999158262 0.768430686 0.846194704 0.033337684 0.079783384 1.531736154 0.030036054 0.007963098 10.93738115 -1.038913347 -0.230727576 RVEHHDHAVVSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVEHHDHAVVSGR 13 1 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 61.038 0.056645 4289700 2597.8 1028 1822.9 2610 4001.3 2400.1 2328.8 1982.9 811.33 FALSE TRUE 2475.007142 1132.754369 1906.481768 2347.637841 4699.125453 2316.983935 1973.498789 1809.266764 937.1469127 2.64100229 1.208726565 2.034346741 2.505090514 5.014288997 2.472380695 2.105858497 1.930611668 1 9.872131421 3.247457543 4.914913815 2.643737057 1.88726188 0.044961326 1.064372379 0.452148584 29.04230792 0.299757805 0.389043055 1767.899378 -3.247457543 -0.756475177 RVEISAPSNFEHR ddPTM_SK-BR-3_Trastuzumab_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 ; 98.942 0.0020046 179188000 196917 189365 179183 220610 219850 213800 246320 245180 220040 FALSE TRUE 187609.1237 208661.5088 187398.7178 198433.8637 258191.7704 206396.0524 208739.36 223710.7394 254162.6794 0.738145837 0.820976192 0.737317997 0.780735646 1.01585241 0.812062782 0.821282497 0.880187209 1 17.95539268 -4.999999979 0.033688701 1.986983104 0.190759035 0.477520114 0.069757376 1044.856512 2.642062425 115.846133 42.05013752 1.00E-05 4.999999979 -1.796224069 RVELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVELLK 6 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 88.029 0.083007 366980000 314070 270880 277970 307410 256950 280040 337380 336070 298760 FALSE TRUE 299224.5335 298482.98 290715.1994 276508.5628 301761.9986 270342.1446 285906.4846 306641.9292 345090.1749 0.867090851 0.864941982 0.84243256 0.801264663 0.874443901 0.783395658 0.828497898 0.888584931 1 18.39661387 0.905913059 3.582169246 0.999889461 0.83947053 0.763447449 0.028685503 0.199271643 5.743961722 0.028150552 0.007257539 8.052172303 -0.905913059 -0.160418931 RVELSGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVELSGPK 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ;;; 114.5 0.0042411 1380270000 2132740 1787070 1624210 1549840 1576450 1548070 1867070 1805430 1843640 FALSE TRUE 2031929.607 1969174.465 1698681.635 1394047.139 1851382.381 1494459.948 1582214.18 1647336.978 2129542.275 0.954162606 0.924693765 0.797674531 0.654622899 0.869380431 0.701775196 0.742983222 0.773563877 1 21.02211194 3.727081222 3.935015955 0.769837326 0.942663267 0.278987023 0.095374553 0.195547334 7.040661795 0.022378384 0.038579563 5334.346493 -3.727081222 0.172825941 RVEQLAGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVEQLAGER 9 1 Q3KQV9 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 90.913 0.017811 539840000 567000 488300 490650 561400 655670 489050 556850 541460 602970 FALSE TRUE 540199.0337 538058.3252 513146.7878 504967.0054 770018.6404 472114.0759 471892.3052 494046.8919 696475.5081 0.775618134 0.772544503 0.736776501 0.725031964 1.105593279 0.677861706 0.677543287 0.709352858 1 19.40971309 -0.279472528 7.886321805 0.999999922 0.769107886 0.251561915 0.12317342 0 0 0.114644117 0.027021878 0.525445253 0.279472528 -0.230892036 RVESQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVESQLK 7 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ;; 125.49 0.0064841 1041510000 1931600 1302370 704390 716590 1568480 839780 1656260 1282680 1342510 FALSE TRUE 1840297.096 1435082.984 736686.9782 644557.0118 1842022.415 810698.208 1403567.118 1170361.739 1550699.594 1.186752807 0.92544229 0.475067499 0.415655627 1.187865414 0.522795138 0.905118646 0.754731441 1 20.5644878 4.138048856 3.066878318 0.745800965 1.133318038 0.241114298 0.242194206 0.304107101 5.556385459 0.057924488 0.15161853 13741.96558 -4.138048856 0.387517073 RVFIMDNCEELIPEYLNFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVFIMDNCEELIPEYLNFIR 20 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 139 1.68E-07 250960000 381650 156202 362680 254930 516370 313680 549760 378630 617150 FALSE TRUE 363610.1609 172119.1614 379309.2367 229303.9521 606424.7645 302817.1829 465884.015 345475.15 712854.47 0.510076286 0.241450631 0.532099121 0.321670077 0.850699252 0.424795236 0.653547161 0.484636296 1 19.44324805 -5 0.123912208 2.725358732 0.249603122 0.501250626 0.161783864 108.9729766 0.866340844 46.63255494 1.260976913 1.00E-05 5 -2.47575561 RVFIMDSCDELIPEYLNFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVFIMDSCDELIPEYLNFIR 20 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 162.09 3.46E-11 331640000 507460 210550 465460 331980 666310 355500 713670 513570 817190 FALSE TRUE 483473.3715 232005.2844 486801.8014 298608.7397 782514.253 343188.9459 604786.5341 468599.0882 943915.6516 0.512199761 0.245790272 0.515725956 0.316351084 0.829008664 0.363580099 0.640720951 0.496441697 1 19.84829842 -4.999999994 0.146893079 2.896567142 0.303095207 0.518316005 0.159583476 95.61719689 0.842370517 52.60925972 0.754141579 1.00E-05 4.999999994 -2.593471935 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR 199.75 2.44E-25 2921050000 1180758 1140792 1107052 1285445 1170441 1138490 1231774 1162504 1197042 TRUE FALSE 1124945.909 1257040.002 1157811.429 1156229.626 1374565.54 1099063.806 1043844.253 1060708.987 1382673.16 0.813602189 0.909137487 0.83737174 0.836227722 0.994136272 0.794883301 0.754946493 0.767143688 1 20.39902874 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 45 3 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.996)PAPGT(0.002)T(0.002)AEEAMSR 82.706 5.22E-05 94204000 34973 24512 38047 34134 39059 35328 45475 36576 46661 TRUE FALSE 33319.8956 27009.80067 39791.49258 30702.78547 45870.87723 34104.5825 38536.95354 33373.21154 53896.94957 0.618214869 0.501137836 0.738288399 0.569657202 0.85108485 0.632773891 0.715011774 0.619204089 1 15.717916 -5 0.145415178 2.218346385 0.531144033 0.561870712 0.095782712 91.28354746 0.799809058 32.26546435 0.481660907 1.00E-05 5 -1.687202352 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 45 3 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENASPAPGTTAEEAMSR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENASPAPGTTAEEAMSR;RVGDPPQPLPEEPMEVQGAERAS(0.97)PEPQRENAS(0.012)PAPGT(0.005)T(0.005)AEEAMS(0.008)R;RVGDPPQPLPEEPMEVQGAERAS(0.974)PEPQRENAS(0.013)PAPGT(0.006)T(0.006)AEEAMS(0.001)R 209.26 8.90E-37 1023537000 109905.7 58414.7 111433.1 93267.4 139635.6 95833 137070 117452.3 155557.9 TRUE FALSE 104710.6754 64367.22434 116542.4179 83891.98376 163988.0044 92514.27918 116157.454 107167.554 179681.0247 0.582758672 0.358230506 0.648607264 0.466893952 0.912661784 0.51488063 0.64646478 0.596432229 1 17.45507853 -5 0.134048559 2.434144409 0.408791989 0.46839888 0.140484437 114.2024072 0.954622826 43.86877465 0.895629163 1.00E-05 5 -2.02535242 RVGFQYEGTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVGFQYEGTYK 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 120.57 0.00069539 1002710000 1643720 1140410 1192740 1500470 1458780 1316360 1978800 1581720 1674660 FALSE TRUE 1566024.613 1256619.076 1247428.309 1349639.905 1713190.77 1270774.123 1676897.717 1443216.212 1934357.72 0.809583769 0.649631174 0.644879846 0.697719916 0.885663883 0.656948873 0.866901556 0.746095821 1 20.88342319 0.236129692 0.394946359 1.035455494 0.706064186 0.494158281 0.084110393 2.678329018 0.668956473 0.251342965 0.0577703 1.722382846 -0.236129692 -0.329391308 RVGMADANS(ph)PPKPLSKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVGMADANSPPKPLSKPR 18 3 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 RVGMADANS(1)PPKPLSKPR;RVGMADANS(1)PPKPLSKPR 106.35 0.0024946 1133220000 1078610 1149720 1056430 1304980 708250 1358460 1363600 1395110 916380 TRUE FALSE 1027626.243 1266877.775 1104868.36 1173800.931 831768.5758 1311416.19 1155557.776 1272946.772 1058487.53 0.970843977 1.196875484 1.043818022 1.108941672 0.785808573 1.238952895 1.091706556 1.202609134 1 20.01357284 RVHNNS(ph)PDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RVHNNSPDTSR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSR;RVHNNS(0.999)PDT(0.001)SR;RVHNNS(1)PDTSR;RVHNNS(1)PDTSR;RVHNNS(1)PDTSR 161.04 1.64E-05 695604000 639012 550706 629739 707517 705172 565557 678311 601977 669669 TRUE FALSE 608807.1692 606823.5675 658613.156 636396.047 828153.7735 545971.6193 574822.1989 549264.7026 773517.8483 0.787062859 0.784498469 0.851451789 0.822729622 1.07063305 0.705829375 0.74312726 0.710086656 1 19.56107506 -0.50852358 7.289507201 1.000032574 0.805979307 0.250345084 0.103486431 0 0 0.097787469 0.023048728 0.310081902 0.50852358 -0.194053268 RVHNNS(ph)PDTSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVHNNSPDTSRR 12 2 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSRR 47.666 0.095212 654830000 10961 10355 11225 13347 13556 10516 10365 13839 11125 TRUE FALSE 10442.89525 11410.18627 11739.67735 12005.3342 15920.16211 10151.82828 8783.628884 12627.18379 12850.20818 0.812663507 0.887937854 0.913578768 0.934252117 1.23890305 0.790012748 0.683539812 0.982644298 1 13.64950411 1.030289774 24.99897412 1.00000182 0.883383852 0.070428349 0.142817336 445.2008094 367434.9475 0.14189338 0.035473345 10.72234493 -1.030289774 -0.116617968 RVIISAPSADAPMFVMGVNHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 364.77 4.56E-113 10854220000 5978250 4573630 4992490 6655750 5471730 5533850 6784340 6277620 5152900 FALSE TRUE 5695669.97 5039688.097 5221400.605 5986701.365 6425997.98 5342211.387 5749264.33 5727918.313 5951985.415 0.956936144 0.846723865 0.877253595 1.005832667 1.079639403 0.897551156 0.965940595 0.962354225 1 22.50493956 3.242438937 24.9997653 0.980671446 0.892627467 0.402212663 0.052431911 102.7557823 662360.9566 0.014794493 0.019299791 1747.587529 -3.242438937 -0.088043979 RVIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVIISAPSADAPMFVMGVNHEKYDNSLK 28 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 322.45 1.76E-83 2005150000 1871700 854500 1851140 1438560 2013750 1831300 3361900 2331300 2312100 FALSE TRUE 1783228.45 941574.5215 1936016.6 1293953.216 2364947.362 1767881.622 2848980.409 2127159.013 2670648.659 0.667713607 0.35256398 0.724923735 0.484508964 0.885532941 0.661967128 1.066774695 0.796495265 1 21.34875876 2.44846921 0.98210245 0.956274757 0.525076277 0.528787919 0.149281373 0.357793089 0.689495118 0.087532678 0.059985126 280.8466253 -2.44846921 -0.431198479 RVLQALEGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVLQALEGLK 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 196.44 5.35E-07 2560800000 5701800 3419700 1496060 1843560 5346200 2689400 6698100 4479500 5309800 FALSE TRUE 5432287.214 3768171.318 1564655.831 1658241.846 6278575.587 2596265.404 5676181.826 4087251.233 6133216.665 0.88571585 0.614387445 0.255111782 0.270370661 1.023700275 0.423312194 0.925482033 0.666412334 1 22.54821249 1.289710159 0.828010933 0.968406391 0.589878486 0.19973702 0.256769014 0.972520563 1.466248746 0.237430015 0.090765895 19.48543739 -1.289710159 -0.378527904 RVLVDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVLVDVER 8 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 122.33 0.0022369 545500000 562480 529950 489350 653410 628990 580040 657420 629660 553010 FALSE TRUE 535892.6851 583952.5075 511787.1815 587727.9854 738685.6569 559953.0694 557118.5047 574523.6324 638767.9664 0.838947338 0.914185648 0.801209842 0.920096211 1.156422513 0.876614199 0.872176649 0.899424615 1 19.28493244 3.011821722 24.77186831 0.949289775 0.86279911 0.244396343 0.085759954 353.015271 739720.6632 0.025221292 0.030123259 1027.594385 -3.011821722 -0.086490666 RVNALK ddPTM_SK-BR-3_Trastuzumab_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 798240000 1510220 1239010 1329240 1534570 1307270 1381260 1841060 1621770 1541200 FALSE TRUE 1438834.894 1365266.528 1390186.969 1380312.108 1535257.474 1333426.62 1560172.484 1479759.221 1780201.425 0.808242749 0.766916883 0.780915547 0.7753685 0.862406609 0.749031318 0.876402222 0.831231343 1 20.76360906 0.238468751 0.446485271 1.02128713 0.781523774 0.756936541 0.036178811 1.311707541 0.4027061 0.085147777 0.019059776 1.731684426 -0.238468751 -0.239763356 RVNDAEPGS(ph)PEAPQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVNDAEPGSPEAPQGK 16 1 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK 218.07 8.37E-15 1409050000 1856340 1618150 1748050 2046150 1598600 1897370 2156120 2072120 1983380 TRUE FALSE 1768594.487 1783041.325 1828199.822 1840467.115 1877395.334 1831663.601 1827164.294 1890674.188 2290952.441 0.771990922 0.778296962 0.798008631 0.803363301 0.819482457 0.79952057 0.797556624 0.825278672 1 21.12751608 -5 0.248360973 2.233181137 0.777052224 0.970954024 0.011093944 30.16593835 0.299277112 18.84892863 0.017984808 1.00E-05 5 -1.456128913 RVNQAIWLLCTGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVNQAIWLLCTGAR 14 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 128.85 0.00011442 1013560000 512860 374120 379850 387260 534730 400080 601160 484620 546430 FALSE TRUE 488618.1242 412243.2533 397266.4982 348331.8891 627986.7427 386225.1293 509442.0009 442184.1037 631167.5736 0.774149599 0.653143904 0.629415253 0.551884957 0.994960402 0.611921692 0.807142227 0.700581149 1 19.26766356 -2.162098758 0.273444948 1.348782648 0.683134767 0.350228932 0.12341053 38.24115324 1.460871776 8.391803324 0.142452241 0.006884957 2.162098758 -0.665647881 RVNS(ph)GDTEVGSSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVNSGDTEVGSSLLR 15 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 RVNS(0.999)GDT(0.001)EVGSSLLR;RVNS(0.922)GDT(0.078)EVGSSLLR;RVNS(0.999)GDT(0.001)EVGSSLLR 212.19 6.14E-10 1387990000 487140 326932 487580 478720 593850 472370 632470 521020 613020 TRUE FALSE 464113.8576 360246.7425 509936.0253 430598.1561 697417.252 456011.7085 535975.0854 475396.7267 708084.0107 0.655450272 0.508762713 0.720163169 0.608117327 0.984935744 0.644007917 0.756937139 0.671384637 1 19.43356101 -4.999999999 0.073911329 2.04849197 0.327716218 0.416469649 0.119122047 250.9066035 1.3267504 44.27493592 4.931773956 1.00E-05 4.999999999 -1.720775752 RVNSGDTEVGS(ph)SLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVNSGDTEVGSSLLR 15 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 RVNS(0.277)GDT(0.013)EVGS(0.355)S(0.355)LLR 197.01 9.15E-09 145460000 223330 163520 226590 234400 257520 223590 294310 253110 300340 TRUE FALSE 212773.6335 180182.8739 236979.3756 210837.6667 302431.4065 215847.0222 249407.6041 230946.3466 346915.1933 0.613330398 0.51938594 0.683104633 0.607749879 0.87177331 0.622189591 0.718929609 0.665714131 1 18.4042235 -4.999999998 0.11948932 2.127010244 0.481786543 0.620844933 0.086113494 93.79583158 0.727577433 25.58148645 0.782425973 1.00E-05 4.999999998 -1.645223701 RVNTTQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RVNTTQK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ;;;; 113.7 0.0097347 1620580000 1732760 1482760 1126100 1531050 1251440 1316000 1801110 1616020 1679920 FALSE TRUE 1650855.869 1633854.93 1177732.799 1377145.945 1469690.74 1270426.59 1526317.59 1474512.722 1940433.414 0.850766564 0.842005151 0.606943166 0.709710488 0.757403335 0.654712798 0.786585914 0.759888338 1 20.8879475 0.302000384 1.759519786 1.000009675 0.75296691 0.525781067 0.075609589 9.021805591 21.51515041 0.078108406 0.021878309 2.004473799 -0.302000384 -0.247042766 RVPDPS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVPDPSPVTK 10 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 RVPDPS(1)PVTK;RVPDPS(0.999)PVT(0.001)K;RVPDPS(1)PVTK 68.83 0.036016 973780000 1300570 993160 1057900 1252180 944650 1189620 1339710 1359470 1073860 TRUE FALSE 1239094.634 1094364.133 1106405.761 1126308.487 1109396.661 1148423.161 1135312.634 1240427.6 1240388.724 0.998956706 0.882275138 0.891983085 0.908028641 0.894394345 0.925857466 0.915287774 1.000031341 1 20.24236089 1.237750537 24.88494474 1.00001572 0.917225377 0.539388607 0.032011815 15.95503237 489969.6783 0.025552893 0.007815362 17.28823022 -1.237750537 -0.082790343 RVPFS(ph)LLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVPFSLLR 8 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 RVPFS(1)LLR 91.961 0.0074212 92664000 71662 22660 26948 40289 84015 36732 76563 48607 78569 TRUE FALSE 68274.67928 24969.07976 28183.59246 36239.07318 98667.1894 35459.96163 64881.90817 44350.7134 90753.07925 0.752312537 0.275132039 0.310552465 0.399315081 1.087204866 0.390730121 0.714927898 0.488696513 1 16.46965897 RVPGS(ph)SGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVPGSSGR 8 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 RVPGS(0.5)S(0.5)GR;RVPGS(0.643)S(0.357)GR 91.701 0.0075342 1041510000 469610 360618 353305 438880 435000 390350 419980 447680 396320 TRUE FALSE 447412.466 397365.3842 369504.3837 394762.9486 510863.8623 376832.0816 355904.3375 408478.7659 457779.2815 0.977354118 0.868028328 0.807167119 0.862343414 1.115961082 0.823174173 0.777458378 0.892305053 1 18.80429264 RVPGSS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RVPGSSGR 8 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 RVPGS(0.029)S(0.971)GR;RVPGS(0.086)S(0.914)GR;RVPGS(0.049)S(0.951)GR;RVPGS(0.113)S(0.887)GR;RVPGS(0.035)S(0.965)GR 95.822 0.0057438 2535060000 1263500 1025980 1062810 1326600 1257760 1129150 1369040 1236640 1286160 TRUE FALSE 1203776.859 1130528.528 1111540.89 1193247.648 1477112.946 1090047.252 1160167.804 1128353.246 1485611.124 0.810290687 0.760985503 0.748204474 0.803203226 0.994279675 0.733736598 0.780936401 0.759521269 1 20.50262509 -2.238656448 2.286358192 1.714780536 0.796545684 0.425428945 0.073403618 4838256.588 899340.878 17869304.25 0.017214226 0.005772229 2.238656448 -0.918234852 RVPLS(ph)PLSLLAGPADAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVPLSPLSLLAGPADAR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 RVPLS(0.708)PLS(0.292)LLAGPADAR;RVPLS(0.941)PLS(0.059)LLAGPADAR;RVPLS(0.988)PLS(0.012)LLAGPADAR;RVPLS(0.999)PLS(0.001)LLAGPADAR 153.36 1.89E-07 171836000 198790 141209 177003 171492 210928 161437 206117 168031 207196 TRUE FALSE 189393.5907 155598.3576 185118.7626 154253.2983 247713.7764 155846.3962 174670.0661 153317.3149 239326.8975 0.791359403 0.650149897 0.773497524 0.644529721 1.035043612 0.651186297 0.729838843 0.640618821 1 17.86862302 -1.073355354 4.274334453 1.000027766 0.737119118 0.323684611 0.118279613 14311802.57 3593928.388 3832.153415 0.02489214 0.084458749 1.073355354 -0.262908647 RVPPPALS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVPPPALSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R 88.021 0.0080034 712630000 282194 273423 268042 310643 419676 265987 314404 280967 387826 TRUE FALSE 268855.2489 301285.1146 280331.9908 279416.5755 492867.3615 256775.8035 266435.8954 256364.04 447968.0753 0.600166091 0.672559343 0.625785645 0.623742161 1.100228763 0.573201122 0.594765364 0.572281942 1 18.7730364 RVPS(ph)PTPAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.895)PT(0.105)PAPK;RVPS(0.905)PT(0.095)PAPK;RVPS(0.962)PT(0.038)PAPK;RVPS(0.899)PT(0.101)PAPK;RVPS(0.883)PT(0.117)PAPK;RVPS(0.941)PT(0.059)PAPK;RVPS(0.899)PT(0.101)PAPK;RVPS(0.998)PT(0.002)PAPK;RVPS(0.645)PT(0.355)PAPK;RVPS(0.96)PT(0.04)PAPK;RVPS(0.905)PT(0.095)PAPK;RVPS(0.99)PT(0.01)PAPK 154.09 1.60E-05 57817910000 24996120 20958470 21703210 25243560 18643160 24094630 26774740 25009150 21355670 TRUE FALSE 23814602.95 23094161.92 22698323.65 22706029.39 21894521.2 23260226.92 22689761.66 22819216.24 24667398.23 0.965428243 0.936222041 0.920175019 0.920487405 0.8875894 0.942954206 0.919827922 0.925075925 1 24.55610222 -1.352005415 5.098669679 1.000035389 0.928751557 0.570399185 0.019810268 8.33E-06 1.06E-06 0.020044172 0.004722112 0.044462572 1.352005415 -0.071283832 RVPVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVPVLGK 7 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 126.2 0.0063733 223780000 773330 604760 577690 734610 653980 695950 850140 755930 794260 FALSE TRUE 736776.2235 666385.7316 604177.6579 660765.6071 768033.9049 671849.077 720435.5291 689736.7618 917429.7843 0.803087316 0.726361562 0.658554658 0.720235617 0.837158242 0.732316618 0.785275932 0.751814224 1 19.80723822 -2.267660136 0.372139208 1.323965067 0.742186226 0.722014283 0.048606559 28.7049543 1.406591465 7.731070822 0.033842546 0.00539933 2.267660136 -0.581778841 RVQDLEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVQDLEQK 8 1 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 130.75 0.0016589 113980000 247650 174310 233940 317590 230950 300410 333220 334040 254140 FALSE TRUE 235944.0753 192072.3872 244666.3804 285665.2498 271227.6069 290006.7264 282381.169 304789.6867 293550.7332 0.803759107 0.654307298 0.833472217 0.973137579 0.923954793 0.987927106 0.96195014 1.038286239 1 18.16325033 3.396884444 3.177118243 0.976532561 0.729187351 0.838324695 0.046431699 0.080765369 1.637732672 0.012650514 0.018119093 2493.931061 -3.396884444 -0.24734521 RVQT(ph)PLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 RVQTPLLR 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR 128.81 0.00065489 4651800000 921382 856998 843711 925225 1077228 835817 1018698 956015 1219942 TRUE FALSE 877830.0989 944327.0705 882395.9839 832219.6252 1265096.222 806872.4477 863276.9104 872301.2584 1409124.375 0.622961404 0.670151682 0.626201633 0.590593449 0.8977889 0.572605557 0.61263358 0.619037804 1 20.42636752 -1.458171427 5.692518759 1.000288263 0.649927115 0.590098196 0.091274074 0.000308538 2.94E-05 0.08165819 0.019231461 0.034819984 1.458171427 -0.350361148 RVS(ph)ADSQPFQHGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.97)ADS(0.03)QPFQHGDK 178.54 1.21E-06 151710000 174900 175580 161820 196840 120040 175110 181400 192630 132910 TRUE FALSE 166632.8236 193471.8016 169239.6071 177053.2692 140974.938 169045.8968 153724.0984 175762.296 153521.004 1.085407334 1.260230174 1.102387313 1.153283685 0.918277853 1.101125529 1.001322909 1.144874587 1 17.22807653 2.941667424 21.91279666 1.036167556 1.159453236 0.370207973 0.07553681 67.26999129 25269.75603 0.02100699 0.022281484 874.3139826 -2.941667424 0.123285679 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(0.995)EVEEEKEPVPQPLPS(0.005)DDTR 150.23 3.00E-08 951050000 1184740 1268060 961080 1316580 753810 1197130 1107600 1212870 729280 TRUE FALSE 1128739.688 1397276.756 1005146.469 1184234.877 885274.2253 1155673.088 938615.2775 1106664.673 842373.0178 1.33995233 1.658738737 1.193232033 1.40583192 1.050928991 1.371925576 1.114251356 1.313746582 1 19.6840997 2.959586831 0.241058594 0.997279416 1.64536688 0.347183812 0.156525052 3.874978173 0.440478235 0.280808759 0.786808452 911.1436034 -2.959586831 0.648087465 RVS(ph)FADPIYQAGLADDIDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSFADPIYQAGLADDIDRR 20 2 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RVS(1)FADPIYQAGLADDIDRR 92.426 0.00086309 17316000 24569 19137 19252 20338 21820 17605 20439 18353 21604 TRUE FALSE 23407.67206 21087.08206 20134.72324 18293.5856 25625.40109 16995.33444 17320.65516 16745.91402 24954.23798 0.938023917 0.845030094 0.806865882 0.733085323 1.026895757 0.681060045 0.694096737 0.671064932 1 14.60699723 2.194252075 24.99965541 0.729602578 0.863673146 0.141095862 0.121543826 188.1583529 106161.0969 0.041138279 0.030382786 156.4055194 -2.194252075 0.134070568 RVS(ph)GPDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVSGPDPK 8 1 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(1)GPDPK;RVS(1)GPDPK;RVS(1)GPDPK;RVS(1)GPDPK 83.045 0.011454 1133210000 3188150 3962640 2497790 3929320 1873960 3281580 2720500 3228780 1694690 TRUE FALSE 3037452.468 4366437.521 2612316.142 3534337.288 2200778.031 3167938.062 2305437.76 2946050.906 1957493.87 1.551704715 2.230626409 1.334520727 1.805541945 1.124283485 1.618364231 1.17774967 1.505011562 1 20.90057636 3.121867763 1.237414973 1.307580912 1.857740557 0.329190986 0.294508738 0.43188414 1.400494069 0.103695225 0.140565921 1323.938353 -3.121867763 0.550159645 RVS(ph)GPDPKPGSNCS(ph)PAQSVLSEVPSVPTNGMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 2 RVS(0.998)GPDPKPGS(0.248)NCS(0.749)PAQS(0.005)VLSEVPSVPTNGMAK 152.41 1.09E-10 159020000 437420 418030 457090 518870 279310 511760 558040 539510 353360 TRUE FALSE 416744.0235 460627.7323 478048.0286 466712.2018 328021.5756 494037.6229 472900.7489 492267.6443 408157.2641 1.02103787 1.128554537 1.171234891 1.143461707 0.803664676 1.210409973 1.15862387 1.206073461 1 18.63876561 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(0.994)GPDPKPGS(0.002)NCS(0.002)PAQS(0.002)VLSEVPSVPTNGMAK;RVS(0.997)GPDPKPGS(0.001)NCS(0.001)PAQS(0.001)VLSEVPSVPTNGMAK;RVS(0.991)GPDPKPGS(0.006)NCS(0.001)PAQS(0.001)VLSEVPSVPTNGMAK;RVS(0.991)GPDPKPGS(0.006)NCS(0.001)PAQS(0.001)VLSEVPSVPTNGMAK;RVS(0.998)GPDPKPGS(0.001)NCSPAQSVLSEVPSVPTNGMAK;RVS(1)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK;RVS(0.949)GPDPKPGS(0.034)NCS(0.01)PAQS(0.003)VLS(0.004)EVPSVPTNGMAK;RVS(0.92)GPDPKPGS(0.027)NCS(0.027)PAQS(0.027)VLS(0.001)EVPSVPTNGMAK;RVS(0.981)GPDPKPGS(0.003)NCS(0.003)PAQS(0.012)VLSEVPSVPTNGMAK;RVS(0.783)GPDPKPGS(0.096)NCS(0.096)PAQS(0.025)VLSEVPSVPTNGMAK 249.56 6.70E-48 16276060000 17613050 15885600 16528170 18981000 10744720 18484760 19554310 19608670 12673990 TRUE FALSE 16780516.03 17504360.7 17286002.94 17072993.82 12618595.77 17844628.13 16570940.87 17891630.9 14639407.64 1.146256491 1.195701434 1.180785683 1.16623529 0.861960817 1.218944684 1.131940669 1.222155387 1 23.80335384 -1.896073909 2.573691524 0.9232363 1.142189142 0.154540335 0.103207978 19943851.41 12568534.84 9304632.989 0.024946812 0.012703579 1.896073909 0.218952843 RVS(ph)HS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK 88.092 0.045557 14559400000 6347450 6235870 5493550 6738560 4470060 6292640 6343470 5718340 3866310 TRUE FALSE 6047418.618 6871312.243 5745434.701 6061187.146 5249637.049 6074724.299 5375657.146 5217611.835 4465877.608 1.354138906 1.538625293 1.286518621 1.357221957 1.175499534 1.360253198 1.203717974 1.168328443 1 22.09051228 1.589110653 0.26515952 0.947165086 1.502832943 0.688404631 0.081489574 0.917896766 0.261510099 0.188226127 0.186993014 38.82492744 -1.589110653 0.555667857 RVS(ph)HS(ph)PPPKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RVSHSPPPKQR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR;RVS(1)HS(1)PPPKQR 81.311 0.011811 1387393000 460368.8 334543 517716 456147 504077 441679.7 676256 457210.1 602186 TRUE FALSE 438608.0792 368633.312 541453.7907 410294.2369 591987.8692 426384.2212 573080.7269 417174.3598 695569.9293 0.630573664 0.529973043 0.778431855 0.589867704 0.851083183 0.612999791 0.823900952 0.59975905 1 19.40783604 -4.999999996 0.111660977 2.036500958 0.491467875 0.467837588 0.107734494 124.2601915 0.918789113 29.49951625 1.123076449 1.00E-05 4.999999996 -1.545033083 RVS(ph)HSPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.592)HS(0.408)PPPK;RVS(0.647)HS(0.353)PPPK 57.836 0.069076 185530000 185804 162087 156297 188920 130408 177068 180773 184806 124417 TRUE FALSE 177021.4131 178603.8496 163463.372 169929.4027 153151.1139 170936.0908 153192.7587 168623.4069 143710.9529 1.231787902 1.242799146 1.137445468 1.182438772 1.065688528 1.189443722 1.06597831 1.173351115 1 17.1328105 7.999999999 0.08039619 0.878887467 1.882657615 0.589936166 0.049998234 109.1345469 0.639128626 1.196282341 12.16732453 99999999.85 -7.999999999 1.003770148 RVS(ph)ISEGDDKIEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSISEGDDKIEYR 14 2 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 1 RVS(0.998)IS(0.002)EGDDKIEYR 88.565 0.0033892 97477000 55200 50954 53641 57300 48533 55456 65545 64253 59456 TRUE FALSE 52590.8054 56146.27053 56100.49291 51540.09514 56997.13983 53535.54481 55544.90643 58626.66669 68676.13282 0.765779948 0.817551429 0.816884857 0.750480451 0.829941022 0.779536392 0.808794907 0.853668724 1 16.06752118 0.773210616 1.613350018 0.999916125 0.794192481 0.876157926 0.024319514 0.232827574 1.038042728 0.020816065 0.005983127 5.932129397 -0.773210616 -0.205723644 RVS(ph)LHCLLDQFDKDLPVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSLHCLLDQFDKDLPVYLK 20 2 Q8IWF6 Q8IWF6 DENND6A Protein DENND6A 1 RVS(1)LHCLLDQFDKDLPVYLK 46.956 0.087305 66233000 58808 69409 77577 83772 73409 52416 80687 58495 81465 TRUE FALSE 56028.26239 76481.85601 81133.98218 75351.0794 86211.50636 50600.82078 68376.71623 53372.8677 94098.17613 0.595423468 0.812787869 0.862226937 0.800770881 0.916186794 0.537744969 0.726652939 0.567204062 1 16.52187914 2.24369412 24.99998652 0.684307918 0.78429071 0.069636251 0.14790155 297.5155576 1448895.668 0.048365244 0.039322984 175.2645653 -2.24369412 0.099982792 RVS(ph)LSEIGFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVSLSEIGFGK 11 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RVS(0.999)LS(0.001)EIGFGK;RVS(0.5)LS(0.5)EIGFGK;RVS(0.623)LS(0.377)EIGFGK;RVS(0.731)LS(0.269)EIGFGK 211.82 8.51E-09 1089400000 2568560 2317130 2214310 2771720 2148210 2494810 2863080 2650720 2349630 TRUE FALSE 2447149.259 2553248.181 2315838.304 2493101.44 2522857.144 2408414.104 2426264.562 2418608.904 2713998.62 0.901676678 0.940769889 0.85329384 0.918608219 0.929572007 0.887404322 0.893981502 0.891160698 1 21.37198856 -2.232169893 2.279923859 1.324954664 0.903961077 0.614307803 0.024347719 1956758.471 456804.9192 3265205.157 0.005690907 0.005859089 2.232169893 -0.420993587 RVS(ph)LVGADDLR ddPTM_SK-BR-3_Trastuzumab_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 159.69 1.74E-05 943840000 1613940 1232060 1251680 1739080 1875410 1308480 1674600 1395830 1587850 TRUE FALSE 1537652.255 1357608.315 1309070.766 1564264.374 2202480.91 1263167.01 1419109.014 1273603.725 1834085.668 0.838375372 0.74020987 0.713745704 0.852885119 1.200860433 0.688717562 0.773741946 0.694407981 1 20.8066296 5.123284672 15.46948304 0.818455002 2.448383026 0 0.160444866 10409453.05 8173957.103 0.036715131 593220038.4 132826.4827 -5.123284672 1.629928024 RVS(ph)PLNLSSVTP ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 RVS(0.999)PLNLS(0.001)SVTP;RVS(1)PLNLSSVTP;RVS(0.889)PLNLS(0.11)S(0.001)VTP;RVS(1)PLNLSSVTP;RVS(1)PLNLSSVTP 122.2 0.00038429 1168565000 1540323 1481802 1293059 1407028 1733769 1384016 1863727 1592308 1896360 TRUE FALSE 1467514.984 1632799.308 1352347.034 1265590.872 2036137.765 1336087.179 1579381.216 1452877.07 2190437.824 0.669964228 0.745421436 0.617386634 0.577779866 0.929557435 0.609963526 0.721034489 0.663281584 1 21.06278783 -1.905983293 2.427553857 1.180289488 0.695044881 0.492645228 0.098244631 11648261.92 5996307.394 11972948.5 0.021899907 0.012417001 1.905983293 -0.485244608 RVS(ph)QDLEVEKPDASPTSLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVSQDLEVEKPDASPTSLQLR 21 2 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RVS(0.999)QDLEVEKPDASPTSLQLR;RVS(1)QDLEVEKPDASPTSLQLR;RVS(0.98)QDLEVEKPDAS(0.01)PT(0.005)S(0.005)LQLR;RVS(1)QDLEVEKPDASPTSLQLR 269.94 3.99E-38 1290760000 1375840 1298470 1215450 1459350 992344 1381740 1529500 1560690 1170230 TRUE FALSE 1310806.77 1430785.569 1271179.585 1312653.365 1165408.479 1333889.997 1296146.684 1424027.71 1351703.292 0.969744453 1.058505648 0.940427972 0.971110578 0.862177733 0.986821594 0.958898814 1.053506135 1 20.36634707 -0.458888511 12.69646838 1.000000952 0.976938343 0.018656627 0.055304887 0 0 0.052279525 0.012322402 0.34762539 0.458888511 -0.023062609 RVS(ph)RT(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;RVS(1)RT(1)PEPK 76.073 0.040243 2192120000 3166150 2737350 2871870 3225190 2153100 3199230 3498180 3087550 2385010 TRUE FALSE 3016492.364 3016289.077 3003548.08 2900987.774 2528599.958 3088439.863 2964468.393 2817187.754 2754865.17 1.094969147 1.094895355 1.090270447 1.053041654 0.917867047 1.121085669 1.076084748 1.022622735 1 21.39355028 3.193457654 4.77273925 1.038492901 1.094241479 0.232704664 0.052282993 0.327493163 16.32779688 0.015184879 0.018816764 1561.196807 -3.193457654 0.055748578 RVS(ph)S(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.5)S(0.5)S(0.5)S(0.5)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.5)S(0.5)S(0.5)S(0.5)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.481)S(0.519)S(0.519)S(0.481)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.5)S(0.5)S(0.5)S(0.5)ELDLPSGDHCEAGLLQLDVPLLR 118.3 0.00010428 35708900 43164.3 32400 39106 39634.3 52871.2 31232 46492.3 40406.4 60006.6 TRUE FALSE 41124.00908 35701.59684 40899.04878 35650.18486 62091.92054 30150.42801 39399.04575 36868.20141 69312.11706 0.593316304 0.515084495 0.590070691 0.51434275 0.895830674 0.434995053 0.568429409 0.531915673 1 16.08081996 -1.508975775 5.699175672 1.00067435 0.576045874 0.541754067 0.121189322 0.000937974 8.08E-05 0.105992968 0.024945073 0.030975921 1.508975775 -0.424628477 RVS(ph)SDLQHATAQLSLEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSSDLQHATAQLSLEHR 18 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RVS(0.664)S(0.336)DLQHATAQLSLEHR 229.71 8.14E-20 119110000 468230 403490 413330 464270 246400 450260 442480 469680 55534 TRUE FALSE 446097.6958 444606.0897 432281.5893 417600.6975 289372.082 434667.3833 374971.5493 428552.3293 64145.92909 6.954419433 6.931166109 6.739033879 6.510166794 4.511152712 6.776227104 5.845601656 6.680896751 1 15.96907009 2.934354686 6.7774462 5.455932227 6.867200639 0.205420275 1.638899335 0.440112442 38.10207089 0.440490897 0.470799589 859.7153607 -2.934354686 1.411268412 RVS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.445)S(0.185)S(0.185)S(0.185)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.568)S(0.236)S(0.098)S(0.098)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.418)S(0.418)S(0.082)S(0.082)ELDLPSGDHCEAGLLQLDVPLLR 185.67 3.40E-18 489146000 362411 274732.5 340064 359236.5 393020 318161.7 446014 365204 402901 TRUE FALSE 345280.5503 302728.0541 355656.2708 323125.3645 461562.5636 307143.6806 377966.3727 333224.8017 465380.8293 0.741931185 0.650495326 0.764226303 0.694324614 0.991795395 0.659983526 0.812165755 0.71602606 1 18.82805226 -5 0.170953956 1.96418147 0.690847943 0.382448307 0.097515471 128.6953673 1.216421617 42.22413919 0.314228692 1.00E-05 5 -1.273333526 RVS(ph)TDLPEGQDVYTAACNSVIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RVSTDLPEGQDVYTAACNSVIHR 23 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RVS(0.992)T(0.008)DLPEGQDVYTAACNSVIHR;RVS(0.79)T(0.21)DLPEGQDVYTAACNSVIHR;RVS(0.965)T(0.035)DLPEGQDVYTAACNSVIHR 325.98 5.13E-75 964600000 342483 291780 339632 373030 418930 354848 447660 359736 394180 TRUE FALSE 326294.5073 321512.7137 355204.4631 335532.3157 491991.2594 342559.5248 379361.2452 328235.6088 455307.4212 0.716646582 0.706144242 0.780142046 0.736935749 1.080569383 0.752369737 0.833198027 0.720909859 1 18.79648145 2.950492893 24.9999371 0.859509805 0.729849601 0.296092498 0.107109329 484.038785 244428.043 0.030352257 0.032193924 892.2630189 -2.950492893 -0.129660204 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR 254.85 1.30E-36 23001630000 12784960 10246070 11969540 12320190 13812350 11191330 13060920 12279810 14619030 TRUE FALSE 12180640.28 11290156.18 12518355.25 11081741.09 16221219.47 10803771.44 11068236.77 11204524.74 16886074.51 0.721342327 0.668607507 0.741341941 0.656265083 0.960627022 0.63980361 0.655465352 0.663536379 1 24.00933065 -1.460434378 2.879946609 1.008095626 0.709057712 0.480970663 0.093478487 31798113.53 35914884.13 2075854.302 0.02150559 0.034639022 1.460434378 -0.299037914 RVSISEGDDKIEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSISEGDDKIEYR 14 2 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 132.84 2.70E-05 92085000 187450 115340 192370 184590 173440 200800 262260 220000 216590 FALSE TRUE 178589.61 127093.2771 201190.3548 166034.6625 203687.8811 193846.2457 222247.4203 200735.6337 250177.671 0.713851117 0.508012072 0.804189894 0.663666992 0.814172905 0.77483432 0.888358339 0.802372302 1 17.93259351 2.133391447 0.365241429 0.995062209 0.584711358 0.610793974 0.081613718 0.763114003 0.25850914 0.091244867 0.109059428 135.9538301 -2.133391447 -0.410350851 RVSLEPHQGPGT(ph)PESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSLEPHQGPGTPESK 16 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RVSLEPHQGPGT(1)PESK 100.28 0.0016063 94489000 144750 136280 151520 158890 126800 159770 193240 195980 145340 TRUE FALSE 137907.9544 150167.0869 158467.3419 142918.0753 148913.8799 154237.1248 163757.6889 178818.9522 167878.5849 0.821474368 0.89449817 0.943940181 0.851318084 0.887033209 0.918742107 0.975453117 1.065168332 1 17.35705868 1.691437315 1.885370529 1.032357691 0.878482719 0.754051185 0.035691701 0.150270962 1.100140662 0.026023895 0.010169353 49.14024469 -1.691437315 -0.153874972 RVSS(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.187)S(0.271)S(0.271)S(0.271)ELDLPS(0.001)GDHCEAGLLQLDVPLLR;RVS(0.2)S(0.267)S(0.267)S(0.267)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.16)S(0.28)S(0.28)S(0.28)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.229)S(0.257)S(0.257)S(0.257)ELDLPS(0.001)GDHCEAGLLQLDVPLLR;RVS(0.203)S(0.266)S(0.266)S(0.266)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.217)S(0.26)S(0.26)S(0.26)ELDLPS(0.002)GDHCEAGLLQLDVPLLR;RVS(0.217)S(0.261)S(0.261)S(0.261)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 152.89 1.18E-08 702307000 183886 143447 167111 187466 219658 158632 212831 180862 226863 TRUE FALSE 175194.0732 158064.4124 174773.2046 168621.5615 257966.2857 153138.5341 180359.722 165024.7645 262043.7554 0.668568014 0.603198547 0.666961914 0.643486281 0.984439737 0.584400624 0.688280939 0.62976034 1 17.9994482 -2.135038837 2.25971863 1.648040024 0.679061442 0.442203035 0.111559382 6244442.984 1383880.48 20778646.32 0.025518671 0.00732759 2.135038837 -0.968978582 RVSSS(ph)S(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.145)S(0.247)S(0.61)S(0.993)ELDLPS(0.005)GDHCEAGLLQLDVPLLR 205.85 7.28E-25 134350000 65756 65601 71580 77488 81980 66176 89154 76712 83770 TRUE FALSE 62647.8442 72285.81648 74862.0138 69698.75902 96277.28604 63884.30853 75551.91987 69994.6906 96760.62376 0.647451843 0.74705819 0.773682629 0.720321514 0.99500481 0.660230433 0.780812658 0.723379903 1 16.56213245 -5 0.192368509 2.036532141 0.709778102 0.390194662 0.09540884 140.4037434 1.377310504 56.18351756 0.23494671 1.00E-05 5 -1.32675404 RVSSS(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.167)S(0.225)S(0.304)S(0.304)ELDLPSGDHCEAGLLQLDVPLLR 143.22 3.39E-08 43732000 28141 19359 24171 27688 29108 25215 30601 29146 34802 TRUE FALSE 26810.8307 21331.70411 25279.26426 24904.74964 34184.42598 24341.79823 25932.25542 26593.82173 40198.91642 0.666954065 0.530653709 0.62885437 0.619537835 0.850381777 0.605533691 0.645098369 0.661555686 1 15.29486899 -5 0.253793461 3.215488003 0.611945597 0.653663096 0.08002306 113.7901229 1.124106881 131.0261946 0.108558312 1.00E-05 5 -2.603542406 RVSVCAETYNPDEEEEDTDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVSVCAETYNPDEEEEDTDPR 21 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 129.84 2.54E-05 107690000 112450 93733 106560 112150 124740 92826 125220 112640 136890 FALSE TRUE 107134.7114 103284.4993 111445.8814 100876.4689 146494.6165 89611.41234 106115.3892 102776.6445 158118.2021 0.6775609 0.653210686 0.704826389 0.637981381 0.926487998 0.566736854 0.671114317 0.649998818 1 17.27064393 -1.242151757 3.25928857 1.00107272 0.682658131 0.530560211 0.092778838 16489608.89 24579250.28 179138.2926 0.020131565 0.057259591 1.242151757 -0.318414589 RVT(ph)QHESDNENEIQIQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVTQHESDNENEIQIQNK 18 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 RVT(0.63)QHES(0.37)DNENEIQIQNK 134.32 8.23E-06 123690000 167130 134880 167690 173560 170260 159440 204800 190910 175340 TRUE FALSE 159230.0961 148624.4253 175378.7524 156113.4191 199953.2901 153918.5528 173553.9986 174192.9083 202530.8317 0.786201759 0.733836049 0.86593607 0.770813104 0.987273337 0.759975909 0.856926312 0.860080941 1 17.62778202 -4.999999992 0.074618744 1.611017536 0.615926145 0.434601987 0.067994806 237.7603699 1.267791981 24.46159762 2.669697943 1.00E-05 4.999999992 -0.995091391 RVTGGLLDRLDDS(ph)PDQCR ddPTM_SK-BR-3_Trastuzumab_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 78.324 0.0095352 99955000 66700 45912 49829 61180 66436 56857 66132 66503 70462 TRUE FALSE 63547.22319 50590.485 52113.70894 55030.07017 78022.41737 54888.02783 56042.3488 60679.64477 81388.88709 0.780785012 0.621589591 0.64030497 0.676137396 0.958637231 0.674392166 0.688574949 0.745551966 1 16.3125442 -5 0.312726089 3.563821144 0.702958271 0.455093761 0.095400147 277.7799253 2.500874865 469.7070475 0.086156505 1.00E-05 5 -2.860862873 RVTQHES(ph)DNENEIQIQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVTQHESDNENEIQIQNK 18 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 RVT(0.004)QHES(0.996)DNENEIQIQNK;RVT(0.005)QHES(0.995)DNENEIQIQNK 216.15 5.59E-19 396120000 312080 303770 302400 359460 257720 333010 368720 342990 296360 TRUE FALSE 297328.5969 334724.5084 316265.3391 323326.3979 302666.2864 321477.7802 312464.992 312955.9773 342317.9952 0.868574253 0.977817448 0.923893408 0.944520599 0.884167034 0.939120305 0.912791604 0.9142259 1 18.38497761 -2.297308248 2.196793729 1.3488285 0.922477027 0.399842324 0.030482308 2992581.775 343642.7074 5207882.869 0.00683435 0.005043032 2.297308248 -0.426351473 RVVFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVFLK 6 1 Q02878;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 99.511 0.062077 424490000 441910 411780 375320 488890 397770 413260 492620 426200 445050 FALSE TRUE 421021.7901 453740.8502 392528.7932 439745.8484 467140.9621 398948.7026 417461.7714 388879.6686 514066.081 0.819003248 0.882650824 0.763576528 0.855426694 0.90871773 0.776065018 0.812078032 0.756477976 1 18.9715943 RVVLGDGVQLPPGDYS(ph)TTPGGT(ph)LFSTTPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.002)S(0.343)T(0.318)T(0.343)PGGT(0.309)LFS(0.245)T(0.227)T(0.21)PGGT(0.002)RIIY(0.001)DRK 115.85 1.08E-05 326590000 148810 81249 162640 115640 159210 154770 211490 169080 202730 TRUE FALSE 141776.0462 89528.36547 170097.2049 104015.6475 186976.1736 149410.2761 179223.3162 154274.4589 234168.333 0.605444999 0.382324819 0.726388588 0.444191775 0.798469081 0.638046461 0.765361029 0.658818624 1 17.83718647 0.545178469 0.187116394 1.190219994 0.399395188 0.549200197 0.117731892 4.326194654 0.435881832 1.045160999 0.492585804 3.508960416 -0.545178469 -0.790824806 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.053)S(0.297)T(0.314)T(0.333)PGGT(0.28)LFS(0.237)T(0.225)T(0.213)PGGT(0.048)R 43.831 0.075095 10177000 6538.1 5770.2 5565.3 5390 6139.4 4948.3 4252.1 5027.4 7152.2 TRUE FALSE 6229.05697 6358.18994 5820.47451 4848.18696 7210.109416 4776.93913 3603.36405 4587.174204 8261.326648 0.754002019 0.76963304 0.704544773 0.586853319 0.872754428 0.578229059 0.436172567 0.555258786 1 13.01215776 3.468245214 3.985590924 0.632625415 0.760060916 0.012306388 0.16417849 0.489570203 17.73790283 0.044714469 0.065509362 2939.308793 -3.468245214 0.1274355 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTRIIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDR 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.107)S(0.272)T(0.288)T(0.305)PGGT(0.308)LFS(0.238)T(0.227)T(0.215)PGGT(0.015)RIIY(0.024)DR 60.959 0.022104 132170000 19128 8270.2 22228 15940 28426 17095 30164 23721 36766 TRUE FALSE 18223.85735 9112.942782 23247.17579 14337.68092 33383.4854 16502.99586 25561.9278 21643.86349 42467.48351 0.429124964 0.214586362 0.547411192 0.337615506 0.786095211 0.388603103 0.601917648 0.509657312 1 15.374071 -4.999999993 0.11418416 2.788077746 0.16321348 0.591347706 0.14433598 98.30495963 0.738664302 40.64209897 1.441686757 1.00E-05 4.999999993 -2.624864267 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.017)S(0.037)T(0.167)T(0.779)PGGT(0.895)LFS(0.038)T(0.035)T(0.031)PGGT(0.001)RIIYDRK;RVVLGDGVQLPPGDYS(0.002)T(0.009)T(0.955)PGGT(0.345)LFS(0.273)T(0.243)T(0.172)PGGT(0.001)RIIYDRK 125.44 1.12E-08 274800000 129309 82000 147433 122641 134323 135858 194170 149689 165767 TRUE FALSE 123196.8198 90355.89323 154192.9489 110312.8937 157748.8887 131153.2034 164545.8003 136581.4376 191473.2997 0.643415139 0.471898136 0.805297392 0.57612677 0.823868857 0.684968628 0.859366818 0.713318451 1 17.5467837 1.846195634 0.156973559 1.144271309 0.375311843 0.533549832 0.102876325 2.969365155 0.430329101 0.808002135 0.978922961 70.17713507 -1.846195634 -0.768959466 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.01)S(0.088)T(0.431)T(0.469)PGGT(0.221)LFS(0.41)T(0.072)T(0.296)PGGT(0.003)R;RVVLGDGVQLPPGDYS(0.01)T(0.057)T(0.931)PGGT(0.012)LFS(0.502)T(0.431)T(0.056)PGGTR 132.49 5.77E-08 1227820000 1029620 814530 914460 1090230 1060640 975520 1156360 1003230 1124340 TRUE FALSE 980951.9031 897531.533 956388.8955 980638.0091 1245615.28 941737.4978 979936.044 915381.8627 1298696.905 0.755335521 0.691101619 0.736421941 0.755093822 0.959127011 0.725140327 0.754553307 0.704846419 1 20.30863334 -2.206307685 2.392911105 1.757243286 0.757043675 0.508302876 0.074061976 7335479.118 1586047.533 30060750.34 0.018815411 0.006218596 2.206307685 -1.000199611 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTRIIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDR 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.127)S(0.247)T(0.267)T(0.338)PGGT(0.105)LFS(0.319)T(0.297)T(0.277)PGGT(0.02)RIIY(0.001)DR 84.247 0.0017271 72204000 15841 8306.9 14541 12400 16853 13399 17908 12824 21947 TRUE FALSE 15092.22732 9153.382554 15207.71923 11153.52844 19792.15786 12934.98927 15175.8057 11701.06258 25350.42867 0.595344068 0.361074074 0.599899885 0.439973958 0.780742532 0.510247359 0.598640989 0.461572573 1 14.62972252 -5 0.293648107 4.668205258 0.512341744 0.597225117 0.116312569 165.1796778 1.545520469 371.9891035 0.110652516 1.00E-05 5 -4.155863514 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.009)S(0.11)T(0.118)T(0.588)PGGT(0.208)LFS(0.333)T(0.31)T(0.287)PGGT(0.01)RIIY(0.026)DRK;RVVLGDGVQLPPGDY(0.037)S(0.069)T(0.371)T(0.493)PGGT(0.129)LFS(0.387)T(0.292)T(0.222)PGGTRIIYDRK 110.58 7.46E-06 691130000 217581 92417 235580 191710 228680 221619 337690 240497 317610 TRUE FALSE 207296.3773 101834.3974 246381.576 172438.9466 268561.7196 213944.2785 286169.1884 219437.8077 366863.3367 0.565050679 0.277581288 0.67158953 0.470035922 0.732048403 0.583171598 0.780043029 0.598145919 1 18.48488321 1.020837756 0.190185879 1.1715034 0.301016356 0.574407313 0.12468596 2.556812296 0.38897256 0.844974199 0.568883415 10.49150414 -1.020837756 -0.870487044 RVVLGDGVQLPPGDYSTT(ph)PGGTLFST(ph)TPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDYS(0.038)T(0.241)T(0.719)PGGT(0.001)LFS(0.177)T(0.527)T(0.296)PGGTR 179.54 1.14E-19 1356000000 1360800 1169100 1279000 1438700 1452400 1342100 1525100 1398000 1578000 TRUE FALSE 1296477.681 1288232.619 1337643.415 1294079.143 1705698.1 1295622.74 1292417.985 1275583.709 1822708.181 0.711291964 0.706768441 0.733876892 0.709976044 0.935804271 0.710822914 0.709064675 0.699828816 1 20.79765217 -1.67856912 2.800405937 1.033156864 0.736492904 0.573651064 0.070481796 13523777.89 12761019.53 3203992.911 0.016536453 0.020961911 1.67856912 -0.29666396 RVVLGDGVQLPPGDYSTT(ph)PGGTLFST(ph)TPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.011)S(0.027)T(0.445)T(0.484)PGGT(0.037)LFS(0.143)T(0.476)T(0.373)PGGT(0.004)RIIYDRK 86.959 0.00043498 202350000 120520 63864 125280 90348 130040 108790 170060 131690 179580 TRUE FALSE 114823.2584 70371.81421 131024.2119 81266.04739 152718.9348 105022.575 144114.2236 120158.5255 207428.3492 0.553556247 0.339258421 0.6316601 0.391778885 0.736249097 0.506307722 0.694766285 0.579277258 1 17.66225356 -4.160280598 0.140290884 2.278812795 0.359250707 0.626168214 0.113681672 58.16763534 0.623780879 21.38809981 0.627295025 6.91E-05 4.160280598 -1.919562087 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDYS(0.029)T(0.181)T(0.789)PGGT(0.001)LFS(0.001)T(0.004)T(0.995)PGGTR;RVVLGDGVQLPPGDYS(0.001)T(0.007)T(0.992)PGGTLFS(0.01)T(0.026)T(0.898)PGGT(0.066)R;RVVLGDGVQLPPGDY(0.003)S(0.03)T(0.132)T(0.775)PGGT(0.059)LFS(0.02)T(0.043)T(0.929)PGGT(0.009)R;RVVLGDGVQLPPGDY(0.001)S(0.058)T(0.235)T(0.702)PGGT(0.005)LFS(0.102)T(0.205)T(0.673)PGGT(0.02)R;RVVLGDGVQLPPGDY(0.003)S(0.059)T(0.214)T(0.718)PGGT(0.006)LFS(0.031)T(0.25)T(0.719)PGGT(0.001)R 178.69 1.21E-19 3532710000 2876970 2268800 2464490 2936140 2935490 2674060 3197080 2827490 3185470 TRUE FALSE 2740981.33 2499993.299 2577489.304 2640993.629 3447438.527 2581456.632 2709306.728 2579899.986 3679456.418 0.74494192 0.679446368 0.700508176 0.717767335 0.936942345 0.701586413 0.73633342 0.701163349 1 21.81106122 -1.991711301 2.904363513 1.248796105 0.737020054 0.558078399 0.072718567 28947493.47 27181165.8 48286410.94 0.016911526 0.010192687 1.991711301 -0.511776051 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.128)S(0.265)T(0.289)T(0.316)PGGT(0.002)LFS(0.165)T(0.153)T(0.676)PGGT(0.005)RIIYDRK;RVVLGDGVQLPPGDY(0.005)S(0.072)T(0.426)T(0.496)PGGT(0.002)LFS(0.08)T(0.069)T(0.849)PGGTRIIYDRK 154.17 7.35E-14 357573000 196848 85643 222738 141033 210384 205012 301643 240781 318958 TRUE FALSE 187543.3852 94370.11907 232950.7576 126856.0949 247074.903 197912.383 255621.8203 219696.9392 368420.3776 0.509047264 0.256147935 0.632296072 0.344324317 0.670633108 0.537191738 0.693831926 0.596321356 1 18.49099333 0.480051395 0.237012035 1.166180033 0.326625877 0.651768019 0.119297307 2.541914414 0.339097467 0.658773367 0.257378176 3.020309128 -0.480051395 -0.839554156 RVVLGDGVQLPPGDYSTTPGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 RVVLGDGVQLPPGDYSTTPGGT(0.003)LFS(0.416)T(0.29)T(0.29)PGGTR 146.58 2.64E-10 158880000 208600 145610 179460 201490 219940 168190 229870 203580 221820 TRUE FALSE 198739.8914 160447.8245 187688.4185 181235.8424 258297.4664 162365.5381 194799.1096 185753.456 256218.7127 0.775665014 0.626214311 0.732532049 0.707348189 1.0081132 0.633698985 0.760284476 0.724980053 1 17.96701632 -5 0.296937564 3.110734168 0.725461504 0.359694856 0.105405692 279.4290985 2.598571537 366.7917722 0.100348685 1.00E-05 5 -2.385272664 RVVLGDGVQLPPGDYSTTPGGTLFST(ph)TPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 RVVLGDGVQLPPGDYSTT(0.001)PGGT(0.14)LFS(0.023)T(0.409)T(0.409)PGGT(0.017)R 175.28 3.99E-15 140100000 278830 203170 249180 263140 281400 236650 296000 238510 300290 TRUE FALSE 265650.2585 223873.254 260605.1495 236688.6673 330476.0709 228454.7512 250839.7636 217624.8 346857.4395 0.765877355 0.645433047 0.751332161 0.682380253 0.952772042 0.658641635 0.723178272 0.627418574 1 18.4039833 -1.096561561 4.161325568 1.00004612 0.724209624 0.466577615 0.092097043 24464667940 64188596.12 11243348.75 0.02031623 0.080064213 1.096561561 -0.275836496 RVVLGDGVQLPPGDYSTTPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 RVVLGDGVQLPPGDYSTTPGGTLFS(0.057)T(0.24)T(0.704)PGGTR;RVVLGDGVQLPPGDYSTTPGGT(0.006)LFS(0.178)T(0.178)T(0.508)PGGT(0.13)R 193.97 1.01E-20 306530000 440370 312964 406850 433290 458960 386170 518170 419740 504160 TRUE FALSE 419554.5828 344855.3874 425504.4749 389734.866 539002.4787 372796.8361 439113.6497 382985.3404 582342.5579 0.720460109 0.592186476 0.730677278 0.669253622 0.925576315 0.640167597 0.754046984 0.657663321 1 19.15150853 -5 0.251248545 2.774536681 0.680743096 0.490150644 0.091007983 148.532099 1.470402025 135.6226635 0.120043828 1.00E-05 5 -2.093793585 RVVNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVNGK 6 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 87.627 0.08374 193470000 641450 662150 433970 668730 454430 543970 593170 640170 557040 FALSE TRUE 611129.9297 729623.8378 453867.9538 601507.9899 533682.4481 525132.1825 502671.0222 584113.321 643422.9182 0.949810634 1.133972411 0.705396001 0.934856333 0.829442709 0.816153991 0.781245131 0.907821752 1 19.2954078 3.746214853 24.99167188 0.841015022 1.041891521 0.408733085 0.093226313 440.802332 1439249.753 0.021552567 0.037930678 5574.614671 -3.746214853 0.200876499 RVVYPLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RVVYPLEK 8 1 O60832;O60832-2;C9IYT0;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 101.65 0.01331 0 425860 339260 362250 454190 360920 393470 500170 419870 422660 FALSE TRUE 405730.4418 373830.9797 378859.5208 408533.9583 423864.3337 379844.0352 423859.8802 383103.9569 488203.9542 0.831067504 0.765727062 0.776027145 0.836810015 0.868211595 0.77804375 0.868202473 0.784721127 1 18.89712445 -5 0.253312412 2.155531832 0.797322351 0.69905942 0.038135626 98.74547733 0.975885375 59.15922293 0.049630711 1.00E-05 5 -1.358209481 RVYATILNAGTNTDGFK ddPTM_SK-BR-3_Trastuzumab_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 ; 275.74 1.59E-35 2730800000 2816240 2874320 2691700 3336100 1963300 2814500 2871270 3110400 2122380 FALSE TRUE 2683121.916 3167216.476 2815117.107 3000748.89 2305698.898 2717033.159 2433205.027 2838036.887 2451507.851 1.094478207 1.291946291 1.148320658 1.224042129 0.940522747 1.108311017 0.992534055 1.157669916 1 21.22523795 2.755924116 24.96709126 1.041161933 1.193859885 0.476553226 0.077997715 634.4795311 912321.2675 0.021506416 0.022756436 570.0646569 -2.755924116 0.152697952 RWDDDVVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RWDDDVVFK 9 1 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ; 110.47 0.0036576 121058000 126334 123122 127245 144586 139784 123926 160019 146477 169497 FALSE TRUE 120362.4422 135668.2718 133079.3091 130051.9406 164162.2853 119634.4115 135605.1626 133650.6974 195781.7291 0.614778727 0.692956756 0.679733036 0.664270058 0.838496453 0.611060144 0.692634411 0.682651532 1 17.57888661 0.066692347 2.557630356 1.000001626 0.682370589 0.718812266 0.061986558 110.0691858 298.2877076 0.055197459 0.014641586 1.165983345 -0.066692347 -0.317631037 RWDDSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RWDDSQK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 204.03 0.00043716 2287720000 2992570 2632060 2712790 3150080 2358630 2979370 3411930 3313100 2693580 FALSE TRUE 2851117.147 2900269.906 2837174.105 2833427.974 2769974.325 2876193.67 2891377.414 3022987.4 3111286.629 0.916378812 0.932177022 0.911897373 0.910693328 0.890298663 0.924438669 0.929318883 0.971619706 1 21.56907988 1.15824987 1.838873615 1.000016802 0.915350455 0.887966944 0.010642665 0.1061938 0.667786564 0.010522151 0.003048701 14.39626625 -1.15824987 -0.084666347 RWDQTADQTPGAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RWDQTADQT(0.014)PGAT(0.986)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK;RWDQT(0.001)ADQT(0.007)PGAT(0.992)PK 187.52 1.97E-07 1298830000 1711940 1740010 1650960 1884230 1256620 1746480 1975150 1985680 1361920 TRUE FALSE 1631019.989 1917318.997 1726658.149 1694823.621 1475774.13 1685998.96 1673804.591 1811803.332 1573119.598 1.036806096 1.218800528 1.097601321 1.077364762 0.938119474 1.071755105 1.064003394 1.151726375 1 20.58519693 3.274902848 3.420122234 1.049633701 1.130799331 0.180431798 0.069468029 0.353677376 8.551392425 0.019605344 0.026219678 1883.227765 -3.274902848 0.08116563 RWEEEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RWEEEGFR 8 1 Q3KQV9 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 145.72 0.0009056 209485000 99520 120898 96295 112086 106083 99817 98962 105585 109429 FALSE TRUE 94815.88683 133217.6436 100710.221 100818.9023 124583.8416 96360.31226 83863.52934 96339.41766 126398.6904 0.750133459 1.053947974 0.796766332 0.797626162 0.98564187 0.762352141 0.663484163 0.762186834 1 16.94762199 2.127650194 10.79717882 0.756697781 0.882164595 0.05112102 0.124725717 0.560651725 51.50648404 0.043542492 0.032156419 134.1683857 -2.127650194 0.125466814 RWLLLCNPGLADTIVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RWLLLCNPGLADTIVEK 17 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 173.28 2.40E-09 152330000 328341 236665 304964 307051 313510 292074 390110 351420 390770 FALSE TRUE 312820.9716 260781.4326 318946.9011 276185.6501 368186.0447 281959.4041 330591.5546 320647.8018 451368.6158 0.693049895 0.577757122 0.706621794 0.611884922 0.815710335 0.624676582 0.732420339 0.710390113 1 18.78394658 -4.999999998 0.204577872 2.522936676 0.627366874 0.711325413 0.064502633 68.4984141 0.680141098 42.58465973 0.128566951 1.00E-05 4.999999998 -1.895569802 RWLPAGDALLQMITIHLPSPVTAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RWLPAGDALLQMITIHLPSPVTAQK 25 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 199.46 4.63E-25 116109000 228120 196864 137536 150099 191701 170380 288990 229480 150770 FALSE TRUE 217337.2197 216924.6654 143842.1616 135010.7634 225133.5937 164479.6979 244899.2678 209385.5146 174150.6416 1.247984031 1.24561508 0.825964006 0.775252747 1.29275202 0.944467941 1.406249587 1.202324107 1 17.40997626 1.744851167 25 1.24073195 1.081648596 0.08786994 0.201111315 2.952304386 11772.05198 0.094640346 0.052482616 55.57137816 -1.744851167 -0.159083354 RWQS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 RWQSPVTK 8 1 A9Z1X7 A9Z1X7 SRRM1 1 RWQS(0.998)PVT(0.002)K;RWQS(1)PVTK;RWQS(0.999)PVT(0.001)K;RWQS(0.999)PVT(0.001)K;RWQS(1)PVTK;RWQS(1)PVTK;RWQS(1)PVTK;RWQS(1)PVTK 105.2 0.0027152 6881540000 7838400 6890750 6812660 8766470 6440820 7661760 8927910 8050570 7194330 TRUE FALSE 7467894.366 7592925.259 7125027.2 7885247.78 7564096.969 7396431.33 7565793.357 7345619.412 8309989.953 0.898664668 0.913710522 0.857405032 0.948887763 0.91024141 0.890065015 0.910445548 0.883950456 1 22.9864153 -1.16309559 4.635933461 1.000012798 0.902953271 0.633932773 0.023464383 2.75E-06 4.97E-07 0.020134995 0.004745238 0.068691723 1.16309559 -0.097059527 RWS(ph)APESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RWSAPESR 8 1 P54253 P54253 ATXN1 Ataxin-1 1 RWS(1)APESR 99.752 0.0040367 285630000 58403 45593 46605 54888 60866 46381 55369 53650 59701 TRUE FALSE 55642.40593 50238.97853 48741.88535 49370.55396 71481.01113 44774.81434 46921.44213 48952.12158 68959.12617 0.806889661 0.728532702 0.706822839 0.715939379 1.036570721 0.649294978 0.680423966 0.709871547 1 16.07345387 -1.326312322 5.143650994 1.000085299 0.751020837 0.337068307 0.108205197 0.000101223 1.33E-05 0.10019469 0.023608051 0.047172368 1.326312322 -0.249064462 RWS(ph)GNEPTDEFSDLPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RWSGNEPTDEFSDLPLR 17 1 Q96II8-3;Q96II8;Q96II8-2;E9PD99;Q96II8-4 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 RWS(1)GNEPTDEFSDLPLR;RWS(1)GNEPTDEFSDLPLR;RWS(1)GNEPTDEFSDLPLR 197.68 9.11E-12 209422000 285903 250521 194858 293030 245735 236311 271300 290665 240374 TRUE FALSE 272388.9318 276049.3747 203792.432 263574.0677 288591.1062 228127.4908 229908.2022 265212.8317 277649.9723 0.981051536 0.994235196 0.733990464 0.949303418 1.039406213 0.821637002 0.828050514 0.955205684 1 18.08290773 2.212097426 24.99955576 0.878258929 0.941912062 0.013418665 0.096338177 572.1901187 540539.7012 0.035646567 0.026333905 162.9661576 -2.212097426 0.063653133 RY(ph)ARKIEPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYARKIEPIR 10 3 Q6P4Q7 Q6P4Q7 CNNM4 Metal transporter CNNM4 1 RY(1)ARKIEPIR 69.349 0.049128 72630000 60554 52206 60818 60485 156710 32294 74006 46315 171370 TRUE FALSE 57691.73243 57525.85075 63606.56546 54404.93289 184040.1744 31175.65068 62715.02549 42259.41307 197945.1844 0.291453074 0.290615056 0.32133424 0.274848479 0.929753229 0.157496384 0.316830266 0.213490483 1 17.59474144 -2.053864074 2.580927221 1.90301951 0.34434642 0.48045335 0.212534645 23636219.19 7978686.357 125962423 0.048267753 0.008833563 2.053864074 -1.55867309 RYDDPEVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RYDDPEVQK 9 1 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 135.43 0.00035449 1907800000 3605390 2958870 3034100 3358240 2450880 2830750 3304790 3463390 2600570 FALSE TRUE 3434970.36 3260382.217 3173216.486 3020663.335 2878312.696 2732720.418 2800583.589 3160117.211 3003853.114 1.143521414 1.085400016 1.056382042 1.005596219 0.958206872 0.909738364 0.932330405 1.052021218 1 21.51838284 3.434859792 1.244371506 0.95823534 1.127138673 0.681904195 0.040322661 0.225857519 0.720103069 0.013955343 0.026238319 2721.822454 -3.434859792 0.168903333 RYDDPEVQKDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYDDPEVQKDIK 12 2 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 100.22 0.0018868 760140000 1873090 610490 2131260 1068340 1636290 1547270 2761500 2068940 2508700 FALSE TRUE 1784552.748 672699.6251 2228980.379 960948.4335 1921658.458 1493687.652 2340182.457 1887772.645 2897736.383 0.615843718 0.232146592 0.76921434 0.331620378 0.663158481 0.515467059 0.807589838 0.65146459 1 21.46649492 1.239914393 0.467184966 1.007069083 0.446144053 0.460752976 0.164063506 0.730541626 0.435848095 0.169956148 0.096946491 17.3745831 -1.239914393 -0.56092503 RYDEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYDEIVK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 87.616 0.054365 0 650780 570814 481176 624899 507782 588623 670716 636449 547581 FALSE TRUE 620018.9191 628980.5956 503238.3955 562082.9653 596339.02 568238.8379 568385.9557 580718.1515 632497.0648 0.980271615 0.994440339 0.795637519 0.888672844 0.942832865 0.898405494 0.898638092 0.918135726 1 19.27069926 RYDFQNPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RYDFQNPSR 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 ;; 119.34 0.001353 573900000 584090 464260 593310 586890 822280 512100 753690 538430 993670 FALSE TRUE 556481.2233 511568.6218 620513.8504 527894.7022 965685.3717 494365.8486 638700.748 491282.2148 1147763.269 0.484839721 0.445709177 0.540628775 0.459933435 0.841362847 0.430721092 0.556474288 0.428034446 1 20.13039368 -2.188267225 2.293946173 2.295356218 0.520808627 0.604947423 0.121006057 4070313.197 827509.4634 27395864.42 0.028128852 0.006482354 2.188267225 -1.774547591 RYDLEQGLGDLLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYDLEQGLGDLLTER 15 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 ; 183.76 7.89E-07 129869000 142909 107638 127451 140811 149572 133464 157486 144160 155150 FALSE TRUE 136153.9748 118606.4346 133294.7544 126656.4108 175657.3094 128842.1082 133458.6183 131536.5862 179209.8696 0.759745962 0.661829813 0.74379137 0.706749082 0.980176537 0.718945382 0.744705738 0.733980703 1 17.45129057 -5 0.258783503 2.580820724 0.730046975 0.444634996 0.084792227 178.6988871 1.757166623 150.3040122 0.109421118 1.00E-05 5 -1.850773749 RYDQDLCYTDILFTEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYDQDLCYTDILFTEQER 18 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 182.95 1.05E-13 103401000 88673 79895 75453 95841 77728 83112 90715 88787 86156 FALSE TRUE 84481.60302 88036.39133 78912.59468 86206.88059 91283.73859 80233.8106 76874.76065 81012.33959 99516.63246 0.848919431 0.884639976 0.792958853 0.866256006 0.917271177 0.806235185 0.772481532 0.814058289 1 16.60265005 RYDSNSGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RYDSNSGGER 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;;; 168.85 7.72E-06 416447000 267881 192491 239958 246674 265855 260463 331326 273229 298636 FALSE TRUE 255218.796 212106.0517 250960.3117 221877.8609 312220.0278 251443.101 280776.1335 249303.6203 344946.9457 0.739878405 0.614894709 0.727533074 0.64322315 0.905124779 0.728932678 0.813969038 0.722730331 1 18.39601496 -5 0.122436384 1.907932758 0.601972771 0.556864659 0.076779226 100.8084586 0.795038267 22.44258378 0.632303323 1.00E-05 5 -1.305959986 RYEDDGIS(ph)DDEIEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYEDDGISDDEIEGKR 16 2 I3VM54;Q9Y2K7;Q9Y2K7-3 I3VM54 KDM2A Lysine-specific demethylase 2A 1 RYEDDGIS(1)DDEIEGKR 105.67 0.00099657 135410000 147620 118640 137020 147160 111640 129840 161430 156570 132370 TRUE FALSE 140642.2952 130729.5509 143302.5025 132367.1972 131109.9807 125343.6082 136800.8886 142859.9008 152897.2635 0.919848347 0.855015635 0.937247006 0.865726398 0.857503775 0.819789742 0.894724245 0.934352241 1 17.22220306 1.014177189 2.404502602 0.99891844 0.877034836 0.593906174 0.03318038 0.19171803 2.438528382 0.030590786 0.008336934 10.33182851 -1.014177189 -0.121883604 RYEEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 152.63 0.0028873 1758005000 2650480 2283080 2252650 2979290 2647420 2809180 3299390 3254890 2916660 FALSE TRUE 2525197.063 2515728.448 2355936.231 2679806.109 3109129.21 2711897.392 2796007.458 2969874.576 3368960.737 0.749547787 0.746737242 0.699306527 0.795439994 0.922874872 0.804965568 0.829931744 0.881540276 1 21.68387218 0.889338299 0.174364961 1.103991392 0.65638259 0.725877693 0.046931432 2.982058661 0.363522515 0.47430947 0.29769964 7.750653088 -0.889338299 -0.447608803 RYEPSDKDRQS(ph)PPPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPSDKDRQS(1)PPPAK;RYEPS(0.119)DKDRQS(0.881)PPPAK;RYEPSDKDRQS(1)PPPAK 184.78 9.77E-09 690510000 873120 803440 731700 914310 481337 885450 841810 978330 570057 TRUE FALSE 831849.348 885311.4494 765249.1688 822401.8217 565282.0204 854786.6445 713376.4236 892662.2387 658458.5281 1.263328384 1.344521199 1.162182789 1.248980439 0.858492975 1.298163222 1.083403727 1.355684832 1 19.32873305 3.530224554 2.293009554 1.137775495 1.303268113 0.168018378 0.145499585 0.458229454 4.76705257 0.038095352 0.063051268 3390.194022 -3.530224554 0.165492618 RYESQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RYESQLR 7 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ;; 193.28 0.00080015 365940000 316103 187031 141302 167335 352652 137914 307865 214398 315243 FALSE TRUE 301161.4376 206089.6715 147780.8365 150514.1679 414154.3971 133138.0036 260894.5399 195624.1745 364129.2744 0.827072852 0.565979409 0.405847173 0.413353659 1.137382864 0.365633891 0.716488781 0.537238251 1 18.47409121 -1.314652468 5.630040361 1.000051726 0.626536974 0.208621813 0.231692445 0.000136157 1.66E-05 0.20304945 0.047852608 0.048455997 1.314652468 -0.373514752 RYLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 111.73 0.044257 698690000 1157740 936290 745390 979420 1094510 943080 1309930 1085700 1200460 FALSE TRUE 1103015.925 1031699.015 779566.8688 880966.8408 1285392.197 910420.9031 1110076.12 990630.3523 1386621.206 0.795470255 0.744038106 0.562206077 0.635333455 0.926995918 0.656575061 0.800561909 0.714420311 1 20.4031423 -1.765182706 0.401945461 1.222097385 0.723473098 0.419233143 0.100358968 36.57188974 2.623281015 7.883113909 0.060634783 0.017171858 1.765182706 -0.498624288 RYNEDLELEDAIHTAILTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYNEDLELEDAIHTAILTLK 20 1 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 176.73 2.15E-14 71285000 175930 124920 146400 160960 160910 156600 215020 181320 162530 FALSE TRUE 167614.1376 137649.49 153112.5848 144779.995 188972.6531 151176.9027 182214.7499 165442.6596 187734.3223 0.892826285 0.733214302 0.815581205 0.771196195 1.006596187 0.805270453 0.970599023 0.881259524 1 17.51833291 2.754455124 24.98698473 0.92364327 0.802185031 0.451258666 0.070582857 726.6932822 1142398.058 0.019439304 0.020555258 568.1396828 -2.754455124 -0.121458238 RYPSGEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYPSGEER 8 1 O00217;E9PPW7;E9PN51;F8W9K7;E9PKH6;H0YDT4 O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" 0 ; 173.39 0.00044579 142864000 198593 154560 160609 172504 212784 146920 182580 188238 245193 FALSE TRUE 189205.9025 170309.8397 167973.0815 155163.5702 249893.4622 141832.1236 154724.0677 171754.8828 283216.2782 0.668061538 0.601341988 0.593091197 0.547862472 0.882341452 0.50079086 0.546310645 0.606444248 1 18.11154466 -0.763949732 6.93005037 0.999999296 0.614420563 0.570725933 0.103992104 1.41E-09 3.04E-10 0.094325003 0.022232616 0.172206788 0.763949732 -0.385578733 RYPSS(ph)IS(ph)SSPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.029)S(0.976)IS(0.898)S(0.074)S(0.022)PQK 128.35 0.0001694 55585000 189190 239500 160950 228900 127430 208850 191800 224430 128010 TRUE FALSE 180247.3636 263905.3223 168329.7167 205890.5371 149653.7517 201617.4721 162537.3874 204777.7194 147861.137 1.219031365 1.7848187 1.138431099 1.392458771 1.012123636 1.363559595 1.099256983 1.384932671 1 17.17388339 3.706505112 24.99864288 1.206551999 1.501925172 0.290852806 0.196556157 661.2551889 515683.055 0.046852288 0.072589296 5087.508078 -3.706505112 0.295373173 RYPSS(ph)IS(ph)SSPQKDLTQAK ddPTM_SK-BR-3_Trastuzumab_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(0.071)S(0.924)IS(0.824)S(0.101)S(0.081)PQKDLTQAK 99.964 0.0046174 818560000 908600 783490 939890 897850 579280 1001600 1133300 1082700 669110 TRUE FALSE 865652.2787 863328.5218 982984.8862 807596.4122 680306.2486 966914.3409 960394.2705 987893.0482 772872.1615 1.120045878 1.117039227 1.27185961 1.044928841 0.880231276 1.251066333 1.242630177 1.278210159 1 19.55987028 RYPSS(ph)ISSS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_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(0.043)S(0.836)IS(0.415)S(0.087)S(0.619)PQK;RYPS(0.029)S(0.962)IS(0.027)S(0.303)S(0.679)PQK 160.03 4.62E-05 305680000 917770 1101940 791480 1095220 599120 980260 871180 994880 577280 TRUE FALSE 874388.8309 1214228.939 827770.1409 985126.4048 703606.3383 946313.3504 738265.4907 907763.033 666801.6341 1.311317769 1.82097475 1.241403888 1.477390508 1.055195882 1.419182711 1.107174087 1.361368939 1 19.34689811 3.234289127 1.635915471 1.212560855 1.548977385 0.288248173 0.200936726 0.382061241 2.117995499 0.060382403 0.086009626 1715.098738 -3.234289127 0.33641653 RYPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RYPS(0.136)S(0.864)ISS(0.001)S(0.999)PQKDLTQAK;RY(0.001)PS(0.439)S(0.56)IS(0.001)S(0.167)S(0.832)PQKDLTQAK;RYPS(0.119)S(0.875)IS(0.006)S(0.323)S(0.677)PQKDLTQAK 227.66 1.53E-19 2010900000 3954800 3436980 3938500 4098100 2402400 4370200 4814000 4818200 3058000 TRUE FALSE 3767864.442 3787212.17 4119084.121 3686151.202 2821377.799 4218858.878 4079535.885 4396292.865 3532219.022 1.066713139 1.072190639 1.166146294 1.043579455 0.798755055 1.194393341 1.154949866 1.244626349 1 21.75214337 RYPSSISS(ph)SPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPS(0.019)S(0.088)IS(0.078)S(0.737)S(0.078)PQK 135.81 0.00012819 231850000 359930 462030 272150 393280 235920 384200 398720 412400 263460 TRUE FALSE 342916.8222 509111.3823 284628.3467 353746.7472 277064.3733 370895.0577 337887.941 376288.0697 304316.0312 1.126844422 1.672969315 0.935305135 1.162432179 0.910449483 1.218782514 1.110319228 1.236504262 1 18.21521081 3.724760795 24.99275454 1.092239692 1.399906891 0.37812428 0.16911199 683.3683086 1237643.066 0.041730043 0.065014159 5305.921196 -3.724760795 0.3076672 RYPSSISSS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPS(0.005)S(0.021)IS(0.008)S(0.082)S(0.884)PQK 185.32 1.40E-05 218870000 351370 438110 265240 399700 222410 365190 375940 374700 229530 TRUE FALSE 334761.4364 482753.9071 277401.5164 359521.3966 261198.2336 352543.3787 318583.4484 341889.2816 265124.3401 1.262658254 1.820858496 1.046307239 1.356048247 0.985191452 1.329728453 1.201637874 1.289543168 1 18.0163096 3.724514614 24.97348146 1.190972936 1.541758396 0.401930525 0.186151514 639.6094306 1137211.257 0.044841058 0.069841168 5302.914366 -3.724514614 0.35078546 RYPSSISSS(ph)PQKDLTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSISS(0.02)S(0.98)PQKDLTQAK;RYPSSISS(0.107)S(0.892)PQKDLTQAK;RYPS(0.012)S(0.012)IS(0.004)S(0.031)S(0.941)PQKDLTQAK;RYPSSIS(0.002)S(0.012)S(0.986)PQKDLTQAK;RYPSSISS(0.004)S(0.996)PQKDLTQAK 276.85 2.13E-39 9164640000 5965760 5304390 5886830 6603820 3776860 7062980 7892710 7608500 4605760 TRUE FALSE 5683770.348 5844913.372 6156746.978 5939991.467 4435543.188 6818387.232 6688532.13 6942259.405 5319997.738 1.068378339 1.098668394 1.157283759 1.116540224 0.833749074 1.28165228 1.257243416 1.304936533 1 22.3429942 RYS(ph)DFEWLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYSDFEWLK 9 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLK;RYS(1)DFEWLK 208.51 6.08E-06 316820000 1160290 1281380 873630 1313870 738120 1059890 978730 1165770 713910 TRUE FALSE 1105445.391 1411954.079 913686.7996 1181797.291 866847.8943 1023185.744 829406.7629 1063688.999 824619.5167 1.340552059 1.712249165 1.108010156 1.433142519 1.05120953 1.240797389 1.0058054 1.289914897 1 19.65336908 3.261462295 1.192261313 1.118995011 1.509910377 0.377245556 0.174166493 0.383461163 1.154486673 0.05972563 0.094377853 1825.838225 -3.261462295 0.390915366 RYS(ph)DFEWLKNELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 RYSDFEWLKNELER 14 2 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLKNELER;RYS(1)DFEWLKNELER 149.95 5.78E-06 128905000 184315 127303 151704 161168 119768 143185 190997 189187 152519 TRUE FALSE 175602.7952 140275.3204 158659.7785 144967.0864 140655.5013 138226.4675 161856.8997 172620.7833 176170.8676 0.996775447 0.79624584 0.900601675 0.822877746 0.798403863 0.784615921 0.918749519 0.979848631 1 17.42661585 1.417423169 3.389617518 0.989379052 0.853797116 0.46004531 0.06258551 0.22760643 4.555052382 0.048273953 0.016375824 26.1470784 -1.417423169 -0.135581937 RYS(ph)DFEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR 247.67 5.01E-11 607666000 300312 296949 239295 321781 326771 281923 348537 317599 356004 TRUE FALSE 286116.8469 327208.4407 250266.9124 289434.9625 383759.7589 272159.9358 295361.2793 289788.3479 411211.2821 0.695790362 0.795718539 0.608609061 0.703859488 0.933242291 0.661849389 0.718271342 0.704718865 1 18.64952032 -0.999187734 4.398835909 1.000010219 0.729974379 0.493278127 0.08668976 8907234.02 4049814.516 864.673397 0.018875722 0.100187206 0.999187734 -0.270035841 RYS(ph)DHAGPAIPSVVAYPK ddPTM_SK-BR-3_Trastuzumab_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(0.381)S(0.616)DHAGPAIPS(0.003)VVAYPK;RY(0.403)S(0.597)DHAGPAIPS(0.001)VVAYPK 117.4 6.24E-05 329490000 829730 748630 724710 877900 694050 810830 902560 859650 724460 TRUE FALSE 790510.3073 824916.2481 757938.6703 789651.8241 815092.1003 782750.7538 764857.8953 784374.4887 836805.5568 0.944676216 0.98579203 0.905752435 0.943650311 0.974051969 0.935403389 0.914021052 0.937343786 1 19.67453291 3.759283591 24.99166222 0.939866489 0.965234119 0.067362285 0.028871936 1549.914122 1869174.078 0.006936951 0.012488305 5744.914779 -3.759283591 0.02536763 RYS(ph)DLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYSDLTTLVAFPSSSVYPTKDEENNPLETEYGLSVYK 37 2 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 1 RYS(0.501)DLT(0.249)T(0.249)LVAFPSSSVYPTKDEENNPLETEYGLSVYK 232.01 1.35E-40 70542000 176090 181690 165760 225270 110030 203150 195480 209760 116090 TRUE FALSE 167766.5747 200204.4176 173360.26 202625.4316 129219.1972 196114.8646 165655.9358 191392.3024 134092.6443 1.251124367 1.493030573 1.292839446 1.51108536 0.963656119 1.462532606 1.235384212 1.427313954 1 17.03287057 RYS(ph)FRVPEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 RYSFRVPEEER 11 2 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6R0;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 RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER 109.83 0.0012732 354545000 392190 296099 332155 399156 409681 322445 420664 402278 454909 TRUE FALSE 373651.9559 326271.8247 347384.6353 359032.0805 481129.2367 311278.6488 356483.9808 367052.4057 525453.9644 0.711103125 0.620933225 0.661113359 0.683279802 0.915644889 0.592399468 0.678430471 0.698543413 1 19.00320485 0.881907207 12.59134692 1.000000001 0.688734017 0.552271772 0.086129764 137.2566737 14636.36922 0.078425095 0.019608804 7.61916199 -0.881907207 -0.311265983 RYS(ph)GNMEYVISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYSGNMEYVISR 12 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 RYS(1)GNMEYVISR 108.49 0.0010415 204570000 109620 100680 95453 106580 102490 100860 113730 110900 110090 TRUE FALSE 104438.4798 110939.4065 99829.61447 95866.37591 120364.2236 97367.19291 96378.39971 101189.0081 127162.1949 0.82130133 0.872424438 0.78505734 0.753890541 0.94654094 0.765692924 0.757917082 0.795747574 1 16.9563103 RYS(ph)PPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR 101.3 0.0033663 48983872100 2342036.6 2106059.5 2107297.9 2407217 2626408.6 2115511.1 2537858.7 2258286.4 2766542.3 TRUE FALSE 2231333.171 2320669.357 2203919.593 2165238.974 3084453.428 2042250.42 2150661.744 2060538.871 3195563.55 0.698259677 0.726215993 0.68968104 0.677576565 0.965229882 0.639089284 0.673014857 0.644812359 1 21.60763895 -1.404616387 3.100917472 1.004070618 0.713624023 0.483586545 0.092803492 33509940.96 41105974.27 1206063.242 0.021731056 0.039389785 1.404616387 -0.290446595 RYS(ph)PS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.126)S(0.875)PS(1)PPPK;RY(0.012)S(0.988)PS(1)PPPK;RY(0.085)S(0.917)PS(0.998)PPPK;RY(0.006)S(0.995)PS(0.999)PPPK 96.82 0.0019252 3542430000 1569170 1298664 1299830 1571890 1123050 1507290 1618700 1403624 1188940 TRUE FALSE 1494998.444 1430999.338 1359428.491 1413880.631 1318909.564 1455092.169 1371737.586 1280715.241 1373314.743 1.088605836 1.042003915 0.989888515 1.029538668 0.960384042 1.059547476 0.998851569 0.932572266 1 20.38923088 4.163122677 1.289195074 0.998079138 1.093665478 0.436468162 0.034592298 0.524813035 1.412688553 0.009633674 0.050555245 14558.7027 -4.163122677 0.095586341 RYS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYSPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.094)S(0.907)PS(0.999)PPPKR 70.332 0.029122 364960000 248100 240040 257180 266620 190490 275380 290580 296750 256070 TRUE FALSE 236372.8047 264500.3489 268971.9574 239818.8511 223711.3957 265843.5215 246246.6841 270764.9968 295780.0278 0.799150661 0.894246819 0.909364839 0.810801368 0.756343819 0.898787939 0.83253317 0.91542691 1 18.17416511 0.973975767 2.787323982 0.999942296 0.845211896 0.532616941 0.048210231 0.215532461 3.982291628 0.044704675 0.011881152 9.418370409 -0.973975767 -0.154730399 RYS(ph)YLTEPGMSPQSPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYSYLTEPGMSPQSPCER 18 1 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 RYS(0.996)YLT(0.004)EPGMSPQSPCER 123.03 1.50E-05 146930000 49592 48473 38943 46724 44788 46902 49915 56527 49008 TRUE FALSE 47247.88444 53412.45381 40728.57507 42027.21475 52599.01302 45277.77198 42299.55 51577.19621 56607.91034 0.834651627 0.94355106 0.719485578 0.742426535 0.929181323 0.79984885 0.74723744 0.911130545 1 15.78871605 -1.470633614 5.866552246 1.000134159 0.828929323 0.314739283 0.079553124 0.000138906 1.25E-05 0.076648348 0.018052091 0.033835016 1.470633614 -0.171204836 RYSPPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 76.1 0.058808 114410000 67631 52595 52752 72533 75263 62897 72833 58325 83295 FALSE TRUE 64434.21666 57954.4903 55170.73138 65241.84504 88388.84337 60718.86112 61720.98818 53217.7538 96211.96319 0.669711068 0.602362621 0.573429016 0.67810533 0.9186887 0.631094711 0.641510537 0.553130318 1 16.55392867 -1.393471589 3.135517802 1.004288391 0.657534676 0.53319834 0.100413963 17099042.31 21039021.64 655911.0282 0.02386047 0.040413681 1.393471589 -0.346753715 RYTCGEAPDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 RYTCGEAPDYDR 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;; 195.87 3.42E-07 5968340000 4319580 3253140 3795080 4143160 4472730 4048830 4847320 4201320 4410960 FALSE TRUE 4115402.014 3584638.665 3969088.172 3726681.685 5252772.696 3908618.002 4107772.307 3833430.148 5094989.149 0.807735187 0.70356159 0.779017983 0.731440554 1.030968377 0.767149426 0.806237695 0.752392211 1 22.28064764 RYWEEETVPTTAGAS(ph)PGPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 RYWEEETVPTTAGASPGPPR 20 1 O15213 O15213 WDR46 WD repeat-containing protein 46 1 RYWEEETVPTTAGAS(1)PGPPR 138.23 1.33E-06 164710000 83270 85140 100050 105980 94595 79485 91143 93113 111790 TRUE FALSE 79333.99213 93815.8628 104637.3915 95326.68905 111092.3381 76732.41452 77237.46139 84959.5321 129125.8223 0.614392929 0.726546102 0.810352179 0.738246521 0.860341767 0.594245312 0.598156589 0.657959273 1 16.97841801 -2.377088808 2.319156178 3.288195756 0.694579058 0.529204959 0.088784641 5267499.481 757582.4853 63016201.35 0.023120534 0.004196732 2.377088808 -2.593616698 S(ph)AEEGELAESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAEEGELAESK 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK 250.69 9.44E-17 878440000 1559740 1683990 1326970 1869220 864580 1671650 1517120 1701270 709750 TRUE FALSE 1486014.181 1855590.496 1387812.887 1681322.454 1015362.478 1613760.341 1285655.48 1552297.78 819814.4051 1.812622677 2.263427532 1.692837889 2.050857418 1.238527247 1.968445945 1.568227482 1.893474633 1 19.64493781 -1.911195651 0.1663372 1.25E-12 2.133822724 0.466813064 0.275283837 30.015158 0.74999135 13.34746228 1.140434715 0.012268864 1.911195651 2.133822724 S(ph)AGEEEDGPVLTDEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK 458.14 1.41E-205 2859480000 5985980 5590420 5582450 6365840 3408550 6638250 6830810 7014240 3803790 TRUE FALSE 5703034.588 6160090.154 5838410.854 5725933.669 4003000.041 6408365.738 5788644.478 6400035.961 4393662.326 1.298013858 1.40203996 1.328825572 1.303225702 0.911085046 1.458547622 1.317498717 1.45665176 1 22.06699257 2.998017105 24.9014525 1.256361438 1.345052348 0.072482678 0.174926563 244.4923858 3070452.002 0.048566278 0.057235184 995.444622 -2.998017105 0.088690911 S(ph)AKSEESLTSLHAVDGDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.541)AKS(0.336)EES(0.086)LT(0.035)S(0.001)LHAVDGDSK;S(0.39)AKS(0.39)EES(0.012)LT(0.174)S(0.034)LHAVDGDSK 197.28 4.82E-16 309860000 635300 514210 556750 670120 342510 658810 759510 751270 368780 TRUE FALSE 605270.628 566608.5836 582277.5382 602758.2645 402243.6356 635995.2445 643632.8001 685484.8161 425968.5189 1.420928076 1.330165396 1.366949698 1.415030073 0.94430367 1.493056919 1.510986778 1.609238208 1 18.70038729 S(ph)APAS(ph)PTHPGLMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 3 S(0.996)APAS(0.99)PT(0.024)HPGLMS(0.991)PR;S(1)APAS(0.773)PT(0.229)HPGLMS(0.998)PR 114.28 0.00028308 116960000 193829 155214 173961 191894 155537 167934 207931 152132 159196 TRUE FALSE 184667.0873 171030.4831 181937.2839 172604.4505 182662.6036 162118.4035 176207.307 138810.5156 183883.3026 1.004262403 0.93010339 0.989417099 0.938662989 0.993361556 0.881637436 0.958256158 0.754883742 1 17.48843096 2.235630796 25 0.901485076 0.967924427 0.226666751 0.066273948 117.505851 1002653.413 0.021569459 0.016628217 172.0405396 -2.235630796 0.066439352 S(ph)APAS(ph)PTHPGLMSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.888)PT(0.112)HPGLMSPR;S(1)APAS(0.82)PT(0.181)HPGLMSPR;S(1)APAS(0.986)PT(0.014)HPGLMSPR;S(1)APAS(0.999)PT(0.001)HPGLMSPR;S(1)APAS(0.995)PT(0.005)HPGLMSPR;S(1)APAS(0.994)PT(0.006)HPGLMSPR 150.61 1.73E-06 2978840000 1594470 1333980 1480870 1576680 1443720 1386470 1682290 1441740 1393100 TRUE FALSE 1519102.563 1469914.079 1548769.354 1418189.131 1695504.311 1338456.196 1425625.763 1315493.602 1609134.833 0.944049269 0.913480989 0.962485755 0.881336419 1.053674482 0.83178623 0.885957928 0.817516081 1 20.61785379 S(ph)APASPT(ph)HPGLMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 3 S(1)APAS(0.306)PT(0.694)HPGLMS(1)PR 183.39 6.02E-12 0 212460 187380 210380 216330 176880 193200 218050 177310 187350 TRUE FALSE 202417.4369 206474.235 220026.1311 194584.0974 207727.816 186509.4356 184782.4677 161783.7964 216403.2811 0.935371385 0.954117858 1.016741197 0.899173508 0.959910658 0.861860479 0.853880157 0.747603251 1 17.72336285 2.209801751 6.103424958 0.853157925 0.952162854 0.288872057 0.066735903 0.185871228 20.69482401 0.022290154 0.016783954 162.1069935 -2.209801751 0.099004929 S(ph)APASPT(ph)HPGLMSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.167)PT(0.833)HPGLMSPR;S(1)APAS(0.309)PT(0.691)HPGLMSPR;S(0.878)APAS(0.277)PT(0.844)HPGLMS(0.001)PR;S(1)APAS(0.299)PT(0.701)HPGLMSPR;S(1)APAS(0.057)PT(0.943)HPGLMSPR 204.13 2.68E-08 2632330000 1465360 1156186 1280300 1458480 1254260 1270120 1528490 1319220 1120310 TRUE FALSE 1396095.337 1274002.668 1339003.021 1311870.819 1473002.547 1226135.426 1295290.778 1203702.103 1294041.953 1.078864046 0.984514192 1.034744676 1.013777657 1.138295821 0.947523705 1.000965057 0.930187851 1 20.30345296 S(ph)APELPEGILK ddPTM_SK-BR-3_Trastuzumab_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 156.14 3.27E-05 150211000 390536 334613 341487 391030 264742 374087 412498 400952 285913 TRUE FALSE 372076.1372 368710.4451 357144.5167 351722.9215 310912.921 361132.2734 349563.8541 365842.5173 330250.9278 1.126646758 1.116455441 1.081433803 1.065017209 0.941444504 1.093508732 1.058479552 1.107771354 1 18.33320309 3.504653578 2.23643069 1.046703226 1.122481347 0.322075758 0.04664907 0.34832851 3.467028285 0.013211007 0.021581537 3196.344474 -3.504653578 0.075778121 S(ph)APPELGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAPPELGIK 9 0 Q96L33 Q96L33 RHOV Rho-related GTP-binding protein RhoV 1 S(1)APPELGIK 88.134 0.013626 95792000 252200 235340 229150 298710 223670 273420 320570 246090 190040 TRUE FALSE 240279.0058 259321.4136 239656.7542 268683.1033 262677.9772 263951.3968 271661.1588 224541.055 219510.4326 1.094613149 1.181362592 1.091778424 1.224010632 1.196653726 1.202454907 1.237577438 1.022917464 1 17.74392998 1.173883761 7.638244219 1.007236353 1.17460524 0.664045358 0.048527081 0.166595083 16.51812696 0.047952127 0.012087278 14.92394917 -1.173883761 0.167368887 S(ph)APPNLWAAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 129.54 0.00025481 861600000 151968 149346 188385 166067 165263 171203 205927 178518 117537 TRUE FALSE 144784.7738 164564.5272 197022.6386 149373.6297 194084.8149 165274.1972 174509.054 162886.0175 135764.0377 1.066444224 1.212136366 1.451213753 1.100244455 1.429574563 1.217363597 1.285384974 1.199772932 1 17.05074185 0.928669839 9.256014832 1.00000008 1.243451897 0.293775933 0.121594289 4.877895939 633.4440283 0.11094789 0.027760253 8.485351531 -0.928669839 0.243451817 S(ph)APSFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAPSFRPK 8 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.996)APS(0.004)FRPK;S(0.985)APS(0.015)FRPK 115.78 0.0014521 395550000 423080 313060 325510 423110 347900 384990 492170 424030 393040 TRUE FALSE 403081.8469 344961.1699 340434.9555 380578.1789 408573.6499 371657.6998 417080.4272 386899.6853 453990.6358 0.887863791 0.759842038 0.749872197 0.838295218 0.899960523 0.81864618 0.918698304 0.852219528 1 18.79230301 0.918856695 0.439286842 1.005293915 0.805740107 0.53285835 0.050839666 0.99963097 0.488153204 0.071215603 0.034254223 8.295769856 -0.918856695 -0.199553809 S(ph)ARHT(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SARHTPAR 8 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 S(1)ARHT(1)PAR 94.122 0.024253 2353100000 24803 20603 18829 27233 21580 18301 26244 18876 11197 TRUE FALSE 23630.61134 22702.46912 19692.32827 24495.4871 25343.54517 17667.23178 22239.9958 17223.11737 12933.37357 1.82710344 1.755340089 1.522597964 1.893975069 1.959546365 1.366018826 1.719581954 1.33168019 1 13.65881102 0.958961247 0.831445933 0.994988174 1.768283461 0.674134216 0.170020111 0.387413425 0.584392276 0.150581912 0.053944689 9.098320832 -0.958961247 0.773295287 S(ph)ARHT(ph)PARS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SARHTPARSR 10 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 3 S(1)ARHT(1)PARS(1)R 92.952 0.014593 961510000 707710 470120 698150 630060 645230 596250 891340 457330 565650 TRUE FALSE 674257.9508 518025.7625 730160.8681 566725.1718 757757.9077 575601.713 755349.7124 417283.7607 653368.1131 1.031972539 0.792854368 1.117533674 0.867390312 1.159771793 0.880976132 1.156085976 0.638665635 1 19.31753652 4.786452226 21.68868163 0.962538355 1.031973916 0.018700485 0.167059662 9889.210436 5882880.813 0.035096325 5.495431377 61157.85238 -4.786452226 0.069435561 S(ph)AS(ph)PERMD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 122.7 0.00092669 1323960000 2210720 2300240 1886890 2284430 1413000 2136330 2103940 1912150 1344590 TRUE FALSE 2106223.647 2534637.071 1973405.773 2054794.756 1659426.753 2062348.356 1782945.311 1744712.009 1553102.15 1.356139805 1.631983493 1.270622008 1.323026149 1.068459504 1.327889705 1.147989726 1.123372348 1 20.56672129 2.853359037 0.445778097 1.048250889 1.541932401 0.571465334 0.117690993 0.850605179 0.340373145 0.107600209 0.174205596 713.4425994 -2.853359037 0.493681512 S(ph)AS(ph)PPPATSSSSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASPPPATSSSSSSR 15 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(1)AS(0.999)PPPATSSSSSSR;S(1)AS(1)PPPATSSSSSSR;S(1)AS(0.999)PPPAT(0.001)SSSSSSR 179.56 9.73E-07 396738000 419427 391601 405757 441170 314076 410761 426615 351019 303992 TRUE FALSE 399601.5169 431505.5871 424361.3598 396822.7534 368850.755 396536.2436 361527.0464 320281.9155 351133.5268 1.138032932 1.228893154 1.20854697 1.130119237 1.050457239 1.12930328 1.029599907 0.912137096 1 18.42166023 2.110327817 0.783639682 0.96335065 1.190512166 0.736508526 0.049508355 0.322419483 0.372414919 0.041075716 0.022795976 128.9222324 -2.110327817 0.227161515 S(ph)AS(ph)PYPSHSLSS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 S(0.997)AS(0.951)PY(0.001)PS(0.045)HS(0.005)LS(0.296)S(0.704)PQR 220.1 1.82E-12 0 276190 210590 240470 259550 208150 242340 279290 180880 183920 TRUE FALSE 263135.0461 232049.3604 251495.7874 233459.5409 244451.2941 233947.705 236679.181 165041.1883 212441.3743 1.238624289 1.09229834 1.183836191 1.098936315 1.150676486 1.101234192 1.114091743 0.776878745 1 17.69670524 1.338227971 6.415231629 0.89096453 1.141230948 0.69925161 0.0686896 0.098210836 5.151232639 0.042045073 0.015097937 21.78853203 -1.338227971 0.250266417 S(ph)ASASHQADIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.694)AS(0.273)AS(0.033)HQADIK;S(0.653)AS(0.314)AS(0.033)HQADIK 150.9 2.17E-05 587790000 1329200 1105200 1240650 1814850 1326990 1512600 1756730 1483640 1181070 TRUE FALSE 1266371.35 1217821.137 1297535.03 1632417.83 1558416.636 1460218.283 1488708.574 1353724.616 1364224.304 0.928272093 0.892683947 0.951115609 1.196590492 1.142346337 1.070365246 1.091249122 0.992303548 1 20.37964944 3.40116409 7.304152139 1.08852683 0.912307913 0.608472256 0.060270313 0.12915391 10.44127632 0.016024199 0.021751227 2518.628365 -3.40116409 -0.176218917 S(ph)ASDNTLVAMDFSGHAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.895)AS(0.104)DNTLVAMDFSGHAGR;S(0.579)AS(0.421)DNTLVAMDFSGHAGR;S(0.591)AS(0.409)DNTLVAMDFSGHAGR;S(0.575)AS(0.425)DNTLVAMDFSGHAGR;S(0.499)AS(0.499)DNT(0.002)LVAMDFSGHAGR;S(0.561)AS(0.439)DNT(0.001)LVAMDFSGHAGR;S(0.582)AS(0.418)DNTLVAMDFSGHAGR;S(0.484)AS(0.484)DNT(0.032)LVAMDFSGHAGR;S(0.46)AS(0.46)DNT(0.081)LVAMDFSGHAGR;S(0.5)AS(0.5)DNTLVAMDFSGHAGR;S(0.583)AS(0.417)DNTLVAMDFSGHAGR;S(0.463)AS(0.463)DNT(0.074)LVAMDFSGHAGR;S(0.487)AS(0.487)DNT(0.027)LVAMDFSGHAGR;S(0.498)AS(0.498)DNT(0.005)LVAMDFSGHAGR;S(0.593)AS(0.407)DNTLVAMDFSGHAGR;S(0.499)AS(0.499)DNT(0.001)LVAMDFSGHAGR;S(0.495)AS(0.495)DNT(0.01)LVAMDFSGHAGR 294.91 1.77E-49 5836600800 1747467.7 1427534.2 1521502.7 1731461.7 1731352.2 1491985.9 1972927.1 1692665 1801077.5 TRUE FALSE 1664868.365 1573001.558 1591265.104 1557411.88 2033299.476 1440318.054 1671920.836 1544446.279 2080379.4 0.800271511 0.756112831 0.764891781 0.748619161 0.977369549 0.692334319 0.803661503 0.742386835 1 20.98841523 -1.101805417 4.167851834 1.000038077 0.785121103 0.446728319 0.074945497 9180730.268 2427001.037 3222.410682 0.015655372 0.079103297 1.101805417 -0.214916974 S(ph)ASEPSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;S(0.5)AS(0.5)EPSLHR;S(0.575)AS(0.425)EPSLHR 99.283 0.0035054 2145020000 1676750 1336340 1568030 1820900 1971260 1601640 2060860 1793520 2042600 TRUE FALSE 1597493.35 1472514.565 1639925.726 1637859.673 2315047.12 1546174.805 1746437.957 1636469.881 2359355.976 0.677088734 0.624117166 0.695073462 0.694197777 0.981219936 0.655337652 0.740218083 0.693608721 1 21.16996168 -5 0.158560852 2.026638078 0.635579315 0.450167605 0.097460921 120.5883996 1.103847904 39.19987272 0.408453812 1.00E-05 5 -1.391058762 S(ph)ASPHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.572)AS(0.428)PHDVDLCLVSPCEFEHR 177.91 1.07E-16 193990000 113290 110620 79258 102580 93928 94098 97407 109230 70082 TRUE FALSE 107935.0062 121892.3038 82892.0577 92268.46351 110309.0135 90839.36267 82545.77315 99665.24214 80949.95863 1.33335468 1.505773515 1.023991353 1.139821009 1.36268153 1.122166882 1.019713593 1.231195714 1 16.30474272 4.362617273 0.282566159 1.024325551 1.68080648 0.317572524 0.138084371 6.543272175 0.512485498 0.171886272 1.472275531 23047.15237 -4.362617273 0.656480929 S(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.566)AS(0.434)PHDVDLCLVSPCEFEHRK 185.45 1.69E-17 250990000 68014 54895 66041 67739 56391 70388 85889 75383 52339 TRUE FALSE 64799.11301 60488.86291 69069.04517 60929.74702 66225.57255 67950.44591 72785.05559 68782.06489 60455.46481 1.071848727 1.000552441 1.14247811 1.00784515 1.09544394 1.123975246 1.203945017 1.13773114 1 15.88358514 2.385769419 3.15895743 1.141085048 1.052893691 0.115287534 0.064486171 0.301976849 6.072434793 0.02206895 0.017964124 243.0913019 -2.385769419 -0.088191357 S(ph)ASPYPS(ph)HSLS(ph)SPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 S(0.986)AS(0.042)PY(0.012)PS(0.644)HS(0.316)LS(0.723)S(0.277)PQR 202.35 5.72E-12 0 167670 126040 159000 164980 129290 150540 181440 116620 115210 TRUE FALSE 159744.5714 138883.6193 166290.3073 148395.897 151838.1351 145326.7621 153757.9956 106408.1346 133076.1784 1.20039945 1.043639974 1.249587336 1.115119917 1.140986591 1.092056924 1.155413369 0.799603174 1 17.02189282 1.25110702 24.99994676 0.89980159 1.137507178 0.65427943 0.073263295 105.665465 210551.4072 0.043399022 0.015610842 17.82818038 -1.25110702 0.237705588 S(ph)ATPVNCEQPDILVSSTPINEGQTVLDK ddPTM_SK-BR-3_Trastuzumab_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 62.683 0.016283 70698000 19897 16959 16888 17492 23920 19437 19169 20413 29821 TRUE FALSE 18956.50824 18687.14138 17662.3315 15733.67093 28091.64043 18763.89182 16244.41699 18625.5295 34445.48838 0.55033356 0.542513469 0.512761826 0.456770151 0.815539037 0.54474164 0.471597813 0.540724791 1 15.07202741 -1.103361164 4.836627078 1.000020707 0.550398122 0.670000531 0.098251165 2.09E-05 3.88E-06 0.090686626 0.021374059 0.078820437 1.103361164 -0.449622585 S(ph)ATREPPYRVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SATREPPYRVPR 12 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.994)AT(0.006)REPPYRVPR;S(0.958)AT(0.042)REPPYRVPR;S(0.98)AT(0.02)REPPYRVPR 88.796 0.0077058 608190000 292245 263490 275833 308183 257605 295802 330450 342745 322765 TRUE FALSE 278431.158 290339.9306 288480.2159 277203.8593 302531.2304 285558.3026 280033.7834 312732.4308 372817.7477 0.74682914 0.778771752 0.773783484 0.743537187 0.81147218 0.765946107 0.751127823 0.838834612 1 18.50811101 0.895476208 3.229192331 0.999874693 0.767421966 0.933433557 0.019673363 0.093465008 2.096624793 0.017843224 0.00464383 7.860971254 -0.895476208 -0.232452727 S(ph)AVDLSCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAVDLSCSR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)AVDLSCSR;S(1)AVDLSCSR;S(1)AVDLSCSR;S(1)AVDLSCSR 180.66 5.08E-05 6359030000 5087880 4041220 4715400 4824480 4474750 4511920 5622270 5249720 4557570 TRUE FALSE 4847385.996 4453024.912 4931605.754 4339514.104 5255144.983 4355671.079 4764489.451 4790026.686 5264334.679 0.920797459 0.845885603 0.936795636 0.82432337 0.998254348 0.827392509 0.905050636 0.909901626 1 22.32781978 0.713751333 2.095070641 0.999928592 0.89104163 0.280091303 0.052889921 1.482859643 9.126278772 0.043065257 0.011805279 5.173105475 -0.713751333 -0.108886962 S(ph)AVFPGEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SAVFPGEGK 9 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)AVFPGEGK;S(1)AVFPGEGK;S(1)AVFPGEGK;S(1)AVFPGEGK;S(1)AVFPGEGK;S(1)AVFPGEGK 121.68 0.00063682 2104440000 4572030 4204920 3746770 4636840 2593150 4281130 4366680 4680550 2768370 TRUE FALSE 4355919.203 4633406.129 3918563.111 4170736.034 3045394.539 4132873.395 3700462.766 4270696.229 3197674.681 1.362214621 1.448992343 1.225441454 1.304302798 0.95237785 1.292462119 1.157235534 1.335563075 1 21.60859174 3.483837976 1.96685285 1.173709405 1.405409404 0.357955574 0.125642887 0.312701654 2.422244806 0.033981234 0.056474238 3046.758109 -3.483837976 0.231699999 S(ph)AVLLVDETATTPIFANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR 292.8 3.36E-49 595627000 129221.3 122949 122341 132272 111789 115875.3 118835 133937 111995 TRUE FALSE 123113.2652 135477.6429 127950.4559 118975.7673 131284.9662 111862.5093 100704.5382 122208.7662 129362.6126 0.95169124 1.047270461 0.989083734 0.919707517 1.014860195 0.864720548 0.778467102 0.944699274 1 16.9810612 2.231235854 24.98301866 0.867299171 0.987355663 0.244197458 0.068064976 155.2753525 529602.5945 0.023836058 0.017960517 170.3083158 -2.231235854 0.120056492 S(ph)AVLLVDETATTPIFANRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAVLLVDETATTPIFANRR 19 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36;A0A087WX73 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(1)AVLLVDETATTPIFANRR;S(1)AVLLVDETATTPIFANRR;S(1)AVLLVDETATTPIFANRR;S(1)AVLLVDETATTPIFANRR 139.69 1.12E-07 190316000 62229.4 39702 64602.6 51010.1 68367.4 56349.5 76167 62151.4 78668.2 TRUE FALSE 59287.93959 43747.67894 67564.69311 45882.46784 80290.65291 54398.10269 64546.32525 56709.09393 90867.66267 0.652464671 0.481443867 0.743550468 0.504937251 0.883599848 0.598651942 0.710333284 0.624084435 1 16.47147935 -4.999999997 0.175995881 2.434621684 0.562741004 0.477059769 0.11527341 103.1609777 0.985577737 51.70058224 0.335729864 1.00E-05 4.999999997 -1.87188068 S(ph)CHDLDLLGQSPGWGQTQAVETNIVCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SCHDLDLLGQSPGWGQTQAVETNIVCK 27 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK;S(1)CHDLDLLGQSPGWGQTQAVETNIVCK 339.98 7.44E-96 2647666000 2071224 1731712 2015679 2037557 1712216 1941903 2374339 2162994 1600519 TRUE FALSE 1973321.346 1908175.422 2108099.876 1832737.899 2010825.928 1874654.412 2012089.978 1973590.779 1848719.312 1.067399109 1.032160701 1.140302837 0.991355414 1.0876859 1.014028685 1.088369643 1.067544849 1 20.81809477 S(ph)CSPLAFSAFGDLTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.5)CS(0.5)PLAFSAFGDLTIK;S(0.5)CS(0.5)PLAFSAFGDLTIK 151.72 6.47E-07 21785600 43258 39471 42111 50624 38878 44697 53223 44659 43341 TRUE FALSE 41213.28007 43493.13977 44041.831 45535.17934 45658.31089 43149.13168 45102.85384 40748.42121 50062.10092 0.823243118 0.86878375 0.879743962 0.909573879 0.912033455 0.861912123 0.900938095 0.813957474 1 15.61143122 S(ph)CSPSPVSPQVQPQAADTISDSVAVPASLLGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.311)CS(0.311)PS(0.311)PVS(0.066)PQVQPQAADTISDSVAVPASLLGMR 49.623 0.04962 76659000 45665 36042 49300 51346 45946 45223 57444 52165 52660 TRUE FALSE 43506.50595 39714.72078 51560.45376 46184.60253 53958.96785 43656.91617 48679.86277 47597.15606 60826.24385 0.715258796 0.652920816 0.84766789 0.759287433 0.887100114 0.717731581 0.80031019 0.782510197 1 15.8924063 -5 0.109633093 1.744395753 0.625525114 0.57140186 0.064459356 116.119593 0.847170647 19.56620696 0.788520704 1.00E-05 5 -1.118870638 S(ph)CTPSPDQISHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.563)CT(0.433)PS(0.004)PDQISHR 93.909 0.0044491 314760000 105930 110730 109140 112220 91266 115100 117360 125430 112360 TRUE FALSE 100922.8988 122013.5129 114144.177 100939.4324 107182.7615 111114.0581 99454.57654 114446.6843 129784.2149 0.777620752 0.940125985 0.879491986 0.777748145 0.825853603 0.856144626 0.766307186 0.881822834 1 16.9857554 -1.745117379 6.841003726 1.002920195 0.838167873 0.463421485 0.054735886 0.002457107 9.15E-05 0.053416646 0.012393358 0.017983848 1.745117379 -0.164752321 S(ph)DEDRYQNGAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDEDRYQNGAER 12 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 S(1)DEDRYQNGAER;S(1)DEDRYQNGAER;S(1)DEDRYQNGAER 166.48 3.14E-05 218408000 192713 200074 184486 223131 168327 201125 208151 198524 149059 TRUE FALSE 183603.8384 220461.7681 192944.8656 200701.448 197683.1755 194159.9908 176393.742 181140.1861 172174.3084 1.066383481 1.280456824 1.120636797 1.165687551 1.148157221 1.127694327 1.024506755 1.052074423 1 17.39351036 1.863119186 1.962003661 1.021187259 1.165228374 0.542878746 0.054604274 0.236418191 1.710066275 0.03364589 0.015462397 72.96577274 -1.863119186 0.144041115 S(ph)DGRMPSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDGRMPSSSR 10 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.987)DGRMPS(0.006)S(0.006)S(0.001)R 65.234 0.042139 160120000 94696 86822 79694 103950 93011 79796 97668 101600 102880 TRUE FALSE 90219.90775 95669.26051 83348.04873 93500.74851 109232.089 77032.64451 82766.9528 92703.36538 118834.105 0.75920888 0.805065688 0.70138155 0.786817459 0.919198146 0.648236839 0.696491574 0.780107406 1 16.85858942 0.954416956 22.03834197 1.000000001 0.758350118 0.513286538 0.073077121 2057.656846 994831.3315 0.0698168 0.0174542 9.003615837 -0.954416956 -0.241649883 S(ph)DSASSEPVGIYQGFEK ddPTM_SK-BR-3_Trastuzumab_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(0.987)DS(0.013)ASSEPVGIYQGFEK 392.63 5.56E-122 78962000 186040 198630 187600 237250 150080 201800 228180 198330 157680 TRUE FALSE 177246.2579 218870.6228 196201.6456 213401.1793 176253.9045 194811.6154 193366.9502 180963.1738 182132.2091 0.973173602 1.201712887 1.077248481 1.171682814 0.967725068 1.069616497 1.061684538 0.993581392 1 17.47462655 2.736706791 24.99954558 1.029803256 1.105565982 0.287100411 0.067165435 242.7232855 3273210.833 0.02040404 0.02012634 545.3895237 -2.736706791 0.075762726 S(ph)DSELEVKPAESLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 S(0.997)DS(0.003)ELEVKPAESLLR;S(0.997)DS(0.003)ELEVKPAESLLR;S(0.879)DS(0.121)ELEVKPAESLLR 189.84 1.46E-07 366510000 603170 536240 378550 625530 292567 555290 537740 623230 260635 TRUE FALSE 574659.3495 590883.4657 395906.8919 562650.536 343590.5922 536060.1681 455697.8867 568656.6772 301052.9447 1.908831518 1.962722757 1.315073973 1.868942144 1.141296235 1.780617588 1.513680217 1.888892593 1 18.1996577 -1.398532514 0.082288557 5.90E-19 2.424437956 0.337477887 0.281224313 98.04414305 1.379950271 33.26709956 11.15373801 0.039945465 1.398532514 2.424437956 S(ph)DSLLSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.985)DS(0.015)LLSFR;S(0.948)DS(0.052)LLSFR;S(0.996)DS(0.004)LLSFR;S(0.999)DS(0.001)LLSFR 142 0.00065516 83160000 126202 100317 97293 119650 99256 100783 118767 115802 106659 TRUE FALSE 120236.6816 110539.4164 101753.9803 107622.5547 116566.215 97292.85944 100646.9128 105661.763 123199.133 0.975953959 0.897241837 0.825930977 0.873565845 0.946161001 0.789720326 0.816944977 0.857650216 1 16.91063258 4.27412926 2.020346801 0.860582267 0.972486308 0.183807528 0.062757456 0.461848145 3.454762911 0.015592663 0.066898942 18798.76245 -4.27412926 0.111904041 S(ph)DSPEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 S(0.5)DS(0.5)PEIPFQAAAGPS(0.097)DGLDAS(0.443)S(0.443)PGNS(0.017)FVGLR 95.212 0.00020818 13201000 30714 31159 23977 30838 22906 29487 27099 27614 23225 TRUE FALSE 29262.21009 34334.13752 25076.36917 27738.10565 26900.79915 28465.8578 22964.54984 25195.97177 26826.61438 1.090790275 1.279853545 0.934757134 1.033977126 1.002765342 1.061105117 0.856036081 0.93921549 1 14.71137737 3.728896295 24.99734788 0.971233041 1.185321912 0.5910868 0.07252131 394.032109 1019187.55 0.019309385 0.030321696 5356.6873 -3.728896295 0.21408887 S(ph)DSSGGYNLSDIIQSPSSTGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSSGGYNLSDIIQSPSSTGLLK 23 0 E9PDR5;Q9P2D0-2;Q9P2D0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 S(0.244)DS(0.244)S(0.244)GGY(0.212)NLS(0.056)DIIQSPSSTGLLK 98.74 0.0018579 25379000 68083 52620 58293 64766 45060 63378 69584 59997 53718 TRUE FALSE 64864.85152 57982.03782 60965.79171 58255.59863 52918.44973 61183.20397 58967.6828 54743.34462 62048.31309 1.045392667 0.934465982 0.982553573 0.938874818 0.852858798 0.986057492 0.950351103 0.882269668 1 15.92110437 5.136605896 0.981187014 0.937447781 1.196269457 0.338137596 0.045612613 4.062623513 1.842545544 0.012944086 1.335198855 136963.8312 -5.136605896 0.258821676 S(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(1)EAEDEDDEDYVPYVPLR 271.68 6.09E-39 488783000 379026 398307 266961 436341 269771 373033 377898 370077 254659 TRUE FALSE 361110.1921 438894.9361 279201.4259 392479.1737 316818.977 360114.7737 320242.7195 337671.096 294150.2171 1.227638707 1.492077553 0.949179738 1.334281435 1.07706525 1.224254659 1.088704685 1.147954604 1 18.16619358 3.597059044 0.212394706 0.983569936 1.51038547 0.225035556 0.140841425 8.967323166 0.596960965 0.294012207 1.291651981 3954.203756 -3.597059044 0.526815534 S(ph)EDEDS(ph)LEEAGSPAPGPCPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEDEDSLEEAGSPAPGPCPR 20 0 Q8TBB5-3;Q8TBB5;Q8TBB5-2 Q8TBB5-3 KLHDC4 Kelch domain-containing protein 4 2 S(1)EDEDS(1)LEEAGSPAPGPCPR 237.73 1.92E-29 89906000 140170 162090 138820 153910 88133 151290 149700 126150 92206 TRUE FALSE 133544.4419 178607.1553 145185.0343 138438.6744 103503.3673 146050.7894 126860.5156 115103.6372 106504.8356 1.25388149 1.676986349 1.363177865 1.299834638 0.971818479 1.371306651 1.191124468 1.080736256 1 16.70055941 3.173686378 2.736103555 1.159391303 1.467071035 0.447111457 0.153620857 0.231749043 3.533032829 0.044301355 0.05673535 1491.71679 -3.173686378 0.307679732 S(ph)EDRRS(ph)SEEREAGEI ddPTM_SK-BR-3_Trastuzumab_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(0.769)EDRRS(0.745)S(0.487)EEREAGEI 97.235 0.0038946 2869100000 988730 784370 868700 983090 869180 917130 1057600 945260 934820 TRUE FALSE 941994.6924 864298.1948 908530.7543 884267.9255 1020764.717 885369.5581 896243.6958 862488.0233 1079787.111 0.872389272 0.800433887 0.841398036 0.818928024 0.94533886 0.819948255 0.830018887 0.798757472 1 20.04231547 -0.95301658 5.050446053 0.999996542 0.839954245 0.578920104 0.042635559 3.69E-07 7.64E-08 0.03841684 0.009054889 0.1114252 0.95301658 -0.160042297 S(ph)EDRRSS(ph)EEREAGEI ddPTM_SK-BR-3_Trastuzumab_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(0.975)EDRRS(0.279)S(0.746)EEREAGEI 123.08 0.0001205 958200000 969700 786540 861250 954440 846750 836680 1034600 881870 903440 TRUE FALSE 923864.2028 866689.3202 900739.1644 858497.8779 994422.9319 807705.5618 876752.7683 804648.7877 1043540.861 0.885316749 0.83052744 0.863156584 0.822677779 0.952931475 0.774004729 0.840171 0.771075497 1 19.99305566 S(ph)EEKEAGEI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEEKEAGEI 9 1 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 S(1)EEKEAGEI;S(1)EEKEAGEI 103.44 0.0090023 630120000 1183260 1006020 965640 1194670 619930 1201380 1189060 1282890 712830 TRUE FALSE 1127329.645 1108534.582 1009915.549 1074579.502 728045.5957 1159775.909 1007647.058 1170553.351 823372.0358 1.369161929 1.34633499 1.226560419 1.305095941 0.884224341 1.408568495 1.223805297 1.421657889 1 19.65118493 3.745902753 2.286443823 1.218821123 1.36546296 0.120488912 0.164880774 0.626196205 6.42499936 0.04263845 0.084133303 5570.609983 -3.745902753 0.146641837 S(ph)EEKET(ph)EENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEEKETEENK 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 S(1)EEKET(1)EENK 109.01 0.052039 187790000 83540 92464 80369 87216 420780 50732 103620 54743 398670 TRUE FALSE 79591.22976 101886.1867 84053.99815 78448.88198 494163.8988 48975.13812 87810.86589 49949.41271 460493.7075 0.172838908 0.221254243 0.182530177 0.170358206 1.073117593 0.106353545 0.190688525 0.108469262 1 18.81282192 -1.842032663 2.553333436 1.287990589 0.270792484 0.386804581 0.28547377 29324377.56 18528533.89 51601816.1 0.069985417 0.014386904 1.842032663 -1.017198105 S(ph)EETQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(1)EETQER;S(0.999)EET(0.001)QER 139.32 0.002832 166035000 200138 293580 250641 278515 115586 256625 124286 230238 91169 TRUE FALSE 190677.8734 323496.1358 262133.1378 250518.1431 135744.1618 247738.0119 105323.888 210077.1402 105307.0229 1.810685253 3.071933162 2.489227504 2.378931017 1.289032375 2.352530772 1.000160152 1.994901521 1 16.68424213 2.813244582 5.767524063 1.553255303 2.485821888 0.441239983 0.507933586 0.198513414 11.73690629 0.144458812 0.153053683 650.4959277 -2.813244582 0.932566585 S(ph)EIQTQASISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEIQTQASISR 11 0 F8VXH2 F8VXH2 WIBG 1 S(0.991)EIQT(0.009)QASISR 56.569 0.076112 196270000 131290 108990 120010 174210 328630 90817 165140 92685 364390 TRUE FALSE 125084.1819 120096.2049 125512.5772 156698.0798 385942.968 87671.98452 139944.86 84569.01005 420897.7402 0.297184256 0.285333451 0.29820207 0.372294895 0.916951865 0.208297589 0.332491355 0.200925313 1 18.68311024 -1.973970387 2.91431726 1.53843305 0.358792635 0.490804696 0.203538068 89152401.96 47074002.24 323596222.6 0.048549849 0.01061768 1.973970387 -1.179640415 S(ph)ESPFRETEPLVSPHQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESPFRETEPLVSPHQDK 18 1 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 S(0.541)ES(0.458)PFRETEPLVSPHQDK 125.58 1.78E-05 39278000 56809 48411 54484 59030 53852 55318 63453 62493 65466 TRUE FALSE 54123.75115 53344.13594 56982.14529 53096.19225 63243.77175 53402.32379 53772.07946 57020.78162 75618.13293 0.715750959 0.705441061 0.753551339 0.702162169 0.836357224 0.706210557 0.711100332 0.754062279 1 16.20644461 -4.999999995 0.447076231 6.965525219 0.727879823 0.809004157 0.040384372 509.1765689 2.979675946 3005.276997 0.020449116 1.00E-05 4.999999995 -6.237645396 S(ph)ET(ph)PPHWR ddPTM_SK-BR-3_Trastuzumab_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 98.754 0.012951 381200000 744030 706980 576020 777280 512740 721070 697580 611400 386050 TRUE FALSE 708861.1764 779022.0658 602431.0868 699146.3377 602161.6937 696099.1651 591151.3591 557862.5748 445916.6623 1.589671874 1.747012686 1.350994788 1.567885654 1.350390655 1.561052151 1.325699192 1.251046713 1 18.76641458 0.940472604 0.182226778 0.75668294 1.824254795 0.725869364 0.110488325 2.256659726 0.303941401 0.879920913 0.564931503 8.719118972 -0.940472604 1.067571855 S(ph)ETPPVPPPPPYLASYPGFPENGAPGPPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SETPPVPPPPPYLASYPGFPENGAPGPPISR 31 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.5)ET(0.5)PPVPPPPPYLASYPGFPENGAPGPPISR 67.641 0.0035717 55656000 97878 88714 94531 98810 70721 83714 105360 92525 86374 TRUE FALSE 93251.50092 97754.05746 98865.33985 88877.43107 83054.72001 80814.96319 89285.39693 84423.02049 99768.43878 0.934679364 0.979809433 0.99094805 0.890837144 0.832474889 0.810025336 0.894926271 0.846189652 1 16.60629588 3.114316253 5.08166774 0.866433814 0.965641711 0.380126417 0.05300702 0.178147345 7.22150027 0.013974233 0.016868878 1301.116704 -3.114316253 0.099207897 S(ph)FAGNLNTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFAGNLNTYK 10 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 S(1)FAGNLNTYK 88.163 0.012988 188820000 322150 307670 208530 300440 242860 274850 308350 305130 213520 TRUE FALSE 306922.6079 339021.9228 218091.3068 270239.2004 285214.7071 265331.8756 261305.5443 278411.1996 246631.5911 1.244457803 1.374608667 0.884279689 1.095720135 1.156440283 1.075822746 1.05949746 1.128854574 1 17.91199808 3.756690335 24.99880235 1.066018564 1.309533251 0.625341369 0.080968039 465.6975916 642141.5067 0.01947077 0.035014335 5710.713001 -3.756690335 0.243514687 S(ph)FDGNTLLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;S(1)FDGNTLLNR 177.83 2.39E-06 789020000 741992 601110 562877 1055173 620722 943310 904469 542997 513800 TRUE FALSE 706919.5086 662363.7924 588685.4672 949105.0053 728975.7203 910642.9382 766475.6423 495449.3041 593477.4799 1.191147992 1.116072328 0.991925536 1.599226656 1.228312354 1.534418692 1.291499119 0.834824102 1 19.17883376 1.244659597 24.99786865 0.917412002 1.270208227 0.402234668 0.182987589 136.9938982 561513.7769 0.129390637 0.044575299 17.56546282 -1.244659597 0.352796225 S(ph)FDYNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.999)FDY(0.001)NYR;S(1)FDYNYR 173.37 0.00090815 15619610000 6804130 7819590 5282940 7429070 4812390 6539400 5745210 6260540 4471700 TRUE FALSE 6482512.259 8616415.111 5525168.025 6682285.769 5651669.292 6312938.938 4868672.696 5712333.928 5165148.398 1.255048599 1.668183457 1.069701701 1.293725805 1.094193014 1.222218309 0.942600739 1.105938008 1 22.30037837 3.130784056 0.923514879 1.044581269 1.44668772 0.417707929 0.155208187 0.448078473 0.84099823 0.070677667 0.102688438 1351.400441 -3.130784056 0.402106451 S(ph)FDYNYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.999)FDY(0.001)NYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR 149.33 0.00031049 4918861000 5258370 3401310 4700460 4551130 4951100 4583060 6265800 5430570 5994600 TRUE FALSE 5009817.271 3747907.356 4915980.74 4093641.766 5814570.272 4424347.483 5309837.131 4955040.502 6924211.952 0.723521652 0.541275654 0.709969708 0.591206883 0.839744698 0.638967656 0.76685075 0.715610749 1 22.72321846 -2.154724011 0.208329537 1.415282116 0.611733506 0.607107864 0.080898132 21.44990986 0.621114016 4.390259117 0.175197792 0.007002869 2.154724011 -0.80354861 S(ph)FEDRVGTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SFEDRVGTIK 10 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 S(0.999)FEDRVGT(0.001)IK;S(1)FEDRVGTIK;S(1)FEDRVGTIK;S(1)FEDRVGTIK;S(1)FEDRVGTIK 177.38 1.41E-06 3178852000 3810530 1739880 3356650 3692800 3534060 4463760 5843230 3506290 3544970 TRUE FALSE 3630413.799 1917175.75 3510555.723 3321592.728 4150398.945 4309178.872 4951737.945 3199260.66 4094705.842 0.886611624 0.468208419 0.85734015 0.811192026 1.013601246 1.052378129 1.209302484 0.781316359 1 21.96532838 2.977469975 1.646422258 1.048751031 0.689183171 0.408077354 0.152189033 0.28493231 1.569117272 0.052656671 0.061307478 949.4453577 -2.977469975 -0.35956786 S(ph)FEEKVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK 207.39 8.05E-08 27401950000 28141090 23618710 20036180 40303830 13802260 39967920 31811110 22843380 9264810 TRUE FALSE 26810916.45 26025483.4 20954858.67 36252412.44 16209369.77 38583820.91 26957740.92 20843092.55 10701549.42 2.505330341 2.431936011 1.958114461 3.387585388 1.514675038 3.605442484 2.519050267 1.947670541 1 23.35131636 0.954930499 3.044209973 1.005295252 2.563504065 0.41221804 0.601461034 0.244914798 5.586185869 0.501847034 0.131733778 9.014268693 -0.954930499 1.558208813 S(ph)FEERVETTVTSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;S(1)FEERVETTVTSLK 242.18 1.09E-17 399545000 458914 309352 381159 557304 448109 603278 658210 394639 387960 TRUE FALSE 437222.0447 340875.3205 398635.5172 501282.7431 526259.0677 582386.3316 557787.9756 360082.317 448122.8554 0.975674504 0.760673812 0.889567475 1.118627932 1.174363372 1.299613096 1.244721105 0.803534818 1 18.77353478 3.238136492 4.432941422 1.145885143 0.861542425 0.335421438 0.147563649 0.177417005 8.400619621 0.041281819 0.053269796 1730.360101 -3.238136492 -0.284342719 S(ph)FEMTEFNQALEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFEMTEFNQALEEIK 15 0 Q9BVS4-2;Q9BVS4;H0Y919 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 S(0.995)FEMT(0.005)EFNQALEEIK;S(1)FEMTEFNQALEEIK 112.72 0.00077756 29674000 38384 61605 35236 50916 30923 54332 37102 53196 21124.7 TRUE FALSE 36569.66439 67882.61954 36851.60545 45797.82695 36315.96141 52450.46922 31441.40848 48537.87623 24400.61059 1.498719233 2.782004954 1.510273906 1.876913153 1.48832183 2.149555604 1.28855007 1.989207445 1 14.57462963 -0.621915789 0.192021357 0.386053029 2.17827771 0.250490924 0.433779003 18.64402931 0.947769219 7.930549674 1.437262518 0.238827433 0.621915789 1.792224681 S(ph)FEVEEVETPNSTPPR ddPTM_SK-BR-3_Trastuzumab_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 358.02 1.53E-87 2555670000 943192 707194 686576 1182365 1174238 937982 1063666 613731 848170 TRUE FALSE 898609.1834 779257.8726 718056.1887 1063511.424 1379024.735 905499.4481 901384.2161 559989.46 979699.8717 0.917229051 0.79540469 0.73293486 1.085548191 1.407599179 0.924262087 0.920061584 0.571592869 1 19.90198033 -2.345002845 2.284229338 1.478370171 0.922144436 0.012918632 0.220390996 21633863.2 2459654.724 54273556.74 0.053822358 0.00451853 2.345002845 -0.556225735 S(ph)FEVEEVETPNSTPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.998)FEVEEVET(0.002)PNSTPPRR;S(0.321)FEVEEVET(0.315)PNS(0.315)T(0.049)PPRR 174.15 8.51E-10 1525450000 404859 339413 333810 457728 507816 377345 500055 311328 432569 TRUE FALSE 385722.1174 373999.5706 349115.5187 411716.3118 596378.9496 364277.448 423762.4256 284066.4699 499649.5913 0.771985256 0.74852372 0.698720713 0.824010104 1.193594391 0.729065838 0.848119228 0.568531376 1 18.93055715 3.013991916 21.09659535 0.862471565 0.748122242 0.114249235 0.161922623 86.82289936 130902.2846 0.044713775 0.053388171 1032.742183 -3.013991916 -0.114349323 S(ph)FGNPFEPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFGNPFEPQAR 11 0 J3KPJ3;Q8N5S9;Q8N5S9-2 J3KPJ3 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 1 S(1)FGNPFEPQAR 132.97 0.0001799 94572000 88150 101910 73918 101240 77751 95860 106380 102840 93084 TRUE FALSE 83983.3242 112294.7449 77307.21341 91063.16286 91310.74978 92540.34416 90149.7772 93834.78441 107518.9913 0.781102233 1.044417767 0.719009846 0.846949564 0.849252292 0.860688359 0.838454454 0.872727536 1 16.71423198 0.949536876 18.87799539 1.000000001 0.858534955 0.242330214 0.082086509 762.618051 285294.3175 0.075188226 0.018797057 8.903010301 -0.949536876 -0.141465046 S(ph)FHIENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFHIENK 7 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3;H0Y534 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(1)FHIENK;S(1)FHIENK;S(1)FHIENK;S(1)FHIENK 131.5 0.0022284 707370000 976477 867040 910747 1058523 759058 891663 1086411 1024532 645785 TRUE FALSE 930320.8674 955392.3617 952505.6508 952118.257 891437.4749 860784.4867 920659.0486 934818.5467 745930.0396 1.247195874 1.280806927 1.276936978 1.276417635 1.195068475 1.153974825 1.234243159 1.2532255 1 19.5086808 -4.778237588 0.202149109 3.15E-11 1.280203845 0.800772387 0.037967579 56.52168005 0.607837113 22.86688965 0.090360289 1.67E-05 4.778237588 1.280203845 S(ph)FILDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFILDK 6 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 1 S(1)FILDK 87.639 0.054767 36391000 73752 92873 79851 100320 66368 88113 91433 105040 80935 TRUE FALSE 70265.88912 102336.8643 83512.24733 90235.643 77942.55819 85061.62472 77483.21657 95842.14075 93485.98644 0.751619486 1.094675985 0.893313004 0.965231758 0.833735206 0.909886369 0.828821725 1.025203289 1 16.5124625 1.215923622 24.97870948 1.012601809 0.903733108 0.216411328 0.090893895 439.4571621 484904.6126 0.083140142 0.020843719 16.44082558 -1.215923622 -0.108868701 S(ph)FKPWLEIFKQNQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFKPWLEIFKQNQQK 15 2 Q96JM4-2;Q96JM4 Q96JM4-2 LRRIQ1 Leucine-rich repeat and IQ domain-containing protein 1 1 S(1)FKPWLEIFKQNQQK 59.185 0.051184 505740000 925330 574440 778130 854300 1020200 699060 1189700 825050 1517200 TRUE FALSE 881591.4847 632976.0891 813808.0302 768424.1409 1198122.557 674851.3769 1008189.415 752804.2481 1752479.627 0.503053771 0.361188843 0.464375173 0.438478216 0.683672745 0.385083722 0.575293087 0.429565192 1 20.74096624 -5 0.286940213 4.996328761 0.445696519 0.746587117 0.094774611 110.0088837 1.041472947 262.7196318 0.092725962 1.00E-05 5 -4.550632242 S(ph)FNDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFNDFR 6 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)FNDFR 121.09 0.020772 115900000 430770 450380 455200 571220 457500 514610 562890 534290 461750 TRUE FALSE 410408.3558 496274.234 476071.3703 513799.8804 537287.8552 496788.9267 477010.7923 487504.7352 533355.8317 0.769483207 0.930474937 0.892596166 0.963334138 1.007372233 0.931439945 0.894357508 0.91403282 1 19.02473883 4.740389893 1.194615937 0.94055215 0.684440256 0.66156579 0.038876623 0.947640097 1.139521425 0.011375683 0.303542638 55003.44522 -4.740389893 -0.256111894 S(ph)FQGDDSDLLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 166.04 5.56E-05 110764000 364165 282941 301447 426050 274042 411630 481330 374680 265939 TRUE FALSE 346951.6422 311773.0096 315268.6431 383222.6446 321834.838 397375.1499 407894.2683 341871.0329 307179.4619 1.129475389 1.014953954 1.026333731 1.247552952 1.047709492 1.293625386 1.327869597 1.112935841 1 18.22872223 3.242439096 24.99434822 1.199859157 1.058292976 0.168652192 0.10856077 127.5043346 821676.7896 0.029597055 0.038612354 1747.588169 -3.242439096 -0.141566181 S(ph)FS(ph)KEVEER ddPTM_SK-BR-3_Trastuzumab_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 2 S(1)FS(1)KEVEER;S(1)FS(1)KEVEER;S(1)FS(1)KEVEER;S(1)FS(1)KEVEER 134.61 0.0029166 849700000 3173460 2671140 2627220 3050370 1483760 3121710 3335360 3402770 1616000 TRUE FALSE 3023456.835 2943332.203 2747680.636 2743741.012 1742527.274 3013604.4 2826489.574 3104805.42 1866601.027 1.619765977 1.576840557 1.472023532 1.469912945 0.933529581 1.614487701 1.514244091 1.663347108 1 20.83198216 3.593588601 2.161760375 1.398378935 1.604591841 0.132769113 0.238010439 0.678290636 6.220686006 0.066291091 0.11695741 3922.731667 -3.593588601 0.206212906 S(ph)FSEDTLMDGPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.999)FS(0.001)EDTLMDGPAR;S(0.994)FS(0.006)EDTLMDGPAR;S(1)FSEDTLMDGPAR 269.14 6.41E-25 365836000 424560 358720 384660 451790 402680 404540 488510 454750 455370 TRUE FALSE 404491.8902 395273.9758 402297.0415 406375.2109 472907.2645 390530.6784 413978.8274 414929.6792 525986.4539 0.769015793 0.75149079 0.76484297 0.772596343 0.899086395 0.742472882 0.78705226 0.78886001 1 19.00466612 -5 0.296943841 2.781299915 0.7693599 0.714326101 0.0429393 137.8290602 1.281737111 152.6083916 0.041744755 1.00E-05 5 -2.011940015 S(ph)FSELPSCDGNESWAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFSELPSCDGNESWAYR 17 0 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 S(0.592)FS(0.408)ELPSCDGNESWAYR;S(1)FSELPSCDGNESWAYR;S(0.999)FS(0.001)ELPSCDGNESWAYR;S(0.997)FS(0.003)ELPSCDGNESWAYR 276.14 1.01E-35 450236000 388219 383446 340792 408771 340472 354553 377912 383255 354786 TRUE FALSE 369868.6572 422519.5833 356417.6503 367680.5625 399850.209 342274.7407 320254.5836 349695.1604 409804.4009 0.902549256 1.031027442 0.869726263 0.897209893 0.975709895 0.835214898 0.781481563 0.853322121 1 18.64457595 2.228167785 24.9829466 0.841526196 0.940626602 0.136121711 0.072005548 245.8380838 590956.8509 0.025227823 0.018834072 169.1094141 -2.228167785 0.099100406 S(ph)FSKEVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.997)FS(0.003)KEVEER;S(0.994)FS(0.006)KEVEER;S(0.997)FS(0.003)KEVEER;S(0.986)FS(0.014)KEVEER;S(0.97)FS(0.03)KEVEER;S(0.969)FS(0.031)KEVEER;S(1)FSKEVEER;S(0.996)FS(0.004)KEVEER;S(0.999)FS(0.001)KEVEER;S(1)FSKEVEER;S(0.998)FS(0.002)KEVEER;S(0.995)FS(0.005)KEVEER 172.13 3.42E-05 25649840000 29126600 25910470 29033540 29724160 19518860 28590770 33596250 33396550 25511660 TRUE FALSE 27749843.34 28550776.35 30364756.53 26736230.96 22922943 27600664.47 28470525.03 30472171.04 29467877.94 0.941698055 0.968877922 1.030435805 0.907300859 0.777895953 0.936635632 0.966154573 1.034080944 1 24.81263984 1.477810596 3.258504531 1.015671533 0.931056086 0.250966154 0.063420654 0.367097393 7.698830693 0.048644722 0.017459806 30.04765582 -1.477810596 -0.084615447 S(ph)FSLDEPPLFIPDNIATIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.5)FS(0.5)LDEPPLFIPDNIATIR;S(0.5)FS(0.5)LDEPPLFIPDNIATIR 123.36 3.29E-05 34356000 61269 55382 53536 69337 58083 61650 69430 56961 59335 TRUE FALSE 58372.93579 61025.48876 55990.67855 62367.11303 68212.65681 59515.04504 58837.17833 51973.19287 68536.36876 0.851707449 0.890410301 0.816948426 0.909985664 0.995276786 0.868371729 0.858481116 0.758330122 1 16.06458214 -2.178770674 2.531150072 1.362708445 0.872059774 0.31235536 0.061047742 8818605.778 2090194.484 18506382.76 0.014207783 0.006625663 2.178770674 -0.490648671 S(ph)FSLEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_SK-BR-3_Trastuzumab_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(0.5)FS(0.5)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER 114.3 2.25E-06 162000000 35970 28982 34080 39299 32909 34674 40849 45395 32169 TRUE FALSE 34269.76939 31935.29875 35642.60171 35348.58986 38648.31918 33473.23069 34616.73481 41419.97315 37157.60422 0.922281458 0.859455269 0.959227659 0.951315097 1.040118705 0.900844696 0.931619127 1.114710542 1 15.18136986 3.09360731 0.390055505 1.013969321 0.869097718 0.285917051 0.061515001 2.382095093 0.659170448 0.061805011 0.141143607 1240.53011 -3.09360731 -0.144871603 S(ph)FSLGDLSHSPQTAQHVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFSLGDLSHSPQTAQHVER 19 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 S(0.569)FS(0.431)LGDLSHSPQTAQHVER 185.41 1.47E-14 139260000 60271 50266 55581 59659 66155 56582 72650 60344 31235 TRUE FALSE 57422.10928 55388.16255 58129.44383 53661.96398 77692.41105 54622.55115 61565.90819 55059.95946 36078.76427 1.591576387 1.535201209 1.611181674 1.48735593 2.153411089 1.513980655 1.706430623 1.52610436 1 15.13886231 0.843246778 4.085460452 1.00002832 1.645247793 0.541600012 0.188705787 0.843537437 21.00502421 0.167961866 0.042869285 6.970224692 -0.843246778 0.645219473 S(ph)FSLSSNFTTPEEVPTGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFSLSSNFTTPEEVPTGTK 19 0 P17029;E9PC66;B3KRF7 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 S(0.5)FS(0.5)LSSNFTTPEEVPTGTK 146.78 1.17E-07 37907000 63202 48360 55001 73444 59159 63838 76513 46672 52682 TRUE FALSE 60214.56671 53287.93898 57522.85025 66061.26959 69476.31087 61627.27405 64839.53659 42585.15226 60851.6555 0.989530461 0.875702371 0.94529639 1.085611707 1.141732469 1.012746055 1.065534472 0.699819124 1 15.89300889 -3.073640566 2.115179044 4.066558406 0.98360234 0.000886667 0.123221161 6005819.125 2269390.314 84449756.74 0.028952612 0.000844033 3.073640566 -3.082956066 S(ph)FSLSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFSLSWR 7 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7;A0A3B3IS41 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.695)FS(0.304)LS(0.001)WR 76.478 0.042641 18929000 42152 34247 39187 41885 50873 41076 54370 38337 54711 TRUE FALSE 40159.5585 37736.80824 40983.76271 37674.64022 59745.23509 39653.52782 46074.85793 34980.00904 63195.30245 0.635483287 0.597145781 0.648525462 0.596162037 0.945406269 0.627475877 0.729086754 0.553522298 1 15.9475297 -5 0.255323802 3.050704123 0.638707364 0.456913617 0.111449354 166.2339029 1.639973143 178.825965 0.142394625 1.00E-05 5 -2.411996759 S(ph)FTCSEKPMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFTCSEKPMAR 11 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.988)FT(0.011)CS(0.001)EKPMAR;S(0.995)FT(0.005)CSEKPMAR 85.45 0.011696 77620000 251710 198800 212523 242380 214017 249290 257370 268620 257700 TRUE FALSE 239812.1671 219057.946 222267.3898 218015.5019 251341.497 240657.0248 218103.4796 245098.2088 297662.7999 0.805650445 0.735926512 0.746708658 0.732424415 0.844383299 0.808488749 0.732719976 0.823408934 1 18.18331941 -2.77031671 0.359418406 1.444908998 0.764842515 0.760442121 0.039481411 37.31251367 1.31918482 12.75168338 0.028622802 0.001697006 2.77031671 -0.680066483 S(ph)FTGGLGQLVVPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFTGGLGQLVVPSK 14 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 S(0.995)FT(0.005)GGLGQLVVPSK;S(0.999)FT(0.001)GGLGQLVVPSK;S(1)FTGGLGQLVVPSK;S(0.988)FT(0.012)GGLGQLVVPSK 235.46 3.23E-17 554885000 954628 793735 835021 940592 660816 925852 1065647 1064415 856195 TRUE FALSE 909504.6263 874617.4989 873307.5388 846041.9052 776062.1012 893789.5131 903062.9782 971209.1798 988969.3478 0.919648954 0.884372707 0.883048136 0.85547839 0.784718053 0.903758559 0.913135458 0.982041741 1 19.91556628 1.363647648 1.893916382 0.999848513 0.873258214 0.657426613 0.035458174 0.219753909 1.394871754 0.033556836 0.010246276 23.10189724 -1.363647648 -0.126590299 S(ph)FTLDDESLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.999)FT(0.001)LDDESLK;S(1)FTLDDESLK;S(0.989)FT(0.011)LDDESLK;S(0.989)FT(0.011)LDDESLK 240.85 2.85E-12 225108000 719240 652670 592400 778320 425965 698370 729830 701530 422034 TRUE FALSE 685242.9506 719177.815 619562.126 700081.7949 500253.1611 674185.2718 618481.0293 640100.3142 487480.8773 1.405681705 1.475294414 1.270946523 1.436121554 1.026200584 1.382998397 1.268728802 1.313077792 1 18.8949861 -4.223650063 0.07142609 7.96E-12 1.746043625 0.460115034 0.118135187 208.6813575 1.23961444 37.04514941 5.706995431 5.98E-05 4.223650063 1.746043625 S(ph)GAAETALLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGAAETALLVR 11 0 Q8WZ26 Q8WZ26 PP6455 Putative uncharacterized protein PP6455 1 S(0.5)GAAET(0.5)ALLVR 67.169 0.06368 10199000 8008.8 6806.3 6850.9 5947.6 7283.3 5854.6 6322.6 6692.5 7831 TRUE FALSE 7630.239896 7499.869708 7165.020541 5349.735948 8553.505214 5651.853734 5357.971247 6106.469221 9045.391485 0.84354999 0.829137105 0.792118346 0.591432218 0.945620234 0.624832407 0.592342659 0.675091756 1 13.14296723 3.464370487 24.63151109 0.709801395 0.832057602 0.055363042 0.139920082 350.215021 676531.0114 0.036022605 0.048805935 2913.201244 -3.464370487 0.122256207 S(ph)GAQASSTPLSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(1)GAQASSTPLSPTR;S(1)GAQASSTPLSPTR;S(1)GAQASSTPLSPTR 151.8 7.17E-06 909640000 449802 423981 435281 487933 432808 450966 508851 473830 478101 TRUE FALSE 428540.7509 467185.1459 455239.0644 438885.0478 508289.5782 435348.9343 431216.4343 432338.9333 552242.4613 0.776001088 0.845978313 0.824346363 0.794732529 0.920410171 0.788329339 0.780846212 0.782878832 1 19.07494229 -1.135505592 4.434647861 1.000027274 0.814016785 0.643595777 0.04345441 19311184144 3764617950 5582480.02 0.009803135 0.07319719 1.135505592 -0.186010489 S(ph)GCCDDSALAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGCCDDSALAR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)GCCDDSALAR;S(1)GCCDDSALAR 230.4 1.92E-12 302060000 204152 166681 174054 215340 181759 176587 221060 194264 204044 TRUE FALSE 194502.1396 183665.9834 182034.5481 193693.6141 213457.7121 170471.7479 187333.237 177253.2143 235686.1014 0.825259268 0.779282199 0.772360131 0.82182875 0.905686465 0.723299961 0.794842105 0.752073259 1 17.84650716 -1.097827916 4.85696957 1.000008436 0.796783114 0.629414703 0.048993641 4.19E-06 7.78E-07 0.044391082 0.010462644 0.079831095 1.097827916 -0.203225322 S(ph)GDEEFKGEDELCDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGDEEFKGEDELCDSGR 17 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 S(1)GDEEFKGEDELCDSGR 85.248 0.004642 0 128120 148990 101620 122660 59693 134060 104680 136860 47581 TRUE FALSE 122064.0215 164172.2504 106279.3775 110329.9838 70103.4403 129417.4686 88709.14342 124875.8129 54959.61847 2.220976508 2.987143196 1.933772113 2.007473611 1.275544523 2.354773781 1.614078589 2.27213755 1 15.74608437 4.158611405 0.080101762 1.54E-15 4.751901695 0.393270352 0.441317689 66.86880584 1.044122431 18.5027183 47.11293226 14408.25563 -4.158611405 4.751901695 S(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.996)GDET(0.004)PGSEVPGDK;S(0.999)GDET(0.001)PGSEVPGDK;S(0.993)GDET(0.007)PGSEVPGDK;S(0.868)GDET(0.132)PGSEVPGDK 308.2 1.25E-55 1271069000 1940820 2786500 1615848 2401890 725803 2160540 1459303 2003590 602470 TRUE FALSE 1849081.285 3070447.518 1689936.229 2160447.454 852382.8134 2085719.958 1236659.525 1828145.038 695897.9706 2.657115501 4.412209329 2.428425287 3.104546277 1.224867508 2.997163444 1.777070171 2.627030276 1 19.40851627 3.216891461 1.788571364 2.06433602 3.479847431 0.3426363 0.797405608 0.332760892 2.196854362 0.232875711 0.321993455 1647.750534 -3.216891461 1.41551141 S(ph)GDETPGSEVPGDKAAEEQGDDQDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGDETPGSEVPGDKAAEEQGDDQDSEK 27 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.769)GDET(0.223)PGS(0.008)EVPGDKAAEEQGDDQDSEK 201.39 2.75E-25 286600000 178180 148670 162260 195540 84231 211990 198310 224790 86177 TRUE FALSE 169757.7845 163819.642 169699.7815 175883.9477 98920.85973 204648.7331 168054.1673 205106.1959 99540.88903 1.705407558 1.645752249 1.704824853 1.766951746 0.99377111 2.055926315 1.68829281 2.060522042 1 16.60300165 S(ph)GEGEVSGLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR 217.42 1.19E-11 4916650000 1992800 1831930 1736920 2128770 1482563 1865208 1979556 1846116 1265499 TRUE FALSE 1898604.293 2018605.75 1816559.5 1914781.995 1741121.518 1800615.379 1677538.375 1684460.296 1461746.122 1.298860497 1.380955092 1.24273256 1.309927878 1.191124431 1.231824975 1.147626356 1.152361735 1 20.47926133 1.592874579 0.343792041 0.982510349 1.365752456 0.85856936 0.039611529 0.38009313 0.145819611 0.053169749 0.04720914 39.16287616 -1.592874579 0.383242107 S(ph)GGDGGDEVEGSGVGAGEGETVQHFPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGGDGGDEVEGSGVGAGEGETVQHFPLAR 29 0 Q96DT7-3;Q96DT7-2;Q96DT7 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 S(1)GGDGGDEVEGSGVGAGEGETVQHFPLAR;S(1)GGDGGDEVEGSGVGAGEGETVQHFPLAR 231.54 1.40E-35 713640000 89896 92615 73734 101173 60449 78775 82270 88532 55298 TRUE FALSE 85646.79424 102052.5738 77114.77683 91002.89782 70991.28646 76047.002 69718.20051 80779.66874 63873.33142 1.340885035 1.597733695 1.207307888 1.424740119 1.111438606 1.19059082 1.09150719 1.264685385 1 15.96292608 2.971068517 1.135140006 1.126298493 1.453075134 0.512066336 0.12144616 0.324572962 0.889622708 0.048581212 0.057071133 935.5532622 -2.971068517 0.326776641 S(ph)GGDGGDEVEGSGVGAGEGETVQHFPLARPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGGDGGDEVEGSGVGAGEGETVQHFPLARPK 31 1 Q96DT7-3;Q96DT7-2;Q96DT7 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 S(0.634)GGDGGDEVEGS(0.344)GVGAGEGET(0.022)VQHFPLARPK 61.372 0.013634 62903000 26711 27646 35274 31982 35497 27168 46982 33492 44968 TRUE FALSE 25448.42397 30463.15883 36891.34779 28767.1086 41687.66556 26227.16535 39814.03302 30559.26293 51941.40778 0.489944825 0.58649082 0.710249286 0.553837677 0.802590214 0.504937515 0.766518173 0.58834106 1 15.6645975 -5 0.142724707 2.293869974 0.493120539 0.577282563 0.102602791 88.01061818 0.763212926 32.4435013 0.521474181 1.00E-05 5 -1.800749435 S(ph)GGGAGSNGSVLDPAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGGGAGSNGSVLDPAER 17 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 S(0.999)GGGAGS(0.001)NGSVLDPAER;S(1)GGGAGSNGSVLDPAER;S(0.998)GGGAGS(0.001)NGSVLDPAER 129.42 3.53E-05 172675000 245578 246138 253638 269968 222838 280640 303765 260770 265484 TRUE FALSE 233970.0146 271219.742 265267.5532 242830.3037 261700.8766 270921.3664 257420.0702 237935.5964 306653.9028 0.762977456 0.884449014 0.865038895 0.791870906 0.853407944 0.88347601 0.839448211 0.775909239 1 18.22625179 -2.240913478 2.43823259 1.63566764 0.835644091 0.60020534 0.042984078 6652097.945 672402.5065 23622528.18 0.009927244 0.005742309 2.240913478 -0.800023549 S(ph)GGGDLTLGLEPSEEEAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(0.986)GGGDLT(0.014)LGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR 352.07 8.91E-91 1653350000 957451 897672 710124 1303690 995980 862709 1056600 1003140 827294 TRUE FALSE 912194.1887 989145.7974 742683.8878 1172640.604 1169678.597 832833.171 895396.2642 915299.7436 955586.5283 0.954590884 1.035119027 0.777202133 1.227142252 1.224042577 0.871541348 0.93701223 0.957840778 1 19.86602699 3.253378797 24.9995085 1.023937458 0.951091194 0.127587457 0.130965219 772.2540065 1302850.211 0.037804271 0.05097755 1792.168323 -3.253378797 -0.072846265 S(ph)GGSIDNVLSQIAAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGGSIDNVLSQIAAQR 16 0 H7C163;A0A0A0MRS7;Q68DC2;Q68DC2-4 H7C163 ANKS6 Ankyrin repeat and SAM domain-containing protein 6 1 S(1)GGSIDNVLSQIAAQR 199.01 4.11E-11 24433000 19616 18072 19918 20120 20202 20851 24023 20265 20502 TRUE FALSE 18688.79056 19913.55735 20831.26 18097.49937 23725.2224 20128.92464 20357.85014 18490.48917 23681.34545 0.789177735 0.840896367 0.8796485 0.764209087 1.001852807 0.849990753 0.859657665 0.780803996 1 14.53146343 -5 0.281676642 2.109083176 0.836674905 0.328078127 0.067462631 267.2916578 2.552152271 173.9525813 0.070241037 1.00E-05 5 -1.272408271 S(ph)GHFDVTTVASIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGHFDVTTVASIK 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.99)GHFDVT(0.003)T(0.007)VASIK 177.21 5.26E-07 0 77899 70935 72219 90796 80541 67579 97715 78989 70243 TRUE FALSE 74216.86865 78163.35715 75530.31258 81669.01358 94587.3249 65238.72228 82806.78209 72072.30441 81135.92569 0.914722646 0.963363103 0.930910838 1.006570306 1.165788448 0.804067024 1.020593299 0.8882909 1 16.30805324 4.273740366 1.28983901 0.976490115 0.913051695 0.03945279 0.093451162 2.502408245 6.226692516 0.025471842 0.169040149 18781.93644 -4.273740366 -0.06343842 S(ph)GLLSSFSLSMTDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGLLSSFSLSMTDLSK 16 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.998)GLLS(0.002)SFSLSMTDLSK;S(1)GLLSSFSLSMTDLSK 252.01 1.69E-26 115776000 379200 346900 358670 390240 274945 354830 416130 397140 295706 TRUE FALSE 361275.9675 382249.5044 375115.3743 351012.3338 322895.3209 342542.1481 352641.7257 362364.3162 341562.5762 1.057715314 1.119119983 1.098233239 1.027666256 0.945347481 1.002867913 1.032436661 1.060901695 1 18.38179039 3.167407447 4.851663161 1.009610416 1.092770112 0.579958007 0.032420862 0.144555587 6.375951628 0.009696243 0.011858444 1470.305044 -3.167407447 0.083159696 S(ph)GNSDSIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)GNSDSIER;S(0.99)GNS(0.01)DSIER;S(0.999)GNS(0.001)DSIER 209.84 8.14E-06 968970000 886040 858290 767960 939560 724240 850080 947660 870410 790650 TRUE FALSE 844158.6452 945750.7268 803171.7256 845113.6438 850547.2267 820641.5164 803077.062 794192.2861 913259.9639 0.924335544 1.035576686 0.879455749 0.925381246 0.931330903 0.898584794 0.879352094 0.869623456 1 19.80066606 3.724081649 24.96843238 0.905929011 0.979956119 0.269124144 0.045752344 762.1167882 1314242.309 0.011224182 0.017480116 5297.630321 -3.724081649 0.074027108 S(ph)GS(ph)IKGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGSIKGSR 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 S(1)GS(1)IKGSR;S(1)GS(1)IKGSR;S(1)GS(1)IKGSR 118.87 0.0010266 1938550000 3903980 3255930 3859870 3706710 1933790 4094160 4203990 3855530 2329390 TRUE FALSE 3719446.602 3587712.969 4036848.857 3334104.469 2271042.364 3952378.213 3562594.114 3517919.354 2690619.904 1.382375339 1.333415011 1.500341557 1.239158479 0.844059155 1.468947065 1.324079298 1.307475407 1 21.35950717 -4.533639228 0.186311274 6.74E-14 1.366547549 0.220586044 0.178711856 183.2758316 2.087191437 69.46074337 0.507552278 2.93E-05 4.533639228 1.366547549 S(ph)GSDAGEARPPTPASPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSDAGEARPPTPASPR 17 1 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 S(0.615)GS(0.385)DAGEARPPTPASPR 70.452 0.019747 186790000 148400 124280 140650 160400 129340 146480 177940 148340 123630 TRUE FALSE 141385.4261 136944.2733 147098.9416 144276.2873 151896.855 141407.3609 150791.9849 135350.5632 142801.909 0.990080785 0.958980691 1.030090863 1.01032464 1.063689247 0.990234387 1.055952165 0.947820405 1 17.12365574 3.735070595 24.95733018 1.018983885 0.974530737 0.179468522 0.033826915 353.8516865 2530410.022 0.007920461 0.012830679 5433.386447 -3.735070595 -0.044453148 S(ph)GSFDSR ddPTM_SK-BR-3_Trastuzumab_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)FDSR 71.692 0.056253 96051000 494980 449430 486920 528510 400360 529860 500490 484830 438970 TRUE FALSE 471583.2764 495227.428 509245.7636 475383.1707 470182.6572 511510.8153 424131.0584 442375.715 507043.2257 0.930065234 0.976696666 1.004343886 0.937559456 0.927302907 1.008811063 0.836479095 0.872461543 1 18.95174922 1.741119695 25 0.888590434 0.962068139 0.233653168 0.049897055 0.459866641 4520.344218 0.02080415 0.011536928 55.09595242 -1.741119695 0.073477705 S(ph)GSMDPSGAHPSVR ddPTM_SK-BR-3_Trastuzumab_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(0.5)GS(0.5)MDPSGAHPSVR;S(0.5)GS(0.5)MDPSGAHPSVR 118.31 0.00084728 495320000 649690 444530 561960 647910 595090 564480 788930 621080 699430 TRUE FALSE 618980.4413 489828.1124 587726.4219 582780.8559 698873.5076 544931.9161 668564.2388 566694.9426 807894.0322 0.766165384 0.606302427 0.727479593 0.72135804 0.86505591 0.674509149 0.827539519 0.701447121 1 19.62380655 -5 0.173761482 2.070578748 0.671344853 0.559937656 0.073295512 89.81348001 0.854128039 33.08258105 0.228194634 1.00E-05 5 -1.399233895 S(ph)GSPRPTEPTDFLMLFEGSPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.491)GS(0.491)PRPT(0.009)EPT(0.009)DFLMLFEGSPSGK;S(0.5)GS(0.5)PRPTEPTDFLMLFEGSPSGK;S(0.559)GS(0.44)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.495)GS(0.495)PRPT(0.007)EPT(0.002)DFLMLFEGSPSGK;S(0.547)GS(0.452)PRPTEPTDFLMLFEGSPSGK 201.1 1.40E-24 663881000 419751 389654 409262 452279 324499 441466 474308 474783 347540 TRUE FALSE 399910.2021 429360.1856 428027.0675 406815.0556 381091.5229 426177.9217 401943.6033 433208.4835 401434.7282 0.996202306 1.069564129 1.066243246 1.013402745 0.949323753 1.061636903 1.001267641 1.07915049 1 18.6148059 3.201762454 24.97998581 1.016331475 1.04265189 0.088185567 0.040040875 407.6501359 276727.6595 0.011004613 0.013153238 1591.338074 -3.201762454 0.026320415 S(ph)GSSPKWTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSSPKWTHDK 11 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.333)GS(0.333)S(0.333)PKWTHDK 140.08 2.34E-05 183320000 274110 77416 288730 173550 178910 239220 438400 289880 260610 TRUE FALSE 261153.3635 85304.77841 301968.5561 156104.4243 210111.8474 230935.7514 371514.0282 264496.5704 301024.0678 0.867549779 0.28338192 1.003137584 0.518577885 0.697990194 0.767167068 1.234167191 0.878655891 1 18.19951931 1.934475358 5.325695411 1.054686279 0.652002627 0.384901145 0.208783441 0.192021325 10.51020371 0.086404551 0.052326038 85.99542714 -1.934475358 -0.402683651 S(ph)GSSS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.622)GS(0.362)S(0.021)S(0.995)PDSEITELKFPSINHD 240.43 3.31E-30 153380000 357690 335390 341430 392370 244580 362730 392960 392960 229490 TRUE FALSE 340782.7026 369566.6223 357084.9032 352928.2221 287234.6746 350168.5691 333006.7348 358550.3392 265078.1371 1.285593396 1.394179944 1.347093001 1.331412036 1.08358493 1.32100132 1.256258771 1.352621318 1 18.01605816 -4.178475536 0.22345352 1.06E-14 1.338556133 0.534515302 0.085779904 80.17003004 1.119751887 36.46460192 0.154338983 6.63E-05 4.178475536 1.338556133 S(ph)GSTESLNPRPQTTISPADLHGMWYPTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.493)GS(0.493)T(0.014)ESLNPRPQTTISPADLHGMWYPTVR;S(0.536)GS(0.443)T(0.02)ESLNPRPQTTISPADLHGMWYPTVR;S(0.527)GS(0.454)T(0.018)ESLNPRPQTTISPADLHGMWYPTVR 189.31 2.74E-18 366255000 311758 271191 321673 317238 247006 306891 362741 334038 242630 TRUE FALSE 297021.8172 298825.6712 336422.0252 285348.6335 290083.7682 296263.2877 307398.1983 304787.8619 280255.8212 1.059823899 1.066260354 1.200410481 1.018172013 1.035067771 1.057117338 1.096848575 1.087534455 1 18.09638481 S(ph)GTPPRQGSITSPQANEQSVTPQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQRR 25 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.532)GT(0.468)PPRQGSITSPQANEQSVTPQRR 72.791 0.018377 442740000 250940 125030 227230 209350 211540 195320 285000 214880 237470 TRUE FALSE 239078.5635 137770.6991 237648.7203 188305.7403 248432.509 188556.0194 241518.0156 196063.968 274295.6348 0.871609071 0.502270841 0.86639629 0.686506515 0.905710764 0.687418958 0.880502586 0.714790697 1 18.06537214 -4.108958886 0.156389205 1.677124425 0.678706715 0.243944386 0.125621171 118.3303616 1.391305704 25.54758241 0.531716412 7.78E-05 4.108958886 -0.99841771 S(ph)GTPTQDEMMDKPTSSSVDTMSLLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.5)GT(0.5)PT(0.001)QDEMMDKPTSSSVDTMSLLSK;S(0.369)GT(0.332)PT(0.299)QDEMMDKPTSSSVDTMSLLSK 115.74 0.0017165 374390000 539430 477280 487240 538440 246940 571260 538710 601900 254730 TRUE FALSE 513932.2129 525915.3746 509580.4359 484314.9882 290006.2578 551477.123 456519.8954 549194.4451 294232.2274 1.746689061 1.787415944 1.731898781 1.646029711 0.985637299 1.874292044 1.551563197 1.866533962 1 18.16659575 -2.004366516 2.835868294 0.328935037 1.652214383 0.39069846 0.254580226 17930001.91 20882891.45 78700308.19 0.057944915 0.009899961 2.004366516 1.323279346 S(ph)HHAASTTTAPTPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.994)HHAAS(0.005)TTTAPTPAAR;S(1)HHAASTTTAPTPAAR;S(0.997)HHAAS(0.003)TTTAPTPAAR 82.859 0.0056814 277906000 84611 87063 98242 121247 120924 112944 128841 92290 70737 TRUE FALSE 80611.60571 95934.81868 102746.4929 109059.0212 142013.1073 109032.721 109183.9391 84208.59834 81706.53269 0.986599273 1.174138903 1.257506462 1.334765014 1.738087551 1.334443127 1.336293874 1.03062259 1 16.31816381 4.032190986 1.531064725 1.331906615 1.004247712 0.171347703 0.202516441 0.608936373 2.625728085 0.056206365 0.198932619 10769.38705 -4.032190986 -0.327658903 S(ph)HHKDHSDSESTSSDNSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHHKDHSDSESTSSDNSGR 19 1 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 S(0.493)HHKDHS(0.119)DS(0.119)ES(0.119)T(0.119)S(0.03)SDNSGR 45.094 0.093345 44167000 2805 5329.6 6809.4 6462.2 6596.7 4341.5 8900.2 7776.3 1395.6 TRUE FALSE 2672.413209 5872.692299 7121.617725 5812.607379 7747.162391 4191.152766 7542.311027 7095.365947 1612.02252 1.657801411 3.643058472 4.417815282 3.605785469 4.805864865 2.599934377 4.67878763 4.401530288 1 10.65465618 4.473643872 2.176730513 3.841255737 1.586615034 0.211540906 1.153298541 0.460438708 3.619286337 0.255391764 1.627683206 29760.75 -4.473643872 -2.254640704 S(ph)HNDFVAILDLPEGEHQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHNDFVAILDLPEGEHQYK 19 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 S(1)HNDFVAILDLPEGEHQYK;S(1)HNDFVAILDLPEGEHQYK 101.86 0.00068234 41184000 143994 165909 138823 192611 107127 160962 163285 126001 34039 TRUE FALSE 137187.689 182815.3157 145188.1719 173249.3763 125809.9149 155387.8456 138372.8743 114967.6845 39317.59427 3.489218797 4.64970757 3.692702327 4.406408366 3.199837559 3.95211987 3.519362689 2.924077289 1 15.26288743 0.512464957 0.643434234 0.922946539 4.035321579 0.832506199 0.409438692 0.582351032 0.412012648 0.446226618 0.146893624 3.254355235 -0.512464957 3.11237504 S(ph)HNNFVAILDLPEGEHQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHNNFVAILDLPEGEHQYK 19 0 Q9Y478 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 S(1)HNNFVAILDLPEGEHQYK 106.03 0.00053835 38705000 82952 82412 94971 103540 72355 102050 117140 78737 24895 TRUE FALSE 79031.02336 90809.87649 99325.51429 93131.96249 84973.68909 98515.98291 99268.14158 71842.37087 28755.58945 2.748370833 3.157990437 3.45412896 3.238742945 2.955032072 3.42597682 3.452133775 2.498379349 1 14.81155479 0.918329227 3.966448166 1.001033461 3.190192202 0.906439199 0.224865431 0.110518757 4.167122521 0.235464425 0.060248035 8.285700415 -0.918329227 2.189158741 S(ph)HS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Trastuzumab_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(0.495)HS(0.534)GT(0.524)S(0.447)PDNTAPPPPPPRPQPSHSR 98.839 0.0097725 106410000 9656.9 9904.6 11102 14762 10756 10832 13006 7443 4806.6 TRUE FALSE 9200.437475 10913.89 11611.03768 13278.09571 12631.84299 10456.88512 11021.69583 6791.251462 5551.982979 1.657144395 1.965764312 2.091331642 2.391595177 2.275194834 1.883450501 1.985181848 1.223211866 1 12.43878743 1.179846916 3.184580776 1.001335766 2.025848798 0.787980006 0.200955871 0.118299419 2.131033966 0.206454687 0.056403036 15.13027829 -1.179846916 1.024513032 S(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.815)HS(0.181)DNDRPNCS(0.004)WNTQYSSAYYTSR;S(0.821)HS(0.179)DNDRPNCSWNTQYSSAYYTSR;S(0.491)HS(0.491)DNDRPNCS(0.018)WNTQYSSAYYTSR;S(0.921)HS(0.079)DNDRPNCSWNTQYSSAYYTSR 268.45 5.87E-45 2039840000 454744 452719 489718 604746 419421 493330 603798 425420 218310.3 TRUE FALSE 433249.1523 498851.5808 512172.0547 543955.7831 492567.8896 476245.8584 511677.5256 388167.9695 252164.7463 1.718119438 1.978276456 2.031100945 2.15714445 1.953357465 1.888629816 2.02913981 1.539342732 1 17.94400707 0.972337552 3.13901765 1.001651492 1.957821038 0.884203373 0.114010236 0.081512432 2.012041812 0.114853695 0.030065966 9.382910039 -0.972337552 0.956169546 S(ph)HSGTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Trastuzumab_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(0.304)HS(0.258)GT(0.219)S(0.219)PDNTAPPPPPPRPQPSHSR;S(0.25)HS(0.25)GT(0.25)S(0.25)PDNTAPPPPPPRPQPSHSR 97.974 0.0048381 690360000 67382 79922 84465 93257 77051 84094 98610 65374 26467.3 TRUE FALSE 64196.9864 88066.14266 88337.8038 83882.62918 90488.67 81181.80369 83565.2334 59649.50599 30571.71371 2.099881839 2.880641351 2.88952738 2.743798728 2.95988216 2.655454793 2.73341672 1.951133867 1 14.8999098 0.971562142 2.640901031 1.003008283 2.704508678 0.845995776 0.238326361 0.107662494 1.750632702 0.232540139 0.062259671 9.366172284 -0.971562142 1.701500395 S(ph)HSLDDLQVEPGAEQDVPTEVTEPPPQIVPEVPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSLDDLQVEPGAEQDVPTEVTEPPPQIVPEVPQK 35 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(0.499)HS(0.499)LDDLQVEPGAEQDVPT(0.001)EVTEPPPQIVPEVPQK 96.492 0.00048914 38752000 25620 29935 27943 34070 24729 32305 34055 27815 12618 TRUE FALSE 24408.99337 32985.41053 29224.21419 30645.21887 29041.72977 31186.26975 28859.28429 25379.37114 14574.735 1.674746977 2.2631911 2.00512834 2.102626146 1.992607741 2.139748665 1.980089813 1.741326422 1 13.83118203 0.811663946 1.980008963 1.000768065 2.032202043 0.823183588 0.149519823 0.258643388 1.801750824 0.134827526 0.037416035 6.481327185 -0.811663946 1.031433978 S(ph)HSQASLAGPGPVDPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.548)HS(0.439)QAS(0.012)LAGPGPVDPSNR 122.22 2.36E-05 211330000 56704 56556 67220 75558 61530 64567 73996 59193 45676 TRUE FALSE 54023.7143 62319.1207 70302.10349 67962.76629 72260.81252 62331.0286 62706.55117 54009.74712 52759.2008 1.023967639 1.181199104 1.332508879 1.288168988 1.369634328 1.181424807 1.188542476 1.023702905 1 15.68713509 1.25300092 2.724429321 0.995149283 1.218432764 0.464016667 0.095163583 0.285839963 3.55532866 0.096486224 0.027773072 17.90609646 -1.25300092 0.223283481 S(ph)HSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.482)HS(0.419)VGGPLQNIDFT(0.074)QRPFHGIS(0.012)T(0.012)VS(0.002)LPNSLQEVVDPLGK;S(0.426)HS(0.426)VGGPLQNIDFT(0.107)QRPFHGIS(0.02)T(0.02)VS(0.001)LPNSLQEVVDPLGK;S(0.499)HS(0.499)VGGPLQNIDFT(0.003)QRPFHGISTVSLPNSLQEVVDPLGK 162.72 3.05E-18 651080000 524620 479499 506033 693131 533322 634870 728856 476143 170918 TRUE FALSE 499822.2523 528360.4932 529235.1136 623456.155 626333.1879 612884.2927 617655.6308 434449.3947 197423.0905 2.531731476 2.67628519 2.680715372 3.157969787 3.172542717 3.104420517 3.128588602 2.200600718 1 17.59093121 3.462875058 24.46667615 2.824237349 2.616423485 0 0.677523839 903.7813954 1552163.876 0.166261064 0.225219704 2903.187316 -3.462875058 -0.207813865 S(ph)HTGEKPY(ph)KCEECGKAFVAS(ph)S(ph)T(ph)LSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHTGEKPYKCEECGKAFVASSTLSK 25 3 A0A1W2PNY2;P35789-3;P35789 A0A1W2PNY2 ZNF93 Zinc finger protein 93 5 S(0.615)HT(0.615)GEKPY(0.939)KCEECGKAFVAS(0.942)S(0.942)T(0.942)LS(0.004)K 41.482 0.081461 67080000 58078 39510 51869 59677 62400 47594 80676 59330 87868 TRUE FALSE 55332.76804 43536.11392 54247.24496 53678.15458 73282.54024 45945.80785 68367.39448 54134.75067 101494.1207 0.545182003 0.428952078 0.534486575 0.528879449 0.722037294 0.45269428 0.673609407 0.533378193 1 16.63103663 -4.999999998 0.198451051 3.051976212 0.47229923 0.730515293 0.086176629 65.05384447 0.642509961 52.80005339 0.18767167 1.00E-05 4.999999998 -2.579676982 S(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.352)HT(0.352)S(0.294)EGAHLDIT(0.002)PNSGAAGNSAGPK;S(0.682)HT(0.133)S(0.092)EGAHLDIT(0.092)PNS(0.001)GAAGNSAGPK;S(0.356)HT(0.288)S(0.356)EGAHLDITPNSGAAGNSAGPK;S(0.357)HT(0.357)S(0.286)EGAHLDITPNSGAAGNSAGPK 207.9 5.08E-25 2165930000 824313 997910 1221830 1506690 987660 1299920 1772470 899450 110978 TRUE FALSE 785349.3581 1099598.164 1277852.114 1355234.659 1159907.591 1254903.444 1502047.148 820689.3897 128187.9014 6.12654821 8.578018293 9.968585956 10.57225092 9.048495047 9.789562278 11.71754222 6.4022375 1 16.96790058 0.960762568 6.946063897 1.000377049 9.281266458 0.775260927 1.447000938 0.187004215 31.43843533 1.592471688 0.399426734 9.13613626 -0.960762568 8.280889409 S(ph)IDQDYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;S(1)IDQDYER 192.14 0.00018617 2915670000 2622460 2340670 2078950 2804110 2313680 2408230 2797920 2406500 2557530 TRUE FALSE 2498501.513 2579186.934 2174271.914 2522235.535 2717185.059 2324832.391 2371045.917 2195774.102 2954138.69 0.845763106 0.873075778 0.736008746 0.853797265 0.919789267 0.786974694 0.802618348 0.743287412 1 21.49430613 S(ph)IDRGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIDRGLER 8 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 S(1)IDRGLER;S(1)IDRGLER;S(1)IDRGLER;S(1)IDRGLER 145.09 0.00034824 649660000 504955 241291 469916 354817 630829 410594 759030 484863 846950 TRUE FALSE 481086.7779 265878.8272 491462.1134 319150.1211 740845.3779 396375.0268 643226.033 442405.8253 978290.6804 0.49176261 0.271778964 0.502368185 0.326232405 0.757285532 0.405171014 0.657499909 0.452223285 1 19.89990367 -5 0.148777593 2.912300075 0.304710464 0.592851154 0.137822279 81.79264617 0.725467753 45.97475674 0.625854677 1.00E-05 5 -2.607589611 S(ph)IEALLEAGQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SIEALLEAGQAR 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR 100.19 0.0035399 51335000 46719.8 42738.9 35908.7 48358 37636 37261.1 37751.7 44263 39087.6 TRUE FALSE 44511.44764 47094.0425 37555.14941 43496.96197 44199.70648 35970.73876 31991.98481 40387.09707 45149.10538 0.985876625 1.043078088 0.831802737 0.963406951 0.978971922 0.79670989 0.708585132 0.894527073 1 15.46240978 2.239638021 24.99933599 0.812091701 0.968436659 0.214110691 0.092937226 28.33749599 657544.6373 0.032059205 0.025413244 173.6352998 -2.239638021 0.156344958 S(ph)IEVENDFLPVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK 242.19 6.69E-17 78620600 205708 188133 198099 231610 154439 216606 246330 222584 181356 TRUE FALSE 195984.5905 207303.9666 207182.0351 208328.1228 181373.1127 209104.8799 208747.8343 203093.365 209479.7622 0.935577683 0.989613337 0.989031269 0.994502383 0.86582642 0.998210413 0.996505973 0.969513058 1 17.67645135 S(ph)IHEVDISNLEAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;S(1)IHEVDISNLEAALR 312.46 2.16E-56 1276196000 731199 726652 616183 795004 664999 649095 707807 714562 554220 TRUE FALSE 696636.6724 800698.6649 644435.6 715088.6875 780974.6151 626616.6774 599818.0424 651991.1631 640165.607 1.088213213 1.250768014 1.006670138 1.117037029 1.219957159 0.978835274 0.936973239 1.018472651 1 19.28808564 2.219031111 24.59099476 0.973906624 1.140926089 0.540841249 0.069714115 140.06883 176369.3262 0.025280644 0.018699716 165.5888581 -2.219031111 0.167019465 S(ph)ILGTPLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SILGTPLSK 9 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 S(1)ILGTPLSK;S(0.999)ILGT(0.001)PLSK 82.171 0.020149 55163000 342080 282250 282050 380140 281700 349780 390250 365260 291360 TRUE FALSE 325910.5563 311011.5959 294982.2715 341927.605 330828.3908 337667.0309 330710.1951 333275.898 336542.6207 0.968407971 0.924137321 0.876507917 1.016000898 0.983020784 1.003341063 0.982669578 0.990293287 1 18.3604297 3.22007181 24.99999957 0.994121966 0.929741948 0.666887862 0.024100783 152.3805011 206043.8107 0.006965726 0.008339805 1659.861339 -3.22007181 -0.064380018 S(ph)INGSLYIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SINGSLYIFR 10 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 S(1)INGSLYIFR;S(0.998)INGS(0.002)LYIFR;S(1)INGSLYIFR;S(1)INGSLYIFR 171.99 4.04E-06 304256000 196416 229515 132509 170186 198195 136235 224842 164357 163242 TRUE FALSE 187131.8049 252902.8394 138584.6687 153078.5799 232760.1452 131517.1478 190538.2234 149965.0298 188556.7356 0.992442961 1.341255928 0.734975965 0.811843605 1.234430287 0.697493767 1.010508708 0.795331067 1 17.52463916 3.737693032 24.99995891 0.902789868 1.16684944 0.285044678 0.177012377 84.42534268 2432781.105 0.042480369 0.070325166 5466.294571 -3.737693032 0.264059572 S(ph)IPLSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIPLSIK 7 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 S(1)IPLSIK;S(0.999)IPLS(0.001)IK;S(1)IPLSIK;S(1)IPLSIK 138.98 0.0028673 437643000 1980640 1798790 1658180 2279810 1519490 2122900 2496110 2404600 1877560 TRUE FALSE 1887019.072 1982088.746 1734209.193 2050639.167 1784488.575 2049383.441 2115282.575 2194040.476 2168722.416 0.870106316 0.913943035 0.799645534 0.9455517 0.822829405 0.944972683 0.975358838 1.011674182 1 21.04841398 1.89639849 2.405504762 0.998072212 0.876600226 0.639141308 0.042757726 0.175731651 1.853411633 0.021667371 0.01086662 78.77682802 -1.89639849 -0.121471986 S(ph)IPQLDLGWPDTIAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIPQLDLGWPDTIAYR 16 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR 164.2 7.83E-09 102378000 51658 40125 33310 54390 41468 44736 52579 45347 50559 TRUE FALSE 49216.22872 44213.78312 34837.29645 48922.61387 48700.00607 43186.7811 44557.10787 41376.17628 58399.4315 0.842751846 0.757092697 0.596534856 0.837724146 0.833912331 0.739506875 0.762971603 0.708503066 1 15.8336667 -1.049526148 5.097420791 1.000003383 0.763295408 0.514607433 0.073223757 2.70E-06 5.04E-07 0.068098207 0.016050672 0.08922239 1.049526148 -0.236707974 S(ph)IPSLQSEYVHY ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIPSLQSEYVHY 12 0 Q9UNH5 Q9UNH5 CDC14A Dual specificity protein phosphatase CDC14A 1 S(0.997)IPS(0.003)LQSEYVHY 76.262 0.033137 24997000 49199 38608 43251 44337 63351 39253 49244 42144 64532 TRUE FALSE 46873.46077 42542.19909 45234.10113 39880.16053 74399.39434 37893.65877 41730.92337 38453.64794 74539.29298 0.628842305 0.570735211 0.606849077 0.535021985 0.998123156 0.508371588 0.559851344 0.515884259 1 16.18571351 -1.39451139 3.484803927 1.003005787 0.612308527 0.422287331 0.141307361 48858220.15 64432670.45 1444070.867 0.031783903 0.040317037 1.39451139 -0.39069726 S(ph)IQDLTVTGTEPGQVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR 224.12 5.01E-19 1271910000 818423 805187 803203 848298 640977 766574 800401 850344 699716 TRUE FALSE 779737.7667 887236.4707 840030.652 763025.4734 752763.1859 740027.3502 678285.1271 775883.3714 808224.3836 0.964754074 1.097760088 1.039353265 0.944076285 0.93137896 0.915621163 0.839228735 0.959985107 1 19.62439635 3.133766562 3.225301429 0.913103911 1.038431668 0.443879517 0.052274201 0.182682123 3.774918809 0.01551215 0.01923195 1360.713087 -3.133766562 0.125327757 S(ph)IQFVDWCPTGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 114.28 0.0007928 191470000 1385100 840930 936860 1120800 857800 1186700 1668500 1354200 1086300 TRUE FALSE 1319629.068 926621.7231 979815.9577 1008135.055 1007400.048 1145604.281 1413939.681 1235619.069 1254757.856 1.051700184 0.738486489 0.780880513 0.803449885 0.802864109 0.913008256 1.126862585 0.984747028 1 20.25897755 1.953668581 5.422944369 1.046270914 0.839057304 0.506880721 0.090568588 0.166264176 11.57051438 0.040255623 0.024833346 89.88114181 -1.953668581 -0.207213609 S(ph)ISESFLTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SISESFLTVK 10 0 F5H527;Q76I76;J3KSQ9;K7EP00;Q76I76-3;Q76I76-4 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 S(0.992)IS(0.008)ESFLTVK;S(0.999)IS(0.001)ESFLTVK 258.48 3.24E-17 149991000 272500 295380 274930 309920 222560 288880 321410 322150 272180 TRUE FALSE 259619.465 325479.5578 287535.8124 278766.2528 261374.3935 278876.0132 272373.0014 293940.8382 314388.2843 0.825792429 1.035278902 0.914588192 0.886694151 0.831374471 0.887043274 0.866358624 0.93496117 1 18.26218793 0.96714149 7.770494352 0.99999787 0.89886104 0.260183144 0.057826802 0.60194404 138.1898912 0.057025546 0.014284951 9.271318273 -0.96714149 -0.10113683 S(ph)ISESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.994)IS(0.006)ESSR;S(0.6)IS(0.396)ES(0.003)SR;S(0.986)IS(0.014)ESSR;S(0.689)IS(0.311)ESSR 162.49 0.0013321 1461920000 1233820 1025290 1113510 1287790 1115420 1143640 1342450 1236210 1274920 TRUE FALSE 1175499.774 1129768.217 1164565.535 1158338.903 1309948.895 1104035.46 1137634.597 1127960.899 1472628.082 0.798232621 0.767178238 0.790807638 0.786579393 0.889531383 0.749704201 0.772519966 0.765950964 1 20.48996169 -1.500956131 3.037831047 1.006447557 0.788396883 0.750202963 0.038060324 6831246.488 8178661.161 368304.4798 0.008695865 0.031553233 1.500956131 -0.218050674 S(ph)ISKDSLASNIVNLTPQNQPHPTATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SISKDSLASNIVNLTPQNQPHPTATK 26 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.546)IS(0.454)KDSLASNIVNLTPQNQPHPTATK;S(0.472)IS(0.472)KDS(0.052)LAS(0.004)NIVNLTPQNQPHPTATK 148.94 9.86E-08 212090000 342950 268360 293310 368200 208911 374880 411540 387260 240940 TRUE FALSE 326739.4332 295706.1891 306758.5536 331187.8365 245345.0123 361897.8116 348752.0145 353349.4614 278303.7446 1.174038939 1.0625304 1.102243716 1.190022926 0.881572803 1.300369896 1.253134466 1.269653996 1 18.0863008 S(ph)ISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.5)IS(0.5)LLEPS(0.001)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.523)IS(0.476)LLEPS(0.001)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.498)IS(0.498)LLEPS(0.004)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.5)IS(0.481)LLEPS(0.019)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 190.33 5.90E-28 99541700 45777.2 30457.7 49095.3 49747.9 86452.9 42096.8 76855.2 41476.2 11889.2 TRUE FALSE 43613.40248 33561.37426 51346.36807 44747.14658 101530.2584 40638.97726 65129.5277 37844.32405 13732.91641 3.175829603 2.443863579 3.738926716 3.258386291 7.393204424 2.959238667 4.742585313 2.755738323 1 13.74535042 3.483498293 2.594135692 4.044204026 2.822481446 0.015414123 1.658173638 0.646680631 8.72320273 0.433404486 0.676901687 3044.376024 -3.483498293 -1.221722579 S(ph)ISQDSLDELSMEDYWIELENIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.5)IS(0.5)QDSLDELSMEDYWIELENIKK 145.18 1.32E-07 34764000 26596 17493 19808 26434 17872 24823 33825 25277 20071 TRUE FALSE 25338.85979 19275.55659 20716.21639 23776.8041 20988.87114 23963.37329 28664.37501 23063.61188 23183.50817 1.092969174 0.831433985 0.893575564 1.025591292 0.905336284 1.033638788 1.236412315 0.99482838 1 14.50081127 2.005342187 8.958087139 1.111294888 0.949224354 0.243661477 0.098319287 0.123739945 111.5737835 0.036058717 0.025685008 101.2376807 -2.005342187 -0.162070534 S(ph)ISTVNLSENSSVVIPPPDYLECLSMGAAADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISTVNLSENSSVVIPPPDYLECLSMGAAADR 32 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.33)IS(0.33)T(0.33)VNLS(0.009)ENS(0.002)S(0.001)VVIPPPDYLECLSMGAAADR 54.326 0.035879 40077000 12680 14472 15160 15526 14126 11155 19413 15032 16461 TRUE FALSE 12080.64153 15946.71325 15855.101 13965.29698 16589.56993 10768.69955 16451.19031 13715.71839 19013.68781 0.635365514 0.838696491 0.833878265 0.734486499 0.872506696 0.566365645 0.865228801 0.721360239 1 14.21475076 -2.163476818 2.218129669 1.547856998 0.762332687 0.363311538 0.10036269 6308166.015 1375661.054 17368486.03 0.022364445 0.006863145 2.163476818 -0.785524311 S(ph)ITST(ph)PLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(1)ITS(0.056)T(0.944)PLSGK 143.42 0.00018037 103200000 401510 316630 341650 392620 271430 310590 365820 338010 257970 TRUE FALSE 382531.418 348894.957 357314.9904 353153.0917 318767.3061 299834.1904 310007.4403 308412.0525 297974.6701 1.283771597 1.170887971 1.199145519 1.185178229 1.069779878 1.006240532 1.040381856 1.035027751 1 18.18483017 2.728456646 1.96068772 1.023118141 1.218867347 0.899711861 0.030311599 0.0974406 0.740471885 0.011332632 0.011085772 535.1267315 -2.728456646 0.195749206 S(ph)IVT(ph)AEVS(ph)S(ph)MPACKFQVMIQK ddPTM_SK-BR-3_Trastuzumab_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 47.38 0.065405 144730000 148170 174470 118970 175020 96017 152400 145580 145390 87344 TRUE FALSE 141166.2977 192248.6914 124424.8922 157426.6571 112762.3344 147122.3498 123369.0972 132658.8808 100888.8614 1.399225799 1.905549222 1.233286712 1.560396805 1.117688641 1.458261573 1.222821781 1.314901159 1 16.62240738 2.309093919 0.276678995 0.986322166 1.736931991 0.369853136 0.200492653 2.020773241 0.420400346 0.3230933 0.541382492 203.7482647 -2.309093919 0.750609826 S(ph)IVVIHPDTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIVVIHPDTGR 11 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 1 S(1)IVVIHPDTGR;S(1)IVVIHPDTGR;S(1)IVVIHPDTGR;S(1)IVVIHPDTGR 126.56 0.00019636 364512000 345797 271207 277721 361064 324928 293545 358283 313958 283734 TRUE FALSE 329451.8611 298843.3016 290454.7826 324769.1607 381595.3403 283379.463 303620.348 286466.1731 327734.0196 1.005241572 0.911847058 0.886251549 0.99095346 1.164344613 0.864662946 0.926423044 0.874081285 1 18.32216591 S(ph)IYGEKFEDENFILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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" 1 S(1)IYGEKFEDENFILK;S(1)IYGEKFEDENFILK 176.67 4.76E-07 78733000 275530 314640 195188 259100 152993 247700 216970 288320 115529 TRUE FALSE 262506.2429 346702.1737 204137.5629 233054.7757 179674.9308 239122.0869 183867.2416 263073.1723 133444.6473 1.967154534 2.598097269 1.529754599 1.746452784 1.346437901 1.791919659 1.377854004 1.971402958 1 17.02588191 3.72376213 24.59314757 1.558341144 2.282625891 0.503096849 0.307254883 409.4600956 680469.2602 0.071650874 0.111533666 5293.734183 -3.72376213 0.724284747 S(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 S(1)KDAS(1)PINRWS(0.952)PT(0.048)R;S(1)KDAS(1)PINRWS(0.593)PT(0.407)R 111.49 0.00042833 424080000 776560 605290 692720 775300 424900 778520 885650 641460 476260 TRUE FALSE 739853.5478 666969.7392 724481.8972 697365.371 499002.4255 751559.6572 750527.8264 585290.3618 550115.9684 1.344904693 1.212416613 1.316962129 1.267669748 0.907085877 1.366184042 1.364308381 1.063939961 1 19.06937626 -4.660269838 0.210726855 5.73E-15 1.281441375 0.231399409 0.142604354 197.0999438 2.238881797 83.46365047 0.296715822 2.19E-05 4.660269838 1.281441375 S(ph)KDEYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 105.46 0.0047974 487960000 1008090 1582390 829260 1285600 491680 1291620 858960 1361870 429600 TRUE FALSE 960439.5835 1743637.34 867282.3913 1156369.046 577428.8363 1246890.876 727909.8761 1242617.443 496220.1739 1.935510957 3.513838074 1.747777372 2.330354763 1.163654496 2.512777475 1.466909075 2.504165506 1 18.92062086 3.701706967 24.95959312 1.850283116 2.724674903 0.256058256 0.640695092 615.9063963 417130.2221 0.151011969 0.233953575 5031.609947 -3.701706967 0.874391787 S(ph)KDRDPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR 87.298 0.012147 1020573000 2922987 2703165 2577017 3090959 1580732 2909105 3055301 3297682 2150219 TRUE FALSE 2784823.197 2978620.587 2695175.778 2780249.929 1856411.16 2808361.964 2589158.718 3008919.482 2483663.981 1.121256023 1.199284851 1.085161197 1.119414683 0.747448598 1.130733459 1.042475447 1.211484124 1 21.24403857 3.300791429 2.599810373 1.034260619 1.156000473 0.136611797 0.122071793 0.487095149 6.707628713 0.034727361 0.048185747 1998.90166 -3.300791429 0.121739854 S(ph)KEDSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.769)KEDS(0.231)RR 65.278 0.055931 1855800000 2044900 2215600 1877200 2621400 1070300 2052500 2185400 3041900 1379000 TRUE FALSE 1948241.63 2441372.159 1963271.477 2357891.892 1256959.981 1981421.41 1851977.092 2775535.11 1592848.277 1.223118145 1.532708541 1.232553976 1.480299113 0.78912725 1.243948616 1.162682673 1.742498108 1 20.60317742 S(ph)KEYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKEYHR 6 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)KEYHR;S(0.986)KEY(0.014)HR;S(1)KEYHR;S(0.939)KEY(0.061)HR 74.376 0.048744 729620000 1270340 1273800 1074510 1383490 719335 1243950 1219530 1404480 770489 TRUE FALSE 1210293.546 1403601.668 1123777.346 1244418.957 844786.7963 1200871.7 1033468.3 1281496.286 889972.499 1.35992241 1.577129259 1.262710193 1.398266753 0.949227979 1.349335739 1.16123622 1.439927961 1 19.76340123 3.33398287 1.919219228 1.206994991 1.460996773 0.272268948 0.166100557 0.370920509 2.797246726 0.046330066 0.069012726 2157.659304 -3.33398287 0.254001782 S(ph)KGHYEVTGSDDETGKLQGSGVSLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.235)KGHY(0.208)EVT(0.235)GS(0.235)DDET(0.087)GKLQGSGVSLASK 68.361 0.01087 896510000 74132 68239 91453 86014 60270 84727 104990 98665 63824 TRUE FALSE 70627.92728 75192.63168 95646.21051 77367.7093 70781.06892 81792.88275 88971.84723 90025.36954 73721.49995 0.958037036 1.01995526 1.297399138 1.04945924 0.960114335 1.109484788 1.206864311 1.221154882 1 16.1697978 2.000998816 24.98525893 1.163787138 1.05197051 0.10286197 0.110805373 57.72150798 1443868.991 0.041661238 0.03052121 100.2302507 -2.000998816 -0.111816627 S(ph)KPAGSDGERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.5)KPAGS(0.5)DGERR 60.628 0.072803 90966000 69097 58499 67666 73732 49329 62232 77776 74654 53223 TRUE FALSE 65830.92175 64460.11461 70768.55303 66320.31928 57931.96198 60076.89024 65909.84275 68116.89999 61476.55101 1.070829782 1.048531734 1.151147094 1.078790501 0.942342422 0.977232607 1.07211354 1.108014338 1 15.90774861 2.955353659 24.97737061 1.023318708 1.083044963 0.287258601 0.052448291 677.5558257 379058.0642 0.016564345 0.017570167 902.3056124 -2.955353659 0.059726256 S(ph)KPLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 S(1)KPLTR;S(1)KPLTR;S(1)KPLTR;S(1)KPLTR;S(0.997)KPLT(0.003)R;S(0.949)KPLT(0.051)R;S(1)KPLTR;S(0.892)KPLT(0.108)R;S(0.976)KPLT(0.024)R;S(1)KPLTR 97.635 0.024738 11515700000 11632190 10238170 10254920 12517810 7727790 11765460 12805890 12767960 9364460 TRUE FALSE 11082359.43 11281451.16 10725118.23 11259495.96 9075514.129 11358019.17 10852116.28 11649929.74 10816652.63 1.024564605 1.042970644 0.99153764 1.040940885 0.839031671 1.05004936 1.003278616 1.077036504 1 23.36675077 -0.321954559 6.456256797 1.000006702 1.009473658 0.001625995 0.06494583 3900959.579 604213.7613 0.057846312 0.014029791 0.476480839 0.321954559 0.009466956 S(ph)KS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 100.02 0.021702 692640000 737100 673140 643570 706800 456900 765360 818280 712110 505100 TRUE FALSE 702258.7438 741733.7313 673078.3211 635751.1212 536583.2153 738855.3913 693436.3573 649753.8733 583428.3283 1.203676115 1.271336504 1.153660678 1.089681612 0.919707168 1.26640301 1.188554487 1.113682421 1 19.15419591 8 0.018286419 2.66E-10 2.600161703 0.209491201 0.098679444 6029.106049 8.505306148 459.9962033 790.6753455 99999999.98 -8 2.600161702 S(ph)KS(ph)PPKS(ph)PEEEGAVSS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPPKSPEEEGAVSS 16 2 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 3 S(1)KS(1)PPKS(1)PEEEGAVSS 84.573 0.0049148 175330000 417230 481160 330530 474370 110390 504100 374810 627140 110180 TRUE FALSE 397508.3648 530190.751 345685.1274 426685.4264 129641.981 486642.8906 317625.8506 572224.2969 127266.1517 3.123441383 4.16599971 2.716237765 3.352701569 1.018668195 3.823820271 2.495760628 4.496280349 1 16.95748924 3.716626618 23.57469672 2.771419411 3.644720547 0.107233779 1.118190127 745.2048112 800947.1477 0.264531555 0.410302391 5207.468103 -3.716626618 0.873301136 S(ph)KSDLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.865)KS(0.132)DLS(0.003)ER 104.79 0.011868 479290000 576590 482100 510970 559750 387480 606820 664300 601190 449030 TRUE FALSE 549335.7334 531226.5381 534398.4799 503482.8665 455056.3893 585805.6712 562948.8343 548546.6165 518663.2791 1.059137509 1.02422238 1.030337989 0.970731661 0.877363807 1.129452758 1.085384019 1.057616065 1 18.98443871 S(ph)KSDSYTLDPDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.792)KS(0.207)DS(0.001)YTLDPDTLR;S(0.491)KS(0.491)DS(0.018)YTLDPDTLR 197.45 1.42E-08 909540000 2727300 2151190 2425540 2937500 2058230 2861800 3202300 2895200 2352250 TRUE FALSE 2598385.934 2370398.707 2536753.408 2642216.919 2417184.66 2762695.148 2713730.321 2641680.94 2717024.916 0.956334967 0.872424354 0.933651139 0.972466945 0.889643906 1.016808912 0.998787425 0.972269678 1 21.37359637 2.231724423 24.99999855 0.997783655 0.923164772 0.579579369 0.030474069 110.4667347 403973.8667 0.010968918 0.008279084 170.5000155 -2.231724423 -0.074618883 S(ph)KSEDMDNVQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.733)KS(0.267)EDMDNVQSK;S(0.5)KS(0.5)EDMDNVQSK 158.74 0.00011017 455350000 795810 772360 759340 959800 434730 906620 927910 921330 464250 TRUE FALSE 758193.6384 851064.3621 794156.4901 863319.0805 510546.7744 875223.5221 786340.2873 840653.4609 536243.5189 1.413897999 1.587085591 1.480962402 1.609938489 0.952080084 1.632138182 1.466386557 1.567671088 1 19.03252878 -1.476518237 3.067232723 0.988381807 1.468796906 0.359316397 0.194517526 66942193.65 86697752.84 6709691.286 0.043866962 0.033379649 1.476518237 0.480415099 S(ph)KSEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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(0.625)KS(0.375)EEAHAEDSVMDHHFR;S(0.656)KS(0.344)EEAHAEDSVMDHHFR;S(0.651)KS(0.349)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.674)KS(0.326)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.679)KS(0.321)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR 270.34 3.14E-39 12544710000 8118980 6496865 7547626 9546480 6230568 8731200 9822320 7411930 1578326 TRUE FALSE 7735211.906 7158902.93 7893692.118 8586849.693 7317177.087 8428836.355 8323744.685 6762902.116 1823084.735 4.242925058 3.926807565 4.32985476 4.710066147 4.013624241 4.623392535 4.565747562 3.70959286 1 20.79795019 0.837969341 3.954818427 1.000239692 4.318500691 0.945622855 0.250489001 0.249274908 5.786705411 0.255038031 0.065224845 6.886036834 -0.837969341 3.318260999 S(ph)KSKDQAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSKDQAEEK 10 2 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 S(0.5)KS(0.5)KDQAEEK;S(0.5)KS(0.5)KDQAEEK 89.959 0.008787 169719000 263180 288920 223130 322630 105108 308510 259200 420090 120742 TRUE FALSE 250740.003 318361.2765 233360.7312 290198.6194 123438.8019 297826.2213 219654.2795 383304.6926 139466.0527 1.797856884 2.282715186 1.673243967 2.0807832 0.885081348 2.135474659 1.574965916 2.748372705 1 17.08955447 3.714870927 24.0828894 1.746163706 2.04028612 0.05202881 0.549580554 1389.830494 1412898.416 0.130684888 0.202617926 5186.458732 -3.714870927 0.294122414 S(ph)KSLCHDEIENLLDSDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;S(0.5)KS(0.5)LCHDEIENLLDSDHR;S(0.878)KS(0.122)LCHDEIENLLDSDHR;S(0.5)KS(0.5)LCHDEIENLLDSDHR 297.99 1.26E-49 975791000 1364030 1097886 1186603 1419950 1032242 1268731 1509392 1450222 649984 TRUE FALSE 1299555.005 1209761.832 1241009.921 1277213.928 1212264.678 1224794.527 1279106.529 1323232.874 750780.1991 1.73093937 1.611339555 1.652960377 1.701182223 1.614673215 1.63136232 1.703703068 1.762477054 1 19.51803108 -1.249152006 3.982871624 0.999319487 1.672136831 0.947539248 0.049986476 3651902.065 1145418.17 21646.34101 0.011278114 0.056344041 1.249152006 0.672817344 S(ph)KSLGDLTSEDIACNFESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSLGDLTSEDIACNFESK 19 1 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(0.5)KS(0.5)LGDLTSEDIACNFESK 177.49 2.43E-14 140350000 269540 238540 272670 297520 153280 298850 310650 310230 180110 TRUE FALSE 256799.3784 262847.4972 285172.1892 267612.7243 180011.9835 288500.7496 263254.637 283064.6166 208040.5389 1.234371819 1.263443647 1.370752982 1.286348929 0.865273588 1.386752558 1.265400668 1.360622396 1 17.66650515 S(ph)KSPASVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.568)KS(0.407)PAS(0.025)VDR 91.858 0.00634 743250000 1041600 970820 1108600 1090100 720080 1080500 1176400 1099500 883910 TRUE FALSE 992365.6323 1069747.662 1159430.407 980521.0769 845661.724 1043082.014 996918.5739 1003221.951 1020982.248 0.971971485 1.047763233 1.135602904 0.960370348 0.828282495 1.021645592 0.976430859 0.982604695 1 19.96152635 3.076563299 24.99999825 0.959449044 1.040576912 0.298416244 0.064403511 48.42128923 15808.81677 0.018573233 0.022199257 1192.788105 -3.076563299 0.081127868 S(ph)KSPIPGQGYLGTERPSSVSSVHSEGDYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSPIPGQGYLGTERPSSVSSVHSEGDYHR 30 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.5)KS(0.5)PIPGQGYLGTERPSSVSSVHSEGDYHR;S(0.575)KS(0.425)PIPGQGYLGTERPSSVSSVHSEGDYHR 105.21 0.00015641 287270000 166988 145911 166727 154426 130669 154836 212430 188466 137122 TRUE FALSE 159094.8082 160779.4968 174371.5979 138902.8051 153457.6322 149473.9905 180019.902 171962.9179 158386.1794 1.004474057 1.015110645 1.100926852 0.876988166 0.968882719 0.943731271 1.136588449 1.085719212 1 17.27308693 1.740871707 25 1.084374871 0.98966983 0.286948609 0.065261293 0.443165757 4824.250108 0.029028734 0.016097833 55.06450091 -1.740871707 -0.094705041 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.499)KS(0.499)PLPPEEEAKDEEEDQT(0.001)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.561)KS(0.439)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.583)KS(0.417)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.499)KS(0.499)PLPPEEEAKDEEEDQT(0.002)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.498)KS(0.498)PLPPEEEAKDEEEDQT(0.004)LVNLDTYTSDLHFQVSK;S(0.497)KS(0.497)PLPPEEEAKDEEEDQT(0.005)LVNLDTYTSDLHFQVSK;S(0.488)KS(0.488)PLPPEEEAKDEEEDQT(0.021)LVNLDT(0.001)Y(0.001)T(0.001)S(0.001)DLHFQVSK;S(0.547)KS(0.453)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.499)KS(0.499)PLPPEEEAKDEEEDQT(0.003)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 250.17 6.77E-51 23394261500 1737110 1457294.4 1512674.8 1751720.9 750489.2 1838574 1861456 1940095 684050.6 TRUE FALSE 1655000.253 1605794.356 1582032.436 1575634.587 881374.2789 1774903.721 1577456.699 1770209.997 790129.6734 2.094593215 2.032317492 2.002244048 1.994146835 1.115480545 2.246344848 1.996452927 2.2404044 1 19.59172992 2.976703059 24.82911722 1.813316309 2.041874815 0.100069552 0.415846702 2037.772032 2171792.626 0.11812915 0.126066335 947.7702208 -2.976703059 0.228558507 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Trastuzumab_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)PPKVPIVIQDDS(0.001)LPAGPPPQIR 149.07 1.04E-07 1679260000 623680 636340 569310 678990 328360 706510 664360 702660 329530 TRUE FALSE 594199.8824 701183.7695 595413.4266 610736.6352 385625.88 682043.3815 562999.6802 641131.3654 380631.8294 1.561088266 1.842157474 1.564276502 1.604533799 1.013120423 1.791871643 1.479118762 1.684387158 1 18.53803668 -2.863479629 0.256725474 1.74E-11 1.642621421 0.365897071 0.228699092 58.4819501 1.537543607 32.87162343 0.306920663 0.001369369 2.863479629 1.642621421 S(ph)KSPRDPDANWDSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.5)KS(0.5)PRDPDANWDSPSR 106.69 0.00061884 215630000 122720 115310 107450 132560 108890 117280 125660 116730 111960 TRUE FALSE 116919.2688 127060.2201 112376.6888 119234.817 127880.3815 113218.5642 106488.2591 106508.5024 129322.185 0.904092897 0.982509073 0.868966827 0.921998163 0.988851074 0.875476734 0.823433807 0.823590341 1 16.98061026 2.052884523 10.63990196 0.859409516 0.933827486 0.122852946 0.060527024 0.631674895 123.9997522 0.020549196 0.015168282 112.9495546 -2.052884523 0.074417969 S(ph)KSPS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.5)KS(0.5)PS(1)PPR 57.836 0.061884 205850000 388080 431060 347010 479330 217050 414290 372490 385750 211690 TRUE FALSE 369736.2275 474985.5041 362920.7517 431146.8377 254903.4513 399943.0334 315659.8093 351971.685 244517.804 1.512103501 1.942539546 1.484230374 1.763253353 1.042473992 1.635639724 1.29094816 1.439452176 1 17.89957999 1.546317181 0.2516555 0.919470078 1.832454978 0.411467544 0.224944734 1.66498841 0.450046245 0.578676221 0.561815434 35.18172914 -1.546317181 0.9129849 S(ph)KSPT(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.979)KS(0.464)PT(0.557)LR 84.882 0.048624 273720000 709740 553790 556770 666480 344460 665140 774510 660880 387200 TRUE FALSE 676191.9968 610221.8306 582298.4552 599484.1642 404533.7149 642106.035 656344.2746 603009.8437 447244.9985 1.511905106 1.364401687 1.301967506 1.340393221 0.904501372 1.43569193 1.467527366 1.348276327 1 18.77070582 4.250696831 1.4303201 1.285436478 1.519757147 0.162848103 0.179357843 1.113164872 3.663165982 0.050763864 0.289576114 17811.34973 -4.250696831 0.234320669 S(ph)KSTAALSGEAASCSPIIMPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSTAALSGEAASCSPIIMPYK 22 1 Q14244-6;Q14244;Q14244-7;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 S(0.447)KS(0.447)T(0.096)AALS(0.011)GEAASCSPIIMPYK 163.39 9.18E-12 115260000 100960 73489 94279 96945 72560 102200 122310 100270 78609 TRUE FALSE 96187.82088 80977.61265 98601.7854 87199.90442 85214.44103 98660.78837 103649.3631 91489.82724 90799.28224 1.059345608 0.891830978 1.085931331 0.960358962 0.938492452 1.086581148 1.141521833 1.007605181 1 16.47039327 2.223888308 24.98470036 1.078872861 0.98401602 0.187368447 0.068698812 277.8616439 473152.5369 0.024114549 0.017884927 167.451217 -2.223888308 -0.09485684 S(ph)KSVIEQVSWDT ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSVIEQVSWDT 12 1 Q6WCQ1 Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.5)KS(0.5)VIEQVSWDT 151.07 0.00018059 69009000 412440 334730 370500 407390 315750 395470 474710 430770 380840 TRUE FALSE 392944.7786 368839.3676 387487.7915 366438.3832 370816.7 381774.7747 402284.2709 393049.4951 439898.7221 0.893261923 0.838464285 0.880856824 0.833006246 0.842959257 0.867869706 0.914492929 0.89349997 1 18.74681188 0.802604669 0.781655391 0.999178554 0.858081458 0.789059909 0.022281503 0.392950197 0.488037776 0.02122967 0.007611236 6.347528644 -0.802604669 -0.141097096 S(ph)KSVPGLNVDMEEEEEEEDIDHLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKSVPGLNVDMEEEEEEEDIDHLVK 25 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 S(0.5)KS(0.5)VPGLNVDMEEEEEEEDIDHLVK;S(0.628)KS(0.372)VPGLNVDMEEEEEEEDIDHLVK;S(0.625)KS(0.375)VPGLNVDMEEEEEEEDIDHLVK 314.72 7.88E-75 159303000 140476 96020 114350 138674 79404 136049 149894 146811 76082 TRUE FALSE 133835.9779 105804.5472 119593.0606 124734.2261 93252.03246 131337.589 127024.9173 133955.4505 87880.40799 1.522933051 1.203960582 1.360861463 1.419363302 1.061124255 1.494503633 1.445429308 1.524292543 1 16.42325395 S(ph)KSYNTPLLNPVQEHEAEGAAAGGTSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSYNTPLLNPVQEHEAEGAAAGGTSIR 28 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.49)KS(0.49)YNT(0.02)PLLNPVQEHEAEGAAAGGTSIR 258 7.95E-54 460570000 181320 132910 157340 159100 152930 197380 196190 191680 130960 TRUE FALSE 172749.3629 146453.6801 164554.1946 143106.9657 179600.9436 190544.6811 166257.6122 174895.483 151268.6079 1.14200405 0.968169682 1.087827784 0.946045367 1.187298184 1.259644573 1.099088664 1.156191529 1 17.2067531 2.71845726 24.72020806 1.152436525 1.039360301 0.263913962 0.085288085 834.6054644 1026275.978 0.025346917 0.023924385 522.946499 -2.71845726 -0.113076223 S(ph)KTLAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKTLAFR 7 1 Q53EV4-2 Q53EV4-2 1 S(0.901)KT(0.099)LAFR;S(0.948)KT(0.052)LAFR 77.674 0.022654 1013820000 269000 148281 270440 227248 1217230 122757 349860 193801 1242630 TRUE FALSE 256284.9031 163391.0025 282839.9415 204404.5993 1429514.527 118505.8943 296482.4314 176830.757 1435330.714 0.178554601 0.113835091 0.197055591 0.142409409 0.995947842 0.082563477 0.206560362 0.123198616 1 20.45295176 -1.851747218 2.640735133 1.30678972 0.244295787 0.434383411 0.266912598 73829767.96 48549026 142811389.9 0.061692538 0.014068662 1.851747218 -1.062493933 S(ph)KTPPKSYSTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKTPPKSYSTAR 12 2 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 S(0.589)KT(0.405)PPKS(0.003)YS(0.003)T(0.001)AR;S(0.54)KT(0.457)PPKS(0.001)YS(0.001)T(0.001)AR;S(0.577)KT(0.4)PPKS(0.022)YS(0.001)TAR 80.609 0.010372 7017550000 1789870 1436390 1672480 1855560 1115090 1944660 2126690 1948570 1229610 TRUE FALSE 1705266.392 1582759.774 1749164.862 1669035.583 1309561.343 1877315.937 1802224.381 1777942.881 1420291.639 1.200645238 1.114390686 1.231553305 1.175135823 0.92203693 1.32178201 1.268911491 1.251815354 1 20.43775577 S(ph)KTPPPPPQTAQTK ddPTM_SK-BR-3_Trastuzumab_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 97.384 0.0018145 271870000 623610 538930 518230 658720 331007 656660 637000 642430 347541 TRUE FALSE 594133.1912 593847.5797 541991.3581 592504.2141 388734.516 633919.6995 539813.9507 586175.4235 401435.8833 1.480020137 1.479308663 1.350131816 1.475962261 0.96836016 1.579130631 1.344707768 1.460196878 1 18.61481006 -3.299048847 0.299277327 1.50E-29 1.424169436 0.346835022 0.166567676 93.76335174 2.217223101 59.02343253 0.156086765 0.000502286 3.299048847 1.424169436 S(ph)LAY(ph)DKKKYT(ph)ANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLAYDKKKYTANK 13 3 P11234-3 P11234-3 RALB Ras-related protein Ral-B 3 S(0.971)LAY(0.659)DKKKY(0.659)T(0.712)ANK;S(0.767)LAY(0.733)DKKKY(0.733)T(0.767)ANK 54.7 0.0468 402530000 2035940 1292100 948050 1024160 2020660 1321730 2889300 2117640 1777420 TRUE FALSE 1939705.151 1423766.459 991519.0302 921209.491 2373062.464 1275958.159 2448484.219 1932208.215 2053053.216 0.944790489 0.693487362 0.482948529 0.448702198 1.155869924 0.621492979 1.19260631 0.941138885 1 20.96933959 2.73262582 24.99277521 0.980393303 0.675709851 0.406530159 0.202202067 551.8241279 2323850.213 0.064800473 0.062556557 540.2886196 -2.73262582 -0.304683451 S(ph)LCHDEIENLLDSDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLCHDEIENLLDSDHR 16 0 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 S(1)LCHDEIENLLDSDHR;S(1)LCHDEIENLLDSDHR 136.49 1.11E-05 103859000 50056 47118 54125 61860 57306 52193 58468 60195 46209 TRUE FALSE 47689.95208 51919.37777 56606.68479 55641.71527 67300.14826 50385.54332 49547.63276 54924.00669 53374.85572 0.893490979 0.972731019 1.060549654 1.042470551 1.260896116 0.943993996 0.928295395 1.029023984 1 15.70387264 4.126460511 2.275422187 1.031858026 0.90514486 0.207594111 0.090403574 0.508807652 5.145363912 0.025210311 0.076550829 13380.13549 -4.126460511 -0.126713166 S(ph)LDADEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 1 S(1)LDADEFR;S(1)LDADEFR;S(1)LDADEFR;S(1)LDADEFR 112.36 0.0032062 470349000 1496680 1243670 1233780 1376960 1185310 1208870 1442870 1352110 1281580 TRUE FALSE 1425934.903 1370401.387 1290350.033 1238545.365 1392027.689 1167006.529 1222733.681 1233712.08 1480320.881 0.963260683 0.925746171 0.871669143 0.836673576 0.940355369 0.788347002 0.825992322 0.833408551 1 20.4974785 3.861201599 1.740480535 0.856218499 0.957561421 0.183224863 0.061757597 0.443188793 2.592443058 0.016301074 0.041250871 7264.43094 -3.861201599 0.101342922 S(ph)LDFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLDFFR 6 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 S(1)LDFFR;S(1)LDFFR;S(1)LDFFR 119.27 0.022187 24786500 91698 90525 70304 97947 69166 82402 85907 84446 60056 TRUE FALSE 87363.61727 99749.60042 73527.50794 88101.18147 81228.5285 79548.39808 72800.30936 77051.46056 69369.17776 1.259401078 1.437952757 1.059944925 1.270033527 1.170959944 1.146739815 1.049461904 1.110744902 1 16.08200716 2.79440845 0.419874631 1.008797454 1.375287089 0.513392035 0.089853267 0.940241677 0.333685527 0.08390764 0.13742891 622.8858277 -2.79440845 0.366489634 S(ph)LDGSGSEPAVCEMCGIVGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDGSGSEPAVCEMCGIVGTR 21 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 S(0.901)LDGS(0.074)GS(0.025)EPAVCEMCGIVGTR 56.819 0.089556 49360000 14286 16625 13768 15897 13080 15617 17101 16716 44762 TRUE FALSE 13610.72909 18319.1064 14399.27642 14299.00336 15361.14786 15076.17937 14491.92837 15252.25842 51703.46235 0.263245989 0.354311018 0.278497334 0.276557946 0.297100951 0.291589358 0.280289321 0.294994914 1 15.65797327 0.850867564 19.42637868 1 0.294101752 0.988165781 0.024346132 15989.2146 2082802.179 0.02319706 0.005799265 7.093614179 -0.850867564 -0.705898248 S(ph)LDTITLSGDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(0.998)LDT(0.001)IT(0.001)LS(0.001)GDER 61.167 0.087514 0 92582 117280 90205 106120 55749 116670 87937 101470 51931 TRUE FALSE 88205.83234 129230.9653 94340.98847 95452.61599 65471.60795 112629.6886 74520.59558 92584.74887 59984.19425 1.470484574 2.154416958 1.57276412 1.591296127 1.091480994 1.877656107 1.242337194 1.543485747 1 15.87229478 1.110355572 0.213942393 0.825570811 1.924787933 0.316746146 0.285056451 3.296201189 0.624613916 1.416926124 0.993281692 12.89304718 -1.110355572 1.099217122 S(ph)LEDLRAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLEDLRAPK 9 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 S(1)LEDLRAPK;S(1)LEDLRAPK 121.02 0.00037886 765910000 1837920 1337280 1606130 1764590 1155810 1824850 1995370 1922400 1282830 TRUE FALSE 1751045.164 1473550.352 1679772.649 1587210.061 1357382.898 1761654.987 1690939.659 1754064.465 1481764.725 1.181729552 0.994456359 1.133629801 1.071161996 0.916058316 1.188889813 1.141166091 1.18376719 1 20.49888496 S(ph)LEEMSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLEEMSLR 8 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 S(1)LEEMSLR;S(1)LEEMSLR;S(1)LEEMSLR 169.41 0.00031595 158202000 182346 179520 149491 192313 166730 170305 197970 183098 164514 TRUE FALSE 173726.866 197813.2921 156345.3102 172981.3319 195807.6592 164407.2951 167766.0405 167064.9685 190025.9909 0.914226865 1.04098019 0.822757505 0.910303538 1.030425671 0.865183201 0.882858391 0.879169042 1 17.53583723 S(ph)LEEMSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLEEMSLRR 9 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 S(1)LEEMSLRR 80.69 0.014332 54245000 42355 29729 28604 38293 44674 32328 45503 36802 47831 TRUE FALSE 40352.96309 32758.4189 29915.52169 34443.71489 52465.13146 31208.47325 38560.68163 33579.42178 55248.38719 0.730391694 0.592929868 0.541473212 0.623433853 0.94962286 0.564875734 0.697951263 0.607790082 1 15.75364473 -1.98061204 2.3963922 1.30268058 0.663102785 0.452300591 0.116349873 12281199.64 5449146.879 20586355.39 0.026314148 0.010456539 1.98061204 -0.639577795 S(ph)LEGGGCPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLEGGGCPAR 10 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR 115.57 0.0012639 1356414000 481248 415807 426985 500804 449422 491611 553869 466022 489623 TRUE FALSE 458500.3608 458178.206 446562.6846 450462.2305 527801.0545 474586.3878 469366.1115 425214.6431 565551.2342 0.810714102 0.810144472 0.789606065 0.796501189 0.933250646 0.839157196 0.829926774 0.751858748 1 19.1092982 -1.950781703 2.635180418 1.132119829 0.821895828 0.594223892 0.046688306 13390968.82 7461370.275 10845507.87 0.011655697 0.011200007 1.950781703 -0.310224001 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLELSSLAGPGEDPLSADSLGKPTR 25 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(0.995)LELS(0.005)SLAGPGEDPLSADSLGKPTR;S(0.998)LELS(0.002)SLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(0.968)LELS(0.032)SLAGPGEDPLSADSLGKPTR 316.44 6.75E-75 1823514000 1115240 1146445 944632 1224280 689635 1090347 1072832 1201270 733732 TRUE FALSE 1062524.815 1263269.049 987944.3116 1101213.048 809907.1257 1052588.01 909151.7745 1096080.43 847515.4112 1.253693799 1.490555844 1.165694805 1.299342801 0.955625249 1.241969168 1.07272595 1.293286725 1 19.69288008 3.35996164 1.869159072 1.130912924 1.36532371 0.323122925 0.129983511 0.320645016 2.288895776 0.036059302 0.055110496 2290.665313 -3.35996164 0.234410786 S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLEPAENVHGAGGGAFPASQTPSKPASADGHR 32 1 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 250.22 7.14E-48 2484470000 1173661 1202443 935318 1439991 852718 1169167 1174656 1207653 568952 TRUE FALSE 1118184.371 1324973.309 978203.2555 1295240.369 1001431.749 1128678.454 995440.6532 1101904.501 657182.1704 1.701483121 2.016143116 1.488481124 1.970900045 1.523826717 1.717451423 1.514710377 1.676710889 1 19.32593381 -2.277044408 0.19469475 2.95E-18 1.89932064 0.642748753 0.169214561 21.4790582 0.553875094 9.851961867 0.425566775 0.005283912 2.277044408 1.89932064 S(ph)LES(ph)VLSLGPRPTGGGSSPPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LES(0.382)VLS(0.14)LGPRPT(0.168)GGGS(0.246)S(0.065)PPEIR 109.08 0.00067577 195890000 185270 173800 200010 195520 168210 188460 220370 206280 201540 TRUE FALSE 176512.6543 191510.4176 209180.6563 175865.9581 197545.7707 181933.5829 186748.5091 188217.0296 232793.7939 0.758236082 0.822661182 0.898566293 0.755458104 0.848586929 0.781522479 0.802205703 0.808513949 1 17.82869307 -0.754896352 4.829203786 1.000000137 0.808114366 0.66795096 0.042208365 11321459.69 25047243.42 35.94841322 0.009372384 0.175834321 0.754896352 -0.191885771 S(ph)LESCLLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLESCLLDLR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(1)LESCLLDLR;S(1)LESCLLDLR;S(0.998)LES(0.002)CLLDLR;S(1)LESCLLDLR;S(1)LESCLLDLR 210.35 8.26E-08 383856000 381047 335373 346802 394111 362277 369475 428512 397813 380073 TRUE FALSE 363035.6635 369547.89 362703.2147 354494.2135 425457.9941 356679.9881 363134.6242 362978.3848 439012.7797 0.826936436 0.841770233 0.826179172 0.807480397 0.969124394 0.812459237 0.827161853 0.826805965 1 18.74390341 -1.330468997 3.04191016 1.001444488 0.841175391 0.535760946 0.04614201 14775871 19688529.96 195342.649 0.010249489 0.04672303 1.330468997 -0.160269097 S(ph)LESINSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 1 S(1)LESINSR 112.83 0.00311 78878000 40962 46050 48219 53290 58211 48865 53266 49367 62869 TRUE FALSE 39025.80744 50742.54735 50429.88885 47933.18796 68362.97997 47172.7928 45139.2934 45044.16377 72618.40343 0.537409329 0.698756031 0.694450531 0.660069427 0.941400206 0.649598319 0.621595784 0.62028579 1 16.14804759 -2.518122142 2.188877686 5.439037374 0.674058055 0.485411035 0.10414107 3880254.064 168134.5112 86429392.01 0.024956191 0.003033038 2.518122142 -4.764979319 S(ph)LESVLSLGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 209.19 1.78E-08 81681000 45972.4 48378.1 40655.6 52341 39417.6 41606.1 49638.4 42919.6 45382 TRUE FALSE 43799.37576 53307.88339 42519.69947 47079.58324 46292.01696 40165.27032 42065.15041 39161.33229 52419.60878 0.835553274 1.016945464 0.811141107 0.898129237 0.883104968 0.76622606 0.802469751 0.747074105 1 15.67781897 2.372234802 6.294982753 0.810105508 0.899989311 0.084194496 0.086782695 0.326363567 17.23224213 0.027635087 0.023014102 235.6322888 -2.372234802 0.089883803 S(ph)LESVLSLGPRPTGGGS(ph)SPPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LES(0.001)VLSLGPRPT(0.008)GGGS(0.792)S(0.199)PPEIR;S(0.996)LES(0.003)VLS(0.004)LGPRPT(0.03)GGGS(0.699)S(0.268)PPEIR 135.52 8.49E-06 460900000 264270 238340 260580 274680 258070 270420 332870 275050 283840 TRUE FALSE 251778.4808 262627.117 272527.8507 247068.6445 303077.3263 261055.2876 282084.5679 250965.1639 327856.4575 0.767953399 0.80104299 0.831241369 0.753587855 0.924420792 0.796248729 0.860390459 0.765472688 1 18.32270479 -5 0.207070385 1.865716275 0.78583365 0.557696456 0.051738019 99.26024578 0.987304094 35.74335351 0.100994045 1.00E-05 5 -1.079882626 S(ph)LESVLSLGPRPTGGGSS(ph)PPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LESVLSLGPRPT(0.135)GGGS(0.394)S(0.471)PPEIR 130.25 2.01E-05 257080000 134930 137890 145980 147880 139310 154500 161150 147540 157230 TRUE FALSE 128552.1263 151941.1478 152673.3274 133014.8214 163605.6199 149149.6263 136563.6078 134620.6154 181612.4254 0.707837727 0.836623086 0.840654636 0.732410358 0.900850366 0.821252323 0.751950796 0.741252231 1 17.47050339 -2.042341087 2.296493155 1.260270633 0.791936389 0.547723022 0.059512573 7988720.751 2582276.45 10929385.85 0.013769842 0.009071078 2.042341087 -0.468334244 S(ph)LGDEGLNR ddPTM_SK-BR-3_Trastuzumab_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 94.363 0.0092024 66475000 145130 159080 117610 211623 114570 171061 162501 132325 120288 TRUE FALSE 138269.9925 175290.4329 123002.5348 190350.254 134550.9717 165137.1147 137708.4879 120737.9215 138941.6487 0.995165912 1.261611867 0.885281958 1.370001405 0.96839913 1.188535736 0.991124614 0.868982934 1 17.0841196 1.563305661 5.021033402 0.932978363 1.115235543 0.21464492 0.145080138 0.199310561 10.8141255 0.072354934 0.032516636 36.58521918 -1.563305661 0.18225718 S(ph)LGDLTSEDIACNFESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLGDLTSEDIACNFESK 17 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(1)LGDLTSEDIACNFESK 197.94 1.54E-11 21100000 73228 75680 64858 93018 61524 73151 91550 81839 64107 TRUE FALSE 69766.65756 83391.87804 67831.80345 83667.65392 72253.76612 70617.76253 77582.36607 74672.7433 74048.38615 0.942176612 1.126180898 0.91604702 1.129905164 0.975764225 0.953670515 1.047725279 1.008431746 1 16.17618067 3.740786145 24.9951459 1.009620011 1.034178742 0.025158736 0.071473183 919.190172 10323307.73 0.017098776 0.028822158 5505.365346 -3.740786145 0.024558731 S(ph)LGSAGPSGTLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLGSAGPSGTLPR 13 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 S(1)LGSAGPSGTLPR;S(1)LGSAGPSGTLPR;S(1)LGSAGPSGTLPR 223.36 1.67E-11 199341000 159118 144597 160765 184268 162618 161039 186231 162946 203077 TRUE FALSE 151596.8075 159331.5987 168136.2343 165745.0306 190978.5277 155462.1791 157818.0406 148677.5844 234569.144 0.646277703 0.679252164 0.716787517 0.706593492 0.814167305 0.662756305 0.672799661 0.63383266 1 17.83965372 -1.416283335 3.399735472 1.003204423 0.690038729 0.788857961 0.050143657 23357789.75 34076088.67 733459.9137 0.012085866 0.0383457 1.416283335 -0.313165694 S(ph)LHGPCPVTTFGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLHGPCPVTTFGPK 14 0 O95544;O95544-2 O95544 NADK NAD kinase 1 S(1)LHGPCPVTTFGPK;S(1)LHGPCPVTTFGPK 109.14 0.00050558 337080000 874390 736620 780110 1059060 943700 927120 1064560 828180 908190 TRUE FALSE 833059.3176 811682.4155 815878.8151 952601.2767 1108280.981 895013.6019 902141.82 755660.1687 1049027.467 0.794125363 0.773747534 0.77774781 0.908080395 1.056484235 0.853184145 0.859979217 0.720343549 1 20.00062102 3.241501839 24.64227487 0.894564695 0.781882508 0.279878744 0.088826857 85.84413197 719213.9408 0.024555058 0.031843747 1743.820742 -3.241501839 -0.112682187 S(ph)LHSAHSLASR ddPTM_SK-BR-3_Trastuzumab_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(1)LHSAHSLASR;S(1)LHSAHSLASR;S(1)LHSAHSLASR;S(1)LHSAHSLASR 210.38 8.35E-09 719392000 262420 242589 275942 253927 324531 203714 305773 241292 164317 TRUE FALSE 250015.9267 267309.0949 288594.2136 228401.7755 381129.1036 196659.3331 259121.7129 220163.1933 189798.4411 1.317270707 1.408384038 1.520529947 1.203391209 2.008072887 1.036148305 1.365246792 1.159984202 1 17.53410862 1.282253186 1.132119646 1.01637576 1.433142978 0.26228437 0.24687566 0.592000271 1.531726019 0.20510249 0.068067975 19.1537223 -1.282253186 0.416767218 S(ph)LIYTDTLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLIYTDTLVR 10 0 Q5SYE7-2 Q5SYE7-2 NHSL1 NHS-like protein 1 1 S(1)LIYTDTLVR;S(1)LIYTDTLVR;S(1)LIYTDTLVR;S(1)LIYTDTLVR 160.72 7.65E-06 154425000 239217 189731 217883 230405 230778 206687 256009 225474 226187 TRUE FALSE 227909.6865 209064.8046 227873.1511 207244.2517 271025.6101 199529.3774 216950.1251 205730.3012 261262.9248 0.872338418 0.800208467 0.872198577 0.793240188 1.037367282 0.76371103 0.830390019 0.78744545 1 17.99514288 -2.431979235 2.305272542 2.557410571 0.842787451 0.286679474 0.076982684 3556224.481 507219.0873 29699438.46 0.016716174 0.003698459 2.431979235 -1.71462312 S(ph)LKEGLTVQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLKEGLTVQER 11 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 S(1)LKEGLTVQER 72.662 0.027666 154340000 118070 72927 103460 94487 83396 102830 120340 109000 105200 TRUE FALSE 112489.0651 80358.34421 108203.7433 84988.98725 97940.236 99268.97132 101979.9228 99455.38215 121513.8787 0.925730182 0.661310009 0.890464073 0.699417944 0.806000409 0.816935254 0.839245063 0.818469324 1 16.89076158 0.154563148 0.624672982 1.00877234 0.792019714 0.378805029 0.078013208 3.210740976 1.601903345 0.139418533 0.028062928 1.427457374 -0.154563148 -0.216752626 S(ph)LLDASEEAIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLLDASEEAIKK 12 1 P18206;P18206-2 P18206 VCL Vinculin 1 S(1)LLDASEEAIKK;S(1)LLDASEEAIKK;S(1)LLDASEEAIKK 187.89 6.07E-06 204856000 518868 207512 211874 514584 275485 327936 664462 426458 348272 TRUE FALSE 494342.1379 228657.7087 221588.6325 462857.0387 323529.4968 316579.4941 563086.1182 389115.0767 402280.243 1.228850152 0.568404024 0.550831507 1.150583571 0.80423909 0.78696257 1.39973595 0.967273644 1 18.61784136 1.76167678 25 1.159406054 0.843775858 0.216239869 0.242426116 16.49579529 17853.61489 0.108165208 0.059985227 57.76659643 -1.76167678 -0.315630197 S(ph)LLGIDTEDAIQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLLGIDTEDAIQGR 14 0 P49454 P49454 CENPF Centromere protein F 1 S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR 192.32 4.07E-07 105996000 51892 67736 63718 74432 55179 58658 77144 73188 74961 TRUE FALSE 49439.168 74638.37541 66639.53333 66949.95395 64802.20013 56626.65875 65374.26595 66779.27073 86585.56903 0.570986234 0.862018651 0.769637875 0.773223006 0.74841802 0.653996496 0.755024962 0.771251739 1 16.40183897 0.648388385 2.11693275 0.999936471 0.735417195 0.541382439 0.076571649 1.568908496 8.440803887 0.070854072 0.019365152 4.45029074 -0.648388385 -0.264519276 S(ph)LLQSEQQPSWTDDLPLCHLSGVGSASNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLLQSEQQPSWTDDLPLCHLSGVGSASNR 29 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 1 S(0.749)LLQS(0.25)EQQPS(0.001)WTDDLPLCHLSGVGSASNR;S(0.999)LLQS(0.001)EQQPSWTDDLPLCHLSGVGSASNR;S(0.998)LLQS(0.002)EQQPSWTDDLPLCHLSGVGSASNR;S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR 308.42 3.60E-92 498340000 57426 44548.5 61331 54956.4 81189 49241 81341 68956 103593 TRUE FALSE 54711.58679 49088.0428 64143.08701 49432.07826 95348.33589 47535.77182 68930.93652 62917.84708 119657.6734 0.457234252 0.410237316 0.536054941 0.413112481 0.796842636 0.397264718 0.576067832 0.525815397 1 16.86855339 -5 0.209322201 3.363961272 0.4339455 0.648296006 0.113930232 83.01984129 0.826899193 82.32795352 0.219119869 1.00E-05 5 -2.930015772 S(ph)LNLEDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLNLEDYK 8 0 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 1 S(1)LNLEDYK 88.021 0.015641 28930000 48484 46439 48133 52611 38330 46398 58836 54351 41074 TRUE FALSE 46192.25741 51171.1869 50339.94566 47322.44233 45014.73986 44791.22563 49859.4876 49591.73831 47443.54614 0.973625733 1.078570028 1.061049389 0.997447412 0.948806393 0.94409523 1.050922447 1.045278912 1 15.53392423 -2.153097038 8.277813421 0.725959231 1.014808343 0.004764584 0.046892883 0.172264299 0.003186005 0.032979867 0.011003268 0.007029152 2.153097038 0.288849112 S(ph)LPAGDALYLSFNPPQPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR 247.61 9.50E-25 2585997000 320844.5 311093.8 316682.6 341900.3 330389.8 306317.8 373354.3 342844.6 350365.7 TRUE FALSE 305678.8163 342794.6119 331202.8105 307531.8323 388009.6765 295709.9378 316392.2444 312823.3093 404698.6233 0.755324577 0.847036763 0.818393717 0.759903332 0.958762037 0.730691731 0.781797185 0.772978437 1 18.62648842 -1.877845785 2.740244402 1.091061632 0.803167011 0.481219749 0.064245666 15248351.91 9702305.303 9003075.845 0.014533878 0.013248119 1.877845785 -0.287894621 S(ph)LPAPQDNDFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLPAPQDNDFLSR 13 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 S(1)LPAPQDNDFLSR;S(1)LPAPQDNDFLSR 153.41 4.32E-05 132904000 90653 84082 84185 102929 95272 93909 113388 104210 111627 TRUE FALSE 86368.01235 92650.05139 88044.96552 92582.38137 111887.4066 90656.90778 96088.57809 95084.81995 128937.545 0.669843778 0.718565344 0.682849712 0.718040516 0.867764363 0.703107134 0.745233501 0.737448661 1 16.97631289 -5 0.206348469 2.27654826 0.686315002 0.738559632 0.05133915 72.30421905 0.718837239 38.15811881 0.10990511 1.00E-05 5 -1.590233257 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK 318.57 1.10E-73 540291700 452944 472649 448822 534056 295953.9 547868 564971 568897 316746 TRUE FALSE 431534.2348 520812.4705 469400.9326 480371.6762 347568.1665 528895.1938 478774.2975 519081.3628 365865.352 1.179489209 1.423508588 1.282988209 1.31297395 0.949989291 1.445600659 1.308607921 1.418777045 1 18.48095327 S(ph)LPNLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 110.53 0.0071141 740161000 694121 591535 587132 681644 598455 628494 757627 670098 669045 TRUE FALSE 661311.2759 651813.089 614052.583 613123.8501 702825.3625 606729.0952 642037.0864 611420.6667 772797.0816 0.855737284 0.843446623 0.7945845 0.793382719 0.909456543 0.785107902 0.830796469 0.791178799 1 19.55973012 -1.012730324 5.521655833 1.000000609 0.82791566 0.672593453 0.038236195 2.64E-07 4.73E-08 0.034159235 0.00805138 0.097111279 1.012730324 -0.172084949 S(ph)LPQGTSAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPQGTSAQK 10 0 A0A087X0J2 A0A087X0J2 UBXN8 1 S(1)LPQGTSAQK 62.298 0.047893 0 129850 121410 111240 156090 142510 126380 153490 132330 138840 TRUE FALSE 123712.2478 133781.817 116340.464 140399.5366 167363.6989 122003.4289 130072.2815 120742.4837 160370.5981 0.771414769 0.834204141 0.725447591 0.875469309 1.043605878 0.760759331 0.811073121 0.752896635 1 17.29105014 -2.51050528 2.275051441 3.585336948 0.821761081 0.279700001 0.089841416 3723953.249 436733.6003 50200252.7 0.02105125 0.003086702 2.51050528 -2.763575866 S(ph)LPRPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLPRPAK 7 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK 111.61 0.0039612 2507460000 2631700 2118880 2235310 2716760 2080010 2588130 3058590 2752310 2426310 TRUE FALSE 2507304.757 2334796.281 2337801.175 2443666.123 2442763.085 2498502.409 2591945.921 2511303.145 2802569.763 0.894644904 0.833091226 0.834163419 0.871937661 0.871615443 0.891504091 0.924846173 0.896071591 1 21.41831886 0.942410466 0.502615798 1.001935613 0.853687517 0.793447198 0.021631589 0.47166311 0.293050631 0.026056637 0.012063274 8.758111431 -0.942410466 -0.148248096 S(ph)LPS(ph)SPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.709)S(0.291)PER;S(1)LPS(0.925)S(0.075)PER 106.4 0.0061444 123410000 607760 590270 534790 637150 579420 621770 661690 580700 562670 TRUE FALSE 579032.3893 650419.1841 559310.6505 573102.4715 680470.6645 600237.949 560737.0377 529850.8295 649925.9899 0.890920502 1.000758847 0.86057591 0.881796513 1.046997158 0.923548155 0.862770602 0.815247948 1 19.30991592 1.870619619 5.901125451 0.879431275 0.938766754 0.060068489 0.071643001 0.475200917 20.39020026 0.029822956 0.017933147 74.2368642 -1.870619619 0.059335479 S(ph)LPS(ph)SPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.591)S(0.409)PERR;S(0.998)LPS(0.592)S(0.41)PERR 89.266 0.0081695 2069680000 1889970 1763140 1684580 1901100 1716020 1737150 1963850 1762110 1739070 TRUE FALSE 1800634.864 1942805.971 1761819.659 1709997.816 2015293.345 1676992.06 1664228.614 1607810.307 2008756.094 0.896392981 0.967168676 0.877069976 0.851271999 1.003254378 0.834841057 0.828487151 0.800400961 1 20.93787097 S(ph)LPS(ph)SPLLTHQSISVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.999)LPS(0.5)S(0.5)PLLTHQSISVR 95.227 0.0020199 204240000 85135 37267 69883 85376 112710 50432 118960 81574 136730 TRUE FALSE 81110.83727 41064.54967 73087.20467 76793.84228 132366.5883 48685.52719 100810.4671 74430.94811 157933.3901 0.513576244 0.260011829 0.462772341 0.486241967 0.838116552 0.308266207 0.638310031 0.471280633 1 17.26895669 -4.999999995 0.165736018 2.971009432 0.355971526 0.502291514 0.158615468 101.9264608 0.951461837 65.95149111 0.565372143 1.00E-05 4.999999995 -2.615037905 S(ph)LPSHMEEAPNVFQLYQRPTSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLPSHMEEAPNVFQLYQRPTSASR 24 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(0.963)LPS(0.037)HMEEAPNVFQLYQRPTSASR;S(0.996)LPS(0.004)HMEEAPNVFQLYQRPTSASR;S(0.999)LPS(0.001)HMEEAPNVFQLYQRPTSASR;S(1)LPSHMEEAPNVFQLYQRPTSASR 276.23 2.91E-52 897561000 84877.8 72096.4 79604.7 89106.8 104802.1 71021.8 104431 101771 92139 TRUE FALSE 80865.79461 79443.10513 83254.65423 80149.61517 123079.5531 68562.29726 88498.13294 92859.39172 106427.4455 0.759820873 0.74645318 0.782266772 0.753091599 1.15646441 0.644216319 0.831534878 0.872513582 1 16.69951072 -4.999999995 0.069745475 1.636797925 0.575976941 0.195357319 0.13076354 505.7089427 2.540168713 52.39337889 6.583429039 1.00E-05 4.999999995 -1.060820984 S(ph)LPSS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.246)S(0.754)PER 91.752 0.01793 336450000 655340 624380 581240 733670 619560 689910 751510 635950 573570 TRUE FALSE 624363.377 688005.0319 607890.4289 659920.0977 727611.0678 666018.2437 636853.3471 580262.8466 662516.3062 0.94241209 1.038472601 0.917547875 0.996081291 1.098253826 1.005285813 0.961264411 0.87584689 1 19.33759644 4.751529248 23.10938253 0.988559722 0.942412041 0.048433315 0.060994724 94.02504633 1420098.731 0.014127506 0.088907406 56432.49445 -4.751529248 -0.046147681 S(ph)LPSS(ph)PERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(0.999)LPS(0.296)S(0.705)PERR;S(0.998)LPS(0.173)S(0.829)PERR;S(1)LPS(0.176)S(0.824)PERR;S(1)LPS(0.129)S(0.871)PERR 99.498 0.0041469 2731670000 2872880 2538370 2603350 2875560 2701440 2589520 3125780 2563950 2804840 TRUE FALSE 2737084.656 2797032.789 2722716.173 2586503.246 3172570.281 2499844.273 2648884.852 2339436.946 3239800.262 0.844831297 0.863334947 0.840396306 0.798352687 0.979248726 0.771604442 0.817607457 0.722092955 1 21.62747344 S(ph)LPSS(ph)PLLTHQSISVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.998)LPS(0.31)S(0.692)PLLTHQSISVR 112.14 0.0004024 213340000 78992 45616 71260 73643 132440 56649 129570 76568 135370 TRUE FALSE 75258.20471 50264.32226 74527.34149 66240.26573 155537.4941 54687.23093 109801.7168 69863.30001 156362.4882 0.481306006 0.321460235 0.476631846 0.423632717 0.994723836 0.349746487 0.702225438 0.446803455 1 17.25453492 -5 0.111257097 2.537696571 0.245150217 0.382799647 0.193459023 156.5774673 1.154699177 54.93651229 2.11531212 1.00E-05 5 -2.292546354 S(ph)LPSSPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.951)LPS(0.036)S(0.013)PER;S(0.998)LPS(0.001)SPER;S(0.972)LPS(0.02)S(0.008)PER 99.815 0.0068662 229165000 785770 691716 655056 773890 596610 689254 761545 700548 494130 TRUE FALSE 748628.2093 762202.6468 685090.9655 696097.1069 700658.5951 665384.9612 645357.3235 639204.3033 570757.1567 1.311640512 1.335423722 1.200319536 1.219602941 1.227594936 1.165793461 1.130703866 1.119923414 1 19.12251752 2.547470383 0.208938886 0.950265102 1.452896872 0.912482284 0.028487113 1.087226045 0.128957284 0.085293128 0.177252644 352.7527299 -2.547470383 0.50263177 S(ph)LPSSPLLTHQSISVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 1 S(0.995)LPS(0.001)S(0.004)PLLTHQSISVR;S(1)LPSSPLLTHQSISVR 228.85 2.40E-15 300630000 196534 111385 186711 173728 234830 168481 302870 225200 294130 TRUE FALSE 187244.2273 122735.2581 195271.884 156264.5314 275784.2777 162646.4607 256661.6189 205480.2941 339742.1782 0.551136242 0.361259997 0.574764915 0.459950343 0.811745775 0.478734968 0.755459979 0.604812435 1 18.37408081 -0.851289279 0.158234273 1.427406288 0.337026184 0.597238003 0.119484148 13.96245091 0.501993373 3.204821178 0.638394915 0.14083504 0.851289279 -1.090380103 S(ph)LPTTVPES(ph)PNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(0.998)LPT(0.002)T(0.001)VPES(0.996)PNY(0.002)R 304.64 4.19E-41 13366353000 4510744 3624951 4188882 4578349 4478434 4417072 5205869 4755967 4851272 TRUE FALSE 4297530.071 3994337.628 4380946.383 4118124.66 5259471.472 4264107.689 4411618.072 4339509.317 5603582.485 0.766925459 0.712818565 0.781811706 0.734909261 0.93859089 0.760960992 0.787285292 0.774416961 1 22.41791804 -5 0.201016154 2.005753213 0.741947951 0.570678443 0.059589831 99.67234484 0.986798512 40.3326681 0.133879918 1.00E-05 5 -1.263805262 S(ph)LPTTVPESPNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 S(0.456)LPT(0.456)T(0.087)VPES(0.001)PNYR;S(0.935)LPT(0.059)T(0.006)VPESPNYR;S(0.998)LPT(0.001)TVPESPNYR 190.1 4.93E-06 2299530000 169138 156863 190064 196653 155193 159461 194840 183088 206851 TRUE FALSE 161143.1819 172847.518 198778.6224 176885.0668 182258.6101 153938.8256 165113.5795 167055.8441 238928.3966 0.674441315 0.723428108 0.831958968 0.740326681 0.762816863 0.644288531 0.691058835 0.699187901 1 17.8662188 -1.689570569 2.585860428 1.044393149 0.718079746 0.742929895 0.051564315 7137033.1 5854356.076 2072473.488 0.013327827 0.020437578 1.689570569 -0.326313403 S(ph)LPVSICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLPVSICR 8 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR 195.79 0.00016507 2246400000 829848 686495 837422 737980 1323247 687810 975031 743071 1605323 TRUE FALSE 790622.7296 756449.621 875818.627 663796.8483 1554020.858 663990.9672 826272.1133 678003.764 1854268.292 0.4263799 0.40795047 0.472325731 0.357983174 0.838077674 0.358087861 0.445605481 0.365644911 1 20.82241857 -1.31259833 4.614914042 1.000365916 0.455897469 0.595163338 0.140201116 0.00048207 7.18E-05 0.123979426 0.029203043 0.048685728 1.31259833 -0.544468447 S(ph)LPVSVPVWGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLPVSVPVWGFK 12 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK 274 9.21E-28 6853420700 13651384 10478691 11472646 13884398 10792033 12698945 16666775 15009415 12921793 TRUE FALSE 13006110.13 11546481.53 11998678.17 12488711.93 12674160.14 12259177.35 14123952.37 13695111.05 14925638.66 0.871393876 0.7736005 0.803897136 0.836728814 0.849153622 0.82135027 0.946287974 0.917556117 1 23.83128933 1.536872307 0.983917584 0.991036115 0.817016481 0.771967423 0.032831536 0.215700001 0.408197927 0.028273432 0.010633666 34.42486986 -1.536872307 -0.174019634 S(ph)LQEEHVAVAQLR ddPTM_SK-BR-3_Trastuzumab_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 171.98 1.56E-05 280760000 320180 273690 288260 428740 331960 389890 426730 250700 306720 TRUE FALSE 305045.7259 301579.3222 301477.0061 385642.2406 389853.7189 376388.0115 361624.5011 228747.379 354284.5711 0.86101894 0.851234704 0.850945908 1.088509837 1.100397112 1.062388945 1.020717611 0.645660008 1 18.43454911 3.262078777 24.6902757 0.999945226 0.854667093 0.185460354 0.128170455 298.2080463 313067.8993 0.034294126 0.046406319 1828.431846 -3.262078777 -0.145278133 S(ph)LQLMDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLQLMDNR 8 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR 147.28 0.00056624 1436360000 1806900 1523120 1493650 1651820 1639960 1546530 2026120 1775050 1858990 TRUE FALSE 1721491.418 1678327.66 1562135.33 1485775.915 1925968.505 1492973.278 1716998.182 1619617.212 2147272.675 0.801710671 0.781609005 0.72749742 0.691936303 0.89693709 0.695288165 0.79961814 0.754267137 1 21.03407398 -1.967104222 2.350444731 1.191698306 0.770921901 0.598583585 0.059523776 5135078.673 2188216.57 5359579.73 0.01282861 0.010786878 1.967104222 -0.420776405 S(ph)LQLPASPAPDPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR 230.82 2.90E-13 892718000 791541 910143 637907 926814 610494 710958 687104 743156 554321 TRUE FALSE 754126.4256 1002887.606 667155.6669 833648.8959 716963.9603 686337.3462 582273.6653 678081.3209 640282.2696 1.177803074 1.566321065 1.041971172 1.302002157 1.119762321 1.071929333 0.909401514 1.059034981 1 19.28834853 2.690662663 0.941884931 0.973123724 1.340360357 0.447482468 0.136475196 0.414305499 0.773910224 0.076638042 0.067280728 490.5267125 -2.690662663 0.367236632 S(ph)LQLPASPAPDPSPRPAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLQLPASPAPDPSPRPAYK 19 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)LQLPASPAPDPSPRPAYK;S(1)LQLPASPAPDPSPRPAYK;S(1)LQLPASPAPDPSPRPAYK;S(1)LQLPASPAPDPSPRPAYK 219.23 1.93E-19 3059610000 3497110 2582200 3088690 3250620 2466360 3123020 3879660 3569020 3093690 TRUE FALSE 3331808.541 2845329.116 3230309.492 2923861.502 2896492.403 3014869.034 3287746.612 3256497.688 3573443.645 0.932380323 0.796242896 0.903976615 0.818219564 0.810560538 0.843687304 0.92004994 0.911305176 1 21.76888361 1.14612432 1.209137212 0.994321291 0.850958396 0.534541422 0.043888841 0.330680257 0.989227967 0.039158482 0.012424325 13.99988023 -1.14612432 -0.143362895 S(ph)LQQLAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 119.25 0.0017307 0 110471 109621 98006 117413 101248 106646 119359 112446 107540 TRUE FALSE 105249.2548 120791.5045 102499.672 105610.4222 118905.6191 102952.8223 101148.5924 102599.6321 124216.754 0.847303213 0.972425222 0.825167852 0.850210771 0.957243007 0.828815912 0.814291061 0.825972575 1 16.92250025 S(ph)LQTLPTDSSTFDTDTFCPPRPKPVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLQTLPTDSSTFDTDTFCPPRPKPVAR 27 2 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.999)LQT(0.001)LPTDSSTFDTDTFCPPRPKPVAR;S(0.999)LQT(0.001)LPTDSSTFDTDTFCPPRPKPVAR 217.57 1.79E-34 576010000 559680 455130 576690 556730 504620 562590 734600 626450 638590 TRUE FALSE 533225.0356 501508.2644 603131.8069 500766.4427 592625.5682 543107.3672 622523.2781 571594.717 737619.2757 0.722900083 0.679901246 0.817673598 0.678895548 0.803430154 0.736297688 0.843962866 0.774918357 1 19.49251683 -4.999999289 0.132351133 1.870624684 0.64901047 0.734821238 0.048470634 61.66323926 0.511423537 14.07048485 0.301069074 1.00E-05 4.999999289 -1.221614214 S(ph)LRLS(ph)AQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLRLSAQK 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 2 S(1)LRLS(1)AQK;S(1)LRLS(1)AQK 96.464 0.005077 146216000 506450 550550 451000 581530 355190 534110 545200 548570 409930 TRUE FALSE 482511.1122 606651.6709 471678.7961 523073.4996 417135.0235 515613.6368 462019.7267 500534.3026 473499.8508 1.019031181 1.281207734 0.996154054 1.104696229 0.880961257 1.088941498 0.975754746 1.057094953 1 18.85300445 3.69708255 24.99364686 1.014202469 1.150119575 0.289967312 0.088029036 489.2204539 294791.9646 0.021264933 0.032943783 4978.317027 -3.69708255 0.135917107 S(ph)LS(ph)GSSPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LS(0.521)GS(0.094)S(0.385)PCPK 90.614 0.015659 535140000 744410 559030 610860 743300 383750 710980 802610 704710 439130 TRUE FALSE 709223.2146 615995.7926 638868.5352 668582.0718 450675.8785 686358.5843 680157.1036 643001.8565 507228.0376 1.398233461 1.214435613 1.259529221 1.318109454 0.888507427 1.353155846 1.340929627 1.267678063 1 18.95227497 -2.020981576 3.091448681 0.696514895 1.26138094 0.244229419 0.140625178 0.107278418 0.000728096 0.04965892 0.030450766 0.009528366 2.020981576 0.564866045 S(ph)LS(ph)PKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(1)LS(1)PKPR 142.43 0.0014168 1468460000 3498370 2884910 2957600 3477170 1719060 3354380 3564210 2784250 1702540 TRUE FALSE 3333008.983 3178885.609 3093208.885 3127638.265 2018863.52 3238216.98 3020424.303 2540446.31 1966561.208 1.694841213 1.616469193 1.572902421 1.590409824 1.026595822 1.646639304 1.535891327 1.291821632 1 20.90724366 -2.560488262 0.101110665 1.24E-12 1.950035898 0.510194991 0.176852313 79.32776997 0.968084873 21.75918523 3.403247762 0.002751134 2.560488262 1.950035898 S(ph)LSDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSDIK 6 0 O14545;F8VNX8 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(1)LSDIK 73.248 0.087547 118190000 230840 244320 203470 287720 207430 265730 270240 298570 226250 TRUE FALSE 219928.6507 269216.4858 212799.3008 258797.839 243605.7263 256527.7035 229009.9247 272425.628 261335.6945 0.841556111 1.030155817 0.814275682 0.990288906 0.932156347 0.981602241 0.87630557 1.042435587 1 17.99554466 7.999999999 0.041356109 1.167979348 0.560571262 0.17179237 0.071679186 1532.848153 4.822626672 19.0031905 64.27376322 99999999.86 -7.999999999 -0.607408086 S(ph)LSDSESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.949)LS(0.05)DSESDDSK;S(0.499)LS(0.499)DS(0.003)ESDDSK;S(1)LSDSESDDSK;S(0.988)LS(0.012)DSESDDSK;S(0.988)LS(0.012)DSESDDSK;S(0.891)LS(0.106)DS(0.003)ESDDSK;S(0.998)LS(0.002)DSESDDSK 318.57 6.93E-46 4337200000 9110600 8975470 7943860 10277740 5556160 8916650 8769820 9066210 5141140 TRUE FALSE 8679959.993 9890080.597 8308093.839 9244602.049 6525152.545 8607864.175 7431822.89 8272324.589 5938401.734 1.461666014 1.665444852 1.399045435 1.556749183 1.098806183 1.449525404 1.25148537 1.393022055 1 22.50164326 -0.371552925 0.084487282 0.269724838 2.030654285 0.525625754 0.138213453 37.23284916 0.822617989 11.67259413 5.625993086 0.425056905 0.371552925 1.760929447 S(ph)LSDSESDDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.993)LS(0.001)DS(0.006)ESDDSKSK;S(0.864)LS(0.031)DS(0.101)ES(0.004)DDSKSK 162.29 2.46E-05 190520000 949000 653320 922880 942120 629120 964920 1202230 892130 769540 TRUE FALSE 904142.6507 719894.0508 965194.9609 847416.3077 738838.3288 931504.5785 1018807.733 814010.3677 888876.3329 1.01717485 0.809892247 1.085859669 0.953356813 0.831204861 1.047957454 1.14617489 0.915774599 1 19.76162319 2.115868726 12.66242438 1.051913522 0.936189808 0.146095482 0.097946673 0.656382096 69.52243124 0.034904966 0.025778948 130.5776131 -2.115868726 -0.115723713 S(ph)LSGS(ph)SPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LS(0.116)GS(0.806)S(0.078)PCPK 145.14 4.53E-05 515860000 1630600 1240400 1507600 1572400 997110 1484800 1810300 1513900 1012300 TRUE FALSE 1553524.77 1366798.17 1576724.951 1414339.365 1171005.668 1433381.004 1534105.487 1381334.89 1169282.314 1.328613929 1.168920588 1.348455315 1.209579028 1.001473857 1.225863922 1.312006064 1.181352761 1 20.15719187 -4.306476668 0.270891382 6.87E-23 1.244359844 0.343472078 0.098332177 171.8207821 2.368914342 95.68870206 0.120424772 4.94E-05 4.306476668 1.244359844 S(ph)LSGSS(ph)PCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LSGS(0.005)S(0.995)PCPK;S(1)LSGSS(1)PCPK;S(0.999)LS(0.46)GS(0.044)S(0.497)PCPK;S(1)LSGSS(1)PCPK;S(1)LSGS(0.013)S(0.987)PCPK;S(1)LS(0.286)GS(0.223)S(0.492)PCPK;S(1)LSGS(0.014)S(0.986)PCPK 265.53 1.82E-17 2572810000 9013220 7565910 8510270 9518660 5859410 9216230 10207510 9072340 6187170 TRUE FALSE 8587182.953 8336884.831 8900474.297 8561826.213 6881289.249 8897069.644 8650166.876 8277917.814 7146644.724 1.201568468 1.166545302 1.245406011 1.198020406 0.962869922 1.244929612 1.210381544 1.158294295 1 22.76883464 0.955930264 20.55448647 0.999999998 1.177937524 0.319652839 0.079887526 1060.493931 494625.5645 0.072843724 0.018210931 9.035043845 -0.955930264 0.177937526 S(ph)LSGSSPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.992)LS(0.006)GS(0.002)SPCPK;S(0.819)LS(0.181)GSSPCPK 206.24 1.61E-07 567920000 612020 531040 587410 677520 500640 583110 744260 645950 628810 TRUE FALSE 583091.0275 585153.5797 614343.3295 609414.4024 587951.4575 562916.7545 630709.4677 589387.1936 726322.6433 0.802798912 0.805638631 0.845827037 0.839040897 0.809490745 0.775023001 0.868359914 0.811467464 1 19.47025103 -4.999999999 0.318674908 2.696995026 0.811974633 0.824481208 0.026114937 123.6661531 1.098494117 141.3899796 0.022324967 1.00E-05 4.999999999 -1.885020393 S(ph)LSKSDSDLLTCSPTEDATMGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.527)LS(0.458)KS(0.015)DSDLLTCSPTEDATMGSR;S(0.326)LS(0.326)KS(0.326)DS(0.022)DLLTCSPTEDATMGSR 103.68 0.00012599 439340000 88845 69392 82711 83254 61292 91766 89965 89566 65812 TRUE FALSE 84645.47292 76463.12369 86503.38116 74885.14975 71981.30539 88588.12041 76239.18693 81723.12622 76017.78884 1.113495594 1.005858298 1.137936034 0.985100342 0.946900804 1.165360395 1.002912451 1.075052662 1 16.21404944 4.697556585 3.720269571 1.042286975 1.118083155 0.10081323 0.068652042 0.554723043 13.44852702 0.014976025 0.106389453 49837.53858 -4.697556585 0.07579618 S(ph)LSLSLADSGHLPDVHGFNSYGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.99)LS(0.009)LSLADSGHLPDVHGFNSYGSHR;S(0.992)LS(0.008)LSLADSGHLPDVHGFNSYGSHR 319.55 1.28E-74 1683060000 433950 358580 426650 441660 502260 388100 567680 460580 50706 TRUE FALSE 413438.0435 395119.7097 446212.3245 397263.4977 589853.985 374659.9997 481069.9898 420249.1735 58569.22751 7.058963573 6.746199779 7.618545497 6.782802413 10.07105625 6.39687453 8.213698734 7.175255529 1 15.83785525 0.941179653 21.87544286 1.000000002 7.494063759 0.796694481 1.034547148 2269.924097 844192.357 0.910734071 0.227683518 8.733325621 -0.941179653 6.494063756 S(ph)LSPILPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.897)LS(0.103)PILPGR;S(0.582)LS(0.418)PILPGR 103.7 0.0035453 307015000 305550 272661 275942 306882 300920 274343 338197 321187 369648 TRUE FALSE 291107.257 300445.4659 288594.2136 276033.6383 353400.3527 264842.4331 286598.8362 293062.1636 426971.1239 0.681796123 0.703666944 0.675910378 0.646492521 0.827691459 0.620281837 0.671237047 0.686374668 1 18.70377898 -1.352799547 6.130507671 1.000033595 0.688154326 0.763935917 0.054296855 2.25E-05 2.38E-06 0.047494165 0.011193279 0.044381344 1.352799547 -0.311879269 S(ph)LSPNHNTLQTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.575)LS(0.425)PNHNTLQTLK;S(0.584)LS(0.416)PNHNTLQTLK 185.25 5.68E-06 1007810000 3012560 2247520 2361750 3237410 2724300 2471970 3164670 2855880 2660270 TRUE FALSE 2870162.259 2476544.843 2470038.574 2911979.396 3199417.057 2386365.059 2681841.468 2605804.007 3072811.085 0.934050998 0.805954149 0.803836782 0.947659754 1.041202003 0.776606499 0.872764838 0.848019594 1 21.55112764 -2.424129184 2.099040468 1.967683176 0.875438018 0.186486062 0.079309866 3726080.716 361328.9194 17115826.14 0.018652726 0.003765918 2.424129184 -1.092245158 S(ph)LSQSFENLLDEPAYGLIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.333)LS(0.333)QS(0.333)FENLLDEPAYGLIQK;S(0.393)LS(0.311)QS(0.296)FENLLDEPAYGLIQK 130.3 1.06E-05 102391300 73122 63076 61096 71431 54555 69109 77498 71581 64046 TRUE FALSE 69665.66797 69503.51611 63897.31203 64250.62017 64069.37473 66715.738 65674.25675 65312.98817 73977.92658 0.941708847 0.939516952 0.863734833 0.868510692 0.866060698 0.901833034 0.887754764 0.882871299 1 16.17480725 -0.422286097 6.285780796 0.999999499 0.898010692 0.583159707 0.027982496 4242693.763 674966.6576 0.031497417 0.007639246 0.378193363 0.422286097 -0.101988807 S(ph)LSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.993)LS(0.007)SLR;S(0.998)LS(0.001)S(0.001)LR 132.57 0.015568 329388000 163981 159657 143300 210134 235980 171861 191733 190046 227206 TRUE FALSE 156229.9431 175926.2298 149870.4467 189010.9311 277134.8373 165909.4105 162480.6094 173404.5647 262439.9461 0.595297878 0.670348521 0.571065682 0.720206409 1.055993348 0.632180478 0.619115389 0.66073998 1 18.0016278 3.074656922 7.053989049 0.758333199 0.623834753 0.217678835 0.148198841 0.425040617 33.27485887 0.042862016 0.0513287 1187.563721 -3.074656922 -0.134498446 S(ph)LSSS(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.992)LS(0.059)S(0.172)S(0.778)PVKK 84.169 0.054853 431890000 2127200 2022200 2035200 2434100 1473700 2248200 2474600 2459300 1157800 TRUE FALSE 2026651.472 2228264.479 2128515.933 2189419.644 1730712.813 2170344.27 2097054.321 2243950.654 1337345.711 1.515428251 1.666184339 1.591597383 1.637138121 1.294140176 1.622874514 1.568071968 1.677913674 1 20.35094103 -1.207504034 4.605137063 0.999871598 1.572967282 0.729449306 0.109411625 7646494.145 2004978.239 9941.353197 0.023770323 0.062014888 1.207504034 0.573095684 S(ph)LSTSGESLYHVLGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.562)LS(0.424)T(0.004)S(0.004)GES(0.005)LYHVLGLDK 177.64 6.55E-10 57659000 84077 72457 48250 99070 68975 73536 83840 80532 61545 TRUE FALSE 80102.84683 79840.45068 50462.31023 89111.29538 81004.21816 70989.42988 71048.66817 73480.19115 71089.08427 1.126795311 1.123104222 0.709846114 1.253515871 1.139474773 0.998598176 0.999431473 1.033635359 1 16.11734043 1.88279415 0.013123157 6.25E-07 2.074467762 0.020807294 0.1414348 2399.485238 26.87699318 2100.801073 2142.187735 76.34738208 -1.88279415 2.074467137 S(ph)LSTSGESLYHVLGLDKNATSDDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSTSGESLYHVLGLDKNATSDDIKK 26 2 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.506)LS(0.403)T(0.076)S(0.015)GESLYHVLGLDKNATSDDIKK 188.44 4.78E-18 134220000 237140 124430 195350 247940 187660 255210 371480 309440 216600 TRUE FALSE 225930.8622 137109.5585 204306.9907 223016.6001 220387.8446 246372.0137 314803.9033 282343.7932 250189.2218 0.903039949 0.548023442 0.816609881 0.891391718 0.880884648 0.984742716 1.25826325 1.12852101 1 17.93266011 2.406929493 1.215159937 1.154784093 0.74280419 0.610217004 0.11740468 0.264096348 0.778548703 0.067279762 0.045121612 255.2286908 -2.406929493 -0.411979903 S(ph)LSVEHLETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.601)LS(0.399)VEHLETK;S(0.965)LS(0.035)VEHLETK;S(0.612)LS(0.388)VEHLETK 152.47 1.16E-05 561356000 1397990 1129320 1226210 1433270 1044740 1347810 1554000 1498950 1019680 TRUE FALSE 1331909.783 1244398.992 1282432.941 1289194.977 1226942.325 1301135.002 1316908.759 1367693.992 1177806.767 1.130838964 1.056539177 1.088831358 1.094572568 1.041717844 1.104710075 1.118102558 1.161221034 1 20.16767144 2.035263951 24.9993426 1.107524463 1.083276125 0 0.046451142 511.3431888 362499.6225 0.015651881 0.011559645 108.4585893 -2.035263951 -0.024248339 S(ph)LT(ph)RS(ph)PPAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)LT(1)RS(1)PPAIR 75.764 0.031821 171430000 213970 161120 171330 207110 151230 178560 216820 154350 160610 TRUE FALSE 203856.0621 177538.3112 179185.65 186290.9093 177604.4641 172376.4224 183740.1268 140834.2957 185516.5785 1.098856306 0.956994316 0.965874055 1.004173917 0.957350904 0.929169909 0.990424297 0.759146686 1 17.50118859 8 0.428860634 0.931001193 4.174402632 0.347726403 0.068660772 85.80441456 1.080225372 0.039830342 240.2653631 100000000 -8 3.243401439 S(ph)LTAHSLLPLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.621)LT(0.251)AHS(0.128)LLPLAEK 140.93 2.55E-05 181340000 654390 594860 577910 719600 502660 658670 730380 699630 505890 TRUE FALSE 623458.2816 655476.9103 604407.7451 647264.4408 590323.7449 635860.0927 618947.1167 638366.6882 584340.8375 1.066942855 1.121737295 1.034341101 1.10768305 1.010238729 1.088166447 1.059222763 1.092456059 1 19.15645059 3.737347856 24.99773038 1.060559724 1.094340074 0.147291603 0.037103785 194.2312386 4003557.793 0.008506642 0.014056018 5461.95171 -3.737347856 0.03378035 S(ph)LTNSHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 S(0.994)LT(0.006)NSHLEK;S(0.989)LT(0.011)NSHLEK;S(0.995)LT(0.005)NSHLEK;S(0.998)LT(0.002)NSHLEK;S(0.994)LT(0.006)NSHLEK 164.64 4.00E-05 882401000 1767290 1388700 1324980 2199200 1558220 1676200 2105610 1790640 1287170 TRUE FALSE 1683753.704 1530210.109 1385731.644 1978132.238 1829973.075 1618152.774 1784360.522 1633842.069 1486777.75 1.132485137 1.029212409 0.932036845 1.33048281 1.230831626 1.088362248 1.200152829 1.098914797 1 20.50375757 3.253033639 24.99999862 1.168635943 1.045272241 0.252745523 0.100821824 316.3855883 546506.0969 0.026378974 0.035559072 1790.744555 -3.253033639 -0.123363703 S(ph)LTSSLENIFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 S(0.997)LT(0.003)SSLENIFSR;S(0.599)LT(0.012)S(0.382)S(0.008)LENIFSR 155.09 6.97E-05 92653000 77725 52957 60215 79431 77590 68040 91519 70603 78702 TRUE FALSE 74051.09329 58353.37851 62975.91731 71446.44497 91121.67143 65683.75774 77556.09569 64420.62703 90906.70421 0.814583412 0.641904016 0.692753278 0.785931528 1.002364702 0.722540305 0.853139451 0.708645502 1 16.47209907 3.007406999 11.18492047 0.843240928 0.717514915 0.270758918 0.104578006 0.343061618 485.0766707 0.028044916 0.03293492 1017.201517 -3.007406999 -0.125726013 S(ph)LVGTPYWMAPELISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 SLVGTPYWMAPELISR 16 0 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.992)LVGT(0.008)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.992)LVGT(0.008)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 405.9 8.15E-140 9813728000 2727550 2543333 2410469 2937499 2423746 2601792 2850083 2760743 2531078 TRUE FALSE 2598624.117 2802501.524 2520991.388 2642216.02 2846446.535 2511691.291 2415250.493 2518997.707 2923584.649 0.888848598 0.958584019 0.862294645 0.903759028 0.973615228 0.859113586 0.826126411 0.861612715 1 21.47930693 2.170231858 24.99999926 0.86681622 0.91731141 0.017715746 0.056148832 89.92411576 32899.71505 0.019133828 0.014131272 147.9898255 -2.170231858 0.050495191 S(ph)LVGTPYWMAPEVISR ddPTM_SK-BR-3_Trastuzumab_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 285.75 7.34E-36 357739000 337375 284420 286061 328528 295233 291195 325040 325348 278989 TRUE FALSE 321427.9524 313402.7214 299177.1798 295503.7413 346721.5417 281110.8441 275449.1782 296858.8043 322253.1892 0.997439166 0.97253567 0.92839168 0.916992449 1.075928969 0.87232913 0.854760131 0.921197413 1 18.29783511 2.152356344 24.80183465 0.894136619 0.974213915 0.216760694 0.057954151 25.34540588 7287.7537 0.020156417 0.014886504 142.0222353 -2.152356344 0.080077296 S(ph)MDELNHDFQALALEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;S(1)MDELNHDFQALALEGR 289.43 3.88E-46 400625000 276765 233105 262431 293035 259963 270182 313278 293889 264687 TRUE FALSE 263682.8669 256858.6645 274463.7209 263578.5651 305300.4649 260825.5296 265481.6874 268154.5212 305733.3081 0.862460386 0.840139617 0.897722668 0.862119233 0.998584246 0.853114537 0.868344012 0.877086382 1 18.22191421 -5 0.253943946 1.742246122 0.86816933 0.404872611 0.044312599 187.9994538 1.8569639 72.73684916 0.060029369 1.00E-05 5 -0.874076792 S(ph)MDLGIADETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMDLGIADETK 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(1)MDLGIADETK 180.09 7.15E-06 68962000 177030 161020 136470 193570 125260 168480 186160 165000 124180 TRUE FALSE 168662.1427 177428.1211 142727.2845 174111.9758 147105.3043 162645.4954 157757.8729 150551.7253 143437.2002 1.175860534 1.236974236 0.995050686 1.213855092 1.025572893 1.13391432 1.099839322 1.049600279 1 17.13005971 8 0.107545937 0.947815069 1.736120081 0.333787206 0.070749061 108.7689261 0.819343524 0.619225334 12.70808169 100000000 -8 0.788305012 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.925)MDS(0.075)SDLSDGAVTLQEYLELKK;S(0.859)MDS(0.116)S(0.025)DLSDGAVTLQEYLELKK;S(0.811)MDS(0.158)S(0.031)DLSDGAVTLQEYLELKK;S(0.995)MDS(0.002)S(0.002)DLSDGAVTLQEYLELKK;S(0.454)MDS(0.454)S(0.091)DLS(0.001)DGAVTLQEYLELKK 268.24 3.77E-38 1232767000 960022 920573 779934 993516 563734 1002708 1069690 1115197 596823 TRUE FALSE 914643.6626 1014380.435 815694.7454 893645.8841 662049.0311 967983.9705 906489.1443 1017544.439 689375.2627 1.326771807 1.471448847 1.18323762 1.296312665 0.960360876 1.404146657 1.314942954 1.476038514 1 19.39493 3.73774575 24.99923281 1.252129568 1.399110327 0.141967853 0.164334416 137.5549723 4220068.943 0.040524806 0.067039567 5466.958161 -3.73774575 0.146980759 S(ph)MFDLTNSSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMFDLTNSSQR 11 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(1)MFDLTNSSQR;S(0.998)MFDLT(0.002)NSSQR 75.102 0.040917 76774000 66689 49768 54159 61637 71811 53259 73607 61122 64285 TRUE FALSE 63536.74313 54839.41578 56642.24372 55441.13166 84334.81566 51414.62748 62376.90026 55769.83365 74253.98948 0.855667737 0.738538308 0.762817515 0.746641791 1.135761408 0.692415692 0.840047797 0.751068516 1 16.18018092 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 250.41 2.84E-25 90240000 68153 61227 52397 71070 54959 62655 66325 64950 65942 TRUE FALSE 64931.54276 67466.10091 54799.45428 63925.90858 64543.8322 60485.24164 56205.90311 59262.63368 76167.94857 0.852478555 0.88575447 0.719455562 0.839275703 0.847388349 0.794103593 0.737920663 0.778052118 1 16.21689642 3.8355432 22.39052151 0.802698011 0.869117861 0.051025526 0.077905945 37.88765408 8739.304764 0.018003232 0.032455788 6847.675943 -3.8355432 0.06641985 S(ph)MMY(ph)KDILLLGNNY(ph)VIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMMYKDILLLGNNYVIHR 18 1 A0A6E1WB48;Q14541;Q14541-2 A0A6E1WB48 HNF4G Hepatocyte nuclear factor 4-gamma 3 S(1)MMY(1)KDILLLGNNY(1)VIHR 46.982 0.052674 167570000 101310 125510 134270 110230 116430 100530 126370 73862 42661 TRUE FALSE 96521.27708 138299.6117 140426.4123 99149.47098 136735.3551 97048.62089 107089.9356 67394.25171 49276.65 1.958762965 2.806595247 2.849755662 2.012098448 2.77485087 1.969464663 2.173238959 1.367671133 1 15.58861656 1.228211186 1.181090604 0.976041652 2.461509657 0.692617981 0.336389036 0.231405364 0.652143688 0.290579584 0.094094655 16.91263148 -1.228211186 1.485468004 S(ph)MPVLGSVSSVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK 239.31 8.74E-17 1361382000 3559450 2939412 3133703 4054430 2969547 3746120 4227300 3723010 3567940 TRUE FALSE 3391201.853 3238941.425 3277386.382 3646870.993 3487435.057 3616390.925 3582347.745 3397003.507 4121237.913 0.822860006 0.785914692 0.795243189 0.884896983 0.846210564 0.87750113 0.869240704 0.824267751 1 21.97464632 -5 0.129538406 1.549377658 0.766588706 0.74238556 0.030739948 69.39113093 0.567816049 9.890169431 0.228762627 1.00E-05 5 -0.782788952 S(ph)MSAPSDLEMIGNEDLEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.493)MS(0.493)APS(0.013)DLEMIGNEDLEFTR 56.215 0.097124 6973900 8204.6 5977.1 9817 8533.7 7676.8 7341.8 8657.1 7849.6 8800.2 TRUE FALSE 7816.784818 6586.173285 10267.11916 7675.876263 9015.631489 7087.551625 7336.300396 7162.247411 10164.89007 0.768998461 0.647933548 1.010057078 0.75513618 0.886938415 0.697258069 0.721729438 0.70460648 1 13.31130699 -2.12518786 2.386840579 1.466430845 0.765614248 0.312032041 0.104754865 6970569.309 1809033.027 17637614.28 0.025230566 0.007495699 2.12518786 -0.700816597 S(ph)MSIDDTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.999)MS(0.001)IDDTPR;S(0.983)MS(0.017)IDDTPR;S(0.993)MS(0.007)IDDTPR;S(0.999)MS(0.001)IDDTPR;S(1)MSIDDTPR;S(1)MSIDDTPR;S(1)MSIDDTPR 239.54 2.63E-10 1225770000 2827910 2453760 2538530 2816980 2575910 2552930 3094740 2792360 2653350 TRUE FALSE 2694240.299 2703800.934 2654924.111 2533811.818 3025147.888 2464521.394 2622580.574 2547846.155 3064817.967 0.879086565 0.882206044 0.866258336 0.826741375 0.987056302 0.804133042 0.855705168 0.831320549 1 21.54736996 -1.132376709 4.990941134 1.000006197 0.867439775 0.42087351 0.049181751 3.06E-06 5.32E-07 0.042986662 0.01013158 0.073726445 1.132376709 -0.132566422 S(ph)MSVDLSHIPLKDPLLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.5)MS(0.5)VDLS(0.001)HIPLKDPLLFK;S(0.5)MS(0.5)VDLSHIPLKDPLLFK 135.91 9.33E-06 207690000 1077820 771600 855890 1230470 974500 1179080 1410660 1066580 976830 TRUE FALSE 1026873.585 850226.9172 895133.4031 1106780.818 1144452.491 1138248.164 1195437.908 973184.6009 1128311.807 0.910097349 0.75353897 0.793338683 0.980917518 1.014305163 1.008806392 1.05949251 0.862513885 1 20.10573438 3.201866421 6.652802796 0.998772534 0.817917644 0.609218507 0.063314893 0.108990798 13.58085255 0.017680487 0.021548744 1591.719077 -3.201866421 -0.18085489 S(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SMVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 32 0 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4;R4GNG3;Q14161-9;Q14161-5;F8WAK2;Q14161-11;Q14161-7;Q14161-10;Q14161-8 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 S(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR;S(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR;S(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR;S(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR;S(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 215.72 5.82E-36 236434000 16781.5 13915.5 13319.7 14535.61 15693 15803.8 13774.6 14406.5 20866.9 TRUE FALSE 15988.27175 15333.50527 13930.42142 13074.46287 18429.85423 15256.51044 11673.03178 13144.99049 24102.83228 0.663335809 0.636170268 0.577957862 0.542445083 0.764634381 0.632975837 0.484301249 0.545371197 1 14.55691506 -1.636473389 2.911906147 1.034406641 0.606166991 0.721077048 0.077030098 28296244.85 28274325.31 7342887.295 0.020619239 0.02309546 1.636473389 -0.42823965 S(ph)NDSGEEAEKEFIFV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.5)NDS(0.5)GEEAEKEFIFV 68.809 0.031205 14137000 138320 120850 124600 144400 90122 137040 156770 153880 102160 TRUE FALSE 131781.8877 133164.7524 130313.0332 129884.6377 105839.2483 132294.2704 132851.8572 140405.4514 118002.451 1.116772462 1.12849141 1.104324801 1.100694405 0.896924151 1.121114598 1.125839811 1.189851992 1 16.8484573 3.182466284 4.148867296 1.076233597 1.119707221 0.068307594 0.078840718 0.693454594 24.30068014 0.023193763 0.028885722 1522.180955 -3.182466284 0.043473624 S(ph)NENLDKIDMSLDDIIK ddPTM_SK-BR-3_Trastuzumab_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(0.996)NENLDKIDMS(0.004)LDDIIK 208.4 3.15E-12 111126000 301679 271534 245020 309752 142091 313731 292550 314288 135078 TRUE FALSE 287419.2315 299203.6233 256254.4094 278615.1405 166871.6254 302866.4168 247916.1245 286767.2766 156025.2064 1.842133321 1.91766209 1.642391094 1.785705957 1.069517095 1.941137742 1.588949185 1.837954798 1 17.25141959 -2.584997203 0.222481739 2.89E-22 1.83173059 0.417735841 0.254951854 43.0833816 1.12425286 22.29308669 0.479716724 0.002600176 2.584997203 1.83173059 S(ph)NGDLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNGDLSPK 8 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 S(1)NGDLSPK;S(1)NGDLSPK 120.53 0.001557 452760000 974430 1065030 862130 1133700 629600 977460 994610 1116690 636740 TRUE FALSE 928370.625 1173557.768 901659.5133 1019738.322 739402.0407 943610.3151 842863.9772 1018906.704 735482.3872 1.262260852 1.595630009 1.22594304 1.386489112 1.005329364 1.282981526 1.146001579 1.385358401 1 19.48833127 3.198357441 1.872220431 1.185350335 1.416643979 0.258436656 0.154906903 0.384762087 2.778113827 0.045294951 0.061345717 1578.910239 -3.198357441 0.231293644 S(ph)NGSLHTLACHPPLSPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNGSLHTLACHPPLSPGPR 19 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 S(0.963)NGS(0.037)LHTLACHPPLSPGPR 90.062 0.0038386 59034000 64468 51132 61847 56439 70972 50675 60045 50216 62547 TRUE FALSE 61420.7254 56342.40893 64682.74613 50765.64449 83349.49433 48920.11204 50884.03245 45818.82083 72246.46931 0.850155391 0.779863839 0.895306674 0.702673016 1.153682597 0.677128066 0.704311684 0.634201522 1 16.14063946 -1.242265247 5.618872638 1.000011113 0.798889007 0.15244493 0.14844196 1.93E-05 2.60E-06 0.134241807 0.03163935 0.05724463 1.242265247 -0.201122105 S(ph)NPDFLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNPDFLKK 8 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(1)NPDFLKK 91.961 0.0074212 285470000 531230 468620 485700 579030 311120 544570 568170 591560 331600 TRUE FALSE 506119.8107 516372.9108 507969.8254 520824.8043 365379.2295 525711.4044 481485.2313 539759.8703 383022.8344 1.321382866 1.348151766 1.326212904 1.359774816 0.953935893 1.372532803 1.25706665 1.409210684 1 18.54707088 -1.693630288 2.832725583 0.960189411 1.29370599 0.344865146 0.127145282 113701770 105960175.2 32503325.92 0.02834106 0.020247421 1.693630288 0.333516579 S(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 234.4 1.41E-38 1518740000 622201 502915 538878 602452 530179 594084 692549 605159 552733 TRUE FALSE 592790.7918 554162.6103 563586.0893 541892.3804 622642.0497 573510.7221 586887.9305 552168.0698 638448.0107 0.928487178 0.867983925 0.882743904 0.848765086 0.975243151 0.898288839 0.919241537 0.86485988 1 19.28420962 2.753879269 24.98189783 0.923246522 0.884867244 0.239278403 0.042345528 1386.678961 2261414.946 0.011896571 0.012575976 567.3868534 -2.753879269 -0.038379279 S(ph)NSFSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.748)NS(0.249)FS(0.003)DER;S(0.555)NS(0.305)FS(0.14)DER;S(0.5)NS(0.5)FSDER 109.42 0.0057667 81576000 480791 506183 395788 555772 337405 412957 405411 452155 323209 TRUE FALSE 458064.9623 557763.6232 413935.2713 499904.7427 396248.3252 398656.1955 343558.1061 412561.9112 373330.601 1.2269687 1.494020639 1.108763306 1.339040361 1.06138721 1.06783691 0.920251662 1.105084636 1 18.51009424 2.714117475 1.267044992 0.995462977 1.332367759 0.566409483 0.110519579 0.266527516 0.87742765 0.047749911 0.043781819 517.746862 -2.714117475 0.336904782 S(ph)NSFSDEREFSGPSTPTGTLEFEGGEVSLEGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNSFSDEREFSGPSTPTGTLEFEGGEVSLEGGK 33 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.327)NS(0.327)FS(0.327)DEREFS(0.013)GPS(0.003)T(0.001)PT(0.001)GT(0.001)LEFEGGEVSLEGGK;S(0.442)NS(0.442)FS(0.116)DEREFSGPSTPTGTLEFEGGEVSLEGGK 261.49 9.86E-60 152068000 106711 65547 94987 94026 77656 98699 108116 115068 87803 TRUE FALSE 101666.9825 72226.31382 99342.2479 84574.32784 91199.18181 95281.02888 91620.91851 104992.0359 101419.0408 1.002444725 0.712157335 0.979522653 0.833909759 0.899231358 0.939478703 0.903389716 1.035230023 1 16.62996901 1.506032559 1.089797507 1.016317721 0.874149985 0.245256217 0.082744442 0.597086932 1.376245248 0.069438464 0.02487144 32.06509705 -1.506032559 -0.142167736 S(ph)NSGRELTDEEILASVMIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.495)NS(0.495)GRELT(0.009)DEEILASVMIK;S(0.333)NS(0.333)GRELT(0.333)DEEILASVMIK;S(0.333)NS(0.333)GRELT(0.333)DEEILASVMIK;S(0.644)NS(0.34)GRELT(0.015)DEEILASVMIK;S(0.489)NS(0.489)GRELT(0.023)DEEILASVMIK;S(0.495)NS(0.495)GRELT(0.01)DEEILASVMIK;S(0.483)NS(0.483)GRELT(0.034)DEEILASVMIK;S(0.64)NS(0.357)GRELT(0.004)DEEILASVMIK;S(0.467)NS(0.467)GRELT(0.066)DEEILASVMIK;S(0.621)NS(0.37)GRELT(0.009)DEEILASVMIK;S(0.488)NS(0.488)GRELT(0.023)DEEILASVMIK;S(0.393)NS(0.393)GRELT(0.214)DEEILASVMIK;S(0.485)NS(0.485)GRELT(0.03)DEEILASVMIK;S(0.455)NS(0.455)GRELT(0.091)DEEILASVMIK;S(0.499)NS(0.499)GRELT(0.002)DEEILASVMIK;S(0.441)NS(0.441)GRELT(0.118)DEEILASVMIK;S(0.499)NS(0.499)GRELT(0.001)DEEILASVMIK 198.56 4.45E-16 1687520100 3094405 2274528 2751180 2977045 2282874 2865902 3542162 3189750 2674246 TRUE FALSE 2948138.608 2506304.989 2877324.324 2677786.781 2681006.503 2766655.095 3001740.131 2910438.58 3088954.412 0.954413117 0.81137649 0.931488116 0.866891001 0.867933335 0.895660708 0.97176576 0.942208331 1 21.55868715 1.783228485 4.071187833 0.968436444 0.883425978 0.483167959 0.040561269 0.175435871 5.571546694 0.01943826 0.010176943 60.70556207 -1.783228485 -0.085010467 S(ph)NSIPTHEAAFELYSGSQMGSTLSLAERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNSIPTHEAAFELYSGSQMGSTLSLAERPK 30 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 S(0.499)NS(0.499)IPT(0.002)HEAAFELYSGSQMGSTLSLAERPK 166.74 3.40E-12 101370000 61175 47744 56667 65556 44543 65697 69405 67162 47699 TRUE FALSE 58283.37899 52609.16788 59265.238 58966.18633 52311.2851 63421.89642 58815.99254 61280.93923 55095.91731 1.057852956 0.954865087 1.075673859 1.070246022 0.949458465 1.151117896 1.06751998 1.11225917 1 15.7496578 2.234311011 24.99999869 1.088360702 1.02047774 0.219547499 0.056784905 143.8799307 846418.4467 0.01911515 0.014617852 171.5185162 -2.234311011 -0.067882962 S(ph)NSLDKHQQSSTLGNSVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNSLDKHQQSSTLGNSVVR 19 1 A0A0A0MSY4;Q9BZ29-5;X6RGR3;Q6ZSL5;A0A088AWN3;Q9BZ29-3;Q9BZ29;Q9BZ29-4 A0A0A0MSY4 DOCK9 Dedicator of cytokinesis protein 9 1 S(0.559)NS(0.441)LDKHQQSSTLGNSVVR;S(0.637)NS(0.363)LDKHQQSSTLGNSVVR 223.69 1.29E-19 882580000 1019190 857700 939040 1078580 679710 979900 1170680 1116270 717420 TRUE FALSE 971014.9085 945100.6051 982095.9128 970159.0892 798251.2088 945965.8173 992071.265 1018523.481 828673.8295 1.171769729 1.14049771 1.185141702 1.170736971 0.963287581 1.141541803 1.197179433 1.229100576 1 19.66044484 S(ph)NTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK 39 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 S(0.669)NT(0.21)QGPAY(0.007)S(0.102)HLT(0.012)EFAPPPTPMVDHLVASNPFEDDFGAPK 150.32 3.32E-13 39242000 69686 63770 61241 79040 50903 74214 80689 75794 36678 TRUE FALSE 66392.08088 70268.2355 64048.96043 71094.74903 59780.46708 71643.95057 68378.41109 69157.07555 42365.83691 1.56711364 1.658606099 1.511806802 1.678115062 1.411053609 1.691078373 1.613998827 1.632378364 1 15.37061375 -1.051854362 4.916427742 0.999986933 1.599308 0.832087621 0.084057348 1.05E-05 2.02E-06 0.070846392 0.016698291 0.088745356 1.051854362 0.599321067 S(ph)NVCINGNHVYLEQPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNVCINGNHVYLEQPEAK 18 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(1)NVCINGNHVYLEQPEAK;S(1)NVCINGNHVYLEQPEAK;S(1)NVCINGNHVYLEQPEAK;S(1)NVCINGNHVYLEQPEAK 252.39 1.13E-30 1335630000 2544120 1914230 2299680 2828550 1715510 2396640 2545570 2541150 1514570 TRUE FALSE 2423864.49 2109292.213 2405122.603 2544218.78 2014694.401 2313643.756 2157196.544 2318633.435 1749441.78 1.385507376 1.205694432 1.374794309 1.454303201 1.151621291 1.322504002 1.23307707 1.325356157 1 20.73846322 -3.889036022 0.257846687 1.28E-19 1.32875677 0.546397454 0.088802882 77.68362897 1.293384701 40.95303575 0.113091212 0.000129111 3.889036022 1.32875677 S(ph)PAFALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPAFALK 7 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 S(1)PAFALK;S(1)PAFALK;S(1)PAFALK 96.964 0.012949 300697000 1054150 1107330 963430 1265140 790620 1087990 1128350 1186380 916030 TRUE FALSE 1004322.419 1220168.186 1007604.218 1137965.724 928503.8777 1050312.633 956199.4839 1082494.278 1058083.254 0.949190354 1.153187314 0.952292 1.075497339 0.877533856 0.992655946 0.903709118 1.023070986 1 20.01302172 2.755034614 24.82482898 0.952175908 1.03892976 0.196714055 0.072129206 976.0172231 1470768.266 0.020104733 0.021268196 568.8982705 -2.755034614 0.086753852 S(ph)PAFRGPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPAFRGPDR 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(1)PAFRGPDR 84.718 0.016238 0 37026 31393 31706 32647 39421 32093 38697 33523 43386 TRUE FALSE 35275.85436 34591.98239 33159.75146 29365.26153 46296.00992 30981.61136 32793.06193 30587.5484 50114.0793 0.703911054 0.690264749 0.661685337 0.585968294 0.923812441 0.618221701 0.654368241 0.610358383 1 15.61292836 -1.191921634 5.151065788 1.000021862 0.682197394 0.534843565 0.0934662 2.14E-05 3.35E-06 0.08241943 0.019425111 0.06428037 1.191921634 -0.317824468 S(ph)PAKSPNPSTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPAKSPNPSTPR 12 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 S(1)PAKSPNPSTPR;S(1)PAKSPNPSTPR 134.14 9.13E-05 204872000 282740 300780 274480 313350 209730 328170 291770 311710 235340 TRUE FALSE 269375.4405 331429.824 287065.1795 281851.4627 246306.8456 316805.3906 247255.1278 284415.0199 271835.3252 0.990950828 1.219230148 1.056026031 1.036846342 0.906088439 1.165431278 0.909576883 1.046276895 1 18.05237342 3.329535972 3.273161175 1.004554178 1.108309414 0.150566776 0.090622777 0.35648498 7.583126129 0.024142225 0.033310388 2135.678973 -3.329535972 0.103755236 S(ph)PALKSPLQSVVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(1)PALKSPLQSVVVR 66.606 0.033251 226570000 278140 191750 271910 260730 236990 272320 323730 296400 281880 TRUE FALSE 264992.8734 211289.543 284377.3425 234520.925 278320.981 262889.4901 274339.0428 270445.6447 325592.5108 0.813878897 0.648938584 0.873414876 0.720289679 0.854813829 0.807418726 0.842584008 0.830626122 1 18.31270799 -0.549377913 0.198841084 1.145127701 0.712512392 0.535695522 0.062810423 9.607756903 0.529873975 1.009130075 0.185373209 0.28224229 0.549377913 -0.432615308 S(ph)PALSDANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 97.452 0.0070088 233739000 456430 533570 418720 574560 311000 463470 466050 539340 354470 TRUE FALSE 434855.4585 587941.3896 437918.7262 516804.1372 365238.3015 447419.9177 394945.5129 492112.5304 409439.3972 1.06207527 1.435966821 1.069556885 1.262223764 0.89204484 1.092762252 0.96460066 1.201917875 1 18.6432904 2.757344433 24.97172537 1.028034544 1.221726461 0.309324944 0.130771704 861.7989957 1145697.881 0.036848604 0.039023597 571.9320481 -2.757344433 0.193691916 S(ph)PAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPAMSR 6 0 Q9BQI6 Q9BQI6 ANKRD32 Ankyrin repeat domain-containing protein 32 1 S(1)PAMSR;S(1)PAMSR 107.29 0.032926 494250000 184476 185584 157831 191239 174106 166907 202973 182886 218049 TRUE FALSE 175756.1851 204495.2206 165067.7075 172015.2924 204470.0313 161126.9687 172005.741 166871.5323 251862.9253 0.697824759 0.811930618 0.655387081 0.682971867 0.811830606 0.639740718 0.682933944 0.662549012 1 17.94227924 -0.695803747 5.689040857 1.000000011 0.710668964 0.702107928 0.060176931 8.54E-09 1.80E-09 0.057310111 0.013508122 0.201463444 0.695803747 -0.289331047 S(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 38 2 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 S(0.774)PAPPPPAVFPAARPEPGDGLS(0.11)S(0.11)PAGGS(0.005)YET(0.002)GDRDDGR 66.324 0.0025239 317660000 8591.6 7426.3 10597 10530 11146 12073 11891 8708 11666 TRUE FALSE 8185.492095 8183.048413 11082.88293 9471.504394 13089.85887 11654.90898 10076.80956 7945.481356 13475.1037 0.607452995 0.607271647 0.822471068 0.702889166 0.971410622 0.864921654 0.747809426 0.589641574 1 13.71800875 3.741644052 24.3182952 0.805332172 0.607362299 0.337272515 0.120022291 190.0614311 1498955.607 0.029497429 0.050444188 5516.251416 -3.741644052 -0.197969873 S(ph)PDLEASLDTLENNCHVGSDIDFRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.998)PDLEAS(0.001)LDT(0.001)LENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK 306.08 1.84E-71 319578000 170788 195965 140438 189384 99855.6 153714 154615 172391 87957 TRUE FALSE 162715.1897 215934.0563 146877.2212 170346.7605 117270.385 148390.8456 131025.6421 157295.5301 101596.9223 1.601575973 2.125399582 1.445685734 1.676692134 1.154271038 1.460584063 1.289661527 1.548231251 1 16.63249717 3.254161158 1.613905072 1.328175603 1.84592248 0.446131138 0.228566958 0.285789023 1.542168188 0.068497774 0.099455315 1795.399742 -3.254161158 0.517746877 S(ph)PDNSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPDNSIK 7 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK 163.91 0.0012769 1339650000 3057050 4213110 3059530 3696250 1231470 3520380 2057950 3826490 1284200 TRUE FALSE 2912549.305 4642430.699 3199812.477 3324695.928 1446237.978 3398468.358 1743971.931 3491422.25 1483347.177 1.96349806 3.129699352 2.157156818 2.241347123 0.974982796 2.291080881 1.175700441 2.353745842 1 20.50042487 3.017869259 3.065952525 1.595971988 2.505681746 0.3332127 0.560740908 0.253672644 4.910440543 0.15625892 0.182568127 1042.003694 -3.017869259 0.909709757 S(ph)PDPFGAVAAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPDPFGAVAAQK 12 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK 115.78 0.00095726 213635000 737680 822300 597310 885680 477430 613250 583880 590050 345670 TRUE FALSE 702811.3283 906093.3049 624697.2543 796649.7637 560693.6408 592012.9987 494798.3823 538382.0939 399274.7382 1.760219872 2.269347941 1.564579961 1.995242092 1.404280279 1.482720899 1.239242895 1.348400093 1 18.60702227 2.377650063 0.647838306 1.096796637 2.014335254 0.686498127 0.206496895 0.37564406 0.315226175 0.158105092 0.120238532 238.5888058 -2.377650063 0.917538617 S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 78.65 0.0044067 29043000 31964 36744 34963 34910 20704 37470 34289 39553 21554 TRUE FALSE 30453.12507 40488.25537 36566.08813 31400.78048 24314.77104 36172.4045 29057.58329 36089.52964 24896.48424 1.22318978 1.626263973 1.468724973 1.261253604 0.976634725 1.452912153 1.167136011 1.449583375 1 14.60365441 -4.69962337 0.106836195 1.60E-07 1.544032355 0.222680774 0.185795094 220.6936802 1.686607899 49.54214361 2.498570999 2.00E-05 4.69962337 1.544032195 S(ph)PDPYR ddPTM_SK-BR-3_Trastuzumab_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 75.131 0.082342 245510000 647910 740560 601860 690390 506260 612570 601640 633310 509840 TRUE FALSE 617284.5783 816023.9059 629455.8763 620990.6855 594551.5837 591356.5473 509848.7681 577854.019 588903.3833 1.048193296 1.385666867 1.068861029 1.054486531 1.009591048 1.004165648 0.865759618 0.98123739 1 19.16767144 3.171089934 1.584918423 0.955520414 1.212779121 0.482068771 0.095307828 0.263406654 1.372157928 0.032116499 0.043692239 1482.825119 -3.171089934 0.257258707 S(ph)PDREASGSGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPDREASGSGGR 12 1 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(0.474)PDREAS(0.248)GS(0.278)GGR 90.229 0.023618 122500000 125860 128770 108540 133870 112080 121250 124350 122650 113540 TRUE FALSE 119910.8472 141891.8094 113516.6664 120413.1333 131626.7165 117051.0821 105378.1237 111910.1158 131147.2033 0.914322564 1.081927832 0.86556681 0.918152505 1.003656298 0.892516799 0.803510262 0.85331683 1 17.00082752 2.065405231 6.073038955 0.859936186 0.963538751 0.138970808 0.076441463 0.24904957 17.15159056 0.027869988 0.020335562 116.2532843 -2.065405231 0.103602565 S(ph)PEAQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SPEAQPK 7 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PEAQPK;S(1)PEAQPK;S(1)PEAQPK;S(1)PEAQPK;S(1)PEAQPK 102.62 0.0089785 1132545000 2936260 3152720 2651000 3488690 1678283 2954590 3124340 3867920 2379940 TRUE FALSE 2797468.809 3473985.752 2772550.972 3138000.253 1970975.024 2852271.807 2647664.551 3529224.42 2749008.94 1.017628123 1.263722974 1.008563825 1.141502382 0.716976578 1.037563671 0.963134209 1.283817003 1 21.39048017 3.283257304 2.302133908 0.999786588 1.133978152 0.064921827 0.155441974 0.59972088 6.503578863 0.044421183 0.061904925 1919.805822 -3.283257304 0.134191564 S(ph)PEASQTDSPVESPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPEASQTDSPVESPR 15 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PEASQTDSPVESPR 182.04 5.91E-07 99950000 32944 32223 30354 32424 43472 29176 40469 27059 47297 TRUE FALSE 31386.80241 35506.56033 31745.76092 29164.67792 51053.50304 28165.6278 34294.71079 24689.57051 54631.5772 0.574517596 0.649927426 0.581088128 0.533842869 0.934505384 0.515555824 0.627745208 0.451928569 1 15.73744745 -1.482384365 3.256324219 1.007960573 0.613841211 0.476701684 0.128761457 59058451.52 80010934 4285176.698 0.027944527 0.032931813 1.482384365 -0.394119362 S(ph)PEDQLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPEDQLGK 8 0 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 S(1)PEDQLGK;S(1)PEDQLGK 105.46 0.0045982 392640000 820580 825690 661760 905470 479440 798760 746050 831490 464340 TRUE FALSE 781792.8096 909828.7497 692102.3506 814450.4353 563054.1842 771098.7409 632226.3704 758680.3276 536347.4757 1.457623733 1.696342 1.290399194 1.518512666 1.049793669 1.437685038 1.178762647 1.414531366 1 19.03280844 7.999999985 0.06826776 0.57420133 3.192390295 0.409804041 0.165172407 208.9507284 1.055435705 7.246778869 52.82157162 99999996.55 -7.999999985 2.618188966 S(ph)PEGTPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPEGTPQK 8 0 C9J0I9;Q86WB0;Q86WB0-3;F8WAU5;F8WBD7;F8WDK5;F8WF13 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 S(0.999)PEGT(0.001)PQK 64.265 0.071415 369430000 323360 369410 331840 415910 218580 342400 359480 355490 265180 TRUE FALSE 308075.4136 407053.299 347055.1922 374101.9366 256700.2828 330542.6021 304634.7237 324361.411 306302.76 1.00578726 1.328924685 1.133046245 1.221346933 0.838060626 1.079136871 0.994554289 1.058956867 1 18.22459884 2.767029146 24.99827458 1.000956468 1.177706135 0.43167808 0.101311062 654.1376873 574398.5837 0.028876783 0.030623531 584.8293309 -2.767029146 0.176749667 S(ph)PEIHRR ddPTM_SK-BR-3_Trastuzumab_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 85.676 0.01264 1118160000 712089 586598 575466 741982 579913 651497 697261 618886 575845 TRUE FALSE 678429.9642 646373.0031 601851.6853 667396.5597 681049.6436 628935.4955 590881.0284 564693.0609 665144.1016 1.019974412 0.9717789 0.904844054 1.003386421 1.023912926 0.945562765 0.888350399 0.848978529 1 19.3433074 1.978901591 5.192885903 0.903119745 0.983710858 0.302387317 0.049718262 0.197771565 15.33309273 0.020220989 0.012903522 95.25802904 -1.978901591 0.080591114 S(ph)PEPEATLTFPFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK 143.38 4.64E-06 495203000 586963 725520 439839 723816 317940 566975 464680 589822 292693 TRUE FALSE 559218.4222 799451.3128 460006.0532 651056.6405 373388.6353 547340.5136 393784.5316 538174.0588 338082.3356 1.654089443 2.364664547 1.360633209 1.925733977 1.104431069 1.61895626 1.164759262 1.591843176 1 18.36701511 3.117703436 1.233699562 1.315802934 1.971091522 0.357237789 0.327790607 0.402889334 1.298987059 0.11532977 0.155765898 1311.304152 -3.117703436 0.655288587 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPEPEVLSTQEDLFDQSNK 19 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(1)PEPEVLSTQEDLFDQSNK 219.23 2.05E-19 88721000 190140 223320 154950 207410 85837 195920 173140 200000 102830 TRUE FALSE 181152.459 246076.5619 162054.6108 186560.7527 100806.9456 189135.2413 146724.3131 182486.9397 118776.3512 1.525155952 2.071763944 1.364367646 1.570689374 0.848712261 1.592364468 1.235299044 1.536391191 1 16.85788809 3.621275978 6.647152814 1.31690417 1.796882484 0.361662746 0.271810708 0.220722202 11.23536472 0.065275032 0.101544073 4180.959671 -3.621275978 0.479978313 S(ph)PEPGQTWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPEPGQTWTR 10 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR 151.15 2.13E-05 2885410000 768259 975919 686449 966811 599318 700373 724311 755965 546081 TRUE FALSE 731944.9196 1075366.256 717923.3656 869625.3215 703838.8694 676118.9074 613804.0541 689768.697 630764.4525 1.160409273 1.704861857 1.138179812 1.378684734 1.115850563 1.071903949 0.97311136 1.093544023 1 19.26674183 2.71189849 1.274577423 1.014057869 1.402227484 0.458470524 0.158122541 0.336849762 1.121295942 0.069692105 0.063818812 515.1082321 -2.71189849 0.388169615 S(ph)PERPTGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPERPTGDLR 10 1 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.996)PERPT(0.004)GDLR;S(1)PERPTGDLR;S(1)PERPTGDLR;S(1)PERPTGDLR 89.43 0.0069753 1373750000 1669690 1518610 1463560 1776270 1625190 1474590 1781780 1635070 1717240 TRUE FALSE 1590767.063 1673358.086 1530665.674 1597715.965 1908622.621 1423524.579 1509936.736 1491894.603 1983540.809 0.801983532 0.843621708 0.77168348 0.805486813 0.962230075 0.71766841 0.761233008 0.752137085 1 20.91964665 S(ph)PESCSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SPESCSKPEK 10 1 Q03111 Q03111 MLLT1 Protein ENL 1 S(0.987)PES(0.009)CS(0.004)KPEK;S(0.997)PES(0.003)CS(0.001)KPEK;S(0.989)PES(0.008)CS(0.003)KPEK;S(0.999)PES(0.001)CS(0.001)KPEK;S(0.998)PES(0.001)CS(0.001)KPEK 112.44 0.00098159 5794550000 5897390 5288700 5385470 6693000 3233610 6620640 6650020 7158880 3677540 TRUE FALSE 5618632.062 5827624.543 5632399.126 6020206.924 3797550.56 6391365.577 5635437.313 6532010.516 4247834.121 1.322705149 1.371904923 1.32594611 1.417241529 0.893996906 1.504617505 1.326661341 1.537727305 1 22.018296 S(ph)PESDRPR ddPTM_SK-BR-3_Trastuzumab_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(0.998)PES(0.002)DRPR 141.88 0.00037938 297961000 107598 112544 99974 124713 110428 96221 118261 127147 137309 TRUE FALSE 102512.0558 124012.3616 104557.9068 112176.6123 129686.6082 92888.84264 100218.1124 116013.3346 158602.1784 0.646347085 0.781908312 0.659246347 0.707282923 0.817684911 0.585671922 0.631883581 0.731473778 1 17.27505306 -2.034576061 1.565481223 1.347199277 0.693480656 0.653952998 0.069673875 77617.41613 18675.79274 96625.76922 0.018897681 0.009234724 2.034576061 -0.653718621 S(ph)PETALEAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPETALEAFK 10 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(1)PETALEAFK 82.287 0.01937 18956000 44180 47562 37512 40622 30712 38605 41051 46568 35189 TRUE FALSE 42091.69896 52408.62187 39231.9623 36538.59938 36068.16308 37268.09917 34787.916 42490.25905 40645.9304 1.035569823 1.289394076 0.965212554 0.89894853 0.887374522 0.916896201 0.855876976 1.045375481 1 15.31082329 3.586251666 6.040430807 0.919922441 1.161209842 0.562718581 0.081772208 0.132983223 6.321392483 0.020417771 0.031768995 3857.018005 -3.586251666 0.2412874 S(ph)PFEGAVTESQSLFSDNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.998)PFEGAVT(0.002)ESQSLFSDNFR 332.61 2.66E-75 607703000 156060 141777 136385 157439 137988.6 138741.7 151631.2 153315.1 139611.7 TRUE FALSE 148683.3531 156224.2375 142638.3872 141612.9326 162053.7682 133937.0401 128497.0755 139890.0171 161261.9694 0.921998867 0.968760571 0.884513489 0.878154553 1.004910015 0.830555652 0.796821941 0.867470598 1 17.29904672 2.210439098 24.99575916 0.849419772 0.931270947 0.118265128 0.065016588 269.4253862 239476.5989 0.022373269 0.016526958 162.3450673 -2.210439098 0.081851175 S(ph)PFLKPDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPFLKPDER 9 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 S(1)PFLKPDER;S(1)PFLKPDER 121.02 0.00037886 469140000 661970 730480 504220 689870 417230 662030 596000 663060 380430 TRUE FALSE 630679.99 804916.7425 527338.9857 620522.9569 489994.7799 639103.7351 505069.2537 604998.9513 439425.1414 1.435238748 1.831749408 1.200065577 1.412124383 1.11508135 1.454408669 1.149386337 1.376796397 1 18.74525789 4.013245884 0.182949162 0.962459049 2.046937294 0.354023171 0.187886352 11.29143232 0.498452395 0.54360539 2.940052201 10309.69658 -4.013245884 1.084478246 S(ph)PGAFDMSGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGAFDMSGVR 11 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 S(1)PGAFDMSGVR;S(1)PGAFDMSGVR 145.14 3.82E-05 305620000 213790 233400 157709 228220 170493 170213 186975 178124 141691 TRUE FALSE 203684.5704 257183.7254 164940.1136 205278.892 200226.9252 164318.4811 158448.5297 162526.5183 163663.7166 1.244531009 1.571415648 1.0077989 1.254272457 1.223404487 1.00400067 0.96813474 0.993051616 1 17.32037499 2.83018225 0.710146792 0.960659472 1.389616403 0.485555073 0.136037918 0.507673298 0.560888478 0.091560367 0.100724486 676.3667502 -2.83018225 0.428956931 S(ph)PGAPGPLTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;S(1)PGAPGPLTLK;S(1)PGAPGPLTLK;S(1)PGAPGPLTLK 179.98 7.20E-06 10280680000 12195500 9555180 10335020 12182450 8983030 10957580 12577110 10955900 8790570 TRUE FALSE 11619042.88 10528863.71 10808890.89 10957846.98 10549667.59 10578116.26 10658240.88 9996543.315 10153766.7 1.144308632 1.036941661 1.064520311 1.079190344 1.038990544 1.041792329 1.049683452 0.984515758 1 23.27551168 8 0.214074829 1.004443686 1.617414652 0.689852763 0.024270241 30.94568916 0.389731201 0.03894034 6.502028719 100000000 -8 0.612970966 S(ph)PGASNFSTLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 S(1)PGASNFSTLPK;S(0.816)PGAS(0.184)NFSTLPK;S(0.711)PGAS(0.289)NFSTLPK;S(1)PGASNFSTLPK 164.93 7.60E-05 988800000 1244080 1238930 1042640 1304460 854910 1131500 1208580 1150830 841400 TRUE FALSE 1185274.804 1365178.376 1090446.075 1173333.202 1004006.033 1092315.871 1024188.924 1050057.224 971880.0147 1.219569068 1.404677897 1.121996603 1.207281953 1.03305554 1.123920499 1.053822394 1.080439157 1 19.89041869 3.285459771 1.417549719 1.067360077 1.307084243 0.61625099 0.072560734 0.222798673 0.932980551 0.022835277 0.035182988 1929.566593 -3.285459771 0.239724166 S(ph)PGEPGGAAPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPGEPGGAAPER 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 S(1)PGEPGGAAPER;S(1)PGEPGGAAPER;S(1)PGEPGGAAPER;S(1)PGEPGGAAPER 133.81 0.00016432 1688300000 130583 114927 114926 127754 122825 124000 138294 103814 130644 TRUE FALSE 124410.6004 126638.192 120195.4708 114911.9252 144245.6411 119705.8489 117194.7104 94723.49581 150903.6043 0.824437567 0.839199253 0.79650497 0.76149225 0.955879363 0.79326037 0.77661969 0.627708637 1 17.20326774 2.017703382 24.9939556 0.778702003 0.833589574 0.01452993 0.101881984 680.6992389 961019.9469 0.034144302 0.025212032 104.1605782 -2.017703382 0.054887571 S(ph)PGETSKPRPFAGGGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(0.993)PGET(0.003)S(0.004)KPRPFAGGGYR;S(0.997)PGET(0.001)S(0.001)KPRPFAGGGYR;S(0.995)PGET(0.004)S(0.001)KPRPFAGGGYR 90.968 0.0028916 1349560000 977830 1035020 885480 1111630 686370 924820 991450 1078670 753920 TRUE FALSE 931609.9138 1140489.715 926080.1339 999886.8404 806072.7107 892793.2515 840186.0933 984215.9364 870834.0631 1.069790392 1.309652163 1.063440411 1.148194453 0.925632959 1.025216272 0.964806189 1.130199171 1 19.73203831 3.094709657 1.94498962 1.006982621 1.180293682 0.350579696 0.087466234 0.288745121 2.231696503 0.026724139 0.033508814 1243.682883 -3.094709657 0.17331106 S(ph)PGEYINIDFGEPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGEYINIDFGEPGAR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 S(1)PGEYINIDFGEPGAR;S(0.998)PGEY(0.002)INIDFGEPGAR 116.06 0.00047947 48508000 27816 23796 23021 28306 21936.9 24279 24969 23595 25023 TRUE FALSE 26501.19281 26220.83945 24076.53562 25460.6271 25762.68841 23438.21214 21159.52046 21528.89672 28903.43904 0.916887183 0.907187529 0.832998993 0.880885734 0.891336439 0.810914304 0.732076222 0.744855887 1 14.81895354 2.181042694 4.682878679 0.790645646 0.889168381 0.091317249 0.077301388 0.259793312 11.59607654 0.026863086 0.019828649 151.7199512 -2.181042694 0.098522734 S(ph)PGGGSEANGLALVSGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFK;S(0.997)PGGGS(0.003)EANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK 361.67 3.89E-91 2697766000 1792202 1596596 1633704 1939105 1340965 1642045 1931603 1854690 1470622 TRUE FALSE 1707488.163 1759290.948 1708610.944 1744182.481 1574828.871 1585180.57 1636901.486 1692283.511 1698678.549 1.005186157 1.035682089 1.005847131 1.026787842 0.927090574 0.933184546 0.963632282 0.996235287 1 20.69598144 2.75382176 24.96550951 0.959404755 1.019098635 0.541860831 0.024624593 531.3505243 869229.059 0.007213929 0.007625073 567.3117254 -2.75382176 0.05969388 S(ph)PGGGSEANGLALVSGFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPGGGSEANGLALVSGFKR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR 192.44 4.57E-15 965350000 728900 495340 708800 659490 581890 719010 897420 787700 757320 TRUE FALSE 694446.3415 545815.7092 741299.1811 593196.8123 683371.4318 694110.5034 760502.0968 718724.8121 874761.3177 0.793869513 0.623959585 0.847430226 0.678124193 0.78120902 0.793485594 0.869382403 0.821623908 1 19.7385299 1.128064859 0.462175909 1.005354552 0.71505247 0.600711194 0.064509174 0.615989475 0.355572269 0.071291402 0.038516564 13.42965509 -1.128064859 -0.290302082 S(ph)PGGPGSHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR 166.45 3.57E-06 2182390000 930040 819724 779483 963333 880452 881753 909504 872599 720997 TRUE FALSE 886078.8524 903254.8075 815223.0666 866496.9366 1034002.55 851217.6725 770742.4606 796189.6056 832805.5324 1.063968499 1.084592708 0.978887669 1.040455308 1.241589434 1.022108571 0.925477114 0.956033041 1 19.66762013 1.997785794 24.99726375 0.957615492 1.078884869 0.403356406 0.06752444 82.8595571 935447.207 0.025108349 0.018241052 99.49145774 -1.997785794 0.121269377 S(ph)PGHMVILDQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 201.76 1.52E-07 2475180000 4739200 4746600 3600810 4846060 3241090 4385190 4578930 4599970 2627390 TRUE FALSE 4515187.408 5230283.936 3765910.7 4358924.842 3806335.07 4233329.771 3880330.131 4197172.241 3034832.222 1.487788147 1.723417821 1.240895847 1.436298458 1.25421598 1.394913939 1.278597908 1.382999762 1 21.53318533 7.829369198 0.041151011 1.38E-11 3.662351584 0.553551668 0.12547579 450.5681523 1.451260416 35.32220509 115.0049864 67510169.36 -7.829369198 3.662351584 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(0.995)PGKAEAES(0.005)DALPDDTVIESEALPSDIAAEAR;S(1)PGKAEAESDALPDDTVIESEALPSDIAAEAR 258.17 1.86E-59 308060000 241101 262993 241569 270581 152537 270778 263644 271183 155539 TRUE FALSE 229704.6335 289792.2857 252645.1776 243381.6838 179139.4045 261400.89 223420.2656 247436.7789 179659.1937 1.278557633 1.613011167 1.406246863 1.354685384 0.997106804 1.454981983 1.243578249 1.377256425 1 17.45490324 -4.437381344 0.117202665 3.80E-18 1.543048617 0.322202966 0.157062684 148.4368799 1.294928053 36.45727001 1.603068585 3.65E-05 4.437381344 1.543048617 S(ph)PGLLDTTPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPGLLDTTPIR 11 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 S(1)PGLLDTTPIR;S(1)PGLLDTTPIR;S(1)PGLLDTTPIR;S(1)PGLLDTTPIR 151.55 3.50E-05 155451000 136719 155808 130454 161061 117192 134825 134703 135748 132188 TRUE FALSE 130256.5638 171685.0123 136435.4449 144870.8423 137630.2477 130155.9764 114151.5834 123861.1855 152687.0399 0.853095088 1.124424263 0.893562708 0.94880903 0.901387883 0.852436307 0.747618026 0.811209553 1 17.22021809 2.558688902 1.59581607 0.821869245 0.974991946 0.171226297 0.095113539 0.429328961 2.206724444 0.039829255 0.033072752 361.9836058 -2.558688902 0.153122701 S(ph)PGLVPPS(ph)PEFAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 157.91 7.56E-06 287856000 658930 823310 636420 775570 568100 653320 610370 680990 525080 TRUE FALSE 627783.6848 907206.225 665600.4865 697608.2301 667176.4601 630695.3646 517246.8463 621358.9054 606506.7247 1.035081161 1.495789227 1.097432987 1.150206917 1.100031431 1.039881899 0.852829532 1.024488073 1 19.21016412 2.616416931 1.137666807 0.94513856 1.247295181 0.388056661 0.128431966 0.405739738 1.078035426 0.06700879 0.054915913 413.4442259 -2.616416931 0.302156621 S(ph)PGMLEPLGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 201.09 1.60E-07 3188052000 1624123 1566024 1377119 1673571 1412319 1446260 1662038 1573361 1401763 TRUE FALSE 1547353.924 1725603.626 1440261.268 1505340.464 1658626.986 1396175.654 1408463.578 1435589.17 1619141.247 0.955663335 1.065752373 0.889521696 0.929715345 1.024386841 0.86229392 0.869883082 0.886636155 1 20.62679741 3.183544509 0.868805412 0.901741101 1.004811195 0.106859107 0.065455358 0.835331475 1.389724561 0.031749131 0.050102278 1525.964776 -3.183544509 0.103070094 S(ph)PGNLTEREELAGSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SPGNLTEREELAGSLAR 17 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTEREELAGSLAR;S(0.99)PGNLT(0.01)EREELAGSLAR;S(1)PGNLTEREELAGSLAR;S(0.998)PGNLT(0.002)EREELAGSLAR;S(1)PGNLTEREELAGSLAR 233.01 2.57E-20 1347190000 101016 78136.7 85954 89777 99305 82398 101088 84307 108554 TRUE FALSE 96241.17387 86098.91856 89895.07592 80752.44539 116623.7606 79544.5366 85665.16899 76924.63214 125387.9999 0.767546926 0.686659957 0.716935241 0.644020524 0.930103045 0.634387156 0.683200697 0.613492776 1 16.93603976 -1.576178718 6.059932535 1.000782448 0.710409833 0.50857477 0.089725899 0.000867373 6.07E-05 0.079445078 0.018677159 0.026535134 1.576178718 -0.290372615 S(ph)PGNTSQPPAFFSK ddPTM_SK-BR-3_Trastuzumab_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 314.17 8.40E-56 1756696000 2250110 2590260 2013880 2582530 1616060 2312920 2331630 2457710 1793950 TRUE FALSE 2143751.76 2854210.439 2106218.39 2322929.178 1897900.352 2232823 1975897.02 2242499.883 2072146.604 1.034556028 1.377417232 1.016442749 1.121025498 0.915910269 1.077541037 0.953550785 1.082211017 1 20.98269465 3.686964571 24.98607994 1.020660243 1.205986713 0.359648236 0.100992238 289.9401402 140407.2724 0.024800963 0.038421519 4863.675265 -3.686964571 0.18532647 S(ph)PGPPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPGPPALK 8 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK 77.674 0.034198 458680000 1167940 1302490 953720 1408180 713600 1178950 1089710 1262090 747450 TRUE FALSE 1112733.791 1435215.212 997449.0054 1266627.071 838051.6141 1138122.666 923454.7256 1151574.709 863360.7286 1.288839941 1.662358692 1.155309678 1.46708905 0.970685354 1.318246972 1.069604738 1.333827994 1 19.71960395 3.164925428 1.459365429 1.157066422 1.454269424 0.270258246 0.182852296 0.425022794 1.887532983 0.057809211 0.079322191 1461.926129 -3.164925428 0.297203002 S(ph)PGPPALKHPATK ddPTM_SK-BR-3_Trastuzumab_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 146.88 2.53E-05 963510000 1614910 1175870 1533930 1474020 1157724 1560090 1935070 1751390 1424250 TRUE FALSE 1538576.405 1295692.49 1604262.208 1325848.709 1359630.699 1506063.692 1639839.532 1598029.007 1645115.416 0.935239187 0.78759975 0.975166965 0.805930512 0.826465235 0.915476007 0.996793 0.971378051 1 20.64975737 1.927749175 3.591773062 0.98688648 0.86397793 0.495291494 0.05655737 0.191948182 4.486016269 0.02566883 0.014549478 84.67382422 -1.927749175 -0.12290855 S(ph)PGSGSQSSGWHEVEPGMPSPTTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.988)PGS(0.012)GSQSSGWHEVEPGMPSPTTLK;S(0.999)PGS(0.001)GSQSSGWHEVEPGMPSPTTLK;S(0.989)PGS(0.01)GSQSSGWHEVEPGMPSPTTLK;S(0.957)PGS(0.042)GSQSSGWHEVEPGMPSPTTLK;S(0.858)PGS(0.063)GS(0.051)QS(0.014)S(0.014)GWHEVEPGMPSPTTLK;S(0.549)PGS(0.113)GS(0.113)QS(0.113)S(0.113)GWHEVEPGMPSPTTLK;S(0.973)PGS(0.024)GS(0.002)QS(0.001)SGWHEVEPGMPSPTTLK;S(0.823)PGS(0.038)GS(0.038)QS(0.05)S(0.05)GWHEVEPGMPSPTTLK 271.47 3.99E-53 2548991000 2076630 1670403 1881352 2304612 1959475 1967957 2760009 2330240 2028145 TRUE FALSE 1978471.815 1840618.965 1967613.85 2072948.023 2301206.82 1899806.156 2338918.936 2126191.832 2342659.368 0.84454097 0.785696371 0.839906081 0.884869585 0.982305345 0.810961329 0.998403339 0.90759752 1 21.15971577 2.621655799 0.425216549 0.987808005 0.790923642 0.473818865 0.056287747 0.976029918 0.368153787 0.05215102 0.073380319 418.4617813 -2.621655799 -0.196884362 S(ph)PGSGSQSSGWHEVEPGMPSPTTLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.74)PGS(0.141)GS(0.04)QS(0.04)S(0.04)GWHEVEPGMPSPTTLKK;S(0.998)PGS(0.002)GS(0.001)QSSGWHEVEPGMPSPTTLKK;S(0.987)PGS(0.012)GS(0.001)QSSGWHEVEPGMPSPTTLKK;S(0.904)PGS(0.017)GS(0.02)QS(0.029)S(0.029)GWHEVEPGMPSPTTLKK;S(0.998)PGS(0.001)GSQSSGWHEVEPGMPSPTTLKK 203.25 2.00E-25 1489260000 2098130 1471070 2011120 2040530 1671520 1965510 2712490 2372610 1869330 TRUE FALSE 1998955.553 1620973.705 2103331.841 1835412.048 1963032.559 1897443.896 2298649.832 2164851.69 2159216.149 0.925778345 0.750723222 0.974118243 0.850036273 0.909141292 0.878765147 1.064576065 1.002609994 1 21.04207624 1.765964188 9.87785786 1.024628604 0.873119689 0.547289714 0.060104748 0.145451246 46.69832823 0.026847479 0.014811778 58.33969955 -1.765964188 -0.151508915 S(ph)PGSISYLPSFFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGSISYLPSFFTK 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(1)PGSISYLPSFFTK;S(0.965)PGS(0.035)ISYLPSFFTK 238.03 2.72E-17 1044680000 885970 802880 797340 937670 726820 899190 981250 927610 868190 TRUE FALSE 844091.9539 884694.3848 833898.8277 843413.6301 853577.1779 868050.8248 831542.2906 846383.5508 1002824.471 0.841714555 0.882202629 0.831550138 0.841038142 0.851173064 0.865605946 0.829200238 0.843999698 1 19.93563768 -2.163384806 2.434355247 1.375907294 0.849573919 0.901638903 0.015740467 3270661.577 592478.7425 6813256.696 0.00404183 0.006864599 2.163384806 -0.526333375 S(ph)PGSNSKVPEIEVTVEGPNNNNPQTSAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.984)PGS(0.016)NSKVPEIEVTVEGPNNNNPQTSAVR;S(0.943)PGS(0.045)NS(0.012)KVPEIEVTVEGPNNNNPQTSAVR;S(0.367)PGS(0.316)NS(0.316)KVPEIEVTVEGPNNNNPQTSAVR;S(0.999)PGS(0.001)NSKVPEIEVTVEGPNNNNPQTSAVR;S(0.963)PGS(0.027)NS(0.009)KVPEIEVTVEGPNNNNPQTSAVR;S(1)PGSNSKVPEIEVTVEGPNNNNPQTSAVR;S(0.989)PGS(0.011)NSKVPEIEVTVEGPNNNNPQTSAVR 421.5 1.45E-196 6817490000 920696 528627 879000 779686 780417 882161 1264671 1053883 1118726 TRUE FALSE 877176.5247 582494.6923 919303.0194 701310.482 916521.4777 851611.5434 1071722.212 961599.4175 1292212.314 0.678817649 0.450773209 0.711417937 0.542720785 0.709265395 0.659033762 0.829370065 0.744149709 1 20.3014117 1.299097016 0.478840815 1.002664505 0.565800952 0.68154388 0.083661291 0.455644423 0.282253612 0.084660165 0.048815684 19.91118082 -1.299097016 -0.436863553 S(ph)PGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 1 S(0.999)PGVVIS(0.001)DDEPGYDLDLFCIPNHYAEDLER;S(0.988)PGVVIS(0.012)DDEPGYDLDLFCIPNHYAEDLER 109.41 0.00015761 8952300 12875.3 9853.2 10387.9 11288.4 11974.2 12220.2 15224.2 9412.2 14859.3 TRUE FALSE 12266.71009 10857.25228 10864.19549 10153.66859 14062.49669 11797.01141 12901.46868 8588.017871 17163.60435 0.714693128 0.632574141 0.632978672 0.59158137 0.819320721 0.687327159 0.751675954 0.500362144 1 14.06706493 -1.965846946 2.610563512 1.26524853 0.674241942 0.586738396 0.087785864 5258469.528 2906524.912 8441614.033 0.019923034 0.010818151 1.965846946 -0.591006587 S(ph)PGYEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPGYEPR 7 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(1)PGYEPR;S(1)PGYEPR;S(1)PGYEPR;S(1)PGYEPR;S(1)PGYEPR;S(1)PGYEPR 114.89 0.0060865 1677630000 2108120 2042980 2055590 2306780 2064830 2053500 2281560 2134120 2093690 TRUE FALSE 2008473.345 2251161.985 2149840.835 2074898.092 2424935.698 1982386.78 1933466.118 1947245.139 2418368.752 0.830507483 0.930859689 0.888963204 0.85797424 1.002715445 0.81972064 0.799491854 0.805189505 1 21.20560281 S(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPHEAGFCVYLK 12 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK 134.37 9.44E-05 723740000 467560 551240 418490 513200 377380 509160 503380 530220 352090 TRUE FALSE 445459.3654 607411.9827 437678.1804 461612.161 443194.9525 491527.6615 426580.1358 483791.1259 406690.319 1.095328176 1.493549156 1.076195228 1.135045855 1.089760272 1.208604283 1.048906541 1.189581122 1 18.63357112 3.688257678 24.99873199 1.111702218 1.294439339 0.324752074 0.11227594 343.2727489 170593.9264 0.027445748 0.042518812 4878.178388 -3.688257678 0.182737121 S(ph)PHKDLGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR 109.6 0.0014632 1356653000 1055532 1037569 872800 1102252 831796 1001502 1057602 1006877 316388 TRUE FALSE 1005639.094 1143298.461 912818.7433 991451.5348 976860.959 966819.7346 896245.3907 918709.5121 365451.8352 2.751769173 3.128451825 2.497781255 2.712947205 2.673022448 2.645546257 2.452430948 2.513900393 1 18.47932175 -1.142625904 0.306245272 4.51E-19 2.901182696 0.922759227 0.15517131 3.910310798 0.281687568 3.488892997 0.157994565 0.072006897 1.142625904 2.901182696 S(ph)PHQLLSPSSFSPSATPSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 S(1)PHQLLSPSSFSPSATPSQK 167.45 8.83E-12 90011000 262830 252830 231160 294270 207340 253380 296280 306640 212640 TRUE FALSE 250406.5468 278593.6644 241758.9146 264689.4205 243500.0304 244605.3871 251077.0444 279788.976 245615.1252 1.019507844 1.134269171 0.984299784 1.077659286 0.991388581 0.995888942 1.022237715 1.139135775 1 17.90603988 5.16432443 9.812238073 1.044413724 0.000304871 0.016117904 0.057150772 884826.0966 815158.4783 0.012738525 20061323.04 145990.4443 -5.16432443 -1.044108852 S(ph)PHSPSPIATPPSQSSSCSDAPMLSTVHSAK ddPTM_SK-BR-3_Trastuzumab_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(0.351)PHS(0.322)PS(0.322)PIAT(0.004)PPSQSSSCSDAPMLSTVHSAK 79.017 0.0034305 72075000 43000 34544 37704 39464 38093 34229 50267 49549 35736 TRUE FALSE 40967.47522 38064.07287 39432.76569 35497.00374 44736.40714 33043.64115 42597.84593 45210.22688 41277.75637 0.992483091 0.922144909 0.955303029 0.859954776 1.083789699 0.800519312 1.031980652 1.095268514 1 15.33307694 1.559342429 9.606193329 1.052007108 0.940323808 0.294671939 0.077789041 0.127662437 19.10159093 0.036299351 0.016930095 36.25287292 -1.559342429 -0.1116833 S(ph)PILEEK ddPTM_SK-BR-3_Trastuzumab_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 91.867 0.016877 2054090000 1791950 2018130 1545230 2102680 1066310 1989260 1779800 2015300 1077470 TRUE FALSE 1707248.075 2223779.741 1616080.324 1891314.612 1252274.126 1920371.427 1508258.822 1838829.648 1244558.545 1.37177 1.786802036 1.298516917 1.51966705 1.006199453 1.543014136 1.211882581 1.477495499 1 20.24720267 -2.443379558 0.07508773 2.22E-08 1.977891292 0.277290746 0.207370732 164.478075 1.536929354 38.12405888 9.819246601 0.003602636 2.443379558 1.97789127 S(ph)PILEEKDIPPLEFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPILEEKDIPPLEFPK 16 1 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK 126.26 4.40E-05 564310000 1023060 712918 924290 977513 608841 1031984 1230387 1237800 717293 TRUE FALSE 974701.9813 785565.1547 966669.6107 879251.5361 715022.6776 996246.1353 1042668.866 1129411.67 828527.135 1.176427349 0.948146562 1.166732591 1.061222378 0.863004538 1.202430305 1.258460733 1.363155921 1 19.66018942 2.027403347 24.94654491 1.234554004 1.047386783 0.278113334 0.127826841 221.3285543 201484.6896 0.043740925 0.032304143 106.513179 -2.027403347 -0.187167221 S(ph)PIRQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR 103.87 0.0050134 5851494000 1413074 1468807 1084980 1461106 996303 1254766 1181802 1303745 1092335 TRUE FALSE 1346280.792 1618480.103 1134727.406 1314232.849 1170057.928 1211313.139 1001496.4 1189582.176 1261728.733 1.067012867 1.282748075 0.899343398 1.04161284 0.927345076 0.960042446 0.79374938 0.942819281 1 20.26697034 3.726828212 24.96933443 0.926466618 1.174880472 0.583726423 0.082786015 415.7345716 884781.6373 0.021968504 0.034346365 5331.239727 -3.726828212 0.248413853 S(ph)PITSSPPKWMAEIERDDIDMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPITSSPPKWMAEIERDDIDMLK 23 2 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 S(0.27)PIT(0.254)S(0.238)S(0.238)PPKWMAEIERDDIDMLK 46.678 0.083775 22761000 51665 39742 48584 56056 28731 54895 54657 66711 29503 TRUE FALSE 49222.89784 43791.75498 50811.62446 50421.14438 33741.6773 52993.97239 46318.07081 60869.43118 34078.17456 1.444411224 1.285038167 1.491031287 1.479572924 0.990125725 1.555070747 1.359171124 1.786170532 1 15.05656044 S(ph)PLAQMEEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEERR;S(1)PLAQMEEERR 97.268 0.0039158 401360000 108923 102837 96479 100247 119247 99436 122892 123992 121098 TRUE FALSE 103774.4257 113316.2072 100902.6576 90169.9811 140043.639 95992.50639 104142.5683 113134.6032 139877.2594 0.741896332 0.81011172 0.721365703 0.644636459 1.001189469 0.686262419 0.74452823 0.80881341 1 17.09380191 0.857877868 4.481055028 0.999985715 0.765287701 0.374824483 0.095093407 1.142620506 34.82145269 0.082603262 0.020978347 7.209047181 -0.857877868 -0.234698013 S(ph)PLPAGPSSCTSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPLPAGPSSCTSPR 14 0 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 S(1)PLPAGPSSCTSPR 105.58 0.0010399 57953000 44619 30533 31012 32177 34846 34115 42654 42330 38011 TRUE FALSE 42509.9483 33644.34741 32433.93088 28942.50683 40923.13137 32933.589 36146.34891 38623.36079 43905.55175 0.968213508 0.766289138 0.738720494 0.659199251 0.932071908 0.750100789 0.823275132 0.879691958 1 15.42211576 0.923989005 2.184743305 0.999509492 0.806578214 0.326641383 0.090153392 0.476397703 4.876333734 0.083977323 0.023065297 8.394387349 -0.923989005 -0.192931278 S(ph)PLPAGPSSCTSPRS(ph)PLPAPPRPFLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPLPAGPSSCTSPRSPLPAPPRPFLYR 27 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 2 S(1)PLPAGPS(0.191)S(0.174)CT(0.144)S(0.132)PRS(0.36)PLPAPPRPFLYR 59.017 0.031354 53639000 19906 14717 15559 17791 17880 11906 16366 20261 24443 TRUE FALSE 18965.08283 16216.67903 16272.39554 16002.61488 20998.26634 11493.69223 13869.06612 18486.83943 28233.4956 0.671722804 0.574377302 0.576350721 0.56679538 0.743735974 0.407094197 0.491227382 0.654783938 1 14.78512014 0.96625261 18.80619228 1.000000003 0.574731127 0.683604462 0.090130007 91.41928563 50945.49738 0.087367036 0.021841749 9.252361871 -0.96625261 -0.425268876 S(ph)PLPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPLPTKR 7 1 D6R9T3;Q96FZ2;E7EMP6 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 1 S(0.999)PLPT(0.001)KR;S(1)PLPTKR;S(1)PLPTKR 72.547 0.031427 452780000 306452 279489 286841 358439 261336 350650 340952 383877 315056 TRUE FALSE 291966.6213 307969.2469 299992.9436 322408.0307 306912.9157 338506.9026 288933.5104 350262.6948 363913.2754 0.802297253 0.846270987 0.824352844 0.885947429 0.843368287 0.930185639 0.793962545 0.962489468 1 18.47323516 -5 0.112661112 1.499402582 0.768027524 0.570411307 0.045128604 112.9608377 0.84064853 12.8199897 0.474577393 1.00E-05 5 -0.731375058 S(ph)PLS(ph)PTETFSWPDVR ddPTM_SK-BR-3_Trastuzumab_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(0.885)PT(0.083)ET(0.029)FS(0.003)WPDVR;S(1)PLS(0.983)PT(0.009)ET(0.006)FS(0.001)WPDVR 106.52 0.0017974 40492000 67060 55583 65528 73097 59784 58674 62024 58686 50218 TRUE FALSE 63890.2067 61246.97089 68532.52362 65749.15068 70210.31067 56642.10467 52561.09965 53547.14273 58005.55096 1.101449872 1.055881202 1.18148216 1.133497563 1.210406754 0.976494555 0.906139133 0.923138249 1 15.82390335 2.095303208 6.093275785 0.934804852 1.123713237 0.779670598 0.048780635 0.09779846 5.201143554 0.019099077 0.014004055 124.5383788 -2.095303208 0.188908385 S(ph)PLSGIPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPLSGIPVR 9 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 S(0.995)PLS(0.005)GIPVR;S(1)PLSGIPVR;S(0.998)PLS(0.002)GIPVR;S(0.997)PLS(0.003)GIPVR 106.4 0.003086 187167000 208385 186555 191275 221755 213385 180390 221326 212466 224421 TRUE FALSE 198535.054 205565.1666 200045.1479 199463.7661 250599.2764 174143.0491 187558.6538 193861.3507 259223.0625 0.765884995 0.79300493 0.771710457 0.769467671 0.96673218 0.67178841 0.72354154 0.747855337 1 17.98383455 -2.349546816 2.283072479 2.419429886 0.774033002 0.464427019 0.075479321 4981903.871 661289.8722 36487278.79 0.017619438 0.004471499 2.349546816 -1.645396884 S(ph)PLSPTETFSWPDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 S(0.999)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR 206.2 4.21E-09 134831000 55861.4 47794 50244.9 55550.2 48423.2 56303.4 53294.9 55638.1 55520.9 TRUE FALSE 53220.94233 52664.26294 52548.67836 49966.18836 56868.19075 54353.59914 45163.78418 50766.13301 64130.79761 0.829881185 0.82120081 0.819398484 0.779129377 0.886753212 0.847542853 0.704244854 0.791603019 1 15.96872973 S(ph)PLTGYVR ddPTM_SK-BR-3_Trastuzumab_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 127780000 55048 49489 55099 51496 67933 49407 58767 53438 72557 TRUE FALSE 52445.99013 54531.98536 57625.34365 46319.52424 79780.49369 47696.0232 49801.01482 48758.68543 83808.76899 0.625781655 0.650671595 0.687581316 0.552681119 0.951934919 0.569105402 0.594222006 0.581785009 1 16.35481358 -1.113809782 3.786151516 1.000151603 0.649341045 0.479555913 0.114000493 31181428.88 53787609.91 58959.56413 0.025309169 0.076946739 1.113809782 -0.350810558 S(ph)PLTILQDDNS(ph)PGTLTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPLTILQDDNSPGTLTLR 18 0 Q99618;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 2 S(0.998)PLT(0.002)ILQDDNS(0.983)PGT(0.016)LT(0.001)LR 125.53 4.32E-05 15630000 23258 24593 23029 28928 22004 23889 25530 26617 23635 TRUE FALSE 22158.64043 27099.05466 24084.90243 26020.10248 25841.49063 23061.71794 21634.92961 24286.27437 27300.19509 0.81166601 0.992632271 0.882224554 0.953110496 0.946567984 0.844745536 0.792482601 0.889600763 1 14.73662364 2.228506772 24.85140144 0.856004701 0.917962175 0.0034636 0.071670965 357.5222953 883727.4983 0.024911173 0.018616984 169.2414634 -2.228506772 0.061957474 S(ph)PNELVDDLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 205.3 3.18E-08 228163000 568786 466336 400883 567410 289844 494727 563622 567614 306078 TRUE FALSE 541900.613 513856.1686 419263.8821 510372.8688 340392.7018 477594.4799 477631.1123 517910.709 353543.013 1.532771383 1.453447387 1.185892145 1.443594839 0.962804211 1.350880833 1.350984448 1.464915696 1 18.43152622 3.887557783 4.810952948 1.273037225 1.504522178 0.257966569 0.169198837 0.278541151 9.8927953 0.04025616 0.075157664 7718.942094 -3.887557783 0.231484953 S(ph)PNSHDSEPWTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPNSHDSEPWTLLR 14 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)PNSHDSEPWTLLR;S(0.996)PNS(0.004)HDSEPWTLLR;S(0.998)PNS(0.002)HDSEPWTLLR 149.47 4.82E-06 104195000 74849 73058 67171 85407 82134 68484 79840 75908 71627 TRUE FALSE 71311.03611 80502.69326 70250.85679 76821.7261 96458.1436 66112.38191 67658.94164 69261.09311 82734.54934 0.861925721 0.973023893 0.849111494 0.928532599 1.165875011 0.799090373 0.817783407 0.83714837 1 16.33620229 -0.77507925 5.185369271 1.000000023 0.903528025 0.074480352 0.106269248 5.21E-08 1.22E-08 0.101297499 0.023876039 0.16784977 0.77507925 -0.096471997 S(ph)PPADAIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK 104.79 0.003359 2804730000 4031900 3052525 3143050 4003930 2591013 3802320 4394810 4277910 3168560 TRUE FALSE 3841320.077 3363580.768 3287161.951 3601447.349 3042884.847 3670644.705 3724301.018 3903313.522 3659924.102 1.04956277 0.919030197 0.898150306 0.984022414 0.831406543 1.002929187 1.017589686 1.066501221 1 21.8033823 2.01746862 24.99309712 1.02505343 0.942468381 0.350653326 0.058162052 283.8321765 406089.2061 0.021464711 0.015849229 104.1042884 -2.01746862 -0.08258505 S(ph)PPAPGLQPMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR 97.163 0.0067886 3276180000 894051 794714 777381 902282 820352 746102 900809 798919 627695 TRUE FALSE 851790.9811 875696.2601 813024.6878 811582.8991 963421.1291 720264.3007 763374.0426 728961.417 725034.7348 1.174827826 1.207799045 1.121359638 1.119371059 1.328793067 0.993420406 1.05287927 1.005415854 1 19.46769059 2.207752385 24.99848465 1.020289543 1.185010776 0.684703841 0.059696811 116.8093141 94780.98097 0.020775866 0.015345679 161.3438385 -2.207752385 0.164721233 S(ph)PPAS(ph)PESWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 S(1)PPAS(1)PESWK 99.531 0.0067716 78495000 170350 213490 137270 208300 101390 182180 160590 166960 90671 TRUE FALSE 162297.8931 235244.8737 143563.9653 187361.2883 119072.3839 175871.0609 136089.0461 152340.0973 104731.7956 1.54965254 2.24616481 1.370777274 1.788962819 1.136926787 1.679251844 1.29940526 1.454573527 1 16.67633997 2.167018986 0.279267586 0.975190375 2.003413999 0.369582317 0.279542962 1.849602539 0.425138672 0.458712344 0.691155038 146.8990497 -2.167018986 1.028223624 S(ph)PPEGDTTLFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR 145.49 4.39E-05 154909000 48616 46940 45549 46006 56225.5 42798 44601 54954 58324 TRUE FALSE 46318.01803 51723.23937 47637.4667 41381.38947 66031.2094 41315.89453 37796.2983 50141.93643 67368.58804 0.687531376 0.767764931 0.707116894 0.614253477 0.980148335 0.613281289 0.561037412 0.744292524 1 16.03978844 0.96661367 23.15684262 1.000000004 0.701178985 0.394109679 0.114212673 1923.204721 1333941.891 0.107428395 0.026857099 9.260057221 -0.96661367 -0.298821019 S(ph)PPGGPDKDFAWLS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPGGPDKDFAWLS 14 1 Q86UZ6 Q86UZ6 ZBTB46 Zinc finger and BTB domain-containing protein 46 1 S(1)PPGGPDKDFAWLS 90.707 0.014851 65389000 132370 145850 113940 144930 87860 131450 133250 137340 92248 TRUE FALSE 126113.1324 160712.2808 119164.2617 130361.3611 103182.7562 126897.8535 112920.2652 125313.7815 106553.3487 1.183567987 1.508279963 1.118353042 1.223437486 0.96836709 1.190932571 1.059753321 1.176066102 1 16.70121641 3.646440633 9.011017018 1.108617466 1.345641266 0.44756827 0.111126495 0.274150586 24.84873339 0.026887016 0.041692318 4430.37648 -3.646440633 0.2370238 S(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(0.996)GAS(0.004)T(0.001)PVGPWDQAVQR 93.812 0.0021303 28616000 50687 44013 44389 44167 36995 45705 40401 46630 35428 TRUE FALSE 48291.12596 48497.97474 46424.27956 39727.24925 43446.91629 44122.22439 34237.08543 42546.83 40921.9933 1.180077559 1.185132268 1.134457924 0.970804353 1.06170088 1.078203206 0.836642663 1.039705708 1 15.3205888 3.255638767 0.895541296 0.965990684 1.2023085 0.53665 0.070847784 0.394379788 0.688599477 0.032877229 0.05638898 1801.518671 -3.255638767 0.236317815 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.903)PPGS(0.096)GAS(0.001)T(0.001)PVGPWDQAVQR;S(0.999)PPGS(0.001)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.999)PPGS(0.001)GASTPVGPWDQAVQR;S(0.99)PPGS(0.01)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.995)PPGS(0.005)GASTPVGPWDQAVQR;S(0.99)PPGS(0.01)GASTPVGPWDQAVQR 321.6 9.40E-67 2637480000 237789 239897 218449 269588 212454.6 203115 247541 249237 245704 TRUE FALSE 226549.1852 264342.777 228465.1027 242488.5021 249506.615 196081.0766 209774.074 227412.487 283806.5214 0.798252218 0.931418967 0.805003005 0.854414835 0.879143346 0.690897008 0.739144657 0.801294085 1 18.11454822 2.278188501 24.9999792 0.777665214 0.857039863 0.013383314 0.08894143 263.6959283 166356.4284 0.027791849 0.023252011 189.7529347 -2.278188501 0.079374649 S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPKVPIVIQDDSLPAGPPPQIR 23 1 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(1)PPKVPIVIQDDSLPAGPPPQIR 189.34 1.12E-17 64014000 80637 87674 68505 85385 43433 79906 71517 82433 44046 TRUE FALSE 76825.44882 96608.08028 71646.02201 76801.93758 51007.70145 77138.83518 60605.76815 75214.72952 50876.42872 1.510040126 1.898876999 1.408236069 1.509578001 1.002580227 1.516199881 1.191234717 1.478380684 1 15.63470978 3.331576739 2.021224337 1.274268342 1.696111501 0.402427522 0.208292988 0.26757621 2.235536695 0.057147082 0.084085738 2145.73823 -3.331576739 0.421843159 S(ph)PPLMAK ddPTM_SK-BR-3_Trastuzumab_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 69.812 0.061601 281670000 634950 746600 506770 698180 423260 585830 574050 636510 424800 TRUE FALSE 604937.1718 822679.3888 530005.9058 627997.6199 497076.41 565542.5602 486468.1293 580773.81 490675.8144 1.232865273 1.676625105 1.080154942 1.279862593 1.013044449 1.152578838 0.991424715 1.183620209 1 18.90441064 3.715933226 24.82261018 1.100092061 1.45474519 0.534616938 0.137563105 443.1822834 486178.06 0.034100208 0.052869032 5199.160524 -3.715933226 0.354653129 S(ph)PPLPAVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 112.01 0.0021318 2630830000 139269 113737 94246 130185 106287 111194 127795 106113 96632 TRUE FALSE 132686.0304 125326.9296 98567.27232 117098.5565 124823.4191 107343.3239 108297.5256 96821.18318 111617.197 1.188759742 1.122828139 0.883083207 1.049108557 1.118317092 0.961709546 0.970258424 0.867439658 1 16.7681998 6.42502059 0.37314519 0.955290367 2.060117904 0.433343651 0.078479578 17.2030081 0.699669879 0.06109144 11.03799597 2660851.21 -6.42502059 1.104827537 S(ph)PPPETIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPPETIK 8 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(1)PPPETIK 63.565 0.076057 124210000 392450 382250 314900 438590 220500 401060 371700 425060 246380 TRUE FALSE 373899.6663 421201.7096 329338.4765 394502.0999 258955.1302 387171.1916 314990.3383 387839.493 284587.3521 1.313830933 1.480043672 1.157249168 1.386224992 0.909931971 1.36046521 1.106831825 1.362813527 1 18.11851202 3.729961785 24.86115897 1.190557088 1.396937303 0.231901547 0.161183859 686.010244 1983411.01 0.037335535 0.058837612 5369.845436 -3.729961785 0.206380215 S(ph)PPRASYVAPLTAQPATYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPPRASYVAPLTAQPATYR 19 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 S(0.974)PPRAS(0.026)YVAPLTAQPATYR;S(0.999)PPRAS(0.001)YVAPLTAQPATYR;S(0.974)PPRAS(0.026)YVAPLTAQPATYR 139.79 1.10E-07 2295890000 118914 50864 143384 79395 198210 128606 185030 127785 263940 TRUE FALSE 113293.1709 56047.09943 149958.2982 71414.06376 232777.7612 124152.342 156800.2752 116595.468 304870.4672 0.371610842 0.183839058 0.49187545 0.234243954 0.763530044 0.407229809 0.514317692 0.382442645 1 18.21783688 -5 0.144471691 3.075360239 0.20484314 0.590738847 0.154758119 86.24709311 0.752991666 51.44881355 0.788189005 1.00E-05 5 -2.870517099 S(ph)PPREGSQGELTPANSQSR ddPTM_SK-BR-3_Trastuzumab_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(0.599)PPREGS(0.401)QGELTPANSQSR 139.36 1.12E-07 496550000 67487 40965 62854 57794 72700 50441 70777 48429 89626 TRUE FALSE 64297.02326 45139.38007 65735.91807 51984.43732 85378.85698 48694.21552 59978.66874 44188.30002 103524.7423 0.621078805 0.436025042 0.634977848 0.502145054 0.824719338 0.470363069 0.579365545 0.426838058 1 16.65961609 -1.312486801 4.976127309 1.000166918 0.559793659 0.578424678 0.11751797 0.000194553 2.69E-05 0.101725136 0.023967846 0.048698233 1.312486801 -0.440373259 S(ph)PPRPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)PPRPPR 99.139 0.0065091 6032390000 538943 403151 490879 463131 793930 431813 677055 500320 909584 TRUE FALSE 513468.2325 444232.5452 513386.2877 416576.192 932391.1406 416859.2075 573757.8248 456509.3284 1050637.641 0.488720575 0.422821844 0.48864258 0.396498446 0.887452633 0.396767821 0.546104387 0.434506923 1 20.00283375 -2.313619796 2.29215039 3.593568332 0.504540514 0.53963766 0.142876387 4420158.184 408756.5696 59875355.76 0.031603653 0.004857135 2.313619796 -3.089027818 S(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.997)PPS(0.002)T(0.001)GSTYGSSQK;S(0.965)PPS(0.03)T(0.005)GSTYGSSQK;S(0.995)PPS(0.004)TGSTYGSSQK;S(0.998)PPS(0.002)TGSTYGSSQK 151.07 7.38E-06 439384000 342835 552373 248080 490965 183386 341423 274670 332541 171902 TRUE FALSE 326629.869 608660.4367 259454.7134 441612.2654 215368.4603 329599.4359 232764.0468 303421.9471 198559.6842 1.644995913 3.065377743 1.306683753 2.224078202 1.08465352 1.659951451 1.172262374 1.528114573 1 17.5992132 3.082157421 1.268357594 1.309666751 2.280582346 0.330557718 0.505331953 0.416217869 1.411563844 0.181378007 0.235591273 1208.251718 -3.082157421 0.970915595 S(ph)PPSTGSTYGSSQKEESAASGGAAYTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPPSTGSTYGSSQKEESAASGGAAYTKR 28 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.999)PPS(0.001)TGSTYGSSQKEESAASGGAAYTKR;S(0.883)PPS(0.065)T(0.041)GS(0.009)T(0.002)YGSSQKEESAASGGAAYTKR 151.31 2.65E-08 878310000 578720 440380 546920 553010 348080 585490 641320 653240 445130 TRUE FALSE 551365.0525 485255.2227 571996.823 497420.3841 408785.0418 565214.3345 543474.8554 596038.8426 514158.487 1.072364001 0.943785302 1.11249126 0.967445635 0.79505649 1.099299824 1.057018155 1.159251199 1 18.97185361 S(ph)PPSYSVLYPSSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPSYSVLYPSSDPK 15 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 S(0.782)PPS(0.214)Y(0.001)S(0.003)VLYPSSDPK 132.65 4.84E-05 52536000 57044 53340 52242 61805 43420 50315 56883 58642 46279 TRUE FALSE 54347.64317 58775.40664 54637.34737 55592.24398 50992.43425 48572.57893 48204.45362 53506.9956 53455.71096 1.016685443 1.099515947 1.022104961 1.039968284 0.953919298 0.908650882 0.901764335 1.000959386 1 15.70605647 2.735979115 3.183020578 0.937690927 1.051448655 0.550072782 0.040017599 0.154276322 3.23950906 0.012818068 0.012784308 544.4764687 -2.735979115 0.113757728 S(ph)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 S(1)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 270.2 5.24E-64 604440000 244900 259850 245370 280180 183820 253080 262830 306550 146920 TRUE FALSE 233324.0623 286329.0104 256620.4572 252015.7741 215878.1498 244315.7761 222730.4563 279706.8569 169703.6032 1.374891622 1.68723 1.512168583 1.485034904 1.27208937 1.439661689 1.312467455 1.64820812 1 17.37265767 2.931679532 4.887210275 1.35897795 1.534543107 0.20094049 0.175830608 0.344044076 15.80085592 0.048541309 0.05253784 854.4359883 -2.931679532 0.175565156 S(ph)PPVTLGPNLAPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPPVTLGPNLAPTSR 15 0 B4DF95;Q15735;C9K0M5 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR 156.72 2.18E-06 593840000 89619 93789 73556 82745 79362 82596 93060 77702 93497 TRUE FALSE 85382.88748 103346.2057 76928.61536 74427.31539 93202.70767 79735.67981 78861.98784 70898.00096 107996.0372 0.790611301 0.956944425 0.712328131 0.689167096 0.8630197 0.738320422 0.730230385 0.65648706 1 16.72061885 3.726378785 24.90695472 0.755919299 0.873777867 0.131061382 0.106505976 992.9432241 2030170.82 0.025330834 0.039565048 5325.725581 -3.726378785 0.117858568 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.513)PPY(0.429)T(0.058)AFLGNLPYDVTEESIK 118.52 5.19E-05 24139000 40697 52692 32136 49419 20095 38511 30489 40390 18970 TRUE FALSE 38773.33346 58061.37471 33609.46739 44451.30823 23599.56164 37177.35441 25837.34308 36853.23748 21911.77071 1.769520773 2.649780132 1.533854467 2.028649752 1.077026679 1.696684166 1.179153589 1.681892256 1 14.41941845 3.12789188 1.457336117 1.35649568 2.169057977 0.415655661 0.372782317 0.319260362 1.411957253 0.120454423 0.160057402 1342.430714 -3.12789188 0.812562298 S(ph)PQALSNGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPQALSNGTK 10 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 S(1)PQALSNGTK;S(1)PQALSNGTK;S(1)PQALSNGTK;S(1)PQALSNGTK 157.43 9.63E-06 479657000 883082 853670 800490 974940 596000 878473 920140 907050 707972 TRUE FALSE 841340.464 940659.9435 837193.2583 876937.1789 699942.2113 848051.2597 779755.7435 827623.8934 817760.6819 1.028834575 1.150287565 1.023763158 1.072364077 0.855925489 1.037040883 0.953525598 1.012061244 1 19.64131917 2.941581074 24.99977103 0.972166153 1.075832435 0.401950451 0.058592765 228.6759184 97859.14084 0.016234384 0.017219194 874.1401608 -2.941581074 0.103666282 S(ph)PQESTGDPGNSSSVSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQESTGDPGNSSSVSEGK 19 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 S(0.999)PQES(0.001)TGDPGNSSSVSEGK 145.52 1.63E-07 0 50730 68391 55605 69034 30202 58217 47992 61808 32824 TRUE FALSE 48332.09344 75360.12065 58154.54425 62094.57116 35469.21924 56200.93069 40669.93897 56395.76386 37914.17828 1.274776235 1.987650111 1.533846885 1.637766503 0.935513332 1.482319629 1.072684173 1.487458424 1 15.21044983 2.76652749 23.98913756 1.213284262 1.630470606 0.404149888 0.247981149 407.2189962 349299.122 0.069184296 0.073363164 584.1541824 -2.76652749 0.417186343 S(ph)PQLSDFGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPQLSDFGLER 11 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 S(1)PQLSDFGLER;S(1)PQLSDFGLER 112.02 0.00082282 42317000 91292 98177 91630 99897 90897 93439 93999 103833 93195 TRUE FALSE 86976.80808 108181.3479 95831.32613 89855.16377 106749.408 90203.184 79657.72614 94740.83207 107647.2046 0.807980183 1.00496198 0.890235157 0.83471897 0.991659824 0.83795194 0.739988803 0.880104898 1 16.71595133 2.039005899 24.9748008 0.830598291 0.907253408 0 0.08909132 283.401768 181456.0826 0.031008862 0.022901535 109.3971226 -2.039005899 0.076655116 S(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 160.57 7.29E-12 28350000 154830 160450 127470 169380 106670 148420 144270 178360 83635 TRUE FALSE 147511.4927 176800.0374 133314.6256 152353.6006 125273.2142 143280.1782 122258.9618 162741.8529 96604.68865 1.526959973 1.830139302 1.380001607 1.57708288 1.296761223 1.48315967 1.265559296 1.684616504 1 16.55980559 -2.713604022 0.099486535 2.91E-12 1.930796034 0.4443827 0.173503137 80.89587224 0.931941779 21.56317652 3.238828978 0.001933731 2.713604022 1.930796034 S(ph)PQPPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQPPSR 7 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(1)PQPPSR 64.207 0.078459 804210000 112810 102650 106040 125720 149040 102000 114260 100150 114840 TRUE FALSE 107477.6949 113110.1517 110902.0389 113082.3867 175032.5288 98467.71442 96827.53847 91380.33507 132648.8007 0.810242492 0.852703915 0.836057607 0.852494604 1.319518367 0.74231892 0.729954119 0.688889267 1 17.01725211 -1.145265091 4.547465553 1.000019385 0.850599135 0.06432513 0.174535348 3.36E-05 6.31E-06 0.165419585 0.038984713 0.071570641 1.145265091 -0.14942025 S(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 328.31 4.90E-105 1689524000 559017 617674 474530.5 630141 378374.6 573997 510104 621736 311506.9 TRUE FALSE 532593.3743 680615.6828 496288.1928 566798.0295 444363.0104 554119.34 432278.2661 567293.4998 359813.7991 1.480191631 1.89157749 1.379291717 1.575253731 1.234980458 1.540016924 1.201394352 1.57663075 1 18.45689099 -1.043231922 0.078669007 2.59E-05 2.227855636 0.418350109 0.18819671 68.49551016 1.046590833 22.35558764 8.903951819 0.090524905 1.043231922 2.227829763 S(ph)PQQTVPYVVPLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 S(0.997)PQQT(0.003)VPYVVPLSPK 111.22 0.00090163 30368000 53479 57857 46830 56086 35273 52135 57266 58281 44311 TRUE FALSE 50951.15366 63752.69408 48977.20182 50448.12872 41424.60003 50329.55188 48529.01994 53177.60667 51182.52357 0.995479513 1.245594973 0.956912602 0.985651453 0.80935048 0.983334708 0.948156061 1.038979772 1 15.64336366 3.666491045 12.32606386 0.954075721 1.120505481 0.384599536 0.083956121 0.972935519 165.1605596 0.021058017 0.032627091 4639.712229 -3.666491045 0.16642976 S(ph)PQREPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 117.14 0.0012943 874560000 258441 251849 221656 281910 188083 279950 275455 279896 231656 TRUE FALSE 246225.0061 277512.6994 231819.1468 253571.8712 220884.6157 270255.2613 233429.2807 255386.8224 267580.0293 0.920192014 1.037120371 0.866354441 0.947648716 0.825489915 1.009997876 0.872371833 0.954431551 1 18.02961092 3.735241773 24.99927394 0.919151849 0.978656191 0.100731882 0.064490112 478.2296698 3602280.879 0.014923582 0.024237446 5435.528444 -3.735241773 0.059504342 S(ph)PQRPGWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)PQRPGWSR;S(1)PQRPGWSR 96.82 0.0043055 2230450000 203384 247671 225607 274368 205285 216448 252008 256302 256032 TRUE FALSE 193770.4414 272908.9565 235951.3041 246788.0074 241086.639 208952.3515 213559.5512 233858.8381 295736.1349 0.655213951 0.922812346 0.797844011 0.83448716 0.815208595 0.70654995 0.722128702 0.790768562 1 18.17395101 S(ph)PQVKPASTMGMGPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQVKPASTMGMGPLGK 17 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 S(1)PQVKPASTMGMGPLGK 90.193 0.0058593 197320000 221540 243750 206730 257890 128530 228490 205950 242980 140500 TRUE FALSE 211068.2432 268588.4021 216208.775 231966.4072 150945.5913 220577.334 174528.545 221703.3831 162288.0224 1.300578072 1.655010629 1.332253433 1.429350138 0.930109253 1.359171988 1.075424682 1.366110572 1 17.308197 2.875914539 9.006404683 1.162376287 1.449507837 0.416165375 0.165430353 0.293919676 20.23972824 0.045430968 0.048225946 751.4750037 -2.875914539 0.28713155 S(ph)PRPDHPGTPPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK 138.57 2.87E-05 460572000 418903 341544 384771 416971 325681 401149 439904 396291 83172 TRUE FALSE 399102.2854 376347.7219 402413.1309 375056.2829 382479.6633 387257.1095 372788.5654 361589.6592 96069.88898 4.154291106 3.917436836 4.188753992 3.903994133 3.981264758 4.03099362 3.88038926 3.763818851 1 16.5517967 -1.096730924 0.536261912 2.63E-15 4.050889419 0.991294505 0.088098627 1.833668786 0.294763283 2.883961031 0.034809866 0.080032996 1.096730924 4.050889419 S(ph)PS(ph)EERGHSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSEERGHSTR 11 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 2 S(1)PS(1)EERGHSTR;S(1)PS(1)EERGHSTR 69.594 0.03077 219970000 211780 157879 191757 214120 166671 175108 242710 172537 156411 TRUE FALSE 201769.5791 173967.0496 200549.2481 192596.2508 195738.3696 169043.9661 205680.1318 157428.7456 180666.419 1.116807319 0.962918568 1.11005271 1.06603237 1.083424195 0.935668991 1.138452475 0.871378015 1 17.46296885 1.232644414 24.99999994 0.935689027 1.054160366 0.339213146 0.071327249 167.4603453 707599.4962 0.055287645 0.015252146 17.08615784 -1.232644414 0.118471339 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSPAPAPAPAAAAGPPTR 19 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(1)PS(1)PAPAPAPAAAAGPPTR;S(1)PS(1)PAPAPAPAAAAGPPTR;S(1)PS(1)PAPAPAPAAAAGPPTR;S(1)PS(1)PAPAPAPAAAAGPPTR 242.24 3.11E-24 789730000 553820 470630 494480 550470 425097 527670 593410 490058 439564 TRUE FALSE 527642.0262 518587.7321 517152.3971 495135.7098 499233.7822 509396.6556 502874.4058 447145.9236 507729.3401 1.039219097 1.021386182 1.018559213 0.975196174 0.983267546 1.003283867 0.990437948 0.880677732 1 18.95370011 3.329641786 0.540544465 0.962502062 1.047332107 0.370031703 0.034205413 1.257783021 0.71816652 0.024391505 0.056563424 2136.199384 -3.329641786 0.084830046 S(ph)PS(ph)PAPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSPAPPPR 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR 72.2 0.069329 1711030000 2448040 2230240 2174100 2640900 1841500 2381090 2438310 2046450 1857320 TRUE FALSE 2332326.001 2457503.992 2273784.635 2375431.715 2162657.017 2298632.256 2066301.027 1867251.989 2145343.7 1.08715727 1.145505959 1.059869631 1.107249955 1.008070183 1.071451748 0.963156173 0.870374285 1 21.03277737 2.049189916 1.03114264 0.93358521 1.105181606 0.641793107 0.047341992 0.292781056 0.575336581 0.033980727 0.016508334 111.9927519 -2.049189916 0.171596395 S(ph)PS(ph)PAPPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;S(1)PS(1)PAPPPRR 94.122 0.029114 999910000 478760 405960 409820 439580 361080 405790 463350 364540 356810 TRUE FALSE 456129.9636 447327.7855 428610.6524 395392.5833 424052.2377 391737.3906 392657.4475 332618.9451 412142.2725 1.106729385 1.08537225 1.039957998 0.959359449 1.028897704 0.950490684 0.952723061 0.807048845 1 18.65278292 3.1954535 0.628224915 0.91818708 1.122481416 0.581130925 0.054638105 0.555426641 0.470650529 0.03422705 0.061966847 1568.38796 -3.1954535 0.204294336 S(ph)PS(ph)PKPR ddPTM_SK-BR-3_Trastuzumab_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 64.297 0.042252 277755000 754540 845980 679570 879970 722230 797320 849990 770930 762920 TRUE FALSE 718874.3896 932186.3238 710728.9567 791513.7438 848186.6833 769708.6085 720308.4144 703423.2822 881229.7371 0.815762745 1.057824407 0.806519488 0.898192277 0.962503474 0.873448292 0.817390045 0.798229171 1 19.74915865 2.010792675 23.3962468 0.850042092 0.915336245 0.016357494 0.088704013 216.2331445 468743.4924 0.030967938 0.022842138 102.5162414 -2.010792675 0.065294153 S(ph)PS(ph)PKPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.979)PS(0.619)PKPT(0.403)K;S(0.998)PS(0.616)PKPT(0.386)K 53.237 0.078441 1197930000 1828980 1950020 1525520 2019910 713410 1864470 1684280 1529840 700470 TRUE FALSE 1742527.74 2148729.255 1595466.601 1816864.809 837828.4781 1799902.936 1427312.152 1395879.099 809095.3101 2.153674256 2.655718341 1.971914286 2.245551033 1.035512711 2.224587034 1.764084075 1.725234446 1 19.62595013 1.572058096 0.101995153 5.91E-11 3.492778536 0.477602301 0.377881995 7.334665997 0.770016906 12.13016201 12.24012965 37.33000909 -1.572058096 3.492778536 S(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_SK-BR-3_Trastuzumab_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(1)PLPTR;S(1)PS(1)PLRGNVVPS(0.999)PLPT(0.001)R 110.06 0.00097012 266420000 290410 265490 249301 330110 216898 274534 290040 230760 232131 TRUE FALSE 276682.8948 292543.7328 260731.6974 296926.7156 254724.9425 265026.8187 245789.071 210553.4311 268128.6899 1.031903356 1.091057182 0.972412529 1.107403746 0.950010022 0.988431409 0.916683221 0.785270055 1 18.03256607 2.168230948 1.296010582 0.892108712 1.050350341 0.450432994 0.067473297 0.351082869 1.125963487 0.039556628 0.021315747 147.3095654 -2.168230948 0.158241629 S(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSPLRGNVVPSPLPTRR 18 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(0.882)PLPT(0.118)RR;S(1)PS(0.999)PLRGNVVPS(0.966)PLPT(0.035)RR;S(1)PS(1)PLRGNVVPS(0.989)PLPT(0.011)RR;S(1)PS(0.999)PLRGNVVPS(0.831)PLPT(0.17)RR 89.829 0.0018613 589420000 437359 316013 457019 409780 347274 399400 527870 333008 432084 TRUE FALSE 416685.9068 348215.084 477973.7732 368588.1359 407838.4756 385568.6779 447333.7365 303848.0541 499089.3799 0.834892353 0.697700849 0.957691733 0.738521296 0.817165205 0.772544344 0.89629985 0.608804888 1 18.92893868 -1.440821804 3.389792361 1.002591528 0.795741477 0.309201487 0.098150196 5910848.804 3840497.717 107021.3901 0.020190033 0.036239166 1.440821804 -0.20685005 S(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 S(1)PS(1)PLRGNVVPSPLPTR;S(1)PS(1)PLRGNVVPSPLPTR 82.975 0.0034342 761550000 145474 150641 116953 154674 97985 125286 106527 128652 100379 TRUE FALSE 138597.7323 165991.4892 122315.4107 139125.8757 115073.553 120947.3144 90274.34965 117386.5489 115945.2627 1.195372102 1.431636665 1.054940995 1.199927211 0.992481714 1.043141493 0.77859455 1.012430747 1 16.82308435 2.924871245 1.006749979 0.915597971 1.300686681 0.56480635 0.112724753 0.300168924 0.657015932 0.052652084 0.059365622 841.1457303 -2.924871245 0.38508871 S(ph)PS(ph)PSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 S(0.999)PS(0.693)PS(0.308)FR;S(1)PS(0.925)PS(0.075)FR 73.985 0.069311 421910000 619080 575000 599930 573380 542420 639890 669570 547450 485530 TRUE FALSE 589817.3153 633593.1537 627437.3839 515742.753 637017.8763 617730.4489 567414.799 499512.3758 560823.5127 1.051698622 1.129754975 1.118778671 0.919616852 1.135861571 1.101470311 1.011752871 0.890676593 1 19.09718731 1.508355153 4.210689716 0.94528878 1.077792545 0.395193133 0.0668768 0.170349481 6.510478783 0.040196876 0.016309793 32.23703961 -1.508355153 0.132503765 S(ph)PS(ph)PSPTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(1)PS(0.967)PS(0.033)PTPEAK 179.19 1.05E-05 260940000 600970 514840 498630 616360 336820 588920 609130 564520 325650 TRUE FALSE 572563.3391 567302.7813 521492.6787 554402.3218 395561.3014 568525.5527 516196.0311 515087.6361 376150.1388 1.522167029 1.508181768 1.386395019 1.47388573 1.051604826 1.511432521 1.372313812 1.36936713 1 18.5209491 -4.043629378 0.125170374 3.31E-14 1.606961492 0.503606164 0.130670722 91.17247192 0.922500939 24.69388851 1.109473028 9.04E-05 4.043629378 1.606961492 S(ph)PS(ph)PYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.996)PS(0.969)PY(0.034)YSR;S(1)PS(0.983)PY(0.014)YS(0.004)R;S(1)PS(0.993)PY(0.007)YSR;S(0.997)PS(0.955)PY(0.048)YSR;S(1)PS(0.965)PY(0.036)YSR;S(1)PS(0.997)PY(0.003)YSR;S(0.999)PS(0.995)PY(0.006)YSR;S(0.998)PS(0.981)PY(0.021)YSR 106.35 0.0061574 5995526000 5507120 4444570 4366830 5509470 4308570 5052820 5845650 4455040 4156520 TRUE FALSE 5246809.352 4897476.736 4567053.475 4955647.608 5059983.244 4877839.576 4953788.73 4064933.08 4801091.893 1.092836686 1.020075609 0.951253085 1.032191784 1.053923432 1.015985464 1.031804606 0.84666846 1 22.19493112 1.268782178 24.97647717 0.923334239 1.029661465 0.429212624 0.05030223 150.8442173 124664.7128 0.031210055 0.011393369 18.56872898 -1.268782178 0.106327226 S(ph)PSFASEWDEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.751)PS(0.249)FASEWDEIEK 128.95 4.76E-05 0 66228 52887 63288 68775 55242 65429 78500 71244 69523 TRUE FALSE 63097.53369 58276.24543 66189.8174 61861.60634 64876.18731 63163.17732 66523.38325 65005.49767 80304.27177 0.785730725 0.725692969 0.824237814 0.77034017 0.807879654 0.786548162 0.828391588 0.809489909 1 16.29318911 -5 0.189529665 1.926530988 0.748501145 0.869610463 0.025873138 40.61514844 0.396943578 14.14359906 0.063818225 1.00E-05 5 -1.178029843 S(ph)PSFGAGEGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.542)PS(0.458)FGAGEGLLR;S(0.525)PS(0.475)FGAGEGLLR 147.02 6.84E-05 153965000 164140 133579 129227 152023 220052 127027 158845 128871 312430 TRUE FALSE 156381.4275 147190.852 135152.1858 136741.3592 258428.9991 122628.0231 134610.2779 117586.3721 360880.0487 0.433333536 0.407866416 0.374507225 0.378910831 0.716107748 0.339802723 0.373005597 0.325832288 1 18.46115986 -1.399675941 3.98042721 1.002352449 0.418058592 0.733286791 0.110181274 34631629.83 12185648.38 713271.4342 0.024413521 0.039840434 1.399675941 -0.584293858 S(ph)PSGHPHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSGHPHVR 9 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.991)PS(0.009)GHPHVR;S(0.966)PS(0.034)GHPHVR;S(0.983)PS(0.017)GHPHVR;S(0.967)PS(0.033)GHPHVR 112.13 0.0012964 240016000 133762 135604.3 135068 174244 170229 136219.4 195266 214844 200471.6 TRUE FALSE 127439.3354 149422.5323 141261.0014 156728.6621 199916.8837 131502.088 165474.5854 196031.1204 231559.7119 0.550351934 0.645287261 0.610041359 0.676839079 0.863349164 0.567897096 0.714608703 0.846568338 1 17.82102474 -5 0.090443781 2.126126997 0.388343916 0.67435358 0.082135093 122.4559775 0.768891355 26.26326516 1.820989874 1.00E-05 5 -1.737783081 S(ph)PSGSAFGSQENLR ddPTM_SK-BR-3_Trastuzumab_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(0.666)PS(0.222)GS(0.11)AFGS(0.001)QENLR 133.48 4.65E-05 104050000 48079 47902 49819 49739 51300 50432 53098 53620 51013 TRUE FALSE 45806.40095 52783.26826 52103.25043 44739.14122 60246.70376 48685.52719 44996.92489 48924.74854 58923.8355 0.77738322 0.895788059 0.884247435 0.75927069 1.022450478 0.826245046 0.763645552 0.830304886 1 15.84656372 4.68175987 3.605112502 0.859002481 0.772793423 0.086064255 0.087905009 0.667959323 14.65306908 0.020009091 0.138943353 48057.35563 -4.68175987 -0.086209058 S(ph)PSLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSLAK 6 0 O15018;O15018-2;A6PVK7;Q5VXU9-3;Q5VXU9;Q5SW96 O15018;Q5SW96 PDZD2;C9orf84;LDLRAP1 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2;Uncharacterized protein C9orf84;Low density lipoprotein receptor adapter protein 1 1 S(0.887)PS(0.113)LAK;S(0.699)PS(0.301)LAK 83.265 0.059984 598210000 1013760 892650 827380 1101230 774410 1053600 1092980 1028230 897740 TRUE FALSE 965841.5739 983612.0499 865316.1914 990532.2682 909466.8588 1017113.568 926225.827 938192.7302 1036956.934 0.931419177 0.948556317 0.834476498 0.9552299 0.877053645 0.980863847 0.893215327 0.904755732 1 19.98392455 2.260240009 24.99921322 0.932855416 0.915382766 0.091776654 0.047298731 1006.207726 1160286.245 0.015270312 0.012765534 182.0706776 -2.260240009 -0.017472651 S(ph)PSLDNPTPFPNLGPSENPLKR ddPTM_SK-BR-3_Trastuzumab_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(0.548)PS(0.451)LDNPTPFPNLGPSENPLKR 107.47 0.00027764 155850000 46453 64670 39367 58864 31778 49300 42792 49141 42002 TRUE FALSE 44257.25875 71259.94652 41172.01589 52946.87889 37320.07314 47592.72864 36263.29447 44837.95353 48515.45564 0.912230096 1.468809178 0.848637106 1.091340444 0.769240908 0.980980762 0.747458598 0.92419937 1 15.5661568 3.701834268 24.98780932 0.895625755 1.190519814 0.326287509 0.16743985 511.0897319 347734.3456 0.041554454 0.064377826 5033.085038 -3.701834268 0.29489406 S(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSLDVTVPEAELNLETPEISVGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.455)PS(0.455)LDVT(0.09)VPEAELNLETPEISVGGK;S(0.451)PS(0.451)LDVT(0.098)VPEAELNLETPEISVGGK 127.28 7.93E-05 42716000 76781 62830 53200 115631 88222 82013 92684 58000 67424 TRUE FALSE 73151.7143 69232.44843 55639.27262 104007.5522 103607.8889 79172.86925 78543.35354 52921.21252 77879.76957 0.939290328 0.888965759 0.714425234 1.3354887 1.330356901 1.016603794 1.008520621 0.679524513 1 16.24896099 3.261021287 24.98687168 1.067638704 0.869537366 0.213766171 0.191883816 399.2169195 444114.7295 0.053959711 0.073008645 1823.985103 -3.261021287 -0.198101338 S(ph)PSLGSDLTFATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 S(0.914)PS(0.081)LGS(0.005)DLTFATR 87.914 0.008548 36014000 90449 102240 74351 112850 45617 111700 81960 94118 41321 TRUE FALSE 86173.65502 112658.3722 77760.06689 101506.1036 53572.59036 107831.801 69455.4967 85876.52897 47728.84964 1.805483595 2.360383145 1.629204715 2.126724284 1.122436236 2.259258327 1.455209946 1.799258302 1 15.54257394 -1.57918793 0.157646162 2.11E-14 2.223422354 0.355309112 0.362363041 32.84676209 0.874213282 14.66929102 1.773173694 0.026351908 1.57918793 2.223422354 S(ph)PSLLQSGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSLLQSGAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3;I3L2H8 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 S(0.976)PS(0.024)LLQSGAK 63.216 0.083946 33730000 85069 104470 91717 113180 73852 90743 90310 89426 66132 TRUE FALSE 81047.95696 115115.6118 95922.31517 101802.9314 86731.76542 87600.54716 76531.55084 81595.38536 76387.4128 1.061011939 1.506997129 1.255734573 1.332718672 1.135419596 1.146792959 1.001886934 1.068178413 1 16.22104731 2.339691388 1.471833889 1.027691824 1.299346638 0.494692513 0.113262826 0.321176137 1.393767579 0.058842258 0.038668425 218.6207539 -2.339691388 0.271654813 S(ph)PSLSLAPLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 S(0.999)PS(0.001)LSLAPLS(1)PR;S(0.999)PS(0.001)LSLAPLS(1)PR 281.14 6.73E-28 400260000 299040 249885 243782 295970 248887 235518 256390 229995 226584 TRUE FALSE 284904.9718 275348.5656 254959.6458 266218.5333 292292.814 227361.9526 217272.9966 209855.4185 261721.4895 1.088580737 1.052067089 0.974163972 1.017182555 1.116808614 0.868717174 0.83016873 0.801827236 1 17.99767286 2.221672184 22.61842666 0.857993965 1.048687145 0.64266838 0.064117384 42.94160631 57509.85028 0.022348839 0.016567007 166.5989209 -2.221672184 0.19069318 S(ph)PSLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.998)PS(0.002)LSSK;S(0.993)PS(0.007)LSSK;S(0.996)PS(0.004)LSSK;S(0.994)PS(0.006)LSSK;S(0.965)PS(0.035)LSSK 88.37 0.019571 2151690000 5174150 4838000 3852940 5375790 3339010 4824540 5535220 5247580 3834540 TRUE FALSE 4929578.184 5330997.7 4029601.11 4835405.376 3921332.287 4657464.97 4690720.528 4788074.076 4429180.879 1.112977392 1.203608036 0.909784725 1.09171549 0.885340291 1.051540928 1.059049214 1.081029248 1 22.07860848 3.754808356 24.99928284 1.016821916 1.15829272 0.421660041 0.071378886 690.1824699 1061933.042 0.016999941 0.030523555 5686.019651 -3.754808356 0.141470804 S(ph)PSMSISEPISVTLPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.608)PS(0.388)MS(0.003)IS(0.001)EPISVTLPPR;S(0.77)PS(0.23)MSISEPISVTLPPR 85.493 0.0052688 51821000 19156.9 18350.9 20655 18899.5 23282.8 17008.3 25654 21637 28444 TRUE FALSE 18251.3913 20220.87757 21602.05218 16999.68635 27343.31295 16419.29831 21740.01113 19742.34958 32854.95025 0.555514197 0.615459084 0.657497638 0.517416287 0.832243322 0.499751124 0.661696669 0.600894216 1 15.00382314 -5 0.390922057 6.822537125 0.607923809 0.624866335 0.093040178 395.8349702 2.852557203 1961.475611 0.051758344 1.00E-05 5 -6.214613316 S(ph)PSPAHLPDDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.5)PS(0.5)PAHLPDDPK 72.209 0.027381 1368700000 1505300 1580700 1413400 1876900 1482200 1692700 1731700 1712100 1310200 TRUE FALSE 1434147.452 1741775.127 1478205.788 1688230.446 1740695.211 1634081.375 1467497.36 1562179.448 1513379.124 0.947645854 1.150917902 0.97675841 1.115537025 1.150204323 1.079756783 0.969682571 1.032245934 1 20.52934202 1.749570304 24.99992176 1.000015328 1.071269499 0.191352025 0.067313746 4.797077904 10912.97128 0.029951665 0.016609588 56.17852133 -1.749570304 0.071254171 S(ph)PSPAHLPDDPKVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPAHLPDDPKVAEK 16 1 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.5)PS(0.5)PAHLPDDPKVAEK;S(0.5)PS(0.5)PAHLPDDPKVAEK 110.41 0.00054131 1015265000 539320 293950 567720 453030 405460 522740 794840 634090 443110 TRUE FALSE 513827.4124 323903.8392 593750.5236 407490.5637 476172.0956 504637.3827 673572.5598 578565.7181 511825.2357 1.003911837 0.632840698 1.160064964 0.796151763 0.930341184 0.985956431 1.316020612 1.130397014 1 18.96529176 1.959940621 4.916628067 1.179711978 0.887580099 0.330663911 0.155157283 0.185278573 10.54462693 0.064243331 0.039520046 91.18861533 -1.959940621 -0.292131879 S(ph)PSPAVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.707)PS(0.293)PAVPLR;S(0.746)PS(0.254)PAVPLR;S(0.705)PS(0.295)PAVPLR 130.66 0.00037247 742300000 1346120 1101810 1122740 1341060 1329080 1147350 1526400 1255000 1135830 TRUE FALSE 1282491.575 1214085.692 1174218.74 1206254.101 1560871.131 1107616.982 1293519.646 1145105.547 1311968.715 0.977532132 0.925392258 0.895005137 0.919422915 1.189716731 0.844240391 0.985937874 0.872814674 1 20.32330189 4.753325362 19.97632464 0.953315256 0.977532369 0.005820334 0.09593718 117.8286057 706714.0007 0.020755782 0.143037442 56666.36595 -4.753325362 0.024217113 S(ph)PSPKPT(ph)K ddPTM_SK-BR-3_Trastuzumab_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 2 S(0.647)PS(0.354)PKPT(1)K 115.65 0.060778 462300000 736000 734320 594370 754840 283330 787090 682940 638770 269220 TRUE FALSE 701210.7386 809148.0429 621622.4524 678962.0491 332742.6623 759832.8759 578744.9599 582835.9125 310969.2626 2.254919772 2.602019364 1.998983588 2.183373506 1.070017852 2.443434022 1.86110021 1.874255698 1 18.24641246 -0.278422147 0.123330945 2.07E-13 2.928279509 0.453473368 0.389735675 22.65120312 0.800197097 13.8109466 5.166316401 0.526717627 0.278422147 2.928279509 S(ph)PSPS(ph)PTPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(0.999)PS(0.288)PS(0.713)PTPEAK 193.46 1.38E-06 242990000 713600 630090 604210 711190 384880 682180 724640 661690 386770 TRUE FALSE 679869.5422 694296.8874 631913.6261 639699.83 452002.9501 658555.9355 614082.8591 603748.9158 446748.3163 1.521817805 1.554111929 1.414473437 1.43190205 1.011761956 1.474109497 1.374561105 1.351429639 1 18.76910277 -2.216085919 0.063507175 3.42E-10 2.06959739 0.490236244 0.137734407 162.3046265 1.361646282 37.00544856 12.46994272 0.006080147 2.216085919 2.06959739 S(ph)PSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK 38 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 S(0.323)PS(0.323)PT(0.085)VHAS(0.115)S(0.122)T(0.033)PAVNIQPDVSGGWDWHAKPGGFGMGSK 57.205 0.014406 200800000 53249 33093 47844 46645 64038 40166 77634 62391 64049 TRUE FALSE 50732.0253 36465.21432 50037.69472 41956.15598 75206.20692 38775.04135 65789.50745 56927.71328 73981.3918 0.685740347 0.492897111 0.676355142 0.567117689 1.016555719 0.524118841 0.889271016 0.76948692 1 16.17487482 1.591889955 0.31351681 1.023393332 0.54762811 0.371658332 0.147498529 1.336989617 0.460347272 0.230252418 0.215561838 39.0741874 -1.591889955 -0.475765222 S(ph)PSPVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.92)PS(0.08)PVLR;S(0.917)PS(0.083)PVLR 107.29 0.0078773 260690000 486520 433760 375910 489170 414430 417610 450360 440990 451270 TRUE FALSE 463523.1638 477960.6371 393145.8453 439997.7022 486706.4608 403148.061 381649.3106 402374.5778 521250.6468 0.889251969 0.916949725 0.754235698 0.844119245 0.933728262 0.773424577 0.732180023 0.771940678 1 18.99161774 2.214971962 24.99920488 0.789271271 0.870116505 0.021576004 0.087513605 404.5744435 428764.2588 0.030498686 0.022536932 164.0483861 -2.214971962 0.080845234 S(ph)PSPYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(1)PSPYYSR;S(0.956)PS(0.044)PYYSR 126.55 0.001274 271430000 350960 319880 269340 355540 369840 354500 360670 346290 393960 TRUE FALSE 334370.8163 352476.1357 281689.5054 319800.4437 434339.9789 342223.5761 305643.1673 315967.0118 455053.3047 0.734794831 0.774582081 0.619025293 0.702775786 0.95448154 0.752051622 0.671664537 0.694351647 1 18.79567603 S(ph)PSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.458)PS(0.458)QDFS(0.083)FIEDTEILDSAMYR;S(0.467)PS(0.467)QDFS(0.064)FIEDT(0.002)EILDSAMYR 129.15 5.69E-05 78714000 26564 24223 20579.2 23162 26522 21487.8 27271 23088 28370 TRUE FALSE 25308.37236 26691.35124 21522.77668 20833.71176 31147.4284 20743.6721 23110.30808 21066.29232 32769.47471 0.772315473 0.81451874 0.65679346 0.635765814 0.950501303 0.633018145 0.705238894 0.64286329 1 15.00006493 -1.443978999 5.837713149 1.000151747 0.732692154 0.42496736 0.099788423 0.000186363 1.78E-05 0.091365178 0.021522851 0.035976673 1.443978999 -0.267459593 S(ph)PSSDLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 140.46 4.26E-10 14444000 12690 10233 10390 13046 12513 14865 14336 12599 13154 TRUE FALSE 12090.16885 11275.75433 10866.39178 11734.59129 14695.26324 14350.22132 12148.7799 11495.76477 15193.85514 0.795727532 0.74212596 0.715183321 0.772324811 0.967184635 0.944475328 0.799585082 0.756606185 1 13.89120035 2.899215015 7.812604866 0.878615126 0.754070897 0.443668287 0.07560906 0.300929084 20.81094421 0.023010054 0.024452708 792.8937882 -2.899215015 -0.124544229 S(ph)PSSDSWTCADTSTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSSDSWTCADTSTER 16 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.974)PS(0.026)SDSWTCADTSTER;S(0.999)PS(0.001)SDSWTCADTSTER;S(0.866)PS(0.134)SDSWTCADTSTER 268.38 1.79E-27 710000000 204853 238652 181454 243732 193109 199198 196306 208456 174353 TRUE FALSE 195170.0047 262970.9101 189773.8454 219231.5963 226787.1485 192299.7233 166355.9143 190202.4875 201390.7728 0.969110958 1.305774373 0.942316486 1.088588088 1.126104962 0.954858659 0.826035434 0.944444897 1 17.61963806 2.125158729 4.588881189 0.901313793 1.098876455 0.333716261 0.106833925 0.198262488 7.085833129 0.039851577 0.028838264 133.4008907 -2.125158729 0.197562661 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSSKPSLAVAVDSAPEVAVK 21 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.941)PS(0.027)S(0.027)KPS(0.006)LAVAVDSAPEVAVK 110.08 0.00016999 112100000 310470 397630 267940 396630 167350 343740 293000 359430 184850 TRUE FALSE 295794.6984 438148.9491 280225.314 356759.9989 196535.787 331836.1976 248297.4687 327956.4037 213515.5939 1.385354076 2.05207002 1.312434885 1.67088498 0.920475097 1.55415439 1.162900864 1.535983381 1 17.70398191 3.189712324 1.804984782 1.273623994 1.692771945 0.238702643 0.290093878 0.406212792 2.729060405 0.085334446 0.115454558 1547.791024 -3.189712324 0.419147951 S(ph)PSSNDKHVMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSSNDKHVMSR 12 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.955)PS(0.033)S(0.012)NDKHVMSR 66.673 0.087103 78605000 117030 90851 108470 117580 95411 117020 144600 130730 107280 TRUE FALSE 111498.2238 100108.8202 113443.4568 105760.635 112050.6482 112967.5681 122538.6142 119282.5882 123916.4345 0.899785604 0.807873634 0.915483545 0.853483523 0.904243643 0.911643145 0.988881053 0.96260507 1 16.91900801 2.02500985 1.119432733 0.993194242 0.862632219 0.714266532 0.031148248 0.23509633 0.544552014 0.021892049 0.010372737 105.9277751 -2.02500985 -0.130562023 S(ph)PSSQTPNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSSQTPNSR 10 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 S(0.995)PS(0.005)SQTPNSR;S(0.936)PS(0.052)S(0.012)QTPNSR;S(0.991)PS(0.009)SQTPNSR 107.79 0.002347 177533000 31575.6 38019.8 38119.9 44911.5 34601.3 33050.1 41454.4 42371.3 42520.1 TRUE FALSE 30083.08396 41894.06084 39867.73512 40396.91069 40635.75576 31905.56675 35129.76992 38661.04435 49113.89995 0.612516701 0.852998049 0.811740366 0.822514822 0.827377907 0.649623972 0.71527144 0.787171135 1 15.58384377 -2.359971741 1.528689894 1.863368341 0.756830218 0.475136532 0.079247694 282541.4898 30472.94937 836857.2912 0.022105463 0.004365442 2.359971741 -1.106538123 S(ph)PSSVTGNALWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 S(0.982)PS(0.018)SVTGNALWK 167.22 0.00016686 0 88884 105690 82392 105760 71092 99472 98784 102520 100890 TRUE FALSE 84682.62947 116459.9312 86169.7547 95128.80387 83490.42229 96027.2597 83712.68651 93542.80531 116535.5059 0.726668055 0.999351487 0.73942919 0.816307469 0.716437635 0.824017186 0.718344901 0.802697895 1 16.83041006 4.771303454 23.87327367 0.815947065 0.726667779 0.078912301 0.101673091 5003.094336 5606314.913 0.023051365 1.004508531 59061.36148 -4.771303454 -0.089279286 S(ph)PSTLLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.597)PS(0.402)T(0.001)LLPK;S(0.499)PS(0.499)T(0.002)LLPK 102.55 0.0051864 458030000 735650 840430 669910 835940 619680 751610 780020 763600 747760 TRUE FALSE 700877.2824 926070.7725 700626.0361 751909.723 727751.9958 725581.5572 661013.6229 696735.1359 863718.8018 0.811464658 1.072190128 0.811173769 0.870549213 0.842579777 0.840066878 0.765311142 0.806668947 1 19.72020217 3.645534898 24.9987763 0.834444184 0.94188689 0.152367651 0.087490735 72.67460002 19525.33244 0.02158544 0.033440023 4421.146418 -3.645534898 0.107442705 S(ph)PSTTYLHTPTPSEDAAIPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSTTYLHTPTPSEDAAIPSK 21 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.966)PS(0.026)T(0.007)T(0.002)YLHTPTPSEDAAIPSK;S(0.268)PS(0.236)T(0.236)T(0.236)Y(0.019)LHT(0.004)PTPSEDAAIPSK 189.45 1.39E-17 324760000 214893 213781 218998 227844 189415 229829 256170 291340 187329 TRUE FALSE 204735.4338 235565.5269 229039.2749 204940.6882 222448.916 221869.9641 217086.5616 265828.7251 216379.0246 0.946188912 1.088670805 1.058509601 0.947137499 1.028052125 1.025376487 1.003269897 1.228532782 1 17.72320113 S(ph)PSVAAMASPQLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.756)PS(0.244)VAAMASPQLCR 96.615 0.012905 195720000 83824 74195 69705 88801 88017 69914 86128 77261 91616 TRUE FALSE 79861.80564 81755.55485 72901.0432 79874.55477 103367.1369 67492.86065 72987.59175 70495.61725 105823.3414 0.754670989 0.772566371 0.688893795 0.754791464 0.976789578 0.637788032 0.689711653 0.666163214 1 16.69129835 S(ph)PSWQRPNQGVPSTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSWQRPNQGVPSTGR 16 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 1 S(0.93)PS(0.07)WQRPNQGVPSTGR;S(0.981)PS(0.019)WQRPNQGVPSTGR;S(0.97)PS(0.03)WQRPNQGVPSTGR;S(0.971)PS(0.029)WQRPNQGVPSTGR 126.51 4.32E-05 1063440000 94771 81533 100021 103535 88872 91460 91298 81856 86784.4 TRUE FALSE 90291.36265 89841.3054 104607.0618 93127.4651 104371.2487 88292.71727 77368.8133 74688.25469 100242.4815 0.900729524 0.896239838 1.043540226 0.929021944 1.041187799 0.880791416 0.77181662 0.745075876 1 16.61313451 2.001542757 24.8317135 0.816783836 0.950703257 0.301663686 0.083978911 47.67307232 767317.5746 0.029669368 0.021747443 100.3558646 -2.001542757 0.133919422 S(ph)PSWTAPPVIALQNGLSEDEALQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSWTAPPVIALQNGLSEDEALQR 24 0 A0A087X0D9;E9PFU9;Q8WV99 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 1 S(0.333)PS(0.333)WT(0.333)APPVIALQNGLSEDEALQR;S(0.459)PS(0.459)WT(0.082)APPVIALQNGLSEDEALQR 79.783 0.011779 19957500 10317.1 10372.6 11214 10082.3 21079.3 7486.5 13350.6 10438.4 18662.5 TRUE FALSE 9829.43113 11429.57973 11728.17299 9068.808049 24755.52325 7227.240628 11313.72077 9524.358359 21556.58519 0.455982756 0.530212909 0.544064512 0.420697804 1.148397255 0.335268344 0.524838265 0.441830572 1 14.39584104 -1.755014878 2.821612185 1.092486266 0.545406645 0.288714911 0.221782783 53143252.73 42784823.8 34177686.92 0.048612226 0.017578634 1.755014878 -0.547079621 S(ph)PSYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 S(0.999)PS(0.001)YGR;S(1)PSYGR;S(0.994)PS(0.006)YGR;S(1)PSYGR;S(1)PSYGR;S(1)PSYGR;S(1)PSYGR 152.31 0.010777 29456000000 4045360 3767400 3306300 4238040 3390960 3756700 3544920 3692930 3055880 TRUE FALSE 3854143.85 4151302.343 3457897.125 3812024.167 3982342.35 3626604.537 3004077.347 3369557.472 3529770.263 1.091896515 1.17608287 0.979638013 1.079963817 1.128215735 1.027433591 0.851068801 0.954610986 1 21.75114286 1.969367118 5.57557501 0.922097014 1.096178158 0.57269553 0.061017303 0.118075786 10.58388138 0.025608978 0.016187097 93.18952931 -1.969367118 0.174081143 S(ph)PTEDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPTEDFR 7 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.985)PT(0.015)EDFR;S(0.98)PT(0.02)EDFR 105.57 0.0082842 245010000 691100 754370 578750 718420 559500 629750 615390 641640 548200 TRUE FALSE 658433.0726 831241.1606 605286.26 646203.0567 657076.6229 607941.5996 521500.9531 585454.6001 633212.0562 1.039830285 1.31273742 0.955898192 1.020516035 1.037688112 0.960091637 0.823580265 0.924579048 1 19.2723292 3.067672027 0.954837741 0.908788031 1.165196916 0.377140455 0.098768777 0.444022435 0.888199187 0.047071872 0.062925956 1168.616534 -3.067672027 0.256408886 S(ph)PTFSEELPVLGDGQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.993)PT(0.007)FSEELPVLGDGQQLR;S(0.995)PT(0.005)FSEELPVLGDGQQLR 232.28 3.47E-20 70652000 46039 35357 38268 41994 36805 33322 43191 41395 35422 TRUE FALSE 43862.82771 38959.9185 40022.62565 37772.68334 43223.78035 32168.05078 36601.41969 37770.23435 40915.06285 1.072045957 0.952214558 0.978188053 0.92319749 1.056427079 0.786215358 0.89457078 0.923137635 1 15.32034445 2.252243103 24.9995132 0.888664686 0.993106379 0.322449045 0.067608056 236.7889186 432640.7058 0.021847626 0.018187153 178.7487867 -2.252243103 0.104441693 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.977)PT(0.023)GPSNSFLANMGGTVAHK;S(0.979)PT(0.021)GPSNSFLANMGGTVAHK;S(0.915)PT(0.085)GPSNSFLANMGGTVAHK;S(0.816)PT(0.184)GPSNSFLANMGGTVAHK;S(0.996)PT(0.004)GPSNSFLANMGGTVAHK;S(0.98)PT(0.02)GPSNSFLANMGGTVAHK;S(0.736)PT(0.264)GPSNSFLANMGGTVAHK;S(0.922)PT(0.078)GPSNSFLANMGGTVAHK;S(0.939)PT(0.061)GPSNSFLANMGGTVAHK 341.59 1.28E-80 9957390000 5511170 6148690 4821910 6440540 3605210 5560980 5488710 6021850 3938940 TRUE FALSE 5250667.916 6775248.501 5042999.343 5793124.683 4233957.483 5368401.868 4651306.482 5494544.89 4549770.698 1.154051108 1.489140652 1.108407363 1.273278384 0.930587004 1.179928006 1.022316682 1.207653145 1 22.11736241 3.22929249 1.771730539 1.080144701 1.30984689 0.295327572 0.132166365 0.34579103 2.240835671 0.038914145 0.054401021 1695.479292 -3.22929249 0.229702189 S(ph)PTGSTTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTGSTTSR 9 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.994)PT(0.006)GSTTSR 64.103 0.075218 78055000 20254 19808 18219 20498 18159 18130 25661 23923 25060 TRUE FALSE 19296.63356 21826.45772 19054.35917 18437.5021 21325.92385 17502.15355 21745.94315 21828.1753 28946.17681 0.666638419 0.754035943 0.658268596 0.636958111 0.736744061 0.60464474 0.751254416 0.75409528 1 14.82108519 0.66086576 1.263904583 0.999563698 0.685859769 0.814290183 0.047224735 0.44897032 1.118192545 0.041632498 0.012563055 4.580002969 -0.66086576 -0.313703928 S(ph)PTKTDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPTKTDPK 8 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.972)PT(0.028)KTDPK;S(0.875)PT(0.125)KTDPK 89.171 0.03221 663430000 2279030 3311400 1664070 3009360 754106 2337080 1697160 2694330 766426 TRUE FALSE 2171304.769 3648835.425 1740369.255 2706853.415 885621.8476 2256146.334 1438227.072 2458400.182 885279.4297 2.452677308 4.121676504 1.96589822 3.057626016 1.000386791 2.548513224 1.624602383 2.776976511 1 19.75577337 3.286060627 1.67518668 1.912250143 3.222021301 0.27586206 0.809747555 0.386481638 2.239589551 0.235811826 0.348621287 1932.238034 -3.286060627 1.309771158 S(ph)PTKTDPKNEEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPTKTDPKNEEEEK 14 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.975)PT(0.013)KT(0.013)DPKNEEEEK;S(0.958)PT(0.039)KT(0.003)DPKNEEEEK 64.83 0.031235 232940000 565920 676410 445410 719600 182814 671720 508800 723220 143088 TRUE FALSE 539170.0831 745336.948 465832.4891 647264.4408 214696.7037 648458.168 431173.2152 659891.0228 165277.3562 3.262213865 4.509613204 2.818489475 3.916231815 1.299008579 3.923454384 2.608785771 3.992628136 1 17.33452956 3.283940996 1.824645523 2.802297769 3.826736265 0.139129608 1.075487505 0.610046401 4.181083421 0.304782375 0.441750997 1922.830472 -3.283940996 1.024438496 S(ph)PTKTDPKNEEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTKTDPKNEEEEKR 15 3 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.985)PT(0.013)KT(0.002)DPKNEEEEKR 88.551 0.037256 49912000 118540 112880 107600 134360 58745 142350 137140 149260 63177 TRUE FALSE 112936.8491 124382.6003 112533.5664 120853.8775 68990.1094 137420.3838 116216.7743 136190.0031 72974.1665 1.547627805 1.704474423 1.542101429 1.656118642 0.945404555 1.883137423 1.592574192 1.866276926 1 16.15509821 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.816)PT(0.184)MEQAVQTASAHLPAPAAVGR;S(0.826)PT(0.174)MEQAVQTASAHLPAPAAVGR;S(0.818)PT(0.182)MEQAVQTASAHLPAPAAVGR;S(0.968)PT(0.032)MEQAVQTASAHLPAPAAVGR;S(0.974)PT(0.026)MEQAVQTASAHLPAPAAVGR;S(0.972)PT(0.028)MEQAVQTASAHLPAPAAVGR 244.75 1.17E-37 1870840000 839630 941078 786921 1014669 663215 900853 934563 991288 727975 TRUE FALSE 799942.3539 1036974.918 823002.1062 912672.5444 778879.486 869656.2347 791978.2499 904485.5676 840865.645 0.95133195 1.233223077 0.978755775 1.0853964 0.926282921 1.034239227 0.941860634 1.075660033 1 19.68151578 2.765457573 24.68296034 0.991118819 1.073733928 0.12364931 0.085173955 1045.018722 958997.3088 0.024370179 0.02584161 582.7168453 -2.765457573 0.082615108 S(ph)PVPAQIAITVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 184 1.04E-05 824880000 924380 744240 726210 901790 628610 855210 965440 991350 746070 TRUE FALSE 880686.3893 820078.9021 759507.4468 811140.3559 738239.385 825593.8633 818144.3965 904542.1385 861766.7252 1.021954508 0.951625165 0.881337634 0.941252815 0.85665803 0.958024764 0.949380351 1.049636882 1 19.71693787 1.318677468 5.749650022 1.024172935 0.940501178 0.386190371 0.045815756 0.222026378 11.40450201 0.033929153 0.011931532 20.82943396 -1.318677468 -0.083671757 S(ph)PVPSAFSDQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPVPSAFSDQSR 12 0 Q9UQ35;Q9UQ35-2;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR 153.64 6.47E-05 2819100000 571810 638870 478500 548940 374230 445360 430150 573390 422480 TRUE FALSE 544781.6745 703971.5793 500439.6983 493759.5083 439495.5935 429937.0715 364522.7173 523180.9319 487996.0407 1.116364948 1.442576416 1.025499505 1.01181048 0.900613031 0.881025737 0.746978842 1.072100772 1 18.89650992 3.44215712 2.515943677 0.901458407 1.27760616 0.548426265 0.122513397 0.167824842 2.142551642 0.034622204 0.052819991 2767.942857 -3.44215712 0.376147752 S(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 258.06 7.52E-31 218217000 538400 558030 464350 624950 348190 539240 545030 541140 371830 TRUE FALSE 512950.899 614893.8914 485640.9068 562128.8387 408914.2258 520565.9836 461875.6633 493754.9128 429491.4974 1.194321429 1.431678846 1.130734624 1.308824138 0.952089222 1.212051896 1.075401181 1.149626747 1 18.71227005 2.76257966 24.83864293 1.093004874 1.278393968 0.437181417 0.105139584 639.272093 661084.6405 0.029435521 0.031206958 578.8681574 -2.76257966 0.185389094 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.5)PVS(0.5)PLAAQGIPLPAQLTK;S(0.939)PVS(0.061)PLAAQGIPLPAQLTK;S(0.581)PVS(0.419)PLAAQGIPLPAQLTK;S(0.996)PVS(0.004)PLAAQGIPLPAQLTK 316.32 1.09E-61 306797000 1006493 1026839 866827 1135497 695665 1016945 1056056 1067928 799093 TRUE FALSE 958918.0706 1131475.062 906571.8754 1021354.684 816988.7557 981727.9397 894935.2614 974414.5629 923012.2612 1.038900685 1.225850521 0.982188334 1.106545088 0.885133156 1.063613108 0.969581119 1.055689728 1 19.81599029 3.717227543 24.90097922 1.007665468 1.132375615 0.321994626 0.074432076 695.5452815 811873.6963 0.017812357 0.027627363 5214.67856 -3.717227543 0.124710147 S(ph)PVSSLQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPVSSLQIR 9 0 P55197-1;P55197;Q5JT35 P55197-1 MLLT10 Protein AF-10 1 S(1)PVSSLQIR;S(1)PVSSLQIR 109.16 0.002617 227300000 94042 85873 98183 106008 178567 62626 87106 74345 91551 TRUE FALSE 89596.82103 94623.55633 102684.7877 95351.87444 209709.0283 60457.24592 73816.37989 67834.95767 105748.2615 0.847265192 0.894800113 0.971030504 0.901687395 1.983096699 0.571709124 0.698038709 0.641475866 1 16.69027442 S(ph)PVSTRPLPSASQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SPVSTRPLPSASQK 14 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.976)PVS(0.02)T(0.004)RPLPSASQK;S(1)PVSTRPLPSASQK;S(0.999)PVS(0.001)TRPLPSASQK;S(1)PVSTRPLPSASQK;S(0.994)PVS(0.004)TRPLPS(0.001)ASQK;S(0.883)PVS(0.116)T(0.001)RPLPSASQK;S(0.997)PVS(0.003)TRPLPSASQK;S(0.995)PVS(0.005)TRPLPSASQK;S(0.98)PVS(0.012)T(0.008)RPLPSASQK;S(0.996)PVS(0.003)T(0.001)RPLPSASQK 197.73 6.06E-08 21123570000 12360180 10441620 11362820 12865470 9434710 12117360 14076690 13084810 11237830 TRUE FALSE 11775938.79 11505632.95 11883816.54 11572208.51 11080120.44 11697732.78 11929032.4 11939034.67 12980535.28 0.907199783 0.886375847 0.915510515 0.891504723 0.853595033 0.901174915 0.918993874 0.919764433 1 23.62984654 0.700123716 0.988261144 0.999694064 0.893003288 0.787581726 0.017157147 0.45521337 0.780488575 0.016283528 0.005278325 5.013300251 -0.700123716 -0.106690776 S(ph)PVVELSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPVVELSK 8 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 S(1)PVVELSK;S(1)PVVELSK;S(1)PVVELSK 112.13 0.0032522 154664000 415339 530316 366715 547865 290789 436533 412566 483622 316833 TRUE FALSE 395706.7486 584355.8033 383529.2455 492792.5693 341502.5095 421415.7528 349621.4794 441273.4938 365965.8435 1.081266888 1.59674957 1.047991916 1.346553451 0.933154051 1.151516624 0.9553391 1.205777812 1 18.48134948 2.950028563 1.765297194 1.048600353 1.30860206 0.223070339 0.177206791 0.417524616 2.620396974 0.057785499 0.0658196 891.3095559 -2.950028563 0.260001707 S(ph)PYCKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPYCKR 6 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 S(0.999)PY(0.001)CKR;S(1)PYCKR;S(0.92)PY(0.08)CKR;S(0.995)PY(0.005)CKR 91.626 0.029204 1627600000 2134880 2070160 1997560 2401820 1520770 2223780 2414350 2300180 1952690 TRUE FALSE 2033968.453 2281111.658 2089150.102 2160384.49 1785991.807 2146769.941 2045996.565 2098764.045 2255503.192 0.901780348 1.01135377 0.926245686 0.957828168 0.79183741 0.951792021 0.907113132 0.930508124 1 21.1050179 -1.638195233 2.121942105 1.012578991 0.926232765 0.157977424 0.05571854 1791830.861 1199393.892 122807.7725 0.014294428 0.023004075 1.638195233 -0.086346226 S(ph)PYKFPS(ph)SPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(0.999)PY(0.001)KFPS(0.917)S(0.083)PLR;S(0.998)PY(0.002)KFPS(0.673)S(0.327)PLR;S(0.994)PY(0.006)KFPS(0.681)S(0.319)PLR 115.8 0.00061136 402510000 1198730 1634600 1156590 1537150 920620 1448880 1314010 1482830 907190 TRUE FALSE 1142068.409 1801167.598 1209620.796 1382632.762 1081175.837 1398704.922 1113533.641 1352985.544 1047872.392 1.089892641 1.718880669 1.154358875 1.319466733 1.031781966 1.334804632 1.062661494 1.291173958 1 19.99903161 S(ph)QDDAMVDYFFQR ddPTM_SK-BR-3_Trastuzumab_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 199.08 1.27E-07 48620000 104963 83678 90874 115085 89419 101848 119799 100006 83319 TRUE FALSE 100001.607 92204.88333 95040.66279 103516.4372 105013.6453 98320.97822 101521.4623 91248.94447 96239.68499 1.039089093 0.95807549 0.987541291 1.075610723 1.091167799 1.021626143 1.05488149 0.948142593 1 16.5543443 5.109613203 16.69806554 1.020183076 2.318359685 0.017535379 0.046948132 16096505.61 14496789.56 0.011385164 787045267.1 128710.2704 -5.109613203 1.29817661 S(ph)QDVELWEGEVVK ddPTM_SK-BR-3_Trastuzumab_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 223.06 1.72E-11 208284000 425537 315670 321014 617440 329968 557450 510060 345085 282153 TRUE FALSE 405422.7093 347837.1319 335732.8094 555373.7581 387514.3147 538145.3667 432240.9791 314867.528 325907.8462 1.243979591 1.067286768 1.030146446 1.704082196 1.189030332 1.651219426 1.326267484 0.966124417 1 18.31410456 S(ph)QEADVQDWEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR 287.85 7.18E-29 3990250000 2312180 2023896 2140789 2699610 2139920 2425310 2841360 2178450 2013118 TRUE FALSE 2202887.834 2230133.303 2238946.293 2428240.074 2513121.37 2341320.907 2407858.347 1987693.369 2325302.058 0.94735556 0.95907252 0.96286256 1.044268664 1.080772006 1.006888932 1.035503469 0.854810825 1 21.1489867 3.367204949 7.182283075 1.011097766 0.954531225 0.11845973 0.058876388 0.385979412 23.04380956 0.015578795 0.021124994 2329.19017 -3.367204949 -0.056566541 S(ph)QEELREDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 109.44 0.0014828 156880000 210320 211180 168640 218940 139600 217280 226520 255720 142700 TRUE FALSE 200378.5904 232699.4821 176372.3108 196931.7352 163946.1958 209755.5391 191960.2137 233327.8011 164829.1872 1.215674201 1.411761388 1.070030823 1.194762521 0.994642991 1.272563086 1.164600863 1.415573328 1 17.33061221 3.738344875 24.99999649 1.167164353 1.313717792 0.187091068 0.133313213 28.91729277 3351133.718 0.03196316 0.053265283 5474.505229 -3.738344875 0.146553439 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_SK-BR-3_Trastuzumab_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 1 S(0.987)QEEPKDT(0.013)FEHDPSESIDEFNK;S(0.943)QEEPKDT(0.057)FEHDPSESIDEFNK 174.15 1.79E-12 242106000 416240 433860 327860 485560 186982 472010 421730 486060 145893 TRUE FALSE 396565.1601 478070.8273 342892.7053 436750.5863 219591.6016 455664.1753 357387.3429 443498.0096 168517.3413 2.353260246 2.836923628 2.034762136 2.59172488 1.303080145 2.703960149 2.120774872 2.631764815 1 17.36253753 3.726943976 24.24911231 2.13118781 2.595091943 0.125331533 0.565926934 906.2543493 1891757.896 0.132025051 0.20658156 5332.660999 -3.726943976 0.463904133 S(ph)QESDGVEYIFISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 S(0.997)QES(0.003)DGVEYIFISK;S(1)QESDGVEYIFISK;S(1)QESDGVEYIFISK 157.22 5.62E-06 114155000 305056 309223 302215 383490 243815 342619 406910 352022 265110 TRUE FALSE 290636.6074 340733.1753 316071.8567 344940.8566 286336.2588 330754.0181 344828.4061 321197.0875 306221.9048 0.949104564 1.112700202 1.032166059 1.12644083 0.935061321 1.080112209 1.126073611 1.048903042 1 18.22421796 S(ph)QGAGSSPRRPQGGSDAPSGHAAPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQGAGSSPRRPQGGSDAPSGHAAPSR 26 2 Q96IQ9-2;M0R0Q5;M0R398 Q96IQ9-2 ZNF414 Zinc finger protein 414 1 S(0.323)QGAGS(0.323)S(0.323)PRRPQGGS(0.03)DAPSGHAAPSR 67.396 0.017995 34615000 12125 6773.4 9956.4 10081 20491 8688.1 12384 9049.6 16428 TRUE FALSE 11551.87528 7463.617161 10412.91079 9067.638727 24064.62391 8387.228919 10494.59335 8257.169049 18975.57034 0.608776183 0.393327685 0.548753508 0.477858561 1.268189756 0.442001414 0.553058125 0.435147345 1 14.21185563 S(ph)QGLSGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQGLSGDK 8 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)QGLSGDK;S(1)QGLSGDK;S(1)QGLSGDK 144.28 0.00061669 3009160000 2911780 3101010 2622440 3504850 1641840 2941490 2828700 3156600 1633450 TRUE FALSE 2774145.93 3417006.445 2742681.468 3152535.819 1928176.376 2839625.464 2397129.862 2880191.37 1886757.083 1.470324905 1.811047365 1.453648428 1.670875306 1.021952637 1.505029709 1.270502644 1.526530042 1 20.84747726 2.769099473 24.99231679 1.30032474 1.613618277 0.411729336 0.197210638 652.1839357 533731.6209 0.053696292 0.056947441 587.62393 -2.769099473 0.313293537 S(ph)QGLSGDKTSGFRPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQGLSGDKTSGFRPIAK 17 2 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)QGLSGDKTSGFRPIAK;S(0.964)QGLS(0.026)GDKT(0.006)S(0.004)GFRPIAK 95.122 0.002084 2494200000 1663310 1273090 1694600 1573630 1003150 1650940 1831090 1895670 1256480 TRUE FALSE 1584688.633 1402819.318 1772299.086 1415445.723 1178099.042 1593767.534 1551723.59 1729675.085 1451328.501 1.091888316 0.966576014 1.221156399 0.975275909 0.811738377 1.098143895 1.069174614 1.191787444 1 20.46894267 -0.57035834 6.866533735 0.999993806 1.04691807 0.017517734 0.117087254 0 0 0.107181855 0.025263006 0.268931491 0.57035834 0.046924264 S(ph)QGLSGDKTSGFRPIAKPAYSPASWSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQGLSGDKTSGFRPIAKPAYSPASWSSR 28 3 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(0.998)QGLS(0.002)GDKTSGFRPIAKPAYSPASWSSR 107.45 0.00058942 477120000 269900 160920 323920 237980 264210 264150 517000 372620 355790 TRUE FALSE 257142.3619 177317.931 338772.0524 214057.7983 310288.1403 255002.4193 438122.1546 339991.4174 410964.0961 0.625705176 0.431468181 0.824334913 0.520867395 0.755024936 0.620498048 1.066083774 0.827301997 1 18.64865283 1.759207644 14.24588899 0.959441654 0.614595282 0.619749568 0.123231439 0.241659025 167.3431832 0.054027482 0.029821405 57.43910233 -1.759207644 -0.344846371 S(ph)QLDLFDDVGTFASGPPK ddPTM_SK-BR-3_Trastuzumab_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 182.39 7.20E-14 8543300 20081 17970 22219 22754 13445 17594 22114 16935 16907 TRUE FALSE 19131.81093 19801.16343 23237.76313 20466.72469 15789.80374 16984.71537 18740.10315 15452.08162 19528.85121 0.97966904 1.013944098 1.189919616 1.04802502 0.808537255 0.869724245 0.959611139 0.791243758 1 14.25331946 2.759120341 23.424371 0.888386864 1.049209115 0.523541623 0.08135773 308.3940623 351362.502 0.024552617 0.026006502 574.2755691 -2.759120341 0.160822251 S(ph)QLFMQVPPY(ph)PEVFRDS(ph)LHT(ph)Y(ph)KLNEQDTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQLFMQVPPYPEVFRDSLHTYKLNEQDTDK 30 2 A0A1B0GUN5 A0A1B0GUN5 5 S(1)QLFMQVPPY(1)PEVFRDS(1)LHT(1)Y(1)KLNEQDTDK 63.331 0.0040612 165980000 178630 78370 164410 146190 96974 157670 222450 184600 115530 TRUE FALSE 170186.5139 86355.9921 171948.3611 131494.7035 113886.2349 152209.8484 188511.1669 168435.4454 133445.8024 1.275323097 0.64712408 1.288525814 0.985379091 0.853426881 1.140611737 1.412642163 1.262201151 1 17.0258944 2.00193338 20.70270273 1.272254499 0.996220569 0.168926107 0.210725938 8.830820112 94551.07129 0.074268263 0.054242503 100.4461695 -2.00193338 -0.276033929 S(ph)QPKAPPVDDAEVDELVLQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQPKAPPVDDAEVDELVLQTK 21 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 S(1)QPKAPPVDDAEVDELVLQTK;S(1)QPKAPPVDDAEVDELVLQTK 101.59 0.00031446 81662000 49053 44601 49408 54497 31197 62980 58174 63411 40992 TRUE FALSE 46734.3619 49145.89261 51673.40567 49018.85802 36637.74692 60798.98681 49298.48786 57858.39668 47348.83 0.987022528 1.037953686 1.091334372 1.035270735 0.773783574 1.284065241 1.041176474 1.22196043 1 15.53104116 2.21628363 24.99999964 1.13475562 0.999572835 0.296023086 0.115046011 317.3364742 356123.7879 0.039301848 0.029048234 164.5445983 -2.21628363 -0.135182785 S(ph)QPLLIPTTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(1)QPLLIPTTGR 136.96 9.27E-05 347331000 214660 183793 198191 217111 191481 191014 227686 227700 237413 TRUE FALSE 204513.4472 202521.7157 207278.2534 195286.5898 224875.2258 184399.1373 192948.319 207761.3809 274229.7955 0.745773984 0.738510982 0.755856062 0.71212754 0.820024773 0.672425609 0.703600856 0.757617824 1 18.06502581 S(ph)QS(ph)IEQESQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 S(1)QS(1)IEQESQEK;S(1)QS(0.997)IEQES(0.003)QEK 261.79 1.53E-20 170642000 1267060 920410 1020220 1216460 585690 1174300 1267540 1091690 549170 TRUE FALSE 1207168.585 1014200.825 1066998.096 1094179.13 687834.1506 1133633.697 1074153.493 996095.8362 634332.4788 1.903053407 1.598847386 1.682080189 1.724930011 1.084343264 1.787128571 1.693360389 1.570305588 1 19.27487969 -2.682807537 0.252344082 4.11E-11 1.720356368 0.474791898 0.212063721 44.10564935 1.237066605 24.82442676 0.305427998 0.002075833 2.682807537 1.720356368 S(ph)QSESSDEVTELDLSHGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.568)QS(0.407)ES(0.016)S(0.009)DEVTELDLSHGKK 86.32 0.0013615 195760000 212380 191170 206160 220590 159570 241460 266370 216320 155260 TRUE FALSE 202341.2183 210650.4403 215612.6399 198415.8741 187398.9575 233098.1797 225730.3643 197377.874 179336.9278 1.128274141 1.174607165 1.202276868 1.106386044 1.044954655 1.299777923 1.258694274 1.100598055 1 17.45231306 4.59598169 3.104097212 1.16697654 1.127479183 0 0.093221212 1.786256172 29.37119455 0.022394252 0.143131241 39444.06718 -4.59598169 -0.039497357 S(ph)QSPVHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSPVHLR 8 0 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 1 S(0.625)QS(0.375)PVHLR;S(0.718)QS(0.282)PVHLR 62.466 0.05027 444280000 415310 360280 366050 419520 643060 368510 465440 389670 620840 TRUE FALSE 395679.1194 396992.9416 382833.7546 377349.0526 755209.4604 355748.4063 394428.5796 355548.429 717116.6964 0.55176392 0.55359601 0.533851403 0.526203133 1.053119338 0.496081611 0.550020076 0.495802748 1 19.45184838 -2.027378063 2.746036792 1.486238044 0.591054918 0.374051956 0.164555037 9785570.427 7312459.694 29925274.99 0.037832605 0.009389056 2.027378063 -0.895183126 S(ph)QSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.499)QS(0.499)VPAS(0.001)T(0.001)GLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.5)QS(0.5)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.374)QS(0.374)VPAS(0.125)T(0.125)GLGWGS(0.003)GLVAPLQEGSIDSTLAGTQDTR 129.57 9.38E-09 168917000 55455.8 42780.4 49702.1 57589.2 43964.5 56564.9 67762.9 60894.1 48568.7 TRUE FALSE 52834.51424 47139.7714 51980.99045 51800.2242 51631.89488 54606.04333 57424.42505 55561.88978 56100.48594 0.94178354 0.840273852 0.926569344 0.923347157 0.92034666 0.973361325 1.023599423 0.990399439 1 15.77572565 2.222847893 1.732690577 1.008842264 0.90043732 0.703933983 0.028290107 0.182687065 1.089353407 0.014901542 0.00915527 167.0505436 -2.222847893 -0.108404944 S(ph)QTPERPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.5)QT(0.5)PERPAKK 70.089 0.028712 57602000 123940 99730 102660 137290 88265 131530 153800 135000 107880 TRUE FALSE 118081.6018 109892.6004 107367.0625 123489.3484 103658.3881 126975.0831 130334.9853 123178.6843 124609.4794 0.947613315 0.881895991 0.861628369 0.991010868 0.831865991 1.018984139 1.045947595 0.988517767 1 16.9270543 2.209966674 24.22292414 1.020336535 0.906163538 0.584976223 0.046059552 94.8034522 80310.48207 0.015627389 0.011544103 162.1685649 -2.209966674 -0.114172997 S(ph)RADLTAEMISAPLGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.5)RADLT(0.5)AEMISAPLGDFR;S(0.5)RADLT(0.5)AEMISAPLGDFR;S(0.979)RADLT(0.021)AEMISAPLGDFR;S(0.908)RADLT(0.092)AEMISAPLGDFR;S(1)RADLTAEMISAPLGDFR;S(0.86)RADLT(0.14)AEMISAPLGDFR;S(0.992)RADLT(0.008)AEMISAPLGDFR;S(0.5)RADLT(0.5)AEMISAPLGDFR;S(0.782)RADLT(0.218)AEMISAPLGDFR;S(1)RADLTAEMISAPLGDFR;S(0.996)RADLT(0.004)AEMISAPLGDFR;S(0.978)RADLT(0.022)AEMISAPLGDFR;S(0.931)RADLT(0.069)AEMISAPLGDFR;S(0.843)RADLT(0.157)AEMISAPLGDFR;S(0.614)RADLT(0.386)AEMISAPLGDFR;S(0.997)RADLT(0.003)AEMISAPLGDFR;S(0.792)RADLT(0.208)AEMISAPLGDFR 232.87 6.68E-22 1542543600 981910 840871 866239 1049059 914402 892878 1093223 971268 943477 TRUE FALSE 935497.0603 926556.7109 905956.915 943605.5962 1073873.419 861957.411 926431.7529 886218.6249 1089786.595 0.85842225 0.850218488 0.831315892 0.86586273 0.985397898 0.79094147 0.850103825 0.813203823 1 20.05561422 -2.431322431 2.359035311 2.504479494 0.855504094 0.439726685 0.051194654 1752590.087 663369.5782 13670603.31 0.01189039 0.003704056 2.431322431 -1.6489754 S(ph)RAS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)RAS(0.997)PVS(0.004)R;S(1)RAS(1)PVSR;S(1)RAS(1)PVSR;S(0.999)RAS(0.992)PVS(0.009)R 92.856 0.0065329 735550000 79618 63343 82599 100792 85475 75304 87713 79006 100022 TRUE FALSE 75854.61493 69797.72372 86386.24585 90660.19667 100381.8129 72696.2036 74330.77089 72087.8158 115532.9009 0.656562887 0.604137204 0.747719872 0.784713237 0.868859105 0.629225121 0.643373189 0.623959195 1 16.81794423 -1.96636003 2.59870904 1.255376777 0.687631935 0.565702307 0.083825013 10541989.36 5865827.465 16224560.14 0.022006229 0.010805378 1.96636003 -0.567744842 S(ph)RASPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.708)RAS(0.285)PVS(0.006)R 64.439 0.040564 1008200000 314300 292750 276300 327970 321420 281150 343280 294400 307990 TRUE FALSE 299443.6619 322581.5578 288968.6283 295001.8325 377475.5462 271413.705 290906.3312 268620.7753 355751.5162 0.841721393 0.90676088 0.81227659 0.82923563 1.061065179 0.762930564 0.817723377 0.755079776 1 18.44051038 -0.541968528 6.018362495 1 0.851538536 0.232046179 0.08652896 5.87E-10 0 0.078798178 0.018572909 0.287098863 0.541968528 -0.148461464 S(ph)RDKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;S(1)RDKEER 80.916 0.022536 6728270000 11301520 10603550 9685550 11806500 5565070 10457290 10789310 13855440 7610080 TRUE FALSE 10767319.55 11684063.8 10129642.05 10619688.19 6535616.446 10095151.43 9143202.6 12642184.22 8790212.339 1.224921439 1.329212919 1.152377401 1.208126468 0.743510645 1.148453648 1.040157194 1.438211471 1 23.06746659 3.334080737 2.320043482 1.077909316 1.271815979 0.148815142 0.174918625 0.468156427 5.134715858 0.049490126 0.071205224 2158.145579 -3.334080737 0.193906663 S(ph)RDREQDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRDREQDRK 9 3 O95232;J3KPP4;H0YA81;H0YBV7;H0YAR4;H0YAX1;H0YAY6 O95232 LUC7L3 Luc7-like protein 3 1 S(1)RDREQDRK;S(1)RDREQDRK;S(1)RDREQDRK;S(1)RDREQDRK 107.09 0.01564 405308000 198784 177015 191348 202871 131100 194982 205599 223766 157983 TRUE FALSE 189387.8743 195053.0297 200121.4951 182478.0217 153963.7985 188229.7244 174231.0965 204171.8628 182482.1968 1.03784302 1.068887997 1.096663119 0.99997712 0.843719558 1.031496375 0.954784081 1.11885908 1 17.47739619 3.106207685 6.538969675 0.981557819 1.063215004 0.207086397 0.069314746 0.297583031 16.30670298 0.018864713 0.02263997 1277.049363 -3.106207685 0.081657184 S(ph)RDRHDDYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRDRHDDYYR 10 2 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 S(1)RDRHDDYYR;S(1)RDRHDDYYR 149.32 1.23E-05 2138800000 349320 182878 374980 290680 426330 351210 650830 321270 537860 TRUE FALSE 332808.3359 201513.4761 392173.2039 261460.2941 500681.817 339047.5096 551533.9302 293137.8956 621268.5818 0.53569156 0.324358067 0.631245834 0.420849053 0.805902361 0.545734195 0.887754421 0.471837631 1 19.24485757 1.35320438 0.163660129 1.194898627 0.226863597 0.441186575 0.159982154 3.202720183 0.518900827 1.356700799 1.19068914 22.55300311 -1.35320438 -0.96803503 S(ph)RECDITK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRECDITK 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)RECDITK 76.326 0.021857 263360000 468570 361530 421530 487930 281460 423750 445350 436140 295670 TRUE FALSE 446421.6247 398370.318 440857.5675 438882.3494 330546.5349 409075.4312 377403.6781 397949.2695 341520.9935 1.307157197 1.166459238 1.290865205 1.285081613 0.967865933 1.197804642 1.105067288 1.165226376 1 18.38161474 8 0.076235907 0.832810437 2.035949159 0.447146894 0.086294671 190.1190874 1.061638879 2.668032605 24.23338488 100000000 -8 1.203138722 S(ph)REDLSALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SREDLSALTR 10 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(0.999)REDLS(0.001)ALTR;S(1)REDLSALTR;S(0.999)REDLS(0.001)ALTR 135.26 0.00039149 712480000 1159480 921170 921940 1123350 796080 1014340 1110060 1071260 837070 TRUE FALSE 1104673.678 1015038.27 964211.8609 1010428.724 934916.1 979213.1515 940699.9593 977454.7953 966878.5404 1.142515458 1.049809493 0.997241971 1.045042041 0.966942652 1.012757146 0.972924644 1.010938556 1 19.88297514 4.651406946 0.76375088 0.992977979 1.225403835 0.816236069 0.021468459 0.782835022 0.378109267 0.00712307 0.152565578 44813.30209 -4.651406946 0.232425856 S(ph)REDLSAQPVQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.995)REDLS(0.005)AQPVQTK;S(0.885)REDLS(0.115)AQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK 210.57 1.75E-08 2603251000 4944610 4966130 4739020 5352900 3292290 5115830 5210680 5279210 3466390 TRUE FALSE 4710888.085 5472184.293 4956308.755 4814816.322 3866464.334 4938667.524 4415695.065 4816934.386 4003940.057 1.17656309 1.366699854 1.237857881 1.202519582 0.96566489 1.233451913 1.102837456 1.203048576 1 21.93298895 3.062107197 3.768885817 1.115285844 1.270400089 0.376778305 0.092846152 0.222459511 6.437198385 0.02560188 0.030591524 1153.737999 -3.062107197 0.155114245 S(ph)REDLTAVVSVSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.974)REDLT(0.026)AVVSVSTK;S(0.975)REDLT(0.025)AVVSVSTK 249.54 1.03E-17 204730000 597740 563890 538740 678590 326790 587510 576020 609880 348780 TRUE FALSE 569486.0148 621351.0321 563441.7619 610376.844 383782.0725 567164.3814 488137.5697 556475.674 402867.0211 1.413583106 1.5423229 1.398580009 1.515082675 0.952627176 1.407820327 1.211659292 1.381288725 1 18.61994418 0.190328653 0.051603996 8.64E-07 2.342277768 0.386597828 0.157210059 95.01421891 1.714796243 44.75056091 32.44236187 1.549989131 -0.190328653 2.342276904 S(ph)REDLTAVVSVSTKFPAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SREDLTAVVSVSTKFPAYER 20 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 S(0.97)REDLT(0.03)AVVSVSTKFPAYER 111.4 0.00013278 86272000 73590 50934 75048 75600 73576 60015 108600 79844 116610 TRUE FALSE 70111.54654 56124.23251 78489.02503 68000.54437 86407.6311 57936.6655 92031.07542 72852.43608 134693.2832 0.520527415 0.416681747 0.582724121 0.504854754 0.641514031 0.430137748 0.683264029 0.540876533 1 17.03931838 -5 0.19577422 3.094851823 0.454380457 0.775077056 0.078976472 55.77455758 0.549320599 45.48742427 0.173658775 1.00E-05 5 -2.640471367 S(ph)RENLSAVMLYNPGLEFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.681)RENLS(0.319)AVMLYNPGLEFER;S(0.86)RENLS(0.14)AVMLYNPGLEFER;S(0.52)RENLS(0.48)AVMLYNPGLEFER;S(0.912)RENLS(0.088)AVMLYNPGLEFER 207.83 1.81E-16 487105000 416262 374225 386779 435257 345273 395824 437439 430866 361241 TRUE FALSE 396586.1202 412358.953 404513.1997 391504.1394 405488.5019 382116.5156 370699.6464 393137.0889 417260.4093 0.950452311 0.988253244 0.96945023 0.938272912 0.971787624 0.915774675 0.888413178 0.942186414 1 18.67058852 2.238614818 24.99999999 0.922717359 0.964910751 0.085150579 0.031811984 1.753072106 808768.136 0.010633513 0.008372806 173.2266946 -2.238614818 0.042193392 S(ph)RERPSQPEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.99)RERPS(0.01)QPEGLR;S(1)RERPSQPEGLR;S(1)RERPSQPEGLR;S(0.999)RERPS(0.001)QPEGLR 156.98 5.18E-05 4644470000 1888630 1745100 1785330 2141040 1606940 1973120 2225230 2077290 1839310 TRUE FALSE 1799358.203 1922927.674 1867189.146 1925818.591 1887189.827 1904790.36 1885730.294 1895391.475 2124540.801 0.84693982 0.905102728 0.878867163 0.906463453 0.888281282 0.896565676 0.887594295 0.892141716 1 21.01871962 -5 0.269537546 1.769997871 0.879163234 0.832532875 0.01596287 79.14400118 0.76879381 33.91459163 0.018703394 1.00E-05 5 -0.890834637 S(ph)RERPSQPEGLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.999)RERPS(0.001)QPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK;S(0.882)RERPS(0.118)QPEGLRK;S(1)RERPSQPEGLRK 154.51 0.00021637 6108360000 2411270 1866970 2294210 2402700 1678505 2448670 2927300 2637790 2011640 TRUE FALSE 2297294.046 2057216.366 2399401.798 2161176.031 1971235.741 2363871.944 2480686.621 2406811.124 2323594.857 0.988680982 0.885359321 1.032624853 0.930100196 0.848356044 1.017333954 1.067607209 1.035813587 1 21.14792711 2.02043948 24.67198629 1.042106793 0.938217434 0.437412218 0.052553811 166.5037155 200981.5385 0.018613586 0.013745625 104.8188715 -2.02043948 -0.103889359 S(ph)RERSPS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRERSPSPLRGNVVPSPLPTR 21 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 S(0.812)RERS(0.376)PS(0.812)PLRGNVVPSPLPTR 70.983 0.024989 131540000 64055 37186 58064 51499 60874 51937 72306 65264 88680 TRUE FALSE 61027.24709 40975.29568 60726.29183 46322.22268 71490.40633 50138.40867 61274.39171 59549.13817 102432.0415 0.595782786 0.400024202 0.59284469 0.452223953 0.697930113 0.489479736 0.598195553 0.581352644 1 16.64430755 -5 0.247354444 3.755854173 0.499868554 0.747781229 0.082699622 78.84934167 0.782813634 109.5440974 0.107296544 1.00E-05 5 -3.255985619 S(ph)RES(ph)SPSHGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.956)RES(0.784)S(0.17)PS(0.09)HGLLK 71.08 0.025919 241010000 481960 413810 428280 533690 331050 468140 541970 459000 326480 TRUE FALSE 459178.706 455977.7095 447917.0616 480042.4673 388785.0152 451928.1944 459282.5225 418807.5267 377108.851 1.217629087 1.209140831 1.187765974 1.272954655 1.030962318 1.198402512 1.217904383 1.110574641 1 18.52462149 -4.999999999 0.172510309 0.244657908 1.232041612 0.488868174 0.062501161 110.4786992 1.047843035 28.44431819 0.202952116 1.00E-05 4.999999999 0.987383704 S(ph)RESASPTIPNLDLLEAHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.326)RES(0.326)AS(0.326)PT(0.022)IPNLDLLEAHTK;S(0.477)RES(0.477)AS(0.046)PT(0.001)IPNLDLLEAHTK 152.41 3.91E-08 48038000 109747 92418 101324 112219 94409 105597 124046 110134 106683 TRUE FALSE 104559.4768 101835.4993 105969.8056 100938.5329 110873.8997 101940.1494 105120.5044 100490.0831 123226.8548 0.848512096 0.826406707 0.859957075 0.819127723 0.899754359 0.827255955 0.853064899 0.815488501 1 16.91095717 -1.175231087 4.727066964 1.00001972 0.843814766 0.798311094 0.024690313 4.44E-06 7.76E-07 0.020709231 0.004880596 0.066798839 1.175231087 -0.156204953 S(ph)RESLNVDVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.981)RES(0.019)LNVDVVK;S(0.997)RES(0.003)LNVDVVK;S(0.997)RES(0.003)LNVDVVK 138.07 3.95E-05 575837000 1194410 1287080 1048110 1422130 717050 1241440 1228350 1340450 752030 TRUE FALSE 1137952.606 1418234.915 1096166.88 1279174.791 842103.293 1198448.622 1040942.647 1223073.092 868650.9716 1.310022833 1.632686731 1.261918672 1.472599275 0.969438037 1.379666472 1.198343963 1.408014418 1 19.72841709 2.81463058 24.99999915 1.218422522 1.433984081 0.301081954 0.169311245 150.1494287 49344.96234 0.046710926 0.049544415 652.5752231 -2.81463058 0.215561559 S(ph)RESMIQLF ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRESMIQLF 9 1 P30520;G3V5D8;G3V232;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 1 S(0.748)RES(0.252)MIQLF 77.379 0.086202 7426300 30832 23339 25610 32364 32669 29408 35802 30022 33774 TRUE FALSE 29374.63246 25717.27063 26784.24383 29110.70923 38366.46326 28389.59359 30339.74735 27393.11452 39011.49943 0.752973685 0.659222819 0.686573042 0.746208417 0.983465486 0.727723723 0.777712926 0.702180509 1 15.25161183 -5 0.177314359 1.977255177 0.697741067 0.420130102 0.089293371 131.0502325 1.25527673 45.33994472 0.284133748 1.00E-05 5 -1.27951411 S(ph)RFHSPSTTWSPNKDTPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRFHSPSTTWSPNKDTPQEK 20 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 S(0.459)RFHS(0.355)PS(0.146)T(0.031)T(0.01)WSPNKDTPQEK 85.801 0.0013545 100360000 111520 48857 105320 88057 87092 108780 158030 139110 123750 TRUE FALSE 106248.6706 53835.58385 110149.0262 79205.34306 102280.8172 105012.9213 133919.6211 126928.7909 142940.518 0.743306881 0.376629276 0.770593445 0.554114006 0.715548108 0.734661682 0.936890554 0.887983287 1 17.1250554 1.984136482 0.973359949 0.981721752 0.585731568 0.617370071 0.112186041 0.320019503 0.557588926 0.084744439 0.039843475 96.41319645 -1.984136482 -0.395990184 S(ph)RGIELS(ph)DEHGNT(ph)ILSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRGIELSDEHGNTILSK 17 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 3 S(1)RGIELS(1)DEHGNT(1)ILSK 68.919 0.0353 5087800 6869.6 4766.2 5164.7 7002 13340 5756 10751 5839.9 18541 TRUE FALSE 6544.887622 5251.881199 5401.506604 6298.145657 15666.49178 5556.668277 9110.737494 5328.527397 21416.24359 0.305603903 0.245228869 0.252215408 0.29408265 0.731523795 0.259460454 0.425412489 0.248807751 1 14.38641783 -5 0.275046748 5.631874002 0.297553415 0.651720496 0.149318679 131.5772458 1.268735887 347.279887 0.166217574 1.00E-05 5 -5.334320587 S(ph)RGPKSDDDGFEIVPIEDPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRGPKSDDDGFEIVPIEDPAK 21 2 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 S(0.5)RGPKS(0.5)DDDGFEIVPIEDPAK 67.43 0.011236 25495000 82692 67567 74504 84509 40743 94302 81150 93251 50774 TRUE FALSE 78783.31304 74452.15412 77920.08209 76013.99476 47848.5663 91036.29809 68769.07708 85085.44809 58647.7726 1.343330011 1.269479655 1.328611107 1.296110515 0.815863317 1.552254997 1.172577815 1.450787375 1 15.8397887 -2.258238737 2.173664973 0.000221158 1.27451543 0.169639339 0.19353944 2757678.802 363831.6559 13629173.83 0.043208514 0.00551774 2.258238737 1.274294272 S(ph)RGQNRPTNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(0.999)RGQNRPT(0.001)NVK 111.07 0.0013461 364989000 389749 402203 379088 472504 300853 421387 451285 507536 363091 TRUE FALSE 371326.3372 443187.943 396469.5598 425007.0002 353321.6679 406794.2625 382433.1848 463093.4572 419397.2979 0.885380853 1.056725795 0.945331698 1.013375628 0.842450988 0.969949651 0.911863731 1.104187985 1 18.67795804 1.242961664 24.99993723 1.052093998 0.95125164 0.308690294 0.065425434 123.7935247 703234.2965 0.043918028 0.014823771 17.49692232 -1.242961664 -0.100842358 S(ph)RGSPSSYNSSSSSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.498)RGS(0.498)PS(0.004)SYNSSSSSPR 128.29 3.73E-05 48658000 14327 8670.1 10417 14319 13889 12864 18719 14364 16360 TRUE FALSE 13649.7911 9553.593047 10894.62975 12879.62692 16311.2372 12418.51645 15863.07275 13106.21201 18897.02524 0.722324859 0.505560686 0.576526179 0.681569017 0.863164281 0.657167797 0.839448143 0.693559533 1 14.20587152 0.928398938 0.267443508 1.059057525 0.563931052 0.543823572 0.096957937 1.838885658 0.413114465 0.328763517 0.185245619 8.480060258 -0.928398938 -0.495126473 S(ph)RKSPHKDLGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.5)RKS(0.5)PHKDLGHR;S(0.5)RKS(0.5)PHKDLGHR;S(0.511)RKS(0.489)PHKDLGHR 138.57 2.93E-05 1359233000 628220 419097 593990 590780 401313 641820 785280 597500 62958.5 TRUE FALSE 598525.2856 461803.4608 621225.029 531393.672 471301.8601 619593.6125 665471.1133 545179.7325 72721.78263 8.230343976 6.35027696 8.542489012 7.307214603 6.480889812 8.52005534 9.1509186 7.496787245 1 16.15009994 3.079936502 16.33178428 7.317654773 7.545485974 0 2.317653705 31.68840573 6438.705523 0.60812783 0.726869962 1202.088664 -3.079936502 0.227831201 S(ph)RLPKSPPYTAFLGNLPYDVTEESIKEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRLPKSPPYTAFLGNLPYDVTEESIKEFFR 30 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.434)RLPKS(0.434)PPY(0.062)T(0.071)AFLGNLPYDVTEESIKEFFR 107.76 0.00019841 55569000 164330 42437 153000 101800 156910 133230 295660 167160 219160 TRUE FALSE 156562.4466 46761.37855 160015.2013 91566.87059 184275.0543 128616.2117 250551.6368 152522.5842 253146.2135 0.618466476 0.18472083 0.632105846 0.361715348 0.727939209 0.508070849 0.98975068 0.602507863 1 17.94961138 2.092648117 0.752470803 0.917809703 0.413321384 0.441964479 0.186621685 0.517940335 0.554183446 0.143056632 0.080373989 123.779327 -2.092648117 -0.504488319 S(ph)RLTPVSPESSSTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.729)RLT(0.271)PVSPESSSTEEK;S(0.5)RLT(0.5)PVS(0.001)PESSSTEEK;S(0.499)RLT(0.499)PVS(0.003)PESSSTEEK 159.14 5.59E-09 1487840000 1157872 922096 968516 1086954 700536 1003420 1171613 1104217 731457 TRUE FALSE 1103141.685 1016058.631 1012923.417 977691.3188 822709.2566 968671.3138 992861.9187 1007525.906 844887.6158 1.305666771 1.202596194 1.198885387 1.157185051 0.97374993 1.146509069 1.175140812 1.192496951 1 19.68839993 3.921563262 1.056327413 1.117711227 1.301284509 0.439552828 0.072947679 0.651365077 1.24508947 0.024471939 0.098775096 8347.631352 -3.921563262 0.183573282 S(ph)RNHIMGRY(ph)FS(ph)NQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRNHIMGRYFSNQSK 15 2 A4D0V7 A4D0V7 CPED1 Cadherin-like and PC-esterase domain-containing protein 1 3 S(0.999)RNHIMGRY(0.806)FS(0.841)NQS(0.354)K 45.723 0.066598 140450000 189250 171000 198910 215240 206550 181670 232240 193810 251620 TRUE FALSE 180304.5276 188425.0944 208030.2202 193603.6663 242572.2546 175378.7223 196807.5226 176838.9689 290639.9445 0.620370775 0.648311073 0.715766102 0.666128899 0.834614303 0.603422639 0.677152354 0.608446885 1 18.14887347 -2.005528291 2.589763838 1.340922454 0.670078833 0.703183476 0.067008422 11971922.02 5013416.432 24319074.72 0.015292342 0.009873513 2.005528291 -0.670843621 S(ph)RPTSFADELAAR ddPTM_SK-BR-3_Trastuzumab_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(0.623)RPT(0.33)S(0.047)FADELAAR;S(0.705)RPT(0.256)S(0.039)FADELAAR 112.24 0.0024116 135984000 223004 164151 190217 252440 255310 204939 235560 207489 226445 TRUE FALSE 212463.0429 180878.1735 198938.6376 227064.2516 299835.9832 197841.911 199620.9956 189320.1632 261560.9341 0.812288898 0.691533597 0.760582379 0.868112252 1.146333202 0.756389373 0.763191171 0.723809019 1 17.99678755 3.263636112 6.673414685 0.86201601 0.748742845 0.160859464 0.127948004 0.343996584 53.11134258 0.03657437 0.048420565 1835.000184 -3.263636112 -0.113273165 S(ph)RQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 2 S(1)RQPS(1)PLLLLPPPAGLTSDPGPSVR 56.383 0.056579 17877000 10600 10274 11006 9584.5 9605.3 9489.9 12756 8357.8 11590 TRUE FALSE 10098.95901 11320.93228 11510.63599 8621.047851 11280.46128 9161.262383 10809.83792 7625.946725 13387.31801 0.754367604 0.845646027 0.859816431 0.643971246 0.842622942 0.684323953 0.807468525 0.569639619 1 13.70857934 5.083598246 10.87517103 0.776449063 0.575266198 0.003257124 0.122864923 405500.2736 1864025.891 0.025388497 1754388.107 121226.6897 -5.083598246 -0.201182864 S(ph)RS(ph)FDYNYR ddPTM_SK-BR-3_Trastuzumab_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 2 S(1)RS(1)FDYNYR;S(1)RS(1)FDYNYR;S(1)RS(1)FDYNYR;S(1)RS(0.999)FDYNYR 124.51 0.00030015 2319720000 2219650 1737580 1749300 2117630 1484540 1958010 2150640 1644690 1286330 TRUE FALSE 2114731.543 1914641.377 1829507.135 1904761.809 1743443.306 1890203.623 1822520.369 1500672.225 1485807.487 1.423287715 1.28862009 1.231321791 1.281970798 1.173397847 1.272172633 1.226619454 1.010004484 1 20.50281577 8 0.067926013 0.681894623 2.508621984 0.762321875 0.062275175 124.2342092 0.624641102 3.022698302 21.82345603 99999999.99 -8 1.826727361 S(ph)RS(ph)KMKT(ph)ENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSKMKTENLK 11 3 P46100;A0A096LNW1;A0A096LNN3;A0A087WWG0;A0A096LNL6;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 3 S(1)RS(1)KMKT(1)ENLK;S(1)RS(1)KMKT(1)ENLK 65.805 0.050908 148168000 223296 74766 155586 209800 393060 205500 470250 157195 539730 TRUE FALSE 212741.2406 82384.7404 162719.772 188710.5054 461609.5396 198383.4835 398504.7258 143430.1725 623428.5718 0.34124397 0.132147842 0.261007883 0.302697877 0.740436933 0.318213653 0.639214729 0.230066729 1 19.24986475 -5 0.115771647 3.068080751 0.031765896 0.551393555 0.181084017 107.9440097 0.819082997 52.4254725 1.77889066 1.00E-05 5 -3.036314855 S(ph)RS(ph)PATAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)RS(0.994)PAT(0.006)AK 105.25 0.052891 233040000 984370 1245600 1010100 1178800 573860 1113700 1015600 1148200 659330 TRUE FALSE 937840.7809 1372528.056 1056414.084 1060304.784 673941.0023 1075132.29 860651.5672 1047657.521 761575.529 1.231448156 1.802221846 1.387142895 1.392251647 0.88492996 1.411721161 1.130093516 1.375644938 1 19.5386276 3.088816209 3.037641819 1.183753135 1.512942367 0.31145567 0.210937428 0.272517412 5.068679277 0.059524858 0.072408773 1226.919895 -3.088816209 0.329189232 S(ph)RS(ph)PAYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPAYSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.999)RS(0.994)PAY(0.004)S(0.003)R;S(0.984)RS(0.943)PAY(0.057)S(0.016)R 64.827 0.037471 1080520000 80131 74880 79776 78989 91851 79684 93294 82718 67882 TRUE FALSE 76343.36643 82510.35713 83433.80851 71048.87565 107869.7853 76924.5231 79060.28684 75474.7734 78408.79387 0.973658217 1.052309991 1.064087386 0.906134021 1.375735807 0.981070098 1.008308927 0.962580467 1 16.25872785 S(ph)RS(ph)PESQVIGENTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.989)RS(0.992)PES(0.019)QVIGENTK 84.249 0.0046706 159800000 213000 217670 183560 237510 122700 235490 168460 196230 114560 TRUE FALSE 202931.9121 239850.8205 191976.4076 213635.0436 144098.8412 227334.9223 142758.333 179047.0609 132325.3797 1.533582693 1.812583656 1.450790529 1.614467641 1.08897357 1.717999395 1.078843177 1.353081785 1 17.01373027 2.023648917 0.357303622 0.992261774 1.732638362 0.441775354 0.208304345 1.044104015 0.359244934 0.234735369 0.26746064 105.5963525 -2.023648917 0.740376588 S(ph)RS(ph)PESQVIGENTKQP ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPESQVIGENTKQP 16 2 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.999)RS(0.999)PES(0.001)QVIGENTKQP;S(0.999)RS(0.999)PES(0.002)QVIGENTKQP 144.08 6.64E-06 1401230000 1241500 833050 1081190 1112580 774810 1141290 1372110 1191780 964020 TRUE FALSE 1182816.755 917938.7421 1130763.631 1000741.345 909936.6187 1101766.841 1162769.419 1087421.425 1113515.298 1.062236646 0.824361141 1.015489983 0.898722583 0.81717478 0.989449218 1.044232999 0.97656622 1 20.08668995 2.017834013 24.84734418 1.013096198 0.923847851 0.211996984 0.075962869 309.9835589 431884.5846 0.027156041 0.020052259 104.1919132 -2.017834013 -0.089248347 S(ph)RS(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK 155.87 3.26E-06 720560000 1022730 811890 888690 1051810 596350 958420 1148280 867550 654520 TRUE FALSE 974387.5798 894622.514 929437.3155 946080.0605 700353.2512 925229.6751 973088.7964 791582.7228 756019.6188 1.288839014 1.183332405 1.229382535 1.251396177 0.926369149 1.223817018 1.287121091 1.047039922 1 19.52806415 -5 0.087748829 0.400327826 1.353700775 0.289676244 0.106417169 314.4190169 1.925583133 35.92681214 2.689985551 1.00E-05 5 0.953372949 S(ph)RS(ph)PLAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRSPLAIR 8 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR;S(1)RS(1)PLAIR 116.24 0.0013144 5995120000 639375 466668 519101 581409 410320 501707 577937 479528 437795 TRUE FALSE 609153.0109 514221.9998 542902.2943 522964.6627 481879.6781 484332.7608 489762.0961 437537.9862 505686.0127 1.204607198 1.016880014 1.073595632 1.034168732 0.952922695 0.957773695 0.968510269 0.865236481 1 18.94788235 7.176154879 0.338782832 0.93563865 2.599953684 0.746607925 0.044798542 15.08649993 0.360620793 0.036692907 14.37468931 15002197.52 -7.176154879 1.664315034 S(ph)RS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 S(0.899)RS(0.899)PLDKDT(0.085)Y(0.1)PPS(0.011)AS(0.005)VVGASVGGHR 50.908 0.071957 738570000 76546 57482 74389 104220 61412 72876 94180 78629 47262 TRUE FALSE 72927.82228 63339.48115 77799.80923 93743.60759 72122.23336 70352.28585 79811.11127 71743.82792 54591.14958 1.335890943 1.160251829 1.425135939 1.71719424 1.321134175 1.288712298 1.461978945 1.314202549 1 15.73637946 0.965738845 21.45314221 0.999999995 1.372032819 0.41192788 0.143657408 825.8102452 517095.6022 0.143813613 0.035953403 9.241422914 -0.965738845 0.372032824 S(ph)RS(ph)PLGFYVHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 S(1)RS(1)PLGFY(0.001)VHLK;S(1)RS(1)PLGFYVHLK 107.69 0.0010166 211993000 546650 447580 431360 486880 347540 482530 584680 451010 284280 TRUE FALSE 520810.9379 493188.9109 451138.2827 437937.8974 408150.866 465819.8651 495476.3276 411517.1734 328364.6905 1.58607473 1.501954763 1.373894014 1.333693634 1.242980374 1.418605223 1.508920849 1.253232109 1 18.32493947 -3.967239887 0.12001354 1.66E-16 1.640851235 0.674820451 0.095496652 78.08342049 0.777914644 20.63913457 1.091077192 0.000107835 3.967239887 1.640851235 S(ph)RS(ph)PLLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPLLNDR 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PLLNDR 89.992 0.0066755 123850000 126550 126510 101450 133710 69514 119090 122970 92680 76365 TRUE FALSE 120568.2323 139401.5128 106101.5828 120269.2168 81637.21959 114965.8834 104208.668 84564.44787 88207.29418 1.36687372 1.58038532 1.202866314 1.363483801 0.925515518 1.303360278 1.181406469 0.958701303 1 16.42861034 3.291321887 1.490535761 1.115898322 1.466689865 0.493406541 0.146849315 0.300756325 1.3874539 0.046148118 0.070524626 1955.788495 -3.291321887 0.350791543 S(ph)RS(ph)PPPVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 103.83 0.0019108 10118328000 8035770 10235210 7072020 9740620 3921960 8723460 7304720 7581580 3677900 TRUE FALSE 7655935.077 11278189.54 7396279.112 8761474.372 4605948.582 8421364.393 6190250.804 6917696.663 4248249.948 1.802138568 2.654784835 1.741017879 2.062372619 1.084199056 1.982313775 1.457129613 1.628363855 1 22.01843722 2.139690269 0.280306965 0.968668379 2.403773079 0.413622476 0.366946742 1.72367655 0.404809928 0.611283399 0.901533744 137.9400151 -2.139690269 1.435104701 S(ph)RS(ph)PQWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 84.882 0.012074 2198950000 405986 327706 315843 375082 321792 313616 385138 366924 374742 TRUE FALSE 386795.8464 361099.614 330324.714 337378.0448 377912.4229 302755.3993 326378.1246 334794.1894 432855.0754 0.893592032 0.834227515 0.763130047 0.779424948 0.873069173 0.699438256 0.75401247 0.773455617 1 18.72352455 4.130181369 2.258102984 0.7891405 0.885224392 0.067900605 0.083151474 0.531303796 5.284498116 0.019776449 0.060678745 13495.26352 -4.130181369 0.096083891 S(ph)RS(ph)PS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;E7EVG6;Q9Y6A9;Q8IYB3;X6R7H2;Q5VV67-2;Q5VV67 A9Z1X7;Q8IYB3;X6R7H2 SRRM1;PPRC1;SPCS1 Serine/arginine repetitive matrix protein 1;Signal peptidase complex subunit 1;Peroxisome proliferator-activated receptor gamma coactivator-related protein 1 3 S(1)RS(1)PS(1)PR 57.885 0.092044 59944000 155100 180940 187350 176370 135780 186380 185650 128940 118220 TRUE FALSE 147768.7304 199377.9917 195940.1828 158640.9525 159459.989 179925.6139 157325.6828 117649.33 136552.9538 1.082134998 1.460078205 1.434902559 1.161754089 1.16775203 1.317625206 1.15212215 0.861565618 1 17.059101 1.430390668 3.643540561 0.934641487 1.274817045 0.561497889 0.122294529 0.166608384 3.939386222 0.090719546 0.031762489 26.93957052 -1.430390668 0.340175559 S(ph)RS(ph)PSS(ph)PELNNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPSSPELNNK 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.999)RS(0.751)PS(0.256)S(0.994)PELNNK;S(0.964)RS(0.682)PS(0.404)S(0.951)PELNNK 155.1 0.00016293 0 827720 551530 738010 778600 438880 711910 936250 527730 482300 TRUE FALSE 788595.316 607731.534 771848.4885 700333.6488 515420.533 687256.3782 793407.8671 481519.1635 557092.6208 1.415555128 1.090898553 1.385494009 1.257122465 0.9251972 1.233648325 1.424193819 0.864343101 1 19.08755768 -3.987003912 0.041358899 6.52E-09 1.850573718 0.218948417 0.179437204 1207.932872 4.442399742 165.6917204 57.99610046 0.000103038 3.987003912 1.850573712 S(ph)RS(ph)PTPPS(ph)SAGLGSNSAPPIPDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(0.992)RS(0.918)PT(0.135)PPS(0.783)S(0.172)AGLGSNSAPPIPDSR 98.583 0.008904 129560000 86056 68873 85942 86091 61029 83842 90671 65945 71942 TRUE FALSE 81988.30343 75891.237 89882.52571 77436.96912 71672.43828 80938.53052 76837.47366 60170.5062 83098.39793 0.986641204 0.913269556 1.081639694 0.931870783 0.862500843 0.974008315 0.924656499 0.72408744 1 16.34253304 3.007596178 24.99378141 0.901139223 0.979453308 0.210251416 0.083898544 318.9370485 1049391.855 0.022751807 0.027143965 1017.644706 -3.007596178 0.078314085 S(ph)RS(ph)PVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PVDLR 74.46 0.023284 209590000 341130 220190 265970 312170 219840 264340 311930 260520 198590 TRUE FALSE 325005.461 242627.6113 278164.9876 280790.0785 258180.0264 255185.8395 264339.3495 237707.4877 229386.3229 1.416847599 1.057724838 1.212648531 1.224092504 1.125524936 1.112471904 1.152376245 1.036275767 1 17.80741985 S(ph)RS(ph)RAS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSRASPVSR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(1)RAS(0.653)PVS(0.347)R 54.859 0.088731 73532000 133810 86754 123110 125910 86270 107010 146710 84829 105720 TRUE FALSE 127485.0665 95594.33123 128754.7153 113253.2876 101315.4607 103304.2169 124326.695 77400.92305 122114.5177 1.04397961 0.782825278 1.054376807 0.927435081 0.829675805 0.845961798 1.018115597 0.63383883 1 16.8978752 2.976255884 23.27555798 0.877705913 0.941361974 0.096961255 0.127319839 1006.8429 986975.1734 0.036053464 0.038492875 946.7948432 -2.976255884 0.063656061 S(ph)RS(ph)RDKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRSRDKEER 9 3 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 2 S(1)RS(1)RDKEER;S(1)RS(1)RDKEER;S(1)RS(1)RDKEER;S(1)RS(1)RDKEER 89.46 0.022041 1306990000 1599018 932661 1578070 1432694 848256 1535690 2181580 1360579 1017829 TRUE FALSE 1523435.588 1027700.216 1650426.07 1288676.877 996191.5778 1482508.67 1848739.904 1241439.49 1175668.723 1.295803451 0.874140986 1.403818982 1.096122447 0.847340376 1.260991843 1.572500712 1.055943282 1 20.16505017 2.021142738 24.98910149 1.309006049 1.098915894 0.007519693 0.229614979 409.9611462 484540.7989 0.080696781 0.059593365 104.9887435 -2.021142738 -0.210090155 S(ph)RS(ph)RS(ph)PPPVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.999)PPPVS(0.002)K;S(1)RS(1)RS(1)PPPVSK;S(1)RS(1)RS(0.999)PPPVS(0.001)K 62.203 0.054456 2364290000 3403880 3109940 2906810 3708010 1662700 3351650 3423600 2391750 1762490 TRUE FALSE 3242985.338 3426846.422 3040090.114 3335273.79 1952674.354 3235581.52 2901266.941 2182315.691 2035807.948 1.592972138 1.683285708 1.493308894 1.63830473 0.959164324 1.589335342 1.425118192 1.071965405 1 20.95717004 1.890025507 0.205419385 0.864245191 1.844732887 0.481690804 0.197749108 2.472265738 0.467559438 0.761170547 0.978901964 77.62927092 -1.890025507 0.980487695 S(ph)RS(ph)RSPHEAGFCVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSRSPHEAGFCVYLK 16 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(0.666)RS(0.666)RS(0.666)PHEAGFCVY(0.001)LK 54.7 0.075615 95191000 137070 79207 114030 125140 111980 113140 158580 115510 110520 TRUE FALSE 130590.9727 87278.28335 119258.3883 112560.6894 131509.2765 109221.9334 134385.7085 105395.332 127658.8771 1.022968208 0.683683621 0.934195811 0.881730217 1.030161627 0.855576485 1.0526938 0.825601277 1 16.96193434 2.924360948 7.681905689 0.956254081 0.864485774 0.091701801 0.108809706 0.564867539 51.51412134 0.030967084 0.032956948 840.1579627 -2.924360948 -0.091768308 S(ph)RS(ph)RT(ph)PLISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSRTPLISR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(0.998)RT(0.995)PLIS(0.007)R 47.548 0.064265 0 312560 211220 275730 300300 223660 252690 360340 192690 243650 TRUE FALSE 297785.9082 232743.5581 288372.4932 270113.2735 262666.2332 243939.2819 305363.5149 175817.0421 281433.9976 1.058102115 0.826991622 1.024654078 0.959774852 0.933313798 0.866772615 1.085027102 0.624718561 1 18.10243709 1.25421775 24.99977845 0.812359018 0.959579037 0.220966251 0.118780532 292.3176788 466748.1284 0.070189433 0.025439075 17.95633712 -1.25421775 0.147220018 S(ph)RSDIDVNAAAGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.695)RS(0.305)DIDVNAAAGAK 224.86 1.81E-12 2686500000 3065620 2664950 2669220 3300370 2242190 3094040 3502610 3402060 2632680 TRUE FALSE 2920714.218 2936511.435 2791606.377 2968610.537 2633227.226 2986892.619 2968222.515 3104157.591 3040942.569 0.960463459 0.965658301 0.918006938 0.976213944 0.865924682 0.982225922 0.976086344 1.02078797 1 21.53608714 1.681448532 2.24359469 1.006426212 0.944233918 0.4074116 0.033343232 0.277756766 3.022871377 0.021511183 0.008714327 48.02291647 -1.681448532 -0.062192294 S(ph)RSDIDVNAAASAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(0.5)RS(0.5)DIDVNAAASAK 165.3 2.34E-07 1494550000 1364070 1124310 1227270 1468610 1159500 1273050 1525410 1446860 2163030 TRUE FALSE 1299593.114 1238878.467 1283541.543 1320982.533 1361716.433 1228963.959 1292680.688 1320165.268 2498461.645 0.52015732 0.495856508 0.513732739 0.528718356 0.545021948 0.491888263 0.517390648 0.528391249 1 21.25260864 0.352540592 2.332321936 1.000001128 0.514682689 0.990293363 0.015012294 1.65321081 5.802416443 0.01419883 0.003818422 2.251855881 -0.352540592 -0.485318439 S(ph)RSESETSTMAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.432)RS(0.432)ES(0.129)ET(0.006)STMAAK;S(0.495)RS(0.495)ES(0.01)ETSTMAAK;S(0.454)RS(0.454)ES(0.092)ETSTMAAK 159.18 2.79E-05 1089550000 1212200 959850 1169900 1259350 877880 1230340 1370290 1300040 1056520 TRUE FALSE 1154901.708 1057659.806 1223541.072 1132757.745 1030981.994 1187733.017 1161227.093 1186201.606 1220359.726 0.946361703 0.866678721 1.002606892 0.928216264 0.844818108 0.97326468 0.951544917 0.972009794 1 20.21887504 S(ph)RSFTLDDESLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.728)RS(0.272)FTLDDESLK 243.83 1.39E-16 403130000 1400200 1131400 1256400 1521900 972750 1432500 1551600 1393000 980330 TRUE FALSE 1334015.321 1246690.946 1314007.183 1368915.721 1142397.292 1382892.166 1314874.923 1271021.535 1132354.57 1.178089758 1.100972239 1.160420259 1.208910846 1.008868885 1.221253663 1.161186574 1.122458962 1 20.11089434 0.85970603 4.87006006 1.000005292 1.147606992 0.377575631 0.059523017 1.385068779 47.13555331 0.051497369 0.013030778 7.239457614 -0.85970603 0.1476017 S(ph)RSGEGEVSGLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.629)RS(0.371)GEGEVSGLMR 135.09 5.33E-05 720040000 527910 471400 491120 477970 502770 419160 470430 474060 478870 TRUE FALSE 502956.7405 519436.1959 513638.3378 429923.5475 590452.9288 404644.3841 398657.2635 432548.7932 553130.7139 0.909290929 0.939083987 0.928602092 0.777254882 1.067474494 0.731552911 0.72072885 0.78200104 1 19.07726093 2.206089252 24.99985135 0.776460453 0.918491531 0.206608443 0.104284899 217.1621502 167192.9279 0.034737061 0.025656909 160.7271529 -2.206089252 0.142031078 S(ph)RSHSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.496)RS(0.496)HS(0.007)DNDRPNCSWNTQYSSAYYTSR;S(0.485)RS(0.485)HS(0.03)DNDRPNCSWNTQYSSAYYTSR;S(0.497)RS(0.497)HS(0.006)DNDRPNCSWNTQYSSAYYTSR 340.6 9.61E-96 2126400000 249370 205967 244882 256245 249405 260038 312183 275451 279343 TRUE FALSE 237582.7743 226955.2715 256110.0819 230486.7658 292901.153 251032.8189 264553.7497 251331.0502 322662.0858 0.736320705 0.703383761 0.793740862 0.71432863 0.907764395 0.778005319 0.819909625 0.778929602 1 18.29966454 -4.999999999 0.110482849 1.729931967 0.643802698 0.654797857 0.053127914 91.93525313 0.674540324 15.16525589 0.596755806 1.00E-05 4.999999999 -1.086129269 S(ph)RSHTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.318)RS(0.225)HT(0.225)S(0.225)EGAHLDIT(0.009)PNSGAAGNSAGPK;S(0.307)RS(0.231)HT(0.231)S(0.231)EGAHLDITPNSGAAGNSAGPK;S(0.307)RS(0.228)HT(0.228)S(0.228)EGAHLDIT(0.008)PNSGAAGNSAGPK;S(0.26)RS(0.186)HT(0.26)S(0.26)EGAHLDIT(0.035)PNSGAAGNSAGPK 137.89 4.76E-06 1494760000 771490 552313 754100 914360 974610 824790 1327080 1156710 287332 TRUE FALSE 735023.1966 608594.3226 788676.2309 822446.7956 1144581.675 796227.3155 1124609.573 1055422.34 331889.9791 2.214659203 1.833723104 2.3763183 2.478070588 3.448678019 2.39907007 3.38850114 3.18003678 1 18.34034554 3.249609798 2.334015714 2.852262731 2.039116646 0.081574019 0.710695381 0.42112581 4.700188514 0.192331167 0.261860109 1776.682391 -3.249609798 -0.813146085 S(ph)RSKDSVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSKDSVPK 9 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.596)RS(0.366)KDS(0.038)VPK;S(0.577)RS(0.405)KDS(0.018)VPK 50.284 0.084667 1042060000 2142580 2027090 1634040 2216130 896370 2044170 1788090 1950500 749080 TRUE FALSE 2041304.49 2233652.776 1708962.35 1993360.402 1052696.644 1973379.88 1515284.03 1779703.88 865243.5006 2.359225453 2.581530834 1.975123013 2.30381436 1.216647849 2.280721992 1.751280453 2.056882113 1 19.72274667 1.136100537 0.10100359 1.21E-14 3.476464638 0.527719793 0.346853867 8.825722464 0.716578634 12.51650332 10.39416547 13.68045486 -1.136100537 3.476464638 S(ph)RSPAPPADKEAEKPVFFPAFAAEAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPAPPADKEAEKPVFFPAFAAEAQK 27 3 C9J0Q5;C9JE98 C9J0Q5 NCOR2 1 S(0.5)RS(0.5)PAPPADKEAEKPVFFPAFAAEAQK 137.34 7.71E-06 295760000 464160 473460 436900 543660 235540 580390 528870 611780 260580 TRUE FALSE 442220.0767 521706.1123 456932.2972 489010.2639 276618.1014 560290.9488 448181.1681 558209.3 300989.4155 1.469221354 1.733303848 1.518100882 1.624675948 0.919029332 1.861497182 1.489026341 1.854581162 1 18.19935323 S(ph)RSPATAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RS(0.5)PATAK;S(0.556)RS(0.444)PATAK;S(0.5)RS(0.5)PATAK;S(0.5)RS(0.5)PATAK 55.401 0.075196 609455000 529909 492996 407875 517855 293467 456814 509413 572489 423171 TRUE FALSE 504861.2517 543232.8529 426576.4722 465799.2315 344647.5519 440994.4166 431692.6908 522358.8282 488794.1974 1.032870796 1.111373367 0.872711817 0.952955731 0.70509747 0.90220878 0.883178837 1.068668227 1 18.89886763 3.735947733 24.95199092 0.898991383 1.072122086 0.316154779 0.096339855 207.4854574 1981406.476 0.023804058 0.038797933 5444.371263 -3.735947733 0.173130702 S(ph)RSPES(ph)QVIGENTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.995)RS(0.009)PES(0.996)QVIGENTK 173.87 3.15E-05 181610000 681770 660410 559410 747680 342650 660880 592810 567420 259850 TRUE FALSE 649544.0832 727706.5298 585059.5018 672521.7859 402408.0515 637993.5599 502365.9468 517733.6967 300146.2109 2.164092231 2.424506802 1.949248335 2.240647263 1.340706752 2.125609242 1.673737427 1.724938307 1 18.19530593 0.071728178 0.124629526 4.44E-12 2.881035855 0.650670617 0.256550179 11.01065279 0.480675059 7.36070415 3.304556432 1.179582113 -0.071728178 2.881035855 S(ph)RSPES(ph)QVIGENTKQP ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPESQVIGENTKQP 16 2 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.875)RS(0.399)PES(0.726)QVIGENTKQP 196.92 2.20E-10 829740000 643730 422750 592850 564260 367550 615440 740960 626000 442790 TRUE FALSE 613302.1586 465828.7056 620032.7589 507539.5128 431650.6036 594127.1585 627912.9433 571184.1214 511455.6117 1.199130764 0.910790096 1.21229046 0.992343228 0.843964938 1.16163973 1.227697827 1.116781414 1 18.96424951 S(ph)RSPHEAGFCVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.632)RS(0.368)PHEAGFCVYLK 168.09 2.15E-06 507190000 430650 326310 315960 351890 347970 346080 460710 369610 329850 TRUE FALSE 410294.028 359561.36 330447.0785 316517.3487 408655.8578 334095.1628 390420.228 337244.989 381001.4534 1.076883105 0.943727004 0.867311858 0.830751027 1.072583462 0.876886846 1.024721099 0.885154075 1 18.53943698 4.486839706 2.565686107 0.938306702 1.076897983 0.245959927 0.076455543 0.42411148 4.945499145 0.017943114 0.099668363 30678.89453 -4.486839706 0.138591281 S(ph)RSPIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.577)RS(0.423)PIER;S(0.633)RS(0.367)PIER 70.1 0.035091 1023480000 321480 256930 335800 305790 277256 327540 375470 354590 406180 TRUE FALSE 306284.2775 283111.4591 351196.7622 275051.4082 325609.3586 316197.2077 318185.1555 323540.2198 469168.3199 0.652823868 0.6034326 0.74855174 0.586253156 0.694013949 0.673952597 0.678189771 0.689603722 1 18.83974607 -5 0.278173092 3.463465046 0.638677676 0.852146303 0.044040749 71.20557662 0.683513461 101.1009456 0.044658649 1.00E-05 5 -2.82478737 S(ph)RSPIIHS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.804)RS(0.209)PIIHS(0.987)PK;S(0.572)RS(0.428)PIIHS(1)PK 54.471 0.077895 311060000 796930 693880 697080 826300 560390 826290 854400 816360 591630 TRUE FALSE 759260.6983 764587.1609 729041.8075 743238.7541 658121.8386 797675.3701 724045.5879 744875.1906 683376.9588 1.111042286 1.118836611 1.066822342 1.087597035 0.963043647 1.16725529 1.059511268 1.089991667 1 19.38232208 -5 0.107766658 0.751065074 1.133720884 0.198559961 0.052173209 267.8824085 1.929698747 15.15224135 0.643513987 1.00E-05 5 0.382655811 S(ph)RSPIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPIQR 7 1 Q9Y252 Q9Y252 RNF6 E3 ubiquitin-protein ligase RNF6 1 S(0.634)RS(0.366)PIQR 64.04 0.045907 54081000 18081 16071 18956 23745 20264 19288 18442 18701 26380 TRUE FALSE 17226.34696 17708.65317 19825.15135 21358.10749 23798.03518 18620.05172 15628.33419 17063.4413 30470.87567 0.5653381 0.581166533 0.650626243 0.700935139 0.781009231 0.611077014 0.51289416 0.559991826 1 14.89514334 -2.079035443 2.565820262 1.616178294 0.613742002 0.705164532 0.077036779 10863030.7 3082082.43 39215215.56 0.020360603 0.008336131 2.079035443 -1.002436292 S(ph)RSPITTNHRPSPDPEQRPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR;S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR 95.123 0.0010508 446620000 160056 149973 144776 170772 160033 142207 179175 160490 173506 TRUE FALSE 152490.4701 165255.4192 151414.1228 153605.6741 187942.7045 137282.3359 151838.563 146436.6448 200412.4243 0.760883316 0.824576719 0.755512655 0.766447862 0.937779707 0.684999128 0.757630489 0.73067648 1 17.61261242 -2.233574902 2.416160633 1.811722591 0.77867586 0.524513947 0.066621431 9281142.885 1182686.698 41456480.09 0.016330827 0.005840165 2.233574902 -1.033046731 S(ph)RSPLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Trastuzumab_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(0.499)RS(0.499)PLDKDT(0.002)YPPSASVVGASVGGHR 163.22 9.56E-12 165670000 91758 72264 86332 95050 88656 91036 120170 101480 97237 TRUE FALSE 87420.78119 79627.78376 90290.40759 85495.39342 104117.5783 87883.40049 101835.8594 92593.87322 112316.0173 0.77834652 0.70896196 0.803896094 0.761203927 0.927005611 0.782465427 0.906690442 0.824404884 1 16.77720416 1.262155804 0.162724706 1.096871594 0.648351548 0.610525738 0.054705882 2.561753073 0.390350665 0.490586679 0.40533774 18.2875617 -1.262155804 -0.448520046 S(ph)RSPLGFYVHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.5)RS(0.5)PLGFYVHLK 113.59 0.00069434 62694000 202620 152480 132670 139130 161860 125380 200870 159770 160090 TRUE FALSE 193042.5542 168017.8854 138753.0507 125144.3881 190088.3328 121038.0592 170223.5923 145779.6918 184915.9396 1.043947615 0.908617644 0.750357438 0.67676366 1.027971592 0.654557197 0.920545804 0.788356548 1 17.49651006 4.175046555 2.511481795 0.825208949 1.023818179 0.219619438 0.12510716 0.35193095 4.349778835 0.028939352 0.088413387 14963.96056 -4.175046555 0.19860923 S(ph)RSPLLVTVVESDPRPQGQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 101.59 0.00027093 1000203000 456412 416274 485317 509230 478940 435215 551130 455850 519240 TRUE FALSE 434838.3093 458692.7939 507569.2645 458041.2329 562466.9844 420143.3954 467044.9963 415933.3574 599761.0873 0.725019209 0.764792521 0.846285755 0.763706153 0.937818402 0.70051793 0.778718403 0.693498405 1 19.1940284 -2.304256682 2.390779705 2.198210281 0.77557971 0.488810681 0.071891827 3759454.041 611305.1305 24526708.1 0.016109763 0.004962989 2.304256682 -1.422630572 S(ph)RSPNRFDAHDPR ddPTM_SK-BR-3_Trastuzumab_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 77.078 0.01405 4650830000 2882320 2360660 2641530 2989730 3220610 2599600 3335070 2983100 2850950 TRUE FALSE 2746078.446 2601213.938 2762646.763 2689196.66 3782283.364 2509575.2 2826243.819 2721883.95 3293060.765 0.833898504 0.789907664 0.838929786 0.816625277 1.148561668 0.762079834 0.858242231 0.826551389 1 21.6509977 -5 0.123399541 1.421916472 0.792627495 0.137748177 0.106989493 303.1936012 2.40375878 32.82063759 0.900240644 1.00E-05 5 -0.629288977 S(ph)RSPPPVS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(1)RS(0.026)PPPVS(0.974)K 131.32 0.0040218 342740000 880040 1091700 775240 1049400 376160 961060 822070 807830 375450 TRUE FALSE 838442.2533 1202945.471 810785.5208 943912.3183 441762.1849 927778.2512 696648.1231 737092.1226 433672.8685 1.933351875 2.773854577 1.869578615 2.176553773 1.018653038 2.139350461 1.606390839 1.699650073 1 18.72624766 1.951619818 0.199596303 0.773737227 2.723678923 0.408460505 0.407461542 2.837198435 0.497455448 1.642200978 2.205668177 89.45813041 -1.951619818 1.949941695 S(ph)RSPQWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RS(0.5)PQWR 99.815 0.0062082 155310000 40130 34249 35522 33960 37900 30793 42737 36228 39365 TRUE FALSE 38233.13443 37739.01204 37150.71884 30546.27628 44509.748 29726.63069 36216.68573 33055.68426 45469.52315 0.840851889 0.829984777 0.81704659 0.671796715 0.978891902 0.653770452 0.79650463 0.726985505 1 15.47261225 3.467462034 24.98390008 0.788479182 0.833434586 0 0.113857659 786.1562462 2033411.349 0.027663946 0.037503152 2934.012999 -3.467462034 0.044955405 S(ph)RSPVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.639)RS(0.361)PVDLR 84.658 0.010474 246210000 202070 166570 149360 187760 168280 141660 190620 176300 172860 TRUE FALSE 192518.5516 183543.6724 156208.3037 168886.0081 197627.9787 136754.2787 161537.418 160862.2374 199666.246 0.964201789 0.919252383 0.782347076 0.845841556 0.989791628 0.684914358 0.809037187 0.805655641 1 17.60723094 2.250039908 24.99947904 0.804562243 0.900847826 0.118189103 0.095373169 345.0376172 751419.0275 0.031249562 0.025935999 177.8442826 -2.250039908 0.096285584 S(ph)RSSSS(ph)PPPKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.712)RS(0.131)S(0.156)S(0.04)S(0.96)PPPKQK 69.729 0.026382 59021000 304540 219630 300440 290680 240160 308630 419790 320400 331190 TRUE FALSE 290144.9977 242010.5467 314215.4712 261460.2941 282043.828 297942.0657 355743.3255 292344.0775 382549.2537 0.75845135 0.63262585 0.82137259 0.683468316 0.737274548 0.778833216 0.929928165 0.764199837 1 18.54528598 1.369318107 0.478407593 0.995815177 0.696482568 0.57707352 0.070358337 0.567928833 0.349111638 0.072872401 0.043495174 23.40550989 -1.369318107 -0.299332609 S(ph)RST(ph)PVRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSTPVRDR 9 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.994)RS(0.165)T(0.841)PVRDR 63.364 0.084485 259850000 302680 216650 265930 262060 245900 276670 314550 278250 270680 TRUE FALSE 288372.9163 238726.8813 278123.1535 235717.2309 288784.8821 267088.8485 266559.6204 253884.9549 312655.672 0.922333871 0.76354566 0.889550961 0.753919574 0.923651506 0.854258766 0.852566079 0.812027344 1 18.25421516 -1.512786556 2.954963984 1.005601911 0.845299761 0.408597693 0.058028353 10703934.76 11613227.55 482058.9468 0.013015109 0.030705307 1.512786556 -0.16030215 S(ph)RSTCGDSEVEEESPGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSTCGDSEVEEESPGKR 18 2 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 S(0.424)RS(0.424)T(0.151)CGDS(0.001)EVEEESPGKR 72.302 0.011525 36868000 61309 47061 71076 71945 60711 69849 77809 79495 76687 TRUE FALSE 58411.04507 51856.5694 74334.9049 64712.95191 71298.97918 67430.11162 65937.80799 72533.99637 88579.2283 0.659421472 0.585425843 0.839191155 0.730565768 0.804917592 0.761240676 0.74439357 0.818860107 1 16.43468081 -5 0.041154166 2.276003302 7.42E-08 0.686444178 0.061865108 431.7601593 1.325464211 67.06093238 19.49251643 1.00E-05 5 -2.276003228 S(ph)RSVDSAFPFGLQGNSEYLIEFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSVDSAFPFGLQGNSEYLIEFSR 24 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.498)RS(0.498)VDS(0.004)AFPFGLQGNSEYLIEFSR 156.26 1.81E-08 35108000 25891 21232 25019 26975 23820 20734 31049 27132 29010 TRUE FALSE 24667.18374 23395.56494 26166.1459 24263.42175 27974.20046 20015.97638 26311.9048 24756.17824 33508.72264 0.736142168 0.698193279 0.78087566 0.724092709 0.834833388 0.597336299 0.785225539 0.738798029 1 15.03224907 0.185761247 1.388929533 1.000219345 0.732689292 0.637172211 0.062378102 4.928812007 7.746371023 0.054170601 0.015339659 1.533773561 -0.185761247 -0.267530053 S(ph)RSVS(ph)PCSNVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.5)RS(0.5)VS(0.939)PCS(0.058)NVES(0.003)R 117.2 0.0062833 263810000 271410 195090 234720 257940 268640 238540 265730 232410 291410 TRUE FALSE 258580.9872 214969.8928 245482.1442 232011.3811 315490.7309 230279.3 225188.008 212058.9483 336600.3745 0.768213605 0.638650189 0.729298488 0.68927844 0.93728574 0.684132632 0.669007004 0.630002116 1 18.36067726 -2.076528953 2.462557457 1.439684665 0.715126709 0.504542747 0.087701732 7125557.618 2433456.489 17581936.74 0.020253845 0.008384382 2.076528953 -0.724557956 S(ph)RT(ph)PDRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTPDRER 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 S(1)RT(1)PDRER 43.382 0.096737 0 69300 50063 57873 69066 45404 62597 64981 67711 49743 TRUE FALSE 66024.32634 55164.47662 60526.53429 62123.35446 53322.44322 60429.25019 55066.95499 61781.86588 57456.89039 1.149110679 0.960102022 1.053425166 1.081216788 0.928042622 1.051731999 0.958404721 1.0752734 1 15.81019229 4.663256524 3.347937438 1.011769447 1.156824728 0.394015543 0.052650335 0.249545844 4.574775912 0.011486712 0.082236755 46052.85131 -4.663256524 0.145055281 S(ph)RT(ph)PPVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTPPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RT(0.999)PPVT(0.001)R 83.617 0.041325 2945200000 618260 589350 446660 613750 329590 460250 463050 600990 351730 TRUE FALSE 589036.0751 649405.435 467139.8028 552054.684 387070.3916 444311.4271 392403.218 548364.1296 406274.492 1.449847546 1.598440089 1.149813272 1.358821917 0.952731218 1.093623734 0.965857384 1.349738023 1 18.63209526 3.4144669 1.348763165 1.072763093 1.528179744 0.535684821 0.150159356 0.26210445 0.981015425 0.046372952 0.082482379 2596.969803 -3.4144669 0.455416651 S(ph)RT(ph)SPAPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.941)RT(0.768)S(0.291)PAPWK 75.479 0.087414 933160000 3131500 3051600 2603600 3330600 1866100 3014700 2900100 2273400 1624700 TRUE FALSE 2983480.201 3362561.509 2722977.635 2995801.76 2191547.249 2910300.183 2457636.481 2074329.044 1876650.178 1.589790274 1.791789194 1.450977741 1.596355994 1.167797427 1.55079525 1.309586896 1.105336023 1 20.83972832 2.023645758 0.340090071 0.962671217 1.763793935 0.679916666 0.141398943 0.754206016 0.243186734 0.177881873 0.212106416 105.5955844 -2.023645758 0.801122718 S(ph)RTGSESSQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.416)RT(0.416)GS(0.167)ES(0.001)SQTGTSTTSSR;S(0.333)RT(0.333)GS(0.333)ES(0.001)SQTGTSTTSSR;S(0.332)RT(0.332)GS(0.332)ES(0.003)SQTGTSTTSSR;S(0.332)RT(0.332)GS(0.332)ES(0.004)S(0.001)QTGTSTTSSR;S(0.321)RT(0.321)GS(0.321)ES(0.036)SQTGTSTTSSR;S(0.332)RT(0.332)GS(0.332)ES(0.005)SQTGTSTTSSR 132.66 8.68E-06 1130569000 101104.1 45159.6 92772.6 76672.8 104651.7 76468.9 127207.6 94515.8 133896.8 TRUE FALSE 96325.10956 49761.41458 97026.31547 68965.50448 122902.9233 73820.76282 107799.7443 86239.49549 154660.8319 0.622815152 0.321745422 0.627348982 0.44591448 0.794660948 0.477307421 0.6970074 0.557603981 1 17.23874835 -5 0.16123667 2.696073942 0.43677375 0.526436985 0.130624162 92.04766109 0.849050531 49.65525859 0.48103848 1.00E-05 5 -2.259300191 S(ph)RTLTAVHDAILEDLVFPSEIVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTLTAVHDAILEDLVFPSEIVGK 24 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 1 S(0.333)RT(0.333)LT(0.333)AVHDAILEDLVFPS(0.001)EIVGK;S(0.333)RT(0.333)LT(0.333)AVHDAILEDLVFPS(0.001)EIVGK 67.992 0.020897 84588000 152410 96110 111001 142280 113104 133865 196375 137191 114945 TRUE FALSE 145205.8813 105903.7183 116090.5056 127977.7441 132829.3018 129229.2215 166414.3871 125177.8287 132770.0835 1.093664156 0.797647448 0.874372468 0.963904975 1.000446021 0.973330874 1.253402744 0.942816525 1 17.01857058 1.974797853 23.29256395 1.098513477 0.940934549 0.176161226 0.110702014 380.7992728 351944.5671 0.043674488 0.028346517 94.36215545 -1.974797853 -0.157578928 S(ph)RTPPSAPSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RT(0.5)PPSAPSQSR 68.481 0.031827 3484600000 237250 194060 220610 236020 223750 212010 251170 220870 248300 TRUE FALSE 226035.6627 213834.9346 230725.1867 212294.8212 262771.9292 204668.0405 212849.4034 201529.4519 286805.0959 0.788115922 0.745575785 0.804466831 0.74020589 0.916203837 0.713613682 0.742139545 0.702670402 1 18.12971113 -1.16110323 4.896512127 1.000018083 0.768293912 0.590425032 0.060428297 1.10E-05 1.89E-06 0.054021417 0.012731977 0.069007576 1.16110323 -0.231724171 S(ph)RTPS(ph)ASNDDQQE ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.607)RT(0.393)PS(0.944)AS(0.055)NDDQQE;S(0.992)RT(0.008)PS(0.97)AS(0.03)NDDQQE;S(0.886)RT(0.114)PS(0.937)AS(0.063)NDDQQE;S(0.968)RT(0.032)PS(0.975)AS(0.024)NDDQQE;S(0.886)RT(0.114)PS(0.999)AS(0.001)NDDQQE;S(1)RTPS(0.993)AS(0.007)NDDQQE 223.29 1.92E-10 434441000 794739 564346 681577 766415 702657 565202 694543 525011 527169 TRUE FALSE 757173.2625 621853.499 712827.9796 689373.5081 825200.1583 545628.913 588577.7092 479038.2536 608919.6761 1.243469857 1.021240606 1.170643695 1.132125525 1.355187212 0.896060572 0.966593349 0.786701879 1 19.21589241 2.209272448 24.99999236 0.915184186 1.164610554 0.641470943 0.100495984 137.3426496 117233.0656 0.035620534 0.026311509 161.9095435 -2.209272448 0.249426367 S(ph)RTPSNDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.5)RT(0.5)PSNDGK;S(0.5)RT(0.5)PSNDGK 107.97 0.0016278 171210000 391620 345470 336210 417130 227760 352350 386950 439580 338990 TRUE FALSE 373108.8987 380673.7858 351625.5611 375199.2999 267481.2719 340148.0312 327913.6707 401088.0448 391558.8379 0.9528808 0.972200724 0.89801462 0.958219464 0.683118975 0.868702219 0.837456951 1.02433659 1 18.57886959 S(ph)RTS(ph)PAPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.993)RT(0.107)S(0.899)PAPWK;S(0.731)RT(0.463)S(0.807)PAPWK 89.359 0.0069194 888970000 2996300 2844900 2419820 3224900 1801060 2830590 2807900 2306220 1646430 TRUE FALSE 2854670.837 3134798.544 2530771.141 2900726.925 2115164.294 2732565.959 2379503.284 2104275.151 1901749.956 1.501075801 1.648375768 1.330759143 1.525293542 1.112219978 1.436869211 1.251217742 1.106494124 1 20.85889614 2.238483596 0.298901035 0.964186227 1.672536195 0.647578723 0.123943875 1.051796126 0.254828069 0.175472391 0.267581055 173.1743619 -2.238483596 0.708349968 S(ph)RTS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.854)RT(0.249)S(0.876)PVS(0.021)R;S(0.93)RT(0.071)S(0.992)PVS(0.007)R;S(0.947)RT(0.053)S(1)PVSR 93.614 0.006227 501610000 94428 88423.5 91239 107281 86075.5 97290 107707.2 121287 96493.2 TRUE FALSE 89964.57558 97433.95518 95422.3984 96496.91006 101087.0399 93920.82291 91274.48846 110666.4673 111456.8726 0.807169387 0.87418526 0.856137411 0.865778016 0.906961029 0.842665155 0.818922031 0.99290842 1 16.76612605 1.229457656 24.99748182 0.996454357 0.852300208 0.821740193 0.027752905 86.64135268 237915.5416 0.025813124 0.006818844 16.96124221 -1.229457656 -0.144154149 S(ph)RTS(ph)PVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.89)RT(0.112)S(0.998)PVTR;S(0.813)RT(0.199)S(0.988)PVTR;S(0.886)RT(0.115)S(0.998)PVTR 92.781 0.0065633 2354050000 258332 271357 242072 328051 231689 263192 279516 225669 244473 TRUE FALSE 246121.1583 299008.5868 253171.2406 295074.6902 272095.4882 254077.595 236870.7005 205908.226 282384.6242 0.871581302 1.058869928 0.896547542 1.044938941 0.963563399 0.899757187 0.838822939 0.729176479 1 18.10730201 2.038051396 2.760772242 0.840600496 0.971449144 0.255786743 0.08599887 0.304548874 4.511548653 0.037802553 0.022537896 109.156951 -2.038051396 0.130848648 S(ph)RTSPAPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 73.466 0.02655 982510000 1932500 2275500 1758600 2527900 1524800 2122900 2120600 2083400 1478300 TRUE FALSE 1841154.555 2507376.037 1839233.549 2273790.689 1790724.637 2049383.441 1797063.523 1900966.451 1707547.214 1.078245181 1.468408028 1.077120172 1.331612193 1.048711639 1.200191376 1.052423914 1.113273142 1 20.70349404 2.17186479 0.70311761 1.03227545 1.258316906 0.24121 0.126875489 0.85844938 0.815860086 0.099322097 0.06137968 148.5473093 -2.17186479 0.226041456 S(ph)RTSPAPWKR ddPTM_SK-BR-3_Trastuzumab_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 59.898 0.053015 75242000 112350 82635 103430 105800 151650 89962 121270 110930 145340 TRUE FALSE 107039.4382 91055.60045 108172.3678 95164.78299 178097.712 86846.59338 102768.0342 101216.3811 167878.5849 0.637600312 0.542389612 0.644348818 0.566866721 1.06087213 0.517317878 0.612156901 0.602914191 1 17.35705868 -2.21159606 2.12088892 2.012223732 0.639839595 0.34364575 0.152481944 6690833.793 1194606.126 32486752.7 0.034681262 0.006143331 2.21159606 -1.372384137 S(ph)RTSPITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.394)RT(0.239)S(0.367)PITR 72.652 0.027615 1326500000 211790 152080 152950 231800 186380 164450 207290 162730 156200 TRUE FALSE 201779.1064 167577.1249 159962.9088 208499.0236 218884.613 158755.0553 175664.1034 148480.4985 180422.6982 1.118368744 0.928802897 0.886600801 1.155614153 1.213176696 0.879906225 0.973625298 0.822959084 1 17.46102132 S(ph)RTSPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.473)RT(0.264)S(0.264)PVSR;S(0.468)RT(0.266)S(0.266)PVSR 91.937 0.0073478 1207970000 195884 169323 169582 185438 170319 135475 163745 179108 166846 TRUE FALSE 186624.9515 186577.2062 177357.5024 166797.4199 200022.5797 130783.4668 138762.6929 163424.354 192719.6255 0.968375437 0.968127692 0.920287708 0.865492653 1.03789419 0.678620387 0.720023674 0.847990201 1 17.55614397 2.240752414 24.99976242 0.77709087 0.950338514 0.316851412 0.096654033 50.87887296 580335.1032 0.031621552 0.02526722 174.0814174 -2.240752414 0.173247644 S(ph)RYMELYDLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRYMELYDLNR 11 1 J3QKP7;J3QLW0;H3BRL0;Q9BXC9 J3QKP7 BBS2 Bardet-Biedl syndrome 2 protein 1 S(0.389)RY(0.306)MELY(0.306)DLNR 79.693 0.040117 783560000 256520 255770 262480 300850 216100 236380 269840 256080 176040 TRUE FALSE 244394.808 281833.2538 274514.9676 270607.9864 253787.7716 228194.1013 228670.952 233656.2776 203339.3841 1.201905912 1.386023937 1.350033437 1.330819347 1.248099441 1.122232677 1.124577774 1.14909504 1 17.63353015 2.342887644 2.424864367 1.106069864 1.317614966 0.745195765 0.06054103 0.14985246 1.80707554 0.024356294 0.018512314 220.2356617 -2.342887644 0.211545102 S(ph)S(ph)KASLGSLEGEAEAEASSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.58)S(0.619)KAS(0.517)LGS(0.284)LEGEAEAEASSPK 100.95 0.00034948 77779000 285120 210160 246460 282300 140710 265510 312440 275310 149120 TRUE FALSE 271642.9427 231575.5429 257760.4348 253922.6677 165249.7794 256315.3221 264771.5396 251202.3969 172244.768 1.577075146 1.344456181 1.496477587 1.474196695 0.959389254 1.488087709 1.537181899 1.458403642 1 17.39410064 -2.173061135 2.163014207 0.000131648 1.422179818 0.362500159 0.173626696 2123545.881 472835.1956 10391943.03 0.040585071 0.006713343 2.173061135 1.42204817 S(ph)S(ph)SPVTELASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.969)S(0.56)S(0.471)PVTELASR 81.709 0.030602 205300000 431190 399720 380440 468850 262690 434600 441820 421820 294840 TRUE FALSE 410808.5032 440451.9224 397883.5503 421720.3072 308503.0528 419549.693 374412.2444 384883.2046 340562.2814 1.20626542 1.293307998 1.168313616 1.238305973 0.905863831 1.231932354 1.09939434 1.130140434 1 18.37755913 4.337639988 0.151585613 0.962353999 1.494849621 0.307296561 0.097281302 22.99328796 0.692393402 0.454770869 2.520974319 21759.05289 -4.337639988 0.532495621 S(ph)SAIGIENIQEVQEK ddPTM_SK-BR-3_Trastuzumab_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(0.5)S(0.5)AIGIENIQEVQEK;S(0.5)S(0.5)AIGIENIQEVQEK 335.95 4.91E-69 149499000 474150 475730 445080 515830 307620 499290 510390 517780 340290 TRUE FALSE 451737.8692 524207.4279 465487.3582 463977.7884 361268.8306 481999.4621 432520.6315 472440.4383 393060.4352 1.149283491 1.333656051 1.184264089 1.180423535 0.91911777 1.22627316 1.100392186 1.201953684 1 18.58439163 7.999995911 0.032032044 0.428768574 2.241535442 0.205802904 0.103878275 1615.249503 3.963232398 69.30700912 178.5545761 99999058.37 -7.999995911 1.812766869 S(ph)SATLWNSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSATLWNSPSR 11 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.968)S(0.032)ATLWNSPSR;S(0.981)S(0.019)ATLWNSPSR;S(0.988)S(0.012)ATLWNSPSR 241.35 1.06E-15 184955000 312047 218709 243934 253915 277010 253783 322439 216677 262198 TRUE FALSE 297297.1567 240995.6958 255118.6152 228390.9818 325320.4563 244994.4311 273245.0086 197703.6132 302858.3267 0.981637718 0.795737394 0.842369493 0.754118218 1.074167119 0.808940714 0.902220558 0.652792398 1 18.20828355 -0.95145919 6.771075073 1.000000011 0.859057104 0.13419968 0.117150531 1.73E-08 2.78E-09 0.100885099 0.023778844 0.11182549 0.95145919 -0.140942907 S(ph)SDEDAAGEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 S(0.992)S(0.008)DEDAAGEPK;S(0.99)S(0.01)DEDAAGEPK 191.53 1.88E-06 217580000 579350 551270 525560 717610 444150 681940 694780 648450 455880 TRUE FALSE 551965.2737 607445.0397 549657.4458 645474.4794 521609.6194 658324.2468 588778.5505 591668.2804 526575.5421 1.048216694 1.153576251 1.043833984 1.225796544 0.990569401 1.250199058 1.118127417 1.123615195 1 19.00628099 4.679141004 3.454202719 1.121872149 1.043539179 0.044997878 0.08595608 0.699992028 13.85138018 0.017819484 0.129595007 47768.43398 -4.679141004 -0.07833297 S(ph)SDGGSEEPPDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSDGGSEEPPDRR 13 1 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4 Q9HCD6 TANC2 Protein TANC2 1 S(0.5)S(0.5)DGGSEEPPDRR;S(0.5)S(0.5)DGGSEEPPDRR 165.49 2.16E-05 79678000 119298 94773 91705 120595 103950 86752 92460 78657 89409 TRUE FALSE 113659.02 104430.4764 95909.76496 108472.5615 122078.8471 83747.75649 78353.52886 71769.37609 103274.0911 1.100556962 1.011197246 0.928691446 1.050336637 1.182085902 0.810927074 0.758694926 0.694940767 1 16.65611884 2.15620794 8.095037342 0.790536683 1.046631898 0.576761961 0.100382098 0.161649547 13.9597356 0.035128397 0.025937884 143.2873793 -2.15620794 0.256095215 S(ph)SDPLGDTASNLGSAVDELMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSDPLGDTASNLGSAVDELMR 21 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR 177.4 6.79E-17 210400000 112091.1 103406.6 100241.6 125549 107042.5 104646.9 121093.3 115862.7 111010.1 TRUE FALSE 106792.7758 113943.8501 104837.7765 112928.576 125710.6781 101022.9516 102618.2931 105717.1478 128224.9793 0.832854693 0.888624437 0.817608059 0.880706525 0.980391487 0.787857032 0.800298768 0.824466093 1 16.96831781 -2.243487865 2.360914774 1.560409877 0.850867848 0.413601359 0.055525385 4740440.342 696952.3811 14288875.31 0.01351526 0.00570837 2.243487865 -0.709542029 S(ph)SDSEEAFETPESTTPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSDSEEAFETPESTTPVK 18 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK 496.07 1.22E-266 1686260000 2502970 2860120 2107860 3024670 1576390 2554870 2437540 2682970 1685490 TRUE FALSE 2384659.569 3151569.48 2204507.466 2720624.425 1851311.917 2466394.211 2065648.505 2448034.923 1946867.181 1.224870187 1.618790183 1.13233583 1.397437099 0.950918447 1.266852837 1.061011519 1.257422667 1 20.89272303 3.180386218 1.570951794 1.125788045 1.402853714 0.281077088 0.166573568 0.393889456 2.017512264 0.05133014 0.070470789 1514.907856 -3.180386218 0.277065669 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 S(0.873)S(0.127)EDLAGPLPSSVSSSSTTSSKPK 248.73 2.37E-38 321650000 332110 314840 293420 376540 145030 341570 334020 378140 152330 TRUE FALSE 316411.8185 346922.5539 306873.5972 338689.4838 170323.1861 329741.3453 283059.1143 345028.057 175952.5584 1.798279157 1.971682351 1.744070106 1.92489093 0.968006306 1.874035525 1.608724061 1.960915261 1 17.42482697 S(ph)SEHLLRPSQVCPQRPLSQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSEHLLRPSQVCPQRPLSQER 21 2 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.849)S(0.151)EHLLRPSQVCPQRPLSQER 105.03 0.00020891 59217000 11123 8761.3 11759 12936 12013 9124.8 13841 13823 12518 TRUE FALSE 10597.23783 9654.086431 12298.16178 11635.6487 14108.0634 8808.805888 11729.30124 12612.58484 14459.22751 0.732904841 0.667676501 0.85054072 0.804721324 0.975713494 0.609216909 0.811198332 0.872286215 1 13.81970286 -4.999999999 0.109431248 1.711859796 0.647250054 0.336618178 0.099936589 189.7399422 1.382403631 30.35973475 1.230455504 1.00E-05 4.999999999 -1.064609742 S(ph)SFSQHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.5)S(0.5)FSQHAR;S(0.497)S(0.497)FS(0.007)QHAR 138.22 0.00046036 796950000 661610 489480 520490 623430 641290 559610 733290 635100 636290 TRUE FALSE 630337.0065 539358.5685 544354.9813 560761.632 753130.773 540230.5654 621413.1427 579487.2771 734962.6035 0.857645006 0.73385852 0.740656707 0.762979816 1.024719856 0.735044971 0.845503077 0.788458181 1 19.48731132 S(ph)SGDGTEWAEPITFPSGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGDGTEWAEPITFPSGGGK 20 0 Q13033-2 Q13033-2 STRN3 Striatin-3 1 S(0.47)S(0.47)GDGT(0.06)EWAEPITFPSGGGK 170.11 2.82E-15 0 19722 18836 22412 23669 14998 25636 23261 22356 25187 TRUE FALSE 18789.78015 20755.40981 23439.61237 21289.74715 17613.64645 24748.21889 19712.10723 20398.39012 29092.87132 0.645855128 0.713419091 0.805682331 0.731785698 0.60542826 0.850662646 0.677557984 0.701147367 1 14.82837807 -2.190901559 2.296000856 1.782057508 0.714982449 0.61204105 0.070940575 3878980.215 851491.0365 15751237.34 0.015902177 0.006443153 2.190901559 -1.067075059 S(ph)SGFLNLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGFLNLIK 9 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.993)S(0.007)GFLNLIK 117.98 0.0017911 0 133310 134050 119880 132550 110150 98962 174000 145350 136430 TRUE FALSE 127008.7005 147709.8474 125376.6166 119225.8222 129360.1251 95534.92113 147453.1043 132622.3835 157586.8676 0.805959928 0.937323329 0.795603203 0.756572067 0.820881379 0.606236564 0.935694113 0.841582712 1 17.26578779 0.885316927 1.470826712 0.995973792 0.811409659 0.306811466 0.091596617 0.718021454 3.043887611 0.084757999 0.02496613 7.679216762 -0.885316927 -0.184564133 S(ph)SGPYGGGGQYFAKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.869)S(0.131)GPYGGGGQYFAKPR;S(0.96)S(0.04)GPYGGGGQYFAKPR;S(0.59)S(0.41)GPYGGGGQYFAKPR 290.92 9.60E-46 1905280000 1333550 1292450 1344920 1596860 1213790 1587330 1839010 1635310 1557740 TRUE FALSE 1270515.734 1424152.124 1406585.912 1436340.599 1425474.592 1532360.364 1558435.249 1492113.587 1799306.363 0.706114178 0.791500632 0.781737864 0.798274617 0.79223562 0.851639496 0.866131127 0.829271556 1 20.77900942 -5 0.05028323 1.866031455 0.374438813 0.917212739 0.021860747 131.1927907 0.487557209 15.04098612 3.33757635 1.00E-05 5 -1.491592642 S(ph)SGREEDDEELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSGREEDDEELLR 13 1 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 S(0.811)S(0.189)GREEDDEELLR;S(0.95)S(0.05)GREEDDEELLR 193.19 1.26E-06 737190000 688050 619720 608680 769300 563550 685070 784310 801030 587360 TRUE FALSE 655527.2401 682870.1726 636588.5801 691968.5024 661832.9416 661345.8541 664649.1047 730887.5667 678444.789 0.966220466 1.006522835 0.938305652 1.019933403 0.975514813 0.974796866 0.979665723 1.077298519 1 19.37187189 1.265242906 24.99571863 1.038649255 0.981260497 0.422415332 0.028421369 159.2829768 149215.2139 0.01630555 0.005950226 18.41801856 -1.265242906 -0.057388757 S(ph)SGRNSPSAASTSSNDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.333)S(0.333)GRNS(0.333)PSAASTSSNDSK 68.41 0.017284 13719000 10816 9556.2 9093.3 11949 5941.6 9477.6 9574.1 9879.4 6350.6 TRUE FALSE 10304.74912 10529.98764 9510.2368 10747.86382 6977.813159 9149.388336 8113.395205 9014.307362 7335.418614 1.404793599 1.435499213 1.29648181 1.465201154 0.951249482 1.247289189 1.106057559 1.228874293 1 12.84066358 2.753001587 24.99531437 1.124249399 1.401027453 0.683685223 0.098901502 431.9677836 747675.5688 0.026783917 0.028289238 566.2413579 -2.753001587 0.276778054 S(ph)SITEPEGPNGPNIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 S(0.5)S(0.5)ITEPEGPNGPNIQK 181.26 2.45E-09 57435000 172420 181230 148420 201200 106950 178940 168490 183630 130790 TRUE FALSE 164270.0483 199697.543 155225.2038 180974.9937 125602.0461 172743.2629 142783.756 167550.3837 151072.2452 1.087360872 1.321867844 1.027489885 1.197936745 0.831403849 1.143448042 0.945135592 1.109074559 1 17.20487911 3.197766502 1.783058297 1.013793238 1.192622619 0.229118722 0.119287252 0.391945384 2.5713468 0.03482487 0.047487583 1576.763297 -3.197766502 0.17882938 S(ph)SLSASHPMVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLSASHPMVGK 12 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 1 S(0.5)S(0.5)LSASHPMVGK;S(0.5)S(0.5)LSASHPMVGK 185.32 8.49E-06 883910000 2069090 1571440 1716630 2113720 1474450 1908800 2200200 2140700 1488230 TRUE FALSE 1971288.216 1731571.523 1795339.183 1901244.85 1731593.613 1842697.777 1864519.081 1953248.959 1719017.108 1.146753111 1.007303252 1.044398672 1.106006939 1.007316103 1.071948481 1.084642539 1.136259174 1 20.71315247 2.0006197 24.99950629 1.081852857 1.061684188 0.00235333 0.052789847 90.55862031 3653344.048 0.018693967 0.01367367 100.142793 -2.0006197 -0.020168669 S(ph)SLTTAALPFTQSILTQVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLTTAALPFTQSILTQVGR 20 0 Q3MII6;C9JMI8 Q3MII6 TBC1D25 TBC1 domain family member 25 1 S(0.5)S(0.5)LTTAALPFTQSILTQVGR 235.24 1.63E-29 41217000 101940 90525 90132 106790 92426 95598 112100 117130 106120 TRUE FALSE 97121.49823 99749.60042 94264.64135 96055.26631 108545.0651 92287.41729 94997.08614 106873.4763 122576.5476 0.792333445 0.813773943 0.769026728 0.783634946 0.885528816 0.752896203 0.775002135 0.871891714 1 16.90332345 0.943387381 3.739578085 0.999780265 0.796485513 0.768394056 0.035936192 0.120629722 4.485555179 0.032857748 0.008447219 8.77783435 -0.943387381 -0.203294753 S(ph)SLVTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.659)S(0.341)LVTSK 203.19 0.00030614 1944000000 6906800 5644600 5888400 7438500 4308900 7041300 8257200 7573000 6046400 TRUE FALSE 6580329.252 6219791.157 6158388.964 6690767.848 5060370.796 6797458.015 6997412.486 6909867.973 6984044.831 0.942194589 0.890571482 0.881779701 0.958007574 0.724561614 0.973283846 1.001914028 0.989379098 1 22.73563139 2.024084366 24.99901083 0.994882631 0.886878377 0.446048842 0.062013914 206.9531049 214811.532 0.021659652 0.015995959 105.7022825 -2.024084366 -0.108004254 S(ph)SLYGIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLYGIAK 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.618)S(0.382)LYGIAK 129.85 0.0011255 128220000 628180 507650 526760 670460 428910 554280 632990 617650 448550 TRUE FALSE 598487.1763 559380.1122 550912.467 603064.087 503711.7682 535085.1446 536415.7498 563565.2916 518108.8431 1.15513793 1.079657527 1.063314156 1.163971808 0.972212258 1.032765898 1.035334094 1.087735326 1 18.98289568 2.740187535 24.99999808 1.028979268 1.111044824 0.533666675 0.04160414 120.6664542 1854229.789 0.012405529 0.012562501 549.7782255 -2.740187535 0.082065556 S(ph)SPATSLFVELDEEEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPATSLFVELDEEEVK 17 0 A0A087WTL4;A0A087WX97;Q9BXK5-4;Q9BXK5 A0A087WTL4 BCL2L13 Bcl-2-like protein 13 1 S(0.499)S(0.499)PAT(0.001)SLFVELDEEEVK 84.566 0.00459 0 18513 17963 15609 22338 11091 18914 18154 16584 12383 TRUE FALSE 17637.92718 19793.45012 16324.68809 20092.5418 13025.26689 18259.00344 15384.27388 15131.81704 14303.2924 1.233137567 1.38383874 1.141323804 1.404749427 0.910648159 1.276559475 1.07557571 1.05792545 1 13.80405965 2.408242082 0.512622122 1.014708096 1.320560991 0.342701626 0.13083958 0.963738931 0.527662058 0.108319568 0.105303012 256.0012475 -2.408242082 0.305852895 S(ph)SPDDPNYSLVDDYSLLYQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPDDPNYSLVDDYSLLYQ 19 0 Q9H939 Q9H939 PSTPIP2 Proline-serine-threonine phosphatase-interacting protein 2 1 S(0.5)S(0.5)PDDPNYSLVDDYSLLYQ;S(0.5)S(0.5)PDDPNYSLVDDYSLLYQ 155.56 2.59E-08 97212000 260600 194992 217642 250982 206852 221494 264107 224671 218004 TRUE FALSE 248281.9545 214861.9065 227621.101 225752.8125 242926.9233 213823.6072 223812.6265 204997.6162 251810.9469 0.985985548 0.853266743 0.90393648 0.896517071 0.96471947 0.849143414 0.88881214 0.814093345 1 17.94198148 2.218300372 24.9997605 0.878767783 0.915704606 0.057420249 0.059259823 608.1586658 750421.7675 0.020133526 0.014887515 165.3104742 -2.218300372 0.036936823 S(ph)SPELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.783)S(0.217)PELTR;S(0.513)S(0.487)PELTR;S(0.882)S(0.118)PELTR;S(0.603)S(0.397)PELTR;S(0.882)S(0.118)PELTR 199.8 0.00038662 3682470000 2946690 2839350 2311100 3148350 2244720 2653860 2827470 2735590 2562970 TRUE FALSE 2807405.803 3128682.993 2417066.221 2831871.877 2636198.457 2561956.163 2396087.521 2496047.237 2960422.298 0.948312613 1.056836721 0.816459943 0.956576999 0.890480544 0.865402265 0.809373556 0.843138913 1 21.49737156 3.739328534 24.99994463 0.873572749 1.002574668 0.36582289 0.064484763 58.71927186 1911615.376 0.015953544 0.026734717 5486.918811 -3.739328534 0.129001919 S(ph)SPEQPRPSTSK ddPTM_SK-BR-3_Trastuzumab_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(0.49)S(0.49)PEQPRPS(0.009)T(0.009)S(0.002)K 78.964 0.063954 19185000 61451 45617 54437 61676 45508 62778 67198 61501 49938 TRUE FALSE 58546.33301 50265.42416 56932.9903 55476.2113 53444.58079 60603.98212 56945.71092 56115.6464 57682.12999 1.014982162 0.871421083 0.987012621 0.96175733 0.926536187 1.050654373 0.987233151 0.972842827 1 15.81583682 2.257596598 24.99985914 1.001828672 0.949005712 0.2592343 0.042064483 309.94138 407043.6509 0.013962462 0.011664602 180.9658378 -2.257596598 -0.052822961 S(ph)SPGAGPSDHHSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR 240.66 4.85E-18 622724100 192834.1 159659.7 192689.1 221605.5 311975.4 169211.9 286881.1 254650 95141.24 TRUE FALSE 183719.2143 175929.2049 201524.0858 199329.2941 366383.811 163352.0495 243112.1193 232351.496 109895.2576 1.671766537 1.600880773 1.833783279 1.81381161 3.333936505 1.48643402 2.212216656 2.114299571 1 16.7457696 2.983706203 24.90934531 2.117429992 1.694566199 0.050842964 0.592955525 1501.3329 2295185.644 0.160852461 0.175001822 963.1772208 -2.983706203 -0.422863793 S(ph)SPGAGPSDHHSASRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPGAGPSDHHSASRDER 18 1 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)PGAGPSDHHSASRDER;S(0.5)S(0.5)PGAGPSDHHSASRDER;S(0.5)S(0.5)PGAGPSDHHSASRDER 136.96 3.11E-06 207110000 34042 26181.7 46652 34265.7 82283 34285.2 68777 42981.9 59375 TRUE FALSE 32432.90212 28849.645 48791.04035 30821.24674 96633.12915 33097.89493 58283.80547 39218.17697 68582.57175 0.472902974 0.420655631 0.711420396 0.449403485 1.409004164 0.48259921 0.849834061 0.571838821 1 16.06555438 S(ph)SPGGQDEGGFMAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.5)S(0.5)PGGQDEGGFMAQGK;S(0.5)S(0.5)PGGQDEGGFMAQGK;S(0.5)S(0.5)PGGQDEGGFMAQGK 161.24 8.92E-09 138390000 458267 460614 408296 539733 313640 477826 499078 528081 366172 TRUE FALSE 436605.6271 507551.0903 427016.7755 485478.0134 368338.7167 461278.7658 422934.4849 481839.4281 422956.0836 1.032271775 1.200008961 1.009600741 1.147821328 0.870867523 1.090606764 0.999948934 1.139218578 1 18.69014835 S(ph)SPGPDTLVVLEFNPASK ddPTM_SK-BR-3_Trastuzumab_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 192.96 1.55E-14 108379000 108321 129654 99248 128200 75367 117239 105266 122126 83390 TRUE FALSE 103200.881 142865.89 103798.619 115313.0924 88510.98094 113178.984 89205.73836 111432 96321.6953 1.07141886 1.483216108 1.077624502 1.19716635 0.918910124 1.175010299 0.92612301 1.156873326 1 16.55557316 3.270074762 1.96551207 1.039079768 1.269460626 0.252253176 0.140691456 0.344905907 2.738655334 0.040503192 0.057316269 1862.407715 -3.270074762 0.230380858 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.499)S(0.499)PGQT(0.001)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.484)S(0.484)PGQT(0.032)PEEGAQALAEFAALHGPALR;S(0.499)S(0.499)PGQT(0.003)PEEGAQALAEFAALHGPALR;S(0.499)S(0.499)PGQT(0.002)PEEGAQALAEFAALHGPALR 206.11 2.02E-25 2511473200 314014.2 278993.3 281462.5 336193.1 291379.3 304813.1 347434.1 313960.8 297120.8 TRUE FALSE 299171.3711 307423.0345 294367.834 302398.3309 342195.7577 294257.3459 294426.647 286468.7279 343196.7762 0.871719643 0.895763177 0.857723191 0.881122294 0.997083252 0.857401253 0.857894559 0.834706931 1 18.38867648 2.972119571 24.97609786 0.897515079 0.877824482 0.056416481 0.056079186 3332.10106 2984994.51 0.016530646 0.017572396 937.8201734 -2.972119571 -0.019690598 S(ph)SPIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;S(0.5)S(0.5)PIMR 144.83 0.011772 369880000 261050 246200 234183 261010 227107 222126 272420 245930 214587 TRUE FALSE 248710.6839 271288.0599 244920.5222 234772.7789 266714.3889 214433.7209 230857.3257 224395.0654 247864.056 1.003415694 1.094503432 0.988124402 0.947183641 1.076051095 0.865126329 0.931386863 0.905315071 1 17.91918955 2.722832579 0.99328975 0.923922117 1.040973749 0.270436565 0.060769344 0.539087121 1.120905807 0.031743765 0.028783118 528.2415752 -2.722832579 0.117051632 S(ph)SPKEELHPAAPSQLAPSFSSSSSSSSGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPKEELHPAAPSQLAPSFSSSSSSSSGPR 30 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 S(0.491)S(0.491)PKEELHPAAPS(0.017)QLAPSFSSSSSSSSGPR 91.615 0.0005994 239810000 61163 58218 57773 68269 41267 74310 61103 72572 38661 TRUE FALSE 58271.9462 64150.48039 60421.9492 61406.47042 48463.95173 71736.62607 51780.61512 66217.21095 44656.35043 1.30489719 1.436536568 1.353042705 1.375089317 1.085264498 1.606414886 1.15953531 1.482817344 1 15.44657773 -1.810617036 2.800412543 0.898004662 1.345890408 0.352668393 0.149099885 23669090.28 17280232.45 16325231.87 0.032135966 0.015466177 1.810617036 0.447885746 S(ph)SPLKITLFLEEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPLKITLFLEEDK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.5)S(0.5)PLKITLFLEEDK;S(0.86)S(0.14)PLKITLFLEEDK 178.43 1.20E-06 86625000 215318 182164 185247 225630 121325 221051 220174 242611 128810 TRUE FALSE 205140.3449 200726.7187 193740.7582 202949.2437 142484.0416 213395.9484 186582.4125 221366.6947 148785.1969 1.378768514 1.349104097 1.302150766 1.364041907 0.957649313 1.434255241 1.254038818 1.487827413 1 17.18287147 -1.43251429 3.118967991 0.99467435 1.313852206 0.32609342 0.142725518 84404774.89 98935513.31 3919876.231 0.031170546 0.036939049 1.43251429 0.319177856 S(ph)SPNPFITGLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.627)S(0.373)PNPFITGLTR;S(0.95)S(0.05)PNPFITGLTR;S(0.552)S(0.448)PNPFITGLTR 184.11 1.55E-05 238215000 353347 317779 317169 370307 333710 345426 400799 371488 369279 TRUE FALSE 336644.9876 350161.0414 331711.5124 333083.0368 391908.9183 333463.811 339649.7514 338958.5413 426544.9013 0.789236928 0.820924222 0.777670795 0.780886223 0.918798741 0.781778917 0.796281354 0.794660868 1 18.70233809 -2.153046522 2.371677711 1.444517315 0.807296893 0.680614508 0.041435273 3674939.319 963047.3742 8775307.291 0.009588534 0.00702997 2.153046522 -0.637220423 S(ph)SPNVANQPPS(ph)PGGK ddPTM_SK-BR-3_Trastuzumab_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(0.988)S(0.012)PNVANQPPS(1)PGGK 287.19 1.92E-27 0 437480 344690 389890 433380 281990 404380 458430 427410 291340 TRUE FALSE 416801.1874 379814.3029 407766.8422 389815.819 331168.9667 390376.2192 388488.0839 389983.7146 336519.5192 1.23856467 1.128654599 1.211718248 1.158375062 0.98410032 1.160040345 1.15442957 1.15887398 1 18.36033066 -4.99999458 0.02687389 0.163636529 1.753204812 0.382474884 0.0640141 2061.821516 4.177997081 184.1511954 81.95244419 1.00E-05 4.99999458 1.589568282 S(ph)SPPLPPPAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.584)S(0.416)PPLPPPAEER 95.094 0.0018613 0 89067 68808 74289 94720 91297 85905 100650 79097 80482 TRUE FALSE 84856.97942 75819.61343 77695.22413 85198.56564 107219.1679 82930.08831 85293.99394 72170.84736 92962.73751 0.912806375 0.815591445 0.835767386 0.916480817 1.153356396 0.892078811 0.917507339 0.776341675 1 16.50436493 3.09406843 5.997885238 0.945326533 0.855618126 0.161326931 0.096503014 0.387764284 20.41138891 0.027639336 0.033187017 1241.847964 -3.09406843 -0.089708407 S(ph)SPPLRTPDVLESSGPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPPLRTPDVLESSGPAVR 19 1 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.565)S(0.435)PPLRTPDVLESSGPAVR;S(0.56)S(0.44)PPLRTPDVLESSGPAVR;S(0.571)S(0.429)PPLRTPDVLESSGPAVR;S(0.595)S(0.405)PPLRTPDVLESSGPAVR;S(0.502)S(0.497)PPLRT(0.001)PDVLESSGPAVR 253.18 4.36E-31 2313720000 293135 192250 295346 261977 248281 283501 343236 253718 215065 TRUE FALSE 279279.0895 211840.4936 308887.9062 235642.5742 291581.1278 273683.2893 290869.0442 231501.1069 248416.1818 1.124238717 0.85276447 1.243429087 0.948579809 1.173760605 1.101712808 1.170894111 0.931908321 1 17.92239963 3.74355298 24.99740984 1.092807657 0.98850161 0.089531915 0.119056323 781.9690731 3915413.542 0.027763912 0.048207162 5540.551293 -3.74355298 -0.104306047 S(ph)SPPSPAYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPPSPAYER 10 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 S(0.987)S(0.013)PPSPAYER 138.25 7.32E-05 175870000 158070 159840 140270 170300 129670 150030 166270 152070 132860 TRUE FALSE 150598.3444 176127.8777 146701.5182 153181.1205 152284.4069 144834.4235 140902.4577 138753.9446 153463.2502 0.981331649 1.147687654 0.95593908 0.998161581 0.9923184 0.943772683 0.918151137 0.904150957 1 17.22753369 3.009903122 1.047332315 0.934920184 1.056829686 0.321574016 0.055199149 0.456785074 1.082274598 0.024463572 0.030173257 1023.064752 -3.009903122 0.121909503 S(ph)SPPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_SK-BR-3_Trastuzumab_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 152 7.63E-08 562140000 53214 50603 65857 78420 63897 51761 64662 72146 10888.7 TRUE FALSE 50698.67968 55759.50323 68876.60859 70537.07261 75040.61657 49968.50359 54796.6243 65828.51377 12577.26398 4.030978418 4.433357152 5.476279156 5.608300239 5.966370481 3.972923177 4.356800046 5.233929562 1 13.6185305 4.124281739 3.761190894 4.715567892 4.129069655 0 1.403380071 0.975851232 25.14171642 0.317696301 0.762053759 13313.178 -4.124281739 -0.586498236 S(ph)SPQLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.981)S(0.019)PQLAK 85.666 0.021654 800900000 577100 696200 1417800 1308700 356220 882490 924220 908280 650700 TRUE FALSE 549821.6267 767143.5715 1482807.532 1177146.99 418344.6552 851929.15 783213.2645 828746.1881 751607.2327 0.731527855 1.020670821 1.97284894 1.566173047 0.556600092 1.133476519 1.042051261 1.102632003 1 19.51961942 2.754661305 24.94969841 0.989423429 1.242865463 0.17772355 0.360867088 2126.861496 3295791.086 0.121014111 0.127982809 568.4094704 -2.754661305 0.253442034 S(ph)SPQLDPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.678)S(0.322)PQLDPLR 108.7 0.0026952 287590000 480810 534940 375040 512590 386420 420810 438690 449470 371370 TRUE FALSE 458083.0642 589450.9942 392235.955 461063.4793 453811.5257 406237.2442 371759.7834 410112.024 428960.1629 1.067891855 1.374139245 0.914387836 1.074839855 1.057933964 0.947027904 0.866653399 0.956060864 1 18.71048415 3.724114318 24.97655839 0.968102326 1.221015556 0.538831454 0.09495034 509.1156988 880222.6128 0.025573363 0.039818114 5298.028841 -3.724114318 0.25291323 S(ph)SPQLDPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.576)S(0.424)PQLDPLRK;S(0.858)S(0.142)PQLDPLRK;S(0.75)S(0.25)PQLDPLRK;S(0.525)S(0.475)PQLDPLRK;S(0.5)S(0.5)PQLDPLRK 152.16 1.13E-05 3499863000 4108150 5054460 3087200 4662600 2166070 3975840 3607290 4104200 2176520 TRUE FALSE 3913965.891 5569515.22 3228751.174 4193906.59 2543831.922 3838155.664 3056931.658 3744814.49 2514043.605 1.556840893 2.215361423 1.284286067 1.668191666 1.011848767 1.526686194 1.215942178 1.489558289 1 21.26157824 3.718938735 24.86340616 1.330748606 1.886101162 0.44981603 0.262622593 544.2743647 689664.4183 0.062492561 0.096966609 5235.265782 -3.718938735 0.555352556 S(ph)SPQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.532)S(0.468)PQLDPLRKS(0.954)PT(0.046)MEQAVQTASAHLPAPAAVGR 173.71 5.53E-15 250810000 172800 117270 152370 165500 127130 153910 209460 197560 135950 TRUE FALSE 164632.0865 129219.9463 159356.3152 148863.6256 149301.4317 148580.0581 177503.03 180260.5991 157032.4317 1.048395447 0.822886998 1.014798749 0.947980134 0.950768132 0.946174345 1.130359048 1.147919555 1 17.26070302 1.754503536 7.779333036 1.102870001 0.948804252 0.460777821 0.06958658 0.105577643 21.40435504 0.031102249 0.016775595 56.8203018 -1.754503536 -0.15406575 S(ph)SPRPTAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPRPTAEK 9 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.5)S(0.5)PRPTAEK;S(0.589)S(0.411)PRPTAEK 57.019 0.071539 592710000 963970 820610 749350 912150 593840 878570 927350 953760 626560 TRUE FALSE 918405.0485 904231.092 783708.4387 820458.949 697405.508 848144.9006 785865.7255 870243.7182 723723.7248 1.268999505 1.249414744 1.082883443 1.133663193 0.963634995 1.171918056 1.085864258 1.202452937 1 19.46507954 3.758034789 7.051443925 1.095730455 1.25995105 0.488518827 0.071252047 0.12760302 30.59131246 0.016638819 0.029108108 5728.419166 -3.758034789 0.164220595 S(ph)SPSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.497)S(0.497)PS(0.006)ARPPDVPGQQPQAAK;S(0.572)S(0.427)PSARPPDVPGQQPQAAK 144.43 8.19E-08 266660000 302875 316349 283506 350119 189417 318705 320882 353413 255590 TRUE FALSE 288558.699 348585.3228 296505.0305 314924.3729 222451.2648 307668.1659 271925.5575 322466.2842 295225.5918 0.977417632 1.180742227 1.004333766 1.066724504 0.753495872 1.042145988 0.921077186 1.092270769 1 18.17145826 2.903092558 23.35644743 0.955654808 1.066123445 0.172250537 0.102740547 39.45626925 9502.948471 0.028677175 0.030416757 800.0047353 -2.903092558 0.110468637 S(ph)SPSIICMPK ddPTM_SK-BR-3_Trastuzumab_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(0.627)S(0.373)PSIICMPK 164.64 6.39E-06 89564000 277480 293170 219810 299610 167360 245550 244270 269420 171860 TRUE FALSE 264364.0703 323044.3563 229888.5059 269492.6336 196547.531 237046.5419 207002.1252 245828.1565 198511.1711 1.331733972 1.627335905 1.158063321 1.357569109 0.990108163 1.194121926 1.04277318 1.238359308 1 17.59886067 3.315146396 1.488457841 1.106318442 1.469420328 0.491336193 0.137529065 0.264108249 1.212694042 0.041450859 0.064753521 2066.076491 -3.315146396 0.363101887 S(ph)SPSPQKR ddPTM_SK-BR-3_Trastuzumab_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(0.908)S(0.092)PSPQKR;S(0.499)S(0.499)PS(0.001)PQKR 111.61 0.0019606 42806000 41672 48367 46538 47166 67482 39200 55114 47741 86155 TRUE FALSE 39702.24715 53295.65229 48671.81333 42424.78407 79250.83943 37842.49417 46705.34706 43560.54495 99515.47738 0.398955501 0.535551391 0.489087875 0.426313426 0.796366972 0.380267423 0.469327468 0.437726333 1 16.6026333 -1.225272417 4.993765313 1.000068907 0.490578956 0.650347755 0.117127485 8.20E-05 1.27E-05 0.103524838 0.024397754 0.059528862 1.225272417 -0.509489951 S(ph)SPVEFECINEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVEFECINEK 12 0 O75131;H0YB26 O75131 CPNE3 Copine-3 1 S(0.5)S(0.5)PVEFECINEK 111.12 0.0014852 73728000 91380 63120 62228 98732 60104 64645 72569 73641 56929 TRUE FALSE 87060.6485 69551.99976 65081.21535 88807.27178 70586.11857 62406.32744 61497.26623 67192.60364 65757.25857 1.323970165 1.057708324 0.989719109 1.350531846 1.073434631 0.949040894 0.935216394 1.021827934 1 16.00486253 2.455239792 5.749182363 0.970044297 1.169914656 0.435467481 0.108955775 0.161023468 16.89653382 0.037059357 0.031587838 285.2592867 -2.455239792 0.19987036 S(ph)SPVESLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.699)S(0.301)PVESLKK 115.29 0.00091909 379260000 1970800 1971100 1613600 2139700 1008200 2028700 2065400 2187500 1093100 TRUE FALSE 1877644.19 2171957.331 1687585.156 1924613.291 1184029.761 1958445.61 1750285.296 1995950.903 1262612.365 1.487110567 1.72020914 1.336582155 1.524310504 0.937761892 1.551105996 1.386241213 1.580810515 1 20.26798035 -4.017622803 0.120371461 5.32E-16 1.670675473 0.274925103 0.212088995 147.6642323 1.456507792 39.90976013 2.035740782 9.60E-05 4.017622803 1.670675473 S(ph)SPVKVGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.677)S(0.323)PVKVGEK 110.31 0.001398 408200000 1443700 1518600 1260100 1705400 751170 1601300 1596700 1813900 792420 TRUE FALSE 1375459.162 1673347.067 1317876.831 1533969.952 882173.8102 1545846.579 1353094.09 1655065.3 915304.4465 1.502734055 1.828186319 1.439823478 1.675912269 0.963803698 1.688887873 1.478299483 1.808212892 1 19.80389216 3.708237156 24.2628169 1.462831339 1.665460233 0.094777195 0.285338616 1024.182853 819482.8142 0.068549275 0.106212229 5107.83849 -3.708237156 0.202628894 S(ph)SPVPEMLEESQELLEPVVDDVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVPEMLEESQELLEPVVDDVPK 24 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.5)S(0.5)PVPEMLEESQELLEPVVDDVPK 146.06 6.74E-07 42514000 191790 178530 166000 200560 106000 216370 193030 216610 121660 TRUE FALSE 182724.4668 196722.41 173611.2642 180399.3278 124486.3664 208877.0526 163579.7283 197642.4801 140526.4114 1.300285583 1.399896347 1.235435121 1.283739661 0.885857435 1.48639 1.164049708 1.406443657 1 17.10048178 S(ph)SPVPPVPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.555)S(0.445)PVPPVPER;S(0.639)S(0.361)PVPPVPER 126.71 0.00039382 702590000 462240 441630 439070 495790 429740 443700 521010 487480 504930 TRUE FALSE 440390.8313 486632.5991 459201.7938 445952.2473 504686.5199 428334.5577 441520.3555 444793.6669 583231.9656 0.755086925 0.834372304 0.787339894 0.764622438 0.865327262 0.734415435 0.757023588 0.762635955 1 19.15371027 -2.137471945 2.446832872 1.46967069 0.783534274 0.749904618 0.039452091 2614689.96 784108.0478 6815445.076 0.009153825 0.007286652 2.137471945 -0.686136416 S(ph)SPVPPVPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVPPVPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.5)S(0.5)PVPPVPERR 54.276 0.081278 1500200000 631780 772920 569440 758300 473340 727530 646860 724500 541330 TRUE FALSE 601917.0115 851681.4267 595549.3873 682074.2433 555890.3461 702335.4537 548169.6266 661058.9392 625276.6917 0.962641051 1.362087278 0.95245736 1.090835869 0.889030974 1.12323946 0.876683289 1.057226262 1 19.25413521 3.678294285 24.99954222 0.99326355 1.162366628 0.233552269 0.123130468 273.2749232 113359.0362 0.029919575 0.046351219 4767.539337 -3.678294285 0.169103078 S(ph)SPVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVTK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(0.965)S(0.035)PVTK 108.7 0.031669 902220000 2015700 2122700 2202100 2919600 1403200 2042500 2795600 3946100 2219300 TRUE FALSE 1920421.856 2339005.543 2303068.463 2626116.261 1647917.636 1971767.713 2369079.875 3600558.564 2563457.709 0.749152931 0.912441635 0.898422648 1.024442982 0.64284955 0.769182852 0.924173575 1.40457108 1 21.28965967 1.403692994 6.334666303 1.199643294 0.840025769 0.535263383 0.140296102 0.149794327 9.180641003 0.08677218 0.032083167 25.33337163 -1.403692994 -0.359617525 S(ph)SQKSPELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSQKSPELGK 10 1 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.335)S(0.335)QKS(0.331)PELGK 60.448 0.059366 103850000 345180 307010 346380 369250 213840 352930 401490 408060 227370 TRUE FALSE 328864.0255 338294.668 362261.8656 332132.2885 251133.6283 340707.9456 340235.3266 372328.1031 262629.3784 1.252198164 1.288106723 1.379365355 1.264642557 0.95622824 1.297295633 1.295496067 1.417694035 1 18.00266878 -1.174345014 4.765106596 0.999968959 1.266853239 0.323497774 0.122164885 3.89E-05 6.75E-06 0.114291285 0.026935584 0.066935265 1.174345014 0.266884279 S(ph)SREKEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.569)S(0.431)REKEQR 76.143 0.019079 67170000 58458 47916 60279 55346 68124 41993 71598 62148 83910 TRUE FALSE 55694.80619 52798.69488 63042.85177 49782.51493 80004.80403 40538.77188 60674.41011 56705.99165 96922.33425 0.574633356 0.544752613 0.650447106 0.513633058 0.825452716 0.418260375 0.626010615 0.585066302 1 16.56454153 -0.128272595 1.991628458 1.000076885 0.588139121 0.600702605 0.104416475 101.4043656 175.5045527 0.128128216 0.023886038 0.744264673 0.128272595 -0.411937764 S(ph)SRLSTNGTHEILDPDLVVSDLVDTDPLQDTLSSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSRLSTNGTHEILDPDLVVSDLVDTDPLQDTLSSTK 36 1 Q9BVI0;Q5JWZ0;Q5JXL1 Q9BVI0 PHF20 PHD finger protein 20 1 S(0.2)S(0.2)RLS(0.2)T(0.2)NGT(0.2)HEILDPDLVVSDLVDTDPLQDTLSSTK 187.89 1.95E-23 20668000 33914 22086 32444 27701 28038 30474 32670 29158 25601 TRUE FALSE 32310.95243 24336.58851 33931.58949 24916.44285 32927.81832 29418.67774 27685.59147 26604.77094 29571.07233 1.092654067 0.822986337 1.147458879 0.842595175 1.113514517 0.994846498 0.93623901 0.899689083 1 14.85189894 4.752855851 24.32906126 0.967790328 1.092654191 0.120899287 0.104115915 208.3315774 1774515.046 0.02189339 0.151994567 56605.13765 -4.752855851 0.124863862 S(ph)SS(ph)PFLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPFLSK 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.995)S(0.007)S(0.998)PFLSK;S(0.999)S(0.001)S(1)PFLSK;S(1)SS(1)PFLSK 227.14 4.05E-06 494480000 2624000 2543000 2097370 2951130 1360290 2501540 2545370 2237170 1300390 TRUE FALSE 2499968.72 2802134.591 2193536.489 2654476.806 1597524.145 2414911.043 2157027.058 2041271.535 1502047.84 1.664373567 1.865542839 1.460363932 1.767238523 1.063564091 1.607745758 1.436057495 1.358992358 1 20.51849933 1.59358167 0.06839275 2.92E-12 2.813946912 0.518772597 0.193632855 14.25146064 0.997287162 19.66540075 19.89626495 39.22669056 -1.59358167 2.813946912 S(ph)SS(ph)PFLSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPFLSKR 9 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.991)S(0.017)S(0.991)PFLSKR;S(0.998)S(0.153)S(0.849)PFLSKR 110.98 0.0076972 436190000 1250390 871240 1112280 1159900 740770 1155890 1511700 1031100 889760 TRUE FALSE 1191286.543 960020.3465 1163279.138 1043304.648 869960.0535 1115861.239 1281062.401 940811.4178 1027739.437 1.159132851 0.934108698 1.131881386 1.015145095 0.846479197 1.085743331 1.246485593 0.915418232 1 19.97104311 2.023932211 24.98265131 1.102545192 1.019170118 0 0.122754521 540.5161869 564238.2989 0.043875963 0.03240299 105.6652565 -2.023932211 -0.083375074 S(ph)SS(ph)PVTELASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.996)S(0.163)S(0.84)PVT(0.001)ELASR 98 0.008549 171210000 419920 403840 397220 413970 293300 421740 426210 382430 280520 TRUE FALSE 400071.2138 444991.7551 415432.9299 372356.9491 344451.4271 407135.0381 361183.8366 348942.4018 324021.6089 1.234705349 1.373339749 1.282114891 1.1491732 1.063050789 1.256505822 1.114690584 1.076910898 1 18.3057305 2.368513678 0.339710948 0.999149813 1.351194974 0.597491761 0.072656559 1.110954406 0.305533099 0.093271729 0.139993487 233.621968 -2.368513678 0.352045161 S(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR 137.9 1.48E-06 9863400 6759 8899.7 8379.9 8666.7 8292.5 6831.9 7703.7 7433.7 7897.6 TRUE FALSE 6439.515465 9806.589548 8764.126704 7795.50685 9738.709374 6595.30959 6528.359077 6782.765819 9122.319473 0.70590769 1.075010536 0.960734463 0.854553151 1.067569427 0.722986035 0.715646837 0.74353522 1 13.15518498 2.21508811 24.99998302 0.764079554 0.929248244 0.194171649 0.132054761 301.7720132 321407.8475 0.0463149 0.034225536 164.092265 -2.21508811 0.16516869 S(ph)SSDALSASFNGEMLGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.913)S(0.085)S(0.001)DALSASFNGEMLGNR;S(0.641)S(0.179)S(0.179)DALSASFNGEMLGNR;S(0.333)S(0.333)S(0.333)DALSASFNGEMLGNR 269.85 4.76E-32 243539000 318999 287139 288393 344942 293850 305898 377677 343435 322512 TRUE FALSE 303920.5495 316398.7905 301616.1043 310267.7748 345097.347 295304.6756 320055.4371 313362.0107 372525.5138 0.815838213 0.849334552 0.809652207 0.832876577 0.92637238 0.792709934 0.859150381 0.841182682 1 18.50697971 -5 0.317101223 2.481838074 0.833494904 0.662707065 0.035803227 179.2940556 1.598402608 178.0411783 0.02924784 1.00E-05 5 -1.64834317 S(ph)SSEDAESLAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.846)S(0.127)S(0.027)EDAESLAPR;S(0.799)S(0.1)S(0.1)EDAESLAPR;S(0.811)S(0.123)S(0.066)EDAESLAPR;S(0.807)S(0.096)S(0.096)EDAESLAPR;S(0.799)S(0.1)S(0.1)EDAESLAPR;S(0.799)S(0.101)S(0.101)EDAESLAPR 291.22 4.17E-36 4224310000 2295170 2055000 2057600 2477380 1995630 2211000 2477890 2189210 2134380 TRUE FALSE 2186681.863 2264406.836 2151942.995 2228349.056 2343667.24 2134432.516 2099842.371 1997511.167 2465368.749 0.88695935 0.918486063 0.872868611 0.903860348 0.950635576 0.86576603 0.851735616 0.810228152 1 21.23337202 S(ph)SSERRPATPAEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSERRPATPAEVR 14 2 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 S(0.333)S(0.333)S(0.333)ERRPATPAEVR 61.87 0.064224 217770000 251630 189350 198040 221960 314400 199990 246090 213140 268260 TRUE FALSE 239735.9486 208644.9803 207120.3299 199648.1591 369231.2605 193064.2962 208544.4507 194476.3317 309860.3907 0.773690203 0.673351569 0.668431126 0.644316489 1.191605225 0.623068653 0.673027134 0.627625658 1 18.24125882 5.387115781 4.759946911 0.743401285 2.890089812 0 0.188535733 10162.70485 2505.492397 0.042044851 231005.1127 243846.0814 -5.387115781 2.146688527 S(ph)SSESLIFSGNQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 S(0.789)S(0.211)SESLIFSGNQGR 458.47 4.49E-198 212880000 367190 354030 336420 393250 290490 376590 402770 431670 360500 TRUE FALSE 349833.6564 390106.0595 351845.1898 353719.7629 341151.364 363548.5939 341320.0391 393870.6864 416404.4988 0.840129387 0.936844008 0.844960107 0.849461915 0.819278766 0.873065961 0.819683841 0.945884801 1 18.66762613 1.047600063 4.864329314 0.999380991 0.859550998 0.693075531 0.033590331 0.101598905 5.074946967 0.033413112 0.008467374 11.15835214 -1.047600063 -0.139829994 S(ph)SSETILSSLAGSDIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.25)S(0.25)S(0.25)ET(0.25)ILSSLAGSDIVK 132.05 1.60E-05 21469000 37962 27501 31530 40529 31266 30366 38659 35317 28093 TRUE FALSE 36167.61149 30303.38317 32975.68169 36454.94792 36718.7805 29314.41781 32760.85953 32224.45625 32449.51896 1.114580821 0.933862323 1.016214808 1.123435696 1.13156625 0.903385281 1.009594613 0.993064221 1 14.98590947 2.235951804 24.99993352 0.97812941 1.051335395 0.298917708 0.064933253 108.688267 1041530.185 0.024544861 0.01896348 172.1677499 -2.235951804 0.073205985 S(ph)SSLEGFHNHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.474)S(0.474)S(0.052)LEGFHNHFK;S(0.382)S(0.382)S(0.236)LEGFHNHFK 197.19 3.31E-07 403310000 565970 429330 475030 750660 636460 648740 752650 444050 51539 TRUE FALSE 539217.7197 473079.2151 496810.5954 675202.2306 747458.4225 626273.9711 637819.4191 405166.6279 59531.4049 9.057701909 7.946716795 8.345353116 11.34195022 12.55569936 10.52006033 10.71399911 6.805930897 1 15.86136332 0.927284502 3.506149159 1.007592832 9.905920859 0.813869782 1.386204272 0.151930477 4.590067784 1.520620586 0.392933587 8.458327606 -0.927284502 8.898328027 S(ph)SSLESLQTAVAEVTLNGDIPFHRPR ddPTM_SK-BR-3_Trastuzumab_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(0.329)S(0.329)S(0.329)LES(0.013)LQTAVAEVTLNGDIPFHRPR;S(0.333)S(0.333)S(0.333)LES(0.001)LQTAVAEVTLNGDIPFHRPR 119.48 0.00022882 54794000 24431 27988 19352.2 28091 21520.3 18479.7 19600 22879 16834.3 TRUE FALSE 23276.19505 30840.00902 20239.51751 25267.23931 25273.43351 17839.74336 16609.66002 20875.59347 19444.87727 1.197034814 1.586022303 1.040866303 1.299429097 1.299747649 0.917452093 0.854192073 1.073578053 1 14.24710251 2.241270369 24.33611905 0.937848008 1.307351541 0.544057642 0.145549523 33.65795363 302283.8022 0.0509256 0.040808292 174.2891569 -2.241270369 0.369503533 S(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.357)S(0.357)S(0.286)LESLQTAVAEVTLNGDIPFHRPRPR;S(0.354)S(0.354)S(0.285)LES(0.008)LQTAVAEVTLNGDIPFHRPRPR;S(0.333)S(0.333)S(0.333)LES(0.001)LQTAVAEVTLNGDIPFHRPRPR 189.2 3.23E-18 286354000 54615.2 48483.5 58849.8 57199 61575.3 58288.2 77804.9 70716.8 74365.8 TRUE FALSE 52033.64773 53424.02377 61548.12154 51449.24785 72314.01282 56269.66502 65934.33352 64524.4621 85898.06846 0.605760393 0.621946741 0.716525094 0.598956982 0.841858427 0.655074858 0.767588081 0.751174773 1 16.39033807 -5 0.10110371 2.044337668 0.468701426 0.741680818 0.062784596 79.24540141 0.543823718 17.24689624 0.883786498 1.00E-05 5 -1.575636243 S(ph)SSLKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.475)S(0.475)S(0.05)LKER;S(0.641)S(0.335)S(0.023)LKER;S(0.683)S(0.286)S(0.031)LKER;S(0.488)S(0.488)S(0.025)LKER;S(0.333)S(0.333)S(0.333)LKER;S(0.333)S(0.333)S(0.333)LKER 134.91 0.0018947 12464270000 9526860 7550340 7791200 9685580 5328320 9306440 10014240 9088370 6369310 TRUE FALSE 9076544.208 8319728.23 8148434.227 8711967.097 6257577.321 8984155.649 8486383.764 8292544.142 7357030.065 1.233723952 1.130854184 1.107571147 1.184169022 0.85055753 1.221166091 1.15350674 1.127159203 1 22.81069206 4.516796462 1.173557909 1.101348022 1.267719133 0.152192897 0.104157291 2.090840718 3.204564877 0.029061104 0.38813878 32869.75462 -4.516796462 0.166371111 S(ph)SSMELHREENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSMELHREENR 12 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.333)S(0.333)S(0.333)MELHREENR;S(0.361)S(0.361)S(0.277)MELHREENR;S(0.333)S(0.333)S(0.333)MELHREENR 85.909 0.0069092 442188000 257489 200107 245387 281507 284587 235827 315866 261357 269538 TRUE FALSE 245318.0053 220498.1308 256638.2367 253209.3815 334218.8827 227660.2519 267674.8404 238471.1955 311336.5764 0.787951124 0.70823073 0.824311231 0.813297893 1.073497006 0.731235162 0.859760339 0.765959459 1 18.24811555 -5 0.035688783 1.820513316 0.293025367 0.223549814 0.101260407 1472.39758 3.93813562 142.6468596 48.7806297 1.00E-05 5 -1.527487949 S(ph)SSPAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.385)S(0.385)S(0.231)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.315)S(0.315)S(0.315)PAGET(0.056)EGDREPQARPGEGTAPLPPPGQK 274.12 6.44E-72 1395470000 846230 668610 807850 822740 610950 862730 1023990 920530 800770 TRUE FALSE 806230.385 736742.1191 844890.7216 740036.6121 717499.4866 832853.4438 867761.5186 839923.5132 924949.3218 0.871648171 0.796521606 0.91344542 0.800083415 0.77571762 0.900431434 0.938171961 0.908075171 1 19.8190148 2.039362342 6.11583095 0.936722193 0.832646122 0.582907878 0.045351156 0.131649872 13.03461728 0.016364534 0.011810174 109.4869461 -2.039362342 -0.104076071 S(ph)SSPAPADIAQTVQEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 89.358 0.0030484 8906000 29994 31558 34115 33571 30619 35763 38965 31338 30627 TRUE FALSE 28576.24306 34773.79608 35679.20649 30196.3793 35958.94391 34524.51834 33020.17361 28593.87859 35376.47874 0.807775225 0.982963746 1.008557317 0.853572215 1.016464758 0.975917321 0.933393452 0.808273735 1 15.11050283 4.622596686 3.14648418 0.946967538 0.802649761 0.291212153 0.068187212 0.347070809 5.686127952 0.01546277 0.105203895 41936.93492 -4.622596686 -0.144317777 S(ph)SSPAPPSQQSLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPAPPSQQSLYK 14 0 I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 I3L3F1 CARD14 Caspase recruitment domain-containing protein 14 1 S(0.333)S(0.333)S(0.333)PAPPSQQSLYK 73.466 0.022098 0 65338 49462 53931 66308 40606 50733 65536 62691 46976 TRUE FALSE 62249.60223 54502.23403 56403.7897 59642.59386 47687.67354 48976.10349 55537.27955 57201.44369 54260.79816 1.147229756 1.004449545 1.039494287 1.099183865 0.878860525 0.902605659 1.023524928 1.05419466 1 15.72762265 6.283175122 0.558780245 0.985036169 1.985877808 0.343445466 0.065192625 21.3612988 1.295519115 0.030903589 20.26629949 1919442.57 -6.283175122 1.000841639 S(ph)SSPATEQSWMENDFDELREEGFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFRR 73.036 0.030885 47793000 23818 19476 21764 23532 22083 22538 24335 25640 25890 TRUE FALSE 22692.17034 21460.62654 22761.90093 21166.51865 25934.26821 21757.50341 20622.24881 23394.82567 29904.88897 0.758811389 0.717629367 0.761143134 0.707794591 0.867225029 0.727556736 0.689594562 0.782307726 1 14.86809374 0.966923803 22.7881091 1.000000001 0.743928442 0.727513281 0.048232534 730.5351684 503309.0802 0.044301396 0.011075266 9.266672251 -0.966923803 -0.256071559 S(ph)SSPCRTPEPDNDAHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPCRTPEPDNDAHLR 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 S(0.327)S(0.327)S(0.327)PCRT(0.019)PEPDNDAHLR;S(0.328)S(0.328)S(0.328)PCRT(0.017)PEPDNDAHLR;S(0.333)S(0.333)S(0.333)PCRTPEPDNDAHLR 179.03 5.67E-10 323752000 433910 309365 423210 428010 506080 420400 543710 472270 555030 TRUE FALSE 413399.9342 340889.6452 442614.5971 384985.6216 594340.1918 405841.4426 460757.0536 430915.5351 641101.2177 0.644827872 0.531725156 0.690397374 0.60050677 0.927061399 0.633038015 0.71869627 0.672148989 1 19.29019262 -5 0.129185677 2.097576425 0.527432221 0.523713873 0.099468802 107.9085853 0.881468835 30.75034877 0.718253126 1.00E-05 5 -1.570144204 S(ph)SSPEDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPEDAR 8 0 Q86TL0;K7EKP6;K7EQN3;K7EPJ0;K7ERK1 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 S(0.904)S(0.081)S(0.015)PEDAR 109.48 0.0037872 13879000 60278 52225 62158 62651 68817 52612 68028 54656 78724 TRUE FALSE 57428.7784 57546.78687 65008.00578 56353.20245 80818.66301 50790.03325 57649.07918 49870.03089 90932.11585 0.631556605 0.63285437 0.714906996 0.619728266 0.888780188 0.5585489 0.6339793 0.548431436 1 16.4725023 -1.283917199 4.075817028 1.000415095 0.652617265 0.566483402 0.095230518 2882565010 506439207.3 11684040.92 0.02051004 0.052009515 1.283917199 -0.347797829 S(ph)SSPELVTHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.455)S(0.455)S(0.09)PELVTHLK;S(0.333)S(0.333)S(0.333)PELVTHLK 253.54 1.33E-20 2504200000 4187400 3859200 3660500 4663600 2846500 4050300 4339400 4258400 2673300 TRUE FALSE 3989469.901 4252456.868 3828337.546 4194806.068 3342928.699 3910037.095 3677344.831 3885511.921 3087861.711 1.29198464 1.377152627 1.239802136 1.358482491 1.082603112 1.266260429 1.190903342 1.258317983 1 21.55817671 -5 0.092230595 0.123945005 1.479426311 0.565307934 0.076247636 132.1975685 0.843408836 22.54479871 1.485653486 1.00E-05 5 1.355481307 S(ph)SSPELVTHLKWDDPYYDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.33)S(0.33)S(0.33)PELVT(0.009)HLKWDDPYYDIAR;S(0.36)S(0.36)S(0.28)PELVTHLKWDDPYYDIAR;S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR;S(0.364)S(0.364)S(0.271)PELVTHLKWDDPYYDIAR 231.21 3.80E-26 570149000 326836 144990 288410 221526 330639 267442 549977 368221 401479 TRUE FALSE 311387.11 159764.6458 301633.8838 199257.7856 388302.3369 258180.4165 466067.9076 335977.6172 463738.3128 0.671471607 0.344514657 0.650439861 0.429677213 0.837330723 0.556737301 1.005023512 0.724498295 1 18.8229514 2.113942671 0.850373919 0.939510444 0.510042756 0.480876242 0.156573941 0.446021407 0.602287825 0.113259034 0.060614377 129.9997961 -2.113942671 -0.429467687 S(ph)SSPGKPQAVSSLNSSHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 199.75 4.10E-16 331980000 384000 271700 375770 426840 311820 340060 517090 436300 360870 TRUE FALSE 365849.081 299386.5389 392999.4262 383933.2323 366201.3093 328283.6369 438198.4235 398095.259 416831.8765 0.877689787 0.718242907 0.942824789 0.921074548 0.8785348 0.787568455 1.051259388 0.955049941 1 18.66910608 2.118735621 0.526377805 1.017578576 0.813380141 0.320039236 0.07999844 0.906156371 0.528646111 0.075425744 0.058937321 131.4424427 -2.118735621 -0.204198435 S(ph)SSPHDKNLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.333)S(0.333)S(0.333)PHDKNLPQK;S(0.333)S(0.333)S(0.333)PHDKNLPQK;S(0.333)S(0.333)S(0.333)PHDKNLPQK 177.88 1.37E-05 992780000 1360170 835586 1263450 1277700 994710 1336400 1857820 1586740 1145090 TRUE FALSE 1295877.46 920733.1634 1321380.432 1149263.169 1168187.109 1290120.133 1574375.438 1447796.634 1322664.709 0.979747513 0.696119853 0.999029023 0.868899851 0.883207287 0.975394689 1.190305772 1.09460593 1 20.33501596 1.999000684 3.757634829 1.112279542 0.873854274 0.506359854 0.093236313 0.154901951 4.697786667 0.040022173 0.0248795 99.77016353 -1.999000684 -0.238425268 S(ph)SSPPPRK ddPTM_SK-BR-3_Trastuzumab_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(0.47)S(0.47)S(0.06)PPPRK 75.378 0.023609 2709940000 3176100 2770470 2762740 3202200 2225050 2813720 3367800 3539100 2963400 TRUE FALSE 3025972.047 3052784.043 2889414.362 2880308.772 2613098.016 2716280.171 2853980.256 3229197.642 3422948.937 0.884024887 0.891857898 0.844130139 0.84146998 0.763405491 0.79354972 0.833778215 0.943396382 1 21.70680834 1.095699729 3.64061076 0.99789115 0.840261873 0.699106189 0.037841769 0.141385454 3.42140905 0.042320979 0.011014729 12.46521372 -1.095699729 -0.157629277 S(ph)SSPRGEASSLNGESH ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPRGEASSLNGESH 16 1 Q8IY57;Q8IY57-5;Q8IY57-3 Q8IY57 YAF2 YY1-associated factor 2 1 S(0.333)S(0.333)S(0.333)PRGEASSLNGESH;S(0.333)S(0.333)S(0.333)PRGEASSLNGESH;S(0.333)S(0.333)S(0.333)PRGEASSLNGESH 131.18 2.78E-05 560620000 602330 344395 570880 498150 631150 560550 743590 576040 709780 TRUE FALSE 573859.0546 379489.242 597055.4127 448075.0156 741222.3602 541138.0129 630141.6885 525598.8838 819849.0573 0.699956961 0.462876963 0.728250411 0.54653355 0.90409613 0.660045905 0.768606956 0.641092259 1 19.64499879 -5 0.116637695 2.099920293 0.492483233 0.438045678 0.117370033 129.2587712 0.985979718 33.51418577 1.109997102 1.00E-05 5 -1.607437059 S(ph)SSPTLTPSQEGSPVFAGFEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.324)S(0.324)S(0.324)PT(0.028)LTPSQEGSPVFAGFEGR 62.203 0.0436 32149000 30042 26831 30916 32892 23723 29952 33556 32412 26233 TRUE FALSE 28621.9742 29565.1094 32333.52918 29585.63367 27860.28369 28914.75473 28436.4159 29573.83345 30301.07966 0.944585953 0.975711418 1.067075152 0.976388762 0.919448548 0.954248332 0.938462135 0.97599933 1 14.88708158 2.9881998 24.82365879 0.951892006 0.988867971 0.164554977 0.037095057 919.0408053 1933359.456 0.011144704 0.012439244 973.1948463 -2.9881998 0.036975964 S(ph)SSPTSSLTQPIEMPTLSSS(ph)PTEERPTVGPGQQDNPLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.166)S(0.166)S(0.166)PT(0.166)S(0.166)S(0.166)LT(0.007)QPIEMPTLS(0.004)S(0.091)S(0.451)PT(0.451)EERPT(0.003)VGPGQQDNPLLK 151.49 2.24E-13 52807000 38909 41462 40428 49586 33658 47979 53026 48964 42061 TRUE FALSE 37069.84868 45687.02494 42281.66379 44601.52107 39527.94454 46317.4752 44935.90981 44676.45259 48583.60506 0.763011486 0.940379473 0.870286668 0.918036466 0.813606658 0.953356078 0.924919214 0.919578786 1 15.56818193 8 0.110626659 1.031114066 0.387665628 0.499345655 0.048861809 92.36229458 0.712347027 0.410528888 9.08174969 100000000 -8 -0.643448438 S(ph)SSQIPEGFGLTSGGSNYSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.333)S(0.333)S(0.333)QIPEGFGLTSGGSNYSLAR 137.61 2.87E-06 36808000 79093 70100 73983 70035 77544 79132 94995 88535 93759 TRUE FALSE 75354.43064 77243.2697 77375.19373 62994.94874 91067.64905 76391.639 80501.76805 80782.40605 108298.6669 0.695802015 0.713243034 0.714461184 0.58167797 0.840893537 0.705379311 0.743331108 0.745922442 1 16.72465596 -4.999988711 0.236509688 2.608899495 0.685685922 0.695628775 0.06006732 86.95272766 0.868164656 67.02952934 0.087140791 1.00E-05 4.999988711 -1.923213573 S(ph)SSQPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.28)S(0.28)S(0.28)QPS(0.073)S(0.073)CCS(0.013)DPSKPGGNVEGATQSLAEQMR 109.97 6.55E-05 329850000 263580 252530 239400 327970 174650 254260 279080 260430 152350 TRUE FALSE 251121.0958 278263.0941 250376.7268 295001.8325 205108.9047 245454.9124 236501.2203 237625.3686 175975.6599 1.427021759 1.581258989 1.422791805 1.676378612 1.165552695 1.394823083 1.343942796 1.350330885 1 17.42501637 -0.034486471 0.252710895 0.829925916 1.553779871 0.577681299 0.12345505 4.641063241 0.477475005 0.936388896 0.211152449 0.923662961 0.034486471 0.723853956 S(ph)SSSELLLTGPGAEEDPLPLIVQDQYVQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSSELLLTGPGAEEDPLPLIVQDQYVQEAR 31 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR;S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR;S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR;S(0.428)S(0.428)S(0.072)S(0.072)ELLLTGPGAEEDPLPLIVQDQYVQEAR 165.55 9.05E-13 93593000 102059 85114 100249 102980 86869 93173 116513 109630 98912 TRUE FALSE 97234.87333 93787.21337 104845.5158 92628.25475 102018.9261 89946.39565 98736.80194 100030.216 114250.7678 0.851065382 0.82088913 0.917678873 0.81074514 0.892938648 0.787271695 0.864211277 0.875532112 1 16.80184433 0.713550709 1.950582681 0.999886701 0.846567425 0.607043819 0.037888558 0.713416479 3.93419844 0.031504828 0.00873564 5.170716291 -0.713550709 -0.153319276 S(ph)SSSESSHSSSSHSHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSSESSHSSSSHSHGK 17 0 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 S(0.321)S(0.321)S(0.321)S(0.037)ESSHSSSSHSHGK;S(0.25)S(0.25)S(0.25)S(0.25)ES(0.001)S(0.001)HSSSSHSHGK 155.03 1.93E-07 41239000 38211 26593 29050 35920 68503 27299 57823 62105 8928.7 TRUE FALSE 36404.84176 29302.85693 30381.97123 32309.25336 80449.90151 26353.62878 49001.03936 56666.75696 10313.31719 3.529886754 2.841264007 2.945897102 3.132770257 7.800584428 2.555300907 4.751239435 5.494522848 1 13.33222082 2.93477703 24.99996124 4.522466764 3.100773306 0.09696372 1.77314126 371.2860482 142313.261 0.47891516 0.507966574 860.5518245 -2.93477703 -1.421693458 S(ph)SSSGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSGDQSSDSLNSPTLLAL 20 0 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 S(0.214)S(0.214)S(0.214)S(0.214)GDQS(0.066)S(0.066)DS(0.012)LNSPTLLAL 66.285 0.018757 0 13903 9563.1 12308 12828 10983 14523 16808 13054 15282 TRUE FALSE 13245.83274 10537.59076 12872.33397 11538.50507 12898.43172 14020.06487 14243.6309 11910.92256 17651.85451 0.750393265 0.596967914 0.729234085 0.653670982 0.730712556 0.794254499 0.806919799 0.674768906 1 14.10753214 -4.302113057 0.167233478 1.867583817 0.638929755 0.673737347 0.062234388 56.23797498 0.651899902 16.40695542 0.229555797 4.99E-05 4.302113057 -1.228654062 S(ph)SSSGSDDYAYTQALLLHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSGSDDYAYTQALLLHQR 20 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 S(0.363)S(0.363)S(0.264)S(0.009)GS(0.001)DDYAYTQALLLHQR 165.58 1.06E-11 51805000 56883 49666 42529 46975 57640 46735 52175 67912 64887 TRUE FALSE 54194.25332 54727.02187 44478.99672 42252.98375 67692.39775 45116.55523 44214.74549 61965.26526 74949.34456 0.723078416 0.730186797 0.593454112 0.563753879 0.903175313 0.601960637 0.589928381 0.826761937 1 16.19362824 0.990113072 5.085213877 0.999675553 0.675864088 0.541004351 0.099580664 0.114769085 11.09471161 0.092880323 0.023475357 9.774916866 -0.990113072 -0.323811464 S(ph)SSSPELQTLQDILGDPGDKADVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.25)S(0.25)S(0.25)S(0.25)PELQT(0.001)LQDILGDPGDKADVGR 86.982 0.0098451 25104000 27213 25458 28328 31523 22405 35503 39667 32806 25549 TRUE FALSE 25926.69542 28052.19914 29626.86682 28354.24815 26312.42491 34273.52221 33615.07062 29933.33272 29511.00843 0.878543188 0.950567284 1.003925938 0.960802414 0.891613886 1.161380923 1.139068856 1.014310737 1 14.8489656 2.242308358 24.99999964 1.098046016 0.93772157 0.565903343 0.06057832 60.82240233 405729.8334 0.02103084 0.016964575 174.7062161 -2.242308358 -0.160324446 S(ph)SSSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.294)S(0.294)S(0.294)S(0.046)QT(0.072)LTQFDSNIAPADPDTAIVHPVPIR 125.42 9.16E-06 105190000 3888.3 3025.5 4501.7 5416.3 4489.4 5081.1 3934.6 6143.9 3193.3 TRUE FALSE 3704.507765 3333.80189 4708.107398 4871.843234 5272.349939 4905.140233 3334.304506 5605.907545 3688.500655 1.004339734 0.9038366 1.276428511 1.320819403 1.429401926 1.329846648 0.903972865 1.519833686 1 11.84881878 3.736413415 24.9928662 1.24407049 0.954088158 0.31383498 0.184081902 208.570653 2427715.374 0.047458331 0.077694767 5450.212242 -3.736413415 -0.289982332 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.347)S(0.347)S(0.289)T(0.017)GNLLDKDDLAIPPPDYGAASR 136.49 1.77E-05 107210000 259900 264290 254600 286210 167240 264380 309030 303800 199690 TRUE FALSE 247615.0421 291221.4515 266273.6618 257439.627 196406.603 255224.4543 261881.7978 277197.6615 230656.9053 1.073521045 1.262574173 1.154414438 1.116114979 0.851509747 1.106511223 1.13537376 1.201774822 1 17.81538896 3.13263027 4.356809121 1.069267859 1.171805389 0.170604475 0.102385196 0.386025045 12.93526617 0.030292445 0.036915665 1357.157558 -3.13263027 0.10253753 S(ph)SSVPHPFQVTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.499)S(0.499)S(0.002)VPHPFQVTLLR;S(0.656)S(0.343)S(0.001)VPHPFQVTLLR 205.31 8.00E-09 304417000 286792 244709 259659 311225 268088 282094 332138 292876 259418 TRUE FALSE 273235.9105 269645.1253 271564.622 279940.0717 314842.4623 272325.014 281464.248 267230.2248 299647.2185 0.911858658 0.899875282 0.906281137 0.934232172 1.050710445 0.908818762 0.939318741 0.891816137 1 18.19290546 3.115237076 4.886458142 0.952859305 0.905817275 0.215638668 0.044469577 0.339021213 13.10063224 0.012534686 0.015150752 1303.878356 -3.115237076 -0.04704203 S(ph)SSYSEANEPDLQMANGGK ddPTM_SK-BR-3_Trastuzumab_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(0.331)S(0.331)S(0.331)YS(0.007)EANEPDLQMANGGK 137.61 3.70E-06 59007000 124650 101110 108630 130730 101870 127370 139480 133660 117190 TRUE FALSE 118758.0415 111413.224 113610.7929 117588.772 119636.0957 122959.145 118199.7643 121956.0218 135363.2267 0.877328684 0.823068618 0.839303227 0.86869067 0.883815337 0.908364465 0.873204394 0.900953862 1 17.04647634 -0.651006617 0.249862331 1.07354486 0.837726538 0.827698777 0.019764251 4.690247741 0.332475562 0.295964764 0.035477295 0.223353819 0.651006617 -0.235818322 S(ph)STPLHSPSPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.333)S(0.333)T(0.333)PLHSPSPIR 140.31 3.84E-05 159910000 300320 261660 361010 326470 1020300 142230 387580 155650 1127700 TRUE FALSE 286124.4688 288323.4515 377562.6656 293652.6153 1198239.997 137304.5394 328447.5526 142020.4608 1302577.957 0.21966015 0.221348327 0.289858019 0.225439571 0.919898875 0.105409844 0.252151935 0.109030297 1 20.31293829 -1.177972412 5.100695331 1.000045686 0.287651317 0.481194678 0.230701505 0.000112121 1.81E-05 0.208955013 0.049248024 0.066378524 1.177972412 -0.712394369 S(ph)STPPGESYFGVSSLQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 224.55 4.77E-19 919600000 1276600 1186600 1186400 1281800 752290 1272900 1355900 1400600 1030100 TRUE FALSE 1216257.648 1307515.889 1240797.614 1152951.029 883489.1378 1228819.154 1149032.552 1277956.039 1189842.647 1.022200415 1.098898155 1.042824962 0.96899454 0.742526031 1.032757699 0.965701267 1.074054659 1 20.18233936 3.259925245 4.685975556 0.956692493 1.061173666 0.18816434 0.088482807 0.283694109 15.19257922 0.024624664 0.032349784 1819.387662 -3.259925245 0.104481172 S(ph)SVKTPESIVPIAPELQPSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSVKTPESIVPIAPELQPSTSR 22 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.344)S(0.344)VKT(0.293)PES(0.018)IVPIAPELQPSTSR 60.687 0.03226 112050000 249860 220640 242630 242050 125310 263930 271920 267620 152000 TRUE FALSE 238049.613 243123.4668 253754.8255 217718.6741 147164.0243 254790.0379 230433.6098 244185.7741 175571.3837 1.355856564 1.384755657 1.44530857 1.240057859 0.838200516 1.451204818 1.312478178 1.390806229 1 17.42169819 -2.263068693 1.941821573 5.19E-05 1.308432117 0.224404662 0.176316739 3598683.446 536895.4876 15765419.88 0.04199231 0.005456715 2.263068693 1.308380174 S(ph)TAALEEDAQILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STAALEEDAQILK 13 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;Q15052-2;Q15052 B1ALK7;Q15052-2 ARHGEF7;ARHGEF6 Rho guanine nucleotide exchange factor 7;Rho guanine nucleotide exchange factor 6 1 S(0.993)T(0.007)AALEEDAQILK;S(0.987)T(0.013)AALEEDAQILK;S(0.989)T(0.011)AALEEDAQILK;S(0.989)T(0.011)AALEEDAQILK;S(0.99)T(0.01)AALEEDAQILK;S(0.995)T(0.005)AALEEDAQILK 307.97 1.72E-50 1601543000 1772480 1433880 1517290 1706980 1163840 1625280 1843170 1815590 1226810 TRUE FALSE 1688698.383 1579994.002 1586859.247 1535391.127 1366813.328 1568996.146 1561960.564 1656607.315 1417057.429 1.19169368 1.114982336 1.119827055 1.083506636 0.964543355 1.107221284 1.10225636 1.169047408 1 20.4344668 4.26308527 1.092252409 1.078273908 1.202791277 0.295289894 0.057500811 1.104010775 1.815765081 0.017599707 0.132288771 18326.74216 -4.26308527 0.12451737 S(ph)TDSSSVSGSLQQETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STDSSSVSGSLQQETK 16 0 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 S(0.915)T(0.085)DS(0.001)SSVSGSLQQETK;S(0.812)T(0.158)DS(0.024)S(0.005)S(0.001)VSGSLQQETK 239.33 8.41E-20 132680000 153160 134901 145453 167276 117598 149976 169720 156843 113714 TRUE FALSE 145920.4303 148647.5653 152122.1639 150461.0987 138107.054 144782.2935 143826.0969 143108.9954 131348.1863 1.110943625 1.131706264 1.158159607 1.145513333 1.051457639 1.102278589 1.094998727 1.089539181 1 17.00303675 0.005913166 0.297563976 0.966797463 1.136530762 0.67966355 0.026038408 3.366182078 0.454105613 0.164105717 0.033347274 1.013708682 -0.005913166 0.169733298 S(ph)TDSVPISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 STDSVPISK 9 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.987)T(0.012)DS(0.001)VPISK;S(0.993)T(0.006)DS(0.001)VPISK;S(0.917)T(0.082)DS(0.001)VPISK;S(0.987)T(0.013)DSVPISK;S(0.983)T(0.017)DSVPISK 198.45 2.76E-05 2400770000 7375120 6532180 5525670 7796470 4497270 7057030 7892450 7904640 5849450 TRUE FALSE 7026512.694 7197816.568 5779027.435 7012754.023 5281592.464 6812643.282 6688311.798 7212467.816 6756552.831 1.039955266 1.065309004 0.855321875 1.037918921 0.781699277 1.008301637 0.989900022 1.067477454 1 22.68785595 2.035049917 24.99999335 1.01327869 0.970820593 0.089705377 0.088805071 633.4430518 451812.5554 0.033680799 0.024874817 108.4051506 -2.035049917 -0.042458097 S(ph)TFHAGQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STFHAGQLR 9 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 S(0.5)T(0.5)FHAGQLR;S(0.5)T(0.5)FHAGQLR 124.67 0.00033699 228963000 362090 182165 269050 310860 546720 289660 519220 287990 506200 TRUE FALSE 344974.7233 200727.8206 281386.2086 279611.7622 642067.7949 279629.0016 440003.4529 262772.0689 584698.9107 0.590004047 0.343301171 0.481249757 0.478214953 1.098116968 0.478244437 0.752529969 0.449414329 1 19.15733438 2.951200199 24.99623848 0.725497094 0.463314433 0.31061013 0.206305835 456.5902915 233874.4796 0.056488686 0.059916385 893.7173705 -2.951200199 -0.262182661 S(ph)TFSTNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.634)T(0.358)FS(0.009)TNYR;S(0.978)T(0.021)FSTNYR;S(0.853)T(0.147)FSTNYR 144.47 0.00061349 6200060000 676929 454024 678979 735004 780711 690881 903390 655884 776767 TRUE FALSE 644931.9077 500289.5618 710110.8588 661120.0015 916866.7512 666955.6177 765561.2636 598451.3199 897224.0592 0.718808085 0.557597132 0.791453207 0.736850505 1.021892739 0.743354585 0.853255389 0.667003201 1 19.77510878 3.482502316 2.546906682 0.834699968 0.639821607 0.313668949 0.117499406 0.290143681 3.770332167 0.030714757 0.048091112 3037.402292 -3.482502316 -0.194878361 S(ph)TGDIAGTVVPETNKEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.975)T(0.025)GDIAGTVVPETNKEPR;S(0.988)T(0.012)GDIAGTVVPETNKEPR;S(0.5)T(0.5)GDIAGTVVPETNKEPR 169.84 1.04E-11 358270000 204157 221978 202662 231198 121596 215367 218355 269296 165828 TRUE FALSE 194506.9032 244597.8106 211954.2532 207957.5378 142802.3039 207908.7868 185040.9344 245715.0146 191543.7593 1.015469801 1.276981362 1.106557864 1.085692056 0.745533576 1.085437539 0.966050447 1.282813992 1 17.5473145 3.111339986 4.000817411 1.008089924 1.146972559 0.111674682 0.145142976 0.392215714 11.59820118 0.040526254 0.049277878 1292.230496 -3.111339986 0.138882634 S(ph)TGSIDQLSHFHNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STGSIDQLSHFHNKR 15 1 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.518)T(0.48)GS(0.002)IDQLSHFHNKR 163.51 7.21E-07 276150000 404860 290590 365760 405010 390740 371140 491290 392770 11212 TRUE FALSE 385723.0702 320201.4514 382530.4578 364297.6253 458884.9323 358287.3287 416334.6873 358376.9766 12950.6997 29.78395602 24.72464491 29.53743556 28.1295709 35.43321543 27.66548041 32.14765975 27.67240265 1 13.66074243 0.945561424 21.964335 1.000000037 29.37199246 0.910498282 2.802647004 1190.443395 480309.1924 2.66482697 0.666206723 8.821885646 -0.945561424 28.37199242 S(ph)TKPSLS(ph)ERDIAMAT(ph)IYGQLYVLFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STKPSLSERDIAMATIYGQLYVLFLR 26 2 K7EIS6;A0A087WZD4;K7ENL9;Q96DM3 K7EIS6 C18orf8 Uncharacterized protein C18orf8 3 S(0.352)T(0.352)KPS(0.352)LS(0.935)ERDIAMAT(0.883)IY(0.063)GQLY(0.063)VLFLR 48.182 0.053061 225770000 25529 11369 43741 17961 159720 15129 67046 19568 18674 TRUE FALSE 24322.29476 12527.51403 45746.56812 16155.52616 187575.1174 14605.07894 56816.90132 17854.52218 21569.86855 1.127605146 0.580787685 2.120855211 0.748985842 8.696164143 0.677105607 2.634086582 0.827752944 1 14.39672976 S(ph)TMVGTPYWMAPEVVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STMVGTPYWMAPEVVTR 17 0 Q13177;H7C1X3;A0A087X294;O75914-2;O75914;O75914-4;O75914-3;H0YCG5;E9PM17;B3KNX7;Q13153;Q13153-2 Q13177;E9PM17 PAK2;PAK3;PAK1 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34;Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 3;Serine/threonine-protein kinase PAK 1 1 S(0.5)T(0.5)MVGTPYWMAPEVVTR 268.13 7.03E-28 64616000 51940 38433 46443 53783 47531 42621 54468 51114 47637 TRUE FALSE 49484.89914 42349.36639 48572.45749 48376.63066 55820.39135 41145.02408 46157.90623 46638.18719 55024.30266 0.899328056 0.769648398 0.882745535 0.87918662 1.014467947 0.747760936 0.838863993 0.847592517 1 15.74778134 -2.284943743 2.08770724 1.574761021 0.853932905 0.263412662 0.072986891 5032231.265 651016.5294 13660648.86 0.017334801 0.005188672 2.284943743 -0.720828116 S(ph)TNTAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STNTAVSR 8 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 S(0.98)T(0.019)NT(0.001)AVSR;S(0.98)T(0.02)NTAVSR 101.3 0.005765 423240000 393530 410780 305363 390416 340364 328822 356435 390180 384403 TRUE FALSE 374928.6168 452638.949 319364.1956 351170.6419 399723.3738 317434.8117 302054.2944 356013.7707 444014.254 0.844406713 1.019424365 0.719265638 0.790899479 0.900248968 0.714920318 0.680280625 0.801807076 1 18.76024647 3.73241586 24.97718162 0.780249877 0.93191554 0.196426808 0.103582768 550.6659051 2238345.156 0.02593656 0.041334568 5400.274803 -3.73241586 0.151665663 S(ph)TPDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPDLLR 7 0 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 S(0.992)T(0.008)PDLLR 109.71 0.0073072 25808000 101840 86364 90419 96150 88640 91506 100230 95496 78391 TRUE FALSE 97026.22503 95164.58979 94564.80059 86484.81933 104098.7879 88337.12428 84938.07265 87133.86398 90547.47591 1.071550853 1.050991083 1.044367053 0.955132304 1.149659744 0.975589031 0.938050142 0.962300308 1 16.4663868 2.026561358 24.99382407 0.959129977 1.051496953 0.427155577 0.048876373 177.2924027 166828.6626 0.016626516 0.012279194 106.3068766 -2.026561358 0.092366976 S(ph)TPLEENVVDREQIDFLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.637)T(0.363)PLEENVVDREQIDFLAAR;S(0.782)T(0.218)PLEENVVDREQIDFLAAR;S(0.576)T(0.424)PLEENVVDREQIDFLAAR 206.85 4.39E-22 182823000 64287 54651 62261.1 61177 55145 58004 70367 65730 70504 TRUE FALSE 61248.28091 60219.99903 65115.83302 55027.37173 64762.27054 55995.30694 59631.22177 59974.33274 81437.40024 0.752090326 0.739463672 0.799581431 0.675701478 0.795239906 0.687587113 0.732233858 0.736447045 1 16.31340389 -1.816131036 2.33642098 1.096993407 0.739169279 0.814512922 0.039022752 3070878.03 1806487.897 1676613.783 0.008467556 0.015271052 1.816131036 -0.357824128 S(ph)TPLSQPSANGVQTEGLDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.5)T(0.5)PLSQPSANGVQTEGLDYDR;S(0.467)T(0.467)PLS(0.065)QPSANGVQTEGLDYDR;S(0.497)T(0.497)PLS(0.007)QPSANGVQTEGLDYDR;S(0.5)T(0.5)PLS(0.001)QPSANGVQTEGLDYDR 192.49 1.12E-17 446350000 420011 346029 374357 462522 363234 433990 480651 453014 435262 TRUE FALSE 400157.9124 381289.7485 391521.6387 416028.4098 426581.8946 418960.8175 407318.8622 413345.6926 502760.2079 0.795922004 0.758392853 0.778744285 0.827488738 0.848479828 0.833321355 0.810165275 0.82215276 1 18.93951094 -5 0.185096626 1.820556026 0.767033099 0.876683635 0.023005791 46.6469572 0.452936457 14.07198967 0.071516598 1.00E-05 5 -1.053522927 S(ph)TPVRDR ddPTM_SK-BR-3_Trastuzumab_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(0.5)T(0.5)PVRDR;S(0.5)T(0.5)PVRDR 82.645 0.014491 289930000 513899 501558 455250 572292 422376 501669 506287 547551 439688 TRUE FALSE 489608.0127 552667.3304 476123.6628 514764.1209 496038.2407 484296.0767 429043.6196 499604.5317 507872.5694 0.964037127 1.088200788 0.937486471 1.01356945 0.976698232 0.953577936 0.844785967 0.983720251 1 18.95410703 2.288924937 2.665342106 0.921583421 1.006855322 0.122041969 0.05753127 0.323070946 4.71226199 0.022457069 0.016706728 194.5023876 -2.288924937 0.085271901 S(ph)TSATDTHHVEMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 STSATDTHHVEMAR 14 0 H3BTL2;H3BS02;O14874-2;O14874-3;O14874;H3BQP2;H3BNP3 H3BTL2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 S(0.853)T(0.127)S(0.019)ATDTHHVEMAR;S(0.865)T(0.125)S(0.01)ATDTHHVEMAR;S(0.497)T(0.497)S(0.006)ATDTHHVEMAR;S(0.88)T(0.117)S(0.002)ATDTHHVEMAR;S(0.645)T(0.178)S(0.178)ATDTHHVEMAR;S(0.868)T(0.13)S(0.002)ATDTHHVEMAR;S(0.862)T(0.131)S(0.007)ATDTHHVEMAR;S(0.813)T(0.179)S(0.008)ATDTHHVEMAR;S(0.812)T(0.182)S(0.005)ATDTHHVEMAR;S(0.966)T(0.026)S(0.008)ATDTHHVEMAR;S(0.984)T(0.015)S(0.001)ATDTHHVEMAR;S(0.935)T(0.061)S(0.004)ATDTHHVEMAR;S(0.976)T(0.018)S(0.005)ATDTHHVEMAR 277.34 2.52E-33 9159860000 2959919 2247334 2566264 2552149 2609516 2062041 2766407 2386243 506654 TRUE FALSE 2820009.495 2476339.89 2683929.743 2295602.134 3064614.764 1990632.003 2344340.804 2177290.913 585223.3147 4.818689591 4.231444352 4.586163393 3.922608816 5.236658703 3.401491282 4.00589099 3.720444586 1 19.15862772 -0.513564538 0.365521225 1.52E-18 4.605467379 0.844620004 0.453459218 2.839022979 0.376482867 3.892236191 0.312271125 0.306503517 0.513564538 4.605467379 S(ph)TSEGAWPQLPSGLSMMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSEGAWPQLPSGLSMMR 18 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 1 S(0.333)T(0.333)S(0.333)EGAWPQLPSGLSMMR 71.601 0.090895 25369000 33643 33025 27603 30660 28323 32037 38660 36142 40464 TRUE FALSE 32052.76206 36390.28505 28868.62485 27577.99855 33262.52223 30927.55066 32761.70696 32977.21488 46738.95046 0.685782666 0.778585841 0.617656678 0.590043171 0.711666007 0.661708283 0.700950848 0.705561733 1 15.51233772 0.197129665 1.300172367 1.000424934 0.683717913 0.793560106 0.051207279 3.320177243 4.872042675 0.053673223 0.015255871 1.574452872 -0.197129665 -0.316707021 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.414)T(0.414)S(0.171)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.296)T(0.296)S(0.296)FRGGMGS(0.055)GGLAT(0.055)GIAGGLAGMGGIQNEK;S(0.32)T(0.32)S(0.32)FRGGMGS(0.022)GGLAT(0.016)GIAGGLAGMGGIQNEK;S(0.332)T(0.332)S(0.332)FRGGMGS(0.004)GGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.391)T(0.303)S(0.303)FRGGMGS(0.001)GGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.327)T(0.327)S(0.327)FRGGMGS(0.009)GGLAT(0.009)GIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.338)T(0.338)S(0.324)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.329)T(0.329)S(0.329)FRGGMGS(0.014)GGLATGIAGGLAGMGGIQNEK 216.6 4.91E-35 2781618000 2604713 2012176 2455589 2905628 2002938 2925118 3243362 2750588 2518591 TRUE FALSE 2481593.379 2217219.022 2568180.185 2613548.753 2352249.753 2823820.43 2748527.558 2509731.933 2909161.229 0.853027104 0.762150616 0.882790599 0.898385668 0.808566308 0.970664809 0.94478351 0.862699498 1 21.47217182 2.415116671 0.368514133 0.987287394 0.788721421 0.441356029 0.053862422 1.185937713 0.365370366 0.059536694 0.08483361 260.0858178 -2.415116671 -0.198565973 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.353)T(0.353)S(0.294)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.353)T(0.353)S(0.294)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.321)T(0.321)S(0.321)FRGGMGS(0.036)GGLAT(0.001)GIAGGLAGMGGIQNEKETMQSLNDR;S(0.333)T(0.333)S(0.333)FRGGMGS(0.001)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.345)T(0.345)S(0.31)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.325)T(0.325)S(0.325)FRGGMGS(0.025)GGLAT(0.001)GIAGGLAGMGGIQNEKETMQSLNDR;S(0.328)T(0.328)S(0.328)FRGGMGS(0.016)GGLAT(0.001)GIAGGLAGMGGIQNEKETMQSLNDR;S(0.268)T(0.268)S(0.268)FRGGMGS(0.18)GGLAT(0.015)GIAGGLAGMGGIQNEKETMQSLNDR;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.322)T(0.322)S(0.322)FRGGMGS(0.034)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 250.97 4.71E-52 5392970000 957865 361293 1063634 768599 1071696 1065898 1743146 1068192 1779554 TRUE FALSE 912588.6198 398109.1675 1112402.671 691337.9683 1258599.443 1028985.685 1477197.063 974655.4456 2055518.146 0.443970111 0.193678255 0.541178716 0.3363327 0.612302765 0.500596741 0.718649488 0.474165333 1 20.97107068 0.201548517 0.184278388 1.304289527 0.190416639 0.670886771 0.124680388 4.695842945 0.362293622 1.415978924 0.517311154 1.590554362 -0.201548517 -1.113872888 S(ph)TSGSPRPAGAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.25)T(0.25)S(0.25)GS(0.25)PRPAGAKPK 50.608 0.089288 40545000 135140 103530 110000 138790 83813 132340 158000 142630 94884 TRUE FALSE 128752.2 114079.8247 115043.6088 124838.5655 98429.96066 127757.0326 133894.1981 130140.5611 109598.1261 1.174766436 1.04089211 1.04968591 1.139057482 0.898098938 1.165686286 1.221683279 1.18743418 1 16.74186361 2.057697808 24.99996452 1.169179202 1.06800995 0.138132199 0.093152876 113.7434342 49283.34556 0.032212558 0.023790547 114.2083371 -2.057697808 -0.101169252 S(ph)TSMFDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSMFDMR 8 0 Q9UPQ0-4;Q9UPQ0-5;E7EPK0;Q9UPQ0-9;E9PDJ9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(0.375)T(0.375)S(0.25)MFDMR 74.376 0.043151 16844000 76594 55412 73405 74935 76612 73650 85644 76435 81331 TRUE FALSE 72973.55341 61058.5458 76770.69186 67402.39143 89973.10854 71099.48203 72577.43484 69741.94619 93943.3961 0.776782152 0.649950378 0.817201581 0.717478761 0.957737449 0.75683321 0.772565586 0.742382638 1 16.51950413 -5 0.203114083 2.051847083 0.731295767 0.432873986 0.079764383 130.2271693 1.291595786 55.84974251 0.175312655 1.00E-05 5 -1.320551316 S(ph)TSPASEKADPGAVKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSPASEKADPGAVKDK 17 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 S(0.331)T(0.331)S(0.331)PAS(0.007)EKADPGAVKDK 65.784 0.022181 160960000 263500 129490 277000 199160 149850 240820 340310 298610 161250 TRUE FALSE 251044.8772 142685.1782 289700.724 179140.0584 175983.7926 232480.343 288389.4593 272462.1254 186255.8264 1.347849793 0.766070952 1.555391472 0.961795729 0.944849865 1.24817756 1.548351344 1.462838133 1 17.50692603 1.999633572 24.23343977 1.398059448 1.101333325 0.119235835 0.260028438 12.54765183 829876.4506 0.090467689 0.066015293 99.9156623 -1.999633572 -0.296726123 S(ph)TSQSIVSLLTGTAGEDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 STSQSIVSLLTGTAGEDEK 19 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 S(0.333)T(0.333)S(0.333)QSIVSLLTGTAGEDEK;S(0.322)T(0.322)S(0.322)QS(0.035)IVSLLTGTAGEDEK;S(0.459)T(0.459)S(0.08)QS(0.003)IVSLLTGTAGEDEK;S(0.333)T(0.333)S(0.333)QS(0.001)IVSLLTGTAGEDEK;S(0.325)T(0.325)S(0.325)QS(0.026)IVSLLTGTAGEDEK 242.18 2.24E-24 203865000 500779 475669 455838 531183 319464 526995 554489 585353 391092 TRUE FALSE 477108.1691 524140.2119 476738.6232 477787.4757 375178.4205 508745.031 469891.5192 534096.3882 451740.5499 1.056155285 1.160268238 1.055337236 1.057659038 0.830517474 1.126188541 1.040180075 1.182307827 1 18.7851349 3.541786943 7.596413245 1.039244199 1.108476579 0.082404921 0.0936282 0.677381348 71.19120929 0.023783368 0.036776202 3481.66469 -3.541786943 0.069232379 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.36)T(0.36)S(0.275)T(0.005)PNVHMVSTTLPVDSR;S(0.352)T(0.352)S(0.289)T(0.008)PNVHMVSTTLPVDSR;S(0.35)T(0.35)S(0.295)T(0.005)PNVHMVSTTLPVDSR;S(0.446)T(0.301)S(0.248)T(0.005)PNVHMVSTTLPVDSR;S(0.351)T(0.351)S(0.29)T(0.008)PNVHMVSTTLPVDSR 197.37 5.10E-16 1489250000 569577 496213 561466 641165 617620 562348 668307 636900 632145 TRUE FALSE 542654.224 546777.6688 587209.7715 576713.8761 725332.7325 542873.7478 566344.4928 581129.6596 730174.8181 0.743183975 0.748831178 0.804204359 0.789829862 0.993368594 0.743484621 0.775628629 0.795877433 1 19.47788239 -5 0.224323936 2.051438305 0.76830705 0.4278453 0.072624186 154.4119447 1.544802669 73.78517549 0.132090451 1.00E-05 5 -1.283131256 S(ph)TTLPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STTLPRPR 8 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.333)T(0.333)T(0.333)LPRPR;S(0.333)T(0.333)T(0.333)LPRPR 54.549 0.078458 925320000 1696900 1372970 1433530 1599200 1792420 1465670 1721040 1612250 1745240 TRUE FALSE 1616690.9 1512877.204 1499258.768 1438445.378 2105017.48 1414913.48 1458463.739 1471072.843 2015882.906 0.801976591 0.750478711 0.743723142 0.713556017 1.044216147 0.701882771 0.723486337 0.729741216 1 20.94298041 -1.453638853 2.945793417 1.005565224 0.773489094 0.334161037 0.099249269 18484696.98 21857436.47 850876.786 0.022873579 0.035185291 1.453638853 -0.23207613 S(ph)TTPANLDSESEHFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STTPANLDSESEHFFR 16 0 Q13315 Q13315 ATM Serine-protein kinase ATM 1 S(0.367)T(0.367)T(0.266)PANLDSESEHFFR 156.49 7.83E-09 0 39839 35033 34193 42535 35333 36455 50057 40224 43942 TRUE FALSE 37955.88942 38602.90253 35760.78287 38259.30099 41495.06401 35192.55421 42419.88529 36701.77332 50756.30094 0.747806454 0.760553898 0.704558492 0.753784265 0.817535227 0.693363259 0.835756044 0.723097874 1 15.63129931 -5 0.302670284 3.054577494 0.745280247 0.744780305 0.045004888 125.4837209 1.153960428 163.7392034 0.0387304 1.00E-05 5 -2.309297247 S(ph)TTPPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR 142.41 1.09E-07 2354760000 1950750 1921030 1739530 2200000 1235080 2011430 2032470 2118740 1443950 TRUE FALSE 1858541.914 2116785.141 1819289.171 1978851.82 1450477.561 1941773.675 1722379.373 1933211.893 1667870.391 1.114320347 1.269154457 1.090785699 1.186454194 0.869658439 1.164223362 1.032681785 1.159090001 1 20.66957575 S(ph)VASSQPAKPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.999)VAS(0.001)SQPAKPTK;S(0.949)VAS(0.05)SQPAKPTK 138.81 4.11E-05 360710000 582210 574210 509900 628820 363760 561920 635540 626210 421860 TRUE FALSE 554690.0871 632722.6518 533279.4194 565609.8189 427199.6288 542460.5695 538576.7005 571375.7327 487279.8942 1.138339779 1.298478881 1.094400622 1.160749347 0.876702761 1.113242258 1.105271748 1.172582205 1 18.89439117 3.605477912 6.157390791 1.076855589 1.21794443 0.295039246 0.092621399 0.263219507 12.0545129 0.023589444 0.036732006 4031.60441 -3.605477912 0.141088841 S(ph)VDEVFDEVVQIFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDEVFDEVVQIFDK 15 0 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 1 S(1)VDEVFDEVVQIFDK 82.651 0.010904 48612000 8262.3 9050.1 6058.5 10269 5578.9 5111.1 6891.6 6858.5 3882.1 TRUE FALSE 7871.757453 9972.315479 6336.288218 9236.74061 6551.858394 4934.101325 5840.159847 6257.933381 4484.116241 1.755475779 2.223919931 1.413051731 2.059879832 1.461125903 1.100350896 1.302410449 1.395577867 1 12.13060796 2.546287007 4.209250614 1.231155708 1.883942211 0.640583176 0.233609235 0.133788593 4.577808379 0.07385493 0.067666295 351.7928487 -2.546287007 0.652786503 S(ph)VDEVFDEVVQIFDKEG ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDEVFDEVVQIFDKEG 17 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 1 S(1)VDEVFDEVVQIFDKEG 206.59 1.80E-11 84561000 42318 34577 37242 38651 22551 36462 42540 28437 28751 TRUE FALSE 40317.71201 38100.43561 38949.58254 34765.72805 26483.88726 35199.3118 36049.7417 25946.90553 33209.55824 1.214039395 1.147273184 1.172842537 1.046859094 0.797477855 1.059915087 1.085523073 0.781308361 1 15.01931091 3.115023791 3.960148664 0.967029222 1.176726539 0.523084962 0.100066929 0.187670419 5.454685707 0.029152521 0.035502887 1303.238168 -3.115023791 0.209697317 S(ph)VDEVNYWDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVDEVNYWDK 10 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK 210.4 8.17E-08 607220000 1095470 1622040 808700 1194130 557460 1046050 658620 913530 383628 TRUE FALSE 1043689.304 1787327.72 845779.6949 1074093.784 654680.8475 1009825.026 558135.4226 833536.4703 443119.0709 2.355324725 4.033515679 1.908696218 2.42393942 1.47743776 2.278902201 1.259560825 1.881066569 1 18.75733489 3.617538325 6.744170109 1.763616522 3.189804468 0.517609412 0.582030295 0.165475634 8.447628464 0.144189713 0.224213146 4145.131617 -3.617538325 1.426187946 S(ph)VDEVNYWDKQDHPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVDEVNYWDKQDHPISR 17 1 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR 292.29 3.07E-46 1754841000 2435522 2107474 2005054 2072660 1435729 1908651 1923669 2188264 1223232 TRUE FALSE 2320399.702 2322227.997 2096987.709 1864312.279 1686119.683 1842553.937 1630177.963 1996648.003 1412924.571 1.642267216 1.643561195 1.484146962 1.319470492 1.19335435 1.304070985 1.153761494 1.413131348 1 20.43025302 3.338668242 1.699399173 1.221981315 1.649924321 0.739821069 0.105109312 0.150490477 0.892989976 0.029578915 0.045498281 2181.063157 -3.338668242 0.427943006 S(ph)VDFDSLTVR ddPTM_SK-BR-3_Trastuzumab_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 216.35 8.14E-09 893050000 976370 804920 823430 1097660 863320 1033430 1246560 861160 804470 TRUE FALSE 930218.9251 886942.2631 861185.08 987321.1314 1013882.735 997642.06 1056374.377 785752.2651 929223.0989 1.001071676 0.954498725 0.926779673 1.062523233 1.091107976 1.073630284 1.136836115 0.845601305 1 19.82566549 3.226586298 24.97662401 1.053306397 0.965192125 0.133780382 0.080114068 319.7352099 666918.3115 0.021798973 0.026245947 1684.947206 -3.226586298 -0.088114272 S(ph)VDISLGDSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDISLGDSPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.998)VDISLGDS(0.001)PR 92.247 0.010635 141660000 80599 66131 70261 78081 69846 71605 81058 70960 75246 TRUE FALSE 76789.245 72869.82408 73482.53635 70232.14954 82027.12029 69125.3009 68691.11337 64746.36622 86914.76538 0.883500573 0.838405578 0.845455154 0.808057748 0.943765078 0.795322873 0.790327317 0.744940931 1 16.40731367 S(ph)VDLDLLCGHYNNDGNAPSFGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVDLDLLCGHYNNDGNAPSFGLLR 24 0 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(1)VDLDLLCGHYNNDGNAPSFGLLR;S(1)VDLDLLCGHYNNDGNAPSFGLLR 200.52 9.80E-25 127912000 43941 32231 34424 41636 41650 45666 49461 42037 39394 TRUE FALSE 41863.99601 35515.37554 36002.37445 37450.67018 48913.74681 44084.57497 41914.81604 38356.01743 45503.02032 0.920026752 0.780505894 0.791208456 0.823037018 1.074956046 0.968827446 0.921143602 0.842933439 1 15.47367469 2.792515454 24.93280853 0.954426857 0.828728471 0.478695139 0.068678865 283.3793479 130950.4374 0.020890869 0.022158101 620.1767111 -2.792515454 -0.125698386 S(ph)VEDVRPHHTDANNQSACFEAPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SVEDVRPHHTDANNQSACFEAPDQK 25 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.985)VEDVRPHHT(0.013)DANNQS(0.003)ACFEAPDQK;S(0.948)VEDVRPHHT(0.052)DANNQSACFEAPDQK;S(0.926)VEDVRPHHT(0.074)DANNQSACFEAPDQK;S(0.892)VEDVRPHHT(0.108)DANNQSACFEAPDQK;S(0.901)VEDVRPHHT(0.099)DANNQSACFEAPDQK;S(0.811)VEDVRPHHT(0.189)DANNQSACFEAPDQK 174.98 1.45E-12 4692310000 4850080 4147690 4627470 5259960 3130000 5092840 5582630 5003200 171711 TRUE FALSE 4620826.33 4570344.327 4839644.077 4731218.828 3675871.009 4916473.674 4730897.261 4565093.284 198339.0649 23.29761075 23.04308699 24.40086162 23.85419549 18.53326782 24.78822655 23.8525742 23.01661191 1 17.59760933 0.890532271 19.79579426 1.000000021 23.16625464 0.94226439 1.719054522 5606.03658 1013780.379 1.554469775 0.388617438 7.771990669 -0.890532271 22.16625462 S(ph)VENLPECGITHEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SVENLPECGITHEQR 15 0 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.999)VENLPECGIT(0.001)HEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR 272.36 1.30E-33 6743620000 3448760 3100630 3269240 3485760 3117096 3318150 3927520 3534645 3484387 TRUE FALSE 3285743.95 3416587.722 3419137.888 3135364.782 3660716.555 3203241.633 3328304.69 3225132.745 4024727.94 0.816389082 0.848899049 0.849532674 0.779025273 0.909556276 0.795890227 0.826963894 0.80132938 1 21.94045983 -1.383098467 5.536509981 1.000065505 0.829488672 0.688428456 0.036263964 2.56E-05 2.85E-06 0.030610919 0.007212297 0.041390582 1.383098467 -0.170576833 S(ph)VEPQDAGPLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVEPQDAGPLER 12 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 S(1)VEPQDAGPLER;S(1)VEPQDAGPLER 138.19 8.28E-05 141050000 187140 168857 191536 230370 170922 194484 225210 192479 182021 TRUE FALSE 178294.2631 186063.7203 200318.1151 207212.7699 200730.7427 187748.9703 190850.0782 175624.5184 210247.887 0.848019286 0.884973081 0.952771121 0.985564102 0.954733698 0.892988619 0.907738389 0.835321205 1 17.68173178 3.974944916 3.667041281 0.928206808 0.859238574 0.261238716 0.047426623 0.299169313 8.688018907 0.01225471 0.025723943 9439.411443 -3.974944916 -0.068968234 S(ph)VGGSGGGSFGDNLVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.891)VGGS(0.098)GGGS(0.011)FGDNLVTR 156.67 8.34E-09 0 46850 42796 46309 47428 41810 48275 55098 48594 49917 TRUE FALSE 44635.49335 47156.96106 48432.31346 42660.44733 49101.65076 46603.22465 46691.78816 44338.85175 57657.87342 0.774143941 0.817875483 0.839994793 0.739889365 0.851603569 0.808271653 0.80980767 0.768999082 1 15.81523001 -1.225558817 4.603253692 1.000053688 0.802835705 0.778221272 0.03332305 1.63E-05 2.74E-06 0.028605195 0.006740476 0.059489618 1.225558817 -0.197217983 S(ph)VHREESCSDSGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVHREESCSDSGTK 14 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK 189.56 7.83E-08 227360000 151662 127323 157202 174096 109189 142753 181471 175730 131484 TRUE FALSE 144493.2378 140297.3585 164409.8672 156595.5393 128231.527 137809.4278 153784.266 160342.1496 151873.8672 0.951402901 0.923775506 1.082542179 1.031089431 0.844329109 0.907393947 1.012578851 1.055758654 1 17.21251412 1.574206308 6.546278822 1.029547781 0.95588219 0.184327932 0.065935295 0.221810025 19.26073782 0.037090029 0.017329481 37.51511727 -1.574206308 -0.073665592 S(ph)VIDPVPAPVGDSHVDGAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVIDPVPAPVGDSHVDGAAK 20 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)VIDPVPAPVGDSHVDGAAK 247.54 2.47E-30 166270000 351320 255190 336180 344100 265230 363520 435690 405720 240160 TRUE FALSE 334713.7998 281194.1511 351594.1855 309510.4143 311486.028 350931.2112 369217.4885 370193.0059 277402.7862 1.206598551 1.013667364 1.267450087 1.115743711 1.122865535 1.265060153 1.330979741 1.334496351 1 18.08162275 2.233830157 24.19785649 1.267970628 1.137107663 0.089806311 0.114468553 108.707863 556066.9108 0.038022773 0.029021373 171.3287147 -2.233830157 -0.130862965 S(ph)VKEDSVPTGAEENVVCESPVEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVKEDSVPTGAEENVVCESPVEIIK 25 1 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 S(0.681)VKEDS(0.296)VPT(0.023)GAEENVVCESPVEIIK;S(0.928)VKEDS(0.072)VPTGAEENVVCESPVEIIK;S(0.633)VKEDS(0.367)VPTGAEENVVCESPVEIIK;S(0.515)VKEDS(0.242)VPT(0.242)GAEENVVCESPVEIIK 243.64 6.16E-39 303518000 363988 256368 272612 491634 213697 412799 502850 335926 197559 TRUE FALSE 346783.0086 282492.1907 285111.5299 442214.0163 250965.6891 398503.6671 426130.997 306510.5386 228195.4407 1.519675448 1.237939679 1.24941817 1.937874021 1.099783976 1.746326157 1.867394877 1.343193087 1 17.79991044 S(ph)VPGLNVDMEEEEEEEDIDHLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVPGLNVDMEEEEEEEDIDHLVK 23 0 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 S(1)VPGLNVDMEEEEEEEDIDHLVK 227.74 5.13E-33 55722000 33358 28293 30878 36199 23885 28894 37038 39528 26701 TRUE FALSE 31781.23345 31176.08887 32293.78684 32560.20775 28050.53644 27893.39353 31387.17285 36066.71877 30841.65471 1.030464602 1.010843587 1.04708347 1.055721817 0.909501669 0.904406518 1.017687707 1.169415815 1 14.91259255 1.45675021 25 1.087656065 0.996021396 0.249062027 0.064828576 10.90675375 13388.62105 0.034412193 0.01592619 28.62531075 -1.45675021 -0.091634669 S(ph)VPSIAAATGTHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVPSIAAATGTHSR 14 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 S(0.998)VPS(0.002)IAAATGTHSR 201.57 5.75E-08 0 64055 64421 67029 72835 75019 63578 81156 79450 81620 TRUE FALSE 61027.24709 70985.57314 70102.34595 65513.48742 88102.28985 61376.27792 68774.16167 72492.93681 94277.21274 0.647317049 0.752945182 0.743576777 0.694902676 0.934502488 0.651019224 0.729488703 0.768933814 1 16.52462149 -5 0.271279148 2.824214329 0.716655482 0.522245063 0.078954622 166.1579565 1.610405585 169.9701311 0.089626084 1.00E-05 5 -2.107558848 S(ph)VS(ph)PCSNVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVSPCSNVESR 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)VS(0.999)PCS(0.001)NVESR;S(1)VS(0.923)PCS(0.077)NVESR;S(1)VS(0.998)PCS(0.002)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.841)PCS(0.159)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.889)PCS(0.111)NVESR 247.73 5.58E-16 8564091000 5271644 4288456 4588680 5023884 4048329 4621295 5426483 4389375 4337312 TRUE FALSE 5022463.836 4725454.542 4799075.517 4518873.636 4754356.296 4461258.395 4598573.354 4005018.055 5009920.193 1.002503761 0.943219524 0.957914564 0.901985154 0.948988429 0.890484923 0.917893535 0.799417536 1 22.25635619 4.139097965 0.589963508 0.900559713 1.024377987 0.245634524 0.050982059 2.455888456 1.044022481 0.025120072 0.189538266 13775.20165 -4.139097965 0.123818274 S(ph)VS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPK;S(1)VS(1)PPPK 84.213 0.034567 480640000 3708300 3312200 3381500 3918500 2400500 3622700 4400500 3540100 2838700 TRUE FALSE 3533016.008 3649716.946 3536545.12 3524604.935 2819146.44 3497244.991 3729122.904 3230110.077 3278911.098 1.077496737 1.113088107 1.078573043 1.074931534 0.859781298 1.066587317 1.13730528 0.985116699 1 21.64478536 2.980580935 24.87224588 1.026211448 1.090952282 0.207251508 0.070609376 1412.016852 1808536.337 0.022378728 0.024085692 956.2708892 -2.980580935 0.064740834 S(ph)VS(ph)PPPKR ddPTM_SK-BR-3_Trastuzumab_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 83.397 0.040954 2558550000 2961410 2640770 2720880 3260870 1972020 3053020 3441050 2618120 2154880 TRUE FALSE 2821430.018 2909867.465 2845635.039 2933081.152 2315939.664 2947293.152 2916054.623 2388863.533 2489047.785 1.133537908 1.169068542 1.143262519 1.178394875 0.93045207 1.184104688 1.171554295 0.959749969 1 21.2471625 0.778794516 0.317670613 0.97426926 1.159375533 0.235257168 0.084697108 3.547899737 0.928649953 0.223542477 0.103510145 6.008893628 -0.778794516 0.185106273 S(ph)VS(ph)PYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(1)VS(0.999)PYSR;S(1)VS(0.992)PY(0.006)S(0.002)R;S(1)VS(0.991)PY(0.009)SR;S(1)VS(0.986)PY(0.014)S(0.001)R;S(1)VS(0.983)PY(0.002)S(0.015)R;S(1)VS(0.904)PY(0.002)S(0.094)R 109.42 0.010281 3128100000 6908650 6127700 6232550 7150130 6334420 6437120 7669730 6336990 7082420 TRUE FALSE 6582091.806 6752119.597 6518318.582 6431385.348 7439140.842 6214200.92 6499571.824 5782089.561 8180725.522 0.804585338 0.825369288 0.796789791 0.786163199 0.909349766 0.75961489 0.794498215 0.706794226 1 22.96379737 -1.887543583 2.647081001 1.100014525 0.801465092 0.609067831 0.050814266 12981662.91 6488214.447 8080823.929 0.011227693 0.012955567 1.887543583 -0.298549434 S(ph)VSGFLHFDTATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSGFLHFDTATK 13 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 1 S(1)VSGFLHFDTATK;S(0.714)VS(0.285)GFLHFDTATK 299.56 4.87E-41 90639000 265396 296095 233249 345240 208869 308684 289519 300895 182707 TRUE FALSE 252851.257 326267.4171 243943.6974 310535.8193 245295.6875 297994.1957 245347.5592 274547.0387 211040.2684 1.198118534 1.54599603 1.155910667 1.47145292 1.16231698 1.412025287 1.162562771 1.300922524 1 17.68715878 0.083492312 0.372794776 0.943080691 1.35500669 0.326772078 0.137312655 4.304714051 0.875091081 0.506454721 0.096555836 1.211971233 -0.083492312 0.411925999 S(ph)VSGS(ph)PEPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)VSGS(1)PEPAAK;S(1)VSGS(1)PEPAAK;S(1)VSGS(1)PEPAAK;S(0.986)VS(0.014)GS(1)PEPAAK;S(0.994)VS(0.006)GS(1)PEPAAK 205.26 4.45E-08 1922410000 6771900 5613720 6019270 6676760 4427790 6721580 7412640 6584610 5198630 TRUE FALSE 6451805.708 6185764.45 6295259.483 6005599.4 5199995.174 6488809.999 6281705.626 6008026.641 6004806.989 1.074440148 1.030135433 1.048369997 1.000131963 0.865972076 1.080602592 1.046112829 1.000536179 1 22.51768644 3.242842874 22.46716799 1.003737496 1.049865987 0.160071148 0.055493606 64.77660226 339841.8139 0.015914681 0.020759923 1749.213716 -3.242842874 0.046128491 S(ph)VSHGSNHTQKPDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.602)VS(0.398)HGSNHTQKPDEQR;S(0.989)VS(0.011)HGSNHTQKPDEQR;S(0.945)VS(0.055)HGSNHTQKPDEQR;S(0.734)VS(0.255)HGS(0.006)NHT(0.006)QKPDEQR;S(0.998)VS(0.002)HGSNHTQKPDEQR;S(0.971)VS(0.029)HGSNHTQKPDEQR;S(0.978)VS(0.022)HGSNHTQKPDEQR;S(0.902)VS(0.098)HGSNHTQKPDEQR;S(0.767)VS(0.233)HGSNHTQKPDEQR;S(0.996)VS(0.004)HGSNHTQKPDEQR 327.16 1.16E-71 1950791000 864133 681637 797677 967059 1070652 796075 1343338 1090243 60001.7 TRUE FALSE 823287.1456 751096.5853 834251.2795 869848.392 1257373.37 768506.7231 1138387.116 994775.5432 69306.45719 11.87893854 10.83732477 12.03713641 12.5507554 18.14222543 11.0885299 16.42541203 14.35328804 1 16.08070215 -0.314982122 11.35402999 0.999830977 13.2954757 0.734549116 2.344358967 0 0 2.296178254 0.541214405 0.4841923 0.314982122 12.29564472 S(ph)VSPLLSTHVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSPLLSTHVLGK 13 0 Q96H12;X6RL08;X6R907;Q96H12-2 Q96H12 MSANTD3 Myb/SANT-like DNA-binding domain-containing protein 3 1 S(0.575)VS(0.425)PLLSTHVLGK 151.9 2.90E-05 193070000 1518300 1311600 1351000 1770400 1616900 1352400 1975600 1715300 1757700 TRUE FALSE 1446532.968 1445253.531 1412944.686 1592436.028 1898886.848 1305566.049 1674185.936 1565099.239 2030275.139 0.71248125 0.711851071 0.69593754 0.784344938 0.935285475 0.643048828 0.824610371 0.770880364 1 20.95324382 -4.999999995 0.149337753 1.873580384 0.677806525 0.507969109 0.077283802 105.8775199 0.94093879 27.41988147 0.367582735 1.00E-05 4.999999995 -1.195773859 S(ph)VSPPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.5)VS(0.5)PPPKR;S(0.987)VS(0.013)PPPKR;S(0.99)VS(0.01)PPPKR 80.231 0.015915 851330000 1256950 1161720 1211920 1464840 1147840 1360370 1537170 1459420 1368120 TRUE FALSE 1197536.465 1280100.589 1267487.731 1317591.5 1348022.933 1313260.046 1302646.484 1331625.448 1580281.062 0.757799668 0.810046149 0.802064747 0.833770354 0.853027328 0.831029414 0.824313165 0.842651019 1 20.59174974 -5 0.154765382 1.670485993 0.761950198 0.909583977 0.018813571 38.93811229 0.352340987 8.015223384 0.092627235 1.00E-05 5 -0.908535795 S(ph)VSQDLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVSQDLIK 8 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(0.991)VS(0.009)QDLIK;S(1)VSQDLIK;S(0.997)VS(0.003)QDLIK;S(0.996)VS(0.004)QDLIK 133.42 0.00096525 537784000 1185790 1136550 867880 1233580 777010 1086890 1213380 1213050 868060 TRUE FALSE 1129740.057 1252365.737 907673.1565 1109578.195 912520.298 1049250.727 1028256.596 1106828.911 1002674.311 1.126726838 1.249025454 0.90525223 1.106618752 0.910086443 1.046452188 1.025514052 1.103876801 1 19.93542164 3.749183711 24.99974936 1.017060383 1.18787615 0.493541097 0.073187105 493.300061 1160899.809 0.016798271 0.029878681 5612.853555 -3.749183711 0.170815767 S(ph)VSSFPVPQDNVDTHPGSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSSFPVPQDNVDTHPGSGK 20 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9JAY7 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 S(0.999)VS(0.001)SFPVPQDNVDTHPGSGK;S(0.965)VS(0.016)S(0.019)FPVPQDNVDTHPGSGK 183.31 2.85E-17 1072840000 419040 324850 348470 434960 407500 355260 465930 437330 351710 TRUE FALSE 399232.8097 357952.5843 364447.6942 391236.9944 478567.871 342957.2571 394843.8211 399035.0668 406251.3905 0.982723552 0.881111038 0.897098946 0.963041613 1.178009189 0.84419959 0.971919925 0.982236802 1 18.63201323 3.009144211 23.04077756 0.988312296 0.921982522 0.140191446 0.083781959 165.1169317 416037.1991 0.023413218 0.027933931 1021.278551 -3.009144211 -0.066329774 S(ph)VSSSPWLPQDGFDPSDYAEPMDAVVKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVSSSPWLPQDGFDPSDYAEPMDAVVKPR 29 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 S(0.948)VS(0.024)S(0.024)S(0.004)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.932)VS(0.051)S(0.013)S(0.004)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.626)VS(0.165)S(0.165)S(0.045)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.747)VS(0.119)S(0.119)S(0.016)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.568)VS(0.144)S(0.144)S(0.144)PWLPQDGFDPSDYAEPMDAVVKPR 173.04 9.42E-13 521158000 439511 359389 382574 466510 374132 415767 478341 430764 365638 TRUE FALSE 418736.1861 396011.1477 400115.3963 419615.5285 439380.5023 401368.8845 405361.2951 393044.0205 422339.2736 0.991468737 0.937661194 0.947379089 0.993550813 1.040349619 0.950347054 0.959800143 0.930635736 1 18.68804289 5.932815435 2.826584661 0.968332872 11.28263714 0.03717648 0.033374901 3526.09783 71.25944283 0.008180675 234608.6755 856673.7015 -5.932815435 10.31430427 S(ph)VSTTNIAGHFNDESPLGLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSTTNIAGHFNDESPLGLRR 21 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.551)VS(0.423)T(0.026)T(0.001)NIAGHFNDESPLGLRR 162.15 8.92E-12 90996000 35757 16981 30525 22719 38812 24570 39343 36950 45703 TRUE FALSE 34066.83747 18711.38321 31924.60144 20435.24296 45580.80051 23719.13474 33340.50277 33714.46212 52790.38782 0.645322735 0.354446784 0.604742696 0.387101588 0.863429923 0.449307833 0.631563891 0.638647745 1 15.68798764 -1.793992671 0.255264444 1.448688923 0.49184034 0.482719319 0.143625791 21.19324906 0.889163275 5.966763522 0.193855898 0.016069684 1.793992671 -0.956848583 S(ph)VTQATQTSPGVPWPSQSANFPEFSFDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.543)VT(0.109)QAT(0.109)QT(0.128)S(0.11)PGVPWPSQSANFPEFSFDFTR 48.088 0.061582 37004000 37884 37140 37959 41662 30910 37384 42503 38831 39475 TRUE FALSE 36093.2984 40924.60822 39699.4577 37474.05661 36300.69421 36089.38271 36018.38673 35430.75178 45596.58139 0.791579046 0.897536767 0.870667416 0.821861102 0.796127541 0.791493169 0.789936123 0.777048426 1 15.47663804 3.09797704 5.947620313 0.812230672 0.853712542 0 0.06972908 0.549823969 28.04070829 0.018115838 0.021760853 1253.074926 -3.09797704 0.04148187 S(ph)VVDMDLDDTDDGDDNAPLFYQPGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVVDMDLDDTDDGDDNAPLFYQPGKR 26 1 E7EMW7;O95071-2;O95071;E7ET84 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 S(1)VVDMDLDDTDDGDDNAPLFYQPGKR;S(1)VVDMDLDDTDDGDDNAPLFYQPGKR;S(1)VVDMDLDDTDDGDDNAPLFYQPGKR 299.63 9.14E-71 267158000 222838 190869 210462 235272 156516 223006 253713 229966 172887 TRUE FALSE 212304.8894 210318.7681 220111.8909 211622.0116 183812.3408 215283.2463 215004.4221 209828.9579 199697.433 1.063132791 1.053187139 1.102226942 1.059713229 0.9204542 1.078047139 1.076650906 1.050734377 1 17.60745626 2.981783144 24.99027165 1.033326269 1.068962999 0.175386556 0.046452037 1695.163907 2325464.292 0.014239394 0.015388017 958.9216949 -2.981783144 0.03563673 S(ph)VVGTPAYLAPEVLLNQGYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVGTPAYLAPEVLLNQGYNR 21 0 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 S(1)VVGTPAYLAPEVLLNQGYNR 97.284 0.0012105 18653000 26166 25478 31554 38242 20304 27962 34357 33307 27937 TRUE FALSE 24929.18504 28074.23717 33000.78211 34397.8415 23845.01117 26993.66893 29115.20864 30390.46251 32269.32728 0.772535009 0.869997596 1.022667186 1.065960911 0.73893735 0.836511672 0.902256449 0.941775521 1 14.97787588 7.99999993 0.019976674 1.592171937 1.11E-06 0.115156393 0.099735238 7664.75862 11.80437648 348.8513063 630.3242247 99999983.91 -7.99999993 -1.592170827 S(ph)VVGTPAYLAPEVLR ddPTM_SK-BR-3_Trastuzumab_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 76.358 0.010366 0 10360 12064 10316 12431 12341 7290.6 14498 11440 12896 TRUE FALSE 9870.303332 13293.33532 10788.9988 11181.41226 14493.26649 7038.124694 12286.06383 10438.25295 14895.84582 0.662621207 0.892418966 0.724295816 0.750639635 0.972973718 0.472489094 0.824797999 0.700749261 1 13.86262242 -1.54732065 6.052079239 1.000443954 0.756224839 0.252264204 0.134836117 0.000713724 5.34E-05 0.115364413 0.027143265 0.028358245 1.54732065 -0.244219115 S(ph)VVSDLEADDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVVSDLEADDVK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.998)VVS(0.002)DLEADDVK;S(0.993)VVS(0.007)DLEADDVK;S(1)VVSDLEADDVK 318.18 1.54E-46 288966000 594372 519091 482620 1081300 324101 871250 718336 532656 284387 TRUE FALSE 566277.2135 571986.9631 504748.6044 972605.6697 380624.1118 841078.394 608740.6501 486013.8169 328488.2835 1.723888619 1.741270516 1.536580237 2.960853457 1.158714423 2.560451731 1.853157877 1.479546886 1 18.32548239 1.015532082 2.909851758 1.007426165 1.923914766 0.27368216 0.50478857 0.297414756 5.794598012 0.425616029 0.112822855 10.36411164 -1.015532082 0.916488601 S(ph)VVSDLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 S(0.791)VVS(0.209)DLEADDVKGS(0.004)VPLS(0.364)S(0.33)S(0.301)PPAT(0.002)HFPDETEITNPVPK 118.02 4.15E-06 23689000 34078 19374 32933 41124 26246 46364 48759 36797 25058 TRUE FALSE 32467.20048 21348.23263 34443.01063 36990.13739 30823.29409 44758.40305 41319.91903 33574.85961 28943.86666 1.121729894 0.737573624 1.189993411 1.277995709 1.06493353 1.546386444 1.42758808 1.159999111 1 14.82097005 3.548204715 5.62662331 1.286408193 0.930642657 0.312803613 0.185248879 0.203167539 11.82428219 0.048503195 0.07507716 3533.496903 -3.548204715 -0.355765535 S(ph)VVSFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVVSFDK 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(1)VVSFDK;S(0.922)VVS(0.078)FDK 107.15 0.0079105 137127000 516540 392150 415300 515190 391400 447990 499770 536070 410610 TRUE FALSE 492124.1779 432110.5308 434341.9158 463402.1224 459660.0361 432475.994 423520.9076 489128.8689 474285.3017 1.037612121 0.911077213 0.915781944 0.977053518 0.96916357 0.911847768 0.892966546 1.031296705 1 18.85539563 S(ph)VVSFDKVKEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVSFDKVKEPR 12 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.5)VVS(0.5)FDKVKEPR 74.816 0.018517 317670000 1268600 834560 1266100 1215400 961730 1418600 1910900 1801700 1388900 TRUE FALSE 1208635.792 919602.6128 1324151.937 1093225.683 1129455.408 1369473.526 1619357.109 1643933.597 1604283.518 0.753380421 0.573217017 0.82538524 0.681441697 0.704024815 0.853635602 1.009395839 1.024715131 1 20.6134977 1.984442212 2.163083467 1.018072059 0.695237333 0.826190858 0.063546733 0.11627292 1.010503294 0.03467286 0.018179562 96.48109232 -1.984442212 -0.322834726 S(ph)WASPVYTEADGTFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.95)WAS(0.044)PVY(0.001)T(0.005)EADGTFSR;S(0.562)WAS(0.438)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.999)WAS(0.001)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR 339.77 6.02E-72 389201000 253175 207817 218199 255686 254390 213929 272974 261733 273959 TRUE FALSE 241207.9195 228993.7886 228203.64 229983.9575 298755.5355 206520.5851 231326.8028 238814.271 316443.1625 0.762247215 0.723649033 0.721152065 0.726778091 0.944104885 0.652630897 0.73102165 0.754682987 1 18.27158687 0.916490435 18.76132601 1 0.748041516 0.522832778 0.074390619 2422.626372 544272.4928 0.066335659 0.016583915 8.250693137 -0.916490435 -0.251958484 S(ph)WDNILAPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SWDNILAPGPR 11 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 S(1)WDNILAPGPR;S(1)WDNILAPGPR;S(1)WDNILAPGPR;S(1)WDNILAPGPR 123.95 0.00037691 54782800 84996 72561 74788 81608 84149 66995 90895 81705 82590 TRUE FALSE 80978.40753 79955.0484 78217.10378 73404.60879 98824.55896 64674.94635 77027.29835 74550.47705 95397.63539 0.848851307 0.838124007 0.819906106 0.769459416 1.035922521 0.677951252 0.807434042 0.781470911 1 16.54166589 S(ph)WDQQIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWDQQIK 7 0 F8W8D3;Q14493;E7EUV9;H0YAE8;Q14493-2 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 S(1)WDQQIK;S(1)WDQQIK 119.68 0.0049587 40047000 167908 146442 124020 169808 111487 155909 175732 181937 127556 TRUE FALSE 159971.3216 161364.6063 129706.4397 152738.5772 130930.2975 150509.8322 148920.8559 166005.6318 147336.733 1.085753147 1.095209613 0.880340137 1.036663255 0.888646672 1.021536376 1.010751717 1.126709059 1 17.16875763 S(ph)WGQQAQEYQEQK ddPTM_SK-BR-3_Trastuzumab_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 339.58 8.20E-63 1082470000 989040 832890 856720 1035170 691440 958870 1159140 1087530 740210 TRUE FALSE 942290.0393 917762.4379 896001.4594 931112.7449 812026.9171 925664.0915 982291.9039 992300.1078 854997.9863 1.102096209 1.073408888 1.047957391 1.089023319 0.949741321 1.08265061 1.148882126 1.160587655 1 19.7055615 1.993715235 24.96215351 1.11871589 1.057519719 0.113993525 0.059344883 445.103603 1767889.066 0.021421722 0.015275662 98.56329977 -1.993715235 -0.061196171 S(ph)WHDVQVSSAYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 S(1)WHDVQVSSAYVK;S(1)WHDVQVSSAYVK 263.15 3.91E-24 217760000 170241 135179 149329 174335 178819 156809 198375 172036 164458 TRUE FALSE 162194.0453 148953.8938 156175.8824 156810.5146 210004.977 151378.665 168109.2503 156971.6158 189961.3067 0.853826751 0.784127549 0.822145757 0.825486607 1.105514489 0.796892102 0.88496575 0.826334681 1 17.53534606 2.958096494 24.98962242 0.908993725 0.817997781 0.239966253 0.087766927 742.311253 442685.3812 0.025056901 0.026579124 908.0222574 -2.958096494 -0.090995944 S(ph)WSTATSPLGGERPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.971)WS(0.022)T(0.007)ATSPLGGERPFR 141.6 9.62E-07 108570000 22701 25980 15535 30932 20836 24757 24652 24434 19427 TRUE FALSE 21627.96872 28627.39154 16247.29512 27822.65659 24469.7918 23899.65888 20890.88463 22294.42943 22439.63994 0.963828688 1.275750931 0.724044377 1.239888727 1.090471677 1.065064277 0.930981276 0.993528839 1 14.45376191 1.755715252 24.99999849 0.970250421 1.072556232 0.061178167 0.151260086 15.89554149 23190.46712 0.064173122 0.035587549 56.97905632 -1.755715252 0.102305811 S(ph)YDNLTTACDNTVPLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SYDNLTTACDNTVPLASR 18 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(1)YDNLTTACDNTVPLASR;S(1)YDNLTTACDNTVPLASR;S(0.928)YDNLT(0.065)T(0.006)ACDNTVPLASR;S(0.999)YDNLTTACDNTVPLASR 329.93 7.56E-75 884040000 525694 519630 509575 558990 458388 468859 548316 581823 464298 TRUE FALSE 500845.4864 572580.8878 532939.5178 502799.2632 538330.7221 452622.2953 464660.3237 530875.4937 536298.9625 0.933892328 1.067652425 0.993735873 0.937535402 1.003788483 0.843973841 0.866420329 0.989887229 1 19.03267794 2.261996849 24.9987182 0.906348693 0.991446692 0.175724807 0.060935274 270.2830739 288301.8521 0.020412726 0.017068989 182.8086952 -2.261996849 0.085097999 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(0.995)Y(0.005)DVPPPPMEPDHPFYSNISK 212.9 4.52E-23 2796966000 3150180 2876198 2986298 3452170 2276247 3262390 3744200 3664470 2503554 TRUE FALSE 3001277.234 3169285.846 3123222.717 3105151.313 2673223.756 3149412.616 3172953.523 3343589.58 2891792.368 1.037860556 1.095958991 1.080030071 1.073780866 0.924417598 1.089086703 1.097227297 1.156234319 1 21.46353254 2.03412502 24.99999689 1.094757315 1.048627427 0.102121107 0.059784406 380.7739474 278953.6531 0.021388872 0.015796668 108.1745308 -2.03412502 -0.046129888 S(ph)YELPDGQVITIGNER ddPTM_SK-BR-3_Trastuzumab_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(0.995)Y(0.005)ELPDGQVITIGNER;S(0.998)Y(0.002)ELPDGQVITIGNER 150.59 7.61E-07 119316000 133571 154850 118675 156404 106295 133844 128848 144356 101973 TRUE FALSE 127257.3635 170629.391 124116.3661 140681.9728 124832.8143 129208.9487 109189.8711 131715.4234 117786.452 1.080407478 1.448633422 1.053740596 1.194381615 1.059823199 1.09697632 0.927015538 1.118256141 1 16.84581408 2.894855504 1.113752994 1.015726354 1.246812129 0.301899035 0.116228222 0.468204601 1.231052315 0.051248924 0.055692818 784.9744187 -2.894855504 0.231085775 S(ph)YS(ph)PAHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.998)Y(0.014)S(0.988)PAHNR;S(0.997)Y(0.076)S(0.927)PAHNR 107.06 0.0021533 433680000 341364 331438 267919 329356 246592 314540 292084 262742 209952 TRUE FALSE 325228.4002 365211.909 280203.3512 296248.5091 289597.5667 303647.4009 247521.2213 239734.9176 242510.2839 1.34109117 1.505964626 1.155428738 1.221591532 1.194166128 1.252101132 1.020662783 0.988555676 1 17.8876864 2.716848116 0.453603241 0.969719065 1.457538735 0.685665301 0.090399378 0.620087337 0.262814782 0.085369184 0.120696724 521.0124676 -2.716848116 0.48781967 S(ph)YSHDVLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.497)Y(0.005)S(0.497)HDVLPK;S(0.5)YS(0.5)HDVLPK;S(0.497)Y(0.006)S(0.497)HDVLPK;S(0.5)YS(0.5)HDVLPK;S(0.5)YS(0.5)HDVLPK 103.08 0.0022415 718971000 3637940 2851060 2993180 4028140 3119590 3706300 4256360 3402120 2368160 TRUE FALSE 3465981.786 3141586.255 3130420.264 3623223.714 3663645.508 3577949.902 3606974.109 3104212.337 2735402.158 1.267083078 1.148491547 1.144409517 1.324567104 1.33934438 1.308016041 1.318626622 1.134828503 1 21.38332152 0.994680435 4.72875633 1.000384425 1.258039101 0.61949734 0.068611359 0.119765778 8.874257664 0.07355053 0.018647912 9.878259601 -0.994680435 0.257654676 S(ph)YSPAHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.777)YS(0.223)PAHNR;S(0.877)Y(0.001)S(0.122)PAHNR 105.4 0.0028315 612320000 405850 361000 366520 415940 500130 364130 480780 404290 424010 TRUE FALSE 386666.2748 397786.3104 383325.3045 374128.921 587352.5137 351520.0868 407428.1809 368888.2243 489763.3053 0.789496213 0.812201131 0.782674611 0.763897411 1.199257901 0.717734634 0.831887927 0.753196943 1 18.90172516 S(ph)YSPDGKES(ph)PSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.499)Y(0.002)S(0.499)PDGKES(1)PSDKK 152.18 3.61E-06 1068800000 1304300 1312100 1202500 1474600 464380 1676500 1388700 1639600 422400 TRUE FALSE 1242648.324 1445804.482 1257635.814 1326370.406 545367.725 1618442.385 1176828.31 1496027.932 487903.6347 2.546913439 2.963299264 2.577631575 2.718508968 1.117777541 3.317135331 2.412009721 3.066236498 1 18.89623671 2.921347535 24.99998339 2.329075786 2.721597751 0.091361631 0.735594485 319.3457221 101503.0099 0.204297729 0.216690528 834.3485871 -2.921347535 0.392521965 S(ph)YSPDGKESPSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.496)Y(0.007)S(0.496)PDGKESPSDKK 58.671 0.05583 4752100 33053 21043 28904 34760 15659 35293 50637 41149 17309 TRUE FALSE 31490.65019 23187.30562 30229.27699 31265.85876 18389.92464 34070.79456 42911.39564 37545.77542 19993.19132 1.575068717 1.159760103 1.511978579 1.563825317 0.919809367 1.704119869 2.146300456 1.877928082 1 14.28722115 2.017514193 24.7308419 1.832884784 1.355019775 0.133992951 0.355613264 241.9292483 341613.6462 0.119761196 0.088430392 104.1152132 -2.017514193 -0.477865009 S(ph)YSPYDYQPCLAGPNQDFHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.499)Y(0.002)S(0.499)PYDYQPCLAGPNQDFHSK 114.35 0.00011551 139040000 95957 96233 95699 107190 81762 100170 118060 103530 84787 TRUE FALSE 91421.30278 106039.2521 100086.8938 96415.05755 96021.26691 96701.08778 100047.7787 94464.36435 97935.33493 0.933486395 1.082747633 1.021969179 0.984476723 0.980455798 0.987397326 1.021569781 0.964558547 1 16.57954186 3.241888447 24.77737725 0.992311398 1.016416096 0.068817194 0.03832539 211.9654342 1578173.287 0.010689197 0.013898037 1745.373776 -3.241888447 0.024104698 S(ph)YVSEPELATLSGDMAQPSLGLVGPESR ddPTM_SK-BR-3_Trastuzumab_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(0.587)YVS(0.412)EPELAT(0.001)LSGDMAQPSLGLVGPESR;S(0.604)YVS(0.396)EPELATLSGDMAQPSLGLVGPESR 177.79 1.13E-17 65551000 63775 47125 55905 65424 60187 53101 71556 60784 67744 TRUE FALSE 60760.48214 51927.09108 58468.29955 58847.45522 70683.59374 51262.09906 60638.81798 55461.43072 78249.39353 0.776497803 0.663610141 0.747204507 0.752049985 0.903311713 0.655111775 0.774942977 0.708777771 1 16.25579195 -1.372130372 3.020394578 1.003218979 0.744748259 0.567729002 0.069148346 13562055.97 17259237 386373.6265 0.015261174 0.042449212 1.372130372 -0.25847072 SAAAGALGS(ph)PGLPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLRK 132.74 2.30E-05 364080000 218880 181350 216200 209210 175470 186460 251000 264370 230630 TRUE FALSE 208533.9762 199829.7712 226112.9839 188179.8133 206071.9124 180002.8434 212705.3401 241220.3613 266394.9225 0.782800116 0.750126051 0.84878864 0.706394144 0.773557959 0.675699228 0.798458687 0.905499095 1 18.02320706 1.121340914 2.495684697 0.996355836 0.75856461 0.763315548 0.04615884 0.114231998 1.344810082 0.039828965 0.010972409 13.22333237 -1.121340914 -0.237791226 SAAEMYGS(ph)SFDLDYDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAAEMYGSSFDLDYDFQR 18 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGS(0.98)S(0.02)FDLDYDFQR;SAAEMYGS(0.985)S(0.015)FDLDYDFQR;SAAEMYGS(0.877)S(0.123)FDLDYDFQR;S(0.002)AAEMYGS(0.985)S(0.013)FDLDYDFQR 178.12 9.48E-14 121922000 171076 124777 178650 198411 190625 181545 209170 188256 256285 TRUE FALSE 162989.5765 137491.9182 186841.2792 178466.3493 223869.9396 175258.0511 177257.2748 171771.3066 296028.3689 0.550587692 0.46445521 0.631160047 0.602869076 0.756244885 0.59203127 0.598784757 0.580252856 1 18.17537591 -5 0.212213028 2.978758866 0.530560172 0.752034582 0.07252702 74.71742916 0.745308211 63.09013259 0.155526926 1.00E-05 5 -2.448198695 SAAEMYGSSFDLDYDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 349.17 5.76E-90 370939000 400815 298015 365325 435476 416580 331483 395965 388822 444649 FALSE TRUE 381869.2693 328383.0673 382075.5126 391701.1251 489231.4201 320003.6606 335553.2669 354774.6844 513602.896 0.74351074 0.639371526 0.743912302 0.762653654 0.952548017 0.623056574 0.653332116 0.690756783 1 18.97029381 -2.080417482 2.506871951 1.448076503 0.718321952 0.457694985 0.093338494 8230371.113 2360923.834 21107900.19 0.023246327 0.008309646 2.080417482 -0.729754551 SAAEMYGSVTEHPS(ph)PSPLLSSSFDLDYDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.999)PS(0.001)PLLSSSFDLDYDFQR;SAAEMYGS(0.006)VT(0.006)EHPS(0.784)PS(0.203)PLLSSSFDLDYDFQR;SAAEMYGS(0.002)VT(0.002)EHPS(0.982)PS(0.013)PLLSSSFDLDYDFQR;SAAEMYGS(0.001)VT(0.009)EHPS(0.94)PS(0.05)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.5)PS(0.5)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.891)PS(0.108)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.663)PS(0.337)PLLSSSFDLDYDFQR 329.98 7.75E-106 400217000 247255 223476 269568 299019 308941 242464 315926 275007 299969 TRUE FALSE 235567.7462 246248.4585 281927.9594 268961.042 362820.2126 234067.4109 267725.6863 250925.9292 346486.6605 0.679875369 0.710701122 0.813676229 0.776252228 1.047140493 0.67554523 0.77268685 0.724200836 1 18.40244029 -5 0.175681961 1.855995121 0.720487387 0.287327464 0.107601532 176.2934272 1.683208393 53.46895419 0.350168277 1.00E-05 5 -1.135507733 SAAEMYGSVTEHPSPS(ph)PLLSSSFDLDYDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.047)PS(0.934)PLLS(0.006)S(0.006)S(0.006)FDLDYDFQR;SAAEMYGSVTEHPS(0.024)PS(0.976)PLLSSSFDLDYDFQR 122.37 2.67E-05 42137000 79753 74616 77920 97551 79676 81188 86890 83732 77491 TRUE FALSE 75983.23375 82219.45523 81492.70907 87744.98815 93571.46917 78376.4392 73633.33466 76399.98219 89507.90851 0.848899667 0.918571963 0.910452612 0.980304306 1.045398901 0.87563703 0.822646131 0.853555663 1 16.44972754 -1.728755815 9.013065891 1.000346552 0.903503909 0.16283376 0.0659114 0.000492222 1.48E-05 0.068439176 0.016074369 0.018674294 1.728755815 -0.096842642 SAALPIFSSFVSNWDEATKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAALPIFSSFVSNWDEATKR 20 1 O76021;J3QSV6;O76021-2;I3L3U9 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 184.78 6.23E-17 168935000 250570 232910 216110 257710 182786 228890 270020 257080 193770 FALSE TRUE 238726.0527 256643.7938 226018.8573 231804.5012 214663.8205 220963.4819 228823.4897 234568.7123 223818.862 1.066603818 1.14665847 1.009829356 1.035679027 0.959096202 0.987242451 1.02236017 1.048029242 1 17.7719721 3.722354144 24.1287001 1.00839417 1.10663114 0.631647641 0.03102872 270.1344333 402184.5668 0.008087094 0.012573966 5276.599646 -3.722354144 0.098236969 SAAMLGNSEDHTALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAAMLGNSEDHTALSR 16 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 160.43 8.78E-09 222510000 261980 267540 270710 291550 249970 279430 349720 312150 297290 FALSE TRUE 249596.7246 294802.6302 283122.3213 262242.8401 293564.6889 269753.269 296363.791 284816.4912 343392.2149 0.726856096 0.858501205 0.824486721 0.763683126 0.854896169 0.785554411 0.863047495 0.82942035 1 18.38949781 -5 0.175485534 1.755518861 0.771939546 0.703102711 0.039924798 70.96989368 0.677335117 18.61727589 0.122572955 1.00E-05 5 -0.983579316 SAAS(ph)PVVSSMPER ddPTM_SK-BR-3_Trastuzumab_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;S(0.001)AAS(0.986)PVVS(0.01)S(0.003)MPER;SAAS(1)PVVSSMPER 226.23 1.17E-11 1049610000 949650 776090 869890 882470 792170 894710 1083560 973930 914420 TRUE FALSE 904761.9265 855174.4533 909775.3169 793762.439 930324.1972 863725.9684 918243.0211 888647.5261 1056223.583 0.856600762 0.809652868 0.861347286 0.751509862 0.880802334 0.817749179 0.869364248 0.841344143 1 20.01048383 -0.424374362 0.508878979 1.026974856 0.827755258 0.669906195 0.036475861 4.381105064 1.024986176 0.244740208 0.015167147 0.37637922 0.424374362 -0.199219598 SAAVETASLS(ph)PSLVPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 SAAVETAS(0.005)LS(0.881)PS(0.115)LVPAR 200.26 1.32E-11 62757000 62881 52404 59028 64561 53420 55966 64521 57035 50365 TRUE FALSE 59908.73975 57744.02718 61734.49219 58071.20562 62736.43109 54027.88339 54677.13644 52040.71304 58175.34697 1.029796002 0.992585866 1.061179613 0.998209871 1.078402353 0.92870754 0.939867818 0.894549251 1 15.82812029 2.219592021 24.99977403 0.935956904 1.026239101 0.608118746 0.036142683 149.9253785 197593.7702 0.012063391 0.008924015 165.8028614 -2.219592021 0.090282197 SACGVCPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SACGVCPGR 9 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ;;; 113.89 0.0040182 214506000 164919 161583 162255 175568 173754 159364 191442 178639 182943 FALSE TRUE 157123.6057 178048.4914 169694.5522 157919.5711 204056.6426 153845.1847 162234.0068 162996.4221 211312.8661 0.743559106 0.84258235 0.803048841 0.747325868 0.965661232 0.72804457 0.767743157 0.771351149 1 17.68902109 -1.71307661 2.494559085 1.039278974 0.795840963 0.467015494 0.06843353 15992193.24 12078986.5 3921954.734 0.015454264 0.019360804 1.71307661 -0.243438011 SACKEDIPSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SACKEDIPSEK 11 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;; 125.61 0.00029611 1060670000 2818690 2375230 2471210 2962130 1575160 2946440 3097160 3234250 1836920 FALSE TRUE 2685456.11 2617268.637 2584517.423 2664371.065 1849867.405 2844404.044 2624631.359 2951041.924 2121780.172 1.265661799 1.233524883 1.218089158 1.255724368 0.871846872 1.340574335 1.236994951 1.39083302 1 21.01684376 -2.317914003 2.034211912 5.13E-05 1.225573772 0.213263759 0.136798446 3068452.829 371210.24 14106500.49 0.030887265 0.004809346 2.317914003 1.22552246 SACMLS(ph)SPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 2 S(0.198)ACMLS(0.401)S(0.401)PES(0.017)S(0.017)LT(0.965)PPLS(0.001)TNLHLESELDALASLENHVK 137.34 2.75E-09 29222000 38631 30716 32829 38660 30354 36661 46014 41395 26208 TRUE FALSE 36804.98919 33845.99532 34334.24212 34773.82335 35647.72799 35391.42038 38993.71919 37770.23435 30272.20279 1.215801488 1.118055252 1.134183804 1.148704757 1.177572978 1.169106214 1.288103131 1.247687016 1 14.88570604 1.97394548 24.08339187 1.215107306 1.158262121 0 0.08071374 1055.646595 975780.58 0.029728872 0.019245772 94.17713611 -1.97394548 -0.056845185 SACMLSS(ph)PESSLTPPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 S(0.32)ACMLS(0.32)S(0.359)PES(0.001)S(0.001)LTPPLSTNLHLESELDALASLENHVK 100.22 0.00018523 43502000 38123 32119 34446 44918 31839 37610 42597 47867 18892 TRUE FALSE 36321.00134 35391.96262 36025.38317 40402.7573 37391.71152 36307.55627 36098.0453 43675.51172 21821.67487 1.664446086 1.621871961 1.650899089 1.851496621 1.713512447 1.663829953 1.654228904 2.001473855 1 14.41347422 -0.806862346 5.344753196 0.999999703 1.70852806 0.790462748 0.11737973 3.88E-07 8.71E-08 0.106245561 0.025042308 0.15600469 0.806862346 0.708528357 SACMLSSPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 SACMLSSPES(0.001)S(0.006)LT(0.984)PPLS(0.007)T(0.001)NLHLESELDALASLENHVK;SACMLSSPESS(0.001)LT(0.999)PPLSTNLHLESELDALASLENHVK;SACMLSSPESSLT(1)PPLSTNLHLESELDALASLENHVK;S(0.002)ACMLS(0.005)S(0.018)PES(0.284)S(0.284)LT(0.29)PPLS(0.079)T(0.023)NLHLES(0.008)ELDALAS(0.008)LENHVK;SACMLS(0.001)S(0.003)PES(0.046)S(0.192)LT(0.751)PPLS(0.003)T(0.003)NLHLES(0.001)ELDALAS(0.001)LENHVK;SACMLSSPESSLT(0.999)PPLS(0.001)TNLHLESELDALASLENHVK;SACMLSSPES(0.004)S(0.021)LT(0.975)PPLSTNLHLESELDALASLENHVK 228.39 9.06E-40 650993000 261403 235425.2 250534 297553 215256 274078 321845 298977 140816.5 TRUE FALSE 249046.9982 259415.2955 262021.2317 267642.4071 252796.5782 264586.6101 272741.6342 272796.9889 162653.6036 1.531149588 1.59489424 1.610915626 1.645474808 1.554202136 1.626687662 1.676825032 1.677165355 1 17.31144326 -0.767554651 7.321888275 1.000003055 1.612266996 0.943931327 0.047076123 0 2.03E-10 0.049770307 0.011730974 0.170783279 0.767554651 0.612263941 SADGVIVSGVKDVDDFFEHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SADGVIVSGVKDVDDFFEHER 21 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ;; 222.51 2.35E-25 89527000 213518 120136 199979 181179 192092 210264 276442 227938 216056 FALSE TRUE 203425.4273 132377.995 209148.235 162966.5427 225592.784 202982.505 234265.6957 207978.5403 249560.861 0.815133537 0.530443734 0.838065048 0.653013225 0.90395899 0.81335873 0.938711682 0.833378037 1 17.92903217 2.629720288 1.145156157 0.912920797 0.68617073 0.431617539 0.102240464 0.398428278 1.073776366 0.049118011 0.040836499 426.3048639 -2.629720288 -0.226750067 SADTLWDIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SADTLWDIQK 10 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;; 240.46 6.54E-12 598158000 1699570 1306700 1034760 1232960 1344370 1255040 1841530 1480120 1402230 FALSE TRUE 1619234.694 1439854.216 1082204.77 1109020.518 1578827.702 1211577.65 1560570.776 1350512.846 1619680.667 0.999724654 0.888974132 0.668159343 0.684715537 0.974777149 0.74803489 0.96350522 0.833814266 1 20.62727797 -1.425954433 7.985560959 1.000003757 0.855832075 0.141094751 0.117450627 7.83E-06 5.63E-07 0.113370838 0.026721067 0.037501235 1.425954433 -0.144171682 SADTLWGIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SADTLWGIQK 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 240 6.81E-12 593870000 2124860 1655290 1144900 1262420 1773330 1394530 2205550 1684840 1724170 FALSE TRUE 2024422.079 1823965.933 1197394.797 1135519.143 2082598.191 1346237.076 1869052.84 1537306.478 1991545.478 1.016508085 0.915854523 0.601238993 0.570169828 1.045719625 0.675976066 0.938493678 0.771916331 1 20.92545699 -1.317881967 8.200311997 1.000000427 0.832376052 0.101072447 0.165979406 1.27E-06 1.06E-07 0.157780446 0.037189113 0.048097005 1.317881967 -0.167624376 SAEFLLHMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAEFLLHMLK 10 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 ; 110.14 0.0019261 171751000 1235210 949790 468870 558750 1080320 635690 1420970 997510 931680 FALSE TRUE 1176824.071 1046574.681 490368.1533 502583.3884 1268727.466 613675.8959 1204174.929 910162.7363 1076160.176 1.093539881 0.972508279 0.455664653 0.467015412 1.178939245 0.57024587 1.11895511 0.845750248 1 20.03746139 1.694073856 18.82746591 0.986530715 0.823850925 0.109261943 0.255096401 0.61175833 243.8364876 0.120269358 0.066595617 49.43947561 -1.694073856 -0.16267979 SAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SAEPSANTTLVSETEEEGSVPAFGAAAK 28 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 S(0.001)AEPS(0.009)ANT(0.063)T(0.135)LVS(0.393)ET(0.393)EEEGS(0.004)VPAFGAAAK;SAEPSANT(0.011)T(0.043)LVS(0.704)ET(0.242)EEEGSVPAFGAAAK;SAEPS(0.002)ANT(0.029)T(0.029)LVS(0.466)ET(0.466)EEEGS(0.008)VPAFGAAAK 131.84 1.32E-05 161582000 392367 529245 316815 508690 236024 413912 350187 397309 246045 TRUE FALSE 373820.5895 583175.6672 331341.2811 457555.5148 277186.5109 399578.1237 296759.5415 362518.5177 284200.402 1.315341523 2.051987482 1.165871965 1.609974904 0.975320615 1.405973112 1.044191139 1.275573557 1 18.11654907 3.136012283 1.39537953 1.158282124 1.64903917 0.308569838 0.270179606 0.403015676 1.64100918 0.089882162 0.121092824 1367.767508 -3.136012283 0.490757046 SAEPSPTVMS(ph)TSLGSNLSELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.481)T(0.481)S(0.038)LGSNLSELDR;SAEPSPTVMS(0.498)T(0.306)S(0.196)LGS(0.001)NLSELDR 164.02 1.51E-11 71968000 201106 184356 173095 222970 140422 209419 222915 207632 159416 TRUE FALSE 191600.1179 203142.086 181031.577 200556.632 164911.5523 202166.7675 188905.2226 189450.6414 184137.4191 1.040527878 1.103209152 0.98313302 1.089168258 0.895589572 1.097912464 1.025892638 1.028854658 1 17.49042331 3.743416907 24.95607087 1.021461921 1.071868513 0.130017119 0.057966616 746.4344468 3835859.452 0.013451257 0.023412185 5538.815608 -3.743416907 0.050406591 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.117)T(0.117)S(0.759)LGS(0.007)NLSELDR;SAEPSPTVMS(0.161)T(0.161)S(0.678)LGS(0.001)NLSELDR 129.2 1.63E-05 59234000 208454 198538 197512 245481 161397 256711 256592 248074 178914 TRUE FALSE 198600.7925 218769.2479 206568.1206 220804.7835 189544.5857 247821.0337 217444.1778 226351.3254 206659.0694 0.961006905 1.058599792 0.999559909 1.06844952 0.917184938 1.199178117 1.052187927 1.095288613 1 17.65689315 2.246021767 24.99999958 1.090715921 1.008192102 0.294846868 0.065195376 203.3918861 681504.3821 0.02030965 0.016684736 176.2064361 -2.246021767 -0.082523819 SAEVGPSSEPEVQTLPYLPHYIPGVDPET(ph)SHGGHPHGNMPGLDRPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQT(0.007)LPY(0.012)LPHY(0.037)IPGVDPET(0.411)S(0.411)HGGHPHGNMPGLDRPLS(0.122)R 41.526 0.025949 53135000 16954 18899 18725 21000 23120 21058 27886 18339 7382.2 TRUE FALSE 16152.61802 20824.82959 19583.55977 18889.0401 27152.12068 20328.75618 23631.47854 16733.13994 8526.993873 1.894292204 2.442224059 2.296654608 2.215205075 3.184254743 2.384047237 2.771372759 1.962372694 1 13.0578215 4.606358387 2.101375773 2.40063005 1.825097121 0.006167556 0.573031254 1.332152806 8.223542033 0.128472998 1.317361628 40397.86254 -4.606358387 -0.575532929 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQTLPY(0.006)LPHY(0.006)IPGVDPET(0.16)S(0.16)HGGHPHGNMPGLDRPLS(0.667)R 101.45 3.17E-07 125580000 28258 28115 26090 33093 35451 26815 37081 30810 8380 TRUE FALSE 26922.30034 30979.95046 27286.25231 29766.42877 41633.64318 25886.38983 31423.61241 28112.11307 9679.527601 2.781365109 3.200564298 2.818965288 3.075194368 4.301206101 2.674344337 3.246399381 2.904285645 1 13.24072092 0.677944639 2.80685899 0.99999114 3.142258377 0.691084286 0.449437314 1.575894108 13.07623717 0.40126907 0.105674235 4.76370258 -0.677944639 2.142267237 SAFLLQNLLVGHPEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAFLLQNLLVGHPEHK 16 0 Q9NZL4;Q9NZL4-3 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 134.85 1.50E-05 96927000 90277 92583 91141 100760 71805 94341 101760 95268 14908 FALSE TRUE 86009.78512 102017.313 95319.905 90631.41337 84327.76927 91073.94751 86234.64305 86925.82887 17219.8565 4.994802664 5.924399716 5.535464538 5.263192139 4.89712381 5.2888912 5.007860724 5.047999608 1 14.0717855 -0.788685729 0.518426606 7.02E-12 5.417352403 0.958292862 0.279390725 2.675094399 0.50294611 4.773259874 0.12822833 0.162672549 0.788685729 5.417352403 SAFS(ph)SLQNIPESLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAFSSLQNIPESLRR 15 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.5)S(0.5)LQNIPESLRR 146.81 2.34E-06 188260000 122120 96703 98658 107860 126280 93930 129810 104500 128790 TRUE FALSE 116347.6296 106557.1456 103181.5669 97017.70788 148303.192 90677.18055 110005.1004 95349.42601 148762.0954 0.782105343 0.716292314 0.693601193 0.652166855 0.996915186 0.609544927 0.739469957 0.640952426 1 17.18264745 -0.989853128 4.513918169 1.000007417 0.730886326 0.385545207 0.107538202 0.076907982 57829396.79 997.6919422 0.022498259 0.102363911 0.989853128 -0.26912109 SAFSNLFGGEPLSYTRFS(ph)LAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAFSNLFGGEPLSYTRFSLAR 21 1 P02786;F8WBE5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 1 SAFSNLFGGEPLS(0.014)YT(0.098)RFS(0.888)LAR;SAFSNLFGGEPLSYT(0.004)RFS(0.996)LAR 138.54 8.89E-07 169589000 111260 74398 100328 119558 174901 119271 169729 100453 149419 TRUE FALSE 106000.9603 81979.24078 104928.138 107539.8027 205403.679 115140.6154 143833.7238 91656.80279 172590.1354 0.614177398 0.47499378 0.607961387 0.623093565 1.190124097 0.667133235 0.833383226 0.531066289 1 17.39699048 2.979084138 24.79814314 0.828124814 0.560986737 0.35242311 0.178638343 732.8386628 868864.9367 0.049877155 0.053449616 952.9807719 -2.979084138 -0.267138077 SAFSS(ph)LQNIPESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAFSSLQNIPESLR 14 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.05)S(0.95)LQNIPESLR;SAFS(0.044)S(0.956)LQNIPESLR;SAFS(0.005)S(0.995)LQNIPESLR;SAFS(0.008)S(0.992)LQNIPESLR 211.9 3.35E-09 463820000 892820 775590 750610 944740 814800 776420 889910 841630 767980 TRUE FALSE 850618.168 854623.5028 785026.211 849772.9403 956900.862 749532.3807 754137.8852 767932.4154 887074.4161 0.95890283 0.963418048 0.884960942 0.957950004 1.078715432 0.844948707 0.850140497 0.865691087 1 19.75869561 2.164022756 24.99999997 0.873582957 0.96287 0.252017004 0.064069109 45.23381481 15169.91282 0.022305465 0.016473674 145.8890702 -2.164022756 0.089287043 SAFSS(ph)LQNIPESLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SAFSSLQNIPESLRR 15 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.099)S(0.901)LQNIPESLRR;SAFS(0.148)S(0.852)LQNIPESLRR;SAFS(0.433)S(0.567)LQNIPESLRR 204.71 2.92E-09 827360000 389120 296413 326481 347080 413490 329471 428790 379225 437100 TRUE FALSE 370727.0688 326617.8217 341450.4768 312190.859 485602.5251 318061.3367 363370.2102 346018.0486 504883.2356 0.734282786 0.646917542 0.676295929 0.618342692 0.961811545 0.629970089 0.71971138 0.685342717 1 18.94559025 -2.340193501 2.119149126 2.544668432 0.706334046 0.47025796 0.096997149 3501783.176 428037.6148 25884264.56 0.024059846 0.004568846 2.340193501 -1.838334386 SAGAENPRPFS(ph)PPRAPPPPPPPPPPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAGAENPRPFSPPRAPPPPPPPPPPPPR 28 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 SAGAENPRPFS(1)PPRAPPPPPPPPPPPPR;S(0.027)AGAENPRPFS(0.973)PPRAPPPPPPPPPPPPR 188.74 3.48E-18 671990000 145665 129221 152841 160575 154284 136558 174975 159720 164410 TRUE FALSE 138779.7041 142388.7668 159848.911 144433.6959 181191.0808 131828.9622 148279.3501 145734.0701 189905.8631 0.730781566 0.749786049 0.841727098 0.760554169 0.954109988 0.69418058 0.780804487 0.767401636 1 17.53492492 -2.559263587 2.045657003 4.058447917 0.780517526 0.474744564 0.070964593 2219583.674 96555.36611 31658970.59 0.016069787 0.002758903 2.559263587 -3.27793039 SAGGRPGS(ph)GPQLGTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 1 SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR 183.09 1.23E-09 1416060000 451076 382665 414224 489403 441817 411809 484567 461204 450606 TRUE FALSE 429754.5314 421658.9986 433216.5801 440207.2806 518869.7449 397547.9511 410637.4045 420818.5328 520483.6771 0.825683014 0.810129149 0.832334613 0.845765775 0.996899168 0.763804839 0.788953473 0.808514371 1 18.98949339 -2.336616451 2.31783095 2.023068862 0.830308254 0.410368804 0.062389511 2777183.107 522811.8513 14884339.25 0.015205152 0.004606632 2.336616451 -1.192760607 SAGGRPGSGPQLGTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 203.06 2.62E-11 171546000 104010 99729 90838 109351 104659 101100 129754 115424 114173 FALSE TRUE 99093.65343 109891.4985 95003.01215 98358.82973 122911.4965 97598.88165 109957.6442 105316.8627 131878.3657 0.751401891 0.833279195 0.720383602 0.745829911 0.932006518 0.740067418 0.833780762 0.798590899 1 17.00884839 -4.999999987 0.235330281 2.141295294 0.773628932 0.540886256 0.060697912 124.1535029 1.240081425 67.58824451 0.090621878 1.00E-05 4.999999987 -1.367666363 SAGGS(ph)SPEGGEDS(ph)DREDGNYCPPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.001)AGGS(0.499)S(0.499)PEGGEDS(1)DREDGNYCPPVKR 138.16 5.18E-06 306600000 388270 286560 334320 333900 270260 349680 412230 340620 296060 TRUE FALSE 369917.2466 315760.7898 349648.9027 300335.7376 317393.2584 337570.4939 349336.7424 310793.5071 341971.4727 1.081719605 0.923354183 1.022450498 0.878247929 0.928127881 0.987130567 1.021537673 0.908828753 1 18.38351645 4.650395051 3.172168313 0.962309664 1.088618953 0.3775228 0.049285696 0.308578796 5.030707284 0.011605488 0.085222533 44709.00978 -4.650395051 0.126309289 SAGGSS(ph)PEGGEDS(ph)DREDGNYCPPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.001)AGGS(0.093)S(0.906)PEGGEDS(1)DREDGNYCPPVKR;SAGGS(0.106)S(0.894)PEGGEDS(0.992)DREDGNY(0.008)CPPVKR;S(0.002)AGGS(0.368)S(0.63)PEGGEDS(1)DREDGNYCPPVKR;S(0.002)AGGS(0.452)S(0.546)PEGGEDS(1)DREDGNYCPPVKR 167.87 5.33E-12 1895510000 1811300 1210960 1561180 1613280 1210920 1490190 1923020 1544700 1286570 TRUE FALSE 1725683.439 1334358.201 1632761.647 1451110.029 1422104.065 1438584.347 1629627.98 1409437.879 1486084.705 1.161228181 0.897901847 1.098700257 0.976465221 0.956946842 0.968036574 1.096591584 0.948423649 1 20.50308492 4.719007347 4.232497018 0.999934387 1.170721179 0.410151999 0.06290173 0.195648267 7.204374109 0.014168291 0.095395714 52360.92945 -4.719007347 0.170786792 SAGGSSPEGGEDS(ph)DREDGNYCPPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 1 SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGS(0.001)S(0.003)PEGGEDS(0.996)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR 346.72 4.26E-110 2820292000 1212090 983763 1097488 1175258 953707 1161810 1361799 1251914 1112767 TRUE FALSE 1154796.908 1084009.568 1147808.91 1057118.833 1120033.199 1121576.228 1154031.551 1142289.773 1285329.223 0.898444451 0.843371137 0.893007713 0.822449855 0.87139791 0.872598404 0.897848995 0.888713765 1 20.29370651 0.347638457 0.696028207 1.002753241 0.865345435 0.762506447 0.022727785 1.011356993 0.70582236 0.027044098 0.007682442 2.226580785 -0.347638457 -0.137407805 SAGVEQLMYIKEDLIIPHHHSFYDFIVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAGVEQLMYIKEDLIIPHHHSFYDFIVTK 29 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 64.315 0.0038314 121630000 125530 94449 177610 203020 141070 157340 210610 161250 40238 FALSE TRUE 119596.4457 104073.4605 185753.5942 182612.0439 165672.5633 151891.2763 178477.5764 147130.0952 46477.90353 2.573189335 2.239202988 3.996600106 3.929007765 3.564544671 3.268032007 3.840052214 3.165592335 1 15.50425737 0.94002797 21.80675528 0.999999991 3.272170474 0.621000274 0.569582639 4744.586622 1725208.166 0.645159607 0.161289902 8.710196855 -0.94002797 2.272170483 SAHATAPVNIAGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAHATAPVNIAGSR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 114.64 0.00046573 114670000 50525 42356 47235 49470 48645 44564 47813 55090 48767 FALSE TRUE 48136.78338 46672.12455 49400.77147 44497.18161 57128.6726 43020.73751 40518.2487 50266.02755 56329.53729 0.854556698 0.828555085 0.876995868 0.789944029 1.01418679 0.763733195 0.719307324 0.892356479 1 15.781604 SAICIQSWWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAICIQSWWR 10 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 98.943 0.01144 0 79541 67496 65750 73691 56477 66637 76974 75469 63633 FALSE TRUE 75781.25457 74373.91914 68764.70254 66283.44068 66326.57092 64329.34398 65230.20258 68860.53427 73500.88065 1.031025124 1.011877932 0.935562975 0.901804714 0.902391513 0.875218683 0.887475116 0.936866792 1 16.16547392 3.685284262 2.448568199 0.906609304 1.026001136 0.586760379 0.035115233 0.15117595 1.777883074 0.008925386 0.016349411 4844.893803 -3.685284262 0.119391833 SAKGEEVDVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAKGEEVDVAR 11 1 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 69.314 0.050811 0 995430 734610 940970 937340 969060 895190 1257600 1023600 1155800 FALSE TRUE 948377.9967 809467.5942 984114.4052 843116.8024 1138063.757 864189.3458 1065730.023 933968.1576 1335035.561 0.71037658 0.606326616 0.737144713 0.631531344 0.852459508 0.6473156 0.798278378 0.699582981 1 20.34844674 -5 0.173361584 2.18133447 0.638325144 0.618338828 0.072611055 76.21562325 0.724197642 30.86457734 0.21520912 1.00E-05 5 -1.543009325 SAKS(ph)EESLTSLHAVDGDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.145)AKS(0.724)EES(0.114)LT(0.018)SLHAVDGDSK;S(0.029)AKS(0.8)EES(0.142)LT(0.025)S(0.003)LHAVDGDSK 206.49 2.19E-16 362330000 432630 353770 420040 483950 235620 429360 504420 519730 271640 TRUE FALSE 412180.4373 389819.5652 439299.2495 435302.4266 276712.0534 414491.1555 427461.4647 474219.6859 313764.5439 1.313661615 1.242395206 1.400092069 1.387353782 0.881909887 1.321026112 1.362363827 1.511387106 1 18.25932281 -1.989052302 2.739816495 0.723384349 1.29644117 0.248431273 0.165063718 38687410.99 33529515.6 67748265.36 0.039214601 0.010255284 1.989052302 0.573056821 SALPVSPSISSAPVPVEIENLPQS(ph)PGTDQHDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SALPVSPSISSAPVPVEIENLPQSPGTDQHDRK 33 1 Q9HCM4-2;Q9HCM4-4;Q9HCM4-3;Q9HCM4 Q9HCM4-2 EPB41L5 Band 4.1-like protein 5 1 SALPVSPSISSAPVPVEIENLPQS(0.847)PGT(0.153)DQHDRK 97.257 5.93E-05 42358000 56199 38247 49784 51353 44230 51269 58918 55320 48544 TRUE FALSE 53542.58465 42144.41278 52066.64564 46190.89888 51943.698 49493.54167 49928.977 50475.88753 56071.95559 0.954890624 0.751613036 0.928568392 0.823778989 0.926375716 0.882679071 0.890444724 0.90019845 1 15.77499177 -0.075102206 0.383597209 1.024706029 0.860791514 0.297317223 0.057640338 5.713766163 1.088210412 0.265823738 0.03952533 0.841197152 0.075102206 -0.163914515 SALQHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SALQHEK 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;; 75.109 0.044361 193470000 415870 409940 345441 396300 354027 396250 510250 475330 391190 FALSE TRUE 396212.6493 451713.3521 361279.8115 356463.1711 415769.1967 382527.7631 432401.9911 433707.5853 451853.7473 0.876860382 0.999689291 0.799550327 0.788890594 0.920141084 0.846574285 0.956951212 0.95984063 1 18.78549636 1.609287256 5.195685383 0.97314183 0.883090369 0.371319401 0.060691812 0.197633498 11.50740554 0.035685304 0.016650128 40.67122529 -1.609287256 -0.090051461 SALS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SALSPSK 7 0 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALS(0.999)PSK 72.365 0.054338 45144000 144310 144060 147500 174130 91832 162700 151420 156060 113530 TRUE FALSE 137488.7523 158739.8778 154263.0209 156626.1216 107847.4717 157065.6582 128318.098 142394.5591 131135.6526 1.048446777 1.210501299 1.176362171 1.194382447 0.822411523 1.197734217 0.978514199 1.085856945 1 17.00070045 SALS(ph)PSKS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 2 S(0.093)ALS(0.896)PS(0.027)KS(0.984)PAK 55.213 0.072126 104250000 409130 491940 368950 522480 168500 492400 404410 516100 173680 TRUE FALSE 389791.2357 542069.2453 385866.7224 469959.3178 197886.3467 475348.0645 342709.827 470907.548 200613.4074 1.942996935 2.702058912 1.923434368 2.342611712 0.986406389 2.369473062 1.708309686 2.347338367 1 17.6140585 SALSPS(ph)KSPAK ddPTM_SK-BR-3_Trastuzumab_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(0.341)PS(0.659)KSPAK 163.33 1.46E-05 393780000 593000 494570 493510 560570 328030 602420 732110 656120 384470 TRUE FALSE 564970.0652 544967.2453 516137.9216 504220.4386 385238.3281 581558.0443 620413.1734 598666.6545 444091.644 1.272192514 1.227150415 1.162232905 1.135397266 0.867474841 1.309545118 1.397038611 1.348070072 1 18.7604979 SALSS(ph)SLRDLSEAGVHH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.123)S(0.672)S(0.205)LRDLSEAGVHH 189.51 2.12E-10 287280000 201250 163170 184700 199920 202910 179440 246910 188680 7116.2 TRUE FALSE 191737.3113 179797.2085 193168.6777 179823.6618 238297.4398 173225.9478 209239.3447 172158.1789 8219.743951 23.32643358 21.87382108 23.50057117 21.87703934 28.99085922 21.07437273 25.45570104 20.9444698 1 13.00487774 0.836518982 5.375305596 1.000096204 23.57289585 0.909419799 2.236100869 0.722180749 23.62277108 1.93268549 0.487362464 6.86307875 -0.836518982 22.57279965 SALSSS(ph)LRDLSEAGVHH ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.001)S(0.291)S(0.708)LRDLSEAGVHH;SALSS(0.067)S(0.933)LRDLSEAGVHH;SALS(0.007)S(0.361)S(0.632)LRDLSEAGVHH 240.94 1.47E-20 864070000 800930 663480 844960 893250 978370 832230 1015400 876010 143208.5 TRUE FALSE 763071.6262 731089.3663 883702.2518 803458.8129 1148997.418 803409.6664 860482.0809 799301.9204 165416.5428 4.613030918 4.419687137 5.342284617 4.857185379 6.946085313 4.856888271 5.201910682 4.832055531 1 17.335744 0.633013944 3.105005806 1.000010784 5.106143545 0.780485057 0.690467571 2.766903634 22.85675725 0.666444302 0.173618016 4.295502186 -0.633013944 4.106132762 SALVTSSSS(ph)LPSFPSTLSWSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SALVTSSSSLPSFPSTLSWSR 21 0 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 SALVTSS(0.001)S(0.012)S(0.987)LPSFPSTLSWSR;SALVTSSSS(0.999)LPS(0.001)FPSTLSWSR 393.11 2.70E-131 66696000 193545 161721 170330 182850 178840 172206 212748 187294 201499 TRUE FALSE 184396.5114 178200.5538 178139.799 164469.5706 210029.6394 166242.463 180289.3852 170893.5445 232746.4358 0.792263524 0.76564246 0.765381426 0.706647 0.902396802 0.71426427 0.774617169 0.73424774 1 17.82839955 -0.962585764 4.416749036 1.000005788 0.770283338 0.64077846 0.05425017 6034987.739 1366386.978 349.4887224 0.011141436 0.108996922 0.962585764 -0.22972245 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_SK-BR-3_Trastuzumab_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 191.64 1.22E-17 176642000 237466 201902 230099 239857 245475 226589 267467 217445 255130 TRUE FALSE 226241.4528 222476.0433 240649.2667 215746.1187 288285.7623 218742.1661 226659.9968 198404.3631 294694.2574 0.767715852 0.754938509 0.81660657 0.732101537 0.97825375 0.742268167 0.769136117 0.673254935 1 18.16885942 -2.225440931 2.466011721 1.792836715 0.779618832 0.433222233 0.079338135 3904243.603 1493501.023 17083997.11 0.017998086 0.005950577 2.225440931 -1.013217883 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.008)S(0.992)PGAAR;SAMDSPVPASMFAPEPS(0.215)S(0.785)PGAAR;SAMDSPVPASMFAPEPS(0.018)S(0.982)PGAAR;SAMDSPVPASMFAPEPSS(1)PGAAR;SAMDSPVPASMFAPEPS(0.01)S(0.99)PGAAR;SAMDSPVPASMFAPEPS(0.002)S(0.998)PGAAR;SAMDSPVPASMFAPEPS(0.359)S(0.641)PGAAR;SAMDSPVPASMFAPEPS(0.029)S(0.971)PGAAR;SAMDSPVPASMFAPEPS(0.001)S(0.999)PGAAR;SAMDSPVPASMFAPEPS(0.02)S(0.98)PGAAR 356.37 7.59E-102 1068272000 1333980 1140189 1216004 1388073 1360306 1204676 1447011 1295623 1387545 TRUE FALSE 1270925.409 1256375.555 1271758.986 1248541.265 1597542.936 1162957.768 1226242.896 1182171.382 1602718.392 0.79298111 0.783902875 0.793501212 0.779014748 0.996770826 0.725615787 0.765101906 0.737603928 1 20.61208953 -1.31117215 3.689644048 1.000586512 0.79532259 0.422728702 0.074602889 17058847.87 34699519.98 110040.996 0.016994356 0.04884587 1.31117215 -0.205263922 SAMPFT(ph)ASPASSTTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 S(0.004)AMPFT(0.713)AS(0.283)PASSTTAR 96.993 0.033622 86455000 102850 92477 102160 109930 98345 105600 123670 109860 120710 TRUE FALSE 97988.48433 101900.5114 106844.1371 98879.62755 115496.3369 101943.0455 104801.8701 100240.076 139429.0903 0.702783645 0.730841112 0.766297312 0.709175017 0.828351792 0.731146171 0.75164996 0.718932296 1 17.08917207 -1.909699576 2.445054664 1.155445325 0.741535854 0.836422203 0.035799806 4659057.324 2326234.264 4152594.479 0.008503751 0.012311201 1.909699576 -0.413909471 SAMPFTAS(ph)PASSTTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.055)AS(0.945)PASSTTAR;SAMPFT(0.001)AS(0.989)PAS(0.008)S(0.001)TT(0.001)AR;SAMPFT(0.001)AS(0.975)PAS(0.019)S(0.004)T(0.001)TAR;SAMPFT(0.002)AS(0.998)PASSTTAR;SAMPFT(0.157)AS(0.843)PASSTTAR;SAMPFT(0.029)AS(0.971)PASSTTAR;SAMPFT(0.302)AS(0.698)PASSTTAR 245.61 4.11E-20 1250937000 1298280 1259976 1368320 1480340 1378840 1333550 1645700 1520640 1656390 TRUE FALSE 1236912.877 1388368.987 1431058.825 1331533.411 1619309.259 1287368.829 1394618.24 1387484.7 1913254.502 0.646496781 0.725658288 0.74797097 0.69595206 0.846363753 0.672868575 0.728924583 0.725196099 1 20.86759736 -5 0.314694514 3.547563099 0.708170623 0.732915697 0.05249283 153.0935091 1.372290217 259.1505926 0.045233145 1.00E-05 5 -2.839392475 SANMDHWQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SANMDHWQQR 10 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 170.89 4.19E-06 392970000 263452 224137 207006 233755 275587 221422 287400 246578 262610 FALSE TRUE 250999.1461 246976.8151 216497.4299 210257.5033 323649.2855 213754.1006 243551.8515 224986.3231 303334.2176 0.8274673 0.814206907 0.71372571 0.693154584 1.066972556 0.704681794 0.802915851 0.741710991 1 18.21054872 SANPTRPS(ph)SPVTSHISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.006)ANPT(0.004)RPS(0.492)S(0.492)PVT(0.006)SHISK;SANPTRPS(0.494)S(0.494)PVT(0.011)SHISK 202.52 6.37E-12 1009050000 281960 203656 266565 296950 269336 276327 376040 298724 311565 TRUE FALSE 268632.3096 224408.7779 278787.2689 267100.0218 316308.1131 266757.7267 318668.1916 272566.1429 359880.9089 0.746447791 0.623563997 0.774665346 0.742190028 0.878924403 0.741238893 0.885482346 0.757378722 1 18.45716005 -4.825918016 0.058658127 1.93745942 0.350356817 0.589011791 0.066385814 235.6419495 1.04225127 32.16127713 5.847168131 1.49E-05 4.825918016 -1.587102602 SANTS(ph)PESSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 S(0.006)ANT(0.056)S(0.933)PES(0.003)S(0.001)S(0.001)R;S(0.002)ANT(0.144)S(0.853)PES(0.002)SSR 81.597 0.022278 250980000 334710 338280 316830 380520 303920 319570 352290 334470 330700 TRUE FALSE 318888.9216 372751.1166 331356.9689 342269.4067 356923.5518 308503.2108 298541.6903 305182.0337 381983.267 0.834824321 0.975831008 0.867464618 0.896032461 0.934395777 0.807635406 0.781556984 0.798940844 1 18.54314992 2.231974671 24.90606829 0.823007836 0.90392197 0.085455213 0.071589392 205.6689911 777771.0667 0.023859979 0.018030319 170.598289 -2.231974671 0.080914134 SAPAS(ph)PTHPGLMSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(0.13)APAS(0.818)PT(0.052)HPGLMSPR;S(0.005)APAS(0.96)PT(0.035)HPGLMSPR;SAPAS(0.487)PT(0.487)HPGLMS(0.026)PR;S(0.009)APAS(0.924)PT(0.067)HPGLMSPR;S(0.036)APAS(0.954)PT(0.009)HPGLMSPR;S(0.05)APAS(0.913)PT(0.037)HPGLMSPR;S(0.015)APAS(0.937)PT(0.047)HPGLMSPR;SAPAS(0.976)PT(0.024)HPGLMSPR;S(0.001)APAS(0.992)PT(0.007)HPGLMSPR;SAPAS(0.499)PT(0.499)HPGLMS(0.003)PR;SAPAS(0.92)PT(0.079)HPGLMS(0.001)PR 257.52 9.06E-25 2150961000 1850583 1611387 1654946 1923211 1981443 1782923 2158437 2011688 2083310 TRUE FALSE 1763109.609 1775589.167 1730826.911 1729886.176 2327006.032 1721179.929 1829127.793 1835533.934 2406379.075 0.732681574 0.737867606 0.719266108 0.718875174 0.96701557 0.715257188 0.760116231 0.762778381 1 21.1984325 -5 0.256052232 2.497220472 0.740520269 0.505091998 0.073678455 155.7143592 1.535172284 122.4864602 0.095708018 1.00E-05 5 -1.756700204 KFPAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 KFPAGK 6 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 91.26 0.077118 1435700000 1351100 1163100 1411300 2879300 2462800 3513100 4305000 3711800 3273900 FALSE TRUE 1287236.181 1281621.212 1476009.501 2589867.294 2892311.54 3391440.466 3648193.183 3386775.115 3781599.691 0.340394618 0.338909805 0.390313524 0.684860246 0.764838105 0.896826936 0.964722203 0.895593239 1 21.85056522 2.949366639 1.125604457 0.950329992 0.317945115 0.972327164 0.042846239 0.061199564 0.164872773 0.017883056 0.020552479 889.952115 -2.949366639 -0.632384878 down SAPGTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAPGTSPR 8 0 Q03111 Q03111 MLLT1 Protein ENL 1 SAPGT(0.018)S(0.982)PR;SAPGT(0.002)S(0.998)PR 140.88 0.00067393 771330000 2023690 1598950 1699040 1999010 1835820 1826910 2186550 1882280 2159360 TRUE FALSE 1928034.184 1761884.823 1776942.665 1798065.717 2155986.427 1763643.649 1852951.639 1717457.585 2494222.52 0.773000071 0.706386382 0.712423471 0.720892263 0.864392174 0.707091542 0.742897486 0.688574324 1 21.25015875 -1.227591361 4.974222297 1.000037446 0.739658927 0.727936008 0.050057516 1.93E-05 2.99E-06 0.044952115 0.010593793 0.059211851 1.227591361 -0.26037852 SAPTTLYLVHT(ph)DHAYQATPPVTIPGSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAPTTLYLVHTDHAYQATPPVTIPGSAK 28 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 S(0.157)APT(0.157)T(0.157)LY(0.135)LVHT(0.212)DHAY(0.182)QATPPVTIPGSAK;S(0.172)APT(0.172)T(0.172)LY(0.172)LVHT(0.252)DHAY(0.052)QAT(0.007)PPVTIPGSAK 100.93 0.0024452 327590000 375880 445070 435810 438290 320570 445300 504660 501130 55328 TRUE FALSE 358112.8973 490423.139 455792.3196 394232.2565 376477.3065 429879.1493 427664.8483 457248.4005 63907.98366 5.603570584 7.673894729 7.132009077 6.168748158 5.890927626 6.726532816 6.691884547 7.1547931 1 15.96370855 3.116020101 5.907944462 6.014208458 6.81483412 0.059640871 1.817657436 0.739924483 35.50882007 0.469538548 0.564795531 1306.231344 -3.116020101 0.800625663 SAQGSSS(ph)PVPSMVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SAQGSS(0.002)S(0.998)PVPSMVQK;SAQGSS(0.001)S(0.999)PVPSMVQK 351.81 2.27E-82 200325000 655180 645040 621070 752700 490790 707730 743560 735740 567880 TRUE FALSE 624210.9398 710770.3093 649546.6738 677037.166 576383.6206 683221.1326 630116.2656 671314.7052 655943.9301 0.951622404 1.083583942 0.990247251 1.032157072 0.878708673 1.041584656 0.960625195 1.023433063 1 19.32321297 SAQSLEYCAELLGLDQDDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 166.48 3.52E-11 25172000 30347 29667 31573 30523 31982 30357 30244 33909 33170 FALSE TRUE 28912.55745 32690.10103 33020.65328 27454.77005 37559.65067 29305.72948 25629.72233 30939.7482 38313.83419 0.754624486 0.853219254 0.861846745 0.716575896 0.980315634 0.764886368 0.668941725 0.807534637 1 15.22557779 SAS(ph)AADVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASAADVSR 9 0 A0A1B0GV45 A0A1B0GV45 1 S(0.103)AS(0.897)AADVSR;S(0.008)AS(0.992)AADVSR 112.83 0.0020342 188170000 332630 299970 337990 347320 393910 312230 383300 315280 431870 TRUE FALSE 316907.2391 330537.284 353487.1758 312406.7337 462607.7793 301417.3968 324820.5452 287672.4118 498842.1939 0.635285553 0.662608913 0.70861523 0.626263651 0.927362972 0.604233965 0.651148899 0.576680191 1 18.92822397 -2.226829461 2.415488108 2.154451926 0.67309614 0.52877844 0.096704506 3701134.216 1152278.783 23147190.98 0.021856475 0.005931582 2.226829461 -1.481355786 SAS(ph)ADNLTLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASADNLTLPR 11 0 Q8ND76-3;Q8ND76-2;Q8ND76 Q8ND76-3 CCNY Cyclin-Y 1 S(0.002)AS(0.997)ADNLTLPR 95.428 0.0081456 300800000 474780 429240 464010 575860 498560 497240 591460 538510 481140 TRUE FALSE 452338.0903 472980.044 485285.3175 517973.4587 585508.7062 480020.4541 501221.9141 491355.2096 555752.7339 0.813919685 0.851062019 0.873203653 0.932021432 1.053541747 0.863730261 0.901879349 0.884125583 1 19.08408361 3.495873108 2.400050588 0.931876939 0.831247277 0.392405666 0.055783925 0.307393999 3.530303117 0.016165669 0.025840058 3132.370374 -3.495873108 -0.100629661 SAS(ph)APTLAETEKETAEHLDLAGASSRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASAPTLAETEKETAEHLDLAGASSRPK 28 2 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.152)AS(0.846)APT(0.001)LAETEKETAEHLDLAGASSRPK;S(0.012)AS(0.419)APT(0.419)LAET(0.131)EKET(0.018)AEHLDLAGASSRPK;S(0.174)AS(0.826)APTLAETEKETAEHLDLAGASSRPK 193.15 1.09E-18 222874000 191495 161990 183216 187906 126839 193255 215189 204524 119412 TRUE FALSE 182443.4109 178496.9652 191616.6348 169017.3319 148959.6814 186562.5309 182357.9658 186614.7943 137929.8031 1.322726537 1.294114551 1.389233005 1.225386596 1.079967332 1.352590424 1.322107056 1.352969338 1 17.07357469 -1.401549063 3.606773556 0.997963826 1.293717263 0.527314522 0.086990359 6945498.508 2699970.925 110034.6563 0.020034401 0.039668971 1.401549063 0.295753436 SAS(ph)ASPLTPCSVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 SAS(0.974)AS(0.026)PLTPCSVTR;SAS(1)ASPLTPCSVTR;S(0.008)AS(0.991)AS(0.001)PLTPCSVTR 172.85 2.93E-06 411540000 408160 311640 349780 390415 344282 364288 394537 382173 369411 TRUE FALSE 388867.0857 343396.4703 365817.759 351169.7425 404324.6718 351672.6152 334343.1345 348707.9061 426697.3712 0.911341649 0.804777562 0.857323676 0.822994858 0.947567759 0.824173381 0.783560334 0.817225344 1 18.7028537 4.71784349 4.207415471 0.845784825 0.915202372 0.03604281 0.068016631 0.510118514 18.37227228 0.014908797 0.100402901 52220.7963 -4.71784349 0.069417548 SAS(ph)DNTLVAMDFSGHAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.056)AS(0.944)DNTLVAMDFSGHAGR;S(0.001)AS(0.976)DNT(0.024)LVAMDFSGHAGR;S(0.051)AS(0.949)DNTLVAMDFSGHAGR;SAS(0.769)DNT(0.231)LVAMDFSGHAGR;S(0.419)AS(0.581)DNTLVAMDFSGHAGR;S(0.154)AS(0.846)DNTLVAMDFSGHAGR 307.35 2.77E-50 5121980000 1627349 1271137 1352514 1612831 1648262 1489650 1984150 1712530 1683868 TRUE FALSE 1550427.438 1400667.305 1414528.105 1450706.164 1935718.371 1438063.047 1681431.476 1562571.795 1944993.649 0.797137532 0.720139783 0.727266182 0.745866787 0.995231204 0.739366449 0.864492013 0.803381438 1 20.89133401 -4.999999971 0.114003064 1.691365645 0.680062006 0.427595785 0.078315489 143.943785 1.080369192 22.88762569 0.816013315 1.00E-05 4.999999971 -1.011303638 SAS(ph)DTNLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASDTNLQK 9 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.003)AS(0.996)DT(0.001)NLQK;S(0.002)AS(0.957)DT(0.042)NLQK 92.112 0.007705 78398000 318790 275140 285540 344710 240170 309040 339450 333110 307770 TRUE FALSE 303721.4285 303177.0788 298632.2914 310059.0959 282055.572 298337.8673 287660.6681 303941.1225 355497.3997 0.854356259 0.852825025 0.840040719 0.872183864 0.793411069 0.839212516 0.809177981 0.854974249 1 18.43947948 0.958349975 22.38946018 1 0.838034807 0.837899156 0.022312686 856.0320486 460170.915 0.021270287 0.005317572 9.085523889 -0.958349975 -0.161965194 SAS(ph)EPSLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.062)AS(0.938)EPSLHR;S(0.115)AS(0.885)EPSLHR;S(0.017)AS(0.982)EPSLHR;S(0.095)AS(0.904)EPS(0.001)LHR 126.19 0.00030941 1273140000 1152120 1105500 1110160 1315460 1388650 1105600 1369660 1266100 1448830 TRUE FALSE 1097661.571 1218151.707 1161061.934 1183227.462 1630830.12 1067312.795 1160693.211 1155233.572 1673507.157 0.655904916 0.727903494 0.693789644 0.707034599 0.974498444 0.637770081 0.693569314 0.690306921 1 20.67444329 -2.130993721 2.366713034 1.57269665 0.719548711 0.466447585 0.093188931 4025790.111 1137529.991 12378249.5 0.023476474 0.00739616 2.130993721 -0.85314794 SAS(ph)MKLPDNTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 S(0.003)AS(0.997)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;S(0.056)AS(0.944)MKLPDNTVK;SAS(1)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;SAS(1)MKLPDNTVK;SAS(1)MKLPDNTVK;S(0.017)AS(0.983)MKLPDNTVK;S(0.045)AS(0.955)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;S(0.1)AS(0.9)MKLPDNTVK;S(0.146)AS(0.854)MKLPDNTVK;S(0.05)AS(0.95)MKLPDNTVK;S(0.04)AS(0.96)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;SAS(1)MKLPDNTVK;S(0.044)AS(0.956)MKLPDNTVK 226.7 8.89E-12 26722140000 47970240 39791320 42149650 50122270 24760930 51033970 53387200 51533930 26315740 TRUE FALSE 45702781.82 43846100.75 44082253.14 45083884.19 29079228.35 49266650.82 45242002.12 47021345.89 30396650.56 1.50354664 1.442464875 1.450233902 1.483185922 0.956658968 1.620792091 1.488387743 1.546925238 1 24.85740902 -1.100926106 4.022737382 0.999905872 1.440369731 0.371697839 0.178298868 9404667.486 5147667.051 8137.279948 0.038992127 0.079263618 1.100926106 0.440463859 SAS(ph)PCIADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPCIADK 9 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(0.002)AS(0.998)PCIADK 108.35 0.0027545 55090000 154660 153470 141920 196780 116220 174850 190370 177350 158690 TRUE FALSE 147349.5283 169108.7675 148427.1724 176999.3005 136488.7312 168794.9007 161325.5601 161820.2938 183298.8347 0.803875969 0.922585066 0.809755133 0.965632437 0.744624107 0.920872743 0.880123217 0.882822272 1 17.48383809 -5 0.216773076 1.666426523 0.850356913 0.312494747 0.064386204 174.1885767 1.740518248 50.4868009 0.110308212 1.00E-05 5 -0.816069609 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.107)AS(0.893)PDDDLGSSNWEAADLGNEER;S(0.104)AS(0.896)PDDDLGSSNWEAADLGNEER;S(0.168)AS(0.832)PDDDLGS(0.001)SNWEAADLGNEER;S(0.16)AS(0.84)PDDDLGSSNWEAADLGNEER;S(0.024)AS(0.976)PDDDLGSSNWEAADLGNEER;S(0.133)AS(0.867)PDDDLGSSNWEAADLGNEER 370.46 1.24E-118 2419280000 1417560 1219460 1272930 1403070 1282830 1288190 1518080 1248140 1344920 TRUE FALSE 1350554.748 1343724.36 1331295.1 1262030.738 1506555.146 1243579.657 1286469.015 1138846.245 1553483.325 0.869371899 0.864975078 0.856974181 0.812387695 0.969791643 0.800510464 0.828118972 0.73309203 1 20.56707532 SAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.005)AS(0.984)PDDDLGS(0.008)S(0.003)NWEAADLGNEERK;SAS(1)PDDDLGSSNWEAADLGNEERK;SAS(1)PDDDLGSSNWEAADLGNEERK;S(0.162)AS(0.813)PDDDLGS(0.023)S(0.002)NWEAADLGNEERK;S(0.066)AS(0.931)PDDDLGS(0.002)SNWEAADLGNEERK;S(0.033)AS(0.965)PDDDLGS(0.001)S(0.001)NWEAADLGNEERK;S(0.069)AS(0.925)PDDDLGS(0.004)S(0.002)NWEAADLGNEERK;S(0.147)AS(0.853)PDDDLGSSNWEAADLGNEERK 308.33 1.32E-73 7144050000 3997249 2770341 3937030 3356364 2799619 3957005 4825664 4328808 3308486 TRUE FALSE 3808306.962 3052641.898 4117546.72 3018975.914 3287871.667 3819972.925 4089420.327 3949754.623 3821549.111 0.996534874 0.798796982 1.077454875 0.78998747 0.860350494 0.999587553 1.07009493 1.033548048 1 21.86572614 2.083434071 5.059399625 1.04074461 0.901706155 0.330505987 0.086518935 0.210761238 9.380078998 0.031061365 0.022439049 121.1808713 -2.083434071 -0.139038455 SAS(ph)PDGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASPDGGPR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.054)AS(0.946)PDGGPR;S(0.083)AS(0.917)PDGGPR 130.79 0.0011853 0 533740 432820 453810 518540 470260 439120 536380 515620 536350 TRUE FALSE 508511.168 476924.8501 474617.6374 466415.374 552273.1951 423913.1643 454545.3797 470469.5793 619524.4187 0.820808918 0.769824136 0.766099968 0.752860355 0.891447017 0.68425578 0.733700506 0.759404416 1 19.24080162 -1.593883168 6.923715025 1.000353125 0.771037106 0.635796756 0.054152419 0.000285439 1.67E-05 0.050702609 0.011932695 0.025475155 1.593883168 -0.229316019 SAS(ph)PDYNR ddPTM_SK-BR-3_Trastuzumab_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;SAS(1)PDYNR;S(0.014)AS(0.986)PDYNR;S(0.003)AS(0.997)PDYNR;S(0.049)AS(0.951)PDYNR;S(0.14)AS(0.86)PDYNR 192.91 0.00018194 1393790000 3351300 3152780 3091230 3632470 3342190 3245780 3551390 3120310 3541710 TRUE FALSE 3192890.691 3474051.866 3232965.953 3267327.214 3925066.878 3133377.825 3009560.23 2847079.115 4090940.298 0.780478437 0.8492062 0.790274538 0.798673893 0.959453473 0.765930959 0.735664666 0.695947363 1 21.96400105 -1.68454428 8.631579643 1.000380049 0.799220113 0.45179304 0.070251638 0.000513333 1.88E-05 0.067960076 0.015988992 0.020675486 1.68454428 -0.201159935 SAS(ph)PHDVDLCLVS(ph)PCEFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.141)AS(0.859)PHDVDLCLVS(1)PCEFEHR;S(0.171)AS(0.829)PHDVDLCLVS(1)PCEFEHR 243.19 4.21E-30 86908000 105799 87333 100809 99178 95958 90129 113989 91089 88404 TRUE FALSE 100798.0909 96232.33199 105431.1924 89208.43901 112693.0448 87007.81013 96597.8845 83112.76427 102113.2408 0.987120672 0.94240797 1.032492863 0.87362264 1.103608542 0.852071773 0.945987844 0.813927397 1 16.63981042 2.162776474 25 0.901926483 0.978455339 0.227756262 0.076548876 55.49899197 18306.09418 0.024786592 0.018306116 145.4710165 -2.162776474 0.076528856 SAS(ph)PHDVDLCLVS(ph)PCEFEHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.085)AS(0.915)PHDVDLCLVS(1)PCEFEHRK;S(0.408)AS(0.592)PHDVDLCLVS(1)PCEFEHRK;S(0.234)AS(0.766)PHDVDLCLVS(1)PCEFEHRK 207.13 3.91E-22 144589000 136427 77651 113606 121815 110615 113062 151982 128342 87265 TRUE FALSE 129978.3661 85563.72518 118814.9475 109569.9248 129906.221 109146.6346 128794.3546 117103.6941 100797.6105 1.289498485 0.848866603 1.178747659 1.08702899 1.288782743 1.082829583 1.277752061 1.161770537 1 16.62110191 SAS(ph)PHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.187)AS(0.813)PHDVDLCLVSPCEFEHR;S(0.035)AS(0.965)PHDVDLCLVSPCEFEHR;S(0.108)AS(0.892)PHDVDLCLVSPCEFEHR;S(0.143)AS(0.857)PHDVDLCLVSPCEFEHR 210.32 2.46E-22 932430000 339703 329519 298176 358402 363352 304106 336836 330163 240515 TRUE FALSE 323645.9124 363097.3607 311847.6645 322374.75 426720.4738 293574.733 285445.4818 301252.1774 277812.8378 1.164978246 1.306985536 1.122509913 1.160402639 1.535999838 1.056735662 1.027474051 1.084370974 1 18.08375374 2.043311686 24.99995003 1.040775741 1.249966359 0.462760243 0.115612505 119.1941779 68799.6003 0.040618703 0.029998881 110.4871284 -2.043311686 0.209190619 SAS(ph)PHDVDLCLVSPCEFEHRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.218)AS(0.782)PHDVDLCLVSPCEFEHRK 127.16 9.53E-06 246520000 123400 97674 102000 132830 102690 108010 158130 142600 100540 TRUE FALSE 117567.1266 107627.0916 106676.8009 119477.676 120599.1035 104269.5866 134004.3642 130113.188 116131.2297 1.012364433 0.926771308 0.918588403 1.028816076 1.03847263 0.897860006 1.153904635 1.120397918 1 16.82539646 1.724962722 11.50810204 1.101526394 0.971545582 0.466238259 0.060647929 0.076068304 36.70611476 0.026762436 0.014611132 53.08388779 -1.724962722 -0.129980811 SAS(ph)PPQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASPPQKR 8 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 S(0.004)AS(0.996)PPQKR;S(0.104)AS(0.896)PPQKR 93.096 0.0069284 535840000 167660 143545 158984 175225 155456 157411 190145 185074 191865 TRUE FALSE 159735.0441 158172.3987 166273.5737 157611.0501 182567.4772 151959.8176 161134.888 168867.9394 221618.4443 0.72076602 0.713714958 0.750269564 0.711182007 0.82379189 0.685682178 0.72708248 0.761976017 1 17.75771843 0.724430637 3.161718834 0.999990264 0.731051619 0.839987116 0.036298971 0.863319006 9.501800378 0.03184692 0.008286214 5.301889068 -0.724430637 -0.268938645 SAS(ph)PSVPGPTKPKPK ddPTM_SK-BR-3_Trastuzumab_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(0.017)AS(0.88)PS(0.103)VPGPTKPKPK;S(0.019)AS(0.598)PS(0.382)VPGPTKPKPK 119.68 0.00010087 1007460000 2427050 1966410 2113990 2562800 1433320 1955070 2301460 2389100 1631830 TRUE FALSE 2312328.156 2166789.415 2210918.533 2305182.475 1683290.554 1887365.436 1950330.008 2179897.739 1884885.862 1.226773569 1.149560012 1.172972102 1.222982527 0.893046411 1.001315503 1.034720482 1.156514451 1 20.84604573 2.759700972 24.89887976 1.019198047 1.188448006 0.631331545 0.066760438 501.3835521 590523.3168 0.019779986 0.020960515 575.0438615 -2.759700972 0.169249958 SAS(ph)PTVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.103)AS(0.892)PT(0.005)VPR;S(0.056)AS(0.878)PT(0.066)VPR;S(0.001)AS(0.626)PT(0.373)VPR 122.33 0.0014634 2032190000 2299580 2071850 2125770 2584630 2164660 2352640 2641620 2093020 2136180 TRUE FALSE 2190883.411 2282973.87 2223238.657 2324818.082 2542176.019 2271167.487 2238592.352 1909744.073 2467447.884 0.887914766 0.925236916 0.901027605 0.942195414 1.030285598 0.92045206 0.907250105 0.773975444 1 21.23458818 -1.266053891 4.784308645 1.000026191 0.914968499 0.164738605 0.062396328 1.66E-05 2.55E-06 0.057608292 0.013574225 0.054193364 1.266053891 -0.085057692 SAS(ph)QSS(ph)LDKLDQELK ddPTM_SK-BR-3_Trastuzumab_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 SAS(1)QS(0.292)S(0.708)LDKLDQELK 216.32 1.26E-12 59474000 423650 465590 375360 536460 176310 506580 392360 443140 140970 TRUE FALSE 403624.9041 513034.1503 392570.6273 482534.0216 207058.4082 489037.0076 332498.2758 404336.3124 162830.9076 2.478797852 3.150717255 2.410909778 2.963405588 1.271616127 3.003342638 2.04198503 2.483166852 1 17.31301504 2.818629167 25 2.111619869 2.76845356 0.280051689 0.603254874 143.3634535 44761.36386 0.162536168 0.17239563 658.6112838 -2.818629167 0.656833691 SAS(ph)QSSLDKLDQELK ddPTM_SK-BR-3_Trastuzumab_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 1 S(0.023)AS(0.971)QS(0.004)S(0.001)LDKLDQELK 142.43 2.78E-06 159010000 103740 94021 89705 134640 57012 105190 97646 116440 54284 TRUE FALSE 98836.41579 103601.8468 93818.06298 121105.7314 66954.87475 101547.2439 82748.30931 106243.8963 62702.08548 1.576285941 1.652287097 1.496251078 1.931446625 1.067825324 1.619519401 1.319705855 1.694423646 1 15.93622581 2.741650436 24.99994656 1.379609252 1.643027568 0.304313487 0.2382424 374.9513224 3033763.063 0.065099776 0.066436378 551.6332511 -2.741650436 0.263418316 SAS(ph)QSSLDKLDQELKEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 S(0.003)AS(0.96)QS(0.03)S(0.006)LDKLDQELKEQQK;S(0.132)AS(0.861)QS(0.007)S(0.001)LDKLDQELKEQQK 170.18 6.62E-12 327540000 439499 285126 388183 393905 198462 433341 499101 475019 204333 TRUE FALSE 418724.7533 314180.6636 405981.5745 354308.921 233073.71 418334.2925 422953.9758 433423.8181 236019.9181 1.774107697 1.33116165 1.720115734 1.50118229 0.987517121 1.772453342 1.792026619 1.836386614 1 17.84854909 SAS(ph)S(ph)GAEGDVSSEREP ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 2 S(0.195)AS(0.827)S(0.977)GAEGDVSSEREP 93.768 0.05165 145960000 218820 176860 224210 225360 189940 206870 243280 210170 193130 TRUE FALSE 208476.8123 194882.2351 234490.2503 202706.3846 223065.4759 199706.04 206163.1679 191766.4006 223079.614 0.934539954 0.873599481 1.051150511 0.908672832 0.999936623 0.895223174 0.92416857 0.859632116 1 17.76719915 -0.041726597 7.624897327 0.999999998 0.928990675 0.125373595 0.057195817 3432899.326 450222.3127 0.050568002 0.012264542 0.908392213 0.041726597 -0.071009324 SAS(ph)SDTSEELNSQDSPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 SAS(0.995)S(0.005)DTSEELNSQDSPPK;SAS(0.877)S(0.123)DTSEELNSQDSPPK;S(0.009)AS(0.932)S(0.056)DT(0.003)SEELNSQDSPPK;S(0.02)AS(0.911)S(0.064)DT(0.005)SEELNSQDSPPK 558.66 0 466320000 958990 1200330 812500 1166010 553690 991680 846340 984630 503370 TRUE FALSE 913660.4432 1322644.992 849753.9287 1048800.46 650253.3607 957337.8729 717215.2889 898410.5773 581430.0487 1.571402175 2.274813616 1.46148953 1.803829131 1.118369032 1.646522871 1.233536675 1.545173971 1 19.14924611 3.121627029 1.531148481 1.344896844 1.894294056 0.362723038 0.289877931 0.352960859 1.71572987 0.092178467 0.121001719 1323.204681 -3.121627029 0.549397212 SAS(ph)SSWLEGTSTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASSSWLEGTSTQAK 15 0 K7EL81;Q9BZL4-3;Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 K7EL81;Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 SAS(0.984)S(0.015)SWLEGTSTQAK;S(0.002)AS(0.495)S(0.495)S(0.007)WLEGTSTQAK;S(0.003)AS(0.913)S(0.084)SWLEGTSTQAK 261.84 6.00E-25 572738000 937220 697340 787140 875510 803460 829110 974680 864910 873420 TRUE FALSE 892919.468 768399.7388 823231.1476 787502.0714 943583.1696 800397.7128 825974.6648 789173.8952 1008865.513 0.885072843 0.761647345 0.815996916 0.780581813 0.935291332 0.793364133 0.818716325 0.782238946 1 19.94430244 -1.275809582 3.751836333 1.000341997 0.82062566 0.534522365 0.052308284 5568985.527 3787497.389 14382.29867 0.011211185 0.052989573 1.275809582 -0.179716337 SAS(ph)TDLGTADVVLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASTDLGTADVVLGR 15 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 SAS(0.949)T(0.051)DLGTADVVLGR 170.98 1.16E-06 35775000 103730 75674 64466 127960 180680 83866 116710 60306 114060 TRUE FALSE 98826.88847 83385.26663 67421.82987 115097.2177 212190.5348 80961.69939 98903.74597 55025.28694 131747.8423 0.750121496 0.632915615 0.511749025 0.873617478 1.610580721 0.614520117 0.750704864 0.417656077 1 17.00741981 SAS(ph)TLCLPSVGAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASTLCLPSVGAAR 14 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 S(0.002)AS(0.851)T(0.147)LCLPSVGAAR;S(0.038)AS(0.908)T(0.054)LCLPSVGAAR;SAS(0.929)T(0.071)LCLPSVGAAR;SAS(0.98)T(0.02)LCLPSVGAAR 216.83 3.98E-08 359840000 750359 778767 636892 888056 541651 769003 775740 773368 519613 TRUE FALSE 714891.0171 858124.2427 666094.1282 798786.9237 636114.7629 742372.2333 657386.6156 705647.798 600191.9302 1.191104014 1.429749718 1.109801873 1.330885811 1.059852242 1.236891394 1.095293993 1.175703575 1 19.1950644 1.853414086 0.308529561 0.991617107 1.328570739 0.343168652 0.103735178 1.435578898 0.443642121 0.152127132 0.173609776 71.3533037 -1.853414086 0.336953632 SAS(ph)TLCLPSVGAARPQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.983)T(0.017)LCLPSVGAARPQVK;SAS(0.943)T(0.057)LCLPSVGAARPQVK;S(0.001)AS(0.835)T(0.164)LCLPSVGAARPQVK 294.09 1.77E-49 4406640000 2864560 2405650 2509010 2899770 2340090 2825350 3128400 3051810 2592670 TRUE FALSE 2729157.926 2650788.47 2624050.59 2608279.61 2748200.955 2727507.421 2651105.123 2784577.338 2994728.022 0.911320796 0.885151657 0.87622334 0.870957092 0.917679647 0.91076966 0.885257393 0.929826454 1 21.51399355 0.910106649 3.112070704 0.99994532 0.894083117 0.82506786 0.015554992 0.148660147 3.257962972 0.014969327 0.003912732 8.130301463 -0.910106649 -0.105862203 SAS(ph)WGSADQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 S(0.152)AS(0.847)WGS(0.001)ADQLK;S(0.001)AS(0.999)WGSADQLK;SAS(1)WGSADQLK;SAS(1)WGSADQLK 302.14 6.69E-36 1171455000 2185140 2006540 1615620 2082260 1400580 1935490 2059250 2155970 1414150 TRUE FALSE 2081852.763 2211008.707 1689697.775 1872947.269 1644840.709 1868463.496 1745073.592 1967181.837 1633449.16 1.274513351 1.353582812 1.034435486 1.146621098 1.006973923 1.143876126 1.068336643 1.204311641 1 20.63949012 3.741140277 24.99998636 1.090535212 1.314048092 0.663249722 0.067396857 108.5679531 1052148.264 0.015338111 0.026127954 5509.856361 -3.741140277 0.22351288 SAS(ph)WGSTDQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASWGSTDQLK 11 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 S(0.013)AS(0.986)WGSTDQLK;S(0.011)AS(0.989)WGSTDQLK;SAS(1)WGSTDQLK;SAS(1)WGSTDQLK 194.06 7.14E-07 324280000 1185120 1219070 1068990 1233200 889830 1222820 1355200 1340020 770860 TRUE FALSE 1129101.726 1343294.619 1118004.249 1109236.393 1045016.07 1180473.437 1148439.35 1222680.745 890401.0318 1.26808223 1.508640007 1.255618771 1.245771684 1.173646518 1.325777256 1.289800111 1.373179838 1 19.76409574 -3.755800017 0.277577165 4.65E-18 1.336989942 0.505120967 0.09204152 88.33102851 1.606781439 50.7507945 0.110451419 0.000175469 3.755800017 1.336989942 SASDNT(ph)LVAMDFSGHAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.316)AS(0.316)DNT(0.367)LVAMDFSGHAGR 73.464 0.074186 7414500 10465 10445 10845 9839 12598 8897.5 12822 10108 11555 TRUE FALSE 9970.34019 11509.35737 11342.25398 8849.965027 14795.08721 8589.377344 10865.76841 9222.889934 13346.89039 0.747015964 0.862325009 0.849804985 0.663073178 1.108504437 0.643548954 0.814104866 0.691014136 1 13.70421604 -0.011984535 7.559059257 0.999999993 0.801143049 0.18547425 0.133211426 1518213.195 200846.8404 0.111852568 0.027128233 0.972781863 0.011984535 -0.198856945 SASDNTLVAMDFSGHAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 154.48 2.57E-08 202820000 181394 156773 156808 201406 188810 167653 181498 201136 192290 FALSE TRUE 172819.8651 172748.3469 163997.8019 181160.2862 221738.4042 161847.1346 153807.1467 183523.4656 222109.3511 0.778084598 0.777762602 0.738365139 0.815635566 0.998329891 0.728682218 0.692483886 0.826275277 1 17.76091061 0.97369303 23.61297929 1.000000004 0.784715516 0.389139231 0.081971692 1390.310958 1247937.112 0.079831686 0.019957922 9.412240811 -0.97369303 -0.215284487 SASEPS(ph)LHR ddPTM_SK-BR-3_Trastuzumab_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 SAS(0.16)EPS(0.84)LHR 111.61 0.0022001 372290000 325740 251040 324500 352880 318570 310540 370520 324460 343730 TRUE FALSE 310342.9158 276621.2614 339378.646 317407.832 374128.5071 299785.9219 313990.3689 296048.5623 397033.8929 0.781653459 0.696719515 0.854785075 0.799447699 0.94230874 0.755063805 0.790840214 0.745650605 1 18.59890264 -2.426724081 2.291814594 2.991393189 0.790530849 0.483225019 0.066161641 5053117.323 833491.8581 51576381.68 0.017343961 0.003743483 2.426724081 -2.20086234 SASQS(ph)SLDKLDQELK ddPTM_SK-BR-3_Trastuzumab_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 1 S(0.001)AS(0.009)QS(0.602)S(0.388)LDKLDQELK 122.22 6.68E-05 94638000 218190 257810 176590 275940 104730 268440 215220 283310 119340 TRUE FALSE 207876.5911 284081.1321 184686.8262 248201.9869 122994.8788 259143.8555 182384.2362 258501.8745 137846.6377 1.508028013 2.060849193 1.339799282 1.80056613 0.892258824 1.879943246 1.323095284 1.875286034 1 17.07270455 3.720547985 24.55344845 1.467435554 1.784438651 0.12923686 0.363124669 1104.382886 1505410.684 0.084676737 0.131502777 5254.700703 -3.720547985 0.317003098 SASQS(ph)SLDKLDQELKEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 S(0.002)AS(0.01)QS(0.583)S(0.405)LDKLDQELKEQQK;SASQS(0.5)S(0.5)LDKLDQELKEQQK 119.02 3.54E-05 803370000 591050 441361 547680 562470 276690 670790 681510 685060 262890 TRUE FALSE 563112.2378 486336.1877 572791.6697 505929.447 324944.6484 647560.3741 577533.1327 625072.5147 303657.6385 1.854431328 1.601593788 1.886307463 1.666117966 1.070102007 2.132534446 1.901921965 2.058477823 1 18.21208614 SASQSS(ph)LDKLDQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.004)QS(0.247)S(0.748)LDKLDQELK;SASQS(0.013)S(0.987)LDKLDQELK;SASQS(0.034)S(0.966)LDKLDQELK;SASQS(0.002)S(0.998)LDKLDQELK;SASQS(0.201)S(0.799)LDKLDQELK 308.02 2.68E-56 1764270000 2374910 2565270 1889280 2706460 905800 2563090 2093670 2542450 871273 TRUE FALSE 2262652.711 2826673.929 1975905.357 2434401.499 1063771.233 2474329.551 1774242.189 2319819.6 1006385.567 2.248296066 2.808738541 1.963368138 2.418955099 1.057021551 2.458629805 1.762984533 2.305100228 1 19.94075171 -0.490999113 0.130081517 3.92E-10 2.944366536 0.367633017 0.469807472 26.18878088 0.883735899 15.61692452 4.933890444 0.322850071 0.490999113 2.944366536 SASQSS(ph)LDKLDQELKEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.206)S(0.794)LDKLDQELKEQQK;S(0.001)AS(0.004)QS(0.157)S(0.838)LDKLDQELKEQQK 268.25 4.53E-32 837170000 737859 607324 710934 653746 273662 862840 795990 878950 261683 TRUE FALSE 702981.8674 669211.0061 743531.0271 588030.21 321388.5662 832959.6344 674547.1061 801984.4784 302263.4631 2.325725577 2.213999003 2.459877285 1.945422725 1.063272957 2.755740392 2.231652808 2.653263051 1 18.20544707 -1.246287165 3.720083696 0.998123241 2.206156254 0.398046807 0.466129952 25229613.7 39938472.7 535054.758 0.106651655 0.056716946 1.246287165 1.208033012 SASS(ph)DTSEELNSQDSPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 S(0.009)AS(0.301)S(0.689)DTSEELNSQDSPPK 491.95 2.79E-240 185480000 287030 358190 252550 377850 162370 296720 270000 301150 148410 TRUE FALSE 273462.6607 394689.9682 264129.6673 339867.8001 190687.2766 286444.512 228806.5411 274779.7095 171424.6648 1.595235207 2.302410617 1.540791505 1.982607348 1.112367796 1.670964399 1.33473524 1.602918167 1 17.38721518 2.751653157 24.96892648 1.389235635 1.883423786 0.433198522 0.287131169 691.9131694 1319554.171 0.079755825 0.084127825 564.4859757 -2.751653157 0.494188151 SASS(ph)GAEGDVSSEREP ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.029)S(0.971)GAEGDVSSEREP;SAS(0.029)S(0.971)GAEGDVSSEREP;SAS(0.002)S(0.998)GAEGDVSSEREP;SAS(0.019)S(0.981)GAEGDVSSEREP 375.01 4.32E-104 4078870000 2592630 2405430 2547460 2892620 2560630 2659850 3100580 2753900 2743470 TRUE FALSE 2470081.518 2650546.052 2664263.561 2601848.342 3007203.061 2567738.728 2627529.575 2512753.917 3168913.316 0.779472731 0.836421128 0.840749902 0.821053807 0.948969808 0.810289986 0.82915792 0.792938672 1 21.59555677 -2.600437826 2.18477442 4.449159513 0.831790944 0.57227576 0.045538502 1418757.892 134342.5895 24366321.09 0.010781846 0.002509355 2.600437826 -3.617368569 SASS(ph)SWLEGTSTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASSSWLEGTSTQAK 15 0 K7EL81;Q9BZL4-3;Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 K7EL81;Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 SAS(0.282)S(0.71)S(0.008)WLEGTSTQAK 343.53 8.72E-70 126500000 152280 116230 147680 156780 122450 134190 168700 159020 144250 TRUE FALSE 145082.0262 128073.9691 154451.2741 141020.1765 143805.2412 129542.9667 142961.7166 145095.3658 166619.5533 0.870738298 0.7686611 0.926969681 0.846360309 0.863075422 0.777477578 0.858012843 0.870818358 1 17.34619819 0.728018852 1.987989549 0.999867453 0.839486955 0.535024276 0.045158629 0.815105978 4.779468956 0.040341589 0.011155686 5.345875643 -0.728018852 -0.160380499 SASSGAEGDVSS(ph)EREP ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SASSGAEGDVS(0.006)S(0.994)EREP;SASSGAEGDVS(0.005)S(0.995)EREP 245.18 1.10E-19 702360000 1240100 1099640 1197070 1281260 1172930 1150770 1389400 1257620 1292090 TRUE FALSE 1181482.931 1211694.566 1251956.844 1152465.311 1377488.621 1110918.546 1177421.512 1147496.126 1492460.718 0.791634189 0.811877024 0.838854134 0.772191386 0.922964741 0.744353625 0.788912899 0.768861861 1 20.50926153 -1.014981967 4.63729032 1.000004077 0.804463111 0.610104507 0.048999772 2.42E-06 5.15E-07 0.042918858 0.010115798 0.096609099 1.014981967 -0.195540966 SAST(ph)LCLPSVGAARPQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.365)T(0.635)LCLPSVGAARPQVK 335.42 7.45E-75 3277700000 1531600 1351200 1262400 1586400 1163100 1453900 1766000 1597100 1192300 TRUE FALSE 1459204.303 1488888.816 1320282.289 1426932.058 1365944.272 1403551.078 1496564.265 1457249.457 1377195.795 1.059547458 1.081101774 0.958674354 1.036114156 0.991830121 1.019136919 1.086675018 1.058128019 1 20.39330225 -0.587815475 7.734270117 1.000000054 1.040778757 0.068129236 0.039458703 0 0 0.039125085 0.009221871 0.258335759 0.587815475 0.040778703 SASVVSSDSISTSADNFS(ph)PDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SASVVSSDSISTSADNFSPDLR 22 0 Q13614 Q13614 MTMR2 Myotubularin-related protein 2 1 SASVVSSDSISTSADNFS(1)PDLR;SASVVSSDSIS(0.001)T(0.001)S(0.002)ADNFS(0.997)PDLR 155.53 1.94E-08 106478000 226830 152938 203313 198054 222330 227037 288560 260950 251490 TRUE FALSE 216108.1954 168522.5561 212635.1022 178145.2356 261104.2816 219174.6518 244534.8722 238099.8346 290489.7848 0.743944217 0.580132469 0.731988226 0.613258176 0.898841527 0.754500376 0.841801967 0.819649596 1 18.14812791 1.560088732 0.388361301 1.002909073 0.640348687 0.607843116 0.078041681 0.664763191 0.298156566 0.091849168 0.072846079 36.3152244 -1.560088732 -0.362560386 SASWGS(ph)ADQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 SAS(0.338)WGS(0.662)ADQLK 199.51 5.25E-08 246320000 788900 661470 545010 716330 462890 628830 728230 726290 469470 TRUE FALSE 751610.2604 728874.545 569999.2476 644323.1475 543617.8694 607053.4594 617125.1386 662692.1973 542273.0099 1.38603664 1.344109944 1.051129666 1.188189594 1.002480041 1.119460951 1.13803403 1.222063767 1 19.04865984 3.787256953 6.699248055 1.110804063 1.367267364 0.691198325 0.072693568 0.111493857 12.35985126 0.017095377 0.03078812 6127.128001 -3.787256953 0.256463302 SASYKPVFVTEITDDLHFYVQDVETGTQLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SASYKPVFVTEITDDLHFYVQDVETGTQLEK 31 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 424.66 3.43E-197 6468759000 1705123 1453343 1478632 1746305 1101730 1753603 1902931 1856529 1062898 FALSE TRUE 1624525.215 1601440.304 1546428.74 1570763.104 1293871.363 1692875.288 1612603.926 1693961.479 1227726.793 1.323197656 1.304394685 1.259587026 1.279407692 1.053875643 1.378869711 1.313487606 1.379754427 1 20.22755812 3.80845606 2.479869229 1.256141271 1.318141287 0.045985441 0.125045634 1.085337574 13.10299619 0.032121394 0.065347034 6433.629684 -3.80845606 0.062000016 SAT(ph)FPNAGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SATFPNAGPR 10 0 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.002)AT(0.998)FPNAGPR;S(0.001)AT(0.999)FPNAGPR;S(0.001)AT(0.999)FPNAGPR;S(0.002)AT(0.998)FPNAGPR 188.27 1.27E-05 777590000 1037260 772440 870440 996450 827980 858930 1102150 967050 860780 TRUE FALSE 988230.7755 851152.5142 910350.535 896284.9529 972379.4499 829185.0387 933996.7751 882369.9753 994265.3661 0.993930604 0.856061715 0.915601172 0.901454464 0.977987852 0.833967537 0.939383797 0.887459229 1 19.92327143 -1.08310732 6.75389726 1.000000056 0.913001104 0.235285756 0.049159354 3.66E-08 4.94E-09 0.042246998 0.009957707 0.082583385 1.08310732 -0.086998952 SAT(ph)RPSPS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.002)AT(0.538)RPS(0.472)PS(0.988)PER 115.83 0.026861 397220000 465250 398270 409140 460110 337140 431000 462840 411050 358930 TRUE FALSE 443258.5545 438854.1658 427899.4737 413858.8686 395937.1093 416074.3619 392225.2574 375056.2829 414591.0312 1.069146511 1.058523057 1.03210017 0.998234012 0.955006451 1.003577817 0.946053406 0.904641574 1 18.66132938 3.215679475 0.975609583 0.954927221 1.071714201 0.703985724 0.02760058 0.262313588 0.54255873 0.011552988 0.018354512 1643.158564 -3.215679475 0.116786981 SATLSGS(ph)ATNLASLTAALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SATLSGS(0.997)AT(0.003)NLASLTAALAK;SATLS(0.005)GS(0.995)ATNLASLTAALAK;SATLSGS(0.996)AT(0.003)NLASLTAALAK;SATLS(0.002)GS(0.998)ATNLASLTAALAK;S(0.004)AT(0.004)LS(0.081)GS(0.62)AT(0.285)NLAS(0.007)LTAALAK 355.04 3.08E-71 106395800 359657 311731 326658 356569 239691 326206 384857 358991 276130 TRUE FALSE 342656.7264 343496.7433 341635.5924 320726.0067 281493.0345 314909.4044 326139.9963 327555.8449 318950.8301 1.074324611 1.076958298 1.07112307 1.005565675 0.882559341 0.987329001 1.022540045 1.026979126 1 18.28297451 3.191572314 4.475423347 0.984891898 1.075342789 0.522256218 0.039445358 0.164908913 7.03064476 0.012000845 0.014929812 1554.434096 -3.191572314 0.090450891 SATREPPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SATREPPYR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 119.62 0.00072797 211535000 143494 108657 135544 148976 133841 130478 152497 140511 154832 FALSE TRUE 136711.323 119729.2718 141758.8265 134000.6494 157182.828 125959.5141 129230.7819 128207.1119 178842.5558 0.764422776 0.669467462 0.792645944 0.749266017 0.878889408 0.704303926 0.722595253 0.716871392 1 17.44833054 -1.605903341 4.730648906 1.00348641 0.744899441 0.654623345 0.057012957 0.002055901 0.000171271 0.054136136 0.012606189 0.024779735 1.605903341 -0.25858697 SATRPS(ph)PS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.15)AT(0.102)RPS(0.749)PS(1)PER;S(0.24)AT(0.243)RPS(0.523)PS(0.994)PER;S(0.001)AT(0.027)RPS(0.984)PS(0.987)PER;S(0.399)AT(0.143)RPS(0.459)PS(0.999)PER;S(0.001)AT(0.038)RPS(0.963)PS(0.998)PER 120.9 0.0050564 8671670000 3002260 2647470 2653740 3082070 2309670 2806480 3050200 2774250 2315130 TRUE FALSE 2860349.12 2917250.203 2775416.604 2772254.468 2712475.717 2709290.894 2584835.969 2531321.963 2674148.536 1.069629858 1.090908064 1.037869275 1.036686792 1.01433248 1.013141513 0.966601494 0.946589888 1 21.35064817 2.739371805 0.767609291 0.968171155 1.081707172 0.808993881 0.018886013 0.237460946 0.301215664 0.012313265 0.011879725 548.7465521 -2.739371805 0.113536017 SATRPS(ph)PS(ph)PERS(ph)STGPEPPAPTPLLAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATRPSPSPERSSTGPEPPAPTPLLAER 28 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.007)AT(0.011)RPS(0.984)PS(0.995)PERS(0.528)S(0.407)T(0.069)GPEPPAPTPLLAER 81.595 0.0033766 119410000 112240 84846 99834 92693 91305 104600 109460 94414 89939 TRUE FALSE 106934.6376 93491.90386 104411.4876 83375.32353 107228.5631 100977.6758 92759.86663 86146.60964 103886.2808 1.029343209 0.899944662 1.005055594 0.802563369 1.032172509 0.97200203 0.892898138 0.82923952 1 16.66464562 1.692116763 6.863487087 0.896019588 0.9545922 0.073700197 0.078787931 0.286943798 28.50558753 0.035857904 0.018455185 49.21718421 -1.692116763 0.058572612 SATRPS(ph)PS(ph)PERSSTGPEPPAPTPLLAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SATRPSPSPERSSTGPEPPAPTPLLAER 28 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.003)AT(0.003)RPS(0.99)PS(0.988)PERS(0.012)S(0.003)T(0.001)GPEPPAPTPLLAER;S(0.009)AT(0.043)RPS(0.861)PS(0.933)PERS(0.079)S(0.071)T(0.004)GPEPPAPTPLLAER;S(0.037)AT(0.045)RPS(0.916)PS(0.964)PERS(0.014)S(0.013)T(0.012)GPEPPAPTPLLAER;S(0.004)AT(0.004)RPS(0.99)PS(0.944)PERS(0.022)S(0.02)T(0.018)GPEPPAPTPLLAER 114.76 0.00021224 681390000 262210 82888 320301 192787 371933 231027 480565 275275 556909 TRUE FALSE 249815.853 91334.38144 334987.1177 173407.6845 436797.9974 223026.4771 407245.9831 251170.4617 643271.6034 0.388352061 0.141984165 0.520755332 0.26957149 0.679025773 0.346706548 0.633085591 0.390457872 1 19.29506848 -4.999999977 0.12032972 2.982580502 0.114402552 0.60360267 0.152431847 88.83333082 0.692401047 42.57685967 1.27207775 1.00E-05 4.999999977 -2.86817795 SATRPS(ph)PSPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.027)AT(0.024)RPS(0.803)PS(0.146)PER;S(0.028)AT(0.024)RPS(0.899)PS(0.05)PER;S(0.041)AT(0.034)RPS(0.897)PS(0.029)PER 73.834 0.025723 287765000 329547 340825 302085 354095 281942 314063 301414 324307 238992 TRUE FALSE 313969.9664 375555.455 315935.8961 318500.6979 331112.5955 303186.9196 255427.7585 295908.9598 276053.6588 1.137351223 1.360443679 1.144472772 1.153763726 1.199450125 1.098289807 0.925283003 1.071925513 1 18.0745892 2.063730323 3.142235166 0.992808353 1.211617061 0.610627236 0.072427096 0.153997272 3.026533727 0.032528889 0.020786491 115.8058032 -2.063730323 0.218808708 SATRPSPS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SAT(0.011)RPS(0.006)PS(0.982)PER;SATRPS(0.003)PS(0.997)PER 104.74 0.0041406 1002140000 930590 710890 763610 896890 896610 796840 944870 826550 852850 TRUE FALSE 886602.855 783330.4992 798622.2738 806732.9132 1052978.5 769245.231 800712.7278 754172.9002 985105.6222 0.900007913 0.795174123 0.810697103 0.818930372 1.068899087 0.780875892 0.812819163 0.765575673 1 19.90991889 -2.498189739 2.207955032 2.977293906 0.842954571 0.238418088 0.08753164 3847099.516 293179.0842 38554309 0.020144667 0.003175486 2.498189739 -2.134339336 SATRPSPS(ph)PERS(ph)STGPEPPAPTPLLAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATRPSPSPERSSTGPEPPAPTPLLAER 28 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.016)AT(0.016)RPS(0.358)PS(0.409)PERS(0.401)S(0.401)T(0.401)GPEPPAPTPLLAER 62.051 0.015474 269190000 78422 29011 88113 52495 102180 56511 126360 69181 174270 TRUE FALSE 74715.14748 31967.25388 92153.06821 47218.10287 120000.1596 54554.0099 107081.4612 63123.14489 201294.9016 0.371172578 0.158808065 0.457801303 0.234571778 0.596141078 0.271015358 0.531963107 0.313585413 1 17.61895111 -5 0.20627778 4.021692699 0.263404907 0.689114211 0.133665812 71.72037529 0.712998352 89.41100778 0.258010643 1.00E-05 5 -3.758287792 SATSPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATSPEGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 83.206 0.048232 0 98197 77646 80498 100430 72050 92897 104010 91733 101980 FALSE TRUE 93555.42242 85558.21568 84188.91292 90334.5856 84615.49719 89679.9536 88141.36423 83700.37221 117794.5376 0.794225474 0.726334323 0.714709822 0.766882637 0.718331248 0.761325232 0.748263596 0.710562425 1 16.84591311 -1.931530215 2.556352319 1.170739836 0.744498019 0.902990666 0.026509553 4064665.653 1773840.772 4132401.081 0.006026669 0.011707651 1.931530215 -0.426241817 SATT(ph)TPSGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 2 SAT(0.024)T(0.463)T(0.463)PS(0.05)GS(1)PR 82.774 0.095586 58282000 144940 111840 126440 150160 146820 131680 159660 127280 149110 TRUE FALSE 138088.9734 123236.6232 132237.3991 135065.6315 172425.3615 127119.8886 135300.9346 116134.6884 172233.2173 0.801755757 0.715521809 0.767781042 0.784201989 1.001115605 0.738068362 0.785568178 0.674287401 1 17.39400389 -1.551356125 2.896198451 1.010876312 0.78275275 0.384873826 0.085996808 37800312.37 41057541.16 3210572.274 0.01968845 0.02809596 1.551356125 -0.228123563 SATTT(ph)PSGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 2 SATT(0.008)T(0.953)PS(0.04)GS(1)PR 112.02 0.0083907 117100000 333430 289410 286370 337490 313250 322680 357660 274450 316930 TRUE FALSE 317669.4247 318901.208 299500.3478 303564.864 367880.7008 311505.5107 303092.3981 250417.703 366077.8857 0.867764585 0.871129397 0.81813286 0.829235733 1.004924676 0.850926873 0.827945117 0.684055806 1 18.4817911 -1.749562988 6.588086896 1.003352748 0.850272469 0.28160697 0.077646426 0.003688795 0.000140224 0.072528483 0.016763803 0.017800697 1.749562988 -0.153080279 SATTTGS(ph)PGTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.017)GS(0.983)PGTEK;SATTT(0.001)GS(0.998)PGT(0.001)EK;SATTT(0.085)GS(0.915)PGTEK;SATTT(0.006)GS(0.994)PGTEK;SATTT(0.026)GS(0.973)PGTEK;SATT(0.001)T(0.239)GS(0.761)PGTEK;SATTT(0.023)GS(0.947)PGT(0.03)EK;SAT(0.003)T(0.029)T(0.464)GS(0.499)PGT(0.005)EK 372.9 1.33E-86 1344436000 3482603 3124575 3397689 3973713 2398406 3784964 4026161 4096287 2905820 TRUE FALSE 3317987.258 3442972.745 3553476.401 3574267.82 2816687.247 3653889.748 3411896.194 3737594.394 3356439.725 0.988543674 1.025781193 1.058704071 1.064898557 0.839188985 1.088620696 1.016522409 1.113559218 1 21.6785003 SATTTPSGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 1 SATTTPSGS(1)PR;SATTTPS(0.007)GS(0.993)PR;SATT(0.001)T(0.001)PS(0.035)GS(0.963)PR;SATT(0.005)T(0.003)PS(0.018)GS(0.973)PR 152.38 3.46E-05 496401000 332672 286106 303093 348997 336066 307577 376962 307195 306937 TRUE FALSE 316947.2539 315260.5267 316990.1138 313915.1585 394675.804 296925.5314 319449.5235 280295.3773 354535.2223 0.893979593 0.88922202 0.894100484 0.885427283 1.113220293 0.837506438 0.901037481 0.790599522 1 18.43556944 -0.61792607 8.491385438 0.999999955 0.902014056 0.124249827 0.082831418 0 0 0.07380077 0.017395008 0.24103157 0.61792607 -0.097985899 SAVADKHELLSLASSNHLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAVADKHELLSLASSNHLGK 20 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 227.95 2.18E-25 300180000 636650 475940 579540 721480 544450 630060 862690 803140 431230 FALSE TRUE 606556.8162 524438.8271 606112.4822 648955.4597 639401.9076 608240.8642 731070.7961 732812.8039 498102.946 1.217733846 1.052872366 1.216841794 1.302854089 1.283674214 1.22111477 1.467710243 1.471207528 1 18.92608442 3.374747253 2.990622631 1.320664933 1.1345506 0.155214636 0.138569094 0.32969273 5.915982408 0.037821955 0.053893138 2369.994035 -3.374747253 -0.186114332 SAVAVYSYSCEGPEEES(ph)EDDSHLEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAVAVYSYSCEGPEEESEDDSHLEGR 26 0 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 1 SAVAVYSYSCEGPEEES(1)EDDSHLEGR;SAVAVYSYSCEGPEEES(0.999)EDDS(0.001)HLEGR 307.68 6.94E-73 275210000 110778 135853 104724 124107 103205 114758 105793 116302 82786 TRUE FALSE 105541.7435 149696.5752 109525.699 111631.5286 121203.9193 110783.9017 89652.33483 106117.9803 95624.03007 1.103715702 1.565470259 1.145378404 1.167400375 1.267504823 1.158536213 0.937550266 1.109741769 1 16.54508559 2.223996429 0.971439275 0.995075429 1.299790225 0.350139391 0.136220799 0.528621655 0.946947163 0.099176399 0.055579717 167.4929104 -2.223996429 0.304714796 SAVAVYSYSCEGPEEES(ph)EDDSHLEGRDPDIWHVGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFK 36 1 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 1 SAVAVYS(0.049)Y(0.002)S(0.053)CEGPEEES(0.862)EDDS(0.034)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(0.5)EDDS(0.5)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(1)EDDSHLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(0.889)EDDS(0.111)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(0.974)EDDS(0.026)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(1)EDDSHLEGRDPDIWHVGFK 328.86 4.23E-129 402153000 116550.2 92957.5 115924.7 124520.7 97307.3 123278 136188.7 130316.7 91478 TRUE FALSE 111041.103 102429.9749 121239.9622 112003.6427 114277.6623 119008.8519 115410.6125 118905.4789 105663.941 1.050889281 0.969393853 1.147410942 1.059998724 1.08151997 1.12629579 1.092242173 1.125317471 1 16.6891236 3.7435515 24.99867034 1.094612424 1.010141568 0.349936869 0.045193074 360.7030906 1806706.111 0.010344923 0.017928947 5540.532413 -3.7435515 -0.084470856 SAVENCQDSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SAVENCQDSWR 11 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 203.02 8.85E-08 1384400000 669270 582330 590340 719130 626760 626550 751630 681850 660450 FALSE TRUE 637634.9335 641670.0891 617407.6729 646841.6861 736066.7456 604852.4164 636955.0389 622143.5993 762869.2129 0.835837812 0.841127258 0.809323096 0.847906398 0.964866235 0.792865155 0.834946578 0.815531141 1 19.54107622 -1.715228817 2.773281785 1.025581885 0.842250786 0.53099571 0.046427228 10192304.13 9186505.673 1818685.553 0.010564459 0.019265096 1.715228817 -0.183331099 SAVGHEYQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAVGHEYQSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 187.97 1.17E-06 1724460000 3878820 3275530 3268630 3964900 3052680 3461670 4396520 4136130 3382710 FALSE TRUE 3695475.866 3609310.231 3418499.919 3566340.719 3585066.425 3341791.5 3725750.126 3773948.53 3907283.39 0.945791614 0.923739046 0.874904525 0.91274176 0.917534273 0.855272363 0.953539775 0.965875303 1 21.89773447 1.521665332 5.759915821 0.976170942 0.909489566 0.600245903 0.026704704 0.109412625 7.837971996 0.01556669 0.006965266 33.24033043 -1.521665332 -0.066681375 SAVRPAS(ph)LNLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SAVRPASLNLNR 12 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SAVRPAS(1)LNLNR;SAVRPAS(1)LNLNR;SAVRPAS(1)LNLNR 123.72 0.00020334 1450940000 1133560 1116500 1108350 1359240 2013500 1014330 1441180 1132060 2242550 TRUE FALSE 1079978.865 1230272.619 1159168.944 1222606.613 2364653.763 979203.4978 1221301.522 1032930.825 2590313.201 0.416929839 0.474951299 0.447501462 0.471991809 0.912883339 0.378025135 0.471487974 0.398766769 1 21.30469512 -1.94724595 2.763861711 1.362178505 0.493179463 0.520471072 0.151832441 47643843.85 30984169.44 111189518.5 0.034858358 0.011291563 1.94724595 -0.868999041 SAVS(ph)S(ph)AQAST(ph)NRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SAVSSAQASTNRK 13 1 F6VGH2 F6VGH2 KIF6 3 S(0.526)AVS(0.737)S(0.737)AQAS(0.059)T(0.942)NRK 50.102 0.092725 192240000 286250 334790 521630 264170 184650 362020 327510 374410 181630 TRUE FALSE 272719.5298 368905.4816 545547.2515 237615.1297 216852.9015 349483.1566 277542.3344 341624.6755 209796.2528 1.299925648 1.758398812 2.600366995 1.132599494 1.033635724 1.66582173 1.322913688 1.628364049 1 17.67862938 SAVSDKQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SAVSDKQDR 9 1 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;;; 103.7 0.0030824 455860000 998540 769000 860150 993660 722560 905970 1147780 994090 858810 FALSE TRUE 951340.9931 847361.9743 899588.7283 893775.409 848574.2352 874596.0317 972665.0806 907042.2096 991989.8686 0.959022892 0.854204263 0.906852738 0.900992477 0.855426312 0.88165823 0.980519168 0.914366405 1 19.91996586 1.748410112 11.52456781 0.95998347 0.893014492 0.466035904 0.036160532 0.09791273 76.18193996 0.016019527 0.008765641 56.02864399 -1.748410112 -0.066968978 SAYNVYVAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAYNVYVAER 10 0 Q00059;H7BYN3 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ; 164.66 1.42E-05 193159000 220390 149707 130439 118686 201285 105052 197291 147935 225060 FALSE TRUE 209972.6015 164962.3135 136419.7572 106755.4578 236389.0403 101414.0229 167190.6345 134981.0271 259961.1554 0.807707602 0.634565242 0.524769776 0.410659268 0.909324472 0.390112218 0.643136988 0.519235372 1 17.98793654 -1.159866214 5.043475292 1.000022402 0.613205779 0.370965061 0.161354177 3.74E-05 6.23E-06 0.143834429 0.033900139 0.069204413 1.159866214 -0.386816623 SAYQEYDS(ph)DSDVPEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 SAYQEYDS(0.997)DS(0.003)DVPEELKR;SAYQEYDS(0.999)DS(0.001)DVPEELKR 210.32 2.61E-16 1700040000 1079120 1103640 805730 1244980 584220 1067150 1021680 1210760 600730 TRUE FALSE 1028112.136 1216102.171 842673.5175 1119832.245 686107.783 1030194.328 865803.9516 1104739.436 693888.1403 1.481668408 1.752591088 1.214422712 1.613851254 0.988787303 1.484669168 1.247757241 1.592100184 1 19.40434358 5.600675281 0.041020485 3.26E-09 3.264518195 0.247422736 0.224349484 532.4562568 2.685988568 72.18557135 154.1315974 398726.6659 -5.600675281 3.264518192 SCAHDWVYE ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 132.57 0.00070124 20870830000 13940920 11146210 11192950 13089280 15582690 11692170 16010990 13395580 14678450 FALSE TRUE 13281960.34 12282021.47 11706157.83 11773520.71 18300306.2 11287267.22 13568219.41 12222592 16954709.06 0.783378841 0.724401783 0.690436963 0.69441007 1.079364213 0.665730517 0.800262592 0.720896593 1 24.01518269 SCATFSSSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 132.78 0.0002146 95356000 122579 84841 78248 91261 152137 84947 156451 118783 173395 FALSE TRUE 116784.9336 93486.39436 81835.7482 82087.2709 178669.6446 82005.26409 132581.5265 108381.7308 200284.211 0.583096056 0.466768668 0.408598101 0.409853929 0.892080528 0.409444477 0.661966941 0.541139665 1 17.61168917 -5 0.214597631 3.270458536 0.481852725 0.497461979 0.145602074 118.7524272 1.18573208 115.9879479 0.268430922 1.00E-05 5 -2.788605812 SCCTSVNEVICHGIPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCCTSVNEVICHGIPDR 17 0 P53582;H0Y955 P53582 METAP1 Methionine aminopeptidase 1 0 ; 176.81 1.06E-09 357870000 587690 600920 528550 651560 526140 595000 671980 640990 552070 FALSE TRUE 559911.0584 662154.4312 552784.5403 586063.9509 617898.6494 574395.0008 569457.1092 584861.5175 637682.196 0.878040914 1.038376852 0.866865256 0.919053338 0.968975852 0.900754332 0.893010833 0.917167707 1 19.28247808 3.706900931 24.99885227 0.918045 0.958208992 0.059635138 0.053449059 1394.201002 1100877.742 0.01326216 0.020547369 5092.146986 -3.706900931 0.040163993 SCDDFSHMGTLPHS(ph)KSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCDDFSHMGTLPHSKSPR 18 1 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 SCDDFSHMGT(0.004)LPHS(0.498)KS(0.498)PR 174.91 2.81E-12 419850000 195240 129270 188620 196160 170370 179080 219040 194420 50259 TRUE FALSE 186011.3921 142442.76 197268.4136 176441.6241 200082.4741 172878.4147 185621.4251 177395.5541 58052.90903 3.204170045 2.453671355 3.398079732 3.039324421 3.446553797 2.977945767 3.197452602 3.0557565 1 15.82508074 0.88744897 19.6775933 1 3.068270865 0.852726549 0.273609099 10860.73098 1898815.923 0.260701034 0.065175259 7.717008345 -0.88744897 2.068270866 SCDDFSHMGTLPHSKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCDDFSHMGTLPHSKSPR 18 1 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 SCDDFSHMGT(0.384)LPHS(0.231)KS(0.385)PR 130.89 1.09E-05 306760000 111540 74576 89745 89686 93806 93897 112540 95202 29504 TRUE FALSE 106267.7253 82175.37919 93859.89702 80670.59289 110165.7367 90645.32335 95369.95606 86865.60818 34079.32963 3.118245763 2.41129682 2.754159135 2.367141424 3.232626283 2.659832934 2.798469251 2.548923618 1 15.05660934 0.685641378 2.786815963 1.000031551 2.750761579 0.809086435 0.266938854 1.025306382 8.617534455 0.232506037 0.061284678 4.848879353 -0.685641378 1.750730028 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 3 SCDEPLT(0.964)PPPHS(0.975)PT(0.031)S(0.031)MLQLIHDPVS(1)PR 111.27 0.0038488 55576000 64191 59545 69069 74846 74346 71741 88716 75871 45710 TRUE FALSE 61156.81864 65612.7032 72235.88197 67322.33788 87311.91886 69256.59118 75180.74482 69227.33302 52798.47335 1.158306572 1.242700765 1.368143384 1.275081146 1.653682641 1.31171579 1.423918914 1.311161642 1 15.68820859 3.938036839 1.72225699 1.368097071 1.16898198 0.089736803 0.161884689 0.600609791 3.416224977 0.041036213 0.115373148 8670.354195 -3.938036839 -0.199115091 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVSPR ddPTM_SK-BR-3_Trastuzumab_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 SCDEPLT(0.993)PPPHS(0.768)PT(0.126)S(0.113)MLQLIHDPVSPR;S(0.007)CDEPLT(0.991)PPPHS(0.738)PT(0.139)S(0.124)MLQLIHDPVSPR 97.243 0.0074732 177357000 223740 200420 224500 237290 261520 219420 268480 226180 118005 TRUE FALSE 213164.2536 220843.0259 234793.5471 213437.1584 307129.0052 211821.4304 227518.445 206374.4801 136304.6127 1.563881437 1.620216818 1.72256494 1.565883605 2.25325467 1.554029803 1.66919109 1.514068204 1 17.05647486 0.728030074 1.490760429 1.000556756 1.701767229 0.547657927 0.202823024 0.71632083 2.59057545 0.183077606 0.053368709 5.346013783 -0.728030074 0.701210472 SCDEPLT(ph)PPPHSPTSMLQLIHDPVSPR ddPTM_SK-BR-3_Trastuzumab_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(1)PPPHSPTSMLQLIHDPVSPR;S(0.001)CDEPLT(0.999)PPPHSPTSMLQLIHDPVSPR 145.86 2.88E-07 226779000 268420 223920 250180 262480 301310 247990 325270 252880 174079 TRUE FALSE 255732.3186 246737.7026 261651.0005 236095.0117 353858.3686 239402.0441 275644.0875 230736.4866 201074.2822 1.27183007 1.227097269 1.301265371 1.174168119 1.759839024 1.190614938 1.370857001 1.147518638 1 17.61736904 1.022752675 3.805313373 1.000874488 1.318046738 0.308885466 0.165410896 0.227909079 7.941619334 0.145716685 0.03749948 10.53786608 -1.022752675 0.31717225 SCDEPLTPPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 SCDEPLT(0.008)PPPHS(0.563)PT(0.216)S(0.236)MLQLIHDPVS(0.976)PR;SCDEPLT(0.075)PPPHS(0.635)PT(0.142)S(0.154)MLQLIHDPVS(0.993)PR 76.476 0.0073196 89020000 77659 67476 78775 78905 83633 75503 96221 81295 42413 TRUE FALSE 73988.21298 74351.88111 82386.91167 70973.31949 98218.56872 72888.31218 81540.71923 74176.37883 48990.19142 1.510265848 1.517689132 1.681702179 1.44872509 2.004861909 1.487814398 1.664429488 1.514106736 1 15.58020531 0.846175545 4.869055196 1.000008028 1.605266446 0.597177869 0.157788536 1.145787477 35.72675882 0.138212339 0.034972343 7.017388895 -0.846175545 0.605258418 SCDEPLTPPPHS(ph)PTSMLQLIHDPVSPR ddPTM_SK-BR-3_Trastuzumab_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 SCDEPLT(0.003)PPPHS(0.719)PT(0.123)S(0.155)MLQLIHDPVSPR;SCDEPLT(0.017)PPPHS(0.4)PT(0.257)S(0.325)MLQLIHDPVSPR;SCDEPLT(0.001)PPPHS(0.987)PT(0.006)S(0.006)MLQLIHDPVSPR;SCDEPLTPPPHS(0.8)PT(0.1)S(0.1)MLQLIHDPVSPR;SCDEPLTPPPHS(0.871)PT(0.053)S(0.076)MLQLIHDPVSPR;SCDEPLTPPPHS(0.936)PT(0.032)S(0.032)MLQLIHDPVSPR;SCDEPLTPPPHS(0.989)PT(0.005)S(0.005)MLQLIHDPVSPR 153.69 4.76E-08 1229304000 885512 733976 806346 915371 930419 788118 1012263 905796 470624 TRUE FALSE 843655.6027 808768.9889 843317.7617 823356.168 1092683.779 760825.276 857823.6879 826479.7003 543605.9663 1.551961632 1.487785343 1.551340151 1.514619447 2.010065832 1.399589635 1.578024785 1.520365396 1 19.05220176 -0.365017943 7.364636161 1.000000202 1.570250217 0.556133208 0.161829488 0 0 0.144043806 0.033951451 0.431501249 0.365017943 0.570250015 SCFESS(ph)PDPELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFES(0.001)S(0.999)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFESS(1)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.002)S(0.998)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.038)S(0.962)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.318)S(0.682)PDPELK;SCFESS(1)PDPELK;SCFES(0.037)S(0.963)PDPELK 305.74 5.04E-37 27004510000 67892900 58294380 59469130 67026700 40499320 67656120 72784700 70864800 43860690 TRUE FALSE 64683737.17 64234643.6 62195848.43 60289048.77 47562388.59 65313171.6 61680057.23 64659502.43 50662381.8 1.276760683 1.267896244 1.227653463 1.190016076 0.938810749 1.289184781 1.217472512 1.276282325 1 25.59441157 -2.340786194 1.958311845 3.52E-05 1.215093891 0.296753424 0.101625173 1971551.281 226922.6565 8714454.534 0.024404515 0.004562615 2.340786194 1.215058721 SCMLTGT(ph)PESVQSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCMLTGTPESVQSAK 15 0 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1 Q96AE4;C9JSZ1 FUBP1 Far upstream element-binding protein 1 1 S(0.002)CMLT(0.03)GT(0.967)PES(0.001)VQSAK 73.887 0.015948 0 89287 88562 86091 104130 63706 84999 100620 95402 71880 TRUE FALSE 85066.58046 97586.56849 90038.35751 93662.65457 74816.30623 82055.46332 85268.57099 87048.09512 83026.78329 1.024567942 1.175362511 1.084449547 1.12810169 0.9011105 0.988301125 1.027000777 1.048433911 1 16.34128918 2.766980144 24.99354433 0.996916238 1.105395456 0.515938837 0.052919654 580.8573349 510834.0363 0.015791563 0.016746577 584.7633479 -2.766980144 0.108479218 SCQGACGPS(ph)PPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SCQGACGPSPPDQK 14 0 P18754-2 P18754-2 RCC1 Regulator of chromosome condensation 1 SCQGACGPS(1)PPDQK;SCQGACGPS(1)PPDQK;SCQGACGPS(1)PPDQK 134.93 1.74E-05 124874000 394640 374176 397160 447260 280682 429583 475742 478746 325159 TRUE FALSE 375986.1493 412304.9598 415370.1788 402300.5751 329632.8519 414706.433 403158.8203 436824.4622 375582.997 1.001073404 1.09777323 1.10593446 1.071136282 0.877656482 1.104167218 1.073421383 1.163057076 1 18.51877223 SCS(ph)FGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCSFGR 6 0 O14974;O14974-5;O14974-2;O14974-4;F8VZN8;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 S(0.054)CS(0.946)FGR;S(0.234)CS(0.766)FGR 77.282 0.076395 152162000 414620 318580 344020 415990 424600 369190 428000 408040 464790 TRUE FALSE 395021.7343 351043.6642 359793.6573 374173.8949 498650.1056 356404.8577 362700.7392 372309.8544 536867.2594 0.735790323 0.653874227 0.67017247 0.696957932 0.92881452 0.663860296 0.675587369 0.693485863 1 19.0342059 -1.108110183 4.58859388 1.000023414 0.710264892 0.558497368 0.079594336 1.84E-05 3.58E-06 0.07451343 0.017561566 0.077963229 1.108110183 -0.289758522 SCS(ph)FSSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SCSFSSESR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SCS(0.769)FS(0.224)S(0.007)ESR;SCS(0.993)FS(0.007)SESR;SCS(0.997)FS(0.002)SESR;SCS(0.994)FS(0.006)SESR;SCS(0.998)FS(0.001)SESR;SCS(0.933)FS(0.067)SESR;S(0.001)CS(0.861)FS(0.138)SESR;S(0.004)CS(0.994)FS(0.002)SESR 195.4 3.28E-05 2434337000 2833710 2134014 2378432 3122150 3108270 2893300 3303840 2241817 3117000 TRUE FALSE 2699766.144 2351472.453 2487485.46 2808305.55 3650351.304 2793104.296 2799778.529 2045511.619 3600368.441 0.749858296 0.653119949 0.690897474 0.780005046 1.013882708 0.775782907 0.777636671 0.568139526 1 21.77971312 3.151736196 4.954921469 0.814212897 0.695919175 0.17402972 0.125983151 0.372624256 15.70884637 0.035173036 0.042774375 1418.195804 -3.151736196 -0.118293722 SCS(ph)PLAFSAFGDLTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.009)CS(0.991)PLAFSAFGDLTIK;S(0.286)CS(0.714)PLAFSAFGDLTIK 181.26 2.45E-09 105432000 370860 299110 361120 385410 287440 383900 432300 426260 359740 TRUE FALSE 353330.1828 329589.6491 377677.7092 346667.8546 337569.445 370605.4467 366344.6953 388934.4147 415526.6419 0.850318962 0.79318536 0.908913343 0.834285506 0.812389414 0.891893345 0.881639487 0.936003557 1 18.66458145 1.16084407 0.818599081 1.000720803 0.836097277 0.718631086 0.032401342 0.292480425 0.442243046 0.029039681 0.010867675 14.48251777 -1.16084407 -0.164623526 SCSSISTALPQVNEDLVSLPHQLPEASEPPQS(ph)PSEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCSSISTALPQVNEDLVSLPHQLPEASEPPQSPSEKR 37 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 SCSSISTALPQVNEDLVSLPHQLPEAS(0.01)EPPQS(0.797)PS(0.192)EKR;SCSSISTALPQVNEDLVSLPHQLPEAS(0.066)EPPQS(0.928)PS(0.006)EKR 288.37 6.58E-78 363740000 102534 87447 100635 104772 82148 98029 113591 112103 80685 TRUE FALSE 97687.42102 96357.94872 105249.2143 94240.11951 96474.58519 94634.23115 96260.60671 102286.667 93197.21772 1.048179585 1.033914435 1.129317128 1.011190267 1.035165937 1.015419059 1.032869962 1.097529192 1 16.50799927 SCSSSCAVHDLIFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCSSSCAVHDLIFWR 15 0 O95197-3;B7Z4M1;O95197-6;O95197-5 O95197-3 RTN3 Reticulon-3;Reticulon 0 101.36 0.0018021 254910000 135460 90789 105600 153950 168250 112760 133540 115450 142020 FALSE TRUE 129057.0743 100040.5023 110441.8645 138474.6535 197592.7467 108855.0929 113166.0204 105340.586 164043.7363 0.786723573 0.609840428 0.673246458 0.844132526 1.204512597 0.663573602 0.689852737 0.642149395 1 17.32372098 5.108009952 17.68923392 0.767041657 2.389256761 0 0.187783867 2524.765293 419771.7681 0.042965839 2502.520502 128235.9969 -5.108009952 1.622215104 SCTKPS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SCTKPSPSK 9 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 SCTKPS(0.994)PS(0.006)K;SCTKPS(0.99)PS(0.01)K;S(0.001)CT(0.005)KPS(0.988)PS(0.006)K;SCTKPS(0.996)PS(0.003)K;SCTKPS(0.997)PS(0.003)K;SCT(0.002)KPS(0.924)PS(0.074)K 108.5 0.0015758 12422310000 14180000 11930200 11953200 14209200 6621350 14748900 14879200 15038300 7171840 TRUE FALSE 13509739.5 13145900.94 12501266.04 12780864.22 7776111.344 14238141.89 12609104.76 13721466.73 8284012.319 1.630820789 1.586900217 1.509083469 1.542835009 0.938689013 1.718749484 1.522101161 1.656379325 1 22.98189827 -1.61935569 2.873263659 0.958113032 1.519805619 0.361202757 0.214321719 21957724.29 22488939.99 6908765.979 0.049970547 0.024023944 1.61935569 0.561692586 SCTKPS(ph)PSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCTKPSPSKK 10 2 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.015)CT(0.004)KPS(0.931)PS(0.05)KK 59.898 0.053015 289580000 1349100 1257000 1294900 1493100 680910 1617600 1516300 1802800 687110 TRUE FALSE 1285330.717 1385089.729 1354272.446 1343010.751 799660.4884 1561582.106 1284960.586 1644937.275 793663.5095 1.619490755 1.745185097 1.706355943 1.692166435 1.007556072 1.96756193 1.619024399 2.072587759 1 19.59816795 SCTKPSPS(ph)KK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCTKPSPSKK 10 2 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.003)CT(0.002)KPS(0.407)PS(0.588)KK 56.122 0.065826 254690000 631780 602260 672400 765210 271000 767420 717030 764660 311280 TRUE FALSE 601917.0115 663630.9787 703230.2051 688289.637 318262.3142 740844.053 607633.9043 697702.3167 359551.7126 1.67407633 1.845717752 1.955852748 1.914299426 0.885164228 2.060465927 1.689976387 1.940478357 1 18.45583976 -1.471593951 2.998313219 0.980592445 1.745954325 0.337968883 0.328018781 122354050.5 141222933.9 19746761.42 0.07420639 0.033760281 1.471593951 0.765361879 SCTPSPDQISHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 105.65 0.00095352 0 53300 44725 52241 55609 55771 51603 55385 53447 67318 FALSE TRUE 50780.61463 49282.52835 54636.30152 50019.07767 65497.44474 49815.97517 46935.00103 48766.89734 77757.33163 0.653065294 0.63379912 0.702651446 0.64327153 0.842331435 0.640659525 0.603608689 0.627167835 1 16.24669109 -1.111918427 4.696724258 1.000020573 0.6640405 0.707832477 0.066918754 1.56E-05 2.95E-06 0.063599204 0.014989466 0.077282573 1.111918427 -0.335980073 SCTPSPDQISHRAS(ph)LEDAPVDDLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SCTPSPDQISHRASLEDAPVDDLTR 25 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPSPDQIS(0.026)HRAS(0.974)LEDAPVDDLTR;SCTPSPDQISHRAS(1)LEDAPVDDLTR;SCTPSPDQISHRAS(1)LEDAPVDDLTR;SCTPSPDQIS(0.128)HRAS(0.872)LEDAPVDDLTR;SCTPSPDQIS(0.001)HRAS(0.999)LEDAPVDDLTR 233.87 1.37E-38 856807000 403696 305660 375478 415138 391486 372361 475467 421922 446848 TRUE FALSE 384614.0901 336807.1015 392694.0377 373407.5395 459761.0345 359466.0452 402925.7766 384976.2729 516142.9057 0.74516977 0.652546219 0.760824247 0.723457662 0.890763061 0.696446742 0.780647709 0.74587148 1 18.97741104 -5 0.199675672 2.159084388 0.701965978 0.627389677 0.060964335 85.94222889 0.849821602 39.7318379 0.136683517 1.00E-05 5 -1.45711841 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 SCVEEPEPEPEAAEGDGDKKGNAEGS(1)S(1)DEEGKLVIDEPAK 148.01 1.12E-13 230420000 180260 141790 133970 174990 44571 204890 157710 216260 46513 TRUE FALSE 171739.467 156238.5622 140112.657 157399.6727 52344.16829 197794.6079 133648.443 197323.1279 53725.99848 3.196580276 2.908062514 2.607911644 2.929674221 0.974280046 3.681543638 2.487593469 3.672767999 1 15.71333277 3.943189158 1.554253745 2.552063864 3.163159885 0.064283562 0.917420886 1.278082903 5.816771694 0.241737482 0.737487205 8773.828836 -3.943189158 0.611096021 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)SDEEGKLVIDEPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 SCVEEPEPEPEAAEGDGDKKGNAEGS(0.5)S(0.5)DEEGKLVIDEPAK;SCVEEPEPEPEAAEGDGDKKGNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 145.86 2.03E-13 175391000 123847 112182 100778 135484 47470 143475 118132 152301 32764 TRUE FALSE 117992.9978 123613.4733 105398.771 121864.8909 55748.75297 138506.4248 100108.7938 138964.717 37844.87378 3.117806613 3.266320137 2.785021073 3.220116194 1.47308598 3.659846392 2.645240524 3.67195615 1 15.20781028 3.377896849 1.912598629 2.695633931 3.178197702 0.067183642 0.852082453 1.012148439 7.543241681 0.235625957 0.36314163 2387.244214 -3.377896849 0.482563771 SCYDLSCHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SCYDLSCHAR 10 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;; 210.27 8.02E-08 2576617000 2357040 1749470 1446530 1769090 2736290 1632100 2751420 2196390 2677310 FALSE TRUE 2245627.39 1927742.982 1512854.831 1591257.712 3213498.11 1575579.968 2331640.346 2004062.448 3092493.561 0.726154266 0.623362003 0.489202257 0.514554899 1.039128472 0.509485286 0.753967729 0.648040944 1 21.56033916 -5 0.25059375 3.064744484 0.633282267 0.310022515 0.159609882 221.0881682 2.189795951 233.5763609 0.210294289 1.00E-05 5 -2.431462216 SCYEDGWLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SCYEDGWLIK 10 0 A0A1W2PQV2;H3BUH9;P23434 A0A1W2PQV2 GCSH "Glycine cleavage system H protein, mitochondrial" 0 129.38 0.0079433 0 87368 50060 70827 82033 89637 69641 103410 94110 88750 FALSE TRUE 83238.28779 55161.17091 74074.48801 73786.88699 105269.6644 67229.31471 87632.90525 85869.22949 102512.8967 0.811978692 0.538090062 0.722587015 0.719781504 1.026891911 0.655813238 0.854847615 0.837643187 1 16.6454459 1.436710206 0.28542798 1.026571965 0.644808944 0.327524531 0.121554658 1.787365034 0.557457501 0.261317742 0.225011366 27.33444157 -1.436710206 -0.381763021 SCYLSSLDLLLEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SCYLSSLDLLLEHR 14 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 240.42 2.13E-17 640170000 1013990 842160 845020 872460 1005150 767690 1043460 944270 868500 FALSE TRUE 966060.7022 927977.0615 883765.0028 784758.6632 1180447.842 741104.7028 884261.0125 861584.7129 1003182.544 0.962995925 0.925033103 0.880961304 0.782269057 1.176702933 0.738753587 0.881455741 0.85885138 1 19.93615272 SDAAKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDAAKLR 7 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 0 58.981 0.096932 117220000 770560 463710 733670 646000 693410 720560 1084400 842310 852630 FALSE TRUE 734137.1559 510962.5762 767309.4952 581062.8527 814340.4845 695606.8265 918954.8636 768552.871 984851.5058 0.745429287 0.518821947 0.779111867 0.590000471 0.826866263 0.706306303 0.933089769 0.780374368 1 19.90954669 1.798795003 0.557234736 0.980291363 0.633318787 0.523157139 0.098412319 0.531987956 0.361088286 0.084807653 0.052763993 62.92091111 -1.798795003 -0.346972577 SDAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDAEEDGGTVSQEEEDRKPK 20 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK 339.67 1.59E-80 611360000 497320 405190 423130 727990 303340 602710 591050 561560 261326 TRUE FALSE 473812.6692 446479.3217 442530.929 654811.0621 356242.4 581838.0016 500874.4671 512386.8294 301851.1014 1.569690046 1.479137626 1.466057029 2.169318114 1.18019248 1.92756627 1.659342851 1.69748206 1 18.20347754 -0.906838359 5.384709465 0.999999177 1.635511849 0.365064584 0.266556062 2.34E-06 4.74E-07 0.228108794 0.053765689 0.123925774 0.906838359 0.635512671 SDAGLES(ph)DTAMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDAGLESDTAMK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 SDAGLES(0.997)DT(0.003)AMK 172.58 0.00014363 0 240360 260840 237400 301840 144690 300920 300460 294330 142520 TRUE FALSE 228998.6591 287419.8926 248285.0248 271498.4697 169923.8902 290499.0649 254619.3087 268556.9049 164621.2737 1.391063585 1.745946232 1.508219559 1.649230768 1.032211004 1.764650816 1.546697477 1.631362088 1 17.32879126 -1.146818408 3.315113023 0.999199891 1.542541438 0.390259386 0.209378915 15569914.66 23971855.05 133637.9262 0.04600976 0.071315116 1.146818408 0.543341547 SDALETLGFLNHYQMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDALETLGFLNHYQMK 16 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 282.35 1.43E-35 1388830000 2297350 1938550 1799570 2214590 1729400 2022370 2393110 2214210 1551850 FALSE TRUE 2188758.818 2136090.449 1882082.065 1991975.206 2031006.812 1952334.82 2027997.117 2020322.034 1792502.972 1.221062867 1.191680283 1.049974306 1.111281396 1.133056315 1.089166852 1.131377269 1.1270955 1 20.77354408 8 0.33020988 1.084143328 2.687785185 0.472502631 0.04590984 46.86053494 0.668230023 0.039270372 45.8658746 100000000 -8 1.603641857 SDAPDSTGDQPGLHQDNSSNGKSEWLDPS(ph)QKSPLHVGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDAPDSTGDQPGLHQDNSSNGKSEWLDPSQKSPLHVGETR 40 2 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SDAPDSTGDQPGLHQDNSSNGKS(0.001)EWLDPS(0.536)QKS(0.46)PLHVGET(0.002)R;SDAPDSTGDQPGLHQDNSSNGKSEWLDPS(0.576)QKS(0.424)PLHVGETR 191.5 7.48E-25 206330000 201893 140845 186749 196807 123090 199994 249159 220549 104500 TRUE FALSE 192349.918 155197.2656 195311.6264 177023.5865 144556.857 193068.1576 211145.2184 201236.5604 120705.3263 1.593549547 1.285753251 1.61808623 1.46657643 1.197601311 1.599499903 1.749261817 1.667172167 1 16.88112981 SDCKEFSSEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDCKEFSSEAR 11 1 Q12931-2;Q12931;I3L0K7;I3L239;I3L2D5 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 96.82 0.0032175 0 352320 210830 368450 284040 258080 369920 419950 381220 299140 FALSE TRUE 335666.5318 232313.8167 385343.7969 255487.7596 303089.0703 357109.5776 355878.9146 347838.3558 345529.1034 0.971456611 0.672342255 1.115228191 0.739410247 0.877173782 1.033515192 1.029953515 1.006683236 1 18.39844771 2.267926466 6.343971276 1.021817873 0.860191406 0.255209504 0.119436873 0.206485662 25.60926326 0.039162467 0.031852892 185.3217815 -2.267926466 -0.161626467 SDDDDRSSDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDDDDRSSDRK 11 2 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 52.693 0.080276 44089000 64574 49713 52282 61833 44011 61218 62428 71218 56432 FALSE TRUE 61521.71499 54778.81122 54679.18141 55617.42936 51686.50447 59098.00531 52903.46203 64981.77437 65183.18635 0.943827978 0.840382533 0.838854074 0.853248092 0.792942281 0.906644928 0.811612089 0.996910062 1 15.99221226 1.226464516 24.99436774 0.998455196 0.857305297 0.654516615 0.043203792 152.5443219 315194.98 0.038877406 0.010018122 16.84474793 -1.226464516 -0.141149899 SDDKHMHDHNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDDKHMHDHNHR 12 1 Q9ULF5 Q9ULF5 SLC39A10 Zinc transporter ZIP10 0 74.46 0.023512 9854400 10176 12305 18227 18907 19152 17983 22384 13486 0 FALSE TRUE 9695.000647 13558.89349 19062.72598 17006.43244 22492.10274 17360.2442 18968.90969 12305.09435 0 0 SDDNRESLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDDNRESLEK 10 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 91.549 0.0091868 573210000 139610 115840 141520 147530 122320 149240 189650 193070 143030 FALSE TRUE 133010.912 127644.2277 148008.832 132700.0041 143652.5693 144071.7814 160715.4093 176163.7673 165210.3619 0.8051003 0.772616355 0.895881047 0.803218409 0.869513072 0.872050516 0.972792551 1.066299748 1 17.33394465 1.784819063 1.365429031 1.03820548 0.816267421 0.830846931 0.038552506 0.150154651 0.528764684 0.029525016 0.011833526 60.9283003 -1.784819063 -0.221938058 SDDNRESLEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDDNRESLEKR 11 2 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 ; 94.122 0.0049156 279165000 553890 221067 567460 379994 533540 536600 892030 642910 823360 FALSE TRUE 527708.7174 243593.9786 593478.6023 341796.2812 626589.2071 518017.4075 755934.4402 586613.3921 951042.4637 0.55487398 0.256133651 0.624029552 0.359391188 0.658844616 0.544683784 0.794848252 0.616810936 1 19.85915023 1.363063443 0.408474066 1.009858712 0.394299444 0.619754449 0.127291627 0.59808943 0.293966437 0.146186727 0.098833748 23.07084191 -1.363063443 -0.615559269 SDDNSYDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDDNSYDEK 9 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 106.88 0.0073163 0 200480 202430 177490 226780 139880 204930 183430 198980 136280 FALSE TRUE 191003.7077 223057.8471 185628.0921 203983.6435 164275.0277 197833.2227 155444.3846 181556.2563 157413.6064 1.213387534 1.417017577 1.179237909 1.295845056 1.04358849 1.256773333 0.987490142 1.153370795 1 17.26420072 2.579531445 0.739125583 1.044883526 1.31351726 0.447391213 0.100588775 0.525058019 0.59475258 0.067008254 0.055821255 379.7794359 -2.579531445 0.268633734 SDEAVKPFGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 156.71 2.82E-05 13890300000 33678810 32497720 31065760 37674850 21279620 35922610 38073830 40097890 24100270 FALSE TRUE 32086879.4 35809274.61 32490155.82 33887702.5 24990778.99 34678601.01 32264967.96 36586706.18 27837616.78 1.152644626 1.286362798 1.16713137 1.217334902 0.897734141 1.245746045 1.159042033 1.314290173 1 24.73053237 -1.351062887 3.632319221 0.999202544 1.181490569 0.198717239 0.113581798 0.000682553 0.000121943 0.102336217 0.024016445 0.044559172 1.351062887 0.182288025 SDEGQLS(ph)PATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(1)PATR;SDEGQLS(0.999)PAT(0.001)R;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR 228.66 3.26E-12 2225830000 2646120 2314830 2203650 2684120 2166280 2279130 2612310 2409520 2275430 TRUE FALSE 2521043.152 2550713.809 2304689.532 2414307.158 2544078.546 2200203.157 2213754.131 2198529.655 2628292.063 0.959194447 0.970483397 0.876877256 0.918584046 0.967958844 0.837122779 0.842278589 0.836486053 1 21.32569417 2.237818511 24.99965376 0.862280005 0.941117928 0.199018922 0.054984081 22.11710268 745026.2857 0.018374683 0.014383379 172.909363 -2.237818511 0.078837923 SDEHVDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDEHVDVR 8 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 0 101.64 0.008668 0 96177 81809 82004 100240 86561 86853 95600 95234 88642 FALSE TRUE 91630.90381 90145.43011 85763.96451 90163.68476 101657.211 83845.25883 81014.46419 86894.80609 102388.1486 0.894936621 0.880428363 0.837635661 0.880606652 0.992861111 0.818896131 0.791248453 0.848680314 1 16.64368921 SDES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDESGEEKNGDEDCQR 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 S(0.013)DES(0.987)GEEKNGDEDCQR;SDES(1)GEEKNGDEDCQR 184.35 1.11E-09 330140000 323220 271420 285666 359156 187672 352597 336498 353733 193463 TRUE FALSE 307942.0312 299078.0066 298764.0687 323052.9565 220401.9374 340386.4775 285159.0499 322758.2633 223464.254 1.378037094 1.338370685 1.336965816 1.445658314 0.986296168 1.523225623 1.276083511 1.444339565 1 17.76968455 -1.38349282 3.121904471 0.99598255 1.338946781 0.356914135 0.143875038 16773478.17 21152775.28 606752.5112 0.030048621 0.041353015 1.38349282 0.34296423 SDES(ph)PKPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 SDES(1)PKPGK;SDES(1)PKPGK;S(0.001)DES(0.999)PKPGK;SDES(1)PKPGK 108.72 0.0015541 1421680000 9121880 8381360 7944830 10189170 3758790 9907050 9375680 10094410 4118469 TRUE FALSE 8690706.81 9235430.113 8309108.314 9164935.273 4414321.786 9563966.374 7945247.82 9210489.947 4757140.138 1.82687635 1.941382815 1.746660404 1.926564071 0.927936041 2.010444531 1.670173169 1.936140134 1 22.18166309 -1.892921826 2.519744804 0.593728232 1.756352612 0.366638715 0.308916178 8100645.948 4868638.259 19580244.21 0.071203741 0.012796116 1.892921826 1.16262438 SDESGEEKNGDEDCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDESGEEKNGDEDCQR 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 0 101.39 0.0015801 122280000 88208 86909 96512 105260 50235 81688 94475 89164 59258 FALSE TRUE 84038.58265 95765.12591 100937.1707 94679.06482 58995.9681 78859.12408 80061.1036 81356.32747 68447.42799 1.227782915 1.399104813 1.474667108 1.383237729 0.861916508 1.152112306 1.169672929 1.18859583 1 16.06270871 2.778605028 24.98205455 1.098291255 1.365662579 0.628314204 0.112546902 368.3128392 229774.5126 0.034232829 0.036308984 600.6272451 -2.778605028 0.267371324 SDFFELLSNHHLDSQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDFFELLSNHHLDSQSR 17 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 109.38 0.00035258 90578000 63940 58158 52616 64706 71015 58708 75973 70820 22115 FALSE TRUE 60917.68292 64084.36632 55028.49564 58201.62995 83399.99352 56674.92724 64381.92351 64618.62536 25544.48125 2.38476884 2.508736258 2.154222476 2.27844243 3.264892823 2.21867599 2.520384848 2.52965111 1 14.64072402 -0.670894211 8.544515215 1.000033326 2.477822351 0.697982774 0.306452536 0 0 0.272137748 0.064143482 0.213356456 0.670894211 1.477789025 SDGS(ph)LEDGDDVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 1 SDGS(1)LEDGDDVHR 177.58 9.87E-06 135120000 128960 97165 124640 162640 104020 119050 144350 131880 107490 TRUE FALSE 122864.3164 107066.224 130354.8673 146291.1182 122161.0551 114927.2686 122326.7563 120331.8881 124159.0002 0.989572372 0.862331557 1.049902682 1.178256252 0.983908173 0.925645893 0.985242762 0.969175717 1 16.92182932 3.728095967 24.95813708 1.011159023 0.925951962 0.196928022 0.07312968 1060.876736 2530185.043 0.020320976 0.031847259 5346.824962 -3.728095967 -0.085207061 SDGSLEDGDDVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 0 117.92 0.00046874 81623000 150700 142030 152440 172340 159520 144470 193640 163090 170360 FALSE TRUE 143576.7097 156503.0185 159429.5248 155016.0558 187340.2375 139466.9677 164096.6616 148808.975 196778.5587 0.729635945 0.795325565 0.810197645 0.787769037 0.952035825 0.708750834 0.833915355 0.756225556 1 17.58621351 -2.776150271 2.03170999 8.691870955 0.796242575 0.480846724 0.066375014 1231171.594 55608.33597 43967506.74 0.015324222 0.001674363 2.776150271 -7.89562838 SDGTETSTNLHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDGTETSTNLHQK 13 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 115.57 0.00065339 107890000 54391 43334 48195 55562 54843 43305 51550 61423 57095 FALSE TRUE 51820.04522 47749.78387 50404.78842 49976.8022 64407.60184 41805.33699 43685.10072 56044.4765 65949.001 0.785759366 0.724041049 0.764299499 0.757809845 0.976627407 0.633904022 0.662407316 0.849815397 1 16.00906319 0.978278427 8.827408355 0.999997379 0.753267331 0.422879615 0.090949856 0.331582444 131.3983835 0.086184133 0.021569276 9.512144227 -0.978278427 -0.246730049 SDHPGISITDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDHPGISITDLSK 13 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 131.26 7.24E-06 141850000 867480 762710 742720 916820 734330 834430 1025550 983840 705220 FALSE TRUE 826475.9396 840431.0161 776774.4467 824659.5118 862396.9195 805533.4799 869083.512 897689.7539 814581.9158 1.014601384 1.031732966 0.953586658 1.012371495 1.058698828 0.988891926 1.066907447 1.102025145 1 19.63570026 1.672574791 7.350976537 1.063291475 1.012743933 0.252118592 0.036650421 0.152887678 15.56988361 0.016956455 0.008753644 47.05164279 -1.672574791 -0.050547542 SDIDEIVLVGGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDIDEIVLVGGSTR 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 137.16 5.32E-05 54653000 119315 101939 104838 121256 102124 105532 118344 113073 118982 FALSE TRUE 113675.2164 112326.7 109644.926 109067.1165 119934.3933 101877.4004 100288.4493 103171.7287 137433.1209 0.827131158 0.817318993 0.797805691 0.793601395 0.872674596 0.741287105 0.729725474 0.750704983 1 17.0683702 2.222297009 24.99971065 0.775722152 0.819237373 0 0.080461128 681.5562864 1047651.441 0.026605994 0.01970618 166.8387814 -2.222297009 0.043515221 SDIYVCMISFAHNVAAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDIYVCMISFAHNVAAQGK 19 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 213.49 3.27E-17 57690000 129090 139580 146030 154290 104010 127730 160500 147350 90987 FALSE TRUE 122988.1715 153803.3607 152725.6199 138780.4761 122149.3111 123306.6781 136012.7772 134447.2528 105096.7993 1.17023708 1.463444765 1.453190021 1.320501452 1.162255292 1.173267682 1.294166694 1.27927067 1 16.68135921 2.881939785 5.149714757 1.207513491 1.359778972 0.3512295 0.112823277 0.291220673 11.14866968 0.03412201 0.036451534 761.9733544 -2.881939785 0.152265481 SDKGS(ph)PGEDGFVPSALGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDKGSPGEDGFVPSALGTR 19 1 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 1 S(0.12)DKGS(0.88)PGEDGFVPSALGTR;S(0.02)DKGS(0.98)PGEDGFVPSALGTR 99.711 0.00045581 364220000 231981 211007 199423 260770 159057 218774 263870 237102 164016 TRUE FALSE 221015.7179 232508.8532 208566.7418 234556.9042 186796.4904 211197.8015 223611.7852 216340.0919 189450.7636 1.166612969 1.227278522 1.100902091 1.238088988 0.985989641 1.11478992 1.180316093 1.141933069 1 17.53146343 -5 0.108307845 0.541694723 1.237598678 0.305788183 0.070181934 202.9115453 1.46713268 20.9862526 0.877828766 1.00E-05 5 0.695903954 SDKLHELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDKLHELEK 9 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;A0A2R8YGU1;A0A2R8Y7D9;A0A2R8Y6B2;A0A087WXD9;A0A2R8YG52 Q3V6T2 CCDC88A Girdin 0 ; 63.816 0.067112 332300000 847850 585620 872170 743050 2305330 531230 1204130 631550 2872100 FALSE TRUE 807773.8108 645295.3438 912159.8572 668357.2023 2707378.822 512833.3719 1020417.853 576248.1339 3317490.599 0.243489405 0.194513089 0.274954768 0.201464686 0.816092387 0.154584725 0.307587263 0.173700005 1 21.66166095 -2.073929243 2.548309881 2.09469506 0.290639836 0.573067517 0.190972734 14640046.22 5094439.803 93102633.07 0.044505848 0.008434722 2.073929243 -1.804055224 SDKNQQGFS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDKNQQGFSPK 11 1 D6RCT7;C9JKA9;Q9NS87-4;Q9NS87-2;Q9NS87 D6RCT7 KIF15 Kinesin-like protein;Kinesin-like protein KIF15 1 SDKNQQGFS(1)PK 73.156 0.026846 138700000 145050 149340 158020 176280 73131 172050 182580 192730 89731 TRUE FALSE 138193.774 164557.9158 165265.3733 158559.9995 85885.02325 166091.8654 154724.0677 175853.5395 103646.0252 1.333324396 1.587691525 1.594517233 1.529822289 0.828637886 1.602491413 1.492812362 1.696674225 1 16.66130526 SDKS(ph)PDLAPTPAPQSTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 S(0.008)DKS(0.992)PDLAPTPAPQSTPR;S(0.003)DKS(0.997)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;S(0.004)DKS(0.996)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(0.999)PDLAPT(0.001)PAPQSTPR;S(0.002)DKS(0.644)PDLAPT(0.35)PAPQS(0.002)T(0.002)PR;S(0.004)DKS(0.996)PDLAPTPAPQSTPR;SDKS(0.999)PDLAPTPAPQSTPR;S(0.001)DKS(0.999)PDLAPTPAPQSTPR 247.64 1.27E-24 8558637000 7910441 7182948 7339402 8587146 4554465 8628891 9113444 8918858 5064283 TRUE FALSE 7536530.131 7914898.568 7675920.841 7723949.77 5348762.254 8330070.341 7723020.738 8137875.512 5849626.143 1.288378086 1.353060584 1.31220708 1.320417678 0.914376769 1.424034654 1.320258859 1.391178737 1 22.47991299 2.917609863 24.99997068 1.241052573 1.320649661 0.085125604 0.159610907 302.7485021 91860.76546 0.046492538 0.049312797 827.1987376 -2.917609863 0.079597088 SDKTEEIAEEEETVFPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDKTEEIAEEEETVFPK 17 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 247.4 8.73E-21 309203000 1208730 1348010 1129330 1449630 669188 1418150 1333570 1434800 656940 FALSE TRUE 1151595.728 1485373.752 1181110.898 1303910.438 785894.1753 1369039.11 1130109.404 1309161.306 758814.9 1.517624032 1.957491546 1.556520434 1.718351127 1.035686273 1.804180585 1.489308399 1.725270953 1 19.53338848 -2.758681016 0.251624065 1.29E-15 1.686391576 0.353170482 0.248490655 54.18086382 1.466943526 30.11266131 0.343695096 0.001743087 2.758681016 1.686391576 SDLDYIRS(ph)PLPFQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 149.52 2.02E-06 128970000 305910 300540 280780 365220 280200 274070 287700 301300 255320 TRUE FALSE 291450.2406 331165.3677 293654.0407 328507.3917 329066.7913 264578.8872 243806.081 274916.5747 294913.7216 0.988255951 1.122922887 0.995728646 1.113910163 1.115806988 0.897139969 0.826703077 0.93219323 1 18.16993342 2.227138938 24.6029588 0.891673964 1.066581508 0.578386773 0.063787811 106.5794368 229576.3114 0.022253847 0.016584639 168.7092667 -2.227138938 0.174907545 SDLHIKDDPDGIPSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDLHIKDDPDGIPSKR 16 2 F6WR09;Q9ULJ6-2;Q9ULJ6 F6WR09 ZMIZ1 Zinc finger MIZ domain-containing protein 1 0 ; 132.59 2.30E-05 172213000 591780 469080 498790 622800 422230 583020 721770 712460 414580 FALSE TRUE 563807.7322 516879.7853 521660.0149 560194.9608 495866.7783 562829.8712 611650.7303 650073.2254 478870.949 1.177368837 1.079371773 1.089354065 1.169824484 1.03549146 1.175326823 1.277276752 1.357512346 1 18.86927739 1.999739614 24.97962328 1.238379127 1.113211728 0.168094667 0.098661186 11.39088203 1092822.268 0.033145331 0.024208365 99.94006189 -1.999739614 -0.125167399 SDLLELDCQLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDLLELDCQLTR 12 0 Q7L5L3-1;Q7L5L3 Q7L5L3-1 GDPD3 Glycerophosphodiester phosphodiesterase domain-containing protein 3 0 105.46 0.0019931 0 63727 32021 50355 67306 66876 54205 70396 55484 76350 FALSE TRUE 60714.751 35283.9763 52663.82656 60540.27301 78539.15323 52327.86726 59655.79729 50625.52682 88189.96806 0.688454167 0.400090589 0.597163461 0.686475733 0.890567884 0.593353965 0.676446523 0.574050858 1 16.42832693 3.300886426 3.720137489 0.716314204 0.539053067 0.240101069 0.14551601 0.312327544 8.679176614 0.038883497 0.052559923 1999.338946 -3.300886426 -0.177261137 SDLPGSDKDTEDGSAWKQDPFQESGLHLS(ph)PTAAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDLPGSDKDTEDGSAWKQDPFQESGLHLSPTAAEAK 36 2 H3BN50;Q15599-3;H3BQS0;Q15599 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 SDLPGSDKDTEDGSAWKQDPFQESGLHLS(0.996)PT(0.004)AAEAK 169.32 3.99E-18 87111000 92407 82094 106240 103460 55737 120980 135720 141840 65414 TRUE FALSE 88039.10424 90459.47193 111111.2091 93060.00424 65457.51515 116790.4323 115013.4213 129419.7377 75558.06903 1.165184677 1.197217889 1.470540612 1.231635554 0.866320646 1.545704301 1.522185821 1.712851312 1 16.20529821 2.169542193 24.99999993 1.494325923 1.200753761 0.222881671 0.23151456 62.16349684 22515.82382 0.079226063 0.058512338 147.7550021 -2.169542193 -0.293572162 SDLYSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDLYSSGR 8 0 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 138.26 0.0016584 280030000 209020 171310 214360 205480 232010 195850 261740 208080 288490 FALSE TRUE 199140.0388 188766.6838 224188.618 184824.76 272472.4705 189067.6654 221806.7558 189859.4121 333227.5558 0.597609758 0.566479814 0.672779349 0.554650289 0.817676887 0.567383045 0.665631494 0.569759039 1 18.34614818 -2.362405177 2.284712882 3.52551271 0.624745214 0.686717634 0.079274481 4858615.986 444468.8285 63682070.79 0.017455666 0.00434105 2.362405177 -2.900767495 SDNKDDDIDIDAI ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDNKDDDIDIDAI 13 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 149.96 0.00035893 289980000 1829580 1690570 1665650 2006840 1109880 1928760 2060310 2101090 1190520 FALSE TRUE 1743099.379 1862841.005 1742021.7 1805108.63 1303442.721 1861966.558 1745971.869 1917107.421 1375139.761 1.267579797 1.354655765 1.26679611 1.312672851 0.947861997 1.354019868 1.269668668 1.394118238 1 20.39114682 -2.120711806 2.456553981 0.459163228 1.273160533 0.325238352 0.122599022 3620269.154 1616281.854 10872569.61 0.027884714 0.007573353 2.120711806 0.813997305 SDPES(ph)PIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDPESPIKK 9 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 SDPES(1)PIKK;SDPES(1)PIKK 110.08 0.0014366 351540000 1785860 1607680 1633850 2010100 926720 1924050 1973310 2023300 984220 TRUE FALSE 1701445.937 1771504.42 1708763.639 1808040.929 1088339.675 1857419.666 1672245.317 1846129.126 1136847.811 1.496634748 1.558259956 1.503071583 1.590398391 0.95733102 1.633833173 1.470949147 1.623901729 1 20.1166077 -1.902594593 2.795611414 0.742558626 1.481947562 0.377378054 0.193451346 6261973.129 7100444.694 10693995.28 0.042731269 0.012514267 1.902594593 0.739388936 SDPFLEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SDPFLEFFR 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56 Q99829 CPNE1 Copine-1 0 ;;;; 148.99 0.00020636 281017000 354042 255654 218821 214936 450525 186169 390593 264345 455605 FALSE TRUE 337307.1363 281705.4333 228854.1593 193330.2249 529096.4174 179721.9208 331000.8641 241197.5504 526257.8965 0.640954062 0.535299204 0.434870737 0.367367837 1.005393783 0.341509214 0.628970827 0.45832576 1 19.00541045 -1.408602533 3.324064399 1.004791466 0.556061201 0.357644056 0.188776919 121176234.5 179581194.3 5628001.172 0.040321093 0.039029903 1.408602533 -0.448730264 SDPMVQCIIEESGEHIIAGAGELHLEICLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SDPMVQCIIEESGEHIIAGAGELHLEICLK 30 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 353.12 1.81E-120 2865024000 2942630.2 2697768.7 2703821.7 3170885.4 2337332.5 2973408.1 3360197.3 3238895.4 838394.5 FALSE TRUE 2803537.902 2972674.398 2827794.599 2852141.975 2744962.548 2870438.232 2847537.488 2955280.548 968408.4371 2.894995329 3.06964942 2.920043332 2.945184971 2.834509121 2.964078091 2.940430276 3.051688146 1 19.88525612 -0.944352486 5.258646108 1.000000256 2.954377923 0.987699684 0.068478402 4.19E-06 8.41E-07 0.062968736 0.014841832 0.113670433 0.944352486 1.954377666 SDPNRETDDTLVLSFVGQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDPNRETDDTLVLSFVGQTR 20 1 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ; 139.11 5.43E-07 196676000 71266 42344 62300 67101 72733 61547 79338 67906 80253 FALSE TRUE 67897.39742 46658.90174 65156.51662 60355.88 85417.61217 59415.61196 67233.53096 61959.79065 92698.22536 0.732456281 0.503341909 0.7028885 0.651100706 0.92145898 0.640957383 0.725294694 0.668403202 1 16.5002541 -4.999999995 0.180528919 2.286429143 0.618594471 0.458795112 0.103916596 115.1389908 1.109473028 53.18034386 0.305607014 1.00E-05 4.999999995 -1.667834672 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK 41 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 347.56 2.86E-154 140140000 149320 107930 125330 138460 116050 131520 171500 142210 10082 FALSE TRUE 142261.9395 118928.1897 131076.5045 124541.7377 136289.0833 126965.4294 145334.5252 129757.3385 11645.46507 12.21608057 10.21240363 11.2555835 10.69444088 11.70318939 10.9025641 12.47992453 11.14230627 1 13.50748064 0.9256911 22.79929385 1.000000018 11.34738551 0.958698186 0.673686903 5096.900922 1563821.602 0.635447172 0.158861791 8.427351337 -0.9256911 10.34738549 SDPVVSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDPVVSYR 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 166.68 0.00073762 1376620000 2447960 2037890 1911740 2286740 2284030 2050970 2662980 2253810 2445730 FALSE TRUE 2332249.782 2245553.308 1999395.17 2056872.551 2682364.109 1979944.395 2256693.492 2056454.448 2825001.317 0.825574759 0.794885756 0.707750173 0.728096139 0.949508976 0.700864946 0.798829182 0.727948138 1 21.42982011 -1.065615314 4.902477364 1.00000571 0.782497407 0.47216379 0.07329912 4.16E-06 7.93E-07 0.064506128 0.015203841 0.085977475 1.065615314 -0.217508303 SDPYLEFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDPYLEFHK 9 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ;;; 150.27 8.56E-05 2302000000 7857640 5384050 4208780 7299480 7367080 4957650 7022230 5816930 5032640 FALSE TRUE 7486224.93 5932690.816 4401756.726 6565722.402 8651896.419 4785965.337 5950859.841 5307568.772 5813076.108 1.287825033 1.020576835 0.757216428 1.129474702 1.48835079 0.823310283 1.023702379 0.913039615 1 22.47087037 4.504224548 2.82685894 1.021759906 1.284653157 0.153074964 0.197605438 0.544361082 7.962864006 0.048281354 0.256175104 31931.88435 -4.504224548 0.262893251 SDQDS(ph)DSDQPSRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDQDSDSDQPSRK 13 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 S(0.001)DQDS(0.955)DS(0.044)DQPSRK;S(0.018)DQDS(0.966)DS(0.014)DQPS(0.001)RK 75.91 0.01844 114063000 140127 150245 147087 165518 123400 158032 167255 155898 145434 TRUE FALSE 133503.4744 165555.1363 153831.0844 148879.8162 144920.9209 152559.3122 141737.1779 142246.7447 167987.1619 0.794724269 0.985522551 0.915731194 0.886257107 0.862690454 0.908160543 0.843738154 0.846771521 1 17.35799146 3.050773673 8.668559143 0.880236342 0.902315473 0 0.063737638 1.377303089 215.6211916 0.017473673 0.020883662 1124.019052 -3.050773673 0.02207913 SDQDYILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDQDYILK 8 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 149.94 0.0011567 437078000 1390550 1235700 1128140 1465580 943680 1265400 1399000 1370690 1036800 FALSE TRUE 1324821.457 1361619.235 1179866.335 1318257.114 1108257.493 1221578.881 1185556.856 1250665.117 1197581.649 1.106247293 1.136974031 0.985207427 1.100765961 0.925412889 1.020038076 0.989959104 1.044325553 1 20.19169259 3.741093821 24.98848207 1.008779258 1.121610668 0.517537192 0.045044149 144.7077204 1427444.105 0.010565776 0.017992712 5509.267009 -3.741093821 0.112831409 SDQWKPLNLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 164.81 5.13E-05 99471000 414150 372830 336810 438930 228730 403540 448890 453680 260180 FALSE TRUE 394573.9503 410821.8009 352253.0717 394807.9225 268620.4396 389565.3086 380403.5861 413953.3741 300527.3856 1.312938418 1.367002878 1.172116381 1.313716957 0.893830155 1.296272244 1.265786761 1.377423137 1 18.19713694 3.739496462 24.99571908 1.20284074 1.339970653 0.149776822 0.147007777 150.6790102 4024472.362 0.036029555 0.060419332 5489.040836 -3.739496462 0.137129913 SDS(ph)ASSEPVGIYQGFEK ddPTM_SK-BR-3_Trastuzumab_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(0.022)DS(0.978)ASSEPVGIYQGFEK 293.2 5.02E-46 97521000 216080 215710 197550 252210 165780 208220 234230 210260 171930 TRUE FALSE 205866.3266 237691.0942 206607.8629 226857.3716 194691.9795 201009.2892 198493.9116 191848.5197 198592.0263 1.036629368 1.196881359 1.040363336 1.142328702 0.980361514 1.012172004 0.999505948 0.966043417 1 17.59944817 2.732354069 24.99042968 0.993959525 1.108493025 0.581674932 0.047289361 331.9505014 1336582.642 0.014073783 0.013572059 539.9506514 -2.732354069 0.1145335 SDS(ph)DAEAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDSDAEAQGK 10 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.001)DS(0.999)DAEAQGK;S(0.004)DS(0.996)DAEAQGK;S(0.017)DS(0.983)DAEAQGK 158.25 8.44E-06 205108000 482260 371394 418720 572400 294044 494110 508650 543190 341639 TRUE FALSE 459464.5255 409239.4708 437918.7262 514861.2645 345325.1805 476998.8468 431046.1005 495625.404 394618.6313 1.164325476 1.037050556 1.109726433 1.30470592 0.87508585 1.208759063 1.092310566 1.255960476 1 18.59009955 SDS(ph)DSSTLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSDSSTLAK 10 0 Q6AWC2-7;Q6AWC2-3;Q6AWC2-2;Q6AWC2-4;Q6AWC2;Q6AWC2-6 Q6AWC2-7 WWC2 Protein WWC2 1 SDS(0.999)DS(0.001)STLAK 185.18 1.55E-06 155850000 302530 331590 262260 345460 175640 306130 301270 332810 188800 TRUE FALSE 288230.0065 365379.398 274284.8804 310733.7045 206271.5604 295528.6413 255305.7283 303667.3921 218078.1397 1.32168225 1.675451737 1.257736703 1.424873235 0.945860785 1.35515023 1.170707567 1.392470572 1 17.73448564 3.289714359 1.952705559 1.203767962 1.487925921 0.287493973 0.177914414 0.350458448 2.744298044 0.050242431 0.072193694 1948.562584 -3.289714359 0.284157959 SDS(ph)DSSTLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDSDSSTLSK 10 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 SDS(0.995)DS(0.002)S(0.002)T(0.001)LSK;SDS(1)DSSTLSK;SDS(0.473)DS(0.11)S(0.11)T(0.307)LSK 195.85 3.61E-07 435160000 1289800 1192190 1117740 1437090 790590 1299000 1320750 1332230 867210 TRUE FALSE 1228833.71 1313675.516 1168989.485 1292630.983 928468.6457 1254015.304 1119245.33 1215572.879 1001692.498 1.226757426 1.31145588 1.167014316 1.290446904 0.92689987 1.251896472 1.117354211 1.213519 1 19.93400826 7.999999999 0.023440915 1.69E-05 2.760873034 0.277050062 0.104923476 2512.846764 4.534042793 187.9226431 376.0862319 99999999.86 -7.999999999 2.760856177 SDS(ph)DYDLSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSDYDLSPK 10 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SDS(1)DYDLSPK;S(0.003)DS(0.997)DYDLSPK 187.85 1.24E-06 1407210000 2566800 2002680 2029240 2674200 1214760 2572500 2531200 2530600 1325970 TRUE FALSE 2445472.451 2206755.369 2122282.661 2405384.335 1426613.759 2483413.68 2145018.951 2309007.248 1531594.655 1.59668385 1.440822061 1.385668626 1.570509747 0.931456475 1.62145622 1.400513474 1.507583772 1 20.5466031 -2.187649877 1.920439172 4.71E-05 1.436139503 0.326376013 0.194884574 2065573.813 387519.7026 8966430.985 0.045573238 0.006491576 2.187649877 1.436092366 SDS(ph)FENPVLQQHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 SDS(1)FENPVLQQHFR;S(0.005)DS(0.995)FENPVLQQHFR;S(0.002)DS(0.998)FENPVLQQHFR;S(0.212)DS(0.788)FENPVLQQHFR;S(0.001)DS(0.999)FENPVLQQHFR;S(0.006)DS(0.994)FENPVLQQHFR;S(0.006)DS(0.994)FENPVLQQHFR 259.14 1.34E-24 987625000 1163843 919202 942414 1341071 929874 1336995 1438075 1087851 1143598 TRUE FALSE 1108830.448 1012869.729 985624.6141 1206263.995 1092043.731 1290694.528 1218670.247 992592.9994 1320941.337 0.839424444 0.766778736 0.746153206 0.913185136 0.826716297 0.97710208 0.922577114 0.751428524 1 20.33313497 3.229649958 24.97362789 0.898719998 0.788303874 0.348063751 0.073720522 200.2009748 561096.6346 0.019886368 0.024100219 1696.875418 -3.229649958 -0.110416124 SDS(ph)IKFQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSIKFQHR 9 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.011)DS(0.989)IKFQHR;S(0.016)DS(0.984)IKFQHR 135.02 0.00014087 289190000 676060 552340 582140 685140 415690 613790 689710 639580 396340 TRUE FALSE 644103.9836 608624.074 608831.6948 616268.4255 488186.2044 592534.2984 584482.0721 583574.9846 457802.383 1.406947643 1.329447151 1.329900668 1.34614508 1.066368858 1.294301472 1.276712603 1.274731208 1 18.80436545 -5 0.085521584 0.073456909 1.556174034 0.607147734 0.079683733 155.3721765 0.931354238 26.94315876 2.149881287 1.00E-05 5 1.482717125 SDS(ph)KSSPQAGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSKSSPQAGRR 12 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.482)KS(0.482)S(0.036)PQAGRR 57.159 0.090717 133810000 153880 93315 152910 125960 101670 146800 180070 161480 145000 TRUE FALSE 146606.3974 102823.9046 159921.0747 113298.2615 119401.2158 141716.2792 152597.0143 147339.9551 167485.8594 0.875335971 0.613925886 0.954833293 0.676464639 0.712903264 0.846138771 0.911103867 0.87971579 1 17.35367977 1.938287302 2.797599911 0.92188297 0.760538681 0.352299837 0.100311932 0.296691846 4.235412349 0.048763979 0.026377351 86.75355936 -1.938287302 -0.161344289 SDS(ph)LLSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 SDS(0.987)LLS(0.013)FR;SDS(0.986)LLS(0.014)FR;SDS(0.997)LLS(0.003)FR;SDS(0.98)LLS(0.02)FR;SDS(1)LLSFR;S(0.002)DS(0.998)LLSFR 209.73 4.70E-05 844346000 1730136 1696178 1421631 1773902 1171997 1584289 1582935 1687952 1248063 TRUE FALSE 1648355.9 1869020.467 1486814.188 1595586.001 1376392.906 1529424.675 1341429.193 1540145.974 1441606.236 1.143416183 1.296484727 1.031359431 1.106811251 0.954763424 1.060917078 0.930510121 1.068354129 1 20.45924573 3.674928392 7.246388436 1.016188932 1.219618857 0.626920698 0.063443845 0.138148388 13.78458514 0.015985788 0.024916481 4730.732505 -3.674928392 0.203429925 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.153)DS(0.847)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.264)DS(0.736)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.149)DS(0.851)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.129)DS(0.871)PEIPFQAAAGPSDGLDASSPGNSFVGLR 175.83 7.43E-14 540580000 857860 876080 783510 934770 654080 852400 868180 876040 638370 TRUE FALSE 817310.6579 965353.548 819434.7085 840805.1437 768151.3449 822881.1743 735723.1958 799329.2934 737365.1593 1.108420499 1.30919333 1.111301094 1.140283255 1.041751614 1.115975123 0.997773202 1.084034529 1 19.49201972 3.059258066 1.398959311 1.045032972 1.204276877 0.475548822 0.063834715 0.300750288 1.224801548 0.022492042 0.02828495 1146.19383 -3.059258066 0.159243905 SDS(ph)PENKYSDSTGHSK ddPTM_SK-BR-3_Trastuzumab_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 SDS(1)PENKYSDSTGHSK 213.5 1.06E-12 332880000 539630 367770 471150 501320 322360 496090 628410 590930 336050 TRUE FALSE 514122.7593 405246.1811 492752.6935 450926.3612 378579.4819 478910.2789 532534.513 539185.0365 388162.9177 1.324502511 1.04401055 1.269448139 1.161693559 0.97531079 1.233786787 1.371935568 1.389068898 1 18.56630277 2.003596395 24.98438236 1.296961062 1.156090526 0.069866572 0.144828663 173.3225389 1204073.914 0.049995344 0.036755059 100.8315388 -2.003596395 -0.140870535 SDS(ph)PVPTAPTSGGPKPSTASAVPELATDPELEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSPVPTAPTSGGPKPSTASAVPELATDPELEKK 34 2 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 S(0.001)DS(0.999)PVPTAPTSGGPKPSTASAVPELATDPELEKK;S(0.169)DS(0.742)PVPT(0.046)APT(0.012)S(0.012)GGPKPS(0.006)T(0.006)AS(0.006)AVPELATDPELEKK 223.92 1.16E-36 940100000 225730 174233 191146 244460 87902 250130 242750 267360 93051 TRUE FALSE 215060.1903 191987.5408 199910.2332 219886.4164 103232.081 241467.9354 205714.0291 243948.541 107480.8738 2.000915908 1.786248417 1.859960996 2.045819023 0.960469312 2.246613065 1.913959403 2.269692572 1 16.71372043 4.762009818 1.533678982 1.807035706 2.087499102 0.017745834 0.453084379 6.606910036 14.00435955 0.109509295 2.858076565 57810.91161 -4.762009818 0.280463397 SDS(ph)RAQAVSEDAGGNEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSRAQAVSEDAGGNEGR 18 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 S(0.002)DS(0.998)RAQAVSEDAGGNEGR;S(0.011)DS(0.989)RAQAVSEDAGGNEGR 176.23 8.44E-13 253340000 60028 49892 68658 64725 79162 61210 87924 74302 92426 TRUE FALSE 57190.5954 54976.05152 71806.03721 58218.72003 92967.82774 59090.28235 74509.57896 67795.72298 106758.952 0.535698359 0.514954957 0.672599682 0.545328695 0.870819973 0.553492529 0.697923477 0.635035486 1 16.70399752 -5 0.121961641 2.235429886 0.439018195 0.600878639 0.099317668 94.77862556 0.745529655 28.8947397 0.824920421 1.00E-05 5 -1.79641169 SDS(ph)VSASER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 SDS(0.999)VS(0.001)ASER;S(0.001)DS(0.998)VS(0.001)ASER;SDS(0.878)VS(0.122)ASER;SDS(0.885)VS(0.115)ASER 217.78 5.81E-07 902920000 843753 775718 819543 1064090 806570 1102100 1139680 834158 836770 TRUE FALSE 803870.4678 854764.5461 857119.8572 957125.6516 947235.5526 1063934.001 965800.8843 761114.7034 966532.018 0.831705989 0.88436237 0.886799238 0.990267921 0.980035358 1.100774709 0.999243549 0.787469726 1 19.882458 3.332308805 2.94178548 0.987356188 0.85986964 0.297662279 0.078022208 0.283281957 4.933840598 0.022335652 0.031148704 2149.358232 -3.332308805 -0.127486548 SDSAFFWEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSAFFWEER 10 0 O75116;C9JFJ0;D6REE7;Q13464;A0A0U1RQV4 O75116;Q13464 ROCK2;ROCK1 Rho-associated protein kinase 2;Rho-associated protein kinase 1 0 ; 156.83 2.39E-05 58005000 79819 103035 69231 88925 67749 72674 66565 79440 58572 FALSE TRUE 76046.11406 113534.3836 72405.30983 79986.09005 79564.40415 70157.28116 56409.2867 72483.81246 67655.04662 1.124027221 1.678136212 1.070212992 1.182263468 1.176030586 1.036985187 0.833777959 1.071373328 1 16.04590993 2.851062468 0.970293206 0.952914011 1.373624751 0.377535514 0.171578139 0.45198284 0.916337988 0.08924496 0.093022849 709.6798401 -2.851062468 0.420710741 SDSDYDLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDSDYDLSPK 10 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SDSDYDLS(1)PK;SDSDYDLS(1)PK;SDSDYDLS(1)PK 145.01 3.27E-05 773123000 3569990 3327480 3207200 3737250 1940850 3461610 3744550 4212810 2224460 TRUE FALSE 3401243.648 3666553.995 3354253.292 3361574.53 2279333.626 3341733.578 3173250.124 3843914.023 2569417.896 1.323740935 1.426997921 1.305452608 1.308301984 0.887101172 1.30058002 1.235007404 1.496025239 1 21.29301012 2.985790938 24.61604336 1.199496672 1.356925345 0.18350437 0.165145973 931.6474377 1614007.007 0.046951932 0.051644336 967.8118551 -2.985790938 0.157428673 SDSEDICLFTKDEPNSTPEKTEQFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSEDICLFTKDEPNSTPEKTEQFYR 26 2 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 55.247 0.053057 106280000 59662 29631 47466 49649 36455 48455 60444 51659 54281 FALSE TRUE 56841.8955 32650.43259 49642.36305 44658.18819 42812.74046 46776.9912 51222.15767 47135.4641 62698.62025 0.906589256 0.520752011 0.79176165 0.712267479 0.682833853 0.746060934 0.816958291 0.751778331 1 15.93614607 0.364159058 0.584469475 1.010049626 0.713903949 0.407852994 0.098744174 2.113343975 1.125104192 0.145083943 0.03995644 2.312911729 -0.364159058 -0.296145677 SDSFENPVLQQHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;; 295.78 1.28E-43 3789772000 2595520 2265840 2200410 2524030 2657170 2188275 2912600 2483190 2612800 FALSE TRUE 2472834.913 2496731.672 2301300.975 2270309.709 3120579.607 2112494.488 2468229.376 2265748.719 3017979.68 0.819367649 0.82728578 0.762530308 0.75226143 1.033996229 0.699969752 0.817841615 0.750750157 1 21.52515166 -1.56985206 2.759703656 1.012336233 0.809887444 0.313108121 0.089332816 23752506.72 23702977.2 2154910.074 0.020858047 0.026924518 1.56985206 -0.202448788 SDSHPSDALTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SDSHPSDALTR 11 0 P49748;P49748-3;K7EQP4;J3QKU9;K7EJW8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;;;; 164.04 2.32E-05 1214140000 1464760 1074071 1148595 1330063 1692860 1025003 1507620 1366600 1559470 FALSE TRUE 1395523.698 1183520.056 1201259.217 1196362.54 1988094.248 989506.8891 1277604.88 1246933.259 1801304.643 0.774729418 0.657034922 0.666882874 0.664164468 1.103696843 0.549327896 0.709266411 0.692238964 1 20.78061076 -1.082345597 4.581819571 1.000017337 0.722346974 0.257845227 0.145262969 0.544646471 81290692.44 2977.859043 0.031157081 0.082728358 1.082345597 -0.277670363 SDSILLTHDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDSILLTHDGR 11 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;; 199.82 4.89E-08 381432000 554923 467264 456016 546596 497527 465031 600210 530646 483167 FALSE TRUE 528692.8895 514878.7328 476924.7847 491651.1316 584295.5513 448926.8599 508636.9409 484179.8231 558094.0707 0.947318593 0.922566212 0.854559849 0.880946703 1.046948144 0.804392814 0.911382091 0.867559518 1 19.09014879 SDSKS(ph)SPQAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.217)KS(0.391)S(0.391)PQAGR;SDS(0.018)KS(0.863)S(0.119)PQAGR 128.46 0.00069814 558293000 431870 463830 433310 500190 285300 437130 468580 518710 355180 TRUE FALSE 411456.361 511094.8043 453177.6921 449909.9509 335056.2297 421992.0785 397089.5149 473289.0025 410259.5004 1.002917326 1.245784202 1.104612304 1.096647245 0.816693408 1.028597944 0.967898402 1.153633254 1 18.64617722 2.976519574 24.52796472 0.988822622 1.125274306 0.262322977 0.099362763 705.2197428 736682.4529 0.028479969 0.030389001 947.3698816 -2.976519574 0.136451684 SDSKS(ph)SPQAGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSKSSPQAGRR 12 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.087)KS(0.456)S(0.456)PQAGRR 100.11 0.0017829 517600000 594430 389810 544150 496680 356340 534150 677400 638880 538830 TRUE FALSE 566332.4719 429532.0822 569099.8157 446752.7828 418485.5832 515652.2516 574050.1887 582936.2803 622389.0044 0.909933286 0.690134432 0.914379611 0.717803142 0.672385888 0.828504758 0.922333436 0.936610827 1 19.24745705 1.723861884 2.735599557 0.958628366 0.781822712 0.478342827 0.082574855 0.21214031 3.395259825 0.048593249 0.02181188 52.94950256 -1.723861884 -0.176805654 SDSKSS(ph)PQAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.001)KS(0.03)S(0.969)PQAGR;SDS(0.002)KS(0.046)S(0.952)PQAGR 141.65 2.30E-05 830950000 1317460 1551440 1325070 1436030 656840 1346240 1320230 1400500 783650 TRUE FALSE 1255186.277 1709533.5 1385825.77 1291677.536 771392.688 1299619.371 1118804.666 1277864.795 905174.4397 1.386678878 1.888623259 1.531004091 1.426992941 0.852203348 1.435766759 1.236010007 1.411733186 1 19.78783632 3.129626641 3.210696944 1.219989307 1.637816114 0.433836158 0.213496522 0.212825483 4.359281243 0.060146205 0.07444386 1347.803689 -3.129626641 0.417826807 SDSPES(ph)DAEREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDSPESDAEREK 12 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 SDS(0.001)PES(0.999)DAEREK 86.641 0.0066596 101390000 180400 180510 178110 197310 126390 194310 198770 207490 180840 TRUE FALSE 171872.8495 198904.1742 186276.5197 177476.0239 148432.376 187580.996 168443.9858 189321.0756 208883.7436 0.822815824 0.952224289 0.891771262 0.849640192 0.710598027 0.898016249 0.806400646 0.906346623 1 17.67234069 -1.742111577 4.651004772 1.009071566 0.856410537 0.321226393 0.066325815 0.006384044 0.000353982 0.065712964 0.01470479 0.018108748 1.742111577 -0.15266103 SDSQASLTVPLS(ph)PQVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 SDSQASLT(0.034)VPLS(0.966)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR 259.56 3.46E-27 749096000 1205150 1079950 1141280 1270300 1154400 1134060 1359220 1336930 1386370 TRUE FALSE 1148184.948 1189998.133 1193608.817 1142607.031 1355726.995 1094787.218 1151846.025 1219861.322 1601361.179 0.717005609 0.743116636 0.745371396 0.713522374 0.84660913 0.683660396 0.719291838 0.761765264 1 20.61086731 0.826583359 5.659956034 0.999999446 0.736981628 0.786932377 0.042470414 1.786361755 58.17014865 0.037589923 0.009465301 6.707850257 -0.826583359 -0.263017818 SDSVLPASHGHLPQAGS(ph)LER ddPTM_SK-BR-3_Trastuzumab_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;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER 187.13 5.06E-17 858262000 1267380 1116350 1218490 1406730 1420400 1125020 1591040 1424680 327992 TRUE FALSE 1207473.459 1230107.334 1274358.972 1265322.828 1668117.31 1086060.275 1348297.627 1299927.466 378855.3242 3.187162439 3.246905232 3.363708757 3.339857584 4.403045711 2.866688696 3.558872056 3.431197567 1 18.5312875 -0.136750753 11.50491554 0.999999778 3.405866109 0.790003455 0.39276317 0 1.08E-18 0.348680221 0.082184716 0.729876274 0.136750753 2.405866332 SDTALEEAVAEVLDHRPIEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDTALEEAVAEVLDHRPIEPK 21 1 A0A3B3ITN0;Q86TP1 A0A3B3ITN0 PRUNE Protein prune homolog 0 ; 199.12 4.92E-22 32889000 94925 89214 85774 111741 62219 100623 103943 115550 70916 FALSE TRUE 90438.08337 98305.00803 89706.82274 100508.5824 73069.9739 97138.40028 88084.58631 105431.8294 81913.29109 1.104070929 1.200110589 1.095143676 1.227011893 0.892040509 1.185868606 1.075339364 1.287115046 1 16.32180994 -1.889037188 2.673177232 0.934232708 1.130275635 0.131787298 0.10729964 41476231.57 16821919.49 17073436.35 0.022742774 0.012911087 1.889037188 0.196042927 SDTDTGVCS(ph)GTDEDPDDKNAPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDTDTGVCSGTDEDPDDKNAPFR 23 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 SDTDT(0.007)GVCS(0.964)GT(0.029)DEDPDDKNAPFR;SDTDT(0.012)GVCS(0.823)GT(0.165)DEDPDDKNAPFR 124.51 1.41E-05 139240000 275070 220025 255752 277590 202503 270343 314376 286647 232730 TRUE FALSE 262067.9862 242445.7976 267478.4822 249686.1258 237819.4591 260980.9541 266412.1673 261546.6691 268820.5798 0.974880667 0.901887042 0.99500746 0.928820725 0.884677279 0.970836959 0.991040818 0.972941392 1 18.03628406 2.014532071 24.92837608 0.985483687 0.937107678 0.352941356 0.03203507 245.7610877 421577.7632 0.011401874 0.008417272 103.4027457 -2.014532071 -0.048376009 SDTFINLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDTFINLR 8 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 117.4 0.0048542 155990000 626140 565970 495240 632910 562390 558890 661040 649170 538380 FALSE TRUE 596543.6031 623642.9865 517947.2439 569288.6843 660470.6379 539535.4992 560186.2072 592325.2333 621869.2207 0.95927501 1.002852313 0.83288773 0.915447598 1.062073208 0.867602835 0.900810313 0.952491639 1 19.24625169 SDTSGHFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SDTSGHFER 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;;;;; 154.01 7.67E-05 7085985000 5621353 4954161 4847895 5728008 5993353 5049628 6348820 5461041 5195000 FALSE TRUE 5355642.784 5458995.638 5070175.781 5152217.753 7038591.866 4874758.116 5380190.905 4982843.299 6000614.068 0.892515787 0.909739499 0.844942821 0.858615084 1.172978596 0.812376544 0.896606721 0.830388897 1 22.51667871 SDTSGHFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDTSGHFQR 9 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ;; 114.5 0.0016287 131624000 205542 169980 145512 224835 238240 159654 215127 178413 184393 FALSE TRUE 195826.437 187301.1553 152183.8691 202234.1586 279788.9806 154125.1419 182305.4251 162790.2119 212987.7247 0.919425931 0.879398827 0.714519437 0.949510865 1.313638995 0.723633919 0.855943343 0.764317343 1 17.70041076 -1.019235743 3.703277207 1.000025186 0.890033136 0.039776197 0.169776612 44159202.67 81470202.43 14357.98099 0.03914375 0.095667463 1.019235743 -0.109992051 SDVLELTDDNFESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 ;;;; 386.98 1.46E-113 4299270000 3746200 3184160 3439490 3935100 3568530 3430830 4142120 3835580 3841900 FALSE TRUE 3569124.55 3508629.524 3597194.019 3539536.272 4190880.502 3312019.497 3510163.519 3499716.282 4437682.23 0.804276729 0.790644607 0.810601984 0.797609222 0.944384993 0.746339942 0.790990282 0.788636072 1 22.08137493 -1.065296595 4.071343882 1.000026225 0.806958905 0.578778402 0.051126586 5329557.507 2789034.856 1327.991834 0.011191686 0.086040595 1.065296595 -0.19306732 SDVS(ph)PIIQPVPSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SDVSPIIQPVPSIK 14 0 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SDVS(1)PIIQPVPSIK;SDVS(1)PIIQPVPSIK 233.14 3.70E-17 146251000 412830 348250 381950 438630 311940 404800 473270 435280 366150 TRUE FALSE 393316.3441 383737.0709 399462.7853 394538.0791 366342.2372 390781.6745 401063.9693 397164.5756 422930.672 0.929978292 0.907328544 0.944511268 0.932867028 0.866199265 0.923985183 0.948297194 0.939077258 1 18.69006167 0.854259749 1.008671455 0.998955636 0.918018155 0.56297641 0.0221477 0.529512729 1.069615423 0.020553891 0.006710576 7.149237892 -0.854259749 -0.080937481 SDWEVKEEMDFPQLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDWEVKEEMDFPQLMK 16 1 O15371-2;O15371;O15371-3;B0QYA5 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 111.06 0.00077138 171660000 242100 201010 216650 265900 169700 247170 276010 290790 157920 FALSE TRUE 230656.4128 221493.1475 226583.6168 239171.2268 199295.6263 238610.4409 233899.6052 265326.886 182409.4271 1.264498313 1.214263709 1.242170542 1.311177995 1.092573062 1.30810367 1.282278054 1.454567838 1 17.47682077 SDYAQLLEDMQNAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SDYAQLLEDMQNAFR 15 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 232.6 8.86E-14 210524000 384157 362304 342895 412763 330164 323848 379205 386916 311937 FALSE TRUE 365998.6599 399223.1895 358617.0749 371271.279 387744.4971 312633.0626 321350.3127 353035.5839 360310.5968 1.015786555 1.107997359 0.995299828 1.030420094 1.076139588 0.867676569 0.891870279 0.979809051 1 18.45888156 2.245265923 24.99872866 0.920112974 1.048100709 0.542673299 0.049454059 98.74844535 368154.6879 0.016549671 0.013552381 175.9000337 -2.245265923 0.127987735 SDYDGIGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 133.68 0.00062852 1767690000 1957030 1687900 1761800 1975640 2200820 1698340 2104660 1893360 2180750 FALSE TRUE 1864525.07 1859898.929 1842580.273 1777044.914 2584642.311 1639526.06 1783555.462 1727567.361 2518929.572 0.74020532 0.73836877 0.731493366 0.70547622 1.026087565 0.650882056 0.708060869 0.685833927 1 21.26437936 -2.255581989 2.280260776 1.971146045 0.746229822 0.373273794 0.10246528 5632300.939 1218076.574 28042011.6 0.024082163 0.005551598 2.255581989 -1.224916223 SDYDMVDYLNELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDYDMVDYLNELR 13 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 118.48 0.00098636 3805200 18189 23026 16474 21693 15973 17223 17574 19055 15599 FALSE TRUE 17329.24202 25372.37558 17229.3492 19512.37843 18758.68614 16626.56319 14892.76353 17386.44318 18018.01325 0.961773186 1.408167217 0.956229133 1.082937289 1.041107356 0.922774501 0.826548595 0.964947852 1 14.13715232 2.778775868 1.146013192 0.904735016 1.160248921 0.259812703 0.132298057 0.481939781 1.320786535 0.062150869 0.060063645 600.8635618 -2.778775868 0.255513905 SDYDRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDYDRSR 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 1 SDYDRS(1)R 61.765 0.054211 258130000 586140 399970 609390 549170 663440 605300 792810 693680 808350 TRUE FALSE 558434.3238 440727.3977 637331.1343 493966.3882 779143.7259 584338.3092 671852.2735 632937.7018 933704.7895 0.598084459 0.472020067 0.682583126 0.52903915 0.834464742 0.625827687 0.719555347 0.67787775 1 19.83260696 -5 0.101527689 2.226618268 0.376454832 0.65138724 0.088779802 97.96749644 0.674484839 25.14617552 1.273230456 1.00E-05 5 -1.850163437 SDYLNTFEFMDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SDYLNTFEFMDK 12 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 87.001 0.025112 28570000 38036 35875 31060 39614 27679 33763 45320 40013 34008 FALSE TRUE 36238.11366 39530.70329 32484.13172 35631.92546 32506.20884 32593.77884 38405.60164 36509.2496 39281.78695 0.922516934 1.006336686 0.826951477 0.907085146 0.827513496 0.829742773 0.977694871 0.929419266 1 15.26157294 -1.168914935 5.130024676 1.000004851 0.911006315 0.184297844 0.062059272 3.55E-06 5.75E-07 0.06192302 0.0145946 0.067777425 1.168914935 -0.088998537 SEAAAPHTDAGGGLS(ph)S(ph)DEEEGTSSQAEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEAAAPHTDAGGGLSSDEEEGTSSQAEAAR 30 0 Q01831-2;Q01831 Q01831-2 XPC DNA repair protein complementing XP-C cells 2 SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR 85.849 0.00070095 181980000 39327 40237 37075 45028 45330 40097 47905 31502 36663 TRUE FALSE 37468.09065 44337.19605 38774.92542 40501.69989 53235.53765 38708.43084 40596.21241 28743.51788 42348.51079 0.884755802 1.046959981 0.915614852 0.956390181 1.257081693 0.914044676 0.95862196 0.678737395 1 15.37002362 1.43789555 5.476620045 0.830930208 0.993668381 0.191510894 0.129332232 0.27349301 15.93441973 0.078000477 0.03009747 27.40914889 -1.43789555 0.162738173 SEAEDLAEPLSSTEGVAPLS(ph)QAPSPLAIPAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEAEDLAEPLSSTEGVAPLSQAPSPLAIPAIK 32 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 SEAEDLAEPLS(0.011)S(0.011)T(0.011)EGVAPLS(0.519)QAPS(0.448)PLAIPAIK 62.051 0.0004309 0 6298 5784.8 4355.5 8452.9 3263.2 5381.8 6744.8 6001.7 5837.5 TRUE FALSE 6000.306021 6374.277697 4555.203983 7603.198433 3832.301047 5195.426917 5715.756883 5476.159331 6742.749686 0.889890075 0.94535286 0.675570679 1.127610958 0.568358789 0.770520508 0.847689318 0.812155216 1 12.71912133 SEAEDLAEPLSSTEGVAPLSQAPS(ph)PLAIPAIK ddPTM_SK-BR-3_Trastuzumab_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(0.011)QAPS(0.989)PLAIPAIK 72.425 8.92E-05 0 12419 12929 11532 13754 6619.6 13744 13758 12705 9651.7 TRUE FALSE 11831.97848 14246.4798 12060.75361 12371.42179 7774.056144 13268.04183 11658.96442 11592.48285 11148.43634 1.061312826 1.277890402 1.081833652 1.109700178 0.697322558 1.19012581 1.045793693 1.039830384 1 13.44455375 3.254990508 2.848112957 1.012077184 1.166611259 0.184184786 0.135636035 0.399402737 6.642737251 0.038470393 0.051486038 1798.831599 -3.254990508 0.154534075 SEAEEAITSFNGHKPPGSSEPITVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEAEEAITSFNGHKPPGSSEPITVK 25 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 135.72 2.23E-05 140820000 186510 139260 160900 201990 140440 178360 246020 200490 148310 FALSE TRUE 177694.0419 153450.7523 168277.4242 181685.5814 164932.6915 172183.3485 208485.1305 182934.0327 171309.1573 1.037271123 0.895753354 0.982302562 1.060571334 0.962778021 1.005103003 1.21701101 1.067859043 1 17.38624275 1.927285818 9.720001436 1.117416361 0.982855941 0.320838278 0.069244963 0.445416864 57.47608386 0.027186006 0.017263846 84.58353226 -1.927285818 -0.13456042 SEAEEGEVRT(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SEAEEGEVRTPTK 13 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SEAEEGEVRT(0.999)PT(0.001)K;SEAEEGEVRT(0.996)PT(0.004)K;SEAEEGEVRT(0.997)PT(0.003)K;SEAEEGEVRT(1)PTK;SEAEEGEVRT(0.999)PT(0.001)K;SEAEEGEVRT(1)PTK 202.33 1.53E-07 2992650000 4406100 3911510 3882840 4802820 3246400 4043120 4492010 4507430 2914510 TRUE FALSE 4197832.385 4310097.316 4060872.055 4320031.409 3812571.132 3903105.741 3806671.373 4112735.534 3366477.326 1.246951035 1.280298929 1.206267461 1.283249816 1.132510563 1.159403544 1.130758061 1.221673321 1 21.68280832 -4.999999998 0.075275106 0.250962365 1.454270415 0.705081256 0.046132377 132.9405955 0.714325916 16.66521983 1.784700697 1.00E-05 4.999999998 1.20330805 SEAHLTELLEEICDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SEAHLTELLEEICDR 15 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;;;;;;; 266.2 2.78E-25 1408191000 1241860.6 920592.1 1102131.1 1235223.5 1382561.1 1000483 1486792 1239701.4 1428597 FALSE TRUE 1183160.311 1014401.482 1152664.901 1111056.487 1623679.318 965836.0228 1259954.574 1131146.573 1650136.526 0.717007527 0.614737911 0.69852699 0.673311856 0.983966655 0.585306735 0.763545654 0.685486658 1 20.65415396 -5 0.240778133 2.649988026 0.681230966 0.402166433 0.108289544 164.6025835 1.640468596 133.1714432 0.154841746 1.00E-05 5 -1.96875706 SEALKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEALKDR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 80.239 0.027773 197724000 609490 598110 541630 641160 494040 598120 658340 633070 502150 FALSE TRUE 580680.6156 659058.089 566464.2712 576709.3787 580200.4196 577406.9544 557898.1418 577635.0347 580020.8574 1.001137473 1.136266189 0.976627416 0.994290759 1.000309579 0.995493433 0.961858758 0.995886661 1 19.14574525 3.7084095 24.95418165 0.9871495 1.068701847 0.484773642 0.034018792 451.5648031 373731.8171 0.008610023 0.013340573 5109.865863 -3.7084095 0.081552347 SEALS(ph)LPT(ph)VR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEALSLPTVR 10 0 Q99592;Q99592-2 Q99592 ZBTB18 Zinc finger and BTB domain-containing protein 18 2 SEALS(1)LPT(1)VR 70.1 0.097588 55882000 9341 12102 9362.2 9607.4 11537 12251 13189 8324.2 14443 TRUE FALSE 8899.469442 13335.20756 9791.46613 8641.645899 13549.04915 11826.7448 11176.77582 7595.288919 16682.74668 0.53345349 0.799341249 0.586921705 0.517998988 0.812159377 0.708920721 0.669960171 0.455278083 1 14.02606922 -1.558720669 3.178735387 1.013846028 0.649233157 0.482193229 0.117944542 34318924.61 43777248.36 4095166.01 0.027327207 0.02762354 1.558720669 -0.36461287 SEAPAEVTHFS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SEAPAEVTHFSPK 13 0 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK 162.29 2.53E-05 966970000 2999130 2447030 2621290 3076150 1837440 3009450 3078550 3121930 1720920 TRUE FALSE 2857367.069 2696385.139 2741478.739 2766929.558 2157888.954 2905231.992 2608860.656 2848557.259 1987791.484 1.437458149 1.356472829 1.379158106 1.391961672 1.085571083 1.461537598 1.312441811 1.433026191 1 20.922735 -1.926024584 2.666308093 0.773451193 1.35686997 0.530054111 0.105701274 11959926.53 8240461.451 16949925.41 0.023835347 0.011857016 1.926024584 0.583418777 SEASLHPVLMSEAPWNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEASLHPVLMSEAPWNTR 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 ;; 157.98 4.17E-10 512680000 298933 249844 278319 327785 345951 266305 356335 325483 400649 FALSE TRUE 284803.0295 275303.3876 291080.2014 294835.429 406284.7449 257082.7911 301969.5512 296981.983 462779.6007 0.615418288 0.594890931 0.628982351 0.637096857 0.877922761 0.555518849 0.652512666 0.641735251 1 18.81996575 -5 0.359403243 5.349335387 0.634922734 0.619750615 0.085829741 310.0309852 2.470975927 1043.126547 0.059667831 1.00E-05 5 -4.714412652 SEAVVEYVFSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEAVVEYVFSGSR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 218.55 5.57E-11 307670000 423700 386160 406130 442040 388650 377290 454570 406200 386130 FALSE TRUE 403672.5407 425510.143 424751.4622 397605.2994 456430.4369 364224.3527 385216.9977 370630.9746 446009.0683 0.90507698 0.954039219 0.952338175 0.891473577 1.023365822 0.816629927 0.86369768 0.830994258 1 18.76671352 2.221381216 24.99992679 0.86439464 0.940680236 0.221381438 0.060209396 290.5704329 422843.4498 0.019725733 0.014603808 166.4873404 -2.221381216 0.076285596 SECDS(ph)SPEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.874)S(0.126)PEPK;S(0.007)ECDS(0.496)S(0.496)PEPK 244.74 1.82E-12 249380000 964554 806517 794354 973018 531000 925339 1001016 954035 564788 TRUE FALSE 918961.444 888701.9992 830775.9166 875208.382 623606.2319 893294.2784 848292.6243 870494.6377 652372.4385 1.408645414 1.362261719 1.273468754 1.341577802 0.955905239 1.36930107 1.300319533 1.33435226 1 19.31533631 -5 0.125380794 0.103325429 1.4264634 0.346148761 0.126009509 171.7159708 1.375821874 39.81328501 1.033511676 1.00E-05 5 1.323137971 SECDSS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.439)S(0.561)PEPK;SECDS(0.299)S(0.701)PEPK;SECDS(0.042)S(0.958)PEPK;SECDS(0.112)S(0.888)PEPK;SECDS(0.13)S(0.87)PEPK 252.69 4.82E-17 1061100000 4400370 3595760 3629910 4395210 2370610 4275310 4410450 4377040 2604880 TRUE FALSE 4192373.231 3962172.032 3796344.964 3953395.14 2784043.633 4127254.943 3737554.849 3993763.173 3008831.487 1.393355942 1.316847437 1.261733992 1.313930394 0.925290647 1.371713558 1.242194807 1.327346909 1 21.52077188 -5 0.060018834 0.172461613 1.641173677 0.292079956 0.130641359 518.2883 2.271853155 66.11481665 11.02531124 1.00E-05 5 1.468712065 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 SEDDS(0.015)AKFDS(0.985)NEEDSASVFSPSFGLK;S(0.001)EDDS(0.087)AKFDS(0.895)NEEDS(0.015)AS(0.002)VFSPSFGLK;SEDDS(0.011)AKFDS(0.989)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;S(0.001)EDDS(0.106)AKFDS(0.893)NEEDSASVFSPSFGLK 347.18 4.81E-110 624990000 1340520 1135041 1198789 1390730 672183 1431320 1496514 1545349 756996 TRUE FALSE 1277156.276 1250702.968 1253754.661 1250931.178 789411.5024 1381753.03 1268193.304 1410030.049 874387.0735 1.460630326 1.430376782 1.433866876 1.430637776 0.902816986 1.580253267 1.450379749 1.612592514 1 19.73791255 2.96352346 24.98245829 1.348395656 1.440720328 0.061492145 0.224704482 2268.012451 1553341.335 0.065461312 0.069453013 919.4401395 -2.96352346 0.092324672 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_SK-BR-3_Trastuzumab_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 194.68 6.46E-18 302310000 955540 929590 905540 1010700 415250 1203000 1002500 1049300 359040 TRUE FALSE 910373.5179 1024316.278 947059.9047 909102.5158 487669.4685 1161339.808 849550.2128 957417.7293 414718.0895 2.195162307 2.469909811 2.28362333 2.192097569 1.175905949 2.800311435 2.048500498 2.30859891 1 18.66177145 2.991450222 24.55490767 1.984483659 2.320116449 0.119694818 0.5203752 801.1330795 2300860.721 0.140582835 0.160478301 980.505925 -2.991450222 0.335632791 SEDES(ph)ET(ph)EDEEEKSQEDQEQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 S(0.001)EDES(0.953)ET(0.81)EDEEEKS(0.236)QEDQEQKR 101.41 0.00010844 0 843550 707850 755320 896790 364320 975180 958090 991750 353150 TRUE FALSE 803677.0633 779980.7198 789952.1691 806642.9654 427857.2927 941409.2721 811915.774 904907.1124 407914.6984 1.97020864 1.912117222 1.936562159 1.977479529 1.048889129 2.307858177 1.990405781 2.21837339 1 18.63790797 SEDFSLPAYMDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEDFSLPAYMDRR 13 1 H3BN72;H3BNV9;P13073;Q86WV2;H3BNI5 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 88.021 0.012988 108900000 35845 21520 28438 36912 49481 24795 46786 32223 49015 FALSE TRUE 34150.67789 23712.91247 29741.91043 33201.53563 58110.47073 23936.34293 39647.93642 29401.3833 56615.99587 0.603198396 0.418837682 0.525326985 0.586433836 1.02639669 0.422784101 0.700295664 0.519312305 1 15.7889221 -5 0.170993821 2.553999202 0.499037098 0.335520716 0.174063555 147.2542144 1.391963966 77.99382848 0.579798071 1.00E-05 5 -2.054962104 SEDHLTESHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEDHLTESHQR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 145.91 2.08E-05 74065000 115270 123310 91280 135040 135880 109250 129560 119890 60051 FALSE TRUE 109821.4155 135875.4292 95465.27829 121465.5226 159577.429 105466.6451 109793.2425 109391.796 69363.40238 1.583276076 1.958892219 1.376306164 1.751147125 2.30059979 1.520494115 1.58286991 1.577082327 1 16.08188705 0.701285609 0.897482677 1.002905081 1.761762664 0.453723651 0.252808763 0.926958965 1.349827844 0.232360344 0.077752676 5.026730579 -0.701285609 0.758857583 SEDKVIAVYDLGGGTFDISILEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SEDKVIAVYDLGGGTFDISILEIQK 25 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 250.99 7.15E-40 318231000 1353091 1130894 1095409 1187385 722723 1108748 1249718 1189593 710929 FALSE TRUE 1289133.07 1246133.384 1145634.586 1068026.804 848765.6624 1070351.779 1059050.566 1085425.93 821176.2384 1.569861632 1.517498103 1.395114146 1.300606075 1.033597446 1.303437348 1.289675123 1.321794129 1 19.64733236 8 0.178072228 1.063337053 3.442276426 0.632511496 0.108935982 35.82271343 0.399978922 0.257168696 23.01506601 100000000 -8 2.378939373 SEDLLDYGPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SEDLLDYGPFR 11 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 223.55 1.60E-11 143374000 447373 353664 378330 501838 611240 389661 561228 431979 517222 FALSE TRUE 426226.5649 389702.7637 395676.8047 451392.2908 717840.0625 376166.9419 475602.3609 394152.6287 597430.1462 0.713433307 0.652298459 0.662298023 0.755556601 1.201546435 0.629641715 0.796080285 0.659746803 1 19.18841051 2.998475885 24.95420576 0.837640588 0.680356584 0.203468241 0.162491871 98.71102826 1616238.871 0.044994494 0.053068555 996.4967468 -2.998475885 -0.157284004 SEDMPFS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SEDMPFS(1)PK;SEDMPFS(1)PK;SEDMPFS(1)PK 227.36 2.13E-07 1440170000 4986610 4458060 4318250 5211550 2790290 5053540 5310430 5307740 3090390 TRUE FALSE 4750902.828 4912341.382 4516246.034 4687675.093 3276915.693 4878534.643 4500226.371 4842966.148 3569631.898 1.330922337 1.376147884 1.265185365 1.313209661 0.91799821 1.366677232 1.260697601 1.356713041 1 21.76734388 -4.898541667 0.178534856 2.41E-29 1.335503457 0.272772107 0.134564473 172.7186582 1.713808903 62.41595047 0.411037191 1.26E-05 4.898541667 1.335503457 SEDPPTT(ph)PIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEDPPTTPIR 10 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C151 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDPPT(0.489)T(0.511)PIR;SEDPPT(0.046)T(0.954)PIR 126.03 0.0043987 1371880000 2312000 2136700 2061690 2419800 2093100 2118000 2236900 2187000 2052370 TRUE FALSE 2202716.342 2354432.159 2156220.526 2176557.107 2458135.977 2044653.129 1895619.822 1995494.686 2370641.058 0.92916485 0.993162652 0.909551667 0.918130182 1.036907705 0.862489546 0.799623298 0.841753196 1 21.17684581 2.099552487 9.502922094 0.851463565 0.955638976 0.25100068 0.064199177 0.284332105 24.69001009 0.021789481 0.016087104 125.7628837 -2.099552487 0.104175411 SEDRRS(ph)S(ph)EEREAGEI ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SEDRRSSEEREAGEI 15 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 S(0.28)EDRRS(0.819)S(0.901)EEREAGEI;S(0.002)EDRRS(0.998)S(1)EEREAGEI;SEDRRS(1)S(1)EEREAGEI;SEDRRS(1)S(1)EEREAGEI 136.62 3.96E-05 32786360000 3983440 3266490 3771640 3989980 3543550 3643550 4450370 3894800 3903440 TRUE FALSE 3795150.686 3599349.045 3944573.425 3588899.63 4161543.998 3517372.95 3771384.32 3553750.664 4508765.539 0.841727221 0.798300336 0.874867719 0.795982758 0.922989666 0.780118842 0.836456074 0.788187062 1 22.10430106 -1.825404172 2.80055667 1.055398567 0.829150085 0.598836484 0.043768763 16842997.13 12163591.98 6285114.013 0.009353478 0.014948438 1.825404172 -0.226248482 SEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 156.17 6.55E-08 1278670000 3590700 3342200 3170850 3610010 2880860 3316510 3963020 3780580 2650132 FALSE TRUE 3420974.727 3682773.98 3316236.609 3247124.936 3383281.072 3201658.427 3358388.513 3449532.373 3061100.936 1.117563517 1.203088058 1.083347684 1.060770293 1.105249759 1.045917301 1.097117862 1.126892724 1 21.54561919 7.999999756 0.028436959 0.579807913 1.845297619 0.393223596 0.041896106 1377.317313 3.006801883 43.66103479 101.2194202 99999943.9 -7.999999756 1.265489706 SEEDNEIES(ph)EEEVQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEEDNEIESEEEVQPK 16 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;C9J7Y7 P52701 MSH6 DNA mismatch repair protein Msh6 1 SEEDNEIES(1)EEEVQPK 165.8 3.44E-09 0 20796 23938 18984 25818 14424 21454 24413 22165 13968 TRUE FALSE 19813.01429 26377.30942 19854.43518 23222.72559 16939.54103 20711.0426 20688.34847 20224.1151 16134.0861 1.2280221 1.634880913 1.23058939 1.439357981 1.049922563 1.283682414 1.282275819 1.253502366 1 13.97782424 -0.019373977 0.166409096 0.779328666 1.500957701 0.321975512 0.147040805 13.6968738 0.804797569 2.445846695 0.825008312 0.956370172 0.019373977 0.721629035 SEEHNDKEHSSDKGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEEHNDKEHSSDKGR 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 115.78 0.00016102 9708000 14644 10147 16995 14168 23182 9188.5 15944 8515.8 3110.3 FALSE TRUE 13951.80714 11180.99084 17774.23756 12743.80572 27224.93346 8870.299941 13511.44997 7770.111407 3592.629439 3.88345288 3.112202643 4.947417445 3.547208511 7.577996541 2.469027238 3.760880491 2.162792333 1 11.81082442 1.173104564 1.389691233 1.026446303 4.23027043 0.414589922 1.35174265 0.393460634 1.490116985 1.186550572 0.363907203 14.89719712 -1.173104564 3.203824127 SEEITTGSAWFSFLESHNKLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEEITTGSAWFSFLESHNKLDK 22 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 190.37 1.08E-17 65438000 325870 323650 259780 346220 174360 290330 301610 326550 136440 FALSE TRUE 310466.7709 356630.303 271691.17 311417.3078 204768.3288 280275.7993 255593.8551 297955.5508 157598.4184 1.969986591 2.262905343 1.723946045 1.976017977 1.299304466 1.77841759 1.621804696 1.89059988 1 17.26589353 -0.135140077 0.09826066 1.08E-14 2.7580382 0.567798953 0.23603514 24.19502599 0.713844043 13.42932722 6.426767527 0.732588207 0.135140077 2.7580382 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR 36 2 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 145.03 1.39E-13 1589787000 361197 237831 314204 332074 253089 351920 403681 378383 95463 FALSE TRUE 344123.9336 262066.2493 328610.5642 298693.2906 297227.6415 339732.9222 342092.0493 345249.7786 110266.9145 3.120826725 2.37665351 2.980137476 2.708820611 2.69552878 3.081005066 3.102399763 3.131036904 1 16.75064045 3.622109554 16.6871833 2.802940567 2.737116293 0 0.654411342 28.14479179 3909.708035 0.15302678 0.237068283 4188.992224 -3.622109554 -0.065824274 SEENTKEEKPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SEENTKEEKPDSK 13 2 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ;;;;; 129.38 8.68E-05 1244224000 2888620 2992730 2749170 3119540 1153320 3501840 2926560 3675110 1183480 FALSE TRUE 2752080.657 3297692.589 2875222.164 2805957.912 1354458.643 3380570.403 2480059.522 3353297.885 1367008.034 2.013214691 2.41234324 2.103295732 2.052627229 0.990819812 2.472970399 1.81422454 2.453019881 1 20.38259029 2.990768109 24.67945352 1.824078431 2.187871562 0.128133906 0.50312314 826.804414 2210290.872 0.13574793 0.154231994 978.9671282 -2.990768109 0.363793131 SEEPAGQILSHLS(ph)SELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEEPAGQILSHLSSELK 17 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SEEPAGQILSHLS(0.982)S(0.018)ELK;SEEPAGQILSHLS(0.98)S(0.02)ELK;SEEPAGQILSHLS(0.75)S(0.25)ELK 198.64 9.03E-12 82900000 108589 109421 98299 118708 75031 109567 115704 114380 66333 TRUE FALSE 103456.2132 120571.1243 102806.1064 106775.2463 88116.38264 105772.6673 98051.22975 104364.2808 76619.58286 1.35025811 1.573633265 1.341773246 1.39357645 1.15005041 1.380491297 1.279715004 1.36210975 1 16.22542555 -4.281068897 0.119834276 1.96E-13 1.557448591 0.566509039 0.100383179 84.76697047 0.781158684 21.41340818 0.958808389 5.24E-05 4.281068897 1.557448591 SEEQLKEEGIEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SEEQLKEEGIEYK 13 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;;;; 206.06 5.92E-08 3114290000 5097730 4037690 3988590 4169960 2557500 4103400 4327400 4799040 2667510 FALSE TRUE 4856770.406 4449135.201 4171470.797 3750787.698 3003527.19 3961298.229 3667175.652 4378810.616 3081173.827 1.576272771 1.443974099 1.353857663 1.217324276 0.974799657 1.285645813 1.19018785 1.42115014 1 21.55504864 3.61786585 1.655376398 1.188153091 1.536487078 0.535022804 0.129231877 0.2675715 1.445151428 0.036962181 0.073692401 4148.258869 -3.61786585 0.348333987 SEETLDEGPPKYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEETLDEGPPKYTK 14 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 200 1.81E-08 615060000 510040 345420 467420 454550 363560 485600 622560 543310 428120 FALSE TRUE 485931.42 380618.6907 488851.6693 408857.7704 426964.7489 468783.5502 527577.0379 495734.8961 494510.6631 0.982651045 0.76968753 0.988556377 0.826792627 0.863408579 0.947974604 1.066866859 1.002475645 1 18.9156421 1.98896207 4.210298208 1.027430012 0.881802449 0.46275644 0.067138791 0.164288285 6.780618944 0.027487369 0.017261541 97.49044886 -1.98896207 -0.145627563 SEETQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 84.227 0.050484 44632000 29043 18803 32833 26978 76328 16043 37264 24877 68520 FALSE TRUE 27670.19495 20719.04708 34338.42553 24266.12019 89639.57903 15487.42689 31578.6924 22698.638 79145.73165 0.349610704 0.261783506 0.433863265 0.306600491 1.132588924 0.195682402 0.398994257 0.286795479 1 16.27222393 -1.991834207 2.491856555 1.563302716 0.409621969 0.323972693 0.262532388 43577283.75 18331311.44 141045418.4 0.061204366 0.010189803 1.991834207 -1.153680747 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;S(0.006)EEVPAFGVAS(0.819)PPPLT(0.124)DT(0.037)PDT(0.007)T(0.007)ANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 267.92 1.20E-67 239187000 431211 383152 391685 486377 335535 467075 486862 477365 377924 TRUE FALSE 410828.5106 422195.6244 409644.1447 437485.4599 394052.1978 450900.0756 412582.2601 435564.3899 436530.5238 0.941122071 0.967161748 0.938408937 1.002187559 0.902691052 1.032917634 0.945139544 0.99778679 1 18.73572301 2.23340951 0.167331872 1.015698412 0.924440113 0.167097429 0.035547953 9.553415983 1.082588215 0.195674106 0.309319653 171.1628505 -2.23340951 -0.091258299 SEEWADNHLPLTDAELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SEEWADNHLPLTDAELAR 18 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;; 164.59 3.03E-11 1077180000 1323810 1146120 1235500 1444800 1339450 1233180 1519970 1355130 1149740 FALSE TRUE 1261236.125 1262910.931 1292148.897 1299565.959 1573049.656 1190474.667 1288070.66 1236467.633 1328035.807 0.949700391 0.950961506 0.972977453 0.978562439 1.184493406 0.896417597 0.969906574 0.931049921 1 20.34086262 3.482061183 2.923992545 0.992038991 0.950765596 0.053713645 0.074995544 0.86856173 15.05548802 0.021041352 0.032235498 3034.318625 -3.482061183 -0.041273395 SEGEGKPQGEGKPASQAKPESQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEGEGKPQGEGKPASQAKPESQPR 24 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 88.09 0.0047925 123060000 155100 126090 122050 150560 70022 153080 160220 156480 82157 FALSE TRUE 147768.7304 138938.7144 127646.1132 135425.4228 82233.81463 147778.8012 135775.4964 142777.7816 94897.48796 1.55714059 1.464092647 1.345094754 1.427070681 0.866554178 1.557246713 1.430759647 1.504547536 1 16.53408228 3.901019207 1.71641013 1.326507431 1.542642382 0.136893014 0.21709893 0.785105472 4.447650918 0.059437512 0.159511598 7961.945612 -3.901019207 0.216134951 SEGEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEGEIAR 7 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 123.99 0.009748 695820000 1051620 1005050 972970 1157810 1255660 922710 1118170 960340 1258290 FALSE TRUE 1001912.007 1107465.738 1017581.637 1041424.739 1474646.706 890756.3213 947572.6299 876247.5385 1453419.187 0.689348273 0.761972697 0.700129492 0.716534327 1.014605229 0.612869521 0.651961002 0.602887004 1 20.47101943 -2.31508629 2.341125614 2.534305287 0.719333699 0.369945134 0.115331728 4748131.538 1064453.413 38217956.35 0.027332585 0.004840762 2.31508629 -1.814971588 SEGEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEGEVAR 7 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 91.906 0.037363 22588000 73389 70113 61419 80778 73136 65116 67599 70726 78581 FALSE TRUE 69920.04741 77257.59441 64235.1219 72658.04197 85890.89524 62861.01659 57285.53101 64532.8565 90766.94014 0.770325047 0.851164469 0.707692931 0.800490155 0.946279506 0.692554101 0.631127709 0.710973141 1 16.4698793 SEGFDTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SEGFDTYR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;;; 214.41 2.06E-05 4847570000 8098020 8780140 7613370 8801420 7723630 8338770 9458730 8949560 8994490 FALSE TRUE 7715242.643 9674846.248 7962450.545 7916684.54 9070628.627 8049996.304 8015627.017 8165889.082 10389309.57 0.742613606 0.931230914 0.766408055 0.76200295 0.873073284 0.774834579 0.771526439 0.785989581 1 23.30859645 -1.468333261 6.775799985 1.000048604 0.805403068 0.537070964 0.057943981 4.13E-05 3.24E-06 0.054516873 0.012846549 0.034014707 1.468333261 -0.194645536 SEGGFIWACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEGGFIWACK 10 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 120.15 0.0063694 0 154680 121530 130260 145460 139540 137910 172450 149810 158340 FALSE TRUE 147368.5829 133914.0452 136232.5498 130838.0844 163875.7318 133134.1421 146139.5852 136691.8422 182894.5585 0.805757067 0.732192616 0.744869344 0.715374397 0.896012069 0.727928393 0.79903736 0.747380585 1 17.48065263 -4.999999988 0.456907568 6.432577135 0.76835022 0.645167588 0.053243666 845.7048599 4.756704051 4656.79092 0.025061973 1.00E-05 4.999999988 -5.664226915 SEGTYLNSVIESHTEFIFTTIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEGTYLNSVIESHTEFIFTTIK 22 0 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 269.11 3.58E-38 83161000 169641 192948 160333 195128 112671 175817 167571 196311 105706 FALSE TRUE 161622.4061 212609.6206 167684.4266 175513.3627 132320.7867 169728.4132 142004.9663 179120.9681 122098.3466 1.323706755 1.741298113 1.373355425 1.437475343 1.083723002 1.390095918 1.163037586 1.467022061 1 16.89768414 3.109259338 2.193284154 1.240838282 1.524132241 0.315339629 0.174971614 0.316803587 3.108679144 0.050584384 0.063422454 1286.054397 -3.109259338 0.283293959 SEHPGLSIGDTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEHPGLSIGDTAK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 158.11 4.34E-05 352160000 757340 672070 648830 835480 573280 736240 839490 791720 552250 FALSE TRUE 721542.0391 740554.6971 678579.4973 751495.9631 673259.8505 710743.8242 711410.3822 722392.7996 637890.1095 1.131138465 1.160944003 1.063787457 1.178096277 1.055448016 1.114210447 1.115255389 1.132472175 1 19.28294838 -5 0.230825714 0.351087909 1.13479186 0.486402412 0.037978425 126.9680152 1.269631841 38.55649729 0.058177689 1.00E-05 5 0.783703951 SEHQNSS(ph)PTCQEDEEDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEHQNSSPTCQEDEEDVR 18 0 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SEHQNS(0.023)S(0.976)PT(0.001)CQEDEEDVR 168.75 1.28E-11 93771000 59699 47900 51008 58172 56168 50387 57330 50382 43078 TRUE FALSE 56877.14658 52781.06446 53346.76725 52324.44004 65963.68142 48642.08556 48583.25556 45970.28499 49758.31623 1.143068152 1.060748604 1.072117614 1.051571757 1.325681543 0.977566952 0.976384638 0.923871394 1 15.60265005 2.045610388 24.99999517 0.967338879 1.118953563 0.502899236 0.07921679 104.6100762 57338.4749 0.028010801 0.02068734 111.0734823 -2.045610388 0.151614684 SEIDLFNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SEIDLFNIR 9 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 180.03 0.00011427 301730000 1021960 1075910 672454 856176 874140 762299 888822 896835 776259 FALSE TRUE 973653.9761 1185546.452 703286.681 770111.5619 1026589.739 735900.3945 753215.8796 818303.373 896637.2811 1.08589504 1.322214096 0.784360294 0.858888625 1.144933142 0.820733657 0.840045239 0.912635901 1 19.77416496 3.73835932 24.99999993 0.900762534 1.204054572 0.523690969 0.116869273 12.04125769 1495523.27 0.029562538 0.049181671 5474.68732 -3.73835932 0.303292038 SEIDLFNIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEIDLFNIRK 10 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 99.283 0.0076982 826710000 2745700 1712650 2345100 2214770 2684200 2383000 3745300 3109700 3272400 FALSE TRUE 2615916.202 1887170.982 2452625.155 1992137.112 3152323.63 2300476.112 3173885.698 2837398.182 3779867.079 0.692065659 0.499269139 0.64886545 0.527038933 0.833977377 0.608612966 0.839681828 0.750660836 1 21.84990407 1.253663418 0.46579989 1.004069942 0.58100493 0.609080932 0.09554041 0.56146092 0.333670778 0.098676172 0.056819784 17.93343231 -1.253663418 -0.423065012 SEIDLLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 ; 133.23 0.00065763 32788000 161987 159265 134544 151050 152564 133432 154851 157616 151096 FALSE TRUE 154330.1955 175494.2846 140712.9755 135866.167 179171.1133 128811.2164 131225.6359 143814.3075 174527.196 0.884275913 1.005541191 0.806252428 0.778481349 1.02660856 0.738058133 0.751892192 0.824022334 1 17.41309234 2.214689479 24.9994327 0.799334129 0.903335875 0.075431423 0.104297149 379.6539192 397596.1489 0.036945082 0.027300112 163.9417169 -2.214689479 0.104001746 SEIDLLNIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEIDLLNIRR 10 1 E5RK69;H0YC77;P08133;P08133-2;E7EMC6;E5RFF0 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;; 206.49 2.40E-07 360954000 997650 427600 645840 973500 1578810 815860 1314890 785650 1208920 FALSE TRUE 950493.0617 471172.9261 675452.4028 875641.9305 1854153.964 787606.5636 1114279.381 716854.321 1396393.139 0.680677264 0.337421399 0.483712204 0.627074071 1.327816581 0.564029242 0.797969676 0.513361389 1 20.41327374 2.992727777 24.71754916 0.820269456 0.499364775 0.30277111 0.237954459 358.0180495 1216873.988 0.065920882 0.075820506 983.3945049 -2.992727777 -0.320904681 SELDMLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SELDMLDIR 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 ;;; 121.96 0.0013943 164813000 615780 492664 417954 827010 782490 526230 602000 486023 467539 FALSE TRUE 586673.2998 542867.0217 437117.6043 743877.3836 918956.0083 508006.5232 510153.8435 443464.2496 540042.5603 1.086346416 1.005230072 0.809413251 1.377442147 1.701636271 0.940678681 0.944654887 0.821165371 1 19.04271358 2.043619124 24.99990179 0.922505353 1.164906484 0.235714624 0.237594371 234.7161763 134524.4493 0.093695513 0.069198684 110.56537 -2.043619124 0.242401131 SELHLMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SELHLMDR 8 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 84.615 0.021884 74982000 141962 147171 116233 135502 131040 105629 120038 133920 99685 FALSE TRUE 135251.7376 162167.8922 121562.398 121881.0815 153893.3345 101971.0412 101723.9985 122193.2548 115143.6407 1.174634889 1.408396428 1.055745652 1.058513356 1.336533512 0.88559855 0.883453032 1.06122452 1 16.81307521 2.230227329 24.99930664 0.938732827 1.217735895 0.51403224 0.119513714 138.3423508 415014.4584 0.044922113 0.033726358 169.913282 -2.230227329 0.279003068 SELISS(ph)TFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SELISSTFK 9 0 H0YHG7;Q92730 H0YHG7 RND1 Rho-related GTP-binding protein Rho6 1 SELIS(0.046)S(0.477)T(0.477)FK 62.2 0.0883 796950000 231710 216750 235970 232240 597040 144160 266680 152770 556400 TRUE FALSE 220757.5275 238837.0714 246789.4579 208894.794 701163.587 139167.7031 225993.0681 139392.6489 642683.6703 0.343493289 0.371624615 0.383998333 0.325035167 1.090993313 0.216541527 0.351639661 0.216891537 1 19.29374929 -2.116987506 2.485340633 2.15532272 0.408512527 0.355578738 0.248494056 27806250.21 8142381.065 181329499.4 0.056078631 0.007638578 2.116987506 -1.746810193 SELKDFFQSYGNVVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SELKDFFQSYGNVVELR 17 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 129.2 3.14E-05 115960000 221700 239910 191460 255370 144540 230860 229450 242450 174870 FALSE TRUE 211220.6804 264357.1018 200238.6304 229699.7224 169747.7302 222865.2603 194443.1884 221219.7927 201987.9465 1.045709331 1.308776619 0.991339502 1.137195196 0.840385445 1.103359206 0.962647483 1.095212841 1 17.62390968 3.710814997 24.91384671 1.016525264 1.177243004 0.285879412 0.104206405 689.6927071 619301.2155 0.024965127 0.03868495 5138.247238 -3.710814997 0.16071774 SELKELLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SELKELLTR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ;;; 154.24 6.95E-05 6404016000 14688240 6846940 14747490 11167250 12440380 13959610 19669090 15082730 16441890 FALSE TRUE 13993956 7544650.97 15423677 10044696.81 14609978.33 13476185.21 16668209.07 13762006.2 18991614.33 0.73684921 0.397262225 0.812130909 0.528901685 0.769285753 0.709586082 0.877661519 0.724635935 1 24.17885921 1.62674027 0.435430582 0.991622031 0.571603451 0.431653961 0.126803388 0.780163408 0.397956105 0.130149481 0.096477679 42.33896817 -1.62674027 -0.420018581 SELLSQLQQHEEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SELLSQLQQHEEESR 15 0 Q92665 Q92665 MRPS31 "28S ribosomal protein S31, mitochondrial" 0 224.97 1.06E-12 131180000 164250 137160 156670 145030 153260 114010 150310 150240 149380 FALSE TRUE 156486.228 151136.7599 163853.4745 130451.3089 179988.4955 110061.8051 127377.4489 137084.1891 172545.0875 0.906929489 0.875926183 0.949627004 0.75604186 1.043138916 0.637872725 0.738227038 0.794483292 1 17.39661387 2.233091376 24.99999324 0.762589541 0.897377122 0.173091598 0.114519495 173.6435969 793719.6452 0.037155765 0.028228121 171.0375143 -2.233091376 0.134787582 SELNEIKENQRS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR 199.41 3.88E-09 4679420000 5405840 4235410 4823860 5512970 3979060 5235900 5854860 5809240 4488530 TRUE FALSE 5150316.657 4667003.094 5045038.752 4958795.782 4673006.804 5054579.47 4961593.575 5300552.149 5184588.308 0.993389706 0.900168503 0.973083773 0.956449285 0.901326494 0.97492398 0.956988922 1.02236703 1 22.305798 1.370230915 2.770316232 1.011445476 0.947182256 0.390439944 0.03065637 0.25426753 3.28267729 0.023926695 0.00746286 23.45475577 -1.370230915 -0.06426322 SELNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 161.58 0.019678 2285720000 2212430 2169020 1849718 2173990 2195870 1969780 2261690 2102230 2160970 FALSE TRUE 2107852.819 2390045.604 1934529.4 1955456.395 2578829.033 1901566.025 1916627.652 1918147.597 2496082.191 0.844464508 0.957518792 0.775026322 0.783410259 1.033150688 0.761820276 0.767854383 0.768463316 1 21.25123401 SELVAMLEEEELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SELVAMLEEEELRK 14 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;;;; 276.45 6.75E-33 485356000 633011 617450 594086 683281 436578 681885 678208 716439 487676 FALSE TRUE 603089.8245 680368.857 621325.4307 614596.2957 512717.065 658271.1515 574734.9135 653703.8031 563302.3034 1.070632626 1.207821898 1.103005308 1.09105944 0.910198772 1.168593041 1.020295692 1.160484875 1 19.10354985 3.278272642 3.197942994 1.056349847 1.140007853 0.146585111 0.081579551 0.396000484 8.301578086 0.021798671 0.029319141 1897.897014 -3.278272642 0.083658005 SEMIEKPLFDFSLITTGIQEPQTDET(ph)RNSPTQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEMIEKPLFDFSLITTGIQEPQTDETRNSPTQK 33 2 H3BSS6;Q9H2Y7;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 SEMIEKPLFDFSLITTGIQEPQT(0.082)DET(0.485)RNS(0.381)PT(0.052)QK 132.6 2.42E-06 48506000 70165 71536 67134 81863 41084 86831 80079 78222 44855 TRUE FALSE 66848.4395 78825.59973 70212.1603 73633.97571 48249.03659 83824.0207 67861.4778 71372.467 51810.88431 1.290239308 1.521410043 1.355162361 1.421206696 0.931252906 1.617884385 1.309791923 1.377557398 1 15.66096759 -1.62274564 2.237178689 0.948181169 1.361865381 0.276658195 0.178910856 2143206.998 1563171.45 642527.525 0.041309343 0.023837152 1.62274564 0.413684213 SEMIEKPLFDFSLITTGIQEPQTDETRNS(ph)PTQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEMIEKPLFDFSLITTGIQEPQTDETRNSPTQK 33 2 H3BSS6;Q9H2Y7;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 SEMIEKPLFDFSLITTGIQEPQT(0.002)DET(0.159)RNS(0.834)PT(0.004)QK 203.75 2.28E-27 50001000 75218 81426 65689 93888 53190 101770 89491 94813 57976 TRUE FALSE 71662.59421 89723.40197 68700.90563 84450.19986 62466.31916 98245.67938 75837.50434 86510.67108 66966.62198 1.070124072 1.339822725 1.025897732 1.261078988 0.932797822 1.467084295 1.132467222 1.291847618 1 16.03115458 2.246039317 24.99999752 1.231350547 1.151629932 0.067095724 0.16338988 528.4163836 1766406.067 0.05105791 0.041925043 176.2135565 -2.246039317 -0.079720615 SENFEELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SENFEELLK 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;; 138.66 0.00030332 211429000 421014 320248 328507 366863 308062 351454 427225 376198 294176 FALSE TRUE 401113.5026 352881.6353 343569.3709 329985.2342 361787.9153 339283.0599 362043.9797 343256.1088 339795.3116 1.18045626 1.038512373 1.011106861 0.97112945 1.064723093 0.99849247 1.065476678 1.010184947 1 18.37430642 4.480521648 1.931413084 1.021429063 1.191285172 0.751127294 0.029153602 0.211953597 1.224311762 0.007231685 0.053664907 30235.81278 -4.480521648 0.169856109 SENKAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SENKAPR 7 1 Q96KM6 Q96KM6 ZNF512B Zinc finger protein 512B 0 81.958 0.040908 0 39874 42392 41820 42324 40269 41585 41819 42538 44458 FALSE TRUE 37989.23504 46711.793 43737.48837 38069.51111 47291.90085 40144.90102 35438.74349 38813.14721 51352.31958 0.739776418 0.909633555 0.851713978 0.741339659 0.920930179 0.781754385 0.690109888 0.755820721 1 15.64814182 2.025344159 24.74747197 0.76964144 0.833098887 0 0.100348614 484.5984386 473186.8557 0.034141852 0.025214559 106.0093469 -2.025344159 0.063457447 SEPHS(ph)PGIPEIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEPHSPGIPEIFR 13 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 SEPHS(1)PGIPEIFR 76.158 0.018957 12554000 28500 20111 25069 27197 24113 21701 28530 28565 19336 TRUE FALSE 27152.86148 22160.33376 26218.43845 24463.10589 28318.29957 20949.48893 24177.22451 26063.69717 22334.52813 1.215734728 0.99220067 1.173897129 1.095304353 1.267915731 0.937986637 1.08250438 1.166968786 1 14.44698815 2.229264008 24.99998986 1.05268817 1.132383226 0.217516429 0.093063614 377.3809005 1014827.118 0.032816607 0.024571555 169.5368102 -2.229264008 0.079695056 SEPQPEEGS(ph)PAGGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SEPQPEEGSPAGGQK 15 0 F8WE91;Q9Y6K1;Q9Y6K1-3 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK 258.12 8.63E-25 231986000 230410 216160 219940 251020 158741 254040 280300 265720 198555 TRUE FALSE 219518.9759 238186.9498 230024.4666 225786.9927 186425.3801 245242.5311 237535.0869 242452.1481 229345.8953 0.957152408 1.038548998 1.002958724 0.984482379 0.812856842 1.069312929 1.035706728 1.057146228 1 17.80716556 SEPRPPISS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(0.001)EPRPPIS(0.311)S(0.688)PR 87.18 0.01005 0 317980 325240 302990 396430 359330 342910 387810 339640 363350 TRUE FALSE 302949.7156 358382.3258 316882.3912 356580.1032 421997.0382 331034.9407 328642.4619 309899.3211 419696.4623 0.72183052 0.853908379 0.755027549 0.84961427 1.005481523 0.788748466 0.783047968 0.738389167 1 18.67898678 -2.512156773 2.247756192 3.658404559 0.812344325 0.348289699 0.080815958 2875009.522 381759.5958 38826018.2 0.019997226 0.003074987 2.512156773 -2.846060234 SEPSDHS(ph)RHSPQQPSNGSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEPSDHSRHSPQQPSNGSLR 20 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.002)EPS(0.08)DHS(0.459)RHS(0.459)PQQPSNGSLR 73.981 0.0086182 34166000 21272 10686 16719 16425 27279 18327 25970 14155 3165.9 TRUE FALSE 20266.51472 11774.91555 17485.58269 14773.92779 32036.44896 17692.33139 22007.79953 12915.51316 3656.851603 5.542066487 3.219959908 4.781594822 4.040067632 8.760664211 4.838132174 6.018236975 3.531866907 1 11.83638637 SEPVKEES(ph)SELEQPFAQDTSSVGPDR ddPTM_SK-BR-3_Trastuzumab_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 SEPVKEES(0.861)S(0.139)ELEQPFAQDTSSVGPDR 256.05 7.74E-53 157820000 201590 172760 175610 215540 122790 213180 199590 212610 131010 TRUE FALSE 192061.2402 190364.4404 183661.8922 193873.5097 144204.5371 205797.5231 169138.8798 193992.7413 151326.3617 1.269185607 1.257972757 1.21368075 1.281161508 0.952937317 1.359958178 1.117709287 1.281949418 1 17.20730381 -5 0.155211756 0.238286927 1.27863718 0.260534959 0.112690194 168.609939 1.527849623 39.88894458 0.455388945 1.00E-05 5 1.040350253 SEPVKEESS(ph)ELEQPFAQDTSSVGPDR ddPTM_SK-BR-3_Trastuzumab_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 S(0.005)EPVKEES(0.44)S(0.554)ELEQPFAQDTSSVGPDR 76.259 0.01416 179130000 50280 49909 50218 53443 32255 48300 52090 51052 36431 TRUE FALSE 47903.36405 54994.78384 52520.54497 48070.8081 37880.26179 46627.35889 44142.7138 46581.61624 42080.53342 1.138373499 1.306893696 1.248095989 1.142352632 0.900184924 1.108050566 1.049005567 1.10696354 1 15.36086537 3.000528028 5.937124986 1.040783353 1.230632347 0.622397933 0.070817718 0.097788337 13.67987437 0.020146877 0.023074786 1001.21657 -3.000528028 0.189848994 SEPVKEESS(ph)ELEQPFAQDTSSVGPDRK ddPTM_SK-BR-3_Trastuzumab_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 1 SEPVKEES(0.395)S(0.605)ELEQPFAQDTSSVGPDRK;SEPVKEES(0.211)S(0.789)ELEQPFAQDTSSVGPDRK 220.78 1.41E-34 303310000 118132 112229 118102 137040 65814 141137 153570 163695 79691 TRUE FALSE 112548.1345 123665.2627 123517.0935 123264.4788 77291.94076 136249.3903 130140.076 149360.998 92049.07327 1.222697095 1.343471024 1.341861348 1.339117 0.8396819 1.480182097 1.413811909 1.622623593 1 16.49011558 SEPVKEESSELEQPFAQDT(ph)SSVGPDRK ddPTM_SK-BR-3_Trastuzumab_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(0.839)S(0.14)S(0.02)VGPDRK 202.75 1.94E-23 204550000 255430 224240 205800 248150 129240 267270 260400 270840 152160 TRUE FALSE 243356.3301 247090.3109 215236.1336 223205.4905 151779.4151 258014.3729 220671.1974 247123.8138 175756.1957 1.384624475 1.405869705 1.224628997 1.269972246 0.863579315 1.468024338 1.255552879 1.406060326 1 17.42321602 3.737024649 23.26777722 1.228381705 1.395247104 0.153367895 0.175418573 90.33946446 1368549.836 0.042949265 0.070703615 5457.888376 -3.737024649 0.1668654 SEPVKEESSELEQPFAQDTSS(ph)VGPDRK ddPTM_SK-BR-3_Trastuzumab_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 1 SEPVKEESSELEQPFAQDT(0.002)S(0.048)S(0.95)VGPDRK;SEPVKEESSELEQPFAQDT(0.001)S(0.168)S(0.83)VGPDRK 259.78 2.72E-53 399800000 489700 414490 450310 504400 262600 538420 561710 579320 288430 TRUE FALSE 466552.8515 456727.0022 470957.1589 453696.7537 308397.3569 519774.3804 476010.823 528591.6696 333158.2513 1.400394106 1.370901067 1.413613972 1.361805544 0.925678279 1.5601426 1.428782932 1.586608369 1 18.3458481 SEPVKEESSELEQPFAQDTSSVGPDR ddPTM_SK-BR-3_Trastuzumab_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 0 169.01 7.90E-12 60558000 64321 62247 65235 68819 43982 74053 71806 79516 52747 FALSE TRUE 61280.6738 68590.04007 68226.08928 61901.18337 51652.44687 71488.52604 60850.67589 72553.1575 60926.73537 1.005809247 1.125779014 1.119805433 1.015993767 0.847779658 1.173352316 0.998751624 1.190826278 1 15.89478782 -0.54628941 6.958873436 0.999998369 1.057325943 0.033020751 0.100872242 0 0 0.088830036 0.02093744 0.284256621 0.54628941 0.057327574 SEPVKEESSELEQPFAQDTSSVGPDRK ddPTM_SK-BR-3_Trastuzumab_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 0 205 1.83E-25 140570000 109670 91629 97699 112910 56955 121700 107290 129350 65419 FALSE TRUE 104486.1164 100966.0993 102178.5958 101560.0723 66887.93397 117485.4985 90920.93998 118023.4283 75563.84441 1.382752787 1.336169435 1.352215422 1.34402998 0.885184369 1.554784559 1.203233381 1.561903437 1 16.20540848 -1.483549455 2.957362507 0.990487342 1.321014557 0.227830193 0.189162104 19377622.46 24051289.46 1529646.586 0.04155298 0.032843584 1.483549455 0.330527215 SEPVS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_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(0.5)PS(0.5)R;SEPVS(0.999)PS(0.001)R;S(0.001)EPVS(0.918)PS(0.081)R;SEPVS(0.887)PS(0.113)R 168 0.00032453 2701990000 3288200 3482780 2735550 3682630 2693930 2962790 3012390 3078160 2680290 TRUE FALSE 3132773.303 3837679.242 2860977.673 3312445.036 3163750.539 2860187.839 2552794.579 2808619.992 3095935.684 1.011898703 1.23958623 0.924107593 1.069933414 1.021904478 0.923852473 0.824563182 0.907195846 1 21.56194407 2.336657296 2.16379278 0.88664821 1.079037675 0.36710899 0.089222582 0.263636079 2.530492446 0.037788706 0.02779341 217.0987365 -2.336657296 0.192389465 SEPVS(ph)PSRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(1)PSRER;SEPVS(0.999)PS(0.001)RER;SEPVS(1)PSRER;SEPVS(1)PSRER;SEPVS(1)PSRER;SEPVS(1)PSRER 177.83 1.38E-06 4054470000 2431110 2011150 2339940 2427450 2396450 2288250 2880380 2577380 3031010 TRUE FALSE 2316196.248 2216088.471 2447228.564 2183438.114 2814390.121 2209007.329 2440925.129 2351690.944 3501043.551 0.661573104 0.632979407 0.698999749 0.623653514 0.803871783 0.630956827 0.697199305 0.671711423 1 21.73935358 -5 0.332347052 4.340810036 0.662341695 0.791989734 0.051898349 145.1299511 1.246869995 342.8925 0.03842419 1.00E-05 5 -3.678468341 SERPPTILMTEEPSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SERPPTILMTEEPSSPK 17 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SERPPTILMTEEPS(0.089)S(0.91)PK 62.589 0.036714 76956000 138400 153110 144770 169430 93362 166650 175860 131950 66226 TRUE FALSE 131858.1063 168712.0831 151407.8477 152398.5745 109644.3032 160878.8687 149029.3271 120395.7585 76495.98984 1.723725735 2.20550232 1.979291307 1.992242663 1.433334002 2.103101993 1.948197904 1.573883268 1 16.2230965 0.938482534 2.916679201 1.001589585 1.92787282 0.656021667 0.211673947 0.17948761 3.627806324 0.19268795 0.050805732 8.679256711 -0.938482534 0.926283235 SES(ph)ELIDELSEDFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.003)ES(0.997)ELIDELSEDFDR;S(0.001)ES(0.999)ELIDELSEDFDR;S(0.015)ES(0.985)ELIDELSEDFDR;S(0.015)ES(0.985)ELIDELSEDFDR;S(0.013)ES(0.987)ELIDELSEDFDR 260.12 7.21E-25 87328000 204356 191413 172475 241519 192173 197916 205900 190034 170818 TRUE FALSE 194696.4969 210918.2023 180383.1494 217241.0513 225687.9104 191062.1193 174486.1734 173393.6155 197307.583 0.986766418 1.068981734 0.914223096 1.10102738 1.143837996 0.96834656 0.884335872 0.878798538 1 17.59008688 2.004330525 24.96520072 0.912730217 1.039684298 0.394139474 0.069589059 110.6000426 637598.4488 0.025130847 0.018484792 101.0021283 -2.004330525 0.126954081 SES(ph)ELIDELSEDFDRSECK ddPTM_SK-BR-3_Trastuzumab_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 1 S(0.001)ES(0.999)ELIDELSEDFDRSECK;S(0.038)ES(0.962)ELIDELSEDFDRSECK 161.68 1.76E-11 46091100 83669.8 63107.4 73766 84496.1 66247.7 82471.1 101366 93168 72239.8 TRUE FALSE 79714.89437 69538.11581 77148.24406 76002.3915 77801.27791 79615.10513 85900.75499 85009.71601 83442.37923 0.955328636 0.833366887 0.924569083 0.910836822 0.932395248 0.95413273 1.029461957 1.018783462 1 16.34849267 2.10353586 1.524483884 1.021280558 0.900205742 0.686030299 0.032175383 0.206660074 0.913070217 0.019459085 0.010245585 126.9216939 -2.10353586 -0.121074816 SES(ph)ENWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESENWR 7 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 1 SES(1)ENWR;SES(1)ENWR 118.67 0.005197 366290000 554340 409250 472750 768940 707720 587070 737690 465470 674610 TRUE FALSE 528137.4468 450953.0403 494426.0551 691644.6903 831146.1439 566739.6187 625141.8419 424710.9792 779225.0734 0.677772655 0.578719879 0.634509941 0.887605794 1.066631673 0.727311836 0.802260943 0.545042753 1 19.57168057 3.251078648 23.54783796 0.829536838 0.626050724 0.316124334 0.143666822 133.2515263 250658.0244 0.03860611 0.051857485 1782.701574 -3.251078648 -0.203486114 SES(ph)FSSEDLIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESFSSEDLIPSR 13 0 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 S(0.026)ES(0.972)FS(0.001)S(0.002)EDLIPSR 112.42 0.00034907 0 88814 65228 78598 89758 76463 83972 87380 77820 81733 TRUE FALSE 84615.93823 71874.80736 82201.79604 80735.35531 89798.12299 81064.02858 74048.57616 71005.66825 94407.73621 0.896281826 0.76132328 0.870710382 0.855177325 0.951173353 0.858658748 0.784348605 0.752117052 1 16.52661747 -2.438621818 2.258601349 2.579322712 0.838661832 0.395993738 0.061553804 4096940.265 368996.033 33280355.63 0.015640484 0.003642321 2.438621818 -1.74066088 SES(ph)LESPRGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESLESPRGER 11 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SES(1)LESPRGER;SES(1)LESPRGER 166.86 1.21E-05 315330000 397200 262830 377320 365840 391780 335900 495160 399360 463350 TRUE FALSE 378425.1432 289612.6758 394620.4952 329065.0681 460106.308 324267.6988 419614.2478 364389.9213 535203.9515 0.70706717 0.541125818 0.73732732 0.614840506 0.859684064 0.605876877 0.784026812 0.680843107 1 19.02972924 -5 0.168304504 2.236818398 0.606955563 0.542023892 0.090176558 89.17780928 0.837733129 36.69243126 0.29337901 1.00E-05 5 -1.629862836 SES(ph)LSNCSIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SESLSNCSIGK 11 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(1)LSNCSIGK;S(0.001)ES(0.999)LSNCSIGK;SES(0.994)LS(0.006)NCSIGK;SES(0.99)LS(0.01)NCSIGK;SES(1)LSNCSIGK;SES(0.998)LS(0.002)NCSIGK 251.91 2.37E-20 864437000 2176108 2061225 1892889 2366287 1474781 2132103 2251163 2217543 1606573 TRUE FALSE 2073247.687 2271266.171 1979679.833 2128423.335 1731982.339 2058267.738 1907706.739 2023363.179 1855712.136 1.117224837 1.22393238 1.066803302 1.146957707 0.933324898 1.109152491 1.028018679 1.090343238 1 20.8235415 3.270078884 1.75291645 1.042653601 1.165578315 0.360062608 0.064401239 0.315447993 1.999621046 0.018613307 0.026906848 1862.425392 -3.270078884 0.122924714 SES(ph)LSNCSIGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESLSNCSIGKK 12 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(1)LSNCSIGKK;SES(0.999)LS(0.001)NCSIGKK 188.47 5.61E-06 1832730000 1278820 830960 1236220 1171520 718670 1241770 1536580 1438390 969770 TRUE FALSE 1218372.713 915635.7687 1292901.91 1053756.584 844005.8205 1198767.194 1302146.5 1312436.946 1120156.979 1.087680331 0.817417368 1.154214931 0.940722242 0.753471019 1.070177856 1.162467872 1.171654483 1 20.09526949 2.013246789 24.97452824 1.126150332 0.950279838 0.271844917 0.123039926 258.2567943 486896.7203 0.043500237 0.032109757 103.0971806 -2.013246789 -0.175870494 SES(ph)PIPVAEQGTLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESPIPVAEQGTLMR 15 0 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SES(1)PIPVAEQGTLMR;SES(1)PIPVAEQGTLMR 241.8 9.22E-18 71681000 148560 130165 125759 167251 145885 140017 166475 146618 151509 TRUE FALSE 141537.8632 143428.9615 131525.1745 150438.6117 171327.2978 135168.1762 141076.1812 133779.3506 175004.2419 0.808768186 0.8195742 0.751554209 0.859628373 0.9789894 0.772370856 0.806130067 0.764434903 1 17.41703037 -2.000658186 2.903422902 1.18065244 0.820129527 0.435819321 0.064297354 8142021.066 17395794.56 9830237.428 0.015045533 0.009984856 2.000658186 -0.360522912 SES(ph)PKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;S(0.023)ES(0.977)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;SES(1)PKEPEQLR;S(0.004)ES(0.996)PKEPEQLR;SES(1)PKEPEQLR;S(0.013)ES(0.987)PKEPEQLR;S(0.012)ES(0.988)PKEPEQLR;S(0.003)ES(0.997)PKEPEQLR;S(0.011)ES(0.989)PKEPEQLR;S(0.058)ES(0.942)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR 205.26 8.00E-08 34885690000 45896510 39060200 36275730 47059740 21366070 44842810 43112470 44810000 21168060 TRUE FALSE 43727072.93 43040478.79 37939008.1 42329205.53 25092305.84 43289892.25 36534870.89 40886198.85 24450694.63 1.788377532 1.76029677 1.55165359 1.731206666 1.026241022 1.77049744 1.494226296 1.672189664 1 24.54337212 -2.823164331 0.126799776 6.71E-16 1.919431178 0.421231347 0.223200617 70.26227214 0.99555375 22.52789486 1.957670474 0.001502573 2.823164331 1.919431178 SES(ph)PKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(0.002)ES(0.998)PKEPEQLRK;S(0.067)ES(0.933)PKEPEQLRK;S(0.18)ES(0.82)PKEPEQLRK;S(0.355)ES(0.645)PKEPEQLRK;S(0.031)ES(0.969)PKEPEQLRK;S(0.007)ES(0.993)PKEPEQLRK;S(0.002)ES(0.998)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK;S(0.002)ES(0.998)PKEPEQLRK;S(0.02)ES(0.98)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK 147.07 5.14E-05 20316160000 7325790 5973813 5913654 7252320 2964469 7272560 7003220 7581240 3070015 TRUE FALSE 6979514.425 6582551.336 6184800.885 6523303.015 3481471.455 7020709.424 5934750.166 6917386.435 3546097.247 1.968224202 1.856280547 1.744114855 1.839572511 0.981775516 1.979841199 1.673600512 1.950704099 1 21.75780067 -2.043964513 2.729109351 0.003706654 1.755746009 0.397323903 0.289908389 417627506.6 355820853.5 2578691944 0.065754235 0.009037233 2.043964513 1.752039355 SES(ph)PPAELPSLR ddPTM_SK-BR-3_Trastuzumab_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 232.78 2.77E-13 796540000 977960 1050840 878090 1090940 838200 980140 943150 923630 778030 TRUE FALSE 931733.7689 1157921.791 918351.295 981276.6385 984381.8146 946197.506 799255.1454 842752.0607 898682.9188 1.036776987 1.288465338 1.02188578 1.091905296 1.095360548 1.052871359 0.889362787 0.937763524 1 19.77745266 1.979075501 2.9893352 0.933027429 1.120710851 0.477917215 0.077077325 0.200463252 3.414499897 0.038005091 0.021754459 95.29618188 -1.979075501 0.187683421 SES(ph)PPAELPSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESPPAELPSLRR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.044)ES(0.956)PPAELPSLRR;S(0.111)ES(0.889)PPAELPSLRR 67.707 0.032106 127820000 258850 187437 260350 228410 253960 238840 310490 272510 291440 TRUE FALSE 246614.6735 206537.0434 272287.305 205449.7928 298250.5436 230568.9109 263119.048 248647.5797 336635.0267 0.732587681 0.613534026 0.808850189 0.610304266 0.885975968 0.68492252 0.781615183 0.738626584 1 18.36082577 -5 0.175896659 2.114745456 0.664144061 0.519845581 0.082313351 92.96103288 0.887953224 36.07668252 0.234900701 1.00E-05 5 -1.450601395 SES(ph)PPPLSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SESPPPLSDPK 11 0 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 SES(1)PPPLSDPK;S(0.011)ES(0.989)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;S(0.389)ES(0.609)PPPLS(0.002)DPK 185.25 4.77E-06 2637160000 5149185 4248909 4384630 5205975 3010559 5038774 5345868 5250465 3327452 TRUE FALSE 4905793.23 4681877.658 4585669.622 4682660.502 3535599.536 4864279.993 4530257.653 4790706.45 3843456.262 1.276401472 1.218142562 1.193110916 1.218346244 0.919901072 1.265600455 1.178693692 1.246457908 1 21.87397282 -5 0.103267864 0.485126568 1.301605171 0.242959359 0.101716784 266.0312649 1.85565717 30.67714069 1.47882963 1.00E-05 5 0.816478603 SES(ph)VKSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESVKSR 7 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 S(0.002)ES(0.998)VKSR;S(0.006)ES(0.994)VKSR 100.48 0.0059139 306570000 536520 217610 571050 406310 385620 505540 738240 578070 650410 TRUE FALSE 511159.7629 239784.7064 597233.2073 365466.9469 452872.0059 488033.023 625607.9293 527451.1263 751272.261 0.680392169 0.319171516 0.79496241 0.48646405 0.602806771 0.649608735 0.832731304 0.702077201 1 19.51897631 1.349005955 0.512781532 0.997073898 0.523792866 0.495104336 0.132652387 0.615238339 0.42036124 0.130174503 0.072485976 22.3360285 -1.349005955 -0.473281032 SES(ph)WER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 S(0.004)ES(0.996)WER;S(0.001)ES(0.999)WER;S(0.003)ES(0.997)WER;SES(1)WER;SES(1)WER 127.46 0.017883 2407380000 1923120 1643980 1658050 1905250 1760600 1791070 1952980 1757610 1579980 TRUE FALSE 1832217.929 1811503.431 1734073.233 1713730.65 2067648.083 1729044.797 1655017.032 1603704.351 1824995.229 1.003957654 0.992607215 0.950179598 0.939032948 1.132960815 0.947424283 0.906861018 0.878744407 1 20.79946126 2.011735499 24.99997102 0.920425407 1.000481217 0.255735939 0.059800117 268.0441807 571008.4733 0.02105096 0.015535719 102.739039 -2.011735499 0.08005581 SESAPTLHPYSPLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 SESAPTLHPYSPLS(1)PK;SESAPTLHPYS(0.001)PLS(0.999)PK;SESAPTLHPYSPLS(1)PK 186.56 9.54E-10 880060000 1651230 1380530 1424270 1784470 1028680 1566170 1667260 1663690 918210 TRUE FALSE 1573179.63 1521207.577 1489574.188 1605091.685 1208081.466 1511933.14 1412888.866 1518008.484 1060601.317 1.483290285 1.434287844 1.404461944 1.513378929 1.139053334 1.425543336 1.332158317 1.431271543 1 20.01645101 -3.810283529 0.187687176 1.54E-12 1.482032794 0.606803627 0.101139209 52.60255262 0.76752599 20.46722335 0.267765927 0.000154781 3.810283529 1.482032794 SESELIDELS(ph)EDFDRSECK ddPTM_SK-BR-3_Trastuzumab_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 1 SESELIDELS(1)EDFDRSECK;SESELIDELS(1)EDFDRSECK 190.79 6.70E-15 56759000 118886 97492 113424 119418 79961 127141 146204 137870 95621 TRUE FALSE 113266.4944 107426.5456 118624.6026 107413.8758 93906.17308 122738.0753 123897.8946 125797.3719 110449.4163 1.025505595 0.972631176 1.074017469 0.972516464 0.850218826 1.111260515 1.121761424 1.138959137 1 16.75302627 SESELIDELSEDFDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 236.61 2.40E-17 99822400 155783 164769 135673 166923 126032 142911 140367 144857 126974.7 FALSE TRUE 148419.4463 181559.1484 141893.7412 150143.5829 148011.9409 137961.9562 118951.4361 132172.5531 146665.288 1.011960283 1.237914921 0.967466421 1.02371587 1.009181811 0.940658544 0.811040143 0.90118497 1 17.16216794 2.773380296 1.008164859 0.886136383 1.109913656 0.403127847 0.084002348 0.398834867 0.859456455 0.043955187 0.042051964 593.4447557 -2.773380296 0.223777272 SESELIDELSEDFDRSECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 265.22 1.95E-31 270212000 344609 256018 306414 326310 252859 317012 361688 366723 278056 FALSE TRUE 328320.0155 282106.5253 320463.385 293508.6989 296957.5295 306033.795 306505.8527 334610.79 321175.5044 1.022244882 0.878356293 0.997782772 0.913857672 0.924595822 0.952855342 0.954325123 1.041831601 1 18.29300234 1.309572322 6.106348856 1.020444095 0.946626792 0.33981534 0.041515601 0.195997499 12.18750922 0.026716818 0.009439703 20.39728301 -1.309572322 -0.073817303 SESGGLGVSMVEYVLSS(ph)SPADKLDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.096)S(0.451)S(0.451)PADKLDS(0.002)R;SESGGLGVSMVEYVLS(0.027)S(0.548)S(0.425)PADKLDS(0.001)R 105.55 0.0019287 66128000 75017 63203 67663 79508 45026 73086 84876 79795 53455 TRUE FALSE 71471.09508 69643.45756 70765.41548 71515.70478 52878.52014 70555.01349 71926.60735 72807.72678 61744.52839 1.157529209 1.127929217 1.146100186 1.158251697 0.856408196 1.142692565 1.164906579 1.179176984 1 15.91402367 1.176811726 0.010010393 7.09E-07 2.188223606 0.08352446 0.096331134 3846.96798 30.99834821 3415.342387 3355.580564 15.0249047 -1.176811726 2.188222897 SESGGLGVSMVEYVLSS(ph)SPGDSCLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPGDSCLRK 26 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.011)S(0.562)S(0.427)PGDS(0.001)CLRK;SESGGLGVSMVEYVLS(0.024)S(0.555)S(0.42)PGDS(0.001)CLRK 128.43 5.37E-05 97818000 110468 80263 103820 101193 80759 99592 134336 122689 97697 TRUE FALSE 105246.3966 88441.89095 108580.2497 91020.88739 94843.34403 96143.10407 113840.576 111945.7007 112847.3518 0.93264392 0.783730318 0.962186954 0.806584168 0.840456976 0.851974836 1.008801484 0.992009994 1 16.78401304 1.731110338 6.148592166 0.999662363 0.859812615 0.598980576 0.052835302 0.090510756 9.026402385 0.024387931 0.012634986 53.84065538 -1.731110338 -0.139849748 SESGGLGVSMVEYVLSSS(ph)PGDSCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.017)S(0.207)S(0.722)PGDS(0.054)CLR 60.472 0.047338 9093100 33848 29778 30926 35730 30736 29780 40764 36049 33984 TRUE FALSE 32248.07212 32812.41205 32343.98769 32138.35252 36096.34867 28748.71113 34544.70312 32892.35845 39254.06515 0.821521847 0.835898446 0.823965303 0.818726733 0.919556956 0.732375386 0.880028679 0.837935086 1 15.26055445 0.135737339 1.002419768 1.001164973 0.830878777 0.55124217 0.047285527 3.539761983 3.491815951 0.05032509 0.012492052 1.366901874 -0.135737339 -0.170286195 SESIRPDEFSLEIFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SESIRPDEFSLEIFER 16 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ;;; 225.01 6.63E-15 230705000 172925 156295 159683 169862 155132 151214 179150 164587 164709 FALSE TRUE 164751.178 172221.6382 167004.6235 152787.149 182186.9717 145977.4213 151817.3772 150174.8897 190251.2305 0.865966425 0.905232716 0.877811003 0.803081003 0.95761258 0.767287659 0.797983681 0.789350425 1 17.53754626 2.222046603 24.99998381 0.817319187 0.879892485 0.04453239 0.074395624 440.0467892 666167.3258 0.024518579 0.018159798 166.742613 -2.222046603 0.062573298 SESLIDASEDS(ph)QLEAAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SESLIDASEDSQLEAAIR 18 0 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 SESLIDAS(0.006)EDS(0.994)QLEAAIR;SESLIDAS(0.296)EDS(0.704)QLEAAIR;SESLIDASEDS(1)QLEAAIR;SESLIDASEDS(1)QLEAAIR 476.83 1.72E-239 543625000 679020 506459 594354 731947 683749 655915 845790 791650 991756 TRUE FALSE 646924.0703 558067.7479 621605.7188 658370.297 802994.6091 633200.4991 716749.2015 722328.9292 1145552.455 0.564726711 0.487160361 0.542625277 0.574718594 0.700967123 0.552746839 0.625679949 0.630550723 1 20.12761209 -5 0.196831924 2.913245852 0.504754753 0.882780866 0.048856402 42.35005234 0.4175803 31.73606398 0.117784444 1.00E-05 5 -2.408491099 SESPKEPEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 160.52 2.50E-05 13602680000 9174790 8081870 8731460 10872560 7697180 10886970 11798210 11331360 8728720 FALSE TRUE 8741115.859 8905421.741 9131806.078 9779629.612 9039565.755 10509951.5 9998176.376 10339126.05 10082325.32 0.866974193 0.883270621 0.905724204 0.96997759 0.896575489 1.042413448 0.991653816 1.025470387 1 23.26532507 2.879273985 0.703677479 1.019357565 0.864817672 0.72266355 0.032801832 0.322469079 0.352202139 0.020333508 0.023738024 757.3105122 -2.879273985 -0.154539893 SESPKEPEQLRK ddPTM_SK-BR-3_Trastuzumab_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 ; 96.059 0.0032045 1392240000 1378700 1072890 1263410 1426890 979330 1525730 1754450 1637680 1029280 FALSE TRUE 1313531.583 1182218.711 1321338.598 1283456.306 1150124.842 1472893.588 1486776.43 1494276.057 1188895.486 1.104833519 0.994384052 1.111400131 1.079536698 0.967389359 1.238875583 1.250552675 1.256860738 1 20.18119046 2.225049988 24.9979293 1.213191926 1.052563056 0.360153446 0.086264584 192.9484621 356998.8369 0.028781507 0.021372717 167.8997264 -2.225049988 -0.16062887 TIVAPMLESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIVAPMLESR 10 0 A0A3B3IT37;Q8IYK4 A0A3B3IT37 COLGALT2 Procollagen galactosyltransferase 2 0 89.296 0.041256 320780000 19784 20595 36675 174900 253960 269100 352950 308290 335200 FALSE TRUE 18848.84953 22693.65391 38356.58503 157318.7197 298250.5436 259780.9995 299100.9951 281294.4933 387181.104 0.048682256 0.058612504 0.099066263 0.406318175 0.770312757 0.670954747 0.772509278 0.726519167 1 18.56264902 2.999458468 1.946237881 0.773924436 0.049435915 0.936229849 0.086073233 0.065437928 0.50000114 0.025928147 0.030473111 998.7538543 -2.999458468 -0.724488521 down SESVEGFLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 SESVEGFLS(0.5)PS(0.5)R 170 4.44E-05 115040000 172240 147150 154210 167980 158670 155810 183890 173940 163840 TRUE FALSE 164098.5565 162144.7523 161280.681 151094.3313 186341.9978 150414.2606 155834.2031 158708.8915 189247.4704 0.867110964 0.856786894 0.852221066 0.798395513 0.984647231 0.794801961 0.823441406 0.838631508 1 17.52991449 -1.376387294 3.150475115 1.001612915 0.851076736 0.437794227 0.052697086 18967312.04 25045825.37 280259.7 0.011568373 0.04203516 1.376387294 -0.150536179 SESWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;;;; 122.51 0.044642 1696760000 1443040 1223280 1313000 1468540 1415180 1288280 1602580 1434510 1498680 FALSE TRUE 1374830.359 1347933.623 1373202.349 1320919.569 1661986.944 1243666.541 1358076.988 1308896.7 1731087.64 0.794200321 0.778662843 0.793259866 0.763057594 0.960082497 0.71843072 0.784522375 0.756112325 1 20.72324734 -1.086745966 4.23892592 1.000024129 0.792353522 0.512554823 0.063265103 0.519949312 32469294.02 1907.190107 0.013451508 0.081894368 1.086745966 -0.207670607 SETAPAETATPAPVEKS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK 202.15 7.20E-22 759440000 690160 703510 666230 831270 466760 821200 792910 868470 528740 TRUE FALSE 657537.5046 775198.4688 696777.3045 747709.1603 548162.7962 792761.6381 671937.0167 792422.1628 610734.2988 1.076634317 1.269289232 1.140884515 1.224278973 0.897547096 1.298046695 1.100211693 1.297490847 1 19.22018534 SETDLLDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SETDLLDIR 9 0 P50995;P50995-2;H0Y6E1 P50995 ANXA11 Annexin A11 0 ; 125.82 0.0011421 88328000 338180 305940 214807 397290 452220 251290 361140 267840 396700 FALSE TRUE 322194.9016 337115.6338 224656.1134 357353.6544 531087.0248 242587.7643 306041.4602 244386.5097 458218.2099 0.70314731 0.735709814 0.490281941 0.779876589 1.159026449 0.529415372 0.667894583 0.533340894 1 18.80567527 SETEDSILHQLFIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ;;; 212.87 6.56E-10 154386000 205068 191088 195272 229274 211722 193709 248392 231823 221328 FALSE TRUE 195374.842 210560.0844 204225.4144 206226.9419 248646.2498 187000.8088 210495.2384 211523.3491 255650.4159 0.764226576 0.823625042 0.7988464 0.806675558 0.972602563 0.731470779 0.82337139 0.82739294 1 17.96381285 -5 0.309954622 2.628004699 0.807097747 0.459900541 0.062068229 258.961754 2.345582789 275.3208314 0.054160816 1.00E-05 5 -1.820906952 SETELKDTYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SETELKDTYAR 11 1 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 208.79 1.67E-08 1862310000 4821420 4145900 4315680 5090010 3839050 4895290 5768550 5420040 4341970 FALSE TRUE 4593521.032 4568371.923 4513558.197 4578352.524 4508579.105 4725764.88 4888451.751 4945432.564 5015300.532 0.91590145 0.910886974 0.899957673 0.912877004 0.898964893 0.942269531 0.974707641 0.986069037 1 22.25790472 1.816089844 1.787434787 0.992477615 0.908491943 0.960748082 0.007337873 0.058169638 0.357025326 0.004853628 0.002088869 65.47716146 -1.816089844 -0.083985673 SEVELAAALSDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEVELAAALSDKR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ;; 224.42 2.27E-11 336729000 555140 444050 471870 569460 489440 513040 610180 571310 572290 FALSE TRUE 528899.6324 489299.1998 493505.7062 512216.7989 574798.181 495273.2962 517085.8343 521283.0677 661037.8103 0.800104962 0.740198506 0.746561995 0.774867626 0.869539037 0.749235957 0.78223337 0.788582831 1 19.33437327 -5 0.360491009 3.739783177 0.772481461 0.779362128 0.036595886 216.766257 1.72203747 460.9012579 0.025664861 1.00E-05 5 -2.967301716 SEVLSESSELLQQELEELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEVLSESSELLQQELEELRK 20 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 97.32 0.0015369 15518000 13894 15047 14358 14609 14003 13595 13365 15711 13804 FALSE TRUE 13237.25816 16580.30641 15016.3285 13140.47556 16445.11877 13124.20174 11325.92378 14335.26155 15944.65382 0.830200411 1.039866189 0.941778271 0.824130503 1.031387633 0.823109858 0.710327356 0.899063831 1 13.96078515 2.135615736 11.91592226 0.819960096 0.933971951 0.067231861 0.102356255 0.648294089 70.66000652 0.035812509 0.026449151 136.6519192 -2.135615736 0.114011855 SEVQQPVHPKPLS(ph)PDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.963)PDS(0.037)R;SEVQQPVHPKPLS(0.999)PDS(0.001)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR 215.08 3.46E-15 13110640000 14246050 12343770 12722130 14887910 9055090 13934730 15569150 15288100 9601340 TRUE FALSE 13572667.45 13601614.2 13305452.24 13391349 10634294.83 13452166.81 13193790.22 13949392.92 11090266.77 1.223835975 1.226446079 1.199741406 1.207486644 0.958885395 1.212970534 1.189672935 1.257804993 1 23.40279073 -2.062681673 2.632664104 0.727130681 1.18659149 0.33081991 0.082470093 27727823.12 21805149.44 45011596.07 0.019274887 0.008656022 2.062681673 0.45946081 SEVQQPVHPKPLSPDSR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 147.56 2.37E-07 2419690000 2292620 1976590 2081720 2291080 1842880 2099800 2579950 2421600 1893530 FALSE TRUE 2184252.396 2178006.768 2177168.921 2060776.286 2164277.689 2027083.399 2186331.243 2209551.866 2187168.962 0.998666511 0.995810935 0.995427861 0.942211746 0.989533834 0.926806952 0.999616985 1.010233734 1 21.06063324 1.527795735 12.36568591 1.005006319 0.978041541 0.235681612 0.023890268 0.189955991 38.29242793 0.012841683 0.005959882 33.71287072 -1.527795735 -0.026964779 SEWETLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SEWETLSR 8 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;; 178.83 0.00057589 237800000 303114 245848 264719 304802 307794 270460 323331 293762 345377 FALSE TRUE 288786.4019 270900.1907 276856.628 274162.7239 361473.1761 261093.9024 274000.9176 268038.6419 398936.3012 0.72389101 0.679056255 0.693987053 0.687234335 0.906092464 0.654475167 0.686828741 0.671883309 1 18.60579888 -1.260499915 3.560977277 1.000648697 0.710594285 0.617096793 0.07104394 19504315.5 31358607.29 143318.7713 0.016170347 0.054890866 1.260499915 -0.290054412 SEWLDPS(ph)QKSPLHVGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.68)QKS(0.32)PLHVGETR 135.54 4.97E-06 338620000 171860 166640 152150 177610 111840 191350 190610 179350 112380 TRUE FALSE 163736.5184 183620.8055 159126.228 159756.3054 131344.8606 184723.5015 161528.9437 163645.1632 129807.3164 1.261381276 1.414564375 1.225864862 1.230718805 1.011844819 1.423059243 1.244374725 1.2606775 1 16.98601218 -4.248971491 0.240051557 2.29E-15 1.298747645 0.332756397 0.113570855 132.3806543 1.837227113 64.80561483 0.174993894 5.64E-05 4.248971491 1.298747645 SEWLDPSQKS(ph)PLHVGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.001)QKS(0.999)PLHVGETR 162.72 2.11E-11 381270000 241360 199950 195110 264390 145120 233510 260830 240190 168140 TRUE FALSE 229951.3911 220325.1323 204055.9865 237813.0149 170428.8821 225423.4901 221035.593 219157.6903 194214.2925 1.184008593 1.134443452 1.050674407 1.224487713 0.877530072 1.16069465 1.13810158 1.128432349 1 17.56728985 7.882829295 0.012427194 3.67E-07 2.400394418 0.123502884 0.094455385 17328.1671 16.9519798 1364.684733 1959.282194 76353560.76 -7.882829295 2.400394051 SEWSDLLSDLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SEWSDLLSDLQK 12 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0;F8VX13;F8VZQ1 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 161.62 0.00049959 0 32464 29452 27074 29256 23069 27532 38215 29866 28739 FALSE TRUE 30929.49106 32453.19228 28315.36968 26315.1313 27092.2263 26578.55994 32384.59988 27250.77471 33195.69734 0.931731927 0.977632491 0.852983126 0.792727173 0.816136682 0.800662799 0.975566187 0.820912856 1 15.01870864 -0.965721402 7.282457 1.000000003 0.883421603 0.234976229 0.070028413 4.32E-09 5.19E-10 0.07246702 0.01708064 0.108212791 0.965721402 -0.116578401 SFAGAVSPQEEEEFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFAGAVSPQEEEEFRR 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 219.97 1.91E-14 646010000 224568 213089 207252 239684 224895 227030 276670 247861 269430 FALSE TRUE 213953.1157 234803.0114 216754.7092 215590.509 264116.6168 219167.8942 234458.9101 226156.9768 311211.8283 0.687483881 0.754479714 0.696486089 0.692745228 0.848671524 0.704240245 0.753374033 0.726697883 1 18.24753737 -5 0.311438285 3.387774911 0.720735537 0.762866512 0.046906622 134.3748225 1.213212069 210.6271137 0.039910885 1.00E-05 5 -2.667039373 SFAPILPHLAEEVFQHIPYIKEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFAPILPHLAEEVFQHIPYIKEPK 24 1 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 172.49 3.46E-12 55266000 50378 31932 45793 40780 38470 40479 54368 44451 26660 FALSE TRUE 47996.73178 35185.9071 47892.65435 36680.71692 45179.15582 39077.20208 46073.16306 40558.63479 30794.29664 1.558624064 1.142611163 1.555244301 1.191152938 1.467127382 1.268975309 1.496158967 1.317082681 1 14.91037556 0.967657397 22.76646097 0.999999996 1.375271525 0.404811242 0.144679343 1259.90556 886869.1978 0.121069696 0.030267424 9.282338396 -0.967657397 0.375271529 SFATASHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFATASHR 8 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 139.88 0.00065854 313989000 689670 569160 485900 519150 870430 450030 794290 597610 1010140 FALSE TRUE 657070.6659 627158.0511 508178.9956 466964.0557 1022232.716 434445.3483 673106.4724 545280.1003 1166787.352 0.563145174 0.537508441 0.435536942 0.400213505 0.876108842 0.37234321 0.576888729 0.4673346 1 20.15411022 -1.239504758 4.398462281 1.000211631 0.531629165 0.526219517 0.140535523 0.000258007 4.46E-05 0.120374615 0.028359888 0.057609651 1.239504758 -0.468582467 SFDFEIETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFDFEIETK 9 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 111.65 0.0048624 64878000 127522 119317 120773 147125 103003 132877 139462 139466 126889 FALSE TRUE 121494.2878 131475.538 126310.5615 132335.7155 120966.6906 128275.4362 118184.5105 127253.6177 146566.2981 0.828937412 0.897037994 0.861798129 0.902906857 0.825337695 0.875204176 0.806355295 0.868232461 1 17.16119388 -2.092423002 3.643953311 1.309748959 0.857365446 0.676525623 0.030803783 0.030741983 0.000779721 0.011828606 0.006733363 0.008083082 2.092423002 -0.452383513 SFDVNKPGCEVDDLKGGVAGGSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFDVNKPGCEVDDLKGGVAGGSILK 25 2 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 266.28 1.11E-45 689660000 797390 720190 703990 827850 398370 832150 904180 946720 485720 FALSE TRUE 759698.955 793578.1798 736268.6378 744632.9452 467845.6019 803332.4368 766230.7346 863820.1779 561042.9769 1.354083352 1.414469501 1.31232128 1.327229777 0.833885497 1.431855437 1.365725561 1.539668463 1 19.09775176 -1.489116621 2.943654987 0.989837206 1.325689595 0.229790144 0.185412891 17849534.21 21122639.94 1487580.56 0.043313174 0.032425253 1.489116621 0.335852389 SFDWGYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFDWGYEER 9 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;A0A0G2JI50 P18615 NELFE Negative elongation factor E 0 107.1 0.0065802 111760000 145400 127330 129590 137890 139110 123380 154380 141640 151400 FALSE TRUE 138527.2302 140305.0718 135531.8297 124029.0352 163370.74 119107.3197 130826.4956 129237.2507 174878.3388 0.79213487 0.802301033 0.775006388 0.709230406 0.934196546 0.681086752 0.748100059 0.739012342 1 17.41599208 -0.868329848 10.99895685 1 0.773463657 0.525378041 0.067911101 0 0 0.060031335 0.014149521 0.135416053 0.868329848 -0.226536343 SFDYNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 86.953 0.045825 103280000 93855 91881 94874 87502 119290 80911 99393 78922 107610 FALSE TRUE 89418.66015 101243.7784 99224.06674 78706.13272 140094.1382 78109.03178 84228.77237 72011.17129 124297.6092 0.719391634 0.814527158 0.79827816 0.633207133 1.127086346 0.628403332 0.677637912 0.579344782 1 16.92343902 SFEEEFGTASDKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFEEEFGTASDKER 14 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 110.98 0.00061822 80902000 77978 76688 92047 90425 90488 82610 107200 93350 97656 FALSE TRUE 74292.13448 84502.59439 96267.446 81335.3072 106269.0786 79749.19499 90844.67114 85175.77912 112799.9937 0.65861825 0.749136517 0.853434852 0.721057728 0.942101813 0.706996449 0.805360605 0.755104467 1 16.78340746 -5 0.128995267 1.715047431 0.676596953 0.45265773 0.07896966 129.5379689 1.057157683 24.37139944 0.572268841 1.00E-05 5 -1.038450477 SFEEKVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ;;; 190.15 8.51E-07 7062590000 12376200 9891680 11371020 10953220 6828970 11231010 12844400 14752000 9203560 FALSE TRUE 11791201.55 10899653.44 11892392.51 9852181.516 8019940.206 10842077.31 10884750.88 13460236.67 10630801.08 1.109154566 1.025289943 1.118673224 0.926758148 0.754406008 1.019873971 1.023888115 1.266154505 1 23.34174698 -1.549212577 7.077522158 0.999983587 1.025448417 0.003949784 0.132024533 3.33E-05 2.12E-06 0.124655132 0.02936256 0.028234976 1.549212577 0.02546483 SFELPPYTPPPILS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SFELPPYTPPPILS(1)PVR;SFELPPYT(0.012)PPPILS(0.988)PVR 144.29 5.43E-07 111620000 194358 225551 161590 248883 190032 189890 205660 217545 183355 TRUE FALSE 185171.0825 248534.9033 168999.0613 223864.808 223173.5206 183314.0617 174282.7898 198495.6065 211788.757 0.8743197 1.173503763 0.797960495 1.057019321 1.053755279 0.865551431 0.822908601 0.937233918 1 17.69226648 2.227368307 24.98869048 0.883366339 0.999718464 0.10669116 0.11220689 336.6405676 751600.5359 0.039059309 0.029111291 168.7983926 -2.227368307 0.116352125 SFEVEEVET(ph)PNSTPPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(0.044)FEVEEVET(0.874)PNS(0.041)T(0.041)PPRR 160.79 5.53E-09 0 43520 26780 33436 45520 63591 39039 50232 32044 59264 TRUE FALSE 41462.89585 29508.91245 34969.07367 40944.24312 74681.25027 37687.06964 42568.18583 29238.05748 68454.35844 0.605701328 0.431074268 0.510837797 0.598124707 1.09096414 0.550543026 0.621847707 0.427117544 1 16.06285478 2.995005493 24.58015806 0.707046979 0.516026702 0.201730803 0.199614108 307.8994042 1515323.031 0.055839735 0.064993482 988.5655983 -2.995005493 -0.191020277 SFEVEEVETPNST(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFEVEEVETPNSTPPR 16 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(0.314)FEVEEVET(0.164)PNS(0.119)T(0.403)PPR 124.81 0.00089935 522000000 75092 69633 78864 83511 86928 78050 95282 91180 99918 TRUE FALSE 71542.54998 76728.68187 82479.99241 75116.31562 102088.2157 75347.10893 80744.98093 83195.79582 115412.7731 0.61988416 0.664819671 0.714652202 0.650849239 0.884548676 0.65284896 0.699619104 0.720854318 1 16.81644338 -5 0.201251651 2.383806245 0.645970844 0.651912019 0.069935157 85.4471308 0.846139144 47.62144278 0.157085522 1.00E-05 5 -1.737835401 SFEVNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFEVNLR 7 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ; 134.85 0.0072917 511970000 950700 1039900 892390 941830 888500 867200 902160 899070 848580 FALSE TRUE 905762.2951 1145866.992 933306.9642 847155.459 1043454.119 837168.6466 764518.9227 820342.6645 980173.4525 0.924083684 1.169045121 0.952185516 0.864291373 1.064560682 0.854102551 0.779983299 0.83693622 1 19.90267755 2.682504531 0.996146193 0.846464451 1.0323365 0.183619614 0.10489175 0.612192506 1.271399633 0.05840079 0.050747589 481.398276 -2.682504531 0.185872049 SFEWLSQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFEWLSQMR 9 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 120.12 0.0016674 50842000 138070 114520 93081 93639 205210 86193 160570 103520 194490 FALSE TRUE 131543.7047 126189.7182 97348.85592 84226.22982 240998.559 83208.1148 136072.0974 94455.24001 224650.5159 0.585548198 0.561715684 0.433334664 0.37492115 1.072771002 0.370389155 0.605705698 0.420454142 1 17.77732285 -1.789967748 3.136220558 1.09702175 0.557823259 0.323302502 0.203087321 10374650.64 13183166.31 6650506.761 0.042502565 0.016219305 1.789967748 -0.539198491 SFFDNIS(ph)CDDNRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFFDNISCDDNRER 14 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 SFFDNIS(1)CDDNRER 56.215 0.076628 41343000 55788 45300 52153 75365 57505 73938 76501 60153 58844 TRUE FALSE 53151.0118 49916.1215 54544.26664 67789.16702 67533.85379 71377.50852 64829.36741 54885.68443 67969.22699 0.78198641 0.734392956 0.802484728 0.99735086 0.993594554 1.05014448 0.953804689 0.807507851 1 16.05259409 3.324232602 4.601927447 0.970916187 0.760156921 0.673321142 0.064055938 0.11284128 4.278321575 0.017779817 0.024138026 2109.757804 -3.324232602 -0.210759266 SFFDNISCDDNRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFFDNISCDDNRER 14 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 115.68 0.00036967 524164000 325221 235247 286898 288625 424680 270295 385379 311854 482380 FALSE TRUE 309848.4479 259218.9368 300052.5571 259611.8666 498744.0575 260934.6164 326582.3556 284546.4105 557185.0267 0.556096149 0.465229546 0.538515112 0.465934751 0.895113891 0.468308737 0.586129095 0.510685673 1 19.08779696 -5 0.335309688 5.62983366 0.539829335 0.540385026 0.126555891 277.9048204 2.369396575 919.5568763 0.095692454 1.00E-05 5 -5.090004325 SFFQAATEHLLPMGTALPLLEAQAATHTLVDPITGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFFQAATEHLLPMGTALPLLEAQAATHTLVDPITGQR 37 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 185.28 2.33E-23 101280000 59797 49354 52419 65056 61055 49742 69677 68181 45596 FALSE TRUE 56970.51432 54383.22871 54822.463 58516.44728 71702.97267 48019.42207 59046.49394 62210.71019 52666.79481 1.081715994 1.032590438 1.040930309 1.111069081 1.361445536 0.91175896 1.121133233 1.181213142 1 15.68460604 3.20651255 8.159863996 1.117955311 1.051926042 0.060439925 0.116022838 0.638622851 139.8973421 0.031557314 0.038231611 1608.838867 -3.20651255 -0.06602927 SFGEKS(ph)YLNVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFGEKSYLNVHR 12 1 Q6ZN11-3;Q6ZN11-2;Q6ZN11 Q6ZN11-3 ZNF793 Zinc finger protein 793 1 S(0.001)FGEKS(0.555)Y(0.445)LNVHR;S(0.001)FGEKS(0.555)Y(0.445)LNVHR 52.247 0.09059 2686860000 3179790 4376600 2551090 3566160 1392660 3233650 1983540 2703640 825470 TRUE FALSE 3029487.628 4822580.516 2668060 3207682.822 1635539.463 3121667.89 1680914.543 2466894.949 953479.6717 3.177296505 5.057874498 2.798234802 3.364185852 1.715337528 3.273974247 1.762926461 2.587254896 1 19.86284265 2.449931834 0.348566689 1.125187882 4.466716106 0.508587894 0.78537832 1.140396984 0.315811466 0.887692299 1.373326999 281.7940595 -2.449931834 3.341528224 SFGS(ph)PNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SFGSPNR 7 0 D6RAD4;P50613;D6REC6;D6R9G1 D6RAD4 CDK7 Cyclin-dependent kinase 7 1 S(0.001)FGS(0.999)PNR;S(0.003)FGS(0.997)PNR;S(0.018)FGS(0.982)PNR;S(0.001)FGS(0.999)PNR;S(0.075)FGS(0.925)PNR;S(0.011)FGS(0.989)PNR;S(0.381)FGS(0.619)PNR 92.051 0.016735 3728260000 4472010 3917160 3976680 4623230 4581310 4080470 4876930 4303530 4766230 TRUE FALSE 4260626.95 4316323.057 4159014.711 4158494.137 5380289.014 3939162.301 4132864.758 3926690.099 5505352.606 0.773906279 0.784022998 0.755449289 0.755354731 0.977283273 0.715514987 0.750699374 0.713249519 1 22.39240354 -2.202776327 2.402362699 1.681083848 0.778178642 0.468429023 0.074259497 17588555.93 4698018.002 64778509.89 0.017355234 0.006269367 2.202776327 -0.902905206 SFGTEDRPTDRPIPPRDEVFEYIIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFGTEDRPTDRPIPPRDEVFEYIIFR 26 3 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 216.14 1.76E-34 84328000 48436 44330 40849 49747 51588 45985 60370 43450 46927 FALSE TRUE 46146.52627 48847.2774 42721.96706 44746.33705 60584.93087 44392.52792 51159.44773 39645.28766 54204.19949 0.85134596 0.901171456 0.788167106 0.825514212 1.11771655 0.818986874 0.943828121 0.731406202 1 15.72611701 SFGTRPLS(ph)S(ph)GFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 S(0.143)FGT(0.135)RPLS(0.756)S(0.764)GFS(0.202)PEEAQQQDEEFEK 65.779 0.026227 37128000 47947 42973 41698 47884 31452 51709 58190 52220 38651 TRUE FALSE 45680.64033 47351.99756 43609.89454 43070.60935 36937.21884 49918.30436 49312.04677 47647.33996 44644.79968 1.023201821 1.060638594 0.976819134 0.964739671 0.827357701 1.118121365 1.104541786 1.067253976 1 15.44620452 SFGTRPLS(ph)SGFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.642)S(0.327)GFS(0.031)PEEAQQQDEEFEK;SFGTRPLS(0.827)S(0.173)GFS(0.001)PEEAQQQDEEFEK;SFGT(0.001)RPLS(0.616)S(0.371)GFS(0.012)PEEAQQQDEEFEK;SFGTRPLS(0.507)S(0.038)GFS(0.455)PEEAQQQDEEFEK;SFGT(0.003)RPLS(0.492)S(0.492)GFS(0.012)PEEAQQQDEEFEK 368.71 6.41E-120 2174080000 1397230 1264640 1292750 1452210 963828 1318140 1528380 1497110 1071326 TRUE FALSE 1331185.707 1393508.254 1352023.866 1306231.092 1131919.298 1272492.481 1295197.56 1366015.112 1237461.765 1.075738859 1.126102069 1.092578296 1.055572891 0.914710523 1.028308525 1.04665663 1.103884702 1 20.23895252 3.119377724 4.123866268 1.021328963 1.100893676 0.356893704 0.048177095 0.238206159 7.341456412 0.014237526 0.017332404 1316.369236 -3.119377724 0.079564713 SFGTRPLSS(ph)GFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.058)S(0.907)GFS(0.035)PEEAQQQDEEFEK;SFGTRPLS(0.337)S(0.57)GFS(0.093)PEEAQQQDEEFEK;SFGT(0.002)RPLS(0.33)S(0.612)GFS(0.056)PEEAQQQDEEFEK;S(0.001)FGT(0.003)RPLS(0.359)S(0.501)GFS(0.136)PEEAQQQDEEFEK 286.74 4.90E-54 5297210000 1036369 964918 989027 1095607 717616 1034286 1123879 1131915 810346 TRUE FALSE 987381.8913 1063244.241 1034374.866 985474.5028 842768.0032 998468.4165 952410.6171 1032798.522 936010.319 1.054883553 1.135932179 1.10508917 1.052845768 0.900383239 1.066728001 1.017521493 1.10340506 1 19.83616491 3.060491124 5.428164879 1.018468471 1.099123993 0.309697307 0.055044917 0.227110306 13.44114527 0.015340734 0.018337891 1149.452751 -3.060491124 0.080655521 SFGWETLDSFMQHDVQELCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFGWETLDSFMQHDVQELCR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 280.43 1.03E-44 220178000 278089 244473 269791 295899 302221 262935 346675 286041 281487 FALSE TRUE 264944.2841 269385.0766 282161.1842 266154.6703 354928.2467 253829.495 293783.3616 260993.7336 325138.5663 0.814865757 0.828523911 0.867818258 0.818588436 1.091621491 0.780680981 0.903563564 0.802715398 1 18.31069517 -5 0.070518397 1.381712119 0.7192374 0.170225782 0.089237617 529.392258 2.685368152 34.56528341 4.247094432 1.00E-05 5 -0.662474719 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 268.24 9.23E-46 6199200000 6004000 3058400 5304700 4368600 5056600 5767000 8400900 6413400 6465700 FALSE TRUE 5720202.819 3370054.437 5547925.742 3929460.028 5938469.439 5567287.344 7119188.412 5851808.696 7468367.734 0.765924098 0.451243773 0.74285653 0.5261471 0.795149576 0.745449011 0.953245564 0.78354587 1 22.83236154 2.229542484 1.260213728 0.913616389 0.614300811 0.526077536 0.113963732 0.321040003 0.985055041 0.065727266 0.037306328 169.6455547 -2.229542484 -0.299315578 SFKLS(ph)GFSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 S(0.001)FKLS(0.997)GFS(0.002)FK;SFKLS(1)GFSFK 125.28 0.00025029 385240000 999660 1375730 1086190 1508540 807770 1343910 1344270 1497390 911500 TRUE FALSE 952408.0529 1515918.451 1135992.886 1356898.693 948644.8323 1297370.06 1139176.922 1366270.593 1052850.765 0.904599289 1.439822719 1.078968572 1.288785399 0.901024973 1.232244971 1.081992777 1.297686851 1 20.00586953 SFLDDFESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFLDDFESK 9 0 Q8TF74;Q8TF74-2;A8MWR2;J3KSA3 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ;; 145.17 0.00022753 56082000 312865 280825 290045 327103 242475 307264 345643 336897 262457 FALSE TRUE 298076.4915 309441.3868 303343.8501 294221.985 284762.5632 296623.3706 292908.8122 307396.5127 303157.4911 0.983239736 1.020728156 1.000614727 0.970525201 0.939322206 0.978446449 0.966193549 1.013982902 1 18.20970795 3.264801569 7.670157111 0.973987735 1.003144596 0.188190026 0.021810679 0.236190745 52.48706181 0.005783495 0.00769373 1839.931137 -3.264801569 0.029156861 SFLDDPIWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFLDDPIWR 9 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 129.47 0.00090379 87373000 362810 427970 365530 446110 344380 337960 386000 409770 358500 FALSE TRUE 345660.6903 471580.6296 382289.9121 401266.1752 404439.763 326256.3605 327108.6106 373888.3665 414094.349 0.83473897 1.138824113 0.923195192 0.969021133 0.976685057 0.787879287 0.789937393 0.902906227 1 18.65959999 2.254347063 24.81635434 0.843639428 0.977525492 0.179587061 0.096254488 252.8662887 397506.1058 0.0316908 0.026428753 179.6168445 -2.254347063 0.133886064 SFLEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 94.662 0.032653 101690000 498940 569450 456690 572700 480240 439420 507090 511360 445360 FALSE TRUE 475356.095 627477.6024 477629.6882 515131.1079 563993.704 424202.7752 429724.1072 466582.6075 514424.1542 0.924054773 1.21976699 0.928474459 1.001374262 1.096359297 0.824616752 0.835349786 0.906999805 1 18.97259886 2.237269058 24.99994345 0.871541549 1.043061305 0.33726267 0.096819858 32.16287058 622537.8478 0.0335566 0.026157044 172.6907431 -2.237269058 0.171519756 SFLEDIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFLEDIRK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 119.27 0.0027669 2371570000 4063480 3431810 2841860 3358390 2876200 3318770 4399790 4025790 3108090 FALSE TRUE 3871407.353 3781515.341 2972162.092 3020798.257 3377808.369 3203840.163 3728521.228 3673270.486 3590076.723 1.078363403 1.053324381 0.827882611 0.84143 0.940873588 0.892415514 1.038563105 1.023173255 1 21.77558325 1.649702882 10.42930453 1.022927746 0.955170341 0.165516425 0.080896793 0.280198071 51.51564545 0.045461445 0.024403751 44.63781029 -1.649702882 -0.067757405 SFLEEVLASGLHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFLEEVLASGLHSR 14 0 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 232.37 1.92E-13 73776000 317300 240680 256380 290500 308400 228390 343280 295980 323780 FALSE TRUE 302301.8578 265205.5656 268135.2766 261298.3881 362184.8624 220480.797 290906.3312 270062.4221 373990.1488 0.808315029 0.709124469 0.716958127 0.698677195 0.968434232 0.589536376 0.777844904 0.722111058 1 18.51264074 -1.282829955 5.514376088 1.000027961 0.748055389 0.400769685 0.096498544 2.91E-05 3.79E-06 0.082040046 0.019334881 0.052139882 1.282829955 -0.251972572 SFLIWVNEEDHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SFLIWVNEEDHTR 13 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;;;;;;;;; 255.45 7.74E-24 3427917700 3692212 2883891.3 3010285.8 3472570.2 3603506.7 2553994.8 3515259 3123543.9 2811644.5 FALSE TRUE 3517688.456 3177763.102 3148310.382 3123500.846 4231957.128 2465549.32 2978941.677 2850029.837 3247659.969 1.083145554 0.978477775 0.96940887 0.961769667 1.303078884 0.759177175 0.917257874 0.877564112 1 21.63096916 2.192762409 24.99999986 0.881052396 1.041845283 0.352091889 0.11350428 141.8940605 77455.22322 0.039218334 0.028964728 155.8699547 -2.192762409 0.160792887 SFLKPGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFLKPGEK 8 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 70.1 0.047611 587630000 1165800 1003600 1100800 1325900 857070 1187600 1432400 1349600 1019300 FALSE TRUE 1110694.944 1105867.981 1151272.769 1192618.013 1006542.737 1146473.114 1213861.072 1231421.869 1177367.838 0.943371229 0.939271437 0.977836095 1.01295277 0.854909319 0.973759497 1.03099561 1.045910912 1 20.16713369 1.842385689 4.266853741 1.028061822 0.946892632 0.436636702 0.041061766 0.2008477 5.741919701 0.018942075 0.01053864 69.56418299 -1.842385689 -0.08116919 SFLSEPSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SFLSEPSSPGR 11 0 Q69YN4-3;Q69YN4;H0YC41 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPS(0.004)S(0.996)PGR;SFLSEPS(0.051)S(0.949)PGR 196.58 6.29E-08 2635620000 3529640 3167160 3257250 3747730 3427920 3469780 3984730 3637880 3871370 TRUE FALSE 3362800.912 3489897.205 3406598.134 3371001.06 4025748.163 3349620.649 3376786.254 3319327.942 4471722.287 0.752014704 0.780436928 0.761808967 0.753848482 0.900267929 0.749067235 0.755142211 0.742292953 1 22.09239916 -1.048831241 4.90786369 1.000004856 0.773815561 0.704221816 0.045955307 2.31E-06 4.47E-07 0.042011479 0.009901988 0.089365267 1.048831241 -0.226189295 SFLVIVDGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFLVIVDGSPK 11 0 Q9H116;Q9H116-4 Q9H116 GZF1 GDNF-inducible zinc finger protein 1 1 SFLVIVDGS(1)PK;SFLVIVDGS(1)PK 126.09 0.00033021 34103000 150330 168410 148262 166838 103120 150588 157183 166885 113765 TRUE FALSE 143224.1988 185571.1705 155059.9594 150067.1273 121104.0954 145373.0998 133201.8465 152271.6647 131407.0952 1.08992744 1.412185318 1.179996857 1.142001709 0.921594798 1.106280446 1.013657948 1.158778105 1 17.00368365 3.167971277 2.755871353 1.044137125 1.252767617 0.413361791 0.101090998 0.221624327 3.423673237 0.028861657 0.036822505 1472.215133 -3.167971277 0.208630492 SFPAAIEHTIQWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFPAAIEHTIQWAR 14 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 204.28 1.39E-08 219770000 360270 303930 305230 359030 366730 318910 396330 376840 389160 FALSE TRUE 343240.7511 334900.8125 319225.0974 322939.6223 430687.5959 307866.0667 335862.5794 343841.8918 449508.9452 0.76359048 0.745037037 0.71016406 0.718427577 0.958129088 0.684894194 0.747176631 0.764927807 1 18.7779903 -1.995734719 2.15764923 1.236013814 0.758925994 0.504595623 0.074213773 3329783.614 1198356.051 3907180.791 0.016876387 0.010098696 1.995734719 -0.477087819 SFPIKPVPS(ph)PSWSGSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.979)PS(0.02)WS(0.001)GSCR 140.48 3.99E-07 642130000 555910 513570 481710 625970 403720 551580 580200 551370 422370 TRUE FALSE 529633.236 565903.3669 503796.88 563046.3063 474128.6402 532478.6463 491679.8339 503089.1198 487868.9824 1.08560547 1.159949469 1.0326479 1.154093264 0.971836 1.091437795 1.007811219 1.031197182 1 18.89613424 2.742642352 24.99830209 1.02575174 1.110033086 0.467500444 0.046253357 296.5099423 1815961.509 0.0128549 0.013190243 552.8946044 -2.742642352 0.084281345 SFPIKPVPSPS(ph)WSGSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.398)PS(0.601)WS(0.002)GSCR 119.41 7.35E-05 575940000 1149800 921570 937510 1118200 811670 1018000 1099900 996600 810830 TRUE FALSE 1095451.233 1015479.031 980495.7608 1005796.412 953224.991 982746.4047 932090.054 909332.4207 936569.3753 1.16964238 1.084253935 1.046901369 1.073915546 1.017783643 1.049304441 0.99521731 0.97091838 1 19.83702634 8 0.255273188 0.981264721 2.254237538 0.871775209 0.020209169 14.30274835 0.196438559 0.023653519 7.874159836 99999999.92 -8 1.272972817 SFQAERPALNVVIFPLLHEGLTDVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFQAERPALNVVIFPLLHEGLTDVIR 26 1 Q96ME1-4 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 93.552 0.0052456 33296000 33127 28128 31797 29148 30552 27168 38631 33467 28949 FALSE TRUE 31561.15236 30994.27518 33254.9239 26217.98766 35880.25913 26227.16535 32737.13144 30536.45206 33438.26307 0.943863391 0.926910441 0.994517085 0.784071458 1.073029991 0.784345924 0.979032056 0.913218847 1 15.02921229 -1.057345263 6.024736239 1.000000155 0.926142869 0.066876232 0.088078514 1.52E-07 2.37E-08 0.070744376 0.016674574 0.087630388 1.057345263 -0.073857285 SFQSLACS(ph)PGLPAADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;SFQS(0.001)LACS(0.999)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR 297.5 1.01E-45 3042223000 2611297 2143447 2355522 2627801 2626789 2230558 2754611 2367698 2663644 TRUE FALSE 2487866.166 2361866.686 2463525.014 2363649.451 3084900.17 2153313.217 2334344.5 2160369.811 3076708.308 0.808612945 0.767660256 0.800701518 0.768239695 1.002662541 0.699875647 0.758714921 0.7021692 1 21.55295624 -2.286126668 2.338467115 1.990118772 0.787897816 0.385001107 0.08397214 4231142.255 861512.198 22074346.93 0.019317147 0.005174559 2.286126668 -1.202220956 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFREPAPAEALPQQYPEPAPAALCGPPPRAPSR 33 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R;SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 172.57 7.39E-15 586180000 206070 120111 196646 174583 209210 165799 221980 189160 257210 TRUE FALSE 196329.4795 132350.4475 205662.4136 157033.5852 245696.1578 160057.3391 188112.8741 172596.1476 297096.8132 0.660826609 0.445479189 0.692240389 0.528560315 0.826990216 0.538737987 0.633170286 0.58094244 1 18.1805736 -5 0.351058532 5.574255184 0.593334455 0.570745666 0.104594442 296.9801043 2.425323381 1023.035807 0.071944258 1.00E-05 5 -4.980920729 SFS(ph)ASQSTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SFSASQSTDR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 SFS(0.988)AS(0.012)QSTDR;SFS(0.986)AS(0.014)QSTDR;SFS(0.996)AS(0.003)QSTDR;S(0.001)FS(0.989)AS(0.01)QSTDR;S(0.001)FS(0.995)AS(0.004)QSTDR 190.66 9.20E-07 544260000 865973 814016 761105 954060 747185 871896 932542 875815 844954 TRUE FALSE 825040.1725 896965.1559 796002.4171 858156.0762 877493.8274 841702.0229 790265.5906 799123.9956 975985.1509 0.845340907 0.919035659 0.815588656 0.879271652 0.899085223 0.862412735 0.80971067 0.818787043 1 19.89649967 1.99939222 24.75278103 0.85028241 0.874129722 0 0.059605176 77.32889794 3149382.621 0.02019555 0.01474813 99.86015143 -1.99939222 0.023847312 SFS(ph)EDTLMDGPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.01)FS(0.989)EDTLMDGPAR 79.089 0.010484 0 169440 157340 157280 177730 154740 156230 186330 185410 177740 TRUE FALSE 161430.907 173373.1249 164491.4436 159864.2427 181726.607 150819.7159 157901.9363 169174.5175 205303.0114 0.786305597 0.844474339 0.801213009 0.778674612 0.88516289 0.734620086 0.769116513 0.824023556 1 17.64739526 0.958659861 21.160278 1.000000001 0.800545013 0.698647612 0.040967927 587.5686319 300752.808 0.038175147 0.009543787 9.09200908 -0.958659861 -0.199454987 SFS(ph)LDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;S(0.004)FS(0.996)LDIK;S(0.015)FS(0.985)LDIK 100.02 0.010598 194477000 1056620 933780 998690 1298100 778670 1280250 1295410 1173510 791090 TRUE FALSE 1006675.667 1028933.244 1044480.924 1167612.522 914469.8015 1235914.621 1097771.413 1070751.243 913768.1969 1.101675097 1.126033109 1.143048016 1.277799474 1.000767815 1.352547206 1.201367498 1.17179745 1 19.80146871 3.468106476 24.7805087 1.186112216 1.117301827 0.021038809 0.108451489 436.7495856 1200564.674 0.026979671 0.036581983 2938.369963 -3.468106476 -0.06881039 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_SK-BR-3_Trastuzumab_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(0.005)FS(0.989)LEGLT(0.006)GGAGVGNKPSSSLEVSSANAEELRHPFSGEER 263.81 1.21E-63 115410000 40953 40674 47487 41462 38837 44682 47005 46377 32529 TRUE FALSE 39017.23285 44818.72684 49664.32592 37294.16099 45610.1605 43134.65114 39833.52394 42315.98402 37573.43118 1.038426133 1.192830291 1.321793734 0.992567349 1.213893942 1.148009372 1.060151354 1.126220914 1 15.19742525 0.925438371 0.731379416 1.002956738 1.150601941 0.1906686 0.093163589 1.32069666 1.565957678 0.0861415 0.032688932 8.422448632 -0.925438371 0.147645202 SFS(ph)LGDLSHSPQTAQHVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSLGDLSHSPQTAQHVER 19 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 S(0.131)FS(0.869)LGDLSHSPQTAQHVER;S(0.151)FS(0.849)LGDLSHSPQTAQHVER 252.13 1.28E-30 453210000 296110 211361 242461 269653 276220 238443 292622 245980 132242 TRUE FALSE 282113.4671 232898.9262 253578.0767 242546.9681 324392.6805 230185.6591 247977.1395 224440.6872 152749.414 1.846903761 1.524712404 1.660091977 1.58787495 2.123691817 1.50694954 1.62342449 1.469339105 1 17.22080732 0.773898637 1.093096296 1.001319101 1.706606174 0.617401645 0.17622924 0.534271729 1.170679434 0.15594675 0.049266045 5.941534693 -0.773898637 0.705287073 SFS(ph)LSWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFSLSWR 7 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7;A0A3B3IS41 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.014)FS(0.91)LS(0.077)WR;S(0.001)FS(0.999)LSWR;SFS(0.986)LS(0.013)WR;S(0.001)FS(0.766)LS(0.233)WR 158.61 0.0014833 179279000 390288 263927 345052 393554 451143 356064 457248 360588 468140 TRUE FALSE 371839.8597 290821.4614 360872.9755 353993.2042 529822.1964 343733.4144 387486.4197 329013.0031 540736.7603 0.687654118 0.53782447 0.667372744 0.654649786 0.979815384 0.635676062 0.71658975 0.608453183 1 19.04456691 2.978060574 24.66632897 0.760052837 0.624334835 0.228209876 0.133148594 1010.743214 1136372.227 0.037457858 0.040065473 950.7373898 -2.978060574 -0.135718002 SFS(ph)MQDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSMQDLR 8 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 1 S(0.012)FS(0.988)MQDLR;S(0.001)FS(0.999)MQDLR 141.08 0.00067049 81153000 297330 296410 304650 447230 429790 393360 417080 315800 399360 TRUE FALSE 283275.8002 326614.516 318618.5038 402273.5907 504745.2399 379737.8446 353446.7858 288146.8778 461290.7092 0.614093877 0.708044861 0.690710863 0.872060899 1.094202051 0.823207225 0.76621267 0.624653547 1 18.81531671 3.282050423 5.703738303 0.853985696 0.668509691 0.336553001 0.127096248 0.232649704 17.95748966 0.036266354 0.048530622 1914.478187 -3.282050423 -0.185476005 SFS(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.121)FS(0.879)PEER;S(0.094)FS(0.906)PEER;S(0.028)FS(0.972)PEER;S(0.022)FS(0.978)PEER;S(0.033)FS(0.967)PEER;S(0.001)FS(0.999)PEER 137.84 0.0029827 2145760000 2606330 2076140 2202980 2574480 2421100 2257440 2615800 2372830 2463350 TRUE FALSE 2483133.946 2287701.026 2303988.812 2315688.379 2843339.073 2179264.287 2216711.668 2165052.426 2845353.737 0.8726978 0.804012871 0.809737215 0.81384903 0.999291946 0.765902762 0.77906365 0.760908002 1 21.44017659 -0.238192159 7.578326952 0.999999998 0.824811542 0.384852644 0.06925258 0 0 0.064790461 0.015271258 0.577840319 0.238192159 -0.175188456 SFS(ph)PLQPGQAPTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSPLQPGQAPTGR 14 0 Q7Z3C6;H7C152;Q7Z3C6-2;H7C1G6 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 S(0.108)FS(0.892)PLQPGQAPTGR;SFS(1)PLQPGQAPTGR 186.72 7.24E-08 60102000 178086 158215 178422 212730 222951 187815 223402 185135 273810 TRUE FALSE 169668.2277 174337.2884 186602.8252 191345.9762 261833.5838 181310.9195 189317.9218 168923.5979 316271.0564 0.536464606 0.551227451 0.590009175 0.605006283 0.82787716 0.573276991 0.59859389 0.534110202 1 18.27080201 -2.273608465 2.314613251 2.724723785 0.59876671 0.688712413 0.084049579 5488042.429 651989.7289 49774951.49 0.020346736 0.005325882 2.273608465 -2.125957075 SFS(ph)PTMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSPTMK 7 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 SFS(0.995)PT(0.005)MK;SFS(0.995)PT(0.005)MK 136.99 0.0030699 435410000 876870 807410 787350 1048910 680450 943730 1010950 1076260 776380 TRUE FALSE 835422.0929 889685.9969 823450.7763 943471.574 799120.2646 911048.3935 856711.0101 982016.9688 896777.0452 0.931582825 0.992092741 0.918233557 1.052069273 0.891102497 1.015914043 0.955322189 1.095051411 1 19.77438982 1.255352948 24.99877498 1.047525719 0.966457956 0.302468305 0.051955169 225.1127403 335128.2755 0.029526455 0.010719107 18.00333439 -1.255352948 -0.081067763 SFS(ph)SQRPGMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 SFS(0.5)S(0.5)QRPGMER;S(0.041)FS(0.834)S(0.125)QRPGMER 85.672 0.039568 535080000 698720 525470 582740 691750 701120 555160 710010 689130 750810 TRUE FALSE 665692.8903 579015.9904 609459.2054 622213.9758 823395.106 535934.67 601684.9343 628786.1239 867241.7802 0.767597809 0.667652324 0.702755817 0.7174631 0.949441234 0.617976073 0.693791452 0.725041319 1 19.72607474 -0.968775034 4.594564187 1.000004942 0.724844802 0.484940701 0.087222604 0.032000272 50344129.89 601.2780129 0.019242362 0.107454589 0.968775034 -0.27516014 SFS(ph)SQRPVDR ddPTM_SK-BR-3_Trastuzumab_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(0.065)FS(0.919)S(0.016)QRPVDR;S(0.261)FS(0.722)S(0.017)QRPVDR 126.83 0.00022537 1337050000 1286580 1060080 1050280 1227220 1277000 1145320 1371990 1293760 1385750 TRUE FALSE 1225765.913 1168103.357 1098436.377 1103857.514 1499708.396 1105657.281 1162667.727 1180471.516 1600645.033 0.765794969 0.729770395 0.686246079 0.689632924 0.936940024 0.690757325 0.726374495 0.737497379 1 20.61022197 -0.951017558 4.913694311 1.00000092 0.743745366 0.54866618 0.072563001 8649518.681 1760288.639 168.1034918 0.015818696 0.111939263 0.951017558 -0.256255555 SFSEFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSEFGK 7 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 130.77 0.0082156 116243000 396980 336000 326520 393620 340020 358800 435410 386050 375890 FALSE TRUE 378215.5421 370238.782 341491.265 354052.5698 399319.3803 346374.666 368980.2076 352245.4154 434181.1014 0.871100886 0.852728921 0.786518031 0.815449057 0.919706959 0.797765414 0.849830189 0.811286844 1 18.72793741 -1.459798651 2.809915406 1.00483843 0.840456806 0.6299798 0.038967698 7108821.561 7614370.78 268487.5005 0.008702313 0.034689764 1.459798651 -0.164381623 SFSERFPEDGPELEEILTQLATADAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFSERFPEDGPELEEILTQLATADAR 26 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 150.18 1.29E-07 127275000 70522.4 64053.7 72325 74986.6 88779 77090 101660 88013.1 98260 FALSE TRUE 67188.94591 70580.84485 75641.17279 67448.8045 104262.0295 74420.35397 86149.89989 80306.20638 113497.659 0.591985302 0.621870491 0.666455797 0.594274852 0.918627137 0.655699462 0.759045611 0.707558263 1 16.79230301 -5 0.0852068 2.040539614 0.393797984 0.614544322 0.084879242 139.7219385 0.83495482 26.81614969 2.159097495 1.00E-05 5 -1.64674163 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.028)FS(0.028)KEELMS(0.472)S(0.472)DLEETAGSTSIPK;SFSKEELMS(0.501)S(0.498)DLEETAGSTSIPK;S(0.053)FS(0.046)KEELMS(0.451)S(0.451)DLEETAGSTSIPK 200.62 3.64E-24 2537740000 762340 562720 703590 754520 542903 720900 844220 808450 645190 TRUE FALSE 726305.699 620061.8078 735850.2974 678674.2161 637585.1113 695935.0522 715418.7338 737657.8321 745242.77 0.974589393 0.8320266 0.987396761 0.910675344 0.85554015 0.933836704 0.959980778 0.989822192 1 19.50735095 1.607048965 2.106385821 0.994129466 0.909803667 0.338349294 0.046636889 0.315011871 3.002316153 0.03353061 0.012355639 40.46215088 -1.607048965 -0.084325799 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.002)FS(0.008)KEELMS(0.205)S(0.785)DLEETAGSTSIPK;S(0.104)FS(0.104)KEELMS(0.359)S(0.432)DLEET(0.001)AGSTSIPK;SFSKEELMS(0.324)S(0.676)DLEETAGSTSIPK;SFSKEELMS(0.125)S(0.875)DLEETAGSTSIPK;SFS(0.001)KEELMS(0.077)S(0.921)DLEETAGSTSIPK;SFS(0.006)KEELMS(0.17)S(0.824)DLEETAGSTSIPK;SFSKEELMS(0.111)S(0.888)DLEETAGSTSIPK;S(0.237)FS(0.198)KEELMS(0.218)S(0.347)DLEETAGSTSIPK 252.77 2.70E-43 4855375000 5635099 4394324 5234267 5679018 3762883 5523448 6629931 6226455 4491999 TRUE FALSE 5368739.038 4842110.612 5474263.319 5108152.321 4419128.604 5332169.611 5618413.259 5681233.592 5188595.263 1.03471918 0.933221877 1.055056917 0.9844962 0.851700389 1.02767114 1.082838991 1.094946378 1 22.30691257 2.006371528 24.99919396 1.065163375 0.973567181 0.31169042 0.060022742 175.6789534 689287.2331 0.02151014 0.015847016 101.4779132 -2.006371528 -0.091596195 SFSKEELMSS(ph)DLEETAGSTSIPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SFSKEELMSSDLEETAGSTSIPKR 24 2 O00567 O00567 NOP56 Nucleolar protein 56 1 SFSKEELMS(0.037)S(0.963)DLEETAGSTSIPKR;SFSKEELMS(0.002)S(0.998)DLEETAGSTSIPKR;SFSKEELMS(0.004)S(0.996)DLEETAGSTSIPKR;SFSKEELMS(0.429)S(0.571)DLEETAGSTSIPKR 250.24 9.67E-39 1061990000 1239810 728840 1301550 1022280 962640 1170630 1642930 1366040 1305470 TRUE FALSE 1181206.638 803109.6246 1361227.355 919518.4722 1130524.111 1130090.79 1392270.854 1246422.296 1507915.62 0.783337358 0.532595865 0.902721171 0.609794381 0.749726375 0.74943901 0.923308198 0.826586235 1 20.52412427 1.626710483 0.742553329 0.983119242 0.685554924 0.43740019 0.105437319 0.501285117 0.562137692 0.088815365 0.040198527 42.33606439 -1.626710483 -0.297564317 SFSLASSSNS(ph)PISQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR 400.08 2.01E-115 497650000 705150 686890 696410 769750 690200 667650 802520 759040 821530 TRUE FALSE 671818.957 756884.8719 728341.0873 692373.2676 810570.6615 644529.1131 680080.8347 692574.4337 948928.6766 0.707976241 0.797620401 0.767540391 0.729636784 0.854195559 0.679217658 0.716682772 0.729848777 1 19.85594013 -1.248407584 3.478006181 1.000611114 0.747746544 0.718884216 0.049555499 10790375.34 16808475.27 70714.72111 0.011258706 0.056440703 1.248407584 -0.25286457 SFSSQRPVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 0 68.355 0.054924 68766000 115930 87426 130680 119320 157740 111320 159960 123840 176800 FALSE TRUE 110450.2187 96334.8088 136671.8073 107325.7269 185249.8061 107464.9605 135555.1641 112995.9131 204217.241 0.540846689 0.471727109 0.669247154 0.525546846 0.907121285 0.526228637 0.663779236 0.553312309 1 17.63974515 -5 0.169473926 2.515689157 0.505127677 0.495070454 0.123762478 104.7828372 0.987047799 53.66742303 0.415720064 1.00E-05 5 -2.01056148 EVSTYIKK ddPTM_SK-BR-3_Trastuzumab_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 ; 99.802 0.01051 6072300000 10122700 6719400 13295900 14445400 14307600 14893400 21584900 18827600 18388800 FALSE TRUE 9644220.032 7404114.499 13905530.17 12993320.95 16802840.91 14377637.82 18291727.07 17178955.53 21240441.19 0.454049892 0.348585721 0.654672379 0.611725568 0.791077773 0.676899208 0.861174535 0.80878525 1 24.3403104 3.065271104 0.344882157 0.985665463 0.245918763 0.831467183 0.078551535 0.739045698 0.156742358 0.083216479 0.206731996 1162.173862 -3.065271104 -0.739746699 down SFYGSTLFLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SFYGSTLFLCR 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 ; 260.06 2.93E-20 878360000 575840 316560 103392 121846 644300 160490 597610 333730 506630 FALSE TRUE 548621.1844 348817.8239 108132.6255 109597.8086 756665.716 154932.1911 506433.6186 304506.832 585195.5929 0.93750054 0.59607049 0.184780314 0.187284064 1.293013353 0.264752833 0.865409147 0.520350522 1 19.15855938 2.806805705 24.99976716 0.743985514 0.53138407 0.154025349 0.344649793 471.3306332 172657.8017 0.102764194 0.108997875 640.9227755 -2.806805705 -0.212601444 SGAGSS(ph)PETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGAGSS(1)PETK;SGAGSS(1)PETK;SGAGS(0.001)S(0.999)PETK;SGAGS(0.002)S(0.998)PETK;SGAGS(0.019)S(0.981)PETK;SGAGS(0.001)S(0.999)PETK;SGAGS(0.263)S(0.737)PETK;S(0.001)GAGS(0.416)S(0.584)PETK;S(0.001)GAGS(0.163)S(0.837)PETK 291.93 4.06E-32 5590217000 9882120 9555000 9309860 11261020 5183960 9861350 10122340 13381360 7376700 TRUE FALSE 9415011.772 10528665.36 9736726.29 10129040.88 6088040.983 9519848.977 8577991.123 12209617.18 8520640.961 1.104965203 1.235665886 1.142722283 1.188765132 0.714505048 1.117269114 1.006730733 1.432945859 1 23.02253053 SGAHSS(ph)ASPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 S(0.001)GAHS(0.117)S(0.653)AS(0.228)PPR 61.212 0.057161 107760000 79574 68699 84595 87867 63710 87435 108780 95619 60817 TRUE FALSE 75812.69472 75699.5062 88473.76443 79034.44222 74821.00383 84407.10403 92183.61312 87246.09345 70248.18975 1.079212076 1.07760081 1.259445471 1.125074433 1.065095116 1.201555575 1.312256066 1.241969277 1 16.10017343 2.082043796 6.769661652 1.228543983 1.118410041 0.05058866 0.097431138 0.311826612 21.13730184 0.034506344 0.025361779 120.7935643 -2.082043796 -0.110133942 SGAHSSAS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHSSAS(1)PPR;SGAHSS(0.003)AS(0.997)PPR;SGAHS(0.001)S(0.04)AS(0.959)PPR;SGAHS(0.001)S(0.092)AS(0.907)PPR 159.77 2.97E-05 844360000 283383 212780 268666 297380 367548 247742 400177 306489 393786 TRUE FALSE 269988.0472 234462.5239 280984.6018 267486.7974 431648.2548 239162.6324 339122.6489 279651.1984 454852.3217 0.593572978 0.515469555 0.617749077 0.588073941 0.948985493 0.525802818 0.74556649 0.614817568 1 18.79503869 -5 0.12486253 2.184987768 0.47283342 0.468087099 0.122484609 121.2831782 0.969098399 36.21265085 0.953680838 1.00E-05 5 -1.712154348 SGAHSSAS(ph)PPRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGAHSSASPPRSR 13 1 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 2 S(0.007)GAHS(0.008)S(0.008)AS(0.977)PPRS(1)R 52.862 0.084942 24821000 36234 27768 32279 44373 43038 30836 43814 39503 46150 TRUE FALSE 34521.29063 30597.59077 33759.02408 39912.54174 50543.81357 29768.14159 37129.3696 36043.9079 53306.7063 0.647597517 0.573991396 0.63329788 0.748733968 0.948169885 0.558431456 0.696523424 0.676160851 1 15.70202942 -5 0.21127148 2.53488275 0.631152112 0.45079632 0.108787963 138.0477654 1.376412308 90.08828774 0.227692969 1.00E-05 5 -1.903730639 SGAHVDFYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGAHVDFYDK 10 0 P35270 P35270 SPR Sepiapterin reductase 0 ;;;; 129.7 0.0002961 1445495000 4676090 3301820 3602480 4042210 3564640 3532520 4923190 4370610 3569630 FALSE TRUE 4455060.493 3638279.212 3767657.271 3635879.371 4186312.087 3410187.947 4172066.945 3987896.218 4123189.989 1.080488773 0.882394268 0.913772414 0.881812233 1.015309044 0.827075142 1.01185416 0.967187112 1 21.97532951 1.60867237 24.99999997 0.992142451 0.937875709 0.130385215 0.07186995 0.198358189 5550.615186 0.033960103 0.017435403 40.61368256 -1.60867237 -0.054266742 SGAQASS(ph)TPLS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 SGAQAS(0.214)S(0.447)T(0.339)PLS(0.999)PT(0.001)R 106.6 0.0013632 367590000 498830 498130 540680 572750 488310 492080 636570 620190 678270 TRUE FALSE 475251.2945 548890.0133 565470.7128 515176.0818 573471.1094 475039.1462 539449.5551 565882.8758 783452.6475 0.606611384 0.700603942 0.721767569 0.657571435 0.731979286 0.606340597 0.688554129 0.722293654 1 19.57948655 0.656538139 2.03163026 0.99993209 0.671865723 0.854870941 0.041996079 0.597013586 3.089941233 0.037692656 0.010369057 4.534591184 -0.656538139 -0.328066367 SGAQASS(ph)TPLSPTR ddPTM_SK-BR-3_Trastuzumab_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(0.228)S(0.644)T(0.128)PLSPTR 134.97 3.74E-05 198990000 252590 215470 233130 249150 249430 240140 301250 254700 249710 TRUE FALSE 240650.5713 237426.638 243819.2411 224104.9686 292930.513 231823.8916 255288.7797 232397.1178 288433.7515 0.834335684 0.823158305 0.845321464 0.776972069 1.015590275 0.80373358 0.885086362 0.805720955 1 18.13788047 -4.999999999 0.235746161 1.828074908 0.832880083 0.330187101 0.0664877 184.0045516 1.837640437 73.06957487 0.096910077 1.00E-05 4.999999999 -0.995194825 SGAQASST(ph)PLS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 SGAQAS(0.002)S(0.125)T(0.873)PLS(1)PTR;SGAQASS(0.052)T(0.948)PLS(0.984)PT(0.016)R;SGAQASS(0.393)T(0.606)PLS(0.999)PT(0.001)R;SGAQAS(0.01)S(0.41)T(0.58)PLS(0.999)PT(0.001)R;SGAQAS(0.003)S(0.386)T(0.612)PLS(0.957)PT(0.043)R 250.6 1.02E-17 3956840000 3579600 3640410 3969290 4134690 3690470 3726360 4615200 4188950 4665340 TRUE FALSE 3410399.402 4011371.918 4151285.873 3719063.106 4334086.8 3597315.219 3911066.476 3822143.331 5388817.1 0.632866052 0.744388211 0.770351971 0.690144616 0.804274244 0.667551923 0.725774582 0.70927316 1 22.36153719 -1.65008686 2.378951166 1.04160537 0.717036271 0.765876273 0.048983297 2110635.496 1614490.323 535289.3485 0.011950984 0.022382734 1.65008686 -0.3245691 SGAQASST(ph)PLSPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQAS(0.02)S(0.086)T(0.894)PLSPTR;SGAQAS(0.01)S(0.429)T(0.561)PLSPTR 229.92 1.23E-11 874410000 861500 724830 811740 905270 805860 812150 991080 846110 810280 TRUE FALSE 820778.6023 798691.0011 848959.0819 814270.5397 946401.7289 784025.0419 839872.5436 772020.1229 935934.0841 0.876961974 0.853362448 0.907071445 0.870008426 1.011184169 0.837692585 0.897362921 0.824865913 1 19.8360474 SGAQASSTPLS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQASSTPLS(0.997)PT(0.003)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.999)PT(0.001)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.98)PT(0.019)R;SGAQASSTPLS(0.994)PT(0.006)R;SGAQASSTPLS(0.973)PT(0.027)R;SGAQASSTPLS(0.892)PT(0.108)R;SGAQASSTPLS(0.988)PT(0.012)R;SGAQASSTPLS(0.993)PT(0.007)R 242.86 1.75E-17 24271600000 5154790 4127580 4381770 5040780 4584480 4682250 5445530 4884210 4904500 TRUE FALSE 4911133.293 4548185.095 4582678.489 4534071.218 5384011.86 4520102.508 4614714.384 4456522.68 5665064.811 0.866915641 0.802847848 0.808936639 0.80035646 0.950388396 0.797890697 0.814591631 0.786667554 1 22.43366103 -1.037079373 4.589513677 1.000006535 0.828365446 0.55380028 0.048357454 3.02E-06 6.33E-07 0.043697542 0.010299217 0.091816477 1.037079373 -0.17164109 SGAQASSTPLSPT(ph)R ddPTM_SK-BR-3_Trastuzumab_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 SGAQASSTPLS(0.272)PT(0.728)R 213.71 7.37E-09 4611800000 884600 694500 737700 868580 725920 784440 933460 809490 757740 TRUE FALSE 842786.7111 765270.3396 771524.2747 781268.6882 852520.2182 757274.6461 791043.5328 738606.7642 875246.4492 0.962913602 0.874348408 0.88149375 0.892627087 0.974034478 0.865213046 0.903795192 0.843884331 1 19.73932978 4.671621644 3.502452501 0.900218121 0.966255285 0.121162422 0.048201892 0.462670171 9.411846384 0.010287726 0.071520868 46948.49168 -4.671621644 0.066037164 SGAVQGAGSLGPGS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGAVQGAGSLGPGSPVR 17 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SGAVQGAGSLGPGS(1)PVR 121.44 0.00053443 0 42441 39932 39193 48626 31653 42616 47703 47367 41354 TRUE FALSE 40434.89804 44001.1162 40990.03782 43738.0221 37173.27318 41140.19723 40425.03122 43219.29437 47766.96711 0.846503358 0.921162026 0.858125192 0.915654159 0.77822134 0.861268775 0.846296796 0.90479461 1 15.54372566 0.913106981 4.181630234 0.999958351 0.864372189 0.554490773 0.039431565 0.310203485 12.50472823 0.036167711 0.009222564 8.186664284 -0.913106981 -0.135586161 SGCSEAQPPES(ph)PETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGCSEAQPPESPETR 15 0 Q9Y6A5;A0A494BZT8;A0A494C117;H0Y8F2 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 SGCSEAQPPES(1)PETR;SGCSEAQPPES(0.994)PET(0.006)R;SGCSEAQPPES(0.998)PET(0.002)R;SGCSEAQPPES(1)PETR 326.38 1.80E-58 430568000 362403 338017 345902 406105 369225 349373 404758 354078 397961 TRUE FALSE 345272.9284 372461.3166 361761.9488 365282.5539 433617.7231 337274.1254 343004.7332 323073.0532 459674.7594 0.751124401 0.810271413 0.78699546 0.794654365 0.94331419 0.733723396 0.746190053 0.702829656 1 18.81025392 -2.198271359 2.490367268 1.67278484 0.784205447 0.523836042 0.064826242 7960029.32 2619326.116 29952975.82 0.016152473 0.006334738 2.198271359 -0.888579392 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ;;;;; 284.06 5.14E-62 1410080000 2420271 2102366 2253305 2566040 2094670 2296050 2783990 2496080 2343597 FALSE TRUE 2305869.586 2316599.486 2356621.263 2308096.784 2459979.785 2216537.213 2359241.194 2277510.003 2707030.053 0.851807901 0.855771617 0.870556003 0.852630646 0.908737523 0.818807759 0.871523828 0.841331628 1 21.36827947 -0.970011869 5.076665378 1.000000832 0.858982687 0.786841005 0.023080745 1.88E-07 3.81E-08 0.019310531 0.004551509 0.107149002 0.970011869 -0.141018145 SGDEGS(ph)EDEAPS(ph)GED ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGDEGSEDEAPSGED 15 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 SGDEGS(1)EDEAPS(1)GED;SGDEGS(1)EDEAPS(1)GED 136.6 3.19E-05 0 506380 475260 449720 534460 353580 464420 458870 408280 323560 TRUE FALSE 482444.4209 523689.5343 470340.1068 480735.0654 415244.2401 448337.0189 388860.9538 372528.8388 373736.0323 1.290869435 1.401228378 1.2584821 1.286295738 1.111062901 1.199608762 1.04046953 0.99676993 1 18.51166014 2.346683051 0.689073644 0.986394846 1.351486969 0.853576316 0.052456461 0.227829465 0.213561329 0.040274526 0.028582235 222.1687908 -2.346683051 0.365092122 SGDET(ph)PGSEVPGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SGDET(1)PGSEVPGDK;S(0.044)GDET(0.956)PGSEVPGDK 277.82 4.19E-32 741190000 1335940 1741640 1101450 1613800 615870 1451410 1069770 1433820 500850 TRUE FALSE 1272792.764 1919115.096 1151952.572 1451577.758 723277.533 1401147.308 906556.9388 1308267.12 578519.26 2.200087105 3.317288168 1.99120868 2.509126071 1.250222046 2.42195447 1.567029832 2.261406335 1 19.14200546 1.923264309 0.156735262 0.484331701 3.462128199 0.385092531 0.522821121 4.270960403 0.582950201 4.147818611 5.278191842 83.80391518 -1.923264309 2.977796499 SGDET(ph)PGSEVPGDKAAEEQGDDQDSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGDETPGSEVPGDKAAEEQGDDQDSEK 27 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.07)GDET(0.893)PGS(0.037)EVPGDKAAEEQGDDQDSEK 232.37 1.85E-35 224470000 316970 278780 302610 280300 107490 340100 306320 362090 114840 TRUE FALSE 301987.4563 307187.9989 316484.9678 252123.7115 126236.222 328322.2517 259585.258 330383.48 132648.8007 2.276593944 2.315799294 2.385886387 1.900685948 0.951657469 2.475124163 1.956936337 2.490663152 1 17.01725211 3.208578206 7.913822252 1.857169116 2.31687117 0.186418645 0.51162252 0.371437103 80.81086042 0.13825651 0.167966254 1616.509293 -3.208578206 0.459702055 SGDGVVTVDDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGDGVVTVDDLR 12 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;; 206.49 2.08E-07 1405747000 1867790 1526430 1560080 1838680 1607730 1627390 1883770 1793700 1756720 FALSE TRUE 1779503.268 1681974.952 1631611.211 1653852.393 1888117.603 1571033.076 1596366.289 1636634.119 2029143.166 0.876972753 0.828908961 0.80408876 0.815049633 0.930499945 0.774234713 0.786719398 0.806564143 1 20.95243923 SGDWMIDYVSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGDWMIDYVSNR 12 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 122.77 0.00047567 0 97249 88295 87333 99640 102400 92521 110870 104130 113510 FALSE TRUE 92652.2325 97292.36088 91337.30443 89623.9979 120258.5276 89316.97457 93954.74523 95011.82517 131112.5511 0.706661809 0.74205223 0.696632807 0.683565358 0.917215984 0.68122368 0.716596119 0.724658504 1 17.00044627 -1.069525477 4.021545357 1.000045862 0.732112215 0.603100266 0.067914545 27749337.78 73305176.42 20040.12686 0.015106522 0.085206852 1.069525477 -0.267933647 SGEHDFGAAFDGDGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGEHDFGAAFDGDGDR 16 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;; 144.33 1.33E-06 653910000 698940 716580 594310 786910 529030 631490 681550 663280 477773 FALSE TRUE 665902.4914 789600.3167 621559.7014 707808.3118 621292.6645 609621.343 577567.03 605199.6869 551863.5967 1.206643264 1.430788915 1.126292267 1.282578369 1.125808385 1.10465946 1.0465757 1.096647234 1 19.0739522 2.649782346 0.844475337 1.038244408 1.306167467 0.587203453 0.079653435 0.368334592 0.551974209 0.048771855 0.041638413 446.4597848 -2.649782346 0.267923059 SGEHDFGAAFDGDGDRNMILGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGEHDFGAAFDGDGDRNMILGK 22 1 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;; 210.38 6.14E-23 591775000 1013480 647296 906770 921680 787730 903060 1253770 1093210 863000 FALSE TRUE 965574.8089 713256.1983 948346.3014 829030.9753 925109.8626 871786.8058 1062484.359 997482.7369 996829.6324 0.968645772 0.715524675 0.95136247 0.831667668 0.928052129 0.874559481 1.065863539 1.000655182 1 19.92698743 1.765241301 10.14219175 1.024367154 0.86934631 0.45987695 0.073051312 0.174322386 59.91958522 0.032347807 0.017832743 58.2426734 -1.765241301 -0.155020844 SGES(ph)S(ph)SQLSQEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGESSSQLSQEQK 13 0 Q6ZMI0-4;Q6ZMI0-3;Q6ZMI0-5;Q6ZMI0-2;Q6ZMI0 Q6ZMI0-4 PPP1R21 Protein phosphatase 1 regulatory subunit 21 2 S(0.28)GES(0.54)S(0.581)S(0.502)QLS(0.097)QEQK 76.24 0.042699 145540000 221210 264660 264550 282450 620860 226370 420550 278480 809460 TRUE FALSE 210753.8417 291629.1549 276679.8792 254057.5894 729137.7874 218530.7501 356387.3736 254094.8149 934986.9227 0.225408331 0.311907202 0.295918448 0.271723147 0.779837418 0.233725996 0.381168298 0.271762961 1 19.83458666 -5 0.325284913 7.410188795 0.315910141 0.615289244 0.161607669 221.1421273 1.933724002 978.6251834 0.130879858 1.00E-05 5 -7.094278653 SGESS(ph)S(ph)QLSQEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGESSSQLSQEQK 13 0 Q6ZMI0-4;Q6ZMI0-3;Q6ZMI0-5;Q6ZMI0-2;Q6ZMI0 Q6ZMI0-4 PPP1R21 Protein phosphatase 1 regulatory subunit 21 2 S(0.123)GES(0.365)S(0.53)S(0.742)QLS(0.24)QEQK 103.46 0.0023518 148720000 230070 239120 292190 292500 614620 229990 362350 275060 768410 TRUE FALSE 219195.0471 263486.5999 305587.2005 263097.3443 721809.5334 222025.3886 307066.8525 250974.2882 887571.0983 0.246960551 0.296862528 0.344296024 0.296423965 0.813241367 0.250149412 0.345963104 0.282765278 1 19.75950316 -1.910022992 2.403867316 1.393109925 0.353016344 0.59779315 0.165009589 16312462.99 8225219.588 36168545.72 0.040287626 0.012302036 1.910022992 -1.040093581 SGETDPGRKS(ph)PSRPILDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGETDPGRKSPSRPILDGK 19 3 O60890 O60890 OPHN1 Oligophrenin-1 1 SGET(0.001)DPGRKS(0.94)PS(0.059)RPILDGK 80.412 0.040528 428980000 470010 338080 382020 446480 218750 442690 441830 461840 215290 TRUE FALSE 447793.5588 372530.7364 399535.9949 401598.9821 256899.9307 427359.5343 374420.7187 421398.8412 248676.0737 1.800710266 1.49805621 1.606652337 1.614948219 1.03307056 1.718539014 1.505656388 1.694569305 1 17.92390818 -2.124129323 2.037554956 3.40E-05 1.558578283 0.415469007 0.208385265 2240294.473 542104.2956 10355950.46 0.048997178 0.007513991 2.124129323 1.558544234 SGEWTEDEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SGEWTEDEVLR 11 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;;;; 280.2 5.68E-27 1735740000 2514813 2313798 2083789 2599152 2058147 2212186 2473333 2394960 1985880 FALSE TRUE 2395942.773 2549576.647 2179332.787 2337880.303 2417087.185 2135577.444 2095980.625 2185244.606 2293840.128 1.044511666 1.11148838 0.950080505 1.019199322 1.053729576 0.931005356 0.913743116 0.952657763 1 21.12933341 2.971964302 0.753508395 0.941032923 1.073758521 0.353913173 0.049793789 0.579625287 0.733743278 0.030931113 0.039152654 937.4849443 -2.971964302 0.132725597 SGEWTEDEVLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGEWTEDEVLRR 12 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;;; 283.43 5.24E-28 4329256000 4211240 2997860 3662140 3768410 3700770 3617150 4493830 4061790 4109320 FALSE TRUE 4012183.031 3303345.342 3830052.741 3389602.267 4346183.116 3491887.189 3808213.699 3706118.135 4746572.358 0.845280073 0.695943324 0.806909166 0.71411579 0.915646658 0.735665007 0.802308152 0.780798828 1 22.17845465 -4.999999996 0.366493765 3.790795004 0.777682471 0.519087842 0.064206914 380.5075168 2.968198538 839.7942239 0.040327653 1.00E-05 4.999999996 -3.013112534 SGFEPASLKEEVGEEAIVELVENGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 244.67 1.56E-45 241349000 517625 433092 416514 556272 297430 534954 553546 606769 286174 FALSE TRUE 493157.8921 477224.5672 435611.5789 500354.4817 349301.6978 516428.4088 469092.3911 553637.0897 330552.4023 1.49192046 1.443718345 1.317829112 1.513691863 1.056721099 1.562319333 1.419116569 1.674884484 1 18.33451947 3.978958003 12.69075203 1.387743467 1.473863619 0.033410038 0.209472578 6.126114933 3697.201332 0.048026391 0.088537053 9527.040307 -3.978958003 0.086120152 SGFEPPGDFPFEDYSQHIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGFEPPGDFPFEDYSQHIYR 20 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;;; 217.97 1.02E-24 546710000 802800 649610 690980 815040 779130 684770 860770 818810 749050 FALSE TRUE 764853.235 715805.9975 722662.1165 733110.6307 915010.0253 661056.2432 729443.7274 747110.6556 865208.8484 0.884009955 0.827321633 0.835245869 0.847322161 1.057559718 0.764042398 0.843083989 0.863503254 1 19.72268889 -2.260533925 2.074065264 1.48106015 0.861393132 0.239535167 0.075168131 4298780.419 614777.5362 9700314.005 0.01703165 0.005488657 2.260533925 -0.619667018 SGFGEISS(ph)PVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGFGEISSPVIR 12 0 P57740;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGFGEIS(0.002)S(0.998)PVIR;SGFGEIS(0.006)S(0.994)PVIR;SGFGEIS(0.009)S(0.991)PVIR 196.11 2.21E-07 293957000 918860 917020 986260 1106970 958800 1013660 1200580 1021920 1179530 TRUE FALSE 875427.3088 1010465.381 1031480.997 995695.2725 1126014.416 978556.7 1017409.471 932435.2673 1362445.488 0.642541163 0.74165564 0.757080562 0.73081476 0.826465665 0.718235488 0.746752424 0.684383541 1 20.37776708 -2.292624538 2.337213096 2.299749603 0.730900894 0.75996865 0.04751218 2727240.62 456992.6749 18719040.44 0.011486365 0.005097714 2.292624538 -1.568848708 SGGASHSELIHNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 270.27 4.91E-27 2487209000 1502843 1173760 1188467 1605640 1509255 1290735 1774663 1451862 333033 FALSE TRUE 1431806.59 1293367.478 1242959.388 1444238.017 1772468.594 1246036.523 1503905.565 1324729.266 384678.0567 3.722090628 3.362207581 3.231167897 3.754407072 4.607667537 3.239167146 3.909517424 3.443734945 1 18.55329201 0.943388001 18.35469297 0.999999996 3.667030025 0.816816712 0.397243928 207.1674315 67168.42306 0.364686622 0.091171561 8.777846888 -0.943388001 2.667030028 SGGASHSELIHNLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGGASHSELIHNLRK 15 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;F8WDT3;F8WAV5;F8WAX2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 210.14 8.27E-10 616520000 663290 370870 582980 608000 706760 607380 924320 744870 158076 FALSE TRUE 631937.5962 408662.0746 609710.2096 546882.6849 830018.7202 586346.2783 783298.0077 679645.234 182589.6187 3.46097221 2.238145178 3.33923809 2.99514665 4.545815507 3.211279384 4.289937254 3.722255617 1 17.47824522 2.956582114 24.80554504 3.61952952 2.942863488 0 1.014822664 944.7814918 539773.1293 0.271790439 0.288296368 904.8615074 -2.956582114 -0.676666032 SGGGLHSVAEGVRLS(ph)PEPGR ddPTM_SK-BR-3_Trastuzumab_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 191.5 8.73E-18 625240000 483313 380525 473166 507872 497859 453374 551520 508962 492095 TRUE FALSE 460467.7523 419300.9301 494861.1291 456819.7417 584685.452 437673.5447 467375.4946 464394.5891 568406.5793 0.810102784 0.737677827 0.870611191 0.803684824 1.028639487 0.770000842 0.822255603 0.817011284 1 19.11656373 -5 0.18213176 1.690374009 0.791096343 0.300188443 0.07859235 165.2524197 1.59681671 41.64289108 0.229199648 1.00E-05 5 -0.899277666 SGGGYGGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SGGGYGGDR 9 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;;;; 107.57 0.006401 1398926000 1434621 1237245 1270222 1492458 1257977 1328447 1498183 1399887 1378233 FALSE TRUE 1366809.308 1363321.672 1328462.935 1342433.286 1477367.791 1282442.547 1269607.667 1277305.473 1591962.335 0.858568874 0.856378095 0.834481386 0.84325694 0.928016799 0.805573423 0.797511122 0.802346541 1 20.60237477 SGGIVIS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGGIVISPFR 10 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR 113.82 0.0015083 279179000 489526 600097 439984 626978 383558 502078 456838 514520 381325 TRUE FALSE 466387.0761 661247.5666 460157.7016 563952.9803 450450.3938 484690.913 387138.9727 469465.9012 440458.9335 1.058866198 1.501269509 1.04472328 1.280375848 1.022684204 1.100422482 0.878944536 1.065856237 1 18.74864799 2.627164867 1.308169282 0.977661307 1.254375407 0.329946762 0.14019475 0.406379236 1.41619927 0.062908149 0.053351989 423.8038199 -2.627164867 0.276714101 SGGIVIS(ph)PFRLEELTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.006)GGIVIS(0.994)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR 342.42 6.16E-73 2449600000 1286184 1249743 1351462 1453835 1377669 1395209 1642812 1516542 1603993 TRUE FALSE 1225388.631 1377093.233 1413427.869 1307692.744 1617934.037 1346892.562 1392170.857 1383745.543 1852732.042 0.661395498 0.743277064 0.762888446 0.705818604 0.873269313 0.72697645 0.751415113 0.746867605 1 20.82122281 -5 0.215725889 2.258448206 0.709012203 0.705109929 0.052080009 80.95330036 0.808632108 44.25217605 0.099400888 1.00E-05 5 -1.549436003 SGGLQT(ph)PECLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R 171.03 0.00020979 2558200000 4849720 4749520 4025980 4904440 3376330 4534730 4415920 4563290 3338890 TRUE FALSE 4620483.347 5233501.488 4210575.165 4411436.373 3965160.883 4377691.163 3742190.3 4163704.136 3856668.009 1.198050581 1.357000778 1.091765004 1.143846544 1.028131245 1.135096709 0.97031694 1.07961176 1 21.87892353 3.621632346 5.081023718 1.060472556 1.27659436 0.648010867 0.065616043 0.11809522 4.444857189 0.016848353 0.026460472 4184.391835 -3.621632346 0.216121804 SGGLQT(ph)PECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 3 S(0.007)GGLQT(0.993)PECLS(1)REGS(1)PIPHDPEFGSK;S(0.126)GGLQT(0.875)PECLS(0.999)REGS(1)PIPHDPEFGSK 115.96 0.0010694 383060000 614330 337980 553810 487750 379360 510100 694990 524820 430980 TRUE FALSE 585291.8384 372420.5463 579202.7363 438720.4433 445520.2639 492435.1091 588956.5111 478863.9786 497814.1773 1.175723523 0.748111571 1.163491846 0.88129359 0.894952945 0.989194626 1.183085051 0.961933188 1 18.92524779 1.978845389 23.9971618 1.073046629 0.963143127 0.04721931 0.138527299 959.8551584 1088829.342 0.052379897 0.034239466 95.24570249 -1.978845389 -0.109903502 SGGLQT(ph)PECLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQT(1)PECLSR;SGGLQT(1)PECLSR 223.03 2.62E-10 430490000 679870 604930 599840 707540 528670 600600 710380 639750 610170 TRUE FALSE 647733.8925 666573.0547 627343.2573 636416.735 620869.8806 579801.0714 601998.484 583730.0985 704792.0473 0.919042567 0.945772668 0.890111147 0.902985125 0.880926343 0.822655525 0.854150506 0.828230257 1 19.42683812 3.148632704 1.369200991 0.862609532 0.930651364 0.100098676 0.050804191 0.54500328 2.141412277 0.016628703 0.022733746 1408.097425 -3.148632704 0.068041832 SGGLQTPECLS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQTPECLS(1)R;SGGLQTPECLS(1)R;SGGLQTPECLS(1)R;SGGLQTPECLS(1)R 147.7 6.79E-05 1792518000 1641112 1639669 1357407 1765192 1336063 1570305 1749104 1634560 1516369 TRUE FALSE 1563539.888 1806753.135 1419645.454 1587751.547 1569071.964 1515924.944 1482246.06 1491429.261 1751519.76 0.892676134 1.031534543 0.810522088 0.906499363 0.895834578 0.865491203 0.846262825 0.851505815 1 20.74017583 3.736505018 24.9998795 0.874791364 0.962105337 0.227274901 0.059943844 198.2516456 2411109.718 0.014209452 0.023256066 5451.361946 -3.736505018 0.087313973 SGGLQTPECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.003)GGLQT(0.021)PECLS(0.976)REGS(1)PIPHDPEFGSK;SGGLQT(0.008)PECLS(0.992)REGS(1)PIPHDPEFGSK;S(0.001)GGLQT(0.012)PECLS(0.987)REGS(1)PIPHDPEFGSK;S(0.003)GGLQT(0.029)PECLS(0.968)REGS(1)PIPHDPEFGSK 158.99 2.64E-11 1025050000 1609110 818510 1516340 1388180 1233600 1446380 2102500 1585710 1351110 TRUE FALSE 1533050.559 901917.0996 1585865.689 1248637.509 1448739.449 1396291.498 1781725.01 1446856.826 1560633.238 0.98232597 0.577917398 1.016168085 0.800083888 0.928302316 0.894695476 1.141667988 0.927095996 1 20.5737001 2.340474417 1.30542736 1.033009237 0.817813095 0.213557302 0.132467543 0.517965902 1.751017916 0.072803653 0.046383248 219.015281 -2.340474417 -0.215196141 SGGMERPFVLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGGMERPFVLAR 12 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 143.31 5.66E-05 1712880000 1548250 1388210 1192940 1465640 1295100 1308720 1617560 1413880 1368370 FALSE TRUE 1475067.291 1529670.177 1247637.479 1318311.083 1520965.03 1263398.698 1370771.513 1290073.172 1580569.831 0.933250314 0.967796644 0.78935929 0.834073292 0.962289043 0.799331149 0.867264126 0.81620764 1 20.59201335 3.762647958 24.75364012 0.860349726 0.950523492 0.201235981 0.068264393 844.8139928 868179.8896 0.015607901 0.02811828 5789.591986 -3.762647958 0.090173767 SGGPPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 100.15 0.010116 183850000 379324 309053 330654 396466 263964 393793 413249 384848 344918 FALSE TRUE 361394.1063 340545.8521 345814.813 356612.4844 309999.238 380155.8497 350200.2752 351148.6689 398406.1218 0.907099782 0.854770631 0.867995731 0.895097904 0.778098581 0.954191788 0.879003248 0.881383718 1 18.60388029 -0.373045589 0.5403966 1.016636335 0.872238572 0.437204713 0.044010753 7.080649152 1.885132138 0.272468987 0.017809804 0.423598497 0.373045589 -0.144397763 SGGPS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGGPSPKR 8 1 Q96E39 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 1 SGGPS(1)PKR;S(0.002)GGPS(0.998)PKR;SGGPS(1)PKR;SGGPS(1)PKR;SGGPS(1)PKR;S(0.001)GGPS(0.999)PKR 108.7 0.0023036 3078030000 5006340 3738850 4520330 4777030 3017180 4929270 5580570 5213190 3762590 TRUE FALSE 4769700.23 4119843.066 4727591.602 4296833.869 3543375.237 4758568.144 4729151.552 4756695.447 4346073.241 1.097473504 0.947946074 1.087784614 0.988670377 0.815304998 1.094912092 1.088143547 1.094481198 1 22.05128106 SGGSGHAVAEPAS(ph)PEQELDQNKGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGGSGHAVAEPASPEQELDQNKGK 24 1 P46013 P46013 MKI67 Antigen KI-67 1 SGGSGHAVAEPAS(1)PEQELDQNKGK 125.62 5.89E-05 56358000 65006 50739 70636 62143 52992 70813 99322 79582 64789 TRUE FALSE 61933.29521 55909.36179 73874.73047 55896.26758 62233.78802 68360.72805 84168.60473 72613.37819 74836.14722 0.827585298 0.747090328 0.987153043 0.746915356 0.831600641 0.91347204 1.124705211 0.97029819 1 16.19144767 1.992671017 4.069351702 1.042371165 0.822200384 0.592225575 0.076653854 0.127949346 4.809671425 0.031787317 0.019937821 98.32659885 -1.992671017 -0.220170781 SGGTEGLLAEKLEALITQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGGTEGLLAEKLEALITQTR 20 1 Q9UHB9;Q9UHB9-4 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 219.34 8.46E-25 159662000 276679 211770 275975 278409 255957 291394 379051 307253 298475 FALSE TRUE 263600.932 233349.6038 288628.7267 250422.7984 300595.8198 281302.9527 321219.8082 280348.2985 344760.9786 0.764590393 0.676844592 0.83718502 0.726366422 0.871896295 0.815936171 0.931717416 0.813167139 1 18.39523697 1.981114491 0.298686345 1.009476569 0.682180396 0.617921258 0.058238601 0.925510319 0.258173863 0.086561476 0.110222641 95.74464458 -1.981114491 -0.327296173 SGHVFTIEPMICEGGWQDETWPDGWTAVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGHVFTIEPMICEGGWQDETWPDGWTAVTR 30 0 P53582;H0Y955;H0Y903 P53582 METAP1 Methionine aminopeptidase 1 0 143.12 4.67E-08 37251000 31264 18256 25526 30363 27404 26208 27540 24601 23829 FALSE TRUE 29786.21268 20116.30716 26696.39235 27310.85355 32183.24892 25300.41039 23338.26719 22446.80602 27524.27962 1.082179555 0.730856808 0.969921564 0.992245898 1.16926762 0.919203363 0.847915641 0.815527466 1 14.74841718 2.001490833 24.99954999 0.874076934 0.96837425 0.117736569 0.120307777 111.4808298 1869383.848 0.046378674 0.034001911 100.3438668 -2.001490833 0.094297317 SGILPILVHCLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGILPILVHCLER 13 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 174.65 1.96E-05 318900000 689650 582980 616320 712260 630230 612120 748250 713560 645260 FALSE TRUE 657051.6113 642386.3248 644578.8816 640662.2716 740141.9125 590922.1309 634090.7199 651076.9036 745323.6253 0.881565523 0.861889122 0.864830873 0.859575961 0.993047701 0.792839662 0.850758917 0.873549263 1 19.50750747 0.922353496 19.51646033 1 0.869690661 0.39880584 0.049226514 3764.813755 946290.9223 0.04410563 0.011026408 8.362834381 -0.922353496 -0.130309339 SGITS(ph)PVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGITSPVEK 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SGIT(0.016)S(0.984)PVEK;SGIT(0.258)S(0.742)PVEK;SGIT(0.112)S(0.887)PVEK 125.74 0.00051723 299183000 967040 921680 788950 1066610 564280 971780 918750 952400 606380 TRUE FALSE 921329.9357 1015600.24 825124.1379 959392.3364 662690.2533 938127.0149 778577.8135 869002.807 700414.3134 1.315407064 1.449999265 1.178051508 1.369749758 0.946140364 1.339388697 1.111596092 1.240698242 1 19.41784904 7.999997114 0.089453042 0.842289976 2.402740643 0.332056862 0.132323371 146.9764153 0.945757932 2.173936203 28.15484178 99999335.46 -7.999997114 1.560450667 SGKNS(ph)QEDS(ph)EDS(ph)EDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 S(0.451)GKNS(0.553)QEDS(0.996)EDS(1)EDKDVK;S(0.168)GKNS(0.832)QEDS(1)EDS(1)EDKDVK 107.87 0.00026915 191123000 770680 620540 611730 767170 204020 839210 779310 899840 182403 TRUE FALSE 734251.4837 683773.7315 639778.4256 690052.6141 239601.0234 810147.9473 660411.9465 821045.2392 210689.1257 3.484999434 3.245415393 3.036599177 3.275217038 1.137225391 3.845229054 3.134532665 3.896951191 1 17.68475633 3.663458104 1.67986258 2.854220469 3.410718857 0.06200521 0.983479018 1.257935139 6.954856653 0.274164092 0.56814645 4607.423191 -3.663458104 0.556498388 SGKNS(ph)QEDSEDSEDKDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.154)GKNS(0.846)QEDSEDSEDKDVK;S(0.016)GKNS(0.984)QEDSEDSEDKDVK 197.37 9.66E-16 449010000 861170 730820 719680 827030 245740 971670 768930 917830 221440 TRUE FALSE 820464.2008 805291.3889 752678.0399 743895.3731 288596.9782 938020.8243 651615.6061 837459.9395 255779.7842 3.207697603 3.148377778 2.942679939 2.90834311 1.128302532 3.66729852 2.547564922 3.274144366 1 17.96454272 2.986019199 24.32052842 2.487921911 3.100488866 0.149058327 0.824203279 974.2877617 1694842.503 0.22525221 0.248174733 968.3206613 -2.986019199 0.612566954 SGKYDLDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 107.06 0.0025861 36743400000 45044600 36842000 33294800 41939600 24181190 45882500 46644000 45924100 23853540 FALSE TRUE 42915431.03 40596241.69 34821399.51 37723751.73 28398381.88 44293577.52 39527601.12 41902742.35 27552625.16 1.557580477 1.473407396 1.263814222 1.369152722 1.030696049 1.607599177 1.434621961 1.520825769 1 24.71568645 3.939436778 4.8422752 1.349317895 1.528500126 0.143580288 0.193131849 0.391835046 18.85534115 0.046983672 0.089548459 8698.347981 -3.939436778 0.179182231 SGKYDLDFKSPDDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SGKYDLDFKSPDDPSR 16 2 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;; 111.06 0.00047572 31540560000 31495090 12557870 27094930 21108200 21929880 29853530 46401860 34737700 28741170 FALSE TRUE 30006379.51 13837531.23 28337259.34 18986363.63 25754444.13 28819694.77 39322404.03 31695882.83 33198203.85 0.903855511 0.416815659 0.853578087 0.571909363 0.775778239 0.868110061 1.184473841 0.954746919 1 24.98460185 2.116860324 2.519417286 1.061929932 0.678195312 0.517271569 0.149636207 0.194285774 2.440513241 0.065629938 0.041163 130.8760937 -2.116860324 -0.38373462 SGLCS(ph)PSYVAVTPFSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGLCSPSYVAVTPFSLR 17 0 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1 H0YBT0 MYC Myc proto-oncogene protein 1 S(0.002)GLCS(0.981)PS(0.017)YVAVTPFSLR 123.92 5.45E-05 99010000 221410 160890 190170 211120 188300 191010 231040 216300 200530 TRUE FALSE 210944.3881 177284.8739 198889.4826 189897.8165 221139.4604 184395.2758 195790.6047 197359.6253 231627.1682 0.910706588 0.765388945 0.858662151 0.819842586 0.954721599 0.796086561 0.845283419 0.852057325 1 17.82144496 0.663371936 4.067266005 0.99999979 0.845892947 0.433600199 0.053591329 10.45876675 125.5369512 0.047084971 0.0120156 4.60650913 -0.663371936 -0.154106843 SGLEPAS(ph)SPSKGSEPRPLVPPVSGHATIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGLEPASSPSKGSEPRPLVPPVSGHATIAR 30 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SGLEPAS(0.538)S(0.445)PS(0.009)KGS(0.009)EPRPLVPPVSGHATIAR 195.08 8.50E-20 158870000 82903 57923 86538 78210 56881 79077 121150 99348 102830 TRUE FALSE 78984.33949 63825.41955 90505.8529 70348.18221 66801.02839 76338.54366 102666.3424 90648.56244 118776.3512 0.664983717 0.537357975 0.761985462 0.592274316 0.562410174 0.642708274 0.864366866 0.76318696 1 16.85788809 1.376249974 0.983387041 0.973043561 0.614702142 0.686768153 0.080341448 0.260813369 0.515847753 0.070562289 0.025281851 23.78208756 -1.376249974 -0.358341418 SGLIFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGLIFYR 7 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ; 138.07 0.0065628 287020000 829150 666450 654540 698760 766360 572200 767630 784730 1227430 FALSE TRUE 789957.7227 734362.0127 684551.3064 628519.3172 900012.9414 552384.5705 650513.945 716014.8811 1417773.576 0.557181863 0.517968472 0.482835425 0.443314312 0.634807248 0.389614096 0.45882781 0.505027667 1 20.43519572 -1.262998493 3.241926932 1.002046524 0.498040206 0.850812151 0.065970416 12075523.98 17261525.81 244599.6995 0.015223358 0.054575976 1.262998493 -0.504006318 SGLLSSFSLS(ph)MTDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGLLSSFSLSMTDLSK 16 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 SGLLSSFS(0.006)LS(0.993)MT(0.001)DLSK;SGLLSSFS(0.005)LS(0.995)MT(0.001)DLSK 251.02 3.98E-21 229780000 470470 421870 415650 516550 316760 519620 538930 549790 349260 TRUE FALSE 448231.8155 464859.0326 434707.9636 464625.4126 372002.8437 501625.4291 456706.3304 501647.473 403421.457 1.111075794 1.152291294 1.077552907 1.151712197 0.922119628 1.243427736 1.132082398 1.243482379 1 18.62192829 SGLS(ph)LEELR ddPTM_SK-BR-3_Trastuzumab_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(0.01)GLS(0.99)LEELR;S(0.017)GLS(0.983)LEELR;SGLS(1)LEELR;S(0.001)GLS(0.999)LEELR 140.78 0.00011358 411294000 1044320 956629 979806 1139800 1006560 969526 1146740 987030 1033770 TRUE FALSE 994957.0632 1054110.583 1024731.074 1025225.139 1182103.745 935951.0715 971783.7517 900600.4206 1194081.772 0.833240308 0.882779226 0.858174958 0.858588719 0.989968839 0.783824939 0.813833503 0.754220056 1 20.18747021 -1.634804519 8.655356582 1.000104407 0.848771212 0.36712889 0.063155822 0.000123384 5.21E-06 0.059295127 0.013966414 0.02318438 1.634804519 -0.151333196 SGLSLEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 0 ;; 72.23 0.047339 1043030000 448896 366604 490622 438581 1614010 223193 475520 249997 1482990 FALSE TRUE 427677.5757 403961.3644 513117.504 394494.0046 1895492.833 215463.7704 402970.6905 228105.9374 1712964.515 0.249671007 0.23582588 0.299549407 0.230298994 1.106556975 0.125784141 0.235247541 0.133164427 1 20.70806383 -1.170382599 3.658553657 1.000600352 0.318564312 0.358568818 0.282676829 90953980.72 156836464.3 669578.8454 0.066562342 0.067548763 1.170382599 -0.68203604 SGLTVPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 SGLTVPT(0.354)S(0.646)PK;SGLTVPT(0.154)S(0.846)PK;SGLTVPT(0.199)S(0.801)PK 125.82 0.00041854 252230000 1460690 1203640 1223320 1468990 810880 1456760 1436090 1596820 972590 TRUE FALSE 1391646.079 1326292.284 1279410.432 1321324.334 952297.2153 1406312.036 1216988.095 1456993.976 1123414.29 1.2387648 1.180590541 1.138858962 1.176168352 0.847681237 1.251819608 1.08329412 1.29693381 1 20.09945863 3.870280696 1.460034763 1.111074577 1.229821238 0.106987762 0.125159676 0.945263316 3.806034515 0.03454087 0.099663011 7417.895239 -3.870280696 0.118746661 SGMLQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGMLQAEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 75.854 0.086804 1140660000 1861280 1572950 1582520 1469260 1225470 1845280 2126110 2018130 1377740 FALSE TRUE 1773300.983 1733235.393 1655080.107 1321567.193 1439191.58 1781377.491 1801732.871 1841411.838 1591392.883 1.114307474 1.089131045 1.0400198 0.830446842 0.904359694 1.119382593 1.132173513 1.157106996 1 20.60185862 -0.026211316 7.954421178 1.000000003 1.053920165 0.018274921 0.104586356 0 0 0.108062345 0.025470539 0.941431409 0.026211316 0.053920162 SGMNVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGMNVAR 7 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 120.52 0.010558 321800000 381020 322430 351670 365660 375370 349360 442420 376990 371080 FALSE TRUE 363009.9397 355285.9836 367794.4173 328903.1621 440834.4092 337261.5756 374920.7034 343978.7571 428625.1912 0.84691695 0.828896646 0.858079331 0.767344451 1.028484602 0.78684497 0.874705246 0.802516427 1 18.70935712 -1.605575144 3.067346113 1.009278181 0.849523018 0.304939395 0.071537338 28784061.86 25484925.19 2095904.766 0.015013645 0.024798468 1.605575144 -0.159755163 SGMS(ph)PEQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.117)GMS(0.883)PEQSR;S(0.007)GMS(0.993)PEQSR;S(0.01)GMS(0.99)PEQSR;S(0.02)GMS(0.98)PEQSR;S(0.002)GMS(0.998)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;S(0.001)GMS(0.999)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR 202.3 2.11E-05 19533906000 13345153 11277687 11412291 13451963 11395610 12202404 13858467 12683242 12302823 TRUE FALSE 12714354.07 12426896.13 11935555.83 12099746.12 13383000.78 11779831.69 11744103.33 11572630.09 14210681.96 0.894704005 0.874475705 0.839900285 0.85145429 0.941756407 0.82894204 0.82642785 0.814361346 1 23.76047245 SGMSHEEDQLIPNLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGMSHEEDQLIPNLYR 16 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 85.734 0.0070483 75923000 106830 89864 95041 107880 97174 99966 122220 108610 92391 FALSE TRUE 101780.3576 99021.24377 99398.72386 97035.69744 114121.1148 96504.15235 103573.0943 99099.53262 106718.5244 0.953727183 0.92787306 0.931410216 0.909267608 1.069365562 0.904286794 0.970525922 0.928606661 1 16.7034511 SGNFGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SGNFGGSR 8 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 144.9 0.0013446 2825210000 1690798 1308116 1222541 1408090 1518265 1296086 1739209 1464759 1558815 FALSE TRUE 1610877.329 1441414.508 1278595.714 1266546.118 1783049.935 1251202.217 1473860.724 1336496.937 1800548.069 0.894659441 0.800542086 0.710114735 0.703422552 0.990281774 0.694900757 0.818562275 0.742272289 1 20.78000468 -1.93602736 4.963326191 1.096973008 0.798549688 0.326714778 0.092606041 0.061010127 0.000786364 0.05505066 0.019462141 0.011587044 1.93602736 -0.298423321 SGNLTEDDKHNNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGNLTEDDKHNNAK 14 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 ;; 250.31 1.48E-18 1366920000 1596680 1330387 1370477 1689430 890812 1689490 1816460 1838480 880804 FALSE TRUE 1521208.101 1465954.948 1433314.726 1519605.287 1046169.331 1630982.538 1539325.665 1677492.945 1017394.586 1.495199721 1.440891242 1.408809076 1.49362431 1.028282778 1.603097324 1.513007526 1.648812534 1 19.95644789 SGNPSSLSDIGNRRS(ph)PPPSLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGNPSSLSDIGNRRSPPPSLAK 22 2 F8VNV8;P54284-5;P54284-2;P54284-3;P54284-4;P54284 F8VNV8 CACNB3 Voltage-dependent L-type calcium channel subunit beta-3 1 SGNPS(0.004)S(0.004)LS(0.004)DIGNRRS(0.987)PPPSLAK 64.779 0.012367 89116000 216720 81227 221690 145380 131160 219060 280390 224070 158210 TRUE FALSE 206476.0751 89504.12365 231854.7058 130766.1262 154034.2625 211473.8973 237611.3558 204449.2429 182744.3988 1.129862674 0.489777658 1.268737687 0.71556845 0.842894576 1.157211377 1.300238789 1.118771597 1 17.47946766 2.215606095 6.944620091 1.184368366 0.865843988 0.231326173 0.223315747 0.192274947 34.98081553 0.077086066 0.058266345 164.2880953 -2.215606095 -0.318524378 SGPASTFNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGPASTFNDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 114.39 0.0053869 0 57562 55703 54394 65495 61658 59920 66516 50562 56691 FALSE TRUE 54841.15834 61379.19903 56888.0187 58911.31817 72411.13568 57844.95538 56367.76255 46134.52323 65482.35074 0.83749526 0.937339578 0.868753459 0.899651853 1.105811487 0.883367117 0.860808476 0.704533706 1 15.99881849 -0.980931286 4.2959001 1.000004266 0.892543909 0.112303447 0.098644008 11950263.73 2781782.946 502.8051593 0.022123245 0.104488553 0.980931286 -0.107460357 SGPFGQIFRPDNFVFGQS(ph)GAGNNWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 SGPFGQIFRPDNFVFGQS(1)GAGNNWAK 139.91 1.97E-07 38168000 58038 42955 43403 54622 44635 51672 55666 50745 43664 TRUE FALSE 55294.65876 47332.16334 45393.07048 49131.29278 52419.32987 49882.58568 47173.12932 46301.49878 50435.19012 1.096350755 0.938474966 0.900027746 0.974147072 1.039340384 0.989043277 0.935321731 0.918039541 1 15.62214308 4.588062235 2.936547222 0.960886633 1.100176024 0.506982625 0.041496898 0.253302871 3.709757126 0.010560051 0.069724648 38731.31434 -4.588062235 0.13928939 SGPFGQIFRPDNFVFGQSGAGNNWAK ddPTM_SK-BR-3_Trastuzumab_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 ; 329.57 5.74E-95 7262800000 5090900 4464900 4090800 4867700 3565700 4772700 5679600 5254500 4146400 FALSE TRUE 4850263.246 4919878.386 4278367.226 4378389.548 4187556.951 4607420.202 4813072.707 4794388.124 4789402.535 1.01270737 1.027242615 0.893298735 0.914182827 0.874338066 0.962003124 1.004942197 1.001040963 1 22.19141426 -0.732324646 7.404008505 0.999996737 0.967046692 0.040626089 0.052866501 0 0 0.056346691 0.013281042 0.185214658 0.732324646 -0.032950045 SGPKPFSAPKPQT(ph)SPSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.5)S(0.5)PSPK 100.64 0.03877 52473000 79319 66411 74686 83054 48132 80196 90213 93715 59154 TRUE FALSE 75569.74807 73178.3564 78110.42697 74705.25413 56526.20556 77418.79241 76449.34997 85508.81779 68327.3002 1.1059964 1.070997335 1.14318035 1.093344152 0.827285805 1.133057975 1.11886976 1.251459044 1 16.0601745 2.070949365 24.99999993 1.134030429 1.056011479 0.117924403 0.103287208 97.30215098 34283.80441 0.037049846 0.02736312 117.7468682 -2.070949365 -0.07801895 SGPKPFSAPKPQTS(ph)PS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFS(0.015)APKPQT(0.075)S(0.911)PS(0.999)PK;SGPKPFS(0.003)APKPQT(0.042)S(0.97)PS(0.985)PK 84.327 0.018885 2350500000 3281500 3035300 3388500 3783700 1301380 4126100 4004600 3772500 1372690 TRUE FALSE 3126389.998 3344600.521 3543866.077 3403355.287 1528340.26 3983212.122 3393624.72 3442159.901 1585559.754 1.971789451 2.109413102 2.235088313 2.146469269 0.963912117 2.51218039 2.140332278 2.170943032 1 20.59656082 SGPKPFSAPKPQTS(ph)PS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.421)S(0.592)PS(0.987)PKR;SGPKPFSAPKPQT(0.18)S(0.821)PS(0.999)PKR 81.477 0.0027911 2773750000 2713200 2215300 2608600 2982900 1214380 3248600 3290600 2517600 1343480 TRUE FALSE 2584952.413 2441041.589 2728206.89 2683053.225 1426167.488 3136100.167 2788558.534 2297145.597 1551820.017 1.665755297 1.573018496 1.758069145 1.728971914 0.919028929 2.02091746 1.796960024 1.480291253 1 20.56552981 0.94744611 8.958533583 1.00000103 1.64270837 0.33484979 0.28219153 1.781099796 303.6357408 0.255157269 0.063852948 8.860252724 -0.94744611 0.642707339 SGPKPFSAPKPQTS(ph)PSPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.141)S(0.758)PS(0.1)PKR 117.43 7.06E-05 3838100000 2765000 1674400 2616400 2227300 1330200 2900000 3377300 3119200 1753500 TRUE FALSE 2634303.93 1845023.264 2736364.528 2003407.572 1562186.459 2799572.273 2862030.857 2846066.312 2025423.824 1.300618615 0.910931945 1.351008364 0.989130052 0.771288676 1.382215534 1.413052825 1.405170749 1 20.9497924 2.157874433 24.99999998 1.34465006 1.074645208 0.231050112 0.206052704 36.62581872 11345.53656 0.071859333 0.053071644 143.8382639 -2.157874433 -0.270004852 SGPKPFSAPKPQTSPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQTSPS(1)PK;SGPKPFSAPKPQT(0.222)S(0.222)PS(0.556)PK 181.81 5.64E-14 10658600000 2660800 2185900 2318500 2769200 1128180 2824300 2799600 3126300 1226080 TRUE FALSE 2535029.257 2408645.695 2424805.518 2490834.755 1324934.235 2726493.783 2372469.602 2852544.598 1416214.224 1.790004092 1.700763665 1.712174243 1.758798007 0.935546482 1.925198699 1.675219441 2.014204171 1 20.43360808 SGPKPFSAPKPQTSPS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQTS(0.045)PS(0.955)PKR 135.76 3.95E-05 5275700000 1242100 800890 1134400 1098100 649920 1328800 1343400 1345600 750780 TRUE FALSE 1183388.395 882501.6015 1186413.362 987716.9017 763265.8422 1282783.323 1138439.657 1227772.131 867207.1279 1.364597172 1.017636471 1.368085344 1.13896308 0.880142491 1.479212153 1.312765567 1.415777259 1 19.72601709 2.199633252 24.99998559 1.331770144 1.163518101 0.12130532 0.189647669 283.3885275 181996.5557 0.064925625 0.047951568 158.3555366 -2.199633252 -0.168252044 SGPKPFSAPKPQTSPSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ; 101.17 0.00040221 1124620000 755420 806650 668550 786360 493570 797740 814280 846780 477460 FALSE TRUE 719712.7937 888848.5521 699203.6788 707313.5988 579648.4517 770114.0638 690046.6307 772631.4541 551502.0583 1.305004728 1.611686736 1.267816989 1.282522138 1.051035881 1.396393816 1.251213156 1.400958424 1 19.07300674 -4.996634552 0.087748827 4.94E-13 1.604889984 0.309867621 0.14399162 248.6913204 1.524052453 47.83519846 3.586424006 1.01E-05 4.996634552 1.604889984 SGPLFNFDVHDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SGPLFNFDVHDDVR 14 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;;;;;;; 208.47 8.00E-09 2202940000 3013700 2513250 2538820 3035670 2780610 2631960 3187600 2869870 2473240 FALSE TRUE 2871248.374 2769353.032 2655227.408 2730518.684 3265547.504 2540814.565 2701273.076 2618568.969 2856777.428 1.005065479 0.969397548 0.92944847 0.955803787 1.143087828 0.889398852 0.945566515 0.916616375 1 21.44595721 SGPPS(ph)PPSTATSFGGPRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(0.998)PPS(0.001)T(0.001)ATSFGGPRPR 243.09 1.17E-24 2209645000 484480 413130 455100 479666 417516 445153 553587 499789 458572 TRUE FALSE 461579.5905 455228.4167 475966.7852 431449.0624 490330.6582 429737.24 469127.1358 456024.8256 529685.0037 0.871422803 0.85943233 0.898584596 0.814538942 0.92570236 0.811307167 0.885671923 0.860935882 1 19.01477514 -1.983222905 2.216243349 1.123049248 0.86594158 0.597705136 0.034562063 3232588.956 1251386.771 2035865.041 0.006993731 0.010393866 1.983222905 -0.257107668 SGPS(ph)PLS(ph)SPNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.927)S(0.073)PNGK;S(0.001)GPS(0.999)PLS(0.585)S(0.415)PNGK;SGPS(1)PLS(0.915)S(0.085)PNGK;SGPS(0.999)PLS(0.614)S(0.386)PNGK 197.79 2.79E-07 720300000 2960820 3029010 2972860 3427640 1959040 3310280 3565820 3393550 2263070 TRUE FALSE 2820867.906 3337669.563 3109168.572 3083087.115 2300695.956 3195644.174 3021788.668 3096392.772 2614015.337 1.079132118 1.276836258 1.189422467 1.179444922 0.88013866 1.222503988 1.155995003 1.184535044 1 21.31783618 -1.616971781 2.489869061 0.983116772 1.151820779 0.153515312 0.106970625 8249292.081 6848966.397 900714.4533 0.024680522 0.024156178 1.616971781 0.168704007 SGPS(ph)PLSSPNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 SGPS(0.997)PLS(0.003)S(0.001)PNGK;SGPS(1)PLSSPNGK 151.7 0.00018063 52885000 227588 215266 209979 229315 159753 217245 253548 246035 208397 TRUE FALSE 216830.3663 237201.8501 219606.7448 206263.8205 187613.8726 209721.7512 214864.5959 224490.8711 240714.1424 0.900779506 0.985408866 0.91231343 0.856882851 0.779405276 0.87124815 0.892613096 0.93260358 1 17.87696138 -0.743384588 5.80822168 1.000000005 0.895515455 0.289959944 0.053059311 4.19E-09 7.94E-10 0.056241448 0.013256236 0.18055745 0.743384588 -0.10448455 SGQGAFGNMCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGQGAFGNMCR 11 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;; 201.61 9.97E-08 316536000 262221 192646 180035 207323 242224 186927 271566 240887 260196 FALSE TRUE 249826.333 212276.8464 188289.7828 186482.4982 284467.7889 180453.6711 230133.619 219793.6573 300545.8668 0.831241952 0.706304328 0.626492671 0.62047933 0.946503747 0.60041974 0.765718795 0.731314856 1 18.19722565 0.010280723 1.449733615 1.000326488 0.728820372 0.399720679 0.104567514 20.19066185 27.96542005 0.112954205 0.026748163 1.02395465 -0.010280723 -0.271506116 SGQGFHGNSEVNAILS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;SGQGFHGNSEVNAILS(1)PR 212.9 9.12E-17 676920000 486894 410534 469219 517366 501849 461602 564111 526436 512568 TRUE FALSE 463879.4856 452367.8813 490733.1553 465359.3867 589371.3067 445616.607 478045.5063 480338.473 592054.4276 0.783508177 0.764064688 0.828864936 0.786007781 0.995468118 0.752661556 0.807435067 0.811307965 1 19.17537028 -5 0.256852332 2.1808332 0.795302606 0.417439167 0.067875083 184.3614795 1.816245865 114.8787868 0.087921411 1.00E-05 5 -1.385530595 SGQKPVLDVHAELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGQKPVLDVHAELDR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ; 103.61 0.00087669 717090000 1336900 1146920 1195590 1404100 1015660 1290780 1520710 1443610 1003650 FALSE TRUE 1273707.386 1263792.452 1250408.984 1262957.2 1192790.782 1246079.965 1288697.76 1317199.855 1159290.916 1.098695219 1.090142633 1.078598104 1.089422148 1.028896859 1.074863908 1.111625858 1.136211659 1 20.14481122 3.974544622 1.944446878 1.079401867 1.097306377 0.034655588 0.038370254 1.52523347 11.20240067 0.010209546 0.027817602 9430.715032 -3.974544622 0.01790451 SGQVYSFGCNDEGALGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGQVYSFGCNDEGALGR 17 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 192.32 2.50E-17 0 22874 24344 23719 22407 23007 20565 29542 27909 26514 FALSE TRUE 21792.79135 26824.68128 24806.53961 20154.60579 27019.41352 19852.82889 25034.82532 25465.14001 30625.65571 0.711586115 0.875889207 0.809992114 0.658095486 0.882247674 0.648241758 0.817446182 0.831496973 1 14.90245311 0.807876403 1.897119729 0.99943033 0.7744575 0.446540163 0.080267031 0.613854018 3.918711969 0.069000005 0.019283938 6.425048389 -0.807876403 -0.22497283 SGS(ph)AAQAEGLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.024)GS(0.976)AAQAEGLCK;SGS(1)AAQAEGLCK;S(0.001)GS(0.999)AAQAEGLCK;S(0.021)GS(0.979)AAQAEGLCK 167.94 5.02E-05 609819000 1620130 1160960 1350540 1925790 1465280 1744900 2029970 1643090 1528200 TRUE FALSE 1543549.666 1279263.144 1412463.595 1732205.93 1720824.368 1684473.675 1720260.794 1499212.329 1765185.451 0.87444051 0.724718835 0.800178584 0.981316682 0.974868883 0.954275753 0.97454961 0.849322845 1 20.75138833 3.245195974 24.91363268 0.956620816 0.794360764 0.651550892 0.053708101 81.32313137 305340.1792 0.014190307 0.018777022 1758.717049 -3.245195974 -0.162260052 SGS(ph)FGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSFGK 6 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 SGS(1)FGK 98.629 0.041662 482740000 1402000 1211100 1051600 1368100 702720 1252800 1347700 1584400 864650 TRUE FALSE 1335730.238 1334512.467 1099816.9 1230575.989 825274.1455 1209415.222 1142083.613 1445661.537 998735.506 1.3374214 1.336202086 1.101209373 1.232134015 0.826319021 1.210946456 1.143529599 1.447491881 1 19.92974314 3.745909399 23.36986764 1.13917645 1.336811792 0.213707006 0.159011356 315.8098254 1004298.052 0.038280472 0.067148474 5570.695227 -3.745909399 0.197635342 SGS(ph)FSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGSFSK 6 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;G3V3H3;Q07866-5;Q07866-10;H0YG16 Q07866-6 KLC1 Kinesin light chain 1 1 S(0.001)GS(0.999)FS(0.001)K;SGS(0.992)FS(0.008)K;SGS(0.97)FS(0.03)K;S(0.009)GS(0.98)FS(0.011)K;SGS(0.99)FS(0.01)K 106.93 0.033257 1761220000 4193530 3631970 3595500 4313420 2217590 4035110 4213420 4927210 3200330 TRUE FALSE 3995310.148 4002071.872 3760357.231 3879826.827 2604336.994 3895373.129 3570585.394 4495757.372 3696620.831 1.080800637 1.0826298 1.017241801 1.049560397 0.704518292 1.053765941 0.96590523 1.216180284 1 21.81777564 3.494819603 2.253622203 0.985274962 1.081697329 0.064444959 0.125274451 0.720247358 7.29386128 0.035050021 0.056742874 3124.781129 -3.494819603 0.096422367 SGS(ph)GGGSAKEPQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGSGGGSAKEPQEER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 S(0.006)GS(0.986)GGGS(0.008)AKEPQEER;S(0.069)GS(0.893)GGGS(0.039)AKEPQEER;S(0.132)GS(0.849)GGGS(0.018)AKEPQEER;S(0.011)GS(0.908)GGGS(0.081)AKEPQEER;S(0.243)GS(0.757)GGGSAKEPQEER;S(0.016)GS(0.984)GGGS(0.001)AKEPQEER 211.67 7.65E-10 1702455000 1443508 1078099 1396455 1500513 990740 1481214 1786536 1615526 1076817 TRUE FALSE 1375276.238 1187958.514 1460483.843 1349678.582 1163524.742 1429919.188 1513967.121 1474061.979 1243804.281 1.105701483 0.95510084 1.174207121 1.085121352 0.935456454 1.149633596 1.217206875 1.185123738 1 20.24632806 2.033172063 24.93845894 1.164538344 1.049495177 0.16403801 0.089546488 222.0140263 166907.1895 0.031147846 0.023004074 107.9374274 -2.033172063 -0.115043167 SGS(ph)GSESTGAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSGSESTGAEER 13 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.008)GS(0.929)GS(0.063)ESTGAEER;S(0.014)GS(0.973)GS(0.011)ES(0.001)TGAEER 186.39 8.24E-06 70840000 84148 92158 86197 106507 89132 91039 98810 84465 80131 TRUE FALSE 80170.49081 101549.005 90149.21771 95800.71401 104676.5926 87886.2966 83734.71973 77068.79682 92557.30623 0.866171392 1.097147369 0.973982729 1.035042158 1.130938192 0.949533864 0.90467974 0.832660326 1 16.49805926 2.008730291 24.79616091 0.908168343 1.017630314 0.279560989 0.080592535 216.6522771 615342.5942 0.029140276 0.021489181 102.0305648 -2.008730291 0.109461971 SGS(ph)IKGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGSIKGSR 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 S(0.063)GS(0.935)IKGS(0.002)R;S(0.017)GS(0.981)IKGS(0.002)R;S(0.055)GS(0.945)IKGSR;S(0.018)GS(0.981)IKGSR 104.07 0.0028167 2224260000 3864200 2195130 3752110 3437330 2459650 3857180 5173510 4852170 3694330 TRUE FALSE 3681546.924 2418816.243 3924147.955 3091803.058 2888612.181 3723604.889 4384196.031 4427288.272 4267227.828 0.86274909 0.566835505 0.919601229 0.724546048 0.676929449 0.872605129 1.027410817 1.037509233 1 22.02486771 1.941690629 3.10698379 1.022452496 0.742315697 0.621288984 0.09629493 0.157931958 2.803068262 0.046184635 0.025704476 87.43606991 -1.941690629 -0.2801368 SGS(ph)ISVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSISVK 7 0 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 SGS(0.719)IS(0.281)VK;S(0.003)GS(0.92)IS(0.077)VK 98.009 0.012145 386870000 1359830 1064670 1191000 1452040 963650 1374660 1467910 1442630 1037650 TRUE FALSE 1295553.531 1173161.083 1245608.528 1306078.181 1131710.255 1327055.18 1243953.369 1316305.669 1198563.462 1.08092193 0.978805979 1.03925121 1.089702983 0.944222221 1.107204767 1.037870258 1.098236106 1 20.19287487 SGS(ph)LSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSLSGR 7 0 Q16512;Q16512-2;Q16512-3 Q16512;REV__Q16512-3 PKN1 Serine/threonine-protein kinase N1 1 S(0.033)GS(0.967)LSGR 110.41 0.0071437 52458000 66055 56026 55789 71358 50788 57837 68052 68069 65668 TRUE FALSE 62932.71106 61735.1131 58346.98083 64184.95827 59645.41112 55834.09019 57669.41754 62108.5175 75851.45805 0.829683604 0.813894877 0.769226885 0.846192808 0.786344952 0.736097784 0.76029412 0.818817714 1 16.21088929 0.96058258 21.33254817 1.000000001 0.792697672 0.799463124 0.032529957 483.170184 261490.702 0.033995881 0.00849897 9.132350677 -0.96058258 -0.207302328 SGS(ph)MDPSGAHPSVR ddPTM_SK-BR-3_Trastuzumab_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(0.153)GS(0.775)MDPS(0.072)GAHPSVR 80.96 0.058014 99283000 109540 69528 98804 119590 125380 103000 144320 111330 139030 TRUE FALSE 104362.2613 76612.98225 103334.2611 107568.586 147246.2323 99433.08417 122301.3334 101581.355 160590.0623 0.649867493 0.477071751 0.6434661 0.669833391 0.916907498 0.619173333 0.76157473 0.632550692 1 17.29302309 -5 0.088238616 2.079272255 0.376310152 0.490447258 0.108437292 171.4694139 1.054978244 35.1854108 2.597905392 1.00E-05 5 -1.702962104 SGS(ph)PKLDPSEVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.111)GS(0.889)PKLDPSEVYLK;S(0.12)GS(0.874)PKLDPS(0.007)EVYLK;S(0.13)GS(0.87)PKLDPSEVYLK;S(0.127)GS(0.873)PKLDPSEVYLK 177.64 1.26E-06 1271340000 6359500 4593990 5646520 6005110 2912180 6415750 6971480 6868790 2988380 TRUE FALSE 6058899.038 5062122.804 5905418.527 5401464.934 3420063.27 6193570.969 5907852.686 6267322.334 3451802.708 1.755285441 1.466515682 1.71082157 1.564824351 0.990804968 1.794300397 1.711526755 1.81566644 1 21.71891858 3.00624782 24.31362297 1.523139652 1.623977017 0.051313856 0.298370209 575.4228164 2239245.765 0.083576462 0.099630464 1014.490115 -3.00624782 0.100837365 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.019)GS(0.979)PRPT(0.002)EPTDFLMLFEGSPSGK;S(0.115)GS(0.885)PRPTEPTDFLMLFEGSPSGK 264.63 3.49E-44 440110000 638630 590342 560901 629020 385740 626310 642960 689660 397403 TRUE FALSE 608443.2255 650498.521 586618.8657 565789.7145 453012.9339 604620.7277 544864.6432 629269.7143 459030.2276 1.325497078 1.417114782 1.277952584 1.232576158 0.986891291 1.317169745 1.18699077 1.370867704 1 18.80822963 8 0.026803301 8.81E-10 2.998647854 0.316998861 0.119288089 1905.796482 3.925115379 146.8717752 324.525565 100000000 -8 2.998647853 SGS(ph)PSDNSGAEEMEVSLAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.399)GS(0.48)PS(0.118)DNS(0.003)GAEEMEVSLAKPK;S(0.005)GS(0.91)PS(0.085)DNSGAEEMEVSLAKPK;S(0.006)GS(0.987)PS(0.007)DNSGAEEMEVSLAKPK 237.01 4.60E-30 1359310000 1242370 1062240 1106270 1285230 663270 1297700 1362940 1367930 721710 TRUE FALSE 1183645.632 1170483.464 1156993.574 1156036.239 778944.078 1252760.324 1154998.471 1248146.797 833629.1008 1.419870817 1.404081818 1.387899694 1.386751299 0.934401255 1.502779021 1.38550642 1.497244753 1 19.66904612 -2.190887089 2.276372544 0.000126746 1.367627202 0.34159023 0.159131731 4826967.448 826982.826 24955411.99 0.039049251 0.006443368 2.190887089 1.367500456 SGS(ph)SS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.105)GS(0.637)S(0.267)S(0.99)PDS(0.001)EITELKFPSINHD;S(0.052)GS(0.475)S(0.475)S(0.995)PDS(0.004)EITELKFPSINHD 220.69 2.61E-25 701950000 596970 531130 524260 627570 396392 586380 653860 618290 367560 TRUE FALSE 568752.4112 585252.7508 548297.8396 564485.4713 465522.6393 566073.5136 554101.648 564149.2498 424559.3276 1.339629998 1.378494625 1.291451639 1.329579719 1.096484305 1.333320167 1.305121834 1.328787788 1 18.69560664 -3.830835305 0.269964333 6.58E-17 1.330830891 0.594907992 0.077154345 73.27704353 1.273400894 40.80979109 0.094245794 0.000147627 3.830835305 1.330830891 SGS(ph)TGSSLSVSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 S(0.009)GS(0.972)T(0.019)GSSLSVSVR;S(0.007)GS(0.959)T(0.032)GS(0.001)S(0.001)LSVSVR 121.56 0.00017907 35672000 126070 93627 122689 127422 105758 111720 142182 123506 127422 TRUE FALSE 120110.9209 103167.6977 128314.412 114613.2985 124202.1617 107851.1084 120489.5245 112691.1599 147181.953 0.816070982 0.70095345 0.871808054 0.778718424 0.843868146 0.732774 0.818643333 0.765658816 1 17.16724126 -2.126419081 2.435692229 1.431211356 0.787795885 0.626383973 0.05065642 3647931.369 939760.8647 8715823.8 0.011069363 0.007474479 2.126419081 -0.643415472 SGS(ph)VSNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSVSNYR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.002)GS(0.987)VS(0.011)NYR;S(0.016)GS(0.934)VS(0.05)NYR 132.39 0.0010115 176704000 397090 311820 359720 422840 411360 368200 496990 415400 477070 TRUE FALSE 378320.3427 343594.8125 376213.5178 380335.3199 483101.0538 355449.1417 421165.0477 379025.3738 551051.5791 0.686542525 0.623525684 0.682719245 0.690199129 0.876689356 0.645037879 0.764293332 0.687821954 1 19.07182784 -5 0.18637181 2.250414982 0.645698971 0.639600287 0.069550754 80.78646108 0.785968038 37.46521308 0.183994671 1.00E-05 5 -1.604716012 SGS(ph)YSGRSPS(ph)PYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.215)GS(0.541)Y(0.013)S(0.215)GRS(0.017)PS(1)PYGR 144.53 0.00010556 310790000 354480 309770 322350 361660 328310 321500 396470 342170 361650 TRUE FALSE 337724.4329 341335.9152 337130.0663 325305.2497 385567.1601 310366.3744 335981.2198 312207.7808 417732.8349 0.808469923 0.817115358 0.807047084 0.778739956 0.92299941 0.742978163 0.80429689 0.747386259 1 18.67222102 -1.195438607 4.876607196 1.000023223 0.805260583 0.60947754 0.049384284 1.11E-05 1.84E-06 0.042673016 0.010056928 0.063761921 1.195438607 -0.194762641 SGSFS(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSFSK 6 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;G3V3H3;Q07866-5;Q07866-10;H0YG16 Q07866-6 KLC1 Kinesin light chain 1 1 SGS(0.189)FS(0.811)K 105.25 0.03476 709950000 1019200 904570 816160 991150 487000 924910 988400 1175600 714400 TRUE FALSE 971024.4359 996746.7114 853581.7433 891517.7189 571932.6458 892880.1348 837601.4268 1072658.232 825185.5034 1.176734724 1.207906231 1.034411947 1.080384611 0.693095848 1.082035653 1.015046221 1.29989951 1 19.65435895 3.704515254 5.437378623 1.020241066 1.192754812 0.174030523 0.146725078 0.276851067 23.31958002 0.03744803 0.060451558 5064.251371 -3.704515254 0.172513746 SGSGS(ph)VGNGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSGSVGNGSSR 12 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 S(0.001)GS(0.011)GS(0.987)VGNGS(0.001)SR 68.856 0.054066 13992000 25995 32129 28507 36960 27900 23704 26542 28299 29955 TRUE FALSE 24766.26787 35402.98163 29814.07415 33244.71058 32765.75117 22883.12454 22492.53042 25820.98954 34600.26841 0.715782536 1.023199624 0.861671759 0.960822332 0.946979682 0.66135685 0.650068091 0.746265585 1 15.07849561 2.241951261 24.99799021 0.723494295 0.902228457 0.197727568 0.125920306 98.05229236 722909.7491 0.041514962 0.033426983 174.5626237 -2.241951261 0.178734162 SGSGSVGNGSS(ph)RYSPSQNSPIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 1 SGSGSVGNGS(0.032)S(0.473)RY(0.02)S(0.473)PS(0.002)QNSPIHHIPSRR;SGSGSVGNGS(0.064)S(0.34)RY(0.251)S(0.278)PS(0.053)QNS(0.011)PIHHIPS(0.003)RR 112.26 0.00025775 350920000 20025.4 13033 24152.8 18166.8 24752.4 17819.8 26148.2 22308.1 9419.9 TRUE FALSE 19078.83903 14361.07752 25260.22977 16340.63875 29069.21072 17202.69586 22158.81185 20354.6845 10880.68998 1.753458564 1.319868275 2.321565067 1.501801703 2.671633028 1.581029869 2.036526349 1.870716336 1 13.40948243 3.75929046 24.92336927 1.907158217 1.536663452 0.065794662 0.466884353 1541.852902 1853754.617 0.103263882 0.18590832 5745.005648 -3.75929046 -0.370494765 SGSGSVGNGSSRYS(ph)PS(ph)QNSPIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 S(0.067)GS(0.075)GS(0.085)VGNGS(0.102)S(0.108)RY(0.047)S(0.545)PS(0.822)QNS(0.15)PIHHIPSRR;S(0.017)GS(0.019)GS(0.022)VGNGS(0.125)S(0.134)RY(0.046)S(0.647)PS(0.589)QNS(0.401)PIHHIPSRR 62.666 0.01361 220720000 79147 43188 87513 75012 84203 76151 116307 91735 29158 TRUE FALSE 75405.87816 47588.9063 91525.55761 67471.65125 98887.97654 73513.87178 98562.23103 83702.19708 33679.67372 2.238913559 1.412985966 2.717531006 2.003334468 2.936132261 2.182737053 2.926460388 2.485243704 1 15.03959054 3.731025359 24.91809251 2.434001534 1.825949756 0.083529974 0.598490001 817.6130867 2703737.576 0.139008145 0.219987466 5383.012133 -3.731025359 -0.608051778 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 SGSGS(0.003)VGNGS(0.021)S(0.025)RY(0.001)S(0.949)PS(0.004)QNS(0.996)PIHHIPSR;SGSGSVGNGSS(0.012)RY(0.01)S(0.973)PS(0.005)QNS(1)PIHHIPSR;SGSGSVGNGS(0.002)S(0.002)RY(0.001)S(0.993)PS(0.003)QNS(1)PIHHIPSR;SGSGSVGNGSS(0.008)RY(0.001)S(0.991)PS(0.022)QNS(0.979)PIHHIPSR;SGSGSVGNGS(0.008)S(0.009)RY(0.024)S(0.94)PS(0.019)QNS(1)PIHHIPSR;SGSGSVGNGS(0.006)S(0.007)RY(0.002)S(0.983)PS(0.001)QNS(1)PIHHIPSR 221.86 3.28E-27 3230250000 791699 647036 753893 887789 769978 795641 946154 828652 190072 TRUE FALSE 754276.9573 712969.704 788459.7398 798546.763 904261.9194 768087.7527 801800.83 756090.8379 219547.395 3.435599667 3.247452351 3.591296265 3.637240893 4.118754948 3.498505426 3.652062599 3.443861577 1 17.74417289 0.741599404 4.989017748 1.000000945 3.568960359 0.930769489 0.221246282 2.62449522 50.54983055 0.227996343 0.057632202 5.515684347 -0.741599404 2.568959414 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.002)GS(0.002)VGNGS(0.004)S(0.004)RY(0.01)S(0.953)PS(0.094)QNS(0.927)PIHHIPS(0.004)RR;SGSGSVGNGS(0.001)S(0.011)RY(0.168)S(0.818)PS(0.037)QNS(0.96)PIHHIPS(0.005)RR;SGSGSVGNGS(0.001)S(0.094)RY(0.11)S(0.786)PS(0.147)QNS(0.853)PIHHIPS(0.009)RR;S(0.071)GS(0.093)GS(0.1)VGNGS(0.109)S(0.113)RY(0.136)S(0.485)PS(0.144)QNS(0.597)PIHHIPS(0.152)RR 160.77 1.69E-11 1837360000 205642 116920 226319 186171 236342 192856 324379 220596 100825 TRUE FALSE 195921.7102 128834.2809 236695.95 167456.7374 277559.97 186177.3484 274889.0259 201279.4448 116460.4261 1.68230288 1.106249438 2.032415285 1.437885323 2.383298597 1.598631867 2.360364248 1.728307646 1 16.82948028 2.808689987 24.99998672 1.917268474 1.52735118 0.041037202 0.454186284 286.6138131 102172.0483 0.124287741 0.131827045 643.7096007 -2.808689987 -0.389917294 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSR ddPTM_SK-BR-3_Trastuzumab_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 1 SGSGSVGNGS(0.006)S(0.006)RYS(0.986)PS(0.001)QNSPIHHIPSR;S(0.001)GS(0.001)GS(0.001)VGNGS(0.155)S(0.155)RYS(0.663)PS(0.021)QNS(0.001)PIHHIPSR;S(0.004)GS(0.004)GS(0.006)VGNGS(0.024)S(0.014)RY(0.002)S(0.747)PS(0.194)QNS(0.005)PIHHIPSR;SGSGSVGNGS(0.042)S(0.031)RYS(0.463)PS(0.463)QNSPIHHIPSR 197.83 3.51E-25 1295160000 262801 200621 250892 272657 253585 248291 305422 252773 101690 TRUE FALSE 250378.9176 221064.508 262395.6464 245249.0003 297810.1437 239692.6204 258824.2644 230638.8561 117459.5658 2.131617938 1.882047719 2.233923176 2.087944039 2.535426907 2.040639421 2.203517973 1.963559583 1 16.84180468 0.78619148 3.425642108 1.000043493 2.13903981 0.824925576 0.166440042 0.624212681 9.49324961 0.157078779 0.040592933 6.112114476 -0.78619148 1.138996317 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_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 1 SGSGSVGNGSS(0.065)RYS(0.934)PS(0.001)QNSPIHHIPSRR 205.58 1.32E-25 90631000 20312 8432.8 16209 16548 20242 13549 23709 19532 8632.5 TRUE FALSE 19351.89201 9292.111907 16952.19868 14884.5636 23772.19839 13079.79473 20091.7566 17821.67453 9971.184011 1.940781756 0.931896543 1.700118929 1.49275789 2.38408983 1.311759438 2.01498203 1.787317786 1 13.28354911 3.277140554 2.708976771 1.75309462 1.435298269 0.010084714 0.450629234 0.634809304 9.515083134 0.121628888 0.165677102 1892.956152 -3.277140554 -0.317796352 SGSLDSELSVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSLDSELSVSPK 13 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SGSLDSELSVS(1)PK;SGSLDSELSVS(1)PK 206.14 6.74E-08 171981000 441320 433120 386570 474380 241310 442900 461940 490020 268900 TRUE FALSE 420459.6782 477255.4204 404294.6169 426694.4211 283394.3876 427562.2619 391462.5689 447111.251 310599.6386 1.35370305 1.536561416 1.301658362 1.373776296 0.912410552 1.376570378 1.260344573 1.439509888 1 18.24469663 -4.097546031 0.056276478 2.23E-11 1.860880773 0.252989346 0.16526556 489.8762582 2.379834785 79.18394873 18.57783635 7.99E-05 4.097546031 1.860880773 SGSLDSELSVS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSLDSELSVSPKR 14 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SGSLDSELS(0.019)VS(0.981)PKR 68.243 0.030832 128920000 215000 170820 211230 203290 176340 200480 238070 226020 209370 TRUE FALSE 204837.3761 188226.7522 220915.1044 182854.903 207093.6402 193537.3273 201748.049 206228.4906 241838.0303 0.847002334 0.778317422 0.913483724 0.756104831 0.856331984 0.800276644 0.83422797 0.852754591 1 17.88368161 0.602861767 1.649055653 0.999969136 0.823216591 0.608771414 0.043358789 1.057746882 3.666755881 0.035511999 0.010110877 4.007391444 -0.602861767 -0.176752544 SGSMDPSGAHPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;; 112.42 0.00045089 463007000 499814 325730 438480 503556 640631 400671 684816 535935 742777 FALSE TRUE 476188.7828 358922.2573 458584.7417 452937.5942 752356.8436 386795.6628 580334.7417 489005.6902 857963.0636 0.555022475 0.418342319 0.534504061 0.527922021 0.876910529 0.450830204 0.676409937 0.569961238 1 19.71055601 -4.999999999 0.154218009 2.581238912 0.438822839 0.548016063 0.123820389 94.04297232 0.849494474 45.44370224 0.53307619 1.00E-05 4.999999999 -2.142416073 SGSPS(ph)DNSGAEEMEVSLAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.092)GS(0.396)PS(0.51)DNS(0.003)GAEEMEVSLAKPK 109.98 0.00042918 362550000 530790 434330 489350 546710 291560 527040 548000 589870 293570 TRUE FALSE 505700.6086 478588.7208 511787.1815 491753.6721 342407.9717 508788.4726 464392.5353 538217.8557 339095.3363 1.491322807 1.411369222 1.509272251 1.450192968 1.009769039 1.500428989 1.369504342 1.587216922 1 18.37133142 -1.851440857 2.795306883 0.84148196 1.412433931 0.412247129 0.156099037 31809355.68 21531514.74 33605256.74 0.035027809 0.014078589 1.851440857 0.57095197 SGSS(ph)PEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)GS(0.002)S(0.996)PEVK;S(0.005)GS(0.041)S(0.954)PEVK;S(0.006)GS(0.029)S(0.964)PEVK;S(0.002)GS(0.017)S(0.981)PEVK;S(0.029)GS(0.23)S(0.74)PEVK 125.75 0.0013099 3324350000 9792900 8569740 7963860 10118800 4801270 9271590 9493290 11086900 6343640 TRUE FALSE 9330009.025 9443006.249 8329010.858 9101639 5638609.968 8950512.513 8044914.254 10116072.26 7327379.292 1.273307775 1.288729008 1.136697109 1.242141103 0.769526149 1.221516201 1.097925184 1.380585317 1 22.80486587 3.584943298 1.967108547 1.112193174 1.284393201 0.145512291 0.160394957 0.570346631 4.348747759 0.04414953 0.079698422 3845.415729 -3.584943298 0.172200027 SGSS(ph)PGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)GS(0.091)S(0.908)PGLR;S(0.004)GS(0.111)S(0.886)PGLR;SGS(0.125)S(0.875)PGLR;S(0.01)GS(0.077)S(0.913)PGLR;SGS(0.058)S(0.942)PGLR;S(0.016)GS(0.082)S(0.901)PGLR 158.37 0.00038329 2331740000 1726572 1547639 1461486 1865150 1421902 1707016 1848750 1892750 1770100 TRUE FALSE 1644960.363 1705345.174 1528496.579 1677661.578 1669881.259 1647901.608 1566689.233 1727010.776 2044598.068 0.804539723 0.834073552 0.747578022 0.820533681 0.816728376 0.805978267 0.766257808 0.844670062 1 20.96338583 0.913648773 6.424165517 0.99999737 0.80144252 0.858976497 0.025464104 0.381291245 28.13304759 0.023930038 0.006009424 8.196883697 -0.913648773 -0.19855485 SGSS(ph)PKWTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSSPKWTHDK 11 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.001)GS(0.02)S(0.979)PKWTHDK 139.86 2.35E-05 233530000 268820 85974 269860 184370 215650 253270 433770 291100 247750 TRUE FALSE 256113.4113 94734.84834 282233.3479 165836.7773 253259.2917 244499.1964 367590.4198 265609.7408 286169.8047 0.894970074 0.33104418 0.986244332 0.579504807 0.884996557 0.854385027 1.28451854 0.928154321 1 18.12651193 2.272578882 1.757008474 1.091980685 0.67455469 0.348578467 0.205023525 0.316545183 1.965812317 0.096875296 0.062867183 187.3177283 -2.272578882 -0.417425995 SGSS(ph)QELDVKPSASPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.024)GS(0.155)S(0.82)QELDVKPSASPQER;S(0.056)GS(0.164)S(0.781)QELDVKPSASPQER 171.5 7.94E-12 597370000 705940 635860 623730 779930 483450 766640 763720 788310 546970 TRUE FALSE 672571.6152 700654.8569 652328.6375 701529.9546 567763.5269 740091.0646 647200.4873 719281.3973 631791.3141 1.064547106 1.108997293 1.032506498 1.110382398 0.898656747 1.171416966 1.024389657 1.138479402 1 19.26908858 3.739941912 24.79585864 1.055947453 1.086772196 0.03020672 0.077108626 445.5206052 7997606.997 0.017781153 0.030109035 5494.673765 -3.739941912 0.030824744 SGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.022)GS(0.147)S(0.833)S(0.994)PDS(0.004)EITELKFPSINHD;S(0.016)GS(0.307)S(0.689)S(0.988)PDSEITELKFPSINHD 196.18 5.57E-22 269730000 123168 109381 111204 128690 86953 126195 141869 121794 81552 TRUE FALSE 117346.0927 120527.0483 116302.8134 115753.8367 102117.5757 121824.8355 120224.2784 111129.0717 94198.66765 1.245729857 1.279498439 1.234654548 1.228826687 1.08406603 1.293275569 1.276284277 1.179730823 1 16.52341903 0.907200986 5.156660308 1.000019129 1.238981555 0.616964996 0.05789637 0.433497867 23.03388328 0.055123966 0.013920476 8.076086951 -0.907200986 0.238962426 SGSSS(ph)PDSEITELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSSSPDSEITELK 14 0 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 SGSS(0.025)S(0.975)PDSEITELK 218.11 4.48E-08 0 445170 491450 353820 530630 266800 456360 431410 460680 271040 TRUE FALSE 424127.6963 541529.3137 370042.997 477290.0643 313329.8355 440556.1388 365590.4811 420340.417 313071.4989 1.354731101 1.729730479 1.181975997 1.524540132 1.000825168 1.40720615 1.167753955 1.34263393 1 18.25613265 2.777339634 0.193730781 0.945901476 1.7378478 0.290934241 0.190847899 6.186483839 0.564790579 0.606862113 1.456520969 598.8797573 -2.777339634 0.791946324 SGSSS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 SGS(0.001)S(0.005)S(0.988)PDS(0.007)EITELKFPSINHD;S(0.003)GS(0.013)S(0.09)S(0.637)PDS(0.258)EITELKFPSINHD;S(0.009)GS(0.036)S(0.145)S(0.788)PDS(0.022)EITELKFPSINHD;SGSS(0.003)S(0.997)PDSEITELKFPSINHD;SGS(0.001)S(0.022)S(0.917)PDS(0.06)EITELKFPSINHD;SGS(0.003)S(0.1)S(0.895)PDS(0.002)EITELKFPSINHD;S(0.004)GS(0.011)S(0.098)S(0.881)PDS(0.006)EITELKFPSINHD;S(0.004)GS(0.024)S(0.17)S(0.8)PDS(0.001)EITELKFPSINHD;SGS(0.001)S(0.039)S(0.861)PDS(0.098)EITELKFPSINHD;S(0.046)GS(0.04)S(0.18)S(0.716)PDS(0.019)EITELKFPSINHD;S(0.004)GS(0.02)S(0.144)S(0.781)PDS(0.051)EITELKFPSINHD;SGS(0.002)S(0.086)S(0.773)PDS(0.138)EITELKFPSINHD;S(0.001)GS(0.005)S(0.023)S(0.97)PDS(0.002)EITELKFPSINHD 292.26 5.65E-55 13267378000 6101339 4666130 5390920 5973971 4322415 5546052 6862303 6191322 4400101 TRUE FALSE 5812940.797 5141613.952 5638099.014 5373456.085 5076242.807 5353990.829 5815332.643 5649177.023 5082446.19 1.143728941 1.011641591 1.109327832 1.057257841 0.998779449 1.053427942 1.14419955 1.111507493 1 22.27709161 SGSTGS(ph)SLSVSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGSTGS(0.94)S(0.06)LSVSVR;SGST(0.001)GS(0.965)S(0.034)LSVSVR;SGST(0.011)GS(0.96)S(0.029)LSVSVR;SGST(0.002)GS(0.966)S(0.032)LSVSVR 241.15 7.43E-17 525310000 480540 417237 459046 512596 414910 422392 506964 491831 474412 TRUE FALSE 457825.8265 459753.9247 480093.7132 461068.8762 487270.1726 407764.4591 429617.3308 448763.6703 547981.39 0.835476961 0.838995508 0.876113171 0.841395136 0.889209345 0.744120999 0.783999856 0.818939618 1 19.06376737 2.275282736 24.99958728 0.812374013 0.85222811 0 0.069299171 442.8096196 301453.2874 0.021395158 0.017900016 188.4875789 -2.275282736 0.039854097 SGSTS(ph)PLGFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGSTSPLGFAR 11 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 S(0.013)GS(0.079)T(0.164)S(0.743)PLGFAR;SGS(0.007)T(0.241)S(0.752)PLGFAR;SGST(0.023)S(0.976)PLGFAR 171.67 1.50E-05 233728000 764110 625510 684030 806920 650650 691500 810410 768670 698160 TRUE FALSE 727992.0346 689250.1801 715393.4521 725806.8686 764123.154 667553.1816 686767.0703 701361.1798 806427.0871 0.902737577 0.854696216 0.88711486 0.900027889 0.947541528 0.82779112 0.851617067 0.869714313 1 19.62118457 -0.918232034 4.68538775 1.000000864 0.877741643 0.563475933 0.033089831 3.73084E+11 86048190636 4429431.358 0.007782008 0.12071687 0.918232034 -0.122259222 SGSYSGRS(ph)PS(ph)PYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.067)GS(0.119)Y(0.003)S(0.402)GRS(0.413)PS(0.992)PY(0.002)GR 102.5 0.013988 40229000 77220 67626 72328 83571 70505 73824 93491 74039 77094 TRUE FALSE 73569.96364 74517.16628 75644.31034 75170.28431 82801.04968 71267.45637 79227.23087 67555.75265 89049.34378 0.826170756 0.836807585 0.849465107 0.844141923 0.92983335 0.800314223 0.889700334 0.758632796 1 16.44231736 -2.348025374 2.477731988 2.129708662 0.844892362 0.537132726 0.046053092 2497978.962 1096209.841 15475300.07 0.009780382 0.004487192 2.348025374 -1.2848163 SGT(ph)PPRQGS(ph)ITSPQANEQS(ph)VTPQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGTPPRQGSITSPQANEQSVTPQRR 25 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.155)GT(0.773)PPRQGS(0.34)IT(0.358)S(0.375)PQANEQS(0.735)VT(0.265)PQRR;S(0.198)GT(0.788)PPRQGS(0.498)IT(0.498)S(0.018)PQANEQS(0.693)VT(0.306)PQRR;S(0.147)GT(0.853)PPRQGS(0.337)IT(0.337)S(0.337)PQANEQS(0.64)VT(0.349)PQRR 94.188 0.017368 1449730000 550140 429230 542970 542180 391290 518760 599410 467720 442030 TRUE FALSE 524135.9725 472969.025 567865.7116 487679.0363 459530.8521 500795.2111 507958.9956 426763.9573 510577.7548 1.026554658 0.926340837 1.112202218 0.955151359 0.900021295 0.980840247 0.994870988 0.835845184 1 18.96177116 3.032684999 24.99904272 0.947417052 1.005923658 0.223536035 0.065729063 347.4191058 265720.4464 0.018024007 0.02154268 1078.164428 -3.032684999 0.058506606 SGT(ph)PPRQGSITSPQANEQSVTPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)GT(0.998)PPRQGSITSPQANEQSVTPQR;S(0.005)GT(0.995)PPRQGSITSPQANEQSVTPQR;S(0.381)GT(0.498)PPRQGS(0.042)IT(0.065)S(0.014)PQANEQSVTPQR 224.06 1.16E-32 569450000 41454.8 34085.7 37918.3 38684 26439.9 37175.4 35643 37039.8 23351.6 TRUE FALSE 39495.31376 37559.07158 39656.89156 34795.41083 31051.01019 35888.00658 30205.00572 33796.39875 26972.84686 1.464261965 1.3924771 1.470252353 1.290016252 1.151195139 1.330523499 1.119830097 1.252978557 1 14.71922018 2.85075159 0.204804062 0.945089228 1.667846867 0.746879873 0.076220586 2.501939254 0.235966512 0.209895252 0.538759715 709.1720156 -2.85075159 0.722757639 SGT(ph)PPRQGSITSPQANEQSVTPQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQRR 25 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.027)GT(0.973)PPRQGSITSPQANEQSVTPQRR 166.2 6.81E-10 333040000 122060 66447 113140 89035 88900 110990 141970 114220 97161 TRUE FALSE 116290.4657 73218.02484 118327.5809 80085.03264 104404.1319 107146.3885 120309.869 104218.2913 112228.2317 1.036196187 0.652402909 1.054347727 0.713590791 0.930284032 0.954718674 1.072010734 0.928628116 1 16.77607611 2.300775564 2.8848074 1.00593827 0.85671644 0.166293082 0.127767912 0.373941213 6.369028642 0.046446621 0.035430431 199.8828643 -2.300775564 -0.14922183 SGT(ph)PTQDEMMDKPTSSSVDTMSLLSK ddPTM_SK-BR-3_Trastuzumab_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(0.155)GT(0.715)PT(0.12)QDEMMDKPT(0.01)SSSVDTMSLLSK;S(0.001)GT(0.99)PT(0.009)QDEMMDKPTSSSVDTMSLLSK;S(0.05)GT(0.689)PT(0.182)QDEMMDKPT(0.033)S(0.02)S(0.025)S(0.001)VDTMSLLSK;S(0.21)GT(0.738)PT(0.05)QDEMMDKPT(0.001)S(0.001)SSVDTMSLLSK 309.63 1.67E-81 932870000 1668260 1462500 1405800 1632410 714160 1693320 1726350 1759380 738810 TRUE FALSE 1589404.656 1611530.413 1470257.321 1468317.045 838709.2779 1634679.904 1462963.601 1605319.36 853380.8815 1.862479803 1.888406979 1.722861799 1.720588166 0.982807673 1.915533778 1.714314947 1.881128808 1 19.70283026 3.377469395 2.459278377 1.578864325 1.870247969 0.15818039 0.321502517 0.557152388 6.831057547 0.090013747 0.132005736 2384.895724 -3.377469395 0.291383644 SGTASVVCLLNNFYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGTASVVCLLNNFYPR 16 0 A0A5H1ZRQ3;P01834 A0A5H1ZRQ3 IGKC Ig kappa chain C region 0 170.04 7.17E-12 0 55443 34897 37116 45105 34428 41175 43901 42492 36311 FALSE TRUE 52822.31927 38453.04397 38817.80531 40570.95971 40432.2323 39749.09943 37203.09615 38771.17522 41941.92443 1.259415727 0.916816395 0.925513215 0.967312784 0.964005177 0.947717587 0.887014524 0.924401437 1 15.35610544 4.564958674 2.364603852 0.936156111 1.281394626 0.899634095 0.033150376 0.106553846 0.942132483 0.008402381 0.0649357 36724.73532 -4.564958674 0.345238515 SGTAT(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGTATPQR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.017)GT(0.29)AT(0.692)PQR 75.387 0.082636 0 124740 110260 128610 141190 119390 109210 132170 138940 154180 TRUE FALSE 118843.7874 121495.6194 134506.8957 126997.313 140211.5782 105428.0303 112005.039 126773.677 178089.447 0.667326388 0.682216838 0.755277182 0.713109705 0.787309864 0.591994821 0.62892575 0.711853954 1 17.4422425 0.955104609 22.92422228 1 0.684930653 0.748972781 0.056090293 2044.686859 1044047.639 0.055689421 0.013922355 9.017883266 -0.955104609 -0.315069348 SGTHNMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SGTHNMYR 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;;;; 162.97 0.00033863 521042000 623871 461682 338410 387996 798033 358515 740426 518652 738868 FALSE TRUE 594381.8542 508727.9207 353926.4332 348993.9049 937209.7025 346099.5357 627460.4148 473236.0813 853447.8758 0.696447752 0.59608552 0.414701874 0.408922343 1.098145217 0.405530959 0.735206487 0.554499103 1 19.70294352 -4.999999154 0.327662723 4.801910046 0.603219146 0.254915015 0.20701077 480.2640218 4.175094194 1270.405098 0.160070421 1.00E-05 4.999999154 -4.1986909 SGTICSSELPGAFEAAGFHLNEHLYNMIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGTICSSELPGAFEAAGFHLNEHLYNMIIR 30 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;A0A075B7C0 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 251.51 6.63E-48 845010000 649230 609030 588050 687360 691160 609150 854850 681120 63487 FALSE TRUE 618542.1845 671090.8494 615012.6742 618265.2669 811698.0852 588054.9828 724426.9321 621477.522 73332.23971 8.434791941 9.15137533 8.386661536 8.431015735 11.06877532 8.019051171 9.878696395 8.474819866 1 16.16215998 0.949355719 22.0664354 0.999999993 9.044747263 0.889943598 0.884268156 980.0174833 427008.4476 0.760753013 0.190188252 8.899297367 -0.949355719 8.044747271 SGTSEFLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGTSEFLNK 9 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 72.638 0.086614 0 41421 34854 41043 43054 43147 41605 44765 50143 37440 FALSE TRUE 39463.11142 38405.66223 42924.86215 38726.13012 50671.82314 40164.20842 37935.27708 45752.2131 43246.00398 0.912526194 0.888074242 0.992574069 0.895484589 1.171711106 0.928738027 0.87719728 1.057952386 1 15.40027921 3.739679142 24.93081982 0.977856474 0.900300216 0.150314664 0.084545116 182.1996024 4061004.933 0.021569796 0.036314042 5491.350217 -3.739679142 -0.077556257 SGTSSPQS(ph)PVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGTSSPQSPVFR 12 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 SGTSSPQS(1)PVFR;SGTSS(0.001)PQS(0.999)PVFR;SGTSS(0.015)PQS(0.985)PVFR;SGTSS(0.008)PQS(0.992)PVFR;SGTSS(0.009)PQS(0.99)PVFR 271.53 1.07E-27 921680000 1702602 1463244 1650770 1773624 1555229 1559735 1977695 1749677 1720083 TRUE FALSE 1622123.378 1612350.227 1726459.437 1595335.946 1826460.445 1505720.986 1675961.305 1596466.006 1986824.687 0.816440116 0.811521136 0.86895409 0.802957582 0.919286164 0.757852968 0.843537588 0.803526359 1 20.92203315 -1.003323719 4.387144794 1.000006617 0.827124803 0.609956886 0.043217731 6884911.047 21942630.42 809.0235054 0.009038002 0.099237606 1.003323719 -0.172881814 SGVLDESTIATILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGVLDESTIATILR 14 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 94.616 0.0095251 10299000 36456 30034 33577 33012 31751 31774 45757 35022 35134 FALSE TRUE 34732.79713 33094.49875 35116.53866 29693.57104 37288.36435 30673.65841 38775.92927 31955.28802 40582.40128 0.8558586 0.815488924 0.86531446 0.731685906 0.918830901 0.755836457 0.95548632 0.787417378 1 15.30856661 -1.194210527 0.347984279 1.08991329 0.826687 0.346880281 0.069448941 18.05752029 1.499269655 1.588284818 0.04924926 0.06394248 1.194210527 -0.26322629 SGVNSELVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGVNSELVKR 10 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ; 95.483 0.011852 134990000 464010 394230 423210 427680 428910 477670 606320 511730 498850 FALSE TRUE 442077.1669 434402.4852 442614.5971 384688.7939 503711.7682 461128.1681 513814.7482 466920.2083 576209.1102 0.767216552 0.753897287 0.768149252 0.667620117 0.874182236 0.800279204 0.891715766 0.81033118 1 19.13623295 1.041098221 0.409870863 1.008363892 0.739496541 0.657127619 0.053018221 0.712288438 0.329487574 0.071419932 0.038773442 10.9925442 -1.041098221 -0.268867351 SGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.087)GVS(0.503)S(0.409)DNEDDDDEEDGNYLHPSLFASK 221.13 1.69E-34 165610000 267450 201790 254380 273160 248530 246590 349400 314450 289150 TRUE FALSE 254808.1685 222352.6304 266043.5746 245701.4378 291873.5533 238050.5265 296092.6128 286915.091 333989.9052 0.762921767 0.66574656 0.796561724 0.735655282 0.873899327 0.712747669 0.886531623 0.859053182 1 18.34944497 1.14234301 0.345871127 1.023778353 0.704840648 0.661174733 0.057110649 0.768274937 0.285807658 0.092465413 0.058361502 13.87851534 -1.14234301 -0.318937705 SGVSDHWALDDHHALHLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SGVSDHWALDDHHALHLTR 19 0 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;D6RD67 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ; 109.42 7.87E-05 147000000 22663 21380 27220 27993 27891 18078.4 24702 20773.4 13094.3 FALSE TRUE 21591.7649 23558.64631 28468.06392 25179.09046 32755.18157 17452.34047 20933.25622 18954.37097 15124.89717 1.42756441 1.55760704 1.882198841 1.664744572 2.165646563 1.153881595 1.38402635 1.253190072 1 13.88463771 2.192713473 24.99998202 1.243592344 1.689464309 0.590571966 0.220525994 108.8078196 59331.11723 0.083543825 0.061701424 155.8523921 -2.192713473 0.445871965 SGVSS(ph)DNEDDDDEEDGNYLHPSLFASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.004)GVS(0.14)S(0.856)DNEDDDDEEDGNYLHPSLFASK;S(0.003)GVS(0.107)S(0.89)DNEDDDDEEDGNYLHPSLFASK;S(0.001)GVS(0.112)S(0.887)DNEDDDDEEDGNYLHPSLFASK 317.49 1.95E-82 764900000 805830 591450 736920 864110 764710 724890 1113870 896550 834410 TRUE FALSE 767740.0129 651719.4274 770708.5109 777248.0211 898075.1819 699786.8775 943928.6739 818043.3291 963806.0412 0.796571073 0.676193549 0.799651048 0.806436137 0.931800739 0.726066083 0.979376175 0.848763438 1 19.87838332 2.069673033 0.364074949 0.999853716 0.71267248 0.472468767 0.0757835 0.986441453 0.341442281 0.08510072 0.09800279 117.4013344 -2.069673033 -0.287181237 SGYFDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SGYFDER 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 101.64 0.020725 2890600000 7992800 6014200 6459700 7523700 7491300 5879800 7650600 6534200 7185600 FALSE TRUE 7614996.184 6627053.818 6755883.635 6767403.382 8797780.348 5676181.052 6483360.457 5962030.808 8299906.149 0.917479794 0.798449247 0.813971088 0.815359025 1.059985522 0.683884968 0.781136598 0.718325087 1 22.98466359 SGYHDDS(ph)DEDLLE ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;S(0.009)GYHDDS(0.991)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE 222.79 1.77E-11 6737500000 5927980 6082100 6045380 7494460 5983850 6639200 7760190 6621770 5070260 TRUE FALSE 5647776.134 6701872.905 6322566.653 6741102.642 7027431.545 6409282.839 6576230.49 6041932.715 5856530.026 0.964355362 1.144341936 1.079575555 1.151040396 1.199930934 1.094382307 1.122888547 1.03165743 1 22.4816147 1.104318098 4.316964041 1.001346299 1.105761514 0.28801851 0.06111303 0.275459727 8.389431373 0.059054093 0.015131338 12.71505074 -1.104318098 0.104415215 SGYLSSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SGYLSSER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 135.83 0.0019006 1110440000 1718340 1184210 904260 1064160 1676780 983840 1619280 1265650 1649100 FALSE TRUE 1637117.474 1304882.345 945721.2154 957188.615 1969209.901 949769.3741 1372229.096 1154822.976 1904834.006 0.859454141 0.685037301 0.496484845 0.502505002 1.033796066 0.498610048 0.720393006 0.606259114 1 20.86123385 -1.941459538 2.734401024 1.219666397 0.682314507 0.26205519 0.170870646 54729886.91 37949679.12 76826627.67 0.037954179 0.011443015 1.941459538 -0.537351891 SGYRIDFYFDENPYFENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SGYRIDFYFDENPYFENK 18 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 64.679 0.03167 131350000 86629 68016 111480 84739 84827 100960 130140 101880 61292 FALSE TRUE 82534.21885 74946.90773 116591.4683 76220.87473 99620.80194 97463.72988 110284.7528 92958.8471 70796.85032 1.165789417 1.058619238 1.646845414 1.076613922 1.407136073 1.376667598 1.557763549 1.313036479 1 16.11139756 3.786056969 24.99460909 1.368359871 1.112204198 0.178312282 0.195677962 499.2905832 262746.392 0.045159662 0.081412479 6110.221712 -3.786056969 -0.256155674 SHAQKNENAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SHAQKNENAR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 134.13 0.00010744 185863000 212157 109600 232314 164833 321814 160523 326053 205337 331650 FALSE TRUE 202128.7591 120768.3646 242965.8267 148263.6737 377938.2597 154964.0483 276307.6265 187356.6037 383080.5882 0.527640307 0.315255767 0.634242074 0.387029983 0.986576379 0.404520754 0.721278068 0.489078824 1 18.5472884 -4.999999967 0.107034313 2.434987927 0.274955516 0.351569639 0.191129437 167.4068732 1.199801068 53.05947281 2.30032782 1.00E-05 4.999999967 -2.160032411 SHCFVTYSTVEEAVATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHCFVTYSTVEEAVATR 17 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 248.25 7.63E-21 188090000 64728 70703 75280 89418 79550 64842 94082 80279 43093 FALSE TRUE 61668.43572 77907.71608 78731.66246 80429.53276 93423.49481 62596.50528 79728.06297 73249.34517 49775.64235 1.238927974 1.565177513 1.581730717 1.615841182 1.876891797 1.257573028 1.60174855 1.471590154 1 15.60315231 0.95290433 20.21007152 0.999999997 1.524230784 0.45651272 0.181432017 829.8366964 356108.0281 0.167867248 0.041966812 8.972311239 -0.95290433 0.524230787 SHEAEVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;;; 95.741 0.0094349 1540390000 2360590 2260190 1840540 2327610 1885060 2200120 2946220 2221030 863520 FALSE TRUE 2249009.589 2490505.931 1924930.58 2093634.221 2213813.867 2123929.293 2496720.028 2026544.839 997430.2714 2.254803823 2.496922344 1.929889873 2.099028153 2.219517425 2.129401276 2.503152451 2.031765926 1 19.92785646 0.969807839 22.09396496 0.999999996 2.253844347 0.832883986 0.172182505 296.9404576 217295.2568 0.16760665 0.041901663 9.328414577 -0.969807839 1.25384435 SHEESHKE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHEESHKE 8 1 P05109 P05109 S100A8 "Protein S100-A8;Protein S100-A8, N-terminally processed" 0 60.91 0.057973 42415000 23741 24964 26778 42011 25781 35708 44267 24695 8436.1 FALSE TRUE 22618.80998 27507.85998 28005.79779 37787.97446 30277.19824 34471.42301 37513.25613 22532.57488 9744.327302 2.321228473 2.822961414 2.874061689 3.877945936 3.107161459 3.537588787 3.849753294 2.312378698 1 13.25034688 4.048423187 1.646178704 3.181197015 2.382669654 0 0.859946521 0.906026679 4.585639549 0.217728947 0.744980329 11179.52077 -4.048423187 -0.798527361 SHEGETAYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 198.72 2.92E-07 2394100000 421340 365980 386180 441430 411900 391380 475210 348710 235034 FALSE TRUE 401424.0932 403273.7781 403886.735 397056.6177 483735.2296 377826.4125 402707.9867 318175.1038 271481.8723 1.478640507 1.485453797 1.487711616 1.462552967 1.781832523 1.391718752 1.483369712 1.17199392 1 18.05049634 1.122962092 2.129215355 0.997358694 1.514761764 0.76009855 0.10164708 0.131687336 1.132318961 0.08851051 0.024942827 13.27278599 -1.122962092 0.517403069 SHEGETSYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHEGETSYIR 10 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 121.9 0.00050283 264990000 58367 51950 50869 61497 58381 45774 61606 68388 46301 FALSE TRUE 55608.10758 57243.76406 53201.39397 55315.20472 68562.62792 44188.8349 52206.87323 62399.58417 53481.12261 1.039770762 1.070354571 0.994769582 1.034294009 1.281996798 0.826251072 0.976173848 1.166759057 1 15.70674213 2.214526143 24.99999603 0.982936739 1.071965036 0.137181278 0.111159903 474.2318259 493279.8131 0.039559746 0.029232184 163.8800708 -2.214526143 0.089028296 SHELDIDENPAS(ph)DFDDSGSLLGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 SHELDIDENPAS(0.834)DFDDS(0.067)GS(0.099)LLGFK 75.275 6.56E-05 0 9284.3 9048.2 6067.6 9660.9 6493.7 7659.4 8765.6 7815.6 4275.5 TRUE FALSE 8845.449539 9970.221867 6345.805462 8689.767977 7626.199224 7394.153057 7428.246729 7131.224631 4938.522704 1.791112458 2.018867274 1.284960269 1.759588545 1.544226823 1.497239863 1.504143481 1.443999564 1 12.26986383 1.653771674 0.072995372 2.04E-12 2.952458449 0.622900766 0.172424851 10.4101649 0.766195176 14.62748517 15.10916719 45.05797548 -1.653771674 2.952458449 SHFEQWGTLTDCVVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 215.48 1.22E-14 585520000 279370 295796 257781 372324 260255 268347 307111 260985 171867 FALSE TRUE 266164.7338 325937.9487 269600.5138 334897.2842 305643.3896 259054.0761 260255.5765 238131.7698 198519.2566 1.340750204 1.641845503 1.358057241 1.686976316 1.539615828 1.304931726 1.310984037 1.199539903 1 17.59891943 1.382419134 0.939551943 1.017232675 1.513550601 0.67660246 0.116468722 0.27971962 0.510008186 0.1010841 0.037028406 24.12232331 -1.382419134 0.496317926 SHFEQWGTLTDCVVMRDPNTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 249.34 7.06E-31 263860000 127210 127320 131690 155140 99865 138780 166770 142230 70678 FALSE TRUE 121197.0354 140294.0528 137728.1168 139545.0325 117281.4244 133974.0138 141326.1736 129775.5872 81638.38327 1.484559475 1.718481517 1.687051008 1.709306663 1.436596607 1.641066474 1.73112411 1.589639358 1 16.31695999 0.950306763 22.58047444 0.999999999 1.63415073 0.801164142 0.097988307 1929.260187 876652.0645 0.092021276 0.023005319 8.918806936 -0.950306763 0.634150731 SHFEQWGTLTDCVVMRDPNTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 200.29 1.00E-22 3339090000 2839270 2119690 3286730 2845180 2791030 3098180 4090530 3144960 2021380 FALSE TRUE 2705063.334 2335688.821 3437429.822 2559177.101 3277784.748 2990889.25 3466444.521 2869570.63 2334845.287 1.158562132 1.000361281 1.472230234 1.096079948 1.403855222 1.280979629 1.484657052 1.229019604 1 21.15489553 3.751953017 24.93889983 1.308981247 1.0794617 0.202602442 0.15881555 853.090414 1588593.247 0.036496609 0.065325299 5648.758622 -3.751953017 -0.229519547 SHHAPMS(ph)PGSSGGGGQPLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHHAPMSPGSSGGGGQPLAR 20 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(0.995)PGS(0.004)S(0.001)GGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR 169.05 3.80E-11 642521000 157429 186855 230629 268819 257008 228518 324327 161010 33669.5 TRUE FALSE 149987.6432 205895.7369 241203.5678 241796.8034 301830.1138 220604.3644 274844.9595 146911.1108 38890.7941 3.856636169 5.294202438 6.20207361 6.217327493 7.760965566 5.672405757 7.06709559 3.777529213 1 15.24714107 4.30633328 1.98949323 5.85135084 3.896451177 0.013409562 1.924419314 0.804842183 5.714708489 0.446813831 2.078167413 20245.72252 -4.30633328 -1.954899663 SHHCTLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SHHCTLAR 8 0 Q9HCN6-3 Q9HCN6-3 0 ;;;;;;; 92.692 0.02698 2809280000 5051740 4541290 4414390 5212990 5322490 4610040 5767130 5045760 5573470 FALSE TRUE 4812954.262 5004052.614 4616794.148 4688970.341 6250730.571 4450393.159 4887248.398 4603926.505 6437775.262 0.747611413 0.777295325 0.717141242 0.728352599 0.970945756 0.69129365 0.759151756 0.71514247 1 22.61813078 -1.288295345 4.936357421 1.000072431 0.763865858 0.477629076 0.077770274 5.67E-05 8.17E-06 0.06885758 0.016224922 0.051487838 1.288295345 -0.236206573 SHHGEHERPEFIAYPHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SHHGEHERPEFIAYPHLR 18 1 P12074;H0YIV9 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ;;;;; 207.53 2.46E-16 2005337000 707115 953926 903247 1315506 1353346 805657 1334082 519670.2 104999.2 FALSE TRUE 673691.0753 1051132.144 944661.7684 1183268.838 1589369.114 777756.8961 1130543.289 474165.1223 121281.9397 5.554751821 8.666848063 7.788973123 9.756348231 13.10474683 6.412800605 9.321612862 3.909610315 1 16.88800521 4.61900518 2.964334506 8.079830433 5.431965266 0.005569466 3.339574753 0.969498106 13.95129715 0.731626397 5.264983723 41591.55709 -4.61900518 -2.647865168 SHIEIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHIEIIR 7 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;;; 128.57 0.0037452 846440000 776220 640041 385108 490437 1094260 423417 1161040 458658 693430 FALSE TRUE 739529.6189 705261.9056 402765.5827 441137.341 1285098.598 408753.9631 983902.024 418495.474 800963.5829 0.923299929 0.880516818 0.502851305 0.5507583 1.604440732 0.510327775 1.228397951 0.522490015 1 19.61137712 SHILEDDENS(ph)VDISMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHILEDDENSVDISMLK 17 0 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 SHILEDDENS(1)VDISMLK;SHILEDDENS(1)VDISMLK;SHILEDDENS(1)VDISMLK;S(0.001)HILEDDENS(0.999)VDISMLK 250.83 1.13E-21 542121000 544336 639609 688298 869348 606788 884030 1012780 806897 334734 TRUE FALSE 518606.3161 704785.8843 719857.1441 781959.4874 712611.6351 853415.8194 858261.81 736240.821 386642.8391 1.341305886 1.822834443 1.861814241 2.022433647 1.843074701 2.207245895 2.219779401 1.904188431 1 18.56064197 4.550569177 1.084161543 1.966525931 1.144514021 0.139251233 0.346991578 1.649795709 1.996267954 0.093845968 1.448358563 35527.87046 -4.550569177 -0.822011909 SHIMAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SHIMAAK 7 0 P48643;E7ENZ3;H0Y914 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 91.041 0.016695 413171000 2189598 1936923 1205079 1560642 2076545 1696722 2819399 1912595 1136504 FALSE TRUE 2086100.042 2134297.656 1260333.064 1403763.301 2438693.791 1637964.092 2389247.901 1745118.042 1312747.236 1.589110215 1.62582529 0.960072914 1.069332513 1.857702476 1.247737605 1.820036512 1.329363334 1 20.32415773 2.749664734 24.92977369 1.510345432 1.374932934 0.009918991 0.325415073 2844.065292 6385186.961 0.098055413 0.10310463 561.9073779 -2.749664734 -0.135412498 SHKDEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHKDEVVK 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 88.417 0.0087904 365150000 805810 839830 770180 969820 641170 849420 1007770 878540 364880 FALSE TRUE 767720.9583 925409.6318 805493.5148 872331.8511 752989.845 820004.3724 854016.1775 801610.3802 421463.7269 1.821558795 2.195704097 1.911181114 2.069767326 1.786606526 1.945610785 2.026310031 1.901967664 1 18.68504895 0.792316473 5.23745175 1.000001174 1.975417166 0.867932791 0.117558834 1.770767353 44.52492384 0.1054472 0.026611149 6.198926296 -0.792316473 0.975415992 SHLEVPLEENVNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHLEVPLEENVNRR 14 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 88.075 0.0043428 99062000 34045 36102 48020 50811 34559 44816 42569 41745 28607 FALSE TRUE 32435.76032 39780.83484 50221.7645 45703.38175 40586.07866 43264.01068 36074.31722 38089.5865 33043.22746 0.981615987 1.203902824 1.519880725 1.383139156 1.22827223 1.309315524 1.091731044 1.15271992 1 15.01206699 SHLGNVHDQDN ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SHLGNVHDQDN 11 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;;;;;; 205.02 3.12E-08 1493732000 1036505 1652521 2092720 2084870 1073027 2042120 1824350 1267700 382887 FALSE TRUE 987511.4628 1820914.769 2188673.282 1875294.907 1260162.569 1971400.872 1546011.901 1156693.467 442263.1604 2.232859417 4.117265311 4.948803061 4.240224089 2.849350074 4.45752902 3.495683202 2.615396377 1 18.75454555 0.956042877 2.1668499 1.009334719 3.761193786 0.572307957 0.778145756 0.26416038 2.705082952 0.747095642 0.205923053 9.037386938 -0.956042877 2.751859067 SHLLNCCPHDVLSGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHLLNCCPHDVLSGTR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 155.92 1.23E-07 453130000 481250 464280 442050 549880 492530 479590 668170 485060 288030 FALSE TRUE 458502.2662 511590.6598 462318.4297 494605.0177 578427.0761 462981.678 566228.3947 442585.5749 332696.2213 1.378140889 1.537711062 1.389611303 1.486656553 1.738604285 1.391604859 1.70193816 1.330299374 1 18.34384596 0.986399713 18.4602937 0.999999992 1.515578328 0.645885255 0.12289248 13.3625005 18138.65853 0.110286867 0.027571936 9.691694428 -0.986399713 0.515578335 SHMS(ph)GSPGPGGSNTAPSTPVIGGSDKPGMEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHMSGSPGPGGSNTAPSTPVIGGSDKPGMEEK 32 1 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 S(0.061)HMS(0.728)GS(0.21)PGPGGSNTAPSTPVIGGSDKPGMEEK 137.91 8.64E-09 157230000 146990 133660 146400 222490 109650 188150 194600 148580 44446 TRUE FALSE 140042.074 147280.106 153112.5848 200124.8825 128772.9253 181634.3183 164910.1959 135569.5475 51338.45868 2.727819993 2.868806539 2.982414914 3.898147464 2.508313038 3.537977629 3.212215562 2.640701552 1 15.64775236 0.848197976 3.669578459 1.000351271 3.083319135 0.735736507 0.394886599 0.422215009 9.357234362 0.361310651 0.092901161 7.050143805 -0.848197976 2.082967864 SHNVAAGSYEAPLPPGS(ph)FHGDFAYGTYR ddPTM_SK-BR-3_Trastuzumab_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 SHNVAAGSYEAPLPPGS(0.362)FHGDFAY(0.138)GT(0.362)Y(0.138)R 82.058 0.0080924 155360000 27310 33582 44451 43739 35990 36552 48654 35461 22595 TRUE FALSE 26019.11042 37004.04398 46489.12232 39342.27262 42266.64461 35286.19507 41230.93871 32355.84685 26098.9172 0.996942142 1.417838284 1.781266325 1.507429305 1.619478857 1.352017588 1.579794993 1.239739051 1 14.67170233 0.989260555 5.392704454 1.000293333 1.446492293 0.360048985 0.204288343 0.178721763 21.36320344 0.208741292 0.052650757 9.755747587 -0.989260555 0.44619896 SHPLDLS(ph)PNVQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 111.33 0.00063673 118350000 86397 71249 84744 94976 92307 82193 97405 87376 79284 TRUE FALSE 82313.18503 78509.3541 88629.59622 85428.83204 108405.3116 79346.6358 82544.07828 79724.89423 91578.95779 0.898822033 0.857285953 0.967794331 0.932843462 1.183736026 0.866428683 0.901343281 0.870559091 1 16.48272853 3.73478993 24.75540911 0.955295976 0.878053992 0.123285569 0.090489339 578.8040985 3799983.867 0.023709058 0.03829248 5429.876226 -3.73478993 -0.077241985 SHPLDPIDTVDFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SHPLDPIDTVDFER 14 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ;;;;;; 220.21 4.73E-12 1975732000 1584570 1462021 1475345 1742820 1493817 1515520 1661068 1557507 1277008 FALSE TRUE 1509670.516 1611002.602 1542991.028 1567628.422 1754338.212 1463037.162 1407641.569 1421123.43 1475039.879 1.023477764 1.092175626 1.04606733 1.062770197 1.189349683 0.991862785 0.954307466 0.963447464 1 20.49232253 2.022876806 24.9434405 0.968902266 1.077293952 0.578081859 0.044808242 151.2466892 164909.2082 0.01601708 0.011828725 105.4087848 -2.022876806 0.108391686 SHPS(ph)GSGAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHPSGSGAKK 10 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 SHPS(0.982)GS(0.017)GAKK 53.252 0.088705 38394000 108390 88399 106950 110410 66521 116200 125650 138040 71367 TRUE FALSE 103266.6195 97406.9586 111853.7633 99311.37703 78122.24134 112175.9649 106479.7848 125952.4858 82434.22987 1.252715282 1.181632421 1.356884919 1.204734698 0.947691772 1.360793508 1.291693814 1.527914872 1 16.3309559 SHPSDGYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHPSDGYNR 9 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8VWU8;F8VPY7;F8VRK2 F8W0Q9 PPHLN1 Periphilin-1 0 85.676 0.014654 14568000 17085 14645 14398 16639 24635 14866 22537 19092 24016 FALSE TRUE 16277.42591 16137.34215 15058.16254 14966.41611 28931.3362 14351.18669 19098.56673 17420.20327 27740.27862 0.586779467 0.581729635 0.542826651 0.539519315 1.042936035 0.517341116 0.688477826 0.627975065 1 14.75969466 -4.999999996 0.170682818 2.407616601 0.550054906 0.373814254 0.149271056 138.1955631 1.305416576 66.00670423 0.494835299 1.00E-05 4.999999996 -1.857561695 SHQGLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 132.08 0.0079173 341326000 380813 478914 401518 530839 389297 445682 437949 393036 195704 FALSE TRUE 362812.7242 527715.8811 419927.9975 477478.0552 457190.2735 430247.9206 371131.8366 358619.6842 226052.7768 1.60499123 2.334480861 1.857654674 2.112241495 2.022493508 1.90330739 1.641792867 1.586442287 1 17.78630011 1.019146098 0.874546163 1.009708806 2.005278151 0.727872941 0.189946559 0.30308722 0.509452398 0.169594587 0.059874698 10.45071726 -1.019146098 0.995569344 SHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.426)HS(0.56)DNDRPNCS(0.013)WNTQYSSAYYTSR 276.3 2.90E-52 503740000 111960 106010 120030 137310 112220 116200 159810 106800 55744 TRUE FALSE 106667.8727 116812.5395 125533.4942 123507.3379 131791.1325 112175.9649 135428.0494 97448.02582 64388.49482 1.656629387 1.814183417 1.949626165 1.918158489 2.046811823 1.742174051 2.103295779 1.513438481 1 15.9745153 0.972251445 5.173531905 1.000428913 1.877310218 0.826147903 0.132758172 0.072409907 7.319996521 0.131265485 0.0331525 9.38104987 -0.972251445 0.876881306 SHS(ph)GPAGSFNKPAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHSGPAGSFNKPAIR 15 1 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 S(0.002)HS(0.998)GPAGSFNKPAIR;S(0.004)HS(0.996)GPAGSFNKPAIR 156.73 1.25E-06 400340000 490390 400920 447380 515920 409690 459250 553140 362850 207938 TRUE FALSE 467210.2366 441774.2038 467892.8155 464058.7414 481139.8063 443346.0573 468748.3339 331076.9304 240183.963 1.945218285 1.83931599 1.948060185 1.932097112 2.003213704 1.845860364 1.951622115 1.378430626 1 17.8737803 1.064254348 3.045669484 1.004257547 1.920955451 0.971197319 0.054614435 0.031979059 0.612781319 0.049628202 0.013146244 11.59456201 -1.064254348 0.916697904 SHS(ph)GTS(ph)PDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Trastuzumab_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(0.397)HS(0.571)GT(0.514)S(0.518)PDNTAPPPPPPRPQPSHSR 88.045 0.02052 83149000 8811.2 6687.5 7847.9 10096 10652 7590.8 10423 5973.2 4526.1 TRUE FALSE 8394.712038 7368.963853 8207.733978 9081.130899 12509.70543 7327.928693 8832.779918 5450.154942 5227.984472 1.605726276 1.409522904 1.56996143 1.737023311 2.39283523 1.401673768 1.689519157 1.042496391 1 12.35203914 1.229453382 8.311887758 1.016890923 1.662673418 0.500092964 0.275753454 0.124346969 61.38162137 0.229746537 0.066744771 16.9610753 -1.229453382 0.645782495 SHS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.079)HS(0.379)GT(0.271)S(0.271)PDNTAPPPPPPRPQPSHSR;S(0.053)HS(0.316)GT(0.316)S(0.316)PDNTAPPPPPPRPQPSHSR;S(0.084)HS(0.336)GT(0.29)S(0.29)PDNTAPPPPPPRPQPSHSR;S(0.01)HS(0.33)GT(0.33)S(0.33)PDNTAPPPPPPRPQPSHSR 114.79 0.0010309 1385580000 186158 195043 206540 235233 186759 217788 254611 178127 69265.7 TRUE FALSE 177358.6803 214918.1034 216010.0633 211586.9319 219329.7105 210245.947 215765.4157 162529.2556 80007.071 2.216787567 2.686238863 2.699887155 2.644602899 2.741379077 2.627842069 2.69682933 2.031436141 1 16.28783989 0.923573374 3.021121027 1.00162438 2.608725058 0.922496906 0.149932163 0.089149632 1.899978138 0.151778195 0.039824369 8.386357546 -0.923573374 1.607100678 SHS(ph)PERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSPERK 7 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 S(0.029)HS(0.971)PERK 55.567 0.0777 113360000 183220 160340 171080 214000 117970 171330 189130 187950 82832 TRUE FALSE 174559.5537 176678.8283 178924.1872 192488.3134 138543.9306 165396.7991 160274.7449 171492.1016 95677.16351 1.824464139 1.846614404 1.87008248 2.011852216 1.448035514 1.728696724 1.675161961 1.792403697 1 16.545887 -2.277301791 0.258933508 4.77E-18 1.874674166 0.755685856 0.140333018 17.70445963 0.60763976 10.54343164 0.188160934 0.005280782 2.277301791 1.874674166 SHS(ph)PSASQSGSQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.162)HS(0.828)PS(0.009)ASQSGSQLR 143.43 5.88E-06 70120000 81367 69981 75885 94763 91406 69750 108140 74812 74259 TRUE FALSE 77520.94316 77112.14346 79364.40231 85237.2432 107347.1775 67334.54001 91641.25687 68261.06468 85774.70646 0.903773926 0.899007955 0.925265799 0.993734012 1.251501543 0.785016269 1.068394876 0.795818109 1 16.38826466 3.338696149 4.375219106 0.989984393 0.903291533 0.064480351 0.130998067 0.535067048 18.15299961 0.033921826 0.04628318 2181.203313 -3.338696149 -0.08669286 SHS(ph)QASLAGPGPVDPSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.143)HS(0.831)QAS(0.025)LAGPGPVDPSNR;S(0.002)HS(0.991)QAS(0.007)LAGPGPVDPSNR 150.69 2.29E-09 587690000 262637 249204 305166 373130 267446 282281 392890 227287 182281 TRUE FALSE 250222.6695 274598.1709 319158.163 335622.2635 314088.4977 272505.5382 332947.4146 207384.5454 210548.2065 1.188434106 1.304205699 1.515843655 1.594040002 1.491765249 1.294266727 1.58133579 0.984974172 1 17.68379106 1.224127424 24.99414495 0.992486569 1.409819108 0.650631536 0.131209129 190.5333425 329939.6473 0.13601342 0.034629897 16.75434384 -1.224127424 0.417332539 SHS(ph)SPASLQLGTGAGAAGSPAQQHAHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.128)HS(0.853)S(0.019)PASLQLGTGAGAAGSPAQQHAHLR;S(0.124)HS(0.858)S(0.018)PASLQLGTGAGAAGSPAQQHAHLR;S(0.118)HS(0.685)S(0.197)PASLQLGTGAGAAGSPAQQHAHLR 279.69 1.77E-61 590460000 140704 102991 146648 156513 191064 132799 215500 133527 22047.4 TRUE FALSE 134053.2008 113485.9 153371.9559 140780.0159 224385.5011 128200.1373 182621.5171 121834.668 25466.39819 5.263924634 4.456299597 6.022522491 5.528069374 8.811041885 5.034089877 7.171077579 4.784134258 1 14.63630731 3.7276236 23.10105983 5.918105733 4.860112124 0 2.018891843 742.6062102 1568528.242 0.469488205 0.736579901 5341.012568 -3.7276236 -1.057993608 SHS(ph)VGGPLQNIDFTQRPFHGISTVS(ph)LPNSLQEVVDPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 S(0.422)HS(0.487)VGGPLQNIDFT(0.078)QRPFHGIS(0.064)T(0.06)VS(0.887)LPNS(0.002)LQEVVDPLGK 77.127 0.0025753 87850000 41164 43140 45861 59122 37109 61163 58549 36894 15601 TRUE FALSE 39218.2593 47536.01505 47963.77221 53178.94424 43580.79785 59044.90997 49616.27472 33663.36577 18020.3234 2.176334932 2.637911318 2.661648803 2.951053821 2.418424846 3.27657327 2.753350959 1.868077782 1 14.13733728 4.579192897 2.778502887 2.583736052 2.161834269 0 0.64134011 1.17341507 15.24237359 0.139742871 0.950092215 37948.34999 -4.579192897 -0.421901783 SHSAHFFEFLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHSAHFFEFLTK 12 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 134.3 8.55E-05 1012580000 1347500 1175040 1453460 1591210 1500250 1396710 2137060 1393720 309360 FALSE TRUE 1283806.345 1294777.912 1520102.579 1431258.548 1761893.125 1348341.582 1811012.247 1271678.488 357333.9688 3.592735249 3.623439205 4.254010845 4.005380604 4.93066229 3.77333727 5.068122276 3.558795411 1 18.44691354 3.756907825 20.38396447 4.078356789 3.608086122 0 1.134409942 286.641404 318449.8545 0.252823205 0.45349562 5713.573591 -3.756907825 -0.470270667 SHSDNDRPNCS(ph)WNTQYSSAYYTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.254)HS(0.254)DNDRPNCS(0.493)WNTQYSSAYYTSR 120.52 9.02E-05 1235000000 91754 92985 92274 101960 86657 102600 109910 71625 44691 TRUE FALSE 87416.97026 102460.2772 96504.85417 91710.78709 101769.9534 99046.93627 93141.21086 65353.13529 51621.45203 1.693423312 1.984839116 1.869471903 1.776602236 1.971466306 1.918716587 1.804312107 1.266007304 1 15.6556831 1.146708074 2.820171919 1.006460977 1.871108058 0.927571753 0.086348686 0.056575645 0.817236206 0.077949054 0.02127383 14.01871072 -1.146708074 0.864647082 SHSGT(ph)SPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Trastuzumab_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(0.034)HS(0.181)GT(0.393)S(0.393)PDNTAPPPPPPRPQPSHSR 104.05 0.006607 408380000 39099 39827 45004 41481 41282 46393 56287 38086 14725 TRUE FALSE 37250.86776 43885.41658 47067.47792 37311.25107 48481.56773 44786.39878 47699.38437 34750.98793 17008.4778 2.190135308 2.580208359 2.767295138 2.193685497 2.850435431 2.633180895 2.804447579 2.043156851 1 14.05396641 0.932085673 4.309258493 1.000673896 2.563791159 0.829075469 0.227702711 0.12270433 5.98073539 0.216432621 0.055102275 8.552354085 -0.932085673 1.563117263 SHSLSQHTATSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHSLSQHTATSSK 13 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 89.747 0.004226 28458000 35670 33617 31273 33794 66919 28932 56043 27016 53387 FALSE TRUE 33983.94979 37042.61052 32706.89798 30396.96292 78589.65241 27930.07759 47492.61105 24650.33582 61665.9833 0.551097185 0.600697638 0.530388007 0.492929185 1.274440919 0.452925196 0.770158984 0.399739605 1 15.91218726 SHSTEPGLVLTLGQGDVGQLGLGENVMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHSTEPGLVLTLGQGDVGQLGLGENVMER 29 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 217.84 2.42E-34 107558000 46553 46093 47146 60924 58582 56379 68288 51898 38236 FALSE TRUE 44352.53195 50789.9291 49307.69073 54799.80377 68798.68225 54426.58109 57869.4114 47353.53599 44165.4436 1.00423608 1.149992505 1.116431461 1.240784634 1.557749151 1.232334075 1.310287109 1.072185223 1 15.43063038 3.256217262 3.92686903 1.270613573 1.086568921 0.147898323 0.152459875 0.300278767 10.14541163 0.041262927 0.054241438 1803.919953 -3.256217262 -0.184044651 SHTEEDCTEELFDFLHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ;;;;;; 402.09 2.48E-147 372228900 206499.5 209472.3 240867 327968 275556 221073.1 318972 189069.3 84721.7 FALSE TRUE 196738.6779 230817.7655 251910.9902 295000.0335 323612.8792 213417.2831 270306.9631 172513.3898 97859.90854 2.010411422 2.35865503 2.574200139 3.014513685 3.306899465 2.180844907 2.762182871 1.76286073 1 16.57843031 1.012733214 3.548051979 1.004083529 2.562192417 0.663943203 0.380876274 0.131992785 4.074629006 0.384857092 0.099636527 10.2975335 -1.012733214 1.558108888 SHTFPELAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHTFPELAYR 10 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 121.83 0.00050465 435020000 255323 234253 182058 219568 287060 196849 285870 209894 178971 FALSE TRUE 243254.3878 258123.647 190405.5394 197496.6075 337123.1731 190032.0698 242255.2811 191514.5686 206724.9086 1.176705746 1.248633504 0.921057557 0.95535951 1.63078158 0.919250955 1.171872721 0.926422316 1 17.65735271 1.432775564 1.780414107 0.9712882 1.162600498 0.098482974 0.210017778 0.778480096 4.582106787 0.173000602 0.054797748 27.0879141 -1.432775564 0.191312298 SHTPS(ph)PTSPK ddPTM_SK-BR-3_Trastuzumab_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 SHTPS(1)PTSPK;SHTPS(1)PTSPK;SHT(0.001)PS(0.992)PT(0.006)S(0.001)PK;SHTPS(1)PTSPK;SHT(0.001)PS(0.995)PT(0.003)SPK 137.01 0.00010766 1056213000 2689250 2347970 2496780 2949440 2025640 2830960 3192380 2657160 1109072 TRUE FALSE 2562134.482 2587230.812 2611259.833 2652956.688 2378910.975 2732923.145 2705323.799 2424484.984 1281061.221 2.000009398 2.019599664 2.038356785 2.070905468 1.856984612 2.13332751 2.111783382 1.892559812 1 20.28890799 0.828424294 4.661547503 1.000016068 2.032926322 0.949030019 0.074642876 0.398278073 10.65920898 0.070229233 0.017801926 6.736344578 -0.828424294 1.032910253 SHTPSPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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(0.003)S(0.996)PK;SHTPSPT(0.004)S(0.996)PK;SHTPSPT(0.016)S(0.984)PK;SHTPSPT(0.006)S(0.994)PK;SHTPSPT(0.009)S(0.991)PK 124.47 0.00028002 1468560000 2459140 2709040 2665790 3218010 1674536 2998800 2991950 2709140 898014 TRUE FALSE 2342901.326 2985094.256 2788019.108 2894529.521 1966574.548 2894950.804 2535473.077 2471913.34 1037273.425 2.258711416 2.87782776 2.687834318 2.790517381 1.89590758 2.790923526 2.444363286 2.383087507 1 19.98436481 -1.523142286 0.423014814 9.64E-10 2.594189192 0.73223022 0.290077238 14.55333798 1.287386109 15.6893887 0.15775938 0.029981801 1.523142286 2.594189191 SHTSSNYDSYKKS(ph)PGSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SHTSSNYDSYKKSPGSTSR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 SHTSSNYDS(0.002)YKKS(0.996)PGS(0.001)TSR 196.2 4.42E-16 76836000 27143 9969.1 40989 21113 51062 26508 78433 34157 45480 TRUE FALSE 25860.00418 10984.96262 42868.38619 18990.68113 59967.19663 25590.02131 66466.60533 31166.032 52532.80612 0.492263903 0.209106717 0.816030769 0.361501365 1.141519006 0.487124584 1.265239956 0.593267984 1 15.68093103 3.053022848 1.023594684 0.92687044 0.365489473 0.30713287 0.287388776 0.488426167 1.111323021 0.116787518 0.151622146 1129.855354 -3.053022848 -0.561380967 SHVATCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SHVATCSK 8 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 ; 114.89 0.0025684 363180000 846780 710320 561480 694890 656280 612560 1033940 699350 377090 FALSE TRUE 806754.3876 782702.4156 587224.4134 625038.337 770735.0242 591346.8936 876193.4634 638111.2065 435567.1913 1.852192736 1.796972846 1.3481833 1.434998663 1.769497427 1.357647925 2.011614926 1.465012102 1 18.73253576 0.985762734 24.49990675 0.999999979 1.673289078 0.467530912 0.219375387 524.7955395 903085.6066 0.207152995 0.051788249 9.677490057 -0.985762734 0.673289099 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.06)S(0.94)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.102)S(0.898)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.053)S(0.947)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.174)S(0.826)PEAPPAEQDPVQLK 270.14 4.51E-60 2577310000 1796010 1693540 1801850 2047020 1468930 1939680 2158140 1817630 804080 TRUE FALSE 1711116.167 1866113.651 1884466.605 1841249.661 1725110.927 1872508.395 1828876.106 1658468.681 928772.6197 1.842341312 2.009225522 2.028985959 1.982454716 1.857409327 2.016110677 1.969132237 1.785656302 1 19.82496592 0.750691262 2.565810755 1.00012537 1.95850259 0.95741703 0.063068216 0.233673249 2.132468835 0.059683832 0.015905504 5.632371108 -0.750691262 0.958377219 SHVSSEPYEPIS(ph)PPQVPVVHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 197.08 3.42E-22 561278000 326153 273245 331334 360924 336417 319772 441963 306874 164907 TRUE FALSE 310736.3941 301088.9762 346525.9916 324643.2338 395088.0183 308698.2155 374533.4271 280002.4857 190479.9353 1.631333996 1.580686048 1.819225689 1.704343469 2.074171317 1.620633769 1.966261835 1.469984149 1 17.53927951 0.963736617 5.953762429 1.00012247 1.754302209 0.718591371 0.155408657 0.124599882 16.78573494 0.148602503 0.037377637 9.198915229 -0.963736617 0.754179739 SICEVLDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SICEVLDLER 10 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ;;;; 200.6 5.98E-07 347390000 588052 487131 437002 528966 619990 463182 638530 534342 634551 FALSE TRUE 560255.9474 536770.2027 457038.974 475793.3327 728116.0597 447141.8912 541110.5211 487552.1818 732953.9282 0.764380851 0.732338258 0.623557575 0.649144939 0.993399492 0.610054567 0.738259937 0.665188033 1 19.48336299 -1.073103308 4.575757639 1.000015808 0.724488365 0.391583426 0.108848091 1.59E-05 3.23E-06 0.09561639 0.022535707 0.08450778 1.073103308 -0.275527444 SIDDLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIDDLEEK 8 0 H7BYY1;P09493-2;P09493-3;Q6ZN40;P09493-9;P09493-8;P09493-7 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 149.65 0.0011673 68871000 181170 156690 158220 200610 127960 181000 202290 197970 139160 FALSE TRUE 172606.4531 172656.8891 165474.5435 180444.3017 150276.1835 174731.9246 171426.9452 180634.6973 160740.2221 1.073822413 1.074136186 1.029453247 1.122583379 0.934900932 1.087045435 1.066484437 1.123767872 1 17.29437145 -0.48891638 6.05856274 0.999999926 1.063620886 0.124548534 0.05333546 0 0 0.045778608 0.010790121 0.324402072 0.48891638 0.06362096 SIDLKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIDLKDK 7 1 P10809;E7EXB4;E7ESH4;P10809-2;C9JCQ4;C9JL25 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 88.819 0.016715 1143260000 2416060 1188480 2486900 1935650 2157400 2508900 3820200 3208800 2826500 FALSE TRUE 2301857.632 1309587.463 2600926.825 1741074.785 2533649.877 2422016.164 3237358.327 2927820.461 3264819.184 0.70504904 0.401120978 0.796652641 0.533283679 0.776046003 0.741853079 0.991588858 0.896778748 1 21.63857166 2.148362853 0.97519744 0.989593643 0.582585344 0.625246887 0.114542207 0.309561281 0.551001488 0.079827465 0.042103225 140.7222768 -2.148362853 -0.407008299 SIEAVHEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIEAVHEDIR 10 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 140.07 3.99E-05 320580000 532090 425600 476840 516780 526160 436390 570180 504500 556830 FALSE TRUE 506939.1602 468969.1239 498703.5857 464832.2926 617922.1374 421277.7049 483188.5689 460323.3055 643180.3525 0.788175755 0.729140935 0.775371299 0.722709098 0.960729187 0.654991564 0.751248957 0.715698643 1 19.29486381 -0.947115581 5.007881461 0.999999946 0.760483054 0.469607671 0.079383476 1.02E-06 2.14E-07 0.068960533 0.016254067 0.112949528 0.947115581 -0.239516891 SIEEIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIEEIVR 7 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 145.88 0.0052498 195984000 383160 339390 338740 388410 387240 329620 411590 382860 412630 FALSE TRUE 365048.7861 373974.2269 354271.5641 349366.2889 454774.5334 318205.1767 348794.3861 349334.7487 476618.553 0.765913924 0.784640515 0.743302085 0.733010259 0.954168759 0.667630697 0.731810342 0.732944084 1 18.86247559 -0.97459217 4.633935004 1.000003874 0.763540678 0.500792954 0.073991965 0.018815769 42565122.75 421.0348983 0.016130875 0.10602489 0.97459217 -0.236463196 SIEEVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIEEVLR 7 0 A0A2R8YF87;Q96AX1;H3BMM5;A0A2R8Y5U3 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 143 0.005702 49794000 86150 72845 74652 88248 88913 74598 97134 85716 97040 FALSE TRUE 82077.86023 80267.98832 78074.86804 79377.14338 104419.399 72014.65255 82314.42431 78210.25263 112088.4676 0.732259634 0.716112817 0.696546841 0.708165122 0.931580218 0.642480481 0.734370146 0.697754678 1 16.77427833 -1.309896383 3.217302728 1.001604521 0.731294605 0.554590961 0.075358742 19852850.22 27343327.73 308206.9466 0.017084719 0.048989569 1.309896383 -0.270309916 SIEHLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIEHLDK 7 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;;; 91.065 0.016678 684919000 2023270 1969990 1904890 2262430 1609250 2115070 2293130 2402820 1590410 FALSE TRUE 1927634.037 2170734.221 1992231.091 2035006.238 1889902.69 2041824.596 1943270.902 2192416.343 1837042.66 1.049313703 1.18164606 1.084477315 1.107762102 1.028774525 1.111473696 1.057825681 1.193448792 1 20.8089537 3.572165799 24.51956849 1.084588002 1.11841024 0.045702295 0.06043382 125.8586774 32458.33418 0.014485922 0.022441479 3733.926794 -3.572165799 0.033822239 SIEIPRPVDGVEVPGCGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIEIPRPVDGVEVPGCGK 18 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 175.33 3.31E-12 328670000 442350 368800 374230 490030 379430 425100 533590 467410 408970 FALSE TRUE 421440.9922 406381.1393 391388.8157 440771.2534 445602.4719 410378.6804 452181.0454 426481.1025 472390.9789 0.892144454 0.860264394 0.828527286 0.933064502 0.943291663 0.868726751 0.957217783 0.902813816 1 18.84962189 0.904671208 0.246540568 1.025249286 0.852497758 0.503537344 0.035737985 2.351371116 0.461586165 0.145942438 0.082538018 8.029180254 -0.904671208 -0.172751528 SIESTLDDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIESTLDDLFR 11 0 A0A087X208;A0A494C0G5;A0A494C1I6;O00468-2;O00468-6;O00468-3;O00468-5;O00468-4;O00468-7;O00468 A0A087X208 AGRN Agrin;Agrin N-terminal 110 kDa subunit;Agrin C-terminal 110 kDa subunit;Agrin C-terminal 90 kDa fragment;Agrin C-terminal 22 kDa fragment 0 ;;; 116.3 0.0018592 30119800 98169 76022 76352 88427 111251 72923 97178 80055 100218 FALSE TRUE 93528.74592 83768.72823 79852.81472 79538.14996 130653.1392 70397.65822 82351.7113 73044.9598 115759.2956 0.807958838 0.723645801 0.689817732 0.687099464 1.128662182 0.608138274 0.711404738 0.631007293 1 16.82076852 6.005483806 1.967026198 0.757588733 5.885886828 0 0.165905167 1186.620348 58.02313964 0.038741802 26612.74392 1012706.986 -6.005483806 5.128298095 SIEVIENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIEVIENR 8 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 102.46 0.011539 231643000 376830 339290 368020 396770 508360 326590 483640 371030 630760 FALSE TRUE 359017.9927 373864.0367 384894.081 356885.9258 597017.823 315280.1064 409851.8353 338540.6462 728575.0393 0.492767352 0.513144174 0.528283375 0.489841 0.819432167 0.432735256 0.562538947 0.464661329 1 19.47471804 -2.135893649 2.392854192 1.979192958 0.53689402 0.651871388 0.106119132 4999318.694 1434809.648 26541602.78 0.023967309 0.007313181 2.135893649 -1.442298938 SIFAS(ph)PESVTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIFASPESVTGK 12 0 O75940 O75940 SMNDC1 Survival of motor neuron-related-splicing factor 30 1 SIFAS(0.999)PES(0.001)VTGK;SIFAS(0.998)PES(0.002)VTGK;SIFAS(0.998)PES(0.002)VTGK;SIFAS(0.825)PES(0.153)VT(0.022)GK 159.52 7.40E-05 185433000 757070 719720 774660 874330 740210 867970 1031110 959430 973570 TRUE FALSE 721284.8015 793060.2863 810178.9272 786440.6873 869302.3896 837911.9813 873795.2319 875417.2229 1124546.263 0.641400736 0.70522691 0.720449619 0.699340448 0.773025013 0.745111169 0.777020262 0.778462613 1 20.10091158 -5 0.1207064 1.929878122 0.58778934 0.957318878 0.019590957 25.78883629 0.201437176 5.804405577 0.171608177 1.00E-05 5 -1.342088782 SIFKPFIFVDDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIFKPFIFVDDVK 13 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 144.68 3.78E-05 110630000 540550 453700 516770 564590 360320 501050 603680 545090 404160 FALSE TRUE 514999.2728 499932.5458 540464.4157 507836.3405 423159.6939 483698.5129 511577.5287 497359.0299 466835.0686 1.103171778 1.070897581 1.157720257 1.087828175 0.906443672 1.036122917 1.095842114 1.065384894 1 18.83255341 2.977491315 24.89824069 1.029972115 1.103747115 0.376353831 0.053521419 937.4363573 1036957.073 0.01677274 0.017916315 949.492012 -2.977491315 0.073775 SIFQHIQSAQSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIFQHIQSAQSQR 13 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 169.19 2.89E-05 1433990000 1353440 1034290 960100 1051640 1356890 1025390 1539200 1292900 1371580 FALSE TRUE 1289465.573 1139685.327 1004121.535 945927.1492 1593531.186 989880.4872 1304366.771 1179686.822 1584277.621 0.813913897 0.719372231 0.633804026 0.597071584 1.005840873 0.624815041 0.82331957 0.744621275 1 20.59539374 -0.899677651 0.413512582 1.093579373 0.731601366 0.31723218 0.118759858 16.4707267 2.066783749 1.99079275 0.067593899 0.125986018 0.899677651 -0.361978007 SIFYVPDMKPSMFDVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIFYVPDMKPSMFDVSR 17 1 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 143.43 5.01E-07 416020000 1087940 980310 864940 888450 827040 790610 968660 1000340 843490 FALSE TRUE 1036515.232 1080204.704 904598.3545 799141.3181 971275.5141 763230.9775 820873.1263 912744.9265 974294.1213 1.063862759 1.108704938 0.928465373 0.820225947 0.99690175 0.783368144 0.842531129 0.936826885 1 19.89399784 3.64090415 4.217698433 0.882231371 1.086224762 0.528884531 0.072029907 0.135715891 4.208671819 0.017975175 0.028791447 4374.255539 -3.64090415 0.203993391 SIGTANRPMGAGEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 186.96 1.29E-09 920670000 694020 642313 535838 727500 630321 615220 693565 669850 619629 FALSE TRUE 661215.05 707765.4249 560406.7023 654370.3178 740248.7828 593914.7771 587748.9211 611194.3829 715717.9007 0.923848697 0.988888813 0.782999422 0.914285247 1.034274513 0.829816855 0.82120193 0.853959894 1 19.44903154 SIIECVDDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIIECVDDFR 10 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 94.692 0.018451 44123000 29192 26536 26165 32369 27544 26695 26739 29984 33021 FALSE TRUE 27812.15201 29240.04857 27364.69113 29115.20662 32347.66488 25770.54546 22659.47445 27358.442 38141.72803 0.729179129 0.766615727 0.717447597 0.76334262 0.848091226 0.675652279 0.594086205 0.717283758 1 15.21908259 -1.005556442 4.861395251 1.00000173 0.722802124 0.635102589 0.065107781 3.18E-06 6.50E-07 0.069890167 0.016473029 0.098728732 1.005556442 -0.277199606 SIIPLPHPVRPEDIE ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SIIPLPHPVRPEDIE 15 1 P61599;A8MZB2 P61599 NAA20 N-alpha-acetyltransferase 20 0 ;; 126.88 7.44E-05 265305000 456900 370340 403103 448000 451920 401510 480900 438400 451460 FALSE TRUE 435303.2425 408078.067 421585.6713 402966.1889 530734.7049 387605.608 407529.8727 400011.3719 521470.1111 0.834761635 0.782553129 0.80845606 0.772750308 1.017766299 0.743294006 0.781501881 0.767083987 1 18.99222504 -0.935409733 4.204015577 1.000006083 0.811370915 0.36825228 0.0767135 1.01818E+11 2.14013E+11 9529735.681 0.017231493 0.116035337 0.935409733 -0.188635168 SIISMFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIISMFDR 8 0 O75340-2;O75340 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 192.11 0.00041331 335370000 467840 401840 291090 327530 441480 306100 441400 359680 379080 FALSE TRUE 445726.1304 442787.9529 304436.7644 294606.0621 518473.9722 295499.6802 374056.3231 328184.5124 437865.7903 1.017951482 1.011241258 0.695274148 0.672822743 1.184093354 0.674863592 0.854271632 0.749509369 1 18.74012921 3.781915176 18.11597867 0.826823372 1.01460068 0.182604868 0.159338401 28.59328302 11946.01132 0.037524534 0.067640209 6052.22655 -3.781915176 0.187777309 SIITVEELTEIERLEDLDT(ph)CMMTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIITVEELTEIERLEDLDTCMMTPK 25 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SIITVEELTEIERLEDLDT(0.5)CMMT(0.5)PK 69.092 0.022103 45460000 74771 38583 67487 65700 60026 57420 89246 80263 79346 TRUE FALSE 71236.72301 42514.65157 70581.3457 59095.71118 70494.5154 55431.531 75629.88358 73234.74622 91650.57244 0.777264354 0.463877643 0.770113528 0.644793694 0.769166122 0.6048138 0.825198158 0.799064799 1 16.48385627 0.988549858 0.573511529 1.006556446 0.642712845 0.518848329 0.099469802 0.660346604 0.524963865 0.098040202 0.043377946 9.739795944 -0.988549858 -0.363843602 SIITVEELTEIERLEDLDTCMMT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIITVEELTEIERLEDLDTCMMTPK 25 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SIITVEELTEIERLEDLDT(0.1)CMMT(0.9)PK 88.917 0.0079902 36897000 71836 48854 77503 73303 58868 69657 91555 90338 83803 TRUE FALSE 68440.45465 53832.27814 81056.58921 65934.44317 69134.56056 67244.76062 77586.60323 82427.52581 96798.74123 0.707038684 0.556125808 0.837372348 0.681149799 0.714209293 0.694686313 0.801524919 0.8515351 1 16.56270067 0.997756869 0.513714608 1.012959645 0.662168524 0.671559021 0.069046477 0.55897219 0.369180673 0.07642549 0.036111676 9.948483168 -0.997756869 -0.350791121 SIKDTICNQDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIKDTICNQDER 12 1 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 63.292 0.065406 149950000 212870 184030 206340 212420 209820 184180 235000 215910 200400 FALSE TRUE 202808.057 202782.8662 215800.8931 191067.138 246412.5416 177801.8004 199146.4339 197003.7758 231477.0085 0.876147736 0.87603891 0.932277873 0.825425986 1.06452275 0.76811862 0.860329219 0.851072757 1 17.82050938 -2.402044016 2.254066292 1.969875654 0.879651148 0.187995802 0.077130725 4993248.336 445276.5608 24995062.89 0.016707346 0.003962379 2.402044016 -1.090224506 SIKEVDEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIKEVDEAK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;D6RAA8;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 69.65 0.049831 65148000 153480 133450 142650 164510 125260 145320 162150 161890 137760 FALSE TRUE 146225.3046 147048.7067 149190.6436 147973.1423 147105.3043 140287.532 137411.0394 147714.0534 159123.1172 0.918944445 0.924119068 0.937579946 0.929928629 0.924474752 0.881628857 0.863551706 0.9283004 1 17.27978392 2.369069438 9.565591983 0.901468974 0.92669137 0 0.037201571 0.680078601 55.82678406 0.011805042 0.009868331 233.921122 -2.369069438 0.025222396 SILCCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SILCCLR 7 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 109.11 0.016523 328550000 188740 137110 110780 109580 200110 108910 210040 137720 203330 FALSE TRUE 179818.6342 151081.6649 115859.3726 98564.81021 235009.1206 105138.4194 177994.5404 125660.5067 234861.3779 0.765637313 0.64328016 0.493309601 0.419672281 1.000629063 0.447661596 0.75787063 0.535041171 1 17.84144996 -1.154139577 3.428304921 1.000447356 0.642505568 0.299734701 0.175799901 27596707.99 44474839.9 137036.4913 0.037271554 0.070122989 1.154139577 -0.357941788 SILDADPEAQALLEISGHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SILDADPEAQALLEISGHSR 20 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ;; 159.26 2.58E-11 95253000 150775 105019 117217 139616 167933 122767 168512 148223 168838 FALSE TRUE 143648.1646 115720.5555 122591.5154 125581.5344 197220.462 118515.548 142802.3995 135243.8083 195020.5347 0.736579688 0.59337626 0.628608241 0.643940058 1.011280491 0.607708046 0.732242887 0.693484963 1 17.57326652 -5 0.218894729 2.508241605 0.661020921 0.378787807 0.118675907 157.4695363 1.574315613 104.7113679 0.216310474 1.00E-05 5 -1.847220684 SILEYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SILEYLR 7 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 138.24 0.0065249 139689000 509300 314750 180783 201593 550280 225350 552170 358440 476450 FALSE TRUE 485226.3983 346823.3828 189072.0794 181328.4886 646248.6578 217546.073 467926.3252 327053.0934 550335.4326 0.881692091 0.630203622 0.343557889 0.329487214 1.174281392 0.395297232 0.850256584 0.59427955 1 19.06995169 2.783272994 24.99929793 0.764497643 0.586243232 0.178499811 0.260355429 1068.705952 597526.1347 0.076964132 0.081632405 607.1178385 -2.783272994 -0.178254411 SILKPSTPIPPQEGEEVGESS(ph)EEQDNAPK ddPTM_SK-BR-3_Trastuzumab_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(0.413)S(0.587)EEQDNAPK 152 1.78E-08 142280000 273230 253260 256650 298420 157810 297200 311560 317500 182050 TRUE FALSE 260314.9594 279067.4819 268417.6564 268422.2546 185332.014 286907.8895 264025.7998 289698.0168 210281.3842 1.237936303 1.327114537 1.276468944 1.276490811 0.881352454 1.364399852 1.255583326 1.377668394 1 17.68196161 2.958075288 24.99683574 1.199020729 1.283421524 0.092850716 0.151662372 1411.364712 841499.5572 0.044034075 0.046708383 907.9779208 -2.958075288 0.084400795 SILPYPVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 SILPYPVS(1)PK;SILPYPVS(1)PK;SILPYPVS(1)PK;SILPYPVS(1)PK;SILPYPVS(1)PK 158.04 8.51E-06 458186000 1610511 1492118 1467505 1724997 1030629 1634780 1729915 1759074 1134069 TRUE FALSE 1534385.337 1644166.521 1534791.556 1551597.024 1210370.371 1578167.159 1465984.695 1605040.155 1309934.628 1.171344969 1.255151581 1.171655075 1.184484317 0.923992957 1.204767875 1.119128133 1.225282636 1 20.32106339 -4.999999992 0.05440073 0.458736774 1.419485979 0.206850899 0.09168409 703.0395448 2.81320409 54.70260267 10.75394141 1.00E-05 4.999999992 0.960749205 SILS(ph)PGGSCGPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK 322.18 3.98E-51 1723863000 3545920 3395730 3177650 3764720 3005590 3797340 4732520 4082340 3973750 TRUE FALSE 3378311.389 3741758.748 3323348.396 3386283.193 3529763.944 3665837.164 4010487.155 3724868.668 4589978.855 0.736018944 0.81520174 0.72404438 0.737755728 0.769015295 0.798661013 0.873748503 0.811521967 1 22.13005608 0.778612142 0.532747045 1.004770831 0.754580402 0.818092025 0.034829406 0.518619575 0.324687685 0.04311623 0.017612473 6.006370836 -0.778612142 -0.250190429 SILYDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SILYDER 7 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;;;;; 143.11 0.0056859 2779830000 9285000 7829270 7753800 9057900 9192600 7868300 9906700 8903000 9863500 FALSE TRUE 8846116.451 8627081.514 8109319.4 8147382.683 10795786.53 7595818.798 8395250.966 8123406.122 11393081.2 0.776446362 0.757221103 0.711775792 0.715116704 0.947573912 0.666704525 0.73687274 0.71301222 1 23.44165463 -1.146884411 3.728797784 1.000157929 0.753206421 0.515816171 0.075179192 21327271.65 34478981.38 40686.14919 0.01670903 0.071304278 1.146884411 -0.246951508 SINHQIES(ph)PSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SINHQIESPSER 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 SINHQIES(1)PSER 181.07 1.95E-05 392750000 199760 151050 143140 192090 263380 183630 219820 200800 255390 TRUE FALSE 190317.7407 166442.1667 149703.1106 172780.7483 309313.3886 177270.8471 186282.4217 183216.8875 294994.5768 0.645156744 0.564221107 0.507477501 0.585708219 1.048539237 0.600929173 0.631477445 0.621085613 1 18.17032891 2.950610026 24.99981342 0.741021465 0.576669719 0.282375518 0.155377825 573.5177004 290298.1673 0.045403342 0.048158277 892.5037025 -2.950610026 -0.164351746 SINNAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SINNAEK 7 0 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 111.74 0.015148 54249000 76211 74451 57976 80668 59072 63527 79513 75022 66291 FALSE TRUE 72608.65707 82037.64154 60634.25695 72559.09938 69374.1381 61327.04406 67381.83149 68452.67596 76571.06971 0.948251831 1.071392131 0.791869007 0.94760462 0.906009781 0.800916642 0.879990729 0.893975704 1 16.22451179 3.746243948 24.9994328 0.881387139 1.00982198 0.352540131 0.067734151 509.1658252 1656679.283 0.015849224 0.027906763 5574.988145 -3.746243948 0.12843484 SINNAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SINNAEKR 8 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;; 185.81 0.00033798 2074790000 1877910 1234934 1421840 1310990 1766370 1616550 2268440 1861920 2483990 FALSE TRUE 1789144.916 1360775.179 1487032.77 1179206.794 2074424.369 1560568.468 1922347.815 1698880.414 2869194.483 0.623570457 0.474270806 0.518275348 0.410988799 0.72299887 0.543904736 0.669995647 0.592110582 1 21.45221433 -0.504038347 0.366919849 1.13323248 0.521575227 0.723422374 0.085754224 4.176238737 0.560318313 0.75965584 0.061512339 0.313300907 0.504038347 -0.611657253 SINNPDMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SINNPDMR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 98.458 0.026681 661200000 1608070 1424650 1416430 1622590 1649950 1532500 1847640 1654620 1683130 FALSE TRUE 1532059.718 1569823.455 1481374.717 1459484.17 1937700.758 1479429.141 1565748.584 1509732.701 1944141.204 0.788039323 0.807463702 0.761968685 0.750708934 0.996687254 0.760967947 0.805367728 0.776555066 1 20.89070158 -1.131555952 3.518941932 1.000168884 0.805721716 0.428795792 0.070378336 13867578.84 24376193.28 27490.29399 0.015614981 0.073865909 1.131555952 -0.194447168 SINPLGGFVHYGEVTNDFVMLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SINPLGGFVHYGEVTNDFVMLK 22 0 P39023;G5E9G0 P39023 RPL3 60S ribosomal protein L3 0 ;;; 214.31 1.52E-25 1286333000 1588415 1615739 1397309 1775405 1413102 1619998 1759241 1772235 1334846 FALSE TRUE 1513333.771 1780384.641 1461377 1596937.916 1659546.541 1563897.063 1490836.475 1617048.708 1541847.1 0.981507032 1.154708947 0.947809286 1.035730402 1.076336649 1.014301005 0.966915899 1.048773713 1 20.55622827 2.013963074 21.65186126 0.998817512 1.045399845 0.061779651 0.057850387 97.53644091 151241.9407 0.020828816 0.015368022 103.2673599 -2.013963074 0.046582333 SIPLDEGEDEAQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIPLDEGEDEAQRR 14 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 167.89 5.73E-06 373680000 179970 142690 164180 174910 182120 148360 191210 177500 221470 FALSE TRUE 171463.1748 157230.2732 171707.8154 157327.7145 213881.6703 143222.256 162037.4027 161957.159 255814.4365 0.670263872 0.614626271 0.671220193 0.615007177 0.836081315 0.559867762 0.633417742 0.633104063 1 17.96473816 -1.427897017 2.930974205 1.00734061 0.650856288 0.695051776 0.071953367 12356569.93 14420774.58 752317.279 0.01683418 0.037333868 1.427897017 -0.356484322 SIPLECPLSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIPLECPLSSPK 12 0 Q92667-2;Q92667;I3L2A2;I3L2N7 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 SIPLECPLS(0.088)S(0.912)PK;SIPLECPLS(0.028)S(0.972)PK 132.5 0.00018863 121579000 300940 231712 262290 381280 232066 289210 324210 283340 221054 TRUE FALSE 286715.1626 255323.7162 274316.2559 342953.01 272538.2369 279194.5852 274745.81 258529.2475 255333.9253 1.122902733 0.999960017 1.074343159 1.343154889 1.067379654 1.093448843 1.076025482 1.012514288 1 17.96202571 1.354988104 1.694899122 0.997441505 1.110305176 0.208733364 0.088108833 0.637223961 3.303774343 0.080953856 0.024905937 22.64582274 -1.354988104 0.112863671 SIQEELQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIQEELQQLR 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 ; 151.83 4.45E-05 92784000 80457 73066 69384 78531 81090 68121 90333 78892 91732 FALSE TRUE 76653.95706 80511.50847 72565.32503 70636.91468 95232.07033 65761.95269 76551.04177 71983.79825 105957.3301 0.723441757 0.759848407 0.684854224 0.666654347 0.898777558 0.620645619 0.722470467 0.679365913 1 16.69312387 -1.144229831 5.455652292 1.000005966 0.721723176 0.586845269 0.073942925 4.80E-06 7.52E-07 0.063981068 0.015080159 0.071741453 1.144229831 -0.27828279 SIQEIQELDKDDESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;;;;;; 288.82 3.91E-37 14837590000 11263050 9994940 9589230 11278150 7055140 11058460 11504600 11860350 7888910 FALSE TRUE 10730667.95 11013435.75 10028905.68 10144448.93 8285554.182 10675502.76 9749361.974 10821794.88 9112281.872 1.177604918 1.208636421 1.100592126 1.113272074 0.909273253 1.17155098 1.069914442 1.187605369 1 23.11938094 3.619693194 3.273735504 1.078383008 1.193484515 0.264146674 0.079813898 0.301816163 6.049134768 0.020359956 0.033414453 4165.749913 -3.619693194 0.115101506 SIQEIQELDKDDESLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SIQEIQELDKDDESLRK 17 2 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;; 321.09 7.93E-59 4604880000 5452740 4725540 4762830 5758060 2967920 5719340 5867360 6114990 3306650 FALSE TRUE 5194999.786 5207077.898 4981210.467 5179248.869 3485524.308 5521277.822 4972186.471 5579529.058 3819428.394 1.360151114 1.363313397 1.304176948 1.356027221 0.912577472 1.445576995 1.301814292 1.460828292 1 21.86492531 -2.221304683 2.27023572 0.000138972 1.314425627 0.296571544 0.151507971 5717289.377 1285327.935 29246282.94 0.034235263 0.006007521 2.221304683 1.314286655 SIQFVDWCPTGFK ddPTM_SK-BR-3_Trastuzumab_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 ; 304.38 7.23E-41 433790000 2284200 2081700 2109900 2375400 1767440 2208500 2500700 2455700 2047900 FALSE TRUE 2176230.393 2293827.597 2206641.002 2136620.279 2075680.976 2132019.091 2119172.286 2240665.89 2365477.873 0.91999609 0.969710021 0.9328521 0.903251011 0.877489069 0.90130587 0.895874914 0.947236039 1 21.17370023 0.958089227 5.926623385 0.999987539 0.917622885 0.551575211 0.024743451 0.248037021 30.31932841 0.027687858 0.006964928 9.08007063 -0.958089227 -0.082364655 SIRDT(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 SIRDT(1)PAK;S(0.023)IRDT(0.977)PAK;S(0.001)IRDT(0.999)PAK;S(0.015)IRDT(0.985)PAK;SIRDT(1)PAK;S(0.001)IRDT(0.999)PAK;S(0.001)IRDT(0.999)PAK 84.198 0.02849 18075520000 14892300 16108400 14906900 17838700 9946970 16484800 16721700 16806400 11696770 TRUE FALSE 14188370.49 17749864.27 15590396.11 16045519.98 11681718.42 15913927.24 14170497.55 15334742.52 13510645.35 1.050162307 1.313768796 1.153934228 1.187620544 0.864630676 1.177880614 1.048839428 1.135011846 1 23.68759325 SIRDT(ph)PAKNAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIRDTPAKNAQK 12 2 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 SIRDT(1)PAKNAQK;S(0.006)IRDT(0.994)PAKNAQK 159.79 0.00011225 311150000 645290 255538 902000 507420 682910 763540 1375170 953750 1172280 TRUE FALSE 614788.4205 281577.6127 943357.5922 456413.1776 802009.2878 737098.4183 1165362.56 870234.5939 1354071.195 0.454029613 0.207948898 0.696682416 0.337067341 0.59229477 0.54435721 0.860636105 0.642680087 1 20.36887217 1.817363388 0.428409107 1.000029211 0.324208174 0.614338922 0.144302403 0.575680556 0.270645073 0.145447456 0.121414973 65.66945137 -1.817363388 -0.675821037 SIRDTPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;; 102.07 0.0045933 2527430000 2106389 883653 2380956 1548177 2386968 2124032 3645580 2601580 3676950 FALSE TRUE 2006824.166 973698.2453 2490125.188 1392551.307 2803254.463 2050476.239 3089379.815 2373771.863 4247152.627 0.472510489 0.229259066 0.586304615 0.3278788 0.660031487 0.482788451 0.727400234 0.558909008 1 22.01806452 0.790784567 0.25542865 1.127616943 0.291311417 0.658205748 0.124661319 1.628308304 0.308025709 0.469049804 0.236274646 6.177099075 -0.790784567 -0.836305525 SIRPDNMSEYSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 86.944 0.011361 297940000 132240 108550 110770 133220 104100 138400 150480 136270 122800 FALSE TRUE 125989.2773 119611.3684 115848.9141 119828.4725 122255.007 133607.1733 127521.5122 124337.4764 141843.1968 0.888229257 0.843264754 0.816739306 0.844795346 0.861902508 0.941935717 0.899031572 0.876583997 1 17.11393743 2.339241639 5.781864274 0.919145756 0.850532881 0.527090342 0.036453652 0.182792664 8.880457593 0.012071928 0.010010603 218.3944707 -2.339241639 -0.068612875 SIRPLLEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIRPLLEGR 9 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 137.98 0.0001364 290440000 227060 147840 104140 141790 241020 146240 245880 185710 242860 FALSE TRUE 216327.3238 162905.0641 108914.922 127536.9998 283053.8117 141175.6721 208366.4901 169448.2479 280521.4884 0.771161329 0.580722229 0.388258748 0.454642532 1.009027199 0.503261525 0.742782634 0.604047301 1 18.09775176 SIS(ph)ADDDLQESSR ddPTM_SK-BR-3_Trastuzumab_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 261.17 4.99E-24 726650000 699090 618760 650680 816120 824290 715910 865190 716950 904540 TRUE FALSE 666045.4012 681812.3475 680514.3216 734082.0671 968045.915 691117.8572 733189.3752 654170.0572 1044811.443 0.637479045 0.652569755 0.651327401 0.702597652 0.926526907 0.661476156 0.701743247 0.626113029 1 19.99481117 SIS(ph)CGPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISCGPSSR 9 0 Q5VU43-13;Q5VU43-2 Q5VU43-13 PDE4DIP Myomegalin 1 S(0.097)IS(0.903)CGPSSR;S(0.033)IS(0.966)CGPSSR;S(0.002)IS(0.998)CGPSSR;SIS(0.959)CGPS(0.04)SR 136.02 0.00021441 798700000 608524 457826 532592 628550 698980 583966 743700 590159 780120 TRUE FALSE 579760.2765 504478.9899 557011.87 565366.9598 820881.8907 563743.111 630234.906 538481.5493 901097.0253 0.643393841 0.559849801 0.618148606 0.627420737 0.91098058 0.625618657 0.699408486 0.597584427 1 19.78132293 -5 0.209267548 2.612983319 0.607124461 0.540035939 0.097318373 111.0144855 1.105699014 75.3389529 0.200809468 1.00E-05 5 -2.005858858 SIS(ph)ESFLTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISESFLTVK 10 0 F5H527;Q76I76;J3KSQ9;K7EP00;Q76I76-3;Q76I76-4 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 S(0.299)IS(0.7)ESFLTVK 208.03 1.27E-07 89806000 106660 106990 96935 120750 85339 105610 117660 111740 88097 TRUE FALSE 101618.3932 117892.4026 101379.5656 108611.9806 100222.0946 101952.6992 99708.80603 101955.4532 101758.6328 0.99862184 1.158549396 0.99627484 1.067349055 0.984900168 1.001907125 0.979855991 1.001934189 1 16.63479167 2.962316941 1.460777015 0.990964699 1.071347225 0.272450814 0.046148863 0.416655587 1.824373922 0.016580059 0.019135902 916.8893771 -2.962316941 0.080382526 SIS(ph)ESSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 SIS(0.974)ES(0.025)SR 118.33 0.005276 825080000 224630 204450 227060 238840 223490 252010 252210 234000 254340 TRUE FALSE 214012.1851 225283.6874 237470.9256 214831.3494 262466.5852 243282.8305 213730.7323 213509.7195 293781.7482 0.728473387 0.766840312 0.808324299 0.73126173 0.89340671 0.828107369 0.727515353 0.72676305 1 18.16438524 -2.070843447 2.494616891 1.338707263 0.774541292 0.624791172 0.054455366 10399046.2 3118668.1 20062521.47 0.013676482 0.008494866 2.070843447 -0.564165972 SIS(ph)ITSALLTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISITSALLTEK 12 0 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2;A0A3B3IS27 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 S(0.001)IS(0.999)ITSALLTEK 123.64 0.00035369 9703300 42125 42363 41170 44178 38947 39892 52934 46093 34397 TRUE FALSE 40133.83473 46679.83786 43057.68522 39737.14351 45739.34447 38510.53004 44857.9461 42056.85257 39731.11108 1.010136229 1.174893845 1.083727186 1.000151831 1.151222385 0.96927896 1.1290383 1.058537036 1 15.27798152 3.468919208 24.90247678 1.059845882 1.098647624 0.055292297 0.068421893 495.0366449 1502985.808 0.017274145 0.023420413 2943.873932 -3.468919208 0.038801742 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 SIS(1)LGDSEGPIVATLAQPLR;SIS(0.999)LGDS(0.001)EGPIVATLAQPLR;S(0.115)IS(0.885)LGDSEGPIVATLAQPLR;S(0.141)IS(0.859)LGDSEGPIVATLAQPLR;S(0.001)IS(0.996)LGDS(0.004)EGPIVATLAQPLR;S(0.001)IS(0.999)LGDSEGPIVATLAQPLR;S(0.024)IS(0.976)LGDSEGPIVATLAQPLR;S(0.008)IS(0.992)LGDSEGPIVATLAQPLR 299.93 8.98E-55 981441000 333464 283486 299060 349605 319360 306110 354651 337553 345139 TRUE FALSE 317701.8176 312373.5457 312772.1968 314462.0412 375056.2829 295509.3339 300542.4763 307995.0698 398661.3934 0.796921455 0.783556047 0.784556022 0.788794818 0.940789073 0.741253953 0.75387906 0.772573103 1 18.60480438 -1.138414729 4.291419165 1.00004158 0.792838893 0.582474897 0.05443307 7492119.402 1987487.377 2914.314583 0.012370657 0.072708514 1.138414729 -0.207202687 SIS(ph)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.141)IS(0.856)LLEPS(0.003)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 141.52 2.09E-13 24652000 13194 6927.7 14377 13979 23666 12106 24690 13731 2651.4 TRUE FALSE 12570.34577 7633.640506 15036.19967 12573.80436 27793.34291 11686.76618 20923.08704 12528.64085 3062.565571 4.104514819 2.49256394 4.909674364 4.105644131 9.075182969 3.816005214 6.831882144 4.090897177 1 11.58052502 3.474101414 2.535683823 5.35545448 3.320849297 0.038727943 2.16202702 0.503457563 6.49602104 0.557027734 0.867714029 2979.212034 -3.474101414 -2.034605183 SIS(ph)NEGLTLNNSHVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISNEGLTLNNSHVSK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.007)IS(0.993)NEGLTLNNSHVSK;SIS(1)NEGLTLNNSHVSK;SIS(1)NEGLTLNNSHVSK;S(0.01)IS(0.99)NEGLTLNNSHVSK 285.25 5.20E-36 2639310000 1430570 1044410 1243050 1580710 1492280 1315740 1884920 1590270 1752720 TRUE FALSE 1362949.791 1150836.566 1300045.072 1421814.028 1752533.16 1270175.594 1597340.835 1451017.528 2024522.866 0.673220251 0.568448293 0.642148871 0.70229586 0.86565244 0.627395035 0.788996194 0.716720741 1 20.94915051 -5 0.111828504 2.031773817 0.511774661 0.643769891 0.075304603 94.99609004 0.703172829 22.22344867 0.84210439 1.00E-05 5 -1.519999156 SIS(ph)PEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISPEWK 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 S(0.01)IS(0.99)PEWK 69.338 0.062947 147720000 229950 241700 217910 259320 169830 244420 267760 284960 201430 TRUE FALSE 219080.7192 266329.5048 227901.389 233252.6609 199448.2982 235955.6741 226908.2943 260007.3917 232666.7356 0.941607397 1.144682346 0.979518574 1.002518303 0.857227389 1.014135835 0.975250259 1.117509948 1 17.82790544 -0.60075405 5.997636775 1 1.005922379 0 0.081424621 0 0 0.075400465 0.01777206 0.250752892 0.60075405 0.005922379 SIS(ph)PSALQDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 S(0.028)IS(0.969)PS(0.003)ALQDLLR;S(0.009)IS(0.966)PS(0.025)ALQDLLR;SIS(1)PSALQDLLR;SIS(1)PSALQDLLR 194.59 1.39E-06 180151000 242547 187247 174561 204675 259038 190007 261108 210124 240332 TRUE FALSE 231082.284 206327.6822 182564.7945 184100.6801 304214.1452 183427.0099 221271.179 191724.4286 277601.4591 0.832424602 0.743251433 0.657650702 0.663183402 1.095866521 0.660756649 0.79708219 0.690646329 1 18.08265563 SIS(ph)PWLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SISPWLAR 8 0 Q86UZ6;A0A494BZW5 Q86UZ6 ZBTB46 Zinc finger and BTB domain-containing protein 46 1 S(0.033)IS(0.967)PWLAR;S(0.006)IS(0.994)PWLAR 98.044 0.0081838 52572000 183828 163554 160821 182140 187706 181718 202328 179357 202857 TRUE FALSE 175138.8148 180220.3385 168194.8019 163830.9412 220441.867 175425.0601 171459.1476 163651.5502 234315.0275 0.747450202 0.76913692 0.717814831 0.699190926 0.940792698 0.748671829 0.731746271 0.698425329 1 17.83808996 -1.054878964 4.798724901 1.000005397 0.757560279 0.550129453 0.069153086 4.93E-06 9.71E-07 0.063127298 0.014878813 0.088129445 1.054878964 -0.242445117 SIS(ph)QDSLDELSMEDYWIELENIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.114)IS(0.868)QDS(0.018)LDELSMEDYWIELENIKK 136.63 1.19E-05 20738000 36435 24384 32018 33300 27716 34968 47586 39369 29454 TRUE FALSE 34712.78976 26868.75732 33486.05697 29952.62073 32549.66162 33757.04939 40325.88172 35921.64165 34021.57589 1.020316927 0.789756401 0.984259432 0.880400744 0.956735859 0.992224743 1.185303169 1.055848846 1 15.05416235 2.052828411 3.194598123 1.099365252 0.916425662 0.435218359 0.077828902 0.182338643 3.721264674 0.032629672 0.020716618 112.9349622 -2.052828411 -0.18293959 SIS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISREPSPALGPNLDGSGLLPR 22 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.439)IS(0.562)REPS(1)PALGPNLDGSGLLPR 105.56 0.00029312 66330000 71808 86495 60973 80165 54990 62099 56551 72042 52548 TRUE FALSE 68413.77815 95308.93884 63768.67236 72106.6619 64580.23859 59948.49606 47923.10632 65733.62056 60696.87546 1.127138384 1.570244565 1.050608814 1.187979799 1.063979622 0.987670215 0.78954816 1.08298195 1 15.88933463 2.945015214 1.122232993 0.932393448 1.327086642 0.423795603 0.150217 0.358498483 0.960138564 0.065476646 0.074923338 881.079739 -2.945015214 0.394693194 SIS(ph)REPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISREPSPALGPNLDGSGLLPRPIFYCSFPTR 32 2 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.486)IS(0.518)REPS(0.997)PALGPNLDGSGLLPRPIFYCSFPTR 51.774 0.036723 178480000 20962 19023 16791 19645 20950 18561 20287 14950 19743 TRUE FALSE 19971.1678 20961.46533 17560.88396 17670.24728 24603.67337 17918.22792 17191.84555 13640.89875 22804.64361 0.875750051 0.919175309 0.770057373 0.774853034 1.078888747 0.785727163 0.753874774 0.598163207 1 14.47704 2.022939674 24.99995557 0.759949172 0.882280248 0.119907382 0.128248616 377.6233016 411537.0762 0.043980479 0.032480064 105.4240447 -2.022939674 0.122331076 SIS(ph)SPKVPPYPEVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISSPKVPPYPEVFR 15 1 Q5VTI5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(0.134)IS(0.748)S(0.118)PKVPPYPEVFR 68.567 0.03164 89440000 283540 243830 251680 283840 190590 309980 331570 322820 191510 TRUE FALSE 270137.6261 268676.5542 263219.7769 255307.8639 223828.8357 299245.3149 280982.9068 294552.1694 221208.3927 1.221190674 1.214585717 1.189917678 1.154150893 1.011846038 1.352775594 1.270218111 1.331559648 1 17.7550466 SIS(ph)SPNVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.001)IS(0.973)S(0.026)PNVNR;S(0.025)IS(0.754)S(0.221)PNVNR;S(0.003)IS(0.499)S(0.499)PNVNR;S(0.002)IS(0.937)S(0.061)PNVNR;S(0.018)IS(0.849)S(0.134)PNVNR 147.42 9.70E-05 1931775000 2224180 1907985 1998520 2287190 2052469 1963880 2252700 2158160 2196949 TRUE FALSE 2119047.419 2102410.841 2090154.119 2057277.316 2410418.944 1895870.343 1909009.241 1969180.069 2537640.63 0.8350463 0.828490376 0.823660409 0.810704751 0.949866153 0.747099617 0.752277221 0.775988548 1 21.27505634 SIS(ph)TVNLSENSSVVIPPPDYLECLSMGAAADRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SISTVNLSENSSVVIPPPDYLECLSMGAAADRR 33 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.044)IS(0.912)T(0.044)VNLSENSSVVIPPPDYLECLSMGAAADRR;S(0.002)IS(0.948)T(0.051)VNLSENSSVVIPPPDYLECLSMGAAADRR;S(0.058)IS(0.882)T(0.058)VNLS(0.001)ENS(0.001)S(0.001)VVIPPPDYLECLSMGAAADRR;S(0.174)IS(0.771)T(0.05)VNLS(0.001)ENS(0.002)S(0.002)VVIPPPDYLECLSMGAAADRR 204.66 2.44E-27 472427000 364232 313223 347039 349070 276646 350302 416358 400478 334036 TRUE FALSE 347015.4752 345140.7798 362951.0814 313980.8204 324892.9748 338170.9539 352834.9402 365410.0233 385836.5969 0.899384553 0.894525772 0.940685991 0.813766301 0.842048104 0.876461582 0.914467272 0.947059004 1 18.55763046 1.146263474 1.629824698 0.997735071 0.880483088 0.590854645 0.0339599 0.262032138 1.332976174 0.032501641 0.009597865 14.0043667 -1.146263474 -0.117251982 SIS(ph)VGENLGLVAEPQAHAPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SISVGENLGLVAEPQAHAPIR 21 0 O60336-4;O60336-3;O60336-6;O60336 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 S(0.014)IS(0.986)VGENLGLVAEPQAHAPIR;S(0.134)IS(0.866)VGENLGLVAEPQAHAPIR 231.68 2.91E-26 185926000 72182 65848 63265 71389 71009 65968 76377 79058 76675 TRUE FALSE 68770.09991 72557.98606 66165.76283 64212.84209 83392.94712 63683.51162 64724.28589 72135.26241 88565.3674 0.776489749 0.819259132 0.747083931 0.725033317 0.94159771 0.719056596 0.730808078 0.814486119 1 16.43445504 0.966458811 21.81372959 1.000000002 0.780074948 0.528161567 0.064898475 667.2455396 433948.9661 0.05899916 0.01474979 9.256755888 -0.966458811 -0.219925054 SISASKAS(ph)PPGDLQNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SISASKASPPGDLQNPK 17 1 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 SISAS(0.001)KAS(0.999)PPGDLQNPK;SISAS(0.001)KAS(0.999)PPGDLQNPK;SISASKAS(1)PPGDLQNPK;SISAS(0.026)KAS(0.974)PPGDLQNPK;SISAS(0.011)KAS(0.989)PPGDLQNPK;SISASKAS(1)PPGDLQNPK 211.17 1.64E-12 4051720000 4318920 3677000 3827990 4492120 2377600 4492260 4664090 4772940 2679220 TRUE FALSE 4114773.211 4051690.48 4003507.128 4040563.563 2792252.687 4336691.91 3952497.409 4354996.071 3094699.754 1.329619523 1.309235403 1.293665766 1.305639928 0.902269334 1.401328806 1.277182836 1.407243486 1 21.56136802 -1.246466991 4.275711511 0.999832315 1.279500717 0.27911003 0.140534353 0.000208478 3.67E-05 0.126282559 0.029747321 0.056693466 1.246466991 0.279668402 SISLYYTGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISLYYTGEK 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 199.46 0.0076274 0 334450 269260 258980 292660 260970 280010 393460 311270 285700 FALSE TRUE 318641.2113 296697.9001 270854.4892 263241.2608 306483.0854 270313.1835 333430.4506 284013.5487 330004.8968 0.9655651 0.899071205 0.820759 0.797688953 0.928722841 0.819118704 1.010380312 0.860634346 1 18.33212791 -1.338017656 6.213296375 1.000008059 0.895443468 0.205712315 0.067838909 7.46E-06 7.94E-07 0.06467473 0.015242805 0.045917934 1.338017656 -0.104564591 SISS(ph)PNVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.003)IS(0.224)S(0.774)PNVNR 120.54 0.00067962 321730000 283130 273620 301860 330800 247490 276340 301620 244840 298400 TRUE FALSE 269747.006 301502.1891 315700.5796 297547.3555 290652.1776 266770.2765 255602.3294 223400.5116 344674.348 0.782614104 0.874745077 0.915938716 0.863270961 0.843266055 0.773977751 0.741576305 0.648149515 1 18.39487441 2.254740112 4.04699867 0.76539232 0.856015112 0.081815474 0.0935403 0.355118648 13.01681179 0.031967054 0.024779823 179.7794769 -2.254740112 0.090622792 SIT(ph)ST(ph)PLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(0.308)IT(0.692)S(0.254)T(0.746)PLSGK 147.62 4.13E-05 86853000 290290 244800 260860 286310 211120 237850 273710 264620 183320 TRUE FALSE 276568.567 269745.3983 272820.689 257529.5748 247939.2612 229613.1949 231950.5125 241448.47 211748.3293 1.30611924 1.273896229 1.288419559 1.216205935 1.17091484 1.08436839 1.095406576 1.140261511 1 17.69199106 2.665985013 0.868021888 1.068203996 1.301902308 0.8771279 0.034648106 0.176406679 0.279960059 0.020450434 0.017660263 463.4309268 -2.665985013 0.233698311 SITFLCGDAGPLAVAAVLYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SITFLCGDAGPLAVAAVLYHK 21 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 140.28 1.67E-07 62169000 354010 372080 370720 400320 331300 364570 451080 438800 269080 FALSE TRUE 337276.6489 409995.375 387717.8787 360079.073 389078.6151 351944.8495 382259.4613 400376.3458 310807.5521 1.085162335 1.319129385 1.24745321 1.158527425 1.251831278 1.13235617 1.229891162 1.288180879 1 18.24566203 -1.665692189 3.089930274 0.980189076 1.213788401 0.471259389 0.071258911 21657691.25 18796420.2 3325776.607 0.016024023 0.021592743 1.665692189 0.233599325 SITHDIEEK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 182.39 4.64E-05 1442870000 3216970 2820500 3019580 3617770 2896860 3268970 4309720 3803730 3252890 FALSE TRUE 3064910.204 3107912.157 3158030.73 3254104.886 3402071.467 3155764.749 3652193.061 3470655.236 3757331.568 0.815714596 0.827159408 0.840498283 0.866068067 0.905448829 0.8398952 0.972017772 0.923702147 1 21.841277 1.957469078 0.402634129 1.005372345 0.804042329 0.79556686 0.028260472 0.426488821 0.176262427 0.029240307 0.028272779 90.67114034 -1.957469078 -0.201330015 SITST(ph)PLSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 SITS(0.023)T(0.977)PLSGK;SITS(0.035)T(0.965)PLSGK 153.34 0.014522 155060000 910580 762960 807350 926470 669210 805610 915170 842220 676740 TRUE FALSE 867538.688 840706.4914 844367.7961 833339.4754 785920.0121 777711.5237 775544.0082 768470.7519 781685.3829 1.109831023 1.075504941 1.0801888 1.066080412 1.005417306 0.994916293 0.992143419 0.983094694 1 19.57622853 2.808290944 1.653542449 0.990353128 1.091015906 0.954721631 0.009641978 0.066584725 0.364125733 0.003653867 0.003742847 643.1184124 -2.808290944 0.100662778 SITVTQDEGIRPSTTMEGLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SITVTQDEGIRPSTTMEGLAK 21 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 147.08 9.38E-08 231600000 198270 175500 172430 217160 176870 206140 247960 217880 192860 FALSE TRUE 188898.17 193383.6495 180336.0861 195330.6642 207716.072 199001.3201 210129.1479 198801.2721 222767.7438 0.847960153 0.868095381 0.809525127 0.876835492 0.932433343 0.893312994 0.943265593 0.892414982 1 17.76518082 1.545152793 0.281174261 1.012428701 0.824332289 0.700676063 0.02902418 0.888647478 0.272025438 0.062163634 0.058663108 35.08752968 -1.545152793 -0.188096412 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 313.24 5.81E-83 934700000 2854900 1675470 1331800 2392500 1840830 1940230 3170000 2429150 1781020 FALSE TRUE 2719954.535 1846202.298 1392864.347 2152001.355 2161870.169 1873039.349 2686358.279 2216440.748 2057211.485 1.322156013 0.897429511 0.677064248 1.046076871 1.050874052 0.910474865 1.305825044 1.077400532 1 20.97225868 1.753684758 25 1.156362512 0.99318588 0.119234605 0.177423947 10.11242459 16737.03697 0.083028788 0.046044108 56.71327905 -1.753684758 -0.163176632 SIVEGIIEEEEEDEEGSESISKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ;; 216.82 3.99E-32 82798000 65870.2 47427.1 49352.4 57377.5 48634.4 56487.3 66189.5 61045.3 58670.6 FALSE TRUE 62756.64619 52259.97541 51615.25636 51609.80469 57116.22396 54531.13064 56091.07612 55699.84991 67768.937 0.926038521 0.771149404 0.761635915 0.76155547 0.84280832 0.804662623 0.827681215 0.821908272 1 16.04833652 -0.192695679 0.927046239 1.003925276 0.813389639 0.594378887 0.048210949 8.526769386 5.730124244 0.172290853 0.0153343 0.641659046 0.192695679 -0.190535637 SIVIRPLEPQPAPHLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SIVIRPLEPQPAPHLAR 17 1 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 153.95 9.37E-08 469550000 780730 659940 674060 799970 748310 672540 882260 812140 786990 FALSE TRUE 743826.4402 727188.6363 704966.3177 719555.4958 878815.0271 649249.7712 747655.0332 741024.7162 909032.3898 0.818261757 0.799958994 0.77551287 0.791561999 0.966758761 0.714220724 0.82247348 0.815179662 1 19.79397217 0.451291778 2.794301818 0.999999355 0.810987586 0.466289641 0.062864875 16.34539714 81.79460752 0.05449466 0.014343369 2.826778489 -0.451291778 -0.189011769 SIWNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIWNNR 6 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;A0A590UJR6;A0A590UJI6;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 0 109.8 0.068051 60885000 363620 312970 289700 356960 358560 317590 362840 361200 356590 FALSE TRUE 346432.4032 344861.9988 302983.0316 321077.7026 421092.7505 306591.7787 307482.094 329571.4132 411888.156 0.841083673 0.837270977 0.735595397 0.779526427 1.022347315 0.74435687 0.746518417 0.800147827 1 18.65189312 -1.899257195 2.281166168 1.110696185 0.812078369 0.334340355 0.082747896 18476488.46 8898528.557 10971964.57 0.021049146 0.012610805 1.899257195 -0.298617815 SIYDDISS(ph)PGLGS(ph)TPLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 SIYDDIS(0.104)S(0.895)PGLGS(0.548)T(0.446)PLT(0.003)S(0.003)R 96.666 0.0018127 47025000 131310 132300 140750 166060 151180 146690 162260 155800 193480 TRUE FALSE 125103.2365 145781.5204 147203.5267 149367.3333 177545.7441 141610.0885 137504.2569 142157.3261 223483.8902 0.559786374 0.652313329 0.658676232 0.668358391 0.79444538 0.633647859 0.615275923 0.636096525 1 17.76981131 -1.73089618 2.634033321 1.068736683 0.648401508 0.774952726 0.058847252 22419367.43 17721320.97 10101725.56 0.014451018 0.018582486 1.73089618 -0.420335174 SIYDDISS(ph)PGLGST(ph)PLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 SIYDDIS(0.083)S(0.917)PGLGS(0.084)T(0.912)PLT(0.002)S(0.002)R 161.75 1.54E-10 49880000 107080 112530 113870 126210 123500 116770 127460 125150 151640 TRUE FALSE 102018.5406 123996.9349 119091.0521 113523.131 145038.3609 112726.2256 108013.636 114191.2025 175155.5567 0.582445356 0.707924643 0.679915924 0.648127488 0.82805458 0.643577787 0.61667262 0.651941649 1 17.41827723 -1.329900038 3.016428239 1.00314303 0.667438637 0.715157188 0.06546903 8552095.768 10967803.95 241624.1762 0.015922958 0.046784281 1.329900038 -0.335704393 SIYGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 126.16 0.040975 3502030000 8048800 6957400 6290200 9501400 5273230 7726750 7531060 8017100 5323740 FALSE TRUE 7668349.175 7666366.97 6578611.892 8546301.221 6192879.642 7459170.71 6382058.48 7315080.223 6149318.409 1.24702425 1.246701904 1.069811555 1.389796503 1.007083912 1.213007721 1.037848108 1.189575777 1 22.55199508 3.317813655 0.106588953 0.864769863 1.517356984 0.271529347 0.107754215 31.71233637 0.990472368 1.85146358 4.219225741 2078.804533 -3.317813655 0.652587121 SIYGEKFEDENFILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 275.83 1.46E-33 44832239000 39136225 25250466 31976264 35327158 24007120 35760702 45537130 40410925 27948280 FALSE TRUE 37286333.2 27823517.19 33442407.33 31776004.96 28193954.13 34522299.92 38589604.47 36872330.18 32282356.52 1.155006549 0.861879992 1.035934515 0.984314913 0.873354896 1.069385994 1.195377557 1.142182113 1 24.94424256 2.005238967 24.44682842 1.133766838 0.982921481 0.282598006 0.094775605 110.647759 516317.1426 0.033521181 0.024669546 101.2136221 -2.005238967 -0.150845357 SIYGERFPDENFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SIYGERFPDENFK 13 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 209.39 3.49E-08 1167560000 1662130 844320 1380160 1360800 1499640 1381050 2428350 1837480 2130810 FALSE TRUE 1583564.409 930357.1679 1443441.701 1224009.799 1761176.741 1333223.892 2057860.608 1676580.51 2461245.132 0.643399712 0.378002644 0.586468078 0.497313243 0.715563321 0.541686756 0.836105506 0.681192007 1 21.23095692 1.288853769 0.488680438 1.000239182 0.500371359 0.651539194 0.103264316 0.481352414 0.307624636 0.103358192 0.058337218 19.44705171 -1.288853769 -0.499867823 SIYYITGESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SIYYITGESK 10 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 150.35 5.05E-05 256990000 512750 526480 488380 571640 399620 537770 557900 533590 477570 FALSE TRUE 488513.3237 580128.9106 510772.7061 514177.6612 469313.6015 519146.8901 472782.1085 486866.0309 551629.1165 0.88558292 1.051664775 0.925935 0.932107544 0.850777429 0.941115823 0.857065181 0.882596687 1 19.07333908 3.285996914 2.681346838 0.898015726 0.969539512 0.107048536 0.059310958 0.380743057 5.584505782 0.016285172 0.022322652 1931.954591 -3.285996914 0.071523786 SKAEELGLPILGVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKAEELGLPILGVLR 15 1 P09110;C9JDE9;H7C131 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 192.96 1.03E-07 454650000 1823380 1405670 1355850 1477690 1462040 1491730 1969870 1764100 1599940 FALSE TRUE 1737192.441 1548909.371 1418017.064 1329149.794 1717019.313 1440071.016 1669330.152 1609626.052 1848050.524 0.9400135 0.838131507 0.767304273 0.719217238 0.929097604 0.779237904 0.903292486 0.870985956 1 20.81757277 0.732518157 0.964587395 0.999069298 0.836590131 0.352391081 0.070042163 1.134346121 1.922101857 0.06644713 0.02177966 5.401546976 -0.732518157 -0.162479167 SKAELMEISEDKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKAELMEISEDKTK 14 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 ; 175.65 1.32E-06 796450000 1583130 1598930 1365020 1703790 868370 1629420 1700020 1759340 964240 FALSE TRUE 1508298.582 1761862.785 1427607.517 1532521.792 1019813.453 1572992.777 1440650.726 1605282.863 1113769.415 1.354228768 1.581891873 1.281780141 1.375977624 0.91564146 1.412314575 1.293491011 1.44130629 1 20.08701915 -5 0.077111268 3.16E-05 1.673460115 0.24348335 0.17363073 358.3146173 1.966181635 63.79913249 6.480206184 1.00E-05 5 1.673428475 SKAEVACIAVYETDVFVVGTER ddPTM_SK-BR-3_Trastuzumab_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 ;; 163.64 1.36E-11 144222000 511900 585190 404080 482420 403520 429670 523580 502580 401040 FALSE TRUE 487703.5015 644821.5263 422607.4677 433926.2251 473893.7602 414790.4202 443698.2548 458571.4309 463231.235 1.052829483 1.392007873 0.91230348 0.936737837 1.023017717 0.895428436 0.957833197 0.989940652 1 18.82137301 3.720681203 24.99837056 0.955510187 1.222418687 0.602141419 0.088867892 433.5863187 606225.3466 0.022145812 0.034386565 5256.312818 -3.720681203 0.266908499 SKCEELSGLHGQLQEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKCEELSGLHGQLQEAR 17 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 125.73 2.76E-05 567270000 1111260 800650 971460 993720 1030030 910690 1200060 1034870 983790 FALSE TRUE 1058732.942 882237.1453 1016002.402 893829.3777 1209666.906 879152.5769 1016968.806 944251.2966 1136351.129 0.931695244 0.776377233 0.894091955 0.78657851 1.064518594 0.773662783 0.8949424 0.830950287 1 20.11597726 -1.235613907 3.860735464 1.000148565 0.866500346 0.179387884 0.087828206 13.75938988 39392790.49 10359.23845 0.017918456 0.058128095 1.235613907 -0.13364822 SKDAS(ph)PINRWS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.023)KDAS(0.977)PINRWS(0.603)PT(0.397)R 84.581 0.039726 578480000 709870 586150 661570 689620 503890 646830 796300 750790 590300 TRUE FALSE 676315.8519 645879.3514 691903.6389 620298.0874 591768.2565 624430.1149 674809.8099 685046.8474 681840.7092 0.991897144 0.947258418 1.014758476 0.90974047 0.867898101 0.915800577 0.989688355 1.004702181 1 19.37907521 1.595443217 5.91988861 1.000508641 0.944700893 0.300108757 0.041003571 0.199404163 14.73945897 0.023980453 0.011276076 39.3951916 -1.595443217 -0.055807748 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 169.26 5.04E-12 762553000 367408 308573 247813 311758 222308 300514 330184 299172 174203 FALSE TRUE 350041.352 340016.9395 259175.4712 280419.4935 261078.4448 290107.1248 279808.3666 272974.9137 201217.5115 1.739616743 1.689797955 1.28803636 1.393613764 1.297493657 1.441758834 1.390576617 1.35661609 1 17.61839634 8 0.1255273 0.972121989 3.527312592 0.710584778 0.111429696 47.81861115 0.408996656 0.686678236 21.51822572 100000000 -8 2.555190603 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 292.26 9.43E-71 955070000 2147500 1424300 1615500 1659900 1298300 1712300 2568200 1939100 1209700 FALSE TRUE 2045991.931 1569437.789 1689572.273 1493043.698 1524723.109 1653002.622 2176373.922 1769302.124 1397294.098 1.464252897 1.123197895 1.209174415 1.068525016 1.091196987 1.183002651 1.55756324 1.266234594 1 20.41420428 SKDEYEKS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 122.66 0.0004564 1549150000 1700450 2200930 1470380 2139820 788870 2086320 1740000 2172640 818880 TRUE FALSE 1620073.098 2425207.269 1537798.377 1924721.228 926448.6782 2014070.215 1474531.043 1982392.124 945867.7281 1.71279033 2.564002552 1.625807004 2.034873557 0.979469592 2.129336011 1.558918862 2.095844974 1 19.85127892 3.698207661 24.57048802 1.668399674 2.138396723 0.175765703 0.45054771 602.8415474 367063.7078 0.106457168 0.164925096 4991.230897 -3.698207661 0.469997049 SKDGVCVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKDGVCVR 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 123.21 0.001238 399100000 397160 313010 342590 386500 342680 377270 434400 432510 348740 FALSE TRUE 378387.0339 344906.0749 358298.0904 347648.2857 402443.2835 364205.0453 368124.3017 394637.1315 402820.8181 0.939343293 0.856227035 0.889472625 0.863034556 0.999062773 0.904136601 0.913866129 0.979684053 1 18.61977872 1.193513265 0.52239108 1.003162779 0.892368818 0.406282168 0.040328184 0.871172994 0.617798062 0.042036106 0.021571636 15.61396728 -1.193513265 -0.11079396 SKDKEEGKEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKDKEEGKEER 11 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 0 69.229 0.024126 80579000 195420 158760 154760 192320 84980 221440 215390 220930 88024 FALSE TRUE 186182.8839 174937.8245 161855.8991 172987.6282 99800.48509 213771.4773 182528.2996 201584.198 101674.3124 1.831169344 1.72057052 1.59190552 1.701389704 0.981570298 2.102512152 1.795225317 1.982646288 1 16.63359571 4.159268689 2.299613398 1.645984248 1.816325322 0.029877227 0.366679982 1.379509105 14.19994802 0.09076334 0.287159008 14430.07834 -4.159268689 0.170341074 SKDQDDQKPGPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SKDQDDQKPGPSER 14 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;;; 149.97 4.13E-06 1573548000 2388480 2065878 2222590 2734240 1450728 2740930 2925230 2997660 1709835 FALSE TRUE 2275581.284 2276393.317 2324497.95 2459389 1703734.504 2646010.907 2478932.438 2735168.999 1974987.479 1.15220036 1.152611518 1.176968449 1.245268148 0.862655851 1.339760852 1.255163622 1.384904475 1 20.91341208 SKDRDPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 0 ; 66.435 0.034698 9098800 6652.4 5871.6 6819.3 7385.6 5284.8 6760.7 8338.4 8954.5 6957.3 FALSE TRUE 6337.954236 6469.922715 7131.97165 6643.185456 6206.467447 6526.575264 7066.223935 8170.396509 8036.202551 0.788675272 0.805097019 0.887480325 0.826657294 0.772313466 0.812146685 0.879298884 1.016698678 1 12.97229821 1.390850981 2.742526513 1.011864675 0.814195421 0.864875132 0.03105005 0.093191113 1.203917184 0.026765222 0.008467297 24.59523525 -1.390850981 -0.197669254 SKDVVDYSEENFAIVFAAMGVNMETAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKDVVDYSEENFAIVFAAMGVNMETAR 27 1 P21281 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 181.62 1.52E-17 22814000 235540 232840 224990 253070 184740 246370 268730 252610 189030 FALSE TRUE 224406.491 256566.6607 235306.014 227630.9228 216958.5975 237838.1451 227730.3029 230490.1292 218343.807 1.027766686 1.175058108 1.077685771 1.042534368 0.993655834 1.089282762 1.042989522 1.055629342 1 17.73624209 3.391104812 4.468430311 1.041549537 1.104936993 0.269969793 0.044051542 0.251967186 9.181074992 0.011827471 0.016338785 2460.961458 -3.391104812 0.063387456 SKDVVEPLLRPQWYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKDVVEPLLRPQWYVR 16 2 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 147.75 5.61E-07 1307890000 738130 602760 632970 711570 605190 657370 828190 736160 681070 FALSE TRUE 703240.0577 664181.9293 661992.3006 640041.6317 710734.9444 634605.1121 701834.4047 671697.9278 786686.8572 0.893926283 0.844277394 0.841494039 0.813591362 0.903453436 0.806680709 0.892139481 0.853831384 1 19.58542996 -0.355677092 0.762258357 1.00805094 0.855047803 0.657963584 0.032601461 6.710902222 3.036772348 0.190417091 0.010018593 0.440882548 0.355677092 -0.153003137 SKEDS(ph)RR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.467)KEDS(0.533)RR;S(0.148)KEDS(0.852)RR 72.848 0.039766 2632100000 1964060 2286210 1990700 2455120 1020770 2083810 2012260 2802140 1322290 TRUE FALSE 1871222.776 2519177.398 2081975.564 2208326.673 1198791.965 2011647.137 1705252.779 2556769.767 1527343.98 1.225148232 1.649384442 1.363134691 1.445860724 0.784886693 1.317088464 1.11648247 1.673997345 1 20.54259358 2.887563283 19.62011144 1.183734113 1.434163258 0.190592832 0.247370539 7.22753377 1243.743745 0.069270824 0.073473081 771.9039858 -2.887563283 0.250429145 SKEEACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKEEACK 7 1 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;H7C366 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 66.073 0.091064 0 138250 142500 127500 164180 95668 139760 155950 185790 114940 FALSE TRUE 131715.1965 157020.912 133346.0011 147676.3145 112352.4689 134920.0762 132156.9633 169521.2427 132764.3082 0.992097939 1.182704254 1.004381396 1.112319392 0.84625507 1.016237557 0.99542539 1.276858555 1 17.01850782 -0.894084415 5.050285711 0.999999871 1.049639527 0.019116628 0.117399086 1.58E-07 3.46E-08 0.105083018 0.02476824 0.127619073 0.894084415 0.049639656 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.998)DEDDNS(0.002)FLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(0.997)DEDDNS(0.003)FLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK 411.74 5.69E-175 9922990000 3868619 3161271 3256790 3994632 2189085 3857882 4201747 4195708 1850464 TRUE FALSE 3685757.047 3483408.109 3406117.043 3593084.002 2570860.731 3724282.579 3560693.325 3828309.565 2137424.506 1.724391685 1.629722172 1.593561332 1.681034344 1.202784343 1.742415963 1.665880275 1.791085277 1 21.02744203 -1.959587372 2.682108229 0.50902238 1.630174465 0.59908775 0.161669074 15117163.83 5661602.357 46085379.2 0.036380488 0.010975205 1.959587372 1.121152085 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLKQQS(ph)PQEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKEGHSLEMENENLVENGADSDEDDNSFLKQQSPQEPK 38 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 2 SKEGHSLEMENENLVENGADS(0.997)DEDDNS(0.003)FLKQQS(1)PQEPK;SKEGHSLEMENENLVENGADS(0.998)DEDDNS(0.002)FLKQQS(1)PQEPK;S(0.005)KEGHS(0.005)LEMENENLVENGADS(0.858)DEDDNS(0.136)FLKQQS(0.996)PQEPK 243.23 2.30E-50 461500000 145511 80028 139508 124222 82467 147517 193048 156989 86669 TRUE FALSE 138632.9834 88182.94418 145904.5798 111734.9686 96849.21869 142408.4493 163594.982 143242.2109 100109.1859 1.384817809 0.880867659 1.457454463 1.116131028 0.967435884 1.42253129 1.634165542 1.430859812 1 16.61121483 2.131153884 8.253357519 1.450453441 1.155237 0.130787219 0.234128667 0.314868036 22.11102197 0.080991165 0.059776615 135.2551731 -2.131153884 -0.295216441 SKEGHSLEMENENLVENGADSDEDDNS(ph)FLKQQS(ph)PQEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKEGHSLEMENENLVENGADSDEDDNSFLKQQSPQEPK 38 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 2 S(0.001)KEGHS(0.001)LEMENENLVENGADS(0.471)DEDDNS(0.543)FLKQQS(0.983)PQEPK 44.023 0.048915 251680000 13649 9512.5 12581 11656 9247.7 11525 14738 13812 9529.8 TRUE FALSE 13003.83882 10481.83456 13157.85129 10484.31674 10860.49595 11125.88636 12489.44742 12602.54806 11007.63271 1.181347449 0.952233313 1.195338874 0.952458808 0.986633206 1.010742877 1.134617019 1.144891766 1 13.42621662 -0.474204815 7.120641652 1.000001289 1.066146459 0.052543996 0.091980668 0 0 0.083096274 0.01958598 0.335579316 0.474204815 0.06614517 SKEGLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKEGLTER 8 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;; 93.178 0.010263 451517000 873480 771530 775530 897320 650100 842270 964030 970080 781500 FALSE TRUE 832192.3315 850149.7842 811088.8176 807119.6888 763477.2342 813101.9787 816949.5179 885134.6525 902691.0287 0.921901631 0.941794875 0.898523184 0.894126188 0.845779131 0.900753362 0.905015661 0.980551068 1 19.78387274 1.184119006 3.975721462 0.998299939 0.903953516 0.701109406 0.024293915 0.139096954 4.076467115 0.025348572 0.006799572 15.27984701 -1.184119006 -0.094346422 SKEHERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKEHERPR 8 2 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 54.608 0.072657 8492300 8422.1 8607.1 8722.7 9472.7 9463.9 7870.4 11775 7935.1 10134 FALSE TRUE 8024.004024 9484.173275 9122.644423 8520.486199 11114.40116 7597.846075 9978.507487 7240.260577 11705.52896 0.685488375 0.810230217 0.779344911 0.727902705 0.949500121 0.649081823 0.852461048 0.618533396 1 13.51490251 -2.242657688 2.317632456 1.853973487 0.766133842 0.371422036 0.098119536 7877279.268 1083917.174 35408895.93 0.020376953 0.005719293 2.242657688 -1.087839645 SKEIEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKEIEAK 7 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 83.948 0.019978 511280000 563160 467870 524410 649800 382050 595500 686070 721840 476810 FALSE TRUE 536540.5429 515546.4849 548454.7172 584480.8695 448679.399 574877.6857 581397.421 658631.8629 550751.2596 0.974197577 0.936078631 0.995830164 1.06124291 0.814667949 1.043806393 1.055644287 1.195878995 1 19.07104136 1.852091599 2.946701714 1.094820388 0.960956047 0.341336607 0.079143299 0.263407462 4.060588995 0.039014865 0.019974819 71.13635354 -1.852091599 -0.13386434 SKEITVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKEITVR 7 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 130.27 0.0032645 518490000 1442200 1166700 1390190 1520310 1196110 1442360 1643790 1523810 1437910 FALSE TRUE 1374030.064 1285588.056 1453931.587 1367485.55 1404711.205 1392410.712 1392999.645 1390377.118 1660893.739 0.827283547 0.774033899 0.875391094 0.823343191 0.845756217 0.838350268 0.838704857 0.837125871 1 20.66352834 -5 0.239912185 1.97912457 0.811485626 0.81870189 0.024818808 66.17359787 0.659773223 31.59323368 0.037574764 1.00E-05 5 -1.167638944 SKELDNFCNPIIYKPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKELDNFCNPIIYKPKPK 18 3 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 129.11 9.59E-06 467710000 627860 503640 566710 655230 395250 667740 710170 711910 459480 FALSE TRUE 598182.3021 554961.4886 592694.2141 589365.0355 464181.4749 644615.9964 601820.5233 649571.3863 530733.8117 1.127085347 1.045649394 1.116744781 1.110471997 0.874603171 1.214574957 1.133940424 1.223911822 1 19.01762894 SKENPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKENPR 6 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;; 83.801 0.051597 82289500 140645 83030 113428 127719 110876 104172 180956 199555 222701 FALSE TRUE 133996.9896 91490.8514 118628.786 114880.4435 130212.7393 100564.4975 153347.8387 182080.9063 257236.3337 0.520910043 0.355668463 0.461166525 0.446594934 0.506198862 0.390942042 0.596135999 0.707835101 1 17.97273491 1.022693313 1.218991537 0.997758679 0.441690131 0.917895384 0.05350551 0.112930441 0.346914503 0.046238346 0.014423945 10.53642579 -1.022693313 -0.556068548 SKEQAELEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 184.34 4.51E-06 2165690000 3994550 3351700 3454360 3882510 2996450 3622410 4411620 4029320 3628220 FALSE TRUE 3805735.538 3693242.041 3612745.823 3492232.719 3519029.931 3496965.033 3738546.344 3676491.38 4190865.827 0.908102453 0.88125991 0.862052371 0.833296236 0.839690431 0.834425433 0.892070159 0.877262965 1 21.9988169 0.410167726 1.307289072 1.000005393 0.865989508 0.750696616 0.024428098 1.751923999 3.313197605 0.026237043 0.007770015 2.571388667 -0.410167726 -0.134015884 SKESSQVTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKESSQVTSR 10 1 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;; 119.45 0.00063017 129940000 226303 173263 200791 229191 197698 203961 266271 230189 249543 FALSE TRUE 215606.1057 190918.6967 209997.466 206152.2852 232176.4686 196897.7794 225646.4685 210032.4309 288240.854 0.748006755 0.662358212 0.728548584 0.715208418 0.80549466 0.683101568 0.782839995 0.728669888 1 18.13691531 -5 0.254504057 2.699537849 0.705814439 0.80751247 0.04129622 71.12851173 0.702228 62.9640907 0.051214156 1.00E-05 5 -1.99372341 SKESVPEFPLS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_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 139.11 6.96E-06 8181240000 4238430 4415090 3558180 4942080 2049360 4695470 4308320 4975730 2096220 TRUE FALSE 4038087.814 4864992.691 3721326.073 4445292.729 2406767.735 4532864.697 3651006.656 4540028.703 2421291.092 1.667741573 2.009255602 1.536918087 1.835918343 0.994001813 1.872085811 1.507875971 1.875044566 1 21.2073451 -2.700785991 0.22173147 9.23E-29 1.781857366 0.319287388 0.290528533 54.44497852 1.353132328 27.64803502 0.536236801 0.001991655 2.700785991 1.781857366 SKESVPEFPLS(ph)PPKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKESVPEFPLSPPKKK 16 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPKKK;SKESVPEFPLS(1)PPKKK;SKESVPEFPLS(1)PPKKK 139.11 1.63E-05 3811920000 4765520 2752520 4742530 4276480 2509970 5348410 6564500 5894400 2751490 TRUE FALSE 4540263.314 3033004.917 4959979.692 3846600.106 2947707.973 5163193.221 5562964.96 5378255.088 3178177.017 1.428574711 0.954322211 1.5606367 1.210316507 0.927483887 1.62457698 1.750363473 1.69224529 1 21.59976805 2.209526555 24.99162017 1.599268444 1.215230474 0.197052557 0.28026859 240.406516 206933.0443 0.095787734 0.070755507 162.0043047 -2.209526555 -0.38403797 SKETSSPGTDDVFTPAPSDS(ph)PSSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKETSSPGTDDVFTPAPSDSPSSQR 25 1 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 SKETSSPGTDDVFTPAPS(0.006)DS(0.992)PS(0.001)S(0.001)QR;SKETSSPGTDDVFT(0.001)PAPS(0.011)DS(0.984)PS(0.003)S(0.001)QR 138.24 6.95E-06 456930000 535110 387150 449840 647700 532170 491560 629560 550360 533170 TRUE FALSE 509816.4108 426601.0252 470465.609 582591.9655 624980.2795 474537.1539 533509.0593 502167.5608 615851.2805 0.827823903 0.692701369 0.763927305 0.945994567 1.014823382 0.770538552 0.866295283 0.81540394 1 19.23222248 2.148422595 0.030473542 1.707938552 1.53E-09 0.255067091 0.0905453 209.740423 4.193753251 111.9483864 121.5657124 140.7416358 -2.148422595 -1.70793855 SKEYFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKEYFSK 7 1 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 117.89 0.0046782 38194300000 25223300 19153150 18933690 22721600 15761450 21178600 26545500 22568400 17869530 FALSE TRUE 24031044.6 21104877.76 19801818.41 20437581.6 18510241.89 20445179.77 22495496.43 20592191.25 20640645.45 1.164258388 1.022491172 0.959360426 0.990161943 0.896786001 0.99053006 1.089864001 0.997652486 1 24.29898475 4.423347046 2.016514302 0.994758507 1.168598599 0.566906872 0.047398962 0.326097173 2.211058981 0.013662876 0.082514216 26506.1741 -4.423347046 0.173840092 SKFDEMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKFDEMAK 8 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 68.657 0.051017 666870000 694030 584850 577130 669200 591880 607170 893790 741630 667300 FALSE TRUE 661224.5773 644446.8799 603591.9814 601930.7446 695103.6846 586143.5507 757425.9199 676688.9456 770781.4759 0.857862569 0.836095443 0.783090928 0.780935665 0.901816801 0.760453603 0.982672708 0.877925802 1 19.55596237 1.7128331 9.48930176 0.946223427 0.82509763 0.595505354 0.05157511 0.075933707 16.44411396 0.022358958 0.01203019 51.62179479 -1.7128331 -0.121125797 SKFDNLYGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKFDNLYGCR 10 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 143 3.17E-05 3941900000 1790850 1357940 1028040 1230110 1587600 1206440 1985800 1447660 1671980 FALSE TRUE 1706200.07 1496315.63 1075176.651 1106457.006 1864476.937 1164660.68 1682829.738 1320895.216 1931262.119 0.883463748 0.774786403 0.55672228 0.572919126 0.965418893 0.603056762 0.871362681 0.683954396 1 20.88111256 -2.865509593 0.554020129 1.758653349 0.74844869 0.254059931 0.139211767 490.8942136 20.03297596 445.0887674 0.056424205 0.001362983 2.865509593 -1.010204659 SKFDS(ph)DEEEEDTENVEAASSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.162)KFDS(0.838)DEEEEDTENVEAASSGK;S(0.253)KFDS(0.747)DEEEEDTENVEAASSGK 212.9 9.36E-24 290690000 276960 243417 254960 309692 137480 285623 318566 310620 120509 TRUE FALSE 263868.6497 268221.469 266650.1682 278561.1718 161456.4685 275731.8039 269962.9058 283420.4661 139196.9202 1.895650056 1.926921002 1.915632671 2.001202119 1.159914086 1.980875751 1.939431601 2.036111615 1 17.08676777 SKFEDMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKFEDMAK 8 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 87.298 0.014066 727400000 1697900 1366600 1304400 1418600 1202300 1618700 2037000 1774200 1415500 FALSE TRUE 1617643.632 1505858.094 1364208.03 1275999.633 1411980.739 1562644.013 1726218.238 1618841.642 1635008.511 0.989379334 0.92100933 0.834373657 0.780423848 0.863592287 0.955740599 1.055785476 0.990112059 1 20.64086671 2.013340438 4.517908034 1.019051633 0.888066038 0.549310008 0.056826372 0.178760833 9.145532684 0.027583917 0.018313135 103.1194144 -2.013340438 -0.130985595 SKFENEEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKFENEEFFR 10 1 Q13951-2;A0A494C0A9;Q13951;H3BSC0;J3KRT0 Q13951-2 CBFB Core-binding factor subunit beta 0 142.08 3.32E-05 155400000 286280 232520 261890 322890 277520 303380 373080 342970 326010 FALSE TRUE 272748.1118 256214.0524 273897.9155 290432.4837 325919.4001 292873.8745 316159.7939 312937.7286 376565.9658 0.724303672 0.680396201 0.727357065 0.771265887 0.865504134 0.777749189 0.839586746 0.831030303 1 18.52254309 0.178605471 0.112482156 1.265221202 0.524416459 0.846575052 0.035378217 7.870941707 0.326420636 1.368271803 0.694632507 1.508708967 -0.178605471 -0.740804744 SKFFIEEMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKFFIEEMIR 10 1 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP1 Q14376 GALE UDP-glucose 4-epimerase 0 ; 146.36 2.63E-05 250680000 326920 235920 219960 248920 308190 224950 388780 302950 340570 FALSE TRUE 311467.1395 259960.5162 230045.3836 223898.0887 361938.2384 217159.9251 329464.4706 276422.092 393383.8562 0.791763908 0.660831684 0.58478603 0.569159321 0.920063782 0.552030597 0.837513958 0.702677773 1 18.58557823 0.090428501 0.539057911 1.022268141 0.684228053 0.390884154 0.118731824 3.627231423 1.356229232 0.287943782 0.04991123 1.231483227 -0.090428501 -0.338040087 SKFGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKFGGR 6 1 P25391 P25391 LAMA1 Laminin subunit alpha-1 0 74.335 0.073505 307600000 772400 655610 626830 802770 676090 637280 843130 788640 791460 FALSE TRUE 735890.1827 722417.4044 655570.7755 722074.0344 793999.8819 615210.8338 714495.0334 719582.5008 914195.5746 0.804959249 0.790221944 0.717101235 0.789846346 0.868522999 0.672953196 0.781555997 0.787120963 1 19.80214331 0.621288301 3.272732368 0.999998131 0.775734953 0.650595301 0.051539251 4.727865008 40.14952701 0.046252378 0.011990639 4.181078307 -0.621288301 -0.224263178 SKFS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKFSPQK 7 1 Q9NS91;F8WE49 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 SKFS(1)PQK 72.434 0.031259 195030000 698760 866780 689060 909550 410890 778760 773770 875510 428220 TRUE FALSE 665730.9996 955105.8674 720654.0826 818120.306 482549.0859 751791.3459 655717.1752 798845.703 494626.1706 1.34592757 1.930965089 1.456967151 1.654017427 0.97558341 1.519918255 1.325682332 1.615049406 1 18.91597905 SKGGVVGIKVDK ddPTM_SK-BR-3_Trastuzumab_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 ; 146 3.50E-05 5334600000 10305000 5579000 10302600 8941400 7433900 11440000 15429600 12725900 9403900 FALSE TRUE 9817903.073 6147506.443 10774984.4 8042593.484 8730369.806 11043829.93 13075531.14 11611552.73 10862208.78 0.903858807 0.565953626 0.991969922 0.740419711 0.803737986 1.016720462 1.203763562 1.068986333 1 23.37281416 2.158359709 3.456959692 1.113059655 0.782306982 0.555622626 0.120688889 0.149316131 3.545557926 0.04656439 0.032957453 143.9990771 -2.158359709 -0.330752672 SKGHYEVTGS(ph)DDETGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVT(0.027)GS(0.973)DDETGK;SKGHYEVT(0.006)GS(0.994)DDETGK;SKGHYEVT(0.016)GS(0.984)DDETGK;SKGHYEVT(0.001)GS(0.999)DDETGK 175.32 2.15E-09 1034640000 1759460 1684640 1401050 2028160 980230 1642740 1801670 1914650 743690 TRUE FALSE 1676293.813 1856306.731 1465289.528 1824285.504 1151181.802 1585851.502 1526792.152 1746993.096 859017.647 1.951407889 2.160964606 1.705773488 2.123688041 1.340114264 1.846122146 1.777369949 2.033710369 1 19.71232824 -2.178238713 0.244342781 7.77E-17 2.00494695 0.548950105 0.241949595 25.735455 0.869952421 15.28668464 0.369565659 0.006633783 2.178238713 2.00494695 SKGHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVT(0.017)GS(0.982)DDET(0.001)GKLQGSGVSLASK;SKGHYEVT(0.007)GS(0.993)DDETGKLQGSGVSLASK 292.86 7.88E-71 3716800000 3533200 2795000 3346900 3744200 2015070 3686300 4386300 4432800 1699440 TRUE FALSE 3366192.638 3079813.678 3500358.676 3367825.902 2366497.57 3558642.507 3717089.375 4044640.532 1962980.476 1.714837554 1.568947687 1.783185681 1.715669587 1.205563478 1.812877179 1.893594675 2.06045887 1 20.90461439 SKGIAYIEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKGIAYIEFK 10 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 121.04 0.0004793 1928400000 5900100 3618200 4033500 4138700 4677000 4916000 7719200 6360300 5340700 FALSE TRUE 5621213.966 3986898.694 4218439.965 3722670.013 5492667.319 4745757.687 6541494.267 5803358.414 6168908.479 0.911216949 0.646289162 0.683822751 0.603456839 0.890379123 0.769302658 1.06039736 0.940743153 1 22.55658381 1.992890229 1.730369265 1.006353194 0.730495857 0.554984561 0.10297954 0.26274261 1.466947595 0.062607236 0.030928885 98.37624209 -1.992890229 -0.275857337 SKGLAPDLPEDLYHLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKGLAPDLPEDLYHLIK 17 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 184.15 3.92E-10 153319000 728470 400860 694750 606910 601710 704640 986340 795910 633170 FALSE TRUE 694036.6668 441708.0897 726604.9747 545902.2537 706648.0335 680238.1401 835855.7176 726215.901 731358.7698 0.948968817 0.603955416 0.99350005 0.74642197 0.966212566 0.930101844 1.142880556 0.992968063 1 19.48021977 2.397174132 1.52235304 1.053878379 0.806400835 0.365753075 0.11862104 0.341769712 1.600504046 0.055617676 0.039115505 249.5595142 -2.397174132 -0.247477544 SKGQENDHVHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKGQENDHVHEK 12 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ; 154.47 4.61E-05 58486000 75842 66938 75393 79840 56731 85375 90742 65867 13163.3 FALSE TRUE 72257.09896 73759.0583 78849.84362 71814.33151 66624.86844 82418.44234 76897.64131 60099.3363 15204.59734 4.752319142 4.851102379 5.185921198 4.723198512 4.381889699 5.420626441 5.057525669 3.952708182 1 13.89221999 0.847073512 3.090771166 1.001316639 4.907132449 0.949719982 0.282407629 0.135578544 2.300780332 0.271420193 0.070887585 7.03191338 -0.847073512 3.90581581 SKGQESFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKGQESFK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;; 101.38 0.004957 11117820000 5621310 4726660 4465510 5361090 3549950 5477520 6651180 6167030 4343400 FALSE TRUE 5355601.817 5208312.028 4670258.05 4822183.048 4169060.156 5287832.109 5636420.334 5627012.16 5016952.289 1.067501046 1.038142627 0.930895448 0.961177777 0.830994579 1.053992903 1.123474972 1.121599696 1 22.25837979 2.010885733 24.95534848 1.093741761 0.97969271 0.355337518 0.071809511 243.047373 557179.2609 0.028517004 0.021042444 102.5382103 -2.010885733 -0.114049051 SKGYAFIEFASFEDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKGYAFIEFASFEDAK 16 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 223.29 8.08E-15 512178000 1770120 1347120 1681660 1763660 1209230 1821960 2031310 1995290 1330520 FALSE TRUE 1686449.936 1484393.06 1758765.774 1586373.546 1420119.329 1758865.068 1721396.352 1820571.83 1536850.246 1.097341748 0.96586708 1.144396325 1.032223894 0.924045354 1.144460934 1.120080734 1.184612381 1 20.55154516 SKGYAFIEFASFEDAKEALNSCNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKGYAFIEFASFEDAKEALNSCNKR 25 3 P19338;H7BY16 P19338 NCL Nucleolin 0 107.05 0.0016317 13752000 39246 11450 52718 26490 47961 45005 95700 51164 71782 FALSE TRUE 37390.91936 12616.76802 55135.17245 23827.17487 56325.38321 43446.46557 81099.20735 46683.80892 82913.58595 0.450962516 0.15216768 0.66497151 0.28737359 0.679326344 0.523996943 0.978117234 0.563041731 1 16.3393209 2.216537187 0.557904226 0.942286329 0.302761398 0.506928464 0.187253464 0.576524836 0.36670761 0.154677961 0.120569919 164.6406937 -2.216537187 -0.639524932 SKHEEEEWT(ph)DDDLVESL ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 S(0.001)KHEEEEWT(0.999)DDDLVESL;S(0.001)KHEEEEWT(0.999)DDDLVESL;S(0.003)KHEEEEWT(0.997)DDDLVESL;S(0.002)KHEEEEWT(0.998)DDDLVESL;S(0.037)KHEEEEWT(0.963)DDDLVESL;S(0.001)KHEEEEWT(0.999)DDDLVESL 214.55 9.54E-15 2006293000 3179900 2706930 3009810 3392120 2514380 3182240 3716590 3331460 2289940 TRUE FALSE 3029592.429 2982769.245 3147812.766 3051137.653 2952887.076 3072038.231 3149555.936 3039739.701 2645052.2 1.14538096 1.127678783 1.190075858 1.153526442 1.116381399 1.161428206 1.190734888 1.149217283 1 21.33486476 -0.746580993 5.938628616 0.999999994 1.154334249 0.811666644 0.023358851 1.76E-09 4.16E-10 0.023668808 0.005578791 0.179233426 0.746580993 0.154334254 SKIEDYFPEFAR ddPTM_SK-BR-3_Trastuzumab_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 63.682 0.062881 466540000 296490 299740 274880 311290 242090 313870 347870 321090 285500 FALSE TRUE 282475.5053 330283.8468 287483.5199 279998.5378 284310.4194 303000.6032 294796.0424 292973.6574 329773.8819 0.856573309 1.001546408 0.871759517 0.8490622 0.862137467 0.918813223 0.89393387 0.888407705 1 18.33111762 -0.741204134 6.341849235 1.000000001 0.89834724 0.364563862 0.04394356 9.61E-10 1.01E-10 0.043012606 0.010138168 0.18146625 0.741204134 -0.101652761 SKIETEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SKIETEIK 8 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;; 134.68 0.00079016 1962380000 4201430 3671420 3604900 4508930 2674360 4207780 4485840 4611340 3000400 FALSE TRUE 4002836.73 4045541.872 3770188.231 4055683.79 3140767.537 4062063.524 3801442.72 4207546.623 3465686.708 1.154990935 1.167313209 1.087861814 1.170239589 0.906246814 1.172080417 1.096880082 1.214058563 1 21.72470981 SKKDQGELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKKDQGELER 10 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 58.476 0.062346 143500000 112800 56991 205260 90202 128070 120570 192120 169680 192710 FALSE TRUE 107468.1675 62798.44769 214671.374 81134.72359 150405.3675 116394.6307 162808.5655 154821.9197 222594.4826 0.482797985 0.282120415 0.964405638 0.364495663 0.675692253 0.522899891 0.731413302 0.695533501 1 17.76405831 -2.413328504 0.078966449 2.063525444 1.90E-10 0.389114126 0.18232959 120.5200411 1.1943122 30.09041082 7.323465251 0.003860748 2.413328504 -2.063525444 SKLEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKLEVGR 7 1 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 101.54 0.0081925 171640000 229970 189900 200780 240920 222880 222260 251390 234990 256210 FALSE TRUE 219099.7739 209251.0259 209985.9616 216702.2639 261750.2014 214563.0805 213035.8384 214413.0298 295941.7383 0.740347661 0.707068314 0.709551694 0.732246371 0.884465311 0.725017977 0.71985736 0.72451095 1 18.17495366 -1.069747197 4.160634632 1.000032904 0.740125859 0.711468973 0.051431161 5721101.283 2941922.741 1698.775523 0.011875327 0.085163363 1.069747197 -0.259907045 SKLNLAQFLNEDLS(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKLNLAQFLNEDLS 14 1 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 1 SKLNLAQFLNEDLS(1);SKLNLAQFLNEDLS(1) 105.28 0.0026545 143223000 672300 643050 731150 738400 593580 732730 894430 810910 769140 TRUE FALSE 640521.7114 708577.5261 764673.9507 664174.6291 697100.1641 707355.3764 757968.2762 739902.4215 888414.303 0.720971859 0.79757555 0.86071774 0.747595606 0.78465662 0.796199897 0.853169826 0.832834882 1 19.76087309 -5 0.144557645 1.736661392 0.726077179 0.779448523 0.035926338 61.66560523 0.538555966 12.96004121 0.198077971 1.00E-05 5 -1.010584213 SKLS(ph)PS(ph)PSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.007)KLS(0.993)PS(0.969)PS(0.031)LR 101.72 0.037543 95549000 407880 321780 341070 405220 256270 380540 423000 344910 293570 TRUE FALSE 388600.3207 354569.7478 356708.3969 364486.5157 300963.4069 367361.8044 358463.5811 314707.8519 339095.3363 1.145991346 1.045634398 1.051941324 1.074879176 0.887548057 1.083358469 1.057117403 0.928080744 1 18.37133142 8 0.413678081 1.004898522 3.605602735 0.350628244 0.060871454 85.14532618 1.10345391 0.038826185 182.3824906 100000000 -8 2.600704213 SKLS(ph)PSPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SKLS(0.995)PS(0.005)PSLR;S(0.016)KLS(0.711)PS(0.27)PS(0.003)LR;SKLS(0.996)PS(0.004)PSLR 166.86 3.28E-06 1221560000 2289710 2111900 1933300 2284080 1734480 2229360 2566100 2430410 1940390 TRUE FALSE 2181479.946 2327105.011 2021943.717 2054479.939 2036972.763 2152156.704 2174594.315 2217590.416 2241295.771 0.973311945 1.038285549 0.90213159 0.916648291 0.908837106 0.96022878 0.97023978 0.98942337 1 21.09590161 -0.844644722 7.321131411 0.999998394 0.962009983 0.086509672 0.041148177 0 0 0.043125986 0.010164892 0.143006335 0.844644722 -0.037988411 SKLSPS(ph)PSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.005)KLS(0.473)PS(0.52)PS(0.002)LR 115.12 0.00076618 761430000 1030800 967840 903110 1031400 749870 970240 1123600 1102000 853680 TRUE FALSE 982076.1268 1066463.996 944518.4868 927721.7125 880647.0906 936640.3455 952174.1837 1005503.038 986064.3344 0.995955429 1.081535919 0.957867001 0.940832844 0.893092935 0.949877521 0.965630893 1.019713423 1 19.91132225 3.71597126 23.23866318 0.955917794 1.038745662 0.397364562 0.039418385 255.7971738 263149.7807 0.010280176 0.015945274 5199.615861 -3.71597126 0.082827868 SKLTFSCLGGSDNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKLTFSCLGGSDNFK 15 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 228.99 4.77E-13 1320870000 4823600 3066700 4199400 4570200 3759000 4561000 6200500 5223700 4817500 FALSE TRUE 4595597.987 3379200.217 4391946.644 4110794.813 4414568.41 4403051.426 5254499.845 4766285.135 5564573.296 0.825867096 0.607270322 0.789269259 0.738743942 0.793334578 0.791264881 0.944277228 0.856540993 1 22.40783963 1.809127595 0.74433479 0.980164567 0.720653987 0.626274995 0.065535057 0.369254718 0.395880871 0.055399636 0.026960053 64.43585489 -1.809127595 -0.25951058 SKNVGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKNVGWR 7 1 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 105.14 0.0072912 495280000 776800 597000 721220 761330 689540 753420 882180 802560 769140 FALSE TRUE 740082.2035 657834.9787 754288.6504 684799.662 809795.5577 727328.8765 747587.2387 732283.5918 888414.303 0.833037245 0.740459689 0.849028036 0.770811163 0.911506664 0.818682088 0.84148492 0.82425912 1 19.76087309 -5 0.18181746 1.751587842 0.78198259 0.612247032 0.044589421 81.7256157 0.789281287 22.15390947 0.122969346 1.00E-05 5 -0.969605251 SKPAGS(ph)DGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SKPAGS(1)DGER;SKPAGS(1)DGER;SKPAGS(1)DGER;S(0.004)KPAGS(0.996)DGER;S(0.003)KPAGS(0.997)DGER;S(0.001)KPAGS(0.999)DGER;S(0.001)KPAGS(0.999)DGER;SKPAGS(1)DGER;S(0.001)KPAGS(0.999)DGER;S(0.001)KPAGS(0.999)DGER;SKPAGS(1)DGER 125.97 0.00023912 3960301000 6337210 5955910 6029930 6901330 4258714 6504070 6527380 6710450 5186450 TRUE FALSE 6037662.642 6562824 6306408.255 6207595.197 5001432.373 6278832.425 5531508.297 6122847.424 5990738.177 1.007832835 1.095495047 1.052693019 1.036198714 0.834860784 1.048089941 0.923343357 1.022052248 1 22.51430235 2.974847182 24.98574852 0.961829586 1.0536941 0.308913637 0.061444141 754.525734 749514.304 0.016594859 0.017672364 943.7287411 -2.974847182 0.091864515 SKPAGS(ph)DGERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.045)KPAGS(0.955)DGERR;S(0.003)KPAGS(0.997)DGERR;S(0.091)KPAGS(0.909)DGERR;S(0.233)KPAGS(0.767)DGERR;S(0.012)KPAGS(0.988)DGERR;S(0.009)KPAGS(0.991)DGERR;S(0.012)KPAGS(0.988)DGERR 89.911 0.0093562 3667987000 3173222 2594396 2808482 3296486 2184596 3074931 3319581 3116345 2733830 TRUE FALSE 3023230.085 2858767.902 2937253.678 2965116.964 2565588.851 2968445.368 2813117.95 2843461.311 3157778.394 0.957391466 0.905309856 0.9301646 0.9389883 0.812466402 0.940042333 0.890853505 0.90046259 1 21.5904785 -1.096978888 3.849091246 1.000028547 0.910460173 0.335854241 0.039990897 11893201.58 26223195.08 4725.759577 0.008979168 0.079987314 1.096978888 -0.089568374 SKPAGSDGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 114.86 0.0011849 252710000 455520 376130 359900 473490 306920 430720 464030 465530 399130 FALSE TRUE 433988.4724 414458.0746 376401.771 425893.8856 360446.7508 415804.0584 393233.701 424765.7253 461025.0419 0.941355529 0.898992543 0.816445392 0.923797727 0.781837684 0.901912088 0.852955187 0.921350657 1 18.81448559 0.947452345 4.792609395 0.999958163 0.877918805 0.41367322 0.048074497 0.264521433 18.23122776 0.043942321 0.011129938 8.860379937 -0.947452345 -0.122039358 SKPAGSDGERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 116.01 0.00058846 186205000 469090 324915 425600 473180 352007 442010 515640 465290 452530 FALSE TRUE 446917.0453 358024.2079 445114.181 425615.0474 413396.9094 426703.0829 436969.6476 424546.7409 522706.0412 0.855006467 0.684943696 0.851557369 0.814253163 0.790878384 0.816334707 0.835975889 0.812209363 1 18.99564031 -4.99999849 0.216348398 1.996760828 0.775886955 0.616471993 0.047676487 93.49658575 0.934111961 40.43161264 0.089336189 1.00E-05 4.99999849 -1.220873872 SKPCGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKPCGSPR 8 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 SKPCGS(1)PR;SKPCGS(1)PR;SKPCGS(1)PR 91.549 0.0075145 1293370000 2530050 2328970 2062590 2715980 1592590 2274930 2458540 2620420 1904210 TRUE FALSE 2410459.551 2566294.691 2157161.792 2442964.53 1870337.192 2196148.604 2083444.569 2390962.133 2199505.161 1.095909931 1.166760022 0.980748684 1.110688246 0.850344534 0.998473949 0.947233317 1.087045475 1 21.06874756 3.484128713 1.602447138 0.980323079 1.130472234 0.309791271 0.076413777 0.350365658 1.814070894 0.021836215 0.038854293 3048.798435 -3.484128713 0.150149155 SKPDLESS(ph)LESLVFDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.206)S(0.794)LESLVFDLR;SKPDLES(0.03)S(0.97)LESLVFDLR;SKPDLES(0.196)S(0.804)LESLVFDLR 258.55 2.19E-27 167108000 259405 273213 257514 318255 200309 272618 320936 308358 234257 TRUE FALSE 247143.4397 301053.7153 269321.2716 286263.4028 235242.8262 263177.1703 271971.3188 281356.5388 270584.3791 0.913369207 1.112605673 0.995331927 1.057945043 0.869388052 0.972625142 1.00512572 1.039810723 1 18.04571903 -4.611619739 4.702599357 2.163917956 0.998888105 0 0.069057422 0 0 0 0.014539542 2.45E-05 4.611619739 -1.165029851 SKPDPEVGPLLGVQPLPGS(ph)PTADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKPDPEVGPLLGVQPLPGSPTADR 24 1 A0A6E1W9L1;Q9H5J0 A0A6E1W9L1 ZBTB3 Zinc finger and BTB domain-containing protein 3 1 SKPDPEVGPLLGVQPLPGS(0.843)PT(0.157)ADR;SKPDPEVGPLLGVQPLPGS(0.86)PT(0.14)ADR 155.25 2.83E-08 289100000 597920 536470 545890 639040 492890 592840 691280 664380 569850 TRUE FALSE 569657.5066 591136.9029 570919.5965 574802.4851 578849.8599 572309.8021 585812.5398 606203.3651 658219.4276 0.865452283 0.898084861 0.867369714 0.873268793 0.879417768 0.869481784 0.889995821 0.920974586 1 19.32820908 0.862445135 1.594471773 0.99984904 0.876970963 0.946790816 0.009331299 0.112408734 0.550337115 0.008538448 0.00247019 7.285261328 -0.862445135 -0.122878077 SKPGAAMVEMADGYAVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SKPGAAMVEMADGYAVDR 18 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;; 241.65 4.82E-24 2362730000 4185230 3464730 3602960 4215610 3323120 3966200 4548770 4150040 3805680 FALSE TRUE 3987402.472 3817789.926 3768159.28 3791848.874 3902671.076 3828849.499 3854771.593 3786640.497 4395845.418 0.907084325 0.868499586 0.857209233 0.86259832 0.887808989 0.871015501 0.876912454 0.86141348 1 22.06770922 -1.975015419 2.794615951 1.106346547 0.875103167 0.880513241 0.014574688 15536862.85 5483469.329 10664101.09 0.003545676 0.010592161 1.975015419 -0.231243381 SKPIPIMPAS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 150.7 2.61E-05 1609120000 3194250 3718090 2642540 3774840 1566730 3252330 2905000 3310130 1502030 TRUE FALSE 3043264.133 4096967.598 2763703.073 3395385.911 1839967.216 3139700.997 2461788.896 3020277.469 1734957.141 1.754086058 2.361422943 1.592951784 1.957043106 1.060526034 1.809670638 1.41893355 1.740836933 1 20.72646859 3.190428991 1.732610532 1.473349396 2.029671866 0.325627058 0.331766402 0.359343886 2.228190126 0.098177529 0.133724569 1550.347277 -3.190428991 0.55632247 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 SKPIPIMPAS(1)PQKGHAVNLLDVPVPVAR;SKPIPIMPAS(1)PQKGHAVNLLDVPVPVAR;S(0.022)KPIPIMPAS(0.978)PQKGHAVNLLDVPVPVAR 221.85 1.19E-34 3398450000 2720950 2169380 2554210 2661120 1863630 2754520 3255780 2983160 2180760 TRUE FALSE 2592336.086 2390442.288 2671323.055 2393619.162 2188646.482 2659130.282 2759050.964 2721938.696 2518941.123 1.029137228 0.948986964 1.06049444 0.950248158 0.868875601 1.055654004 1.095321736 1.080588455 1 21.26438597 2.028937077 24.9995971 1.070793061 0.975572248 0.360075126 0.056295362 198.7155172 171675.3916 0.020186782 0.014908704 106.89 -2.028937077 -0.095220813 SKPLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 79.597 0.060858 538660000 1024290 942980 966230 1138280 901590 986240 1242540 1082040 1057910 FALSE TRUE 975873.8416 1039070.734 1010532.601 1023857.932 1058827.011 952086.2615 1052967.702 987290.8413 1221965.28 0.798610122 0.850327543 0.826973252 0.837878088 0.866495168 0.779143464 0.861700181 0.807953268 1 20.22077186 -1.282509274 3.550916347 1.000480559 0.830271064 0.791140173 0.027659659 1358241.796 984319.883 4558.029653 0.005658831 0.052178396 1.282509274 -0.170209495 SKPNLPSES(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.006)ES(0.994)R 53.754 0.085728 207430000 220900 288430 200270 256380 134430 240510 203350 251750 149330 TRUE FALSE 210458.4948 317821.3449 209452.5776 230608.1953 157874.5494 232181.0784 172325.2227 229705.4354 172487.3337 1.220138837 1.842577875 1.214307005 1.336957273 0.915281986 1.346076105 0.999060157 1.331723498 1 17.3961309 3.556027744 9.213727587 1.156937484 1.532108714 0.34793258 0.210929259 0.389165744 43.11990062 0.051161318 0.07925819 3597.723175 -3.556027744 0.37517123 SKPVNKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKPVNKDR 8 2 P62316;P62316-2;K7EJB5 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 ; 69.375 0.030418 1092430000 3111280 1719530 2896960 2512000 2813010 3208430 5136200 3807170 4774000 FALSE TRUE 2964215.96 1894752.062 3029788.481 2259488.988 3303598.053 3097321.265 4352578.357 3473794.012 5514327.538 0.53754804 0.343605281 0.54943934 0.409748781 0.599093549 0.561686125 0.789321695 0.629957867 1 22.39475353 1.289939254 0.471505079 1.001649493 0.425792587 0.773901714 0.087756693 0.373719697 0.226271764 0.090608738 0.052656504 19.49571891 -1.289939254 -0.575856906 SKPYEGSQRNS(ph)TELAPPLPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKPYEGSQRNSTELAPPLPVR 21 2 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SKPYEGSQRNS(0.786)T(0.214)ELAPPLPVR 180.21 2.85E-17 188230000 101710 97274 116380 131760 79700 133440 132570 133590 105890 TRUE FALSE 96902.36987 107186.3312 121716.1381 118515.2345 93599.65477 128818.9393 112344.0117 121892.1514 122310.8804 0.792262876 0.876343387 0.995137454 0.968967226 0.765260249 1.053209158 0.918512003 0.996576519 1 16.90019322 6.582938338 0.407425503 0.967365457 8.03E-19 0.317921537 0.077569485 25.69442106 1.004277943 0.050693442 16.56714199 3827703.929 -6.582938338 -0.967365457 SKPYEGSQRNS(ph)TELAPPLPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKPYEGSQRNSTELAPPLPVRR 22 3 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SKPYEGS(0.069)QRNS(0.912)T(0.019)ELAPPLPVRR 119.28 5.11E-05 76755000 137910 70897 129860 122900 125180 129860 198980 146430 156400 TRUE FALSE 131391.2676 78121.4849 135814.2094 110545.8585 147011.3524 125362.9156 168621.9465 133607.8129 180653.7132 0.727310086 0.432437748 0.751793069 0.611921319 0.813774319 0.693940431 0.93339873 0.739579666 1 17.46286738 2.019403805 0.480738878 0.973334974 0.574922324 0.49371344 0.112165928 0.669675228 0.347170611 0.102970356 0.084241294 104.5692046 -2.019403805 -0.39841265 SKQEALKNDLVEALKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKQEALKNDLVEALKR 16 3 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 162.4 3.54E-09 502050000 634820 558560 628520 695540 387250 702370 809630 864060 466440 FALSE TRUE 604813.3167 615477.899 657338.2637 625622.9978 454786.2774 678046.7508 686106.0736 788398.3257 538773.133 1.122575124 1.142369323 1.220065039 1.161199324 0.844114618 1.258501416 1.273460074 1.463321531 1 19.03931838 2.039903525 24.99996985 1.273479971 1.109462833 0.194438782 0.148100968 214.2002611 134197.8046 0.05106076 0.037710816 109.623465 -2.039903525 -0.164017138 SKQELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKQELER 7 1 H0Y626;O95361;K7ENN8;B3KP96;O95361-2;J3QR69;J3QKY5;J3QLP0;K7EL43 H0Y626 TRIM16 Tripartite motif-containing protein 16 0 63.486 0.072179 104990000 217410 182520 175460 225820 177190 198460 212110 214670 149300 FALSE TRUE 207133.4602 201118.9955 183505.0146 203120.1446 208091.8799 191587.2804 179748.7238 195872.3568 172452.6815 1.201103157 1.166227128 1.064089076 1.177831176 1.206660738 1.110955648 1.042307503 1.135803486 1 17.39584104 -4.999999964 0.049376429 0.365423475 1.452174298 0.505884931 0.048809633 447.5361539 1.634839108 36.95082706 8.421429652 1.00E-05 4.999999964 1.086750823 SKRPPKS(ph)PEEEGQMS(ph)S ddPTM_SK-BR-3_Trastuzumab_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(0.538)S(0.462) 84.573 0.0030248 135640000 183570 143780 167990 186690 97503 175390 213040 143900 95158 TRUE FALSE 174893.0099 158431.3455 175692.5077 167923.5665 114507.4923 169316.2003 180536.8353 131299.3531 109914.6166 1.591171541 1.441403794 1.598445348 1.527763746 1.04178585 1.540433889 1.6425189 1.194557714 1 16.74602373 -3.210860035 0.230796013 3.06E-13 1.535141173 0.407718713 0.181934435 66.82447826 1.400552276 32.43694877 0.320862456 0.000615375 3.210860035 1.535141173 SKS(ph)AT(ph)TTPSGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 S(0.018)KS(0.98)AT(0.496)T(0.496)T(0.01)PS(0.288)GS(0.712)PR 105.14 0.01062 51783000 202150 163470 191040 205420 128980 191690 218180 163940 153390 TRUE FALSE 192594.7701 180127.7788 199799.373 184770.7913 151474.0712 185051.7272 184892.6338 149584.5445 177176.9378 1.087019409 1.016654769 1.12768273 1.042860282 0.854931082 1.044445906 1.04354797 0.844266451 1 17.4348313 2.981724943 24.67455451 0.971745215 1.068038563 0.361875135 0.072796313 800.575257 1080919.129 0.021207102 0.022890797 958.793195 -2.981724943 0.096293348 SKS(ph)ATTTPS(ph)GS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 S(0.001)KS(0.983)AT(0.037)T(0.103)T(0.253)PS(0.624)GS(0.999)PR 139.03 2.64E-06 0 226880 192500 231590 228850 158550 239740 260410 208940 200590 TRUE FALSE 216155.832 212115.9689 242208.6306 205845.5632 186201.0698 231437.7437 220679.6717 190644.1059 231696.4727 0.932926727 0.915490712 1.045370384 0.888427695 0.803642229 0.998883328 0.952451581 0.822818335 1 17.82187656 SKS(ph)DATASISLSSNLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSDATASISLSSNLKR 17 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.004)KS(0.648)DAT(0.345)AS(0.003)ISLSSNLKR;S(0.054)KS(0.939)DAT(0.008)ASISLSSNLKR 148.29 2.90E-07 1325580000 1539650 1124110 1496210 1541500 1097110 1674770 1988700 1910320 1424830 TRUE FALSE 1466873.796 1238658.087 1564812.708 1386545.491 1288445.637 1616772.295 1685287.29 1743042.254 1645785.359 0.891291071 0.75262432 0.950799993 0.842482577 0.782875865 0.982371295 1.024001873 1.059094519 1 20.65034476 2.10802573 5.08936877 1.024061448 0.841095815 0.706832826 0.055643213 0.108992357 4.464450973 0.020666122 0.015027064 128.2406557 -2.10802573 -0.182965633 SKS(ph)DGEAKPEPSPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 S(0.276)KS(0.724)DGEAKPEPSPSPR 94.911 0.0020514 54323000 58307 66874 62612 79064 43819 80232 66284 68059 35171 TRUE FALSE 55550.94366 73688.53663 65482.82213 71116.33651 51461.01973 77453.54572 56171.15841 62099.39316 40625.13905 1.367403164 1.813865462 1.611879335 1.750549984 1.266728458 1.906542292 1.382669936 1.528595215 1 15.31008513 0.359766514 0.774402906 0.991838045 1.613052409 0.456442975 0.201733514 1.882805501 1.571705905 0.207093019 0.061404357 2.289636363 -0.359766514 0.621214364 SKS(ph)DLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.358)KS(0.642)DLSER;S(0.028)KS(0.972)DLSER;S(0.169)KS(0.809)DLS(0.023)ER;S(0.357)KS(0.643)DLSER 136.38 0.00048061 3286730000 2817130 2445100 2436910 2910770 1888930 2860580 3115550 2945910 2289470 TRUE FALSE 2683969.848 2694258.47 2548644.734 2618173.869 2218358.794 2761517.397 2640215.626 2687950.503 2644509.315 1.014921684 1.018812244 0.963749577 0.990041463 0.838854596 1.044245669 0.998376376 1.016426937 1 21.33456863 -0.76358407 7.426819126 1 0.988820023 0.003597867 0.056397346 0 0 0.05211817 0.01228437 0.172351842 0.76358407 -0.011179977 SKS(ph)DSYTLDPDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.203)KS(0.79)DS(0.006)YTLDPDTLR;S(0.279)KS(0.705)DS(0.01)Y(0.001)T(0.005)LDPDTLR;S(0.025)KS(0.788)DS(0.14)YT(0.047)LDPDTLR;S(0.2)KS(0.785)DS(0.012)YT(0.003)LDPDTLR;S(0.083)KS(0.765)DS(0.143)YT(0.009)LDPDTLR 151.8 5.90E-06 590848000 1547500 1266509 1348185 1667070 1144160 1514844 1764300 1569368 1280700 TRUE FALSE 1474352.742 1395567.707 1410000.616 1499492.956 1343701.142 1462384.572 1495123.631 1431945.818 1479304.415 0.996652702 0.943394539 0.95315109 1.01364732 0.908333084 0.988562298 1.010693686 0.967985902 1 20.49648753 2.02213812 24.99936847 0.995468071 0.963863294 0.182902457 0.030145107 348.4876049 393526.3868 0.01036417 0.007653849 105.2296485 -2.02213812 -0.031604778 SKS(ph)EDMDNVQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.063)KS(0.937)EDMDNVQSK;S(0.004)KS(0.996)EDMDNVQSK 132.14 0.00011284 245490000 311438 324431 314085 385915 181477 351053 358542 354111 182128 TRUE FALSE 296716.943 357490.8877 328486.1079 347122.091 213126.5313 338895.9466 303839.8328 323103.1636 210371.4801 1.410442817 1.699331524 1.561457417 1.650043489 1.013096125 1.610940544 1.444301446 1.535869613 1 17.68257961 -3.030902805 0.267094417 1.61E-13 1.547616214 0.390575266 0.191423008 62.92777729 1.581031984 35.78717967 0.231353326 0.000931316 3.030902805 1.547616214 SKS(ph)EEAHAEDSVMDHHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.249)KS(0.751)EEAHAEDSVMDHHFR 189.39 1.66E-14 934870000 487270 367430 444290 463910 327570 403810 579470 428950 209330 TRUE FALSE 464237.7128 404871.5347 464661.136 417276.8854 384698.1043 389825.9584 491061.2088 391388.864 241791.8273 1.919989265 1.674463274 1.921740454 1.725769188 1.59103022 1.612237944 2.030925587 1.618701791 1 17.88340596 0.976047224 23.9668169 0.999999994 1.783669095 0.74918902 0.141640918 620.3883539 620753.0186 0.132350821 0.033087705 9.463400573 -0.976047224 0.783669101 SKS(ph)ERECPHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSERECPHSK 11 2 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 S(0.251)KS(0.749)ERECPHSK 66.387 0.032793 20907000 21072 16148 23970 23733 16862 23484 31485 26828 23798 TRUE FALSE 20075.96832 17793.49956 25069.04821 21347.31375 19802.72746 22670.74319 26681.38499 24478.7981 27488.4723 0.730341363 0.647307692 0.911984047 0.776591493 0.720401165 0.824736382 0.970639063 0.890511405 1 14.74653911 2.009221352 0.46450753 1.011640791 0.697099535 0.571281965 0.074738329 0.650877092 0.322034454 0.076920306 0.065104159 102.1459971 -2.009221352 -0.314541256 SKS(ph)HESQLGNR ddPTM_SK-BR-3_Trastuzumab_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(0.061)KS(0.938)HESQLGNR;S(0.005)KS(0.948)HES(0.047)QLGNR 97.797 0.0036328 193054000 196632 123756 162741 214730 163699 174615 242010 201920 177593 TRUE FALSE 187337.595 136366.8771 170202.8358 193144.9324 192248.0538 168568.0388 205086.9297 184238.8144 205133.2154 0.91324847 0.664772289 0.829718559 0.941558548 0.937186371 0.821749118 0.999774363 0.898142283 1 17.64620159 3.356387056 4.493709088 0.929958119 0.78315016 0.391381797 0.077431014 0.191705785 6.636811782 0.020660486 0.028282128 2271.888724 -3.356387056 -0.146807959 SKS(ph)LDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.014)KS(0.986)LDSR;S(0.006)KS(0.994)LDSR;S(0.229)KS(0.771)LDSR;S(0.056)KS(0.944)LDSR 152.54 0.0010942 1629610000 8364400 7030600 7238300 9080500 5438200 8274900 9314500 8930800 6752100 TRUE FALSE 7969031.389 7747026.133 7570183.215 8167710.888 6386620.358 7988338.138 7893401.952 8148771.807 7799181.183 1.021777954 0.993312753 0.970638204 1.047252358 0.818883445 1.024253438 1.012080854 1.044824016 1 22.89489124 -0.539288071 4.971924161 1.000000002 0.992386654 0.001492381 0.065493291 0 39958218.96 0.05819156 0.014113528 0.288876311 0.539288071 -0.007613348 SKS(ph)LGDLTSEDIACNFESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSLGDLTSEDIACNFESK 19 1 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(0.192)KS(0.807)LGDLTSEDIACNFESK 298.32 5.23E-50 161840000 426370 354500 420380 447740 230000 464370 514740 514570 271810 TRUE FALSE 406216.3351 390623.953 439654.8388 402732.3245 270111.9272 448288.7505 436206.9592 469511.5229 313960.9066 1.293843681 1.24418023 1.400348991 1.282746725 0.86033618 1.427848949 1.389367115 1.495445812 1 18.2602254 SKS(ph)LKEGLTVQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSLKEGLTVQER 13 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.079)KS(0.921)LKEGLTVQER;S(0.254)KS(0.746)LKEGLTVQER;S(0.001)KS(0.991)LKEGLT(0.008)VQER;S(0.003)KS(0.997)LKEGLTVQER 134.52 4.94E-05 1930280000 1921760 1205870 1765740 1794700 1098960 1878800 2318850 2022840 1357230 TRUE FALSE 1830922.213 1328749.524 1846700.926 1614293.346 1290618.276 1813736.685 1965066.844 1845709.406 1567702.297 1.167901723 0.847577711 1.177966588 1.029719322 0.823254695 1.156939483 1.253469392 1.177334121 1 20.58022019 2.032397237 24.8819987 1.180124586 1.008569785 0.20033659 0.130222669 216.7198502 166446.142 0.045450873 0.033567436 107.7450276 -2.032397237 -0.171554801 SKS(ph)NPDFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSNPDFLK 9 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.201)KS(0.799)NPDFLK 79.466 0.016268 208720000 540300 493430 442750 586400 302500 516070 557950 572660 342240 TRUE FALSE 514761.0898 543711.078 463050.5254 527453.9579 355255.9042 498198.3665 472824.48 522514.8545 395312.8313 1.302161349 1.37539446 1.171352126 1.334269764 0.898670309 1.260263586 1.196076734 1.321775599 1 18.59263526 3.504316004 1.773597734 1.169013055 1.337728279 0.199651271 0.136305785 0.520589632 3.277953776 0.038405522 0.067058378 3193.860944 -3.504316004 0.168715225 SKS(ph)NPDFLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.03)KS(0.97)NPDFLKK;S(0.007)KS(0.993)NPDFLKK 115.1 0.00099832 2430900000 1945380 1741060 1690890 2004380 989010 1938360 2161100 2209500 1080890 TRUE FALSE 1853425.743 1918475.993 1768418.979 1802895.914 1161493.031 1871234.107 1831384.504 2016024.467 1248508.901 1.484511437 1.53661379 1.416424807 1.444039296 0.930304165 1.498775144 1.466857387 1.61474577 1 20.25177468 3.380041923 2.562015662 1.349437111 1.50703428 0.108163008 0.214468288 0.682968451 9.077458124 0.060973842 0.08899743 2399.064492 -3.380041923 0.157597169 SKS(ph)PASVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.282)KS(0.69)PAS(0.027)VDR;S(0.023)KS(0.976)PAS(0.001)VDR;S(0.035)KS(0.784)PAS(0.181)VDR;S(0.306)KS(0.692)PAS(0.001)VDR 107.17 0.0017064 1503245000 2126020 2157370 2053010 2275370 1548330 2182770 2335300 2374670 1811630 TRUE FALSE 2025527.248 2377208.456 2147142.539 2046645.485 1818358.262 2107180.128 1979007.094 2166731.306 2092568.328 0.967962298 1.136024293 1.026080014 0.978054316 0.868960042 1.006982711 0.945731171 1.035441126 1 20.9968433 3.307483812 3.913053707 0.965478758 1.055534288 0.239294664 0.059565869 0.250165539 7.557186133 0.016117023 0.021819888 2029.942856 -3.307483812 0.09005553 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.315)KS(0.685)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.146)KS(0.854)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.212)KS(0.788)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.099)KS(0.823)PLPPEEEAKDEEEDQT(0.078)LVNLDTYTSDLHFQVSK;S(0.166)KS(0.834)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 318.86 3.87E-110 8513693000 2893720 2294790 2334450 2865090 1143051 3065180 2914250 3273210 1040854 TRUE FALSE 2756939.59 2528631.71 2441486.842 2577085.71 1342398.732 2959032.048 2469627.639 2986590.38 1202264.322 2.293122684 2.103224443 2.030740492 2.143526729 1.116558736 2.461215885 2.05414699 2.484137909 1 20.19732268 4.018382489 1.288217631 1.950208128 2.283146791 0.062036319 0.493592184 1.78174502 5.170001484 0.137812182 0.553557615 10432.35816 -4.018382489 0.332938663 SKS(ph)PS(ph)PPRLTEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSPSPPRLTEDR 13 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.42)KS(0.58)PS(0.99)PPRLT(0.01)EDR;S(0.415)KS(0.585)PS(0.961)PPRLT(0.039)EDR 83.418 0.0054771 288430000 185920 107145 194917 183515 147595 195410 256150 191208 181212 TRUE FALSE 177131.9301 118063.1973 203854.1372 165067.7235 173335.5213 188642.9027 217069.613 174464.8139 209313.4315 0.846252096 0.564049791 0.973918089 0.788615056 0.828114661 0.901246047 1.037055346 0.833509883 1 17.67530537 2.765020544 0.726486344 0.971078123 0.725004838 0.284855555 0.112789354 0.702399087 0.802824135 0.07584462 0.076904396 582.1307548 -2.765020544 -0.246073285 SKS(ph)PSGQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.026)KS(0.868)PS(0.106)GQKR;S(0.026)KS(0.97)PS(0.004)GQKR;S(0.004)KS(0.975)PS(0.021)GQKR 105.03 0.0016508 2990120000 3992770 3787350 3686170 4585130 2606300 4007210 4739510 5838050 3699680 TRUE FALSE 3804039.675 4173285.271 3855184.541 4124224.021 3060837.895 3868439.313 4016410.702 5326839.393 4273407.479 0.890165446 0.976570873 0.902133616 0.96509028 0.71625229 0.905235303 0.939861392 1.246508651 1 22.02695546 1.382758373 6.319842687 1.121428399 0.901253952 0.514501892 0.091133078 0.161266522 8.464919908 0.057643294 0.020962212 24.14117326 -1.382758373 -0.220174447 SKS(ph)PSPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.061)KS(0.626)PS(0.313)PPR;S(0.061)KS(0.626)PS(0.313)PPR 63.694 0.043417 263590000 271380 269000 213580 287780 171182 264010 257840 275240 186481 TRUE FALSE 258552.4052 296411.4058 223372.8543 258851.8077 201036.0866 254867.2675 218501.7724 251138.5265 215399.5211 1.200338812 1.37610058 1.037016485 1.201728799 0.93331724 1.183230428 1.014402313 1.165919614 1 17.71665552 3.73080534 24.99693945 1.078951615 1.288219698 0.458388741 0.095641548 406.8885946 1311491.261 0.02217401 0.035082381 5380.285723 -3.73080534 0.209268083 SKS(ph)PTISDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.247)KS(0.643)PT(0.11)IS(0.001)DK;S(0.003)KS(0.796)PT(0.2)IS(0.001)DK;S(0.206)KS(0.772)PT(0.022)ISDK;S(0.012)KS(0.981)PT(0.007)ISDK 124.12 0.00032619 1056820000 1321420 1238120 1146820 1413130 668150 1367870 1327810 1492680 786100 TRUE FALSE 1258959.095 1364285.836 1199402.831 1271079.488 784675.1485 1320500.319 1125228.198 1361973.026 908004.3732 1.38651215 1.502510204 1.320921866 1.399860535 0.864175517 1.454288501 1.239232135 1.499963069 1 19.79233972 -5 0.085402888 0.065700271 1.60687545 0.208459017 0.189013261 339.6453382 2.033582119 61.13997709 4.895146093 1.00E-05 5 1.541175179 SKS(ph)PVGNPQLIQFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 S(0.269)KS(0.731)PVGNPQLIQFSR;S(0.229)KS(0.771)PVGNPQLIQFSR;S(0.036)KS(0.964)PVGNPQLIQFSR 161.47 9.99E-07 950000000 356078 277460 318147 365547 233429 368558 403190 391470 321586 TRUE FALSE 339246.8986 305733.4894 332734.3546 328801.5211 274138.9437 355794.744 341675.9604 357190.8115 371455.9144 0.913289802 0.823068035 0.895757321 0.885169702 0.738012058 0.957838414 0.919829103 0.961596781 1 18.50283147 SKS(ph)TAALSGEAASCSPIIMPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSTAALSGEAASCSPIIMPYK 22 1 Q14244-6;Q14244;Q14244-7;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 S(0.183)KS(0.632)T(0.183)AALS(0.002)GEAASCSPIIMPYK;S(0.151)KS(0.69)T(0.151)AALS(0.009)GEAASCSPIIMPYK 165.34 7.83E-12 1575000000 3128600 2160700 2838100 3060500 2229200 3112900 3858500 3280600 2459700 TRUE FALSE 2980717.278 2380877.787 2968229.692 2752852.725 2617971.774 3005099.492 3269814.959 2993333.272 2841137.714 1.049128053 0.838001543 1.044732777 0.968926185 0.921451911 1.057709902 1.150882248 1.053568526 1 21.43803733 2.113093637 5.438987043 1.089296554 0.959181451 0.320832012 0.070555709 0.189054755 8.299224524 0.025473805 0.018617276 129.7458983 -2.113093637 -0.130115103 SKS(ph)VIEQVSWDT ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSVIEQVSWDT 12 1 Q6WCQ1 Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.168)KS(0.831)VIEQVS(0.001)WDT 88.561 0.026086 95565000 294400 253550 276140 301440 258160 286690 369180 351450 288160 TRUE FALSE 280484.2954 279387.0333 288801.2921 271138.6785 303183.0223 276761.8534 312854.8105 320675.1748 332846.3811 0.842683927 0.839387324 0.86767142 0.814606058 0.910879732 0.831500263 0.939937546 0.963432962 1 18.34449696 1.479858703 1.333124003 0.999005898 0.847255734 0.801568504 0.027710595 0.148657927 0.505174775 0.021505672 0.007229066 30.18969347 -1.479858703 -0.151750165 SKSEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;; 169.43 6.92E-12 3314540000 3960910 3113860 3637000 3991530 3576770 3772800 4881030 4114730 451947.6 FALSE TRUE 3773685.634 3431165.874 3803760.047 3590293.821 4200557.556 3642146.99 4136339.227 3754422.428 522033.3256 7.228821321 6.572695087 7.286431462 6.877518436 8.046531418 6.976847668 7.923515654 7.191920982 1 18.99378238 0.910649524 22.47937777 1.000000004 7.252625635 0.951922005 0.442361559 12174.21263 3062871.234 0.428292062 0.107073015 8.140470822 -0.910649524 6.252625631 SKSERPPTILMTEEPSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKSERPPTILMTEEPSSPK 19 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SKSERPPTILMTEEPS(0.017)S(0.983)PK;SKSERPPTILMTEEPS(0.016)S(0.984)PK;SKSERPPTILMTEEPS(0.05)S(0.95)PK 163.72 1.31E-11 462260000 958750 863860 831820 1080940 455110 942450 850250 900590 398590 TRUE FALSE 913431.7876 951888.3161 869959.7698 972281.8575 534481.0399 909812.7202 720528.7466 821729.5653 460401.3015 1.983990455 2.067518734 1.889568442 2.111813877 1.160902539 1.976129775 1.565001542 1.78481156 1 18.81253239 -1.317797356 0.135485977 1.31E-13 2.334611312 0.542392143 0.256815392 26.16468489 0.649042087 11.27995715 2.085309413 0.048106376 1.317797356 2.334611312 SKSPS(ph)GQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 SKS(0.123)PS(0.877)GQKR 80.318 0.019256 173600000 282640 264820 262070 297620 166010 277060 321510 371740 257890 TRUE FALSE 269280.1673 291805.4591 274086.1687 267702.6722 194962.0914 267465.3427 272457.7446 339188.4749 297882.2641 0.903981874 0.979599977 0.92011577 0.898686174 0.654493788 0.897889452 0.914649099 1.138666231 1 18.1843827 1.355196535 5.522530819 1.067138731 0.886424875 0.427237735 0.090747653 0.209713158 8.610870067 0.065209804 0.023147351 22.6566938 -1.355196535 -0.180713856 SKSPS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.034)KS(0.134)PS(0.832)PPR;SKS(0.013)PS(0.987)PPR 53.567 0.082222 294180000 194477 192841 177498 214262 120799 172162 181401 210679 138841 TRUE FALSE 185284.4576 212491.7171 185636.4589 192723.9767 141866.3074 166199.9868 153724.9458 192230.8299 160371.7532 1.155343469 1.324994664 1.157538377 1.20173268 0.88460907 1.036342021 0.958553752 1.198657657 1 17.29106053 2.856013921 6.942370817 1.010676506 1.22236259 0.529691593 0.090720549 0.175018573 9.383807949 0.025804571 0.027422419 717.8172996 -2.856013921 0.211686084 SKT(ph)FDWAEFRPIQQALAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.208)KT(0.792)FDWAEFRPIQQALAQER;SKT(1)FDWAEFRPIQQALAQER;S(0.251)KT(0.749)FDWAEFRPIQQALAQER 271.77 9.91E-43 2045690000 550010 395038 452190 524730 357278 484990 545170 529650 382499 TRUE FALSE 524012.1173 435292.8213 472923.3588 471983.1435 419587.1701 468194.6747 461994.3038 483271.0381 441814.9914 1.186044221 0.98523778 1.070410393 1.068282319 0.949689753 1.059707533 1.045673671 1.093831236 1 18.75308285 4.654427542 3.270709331 1.036856006 1.194081911 0.534584557 0.044352937 0.204531259 3.564331978 0.009978641 0.071466906 45126.07307 -4.654427542 0.157225904 SKTDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKTDLLVNDNPDPAPLSPELQDFK 24 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 SKTDLLVNDNPDPAPLS(1)PELQDFK 150.98 7.18E-08 191160000 398420 419990 354080 441990 196680 422270 363890 411020 232500 TRUE FALSE 379587.4762 462787.4585 370314.9182 397560.3255 230980.9297 407646.684 308371.8972 375028.9098 268554.9126 1.413444545 1.723250765 1.37891694 1.480368844 0.860088268 1.517926744 1.148263848 1.396470116 1 18.03485759 2.968454305 24.60146744 1.212812642 1.525172852 0.365143592 0.203798321 543.7016352 424015.4367 0.055910099 0.0593631 929.9386647 -2.968454305 0.31236021 SKTPSS(ph)PCPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKTPSSPCPASK 12 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 S(0.001)KT(0.004)PS(0.284)S(0.711)PCPASK 108.18 0.0010498 160510000 318470 281340 315960 360050 210230 329570 357190 351410 250010 TRUE FALSE 303416.5542 310008.8659 330447.0785 323857.0899 246894.0454 318156.9083 302694.1053 320638.6775 288780.2739 1.050683103 1.073511226 1.144285494 1.121465416 0.854954676 1.101726596 1.048181377 1.110320567 1 18.13961267 -5 0.199698286 0.739218785 1.07150056 0.051572994 0.080224069 503.8516787 4.982333782 53.12678881 0.182653702 1.00E-05 5 0.332281775 SKVDDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKVDDLR 7 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 78.496 0.032082 691160000 3887600 3405100 3681600 4028200 3432300 4113200 4951200 4310500 3989200 FALSE TRUE 3703840.852 3752083.561 3850405.002 3623277.683 4030892.033 3970758.853 4195803.505 3933049.769 4607824.762 0.803815476 0.814285212 0.835623141 0.786331484 0.874792823 0.861742592 0.910582264 0.853558886 1 22.13565442 0.418992161 0.221786558 1.06298666 0.774651427 0.820806707 0.025899303 2.066047803 0.239401158 0.178899639 0.068791393 2.624171179 -0.418992161 -0.288335233 SKVDEAVAVLQAHQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 184.01 1.14E-09 503050000 1693000 1536900 1310700 2100400 1021600 1566900 1887600 1890300 1046800 FALSE TRUE 1612975.245 1693511.857 1370796.891 1889263.802 1199766.717 1512637.86 1599611.952 1724775.311 1209132.398 1.333993902 1.400600844 1.133702888 1.562495393 0.992254214 1.251010942 1.322941933 1.426456949 1 20.20554079 -1.795842737 2.91580776 0.922324756 1.305902369 0.269013114 0.156865677 34074047.93 27382920.19 18742625.6 0.033940368 0.016001374 1.795842737 0.383577613 SKVGS(ph)TENIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.559)T(0.44)ENIK;SKVGS(0.582)T(0.418)ENIK;SKVGS(0.899)T(0.101)ENIK;SKVGS(0.5)T(0.5)ENIK;SKVGS(0.805)T(0.194)ENIK;SKVGS(0.921)T(0.079)ENIK 154.23 3.91E-05 3711880000 6688360 5732080 5581190 6963290 3342040 6633830 6607430 6717590 3582460 TRUE FALSE 6372214.478 6316185.469 5837093.082 6263326.86 3924890.718 6404098.804 5599345.2 6129362.207 4138009.6 1.539922594 1.526382507 1.410604045 1.513608586 0.948497248 1.547627827 1.353149398 1.48123441 1 21.98050556 -4.140696871 0.118507408 1.31E-15 1.635210254 0.355437136 0.17637584 132.7123942 1.254008942 34.65988959 1.728949279 7.23E-05 4.140696871 1.635210254 SKVGS(ph)TENIKHQPGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKVGSTENIKHQPGGGR 17 2 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 SKVGS(0.5)T(0.5)ENIKHQPGGGR;SKVGS(0.5)T(0.5)ENIKHQPGGGR;SKVGS(0.967)T(0.033)ENIKHQPGGGR 186.13 2.82E-10 2622870000 1304740 541999 1468740 893740 1113140 1273450 2040250 1433510 1467870 TRUE FALSE 1243067.526 597229.3143 1536083.182 803899.5572 1307271.264 1229350.107 1728972.391 1307984.265 1695499.783 0.733156995 0.352243816 0.905976631 0.474137222 0.771024141 0.725066508 1.01974203 0.771444667 1 20.69327917 2.18886065 1.360365774 0.935716111 0.597812727 0.371571861 0.166223697 0.393641705 1.403155429 0.095276274 0.052834895 154.47587 -2.18886065 -0.337903384 SKVGST(ph)ENIK ddPTM_SK-BR-3_Trastuzumab_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 SKVGS(0.304)T(0.696)ENIK;SKVGS(0.275)T(0.725)ENIK;SKVGS(0.258)T(0.742)ENIK;SKVGS(0.118)T(0.882)ENIK 164.13 3.98E-05 1833450000 2368610 1966460 1865900 2300580 1109160 2217260 2223150 2377370 1183290 TRUE FALSE 2256650.499 2166844.51 1951453.361 2069321.328 1302597.153 2140475.73 1883967.637 2169194.88 1366788.57 1.651060412 1.585354573 1.42776535 1.514002512 0.95303486 1.566062065 1.378389956 1.587074203 1 20.38235866 3.946509477 0.041505806 2.71E-15 3.06832268 0.343620138 0.197259622 297.6174215 2.557226915 74.3339572 116.9770994 8841.164624 -3.946509477 3.06832268 SKVGST(ph)ENIKHQPGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKVGSTENIKHQPGGGR 17 2 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 SKVGS(0.351)T(0.649)ENIKHQPGGGR;S(0.002)KVGS(0.392)T(0.606)ENIKHQPGGGR 176.67 5.13E-08 1809130000 550500 248860 591820 386270 490390 535660 845700 631840 631000 TRUE FALSE 524478.956 274219.1169 618955.5324 347441.4057 575913.8607 517109.9599 716672.9327 576512.74 728852.2573 0.719595708 0.37623416 0.849219477 0.476696618 0.790165435 0.709485297 0.983289721 0.790987109 1 19.47526688 2.161031059 0.93248555 0.949748889 0.581305836 0.438766564 0.147036291 0.452764115 0.73806654 0.102717251 0.055202358 144.8875467 -2.161031059 -0.368443053 SKVTLLEGDHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKVTLLEGDHVR 12 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 116.98 0.00047045 118610000 347080 284270 327040 330640 303220 319870 405750 390730 338880 FALSE TRUE 330674.2162 313237.4362 342035.1075 297403.439 356101.472 308792.8217 343845.3854 356515.6098 391431.7796 0.84478122 0.800235066 0.873805157 0.75978358 0.90974083 0.788880305 0.878429916 0.910798837 1 18.57840136 1.028640988 1.285947631 0.99940447 0.828284253 0.619419855 0.043140695 0.259513976 0.881827834 0.034465826 0.010599128 10.68171505 -1.028640988 -0.171120216 SKVYEDPALS(ph)AIFLHNNYNYILKS(ph)LEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKVYEDPALSAIFLHNNYNYILKSLEK 27 2 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5 A0A0A0MRE1 EXOC7 Exocyst complex component 7 2 S(0.019)KVY(0.018)EDPALS(0.502)AIFLHNNY(0.48)NY(0.48)ILKS(0.502)LEK 48.097 0.065732 184940000 67936 51545 63885 70197 43825 68941 72860 70808 46210 TRUE FALSE 64724.79992 56797.4941 66814.19044 63140.66419 51468.06612 66553.55588 61743.86883 64607.67614 53376.01079 1.212619657 1.064101518 1.251764406 1.182940862 0.964254641 1.246881415 1.156771889 1.210425342 1 15.70390387 SKYDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKYDEER 7 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 121.09 0.0040782 765280000 1475940 1443210 1321570 1658100 1109170 1526240 1599130 1619880 1240840 FALSE TRUE 1406175.241 1590274.74 1382165.292 1491424.638 1302608.897 1473385.926 1355153.348 1478034.72 1433263.13 0.981100547 1.109548349 0.964348599 1.040579784 0.908841419 1.02799402 0.945502134 1.031237523 1 20.45087206 3.7067464 24.90384642 0.985026075 1.045324494 0.175596961 0.050919764 803.3846535 628881.2264 0.012122924 0.018783368 5090.335418 -3.7067464 0.060298419 SKYHPDEVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKYHPDEVGK 10 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 59.198 0.063782 57456000 132640 107170 142770 163530 116180 142730 203130 204990 132850 FALSE TRUE 126370.3701 118090.7448 149316.1457 147091.6537 136441.7552 137787.2243 172138.7878 187039.9889 153451.6995 0.823518869 0.769562965 0.973049801 0.958553435 0.889151151 0.897919181 1.121778308 1.218885092 1 17.2274251 1.751801967 4.004637691 1.130962861 0.871348942 0.647593453 0.078833529 0.119729272 4.071886544 0.043934684 0.02215174 56.46794292 -1.751801967 -0.259613919 SKYNDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SKYNDDIR 8 1 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ; 70.919 0.045678 291820000 1205710 1025430 845940 1359060 825550 975440 1102580 1076000 844810 FALSE TRUE 1148718.478 1129922.483 884727.1857 1222444.707 969525.6586 941660.2682 934361.1707 981779.7358 975818.8201 1.17718418 1.157922413 0.906651079 1.252737375 0.993550891 0.964994986 0.957515014 1.00610863 1 19.89625378 2.536971636 14.63380452 0.976291892 1.123244452 0.381563985 0.088017973 3.304409337 807.1620886 0.026834641 0.025294914 344.3274419 -2.536971636 0.146952561 SKYNDDIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SKYNDDIRK 9 2 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ;; 57.598 0.064305 559880000 2661060 1903810 1903320 2452190 1661860 2298290 2723220 2555440 1770780 FALSE TRUE 2535276.968 2097810.403 1990589.105 2205691.202 1951687.858 2218699.641 2307742.774 2331672.126 2045383.519 1.239511781 1.025631812 0.97321069 1.078375367 0.954191642 1.084735269 1.128268979 1.13996818 1 20.96393995 4.583242646 2.900627643 1.053923502 1.244693691 0.47830447 0.062299363 0.280694991 4.019664071 0.015916049 0.104845735 38303.86918 -4.583242646 0.190770189 SKYTTPSGEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SKYTTPSGEVR 11 1 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 93.959 0.008081 130280000 338090 237050 232460 289550 294350 300230 385120 325480 372460 FALSE TRUE 322109.1557 261205.6645 243118.5209 260443.8839 345684.5468 289832.9598 326362.8708 296979.2457 430219.1945 0.748709402 0.607145538 0.565103845 0.605374858 0.803507959 0.673686724 0.758596722 0.690297526 1 18.71471237 -0.466930432 0.362719276 1.096431339 0.645539909 0.673764885 0.071364008 4.861463495 0.656001313 0.647466965 0.056379285 0.341247571 0.466930432 -0.45089143 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_SK-BR-3_Trastuzumab_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;SLAALDALNT(1)DDENDEEEYEAWK 269.83 1.80E-44 737527000 490980 506502 504867 536917 361180 540440 545560 516213 387848 TRUE FALSE 467772.3484 558115.1296 528015.6513 482945.0831 424169.6776 521724.4273 462324.8021 471010.6531 447993.487 1.044149886 1.245810812 1.178623499 1.07801809 0.946821081 1.164580384 1.031990008 1.05137835 1 18.77311823 3.120616337 5.099268043 1.047305998 1.15883953 0.346674592 0.072732146 0.230629238 9.364243127 0.020344898 0.02457791 1320.128895 -3.120616337 0.111533532 SLADELALVDVLEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;; 220.9 3.74E-12 141237000 514444 620380 428264 638070 300605 494091 459922 566783 289932 FALSE TRUE 490127.2516 683597.4273 447900.328 573929.9913 353030.4168 476980.5048 389752.4519 517152.4758 334893.1738 1.46353312 2.041240255 1.337442394 1.713770349 1.054158294 1.424276582 1.163811276 1.544231165 1 18.35334144 3.047155324 1.597084122 1.258864855 1.71769198 0.339295343 0.253029045 0.356117958 1.865031102 0.081141131 0.099854487 1114.693129 -3.047155324 0.458827126 SLADIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLADIAR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;; 101.69 0.020643 148855000 699850 552040 439560 502990 737040 524730 767140 611490 741120 FALSE TRUE 666769.4775 608293.5036 459714.2608 452428.4896 865579.5426 506558.4685 650098.7035 557944.6939 856049.1045 0.778891624 0.710582489 0.537018564 0.528507637 1.011133051 0.591739967 0.759417538 0.65176716 1 19.70733403 SLADLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLADLFR 7 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;A0A0U1RRM9;H0Y9C3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 127.84 0.0088763 26121000 209600 151630 76277 87884 255190 95913 226390 158460 233880 FALSE TRUE 199692.6234 167081.2694 79774.3759 79049.73335 299695.0552 92591.50876 191850.0476 144584.4024 270148.9159 0.739194613 0.6184784 0.295297783 0.292615401 1.109369824 0.342742478 0.710164048 0.535202601 1 18.04339537 -4.819870023 0.471257102 9.82872272 0.585892338 0.221698104 0.246468796 2197.440565 13.98649343 20256.5688 0.114566612 1.51E-05 4.819870023 -9.242830382 SLAEDFAEQPIKDAVITVPVFFNQAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLAEDFAEQPIKDAVITVPVFFNQAER 27 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 239.34 3.65E-45 507630000 631220 533490 562640 677850 534510 632980 738620 637610 608800 FALSE TRUE 601383.4816 587853.2375 588437.6005 609711.2302 627728.3748 611059.7439 625929.9533 581777.4882 703209.5947 0.855198061 0.835957362 0.836788356 0.867040545 0.892661846 0.8689582 0.890104399 0.827317336 1 19.42359523 -5 0.238305456 1.787063098 0.845454731 0.782078466 0.023035625 74.50366275 0.743350037 28.41717798 0.035247327 1.00E-05 5 -0.941608366 SLAEGYFDAAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLAEGYFDAAGR 12 0 O43813;E9PHS0;F8WDS9 O43813 LANCL1 LanC-like protein 1 0 ;;; 248.09 2.41E-16 487104000 486795 438717 457260 512674 513160 455927 545192 512915 549584 FALSE TRUE 463785.1651 483422.7611 478225.8233 461139.0355 602654.9415 440138.1337 462012.9473 468001.4435 634810.6798 0.730588158 0.761522729 0.753336134 0.726419782 0.94934594 0.693337632 0.727796431 0.737229946 1 19.27596687 -1.9500388 2.653398021 1.178639124 0.757585392 0.538073765 0.069869174 7468063.056 4801169.164 8244786.208 0.015600169 0.011219182 1.9500388 -0.421053732 SLAGSSGPGASSGTSGDHGELVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLAGSSGPGASSGTSGDHGELVVR 24 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1 P29692 EEF1D Elongation factor 1-delta 0 ;;; 395.65 1.23E-137 2184990000 463473 314998 396742 490871 529851 410836 575155 497073 602329 FALSE TRUE 441565.5498 347096.6543 414933.0131 441527.7145 622256.8466 396608.6463 487404.5413 453546.653 695735.105 0.634674816 0.498891966 0.596395108 0.634620434 0.894387594 0.570056971 0.700560512 0.651895599 1 19.40817859 -5 0.14994389 2.294200639 0.524592506 0.566155756 0.099443599 95.15645386 0.84744191 36.65536208 0.483301211 1.00E-05 5 -1.769608132 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SLAPDRSDDEHDPLDNTSRPR 21 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR 205.26 2.53E-22 42093920000 5577590 4519380 5057190 5438230 5280000 4904300 5866780 5407210 5294700 TRUE FALSE 5313948.374 4979909.96 5289067.164 4891568.788 6200830.328 4734462.861 4971694.96 4933726.027 6115775.034 0.868892061 0.814272914 0.864823695 0.79982811 1.013907525 0.774139473 0.812929667 0.806721307 1 22.54410391 -1.623325823 2.654677438 1.015773334 0.842201105 0.349104007 0.066692294 14447169.62 12910863.23 1570209.69 0.01483726 0.023805328 1.623325823 -0.173572228 SLAQAEAEKQKEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLAQAEAEKQKEEAER 16 2 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 0 207.43 9.83E-12 357010000 419920 206460 464830 356180 299500 505710 645990 553110 382770 FALSE TRUE 400071.2138 227498.5087 486142.9153 320376.1097 351732.7052 488197.1359 547432.3611 504676.7562 442128.0167 0.904876413 0.514553478 1.099552385 0.724622954 0.795544937 1.104198597 1.23817614 1.141472011 1 18.75410463 2.210160887 4.578086606 1.156166514 0.784410559 0.489321866 0.157029882 0.142075584 6.966718578 0.056772551 0.042674062 162.2411018 -2.210160887 -0.371755955 SLAVPTIEELEDEEERNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLAVPTIEELEDEEERNHR 19 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 0 ;; 195.27 7.81E-16 81082000 118358 92166 105795 109854 123297 103875 133806 115579 112928 FALSE TRUE 112763.4519 101557.8202 110645.8054 98811.26721 144799.9578 100277.7827 113391.4372 105458.29 130440.2975 0.864483247 0.778577036 0.848248643 0.75752102 1.110086074 0.76876383 0.869297597 0.808479374 1 16.99303011 SLDADEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;;;; 273.93 1.11E-18 9721060000 12033770 9944790 10163670 11473790 11820860 10477230 12688800 11229230 12688440 FALSE TRUE 11464957.54 10958175.41 10629684.32 10320422.83 13882414.24 10114400.9 10752890.51 10245939.09 14656098.47 0.782265319 0.747687076 0.725273806 0.704172591 0.947210765 0.690115512 0.733680286 0.699090492 1 23.80499777 -1.82174263 2.463162904 1.089522934 0.753947513 0.524011927 0.073775999 7532573.295 4631271.53 3994619.107 0.017602667 0.015075002 1.82174263 -0.335575421 SLDAFPEDFCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 140.16 9.01E-05 101322000 183849 141221 148001 177548 208506 141522 207174 179985 222394 FALSE TRUE 175158.8221 155611.5805 154786.9922 159700.5377 244869.3804 136621.0577 175565.8013 164224.5592 256881.7257 0.681865639 0.605771314 0.602561322 0.621688979 0.953237836 0.531844207 0.683449945 0.63930028 1 17.97074474 -2.109852471 2.293476488 1.604212757 0.661780081 0.472141023 0.111285644 5912146.061 1613064.48 18619240.63 0.024739259 0.007765109 2.109852471 -0.942432675 SLDFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLDFYTR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 139.68 0.0062246 1500180000 1039630 668400 758700 902870 1014450 848580 1226630 974980 1134080 FALSE TRUE 990488.7502 736510.7199 793487.1455 812111.7923 1191369.759 819193.4618 1039485.065 889605.5825 1309947.334 0.756128681 0.562244527 0.605739731 0.61995759 0.909479128 0.625363662 0.793531952 0.679115533 1 20.32107738 -2.59915786 0.205915308 1.493269676 0.624715779 0.484247661 0.101287249 37.11240383 0.896353611 8.422540075 0.230655029 0.002516762 2.59915786 -0.868553897 SLDGAAAVDSADRS(ph)PRPTSAPAITQGQVAEGGVLDASAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 SLDGAAAVDSADRS(0.999)PRPTSAPAITQGQVAEGGVLDASAK;S(0.003)LDGAAAVDS(0.044)ADRS(0.919)PRPT(0.011)S(0.011)APAIT(0.011)QGQVAEGGVLDASAK 241.39 1.50E-50 128323000 79599 78622 71448 103079 63508 72697 77828 78766 64362 TRUE FALSE 75836.51302 86633.67119 74723.96147 92717.30308 74583.77509 70179.48466 65953.90919 71868.83148 74342.93024 1.020090448 1.165324946 1.005125319 1.247156963 1.003239647 0.943996752 0.887157783 0.966720457 1 16.18190793 2.496786333 9.915117181 0.939307992 1.105277381 0.515572932 0.073181939 0.280879317 137.7260711 0.022036152 0.020075483 313.8963989 -2.496786333 0.165969389 SLDGAEFSRPASVS(ph)ENHDAGPDGDKRDEDGESGGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDGAEFSRPASVSENHDAGPDGDKRDEDGESGGQR 36 3 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.001)RPAS(0.16)VS(0.84)ENHDAGPDGDKRDEDGESGGQR 153.71 1.03E-13 360660000 70173 62144 66711 79384 48878 79844 82617 77782 48149 TRUE FALSE 66856.06136 68476.54425 69769.76534 71404.1695 57402.30772 77078.98226 70012.25928 70970.99573 55615.70101 1.202107681 1.231244829 1.254497634 1.283885094 1.032124143 1.385921257 1.258857805 1.276096398 1 15.76320461 -0.943068346 4.754512397 0.999997728 1.240796879 0.424306597 0.088071972 1.93E-06 4.29E-07 0.077541342 0.018276497 0.114007036 0.943068346 0.240799151 SLDGAEFSRPASVSENHDAGPDGDKRDEDGES(ph)GGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDGAEFSRPASVSENHDAGPDGDKRDEDGESGGQR 36 3 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.002)RPAS(0.008)VS(0.01)ENHDAGPDGDKRDEDGES(0.98)GGQR 81.068 0.0012507 506750000 21341 19607 19085 26259 14718 17993 21358 24373 17753 TRUE FALSE 20332.25322 21604.97559 19960.06613 23619.39543 17284.81454 17369.8979 18099.44483 22238.77091 20506.04457 0.991524872 1.05359059 0.973374756 1.151826007 0.842913146 0.84706233 0.882639495 1.084498321 1 14.32376162 2.724652716 24.99723522 0.913807343 1.034896947 0.277886548 0.086090967 902.4255532 1621963.906 0.026158593 0.024777532 530.4600912 -2.724652716 0.121089605 SLDGIPFTVDAGGLIHCIEDFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLDGIPFTVDAGGLIHCIEDFHK 23 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 ; 186.06 1.65E-17 64414000 136954 126267 127406 145333 111105 135639 143127 128417 42365 FALSE TRUE 130480.4558 139133.7509 133247.6911 130723.8507 130481.6768 130941.7874 121290.3474 117172.1267 48934.74783 2.666417252 2.843250594 2.722966747 2.671391118 2.666442203 2.675844737 2.478613926 2.394456534 1 15.57857164 -0.202200352 0.508485255 0.786074439 2.757606355 0.990279353 0.052260974 0.477679074 0.130584546 0.244480746 0.024161548 0.627768685 0.202200352 1.971531917 SLDIVCKPVPFFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDIVCKPVPFFLR 14 1 Q9P015;E5RIZ4 Q9P015 MRPL15 "39S ribosomal protein L15, mitochondrial" 0 79.646 0.016879 51358000 129160 91109 90466 88258 137000 88161 144650 109140 125200 FALSE TRUE 123054.8628 100393.1107 94613.95558 79386.13816 160892.7566 85107.96246 122580.9858 99583.12301 144615.3766 0.850911332 0.694207719 0.654245474 0.548946731 1.112556358 0.588512539 0.847634524 0.68860674 1 17.14186143 SLDLFNCEVTNLNDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 429.98 6.66E-160 1283665000 427035 402097.5 379013.9 463881.4 418037.3 390514.3 436465.3 444172 447566 FALSE TRUE 406849.9019 443071.6924 396392.0622 417251.1604 490942.8728 376990.6919 369874.5022 405277.945 516972.2494 0.78698596 0.857051211 0.766756944 0.807105528 0.949650341 0.729228101 0.715462972 0.783945261 1 18.97972731 SLDLFNCEVTNLNDYRENVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLDLFNCEVTNLNDYRENVFK 21 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 322.26 3.87E-67 812160000 729760 442460 681270 614200 644740 668090 876090 736730 794290 FALSE TRUE 695265.691 487547.177 712506.9034 552459.4491 757182.4519 644953.8758 742426.38 672218.0155 917464.4365 0.757812143 0.531407167 0.776604384 0.60215898 0.825298967 0.702974252 0.809215432 0.732691087 1 19.80729271 -0.185012405 0.252824762 1.123850475 0.63126624 0.538393879 0.086113123 5.411098203 0.507534124 0.730631099 0.140925243 0.653111897 0.185012405 -0.492584235 SLDLLAALPT(ph)PPHNQTEDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDLLAALPTPPHNQTEDVR 20 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SLDLLAALPT(1)PPHNQTEDVR 116.65 0.00033766 38881000 58949 57572 50660 61842 44812 47249 51753 55649 42726 TRUE FALSE 56162.5976 63438.65225 52982.81111 55625.52467 52627.19861 45612.75528 43857.12934 50776.07855 49351.72987 1.138006667 1.285439283 1.073575562 1.127124111 1.066369887 0.924238226 0.88866448 1.02886117 1 15.59081303 2.767812237 1.224146536 0.94246119 1.196846698 0.650663427 0.066516806 0.2310692 0.715601986 0.030231716 0.029067054 585.8848086 -2.767812237 0.254385508 SLDQEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLDQEIAR 8 0 P48681 P48681 NES Nestin 0 ;;;; 125.25 0.0029544 3549990000 4269530 3917920 3253310 4503030 4031950 3601710 4309480 4101870 4045760 FALSE TRUE 4067717.778 4317160.502 3402477.481 4050376.869 4735120.803 3476981.88 3651989.677 3742688.517 4673155.798 0.870443434 0.923821223 0.728089888 0.866732684 1.013259777 0.744032947 0.781482543 0.800891021 1 22.15596571 SLDRALEEAGS(ph)SGILSLSGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLDRALEEAGSSGILSLSGRK 21 2 Q5VUJ6-2;Q5VUJ6 Q5VUJ6-2 LRCH2 Leucine-rich repeat and calponin homology domain-containing protein 2 1 SLDRALEEAGS(0.25)S(0.25)GILS(0.25)LS(0.25)GRK;SLDRALEEAGS(0.25)S(0.25)GILS(0.25)LS(0.25)GRK;SLDRALEEAGS(0.25)S(0.25)GILS(0.25)LS(0.25)GRK 46.027 0.089 143541000 27205 17161.4 52011 20413.1 371653 4293.6 34978.7 10887.2 262764 TRUE FALSE 25919.07357 18910.16617 54395.7558 18361.13641 436469.1655 4144.911555 29642.05689 9933.859051 303512.0991 0.085397167 0.062304489 0.179221046 0.060495567 1.438061833 0.013656495 0.09766351 0.032729697 1 18.2113945 -2.41809636 2.205790661 7.455678239 0.228019983 0.234134997 0.427334485 53193361.96 4276319.026 1717565699 0.099616939 0.003818595 2.41809636 -7.227658256 SLDS(ph)DES(ph)EDEEDDYQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.001)LDS(0.999)DES(1)EDEEDDYQQK;S(0.023)LDS(0.977)DES(1)EDEEDDYQQK 284.48 1.79E-36 1100970000 1100810 881660 946980 1130630 647300 1072450 1102160 1016780 589970 TRUE FALSE 1048776.893 971502.1564 990399.9697 1016976.924 760188.9151 1035310.788 934005.2494 927745.3529 681459.5345 1.539015657 1.425619728 1.453351108 1.492351156 1.115530529 1.519254974 1.370595321 1.361409308 1 19.37826847 -3.725799904 0.176026725 1.67E-18 1.520877286 0.589497409 0.112457905 54.46783738 0.782213398 20.01554949 0.359616065 0.000188018 3.725799904 1.520877286 SLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;S(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR 256.06 4.90E-30 24737200000 14237040 10571900 12543990 13839630 8225970 13205960 16090780 13216100 8597000 TRUE FALSE 13564083.33 11649188.63 13119144.35 12448444.1 9660576.564 12748634.29 13635835.98 12058828.22 9930178.853 1.365945522 1.173109649 1.321138777 1.253597169 0.972850208 1.283827259 1.373171237 1.214361634 1 23.24338827 -2.105900558 2.027781913 0.588645094 1.250874458 0.308093312 0.114942617 6375190.523 1581337.394 12085932.83 0.027501744 0.00783609 2.105900558 0.662229365 SLDSDES(ph)EDEEDDYQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 SLDSDES(1)EDEEDDYQQK 358.55 4.87E-88 65228000 156610 119180 132420 158040 93652 150850 143890 139990 90706 TRUE FALSE 149207.3557 131324.5775 138491.588 142153.5189 109984.8791 145626.0267 121936.9378 127731.7335 104772.2232 1.424111764 1.253429329 1.321834965 1.356786318 1.04975227 1.389929718 1.163828866 1.219137378 1 16.67689676 -4.516357293 0.05982494 1.07E-11 1.733793037 0.517483011 0.097382304 274.3911619 1.306516817 42.04359249 8.046168459 3.05E-05 4.516357293 1.733793037 SLDSDES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 SLDS(0.034)DES(0.965)EDEEDDYQQKR 84.946 0.0022813 81230000 55543 45613 46477 52113 42997 49410 51872 58099 48849 TRUE FALSE 52917.59247 50261.01656 48608.01642 46874.50223 50495.66319 47698.91931 43957.97371 53011.54356 56424.25343 0.937851885 0.890769722 0.861473807 0.830750952 0.894928335 0.845361993 0.779061681 0.939516969 1 15.7840278 4.189340622 1.751248837 0.861380871 0.935668185 0.024466741 0.061934478 0.754181796 4.203771274 0.015672622 0.064953921 15464.66875 -4.189340622 0.074287314 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_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 SLDSEPSVPS(0.002)AAKPPS(0.998)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK 258.47 3.01E-31 1402670000 2583210 2930610 2203670 3154860 1001344 3163080 2442010 3118870 985952 TRUE FALSE 2461106.783 3229242.491 2304710.449 2837727.479 1175978.077 3053541.746 2069436.524 2845765.209 1138848.401 2.161048636 2.835533236 2.023720144 2.491751736 1.032602826 2.681253927 1.817130816 2.498809505 1 20.11914428 SLEAQVAHADQQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLEAQVAHADQQLR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 199.84 2.01E-08 1026410000 1193190 1072260 1065350 1188560 1210850 1070640 1329290 1214660 1257310 FALSE TRUE 1136790.273 1181524.513 1114197.351 1069083.691 1422021.857 1033563.468 1126482.396 1108297.931 1452287.213 0.782758578 0.81356119 0.767201791 0.736137922 0.979160213 0.711679796 0.775660893 0.763139633 1 20.46989537 -2.214432861 2.348885934 1.666021229 0.791202017 0.452741871 0.072157531 7121970.198 839403.4579 25406725.5 0.017085349 0.006103334 2.214432861 -0.874819212 SLEDALSSDTSGHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLEDALSSDTSGHFR 15 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 275.19 1.68E-33 2622000000 1829740 1176330 1168380 2798000 2779200 1540650 2001230 1461800 1725950 FALSE TRUE 1743251.816 1296199.364 1221951.379 2516739.724 3263891.6 1487296.904 1695905.608 1333797.043 1993601.511 0.874423402 0.650179766 0.612936623 1.262408616 1.63718355 0.746035201 0.850674319 0.66903894 1 20.92694564 3.255864295 24.99803246 1.017224776 0.722286087 0.218279845 0.280392492 419.3483383 605814.5071 0.081568882 0.11018597 1802.454438 -3.255864295 -0.294938689 SLEDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLEDDIR 7 0 P09525;Q6P452;P09525-2;B4E1S2 P09525 ANXA4 Annexin A4;Annexin 0 81.381 0.063639 85183000 545040 475290 402350 569300 514220 474850 521610 478860 428580 FALSE TRUE 519277.0394 523722.5914 420798.1455 512072.8824 603899.8052 458405.8254 442028.8145 436928.4798 495041.9975 1.048955527 1.057935678 0.850025145 1.034402909 1.219896106 0.92599381 0.892911746 0.882608914 1 18.9171914 2.036680816 24.99982615 0.912318916 1.038986797 0.276802526 0.093012202 204.9976157 139715.3966 0.034116049 0.025196299 108.813008 -2.036680816 0.126667881 SLEDQVEMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLEDQVEMLR 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 185.6 3.33E-06 406718000 478762 383408 417418 473590 513930 389275 509979 448401 497079 FALSE TRUE 456131.8691 422477.7111 436557.0282 425983.8334 603559.2293 375794.3091 432172.3371 409136.6313 574163.4726 0.794428575 0.73581433 0.760335774 0.741920818 1.051197539 0.654507518 0.752699114 0.712578648 1 19.13110203 -2.224336417 2.184857275 1.702112329 0.772880838 0.312570292 0.104599887 10737376.59 1804892.691 37274364.37 0.023642949 0.00596573 2.224336417 -0.929231491 SLEELRLEDYQANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLEELRLEDYQANR 14 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 ; 244.36 1.26E-17 231640000 309440 189703 310250 290000 455760 251530 428800 319680 544470 FALSE TRUE 294813.3845 209033.9514 324475.2694 260848.649 535244.3997 242819.453 363378.6845 291687.1245 628903.6268 0.468773548 0.332378353 0.515937984 0.414767284 0.85107539 0.386099623 0.577797089 0.46380258 1 19.26247943 -5 0.191716846 3.18722527 0.401029701 0.551970891 0.141324406 96.86827768 0.949463001 81.02877266 0.34480724 1.00E-05 5 -2.78619557 SLEICHPQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLEICHPQER 10 0 H7C5Q2;Q9Y305-3;Q9Y305-2;Q9Y305;Q9Y305-4 H7C5Q2 ACOT9 "Acyl-coenzyme A thioesterase 9, mitochondrial" 0 65.179 0.069743 150310000 173160 187060 155470 221200 222920 194990 211620 209300 230600 FALSE TRUE 164975.07 206121.6267 162598.4533 198964.5557 261797.1774 188237.4474 179333.4823 190972.5824 266360.2703 0.619368158 0.773845238 0.610445594 0.746975349 0.982868718 0.706702419 0.673274142 0.716970974 1 18.02301938 -2.400681535 2.174729146 3.038105526 0.725976453 0.403201402 0.103638711 5280117.733 533729.4497 52924804.64 0.024571786 0.003974829 2.400681535 -2.312129074 SLELYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLELYR 6 0 D6RHI9;O00584;H0YAE9;D6REQ6;A0A087WZM2;Q07343-4;Q07343-2 D6RHI9 RNASET2 Ribonuclease T2 0 ; 106.85 0.073919 145888000 295350 241900 222960 249000 324470 228410 312060 256570 328930 FALSE TRUE 281389.3908 266549.885 233182.9365 223970.0469 381057.4653 220500.1044 264449.5156 234103.3706 379938.7845 0.740617706 0.701560083 0.613738176 0.589489823 1.002944371 0.580356924 0.696031904 0.616160761 1 18.53540747 -1.085935181 4.687191278 1.000013166 0.695150067 0.385045809 0.122045194 1.83E-05 3.56E-06 0.106932895 0.025203017 0.082047399 1.085935181 -0.304863099 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.978)PT(0.019)S(0.003)KPPKPDQPLK;SLENETLNKEEDCHS(0.833)PT(0.135)S(0.032)KPPKPDQPLK;SLENETLNKEEDCHS(0.969)PT(0.026)S(0.005)KPPKPDQPLK;SLENETLNKEEDCHS(0.946)PT(0.024)S(0.03)KPPKPDQPLK 160.9 6.78E-12 2520550000 2489370 2062400 2079010 2521760 1151372 2601910 2582790 2637410 1035149 TRUE FALSE 2371702.414 2272560.905 2174334.665 2268267.894 1352170.912 2511805.204 2188737.949 2406464.399 1195674.62 1.983568417 1.900651621 1.818500308 1.89706117 1.130885351 2.100743097 1.830546465 2.012641532 1 20.18939341 2.945856521 24.99991164 1.698993947 1.905804346 0.116346407 0.349939513 825.7135331 381259.8988 0.098613257 0.104595704 882.7882032 -2.945856521 0.206810399 SLENYHFVDEHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLENYHFVDEHGK 13 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 143.46 2.36E-05 179907000 258078 215035 200620 261282 139133 224112 209136 257326 71879 FALSE TRUE 245879.1644 236947.311 209818.6254 235017.437 163397.7511 216350.9452 177228.4622 234793.1713 83025.62821 2.961485143 2.853905668 2.527154927 2.830661351 1.968039925 2.605833282 2.134623561 2.827960189 1 16.34126911 -1.017290184 0.214671591 2.42E-17 3.002649379 0.712794306 0.317762275 8.987703029 0.435343568 6.680467485 0.717761608 0.096096997 1.017290184 3.002649379 SLEPEPQQSLEDGS(ph)PAKGEPSQAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLEPEPQQSLEDGSPAKGEPSQAWR 25 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQS(0.001)LEDGS(0.999)PAKGEPSQAWR;SLEPEPQQS(0.003)LEDGS(0.997)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQS(0.001)LEDGS(0.999)PAKGEPSQAWR 242.9 6.73E-39 1276867000 952649 953512 986323 1170213 668079 1200347 1217698 1191909 895368 TRUE FALSE 907619.1697 1050675.957 1031546.885 1052580.966 784591.7661 1158778.682 1031915.806 1087539.129 1034217.097 0.877590569 1.015914319 0.997418133 1.0177563 0.758633529 1.120440463 0.997774847 1.051557872 1 19.98010763 SLEQYDQVLDGAHGAS(ph)LTDLANLSEGVSLAER ddPTM_SK-BR-3_Trastuzumab_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(0.99)LT(0.01)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.971)LT(0.029)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.997)LT(0.003)DLANLSEGVSLAER;S(0.01)LEQYDQVLDGAHGAS(0.977)LT(0.013)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.901)LT(0.099)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.783)LT(0.217)DLANLSEGVSLAER 168.33 2.51E-14 337935000 219826 206600 214283 250600 239767 224478 252422 245736 244936 TRUE FALSE 209435.2606 227652.7749 224108.0875 225409.2119 281582.2889 216704.2706 213910.3879 224218.0531 282919.4239 0.740264693 0.804655869 0.792126905 0.796725827 0.995273796 0.765957556 0.756082368 0.792515586 1 18.1100317 -2.601873676 2.123615498 4.769637267 0.801349262 0.427719372 0.070581011 3276865.183 212298.9613 59446573.96 0.017201062 0.002501073 2.601873676 -3.968288005 SLESINSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 156.01 0.00093025 583840000 519080 482130 468420 523190 524470 472820 541210 501300 548360 FALSE TRUE 494544.1171 531259.5951 489897.5203 470597.9472 615937.4019 456446.1248 458638.4745 457403.5144 633396.8682 0.780780806 0.838746798 0.77344481 0.742974856 0.972435187 0.720632115 0.724093373 0.722143631 1 19.27275021 -0.344761639 8.176242398 1.000000632 0.785654983 0.443861654 0.075829869 0 0 0.071085656 0.01675505 0.452104012 0.344761639 -0.214345649 SLESLHSFVAAATK ddPTM_SK-BR-3_Trastuzumab_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 0 136.99 2.39E-05 118690000 384150 328640 289920 318030 360260 308640 443790 402970 403890 FALSE TRUE 365991.9908 362128.7896 303213.1188 286061.0202 423089.2299 297951.7194 376081.6847 367683.8105 466523.1984 0.784509735 0.776228901 0.64994221 0.61317641 0.906898588 0.638664316 0.806137157 0.788136178 1 18.8315893 0.525008399 0.976606627 1.000557258 0.737099081 0.47288126 0.087142287 1.403792913 1.975141498 0.078779842 0.02508908 3.349719171 -0.525008399 -0.263458177 SLETEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLETEHK 7 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 69.998 0.058219 132000000 192860 135110 150640 202330 196970 182840 251710 190550 204410 FALSE TRUE 183743.89 148877.8626 157546.993 181991.404 231321.5056 176508.205 213307.0165 173864.4318 236108.8588 0.77821684 0.630547551 0.667264218 0.770794476 0.979723958 0.747571293 0.90342657 0.73637403 1 17.84909265 2.994192864 6.653734687 0.861772379 0.693911256 0.451484813 0.09152076 0.122821472 28.01428299 0.024464669 0.027756082 986.7175766 -2.994192864 -0.167861123 SLETENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLETENR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 171.08 0.0022125 34705700000 11745350 10826000 11039200 12053290 11921180 11107180 13147760 11620050 12646350 FALSE TRUE 11190170.58 11929181.71 11545358.24 10841670.39 14000230.02 10722535.57 11141827.74 10602536.82 14607481.37 0.766057495 0.816648771 0.790372957 0.742199844 0.958428744 0.734044104 0.762748037 0.725829221 1 23.80020411 -1.136211429 3.857462631 1.000094407 0.788055184 0.502730111 0.066555278 7470255022 8443969582 8203996.788 0.014824022 0.073078323 1.136211429 -0.212039223 SLETENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SLETENRR 8 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;; 146.81 0.00087765 30599090000 19285550 17685790 17054480 19124330 19571890 17438720 21688240 18602950 20626770 FALSE TRUE 18373960.27 19487992.11 17836444.78 17201916.01 22985221.42 16834812.75 18379300.66 16973977.08 23825464.14 0.771190024 0.817948057 0.748629478 0.7219971 0.964733416 0.706589078 0.77141417 0.71243007 1 24.50600098 -1.065505933 4.658677549 1.000009399 0.779577707 0.4691947 0.074536629 6.83E-06 1.37E-06 0.065217645 0.015371265 0.085999132 1.065505933 -0.220431692 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.035)LFS(0.925)PQNT(0.039)LAAPTGHPPTSGVEK 71.085 0.014467 100680000 52960 47968 50161 55969 42396 47666 66354 62478 53700 TRUE FALSE 50456.68576 52855.99374 52460.93147 50342.88979 49789.84898 46015.31447 56230.47863 57007.0951 62027.52174 0.81345642 0.852137765 0.84576862 0.811621815 0.80270576 0.741853184 0.906540791 0.919061305 1 15.92062086 1.291837151 1.945471244 0.985145402 0.818200018 0.75088708 0.036077042 0.157776843 1.032108872 0.032376276 0.009605637 19.58110295 -1.291837151 -0.166945384 SLGGES(ph)SGGTTPVGSFHTEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.035)LGGES(0.441)S(0.441)GGT(0.078)T(0.004)PVGSFHTEAAR;S(0.002)LGGES(0.56)S(0.436)GGT(0.001)TPVGSFHTEAAR 137.86 1.52E-06 210080000 118169 110031 128567 132057 256091 103953 144202 118393 260319 TRUE FALSE 112583.3856 121243.284 134461.9241 118782.3795 300753.1893 100353.0815 122201.3364 108025.8813 300687.941 0.374419357 0.403219642 0.447180967 0.395035395 1.000216997 0.333744949 0.406405844 0.359262433 1 18.19790748 -2.109985722 2.403555496 1.996962528 0.457667215 0.430599421 0.193205615 21714399.11 6034492.42 118287221.2 0.04431032 0.007762726 2.109985722 -1.539295313 SLGGQQGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 123.28 0.00048919 425220000 934310 809250 860710 1055460 551023 971360 1068280 1096800 686820 TRUE FALSE 890147.0179 891713.495 900174.4049 949363.1556 647121.2367 937721.5596 905294.2657 1000758.377 793328.5378 1.122040839 1.124015402 1.134680478 1.19668348 0.815703969 1.182009111 1.141134124 1.261467765 1 19.59755892 -0.269446938 7.36638788 1.000000015 1.120062508 0.097171936 0.116911628 0 0 0.103976904 0.024507591 0.537716127 0.269446938 0.120062493 SLGLALTHSFGPSLADTDLS(ph)PMDGISTCGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLGLALTHSFGPSLADTDLSPMDGISTCGPK 31 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 SLGLALTHSFGPSLADTDLS(1)PMDGISTCGPK;SLGLALTHSFGPSLADT(0.001)DLS(0.999)PMDGISTCGPK 393.03 1.19E-155 371410000 534960 487243 475406 619250 380286 533772 596090 600340 394259 TRUE FALSE 509673.501 536893.6156 497203.8353 557001.8135 446607.758 515287.3418 505145.5226 547771.047 455398.6721 1.119180912 1.178952967 1.091799045 1.22310812 0.980696224 1.131508222 1.109238023 1.202838481 1 18.79677056 2.777801194 24.99967668 1.096844245 1.150341241 0.173426836 0.071469475 1099.621476 700553.8233 0.019764901 0.020963509 599.5165745 -2.777801194 0.053496996 SLGLALTHSFGPSLADTDLS(ph)PMDGISTCGPKEEVTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLGLALTHSFGPSLADTDLSPMDGISTCGPKEEVTLR 37 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 SLGLALTHSFGPSLADTDLS(1)PMDGISTCGPKEEVTLR 309.91 7.46E-110 80633000 70357 32756 64014 49240 51520 59496 91040 68791 93661 TRUE FALSE 67031.36404 36093.87364 66949.10522 44290.30165 60505.07169 57435.6386 77150.17594 62767.29536 108185.4695 0.619596738 0.333629588 0.618836388 0.409392332 0.559271702 0.530899749 0.713128817 0.580182308 1 16.72314722 0.451204888 0.455519773 1.035712782 0.476609355 0.690623532 0.099414514 1.138457377 0.426249904 0.179500822 0.053802042 2.826212988 -0.451204888 -0.559103427 SLGLSLS(ph)GGDQEDAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SLGLSLSGGDQEDAGR 16 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 1 SLGLSLS(1)GGDQEDAGR;SLGLS(0.004)LS(0.996)GGDQEDAGR;SLGLS(0.002)LS(0.998)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR 259.95 9.57E-27 783733000 1231765 1012151 1138248 1241561 1147538 1093653 1328976 1218614 1228740 TRUE FALSE 1173541.91 1115290.338 1190437.797 1116756.929 1347668.264 1055779.522 1126216.303 1111905.698 1419286.724 0.826853299 0.785810449 0.838757791 0.786843779 0.949539118 0.743880362 0.793508658 0.783425702 1 20.43673464 -1.170665451 4.049146981 1.00007518 0.811436897 0.533430606 0.05475987 7209375.789 2084334.121 5227.70663 0.011718783 0.067504783 1.170665451 -0.188638283 SLGNILQAKPTS(ph)SPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SLGNILQAKPT(0.014)S(0.664)S(0.322)PAK 227.08 5.73E-20 703650000 2398700 3021600 1928400 2890300 1101400 2735600 2516700 2913800 1167600 TRUE FALSE 2285318.205 3329504.475 2016819.047 2599761.553 1293483.811 2640865.486 2132731.193 2658652.225 1348665.445 1.694503417 2.468740108 1.495418345 1.9276549 0.959084268 1.958132387 1.581364156 1.971320786 1 20.36310108 3.714824006 24.87205453 1.594472 2.081621829 0.224037872 0.40167622 916.4240564 960261.3572 0.095799036 0.148497273 5185.898428 -3.714824006 0.487149829 SLGNILQAKPTS(ph)SPAKGPPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.018)S(0.58)S(0.402)PAKGPPQK;SLGNILQAKPT(0.007)S(0.893)S(0.1)PAKGPPQK 167.23 9.75E-12 1468700000 1621870 1461170 1533180 1694880 819910 1850700 1840750 1995130 908860 TRUE FALSE 1545207.419 1610064.884 1603477.82 1524507.442 962902.0444 1786609.795 1559909.78 1820425.84 1049801.367 1.47190456 1.533685262 1.52741068 1.452186566 0.917223081 1.701855085 1.485909458 1.734066936 1 20.00168495 3.003935479 24.48654624 1.407706508 1.507716522 0.048921643 0.25997725 386.155347 2402611.465 0.071427958 0.084994117 1009.102958 -3.003935479 0.100010014 SLGNILQAKPTSS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SLGNILQAKPT(0.001)S(0.14)S(0.86)PAK 197 2.69E-11 789340000 2139500 2528700 1609500 2519100 927020 2216000 1962300 2335700 956610 TRUE FALSE 2038370.075 2786377.405 1683297.167 2265875.282 1088691.994 2139259.364 1662915.095 2131173.726 1104956.193 1.844751935 2.521708482 1.523406247 2.050647162 0.985280685 1.936058079 1.504960201 1.928740469 1 20.07555774 3.967417019 0.069318461 4.34E-13 3.948537103 0.298235697 0.394625947 98.54742385 1.424420791 26.81760638 57.04107256 9277.202122 -3.967417019 3.948537103 SLGS(ph)VQAPSYGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR 303.02 4.58E-41 5138096000 3290284 3289343 3234647 4235330 3370129 3680861 4031726 3609264 3426178 TRUE FALSE 3134758.796 3624530.791 3382958.764 3809586.582 3957878.431 3553391.861 3416612.151 3293217.71 3957492.186 0.792107387 0.915865559 0.854823865 0.962626432 1.000097598 0.897889798 0.86332758 0.832147622 1 21.91615507 4.755832964 1.344349804 0.912072537 0.734678341 0.306024636 0.058107413 1.766705787 2.749053297 0.016033399 0.43430682 56994.50214 -4.755832964 -0.177394196 SLGSVQAPS(ph)YGARPVSSAASVYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(0.001)VQAPS(0.593)Y(0.019)GARPVS(0.366)S(0.02)AAS(0.001)VYAGAGGSGSR 92.126 0.0002976 194830000 31715 20873 31916 29561 29429 29185 36546 29410 32918 TRUE FALSE 30215.8948 22999.98243 33379.38017 26589.47212 34561.40828 28174.31613 30970.23649 26834.70449 38022.75532 0.794679253 0.604900467 0.877879046 0.69930419 0.908966433 0.740985652 0.81451847 0.705753811 1 15.21457546 -5 0.201952219 2.068238873 0.72560508 0.372165852 0.090894946 137.889712 1.366278519 59.65508728 0.193141553 1.00E-05 5 -1.342633793 SLGSVQAPSYGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 207.44 1.25E-07 1257240000 450937 483447 382569 496279 377926 427201 436072 418667 407960 FALSE TRUE 429622.1017 532710.7989 400110.1671 446392.0921 443836.1747 412406.9223 369541.2074 382006.298 471224.3532 0.911714555 1.130482318 0.849086352 0.947302679 0.941878686 0.875181682 0.784215003 0.810667563 1 18.84605458 2.903833226 0.978809803 0.846150032 1.005041079 0.160973102 0.091255618 0.617414282 1.280126923 0.044880705 0.049558448 801.3702692 -2.903833226 0.158891047 SLGSVQAPSYGARPVSS(ph)AASVYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVS(0.238)S(0.741)AAS(0.017)VY(0.002)AGAGGS(0.001)GS(0.001)R;SLGSVQAPS(0.002)Y(0.001)GARPVS(0.173)S(0.746)AAS(0.07)VY(0.007)AGAGGSGSR 80.011 9.72E-07 784450000 102746 62584 98502 83924 110861 87957 119333 97071 120613 TRUE FALSE 97889.4002 68961.38075 103018.4141 75487.80007 130195.1233 84911.02704 101126.5591 88570.94863 139317.048 0.702637628 0.494995995 0.739453036 0.5418418 0.934523988 0.609480521 0.725873542 0.635750972 1 17.08801228 -4.999999999 0.190520212 2.436780742 0.604181944 0.413147703 0.121340952 122.364361 1.197500047 66.75649968 0.293325461 1.00E-05 4.999999999 -1.832598798 SLGSVQAPSYGARPVSSAAS(ph)VYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVS(0.012)S(0.148)AAS(0.528)VYAGAGGS(0.243)GS(0.069)R 229.91 9.15E-36 1962900000 439660 141990 492890 370790 518500 393840 575710 486860 744840 TRUE FALSE 418878.1431 156458.9424 515489.494 333517.4847 608926.2358 380201.222 487874.8659 444227.9574 860345.9831 0.486871737 0.181855841 0.599165341 0.387655073 0.707769023 0.441916659 0.567068221 0.516336411 1 19.71455742 -4.999999999 0.138667902 2.857825667 0.268669856 0.609479487 0.133114802 83.91870655 0.715815877 42.93412358 0.771627536 1.00E-05 4.999999999 -2.589155811 SLGSVQAPSYGARPVSSAASVYAGAGGS(ph)GSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVSSAASVYAGAGGS(0.901)GS(0.099)R;SLGSVQAPSYGARPVSSAASVYAGAGGS(0.959)GS(0.041)R;SLGSVQAPSYGARPVSSAASVYAGAGGS(0.943)GS(0.057)R 274.68 7.20E-72 3634050000 489350 188838 555070 359283 609030 471680 770800 512680 818770 TRUE FALSE 466219.3953 208080.8069 580520.5085 323167.1902 715244.6392 455345.6033 653200.3033 467787.0213 945740.6699 0.492967481 0.220018884 0.613826313 0.34170804 0.756279879 0.481469834 0.690675916 0.494625045 1 19.85108511 -5 0.097149297 2.679269381 0.122502063 0.54773292 0.146993659 123.0768499 0.818631574 41.71272262 2.390540004 1.00E-05 5 -2.556767319 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 320.97 4.50E-93 579020000 128055.8 60490.4 125210 103019.7 143901.5 105743 184151 131870.2 199868 FALSE TRUE 122002.8561 66654.44053 130951.0023 92663.96403 168997.876 102081.0934 156055.3828 120322.9462 230862.5087 0.528465435 0.288719207 0.567225069 0.401381604 0.732028241 0.442172677 0.675966763 0.521188767 1 17.81667438 -5 0.140515549 2.751491917 0.328079688 0.625635283 0.12071195 77.58732512 0.666898982 37.75974181 0.644957162 1.00E-05 5 -2.423412229 SLGTADVHFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SLGTADVHFER 11 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;;;;;;; 212.09 7.11E-09 8858860000 6633880 6155350 6155830 6974130 7283610 6106490 7249430 6531250 6399170 FALSE TRUE 6320309.639 6782587.163 6438080.894 6273077.202 8553869.278 5895020.72 6143396.309 5959339.126 7391520.601 0.855075698 0.917617298 0.87100899 0.848685614 1.157254338 0.797538293 0.831141066 0.80623994 1 22.81743976 -2.015550019 8.733451843 1.156922275 0.885216557 0.109809155 0.102387142 0.06436033 0.000114594 0.020395393 0.022050678 0.009648282 2.015550019 -0.271705718 SLGTIQQCCDAIDHLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLGTIQQCCDAIDHLCR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 184.61 6.26E-10 531550000 553560 488160 549240 596840 618900 649320 740330 606720 457720 FALSE TRUE 527394.3159 537904.059 574423.1973 536844.5093 726835.964 626833.8856 627379.0614 553592.3804 528700.8799 0.997528727 1.017407157 1.086480502 1.015403094 1.374758378 1.18561158 1.186642741 1.047080498 1 19.0120922 SLGYHGSSYSPEGVEPVS(ph)PVSSPSLTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SLGYHGSSYSPEGVEPVS(0.954)PVS(0.037)S(0.009)PSLTHDK 245.62 1.88E-45 108270000 57207 38581 53447 67378 85697 52547 87375 78159 77476 TRUE FALSE 54502.93848 42512.44776 55897.59782 60605.03543 100642.5297 50727.28421 74044.339 71314.98361 89490.58239 0.609035465 0.475049403 0.624619891 0.677222494 1.124615876 0.566844945 0.827398113 0.796899313 1 16.44944825 3.107548373 3.303759063 0.830725264 0.552387675 0.433989916 0.150634177 0.218417561 4.71802585 0.041799188 0.051139199 1280.997768 -3.107548373 -0.278337589 SLGYTGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLGYTGAR 8 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;; 104.75 0.010518 548250000 1031100 850690 879720 949350 828190 921300 1117750 1062960 900310 FALSE TRUE 982361.9464 937376.2782 920056.0322 853919.5344 972626.0738 889395.15 947216.7086 969881.5873 1039925.477 0.944646485 0.901387935 0.884732659 0.821135315 0.935284398 0.855248929 0.910850566 0.93264528 1 19.98804871 0.915030074 1.947034698 0.99957813 0.894320882 0.483758557 0.035570835 0.37956177 2.983027732 0.032975616 0.009225545 8.2229959 -0.915030074 -0.105257248 SLHDAIMIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLHDAIMIVR 10 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 188.87 1.07E-06 1242730000 179794 136719 136453 130329 224150 147528 188395 174788 195311 FALSE TRUE 171295.4939 150650.8215 142709.505 117228.0813 263241.689 142419.0684 159651.8826 159482.6361 225598.8324 0.759292467 0.66778192 0.632580867 0.519630709 1.166857498 0.631293464 0.707680447 0.706930237 1 17.78340008 SLHDALCVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLHDALCVIR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 202.2 2.28E-07 975620000 446632 439505 348091 368295 469311 355943 549388 424845 477505 FALSE TRUE 425520.5905 484291.0592 364051.3167 331273.2869 551158.6898 343616.6047 465568.7704 387643.3196 551554.0366 0.771493928 0.878048255 0.660046509 0.600618008 0.999283213 0.622997171 0.844103641 0.702820202 1 19.07314271 -1.750741729 2.729386358 1.048014853 0.770001888 0.269533408 0.123217103 47508817.31 34584173.95 15288492.89 0.027343821 0.017752449 1.750741729 -0.278012965 SLHDALCVLAQTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLHDALCVLAQTVK 14 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 162.67 4.40E-06 368540000 727090 562700 518060 636590 736460 572050 936260 743600 779360 FALSE TRUE 692721.8967 620039.7697 541813.5634 572598.7638 864898.3908 552239.7651 793416.3414 678486.4419 900219.1684 0.769503606 0.688765349 0.601868503 0.636065954 0.960764246 0.613450351 0.881359084 0.753690285 1 19.77991676 0.602614645 0.423643888 1.019944387 0.693724924 0.391143644 0.110105943 1.930179513 0.716519981 0.193100943 0.069566115 4.005111812 -0.602614645 -0.326219463 SLHDALCVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLHDALCVVK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 90.827 0.010566 1114970000 3285600 2947700 2161210 2772700 2970000 2405500 3556700 3280500 2586100 FALSE TRUE 3130296.199 3248073.981 2260303.616 2493982.928 3487967.06 2322196.932 3014060.092 2993242.029 2987139.18 1.047924456 1.087352743 0.756678374 0.834906838 1.167661381 0.777398304 1.009012272 1.002043041 1 21.51033303 SLHDPDGLVATYISEVHEHDGHLYLGSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLHDPDGLVATYISEVHEHDGHLYLGSFR 29 0 Q9HDC9;H0Y512 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 44.555 0.038742 12237000 4346.6 3991.9 3688.3 4062.8 6555 3982.2 6053 4451 3751.6 FALSE TRUE 4141.144832 4398.679148 3857.412203 3654.399625 7698.189925 3844.295415 5129.503679 4061.246844 4333.378967 0.955638744 1.015069114 0.890162673 0.84331411 1.776486659 0.887135753 1.183719153 0.93720094 1 12.08127669 SLHINNIS(ph)PGNTISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLHINNISPGNTISR 15 0 Q8IZ41 Q8IZ41 RASEF Ras and EF-hand domain-containing protein 1 SLHINNIS(1)PGNTISR 121.47 7.40E-05 106960000 120320 82574 103240 113820 136150 98243 132350 104600 133840 TRUE FALSE 114632.7121 90988.38448 107973.6561 102378.5974 159894.5169 94840.82028 112157.5767 95440.66948 154595.2236 0.741502288 0.588558833 0.69842815 0.662236484 1.034278506 0.613478334 0.725491862 0.617358462 1 17.23813622 -1.911610425 2.686426172 1.170072698 0.706154726 0.344904421 0.125423543 28027779.94 17911194.94 30101810.56 0.028335902 0.012257152 1.911610425 -0.463917972 SLHLS(ph)PQEQSASYQDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLHLSPQEQSASYQDRR 17 1 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 SLHLS(1)PQEQSASYQDRR 122.18 2.72E-05 97565000 151220 165460 112730 163760 139100 149410 152090 132430 147990 TRUE FALSE 144072.1303 182320.5621 117898.782 147298.5337 163358.996 144235.8942 128885.8772 120833.7271 170939.5334 0.842825106 1.066579266 0.689710447 0.861699636 0.955653691 0.843783128 0.753985194 0.70687994 1 17.38312656 2.000741796 24.41122594 0.794436081 0.89523498 0.036491881 0.120498921 37.34064901 1228775.591 0.043326911 0.031704942 100.1709507 -2.000741796 0.100798898 SLHPWYGITPTSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SLHPWYGITPTS(0.052)S(0.948)PK;SLHPWYGITPTS(0.001)S(0.999)PK 223.06 8.49E-13 620420000 1158520 844330 921830 1118440 814240 1008050 1325770 1285820 787880 TRUE FALSE 1103759.056 930368.1869 964096.8173 1006012.286 956243.1982 973140.9757 1123499.437 1173226.784 910060.4065 1.21284153 1.022314761 1.05937673 1.105434627 1.050746952 1.069314706 1.234532817 1.289174626 1 19.79560278 1.749820579 14.75545467 1.195941983 1.087240921 0.164836802 0.089024297 0.256562669 326.8322795 0.038067734 0.02100146 56.21090525 -1.749820579 -0.108701062 SLIEEGGDWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLIEEGGDWDR 11 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 135.43 0.00027968 47114000 108100 109590 107100 129750 114590 95603 116970 125960 127360 FALSE TRUE 102990.3272 120757.3456 112010.6409 116707.2835 134574.4597 92292.24414 99124.0782 114930.2746 147110.3383 0.700088984 0.820862401 0.761405637 0.793331623 0.914785876 0.627367493 0.673807696 0.781252194 1 17.16653911 0.9614029 23.17213059 1.000000001 0.75335471 0.476118663 0.079803944 2616.406757 1570786.702 0.078012972 0.019503243 9.14961669 -0.9614029 -0.246645292 SLIEEGGDWDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLIEEGGDWDRR 12 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;;; 227.48 2.06E-11 2084590000 2158810 2010790 2074530 2095050 2260820 2196980 2664390 2351610 2443680 FALSE TRUE 2056767.33 2215691.787 2169649.252 1884451.594 2655106.292 2120898.032 2257888.371 2145690.562 2822633.414 0.72866966 0.784973272 0.768661365 0.667621798 0.940648644 0.751389827 0.799922639 0.760173302 1 21.42861034 -5 0.239442122 2.275113207 0.752251253 0.519246247 0.068386389 129.7145525 1.293575107 80.54945584 0.096984111 1.00E-05 5 -1.522861954 SLIGS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLIGSPGR 8 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SLIGS(1)PGR;SLIGS(1)PGR;SLIGS(1)PGR;SLIGS(1)PGR 119.21 0.0018234 617710000 1045690 1049870 1010210 1130440 1051780 1042380 1216080 1137240 1205780 TRUE FALSE 996262.3061 1156852.947 1056529.128 1016806.024 1235210.099 1006282.119 1030544.661 1037657.237 1392766.204 0.715311948 0.83061532 0.75858326 0.730062246 0.88687541 0.722506129 0.739926528 0.745033326 1 20.40952167 -1.056460667 4.944759221 1.000005029 0.767175244 0.653984625 0.053460118 2.76E-06 5.26E-07 0.048148609 0.011348491 0.087809061 1.056460667 -0.232829785 SLIGVEYKPVSATGAEDKDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLIGVEYKPVSATGAEDKDKK 21 3 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 194.25 1.91E-18 377880000 573970 489090 552660 679180 243510 692320 649820 755640 266210 FALSE TRUE 546839.5756 538928.827 578000.0077 610907.536 285978.0669 668344.7848 550678.0242 689472.1557 307492.4872 1.778383533 1.752656892 1.879720747 1.986739714 0.930032696 2.173532079 1.790866597 2.242240654 1 18.23019164 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.557)RIS(0.442)EDET(0.001)ER 97.605 2.87E-05 441890000 101890 106320 87008 115010 69016 104430 94238 100070 57983 TRUE FALSE 97073.86163 117154.1289 90997.40286 103448.9763 81052.36855 100813.5629 79860.2623 91307.3403 66974.7075 1.449410759 1.749229422 1.358683095 1.544597657 1.210193692 1.505248275 1.192394342 1.363310774 1 16.03132876 1.523172166 0.257365636 0.930854881 1.674851285 0.545937902 0.140782134 1.210551464 0.335934845 0.343928251 0.326284444 33.35586185 -1.523172166 0.743996404 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.497)RIS(0.497)EDET(0.006)ERNGDDGTHDK;SLIPDIKPLAGQEAVVDLHADDS(0.33)RIS(0.33)EDET(0.33)ERNGDDGT(0.011)HDK;SLIPDIKPLAGQEAVVDLHADDS(0.498)RIS(0.498)EDET(0.003)ERNGDDGTHDK;SLIPDIKPLAGQEAVVDLHADDS(0.692)RIS(0.146)EDET(0.16)ERNGDDGT(0.002)HDK;SLIPDIKPLAGQEAVVDLHADDS(0.61)RIS(0.307)EDET(0.084)ERNGDDGTHDK 248.43 1.77E-55 2356716000 1100354 909701 997483 1110226 673109 1145003 1302674 1199134 534198 TRUE FALSE 1048342.447 1002400.566 1043218.582 998623.9732 790498.9965 1105351.259 1103927.156 1094131.47 617038.6975 1.69898979 1.624534361 1.69068583 1.618413849 1.281117375 1.791380773 1.789072809 1.77319749 1 19.23500145 -2.024532377 2.769604374 0.226110132 1.66177027 0.663025766 0.147499592 51113183.71 50524723.57 250049061.5 0.036779918 0.009450779 2.024532377 1.435660138 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.047)RIS(0.953)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.011)RIS(0.986)EDET(0.003)ER;SLIPDIKPLAGQEAVVDLHADDS(0.13)RIS(0.87)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.204)RIS(0.796)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.004)RIS(0.996)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.186)RIS(0.814)EDETER 237.11 6.49E-47 1783804000 1238524 1352274 1078909 1464071 906996 1285490 1226440 1355904 809676 TRUE FALSE 1179981.425 1490072.258 1128378.045 1316899.802 1065175.815 1240973.159 1039324.053 1237173.858 935236.4188 1.261693195 1.593257307 1.206516365 1.408092943 1.138937486 1.326908506 1.111295531 1.322846109 1 19.83497159 1.578206877 0.265385043 0.966809297 1.466454668 0.365449212 0.132379941 1.604657519 0.458396007 0.297310664 0.292749127 37.86228997 -1.578206877 0.499645371 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.438)RIS(0.544)EDET(0.017)ERNGDDGT(0.001)HDK 109.19 2.70E-06 63425000 65400 48602 66737 64110 45421 66817 72566 74466 38691 TRUE FALSE 62308.67161 53554.59906 69796.95746 57665.541 53342.40802 64503.11054 61494.72393 67945.36227 44691.00267 1.394210644 1.198330667 1.561767543 1.290316564 1.193582709 1.443313121 1.375997858 1.520336493 1 15.44769679 SLIPDIKPLAGQEAVVDLHADDSRISEDET(ph)ERNGDDGTHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.099)RIS(0.133)EDET(0.768)ERNGDDGTHDK 161.98 9.01E-20 986570000 510750 407770 458210 518210 270140 529150 595390 518990 252460 TRUE FALSE 486607.8597 449322.2266 479219.3817 466118.5463 317252.3305 510825.4028 504552.3204 473544.4843 291610.2074 1.668692821 1.540831614 1.643355992 1.598430146 1.087932872 1.751740474 1.730228598 1.623895434 1 18.15368169 -2.090885732 2.38582453 0.030763356 1.588280714 0.490874625 0.185693443 3146467.892 1008191.304 16564624.56 0.045887724 0.008111745 2.090885732 1.557517358 SLKDMEESIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLKDMEESIR 10 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 187.85 1.08E-06 3204090000 5309200 3941220 5344270 5574460 5593910 6086230 8183320 6835400 6899730 FALSE TRUE 5058244.638 4342834.799 5589310.066 5014104.69 6569486.133 5875462.329 6934804.237 6236856.139 7969704.889 0.634684058 0.544917893 0.701319577 0.629145591 0.824307327 0.737224579 0.870145675 0.782570525 1 22.92609487 2.089563377 0.330543865 1.005762142 0.532567214 0.786172189 0.060867948 0.572371118 0.172312521 0.075305765 0.096118602 122.9032528 -2.089563377 -0.473194928 SLKEEGVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLKEEGVQR 9 1 P40222 P40222 TXLNA Alpha-taxilin 0 67.726 0.06476 0 107730 100090 95736 104000 107920 93174 140120 119420 114180 FALSE TRUE 102637.8164 110289.2848 100125.5903 93545.72241 126741.2138 89947.36102 118742.1205 108962.9517 131886.4512 0.778228661 0.836244237 0.75918026 0.709289859 0.960987369 0.682006075 0.900336004 0.826187608 1 17.00893684 0.345460154 0.54970392 1.010196074 0.791102876 0.381886634 0.080856585 2.325270729 1.100673601 0.123022833 0.032560492 2.215440824 -0.345460154 -0.219093198 SLKES(ph)EQES(ph)EEEILAQKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLKESEQESEEEILAQKK 18 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 SLKES(1)EQES(1)EEEILAQKK;S(0.031)LKES(0.969)EQES(1)EEEILAQKK 130.3 1.04E-05 252055000 272820 216054 251840 260020 128031 281670 312610 317340 156316 TRUE FALSE 259924.3393 238070.1482 263387.1131 233882.2956 150359.5659 271915.6973 264915.603 289552.0273 180556.6869 1.439571936 1.318534097 1.458750255 1.295339982 0.832755454 1.505985194 1.467215685 1.603662718 1 17.46209233 SLKNEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLKNEPR 7 1 Q13393-3;Q13393-4;Q13393-2;Q13393;F8WBV7;C9IY79 Q13393-3 PLD1 Phospholipase D1 0 78.496 0.032082 247540000 648510 539550 646940 664490 670240 688280 858800 726540 840000 FALSE TRUE 617856.2175 594530.7584 676602.8389 597694.2028 787129.6438 664444.691 727774.2871 662920.306 970262.9099 0.636792576 0.612752227 0.697339692 0.616012626 0.811253976 0.684808915 0.750079468 0.68323781 1 19.8880162 -4.999999999 0.149021691 2.143163544 0.580149619 0.776637977 0.054562883 54.93960799 0.487711014 18.54841756 0.250816804 1.00E-05 4.999999999 -1.563013926 SLKPDSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLKPDSVR 8 1 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 87.913 0.013668 108290000 493950 368570 352620 429880 384620 431050 507040 509110 457340 FALSE TRUE 470601.9624 406127.702 368787.9758 386667.6457 451697.6062 416122.6304 429681.7356 464529.6294 528261.9514 0.890849627 0.768799837 0.698115726 0.731961945 0.855063676 0.787720239 0.813387628 0.879354699 1 19.01089398 0.894658986 1.334071441 1.000268476 0.789424831 0.610069872 0.0543813 0.409923098 1.438999106 0.053521802 0.016132829 7.846192994 -0.894658986 -0.210843646 SLLDSDDSSDLLDFALSASRPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLLDSDDSSDLLDFALSASRPESR 24 1 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 0 59.324 0.068008 35009000 10719 8986.8 8791.5 13189 11617 9052 12247 10916 13020 FALSE TRUE 10212.33411 9902.565137 9194.598971 11863.21666 13643.00112 8738.52697 10378.49522 9960.137171 15039.0751 0.679053336 0.658455727 0.611380614 0.788826213 0.907170223 0.581054813 0.690101961 0.662283891 1 13.87642822 -1.906242223 2.694603619 1.17116133 0.693685232 0.515219556 0.092220391 16333135.84 8380645.653 17650926.29 0.021581165 0.0124096 1.906242223 -0.477476098 SLLEAVSFLHANNIVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLLEAVSFLHANNIVHR 17 0 J3KNN3;P15735-2;P15735;H3BTI9;H3BP07;H3BTW6 J3KNN3 PHKG2 "Phosphorylase b kinase gamma catalytic chain, liver/testis isoform" 0 130.29 1.78E-05 40452000 43836 36143 37123 42501 47441 35840 43544 46251 14707 FALSE TRUE 41763.95915 39826.01279 38825.12627 38228.71873 55714.69538 34598.85181 36900.56306 42201.01725 16987.68645 2.458484225 2.34440475 2.285486396 2.25037817 3.279710604 2.036701815 2.172194735 2.48421216 1 14.05220176 -1.060323786 0.515198219 0.531022131 2.432492507 0.636325165 0.335310471 13.95914736 2.170934798 10.0150248 0.14656126 0.087031449 1.060323786 1.901470376 SLLELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLLELAR 7 0 P49321;P49321-3;P49321-2;E9PPR5;E9PI86;E9PPQ8 P49321 NASP Nuclear autoantigenic sperm protein 0 110.63 0.015726 35019000 104300 83232 79386 87490 155390 77270 108700 87346 139460 FALSE TRUE 99369.9457 91713.43543 83025.92662 78695.33898 182489.9668 74594.12052 92115.81859 79697.52119 161086.7445 0.61687227 0.569341914 0.515411289 0.488527713 1.132867681 0.463068024 0.571839842 0.494749096 1 17.29747826 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_SK-BR-3_Trastuzumab_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(1)PS(0.677)QS(0.323)PVVGR;SLLGDSAPTLHLNKGT(0.999)PS(0.654)QS(0.346)PVVGR 149.66 2.85E-06 866570000 315414 244769 298116 333779 288680 304359 410500 364029 360440 TRUE FALSE 300505.0053 269711.2394 311784.9135 300226.9008 339025.7006 293818.9715 347870.6857 332152.6909 416335.1943 0.721786218 0.647822339 0.748879551 0.721118236 0.814309492 0.705726961 0.835554357 0.797801136 1 18.66738599 -0.504890618 0.199475606 1.177157323 0.645177099 0.808289828 0.042227256 5.001855421 0.283431987 0.649650075 0.123426786 0.31268668 0.504890618 -0.531980224 SLLGDSAPTLHLNKGT(ph)PSQS(ph)PVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.167)QS(0.833)PVVGR;SLLGDSAPTLHLNKGT(0.964)PS(0.253)QS(0.783)PVVGR;SLLGDSAPTLHLNKGT(0.931)PS(0.08)QS(0.989)PVVGR 222.95 1.50E-32 1590370000 1668600 1206240 1430830 1641320 1339670 1492650 1956750 1759260 1630330 TRUE FALSE 1589728.585 1329157.227 1496434.971 1476331.395 1573308.024 1440959.156 1658211.849 1605209.868 1883153.25 0.844184394 0.70581469 0.794643225 0.783967739 0.835464678 0.765184223 0.880550667 0.85240533 1 20.84471898 0.834958791 0.563250676 1.004331619 0.774642775 0.710053152 0.042160383 0.54813569 0.391822696 0.04446391 0.018460286 6.838467553 -0.834958791 -0.229688844 SLLGDSAPTLHLNKGT(ph)PSQSPVVGR ddPTM_SK-BR-3_Trastuzumab_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 1 SLLGDSAPTLHLNKGT(0.999)PS(0.001)QSPVVGR 153.06 1.63E-07 207510000 302180 220510 282180 298700 243060 307020 333810 321000 319800 TRUE FALSE 287896.5503 242980.2197 295118.2321 268674.1085 285449.587 296387.8204 282881.1537 292891.5383 369392.9507 0.779377489 0.657782503 0.798927623 0.727339566 0.772753206 0.802364582 0.765800087 0.792899642 1 18.49479681 -5 0.196040834 2.106644049 0.713191598 0.788352418 0.039612753 56.23069188 0.553975016 24.24612199 0.091908163 1.00E-05 5 -1.393452451 SLLLAGAAEYDNFFQHLR ddPTM_SK-BR-3_Trastuzumab_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 72.627 0.02155 38551000 135160 117270 119660 120990 102880 117700 158690 157550 72266 FALSE TRUE 128771.2547 129219.9463 125146.5294 108827.8553 120822.2394 113624.0195 134478.926 143754.0868 83472.6422 1.542676154 1.548051468 1.499252043 1.303754769 1.447447166 1.361212686 1.611053902 1.722170079 1 16.34901582 3.472564531 24.96296012 1.44403432 1.541745156 0.06636373 0.191198436 400.2270715 2192539.606 0.049161707 0.066823562 2968.687823 -3.472564531 0.097710837 SLLLTTIPQIGSTEWSETLHNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLLLTTIPQIGSTEWSETLHNLK 23 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ; 215.42 2.71E-32 100298000 372370 307340 336580 393830 289950 333500 426780 399500 301510 FALSE TRUE 354768.8081 338658.2954 352012.5259 354241.4602 340517.1882 321950.8114 361666.8726 364517.6621 348266.6309 1.018670112 0.972410979 1.010755825 1.017155905 0.977748535 0.924437723 1.038476961 1.046662614 1 18.40983272 1.607190152 25 1.031931574 0.98880915 0.297626826 0.029798541 0.091636873 2954.096835 0.014395024 0.007278759 40.47530701 -1.607190152 -0.043122424 SLLNEIESVYDEHQEQHSEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLLNEIESVYDEHQEQHSEGR 21 0 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 0 101.94 0.00027383 8690300 11874 9084.8 9881.7 12896 13811 11356 15409 11232 9907.6 FALSE TRUE 11312.73955 10010.55145 10334.78572 11599.66958 16219.63403 10962.73887 13058.07404 10248.46654 11444.02001 0.988528467 0.87474082 0.903073021 1.013600952 1.417302138 0.957944749 1.141039079 0.895530288 1 13.4823063 3.000677766 24.98689139 1.097793325 0.926061226 0.20602106 0.141834007 31.23631642 1151484.516 0.038074426 0.045130397 1001.561833 -3.000677766 -0.171732098 SLLVNPEGPTLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLLVNPEGPTLMR 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 0 103.44 0.0037466 154530000 174120 165160 166050 172100 149490 156880 177000 157920 124480 FALSE TRUE 165889.6927 181989.9918 173663.5567 154800.181 175561.0087 151447.2063 149995.3992 144091.6876 143783.7226 1.153744594 1.265720406 1.207810965 1.076618258 1.221007534 1.053298687 1.043201528 1.002141863 1 17.13354084 2.107620486 0.881264592 0.990599612 1.205736584 0.686722675 0.052918958 0.30908349 0.447083148 0.040273932 0.021173861 128.1210492 -2.107620486 0.215136972 SLNS(ph)TPPPPPAPAPAPPPALARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.007)LNS(0.497)T(0.497)PPPPPAPAPAPPPALARPR 79.388 0.011406 323720000 424050 367070 486030 442880 485310 465980 570440 470140 611920 TRUE FALSE 404005.9969 404474.8503 508314.9562 398360.861 569947.9103 449842.9958 483408.9012 428972.0492 706813.4283 0.571587891 0.572251225 0.71916426 0.56360115 0.806362595 0.636438101 0.683927161 0.606909875 1 19.43096992 -5 0.20048605 2.614034053 0.583015884 0.679306385 0.076418391 76.67716663 0.758774966 49.68400474 0.167267298 1.00E-05 5 -2.031018169 SLNST(ph)PPPPPAPAPAPPPALARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.021)LNS(0.195)T(0.783)PPPPPAPAPAPPPALARPR;S(0.023)LNS(0.434)T(0.543)PPPPPAPAPAPPPALARPR;S(0.023)LNS(0.181)T(0.795)PPPPPAPAPAPPPALARPR 94.834 0.011818 1424320000 1269080 1011550 1363010 1263860 1300860 1280510 1556170 1415150 1602680 TRUE FALSE 1209093.103 1114628.095 1425505.357 1136814.392 1527729.572 1236165.618 1318747.685 1291231.964 1851215.429 0.653134738 0.602106096 0.77003753 0.614090815 0.825257584 0.667758921 0.712368569 0.697504971 1 20.82004136 -4.999999999 0.204748663 2.459522933 0.63786926 0.684829764 0.066011245 75.27996489 0.747572083 45.02715528 0.135324841 1.00E-05 4.999999999 -1.821653674 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLPAPVAQRPDSPGGGLQAPGQK 23 1 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 SLPAPVAQRPDS(1)PGGGLQAPGQK;SLPAPVAQRPDS(1)PGGGLQAPGQK;SLPAPVAQRPDS(1)PGGGLQAPGQK;SLPAPVAQRPDS(1)PGGGLQAPGQK 211.62 2.74E-25 1756740000 2033230 1800400 1742090 2127330 1487070 1951260 2204090 2095590 1696380 TRUE FALSE 1937123.247 1983862.807 1821966.55 1913486.747 1746414.537 1883687.377 1867815.59 1912089.03 1959445.946 0.988607647 1.012461104 0.929837617 0.976544798 0.891279772 0.961336739 0.953236599 0.975831476 1 20.90201434 3.74619203 24.95744888 0.952197007 1.000534378 0.278212514 0.029844953 575.8623353 1883270.522 0.006944778 0.012235629 5574.321716 -3.74619203 0.048337371 SLPDCTPHPNSIS(ph)IDAGPR ddPTM_SK-BR-3_Trastuzumab_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(0.021)IS(0.979)IDAGPR;SLPDCTPHPNS(0.093)IS(0.907)IDAGPR;SLPDCTPHPNS(0.033)IS(0.967)IDAGPR 235.99 2.28E-24 849800000 545325 315463 499067 920460 690964 880558 961020 487741 532047 TRUE FALSE 519548.568 347609.0384 521949.7156 827933.612 811467.9028 850064.0557 814398.7487 445031.8124 614554.1314 0.845407331 0.565628023 0.849314469 1.347210229 1.320417293 1.383220797 1.325186354 0.724153967 1 19.22918057 3.374561527 4.775938318 1.226191714 0.705664641 0.478708045 0.211563698 0.14547431 5.552172057 0.056616082 0.077584671 2368.980724 -3.374561527 -0.520527073 SLPELDRDKSDS(ph)DTEGLLFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLPELDRDKSDSDTEGLLFSR 21 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLPELDRDKS(0.101)DS(0.899)DTEGLLFSR;SLPELDRDKS(0.015)DS(0.961)DT(0.024)EGLLFSR;SLPELDRDKS(0.378)DS(0.618)DT(0.004)EGLLFSR;SLPELDRDKS(0.102)DS(0.897)DTEGLLFSR;SLPELDRDKS(0.066)DS(0.934)DT(0.001)EGLLFSR;SLPELDRDKS(0.002)DS(0.998)DTEGLLFSR 262.63 5.48E-37 631500000 786646 644519 740580 812745 591214 826385 987665 966605 698414 TRUE FALSE 749462.8026 710196.2189 774536.3255 731046.3285 694321.5344 797767.0802 836978.5645 881963.9419 806720.4761 0.929024147 0.880349811 0.960104954 0.906195331 0.860671763 0.988901489 1.037507525 1.093270802 1 19.62170935 1.994163345 3.374744158 1.044745999 0.908059546 0.760917456 0.035047863 0.108480788 2.489199596 0.015438582 0.009280381 98.66505107 -1.994163345 -0.136686453 SLPLSPELES(ph)SP ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.5)S(0.5)P 138.71 7.30E-05 18762000 39487 34524 36177 43004 40547 33954 44573 38586 52865 TRUE FALSE 37620.52777 38042.03485 37835.75123 38681.15622 47618.38396 32778.16447 37772.57021 35207.20528 61063.0342 0.616093325 0.622996144 0.619617936 0.633462728 0.779823417 0.536792265 0.618583251 0.576571501 1 15.89801166 -1.62648127 2.942071489 1.02984385 0.624931872 0.784127106 0.061753896 10683336.47 12042490.73 2469341.593 0.014711235 0.023632993 1.62648127 -0.404911979 SLPLSPELESS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.003)S(0.997)P 241.4 3.80E-07 0 52141 45771 47594 57450 54219 47066 55306 55105 63186 TRUE FALSE 49676.39826 50435.11694 49776.23198 51675.01685 63674.77643 45436.09262 46868.05394 50279.71407 72984.56217 0.680642547 0.691038152 0.682010421 0.708026675 0.872441713 0.622543881 0.642163939 0.688908895 1 16.15530371 -1.508965708 6.297400895 1.0002471 0.694428686 0.667683372 0.066798874 0.000227559 1.77E-05 0.063510374 0.014957636 0.030976639 1.508965708 -0.305818414 SLPSRS(ph)PPITPNWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLPSRSPPITPNWR 14 1 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.004)LPS(0.026)RS(0.97)PPITPNWR 78 0.013991 406870000 309290 271720 253970 327410 344740 278580 339690 303590 286340 TRUE FALSE 294670.4747 299408.5769 265614.7757 294498.1248 404862.5469 268932.7047 287864.0517 277006.0502 330744.1448 0.890931795 0.905257377 0.803082322 0.890410698 1.224095886 0.813114031 0.870352677 0.837523671 1 18.33535609 2.981421474 24.96683401 0.937265885 0.874308914 0.093314333 0.116597095 2365.832966 3179338.229 0.035137805 0.03787325 958.1234592 -2.981421474 -0.062956971 SLPTTVPES(ph)PNYR ddPTM_SK-BR-3_Trastuzumab_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;SLPTT(0.012)VPES(0.988)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR 388.18 4.79E-108 29041640000 7416320 7590180 6978340 7821070 7319870 7041660 7675950 7085110 7377770 TRUE FALSE 7065765.251 8363627.971 7298303.792 7034881.185 8596453.01 6797805.549 6504842.849 6464700.208 8521876.891 0.829132519 0.981430274 0.856419763 0.825508427 1.008751138 0.797688776 0.763311056 0.758600516 1 23.02273978 SLQALGEVIEAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLQALGEVIEAELR 14 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 176.91 5.02E-06 64781000 106312 91747 100769 108160 122926 90479 127346 107747 129832 FALSE TRUE 101286.8425 101096.1236 105389.3583 97287.55131 144364.2555 87345.68954 107917.0288 98312.10148 149965.6835 0.675400132 0.674128382 0.702756497 0.64873209 0.962648602 0.582437845 0.719611489 0.655563988 1 17.19427288 -1.584286798 2.938231512 1.017933939 0.700662365 0.468693322 0.099470896 17193509.75 19012960.85 2416597.742 0.022140571 0.026044331 1.584286798 -0.317271573 SLQAMKEILCGTNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLQAMKEILCGTNEK 15 1 Q9H9S4;B7ZBJ5;Q5TAW7;B7ZBJ6;B7ZBJ7 Q9H9S4 CAB39L Calcium-binding protein 39-like 0 ; 67.275 0.07543 247250000 485090 360460 417700 477000 486250 417720 567580 487040 592240 FALSE TRUE 462160.7571 397191.2838 436851.9582 429051.0538 571051.846 403254.2517 480985.2467 444392.1956 684081.5545 0.675593069 0.580619783 0.638596313 0.627192841 0.834771589 0.589482714 0.703110972 0.649618737 1 19.3838088 -5 0.277773617 3.463340359 0.635842354 0.689393385 0.071188866 119.571677 1.148463048 169.5966233 0.075686302 1.00E-05 5 -2.827498005 SLQARPVS(ph)MPVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLQARPVSMPVDR 13 1 A0A2U3TZV8;Q4KWH8-2;Q4KWH8;Q4KWH8-3;Q4KWH8-4 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(0.006)LQARPVS(0.994)MPVDR;SLQARPVS(1)MPVDR;SLQARPVS(1)MPVDR;SLQARPVS(1)MPVDR;SLQARPVS(1)MPVDR;SLQARPVS(1)MPVDR 116.29 0.00036141 1255457000 1246881 966739 1234181 1297721 1469290 1183900 1445795 1265488 1573250 TRUE FALSE 1187943.406 1065250.803 1290769.42 1167271.62 1725533.711 1142901.246 1225212.419 1154675.162 1817221.575 0.653714122 0.586197532 0.710298313 0.642338631 0.949545028 0.628927843 0.67422291 0.635406919 1 20.79330291 -2.390288016 2.255776456 3.438459696 0.678864046 0.496135346 0.099562212 5547154.035 607013.5661 69013991.69 0.023691434 0.004071102 2.390288016 -2.75959565 SLQEEHVAVAQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 183.96 9.91E-06 1675370000 2305920 1963010 1911350 2089690 2273540 1925990 2435460 2173620 2145040 FALSE TRUE 2196923.731 2163042.951 1998987.288 1879630.391 2670044.656 1859292.483 2063885.847 1983286.31 2477681.848 0.886685162 0.873010775 0.806797406 0.758624596 1.07763822 0.750416154 0.832990664 0.800460443 1 21.24055952 SLQELFLAHILSPWGAEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLQELFLAHILSPWGAEVK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 101.49 0.00046745 68975000 247530 216750 232120 272610 213050 222010 302360 293810 203710 FALSE TRUE 235829.7475 238837.0714 242762.9316 245206.7249 250205.8525 214321.738 256229.4288 268082.4388 235300.3064 1.002250065 1.015030856 1.031715323 1.042101171 1.063346905 0.910843429 1.088946431 1.139320398 1 17.84414367 1.602757843 25 1.085612412 1.013656493 0.250182636 0.052209383 0.561349603 2735.043241 0.024280203 0.011774212 40.0643262 -1.602757843 -0.071955919 SLQSVAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLQSVAEER 9 0 P61313;A0A2R8YEM3;E7EQV9;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 212.03 9.72E-06 971400000 1179310 1047310 1036110 1271670 1235000 1158290 1427450 1166640 1369970 FALSE TRUE 1123566.353 1154032.08 1083616.668 1143839.316 1450383.609 1118178.127 1209666.286 1064482.817 1582417.951 0.71003135 0.729283992 0.684785374 0.722842733 0.916561651 0.706626291 0.764441711 0.672693846 1 20.59369927 -1.948719156 2.843502812 1.186140494 0.739581916 0.59287452 0.068119232 22495142.72 10926710.07 27618511.95 0.015479725 0.011253325 1.948719156 -0.446558578 SLRDDYEVSCPELDQLVEAALAVPGVYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLRDDYEVSCPELDQLVEAALAVPGVYGSR 30 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 132.16 6.71E-06 408910000 225346 173890 172306 211114 241116 181672 244831 207327 271450 FALSE TRUE 214694.3412 191609.5887 180206.4005 189892.4196 283166.5541 175380.6531 207477.5343 189172.3488 313545.0796 0.684731974 0.611106986 0.57473841 0.605630361 0.903112734 0.559347489 0.661715166 0.603333814 1 18.25831335 -1.270186124 3.971022999 1.000442457 0.649742399 0.561076246 0.097155835 13752828.92 4399137.714 52417.54456 0.020959666 0.053680169 1.270186124 -0.350700059 SLRQS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR 126.49 0.0023906 3294030000 2145730 1970720 1795360 2407650 1911180 2022640 2230550 1920500 1907100 TRUE FALSE 2044305.595 2171538.609 1877679.032 2165628.448 2244489.187 1952595.47 1890238.631 1752330.839 2202843.328 0.928030409 0.985788949 0.852388823 0.98310598 1.018905502 0.886397795 0.858090363 0.795485914 1 21.07093546 2.030325909 19.6314768 0.869629243 0.952454087 0.198015108 0.066418729 24.23239531 15685.89556 0.022784624 0.016826131 107.232371 -2.030325909 0.082824845 SLRVDIAEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLRVDIAEGR 10 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;; 172.13 3.48E-06 4236970000 2186551 1210685 2141532 1794925 2611050 1986461 2866740 2194448 3117400 FALSE TRUE 2083197.068 1334055.178 2239723.36 1614495.729 3066416.293 1917669.357 2429366.162 2002290.5 3600830.471 0.578532393 0.370485417 0.622001891 0.448367604 0.851585855 0.532563078 0.674668297 0.556063529 1 21.77989825 -4.999999995 0.140097482 2.498980715 0.412262413 0.534888375 0.125725226 96.10390658 0.824644312 40.12647398 0.69331704 1.00E-05 4.999999995 -2.086718302 SLS(ph)ASPALGSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSASPALGSTK 12 0 O95544;O95544-2 O95544 NADK NAD kinase 1 SLS(0.742)AS(0.258)PALGSTK;SLS(0.931)AS(0.069)PALGSTK;SLS(0.999)ASPALGSTK 265.27 1.38E-21 647796000 2191330 1735360 1897570 2194820 1789740 2029490 2624140 2340830 2351430 TRUE FALSE 2087750.174 1912195.157 1984575.461 1974192.524 2101870.089 1959208.252 2223779.247 2135854.516 2716077.755 0.768663625 0.704028135 0.730676969 0.7268542 0.773862267 0.721337321 0.818746534 0.786374584 1 21.37309335 0.242941191 0.523802514 1.017404467 0.729976535 0.897183629 0.027158885 0.753150337 0.302920336 0.052734623 0.011863504 1.749609754 -0.242941191 -0.287427933 SLS(ph)CLSDLDGGVALEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 SLS(1)CLSDLDGGVALEPR;S(0.205)LS(0.795)CLSDLDGGVALEPR;S(0.002)LS(0.998)CLSDLDGGVALEPR;SLS(1)CLSDLDGGVALEPR;SLS(0.997)CLS(0.003)DLDGGVALEPR;SLS(1)CLSDLDGGVALEPR 324.59 5.14E-59 747235000 807840 488379 613444 655475 1342665 681028 1069005 566205 980714 TRUE FALSE 769655.0042 538145.3753 641571.0142 589585.4077 1576825.351 657443.8296 905908.6536 516625.0886 1132798.118 0.679428216 0.4750585 0.566359534 0.520468209 1.391973844 0.580371576 0.799708826 0.456061041 1 20.11145934 SLS(ph)DPIPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.002)LS(0.998)DPIPQR;S(0.022)LS(0.978)DPIPQR 88.576 0.013312 335720000 534450 455490 463160 534100 607530 471220 559360 533440 645630 TRUE FALSE 509187.6077 501904.9488 484396.3441 480411.2533 713483.0396 454901.5332 474019.3586 486729.1657 745751.003 0.682785012 0.673019475 0.64954166 0.644197931 0.956730915 0.609991179 0.635626847 0.65266981 1 19.50833449 -1.278930939 3.561883368 1.000844972 0.684801148 0.50108997 0.097768201 47350354.61 88732716.53 455844.1596 0.022346843 0.052610092 1.278930939 -0.316043824 SLS(ph)DS(ph)ESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 SLS(1)DS(0.999)ES(0.001)DDSK;SLS(1)DS(0.999)ES(0.001)DDSK 311.12 1.88E-45 497380000 2184260 2146470 2012570 2509050 1138290 2461120 2468100 2364520 964890 TRUE FALSE 2081014.359 2365197.733 2104848.325 2256835.527 1336807.416 2375890.797 2091546.015 2157470.094 1114520.213 1.867184044 2.122166745 1.888569001 2.024939073 1.199446542 2.131761066 1.876633542 1.935783728 1 20.08799135 SLS(ph)DSES(ph)DDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 S(0.108)LS(0.881)DS(0.03)ES(0.981)DDSKSK 89.484 0.0042268 206130000 579130 487180 516790 586330 268610 627740 661570 683510 307040 TRUE FALSE 551755.6726 536824.1959 540485.3327 527390.9944 315455.499 606001.2064 560635.3459 623658.2409 354654.1951 1.555756792 1.513655283 1.5239784 1.487056975 0.889473474 1.708710104 1.580794345 1.758496726 1 18.43605349 2.995769398 24.92631462 1.435200303 1.527730429 0.040572901 0.276634647 882.0270665 5196872.518 0.078271742 0.091432653 990.3059708 -2.995769398 0.092530126 SLS(ph)DSESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.029)LS(0.713)DS(0.258)ESDDSK;SLS(0.981)DS(0.019)ESDDSK;SLS(0.999)DS(0.001)ESDDSK;SLS(0.991)DS(0.009)ESDDSK;SLS(0.983)DS(0.017)ESDDSK 291.22 1.98E-35 965540000 2073550 1918440 1768560 2256880 1214010 2131610 2115560 2178900 1287570 TRUE FALSE 1975537.401 2113931.217 1849650.225 2030014.135 1425732.96 2057791.811 1792792.467 1988103.965 1487239.78 1.328324745 1.421378883 1.243679903 1.364954167 0.958643643 1.383631503 1.205449512 1.336774333 1 20.50420583 -4.999999997 0.092774848 0.135959139 1.501404644 0.312935558 0.130626249 226.2963998 1.450657121 39.10333503 2.537255252 1.00E-05 4.999999997 1.365445505 SLS(ph)DSESDDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(0.565)DS(0.217)ES(0.217)DDSKSK;SLS(0.558)DS(0.417)ES(0.024)DDSKSK 234.85 2.99E-16 697940000 415310 246730 439240 362470 288200 480330 614830 562150 359850 TRUE FALSE 395679.1194 271872.0675 459379.5885 326033.827 338461.9888 463696.0517 521026.3914 512925.1659 415653.7001 0.951944177 0.654083116 1.105197881 0.784388126 0.814288406 1.115582639 1.253510774 1.234020449 1 18.66502253 2.152555064 4.539392026 1.188497989 0.849315781 0.529516992 0.13440479 0.140671099 5.232874207 0.048604618 0.035423625 142.0872353 -2.152555064 -0.339182208 SLS(ph)EINKPNFYNNDFDDDFSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSEINKPNFYNNDFDDDFSHR 22 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 S(0.439)LS(0.561)EINKPNFYNNDFDDDFSHR 140.11 7.98E-08 35914000 30389 27610 32548 35127 31132 32870 35656 37712 32113 TRUE FALSE 28952.5722 30423.49039 34040.35799 31595.96722 36561.41094 31731.70366 30216.02233 34409.73736 37092.92003 0.780541736 0.820196694 0.917704995 0.851805876 0.985670875 0.855465238 0.814603496 0.927663213 1 15.17885622 7.999999986 0.029805547 1.469072932 2.21E-07 0.434023088 0.055098946 1429.999184 3.269389488 51.5025163 124.295891 99999996.68 -7.999999986 -1.469072712 SLS(ph)ELCLAVPAPGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSELCLAVPAPGIR 15 0 A0A5F9ZHW8;O94827-5;O94827-3;O94827;O94827-7;O94827-2;O94827-6 A0A5F9ZHW8 PLEKHG5 Pleckstrin homology domain-containing family G member 5 1 S(0.006)LS(0.994)ELCLAVPAPGIR;SLS(1)ELCLAVPAPGIR 210.14 2.13E-09 143530000 136418 113275 122409 138965 133572 130401 154082 149069 164758 TRUE FALSE 129969.7915 124817.8513 128021.5737 124995.9742 156866.9145 125885.1807 130573.961 136015.7281 190307.8292 0.682945058 0.655873444 0.672707866 0.656809416 0.82427988 0.66148188 0.686119754 0.714714306 1 17.53797539 -5 0.312381682 3.795584027 0.675725844 0.798776351 0.048444171 125.0164199 1.126388161 230.183253 0.042590177 1.00E-05 5 -3.119858183 SLS(ph)ELESLKLPAESNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSELESLKLPAESNEK 17 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 S(0.003)LS(0.995)ELES(0.002)LKLPAESNEK 133.48 1.22E-05 82216000 304510 245450 268230 321880 188300 288220 318390 328300 204450 TRUE FALSE 290116.4158 270461.6341 280528.6108 289524.0109 221139.4604 278238.8691 269813.7579 299552.3116 236155.0618 1.228499671 1.145271382 1.187900055 1.225991129 0.936416347 1.17820413 1.142527947 1.268456027 1 17.84937493 -2.168506929 2.53921826 0.567915973 1.161292976 0.24819584 0.089665274 2708516.162 2829093.65 6577734.493 0.020060303 0.006784113 2.168506929 0.593377002 SLS(ph)ESSVIMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSESSVIMDR 11 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 SLS(0.992)ES(0.006)S(0.002)VIMDR;SLS(0.568)ES(0.146)S(0.286)VIMDR;SLS(0.925)ES(0.065)S(0.011)VIMDR;SLS(0.967)ES(0.028)S(0.005)VIMDR;S(0.002)LS(0.998)ESSVIMDR 224.49 6.47E-12 820534000 1481671 1165834 1087384 1333514 1477028 1203380 1645481 1361002 1602737 TRUE FALSE 1411635.348 1284633.81 1137241.632 1199466.639 1734621.216 1161706.649 1394432.652 1241825.45 1851281.268 0.762518031 0.693916063 0.614299756 0.647911617 0.936984155 0.627514937 0.753225712 0.670792424 1 20.82009267 -1.881798601 2.737074857 1.13511733 0.715327904 0.484358587 0.092915303 13812467.32 8205295.514 12053856.82 0.021094499 0.013128086 1.881798601 -0.419789426 SLS(ph)FSDEMSSCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSFSDEMSSCR 12 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 S(0.002)LS(0.997)FS(0.001)DEMSSCR;SLS(1)FSDEMSSCR;SLS(0.952)FS(0.048)DEMSSCR 314.35 2.25E-46 334961000 294207 293850 289968 299546 321468 306084 336290 312183 372150 TRUE FALSE 280300.4182 323793.6491 303263.3196 269435.067 377531.9174 295484.2343 284982.7841 284846.6015 429861.1213 0.65207204 0.753251767 0.705491389 0.626795618 0.87826486 0.687394648 0.662964781 0.662647975 1 18.71351111 -1.048805943 4.43019837 1.000016226 0.704155678 0.633756497 0.070808045 1.17E-05 2.52E-06 0.063670241 0.015006303 0.089370473 1.048805943 -0.295860548 SLS(ph)GSSPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLS(0.905)GS(0.093)S(0.002)PCPK 156.58 1.12E-05 272440000 295830 216880 262730 283480 223670 270030 325620 290520 245950 TRUE FALSE 281846.7022 238980.3186 274776.4304 254984.0518 262677.9772 260678.7934 275940.6886 265080.5287 284090.6699 0.992101227 0.84121143 0.967213849 0.897544618 0.924627258 0.917590125 0.971312042 0.933084247 1 18.11599193 1.023784954 0.697959745 0.997905245 0.918632924 0.21900759 0.042030489 1.006741248 1.138549639 0.038067734 0.015165449 10.56294344 -1.023784954 -0.079272321 SLS(ph)KSDSDLLTCSPTEDATMGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.088)LS(0.479)KS(0.414)DS(0.019)DLLTCSPTEDATMGSR;S(0.065)LS(0.466)KS(0.466)DS(0.003)DLLTCSPTEDATMGSR;S(0.05)LS(0.616)KS(0.332)DS(0.002)DLLTCSPTEDATMGSR 157.61 7.18E-09 757750000 655390 520770 598090 646690 445190 604960 741360 694910 576320 TRUE FALSE 624411.0136 573837.0551 625513.0181 581683.4926 522830.995 584010.0835 628251.916 634059.9965 665692.7622 0.937986785 0.862014863 0.93964221 0.873801738 0.78539384 0.87729673 0.943756567 0.952481434 1 19.34449696 1.577144879 2.86252135 0.97258507 0.880453295 0.469645671 0.044018183 0.223142281 4.166566377 0.031044505 0.012019788 37.76981687 -1.577144879 -0.092131775 SLS(ph)LGDKEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.017)LS(0.983)LGDKEISR;S(0.021)LS(0.979)LGDKEISR;S(0.044)LS(0.956)LGDKEISR 138.21 3.77E-05 564270000 838910 703690 756700 933040 660350 840110 1002110 943700 803560 TRUE FALSE 799256.3869 775396.811 791395.4435 839249.0465 775514.8309 811016.78 849219.7145 861064.6251 928171.9808 0.861108074 0.835402088 0.8526388 0.904195627 0.835529241 0.873778563 0.914937891 0.927699438 1 19.82403262 1.132087315 0.745136591 1.00027781 0.852601252 0.841214808 0.020049247 0.227102374 0.29200033 0.01838198 0.007218644 13.55461899 -1.132087315 -0.147676559 SLS(ph)LQASDFDGASSSGNPEAVALAPDAYSTGSSSASSTLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSLQASDFDGASSSGNPEAVALAPDAYSTGSSSASSTLKR 41 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.186)LS(0.814)LQASDFDGASSSGNPEAVALAPDAYSTGSSSASSTLKR 166.16 4.82E-20 125440000 143540 104280 142180 151380 143380 153740 189230 156210 176500 TRUE FALSE 136755.1487 114906.2506 148699.0936 136162.9948 168385.4266 148415.9453 160359.4881 142531.4243 203870.7186 0.670793479 0.56362312 0.729379357 0.667888924 0.825942184 0.727990495 0.7865744 0.699126512 1 17.63729505 -5 0.08896585 1.984098393 0.446037067 0.703034071 0.062968697 105.6030276 0.654152461 19.72706453 1.426638688 1.00E-05 5 -1.538061327 SLS(ph)LSLADSGHLPDVHGFNSYGSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.042)LS(0.95)LS(0.008)LADSGHLPDVHGFNSYGSHR;S(0.455)LS(0.521)LS(0.024)LADSGHLPDVHGFNSYGSHR;S(0.254)LS(0.559)LS(0.181)LADS(0.006)GHLPDVHGFNSYGSHR;S(0.002)LS(0.998)LSLADSGHLPDVHGFNSYGSHR 288.95 1.22E-55 1432930000 435690 385098 434087 476944 625891 423909 598277 445131 184841 TRUE FALSE 415095.7972 424339.924 453990.3183 429000.683 735046.1922 409228.925 506998.8555 406152.9699 213505.1982 1.944195273 1.987492237 2.126366581 2.009321958 3.442755485 1.916716447 2.374644082 1.902309514 1 17.70391167 0.888564163 3.939821594 1.000203205 2.225574085 0.440038328 0.446389506 0.522445026 16.2017314 0.409478788 0.104787589 7.736849752 -0.888564163 1.22537088 SLS(ph)MDSQVPVYSPSIDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 S(0.004)LS(0.996)MDS(0.001)QVPVYSPSIDLK;S(0.132)LS(0.868)MDSQVPVYSPSIDLK;S(0.127)LS(0.661)MDS(0.212)QVPVYSPSIDLK;S(0.313)LS(0.686)MDS(0.001)QVPVYSPSIDLK;S(0.143)LS(0.856)MDS(0.001)QVPVYSPSIDLK;S(0.085)LS(0.915)MDSQVPVYSPSIDLK 312.5 3.53E-61 668757000 1662670 1515040 1497430 1796740 1232170 1790610 1879070 1815250 1382830 TRUE FALSE 1584078.884 1669424.298 1566088.647 1616128.282 1447060.058 1728600.727 1592383.36 1656297.087 1597272.214 0.991740087 1.045172065 0.980476986 1.011805169 0.905957072 1.082220495 0.996939248 1.036953546 1 20.60717877 SLS(ph)MVDLQDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SLSMVDLQDAR 11 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 S(0.002)LS(0.998)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;S(0.027)LS(0.973)MVDLQDAR;S(0.003)LS(0.997)MVDLQDAR;S(0.001)LS(0.999)MVDLQDAR;SLS(1)MVDLQDAR 322.75 3.25E-46 993426000 2169727 1816323 1897793 2120222 2248096 1880504 2417458 2138387 2273633 TRUE FALSE 2067168.305 2001408.379 1984808.686 1907093.256 2640163.231 1815381.675 2048630.382 1951138.498 2626216.394 0.787127942 0.762088145 0.755767381 0.726175216 1.00531062 0.691253653 0.780069147 0.742946584 1 21.32455436 -1.444223557 4.12678495 1.001118063 0.780195637 0.39949839 0.084238962 0.000783692 0.000105544 0.073765216 0.017300612 0.03595642 1.444223557 -0.220922426 SLS(ph)PDEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSPDEER 8 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 S(0.079)LS(0.921)PDEER;S(0.025)LS(0.975)PDEER 112.3 0.0032187 250420000 817470 794380 789570 949100 889770 891660 968860 838560 958580 TRUE FALSE 778829.8132 875328.2251 825772.5655 853694.6648 1044945.606 860781.5906 821042.6127 765131.2409 1107231.691 0.703402747 0.79055561 0.745799251 0.771017188 0.943746115 0.777417769 0.741527378 0.691030836 1 20.07852571 -2.303870311 2.429083095 2.253764401 0.770901964 0.522671777 0.068906049 3196134.05 716786.2125 22202414.84 0.016783388 0.004967406 2.303870311 -1.482862437 SLS(ph)PFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSPFR 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.018)LS(0.982)PFR;S(0.082)LS(0.918)PFR 103.74 0.036114 259510000 214508 165703 168117 201693 239440 161285 206643 225877 234775 TRUE FALSE 204368.632 182588.3241 175825.3307 181418.4364 281198.2602 155699.66 175115.8151 206098.0124 271182.7079 0.753619704 0.673303713 0.648364832 0.668989693 1.036932857 0.574150399 0.645748457 0.759996882 1 18.04890566 0.966567406 20.21337521 1.000000006 0.709422328 0.340145832 0.123934025 378.7303482 228982.4979 0.112683114 0.028170778 9.259070813 -0.966567406 -0.290577678 SLS(ph)PFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSPFRR 7 1 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)PFRR 104.2 0.0050255 206570000 134080 118320 123150 127270 131880 107920 142170 134440 153270 TRUE FALSE 127742.3041 130376.9425 128796.5493 114476.5778 154879.8302 104182.7033 120479.3554 122667.7209 177038.3288 0.721551683 0.736433423 0.727506581 0.646620303 0.874837846 0.588475411 0.680526958 0.692887928 1 17.43370221 -0.647264384 9.444035689 0.999999988 0.708108868 0.610053909 0.073214494 0 0 0.064472692 0.015196359 0.225286732 0.647264384 -0.291891119 SLS(ph)PGGAALGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 SLSPGGAALGYR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 SLS(1)PGGAALGYR;S(0.012)LS(0.988)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;S(0.004)LS(0.996)PGGAALGYR;S(0.014)LS(0.986)PGGAALGYR;SLS(1)PGGAALGYR;S(0.003)LS(0.997)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR 266.97 9.13E-22 19169420000 5687727 4812452 4676969 5358362 5852498 4935112 6271796 5325614 6010470 TRUE FALSE 5418879.417 5302846.33 4891412.655 4819729.272 6873171.798 4764207.834 5314918.331 4859275.005 6942542.99 0.780532353 0.763819012 0.704556336 0.694231102 0.990007812 0.686233825 0.765557857 0.699927247 1 22.72703278 -1.442048903 5.544270361 1.000191766 0.762198861 0.421673803 0.088089387 0.000189267 1.90E-05 0.077309765 0.018207513 0.036136917 1.442048903 -0.237992905 SLS(ph)PIIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SLSPIIGK 8 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK 148.91 0.00053875 2585243000 4288350 4386750 3914170 5071950 3237750 4412110 4752890 4852960 3595010 TRUE FALSE 4085648.194 4833764.812 4093638.566 4562107.95 3802412.575 4259317.524 4027749.338 4428009.095 4152505.79 0.983899458 1.16405974 0.985823686 1.098639756 0.915691095 1.025722236 0.969956345 1.066346278 1 21.98555075 2.764182088 24.97563852 0.994256763 1.063503873 0.189363077 0.063857591 1084.617099 1057275.309 0.017832398 0.018908433 581.0079674 -2.764182088 0.06924711 SLS(ph)PILPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.033)LS(0.967)PILPGR;S(0.401)LS(0.599)PILPGR;S(0.193)LS(0.807)PILPGR;S(0.029)LS(0.971)PILPGR;S(0.415)LS(0.585)PILPGR;S(0.143)LS(0.857)PILPGR 160.33 6.86E-05 737868000 1013495 902277 895259 1012218 1021170 892081 1124155 995981 1122505 TRUE FALSE 965589.0999 994220.0521 936307.5107 910467.9236 1199261.725 861188.0113 952644.5082 908767.6236 1296577.342 0.744721559 0.766803506 0.722137801 0.702208726 0.924944225 0.664201034 0.734737896 0.70089735 1 20.30627684 -1.062208064 4.145659175 1.000031988 0.745951305 0.568748745 0.069756716 18679770976 36435860659 8454139.377 0.01527918 0.086654663 1.062208064 -0.254080683 SLS(ph)PLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSPLIK 7 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 S(0.022)LS(0.978)PLIK;SLS(1)PLIK 109.71 0.0073072 95435000 485570 414120 446060 533890 368510 512820 559270 552830 428720 TRUE FALSE 462618.0684 456319.2988 466512.2922 480222.3629 432778.0273 495060.9148 473943.0898 504421.2745 495203.708 0.934197505 0.921477952 0.942061387 0.969747106 0.873939392 0.999711648 0.957066924 1.018613686 1 18.91766259 1.766418824 1.467652047 1.003014409 0.931753585 0.46417086 0.031375176 0.326067738 1.34429312 0.021668914 0.008620731 58.4008037 -1.766418824 -0.071260824 SLS(ph)PNHNTLQTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.116)LS(0.884)PNHNTLQTLK;S(0.001)LS(0.999)PNHNTLQTLK;S(0.223)LS(0.777)PNHNTLQTLK;S(0.004)LS(0.996)PNHNTLQTLK;S(0.029)LS(0.971)PNHNTLQTLK 262.83 4.09E-24 3212400000 5161430 4010780 4016530 5102070 4334970 4414210 5699190 5053320 4434680 TRUE FALSE 4917459.433 4419483.042 4200691.873 4589200.23 5090987.395 4261344.801 4829673.893 4610824.511 5122387.525 0.959993637 0.862777957 0.820065224 0.895910395 0.993870021 0.831905977 0.942856016 0.900131919 1 22.28838497 -0.270279322 0.499874937 1.014082855 0.895159101 0.251273947 0.054261429 9.178877751 2.326264915 0.292089447 0.025411572 0.536686508 0.270279322 -0.118923754 SLS(ph)PSHLTEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(1)PSHLTEDR;S(0.056)LS(0.944)PSHLTEDR;S(0.114)LS(0.881)PS(0.006)HLTEDR;S(0.229)LS(0.617)PS(0.155)HLTEDR;S(0.463)LS(0.496)PS(0.041)HLTEDR;SLS(1)PSHLTEDR 256.7 1.75E-20 2413100000 1643920 1765201 1636430 1791760 3906930 1521025 1968840 1607480 3925610 TRUE FALSE 1566215.16 1945076.989 1711461.934 1611648.881 4588297.355 1468351.523 1668457.298 1466720.529 4534373.55 0.345409381 0.428962671 0.37744176 0.355429226 1.011892228 0.323826766 0.36795762 0.323467071 1 22.11247182 -1.938664648 2.589763079 1.390466652 0.436979564 0.421664481 0.205378195 40567826.35 19387255.26 95538180.02 0.05089412 0.011516894 1.938664648 -0.953487087 SLS(ph)PSLLGYQQPALMAAPLSLADAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSPSLLGYQQPALMAAPLSLADAHR 26 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 S(0.322)LS(0.515)PS(0.163)LLGYQQPALMAAPLSLADAHR 129.33 5.18E-05 162660000 164150 125270 151150 173960 114860 137060 177450 178160 153200 TRUE FALSE 156390.9548 138035.1554 158080.377 156473.2103 134891.5476 132313.5778 150376.7434 162559.3659 176957.4736 0.883777055 0.780047051 0.893324107 0.884241887 0.762282287 0.747713986 0.849790294 0.91863521 1 17.43304317 1.063765298 2.557900832 0.997829445 0.825351391 0.557246011 0.051498475 0.192047805 2.601743021 0.048631065 0.013209564 11.58151298 -1.063765298 -0.172478054 SLS(ph)PSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSPSVR 7 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.032)LS(0.959)PS(0.009)VR;S(0.065)LS(0.917)PS(0.018)VR;S(0.021)LS(0.977)PS(0.002)VR 112.84 0.0065702 161660000 210418 181853 195293 222757 223284 203828 234784 219580 273937 TRUE FALSE 200471.9581 200384.0274 204247.3772 200365.0431 262224.6589 196769.3853 198963.3887 200352.4111 316417.7509 0.633567357 0.633289463 0.645499112 0.633229465 0.828729293 0.621865824 0.628799706 0.633189543 1 18.27147101 -1.314483434 3.382148093 1.001654596 0.65427134 0.754404928 0.06143429 65353018.44 97256748.03 1099897.481 0.014254025 0.04847486 1.314483434 -0.347383256 SLS(ph)PVAAPPLREPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.011)LS(0.989)PVAAPPLREPR;S(0.038)LS(0.962)PVAAPPLREPR;S(0.05)LS(0.95)PVAAPPLREPR;S(0.046)LS(0.954)PVAAPPLREPR;S(0.26)LS(0.74)PVAAPPLREPR;S(0.05)LS(0.95)PVAAPPLREPR 125.86 5.38E-05 2078860000 2930060 2477130 2625510 2832940 2782470 2545170 3055540 2823170 3028610 TRUE FALSE 2791561.871 2729552.363 2745892.23 2548167.489 3267731.887 2457030.125 2589361.254 2575958.268 3498271.371 0.797983225 0.780257468 0.784928309 0.72840761 0.934099028 0.702355496 0.740183073 0.736351756 1 21.73821078 -0.998634193 4.615921466 1.000004893 0.77505174 0.553463549 0.063351287 0.025572377 36205461.33 448.1240661 0.013774299 0.100314984 0.998634193 -0.224953154 SLS(ph)RS(ph)PLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSRSPLPR 9 1 Q9NYV4-3;J3QSD7 Q9NYV4-3 CDK12 Cyclin-dependent kinase 12 2 S(0.432)LS(0.602)RS(0.966)PLPR 50.207 0.092616 85593000 101890 87536 90139 106350 87990 86520 106840 92201 84295 TRUE FALSE 97073.86163 96456.01792 94271.96231 95659.49595 103335.4281 83523.79071 90539.59575 84127.39165 97367.03808 0.996988956 0.990643444 0.968212284 0.982462832 1.06129785 0.857824089 0.929879326 0.864023322 1 16.57114584 2.232526993 24.99999852 0.90777076 0.996154521 0.471544418 0.045517402 114.5431871 474598.6586 0.014818578 0.011226483 170.8153884 -2.232526993 0.088383761 SLS(ph)RS(ph)PLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSRSPLPSR 10 1 Q9NYV4;Q9NYV4-2 Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.402)LS(0.61)RS(0.985)PLPS(0.004)R 56.139 0.071722 165140000 325700 301970 272790 365940 296500 285230 336610 326940 284450 TRUE FALSE 310304.8065 332741.0863 285297.6913 329155.016 348209.5061 275352.4136 285253.9622 298311.4004 328561.0532 0.944435755 1.012722242 0.868324741 1.00180777 1.059801528 0.838055548 0.868191648 0.907932932 1 18.32580195 2.224069649 24.9998527 0.888003387 0.975383962 0.229196346 0.064520373 282.8696785 488004.1609 0.022537771 0.016719496 167.5211513 -2.224069649 0.087380575 SLS(ph)SPPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.891)S(0.109)PPSSK;SLS(0.883)S(0.117)PPSSK 161.67 6.75E-05 486180000 1122860 843230 1011260 1163670 876720 1150300 1320580 1178520 1060160 TRUE FALSE 1069784.633 929156.0957 1057627.271 1046695.681 1029619.69 1110464.823 1119101.267 1075322.541 1224564.198 0.873604368 0.758764707 0.86367646 0.854749536 0.840804992 0.906824505 0.913877172 0.878126719 1 20.22383698 1.25330759 0.358282766 1.007678059 0.809933916 0.646378432 0.03620045 0.739459511 0.299767377 0.056147041 0.038126668 17.91874505 -1.25330759 -0.197744142 SLS(ph)SPTVTLSAPLEGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.5)S(0.5)PTVTLSAPLEGAK;SLS(0.5)S(0.5)PTVTLSAPLEGAK;S(0.023)LS(0.977)SPTVTLSAPLEGAK 364.38 1.44E-104 291739000 840890 696420 740800 846600 535590 769270 877980 883390 680880 TRUE FALSE 801142.7962 767385.9898 774766.4128 761498.1596 628996.7264 742629.987 744028.0258 806035.6885 786467.3929 1.0186599 0.975737833 0.985122104 0.968251407 0.799774704 0.944260364 0.946037983 1.024881255 1 19.58502743 1.242267543 24.91899089 1.012440639 0.952083181 0.173900564 0.057687027 169.0842931 1136698.417 0.043938276 0.014645724 17.46897982 -1.242267543 -0.060357459 SLS(ph)SYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSYR 6 0 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.364)LS(0.625)S(0.011)YR 73.26 0.087515 37212000 82779 63056 75750 82513 110790 80524 99641 74510 134380 TRUE FALSE 78866.20072 69481.47809 79223.21243 74218.63648 130111.7409 77735.43369 84438.93542 67985.5094 155218.9641 0.508096425 0.447635239 0.510396477 0.478154438 0.83824642 0.500811445 0.543998834 0.437997443 1 17.24394531 -2.383292814 2.312986287 4.616914896 0.530364451 0.6277276 0.11296354 4907331.29 294301.7638 94041177.74 0.027079759 0.004137206 2.383292814 -4.086550445 SLS(ph)TNGENMGLAVQYLDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSTNGENMGLAVQYLDPR 19 0 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 1 S(0.11)LS(0.874)T(0.017)NGENMGLAVQYLDPR 96.79 0.0012797 38972000 10984 13522 11835 16301 14821 11910 15783 14807 17329 TRUE FALSE 10464.80809 14899.90717 12377.64646 14662.39251 17405.77771 11497.55371 13375.01348 13510.42058 20016.29282 0.522814498 0.744388949 0.618378566 0.732522882 0.86958049 0.574409748 0.668206326 0.67497117 1 14.28888718 -2.455671665 1.825898618 3.217656633 0.67353395 0.531028767 0.09577108 2420028.39 180737.7888 22143329.01 0.022936026 0.003502098 2.455671665 -2.544122682 SLS(ph)TSGESLYHVLGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.005)LS(0.973)T(0.021)S(0.001)GESLYHVLGLDK;S(0.001)LS(0.3)T(0.3)S(0.3)GES(0.097)LYHVLGLDK;S(0.069)LS(0.769)T(0.069)S(0.086)GES(0.008)LYHVLGLDK;SLS(0.924)T(0.058)S(0.018)GESLYHVLGLDK 299.43 1.76E-46 2182540000 2661940 2295310 1607853 2984790 2237180 2267930 2793250 2633460 1797933 TRUE FALSE 2536115.372 2529204.699 1681574.65 2684753.238 2627343.484 2189391.015 2367088.411 2402860.282 2076747.267 1.22119596 1.217868317 0.809715596 1.292768398 1.265124325 1.05424047 1.139805719 1.15703067 1 20.98589423 -5 0.180357552 0.398570904 1.1802753 0.093299491 0.13719049 324.2820788 3.123808702 70.11185097 0.404769231 1.00E-05 5 0.781704396 SLS(ph)VEHLETK ddPTM_SK-BR-3_Trastuzumab_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(0.144)LS(0.856)VEHLETK;S(0.269)LS(0.731)VEHLETK 153.75 1.01E-05 432510000 2609400 2206900 2322400 2527800 1769360 2437200 2802200 2678900 1710540 TRUE FALSE 2486058.833 2431785.619 2428884.337 2273700.741 2077935.824 2352799.153 2374672.924 2444321.314 1975801.807 1.258253143 1.230784186 1.229315779 1.150773693 1.05169244 1.190807269 1.201878101 1.237128798 1 20.91400681 -5 0.159071656 0.32052139 1.248480376 0.500157432 0.059701082 120.2162709 1.102082039 26.17686524 0.268987174 1.00E-05 5 0.927958987 SLS(ph)VPVDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR;S(0.001)LS(0.999)VPVDLSR;S(0.001)LS(0.999)VPVDLSR 201.09 2.60E-07 397253000 917138 776328 779648 856827 934240 817556 1110320 868099 1020800 TRUE FALSE 873786.7043 855436.7058 815395.632 770697.1221 1097171.16 789243.8307 940920.2916 792083.6495 1179100.45 0.741062141 0.725499431 0.69154043 0.653631437 0.930515428 0.669360978 0.797998416 0.67176944 1 20.1692552 -2.111244322 2.525221876 1.499867367 0.738263347 0.512554472 0.081113406 8684716.081 2049889.159 25007942.55 0.017418605 0.007740262 2.111244322 -0.761604021 SLS(ph)YEEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSYEEPR 8 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 S(0.001)LS(0.999)YEEPR;S(0.001)LS(0.999)YEEPR;S(0.096)LS(0.898)Y(0.005)EEPR;S(0.007)LS(0.992)Y(0.001)EEPR 113.1 0.0030571 525147000 1565760 1341330 1483390 1743170 1632800 1563610 1851200 1575420 1717580 TRUE FALSE 1491749.628 1478013.052 1551404.899 1567943.24 1917559.803 1509461.794 1568765.44 1437467.873 1983933.534 0.751915123 0.744991214 0.781984311 0.790320448 0.966544378 0.760842925 0.790734878 0.724554451 1 20.91993226 -2.364353256 2.362884461 2.546694594 0.786983828 0.497993129 0.06655504 7265382.804 668766.7045 60522972.52 0.016931274 0.004321622 2.364353256 -1.759710766 SLS(ph)YS(ph)PVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(0.985)Y(0.016)S(0.999)PVER;S(0.001)LS(0.942)Y(0.084)S(0.973)PVER;SLS(0.994)Y(0.007)S(0.999)PVER;S(0.002)LS(0.98)Y(0.04)S(0.978)PVER;SLS(0.99)Y(0.028)S(0.982)PVER 170.68 8.41E-05 3629280000 4602830 3908260 4070860 4562390 4128730 4095790 4979510 4004390 4501770 TRUE FALSE 4385263.348 4306516.137 4257512.958 4103769.889 4848779.205 3953951.765 4219794.295 3653744.383 5199881.5 0.843339093 0.828195054 0.81877115 0.789204502 0.932478789 0.760392668 0.811517396 0.702659163 1 22.31004732 SLS(ph)YSPVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLS(1)YSPVER 169.37 6.14E-05 135020000 56699 58635 77653 79110 62768 63354 62882 61922 66482 TRUE FALSE 54018.95064 64609.97316 81213.46686 71157.7125 73714.71933 61160.03509 53288.19599 56499.78141 76791.68902 0.703447877 0.841366741 1.057581464 0.926632991 0.959930954 0.796440811 0.693931813 0.735753857 1 16.22866256 2.041881527 11.40825795 0.76821828 0.8808249 0.082762959 0.121524565 1.272665086 342.6243628 0.046866185 0.034586525 110.1238856 -2.041881527 0.11260662 SLSAS(ph)PALGSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSASPALGSTK 12 0 O95544;O95544-2 O95544 NADK NAD kinase 1 SLS(0.103)AS(0.897)PALGSTK;SLS(0.311)AS(0.689)PALGSTK 260.67 2.63E-21 972460000 2223200 1702410 1766850 2073530 1721540 2035180 2493100 2228900 2109700 TRUE FALSE 2118113.742 1875887.514 1847861.82 1865094.825 2021776.031 1964701.206 2112731.806 2033725.7 2436861.501 0.869197425 0.769796525 0.758295791 0.765367594 0.829663906 0.806242458 0.866988873 0.834567619 1 21.21659283 0.494580222 0.620395704 1.004351981 0.796517707 0.747051052 0.035655007 0.900225576 0.590228679 0.046030388 0.01486997 3.123059237 -0.494580222 -0.207834275 SLSCLS(ph)DLDGGVALEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 SLSCLS(1)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR 238.81 2.62E-20 114161000 225573 137639 166300 245490 208504 203212 240874 177611 229701 TRUE FALSE 214910.6113 151664.5706 173925.0195 220812.8788 244867.0316 196174.7175 204124.2473 162058.4393 265321.8579 0.809999647 0.571624863 0.655524655 0.832245336 0.922905612 0.739383928 0.769345763 0.610799429 1 18.01738401 3.242482702 24.98945993 0.799063009 0.674737225 0.214754013 0.118321048 156.7747096 998877.5375 0.03161287 0.041255415 1747.763646 -3.242482702 -0.124325785 SLSDSES(ph)DDSKSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(0.003)DS(0.02)ES(0.802)DDS(0.174)KSK;SLS(0.142)DS(0.283)ES(0.575)DDSKSK 256.13 1.94E-23 317311000 680160 356989 708700 570760 400656 769760 989420 883380 540980 TRUE FALSE 648010.1847 393366.585 741194.596 513386.1204 470530.2795 743103.0182 838465.8071 806026.5641 624872.4155 1.03702799 0.629515042 1.186153489 0.821585507 0.753002162 1.189207588 1.341819204 1.289905818 1 19.25320213 2.140933817 5.923565373 1.251377573 0.875913543 0.445542259 0.174798374 0.160266382 8.130776659 0.061765166 0.045419108 138.3355549 -2.140933817 -0.375464029 SLSDSESDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 157.78 7.08E-05 43428000 89134 71779 75454 85301 53674 77020 85307 88511 56991 FALSE TRUE 84920.81247 79093.36171 78913.64053 76726.38142 63034.72861 74352.77809 72291.85038 80760.50761 65828.87321 1.290023789 1.201499553 1.198769426 1.165542986 0.957554422 1.129485809 1.098178457 1.226825004 1 16.00643288 3.203427776 2.414993001 1.09189911 1.239586361 0.435462824 0.076243407 0.259694816 3.100696926 0.022200571 0.029258188 1597.451846 -3.203427776 0.147687251 SLSEEIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSEEIKR 8 1 P15924 P15924 DSP Desmoplakin 0 120.12 0.0025063 184530000 245540 236930 267050 311800 228620 326280 383470 358170 303230 FALSE TRUE 233933.8108 261073.4364 279294.5066 280457.2716 268491.2556 314980.8418 324964.6086 326806.736 350253.3597 0.667898835 0.745384531 0.797407074 0.800726856 0.76656297 0.899294277 0.927798691 0.933058105 1 18.41803936 2.645748543 0.34798168 1.017577905 0.636755118 0.915182436 0.029565292 0.456485199 0.116424681 0.035770652 0.063676513 442.3321876 -2.645748543 -0.380822787 SLSEINKPNFYNNDFDDDFSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSEINKPNFYNNDFDDDFSHR 22 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ;; 235.92 1.06E-30 483920000 792820 716410 724140 871560 699490 784510 865530 805090 627588 FALSE TRUE 755344.9698 789412.9935 757342.5353 783949.1329 821480.8345 757342.222 733477.502 734592.0515 724911.1418 1.041982839 1.088978977 1.04473844 1.081441694 1.133215904 1.044738008 1.011817118 1.013354616 1 19.46744464 1.922105296 4.088117019 1.011429873 1.075824237 0.603263756 0.025578185 0.166700852 4.959102917 0.011956435 0.006908724 83.5805637 -1.922105296 0.064394364 SLSGS(ph)SPCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLS(0.07)GS(0.928)S(0.003)PCPK 183.85 1.70E-06 286130000 600550 472000 486730 560300 435190 558390 656500 605680 461350 TRUE FALSE 572163.1917 520097.3366 509047.0519 503977.5795 511086.9982 539052.8143 556338.8676 552643.4483 532893.8018 1.073690836 0.975986838 0.955250465 0.945737364 0.959078519 1.011557673 1.043995756 1.03706113 1 19.02348853 2.005117105 22.03219445 1.030874728 0.986508241 0.236687969 0.036918663 50.71934863 218371.771 0.015292129 0.011235678 101.1852258 -2.005117105 -0.044366487 SLSGSS(ph)PCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.032)S(0.968)PCPK;SLS(0.001)GS(0.104)S(0.895)PCPK;SLSGS(0.001)S(0.999)PCPK;SLSGS(0.074)S(0.926)PCPK;SLSGS(0.161)S(0.839)PCPK;SLSGS(0.003)S(0.997)PCPK;SLSGS(0.207)S(0.793)PCPK;SLSGS(0.009)S(0.991)PCPK 231.05 9.08E-10 3971060000 9940220 7927640 8289080 9643240 6261040 9278490 10487650 9801590 7300330 TRUE FALSE 9470365.5 8735475.529 8669142.517 8673883.194 7352963.394 8957173.565 8887566.374 8943310.818 8432427.891 1.123088821 1.035938361 1.028071942 1.028634138 0.871986513 1.062229488 1.053974785 1.060585508 1 23.00751665 4.483809511 1.415644507 1.016744156 1.140570046 0.27711812 0.054603201 1.027472779 2.646422199 0.01528402 0.158785955 30465.58427 -4.483809511 0.12382589 SLSKS(ph)DSDLLTCSPTEDATMGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.045)LS(0.214)KS(0.737)DS(0.003)DLLTCSPTEDATMGSR;S(0.001)LS(0.058)KS(0.94)DSDLLTCSPTEDATMGSR;S(0.031)LS(0.261)KS(0.701)DS(0.007)DLLTCSPTEDATMGSR 183.12 5.67E-17 671734000 657440 562389 621880 667550 439873 663230 756360 703730 624920 TRUE FALSE 626364.1141 619697.0785 650393.8131 600446.6057 516586.7119 640262.1788 640963.3905 642107.6705 721829.402 0.86774536 0.858509056 0.901035357 0.83184005 0.715663162 0.886999306 0.887970743 0.889555993 1 19.46129838 0.852427428 1.085193308 0.998120774 0.846246753 0.475748471 0.050776126 0.638585769 1.471941397 0.048252202 0.015368082 7.119138272 -0.852427428 -0.151874021 SLSNS(ph)NPDISGTPTS(ph)PDDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSNSNPDISGTPTSPDDEVR 21 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 2 SLSNS(1)NPDISGTPT(0.061)S(0.939)PDDEVR;SLSNS(1)NPDISGTPT(0.341)S(0.659)PDDEVR;SLS(0.001)NS(0.999)NPDISGTPT(0.002)S(0.998)PDDEVR;SLSNS(1)NPDISGTPT(0.001)S(0.999)PDDEVR 362.44 3.69E-96 502440000 676486 604550 666239 677430 635670 649785 756360 701070 753080 TRUE FALSE 644509.8474 666154.3323 696786.7172 609333.4494 746530.6467 627282.7825 640963.3905 639680.5942 869863.8002 0.740931911 0.765814524 0.801029675 0.700492938 0.858215558 0.721127586 0.736854885 0.735380176 1 19.73043 -0.978402233 4.527466823 1.000005089 0.756733776 0.745194415 0.044565578 83902623105 18926999322 5300271.551 0.009308774 0.105098802 0.978402233 -0.243271313 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_SK-BR-3_Trastuzumab_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 SLSNS(0.993)NPDIS(0.003)GT(0.003)PTSPDDEVR;SLSNS(0.964)NPDIS(0.007)GT(0.022)PT(0.007)SPDDEVR 366.99 2.97E-112 591300000 408990 363160 405760 423850 368610 367800 440300 401760 461250 TRUE FALSE 389657.8532 400166.4169 424364.4974 381243.7927 432895.4673 355062.9938 373124.1483 366579.7645 532778.2943 0.73136961 0.751093694 0.796512362 0.715576811 0.812524594 0.666436673 0.700336617 0.688053114 1 19.02317578 -0.824231731 7.275602069 1.000000001 0.732690029 0.774285828 0.045349082 6.39E-10 8.79E-11 0.0429118 0.010114408 0.149888485 0.824231731 -0.267309972 SLSNSNPDISGT(ph)PTSPDDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SLSNS(0.081)NPDIS(0.246)GT(0.646)PT(0.027)SPDDEVR 239.63 6.96E-29 162120000 110890 100330 120290 120390 102090 106090 133790 104100 132350 TRUE FALSE 105648.4495 110553.7411 125805.4155 108288.1685 119894.4637 102416.0767 113377.8783 94984.45213 152874.162 0.691081135 0.723168255 0.822934457 0.708348403 0.784268984 0.669937126 0.741641863 0.621324433 1 17.22198507 -1.028350115 4.640854522 1.000008004 0.722620644 0.709408134 0.056234033 4.51E-06 9.44E-07 0.04916893 0.011588869 0.093680648 1.028350115 -0.27738736 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.057)LS(0.043)QS(0.9)FENLLDEPAYGLIQK 229.69 1.41E-25 92767000 170190 152290 151160 182510 136190 173450 190670 168410 142980 TRUE FALSE 162145.456 167808.5241 158090.8355 164163.7481 159941.4929 167443.383 161579.7896 153663.1276 165152.6082 0.981791676 1.016081587 0.957240926 0.994012446 0.968446667 1.013870655 0.978366563 0.930431129 1 17.33344023 1.46406236 11.62445454 0.961611411 0.989803108 0.130886191 0.024299178 0.1817813 118.6613193 0.011765331 0.005405289 29.11135093 -1.46406236 0.028191698 SLSS(ph)PPSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.303)S(0.697)PPSSK;SLS(0.245)S(0.755)PPSSK 210.44 7.11E-06 627120000 819560 645930 698540 907400 685360 822180 980110 896370 817420 TRUE FALSE 780821.023 711751.0014 730568.75 816186.4281 804886.567 793707.7004 830576.2185 817879.0908 944181.3188 0.826982072 0.753828727 0.773758954 0.86443823 0.852470337 0.840630591 0.879678725 0.866230961 1 19.84870441 0.509535811 0.251710206 1.052050314 0.765484432 0.798015212 0.02978561 1.79561287 0.267633795 0.161168572 0.062648967 3.232479733 -0.509535811 -0.286565882 SLSS(ph)PTDNLELSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SLSSPTDNLELSLR 14 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SLS(0.001)S(0.999)PTDNLELSLR;SLS(0.023)S(0.977)PTDNLELSLR;SLS(0.001)S(0.999)PTDNLELSLR;SLS(0.025)S(0.975)PTDNLELSLR;SLS(0.273)S(0.62)PT(0.106)DNLELSLR 356.37 3.95E-82 1495460000 2189050 1875820 1869980 2166470 2010950 1939700 2216360 2044640 2140010 TRUE FALSE 2085577.945 2066968.191 1955720.433 1948692.32 2361659.043 1872527.703 1878213.576 1865600.482 2471871.821 0.843724147 0.836195539 0.791190067 0.788346832 0.955413231 0.757534305 0.759834535 0.754731886 1 21.2371725 SLSS(ph)SPDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 SLS(0.001)S(0.532)S(0.467)PDKR;S(0.276)LS(0.132)S(0.296)S(0.296)PDKR;S(0.07)LS(0.053)S(0.504)S(0.374)PDKR 156.58 4.32E-05 1155190000 821200 797091 800408 952282 567960 925387 1040276 1041550 661037 TRUE FALSE 782383.5035 878315.4791 837107.4985 856556.8041 667012.0442 893340.6162 881562.7902 950346.3604 763547.2419 1.024669412 1.150309281 1.096340151 1.121812453 0.873570105 1.169987353 1.154562209 1.244646445 1 19.5423579 SLSS(ph)SPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.005)S(0.588)S(0.407)PVKK 94.465 0.005331 337930000 872270 847110 814760 964060 503590 995160 1062200 1005300 585680 TRUE FALSE 831039.5258 933431.4721 852117.5519 867150.8572 591415.9366 960697.3597 900141.8814 917270.6026 676504.2632 1.22843206 1.379786533 1.25958933 1.281811371 0.874223518 1.420090622 1.330578284 1.355897742 1 19.3677395 3.318830212 3.345331787 1.232248494 1.304367693 0.039266659 0.16887853 0.999781591 22.27336927 0.047739931 0.065427852 2083.676107 -3.318830212 0.072119198 SLSSPTDNLELS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSPTDNLELSLR 14 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SLSSPT(0.001)DNLELS(0.999)LR 62.378 0.081305 16303000 24157 19277 19298 26112 21248 20027 24276 28410 27706 TRUE FALSE 23015.14648 21241.34822 20182.83239 23487.17215 24953.64447 19333.45997 20572.25034 25922.26979 32002.50498 0.719167031 0.663740174 0.630664143 0.733916678 0.779740351 0.604123333 0.642832502 0.810007523 1 14.96589722 0.961472317 3.841768871 0.999538147 0.680997208 0.795263567 0.05215762 0.098743493 4.106432194 0.050563591 0.012976672 9.151079255 -0.961472317 -0.318540939 SLSSS(ph)LDDTEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 SLS(0.001)S(0.01)S(0.989)LDDTEVKK;SLS(0.001)S(0.012)S(0.987)LDDTEVKK 236.17 6.40E-17 552620000 856270 688390 804470 1188140 685270 1030800 1104030 978570 620650 TRUE FALSE 815795.8141 758537.7236 841355.7452 1068705.91 804780.871 995103.1375 935589.9466 892881.2231 716897.2322 1.137953639 1.058084325 1.173607189 1.49073795 1.122588894 1.388069437 1.305054483 1.245480081 1 19.4514068 3.470029975 24.98756156 1.282811128 1.100990082 0.18302485 0.135425976 194.135272 684071.5626 0.032624977 0.044265296 2951.412929 -3.470029975 -0.181821046 SLSSS(ph)PDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 S(0.007)LS(0.023)S(0.109)S(0.861)PDKR;SLSS(0.033)S(0.967)PDKR;SLS(0.001)S(0.01)S(0.989)PDKR;S(0.08)LS(0.228)S(0.228)S(0.464)PDKR 129 0.00024594 3509050000 2239640 2026070 2024530 2482770 1465180 2291880 2528110 2533460 1680540 TRUE FALSE 2133776.656 2232528.836 2117356.703 2233197.243 1720706.928 2212511.621 2142400.388 2311616.812 1941149.56 1.099233516 1.150106557 1.090774635 1.150450892 0.88643707 1.139794515 1.103676106 1.190849412 1 20.88847985 0.192110929 0.007911461 4.84E-07 2.145506954 0.055716566 0.085532827 15705.40977 42.81780312 5949.257637 5660.271396 1.556363114 -0.192110929 2.14550647 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLS(0.003)S(0.018)S(0.979)PQAQPPRPAELSDEEVAELFQR 237.28 2.83E-45 187750000 61027 59055 56241 72262 70258 61437 77136 73877 64591 TRUE FALSE 58142.37465 65072.77164 58819.70548 64998.08647 82510.97296 59309.42129 65367.4865 67407.93823 74607.44239 0.779310653 0.87220215 0.788389249 0.871201108 1.105934881 0.794953149 0.876152357 0.903501528 1 16.18703193 8 0.130793491 0.993870169 0.329464229 0.255355197 0.086935416 125.9815521 1.113595914 0.438910272 15.46308273 100000000 -8 -0.664405939 SLSSS(ph)PVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.001)LS(0.03)S(0.193)S(0.776)PVKK 67.385 0.037393 618700000 1190100 1158200 1035200 1453300 658250 1300400 1313200 1345400 759930 TRUE FALSE 1133846.332 1276221.897 1082664.944 1307211.523 773048.5916 1255366.822 1112847.221 1227589.644 877776.0632 1.291726192 1.45392652 1.233418168 1.489231226 0.880689989 1.430167527 1.267803108 1.398522579 1 19.7434934 -2.266855615 1.900218772 5.58E-05 1.311105228 0.23643374 0.172397386 2526985.415 357597.0342 10836943.95 0.039345947 0.005409341 2.266855615 1.311049446 SLSTSGES(ph)LYHVLGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.169)LS(0.169)T(0.206)S(0.206)GES(0.251)LYHVLGLDK 125.12 3.09E-05 68632000 67014 53500 40129 77818 56285 59616 75491 65442 48287 TRUE FALSE 63846.38103 58951.71082 41968.95434 69995.5868 66101.08618 57551.48297 63973.46146 59711.55155 55775.10134 1.144711161 1.056953899 0.752467559 1.254961176 1.185136102 1.031849008 1.146989605 1.070577195 1 15.76733361 4.571094689 3.550379103 1.070460859 1.142890123 0.032848881 0.133685064 1.125684161 25.93625306 0.031423112 0.167299894 37247.29078 -4.571094689 0.072429265 SLSYS(ph)PVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLSYS(1)PVER;S(0.002)LS(0.284)Y(0.003)S(0.712)PVER 220.17 4.89E-07 1926106000 2968825 2365705 2451625 2692839 2670056 2465566 2977325 2589724 2860303 TRUE FALSE 2828494.526 2606773.029 2564034.431 2422149.708 3135712.921 2380182.831 2523079.389 2362954.038 3303864.181 0.856117071 0.789007322 0.776071379 0.733126295 0.949104669 0.720423934 0.763675276 0.715209194 1 21.65572295 4.548430718 2.627833363 0.792990999 0.857959816 0.010665234 0.096215761 1.179539761 13.85404928 0.021373243 0.139525667 35353.36184 -4.548430718 0.064968817 SLT(ph)PPPSSTESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLTPPPSSTESK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 S(0.004)LT(0.968)PPPS(0.009)S(0.016)T(0.004)ESK;SLT(1)PPPSSTESK;SLT(0.999)PPPSSTESK;S(0.004)LT(0.995)PPPS(0.001)STESK 160.18 0.00076846 478602000 1485290 1261000 1335160 1507800 952060 1429280 1613110 1502500 1062160 TRUE FALSE 1415083.285 1389497.334 1396378.407 1356233.079 1118098.963 1379783.675 1367000.443 1370933.135 1226874.348 1.153405226 1.132550645 1.138159265 1.105437636 0.911339425 1.124633242 1.114213892 1.117419349 1 20.22655607 2.996439175 24.73091618 1.064603976 1.138775316 0.277971057 0.0639192 193.4995529 1343928.103 0.018589803 0.021772275 991.8344188 -2.996439175 0.07417134 SLTAEIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLTAEIDR 8 0 P54136;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 188.76 0.00045427 159388000 306300 249958 248636 301920 325960 264804 315240 301990 337490 FALSE TRUE 291821.806 275429.0044 260036.2065 271570.428 382807.3208 255633.7711 267144.3482 275546.1547 389826.2255 0.748594597 0.706543035 0.667056728 0.696644839 0.981994786 0.6557634 0.685290857 0.706843554 1 18.57247163 -0.941657316 4.413849661 1.000005626 0.727932841 0.452777528 0.092848903 9773105.882 4428780.853 513.4077572 0.020685951 0.114378049 0.941657316 -0.272072785 SLTAHS(ph)LLPLAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.131)LT(0.131)AHS(0.738)LLPLAEK 137.59 3.80E-05 241470000 688450 665490 631940 785180 543790 695750 812380 808730 585010 TRUE FALSE 655908.3329 733304.1876 660915.0741 706252.2147 638626.8038 671656.003 688436.5106 737913.3139 675730.363 0.97066577 1.085202364 0.978075147 1.045168685 0.945091177 0.993970435 1.018803577 1.092023319 1 19.36608816 1.442309637 13.25428278 1.049160135 1.008564405 0.125334322 0.044814429 1.261476081 474.3178084 0.023774747 0.010459384 27.68915086 -1.442309637 -0.04059573 SLTDPSQESHTEAIS(ph)DAETSSSDISFSGIATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR 194.08 1.03E-20 105570000 27510 26239 26804 26623 32273 24910 29158 25751 31373 TRUE FALSE 26209.65682 28912.78393 28032.98991 23946.80546 37901.40098 24047.36045 24709.41158 23496.10593 36238.16461 0.723261156 0.797854534 0.773576427 0.660817282 1.045897368 0.663592119 0.681861563 0.648380131 1 15.14522227 4.728009836 4.571577908 0.76720171 0.720919704 0.005757236 0.139961108 1.410469246 69.02734147 0.030738519 0.201186485 53457.64661 -4.728009836 -0.046282006 SLTNDWEDHLAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;;; 253.06 8.99E-24 34131387000 36582790 39168240 34688830 39115590 25913000 37551790 36689360 39086960 22259450 FALSE TRUE 34853594.02 43159528.19 36279347.17 35183616.58 30432219 36251362.1 31091724.29 35664298.57 25711331.82 1.355573265 1.678618925 1.411025591 1.36840895 1.183611149 1.409937157 1.209261523 1.387104286 1 24.61590101 0.610678748 0.156211499 0.757254648 1.668307558 0.515817474 0.123750998 6.364766525 0.534772292 1.769581051 0.959508023 4.080174605 -0.610678748 0.91105291 SLTSS(ph)LENIFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 SLTS(0.013)S(0.987)LENIFSR;SLTS(0.04)S(0.959)LENIFSR;SLTS(0.004)S(0.996)LENIFSR;SLTS(0.018)S(0.982)LENIFSR;SLT(0.001)S(0.291)S(0.708)LENIFSR;SLT(0.009)S(0.292)S(0.699)LENIFSR;SLT(0.001)S(0.204)S(0.795)LENIFSR;SLT(0.059)S(0.204)S(0.736)LENIFSR 289.88 4.51E-36 1570142000 2708851 2101508 2329276 2905328 2988775 2606926 3288874 2777278 3208026 TRUE FALSE 2580808.982 2315654.054 2436075.609 2613278.91 3510016.414 2516647.499 2787095.867 2534084.815 3705510.288 0.696478698 0.624921772 0.65741974 0.705241305 0.947242388 0.679163544 0.752149003 0.683869324 1 21.8212408 -5 0.162248486 2.055653326 0.63867236 0.507482591 0.087492555 108.0592024 0.999518237 36.85623629 0.347353651 1.00E-05 5 -1.416980966 SLTTECHLLDS(ph)PGLNCSNPFTQLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLTTECHLLDSPGLNCSNPFTQLER 25 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 SLTTECHLLDS(1)PGLNCSNPFTQLER;SLTTECHLLDS(1)PGLNCSNPFTQLER 187.45 8.82E-18 135310000 62207 63260 68528 66155 71409 64977 69183 69267 69341 TRUE FALSE 59266.59839 69706.26592 71670.07658 59504.97371 83862.70699 62726.8302 58627.86272 63201.61427 80094.04814 0.739962579 0.870305192 0.894824001 0.742938771 1.04705292 0.783164688 0.731987758 0.78909252 1 16.28940742 -2.449377576 2.219106816 2.772612465 0.821621059 0.24886837 0.095439615 3383439.324 446866.8656 30028655.95 0.022345244 0.003553223 2.449377576 -1.950991406 SLVDTVYALKDEVQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLVDTVYALKDEVQELR 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 197.38 1.38E-11 124770000 348480 314120 320450 341110 248270 317760 382110 359410 301970 FALSE TRUE 332008.041 346129.1851 335142.9495 306820.9747 291568.2094 306755.8915 323812.1016 327938.155 348797.9654 0.951863468 0.992348636 0.960851217 0.879652421 0.835922908 0.879465828 0.928365798 0.940195149 1 18.4120321 3.339863614 5.957869225 0.903203624 0.972595057 0.26331505 0.044564477 0.229559169 11.5200374 0.012013174 0.016299097 2187.074687 -3.339863614 0.069391433 SLVEIIEHGLVDEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLVEIIEHGLVDEQQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 295.09 1.19E-45 213632000 461971 472154 418637 536692 341891 512179 490625 553088 315906 FALSE TRUE 440134.5464 520267.0294 437831.9205 482742.7005 401516.6822 494442.1128 415771.1453 504656.6826 364895.0891 1.206194765 1.425798935 1.199884388 1.322962997 1.100361979 1.355025397 1.13942653 1.383018565 1 18.47712221 -4.145757429 0.255522166 7.66E-18 1.291255232 0.352002336 0.108986014 119.2750411 1.760258938 62.38171069 0.134049401 7.15E-05 4.145757429 1.291255232 SLVESVS(ph)SSPNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.001)LVES(0.012)VS(0.326)S(0.284)S(0.284)PNKES(0.092)NEEEQVWHFLGK 90.974 0.0061698 1630600000 114130 117510 121990 136540 94654 144120 142450 143230 96924 TRUE FALSE 108735.3011 129484.4026 127583.3622 122814.7398 111161.6276 139129.0883 120716.6362 130688.0219 111954.4789 0.971245654 1.156580816 1.13960034 1.097006042 0.992918092 1.242729095 1.078265358 1.167331787 1 16.77255272 4.638447402 3.206466413 1.113735593 0.964830197 0.245432509 0.075435277 0.355029193 5.974212077 0.016338732 0.114033706 43495.80796 -4.638447402 -0.148905396 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.006)LVES(0.051)VS(0.058)S(0.442)S(0.442)PNKES(0.001)NEEEQVWHFLGK;S(0.003)LVES(0.086)VS(0.108)S(0.634)S(0.168)PNKESNEEEQVWHFLGK 180.65 1.28E-17 1144757000 887460 737035 727515 837118 476412 885201 905843 925170 463891 TRUE FALSE 845511.5246 812139.7044 760872.2824 752969.3082 559498.102 854546.2674 767640.0134 844157.2102 535828.8471 1.577950738 1.515669992 1.419991265 1.405242201 1.044173163 1.594811985 1.432621662 1.575423225 1 19.03141273 -2.037381826 2.502250085 0.440324 1.451215082 0.438995004 0.158247827 6629787.03 2220796.007 21279675.92 0.037463327 0.009175256 2.037381826 1.010891082 SLVESVSSS(ph)PNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 SLVES(0.002)VS(0.054)S(0.388)S(0.556)PNKESNEEEQVWHFLGK 292.43 1.70E-70 1230000000 1251900 1049400 1069200 1246800 744900 1361100 1408500 1341100 714440 TRUE FALSE 1192725.168 1156335.053 1118223.878 1121469.295 874810.3242 1313964.766 1193607.456 1223666.174 825231.7063 1.445321549 1.401224704 1.35504231 1.358975045 1.060078421 1.592237375 1.446390689 1.482815269 1 19.65443973 -1.92857696 2.598327158 0.740991925 1.397194496 0.450577002 0.136222917 6675847.055 4173011.547 10517360.67 0.031324385 0.011787536 1.92857696 0.656202572 SLVESVSSSPNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 105.56 0.0019131 231120000 609620 442890 524590 530960 406630 524510 645400 632880 417310 FALSE TRUE 580804.4708 488020.9945 548642.9704 477586.892 477546.1433 506346.0872 546932.3764 577461.6721 482024.3035 1.204927773 1.01244064 1.138206033 0.990794216 0.99070968 1.050457588 1.134657262 1.197992856 1 18.87874636 -0.45258895 7.128194434 0.999999714 1.087215975 0.112147675 0.07925444 0 0 0.074802571 0.017631135 0.35270454 0.45258895 0.08721626 SLVGS(ph)WLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLVGSWLK 8 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 SLVGS(1)WLK;SLVGS(1)WLK 119.22 0.0018204 171461000 639750 582760 585240 642350 520460 630170 663600 610920 520170 TRUE FALSE 609510.2854 642143.9065 612073.8329 577779.7576 611228.0592 608347.0549 562355.6321 557424.6061 600835.3069 1.014438197 1.068751951 1.018704836 0.961627506 1.017297173 1.012502175 0.935956369 0.927749418 1 19.19661007 2.736356964 0.746715398 0.955827783 1.041417051 0.37845123 0.033581874 0.603453445 0.724250017 0.023288872 0.022635084 544.9503853 -2.736356964 0.085589268 SLVHEVGKPPQDVTDDS(ph)PPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SLVHEVGKPPQDVTDDSPPSK 21 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SLVHEVGKPPQDVT(0.001)DDS(0.993)PPS(0.006)K 97.771 0.00065366 207010000 88132 74914 94497 102860 61550 101950 108220 118690 76378 TRUE FALSE 83966.17502 82547.82177 98829.78092 92520.31738 72284.30051 98419.44594 91709.0514 108296.8744 88222.31016 0.951756703 0.935679667 1.120235695 1.048717917 0.81934264 1.115584547 1.039522217 1.227545212 1 16.42885592 SLVLQRPQTWADCVTWACHHWHTQYSNNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLVLQRPQTWADCVTWACHHWHTQYSNNIR 30 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 198.06 8.77E-26 604373000 251106 203454 207113 241699 313280 225962 327050 252387 194211 FALSE TRUE 239236.717 224186.1939 216609.3359 217402.9573 367915.9328 218136.8793 277152.5158 230286.6563 224328.25 1.066458268 0.999366749 0.965590985 0.969128754 1.640078469 0.972400397 1.235477546 1.026561105 1 17.77525179 SLVQDSLSTNSSDLVAPS(ph)PDAFR ddPTM_SK-BR-3_Trastuzumab_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 85.35 8.45E-05 36939000 86156 71449 83862 87213 100114 74122 95476 75638 96666 TRUE FALSE 82083.57662 78729.73433 87707.15565 78446.18355 117573.8499 71555.13655 80909.38266 69014.73574 111656.4696 0.735143937 0.705106785 0.785508945 0.702567293 1.052996305 0.640850788 0.724627807 0.618098853 1 16.76870732 -2.184035089 2.364021404 1.696492484 0.744284129 0.311062803 0.118962625 9423123.332 2668240.14 34952243.2 0.026926247 0.006545833 2.184035089 -0.952208356 SLYDEVAAQGEVVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLYDEVAAQGEVVRK 15 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 179.17 1.09E-06 237340000 161360 124625 201131 180942 157574 211358 260790 206071 186833 FALSE TRUE 153732.8326 137324.4292 210353.0553 162753.3664 185054.8557 204038.6195 221001.6958 188026.3308 215806.1074 0.712365532 0.636332451 0.974731706 0.754164784 0.857505183 0.945471942 1.024075261 0.871274372 1 17.71937617 3.333453347 0.550595497 0.986743492 0.631181634 0.534121571 0.088118277 0.750926436 0.447830998 0.062034439 0.143197429 2155.030132 -3.333453347 -0.355561859 SLYGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SLYGER 6 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 0 ;;; 139.92 0.027558 1348020000 1479390 1380990 1265260 1496490 1380170 1297090 1608310 1521250 1508210 FALSE TRUE 1409462.167 1521714.451 1323273.423 1346059.982 1620871.211 1252171.448 1362932.771 1388041.285 1742095.504 0.809061365 0.873496572 0.759587187 0.772667158 0.930414669 0.718773136 0.782352499 0.796765322 1 20.73239229 -0.931606023 5.150730788 1.000000605 0.807352115 0.515668849 0.059245472 3.92E-07 8.14E-08 0.054656779 0.012882686 0.11705608 0.931606023 -0.19264849 SLYHDISGDTSGDYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SLYHDISGDTSGDYRK 16 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 159.22 5.98E-09 762290000 634290 419570 451530 763650 850750 509710 833760 631820 783590 FALSE TRUE 604308.3687 462324.66 472233.0971 686886.4512 999120.5306 492058.6149 706554.5989 576494.4913 905105.1352 0.66766649 0.510796638 0.521743915 0.758902391 1.103872348 0.54364802 0.780632627 0.636936494 1 19.78772586 3.179407627 6.527193043 0.789810962 0.569439749 0.315275329 0.164236495 0.248781102 20.91878151 0.044774936 0.054094363 1511.498174 -3.179407627 -0.220371213 SLYQSAGVAPES(ph)FEYIEAHGTGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;SLYQSAGVAPES(1)FEYIEAHGTGTK;SLYQSAGVAPES(1)FEYIEAHGTGTK;SLYQSAGVAPES(1)FEYIEAHGTGTK 274.13 3.62E-52 785780000 1184110 1038180 1213640 1437340 1091980 1314870 1568230 1436430 1113180 TRUE FALSE 1128139.467 1143971.722 1269286.594 1292855.852 1282420.966 1269335.722 1328967.711 1310648.574 1285806.269 0.877379038 0.889692133 0.987152283 1.005482617 0.997367175 0.987190491 1.033567609 1.019320411 1 20.29424186 3.701935421 2.950876374 1.008364738 0.880145657 0.941355751 0.01263446 0.052959023 0.923810513 0.003737982 0.006626038 5034.257448 -3.701935421 -0.12821908 SLYQSAGVAPESFEYIEAHGTGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 336.87 4.62E-87 8767217000 6782130 5917667 6581461 7520604 5928204 6801476 8267861 7808302 6670240 FALSE TRUE 6461552.156 6520683.995 6883227.497 6764618.598 6962080.901 6565939.181 7006446.955 7124565.682 7704626.752 0.838658687 0.846333535 0.893388832 0.877994329 0.903623384 0.852207302 0.909381749 0.924712632 1 22.87729364 -5 0.089708613 1.425158946 0.768259382 0.842657557 0.018626985 75.00549265 0.467809904 6.032652404 0.427133884 1.00E-05 5 -0.656899564 SMDELNHDFQALALEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 0 ; 234.48 3.90E-20 106523000 129282 111444 123303 144207 142852 119781 146375 134142 133930 FALSE TRUE 123171.0961 122800.2703 128956.5645 129711.0384 167765.3436 115632.9539 124042.8054 122395.8153 154699.1804 0.79619747 0.793800394 0.833595654 0.838472693 1.084461748 0.747469726 0.801832337 0.791185933 1 17.23910603 -2.46183688 2.228161285 2.806955469 0.83103221 0.237397858 0.092081595 5085074.772 331455.8045 47220384.92 0.022308709 0.003452734 2.46183688 -1.975923259 SMDFEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMDFEEAER 9 0 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 158.61 0.00015512 254450000 474230 523630 433390 536310 381900 509100 464180 465370 408690 FALSE TRUE 451814.0877 576988.4923 453261.3602 482399.0999 448503.2391 491469.7393 393360.8157 424619.7357 472067.5579 0.957096246 1.222258303 0.960162063 1.021885728 0.95008274 1.041100434 0.833272292 0.899489339 1 18.84863381 2.770561832 0.979468874 0.913660514 1.077803156 0.225179257 0.089923522 0.592043538 1.207833069 0.047602452 0.045433361 589.605915 -2.770561832 0.164142642 SMDIDDFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMDIDDFIR 9 0 A0A494C0G7;Q9UNQ2 A0A494C0G7 DIMT1 Probable dimethyladenosine transferase 0 79.893 0.059685 16118000 75108 76256 86331 81972 103330 69277 99608 82039 124260 FALSE TRUE 71557.79369 84026.5731 90289.36174 73732.01882 121350.7193 66877.92012 84410.97017 74855.23024 143529.6062 0.498557723 0.585430249 0.629064373 0.513705993 0.845475178 0.465952091 0.588108422 0.521531635 1 17.13098883 -1.809002835 2.489751392 1.140729946 0.579286883 0.608382929 0.105645144 9426963.18 6284980.177 7995118.972 0.024007284 0.015523769 1.809002835 -0.561443063 SMEAEMIQLQEELAAAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 223.96 1.13E-18 143182600 195678.2 165266.9 171062.3 201398.2 204754.6 170627 204011.6 196545.5 216160.8 FALSE TRUE 186428.8793 182107.785 178905.6757 181153.2703 240463.7374 164718.1442 172885.8835 179334.9341 249681.9129 0.746665536 0.729359139 0.716534384 0.725536216 0.963080323 0.65971196 0.692424539 0.718253605 1 17.92973179 -2.455764739 2.199466778 3.608728526 0.740607936 0.493053658 0.0815335 3574366.604 315955.0803 46463576.9 0.020729116 0.003501348 2.455764739 -2.868120591 SMEMLVEHQAHDILT ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMEMLVEHQAHDILT 15 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 157.23 1.99E-06 180518000 206388 207409 200167 229387 228055 201033 247138 205707 9051.4 FALSE TRUE 196632.4483 228544.2129 209344.8549 206328.583 267827.7198 194071.1768 209432.5591 187694.2046 10455.04488 18.80742268 21.85970653 20.02333393 19.73483474 25.61707987 18.5624432 20.03172262 17.95250108 1 13.35191164 0.303327419 1.063399074 0.932521794 20.84047968 0.907126339 1.96411594 0.859155201 1.083668468 1.819991825 0.540523365 2.010608061 -0.303327419 19.90795788 SMESS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SMESSPR 7 0 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 SMES(0.093)S(0.907)PR;SMES(0.029)S(0.971)PR;SMES(0.008)S(0.992)PR;SMES(0.188)S(0.812)PR 102.95 0.019225 355607000 1158420 1075160 1056760 1334460 1260880 1075620 1337670 1174330 1384750 TRUE FALSE 1103663.782 1184720.026 1105213.491 1200317.545 1480777.073 1038371.01 1133583.874 1071499.44 1599489.958 0.690009823 0.74068613 0.6909787 0.750437688 0.925780788 0.649188827 0.708715843 0.669900698 1 20.6091805 -1.519363309 3.111184658 1.008704972 0.727553987 0.555408916 0.076417838 95865913.56 113039947.6 7069505.78 0.01759326 0.030243823 1.519363309 -0.281150985 SMGFIGHYLDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SMGFIGHYLDQK 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 184.31 1.45E-05 3272930000 9924260 9691480 8119220 10285230 7331090 9648170 10695030 10345320 6762480 FALSE TRUE 9455159.898 10679052.83 8491494.268 9251339.14 8609629.775 9314051.454 9063306.746 9439428.937 7811170.86 1.210466403 1.367151356 1.087096214 1.184372907 1.102220132 1.192401449 1.160300665 1.208452498 1 22.89710739 -5 0.034447929 7.14E-08 1.835884347 0.380464419 0.075642392 1034.065626 2.672171418 118.3982218 42.01410528 1.00E-05 5 1.835884276 SMGFIGHYLDQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMGFIGHYLDQKR 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 135.58 5.34E-05 226800000 356050 131710 315590 199150 419750 279580 594030 386330 538140 FALSE TRUE 339220.2221 145131.3987 330060.1137 179131.0636 492954.2671 269898.0745 503399.8134 352500.8971 621592.0028 0.545728099 0.233483375 0.53099157 0.288181094 0.793051173 0.434204548 0.809855679 0.567093681 1 19.24560842 1.330989103 0.388325706 1.012872397 0.359960702 0.513537748 0.165185715 0.792302525 0.363035552 0.202179544 0.138677466 21.42836833 -1.330989103 -0.652911695 SMGSQEDDSGNKPS(ph)SYS ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMGSQEDDSGNKPSSYS 17 1 Q9UNS2-2;Q9UNS2;H7C3P9 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 1 SMGSQEDDS(0.1)GNKPS(0.3)S(0.3)YS(0.3) 85.087 0.0057121 0 292610 318760 274090 349730 202470 338310 330670 276240 197750 TRUE FALSE 278778.9052 351242.0064 286657.2976 314574.476 237780.7039 326594.2399 280220.2183 252050.9612 228416.06 1.220487321 1.53772903 1.254978733 1.377199466 1.040998185 1.429821703 1.226797355 1.103473027 1 17.80130457 1.02113352 0.422437952 0.976435446 1.367344231 0.3768859 0.134170444 1.221020036 0.587872471 0.177560146 0.093726557 10.49865151 -1.02113352 0.390908785 SMGSQEDDSGNKPSSYS(ph) ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMGSQEDDSGNKPSSYS 17 1 Q9UNS2-2;Q9UNS2;H7C3P9 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 1 SMGSQEDDSGNKPS(0.02)S(0.02)Y(0.002)S(0.957) 90.754 0.0097977 78591000 160330 171110 172160 192680 123120 193480 216040 208700 155460 TRUE FALSE 152751.5186 188546.3035 180053.7063 173311.4403 144592.089 186779.7391 183079.1302 190425.1216 179567.9428 0.850661406 1.049999797 1.002705179 0.965158021 0.805222172 1.040161936 1.019553531 1.06046279 1 17.45417029 SMGTGDT(ph)PGLEVPSSPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDT(0.68)PGLEVPS(0.221)S(0.099)PLRK 148.03 1.93E-07 133500000 186090 167290 171590 192790 150390 193980 219330 215980 187920 TRUE FALSE 177293.8945 184337.0412 179457.5712 173410.3829 176617.9684 187262.424 185867.1802 197067.6462 217061.6738 0.816790414 0.849238089 0.826758442 0.798899132 0.813676432 0.862715286 0.856287418 0.907887803 1 17.72774549 0.942068026 0.965284574 1.000035105 0.824905017 0.925280806 0.016010207 0.162254738 0.317495306 0.015499103 0.005190996 8.751208397 -0.942068026 -0.175130087 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDT(0.005)PGLEVPS(0.498)S(0.498)PLRK 231.21 4.14E-20 139920000 170220 153110 163260 187980 124420 169130 196360 188470 150890 TRUE FALSE 162174.0379 168712.0831 170745.6325 169083.8933 146118.8086 163272.9857 166401.6756 171966.5677 174289.2506 0.930487895 0.968000508 0.979668178 0.970133802 0.838369596 0.936793205 0.954744341 0.986673401 1 17.41112407 1.266110162 2.533494865 0.998703654 0.939763914 0.257642351 0.039030713 0.419507764 4.481964569 0.035707461 0.010352803 18.45483482 -1.266110162 -0.05893974 SMGTGDTPGLEVPSS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.001)S(0.999)PLR;SMGTGDTPGLEVPS(0.005)S(0.995)PLR;SMGTGDTPGLEVPSS(1)PLR;SMGTGDTPGLEVPS(0.203)S(0.797)PLR;SMGTGDTPGLEVPS(0.001)S(0.999)PLR;SMGTGDTPGLEVPS(0.001)S(0.999)PLR 297.56 2.29E-49 972330000 2094499 1968631 1932444 2185080 2040529 2004189 2271562 2145577 2166673 TRUE FALSE 1995496.183 2169236.737 2021048.469 1965431.607 2396396.612 1934783.432 1924993.497 1957698.903 2502669.583 0.79734704 0.86676913 0.807557051 0.785334037 0.957536156 0.773087844 0.769176047 0.782244255 1 21.2550364 -2.284842226 2.322893003 1.835530912 0.81792098 0.504352824 0.056891764 4158834.825 881373.1934 18134786.26 0.013302695 0.005189885 2.284842226 -1.017609933 SMIEISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMIEISR 7 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 150.17 0.0045767 199893000 341910 312090 291730 365700 366120 290880 346690 331180 389240 FALSE TRUE 325748.5919 343892.3258 305106.1091 328939.1412 429971.2121 280806.7527 293796.0731 302180.1235 449601.3512 0.724527609 0.764882768 0.678614751 0.731624005 0.95633879 0.624568302 0.653459053 0.672106796 1 18.77828685 4.761937901 18.84703316 0.740613496 0.724527228 0 0.126529735 676.247552 1066510.216 0.027717144 0.340472427 57801.33929 -4.761937901 -0.016086269 SMIGSTAQQFLTFLSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMIGSTAQQFLTFLSHR 17 0 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 77.468 0.01772 17404000 35039 23766 36072 29624 35498 29941 51242 27113 24478 FALSE TRUE 33382.77591 26187.78242 37725.93688 26646.13924 41688.83996 28904.13566 43424.09178 24738.84198 28273.92322 1.180691326 0.92621679 1.334301454 0.942428082 1.474462516 1.022289529 1.535835386 0.874970261 1 14.78718446 2.770221592 24.99937046 1.227538832 1.090291561 0.011213201 0.233504943 1719.13773 1357420.626 0.063409222 0.067248991 589.1441806 -2.770221592 -0.137247271 SMIIDRR ddPTM_SK-BR-3_Trastuzumab_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 ; 129.68 0.0058311 577280000 464210 409280 358100 466820 447500 407840 523590 454880 495020 FALSE TRUE 442267.7133 450986.0973 374519.2392 419894.3667 525543.8583 393716.3985 443706.7291 415048.2957 571785.1734 0.773485802 0.788733458 0.654999914 0.734356864 0.919128167 0.68857399 0.776002509 0.725881529 1 19.12511369 -1.082183669 4.389259487 1.000019317 0.760500302 0.539244921 0.070359803 1.42E-05 2.97E-06 0.062657216 0.014767065 0.082759209 1.082183669 -0.239519015 SMNLRPEEDDIPWEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMNLRPEEDDIPWEDLR 17 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 63.145 0.05116 44220000 29050 33287 25703 36081 23879 28814 26836 30902 26882 FALSE TRUE 27676.86407 36678.98314 26881.50797 32454.06933 28043.49004 27816.16396 22741.67532 28196.05706 31050.72327 0.89134362 1.181260186 0.865728883 1.045195278 0.903150944 0.895829824 0.732404045 0.908064421 1 14.92233925 2.501213565 2.245420774 0.847500068 1.009164538 0.15503547 0.109635608 0.362354809 3.680733303 0.040320913 0.034093178 317.1126489 -2.501213565 0.16166447 SMQHS(ph)PNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 1 SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;S(0.002)MQHS(0.998)PNLR;S(0.004)MQHS(0.996)PNLR;S(0.001)MQHS(0.999)PNLR 148.78 5.74E-05 6246310000 2776290 2027910 2553570 2854190 3536720 1970300 2828040 2190990 2547390 TRUE FALSE 2645060.274 2234556.335 2670653.71 2567281.399 4153522.848 1902068.017 2396570.557 1999135.3 2942426.231 0.898938517 0.759426459 0.90763659 0.872504932 1.411597954 0.646428446 0.814487899 0.679417305 1 21.48857482 SMQNHAAVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMQNHAAVFR 10 0 P31040;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 67.726 0.054369 0 58045 56145 45293 58181 58692 49470 66927 74140 60216 FALSE TRUE 55301.32788 61866.23933 47369.72885 52332.53534 68927.86622 47756.8415 56716.05695 67647.90856 69553.98974 0.795084913 0.889470749 0.681049772 0.752401631 0.990998021 0.686615415 0.815424926 0.97259566 1 16.08584565 1.224716005 5.248542557 0.992980954 0.804702066 0.418710078 0.090730218 0.166011756 12.58649393 0.073078525 0.020852588 16.77706569 -1.224716005 -0.188278888 SMS(ph)APGNLLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMSAPGNLLVK 11 0 J3KPJ3;Q8N5S9 J3KPJ3 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 1 S(0.016)MS(0.984)APGNLLVK 83.314 0.01312 0 48897 45812 48912 60699 47899 52641 62968 60276 79989 TRUE FALSE 46585.73571 50480.29488 51154.66358 54597.4212 56252.57043 50818.02897 53361.07511 54997.9139 92393.28559 0.504211268 0.54636324 0.553662133 0.590924122 0.608838295 0.550018637 0.577542781 0.595258774 1 16.49550039 -5 0.287039887 4.362290567 0.535180165 0.96844589 0.024812269 40.42041875 0.38260297 81.22210944 0.028594185 1.00E-05 5 -3.827110403 SMS(ph)APSDLEMIGNEDLEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.013)MS(0.968)APS(0.019)DLEMIGNEDLEFTR;S(0.014)MS(0.983)APS(0.003)DLEMIGNEDLEFTR 209.25 5.11E-22 134492000 34663 26543 33487 38870 35927 29211 40424 35041 40050 TRUE FALSE 33024.54869 29247.76188 35022.41207 34962.71375 42192.65743 28199.41575 34256.57636 31972.62428 46260.74945 0.713878376 0.632237096 0.757065385 0.75577491 0.912061692 0.609575419 0.740510622 0.691139349 1 15.49750102 -2.048988407 2.454513955 1.368204894 0.720881617 0.521985725 0.082085657 7856412.428 2756674.962 16235800.73 0.019218405 0.008933293 2.048988407 -0.647323276 SMS(ph)FQGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SMSFQGIR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 SMS(1)FQGIR;S(0.003)MS(0.997)FQGIR;S(0.001)MS(0.999)FQGIR;SMS(1)FQGIR 160.33 0.00037128 383692000 448193 327801 332861 512136 491617 443411 504428 371373 522439 TRUE FALSE 427007.8051 361204.2946 348123.0061 460655.1163 577354.8491 428055.5659 427468.2441 338853.6113 603456.1719 0.707603675 0.598559285 0.576882005 0.763361347 0.956746945 0.709339942 0.708366679 0.561521494 1 19.20288947 3.220848209 23.60391982 0.767712936 0.632858612 0.239199237 0.128690423 193.8587374 258339.0535 0.035668935 0.042740324 1662.831371 -3.220848209 -0.134854325 SMS(ph)VDLSHIPLKDPLLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.104)MS(0.895)VDLS(0.001)HIPLKDPLLFK;S(0.002)MS(0.993)VDLS(0.005)HIPLKDPLLFK 195.39 1.46E-15 556650000 3008900 2247120 2447110 3423290 2794490 3181540 3947770 3059840 2434790 TRUE FALSE 2866675.26 2476104.083 2559312.414 3079174.385 3281848.171 3071362.472 3345465.181 2791904.188 2812364.798 1.019311315 0.880434887 0.910021494 1.094870192 1.166935446 1.092092489 1.189555915 0.992724767 1 21.42335231 3.210714657 8.082809959 1.108888129 0.936350601 0.489095428 0.071794725 0.139148738 33.64429334 0.019343049 0.023522284 1624.48108 -3.210714657 -0.172537527 SMSCPSTGLTEDILTHIGNVASSVPVENFTIHGGLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMSCPSTGLTEDILTHIGNVASSVPVENFTIHGGLSR 37 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 256.93 2.26E-62 35469000 37833 25381 31439 28673 37568 25541 39961 28910 30666 FALSE TRUE 36044.70907 27967.35276 32880.50925 25790.73556 44119.84731 24656.50877 33864.21552 26378.48714 35421.52666 1.017593324 0.789558085 0.92826347 0.728109091 1.245565944 0.696088257 0.956034895 0.744702152 1 15.11233877 -1.006571379 5.302738264 0.9999962 0.890493464 0.043444943 0.164505393 9.80E-07 1.84E-07 0.13588028 0.032027116 0.098498274 1.006571379 -0.109502736 SMSHQAAIASQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMSHQAAIASQR 12 0 Q4G0F5 Q4G0F5 VPS26B Vacuolar protein sorting-associated protein 26B 0 ; 78.763 0.012051 18744000 16894.1 14869.3 16115.9 15784.5 23137.7 16603.7 21319.5 13509 20285.9 FALSE TRUE 16095.54937 16384.49857 16854.82996 14197.81207 27172.90755 16028.70971 18066.81872 12326.08034 23431.73377 0.686912438 0.699243971 0.719316382 0.605922388 1.159662696 0.684059911 0.771040628 0.526042181 1 14.51617609 SMSSIPPYPAS(ph)SLASSSPPGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPY(0.149)PAS(0.189)S(0.189)LAS(0.149)S(0.149)S(0.149)PPGS(0.025)GR 55.899 0.097696 62876000 37343 30517 34411 37831 35456 32367 39711 36680 39785 TRUE FALSE 35577.8704 33626.71699 35988.77839 34028.15601 41639.51517 31246.12267 33652.35761 33468.10475 45954.65461 0.774195143 0.731736911 0.78313674 0.740472457 0.906100057 0.679933794 0.732294865 0.728285416 1 15.48792337 -1.155627861 5.41289483 1.000006533 0.757011508 0.619857695 0.059155746 4.32E-06 6.74E-07 0.053051628 0.012504053 0.069883096 1.155627861 -0.242995025 SMSSIPPYPASSLASS(ph)SPPGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLAS(0.136)S(0.541)S(0.317)PPGS(0.006)GR 141.07 1.97E-07 95621000 36576 31934 28896 38891 35824 32504 37787 32980 40826 TRUE FALSE 34847.12497 35188.11091 30220.91018 34981.60279 42071.69426 31378.37833 32021.89914 30092.09636 47157.08757 0.738958379 0.746189231 0.640856163 0.741810078 0.892160573 0.665401108 0.679047431 0.638124573 1 15.525187 -1.527719089 3.184299811 1.008770094 0.719852058 0.591884201 0.073621204 19272694.91 25979711.29 1484772.062 0.017553205 0.029667497 1.527719089 -0.288918035 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLASS(0.043)S(0.957)PPGSGR;SMSSIPPYPASSLAS(0.007)S(0.05)S(0.943)PPGSGR 399.22 9.21E-138 143036000 116054 99780 103813 114669 106833 104644 129184 117328 118265 TRUE FALSE 110568.3574 109947.6954 108572.9287 103142.2543 125464.6414 101020.152 109474.6082 107054.1383 136604.9322 0.809402381 0.8048589 0.794795085 0.755040485 0.918448839 0.739505891 0.801395721 0.783676963 1 17.05965005 -0.980445218 4.535522697 1.000004365 0.800994078 0.636646706 0.047272565 0.013786149 25160996.87 279.2483244 0.009742143 0.104605563 0.980445218 -0.199010286 SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR 32 1 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 0 204.58 3.30E-27 107830000 111040 101300 102740 122700 101020 105820 136190 116290 89879 FALSE TRUE 105791.3593 111622.5852 107450.7306 110365.9629 118637.856 102155.4269 115411.7142 106107.0311 103816.9763 1.01901792 1.075186248 1.035001543 1.06308204 1.142759694 0.983995398 1.111684412 1.022058578 1 16.66368285 1.01008502 24.47097995 0.999999972 1.060996546 0.190997028 0.044506293 185.189625 449354.0344 0.037684353 0.009421088 10.23493338 -1.01008502 0.060996574 SMVNTKPEKTEEDSEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SMVNTKPEKTEEDSEEVR 18 2 Q16543 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 150.7 2.98E-08 301520000 514450 443890 447380 572750 274250 547960 578440 617280 300540 FALSE TRUE 490132.968 489122.8957 467892.8155 515176.0818 322079.1132 528984.0078 490188.3542 563227.6908 347146.2083 1.41189204 1.408982394 1.347826375 1.484032 0.927790958 1.523807535 1.412051587 1.622450937 1 18.40518389 SNAAAYLQHLCYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 126.95 0.00018262 603370000 469370 399370 398500 401750 454370 373480 472460 490150 501660 FALSE TRUE 447183.8103 440066.257 416771.6192 361365.3267 533611.9841 360546.294 400377.5497 447229.8676 579454.8707 0.771731903 0.759448715 0.719247762 0.623629803 0.920886183 0.622216349 0.690955534 0.771811387 1 19.14433678 0.921675136 9.495290795 0.999999959 0.730644513 0.501356534 0.084079181 4.370286852 530.1912454 0.074391718 0.018611531 8.349781978 -0.921675136 -0.269355446 SNDRNS(ph)MDIQCEVDALLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SNDRNSMDIQCEVDALLER 19 1 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 S(0.023)NDRNS(0.977)MDIQCEVDALLER;S(0.007)NDRNS(0.993)MDIQCEVDALLER;S(0.014)NDRNS(0.986)MDIQCEVDALLER;S(0.054)NDRNS(0.946)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.006)NDRNS(0.994)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.07)NDRNS(0.93)MDIQCEVDALLER;S(0.181)NDRNS(0.819)MDIQCEVDALLER;S(0.202)NDRNS(0.798)MDIQCEVDALLER;S(0.006)NDRNS(0.994)MDIQCEVDALLER 252.39 4.56E-31 642285600 482000.6 457904 475567.9 510041.9 480441.5 490483.6 551912.5 519728.2 531727.2 TRUE FALSE 459217.3869 504564.9382 497373.1586 458771.5192 564230.3455 473498.0299 467708.1116 474218.0436 614184.7385 0.747686092 0.821519824 0.809810351 0.746960142 0.918665525 0.770937473 0.761510474 0.77210978 1 19.22831314 -1.132801211 5.056977704 1.000008528 0.792865251 0.622219875 0.050527335 4.52E-06 7.76E-07 0.045547111 0.010735115 0.073654416 1.132801211 -0.207143277 SNDS(ph)GEEAEKEFIFV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SNDS(1)GEEAEKEFIFV;S(0.001)NDS(0.999)GEEAEKEFIFV;S(0.002)NDS(0.998)GEEAEKEFIFV 184.22 1.24E-06 699898000 1426620 1327080 1446780 1583100 948290 1537920 1739440 1741040 1040510 TRUE FALSE 1359186.5 1462310.961 1513116.294 1423963.78 1113671.476 1484661.445 1474056.481 1588585.308 1201866.977 1.130895953 1.216699509 1.25897152 1.184793166 0.926617918 1.23529598 1.226472238 1.32176467 1 20.1968458 SNEDQSMGNWQIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 309.23 1.80E-55 6562170000 2265010 1480271 2015900 2381120 2102110 2428840 2946540 2694750 2431020 FALSE TRUE 2157947.466 1631112.298 2108331.009 2141765.294 2468717.318 2344728.662 2496991.206 2458783.404 2808010.166 0.768497028 0.580878345 0.750827413 0.762734167 0.879169651 0.835014307 0.889238663 0.875631945 1 21.42111673 2.940027754 1.31972433 0.894381181 0.675596345 0.683094898 0.062729049 0.225834809 0.815812759 0.023917146 0.027119647 871.0192508 -2.940027754 -0.218784836 SNEEGSEEKGPEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;; 222.57 3.51E-12 1176365000 2285146 1974608 2062103 2618465 1520997 2439822 2640728 2643824 1731928 FALSE TRUE 2177131.677 2175822.8 2156652.462 2355251.923 1786258.395 2355330.352 2237836.443 2412316.755 2000506.549 1.088290203 1.08763593 1.078053188 1.177327775 0.892903048 1.177366979 1.1186349 1.205852966 1 20.93193392 SNEHDHS(ph)KSKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNEHDHSKSKEK 12 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SNEHDHS(0.5)KS(0.5)KEK 63.037 0.034913 28248000 65651 49272 63971 68245 29931 71425 76169 78021 1332 TRUE FALSE 62547.80734 54292.87282 66904.13363 61384.88294 35150.95692 68951.53434 64548.02011 71189.06762 1538.559757 40.65347937 35.28811446 43.48491069 39.89762676 22.84666342 44.8156362 41.95353467 46.26993999 1 10.58736476 -1.315790613 4.25494158 0.953897098 39.19826418 0.769384899 6.606404291 15305922.04 6151345.143 6572312.166 1.469878097 0.048329176 1.315790613 38.24436708 SNEHDHSKS(ph)KEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNEHDHSKSKEK 12 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SNEHDHS(0.114)KS(0.886)KEK;SNEHDHS(0.006)KS(0.994)KEK;SNEHDHS(0.007)KS(0.993)KEK 127.57 0.00012697 82333000 202538 175487 202406 223645 85866 239153 256225 265093 15878.5 TRUE FALSE 192964.4301 193369.3248 211686.5153 201163.7797 100841.0032 230871.0716 217133.1704 241880.0516 18340.85668 10.5210151 10.54309121 11.54180085 10.9680689 5.498162106 12.58780196 11.83876926 13.18804545 1 14.16277341 2.896865391 18.53834952 9.813835817 10.83068524 0.036845818 3.65446414 25.68072688 4585.469652 1.02460331 1.086762973 788.6156486 -2.896865391 1.016849425 SNFAEALAAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNFAEALAAHK 11 0 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 ;; 144.57 3.67E-05 3391660000 7204260 5856280 4857300 5522840 5253000 5638980 7188200 6468280 5410620 FALSE TRUE 6863728.907 6453041.59 5080012.01 4967673.63 6169121.537 5443700.709 6091508.07 5901883.113 6249671.316 1.098254382 1.032540955 0.812844669 0.794869583 0.987111358 0.871037921 0.97469255 0.944350961 1 22.57534889 3.928745313 6.204994606 0.910894487 1.074367237 0.462575662 0.070099963 0.172456504 11.92407189 0.017756783 0.032654323 8486.826289 -3.928745313 0.16347275 SNFLNCYVSGFHPSDIEVDLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNFLNCYVSGFHPSDIEVDLLK 22 0 P61769 P61769 B2M Beta-2-microglobulin;Beta-2-microglobulin form pI 5.3 0 221.04 9.67E-26 119620000 167740 125590 147580 159110 159100 136430 204550 192900 166480 FALSE TRUE 159811.2626 138387.7638 154346.689 143115.9605 186846.9896 131705.3949 173342.1407 176008.6534 192296.8681 0.831065343 0.719656878 0.80264796 0.744244885 0.971659037 0.684906604 0.901429869 0.915296516 1 17.55297574 1.277184693 1.545465088 0.993834915 0.791361099 0.431889648 0.080061442 0.311286675 1.371544835 0.066297922 0.020249351 18.93148549 -1.277184693 -0.202473816 SNGELSES(ph)PGAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNGELSESPGAGK 13 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 SNGELS(0.043)ES(0.957)PGAGK;SNGELS(0.005)ES(0.995)PGAGK 201.65 1.05E-07 276864000 683770 718610 688490 799670 505330 778380 826470 817410 591990 TRUE FALSE 651449.5472 791837.176 720057.9475 719285.6523 593459.392 751424.5054 700376.8223 745833.247 683792.7857 0.952700234 1.158007502 1.053035309 1.05190588 0.867893614 1.098906746 1.024253015 1.090729915 1 19.38319968 -1.607977395 2.746419149 0.996619958 1.040376308 0.019460358 0.080131081 27168789.08 30017505.3 672252.4079 0.018096117 0.024661677 1.607977395 0.04375635 SNMGHPEPASGLAALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNMGHPEPASGLAALAK 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 ;; 157.11 3.78E-08 552330000 1223790 1009220 1136980 1323540 954030 1234480 1412210 1368800 1113110 FALSE TRUE 1165943.872 1112060.665 1189111.658 1190495.245 1120412.53 1191729.648 1196751.427 1248940.616 1285725.414 0.906837385 0.864928587 0.924856618 0.925932732 0.871424425 0.926892815 0.93079861 0.971389849 1 20.29415114 1.305020912 1.066691615 1.000718314 0.896797472 0.735647815 0.020725059 0.225680488 0.524074063 0.018692685 0.006369692 20.18463551 -1.305020912 -0.103920842 SNNVEMDWVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 169.65 3.87E-05 54169000 131070 96349 114900 128600 111470 117850 145690 134390 123560 FALSE TRUE 124874.5809 106167.0726 120168.2787 115672.8837 130910.3327 113768.8249 123462.3147 122622.0992 142721.0537 0.874955569 0.743878145 0.841980041 0.81048227 0.917246119 0.79714115 0.86506028 0.859173163 1 17.12283865 -2.130174309 0.243577607 1.206102359 0.807757741 0.55947586 0.046004493 23.38402094 0.804333539 2.735688564 0.070386478 0.007410128 2.130174309 -0.398344618 SNNWS(ph)LEDVTASDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 S(0.004)NNWS(0.992)LEDVT(0.001)AS(0.002)DK;SNNWS(1)LEDVTASDK 169.25 3.53E-06 59976000 74479 82941 66038 89636 60896 77177 71474 77552 61153 TRUE FALSE 70958.52527 91392.7822 69065.90762 80625.61898 71516.24312 74504.34114 60569.32859 70761.13575 70636.29491 1.004561824 1.29385017 0.977767983 1.14141914 1.012457451 1.054760038 0.857481677 1.001767375 1 16.10812205 2.425656655 1.276260017 0.944123158 1.124492534 0.263355321 0.097933124 0.458445238 1.498677656 0.051284798 0.035415189 266.4751131 -2.425656655 0.180369377 SNPKS(ph)PQKPIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNPKSPQKPIVR 12 2 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.002)NPKS(0.998)PQKPIVR;S(0.003)NPKS(0.997)PQKPIVR 88.427 0.0078691 897800000 1084310 952500 992900 1219490 669640 1169210 1222330 1235020 746350 TRUE FALSE 1033056.815 1049560.833 1038425.447 1096904.548 786425.004 1128719.965 1035841.109 1126875.102 862090.1462 1.198316464 1.217460654 1.204543924 1.272378014 0.912230592 1.30928299 1.201546165 1.307143002 1 19.71747921 SNQNGKDSKPSSTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNQNGKDSKPSSTPR 15 2 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 62.377 0.045891 30256000 36294 20263 46345 24372 51711 40125 79824 48486 88449 FALSE TRUE 34578.45455 22327.82274 48469.96409 21922.08026 60729.38203 38735.46119 67645.38273 44240.3088 102165.2192 0.338456226 0.218546223 0.474427251 0.214574788 0.594423254 0.379145285 0.662117531 0.433027102 1 16.64054461 -2.119415028 0.145528782 1.909193966 0.117473738 0.72096818 0.122991457 21.37218359 0.431452471 7.184027141 0.707878815 0.007596 2.119415028 -1.791720228 SNRDELELELAENRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNRDELELELAENRK 15 2 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 68.257 0.029904 128180000 48215 43914 47123 46664 40873 43155 55803 55166 45149 FALSE TRUE 45935.9725 48388.88653 49283.63616 41973.24606 48001.23826 41660.53153 47289.22746 50335.37259 52150.47633 0.880835147 0.927870461 0.945027536 0.804848757 0.920437197 0.798852368 0.90678419 0.965194877 1 15.67039281 1.190576373 3.241423555 0.995483621 0.884203198 0.437023363 0.048039928 0.218519485 4.082652322 0.041722699 0.011459597 15.50873491 -1.190576373 -0.111280423 SNRNS(ph)IER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SNRNSIER 8 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 SNRNS(1)IER;SNRNS(1)IER;SNRNS(1)IER;SNRNS(1)IER;SNRNS(1)IER;SNRNS(1)IER 135.99 0.00049071 840262000 1065019 925997 915330 1082066 989071 953787 1108488 1003362 1044227 TRUE FALSE 1014677.663 1020357.147 957298.7859 973294.6699 1161564.669 920757.117 939367.7968 915502.3041 1206160.39 0.841246049 0.84595478 0.793674534 0.806936356 0.963026708 0.763378672 0.778808361 0.759022027 1 20.20199033 SNS(ph)APLIHGLSDTSPVFQAEAPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.26)NS(0.74)APLIHGLSDTSPVFQAEAPSAR 267.46 8.98E-46 736320000 469240 348570 397970 449030 411940 453640 476820 449260 374690 TRUE FALSE 447059.9551 384089.6793 416217.3181 403892.6513 483782.2056 437930.3331 404072.3516 409920.4127 432795.0115 1.032960046 0.887463277 0.9616962 0.933219285 1.117809107 1.011865482 0.933634494 0.947146806 1 18.72332435 7.320711308 7.136353159 0.975534293 1.014174718 0 0.064771706 0 0 0.014105934 0 20927208.83 -7.320711308 0.038640424 SNS(ph)AWQIYLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SNSAWQIYLQR 11 0 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 S(0.013)NS(0.987)AWQIYLQR;SNS(1)AWQIYLQR;SNS(1)AWQIYLQR;S(0.001)NS(0.999)AWQIYLQR;S(0.001)NS(0.999)AWQIYLQR 222.55 7.97E-12 1172770000 780642 661771 676629 741690 790743 648020 952820 844673 873439 TRUE FALSE 743742.5997 729206.2173 707653.1089 667133.9121 928648.3288 625578.9049 807449.8093 770708.9542 1008887.459 0.737190846 0.722782517 0.701419274 0.661257017 0.92046771 0.620068075 0.800336848 0.76391965 1 19.94433382 -3.119737 0.279486852 1.581257465 0.717178528 0.520822955 0.0795344 51.18402451 1.272056427 17.41414363 0.081921158 0.000759037 3.119737 -0.864078937 SNS(ph)DNNLNASAPDWAVCSTATSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.187)NS(0.813)DNNLNASAPDWAVCSTATSHR;S(0.242)NS(0.758)DNNLNASAPDWAVCSTATSHR;S(0.204)NS(0.796)DNNLNASAPDWAVCSTATSHR;S(0.2)NS(0.8)DNNLNASAPDWAVCSTATSHR 312.24 1.09E-73 1016460000 375386 294139 348214 361269 312196 308705 366104 333847 301169 TRUE FALSE 357642.2477 324112.0985 364179.9563 324953.5538 366642.8836 298014.4684 310248.1108 304613.5868 347872.7504 1.028083537 0.931697289 1.046876928 0.934116149 1.053956894 0.856676667 0.891843671 0.875646588 1 18.40820015 2.229767708 24.99995861 0.895032018 0.991656567 0.396608269 0.055816117 167.3103305 475692.1665 0.018195652 0.013641258 169.7335554 -2.229767708 0.096624548 SNS(ph)ELEDEILCLEK ddPTM_SK-BR-3_Trastuzumab_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(0.122)NS(0.878)ELEDEILCLEK 188.04 9.22E-07 18874000 38489 27568 34073 47133 30731 39007 46753 41925 30675 TRUE FALSE 36669.70125 30377.21054 35635.28075 42395.10129 36090.47667 37656.17781 39619.97117 38253.82474 35431.92233 1.034934004 0.857340176 1.005739413 1.196522754 1.018586469 1.062775467 1.118199876 1.079642938 1 15.11276212 3.472884786 24.99511587 1.08490393 0.943704199 0.40159966 0.067883097 92.24417202 544235.8563 0.017198171 0.023380034 2970.877784 -3.472884786 -0.141199731 SNS(ph)FIGVPNGEVEMPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 S(0.16)NS(0.84)FIGVPNGEVEMPLK;SNS(1)FIGVPNGEVEMPLK 183.54 7.19E-10 60493000 131635 135354 119888 172443 93677 157206 156378 138763 97002 TRUE FALSE 125412.8744 149146.7265 125384.9834 155108.702 110014.2391 151761.9168 132519.664 126612.1761 112044.5747 1.119312334 1.331137423 1.119063406 1.38434817 0.981879215 1.354478047 1.182740568 1.130016124 1 16.77371327 0.964265696 2.282244889 1.001326515 1.21785534 0.234495421 0.122547669 0.419006007 4.842707605 0.09975367 0.027286366 9.210128644 -0.964265696 0.216528825 SNS(ph)FSDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.004)NS(0.969)FS(0.027)DER;S(0.045)NS(0.95)FS(0.005)DER;S(0.018)NS(0.931)FS(0.051)DER;S(0.108)NS(0.85)FS(0.041)DER;S(0.033)NS(0.962)FS(0.005)DER;S(0.004)NS(0.993)FS(0.002)DER;SNS(0.994)FS(0.006)DER 185.99 0.00022011 11726512000 10237480 12702030 8747451 12229500 7903642 10581700 9369980 10591990 6985144 TRUE FALSE 9753574.609 13996381.3 9148530.281 11000167.43 9282034.662 10215253.08 7940417.46 9664499.204 8068364.456 1.208866389 1.734723484 1.133876677 1.363370171 1.150423325 1.266087214 0.98414214 1.197826307 1 22.94384482 2.740965523 0.821464621 1.064534609 1.445937502 0.339574359 0.172207409 0.582205569 0.843795402 0.104436444 0.098855149 550.7639713 -2.740965523 0.381402893 SNS(ph)GRELTDEEILASVMIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.065)NS(0.483)GRELT(0.452)DEEILASVMIK;S(0.202)NS(0.798)GRELTDEEILASVMIK;S(0.187)NS(0.813)GRELTDEEILASVMIK;S(0.142)NS(0.587)GRELT(0.271)DEEILASVMIK 228.19 1.66E-19 648871000 1155760 885358 1072019 1122870 845818 1108430 1377160 1246650 1040830 TRUE FALSE 1101129.515 975576.9868 1121172.132 1009996.974 993328.3914 1070044.791 1167048.949 1137486.717 1202236.601 0.915900842 0.81146838 0.93257195 0.840098342 0.826233697 0.890045096 0.970731508 0.946142146 1 20.19728942 1.813362692 3.536479144 0.969916999 0.864045622 0.610263783 0.0390922 0.150468225 3.34102794 0.019096227 0.009946847 65.06728593 -1.813362692 -0.105871377 SNS(ph)LDKHQQSSTLGNSVVR ddPTM_SK-BR-3_Trastuzumab_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(0.33)NS(0.67)LDKHQQSSTLGNSVVR 222.4 1.48E-19 244800000 490950 444880 443940 536070 328090 499750 590390 547470 341830 TRUE FALSE 467743.7665 490213.7778 464295.0881 482183.2251 385308.7921 482443.5322 500315.1622 499530.6245 394839.2506 1.184643537 1.241552802 1.175909151 1.221214012 0.975862434 1.221873285 1.267136338 1.265149358 1 18.59090589 3.407474629 2.640108925 1.173949021 1.211920451 0.028908768 0.101616934 1.353141713 19.08011418 0.029318919 0.043355023 2555.49261 -3.407474629 0.037971431 SNS(ph)LPHSAVSNAGSK ddPTM_SK-BR-3_Trastuzumab_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(0.227)NS(0.773)LPHSAVSNAGSK;S(0.214)NS(0.784)LPHS(0.001)AVSNAGSK 281.36 6.00E-34 896140000 1214860 972180 1051100 1378110 948890 1159530 1459510 1335950 967690 TRUE FALSE 1157435.975 1071246.247 1099293.975 1239579.765 1114376.116 1119375.185 1236834.944 1218967.136 1117754.423 1.035501137 0.958391419 0.983484343 1.108991151 0.996977594 1.001450017 1.106535495 1.090550045 1 20.09217182 3.273500582 24.99390147 1.05359114 0.991307606 0.260614434 0.046105896 226.1034719 161739.1464 0.012571213 0.017020725 1877.156935 -3.273500582 -0.062283534 SNS(ph)LSTPRPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.046)NS(0.927)LS(0.026)T(0.001)PRPTR 98.592 0.0032736 385200000 427480 466420 415170 502570 698000 342660 559310 405380 774050 TRUE FALSE 407273.8676 513948.7283 434205.9552 452050.7088 819730.979 330793.5983 473976.9871 369882.7781 894085.7207 0.455519933 0.574831603 0.485642422 0.505601083 0.916837122 0.369979735 0.53012477 0.413699458 1 19.77005363 -1.684889934 2.958654288 1.054595198 0.532794589 0.495148465 0.148656734 22348160.44 21336685.27 9146256.809 0.033615468 0.020659037 1.684889934 -0.521800609 SNS(ph)LVSTFTMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SNSLVSTFTMEK 12 0 Q9HB21 Q9HB21 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 S(0.002)NS(0.998)LVSTFTMEK;SNS(0.998)LVS(0.002)TFTMEK;SNS(0.771)LVS(0.227)T(0.002)FTMEK;SNS(1)LVSTFTMEK;SNS(0.992)LVS(0.008)TFTMEK;S(0.023)NS(0.974)LVS(0.002)T(0.001)FTMEK;S(0.031)NS(0.969)LVSTFTMEK;S(0.012)NS(0.985)LVS(0.002)TFTMEK 320.06 1.19E-46 617196000 2594059 2229500 1942368 2435833 1671639 2175974 2455381 2525353 1692767 TRUE FALSE 2471442.972 2456688.585 2031427.494 2190978.439 1963172.312 2100619.475 2080767.532 2304219.704 1955272.661 1.263988916 1.256442968 1.038948447 1.120548803 1.004040179 1.074335829 1.064182799 1.178464646 1 20.89893837 3.74527439 24.5378411 1.070696608 1.260215966 0.69846688 0.05231568 184.9489476 675958.4072 0.01216271 0.02129623 5562.555922 -3.74527439 0.189519358 SNS(ph)MLELAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNSMLELAPK 10 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 SNS(1)MLELAPK;SNS(1)MLELAPK;S(0.007)NS(0.993)MLELAPK 146.88 2.92E-05 337474000 853470 771940 772450 877360 643750 853470 989690 961980 677770 TRUE FALSE 813128.1645 850601.5636 807867.5966 789166.1059 756019.7962 823914.1199 838694.6136 877743.9314 782875.11 1.038643526 1.086509908 1.031923976 1.008035759 0.965696554 1.05242089 1.071300649 1.12118002 1 19.57842265 2.002378614 24.99049693 1.069527089 1.032805134 0.139924077 0.041554965 149.569406 1571411.395 0.015993015 0.011732966 100.5491987 -2.002378614 -0.036721955 SNS(ph)PDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SNSPDKFK 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.006)NS(0.994)PDKFK;SNS(1)PDKFK;S(0.002)NS(0.998)PDKFK;S(0.001)NS(0.999)PDKFK;S(0.003)NS(0.997)PDKFK 145.01 0.00034895 5582020000 14209250 15937600 11180410 15927200 5076460 14379640 11659210 14497660 4186100 TRUE FALSE 13537606.91 17561659.56 11693042.86 14326167.6 5961793.017 13881669.46 9880383.378 13228168.03 4835259.008 2.799768717 3.63199976 2.418286763 2.962854228 1.232983178 2.870925722 2.043403127 2.735772378 1 22.20516174 3.248655309 1.778614863 2.131846652 3.177238321 0.309063669 0.665981835 0.376159021 2.455447446 0.1917031 0.271801413 1772.781902 -3.248655309 1.045391669 SNS(ph)PGTASSGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNSPGTASSGSSR 13 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 SNS(0.985)PGT(0.015)ASSGSSR;SNS(0.996)PGT(0.004)ASSGSSR;S(0.002)NS(0.947)PGT(0.051)AS(0.001)SGSSR;S(0.007)NS(0.97)PGT(0.02)AS(0.004)SGSSR 258.61 6.39E-24 422229000 444350 489499 453713 526610 421453 484756 531599 491700 456233 TRUE FALSE 423346.4561 539379.5046 474516.1898 473674.1623 494954.2698 467968.7782 450493.8091 448644.1413 526983.2835 0.80333944 1.023522987 0.900438789 0.898840963 0.939221955 0.888014464 0.854854078 0.851344161 1 19.00739767 2.09398191 8.015633651 0.882366308 0.916857801 0 0.067426309 0.77685339 58.15638437 0.023823237 0.017570582 124.1600591 -2.09398191 0.034491494 SNS(ph)PLPVPPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.005)NS(0.995)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;S(0.009)NS(0.99)PLPVPPSK;SNS(1)PLPVPPSK;S(0.004)NS(0.996)PLPVPPSK 176.58 8.90E-06 3295500000 7299470 8172260 6956040 8543070 4405110 8294460 7789700 8234690 4530200 TRUE FALSE 6954438.519 9005022.585 7274981.314 7684304.373 5173359.789 8007220.77 6601238.197 7513616.889 5232720.279 1.32902929 1.720906547 1.390286682 1.468510443 0.988655902 1.530221442 1.261530876 1.435891179 1 22.31912971 -3.835334631 0.112341666 1.43E-16 1.654656455 0.305513831 0.18724584 130.9699689 1.273806418 32.63968686 2.205897258 0.000146105 3.835334631 1.654656455 SNS(ph)TTQVSQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SNSTTQVSQPR 11 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SNS(0.776)T(0.202)T(0.022)QVSQPR;SNS(0.574)T(0.37)T(0.055)QVSQPR;SNS(0.822)T(0.164)T(0.014)QVSQPR;SNS(0.973)T(0.025)T(0.002)QVSQPR;S(0.005)NS(0.869)T(0.029)T(0.097)QVSQPR;S(0.005)NS(0.885)T(0.09)T(0.019)QVS(0.001)QPR 232.92 1.93E-15 701904000 718175 650364 715441 788889 661451 736883 818478 750092 742080 TRUE FALSE 684228.291 716636.831 748244.6775 709588.3789 776807.845 711364.5569 693604.1487 684409.968 857157.9764 0.798252259 0.836061555 0.872936726 0.827838506 0.906259834 0.829910678 0.809190567 0.798464212 1 19.7092016 -2.530158693 2.258786191 3.619464026 0.83378638 0.708773918 0.033259938 1492388.57 170898.1557 20116767.67 0.008097351 0.002950131 2.530158693 -2.785677646 SNS(ph)VGIQDAFNDGSDSTFQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNSVGIQDAFNDGSDSTFQKR 21 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 S(0.427)NS(0.573)VGIQDAFNDGSDSTFQKR;S(0.034)NS(0.966)VGIQDAFNDGSDSTFQKR 177.82 3.88E-17 573050000 542460 377409 527343 512040 428805 551000 672290 595131 553829 TRUE FALSE 516818.9909 415867.4062 551522.1982 460568.7664 503588.4562 531918.7318 569719.813 543018.1747 639713.9728 0.807890734 0.650083356 0.86213874 0.71996046 0.78720878 0.831494628 0.890585226 0.848845262 1 19.28706747 1.384986356 0.484659351 0.999788228 0.735320983 0.612030929 0.058793409 0.518522642 0.324087432 0.059311229 0.035260099 24.2653386 -1.384986356 -0.264467245 SNS(ph)WVNTGGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNSWVNTGGPK 11 0 Q96N67-2;Q96N67-6;Q96N67;A0A1B0GWE0;A0A0U1RRC1 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SNS(1)WVNTGGPK;SNS(1)WVNTGGPK;SNS(1)WVNTGGPK 236.22 1.59E-15 493780000 1063260 871970 923830 1115700 723840 1089030 1201040 1092220 782320 TRUE FALSE 1013001.807 960824.7343 966188.5193 1003547.716 850077.4668 1051316.618 1017799.289 996579.4266 903638.1901 1.121025891 1.06328478 1.069220546 1.110563639 0.94072769 1.163426501 1.126334965 1.102852267 1 19.78538572 SNSDES(ph)NFSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNSDESNFSEK 11 0 A0A087WWW9;O95999 A0A087WWW9 BCL10 B-cell lymphoma/leukemia 10 1 SNS(0.045)DES(0.947)NFS(0.008)EK 167.09 0.00081173 0 271640 264630 262520 341970 194240 335960 315670 289720 176990 TRUE FALSE 258800.1155 291596.0979 274556.8017 307594.5259 228115.3945 324325.621 267508.7438 264350.5809 204436.7053 1.265918051 1.426339255 1.342991716 1.504595398 1.11582406 1.586435374 1.308516215 1.293068094 1 17.64129472 0.749818429 1.982389877 1.000470567 1.368230635 0.443529768 0.127912725 0.813506438 4.981770173 0.105565066 0.029224548 5.621062691 -0.749818429 0.367760068 SNSFS(ph)DER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.135)NS(0.392)FS(0.473)DER 82.494 0.021112 95137000 300580 331540 243770 344750 217110 272100 271130 295570 207400 TRUE FALSE 286372.1791 365324.3029 254947.0956 310095.075 254973.9153 262677.1088 229764.1389 269688.3239 239562.5327 1.195396358 1.52496427 1.064219403 1.29442226 1.064331356 1.096486607 0.959098805 1.12575335 1 17.87004276 2.960737808 1.025333732 1.024997183 1.340239133 0.435679086 0.122809936 0.387407569 0.879780157 0.054811155 0.064187221 913.5615404 -2.960737808 0.31524195 SNSLSEQLAINT(ph)SPDAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 SNSLSEQLAINT(0.683)S(0.317)PDAVK;SNSLSEQLAINT(0.656)S(0.344)PDAVK 230.06 1.72E-18 76969000 189561 171187 171432 204923 133452 183332 206769 207699 147772 TRUE FALSE 180600.8272 188631.1499 179292.3268 184323.7507 156725.9865 176983.1669 175222.5915 189511.7745 170687.727 1.058077404 1.105124271 1.050411356 1.079888718 0.918203021 1.036882791 1.026568193 1.110283544 1 17.3809998 SNT(ph)ENLSQHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.01)NT(0.99)ENLSQHFR;S(0.013)NT(0.987)ENLSQHFR;S(0.184)NT(0.816)ENLSQHFR;S(0.28)NT(0.72)ENLSQHFR 203.93 1.29E-07 955090000 662732 464194 534195 651936 669216 567376 780694 637369 600044 TRUE FALSE 631405.9718 511495.8963 558688.3691 586402.1547 785927.0585 547727.6269 661584.7919 581557.5915 693095.7589 0.910993847 0.737987341 0.806076739 0.846062246 1.133937192 0.790262557 0.954535911 0.8390725 1 19.40269517 2.981164984 24.94498222 0.935257875 0.815828878 0.259069978 0.099734484 975.4988605 1291946.564 0.027725401 0.029871515 957.5577689 -2.981164984 -0.119428997 SNT(ph)PILVDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNTPILVDGK 10 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.009)NT(0.991)PILVDGK;S(0.006)NT(0.994)PILVDGK;S(0.007)NT(0.993)PILVDGK 124.62 0.0048149 238108000 723640 935360 627060 881070 383770 799900 657900 827140 346883 TRUE FALSE 689434.9713 1030674.247 655811.3212 792503.1697 450699.3665 772199.2624 557525.2718 754711.2367 400675.844 1.72068015 2.572339368 1.636762812 1.977916017 1.124847862 1.927241869 1.391462151 1.88359555 1 18.61207601 3.258738952 1.866835326 1.531390598 2.122885995 0.273106148 0.385866425 0.374017148 2.684392539 0.110192327 0.156047553 1814.424713 -3.258738952 0.591495398 SNT(ph)PILVDGKDVMPEVNK ddPTM_SK-BR-3_Trastuzumab_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(0.117)NT(0.883)PILVDGKDVMPEVNK 178.35 1.44E-13 147170000 591200 492690 495650 652630 269900 634890 632490 681320 242750 TRUE FALSE 563255.1476 542895.6711 518376.0428 587026.3925 316970.4745 612903.6001 535992.034 621660.0089 280394.4302 2.008795778 1.936185647 1.84873873 2.093573656 1.130444975 2.18586225 1.911564483 2.217091147 1 18.09709817 SNTENLSQHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;;;; 247.29 4.25E-16 1936420000 1535970 1133111 1145269 1313080 1721490 1154500 1911350 1453040 1861450 FALSE TRUE 1463367.742 1248576.299 1197780.716 1181086.704 2021717.311 1114519.376 1619738.453 1325804.115 2150114.159 0.680600021 0.580702329 0.557077731 0.549313486 0.940283707 0.518353582 0.753326723 0.616620336 1 21.03598183 -5 0.230630964 2.905858665 0.609182736 0.44522966 0.123409513 141.1843673 1.411837099 125.4954048 0.190329774 1.00E-05 5 -2.29667593 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR 38 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 179.58 2.18E-23 373210000 548700 442430 477110 553740 490350 511250 622710 551160 482850 FALSE TRUE 522764.0384 487514.12 498985.9654 498077.0032 575866.8847 493545.2843 527704.1526 502897.5085 557727.9119 0.93731016 0.874107445 0.894676337 0.893046578 1.032522978 0.884921256 0.94616773 0.901689691 1 19.08920195 SNTTSKPSHLVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SNTTSKPSHLVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLR 46 2 Q16576;E9PC52;Q16576-2;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 49.322 0.0067782 78279000 28797 16855 30945 26084 32615 26049 55668 31590 22391 FALSE TRUE 27435.82288 18572.54366 32363.85886 23461.98676 38303.04567 25146.9166 47174.82419 28823.81213 25863.28192 1.060802065 0.718104675 1.251343853 0.907154275 1.48098164 0.97230184 1.824007654 1.114468466 1 14.65861774 2.934522632 1.294353624 1.356564197 0.919999292 0.136848713 0.290983427 0.52250735 1.819727028 0.110079696 0.124216126 860.0478847 -2.934522632 -0.436564905 SNVSDAVAQSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SNVSDAVAQSTR 12 0 P60174;P60174-3;P60174-4 P60174 TPI1 Triosephosphate isomerase 0 ;;; 226.33 3.62E-11 953620000 634190 413759 457835 537100 595350 510623 718900 579493 729870 FALSE TRUE 604213.0955 455921.5125 478827.1876 483109.6876 699178.8515 492939.9975 609218.6015 528749.5208 843054.5119 0.716695169 0.540797192 0.567967054 0.573046797 0.829340027 0.584707146 0.722632514 0.627183075 1 19.68526639 -5 0.244858671 3.11543166 0.608919782 0.616128484 0.088325217 111.993301 1.113656 118.0930161 0.123440631 1.00E-05 5 -2.506511878 SNVVS(ph)PTKNEDNGAPENSVEKPHEKPEAR ddPTM_SK-BR-3_Trastuzumab_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(0.001)NVVS(0.787)PT(0.212)KNEDNGAPENSVEKPHEKPEAR;S(0.005)NVVS(0.498)PT(0.498)KNEDNGAPENSVEKPHEKPEAR 223.16 1.12E-34 440680000 247566 248255 240185 278665 105293 309710 280450 317320 108389 TRUE FALSE 235864.0458 273552.4667 251197.7198 250653.0648 123656.0659 298984.665 237662.2017 289533.7786 125197.4125 1.883937064 2.184969012 2.00641303 2.00206266 0.98768867 2.388105784 1.898299628 2.31261791 1 16.93384522 2.968714635 24.98206325 1.803889836 2.034826329 0.077519568 0.467566592 2101.641577 1678208.789 0.131757089 0.139893872 930.4962667 -2.968714635 0.230936493 SNYNFEKPFLWLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 237.46 2.46E-17 5985300000 8528200 7262300 6528200 8056700 7595600 7891000 10400500 9042000 8608300 FALSE TRUE 8125088.887 8002336.627 6827524.427 7246825.209 8920270.235 7617732.691 8813712.707 8250234.545 9943231.199 0.817147738 0.80480243 0.686650475 0.728819944 0.897119865 0.766122454 0.886403276 0.829733754 1 23.24528332 0.750354063 0.547336812 1.003778138 0.777182568 0.568591538 0.058722573 0.944080393 0.607966634 0.069475051 0.027650254 5.627999662 -0.750354063 -0.226595569 SNYNLPMHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SNYNLPMHK 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 101.65 0.003842 514697000 831520 689420 690230 828980 666060 763780 913560 895350 735140 FALSE TRUE 792215.6975 759672.6818 721877.7282 745649.3554 782220.6531 737330.1071 774179.6433 816948.4075 849141.7566 0.932960476 0.894635879 0.850126286 0.878121173 0.921189715 0.86832393 0.911720142 0.962087191 1 19.69564589 1.145794762 2.368123177 0.998766042 0.893340782 0.713203054 0.023915194 0.153857012 1.583072637 0.02291574 0.00639351 13.98926066 -1.145794762 -0.10542526 SPAAECLSEKETEELMAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPAAECLSEKETEELMAWMR 20 1 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 247.89 3.20E-30 81208000 82742 63739 64836 71467 53958 61741 68651 74839 53788 FALSE TRUE 78830.94964 70234.07657 67808.79473 64283.00138 63368.25812 59602.89369 58177.02909 68285.70041 62129.16833 1.268823513 1.130452547 1.091416424 1.034667019 1.019943769 0.959338348 0.936388345 1.099092459 1 15.92298312 4.092844832 0.715090624 0.985540521 1.32029525 0.787675467 0.044075494 0.556523603 0.378372187 0.019210847 0.131399684 12383.5406 -4.092844832 0.334754729 SPAAPYFLGSSFS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGS(0.001)S(0.007)FS(0.993)PVR 130.92 7.16E-05 0 155070 122840 137660 169670 131480 152270 191920 162110 138040 TRUE FALSE 147740.1484 135357.5357 143971.8472 152614.4492 154410.0704 146996.8517 162639.0791 147914.789 159446.5382 0.926581098 0.848921132 0.902947463 0.957151224 0.968412812 0.921919368 1.020022642 0.92767639 1 17.28271325 3.253487747 3.376285373 0.968722808 0.886099725 0.507426182 0.034232468 0.166154313 3.958304472 0.00939622 0.012414018 1792.617977 -3.253487747 -0.082623083 SPAGLQVLNDYLADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPAGLQVLNDYLADK 15 0 P24534;C9JZW3;F2Z2G2;F8WF65 P24534 EEF1B2 Elongation factor 1-beta 0 162.93 3.65E-06 26183000 137440 143040 128040 156510 113420 143430 144680 141000 109260 FALSE TRUE 130943.4836 157615.9386 133910.7606 140777.3175 133200.4121 138462.9831 122606.4088 128653.2925 126203.4828 1.037558399 1.248903241 1.061070247 1.115478863 1.05544165 1.097140745 0.971497823 1.019411586 1 16.9453922 2.250837055 0.920451501 0.991322908 1.133031488 0.383651846 0.060391523 0.513794912 0.830054583 0.043220624 0.024997996 178.1710155 -2.250837055 0.14170858 SPAGPAATPAQAQAAS(ph)TPR ddPTM_SK-BR-3_Trastuzumab_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(0.645)T(0.355)PR 154.55 3.64E-08 112090000 113340 149710 110210 139350 108090 112630 114590 112270 110860 TRUE FALSE 107982.6428 164965.6192 115263.2375 125342.2733 126940.8618 108729.5949 97107.19091 102439.0436 128051.6026 0.843274435 1.288274538 0.900131159 0.978841894 0.991325834 0.849107646 0.758344206 0.799982519 1 16.96636578 2.263831391 3.057496506 0.820012898 1.02422458 0.219529195 0.131881037 0.287430672 5.559060815 0.050921959 0.038213085 183.5825472 -2.263831391 0.204211682 SPAGPAATPAQAQAAST(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.004)T(0.996)PR;SPAGPAATPAQAQAAS(0.025)T(0.975)PR;SPAGPAATPAQAQAAS(0.376)T(0.624)PR;SPAGPAATPAQAQAAS(0.037)T(0.963)PR 255.47 6.97E-30 772569000 718785 878403 633477 837097 643735 670094 673536 734939 627707 TRUE FALSE 684809.4575 967913.2644 662522.547 752950.4192 756002.1802 646888.4768 570775.7129 670583.845 725048.5957 0.94450146 1.334963298 0.913762955 1.038482694 1.042691738 0.892200165 0.787224079 0.924881241 1 19.46771817 2.650525489 1.138576525 0.872124641 1.108957903 0.226488976 0.126748796 0.507642945 1.356124084 0.064603668 0.054814055 447.2243993 -2.650525489 0.236833261 SPALKS(ph)PLQSVVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)PALKS(0.998)PLQSVVVR;S(0.002)PALKS(0.995)PLQS(0.004)VVVR 70.837 0.026098 602140000 538030 576750 526390 666180 463720 578120 670100 653540 519580 TRUE FALSE 512598.3882 635521.4807 550525.5022 599214.3207 544592.6212 558099.5594 567863.9378 596312.573 600153.8128 0.854111692 1.058931006 0.917307348 0.998434581 0.907421747 0.929927541 0.946197334 0.993599574 1 19.19497277 1.219368415 7.073011326 0.997587886 0.948697708 0.134028785 0.054402091 0.363157207 74.67188642 0.044289307 0.012280265 16.5717516 -1.219368415 -0.048890178 SPALLLSQLLPYMENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPALLLSQLLPYMENR 16 0 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 88.075 0.022221 27418000 43615 37812 43565 37198 41678 34012 45521 40811 45197 FALSE TRUE 41553.40539 41665.08579 45562.49834 33458.78637 48946.63 32834.15591 38575.9354 37237.37249 52205.91993 0.795951981 0.79809121 0.872745819 0.640900235 0.937568576 0.628935492 0.738918794 0.713278734 1 15.67192579 SPALLLSQLLPYMENRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPALLLSQLLPYMENRR 17 1 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 212.9 1.85E-12 2848700000 324550 252386 294520 260681 380680 222292 329070 308610 364580 FALSE TRUE 309209.1647 278104.4203 308024.0333 234476.8506 447070.4715 214593.9723 278864.3277 281586.4724 421117.2044 0.73425916 0.66039672 0.731444904 0.55679713 1.061629558 0.509582534 0.662201223 0.668665325 1 18.68386229 -0.98120337 4.567136905 1.000006033 0.693732961 0.294366284 0.146745893 16532916.95 3619973.496 1126.08634 0.030425687 0.104423112 0.98120337 -0.306273072 SPAPEQFQS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPAPEQFQSR 10 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SPAPEQFQS(1)R 110.58 0.002629 0 70030 76684 63189 71978 74460 58399 71826 69687 88898 TRUE FALSE 66719.82069 84498.18678 66086.27815 64742.63469 87445.80043 56376.62799 60867.62453 63584.83685 102683.8478 0.649759647 0.822896576 0.64358981 0.630504564 0.851602295 0.54903112 0.592767274 0.619229199 1 16.64784974 -0.998287436 8.876904807 0.999975493 0.674375336 0.540013333 0.095660525 1.40E-09 7.86E-11 0.093646296 0.022072644 0.100395111 0.998287436 -0.325600156 SPAPEQFQS(ph)REDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPAPEQFQSREDFR 14 1 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 S(0.003)PAPEQFQS(0.997)REDFR;SPAPEQFQS(1)REDFR;SPAPEQFQS(1)REDFR;SPAPEQFQS(1)REDFR 119.38 0.00011562 1068400000 1368050 908140 1161530 1161730 1342630 1032640 1401060 1236000 1517290 TRUE FALSE 1303384.988 1000680.498 1214787.299 1044950.693 1576784.247 996879.4179 1187302.565 1127769.288 1752583.584 0.743693482 0.570974479 0.693140864 0.596234441 0.899691325 0.568805635 0.677458454 0.643489588 1 20.74105182 -1.074528173 4.373946632 1.000027242 0.669908234 0.525773428 0.097169205 11661602.34 2864854.966 3290.994268 0.02020897 0.084230975 1.074528173 -0.330119008 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.111)S(0.889)PLPSK;SPAVATSTAAPPPPS(0.001)S(0.999)PLPSK;SPAVATSTAAPPPPS(0.001)S(0.999)PLPSK;SPAVATSTAAPPPPS(0.008)S(0.992)PLPSK 325.98 5.05E-68 1493440000 3016460 2672600 2885750 3223370 2339830 2851860 3310700 2971210 2527130 TRUE FALSE 2873877.914 2944940.978 3018064.492 2899350.724 2747895.611 2753099.373 2805591.91 2711035.101 2919024.414 0.984533703 1.008878502 1.033929171 0.993260183 0.941374659 0.943157365 0.961140269 0.928746977 1 21.47705485 2.857776254 4.750587053 0.952432882 1.00633474 0.565700006 0.022078065 0.152875592 5.309817651 0.006334806 0.006754668 720.7360641 -2.857776254 0.053901858 SPDDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPDDPSR 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 110.61 0.015737 2288900000 7619800 7127300 5646500 7472800 6635600 6612000 7204200 7291200 6601600 FALSE TRUE 7259627.155 7853579.973 5905397.61 6721619.947 7792846.539 6383024.782 6105066.976 6652743.875 7625342.412 0.952039497 1.029931451 0.774443598 0.881484343 1.021966768 0.837080414 0.800628568 0.872451821 1 22.86237069 3.758532207 24.97661298 0.874031136 0.990985479 0.229229164 0.079941444 978.0908293 1223203.784 0.020022012 0.03603512 5734.983956 -3.758532207 0.116954343 SPDKPGGS(ph)PSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 SPDKPGGS(0.996)PS(0.004)ASR;SPDKPGGS(0.982)PS(0.018)ASR;SPDKPGGS(0.999)PS(0.001)ASR 140.3 2.38E-05 1053100000 1377460 1272300 1299640 1480110 907070 1454500 1525170 1345610 1116420 TRUE FALSE 1312350.196 1401948.816 1359229.78 1331326.531 1065262.721 1404130.3 1292477.305 1227781.255 1289548.712 1.017681755 1.087162357 1.054035235 1.03239724 0.826074045 1.088854021 1.002271022 0.952101494 1 20.29843484 2.984367203 24.80202886 0.980266586 1.053745089 0.236254763 0.066375035 948.0956944 1504193.269 0.019013168 0.020737648 964.6443005 -2.984367203 0.073478504 SPDKPGGSPSASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 61.212 0.078379 33009000 52407 49534 48524 63339 42428 58085 59064 49740 43043 FALSE TRUE 49929.82497 54581.57092 50748.8734 56972.04338 49827.42977 56073.50189 50052.70202 45384.50191 49717.88861 1.004262779 1.097825601 1.020736697 1.145906332 1.002203254 1.127833531 1.006734264 0.912840492 1 15.60147741 1.497032743 5.761764434 0.956685193 1.064311761 0.431867622 0.052723193 0.118205104 8.96538927 0.026722113 0.01168363 31.40745477 -1.497032743 0.107626568 SPDTNYLFMGDYVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 126.63 0.00019336 107169000 64687 77213 60244 72862 63699 73132 68270 74781 63164 FALSE TRUE 61629.37371 85081.09248 63006.24699 65537.77333 74808.08543 70599.4205 57854.15764 68232.7792 72959.15052 0.844710681 1.166146972 0.863582519 0.898280378 1.025342056 0.967656833 0.792966437 0.935218937 1 16.15480131 1.949672327 24.72296981 0.88487138 0.972371375 0.027259199 0.104462972 648.083769 318363.3021 0.041327661 0.026671566 89.05787465 -1.949672327 0.087499994 SPEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPEDKR 6 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 86.113 0.0865 83858000 222530 223910 211830 260530 178276 217970 234950 283570 239710 FALSE TRUE 212011.4479 246726.6836 221542.615 234341.0294 209367.278 210421.6442 199104.0623 258739.1075 276883.0025 0.765707703 0.89108642 0.800130788 0.846353974 0.75615793 0.759965915 0.719090954 0.934470896 1 18.07891697 1.064634174 5.539069254 0.998917071 0.795579727 0.699919257 0.048824634 0.106781464 5.768101681 0.051019458 0.012866087 11.60470684 -1.064634174 -0.203337343 SPEDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPEDLER 7 0 P06744;A0A2U3TZU2;P06744-2;Q8N196 P06744 GPI;SIX5 Glucose-6-phosphate isomerase;Homeobox protein SIX5 0 ;;;;; 166.05 0.002647 10377800000 7146810 6174350 6347810 7302270 7528670 6574380 8065980 6934340 7918230 FALSE TRUE 6808994.455 6803523.285 6638863.367 6568231.946 8841667.664 6346707.572 6835366.609 6327132.428 9146148.668 0.744465753 0.743867559 0.725864362 0.71814183 0.966709375 0.693921322 0.747349169 0.691781061 1 23.12473294 -2.102259424 2.420198255 1.435294842 0.753800164 0.494232337 0.078203089 6078568.818 1690622.612 14579017 0.017496809 0.007902065 2.102259424 -0.681494678 SPEEAGFPGDPHEDKQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPEEAGFPGDPHEDKQ 16 1 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 0 71.98 0.062742 42012000 109360 106870 95427 110200 78445 118970 114460 118340 85182 FALSE TRUE 104190.7695 117760.1745 99802.42234 99122.48663 92125.78316 114850.0391 96997.0248 107977.5222 98391.58951 1.058939794 1.196852039 1.014338958 1.007428451 0.936317663 1.167274964 0.985826383 1.097426343 1 16.58624738 3.717242597 24.81743163 1.030194718 1.127895923 0.248413525 0.070933351 827.752923 963631.5342 0.01734559 0.02689943 5214.859321 -3.717242597 0.097701205 SPEEGAETPVYLALLPPDAEGPHGQFVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPEEGAETPVYLALLPPDAEGPHGQFVSEK 30 0 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ; 126.18 1.34E-05 261800000 407920 378990 342430 434920 365120 378530 426740 410330 378470 FALSE TRUE 388638.43 417609.5119 358130.7542 391201.0153 428796.8124 365421.4112 361632.9754 374399.3299 437161.1946 0.889004868 0.955275804 0.819218994 0.894866745 0.980866595 0.835896268 0.827230275 0.856433129 1 18.73780582 SPEPEAT(ph)LTFPFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.306)PEPEAT(0.694)LTFPFLDK 140.08 1.84E-05 15793000 76175 98434 61630 93274 41233 76915 60641 76977 39204 TRUE FALSE 72574.35871 108464.5365 64455.79646 83897.92031 48424.02215 74251.41426 51389.1017 70236.4858 45283.55609 1.602664741 2.395230098 1.423381952 1.85272376 1.069351136 1.639699279 1.134829199 1.551037327 1 15.46669964 3.133865892 1.442412439 1.304706942 1.964386348 0.376833152 0.325483854 0.347261213 1.506273655 0.105651777 0.141337777 1361.024339 -3.133865892 0.659679406 SPFEGAVT(ph)ESQSLFSDNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.382)PFEGAVT(0.618)ESQSLFSDNFR 348.22 1.26E-89 197630000 16559 15170 12191 19062 15094 11594 16296 16960 14275 TRUE FALSE 15776.28889 16715.84025 12749.96941 17145.85154 17726.38882 11192.49687 13809.7459 15474.89249 16488.69409 0.956794322 1.013775873 0.773255258 1.039855033 1.075063235 0.678798261 0.837528177 0.938515349 1 14.00918952 2.255969399 24.99999776 0.842695983 0.970193502 0.170512691 0.114275103 346.6429661 497798.0445 0.037517355 0.031320565 180.2890702 -2.255969399 0.12749752 SPFIEEQLHTVLEKS(ph)PENSPPVKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPFIEEQLHTVLEKSPENSPPVKPK 25 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SPFIEEQLHTVLEKS(0.997)PENS(0.003)PPVKPK;SPFIEEQLHTVLEKS(0.999)PENSPPVKPK 152.16 6.21E-08 411100000 666780 526050 552970 686420 326740 683750 696390 762310 283340 TRUE FALSE 635262.6308 579655.0931 578324.2215 617419.7575 383723.3526 660071.5661 590142.9154 695558.0951 327278.9201 1.941043531 1.771134826 1.76706835 1.886524672 1.172465836 2.016847177 1.803180343 2.125276186 1 18.32016116 4.582494717 0.969404598 1.721708391 2.022746895 0.045145898 0.350646963 6.005192514 5.348359108 0.101465834 1.795291881 38237.96024 -4.582494717 0.301038504 SPGGPGSHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 100.48 0.003987 13708000 22712 19554 16881 22234 24333 17223 21006 19275 23445 FALSE TRUE 21638.44877 21546.57483 17655.01055 19998.99608 28576.6675 16626.56319 17801.1489 17587.17882 27080.73086 0.799034889 0.795642294 0.651939958 0.738495434 1.055239892 0.613962868 0.657336354 0.649435161 1 14.72497905 SPGHILCCECGVPIS(ph)PNPANICVACLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGHILCCECGVPISPNPANICVACLR 27 0 C9JA08;Q96D46;C9J0B9;C9IZW9;C9K0C2;C9IY70 C9JA08 NMD3 60S ribosomal export protein NMD3 1 SPGHILCCECGVPIS(1)PNPANICVACLR 131.81 2.59E-05 90140000 47610 48317 58588 57743 65359 48034 62266 56378 73841 TRUE FALSE 45359.56965 53240.55723 61274.31775 51938.56394 76757.58891 46370.57054 52766.17811 51441.24344 85291.88515 0.531815771 0.624215975 0.718407357 0.608950826 0.899940115 0.543669195 0.618654143 0.60312002 1 16.38012087 -2.121297419 2.370613867 1.701659387 0.638112139 0.535155257 0.104278553 5817948.726 1647632.112 21966443.92 0.02451567 0.007563148 2.121297419 -1.063547248 SPGLVPPS(ph)PEFAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 SPGLVPPS(1)PEFAPR;SPGLVPPS(1)PEFAPR 120.92 0.00069671 0 157672 202367 152413 195672 152494 163392 164404 159091 154385 TRUE FALSE 150219.157 222988.4274 159401.2868 176002.6788 179088.9053 157733.6941 139321.1503 145160.1486 178326.2373 0.842383932 1.250452153 0.893874559 0.986970182 1.004276813 0.8845232 0.781271183 0.814014532 1 17.44415946 2.17117003 3.637361562 0.839157738 1.012505581 0.195953917 0.120347249 0.278855611 7.395048337 0.046281801 0.033295297 148.3098617 -2.17117003 0.173347844 SPGLYAIGYEECIERPLS(ph)PHMEQSSLDPGKEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGLYAIGYEECIERPLSPHMEQSSLDPGKEGR 33 2 A0A6I8PS01;Q6P1R3-3;Q6P1R3;Q6P1R3-2 A0A6I8PS01 MSANTD2 Myb/SANT-like DNA-binding domain-containing protein 2 1 SPGLYAIGYEECIERPLS(0.98)PHMEQS(0.01)S(0.01)LDPGKEGR 84.98 0.00020153 41341000 22215 19919 16449 11044 21466 12302 29018 14888 12939 TRUE FALSE 21164.94098 21948.76875 17203.20292 9933.836138 25209.6636 11875.97866 24590.77115 13584.32779 14945.51404 1.416140049 1.468585737 1.151061307 0.664670089 1.686771264 0.79461828 1.64536135 0.908923424 1 13.8674249 3.736611516 24.33852437 1.161961119 1.4423629 0.131333214 0.330503685 226.1481197 2823944.72 0.07862007 0.1289636 5452.698891 -3.736611516 0.280401781 SPGS(ph)PPGPELPIETALDDRER ddPTM_SK-BR-3_Trastuzumab_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(0.014)PGS(0.986)PPGPELPIETALDDRER 111.84 0.00014475 36785000 34962 28897 36393 40533 28533 30968 37864 40184 37750 TRUE FALSE 33309.41555 31841.63715 38061.65505 36458.54583 33509.14617 29895.57039 32087.15138 36665.27593 43604.0772 0.763905985 0.730244491 0.872892112 0.83612699 0.768486534 0.685614106 0.735875025 0.840868063 1 15.41217542 0.924886598 4.247000341 0.999890963 0.766428165 0.654642907 0.052751598 0.225774196 10.16771417 0.053708335 0.013684261 8.411754675 -0.924886598 -0.233462799 SPGS(ph)PVGEGTGSPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 214.73 2.55E-12 107130000 234830 220810 202400 268800 167790 214370 211990 232700 182700 TRUE FALSE 223730.0513 243310.79 211680.2402 241779.7133 197052.5229 206946.3131 179647.032 212323.5544 211032.1829 1.060170294 1.152955851 1.003070893 1.14570067 0.933755791 0.980638641 0.851277893 1.006119311 1 17.6871035 2.727375727 24.70977994 0.939695967 1.092665119 0.547614538 0.060652715 394.1678853 870798.3961 0.018058431 0.017171013 533.7965062 -2.727375727 0.152969152 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 SPGS(0.995)T(0.005)PT(0.019)T(0.976)PT(0.004)S(0.001)SQAPQK;SPGS(0.998)T(0.002)PTT(0.785)PT(0.206)S(0.009)SQAPQK;SPGS(0.958)T(0.042)PT(0.005)T(0.993)PT(0.002)SSQAPQK 306.37 2.39E-46 355569000 813740 940670 767990 1042930 566960 844110 819340 833850 551800 TRUE FALSE 775276.1229 1036525.342 803203.1011 938092.695 665837.6445 814878.259 694334.6348 760833.6735 637370.3258 1.21636683 1.626252903 1.260182768 1.471817336 1.044663703 1.278500467 1.089373958 1.193707398 1 19.28177233 2.741868974 24.98476113 1.136662341 1.405307485 0.500644261 0.134473849 227.1898727 1715745.139 0.038299059 0.03911399 551.9109037 -2.741868974 0.268645144 SPGS(ph)TPTTPT(ph)SSQAPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 SPGS(0.998)T(0.002)PTT(0.224)PT(0.769)S(0.006)SQAPQK 302.9 8.45E-46 305580000 963330 1097000 901550 1162300 662660 969730 907270 983020 625250 TRUE FALSE 917795.3 1208785.547 942886.9593 1045463.396 778227.6942 936148.0069 768849.2983 896941.5575 722210.5767 1.270813984 1.673730054 1.305556841 1.447588044 1.077563413 1.296225834 1.064577733 1.241939105 1 19.46206002 2.746383891 24.52799287 1.147038962 1.442302339 0.523913675 0.13589385 336.3865374 1054659.011 0.038751303 0.040401174 557.6784865 -2.746383891 0.295263377 SPGS(ph)TPTTPTSSQAPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 S(0.001)PGS(0.947)T(0.053)PTTPTSSQAPQK;S(0.025)PGS(0.821)T(0.153)PT(0.001)TPTSSQAPQK 186.96 5.18E-10 139812000 120982 114567 96178 132356 82484 122825 112928 121419 89393 TRUE FALSE 115263.4206 126241.5076 100587.8564 119051.3234 96869.18348 118571.5395 95698.75953 110786.9087 103255.6099 1.116292091 1.222611611 0.974163598 1.152976807 0.938149352 1.148330242 0.926814143 1.072938398 1 16.65586064 3.739137691 24.99940515 1.029645172 1.169451853 0.334626559 0.081462887 47.222735 2045694.215 0.018764602 0.031456241 5484.508209 -3.739137691 0.13980668 SPGSNS(ph)KVPEIEVTVEGPNNNNPQTSAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.125)PGS(0.388)NS(0.487)KVPEIEVTVEGPNNNNPQTSAVR 201.58 1.91E-25 247600000 85885 43716 95970 73793 85667 78973 135040 109680 122530 TRUE FALSE 81825.38626 48170.7101 100370.3194 66375.18744 100607.2977 76238.14521 114437.1678 100075.8377 141531.3266 0.578143286 0.340353696 0.709173876 0.46897877 0.710848263 0.538666223 0.808564228 0.707093194 1 17.11076189 1.277652188 0.350397511 1.034505275 0.449249355 0.620081343 0.11333766 0.742398588 0.293382857 0.166789632 0.116629225 18.95187519 -1.277652188 -0.58525592 SPGTGPSPFSSS(ph)LGHLNHLGGSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFSS(0.086)S(0.914)LGHLNHLGGSLDR;SPGTGPSPFSS(0.035)S(0.965)LGHLNHLGGSLDR;SPGTGPSPFSS(0.066)S(0.934)LGHLNHLGGSLDR 240.74 2.32E-38 299089000 256851 244166 259410 274230 323350 228945 311291 274465 40600.1 TRUE FALSE 244710.1623 269046.793 271304.2051 246663.8794 379742.1376 221016.5772 263797.8407 250431.3896 46896.15615 5.218128357 5.737075596 5.785211995 5.259788853 8.097510943 4.712893239 5.625148463 5.340126145 1 15.51718206 0.068034965 0.955680624 0.950474599 5.787052072 0.73914676 0.886391394 2.809786275 2.443442962 1.199284471 0.252234075 1.169593552 -0.068034965 4.836577473 SPGTGPSPFSSSLGHLNHLGGS(ph)LDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFSSSLGHLNHLGGS(1)LDR 158.15 4.21E-11 56986000 30215 23401 29963 33092 45355 28353 40504 32166 10503 TRUE FALSE 28786.79683 25785.5885 31336.83319 29765.52929 53264.89764 27371.1285 34324.37089 29349.37452 12131.7516 2.372847531 2.125462947 2.583042765 2.453522811 4.390536454 2.256156358 2.829300503 2.419219869 1 13.56650024 3.493712842 2.817817442 2.718933443 2.253285515 0 0.828030687 0.809120507 12.91422738 0.215406121 0.33442499 3116.828041 -3.493712842 -0.465647929 SPGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 165.47 3.04E-12 96393000 78710 63816 72676 79219 81434 73263 89010 79316 80807 FALSE TRUE 74989.53429 70318.92295 76008.26649 71255.75561 95636.06382 70725.88394 75429.88972 72370.67056 93338.13686 0.803417947 0.753378258 0.814332373 0.763415234 1.024619379 0.75773833 0.808135798 0.775360137 1 16.51017905 -2.292433754 2.190719868 1.834660954 0.809096581 0.359495952 0.078512419 4193986.72 451451.8272 17420773.51 0.018546027 0.005099954 2.292433754 -1.025564373 SPHT(ph)PQPDQIANGFFLHSQEMSILNSNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPHTPQPDQIANGFFLHSQEMSILNSNIK 29 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.189)PHT(0.811)PQPDQIANGFFLHSQEMSILNSNIK 58.722 0.078462 49839000 54782 44895 51199 59309 45782 51595 58390 53888 36951 TRUE FALSE 52192.56343 49469.85154 53546.52479 53347.14664 53766.3663 49808.25221 49481.53309 49169.28104 42681.17236 1.222847465 1.159055593 1.25457015 1.249898812 1.259720934 1.166984163 1.159329286 1.152013366 1 15.38131218 0.786597518 0.801378126 1.000705388 1.218615745 0.807419261 0.033629888 0.426579617 0.547141298 0.035010483 0.012385659 6.11783159 -0.786597518 0.217910357 SPIIFIGTGEHIDDFEPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPIIFIGTGEHIDDFEPFK 19 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 153.14 4.87E-08 63927000 219260 193480 186080 243900 139250 209210 220830 213600 133870 FALSE TRUE 208896.0143 213195.832 194611.9521 219382.7086 163535.1559 201965.0052 187138.3277 194896.0516 154629.8759 1.350942133 1.378749292 1.258566308 1.418760168 1.057590941 1.306118912 1.210233964 1.260403596 1 17.23845956 -5 0.077518745 0.012816979 1.599121873 0.535734987 0.090755857 179.9018519 0.991700835 30.50632076 3.06245174 1.00E-05 5 1.586304894 SPILLGSLAHQIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPILLGSLAHQIYR 14 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 ; 276.71 4.12E-33 616620000 1069700 653590 501720 552600 1105000 516870 1002110 749010 995160 FALSE TRUE 1019137.401 720191.5641 524724.3583 497051.5981 1297711.65 498970.6623 849219.7145 683422.7136 1149484.33 0.886603996 0.626534477 0.456486743 0.432412679 1.128951144 0.434082179 0.738783202 0.594547221 1 20.13255537 -1.474725369 3.105627307 1.007707978 0.668443005 0.191251773 0.217916241 85681459.55 103325338.7 5714755.088 0.049556158 0.033517732 1.474725369 -0.339264973 SPITS(ph)SPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.058)S(0.628)S(0.314)PPK 93.111 0.010092 26319000 207510 233430 182440 231670 121280 197650 191210 226590 142710 TRUE FALSE 197701.4135 257216.7824 190805.0545 208382.0915 142431.1936 190805.3309 162037.4027 206748.5784 164840.7379 1.199348025 1.560395723 1.157511528 1.264141947 0.864053361 1.157513205 0.982993674 1.254232303 1 17.3307133 3.253049153 1.981099581 1.059095466 1.370402962 0.381632603 0.149688908 0.267175516 2.156052137 0.042815926 0.059782398 1790.808526 -3.253049153 0.311307496 SPKFQLFGSPSGQKDLLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPKFQLFGSPSGQKDLLFK 19 2 E7EQB2;E7ER44;P02788-2;P02788 E7EQB2 LTF Lactotransferrin;Lactoferricin-H;Kaliocin-1;Lactoferroxin-A;Lactoferroxin-B;Lactoferroxin-C 0 1.4616 0.09787 783660 0 0 0 864.2 955.99 0 1321 0 0 FALSE TRUE 0 0 0 777.3289741 1122.714353 0 1119.457188 0 0 0 SPLAPSEGAGS(ph)DVFDGDLGMGAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.166)EGAGS(0.833)DVFDGDLGMGAAK 89.483 0.034134 27090000 50842 38056 39316 62972 43979 41983 43398 51663 40810 TRUE FALSE 48438.79942 41933.94967 41118.67749 56641.93492 51648.92368 40529.11818 36776.83804 47139.11384 47138.60637 1.02758234 0.889588236 0.872293024 1.201603935 1.095682025 0.859786093 0.780185094 1.000010765 1 15.52462149 2.214538491 24.97440715 0.878592923 1.002639793 0.148367054 0.114579641 372.9322316 387713.4679 0.043879748 0.032424126 163.8847303 -2.214538491 0.12404687 SPLAQMEEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 0 ; 148.68 5.57E-05 1019670000 426430 355760 397050 457560 444950 376230 487430 435050 479100 FALSE TRUE 406273.499 392012.3485 415255.1352 411565.1995 522549.1391 363201.0608 413063.6012 396954.7157 553396.3811 0.734145565 0.708375338 0.750375589 0.74370779 0.944258324 0.656312678 0.746415436 0.717306309 1 19.07795368 -1.45897482 2.963652444 1.006289644 0.746804375 0.527166431 0.074316497 14376552.61 17035132.17 752774.6286 0.016972314 0.034755631 1.45897482 -0.259485268 SPLDPMT(ph)SPGSGLILQANFVHSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPLDPMTSPGSGLILQANFVHSQR 24 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SPLDPMT(0.563)S(0.436)PGS(0.001)GLILQANFVHSQR;SPLDPMT(0.546)S(0.454)PGSGLILQANFVHSQR 169.7 3.27E-11 345409000 379780 295142 345330 405090 433020 347780 442380 378150 397190 TRUE FALSE 361828.5521 325217.3053 361163.7221 364369.5836 508538.5509 335736.2914 374886.8061 345037.1813 458784.1966 0.788668299 0.708867715 0.787219187 0.79420692 1.108448274 0.731795676 0.817131037 0.752068584 1 18.80745617 -5 0.133024635 1.588335978 0.733481189 0.203340831 0.112023587 228.9005342 1.904419058 36.77261906 0.772308959 1.00E-05 5 -0.85485479 SPLDPMTS(ph)PGSGLILQANFVHSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPLDPMTSPGSGLILQANFVHSQR 24 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SPLDPMT(0.295)S(0.696)PGS(0.01)GLILQANFVHSQR;SPLDPMT(0.256)S(0.74)PGS(0.004)GLILQANFVHSQR;SPLDPMT(0.193)S(0.764)PGS(0.043)GLILQANFVHSQR 114.73 0.00076871 394772000 264704 242659 257927 282101 307702 258489 334243 275146 343679 TRUE FALSE 252191.9665 267386.228 269753.2081 253743.6715 361365.1314 249537.4611 283248.0916 251052.7576 396974.9841 0.635284279 0.67355939 0.679521932 0.639193102 0.910296986 0.628597446 0.713516224 0.632414554 1 18.59868857 -2.117600826 2.475854049 1.609152839 0.688447144 0.580450023 0.083080287 6337086.326 1137741.812 21847746.68 0.018309162 0.007627798 2.117600826 -0.920705695 SPLEHSS(ph)PEKEAPSPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPLEHSSPEKEAPSPEK 17 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 SPLEHS(0.029)S(0.971)PEKEAPSPEK 109.09 0.00037673 66243000 154130 148870 127100 169900 98540 163790 156230 164980 89040 TRUE FALSE 146844.5804 164040.0223 132927.6607 152821.3292 115725.3448 158117.9112 132394.2441 150533.4766 102847.8684 1.427784383 1.594977365 1.292468796 1.485896903 1.125208977 1.537396094 1.287282334 1.463651886 1 16.65015237 -3.808582396 0.177584603 8.46E-12 1.507758309 0.446190968 0.138642896 69.27495545 0.974631316 25.66560476 0.417481943 0.000155388 3.808582396 1.507758309 SPLS(ph)PTETFSWPDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SPLS(0.941)PT(0.059)ETFSWPDVR;SPLS(0.999)PT(0.001)ETFSWPDVR;S(0.015)PLS(0.984)PT(0.001)ETFSWPDVR 290.64 7.01E-44 181916000 70132 66808 62320 78016 71270 75728 95087 91610 95175 TRUE FALSE 66816.99935 73615.81115 65177.43364 70173.68346 83699.46544 73105.52037 80579.73176 83588.14274 109934.2529 0.607790544 0.669634888 0.592876487 0.638324104 0.761359296 0.664993107 0.732981119 0.760346667 1 16.74628144 -1.079313273 0.227544506 1.250711362 0.593491139 0.896098979 0.037620501 4.960960609 0.251184091 0.836097328 0.07597348 0.083308004 1.079313273 -0.657220223 SPPAS(ph)PESWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 S(0.094)PPAS(0.905)PES(0.001)WK;S(0.01)PPAS(0.99)PESWK 101.71 0.0032991 177122000 438890 410830 444390 469520 381590 466190 581780 522590 453700 TRUE FALSE 418144.5395 452694.0441 464765.7211 422322.9576 448139.1752 450045.7234 493018.7759 476829.2492 524057.4788 0.797898239 0.863825176 0.886860201 0.805871445 0.855133632 0.858771684 0.940772331 0.909879676 1 18.99936553 1.378094626 0.712852213 0.996555442 0.83520603 0.748861059 0.030160628 0.297573621 0.339811473 0.02782436 0.011965042 23.88331609 -1.378094626 -0.161349412 SPPMELQPPVS(ph)PQQSECNPVGALQELVVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPMELQPPVSPQQSECNPVGALQELVVQK 30 0 H3BV98;F8VSA1;Q15633-2;Q15633;F8VW32;F8VZ57 H3BV98 TARBP2 RISC-loading complex subunit TARBP2 1 SPPMELQPPVS(0.962)PQQS(0.038)ECNPVGALQELVVQK 91.113 0.00065806 19566000 43604 34274 36134 35673 32798 39413 42612 38689 34318 TRUE FALSE 41542.92533 37766.55957 37790.77964 32087.08227 38517.96082 38048.11793 36110.75678 35301.18606 39639.86017 1.048008877 0.952741998 0.953353001 0.809465072 0.971697697 0.959844908 0.910970842 0.890547694 1 15.27466425 4.371113851 1.536425295 0.923029825 1.056198292 0.338155508 0.052291695 0.576408872 2.06319136 0.013433654 0.094619054 23502.48864 -4.371113851 0.133168467 SPPS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPPSPGR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 1 SPPS(1)PGR;SPPS(1)PGR 95.358 0.014187 225170000 203610 179047 171984 225150 197617 174565 202849 185236 225330 TRUE FALSE 193985.7588 197292.0929 179869.6365 202517.4942 232081.3422 168519.7703 171900.6595 169015.7538 260273.0256 0.745316417 0.758019746 0.691080592 0.778096362 0.891684191 0.647473052 0.660462832 0.64937868 1 17.98966627 SPPS(ph)TGSTYGSSQKEESAASGGAAYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.193)PPS(0.214)T(0.214)GS(0.155)T(0.155)Y(0.021)GS(0.023)S(0.023)QKEES(0.001)AASGGAAYTK 71.002 0.0015153 0 193270 211360 141680 210760 86077 198280 142710 173810 77706 TRUE FALSE 184134.5101 232897.8243 148176.1681 189574.0044 101088.8015 191413.5139 120936.9685 158590.275 89756.24961 2.051495143 2.594781147 1.65087299 2.112098101 1.126259196 2.132592602 1.34739329 1.766899527 1 16.45372477 3.469246048 0.151024385 0.713612159 3.278386542 0.435499537 0.371948487 11.41345536 0.500269909 2.046224326 6.677298406 2946.090258 -3.469246048 2.564774383 SPPSTGSTYGS(ph)SQKEESAASGGAAYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.017)PPS(0.087)T(0.087)GS(0.087)T(0.087)Y(0.08)GS(0.456)S(0.094)QKEES(0.005)AAS(0.001)GGAAYTK 53.865 0.053718 28855000 38121 49426 29136 43143 20510 38119 36065 38910 18116 TRUE FALSE 36319.09588 54462.56559 30471.91442 38806.18367 24086.93751 36798.92947 30562.62187 35502.83413 20925.33676 1.735651679 2.602709157 1.456220981 1.854507009 1.1510896 1.758582426 1.460555795 1.696643382 1 14.35296322 3.403092514 0.151843452 0.789163571 2.884864361 0.343962616 0.353428966 13.34729595 0.60930713 2.058135878 6.479411251 2529.836847 -3.403092514 2.09570079 SPPSYS(ph)VLYPSSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPSYSVLYPSSDPK 15 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 S(0.18)PPS(0.251)Y(0.212)S(0.356)VLY(0.002)PSSDPK 68.551 0.054853 72573000 54346 49075 46143 58652 41011 56160 60058 58848 43384 TRUE FALSE 51777.17228 54075.79829 48258.70219 52756.18953 48163.30542 54215.16512 50895.04906 53694.95715 50111.76915 1.033233773 1.079103756 0.963021322 1.052770446 0.961117642 1.081884875 1.015630658 1.071503921 1 15.61286185 -0.567531513 7.520628961 1.000004136 1.033816427 0.05134435 0.043165369 0 0 0.037022884 0.008726377 0.270687678 0.567531513 0.033812291 SPPYT(ph)AFLGNLPYDVTEESIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.329)PPY(0.275)T(0.395)AFLGNLPYDVTEESIK 119.31 0.00022745 22362000 42845 62630 33916 56655 23009 44693 31049 48622 21763 TRUE FALSE 40819.80176 69012.0682 35471.08215 50959.93176 27021.76232 43145.2702 26311.9048 44364.39992 25137.89489 1.623835327 2.745339994 1.411060166 2.027215564 1.074941336 1.716343807 1.046702793 1.764841492 1 14.61757622 3.129671929 1.426152357 1.334407721 2.134264978 0.307489024 0.439741393 0.393006275 1.667812687 0.144539212 0.192976161 1347.944246 -3.129671929 0.799857257 SPQDPGDPVQYNRTT(ph)DEELSELEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQDPGDPVQYNRTTDEELSELEDR 25 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 SPQDPGDPVQYNRT(0.436)T(0.564)DEELSELEDR 108.32 0.0054884 160570000 83871 57106 82535 80345 96431 65429 87883 84329 120100 TRUE FALSE 79906.58405 62925.16632 86319.31139 72268.56795 113248.5359 63163.17732 74474.83427 76944.7057 138724.4946 0.576009192 0.453598094 0.622235544 0.520950306 0.816355729 0.455313804 0.536854248 0.554658396 1 17.08186302 -1.861660456 2.357632323 1.208343063 0.55848295 0.637577135 0.102418405 8356122.856 4583814.184 9755284.183 0.02344831 0.013751167 1.861660456 -0.649860113 SPQLSLSPRPAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPQLSLSPRPASPK 14 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 SPQLSLS(0.014)PRPAS(0.986)PK;SPQLSLSPRPAS(1)PK 122.14 6.69E-05 556100000 810570 753070 708780 873910 442240 836410 836010 876930 510700 TRUE FALSE 772255.9625 829808.6892 741278.2641 786062.9065 519366.516 807444.912 708461.3201 800141.3603 589896.7477 1.309137515 1.406701584 1.256623751 1.332543211 0.88043631 1.368790242 1.200992077 1.356409174 1 19.17010293 -4.999999994 0.0652943 0.166455453 1.604750633 0.22237907 0.149794256 492.2868448 2.330411973 65.57590286 9.376532333 1.00E-05 4.999999994 1.43829518 SPQNSHSHS(ph)TPSSSVRPNSPSPTALAFGDHPIVQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQNSHSHSTPSSSVRPNSPSPTALAFGDHPIVQPK 36 1 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 S(0.003)PQNS(0.002)HS(0.011)HS(0.207)T(0.176)PS(0.15)S(0.15)S(0.15)VRPNS(0.15)PS(0.002)PT(0.002)ALAFGDHPIVQPK 80.125 0.0010168 135580000 29344 25810 33259 33473 50398 29444 51786 38840 9722.1 TRUE FALSE 27956.96727 28440.06834 34783.95805 30108.23045 59187.39524 28424.3469 43885.09458 35438.9637 11229.75361 2.489544137 2.532563876 3.097481854 2.681112291 5.270587163 2.531163895 3.907930315 3.15580955 1 13.45503865 3.488213419 1.926789432 3.345455188 2.504277859 0.016821081 1.086286308 0.747754717 5.557439184 0.290947726 0.488120723 3077.608825 -3.488213419 -0.84117733 SPQPVPS(ph)PRPQSQPPHSSPSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.974)PRPQS(0.005)QPPHS(0.006)S(0.016)PSPR 86.982 0.0017537 53962000 22462 19400 20525 24215 35548 22427 32138 24063 45040 TRUE FALSE 21400.26578 21376.88206 21466.09155 21780.86219 41747.55995 21650.34737 27234.75785 21955.91615 52024.57317 0.411349185 0.410899711 0.412614467 0.41866489 0.802458481 0.416156175 0.523497959 0.422029722 1 15.6669056 -5 0.245224758 4.078784884 0.423350938 0.645863124 0.121307604 107.8829921 1.072542183 166.2492297 0.172127243 1.00E-05 5 -3.655433946 SPQYCQVIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SPQYCQVIHR 10 0 Q13228;Q13228-4;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;;; 192.38 6.89E-07 18567800000 11374170 8044230 6778950 7754430 11697220 7385650 12223700 8976870 10743220 FALSE TRUE 10836535.53 8863946.183 7089771.563 6974939.964 13737211.46 7129883.089 10358750.06 8190807.673 12409223.69 0.873264581 0.714303038 0.571330789 0.56207706 1.107016185 0.574563185 0.834762135 0.660058024 1 23.56490953 SPS(ph)FASEWDEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SPS(1)FASEWDEIEK;S(0.163)PS(0.837)FASEWDEIEK;SPS(1)FASEWDEIEK;S(0.002)PS(0.998)FASEWDEIEK;S(0.002)PS(0.998)FASEWDEIEK;SPS(1)FASEWDEIEK 410.88 1.78E-126 1387950000 1546154 1313098 1325202 1640242 1027896 1542794 1623701 1546524 1098855 TRUE FALSE 1473070.365 1446904.179 1385963.823 1475361.758 1207160.737 1489366.657 1375975.591 1411102.16 1269259.821 1.160574328 1.139959018 1.091946502 1.162379627 0.951074569 1.173413538 1.084077167 1.111752012 1 20.27555599 -2.791857372 0.016471637 2.07E-06 2.006372003 0.265936996 0.061989535 3943.280924 7.415424364 531.4193623 382.1525069 0.001614889 2.791857372 2.006369931 SPS(ph)FGAGEGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.112)PS(0.888)FGAGEGLLR;S(0.073)PS(0.927)FGAGEGLLR;S(0.293)PS(0.707)FGAGEGLLR 158.59 6.47E-05 419352000 338302 269111 285352 302314 424310 265365 325564 327037 600790 TRUE FALSE 322311.1349 296533.7169 298435.6715 271924.8224 498309.5297 256175.3435 275893.2324 298399.9065 693957.4448 0.464453746 0.427308215 0.430048951 0.391846538 0.71806929 0.369151373 0.397565059 0.429997414 1 19.40448767 -1.405542811 2.829888927 1.011421474 0.449548838 0.755023963 0.097796935 7673079.218 8796337.271 709745.2933 0.023385456 0.03930585 1.405542811 -0.561872636 SPS(ph)GSAFGSQENLR ddPTM_SK-BR-3_Trastuzumab_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(0.225)PS(0.382)GS(0.1)AFGS(0.294)QENLR 124.86 9.92E-05 277530000 78429 64064 79293 93493 68316 76044 89105 82336 94270 TRUE FALSE 74721.8166 70592.19443 82928.66248 84094.90601 80230.28877 73410.57721 75510.39572 75126.22335 108888.9101 0.686220631 0.648295537 0.761589609 0.772300007 0.736808631 0.674178639 0.693462683 0.68993457 1 16.7324975 -2.380272991 2.227311114 3.085523925 0.703370042 0.846608314 0.03904002 1590370.929 185160.4396 16708748.64 0.010876846 0.004166074 2.380272991 -2.382153883 SPS(ph)LDNPTPFPNLGPSENPLKR ddPTM_SK-BR-3_Trastuzumab_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(0.001)PS(0.999)LDNPTPFPNLGPSENPLKR 296.86 8.72E-56 180110000 161020 186300 130250 215250 99628 179580 159130 167670 102290 TRUE FALSE 153408.9037 205284.1818 136222.0913 193612.6611 117003.0917 173361.0996 134851.7959 152987.9259 118152.6108 1.298396224 1.737449392 1.152933401 1.638665957 0.990270895 1.467264231 1.141335727 1.294833224 1 16.85029198 1.79522847 0.324896551 0.990741276 1.536035945 0.245311267 0.218000699 1.64236628 0.55314255 0.295023587 0.31279531 62.40630511 -1.79522847 0.545294669 SPS(ph)LNLLQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSLNLLQNK 10 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 S(0.005)PS(0.995)LNLLQNK;S(0.359)PS(0.641)LNLLQNK 135.02 0.0001629 131730000 295520 261430 235840 307360 236650 307260 347990 302280 259840 TRUE FALSE 281551.3553 288070.0142 246653.4973 276463.5889 277921.6851 296619.5092 294897.7342 275810.7607 300134.6601 0.938083443 0.959802557 0.821809441 0.92113183 0.925989971 0.988288087 0.982551412 0.918956713 1 18.19525041 2.327892776 5.653256621 0.972703085 0.917428269 0.334247151 0.04133813 0.274593529 13.7258117 0.014769023 0.012220331 212.7613687 -2.327892776 -0.055274815 SPS(ph)MSISEPISVTLPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.058)PS(0.942)MSISEPISVTLPPR 178.14 1.04E-09 12488000 7571.7 5163.2 4792.8 7325.8 7780.8 6442.2 6410.2 6636.5 6651.3 TRUE FALSE 7213.800747 5689.33595 5012.554621 6589.396666 9137.769057 6219.104999 5432.206259 6055.372878 7682.749634 0.938960801 0.740533822 0.652442792 0.857687284 1.189387848 0.809489479 0.707065376 0.788177823 1 12.90740702 4.738287973 5.212181065 0.828279062 0.943564717 0.028812184 0.15492899 0.57621596 47.92298168 0.037246003 0.234311621 54737.87997 -4.738287973 0.115285655 SPS(ph)PAHLPDDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.12)PS(0.88)PAHLPDDPK;S(0.052)PS(0.948)PAHLPDDPK;S(0.018)PS(0.982)PAHLPDDPK;S(0.013)PS(0.987)PAHLPDDPK;S(0.019)PS(0.981)PAHLPDDPK;S(0.432)PS(0.568)PAHLPDDPK;S(0.09)PS(0.91)PAHLPDDPK 174.83 1.89E-05 9997500000 22083160 21589020 19245340 24476990 13548470 22223890 22385050 23036060 11408070 TRUE FALSE 21039332.79 23788965.68 20127757.88 22016516.46 15911318.88 21454271.12 18969799.49 21018900.46 13177175.23 1.596649693 1.805316031 1.527471368 1.670806988 1.207490877 1.628138864 1.439595297 1.595099109 1 23.6515378 -2.917912352 0.158778478 9.10E-14 1.76751604 0.577243093 0.15280277 40.37224226 0.687423721 14.68431216 0.678732864 0.001208058 2.917912352 1.76751604 SPS(ph)PAHLPDDPKVAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSPAHLPDDPKVAEK 16 1 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.472)PS(0.528)PAHLPDDPKVAEK;S(0.469)PS(0.531)PAHLPDDPKVAEK;S(0.154)PS(0.846)PAHLPDDPKVAEK;S(0.074)PS(0.926)PAHLPDDPKVAEK 186.11 1.07E-09 1282680000 1494645 687630 1566330 1184535 1047443 1476418 2116420 1711660 1084549 TRUE FALSE 1423996.093 757700.2788 1638147.78 1065463.291 1230116.728 1425289.274 1793521.258 1561777.976 1252735.32 1.136709463 0.604836686 1.307656736 0.850509501 0.981944636 1.13774175 1.431684115 1.246694295 1 20.2566502 2.110359929 3.523832718 1.276054565 0.948789342 0.21433595 0.209807582 0.258617506 6.225958471 0.081588154 0.056158365 128.9317654 -2.110359929 -0.327265222 SPS(ph)PAVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.095)PS(0.905)PAVPLR 138.66 0.00013676 383460000 460080 375790 362220 451170 431210 399820 457480 458120 469520 TRUE FALSE 438332.9302 414083.4282 378828.1453 405817.5344 506412.8875 385974.1331 387683.0238 418004.5842 542330.7636 0.808239103 0.763525612 0.698518636 0.748284187 0.933771273 0.711695074 0.714846086 0.770755805 1 19.04881348 0.920034349 21.23735159 1 0.76616715 0.540720095 0.066970432 11098.75965 2947623.909 0.06309178 0.015772945 8.318295599 -0.920034349 -0.23383285 SPS(ph)PGLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.11)PS(0.89)PGLFR;S(0.001)PS(0.999)PGLFR;S(0.008)PS(0.992)PGLFR 152.38 0.00048042 178223000 475480 479752 465106 514960 484401 476432 559849 516206 574807 TRUE FALSE 453005.0027 528639.2742 486431.5702 463195.2424 568880.381 459933.0404 474433.7527 471004.2661 663945.1339 0.682292828 0.796209276 0.732638204 0.697640842 0.85681836 0.692727481 0.714567708 0.709402392 1 19.3407045 -1.354190532 3.838622667 1.000874012 0.73646424 0.708392208 0.053370535 254.0230167 25266630.72 32859.56098 0.011559147 0.044239424 1.354190532 -0.264409772 SPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Trastuzumab_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(0.142)PS(0.719)PGPNHT(0.032)S(0.032)NS(0.032)S(0.032)NAS(0.009)NAT(0.001)VVPQNSSAR 56.041 0.040484 56601000 6291.4 5572.7 6823.3 9020.2 11603 7117.9 7677.6 6306.7 12630 TRUE FALSE 5994.01799 6140.564466 7136.155054 8113.472359 13626.55953 6871.405338 6506.241111 5754.451914 14588.59589 0.410870109 0.420915386 0.489159828 0.556151697 0.934055589 0.47101211 0.44598131 0.394448647 1 13.83255341 -2.151923165 2.449092114 2.161256806 0.507030803 0.486924094 0.156149601 14499685.7 4533524.263 93131704.2 0.0416335 0.007048178 2.151923165 -1.654226003 SPS(ph)PISISSSETSSIMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPISISSSETSSIMQK 18 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 SPS(1)PISISSSETSSIMQK 215.49 9.94E-19 67248000 93078 77215 104810 80622 95958 79656 106520 73790 123620 TRUE FALSE 88678.3874 85083.29629 109615.6422 72517.72339 112693.0448 76897.49275 90268.41763 67328.55641 142790.3582 0.621039043 0.595861635 0.767668374 0.507861485 0.789220268 0.53853421 0.63217446 0.471520327 1 17.12353904 -1.260586461 4.922703268 1.000087488 0.618174722 0.587262394 0.101284053 8.33E-05 1.25E-05 0.083960571 0.019785183 0.054879929 1.260586461 -0.381912766 SPS(ph)PPTQHTGQPPGQPSAPSQLSAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 SPS(1)PPTQHTGQPPGQPSAPSQLSAPR;S(0.007)PS(0.992)PPTQHTGQPPGQPSAPSQLSAPR;S(0.001)PS(0.997)PPT(0.002)QHTGQPPGQPSAPSQLSAPR;S(0.001)PS(0.998)PPT(0.001)QHTGQPPGQPSAPSQLSAPR;S(0.063)PS(0.936)PPT(0.001)QHTGQPPGQPSAPSQLSAPR;S(0.198)PS(0.8)PPT(0.002)QHTGQPPGQPSAPSQLSAPR 259.93 5.99E-53 9406250000 590559 503652 551614 562806 557100 512283 597164 567102 583244 TRUE FALSE 562644.4464 554974.7114 576906.0475 506231.6716 654258.0636 494542.5113 506055.6641 517443.5425 673690.5007 0.835167552 0.823782896 0.856336919 0.751430621 0.971155245 0.734079686 0.751169363 0.768073087 1 19.36172643 SPS(ph)PQGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPQGTK 8 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.03)PS(0.97)PQGTK;S(0.047)PS(0.953)PQGTK 78.342 0.026352 268740000 481430 484140 439100 557930 320360 476290 467890 549560 386970 TRUE FALSE 458673.758 533474.4164 459233.1693 501845.8164 376230.6826 459795.9579 396504.7871 501437.613 446979.3312 1.026163238 1.193510257 1.027414776 1.12274949 0.841718299 1.028673869 0.887076335 1.121836242 1 18.7698486 2.773380132 24.99802181 0.966589732 1.098321425 0.294898132 0.088744099 629.4919575 451930.989 0.024329586 0.025804384 593.4445306 -2.773380132 0.131731693 SPS(ph)PSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.306)PS(0.694)PSFR 126.07 0.0041833 105730000 225260 200070 227040 237570 247100 222310 272290 214370 263570 TRUE FALSE 214612.4062 220457.3605 237450.0086 213689.0122 290194.1618 214611.349 230747.1596 195598.6264 304443.0895 0.704934399 0.724133239 0.779948755 0.701901339 0.953196744 0.704930926 0.757932 0.642480099 1 18.21581304 -1.773457417 2.802560027 1.058701767 0.746608729 0.485275834 0.082150839 23599380.54 19090910.13 9525149.604 0.0181366 0.016847776 1.773457417 -0.312093038 SPS(ph)PSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSPSVR 7 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.023)PS(0.974)PS(0.003)VR;S(0.041)PS(0.944)PS(0.016)VR;S(0.023)PS(0.894)PS(0.083)VR 100.98 0.011703 739750000 569580 546570 581490 652270 545460 582990 564930 551460 639390 TRUE FALSE 542657.0822 602266.1044 608151.8917 586702.5804 640588.0513 562800.9101 478739.5528 503171.2389 738543.3356 0.734766744 0.815478355 0.823447809 0.794405084 0.86736691 0.762041823 0.648221343 0.681302254 1 19.49432305 2.003879715 24.95920034 0.729348904 0.802901042 0 0.100881035 237.6538596 1528878.997 0.034016796 0.025010846 100.8973395 -2.003879715 0.073552138 SPS(ph)PTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK 38 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 S(0.19)PS(0.798)PT(0.01)VHAS(0.001)STPAVNIQPDVSGGWDWHAKPGGFGMGSK 129.29 7.27E-09 216640000 179180 114310 168300 179040 200360 137280 270370 208680 207540 TRUE FALSE 170710.5165 125958.319 176016.7215 161042.559 235302.7206 132525.9592 229120.0908 190406.8729 239724.2432 0.712112026 0.525430041 0.734246646 0.671782532 0.981555797 0.552826687 0.955765206 0.794274581 1 17.87101629 1.971760139 0.324134215 1.011172176 0.578725958 0.371000922 0.133237819 1.363289836 0.423389388 0.174738809 0.20933297 93.70443344 -1.971760139 -0.432446218 SPS(ph)PVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.047)PS(0.953)PVLR;S(0.019)PS(0.981)PVLR 88.819 0.019225 494560000 629980 510090 548710 616320 648680 623540 794840 688860 565830 TRUE FALSE 600202.0939 562068.7509 573868.8962 554366.3427 761809.5866 601946.6535 673572.5598 628539.7665 653576.0265 0.918335541 0.859989853 0.878044593 0.84820483 1.165602096 0.921004794 1.030595573 0.961693424 1 19.31799554 2.799190868 24.99998397 1.010816806 0.878244907 0.533337472 0.064797995 177.4424043 73165.34614 0.017520528 0.018583321 629.7829053 -2.799190868 -0.132571899 SPS(ph)PVQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.013)PS(0.987)PVQGK;S(0.214)PS(0.786)PVQGK;S(0.072)PS(0.928)PVQGK 101.3 0.005765 2010110000 4464660 3961080 3895440 4825210 3138020 4263110 4820620 4377480 3598460 TRUE FALSE 4253624.37 4364718.555 4074049.777 4340170.724 3685289.694 4115477.432 4085145.882 3994164.645 4156490.798 1.023369129 1.050097009 0.980165715 1.044191106 0.886634874 0.990132694 0.9828353 0.960946346 1 21.98693459 SPS(ph)SLLIANLHLQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SPSSLLIANLHLQ 13 0 Q658Y4 Q658Y4 FAM91A1 Protein FAM91A1 1 S(0.004)PS(0.972)S(0.023)LLIANLHLQ;S(0.027)PS(0.911)S(0.063)LLIANLHLQ;S(0.004)PS(0.763)S(0.233)LLIANLHLQ;S(0.008)PS(0.964)S(0.028)LLIANLHLQ;SPS(0.999)S(0.001)LLIANLHLQ 227.47 9.49E-12 258101000 548857 543698 604696 677445 670275 651486 665744 709042 640933 TRUE FALSE 522913.6173 599101.4443 632421.9097 609346.9415 787170.7478 628924.8765 564172.5256 646954.5236 740325.6162 0.706329223 0.809240463 0.854248314 0.82307964 1.063276389 0.849524672 0.762059982 0.873878344 1 19.49780042 4.201113867 1.177769881 0.878435179 0.694583535 0.325895502 0.085851237 0.91191059 1.90666988 0.026646936 0.164281845 15889.63302 -4.201113867 -0.183851644 SPSDEYKDNLHQVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSDEYKDNLHQVSK 15 1 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 142.97 2.70E-06 129280000 309750 317120 280660 350670 180990 331180 318020 325090 180670 FALSE TRUE 295108.7314 349434.8885 293528.5386 315419.9854 212554.5987 319711.1536 269500.2082 296623.3962 208687.3809 1.414118717 1.674441871 1.40654666 1.511447334 1.018531153 1.532009996 1.291406347 1.421376774 1 17.67098384 -3.563694184 0.104839349 8.48E-14 1.724404753 0.39538356 0.166178539 110.465509 1.078674314 26.90177431 2.454618161 0.00027309 3.563694184 1.724404753 SPSDSSTAS(ph)TPVAEQIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 SPSDSSTAS(0.5)T(0.5)PVAEQIER 186.72 1.27E-15 0 97729 78845 88652 97301 89462 83814 105020 93501 91920 TRUE FALSE 93109.54385 86879.39514 92716.78189 87520.11862 105064.1445 80911.50016 88997.27018 85313.55676 106174.4841 0.876948399 0.81827 0.873249186 0.824304628 0.989542312 0.762061627 0.838217119 0.803522216 1 16.69607757 -0.939949263 4.126232034 1.000006199 0.847021795 0.38678832 0.060024325 2921188.122 1415977.317 157.1116738 0.012670182 0.114828776 0.939949263 -0.152984403 SPSFGDPQLS(ph)PEARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR 122.19 5.73E-05 289890000 417230 339150 372770 418470 429520 382480 452460 451320 495250 TRUE FALSE 397508.3648 373709.7706 389861.8732 376404.6006 504428.152 369234.6217 383428.917 411800.0282 572050.8406 0.694882931 0.653280695 0.681516127 0.657991517 0.881789023 0.645457703 0.670270699 0.719866136 1 19.12578385 0.865217177 7.650827234 0.999999945 0.693803511 0.659399235 0.067746837 4.786899782 271.9158005 0.061539214 0.015417682 7.33191087 -0.865217177 -0.306196434 SPSGS(ph)AFGSQENLR ddPTM_SK-BR-3_Trastuzumab_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(0.288)PS(0.107)GS(0.373)AFGS(0.232)QENLR 141.6 1.01E-05 301310000 143030 139760 159400 162990 143710 147420 176710 148410 168310 TRUE FALSE 136269.2554 154001.7029 166708.6477 146605.9355 168772.9785 142314.8084 149749.644 135414.4336 194410.6552 0.700935117 0.792146412 0.857507771 0.754104426 0.868126175 0.732031937 0.770274879 0.696538127 1 17.56874777 -2.300378815 2.460195791 2.249477477 0.772132708 0.610454882 0.057372446 4256353.449 1096255.057 29384688.9 0.012983025 0.005007503 2.300378815 -1.477344768 SPSGSAFGS(ph)QENLR ddPTM_SK-BR-3_Trastuzumab_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 SPSGSAFGS(1)QENLR;SPSGS(0.001)AFGS(0.999)QENLR;S(0.021)PS(0.134)GS(0.377)AFGS(0.468)QENLR 212.5 2.47E-09 787387000 411372 326585 387816 410174 393079 414793 429621 429020 435798 TRUE FALSE 391927.2608 359864.3828 405597.7472 368942.5302 461631.8531 400428.6144 364074.4259 391452.7344 503379.3281 0.778592284 0.714897022 0.805749709 0.732931429 0.917065575 0.795480847 0.723260582 0.777649603 1 18.94128645 -2.116528626 2.261711725 1.413049499 0.774885447 0.589022617 0.057384881 5684724.178 1455376.747 12067241.91 0.013536571 0.007646653 2.116528626 -0.638164052 SPSLSLAPLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 SPSLSLAPLS(1)PR;SPSLSLAPLS(1)PR;SPSLSLAPLS(1)PR;SPSLSLAPLS(1)PR 179.27 2.20E-05 864470000 955490 801630 746340 813870 1005890 869820 1166550 1065750 1283440 TRUE FALSE 910325.8813 883317.0084 780560.4272 732058.2413 1181316.898 839697.9153 988571.3723 972427.2801 1482469.32 0.61406052 0.595841679 0.526527205 0.493810045 0.796857568 0.56641841 0.666841033 0.655951032 1 20.49957082 -1.631715084 0.309847819 1.325537425 0.57569003 0.714971666 0.078534511 12.79932154 0.726630121 3.233932157 0.073104139 0.023349894 1.631715084 -0.749847395 SPSPGGPQLS(ph)PQLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR 236.43 1.10E-17 1304583000 739982 635271 694041 749373 762751 686918 734853 707059 709319 TRUE FALSE 705004.5174 700005.8371 725863.4664 674044.6023 895774.5329 663129.8574 622737.6783 645145.1656 819316.5678 0.860478776 0.854377739 0.885937737 0.822691288 1.093319198 0.80936952 0.760069676 0.787418674 1 19.64406146 -1.374540941 6.674966143 1.000009616 0.85614598 0.190774592 0.090934614 1.28E-05 1.20E-06 0.086791097 0.020455491 0.042214248 1.374540941 -0.143863636 SPSQDFS(ph)FIEDTEILDSAMYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.283)PS(0.283)QDFS(0.434)FIEDTEILDSAMYR 100.92 0.0020722 10783000 8272.9 7326.1 7182 8810.9 7766 6975 10034 9792.6 6724 TRUE FALSE 7881.856412 8072.637919 7511.301804 7925.211592 9120.387941 6733.454001 8503.129013 8935.10803 7766.723579 1.014823861 1.039387824 0.967113317 1.020406033 1.174290272 0.866961973 1.094815456 1.150434664 1 12.92309041 1.589874875 25 1.091994633 1.018584449 0.123600457 0.083146486 1.708018031 2366.52159 0.039884561 0.018523509 38.89330732 -1.589874875 -0.073410183 SPSS(ph)LLIANLHLQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSSLLIANLHLQ 13 0 Q658Y4 Q658Y4 FAM91A1 Protein FAM91A1 1 S(0.001)PS(0.039)S(0.96)LLIANLHLQ;S(0.002)PS(0.077)S(0.921)LLIANLHLQ 185.32 9.18E-06 162263000 146160 138468 121172 139834 171496 141200 176977 148255 147275 TRUE FALSE 139251.3065 152578.0466 126727.8561 125777.6207 201404.8481 136310.2086 149975.9082 135273.0063 170113.6548 0.818578065 0.89691828 0.744959928 0.739374043 1.183942866 0.801289048 0.88162181 0.795191934 1 17.37613942 SPSSES(ph)SPQHPTPPARPR ddPTM_SK-BR-3_Trastuzumab_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(0.017)PS(0.076)S(0.076)ES(0.416)S(0.416)PQHPTPPARPR 74.047 0.011625 11707000 5700.5 4253.6 5814.3 6129.2 7193.8 5497.9 5194 5545.6 5982.4 TRUE FALSE 5431.048662 4687.046676 6080.891406 5513.081171 8448.396442 5307.506344 4401.559906 5059.997865 6910.120038 0.785955762 0.678287302 0.879997941 0.79782712 1.22261211 0.7680773 0.636973002 0.73225904 1 12.75449506 -1.312428867 3.92231369 1.000404299 0.798825772 0.113009731 0.160711217 25654199.09 8584207.666 88179.4999 0.038170422 0.048704729 1.312428867 -0.201578527 SPSVPKS(ph)PTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SPSVPKSPTPK 11 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPS(0.003)VPKS(0.993)PT(0.004)PK;SPS(0.001)VPKS(0.973)PT(0.025)PK;SPSVPKS(0.981)PT(0.018)PK;SPSVPKS(0.852)PT(0.148)PK 113.76 0.00081687 1037280000 1623220 1897480 1459190 2079370 834040 1758930 1616490 1949600 845700 TRUE FALSE 1546493.608 2090835.369 1526095.305 1870347.777 979496.3119 1698017.813 1369864.762 1778882.689 976846.8368 1.583148503 2.14039222 1.562266721 1.914678644 1.002712273 1.738264126 1.402333211 1.821045656 1 19.89777285 2.795101759 24.99975831 1.4447921 1.819511186 0.292114203 0.308551089 356.5855781 157664.079 0.084302739 0.08941653 623.8809987 -2.795101759 0.374719086 SPSVPKS(ph)PTPKS(ph)PPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.116)PS(0.242)VPKS(0.642)PT(0.041)PKS(0.924)PPS(0.036)R;S(0.081)PS(0.106)VPKS(0.81)PT(0.007)PKS(0.887)PPS(0.108)R 78.708 0.010933 212800000 893180 704210 875060 962410 480360 996540 1047090 1049480 577510 TRUE FALSE 850961.1515 775969.7996 915182.3666 865666.7183 564134.6319 962029.5699 887337.1894 957581.9676 667067.3013 1.275675108 1.163255639 1.371949074 1.29772021 0.845693727 1.442177675 1.330206394 1.435510279 1 19.3474728 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.375)PT(0.625)GPSNSFLANMGGTVAHK 343.8 2.78E-80 2223600000 1594700 1916200 1391600 1905800 968400 1619000 1392100 1706200 968880 TRUE FALSE 1519321.691 2111462.959 1455406.236 1714225.363 1137288.653 1562933.624 1179709.577 1556796.083 1119128.962 1.357593041 1.886702096 1.300481254 1.531749621 1.01622663 1.396562574 1.054131934 1.391078362 1 20.09394486 3.089293482 1.635715181 1.184795411 1.600336938 0.368924096 0.212457364 0.324433399 1.786951251 0.066687513 0.084637522 1228.268976 -3.089293482 0.415541527 SPTDWALFTYEGNSNDIR ddPTM_SK-BR-3_Trastuzumab_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 0 206.18 2.05E-15 46882000 24518 27258 25374 33136 29260 27528 33904 29623 31325 FALSE TRUE 23359.08273 30035.62119 26537.423 29805.10633 34362.93474 26574.69846 28731.32211 27029.05308 36182.72101 0.64558668 0.83010952 0.733428063 0.823738666 0.949705654 0.734458264 0.794061953 0.74701549 1 15.14301329 -5 0.175816669 1.822978667 0.735666874 0.426047364 0.079425454 134.7109513 1.286537135 39.1627397 0.255545745 1.00E-05 5 -1.087311794 SPTEYHEPVYANPFYRPTT(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTEYHEPVYANPFYRPTTPQR 22 1 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SPTEYHEPVYANPFYRPT(0.401)T(0.599)PQR 130.15 2.06E-05 314340000 130030 124890 105340 133030 138110 122130 131360 126630 114390 TRUE FALSE 123883.7396 137616.433 110169.9432 119657.5717 162196.3403 117900.6075 111318.6194 115541.6059 132129.017 0.93759677 1.041530741 0.833805819 0.905611609 1.227560334 0.892314271 0.842499414 0.874460497 1 17.01158781 2.040272443 24.99999839 0.882965284 0.987391357 0.123699407 0.109936901 256.4938079 159223.0424 0.039387324 0.029089433 109.7166257 -2.040272443 0.104426073 SPTLSQVHSPLVTS(ph)PSANLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTLSQVHSPLVTSPSANLK 20 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 SPTLSQVHSPLVT(0.041)S(0.896)PS(0.063)ANLK 181.35 3.30E-17 137770000 130160 119690 126370 123320 103000 115020 143160 150040 116200 TRUE FALSE 124007.5948 131886.5471 132164.1895 110923.6393 120963.1674 111036.8286 121318.3127 136901.7022 134219.7025 0.923914987 0.982616893 0.98468546 0.826433357 0.901232569 0.82727667 0.903878569 1.019982161 1 17.03423694 1.23953747 24.99688819 1.009991119 0.911090007 0.393059714 0.052953975 29.01757412 742711.4211 0.043456649 0.013774342 17.35951032 -1.23953747 -0.098901113 SPTLYGISHDDLKGDPLLDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPTLYGISHDDLKGDPLLDQR 21 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 152.32 3.22E-08 66819000 95213 63815 80818 84968 81929 96851 127040 110790 98396 FALSE TRUE 90712.47018 70317.82105 84523.58524 76426.85521 96217.39166 93497.02559 107657.7148 101088.6403 113654.7491 0.798140604 0.618696725 0.743687227 0.672447529 0.846576077 0.822640728 0.947234634 0.88943613 1 16.79429844 2.195847713 1.052521733 0.956301002 0.701902871 0.740581456 0.05942963 0.239678001 0.502765997 0.039416454 0.021422994 156.9812247 -2.195847713 -0.254398131 SPTPKS(ph)PPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPTPKSPPSR 10 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPT(0.001)PKS(0.999)PPSR;SPT(0.017)PKS(0.983)PPSR 87.719 0.0076817 672600000 276430 170969 258490 251720 256479 260770 342510 295970 331070 TRUE FALSE 263363.7017 188390.9355 270342.0222 226416.6274 301208.8564 251739.4695 290253.8089 270053.2978 382410.6447 0.688693438 0.492640407 0.706941676 0.592077209 0.787658138 0.658296188 0.759010799 0.706186665 1 18.54476316 -1.805736413 0.17477613 1.416252252 0.544594877 0.673043601 0.075482239 17.60567063 0.482495547 3.320164673 0.275722416 0.015640967 1.805736413 -0.871657375 SPVDIVTGGIS(ph)PVRDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPVDIVTGGISPVRDLDR 18 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 SPVDIVT(0.276)GGIS(0.724)PVRDLDR 65.901 0.019802 33311000 30480 25553 26108 32226 59089 26738 32732 30229 56001 TRUE FALSE 29039.27081 28156.87975 27305.07762 28986.58125 69394.10289 25812.05636 27738.13224 27581.98851 64685.34907 0.448931191 0.43528991 0.422121516 0.44811664 1.07279475 0.399040227 0.428816303 0.426402406 1 15.98115136 -1.529599267 3.010429268 1.019062862 0.501719581 0.368762434 0.201126304 42317370.66 49365929 6627120.142 0.046554545 0.029539336 1.529599267 -0.517343281 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)PVGKS(0.965)PPS(0.034)TGSTYGSSQK;S(0.002)PVGKS(0.958)PPS(0.037)T(0.004)GSTYGSSQK 171.05 6.68E-12 676640000 644880 699180 537520 749280 312850 653000 575800 658730 337200 TRUE FALSE 614397.8004 770427.2369 562165.8237 673960.9509 367410.9409 630386.4463 487951.1347 601048.1091 389491.2538 1.577436706 1.978034755 1.443333626 1.730362221 0.943309862 1.618486783 1.252790993 1.543162018 1 18.57123141 2.786160343 24.99310393 1.312941863 1.706656464 0.400514516 0.246031268 382.8179191 201004.7815 0.067695458 0.071801718 611.1676282 -2.786160343 0.393714601 SPVGKS(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQKEESAASGGAAYTK 32 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.069)PVGKS(0.818)PPS(0.042)T(0.054)GS(0.016)T(0.001)YGSSQKEESAASGGAAYTK;SPVGKS(0.985)PPS(0.014)T(0.001)GSTYGSSQKEESAASGGAAYTK 288.67 2.55E-75 557510000 318720 276390 288290 363920 174204 332270 351430 357750 194476 TRUE FALSE 303654.7372 304554.4552 301508.3817 327338.0702 204585.1224 320763.4066 297812.899 326423.5134 224634.3448 1.351773423 1.355778679 1.342218537 1.457204019 0.910747297 1.427935727 1.325767434 1.453132706 1 17.777219 -1.603423251 2.753427234 0.973457503 1.328084678 0.305020752 0.155628757 28325136.81 27934219.05 5444401.763 0.033816258 0.024921648 1.603423251 0.354627175 SPVGKS(ph)PPSTGSTYGSSQKEESAASGGAAYTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQKEESAASGGAAYTKR 33 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.063)PVGKS(0.883)PPS(0.04)T(0.01)GS(0.002)T(0.002)YGSSQKEESAASGGAAYTKR;S(0.051)PVGKS(0.838)PPS(0.084)T(0.013)GS(0.006)T(0.006)YGS(0.001)S(0.001)QKEESAASGGAAYTKR 113.22 3.86E-06 1037160000 473920 242451 438230 336230 290964 452080 616010 543810 357780 TRUE FALSE 451518.7408 267157.0325 458323.279 302431.5216 341708.0295 436424.3562 522026.3607 496191.1135 413262.6951 1.09257077 0.646458138 1.109036176 0.731814231 0.826854283 1.056045855 1.263182878 1.200667564 1 18.65669961 2.054746073 4.268848329 1.180015781 0.873303048 0.394041562 0.155563112 0.1777149 6.748984812 0.058406996 0.040327973 113.4347382 -2.054746073 -0.306712733 SPVKAEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPVKAEAK 8 1 P12036-2;P12036 P12036-2 NEFH Neurofilament heavy polypeptide 0 ;; 59.245 0.059989 841680000 2537550 2035740 2171760 2422690 3473490 1488680 2972170 1868130 5663600 FALSE TRUE 2417605.04 2243184.22 2271337.344 2179156.598 4079265.556 1437126.638 2518710.879 1704546.634 6541882.162 0.369558023 0.342895846 0.347199367 0.333108507 0.623561454 0.219680912 0.385013184 0.260559055 1 22.64127434 -1.989916676 2.79188174 1.598567802 0.361346008 0.782812743 0.105908459 26374084.1 12609396.58 101657519.8 0.02286543 0.010234893 1.989916676 -1.237221794 SPVPSPGSSS(ph)PQLQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.01)S(0.327)S(0.664)PQLQVK 329.46 2.86E-47 0 380320 346550 337020 420300 270010 363040 355610 373850 284780 TRUE FALSE 362343.0273 381863.839 352472.7004 378050.6455 317099.6585 350467.8338 301355.1633 341113.7121 328942.2279 1.101540017 1.160884212 1.071533754 1.149291922 0.963998026 1.065438864 0.916134013 1.03700189 1 18.3274747 2.738619375 24.99999999 0.990900648 1.12261201 0.638911614 0.046317107 2.944460363 1252956.882 0.013252851 0.013263263 547.7966538 -2.738619375 0.131711362 SPWSNKYDPPLEDGAMPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPWSNKYDPPLEDGAMPSAR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 78.975 0.0085387 977970000 1479860 1204720 1233010 1448510 1246320 1347220 1638510 1473870 1472910 FALSE TRUE 1409909.951 1327482.338 1289544.728 1302903.023 1463677.813 1300565.434 1388525.206 1344810.129 1701321.36 0.828714659 0.780265486 0.757966577 0.765818295 0.860318249 0.76444431 0.816145167 0.790450388 1 20.69822424 -4.999995211 0.468667103 6.247074855 0.793945129 0.800781844 0.032051756 678.5443049 3.635860258 3711.438133 0.015101079 1.00E-05 4.999995211 -5.453129726 SPWWVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SPWWVR 6 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 120.06 0.047651 635300000 738840 679830 662880 788070 768630 613980 855960 761380 739840 FALSE TRUE 703916.4974 749105.4499 693273.7037 708851.7064 902678.8286 592717.7186 725367.5812 694709.5309 854570.6086 0.823707825 0.876586958 0.811253859 0.8294829 1.056295196 0.693585425 0.848809418 0.812934032 1 19.70484017 4.724916449 4.424254926 0.855311583 0.821931924 0.007131916 0.101315992 1.453939268 62.97991575 0.021828448 0.144943877 53078.23209 -4.724916449 -0.033379659 SPYGSRS(ph)PFEHSVEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SPYGSRSPFEHSVEHK 16 1 O14646 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 S(0.004)PYGS(0.143)RS(0.853)PFEHSVEHK;SPYGS(0.009)RS(0.991)PFEHSVEHK;S(0.246)PY(0.003)GS(0.246)RS(0.505)PFEHSVEHK 223.54 5.21E-15 434561000 649960 478158 597547 655215 556348 654672 822061 710721 81963 TRUE FALSE 619237.6789 526882.8438 624945.121 589351.5434 653374.9151 632000.5445 696640.4963 648486.5015 94673.40343 6.540777626 5.565267802 6.601063217 6.225101475 6.901356573 6.675587035 7.358354839 6.849722076 1 16.53067157 6.666714703 13.27869076 6.264890513 35.30258543 0 1.841216563 0 0 0.341841011 0 4642102.258 -6.666714703 29.03769491 SPYLYPLYGLGELPQGFAR ddPTM_SK-BR-3_Trastuzumab_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 ; 206.18 8.76E-16 192139000 187757 167024 160371 182885 183013 149472 210238 179184 190139 FALSE TRUE 178882.0987 184043.9355 167724.169 164501.0523 214930.4093 144295.7472 178162.3318 163493.699 219624.785 0.814489579 0.837992558 0.763685068 0.749009509 0.978625474 0.657010306 0.811212322 0.744422807 1 17.74468135 -1.016091881 4.638970066 1.000005152 0.797699056 0.380394375 0.082314958 4.17E-06 8.84E-07 0.070739255 0.016672948 0.096362513 1.016091881 -0.202306096 SPYQEFTDHLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 200.21 1.63E-07 3791660000 6059610 5258530 5016250 6005170 4874700 5613390 6649510 6129810 4758830 FALSE TRUE 5773184.244 5794380.185 5246250.024 5401518.903 5724846.137 5418996.897 5635005.123 5593051.34 5496805.052 1.05027997 1.054136017 0.954418062 0.982665176 1.041486115 0.98584484 1.025141891 1.017509496 1 22.39016188 3.806980806 24.99826042 1.003344885 1.052208128 0.433585441 0.024214001 151.7728894 55451.43653 0.006052759 0.010911767 6411.812381 -3.806980806 0.048863243 SQAAPGS(ph)SPCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQAAPGSSPCR 11 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 SQAAPGS(0.5)S(0.5)PCR;SQAAPGS(0.595)S(0.405)PCR 96.866 0.0030934 0 197619 187901 190077 218345 202804 199010 232720 201074 197806 TRUE FALSE 188277.9415 207048.3255 198792.2185 196396.5458 238172.9534 192118.2338 197214.2898 183466.8946 228480.7442 0.824042928 0.906195952 0.870061147 0.859575919 1.042420245 0.840850875 0.863154969 0.802986244 1 17.80171306 4.620742413 2.803896155 0.891542303 0.819689685 0.086453192 0.072634511 0.89066286 11.22258275 0.016685705 0.128765888 41758.26187 -4.620742413 -0.071852618 SQANGAGALSYVS(ph)PNTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.999)PNT(0.001)SK 177.09 1.00E-13 132310000 169390 158560 153920 194490 112410 178840 184380 184210 142170 TRUE FALSE 161383.2704 174717.4443 160977.3842 174939.4957 132014.2684 172646.726 156249.4446 168079.5958 164216.9975 0.982744009 1.063942509 0.980272363 1.065294692 0.803901365 1.051332862 0.951481558 1.023521307 1 17.32524394 SQAPGQPGASQWGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQAPGQPGASQWGSR 15 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 113.25 0.0016274 23665000 16536 13909 16538 15212 15881 17712 18619 17927 20091 FALSE TRUE 15754.37605 15326.34291 17296.28366 13682.86086 18650.64137 17098.629 15778.32959 16357.21684 23206.60967 0.678874522 0.660430073 0.745317128 0.589610506 0.803677988 0.736799957 0.679906708 0.704851638 1 14.50224815 -5 0.301149996 3.543890163 0.680434829 0.738924439 0.056183838 128.6806467 1.186954408 206.7616069 0.050829004 1.00E-05 5 -2.863455334 SQAPLESSLDSLGDVFLDS(ph)GRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQAPLESSLDSLGDVFLDSGRK 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 SQAPLESSLDSLGDVFLDS(1)GRK 211.11 2.25E-23 18240000 23188 26532 25956 27595 17069 25577 31908 26398 23234 TRUE FALSE 22091.94919 29235.64096 27146.10827 24821.09817 20045.8282 24691.26208 27039.84857 24086.45118 26837.01006 0.82318966 1.089377725 1.01151761 0.924883142 0.746947151 0.920045192 1.007558164 0.897508743 1 14.71193633 -0.950373567 5.019999825 1.000000335 0.93777516 0.043168079 0.097147117 3.64E-07 7.61E-08 0.094122123 0.022184678 0.112105374 0.950373567 -0.062225175 SQATS(ph)PGQTNGDSSLEVLATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 SQATS(1)PGQTNGDSSLEVLATR;SQATS(1)PGQTNGDSSLEVLATR;SQAT(0.003)S(0.997)PGQTNGDSSLEVLATR;SQATS(1)PGQTNGDSSLEVLATR;SQAT(0.023)S(0.976)PGQTNGDSSLEVLATR;S(0.001)QAT(0.008)S(0.991)PGQTNGDSSLEVLATR 391.76 3.14E-131 1273280000 1306830 1149200 1253620 1360410 1297050 1218970 1490270 1333080 1433360 TRUE FALSE 1245058.736 1266304.787 1311099.717 1223659.002 1523255.109 1176756.763 1262901.941 1216348.448 1655638.148 0.752011384 0.764843929 0.79189992 0.739086016 0.92004108 0.710757217 0.762788622 0.734670465 1 20.65895597 -1.162063823 3.833457942 1.00013141 0.77086069 0.613621813 0.056848614 24807307.42 57460337.46 46251.1648 0.012446765 0.06885511 1.162063823 -0.22927072 SQDADS(ph)PGSSGAPENLTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQDADSPGSSGAPENLTFK 19 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 SQDADS(0.99)PGS(0.01)SGAPENLTFK;SQDADS(0.999)PGS(0.001)SGAPENLTFK 195.86 9.04E-16 198472000 507020 480240 444540 572150 390280 516850 560980 545910 539350 TRUE FALSE 483054.1694 529177.002 464922.5987 514636.395 458344.7084 498951.3549 475392.1979 498107.2263 622989.6434 0.775380738 0.849415408 0.746276609 0.826075362 0.735718022 0.800898314 0.763082024 0.79954335 1 19.24884865 0.943259818 22.1241661 1 0.788418029 0.791307304 0.034415091 2373.150693 925341.8153 0.030516429 0.007629107 8.775256462 -0.943259818 -0.211581971 SQDATFS(ph)PGSEQAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQDATFSPGSEQAEK 15 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFS(1)PGSEQAEK;SQDATFS(0.998)PGS(0.002)EQAEK;SQDATFS(0.986)PGS(0.014)EQAEK 401.46 8.53E-133 800190000 1366360 1165660 1190870 1424530 876950 1387800 1452410 1477030 957170 TRUE FALSE 1301774.871 1284442.079 1245472.567 1281333.538 1029889.802 1339740.138 1230818.179 1347693.423 1105603.035 1.177434241 1.161757013 1.126509722 1.158945388 0.93151861 1.211773209 1.113255065 1.218966826 1 20.07640205 -1.680582311 3.073842585 0.985644709 1.137733082 0.224902764 0.080231402 6318412.503 3494539.525 605313.4909 0.017197741 0.020864966 1.680582311 0.152088373 SQDATFS(ph)PGSEQAEKS(ph)PGPIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 S(0.001)QDAT(0.106)FS(0.882)PGS(0.012)EQAEKS(0.997)PGPIVS(0.002)R;S(0.006)QDAT(0.083)FS(0.896)PGS(0.054)EQAEKS(0.945)PGPIVS(0.015)R 91.151 0.0030117 407250000 886610 800580 897690 1000490 620990 996180 1068490 981250 705510 TRUE FALSE 844701.7024 882160.0122 938849.9744 899918.8444 729290.4594 961682.0368 905472.2263 895326.5481 814916.8876 1.036549512 1.082515316 1.152080646 1.104307517 0.894926183 1.180098304 1.111122177 1.098672223 1 19.6362934 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR 259.2 6.82E-44 1731310000 1647620 1372890 1553930 1689060 1053490 1654090 1770960 1680510 1171640 TRUE FALSE 1569740.268 1512789.052 1625179.228 1519272.48 1237218.322 1596808.449 1500767.526 1533355.635 1353331.947 1.15990779 1.117825567 1.20087258 1.122616283 0.914201667 1.179908929 1.108942657 1.133022566 1 20.36808432 0.745375039 0.013979274 1.76E-05 2.158145642 0.189635486 0.077389388 1713.432385 12.62081099 998.5009077 947.533345 5.563845212 -0.745375039 2.158128091 SQDIYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SQDIYLR 7 0 J3QQ67;Q07020;F8VYV2;G3V203;A0A075B7A0;F8VXR6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;;;;; 221.53 6.01E-05 2432500000 2963380 3122610 2439850 3150540 2756370 2824490 3187210 3014020 2800090 FALSE TRUE 2823306.9 3440807.509 2551719.536 2833841.734 3237080.055 2726677.203 2700942.577 2750096.43 3234313.656 0.872923037 1.063844721 0.788952404 0.876180246 1.000855328 0.843046622 0.835089872 0.850287487 1 21.62502816 3.735879467 24.99993164 0.87740639 0.968383875 0.14818663 0.081667833 355.3061532 3313002.737 0.020366874 0.033255752 5443.515544 -3.735879467 0.090977486 SQDLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQDLAK 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 139.92 0.027558 1225830000 1770740 1568880 1414380 1719990 1147420 1562650 1840500 1816140 1386860 FALSE TRUE 1687040.629 1728750.656 1479230.722 1547093.337 1347529.685 1508535.039 1559697.922 1657109.154 1601927.166 1.053131919 1.079169323 0.923406977 0.965770087 0.841192854 0.941700142 0.973638475 1.034447251 1 20.61137712 3.742597798 24.78248573 0.94977218 1.066150629 0.452097627 0.05099778 239.3275199 1469121.074 0.013040805 0.022475756 5528.378869 -3.742597798 0.116378449 SQDLHCGACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQDLHCGACR 10 0 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 90.05 0.011095 1024330000 2426840 1715640 1343040 1511500 2423630 1467210 2587610 1969480 2295420 FALSE TRUE 2312128.083 1890465.667 1404619.712 1359561.148 2846310.305 1416400.15 2192822.57 1797021.89 2651382.01 0.87204638 0.713011425 0.529768893 0.512774524 1.073519506 0.534212024 0.827048898 0.677768003 1 21.33831312 -1.222951923 4.355391917 1.000113627 0.724682755 0.203862729 0.174926895 24217569.14 6800072.858 26214.24004 0.03751746 0.059847784 1.222951923 -0.275430872 SQDQDS(ph)EVNELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQDQDSEVNELSR 13 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SQDQDS(1)EVNELSR;SQDQDS(1)EVNELSR 263.04 3.97E-24 221030000 451300 388760 346800 469700 333210 387940 419290 413980 319640 TRUE FALSE 429967.9434 428375.086 362701.123 422484.8636 391321.7185 374505.5405 355319.6097 377729.7166 369208.1387 1.164567891 1.160253638 0.982375752 1.144299974 1.059894616 1.014348009 0.962382928 1.023080688 1 18.49407483 3.596147224 0.452703976 0.981113151 1.218232039 0.539708604 0.050871698 1.246404621 0.406405949 0.041084269 0.14450329 3945.910443 -3.596147224 0.237118888 SQDVAVS(ph)PQQQQCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK;SQDVAVS(1)PQQQQCSK 395.34 9.78E-115 3322011000 4805271 3937063 4496005 4969118 3657418 4771737 5648500 4953167 4242664 TRUE FALSE 4578135.363 4338254.196 4702151.276 4469612.818 4295270.541 4606490.551 4786717.583 4519441.439 4900594.665 0.934199965 0.885250565 0.959506264 0.912055194 0.876479455 0.939986036 0.976762599 0.922223066 1 22.22452539 1.207677044 0.663603897 0.995599838 0.913041958 0.394760119 0.029767455 0.656022781 0.689842502 0.028222713 0.012181508 16.13158513 -1.207677044 -0.08255788 SQDVELWEGEVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQDVELWEGEVVK 13 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 124.86 0.00048139 32379000 84371 71637 79613 90987 71652 80498 90784 97119 83781 FALSE TRUE 80382.95004 78936.89174 83263.3348 81840.8139 84148.08611 77710.33408 76933.23344 88614.7455 96773.32959 0.830631233 0.815688497 0.860395474 0.84569596 0.869537986 0.803013954 0.794983843 0.915693878 1 16.56232188 1.00650539 4.407563909 0.999589013 0.829864676 0.849807918 0.023572092 0.062328226 3.468879473 0.024164857 0.006150426 10.15091964 -1.00650539 -0.169724338 SQEADVQDWEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 137.6 0.00020781 84663000 312420 342190 285390 328410 294020 308410 287640 316130 271940 FALSE TRUE 297652.5258 377059.55 298475.4138 295397.6029 345296.9949 297729.6844 243755.2351 288447.9813 314111.0663 0.947602799 1.200401993 0.950222535 0.940424055 1.099283126 0.947848441 0.77601607 0.918299329 1 18.26091525 2.007182859 8.452606561 0.870295274 1.035515275 0.262534256 0.09621724 0.127633069 80.98986632 0.035857159 0.025547412 101.6676674 -2.007182859 0.165220001 SQEPIPDDQKVS(ph)DDDKEKGEGALPTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQEPIPDDQKVSDDDKEKGEGALPTGK 27 3 E5RJU9;Q86UE4;H0YBJ8 E5RJU9 MTDH Protein LYRIC 1 S(0.001)QEPIPDDQKVS(0.999)DDDKEKGEGALPTGK;SQEPIPDDQKVS(1)DDDKEKGEGALPTGK 178.76 1.44E-17 1296740000 1740770 1506330 1497490 2362320 535010 2415690 2017610 2056500 355745 TRUE FALSE 1658487.252 1659826.74 1566151.398 2124855.105 628315.5746 2332034.05 1709786.539 1876421.958 410912.1177 4.036111812 4.039371603 3.811402318 5.171069467 1.529075312 5.675262298 4.160954289 4.566479977 1 18.64847035 SQEPLDLVLVPDDCRPGT(ph)PPSDLIEIQVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQEPLDLVLVPDDCRPGTPPSDLIEIQVVK 30 1 Q8NCA9 Q8NCA9 ZNF784 Zinc finger protein 784 1 SQEPLDLVLVPDDCRPGT(0.95)PPS(0.05)DLIEIQVVK 64.668 0.013614 12630000 15648 18153 15029 19720 14898 14817 20598 21376 18711 TRUE FALSE 14908.35005 20002.81134 15718.09452 17737.70813 17496.20648 14303.88357 17455.39679 19504.20412 21612.60632 0.689798807 0.925515925 0.72726511 0.820711203 0.809537093 0.661830571 0.807648857 0.902445722 1 14.39958544 1.071518883 2.775723478 0.997052353 0.781687954 0.51355004 0.073894554 0.195861447 3.085555787 0.066476777 0.017861737 11.79013786 -1.071518883 -0.215364399 SQEQILEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQEQILEILR 10 0 P12270 P12270 TPR Nucleoprotein TPR 0 ; 94.465 0.01881 35901000 66522 53414 50387 65983 79857 58979 72088 58080 68139 FALSE TRUE 63377.63689 58856.94733 52697.29379 59350.26348 93784.03552 56936.54244 61089.65161 52994.2073 78705.64811 0.805248904 0.747810973 0.669549074 0.754078836 1.191579483 0.723411138 0.776178751 0.673321529 1 16.26417955 5.163867819 15.99030505 0.802992858 1.752530087 0 0.162249172 11915.78626 1144809.678 0.035419763 6414.48845 145837.0325 -5.163867819 0.949537229 SQERVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SQERVEGK 8 1 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;;; 127.76 0.0010601 691855000 630657 319603 652335 507985 669371 619601 889274 748625 881493 FALSE TRUE 600847.0935 352170.9091 682245.205 456921.3827 786109.0905 598144.062 753598.9187 683071.4263 1018190.432 0.590112688 0.345879217 0.670056586 0.448758276 0.772064896 0.587457948 0.740135533 0.670868046 1 19.95757598 0.724936574 0.236232409 1.125463349 0.411846111 0.615626792 0.110669968 2.183067474 0.350019162 0.5229767 0.255755236 5.308069177 -0.724936574 -0.713617238 SQESGYYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 137.69 0.00036641 3981970000 3050290 2834120 2641100 3418730 2806820 2853070 3156710 3113990 2977680 FALSE TRUE 2906108.837 3122920.05 2762197.047 3075072.765 3296328.519 2754267.471 2675095.913 2841312.527 3439443.407 0.844935791 0.907972506 0.803094199 0.894061161 0.958390103 0.800788716 0.777770004 0.826096607 1 21.71374369 SQESGYYDRMDYEDDRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQESGYYDRMDYEDDRLR 18 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 103.1 0.00030667 125890000 94169 29699 95567 58740 132360 87398 180720 101650 219720 FALSE TRUE 89717.81799 32725.36186 99948.84148 52835.3436 155443.5421 84371.38535 153147.8448 92748.98712 253793.0554 0.353507774 0.128945064 0.393820238 0.208182779 0.612481464 0.332441663 0.603435916 0.365451241 1 17.95329307 -4.999999968 0.128740208 3.20693205 0.083590953 0.695213132 0.136120389 69.94567614 0.570105054 39.48780487 0.933800228 1.00E-05 4.999999968 -3.123341098 SQET(ph)PEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQETPEKPR 9 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 S(0.029)QET(0.971)PEKPR 100.55 0.0074091 293290000 497680 510640 491330 547940 343200 533980 594540 578370 414190 TRUE FALSE 474155.6527 562674.7965 513857.9665 492860.0302 403053.9713 515488.1387 503832.0035 527724.8567 478420.4698 0.99108563 1.176109368 1.074071865 1.030181736 0.842468073 1.07747927 1.053115482 1.1030566 1 18.86791959 3.254801193 4.796771949 1.018279564 1.089216785 0.114735404 0.081982592 0.387646402 22.62943976 0.023406207 0.030604881 1798.047634 -3.254801193 0.070937221 SQFSDKPVQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQFSDKPVQDR 11 1 Q9BWS9-3;Q9BWS9;E9PKF1;E9PI70;E9PIP0;E9PRL3;E9PPH0;E9PPA0 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 106.17 0.0021586 599730000 1007690 898680 949950 1073680 778310 985740 1132600 1039080 880280 FALSE TRUE 960058.4907 990256.5137 993506.1471 965751.6465 914047.0176 951603.5766 959801.0684 948092.6467 1016789.327 0.944205909 0.9739053 0.977101275 0.949805059 0.898954182 0.935890604 0.943952738 0.932437647 1 19.95558936 -0.928186683 4.54896644 1.000000714 0.946346226 0.38776732 0.021798122 3.90052E+11 91980854826 3080028.729 0.005417481 0.117981338 0.928186683 -0.053654488 SQGDEAGGHGEDRPEPLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK;SQGDEAGGHGEDRPEPLS(1)PK 219.26 5.64E-25 7043098000 7124380 6010290 6318160 7303670 4008572 7417800 7803770 7492130 3672609 TRUE FALSE 6787624.677 6622745.384 6607853.886 6569491.216 4707665.688 7160919.726 6613161.56 6836079.379 4242138.447 1.600047891 1.561180868 1.557670493 1.548627254 1.109738814 1.688044795 1.558921672 1.611470126 1 22.01636027 -1.877849237 2.697367035 0.749807149 1.534337558 0.535187967 0.155009267 36513411.08 26213869.71 58585600.46 0.035774367 0.013248014 1.877849237 0.784530409 SQGLS(ph)GDKTSGFRPIAKPAYSPASWSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQGLSGDKTSGFRPIAKPAYSPASWSSR 28 3 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(0.005)QGLS(0.98)GDKT(0.014)S(0.001)GFRPIAKPAYSPASWSSR 131.76 0.00011457 967950000 480390 249550 565960 376980 472980 487730 812800 603750 649370 TRUE FALSE 457682.9167 274979.4287 591909.8258 339085.2542 555467.5622 470839.7878 688792.4319 550882.4493 750070.9831 0.610186138 0.366604541 0.789138414 0.452070886 0.740553327 0.627726973 0.918302997 0.734440422 1 19.51666761 1.881908374 0.498962039 0.988347936 0.49664081 0.527530467 0.132401789 0.585255815 0.331363161 0.118752263 0.086567074 76.19182466 -1.881908374 -0.491707127 SQGS(ph)SQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 SQGS(0.956)S(0.044)QFR;SQGS(0.796)S(0.204)QFR 126.33 0.0012837 811240000 462220 424230 452270 495560 440720 460520 534590 456960 493000 TRUE FALSE 440371.7766 467459.5193 473007.0269 445745.3673 517581.4285 444572.0769 453028.4771 416946.1599 569451.9221 0.773325648 0.820893742 0.830635579 0.782762073 0.908911549 0.780701688 0.795551757 0.73218852 1 19.11921452 -1.92661277 2.84565967 1.120787709 0.804624592 0.642318405 0.046159417 7329245.794 4032791.766 5820109.92 0.010305603 0.011840969 1.92661277 -0.316163117 SQGSS(ph)QFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 S(0.003)QGS(0.169)S(0.828)QFR 94.465 0.010846 365100000 174060 149640 144030 173330 147040 151390 171980 163800 157410 TRUE FALSE 165832.5288 164888.4861 150633.918 155906.5391 172683.7294 146147.3263 145741.2924 149456.8036 181820.3389 0.912068088 0.906875915 0.82847672 0.857475792 0.949749244 0.803800759 0.801567598 0.822002668 1 17.47215407 2.219372836 24.99998882 0.834852325 0.890666098 0.016454031 0.065567346 450.8952684 587473.3037 0.02243077 0.016591663 165.7192031 -2.219372836 0.055813773 SQHDEQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQHDEQVR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 80.688 0.026551 0 32599 20596 28750 33677 42818 27066 39187 33917 39591 FALSE TRUE 31058.10987 22694.75582 30068.21594 30291.72398 50285.44564 26128.69763 33208.30343 30947.04767 45730.57008 0.679154225 0.496271002 0.657508006 0.662395503 1.099602423 0.57136173 0.72617296 0.676725604 1 15.48087128 2.987172778 24.56446696 0.782803044 0.604113983 0.255280764 0.158750416 712.0065272 1363515.089 0.044824068 0.049729856 970.8961476 -2.987172778 -0.178689061 SQIDVALS(ph)QDSTYQGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 SQIDVALS(0.999)QDS(0.001)TYQGER;SQIDVALS(1)QDSTYQGER 306.99 2.58E-47 341300000 508920 457320 475540 524740 495490 434750 530280 496910 537020 TRUE FALSE 484864.3602 503921.4279 497343.9794 471992.1383 581903.2991 419694.4985 449376.0467 453397.9261 620298.3189 0.781663186 0.81238561 0.801781924 0.760911523 0.938102331 0.676601057 0.724451499 0.730935281 1 19.24260269 2.192999383 24.99999919 0.753242558 0.811260985 0 0.09870313 330.1204162 181139.1005 0.032638438 0.024105175 155.9550288 -2.192999383 0.058018427 SQIHDIVLVGGSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 173.51 2.69E-06 16202530000 6711330 5919530 5975130 7382030 6770990 6198970 7351070 7054330 6787030 FALSE TRUE 6394098.731 6522736.837 6249095.621 6639974.319 7951848.512 5984298.115 6229529.26 6436615.468 7839527.949 0.815622927 0.832031837 0.797126518 0.846986497 1.014327465 0.763349293 0.794630659 0.821046307 1 22.90233536 -2.46989724 2.089591345 2.606061147 0.832576299 0.367769737 0.067618813 3145787.026 177439.69 24044933.23 0.01603218 0.003389243 2.46989724 -1.773484848 SQLDDHPES(ph)DDEENFIDANDDEDMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQLDDHPESDDEENFIDANDDEDMEK 26 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK 226.5 1.30E-40 203498000 405860 486570 367470 505260 236554 479930 360820 422070 176991 TRUE FALSE 386675.8021 536152.0362 384318.863 454470.3049 277808.9427 463309.9038 305770.2821 385111.3133 204437.8603 1.891409945 2.622567245 1.879881067 2.22302417 1.358891852 2.266262731 1.495663678 1.883757307 1 17.64130287 0.366950509 0.222325561 0.608446697 2.38624093 0.472661919 0.342511273 4.494588316 0.503274898 2.363598519 0.866474599 2.327825971 -0.366950509 1.777794233 SQLDDHPES(ph)DDEENFIDANDDEDMEKFTDADKETEIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQLDDHPESDDEENFIDANDDEDMEKFTDADKETEIVK 38 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEKFTDADKETEIVK 165.01 3.40E-18 82727000 107760 81739 90187 110180 43628 116150 116900 126340 37777 TRUE FALSE 102666.3984 90068.29703 94322.16316 99104.49707 51236.70939 112127.6964 99064.75798 115276.9998 43635.26422 2.352830908 2.064117146 2.161604034 2.271201947 1.174204174 2.569657784 2.270291237 2.64183114 1 15.41320691 -0.457925807 8.401879205 0.999980718 2.182012591 0.466197891 0.3995306 0 0 0.357823016 0.084339694 0.348396829 0.457925807 1.182031873 SQLDIIIHSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQLDIIIHSLK 11 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 101.72 0.0030737 286262000 1486730 1480140 1323080 1549040 1273560 1379590 1479180 1502100 1299070 FALSE TRUE 1416455.219 1630967.949 1383744.527 1393327.556 1495668.461 1331814.452 1253503.924 1370568.161 1500523.141 0.943974259 1.086932887 0.922174733 0.928561192 0.996764675 0.887566753 0.835377936 0.913393552 1 20.51703414 3.014795907 1.030041235 0.896739145 1.008437107 0.1418998 0.063989404 0.601407852 1.382209374 0.029297597 0.036407047 1034.655826 -3.014795907 0.111697962 SQLDIIIHSLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQLDIIIHSLKK 12 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 166.38 3.38E-05 352990000 1336990 1345840 1290250 1424120 888220 1489440 1443510 1501910 872920 FALSE TRUE 1273793.132 1482982.626 1349409.239 1280964.752 1043125.287 1437860.319 1223276.038 1370394.798 1008287.975 1.263322745 1.470792732 1.338317298 1.270435415 1.034550954 1.426041324 1.213220893 1.359130359 1 19.94347631 -4.522751993 0.18162503 8.90E-17 1.366682323 0.358222569 0.121950353 117.5563003 1.328212693 43.07365291 0.356608103 3.00E-05 4.522751993 1.366682323 SQLIDELADKFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQLIDELADKFNR 13 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 ; 118.16 0.00040973 106288000 364760 325400 341050 422750 315360 382410 435680 402330 361460 FALSE TRUE 347518.5177 358558.6299 356687.4798 380254.3668 370358.6842 369167.0458 369209.0142 367099.8523 417513.3707 0.832353026 0.858795562 0.854313909 0.910759735 0.88705826 0.884204128 0.884304648 0.879252925 1 18.67146287 -5 0.138683002 1.434328245 0.824839089 0.840319726 0.017995126 53.29859961 0.454659125 6.419852599 0.115331861 1.00E-05 5 -0.609489156 SQLLGSAHEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQLLGSAHEVQR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 134.04 0.00015247 371930000 318100 248040 296280 307020 292940 284090 363470 321710 320860 FALSE TRUE 303064.0434 273315.558 309864.7311 276157.7663 344028.6433 274251.8921 308015.9759 293539.3669 370617.3301 0.817727664 0.737460275 0.836077285 0.745129123 0.928258382 0.739986692 0.831088972 0.792028173 1 18.49957082 -5 0.304599808 2.708414878 0.790481343 0.532896811 0.057568683 198.0293937 1.813979925 216.4989813 0.04876677 1.00E-05 5 -1.917933535 SQLQALHIGLDSS(ph)SIGS(ph)GPGDAEADDGFPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.327)S(0.361)S(0.327)IGS(0.985)GPGDAEADDGFPESR 110.33 2.00E-06 149060000 36113 37719 40822 44280 40319 34556 52111 45039 40311 TRUE FALSE 34406.01006 41562.60898 42693.72908 39828.89027 47350.62083 33359.31706 44160.50987 41095.14639 46562.224 0.738925401 0.892625081 0.916917737 0.855390633 1.016932113 0.716445955 0.948419256 0.882585557 1 15.50687235 4.525592601 2.083883822 0.898194321 0.726801074 0.275753968 0.083363726 0.536367158 3.588206341 0.0188405 0.147434816 33542.28164 -4.525592601 -0.171393248 SQLQALHIGLDSS(ph)SIGSGPGDAEADDGFPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.096)S(0.758)S(0.139)IGS(0.007)GPGDAEADDGFPESR;SQLQALHIGLDS(0.059)S(0.513)S(0.339)IGS(0.089)GPGDAEADDGFPESR;SQLQALHIGLDS(0.078)S(0.771)S(0.15)IGSGPGDAEADDGFPESR 263.28 1.14E-59 373696000 126916 113081 125355 134338 130394 118775 147503 139285 143903 TRUE FALSE 120916.9322 124604.0825 131102.6507 120834.089 153134.6723 114661.792 124998.7083 127088.467 166218.7423 0.727456667 0.749639185 0.788735668 0.726958268 0.921284027 0.689824688 0.75201332 0.764585661 1 17.34272354 0.887741124 16.64966834 1 0.761408837 0.590212385 0.061461383 1988.462814 294922.664 0.054069692 0.013517423 7.722201391 -0.887741124 -0.238591163 SQLQALHIGLDSSS(ph)IGS(ph)GPGDAEADDGFPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.07)S(0.393)S(0.538)IGS(1)GPGDAEADDGFPESR 111.46 1.80E-06 179880000 76518 73574 85625 102190 79479 85513 107600 95010 83964 TRUE FALSE 72901.14578 81071.27425 89550.99094 91917.66705 93340.11244 82551.66337 91183.64379 86690.42072 96984.70829 0.751676703 0.835918112 0.923351655 0.947754225 0.962420923 0.851182262 0.940185782 0.893856591 1 16.56546967 4.011549408 1.853660075 0.927684994 0.763215269 0.689670281 0.040196706 0.179679987 1.188671777 0.010336801 0.03057332 10269.50258 -4.011549408 -0.164469724 SQLQALHIGLDSSS(ph)IGSGPGDAEADDGFPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.047)S(0.248)S(0.705)IGSGPGDAEADDGFPESR 144.92 3.18E-10 196600000 101700 88786 109760 105780 103150 93933 124100 102610 99549 TRUE FALSE 96892.84255 97833.39434 114792.6046 95146.79343 121139.3273 90680.07666 105166.2657 93624.92443 114986.5505 0.842645006 0.850824674 0.998313316 0.827460194 1.053508665 0.788614636 0.914596231 0.814225003 1 16.8111056 3.958410745 24.98454798 0.90677406 0.845712218 0.090024757 0.086596008 1031.36555 619588.3283 0.019558401 0.035260733 9086.795312 -3.958410745 -0.061061841 SQNHS(ph)RS(ph)PS(ph)EERGHSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQNHSRSPSEERGHSTR 17 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 3 S(0.265)QNHS(0.794)RS(0.942)PS(0.999)EERGHSTR 62.237 0.046932 321960000 38514 22392 37053 34051 31494 28713 46706 30588 34787 TRUE FALSE 36693.51955 24673.77026 38751.9167 30628.12879 36986.54363 27718.66161 39580.14189 27909.55256 40181.59029 0.913192317 0.614056589 0.964419686 0.762242822 0.920484813 0.689834857 0.985031742 0.694585564 1 15.29424704 -5 0.220629319 1.922294347 0.794457393 0.14119835 0.129117902 267.9980172 2.680213975 110.0019086 0.217069637 1.00E-05 5 -1.127836954 SQNHS(ph)RS(ph)PSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQNHSRSPSEER 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 2 S(0.156)QNHS(0.807)RS(0.91)PS(0.127)EER 49.595 0.096052 138160000 134260 143110 130830 153030 149290 120680 155920 146910 143640 TRUE FALSE 127913.7959 157693.0717 136828.6849 137647.1337 175326.1287 116500.8213 132131.5403 134045.7816 165914.9576 0.770960001 0.95044518 0.824691679 0.82962462 1.056722861 0.702171902 0.796381124 0.807918608 1 17.34008443 -1.32876192 8.550231186 1.000000285 0.843479258 0.203959441 0.097848564 5.03E-07 3.95E-08 0.089481096 0.021090858 0.046907046 1.32876192 -0.156521027 SQNHSRS(ph)PS(ph)EERGHSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQNHSRSPSEERGHSTR 17 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 2 S(0.004)QNHS(0.037)RS(0.959)PS(1)EERGHSTR 134.47 9.05E-06 243380000 149610 66283 151110 128840 225540 137900 241270 143110 171080 TRUE FALSE 142538.2318 73037.31306 158038.543 115888.7584 264874.1046 133124.4884 204459.8303 130578.5297 197610.2126 0.721310047 0.369602927 0.799748863 0.586451261 1.340386719 0.673672108 1.034662265 0.660788367 1 17.59229798 SQNKEDYAGLKEEFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQNKEDYAGLKEEFRK 16 3 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 116.06 0.00020024 790930000 1110200 834210 995350 1104200 717460 1147700 1390500 1358300 916190 FALSE TRUE 1057723.046 919216.9474 1040987.782 993203.7182 842584.7968 1107954.861 1178353.687 1239360.051 1058268.066 0.999484989 0.868605013 0.983671166 0.938518085 0.796192216 1.046951048 1.113473726 1.17112109 1 20.01327369 2.034622478 10.53807062 1.100698429 0.921962108 0.586526262 0.069937025 0.302315495 90.09466713 0.024390868 0.017972881 108.2985091 -2.034622478 -0.178736321 SQPERDWVLNEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQPERDWVLNEFR 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 225.32 1.15E-11 987691000 1196301 663826 1012373 879846 1419858 996591 1582173 1161908 1646530 FALSE TRUE 1139754.223 731470.6241 1058791.303 791402.2085 1667480.786 962078.8038 1340783.45 1060165.176 1901865.463 0.599282255 0.384606923 0.556711988 0.416118923 0.876760643 0.5058606 0.704983332 0.55743437 1 20.85898376 -4.999999681 0.142637631 2.547084409 0.413343117 0.507691535 0.135540777 100.4934886 0.871164079 43.86238282 0.706703504 1.00E-05 4.999999681 -2.133741292 SQPPGEDS(ph)DT(ph)DVDDDSRPPGRPAEVHLER ddPTM_SK-BR-3_Trastuzumab_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;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER 244.85 2.40E-45 3277250000 209332 198325 182974 232804 203479 205278 244780 217138 219710 TRUE FALSE 199437.2912 218534.543 191363.5389 209402.0996 238965.6732 198169.1714 207434.3153 198124.2456 253781.5047 0.785862199 0.861112961 0.754048405 0.825127504 0.941619735 0.780865302 0.817373652 0.780688277 1 17.95322741 -1.064983217 4.178988673 1.000021775 0.820296809 0.538483242 0.052826092 6542541.467 1667316.658 1320.257157 0.011489063 0.086102703 1.064983217 -0.179724966 SQPPGEDS(ph)DTDVDDDSRPPGRPAEVHLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQPPGEDS(0.977)DT(0.023)DVDDDSRPPGRPAEVHLER;S(0.002)QPPGEDS(0.964)DT(0.035)DVDDDSRPPGRPAEVHLER;S(0.006)QPPGEDS(0.958)DT(0.036)DVDDDSRPPGRPAEVHLER;S(0.027)QPPGEDS(0.81)DT(0.162)DVDDDSRPPGRPAEVHLER;SQPPGEDS(0.979)DT(0.021)DVDDDSRPPGRPAEVHLER;S(0.069)QPPGEDS(0.712)DT(0.219)DVDDDSRPPGRPAEVHLER 192.52 1.13E-18 1586601000 316829 336572 342514 396379 362701 358292 427575 381657 373494 TRUE FALSE 301853.1211 370869.0695 358218.6057 356534.2298 425955.9396 345884.2582 362340.5808 348237.0898 431413.542 0.699683927 0.859660241 0.830336952 0.826432634 0.987349487 0.801746409 0.839891532 0.807200182 1 18.71871194 -5 0.022647241 2.08887036 3.00E-11 0.407420323 0.067528014 2685.508898 4.59663001 297.022627 150.0542374 1.00E-05 5 -2.08887036 SQPVYIQYSNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQPVYIQYSNHR 12 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;O95758-7;X6R242 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 97.69 0.0047799 216630000 192470 128330 125610 148780 261740 138640 260810 216400 253170 FALSE TRUE 183372.3245 141406.9729 131369.3427 133824.3517 307387.3731 133838.862 221018.6444 197450.8688 292430.3106 0.627063331 0.483557852 0.44923299 0.457628183 1.051147443 0.457677803 0.75579937 0.675206576 1 18.15773333 0.202881211 0.249488363 1.136849516 0.487042838 0.363107424 0.175753449 6.054428837 0.714543635 1.138624555 0.329879378 1.5954427 -0.202881211 -0.649806678 SQPWDLTPMLSS(ph)SEPWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 SQPWDLTPMLS(0.012)S(0.494)S(0.494)EPWGR 142.3 1.19E-07 8406000 31357 25462 27791 34705 30339 28415 38051 32452 33874 TRUE FALSE 29874.81675 28056.60675 29065.24484 31216.38746 35630.11199 27430.98143 32245.6211 29610.33084 39127.00692 0.763534426 0.717064988 0.742843553 0.797822014 0.910627078 0.701075385 0.824126956 0.756774749 1 15.25587713 -5 0.215792309 2.113571873 0.743697324 0.58118279 0.059443819 102.9945867 1.02882209 49.79734959 0.111660236 1.00E-05 5 -1.369874549 SQQALADALEEGS(ph)QHEEACQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQQALADALEEGSQHEEACQR 21 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 SQQALADALEEGS(1)QHEEACQR 57.156 0.05328 209850000 100700 104220 101940 106880 123170 115250 120470 110080 109960 TRUE FALSE 95940.11057 114840.1365 106614.0498 96136.21934 144650.809 111258.8636 102090.0889 100440.8116 127012.0352 0.755362359 0.904167359 0.839401161 0.756906377 1.138874822 0.875971032 0.803782797 0.790797592 1 16.95460568 4.618973491 2.68160028 0.879604866 0.746037647 0.117400122 0.111943749 0.817251724 9.260480609 0.026619907 0.215121395 41588.52242 -4.618973491 -0.133567218 SQQALADALEEGSQHEEACQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQQALADALEEGSQHEEACQR 21 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 246.92 2.43E-30 364340000 263520 245750 235980 281330 284470 229807 253480 282720 255240 FALSE TRUE 251063.9318 270792.2044 246799.9164 253050.1739 334081.4779 221848.726 214806.9705 257963.538 294821.3156 0.851579986 0.918496018 0.837116936 0.858317091 1.133165956 0.752485367 0.728600543 0.874982657 1 18.16948131 SQQLSNDHICYFLYQILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQQLSNDHICYFLYQILR 18 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 185.33 5.36E-14 81591000 135990 152190 119140 162720 139290 129510 172750 152720 130230 FALSE TRUE 129562.0222 167698.334 124602.6868 146363.0765 163582.1319 125025.0362 146393.8147 139347.0272 150425.4033 0.861304137 1.114827219 0.828335402 0.97299441 1.087463476 0.831143102 0.973198752 0.926353024 1 17.1986887 2.229264921 24.9971917 0.931475272 0.97559972 0.041163413 0.096138867 692.5095891 1862221.898 0.033318474 0.024944514 169.5371667 -2.229264921 0.044124448 SQREPGPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQREPGPGAK 10 1 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 66.595 0.070496 0 45927 43237 43390 46031 42892 43719 60493 51519 43644 FALSE TRUE 43756.12173 47642.89946 45379.47442 41403.87643 50372.35122 42205.00007 51263.68182 47007.72324 50412.08862 0.867968833 0.945068946 0.900170488 0.821308491 0.999211749 0.83719999 1.016892639 0.932469265 1 15.62148211 1.711435823 11.59140727 0.980249987 0.900203023 0.360755386 0.054853377 0.122072615 37.98431169 0.022904878 0.012504328 51.4559763 -1.711435823 -0.080046963 SQS(ph)CSDTAQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSCSDTAQER 11 0 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.001)QS(0.998)CS(0.001)DTAQER;SQS(0.998)CS(0.002)DTAQER 155.14 3.32E-05 124141000 190890 152337 168163 189002 178062 174427 203228 183550 217210 TRUE FALSE 181867.008 167860.3135 175873.4399 170003.1599 209115.9564 168386.5493 172221.8361 167477.3889 250893.8174 0.724876403 0.669049223 0.70098754 0.677590072 0.833483896 0.671146667 0.686433161 0.667522981 1 17.93671739 -1.241475003 4.815043046 1.000066276 0.702362075 0.780867949 0.049291659 3.27E-05 5.15E-06 0.0445286 0.010493161 0.057348887 1.241475003 -0.297704201 SQS(ph)DIFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSDIFSR 8 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(0.008)QS(0.991)DIFSR 117.86 0.0020957 91670000 154080 121800 137790 145070 196600 141250 178030 144180 198670 TRUE FALSE 146796.9438 134211.5585 144107.8078 130487.288 230886.9778 136358.4771 150868.2538 131554.8349 229478.7289 0.639697389 0.584854026 0.627978935 0.568624764 1.006136729 0.594209658 0.657438946 0.573276815 1 17.80800091 -2.206947113 2.343198119 2.058320967 0.653562803 0.416069396 0.127834178 5743817.04 1264051.907 32189660.9 0.029045557 0.006209446 2.206947113 -1.404758164 SQS(ph)DRTEYNQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.01)QS(0.99)DRTEYNQK;S(0.02)QS(0.98)DRTEYNQK;S(0.008)QS(0.992)DRTEYNQK;S(0.001)QS(0.999)DRTEYNQK;S(0.001)QS(0.998)DRTEYNQK;S(0.137)QS(0.863)DRTEYNQK 196.37 3.68E-08 3272838000 1431011 1285724 1368710 1539885 1054602 1516728 1731021 1612451 1271591 TRUE FALSE 1363369.946 1416740.737 1431466.707 1385092.834 1238524.255 1464203.329 1466921.954 1471256.242 1468782.838 0.928231125 0.964567873 0.974593841 0.943020846 0.843231704 0.996882106 0.998733044 1.001683982 1 20.48618968 2.054850112 24.99999994 0.999452187 0.936201208 0.483030788 0.035020341 82.39754781 37555.29879 0.013021749 0.009617198 113.4619158 -2.054850112 -0.063250979 SQS(ph)ESS(ph)DEVTELDLSHGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 S(0.172)QS(0.827)ES(0.197)S(0.804)DEVTELDLSHGKK 100.93 0.0019529 83154000 251770 180620 230520 262730 173020 263250 316340 248700 158030 TRUE FALSE 239869.3311 199025.3833 241089.57 236319.8812 203194.6332 254133.5865 268076.523 226922.5096 182536.4853 1.314089787 1.090332067 1.320774691 1.294644634 1.113172706 1.392234468 1.468618849 1.243162479 1 17.47782533 3.681524307 24.99654793 1.294828471 1.20220982 0 0.144526076 708.5446706 310524.3155 0.037305126 0.057792912 4803.129618 -3.681524307 -0.09261865 SQS(ph)ESSDEVTELDLSHGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.264)QS(0.687)ES(0.039)S(0.01)DEVTELDLSHGKK 125.35 1.29E-05 144800000 261620 213280 240350 240090 166600 281480 322970 300660 196120 TRUE FALSE 249253.7411 235013.4745 251370.2852 215955.6971 195654.9873 271732.277 273694.9947 274332.6165 226533.288 1.100296311 1.037434615 1.109639504 0.953306682 0.863691994 1.199524712 1.208188859 1.211003553 1 17.78936354 2.182507011 24.99999725 1.176885115 1.025859959 0.348711828 0.09321496 88.35416047 39405.35846 0.033824419 0.024981001 152.2323708 -2.182507011 -0.151025156 SQS(ph)FALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSFALR 7 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 SQS(1)FALR;SQS(1)FALR 148.91 0.0021522 261540000 526540 413250 466870 516140 569410 428580 551760 479920 536740 TRUE FALSE 501651.4977 455360.6448 488276.4513 464256.6266 668714.9237 413738.1671 467578.8782 437895.6606 619974.8979 0.809148079 0.73448239 0.78757455 0.748831329 1.078616128 0.667346643 0.754190016 0.70631192 1 19.24185028 -2.056225034 2.476121062 1.299214988 0.782854542 0.267088117 0.111409402 11246540.56 4782412.716 19005121.74 0.025152429 0.008785672 2.056225034 -0.516360446 SQS(ph)FSHQQPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 S(0.045)QS(0.945)FS(0.01)HQQPSR;SQS(0.994)FS(0.006)HQQPSR;SQS(0.737)FS(0.263)HQQPSR;S(0.162)QS(0.676)FS(0.162)HQQPSR;S(0.001)QS(0.976)FS(0.023)HQQPSR;S(0.215)QS(0.765)FS(0.02)HQQPSR;S(0.414)QS(0.495)FS(0.091)HQQPSR 222.48 8.02E-12 1316759000 1190884 902562 1034235 1126211 1140872 985251 1272760 1092056 1186178 TRUE FALSE 1134593.273 994534.0939 1081655.698 1013002.131 1339839.716 951131.5108 1078577.086 996429.7873 1370124.426 0.828095063 0.72587137 0.789458006 0.739350464 0.977896379 0.694193529 0.787211049 0.727254962 1 20.38587548 -1.862087502 3.618490838 1.069039752 0.782161652 0.425012684 0.079060612 0.038926161 0.001483603 0.067670464 0.016099098 0.013737652 1.862087502 -0.2868781 SQS(ph)FSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSFSK 6 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75;REV__E7ESW5 COBLL1 Cordon-bleu protein-like 1 1 SQS(0.998)FS(0.002)K;SQS(1)FSK 139.74 0.012449 271780000 963720 980740 891020 1066680 637350 900230 941750 1050230 776150 TRUE FALSE 918166.8655 1080678.521 931874.1483 959455.2998 748503.6382 869054.8094 798068.7411 958266.2936 896511.378 1.024155285 1.205426442 1.039444865 1.070209842 0.834907015 0.969373988 0.890193656 1.068883583 1 19.77396237 2.911624947 6.768352106 0.942766737 1.099222657 0.411177937 0.078043139 0.203058389 13.20942833 0.022250073 0.023702913 815.8774813 -2.911624947 0.15645592 SQS(ph)GEDESMNQPGPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 SQS(1)GEDESMNQPGPIK;S(0.05)QS(0.95)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK;S(0.079)QS(0.921)GEDESMNQPGPIK;S(0.021)QS(0.979)GEDESMNQPGPIK 472.38 8.05E-191 288866000 772869 695198 651618 820000 519298 740248 809260 775047 586996 TRUE FALSE 736337.014 766039.4666 681495.3298 737572.0421 609863.4068 714613.0261 685792.5239 707179.7759 678024.3417 1.086003804 1.129811158 1.005119268 1.087825314 0.899471257 1.053963674 1.011457085 1.043000571 1 19.37097754 3.734154117 24.97067772 1.015361394 1.107907483 0.379228814 0.049722859 312.7372155 1772214.555 0.011885449 0.019142205 5421.932631 -3.734154117 0.092546089 SQS(ph)GSPVRYQQETSVSQLPGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSGSPVRYQQETSVSQLPGRPK 23 2 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 S(0.036)QS(0.59)GS(0.374)PVRYQQETSVSQLPGRPK 69.444 0.012755 107240000 41392 23713 48149 31458 38549 42683 46303 38863 56085 TRUE FALSE 39435.48219 26129.38166 50356.67928 28295.78207 45271.93339 41204.87701 39238.62694 35459.94969 64782.37536 0.608737824 0.403340901 0.777320668 0.436782102 0.698831019 0.636050728 0.605699108 0.547370323 1 15.98331375 -5 0.259743921 3.689796473 0.547263684 0.564011736 0.112172083 131.2552467 1.289398723 188.4247371 0.13380486 1.00E-05 5 -3.142532789 SQS(ph)IEQESQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 318.96 6.59E-46 2031260000 4377590 3528720 3627180 4299940 2557520 4185570 4441790 4318110 2964810 TRUE FALSE 4170669.996 3888300.58 3793489.791 3867701.862 3003550.678 4040622.661 3764113.356 3939993.397 3424577.593 1.217864067 1.135410273 1.107724876 1.129395307 0.877057271 1.179889359 1.099146757 1.150504928 1 21.70749462 4.156145175 1.182932059 1.07957692 1.223674823 0.228058509 0.085236886 1.00386221 2.19139552 0.024860213 0.139254541 14326.66727 -4.156145175 0.144097903 SQS(ph)LNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SQSLNIR 7 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 S(0.03)QS(0.97)LNIR;SQS(1)LNIR;SQS(1)LNIR;SQS(1)LNIR;S(0.007)QS(0.993)LNIR 174.02 0.00088281 1494740000 2156110 1767510 1854290 2210010 2099860 2034150 2267710 2045580 2128920 TRUE FALSE 2054194.953 1947621.278 1939311.031 1987855.596 2466074.919 1963706.875 1921729.19 1866458.171 2459062.041 0.835357107 0.792017951 0.788638513 0.808379603 1.002851851 0.798559306 0.781488697 0.759012233 1 21.2296767 -2.219066501 2.351678472 1.591562268 0.819364292 0.408899 0.06769687 4090804.659 803546.045 12905178.59 0.015969138 0.006038562 2.219066501 -0.772197977 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.274)QS(0.718)LPHS(0.006)AT(0.002)VTLGGTSDPSTLSSSALSER 137.4 5.28E-14 0 61343 43004 66518 63637 61829 63632 83876 48688 40835 TRUE FALSE 58443.43796 47386.15649 69567.9161 57240.08786 72611.95802 61428.40788 71079.17571 44424.62061 47167.48324 1.239062039 1.004636102 1.474912616 1.213549758 1.53944949 1.302346525 1.506952901 0.941848442 1 15.525505 3.744513984 24.98237283 1.323503095 1.121849077 0.067787594 0.209109534 804.8665293 3377485.711 0.048342525 0.084284478 5552.824965 -3.744513984 -0.201654019 SQS(ph)LPNSLDYTQTSDPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;SQS(1)LPNSLDYTQTSDPGR;S(0.015)QS(0.985)LPNSLDYTQTSDPGR;S(0.004)QS(0.996)LPNSLDYTQTSDPGR;S(0.042)QS(0.958)LPNSLDYTQTSDPGR;S(0.002)QS(0.983)LPNS(0.015)LDYTQTSDPGR 396.08 6.26E-127 3087925000 1888054 1347658 1569970 1827441 1579490 1400257 1831082 1532962 1762588 TRUE FALSE 1798809.429 1484985.882 1641954.677 1643743.159 1854952.556 1351765.749 1551716.811 1398727.721 2035921.145 0.883535904 0.729392632 0.806492276 0.807370739 0.911112182 0.663957812 0.762169407 0.687024507 1 20.95725025 2.237337316 24.9999371 0.75548985 0.817401077 0.028944377 0.102206846 83.18967388 1700049.658 0.033009244 0.025747904 172.7178869 -2.237337316 0.061911226 SQS(ph)LPTTLLS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 2 S(0.113)QS(0.885)LPT(0.021)T(0.017)LLS(0.964)PVR;S(0.204)QS(0.795)LPT(0.006)T(0.005)LLS(0.989)PVR 96.143 0.0063925 57574000 223251 210790 216474 247100 232773 220948 263510 245785 268420 TRUE FALSE 212698.3677 232269.7406 226399.547 222261.0385 273368.5375 213296.5154 223306.7098 224262.7624 310045.2027 0.686023734 0.749147991 0.730214643 0.716866562 0.881705426 0.687952961 0.720239203 0.723322794 1 18.24211904 -1.107437518 3.492958827 1.000200207 0.735200707 0.694608521 0.054807559 49482892.29 83865457.95 115175.5761 0.012405234 0.078084077 1.107437518 -0.2649995 SQS(ph)LPTTLLSPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 S(0.001)QS(0.997)LPT(0.002)T(0.001)LLSPVR;SQS(0.882)LPT(0.036)T(0.082)LLSPVR;S(0.054)QS(0.532)LPT(0.207)T(0.207)LLSPVR;S(0.001)QS(0.825)LPT(0.087)T(0.087)LLSPVR 164.7 3.84E-05 871230000 1241550 991920 939530 1077180 1269350 1083730 1383480 1063810 1298680 TRUE FALSE 1182864.392 1092997.776 982608.3798 968899.8199 1490724.238 1046200.158 1172404.717 970657.1568 1500072.662 0.788538064 0.728629888 0.655040522 0.645901925 0.99376802 0.697432988 0.781565285 0.647073426 1 20.51660095 SQS(ph)MDAMGLSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SQSMDAMGLSNK 12 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.004)QS(0.996)MDAMGLSNK;SQS(1)MDAMGLSNK;SQS(1)MDAMGLSNK;S(0.216)QS(0.784)MDAMGLSNK;S(0.023)QS(0.977)MDAMGLSNK 222.07 2.69E-11 532191000 1865850 1821320 1454731 2082470 1183596 1845324 1833500 1966550 1236584 TRUE FALSE 1777654.968 2006914.579 1521431.855 1873136.159 1390014.768 1781419.967 1553765.9 1794348.457 1428347.131 1.244553883 1.405060811 1.065169539 1.311401212 0.973163132 1.247189796 1.087806925 1.25624116 1 20.44591521 7.999999998 0.104498852 0.935849516 2.095306836 0.229414212 0.123862217 135.4411004 0.995918407 1.18578581 22.57178623 99999999.64 -7.999999998 1.159457319 SQS(ph)MDIDGVSCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSMDIDGVSCEK 13 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 SQS(1)MDIDGVSCEK 233.48 1.29E-16 99975000 149870 108840 131990 187470 160400 184130 202850 148720 151510 TRUE FALSE 142785.9421 119930.9197 138041.8721 168625.1594 188373.7092 177753.5319 171901.5069 135697.2884 175005.397 0.815894507 0.685298407 0.788786371 0.963542624 1.076388 1.015703144 0.982264032 0.775389164 1 17.41703989 3.271349209 4.189345908 0.978395874 0.74931098 0.580477592 0.082600619 0.13162492 5.061812374 0.023069288 0.030595972 1867.881018 -3.271349209 -0.229084894 SQS(ph)PAASDCSSSSSSASLPSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SQS(0.996)PAAS(0.003)DCSSSSSSASLPSSGR;SQS(1)PAASDCSSSSSSASLPSSGR;SQS(1)PAASDCSSSSSSASLPSSGR;S(0.003)QS(0.996)PAAS(0.001)DCSSSSSSASLPSSGR;S(0.004)QS(0.996)PAASDCSSSSSSASLPSSGR;S(0.066)QS(0.927)PAAS(0.007)DCSSSSSSASLPSSGR 449.43 2.11E-203 2950480000 904333 735691 803716 859069 851569 798326 987254 887199 924794 TRUE FALSE 861586.9713 810658.7493 840567.1736 772713.752 1000082.364 770679.7704 836630.2701 809511.1522 1068206.33 0.806573549 0.758897159 0.786895892 0.723374998 0.936225835 0.721470889 0.783210365 0.757822837 1 20.02675891 -0.997656652 5.343119222 1.000000955 0.783332837 0.559145687 0.060183807 6.02E-07 1.13E-07 0.051241959 0.012077792 0.100541034 0.997656652 -0.216668119 SQS(ph)PHYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 S(0.029)QS(0.971)PHYFR;S(0.009)QS(0.991)PHYFR;SQS(1)PHYFR 129.82 0.00069204 1136500000 912510 739730 734260 871260 951650 769270 1051630 897960 846220 TRUE FALSE 869377.4607 815109.328 767926.5473 783679.2895 1117617.459 742629.987 891184.529 819329.862 977447.4757 0.889436499 0.833916244 0.785644821 0.801761024 1.143404108 0.759764597 0.911746719 0.838234158 1 19.89865965 SQS(ph)PINCIRPSVLGPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSPINCIRPSVLGPLK 17 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.007)QS(0.993)PINCIRPSVLGPLK 144.22 3.15E-07 368330000 320480 279020 232010 295410 222940 256140 298960 306600 237060 TRUE FALSE 305331.5455 307452.4552 242647.888 265714.8256 261820.6654 247269.8076 253348.1612 279752.4786 273822.0541 1.115072877 1.122818453 0.886151734 0.970392346 0.956170847 0.903031016 0.925229204 1.021657951 1 18.06287912 3.750103955 24.91951357 0.945464694 1.118945685 0.73868165 0.041195526 283.1625413 611283.2922 0.009790145 0.017464203 5624.759463 -3.750103955 0.173480992 SQS(ph)PVHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSPVHLR 8 0 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 1 S(0.15)QS(0.85)PVHLR 87.184 0.0099865 280330000 141310 132060 137210 156030 144870 148270 163260 138310 160660 TRUE FALSE 134630.5563 145517.0641 143501.2142 140345.568 170135.2821 143135.3727 138351.6885 126198.8432 185574.3323 0.725480484 0.78414435 0.773281587 0.756276831 0.916803957 0.771310186 0.74553246 0.680044711 1 17.50163765 -2.214092521 2.409057233 1.753465326 0.770254903 0.592165871 0.060211694 3192547.06 918296.5745 13046561.56 0.014249903 0.006108119 2.214092521 -0.983210423 SQS(ph)SDTEQQSPTSGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.038)QS(0.923)S(0.038)DTEQQSPTSGGGK;S(0.199)QS(0.783)S(0.018)DTEQQSPTSGGGK 160.97 3.17E-09 113006000 205754 173677 208089 291768 197096 257147 285597 206344 207716 TRUE FALSE 196028.4162 191374.8838 217630.0865 262438.9263 231469.48 248241.9349 242023.9323 188275.4255 239927.5364 0.817031755 0.797636181 0.907065899 1.093825787 0.964747454 1.03465379 1.008737621 0.784717871 1 17.87223922 3.533067483 4.331711575 0.987522545 0.810073995 0.445652871 0.079204244 0.167129284 6.429091318 0.020302639 0.031284687 3412.45932 -3.533067483 -0.17744855 SQS(ph)SLSGKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSSLSGKPK 10 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.001)QS(0.656)S(0.343)LSGKPK 117.93 0.00054023 287200000 382170 298000 326050 507440 327810 520050 518600 383740 273850 TRUE FALSE 364105.5815 328366.5388 340999.715 456431.1671 384979.9602 502040.5381 439478.0453 350137.6913 316317.2594 1.151077188 1.038092387 1.078030695 1.442953723 1.217069094 1.587142412 1.389358412 1.106919338 1 18.27101275 3.254151357 24.73295391 1.331886706 1.08700221 0.213550691 0.170396546 235.1371161 373016.0382 0.043531083 0.058730862 1795.359224 -3.254151357 -0.244884496 SQS(ph)SSQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSSSQFR 8 0 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.074)QS(0.82)S(0.057)S(0.05)QFR;S(0.001)QS(0.865)S(0.073)S(0.061)QFR 115.91 0.0024882 178090000 197214 168492 182865 189484 192337 173281 205932 174593 198327 TRUE FALSE 187892.0851 185661.5264 191249.5411 170436.7083 225880.5119 167280.2355 174513.2912 159304.7113 229082.5382 0.820193833 0.810456911 0.83484993 0.743996944 0.98602239 0.730218186 0.761792202 0.695403118 1 17.80550797 -1.481810845 8.663583663 1.000006494 0.799589889 0.390161726 0.079393199 9.21E-06 5.51E-07 0.071100323 0.016757964 0.03297533 1.481810845 -0.200416606 SQS(ph)TSEQEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSTSEQEKR 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 S(0.013)QS(0.941)T(0.042)S(0.004)EQEKR 104.81 0.0016128 72885000 127990 103700 121530 149990 107210 159430 160790 143510 135190 TRUE FALSE 121940.1664 114267.1479 127102.2707 134912.7202 125907.3901 153908.8991 136258.5324 130943.5036 156154.5747 0.780893973 0.731756646 0.81395163 0.863969054 0.806299721 0.985618893 0.872587515 0.838550544 1 17.25261531 3.050144787 0.921488999 0.911394567 0.751861363 0.527387053 0.057738146 0.408327869 0.764122555 0.026931967 0.035513022 1122.392579 -3.050144787 -0.159533204 SQS(ph)TTFNPDDMSEPEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSTTFNPDDMSEPEFK 17 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.178)QS(0.779)T(0.041)T(0.002)FNPDDMSEPEFK 256.67 4.39E-27 82616000 148960 142230 124510 172310 96748 148540 145240 151990 103650 TRUE FALSE 141918.956 156723.3987 130218.9067 154989.0714 113620.8206 143396.0226 123080.9705 138680.9499 119723.5126 1.185389176 1.309044441 1.087663599 1.294558337 0.949026787 1.19772649 1.028043429 1.158343477 1 16.86934699 2.752312613 24.99951627 1.075895487 1.223085662 0.396216312 0.093120895 759.0333859 1379832.086 0.025164426 0.026558052 565.3437724 -2.752312613 0.147190176 SQS(ph)TTFNPDDMSEPEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSTTFNPDDMSEPEFKR 18 1 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.118)QS(0.755)T(0.118)T(0.008)FNPDDMSEPEFKR 132.36 6.42E-06 184750000 347070 280280 296440 342990 239530 358910 389630 358140 302700 TRUE FALSE 330664.6889 308840.8507 310032.0672 308511.9936 281303.9562 346480.8567 330184.7875 326779.363 349641.17 0.945725839 0.883308023 0.886714992 0.882367467 0.804550437 0.990961267 0.944353285 0.934613515 1 18.41551555 2.207221358 24.99995942 0.961867729 0.887202562 0.546623438 0.038937577 177.3192905 141450.145 0.014477049 0.010693035 161.1466782 -2.207221358 -0.074665167 SQS(ph)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.185)QS(0.814)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.039)QS(0.961)VPAS(0.001)TGLGWGSGLVAPLQEGSIDSTLAGTQDTR 252.02 4.51E-62 633340000 88861 75105 88622 96785 97845 98878 101770 84619 105575 TRUE FALSE 84660.71664 82758.28489 92685.40636 87055.98792 114909.137 95453.83007 86243.11737 77209.31177 121947.0318 0.694241716 0.67864124 0.760046432 0.713883615 0.942287281 0.782748286 0.707217848 0.633138098 1 16.89589512 -2.339302362 2.457395463 2.796196278 0.736650141 0.49296392 0.083147717 6124270.619 1431333.64 60687097.16 0.020338548 0.00457823 2.339302362 -2.059546137 SQS(ph)WEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SQSWEER 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 1 SQS(1)WEER;SQS(1)WEER;SQS(1)WEER;SQS(1)WEER;SQS(1)WEER;SQS(1)WEER 183.78 0.00066889 2796590000 4458640 3987630 3992100 5257960 4776840 4539720 5137780 4253720 4734230 TRUE FALSE 4247888.923 4393974.031 4175141.734 4729419.871 5609919.384 4382508.358 4353917.299 3881241.726 5468390.209 0.776807938 0.803522401 0.76350472 0.864865105 1.025881323 0.801425683 0.79619726 0.709759468 1 22.38268476 -2.430415348 2.360442479 2.891742065 0.817693269 0.319965043 0.083501626 3342802.714 769283.2562 33821345.89 0.02036796 0.003711801 2.430415348 -2.074048796 SQS(ph)WEERGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQSWEERGDR 10 1 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 S(0.001)QS(0.999)WEERGDR;SQS(1)WEERGDR;S(0.006)QS(0.994)WEERGDR 175.29 1.72E-06 1415040000 1568240 1207100 1395650 1728500 1656180 1503320 1887500 1601810 1754000 TRUE FALSE 1494112.403 1330104.862 1459641.933 1554747.896 1945017.268 1451259.651 1599527.209 1461547.025 2026001.362 0.737468608 0.65651726 0.720454567 0.767397261 0.960027621 0.716317214 0.789499572 0.721394888 1 20.95020371 -5 0.145533162 1.836589881 0.673047054 0.471210967 0.079983801 118.9798871 1.042939281 29.03165721 0.431984767 1.00E-05 5 -1.163542827 SQSDLDDQHDYDS(ph)VAS(ph)DEDTDQEPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 SQSDLDDQHDYDS(1)VAS(0.988)DEDT(0.012)DQEPLR;SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR;SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR 293.99 1.34E-70 787310000 765874 626692 655916 783488 716417 649844 846496 727781 662294 TRUE FALSE 729672.6538 690552.6273 685990.3974 704730.2977 841359.898 627339.7393 717347.4882 664052.6374 764999.171 0.953821496 0.902684151 0.896720445 0.921217074 1.099818052 0.820052836 0.937710151 0.868043604 1 19.54509866 4.746283436 6.532823394 0.926967502 0.954403751 0.006821268 0.075841124 0.802176153 187.0622269 0.016415821 0.098291023 55754.95062 -4.746283436 0.027436249 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SQSDLDDQHDYDSVAS(1)DEDTDQEPLR 208.29 1.48E-25 320300000 118220 109680 109290 129230 114490 125200 133100 118190 102570 TRUE FALSE 112631.9749 120856.5167 114301.0546 116239.5549 134457.0198 120864.2926 112793.1505 107840.657 118476.0317 0.950673087 1.020092545 0.964760998 0.981122959 1.134887941 1.020158177 0.952033494 0.910231846 1 16.8542357 1.678154689 5.65012614 0.947623152 1.0098135 0.198754239 0.054128963 0.230266509 16.17996594 0.028332445 0.014035708 47.66007143 -1.678154689 0.062190348 SQSLPT(ph)TLLSPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 SQS(0.329)LPT(0.335)T(0.335)LLSPVR 98.654 0.036 56562000 110990 95450 97937 105220 106320 98247 136420 108200 121340 TRUE FALSE 105743.7227 105176.4635 102427.5083 94643.0857 124862.1743 94844.68176 115606.6235 98725.4344 140156.7875 0.754467369 0.75042005 0.730806621 0.675265803 0.890874974 0.676704164 0.824837852 0.704392817 1 17.09668209 -1.755502331 2.464034353 1.061345956 0.754377833 0.585510056 0.065792414 6196477.261 4351042.112 2307009.71 0.014362374 0.017558915 1.755502331 -0.306968122 SQSQENMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSQENMR 8 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 0 60.436 0.092303 285690000 39889 50301 46856 44865 38656 51193 42178 54059 32573 FALSE TRUE 38003.52602 55426.72909 49004.39395 40355.08496 45397.59416 49420.17357 35742.97145 49325.30738 37624.25448 1.010080507 1.473164847 1.302468172 1.07258165 1.206604484 1.313519012 0.949998131 1.310997601 1 15.19937537 1.300193242 0.494448887 1.015400444 1.250565874 0.109981255 0.161059244 1.66676323 1.083652648 0.169919732 0.095494512 19.96150316 -1.300193242 0.235165431 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 SQS(0.005)S(0.995)DTEQQS(0.99)PT(0.01)SGGGK;SQS(0.005)S(0.995)DTEQQS(0.996)PT(0.004)SGGGK;SQS(0.001)S(0.999)DTEQQS(0.993)PT(0.007)SGGGK;SQS(0.006)S(0.994)DTEQQS(0.998)PT(0.002)SGGGK;SQS(0.038)S(0.962)DTEQQS(1)PTSGGGK;SQS(0.027)S(0.973)DTEQQS(0.998)PT(0.002)SGGGK;S(0.009)QS(0.427)S(0.564)DTEQQS(1)PTSGGGK;S(0.004)QS(0.136)S(0.86)DTEQQS(0.998)PT(0.002)SGGGK;SQS(0.004)S(0.996)DTEQQS(0.999)PT(0.001)SGGGK 357.92 7.59E-88 3904237000 6557297 5681689 6134997 6705758 4237281 6690921 7510035 6533483 4724291 TRUE FALSE 6247346.566 6260659.569 6416292.681 6031682.466 4976261.465 6459212.728 6364241.229 5961376.592 5456909.92 1.144850595 1.147290254 1.175810628 1.105329308 0.911919298 1.183675894 1.166271997 1.092445483 1 22.3796528 -5 0.262479429 0.214174184 1.131783665 0.180002847 0.077993113 359.5592659 3.52196536 152.9400359 0.101187973 1.00E-05 5 0.91760948 SQSS(ph)DTEQQSPTSGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQS(0.001)S(0.999)DTEQQSPTSGGGK;SQS(0.019)S(0.981)DTEQQSPTSGGGK;SQS(0.005)S(0.987)DT(0.008)EQQSPTSGGGK;SQS(0.005)S(0.995)DTEQQSPTSGGGK;SQS(0.139)S(0.861)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;S(0.003)QS(0.022)S(0.975)DTEQQSPTSGGGK;S(0.003)QS(0.015)S(0.982)DTEQQSPTSGGGK;SQS(0.044)S(0.955)DT(0.001)EQQSPTSGGGK;SQS(0.022)S(0.978)DTEQQSPTSGGGK 452.76 6.45E-183 6587631000 5199043 4635564 4808593 5373789 3534578 5313626 6017483 5534294 4129474 TRUE FALSE 4953294.541 5107933.242 5029071.745 4833605.52 4151007.284 5129613.799 5099405.45 5049681.878 4769851.737 1.038458806 1.070878829 1.054345506 1.013365988 0.870259185 1.07542416 1.069090976 1.058666423 1 22.18551299 -0.806975806 6.647402407 1 1.035134947 0.022589603 0.060226965 8.67E-10 1.39E-18 0.058157929 0.013707955 0.155963939 0.806975806 0.035134947 SQSS(ph)LSGKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQSSLSGKPK 10 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.001)QS(0.185)S(0.813)LS(0.001)GKPK;S(0.008)QS(0.354)S(0.633)LS(0.005)GKPK 90.689 0.0069437 211430000 790690 629230 622600 941230 646730 929140 1015710 739220 651270 TRUE FALSE 753315.6507 693349.2524 651146.8258 846615.7722 759519.5072 896963.6488 860744.7847 674489.9779 752265.6254 1.001395817 0.921681423 0.865580991 1.125421319 1.009642713 1.192349642 1.144203265 0.896611456 1 19.52088264 3.231803165 24.99983786 1.080152757 0.938129325 0.306453868 0.090283424 165.1312955 610918.5515 0.025041323 0.030570745 1705.309319 -3.231803165 -0.142023432 SQSSDTEQQS(ph)PTSGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.934)PT(0.066)SGGGK;SQSSDTEQQS(0.812)PT(0.181)S(0.007)GGGK;SQSSDTEQQS(0.494)PT(0.494)S(0.013)GGGK;SQSSDTEQQS(0.948)PT(0.051)S(0.001)GGGK;SQSSDTEQQS(0.987)PT(0.013)SGGGK;SQSSDTEQQS(0.999)PT(0.001)SGGGK;SQSSDTEQQS(0.999)PT(0.001)SGGGK;SQSSDTEQQS(0.999)PTSGGGK;SQSSDT(0.001)EQQS(0.996)PT(0.002)S(0.002)GGGK;SQSSDTEQQS(0.5)PT(0.5)S(0.001)GGGK;SQSSDTEQQS(0.936)PT(0.063)SGGGK 425.09 1.63E-160 7488821000 7313276 6276083 6652724 7252568 4625060 7095797 7862137 7504218 5755471 TRUE FALSE 6967591.937 6915622.993 6957757.976 6523526.086 5431669 6850067.771 6662623.603 6847108.89 6648000.048 1.048073389 1.040256159 1.046594152 0.98127648 0.817038051 1.030395265 1.002199692 1.029950187 1 22.66448896 3.221210023 6.972162389 0.974826905 1.04452948 0.222357465 0.060063064 0.232613433 48.35937421 0.017286687 0.021426744 1664.217264 -3.221210023 0.069702575 SQSSDTEQQSPT(ph)SGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.268)PT(0.727)S(0.005)GGGK 395.29 4.10E-121 1168200000 444810 398150 391710 442330 282590 458240 488630 453300 348420 TRUE FALSE 423784.7128 438721.9377 409670.291 397866.148 331873.6065 442371.0339 414080.5192 413606.6489 402451.1941 1.053008959 1.090124577 1.017937819 0.9886072 0.824630692 1.099191754 1.028896237 1.027718777 1 18.61845431 3.585302489 4.423246037 0.998172754 1.071093519 0.168846537 0.069097558 0.394994673 12.6973765 0.018737848 0.029450875 3848.597465 -3.585302489 0.072920765 SQSSHS(ph)YDDSTLPLIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 S(0.001)QS(0.007)S(0.259)HS(0.733)YDDSTLPLIDR 176.1 7.39E-10 62447000 74076 57605 73076 81134 76423 74371 98528 68259 80419 TRUE FALSE 70574.57428 63475.01499 76426.60688 72978.25618 89751.147 71795.51362 83495.74401 62281.8801 92889.9678 0.7597653 0.683335526 0.82276492 0.785641958 0.96620926 0.772909231 0.898867187 0.670490921 1 16.50323517 -4.999600056 0.028321073 2.132347754 8.51E-07 0.292807102 0.092128313 1762.771953 3.761294556 215.5084352 91.84396306 1.00E-05 4.999600056 -2.132346903 SQSSHSYDDSTLPLIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 253.48 5.17E-27 715042000 600336 467345 568020 590298 730054 531570 773631 624611 769753 FALSE TRUE 571959.307 514967.9868 594064.2788 530960.1235 857375.1865 513161.5976 655599.3822 569916.7496 889122.3639 0.643285256 0.579186856 0.668146819 0.597173286 0.964293804 0.577155202 0.737355632 0.640987982 1 19.76202246 -5 0.179422428 2.324377348 0.602021372 0.450498558 0.112674627 114.8062496 1.104057674 54.31346704 0.321562394 1.00E-05 5 -1.722355976 SQT(ph)PPGVATPPIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SQT(1)PPGVATPPIPK;S(0.019)QT(0.981)PPGVATPPIPK;S(0.002)QT(0.998)PPGVATPPIPK;S(0.002)QT(0.998)PPGVATPPIPK 179.27 2.11E-05 1907730000 2212560 1852490 1908710 2235820 1311420 2237610 2326020 2256160 1544790 TRUE FALSE 2107976.674 2041260.837 1996226.241 2011071.126 1540131.233 2160121.005 1971142.929 2058598.67 1784348.144 1.181370733 1.14398126 1.118742578 1.127062078 0.863133822 1.210593915 1.104685168 1.15369788 1 20.7669657 3.622346521 1.797102699 1.083746883 1.168214414 0.129674534 0.093746224 0.757457953 4.81078653 0.026738777 0.051635873 4191.278511 -3.622346521 0.084467531 SQT(ph)PPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQTPPRR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.03)QT(0.97)PPRR;S(0.012)QT(0.988)PPRR;S(0.046)QT(0.954)PPRR;S(0.053)QT(0.947)PPRR 79.986 0.018248 2052320000 373124 326714 308190 410532 284636 352602 366465 366942 301761 TRUE FALSE 355487.168 360006.528 322320.8163 369264.5434 334276.4283 340391.3043 310554.0337 334810.6132 348556.5547 1.019883755 1.032849686 0.924730326 1.059410699 0.959030676 0.976574102 0.890971722 0.960563239 1 18.41103323 2.408529237 2.460489612 0.94117437 1.009608674 0.200305788 0.045106617 0.324840446 4.021045927 0.016587891 0.013288521 256.1705712 -2.408529237 0.068434304 SQTDKDYYQLQAILEAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQTDKDYYQLQAILEAERR 19 2 Q13464;A0A0U1RQV4 Q13464 ROCK1 Rho-associated protein kinase 1 0 48.229 0.090836 55311000 35874 34521 31393 42684 34421 30077 41743 34676 32316 FALSE TRUE 34178.30712 38038.72915 32832.4001 38393.32323 40424.0115 29035.42595 35374.33869 31639.58561 37327.40023 0.915635884 1.019056482 0.879579073 1.028556047 1.082958129 0.777858243 0.947677536 0.847623607 1 15.18794741 2.242887624 24.9999977 0.891257231 0.980633308 0.241749175 0.080589101 154.3546969 891813.2871 0.026120606 0.021148611 174.9393965 -2.242887624 0.089376078 SQTEAVTFLANHDDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQTEAVTFLANHDDSR 16 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 ;;; 241.68 6.49E-20 1285440000 1127600 903140 1079340 1046350 1123710 881920 1131570 1080030 1112930 FALSE TRUE 1074300.583 995170.9928 1128828.807 941168.9101 1319684.668 851378.8893 958928.2138 985456.8476 1285517.5 0.835695027 0.77414037 0.87811236 0.73213232 1.026578532 0.662284947 0.745947226 0.766583767 1 20.29391782 SQTGDVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQTGDVSPK 9 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2;H0YBM4 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 SQTGDVS(1)PK 82.774 0.018357 71243000 180700 162070 140840 170750 104610 171000 161770 158100 95842 TRUE FALSE 172158.6691 178585.1173 147297.6533 153585.8856 122853.9509 165078.2271 137089.0154 144255.9259 110704.6879 1.555116341 1.613166711 1.330545762 1.387347623 1.109744793 1.491158417 1.238330716 1.303069713 1 16.75635679 8 0.086832502 0.754936005 3.129085168 0.610341494 0.118855108 98.28344662 0.616178045 2.303549394 27.83828188 100000000 -8 2.374149164 SQTTTERDS(ph)DT(ph)DVEEEELPVENR ddPTM_SK-BR-3_Trastuzumab_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;SQTTT(0.001)ERDS(0.999)DT(1)DVEEEELPVENR 221.3 4.12E-32 2257400000 436660 395540 417110 450660 406640 398620 485420 410950 411850 TRUE FALSE 416019.9472 435845.9757 436234.9061 405358.8006 477557.8873 384815.6894 411360.2637 374965.0394 475717.5946 0.874510323 0.916186369 0.917003935 0.85209966 1.003868456 0.808916243 0.86471526 0.788209315 1 18.85974586 SQTTTERDS(ph)DTDVEEEELPVENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQT(0.002)T(0.001)T(0.002)ERDS(0.97)DT(0.024)DVEEEELPVENR;SQTTTERDS(0.999)DT(0.001)DVEEEELPVENR 301.75 3.49E-62 651210000 227908 217939 225285 260480 193783 213724 243130 210040 202780 TRUE FALSE 217135.2405 240147.2319 235614.5401 234296.0555 227578.6938 206322.6843 206036.0531 191647.7841 234226.0867 0.927032695 1.025279614 1.005927834 1.000298723 0.971619759 0.880869792 0.879646055 0.818217077 1 17.83754224 2.290261327 4.395658081 0.883450971 0.989065767 0.436796818 0.051100155 0.163354136 6.572924571 0.01706746 0.013695395 195.1018229 -2.290261327 0.105614795 SQVDHVIWPDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SQVDHVIWPDGKR 13 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 127.71 0.00011278 168063000 376400 343040 361710 385630 313000 391340 427580 408100 359820 FALSE TRUE 358608.318 377996.166 378294.7613 346865.7398 367587.1009 377787.7977 362344.818 372364.6005 415619.0479 0.862829362 0.909477484 0.910195919 0.834576138 0.884432758 0.90897614 0.871819566 0.895927659 1 18.66490225 0.948243907 18.44948349 1 0.884386998 0.704543932 0.023579781 221.5872922 78990.12287 0.021440048 0.005360012 8.876543927 -0.948243907 -0.115613002 SQVDKLTLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SQVDKLTLTSR 11 1 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 118.76 0.00061791 438090000 607590 400170 496360 449280 486120 403680 546040 490400 563390 FALSE TRUE 578870.4248 440947.778 519118.597 404117.5208 570899.1741 389700.4604 462731.5693 447457.9762 650757.6438 0.889533039 0.677591392 0.797714175 0.620995427 0.877283854 0.598841157 0.711065899 0.687595421 1 19.31176083 -1.165194738 4.375026235 1.000056775 0.732378369 0.425970025 0.097561178 5.13E-05 9.79E-06 0.085471945 0.020141453 0.068360505 1.165194738 -0.267678405 SQVEEELFSVR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 227.37 9.42E-12 254699000 373141 354517 345471 395440 370274 348919 431483 397708 450225 FALSE TRUE 355503.3644 390642.6854 361311.1871 355689.6199 434849.6684 336835.8475 365652.3436 362882.5791 520043.5936 0.683603007 0.75117296 0.694770961 0.683961161 0.836179262 0.647706946 0.703118639 0.697792615 1 18.98827304 -1.174224144 5.400051128 1.000009977 0.712775276 0.759806776 0.050837403 5.52E-06 8.45E-07 0.044524561 0.010494175 0.066953896 1.174224144 -0.287234701 SQWLDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SQWLDVK 7 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 143.12 0.0056838 1367850000 3384670 3223150 2816640 3440100 2225030 3330670 3374340 3444000 2246990 FALSE TRUE 3224683.357 3551592.649 2945785.73 3094294.612 2613074.528 3215328.063 2859522.459 3142425.102 2595441.733 1.242441052 1.368396217 1.134984343 1.192203459 1.006793755 1.238836542 1.101747892 1.210747697 1 21.30754867 7.999999998 0.114444595 0.958400874 2.063860484 0.362396146 0.089391712 91.89305635 0.728925144 0.664642309 16.11335302 99999999.53 -7.999999998 1.105459611 SRADLES(ph)PQRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRADLESPQRK 11 2 A0A087X1K6;Q9Y2Y9 A0A087X1K6 KLF13 Krueppel-like factor 13 1 SRADLES(1)PQRK;SRADLES(1)PQRK;SRADLES(1)PQRK 101.61 0.001647 263412000 236591 193767 208746 232895 190083 225997 260360 258388 248641 TRUE FALSE 225407.8123 213512.0776 218317.2106 209483.9521 223233.415 218170.6672 220637.3002 235762.1769 287198.9764 0.78484894 0.743429104 0.760160128 0.729403547 0.777277892 0.759649877 0.768238463 0.82090187 1 18.13169108 0.71105268 1.548074653 1.00000184 0.758289552 0.959852686 0.015411037 0.169322639 0.636756291 0.013693477 0.003958736 5.141060089 -0.71105268 -0.241712287 SRAS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.346)RAS(0.65)PVS(0.004)R;S(0.321)RAS(0.652)PVS(0.028)R;S(0.195)RAS(0.786)PVS(0.018)R;S(0.032)RAS(0.968)PVSR;S(0.073)RAS(0.924)PVS(0.003)R;S(0.199)RAS(0.8)PVS(0.001)R 70.488 0.031007 2991413000 674559 549835 645708.9 752152 640961 647391 655817 702227 648795 TRUE FALSE 642673.9329 605863.8116 675315.2918 676544.252 752744.3955 624971.6873 555760.0717 640736.2811 749406.815 0.857576846 0.808457836 0.901133107 0.902773018 1.00445363 0.833955169 0.74159997 0.854991265 1 19.51538957 0.871119331 20.56022829 1 0.854666512 0.275641462 0.068529211 187143.6581 29854877.31 0.071139941 0.017784985 7.432233245 -0.871119331 -0.145333488 SRDEIVEMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRDEIVEMIR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 191.52 7.15E-07 239240000 236460 188563 166156 208950 223890 175089 239720 198172 247590 FALSE TRUE 225283.0044 207777.7841 173774.417 187945.949 262936.3451 169025.624 203146.3112 180819.0091 285984.9927 0.787744148 0.726533872 0.607634741 0.657188153 0.919406094 0.591029699 0.710339061 0.632267475 1 18.12557992 -1.308521251 4.17878306 1.000376205 0.70828169 0.48211831 0.096316446 0.000314077 5.20E-05 0.086765532 0.020424766 0.049144933 1.308521251 -0.292094515 SRDLLVQQASQCLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRDLLVQQASQCLSK 15 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 117.07 0.00036386 343990000 354490 278800 347630 353940 271800 367560 446170 379750 316930 FALSE TRUE 337733.9602 307210.037 363569.1794 318361.2788 319201.8339 354831.305 378098.572 346497.0768 366077.8857 0.922574057 0.839193103 0.993147069 0.869654495 0.871950605 0.969278175 1.032836417 0.946511904 1 18.4817911 2.101074443 4.994333921 0.997724845 0.896484326 0.483357661 0.045436304 0.156937078 6.384398617 0.016518371 0.011974671 126.2043846 -2.101074443 -0.101240519 SRDPFWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRDPFWNR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;;; 135.71 0.00074973 884360000 367364 301962 238308 273951 345214 259140 358216 314995 360674 FALSE TRUE 349999.4318 332732.2711 249234.6575 246412.925 405419.2123 250165.9168 303563.5701 287412.3679 416605.4819 0.840122003 0.798674731 0.598251027 0.591477875 0.97314901 0.600486378 0.728659567 0.689890989 1 18.6683223 -1.392421142 8.431362656 1.000002005 0.733990537 0.333490722 0.120727577 4.33E-06 3.12E-07 0.111309758 0.026235764 0.04051155 1.392421142 -0.266011468 SRDPQLCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRDPQLCR 8 1 Q8TAT6;Q8TAT6-2;I3L4S2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;; 166.52 0.00029002 313227000 273121 215710 211129 240500 297746 221424 322395 254067 271986 FALSE TRUE 260211.1116 237691.0942 220809.4735 216324.4831 349672.8081 213756.0314 273207.7216 231819.5466 314164.1998 0.828264684 0.756582368 0.702847344 0.688571401 1.113025636 0.680395893 0.869633528 0.737892945 1 18.26115926 SREDAGDNDDTEGAIGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SREDAGDNDDTEGAIGVR 18 1 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 ;; 181.15 6.84E-14 895430000 185169 164944 185960 182901 211879 169377 223456 192536 205875 FALSE TRUE 176416.4283 181751.9811 194486.4499 164515.444 248830.6305 163511.432 189363.6831 175676.5271 237801.0435 0.741865661 0.764302706 0.817853644 0.691819689 1.046381575 0.687597622 0.796311405 0.738754231 1 17.85939552 -2.463218686 2.238679107 3.356635882 0.783598023 0.306993587 0.101189856 3659542.678 308222.4016 44108454.2 0.021659126 0.003441766 2.463218686 -2.573037858 SREDMIDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SREDMIDIK 9 1 P20340-2;P20340;P20340-4;P20340-3;F5H3K7 P20340-2 RAB6A Ras-related protein Rab-6A 0 ; 98.634 0.0053639 549240000 314420 290210 285270 397370 293480 341580 412990 359770 306370 FALSE TRUE 299557.9897 319782.7289 298349.9117 357425.6126 344662.8191 329750.999 349980.7904 328266.6315 353880.2949 0.846495253 0.90364661 0.843081449 1.01001841 0.973953125 0.93181509 0.988980725 0.927620544 1 18.4329019 3.243035683 24.99980775 0.970058695 0.870257154 0.729502648 0.030818568 55.40294759 309504.442 0.007917535 0.01036317 1749.990468 -3.243035683 -0.099801541 SREDMTEAEQIIFDHFSDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SREDMTEAEQIIFDHFSDPK 20 1 Q14997;Q14997-3;Q14997-2 Q14997 PSME4 Proteasome activator complex subunit 4 0 49.224 0.089537 13720000 12963 11762 11385 13010 13272 13137 16662 14006 13206 FALSE TRUE 12350.26468 12960.56117 11907.01351 11702.21008 15586.6326 12682.0624 14119.90588 12779.56039 15253.91903 0.809645354 0.849654515 0.780587171 0.767160889 1.021811678 0.831396992 0.925657587 0.83778866 1 13.89689233 2.76627706 24.99973432 0.911733596 0.809443621 0.468270376 0.0634747 697.8837086 629477.3835 0.017492679 0.018550376 583.8174343 -2.76627706 -0.102289975 SRENLS(ph)AVMLYNPGLEFER ddPTM_SK-BR-3_Trastuzumab_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(0.187)RENLS(0.813)AVMLYNPGLEFER;S(0.322)RENLS(0.678)AVMLYNPGLEFER 207.55 1.89E-16 273195000 189023 163301 168632 191088 142363 173663 188155 188226 149210 TRUE FALSE 180088.2574 179941.5576 176363.944 171879.4712 167191.0621 167649.0068 159448.499 171743.9336 172348.7247 1.044906237 1.044055057 1.023297064 0.997277302 0.970074263 0.972731345 0.925150443 0.996490887 1 17.3949711 3.133314611 1.438857747 0.963234538 1.045418956 0.657077062 0.021101582 0.191946289 0.82863975 0.007269482 0.009723817 1359.29779 -3.133314611 0.082184418 SRERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRERSPSPLRGNVVPSPLPTR 21 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 S(0.442)RERS(0.617)PS(0.941)PLRGNVVPSPLPTR 96.466 0.0018297 160620000 70022 44694 64222 54168 57640 68311 86518 52232 85841 TRUE FALSE 66712.19883 49248.36941 67166.64222 48722.92973 67692.39775 65945.37294 73318.09009 47658.28918 99152.78386 0.672822247 0.496691747 0.677405511 0.491392453 0.68270799 0.665088466 0.739445603 0.480655079 1 16.59736566 -5 0.279226803 3.775558522 0.592452683 0.605013495 0.096014708 145.8283869 1.397631761 234.5492637 0.100843965 1.00E-05 5 -3.183105839 SRES(ph)LNVDVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.406)RES(0.594)LNVDVVK 77.912 0.018968 112420000 65292 65568 58643 73371 61426 57733 66536 65312 58553 TRUE FALSE 62205.77656 72249.45374 61331.83956 65995.60768 72138.67495 55733.69173 56384.71118 59592.93504 67633.10019 0.91975344 1.068255832 0.906831705 0.975788593 1.066617895 0.824059397 0.833685149 0.881120855 1 16.04544187 2.227657506 24.99936305 0.865202761 0.988119872 0.327014933 0.070810668 197.0586453 451825.6214 0.024312619 0.018129127 168.9108337 -2.227657506 0.122917111 SRES(ph)S(ph)PSHGLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.502)RES(0.76)S(0.725)PS(0.013)HGLLK 63.709 0.039125 339120000 442860 345520 409770 441150 276250 430710 488780 412050 286740 TRUE FALSE 421926.8855 380728.8808 428558.3598 396804.7639 324427.9125 415794.4047 414207.6339 375968.7176 331206.1747 1.273910083 1.149522291 1.293932277 1.19805968 0.979534614 1.255394484 1.250603598 1.135150086 1 18.33737004 -4.586022944 0.262798176 3.93E-11 1.213088269 0.323669684 0.089896496 195.8465121 2.352624556 105.4399628 0.113848232 2.59E-05 4.586022944 1.213088269 SRESAS(ph)PTIPNLDLLEAHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.183)RES(0.183)AS(0.537)PT(0.097)IPNLDLLEAHTK 268.24 3.12E-37 85855000 156570 129570 153220 168810 120330 148890 180270 163800 126400 TRUE FALSE 149169.2464 142773.3303 160245.2886 151840.8981 141315.5139 143733.902 152766.5006 149456.8036 146001.4664 1.021696905 0.977889701 1.097559446 1.039995705 0.967904757 0.984468892 1.046335385 1.023666455 1 17.15562333 -1.650701508 2.620713702 0.997800207 1.01815601 0.02479263 0.037859747 166322978.2 158743487.6 2494964.886 0.009016965 0.022351079 1.650701508 0.020355803 SRESASPT(ph)IPNLDLLEAHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.199)RES(0.1)AS(0.236)PT(0.466)IPNLDLLEAHTK 269.94 1.35E-37 91115000 181750 155530 168400 191700 131470 178170 196270 179340 154940 TRUE FALSE 173159.0377 171378.6838 176121.3066 172429.9518 154398.3264 171999.9282 166325.4068 163636.0389 178967.3039 0.967545657 0.957597729 0.984097669 0.963471808 0.862718067 0.961069003 0.929361974 0.914334827 1 17.44933652 2.963888623 24.99826597 0.929682496 0.96769861 0.19190259 0.034992909 811.4746218 561746.7175 0.009470471 0.010047663 920.2135488 -2.963888623 0.038016115 SRFS(ph)GGFGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRFSGGFGAR 10 1 A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A2R8YFS5 1 S(0.2)RFS(0.8)GGFGAR;S(0.301)RFS(0.699)GGFGAR;S(0.164)RFS(0.836)GGFGAR;S(0.001)RFS(0.999)GGFGAR;S(0.01)RFS(0.99)GGFGAR;S(0.151)RFS(0.849)GGFGAR 138.21 4.28E-05 1342590000 754375 717371 730129 825449 1110713 735309 956716 793851 1230058 TRUE FALSE 718717.1888 790471.9205 763606.1368 742473.2983 1304420.996 709845.065 810751.4029 724337.198 1420809.112 0.505850633 0.556353358 0.537444566 0.52257076 0.918083213 0.499606216 0.570626551 0.509806132 1 20.43828131 -2.13885538 2.317469535 1.891991983 0.574884993 0.536595464 0.123357225 7433417.02 1974204.976 34820979.36 0.028386841 0.007263478 2.13885538 -1.31710699 SRGSDS(ph)PAADVEIEYVTEEPEIYEPNFIFFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRGSDSPAADVEIEYVTEEPEIYEPNFIFFK 31 1 Q13435;E9PPJ0;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 1 S(0.204)RGS(0.204)DS(0.589)PAADVEIEY(0.003)VTEEPEIYEPNFIFFK 131.2 2.32E-06 8052900 8151.5 6857.8 8337.5 9425 6114.2 8715.5 12722 8079.5 11252 TRUE FALSE 7766.19475 7556.617617 8719.782622 8477.581094 7180.514544 8413.68005 10781.02524 7372.016148 12996.90269 0.597541963 0.581416803 0.670912357 0.65227703 0.552478903 0.647360394 0.829507268 0.567213306 1 13.66588023 -5 0.169175027 2.422374399 0.553269072 0.679094089 0.078339716 73.73939953 0.694135274 35.02940337 0.273551908 1.00E-05 5 -1.869105327 SRHS(ph)SIS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRHSSISPVRLPLNSSLGAELSR 23 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.017)RHS(0.551)S(0.432)IS(1)PVRLPLNSSLGAELSR 189.98 8.90E-18 112760000 51290 25894 50862 42145 55999 43585 78060 58953 83144 TRUE FALSE 48865.62335 28532.62804 53194.07301 37908.50453 65765.20787 42075.64052 66150.51333 53790.76279 96037.54688 0.508817904 0.297098676 0.553888294 0.394725873 0.68478642 0.438116569 0.688798449 0.560101383 1 16.55131093 -1.043799876 0.200175665 1.416447016 0.345187975 0.694155661 0.107312539 9.380176506 0.411470857 2.386509315 0.283432549 0.090406597 1.043799876 -1.071259041 SRHSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRHSSISPVRLPLNSSLGAELSR 23 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.248)RHS(0.353)S(0.398)IS(0.999)PVRLPLNSSLGAELSR 78.311 0.0073569 120160000 19541 12698 19949 17382 23582 18416 29429 18028 28128 TRUE FALSE 18617.33566 13991.94064 20863.68138 15634.72834 27694.69333 17778.2493 24939.06555 16449.37275 32489.94658 0.573018352 0.430654467 0.64215807 0.481217422 0.852408091 0.547192322 0.767593307 0.50629116 1 14.98770575 -5 0.122208168 2.320399354 0.405299183 0.490353176 0.128332454 111.349748 0.877071477 36.27379282 1.02850144 1.00E-05 5 -1.915100171 SRIPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;S(0.08)RIPS(0.92)PLQPEMQGTPDDEPSEPEPSPSTLIYR;S(0.044)RIPS(0.945)PLQPEMQGT(0.011)PDDEPSEPEPSPSTLIYR;S(0.013)RIPS(0.987)PLQPEMQGTPDDEPSEPEPSPSTLIYR;S(0.045)RIPS(0.954)PLQPEMQGT(0.001)PDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR 247.42 2.17E-47 1547960000 642714 573662 603355 648564 644018 645568 769658 695133 770623 TRUE FALSE 612334.183 632118.81 631019.4235 583369.1145 756334.5353 623211.8183 652232.5364 634263.4694 890127.279 0.687917557 0.710144296 0.708909207 0.65537719 0.84969257 0.700137871 0.732740757 0.712553681 1 19.76365212 -5 0.300146839 3.342142114 0.703524996 0.75619371 0.050112836 122.623246 1.133317248 180.7231457 0.045573212 1.00E-05 5 -2.638617118 SRKS(ph)PS(ph)PAGGGS(ph)SPYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRKSPSPAGGGSSPYSR 17 2 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 3 S(0.439)RKS(0.566)PS(0.975)PAGGGS(0.525)S(0.458)PY(0.011)S(0.027)R 53.304 0.08998 273400000 350880 246350 280470 325170 197630 300740 374650 220720 254210 TRUE FALSE 334294.5978 271453.3451 293329.8269 292483.2938 232096.6094 290325.2984 317490.2616 201392.5867 293631.5885 1.138483089 0.92446915 0.998972312 0.996089335 0.790434744 0.988740005 1.081253768 0.68586826 1 18.16364765 4.616243626 2.149556487 0.945090609 1.165255518 0.228907297 0.115915923 0.740331741 4.781603256 0.027574938 0.286019193 41327.92745 -4.616243626 0.220164909 SRKS(ph)PS(ph)PAGGGSS(ph)PYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRKSPSPAGGGSSPYSR 17 2 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 3 S(0.024)RKS(0.977)PS(0.999)PAGGGS(0.175)S(0.623)PY(0.028)S(0.175)R 109.03 0.00041381 518720000 382670 260960 343250 361940 212710 342870 417830 250630 297450 TRUE FALSE 364581.9475 287552.1207 358988.352 325557.1036 249806.5567 330996.3259 354082.3595 228683.5085 343577.0268 1.061135987 0.836936402 1.044855517 0.947552013 0.727075844 0.963383172 1.030576354 0.66559604 1 18.39027405 4.695392037 3.715268847 0.912043736 1.070468432 0.13066674 0.126480477 0.500575468 12.05060346 0.028305015 0.199537661 49589.76344 -4.695392037 0.158424696 SRLDQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRLDQELK 8 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 87.806 0.013737 957920000 1366520 1098120 915210 1248020 1197020 1179280 1446590 1375070 1172990 FALSE TRUE 1301927.308 1210019.676 957173.2838 1122566.659 1405779.909 1138441.238 1225886.127 1254661.581 1354891.298 0.960909048 0.893075096 0.706457621 0.828528945 1.037559183 0.840245442 0.904785593 0.926023794 1 20.36974568 SRLNS(ph)HGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRLNSHGGR 9 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(0.033)RLNS(0.967)HGGR;S(0.004)RLNS(0.996)HGGR;S(0.03)RLNS(0.97)HGGR 73.848 0.025896 145395000 67951 41284 60909 64290 82159 57294 78108 60415 72252 TRUE FALSE 64739.0909 45490.88654 63701.7379 57827.44706 96487.50359 55309.89441 66191.19005 55124.74232 83456.47115 0.775722841 0.545085191 0.763292972 0.69290549 1.156141666 0.662739434 0.79312232 0.660520887 1 16.3487363 2.957353811 24.99891051 0.832176736 0.6809497 0.192177091 0.158828849 794.7407588 465871.5024 0.045499398 0.04826282 906.4707838 -2.957353811 -0.151227037 SRLT(ph)PVSPESSSTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.254)RLT(0.746)PVSPESSSTEEK;S(0.086)RLT(0.812)PVS(0.102)PESSSTEEK;S(0.002)RLT(0.997)PVS(0.002)PESSSTEEK 237.14 1.53E-19 2743030000 2452860 1928640 1962480 2357050 1488590 2198220 2451420 2450360 1725710 TRUE FALSE 2336918.169 2125170.609 2052461.649 2120114.856 1748199.625 2122095.09 2077410.856 2235793.488 1993324.293 1.172372291 1.066143937 1.029667704 1.063607594 0.877027201 1.064601027 1.042184086 1.121640616 1 20.92674501 4.39303035 1.378320398 1.027517377 1.189309167 0.344099681 0.062524687 0.743788384 1.97112237 0.016985156 0.141122789 24718.96884 -4.39303035 0.161791789 SRLTPVS(ph)PESSSTEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 SRLTPVS(1)PESSSTEEK;SRLTPVS(1)PESSSTEEK;S(0.229)RLT(0.138)PVS(0.633)PESSSTEEK;SRLTPVS(1)PESSSTEEK 233.89 7.01E-20 1396070000 1015790 763710 1006880 882690 622590 991460 1232730 1250930 965010 TRUE FALSE 967775.6198 841532.9173 1053046.444 793960.3242 731169.4989 957125.4916 1044654.398 1141391.938 1114658.822 0.868225865 0.754969055 0.944725348 0.712289993 0.655958114 0.858671257 0.937196546 1.023983227 1 20.08817076 1.686126412 2.513772929 1.004662784 0.79302656 0.565805617 0.080448756 0.187264624 2.614683306 0.051972948 0.021880816 48.54297757 -1.686126412 -0.211636225 SRLTVADIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRLTVADIR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 71.349 0.045447 422240000 569220 425590 359350 322460 536650 379520 672160 592160 740660 FALSE TRUE 542314.0987 468958.1049 375826.5529 290045.7082 630241.5901 366377.1272 569609.6469 540307.3312 855517.77 0.633901618 0.548157059 0.439297191 0.339029437 0.73667855 0.42825192 0.665806915 0.631555942 1 19.7064383 0.544524532 0.823208536 1.00255628 0.528572957 0.619331341 0.114731592 0.972442499 1.061959463 0.10900473 0.036089024 3.503680794 -0.544524532 -0.473983323 SRNPS(ph)KSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SRNPSKSHLR 10 2 Q92615 Q92615 LARP4B La-related protein 4B 1 SRNPS(0.952)KS(0.047)HLR;SRNPS(0.802)KS(0.198)HLR;SRNPS(0.997)KS(0.003)HLR;SRNPS(0.975)KS(0.025)HLR;SRNPS(0.796)KS(0.204)HLR 124.3 0.00022915 388208000 394564 249947 322079 335515 321032 319331 432597 381105 349667 TRUE FALSE 375913.7417 275416.8835 336846.6407 301788.3948 377019.8792 308272.4874 366596.3825 347733.4258 403891.5725 0.930729352 0.681907973 0.834002647 0.747201515 0.933468051 0.763255558 0.907660391 0.86095737 1 18.62360852 0.859710473 0.566817887 1.002286419 0.801866437 0.333209563 0.079832464 1.123347973 0.823652686 0.081550645 0.034215293 7.239531682 -0.859710473 -0.200419983 SRNPTPDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRNPTPDQK 9 1 Q96GT9 Q96GT9 XAGE2 X antigen family member 2 0 ; 101.48 0.0044797 149820000 169691 158623 162213 182152 119855 188456 190856 187600 121346 FALSE TRUE 161670.0427 174786.864 169650.6265 163841.7349 140757.6741 181929.7215 161737.4119 171172.7495 140163.7179 1.153437174 1.247019319 1.21037476 1.168931142 1.004237588 1.297980135 1.15391782 1.221234368 1 17.09675342 -2.229470037 2.424413699 0.336485615 1.184295486 0.355328936 0.077053399 3929968.675 1047115.298 14320164.54 0.018220539 0.005895627 2.229470037 0.847809871 SRNS(ph)FSSYAQLPKPTSTYSLSSFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRNSFSSYAQLPKPTSTYSLSSFFR 25 2 G3V4K3;Q9H9C1 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 1 S(0.198)RNS(0.764)FS(0.03)S(0.009)YAQLPKPTSTYSLSSFFR 107.71 0.0018534 101840000 130520 89918 112530 151240 124290 129510 178330 138620 127480 TRUE FALSE 124350.5783 99080.74643 117689.6118 136037.0679 145966.1366 125025.0362 151122.4832 126481.6979 147248.9473 0.844492137 0.672879149 0.799256049 0.92385766 0.99128815 0.84907253 1.026306035 0.85896504 1 17.16789779 3.274557572 3.606949304 0.946296517 0.755887745 0.573992558 0.069469469 0.137250504 3.722244251 0.01836994 0.024505334 1881.731141 -3.274557572 -0.190408771 SRNS(ph)PLLER ddPTM_SK-BR-3_Trastuzumab_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(0.035)RNS(0.965)PLLER;S(0.013)RNS(0.987)PLLER;SRNS(1)PLLER;SRNS(1)PLLER;SRNS(1)PLLER;SRNS(1)PLLER;S(0.003)RNS(0.997)PLLER 147.66 5.56E-05 14858570000 2480228 2459543 2277700 2620058 2352141 2326835 2771417 2284126 2580515 TRUE FALSE 2362992.538 2710173.228 2382134.798 2356684.792 2762353.646 2246256.121 2348586.436 2084115.819 2980688.087 0.792767465 0.909244157 0.799189559 0.79065126 0.926750323 0.753603213 0.787934318 0.699206276 1 21.50721398 SRNTDEMVELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SRNTDEMVELR 11 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 175.48 8.91E-06 2966060000 4631430 3546502 4175810 4115291 3771120 4335520 5227260 5055470 5264640 FALSE TRUE 4412511.483 3907894.586 4367275.019 3701614.13 4428802.134 4185379.855 4429745.482 4612786.246 6081053.483 0.725616292 0.642634471 0.718177374 0.608712642 0.728295212 0.688265589 0.728450341 0.758550514 1 22.53588985 0.38442847 0.736150821 1.005450423 0.679173294 0.875222581 0.036836489 0.611090198 0.481694937 0.038327094 0.011496445 2.423418785 -0.38442847 -0.326277129 SRPALS(ph)PLGDIDFCPPNPGPDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRPALSPLGDIDFCPPNPGPDGPR 24 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.003)RPALS(0.997)PLGDIDFCPPNPGPDGPR;S(0.276)RPALS(0.724)PLGDIDFCPPNPGPDGPR;S(0.008)RPALS(0.992)PLGDIDFCPPNPGPDGPR;S(0.006)RPALS(0.994)PLGDIDFCPPNPGPDGPR 186.86 1.23E-17 438373000 361353 320032 328476 375686 391514 326638 390897 335868 436765 TRUE FALSE 344272.5598 352643.6246 343536.9495 337921.3295 459793.9176 315326.4442 331258.4833 306457.6174 504496.2855 0.682408513 0.699001429 0.680950404 0.669819262 0.911392077 0.625032241 0.656612334 0.607452673 1 18.94448412 -1.183506157 3.72564518 1.000269596 0.691696363 0.577840149 0.08284652 24886602.08 38962688.73 80047.78235 0.018897884 0.065538099 1.183506157 -0.308573234 SRPEFMLPVHFYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRPEFMLPVHFYGK 14 1 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 113.63 0.0003151 264000000 1551650 1300110 1268460 1511920 1315140 1311550 1657460 1489660 1327330 FALSE TRUE 1478306.58 1432592.687 1326620.146 1359938.929 1544500 1266130.695 1404584.036 1359217.473 1533165.557 0.964218491 0.93440182 0.86528173 0.887013749 1.007392836 0.825827771 0.916133309 0.886543183 1 20.54808206 3.98706294 13.1854957 0.906704303 0.953046198 0.071760736 0.055883836 2.805916145 2864.262239 0.012793469 0.024162609 9706.506293 -3.98706294 0.046341895 SRPERS(ph)ELVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRPERSELVR 10 2 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6;B0QY74;B0QY84 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1;Phosphatase and actin regulator 1 S(0.131)RPERS(0.869)ELVR 95.531 0.085115 1297200000 6259.7 6331 8347.7 8018.3 11356 6293.4 7555.3 4895.8 14294 TRUE FALSE 5963.816387 6976.136098 8730.450302 7212.28525 13336.4828 6075.45798 6402.600222 4467.097798 16510.64052 0.36121048 0.42252365 0.528777202 0.436826496 0.807750783 0.367972277 0.387786302 0.270558722 1 14.01110847 -1.417133342 3.7828059 1.003459012 0.445416342 0.593119037 0.143688614 109254757.1 178180434.9 4076080.235 0.033588584 0.038270722 1.417133342 -0.558042671 SRPFTVAASFQSTSVKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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;SRPFTVAASFQSTSVKS(1)PK 208.77 2.00E-16 902290000 1381110 1086210 1259220 1544670 753000 1315570 1443370 1437680 652260 TRUE FALSE 1315827.667 1196896.034 1316956.483 1389396.837 884322.9616 1270011.481 1223157.397 1311789.118 753409.1495 1.746498126 1.588640163 1.747996402 1.844146488 1.173761909 1.685686299 1.623496871 1.741137758 1 19.52307403 -1.913900208 2.704924842 0.625250625 1.640727368 0.553504003 0.181733535 21977208.35 10969163.02 52102593 0.040793496 0.012192697 1.913900208 1.015476742 SRPQGLTEAEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 93.348 0.0056298 168590000 206227 170288 179996 215358 215443 188437 210924 211637 237510 FALSE TRUE 196479.0584 187640.5408 188248.9946 193709.8047 253016.191 181911.3794 178743.6699 193104.9423 274341.8378 0.716183357 0.683966187 0.686184055 0.706089185 0.922266152 0.663082893 0.651536315 0.703884409 1 18.06561513 -1.798743674 2.307797016 1.098888306 0.711717975 0.578518385 0.075904087 3848110.914 2312339.914 2128796.607 0.018861798 0.015894846 1.798743674 -0.38717033 SRPT(ph)S(ph)EGSDIESTEPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.03)RPT(0.741)S(0.796)EGS(0.433)DIESTEPQK;S(0.004)RPT(0.94)S(0.69)EGS(0.366)DIESTEPQK 162.32 6.54E-09 1134580000 1549570 1421540 1405360 1764680 1024950 1581010 1595320 1475380 1053150 TRUE FALSE 1476324.897 1566396.542 1469797.146 1587291.014 1203700.955 1526259.227 1351924.634 1346187.906 1216467.123 1.213616767 1.2876604 1.208250612 1.304836755 0.989505538 1.254665414 1.111353203 1.106637311 1 20.2142659 1.564631548 0.342314016 0.987730809 1.275693217 0.449161186 0.082488164 1.067119501 0.4096406 0.113122082 0.098769848 36.69708329 -1.564631548 0.287962407 SRPT(ph)SEGS(ph)DIESTEPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.013)RPT(0.648)S(0.564)EGS(0.775)DIESTEPQK 158.77 7.55E-09 623680000 1009700 926180 963290 1096900 622640 1047000 1065600 975340 680810 TRUE FALSE 961973.482 1020558.795 1007457.799 986637.528 731228.2189 1010742.127 903023.1489 889934.059 786386.5377 1.223283253 1.297782637 1.281122897 1.254647022 0.929858516 1.285299378 1.148319695 1.131675094 1 19.5848791 0.981706643 0.147783196 0.870500986 1.377479606 0.352131249 0.100542339 7.426205018 0.802137997 1.398303754 0.983130667 9.587527954 -0.981706643 0.506978621 SRPTPQDYEMRVS(ph)PSDTTPLVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRPTPQDYEMRVSPSDTTPLVSR 23 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 SRPTPQDYEMRVS(0.917)PS(0.083)DTTPLVSR 162.1 8.88E-12 595860000 99735 58619 103440 91883 123870 94479 132870 94253 134370 TRUE FALSE 95020.72421 64592.34274 108182.8263 82646.74627 145472.8888 91207.16854 112598.2412 85999.70765 155207.4133 0.612217691 0.416167897 0.697020999 0.53249226 0.937280544 0.587646985 0.725469478 0.554095361 1 17.24383794 -4.999999999 0.109288792 2.167836061 0.409295624 0.40562825 0.138610761 151.165315 1.100300697 39.89670517 1.623464364 1.00E-05 4.999999999 -1.758540437 SRPTS(ph)EGS(ph)DIESTEPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.004)RPT(0.068)S(0.928)EGS(0.858)DIES(0.119)T(0.023)EPQK;S(0.009)RPT(0.272)S(0.886)EGS(0.833)DIESTEPQK 242.48 2.48E-19 656450000 1709060 1500460 1504210 1846170 1133690 1767200 1763420 1582350 1071670 TRUE FALSE 1628276.121 1653358.58 1573179.516 1660589.484 1331405.177 1706001.421 1494377.892 1443791.045 1237859.11 1.315396968 1.335659742 1.270887376 1.341501202 1.075570851 1.378187071 1.207227769 1.166361368 1 20.23941569 -4.999998756 0.120468088 0.058339974 1.410010745 0.564083539 0.081098503 101.8586153 0.79454876 23.03727304 0.685640427 1.00E-05 4.999998756 1.351670771 SRPTS(ph)EGSDIESTEPQKQCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRPTSEGSDIESTEPQKQCSK 21 2 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 SRPT(0.225)S(0.344)EGS(0.344)DIES(0.069)T(0.018)EPQKQCSK 147.17 8.03E-08 101300000 45096 17555 47711 32816 39702 43028 77945 51551 63816 TRUE FALSE 42964.40145 19343.87446 49898.59654 29517.27333 46626.01623 41537.92957 66053.05869 47036.92115 73712.25935 0.58286643 0.262424115 0.676937554 0.400439134 0.632540864 0.563514535 0.896093259 0.638115309 1 16.16961696 1.708044201 0.543705178 0.976157929 0.431102251 0.558790044 0.14080154 0.503832796 0.339146599 0.125792431 0.077042843 51.05569603 -1.708044201 -0.545055678 SRPTS(ph)FADELAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.181)RPT(0.127)S(0.692)FADELAAR 89.846 0.0043981 78855000 67062 57349 65297 85908 74800 61802 77779 86773 59076 TRUE FALSE 63892.11216 63192.9283 68290.93204 77272.36463 87845.09632 59661.78124 65912.38504 79174.69611 68237.20436 0.936323707 0.926077334 1.000787366 1.132408125 1.287348993 0.874329214 0.965930326 1.16028634 1 16.05827092 3.528835255 4.380403077 1.058702974 0.933337416 0.202077726 0.112729698 0.366460965 14.76885041 0.031821727 0.048891113 3379.366196 -3.528835255 -0.125365558 SRPTSEGS(ph)DIESTEPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.004)RPT(0.097)S(0.169)EGS(0.73)DIESTEPQK;SRPT(0.018)S(0.156)EGS(0.826)DIESTEPQK;S(0.005)RPT(0.192)S(0.192)EGS(0.611)DIESTEPQK;SRPT(0.184)S(0.184)EGS(0.631)DIESTEPQK;S(0.001)RPT(0.033)S(0.033)EGS(0.932)DIESTEPQK;S(0.007)RPT(0.285)S(0.285)EGS(0.423)DIESTEPQK;SRPT(0.038)S(0.038)EGS(0.923)DIESTEPQK;S(0.001)RPT(0.17)S(0.17)EGS(0.66)DIESTEPQK 235.92 2.16E-20 7362730000 10114140 9243570 8741420 10890540 6345080 10222840 9909230 9577280 6766600 TRUE FALSE 9636064.646 10185500.29 9142222.753 9795802.229 7451659.943 9868820.487 8397394.968 8738642.591 7815929.769 1.23287503 1.303171931 1.169691006 1.253312468 0.953393923 1.262654704 1.074394885 1.118055414 1 22.89798607 3.046556888 0.221719529 0.981952945 1.387135976 0.397435707 0.09035473 4.6678606 0.44190892 0.188188331 0.562540376 1113.158194 -3.046556888 0.405183031 SRPTSEGS(ph)DIESTEPQKQCSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRPTSEGSDIESTEPQKQCSK 21 2 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.002)RPT(0.001)S(0.001)EGS(0.995)DIESTEPQKQCSK;SRPTSEGS(1)DIESTEPQKQCSK;SRPTSEGS(1)DIESTEPQKQCSK 247.39 1.14E-30 590671000 931950 317231 969790 640474 780330 883450 1436270 988050 1136840 TRUE FALSE 887898.5704 349557.1996 1014255.831 576092.3367 916419.3049 852855.905 1217140.633 901531.104 1313135.341 0.676166837 0.266200435 0.772392456 0.438715126 0.697886407 0.649480582 0.926896562 0.686548504 1 20.32458419 1.960945079 0.625123908 0.95499445 0.491284462 0.443264119 0.157821496 0.583122885 0.455770632 0.132083177 0.079489018 91.39976497 -1.960945079 -0.463709988 SRPVS(ph)MDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SRPVSMDAR 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 S(0.058)RPVS(0.942)MDAR;S(0.001)RPVS(0.999)MDAR;S(0.003)RPVS(0.997)MDAR;S(0.024)RPVS(0.976)MDAR;S(0.01)RPVS(0.99)MDAR;S(0.004)RPVS(0.996)MDAR;S(0.006)RPVS(0.994)MDAR;S(0.016)RPVS(0.984)MDAR 91.961 0.009412 3355460000 3866250 3257970 3376720 3767460 3746620 3460760 4155570 3953320 3984270 TRUE FALSE 3683500.025 3589960.847 3531545.952 3388747.763 4400029.342 3340913.013 3521561.474 3607146.343 4602130.243 0.800390217 0.780065026 0.767372014 0.736343299 0.956085358 0.725949253 0.76520248 0.783799274 1 22.13387038 -0.960979952 4.609778652 1.00000345 0.787453529 0.522746141 0.063215156 0.010745625 35549023.52 293.4341375 0.013542585 0.109400687 0.960979952 -0.212549921 SRQELAS(ph)GLPS(ph)PAATQELPVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRQELASGLPSPAATQELPVER 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 S(0.404)RQELAS(0.598)GLPS(0.977)PAAT(0.02)QELPVER 58.98 0.037816 50615000 52901 41158 46585 50163 46744 39483 56557 48931 54145 TRUE FALSE 50400.47457 45352.04699 48720.96833 45120.51994 54896.1388 38115.69381 47928.19091 44646.34224 62541.53007 0.805872106 0.725150903 0.779017851 0.72144893 0.877754969 0.609446136 0.766341835 0.713867125 1 15.93252689 -0.933606431 6.339402311 1.000000043 0.749781723 0.563707271 0.069158137 3.71E-08 6.27E-09 0.058631944 0.013819679 0.116518147 0.933606431 -0.25021832 SRQELASGLPS(ph)PAATQELPVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SRQELASGLPSPAATQELPVER 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 SRQELASGLPS(1)PAATQELPVER;S(0.001)RQELAS(0.001)GLPS(0.997)PAAT(0.001)QELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER 264.56 1.04E-37 11330840000 6520930 4958077 5826992 6068915 6458958 5289605 6357695 5361102 6051615 TRUE FALSE 6212698.562 5463310.683 6094165.347 5458856.134 7585398.23 5106424.653 5387711.861 4891655.488 6990068.547 0.888789362 0.781581847 0.871831986 0.780944578 1.085167932 0.730525691 0.770766671 0.69980079 1 22.73687517 -0.827811818 5.358599993 1.000000055 0.825311126 0.203169051 0.108172752 1.10E-07 2.42E-08 0.097747723 0.023039347 0.148657964 0.827811818 -0.174688929 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.049)RQPS(0.951)PLLLLPPPAGLTSDPGPSVR;S(0.056)RQPS(0.944)PLLLLPPPAGLTSDPGPSVR;S(0.055)RQPS(0.945)PLLLLPPPAGLTSDPGPSVR;S(0.069)RQPS(0.931)PLLLLPPPAGLTSDPGPSVR 95.435 0.0060049 479303000 315786 270650 300245 324832 321629 294880 359831 319196 352014 TRUE FALSE 300859.4216 298229.5427 314011.5302 292179.2702 377720.9958 284668.2317 304932.1722 291245.5061 406602.5333 0.739934941 0.733467006 0.772281293 0.71858694 0.928968624 0.70011426 0.749951481 0.716290437 1 18.63325968 -1.699877379 2.785492402 1.035638448 0.755665077 0.584903904 0.064199428 17910579.87 15548934.55 4476728.863 0.014072346 0.019958257 1.699877379 -0.27997337 SRRPS(ph)LGELLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRRPSLGELLLR 12 2 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 S(0.002)RRPS(0.998)LGELLLR;S(0.055)RRPS(0.945)LGELLLR 124.68 0.00025106 247990000 126858 104773 113696 101566 137379 111476 159746 143013 200285 TRUE FALSE 120861.6737 115449.4878 118909.0741 91356.39272 161337.8541 107615.5582 135373.8138 130490.0236 231344.1749 0.522432319 0.499037799 0.513992082 0.394893854 0.697393199 0.465175137 0.585161973 0.564051477 1 17.81968125 -4.999978354 0.270768979 4.286710226 0.493439846 0.797343359 0.075340881 81.49056273 0.79034402 149.6415083 0.079951706 1.00E-05 4.999978354 -3.79327038 SRS(ph)APDGGDEENQEQLQDQIAEGSSIEEEEKTDNATLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSAPDGGDEENQEQLQDQIAEGSSIEEEEKTDNATLLR 39 2 Q8IZQ1-2;Q8IZQ1;H0Y9T6 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.162)RS(0.838)APDGGDEENQEQLQDQIAEGSSIEEEEKTDNATLLR 228.76 2.60E-40 50197000 48424 46433 53959 53017 40786 56021 63394 55193 47034 TRUE FALSE 46135.09349 51164.57549 56433.07352 47687.63043 47899.06549 54080.97872 53722.08099 50360.00832 54327.7925 0.84919875 0.941775344 1.038751455 0.877775964 0.881667804 0.995456952 0.988850798 0.926965849 1 15.72940281 4.411121749 2.520832555 0.957673131 0.852377491 0.299895107 0.051672752 0.369392072 4.276822941 0.012997828 0.060658721 25770.43495 -4.411121749 -0.10529564 SRS(ph)APPNLWAAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRSAPPNLWAAQR 13 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(0.017)RS(0.983)APPNLWAAQR;S(0.194)RS(0.806)APPNLWAAQR;S(0.027)RS(0.973)APPNLWAAQR;S(0.004)RS(0.996)APPNLWAAQR 227 5.96E-12 3678310000 907430 619030 678910 737250 889790 718910 1080700 884320 999660 TRUE FALSE 864537.5823 682109.8608 710038.695 663140.2293 1044969.094 694013.9664 915819.3666 806884.2527 1154682.167 0.748723421 0.590733866 0.614921331 0.574305422 0.90498418 0.601043288 0.793135455 0.698793378 1 20.13906437 -0.604195466 0.31819763 1.12543186 0.64484236 0.494000685 0.10119156 7.748338791 0.792488963 1.087839206 0.094364399 0.248773739 0.604195466 -0.480589501 SRS(ph)AVTLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRSAVTLPR 9 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.002)RS(0.998)AVTLPR;S(0.063)RS(0.937)AVTLPR;S(0.002)RS(0.998)AVTLPR;SRS(1)AVTLPR 122.97 0.00034574 561602000 222959 159545 177785 180814 219303 142211 192992 172995 179958 TRUE FALSE 212420.1699 175802.8169 185936.6181 162638.2332 257549.3738 137286.1974 163547.5259 157846.6407 207864.9675 1.021914238 0.84575491 0.894506757 0.782422527 1.23902251 0.660458561 0.786796966 0.75937106 1 17.66528711 SRS(ph)DIDVNAAAGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SRSDIDVNAAAGAK 14 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.49)RS(0.51)DIDVNAAAGAK;S(0.209)RS(0.791)DIDVNAAAGAK;S(0.081)RS(0.919)DIDVNAAAGAK;S(0.19)RS(0.81)DIDVNAAAGAK;S(0.171)RS(0.829)DIDVNAAAGAK;S(0.214)RS(0.786)DIDVNAAAGAK 251 6.91E-19 6952860000 10268430 9178720 9463770 11058070 7699180 10950240 12145130 11811460 9293630 TRUE FALSE 9783061.664 10114042 9897693.215 9946491.795 9041914.554 10571030.44 10292167.36 10777185.95 10734838.68 0.911337558 0.942169911 0.922016019 0.926561833 0.842296268 0.984740504 0.958763114 1.003944845 1 23.35579717 2.128185487 20.74216067 0.98084836 0.914887724 0.633871304 0.029093381 2.061450616 377.5600816 0.010435093 0.007706835 134.3338577 -2.128185487 -0.065960636 SRS(ph)DIDVNAAASAK ddPTM_SK-BR-3_Trastuzumab_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(0.009)RS(0.97)DIDVNAAAS(0.022)AK;S(0.007)RS(0.993)DIDVNAAASAK;S(0.021)RS(0.976)DIDVNAAAS(0.002)AK 188.82 9.31E-08 536570000 1180860 992300 1052000 1238070 819010 1158650 1310330 1201670 922880 TRUE FALSE 1125043.088 1093416.498 1100235.241 1113616.851 961845.0847 1118525.66 1110415.093 1096445.404 1065995.517 1.055391951 1.025723355 1.032119951 1.044673109 0.902297495 1.049278015 1.041669571 1.028564742 1 20.02376994 4.246408831 1.050490295 1.014819282 1.058402935 0.094052925 0.042204178 2.455216374 3.712338292 0.013358437 0.099935615 17636.35494 -4.246408831 0.043583653 SRS(ph)DVDMDAAAEATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSDVDMDAAAEATR 15 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.002)RS(0.986)DVDMDAAAEAT(0.012)R 180.31 1.67E-06 198500000 179060 152420 170670 194730 188570 159240 193650 187250 186930 TRUE FALSE 170596.1887 167951.7713 178495.3883 175155.3704 221456.5483 153725.4789 164105.1359 170853.3973 215918.1497 0.790096566 0.777849252 0.826680798 0.811211891 1.025650454 0.71196182 0.760034004 0.791287798 1 17.72012499 -1.874315529 2.60239318 1.091167326 0.806378597 0.339026288 0.082249483 40018900.1 22981753.38 22468862.82 0.019080307 0.013356248 1.874315529 -0.284788729 SRS(ph)ESETSTMAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.011)RS(0.441)ES(0.441)ET(0.061)S(0.023)T(0.023)MAAK 114.35 0.0019731 171800000 224480 198710 200630 235280 154150 220680 261820 246110 197550 TRUE FALSE 213869.2753 218958.7749 209829.084 211629.2074 181033.7112 213037.7963 221874.5503 224559.3037 228185.0451 0.937262454 0.959566719 0.919556687 0.927445562 0.79336361 0.933618574 0.972344837 0.984110522 1 17.79984472 1.71538251 3.523442644 0.986676438 0.915121923 0.383962096 0.044539432 0.25340774 7.034534806 0.026479904 0.012540508 51.92571792 -1.71538251 -0.071554515 SRS(ph)FDYNYR ddPTM_SK-BR-3_Trastuzumab_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(0.038)RS(0.962)FDYNYR;SRS(1)FDYNYR;S(0.008)RS(0.992)FDYNYR;S(0.024)RS(0.976)FDYNYR 204.32 1.02E-05 1154820000 997790 950690 740200 1108110 955730 860160 1006850 952810 910180 TRUE FALSE 950626.4441 1047566.392 774138.9022 996720.6775 1122409.009 830372.4435 853236.5404 869376.9052 1051326.066 0.904216565 0.996423874 0.7363452 0.948060464 1.067612652 0.789833402 0.811581267 0.826933654 1 20.00377876 SRS(ph)FIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSFIFK 7 1 Q9UN19 Q9UN19 DAPP1 Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide 1 S(0.156)RS(0.844)FIFK;S(0.254)RS(0.746)FIFK 96.009 0.018877 184880000 466590 371070 348200 487250 375170 376350 494400 407830 350070 TRUE FALSE 444535.2154 408882.4549 364165.3144 438270.7043 440599.5292 363316.9051 418970.1997 372118.2432 404357.0677 1.099363041 1.011191562 0.900603312 1.083870518 1.089629846 0.898505144 1.036139178 0.920271396 1 18.6252703 4.393656359 2.623280194 0.994018134 1.094770685 0.193951231 0.068724478 0.45245035 5.754967324 0.016305314 0.070637316 24754.62541 -4.393656359 0.100752552 SRS(ph)FTLDDESLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.172)RS(0.826)FT(0.001)LDDESLK;S(0.154)RS(0.846)FTLDDESLK 233.48 3.24E-16 285930000 1021040 770140 892720 1069780 668000 1024580 1114560 1015400 741390 TRUE FALSE 972777.4627 848618.1416 933652.095 962243.682 784498.9885 989098.5377 944513.4017 926486.193 856360.9747 1.135943243 0.990958447 1.090255304 1.123642611 0.916084469 1.155001882 1.102938398 1.081887452 1 19.70785953 SRS(ph)GEGEVSGLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.009)RS(0.991)GEGEVSGLMR;S(0.055)RS(0.945)GEGEVSGLMR;S(0.003)RS(0.997)GEGEVSGLMR;S(0.059)RS(0.941)GEGEVSGLMR;S(0.013)RS(0.987)GEGEVSGLMR;S(0.007)RS(0.993)GEGEVSGLMR;S(0.083)RS(0.917)GEGEVSGLMR;S(0.009)RS(0.987)GEGEVS(0.004)GLMR;S(0.001)RS(0.991)GEGEVS(0.007)GLMR;S(0.071)RS(0.929)GEGEVSGLMR;S(0.35)RS(0.649)GEGEVS(0.001)GLMR;S(0.008)RS(0.719)GEGEVS(0.272)GLMR;S(0.059)RS(0.922)GEGEVS(0.019)GLMR;S(0.014)RS(0.984)GEGEVS(0.002)GLMR 210.06 1.99E-08 17625030000 7947120 6250390 6547290 6995540 7278620 6280560 7964630 6491400 6718730 TRUE FALSE 7571475.387 6887311.847 6847489.723 6292335.029 8548009.024 6063062.632 6749479.413 5922978.603 7760636.334 0.975625588 0.887467413 0.882336116 0.810801429 1.101457233 0.78125844 0.869706957 0.763207854 1 22.88774352 SRS(ph)IDKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSIDKDR 8 2 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.148)RS(0.852)IDKDR 67.153 0.04712 277460000 415630 352940 391500 431850 297320 449630 495470 453150 347490 TRUE FALSE 395983.9936 388904.9873 409450.6622 388439.6175 349172.5139 434059.2004 419876.9516 413469.7837 401376.9745 0.986563801 0.968926999 1.020114975 0.967767566 0.869936584 1.081425263 1.046091276 1.030128308 1 18.61459833 2.199126986 24.99999945 1.044919669 0.968532442 0.440114426 0.042528976 143.9757621 91276.44476 0.015225024 0.011244584 158.1710458 -2.199126986 -0.076387227 SRS(ph)LGPGAGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSLGPGAGPR 11 1 P78549-3;P78549-2;P78549;H3BUV2 P78549-3 NTHL1 Endonuclease III-like protein 1 1 S(0.02)RS(0.98)LGPGAGPR;S(0.003)RS(0.997)LGPGAGPR 140.82 2.33E-05 207076000 77209 58295 76763 99747 119187 87353 107661 79097 113382 TRUE FALSE 73559.48358 64235.32678 80282.65948 89720.24205 139973.1751 84327.94371 91235.33712 72170.84736 130964.7015 0.561674121 0.490478167 0.613009907 0.68507194 1.068785508 0.643898262 0.696640668 0.551070987 1 16.99881849 3.290290965 2.909335177 0.762792039 0.530576489 0.317431582 0.156308453 0.305323951 5.262621275 0.0442004 0.060274974 1951.151377 -3.290290965 -0.232215549 SRS(ph)MLEVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSMLEVPR 9 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.007)RS(0.993)MLEVPR;S(0.157)RS(0.843)MLEVPR 140.16 6.65E-05 200856000 106112 92614 99260 105891 98567 102946 120673 103655 105521 TRUE FALSE 101096.2961 102051.4719 103811.1692 95246.6355 115757.0536 99380.95421 102262.1175 94578.41869 121884.6578 0.829442343 0.837279062 0.85171646 0.781448931 0.949726206 0.815368858 0.839007299 0.775966561 1 16.89515701 -1.105092822 4.436299389 1.000017516 0.836501449 0.544263593 0.047434043 7.25E-06 1.46E-06 0.040545904 0.009555738 0.078506782 1.105092822 -0.163516067 SRS(ph)PAYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SRSPAYSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.139)RS(0.861)PAYSR;S(0.017)RS(0.983)PAYSR;S(0.019)RS(0.981)PAYSR;S(0.139)RS(0.861)PAYSR;S(0.153)RS(0.847)PAYSR 84.479 0.010551 1197320000 196388 182574 201826 220756 212418 180942 233227 201761 249308 TRUE FALSE 187105.1284 201178.4982 211079.9217 198565.1875 249463.6319 174675.9332 197643.9376 184093.7372 287969.4114 0.649739594 0.698610652 0.732994247 0.689535692 0.866285175 0.606578082 0.686336569 0.639282264 1 18.13555605 -1.10584941 4.666136094 1.000020519 0.694942268 0.651572522 0.069819321 1.38E-05 2.65E-06 0.062704462 0.01477859 0.078370134 1.10584941 -0.305078251 SRS(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.014)RS(0.986)PHEAGFCVYLK 206.64 6.39E-09 449580000 428360 324040 355930 404710 341660 371000 476930 406340 360830 TRUE FALSE 408112.2717 357060.0444 372249.7426 364027.7819 401245.3958 358152.177 404165.5691 370758.7155 416785.6735 0.979189779 0.856699419 0.893144285 0.873417214 0.962713983 0.859319789 0.969720398 0.889566842 1 18.66894616 -0.293984805 0.504503233 1.012410245 0.906539879 0.26686639 0.045759153 8.71388982 2.203426813 0.247577646 0.020367948 0.508177222 0.293984805 -0.105870365 SRS(ph)PIIHS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.206)RS(0.796)PIIHS(0.998)PK 75.376 0.022294 166790000 1326900 1158000 1168200 1329800 808210 1297900 1407800 1277200 793400 TRUE FALSE 1264180.067 1276001.517 1221763.126 1196125.978 949161.5681 1252953.398 1193014.254 1165361.597 916436.4199 1.379452016 1.392351383 1.333167363 1.305192539 1.035709131 1.367201663 1.301797078 1.271622965 1 19.80567527 -5 0.118592354 0.031672983 1.459761852 0.511612339 0.096110076 129.6616619 1.000576168 30.43421463 0.954439495 1.00E-05 5 1.428088869 SRS(ph)PITTNHRPS(ph)PDPEQRPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.427)RS(0.573)PIT(0.005)T(0.009)NHRPS(0.987)PDPEQRPLR;S(0.441)RS(0.557)PIT(0.224)T(0.027)NHRPS(0.752)PDPEQRPLR;S(0.425)RS(0.574)PIT(0.094)T(0.066)NHRPS(0.839)PDPEQRPLR 98.151 0.0014733 306467000 87265 74311 70512 83743 80608 74225 87652 91060 74006 TRUE FALSE 83140.15639 81883.37538 73745.04495 75324.99454 94666.00968 71654.56964 74279.07756 83086.30366 85482.47251 0.972598873 0.957896666 0.862691997 0.881174729 1.107431815 0.83823698 0.868939274 0.971968887 1 16.38334102 SRS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Trastuzumab_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(0.393)RS(0.602)PLDKDT(0.004)YPPSASVVGASVGGHR 187.32 7.26E-18 154750000 108000 101380 116380 120660 95346 107350 128470 128350 119540 TRUE FALSE 102895.054 111710.7373 121716.1381 108531.0276 111974.3122 103632.4426 108869.542 117110.9936 138077.6527 0.745197011 0.809042847 0.881504978 0.786014431 0.810951737 0.750537401 0.788466054 0.848153132 1 17.07512032 0.860068554 3.086463039 0.999900387 0.794661692 0.746470594 0.037368495 0.298266375 5.326572589 0.035909948 0.009382579 7.245503222 -0.860068554 -0.205238694 SRS(ph)PLGFYVHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.395)RS(0.605)PLGFYVHLK 116.43 0.00050877 63143000 156630 120770 101960 107170 135950 118840 161600 131640 124690 TRUE FALSE 149226.4103 133076.6003 106634.9669 96397.06799 159659.637 114724.541 136944.952 120112.9037 144026.2884 1.036105367 0.923974379 0.74038544 0.669301897 1.108545105 0.796552784 0.950833029 0.83396514 1 17.13597264 -1.363875785 6.000398279 1.000016454 0.892035208 0.068426321 0.132164395 2.79E-05 2.95E-06 0.122507746 0.028870954 0.043263755 1.363875785 -0.107981247 SRS(ph)QPCVLNDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSQPCVLNDKK 12 2 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 S(0.068)RS(0.932)QPCVLNDKK 64.565 0.032926 87745000 305600 282590 248810 298020 193180 305490 340600 324040 260870 TRUE FALSE 291154.8936 311386.2423 260218.1846 268062.4634 226870.5308 294910.8047 288635.2145 295665.3398 301324.3873 0.966250679 1.033392103 0.863581561 0.889614232 0.752911282 0.978715355 0.957888663 0.981219418 1 18.20095791 -3.053890153 9.41246772 0.999711041 0.938744719 0 0.081535628 0 0 0 0.018456306 0.000883303 3.053890153 -0.060966323 SRS(ph)SDIVSSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.077)RS(0.922)S(0.001)DIVSSVR;S(0.02)RS(0.926)S(0.052)DIVS(0.001)SVR;S(0.021)RS(0.754)S(0.225)DIVSSVR;S(0.004)RS(0.735)S(0.261)DIVSSVR 178.03 4.68E-06 2097480000 1162900 680190 842960 1221740 1494590 1096040 1362130 908250 1313700 TRUE FALSE 1107932.022 749502.1343 881610.5498 1098928.374 1755246.023 1058083.86 1154312.051 828718.8151 1517421.887 0.730141058 0.49393128 0.580992378 0.724207542 1.15672908 0.697290496 0.760706078 0.546136063 1 20.53319082 3.052553016 5.85076122 0.814607347 0.600902759 0.266865467 0.172945391 0.267615133 19.99071091 0.048839855 0.058282962 1128.633705 -3.052553016 -0.213704588 SRS(ph)VS(ph)PCSNVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.199)RS(0.802)VS(0.993)PCS(0.006)NVESR 71.269 0.024313 146990000 123080 98328 100280 116390 105830 106210 126400 107510 122300 TRUE FALSE 117262.2523 108347.735 104877.9372 104690.2561 124286.7185 102531.9211 107115.3585 98095.85445 141265.6594 0.830083212 0.766978581 0.742416364 0.741087795 0.879808434 0.725809241 0.758254759 0.694406941 1 17.10805127 -0.943054555 6.259247162 1.000000056 0.770147264 0.656989192 0.052794438 3.84E-08 6.54E-09 0.048198464 0.011360484 0.114010656 0.943054555 -0.229852792 SRS(ph)VSPCS(ph)NVESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.006)RS(0.987)VS(0.472)PCS(0.534)NVES(0.002)R 124.3 0.002552 292970000 410170 301350 359880 388370 400300 337750 405200 350710 444940 TRUE FALSE 390782.077 332057.9076 376380.854 349330.3097 470112.1933 326053.6328 343379.298 319999.9732 513939.0228 0.760366619 0.646103707 0.732345351 0.679711589 0.914723678 0.634420852 0.668132371 0.622641907 1 18.97123767 -1.296406435 3.436248726 1.001113117 0.705086817 0.539272925 0.085000576 133618814.7 194966402.9 1547509.4 0.019230633 0.050535151 1.296406435 -0.2960263 SRS(ph)WEDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.002)RS(0.998)WEDS(1)PER;S(0.004)RS(0.996)WEDS(1)PER;S(0.003)RS(0.997)WEDS(1)PER;S(0.02)RS(0.98)WEDS(1)PER;S(0.259)RS(0.741)WEDS(1)PER;S(0.333)RS(0.667)WEDS(1)PER 160.48 8.81E-05 11010480000 5643330 4652470 4951410 5363800 4838020 5116150 5775950 4533830 4764250 TRUE FALSE 5376580.975 5126561.982 5178437.046 4824620.633 5681769.156 4938976.443 4894722.745 4136823.81 5503065.558 0.977015614 0.931582938 0.941009514 0.876715093 1.032473464 0.897495476 0.889453831 0.751730788 1 22.39180408 1.895398918 3.248186022 0.867763957 0.948059804 0.164715559 0.071101032 0.373340515 6.848678647 0.032492866 0.01758311 78.59572384 -1.895398918 0.080295847 SRS(ph)WEDSPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.003)RS(0.995)WEDS(0.001)PER;S(0.014)RS(0.529)WEDS(0.457)PER;S(0.123)RS(0.688)WEDS(0.189)PER;S(0.031)RS(0.96)WEDS(0.009)PER 145.31 8.06E-05 1143970000 1320280 1136180 1134580 1259070 1162530 1143240 1341600 1184340 1075960 TRUE FALSE 1257872.981 1251958.034 1186601.615 1132505.892 1365274.864 1103649.312 1136914.28 1080632.911 1242814.382 1.012116531 1.007357215 0.954769781 0.911242989 1.098534813 0.888024252 0.91479009 0.869504672 1 20.24517941 SRS(ph)WPASPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRSWPASPR 9 1 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 S(0.003)RS(0.997)WPASPR;S(0.007)RS(0.993)WPASPR;S(0.13)RS(0.87)WPASPR 100.38 0.0028475 568070000 65383 60761 59125 68956 89914 70650 89472 71251 70297 TRUE FALSE 62292.47517 66952.61498 61835.93973 62024.41187 105594.9731 68203.37278 75821.40313 65011.88471 81198.29973 0.767164773 0.824556859 0.761542298 0.763863432 1.300457934 0.839960603 0.933780675 0.800655739 1 16.3091619 SRS(ph)YER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRSYER 6 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4;Q96S94;Q96S94-3;A0A0A0MSF3 O75494-2;O75494-6;Q5JRI1;Q96S94 SRSF10;CCNL2 Serine/arginine-rich splicing factor 10;Cyclin-L2 1 S(0.167)RS(0.832)Y(0.001)ER;S(0.145)RS(0.855)YER;S(0.165)RS(0.835)YER 69.598 0.05637 214608000 154754 161590 162841 183239 171503 177415 188473 163583 212918 TRUE FALSE 147439.0851 178056.2047 170307.4209 164819.4676 201413.0689 171271.0741 159717.9823 149258.8053 245936.236 0.599501267 0.723993372 0.692486084 0.670171546 0.818964591 0.696404389 0.649428425 0.606900422 1 17.90792479 -1.444443812 3.3867327 1.004155995 0.683175911 0.722370975 0.06190827 24446870.87 27421504.23 935673.0396 0.014631069 0.035938189 1.444443812 -0.320980084 SRSDVDMDAAAEAT(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSDVDMDAAAEATR 15 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.027)RS(0.348)DVDMDAAAEAT(0.625)R 170.47 1.45E-10 0 153030 146650 149050 170640 148620 142060 162610 160520 180450 TRUE FALSE 145796.5752 161593.8017 155884.0899 153486.943 174539.2809 137140.4266 137800.858 146464.0178 208433.2644 0.699488038 0.775278371 0.747884894 0.736384106 0.83738688 0.657958445 0.661126996 0.702690227 1 17.66922601 -0.964348158 5.527664388 1.000000516 0.726133781 0.721597488 0.053233216 3.52E-07 6.59E-08 0.053534295 0.01261813 0.108555502 0.964348158 -0.273866736 SRSFT(ph)LDDESLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.27)RS(0.195)FT(0.534)LDDESLK 86.378 0.018018 382770000 162650 128770 145120 167130 115120 152840 179900 162470 119030 TRUE FALSE 154961.8568 141891.8094 151773.8955 150329.7749 135196.8916 147547.1125 152452.9509 148243.2655 137488.5645 1.12708906 1.032026263 1.103901958 1.093398389 0.983331902 1.073159161 1.108840953 1.078222513 1 17.0689521 4.703680748 3.872891852 1.065558664 1.130890491 0.185587083 0.042854801 0.400597418 10.92931608 0.009868728 0.068417526 50545.29644 -4.703680748 0.065331827 SRSS(ph)S(ph)SPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.306)RS(0.403)S(0.445)S(0.505)S(0.341)PPPK 60.628 0.055112 263210000 652280 776340 587630 742860 345130 617020 604400 676110 482660 TRUE FALSE 621448.0171 855449.9286 614573.4167 668186.3015 405320.5627 595652.4427 512187.6794 616906.2241 557508.4477 1.114688073 1.534416083 1.102357138 1.19852229 0.727021383 1.068418685 0.918708374 1.106541482 1 19.08863414 3.209116896 2.121733354 0.968704852 1.313923794 0.407573488 0.158116554 0.243769125 2.252934547 0.045494402 0.061048539 1618.515622 -3.209116896 0.345218942 SRSS(ph)S(ph)SPPPKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.261)RS(0.346)S(0.398)S(0.54)S(0.454)PPPKQK 55.213 0.069174 68181000 150310 84783 150820 140010 99866 148310 201240 143640 150370 TRUE FALSE 143205.1442 93422.48409 157735.2462 125935.9288 117282.5988 143173.9875 170537.142 131062.1201 173688.6116 0.824493574 0.5378734 0.908149617 0.725067278 0.675246337 0.824314192 0.981855635 0.754580965 1 17.40614364 2.01980469 5.408137912 0.909215486 0.724151778 0.333226638 0.114771334 0.180194128 15.86297265 0.043042601 0.029900034 104.6657741 -2.01980469 -0.185063708 SRSS(ph)SS(ph)PPPKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.245)RS(0.343)S(0.412)S(0.023)S(0.977)PPPKQK;S(0.22)RS(0.344)S(0.433)S(0.005)S(0.997)PPPKQK 81.632 0.0091841 541250000 390250 238220 386710 338220 253510 383480 521480 382420 375030 TRUE FALSE 371803.6559 262494.8888 404441.036 304221.483 297722.0637 370199.9914 441918.6484 348933.2775 433187.737 0.858296817 0.605961034 0.933639163 0.702285538 0.687281837 0.854594809 1.020155029 0.805501282 1 18.72463288 2.012832006 6.161371532 0.943066659 0.75238157 0.390208768 0.10563001 0.140458071 21.03911856 0.03846224 0.026910607 102.9987624 -2.012832006 -0.190685088 SRSWEDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_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 SRSWEDS(1)PER;SRSWEDS(1)PER 132.31 0.0001375 669510000 213976 153185 190064 160980 184783 175866 208462 205193 249372 TRUE FALSE 203861.7785 168794.7257 198778.6224 144797.9846 217009.0967 169775.7163 176657.2932 187225.2131 288043.3361 0.707746901 0.58600462 0.690099709 0.502695138 0.753390443 0.589410325 0.613301094 0.64998974 1 18.13592636 0.922044018 16.78513955 1 0.632793892 0.72400447 0.070571054 286.39592 61666.6725 0.058750074 0.014687486 8.356877154 -0.922044018 -0.367206108 SRT(ph)AS(ph)GSSVTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.411)RT(0.589)AS(0.978)GS(0.021)SVTSLDGTR;S(0.047)RT(0.952)AS(0.924)GS(0.035)S(0.026)VT(0.015)SLDGTR 144.3 3.33E-05 142540000 433460 365440 437300 575890 414670 528020 563720 453900 498060 TRUE FALSE 412971.2048 402678.7515 457350.6375 518000.4431 486988.3167 509734.535 477714.1606 414154.1097 575296.6011 0.717840509 0.699949818 0.794982339 0.900405881 0.846499555 0.8860378 0.830378903 0.719896674 1 19.13394642 8 0.090408586 1.060808059 0.056968158 0.458786327 0.069143973 132.3536422 0.859589924 1.240905456 16.47945538 100000000 -8 -1.003839901 SRT(ph)ASGSSVTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.086)RT(0.455)AS(0.444)GS(0.016)SVTSLDGTR;S(0.042)RT(0.868)AS(0.084)GS(0.003)S(0.004)VTSLDGTR 178.32 4.54E-09 562891000 220281 120996 268276 162752 275283 220132 398317 321120 625641 TRUE FALSE 209868.7537 133325.63 280576.72 146391.8598 323292.268 212508.7736 337546.4261 293001.0304 722662.2109 0.290410583 0.184492323 0.388254313 0.202573011 0.447362908 0.294063769 0.467087418 0.40544673 1 19.46296193 -5 0.184414806 3.894362732 0.188631034 0.885306958 0.077791069 35.32822454 0.342662756 37.30224027 0.193082754 1.00E-05 5 -3.705731698 SRT(ph)GS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.43)RT(0.572)GS(0.94)ES(0.046)S(0.011)QT(0.001)GTSTTSSR 65.833 0.075189 286940000 31021 31839 37417 37336 37653 32512 37880 28899 34229 TRUE FALSE 29554.69881 35083.4303 39132.60646 33582.91435 44219.67128 31386.10129 32100.71029 26368.45036 39537.0585 0.747518908 0.887355601 0.989770305 0.849403461 1.118436043 0.79384007 0.81191448 0.666929998 1 15.27091792 -0.744418925 7.038158384 0.999994073 0.85918798 0.11246384 0.125205919 0 1.23E-10 0.116580517 0.027478291 0.180127937 0.744418925 -0.140806093 SRT(ph)GSES(ph)SQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.126)RT(0.794)GS(0.079)ES(0.758)S(0.241)QT(0.001)GTSTTSSR 100.45 0.021277 119830000 61293 42262 60454 61045 63441 62745 77533 54519 70910 TRUE FALSE 58395.80136 46568.54585 63225.8757 54908.64062 74505.09031 60572.12492 65703.91686 49745.02734 81906.36064 0.712958077 0.568558357 0.771928764 0.670383108 0.909637417 0.73952895 0.802183327 0.607340223 1 16.32168787 -5 0.123559569 1.869566044 0.595326676 0.404326334 0.100354994 137.6158856 1.091980057 30.20981238 0.824946814 1.00E-05 5 -1.274239368 SRT(ph)HS(ph)TSSSLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTHSTSSSLGSGESPFSR 19 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 S(0.418)RT(0.588)HS(0.832)T(0.111)S(0.027)S(0.023)S(0.001)LGSGESPFSR;S(0.425)RT(0.582)HS(0.938)T(0.044)S(0.01)S(0.002)SLGSGESPFSR 92.463 0.0043825 423330000 300610 194975 251050 301920 314260 249620 368190 265070 297040 TRUE FALSE 286400.7611 214843.1742 262560.8908 271570.428 369066.8445 240975.5968 312015.8532 241859.0656 343103.4461 0.834735892 0.626176089 0.765252852 0.791511805 1.075672217 0.70234094 0.909392945 0.704915874 1 18.38828409 3.090803133 3.999387985 0.866860131 0.731010213 0.194185101 0.124938493 0.332110743 10.07329679 0.03378371 0.040811323 1232.545991 -3.090803133 -0.135849919 SRT(ph)PSASNDDQQE ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.024)RT(0.896)PS(0.08)ASNDDQQE;S(0.137)RT(0.851)PS(0.012)ASNDDQQE;S(0.133)RT(0.866)PS(0.001)ASNDDQQE;S(0.255)RT(0.721)PS(0.024)ASNDDQQE 179.66 8.64E-05 477268000 586346 540461 548070 610263 568610 559534 652961 624570 628303 TRUE FALSE 558630.5866 595534.5904 573199.5516 548918.2038 667775.404 540157.1973 553339.807 569879.3397 725737.0203 0.769742442 0.820592823 0.789817159 0.756359657 0.920134133 0.744287782 0.762452227 0.785242207 1 19.46908734 -0.910068108 4.907065563 1.000000594 0.792667273 0.630547247 0.049652354 4.68E-07 1.04E-07 0.044585978 0.010508969 0.123007585 0.910068108 -0.20733332 SRT(ph)PSRHS(ph)CSGS(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTPSRHSCSGSSPPR 16 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.154)RT(0.486)PS(0.363)RHS(0.771)CS(0.413)GS(0.655)S(0.159)PPR 65.278 0.092521 283610000 121430 102290 123430 126780 126730 112610 147480 123230 122350 TRUE FALSE 115690.2446 112713.4673 129089.3876 114035.8335 148831.6719 108710.2875 124979.2173 112439.3279 141323.4131 0.81862051 0.797556928 0.913432422 0.80691395 1.053128201 0.769230555 0.884348988 0.795617127 1 17.10864097 SRT(ph)SPAPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.073)RT(0.463)S(0.463)PAPWK;S(0.167)RT(0.666)S(0.167)PAPWK 78.548 0.047627 1816900000 2858300 3275400 2473000 3481000 2054130 3052300 2974800 2898800 1953130 TRUE FALSE 2723193.824 3609166.984 2586389.496 3131083.267 2412369.622 2946598.086 2520939.624 2644965.704 2256011.425 1.207083348 1.599799958 1.146443439 1.38788449 1.06930736 1.306109558 1.117432118 1.172407939 1 21.10534294 2.072618759 0.405369404 1.012847947 1.404208712 0.331024463 0.141466799 1.130909284 0.453443408 0.144711533 0.148699188 118.2003489 -2.072618759 0.391360765 SRT(ph)SPVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.015)RT(0.424)S(0.424)PVT(0.138)R;S(0.097)RT(0.451)S(0.451)PVTR 91.752 0.078113 1398780000 1907288 1747916 1795395 1951686 1922344 1881167 2138677 1990603 1976937 TRUE FALSE 1817134.276 1926030.628 1877715.637 1755498.815 2257600.185 1816021.715 1812382.544 1816295.248 2283510.293 0.795763558 0.843451695 0.822293485 0.768772018 0.988653387 0.795276343 0.793682669 0.795396129 1 21.12282186 -0.947538969 4.237778087 1.000005742 0.824683059 0.444245056 0.061364236 16607279.01 44232880.7 1613.725156 0.013749531 0.112839468 0.947538969 -0.175322682 SRT(ph)SVQTEDDQLIAGQSAR ddPTM_SK-BR-3_Trastuzumab_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(0.096)RT(0.452)S(0.452)VQTEDDQLIAGQSAR 281.23 1.80E-39 197580000 126290 100550 125320 129350 120810 105530 136910 123480 123290 TRUE FALSE 120320.522 110796.1593 131066.046 116347.4923 141879.2258 101875.4696 116021.865 112667.4366 142409.1835 0.844892998 0.778012742 0.920348272 0.816994307 0.996278626 0.715371489 0.814707746 0.791152886 1 17.11968266 -2.457385844 2.135700237 2.606554533 0.830570811 0.309975488 0.07727812 2905626.761 195505.2649 22716120.67 0.01721266 0.003488303 2.457385844 -1.775983722 SRTAS(ph)GS(ph)SVTS(ph)LDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 3 S(0.009)RT(0.029)AS(0.91)GS(0.529)S(0.508)VT(0.224)S(0.789)LDGT(0.002)R 84.113 0.0061955 106780000 112530 73530 113290 123100 113170 106600 156410 115570 166460 TRUE FALSE 107210.9299 81022.7906 118484.4586 110725.7541 132906.8122 102908.4153 132546.7818 105450.0781 192273.7666 0.557595203 0.42139285 0.616227895 0.575875514 0.691237367 0.535218179 0.689364879 0.548437158 1 17.55280241 -5 0.169536535 2.667678591 0.470030059 0.752274286 0.076309105 59.13485 0.557127807 33.12188883 0.256134914 1.00E-05 5 -2.197648532 SRTAS(ph)GSSVTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 SRT(0.032)AS(0.54)GS(0.053)S(0.374)VT(0.001)SLDGTR;SRT(0.026)AS(0.878)GS(0.025)S(0.062)VT(0.005)S(0.005)LDGTR;S(0.028)RT(0.105)AS(0.833)GS(0.033)SVTSLDGTR 172.74 1.18E-08 960060000 534410 323473 566430 436120 577950 556680 832620 686400 1195760 TRUE FALSE 509149.4984 356435.2665 592401.3758 392280.389 678744.297 537402.032 705588.5269 626295.1772 1381192.354 0.368630406 0.258063452 0.428905774 0.284015755 0.491419095 0.389085583 0.510854643 0.453445297 1 20.39748282 -5 0.185059269 3.624355633 0.267252777 0.900553487 0.064891425 33.1348994 0.321717176 31.8435067 0.161997514 1.00E-05 5 -3.357102856 SRTDEEGNAYGS(ph)EREEEDEEEDEEDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTDEEGNAYGSEREEEDEEEDEEDGKR 28 3 P78415 P78415 IRX3 Iroquois-class homeodomain protein IRX-3 1 SRTDEEGNAYGS(1)EREEEDEEEDEEDGKR 200.66 2.42E-24 108790000 28916 20976 24845 27026 14878 28293 29176 29901 18758 TRUE FALSE 27549.19799 23113.47825 25984.16783 24309.29513 17472.71849 27313.20632 24724.66535 27282.70992 21666.89484 1.271488056 1.066764685 1.199256655 1.121955652 0.806424669 1.260596247 1.141126383 1.259188736 1 14.40320479 8 0.010514681 2.15E-08 2.419097847 0.06223804 0.138516235 43713.90768 35.5429077 3495.507474 4774.010319 99999999.91 -8 2.419097826 SRTGS(ph)ESS(ph)QTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.183)RT(0.262)GS(0.555)ES(0.026)S(0.969)QT(0.005)GT(0.001)STTSSR 83.31 0.002292 321420000 137500 89796 134680 143010 161300 129410 176840 133260 160820 TRUE FALSE 131000.6475 98946.31449 140855.2112 128634.3631 189430.6689 124928.4993 149859.8101 121591.0479 185759.1442 0.705217759 0.532659186 0.758267981 0.692479305 1.019764974 0.672529472 0.806742574 0.65456292 1 17.50307371 -4.999999745 0.042243181 2.185038912 0.047455277 0.310024866 0.125448606 817.8952958 2.574711127 121.0412198 34.06441134 1.00E-05 4.999999745 -2.137583635 SRTGS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.013)RT(0.248)GS(0.724)ES(0.014)S(0.001)QTGTSTTSSR;S(0.069)RT(0.069)GS(0.862)ESSQTGTSTTSSR;S(0.015)RT(0.004)GS(0.744)ES(0.235)S(0.002)QTGTSTTSSR 202.15 8.02E-16 3243100000 304734 153427 306381 222890 339016 252104 436830 313239 417600 TRUE FALSE 290329.8277 169061.3857 320428.8719 200484.6737 398140.2831 243373.5753 370183.5606 285810.1326 482359.2752 0.601895398 0.350488514 0.664295036 0.4156335 0.825401943 0.504548348 0.767443645 0.592525421 1 18.87974858 -1.240899209 0.166721208 1.441757303 0.396874114 0.493666381 0.137663993 19.282239 0.624381517 4.250063515 0.591911767 0.057424972 1.240899209 -1.044883189 SRTLT(ph)AVHDAILEDLVFPSEIVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTLTAVHDAILEDLVFPSEIVGK 24 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 1 S(0.297)RT(0.297)LT(0.407)AVHDAILEDLVFPSEIVGK 129.71 0.00011074 97396000 117430 104890 117390 127490 93356 117370 139400 119860 95641 TRUE FALSE 111879.3166 115578.4103 122772.4476 114674.463 109637.2568 113305.4475 118131.9697 109364.423 110472.5178 1.012734378 1.046218666 1.111339273 1.038036113 0.992439197 1.02564375 1.069333551 0.989969498 1 16.75332799 2.998965956 24.99983287 1.023721638 1.051523563 0.222031594 0.033124877 84.9829452 2054680.985 0.010009202 0.01180695 997.6218575 -2.998965956 0.027801925 SRTPS(ph)ASNDDQQE ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 SRTPS(1)ASNDDQQE;S(0.006)RT(0.002)PS(0.991)AS(0.001)NDDQQE 216.78 7.08E-11 1541830000 1619290 1175610 1435650 1773840 1587880 1321730 1542050 1169750 1453540 TRUE FALSE 1542749.371 1295405.996 1501475.973 1595530.233 1864805.769 1275958.159 1306781.951 1067320.489 1678947.56 0.918878831 0.771558342 0.894295932 0.950315705 1.110699235 0.759974992 0.778333989 0.635708056 1 20.67912574 -0.836281172 4.390674544 1.00000108 0.851467675 0.114195335 0.129102724 7673329.054 2621490.566 81.42508491 0.030095928 0.14578701 0.836281172 -0.148533406 SRTPS(ph)NDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SRTPS(0.999)NDGK 76.522 0.021313 14523000 37555 36128 29934 39347 28600 40550 37679 40804 37312 TRUE FALSE 35779.84958 39809.48427 31306.50351 35391.76481 33587.83094 39145.74333 31930.37653 37230.98544 43098.1544 0.830194473 0.923693481 0.726400096 0.8211898 0.779333394 0.9082928 0.740875728 0.86386496 1 15.39533847 -0.791944321 6.598602669 1.000000002 0.826515428 0.424649509 0.064248977 1.32E-09 3.33E-10 0.058961689 0.013897403 0.161456554 0.791944321 -0.173484574 SRTS(ph)PAPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.085)RT(0.372)S(0.542)PAPWK 71.085 0.030631 607280000 1479000 1656100 1300800 1830800 1095200 1482000 1515600 1618400 1044100 TRUE FALSE 1409090.601 1824858.473 1360442.967 1646764.506 1286202.533 1430677.968 1284367.384 1476684.316 1206013.695 1.168386898 1.513132462 1.128049351 1.365460867 1.066490819 1.186286668 1.064969153 1.224434119 1 20.20181486 2.736776262 24.97668656 1.114910839 1.30718385 0.362994293 0.121242569 158.2877487 2215633.089 0.035235076 0.034817428 545.4767722 -2.736776262 0.192273011 SRTS(ph)PAPWKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SRTSPAPWKR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.062)RT(0.335)S(0.603)PAPWKR 95.417 0.0038801 344100000 516680 350560 520980 470040 483440 502910 686820 553370 648090 TRUE FALSE 492257.5604 386282.4626 544867.4483 422790.6862 567751.7829 485494.1006 582032.9947 504913.9892 748592.4872 0.657577479 0.516011674 0.727855886 0.56478083 0.758425702 0.648542577 0.77750312 0.674484446 1 19.51382104 -5 0.133872814 2.204660319 0.518731413 0.688705267 0.073775509 68.37591364 0.571099612 21.82919412 0.447837007 1.00E-05 5 -1.685928906 SRTS(ph)PITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.09)RT(0.362)S(0.548)PITR;S(0.054)RT(0.054)S(0.892)PITR 72.29 0.028182 2329820000 346690 531930 477140 421860 262216 497810 308930 386900 236646 TRUE FALSE 330302.6508 586134.2718 499017.341 379453.8313 307946.3874 480570.7149 261797.0546 353020.9849 273343.8531 1.208377825 2.144311149 1.825602937 1.388192297 1.126589766 1.758117878 0.957757241 1.291490483 1 18.06035741 2.342466515 0.782668846 1.085505477 1.715831069 0.31612521 0.319240896 0.73766355 0.882030917 0.245249314 0.161278734 220.0222061 -2.342466515 0.630325591 SRTS(ph)PVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.288)RT(0.16)S(0.552)PVSR;S(0.257)RT(0.1)S(0.642)PVS(0.001)R;S(0.132)RT(0.053)S(0.815)PVSR;S(0.214)RT(0.088)S(0.698)PVSR 94.767 0.0061323 1656080000 208308 231818 225021 247066 237921 219178 280502 233769 266896 TRUE FALSE 198461.6937 255440.5178 235338.4354 222230.4563 279414.3471 211587.8109 237706.2681 213298.9471 308284.8686 0.643760735 0.828585973 0.763379781 0.720860733 0.906351156 0.686338619 0.771060446 0.691889122 1 18.23390455 -1.597751002 2.843836705 1.017610143 0.754380827 0.51872517 0.075170868 15646598.06 15570131.4 2060279.074 0.016307355 0.02524928 1.597751002 -0.263229316 SRTS(ph)PVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.1)RT(0.224)S(0.675)PVTR;S(0.043)RT(0.182)S(0.775)PVTR;S(0.288)RT(0.139)S(0.573)PVTR;S(0.027)RT(0.116)S(0.857)PVTR;S(0.008)RT(0.114)S(0.877)PVT(0.001)R;S(0.053)RT(0.112)S(0.835)PVTR;S(0.016)RT(0.036)S(0.943)PVT(0.004)R 98.898 0.0043579 16336956000 1308718 1260592 1228208 1506483 1441680 1238833 1569787 1265572 1279277 TRUE FALSE 1246857.494 1389047.758 1284522.552 1355048.467 1693108.536 1195931.903 1330287.162 1154751.806 1477660.744 0.84380498 0.940031576 0.869294632 0.917022715 1.145803286 0.809341324 0.900265618 0.781472886 1 20.49488365 -0.44840433 6.080045304 1.000000158 0.903489233 0.089097473 0.09929098 0 0 0.089149124 0.02101265 0.35611943 0.44840433 -0.096510925 SRVPVRPPQQYS(ph)DDEDDYEDDEEDDVQNTNSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR 34 2 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.106)RVPVRPPQQYS(0.894)DDEDDYEDDEEDDVQNTNSALR;S(0.021)RVPVRPPQQYS(0.979)DDEDDYEDDEEDDVQNTNSALR 180.9 4.15E-20 150593000 38108 21878.9 20251.6 35276 30937 24954 42901 37405 33852 TRUE FALSE 36306.71036 24108.38478 21180.15589 31729.98946 36332.403 24089.83672 36355.66452 34129.6199 39101.59527 0.928522484 0.616557576 0.541669867 0.811475574 0.929179558 0.61608322 0.929774457 0.872844693 1 15.25493985 1.346931388 0.842782757 0.998351802 0.733301056 0.293136708 0.134245446 0.699639862 1.069447731 0.122938469 0.047181052 22.22958668 -1.346931388 -0.265050747 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.173)T(0.827)PVLTPGK;SRWDETPASQMGGS(0.153)T(0.847)PVLTPGK 194.25 2.74E-24 276290000 359580 345150 330600 394980 254690 368480 364210 394130 264360 TRUE FALSE 342583.366 380321.1774 345758.337 355275.86 299107.8554 355719.4452 308643.0753 359617.8878 305355.5986 1.121916112 1.245502552 1.13231373 1.163482384 0.979539451 1.164935068 1.01076606 1.177701963 1 18.22013077 2.914003708 11.1893962 1.070698521 1.173474625 0.316467826 0.072088829 0.73991742 93.90239932 0.019478263 0.020667067 820.3585488 -2.914003708 0.102776103 SS(ph)ATLWNSPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSATLWNSPSR 11 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.164)S(0.836)ATLWNSPSR 196.58 6.29E-08 239290000 127800 112350 105810 137750 120220 117590 140180 125090 107620 TRUE FALSE 121759.1473 123798.5927 110661.4932 123903.1083 141186.3299 113517.8288 118792.9664 114136.4565 124309.16 0.979486526 0.995892763 0.890211898 0.996733534 1.13576771 0.913189574 0.955625205 0.918166099 1 16.92357308 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.382)S(0.618)DEENGPPS(0.325)S(0.675)PDLDR;S(0.023)S(0.977)DEENGPPS(0.002)S(0.998)PDLDR 483.84 5.78E-231 612460000 877760 851810 777920 934450 624620 825760 883860 853720 679150 TRUE FALSE 836270.0244 938610.4074 813588.4015 840517.3107 733553.5302 797163.7241 749010.9238 778963.7509 784469.1134 1.066033079 1.196491221 1.037119738 1.071447296 0.93509549 1.016182423 0.954799763 0.992982053 1 19.58135712 3.192801073 1.707179807 0.979356584 1.12708613 0.592377878 0.046582019 0.196148486 1.181660055 0.014116895 0.01930831 1558.838321 -3.192801073 0.147729546 SS(ph)DTEEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSDTEEESR 9 0 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 S(0.128)S(0.872)DTEEESR;S(0.347)S(0.653)DTEEESR 307.09 3.52E-30 269380000 496540 419840 456550 482980 371850 442330 477330 486600 438120 TRUE FALSE 473069.5382 462622.1733 477483.2691 434429.9328 436700.5223 427012.0012 404504.5417 443990.7244 506061.412 0.934806581 0.91416212 0.943528311 0.858452991 0.862939778 0.843794826 0.799319079 0.877345543 1 18.94895295 3.22974785 24.42692968 0.856931181 0.927827896 0.162725295 0.052596504 164.0593224 454733.6193 0.013776791 0.01671134 1697.257943 -3.22974785 0.070896715 SS(ph)FSQHAR ddPTM_SK-BR-3_Trastuzumab_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 1 S(0.368)S(0.63)FS(0.002)QHAR;S(0.365)S(0.635)FS(0.001)QHAR;S(0.355)S(0.644)FS(0.001)QHAR;S(0.346)S(0.632)FS(0.022)QHAR 161.67 0.00022299 1835570000 1928540 1642480 1672660 1979470 1937520 1799800 2154890 1877480 1918230 TRUE FALSE 1837381.736 1809850.579 1749353.115 1780489.915 2275422.875 1737472.475 1826121.953 1713077.898 2215699.311 0.829255904 0.816830411 0.789526407 0.803579216 1.026954724 0.784164379 0.824174085 0.773154502 1 21.07933068 -2.31578098 2.326547129 1.918688934 0.830796225 0.352489611 0.072003464 3272232.399 814157.4327 15645492.45 0.016311717 0.004833025 2.31578098 -1.087892709 SS(ph)GFISELPSEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.16)S(0.84)GFISELPSEEGK;S(0.193)S(0.807)GFISELPSEEGK;S(0.002)S(0.998)GFISELPSEEGK;S(0.071)S(0.929)GFISELPSEEGK;S(0.257)S(0.743)GFISELPSEEGK;S(0.215)S(0.785)GFISELPSEEGK 448.81 7.56E-175 731441000 3188890 2856680 2941790 3470390 2028642 3466820 3630200 3686720 2177400 TRUE FALSE 3038157.489 3147778.94 3076673.981 3121539.804 2382436.523 3346763.154 3076346.317 3363891.252 2515060.071 1.207986053 1.25157207 1.223300396 1.241139263 0.947268238 1.330689152 1.223170115 1.337499367 1 21.26216143 SS(ph)GPTSLFAVTVAPPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGPTSLFAVTVAPPGAR 18 0 Q00839;A0A1X7SBS1;A0A1W2PP22;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.211)S(0.782)GPT(0.006)S(0.001)LFAVTVAPPGAR 101.78 0.00063069 21269000 41599 38388 37087 43931 35829 40583 44635 43482 39258 TRUE FALSE 39632.69771 42299.78084 38787.47563 39514.97242 42077.56626 39177.60053 37825.11097 39674.48557 45345.93014 0.874007824 0.932824196 0.855368398 0.871411664 0.927923766 0.863971704 0.834145663 0.874929359 1 15.46868545 SS(ph)GRNSPSAASTSSNDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.103)S(0.535)GRNS(0.342)PS(0.021)AASTSSNDSK 100.9 0.00046298 540550000 151140 153340 142800 166480 93693 149920 151560 156190 97466 TRUE FALSE 143995.9117 168965.5203 149347.5212 149745.1141 110033.0295 144728.2328 128436.7384 142513.1756 112580.5295 1.279048095 1.500841407 1.32658393 1.330115561 0.977371754 1.285552959 1.140843261 1.265877645 1 16.78059781 2.938557494 9.080343955 1.154525836 1.377448111 0.497710463 0.111812226 0.345375243 49.0632397 0.031007107 0.032976318 868.0754895 -2.938557494 0.222922275 SS(ph)GSETEQVVDFSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 S(0.009)S(0.963)GS(0.029)ETEQVVDFSDR 222.09 1.52E-12 89682000 64185 63352 57594 60099 57256 58289 63537 57352 51199 TRUE FALSE 61151.10225 69807.64083 60234.74187 54057.73434 67241.42827 56270.43731 53843.26371 52329.95484 59138.67943 1.034028877 1.18040581 1.018533766 0.914084231 1.137012678 0.951499727 0.91045766 0.884868505 1 15.85181441 2.74093866 0.726637685 0.9230604 1.10063819 0.292062904 0.081150915 0.714020799 0.812378222 0.056212316 0.055546206 550.729906 -2.74093866 0.17757779 SS(ph)KAS(ph)LGSLEGEAEAEASSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.487)S(0.524)KAS(0.513)LGS(0.476)LEGEAEAEASSPK 58.08 0.042916 52673000 113610 83573 90877 95655 52778 100160 104970 92956 59757 TRUE FALSE 108239.8805 92089.18371 95043.80034 86039.57767 61982.46649 96691.43409 88954.89859 84816.27985 69023.81036 1.568152785 1.33416546 1.37697122 1.246520255 0.897986741 1.400841732 1.288756708 1.228797416 1 16.0748065 7.999999994 0.364724089 1.178497061 6.478563028 0.420445334 0.146790218 63.84246134 0.887922326 0.11330161 235.9027384 99999998.56 -7.999999994 5.300065968 SS(ph)KASLGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.42)S(0.479)KAS(0.382)LGS(0.719)LEGEAEAEASSPK 146.45 6.19E-08 81859000 228600 180480 203990 235650 103390 217650 244170 220230 121950 TRUE FALSE 217794.531 198871.1172 213343.1433 211962.0143 121421.1833 210112.7259 206917.382 200945.4937 140861.3832 1.546162093 1.411821414 1.5145609 1.50475602 0.861990565 1.491627593 1.468943279 1.426547782 1 17.10391663 -3.60686088 0.228052695 1.29E-17 1.464912898 0.293465669 0.196809219 105.2158957 1.865796659 50.36089714 0.347640207 0.000247252 3.60686088 1.464912898 SS(ph)LETLEDIEENAPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.165)S(0.835)LETLEDIEENAPLRR;S(0.167)S(0.833)LETLEDIEENAPLRR 136.49 6.21E-06 64141000 22783 19726.3 17732.6 22377 21300.5 19652 26265 20108.1 20711.1 TRUE FALSE 21706.09274 21736.4324 18545.65725 20127.62145 25015.30046 18971.44631 22257.79186 18347.32816 23922.87161 0.907336422 0.90860465 0.775227053 0.841354741 1.04566462 0.793025462 0.930397998 0.766936698 1 14.54610296 SS(ph)LGSLQTPEAVTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.217)S(0.783)LGSLQTPEAVTTR;S(0.001)S(0.999)LGSLQTPEAVTTR;SS(1)LGSLQTPEAVTTR 339.4 3.07E-69 459351000 839480 744250 750900 905910 744850 804220 960640 880060 916700 TRUE FALSE 799799.4441 820089.9211 785329.5077 814846.2057 874751.6042 776369.6597 814076.7246 802997.2809 1058857.154 0.755342154 0.774504774 0.741676537 0.769552534 0.826128058 0.733214728 0.768825825 0.758362238 1 20.01407654 -1.071108149 4.17288682 1.000028602 0.766007304 0.897735237 0.024825517 2571100.83 1319914.696 680.9423718 0.005326355 0.084896904 1.071108149 -0.234021298 SS(ph)LS(ph)GDEEDELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 S(0.029)S(0.971)LS(1)GDEEDELFK;S(0.042)S(0.958)LS(1)GDEEDELFK;S(0.134)S(0.866)LS(1)GDEEDELFK;S(0.393)S(0.607)LS(1)GDEEDELFK 255.39 1.14E-23 416416000 2089920 1758590 1774220 2164920 1023680 1994550 2071060 2057210 872790 TRUE FALSE 1991133.623 1937792.32 1855569.742 1947298.129 1202209.468 1925478.233 1755081.759 1877069.786 1008137.816 1.975060942 1.922150216 1.840591349 1.931579292 1.192505081 1.90993553 1.740914518 1.861917842 1 19.94326144 -2.313015661 0.233140052 1.44E-12 1.934266832 0.554459763 0.224412371 28.74371702 0.875636359 15.98629045 0.38901542 0.004863897 2.313015661 1.934266832 SS(ph)LVTSK ddPTM_SK-BR-3_Trastuzumab_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(0.081)S(0.919)LVTSK;S(0.169)S(0.831)LVTSK;S(0.266)S(0.734)LVTSK;S(0.212)S(0.788)LVTSK 163.69 0.0012856 2365380000 9771660 8143890 8246320 10144070 5979440 10045800 12054930 10682890 8430440 TRUE FALSE 9309772.997 8973761.65 8624421.929 9124368.811 7022252.443 9697911.427 10215729.02 9747439.518 9737789.578 0.956045817 0.921539902 0.885665259 0.937006159 0.721134133 0.995904805 1.049080897 1.000990978 1 23.2151629 2.023346916 24.98794322 1.022231356 0.895024797 0.482640804 0.065133111 192.9260687 206485.7101 0.023639553 0.01745801 105.522948 -2.023346916 -0.127206559 SS(ph)LYGIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLYGIAK 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.132)S(0.868)LYGIAK;S(0.123)S(0.877)LYGIAK 201.18 0.00011942 821990000 2478440 1992920 1940840 2448130 1536940 2308710 2609350 2328570 1636270 TRUE FALSE 2361289.053 2196000.814 2029829.434 2202039.321 1804981.849 2228758.794 2211245.733 2124668.066 1890014.395 1.249349772 1.161896343 1.073975648 1.165091296 0.955009578 1.179228476 1.169962377 1.124154436 1 20.84996579 4.209801178 1.912155019 1.108134213 1.244393052 0.298253394 0.074026762 0.458182355 3.103572126 0.018982041 0.075574909 16210.67796 -4.209801178 0.136258839 SS(ph)PELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.087)S(0.913)PELTR 180.45 0.00071991 701480000 447810 423100 330270 456980 324780 370320 417860 408200 358330 TRUE FALSE 426642.9088 466214.371 345413.2062 411043.5022 381421.5292 357495.7255 354107.7825 372455.844 413897.9863 1.030792424 1.126399225 0.834537054 0.993103411 0.921535117 0.863729077 0.855543622 0.899873535 1 18.6589157 3.74246208 24.99996299 0.902079101 1.07859583 0.586071498 0.058713877 190.859501 1222993.645 0.014482013 0.024913351 5526.651503 -3.74246208 0.176516729 SS(ph)PELTRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPELTRK 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.251)S(0.749)PELTRK 62.005 0.050459 176210000 124260 106470 114860 119810 129130 118680 130840 116590 135570 TRUE FALSE 118386.4761 117319.414 120126.4446 107766.4712 151650.2311 114570.0818 110877.955 106380.7615 156593.5032 0.756011416 0.749197199 0.767122787 0.688192479 0.968432457 0.731640071 0.708062293 0.679343391 1 17.25666483 -1.012684414 4.104666392 1.000020752 0.75541623 0.474244696 0.080736745 4507025.212 1668214.264 840.8292464 0.01777115 0.097121546 1.012684414 -0.244604522 SS(ph)PEQPRPSTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.165)S(0.835)PEQPRPSTSK;S(0.046)S(0.954)PEQPRPSTSK;S(0.346)S(0.654)PEQPRPSTSK;S(0.16)S(0.84)PEQPRPSTSK;S(0.107)S(0.893)PEQPRPSTSK;S(0.113)S(0.887)PEQPRPSTSK 147.12 3.96E-05 6094633000 3351960 2771630 2984620 3395220 2324820 3237950 3766150 3267950 2663900 TRUE FALSE 3193519.494 3054062.248 3121467.779 3053926.035 2730267.872 3125818.98 3191554.647 2981790.974 3077004.007 1.037866537 0.992544125 1.014450346 0.992499857 0.88731372 1.015864449 1.037227979 0.969056578 1 21.55309489 -0.837426661 6.627691267 0.999999984 0.997360196 0 0.043234276 0 4.64E-11 0.041298299 0.009734102 0.145402991 0.837426661 -0.002639788 SS(ph)PGAGPSDHHSASR ddPTM_SK-BR-3_Trastuzumab_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(0.206)S(0.794)PGAGPSDHHSASR 267.46 1.24E-25 119430000 49366 45021 46068 57049 77923 42329 91026 55766 17112 TRUE FALSE 47032.56701 49608.69108 48180.26337 51314.32613 91512.74653 40863.13612 77138.31189 50882.83341 19765.64156 2.379511278 2.509844718 2.437576499 2.596137645 4.629890016 2.067382229 3.902646501 2.574307201 1 14.27070716 2.978373854 24.96054434 3.080319685 2.456441478 0 0.982985055 1777.408982 2051458.468 0.26044411 0.278708572 951.4234566 -2.978373854 -0.623878206 SS(ph)PGGQDEGGFMAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.205)S(0.795)PGGQDEGGFMAQGK 266.44 3.58E-27 102780000 245130 261360 245420 301120 169330 282770 270930 290800 191520 TRUE FALSE 233543.1907 287992.8811 256672.7498 270850.8455 198861.0984 272977.604 229594.6525 265336.0104 221219.9435 1.05570586 1.301839593 1.160260444 1.224350939 0.898929343 1.233964713 1.037856935 1.199421744 1 17.75512193 SS(ph)PGQTPEEGAQALAEFAALHGPALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.416)S(0.584)PGQTPEEGAQALAEFAALHGPALR;S(0.158)S(0.842)PGQTPEEGAQALAEFAALHGPALR;S(0.424)S(0.576)PGQTPEEGAQALAEFAALHGPALR;S(0.001)S(0.999)PGQTPEEGAQALAEFAALHGPALR;S(0.424)S(0.576)PGQTPEEGAQALAEFAALHGPALR;S(0.147)S(0.853)PGQTPEEGAQALAEFAALHGPALR 339.99 1.35E-95 19430030000 1608300 1395330 1460490 1691440 1416170 1529450 1760370 1678780 1467900 TRUE FALSE 1532278.846 1537515.713 1527454.911 1521413.238 1663149.6 1476484.763 1491793.225 1531777.123 1695534.435 0.903714377 0.906803001 0.900869295 0.897306009 0.980899925 0.87080789 0.879836584 0.903418469 1 20.69330865 -0.958345008 4.575146234 1.000001647 0.903991192 0.508523522 0.029178148 4.72E-07 1.07E-07 0.027173401 0.006404722 0.110066458 0.958345008 -0.096010454 SS(ph)PIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.165)S(0.835)PIMR;S(0.084)S(0.916)PIMR 142.64 0.012064 660960000 562180 512820 442840 598190 486220 558700 625440 594300 507210 TRUE FALSE 535606.8655 565076.941 463144.652 538058.8047 571016.6141 539352.0789 530017.641 542259.9414 585865.5363 0.914214666 0.964516439 0.790530631 0.918399823 0.974654726 0.920607282 0.904674551 0.925570643 1 19.16021006 2.998714151 24.99999456 0.935608677 0.902418408 0.171079734 0.05106396 132.0363818 2567202.042 0.014860893 0.017537978 997.043603 -2.998714151 -0.033190269 SS(ph)PNPFITGLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.261)S(0.739)PNPFITGLTR;S(0.121)S(0.879)PNPFITGLTR;S(0.144)S(0.856)PNPFITGLTR;S(0.174)S(0.826)PNPFITGLTR 263.12 1.96E-21 934906000 868730 741994 760567 871380 711490 811660 947460 898780 931390 TRUE FALSE 827666.8546 817604.0322 795439.7493 783787.2269 835573.6307 783552.0107 802907.5757 820078.0585 1075825.204 0.769332092 0.759978507 0.739376384 0.728545143 0.77668159 0.728326505 0.746317871 0.762278161 1 20.03701226 0.676758087 4.049840456 0.999999732 0.750767971 0.96076627 0.015809225 1.722449464 21.4203498 0.015046234 0.003840662 4.750705261 -0.676758087 -0.24923176 SS(ph)PNVANQPPS(ph)PGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.427)S(0.573)PNVANQPPS(1)PGGK;S(0.422)S(0.578)PNVANQPPS(1)PGGK;S(0.412)S(0.588)PNVANQPPS(1)PGGK;S(0.416)S(0.584)PNVANQPPS(1)PGGK 208.17 2.44E-11 255410000 954527 945292 853455 1070110 538217 936239 878298 880357 539274 TRUE FALSE 909408.4004 1041618.33 892586.7559 962540.5097 632081.8744 903816.8087 744297.5091 803268.274 622901.8577 1.459954548 1.672202959 1.43294926 1.54525227 1.014737501 1.450977867 1.194887284 1.289558321 1 19.24864535 2.300817424 0.313634125 1.004230591 1.664929018 0.515344231 0.152670104 1.297983572 0.326186371 0.199426428 0.306623262 199.9021311 -2.300817424 0.660698427 SS(ph)PPLPPPAEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.311)S(0.689)PPLPPPAEER;S(0.056)S(0.944)PPLPPPAEER 112.02 0.0013831 477070000 261270 219480 247430 276120 194601 254500 268680 267980 230470 TRUE FALSE 248920.2849 241845.2615 258774.9102 248363.893 228539.3528 245686.6012 227687.9314 244514.2505 266210.1105 0.935051957 0.908475118 0.972070181 0.932961909 0.858492385 0.922904846 0.855294079 0.918500992 1 18.02220584 2.942601577 24.99777954 0.898981161 0.934209657 0.042962183 0.043208113 509.3560642 221830.9666 0.011790628 0.012505906 876.1966264 -2.942601577 0.035228496 SS(ph)PPLRTPDVLESSGPAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPPLRTPDVLESSGPAVR 19 1 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.471)S(0.526)PPLRT(0.002)PDVLESSGPAVR 53.266 0.073105 129380000 64887 44702 88578 73338 59840 92158 90548 68747 24544 TRUE FALSE 61819.9201 49257.18462 92639.38892 65965.92491 70276.07705 88966.54535 76733.23957 62727.14823 28350.15817 2.180584663 1.737457136 3.267685082 2.326827403 2.47886014 3.13813224 2.706624743 2.212585477 1 14.79106916 3.776392316 24.97261407 2.564292416 1.959020832 0.07136583 0.630422297 914.5093206 603662.4934 0.142203634 0.256353913 5975.748569 -3.776392316 -0.605271584 SS(ph)PQKEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPQKEVK 8 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 S(0.034)S(0.966)PQKEVK;S(0.113)S(0.887)PQKEVK 88.596 0.0087829 965020000 2035270 1535770 2026430 2157300 1110870 2375000 2547600 2511800 1292560 TRUE FALSE 1939066.821 1692266.709 2119343.82 1940444.105 1304605.376 2292753.154 2158916.83 2291853.476 1493003.603 1.298769016 1.133464585 1.419516882 1.299691509 0.873812611 1.53566485 1.446022518 1.535062254 1 20.50978622 SS(ph)PQLDPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.017)S(0.983)PQLDPLR;S(0.02)S(0.98)PQLDPLR;S(0.05)S(0.95)PQLDPLR 129.69 0.00040101 519230000 1163980 1251160 848670 1165400 886240 959170 1035480 1079950 875950 TRUE FALSE 1108960.972 1378654.626 887582.3589 1048251.778 1040799.975 925953.7024 877498.5081 985383.8528 1011787.852 1.096041003 1.362592586 0.877241565 1.036039102 1.028674117 0.915165862 0.867275196 0.973903621 1 19.94847539 3.730913837 24.99959143 0.950021088 1.229316797 0.637204862 0.085334114 305.360755 998315.0121 0.022379835 0.035397949 5381.630023 -3.730913837 0.27929571 SS(ph)PQLDPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.402)S(0.598)PQLDPLRK;S(0.113)S(0.887)PQLDPLRK;S(0.195)S(0.805)PQLDPLRK 138.02 4.64E-05 2398220000 4401210 5186720 3351530 4773060 2186000 3988870 3666460 4265220 2296810 TRUE FALSE 4193173.526 5715252.665 3505200.966 4293262.941 2567237.708 3850734.432 3107074.188 3891734.725 2652987.564 1.58054775 2.154270431 1.321227816 1.618274808 0.967678003 1.451470969 1.171160479 1.466925355 1 21.33918648 3.68956305 11.00450019 1.295210037 1.867255341 0.496774311 0.2434341 0.601619925 134.1716617 0.058509882 0.090761046 4892.862935 -3.68956305 0.572045304 SS(ph)PQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.474)S(0.526)PQLDPLRKS(0.826)PT(0.175)MEQAVQTASAHLPAPAAVGR;S(0.206)S(0.794)PQLDPLRKS(0.5)PT(0.5)MEQAVQT(0.001)ASAHLPAPAAVGR;S(0.448)S(0.552)PQLDPLRKS(0.849)PT(0.151)MEQAVQTASAHLPAPAAVGR;S(0.474)S(0.526)PQLDPLRKS(0.944)PT(0.056)MEQAVQTASAHLPAPAAVGR;S(0.467)S(0.533)PQLDPLRKS(0.881)PT(0.118)MEQAVQTASAHLPAPAAVGR 210.07 9.24E-28 1670930000 1140986 777068 1057139 1071433 808994 1007452 1342724 1247194 930994 TRUE FALSE 1087053.853 856252.1127 1105609.869 963730.5193 950082.2975 972563.6846 1137866.793 1137983.082 1075367.795 1.010867034 0.796241172 1.02812254 0.89618689 0.883495212 0.904400977 1.058118719 1.058226857 1 20.03639874 1.738108618 7.062243833 1.042374842 0.914407691 0.411489557 0.066650448 0.114366408 16.96221089 0.030548633 0.016116184 54.71527902 -1.738108618 -0.12796715 SS(ph)PSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.164)S(0.836)PSARPPDVPGQQPQAAK;S(0.185)S(0.814)PSARPPDVPGQQPQAAK 202.99 3.19E-16 826600000 875930 788310 781930 897880 545670 888440 915460 885410 630480 TRUE FALSE 834526.5248 868639.6852 817782.2639 807623.3965 640834.6752 857673.1 775789.7634 807878.8065 728251.6184 1.145931576 1.192774123 1.122939165 1.108989498 0.87996327 1.177715337 1.065277088 1.109340215 1 19.47407748 3.267249026 2.840417655 1.058637597 1.16648012 0.274147824 0.078303772 0.326821848 5.396528453 0.021856428 0.029469915 1850.329301 -3.267249026 0.107842523 SS(ph)PSIICMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.349)S(0.651)PSIICMPK;S(0.182)S(0.818)PSIICMPK 187.42 1.29E-06 144659000 577490 643860 450710 621630 354810 484080 493020 542190 338440 TRUE FALSE 550193.1922 709470.066 471375.4993 559142.5714 416688.7517 467316.1882 417800.7441 494712.9693 390923.5467 1.407418911 1.814856311 1.20579971 1.430311825 1.065908552 1.19541581 1.068753079 1.265498007 1 18.57652696 3.278392288 1.406239278 1.129050194 1.597330546 0.536530962 0.161446029 0.255541486 1.054194089 0.051133107 0.078431258 1898.419947 -3.278392288 0.468280352 SS(ph)PVEFECINEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSPVEFECINEK 12 0 O75131;H0YB26 O75131 CPNE3 Copine-3 1 S(0.049)S(0.951)PVEFECINEK;S(0.154)S(0.846)PVEFECINEK;S(0.043)S(0.957)PVEFECINEK;S(0.204)S(0.796)PVEFECINEK 261.9 2.30E-21 419678000 1628580 1221250 1110010 1825150 1075180 1265950 1320600 1283100 926510 TRUE FALSE 1551600.251 1345696.763 1160905.056 1641682.454 1262691.052 1222109.834 1119118.216 1170744.962 1070188.439 1.44983836 1.257439078 1.084766957 1.534012511 1.179877305 1.141957612 1.045720711 1.093961511 1 20.02943342 2.328129819 2.5780683 1.064843437 1.320306696 0.496576302 0.122748355 0.235373073 3.205215263 0.047489482 0.03615293 212.8775284 -2.328129819 0.255463259 SS(ph)PVESLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.101)S(0.899)PVESLKK 122.7 0.00035432 589230000 1257300 1216800 1059100 1386600 662450 1258300 1383400 1436000 749080 TRUE FALSE 1197869.921 1340793.303 1107660.783 1247216.334 777981.0703 1214724.755 1172336.922 1310256.227 865243.5006 1.384430995 1.54961384 1.280172323 1.441462817 0.899146968 1.40391087 1.354921385 1.514320797 1 19.72274667 -2.230542993 1.916557877 5.36E-05 1.361544359 0.277468728 0.178852308 2010388.238 335725.496 8693990.254 0.043105491 0.005881079 2.230542993 1.361490735 SS(ph)PVKVGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.056)S(0.944)PVKVGEK;S(0.302)S(0.698)PVKVGEK 147.24 5.62E-05 732840000 2471600 2588900 2189200 2800800 1239810 2815100 2690100 3034100 1328200 TRUE FALSE 2354772.366 2852711.853 2289576.985 2519258.263 1456032.471 2717612.381 2279675.838 2768418.119 1534170.472 1.534883123 1.859449067 1.492387597 1.642097999 0.949068241 1.771388793 1.485933851 1.80450489 1 20.54902737 3.609514449 7.978787196 1.475494624 1.696815819 0.104503688 0.294319086 0.600123339 36.00500145 0.07109446 0.110296317 4069.250717 -3.609514449 0.221321195 SS(ph)PVNRPSSATNK ddPTM_SK-BR-3_Trastuzumab_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(0.18)S(0.82)PVNRPSSATNK 75.911 0.018231 65548000 66831 74078 61168 73605 54874 79343 76442 74643 54546 TRUE FALSE 63672.03108 81626.63242 63972.6133 66206.08556 64444.00823 76595.33202 64779.36895 68106.86321 63004.7151 1.010591524 1.295563868 1.015362314 1.050811601 1.022844213 1.215707934 1.028167001 1.080980417 1 15.94317218 -0.120476366 0.212552403 0.947010464 1.136742657 0.068353349 0.094946602 21.70778365 1.658454388 1.081597117 0.266703988 0.757745967 0.120476366 0.189732194 SS(ph)PVPPVPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.252)S(0.748)PVPPVPER;S(0.105)S(0.895)PVPPVPER;S(0.082)S(0.918)PVPPVPER;S(0.004)S(0.996)PVPPVPER;S(0.067)S(0.933)PVPPVPER 181.68 1.95E-06 2764030000 2638804 2453263 2501510 2680640 2229884 2497220 2812030 2765385 2620560 TRUE FALSE 2514072.965 2703253.289 2616206.708 2411176.974 2618775.064 2410740.645 2383003.177 2523233.229 3026943.061 0.830565 0.893063805 0.864306548 0.796571632 0.865155046 0.796427484 0.787263959 0.833591243 1 21.52943011 -1.485674553 3.081533373 1.004311349 0.834166386 0.703734163 0.033974437 10360410.69 13844213.45 387324.1648 0.009296991 0.032683266 1.485674553 -0.170144963 SS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSPVTK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(0.376)S(0.624)PVTK;S(0.027)S(0.973)PVTK;S(0.395)S(0.605)PVTK;S(0.104)S(0.896)PVTK;S(0.135)S(0.865)PVTK 109.86 0.030624 1876927000 7812270 8250480 8677500 11303880 5759320 8173530 10579470 14925890 8668850 TRUE FALSE 7442999.48 9091213.292 9075371.958 10167592.51 6763743.585 7890478.607 8965377.546 13618899.94 10013170.98 0.743320921 0.907925502 0.906343452 1.01542184 0.675484679 0.788009974 0.895358479 1.360098611 1 23.25539559 1.367887475 6.773959668 1.17628386 0.843957486 0.547046082 0.126615817 0.148610792 8.002135767 0.07931849 0.028791119 23.32853548 -1.367887475 -0.332326374 SS(ph)REKEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.427)S(0.573)REKEQR;S(0.071)S(0.929)REKEQR;S(0.443)S(0.557)REKEQR;S(0.441)S(0.559)REKEQR 95.573 0.0049852 1104271000 608000 532304 565723 592946 674334 514409 705432 621326 869734 TRUE FALSE 579261.0449 586546.3828 591661.9591 533341.9416 791937.6361 496594.8873 597805.3923 566919.4016 1004607.907 0.576604107 0.583856029 0.588948141 0.530895624 0.788305199 0.49431712 0.595063396 0.564319072 1 19.9382011 -1.599794002 4.427222996 1.006948551 0.589138486 0.73829816 0.076657145 0.004685677 0.000423569 0.066150171 0.01540988 0.025130782 1.599794002 -0.417810065 SS(ph)RSS(ph)PELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.416)S(0.522)RS(0.172)S(0.889)PELTR;S(0.409)S(0.549)RS(0.101)S(0.938)PELT(0.003)R;S(0.399)S(0.599)RS(0.003)S(0.998)PELTR;S(0.398)S(0.602)RS(0.013)S(0.988)PELTR 125.5 0.00023188 1622470000 1332170 1047930 1263010 1315330 1117100 1155300 1312580 1057810 1179290 TRUE FALSE 1269200.964 1154715.258 1320920.258 1183110.529 1311921.886 1115291.671 1112321.814 965182.5486 1362168.27 0.931750498 0.847703829 0.969718857 0.86854947 0.963112939 0.81876204 0.816581797 0.708563376 1 20.3774735 2.214040468 24.66276571 0.820182589 0.908517613 0.184732967 0.079840059 271.730708 273309.1401 0.026410755 0.019514991 163.6969049 -2.214040468 0.088335024 SS(ph)S(ph)AS(ph)T(ph)AAT(ph)WLWQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSASTAATWLWQAR 15 0 J3QKM6 J3QKM6 LLGL2 5 S(0.635)S(0.683)S(0.683)AS(1)T(1)AAT(1)WLWQAR 43.184 0.064388 0 5376.6 6370.2 6615.5 7874.4 8391.2 5952.6 8186.9 7272.9 7962.5 TRUE FALSE 5122.458773 7019.330622 6918.827219 7082.850352 9854.622623 5746.459969 6937.838042 6636.04632 9197.283833 0.55695343 0.763196042 0.752268533 0.7701024 1.071470969 0.624799677 0.754335537 0.721522402 1 13.16699215 -1.221499052 0.037655655 1.82128614 2.55E-39 0.282804291 0.130104386 548.7186129 3.680911544 111.8622239 69.24994441 0.060048332 1.221499052 -1.82128614 SS(ph)SAPNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.096)S(0.521)S(0.383)APNVHINTIEPVNIDDLIR 301.05 5.64E-56 686950000 87901 84845 86753 101270 85645 92207 107250 117630 107080 TRUE FALSE 83746.09393 93490.80196 90730.71086 91090.1472 100581.4609 89013.84847 90887.04272 107329.6936 123685.4195 0.67708946 0.755875691 0.733560279 0.736466332 0.813203863 0.7196794 0.734824226 0.867763509 1 16.91631591 -5 0.177883808 2.057615627 0.690943382 0.808378939 0.040770391 55.33787068 0.530638978 20.53682525 0.126737335 1.00E-05 5 -1.366672246 SS(ph)SESLIFSGNQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 S(0.05)S(0.812)S(0.138)ESLIFSGNQGR;S(0.008)S(0.992)SESLIFSGNQGR;SS(1)SESLIFSGNQGR;S(0.003)S(0.996)SESLIFSGNQGR;S(0.002)S(0.998)SESLIFSGNQGR 423.52 1.01E-152 902310000 1428070 1341900 1399120 1561090 1132090 1419600 1561720 1601290 1456680 TRUE FALSE 1360567.961 1478641.136 1463271.036 1404166.267 1329526.138 1370438.896 1323450.931 1461072.559 1682574.495 0.808622718 0.878796832 0.869661962 0.834534383 0.790173714 0.814489284 0.786563053 0.868355347 1 20.68223895 0.974141515 19.86947302 1.000000001 0.828030202 0.768689616 0.029935864 80.54527903 61891.21825 0.03160628 0.00790157 9.42196562 -0.974141515 -0.171969799 SS(ph)SKESLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.067)S(0.453)S(0.453)KES(0.026)LVR;S(0.06)S(0.47)S(0.47)KES(0.001)LVR;S(0.08)S(0.361)S(0.361)KES(0.198)LVR 100.93 0.0026199 2123900000 2168430 1779170 1850240 2099180 1112633 2120160 2210900 2139740 1239970 TRUE FALSE 2065932.611 1960469.446 1935075.334 1888166.438 1306675.843 2046738.328 1873586.599 1952373.022 1432258.215 1.442430276 1.368796091 1.35106597 1.318314267 0.912318623 1.429028863 1.30813465 1.363143183 1 20.44986018 -5 0.108094131 0.107435902 1.490487879 0.301355943 0.148534345 221.9147827 1.602182545 45.51708005 1.915393244 1.00E-05 5 1.383051977 SS(ph)SLDMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSLDMNR 8 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.138)S(0.516)S(0.347)LDMNR;S(0.163)S(0.503)S(0.333)LDMNR 74.267 0.043448 606600000 1092440 1033180 1006560 1219470 1108920 1150910 1320060 1207600 1178250 TRUE FALSE 1040802.526 1138462.217 1052711.772 1096886.559 1302315.297 1111053.698 1118660.602 1101856.142 1360966.992 0.764752218 0.836509793 0.773502794 0.805961177 0.956904395 0.81637079 0.821960127 0.809612686 1 20.37620065 -5 0.210844204 1.83983836 0.797227573 0.540127385 0.05167326 116.3823164 1.160147262 41.47940185 0.106031198 1.00E-05 5 -1.042610787 SS(ph)SPELVTHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.114)S(0.611)S(0.275)PELVTHLK 235.21 1.04E-15 438740000 605930 516710 522670 675920 416870 580660 626400 594910 364390 TRUE FALSE 577288.8897 569363.3365 546634.9365 607975.2374 489571.996 560551.5986 530831.1754 542816.5266 420897.7402 1.371565667 1.352735551 1.298735736 1.444472563 1.163161379 1.331799972 1.261187991 1.289663676 1 18.68311024 -4.385864368 0.170568187 1.64E-12 1.399052199 0.701839987 0.067185843 51.79148335 0.591820948 17.74237677 0.214839087 4.11E-05 4.385864368 1.399052199 SS(ph)SPFLSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPFLSKR 9 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.109)S(0.52)S(0.371)PFLSKR 84.507 0.0094602 136440000 89386 57445 81158 71542 74035 68018 96042 80870 94809 TRUE FALSE 85160.90093 63298.71081 84879.17458 64350.46224 86946.68056 65662.5196 81389.02897 73788.59408 109511.4955 0.777643484 0.578009738 0.775070911 0.587613766 0.793950262 0.599594767 0.743200781 0.673797703 1 16.74072279 -2.902029807 0.513281665 1.912814655 0.685638161 0.583644833 0.08185018 157.668934 6.082150434 158.6985874 0.031917038 0.001253055 2.902029807 -1.227176493 SS(ph)SPGKPQAVSSLNSSHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.104)S(0.448)S(0.448)PGKPQAVSSLNSSHSR 103.84 0.00022094 190220000 140740 96451 121010 151730 112810 128260 164090 144670 127380 TRUE FALSE 134087.4991 106279.4666 126558.4282 136477.8121 132484.0283 123818.324 139055.0568 132001.9279 147133.4398 0.911332592 0.722333867 0.860160874 0.927578478 0.90043452 0.841537615 0.945094854 0.8971579 1 17.16676565 1.567389452 0.327760304 1.006905928 0.811748858 0.364223373 0.058540129 1.32893406 0.484216119 0.094921584 0.085238766 36.9308626 -1.567389452 -0.19515707 SS(ph)SPHDKNLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.084)S(0.508)S(0.408)PHDKNLPQK 83.499 0.0077304 352440000 108870 71681 107510 107410 78760 113510 147600 125990 93119 TRUE FALSE 103723.9309 78985.37539 112439.4398 96612.94273 92495.71906 109579.1202 125080.9091 114957.6477 107559.4189 0.964340751 0.734341782 1.045370466 0.898228567 0.85994997 1.01877754 1.162900566 1.068782714 1 16.71477434 2.072732582 4.371778764 1.094875423 0.89081063 0.46011539 0.087865646 0.157780878 5.839127594 0.033813187 0.023792794 118.231332 -2.072732582 -0.204064793 SS(ph)SPVTELASRS(ph)PIRQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.273)S(0.364)S(0.364)PVTELAS(0.142)RS(0.858)PIRQDR;S(0.277)S(0.362)S(0.362)PVTELAS(0.061)RS(0.939)PIRQDR 186.96 2.43E-14 803760000 306130 213361 322090 275481 303330 269135 374790 323000 406730 TRUE FALSE 291659.8416 235102.7285 336858.1451 247789.1265 356230.656 259814.7875 317608.902 294716.4077 469803.6111 0.62081226 0.500427674 0.717019063 0.527431294 0.758254401 0.553028502 0.676046106 0.627318311 1 18.84169828 -5 0.240419419 3.210329566 0.576909828 0.686857499 0.080374121 86.16968405 0.858936462 93.05808491 0.109219706 1.00E-05 5 -2.633419738 SS(ph)SS(ph)PPPKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSPPPKQK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.429)S(0.571)S(0.311)S(0.689)PPPKQK 69.815 0.031778 108620000 317740 230500 335700 302400 197520 329150 396720 355320 280490 TRUE FALSE 302721.0599 253988.2121 351092.1771 272002.1775 231967.4255 317751.453 336193.0777 324206.2971 323986.9567 0.934361874 0.783945794 1.083661456 0.839546691 0.715977667 0.980753843 1.03767473 1.000677004 1 18.30557621 2.020178965 24.9724696 1.015031113 0.871374192 0.327024975 0.095906687 257.2206587 318321.9572 0.034565149 0.025525499 104.7560141 -2.020178965 -0.143656921 SS(ph)SVPHPFQVTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.273)S(0.628)S(0.099)VPHPFQVTLLR;S(0.123)S(0.874)S(0.003)VPHPFQVTLLR;S(0.146)S(0.853)SVPHPFQVTLLR;S(0.014)S(0.985)S(0.001)VPHPFQVTLLR;S(0.014)S(0.985)S(0.001)VPHPFQVTLLR 231.37 3.64E-13 4457780000 2931160 2461090 2532190 2970590 2711190 2715740 3141460 3063720 2500210 TRUE FALSE 2792609.876 2711877.869 2648293.416 2671980.649 3184020.678 2621693.243 2662172.58 2795444.435 2887929.797 0.966993685 0.939038709 0.917021397 0.925223547 1.102527035 0.907810586 0.921827318 0.967975204 1 21.46160424 SS(ph)TPLPTISSSAENTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.023)S(0.754)T(0.223)PLPTISSSAENTR 219.12 1.33E-14 2486700000 727300 685920 706710 987840 821020 845040 976860 791320 851460 TRUE FALSE 692921.9704 755816.0278 739113.3525 888540.4464 964205.6281 815776.0529 827822.0657 722027.8257 983500.0681 0.704546947 0.768496162 0.75151327 0.903447265 0.980381862 0.829462121 0.841710227 0.734141104 1 19.90756563 3.269464667 9.423121322 0.872543576 0.7417737 0.422236529 0.076727254 0.317999153 91.20986795 0.020617511 0.027679614 1859.79325 -3.269464667 -0.130769876 SS(ph)TPPRQS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.293)S(0.353)T(0.353)PPRQS(1)PSR;S(0.29)S(0.355)T(0.355)PPRQS(1)PSR 92.935 0.0054768 677150000 490120 385100 409570 466850 384620 439860 493310 441600 422530 TRUE FALSE 466952.9989 424342.1278 428349.1896 419921.351 451697.6062 424627.5379 418046.4992 402931.1629 488053.7944 0.956765431 0.869457696 0.877667984 0.860399726 0.925507826 0.870042489 0.85655824 0.825587604 1 18.89668065 4.582594657 2.618660407 0.878907612 0.960905174 0.164229007 0.048009644 0.500437731 5.599670513 0.010530173 0.077139571 38246.76058 -4.582594657 0.081997563 SS(ph)VEKENQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSVEKENQK 9 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.16)S(0.84)VEKENQK;S(0.147)S(0.853)VEKENQK 110.64 0.0025531 217500000 476340 454000 432060 544490 214943 504350 508720 600490 294910 TRUE FALSE 453824.3522 500263.1162 451870.3784 489756.8307 252428.9911 486884.233 431105.4207 547907.9122 340643.1366 1.332257437 1.468584164 1.326521306 1.437741666 0.741036481 1.429308801 1.265563208 1.608451348 1 18.37790161 -2.066021243 2.722152607 0.507901086 1.325328646 0.167758031 0.228314559 4709142.101 7505798.693 14422605.21 0.050969277 0.008589715 2.066021243 0.81742756 SS(ph)WPNSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSWPNSEK 8 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.141)S(0.859)WPNSEK;S(0.165)S(0.835)WPNSEK;S(0.02)S(0.98)WPNSEK 167.12 0.00032992 237970000 779680 679410 701220 827390 523950 846800 869680 843560 605220 TRUE FALSE 742826.0716 748642.6514 733371.6306 744219.1853 615326.7141 817475.1037 736994.3432 769693.4144 699074.4266 1.062585103 1.070905504 1.049060876 1.0645779 0.880202008 1.169367771 1.054243032 1.101017839 1 19.41508653 -0.508278533 7.586648351 0.999981558 1.057701857 0.057650382 0.071634752 0 0 0.062594483 0.014753661 0.310256913 0.508278533 0.057720299 SSAQLLEDWGMEDIDHVFSEEDYR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 163.74 1.64E-11 222884000 146013 149547 139234.5 170573.1 134216.5 141298.7 164216.1 166239.4 130167.3 FALSE TRUE 139111.2549 164786.0093 145618.5395 153426.7679 157623.8151 136405.4906 139161.9179 151682.5968 150352.9801 0.925231111 1.095994301 0.968511163 1.020443811 1.048358436 0.907235031 0.925568072 1.008843302 1 17.19799394 2.242709187 24.9992936 0.949462637 1.013773479 0.168817873 0.054081753 144.7780894 872437.7664 0.018216027 0.014730191 174.8675345 -2.242709187 0.064310842 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR 362.96 3.07E-96 3957220000 2569711 3256040 2276719 3034001 1943044 2525334 2343884 2689460 1962143 TRUE FALSE 2448245.854 3587834.178 2381108.818 2729017.455 2281910.258 2437881.05 1986281.447 2453956.625 2266422.115 1.080225011 1.583038814 1.050602534 1.204108201 1.006833742 1.07565181 0.876395193 1.08274474 1 21.11198515 3.097757473 1.360261692 0.990096534 1.31391831 0.348191147 0.15132127 0.363911358 1.409127574 0.053889598 0.070381512 1252.441567 -3.097757473 0.323821776 SSDEENGPPSS(ph)PDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 SSDEENGPPSS(1)PDLDR;SSDEENGPPS(0.001)S(0.999)PDLDR 416.41 2.08E-140 337500000 673230 556080 643520 692630 638950 635210 744680 669970 713660 TRUE FALSE 641407.7521 612745.1842 673026.0285 623005.5165 750382.6777 613212.5184 631065.389 611303.8751 824330.7479 0.778095144 0.743324431 0.816451443 0.755771295 0.910293204 0.743891357 0.765548769 0.741575971 1 19.65286378 -1.411612603 3.368225817 1.002297321 0.779534537 0.645086492 0.050821598 35107559.01 63348516.75 822734.0158 0.011418834 0.038760324 1.411612603 -0.222762785 SSDGRPDS(ph)GGTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDGRPDSGGTLR 13 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 S(0.001)S(0.012)DGRPDS(0.572)GGT(0.414)LR 101.71 0.0047864 84202000 201510 156510 182200 215060 180520 189420 215950 188190 191590 TRUE FALSE 191985.0217 172458.5469 190554.0502 193441.7602 212002.6308 182860.3379 183002.8613 171711.0859 221300.7987 0.867529728 0.779294733 0.861063545 0.874112346 0.957984029 0.826297686 0.826941712 0.775917154 1 17.75564913 -2.293055033 2.429416204 1.804245234 0.843897977 0.464888498 0.051826537 4929257.555 1638586.071 21382548.68 0.012631797 0.005092663 2.293055033 -0.960347257 SSDKPIRT(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDKPIRTPSR 11 2 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 S(0.002)S(0.006)DKPIRT(0.969)PS(0.023)R 67.115 0.097847 213660000 308790 252130 292440 311470 236830 306040 352210 340000 259290 TRUE FALSE 294194.1087 277822.3336 305848.6633 280160.4438 278133.077 295441.7581 298473.8957 310227.7975 299499.3689 0.982286239 0.927622434 1.021199692 0.935429162 0.928659977 0.986452022 0.996576042 1.035821206 1 18.19219344 1.76721828 2.345966158 1.015793058 0.958984803 0.383892454 0.029713184 0.268082736 2.955596748 0.017584837 0.00785972 58.50840785 -1.76721828 -0.056808255 SSDKPIRTPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDKPIRTPSR 11 2 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 SS(0.005)DKPIRT(0.231)PS(0.763)R 70.225 0.041228 208710000 312110 274700 265430 337480 222600 264050 326200 323230 277140 TRUE FALSE 297357.1788 302692.2423 277600.228 303555.8692 261421.3695 254905.8823 276432.1989 294926.2676 320117.4558 0.928900232 0.945566188 0.867182414 0.948264032 0.816642032 0.796288605 0.863533662 0.921306422 1 18.28824182 3.388482314 1.419185759 0.868787877 0.936001201 0.033819468 0.0619848 0.71558871 2.968839178 0.019519641 0.033181077 2446.14566 -3.388482314 0.067213323 SSDQPLTVPVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 279.29 2.52E-32 1299170000 3979420 3813890 4040510 4672940 2432110 4664280 4819520 4749310 2797770 TRUE FALSE 3791320.703 4202529.727 4225771.38 4203207.193 2856269.214 4502754.814 4084213.707 4333435.239 3231633.883 1.173190046 1.300434975 1.307626895 1.300644611 0.883846784 1.393336924 1.263823148 1.340942507 1 21.62383233 SSDS(ph)EEAFETPESTTPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDSEEAFETPESTTPVK 18 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.212)S(0.212)DS(0.577)EEAFETPESTTPVK 462.36 3.21E-214 393060000 639870 700420 543420 735210 379240 638120 590440 662690 384580 TRUE FALSE 609624.6132 771793.5943 568336.3445 661305.294 445379.3359 616021.7444 500357.5338 604661.3505 444218.7022 1.372352425 1.737418057 1.279406611 1.488693048 1.002612753 1.386753285 1.12637656 1.361179409 1 18.76091061 3.157935948 1.651172702 1.200007147 1.537746409 0.363975082 0.178748279 0.329942956 1.86010176 0.0540862 0.072353029 1438.586392 -3.157935948 0.337739262 SSDYQFPS(ph)SPFTDTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.857)S(0.143)PFTDTLK 160.47 9.20E-09 61108000 327070 416080 281630 399190 215890 338120 333990 377970 226080 TRUE FALSE 311610.0493 458479.025 294543.0141 359062.6628 253541.1476 326410.8196 283033.6914 344872.9431 261139.3317 1.193271221 1.755687364 1.127915171 1.374984995 0.970903716 1.249948897 1.083841677 1.32064726 1 17.99446024 3.701500383 24.99652849 1.165966934 1.474479433 0.332207096 0.184574803 522.6766085 352536.8586 0.044693475 0.069240674 5029.217099 -3.701500383 0.308512499 SSDYQFPSS(ph)PFTDTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.162)S(0.838)PFTDTLK 237.06 9.97E-20 83168000 281990 317600 237550 335150 169010 302630 274930 315290 187890 TRUE FALSE 268660.8916 349963.8011 248441.9025 301460.0853 198485.2905 292149.8472 232984.3791 287681.5361 217027.0216 1.237914475 1.612535612 1.144751011 1.389044014 0.914564873 1.346145033 1.073527054 1.325556302 1 17.72751516 3.712981081 24.92470282 1.176438787 1.425225068 0.266066269 0.175661064 775.2650098 755418.5195 0.041430547 0.064208743 5163.938737 -3.712981081 0.248786281 SSECMKDDPITLFVALSPQGTAQGELFLDDGHTFNYQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSECMKDDPITLFVALSPQGTAQGELFLDDGHTFNYQTR 39 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 236.29 2.59E-50 110295000 198652 176366 177473.1 211342.2 141979.3 191281 224708 215652.6 132570.5 FALSE TRUE 189262.1137 194337.8959 185610.4172 190097.6805 166740.445 184656.891 190424.6676 196768.9151 153128.8561 1.235966352 1.269113483 1.212119139 1.241422978 1.088889771 1.205892186 1.24355835 1.284989127 1 17.22438665 -1.770868092 2.906537097 0.951539545 1.224591482 0.635106458 0.053043683 16935243.98 17526950.81 5934030.037 0.013203244 0.016948525 1.770868092 0.273051937 SSEIEQAVQSLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSEIEQAVQSLDR 13 0 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ; 125.89 0.00045339 31000000 64381 53018 59365 73125 55584 57901 72084 67871 73587 FALSE TRUE 61337.83772 58420.59448 62086.94397 65774.33607 65277.832 55895.87385 61086.26189 61927.85543 84998.49613 0.721634388 0.687313272 0.730447558 0.77382941 0.767988082 0.657610151 0.71867462 0.728575895 1 16.3751497 0.62496875 3.886032984 0.999999768 0.719366183 0.868516227 0.033830254 5.172290514 53.2222596 0.032901981 0.008419376 4.216661607 -0.62496875 -0.280633585 SSENGVDYVIMGMPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSENGVDYVIMGMPHR 16 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q02218-3 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 83.106 0.0081331 42105000 46195 35132 34273 38931 51885 34418 38120 40346 45778 FALSE TRUE 44011.4539 38711.99074 35844.45095 35017.58192 60933.72757 33226.09603 32304.09388 36813.09035 52877.01844 0.832336149 0.732113721 0.67788336 0.662245772 1.152366933 0.628365536 0.610928809 0.696202082 1 15.69035321 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKETVQTTQS(0.997)PT(0.003)PVEK;SSEPVKETVQTT(0.004)QS(0.995)PT(0.001)PVEK;SSEPVKETVQTT(0.001)QS(0.998)PT(0.001)PVEK;SSEPVKETVQTTQS(1)PTPVEK 341.46 1.24E-80 1469620000 2169690 2188670 1894670 2460550 1200370 2309480 2236890 2437760 1371780 TRUE FALSE 2067133.054 2411697.961 1981542.494 2213210.839 1409714.148 2229502.129 1895611.347 2224296.811 1584508.636 1.304589326 1.522047849 1.250572227 1.396780547 0.889685367 1.40706215 1.19634018 1.40377702 1 20.59560409 -5 0.064218806 1.71E-07 1.708493877 0.212919877 0.172545893 487.9181049 2.275195919 76.20836878 11.24328095 1.00E-05 5 1.708493706 SSEPVQADESQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSEPVQADESQSPR 14 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR 322.75 2.53E-56 1303100000 1176420 1072537 1136854 1329461 1113452 1158679 1318875 1186179 1150722 TRUE FALSE 1120812.958 1181829.74 1188979.88 1195821.054 1307637.676 1118553.656 1117656.396 1082310.878 1329170.091 0.843242686 0.889148611 0.894528013 0.899674965 0.983800106 0.841542902 0.84086785 0.814275679 1 20.3420943 SSEPVQHEESIRKPS(ph)PEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SSEPVQHEESIRKPSPEPR 19 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SSEPVQHEES(0.066)IRKPS(0.934)PEPR;SSEPVQHEES(0.043)IRKPS(0.957)PEPR;SSEPVQHEES(0.132)IRKPS(0.868)PEPR;SSEPVQHEES(0.002)IRKPS(0.998)PEPR;SSEPVQHEES(0.01)IRKPS(0.99)PEPR;SSEPVQHEES(0.025)IRKPS(0.975)PEPR;SSEPVQHEES(0.207)IRKPS(0.793)PEPR;SSEPVQHEES(0.127)IRKPS(0.873)PEPR 151.33 3.17E-08 4134160000 1526468 1145400 1464346 1466869 1188015 1376054 1770500 1626950 1433248 TRUE FALSE 1454314.883 1262117.562 1531487.713 1319416.541 1395204.44 1328400.905 1500377.708 1484485.633 1655508.78 0.878470051 0.76237443 0.925085829 0.796985529 0.842764748 0.80241248 0.90629402 0.896694509 1 20.65884323 1.038224816 1.064663254 0.997330352 0.832025999 0.538274251 0.047630215 0.36301907 0.870831288 0.040319285 0.013159822 10.92005476 -1.038224816 -0.165304353 SSESPS(ph)SSPS(ph)SPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSES(0.001)PS(0.544)S(0.397)S(0.059)PS(0.849)S(0.151)PAR 90.853 0.0081689 189240000 163260 142700 157740 176760 161130 146080 173290 145330 165420 TRUE FALSE 155543.0234 157241.2922 164972.535 158991.749 189231.021 141021.213 146851.4278 132604.1348 191072.4888 0.814052428 0.822940515 0.863402869 0.832101733 0.990362465 0.738050851 0.768563956 0.693999098 1 17.54376054 -1.678800098 8.610754297 1.000315261 0.816158372 0.35021486 0.079002555 0.000467085 1.74E-05 0.074725424 0.017583486 0.020950766 1.678800098 -0.18415689 SSESPSS(ph)SPS(ph)SPARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSES(0.001)PS(0.112)S(0.879)S(0.023)PS(0.634)S(0.351)PARK 83.758 0.030063 250690000 333830 259790 337540 350180 262150 324770 379390 332830 297510 TRUE FALSE 318050.5175 286262.8964 353016.5429 314979.2411 307868.877 313523.1335 321507.0875 303685.6408 343646.3313 0.925516988 0.833016012 1.02726702 0.91657967 0.895888735 0.912342443 0.935575498 0.883715649 1 18.39056503 -2.31659309 2.163559099 1.418716465 0.913527107 0.225161634 0.048601843 5401262.378 585624.3807 11097492.13 0.012224021 0.004823996 2.31659309 -0.505189358 SSESPSSSPS(ph)SPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPS(0.002)S(0.001)S(0.005)PS(0.496)S(0.496)PAR 103.88 0.0024108 0 48366 43557 45867 48977 41996 47512 51722 45862 48948 TRUE FALSE 46079.83503 47995.50782 47970.04732 44053.73891 49320.0891 45866.64753 43830.85896 41846.08015 56538.60585 0.81501541 0.848897972 0.848447651 0.779179788 0.87232588 0.811244756 0.775237704 0.740132862 1 15.78694869 SSFDEMLPGTHFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSFDEMLPGTHFQR 14 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 83.499 0.0064518 112050000 186990 89910 153440 126740 141360 158840 235290 184410 165480 FALSE TRUE 178151.3533 99071.93122 160475.3758 113999.8544 166013.1392 153339.331 199392.1891 168262.0828 191141.7932 0.932037679 0.518316426 0.839561945 0.596415114 0.868533963 0.80222817 1.043163746 0.880299802 1 17.54428373 2.153116307 1.669866293 0.974545271 0.72105421 0.383824713 0.128537957 0.342349433 1.851674539 0.067359777 0.038157472 142.2709748 -2.153116307 -0.253491061 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.296)S(0.704)PSSDSLLFAHK;SSFDWLTGSSTDPLVDHT(0.361)S(0.583)PS(0.019)S(0.037)DSLLFAHK;SSFDWLTGSSTDPLVDHT(0.003)S(0.972)PS(0.022)S(0.004)DSLLFAHK;SSFDWLTGSSTDPLVDHT(0.035)S(0.748)PS(0.078)S(0.139)DSLLFAHK 402.81 1.57E-174 1013950000 836350 903625 822571 1189060 798188 1085803 1086859 968855 421997 TRUE FALSE 796817.393 995705.4148 860286.694 1069533.43 937391.7345 1048201.37 921038.698 884016.92 487438.1395 1.63470465 2.042731855 1.76491461 2.194193156 1.923098868 2.150429531 1.889549921 1.813598175 1 18.89485961 0.641770217 2.097412997 1.000178367 1.942106064 0.76037414 0.165115805 0.951983108 4.985111941 0.148924215 0.04075512 4.382987349 -0.641770217 0.941927698 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHKR 31 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.009)S(0.989)PS(0.002)SDSLLFAHKR 156.51 1.04E-09 237660000 152760 101400 157070 168310 192610 180920 256760 198560 130360 TRUE FALSE 145539.3375 111732.7753 164271.8149 151391.159 226201.123 174654.695 217586.5463 181173.0338 150575.563 0.966553501 0.742037905 1.090959327 1.005416523 1.502243249 1.159913943 1.445032261 1.203203429 1 17.20012813 3.172725879 1.844512157 1.289664388 0.86797356 0.441235058 0.168056196 0.227212445 1.591794707 0.048797292 0.065007851 1488.421309 -3.172725879 -0.421690828 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 182.44 3.58E-18 68143000 79350 56713 68512 89341 101020 76008 114960 85676 53380 FALSE TRUE 75599.28276 62492.11918 71653.34297 80360.27294 118637.856 73375.8239 97420.74061 78173.75524 61657.89777 1.226108666 1.013529839 1.162111352 1.303324892 1.924130733 1.190047448 1.58002047 1.267862805 1 15.91199808 3.133936327 4.102248417 1.43843931 1.120673325 0.16263424 0.251068234 0.277962647 8.551725062 0.066268975 0.081040887 1361.245093 -3.133936327 -0.317765985 SSFFSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 157.21 0.0034697 2984590000 4252070 3392190 3430640 3890740 3669260 3813230 4756150 4348080 3936120 FALSE TRUE 4051083.078 3737858.018 3587938.237 3499635.423 4309177.782 3681176.889 4030511.965 3967339.065 4546513.387 0.891030716 0.822137251 0.789162581 0.769740486 0.947798327 0.809670307 0.886506125 0.872611324 1 22.11632917 0.362217917 0.574785126 1.006609144 0.835315852 0.486160089 0.051248149 1.933510169 0.999561826 0.07776156 0.021272533 2.302596905 -0.362217917 -0.171293293 SSFFSDRGS(ph)GSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 SSFFS(0.001)DRGS(0.963)GS(0.036)R;SSFFSDRGS(0.975)GS(0.025)R;SSFFSDRGS(0.987)GS(0.013)R 175.27 1.70E-05 976020000 1025360 692070 700410 1310400 928780 815780 1268820 819880 991850 TRUE FALSE 976893.2649 762592.7198 732524.4913 1178676.102 1090758.938 787529.334 1075238.206 748086.9607 1145661.032 0.852689615 0.665635557 0.639390248 1.028817485 0.952078239 0.687401694 0.938530835 0.652974082 1 20.12774883 -5 0.159321691 1.678877313 0.752808086 0.131491167 0.142470907 262.5878134 2.409015387 57.17673953 0.583546426 1.00E-05 5 -0.926069227 SSFS(ph)HYSGLKHEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSFSHYSGLKHEDKR 15 2 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.28)S(0.28)FS(0.439)HYSGLKHEDKR 79.97 0.0087205 53519000 110310 76519 93322 97328 87408 100790 130080 124980 71666 TRUE FALSE 105095.8649 84316.37309 97600.90601 87544.40453 102651.9275 97299.61703 110233.9069 114036.0886 82779.59726 1.26958657 1.018564669 1.179045432 1.057560165 1.240063143 1.175405779 1.331655511 1.377586898 1 16.33698761 2.407236381 2.115817248 1.260721677 1.131780714 0.079920803 0.122610146 0.512725798 4.691401511 0.047011619 0.036528767 255.4091085 -2.407236381 -0.128940963 SSFSQHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 165.26 0.0003253 2677898000 3133390 1912944 1607292 1867157 4403630 1611074 4004720 2788260 5079260 FALSE TRUE 2985280.864 2107875.168 1680987.928 1679466.831 5171621.678 1555282.103 3393726.412 2544105.173 5866925.7 0.508832226 0.35928104 0.286519382 0.286260116 0.881487502 0.265093199 0.578450552 0.433635144 1 22.48417329 -5 0.244816931 4.267785247 0.395024167 0.478947926 0.181867539 145.8759945 1.450620775 237.6094072 0.248639714 1.00E-05 5 -3.87276108 SSFTPSS(ph)PENVIGDFLLQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 SSFTPS(0.07)S(0.93)PENVIGDFLLQDR;SSFTPS(0.128)S(0.871)PENVIGDFLLQDR;SSFTPS(0.15)S(0.85)PENVIGDFLLQDR 170.11 1.03E-11 149132000 212342 207424 209879 226620 211407 213894 243334 225598 243680 TRUE FALSE 202305.0145 228560.7414 219502.1597 203839.7271 248276.3139 206486.7971 206208.9292 205843.4431 281468.6499 0.718747948 0.812029125 0.779845854 0.724200465 0.882074483 0.733604958 0.732617751 0.731319254 1 18.10261472 -1.155614462 4.204652716 1.000066218 0.764860428 0.68118814 0.050672897 2.205306901 26718400.9 3439.889378 0.01115923 0.069885252 1.155614462 -0.23520579 SSFYVNGLTLGGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSFYVNGLTLGGQK 14 0 P07737;K7EJ44;I3L3D5 P07737 PFN1 Profilin-1 0 202.44 2.48E-07 0 224780 158160 146860 174470 156800 168560 227020 189070 166590 FALSE TRUE 214155.0949 174276.6838 153593.6763 156931.9441 184145.8704 162722.7249 192383.9295 172514.0285 192423.9264 1.112933817 0.90569134 0.798204668 0.815553175 0.956980111 0.845647046 0.999792142 0.896531069 1 17.55392867 -0.63323944 7.602748609 1.000003618 0.924323073 0.068717013 0.092725564 0 0 0.092146437 0.021719123 0.232680806 0.63323944 -0.075680545 SSGEIVYCGQVFEKS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SSGEIVYCGQVFEKS(1)PLR 277.05 2.43E-39 2853772000 3377180 3281910 2886090 3457290 2005985 3240600 3377790 3470160 2182875 TRUE FALSE 3217547.394 3616340.36 3018420.081 3109756.641 2355828.149 3128377.209 2862446.098 3166294.394 2521384.106 1.276103623 1.434267929 1.197128226 1.233352996 0.934339256 1.240738054 1.135267765 1.255776296 1 21.26578448 3.45962212 2.458076093 1.135963528 1.353403526 0.398091087 0.109830987 0.250603593 3.043728918 0.02929425 0.045427055 2881.523198 -3.45962212 0.217439997 SSGFGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGFGSPR 8 0 A1L390-3;A1L390;A1L390-2;G3V311;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SSGFGS(1)PR 79.986 0.024598 0 122430 106710 108550 118790 130060 109780 131560 127720 124060 TRUE FALSE 116642.9765 117583.8703 113527.1249 106849.0035 152742.4228 105978.2911 111488.1057 116536.1597 143298.5912 0.813985508 0.820551475 0.792241738 0.745638897 1.065903172 0.739562687 0.778012574 0.813240094 1 17.1286649 -1.4087492 3.059931222 1.002810584 0.818199809 0.274048188 0.091373813 21770858.36 28282926.05 541121.279 0.020338889 0.039016724 1.4087492 -0.184610775 SSGGGYGGGPAGGHGGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-2;Q9H2U1;Q9H2U1-3 Q9H2U1-2 DHX36 ATP-dependent RNA helicase DHX36 0 ;; 157.58 3.36E-09 49158700 22048.1 21111.9 18998.2 22273.3 21414.9 21137.5 27678.3 24080.1 28309.5 FALSE TRUE 21005.93001 23263.22661 19869.28626 20034.34557 25149.65178 20405.50307 23455.46699 21971.51879 32699.59268 0.642391183 0.71142252 0.607631002 0.61267875 0.769112081 0.624029274 0.717301503 0.671920259 1 14.99698504 -5 0.329633134 4.319454177 0.659190254 0.810236994 0.050486516 138.147432 1.195072538 321.1798127 0.038519754 1.00E-05 5 -3.660263923 SSGHSSSELS(ph)PDAVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSGHSSSELS(1)PDAVEK;SSGHSSSELS(1)PDAVEK;SSGHSSSELS(1)PDAVEK 263.45 6.34E-27 1209882000 1207230 712780 966630 1159800 1131830 1035570 1593960 1392000 1288770 TRUE FALSE 1150166.63 785413.0924 1010950.942 1043214.701 1329220.794 999707.9512 1350772.127 1270109.101 1488625.869 0.772636466 0.527609461 0.67911687 0.700790388 0.892917973 0.671564274 0.907395306 0.853209075 1 20.50554978 1.818871429 0.511793426 0.992283621 0.638750339 0.56732785 0.091639012 0.571880927 0.341601297 0.086397275 0.059360325 65.89787786 -1.818871429 -0.353533282 SSGNS(ph)PTPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSGNSPTPVSR 11 0 H0YBT1;O95429-2;O95429 H0YBT1 BAG4 BAG family molecular chaperone regulator 4 1 SSGNS(0.982)PT(0.018)PVSR;S(0.002)S(0.012)GNS(0.978)PT(0.007)PVSR;SSGNS(0.999)PTPVSR;SSGNS(0.998)PT(0.002)PVSR 160.07 2.93E-05 260951000 508071 453201 458230 525290 429971 459580 517176 476411 503662 TRUE FALSE 484055.4907 499382.6971 479240.2988 472486.8512 504957.8063 443664.6294 438271.3026 434693.9272 581767.3306 0.832043096 0.858389034 0.823766261 0.812157759 0.867972091 0.762615235 0.753344644 0.747195493 1 19.15008276 2.237154795 24.9999063 0.789581097 0.839007365 0 0.074780565 86.03064878 1529843.666 0.023871626 0.018593852 172.6453141 -2.237154795 0.049426268 SSGNSSSSGSGSGSTSAGS(ph)SSPGARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGARR 26 1 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGST(0.001)S(0.008)AGS(0.351)S(0.351)S(0.289)PGARR;SSGNSSSSGSGSGS(0.001)T(0.003)S(0.008)AGS(0.353)S(0.353)S(0.283)PGARR 74.28 0.015841 36014000 6138.4 2024.24 4256.6 6659.1 6757.6 5096.1 8899.5 5654.3 8599.8 TRUE FALSE 5848.249997 2230.512357 4451.76932 5989.714617 7936.1233 4919.620779 7541.717824 5159.179517 9933.413062 0.588745274 0.224546422 0.4481611 0.602986565 0.798932175 0.495259862 0.759227244 0.51937632 1 13.27807379 -0.216367509 0.138691487 1.422547832 0.213147668 0.491972496 0.151460434 15.5412649 0.651667514 4.152517216 1.449411248 0.607620602 0.216367509 -1.209400164 SSGNSSSSGSGSGSTSAGSS(ph)SPGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGS(0.067)S(0.467)S(0.467)PGAR 139.47 4.34E-07 13237000 14201 14238 15011 20101 17003 16936 17757 17126 17423 TRUE FALSE 13529.74687 15688.86839 15699.2692 18080.40929 19968.31782 16349.50207 15047.84352 15626.35665 20124.86986 0.672289907 0.779576141 0.780092955 0.89841124 0.992220966 0.812402872 0.747723768 0.776469948 1 14.29669183 4.079532237 1.345256047 0.849135722 0.677287682 0.339683204 0.08554101 0.671652506 2.101124761 0.026327761 0.113280193 12009.70217 -4.079532237 -0.17184804 SSGNSSSSGSGSGSTSAGSSS(ph)PGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGSSS(1)PGAR;SSGNSSSSGSGSGSTSAGS(0.028)S(0.15)S(0.823)PGAR 326.48 1.02E-87 68206000 73452 78381 81542 114825 97404 79995 95016 74667 78315 TRUE FALSE 69980.06953 86368.11301 85280.78136 103282.5728 114391.2268 77224.75309 80519.56411 68128.76165 90459.69022 0.77360501 0.954769056 0.942748987 1.141752449 1.264554704 0.853692434 0.890115408 0.753139453 1 16.46498744 -1.592620442 7.993717208 1.00003094 0.944153694 0.011134153 0.155810927 8.78E-05 4.47E-06 0.154129246 0.036308508 0.025549333 1.592620442 -0.055877245 SSGNSSSSGSGSGSTSAGSSS(ph)PGARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGARR 26 1 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGS(0.165)S(0.165)S(0.669)PGARR 78.909 0.012288 118160000 12785 5057.5 13214 17599 17632 13114 23614 12836 24138 TRUE FALSE 12180.67839 5572.865 13819.87497 15829.91508 20707.01522 12659.85889 20011.2506 11712.01179 27881.19776 0.436877873 0.199878967 0.49567006 0.567763093 0.742687434 0.454064384 0.717732817 0.420068459 1 14.76700492 -1.555980079 0.098668398 1.848540733 1.31E-15 0.556868806 0.14579263 46.7426392 0.754754346 12.96544802 3.304221968 0.027798408 1.555980079 -1.848540733 SSGPYGGGGQYFAKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;; 328.3 1.64E-71 8197710000 3192753 2418478 2709945 3243677 3081185 3393978 4348200 3768330 3704842 FALSE TRUE 3041837.893 2664923.658 2834198.659 2917616.425 3618542.688 3276443.691 3684802.23 3438355.048 4279369.976 0.710814421 0.622737383 0.662293439 0.681786441 0.84557837 0.76563693 0.86106185 0.803472256 1 22.02896698 1.650965602 0.388179196 1.000495527 0.633671424 0.795234195 0.05060449 0.447113142 0.195806482 0.061007191 0.051132134 44.76778449 -1.650965602 -0.366824103 SSGQPS(ph)PESQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSGQPSPESQTR 12 0 C9J6N8 C9J6N8 TFAP2A 1 SSGQPS(0.999)PESQTR;SSGQPS(0.979)PES(0.019)QT(0.002)R 157.54 6.59E-05 312260000 307710 237900 256890 290780 248630 258180 313990 263130 274490 TRUE FALSE 293165.1581 262142.2805 268668.6606 261550.242 291990.9933 249239.1619 266085.0587 240088.9423 317056.5073 0.9246464 0.826799875 0.847384155 0.824932578 0.92094307 0.786103285 0.839235444 0.757243383 1 18.27438046 2.227536699 24.99974536 0.831349064 0.865278524 0.006922758 0.071566497 699.2654224 1585764.956 0.023629586 0.017611215 168.8638546 -2.227536699 0.033929461 SSGRNS(ph)PSAASTSSNDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.004)S(0.015)GRNS(0.95)PS(0.031)AASTSSNDSK;SSGRNS(0.991)PS(0.008)AASTSSNDSK;S(0.01)S(0.063)GRNS(0.925)PS(0.002)AASTSSNDSK;S(0.038)S(0.038)GRNS(0.48)PS(0.444)AASTSSNDSK 232.38 1.66E-20 787800000 566030 539110 507240 651910 346483 600560 593510 605490 378950 TRUE FALSE 539274.8837 594045.9219 530497.4557 586378.7683 406909.5255 579762.4566 502959.1489 552470.0857 437715.6306 1.232021079 1.357150352 1.21196827 1.339634062 0.929620733 1.324518514 1.149054577 1.262166683 1 18.73963438 -4.999999999 0.103049268 0.26905501 1.381026914 0.259886442 0.12180923 219.7944972 1.530655038 34.44108201 1.670544458 1.00E-05 4.999999999 1.111971904 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.01)S(0.027)GS(0.962)PY(0.001)GGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.003)GS(0.937)PYGGGYGS(0.06)GGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.102)S(0.102)GS(0.619)PY(0.176)GGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR 585.5 0 12030660000 2015662 1728254 1795555 2064226 1751698 1917702 2259893 1981826 2056496 TRUE FALSE 1920385.652 1904365.047 1877882.973 1856726.081 2057193.577 1851291.499 1915104.817 1808286.809 2375406.897 0.808444926 0.801700563 0.790552126 0.781645487 0.866038395 0.779357634 0.806221797 0.761253498 1 21.17974323 -1.073507893 4.965685349 1.000004995 0.80084616 0.839379095 0.027570848 1.36E-06 2.54E-07 0.023813923 0.005612855 0.08442909 1.073507893 -0.199158834 SSGSPYGGGYGSGGGSGGYGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 151.8 1.07E-07 39285000 8879.3 7477.5 8704.9 7403.2 7419.8 8159.9 7844.6 7447.7 8847.3 FALSE TRUE 8459.593086 8239.465751 9104.028275 6659.016271 8713.810771 7877.320617 6647.762194 6795.539905 10219.2941 0.827806011 0.806265645 0.890866648 0.651612157 0.852682258 0.770828253 0.650510899 0.664971557 1 13.31900792 3.253718081 24.95623405 0.745773491 0.8320874 0.080373738 0.108165892 465.9014623 767085.8461 0.027449993 0.037023863 1793.568968 -3.253718081 0.086313908 SSHKDS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSHKDSPR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.009)S(0.009)HKDS(0.982)PR;S(0.005)S(0.005)HKDS(0.991)PR;SSHKDS(1)PR;S(0.028)S(0.028)HKDS(0.943)PR 80.755 0.014915 530823000 1266010 1511670 1390500 1889780 1016553 1394280 1605150 2005360 754859 TRUE FALSE 1206168.216 1665710.892 1454255.8 1699815.724 1193839.521 1345995.734 1360254.887 1829760.047 871918.6784 1.383349441 1.910397074 1.667880086 1.949511768 1.369209711 1.543717054 1.560070819 2.098544386 1 19.73383406 2.727569073 24.94954438 1.551687716 1.716621414 0.100214138 0.305882417 2078.803611 4718640.447 0.090497915 0.086103122 534.0342033 -2.727569073 0.164933698 SSHSSDS(ph)GGS(ph)DVDLDPTDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSHSSDSGGSDVDLDPTDGK 20 0 P78545-2;P78545;Q5SR36 P78545-2 ELF3 ETS-related transcription factor Elf-3 2 S(0.011)S(0.012)HS(0.031)S(0.031)DS(0.936)GGS(0.979)DVDLDPTDGK;S(0.002)S(0.002)HS(0.092)S(0.436)DS(0.67)GGS(0.797)DVDLDPTDGK 108.94 0.00010128 78445000 300390 277910 277210 372910 249920 298880 340950 284380 196845 TRUE FALSE 286191.16 306229.345 289920.3527 335424.3783 293505.9689 288529.7107 288931.8155 259478.1796 227370.7173 1.258698409 1.346828425 1.275099785 1.47523121 1.290869697 1.268983597 1.270752096 1.14121195 1 17.79468694 1.055391651 1.164888801 0.999021855 1.3260438 0.759972108 0.060432273 0.22210989 0.62812762 0.053624357 0.017016505 11.3603484 -1.055391651 0.327021945 SSHYDELLAAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 258.78 6.01E-24 7744130000 4412090 3705790 4013520 4622820 5278120 4001540 5668820 4294270 3242750 FALSE TRUE 4203539.25 4083414.214 4197543.862 4158125.351 6198622.457 3862965.666 4803937.394 3918240.953 3745619.108 1.12225486 1.090184051 1.12065422 1.110130323 1.654899304 1.031329015 1.282548293 1.046086332 1 21.83677277 2.923038557 24.99999997 1.228148692 1.10903324 0.048241411 0.18549548 285.3971155 92706.1614 0.051362603 0.054478284 837.6036422 -2.923038557 -0.119115452 SSHYGGS(ph)LPNVNQIGSGLAEFQSPLHSPLDSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 S(0.002)S(0.002)HYGGS(0.906)LPNVNQIGS(0.091)GLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR 260.29 3.10E-59 828340000 229403 181526 237893 261401 311338 214623 327538 235685 142895 TRUE FALSE 218559.5748 200023.7058 248800.6294 235124.4749 365635.2486 207190.5517 277566.0625 215047.172 165054.4268 1.324166695 1.211865138 1.507385377 1.424526924 2.215240486 1.255286245 1.681663848 1.302886424 1 17.33258231 3.669387596 5.155694232 1.536378403 1.268306837 0.054701188 0.32017717 0.414623358 21.14368661 0.077395849 0.122756642 4670.760473 -3.669387596 -0.268071566 SSIIVAADESTISWGPSPTFGELGYGDHKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSIIVAADESTISWGPSPTFGELGYGDHKPK 31 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 96.44 0.00021356 188075000 286940 291540 265020 301720 178724 299690 305110 296510 169571 FALSE TRUE 273376.9149 321248.2575 277171.4291 271390.5324 209893.409 289311.6602 258559.8658 270546.0125 195867.2046 1.39572582 1.640132957 1.415098713 1.385584345 1.071610786 1.477080661 1.320077377 1.381272649 1 17.57951633 -3.916015604 0.106215054 7.37E-17 1.668486081 0.463670325 0.135774666 111.142693 1.00974446 26.50601428 1.981932945 0.000121335 3.916015604 1.668486081 SSILLDVKPWDDETDMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSILLDVKPWDDETDMAK 18 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 215.75 8.51E-19 403250000 1355900 1479600 1156400 1548100 616200 1593300 1310700 1612900 607180 FALSE TRUE 1291809.294 1630372.922 1209422.084 1392482.047 723665.0849 1538123.621 1110728.642 1471665.925 701338.3734 1.841920168 2.324659514 1.724448754 1.985463935 1.031834436 2.193126285 1.583727177 2.098367894 1 19.41975114 -2.212509901 0.205648238 1.02E-17 2.044748871 0.321497339 0.370241689 41.95869691 1.172303695 21.69044033 0.851195463 0.006130418 2.212509901 2.044748871 SSILLDVKPWDDETDMAQLEACVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSILLDVKPWDDETDMAQLEACVR 24 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;A0A087X1X7;E9PQZ1;H0YE72;H0YE58;P29692-3 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 137.89 1.10E-05 117050000 154621 128186 138300 163796 104680 149482 162857 160796 115095 FALSE TRUE 147312.3718 141248.2991 144641.1918 147330.9149 122936.1589 144305.4009 138010.1736 146715.8498 132943.3448 1.108083838 1.062469877 1.087991219 1.10822332 0.924725935 1.0854654 1.038112692 1.103596799 1 17.02045203 SSISSVLKDPDSNPYSLLDNT(ph)ESDQTADTDASESHHSTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SSISSVLKDPDS(0.016)NPY(0.001)S(0.053)LLDNT(0.422)ES(0.422)DQT(0.048)ADT(0.012)DAS(0.013)ES(0.014)HHS(0.001)T(0.001)NR 56.273 0.03274 29326000 18828 15416 18708 19478 17585 15356 23870 20676 19092 TRUE FALSE 17938.03775 16986.90793 19565.7803 17520.03443 20651.81843 14824.21787 20228.1931 18865.49983 22052.68985 0.813417224 0.770287345 0.887228743 0.794462469 0.936476166 0.672218127 0.917266476 0.855473865 1 14.42866702 0.799395337 1.05373218 0.998753408 0.816321168 0.349514544 0.075228267 0.792719212 1.662976627 0.062860585 0.020126938 6.300794817 -0.799395337 -0.18243224 SSKAS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.445)S(0.478)KAS(0.603)LGS(0.474)LEGEAEAEASSPK 122.06 1.63E-05 65142000 171820 137500 153360 157400 82556 168550 171850 157610 102420 TRUE FALSE 163698.4091 151511.4063 160391.7077 141577.853 96953.74026 162713.0712 145631.1263 143808.8329 118302.7705 1.383724222 1.28070886 1.355773047 1.196741652 0.819539051 1.375395272 1.231003514 1.215599873 1 16.85212433 8 0.204282962 1.100498413 2.523400009 0.233993525 0.154617138 82.83569799 1.013987592 0.268757184 38.00457154 100000000 -8 1.422901596 SSLDVLPSQVYSLVGSS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLDVLPSQVYSLVGSSPLR 20 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3;Q86Z02-2 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 SSLDVLPSQVYSLVGS(0.029)S(0.971)PLR 238.64 1.29E-29 35697000 168950 138120 151020 159040 162600 150830 178740 157800 183400 TRUE FALSE 160964.0683 152194.585 157944.4164 143052.997 190957.3885 145606.7193 151469.9302 143982.1954 211840.7353 0.759835298 0.718438712 0.745580949 0.675285595 0.901419589 0.687340511 0.715017959 0.679671902 1 17.69262051 -1.48255014 5.817891687 1.000258592 0.735100002 0.621046941 0.064975024 0.000197235 1.75E-05 0.056935993 0.013407016 0.032919245 1.48255014 -0.26515859 SSLFPFEDAFLDDSHGDQALSSGLS(ph)SPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALS(0.012)S(0.009)GLS(0.493)S(0.418)PT(0.069)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.492)S(0.492)PT(0.016)R 181.9 6.44E-18 99017000 45070 33003 44139 45061 41597 38745 46395 43177 37229 TRUE FALSE 42939.63042 36366.04322 46162.81681 40531.38267 48851.50363 37403.25093 39316.59065 39396.19298 43002.28318 0.998543036 0.845677032 1.07349688 0.942540248 1.13602116 0.869796861 0.914290771 0.91614189 1 15.39212564 -0.677000623 7.987515832 1 0.954614481 0.011583072 0.088997161 0 0 0.080774022 0.019038619 0.210377542 0.677000623 -0.045385519 SSLFPFEDAFLDDSHGDQALSSGLSS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALSSGLS(0.204)S(0.771)PT(0.026)R;SSLFPFEDAFLDDSHGDQALS(0.002)S(0.011)GLS(0.161)S(0.665)PT(0.161)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.031)S(0.966)PT(0.004)R;SSLFPFEDAFLDDSHGDQALS(0.001)S(0.001)GLS(0.168)S(0.662)PT(0.168)R 205.96 1.32E-25 228916000 158938 119025 141476 167724 157383 136643 172158 146529 123359 TRUE FALSE 151425.3157 131153.7828 147962.8145 150864.0649 184830.5454 131911.0186 145892.1352 133698.144 142488.8837 1.062716696 0.920449227 1.038416547 1.058777786 1.297157649 0.925763577 1.02388433 0.938305786 1 17.12048985 SSLFS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 S(0.006)S(0.017)LFS(0.976)PR;SSLFS(1)PR 83.948 0.022978 76751000 197260 183056 165547 194836 185565 166625 209375 187626 216110 TRUE FALSE 187935.9107 201709.6145 173137.4937 175250.7151 217927.4772 160854.7345 177430.9983 171196.4728 249623.2351 0.752878275 0.808056247 0.693595264 0.702060908 0.873025611 0.644390072 0.710795204 0.685819462 1 17.9293927 -1.187255206 8.266514804 1.00000005 0.737612315 0.618184321 0.065680713 5.85E-08 5.75E-09 0.061342613 0.01445859 0.064974776 1.187255206 -0.262387736 SSLGQS(ph)AS(ph)ETEEDTVSVSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 2 SSLGQS(0.999)AS(0.827)ET(0.174)EEDTVSVSKK 91.722 0.0061388 118430000 243280 201310 245660 247640 140060 274900 310470 265330 178690 TRUE FALSE 231780.6365 221823.7179 256923.754 222746.7567 164486.4197 265380.1441 263102.0993 242096.2986 206400.3326 1.122966391 1.074725584 1.244783624 1.079197664 0.796929044 1.28575444 1.274717419 1.172945293 1 17.65508577 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQS(0.002)AS(0.965)ET(0.033)EEDTVSVSKK;SSLGQSAS(0.995)ET(0.005)EEDTVSVSKK;SSLGQS(0.017)AS(0.98)ET(0.003)EEDTVSVSKK;SSLGQS(0.004)AS(0.991)ET(0.005)EEDTVSVSKK 213.39 4.83E-23 1701790000 1065502 858096 1103190 1139750 670708 1270890 1396410 1294030 836701 TRUE FALSE 1015137.832 945536.958 1153772.353 1025180.165 787679.2628 1226878.761 1183362.008 1180717.873 966452.3178 1.050375495 0.978358622 1.193822325 1.060766419 0.81502134 1.269466417 1.224439102 1.221703183 1 19.88233903 2.198081684 24.99998812 1.203046993 1.026610611 0.303784271 0.117016137 161.1639008 99534.70839 0.040725555 0.030078164 157.7908022 -2.198081684 -0.176436381 SSLGQSASET(ph)EEDTVSVSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(0.333)ET(0.667)EEDTVSVSKK 272.96 1.13E-44 270620000 387460 309250 398220 408660 237960 448380 541540 480150 276210 TRUE FALSE 369145.5337 340762.9266 416478.7809 367580.7204 279460.1487 432852.4882 458918.1269 438105.5206 319043.2361 1.157039209 1.068077577 1.305399187 1.152134503 0.875931902 1.356720467 1.43841986 1.373185421 1 18.28339242 2.131430633 20.49230942 1.341439534 1.12006533 0.215565027 0.158566261 3.291484588 615.7151643 0.05458258 0.040311928 135.3413902 -2.131430633 -0.221374204 SSLLCLQGNY(ph)AGHDWFVS(ph)S(ph)LFMIMLGDKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLLCLQGNYAGHDWFVSSLFMIMLGDKEK 30 1 Q96NH3;Q96NH3-4 Q96NH3 TBC1D32 Protein broad-minded 3 S(0.241)S(0.252)LLCLQGNY(0.508)AGHDWFVS(0.999)S(0.999)LFMIMLGDKEK 44.534 0.062256 236550000 130510 163560 120120 176440 40259 165080 102260 169650 34133 TRUE FALSE 124341.0509 180226.95 125627.6208 158703.916 47280.15685 159363.2382 86658.35887 154794.5466 39426.17131 3.153769357 4.571251632 3.186401739 4.025344351 1.199207412 4.04206731 2.197990725 3.926187643 1 15.266866 SSLLGSGDWHQYYDIVYMKPHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSLLGSGDWHQYYDIVYMKPHGR 23 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 129.85 2.38E-05 92813000 84529 86532 78075 95892 78516 95698 105840 102840 41227 FALSE TRUE 80533.48169 95349.70918 81654.81598 86252.75398 92209.16554 92383.95426 89692.16412 93834.78441 47620.2726 1.691159611 2.002292385 1.714707025 1.811261239 1.936342665 1.940013133 1.883486994 1.970479783 1 15.53928826 -1.176033373 5.084860885 0.999943797 1.869985361 0.874084545 0.103619113 6.18E-05 1.00E-05 0.093941591 0.022140825 0.066675553 1.176033373 0.870041564 SSLS(ph)GDEEDELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK;S(0.036)S(0.036)LS(0.927)GDEEDELFK 234.83 1.19E-16 352610000 1060379 1011173 962936 1135913 703191 1111112 1125400 1206650 796517 TRUE FALSE 1010256.986 1114212.678 1007087.568 1021728.867 825827.2878 1072633.913 953699.5606 1100989.329 920036.7883 1.098061511 1.211052311 1.094616629 1.110530448 0.897602464 1.165859807 1.036588507 1.19667968 1 19.81133202 3.410068501 2.870339871 1.065952234 1.154091328 0.13507218 0.087828421 0.441595378 7.363491427 0.023242102 0.034004693 2570.801243 -3.410068501 0.088139094 SSLS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSLSPGR 7 0 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 SS(0.002)LS(0.997)PGR;S(0.001)S(0.017)LS(0.983)PGR 110.38 0.0071513 1207400000 2075600 1888410 1840550 2169640 2470900 1918550 2205300 1923470 2352000 TRUE FALSE 1977490.501 2080841.126 1924941.038 1951543.665 2901824.178 1852110.132 1868840.982 1755040.77 2716736.148 0.727891998 0.765934199 0.708549132 0.718341259 1.068128821 0.681740895 0.687899332 0.646010755 1 21.37344303 -2.121483739 2.522333657 1.506154182 0.750123742 0.308443045 0.11737766 22699349.77 5110262.731 66032811.96 0.027041118 0.007559904 2.121483739 -0.756030441 SSMIT(ph)SLEGLGTDNVFSLHEDNHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.016)S(0.016)MIT(0.484)S(0.484)LEGLGTDNVFSLHEDNHYR 100.27 0.011741 29034000 11105 8452.5 10109 11788 12553 10649 14463 10718 5951.8 TRUE FALSE 10580.08866 9313.81936 10572.50765 10603.04784 14742.23923 10280.22246 12256.40372 9779.4751 6874.774746 1.53897241 1.35478175 1.537869681 1.542312037 2.144395965 1.495354079 1.782808044 1.422515713 1 12.74709673 0.95844172 8.581109001 1.000002778 1.608347095 0.465906703 0.213175952 0.787076263 161.9566556 0.205559157 0.051453651 9.08744342 -0.95844172 0.608344316 SSMITS(ph)LEGLGTDNVFSLHEDNHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.013)S(0.013)MIT(0.46)S(0.513)LEGLGTDNVFSLHEDNHYR 79.395 0.041752 16234000 4300.6 5434.8 4866.8 5500.6 7181 5939.4 7329.3 6666.1 4965.2 TRUE FALSE 4097.319161 5988.612299 5089.947594 4947.669238 8433.364126 5733.717089 6211.080673 6082.380945 5735.177857 0.714418849 1.044189465 0.887496032 0.862688021 1.470462527 0.999745297 1.082979609 1.060539201 1 12.48562251 5.556752957 0.546701168 1.092469517 1.57E-10 0.316287563 0.161947889 10.35413671 1.206746031 0.076925156 8.746475402 360373.5905 -5.556752957 -1.092469516 SSPAFGDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;; 91.087 0.017622 425617000 389971 311136 300736 316810 409700 294384 440972 342744 402232 FALSE TRUE 371537.8437 342841.1121 314525.0431 284963.6569 481151.5503 284189.4083 373693.6224 312731.5184 464608.0842 0.799680109 0.737914651 0.676968511 0.613342011 1.035607357 0.611675556 0.804320103 0.673108215 1 18.82565473 -1.16142032 3.760322493 1.00017242 0.747921811 0.299288743 0.122940372 6572379122 12757390305 14440007.22 0.026090765 0.06895721 1.16142032 -0.252250609 SSPDLTGVVTIYEDLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSPDLTGVVTIYEDLRR 17 1 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01 O60784 TOM1 Target of Myb protein 1 0 ;; 133.48 3.23E-05 63537000 135636 107926 125935 126740 120001 124475 157761 120883 142192 FALSE TRUE 129224.7551 118923.7821 131709.2443 113999.8544 140929.1364 120164.3995 133691.662 110297.8437 164242.4091 0.786792862 0.724074755 0.801919827 0.694095118 0.858055706 0.73162833 0.813989899 0.671555199 1 17.32546717 -1.126251085 4.244396257 1.000044364 0.76329536 0.634869881 0.057095854 13695832923 2819420658 6461148.648 0.011346105 0.074773707 1.126251085 -0.236749004 SSPINPAQSGSPNHVDS(ph)AYFPGSSTSSSSDNDEGSGGATNHISGNK ddPTM_SK-BR-3_Trastuzumab_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 SSPINPAQS(0.031)GS(0.117)PNHVDS(0.85)AYFPGS(0.001)S(0.001)T(0.001)SSSSDNDEGSGGATNHISGNK 193.9 1.78E-29 83633000 17786 9884.1 15090 15239 20863 13137 22944 15588 20780 TRUE FALSE 16945.29103 10891.30103 15781.89143 13707.14677 24501.50059 12682.0624 19443.4714 14223.03208 24002.45627 0.705981539 0.45375777 0.657511517 0.571072669 1.020791386 0.528365191 0.810061736 0.592565691 1 14.55089443 SSPINPAQSGSPNHVDSAYFPGS(ph)STSSSSDNDEGSGGATNHISGNK ddPTM_SK-BR-3_Trastuzumab_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 SSPINPAQSGSPNHVDS(0.002)AY(0.001)FPGS(0.3)S(0.3)T(0.3)S(0.059)S(0.015)S(0.018)S(0.005)DNDEGSGGATNHISGNK 142.59 1.31E-14 157080000 27198 20663 29496 29877 30425 28085 44378 36322 32781 TRUE FALSE 25912.40444 22768.58319 30848.42078 26873.7072 35731.11037 27112.40941 37607.32104 33141.45312 37864.51006 0.684345431 0.601317253 0.814705399 0.709733393 0.943657011 0.716037508 0.99320765 0.87526428 1 15.20855864 2.76652234 0.426773215 0.991567331 0.596500213 0.591627629 0.087768717 0.766641025 0.283344966 0.076650769 0.120564195 584.1472551 -2.76652234 -0.395067119 SSPNVANQPPS(ph)PGGK ddPTM_SK-BR-3_Trastuzumab_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 277.28 1.50E-33 1204180000 2065287 1671635 1885932 2125836 1283800 2000281 2204912 2033356 1408969 TRUE FALSE 1967664.977 1841976.507 1972403.848 1912142.926 1507694.314 1931010.767 1868512.178 1855304.569 1627464.717 1.20903695 1.131807337 1.211948762 1.174921279 0.926406759 1.186514674 1.148112251 1.1399968 1 20.63419484 -5 0.09307321 0.582884835 1.247455268 0.264535762 0.07920375 297.8025068 1.914007716 25.1256287 1.616528297 1.00E-05 5 0.664570432 SSPS(ph)PEVVKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSPSPEVVKPK 11 1 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(0.057)S(0.057)PS(0.887)PEVVKPK 87.863 0.0081196 270560000 518410 455520 452430 592170 334540 579190 633630 652330 424750 TRUE FALSE 493905.7867 501938.0059 473174.363 532643.9466 392883.6701 559132.5051 536958.1061 595208.527 490618.0607 1.006701192 1.023072826 0.964445464 1.085659068 0.800793329 1.13964925 1.094452384 1.213181036 1 18.90424082 SSPS(ph)PQKR ddPTM_SK-BR-3_Trastuzumab_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 SSPS(1)PQKR;SSPS(1)PQKR;SSPS(1)PQKR;S(0.001)S(0.001)PS(0.998)PQKR 148.32 0.00032042 669378000 1220832 1101656 1144555 1289640 743379 1238540 1356850 1309550 1080601 TRUE FALSE 1163125.691 1213915.999 1197033.979 1160002.937 873024.0622 1195649.049 1149837.612 1194878.86 1248175.084 0.931861007 0.972552661 0.959027298 0.929359151 0.699440386 0.957917735 0.921215002 0.957300682 1 20.25138889 -0.439950188 7.844463226 0.999999995 0.919310815 0.099411425 0.078846493 0 0 0.074087862 0.017462677 0.363119701 0.439950188 -0.08068918 SSPSGASS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSPSGASSPR 10 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SSPSGAS(0.001)S(0.999)PR;SSPSGAS(0.01)S(0.99)PR;SSPSGAS(0.004)S(0.996)PR;SSPSGAS(0.002)S(0.998)PR;SSPSGAS(0.013)S(0.987)PR;SSPSGAS(0.006)S(0.994)PR 166.11 5.92E-06 1244266000 3229970 2725778 2963010 3504920 2877147 3006041 3559960 3262870 3537370 TRUE FALSE 3077295.719 3003537.877 3098866.939 3152598.783 3378920.526 2901941.046 3016822.719 2977155.805 4085927.273 0.753145006 0.735093328 0.7584244 0.771574865 0.826965411 0.710228267 0.738344693 0.728636514 1 21.96223209 -1.12922976 5.389472154 1.000005043 0.751304896 0.860246115 0.03130741 1.86E-06 3.01E-07 0.029745996 0.007011056 0.074262615 1.12922976 -0.248700147 SSQCHTGS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSQCHTGSSPR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 1 SSQCHT(0.025)GS(0.866)S(0.109)PR;SSQCHT(0.025)GS(0.488)S(0.488)PR;SSQCHT(0.002)GS(0.499)S(0.499)PR 97.273 0.0041157 777424000 665340 492083 687633 660569 662308 634763 746161 767082 671382 TRUE FALSE 633890.6968 542226.8172 719161.6532 594167.3491 777814.3055 612780.9981 632320.4353 699912.2335 775496.4916 0.817399825 0.699199575 0.927356424 0.766176708 1.002988813 0.790178943 0.815374979 0.902534365 1 19.56476073 -4.999999997 0.076903365 1.574341721 0.642740167 0.303946215 0.083287591 301.9168083 1.652828937 29.85563349 3.050706681 1.00E-05 4.999999997 -0.931601554 SSQCHTGSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSQCHTGSSPR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 1 SSQCHT(0.001)GS(0.468)S(0.531)PR 101.75 0.0019634 258130000 289810 218230 263380 292700 280340 260870 356390 307300 319310 TRUE FALSE 276111.2556 240467.8851 275456.2335 263277.2399 329231.2072 251836.0065 302016.1599 280391.1829 368826.964 0.748620038 0.65198022 0.746844077 0.71382319 0.892644083 0.682802591 0.818855966 0.760224198 1 18.49258461 -4.999999999 0.155198015 1.944334087 0.671323441 0.610378977 0.064226999 80.27356204 0.72736309 23.23514771 0.265361759 1.00E-05 4.999999999 -1.273010646 SSQKS(ph)PELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSQKSPELGK 10 1 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.053)S(0.289)QKS(0.658)PELGK 53.001 0.088693 127770000 148600 138670 143790 153780 91058 152080 162760 164630 83636 TRUE FALSE 141575.9725 152800.6307 150382.9137 138321.7422 106938.4864 146813.4315 137927.9727 150214.1244 96605.84373 1.465501123 1.581691384 1.556664772 1.431815477 1.106956704 1.519715845 1.427739435 1.554917577 1 16.55982284 -2.935420387 0.354544867 2.33E-40 1.478494654 0.515814636 0.136750746 73.31587996 2.328200099 55.53339538 0.102419852 0.001160325 2.935420387 1.478494654 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SSQQPS(0.028)T(0.972)PQQAPPGQPQQGTFVAHK;SSQQPS(0.045)T(0.955)PQQAPPGQPQQGTFVAHK 192.22 2.04E-17 1133980000 660560 551950 596190 684010 493080 607770 762010 702840 555340 TRUE FALSE 629336.6379 608194.3325 623525.9012 615252.0153 579072.9959 586722.7725 645751.3792 641295.6036 641459.2909 0.981101446 0.948141747 0.972042825 0.959144289 0.902743173 0.914668757 1.006691131 0.99974482 1 19.29099818 1.651945403 8.117638612 1.002508502 0.949133317 0.549826143 0.023676063 0.101579178 12.3956908 0.012566114 0.00652077 44.86889801 -1.651945403 -0.053375185 SSQRHS(ph)PPFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSQRHSPPFSK 11 1 Q8WV28-3;Q8WV28;Q8WV28-2 Q8WV28-3 BLNK B-cell linker protein 1 SS(0.006)QRHS(0.993)PPFS(0.001)K 73.834 0.025723 135890000 227610 166120 197370 209710 193790 201480 288330 259980 215590 TRUE FALSE 216851.3264 183047.8169 206419.6097 188629.5524 227586.9146 194502.6971 244339.963 237214.773 249022.5961 0.870809837 0.735065089 0.828919194 0.757479664 0.913920737 0.78106445 0.981195951 0.952583326 1 17.92591713 1.703634799 6.178182875 0.975128773 0.811951848 0.676150754 0.053137857 0.075891974 6.743901073 0.025090512 0.012777855 50.539949 -1.703634799 -0.163176925 SSRFS(ph)GGFGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSRFSGGFGAR 11 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1 A0A0D9SFB3 DDX3X ATP-dependent RNA helicase DDX3X 1 SS(0.001)RFS(0.999)GGFGAR;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR 182.37 3.52E-06 3137650000 909394 746021 814445 973991 875030 887550 1099058 966464 1068140 TRUE FALSE 866408.7479 822041.3881 851788.1088 876083.5742 1027634.955 856813.921 931376.5165 881835.2886 1233781.696 0.70223829 0.666277828 0.690388025 0.710079893 0.832914736 0.694461527 0.754895716 0.71474175 1 20.23465572 -5 0.21830035 2.420694154 0.680745527 0.798718974 0.044397287 62.73172546 0.627080392 39.14434259 0.08214304 1.00E-05 5 -1.739948627 SSRPS(ph)MDS(ph)EGGSLLLDEDSEVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSRPSMDSEGGSLLLDEDSEVFK 23 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;H0YBP7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 2 S(0.01)S(0.011)RPS(0.958)MDS(0.626)EGGS(0.394)LLLDEDSEVFK 76.237 0.009233 11027000 23736 19179 20149 24965 15158 23813 29249 22677 15028 TRUE FALSE 22614.04632 21133.3619 21072.85158 22455.47077 17801.5504 22988.34984 24786.52786 20691.28166 17358.46549 1.302767594 1.217467173 1.213981247 1.29363225 1.025525581 1.324330763 1.427921602 1.19199947 1 14.0833518 SSRPS(ph)MDSEGGSLLLDEDSEVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSRPSMDSEGGSLLLDEDSEVFK 23 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;H0YBP7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 S(0.021)S(0.021)RPS(0.369)MDS(0.294)EGGS(0.294)LLLDEDSEVFK;SSRPS(1)MDSEGGSLLLDEDSEVFK;S(0.001)S(0.001)RPS(0.937)MDS(0.06)EGGS(0.002)LLLDEDSEVFK;S(0.04)S(0.04)RPS(0.918)MDS(0.001)EGGSLLLDEDSEVFK 264.23 3.74E-44 214986000 270657 237865 252337 300486 181055 309168 341681 320762 251459 TRUE FALSE 257863.58 262103.7139 263906.901 270280.5764 212630.9347 298461.4346 289551.288 292674.3788 290453.9774 0.887794969 0.902393268 0.908601436 0.930545275 0.732064118 1.027568764 0.996892143 1.007644589 1 18.14795006 SSRPSMDS(ph)EGGSLLLDEDSEVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSRPSMDSEGGSLLLDEDSEVFK 23 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;H0YBP7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 S(0.004)S(0.004)RPS(0.151)MDS(0.57)EGGS(0.272)LLLDEDSEVFK 154.63 5.72E-08 20330000 43237 39303 44027 48100 33566 49166 52854 49781 39556 TRUE FALSE 41193.2727 43308.02038 46045.6815 43264.89662 39419.89977 47463.36909 44790.15157 45421.91173 45690.14246 0.901578995 0.947863545 1.007781526 0.946919714 0.862765963 1.038809829 0.980302296 0.994129352 1 15.47959532 2.216875457 24.99999827 1.000706066 0.93646265 0.437317311 0.039279295 249.9881814 288200.158 0.014614576 0.010803298 164.7689814 -2.216875457 -0.064243417 SSRS(ph)SPELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.01)S(0.01)RS(0.567)S(0.412)PELTR 119.01 0.00045329 353930000 125010 63731 86902 84329 110620 103850 117460 104420 149300 TRUE FALSE 119101.025 70225.26136 90886.54266 75852.08871 129912.093 100253.6485 99539.3197 95276.43123 172452.6815 0.690630172 0.407214668 0.527023076 0.439842907 0.753320226 0.581340038 0.577197866 0.552478688 1 17.39584104 -5 0.313507732 4.991740055 0.541027266 0.639230322 0.102312733 188.4348639 1.693561834 497.4033428 0.089455842 1.00E-05 5 -4.450712789 SSRSS(ph)PELTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSRS(0.164)S(0.835)PELTR;S(0.002)S(0.002)RS(0.289)S(0.708)PELTR;S(0.001)S(0.001)RS(0.477)S(0.521)PELTR;S(0.004)S(0.004)RS(0.108)S(0.884)PELTR;S(0.006)S(0.006)RS(0.213)S(0.776)PELTR;S(0.006)S(0.006)RS(0.095)S(0.893)PELTR 162.72 4.05E-06 1942721000 526727 219735 441209 408558 499327 410412 642613 481432 680159 TRUE FALSE 501829.6586 242126.2463 461438.8691 367488.9736 586409.4707 396199.3295 544570.5845 439275.2618 785634.5839 0.638757087 0.30819194 0.587345413 0.467760688 0.746415042 0.504304848 0.693160148 0.559134324 1 19.58349891 -3.695969052 0.174542069 2.107910337 0.43537234 0.579394031 0.119197323 50.61832685 0.729472237 20.2095847 0.383612245 0.000201387 3.695969052 -1.672537998 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.094)S(0.094)S(0.811)APLIHGLSDLSQVFQPYTLR;S(0.094)S(0.094)S(0.813)APLIHGLSDLSQVFQPYTLR 345.15 6.60E-90 1732770000 547910 499270 504490 582940 563630 484990 539750 552460 557680 TRUE FALSE 522011.3802 550146.1806 527621.3655 524341.7637 661926.8935 468194.6747 457401.2243 504083.6736 644162.1662 0.810372617 0.854049197 0.819081581 0.813990314 1.027578036 0.726827341 0.710071545 0.782541571 1 19.2970644 -1.518403775 8.581308732 1.000013623 0.815069423 0.305934924 0.086015461 2.28E-05 1.28E-06 0.084636584 0.019947566 0.030310718 1.518403775 -0.1849442 SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.116)S(0.116)S(0.768)APNVHINTIEPVNIDDLIR;S(0.016)S(0.088)S(0.896)APNVHINTIEPVNIDDLIR;S(0.091)S(0.091)S(0.818)APNVHINTIEPVNIDDLIR;S(0.127)S(0.127)S(0.747)APNVHINTIEPVNIDDLIR;S(0.002)S(0.115)S(0.882)APNVHINTIEPVNIDDLIR;S(0.146)S(0.146)S(0.707)APNVHINTIEPVNIDDLIR 305.1 2.22E-56 2337017000 618869 582340 581729 665803 518865 582575 718030 671163 579811 TRUE FALSE 589616.2889 641681.1081 608401.8501 598875.2175 609354.8917 562400.2817 608481.336 612392.4097 669725.1286 0.880385495 0.958126074 0.908435154 0.894210463 0.909858188 0.839747917 0.908553838 0.914393657 1 19.35320957 0.716170145 2.836585759 0.999984472 0.902359025 0.531170699 0.029263513 1.769320077 16.61748326 0.028286886 0.007443248 5.201997568 -0.716170145 -0.097625447 SSS(ph)ASSPEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)S(0.251)S(0.747)ASSPEMK;SSS(0.997)AS(0.003)SPEMK 220.45 6.13E-09 170530000 1063510 870630 917800 1098490 726620 1034660 1155030 1014250 743980 TRUE FALSE 1013239.99 959348.1868 959882.0378 988067.6982 853342.2979 998829.4648 978808.9599 925436.8931 859352.6187 1.179073605 1.11636151 1.116982734 1.149781448 0.99300599 1.162304557 1.139007363 1.076900068 1 19.71289071 -5 0.144116378 0.586167064 1.162155287 0.387552068 0.049870402 147.0550839 1.282141989 17.5484947 0.271477458 1.00E-05 5 0.575988222 SSS(ph)EITLSECDAEDAGEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 SSS(1)EITLSECDAEDAGEPR;SSS(1)EITLSECDAEDAGEPR 507.15 1.91E-267 246850000 233139 215421 242657 236224 228342 228516 261573 249444 256811 TRUE FALSE 222118.9815 237372.6448 253783.0635 212478.3147 268164.7725 220602.4336 221665.2347 227601.361 296635.9383 0.748793227 0.800215396 0.855537144 0.716293231 0.904019837 0.743680738 0.747263585 0.767275072 1 18.17833387 -1.044385902 5.072051548 1.000003079 0.783527712 0.586245189 0.056643295 6898010.027 1420368.468 238.4480696 0.012090677 0.090284687 1.044385902 -0.216475368 SSS(ph)ENDVELLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 SS(0.012)S(0.988)ENDVELLTK 188.19 9.98E-06 63051000 190390 158050 163650 190820 143320 185310 215810 212790 171770 TRUE FALSE 181390.642 174155.4747 171153.5144 171638.4111 168314.9626 178892.6682 182884.2209 194156.9795 198407.2143 0.914234105 0.877767854 0.862637556 0.865081502 0.848330859 0.901643969 0.921761951 0.978578225 1 17.59810496 1.37987991 1.603544546 0.999871697 0.877501751 0.867698842 0.018019192 0.133120643 0.629043787 0.017690832 0.005533766 23.98169692 -1.37987991 -0.122369946 SSS(ph)ERRPATPAEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSERRPATPAEVR 14 2 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 S(0.311)S(0.231)S(0.458)ERRPATPAEVR 75.143 0.024473 127390000 106290 88672 98282 103650 111580 87696 124980 101640 116310 TRUE FALSE 101265.8823 97707.77761 102788.3269 93230.90508 131039.5167 84659.06553 105912.0056 92739.86277 134346.7608 0.753764972 0.727280487 0.765097173 0.693957223 0.975382778 0.630153381 0.78834804 0.690302187 1 17.03560201 -1.290491693 3.930453072 1.000400896 0.75313243 0.422774556 0.090688983 0.000276336 4.99E-05 0.076033646 0.017892439 0.051228107 1.290491693 -0.247268467 SSS(ph)ETILSSLAGSDIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.024)S(0.024)S(0.951)ETILSSLAGSDIVK;S(0.027)S(0.027)S(0.947)ETILSSLAGSDIVK;S(0.042)S(0.042)S(0.915)ETILSSLAGSDIVK;SS(0.002)S(0.998)ETILSSLAGSDIVK;S(0.033)S(0.033)S(0.934)ETILSSLAGSDIVK 382.49 8.03E-107 385848000 1173160 933354 1024839 1239810 879466 1125860 1266880 1096740 906389 TRUE FALSE 1117707.052 1028463.834 1071828.882 1115181.943 1032844.592 1086871.186 1073594.188 1000703.631 1046947.177 1.067586862 0.982345486 1.02376596 1.065174985 0.986529803 1.038133738 1.025452107 0.955830106 1 19.99775722 1.256290715 24.77047374 0.977915068 1.025625839 0.322032716 0.029555934 211.9430178 296104.8586 0.018212473 0.006617885 18.04225076 -1.256290715 0.047710771 SSS(ph)FSLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 SS(0.011)S(0.988)FSLPSR;SS(0.001)S(0.999)FSLPSR;SS(0.013)S(0.987)FSLPSR;SS(0.002)S(0.998)FSLPSR;SS(0.015)S(0.984)FSLPSR 238.51 5.89E-06 225600000 2490550 2402920 2374020 2762750 2503550 2497420 2910520 2689720 2895610 TRUE FALSE 2372826.637 2647780.28 2482871.165 2485033.121 2940168.327 2410933.719 2466466.719 2454193.858 3344646.41 0.709440206 0.791647294 0.742341898 0.742988291 0.879067012 0.720833662 0.73743721 0.733767806 1 21.67342227 -1.181846574 3.703247994 1.000219207 0.757100921 0.713878547 0.048309337 12059956.96 22465022.58 32782.48979 0.010961998 0.065789021 1.181846574 -0.243118286 SSS(ph)FSSWDDSSDSYWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSFSSWDDSSDSYWK 16 0 Q9NP61;Q9NP61-2 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 S(0.171)S(0.171)S(0.655)FS(0.003)S(0.001)WDDSSDSYWK 103.6 0.001496 38334000 106710 69116 92491 122500 91047 110280 133050 98671 104000 TRUE FALSE 101666.0298 76158.99898 96731.80384 110186.0673 106925.568 106460.9759 112750.7789 90030.84415 120127.7888 0.846315667 0.633983192 0.805240859 0.917240451 0.890098528 0.886231046 0.938590313 0.749458931 1 16.8742104 3.42944049 4.794811831 0.894961041 0.736740538 0.40456336 0.079921553 0.16381399 8.295118649 0.020537415 0.028651262 2688.069478 -3.42944049 -0.158220503 SSS(ph)FTLLQSLAIEDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSFTLLQSLAIEDSR 16 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.044)S(0.044)S(0.912)FTLLQSLAIEDSR;S(0.098)S(0.098)S(0.803)FTLLQSLAIEDSR;S(0.003)S(0.018)S(0.976)FT(0.003)LLQSLAIEDSR 181.86 2.35E-09 102169000 163557 127567 137254 162082 143147 133524 156517 147643 136908 TRUE FALSE 155825.9847 140566.2223 143547.2317 145789.2094 168111.7915 128900.0304 132637.457 134714.5962 158138.9934 0.985373572 0.888877685 0.907728249 0.92190551 1.063063498 0.815105924 0.838739732 0.851874628 1 17.27083362 SSS(ph)FVLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSFVLPK 8 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 SS(0.005)S(0.995)FVLPK;SS(0.035)S(0.965)FVLPK;SS(0.002)S(0.998)FVLPK;SSS(1)FVLPK;S(0.024)S(0.03)S(0.947)FVLPK;SS(0.009)S(0.991)FVLPK 124.81 0.0013521 799531000 4804140 3873890 4006630 4791950 3400220 4421560 5284510 4782750 3898250 TRUE FALSE 4577057.823 4268643.795 4190337.949 4310254.082 3993217.291 4268440.269 4478260.943 4363947.055 4502770.7 1.016498091 0.948003813 0.930613222 0.957244854 0.886835586 0.947958613 0.994556739 0.969169284 1 22.10238158 1.752760162 9.563344801 0.986030995 0.95049944 0.250857353 0.032346901 0.216762486 85.47638183 0.016260416 0.008838851 56.59266712 -1.752760162 -0.035531555 SSS(ph)KESLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.011)S(0.059)S(0.93)KESLVR;S(0.122)S(0.279)S(0.594)KES(0.005)LVR;S(0.002)S(0.041)S(0.931)KES(0.026)LVR 114.87 0.00094985 1090810000 2192640 1866150 1807610 2206250 1176010 2136510 2285710 2250450 1355550 TRUE FALSE 2088998.253 2056312.807 1890490.706 1984473.558 1381105.772 2062522.123 1936982.96 2053388.668 1565761.771 1.33417375 1.313298642 1.207393578 1.267417302 0.882066351 1.317264326 1.237086635 1.311431091 1 20.57843329 3.671071495 1.965349999 1.18227762 1.330975934 0.173419907 0.136716858 0.586794905 4.434439409 0.037846854 0.073724966 4688.905661 -3.671071495 0.148698313 SSS(ph)LDMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SSSLDMNR 8 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 SS(0.019)S(0.981)LDMNR;S(0.003)S(0.135)S(0.862)LDMNR;SS(0.02)S(0.98)LDMNR;S(0.034)S(0.119)S(0.847)LDMNR;S(0.025)S(0.125)S(0.851)LDMNR;S(0.007)S(0.011)S(0.982)LDMNR;S(0.057)S(0.093)S(0.85)LDMNR 157.34 0.00039692 1409872000 3755820 3287300 3377050 3834180 3447560 3525940 4154020 3742250 3848390 TRUE FALSE 3578289.832 3622279.607 3531891.083 3448760.942 4048813.372 3403835.814 3520247.955 3414558.751 4445178.666 0.804982229 0.814878294 0.794544235 0.775843043 0.910832539 0.765736558 0.791924964 0.768148821 1 22.08380998 -1.132114695 4.834893423 1.000012476 0.804025235 0.691806058 0.04124478 5.08E-06 9.12E-07 0.036571203 0.008619367 0.073770938 1.132114695 -0.195987241 SSS(ph)LESLQTAVAEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 SS(0.003)S(0.997)LESLQTAVAEVR;S(0.001)S(0.021)S(0.978)LESLQTAVAEVR;S(0.001)S(0.029)S(0.971)LESLQTAVAEVR;SS(0.016)S(0.984)LESLQTAVAEVR 243.83 5.61E-18 147246000 271508 255397 259165 297199 250311 244747 290189 282485 262302 TRUE FALSE 258674.3549 281422.2447 271047.9716 267323.9919 293965.1591 236271.35 245915.3384 257749.1159 302978.4545 0.853771452 0.928852334 0.894611374 0.882320138 0.970251035 0.779828884 0.811659492 0.85071764 1 18.20885568 2.233982485 24.99999628 0.838977244 0.902747744 0.064935988 0.065346325 183.0453618 999551.8615 0.021570798 0.016460427 171.3888185 -2.233982485 0.0637705 SSS(ph)LESQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSLESQGK 9 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SS(0.001)S(0.997)LES(0.002)QGK;SSS(1)LESQGK;SSS(1)LESQGK;SS(0.002)S(0.998)LESQGK;S(0.001)S(0.009)S(0.991)LESQGK;SSS(1)LESQGK 230.93 7.57E-08 1114381000 4208780 3766140 3699710 4652300 2881470 4324360 4720510 4540760 3191380 TRUE FALSE 4009839.31 4149913.948 3869345.363 4184641.965 3383997.456 4174606.329 4000309.501 4143146.982 3686282.911 1.087773078 1.125771963 1.049660446 1.13519284 0.917997218 1.132470412 1.08518787 1.123936248 1 21.81373537 0.418336969 0.007496991 4.11E-07 2.119147634 0.077053634 0.066443921 12124.38153 36.60379923 5273.916447 5070.106239 2.620215245 -0.418336969 2.119147223 SSS(ph)LGNLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSLGNLKK 9 1 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YGH8;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.005)S(0.196)S(0.799)LGNLKK;SS(0.007)S(0.993)LGNLKK;S(0.007)S(0.162)S(0.831)LGNLKK;S(0.002)S(0.168)S(0.83)LGNLKK 113.61 0.0010857 3942260000 2928210 2474640 2576480 2944570 1844950 2981240 3153060 3380420 2010230 TRUE FALSE 2789799.316 2726808.629 2694614.156 2648576.229 2166708.696 2877998.911 2672002.787 3084412.504 2321966.202 1.201481449 1.174353282 1.160488105 1.140660974 0.933135329 1.239466324 1.150750078 1.32836236 1 21.14691554 -2.297771947 2.400519403 0.152449912 1.163402096 0.216982714 0.099037666 4347811.015 1069209.579 20393177.49 0.022953742 0.005037651 2.297771947 1.010952184 SSS(ph)LIQLTSQNSSPNQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 S(0.026)S(0.026)S(0.948)LIQLTSQNSSPNQQR;SS(0.013)S(0.987)LIQLTSQNSSPNQQR 321.92 1.15E-61 160060000 145842 109952 128193 156192 143765 147759 185388 132353 148607 TRUE FALSE 138948.3377 121156.2338 134070.7759 140491.2834 168837.5705 142642.0688 157103.6557 120763.4697 171652.2146 0.80947594 0.70582389 0.781060566 0.81846473 0.983602635 0.830994631 0.915243978 0.703535751 1 17.38912894 3.089923932 3.490508695 0.881229438 0.758668162 0.291391253 0.085774435 0.269397966 6.485163024 0.023369782 0.028313983 1230.053304 -3.089923932 -0.122561276 SSS(ph)LKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.007)S(0.019)S(0.975)LKER;S(0.002)S(0.002)S(0.996)LKER;SS(0.01)S(0.989)LKER;S(0.289)S(0.289)S(0.422)LKER 106.16 0.011042 1624647000 3770110 2935610 3060870 3652460 2114690 3470470 3959170 3417790 2709310 TRUE FALSE 3591904.372 3234751.997 3201213.917 3285307.782 2483491.266 3350286.754 3355125.901 3118510.189 3129455.958 1.147772782 1.033646755 1.022929851 1.049801571 0.793585626 1.070565235 1.072111558 0.996502341 1 21.57748044 4.508479425 1.223137399 1.004188345 1.181168742 0.256988878 0.078630841 1.421387093 2.442653377 0.022756983 0.287955023 32246.26548 -4.508479425 0.176980397 SSS(ph)MAAGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 SS(0.001)S(0.999)MAAGLER;SS(0.003)S(0.997)MAAGLER;S(0.005)S(0.097)S(0.898)MAAGLER;S(0.001)S(0.061)S(0.938)MAAGLER;S(0.007)S(0.024)S(0.969)MAAGLER;S(0.026)S(0.074)S(0.9)MAAGLER;S(0.028)S(0.158)S(0.814)MAAGLER;S(0.007)S(0.03)S(0.964)MAAGLER 202.2 2.39E-07 3353420000 5346540 4935270 4643050 4919650 5336110 4811140 5991440 5709790 5625240 TRUE FALSE 5093819.65 5438179.624 4855938.435 4425117.435 6266725.895 4644529.015 5077335.788 5209810.518 6497573.489 0.78395722 0.836955462 0.747346443 0.681041537 0.964471722 0.714809771 0.781420294 0.801808633 1 22.63146962 0.776013613 5.307407927 0.999999786 0.789044698 0.432888237 0.076062091 7.132545737 168.6845148 0.066016504 0.016653164 5.97054001 -0.776013613 -0.210955088 SSS(ph)MELHREENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSMELHREENR 12 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.176)S(0.176)S(0.647)MELHREENR 112.17 0.00078876 396130000 143610 125860 145660 152940 152430 139640 169370 162550 141420 TRUE FALSE 136821.8399 138685.2771 152338.6551 137566.1806 179013.7437 134804.2318 143529.4958 148316.2603 163350.6913 0.83759572 0.849003307 0.932586534 0.842152424 1.095886049 0.82524433 0.878658637 0.907962244 1 17.31761303 7.999999999 0.020096592 1.595347609 1.43E-06 0.176002127 0.077055125 5305.213903 8.219038454 241.4893224 437.8863807 99999999.71 -7.999999999 -1.595346183 SSS(ph)MSYVDGFIGTWPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 SS(0.024)S(0.976)MSYVDGFIGTWPK;SS(0.023)S(0.977)MSYVDGFIGTWPK;S(0.117)S(0.117)S(0.766)MS(0.001)YVDGFIGTWPK 399.78 2.80E-122 268558000 813910 696540 737340 915590 691540 808090 929720 804730 684040 TRUE FALSE 775438.0873 767518.2179 771147.7683 823553.1537 812144.3571 780105.6407 787874.1385 734263.5751 790117.4296 0.981421316 0.971397654 0.975991339 1.042317411 1.027878043 0.987328733 0.997160813 0.929309426 1 19.59170756 SSS(ph)PAELDLKDDLQQTQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.03)S(0.13)S(0.84)PAELDLKDDLQQTQGK 107.21 0.000181 84342000 125270 104920 108090 131530 74460 123880 132640 146230 77174 TRUE FALSE 119348.7354 115611.4673 113046.0334 118308.3545 87445.80043 119590.0045 112403.3319 133425.326 89141.74977 1.338864625 1.296939622 1.268160359 1.327193541 0.980974691 1.341571204 1.260950477 1.496777058 1 16.44381366 3.749138965 1.479360552 1.245645637 1.3286004 0.049678128 0.152500194 1.535913259 6.491895942 0.04316205 0.105620107 5612.275285 -3.749138965 0.082954762 SSS(ph)PAGETEGDREPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPAGETEGDREPQAR 17 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.031)S(0.173)S(0.796)PAGETEGDREPQAR;SS(0.004)S(0.996)PAGETEGDREPQAR;S(0.008)S(0.087)S(0.905)PAGETEGDREPQAR;S(0.025)S(0.012)S(0.963)PAGETEGDREPQAR 235.26 2.26E-20 1453330000 616740 700600 512740 707760 454467 594640 557470 543710 451627 TRUE FALSE 587587.9225 771991.9365 536249.6362 636614.6201 533725.9009 574047.4677 472417.7129 496099.87 521663.0086 1.126374523 1.479867125 1.027961783 1.220356072 1.023123917 1.100418198 0.90559941 0.950996835 1 18.99275861 2.799572319 0.889975209 0.953372285 1.283551912 0.45373285 0.120719372 0.429355196 0.734130065 0.066710897 0.066287687 630.3363016 -2.799572319 0.330179627 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.029)S(0.182)S(0.789)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.126)S(0.15)S(0.627)PAGET(0.097)EGDREPQARPGEGTAPLPPPGQK;S(0.134)S(0.134)S(0.729)PAGET(0.003)EGDREPQARPGEGTAPLPPPGQK 166.32 6.82E-13 958700000 850020 675280 799420 866910 665420 864260 981880 925970 809110 TRUE FALSE 809841.2392 744091.7997 836074.1977 779766.5598 781469.0373 834330.4595 832076.1725 844887.1579 934582.6464 0.866527152 0.796175493 0.894596322 0.834347356 0.836169 0.892730528 0.890318449 0.904026157 1 19.83396272 0.798156718 0.477796449 1.006785233 0.835932297 0.751990411 0.027109346 0.603978786 0.316904231 0.034569293 0.014739343 6.282850384 -0.798156718 -0.170852936 SSS(ph)PAPADIAQTVQEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 SS(0.004)S(0.996)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.009)S(0.178)S(0.813)PAPADIAQTVQEDLR;S(0.047)S(0.047)S(0.906)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.109)S(0.109)S(0.782)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;SS(0.002)S(0.998)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.002)S(0.002)S(0.997)PAPADIAQTVQEDLR;SS(0.005)S(0.994)PAPADIAQTVQEDLR;S(0.001)S(0.002)S(0.997)PAPADIAQTVQEDLR 439.12 1.60E-190 1.14981E+11 27294282 23549457 23461076 26111852 26010085 25051233 29803855 26838057 27989119 TRUE FALSE 26004135.38 25949173.44 24536789.54 23487039.03 30546235.59 24183702.52 25256729.53 24487974.45 32329528.63 0.804346258 0.802646204 0.758959087 0.726488756 0.944840116 0.748037585 0.781227893 0.757449165 1 24.94634914 -1.379223176 5.226246567 1.000118786 0.791500844 0.547468031 0.059853338 7.54E-05 8.96E-06 0.052751842 0.012426674 0.041761571 1.379223176 -0.208617942 SSS(ph)PATEQSWMENDFDELREEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.008)S(0.05)S(0.942)PATEQSWMENDFDELREEGFR;S(0.103)S(0.103)S(0.793)PATEQSWMENDFDELREEGFR 236.94 1.21E-37 135227000 11740.8 12589.8 13692.2 16587 15892.1 13073.3 15457.6 14971 15392.1 TRUE FALSE 11185.83565 13872.71493 14320.00091 14919.64325 18663.67721 12620.56834 13099.25922 13660.05987 17779.02826 0.629159001 0.78028533 0.805443397 0.839170906 1.049758004 0.709857038 0.736781506 0.768324324 1 14.11788885 4.399094061 1.430317637 0.828345231 0.608222942 0.276002034 0.108030365 0.925378546 2.682354128 0.030091181 0.244934621 25066.52094 -4.399094061 -0.220122289 SSS(ph)PATEQSWMENDFDELREEGFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.103)S(0.103)S(0.793)PAT(0.001)EQSWMENDFDELREEGFRR;S(0.299)S(0.299)S(0.401)PATEQSWMENDFDELREEGFRR 265.71 1.17E-45 283250000 31864 23012 27264 25896 28724 25544 41134 28715 34636 TRUE FALSE 30357.85187 25356.94896 28514.08137 23292.88488 33733.45651 24659.40487 34858.25282 26200.56237 40007.17398 0.758810204 0.63381005 0.712724207 0.582217702 0.843185188 0.616374575 0.871300053 0.654896604 1 15.2879711 -1.158220599 0.311465257 1.172967584 0.679640234 0.478405709 0.094858937 12.91124404 0.943299849 1.982973327 0.084569304 0.069467137 1.158220599 -0.49332735 SSS(ph)PELVTHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.081)S(0.314)S(0.604)PELVTHLK;S(0.173)S(0.05)S(0.778)PELVTHLK;S(0.001)S(0.047)S(0.952)PELVTHLK;S(0.001)S(0.037)S(0.962)PELVTHLK;S(0.274)S(0.274)S(0.452)PELVTHLK 259.51 8.55E-21 10311060000 12090910 11329730 10993710 13523150 8692940 12296190 12803950 12857300 8041120 TRUE FALSE 11519396.65 12484242.37 11497782.48 12163777.27 10208985.98 11870369.86 10850472.27 11731446.65 9288095.821 1.240232322 1.344112142 1.237905239 1.309609365 1.099147358 1.278019745 1.168212783 1.263062621 1 23.14695143 -5 0.148953448 0.10987811 1.325688347 0.570407307 0.067302653 86.82476645 0.770577725 22.78864316 0.308730925 1.00E-05 5 1.215810237 SSS(ph)PELVTHLKWDDPYYDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.166)S(0.166)S(0.668)PELVTHLKWDDPYYDIAR;S(0.112)S(0.112)S(0.762)PELVT(0.014)HLKWDDPYYDIAR 265.49 3.98E-37 259100000 283340 110177 260970 165401 297770 223715 460530 294610 333040 TRUE FALSE 269947.0797 121404.1616 272935.7326 148774.5772 349700.9937 215967.6935 390267.6903 268812.3866 384686.1423 0.701733309 0.31559276 0.709502378 0.386742752 0.909055345 0.56141272 1.014509356 0.69878365 1 18.55332233 2.306540045 0.929416504 0.908684935 0.515906101 0.366801609 0.187147787 0.525018631 0.87557969 0.120682583 0.073001366 202.5536368 -2.306540045 -0.392778834 SSS(ph)PGKLLGSGYGGLTGGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPGKLLGSGYGGLTGGSSR 21 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.002)S(0.022)S(0.975)PGKLLGSGYGGLTGGSSR;S(0.063)S(0.063)S(0.873)PGKLLGSGYGGLTGGSSR 120.79 1.86E-05 488430000 255260 138489 289880 206823 195064 249446 380860 295560 289090 TRUE FALSE 243194.3657 152601.1865 303171.2847 186032.7591 229083.0998 240807.6225 322752.812 269679.1995 333920.6007 0.728299977 0.456998419 0.907914289 0.557116748 0.686040632 0.72115234 0.966555556 0.807614741 1 18.34914558 1.897301159 3.408746457 0.917396874 0.651897002 0.46575779 0.125506059 0.203331159 4.074521204 0.05893704 0.032282712 78.94073382 -1.897301159 -0.265499872 SSS(ph)PHDKNLPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.004)S(0.104)S(0.892)PHDKNLPQK 149.35 4.07E-05 110990000 186370 110200 178970 182930 138730 189910 244630 213800 157640 TRUE FALSE 177560.6594 121429.5053 187175.9515 164541.5289 162924.4681 183333.3691 207307.2006 195078.5386 182086.0061 0.975147203 0.666879943 1.027953523 0.903647306 0.894766553 1.006850406 1.138512536 1.071353822 1 17.47426053 2.137460215 2.856673914 1.084233537 0.874402778 0.394743566 0.099099988 0.228986721 3.737056074 0.043196251 0.028744046 137.2335239 -2.137460215 -0.209830759 SSS(ph)PIPLTPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SS(0.012)S(0.988)PIPLTPSK 171.92 1.46E-05 152400000 439800 370110 363760 453260 340110 413130 480980 432970 367950 TRUE FALSE 419011.5256 407824.6298 380438.7558 407697.4437 399425.0763 398823.2045 407597.6672 395056.8515 425009.8068 0.985886723 0.959565222 0.895129359 0.959265968 0.939802023 0.938385887 0.959031205 0.929524084 1 18.69713661 -1.646799123 5.954901617 1.000405217 0.948599853 0.331457253 0.023892897 0.000129469 7.68E-06 0.023301669 0.005449456 0.022552821 1.646799123 -0.051805364 SSS(ph)PPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSPPPR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SS(0.01)S(0.989)PPPR;SS(0.004)S(0.996)PPPR;S(0.001)S(0.03)S(0.969)PPPR;S(0.042)S(0.042)S(0.917)PPPR;SS(0.01)S(0.989)PPPR;S(0.005)S(0.22)S(0.774)PPPR 122.18 0.0045797 2630276000 3441240 3048300 2891470 3563550 2840010 3069350 3285150 3429410 3335140 TRUE FALSE 3278579.405 3358925.236 3024046.76 3205335.184 3335306.845 2963057.64 2783940.032 3129112.68 3852336.478 0.851062576 0.871918965 0.784990298 0.832049641 0.865788039 0.769158576 0.722662739 0.812263596 1 21.87730229 2.239563814 24.99908302 0.793106491 0.843288661 0 0.077186004 64.81665523 1615238.789 0.025244904 0.020008128 173.6056337 -2.239563814 0.050182171 SSS(ph)PPPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.3)S(0.3)S(0.4)PPPRK;S(0.293)S(0.293)S(0.414)PPPRK;S(0.293)S(0.293)S(0.414)PPPRK;S(0.3)S(0.3)S(0.4)PPPRK;S(0.301)S(0.301)S(0.399)PPPRK 78.934 0.017971 5464930000 4932670 4240410 4204090 4930020 3136640 4339810 5171510 5248770 4450140 TRUE FALSE 4699512.465 4672512.6 4396851.685 4434445.023 3683669.023 4189521.292 4382501.168 4789159.873 5140244.983 0.91425846 0.909005819 0.855377847 0.862691377 0.716632969 0.815043117 0.85258605 0.931698759 1 22.29340569 1.041484765 3.067477402 0.998956225 0.851959639 0.472677216 0.054779938 0.23392961 4.813584723 0.058025317 0.015312631 11.0023325 -1.041484765 -0.146996586 SSS(ph)PQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSPQPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)S(0.069)S(0.929)PQPK;S(0.001)S(0.025)S(0.974)PQPK;S(0.001)S(0.022)S(0.977)PQPK;SS(0.019)S(0.98)PQPK;S(0.002)S(0.02)S(0.978)PQPK 78.149 0.037887 418515000 1722240 1786220 2033830 2887130 1460730 1862730 2688770 3730670 2161920 TRUE FALSE 1640833.128 1968237.849 2127083.117 2596910.207 1715480.85 1798223.193 2278548.754 3403992.757 2497179.512 0.65707456 0.788184365 0.851794237 1.039937335 0.686967373 0.720101692 0.912448922 1.363134985 1 21.2518681 1.428695269 5.152379103 1.178887872 0.790627318 0.578134241 0.136087793 0.13187217 6.33935802 0.087765009 0.032963626 26.83460882 -1.428695269 -0.388260554 SSS(ph)PTLTPSQEGSPVFAGFEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.111)S(0.111)S(0.777)PT(0.001)LTPSQEGSPVFAGFEGR;S(0.114)S(0.114)S(0.772)PTLTPSQEGSPVFAGFEGR;S(0.014)S(0.014)S(0.971)PTLTPSQEGSPVFAGFEGR;S(0.115)S(0.115)S(0.768)PT(0.001)LTPSQEGSPVFAGFEGR 277.1 1.80E-45 239359000 250624 215903 220307 268086 218956 214108 253274 226013 247302 TRUE FALSE 238777.5002 237903.7612 230408.2939 241137.4859 257141.8571 206693.3863 214632.3996 206222.1035 285652.3311 0.835902509 0.832843759 0.806603933 0.84416425 0.900191698 0.723583755 0.751376328 0.721933907 1 18.12390078 2.233216999 24.99923918 0.773636772 0.840010132 0.027529466 0.082823525 249.9348198 1169265.728 0.026824377 0.020391134 171.0869954 -2.233216999 0.06637336 SSS(ph)PTQYGLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPTQYGLTK 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 SSS(0.997)PT(0.003)QYGLTK;SS(0.002)S(0.998)PTQYGLTK 246.31 5.48E-16 178927000 757780 660720 676250 795450 590250 761820 876520 836610 666190 TRUE FALSE 721961.2412 728048.1192 707256.7314 715489.8547 693189.4131 735437.9824 742790.7756 763351.9933 769499.3428 0.938222037 0.946132217 0.919112847 0.929812171 0.900831716 0.955735686 0.965290981 0.992011235 1 19.55356057 1.580310116 1.682255801 0.997318271 0.930690192 0.801347597 0.013667878 0.157411865 0.889910335 0.01157984 0.004042469 38.04609747 -1.580310116 -0.066628078 SSS(ph)PTSYWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SS(0.011)S(0.988)PT(0.001)SYWK;SS(0.01)S(0.989)PTSYWK;SS(0.004)S(0.994)PT(0.002)SYWK;SS(0.019)S(0.98)PT(0.001)SYWK 181.87 4.93E-05 2635860000 8233300 8106200 6191700 8422300 5199100 7447200 7672000 7797200 5238950 TRUE FALSE 7844128.226 8932230.996 6475595.569 7575674.403 6105821.394 7189301.597 6501495.494 7114435.832 6051379.609 1.296254529 1.476065224 1.070102355 1.251892113 1.008996591 1.188043399 1.074382358 1.175671713 1 22.52883266 3.732930961 24.97652854 1.116775967 1.38615988 0.621222793 0.089566088 230.9993429 1024852.498 0.020821579 0.033252211 5406.683665 -3.732930961 0.269383913 SSS(ph)PVGLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.001)S(0.002)S(0.997)PVGLAK;SS(0.001)S(0.999)PVGLAK;SS(0.001)S(0.998)PVGLAK;SS(0.001)S(0.999)PVGLAK;S(0.002)S(0.077)S(0.921)PVGLAK;S(0.001)S(0.014)S(0.985)PVGLAK 190.57 3.87E-05 3824730000 13229630 11668460 11847290 13819840 9268990 13355930 15049500 14403440 10991210 TRUE FALSE 12604291.61 12857489.34 12390499.97 12430643.43 10885498.92 12893410.8 12753422.37 13142198.44 12695670.71 0.992802341 1.012745969 0.975962613 0.979124594 0.857418184 1.015575395 1.004548926 1.035171653 1 23.59783328 SSS(ph)PVQVEEEPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSPVQVEEEPVR 13 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 SS(0.032)S(0.968)PVQVEEEPVR;SS(0.001)S(0.999)PVQVEEEPVR 303.02 4.58E-41 1100080000 654390 573580 609230 665510 610260 572910 683460 615300 708010 TRUE FALSE 623458.2816 632028.4541 637163.7981 598611.6704 716689.1508 553069.983 579185.6244 561421.0701 817804.5748 0.76235607 0.772835557 0.779114984 0.731973981 0.876357473 0.676286243 0.708220084 0.686497835 1 19.64139661 -1.089532356 4.893598367 1.000008763 0.749904764 0.658260232 0.056787745 5.28E-06 9.82E-07 0.053469349 0.012602405 0.081370624 1.089532356 -0.250103999 SSS(ph)PVTELAS(ph)RSPIRQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.268)S(0.328)S(0.404)PVTELAS(0.601)RS(0.399)PIRQDR 95.209 0.00097647 546630000 99906 77219 100320 107340 98239 107140 122860 110350 117110 TRUE FALSE 95183.64137 85087.70389 104919.7712 96549.97927 115371.8505 103429.7149 104115.4505 100687.169 135270.8207 0.703652428 0.629017429 0.77562752 0.713753186 0.852895324 0.764612164 0.769681517 0.744337681 1 17.04549114 -5 0.114693443 1.844183364 0.596505443 0.711779382 0.053047398 82.1891931 0.619532107 16.23179249 0.567637697 1.00E-05 5 -1.247677921 SSS(ph)PVTELASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.001)S(0.999)PVTELASR;SS(0.002)S(0.998)PVTELASR;SS(0.001)S(0.998)PVTELASR;SSS(1)PVTELASR 321.08 4.72E-46 2625940000 3506580 3941320 2993430 3917360 2870960 3222760 3287450 3583700 2812280 TRUE FALSE 3340830.913 4342944.989 3130681.726 3523579.53 3371654.515 3111155.013 2785889.124 3269892.23 3248394.019 1.028456183 1.336951418 0.963762926 1.084714326 1.037945057 0.957751737 0.857620445 1.006618104 1 21.63129521 2.963318764 1.050589933 0.937348628 1.165208813 0.308989609 0.102951303 0.456909393 1.085405918 0.046946821 0.055011896 919.0068838 -2.963318764 0.227860185 SSS(ph)PVTELASRS(ph)PIRQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.262)S(0.327)S(0.411)PVTELAS(0.287)RS(0.713)PIRQDR 119.52 3.83E-05 196760000 92716 73013 105640 108380 92847 89027 108490 97339 110070 TRUE FALSE 88333.49843 80453.10771 110483.6985 97485.43649 109039.4874 85943.97267 91937.85794 88815.48113 127139.0934 0.69477842 0.632795984 0.868998634 0.766762086 0.857639334 0.675983841 0.723128154 0.698569407 1 16.95604818 -2.443352266 2.231580023 3.613653173 0.732197458 0.537844582 0.075497499 3925880.46 317142.3115 52027337.96 0.018706572 0.003602863 2.443352266 -2.881455714 SSS(ph)QGPLSSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSQGPLSSIR 11 0 A0A0U1RQE4 A0A0U1RQE4 1 S(0.001)S(0.022)S(0.977)QGPLSSIR;S(0.003)S(0.179)S(0.818)QGPLSSIR;SS(0.007)S(0.993)QGPLSSIR;SS(0.004)S(0.996)QGPLSSIR 188.96 3.06E-06 493377000 1075260 813400 776190 857520 933850 793290 1063140 950950 1054580 TRUE FALSE 1024434.591 896286.3848 811779.0793 771320.4604 1096713.144 765818.1684 900938.4671 867679.7767 1218118.88 0.840997219 0.735795495 0.666420242 0.633206227 0.900333426 0.628689187 0.739614566 0.712311245 1 20.21622351 -1.787413577 4.414165747 1.030559718 0.734819829 0.493185443 0.085288079 0.024323348 0.001171413 0.078308632 0.018145303 0.016314975 1.787413577 -0.295739889 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.107)S(0.107)S(0.785)QIPEGFGLTSGGSNYSLAR;S(0.024)S(0.024)S(0.951)QIPEGFGLTSGGSNYSLAR;S(0.113)S(0.113)S(0.774)QIPEGFGLTSGGSNYSLAR 204.17 1.26E-22 245191000 155105 145296 159884 173122 167134 167589 199204 181788 201322 TRUE FALSE 147773.494 160101.8276 167214.8395 155719.4476 196282.1167 161785.3509 168811.7712 165869.679 232541.9875 0.63547016 0.688485676 0.719073752 0.669640134 0.844071726 0.695725329 0.725941035 0.71328916 1 17.82713171 -5 0.201028313 2.324893333 0.660826683 0.760444954 0.051632961 65.65321075 0.650001695 34.98361329 0.116086724 1.00E-05 5 -1.66406665 SSS(ph)QPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.014)S(0.056)S(0.713)QPS(0.008)S(0.06)CCS(0.146)DPS(0.003)KPGGNVEGATQSLAEQMR;S(0.001)S(0.009)S(0.99)QPSSCCSDPSKPGGNVEGATQSLAEQMR 249.53 7.66E-47 757200000 573950 547010 532360 698530 404160 604010 630890 611410 406590 TRUE FALSE 546820.521 602750.9409 556769.2326 628312.4373 474645.376 583092.9822 534636.1434 557871.6991 469641.9006 1.16433504 1.283426671 1.185518651 1.337854302 1.01065381 1.241569335 1.138391065 1.187866113 1 18.8412016 -1.171199793 0.237029329 0.849749517 1.240364908 0.352148263 0.085688407 18.3958236 0.939149827 1.896015367 0.144804669 0.067421779 1.171199793 0.390615391 SSS(ph)SPELQTLQDILGDPGDKADVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.15)S(0.15)S(0.677)S(0.023)PELQTLQDILGDPGDKADVGR 97.639 0.0050036 98346000 66642 64424 73486 86164 54115 90269 95570 92784 68771 TRUE FALSE 63491.96473 70988.87884 76855.40579 77502.63102 63552.63887 87142.9619 80989.04124 84659.34108 79435.65545 0.799287982 0.893665174 0.967517739 0.975665532 0.800051797 1.09702578 1.019555271 1.065759961 1 16.2774991 4.545651325 0.340020312 1.049153008 0.639305755 0.468125725 0.073402569 4.63262335 0.477668145 0.07035051 0.779479472 35127.83018 -4.545651325 -0.409847253 SSS(ph)TEPPPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SS(0.004)S(0.981)T(0.015)EPPPPVR 103.89 0.0028044 111330000 213700 191650 180630 216720 164350 196350 190390 190700 181630 TRUE FALSE 203598.8245 211179.3529 188912.0642 194934.8939 193012.588 189550.3503 161342.5087 174001.297 209796.2528 0.970459776 1.006592587 0.900454902 0.929162896 0.920000169 0.903497311 0.769043806 0.829382292 1 17.67862938 2.919006472 0.915868049 0.849721047 0.98467022 0.224152296 0.064251396 0.551858406 1.012567272 0.033206781 0.037599084 829.8631351 -2.919006472 0.134949173 SSS(ph)TGNLLDKDDLAIPPPDYGAASR ddPTM_SK-BR-3_Trastuzumab_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(0.099)S(0.099)S(0.786)T(0.015)GNLLDKDDLAIPPPDYGAASR;S(0.26)S(0.26)S(0.474)T(0.006)GNLLDKDDLAIPPPDYGAASR;S(0.097)S(0.097)S(0.802)T(0.003)GNLLDKDDLAIPPPDYGAASR 184.44 1.14E-17 487587000 674180 716600 669460 751540 449010 741660 825110 893760 573370 TRUE FALSE 642312.8475 789622.3547 700155.4032 675993.7714 527317.2018 715976.1282 699224.3153 815497.6363 662285.2912 0.969843142 1.192269201 1.057180965 1.020698754 0.796208536 1.081069046 1.055775094 1.231338891 1 19.33709329 -0.522363603 7.1616756 0.999999318 1.051799287 0.017626973 0.118264506 0 0 0.110232839 0.025982129 0.300356059 0.522363603 0.051799969 SSS(ph)TSDILEPFTVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.002)S(0.997)T(0.002)SDILEPFTVER;SSS(0.99)T(0.01)SDILEPFTVER;SSS(1)TSDILEPFTVER;SSS(0.725)T(0.271)S(0.003)DILEPFTVER;SSS(0.959)T(0.041)SDILEPFTVER;SSS(0.98)T(0.018)S(0.001)DILEPFTVER;SS(0.024)S(0.92)T(0.055)SDILEPFTVER;S(0.026)S(0.026)S(0.942)T(0.005)SDILEPFTVER 342.32 1.52E-69 2001730000 3692902 3259349 3479765 4074865 3585075 3694674 4331709 3779767 3942310 TRUE FALSE 3518345.841 3591480.369 3639315.667 3665251.828 4210310.945 3566726.513 3670827.235 3448790.564 4553663.3 0.772640753 0.788701345 0.79920614 0.804901809 0.924598651 0.783265314 0.806126187 0.757366177 1 22.11859619 -2.218641282 2.453559634 1.674463531 0.80390902 0.648474038 0.045209861 7619885.912 1017042.951 28744855.69 0.010966389 0.006044477 2.218641282 -0.870554511 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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(0.007)S(0.993)VGS(0.997)S(0.003)SSYPISPAVSR;S(0.07)S(0.099)S(0.831)VGS(0.97)S(0.029)S(0.001)SYPISPAVSR 302.9 1.52E-49 475550000 746800 639450 760550 936720 796070 921290 1065920 847070 1006910 TRUE FALSE 711500.244 704610.682 795421.9698 842559.1259 934904.356 889385.4963 903294.327 772896.0602 1163056.46 0.611750391 0.605826721 0.683906583 0.724435274 0.803834025 0.764696751 0.776655612 0.664538728 1 20.1494897 -5 0.045536716 2.264401018 0.020101315 0.75200372 0.056803142 301.0363932 1.018269251 48.84077098 12.46777665 1.00E-05 5 -2.244299703 SSS(ph)VGSSSSYPISPAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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(0.999)VGS(0.001)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.996)VGS(0.004)SSSYPISPAVSR;SS(0.002)S(0.998)VGSSSSYPISPAVSR;SS(0.002)S(0.998)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.981)VGS(0.019)SSSYPISPAVSR;SS(0.005)S(0.995)VGSSSSYPISPAVSR 444.34 1.14E-190 21547110000 7026210 6147650 6539060 7384070 7013700 7538850 9289140 8185510 8803860 TRUE FALSE 6694094.978 6774102.524 6838882.369 6641809.255 8236887.059 7277777.734 7871911.086 7468743.35 10169117.64 0.658276874 0.666144572 0.672514825 0.653135256 0.80999034 0.715674456 0.774099717 0.734453432 1 23.27769117 -5 0.136944501 2.033790321 0.592696383 0.85876389 0.039306338 44.22126862 0.374434012 12.40242559 0.233749498 1.00E-05 5 -1.441093938 SSSAS(ph)SPEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)S(0.001)S(0.003)AS(0.577)S(0.419)PEMK 58.981 0.093943 0 165240 158640 148980 178470 97417 184500 189670 202320 128310 TRUE FALSE 157429.4327 174805.5964 155810.8804 160529.8565 114406.494 178110.7187 160732.358 184603.7882 148207.6595 1.062221974 1.179463983 1.051301133 1.083141432 0.771933747 1.201764601 1.084507768 1.245575221 1 17.17726048 -0.195087609 7.340594169 1.000005183 1.086746059 0.041415361 0.128251121 0 0 0.11541585 0.027203777 0.638134745 0.195087609 0.086740875 SSSGLLEWESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSGLLEWESK 11 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 182.28 1.36E-05 345966000 761650 672360 640056 771080 519081 725540 771150 784120 572376 FALSE TRUE 725648.3139 740874.2484 669403.2007 693569.5734 609608.5621 700414.3679 653496.9044 715458.2959 661137.1468 1.097576074 1.120605992 1.012502782 1.04905552 0.922060672 1.059408583 0.988443786 1.082163208 1 19.33459005 3.734916197 24.47639132 1.014317004 1.109091036 0.433459189 0.04409237 172.0147761 1155276.179 0.010378867 0.016814278 5431.45514 -3.734916197 0.094774033 GINESYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 GINESYKK 8 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2;E9PIA8 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 107.15 0.0065062 523650000 858890 692050 1028500 1329400 1193600 1404500 1820800 1630700 1492900 FALSE TRUE 818291.9719 762570.6818 1075657.742 1195766.186 1401763.462 1355861.813 1543003.519 1487907.263 1724411.307 0.474534102 0.442220878 0.623782585 0.693434438 0.812893917 0.786275181 0.894800163 0.862849401 1 20.7176725 3.075148206 0.543622843 0.948508336 0.382443054 0.937389213 0.04479183 0.207846178 0.128367841 0.033877193 0.057700633 1188.907881 -3.075148206 -0.566065282 down SSSISEEKGDS(ph)DDEKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SSSISEEKGDSDDEKPR 17 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;S(0.006)S(0.006)S(0.005)IS(0.005)EEKGDS(0.978)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR 249.32 2.71E-21 15235840000 10379880 9533370 8958950 10722500 4164530 11701130 10688050 12175960 4276720 TRUE FALSE 9889243.643 10504831.24 9369726.719 9644653.929 4890822.713 11295916.93 9057391.673 11109768.39 4939931.895 2.001898782 2.126513374 1.896731963 1.952386011 0.990058733 2.286654386 1.833505373 2.248971976 1 22.23605972 3.324945344 2.651851245 1.766266008 2.055006521 0.091802791 0.439413118 0.709889022 10.1323979 0.120385006 0.169081252 2113.223075 -3.324945344 0.288740513 SSSQRS(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Trastuzumab_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(0.367)S(0.376)S(0.387)QRS(0.395)PS(0.36)PGPNHT(0.041)S(0.041)NS(0.016)S(0.016)NASNATVVPQNSSAR 100.81 5.30E-05 117560000 35464 22782 38120 40203 64661 33855 61046 52534 84145 TRUE FALSE 33787.687 25103.5117 39867.83971 36161.71806 75937.85793 32682.59286 51732.31151 47933.84446 97193.77685 0.347632205 0.258283118 0.410189222 0.372057957 0.781303705 0.336262196 0.532259505 0.493178123 1 16.56857632 -5 0.128610019 2.931931859 0.17740891 0.66886903 0.130517516 80.86994108 0.658718976 40.21589863 0.954457425 1.00E-05 5 -2.754522949 SSSQRSPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Trastuzumab_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(0.176)S(0.176)S(0.176)QRS(0.176)PS(0.288)PGPNHT(0.001)S(0.001)NS(0.001)S(0.001)NASNATVVPQNSSAR 110.7 4.35E-06 72068000 25100 15699 30285 20887 54135 21890 46885 28430 68832 TRUE FALSE 23913.57274 17298.74595 31673.59721 18787.39908 63576.12686 21131.94381 39731.83215 25940.51848 79506.11501 0.300776522 0.217577553 0.398379385 0.236301309 0.799638202 0.26579017 0.499733035 0.326270734 1 16.27877821 -5 0.174184208 3.475765507 0.230893417 0.575705882 0.168336355 87.98391933 0.837472009 75.39823664 0.51416901 1.00E-05 5 -3.244872091 SSSQSTFHIPLS(ph)PVEVKPGNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSQSTFHIPLSPVEVKPGNVR 22 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR 94.73 0.0010414 120829000 250130 175847 216820 242580 209810 189622 257660 250600 212980 TRUE FALSE 238306.8506 193766.0092 226761.4115 218195.3975 246400.7976 183055.3426 218349.2347 228656.1355 246007.8506 0.968696121 0.787641568 0.921764939 0.886944855 1.001597294 0.744103662 0.88757019 0.929466823 1 17.90834483 0.971591346 3.189813354 0.99938456 0.880142572 0.189785573 0.075637632 0.374343709 9.619915846 0.066450552 0.017362568 9.36680213 -0.971591346 -0.119241988 SSSS(ph)PPPKQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSPPPKQK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSS(0.016)S(0.983)PPPKQK 107.09 0.0014112 152330000 162810 97219 169530 139120 104130 164000 225960 201410 160780 TRUE FALSE 155114.294 107125.7266 177303.1182 125135.3933 122290.239 158320.6389 191485.652 183773.4727 185712.9412 0.83523686 0.576835012 0.95471601 0.673810842 0.65849067 0.852501919 1.031084052 0.989556632 1 17.50271483 1.94527872 3.635168647 1.004787667 0.733375512 0.582839729 0.102715979 0.157545506 3.949367227 0.046483497 0.026836946 88.16144909 -1.94527872 -0.271412155 SSSSESSHSSSSHSHGKT(ph)TPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSESSHSSSSHSHGKTTPTK 22 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 SSSSESSHSSSSHSHGKT(0.458)T(0.458)PT(0.085)K 99.059 0.00059051 17141000 8099.9 3929.5 5735.7 7759.6 13808 6567.1 18169 20071 2831.7 TRUE FALSE 7717.033779 4329.920517 5998.687518 6979.590266 16216.11083 6339.67968 15396.98535 18313.47684 3270.825574 2.359353504 1.323800496 1.833997987 2.133892532 4.957803607 1.938250615 4.707369747 5.599038048 1 11.67543911 2.885909805 6.510201759 3.789054904 1.824815049 0.276206888 1.383895972 0.270040804 13.68079034 0.383943657 0.408635922 768.9707227 -2.885909805 -1.964239855 SSSSGDQSSDSLNS(ph)PTLLAL ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSGDQSSDSLNSPTLLAL 20 0 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 SSSSGDQS(0.004)S(0.016)DS(0.013)LNS(0.797)PT(0.17)LLAL 59.9 0.065924 10391000 32083 25426 29634 30864 28336 25980 33102 27453 29683 TRUE FALSE 30566.50017 28016.93831 30992.74821 27761.49208 33277.78943 25080.30609 28051.68194 25049.06978 34286.08804 0.891513203 0.817151793 0.903945302 0.809701359 0.970591611 0.731500953 0.818165138 0.730589904 1 15.06533569 2.222104064 24.99956242 0.80370942 0.869401771 0.08308931 0.086612337 479.0450506 727724.9546 0.028100496 0.020811464 166.764676 -2.222104064 0.065692351 SSSSPELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_SK-BR-3_Trastuzumab_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 1 SSSSPELQTLQDILGDPGDKADVGRLS(1)PEVK 98.342 0.00015418 37994000 19459 16434 17796 18398 9908.5 21053 22397 22089 9427.7 TRUE FALSE 18539.21163 18108.64328 18611.9642 16548.59809 11636.53926 20323.92933 18979.9263 20154.77006 10889.69957 1.702453913 1.662914865 1.709134774 1.519656074 1.068582213 1.866344357 1.742924696 1.850810478 1 13.41067653 -1.918844059 2.632096434 0.605760248 1.644897719 0.443778283 0.225249675 7116352.018 4556567.726 17324742.25 0.053459996 0.012054687 1.918844059 1.039137471 SSSSS(ph)QESLNRPFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSSQESLNRPFSSK 16 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.019)S(0.077)S(0.068)S(0.375)S(0.44)QES(0.021)LNRPFSSK 52.185 0.097998 250570000 63695 49478 59087 63094 54481 66627 71277 75621 58153 TRUE FALSE 60684.26358 54519.86445 61796.1974 56751.67125 63982.46915 64319.69028 60402.38456 68999.22435 67171.07024 0.903428565 0.811656927 0.919982325 0.844882641 0.952530143 0.957550476 0.89923213 1.027216391 1 16.0355524 2.044697729 0.564884409 1.003357244 0.85735522 0.544342219 0.044036387 0.601962904 0.396005055 0.038772841 0.026932594 110.8403094 -2.044697729 -0.146002024 SSSSSASPS(ph)SPSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSS(0.001)AS(0.124)PS(0.495)S(0.379)PSSR 89.231 0.0065365 20473000 25314 31716 26451 33387 24875 31291 33854 32279 28224 TRUE FALSE 24117.45739 34947.89646 27663.80451 30030.87533 29213.19212 30207.38482 28688.95053 29452.47964 32600.83377 0.739780386 1.071993947 0.848561258 0.921168935 0.89608727 0.926583198 0.88000665 0.90342719 1 14.99262124 SSSSSASPSS(ph)PSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPS(0.02)S(0.979)PSSR;SSSSSASPSS(0.974)PS(0.025)SR;SSSSSASPS(0.028)S(0.961)PS(0.011)SR;SSSSSASPSS(1)PSSR;SSSSSASPS(0.01)S(0.988)PS(0.001)SR 335.79 1.39E-68 2061138000 1186330 1249390 1206410 1428290 1096350 1284790 1387390 1309140 1249020 TRUE FALSE 1130254.532 1376704.261 1261725.092 1284715.576 1287553.093 1240297.4 1175718.174 1194504.761 1442711.642 0.783423727 0.954247696 0.874551126 0.890486732 0.892453526 0.859698753 0.81493636 0.82795808 1 20.46035154 2.118825874 6.844683768 0.854811025 0.880826531 0 0.065439549 0.887131868 49.65275284 0.022810809 0.016800771 131.469761 -2.118825874 0.026015506 SSSSSASPSS(ph)PSSREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSSSASPSSPSSREEK 17 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSS(0.001)ASPS(0.011)S(0.954)PS(0.023)S(0.011)REEK;SSSSSASPS(0.044)S(0.953)PS(0.002)S(0.001)REEK 116.73 0.00015261 443280000 206673 91317 222124 148937 170723 222144 297100 226977 239510 TRUE FALSE 196903.9769 100622.3061 232308.6051 133965.5698 200497.0371 214451.0976 251771.9384 207101.6906 276651.9876 0.711738884 0.36371438 0.83971421 0.484238595 0.724726538 0.775165577 0.91006734 0.748600046 1 18.07771276 2.14235711 0.74578395 0.936766055 0.563244202 0.437648536 0.140217078 0.541361454 0.571746353 0.108728786 0.063397421 138.7896593 -2.14235711 -0.373521853 SSSSSGVPYS(ph)PAIPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;SSSSSGVPYS(1)PAIPNK;SSSSS(0.002)GVPYS(0.998)PAIPNK 289.13 1.84E-45 627751000 1270280 1046150 1156660 1299950 866980 1191770 1375560 1319410 1028660 TRUE FALSE 1210236.382 1152753.874 1209694.005 1169276.556 1018181.038 1150498.706 1165693.058 1203875.466 1188179.339 1.018563732 0.970185086 1.018107255 0.984090968 0.856925385 0.968287083 0.981075011 1.013210234 1 20.18032118 1.383846748 4.052304361 1.006219273 0.97160199 0.102865266 0.044460929 0.594996903 15.54679215 0.033901972 0.011611836 24.20174875 -1.383846748 -0.034617283 SSSSSGVPYS(ph)PAIPNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSSSSGVPYSPAIPNKR 17 1 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 SSSSSGVPYS(1)PAIPNKR;SSSSSGVPYS(1)PAIPNKR;SSSSS(0.001)GVPYS(0.999)PAIPNKR 108.45 0.00040134 506950000 500690 473960 476270 530740 397780 497060 555630 577020 494900 TRUE FALSE 477023.376 522257.0628 498107.4506 477389.0069 467152.7061 479846.6876 470858.4387 526493.0698 571646.5644 0.834472567 0.913601332 0.871355627 0.835112177 0.817205482 0.839411478 0.823688041 0.921011518 1 19.12476391 0.991423639 4.271175422 0.999728918 0.851400948 0.765058809 0.02783394 0.093937008 5.150554756 0.029679576 0.007566072 9.80445909 -0.991423639 -0.14832797 SSSSSSQPEHSAMLVSTAAS(ph)PSLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSSSSQPEHSAMLVSTAASPSLIK 25 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SSSSSSQPEHSAMLVST(0.003)AAS(0.997)PSLIK;SSSSSSQPEHSAMLVSTAAS(0.997)PS(0.003)LIK 253.88 5.17E-45 373690000 546760 536900 575840 680430 455510 620330 742950 715540 568940 TRUE FALSE 520915.7384 591610.7204 602242.8336 612031.8837 534950.7998 598847.8166 629599.3323 652883.5243 657168.3095 0.792667161 0.900242315 0.916420991 0.931316795 0.814024036 0.911254861 0.958048833 0.993479927 1 19.32590339 7.999999998 0.116095055 1.051016536 0.324126251 0.586999364 0.043303992 71.6029313 0.574712092 0.33273646 8.388315087 99999999.57 -7.999999998 -0.726890285 SSSSVGS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSSSVGSPTR 10 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 SSSSVGS(0.985)PT(0.015)R;SSSSVGS(0.978)PT(0.022)R;SSSSVGS(0.999)PT(0.001)R;SSSSVGS(0.991)PT(0.009)R 196.44 3.50E-07 829560000 909640 717230 813870 975110 864950 768700 990710 854830 918760 TRUE FALSE 866643.1199 790316.5524 851186.7445 877090.0902 1015797.006 742079.7263 839558.9939 779976.5535 1061236.608 0.816635153 0.744712862 0.802070658 0.826479301 0.957182402 0.699259449 0.791113864 0.734969513 1 20.01731492 -2.060207914 2.469274718 1.289586428 0.794363463 0.460001595 0.069237932 16652288.96 7267974.725 27127347.64 0.016676611 0.008705467 2.060207914 -0.495222965 SSSTGS(ph)SSSTGGGGQESQPSPLALLAATCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSSTGSSSSTGGGGQESQPSPLALLAATCSR 31 0 P08047;H3BVI2;P08047-2 P08047 SP1 Transcription factor Sp1 1 S(0.149)S(0.149)S(0.149)T(0.149)GS(0.173)S(0.173)S(0.04)S(0.01)T(0.01)GGGGQESQPSPLALLAATCSR 80.733 4.75E-07 0 5809.2 6653.3 7747.8 7381.6 11100 5267.8 8359.6 7608.8 9325.8 TRUE FALSE 5534.610629 7331.278834 8103.044294 6639.587544 13035.83649 5085.374765 7084.189485 6942.533135 10771.99743 0.513796133 0.68058676 0.75223229 0.61637478 1.210159635 0.472092088 0.657648642 0.644498217 1 13.39499817 4.38522417 1.430884829 0.741364439 0.490661239 0.120284261 0.208570955 1.438316967 4.230853713 0.054859047 0.430558274 24278.62961 -4.38522417 -0.2507032 SSSTGSSSSTGGGGQESQPS(ph)PLALLAATCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSSTGSSSSTGGGGQESQPSPLALLAATCSR 31 0 P08047;H3BVI2;P08047-2 P08047 SP1 Transcription factor Sp1 1 SSSTGSSSSTGGGGQES(0.001)QPS(0.999)PLALLAATCSR;SSSTGSSSSTGGGGQES(0.001)QPS(0.999)PLALLAATCSR 124.82 4.40E-06 92497000 22986 22812.7 20656 27057 24151 22310 25855 20981.3 28449 TRUE FALSE 21899.49733 25137.34007 21603.09803 24337.17896 28362.92675 21537.39911 21910.34489 19144.06614 32860.72562 0.666433772 0.764966068 0.657413907 0.740615994 0.863125394 0.655414593 0.666763879 0.582581966 1 15.00407672 -1.159785053 4.40335385 1.000058248 0.703636093 0.604272644 0.076321829 2.982470992 43436077.16 4971.817233 0.01732291 0.069217347 1.159785053 -0.296422155 SSSVGSSSSYPIS(ph)PAVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR 404.04 4.02E-147 2252030000 1614635 1521639 1722509 1844521 1617246 1643812 1884403 1763740 1989973 TRUE FALSE 1538314.403 1676695.744 1801487.741 1659106.245 1899293.19 1586886.378 1596902.713 1609297.575 2298567.849 0.669249073 0.729452361 0.783743557 0.721799987 0.82629416 0.690380481 0.694738123 0.700130551 1 21.13230382 -1.386468465 5.404173695 1.000133243 0.724402051 0.771546368 0.046671506 7.43E-05 8.43E-06 0.044805797 0.010555754 0.041070646 1.386468465 -0.275731192 SST(ph)DFSELEQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSTDFSELEQPR 12 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 SS(0.026)T(0.973)DFSELEQPR;S(0.002)S(0.021)T(0.977)DFSELEQPR;S(0.002)S(0.044)T(0.954)DFSELEQPR 227.06 1.55E-10 129088000 313028 241633 309210 349900 318004 337690 405050 312500 347930 TRUE FALSE 298231.7868 266255.6774 323387.5844 314727.3872 373463.7969 325995.7106 343252.1832 285135.8433 401885.2074 0.742082021 0.66251674 0.804676506 0.783127573 0.929279779 0.811166235 0.854105045 0.709495742 1 18.61642395 -4.99995359 0.031655396 2.183064457 5.64E-07 0.456645957 0.073501513 1051.766582 2.502718667 137.839707 53.16546528 1.00E-05 4.99995359 -2.183063893 SST(ph)PLPTISSSAENTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 SST(1)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;SS(0.007)T(0.992)PLPTISSSAENTR;SS(0.002)T(0.997)PLPTISSSAENTR;SST(1)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;SS(0.004)T(0.996)PLPTISSSAENTR;SST(1)PLPTISSSAENTR;SS(0.001)T(0.999)PLPTISSSAENTR;S(0.001)S(0.025)T(0.975)PLPTISSSAENTR;S(0.024)S(0.197)T(0.779)PLPTISSSAENTR 355.35 2.38E-86 14030390000 4463100 3802051 4219580 5468890 4497220 4848730 5575030 5155770 4910910 TRUE FALSE 4252138.108 4189484.319 4413051.917 4919146.787 5281533.744 4680817.264 4724456.781 4704303.446 5672468.841 0.749609778 0.738564536 0.777977286 0.867196793 0.931082019 0.825181662 0.832874876 0.829322043 1 22.43554535 5.493426315 0.042527578 1.447288744 5.04E-12 0.656795585 0.046752411 260.4654173 1.399834443 16.01874113 34.43111899 311477.2382 -5.493426315 -1.447288744 SST(ph)PPGESYFGVSSLQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.006)S(0.006)T(0.989)PPGESYFGVSSLQLK;S(0.228)S(0.228)T(0.544)PPGESYFGVSSLQLK;S(0.023)S(0.023)T(0.953)PPGESYFGVSSLQLK;S(0.164)S(0.164)T(0.672)PPGESYFGVSSLQLK;S(0.012)S(0.012)T(0.976)PPGESYFGVSSLQLK;S(0.096)S(0.096)T(0.808)PPGESYFGVSSLQLK;S(0.151)S(0.151)T(0.699)PPGESYFGVSSLQLK 304.71 7.27E-49 6371792000 2913480 2525080 2643310 2943060 1851847 2801290 3159200 2963730 2180840 TRUE FALSE 2775765.574 2782388.523 2764508.378 2647218.017 2174808.53 2704280.625 2677206.017 2704210.089 2519033.529 1.101916883 1.104546045 1.097448028 1.050886376 0.86335037 1.073538956 1.062790942 1.073510955 1 21.26443889 3.145575819 4.560790511 1.02113396 1.102106578 0.293507733 0.060402311 0.283150312 10.36873327 0.017863294 0.021789205 1398.220994 -3.145575819 0.080972619 SST(ph)PPRQS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.004)S(0.02)T(0.976)PPRQS(0.901)PS(0.099)R 121.45 0.010317 1485600000 79293 61092 61560 73289 68005 70637 82462 66773 70454 TRUE FALSE 75544.97703 67317.34426 64382.58689 65921.85048 79865.05047 68190.82298 69880.90738 60926.00213 81379.64649 0.928303087 0.827201237 0.79113869 0.810053291 0.981388516 0.837934618 0.858702518 0.748663883 1 16.31238039 4.641802551 3.331398407 0.851719881 0.931271453 0.071467615 0.07867002 0.670899618 12.22816433 0.017357439 0.116973426 43833.13682 -4.641802551 0.079551572 SST(ph)PPRQS(ph)PSRS(ph)S(ph)SPQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSTPPRQSPSRSSSPQPK 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 4 S(0.264)S(0.328)T(0.408)PPRQS(0.999)PS(0.002)RS(0.93)S(0.681)S(0.388)PQPK 138.49 1.15E-06 165020000 217450 164850 193130 214780 125190 222900 253230 153190 161740 TRUE FALSE 207171.5694 181648.4024 201985.2015 193189.9063 147023.0964 215180.9171 214595.1126 139775.8715 186821.8131 1.108926019 0.972308315 1.081164978 1.034086454 0.786969647 1.151797606 1.148661974 0.74817747 1 17.51130339 4.662118558 3.263610821 1.008851066 1.115057175 0.055734222 0.135194128 0.969336388 16.7741745 0.031406847 0.231427547 45932.33866 -4.662118558 0.106206109 SSTAISSIAADGEFLHELEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SSTAISSIAADGEFLHELEEK 21 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;; 249.5 1.09E-30 87718000 185182 175405 164159 194422 116334 192065 185213 199589 109357 FALSE TRUE 176428.8139 193278.9689 171685.8525 174878.3312 136622.6128 185413.7409 156955.3552 182111.9291 126315.525 1.396731034 1.530128374 1.359182511 1.384456353 1.081597949 1.467861855 1.24256583 1.441722457 1 16.94667244 -4.418536299 0.128618248 2.36E-14 1.529910246 0.446294037 0.125884448 104.3402236 0.981363611 28.08300143 0.935582558 3.81E-05 4.418536299 1.529910246 SSTGPEPPAPT(ph)PLLAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSTGPEPPAPTPLLAER 17 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSTGPEPPAPT(1)PLLAER 113.33 0.0046663 50172000 112830 87772 110260 113840 120920 103580 133720 99376 126380 TRUE FALSE 107496.7495 96716.06659 115315.5301 102396.5869 142008.4097 99992.99863 113318.5581 90674.11061 145978.3649 0.736388228 0.662536991 0.789949457 0.70145043 0.972804496 0.684985057 0.776269539 0.621147597 1 17.15539504 -2.138116493 2.450717239 1.561504582 0.742481629 0.415141512 0.095790908 4361769.703 1480091.237 13590185.95 0.022180706 0.007275846 2.138116493 -0.819022954 SSTRAPS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSTRAPSPTK 10 1 Q15287;H3BTC0;H3BMM9;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 SSTRAPS(0.849)PT(0.151)K;SSTRAPS(0.802)PT(0.197)K;SSTRAPS(0.941)PT(0.059)K;SSTRAPS(0.991)PT(0.007)K 73.219 0.027643 1117754000 917313 202104 1168451 449854 1006885 879316 1965230 1068984 1764720 TRUE FALSE 873953.4324 222698.6274 1222025.634 404633.8213 1182485.425 848865.0664 1665398.07 975378.0939 2038383.765 0.428748231 0.109252552 0.599507146 0.198507184 0.580109323 0.416440261 0.817018904 0.478505623 1 20.95899426 1.391706371 0.37935363 1.01845952 0.251706493 0.5461247 0.176981424 0.739805669 0.328811257 0.220123874 0.159651467 24.64372595 -1.391706371 -0.766753027 SSTSPCGTSKS(ph)PNREWEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSTSPCGTSKSPNREWEGK 19 2 H0Y459 H0Y459 NCOR1 1 SSTS(0.002)PCGT(0.001)S(0.005)KS(0.991)PNREWEGK;SSTSPCGT(0.068)S(0.266)KS(0.665)PNREWEGK;SSTSPCGT(0.031)S(0.173)KS(0.796)PNREWEGK;SSTSPCGT(0.02)S(0.13)KS(0.85)PNREWEGK 166.91 9.91E-12 486124000 579467 452540 529335 575128 337829 578049 665927 592399 362672 TRUE FALSE 552076.7433 498654.3405 553605.5333 517315.0408 396746.2706 558031.0182 564327.6056 540525.4031 418913.3215 1.317878222 1.190352073 1.321527641 1.234897565 0.947084397 1.332091842 1.347122607 1.290303687 1 18.67629224 3.007673841 24.54914171 1.2148867 1.265781984 0.063210349 0.13593983 685.931373 2194317.437 0.039437366 0.047045411 1017.826703 -3.007673841 0.050895284 SSVKT(ph)PESIVPIAPELQPSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSVKTPESIVPIAPELQPSTSR 22 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.036)S(0.036)VKT(0.891)PES(0.037)IVPIAPELQPSTSR 82.234 0.0073176 113770000 188020 179240 179880 203500 123080 214260 221250 218490 141240 TRUE FALSE 179132.6672 197504.7598 188127.6759 183043.7934 144545.113 206840.1225 187494.249 199357.8573 163142.7778 1.098011629 1.210625211 1.153147436 1.121985268 0.88600375 1.267847251 1.149264782 1.221983958 1 17.3157756 -2.399394909 2.126818321 0.000193756 1.141404892 0.15195205 0.10271948 3005990.119 323719.2296 14481259.42 0.025118806 0.003986622 2.399394909 1.141211136 SSVKT(ph)PETVVPTALELQPSTSTDRPVTSEPTSQATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SSVKTPETVVPTALELQPSTSTDRPVTSEPTSQATR 36 2 Q14676;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.007)S(0.007)VKT(0.986)PETVVPTALELQPSTSTDRPVTSEPTSQATR;SSVKT(0.661)PET(0.339)VVPTALELQPSTSTDRPVTSEPTSQATR 166.52 5.52E-16 355680000 18447.3 15746.7 15459.8 17817 5686.8 22906 21976.5 19813.9 14437.9 TRUE FALSE 17575.33269 17351.30663 16168.64712 16026.00131 6678.576119 22112.75948 18623.5813 18078.88988 16676.85579 1.053875677 1.040442326 0.96952611 0.96097259 0.400469741 1.325954949 1.116732166 1.084070649 1 14.02555969 SSVQGAS(ph)SREGS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.021)S(0.024)VQGAS(0.509)S(0.446)REGS(1)PAR 64.87 0.035979 326740000 395040 239780 366250 359160 366790 319080 462870 337400 444560 TRUE FALSE 376367.2421 264213.8546 383042.9248 323056.5544 430758.0599 308030.1796 392250.6803 307855.4673 513500.0943 0.732944835 0.514535163 0.745945189 0.629126573 0.838866564 0.59986392 0.76387655 0.599523682 1 18.97000502 -5 0.285394594 3.451114443 0.654809189 0.508129178 0.097622021 179.9446859 1.70794516 262.0949918 0.096231021 1.00E-05 5 -2.796305254 SSVQGASS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SSVQGASSR 9 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSVQGAS(0.033)S(0.967)R 64.86 0.071532 375500000 1383200 1336100 1159700 1408700 982270 1196600 1300200 1347800 1115300 TRUE FALSE 1317818.877 1472250.109 1212873.392 1267094.8 1153577.577 1155161.442 1101830.61 1229779.487 1288255.028 1.022948755 1.142825044 0.941485471 0.983574504 0.895457462 0.896686927 0.855289198 0.954608723 1 20.29698679 3.625648862 5.168720286 0.918879232 1.082198435 0.58235785 0.052210695 0.128681464 4.997501335 0.013897955 0.021819142 4223.270143 -3.625648862 0.163319203 SSVQGASS(ph)REGS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 SSVQGAS(0.098)S(0.959)REGS(0.943)PAR;SSVQGAS(0.153)S(0.847)REGS(1)PAR;SSVQGAS(0.178)S(0.822)REGS(1)PAR;SSVQGAS(0.164)S(0.836)REGS(1)PAR 139.44 2.91E-06 3179900000 4181450 2557400 4082410 3975410 4130210 3539730 4959230 4096120 5163650 TRUE FALSE 3983801.145 2818001.968 4269592.537 3575794.234 4850517.316 3417148.263 4202608.381 3737442.018 5964402.47 0.667929632 0.472470123 0.715845813 0.599522626 0.813244468 0.572923823 0.704615157 0.626624718 1 22.50794618 -5 0.212371897 2.756619691 0.587812164 0.590881172 0.091886437 94.83102152 0.946010236 71.00877861 0.174312267 1.00E-05 5 -2.168807527 SSYSS(ph)PTSLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 2 SSYS(0.001)S(0.999)PTS(0.002)LS(0.998)PR;SSYSS(1)PTSLS(1)PR;SSYS(0.002)S(0.998)PTS(0.034)LS(0.966)PR;SSYS(0.15)S(0.85)PTS(0.171)LS(0.829)PR;S(0.038)S(0.018)Y(0.025)S(0.093)S(0.826)PT(0.001)S(0.024)LS(0.975)PR;S(0.057)S(0.044)Y(0.032)S(0.234)S(0.633)PT(0.002)S(0.033)LS(0.964)PR;SSYS(0.005)S(0.995)PTS(0.303)LS(0.697)PR;SS(0.001)YS(0.052)S(0.947)PTS(0.13)LS(0.87)PR 318.04 2.18E-46 4447530000 5527640 4806510 5083930 5567550 4632530 5150060 5956590 5366040 5316740 TRUE FALSE 5266359.412 5296298.834 5317033.219 5007889.296 5440441.765 4971712.131 5047802.795 4896161.09 6141232.885 0.857541069 0.862416217 0.865792475 0.81545341 0.885887552 0.809562546 0.821952675 0.797260287 1 22.55009688 -1.437003 5.86226249 1.000079465 0.84128579 0.758436106 0.028453303 2.93E-05 2.81E-06 0.02727362 0.006425244 0.036559227 1.437003 -0.158793675 SSYSSPTSLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR 280.91 4.98E-28 7688370000 4865610 4298180 4418580 5003000 4404160 4597000 5385170 4827500 4781260 TRUE FALSE 4635622.258 4736169.429 4621176.264 4500088.935 5172244.11 4437804.737 4563563.411 4404778.508 5522713.382 0.839374043 0.857580161 0.836758301 0.814832968 0.936540384 0.803555142 0.826326317 0.797575069 1 22.39694583 -1.561778773 4.332831111 1.002017195 0.840233219 0.628654069 0.038862111 0.000706917 7.15E-05 0.035126336 0.008179436 0.027429711 1.561778773 -0.161783976 ST(ph)FHAGQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STFHAGQLR 9 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 S(0.373)T(0.627)FHAGQLR 123.62 0.0020334 268070000 200990 134070 158860 195350 243560 184320 253490 196800 230580 TRUE FALSE 191489.601 147731.8854 166143.8881 175713.0469 286036.7869 177936.9522 214815.4448 179567.1487 266337.1688 0.718974381 0.554679942 0.623810371 0.659739111 1.07396496 0.668089073 0.806554511 0.674209873 1 18.02289425 2.970548052 24.867366 0.821033975 0.629870697 0.371246422 0.131145331 694.8748592 586708.7773 0.036554022 0.038833532 934.4327507 -2.970548052 -0.191163278 ST(ph)FSTNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.131)T(0.515)FS(0.282)T(0.072)NYR 131.52 0.011197 384410000 687120 502650 619390 639230 610630 689480 822830 668750 697290 TRUE FALSE 654641.1993 553870.6065 647789.6442 574973.3859 717123.6787 665603.1347 697292.1712 610190.7047 805422.1719 0.812792622 0.687677377 0.804285835 0.713878269 0.890369925 0.826402796 0.865747425 0.75760356 1 19.61938566 2.73676725 24.98837582 0.856907994 0.752711417 0.385733656 0.070294786 164.9103034 2297807.799 0.019695302 0.019459314 545.4654527 -2.73676725 -0.104196577 ST(ph)GSIDQLSHFHNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STGSIDQLSHFHNKR 15 1 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.41)T(0.57)GS(0.019)IDQLSHFHNKR 158.98 1.37E-06 289750000 227530 167740 217140 238300 211830 190800 279240 236020 17698 TRUE FALSE 216775.1078 184832.8967 227096.0838 214345.6313 248773.0849 184192.5482 236636.8094 215352.8376 20442.51545 10.6041308 9.041592614 11.10900879 10.4852865 12.16939694 9.010268262 11.57571875 10.53455667 1 14.31928511 -0.322246774 9.662939155 1 10.50392525 0.903655227 0.981462521 0 0 0.889001039 0.209539554 0.476160347 0.322246774 9.503925248 ST(ph)PLSQPSANGVQTEGLDYDRLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPLSQPSANGVQTEGLDYDRLK 23 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.46)T(0.539)PLS(0.001)QPSANGVQTEGLDYDRLK 117.03 0.00067667 88935000 26516 20938 19862 26183 23416 27007 30244 27968 33006 TRUE FALSE 25262.64123 23071.606 20772.69235 23551.0351 27499.74299 26071.74082 25629.72233 25518.97365 38124.40191 0.66263705 0.605166372 0.544866052 0.617741759 0.72131605 0.683859668 0.672265558 0.669360629 1 15.21842708 -5 0.230347148 2.938049235 0.604411866 0.871378318 0.043428369 55.89248308 0.558948956 50.39468074 0.077001575 1.00E-05 5 -2.333637369 ST(ph)PPPNNLVNPVQELETERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPPPNNLVNPVQELETERR 20 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(0.476)T(0.524)PPPNNLVNPVQELETERR 52.483 0.071911 34094000 21504 15132 16592 20192 13747 21856 24615 22854 25956 TRUE FALSE 20487.54854 16673.968 17352.75961 18162.2618 16144.47245 21099.12124 20859.52966 20852.7826 29981.12392 0.683348249 0.556148864 0.578789496 0.605789891 0.5384879 0.703746841 0.695755427 0.695530383 1 14.87176685 0.484703397 0.603673124 1.010676438 0.596937399 0.85596125 0.049669119 0.627091196 0.389483698 0.064192525 0.020475109 3.052835458 -0.484703397 -0.413739039 ST(ph)PVRDR ddPTM_SK-BR-3_Trastuzumab_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(0.41)T(0.59)PVRDR 94.692 0.022657 164790000 368950 342930 298410 405200 281390 332140 360550 363700 307980 TRUE FALSE 351510.4647 377874.9569 312092.3937 364468.5262 330464.3269 320637.9085 305541.4755 331852.4999 355739.9655 0.988110696 1.062222392 0.877304841 1.024536351 0.928949117 0.901326642 0.858889934 0.93285133 1 18.44046354 3.237554417 0.932557451 0.908441899 1.020509664 0.171471246 0.059710401 0.629890664 1.192351596 0.025709981 0.04253956 1728.042489 -3.237554417 0.112067764 ST(ph)SFRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.093)T(0.515)S(0.392)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.067)T(0.466)S(0.466)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.086)T(0.494)S(0.42)FRGGMGSGGLATGIAGGLAGMGGIQNEK 230.52 1.94E-35 9835700000 5757890 4228200 5465600 6357690 4401850 6713710 8043240 6527660 5629440 TRUE FALSE 5485725.951 4659058.387 5716203.166 5718602.922 5169531.246 6481212.539 6816096.014 5956063.485 6502424.804 0.84364312 0.716510921 0.879087931 0.879456986 0.795015921 0.996737792 1.048239114 0.915975757 1 22.63254638 2.2340723 24.9221209 1.000130376 0.815295835 0.683436983 0.056339614 58.25124617 323445.6885 0.020987944 0.016027085 171.4242666 -2.2340723 -0.184834541 ST(ph)SFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.107)T(0.446)S(0.446)FRGGMGS(0.002)GGLATGIAGGLAGMGGIQNEKETMQSLNDR 143.12 4.68E-13 215870000 86359 36762 114320 78942 102830 99816 161950 97391 187150 TRUE FALSE 82276.98122 40508.08959 119561.6851 71006.60018 120763.5194 96359.34689 137241.5531 88862.92774 216172.2662 0.380608404 0.187388005 0.553085219 0.328472294 0.558644833 0.445752587 0.634871233 0.411074599 1 17.72182192 -4.999999982 0.116451972 2.914429036 0.12188364 0.710933035 0.117068348 73.26663161 0.558249218 32.94292686 1.096754501 1.00E-05 4.999999982 -2.792545397 ST(ph)SYGYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 S(0.317)T(0.342)S(0.342)YGYSR 123.29 0.015136 518400000 821170 581600 619890 729910 718090 639640 744380 701310 712780 TRUE FALSE 782354.9215 640865.7012 648312.5697 656538.0601 843324.6686 617489.1064 630811.1595 639899.5785 823314.282 0.950250638 0.778397406 0.787442394 0.7974331 1.024304676 0.750004123 0.766185129 0.77722395 1 19.65108373 ST(ph)TPPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.099)T(0.45)T(0.45)PPPAEPVSLPQEPPKPR 164.05 3.03E-11 301210000 498360 475290 449400 570080 306470 526080 540730 536590 342370 TRUE FALSE 474803.5105 523722.5914 470005.4345 512774.4753 359918.271 507861.7177 458231.7073 489603.335 395462.991 1.200626914 1.324327695 1.188494107 1.296643395 0.910118719 1.284220595 1.1587221 1.238050958 1 18.59318316 -4.999999998 0.118485449 0.356039634 1.306874564 0.22699945 0.115312188 214.5439277 1.654563093 33.49439431 1.053546124 1.00E-05 4.999999998 0.950834931 ST(ph)TPTSSPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.012)T(0.492)T(0.492)PT(0.005)SSPFR 183.78 1.82E-05 305090000 438440 368760 351120 376190 413740 354810 480530 410270 450730 TRUE FALSE 417715.8101 406337.0632 367219.1993 338374.6665 485896.125 342522.8407 407216.323 374344.5838 520626.9064 0.802332352 0.780476495 0.705340417 0.649936955 0.93329046 0.657904608 0.782165343 0.71902658 1 18.98989035 -1.578736759 6.288485003 1.000544109 0.75745422 0.473716956 0.081469636 0.000554373 3.71E-05 0.070364602 0.016549003 0.026379298 1.578736759 -0.243089889 STAGDTHLGGEDFDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 240.2 7.45E-20 99577770000 28679010 23227000 25310660 29404630 27758050 25824320 31788370 27715950 27063050 FALSE TRUE 27323410.03 25593857.71 26471178.8 26448820.73 32599045.13 24930017.32 26938470.32 25288994.49 31259849.58 0.874073625 0.818745389 0.846810818 0.846095585 1.042840755 0.79750919 0.861759435 0.80899284 1 24.8978075 -2.293484084 2.32600869 1.671404416 0.860590996 0.285810742 0.068468056 3749100.856 1026503.455 13074854.87 0.015351836 0.005087635 2.293484084 -0.81081342 STANQS(ph)FRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STANQSFRK 9 1 Q13464;J3KRH6 Q13464 ROCK1 Rho-associated protein kinase 1 1 STANQS(1)FRK;S(0.001)T(0.002)ANQS(0.997)FRK 75.695 0.022989 1093650000 832880 641780 696670 872330 763650 739190 952480 828710 730560 TRUE FALSE 793511.413 707178.1116 728613.0086 784641.7311 896830.3182 713591.665 807161.6825 756143.7591 843851.5136 0.940344836 0.838036195 0.863437461 0.929833885 1.062782141 0.845636529 0.956520987 0.896062574 1 19.68662964 3.124120668 5.847629287 0.946331763 0.880404454 0.211925447 0.062312743 0.324937461 15.43431764 0.017008693 0.020476292 1330.824134 -3.124120668 -0.065927308 STAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASASAAASS(1)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.431)S(0.569)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.131)S(0.869)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.008)S(0.992)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAASS(1)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.139)S(0.861)PAGGGAEALELLEHCGVCR 364.17 3.10E-161 13591090000 1379673 1296858 1421454 1701764 1554460 1522806 1805679 1663959 1619598 TRUE FALSE 1314458.592 1429009.305 1486629.072 1530699.45 1825557.332 1470070.846 1530189.505 1518253.929 1870756.986 0.702634603 0.763866881 0.794667123 0.818224634 0.975838842 0.78581604 0.817952046 0.811571968 1 20.83519073 6.120271208 0.045259995 1.3824866 1.41E-17 0.545925795 0.06134485 332.7180492 1.637513714 15.35951847 39.44531776 1319080.218 -6.120271208 -1.3824866 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STAQQELDGKPASPTPVIVASHTANK 26 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.975)PT(0.025)PVIVASHTANK;STAQQELDGKPAS(0.709)PT(0.291)PVIVASHTANK;STAQQELDGKPAS(0.99)PT(0.01)PVIVASHTANK;STAQQELDGKPAS(0.988)PT(0.012)PVIVASHTANK;STAQQELDGKPAS(0.996)PT(0.004)PVIVASHTANK;STAQQELDGKPAS(0.961)PT(0.039)PVIVASHTANK 300.15 8.44E-71 5725410000 4176440 5011570 3417930 5471410 2002070 4631630 3950070 4662030 1848680 TRUE FALSE 3979027.958 5522254.681 3574645.471 4921413.472 2351230.374 4471235.492 3347414.273 4253797.938 2135363.853 1.863395764 2.586095421 1.674021721 2.30471892 1.101091213 2.093898652 1.567608382 1.992071718 1 21.02605049 -0.9616013 0.134622106 1.71E-15 2.517729842 0.345312993 0.399887892 31.27233103 0.887912992 15.02393107 3.466834025 0.109244278 0.9616013 2.517729842 STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.939)PT(0.06)PVIVASHTANKEEK;STAQQELDGKPAS(0.944)PT(0.056)PVIVASHTANKEEK;STAQQELDGKPAS(0.955)PT(0.045)PVIVASHTANKEEK;STAQQELDGKPAS(0.977)PT(0.023)PVIVASHTANKEEK;STAQQELDGKPAS(0.966)PT(0.034)PVIVASHTANKEEK;STAQQELDGKPAS(0.961)PT(0.039)PVIVASHTANKEEK;STAQQELDGKPAS(0.938)PT(0.062)PVIVASHTANKEEK;STAQQELDGKPAS(0.996)PT(0.004)PVIVASHTANKEEK;STAQQELDGKPAS(0.947)PT(0.053)PVIVASHTANKEEK;STAQQELDGKPAS(0.941)PT(0.059)PVIVASHTANKEEK;STAQQELDGKPAS(0.969)PT(0.031)PVIVASHTANKEEK 213.27 1.07E-26 30986869000 7974245 6818600 7164055 8215010 3223869 8999090 8493100 9501200 3232731 TRUE FALSE 7597318.242 7513423.092 7492534.008 7389221.587 3786110.733 8687449.257 7197321.609 8669224.559 3734046.413 2.034607341 2.012139717 2.006545495 1.97887781 1.013943137 2.326550957 1.927485846 2.321670274 1 21.83230843 2.972823465 24.94625104 1.803515707 2.015683719 0.076589944 0.450547214 2381.345892 2185918.667 0.127457347 0.135524286 939.3414036 -2.972823465 0.212168012 STAS(ph)PASTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.999)PAS(0.001)TK;STAS(0.995)PAS(0.004)T(0.001)K;STAS(0.861)PAS(0.139)TK;STAS(0.998)PAS(0.001)TK;STAS(0.999)PAS(0.001)TK;STAS(0.989)PAS(0.011)TK;STAS(1)PASTK;STAS(0.999)PAS(0.001)TK;STAS(0.996)PAS(0.004)TK;STAS(1)PASTK 183.57 4.72E-05 1795648000 6661530 6056070 5303200 6829830 3991473 5733720 6177810 7050390 5047100 TRUE FALSE 6346652.679 6673190.418 5546356.966 6143282.513 4687584.627 5535159.839 5235271.621 6433020.475 5829778.491 1.088661034 1.144673066 0.951383826 1.053776318 0.804075941 0.949463148 0.898022391 1.10347597 1 22.47500964 3.733033294 24.61104283 0.954142138 1.116667054 0.35894721 0.082729797 300.3755744 1337458.678 0.020378395 0.032608655 5407.9578 -3.733033294 0.162524916 STAYEDYYYHPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STAYEDYYYHPPPR 14 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 194.06 1.88E-07 3620270000 2008040 1688820 1754410 2079890 1928050 1808150 2162390 1906580 1709820 FALSE TRUE 1913123.929 1860912.678 1834851.434 1870815.506 2264301.31 1745533.312 1832477.69 1739629.748 1974970.153 0.968684983 0.942248507 0.929052741 0.947262673 1.146499002 0.883827692 0.927850827 0.8808385 1 20.91339942 -0.908540136 4.302249091 1.000000906 0.953085925 0.038052119 0.073812154 6441489.075 1497237.677 56.77072074 0.01686191 0.123441123 0.908540136 -0.046914982 STCAPS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STCAPSPQR 9 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 STCAPS(1)PQR;STCAPS(1)PQR;STCAPS(1)PQR 101.64 0.0040322 930610000 551160 492980 432700 594260 512730 487190 573260 496330 516040 TRUE FALSE 525107.7591 543215.2225 452539.723 534523.8558 602149.9497 470318.4881 485798.6584 452868.714 596064.8476 0.880957435 0.911335779 0.759212231 0.896754536 1.010208792 0.789039129 0.815009743 0.75976417 1 19.18510977 STCAPS(ph)PQREVLTVPEANSEPWTLDTLGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STCAPSPQREVLTVPEANSEPWTLDTLGGER 31 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.01)T(0.01)CAPS(0.98)PQREVLTVPEANSEPWTLDTLGGER;STCAPS(1)PQREVLTVPEANSEPWTLDTLGGER;S(0.023)T(0.023)CAPS(0.945)PQREVLT(0.01)VPEANSEPWTLDTLGGER 259.57 9.06E-59 503704000 127372 68874.7 126287 107848 127343 100017 161938 137096 189565 TRUE FALSE 121351.378 75893.11023 132077.3839 97006.91414 149551.5789 96553.38621 137231.3839 125091.1474 218961.772 0.554212623 0.346604385 0.603198369 0.44303128 0.683003145 0.440960015 0.626736725 0.571292177 1 17.74031949 -4.99999997 0.195042102 3.147392709 0.439449479 0.711186398 0.095258913 65.65409266 0.64609474 54.63434237 0.212700445 1.00E-05 4.99999997 -2.707943231 STDEPSEKDALQPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STDEPSEKDALQPGR 15 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;; 207.4 3.11E-09 744250000 1175780 936490 982170 1184330 841610 1170630 1233780 1193150 945160 FALSE TRUE 1120203.21 1031919.396 1027203.466 1065278.898 988386.5175 1130090.79 1045544.201 1088671.461 1091730.586 1.026080266 0.945214332 0.940894649 0.975770865 0.905339221 1.035137061 0.957694339 0.997197912 1 20.05818545 2.219968785 24.9997324 0.991563704 0.962925746 0.214688609 0.035617501 505.5096624 679734.9846 0.012952884 0.009584359 165.9467628 -2.219968785 -0.028637958 STEDGAELEEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STEDGAELEEQK 12 0 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 0 91.549 0.008235 232170000 461550 448700 377540 556250 486090 351390 458550 399780 486740 FALSE TRUE 439733.4462 494423.0401 394850.5824 500334.6932 570863.9421 339221.2762 388589.7757 364773.1438 562221.1533 0.782136075 0.879410241 0.702304743 0.889925059 1.015372579 0.603359148 0.691168899 0.648807221 1 19.10077821 2.220038505 24.99998685 0.704257728 0.845553641 0.144619657 0.132239596 357.0454966 481914.7478 0.044894732 0.033216179 165.9734055 -2.220038505 0.141295914 STEEEEERLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STEEEEERLER 11 1 Q5T8U9;Q8N4J0 Q5T8U9 C9orf41 UPF0586 protein C9orf41 0 ; 158.56 2.71E-05 424720000 226110 208362 202808 243368 222990 225166 241753 222080 242498 FALSE TRUE 215422.2284 229594.3247 212106.9474 218904.1863 261879.3854 217368.445 204869.1398 202633.4979 280103.3513 0.769081224 0.819677178 0.757245304 0.7815122 0.934938422 0.776029433 0.731405529 0.723424039 1 18.09559972 -2.125608303 2.532226805 1.442438222 0.78731633 0.562632561 0.059109708 4854430.79 1307043.733 12424877.57 0.014469365 0.007488446 2.125608303 -0.655121892 STELDSNWNWFQLR ddPTM_SK-BR-3_Trastuzumab_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 84.289 0.019059 46035000 83995 103070 81329 79930 70982 85350 109280 96994 85115 FALSE TRUE 80024.72281 113572.9502 85058.0151 71895.28454 83361.23833 82394.3081 92607.32894 88500.69116 98314.19949 0.813969124 1.155203936 0.865165109 0.731280781 0.847906394 0.838071291 0.941952733 0.900182188 1 16.58511218 3.588635289 21.91463531 0.86784724 0.988859595 0.151945215 0.10656401 14.23688021 2776.475509 0.027335404 0.042347794 3878.245423 -3.588635289 0.121012355 STELKTEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STELKTEIKEEEDQPSTSATQSSPAPGQSK 30 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 STELKTEIKEEEDQPSTSAT(0.003)QS(0.06)S(0.937)PAPGQSK 134.42 2.63E-06 305110000 219660 137900 209760 189010 95036 228920 240440 254290 95840 TRUE FALSE 209277.1071 151952.1668 219377.7035 170010.3557 111610.2483 220992.443 203756.462 232023.0195 110702.3777 1.890448168 1.372618817 1.981689174 1.535742585 1.008201004 1.996275487 1.840578913 2.095917218 1 16.75632668 STELVLS(ph)PDMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STELVLSPDMPR 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 STELVLS(1)PDMPR;STELVLS(1)PDMPR 143.98 6.57E-05 58087000 130624 113490 122404 149594 137399 129404 147280 141856 157089 TRUE FALSE 124449.6624 125054.76 128016.3445 134556.5269 161361.3421 124922.707 124809.731 129434.3366 181449.5598 0.685863678 0.689198476 0.705520281 0.741564361 0.889290347 0.688470709 0.687848078 0.713335082 1 17.46920903 -2.23524998 2.185044948 1.913552791 0.7203138 0.666597388 0.06100564 3995987.357 690786.5562 18027249.49 0.015033075 0.005817683 2.23524998 -1.193238991 STFDAHIYEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STFDAHIYEGR 11 0 Q05655;Q05655-2;A0A494C1T7;C9K0E3;C9JZU8;C9J9P1 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ; 117.23 0.00088222 434180000 1173050 1185600 977490 1096930 1265720 1080180 1313150 1239130 1099150 FALSE TRUE 1117602.251 1306413.988 1022308.883 986664.5124 1486461.167 1042773.096 1112804.85 1130625.208 1269600.568 0.880278632 1.028996064 0.805220877 0.777145613 1.170810099 0.8213395 0.876499962 0.890536155 1 20.27594325 -1.012285028 4.743903269 1.000001847 0.910457275 0.059501712 0.11599062 2.10E-06 4.37E-07 0.103967788 0.024504937 0.097210902 1.012285028 -0.089544572 STFETEHAGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STFETEHAGQR 11 0 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 62.633 0.079739 69909000 69466 51025 56462 69955 114540 53948 84430 60695 122130 FALSE TRUE 66182.47985 56224.50551 59050.83855 62922.99049 134515.7397 52079.76723 71548.65284 55380.22404 141069.2966 0.469148719 0.39855948 0.418594549 0.446043129 0.953543705 0.369178613 0.507187989 0.392574609 1 17.1060445 -2.23646442 2.28621578 2.771205437 0.489955206 0.470994139 0.168354109 10688700.71 1776541.131 97961713.98 0.038501629 0.005801437 2.23646442 -2.281250231 STFREES(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR 220.32 3.57E-09 26744770000 15921230 11802100 13959360 14728940 15137980 13065100 17515400 15041380 16396820 TRUE FALSE 15168665.01 13004747.41 14599410.46 13248358.97 17778038.92 12612652.31 14843104.04 13724277.03 18939555.1 0.800898697 0.68664482 0.770842313 0.699507401 0.938672467 0.665942375 0.783709224 0.724635661 1 24.17489911 -1.450806486 4.021268128 1.001505473 0.756708321 0.491491181 0.077057345 0.000914696 0.000124922 0.065618338 0.015374301 0.035415511 1.450806486 -0.244797152 STFS(ph)PISDIGLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STFSPISDIGLAK 13 0 Q8TEK3;Q8TEK3-1;H7C2S2 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 STFS(1)PISDIGLAK;STFS(1)PISDIGLAK 215.87 2.98E-11 76591000 304440 267660 269240 318680 226910 296530 321620 312700 259570 TRUE FALSE 290049.7245 294934.8583 281584.9203 286645.6809 266483.0322 286261.0917 272550.962 285318.3303 299822.7899 0.967403861 0.983697265 0.93917117 0.956050342 0.888801789 0.954767621 0.909040177 0.951623225 1 18.19375052 3.708809214 8.694144305 0.936425483 0.975546381 0.145490716 0.030097011 0.396293772 109.9768353 0.007073562 0.011115381 5114.571031 -3.708809214 0.039120898 STFS(ph)TNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.062)T(0.163)FS(0.752)T(0.024)NYR;S(0.001)T(0.262)FS(0.723)T(0.013)NYR;S(0.018)T(0.461)FS(0.485)T(0.037)NYR 185.08 0.00022515 1552600000 1459900 1274460 1280390 1458840 1340040 1382590 1732110 1370590 1503360 TRUE FALSE 1390893.42 1404328.923 1339097.148 1312194.632 1573742.552 1334710.562 1467844.807 1250573.874 1736493.391 0.80097824 0.808715386 0.771150155 0.755657717 0.906276154 0.768624038 0.845292481 0.720171974 1 20.72774549 -1.418358067 5.33211164 1.000157087 0.801609788 0.606113134 0.051287505 8.40E-05 9.17E-06 0.04357815 0.01026338 0.03816295 1.418358067 -0.198547299 STFSTNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 186.09 0.000487 26222940000 18178220 15342280 13824270 16489480 17430750 16679890 22839720 19666770 19597390 FALSE TRUE 17318971.57 16905675.77 14458126.45 14831926.14 20470667.28 16102261.23 19355101.23 17944643.36 22636453.15 0.765092104 0.746834129 0.638709888 0.655223062 0.904323091 0.71134206 0.855041252 0.792732114 1 24.43214459 0.668777855 0.465778561 1.012399218 0.721196944 0.553982991 0.074150456 1.218978225 0.559599473 0.110011028 0.04201788 4.664207414 -0.668777855 -0.291202274 STFVLDEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 202.56 3.55E-07 5831170000 11042170 7969400 7771280 8878790 7932920 9040470 11766910 10482890 8671620 FALSE TRUE 10520228.51 8781490.92 8127600.875 7986277.161 9316418.736 8727396.257 9971651.765 9564952.578 10016370.54 1.050303447 0.876713864 0.81143173 0.797322456 0.930119218 0.871313239 0.995535431 0.954931983 1 23.2558565 1.720473803 7.988025853 0.980416846 0.895474127 0.282380246 0.070016215 0.185544901 31.72657392 0.036868884 0.019523681 52.53803231 -1.720473803 -0.08494272 STGNFLTLTQAIDKFSADGMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STGNFLTLTQAIDKFSADGMR 21 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 191.5 1.30E-17 194061000 304700 253680 309870 320530 271110 298910 397830 334910 313610 FALSE TRUE 290297.4349 279530.2804 324077.846 288309.7154 318391.4982 288558.6717 337133.7269 305583.5049 362243.0371 0.801388585 0.77166502 0.89464203 0.795901331 0.878944426 0.796588594 0.930683802 0.843586967 1 18.46659843 -5 0.083425126 1.570584253 0.674533141 0.593355926 0.045447535 137.6567475 0.80809474 14.09443144 1.194184461 1.00E-05 5 -0.896051112 STGS(ph)PTQETQAPFIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STGSPTQETQAPFIAK 16 0 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 STGS(1)PTQETQAPFIAK;S(0.011)T(0.048)GS(0.941)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;S(0.003)T(0.004)GS(0.993)PTQETQAPFIAK;S(0.02)T(0.02)GS(0.832)PT(0.128)QETQAPFIAK;S(0.018)T(0.018)GS(0.964)PTQETQAPFIAK 433.68 1.73E-160 1346644000 1763311 1522891 1540801 1802210 1171730 1663533 1841631 1739439 1422691 TRUE FALSE 1679962.784 1678075.324 1611448.25 1621048.427 1376079.341 1605924.435 1560656.367 1587124.5 1643314.654 1.022301346 1.021152778 0.980608459 0.986450418 0.837380314 0.977247073 0.949700268 0.96580682 1 20.64817732 3.38459562 2.090439409 0.94554027 1.021055184 0.296419721 0.043935987 0.327745116 2.909602782 0.012513022 0.01899982 2424.351684 -3.38459562 0.075514914 STHALSEVEVESDSFMNAVLWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STHALSEVEVESDSFMNAVLWLR 23 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;; 202.53 2.06E-24 254255000 193206 182548 113388 142486 209340 146880 218242 188438 171916 FALSE TRUE 184073.5353 201149.8487 118586.952 128163.0366 245848.8297 141793.5088 184945.1746 171937.3697 198575.8553 0.926968362 1.012962268 0.597187165 0.645410976 1.238060032 0.714052112 0.931357815 0.865852344 1 17.59933069 STHDHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STHDHWK 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 90.706 0.016941 126990000 367190 303370 326280 381970 502460 280660 454020 333850 263570 FALSE TRUE 349833.6564 334283.7479 341240.2607 343573.6499 590088.8649 270940.6738 384750.9104 304616.3241 304443.0895 1.149093767 1.098017198 1.120867159 1.12853161 1.938256723 0.889955079 1.263785987 1.000569022 1 18.21581304 1.229107739 1.867720396 0.985652585 1.219715875 0.096576703 0.273357309 0.851702699 5.26513829 0.238593591 0.069921963 16.9475818 -1.229107739 0.23406329 STHTLDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STHTLDLSR 9 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EJY8 Q08380 LGALS3BP Galectin-3-binding protein 0 ;; 144.77 9.88E-05 487910000 238180 149114 104156 117992 239876 120610 254857 150783 158745 FALSE TRUE 226921.7034 164308.8861 108931.6556 106131.22 281710.2985 116433.2455 215973.8839 137579.6412 183362.3638 1.237558781 0.896088394 0.594078596 0.578805911 1.536358348 0.63498988 1.177852856 0.750315595 1 17.48433802 STIGGQIMYLTGMVDKR ddPTM_SK-BR-3_Trastuzumab_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 ; 212.37 2.62E-12 382760000 401160 324500 358490 373890 330680 347050 456570 397430 421020 FALSE TRUE 382197.9618 357566.9189 374927.1211 336305.8669 388350.4873 335031.5715 386911.861 362628.9223 486309.6313 0.785914852 0.735265962 0.770963799 0.691546795 0.798566309 0.688926457 0.795608057 0.745674975 1 18.89151564 -0.665207278 0.802302084 1.021164325 0.750664226 0.801610688 0.038828835 10.16247886 3.959045893 0.655306282 0.011065331 0.216168656 0.665207278 -0.270500099 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.033)AS(0.967)HNPEEDNGVK;STIGVMVT(0.004)AS(0.996)HNPEEDNGVK;STIGVMVT(0.022)AS(0.978)HNPEEDNGVK;STIGVMVT(0.011)AS(0.989)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.312)AS(0.688)HNPEEDNGVK;STIGVMVT(0.018)AS(0.982)HNPEEDNGVK;STIGVMVT(0.036)AS(0.964)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;S(0.004)T(0.004)IGVMVT(0.031)AS(0.961)HNPEEDNGVK;STIGVMVT(0.023)AS(0.977)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;STIGVMVT(0.111)AS(0.889)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK 297.64 7.14E-55 12563330000 13230200 12458160 12851780 14337380 10088006 13865680 14778690 14741800 9902847 TRUE FALSE 12604834.67 13727660.67 13441046.83 12896159.32 11847351.05 13385508.02 12523929.41 13450929.84 11438529.94 1.101962817 1.200124557 1.175067679 1.127431531 1.035740704 1.170212265 1.09488977 1.17593169 1 23.44739832 3.011286189 11.87649687 1.104304976 1.158661031 0.193181166 0.05806749 0.801238445 826.7747389 0.01535627 0.018155662 1026.328029 -3.011286189 0.054356055 STKPGAAPTEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STKPGAAPTEHK 12 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;;; 138.42 4.49E-05 315289000 793587 674241 707085 828177 496164 795852 891498 848174 533010 FALSE TRUE 756075.7152 742946.9244 739505.5467 744927.0745 582694.8445 768291.4457 755483.6066 773903.3881 615666.4686 1.228060572 1.206736053 1.201146375 1.209952324 0.946445639 1.247902046 1.227098835 1.257017277 1 19.23178947 2.945122971 24.99968344 1.156569548 1.21220515 0.10271062 0.101365913 909.6286589 414388.448 0.030060222 0.031883843 881.2983786 -2.945122971 0.055635602 STLDIVLANKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STLDIVLANKDR 12 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 129.71 0.00020927 577350000 1131570 878570 1006470 978300 1179430 1032670 1381460 1232850 1356760 FALSE TRUE 1078082.929 968097.2819 1052617.645 879959.4254 1385122.219 996908.379 1170692.905 1124895.118 1567159.411 0.687921676 0.617740145 0.67167235 0.561499627 0.883842581 0.636124425 0.74701584 0.717792402 1 20.57972051 -5 0.182868403 2.334314906 0.620994733 0.602544961 0.081862073 83.1359656 0.804333377 40.13008985 0.216538999 1.00E-05 5 -1.713320173 STLESEKPGS(ph)PEAAETS(ph)PPSNIIDHCEK ddPTM_SK-BR-3_Trastuzumab_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(0.994)PEAAET(0.463)S(0.532)PPS(0.005)NIIDHCEK 115.13 0.0004962 169380000 182130 146860 155540 185820 91638 191180 197880 203790 96255 TRUE FALSE 173521.0758 161825.201 162671.6629 167141.0206 107619.6382 184559.3887 167689.7717 185945.0672 111181.7338 1.560697697 1.455501686 1.463115004 1.503313673 0.967961503 1.659979408 1.508249296 1.672442594 1 16.76256026 4.403389741 1.200756082 1.423510958 1.58099745 0.037810184 0.240203773 3.764302017 6.918628325 0.066219826 0.640704333 25315.68835 -4.403389741 0.157486492 STLHNWMSEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STLHNWMSEFKR 12 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 56.951 0.075728 156820000 190600 177140 167100 177820 151450 171580 198840 191690 142810 FALSE TRUE 181590.7157 195190.7674 174761.7003 159945.1958 177862.832 165638.1416 168503.3061 174904.6074 164956.2454 1.100841713 1.183288131 1.059442762 0.969621946 1.078242485 1.0041338 1.021503039 1.060309096 1 17.33172388 3.558081711 5.310290294 1.023709662 1.140873055 0.64797129 0.036001699 0.112009943 5.399772758 0.008780001 0.013634219 3614.778673 -3.558081711 0.117163392 STLINSLFLTDLYS(ph)PEYPGPSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 1 STLINSLFLTDLYS(1)PEYPGPSHR;STLINSLFLTDLY(0.005)S(0.995)PEYPGPSHR 162.07 1.10E-11 143185000 110042 85398 102583 105980 115410 90970 127794 93502 106191 TRUE FALSE 104840.5327 94100.15329 107286.532 95326.68905 135537.4675 87819.68609 108296.6782 85314.46919 122658.5579 0.854734757 0.767171528 0.874676287 0.777171122 1.104998051 0.715968682 0.882911719 0.695544368 1 16.90428837 -2.402293518 2.259881013 2.336771726 0.835238654 0.170721935 0.114854052 8011216.036 472271.0194 55594334.49 0.024377132 0.003960103 2.402293518 -1.501533072 STLINSLFLTDLYSPEYPGPSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 206.85 2.96E-24 474840000 466920 428260 407410 509550 460040 452230 551720 510310 453980 FALSE TRUE 444849.6169 471900.1809 426090.1515 458329.0659 540270.8303 436569.1617 467544.981 465624.5511 524380.8998 0.848332991 0.899918706 0.812558489 0.874038444 1.030302268 0.832542074 0.891613293 0.887951013 1 19.00025561 -5 0.188732895 1.489153642 0.862134069 0.295305931 0.057806277 177.678793 1.734587501 32.74654487 0.150948035 1.00E-05 5 -0.627019573 STLNPQWNES(ph)FTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STLNPQWNESFTFK 14 0 P17252;J3KRN5 P17252 PRKCA Protein kinase C alpha type 1 STLNPQWNES(1)FTFK 397.75 3.99E-101 0 217060 166560 190600 212260 154630 195030 222430 218670 153870 TRUE FALSE 206800.004 183532.6534 199339.1985 190923.2215 181597.423 188276.0622 188494.2183 199522.0956 177731.3737 1.163553736 1.032640718 1.121575748 1.074223518 1.021752205 1.059329359 1.060556807 1.122604813 1 17.43933885 4.649905948 3.133833946 1.064447312 1.1695379 0.397177571 0.039205039 0.282672002 4.484304013 0.008683231 0.064633723 44658.6868 -4.649905948 0.105090587 STLPDADRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STLPDADRER 10 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 131.46 0.00022763 4701540000 5189980 2996770 2827630 3877270 4726120 3254790 5696570 4198180 5301190 FALSE TRUE 4944659.931 3302144.27 2957279.632 3487519.453 5550353.832 3142075.806 4827453.622 3830565.103 6123271.47 0.807519306 0.539277784 0.482957459 0.569551664 0.906436022 0.51313678 0.788378181 0.625574927 1 22.54587121 -0.903457675 0.393065382 1.135183954 0.631706906 0.378805459 0.139488666 14.2203653 1.654810378 2.356126009 0.088386204 0.124894216 0.903457675 -0.503477047 STLTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 6713160000 3307110 2747290 2875820 3266130 2957630 2830290 3489380 3086260 3241580 FALSE TRUE 3150789.464 3027241.974 3007679.192 2937812.407 3473439.736 2732276.348 2957010.994 2816010.713 3744267.671 0.841496854 0.808500417 0.803275689 0.784616023 0.92766865 0.729722495 0.789743484 0.752085844 1 21.83625214 STMGKPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STMGKPQR 8 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;; 109.86 0.0032254 2446700000 3803120 3164500 3052680 3876900 3069340 3456050 4372930 3699920 3190200 FALSE TRUE 3623354.055 3486966.148 3192648.398 3487186.646 3604631.924 3336366.122 3705759.214 3375935.39 3684919.923 0.983292481 0.946280033 0.866409166 0.946339872 0.978211739 0.905410753 1.00565529 0.916148915 1 21.81320184 1.735371441 25 0.972661234 0.941315601 0.144302267 0.040964841 0.865021236 6685.194435 0.018267796 0.010130401 54.37151586 -1.735371441 -0.031345633 STNGDTFLGGEDFDQALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 STNGDTFLGGEDFDQALLR 19 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 302.15 1.19E-49 611257000 455888 404327 403048 403431 439792 341881 438114 420832 484450 FALSE TRUE 434339.0777 445528.381 421528.1495 362877.3494 516491.5856 330041.5752 371271.6628 383981.7191 559576.0318 0.776193141 0.796189178 0.753299151 0.648486227 0.923005197 0.58980649 0.663487429 0.686201155 1 19.09397464 2.218000387 24.99987169 0.698007732 0.774284542 0 0.126097336 609.2893841 740851.005 0.041809114 0.030913015 165.1963272 -2.218000387 0.07627681 STNS(ph)PTIVSPAIVSPTQDSRPNMSRPLITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STNSPTIVSPAIVSPTQDSRPNMSRPLITR 30 2 A0A2U3U043 A0A2U3U043 1 S(0.135)T(0.135)NS(0.723)PT(0.006)IVSPAIVSPTQDSRPNMSRPLITR;S(0.183)T(0.183)NS(0.549)PT(0.085)IVSPAIVSPTQDSRPNMSRPLITR 121.2 9.67E-06 99009000 46788 39196 47164 48579 47945 41724 48359 51882 55022 TRUE FALSE 44576.42396 43190.11696 49326.51605 43695.74663 56306.59282 40279.08742 40980.94638 47338.93704 63554.53075 0.70138861 0.679575735 0.776129026 0.687531575 0.88595718 0.633772084 0.644815498 0.744855425 1 15.95570736 0.961035845 22.05771362 1.000000002 0.70959363 0.600548619 0.072212114 1010.963917 572310.8775 0.066890546 0.016722637 9.141886914 -0.961035845 -0.290406372 STPCIQNGS(ph)VK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPCIQNGSVK 11 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 STPCIQNGS(1)VK 100.22 0.0043949 23963000 65305 54238 62796 70294 52843 67055 69412 73636 68336 TRUE FALSE 62218.16207 59764.91386 65675.25871 63227.91357 62058.80247 64732.86854 58821.92456 67188.04147 78933.19787 0.788238203 0.757158147 0.832035956 0.801030685 0.786219286 0.82009687 0.745211472 0.851201311 1 16.26834458 0.930895037 5.33551547 0.999976232 0.787968779 0.869486914 0.025706763 0.136096351 9.69039144 0.02384579 0.006015364 8.528939565 -0.930895037 -0.212007452 STPDGTEHGEFLALDLGGTNFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPDGTEHGEFLALDLGGTNFR 22 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 207.22 8.34E-23 107060000 85015 84276 75225 88019 77073 74379 78278 76369 69714 FALSE TRUE 80996.50943 92863.82021 78674.14066 79171.16289 90514.5068 71803.23658 66335.25343 69681.7255 80524.89107 1.005856802 1.153231243 0.977016418 0.983188699 1.124056246 0.891689956 0.823785696 0.865343928 1 16.29714718 2.163172767 7.192977636 0.873048323 1.052567762 0.519044796 0.07206959 0.151383859 12.06809197 0.025774188 0.019032111 145.6038192 -2.163172767 0.179519438 STPENHPET(ph)PKKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPENHPETPKKK 13 2 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 STPENHPET(1)PKKK 83.106 0.010585 60282000 60701 35802 68110 52609 37416 69876 89833 75284 38656 TRUE FALSE 57831.78403 39450.2645 71232.91087 47320.64337 43941.33855 67456.1766 76127.32595 68691.73385 44650.57505 1.295208045 0.883533179 1.595341399 1.059799192 0.984115848 1.510757174 1.704957346 1.538428873 1 15.44639114 2.219041879 23.41493873 1.520014861 1.152279574 0.1824508 0.26474991 133.5846944 160247.7858 0.091541141 0.067735116 165.5929636 -2.219041879 -0.367735287 STPEYFAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPEYFAER 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 90.761 0.026082 153800000 298370 253640 223800 276770 374750 243190 299920 242600 302650 FALSE TRUE 284266.6414 279486.2044 234061.4514 248948.5538 440106.2813 234768.2693 254161.6956 221356.6579 349583.4163 0.813158257 0.799483589 0.669543921 0.712129186 1.258944964 0.671565808 0.727041627 0.633201255 1 18.41527722 -1.103148761 5.049917635 1.000006289 0.787376221 0.125848661 0.177500292 1.18E-05 2.10E-06 0.161754973 0.038124885 0.078858995 1.103148761 -0.212630068 STPFIVPS(ph)SPTEQEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.835)S(0.165)PTEQEGR;STPFIVPS(0.754)S(0.246)PTEQEGR 285.43 8.06E-36 417040000 555710 454480 503350 574900 487660 518810 599440 510350 546330 TRUE FALSE 529442.6896 500792.0287 526429.0954 517109.9598 572707.7496 500843.4796 507984.4185 465661.0485 631052.0661 0.838984163 0.793582742 0.834208655 0.819441037 0.90754437 0.793664274 0.8049802 0.737912248 1 19.26739952 -2.465415857 2.41184359 3.425931412 0.817050295 0.645447911 0.042787003 1319701.489 492123.5716 17659966.06 0.009956666 0.003424397 2.465415857 -2.608881117 STPFIVPSS(ph)PTEQEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.184)S(0.816)PTEQEGR;STPFIVPS(0.139)S(0.858)PT(0.003)EQEGR;STPFIVPS(0.159)S(0.839)PT(0.002)EQEGR;STPFIVPS(0.001)S(0.999)PTEQEGR;STPFIVPS(0.158)S(0.838)PT(0.003)EQEGR;STPFIVPSS(1)PTEQEGR;STPFIVPS(0.213)S(0.661)PT(0.126)EQEGR;STPFIVPS(0.182)S(0.81)PT(0.008)EQEGR 408.93 6.40E-140 10878400000 5744150 4896390 5208480 5847050 5401730 5310550 6176590 5505580 5466230 TRUE FALSE 5472635.413 5395337.708 5447293.96 5259293.425 6343790.002 5126644.322 5234237.755 5023482.228 6313905.031 0.866759222 0.854516766 0.862745628 0.832969992 1.004733199 0.811960949 0.82900166 0.795622076 1 22.59010113 -2.316992379 2.281637057 1.754633343 0.857302545 0.383391449 0.056878009 4011218.076 361473.7498 15804064.27 0.013731907 0.004819563 2.316992379 -0.897330798 STPKEDDSSASTSQSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STPKEDDSSASTSQSTR 17 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 184.8 5.61E-10 608273000 615980 555473 644877 616106 451632 659967 727371 664983 555337 FALSE TRUE 586863.8462 612076.3302 674445.2483 554173.8544 530396.4778 637112.1773 616397.1949 606753.5632 641455.8257 0.914893626 0.954198724 1.051428986 0.863931439 0.826863607 0.993228453 0.960934752 0.945900776 1 19.29099039 1.223865908 1.081221153 0.992016223 0.933702748 0.091102541 0.062311911 1.265607354 3.067583304 0.057966609 0.019333514 16.74425802 -1.223865908 -0.058313476 STPLASPSPSPGRS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STPLASPSPSPGRSPQR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 STPLASPSPS(0.016)PGRS(0.984)PQR;STPLASPSPS(0.022)PGRS(0.978)PQR;STPLASPSPS(0.004)PGRS(0.996)PQR 179.19 5.63E-10 692526000 389862 331201 385317 396041 357292 417921 475835 399046 419071 TRUE FALSE 371433.9959 364950.7584 402984.1656 356230.2063 419603.6117 403448.291 403237.6314 364103.4168 484058.3904 0.767333039 0.753939536 0.832511477 0.73592404 0.866845034 0.833470298 0.833035104 0.752189042 1 18.88482156 -5 0.185767868 1.845165763 0.757173809 0.664244399 0.044843947 75.89271245 0.737677677 23.75876271 0.118588923 1.00E-05 5 -1.087991954 STPLEENVVDREQIDFLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;;; 220.63 7.65E-25 343171000 189543 150315 187820 202378 211142 174811 227782 218723 243342 FALSE TRUE 180583.678 165632.2694 196431.7328 182034.5789 247965.0979 168757.2512 193029.6724 199570.4546 281078.2345 0.642467669 0.589274618 0.698850742 0.64762958 0.882192456 0.600392455 0.686747135 0.710017462 1 18.10061222 -5 0.209521344 2.558672799 0.625997297 0.6196678 0.07933708 93.27443088 0.929141978 61.09205836 0.161742722 1.00E-05 5 -1.932675503 STPS(ph)PVLQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPSPVLQPR 10 0 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 S(0.067)T(0.143)PS(0.79)PVLQPR 84.479 0.015622 84532000 341960 300140 335070 343750 390540 291580 403410 307280 448240 TRUE FALSE 325796.2285 330724.6072 350433.2909 309195.5969 458650.0524 281482.5115 341862.3954 280372.9342 517750.7699 0.629253006 0.638771831 0.676837798 0.597190028 0.885851029 0.54366411 0.660283703 0.541521038 1 18.98189827 -1.497689641 2.884863822 1.012516944 0.647806205 0.572684298 0.095913048 20939415.63 23067101.83 2075719.252 0.020483484 0.031791452 1.497689641 -0.364710739 STPSHGSVSSLNSTGSLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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;STPSHGSVSSLNSTGS(0.001)LS(0.999)PK;STPSHGSVSSLNSTGSLS(1)PK 248.16 7.68E-30 1167830000 857300 609828 786020 790040 668970 834430 1092640 998950 804780 TRUE FALSE 816777.128 671970.1665 822059.7945 710623.6782 785638.1562 805533.4799 925937.7003 911476.6422 929581.1722 0.878650679 0.722874114 0.884333525 0.764455757 0.845152828 0.866555287 0.996080523 0.980523992 1 19.82622132 1.902324343 2.015729493 0.997956878 0.810295666 0.722994151 0.048807013 0.152947894 1.152129913 0.027673908 0.013241904 79.85908735 -1.902324343 -0.187661212 STPST(ph)KQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STPSTKQR 8 1 Q9NQ75-2;Q9NQ75 Q9NQ75-2 CASS4 Cas scaffolding protein family member 4 1 S(0.003)T(0.003)PS(0.002)T(0.993)KQR;S(0.016)T(0.016)PS(0.016)T(0.951)KQR 71.451 0.078747 188821000 198571 219734 216388 273800 317330 155922 258070 268100 478590 TRUE FALSE 189184.9424 242125.1444 226309.6038 246277.1038 372672.2515 150522.382 218696.6817 244623.7427 552807.2929 0.342225844 0.43799195 0.40938245 0.445502632 0.674144962 0.272287258 0.395611065 0.442511786 1 19.07641712 -2.007260002 1.687915748 1.594780771 0.421773768 0.755022676 0.102447391 126827.8123 34791.9525 292835.1164 0.026361785 0.009834222 2.007260002 -1.173007003 STPTDLILCVPHLYSCLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STPTDLILCVPHLYSCLEDR 20 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 77.221 0.010291 85921000 154750 132670 147690 151610 159620 151820 202350 171080 159510 FALSE TRUE 147435.2742 146189.2238 154461.7326 136369.8748 187457.6775 146562.4353 171477.7911 156099.3282 184245.9961 0.800208836 0.793445865 0.838345125 0.740151089 1.017431485 0.795471481 0.930700231 0.847233218 1 17.49127374 0.013913745 0.064396958 1.3574098 0.50931009 0.380206611 0.072577229 67.954699 1.384970585 11.05408152 7.046149735 1.032556311 -0.013913745 -0.84809971 STQIENQHQGAQDTSDLMS(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STQIENQHQGAQDTSDLMSPSKR 23 1 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 STQIENQHQGAQDT(0.017)S(0.017)DLMS(0.769)PS(0.197)KR;STQIENQHQGAQDT(0.003)S(0.003)DLMS(0.817)PS(0.178)KR 99.446 0.001251 288400000 287330 249588 235010 289624 162311 308730 318700 331130 207543 TRUE FALSE 273748.4803 275021.301 245785.441 260510.4453 190617.987 298038.6027 270076.4617 302134.5018 239727.7085 1.141914225 1.147223668 1.025269221 1.086693094 0.795143741 1.243238025 1.126596769 1.260323655 1 17.87103714 -0.870910873 8.025637934 1.000000355 1.105365601 0.059436693 0.12891046 0 0 0.117778652 0.027760695 0.134613658 0.870910873 0.105365246 STRHPS(ph)GGSSPPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STRHPSGGSSPPPR 14 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.001)T(0.003)RHPS(0.989)GGS(0.003)S(0.003)PPPR;S(0.03)T(0.03)RHPS(0.859)GGS(0.035)S(0.046)PPPR 76.068 0.017257 46924000 20348.9 10961.8 17085.3 14688.4 20851.5 14049.9 26810 18440 28120 TRUE FALSE 19387.04782 12078.81988 17868.6779 13211.89413 24487.995 13563.34844 22719.6421 16825.29584 32480.70598 0.596878893 0.371876766 0.550132067 0.406761298 0.753924345 0.417581701 0.699481166 0.518008933 1 14.98729537 -4.674856994 0.203349714 2.886065824 0.459273728 0.591942692 0.121325327 75.63149193 0.846239815 57.89249578 0.244157645 2.11E-05 4.674856994 -2.426792096 STRPHS(ph)LDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STRPHSLDR 9 1 Q3KP66-3;Q3KP66 Q3KP66-3 C1orf106 Uncharacterized protein C1orf106 1 S(0.007)T(0.007)RPHS(0.985)LDR 53.557 0.085278 73717000 114140 80919 108040 128730 143790 100160 145920 124870 140010 TRUE FALSE 108744.8284 89164.7381 112993.7409 115789.8158 168866.9305 96691.43409 123657.224 113935.7208 161722.0357 0.672418127 0.551345633 0.698691062 0.715980449 1.044180094 0.597886575 0.764628169 0.704515747 1 17.30315674 -4.999999998 0.070415483 1.942172334 0.365519503 0.336651574 0.128415424 338.2468224 1.713546117 52.49724967 6.469685183 1.00E-05 4.999999998 -1.57665283 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.018)T(0.018)S(0.964)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.101)T(0.101)S(0.521)FRGGMGS(0.111)GGLAT(0.164)GIAGGLAGMGGIQNEK;S(0.12)T(0.12)S(0.76)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.004)T(0.136)S(0.86)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.031)T(0.031)S(0.935)FRGGMGS(0.002)GGLATGIAGGLAGMGGIQNEK;S(0.149)T(0.149)S(0.701)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.008)T(0.033)S(0.958)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.191)T(0.191)S(0.564)FRGGMGS(0.052)GGLAT(0.003)GIAGGLAGMGGIQNEK;S(0.116)T(0.116)S(0.768)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.167)T(0.167)S(0.666)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.083)T(0.083)S(0.833)FRGGMGSGGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.028)T(0.141)S(0.831)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.176)T(0.176)S(0.643)FRGGMGS(0.006)GGLATGIAGGLAGMGGIQNEK;S(0.148)T(0.148)S(0.7)FRGGMGS(0.003)GGLATGIAGGLAGMGGIQNEK 293.62 1.72E-81 16795689000 16085944 11279385 15505996 17059277 12094604 18560649 20505634 16553180 15743917 TRUE FALSE 15325593.31 12428767.16 16216961.25 15344446.07 14203899.11 17917889.07 17377122.92 15103695.81 18185403.24 0.842741462 0.683447433 0.891757034 0.843778159 0.781060443 0.985289621 0.955553346 0.830539505 1 24.11627758 2.607596839 0.888782706 0.947702267 0.776834494 0.366512607 0.076735691 0.54618034 0.8956763 0.04784429 0.03874335 405.1322714 -2.607596839 -0.170867774 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.152)T(0.152)S(0.697)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.01)T(0.185)S(0.805)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.175)T(0.175)S(0.65)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.181)T(0.181)S(0.638)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.014)T(0.049)S(0.936)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.145)T(0.145)S(0.708)FRGGMGS(0.002)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.151)T(0.151)S(0.697)FRGGMGS(0.002)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.165)T(0.165)S(0.668)FRGGMGS(0.003)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.081)T(0.081)S(0.837)FRGGMGS(0.001)GGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.16)T(0.16)S(0.68)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 320.6 2.78E-111 7951340000 2673586 1113983 3107467 2164277 2954845 2986847 4999052 2978238 4797931 TRUE FALSE 2547210.888 1227499.134 3249947.436 1946719.764 3470169.032 2883411.739 4236354.804 2717447.692 5541969.635 0.45962195 0.221491494 0.58642462 0.351268573 0.626161683 0.520286456 0.764413211 0.490339693 1 22.40196738 0.725801764 0.201756228 1.204401742 0.223230351 0.633950173 0.129931319 2.720264436 0.350076065 0.887029088 0.464463622 5.318654312 -0.725801764 -0.981171391 STS(ph)FRQGPEESGLGDGTGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STSFRQGPEESGLGDGTGPK 20 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 S(0.011)T(0.011)S(0.978)FRQGPEESGLGDGTGPK;S(0.005)T(0.036)S(0.958)FRQGPEESGLGDGTGPK;S(0.044)T(0.044)S(0.913)FRQGPEESGLGDGTGPK 200.63 8.11E-22 1295710000 1534920 516510 1676000 1112380 1570140 1527180 2721360 1722620 2321410 TRUE FALSE 1462367.374 569142.9562 1752846.258 1000561.449 1843971.919 1474293.374 2306166.551 1571778.261 2681402.407 0.545374081 0.212255704 0.653705036 0.373148561 0.687689365 0.549821754 0.86005985 0.586177687 1 21.35455631 1.737830925 0.39006753 0.99531701 0.357839405 0.537080754 0.151322288 0.721146144 0.30920992 0.16664164 0.146401333 54.68030452 -1.737830925 -0.637477605 STS(ph)GSPRPAGAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.013)T(0.089)S(0.556)GS(0.343)PRPAGAKPK 77.562 0.012692 223940000 676290 557430 602940 699340 402740 678570 721180 744050 486600 TRUE FALSE 644323.112 614232.7507 630585.3954 629041.0145 472977.7285 655070.9508 611150.7456 678897.0375 562059.4428 1.146361155 1.092825249 1.121919405 1.119171687 0.841508375 1.165483401 1.087341834 1.207874089 1 19.10036319 STS(ph)PAGQHHS(ph)PISSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSPAGQHHSPISSR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.268)T(0.329)S(0.403)PAGQHHS(0.996)PIS(0.003)S(0.002)R;S(0.265)T(0.328)S(0.406)PAGQHHS(0.988)PIS(0.011)S(0.001)R 136.14 1.30E-05 263900000 389890 357010 362080 406960 379230 356810 431760 362040 178492 TRUE FALSE 371460.6724 393389.7249 378681.7261 366051.6076 445367.5919 344453.5802 365887.0822 330337.8583 206171.6277 1.801706066 1.908069162 1.836730545 1.775470328 2.160178861 1.670712813 1.774672326 1.602246933 1 17.65348628 0.655023913 0.934469456 0.998299907 1.872754782 0.830419706 0.121999094 0.406532604 0.607323593 0.106178873 0.03485514 4.51880825 -0.655023913 0.874454875 STS(ph)PIIGS(ph)PPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 STS(1)PIIGS(1)PPVR;S(0.007)T(0.022)S(0.971)PIIGS(1)PPVR 169.54 6.37E-05 147546000 389460 322280 349590 399050 362480 389820 472070 411440 428690 TRUE FALSE 371050.9976 355120.6984 365619.0473 358936.7359 425696.3972 376320.4357 400047.0513 375412.1324 495169.0558 0.749342055 0.717170619 0.738372164 0.724877154 0.859699111 0.75998375 0.807899942 0.75814942 1 18.91756163 -5 0.182416263 1.992658615 0.713693281 0.787594268 0.039183125 55.45539662 0.536118668 19.91625703 0.108781824 1.00E-05 5 -1.278965334 STS(ph)PIIGSPPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 S(0.128)T(0.128)S(0.745)PIIGSPPVR;S(0.005)T(0.005)S(0.99)PIIGSPPVR;ST(0.003)S(0.997)PIIGSPPVR;ST(0.006)S(0.994)PIIGSPPVR 229.56 8.30E-12 1404150000 2285240 2351580 2084820 2511280 1974070 2146340 2206040 2225270 2107290 TRUE FALSE 2177221.234 2591208.676 2180411.059 2258841.363 2318347.183 2072011.708 1869468.081 2030413.562 2434077.771 0.894474803 1.064554595 0.895785289 0.928007063 0.95245403 0.851251235 0.768039585 0.834161335 1 21.21494383 2.213338723 4.833953547 0.834425562 0.955629282 0.189119033 0.075883886 0.199930401 11.53628499 0.02694211 0.020338787 163.4326124 -2.213338723 0.12120372 STS(ph)PVTDPSIPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSPVTDPSIPIR 13 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 S(0.094)T(0.094)S(0.812)PVTDPSIPIR;S(0.264)T(0.264)S(0.473)PVTDPSIPIR 136.53 7.47E-05 259300000 572930 546940 538620 641080 560400 554240 694810 652860 710210 TRUE FALSE 545848.7343 602673.8078 563316.2598 576637.4204 658133.5826 535046.5298 588803.9734 595692.1174 820345.7395 0.665388638 0.734658302 0.68668152 0.702919992 0.802263669 0.65222077 0.717750998 0.726147633 1 19.64587254 -4.999999987 0.427380189 6.63582515 0.705521315 0.831923837 0.040904684 366.1352706 2.31345777 1941.461399 0.02118353 1.00E-05 4.999999987 -5.930303835 STS(ph)QGSINSPVYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STSQGSINSPVYSR 14 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 ST(0.001)S(0.999)QGSINSPVYSR;ST(0.003)S(0.997)QGSINSPVYSR;ST(0.001)S(0.999)QGSINSPVYSR 234.78 3.37E-17 768200000 1660060 1454830 1587800 1808020 1699430 1669030 1970370 1709020 1867830 TRUE FALSE 1581592.254 1603078.831 1660602.201 1626274.395 1995810.054 1611231.073 1669753.868 1559369.149 2157483.537 0.733072687 0.743031779 0.769694031 0.753782992 0.925063863 0.746810367 0.773935856 0.722772212 1 21.04091812 -2.146650905 2.479586752 1.532476663 0.769536893 0.614782735 0.056952017 2897000.166 1151475.094 8634861.921 0.013223126 0.007134263 2.146650905 -0.76293977 STS(ph)TPNVHMVSTTLPVDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.111)T(0.111)S(0.764)T(0.013)PNVHMVSTTLPVDSR;S(0.069)T(0.311)S(0.618)T(0.002)PNVHMVSTTLPVDSR;S(0.201)T(0.201)S(0.592)T(0.005)PNVHMVSTTLPVDSR;S(0.125)T(0.125)S(0.72)T(0.029)PNVHMVSTTLPVDSR 223.68 1.38E-19 1559050000 569409 490305 533310 596373 568218 514520 645590 541758 619050 TRUE FALSE 542494.165 540267.6369 557762.791 536424.453 667315.0393 496702.0434 547093.3884 494318.7975 715049.1123 0.758680985 0.755567174 0.78003424 0.750192461 0.933243644 0.694640459 0.765113024 0.691307477 1 19.44768281 -1.42369029 3.389756399 1.002595285 0.76635043 0.553360114 0.066040448 25698423.26 44028463.03 671255.5711 0.014996009 0.037697253 1.42369029 -0.236244855 STS(ph)TPT(ph)SPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.003)T(0.023)S(0.956)T(0.061)PT(0.553)S(0.403)PGPR 110.38 0.0095616 90939000 297630 254660 301990 318170 297910 272750 320610 295550 317170 TRUE FALSE 283561.6197 280610.1435 315836.5402 286186.9471 349865.4097 263304.5991 271695.0561 269670.0752 366355.1037 0.77400756 0.765951233 0.862104928 0.781173632 0.954989861 0.718714156 0.741616681 0.736089309 1 18.48288319 -2.262059159 2.361618855 1.880196953 0.788338674 0.46767887 0.069707733 2555971.306 565035.8335 12041059.61 0.016458387 0.005469415 2.262059159 -1.091858279 STS(ph)TPTS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ST(0.001)S(0.999)TPT(0.003)S(0.997)PGPR;ST(0.004)S(0.995)T(0.009)PT(0.262)S(0.73)PGPR;ST(0.001)S(0.998)T(0.001)PT(0.034)S(0.966)PGPR;ST(0.001)S(0.999)T(0.005)PT(0.099)S(0.896)PGPR;ST(0.001)S(0.999)TPT(0.004)S(0.996)PGPR 183.39 7.85E-06 435799000 1935140 1636270 1847450 2023990 1836900 1741400 2054640 1832740 1952120 TRUE FALSE 1843669.767 1803007.773 1932157.41 1820534.68 2157254.778 1681094.881 1741166.932 1672255.57 2254844.8 0.817648189 0.799615022 0.85689153 0.807388021 0.95671985 0.745547934 0.772189258 0.741627792 1 21.10459671 STS(ph)YGYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 S(0.008)T(0.098)S(0.894)YGYSR;S(0.001)T(0.03)S(0.969)YGYSR;S(0.002)T(0.093)S(0.905)YGYSR;ST(0.009)S(0.991)YGYSR 170.68 0.00030815 3577010000 3378210 2563890 2741510 3141920 2970750 2784790 3253020 2941920 3164410 TRUE FALSE 3218528.708 2825153.306 2867210.945 2826088.232 3488847.859 2688352.024 2756712.053 2684309.889 3655130.541 0.88055096 0.772928155 0.784434622 0.77318394 0.954507047 0.735500961 0.754203447 0.734395081 1 21.8014915 STSAPQMS(ph)PGSSDNQSSSPQPAQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 STSAPQMS(0.998)PGS(0.002)SDNQSSSPQPAQQK;STSAPQMS(0.934)PGS(0.066)SDNQSSSPQPAQQK;STSAPQMS(0.837)PGS(0.138)S(0.025)DNQSSSPQPAQQK 190.23 3.00E-17 406540000 309463 266661 280188 333737 228356 305036 331470 317744 274221 TRUE FALSE 294835.2973 293834.0591 293034.8969 300189.1227 268181.2141 294472.5268 280898.1636 289920.6509 316745.7922 0.930826248 0.927665233 0.925142194 0.947728842 0.846676486 0.929680943 0.886825242 0.915310189 1 18.27296593 -0.82693784 4.330205841 1.000000716 0.914037399 0.477070757 0.028382991 2942833.889 1359242.787 18.35445826 0.006270385 0.148957426 0.82693784 -0.085963317 STSESFIQHIVSLVHHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 254.59 5.37E-31 176572000 307060 228270 252560 304800 306090 271250 379920 321070 46778 FALSE TRUE 292545.8823 251530.9725 264140.1258 274160.9249 359471.9991 261856.5445 321956.2263 292955.4087 54032.09333 5.414298509 4.655214281 4.888578427 5.074038558 6.652934893 4.846315002 5.958611011 5.421877826 1 15.72152896 2.991928114 24.28250336 5.226609297 4.976945476 0 1.524605898 2444.087524 7352536.963 0.392363228 0.448734175 981.5854545 -2.991928114 -0.24966382 STSGPRPGCQPS(ph)SPCVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(0.001)T(0.001)S(0.001)GPRPGCQPS(0.498)S(0.498)PCVPK 53.625 0.074315 211490000 82878 71086 80109 98490 65804 88929 101600 91026 75290 TRUE FALSE 78960.52119 78329.74422 83782.07689 88589.59808 77280.19677 85849.36643 86099.05399 83055.28088 86965.58867 0.907951322 0.900698143 0.963393431 1.018674161 0.888629606 0.987164783 0.99003589 0.955036149 1 16.40815703 3.70164092 5.323252384 0.972380148 0.90411623 0.397312205 0.03466899 0.164089726 12.58725464 0.008630872 0.013923837 5030.844808 -3.70164092 -0.068263918 STSGPRPGCQPSS(ph)PCVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 STSGPRPGCQPS(0.023)S(0.977)PCVPK;STSGPRPGCQPS(0.019)S(0.981)PCVPK 158 1.78E-10 441440000 269098 220154 251692 284060 198289 265151 309100 294160 232893 TRUE FALSE 256378.2708 242587.9429 263232.3272 255505.7491 232870.5388 255968.7544 261941.118 268401.791 269008.857 0.953047694 0.901784222 0.978526618 0.949804226 0.865661233 0.951525378 0.973726742 0.997743323 1 18.03729415 1.66698461 2.548157046 0.995962056 0.930281694 0.452201451 0.030767486 0.223459655 3.263483172 0.01977937 0.008188196 46.44988146 -1.66698461 -0.065680362 STSGS(ph)PRPAGAKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.017)T(0.017)S(0.4)GS(0.567)PRPAGAKPK 84.213 0.0064756 94317000 118180 96065 99169 121510 74871 116130 126520 128940 92209 TRUE FALSE 112593.8656 105854.1327 103715.9967 109295.5839 87928.47869 112108.389 107217.0503 117649.33 106508.3008 1.057137 0.993858056 0.973783226 1.026169633 0.825555173 1.05257889 1.006654406 1.104602451 1 16.70060635 -0.572338148 6.301075302 1 1.003829918 0.000222707 0.073533347 0 0 0.065734029 0.015493659 0.26770831 0.572338148 0.003829918 STSQGSINS(ph)PVYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STSQGSINSPVYSR 14 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 STSQGS(0.017)INS(0.983)PVYSR 125.39 9.60E-05 53191000 111990 103890 104900 127170 117890 117670 126700 137810 144960 TRUE FALSE 106696.4546 114476.5091 109709.7688 114386.63 138449.9787 113595.0584 107369.588 125742.6258 167439.6564 0.637223325 0.683688151 0.655219744 0.683151366 0.826864923 0.678423862 0.64124348 0.750972789 1 17.35328173 -5 0.286508689 3.382317929 0.668870637 0.762396782 0.054323468 117.7493724 1.115558831 167.3267437 0.059711873 1.00E-05 5 -2.713447292 STSSFPCPAGHFNGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSSFPCPAGHFNGFR 16 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 187.16 1.38E-09 2660000000 2667400 2118640 1105550 1227930 2579100 1149980 2514420 1285330 1281650 FALSE TRUE 2541317.288 2334531.825 1156240.561 1104496.143 3028894.223 1110155.904 2130799.049 1172779.691 1480401.736 1.716640305 1.576958313 0.781031616 0.74607866 2.045994779 0.749901785 1.439338388 0.792203672 1 20.4975573 3.893674633 6.779120331 1.123044645 1.664697508 0.250566726 0.405249131 0.304988459 16.80405618 0.095878458 0.174523723 7828.429285 -3.893674633 0.541652863 STST(ph)PTSPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 STS(0.008)T(0.522)PT(0.043)S(0.427)PGPR 163.09 0.00027226 1786400000 3401500 2946100 3124900 3497700 3146100 2951200 3639700 2979200 3223500 TRUE FALSE 3240717.836 3246310.939 3268179.756 3146104.551 3694778.844 2848999.204 3084396.917 2718325.454 3723383.917 0.870368973 0.871871129 0.8777445 0.844958409 0.992317453 0.765163966 0.828385411 0.730068538 1 21.82818295 2.195956521 24.99984937 0.816028587 0.88412956 0.108277298 0.079995827 249.9534497 146669.886 0.026169324 0.019327471 157.0205596 -2.195956521 0.068100973 STSTLEIQPSRAS(ph)PTSDIESVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 STSTLEIQPS(0.053)RAS(0.909)PT(0.031)S(0.007)DIESVER;STSTLEIQPS(0.012)RAS(0.775)PT(0.204)S(0.01)DIESVER 137.42 1.67E-09 0 142302 126824 126035 150641 143417 125870 153006 126089 160976 TRUE FALSE 135575.6665 139747.5098 131813.8294 135498.2805 168428.8794 121511.0903 129662.1246 115047.9787 185939.3359 0.729139242 0.751575825 0.708907713 0.728723053 0.905827046 0.653498571 0.697335633 0.618739322 1 17.50447248 STSTPTS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_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 STSTPT(0.002)S(0.998)PGPR;STS(0.001)T(0.133)PT(0.006)S(0.86)PGPR;STS(0.001)T(0.01)PT(0.003)S(0.985)PGPR;STST(0.004)PT(0.079)S(0.917)PGPR;STST(0.004)PT(0.002)S(0.994)PGPR;STST(0.005)PT(0.107)S(0.888)PGPR;STS(0.001)T(0.062)PT(0.106)S(0.83)PGPR 189.43 2.85E-06 10127330000 11331800 10075520 10819040 12090890 10912000 10370640 12261810 10976480 11212920 TRUE FALSE 10796168.27 11102226.94 11315103.69 10875490.77 12815049.35 10011502.14 10391045.68 10015321.22 12951762.37 0.833567507 0.857198166 0.873634287 0.839691963 0.989444446 0.772983773 0.802288166 0.773278643 1 23.62664509 -0.067642384 7.891065551 0.999999999 0.842582143 0.39185934 0.061559844 7838552.88 993345.1351 0.05766779 0.013986493 0.855771101 0.067642384 -0.157417856 STSTSS(ph)MKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 STSTSSMKK 9 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 STS(0.002)T(0.001)S(0.187)S(0.809)MKK;ST(0.005)S(0.006)T(0.005)S(0.138)S(0.846)MKK 64.64 0.042151 476740000 583810 392880 415890 738020 365140 515410 678710 506380 456390 TRUE FALSE 556214.4583 432914.9187 434958.9679 663832.8275 428820.3004 497561.2225 575160.3241 462038.6827 527164.6303 1.055105799 0.821213894 0.825091334 1.259251455 0.813446646 0.943844093 1.091044981 0.876459945 1 19.00789405 STT(ph)PPPAEPVSLPQEPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.065)T(0.065)T(0.87)PPPAEPVSLPQEPPK 142.77 1.23E-06 53967000 66224 68010 58650 77541 38745 65685 64201 71646 45397 TRUE FALSE 63093.72276 74940.29632 61339.16051 69746.43136 45502.11573 63410.31198 54405.95832 65372.29642 52436.9349 1.203230564 1.429150969 1.169770137 1.330101225 0.867749341 1.209268087 1.037550315 1.246684165 1 15.67829574 2.781784668 24.99563658 1.082862807 1.292246875 0.409507824 0.125215014 425.3556768 245974.2059 0.03423017 0.036306441 605.0408085 -2.781784668 0.209384069 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.297)T(0.297)T(0.405)PPPAEPVSLPQEPPKPR;S(0.004)T(0.006)T(0.99)PPPAEPVSLPQEPPKPR;S(0.018)T(0.018)T(0.963)PPPAEPVSLPQEPPKPR;S(0.002)T(0.134)T(0.864)PPPAEPVSLPQEPPKPR;S(0.008)T(0.008)T(0.984)PPPAEPVSLPQEPPKPR;S(0.004)T(0.025)T(0.971)PPPAEPVSLPQEPPKPR;S(0.1)T(0.1)T(0.799)PPPAEPVSLPQEPPKPR 222.46 1.15E-24 13286600000 6451360 6123840 5803930 7067120 3982760 6605660 6548780 6801520 4532870 TRUE FALSE 6146416.998 6747866.258 6070045.931 6356719.671 4677352.083 6376904.338 5549643.334 6205942.852 5235804.329 1.173920302 1.288792673 1.159333992 1.214086561 0.893339741 1.217941683 1.059940935 1.185289301 1 22.31997975 2.925713482 24.99999946 1.08268615 1.215866719 0.334265596 0.095627472 146.1654662 49189.12774 0.026133391 0.027718654 842.7785665 -2.925713482 0.133180569 STT(ph)PTSSPFR ddPTM_SK-BR-3_Trastuzumab_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 ST(0.003)T(0.996)PT(0.001)SSPFR;S(0.006)T(0.003)T(0.99)PT(0.001)SSPFR;S(0.003)T(0.055)T(0.942)PTSSPFR 190.53 9.97E-06 1555020000 2785470 2417940 1997860 2323500 2594150 2217590 2937300 2481620 2758010 TRUE FALSE 2653806.353 2664330.835 2089463.857 2089937.366 3046568.939 2140794.302 2489160.938 2264316.197 3185708.105 0.833035001 0.836338656 0.655886788 0.656035423 0.956323944 0.671999515 0.781352483 0.710773279 1 21.60318265 -1.771171836 8.52790536 1.002575312 0.769720774 0.376273348 0.095632084 0.004454948 0.000119539 0.088095686 0.020587185 0.016936675 1.771171836 -0.232854538 STTGPFDREHLLSYLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STTGPFDREHLLSYLEK 17 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 92.551 0.0019713 107620000 327320 188810 303010 294820 301370 298200 427470 362280 346690 FALSE TRUE 311848.2323 208049.9537 316903.3082 265184.1335 353928.8326 287873.2592 362251.6005 330556.8426 400452.9146 0.778738825 0.51953662 0.791362222 0.662210522 0.883821343 0.718869182 0.90460473 0.825457452 1 18.61127309 1.838266264 0.437409932 0.992894189 0.644181735 0.497326585 0.095089635 0.716960461 0.34396824 0.094250115 0.077787523 68.90746361 -1.838266264 -0.348712454 STTS(ph)VSEEDVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STT(0.31)S(0.685)VS(0.005)EEDVSSR;STT(0.007)S(0.992)VSEEDVSSR;STT(0.025)S(0.975)VSEEDVSSR 285.55 8.99E-33 988090000 1733510 1389850 1441810 2526220 1991230 2442870 2420320 1494640 1743020 TRUE FALSE 1651570.418 1531477.295 1507918.415 2272279.566 2338499.882 2358272.799 2051055.732 1363761.398 2013318.639 0.82032242 0.760673082 0.748971566 1.128623916 1.161515041 1.171336098 1.018743726 0.677369876 1 20.94114409 3.245997116 24.99945738 1.042642935 0.7794689 0.410155849 0.140179122 155.9922666 524399.6136 0.038832958 0.051563002 1761.964346 -3.245997116 -0.263174035 STTSVS(ph)EEDVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STTSVS(1)EEDVSSR 183.06 1.12E-05 101960000 77847 61016 66754 80398 68731 75696 82235 72590 78778 TRUE FALSE 74167.32659 67233.59977 69814.73693 72316.24029 80717.66464 73074.62854 69688.5404 66233.63478 90994.4899 0.81507492 0.738875506 0.767241368 0.794732081 0.887061016 0.803066522 0.765854509 0.727886214 1 16.47349157 -1.1313982 4.743987331 1.000016171 0.786511758 0.693128931 0.044437069 7.63E-06 1.40E-06 0.043216518 0.01018546 0.073892745 1.1313982 -0.213504413 STTTGHLIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 215.38 1.91E-08 21894330000 34923200 29513310 30095860 34605280 28719300 32969400 41249770 35539980 32220360 FALSE TRUE 33272449.55 32520749.84 31475784.95 31126691.51 33727936.83 31827661.41 34956359.98 32427910.94 37216928.87 0.894013841 0.873816052 0.845738375 0.836358411 0.906252554 0.855193117 0.939259661 0.871321518 1 25.14945567 0.238978939 0.505404589 1.008539089 0.868754308 0.638126377 0.029367578 1.800992062 0.680418064 0.063021862 0.0140432 1.733719921 -0.238978939 -0.139784782 STVDGLQVTQLNVDHTTENEDELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 STVDGLQVTQLNVDHTTENEDELFR 25 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 183.49 2.05E-17 38583000 17045 13962 15779 19126 19446 15506 22144 20596 18827 FALSE TRUE 16239.31663 15384.74367 16502.48276 17203.41814 22837.37624 14969.02333 18765.5261 18792.50505 21746.59501 0.746752153 0.70745529 0.758853639 0.791085599 1.050158714 0.688338718 0.8629179 0.864158506 1 14.40850191 4.07709365 0.045738237 1.510159358 1.65E-07 0.376283232 0.094261923 226.4354421 2.039713541 25.46194135 43.09580114 11942.45601 -4.07709365 -1.510159194 STVLSLDWHPNNVLLAAGSCDFK ddPTM_SK-BR-3_Trastuzumab_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 ; 234.51 4.53E-37 196206000 746280 782990 724090 837550 501950 814280 801860 931700 495760 FALSE TRUE 711004.8234 862777.5712 757290.2427 753357.8828 589489.9211 786081.2794 679521.5298 850115.4087 572639.9288 1.241626348 1.506666804 1.322454486 1.315587413 1.029425109 1.372732218 1.186647133 1.484554894 1 19.12726874 -4.270044311 0.212598433 3.71E-12 1.3522986 0.285267728 0.142544786 130.6276653 1.727042257 56.76466937 0.281075966 5.37E-05 4.270044311 1.3522986 STVPGHAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 STVPGHAGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;;;;;;;;; 112.84 0.001897 1504435000 2796710 2607588 2454390 2824750 2656528 2469008 2918460 2736276 2472455 FALSE TRUE 2664515.061 2873304.182 2566926.209 2540800.763 3119825.642 2383505.634 2473195.326 2496673.168 2855870.694 0.932995694 1.006104439 0.898824381 0.889676402 1.092425385 0.834598583 0.866003958 0.874224864 1 21.44549923 STVTGERQS(ph)GDGQESTEPVENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK 322.6 5.13E-68 3468060000 2553610 2144250 2380110 2661580 1581930 2670310 2671250 2713040 1858470 TRUE FALSE 2432905.916 2362751.513 2489240.398 2394032.922 1857818.091 2577836.495 2263701.752 2475471.835 2146672.036 1.133338431 1.10065789 1.159581136 1.115229938 0.865441046 1.200852507 1.054516812 1.153167225 1 21.03367037 1.366446667 0.01108503 1.68E-07 2.148581061 0.088197169 0.091948988 2171.600483 22.89842686 2227.954609 2206.080716 23.25126936 -1.366446667 2.148580894 STVTGERQS(ph)GDGQESTEPVENKVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 STVTGERQSGDGQESTEPVENKVGK 25 2 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 S(0.005)T(0.005)VT(0.004)GERQS(0.976)GDGQES(0.007)T(0.002)EPVENKVGK;STVTGERQS(1)GDGQESTEPVENKVGK;S(0.001)T(0.001)VT(0.022)GERQS(0.977)GDGQESTEPVENKVGK;S(0.002)T(0.002)VT(0.009)GERQS(0.987)GDGQESTEPVENKVGK 230.44 1.26E-34 425848000 464082 159421 507336 322454 391647 458140 842210 545202 591326 TRUE FALSE 442145.7636 175666.1811 530597.8574 290040.3113 459950.1128 442274.4969 713715.3963 497461.2226 683025.816 0.647333898 0.257188201 0.776834265 0.424640335 0.673400773 0.647522373 1.044931801 0.728319795 1 19.38158058 2.101845074 1.65348094 0.929139582 0.510890297 0.497276639 0.165898265 0.272112329 1.419984386 0.0907634 0.048808364 126.428526 -2.101845074 -0.418249285 SVAAEGALLPQTPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQT(0.001)PPS(0.999)PR 347.9 1.46E-87 656976000 1057340 883210 950400 1088140 1028470 967630 1192720 1036440 1150410 TRUE FALSE 1007361.634 973210.1031 993976.7801 978758.0999 1207834.842 934120.7305 1010748.658 945683.8191 1328809.707 0.758093223 0.732392379 0.748020408 0.736567542 0.908959978 0.702975547 0.760642139 0.711677386 1 20.34170309 -1.72999652 4.010202379 1.020108751 0.7566935 0.641850415 0.056945902 0.009791865 0.000659278 0.052734919 0.011876573 0.018621021 1.72999652 -0.263415251 SVAGKEDNTDT(ph)DQEKKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVAGKEDNTDTDQEKKEEK 19 3 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 SVAGKEDNT(0.3)DT(0.7)DQEKKEEK 78.976 0.0049644 124730000 170460 136520 162390 168960 59538 196410 186370 221410 62028 TRUE FALSE 162402.6936 150431.5432 169835.7421 151975.8198 69921.40835 189608.2725 157935.8336 202022.1666 71646.98544 2.266706584 2.099621391 2.37045203 2.121175355 0.975915566 2.64642359 2.204361183 2.819688301 1 16.12861838 3.000780412 24.99848708 2.025839795 2.22089033 0.042518899 0.600097376 136.2119334 4362874.74 0.164006418 0.194385584 1001.798582 -3.000780412 0.195050536 SVAPLPPQRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVAPLPPQRSPR 12 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR 131.72 0.00011733 1730980000 1746070 1552980 1701660 1913640 1654620 1812510 2113990 1851250 2029930 TRUE FALSE 1663536.731 1711230.428 1779682.794 1721277.272 1943185.204 1749742.324 1791461.999 1689144.736 2344721.177 0.709481685 0.729822567 0.759016813 0.734107445 0.828748946 0.746247503 0.764040525 0.720403241 1 21.16098494 -5 0.327095269 3.490823723 0.737931899 0.843852784 0.033754647 126.6638398 1.102676284 219.1616456 0.028009678 1.00E-05 5 -2.752891824 SVAVS(ph)DEEEVEEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER 380.2 5.42E-105 2319901000 457643 395976 444693 444393 426211 433208 484929 442788 486720 TRUE FALSE 436011.1224 436326.4046 465082.6139 399721.7713 500542.0635 418205.8983 410944.1747 404015.1354 562198.0518 0.775547195 0.776107998 0.827257605 0.710998144 0.890330484 0.743876463 0.730959799 0.71863489 1 19.10071893 -1.102485411 5.09894561 1.000004541 0.771454349 0.639362105 0.053881705 3.43E-06 6.03E-07 0.048144704 0.011347515 0.078979538 1.102485411 -0.228550192 SVAVS(ph)DEEEVEEEAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVAVSDEEEVEEEAERR 17 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 S(0.001)VAVS(0.999)DEEEVEEEAERR 104.03 0.00053313 207200000 37987 29449 37562 38279 34738 36758 37926 34423 39792 TRUE FALSE 36191.42979 32449.88658 39284.25485 34431.12219 40796.2962 35485.06124 32139.69214 31408.73963 45962.74013 0.787408011 0.706004178 0.854697843 0.749109433 0.887594954 0.772039725 0.699255354 0.683352201 1 15.48817719 3.764962339 24.95045974 0.787732744 0.746706109 0.03577329 0.096199473 2904.492668 2744828.564 0.023094091 0.041617814 5820.527419 -3.764962339 -0.041026636 SVDEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVDEALR 7 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;;; 170.44 0.0022673 3257221000 7295010 6131380 6172190 7125920 7651970 6244700 8110340 7192520 8263410 FALSE TRUE 6950189.335 6756174.593 6455191.017 6409608.983 8986471.145 6028444.473 6872958.676 6562704.819 9544857.419 0.728160624 0.707833999 0.676300413 0.671524854 0.941498731 0.631590836 0.720069287 0.687564469 1 23.18629222 -1.359827832 5.528358131 1.000080997 0.719731565 0.526530411 0.083271346 7.53E-05 8.72E-06 0.073042619 0.017211355 0.043668892 1.359827832 -0.280349432 SVDETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SVDETLR 7 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;;; 217.5 8.14E-05 13782940000 15537520 12165600 13247790 14867510 15598300 13448670 16329300 13830240 15898790 FALSE TRUE 14803092.22 13405288.47 13855214.28 13372999.65 18318638.58 12982939.19 13837965.38 12619190.87 18364293.15 0.806080152 0.729964849 0.754464882 0.728206609 0.997513949 0.706966453 0.75352562 0.687159084 1 24.13040003 -1.072611003 4.1840678 1.000028637 0.769948578 0.408621458 0.086771018 15790905.83 44891301.54 6933.419981 0.019398792 0.08460363 1.072611003 -0.230080059 SVDGPIRLPIVDKYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDGPIRLPIVDKYK 15 2 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 75.961 0.017028 357310000 971120 618240 764400 757280 751420 813320 1242700 1074700 1024300 FALSE TRUE 925217.0822 681239.3589 799448.4961 681156.7757 882467.4101 785154.5245 1053103.291 980593.5707 1183143.213 0.781999231 0.575787742 0.67569884 0.575717942 0.745866942 0.663617486 0.89008945 0.828803783 1 20.17419328 1.513146797 1.02042587 0.975880657 0.655894115 0.695260439 0.074306109 0.249437566 0.507883446 0.062007481 0.022796921 32.59468568 -1.513146797 -0.319986542 SVDIS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDISPTR 8 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SVDIS(0.952)PT(0.048)R 73.327 0.046001 85728000 595100 570580 533110 600170 500910 575320 634270 630260 524520 TRUE FALSE 566970.8024 628722.7507 557553.6208 539839.7714 588268.5454 555396.5241 537500.4623 575071.0932 605859.8827 0.935811759 1.03773623 0.920268261 0.891030726 0.970964677 0.916707873 0.887169588 0.949181667 1 19.20862465 3.704629814 24.71161963 0.925421128 0.986774008 0.195585561 0.042352279 587.1457293 427614.8875 0.01047729 0.01623238 5065.587412 -3.704629814 0.06135288 SVDISLGDS(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVDISLGDSPRR 12 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PRR;SVDISLGDS(1)PRR;SVDISLGDS(1)PRR 177.74 1.40E-05 626820000 603840 506335 535861 575217 566078 546760 678800 599900 661560 TRUE FALSE 575297.6799 557931.1122 560430.7569 517395.0943 664801.824 527825.5641 575236.593 547369.5757 764151.346 0.752858296 0.730131688 0.733402826 0.677084581 0.869987114 0.690734325 0.752778355 0.716310425 1 19.54349888 -1.257199469 4.982416727 1.000051629 0.740680455 0.711294421 0.051974418 2.59E-05 3.87E-06 0.043807673 0.010323516 0.055309602 1.257199469 -0.259371174 SVDQGGGGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVDQGGGGSPR 11 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 SVDQGGGGS(1)PR;SVDQGGGGS(1)PR 162.67 2.61E-05 563360000 567240 514780 582280 674930 596080 584200 680210 602560 690150 TRUE FALSE 540427.6894 567236.6673 608978.114 607084.7541 700036.1633 563969.0075 576431.4716 549796.652 797174.9372 0.6779286 0.711558581 0.763920296 0.761545209 0.878146227 0.707459531 0.723092818 0.689681306 1 19.60453683 -2.325571011 2.393637146 2.587068085 0.736196214 0.677720455 0.056494114 2780915.987 461945.3902 24045636.8 0.013986378 0.004725296 2.325571011 -1.850871871 SVDYPCLLRPSYVLSGSAMNVVFSEDEMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVDYPCLLRPSYVLSGSAMNVVFSEDEMKK 30 2 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 268.66 2.54E-59 79948000 187090 130580 162990 150930 113400 160250 173490 186550 114230 FALSE TRUE 178246.6265 143886.2505 170463.2527 135758.2297 133176.9241 154700.5023 147020.9141 170214.693 131944.205 1.350924252 1.090508298 1.291934365 1.028906345 1.00934273 1.172469093 1.114265792 1.290050541 1 17.00956846 5.745855646 0.894647047 1.122424124 2.436562923 0.314549352 0.104140651 12.85678173 2.071032134 0.030316657 25.20566923 557000.5782 -5.745855646 1.314138799 SVEDEMDS(ph)PGEEPFYTGQGR ddPTM_SK-BR-3_Trastuzumab_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 372.64 3.45E-112 1178137000 1871830 1778910 1652280 1976330 1713330 1785180 1938320 1866740 1639130 TRUE FALSE 1783352.306 1960182.951 1728038.672 1777665.554 2012134.21 1723358.769 1642593.684 1703278.349 1893317.909 0.941919103 1.035316331 0.912703917 0.938915512 1.0627556 0.910232117 0.867574155 0.899626176 1 20.85248525 2.039029343 24.99881876 0.902990253 0.97871779 0.191907985 0.056014336 182.0446511 116601.2857 0.019488206 0.014392967 109.4030283 -2.039029343 0.075727537 SVEDVRPHHT(ph)DANNQSACFEAPDQK ddPTM_SK-BR-3_Trastuzumab_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(0.375)VEDVRPHHT(0.625)DANNQSACFEAPDQK 113.47 0.0030088 507280000 164300 151960 162000 194480 113910 191320 213250 194580 9526.9 TRUE FALSE 156533.8646 167444.8968 169427.8602 174930.5009 133775.8679 184694.5404 180714.7959 177541.5437 11004.283 14.22481271 15.21633866 15.3965379 15.89658327 12.15670916 16.78387774 16.4222236 16.1338584 1 13.42577753 -0.939646698 5.763502341 0.999988942 15.29090755 0.920918567 1.314987166 0.000182693 3.36E-05 1.244956463 0.293438849 0.114908803 0.939646698 14.2909186 SVEEEEQVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVEEEEQVWR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 232.46 4.78E-10 1513350000 857000 707440 756150 878090 838360 711000 845280 776650 801640 FALSE TRUE 816491.3084 779528.9403 790820.2254 789822.7249 984569.7186 686377.8917 716317.0114 708642.4087 925954.237 0.881783652 0.841865515 0.85405973 0.852982462 1.063302785 0.741265458 0.773598719 0.765310401 1 19.82058137 SVEETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SVEETLR 7 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;;;; 158.36 0.003312 1743160000 3421820 2588890 2916420 2829170 3273500 2523640 3279970 3028100 3444780 FALSE TRUE 3260077.35 2852700.834 3050140.742 2544776.457 3844397.364 2436245.714 2779550.336 2762943.511 3978978.889 0.819325119 0.716942943 0.766563691 0.639555154 0.966176869 0.612279125 0.698558704 0.694385064 1 21.92396681 -1.096708285 4.744607237 1.000006839 0.737998618 0.40471938 0.099382971 1.29E-05 2.45E-06 0.086899305 0.020481303 0.080037168 1.096708285 -0.262008221 SVEGWILFVTGVHEEATEEDIHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVEGWILFVTGVHEEATEEDIHDK 24 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 122.18 7.05E-05 33928000 52106 50847 50256 58868 38455 53221 57818 59535 25537 FALSE TRUE 49643.05264 56028.36711 52560.28731 52950.4768 45161.53982 51377.94343 48996.8022 54321.79979 29497.14754 1.682978077 1.899450347 1.781876951 1.795104992 1.531047698 1.741793621 1.661069164 1.841595013 1 14.84828783 -2.290705554 0.423662471 2.55E-16 1.762458119 0.828994092 0.105237025 26.8989324 1.464801989 25.46636161 0.058615365 0.005120289 2.290705554 1.762458119 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIK 32 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 159.59 5.13E-14 129170000 163980 163930 175030 186000 133340 176130 244670 191360 110860 FALSE TRUE 156228.9904 180634.6534 183055.2986 167302.9266 156594.4538 170030.5739 207341.0978 174603.5039 128051.6026 1.220047131 1.410639537 1.429543207 1.306527394 1.222901163 1.327828551 1.619199554 1.36354017 1 16.96636578 4.633272904 3.212374055 1.3679014 1.214079788 0.01268316 0.160098605 0.776429935 13.17063739 0.037321104 0.255929662 42980.64259 -4.633272904 -0.153821612 SVEMHHEALSEALPGDNVGFNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVEMHHEALSEALPGDNVGFNVK 23 0 A0A2U3TZH3;Q05639;P68104;A0A087WVQ9;A0A087WV01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 132.13 1.62E-05 151778000 251440 211508 232620 241100 193689 224000 265660 244350 60783 FALSE TRUE 239554.9295 233060.9057 243285.8571 216864.1699 227468.3003 216242.8238 225128.6878 222953.4186 70208.9172 3.412029968 3.319534255 3.465170334 3.088840828 3.23987763 3.079990868 3.20655405 3.175571245 1 16.09936666 -1.247391254 0.474605466 2.99E-13 3.325461919 0.975359673 0.112631364 3.40951283 0.417940131 4.534978496 0.055166981 0.05657294 1.247391254 3.325461919 SVES(ph)TSPEPSKIMLVEPPVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVESTSPEPSKIMLVEPPVAK 21 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 1 S(0.053)VES(0.34)T(0.303)S(0.303)PEPS(0.002)KIMLVEPPVAK 72.532 0.0094517 61835000 61352 21772 77699 39383 70225 58407 131120 75419 115160 TRUE FALSE 58452.01255 23990.59155 81261.576 35424.14602 82472.21777 56384.35094 111115.2358 68814.91254 133018.4246 0.439427942 0.180355403 0.610904664 0.26631007 0.620005973 0.423883767 0.835337181 0.517333691 1 17.02126656 1.39550712 0.355120841 1.028586069 0.283691786 0.565775703 0.161184887 0.767664162 0.312949985 0.219126957 0.166035598 24.86034319 -1.39550712 -0.744894282 SVESTS(ph)PEPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 SVES(0.001)T(0.025)S(0.974)PEPSK;SVEST(0.229)S(0.771)PEPSK;SVEST(0.033)S(0.967)PEPSK;SVEST(0.001)S(0.999)PEPSK;SVEST(0.24)S(0.76)PEPSK;SVEST(0.155)S(0.845)PEPSK 314.35 1.06E-45 4964030000 9612130 8982290 8871570 10380790 6536220 10135260 10740890 10278660 7213220 TRUE FALSE 9157783.664 9897595.563 9278340.26 9337293.267 7676134.699 9784273.405 9102169.961 9378606.04 8331809.318 1.099135052 1.187928718 1.113604489 1.120680144 0.921304654 1.174327572 1.092460186 1.125638584 1 22.99019839 1.432995691 0.012787385 6.93E-05 2.167006397 0.145972773 0.072927709 1101.790701 13.95071048 1184.904312 1176.097412 27.10164741 -1.432995691 2.166937142 SVFALTNGIYPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVFALTNGIYPHK 13 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 164.64 3.67E-05 2706300000 2184250 1894750 2023220 2270200 1902120 2167200 2525800 2357800 2010020 FALSE TRUE 2081004.831 2087827.179 2115986.638 2041995.183 2233849.126 2092149.321 2140442.821 2151338.533 2321723.636 0.896318924 0.899257408 0.911386095 0.879516903 0.962151176 0.901119017 0.921919727 0.926612668 1 21.14676482 -5 0.161870596 1.343642726 0.886218821 0.679434231 0.020015553 69.92755554 0.646143492 7.67616829 0.073091872 1.00E-05 5 -0.457423905 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR 31 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;; 304.07 4.44E-82 282119000 741645 711904 673323 807550 585987 720972 748505 785526 569361 FALSE TRUE 706588.9106 784447.827 704195.5256 726373.5398 688182.9473 696004.5589 634306.815 716741.1791 657654.596 1.074407318 1.192796084 1.070768044 1.104490935 1.046420038 1.058313229 0.964498414 1.089844401 1 19.32697055 2.736665359 1.167943921 1.016071453 1.128219003 0.426706141 0.04606706 0.3641437 1.029872938 0.021125752 0.019605025 545.3374947 -2.736665359 0.11214755 SVGGS(ph)GGGSFGDNLVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.112)VGGS(0.664)GGGS(0.224)FGDNLVTR 261.06 2.98E-27 257860000 538680 417860 485110 553410 399480 538240 640710 571610 375240 TRUE FALSE 513217.664 460440.4091 507352.7733 497780.1754 469149.1855 519600.6138 542957.9221 521556.7981 433430.3027 1.184083486 1.06231707 1.170552151 1.148466483 1.08240975 1.198810075 1.252699497 1.203323337 1 18.7254405 2.213822603 24.95337959 1.192546641 1.128073796 0 0.076459472 415.2844988 418897.3215 0.025890678 0.01913031 163.6148066 -2.213822603 -0.064472845 SVGGSGGGS(ph)FGDNLVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.053)VGGS(0.094)GGGS(0.853)FGDNLVTR;S(0.219)VGGS(0.039)GGGS(0.742)FGDNLVTR;S(0.187)VGGS(0.169)GGGS(0.644)FGDNLVTR 245.31 1.50E-20 725360000 862080 637630 772660 843290 568220 849790 960970 830690 585820 TRUE FALSE 821331.1869 702605.2219 808087.2253 758520.8871 667317.3881 820361.5592 814356.3771 757950.3798 676665.9736 1.213791174 1.038333904 1.194218797 1.120967976 0.986184342 1.212358226 1.203483563 1.120124861 1 19.36808432 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR 30 2 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ;; 143.09 2.63E-08 199784000 240811 207525.7 223113 240512 189805.3 235571 286405 268680 207244.1 FALSE TRUE 229428.3413 228672.8048 233342.9517 216335.2768 222907.2842 227413.1172 242708.6571 245152.9548 239382.4566 0.958417524 0.955261334 0.974770479 0.903722353 0.931176359 0.949999095 1.013894922 1.024105769 1 17.8689579 1.73763162 4.727159397 1.01473171 0.946344415 0.726003745 0.019421457 0.094952567 4.940576815 0.010323444 0.005245051 54.6552166 -1.73763162 -0.068387295 SVHELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVHELEK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 145.34 0.0022931 8273980000 13969690 10455190 12386240 14842150 13131800 12956600 18126520 16084970 14601700 FALSE TRUE 13309370.44 11520585.75 12954161.36 13350188.88 15421981.76 12507909.69 15360986.46 14676484.76 16866057.06 0.78912163 0.683063368 0.768061042 0.791541783 0.914379793 0.741602477 0.91076334 0.870178768 1 24.0076194 1.568806119 0.332227877 1.014562112 0.712835168 0.624618967 0.057961792 0.778608325 0.288202166 0.086043028 0.076743017 37.0515277 -1.568806119 -0.301726944 SVHPYEVAEVIALPVEQGNFPYLQWVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVHPYEVAEVIALPVEQGNFPYLQWVR 27 0 O60888-3;O60888;O60888-2 O60888-3 CUTA Protein CutA 0 ; 208.97 1.85E-25 454430000 360940 289970 274490 324420 424830 295450 436940 400460 394520 FALSE TRUE 343879.0815 319518.2727 287075.638 291808.6852 498920.2175 285218.4924 370276.778 365393.5994 455700.1467 0.754617009 0.70115903 0.629966086 0.640352406 1.094843223 0.625890719 0.812544786 0.801829014 1 18.79772531 SVICDIS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVICDISPLR 10 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 SVICDIS(1)PLR 85.845 0.014646 37507000 89191 97804 97926 100730 93838 101940 111140 95598 117970 TRUE FALSE 84975.11819 107770.3388 102416.004 90604.42903 110203.3175 98409.79224 94183.55177 87226.93232 136264.1851 0.623605668 0.790892623 0.751598844 0.66491741 0.808747489 0.722198516 0.691183466 0.640131024 1 17.0560469 -1.466797951 3.54388403 1.003674447 0.714895403 0.691273438 0.060523506 215981499.5 261949461.2 7659937.496 0.013791049 0.034135168 1.466797951 -0.288779044 SVIDLRPEDVVHES(ph)GSLGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 SVIDLRPEDVVHES(0.5)GS(0.5)LGDR 110.94 0.00010593 165490000 73469 63874 72162 76617 97785 61279 92918 79835 97400 TRUE FALSE 69996.26597 70382.83322 75470.69908 68915.3136 114838.673 59156.89286 78741.65254 72844.22417 112504.2945 0.62216528 0.625601303 0.670825051 0.612557182 1.020749239 0.525818975 0.699899083 0.647479498 1 16.77962055 -5 0.323874265 4.155098606 0.659616538 0.372343561 0.130535238 346.4901974 3.040175257 751.0330201 0.104060803 1.00E-05 5 -3.495482068 SVIDLRPEDVVHESGS(ph)LGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 SVIDLRPEDVVHES(0.057)GS(0.943)LGDR;SVIDLRPEDVVHES(0.043)GS(0.957)LGDR;SVIDLRPEDVVHES(0.14)GS(0.86)LGDR 171.29 4.86E-12 564530000 1514490 1273990 1505200 1602830 1958360 1291040 1863490 1695100 2005080 TRUE FALSE 1442903.059 1403811.029 1574214.909 1441710.483 2299897.364 1246330.961 1579180.375 1546668.058 2316017.566 0.623010413 0.606131426 0.679707672 0.622495487 0.993039689 0.538135366 0.68185164 0.667813613 1 21.14321476 -5 0.277650691 3.36447361 0.647279711 0.413987382 0.120552493 213.6828913 2.052753541 291.0779598 0.130310279 1.00E-05 5 -2.717193899 SVIDLRPEDVVHESGSLGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 0 72.644 0.0095605 33070000 46485 36703 39967 46745 74819 37757 61780 50034 77275 FALSE TRUE 44287.74617 40443.07743 41799.52648 42046.10379 87867.40991 36449.46562 52354.32633 45652.75771 89258.41233 0.496174478 0.453101017 0.468297894 0.471060404 0.984416008 0.408358884 0.586547811 0.511467284 1 16.44570052 -5 0.216640462 3.25851565 0.479928891 0.435221776 0.162114945 139.2246347 1.391098003 137.2789368 0.300992856 1.00E-05 5 -2.77858676 SVIDYQTHFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVIDYQTHFR 10 0 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ;; 195.83 6.49E-06 241540000 659290 594170 420810 516660 769090 485720 737450 502870 557260 FALSE TRUE 628126.6683 654716.5985 440104.5547 464724.3552 903219.0525 468899.3946 624938.4583 458836.0369 643677.0347 0.975841353 1.017150781 0.683735058 0.721983744 1.403217769 0.728469977 0.970888232 0.712835805 1 19.29597747 SVISHSVTSDMQTIEQES(ph)PIMAKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVISHSVTSDMQTIEQESPIMAKPR 25 1 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 SVISHSVTSDMQTIEQES(1)PIMAKPR 252.28 5.32E-45 66807000 50260 31686 50289 42296 48624 46094 57861 54065 50366 TRUE FALSE 47884.30941 34914.83942 52594.80039 38044.32572 57104.01021 44497.75322 49033.24176 49330.78198 58176.50205 0.823086774 0.600153639 0.904055736 0.6539466 0.981564862 0.764875021 0.842835854 0.847950293 1 15.82814893 0.450176833 0.184544904 1.109656746 0.673091529 0.292374551 0.107016941 8.12246347 0.747757965 1.041928097 0.460229381 2.819530733 -0.450176833 -0.436565218 SVKEDSVPTGAEENVVCES(ph)PVEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVKEDSVPTGAEENVVCESPVEIIK 25 1 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK 239.24 9.56E-39 966400000 1311759 882840 1210984 1137520 842943 1320602 1577279 1423062 1044489 TRUE FALSE 1249754.752 972802.3997 1266508.814 1023174.328 989951.9923 1274869.222 1336636.12 1298451.147 1206463.02 1.035883182 0.806325916 1.049770108 0.848077655 0.820540685 1.056699792 1.107896469 1.076246123 1 20.20235226 2.130570252 7.493647718 1.075227631 0.912578639 0.426146082 0.084826113 0.196189507 12.37356175 0.029958363 0.022096902 135.0735308 -2.130570252 -0.162648993 SVKHDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVKHDSIPAADTFEDLSDVEGGGSEPTQR 29 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 SVKHDSIPAADT(0.001)FEDLS(0.999)DVEGGGSEPTQR 84.226 0.0012834 29686000 53450 34995 56970 48873 89137 48681 99105 74630 124040 TRUE FALSE 50923.52443 38561.03029 59582.13085 43960.19319 104682.4646 46995.16476 83984.71206 68095.00156 143275.4897 0.355423838 0.269139058 0.415857108 0.306822844 0.730637632 0.328005613 0.586176409 0.475273208 1 17.1284323 -4.999999999 0.132399556 3.002923071 0.182131237 0.696695525 0.124412026 69.93460052 0.580156044 36.8639297 0.787728876 1.00E-05 4.999999999 -2.820791834 SVLLLAYKPMEGNFEEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVLLLAYKPMEGNFEEIAR 19 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 156.85 1.07E-08 349640000 596430 572180 530730 670820 459840 557480 612340 609280 468960 FALSE TRUE 568237.9359 630485.7925 555064.4955 603387.8991 540035.9504 538174.3278 518916.2866 555928.2132 541683.9217 1.049021234 1.163936693 1.024701811 1.113911407 0.996957688 0.993520956 0.957968782 1.026296316 1 19.04709174 2.705397732 7.973465848 0.989207361 1.092729694 0.564666413 0.040279759 0.177840038 38.58622173 0.012263175 0.011672114 507.4552292 -2.705397732 0.103522333 SVMEELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVMEELKR 8 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 140.35 0.0010437 1141670000 835990 723800 745010 852680 720470 762660 968540 859180 578090 FALSE TRUE 796474.4095 797556.0429 779169.4454 766966.9864 846119.7399 736248.893 820771.4345 783945.6444 667737.2447 1.192796142 1.194415991 1.166880313 1.148605971 1.267144744 1.102602706 1.229183247 1.174033125 1 19.34892099 0.94991407 22.53147303 1 1.186978056 0.637116889 0.043833884 2562.772093 1152881.181 0.03608399 0.009020998 8.910746122 -0.94991407 0.186978056 SVNEILGLAES(ph)SPNEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.618)S(0.382)PNEPK 112.82 0.00046402 30101000 95757 87159 84199 97674 63835 86345 96201 101440 77321 TRUE FALSE 91230.75638 96040.60119 88059.60743 87855.62395 74967.80379 83354.851 81523.7706 92557.37583 89311.54578 1.021488942 1.075343623 0.985982346 0.983698392 0.839396554 0.933304314 0.912802145 1.036342782 1 16.44655907 3.362526946 2.291131295 0.936118536 1.047027943 0.325876471 0.05527446 0.261861551 2.794501275 0.015572034 0.022879312 2304.235941 -3.362526946 0.110909408 SVNEILGLAESS(ph)PNEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.021)S(0.979)PNEPK;SVNEILGLAES(0.044)S(0.956)PNEPK;SVNEILGLAES(0.251)S(0.749)PNEPK;SVNEILGLAES(0.041)S(0.959)PNEPK;SVNEILGLAESS(1)PNEPK 227.88 1.69E-15 244221000 616717 547512 561213 642982 404017 642029 671740 680120 463115 TRUE FALSE 587566.0096 603304.0953 586945.1712 578348.2278 474477.4369 619795.3747 569253.7256 620565.0873 534932.5089 1.098392788 1.127813481 1.097232195 1.081161115 0.886985608 1.158642192 1.064159901 1.160081089 1 19.02899736 0.08033324 0.008461719 1.41E-05 2.108535818 0.060649741 0.078602534 12917.69626 35.13812449 4503.152238 4251.301746 1.203187302 -0.08033324 2.10852175 SVNELIYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVNELIYKR 9 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 153.1 0.00012649 1908690000 2142110 1296320 1999940 1905400 2291200 2380800 3500200 2647300 3215200 FALSE TRUE 2040856.706 1428416.482 2091639.227 1713865.572 2690784.555 2298352.299 2966180.204 2415488.378 3713796.795 0.549533757 0.384624297 0.563207774 0.461486093 0.724537368 0.61886862 0.798692112 0.650409409 1 21.82446345 1.478052574 0.347818692 1.018941235 0.421929741 0.747320789 0.087650517 0.541423597 0.214428731 0.121983811 0.099235509 30.06440232 -1.478052574 -0.597011494 SVNESLNNLFITEEDYQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVNESLNNLFITEEDYQALR 20 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 231.71 1.87E-25 63558000 62693 57492 60025 72106 62400 64606 69974 69657 79989 FALSE TRUE 59729.62614 63350.50016 62777.20562 64857.76789 73282.54024 62368.67802 59298.18114 63557.46381 92393.28559 0.646471502 0.685661298 0.679456361 0.701974905 0.793158721 0.675034745 0.641801845 0.687901327 1 16.49550039 -2.115134198 2.253744377 1.571724265 0.685443208 0.84758284 0.041432086 3281023.647 855955.4082 9605232.38 0.010366128 0.007671244 2.115134198 -0.886281057 SVNVKPLVTHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVNVKPLVTHR 11 1 Q00796 Q00796 SORD Sorbitol dehydrogenase 0 ; 105.65 0.0014645 674370000 1069330 988290 910630 1184830 885910 913260 1079920 1029190 859710 FALSE TRUE 1018784.89 1088997.875 952383.2862 1065728.637 1040412.424 881633.5772 915158.3699 939068.6675 993029.436 1.025936244 1.096642088 0.959068535 1.073209513 1.047715592 0.887822199 0.921582318 0.945660454 1 19.92147696 2.250679977 24.99266852 0.929504417 1.044626964 0.553243197 0.045009235 136.7920324 282093.7918 0.01451917 0.012062095 178.1065852 -2.250679977 0.115122547 SVPGTTSSPLVGDIS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVPGTTSSPLVGDISPK 17 0 Q9UQR0;H0Y6S1;B4DRC2;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK 250.55 2.51E-21 165429000 191243 184647 179830 207157 120206 202871 194678 219800 139541 TRUE FALSE 182203.3224 203462.7392 188075.3834 186333.1848 141169.8883 195845.5264 164976.2956 200553.1468 161180.3056 1.130431672 1.262330025 1.166863301 1.156054296 0.87585073 1.21507107 1.023551202 1.244278239 1 17.29831595 2.984981809 24.8421492 1.074482172 1.190602906 0.198499227 0.108279923 925.8968934 1531564.01 0.029309401 0.032070856 966.010416 -2.984981809 0.116120734 SVPGYKVEEKS(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVPGYKVEEKSP 12 2 S5FZ81 S5FZ81 PHF10 1 SVPGYKVEEKS(1)P 80.706 0.01545 164550000 259250 167320 235430 247770 145140 269190 303540 307040 176670 TRUE FALSE 246995.7663 184370.0982 246224.6984 222863.6889 170452.37 259867.8828 257229.3981 280153.9499 204067.0813 1.210365556 0.903477901 1.206587054 1.092109945 0.83527617 1.273443424 1.260513927 1.372852241 1 17.63868395 2.1536287 24.99999999 1.250605678 1.053295748 0.25385933 0.14833224 29.19695604 8590.265859 0.050761086 0.037489316 142.4389292 -2.1536287 -0.19730993 SVPTAYRVS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVPTAYRVSR 10 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 SVPT(0.001)AY(0.002)RVS(0.997)R 52.555 0.09045 64776000 100210 84338 68449 86864 93331 81995 111000 82826 109510 TRUE FALSE 95473.2719 92932.13808 71587.45436 78132.26569 109607.8969 79155.49259 94064.91135 75573.31635 126492.2515 0.754775654 0.734686409 0.565943396 0.617684204 0.866518665 0.62577345 0.743641687 0.597454116 1 16.94868949 -1.266836896 3.376037418 1.001012175 0.696693165 0.536642479 0.090724149 107346201.5 160064853.1 1121814.013 0.020396304 0.054095745 1.266836896 -0.30431901 SVQNHNNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVQNHNNK 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 81.548 0.022576 221920000 231478 212569 218647 265765 176156 219630 259965 311640 251888 FALSE TRUE 220536.4937 234230.0228 228672.1812 239049.7973 206877.5506 212024.158 220302.5647 284351.1495 290949.5046 0.757988896 0.805053864 0.785951437 0.821619537 0.711042801 0.728731806 0.757184876 0.977321305 1 18.15040926 1.225765626 8.085086791 0.990553941 0.768065689 0.886425593 0.033018197 0.050563301 19.52497588 0.029252198 0.008313811 16.81766225 -1.225765626 -0.222488252 SVQPQSHKPQPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVQPQSHKPQPTR 13 1 Q6PKG0;Q6PKG0-3;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 0 82.55 0.0072371 51882000 20272 20909 21626 25422 25908 25748 28754 27495 23649 FALSE TRUE 19313.78274 23039.65087 22617.57349 22866.53226 30426.347 24856.3403 24367.0492 25087.39204 27316.36614 0.707040704 0.843437621 0.827986174 0.837100079 1.11385046 0.909943152 0.892031139 0.918401515 1 14.73747796 3.882540654 0.808219807 0.946863049 0.702993407 0.535415964 0.07380648 0.781431277 0.824776264 0.030598766 0.138208838 7630.283138 -3.882540654 -0.243869642 SVRPTDS(ph)NVSPAISIHEIGAVGATK ddPTM_SK-BR-3_Trastuzumab_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(0.107)VRPT(0.107)DS(0.392)NVS(0.392)PAISIHEIGAVGATK 136.73 1.62E-05 117450000 101250 88731 103360 113470 102310 94349 139630 135960 149420 TRUE FALSE 96464.11316 97772.78978 108099.1582 102063.78 120152.8316 91081.67047 118326.879 124054.6216 172591.2905 0.55891646 0.566498979 0.62633032 0.591361127 0.696169727 0.527730398 0.685590094 0.718776836 1 17.39700014 -1.833753361 0.243365179 1.4135082 0.547743812 0.87203633 0.048171935 8.480208711 0.331340543 2.083787089 0.074120114 0.014663804 1.833753361 -0.865764388 SVRPTDSNVS(ph)PAISIHEIGAVGATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVRPTDSNVSPAISIHEIGAVGATK 25 1 A6NIT2;A6NMN0;P46020-3;P46020-2;P46020 A6NIT2 PHKA1 "Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform" 1 S(0.181)VRPT(0.181)DS(0.111)NVS(0.523)PAIS(0.002)IHEIGAVGATK;S(0.046)VRPT(0.046)DS(0.082)NVS(0.825)PAISIHEIGAVGATK;S(0.002)VRPT(0.002)DS(0.002)NVS(0.994)PAISIHEIGAVGATK 226.85 3.61E-34 405779000 752920 605840 737420 803720 705540 765990 1003960 925700 984080 TRUE FALSE 717330.9637 667575.7848 771231.4364 722928.5386 828585.9526 739463.5742 850787.463 844640.8006 1136686.1 0.63107217 0.587300033 0.67849113 0.635996638 0.728948786 0.650543342 0.748480572 0.743073044 1 20.11640247 -3.021664082 0.162970099 1.651881405 0.555276953 0.918723801 0.032685523 13.73478299 0.231756695 3.196160215 0.127122602 0.00095134 3.021664082 -1.096604452 SVS(ph)ANPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 S(0.002)VS(0.998)ANPK;S(0.001)VS(0.999)ANPK;SVS(1)ANPK;S(0.084)VS(0.916)ANPK;S(0.004)VS(0.996)ANPK;S(0.201)VS(0.799)ANPK;S(0.001)VS(0.999)ANPK;S(0.001)VS(0.999)ANPK;SVS(1)ANPK;S(0.003)VS(0.997)ANPK 105.2 0.008372 4586982000 12026340 9168840 10075550 12652650 8050820 11083920 12789130 12708130 10230750 TRUE FALSE 11457878.74 10103155.22 10537523.93 11380781.58 9454880.459 10700081.07 10837913.33 11595338.77 11817282.46 0.969586602 0.854947426 0.891704499 0.9630625 0.800089233 0.90546038 0.917123998 0.98121872 1 23.49439497 1.253151564 2.420765143 1.00026281 0.897154536 0.386930327 0.048189302 0.283644886 2.786774001 0.041272679 0.011906905 17.91230867 -1.253151564 -0.103108274 SVS(ph)LRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSLRK 6 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 S(0.003)VS(0.997)LRK;S(0.002)VS(0.998)LRK 75.738 0.047102 944760000 1256330 1113330 1179500 1317080 991800 1212530 1393500 1230920 1073930 TRUE FALSE 1196945.771 1226779.593 1233581.242 1184684.616 1164769.606 1170539.782 1180895.982 1123134.119 1240469.58 0.964913441 0.988963867 0.994446992 0.955029156 0.938974744 0.94362635 0.951974963 0.905410449 1 20.24245493 3.087364198 5.380000414 0.945440316 0.98136732 0.303350523 0.023977992 0.216775853 10.30067357 0.00626246 0.007524491 1222.824687 -3.087364198 0.035927004 SVS(ph)PLLSTHVLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSPLLSTHVLGK 13 0 Q96H12;X6RL08;X6R907;Q96H12-2 Q96H12 MSANTD3 Myb/SANT-like DNA-binding domain-containing protein 3 1 S(0.363)VS(0.637)PLLSTHVLGK 130.01 9.47E-05 214180000 661950 534040 571640 727960 666520 563650 782660 656580 708770 TRUE FALSE 630660.9354 588459.2832 597850.2594 654784.0778 782760.877 544130.6592 663250.8425 599086.3745 818682.4317 0.770336471 0.718788214 0.730259056 0.799802283 0.956122724 0.664641915 0.810144223 0.731768939 1 19.64294441 -2.289264074 2.249727046 2.025389789 0.770864902 0.459951917 0.077368968 3787594.23 458670.395 19837213.53 0.017425989 0.005137312 2.289264074 -1.254524887 SVS(ph)PQTLEAYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSPQTLEAYIR 12 0 A0A2R8Y7K2;A0A2R8Y481;A0A2R8YGN6;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0 A0A2R8Y7K2 SPAST Spastin 1 SVS(0.998)PQT(0.002)LEAYIR 94.717 0.0067686 14516000 30965 26223 25719 30642 36961 26773 32287 31064 34497 TRUE FALSE 29501.34582 28895.15351 26898.24159 27561.80794 43406.9867 25845.8443 27361.02516 28343.87148 39846.61857 0.740372631 0.725159488 0.675044522 0.691697537 1.089351826 0.648633315 0.686658646 0.711324386 1 15.28216968 -2.268036362 2.106352782 1.947473251 0.74185114 0.289037615 0.125026088 8709657.016 1299204.358 39263927.68 0.028763035 0.005394655 2.268036362 -1.205622111 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.013)VS(0.987)PSPVPLLFQPDQNAPPIR;S(0.002)VS(0.998)PSPVPLLFQPDQNAPPIR;S(0.003)VS(0.997)PSPVPLLFQPDQNAPPIR;SVS(1)PSPVPLLFQPDQNAPPIR;S(0.015)VS(0.982)PS(0.003)PVPLLFQPDQNAPPIR;S(0.002)VS(0.998)PSPVPLLFQPDQNAPPIR 438.74 9.32E-198 1025470000 372946.2 343840.5 363687.8 384247.1 322733 363783 442873 397203 424184 TRUE FALSE 355317.7722 378878.2379 380363.2454 345621.8515 379017.533 351185.1035 375304.5899 362421.7996 489964.2883 0.725191163 0.773277251 0.776308099 0.705402128 0.773561547 0.716756531 0.76598356 0.739690235 1 18.90231707 -1.868722098 2.529393872 1.117102333 0.748446973 0.907370524 0.025398414 7156423.562 4329437.74 5034064.137 0.005395326 0.01352938 1.868722098 -0.368655359 SVS(ph)PSPVPLSSNYIAQISNGQQLMSQPQLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSPSPVPLSSNYIAQISNGQQLMSQPQLHR 31 0 Q02241;H7BYN4 Q02241 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 S(0.076)VS(0.87)PS(0.05)PVPLS(0.002)S(0.002)NYIAQISNGQQLMSQPQLHR 101.47 0.00012681 68977000 23732 21564 22638 25254 26698 23526 25658 21326 25584 TRUE FALSE 22610.23539 23761.39612 23675.97469 22715.41994 31354.12275 22711.28872 21743.40086 19458.58238 29551.43606 0.765114607 0.804069084 0.801178482 0.768673979 1.061001661 0.768534182 0.735781531 0.658464866 1 14.85094062 -0.483151959 6.221210047 0.999979891 0.795944468 0.280856935 0.102910114 0 1.15E-10 0.096158098 0.022664681 0.328736586 0.483151959 -0.204035422 SVS(ph)PTFLNPSDENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 SVS(1)PTFLNPSDENLK;S(0.002)VS(0.998)PTFLNPSDENLK;SVS(0.99)PT(0.01)FLNPSDENLK 316.8 2.43E-56 564911000 557820 523420 536470 614270 432981 590390 647860 607400 498600 TRUE FALSE 531452.9541 576757.0931 561067.6801 552522.4126 508492.7493 569944.6463 549017.0582 554212.836 575920.3415 0.922788997 1.001452895 0.974210563 0.959372977 0.882922017 0.989624094 0.953286451 0.962308146 1 19.13550975 0.330186176 1.223115796 1.000048473 0.956823665 0.149352251 0.033354074 7.750504859 12.1790084 0.030964961 0.009189266 2.138878799 -0.330186176 -0.043224808 SVS(ph)SDS(ph)LGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 S(0.42)VS(0.474)S(0.147)DS(0.603)LGPPRPAPART(0.304)PT(0.054)QPPPEPGDLPTIEEALQIIHSAEPR;S(0.416)VS(0.459)S(0.159)DS(0.593)LGPPRPAPART(0.342)PT(0.032)QPPPEPGDLPTIEEALQIIHSAEPR 73.719 0.0018745 47342000 6108.5 5880.7 5858.2 6861.2 6115 4766.3 6948.9 4800.9 7505.2 TRUE FALSE 5819.763311 6479.950016 6126.804265 6171.499141 7181.454064 4601.241836 5888.71768 4380.507745 8669.068085 0.671325136 0.747479424 0.706743124 0.711898797 0.828399777 0.530765451 0.679279205 0.505303189 1 13.0816612 -1.523315564 5.987046084 1.000448325 0.679723854 0.538947549 0.094951757 0.000531054 4.23E-05 0.085924642 0.020225099 0.029969841 1.523315564 -0.320724471 SVS(ph)SDSLGPPRPAPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 SVS(0.745)S(0.25)DS(0.004)LGPPRPAPAR;S(0.008)VS(0.798)S(0.194)DSLGPPRPAPAR;S(0.002)VS(0.778)S(0.218)DS(0.002)LGPPRPAPAR;S(0.001)VS(0.958)S(0.04)DSLGPPRPAPAR;S(0.002)VS(0.958)S(0.038)DS(0.001)LGPPRPAPAR;S(0.002)VS(0.78)S(0.193)DS(0.025)LGPPRPAPAR;S(0.016)VS(0.918)S(0.066)DS(0.001)LGPPRPAPAR 174.19 2.40E-09 2868350000 3136910 2390926 2578650 3106410 2652030 2883150 3245360 2794790 2830260 TRUE FALSE 2988634.481 2634564.078 2696883.653 2794147.765 3114543.192 2783305.793 2750220.727 2550063.371 3269162.266 0.914189703 0.805883546 0.824946403 0.854698402 0.952703763 0.851381965 0.841261615 0.780035729 1 21.64048956 -1.211551445 4.944714048 1.000018473 0.853719694 0.463800933 0.049622598 9.75E-06 1.56E-06 0.046373709 0.010929008 0.061439625 1.211551445 -0.146298779 SVS(ph)TMNLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 SVS(0.639)T(0.36)MNLSK;SVS(0.969)T(0.031)MNLSK;SVS(0.989)T(0.011)MNLSK;SVS(0.5)T(0.5)MNLSK;SVS(0.5)T(0.5)MNLSK;SVS(0.5)T(0.5)MNLSK;SVS(0.851)T(0.149)MNLSK 216.97 6.12E-07 3357380000 5007900 3884590 4282070 4497080 3867470 4522560 5663120 4915560 4505800 TRUE FALSE 4771186.492 4280434.137 4478407.145 4045024.975 4541955.544 4365942.613 4799107.034 4485127.507 5204536.452 0.916736108 0.822442916 0.860481464 0.777211383 0.872691658 0.838872521 0.922100763 0.861772715 1 22.31133824 0.5433713 0.688072199 1.001027226 0.849721485 0.545535515 0.041194124 1.163555847 0.945289938 0.043862916 0.014784621 3.494389407 -0.5433713 -0.151305741 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.138)VS(0.778)T(0.075)T(0.009)NIAGHFNDESPLGLR;S(0.014)VS(0.913)T(0.06)T(0.013)NIAGHFNDESPLGLR;SVS(0.956)T(0.038)T(0.006)NIAGHFNDESPLGLR;S(0.005)VS(0.976)T(0.013)T(0.006)NIAGHFNDESPLGLR;SVS(0.333)T(0.333)T(0.333)NIAGHFNDESPLGLR;S(0.002)VS(0.858)T(0.135)T(0.005)NIAGHFNDESPLGLR;SVS(0.984)T(0.015)T(0.001)NIAGHFNDESPLGLR;SVS(0.738)T(0.241)T(0.021)NIAGHFNDESPLGLR;S(0.16)VS(0.811)T(0.024)T(0.005)NIAGHFNDESPLGLR;SVS(0.893)T(0.074)T(0.032)NIAGHFNDESPLGLR 389.55 4.32E-131 6540060000 3344610 3068750 3253228 3530060 3054448 3016182 3472568 3507570 2901242 TRUE FALSE 3186516.914 3381459.114 3402391.722 3175211.662 3587142.764 2911730.861 2942763.974 3200428.576 3351151.792 0.950872151 1.009043852 1.015290244 0.947498609 1.070420854 0.868874656 0.878135088 0.955023459 1 21.6762256 2.223011542 24.99999937 0.909705336 0.99413828 0.315339673 0.050997317 230.4485507 370515.7924 0.017491075 0.012962382 167.1135028 -2.223011542 0.084432944 SVS(ph)TTNIAGHFNDESPLGLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSTTNIAGHFNDESPLGLRR 21 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.136)VS(0.7)T(0.136)T(0.027)NIAGHFNDESPLGLRR;S(0.101)VS(0.883)T(0.014)T(0.002)NIAGHFNDESPLGLRR 162.45 8.74E-12 719792000 134992 92386 157916 102778 168696 112183 208271 140230 192269 TRUE FALSE 128611.1957 101800.2384 165156.6048 92446.56017 198116.529 108298.0746 176495.4338 127950.7178 222085.0945 0.579107733 0.45838393 0.743663617 0.416266388 0.892074857 0.487642247 0.794719853 0.576133748 1 17.76075304 -5 0.126625213 2.305806123 0.438846926 0.400002904 0.150097404 125.7873095 1.014360776 41.6290181 1.043933825 1.00E-05 5 -1.866959197 SVS(ph)VATGLNMMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSVATGLNMMK 12 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.002)VS(0.991)VAT(0.007)GLNMMK 90.229 0.0094174 234900000 685370 494410 582810 650490 462540 667100 800570 740540 503430 TRUE FALSE 652973.9184 544790.9411 609532.415 585101.5093 543206.8296 643998.1597 678428.343 675694.3918 581499.3532 1.122914264 0.936872824 1.048208242 1.0061946 0.934148639 1.107478721 1.166688044 1.161986489 1 19.14941806 2.080429879 7.927257099 1.130296993 1.011851206 0.315818794 0.070449244 0.234698982 20.13358462 0.02459965 0.018134658 120.3455065 -2.080429879 -0.118445788 SVS(ph)VDESRPELIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.005)VS(0.995)VDESRPELIFR;S(0.029)VS(0.971)VDESRPELIFR;S(0.017)VS(0.983)VDESRPELIFR;S(0.004)VS(0.996)VDESRPELIFR 194.94 5.24E-08 399074000 528529 570640 451930 600767 605613 524163 595859 563687 581187 TRUE FALSE 503546.4816 628788.8648 472651.4375 540376.7598 711231.7155 506011.1039 504949.7658 514327.578 671314.5117 0.750090267 0.936653169 0.704068554 0.804953193 1.059461256 0.753761605 0.75218062 0.766149948 1 19.3566293 -0.905575512 7.399667553 1.000000001 0.818657579 0.22881833 0.106101118 1.46E-09 3.95E-10 0.098138693 0.023131512 0.124286652 0.905575512 -0.181342423 SVS(ph)VDSGEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVSVDSGEQR 10 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 SVS(1)VDSGEQR;S(0.002)VS(0.998)VDSGEQR;SVS(1)VDSGEQR 152.96 1.79E-05 281850000 651430 632640 686100 800220 878750 691980 860200 692120 1020150 TRUE FALSE 620638.1949 697106.7353 717558.3636 719780.3653 1032003.722 668016.5591 728960.6913 631514.3036 1178349.652 0.526701216 0.591595826 0.608951989 0.610837678 0.875804325 0.566908607 0.618628512 0.535931167 1 20.16833626 -2.193264019 2.458229316 2.150753648 0.614633223 0.60536987 0.097186765 8661435.404 863297.1002 56109912.71 0.024617461 0.006408199 2.193264019 -1.536120426 SVSDQFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSDQFYR 8 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11;H0YK29 P55010 EIF5 Eukaryotic translation initiation factor 5 0 111.74 0.0073876 209590000 246120 241260 230990 247140 292130 204520 252880 265590 334430 FALSE TRUE 234486.3954 265844.6683 241581.12 222297.0177 343077.3795 197437.4211 214298.5115 242333.5316 386291.6964 0.60701899 0.688196694 0.625385226 0.575464137 0.88813035 0.511109669 0.554758266 0.627333007 1 18.55933114 -1.338424278 5.863926616 1.00004857 0.632037693 0.559847871 0.101776373 6.11E-05 6.89E-06 0.093174475 0.021958545 0.045874962 1.338424278 -0.368010877 SVSDYDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVSDYDGK 8 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;; 153.78 0.0010134 652540000 1913780 1718650 1420240 2232920 1255690 1807200 1906370 1954030 1343870 FALSE TRUE 1823319.412 1893782.389 1485359.409 2008462.639 1474681.938 1744616.211 1615518.244 1782924.774 1552270.496 1.174614487 1.220007978 0.956894699 1.293887015 0.950016084 1.123912498 1.040745313 1.148591549 1 20.56594855 7.999999998 0.164891182 1.009251813 1.794699827 0.141949202 0.105602728 92.36273464 0.975576383 0.252945759 17.77273728 99999999.53 -7.999999998 0.785448014 SVSDYDGKLSNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSDYDGKLSNFK 13 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 229.97 4.44E-12 1584850000 3676900 1985390 3264400 3412000 3226700 3986200 6332700 4761900 4839900 FALSE TRUE 3503100.224 2187703.498 3414075.969 3069019.278 3789435.458 3848156.894 5366530.307 4344922.792 5590446.973 0.626622565 0.391328906 0.610698212 0.548975653 0.677841231 0.68834512 0.959946554 0.777204902 1 22.4145322 2.11313708 0.925675838 0.947808916 0.516139948 0.757886393 0.089169141 0.241729149 0.385541451 0.064975988 0.033775265 129.7588776 -2.11313708 -0.431668969 SVSEINS(ph)DDELSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVSEINSDDELSGK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK 319.53 4.74E-56 1925464000 3595680 3279360 3179250 3802260 2366510 3582750 3705690 3750640 2493090 TRUE FALSE 3425719.332 3613530.512 3325021.757 3420049.601 2779228.595 3458678.469 3140318.931 3422214.078 2879705.664 1.189607457 1.254826338 1.154639448 1.187638599 0.965108563 1.201052771 1.090499967 1.188390231 1 21.45748993 7.999999994 0.04770736 0.714934209 1.926866019 0.321135576 0.076085571 553.9370254 1.999299704 12.37689159 50.31533667 99999998.69 -7.999999994 1.211931809 SVSGS(ph)PEPAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.001)GS(0.999)PEPAAK 206.03 2.92E-08 650990000 1911760 1647580 1663090 1983030 1381290 1783780 2014370 1900130 1539930 TRUE FALSE 1821394.894 1815470.275 1739344.322 1783692.057 1622186.539 1722007.251 1707040.86 1733744.544 1778734.48 1.023983576 1.020652771 0.977854953 1.002787137 0.911989146 0.968108097 0.959694029 0.974706773 1 20.76241974 3.518444117 1.4730026 0.962578555 1.024793472 0.430302214 0.024747027 0.300823205 1.312543908 0.007237428 0.013786969 3299.469491 -3.518444117 0.062214917 SVSLVGEDERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSLVGEDERK 11 1 B7Z6D5;Q96GQ7 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 ; 89.266 0.01982 393320000 593110 620820 503730 628150 474070 526890 574880 573930 476100 FALSE TRUE 565074.8657 684082.2638 526826.5188 565007.1686 556747.6579 508643.6672 487171.4976 523673.6466 549931.1564 1.027537464 1.243941639 0.957986309 1.027414363 1.012395191 0.92492244 0.885877245 0.952253097 1 19.0688915 3.200285375 1.165178501 0.934832997 1.127627846 0.395613106 0.074999056 0.363913186 1.05312828 0.02868506 0.042703697 1585.93497 -3.200285375 0.192794848 SVSMLSLNT(ph)PNSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSMLSLNTPNSNR 14 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 SVSMLSLNT(1)PNSNR;SVSMLSLNT(1)PNSNR 313.16 9.70E-55 293560000 753200 693870 894980 777800 824580 840370 980240 759320 583680 TRUE FALSE 717597.7287 764576.1419 936015.7183 699614.0663 968386.4909 811267.7762 830686.3847 692829.9154 674194.1134 1.064378514 1.134059356 1.38834751 1.037704205 1.436361534 1.203314832 1.232117528 1.027641597 1 19.36280451 1.209613569 7.771285011 1.011169597 1.204251288 0.303741739 0.125226224 0.284976175 59.08184628 0.108405 0.028691359 16.20367668 -1.209613569 0.193081691 SVSSDSLGPPRPAPART(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.002)VS(0.002)S(0.002)DS(0.009)LGPPRPAPART(0.807)PT(0.179)QPPPEPGDLPTIEEALQIIHSAEPR;S(0.028)VS(0.028)S(0.028)DS(0.157)LGPPRPAPART(0.752)PT(0.006)QPPPEPGDLPTIEEALQIIHSAEPR 112.76 7.50E-05 64828000 18100.8 11749.1 13970.4 17078.9 15548.4 15508.8 17731.9 15882.5 18882.9 TRUE FALSE 17245.21106 12946.34665 14610.95666 15362.09652 18260.03604 14971.72637 15026.57299 14491.7441 21811.16369 0.790659834 0.59356515 0.669884325 0.704322646 0.837187612 0.686424923 0.688939536 0.664418658 1 14.41277912 -1.272640849 5.015607755 1.000067251 0.700877888 0.655221794 0.067338546 4.93E-05 7.15E-06 0.063460386 0.014954403 0.053377613 1.272640849 -0.299189363 SVSSNVASVS(ph)PIPAGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSSNVASVSPIPAGSK 17 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 SVSSNVASVS(1)PIPAGSK 389.24 2.99E-92 0 150930 158070 168730 197430 128250 167580 202200 195160 172710 TRUE FALSE 143795.838 174177.5127 176466.4374 177583.9613 150616.7594 161776.6626 171350.6763 178070.7558 199492.9847 0.72080649 0.873100941 0.884574651 0.890176472 0.754997774 0.810939105 0.858930837 0.89261663 1 17.60597849 -5 0.158784279 1.629536181 0.785775632 0.509868071 0.054647296 117.8081627 1.07910296 23.27086446 0.241005396 1.00E-05 5 -0.843760549 SVSSVLSSLT(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVSSVLSSLTPAK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SVSSVLS(0.009)S(0.024)LT(0.967)PAK 170.74 0.00029374 50261000 191390 197750 203760 193370 158450 198320 211930 226750 195580 TRUE FALSE 182343.374 217900.9498 213102.5975 173932.0802 186083.6298 191452.1287 179596.1861 206894.5679 225909.5475 0.807152137 0.964549539 0.94330939 0.769919121 0.823708568 0.847472499 0.794991571 0.915829234 1 17.78538572 0.988051811 11.84682913 0.999999929 0.855070657 0.386891055 0.06143606 0.748988828 741.3324709 0.061539963 0.015387965 9.728632778 -0.988051811 -0.144929272 SVST(ph)PSEAGSQDSGDGAVGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 SVS(0.023)T(0.977)PSEAGSQDSGDGAVGSR;SVS(0.035)T(0.964)PS(0.001)EAGSQDSGDGAVGSR 280.31 4.46E-43 0 103027 87381 88832 107008 97650 89894 111220 92472 107574 TRUE FALSE 98157.11789 96285.22324 92905.03507 96251.35254 114680.1291 86780.94824 94251.3463 84374.66146 124256.0265 0.789958609 0.774893789 0.747690375 0.774621201 0.922934141 0.69840434 0.758525352 0.679038786 1 16.9229563 -1.306302393 3.491575449 1.000864494 0.770332333 0.557439625 0.064869026 880842852.9 1407308943 8106891.993 0.014636824 0.049396663 1.306302393 -0.230532161 SVSTPSEAGS(ph)QDSGDGAVGSR ddPTM_SK-BR-3_Trastuzumab_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 SVSTPSEAGS(0.997)QDS(0.003)GDGAVGSR 281.36 5.32E-45 92089000 40543 26098 29979 44741 38839 37904 48925 37133 33723 TRUE FALSE 38626.61274 28757.41587 31353.5668 40243.54968 45612.5093 36591.37498 41460.59268 33881.43767 38952.59061 0.99163142 0.738267094 0.804916087 1.033141803 1.170974988 0.939382321 1.064386015 0.869812178 1 15.24943166 3.233356937 24.99044929 1.021550268 0.843036272 0.386083777 0.099469543 116.641399 560165.0466 0.027374577 0.033657968 1711.421315 -3.233356937 -0.178513996 SVSTPSEAGSQDS(ph)GDGAVGSR ddPTM_SK-BR-3_Trastuzumab_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 SVSTPSEAGS(0.016)QDS(0.984)GDGAVGSR 191.07 1.65E-17 72198000 25559 21820 23072 29285 26134 24352 27311 27423 26681 TRUE FALSE 24350.87672 24043.48281 24129.87402 26341.21616 30691.76133 23508.68413 23144.20535 25021.69674 30818.55321 0.79013692 0.780162607 0.782965828 0.854719428 0.995885859 0.762809466 0.750982864 0.811903679 1 14.91151152 -2.329754134 2.162686973 1.981071741 0.810130666 0.4018055 0.070134645 6256325.033 648356.7958 30091981.37 0.017363379 0.00468 2.329754134 -1.170941075 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 213.57 3.91E-23 115910000 88519 91345 82086 114360 85905 78532 92617 96104 101780 TRUE FALSE 84334.8823 100653.1594 85849.72429 102864.3155 100886.8048 75812.41715 78486.57562 87688.62428 117563.5226 0.717355864 0.856159778 0.73024117 0.87496796 0.858147175 0.644863436 0.667609935 0.745882927 1 16.84308097 2.251709219 24.95064411 0.72618037 0.80540981 0 0.110054175 477.6597804 906401.1262 0.03473106 0.028897775 178.5291834 -2.251709219 0.07922944 SVT(ph)PASTLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVTPASTLTK 10 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 S(0.002)VT(0.996)PAS(0.002)T(0.001)LTK;SVT(0.999)PAS(0.001)TLTK 138.51 0.00070135 231550000 833890 727120 707030 836850 608440 770500 838930 861760 760080 TRUE FALSE 794473.6723 801214.3547 739448.0248 752728.2481 714551.7434 743817.3918 710935.8205 786299.7259 877949.3244 0.904919738 0.912597495 0.84224454 0.857370952 0.81388723 0.847221327 0.809768629 0.895609466 1 19.74377814 0.980167721 23.12178329 1.000000003 0.859294918 0.653359906 0.033128855 410.4747942 478560.1658 0.037978098 0.009494525 9.553614678 -0.980167721 -0.140705084 SVTDSIRDEYAFLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 285.58 3.82E-34 293730000 348450 287548 310272 379900 297300 358270 417430 385050 339710 FALSE TRUE 331979.4591 316849.4681 324498.2781 341711.7302 349149.0259 345863.0201 353743.3869 351332.9807 392390.4918 0.846043587 0.807485081 0.826977934 0.870846102 0.889799914 0.881425588 0.901508559 0.895365683 1 18.58193056 0.741407812 0.221271724 1.048093125 0.794952865 0.888092971 0.01745501 1.27065673 0.188089347 0.108310917 0.055227842 5.513251593 -0.741407812 -0.25314026 SVTDYDFAPFLNNS(ph)PQQNPAAQIPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVTDYDFAPFLNNSPQQNPAAQIPAR 26 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2 Q9UM54-1 MYO6 Unconventional myosin-VI 1 SVTDYDFAPFLNNS(1)PQQNPAAQIPAR;SVTDYDFAPFLNNS(1)PQQNPAAQIPAR 122.18 8.87E-05 62627000 95208 84822 100143 99702 117277 99240 120797 102521 127365 TRUE FALSE 90707.70652 93465.45823 104734.6556 89679.76554 137730.0717 95803.29392 102367.1991 93543.71774 147116.1137 0.616572204 0.635317613 0.711918314 0.609584928 0.936199769 0.651208705 0.695825878 0.635849571 1 17.16659575 -5 0.245156732 2.837219822 0.652726589 0.509169345 0.095618959 141.5112787 1.406924357 130.269083 0.135114376 1.00E-05 5 -2.184493233 SVTEQGAELSNEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 388.54 1.30E-113 3163790000 1645951 1575242 1497160 1771143 1596717 1580230 1747582 1658256 1667981 FALSE TRUE 1568150.158 1735760.951 1565806.267 1593104.341 1875183.939 1525506.239 1480956.269 1513050.314 1926642.975 0.813928776 0.900925067 0.812712209 0.826880933 0.97329083 0.791794982 0.768671876 0.785329889 1 20.87765782 SVTLLEVCGS(ph)WPEGFGLR ddPTM_SK-BR-3_Trastuzumab_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 174.95 4.79E-12 26962000 77841 59555 78668 78340 78862 74075 97812 96029 96761 TRUE FALSE 74161.6102 65623.72221 82275.00561 70465.11436 92615.50783 71509.76418 82888.98296 87620.19168 111766.2017 0.663542369 0.587151762 0.736134935 0.630468901 0.82865398 0.639815643 0.741628343 0.783959644 1 16.77012445 -5 0.137185402 2.104072705 0.569358611 0.721273592 0.063056761 65.20679932 0.55270019 19.51773029 0.365415502 1.00E-05 5 -1.534714093 SVTQATQTS(ph)PGVPWPSQSANFPEFSFDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 SVTQAT(0.001)QT(0.027)S(0.972)PGVPWPSQSANFPEFSFDFTR;SVTQATQT(0.009)S(0.991)PGVPWPSQSANFPEFSFDFTR 167.7 1.57E-12 199350000 297131 235793 260074 285639 291008 251160 309208 268365 296872 TRUE FALSE 283086.2065 259820.5748 271998.6501 256926.025 341759.7031 242462.2662 262032.6406 244865.5379 342909.3935 0.825542291 0.757694539 0.793208513 0.749253388 0.996647247 0.707073853 0.764145414 0.714082328 1 18.3874679 -1.126637059 4.235137207 1.000041827 0.787699844 0.398741743 0.081632484 23197270768 4783603254 10017281.77 0.01759083 0.074707283 1.126637059 -0.212341983 SVTVVEDDEDEDGDDLLHHHHGS(ph)HCSSSGDPAEYNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 SVTVVEDDEDEDGDDLLHHHHGS(0.25)HCS(0.25)S(0.25)S(0.25)GDPAEYNLR 85.767 0.00041194 117390000 37144 32548 31512 40072 59318 35342 48443 44170 4784.4 TRUE FALSE 35388.27673 35864.6782 32956.85637 36043.88643 69663.04042 34118.09768 41052.13063 40302.24064 5526.340317 6.403564512 6.48977011 5.963595161 6.522198121 12.60563708 6.173723608 7.428447812 7.292754034 1 12.43210869 2.971920703 24.99544058 7.473060866 6.333311892 0 2.791509724 2665.764184 2372993.673 0.763501628 0.811479504 937.3908354 -2.971920703 -1.139748974 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;; 140.24 1.68E-13 1842930000 470079 336684 330658 444238 812178 346231 581865 548316 32392.1 FALSE TRUE 447859.2973 370992.4824 345818.9964 399582.3522 953821.5861 334240.9337 493090.8076 500302.5442 37415.30143 11.96995026 9.915528358 9.242715764 10.67965076 25.49282111 8.933268499 13.17885434 13.37160266 1 15.19134078 -0.661142681 8.803801136 0.999997931 12.60560797 0.379627233 4.750913866 0 0 4.339506527 1.022831497 0.218201293 0.661142681 11.60561004 SVTVVEDDEDEDGDDLLHHHHVS(ph)GSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SVTVVEDDEDEDGDDLLHHHHVS(0.5)GS(0.5)R 199.03 2.67E-25 155950000 2760.6 1530.5 3511.8 0 3865.6 2285.1 3041.2 2788.8 5616.7 TRUE FALSE 2630.111909 1686.45969 3672.819504 0 4539.759416 2205.966414 2577.209085 2544.597888 6487.70915 0.405399171 0.25994687 0.56611963 0 0.699747678 0.340022397 0.397244856 0.392218244 1 12.66349343 -5 0.325446627 7.142482513 0.349948684 0.533415605 0.181748966 238.0302002 2.080577228 1009.241183 0.134427933 1.00E-05 5 -6.792533829 SVTVVEDDEDEDGDDLLHHHHVSGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SVTVVEDDEDEDGDDLLHHHHVS(0.393)GS(0.607)R 197.1 3.01E-25 237970000 4798 3552 2791.5 6206.1 6581.9 3070.7 6022.1 2780.8 7441.7 TRUE FALSE 4571.208049 3913.952838 2919.493036 5582.251037 7729.781276 2964.360889 5103.318042 2537.29841 8595.720829 0.531800432 0.455337361 0.339644934 0.649422096 0.899259228 0.344864724 0.593704489 0.295181575 1 13.06940291 -1.691268639 3.03166453 1.055858858 0.517976167 0.425297722 0.177611106 211328395.8 222369510.8 91230717.08 0.040104702 0.020357824 1.691268639 -0.537882691 SVTVVEDDEDEDGDDLLHHHHVSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 15 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;;;;;;; 247.54 5.00E-46 12736710000 1310621.2 1103492.7 1098173.5 1435932.3 1799753.9 1148998.2 1502596.8 1328585.5 125504.3 FALSE TRUE 1248670.733 1215939.861 1148525.841 1291589.657 2113630.41 1109208.104 1273348.061 1212247.51 144966.8659 8.613490579 8.387708829 7.922678292 8.90955081 14.58009317 7.651459509 8.783717945 8.362238524 1 17.14536366 0.304269412 1.181574039 0.986987203 9.222168991 0.637463539 1.94569798 2.505898727 3.652332608 1.853379668 0.548745731 2.014973841 -0.304269412 8.235181789 SVVEFLQGYIGVPHGGFPEPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVEFLQGYIGVPHGGFPEPFR 22 0 P11498 P11498 PC "Pyruvate carboxylase, mitochondrial" 0 122.19 2.61E-05 64991000 76398 59570 68452 67392 73172 69990 78052 60422 67718 FALSE TRUE 72786.81795 65640.25073 71590.59191 60617.62812 85933.17363 67566.22875 66143.73388 55131.12936 78219.36158 0.930547328 0.839181622 0.915254107 0.77496961 1.098617681 0.863804401 0.845618432 0.704827146 1 16.25523814 2.00818357 24.99978352 0.838424078 0.904458162 0.063152425 0.107253648 483.4386714 1476837.863 0.036755212 0.027104115 101.9022023 -2.00818357 0.066034084 SVVLFGVETHVCIQQTALELVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVVLFGVETHVCIQQTALELVGR 23 0 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;;;; 238.03 3.60E-37 187953000 169688 171345 168398 183510 171880 162760 203011 183907 158312 FALSE TRUE 161667.1845 188805.2503 176119.2149 165063.2262 201855.8176 157123.5804 172037.9434 167803.1281 182862.2164 0.884092885 1.032500065 0.963125233 0.902664473 1.103868374 0.85924574 0.940806399 0.917647896 1 17.48039749 -0.221166496 8.361838782 1 0.952446718 0.044032783 0.071983395 0 0 0.063073317 0.014866523 0.600943308 0.221166496 -0.047553282 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK 30 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 170.36 1.03E-12 2999390000 5025730 4019410 4223790 4897690 3175320 5033850 5660630 5364090 3393430 FALSE TRUE 4788173.703 4428992.449 4417454.949 4405364.896 3729094.803 4859526.512 4796996.929 4894381.843 3919665.793 1.221577031 1.129941348 1.126997857 1.123913397 0.951380806 1.23978083 1.223828046 1.248673255 1 21.90229922 SVVNMEWDKIWAFNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVVNMEWDKIWAFNKK 16 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 179.78 1.45E-09 365600000 904530 693490 877840 869050 601870 958000 1098030 1005530 731090 FALSE TRUE 861774.6595 764157.4194 918089.8323 781691.4429 706835.9374 924824.2198 930505.3568 917480.4626 844463.7033 1.020499349 0.904902622 1.087186849 0.925666124 0.837023468 1.095161599 1.101889108 1.086465243 1 19.68767589 2.190383416 24.99978735 1.082346771 0.958835812 0.386008191 0.07185462 110.2061831 57186.72477 0.025507674 0.018838704 155.0184591 -2.190383416 -0.123510958 SVVS(ph)DLEADDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 323.76 5.00E-47 2010280000 4163630 5425575 3815637 5497644 2280444 4894097 4059211 4963290 2292238 TRUE FALSE 3966823.461 5978447.261 3990587.731 4945010.38 2678152.712 4724613.194 3439903.809 4528678.016 2647706.562 1.498211138 2.257971992 1.507186555 1.867658014 1.011499065 1.784417224 1.299201301 1.710415376 1 21.33631181 2.781489457 24.99506975 1.407845767 1.815033885 0.283010596 0.327057111 581.3750668 338501.3075 0.09007162 0.095534776 604.6296728 -2.781489457 0.407188118 SVVS(ph)DLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 S(0.138)VVS(0.86)DLEADDVKGS(0.046)VPLS(0.689)S(0.138)S(0.127)PPAT(0.001)HFPDETEITNPVPK;S(0.13)VVS(0.87)DLEADDVKGSVPLS(0.374)S(0.322)S(0.278)PPAT(0.024)HFPDET(0.001)EITNPVPK 155.35 1.00E-13 153885000 168268 143351 173777 175681 109803 188446 229147 214887 119753 TRUE FALSE 160314.3051 157958.6299 181744.8473 158021.2121 128952.6084 181920.0678 194186.4166 196070.3551 138323.6836 1.158979438 1.141949272 1.313909828 1.142401706 0.932252562 1.31517657 1.403855157 1.41747494 1 17.07768867 2.043620778 24.99939485 1.328866715 1.146500924 0.167297245 0.147478562 169.0468009 96881.28963 0.050770668 0.037496602 110.5657913 -2.043620778 -0.182365791 SVVS(ph)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.03)VVS(0.97)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 297.75 1.31E-92 165320000 205370 183530 228680 205020 139570 242210 279730 265360 139740 TRUE FALSE 195662.5671 202231.9157 239165.2042 184411.0001 163910.9638 233822.207 237052.0509 242123.6716 161410.1655 1.212207214 1.252906934 1.481723307 1.142499294 1.015493437 1.44862132 1.468631484 1.500052186 1 17.30037192 SVVS(ph)FDKVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;SVVS(1)FDKVK 150.06 5.22E-05 2077600000 7401640 6691390 5329390 8131690 4053490 7717420 8174320 8959300 4495200 TRUE FALSE 7051779.146 7373250.248 5573747.803 7314277.072 4760417.373 7450163.81 6927177.352 8174776.196 5192292.658 1.358124361 1.420037493 1.073465648 1.408679663 0.916823778 1.434850518 1.334126909 1.5744059 1 22.30794027 SVVS(ph)FDKVKEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVVSFDKVKEPR 12 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 SVVS(1)FDKVKEPR;SVVS(1)FDKVKEPR;S(0.037)VVS(0.963)FDKVKEPR 126.88 0.00022026 1640650000 2400580 1415130 2406180 2263430 1718620 2775200 3434990 3209340 2518020 TRUE FALSE 2287109.341 1559333.356 2516505.733 2035905.716 2018346.784 2679094.128 2910919.188 2928313.176 2908501.681 0.786353109 0.536129433 0.865224094 0.69998437 0.693947264 0.921125178 1.000831186 1.006811581 1 21.47184471 2.135593048 3.303939682 0.996473387 0.702898554 0.720512938 0.083102751 0.123721292 2.664769931 0.034021592 0.023484771 136.6447808 -2.135593048 -0.293574834 SVVSDLEADDVKGSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGSVPLS(0.101)S(0.438)S(0.438)PPAT(0.023)HFPDETEITNPVPK 224.63 1.03E-39 2628900000 649230 419750 715160 588040 377500 667920 787310 728300 490630 TRUE FALSE 618542.1845 462523.0022 747950.7934 528929.102 443335.8805 644789.7629 667191.3996 664526.191 566714.3946 1.091453103 0.816148322 1.319802003 0.933325688 0.782291547 1.137768458 1.177297429 1.172594516 1 19.11226232 2.063688269 24.99999547 1.141637851 0.984732991 0.148029551 0.155634068 98.61122787 38707.58388 0.055390976 0.040908951 115.7945899 -2.063688269 -0.15690486 SVVSDLEADDVKGSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGSVPLS(0.048)S(0.246)S(0.567)PPAT(0.132)HFPDET(0.007)EITNPVPK 160.77 4.89E-18 61968000 118980 89347 135420 118900 91879 138920 169220 163730 93699 TRUE FALSE 113356.0512 98451.56088 141629.1409 106947.9461 107902.6685 134109.1656 143402.3811 149392.9332 108229.3624 1.047368743 0.909656665 1.308601823 0.988160179 0.996981467 1.239119982 1.324985918 1.380336444 1 16.72373243 2.174251638 5.747977854 1.272486986 1.039813776 0.281334038 0.142560304 0.203576187 12.77184855 0.050422345 0.037262696 149.3659611 -2.174251638 -0.23267321 SVWGSLAVQNS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SVWGSLAVQNSPK 13 0 P18615;P18615-3;P18615-4 P18615 NELFE Negative elongation factor E 1 SVWGSLAVQNS(1)PK;SVWGSLAVQNS(1)PK 190.18 4.86E-06 205928000 388330 433370 357640 445000 223960 438950 407570 430270 240134 TRUE FALSE 369974.4105 477530.8957 374038.1478 400267.7546 263018.5531 423749.0514 345387.711 392593.2778 277372.7543 1.333852748 1.721621494 1.348503564 1.443068032 0.948249419 1.527724136 1.245211383 1.415399572 1 18.08146656 -3.510171577 0.083725902 6.98E-13 1.793135548 0.271729009 0.195990202 194.274737 1.55747407 40.9761416 6.064676002 0.000308907 3.510171577 1.793135548 SVWVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 SVWVAR 6 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;; 148.53 0.025017 2655810000 3011370 2463020 2212220 2680330 2825800 2400220 3249760 2780630 2952000 FALSE TRUE 2869028.508 2714004.538 2313652.475 2410898.136 3318618.625 2317099.78 2753949.426 2537143.296 3409781.083 0.841411351 0.795946858 0.678534023 0.707053643 0.973264425 0.679545027 0.807661653 0.744078061 1 21.70124769 -1.364840203 2.912497863 1.003074333 0.781957558 0.386112329 0.087698778 12738142.76 15248946.74 331828.2757 0.019161302 0.043167788 1.364840203 -0.221116774 SVYAHFPINVVIQENGSLVEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SVYAHFPINVVIQENGSLVEIR 22 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 304.43 4.32E-56 1056792000 936538 1000812 919331 1090504 922663 952583 1035329 1068310 834625 FALSE TRUE 892269.7048 1102795.881 961483.2357 980884.4661 1083575.135 919594.8119 877370.5459 974763.1129 964054.3823 0.925538767 1.143914597 0.997332986 1.017457608 1.123977189 0.953882715 0.91008408 1.011108015 1 19.87875501 2.180757413 24.99936113 0.955526497 1.041921726 0.215525558 0.067001002 101.4809569 43888.64604 0.023835851 0.017603951 151.6203213 -2.180757413 0.086395229 SVYATMGDHENRS(ph)PVKEPVEQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVYATMGDHENRSPVKEPVEQPR 23 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SVYATMGDHENRS(1)PVKEPVEQPR 206 6.88E-25 164540000 244590 208260 237280 266920 147090 275500 287020 284090 159210 TRUE FALSE 233028.7154 229481.9308 248159.5227 240088.6945 172742.4494 265959.3659 243229.8275 259213.5735 183899.4737 1.267152705 1.247866164 1.349430304 1.30554313 0.939330853 1.446221463 1.322623837 1.409539508 1 17.48855783 SVYRGS(ph)LTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SVYRGSLTQR 10 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 SVYRGS(1)LTQR 139.77 2.45E-05 543970000 319050 201480 280830 305080 349690 287470 352550 249300 325230 TRUE FALSE 303969.1388 222011.0411 293706.3333 274412.7788 410675.8253 277514.8418 298762.0225 227469.9704 375665.0074 0.809149463 0.590981424 0.781830427 0.730472025 1.09319691 0.73872955 0.7952884 0.6055128 1 18.51908721 2.966765263 24.94838946 0.830908349 0.7155892 0.136670694 0.144000255 1241.660247 932079.9255 0.041548157 0.044097274 926.3290055 -2.966765263 -0.11531915 SWAQASVTHGAHGDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWAQASVTHGAHGDGGR 17 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 61.102 0.042063 67368000 37198 37227 36641 45532 83324 38346 54355 46693 97785 FALSE TRUE 35439.72426 41020.47362 38321.02609 40955.03685 97855.67922 37018.0684 46062.14645 42604.31338 112948.9984 0.313767495 0.363176958 0.339277255 0.36259761 0.866370491 0.327741449 0.407813678 0.377199568 1 16.78531195 -5 0.287496494 5.470761155 0.377282922 0.557381719 0.161957052 181.7958331 1.719480416 487.2583299 0.169550445 1.00E-05 5 -5.093478233 SWDIFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWDIFFR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;Q02218-3;C9J4G7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 173.85 0.001973 361930000 1472670 1101130 1164080 1160530 1501280 857030 1361420 1240990 1462730 FALSE TRUE 1403059.808 1213336.399 1217454.219 1043871.32 1763102.757 827350.8362 1153710.375 1132322.337 1689562.698 0.830427784 0.718136356 0.720573567 0.617835207 1.04352609 0.489683418 0.682845553 0.670186634 1 20.68821846 SWDSSSPVDRPEPEAAS(ph)PTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDSSSPVDRPEPEAAS(0.993)PT(0.006)T(0.001)R;SWDSSSPVDRPEPEAAS(0.941)PT(0.029)T(0.029)R;SWDSSSPVDRPEPEAAS(0.998)PT(0.002)TR 233.22 5.79E-30 1284210000 974690 871796 913209 1110430 859460 967060 1086610 1009320 894580 TRUE FALSE 928618.3353 960633.0035 955080.5359 998807.4667 1009349.552 933570.4697 920827.6875 920938.5901 1033306.898 0.898685896 0.929668626 0.924295133 0.9666126 0.976814879 0.903478407 0.891146367 0.891253695 1 19.97883738 2.511041259 0.004408099 1.853106178 6.06E-08 0.127263649 0.035700946 36125.03757 74.33167605 15471.11995 15773.5314 324.3704318 -2.511041259 -1.853106117 SWEDS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;SWEDS(1)PER;SWEDS(1)PER;SWEDS(1)PER;SWEDS(1)PER 234.28 1.55E-08 3375930000 5793720 5093490 4821990 5734020 5308740 5040290 5626250 5152180 3230140 TRUE FALSE 5519862.338 5612522.422 5043083.011 5157625.416 6234582.575 4865743.493 4767862.229 4701027.806 3731053.614 1.479437957 1.504272788 1.351651178 1.382350925 1.670997852 1.304120497 1.277886282 1.259973266 1 21.83115166 1.172097034 0.806609548 1.008677188 1.472689724 0.690587013 0.098433186 0.321760802 0.473824131 0.089565659 0.033870335 14.86267679 -1.172097034 0.464012536 SWEEQMIEVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SWEEQMIEVGR 11 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ;;; 202.34 9.39E-08 261539000 249579 235776 211164 239515 246243 189511 233317 194551 239227 FALSE TRUE 237781.8953 259801.8425 220846.0783 215438.4972 289187.7012 182948.1866 197720.2065 177515.0831 276325.1014 0.860515003 0.940203554 0.79922554 0.779655906 1.046548793 0.662075887 0.715534729 0.642413889 1 18.0760071 2.211933707 24.99994901 0.727139154 0.881771413 0.204522187 0.122137695 269.0093694 252570.6834 0.04083908 0.030170011 162.9047349 -2.211933707 0.154632259 SWEEQMIEVGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWEEQMIEVGRK 12 1 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 108.01 0.0028098 130080000 318740 273960 341880 330990 618990 241010 433460 287480 758050 FALSE TRUE 303673.7919 301876.8355 357555.5362 297718.2564 726941.66 232663.7633 367327.716 262306.7272 875604.5224 0.346816153 0.344763906 0.408352775 0.340014526 0.830216886 0.265717864 0.419513269 0.299572148 1 19.73991988 -1.176910899 4.078628331 1.000258479 0.403299188 0.58380914 0.157359015 92743689.51 158108861.6 305181.4672 0.035024977 0.066540966 1.176910899 -0.596959292 SWEQKLEEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWEQKLEEMR 10 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 121.02 0.00047978 328740000 1230180 705790 1082020 1007100 1353010 1066040 1703290 1264320 1617420 FALSE TRUE 1172031.829 777710.8034 1131631.687 905864.3946 1588974.516 1029122.767 1443421.827 1153609.438 1868241.233 0.627345018 0.416279648 0.605720325 0.484875496 0.85051892 0.550851116 0.772609983 0.617484197 1 20.83324932 -0.810853916 0.181156024 1.327920522 0.446425127 0.544523677 0.117403596 12.73319447 0.549396061 2.547715326 0.430838429 0.154577431 0.810853916 -0.881495395 SWGHES(ph)PEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWGHESPEER 10 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 SWGHES(1)PEER;SWGHES(1)PEER 131.06 0.00016757 195971000 206667 159886 199579 211505 229670 172955 231932 190041 177807 TRUE FALSE 196898.2605 176178.5652 208729.8946 190244.1156 269724.3753 166965.525 196546.5137 173400.0026 205380.4014 0.958700339 0.857815857 1.016308728 0.926301216 1.313291694 0.812957438 0.956987679 0.844286998 1 17.64793899 -2.09473355 7.822553258 1.241989265 0.956072364 0.006721217 0.139347816 0.179531646 0.002174184 0.041188956 0.029256845 0.008040193 2.09473355 -0.285916901 SWHDIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWHDIEK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 109.86 0.0069328 228970000 585840 583550 515900 726560 611270 577940 716150 670180 440190 FALSE TRUE 558148.5042 643014.4084 539554.5253 653524.8084 717875.2945 557925.7929 606888.1645 611495.4864 508452.417 1.097739898 1.264650117 1.061170145 1.285321471 1.411882942 1.09730188 1.19359874 1.202660202 1 18.95575324 -0.697876569 6.186426186 0.999999998 1.200575849 0.27236394 0.103637048 2.80E-09 4.52E-10 0.09390747 0.022134203 0.20050418 0.697876569 0.200575851 SWHDIEKDNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWHDIEKDNAR 11 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 69.451 0.032726 234250000 31703 23933 28932 36801 37500 30699 44283 31708 36651 FALSE TRUE 30204.46202 26371.79991 30258.56082 33101.69356 44039.98813 29635.88593 37526.81504 28931.47943 42334.64989 0.71346904 0.62293653 0.714746925 0.781905452 1.040282328 0.700038527 0.88643263 0.68339952 1 15.36955134 3.202855877 3.23662276 0.848712521 0.670687873 0.332908793 0.113849078 0.252887512 5.450897717 0.030433122 0.039099177 1595.349635 -3.202855877 -0.178024648 SWHDVQVS(ph)SAYVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 S(0.027)WHDVQVS(0.964)S(0.008)AYVK 211.82 1.98E-08 83479000 135710 106200 127720 132650 116040 128070 163230 137560 125020 TRUE FALSE 129295.2573 117021.9007 133576.0883 119315.77 136277.3393 123634.9038 138326.2656 125514.5171 144407.4631 0.895350244 0.810359093 0.924994356 0.826243793 0.943700113 0.856153146 0.95788862 0.869169186 1 17.13978578 -0.144359092 0.212774739 1.061294449 0.840851238 0.379652988 0.04713074 8.557346159 0.645482627 0.493689695 0.11905167 0.717201036 0.144359092 -0.220443212 SWLKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWLKPR 6 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ; 110.54 0.026101 3925200000 6257900 5450900 5118200 5722800 7530200 4970900 7163500 5449400 7911900 FALSE TRUE 5962101.469 6006352.907 5352874.533 5147533.271 8843464.496 4798756.487 6070576.508 4972221.647 9138837.044 0.652391704 0.657233834 0.585728196 0.563259116 0.967679416 0.525094874 0.66426138 0.544075972 1 23.12357916 -1.556901399 3.10034121 1.014886278 0.647795024 0.44525014 0.124507459 188292215 210200052.4 23214679.53 0.026953919 0.027739498 1.556901399 -0.367091254 SWNSWQGFNPFSSGGPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWNSWQGFNPFSSGGPFR 18 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 142.91 2.54E-07 27572000 37510 32847 32910 32274 37454 36183 45173 37935 41834 FALSE TRUE 35736.97664 36194.14664 34418.95605 29029.7562 43985.96574 34929.97364 38281.02919 34613.21029 48321.40306 0.739568274 0.749029299 0.712292149 0.600763934 0.910279151 0.722867537 0.792216839 0.716312195 1 15.56037472 -4.999999998 0.274823298 2.808067225 0.727601969 0.528375667 0.076436419 165.3288876 1.594685668 169.9954221 0.081832667 1.00E-05 4.999999998 -2.080465256 SWPS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SWPSPK 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 SWPS(1)PK;SWPS(1)PK;SWPS(1)PK;S(0.004)WPS(0.996)PK 90.657 0.051169 1080670000 4330930 4062970 3868610 4629730 2693950 4605950 4722240 4982650 3031660 TRUE FALSE 4126215.522 4476991.262 4045989.595 4164340.744 3163774.027 4446444.797 4001775.558 4546342.751 3501794.349 1.178314633 1.278484918 1.155404684 1.189201972 0.903472252 1.269761829 1.142778576 1.298289476 1 21.73966293 -2.323378765 2.30902437 0.000161091 1.179135476 0.201357138 0.110683897 1860099.628 723379.2459 9551240.816 0.025044052 0.004749208 2.323378765 1.178974385 SWS(ph)LATFR ddPTM_SK-BR-3_Trastuzumab_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(0.004)WS(0.996)LATFR;S(0.007)WS(0.993)LATFR;SWS(1)LATFR 146.68 0.00057634 107406000 250456 247863 218522 237703 262044 235889 269454 230816 251482 TRUE FALSE 238617.4412 273120.5215 228541.4498 213808.6428 307744.3906 227720.1048 228343.8434 210604.5274 290480.5442 0.821457568 0.940236883 0.786770248 0.736051509 1.059432023 0.783942709 0.786089974 0.725021113 1 18.14808201 SWS(ph)PPPEVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 SWSPPPEVSR 10 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;S(0.015)WS(0.985)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;S(0.003)WS(0.997)PPPEVSR 187.76 1.25E-06 19374420000 3648680 3056210 3174930 3700910 3565060 3335750 3883580 3498270 3809170 TRUE FALSE 3476214.127 3367641.274 3320503.681 3328887.496 4186805.335 3220232.141 3291068.544 3191942.933 4399876.629 0.790070818 0.765394478 0.754681088 0.756586554 0.951573348 0.731891463 0.747991096 0.725461917 1 22.06903164 -1.179602949 4.866383192 1.000022679 0.777164813 0.540679191 0.064313811 1.50E-05 2.53E-06 0.059036113 0.01391353 0.066129776 1.179602949 -0.222857865 SWS(ph)TATSPLGGERPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.396)WS(0.563)T(0.04)ATSPLGGERPFR 130.95 2.86E-05 130940000 20690 20932 24430 25396 19424 27195 22064 24247 21208 TRUE FALSE 19712.0247 23064.9946 25550.13966 22843.14583 22811.53945 26253.23033 18697.73157 22123.80414 24496.82832 0.804676607 0.94155024 1.042997866 0.932494016 0.931203793 1.07169916 0.763271527 0.903129329 1 14.58030735 -0.201594065 7.238253463 0.999999999 0.917485967 0.05878106 0.092641251 0 0 0.088062866 0.020756617 0.628645679 0.201594065 -0.082514032 SWSHYTVPAGMTVIQWVSDFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWSHYTVPAGMTVIQWVSDFSER 23 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 267.77 2.58E-44 234410000 248340 243860 250810 284130 328370 260550 373780 295670 288740 FALSE TRUE 236601.4604 268709.6112 262309.8866 255568.7126 385637.624 251527.0882 316752.9961 269779.5674 333516.3245 0.709414931 0.805686533 0.786497893 0.766285467 1.156278106 0.754167247 0.949737607 0.80889464 1 18.34739785 2.896734276 21.49974735 0.921772513 0.76801467 0.361576204 0.109508573 12.38765502 2571.071355 0.02982356 0.031632683 788.3776004 -2.896734276 -0.153757843 SWSTATS(ph)PLGGERPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 SWST(0.001)AT(0.043)S(0.956)PLGGERPFR 110.57 0.0023257 87350000 98418 78598 79673 96864 94440 83643 103550 86076 93952 TRUE FALSE 93765.97619 86607.22556 83326.08586 87127.04669 110910.3061 80746.42194 87751.54567 78538.72912 108521.5963 0.864030565 0.798064427 0.767829526 0.802854452 1.022011377 0.744058553 0.808609057 0.723715203 1 16.72762265 -1.344383946 3.727140856 1.000654782 0.817946659 0.328087647 0.082547731 795467.3101 38110359.61 42191.95023 0.018030524 0.045249736 1.344383946 -0.182708124 SWSYNGYYS(ph)DLSTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SWSYNGYYSDLSTAR 15 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 SWSYNGYYS(1)DLSTAR;SWSYNGYYS(1)DLSTAR 130.06 6.51E-05 64052000 80557 81888 80134 87297 104974 82309 101425 89607 118089 TRUE FALSE 76749.23026 90232.4803 83808.22316 78521.73971 123281.4324 79458.61869 85950.75345 81760.53604 136401.639 0.56267088 0.661520499 0.614422406 0.575665661 0.903811958 0.582534193 0.630129917 0.599410217 1 17.05750145 -1.918459756 2.607314405 1.220583773 0.640095181 0.571156461 0.097683275 24175246.69 12948319.97 32550590.98 0.021692307 0.012065359 1.918459756 -0.580488592 SWTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 SWT(0.003)S(0.997)PK;SWT(0.016)S(0.984)PK;SWT(0.002)S(0.998)PK;SWT(0.004)S(0.996)PK;SWT(0.004)S(0.996)PK;SWT(0.116)S(0.884)PK 143.73 0.011918 3221375000 15929660 15171570 14361280 17737000 9859810 17313600 17857700 17967400 10627830 TRUE FALSE 15176696.54 16717570.23 15019758.89 15954043.06 11579357.74 16714025.69 15133179.89 16394079.2 12275939.6 1.236296124 1.361815941 1.223511958 1.299618896 0.943256331 1.361527202 1.23275125 1.33546431 1 23.54933012 -1.660173637 2.560221072 0.965794185 1.253647842 0.297398438 0.120247146 16271608.7 13784838.9 3650693.364 0.028694858 0.021868871 1.660173637 0.287853656 SWVIGS(ph)PEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 139.78 4.08E-05 114077000 175667 169794 173561 190091 181219 168859 190698 184273 194448 TRUE FALSE 167363.569 187096.2016 181518.9435 170982.6915 212823.5362 163011.3705 161603.5177 168137.0792 224602.0027 0.745156174 0.83301217 0.808180432 0.761269666 0.947558497 0.725778793 0.719510582 0.748600089 1 17.77701127 -2.333557295 2.248451048 2.208981056 0.785027813 0.500666228 0.067114248 3117282.669 516898.3229 19068993.14 0.015941994 0.004639196 2.333557295 -1.423953243 SWWDAVCTLIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SWWDAVCTLIHR 12 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;F8W705;Q99666-2;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;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 0 99.5 0.0037613 35242000 62755 49822 29344 32103 53113 30606 52433 40927 37288 FALSE TRUE 59788.69552 54898.91844 30689.45143 28875.94545 62375.89038 29546.10655 44433.38285 37343.21491 43070.4326 1.388161017 1.274631229 0.712541054 0.670435464 1.448229948 0.685995119 1.031644685 0.867026697 1 15.39441019 3.877602604 5.894679091 0.922955578 1.34581971 0.369163635 0.226951974 0.208572871 9.152780234 0.054074387 0.099028501 7544.016056 -3.877602604 0.422864132 SYCAEIAHNVSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SYCAEIAHNVSSK 13 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;;;; 198.14 1.28E-07 5901170000 9590160 8220530 7879730 9801640 7762240 8778820 11313980 9918780 8956540 FALSE TRUE 9136852.143 9058211.353 8241023.415 8816360.525 9115972.198 8474807.262 9587824.556 9050239.04 10345474.48 0.883173813 0.875572345 0.796582451 0.852194894 0.881155545 0.819180143 0.926765087 0.874801737 1 23.30249648 0.587301071 0.744843447 1.000545793 0.856488219 0.628460858 0.034036902 0.908267889 0.87461336 0.034233567 0.011713064 3.866349152 -0.587301071 -0.144057574 SYDQVHSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYDQVHSGK 9 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 112.11 0.0020162 268450000 876000 953970 835930 1010890 686170 859000 911620 991160 700850 FALSE TRUE 834593.2161 1051180.628 874258.2173 909273.4166 805837.8308 829252.6146 772535.626 904368.7759 809534.2386 1.030954809 1.298500517 1.07995212 1.123205633 0.995433908 1.02435768 0.95429642 1.117147037 1 19.62673257 2.967242047 1.929995419 1.010074172 1.159445762 0.323578761 0.079841137 0.317856718 2.377604121 0.0260784 0.029999833 927.3465204 -2.967242047 0.149371589 SYDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;; 179.03 5.90E-17 447680000 768090 726920 732550 852040 650250 743170 883840 840420 675950 FALSE TRUE 731783.9079 800993.9744 766138.1421 766391.3204 763653.3941 717433.8366 748993.9752 766828.3695 780772.8737 0.937255805 1.025898826 0.981256096 0.981580363 0.978073675 0.918876489 0.959298152 0.982140127 1 19.5745434 2.454959415 24.96995345 0.95847363 0.983554589 0.045071245 0.029437218 449.3968122 506336.9091 0.009721506 0.008134241 285.0751853 -2.454959415 0.025080959 SYEALVQHVIEDHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 SYEALVQHVIEDHER 15 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;;;; 223.76 7.08E-13 679281000 497596 425749 428109 504178 527585 426070 554902 460200 66408.7 FALSE TRUE 474075.6232 469133.3071 447738.2211 453497.0696 619595.657 411315.0891 470241.5084 419902.4483 76707.02203 6.180341913 6.115910835 5.836991312 5.912067208 8.07743073 5.362156921 6.13035803 5.474107027 1 16.22707103 0.327777234 1.09671506 0.98606641 6.25936705 0.84484956 0.699669007 1.109877565 1.499423968 0.637666907 0.191055837 2.127047723 -0.327777234 5.27330064 SYEDMIGEEVPSDQYYWAPLAQHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 183.25 2.09E-17 185809000 201119 186424 185159 208590 211620 182765 215200 205060 184306 FALSE TRUE 191612.5034 205420.8175 193648.7233 187622.1369 248526.461 176435.8022 182367.2876 187103.8593 212887.2332 0.900065732 0.964927838 0.909630514 0.881321694 1.167408948 0.828775872 0.856637971 0.878887177 1 17.69972991 -0.871741154 5.19246473 1.000000107 0.922250058 0.061588463 0.093792627 1.11E-07 2.41E-08 0.086294267 0.020339726 0.134356551 0.871741154 -0.077750049 SYELPDGQVITIGNER ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;;;;;;;; 338.79 1.58E-71 20854376000 5434599 4790894 4985168 5561809 5490301 4999091 5816920 5495646 5982924 FALSE TRUE 5177716.276 5279091.545 5213742.884 5002725.393 6447807.756 4825971.225 4929442.019 5014418.102 6910725.297 0.749229068 0.763898335 0.754442213 0.72390743 0.933014623 0.698330641 0.713303135 0.725599396 1 22.7204057 -1.383953271 3.212041864 1.002548091 0.756040159 0.575025795 0.065444337 62823461.89 83647798.12 1494141.09 0.014957008 0.041309195 1.383953271 -0.246507932 SYETLVDFDNHLDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 141 1.65E-06 42111000 70893 78330 57583 84737 69396 66313 68119 68498 52714 FALSE TRUE 67542.02839 86311.91605 60223.23751 76219.07577 81498.64043 64016.56418 57726.19546 62499.95199 60888.61789 1.109271827 1.417537777 0.989072171 1.251778713 1.338487278 1.051371609 0.948062174 1.026463634 1 15.89388495 2.078002861 6.036394388 0.988969437 1.227945224 0.459265734 0.117043282 0.167884573 10.05404725 0.042356718 0.030975719 119.6748414 -2.078002861 0.238975787 SYGPAPGAGHVQEESNLSLQALESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SYGPAPGAGHVQEESNLSLQALESR 25 0 Q13155 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ;; 379.32 2.50E-120 604032000 448639 357550 402880 471714 430102 402870 490096 461841 492949 FALSE TRUE 427432.7236 393984.7515 421352.4465 424296.4125 505111.6526 388918.5109 415322.854 421399.7537 569393.0133 0.750681364 0.691938156 0.740002839 0.745173198 0.887105463 0.683040539 0.72941333 0.740085923 1 19.11906527 -1.546480725 6.413277422 1.00031889 0.741663202 0.676958111 0.055087405 0.000240254 1.70E-05 0.051019152 0.012010771 0.028413143 1.546480725 -0.258655689 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 132.57 6.59E-08 106688000 182193 184222 175020 207054 174274 187261 211908 202577 153899 FALSE TRUE 173581.098 202994.4312 183044.8401 186240.5385 204667.3304 180776.1046 179577.5426 184838.284 177764.8709 0.976464568 1.141926581 1.029701983 1.047679092 1.151337322 1.016939419 1.010197019 1.039790837 1 17.43961073 2.082612559 24.98512903 1.016703571 1.06940422 0.207848361 0.051113128 41.83473453 12648.10723 0.018161556 0.013413198 120.9518622 -2.082612559 0.052700649 SYIYSGSHDGHINYWDSETGENDSFAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYIYSGSHDGHINYWDSETGENDSFAGK 28 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 158.61 6.29E-12 526050000 170942 152166 174691 193940 197956 163272 246265 191466 22738.2 FALSE TRUE 162861.9104 167671.8884 182700.7551 174444.7827 232479.4637 157617.8497 208692.7513 174700.222 26264.32393 6.2008796 6.384016923 6.956232936 6.64189123 8.851530479 6.001214809 7.945864203 6.651616943 1 14.68081683 0.942671656 22.15835068 0.999999996 6.954895704 0.829828149 0.848604458 2289.556086 884952.7101 0.780167312 0.195041828 8.763380233 -0.942671656 5.954895708 SYKDDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYKDDSK 7 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 64.091 0.068854 434140000 650250 576220 617830 871840 418630 756020 813770 933290 590590 FALSE TRUE 619513.9712 634937.4731 646158.1166 784200.9868 491638.9395 729838.8378 689614.4406 851566.1799 682175.6809 0.908144322 0.930753603 0.947201923 1.149558697 0.720692562 1.069869329 1.010904463 1.248309202 1 19.3797838 1.716210669 2.277128631 1.113923933 0.941252839 0.233717977 0.124836128 0.356582642 3.901287013 0.074545679 0.03143727 52.02482989 -1.716210669 -0.172671094 SYLYLSPSGNSS(ph)PPGS(ph)PTLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYLYLSPSGNSSPPGSPTLQK 21 0 H0YC42;P55327-8 H0YC42 2 SYLYLSPSGNS(0.032)S(0.968)PPGS(0.751)PT(0.249)LQK 185.06 1.97E-17 107520000 275630 186520 233550 247040 187810 233180 254910 231060 220290 TRUE FALSE 262601.5161 205526.6001 244258.4985 222207.0699 220564.0045 225104.9181 216018.7978 210827.1615 254451.4481 1.032029953 0.80772423 0.959941475 0.873278857 0.866821573 0.884667467 0.848958807 0.828555558 1 17.95703088 4.684225399 3.573157755 0.877968718 1.041357718 0.389336034 0.057835916 0.219845245 4.734660801 0.01224709 0.086844122 48330.95744 -4.684225399 0.163389 SYMNPGDQS(ph)PADSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;S(0.016)Y(0.001)MNPGDQS(0.984)PADSNK 449.14 2.60E-175 3179860000 5942944 6541700 5425434 6919479 3895296 6242244 6618094 6475975 4415079 TRUE FALSE 5662032.815 7208306.667 5674195.515 6223919.825 4574634.389 6026073.525 5608382.211 5908904.298 5099746.902 1.110257611 1.41346361 1.112642573 1.220437003 0.897031652 1.181641685 1.099737363 1.158666187 1 22.28199422 3.316694542 2.220009208 1.089035336 1.256822938 0.234386729 0.118380142 0.370596485 3.731464614 0.033297245 0.047690306 2073.454654 -3.316694542 0.167787602 SYNPFDDDGEDEGARPAPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;; 211.43 2.48E-22 224820000 132045 113383 118442 127754 132192 120244 142676 127436 152028 FALSE TRUE 125803.4945 124936.8566 123872.6829 114911.9252 155246.2429 116079.9201 120908.1558 116277.0283 175603.7258 0.716405611 0.71147042 0.705410334 0.654382045 0.884071464 0.661033356 0.688528419 0.662155816 1 17.42196393 -1.016679419 4.816520466 1.000005316 0.71039805 0.658780209 0.065493708 3.41E-06 6.97E-07 0.057867191 0.013639177 0.096232237 1.016679419 -0.289607266 SYQNS(ph)PS(ph)SDDGIRPLPEYSTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 S(0.001)Y(0.003)QNS(0.807)PS(0.638)S(0.551)DDGIRPLPEYSTEK 107.29 0.00026131 396290000 592970 494380 519670 587920 412660 578450 653170 545280 442110 TRUE FALSE 564941.4833 544757.8841 543497.3835 528821.1646 484627.7733 558418.1315 553516.9202 497532.3925 510670.1608 1.106274708 1.06675096 1.064282633 1.035543498 0.949003507 1.093500608 1.083903002 0.974273476 1 18.96203224 3.911881759 1.287589685 1.033423659 1.101496425 0.25562196 0.045186818 0.804141564 2.428056895 0.014242614 0.048170526 8163.600784 -3.911881759 0.068072767 SYQNS(ph)PSS(ph)DDGIRPLPEYSTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.044)S(0.956)DDGIRPLPEYSTEK 258.24 2.04E-37 364840000 711610 641510 675890 766360 576410 804100 844300 757840 648140 TRUE FALSE 677973.6056 706880.5983 706880.225 689324.0368 676935.7215 776253.8154 715486.5284 691479.512 748650.241 0.905594587 0.944206733 0.944206235 0.92075578 0.904208246 1.036871122 0.955701994 0.923634929 1 19.51393234 2.27696399 24.99999959 0.975451316 0.925713002 0.426600433 0.031668111 164.7373559 107240.8453 0.010461785 0.008752791 189.2186719 -2.27696399 -0.049738314 SYQNSPS(ph)SDDGIRPLPEYSTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SYQNS(0.143)PS(0.429)S(0.429)DDGIRPLPEYSTEK;SYQNS(0.114)PS(0.443)S(0.443)DDGIRPLPEYSTEK 229.6 1.63E-26 375590000 624390 554360 555160 671740 471360 657770 699390 664220 559550 TRUE FALSE 594876.3221 610849.9143 580614.6351 604215.419 553565.0348 634991.26 592685.2103 606057.3755 646322.1562 0.920402181 0.945116779 0.89833627 0.934851781 0.856484695 0.982468656 0.917012058 0.937701686 1 19.30189392 0.185096264 0.687449831 1.002315354 0.921530419 0.37127846 0.031910686 3.324494708 1.978154159 0.047615249 0.010550822 1.531426874 -0.185096264 -0.080784936 SYQSELEALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYQSELEALRR 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 100.38 0.0065343 90229000 71856 65110 67652 80204 63677 73391 85887 78260 74296 FALSE TRUE 68459.50928 71744.78302 70753.91112 72141.74154 74782.24864 70849.45127 72783.36073 71407.13952 85817.44423 0.797734189 0.83601631 0.824470033 0.840641925 0.871410811 0.825583329 0.848118484 0.832081871 1 16.38898332 -5 0.26291531 2.090713846 0.820740091 0.89434368 0.017958031 58.20116333 0.569822044 34.34195058 0.022467047 1.00E-05 5 -1.269973755 SYS(ph)AGNASQLEQLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSAGNASQLEQLSR 15 0 Q14678;Q14678-2 Q14678 KANK1 KN motif and ankyrin repeat domain-containing protein 1 1 SYS(0.999)AGNAS(0.001)QLEQLSR;SYS(1)AGNASQLEQLSR 260.38 7.04E-25 294870000 176786 174657 179335 208644 195544 196520 226477 208097 224120 TRUE FALSE 168429.6761 192454.7469 187557.6871 187670.7087 229646.8117 189714.4631 191923.7741 189874.9235 258875.385 0.650620669 0.743426212 0.724509544 0.724946131 0.887094042 0.732840873 0.741375137 0.733460709 1 17.98189827 -5 0.202937734 2.180049922 0.698954716 0.675032776 0.056750551 85.37729458 0.846653112 41.01792453 0.129361368 1.00E-05 5 -1.481095206 SYS(ph)EPEKMNEVGIVEEAEPAPLGPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSEPEKMNEVGIVEEAEPAPLGPQR 26 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.001)YS(0.999)EPEKMNEVGIVEEAEPAPLGPQR;S(0.15)Y(0.041)S(0.81)EPEKMNEVGIVEEAEPAPLGPQR 340.53 1.13E-95 327360000 302084 229978 270128 309105 202693 296083 332535 305897 207363 TRUE FALSE 287805.088 253413.0197 282513.636 278033.1781 238042.595 285829.5715 281800.6783 279111.037 239519.795 1.201592077 1.058004495 1.179500158 1.160794156 0.99383266 1.193344256 1.176523545 1.165294238 1 17.86978537 4.746319257 6.524709592 1.126199915 1.203236174 0.100712232 0.07505934 0.289320735 67.06197454 0.016586363 0.099415438 55759.54953 -4.746319257 0.077036258 SYS(ph)LSELSVLQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.835)LS(0.165)ELSVLQAK;SYS(0.892)LS(0.108)ELSVLQAK;SYS(0.951)LS(0.048)ELSVLQAK;SYS(1)LSELSVLQAK;SYS(0.507)LS(0.493)ELSVLQAK;SYS(0.998)LS(0.002)ELSVLQAK;SYS(0.908)LS(0.092)ELSVLQAK 369.89 3.28E-91 4451375000 5981862 5082276 5319808 5983769 4523658 5527237 6369522 6136020 5370554 TRUE FALSE 5699111.238 5600165.702 5563726.459 5382269.172 5312582.523 5335827.397 5397734.435 5598717.56 6203392.085 0.918708855 0.902758624 0.89688454 0.86763324 0.856399604 0.860146727 0.870126273 0.90252518 1 22.56462588 -1.717266413 7.216919044 1.001048272 0.884935996 0.754811416 0.020704122 0.000406966 1.59E-05 0.023362344 0.00545849 0.019174921 1.717266413 -0.116112276 SYS(ph)PAHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.124)YS(0.876)PAHNR;S(0.002)YS(0.998)PAHNR;S(0.009)YS(0.991)PAHNR 89.827 0.0087794 489987000 471554 473428 495812 529090 519127 435074 542714 475229 457433 TRUE FALSE 449264.5769 521670.8514 518545.4706 475904.868 609662.5844 420007.2783 459913.0117 433615.4294 528369.3734 0.850285046 0.987322274 0.981407131 0.90070487 1.153856781 0.794912233 0.870438437 0.820667229 1 19.01118732 SYS(ph)PDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(1)PDGK;S(0.003)YS(0.997)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK 152.86 0.0018727 34091440000 43595190 46193040 35198440 48706350 24201780 43491810 39640260 42891940 24590230 TRUE FALSE 41534531.77 50900163.29 36812323.29 43810295.16 28422562.77 41985677.71 33592410.29 39136094.35 28403557.28 1.462300351 1.792034807 1.296046229 1.542422829 1.000669124 1.478183782 1.18268321 1.377858906 1 24.75956829 3.190362039 0.207331682 0.968015494 1.902017882 0.377370308 0.19285927 5.770110955 0.454851913 0.463953702 1.517102337 1550.108292 -3.190362039 0.934002388 SYS(ph)PDGKES(ph)PSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.063)Y(0.002)S(0.934)PDGKES(0.987)PS(0.013)DKK;S(0.003)YS(0.997)PDGKES(0.649)PS(0.351)DKK;S(0.457)Y(0.008)S(0.535)PDGKES(0.976)PS(0.024)DKK;S(0.001)YS(0.999)PDGKES(0.5)PS(0.5)DKK 148.24 3.84E-05 2156970000 2849190 2827980 2699630 3312800 1061340 3567840 3150250 3518860 998180 TRUE FALSE 2714514.435 3116154.377 2823410.706 2979791.05 1246437.36 3444284.806 2669621.504 3210729.964 1152972.656 2.354361502 2.702713165 2.44880977 2.58444208 1.081064111 2.987308317 2.315424819 2.784740771 1 20.13692687 SYS(ph)PDGKESPSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.007)Y(0.001)S(0.958)PDGKES(0.033)PS(0.001)DK;S(0.042)YS(0.951)PDGKES(0.007)PSDK 132.08 0.00021125 74461000 337100 250290 297520 320040 183192 349770 391500 393850 225690 TRUE FALSE 321165.9511 275794.8356 311161.5863 287868.9712 215140.6268 337657.3772 331769.4846 359362.4061 260688.8525 1.231989584 1.05794641 1.193612935 1.104262681 0.825277432 1.295250541 1.27266464 1.378510828 1 17.99196937 SYS(ph)PDGKESPSDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.024)YS(0.968)PDGKES(0.003)PS(0.005)DKK;S(0.011)YS(0.988)PDGKESPSDKK;S(0.154)Y(0.002)S(0.771)PDGKES(0.068)PS(0.004)DKK;S(0.001)YS(0.99)PDGKES(0.009)PSDKK;S(0.001)YS(0.992)PDGKES(0.007)PSDKK;S(0.003)YS(0.997)PDGKESPSDKK;S(0.002)Y(0.001)S(0.996)PDGKES(0.001)PSDKK 147.56 4.17E-06 44288370000 10554690 7429960 9460160 9607630 4484820 11658920 12229590 12226770 4895780 TRUE FALSE 10055790.72 8187081.371 9893917.693 8641852.779 5266971.188 11255168.68 10363741.43 11156129.2 5654992.558 1.778214669 1.447761653 1.74958987 1.528181105 0.931384283 1.990306541 1.8326711 1.972792906 1 22.4310937 SYS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.051)YS(0.949)PDHR;S(0.001)YS(0.999)PDHR;S(0.035)YS(0.965)PDHR;S(0.188)YS(0.812)PDHR;S(0.235)YS(0.765)PDHR;S(0.025)YS(0.975)PDHR;SYS(1)PDHR;S(0.005)YS(0.995)PDHR 153.08 0.0018574 1439126000 2594786 2828200 2415731 2711720 2564710 2783369 2783630 2443891 2006300 TRUE FALSE 2472135.608 3116396.795 2526494.656 2439132.754 3011994.612 2686980.234 2358936.119 2229890.948 2317426.757 1.066758896 1.344766037 1.090215537 1.052517732 1.299715127 1.159467166 1.017911833 0.962227152 1 21.14409231 1.697777021 3.584194078 0.984358942 1.179958786 0.43816375 0.093997328 0.176371123 5.205202886 0.052505994 0.024510593 49.86284115 -1.697777021 0.195599844 SYS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.017)YS(0.983)PER;S(0.024)YS(0.976)PER;S(0.179)Y(0.001)S(0.82)PER;S(0.009)YS(0.991)PER;S(0.077)YS(0.923)PER;S(0.007)YS(0.993)PER 114.43 0.026529 4076020000 2663390 2525790 2529640 2715100 2616310 2546430 2790200 2528830 2819900 TRUE FALSE 2537496.833 2783170.873 2645626.496 2442172.99 3072593.636 2458246.491 2364503.744 2307392.239 3257195.69 0.779043409 0.854468425 0.812240574 0.749777791 0.94332485 0.754712558 0.725932357 0.708398407 1 21.63519897 SYS(ph)PYDYQPCLAGPNQDFHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.017)YS(0.983)PYDYQPCLAGPNQDFHSK 201.46 4.45E-22 168480000 204530 194960 179430 225330 165890 216640 236160 225890 184860 TRUE FALSE 194862.2722 214826.6457 187657.043 202679.4003 194821.1635 209137.7025 200129.4546 206109.8741 213527.1447 0.912587824 1.006085882 0.878843967 0.949197352 0.912395301 0.979443165 0.937255331 0.965263102 1 17.70405996 0.700706706 0.89754655 1.000202356 0.941154196 0.235685288 0.035424449 1.628174964 2.370003785 0.031717898 0.010612371 5.020034547 -0.700706706 -0.059048161 SYS(ph)SPDITQAIQEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSSPDITQAIQEEEK 16 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.913)S(0.087)PDITQAIQEEEK 285.26 8.43E-36 57194000 97564 87039 82056 115780 64697 105470 105220 105890 74564 TRUE FALSE 92952.34307 95908.37306 85818.34876 104141.5744 75980.13632 101817.5475 89166.7565 96617.71024 86127.0043 1.079247372 1.113569128 0.996416275 1.209162855 0.882187148 1.182179135 1.035293834 1.121805072 1 16.39417803 SYS(ph)SPDITQAIQEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.913)S(0.087)PDITQAIQEEEKR;SYS(0.5)S(0.5)PDITQAIQEEEKR;SYS(0.5)S(0.5)PDITQAIQEEEKR;SYS(0.5)S(0.5)PDITQAIQEEEKR;SYS(0.735)S(0.265)PDITQAIQEEEKR;S(0.006)YS(0.839)S(0.155)PDITQAIQEEEKR;SYS(0.812)S(0.188)PDITQAIQEEEKR;S(0.014)YS(0.825)S(0.162)PDITQAIQEEEKR 325.01 2.33E-59 6137345000 3865880 3217850 3263030 3873320 2570770 3853400 4057940 4114940 2879090 TRUE FALSE 3683147.514 3545752.573 3412643.153 3483966.515 3019111.474 3719955.792 3438826.724 3754614.039 3325564.573 1.107525484 1.066210713 1.026184601 1.047631594 0.907849301 1.118593764 1.034058022 1.129015527 1 21.66516785 4.169446254 2.060941783 1.038870323 1.103330098 0.117412306 0.061073579 0.68728816 5.575974769 0.015235512 0.053089119 14772.23658 -4.169446254 0.064459775 SYSDMKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYSDMKR 7 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 78.616 0.055886 329170000 521060 355970 423430 463590 433340 463090 628210 561950 530570 FALSE TRUE 496430.5264 392243.7477 442844.6843 416989.0524 508914.3588 447053.0772 532365.0266 512742.6789 612848.0858 0.810038471 0.640034222 0.722601073 0.680411773 0.830408662 0.729468016 0.86867372 0.83665543 1 19.22516997 1.200822228 0.616789469 0.997687839 0.713023887 0.690286463 0.057834895 0.38215428 0.355706236 0.053373196 0.024238777 15.87896632 -1.200822228 -0.284663953 SYSEDDIHR ddPTM_SK-BR-3_Trastuzumab_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 ; 214.93 6.58E-07 1908410000 2109890 1962180 1835210 2225400 1981090 1931870 2240900 2025530 1872720 FALSE TRUE 2010159.681 2162128.373 1919356.194 2001698.564 2326591.469 1864968.857 1899009.548 1848163.855 2163131.853 0.929282086 0.999536098 0.8873043 0.925370574 1.075566182 0.862161433 0.877898194 0.854392603 1 21.04469018 SYSFDEIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 158.57 0.00010697 2493810000 3622800 2879980 2895530 3244870 2846290 3113240 3938560 3536690 3209840 FALSE TRUE 3451557.424 3173453.236 3028292.915 2918689.503 3342682.075 3005427.718 3337660.335 3226998.674 3707605.594 0.93093975 0.855930642 0.816778602 0.787216825 0.901574342 0.810611496 0.9002199 0.870372696 1 21.82205635 0.383566102 0.984563495 1.000383324 0.857273592 0.505427963 0.044306404 2.120493377 2.604718637 0.044184885 0.013576085 2.418611433 -0.383566102 -0.143109732 SYSLS(ph)ELSVLQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.024)LS(0.976)ELSVLQAK 307.77 1.74E-50 307450000 322730 276060 300130 303850 249160 293110 343030 310720 276260 TRUE FALSE 307475.1925 304190.8279 313891.2574 273306.4207 292613.4251 282959.5272 290694.4733 283511.7096 319100.9899 0.963567028 0.953274473 0.983673719 0.85648879 0.91699316 0.886739735 0.910979541 0.888470166 1 18.28365356 3.25658214 24.99980458 0.904707526 0.963464515 0.330786691 0.037556978 231.4359006 321050.3517 0.008951454 0.012095958 1805.436175 -3.25658214 0.058756989 SYSPDGKES(ph)PSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.105)YS(0.272)PDGKES(0.619)PS(0.004)DK 90.759 0.018003 92608000 134520 99269 130930 131430 73458 155380 171550 173110 101170 TRUE FALSE 128161.5062 109384.624 136933.27 118218.4067 86269.05194 149999.1516 145376.8968 157951.5707 116858.9269 1.096719862 0.936039949 1.17178271 1.011633513 0.73823245 1.283591726 1.244037581 1.351643173 1 16.83440842 2.181698019 24.99996704 1.242122583 1.002188134 0.381992722 0.143053217 78.46650724 34497.56647 0.049284518 0.036399048 151.9490604 -2.181698019 -0.239934449 SYSS(ph)PDITQAIQEEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.378)S(0.622)PDITQAIQEEEKR 314.79 1.88E-58 920250000 739220 602930 606340 716000 518650 673040 733830 723310 538490 TRUE FALSE 704278.5356 664369.2525 634141.2888 644026.3197 609102.3958 649732.456 621870.7558 659973.1419 621996.279 1.132287378 1.068124159 1.019525856 1.035418284 0.97927016 1.044592191 0.999798193 1.061056415 1 19.24654642 4.174215716 1.332428887 1.017693879 1.136675428 0.698704217 0.023907105 0.262301951 0.760979851 0.006176375 0.032129791 14935.36072 -4.174215716 0.118981549 SYSSGGEDGYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 146.48 0.00013706 397060000 510490 402953 461530 487390 567320 461991 560580 487780 599730 FALSE TRUE 486360.1494 444014.3688 482691.607 438396.6312 666260.4284 445992.1358 475053.2252 445067.3973 692733.0654 0.702088833 0.640960264 0.696793081 0.632850737 0.961785227 0.643815285 0.685766638 0.642480372 1 19.40194001 -1.044732004 4.163985841 1.000031104 0.69772912 0.488353393 0.096194043 9933130.047 4984387.816 2681.468 0.0209011 0.090212765 1.044732004 -0.302301983 SYSYVCGISSKDEPDWESLIFLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYSYVCGISSKDEPDWESLIFLAR 24 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 216.89 1.18E-32 84698000 117460 63675 115280 102650 114640 119120 151350 127550 139290 FALSE TRUE 111907.8986 70163.55489 120565.702 92331.42698 134633.1797 114994.8445 128258.7778 116381.0458 160890.3818 0.695553689 0.436095397 0.749365504 0.573877854 0.836800673 0.71474033 0.797181139 0.723356142 1 17.29571856 1.193915283 0.225284257 1.081932049 0.503776799 0.534594896 0.102003577 1.812573938 0.388065523 0.417697623 0.309988201 15.62842752 -1.193915283 -0.57815525 SYVAWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 SYVAWDR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 101.41 0.02112 1376450000 794710 682310 651860 851460 756840 777100 962690 861450 775490 FALSE TRUE 757145.6333 751838.1647 681748.4258 765869.6231 888832.6564 750188.8321 815813.9595 786016.8712 895749.0285 0.845265369 0.839340195 0.761093123 0.855004693 0.992278672 0.837498907 0.910761757 0.877496761 1 19.77273505 2.990235872 24.91451844 0.911727224 0.822609071 0.461039169 0.05327139 430.2774869 1097916.278 0.014417023 0.016321621 977.7681172 -2.990235872 -0.089118153 SYVDPSTDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SYVDPSTDER 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 93.467 0.014752 0 122830 117780 113910 118550 132080 112520 106190 114920 131820 FALSE TRUE 117024.0693 129781.9159 119132.8862 106633.1288 155114.7102 108623.4042 89988.76519 104856.9956 152261.9724 0.76857056 0.852359351 0.782420484 0.700326727 1.018735721 0.713398116 0.591012738 0.688661745 1 17.21619615 2.034613279 24.99999801 0.698887258 0.819847463 0.019789828 0.133890181 302.4688964 218461.8256 0.045214951 0.033393322 108.2962152 -2.034613279 0.120960205 SYVS(ph)EPELATLSGDMAQPSLGLVGPESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.061)YVS(0.939)EPELATLSGDMAQPSLGLVGPESR;S(0.014)Y(0.001)VS(0.984)EPELAT(0.001)LSGDMAQPSLGLVGPESR;S(0.012)YVS(0.988)EPELATLSGDMAQPSLGLVGPESR;S(0.011)Y(0.002)VS(0.986)EPELAT(0.001)LSGDMAQPSLGLVGPESR;S(0.034)YVS(0.966)EPELATLSGDMAQPSLGLVGPESR;S(0.035)YVS(0.965)EPELATLSGDMAQPSLGLVGPESR;S(0.183)Y(0.001)VS(0.815)EPELAT(0.001)LSGDMAQPSLGLVGPESR 212.24 4.02E-26 815906000 280913 257641 258931 291787 288404 282435 324094 301250 318848 TRUE FALSE 267634.7992 283894.9108 270803.2425 262456.0164 338701.5663 272654.2051 274647.5079 274870.953 368293.3194 0.726689259 0.770839154 0.735292302 0.712627687 0.91965167 0.740318086 0.745730355 0.746337059 1 18.4904957 -2.113355626 2.308021005 1.436319673 0.761131313 0.623750984 0.058040894 6926996.396 2071178.91 15826908.45 0.013562053 0.007702725 2.113355626 -0.67518836 T(ph)AS(ph)PPPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;T(1)AS(1)PPPPPK 124.67 0.0027755 2284490000 6281740 4974210 5469500 6226350 4113840 5777580 6647470 5339790 4503340 TRUE FALSE 5984814.599 5481087.654 5720281.985 5600465.469 4831292.394 5577500.956 5633276.362 4872209.68 5201694.967 1.150550856 1.053711855 1.099695776 1.076661647 0.928791946 1.072246833 1.082969378 0.936658091 1 22.31055037 8 0.267757359 1.004884135 1.999536326 0.395072712 0.054789014 56.11516649 0.783390667 0.062728282 25.72446169 100000000 -8 0.994652191 T(ph)ASFGNILDVPEIVISGNGQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 119.06 3.08E-05 0 17438 16769 16070 19170 16800 16511 21453 16378 17578 TRUE FALSE 16613.7403 18477.78016 16806.8254 17242.99518 19729.91468 15939.21993 18179.95084 14943.85549 20303.90646 0.81825339 0.910060347 0.827763141 0.849245204 0.971729983 0.785032179 0.895391775 0.736008882 1 14.30946971 4.743768025 5.892542693 0.867555358 0.816762632 0.040512667 0.079588447 0.490961214 70.17070006 0.016358932 0.100003843 55432.95436 -4.743768025 -0.050792726 T(ph)ASGSSVTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 T(0.628)AS(0.372)GSSVTSLDGTR;T(0.983)AS(0.016)GS(0.001)SVTSLDGTR 162.32 4.98E-05 257920000 295770 224000 271950 324480 240630 277600 310230 292790 299110 TRUE FALSE 281789.5383 246825.8547 284419.1765 291862.6539 282595.7958 267986.6424 262898.7157 267151.7554 345494.4512 0.815612341 0.714413369 0.823223573 0.844767993 0.817945975 0.775661205 0.760934698 0.773244706 1 18.39830301 -1.225173817 4.835719205 1.000038295 0.786212291 0.752601951 0.037629068 1.61E-05 2.57E-06 0.037655049 0.008873792 0.059542379 1.225173817 -0.213826004 T(ph)CFSPNRVIGLSSDLQQVGGASAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCFSPNRVIGLSSDLQQVGGASAR 24 1 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 1 T(0.534)CFS(0.466)PNRVIGLSSDLQQVGGASAR 89.181 0.016737 109780000 26002 20761 28941 23612 26579 24895 32642 31382 28919 TRUE FALSE 24772.93699 22876.5695 30267.97348 21238.4769 31214.36918 24032.87991 27661.86339 28634.02571 33403.61082 0.741624524 0.684853192 0.906128791 0.635813805 0.934460929 0.719469522 0.828109977 0.857213487 1 15.02771644 -5 0.105832178 1.750286241 0.634649639 0.402673447 0.090067588 150.9482035 1.072708098 24.41258365 1.094796419 1.00E-05 5 -1.115636601 T(ph)CNSPQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.507)CNS(0.375)PQNS(0.078)T(0.017)DS(0.022)VSDIVPDSPFPGALGSDTR 113.65 0.00058635 68316000 45215 41741 50305 48289 43298 48038 55238 45294 51096 TRUE FALSE 43077.77656 45994.45536 52611.53401 43434.89798 50849.15749 46374.43201 46810.42858 41327.81724 59019.70672 0.729888015 0.779306742 0.891423169 0.735938899 0.861562355 0.785744874 0.793132179 0.700237591 1 15.84890913 -1.52312994 3.017130479 1.007790553 0.785549164 0.579379824 0.057659177 9522262.361 11101199.53 610797.2766 0.013642976 0.029982653 1.52312994 -0.222241389 T(ph)ES(ph)KIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;T(1)ES(1)KIRR;T(1)ES(1)KIRR 69.176 0.066713 2940600000 3540060 2684120 2978230 3194820 3132930 3100700 4017320 3575420 3353200 TRUE FALSE 3372728.38 2957634.88 3114784.791 2873670.624 3679312 2993321.982 3404404.051 3262337.27 3873197.13 0.870786657 0.763615892 0.804189585 0.741937611 0.949941838 0.772829753 0.878964828 0.842285368 1 21.8850935 -0.109608781 0.403472995 1.032529341 0.806656587 0.459496184 0.060496628 4.2976646 0.866524113 0.273143071 0.037113334 0.776946686 0.109608781 -0.225872754 T(ph)FCGTPDYIAPEIIAYQPYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFCGTPDYIAPEIIAYQPYGK 21 0 P05771;P05771-2;P05129-2;P05129;P17252 P05771;P17252 PRKCB;PRKCG;PRKCA Protein kinase C beta type;Protein kinase C gamma type;Protein kinase C alpha type 1 T(0.333)FCGT(0.333)PDY(0.333)IAPEIIAYQPYGK;T(0.715)FCGT(0.284)PDY(0.001)IAPEIIAYQPYGK 153.75 1.48E-07 112193000 234908 132517 256735 294954 241786 322302 330338 250882 224379 TRUE FALSE 223804.3644 146020.633 268506.5537 265304.6635 283953.4018 311140.6009 279938.871 228913.4421 259174.5494 0.863527553 0.563406528 1.036006639 1.023652454 1.095606812 1.200505998 1.080117132 0.883240436 1 17.98356453 3.669052619 7.5259652 1.061720551 0.714076798 0.621608263 0.107198538 0.149240732 14.41740507 0.02776764 0.043202015 4667.159243 -3.669052619 -0.347643752 T(ph)FSLDAVPPDHSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFSLDAVPPDHSPR 14 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 T(0.5)FS(0.5)LDAVPPDHSPR;T(0.576)FS(0.424)LDAVPPDHSPR;T(0.57)FS(0.43)LDAVPPDHSPR;T(0.5)FS(0.5)LDAVPPDHSPR;T(0.555)FS(0.445)LDAVPPDHSPR;T(0.5)FS(0.5)LDAVPPDHSPR 158.64 1.85E-05 2716390000 855713 764442 795184 913844 730817 869522 998402 954738 809758 TRUE FALSE 815265.1423 842339.5089 831643.9729 821982.6649 858271.2534 839410.2351 846077.438 871136.0793 935331.135 0.871632636 0.900578926 0.8891439 0.878814608 0.917612192 0.897447122 0.904575296 0.931366493 1 19.83511769 -2.388325192 0.207942583 1.151640315 0.874476511 0.905577372 0.011112156 10.84258391 0.286336499 0.778590447 0.02514413 0.004089543 2.388325192 -0.277163804 T(ph)FSLTEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.896)FS(0.103)LTEVR 167.12 0.0035154 101950000 161830 155280 155660 190640 164640 175720 216310 187300 189370 TRUE FALSE 154180.6166 171103.2085 162797.165 171476.505 193353.1639 169634.7723 183307.9367 170899.0191 218736.5324 0.704869072 0.782234255 0.744261433 0.783940858 0.883954599 0.775520991 0.838030733 0.78130076 1 17.73883467 -5 0.110444393 1.681032141 0.663184328 0.743834159 0.041732882 78.65062406 0.576922309 12.15361826 0.478763571 1.00E-05 5 -1.017847813 T(ph)GSPGDAPERPPLCDFSEGLSAPMDFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TGSPGDAPERPPLCDFSEGLSAPMDFYR 28 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 T(0.5)GS(0.5)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.5)GS(0.5)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.5)GS(0.5)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.53)GS(0.47)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.5)GS(0.5)PGDAPERPPLCDFSEGLSAPMDFYR 113.37 0.00077158 223552000 80790 67454.2 74396 80103 54856.3 74550.9 84707 74876.9 63333.8 TRUE FALSE 76971.21681 74327.85967 77807.13019 72050.89425 64423.22135 71969.18364 71783.3914 68320.28169 73155.28224 1.052162119 1.016028609 1.063588682 0.98490351 0.880636632 0.983786562 0.981246866 0.933907704 1 16.15867442 3.0625008 5.928959813 0.95679775 1.038310585 0.569802154 0.034764363 0.14277529 9.738821014 0.009644009 0.011536995 1154.784112 -3.0625008 0.081512835 T(ph)GTCRISMSEVDLNVAAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGTCRISMSEVDLNVAAPK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 T(0.363)GT(0.363)CRIS(0.259)MS(0.014)EVDLNVAAPK 99.441 0.0012867 146830000 170880 91310 186130 116920 187860 167290 262550 187850 245120 TRUE FALSE 162802.8411 100614.5928 194664.2446 105166.9795 220622.7245 161496.7054 222493.1754 171400.8581 283131.9577 0.575006942 0.355362897 0.687538935 0.371441572 0.779222262 0.570393772 0.785828549 0.605374468 1 18.11111507 0.722475143 0.243737966 1.117437439 0.410667442 0.530455588 0.132364115 2.419608874 0.405142209 0.574235445 0.27659823 5.278069964 -0.722475143 -0.706769997 T(ph)HSFENVSCHLPDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THSFENVSCHLPDSR 15 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 T(0.576)HS(0.424)FENVSCHLPDSR;T(0.767)HS(0.233)FENVSCHLPDSR 157.97 6.83E-06 563210000 311920 298423 356030 461020 477870 406770 554820 282170 150554 TRUE FALSE 297176.1598 328832.643 372354.3277 414677.3937 561210.3767 392683.4529 470172.019 257461.6989 173901.1454 1.70887983 1.890917062 2.141183871 2.384558151 3.22718045 2.258084339 2.703674079 1.480506056 1 17.40790791 1.048083473 5.17880746 1.005117811 2.285003931 0.550322408 0.420078913 0.144506661 8.170992775 0.446533683 0.112851965 11.17077933 -1.048083473 1.27988612 T(ph)HSTSSSLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.374)HS(0.374)T(0.079)S(0.171)S(0.002)SLGSGESPFSR 176.39 4.09E-09 3510900000 182330 156770 206540 210590 203120 206400 245370 162560 110000 TRUE FALSE 173711.6222 172745.0412 216010.0633 189421.0931 238544.0637 199252.3162 207934.3 148325.3846 127058.2382 1.367181103 1.359573717 1.700087034 1.490821027 1.87743878 1.56819675 1.636527493 1.16738109 1 16.95513039 1.103836405 4.311159811 1.007517266 1.55212526 0.640177854 0.153787836 0.141719784 4.312060384 0.158450266 0.040601404 12.70095581 -1.103836405 0.544607994 T(ph)IHTFPCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIHTFPCLK 9 0 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 T(1)IHTFPCLK 142.89 0.00037985 149700000 710600 500800 555180 700310 886330 576050 699840 643540 653390 TRUE FALSE 677011.3463 551832.0894 580635.5521 629913.5083 1040905.671 556101.2441 593066.5546 587188.226 754714.3841 0.897043121 0.731180034 0.769344754 0.83463827 1.37920476 0.736836684 0.785815889 0.778027077 1 19.52557125 5.113110457 16.44628237 0.860633048 3.538479792 0 0.194894281 15992473.48 11741628.16 0.045215372 1591604307 129750.9233 -5.113110457 2.677846745 T(ph)ISEPDEQRSELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.551)IS(0.449)EPDEQRSELPR 64.565 0.097974 168640000 217450 193240 200100 220260 146370 216550 209470 224300 142980 TRUE FALSE 207171.5694 212931.3757 209274.7829 198119.0463 171896.8817 209050.8192 177511.5043 204659.1029 165152.6082 1.254425054 1.289300714 1.267160024 1.199611974 1.040836615 1.265803922 1.074833188 1.239212055 1 17.33344023 4.812783487 0.027016507 1.63E-07 2.558356472 0.464411355 0.076813383 650.4094142 2.676830202 102.9804539 154.1910964 64980.56559 -4.812783487 2.55835631 T(ph)KFASDDEHDEHDENGATGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.5)KFAS(0.5)DDEHDEHDENGATGPVK;T(0.627)KFAS(0.373)DDEHDEHDENGATGPVK;T(0.5)KFAS(0.5)DDEHDEHDENGATGPVK;T(0.606)KFAS(0.394)DDEHDEHDENGATGPVK 208.26 1.04E-22 1908750000 1721530 1710210 1597040 2006370 863630 1851760 1737270 1754910 262032 TRUE FALSE 1640156.689 1884482.343 1670265.864 1804685.876 1014246.799 1787633.087 1472217.554 1601240.777 302666.5843 5.419021371 6.226264944 5.518501052 5.962620155 3.35103659 5.906278326 4.864156239 5.290444536 1 18.20736988 2.774834116 24.92674978 4.514197184 5.800809206 0.246066979 1.366182921 904.037949 621243.2516 0.368700011 0.391054188 595.4346672 -2.774834116 1.286612021 T(ph)KFASDDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.5)KFAS(0.5)DDEHDEHDENGATGPVKR 63.803 0.035518 2276400000 82617 50602 65231 82192 45198 74031 91208 60504 69809 TRUE FALSE 78711.85814 55758.40133 68221.90587 73929.90401 53080.51689 71467.28791 77292.54445 55205.94901 80634.62319 0.976154598 0.691494536 0.84606219 0.916850617 0.658284429 0.886310186 0.958552808 0.684643232 1 16.29911182 -1.183789522 4.605944021 1.000028862 0.834135976 0.180127664 0.11497505 3.17E-05 5.62E-06 0.103578295 0.024409393 0.065495352 1.183789522 -0.165892887 T(ph)KSDES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.5)KS(0.5)DES(1)GEEKNGDEDCQR;T(0.5)KS(0.5)DES(1)GEEKNGDEDCQR;T(0.5)KS(0.5)DES(1)GEEKNGDEDCQR 181.81 1.35E-13 697950000 809469 788587 782722 901349 260332 960475 904164 1154130 233566 TRUE FALSE 771207.0046 868944.9118 818610.5779 810743.6861 305733.8184 927213.5099 766217.1757 1053068.259 269786.2224 2.858585578 3.220864669 3.034293489 3.005133764 1.133244743 3.436845298 2.840090087 3.903343356 1 18.04145715 2.961520932 24.99486939 2.616722313 3.047528236 0.075926484 0.898041407 1777.999168 1154935.972 0.253444034 0.268868461 915.2103688 -2.961520932 0.430805922 T(ph)KSPKPAESPQSATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKSPKPAESPQSATK 15 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 T(0.5)KS(0.5)PKPAESPQSATK;T(0.5)KS(0.5)PKPAESPQSATK 211.43 6.59E-08 158783000 226550 183407 194888 237090 106958 240170 228320 237470 95068 TRUE FALSE 215841.4305 202096.3818 203823.8076 213257.2628 125611.4413 231852.8527 193485.5906 216675.8679 109810.6599 1.96557812 1.84040768 1.856138628 1.94204518 1.143891144 2.111387482 1.761992786 1.973176995 1 16.74465859 -1.31588329 3.646440622 0.997356191 1.826399208 0.498937017 0.259605023 5583469.656 2724963.442 112689.0321 0.054811591 0.048318863 1.31588329 0.829043016 T(ph)KSPTDDEVTPSAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.529)KS(0.293)PT(0.178)DDEVTPSAVVR 125.73 0.00012203 352010000 301150 297900 232600 303150 186260 298490 356890 289700 242120 TRUE FALSE 286915.2363 328256.3487 243264.9401 272676.7861 218743.685 288153.2165 302439.8758 264332.3322 279666.733 1.025918361 1.173741135 0.869838673 0.975006155 0.782158402 1.030344987 1.081429573 0.945169021 1 18.09334913 3.74371397 24.98559873 0.963772939 1.099829745 0.306285844 0.089933863 525.8368279 2549468.719 0.023979204 0.041635798 5542.605524 -3.74371397 0.136056806 T(ph)KSVSSMSEFESLLDCSPYLAGGDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKSVSSMSEFESLLDCSPYLAGGDAR 26 1 O94964-2;H0YDM2;O94964;O94964-3;X6R3R3;O94964-4 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 T(0.334)KS(0.334)VS(0.111)S(0.111)MS(0.111)EFESLLDCSPYLAGGDAR;T(0.352)KS(0.352)VS(0.099)S(0.099)MS(0.099)EFESLLDCSPYLAGGDAR 217.17 6.11E-34 289710000 185457 173319 189704 201788 133197 189415 231640 210090 171370 TRUE FALSE 176690.8152 190980.4031 198402.116 181503.8869 156426.5146 182855.5111 196299.0636 191693.4058 197945.1844 0.892624975 0.964814596 1.002308375 0.916940149 0.790251681 0.923768424 0.991683957 0.968416617 1 17.59474144 1.764708204 6.178566638 0.984607211 0.917556889 0.275571001 0.054596275 0.266458765 25.81248109 0.027704879 0.015010283 58.17122429 -1.764708204 -0.067050322 T(ph)KTLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKTLLR 6 1 E7ENT7;A0A0A0MTJ2;Q9BQ16-9;Q9BQ16-7;Q9BQ16-2;Q9BQ16-5;Q9BQ16-6;Q9BQ16-4;Q9BQ16-1;Q9BQ16 E7ENT7 SPOCK3 Testican-3 1 T(0.963)KT(0.037)LLR;T(0.964)KT(0.036)LLR 99.511 0.06259 1143470000 1003140 827420 726840 761740 3383300 659130 987190 725630 2580500 TRUE FALSE 955723.5602 911735.0387 760166.3329 685168.448 3973346.449 636304.1628 836576.0345 662089.9904 2980670.761 0.320640432 0.305882505 0.255031969 0.229870557 1.333037684 0.213476836 0.280667038 0.222127851 1 21.5072056 T(ph)LQRLSSGFDDIDLPSAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 T(0.42)LQRLS(0.214)S(0.366)GFDDIDLPSAVK 102.07 0.0006458 52897000 83695 59132 82720 86421 74170 86865 108830 94440 80772 TRUE FALSE 79738.90322 65157.61803 86512.79382 77733.79689 87105.22452 83856.84327 92225.9847 86170.33294 93297.70923 0.854671608 0.6983839 0.92727672 0.833180123 0.933626616 0.898809241 0.988512853 0.923606095 1 16.50955404 2.915237244 0.777674968 0.969442133 0.780870296 0.52095122 0.059825499 0.43621518 0.584918845 0.034694899 0.040613467 822.6919437 -2.915237244 -0.188571837 T(ph)LTPPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.857)LT(0.143)PPLRR;T(0.716)LT(0.284)PPLRR;T(0.75)LT(0.25)PPLRR;T(0.592)LT(0.408)PPLRR 79.986 0.015599 1530610000 1205720 994480 1051340 1178770 908140 1074350 1257130 1173830 957660 TRUE FALSE 1148728.005 1095818.643 1099544.979 1060277.8 1066519.328 1037144.99 1065331.73 1071043.222 1106169.022 1.038474214 0.99064304 0.994011726 0.958513373 0.964155846 0.937600827 0.963082231 0.96824554 1 20.07714041 4.231184758 0.862763877 0.961361879 1.05069843 0.63691204 0.01687731 0.632381661 0.5965371 0.005609656 0.046358207 17028.82796 -4.231184758 0.089336551 T(ph)MIISPERLDPFADGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.618)MIIS(0.382)PERLDPFADGGK;T(0.895)MIIS(0.105)PERLDPFADGGK 86.539 0.013164 111959000 339620 368920 281053 419610 200864 363940 329320 339310 215959 TRUE FALSE 323566.8357 406513.3674 293939.558 377430.0056 235894.618 351336.6665 279076.1856 309598.2176 249448.8188 1.297127151 1.629646392 1.178356184 1.513055895 0.9456634 1.408451915 1.118771326 1.241129219 1 17.92838431 2.319193731 0.324529248 1.01061911 1.508735938 0.279498374 0.182811615 1.874721602 0.491439569 0.220472399 0.333690605 208.5420946 -2.319193731 0.498116827 T(ph)NHRLSLPMPASGTSLSAAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.58)NHRLS(0.42)LPMPASGTSLSAAIHR;T(0.5)NHRLS(0.5)LPMPASGTSLSAAIHR;T(0.785)NHRLS(0.215)LPMPASGTSLSAAIHR;T(0.945)NHRLS(0.055)LPMPASGTSLSAAIHR 251.07 8.70E-32 1385460000 615800 651780 642840 766420 589070 665480 712440 611290 288642 TRUE FALSE 586692.3544 718197.123 672314.8499 689378.0055 691803.6215 642434.2607 603744.1931 557762.2069 333403.1272 1.759708613 2.154140332 2.016522327 2.067701078 2.074976403 1.926899325 1.81085342 1.672936339 1 18.34690811 0.753189203 0.929961279 0.999929742 2.013020538 0.900362983 0.104405393 0.261221215 0.422923775 0.098849134 0.032884775 5.664860287 -0.753189203 1.013090797 T(ph)NSSDSERSPDLGHSTQIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 T(0.327)NS(0.327)S(0.327)DS(0.017)ERS(0.002)PDLGHSTQIPR;T(0.316)NS(0.316)S(0.316)DS(0.03)ERS(0.023)PDLGHSTQIPR 109.39 0.00029052 143370000 120370 89534 106202 111129 119373 104698 153929 113735 142500 TRUE FALSE 114680.3487 98657.61639 111071.4667 99958.10179 140191.6134 101072.282 130444.3039 103775.7605 164598.1722 0.696729175 0.599384641 0.674803768 0.607285612 0.851720353 0.614054705 0.792501534 0.630479422 1 17.32858879 -5 0.211040948 2.534183947 0.637882461 0.58756271 0.082926725 92.37452246 0.920919294 59.95706367 0.152467047 1.00E-05 5 -1.896301486 T(ph)PDRER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPDRER 6 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 T(1)PDRER;T(1)PDRER 97.431 0.066413 387750000 418119 468466 410315 471340 357502 385569 415604 521120 496890 TRUE FALSE 398355.3435 516203.218 429128.3486 423960.0077 419850.2356 372216.6489 352195.9767 475487.9702 573945.1634 0.694065163 0.899394665 0.747681793 0.738676854 0.731516288 0.648523017 0.613640465 0.8284554 1 19.13055338 0.98981272 24.18320108 1.000000006 0.731177195 0.58107412 0.075018352 250.3865747 594385.5294 0.082120986 0.020530247 9.768158991 -0.98981272 -0.268822811 T(ph)PDSTFSETFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(0.968)PDS(0.032)TFSETFK;T(0.682)PDS(0.066)T(0.243)FS(0.008)ETFK;T(0.793)PDS(0.169)T(0.036)FS(0.002)ETFK;T(1)PDSTFSETFK;T(0.94)PDS(0.06)TFSETFK 244.45 7.89E-15 1841100000 3068800 3165620 2751530 3572430 2296290 3001570 3270960 3093360 2545730 TRUE FALSE 2923743.906 3488200.277 2877690.372 3213322.549 2696762.249 2897624.878 2771914.977 2822488.999 2940508.807 0.994298639 1.186257381 0.978636883 1.092777734 0.917107353 0.985416154 0.942665082 0.959864155 1 21.48763438 2.744681452 24.97165282 0.958330287 1.071217682 0.411581036 0.060188414 419.4787324 1711379.997 0.017384445 0.018026546 555.4966594 -2.744681452 0.112887395 T(ph)PELPEPSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;T(1)PELPEPSVK 163.9 7.07E-05 570156000 1557360 1215960 1429500 1463620 1218188 1455960 1712080 1597620 1524670 TRUE FALSE 1483746.679 1339867.706 1495043.989 1316494.137 1430639.602 1405539.74 1450870.751 1457723.923 1761108.037 0.842507472 0.76080949 0.848922359 0.747537408 0.812351981 0.798099668 0.82383972 0.827731118 1 20.74805198 0.167578797 0.837313866 1.002984008 0.800041047 0.791605282 0.031320879 1.473673537 1.162718086 0.03785717 0.009012724 1.470885263 -0.167578797 -0.202942961 T(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.987)PES(0.013)FLGPNAALVDLDSLVSRPGPTPPGAK 118.99 8.36E-05 117240000 51448 45652 49471 56742 41612 55036 54034 58695 46554 TRUE FALSE 49016.155 50303.9907 51739.29428 51038.18636 48869.11963 53130.08952 45790.1209 53555.35464 53773.35656 0.911532367 0.935481694 0.962173418 0.949135215 0.908798014 0.988037439 0.851539198 0.995945912 1 15.71460391 1.048771274 24.99994472 1.00000149 0.928722246 0.38292248 0.036131461 91.37490116 46838.03446 0.032019603 0.008004901 11.18848474 -1.048771274 -0.071279244 T(ph)PPPPSPLPFPTQAILPPAPSSYFSHPTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPPPPSPLPFPTQAILPPAPSSYFSHPTIR 30 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 T(0.881)PPPPS(0.118)PLPFPTQAILPPAPSSYFSHPTIR 66.825 0.028011 58380000 12392 15307 12690 13969 14345 12981 13127 12538 13381 TRUE FALSE 11806.25472 16866.8007 13271.84905 12564.80958 16846.76346 12531.46472 11124.23506 11440.10625 15456.05714 0.763859412 1.091274479 0.858682711 0.812937573 1.089978078 0.810780175 0.719733044 0.74016977 1 13.91588471 2.02468846 24.98198499 0.782934197 0.926004931 0.120888435 0.129421636 317.3512185 321122.8497 0.04480784 0.033091582 105.8494145 -2.02468846 0.143070734 T(ph)PPRDLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.96)PPRDLPT(0.043)IPGVT(0.453)S(0.411)PS(0.107)S(0.026)DEPPMEASQSHLR;T(1)PPRDLPT(0.166)IPGVT(0.431)S(0.389)PS(0.012)S(0.002)DEPPMEASQSHLR;T(0.582)PPRDLPT(0.426)IPGVT(0.472)S(0.426)PS(0.077)S(0.016)DEPPMEASQSHLR 102.49 0.00047521 168542000 76756 70412 73761.8 85421 70885.3 74531.3 86754 79857 74780 TRUE FALSE 73127.896 77587.06285 77143.85149 76834.31879 83247.67388 71950.26239 73518.08395 72864.29773 86376.50048 0.846617953 0.898242721 0.893111565 0.889528036 0.963776877 0.832984226 0.851135246 0.843566217 1 16.39835125 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.994)PPRDLPT(0.006)IPGVT(0.001)S(0.001)PS(0.001)S(0.001)DEPPMEAS(0.405)QS(0.397)HLRNS(0.194)PEDKR 88.033 0.00060096 260300000 48398 49998 59145 61316 46977 58985 64306 60927 41731 TRUE FALSE 46110.32246 55092.85304 61856.85675 55152.39919 55169.77393 56942.33466 54494.93864 55591.90889 48202.43035 0.95659746 1.14294762 1.283272572 1.144182955 1.144543408 1.181316673 1.130543382 1.153300954 1 15.55681827 4.465871772 2.548957667 1.157270898 0.95829035 0.426315594 0.068724059 0.251002069 2.914641372 0.01566152 0.082679404 29232.89135 -4.465871772 -0.198980548 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 28 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.99)PPRDLPT(0.01)IPGVTSPSSDEPPMEASQSHLR;T(0.971)PPRDLPT(0.029)IPGVTSPSSDEPPMEASQSHLR;T(0.987)PPRDLPT(0.013)IPGVTSPSSDEPPMEASQSHLR;T(1)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;T(0.993)PPRDLPT(0.007)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.991)PPRDLPT(0.009)IPGVTSPSSDEPPMEASQSHLR;T(0.995)PPRDLPT(0.005)IPGVTSPSSDEPPMEASQSHLR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.956)PPRDLPT(0.044)IPGVTSPSSDEPPMEASQSHLR;T(0.988)PPRDLPT(0.012)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.888)PPRDLPT(0.06)IPGVT(0.008)S(0.009)PS(0.017)S(0.017)DEPPMEASQSHLR;T(0.934)PPRDLPT(0.066)IPGVTSPSSDEPPMEASQSHLR;T(0.994)PPRDLPT(0.006)IPGVTSPSSDEPPMEASQSHLR;T(0.824)PPRDLPT(0.176)IPGVTSPSSDEPPMEASQSHLR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.776)PPRDLPT(0.224)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(1)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;T(0.893)PPRDLPT(0.101)IPGVT(0.005)S(0.001)PSSDEPPMEASQSHLR;T(0.992)PPRDLPT(0.007)IPGVTSPSSDEPPMEASQSHLR;T(0.995)PPRDLPT(0.005)IPGVTSPSSDEPPMEASQSHLR;T(0.989)PPRDLPT(0.011)IPGVTSPSSDEPPMEASQSHLR;T(0.973)PPRDLPT(0.026)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR 184.03 1.09E-17 21177800000 1436438 1290763.3 1246589.9 1514593.7 1380934 1321517 1478700 1392035 1306705 TRUE FALSE 1368540.422 1422293.548 1303747.28 1362343.864 1621768.452 1275752.535 1253097.157 1270141.036 1509342.138 0.906713189 0.942326801 0.86378512 0.902607719 1.074486965 0.845237473 0.830227372 0.841519629 1 20.52548844 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEAS(0.372)QS(0.254)HLRNS(0.374)PEDKR 125.89 1.50E-08 273780000 94719 79823 93006 107810 70498 101700 118500 109780 84354 TRUE FALSE 90241.82058 87957.05445 97270.4171 96972.73397 82792.82888 98178.1035 100420.6486 100167.0812 97435.1875 0.926172802 0.902723715 0.998308923 0.995253732 0.849722067 1.00762472 1.030640482 1.028038061 1 16.57215526 2.028256646 24.99442956 1.022006188 0.934498712 0.475679933 0.042978254 170.9926232 151250.8383 0.015735167 0.01162104 106.7226611 -2.028256646 -0.087507477 T(ph)PRT(ph)MEVT(ph)EMS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPRTMEVTEMSPSK 14 1 Q8IZF6-2;Q8IZF6-3;Q8IZF6 Q8IZF6-2 GPR112 Probable G-protein coupled receptor 112 4 T(1)PRT(1)MEVT(1)EMS(0.5)PS(0.5)K 44.425 0.064154 107390000 104310 139460 114790 148710 207450 84734 102810 101980 195060 TRUE FALSE 99379.47302 153671.1326 120053.235 133761.3883 243629.2143 81799.64033 87124.44626 93050.09057 225308.9086 0.441080975 0.682046411 0.532838385 0.59367998 1.081311946 0.363055508 0.386688866 0.412988954 1 17.78154483 -2.135900511 2.480779501 1.958206409 0.559125277 0.302743788 0.209003325 11430927.55 3656288.667 61536443.64 0.05002406 0.007313066 2.135900511 -1.399081132 T(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(1)PRT(1)PQLK;T(1)PRT(1)PQLK 116.24 0.011373 647200000 1316010 1182460 1271660 1462820 1036860 1355850 1544010 1456320 1226220 TRUE FALSE 1253804.815 1302954.018 1329966.869 1315774.554 1217688.056 1308896.575 1308442.917 1328796.9 1416375.935 0.88522036 0.919921037 0.938992845 0.928972684 0.859720944 0.924116643 0.923796349 0.938166815 1 20.43377281 0.777306258 1.11688967 0.999777962 0.909103163 0.608217657 0.022738716 0.554525863 1.266812559 0.021139365 0.006636657 5.988337345 -0.777306258 -0.090674799 T(ph)PRT(ph)PRTPQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.995)PRT(0.865)PRT(0.14)PQLK 89.466 0.019592 889310000 1437500 1001700 1453100 1416800 1217000 1518500 1869000 1648500 1555100 TRUE FALSE 1369552.224 1103774.369 1519726.072 1274380.572 1429244.415 1465913.964 1583849.723 1504148.601 1796256.966 0.762447829 0.614485783 0.846051596 0.709464512 0.795679261 0.816093684 0.88175008 0.837379411 1 20.77656232 1.598584004 0.353658433 1.010960684 0.678203978 0.653743898 0.060154585 0.651592209 0.258262227 0.079451856 0.069450906 39.68112751 -1.598584004 -0.332756706 T(ph)PRTPQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.843)PRT(0.157)PQLK 93.096 0.018287 1079700000 784590 542730 742900 740930 681680 814690 1008700 894110 775990 TRUE FALSE 747503.9856 598034.804 776962.6998 666450.3087 800564.7762 786477.081 854804.289 815816.9884 896326.566 0.833963885 0.667206381 0.866829936 0.743535151 0.893161942 0.877444796 0.953675057 0.910178298 1 19.77366493 2.349903232 0.809005465 0.969371975 0.757317896 0.614901482 0.059863124 0.368626034 0.471046599 0.041951436 0.027369067 223.8222369 -2.349903232 -0.212054079 T(ph)PS(ph)PESHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSPESHR 8 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(0.996)PS(0.959)PES(0.045)HR;T(1)PS(1)PESHR 100.88 0.010277 90915000 93382 95201 70289 91876 85539 84769 80209 68530 50226 TRUE FALSE 88968.01793 104902.0901 73511.82018 82640.44993 100456.9745 81833.42827 67971.64391 62529.1499 58014.79156 1.533540249 1.808195588 1.267122025 1.424472065 1.731575204 1.410561446 1.171626099 1.07781392 1 15.82413316 1.73557083 2.135582688 1.047290835 1.568517732 0.670950537 0.151202769 0.173310271 1.623979918 0.104120411 0.043896659 54.39648406 -1.73557083 0.521226897 T(ph)PS(ph)PPPPIPEDIALGK ddPTM_SK-BR-3_Trastuzumab_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 133.66 0.0001724 76745000 163597 208299 141277 209087 101482 165095 150773 158005 94799 TRUE FALSE 155864.094 229524.9049 147754.6902 188069.1775 119180.4287 159377.7188 127769.8097 144169.2446 109499.9448 1.423417102 2.096118911 1.349358582 1.717527602 1.08840629 1.455505015 1.166848166 1.31661477 1 16.74057062 2.940637242 1.434166698 1.222522855 1.726573411 0.411098288 0.244014937 0.345948494 1.460066066 0.086523357 0.098083766 872.2424972 -2.940637242 0.504050556 T(ph)PS(ph)PSYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSPSYQR 8 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 T(1)PS(0.953)PS(0.047)YQR;T(0.999)PS(0.5)PS(0.5)Y(0.001)QR 85.533 0.046274 310690000 824460 834120 781190 964720 852200 793330 870030 729340 801940 TRUE FALSE 785489.4097 919117.7763 817008.3342 867744.5128 1000823.41 765856.7832 737290.9443 665475.1231 926300.7595 0.847985281 0.992245517 0.882011945 0.936784844 1.080451894 0.826790624 0.795952002 0.718422301 1 19.82112117 2.038838474 24.99879255 0.814432225 0.942382791 0.252826151 0.093173111 177.1389974 114016.6567 0.031841896 0.023516764 109.354957 -2.038838474 0.127950566 T(ph)PSEADRWLEEVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPSEADRWLEEVSK 14 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 T(0.991)PS(0.009)EADRWLEEVSK;T(0.987)PS(0.013)EADRWLEEVSK;T(0.995)PS(0.005)EADRWLEEVSK;T(0.997)PS(0.003)EADRWLEEVSK 173.98 4.22E-06 286879000 381241 288816 334291 364857 288288 377647 441180 413637 324342 TRUE FALSE 363220.4935 318246.6788 349618.573 328180.8812 338565.3359 364568.9897 373869.8882 377416.7515 374639.3009 0.96952053 0.84947489 0.93321382 0.875991602 0.903710142 0.973119982 0.997946257 1.007413666 1 18.51514273 2.12708018 3.126005205 0.99937834 0.903787595 0.663324952 0.031688656 0.146860472 2.846580076 0.013000316 0.008792612 133.9924043 -2.12708018 -0.095590745 T(ph)PSFLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSFLKK 7 1 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 T(0.816)PS(0.184)FLKK;T(0.85)PS(0.15)FLKK 65.157 0.041809 1523530000 4475500 3755900 3649600 4516000 2640400 4504000 4810500 4856000 2742400 TRUE FALSE 4263951.985 4138630.48 3816937.77 4062043.1 3100884.924 4348025.351 4076569.874 4430782.897 3167677.386 1.346081518 1.306518934 1.204964176 1.282341162 0.978914374 1.372622531 1.286927101 1.398748154 1 21.59499398 3.906177978 4.082920667 1.235190932 1.332831472 0.088132803 0.138535571 0.56779907 16.88733765 0.033658894 0.064912795 8057.085614 -3.906177978 0.09764054 T(ph)PSPAAEDAREPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.791)PS(0.209)PAAEDAREPEAK 143.83 7.02E-06 482270000 480030 469490 442960 634640 340220 539480 503640 598800 355300 TRUE FALSE 457339.9332 517331.5648 463270.1541 570844.7815 399554.2603 520797.6723 426800.468 546365.8976 410398.1094 1.114381189 1.260560302 1.128831112 1.390953731 0.973577244 1.269006022 1.039966945 1.331307053 1 18.64666456 2.729091075 24.98816599 1.130277694 1.212414082 0.120013157 0.133388629 1641.737681 4332199.495 0.037637117 0.035942107 535.9090307 -2.729091075 0.082136388 T(ph)PSPSQPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.572)PS(0.428)PSQPKK 108.35 0.0015388 401960000 855530 711340 841260 900290 543800 1006200 1082500 1010000 741910 TRUE FALSE 815090.7924 783826.3547 879832.6031 809791.1388 638638.5478 971355.0417 917344.7435 921559.0457 856961.6136 0.951140377 0.914657486 1.026688464 0.94495614 0.745235886 1.133487225 1.070461884 1.07537961 1 19.70887106 2.198385139 24.99999944 1.077206087 0.925723674 0.492818143 0.076800931 126.3247005 78607.35006 0.027131657 0.020038325 157.9010941 -2.198385139 -0.151482413 T(ph)PTAPAVNLAGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPTAPAVNLAGAR 13 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.998)PT(0.002)APAVNLAGAR 94.673 0.056419 73743000 12302 11894 12300 15196 14849 12447 11372 14234 16002 TRUE FALSE 11720.50884 13106.01212 12863.96717 13668.46921 17438.6609 12015.95727 9636.992539 12987.5955 18483.50843 0.634106284 0.709065174 0.695969989 0.739495386 0.943471363 0.650090718 0.521383295 0.702658564 1 14.17395101 4.503769268 1.530650813 0.719825173 0.621306058 0.033182514 0.139027995 2.977222962 9.174628484 0.038063792 0.388782224 31898.42708 -4.503769268 -0.098519115 T(ph)PTPEPAEVETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.746)PT(0.254)PEPAEVETR 95.417 0.067725 548250000 101300 89599 92625 116860 97959 104560 99129 96865 102840 TRUE FALSE 96511.74976 98729.23997 96871.94787 105113.0108 115043.0186 100939.061 84005.05042 88382.98709 118787.902 0.812471204 0.831138848 0.815503484 0.884879765 0.968474202 0.849741929 0.707185235 0.744040307 1 16.85802839 -0.609662962 7.248600297 1.000000045 0.82416937 0.369231744 0.071125917 0 0 0.074121563 0.01747062 0.245661465 0.609662962 -0.175830675 T(ph)PVDRDT(ph)EDGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPVDRDTEDGLK 12 1 Q9NVR0 Q9NVR0 KLHL11 Kelch-like protein 11 2 T(1)PVDRDT(1)EDGLK 87.258 0.03441 219210000 279340 254470 282400 308330 441060 258110 398660 307880 574620 TRUE FALSE 266136.1518 280400.7823 295348.3193 277336.0826 517980.7244 249171.586 337837.0951 280920.395 663729.1348 0.400971025 0.42246267 0.444983207 0.417845275 0.780409804 0.375411554 0.508998441 0.423245538 1 19.34023508 -5 0.320254975 6.024872072 0.445416606 0.669700611 0.116111987 185.4335309 1.641098828 631.788191 0.095870448 1.00E-05 5 -5.579455467 T(ph)RHGSASQVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TRHGSASQVQK 11 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 T(0.685)RHGS(0.314)AS(0.001)QVQK;T(0.681)RHGS(0.312)AS(0.007)QVQK;T(0.505)RHGS(0.495)ASQVQK 102.73 0.0045746 133504000 165655 129299 173377 166111 156570 175481 228900 200984 189704 TRUE FALSE 157824.8164 142474.7151 181326.5069 149413.2067 183875.7584 169404.049 193977.101 183384.7755 219122.3274 0.720258945 0.650206288 0.827512691 0.681871211 0.839146611 0.773102636 0.885245713 0.836905931 1 17.74137697 1.587672476 0.282848365 1.030619217 0.648518358 0.712627173 0.054893317 0.738607253 0.226262233 0.103040051 0.100357052 38.69657039 -1.587672476 -0.382100859 T(ph)RKSPSSDSWTCADTSTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRKSPSSDSWTCADTSTER 19 2 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 T(0.489)RKS(0.489)PS(0.016)S(0.005)DSWTCADTSTER 186.11 1.01E-12 278120000 125030 89206 122680 117980 86975 112800 144250 128940 105610 TRUE FALSE 119120.0797 98296.19282 128304.9993 106120.4263 102143.4125 108893.7077 122242.0132 117649.33 121987.4594 0.976494471 0.805789327 1.051788438 0.869928981 0.837327156 0.892663133 1.002086721 0.964437907 1 16.89637332 1.744033378 8.160234655 0.986429721 0.901186775 0.238994761 0.069541049 0.163618464 38.89665947 0.031645385 0.016950116 55.46683406 -1.744033378 -0.085242945 T(ph)RKSPSSDSWTCADTSTERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRKSPSSDSWTCADTSTERR 20 3 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 T(0.793)RKS(0.188)PS(0.013)S(0.005)DSWTCADTSTERR 55.881 0.098001 206350000 53930 20520 54954 37080 41522 43865 79664 52856 53428 TRUE FALSE 51380.83578 22611.01133 57473.69526 33352.64795 48763.42365 42345.94405 67509.79367 48227.64843 61713.34137 0.832572579 0.366387734 0.931300979 0.540444695 0.790160159 0.68617163 1.093925433 0.781478484 1 15.91329479 1.758082523 25 0.961023177 0.671820131 0.343011952 0.172996128 8.384787812 10747.7014 0.073366663 0.040686306 57.29048812 -1.758082523 -0.289203046 T(ph)RLSTASEETVQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRLSTASEETVQNR 14 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 T(0.626)RLS(0.36)T(0.015)ASEETVQNR 114.56 0.0013289 0 437900 352640 327930 372260 227040 437720 440350 406390 212840 TRUE FALSE 417201.3348 388574.4169 342965.9149 334839.7176 266635.7041 422561.6466 373166.5199 370804.3372 245846.1402 1.697001769 1.580559356 1.39504291 1.361988914 1.084563312 1.718805292 1.51788643 1.508278051 1 17.90739618 3.915864655 2.651153121 1.406368539 1.666121186 0.215801465 0.208994812 0.430586047 5.934014828 0.053906768 0.118107002 8238.813182 -3.915864655 0.259752647 T(ph)RPASQPTPFALHHAASCEVDPSSGDSISLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.507)RPAS(0.365)QPT(0.128)PFALHHAASCEVDPSSGDSISLAR 159.32 1.18E-13 106780000 56638 38944 57304 57372 53737 53156 77350 64514 10350 TRUE FALSE 53960.83399 42912.43788 59931.44508 51604.85756 63108.71579 51315.19439 65548.83687 58864.81215 11955.02514 4.513652908 3.589489556 5.013075622 4.31658294 5.278844256 4.292353533 5.482952658 4.923855154 1 13.54532954 3.735297787 24.9411352 4.602474276 4.051571257 0 1.294748648 982.4834591 7510125.133 0.295301314 0.478977819 5436.229545 -3.735297787 -0.550903019 T(ph)RS(ph)RS(ph)PESQVIGENTKQP ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRSRSPESQVIGENTKQP 18 3 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 3 T(1)RS(0.992)RS(0.994)PES(0.014)QVIGENTKQP 97.346 0.0011253 88314000 193190 125970 188600 183050 127930 165390 231600 119720 160320 TRUE FALSE 184058.2916 138806.4862 197247.4966 164649.4662 150240.9515 159662.5028 196265.1664 109236.6821 185181.6068 0.993933981 0.74956951 1.065157064 0.889124298 0.811316815 0.862194176 1.059852378 0.589889482 1 17.49858128 3.018414731 24.98039394 0.880656033 0.913552419 0.0340751 0.146205269 1735.783721 2354649.807 0.039872383 0.047649922 1043.313269 -3.018414731 0.032896387 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.497)RS(0.497)PDVIS(0.002)S(0.002)AS(0.001)T(0.001)ALSQDIPEIASEALSR;T(0.498)RS(0.498)PDVIS(0.001)S(0.001)AS(0.001)T(0.001)ALSQDIPEIASEALSR;T(0.568)RS(0.431)PDVISSASTALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.577)RS(0.422)PDVISSASTALSQDIPEIASEALSR;T(0.499)RS(0.499)PDVISSASTALSQDIPEIASEALSR;T(0.438)RS(0.438)PDVIS(0.031)S(0.031)AS(0.031)T(0.031)ALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.496)RS(0.496)PDVIS(0.002)S(0.002)AS(0.002)T(0.002)ALSQDIPEIASEALSR;T(0.587)RS(0.413)PDVISSASTALSQDIPEIASEALSR 176.44 3.01E-13 3621926000 450573.6 393786.5 417170 462671.3 413339.7 431368 506917 455870 476284 TRUE FALSE 429275.8789 433913.792 436297.6571 416162.7019 485426.0128 416429.618 429577.5015 415951.6061 550143.6902 0.780297741 0.788728108 0.793061276 0.756461829 0.882362229 0.756947004 0.780846003 0.756078118 1 19.06944896 -1.040645887 4.555165084 1.000007607 0.786959655 0.770806924 0.036527482 3.03E-06 6.38E-07 0.031767289 0.007487303 0.09106555 1.040645887 -0.213047952 T(ph)RSWDSSSPVDRPEPEAASPTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRSWDSSSPVDRPEPEAASPTTR 23 2 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 T(0.499)RS(0.499)WDS(0.003)SSPVDRPEPEAASPTTR 220.96 8.81E-31 561570000 61678 46284 42699 61592 55287 54838 61932 55697 40141 TRUE FALSE 58762.60317 51000.39222 44656.79139 55400.65514 64929.0353 52938.94631 52483.13594 50819.87541 46365.86127 1.267367877 1.099955675 0.963139477 1.194858752 1.400362972 1.141765619 1.131934887 1.096062362 1 15.50077533 1.049160851 1.53382549 1.003294687 1.174101798 0.208567141 0.111494632 0.67370825 3.20829132 0.106680398 0.031531666 11.19852569 -1.049160851 0.170807111 T(ph)RSYDNLTTACDNTVPLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.646)RS(0.354)YDNLTTACDNTVPLASR 230.88 2.23E-25 208150000 110400 73746 101650 136890 113470 138090 145780 106490 129970 TRUE FALSE 105181.6108 81260.80124 106310.753 123129.5571 133259.1321 133307.9087 123538.5836 97165.17106 150125.0838 0.700626492 0.5412873 0.708147835 0.820179773 0.887654006 0.887978913 0.822904344 0.647228089 1 17.19580553 3.363448261 3.144192417 0.840934928 0.620792286 0.49703119 0.094907641 0.184063475 3.620533453 0.025695246 0.036187299 2309.129349 -3.363448261 -0.220142641 T(ph)RTDSYSAGQSVEILDGVELGEPAHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRTDSYSAGQSVEILDGVELGEPAHKK 27 2 P42345;B1AKP8;B1AKQ2 P42345 MTOR Serine/threonine-protein kinase mTOR 1 T(0.563)RT(0.11)DS(0.323)Y(0.002)S(0.002)AGQSVEILDGVELGEPAHKK 154.43 4.58E-08 161600000 281390 250710 294650 338900 235260 320870 396890 362140 246300 TRUE FALSE 268089.2524 276257.634 308159.9939 304833.1281 276289.2695 309758.1914 336337.1411 330429.1018 284494.9461 0.942333971 0.971045841 1.083182665 1.071488729 0.971157039 1.088800331 1.182225364 1.1614586 1 18.1180435 3.697759518 0.567312307 1.118979987 0.906687822 0.355717188 0.065244826 1.309113272 0.695867301 0.042792532 0.161296336 4986.083168 -3.697759518 -0.212292165 T(ph)RTPASINATPANINLADLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.5)RT(0.5)PASINATPANINLADLTR;T(0.63)RT(0.37)PASINATPANINLADLTR 216.51 9.96E-25 332850000 177028 157233 191299 193487 174099 173084 208830 185757 174864 TRUE FALSE 168660.2373 173255.2215 200070.2484 174037.3192 204461.8105 167090.0577 176969.1481 169491.1323 201981.016 0.835030146 0.85777973 0.990539865 0.861651865 1.012282315 0.827256249 0.876167234 0.839143874 1 17.62386018 3.978119812 24.33732243 0.906238589 0.843561209 0.146188894 0.067369735 955.0951554 1062354.285 0.015986134 0.028932396 9508.670791 -3.978119812 -0.06267738 T(ph)SLMAFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSLMAFLR 8 0 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 T(0.972)S(0.028)LMAFLR;T(0.52)S(0.48)LMAFLR;T(0.5)S(0.5)LMAFLR;T(0.984)S(0.016)LMAFLR 234.26 1.65E-07 175692000 514056 362031 290703 338844 405782 330466 524277 396470 344089 TRUE FALSE 489757.5916 398922.3705 304032.0201 304782.7574 476550.2523 319021.8796 444288.9146 361752.985 397448.5648 1.23225402 1.003708167 0.764959411 0.766848303 1.199023709 0.80267463 1.117852608 0.910188178 1 18.60040864 4.358693701 2.549005753 0.945446456 1.217586557 0.287316164 0.14335127 0.355505988 4.307470343 0.034752201 0.143918359 22839.87383 -4.358693701 0.272140101 T(ph)SNRYSPESQAQSVHHQRPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.298)S(0.298)NRY(0.102)S(0.298)PES(0.005)QAQSVHHQRPGSR 109.97 0.0003743 102760000 27720 17174 24760 28512 23869 22349 29743 26636 10398 TRUE FALSE 26409.73054 18924.05013 25895.27049 25645.91959 28031.74604 21575.04853 25205.15908 24303.61063 12010.46873 2.198892576 1.575629606 2.156058274 2.135297144 2.333942718 1.796353581 2.098599117 2.023535565 1 13.55200484 -0.698868661 6.455040805 0.999999996 2.017942389 0.696692417 0.215181139 1.50E-08 2.33E-09 0.201989304 0.047609335 0.200046676 0.698868661 1.017942394 T(ph)SPAPWKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.87)S(0.13)PAPWKR;T(0.66)S(0.34)PAPWKR 104.89 0.0026332 459560000 1604330 1301260 1259470 1392000 1189870 1371670 1744710 1454320 1475580 TRUE FALSE 1528496.5 1433859.873 1317217.945 1252073.515 1397382.951 1324168.724 1478522.446 1326972.031 1704405.41 0.896791627 0.84126691 0.772831357 0.734610151 0.819865358 0.776909482 0.867471106 0.778554224 1 20.70083711 -1.940602068 8.435374071 1.057453561 0.817878708 0.594141741 0.048791414 0.03238844 0.000228064 0.029023713 0.011658157 0.01146563 1.940602068 -0.239574853 T(ph)SPDSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSPDSLRR 8 1 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 T(0.5)S(0.5)PDSLRR;T(0.5)S(0.5)PDSLRR;T(0.5)S(0.5)PDSLRR;T(0.569)S(0.431)PDSLRR 85.355 0.0098458 743546000 961960 812292 846029 1000100 1326210 793237 994890 857836 1310530 TRUE FALSE 916490.0572 895065.4783 884820.2665 899568.0479 1557500.604 765767.0038 843101.2581 782719.3322 1513760.299 0.605439354 0.591286136 0.584518082 0.594260563 1.028895133 0.505870714 0.556958231 0.517069534 1 20.52970534 -2.121673846 2.406582163 1.747055631 0.619347382 0.389532562 0.148242587 12034427.67 3442235.825 49108485.14 0.034421055 0.007556595 2.121673846 -1.127708249 T(ph)SPDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.719)S(0.281)PDTLR;T(0.883)S(0.117)PDTLR 201.39 0.0037181 5758400000 5952100 6228600 4676700 6736900 3655510 5641800 5221700 5628000 3691280 TRUE FALSE 5670756.029 6863301.421 4891131.321 6059694.013 4293029.787 5446423.051 4425033.762 5135182.484 4263704.85 1.330006703 1.609703688 1.147155231 1.421227366 1.006877806 1.277392137 1.03783773 1.204394456 1 22.02367614 3.138366221 1.115578572 1.110249434 1.4564021 0.425627008 0.147299813 0.377902709 1.00958817 0.054511192 0.076627693 1375.201133 -3.138366221 0.346152667 T(ph)SPDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.624)S(0.376)PDTLRR;T(0.952)S(0.048)PDTLRR;T(0.929)S(0.071)PDTLRR;T(0.637)S(0.363)PDTLRR;T(0.986)S(0.01)PDT(0.003)LRR;T(0.634)S(0.366)PDTLRR;T(0.644)S(0.356)PDTLRR;T(0.98)S(0.02)PDTLRR;T(0.612)S(0.388)PDTLRR;T(0.955)S(0.045)PDTLRR;T(0.754)S(0.246)PDTLRR 139.43 0.00039008 20225865000 6892640 6018560 5570260 6656760 4574828 5938480 6219300 6242230 4707673 TRUE FALSE 6566838.567 6631858.107 5825661.931 5987609.838 5372676.555 5732828.949 5270431.56 5695627.249 5437714.885 1.207646724 1.219603868 1.071343764 1.10112611 0.9880394 1.054271706 0.969236466 1.047430284 1 22.37456908 3.470674934 1.160838792 1.00942704 1.225788657 0.817774572 0.036203595 0.155683669 0.429982558 0.011517779 0.023299005 2955.799249 -3.470674934 0.216361618 T(ph)SPGGRTS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.974)S(0.026)PGGRT(0.003)S(0.997)PEAR 161.94 0.0032936 0 170620 158250 156300 193060 124790 172010 181330 161080 144710 TRUE FALSE 162555.1307 174375.8549 163466.5096 173653.242 146553.3365 166053.2506 153664.7781 146974.9813 167150.8877 0.972505339 1.043224223 0.977957771 1.038901105 0.876772708 0.993433256 0.919317751 0.879295248 1 17.35079149 2.750939563 24.98052615 0.933050062 1.008355913 0.396222254 0.045621442 710.6048055 1433989.358 0.012537255 0.013210459 563.5592249 -2.750939563 0.075305851 T(ph)SPINEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPINEDIR 9 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 T(0.906)S(0.094)PINEDIR;T(0.845)S(0.155)PINEDIR 129.89 0.0042099 283959000 488440 499880 423580 487870 351430 524570 495620 516370 358770 TRUE FALSE 465352.4092 550818.3403 443001.562 438828.3807 412719.2807 506404.0094 420004.0663 471153.9054 414406.2193 1.122937803 1.329174889 1.06900317 1.058932903 0.995929263 1.221999058 1.013508115 1.136937342 1 18.66068613 3.711175533 24.39871881 1.073483078 1.226056344 0.374026486 0.083395606 455.2218186 405579.4353 0.020192752 0.031291946 5142.514597 -3.711175533 0.152573265 T(ph)SPINLGLNVNDLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.697)S(0.303)PINLGLNVNDLLK;T(0.703)S(0.297)PINLGLNVNDLLK 214.81 2.71E-11 187247000 804350 815740 796720 895040 471390 871520 900970 887820 534090 TRUE FALSE 766329.9696 898864.8334 833250.4001 805068.8787 553600.2668 841339.0439 763510.4791 810077.7742 616913.9494 1.242199127 1.457034379 1.350675245 1.304993799 0.897370318 1.363786707 1.237628813 1.313113077 1 19.23470974 -5 0.122040159 0.113453852 1.410057008 0.250067042 0.146975917 207.4704292 1.632673723 45.68645811 1.301462172 1.00E-05 5 1.296603156 T(ph)SPKPAVVETVTTAKPQQIQALMDEVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPKPAVVETVTTAKPQQIQALMDEVTK 28 2 P56192;H0YIP0;H0YI94 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK 156.69 1.37E-08 96086000 204210 172180 193570 220660 99403 211410 243270 245700 93867 TRUE FALSE 194557.398 189725.3378 202445.376 198478.8376 116738.8517 204088.8187 206154.6935 224185.2055 108423.415 1.79442234 1.749855765 1.86717395 1.83059017 1.076694105 1.882331587 1.901385357 2.067682572 1 16.72631683 T(ph)SPLKDNPS(ph)PEPQLDDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.5)S(0.5)PLKDNPS(1)PEPQLDDIKR;T(0.853)S(0.147)PLKDNPS(1)PEPQLDDIKR 175.76 3.66E-12 726000000 1593290 1405620 1330290 1628510 619280 1686090 1537390 1634600 553940 TRUE FALSE 1517978.339 1548854.276 1391285.112 1464809.081 727282.2359 1627700.281 1302832.919 1491465.758 639842.1861 2.372426158 2.420681708 2.174419166 2.289328701 1.136658776 2.543908976 2.036178526 2.330990033 1 19.28735659 2.964170565 24.99205575 1.923775322 2.335827172 0.194834334 0.479644507 1058.748487 738507.6242 0.13343884 0.141582671 920.8111411 -2.964170565 0.412051849 T(ph)SPLKDNPSPEPQLDDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.564)S(0.202)PLKDNPS(0.234)PEPQLDDIKR 107.75 0.013744 421650000 385750 340510 353790 435960 189800 461090 382050 440240 204300 TRUE FALSE 367516.362 375208.3561 370011.6214 392136.4725 222901.0599 445122.3377 323761.2557 401690.2517 235981.8006 1.55739282 1.58998853 1.567966769 1.661723368 0.944568858 1.886257061 1.371975529 1.702208606 1 17.84831607 -1.914258604 2.51358726 0.67591681 1.532349426 0.317511791 0.246591025 22613666.4 10031867.35 43058121.63 0.052040509 0.01218264 1.914258604 0.856432616 T(ph)SPPCS(ph)PANLSR ddPTM_SK-BR-3_Trastuzumab_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(0.878)S(0.122)PPCS(1)PANLSR 133.47 0.00086284 829220000 545110 477070 439650 546880 378946 458000 532830 522610 408390 TRUE FALSE 519343.7306 525683.9754 459808.3874 491906.5834 445034.0624 442139.3452 451536.9974 476847.4979 471721.0354 1.100955208 1.114395874 0.974746413 1.042791282 0.943426366 0.937289864 0.957211919 1.010867572 1 18.84757441 3.737179061 24.66964713 0.976314707 1.107675548 0.729044213 0.032035245 44.92960659 802288.9155 0.008490151 0.013981133 5459.829248 -3.737179061 0.131360841 T(ph)SPPLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.634)S(0.366)PPLLDR;T(0.691)S(0.309)PPLLDR;T(0.551)S(0.449)PPLLDR;T(0.662)S(0.338)PPLLDR 162.34 0.0038264 21670820000 9194300 9108700 7373600 9636400 6002500 8469700 8315000 8571500 5678260 TRUE FALSE 8759703.66 10036886.89 7711686.853 8667730.764 7049334.1 8176392.165 7046394.035 7820934.02 6558815.56 1.335561822 1.530289546 1.175774312 1.321539032 1.074787671 1.246626329 1.074339409 1.192430851 1 22.64500388 3.279961493 1.170831844 1.125553671 1.429492234 0.534883781 0.105159319 0.301537789 0.875479618 0.03580841 0.05805354 1905.291775 -3.279961493 0.303938563 T(ph)SPSKSPFLHSGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPSKSPFLHSGMK 14 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;H0YEW5 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 T(0.499)S(0.499)PS(0.002)KSPFLHSGMK 138.97 2.45E-05 307610000 444290 415130 370710 479910 300870 471410 474990 494550 296930 TRUE FALSE 423289.2922 457432.219 387707.4202 431668.535 353341.6327 455084.9535 402521.5517 451244.5802 342976.3879 1.234164529 1.333713442 1.130420151 1.25859549 1.030221453 1.326869632 1.173613012 1.315672437 1 18.38774973 -2.323776292 1.980614285 2.92E-05 1.228412627 0.356969902 0.095000424 2808295.906 296862.0369 12587404.61 0.021034405 0.004744863 2.323776292 1.228383388 T(ph)SPTPPESATTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.948)S(0.052)PTPPESATTVK 142.85 0.00045315 170610000 745070 680060 696810 835230 483110 768030 851200 781230 576840 TRUE FALSE 709852.0177 749358.8872 728759.4277 751271.0936 567364.231 741432.9285 721333.8066 712821.3596 666293.4011 1.065374528 1.124668031 1.093751531 1.127537947 0.851523113 1.112772432 1.08260686 1.069831036 1 19.34579808 3.614860311 0.009548492 0.000137162 2.156117956 0.072462275 0.078865327 12086.90845 27.33682001 2947.811179 3226.440037 4119.649911 -3.614860311 2.155980794 T(ph)SPTVATQTGASATSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.619)S(0.372)PT(0.009)VATQTGASATSTR;T(0.558)S(0.442)PTVATQTGASATSTR 216.6 5.86E-14 218413000 242241 218991 229701 251886 186636 241828 271645 242227 216449 TRUE FALSE 230790.748 241306.4319 240233.0181 226565.9407 219185.2593 233453.4357 230200.5661 221016.3198 250014.8055 0.923108324 0.965168568 0.960875167 0.906210096 0.876689118 0.933758444 0.920747736 0.884012926 1 17.93165401 5.121217818 17.93527939 0.92926384 0.001366069 0.002518532 0.037606113 2177.455553 300249.7518 0.008291999 5640.613311 132195.8489 -5.121217818 -0.927897772 T(ph)SPYILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.5)S(0.5)PYILR;T(0.898)S(0.102)PYILR 141.52 0.02852 123760000 399460 466290 397170 507490 349600 408370 427260 467290 332760 TRUE FALSE 380578.3175 513805.4811 415380.6374 456476.141 410570.1293 394228.0445 362073.6398 426371.6103 384362.7213 0.990154082 1.33677241 1.080699595 1.187618142 1.068184053 1.025666701 0.942010293 1.10929491 1 18.55210889 2.495357794 2.68512842 1.006729971 1.158959219 0.28252062 0.095720004 0.302886489 4.412139138 0.034002638 0.029262813 312.8655855 -2.495357794 0.152229248 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.328)S(0.328)S(0.328)DS(0.017)ALHTSVMNPSPQDTYPGPTPPSILPSR 168.18 1.46E-13 410830000 57678 44278 66312 74282 93050 57815 103270 76368 103460 TRUE FALSE 54951.67525 48789.97854 69352.47079 66815.03223 109277.8905 55812.85205 87514.26482 69680.81307 119504.0484 0.459831077 0.408270508 0.580335744 0.559102667 0.914428356 0.467037333 0.732312135 0.583083285 1 16.86669997 -2.168437483 0.075606745 1.974133636 3.37E-12 0.537310336 0.132696393 95.78291105 0.97170436 22.88363813 6.417895032 0.006785198 2.168437483 -1.974133636 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSRR 33 1 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.332)S(0.332)S(0.332)DS(0.003)ALHTSVMNPSPQDTYPGPTPPSILPSRR 69.537 0.0030966 41334000 14450 11392 14441 17141 11187 15238 14977 15978 10384 TRUE FALSE 13766.97714 12552.85775 15103.13413 15417.95411 13138.00926 14710.30424 12691.98358 14578.88162 11994.29769 1.147793518 1.046568801 1.259192871 1.285440342 1.09535461 1.226441483 1.058168132 1.215484391 1 13.55006106 -0.697945855 6.306101286 1.000000004 1.154547118 0.276847809 0.082639451 2.32E-09 1.84E-10 0.07798651 0.018381597 0.200472195 0.697945855 0.154547114 T(ph)SSEEEDSRREEPSLLLVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK 191.4 7.03E-16 70172000 102734 86119 93885 99909 62760 105069 124864 116619 78213 TRUE FALSE 97877.96742 94894.62401 98189.72011 89865.95751 73705.32413 101430.4342 105813.7035 106407.2221 90341.87258 1.083417519 1.050394698 1.086868329 0.994732065 0.815848975 1.122740002 1.171258692 1.177828388 1 16.4631072 2.03312731 24.99999058 1.138293565 1.01799971 0.259166928 0.090217593 234.2380797 176770.1187 0.033424645 0.024685595 107.9263053 -2.03312731 -0.120293855 T(ph)SSESIYSRPGSSIPGSPGHTIYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSESIYSRPGSSIPGSPGHTIYAK 25 1 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;A0A0A0MRL6;A0A3B3IS55;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 T(0.494)S(0.494)S(0.012)ES(0.001)IYSRPGSSIPGSPGHTIYAK;T(0.477)S(0.477)S(0.015)ES(0.013)IY(0.001)S(0.013)RPGS(0.003)S(0.003)IPGSPGHTIYAK 137.25 3.48E-05 412140000 230544 191851 183924 250627 174196 184001 240393 261577 191005 TRUE FALSE 219646.642 211400.835 192357.0973 225433.4978 204575.7272 177628.9992 203716.6327 238671.9312 220625.0799 0.995565156 0.958190407 0.871873213 1.021794521 0.927255085 0.805116985 0.923361174 1.08179873 1 17.75123728 1.249449384 24.9778126 1.040899365 0.930900338 0.351286475 0.06316587 214.2855873 491558.2584 0.043630789 0.015592176 17.76026263 -1.249449384 -0.109999027 T(ph)SSISGPLSPAYTGQVPYNYNQLEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 T(0.319)S(0.319)S(0.319)IS(0.041)GPLS(0.001)PAYTGQVPYNYNQLEGR;T(0.363)S(0.363)S(0.269)IS(0.006)GPLSPAYTGQVPYNYNQLEGR 208.41 8.25E-25 325880000 343720 238240 287810 383400 311540 344080 407540 340340 371380 TRUE FALSE 327473.0368 262516.9269 301006.3732 344859.9036 365872.4774 332164.4233 345362.288 310538.0253 428971.7137 0.763390747 0.611967919 0.701692824 0.803922246 0.852905834 0.774327101 0.805093383 0.723912593 1 18.71052299 -4.999999992 0.116469788 1.814249142 0.618113632 0.593682246 0.064693861 107.2339763 0.817148394 20.65585961 0.687344012 1.00E-05 4.999999992 -1.19613551 T(ph)SSKHKEDVYENLHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSKHKEDVYENLHTK 16 2 P29350-2;P29350;P29350-3 P29350-2 PTPN6 Tyrosine-protein phosphatase non-receptor type 6 1 T(0.333)S(0.333)S(0.333)KHKEDVYENLHTK;T(0.333)S(0.333)S(0.333)KHKEDVYENLHTK 100.28 0.0021178 156866000 397010 250820 364990 461630 223800 438480 511180 461760 153550 TRUE FALSE 378244.1241 276378.8432 381725.1525 415226.0754 262830.6491 423295.3277 433190.1025 421325.8465 177361.7498 2.13261385 1.558277608 2.152240565 2.341125276 1.481890258 2.386621288 2.442409951 2.37551697 1 17.43633538 3.681487033 24.9844161 2.117245703 1.845444149 0 0.484560678 759.861108 332634.6869 0.118258567 0.18320547 4802.717397 -3.681487033 -0.271801554 T(ph)SSKSEAGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.937)S(0.027)S(0.037)KSEAGAR;T(0.45)S(0.095)S(0.45)KS(0.005)EAGAR 109.96 0.0031521 143714000 181698 161348 165183 197396 90851 185869 177891 232234 129721 TRUE FALSE 173109.4956 177789.5446 172756.8039 177553.3791 106695.3856 179432.3099 150750.4608 211898.3598 149837.4702 1.155315125 1.186549295 1.152961297 1.18497315 0.712074126 1.197512943 1.006093206 1.41418805 1 17.19303892 T(ph)SSLDTITGPYLTGQWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 T(0.324)S(0.324)S(0.324)LDT(0.027)ITGPYLTGQWPR 193.17 5.06E-14 17368000 27710 18971 21772 28023 22570 21938 28346 22513 21149 TRUE FALSE 26400.20322 20904.16647 22770.26774 25206.0748 26506.20085 21178.28156 24021.29709 20541.64237 24428.67891 1.080705318 0.855722348 0.932112122 1.031823084 1.085044384 0.866943384 0.983323625 0.840882245 1 14.57628822 -0.852432859 4.29412297 1.000000451 0.960165304 0.020180281 0.088449553 10440750.04 2431429.708 45.5207684 0.019329471 0.140464682 0.852432859 -0.039835147 T(ph)SSLDTLAAPYLAGHWPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.333)S(0.333)S(0.333)LDTLAAPYLAGHWPR;T(0.553)S(0.221)S(0.226)LDTLAAPYLAGHWPR 290.57 1.35E-48 300720000 151762 153530 146447 170425 114306 150945 164535 160592 121571 TRUE FALSE 144588.511 169174.8815 153161.7398 153293.5552 134240.9302 145717.7368 139432.1639 146529.7131 140423.6098 1.029659551 1.204746708 1.090712168 1.091650866 0.955971225 1.037701118 0.992939607 1.043483452 1 17.09942599 2.902712006 5.080020173 1.007409699 1.115042888 0.503191571 0.04846014 0.170630029 6.932051255 0.014273099 0.015299608 799.3040366 -2.902712006 0.107633189 T(ph)SSPHKEESPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.333)S(0.333)S(0.333)PHKEESPK 109.44 0.0014449 0 309880 285540 264930 323850 119150 325690 320950 350940 119270 TRUE FALSE 295232.5865 314636.8506 277077.3026 291295.9827 139929.7223 314411.2736 271983.1828 320209.8332 137765.7825 2.143003736 2.2838534 2.01122004 2.114429124 1.015707382 2.282216005 1.974243372 2.324305988 1 17.07185808 2.967645554 24.99950367 1.813924395 2.161090924 0.157725245 0.452520221 1335.025794 1031542.831 0.128199276 0.13608624 928.2085285 -2.967645554 0.347166529 T(ph)SSPPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.333)S(0.333)S(0.333)PPRK 60.59 0.056603 1287900000 379920 304850 318010 363720 204360 351000 387720 361160 249370 TRUE FALSE 361961.9345 335914.5616 332591.0731 327158.1746 240000.3193 338844.782 328566.193 329534.9158 288041.026 1.256633264 1.166203878 1.154665631 1.135804087 0.833215749 1.176376805 1.140692344 1.144055485 1 18.13591479 3.775054296 1.345021154 1.081498177 1.237184602 0.270424463 0.099652546 0.650862863 2.245033255 0.031013642 0.08357254 5957.366189 -3.775054296 0.155686425 T(ph)SSVPEYVYNLHLVENDFVGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.333)S(0.333)S(0.333)VPEYVYNLHLVENDFVGGR 208.96 2.30E-22 49436000 23947 19086 18458 19199 17244 18749 23897 18551 16763 TRUE FALSE 22815.07277 21030.8851 19304.31756 17269.08004 20251.34814 18099.71743 20251.07375 16926.57609 19362.52043 1.178311101 1.086164644 0.996994045 0.891881824 1.045904546 0.934781063 1.045890375 0.874192808 1 14.24097914 3.943257983 1.979285247 0.972586871 1.160680103 0.600123768 0.057682374 0.200627134 1.530467558 0.014569114 0.037740892 8775.219395 -3.943257983 0.188093231 T(ph)TFQDELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTFQDELIR 9 0 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;C9JXH8 E7ETZ8 MAP9 Microtubule-associated protein 9 1 T(0.5)T(0.5)FQDELIR 96.253 0.083763 30429000 2581.5 2391.2 3585.9 3048 4592.8 3327.4 2943.4 2618.8 4171.8 TRUE FALSE 2459.477611 2634.865999 3750.317062 2741.609249 5393.782866 3212.171304 2494.330271 2389.483989 4818.741437 0.510398336 0.546795472 0.778277297 0.568947159 1.119334361 0.666599639 0.517631067 0.495873045 1 12.23444068 3.831833966 5.966953245 0.708302256 0.524910417 0.14536 0.2005568 0.457779729 23.86708285 0.050622301 0.092316615 6789.440183 -3.831833966 -0.183391839 T(ph)TGTPPDSSLVTYELHSRPEQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.347)T(0.347)GT(0.306)PPDSSLVTYELHSRPEQDK 91.722 0.007493 33652000 39114 44872 31293 48860 21441 41237 37411 40873 20205 TRUE FALSE 37265.15874 49444.50782 32727.815 43948.49997 25180.30361 39808.95235 31703.26485 37293.94344 23338.28821 1.596739161 2.118600446 1.402322857 1.883107261 1.078926757 1.705735742 1.358422887 1.597972529 1 14.51041113 -0.424992125 0.088926274 2.65E-09 2.434722154 0.353631351 0.273443466 47.16740196 1.0729608 20.4587414 9.31089616 0.375844219 0.424992125 2.434722151 T(ph)TPDQELAPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIRR 113.54 0.07509 62949000 37444 28878 34195 39423 22880 35941 41119 34790 33658 TRUE FALSE 35674.09633 31820.70103 35762.87457 35460.12514 26870.26476 34696.35416 34845.54135 31743.60317 38877.51074 0.917602379 0.818486071 0.919885916 0.912098652 0.691151883 0.892453079 0.896290444 0.816502975 1 15.24664823 -1.382424739 4.889766153 1.000133055 0.860739426 0.287957688 0.070032729 9.42E-05 1.19E-05 0.062907296 0.014813272 0.041454842 1.382424739 -0.139393628 T(ph)TPDQELVPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 124.06 0.0058414 154850000 53160 49617 41552 60959 38885 55440 49669 66592 44610 TRUE FALSE 50647.23215 54673.02871 43457.2003 54831.28551 45666.53169 53520.0989 42091.08182 60760.85145 51527.89096 0.982909085 1.06103758 0.843372385 1.064108864 0.886248803 1.038662711 0.816860171 1.179183745 1 15.65306592 1.22202613 24.9999876 1.089591762 0.962673226 0.246949774 0.096342527 390.4183201 590292.8666 0.082656214 0.020902486 16.67347528 -1.22202613 -0.126918536 T(ph)TPNSGDVQVTEDAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPNSGDVQVTEDAVR 16 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 T(0.5)T(0.5)PNSGDVQVTEDAVR 97.904 0.032585 36842000 90975 90084 92756 104690 88710 99897 97625 95301 86916 TRUE FALSE 86674.79205 99263.66202 97008.95435 94166.3623 104180.9959 96437.54184 82730.51324 86955.93922 100394.4894 0.863342127 0.988736161 0.966277681 0.937963457 1.037716279 0.960586009 0.824054326 0.866142552 1 16.61532056 -0.612064615 5.545795892 0.999999995 0.929731133 0.10327902 0.064218745 8722340.118 1572784.729 0.137911502 0.015815499 0.244306704 0.612064615 -0.070268862 T(ph)TPPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK 121.45 3.10E-05 66378000 37552 35965 31801 40994 28008 39889 41195 43940 24927 TRUE FALSE 35776.99138 39629.87439 33259.10731 36873.20524 32892.58633 38507.63393 34909.94615 40092.38066 28792.55185 1.242577996 1.376393263 1.15512885 1.280650823 1.142399135 1.3374165 1.212464471 1.392456663 1 14.81340804 -2.115058259 2.527215726 0.476405848 1.268007323 0.496521361 0.084632061 5988914.913 1440856.526 18102660.95 0.018752178 0.007672586 2.115058259 0.791601475 T(ph)TPPPGRPPAPSSEEEDGEAVAH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.863)T(0.137)PPPGRPPAPSSEEEDGEAVAH 130.78 5.38E-05 359770000 82494 74487 86758 95556 71046 96459 107170 91888 67543 TRUE FALSE 78594.67211 82077.30998 90735.94012 85950.52934 83436.39991 93118.60064 90819.24819 83841.79959 78017.22348 1.007401553 1.0520409 1.163024472 1.101686596 1.069461283 1.193564658 1.164092288 1.074657567 1 16.25150504 3.93011771 4.519341418 1.121819734 1.022615033 0.246157502 0.056917369 0.216781722 8.518347564 0.013869563 0.026591134 8513.687595 -3.93011771 -0.099204701 T(ph)VHRDSEEEDDYLFDDPLPIPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.561)VHRDS(0.439)EEEDDYLFDDPLPIPLR;T(0.569)VHRDS(0.431)EEEDDYLFDDPLPIPLR;T(0.35)VHRDS(0.35)EEEDDY(0.301)LFDDPLPIPLR;T(0.462)VHRDS(0.462)EEEDDY(0.077)LFDDPLPIPLR;T(0.459)VHRDS(0.459)EEEDDY(0.083)LFDDPLPIPLR 113.6 0.001214 162187000 166646 129449 116612 142581 129373 130954 149181 148185 119394 TRUE FALSE 158768.9738 142640.0003 121958.7755 128248.487 151935.6102 126419.0301 126420.6986 135209.1358 137909.0117 1.151258876 1.034305144 0.884342321 0.929950011 1.101709078 0.916684331 0.916696429 0.980422774 1 17.07335721 4.164292302 2.473984125 0.957352831 1.133886633 0.483008573 0.061644601 0.217570291 2.608105513 0.015795547 0.047972994 14597.96445 -4.164292302 0.176533802 T(ph)VQEEEQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVQEEEQLK 9 0 A0A0U1RRH1;A0A0X1KG73;A0A087X080;Q15413-3;Q15413-2;Q15413;A0A1B0GTF2 A0A0U1RRH1 RYR3 Ryanodine receptor 3 1 T(1)VQEEEQLK 81.594 0.076676 94106000 44057 47460 45990 53622 352910 39727 45389 41470 288650 TRUE FALSE 41974.51292 52296.22796 48098.68699 48231.81468 414457.3923 38351.24403 38464.07442 37838.66695 333412.3678 0.125893689 0.156851494 0.144261856 0.144661144 1.243077439 0.115026459 0.11536487 0.113489092 1 18.3469481 -1.844356996 2.420320349 1.312786485 0.255310334 0.303038004 0.347383758 19897793.95 11699912.12 35997163.63 0.084282362 0.014310111 1.844356996 -1.057476151 T(ph)VSPPTVCTIPTVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSPPTVCTIPTVVGR 16 0 A0A0C4DH56;Q9BWT3-2;Q9BWT3 A0A0C4DH56 PAPOLG Poly(A) polymerase gamma 1 T(0.631)VS(0.358)PPT(0.01)VCT(0.001)IPTVVGR 117.08 0.0042229 33544000 56426 51406 50830 61112 44232 48425 56462 52793 43746 TRUE FALSE 53758.85481 56644.32984 53160.60578 54968.90565 51946.0468 46748.03011 47847.6849 48170.16505 50529.90626 1.063901732 1.121006035 1.052062228 1.087848954 1.02802579 0.925155686 0.946918141 0.953300107 1 15.62484988 2.454844304 3.377939793 0.950686807 1.083590365 0.833723369 0.026149065 0.079719362 1.918404024 0.008863453 0.007548334 284.9996353 -2.454844304 0.132903559 T(ph)WSEKDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWSEKDLR 8 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2;F5H0D8;E9PKU1;F5H4Y5;E9PQK4;E9PSH0;E9PKA1 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 T(0.5)WS(0.5)EKDLR;T(0.5)WS(0.5)EKDLR 97.456 0.013287 185458000 662210 508700 542680 663630 441520 605700 668790 633030 423010 TRUE FALSE 630908.6457 560537.1083 567562.4148 596920.6516 518520.9482 584724.4571 566753.8023 577598.5373 488608.2304 1.291236223 1.147211761 1.16158996 1.221675392 1.06122025 1.196714302 1.15993503 1.182130184 1 18.89831864 -5 0.112869736 0.463051929 1.272528018 0.52914201 0.055251907 130.5867721 0.973116665 16.43660869 0.604913336 1.00E-05 5 0.80947609 T(ph)WTLCGTPEYLAPEIILSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWTLCGTPEYLAPEIILSK 19 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;P22612;P17612-2;P17612;Q15136;K7ERP6 P22694-2;P17612-2 PRKACB;PRKACG;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit gamma;cAMP-dependent protein kinase catalytic subunit alpha 1 T(0.496)WT(0.496)LCGT(0.008)PEYLAPEIILSK;T(0.48)WT(0.48)LCGT(0.037)PEY(0.003)LAPEIILSK 150.28 2.84E-07 97558000 118508 94622 111734 140738 88865 167256 173081 140847 98813 TRUE FALSE 112906.3617 104264.0894 116857.1144 126590.7489 104363.0279 161463.8828 146674.3146 128513.69 114136.4154 0.989222952 0.913504152 1.023837257 1.109117966 0.914370997 1.414657033 1.285079036 1.12596571 1 16.80039963 2.252868327 24.99979927 1.242652271 0.986457867 0.43013351 0.120577686 175.505116 306658.89 0.039278679 0.032721176 179.0063044 -2.252868327 -0.256194404 T(ph)Y(ph)T(ph)WLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYTWLK 6 0 Q6YHK3-2;Q6YHK3-4;Q6YHK3 Q6YHK3-2 CD109 CD109 antigen 3 T(1)Y(1)T(1)WLK 63.486 0.055775 199560000 0 2121 1695.6 2933.8 3553.8 0 0 0 3205.1 TRUE FALSE 0 2337.132311 1773.344937 2638.88885 4173.581595 0 0 0 3702.130539 0 0.631293869 0.479006593 0.712802756 1.127345876 0 0 0 1 11.85414005 4.656705816 3.76066078 0.440571641 1.45E-14 0.115392295 0.405506888 0.605393506 14.12583286 0.101142807 0.617407823 45363.42284 -4.656705816 -0.440571641 T(ph)YTHEVVTLWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.562)YT(0.438)HEVVTLWYR;T(0.515)YT(0.485)HEVVTLWYR;T(0.564)YT(0.436)HEVVTLWYR 183.96 5.49E-05 431359000 523830 482939 383788 471738 417980 481829 560940 467850 333761 TRUE FALSE 499069.594 532151.0332 401385.0594 424318 490875.5797 465143.1409 475358.3006 426882.5738 385518.9513 1.294539717 1.380349867 1.041155196 1.100641093 1.273285212 1.20653768 1.233034846 1.107293357 1 18.55644226 7.999999954 0.024894326 9.86E-09 2.85051341 0.364829644 0.095307758 2141.736545 4.101071722 161.6614406 337.6851692 99999989.3 -7.999999954 2.8505134 TAAAAAEHSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TAAAAAEHSQR 11 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;;;;; 159.99 2.80E-05 975045000 1510676 1408107 1450359 1611025 1409502 1561568 1741804 1586991 1473454 FALSE TRUE 1439269.339 1551594.704 1516859.395 1449081.706 1655318.703 1507490.509 1476059.809 1448025.655 1701949.721 0.845659141 0.911657192 0.891248065 0.851424509 0.972601412 0.885743268 0.867275802 0.850804014 1 20.69875699 TAADKDRGEEDADGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 234.04 6.46E-20 1034212000 1845700 1894610 1618930 2234520 795047 2046000 1800780 2141420 753699 FALSE TRUE 1758457.419 2087672.913 1693159.542 2009901.804 933702.9451 1975146.507 1526037.937 1953905.912 870578.7916 2.019871648 2.398028683 1.944866517 2.308696035 1.07250826 2.268773977 1.752900429 2.244375732 1 19.73161535 TAADKDRGEEDADGSKTQDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAADKDRGEEDADGSKTQDLFR 22 3 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 0 174.7 1.02E-12 157400000 295120 173490 317530 264150 185070 344100 422650 383190 235810 FALSE TRUE 281170.2625 191168.8282 332089.0646 237597.1401 217346.1494 332183.7307 358166.98 349635.8522 272378.2104 1.032278838 0.701850665 1.219220378 0.872305974 0.797957183 1.219567932 1.31496194 1.28364105 1 18.05525177 2.207004341 12.51631466 1.239545894 0.915131855 0.420233571 0.160782306 0.819639774 323.1655489 0.056250173 0.041683673 161.0661733 -2.207004341 -0.324414038 TAAESFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAAESFK 7 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 91.9 0.037373 63153000 191990 179880 155140 190550 145050 170340 219480 196580 148400 FALSE TRUE 182915.0132 198209.9765 162253.3225 171395.552 170346.6741 164441.0831 185994.295 179366.4131 171413.1141 1.067100462 1.156329127 0.946563064 0.999897545 0.993778539 0.959326152 1.085064559 1.046398428 1 17.38711796 3.744721087 24.99694017 1.009169675 1.111714794 0.497319911 0.044644029 400.0722686 1623343.735 0.011829064 0.020650878 5555.47358 -3.744721087 0.102545119 TAAGSSWEDPSLLEWDADDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAAGSSWEDPSLLEWDADDFR 21 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 120.53 7.69E-05 15765000 43395 41799 39525 45727 38868 40326 51061 42028 41744 FALSE TRUE 41343.80435 46058.36562 41337.26035 41130.43508 45646.56689 38929.50051 43270.70665 38347.80552 48217.44632 0.857444919 0.955222002 0.8573092 0.853019772 0.946681552 0.807373751 0.89740768 0.795309757 1 15.55726762 TAALESNLPGS(ph)PNTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALES(0.001)NLPGS(0.96)PNT(0.02)S(0.02)R;TAALES(0.008)NLPGS(0.947)PNT(0.022)S(0.022)R 481.09 5.18E-231 1078655000 1348635 1254671 1324684 1449078 1217568 1287520 1481033 1442082 1327874 TRUE FALSE 1284887.696 1382523.401 1385422.072 1303413.926 1429911.474 1242932.86 1255074.215 1315805.655 1533793.918 0.837718602 0.90137494 0.90326481 0.849797297 0.932270924 0.810364968 0.818280866 0.857876433 1 20.54867322 2.227316961 24.99976622 0.850746551 0.882086545 0 0.05903132 638.6336828 1419964.317 0.019767275 0.014728164 168.7784369 -2.227316961 0.031339994 TAAPS(ph)PSLLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 TAAPS(0.996)PS(0.004)LLYK;TAAPS(0.963)PS(0.036)LLYK;TAAPS(0.986)PS(0.014)LLYK;TAAPS(0.987)PS(0.013)LLYK 182.41 6.08E-06 272189000 1242540 1115170 1210060 1422960 974570 1279490 1524890 1408350 1219910 TRUE FALSE 1183807.597 1228807.091 1265542.448 1279921.357 1144534.699 1235180.94 1292240.024 1285027.408 1409087.412 0.840123605 0.872058809 0.898129127 0.90833354 0.812252448 0.876582198 0.917075841 0.911957198 1 20.42632968 0.921749438 0.882178865 0.998985764 0.866413657 0.67300802 0.028701681 0.413376126 0.681954805 0.027221164 0.009439931 8.351210647 -0.921749438 -0.132572107 TAAQCLEHYEFLLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAAQCLEHYEFLLDK 15 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 142.01 4.66E-06 42769000 120020 107800 114340 118420 82730 113990 128960 130190 90806 FALSE TRUE 114346.8925 118784.9426 119582.6021 106516.1966 97158.08581 110042.4977 109284.7835 118789.8734 104887.7307 1.090183682 1.132496068 1.140100956 1.0155258 0.926305538 1.049145567 1.041921517 1.132543078 1 16.6784864 3.235029099 24.99927731 1.027325091 1.119014126 0.417437534 0.051970575 88.73673801 628160.6071 0.014838747 0.018421582 1718.023497 -3.235029099 0.091689035 TAAYGHFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAAYGHFGR 9 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 156.01 7.20E-05 1436330000 3029000 2499180 2255020 2580010 2759430 2509370 3477450 2893930 2697810 FALSE TRUE 2885825.173 2753849.283 2358414.898 2320662.493 3240673.718 2422469.888 2946901.135 2640522.148 3116172.596 0.926080018 0.883728099 0.756830639 0.744715648 1.039953218 0.777386301 0.94567969 0.847360686 1 21.57134371 2.75704791 24.99801373 0.908967708 0.844124359 0.194690417 0.090485375 1893.839876 2560795.082 0.02678831 0.028367328 571.5416842 -2.75704791 -0.064843349 TADEDRGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TADEDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 93.667 0.0062916 0 359830 274560 308090 351750 299860 310730 385920 359320 348570 FALSE TRUE 342821.549 302537.9761 322216.2312 316391.4217 352155.4891 299969.3422 327040.8161 327856.0359 402624.4554 0.851467278 0.751414804 0.800289766 0.785822663 0.874650023 0.745035077 0.812272607 0.814297372 1 18.61907528 0.491190948 2.090222437 0.999993028 0.800637036 0.710221332 0.039316821 2.700950253 10.47817857 0.034052703 0.009305872 3.098781453 -0.491190948 -0.199355992 TADGIVSHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TADGIVSHLK 10 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 141.95 3.66E-05 829540000 2976390 2949140 2346250 3060200 2049320 2693560 2800860 2843880 1890440 FALSE TRUE 2835701.943 3249660.719 2453827.883 2752582.882 2406720.759 2600281.342 2373537.366 2594854.791 2183599.78 1.298636302 1.488212606 1.123753494 1.260571148 1.102180345 1.190823229 1.086983699 1.188338089 1 21.05827703 3.72771328 24.8695891 1.143245975 1.393424454 0.62426686 0.082853879 342.569869 785407.017 0.0198237 0.031045326 5342.115583 -3.72771328 0.250178479 TADGRVS(ph)PAGGTLDDKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TADGRVSPAGGTLDDKPK 18 2 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 T(0.007)ADGRVS(0.993)PAGGTLDDKPK 98.199 0.00066061 142520000 480680 438880 441430 513120 208780 518800 490110 541220 207100 TRUE FALSE 457959.209 483602.371 461670.0021 461540.2027 245191.1659 500833.8259 415334.718 493827.9076 239216.0103 1.914417051 2.021613731 1.929929362 1.929386759 1.024978076 2.093646764 1.736232945 2.064359769 1 17.86795442 2.961856728 24.98719506 1.659653526 1.959430057 0.182091501 0.365562072 1034.188709 677484.3871 0.101808375 0.108006806 915.9182829 -2.961856728 0.299776531 TAEALDKDGWLHTGDIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TAEALDKDGWLHTGDIGK 18 1 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;; 155.11 1.27E-08 349254000 1975620 1479520 1653190 2065730 1185890 1884480 2143230 1956690 1108820 FALSE TRUE 1882236.358 1630284.77 1728990.397 1858078.896 1392708.841 1819219.985 1816240.9 1785351.851 1280770.143 1.469612927 1.27289411 1.349961511 1.450751258 1.087399522 1.420410989 1.418084979 1.393967419 1 20.28858015 -2.221969743 2.006284353 2.72E-05 1.358641632 0.50769255 0.110752974 1700113.866 290402.9241 7706129.564 0.025458819 0.005998329 2.221969743 1.358614401 TAEAVCFDVDNGTSAGRS(ph)PLDPMTSPGSGLILQANFVHSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAEAVCFDVDNGTSAGRSPLDPMTSPGSGLILQANFVHSQR 41 1 Q08499-10 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 T(0.012)AEAVCFDVDNGT(0.182)S(0.182)AGRS(0.569)PLDPMT(0.026)S(0.026)PGS(0.002)GLILQANFVHSQR 49.191 0.020098 28917000 25330 20176 24790 27155 32272 22386 30208 28994 40301 TRUE FALSE 24132.7011 22231.95734 25926.64602 24425.32781 37900.22658 21610.76721 25599.21479 26455.13165 46550.67325 0.518417875 0.477586161 0.556955339 0.524704072 0.814171395 0.464241776 0.549921473 0.56830825 1 15.50651441 -5 0.314899484 5.10276003 0.530868909 0.673363515 0.096457836 177.9138471 1.594037505 485.3596241 0.084279894 1.00E-05 5 -4.57189112 TAELSLGRNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAELSLGRNER 11 1 Q9H611-2;Q9H611;Q9H611-3 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 0 64.439 0.041035 63981000 75831 44923 69475 53384 203990 51756 73677 52829 174800 FALSE TRUE 72246.61891 49500.70477 72660.49747 48017.7389 239565.7914 49963.67674 62436.22048 48203.0127 201907.0912 0.357821107 0.245165757 0.359870954 0.237820963 1.186514995 0.247458752 0.30923243 0.238738582 1 17.62333206 -2.207694999 2.222217526 2.774621167 0.386874611 0.30545695 0.284937784 23621737.86 4290542.389 210857764.7 0.065245522 0.006198763 2.207694999 -2.387746556 TAENATSGETLEENEAGD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 281.1 6.17E-39 615140000 1533830 1335190 1433330 1604600 1355550 1472270 1675500 1505350 1470380 FALSE TRUE 1461328.896 1471247.379 1499049.598 1443302.559 1591957.491 1421284.921 1419871.702 1373533.574 1698399.021 0.860415531 0.866255433 0.882625096 0.849801809 0.937328314 0.836838048 0.836005959 0.808722542 1 20.69574401 -2.357928769 2.338671998 1.960517795 0.860238965 0.627508642 0.033957253 3998396.81 339923.3501 20559403.25 0.008958836 0.004386026 2.357928769 -1.10027883 TAENFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 189.49 0.003225 54986900000 19929760 14033970 16252970 19371700 16948450 17207960 21633290 18217100 17312140 FALSE TRUE 18987719.74 15464047.5 16998184.75 17424419.91 19904254.31 16612044.03 18332734.29 16621914.15 19996818.25 0.949537046 0.773325401 0.850044469 0.871359618 0.995371067 0.830734361 0.916782563 0.831227945 1 24.25326713 2.987709182 24.16298693 0.906356819 0.853698429 0.123208925 0.069779492 813.0265796 1598365.243 0.019364457 0.021540158 972.0960574 -2.987709182 -0.05265839 TAESQT(ph)PTPSATSFFSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 TAESQT(1)PTPSATSFFSGK;TAESQT(0.998)PT(0.001)PSATSFFSGK 401.24 8.07E-128 239850000 733390 744810 637450 870500 474210 694960 668590 688520 431240 TRUE FALSE 698724.1081 820706.9858 666677.713 782995.6862 556912.0739 670893.3609 566584.316 628229.5387 498114.4967 1.40273795 1.647627184 1.338402551 1.571919089 1.118040285 1.346865761 1.137457994 1.261215128 1 18.92611787 2.234509329 0.499969471 1.04524661 1.548123559 0.568204425 0.131116874 0.595051727 0.315495637 0.112764541 0.100203404 171.5968572 -2.234509329 0.502876949 TAESQTPTPSATSFFSGKS(ph)PVTTLLECMHK ddPTM_SK-BR-3_Trastuzumab_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 TAESQTPTPSATSFFSGKS(0.993)PVT(0.002)T(0.004)LLECMHK 242.39 6.86E-46 131720000 353130 334660 369550 422840 204680 401420 416280 455170 213970 TRUE FALSE 336438.2447 368762.2345 386494.233 380335.3199 240376.1272 387518.7247 352768.8405 415312.9018 247151.3748 1.361263902 1.492050104 1.563795602 1.538876003 0.972586648 1.567940802 1.427339179 1.680398914 1 17.91503541 TAFDDAIAELDTLNEDSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TAFDDAIAELDTLNEDSYK 19 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 259 1.10E-30 52083800 179665 188824 141852 207831 86816.2 166301 151207 168876 92292 FALSE TRUE 171172.5915 208065.3803 148356.0545 186939.433 101956.9178 160541.9547 128137.595 154088.3222 106604.172 1.605683796 1.95175645 1.391653363 1.753584588 0.956406451 1.50596315 1.201994187 1.445424877 1 16.70190437 2.760260706 24.7131075 1.25518311 1.698129203 0.513550833 0.217606498 530.5493057 604214.0744 0.060435844 0.064046114 575.7854768 -2.760260706 0.442946094 TAFDEAIAELDTLSEESYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 220.97 6.46E-19 97880000 182120 195550 148210 194550 90946 167760 147950 178520 93533 FALSE TRUE 173511.5485 215476.7673 155005.5751 174993.4644 106806.9536 161950.4291 125377.5102 162887.8424 108037.6199 1.60602898 1.994460517 1.434737041 1.619745645 0.988608909 1.499018853 1.160498633 1.507695583 1 16.72117424 3.241235208 1.69198315 1.263022491 1.785216513 0.463528897 0.224880138 0.263429535 1.559539563 0.065553817 0.093283603 1742.750467 -3.241235208 0.522194021 TAFQEALDAAGDKLVVVDFSATWCGPCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAFQEALDAAGDKLVVVDFSATWCGPCK 28 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ;;; 308.57 1.19E-82 1094974000 2404280 1764850 1929660 2404850 1475430 2271860 3015510 2639720 1988630 FALSE TRUE 2290634.449 1944690.221 2018136.82 2163109.909 1732744.525 2193184.919 2555438.566 2408572.123 2297016.584 0.997221555 0.846615664 0.878590444 0.941704089 0.754345675 0.954797163 1.112503316 1.048565404 1 21.13132984 1.972515341 7.969896851 1.05862485 0.8883124 0.568932556 0.067449592 0.169062792 42.408401 0.026630133 0.017286597 93.86751936 -1.972515341 -0.17031245 TAFYNEDDS(ph)EEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR 330.82 2.13E-68 1631330000 2099940 2127720 2026810 2338900 1624170 1900970 1933390 1988270 1451780 TRUE FALSE 2000679.998 2344537.087 2119741.243 2103789.328 1907424.734 1835138.932 1638415.846 1814166.538 1676914.628 1.193072065 1.398125491 1.264072248 1.25455959 1.137460848 1.094354418 0.977041895 1.081847882 1 20.67737781 2.511673561 1.389880475 1.017986274 1.297269316 0.797956112 0.057523344 0.163105826 0.638075132 0.02747365 0.021111625 324.8430363 -2.511673561 0.279283042 TAGAMQVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TAGAMQVEK 9 0 Q5M9N0 Q5M9N0 CCDC158 Coiled-coil domain-containing protein 158 0 ;; 75.378 0.02915 935211000 571718 461384 638272 487977 1942220 339152 798440 351711 2386890 FALSE TRUE 544694.0232 508399.5542 667537.4025 438924.6249 2280942.553 327407.0812 676623.3136 320913.3203 2757036.711 0.197565024 0.18440072 0.242121333 0.159201589 0.827316714 0.118753254 0.245416868 0.116397913 1 21.39468705 -1.550052004 2.962410925 1.034470801 0.256726781 0.55870013 0.206259097 62959967.96 68675252.49 17285170.83 0.048002124 0.028180455 1.550052004 -0.777744021 TAGTICLETFKDFPQMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAGTICLETFKDFPQMGR 18 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 ; 111.34 0.00028036 178132000 390710 452540 379190 417460 231378 418470 365400 351390 196165 FALSE TRUE 372241.9126 498654.3405 396576.2366 375496.1277 271730.2499 403978.279 309651.519 320620.4288 226585.2663 1.642833705 2.200735946 1.750229585 1.657195694 1.199240596 1.782897386 1.366600415 1.415010049 1 17.78969453 1.89202732 0.304087714 0.964926454 2.030966777 0.546122634 0.226226387 1.117750889 0.333411684 0.364202427 0.430839195 77.98791678 -1.89202732 1.066040323 TAHETDKSEGGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAHETDKSEGGKR 13 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 171.29 1.52E-05 354755000 335001 250459 290022 336738 197371 337399 400762 361456 199622 FALSE TRUE 319166.1666 275981.0568 303319.7956 302888.4565 231792.4399 325714.788 339618.3964 329804.9964 230578.3602 1.384198267 1.196907882 1.315473817 1.313603133 1.005265367 1.412599117 1.47289796 1.430338025 1 17.8148976 TAHSLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAHSLFK 7 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 91.041 0.016695 691780000 2983000 2659400 1700230 2246800 2291400 2292200 3204600 2553200 1904120 FALSE TRUE 2841999.502 2930395.883 1778187.227 2020947.395 2691019.435 2212820.539 2715679.413 2329628.273 2199401.205 1.292169658 1.33236077 0.808486975 0.918862548 1.22352367 1.006101358 1.234735803 1.059210238 1 21.06867937 3.7892452 24.99965497 1.057351372 1.312265444 0.440391051 0.127766293 328.2238827 161891.9661 0.033173045 0.059803463 6155.242958 -3.7892452 0.254914071 TAIHEVMEQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAIHEVMEQGR 11 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 77.744 0.024105 30330000 78267 62648 58177 74400 69760 56828 83024 79790 71700 FALSE TRUE 74567.47402 69031.90242 60844.47299 66921.17065 81926.12191 54860.03211 70357.16396 72803.16461 82818.86981 0.900368167 0.83352867 0.734669202 0.808042549 0.989220477 0.662409814 0.849530598 0.879064937 1 16.33767189 0.891610257 2.640123283 0.999492574 0.826394404 0.288829509 0.086997702 0.548797584 8.062928483 0.077363146 0.020622154 7.791305927 -0.891610257 -0.173098169 TAIT(ph)TPNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAITTPNFK 9 0 H0YMD2;Q9BXS6-7;Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6 H0YMD2 NUSAP1 Nucleolar and spindle-associated protein 1 1 TAIT(0.5)T(0.5)PNFK 113.22 0.0056455 0 397270 419260 384280 452650 301550 408340 467770 460210 388400 TRUE FALSE 378491.8344 461983.0707 401899.6181 407148.762 354140.2245 394199.0834 396403.0953 419911.5727 448631.0883 0.843659399 1.029761607 0.895835417 0.907535774 0.78937959 0.878670903 0.883583652 0.935984116 1 18.77517007 0.949502553 3.965260252 0.999898387 0.89706058 0.254553973 0.060287653 0.398386703 17.49937419 0.059413377 0.015209068 8.902306718 -0.949502553 -0.102837807 TAITT(ph)PNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAITTPNFK 9 0 H0YMD2;Q9BXS6-7;Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6 H0YMD2 NUSAP1 Nucleolar and spindle-associated protein 1 1 TAIT(0.038)T(0.962)PNFK 158.05 0.003323 0 370740 395330 417200 440030 309760 414620 470980 457080 380650 TRUE FALSE 353215.8549 435614.5765 436329.0327 395797.3484 363782.0459 400261.6054 399123.3509 417055.6521 439679.2579 0.803348915 0.990755349 0.992380297 0.900195634 0.827380504 0.910349074 0.907760245 0.948545206 1 18.74609195 0.976981624 2.454483198 0.999786833 0.906549994 0.21923397 0.059113868 0.499774975 6.834746094 0.056662563 0.015341744 9.483783333 -0.976981624 -0.09323684 TALAEAELEYNPEHVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TALAEAELEYNPEHVSR 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ;; 247.46 9.43E-21 439580000 462650 326296 399660 416460 517660 323051 517600 434120 535060 FALSE TRUE 440781.4514 359545.9334 417984.8063 374596.6496 607939.7401 311863.6629 438630.6136 396106.1514 618034.3721 0.713198928 0.58175718 0.676313204 0.606109735 0.983666552 0.504605693 0.709718801 0.640912819 1 19.23732755 -1.441701181 2.704820092 1.0100983 0.672717027 0.395146399 0.125474041 9102615.242 9683224.614 699066.8612 0.028021722 0.036165862 1.441701181 -0.337381273 TALIHDGLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;;; 197.21 3.19E-07 16188000000 10310890 8584940 8360050 9885950 8653240 9113220 10734130 9693490 8742660 FALSE TRUE 9823514.664 9459755.146 8743366.562 8892195.524 10162362.32 8797626.906 9096441.323 8844676.627 10098427.06 0.972776711 0.936755307 0.865814697 0.880552533 1.006331209 0.871187845 0.900778039 0.875846958 1 23.26762726 4.102275119 3.342277864 0.909126895 0.964283075 0.106750596 0.050810973 0.414248776 8.902422392 0.011958199 0.029290895 12655.37792 -4.102275119 0.05515618 TALINSTGEEVAMR ddPTM_SK-BR-3_Trastuzumab_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 ; 190.26 1.45E-06 114645000 57387 42603 52106 58323 53949 45190 59724 50695 59687 FALSE TRUE 54674.43024 46944.29414 54495.11164 52460.26123 63357.68852 43625.05897 50612.00689 46255.87705 68942.95512 0.793038682 0.680915027 0.790437711 0.760922724 0.918987131 0.632770366 0.734114266 0.670929712 1 16.07311552 -1.405197361 3.193214861 1.003204962 0.745276613 0.496970214 0.07971687 17245098.55 23452268.66 509953.0736 0.017896895 0.039337127 1.405197361 -0.257928349 TALPTSGSSAGELELLAGEVPARS(ph)PGAFDMSGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TALPTSGSSAGELELLAGEVPARSPGAFDMSGVR 34 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPT(0.002)S(0.002)GS(0.002)S(0.002)AGELELLAGEVPARS(0.991)PGAFDMS(0.002)GVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(0.982)PGAFDMS(0.018)GVR 286.97 8.10E-75 802688000 313952 201916 319986 321630 335626 269828 367363 287576 348054 TRUE FALSE 299112.1112 222491.47 334657.6746 289299.1413 394159.0681 260483.7887 311315.0273 262394.3209 402028.4367 0.744007348 0.55342222 0.832422894 0.719598702 0.980425841 0.647923791 0.774360714 0.652676022 1 18.61693803 -5 0.233341316 2.437123729 0.701557306 0.3092237 0.117478616 193.8312182 1.937163773 132.3321076 0.186923026 1.00E-05 5 -1.735566422 TAMLLALQRPELVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAMLLALQRPELVER 15 1 Q8NFV4;Q8NFV4-4 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 135.55 2.58E-05 548630000 429370 356040 442510 416640 839000 348800 457370 365060 734760 FALSE TRUE 409074.531 392320.8808 462799.5212 374758.5556 985321.3344 336720.9685 387589.8063 333093.4111 848702.8282 0.481999726 0.462259424 0.545302202 0.441566286 1.160973313 0.396747787 0.456684947 0.392473549 1 19.69489996 TAMPS(ph)PGVSQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAMPSPGVSQNK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 TAMPS(0.999)PGVS(0.001)QNK 135.02 0.00014178 81314000 127610 147160 122740 161640 85701 123380 128740 143550 87322 TRUE FALSE 121578.1282 162155.7713 128367.7504 145391.6401 100647.2273 119107.3197 109098.3485 130980.001 100863.4498 1.205373487 1.607676236 1.272688478 1.441470031 0.997856285 1.180876917 1.081644032 1.29858736 1 16.62204395 2.748189844 24.97122122 1.11957329 1.393782724 0.494768006 0.135212589 518.0130657 1343349.647 0.03823419 0.040086441 560.002343 -2.748189844 0.274209434 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.015)EPS(0.036)EPS(0.475)RPS(0.475)PQPKPR 172.1 5.31E-15 679290000 855140 883140 828860 941540 654650 915570 1101800 1018700 721970 TRUE FALSE 814719.2269 973132.97 866864.0509 846894.6104 768820.7527 883863.5813 933700.1741 929497.2275 833929.4203 0.976964246 1.166924858 1.039493307 1.015547107 0.921925446 1.059878162 1.119639326 1.114599395 1 19.66956576 -0.724182387 7.47094007 0.999999971 1.057375001 0.044602103 0.071523666 0 0 0.069911086 0.016478201 0.188719863 0.724182387 0.05737503 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.004)EPS(0.05)EPS(0.193)RPS(0.753)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.012)EPS(0.214)RPS(0.774)PQPKPR;TAPAAPAEDAVAAAAAAPS(0.022)EPS(0.083)EPS(0.234)RPS(0.662)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.039)EPS(0.039)RPS(0.922)PQPKPR 170.4 7.26E-15 2588860000 2576120 2561530 2647870 2840840 1783620 2933590 3342640 3249770 2276010 TRUE FALSE 2454351.913 2822552.819 2769277.459 2555273.366 2094682.763 2831999.043 2832658.876 2965202.911 2628962.007 0.933582116 1.073637737 1.053372948 0.971970443 0.79677179 1.077230875 1.077481861 1.127898731 1 21.32606186 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;TAPPALPT(0.04)GYDS(0.96)EEEEES(0.001)RPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK 233.33 4.43E-45 739510000 960180 1012250 804291 1086380 615093 992180 898260 929860 569252 TRUE FALSE 914794.1943 1115399.426 841168.5379 977175.0184 722365.0245 957820.5578 761213.9393 848436.5289 657528.6928 1.391261255 1.696350955 1.279287957 1.486132893 1.098606087 1.456697735 1.157689311 1.290341453 1 19.32669433 2.087174285 0.260240612 0.964789672 1.633388602 0.45258617 0.1506713 1.688241208 0.371741294 0.286537718 0.418464487 122.2290075 -2.087174285 0.66859893 TAPPALPTGYDS(ph)EEEEESRPMSYDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;TAPPALPT(0.003)GY(0.003)DS(0.385)EEEEES(0.32)RPMS(0.284)Y(0.005)DEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPT(0.189)GY(0.058)DS(0.749)EEEEES(0.003)RPMS(0.001)YDEKR 336.8 9.72E-96 3832639000 3722582 2741268 3348745 3392781 2571134 3322213 4182584 3786442 3191432 TRUE FALSE 3546622.926 3020606.326 3502288.271 3051732.208 3019538.956 3207163.931 3544453.992 3454881.065 3686342.975 0.962097925 0.819404582 0.950071194 0.827848149 0.819115035 0.870012354 0.961509555 0.937210967 1 21.81375887 1.714612438 5.244150161 0.962643814 0.873938435 0.411958875 0.051394216 0.159739465 10.6121245 0.02564491 0.012877784 51.83372707 -1.714612438 -0.088705379 TAPPAS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPPAS(1)PEAR 97.163 0.0065521 354430000 293500 286700 298710 335800 283240 285690 322080 339990 309440 TRUE FALSE 279626.8367 315915.056 312406.149 302044.746 332636.9663 275796.4837 272940.7806 310218.6732 357426.3748 0.782334087 0.883860504 0.874043358 0.845054443 0.930644714 0.771617606 0.76362798 0.867923285 1 18.44728657 -1.786009432 1.785160135 1.06811858 0.835827725 0.464959541 0.053821009 196655.2957 86333.46587 57961.83749 0.014958766 0.01636781 1.786009432 -0.232290856 TAPTALGITLSS(ph)SPTSTPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGIT(0.001)LS(0.053)S(0.529)S(0.417)PTSTPELR 133.16 1.09E-05 70870000 112180 81916 106450 105650 122360 105440 125120 115170 120600 TRUE FALSE 106877.4737 90263.33353 111330.8378 95029.86128 143699.5453 101788.5864 106030.646 105085.1042 139302.0321 0.767235568 0.647968534 0.799204693 0.68218575 1.031568191 0.730704246 0.761156492 0.754368782 1 17.08785678 -5 0.174226573 1.913210802 0.711446145 0.325389169 0.10244428 151.2248572 1.439556309 48.01117597 0.327031847 1.00E-05 5 -1.201764656 TAPTALGITLSSS(ph)PTSTPELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGITLSS(0.059)S(0.89)PT(0.039)S(0.01)T(0.002)PELR 171.04 7.79E-12 75899000 81405 65075 70985 87768 79085 76406 97748 89417 90838 TRUE FALSE 77557.14698 71706.21648 74239.73246 78945.39389 92877.39896 73760.04106 82834.74733 81587.17345 104924.6931 0.739169634 0.683406492 0.707552534 0.752400522 0.885181517 0.702980765 0.789468569 0.777578385 1 16.67899472 -5 0.16867298 1.98403463 0.68761584 0.696148218 0.052764329 71.57198901 0.672935164 23.49085615 0.185957686 1.00E-05 5 -1.29641879 TAPTLS(ph)PEHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPTLS(1)PEHWK;TAPT(0.002)LS(0.998)PEHWK;TAPT(0.003)LS(0.997)PEHWK;TAPTLS(1)PEHWK 228.7 1.98E-12 1784160000 1600160 1504920 1413470 1681440 1113260 1595490 1770990 1672120 1072900 TRUE FALSE 1524523.608 1658273.059 1478278.998 1512418.457 1307412.192 1540237.781 1500792.949 1525700.308 1239279.852 1.230168961 1.3380941 1.192853248 1.220401069 1.054977364 1.242849045 1.211020212 1.231118464 1 20.24107058 -5 0.148225442 0.235692157 1.292746213 0.485175652 0.069202609 114.7693776 1.015967832 26.02956577 0.359743365 1.00E-05 5 1.057054055 TAQALSSGSGS(ph)QETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TAQALSSGSGSQETK 15 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TAQALSSGSGS(1)QETK;TAQALSSGS(0.001)GS(0.999)QETK;TAQALSSGS(0.018)GS(0.982)QETK 251.35 1.81E-19 261543000 1074970 1027140 933660 1369880 616859 1206040 1113020 1147160 618036 TRUE FALSE 1024158.298 1131806.734 976469.2345 1232177.06 724439.0143 1164274.532 943208.357 1046708.589 713877.8664 1.434640779 1.58543469 1.367837946 1.726033426 1.014794054 1.630915577 1.321246114 1.466229222 1 19.44531775 -3.31967126 0.22585165 6.84E-13 1.515064068 0.343956228 0.193734665 68.31111371 1.350000453 32.30537328 0.312559081 0.000478993 3.31967126 1.515064068 TAQALSSGSGS(ph)QETKIPISLVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAQALSSGSGSQETKIPISLVLR 23 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TAQALSS(0.003)GS(0.014)GS(0.983)QETKIPISLVLR;TAQALSSGS(0.002)GS(0.998)QETKIPISLVLR 246.98 7.43E-38 1166610000 461620 330920 462440 496930 330210 539730 652890 575590 423230 TRUE FALSE 439800.1374 364641.1242 483643.3314 446977.6523 387798.5195 521039.0148 553279.6394 525188.2882 488862.3468 0.899640032 0.74589734 0.989324162 0.91432211 0.793267311 1.065819485 1.131769798 1.074307096 1 18.89906876 2.187346829 7.814270106 1.085368424 0.862311275 0.642657524 0.073355194 0.136507993 17.96056585 0.027047072 0.020036033 153.9383507 -2.187346829 -0.223057149 TAQEVETYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TAQEVETYRR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 119.74 0.0010452 579160000 739830 549870 659580 680170 634730 660130 864830 732740 726340 FALSE TRUE 704859.7021 605902.3782 689822.3954 611798.0194 745426.711 637269.5326 732884.2998 668577.4011 838977.0976 0.840141768 0.722191797 0.822218386 0.729218975 0.888494708 0.759579176 0.873545061 0.79689589 1 19.6782719 -1.316316624 0.287995706 1.140930297 0.776367297 0.560513368 0.05504894 12.37884988 0.753170373 1.369201513 0.057219077 0.048270675 1.316316624 -0.364563 TAQVPS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;TAQVPS(1)PPR;TAQVPS(1)PPR 130.36 0.00038116 8931880000 2918737 2841844 2519534 3275932 2107657 2873939 2696854 2875958 2085205 TRUE FALSE 2780774.086 3131431.135 2635057.126 2946629.091 2475231.713 2774413.772 2285399.391 2624123.871 2408567.942 1.15453421 1.30012157 1.094034792 1.223394632 1.027677763 1.151893506 0.948862331 1.089495474 1 21.19974419 2.628848027 0.899783294 1.01354823 1.218806106 0.468960993 0.07614327 0.41361224 0.698150613 0.04332715 0.035801115 425.4495091 -2.628848027 0.205257876 TAQVPS(ph)PPRGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK;TAQVPS(1)PPRGK 124.21 0.0009311 12799280000 5911270 3255890 5855430 4934220 4509770 5621920 7468460 6212650 5754290 TRUE FALSE 5631855.982 3587668.893 6123907.257 4438222.831 5296272.46 5427231.501 6329009.259 5668637.431 6646635.904 0.84732428 0.539772141 0.921354403 0.667739725 0.796835051 0.816538107 0.95221242 0.852858124 1 22.6641929 1.943931906 0.812709182 0.971298512 0.719926463 0.368568542 0.107336628 0.56850178 0.700666902 0.085650494 0.042220334 87.8884703 -1.943931906 -0.251372049 TARPFGIQAPGGTSQMERS(ph)PMLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TARPFGIQAPGGTSQMERSPMLER 24 2 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 TARPFGIQAPGGT(0.001)S(0.018)QMERS(0.981)PMLER 155.15 2.53E-08 304680000 74365 63845 72188 59509 70348 70973 92172 62824 99382 TRUE FALSE 70849.91383 70350.87809 75497.8912 53527.04226 82616.66893 68515.18721 78109.46855 57322.79751 114793.653 0.617193651 0.61284641 0.657683498 0.466289214 0.719697185 0.596855187 0.680433687 0.499355113 1 16.80868335 -1.330742606 3.512355 1.001717233 0.61288959 0.723077621 0.076473626 20801817 31131270.54 372618.9814 0.016016371 0.046693604 1.330742606 -0.388827643 TAS(ph)APAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASAPAK 7 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8;Q4KWH8-3;Q4KWH8-4 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 TAS(1)APAK;TAS(1)APAK 82.287 0.026118 195562000 754320 657880 677540 826880 466660 721620 777170 869790 625650 TRUE FALSE 718664.7885 724918.7199 708605.8792 743760.4514 548045.3562 696630.1185 658598.4428 793626.5766 722672.6066 0.994454172 1.003108065 0.980535131 1.029180357 0.758359112 0.963963643 0.911337218 1.098182731 1 19.46298268 1.241188133 24.99984514 1.049091368 0.953189735 0.219116802 0.078431544 103.8292563 987977.8934 0.056801435 0.018584743 17.42561573 -1.241188133 -0.095901634 TAS(ph)EINFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TASEINFDK 9 0 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 T(0.001)AS(0.999)EINFDK;T(0.003)AS(0.997)EINFDK;TAS(1)EINFDK;TAS(1)EINFDK 159.44 6.93E-05 161572000 379507 416255 336330 491748 249201 404523 382018 438097 222348 TRUE FALSE 361568.4562 458671.8577 351751.0632 442316.5568 292661.5755 390514.2671 323734.1379 399734.9042 256828.5922 1.407820107 1.785906521 1.369594639 1.722224745 1.139521005 1.52052489 1.260506609 1.556426801 1 17.9704463 -3.207400559 0.135913264 2.11E-11 1.704147788 0.37346404 0.193366842 71.47509193 0.969375576 21.7733437 1.271498649 0.000620297 3.207400559 1.704147788 TAS(ph)EINFDKLQFEPPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASEINFDKLQFEPPLR 17 1 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 T(0.097)AS(0.903)EINFDKLQFEPPLR 70.917 0.019148 40196000 54306 48736 49773 59356 43898 49120 54759 61458 48361 TRUE FALSE 51739.063 53702.25381 52055.14128 53389.42211 51553.7973 47418.96208 46404.50883 56076.41171 55860.57689 0.926217842 0.96136232 0.931876185 0.955762097 0.922901269 0.848880637 0.830720186 1.003863813 1 15.76954285 2.472041426 24.71913934 0.895213534 0.943635881 0 0.057729413 239.1410978 1163677.253 0.018845412 0.015816948 296.511421 -2.472041426 0.048422347 TAS(ph)FGNILDVPEIVISGNGQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.109)AS(0.891)FGNILDVPEIVISGNGQPR;T(0.105)AS(0.895)FGNILDVPEIVISGNGQPR 188.69 2.51E-17 99585000 224700 219190 208910 233580 171585 211040 245330 249930 222580 TRUE FALSE 214078.8763 241525.7102 218488.7301 210100.0946 201509.3697 203731.6319 207900.4027 228044.8042 257096.5696 0.832678851 0.939435756 0.849831371 0.817203026 0.783788636 0.792432323 0.808647128 0.887000572 1 17.97195084 0.929120351 5.0607906 0.999970512 0.838055693 0.602539404 0.04318935 0.33830681 21.72750711 0.048176142 0.012174829 8.494158319 -0.929120351 -0.161914819 TAS(ph)FSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(1)FSESR;TAS(0.997)FS(0.003)ESR;TAS(0.979)FS(0.021)ESR;T(0.001)AS(0.837)FS(0.162)ESR;TAS(1)FSESR;TAS(1)FSESR 218.93 7.03E-06 26467500000 21664200 21262400 18592900 26291800 17255200 24363300 24624400 21417000 16789600 TRUE FALSE 20640176.2 23429062.73 19445402.86 23648898.31 20264501.42 23519592.81 20867495.52 19541613.94 19393245.42 1.064297169 1.208104277 1.002689464 1.219439955 1.044925745 1.212772401 1.076018741 1.007650526 1 24.20905092 1.382807058 3.796494467 1.004307394 1.127036017 0.312180553 0.073711141 0.24305852 5.661067815 0.048408892 0.016326601 24.14387966 -1.382807058 0.122728622 TAS(ph)FSESRADEVAPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.003)AS(0.996)FS(0.001)ESRADEVAPAK;T(0.001)AS(0.998)FS(0.001)ESRADEVAPAK;T(0.001)AS(0.999)FSESRADEVAPAK;T(0.012)AS(0.988)FSESRADEVAPAK;T(0.017)AS(0.981)FS(0.002)ESRADEVAPAK;T(0.035)AS(0.959)FS(0.006)ESRADEVAPAK 252.33 4.17E-26 1919990000 1914970 1349050 1892170 2072380 1455640 2167910 2665430 2284640 1811850 TRUE FALSE 1824453.163 1486519.729 1978927.866 1864060.425 1709503.155 2092834.733 2258769.7 2084584.81 2092822.444 0.871766818 0.710294241 0.94557848 0.890692103 0.816840989 1.000005872 1.079293518 0.996063864 1 20.99701849 2.171835248 4.844776161 1.034613724 0.836947484 0.634323498 0.064475957 0.122224542 5.524780323 0.025312083 0.018631084 148.5372053 -2.171835248 -0.197666241 TAS(ph)FSESRADEVAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.004)AS(0.968)FS(0.028)ESRADEVAPAKK;T(0.001)AS(0.959)FS(0.04)ESRADEVAPAKK;T(0.001)AS(0.997)FS(0.002)ESRADEVAPAKK;T(0.124)AS(0.786)FS(0.089)ES(0.001)RADEVAPAKK;T(0.007)AS(0.962)FS(0.031)ESRADEVAPAKK;T(0.032)AS(0.95)FS(0.018)ESRADEVAPAKK 215.98 2.84E-15 8391070000 3849492 2024963 3718150 3456090 2633168 4243080 5757670 4436610 3412710 TRUE FALSE 3667534.142 2231309.032 3888630.855 3108677.267 3092391.666 4096141.076 4879231.695 4048116.908 3941935.637 0.930389149 0.566044004 0.986477511 0.788616952 0.78448558 1.039119218 1.237775586 1.026936328 1 21.91047279 2.15701697 4.228943537 1.119272747 0.794995203 0.511500844 0.127123525 0.145702107 4.909548825 0.0473742 0.034396613 143.5545525 -2.15701697 -0.324277544 TAS(ph)GSS(ph)VTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 T(0.038)AS(0.883)GS(0.366)S(0.664)VT(0.041)S(0.007)LDGTR;TAS(1)GSS(0.947)VT(0.053)SLDGTR;TAS(1)GS(0.01)S(0.979)VT(0.011)SLDGTR 244.05 2.11E-17 1233190000 2091930 1984510 2067030 2590530 1760510 2468030 2600740 2465360 1851560 TRUE FALSE 1993048.615 2186733.825 2161805.37 2330125.003 2067542.387 2382561.502 2203949.347 2249480.009 2138690.468 0.931901387 1.022463913 1.01080797 1.089510164 0.966732876 1.114028204 1.030513475 1.051802513 1 21.02829627 4.734406922 0.939728881 1.044082269 0.868597367 0.380478586 0.042081503 1.776080588 1.23996718 0.011777902 0.319195143 54250.89688 -4.734406922 -0.175484902 TAS(ph)GSSVT(ph)SLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(1)GS(0.001)S(0.003)VT(0.898)S(0.098)LDGTR 213.55 4.65E-09 192450000 500650 407780 444410 528450 370020 539620 573980 537430 474000 TRUE FALSE 476985.2667 449333.2456 464786.6381 475329.202 434551.3708 520932.8241 486408.8091 490369.7801 547505.4991 0.871197216 0.820691749 0.84891684 0.868172471 0.793693162 0.951465921 0.888408993 0.89564357 1 19.06251393 0.911725301 0.468608067 1.003994518 0.839285309 0.602772263 0.037543806 0.769039626 0.417387065 0.045489493 0.021255033 8.160660312 -0.911725301 -0.164709208 TAS(ph)GSSVTS(ph)LDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(0.993)GS(0.007)S(0.002)VT(0.099)S(0.899)LDGTR 162.86 6.39E-06 188580000 474170 428970 457190 574010 399360 528670 605680 563150 476140 TRUE FALSE 451756.9238 472682.5307 478152.6137 516309.4243 469008.2576 510362.0253 513272.3919 513837.6006 549977.3594 0.821410038 0.859458162 0.869404177 0.938783052 0.852777391 0.927969155 0.933260948 0.934288643 1 19.0690127 8 0.092496008 1.073383877 0.355748323 0.790373784 0.024322825 55.87761945 0.370174327 0.3626906 5.086533769 100000000 -8 -0.717635553 TAS(ph)GSSVTSLDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TAS(0.856)GS(0.144)S(0.001)VTSLDGTR;TAS(0.808)GS(0.192)SVTSLDGTR;T(0.001)AS(0.981)GS(0.017)S(0.001)VTSLDGTR;TAS(0.992)GS(0.008)SVTSLDGTR;TAS(0.994)GS(0.006)SVTSLDGTR;T(0.002)AS(0.874)GS(0.125)SVTSLDGTR;TAS(1)GSSVTSLDGTR;TAS(0.985)GS(0.008)S(0.008)VTSLDGTR;TAS(0.993)GS(0.007)SVTSLDGTR;TAS(1)GSSVTSLDGTR 393.16 3.73E-114 34912930000 7979320 6784660 7188740 8172880 6502760 7839120 8766730 8143060 7211770 TRUE FALSE 7602153.357 7476024.568 7518350.84 7351326.575 7636839.285 7567649.309 7429204.326 7430010.497 8330134.459 0.912608721 0.897467454 0.902548557 0.882497949 0.916772631 0.908466646 0.891846868 0.891943646 1 22.98990835 -1.548760857 3.04893937 1.004180352 0.900672597 0.901547709 0.01033133 2039832.273 2822887.051 71517.07152 0.002455009 0.028264359 1.548760857 -0.103507755 TAS(ph)LPGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TASLPGYGR 9 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR 210.64 6.77E-06 1063360000 1494610 1376800 1396510 1585060 1290050 1508140 1599680 1545480 1289800 TRUE FALSE 1423962.747 1517097.485 1460541.365 1425726.757 1515034.312 1455912.734 1355619.436 1410149.578 1489815.597 0.955797986 1.018312259 0.980350433 0.956982032 1.016927407 0.977243584 0.909924315 0.946526256 1 20.50670234 1.975843098 23.20873124 0.942502298 0.986797771 0.183453204 0.030140401 340.1491548 326796.9209 0.011323304 0.007363726 94.58953666 -1.975843098 0.044295473 TAS(ph)NPKVENEDEPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 T(0.017)AS(0.983)NPKVENEDEPVR;T(0.144)AS(0.856)NPKVENEDEPVR;T(0.022)AS(0.978)NPKVENEDEPVR 242.45 3.81E-18 883530000 1461730 1349750 1370840 1639820 801520 1582190 1697430 1734750 913630 TRUE FALSE 1392636.92 1487291.06 1433694.37 1474982.178 941304.8342 1527398.364 1438455.878 1582846.094 1055311.074 1.319645888 1.409339005 1.358551431 1.397675258 0.891969067 1.447344201 1.363063378 1.499885799 1 20.00923689 TAS(ph)PLPLRPDAPVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TASPLPLRPDAPVEK 15 1 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 T(0.004)AS(0.996)PLPLRPDAPVEK;T(0.015)AS(0.985)PLPLRPDAPVEK;T(0.001)AS(0.999)PLPLRPDAPVEK;T(0.013)AS(0.987)PLPLRPDAPVEK;T(0.002)AS(0.998)PLPLRPDAPVEK;T(0.026)AS(0.974)PLPLRPDAPVEK 182.64 3.26E-07 1654477000 4118020 3838590 3663800 4540970 2545600 4278860 4407620 4614270 2925130 TRUE FALSE 3923369.356 4229746.685 3831788.854 4084503.068 2989551.834 4130682.005 3735156.618 4210220.057 3378744.221 1.161191585 1.251869455 1.134086691 1.208881999 0.884811527 1.222549484 1.105486646 1.246090199 1 21.68805571 0.333040722 0.017700624 6.53E-07 2.188557989 0.125007395 0.108684914 1555.176619 10.44194024 676.8912024 612.5585342 2.1529836 -0.333040722 2.188557336 TAS(ph)PLPLRPDAPVEKS(ph)PEETATQVPSLESLTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASPLPLRPDAPVEKSPEETATQVPSLESLTLK 33 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 2 T(0.1)AS(0.9)PLPLRPDAPVEKS(0.999)PEET(0.001)ATQVPSLESLTLK 309.99 2.14E-104 126220000 93010 91148 90272 103390 45237 110750 107890 116120 45819 TRUE FALSE 88613.60163 100436.0848 94411.06049 92997.04077 53126.31848 106914.6997 91429.39896 105951.9172 52924.37651 1.674343799 1.897728258 1.783886117 1.757168377 1.00381567 2.02014094 1.727547966 2.001949276 1 15.69164475 2.97529297 24.96234539 1.618521392 1.790675249 0.077284889 0.350503333 2394.722512 2419471.296 0.099515094 0.106027144 944.6979431 -2.97529297 0.172153858 TAS(ph)PPGPPPYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TASPPGPPPYGK 12 0 P54259 P54259 ATN1 Atrophin-1 1 T(0.002)AS(0.998)PPGPPPYGK;TAS(1)PPGPPPYGK;T(0.01)AS(0.99)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK 173.72 4.73E-05 969160000 1498470 1270090 1320890 1500210 1002760 1442600 1646890 1522500 1119790 TRUE FALSE 1427640.293 1399513.615 1381454.113 1349406.041 1177641.027 1392642.4 1395626.683 1389181.829 1293441.314 1.103753435 1.082007819 1.068045452 1.043268083 0.91047117 1.076695467 1.07900271 1.074019991 1 20.30278317 3.485527722 2.497873668 1.035537019 1.093142484 0.216260655 0.049700763 0.482968604 6.028021232 0.01493123 0.02351048 3058.635482 -3.485527722 0.057605465 TAS(ph)PPPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;TAS(1)PPPPPK;T(0.01)AS(0.99)PPPPPK;T(0.002)AS(0.998)PPPPPK;TAS(1)PPPPPK;T(0.094)AS(0.906)PPPPPK;T(0.01)AS(0.99)PPPPPK 142.83 0.00010846 6517744000 6698450 5408930 5797850 6794880 4340060 6429760 7134810 6638840 4708050 TRUE FALSE 6381827.544 5960106.116 6063687.157 6111845.753 5096965.09 6207095.799 6046263.695 6057507.975 5438150.349 1.173529074 1.095980386 1.115027494 1.123883188 0.93726079 1.141398343 1.111823563 1.113891229 1 22.37468461 6.372914751 0.011887268 6.03E-08 2.314459195 0.231827367 0.061215725 10580.19602 12.99366933 1107.625247 1441.337921 2360014.933 -6.372914751 2.314459134 TAS(ph)PPPPPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.041)AS(0.959)PPPPPKR;T(0.027)AS(0.973)PPPPPKR;T(0.027)AS(0.973)PPPPPKR;T(0.001)AS(0.999)PPPPPKR;T(0.026)AS(0.974)PPPPPKR;T(0.118)AS(0.882)PPPPPKR;T(0.006)AS(0.994)PPPPPKR;T(0.051)AS(0.949)PPPPPKR;T(0.023)AS(0.977)PPPPPKR 121.02 0.00032222 13068630000 5262660 4546970 4777810 5318510 3536540 5151980 5734120 5368760 3869380 TRUE FALSE 5013904.491 5010311.412 4996877.314 4783883.27 4153311.456 4973565.641 4859274.68 4898642.913 4469423.688 1.121823492 1.121019568 1.118013789 1.070357971 0.929272261 1.112797977 1.087226233 1.096034579 1 22.09165738 3.190277782 4.811104032 1.053883328 1.120974541 0.289606302 0.052580609 0.273112264 13.60152436 0.015218449 0.018812021 1549.807583 -3.190277782 0.067091213 TAS(ph)PWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 89.752 0.052248 735180000 3335600 3161500 3088400 3562600 1963790 3431600 3572200 3766000 2305700 TRUE FALSE 3177932.799 3483660.444 3230006.195 3204480.68 2306274.354 3312762.832 3027195.282 3436229.075 2663256.18 1.193250887 1.308045569 1.212803417 1.203219091 0.865960388 1.243876896 1.136651932 1.290236028 1 21.34475978 -4.99987461 0.027447623 6.77E-06 1.900628901 0.147770188 0.124715661 3065.455242 6.342304264 330.0009026 144.3596916 1.00E-05 4.99987461 1.900622136 TAS(ph)TDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASTDLK 7 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 TAS(0.972)T(0.028)DLK;TAS(0.997)T(0.003)DLK 146.79 0.002303 554340000 2972300 2411300 2435900 3510600 1544390 3023600 3107800 3227700 1649780 TRUE FALSE 2831805.27 2657014.211 2547588.424 3157707.818 1813731.127 2918891.974 2633648.031 2945065.477 1905619.456 1.486028735 1.394304725 1.336882039 1.657050576 0.951780336 1.53172868 1.382043 1.545463585 1 20.86182862 -1.681309778 2.735328271 0.945115665 1.408589727 0.321455024 0.187484179 16315397.13 14815990.9 6236419.231 0.040482499 0.020830046 1.681309778 0.463474062 TAS(ph)TPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Trastuzumab_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 1 T(0.115)AS(0.479)T(0.399)PT(0.007)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.065)AS(0.529)T(0.405)PT(0.001)PPQTGGGLEPQANGETPQVAVIVRPDDR 151.72 6.81E-11 360229000 52516.5 50909.5 52647.5 50608.6 49053.3 51940.8 56282.3 58384.9 54027 TRUE FALSE 50034.14912 56097.23593 55061.43995 45521.32738 57608.17999 50142.07707 47695.40144 53272.40864 62405.23123 0.801762098 0.898918806 0.882320903 0.729447299 0.923130623 0.803491568 0.764285309 0.853652932 1 15.92937935 0.96609253 23.26101436 1.000000002 0.829848612 0.443529222 0.059710489 1930.688995 1324482.663 0.055127291 0.013781823 9.248952092 -0.96609253 -0.170151389 TASESISNLS(ph)EAGS(ph)IKKGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASESISNLSEAGSIKKGER 20 2 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 2 TASESISNLS(0.999)EAGS(1)IKKGER;TASESISNLS(1)EAGS(1)IKKGER 90.694 0.0010192 141059000 188699 123949 164104 168944 110595 185915 217672 198359 124684 TRUE FALSE 179779.5722 136579.544 171628.3307 151961.4281 129882.733 179476.7169 184462.1386 180989.6344 144019.3579 1.248301442 0.94834157 1.191703207 1.055145852 0.901842189 1.246198563 1.280814894 1.256703522 1 17.13590321 2.148342059 23.92425883 1.22688228 1.073767939 0.179292025 0.127216388 18.58867375 4922.191727 0.04414804 0.032605499 140.7155392 -2.148342059 -0.15311434 TASESISNLSEAGS(ph)IK ddPTM_SK-BR-3_Trastuzumab_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 353.41 2.74E-87 685780000 1261250 1239420 1010740 1342070 503690 1177620 1159180 1285580 580921 TRUE FALSE 1201633.212 1365718.307 1057083.429 1207162.574 591533.3765 1136838.724 982325.8012 1173007.8 671007.2617 1.790790176 2.035325674 1.575368091 1.799030566 0.88156032 1.694227155 1.463957035 1.748129814 1 19.35596885 3.291420946 1.905618839 1.427810491 1.897890698 0.309431255 0.299979872 0.368690619 2.751157685 0.086256881 0.124664564 1956.234643 -3.291420946 0.470080207 TASFS(ph)ESRADEVAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(0.318)FS(0.617)ES(0.065)RADEVAPAKK 181.61 6.25E-10 187120000 291540 160220 301510 267150 218150 351760 486940 381020 297550 TRUE FALSE 277759.482 176546.6002 315334.5317 240295.5744 256195.2909 339578.463 412648.3597 347655.8689 343692.5343 0.808162687 0.513675982 0.917490199 0.699158551 0.745420006 0.988029791 1.200632305 1.011531628 1 18.39075899 2.168453444 3.405717554 1.093544077 0.716474466 0.649784902 0.114617873 0.126920367 2.958644281 0.04481337 0.031851819 147.3850538 -2.168453444 -0.377069611 TASFSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 140.09 0.0015242 387780000 484800 370190 376750 449280 405710 421480 529810 469190 474600 FALSE TRUE 461884.4648 407912.7819 394024.3602 404117.5208 476465.6955 406884.0419 448977.7539 428105.2363 548198.5441 0.842549601 0.744096799 0.718762143 0.737173648 0.86914805 0.742220216 0.819005739 0.780930998 1 19.06433897 -1.372351032 0.450699949 1.117269635 0.774783708 0.665469481 0.048775527 16.29498723 1.71955765 2.286526153 0.02513842 0.042427649 1.372351032 -0.342485928 TASFSESRADEVAPAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 84.559 0.0029547 89987000 85536 40602 108650 54439 92854 81812 145550 101090 156270 FALSE TRUE 81492.8828 44739.38996 113631.71 48966.68829 109047.7082 78978.82993 123343.6743 92238.02369 180503.5535 0.451475227 0.247858777 0.629526166 0.271278251 0.604130534 0.437547231 0.683331003 0.511003922 1 17.46166771 -0.938258531 0.200665122 1.4274178 0.293832161 0.640447911 0.129679043 9.75924033 0.450652049 2.637700736 0.341977926 0.115276682 0.938258531 -1.133585639 TASGSS(ph)VTS(ph)LDGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(0.002)GS(0.111)S(0.882)VT(0.061)S(0.944)LDGTR;TAS(0.005)GS(0.128)S(0.855)VT(0.246)S(0.767)LDGTR 122.63 0.00015733 295300000 767610 583080 678220 1100760 644500 844440 985360 863920 712810 TRUE FALSE 731326.5966 642496.5149 709317.0579 990109.5135 756900.5959 815196.8311 835025.2346 788270.5849 823348.9343 0.888234096 0.780345353 0.86150237 1.202539376 0.919295045 0.990098848 1.014181473 0.957395525 1 19.65114445 3.448937537 24.9974355 1.010602958 0.83206198 0.518650904 0.077734103 141.0467995 125100.4773 0.019506915 0.026412937 2811.496433 -3.448937537 -0.178540978 TASLVS(ph)GLLNELYSCTEEEEAAGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TASLVSGLLNELYSCTEEEEAAGGGR 26 0 Q9Y2I9 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.231)AS(0.231)LVS(0.539)GLLNELYSCTEEEEAAGGGR 148.09 1.15E-07 84559000 73418 57469 71181 70008 72909 68079 76772 59010 79884 TRUE FALSE 69947.67664 63325.15644 74444.71926 62970.66283 85624.30652 65721.40716 65059.02139 53842.77157 92272.00273 0.758059591 0.686287872 0.806796396 0.68244604 0.927955436 0.712257296 0.705078675 0.583522303 1 16.49360535 -1.938234996 2.558478241 1.185111694 0.733624281 0.467164325 0.089677073 21056526.41 10549029.88 23240389.3 0.021426783 0.011528293 1.938234996 -0.451487413 TAST(ph)PTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Trastuzumab_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(0.008)T(0.986)PT(0.007)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.009)T(0.981)PT(0.011)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.028)T(0.971)PT(0.001)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.005)T(0.995)PTPPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.005)T(0.989)PT(0.007)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.023)AS(0.119)T(0.855)PT(0.003)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.008)AS(0.15)T(0.767)PT(0.07)PPQT(0.003)GGGLEPQANGETPQVAVIVRPDDR 223.55 3.75E-36 3601930000 65675.5 68872.6 71675.6 84709.8 66197.1 64831.9 84170.1 66459.7 64984.7 TRUE FALSE 62571.14927 75890.79624 74961.99716 76194.60997 77741.85328 62586.75505 71328.40536 60640.13634 75062.19538 0.833590717 1.011038857 0.998665131 1.01508635 1.035699168 0.833798622 0.950257383 0.807865211 1 16.19579887 2.238930732 24.99999312 0.897736181 0.972558638 0.213881696 0.076485932 17.01856211 1149640.426 0.02681866 0.02115745 173.3527484 -2.238930732 0.074822457 TATAVAHCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TATAVAHCK 9 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;; 123.35 0.001711 393740000 3296400 2759110 2279270 2814970 2206490 2695230 3278700 2811550 2145450 FALSE TRUE 3140585.705 3040266.446 2383776.784 2532003.868 2591301.157 2601893.509 2778474.098 2565355.777 2478155.429 1.2673078 1.226826377 0.961915769 1.021729242 1.045657237 1.049931525 1.121186373 1.035187603 1 21.24083524 3.833093283 6.1204357 1.04460606 1.251055947 0.815877288 0.041983904 0.093111827 4.973308376 0.011457971 0.02087646 6809.15598 -3.833093283 0.206449888 TATESFASDPILYRPVAVALDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 280.2 5.90E-52 1479257000 3582630 3405230 2914410 3955330 2170040 3429110 3513850 3687190 2202080 FALSE TRUE 3413286.18 3752226.808 3048038.581 3557732.714 2548494.289 3310359.061 2977747.646 3364320.097 2543567.32 1.341928776 1.475182819 1.198332184 1.398717732 1.001937031 1.30146312 1.170697399 1.322677828 1 21.27842185 7.999999922 0.051063634 0.525540416 2.654316837 0.368413226 0.124824815 419.1665861 1.614129381 15.5873462 69.79460074 99999982.13 -7.999999922 2.128776421 TATESFASDPILYRPVAVALDTKGPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TATESFASDPILYRPVAVALDTKGPEIR 28 2 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 302.05 7.03E-72 2233250000 3675300 1637590 3539300 2841800 3129500 3456200 5329700 4032300 4049600 FALSE TRUE 3501575.853 1804462.283 3701580.406 2556136.865 3675283.809 3336510.927 4516556.378 3679210.435 4677591.286 0.748585252 0.385767412 0.791343275 0.546464346 0.78572145 0.713296807 0.965573113 0.786560905 1 22.15733438 2.144267245 0.801946934 0.952243621 0.586484647 0.476426419 0.12958592 0.47192392 0.571340792 0.097474529 0.054667445 139.4014352 -2.144267245 -0.365758975 TATPPGYKPGS(ph)PPSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 TATPPGYKPGS(0.998)PPS(0.002)FR;TATPPGYKPGS(0.997)PPS(0.003)FR 141.83 9.49E-07 1080900000 1870400 1611660 1655910 1910960 1164820 1735300 1962970 1922760 1398860 TRUE FALSE 1781989.899 1775889.986 1731835.111 1718866.67 1367964.239 1675206.126 1663482.874 1754392.941 1615788.064 1.10286116 1.099085966 1.071820711 1.063794633 0.846623557 1.036773425 1.029517986 1.085781595 1 20.62380655 2.985759575 24.85853538 1.001773152 1.091243715 0.328267433 0.061192295 722.8489553 1261831.449 0.018034577 0.019864616 967.7419671 -2.985759575 0.089470563 TATPQQAQEVHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TATPQQAQEVHEK 13 0 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ;;;;;;; 229.9 5.00E-12 11364960000 13900190 8762430 10835300 12751160 9346110 11979370 15722130 13514140 9978020 FALSE TRUE 13243155.57 9655331.579 11332109.22 11469389.17 10976068.62 11564521.41 13323430.31 12330770.26 11525360.38 1.149044813 0.837746609 0.983232528 0.995143648 0.9523406 1.003397814 1.156009866 1.069881535 1 23.45830853 1.925277 7.578485363 1.090202 0.979074019 0.195186316 0.083493397 0.383218958 34.63050076 0.034216199 0.021380336 84.19319681 -1.925277 -0.111127981 TAVIPINGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 123.95 0.00037696 1241453000 2334117 2480340 2311766 2658668 2210697 2498940 2771612 2633817 2531444 TRUE FALSE 2223787.915 2733089.466 2417762.758 2391413.642 2596241.857 2412401.081 2348751.685 2403186.021 2924007.407 0.760527456 0.934706752 0.826866154 0.817854851 0.887905363 0.82503248 0.803264615 0.821880962 1 21.47951554 -1.562072055 2.627769253 1.011497004 0.837156323 0.548135747 0.047106195 6123392.566 5806416.33 493677.0261 0.011943443 0.027411193 1.562072055 -0.174340682 TAWLDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TAWLDGK 7 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 111.82 0.015108 573620000 2890450 2326870 2271270 2787900 2169220 2711640 3529610 2975450 2620130 FALSE TRUE 2753824.157 2563980.698 2375409.976 2507654.995 2547531.281 2617735.227 2991103.169 2714903.824 3026446.379 0.909920022 0.847191847 0.78488421 0.828580679 0.841756622 0.864953447 0.988321878 0.897059946 1 21.52919336 1.843766288 5.251432239 0.957525429 0.846724993 0.646992001 0.040381392 0.150615039 5.831084037 0.01882053 0.010964263 69.78567576 -1.843766288 -0.110800436 TCAYTNHTVLPEALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TCAYTNHTVLPEALER 16 0 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 154.51 3.48E-07 616720000 1007740 769290 872880 1014750 770010 924780 1053760 984060 858260 FALSE TRUE 960106.1273 847681.5256 912902.4114 912745.4021 904299.5002 892754.6367 892989.5584 897890.4896 991354.5774 0.968479038 0.855074002 0.920863667 0.920705288 0.912185731 0.900540187 0.900777158 0.905720829 1 19.91904163 -2.215793323 2.208179717 1.273677216 0.908659044 0.506867203 0.027674626 3286655.106 678731.2885 4482504.797 0.006426553 0.006084245 2.215793323 -0.365018172 TCDISFSDPDDLLNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TCDISFSDPDDLLNFK 16 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 194.24 5.69E-10 103297000 329110 290151 298541 331460 235557 330146 343600 361090 268458 FALSE TRUE 313553.6225 319717.7168 312229.4001 298141.0111 276638.0662 318712.9612 291177.5094 329471.0453 310089.0955 1.011172682 1.031051144 1.006902225 0.961468866 0.892124458 1.027810929 0.939012411 1.062504455 1 18.24232327 3.393269103 4.95921605 0.974278768 1.020836394 0.111243607 0.046763707 0.338261442 14.54165778 0.012017019 0.01650067 2473.25618 -3.393269103 0.046557626 TCEEHQLCVVAVLPHILDTGAAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TCEEHQLCVVAVLPHILDTGAAGR 24 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;; 218 6.97E-33 575546000 368352 284359 309317 322667 324589 298071 392661 331098 305970 FALSE TRUE 350940.731 313335.5054 323499.4904 290231.9001 381197.2188 287748.7265 332753.3527 302105.3039 353418.2649 0.992989796 0.886585489 0.915344572 0.821213641 1.078600787 0.81418748 0.941528454 0.854809538 1 18.43101708 TCEERPAEDGS(ph)DEEDPDS(ph)MEAPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TCEERPAEDGSDEEDPDSMEAPTR 24 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 2 TCEERPAEDGS(1)DEEDPDS(0.999)MEAPT(0.001)R;TCEERPAEDGS(1)DEEDPDS(1)MEAPTR 152.02 6.62E-08 261050000 276120 246901 257160 279780 249649 267545 285430 267060 306830 TRUE FALSE 263068.3548 272060.4926 268951.0404 251655.9829 293187.7066 258279.8496 241882.4112 243674.8106 354411.6293 0.742267841 0.767639857 0.758866296 0.710066945 0.827251936 0.7287567 0.682490052 0.687547446 1 18.43506642 -1.211099677 6.630800467 1.000001534 0.73882394 0.794223462 0.041892089 9.70E-07 1.15E-07 0.041391001 0.009755895 0.06150357 1.211099677 -0.261177595 TCEERPAEDGS(ph)DEEDPDSMEAPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR 317.81 6.22E-74 30615880000 11267014 9513265 9873582 11404897 10215847 10455817 12491401 10929764 10877271 TRUE FALSE 10734444.58 10482677.52 10326295.5 10258455.09 11997487.48 10093729.44 10585608.36 9972695.922 12564062.63 0.854376876 0.834338209 0.821891438 0.816491877 0.9549051 0.803381019 0.84253069 0.793747708 1 23.5827997 -1.552254919 5.916980171 1.000356193 0.841151217 0.560158422 0.044492055 0.00019007 1.44E-05 0.039166326 0.009211154 0.028037874 1.552254919 -0.159204976 TCEESSFCKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TCEESSFCKR 10 1 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 247.08 1.83E-12 2823470000 2672250 1809410 2408420 2602520 2266120 2553790 3565130 3033690 2809490 FALSE TRUE 2545938.038 1993790.936 2518848.439 2340909.745 2661330.611 2465351.612 3021203.94 2768044.021 3245171.36 0.784531156 0.614386951 0.776183492 0.721351659 0.820089393 0.759698438 0.930984409 0.852973145 1 21.62986323 1.737421547 0.585253442 0.991079768 0.700185499 0.688561732 0.059710655 0.373365071 0.277405868 0.05249598 0.030266054 54.62878566 -1.737421547 -0.290894269 TCFETFPDKVAIQLNDTHPALSIPELMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TCFETFPDKVAIQLNDTHPALSIPELMR 28 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 196.32 3.47E-25 282300000 585230 446420 547260 582010 515910 557660 745380 619630 547630 FALSE TRUE 557567.3377 491910.7055 572352.4123 523505.2491 605884.5407 538348.0944 631658.5912 565371.9123 632553.6635 0.881454602 0.777658456 0.904828231 0.827606066 0.957838956 0.851071024 0.998584986 0.893792804 1 19.27082835 2.224139982 0.544722785 0.984612424 0.828195543 0.411506138 0.054883741 0.705892616 0.431293841 0.045242644 0.036337534 167.5482833 -2.224139982 -0.156416881 TCFSLHLDGNVLDHFSELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCFSLHLDGNVLDHFSELR 19 0 K7EIG1;A0A494C0R8;O75153;I3L2B0;I3L318 K7EIG1 CLUH Clustered mitochondria protein homolog 0 100.67 0.00034638 8950500 9934.2 9814.2 8574.3 10014 11588 10043 12561 9116.9 3120.3 FALSE TRUE 9464.630054 10814.27814 8967.440136 9007.373695 13608.94353 9695.208392 10644.58875 8318.575904 3604.180188 2.626014672 3.0004821 2.488066542 2.499146332 3.775877682 2.689989925 2.953400828 2.308035523 1 11.81545542 0.871688559 2.789468382 1.000770585 2.862185362 0.717442718 0.369310648 0.255333846 3.956603973 0.328958511 0.086995628 7.44198103 -0.871688559 1.861414777 TCFVDCLIEQTHPEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TCFVDCLIEQTHPEIR 16 0 Q15029;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 222.57 9.52E-15 805240000 478376 435022 416935 504302 427025 427492 533687 465950 461450 FALSE TRUE 455764.1145 479351.2364 436051.8822 453608.6048 501498.0248 412687.8448 452263.2463 425148.9478 533009.3092 0.855077213 0.899329952 0.818094308 0.851033175 0.940880424 0.774260107 0.848509094 0.797638879 1 19.0238012 2.235079669 24.99990887 0.840687668 0.87138713 0 0.06736135 301.6586961 2166461.372 0.021740105 0.016701511 171.8223558 -2.235079669 0.030699462 TCGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWK 42 2 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 78.542 0.00030886 124560000 165300 118820 161180 122290 93001 137720 151860 156600 12617 FALSE TRUE 157486.5966 130927.8931 168570.2624 109997.1769 109220.345 132950.7219 128690.9679 142887.2738 14573.57992 10.80630823 8.983921164 11.56683967 7.547711507 7.494407383 9.122722254 8.830429352 9.80454182 1 13.83106769 3.221595014 24.82117567 7.893363252 10.18825637 0.233651909 2.529207803 364.38606 533106.3327 0.64640526 0.774511357 1665.693203 -3.221595014 2.294893116 TCNCETEDYGEKFDENDVITCFANFESDEVELSYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCNCETEDYGEKFDENDVITCFANFESDEVELSYAK 36 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 131.79 6.76E-09 13995000 61373 58194 53686 66372 34209 63788 63075 70967 36470 FALSE TRUE 58472.01992 64124.03476 56147.5562 59700.16046 40175.03877 61579.00557 53451.7503 64752.75326 42125.58134 1.388040665 1.522211272 1.332861279 1.417194934 0.953696958 1.461795983 1.268866769 1.537136135 1 15.36240898 -4.108453206 0.196832934 1.70E-26 1.425737426 0.280321764 0.170039049 120.0831643 1.62573231 49.00190063 0.404321259 7.79E-05 4.108453206 1.425737426 TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.131)CNS(0.403)PQNS(0.37)T(0.08)DS(0.013)VS(0.003)DIVPDSPFPGALGSDTR;T(0.039)CNS(0.815)PQNS(0.141)T(0.005)DSVSDIVPDSPFPGALGSDTR 163.66 2.27E-12 295923000 196539 155944 190730 224633 164402 203507 221730 210926 192619 TRUE FALSE 187248.991 171834.8709 199475.1592 202052.4641 193073.6567 196459.5016 187901.0161 192456.2013 222489.3708 0.841608704 0.77232845 0.8965604 0.908144346 0.867788228 0.883006235 0.844539294 0.865013014 1 17.76337689 -5 0.145914477 1.499376828 0.806005749 0.579906529 0.037412479 100.9816545 0.886431392 14.7311629 0.216914475 1.00E-05 5 -0.693371079 TCNSPQNS(ph)TDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.069)CNS(0.348)PQNS(0.485)T(0.095)DS(0.004)VSDIVPDSPFPGALGSDTR;T(0.071)CNS(0.323)PQNS(0.498)T(0.108)DSVSDIVPDSPFPGALGSDTR;T(0.068)CNS(0.199)PQNS(0.482)T(0.222)DS(0.028)VSDIVPDSPFPGALGSDTR 167.22 1.66E-12 386353000 171484 143164 157076 168143 148816 155577 183834 166810 170721 TRUE FALSE 163378.2912 157752.5744 164278.09 151240.9462 174769.4633 150189.3295 155786.747 152203.2321 197195.5408 0.828509055 0.799980434 0.833072033 0.766959261 0.886274926 0.761626398 0.79001151 0.771839117 1 17.5892674 -2.121003688 2.500102079 1.391617622 0.80487645 0.72851102 0.037452023 7886178.136 2035658.695 17563625.43 0.008200832 0.007568265 2.121003688 -0.586741172 TCNTNPHLNALSTDSACRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCNTNPHLNALSTDSACRR 19 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 139.11 3.94E-07 107340000 61903 36707 63413 49381 49302 52540 75390 64234 59533 FALSE TRUE 58976.96787 40447.48503 66320.54877 44417.12806 57900.25319 50720.52663 63887.87087 58609.33043 68765.07359 0.857658762 0.588198091 0.96445107 0.645925697 0.84200089 0.737591396 0.92907442 0.85231248 1 16.06938837 1.359171 0.717110985 0.993913428 0.751317393 0.290516322 0.11187915 0.673038653 0.78070287 0.094840134 0.040396915 22.86498918 -1.359171 -0.242596034 TCNVLVALEQQS(ph)PDIAQGVHLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 TCNVLVALEQQS(1)PDIAQGVHLDR 48.852 0.093183 21935000 7673.2 7712.9 6496.7 7300.3 8376.6 7608.1 7591.2 7194.9 6073.9 TRUE FALSE 7310.503043 8498.853279 6794.580121 6566.459974 9837.476388 7344.629589 6433.023018 6564.876413 7015.809391 1.042004227 1.211386001 0.968467035 0.935951878 1.402186952 1.046868462 0.916932411 0.935726165 1 12.77639384 1.994102729 24.97695835 0.951717426 1.114651194 0.239591687 0.130984391 356.0317384 1507918.097 0.048464544 0.03465195 98.65128104 -1.994102729 0.162933768 TCNVLVALEQQSPDIAQGVHLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 197.15 3.02E-24 363053000 537811 551791 450870 602689 443257 498118 552182 560324 352208 FALSE TRUE 512389.7399 608019.1302 471542.8355 542105.5567 520560.8805 480868.0488 467936.4944 511259.0601 406826.6178 1.259479389 1.494541172 1.159075672 1.33252234 1.279564457 1.181997509 1.150211107 1.256700122 1 18.63405455 1.311144781 0.256124926 0.952611921 1.407858254 0.498593028 0.091694194 1.468497491 0.390847997 0.264512092 0.210929244 20.47126974 -1.311144781 0.455246333 TCS(ph)FGGFDLTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TCSFGGFDLTNR 12 0 O94885;A0A1B0GWB9 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 T(0.005)CS(0.995)FGGFDLTNR;T(0.001)CS(0.999)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;T(0.044)CS(0.956)FGGFDLTNR 292.95 3.74E-36 1971480000 3156609 2494098 2711923 3300284 2751482 2953481 3380730 2884846 2744922 TRUE FALSE 3007402.348 2748249.422 2836267.352 2968533.182 3231339.59 2851201.212 2864937.547 2632233.591 3170590.485 0.94853068 0.866794193 0.894554931 0.936271397 1.019160187 0.899265051 0.903597472 0.830202955 1 21.59632012 3.985877173 0.00440482 1.821952555 9.07E-08 0.042398323 0.056039074 124022.2843 110.3133392 22255.99876 23379.32845 9680.040467 -3.985877173 -1.821952465 TCTFILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TCTFILR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 106.42 0.01793 26607000 97985 81126 84108 89483 89800 73278 99081 89382 92973 FALSE TRUE 93353.44324 89392.83163 87964.43499 80487.99883 105461.0916 70740.36449 83964.3737 81555.23824 107390.778 0.869287335 0.832406965 0.819106041 0.749487063 0.982031172 0.658719173 0.781858324 0.759424969 1 16.71251058 2.227955483 24.99989184 0.777429547 0.843697488 0.035055979 0.101856352 497.0315754 1171663.488 0.033463074 0.02497512 169.0267663 -2.227955483 0.066267941 TDCSSGDASRPSSDNADS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDCSSGDASRPSSDNADSPK 20 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TDCSSGDASRPS(0.036)S(0.036)DNADS(0.928)PK 88.168 0.0013683 42845000 21297 19794 21510 24556 13315 22228 23259 22746 12741 TRUE FALSE 20290.33302 21811.0311 22496.25478 22087.58423 15637.13178 21458.23879 19710.41237 20754.23966 14716.80921 1.378718221 1.482048914 1.528609528 1.500840564 1.06253547 1.458076848 1.339312897 1.410240451 1 13.84517729 -3.613829456 0.21478409 2.87E-12 1.462131781 0.4865262 0.129394238 64.73043262 1.104177348 28.72880783 0.256587251 0.000243316 3.613829456 1.462131781 TDDCHPWVLPVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDDCHPWVLPVVK 13 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 153.38 3.92E-05 1105720000 2854350 2331700 2316490 2750720 2074590 2588420 3099890 2875340 2011770 FALSE TRUE 2719430.532 2569302.881 2422703.358 2474212.4 2436397.839 2498782.366 2626944.847 2623559.986 2323745.017 1.170279231 1.105673326 1.042585714 1.064752106 1.048478995 1.075325541 1.130478959 1.129022318 1 21.14802034 4.27325457 2.29398207 1.077833782 1.165047645 0.379565384 0.039442674 0.338591131 3.376361538 0.010331058 0.03965247 18760.93895 -4.27325457 0.087213863 TDDEVVQREEEAIQLDGLNASQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;;; 359.31 2.06E-102 2309782000 1598530 1180873 1490941 1558480 1269103 1533178 1800641 1626600 1524919 FALSE TRUE 1522970.655 1301205.301 1559302.12 1401818.629 1490434.161 1480083.661 1525920.144 1484166.281 1761395.65 0.864638592 0.738735389 0.885265113 0.795856757 0.846166596 0.84029029 0.86631311 0.842608122 1 20.74828758 -2.161130175 0.240738177 1.213442581 0.803928815 0.625774401 0.040578121 20.31691532 0.681345104 2.42533909 0.062602625 0.006900329 2.161130175 -0.409513766 TDDIPVWDQEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 169.23 6.71E-05 35687000 182002 152603 144288 194372 134009 171096 189431 188211 144765 FALSE TRUE 173399.1262 168153.4192 150903.7475 174833.3573 157380.1272 165170.9026 160529.8218 171730.2471 167214.4168 1.036986699 1.005615559 0.902456561 1.045563897 0.941187549 0.987779079 0.960023812 1.027006225 1 17.35133971 3.993626621 24.67770442 0.977450111 1.025222538 0.15957924 0.040949235 478.8799951 1854233.344 0.009103278 0.017694947 9854.319084 -3.993626621 0.047772426 TDDVHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TDDVHAK 7 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 94.887 0.013871 930330000 3769170 3175100 3110210 3843510 2043260 3240910 3717420 4181870 2498790 FALSE TRUE 3591008.804 3498646.3 3252816.205 3457153.073 2399603.897 3128676.474 3150259.304 3815683.293 2886289.591 1.244160951 1.212160523 1.126988856 1.197784548 0.831380158 1.083978712 1.09145642 1.322002929 1 21.46078463 3.499848648 1.656449817 1.078058389 1.232796007 0.185538587 0.124225897 0.573292547 3.159040168 0.037288787 0.066472279 3161.175797 -3.499848648 0.154737618 TDDYLDQPCYETINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TDDYLDQPCYETINR 15 0 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 376.83 1.62E-97 1918620000 2079950 1848490 1839940 2103360 1661290 1939370 2230690 2065880 1789070 FALSE TRUE 1981634.886 2036853.233 1924303.069 1891926.257 1951018.45 1872209.131 1890357.271 1884980.595 2066509.838 0.958928358 0.98564894 0.931185051 0.915517662 0.944112829 0.905976394 0.914758418 0.912156604 1 20.9787648 3.666324133 6.076779426 0.925748399 0.972179908 0.244373715 0.027940769 0.21335118 14.11220974 0.006579366 0.010309663 4637.929399 -3.666324133 0.046431509 TDEAAFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDEAAFQK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ;; 163.77 0.00077691 1748140000 2000190 1680500 1591190 2098550 1360720 1877560 2061680 2019620 1357640 FALSE TRUE 1905644.983 1851744.861 1664147.635 1887599.767 1598029.137 1812539.626 1747132.851 1842771.366 1568175.877 1.215198506 1.180827283 1.061199614 1.203691368 1.019036933 1.155826749 1.114117923 1.175105033 1 20.58065594 4.916730379 0.016884648 1.99E-08 2.375267117 0.346119681 0.0614343 2376.511116 5.919057278 364.6152103 473.2345665 82552.52837 -4.916730379 2.375267097 TDEFPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDEFPR 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 106.76 0.074087 47840000 96668 91615 87027 89875 83248 85018 97997 100680 90034 FALSE TRUE 92098.69522 100950.6727 91017.27403 80840.59425 97766.42484 82073.80534 83045.75781 91863.92546 103996.0129 0.885598329 0.97071676 0.87519965 0.777343208 0.940097818 0.789201461 0.798547516 0.883340841 1 16.66616869 3.488655643 23.68867733 0.84743351 0.927291009 0.082244809 0.072625433 405.7250879 833253.9907 0.017821328 0.025940132 3080.744223 -3.488655643 0.079857498 TDEGIAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TDEGIAYR 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;;;;;; 147.69 0.0012404 7711412000 10071598 8866948 8733902 10603890 9634470 8470119 10464730 9206027 10130650 FALSE TRUE 9595533.523 9770500.082 9134360.046 9537966.831 11314718.52 8176796.655 8868143.241 8399898.472 11701659.46 0.820014764 0.83496705 0.780603817 0.815095232 0.966932814 0.698772399 0.757853471 0.717838226 1 23.4802098 TDEVPAGGS(ph)RS(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 2 TDEVPAGGS(1)RS(1)EAEDEDDEDYVPYVPLR 118.93 8.53E-05 56651000 73568 48142 47373 66272 58646 55599 76328 70027 60921 TRUE FALSE 70090.58644 53047.72453 49545.09891 59610.21265 68873.84383 53673.59269 64682.76174 63895.06464 70368.31754 0.99605318 0.753858077 0.704082471 0.847117208 0.978762123 0.762752252 0.919202903 0.908008986 1 16.1026384 1.015562945 0.875126687 0.999826994 0.839387879 0.226717103 0.093317328 0.975272014 1.639871997 0.08762717 0.030910035 10.36484818 -1.015562945 -0.160439115 TDEVPAGGS(ph)RSEAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 TDEVPAGGS(0.589)RS(0.411)EAEDEDDEDYVPYVPLR 179.54 9.55E-18 65986000 45798 25202 37545 44091 38164 30817 47877 42356 42560 TRUE FALSE 43633.2193 27770.11245 39266.47539 39658.88891 44819.78952 29749.79956 40572.48433 38647.0841 49159.98743 0.887575884 0.564892586 0.798748686 0.806731063 0.911712794 0.60516288 0.825315189 0.786149186 1 15.58519693 0.451552162 1.209197555 1.000094752 0.758655939 0.294049888 0.109994572 2.851542221 5.090508642 0.099438187 0.029991804 2.828473814 -0.451552162 -0.241438813 TDFEEFFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TDFEEFFLR 9 0 B1AKV2;B1AKV6;B1AKV3;Q9NVA1-5;Q9NVA1-2;Q9NVA1 B1AKV2 UQCC1 Ubiquinol-cytochrome-c reductase complex assembly factor 1 0 ;;;;; 256.03 1.32E-14 227187000 361850 379356 264385 290425 256056 232296 293411 320115 231790 FALSE TRUE 344746.0676 418012.8077 276507.3138 261230.9272 300712.0853 224251.5313 248645.7631 292084.0336 267734.8094 1.287640066 1.56129421 1.032765647 0.975707745 1.123171417 0.837588253 0.928701664 1.090945306 1 18.0304452 3.662470014 6.055332598 0.983561171 1.423326111 0.748758319 0.102500912 0.091437485 5.750068812 0.026578892 0.041623202 4596.952474 -3.662470014 0.439764939 TDFGIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDFGIFR 7 0 Q9HCC0-2;Q9HCC0 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 111.28 0.015389 75500000 189170 124340 64344 65619 174680 61256 163600 107790 143400 FALSE TRUE 180228.309 137010.3874 67294.23604 59022.85345 205144.1367 59134.68936 138639.8153 98351.33617 165637.7396 1.088087228 0.827168903 0.406273571 0.356336989 1.238510844 0.357012173 0.837006202 0.593773716 1 17.33767189 4.183923515 2.92746391 0.674541717 1.042446651 0.159951885 0.286711646 0.388000187 6.570000021 0.066880444 0.189086878 15272.97059 -4.183923515 0.367904934 TDGCHAYLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TDGCHAYLSK 10 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;;;;; 167.12 5.34E-06 4760000000 15455520 12762000 11398300 14591000 10659910 13261640 16216530 14597640 10174060 FALSE TRUE 14724968.2 14062462.31 11920923.33 13124284.96 12518994.93 12802386.08 13742400.51 13319393.25 11751801.26 1.2529967 1.196621862 1.014391161 1.116789219 1.06528307 1.089397769 1.169386735 1.133391636 1 23.48637857 3.931776292 6.173360889 1.096437753 1.232539949 0.556418104 0.052290795 0.151669331 10.80027669 0.013128488 0.024176467 8546.263753 -3.931776292 0.136102196 TDGFAEAIHS(ph)PQVAGVPR ddPTM_SK-BR-3_Trastuzumab_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 240.31 3.86E-24 3519560000 1832980 1714540 1798100 2218080 1615260 1648550 1738080 1534790 1104004 TRUE FALSE 1746338.668 1889253.575 1880544.664 1995114.384 1896960.833 1591460.3 1472903.974 1400395.651 1275207.302 1.369454727 1.481526629 1.47469722 1.564541217 1.487570554 1.248001245 1.155031007 1.098170979 1 20.28230036 1.90567351 1.707965147 1.065752201 1.472048402 0.901380803 0.059616929 0.112298618 0.61178306 0.041634304 0.019053381 80.47732081 -1.90567351 0.406296201 TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.022)DGS(0.978)IS(1)GDRQPVTVADYISR;T(0.008)DGS(0.992)IS(1)GDRQPVTVADYISR;T(0.053)DGS(0.947)IS(0.998)GDRQPVT(0.002)VADYISR;T(0.017)DGS(0.981)IS(0.744)GDRQPVT(0.249)VADY(0.001)IS(0.007)R;T(0.003)DGS(0.997)IS(1)GDRQPVTVADYISR 165.42 9.50E-12 1445530000 1888756 1705355 1746160 2163020 1516208 1922391 2070170 1836390 1827740 TRUE FALSE 1799478.247 1879132.613 1826223.163 1945589.12 1780634.195 1855818.118 1754327.545 1675585.956 2111176.584 0.852357998 0.890087844 0.86502625 0.921566265 0.843432145 0.879044478 0.830971487 0.793673996 1 21.00961582 2.626254161 17.98669309 0.85763267 0.879620887 0 0.056329039 11.53055812 1814.099887 0.016185135 0.015259369 422.9160438 -2.626254161 0.021988217 TDGS(ph)ISGDRQPVTVADYISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 T(0.01)DGS(0.99)ISGDRQPVTVADYISR;TDGS(0.999)IS(0.001)GDRQPVTVADYISR;TDGS(0.999)IS(0.001)GDRQPVTVADYISR;T(0.012)DGS(0.988)IS(0.001)GDRQPVTVADYISR;T(0.004)DGS(0.995)IS(0.001)GDRQPVTVADYISR 275.6 9.80E-45 2556450000 1523450 1289710 1374690 1563580 1359430 1490820 1612000 1616460 1428790 TRUE FALSE 1451439.538 1421132.915 1437720.896 1406405.968 1596514.162 1439192.53 1366059.794 1474914.193 1650359.456 0.879468732 0.861105082 0.871156215 0.852181604 0.967373596 0.872047919 0.827734703 0.893692697 1 20.65434885 0.969456162 23.58156653 1.000000001 0.873449088 0.537729772 0.035838767 1440.69597 1112300.35 0.033863412 0.008465853 9.320863811 -0.969456162 -0.126550914 TDIIDRLEQELLCASNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDIIDRLEQELLCASNR 17 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A6I8PUD8;A0A2R8Y590 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 159.81 2.89E-09 9790300 8311.6 5989.4 5891.8 8131.1 7438.5 5491.3 10036 9409.6 7181.1 FALSE TRUE 7918.72714 6599.726669 6161.944858 7313.74638 8735.772045 5301.134904 8504.823876 8585.645541 8294.708312 0.954672165 0.795655064 0.742876618 0.881736416 1.05317411 0.639098411 1.025331278 1.03507504 1 13.01797553 1.604458369 25 1.022680898 0.851430833 0.352070391 0.112018467 0.362464294 2638.704026 0.053197822 0.026178 40.22150982 -1.604458369 -0.171250065 TDKLDEALEDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDKLDEALEDYK 12 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 114.56 0.00095231 85974000 239850 244060 201240 291350 123200 266630 237400 284200 123680 FALSE TRUE 228512.7658 268929.9915 210467.0531 262062.9445 144686.041 257396.5362 201180.2698 259313.9414 142859.6627 1.599561146 1.882476735 1.473243385 1.834408254 1.012784422 1.801743973 1.408237049 1.815165572 1 17.12423909 -2.849657353 0.227275205 4.61E-14 1.699491199 0.315702675 0.267766657 58.03786368 1.389249287 29.3577244 0.448165416 0.001413652 2.849657353 1.699491199 TDKLVNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDKLVNER 8 1 P05023-4;P05023;P05023-3;Q5TC05;M0R116;A0A2R8YEY8;A0A0A0MT26;P13637;P13637-2;P13637-3 P05023-4 ATP1A1;ATP1A3 Sodium/potassium-transporting ATPase subunit alpha-1;Sodium/potassium-transporting ATPase subunit alpha-3 0 ; 107.21 0.0036916 236830000 479290 290960 363110 561260 413720 403880 558370 508670 413720 FALSE TRUE 456634.9116 320609.1548 379758.9527 504841.0785 485872.637 389893.5343 473180.4013 464128.1582 477877.5846 0.955547877 0.670902267 0.794678313 1.056423433 1.016730336 0.815885798 0.990170739 0.971228141 1 18.86628157 3.258238719 24.78193065 0.966695504 0.799084766 0.423908751 0.091839151 203.8950462 256776.6658 0.025012871 0.033818616 1812.336008 -3.258238719 -0.167610738 TDKTLVLLMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDKTLVLLMGK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 122.45 0.00096813 0 1746500 1403100 1672700 1112000 1525600 1652000 2586100 1907500 1873300 FALSE TRUE 1663946.406 1546077.485 1749394.95 1000219.647 1791664.157 1594790.826 2191542.948 1740469.188 2163801.797 0.768992062 0.714518995 0.808482067 0.462251048 0.828016762 0.737031843 1.01282056 0.804357031 1 21.04513692 1.755254702 25 0.933934843 0.720698744 0.452744282 0.113545612 5.382235334 8069.224348 0.047789317 0.026501687 56.91866462 -1.755254702 -0.213236098 TDKVFEVMLATDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDKVFEVMLATDR 13 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;F8WDT3;F8WAV5;F8WAX2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ; 172.91 2.06E-05 741790000 2052930 1344830 1653250 1793520 1492160 1739590 2353900 2044560 1793920 FALSE TRUE 1955892.067 1481869.706 1729053.148 1613231.962 1752392.232 1679347.562 1994769.323 1865527.488 2072111.952 0.943912353 0.715149442 0.834440025 0.778544789 0.845703453 0.810452138 0.962674493 0.90030246 1 20.98267052 1.740035279 6.784055618 0.947554573 0.818229059 0.504751998 0.06181779 0.111242799 14.84225849 0.028777893 0.015157076 54.95855161 -1.740035279 -0.129325515 TDLADKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 75.854 0.067891 142580000 407640 410610 350910 545580 303910 449710 459930 446500 270630 FALSE TRUE 388371.6651 452451.6258 366999.5706 490737.2619 356911.8078 434136.4299 389759.2313 407402.093 312597.9182 1.242400037 1.447391679 1.174030757 1.569867338 1.141760028 1.388801411 1.246838858 1.30327833 1 18.25394864 -0.583416093 0.443114783 0.920629943 1.338851865 0.377771378 0.127646245 8.999979189 1.528825037 1.149671801 0.061841451 0.260965987 0.583416093 0.418221921 TDLCDHALHISHDEL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDLCDHALHISHDEL 15 0 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ; 203.82 3.02E-09 255880000 185376 151417 175813 206508 234140 170493 247860 164065 6595 FALSE TRUE 176613.6439 166846.5644 183874.2 185749.4235 274973.9419 164588.7847 210044.4047 149698.5988 7617.718917 23.18458396 21.90243119 24.13769817 24.38386419 36.09662484 21.60604591 27.57313666 19.65136814 1 12.89514334 0.863635715 3.813656171 1.002881487 25.19186761 0.77525604 4.144473655 0.336351475 8.56332453 3.847175588 0.986515543 7.305260631 -0.863635715 24.18898612 TDLEKDIISDTSGDFR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 155.22 2.56E-07 440949000 1554642 1352494 1047243 1769680 1058264 1311572 1290185 1232552 840310 FALSE TRUE 1481157.154 1490314.676 1095260.127 1591788.404 1242824.907 1266151.933 1093343.582 1124623.213 970620.9831 1.525989217 1.535423922 1.128411755 1.639969084 1.280443065 1.30447616 1.1264372 1.158663611 1 19.88854852 2.020784602 0.42967706 0.980567957 1.541887493 0.566038157 0.137485975 0.690351032 0.305168175 0.135728574 0.126553649 104.9022013 -2.020784602 0.561319536 TDLEKDIISDTSGDFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDLEKDIISDTSGDFRK 17 2 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 ; 247.46 5.30E-21 355960000 1328210 1054290 958910 1355200 788970 1150810 1235930 1100980 671430 FALSE TRUE 1265428.146 1161723.35 1002876.972 1218972.721 926566.1182 1110957.161 1047366.179 1004572.355 775551.9352 1.631648492 1.497931082 1.29311388 1.571748668 1.194718337 1.43247294 1.350478455 1.295299913 1 19.56486387 1.314607303 0.052146748 1.67E-12 2.590138533 0.674366395 0.105649111 20.90190992 1.00256598 25.08319939 23.67668653 20.63513447 -1.314607303 2.590138533 TDLFYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TDLFYER 7 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;;;; 166.86 0.0025772 577600000 1328200 1057990 808150 984230 1125050 905750 1384070 1086180 1119590 FALSE TRUE 1265418.618 1165800.384 845204.4769 885293.3305 1321258.364 874383.6504 1172904.701 991068.321 1293210.299 0.978509543 0.901477807 0.65357079 0.684570275 1.021688711 0.676134153 0.906971358 0.766362843 1 20.30252547 6.065741762 11.49135592 0.843967624 0.85235992 0 0.140300611 0 0 0.029230111 0 1163434.03 -6.065741762 0.008392296 TDLKGDDLEEGVTSEEFDKFLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDLKGDDLEEGVTSEEFDKFLEER 24 2 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 108.59 0.0012943 22932000 40081 33240 39274 41543 19478 36925 41499 37382 24024 FALSE TRUE 38186.45056 36627.19379 41074.75175 37367.01871 22874.95703 35646.27799 35167.56537 34108.63391 27749.51922 1.37611215 1.319921743 1.480196879 1.346582563 0.824337058 1.284572814 1.26732161 1.229161256 1 14.76017516 7.999998788 0.052318073 0.558575845 2.584075473 0.298846787 0.159629745 581.7872591 2.292532887 20.17392029 93.64269281 99999720.82 -7.999998788 2.025499628 TDLLLEPYNKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDLLLEPYNKYR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 133.32 0.00015074 206180000 647520 271950 485110 395650 633210 481120 896030 674960 842630 FALSE TRUE 616913.0129 299662.0142 507352.7733 355878.5103 743641.6235 464458.6938 759324.1668 615856.9242 973300.7568 0.633835953 0.307882237 0.521270296 0.365640844 0.764040938 0.477199561 0.78015368 0.632750894 1 19.89252615 1.111070456 0.470648892 1.00652169 0.449805633 0.566710502 0.135675662 0.662172456 0.391938798 0.147074492 0.077810703 12.91428767 -1.111070456 -0.556716057 TDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDLLVNDNPDPAPLSPELQDFK 22 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 TDLLVNDNPDPAPLS(1)PELQDFK 121.23 1.78E-05 13391000 22257 29396 18448 28446 13155 25956 19139 24018 8771.3 TRUE FALSE 21204.95572 32391.48582 19293.85905 25586.55404 15449.22783 25057.13721 16218.99404 21914.85659 10131.50841 2.092971241 3.197103977 1.904342204 2.525443696 1.524869468 2.473189204 1.600846921 2.163039867 1 13.30656136 0.452757862 0.187330066 0.37983018 2.895557222 0.430950017 0.459317856 5.884403349 0.553709594 4.366378481 1.915126652 2.836337206 -0.452757862 2.515727042 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(1)PSKVEGVHTPR;TDLQGSAS(0.974)PS(0.026)KVEGVHTPR;TDLQGSAS(0.999)PS(0.001)KVEGVHTPR 282.38 5.74E-40 640302000 707760 670440 676390 833220 481492 781840 843310 846590 518378 TRUE FALSE 674305.5874 738758.5982 707403.1505 749463.1426 565464.0524 754764.6848 714647.571 772458.0915 598765.4127 1.126159883 1.23380306 1.181436228 1.251680753 0.944383293 1.260534875 1.193535157 1.290084689 1 19.19163136 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 45 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 131.79 2.57E-10 241840000 219570 165830 164350 236960 142440 215180 251460 225500 52008 FALSE TRUE 209191.3612 182728.2655 171885.6101 213140.3306 167281.4909 207728.2626 213095.1586 205754.0245 60073.13502 3.482278079 3.041763435 2.861272514 3.548014109 2.784630615 3.45792279 3.547262159 3.42505888 1 15.87443233 4.591965473 3.013174336 3.109024136 3.49154878 0.011559523 0.762057554 1.376859523 21.28847842 0.161964005 1.054132085 39080.98244 -4.591965473 0.382524643 TDNSSLS(ph)SPLNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDNSSLSSPLNPK 13 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 T(0.001)DNS(0.079)S(0.079)LS(0.42)S(0.42)PLNPK;TDNS(0.015)S(0.033)LS(0.476)S(0.476)PLNPK 94.532 0.0053622 145999000 332600 349570 348290 396490 202139 399890 391580 407100 257900 TRUE FALSE 316878.6571 385191.5804 364259.441 356634.0719 237391.9776 386041.709 331837.2791 371452.1658 297893.8148 1.063730233 1.293049943 1.222782827 1.197185219 0.796901331 1.295903741 1.113944844 1.246928091 1 18.18443864 -2.081849695 2.37592766 0.754744492 1.156763225 0.098388387 0.146076661 21861310.35 6675582.235 29029581.46 0.032534172 0.008282288 2.081849695 0.402018733 TDPVPEEGEDVAATIS(ph)ATETLSEEEQEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 1 TDPVPEEGEDVAAT(0.012)IS(0.978)AT(0.009)ET(0.001)LSEEEQEELRR 148.89 8.10E-09 23443000 14047 9267.2 10583 10859 9914 10222 13486 12025 13279 TRUE FALSE 13383.02615 10211.53822 11068.24102 9767.432689 11642.99846 9868.009577 11428.46301 10972.02725 15338.2395 0.872526873 0.665756863 0.721610914 0.636802724 0.759083105 0.643359988 0.745096138 0.71533811 1 13.90484528 -0.913106615 6.117062526 1.000000063 0.721286821 0.628507549 0.067657814 5.45E-08 9.82E-09 0.062025564 0.014619562 0.122149976 0.913106615 -0.278713242 TDPVPEEGEDVAATISATETLSEEEQEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;;;;;;;;;;;;; 315.57 1.57E-92 3256894000 238375.6 160060.1 174398.3 190305.6 164454.3 178984.7 207584.6 180189.9 183320.7 FALSE TRUE 227108.0578 176370.4062 182394.6346 171175.7195 193135.0779 172786.415 175913.7567 164411.5171 211749.1379 1.072533565 0.832921484 0.861371321 0.808389216 0.91209381 0.815995837 0.830764925 0.7764448 1 17.69199657 4.5716084 2.27415006 0.846149698 1.091504091 0.531100192 0.063512531 0.270022686 2.143374602 0.013968406 0.115411548 37291.37525 -4.5716084 0.245354393 TDQAQKAEGAGDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDQAQKAEGAGDAK 14 1 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;; 146.3 7.61E-06 250480000 674010 367689 693770 582901 444939 729700 922250 801390 510594 FALSE TRUE 642150.8831 405156.9271 725580.0407 524306.684 522536.2207 704430.306 781543.8242 731216.0432 589774.3098 1.088807824 0.68696944 1.230267288 0.88899546 0.885993527 1.194406563 1.325157456 1.23982349 1 19.16980346 2.182974247 6.197178847 1.231070661 0.941083099 0.322933152 0.162914962 0.185186287 14.78311982 0.05743687 0.042564165 152.3962382 -2.182974247 -0.289987562 TDQDEEHCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TDQDEEHCR 9 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;;;;; 190.03 3.75E-05 723921300 680441.3 596874 534861.7 671101.2 593510.8 587256.2 831634.8 608452.2 593685.5 FALSE TRUE 648278.1883 657696.1392 559385.638 603640.8324 697018.8956 566919.3705 704753.6372 555172.8998 685751.2152 0.945354779 0.959088551 0.815726791 0.88026214 1.016431149 0.826712892 1.027710373 0.809583545 1 19.38732575 TDQVIQSLIALVNDPQPEHPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLR 22 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 196.4 2.13E-22 739100000 450940 405130 381170 486180 328970 409660 431940 439790 286470 FALSE TRUE 429624.9599 446413.2076 398647.0215 437308.2627 386342.2638 395473.3715 366039.6199 401279.6561 330894.3045 1.298375203 1.349111186 1.204756371 1.321595013 1.167570002 1.195165242 1.106213117 1.212712491 1 18.33601093 1.898322228 0.236456337 0.960890064 1.401110277 0.727563273 0.054022308 1.026479362 0.226810492 0.136712731 0.176403164 79.12654954 -1.898322228 0.440220213 TDQVIQSLIALVNDPQPEHPLRADLAEEYSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLRADLAEEYSK 31 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 219.21 4.17E-35 371560000 277960 217640 249040 272330 180628 292190 329400 312980 201546 FALSE TRUE 264821.3817 239817.7634 260458.7303 244954.871 212129.466 282071.387 279143.9802 285573.812 232800.7243 1.137545351 1.030141827 1.118805498 1.052208371 0.911206211 1.211643082 1.199068349 1.226687816 1 17.82873602 2.174850206 24.99999982 1.179692497 1.05846117 0.264486374 0.087124049 71.35808307 28000.03712 0.029969648 0.022134058 149.5719674 -2.174850206 -0.121231327 TDQVIQSLIALVNDPQPEHPLRADLAEEYSKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLRADLAEEYSKDR 33 2 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 163.89 2.62E-14 367890000 214014 139003 220660 203737 185271 210352 312940 231460 185941 FALSE TRUE 203897.9824 153167.5637 230777.4793 183256.9697 217582.2037 203067.4575 265195.2555 211192.1354 214775.7806 0.94935277 0.713151005 1.074504204 0.853247834 1.013066758 0.945485831 1.234754006 0.983314481 1 17.71247179 2.617646612 1.029423218 1.087593471 0.861473096 0.231628977 0.118481376 0.533447522 1.167433714 0.064372124 0.052329835 414.6165294 -2.617646612 -0.226120375 TDRDKYNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TDRDKYNR 8 2 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ;;; 148.52 0.00029241 824630000 870110 503264 753050 743830 659590 814410 1118250 928850 841420 FALSE TRUE 828981.6247 554547.1738 787578.0874 669058.7952 774622.2872 786206.7775 947640.4244 847514.9699 971903.1162 0.852946771 0.570578656 0.810346293 0.68840071 0.797015952 0.80893534 0.975035895 0.872015899 1 19.89045298 2.045354685 1.408978316 0.9562271 0.721306487 0.556844521 0.083174839 0.283619925 1.054063091 0.052089491 0.025587685 111.0081041 -2.045354685 -0.234920613 TDRLEVCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 158.76 0.00033118 360320000 367520 268490 282690 303370 313120 290780 370110 331790 346020 FALSE TRUE 350148.058 295849.4362 295651.6161 272874.6712 367728.0289 280710.2157 313642.922 302736.7087 399679.0144 0.876073162 0.740217589 0.739722641 0.682734548 0.920058386 0.702339141 0.784737028 0.757449598 1 18.6084823 -1.220210639 5.547752182 1.000010566 0.776129506 0.483391309 0.072961213 8.67E-06 1.22E-06 0.064248114 0.015142711 0.060226741 1.220210639 -0.22388106 TDRVGVEASEETPQTSSSS(ph)ARPGTPSDHQSQEASQFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDRVGVEASEETPQTSSSSARPGTPSDHQSQEASQFER 38 2 Q6Y7W6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 TDRVGVEASEETPQT(0.004)S(0.001)S(0.004)S(0.117)S(0.755)ARPGT(0.117)PSDHQSQEASQFER 234.04 4.44E-50 114250000 11447 6154.7 13069 10558 14730 10797 19793 14072 22708 TRUE FALSE 10905.923 6781.870927 13668.22658 9496.689781 17298.90734 10423.09718 16773.21433 12839.78108 26229.44066 0.415789385 0.258559495 0.52110248 0.36206223 0.65952254 0.397381603 0.639480443 0.489517914 1 14.67889942 -5 0.126608819 2.865032676 0.209037661 0.725200993 0.108255009 65.47766687 0.527973524 30.82329931 0.773309509 1.00E-05 5 -2.655995015 TDS(ph)IGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDSIGEK 7 0 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;Q7Z3U7-3 A0A286YFF8 MON2 Protein MON2 homolog 1 TDS(1)IGEK;T(0.004)DS(0.996)IGEK 107.21 0.0078984 452870000 1406730 1102220 1137560 1694070 909000 1634830 1662180 1455560 1020460 TRUE FALSE 1340236.661 1214537.471 1189718.251 1523778.865 1067529.312 1578215.427 1408583.913 1328103.45 1178707.725 1.137039007 1.030397481 1.009341184 1.292753778 0.905677709 1.338937036 1.195023909 1.126745352 1 20.1687746 3.28209804 24.99992253 1.158139726 1.063971715 0.077882822 0.129679346 297.2390398 170677.5608 0.032827059 0.044447791 1914.68811 -3.28209804 -0.094168011 TDS(ph)PDMHEDT ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TDSPDMHEDT 10 0 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT 244.28 1.94E-12 2578550000 4063298 3507977 3619684 4105091 3039251 3927863 4228919 3884428 2591594 TRUE FALSE 3871233.956 3865443.845 3785650.092 3692439.454 3569295.412 3791840.119 3583719.737 3544286.892 2993485.161 1.293219691 1.291285454 1.26462965 1.233491818 1.19235447 1.266697483 1.197173042 1.184000154 1 21.51339469 -5 0.131716282 0.137181635 1.350913155 0.928532719 0.022791521 32.76238264 0.270914839 7.38506672 0.160820263 1.00E-05 5 1.213731521 TDS(ph)PWIKPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDSPWIKPAR 10 1 A0A1B0GV09;Q9H9B1-3;Q9H9B1;A0A0C4DGF8;A0A1B0GU48;Q9H9B1-4;A0A1W2PPZ7;A0A0D9SEQ1;A0A1B0GVZ8;A0A1B0GUD1;A0A0D9SER9 A0A1B0GV09 EHMT1 Histone-lysine N-methyltransferase EHMT1 1 TDS(1)PWIKPAR 137.16 5.97E-05 127490000 129640 119270 123880 145900 96418 131270 129430 134260 111750 TRUE FALSE 123512.1741 131423.7486 129560.0205 131233.8548 113233.2687 126724.087 109683.0764 122503.4826 129079.6193 0.956868132 1.018160337 1.003721744 1.0166892 0.877235843 0.981751323 0.849731948 0.949053641 1 16.9779017 2.749911424 24.99369558 0.920570839 0.997680961 0.318445934 0.047425125 707.824438 1558578.925 0.013206134 0.013890566 562.2266452 -2.749911424 0.077110121 TDS(ph)SPNQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 T(0.002)DS(0.588)S(0.411)PNQAR 83.081 0.017446 12818000 21109 19747 15611 20076 12943 17593 22705 20797 14860 TRUE FALSE 20111.2194 21759.24175 16326.77979 18057.92234 15200.2551 16983.75 19240.93524 18975.90443 17164.41291 1.17168117 1.267695078 0.951199431 1.052055927 0.885568017 0.989474565 1.120978349 1.105537634 1 14.06713289 3.742332076 24.99999998 1.020720131 1.219688131 0.578438178 0.07252726 225.0985461 1492112.439 0.019575984 0.033682284 5524.997377 -3.742332076 0.198968 TDS(ph)TSDGRPAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TDS(0.746)T(0.111)S(0.142)DGRPAWMR;TDS(0.941)T(0.035)S(0.023)DGRPAWMR;T(0.007)DS(0.952)T(0.04)S(0.001)DGRPAWMR;T(0.007)DS(0.95)T(0.04)S(0.003)DGRPAWMR;T(0.001)DS(0.974)T(0.024)S(0.001)DGRPAWMR;T(0.002)DS(0.447)T(0.32)S(0.231)DGRPAWMR;T(0.002)DS(0.931)T(0.044)S(0.024)DGRPAWMR;T(0.011)DS(0.945)T(0.042)S(0.002)DGRPAWMR;TDS(0.969)T(0.03)S(0.001)DGRPAWMR;TDS(0.955)T(0.043)S(0.001)DGRPAWMR;TDS(0.496)T(0.496)S(0.007)DGRPAWMR 211.49 1.30E-08 7359216000 4071970 3169995 3597760 4145330 3018897 3820520 4139210 3472770 2795728 TRUE FALSE 3879496.048 3493021.094 3762720.855 3728633.553 3545391.681 3688214.434 3507697.493 3168675.848 3229275.22 1.201351939 1.081673396 1.165190515 1.154634802 1.097890839 1.142118334 1.086218193 0.981234374 1 21.62277897 1.405565358 2.690596717 0.988334979 1.138159732 0.763881933 0.033938964 0.123176583 1.561675137 0.026566636 0.008475255 25.44282661 -1.405565358 0.149824753 TDS(ph)YSAGQSVEILDGVELGEPAHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDSYSAGQSVEILDGVELGEPAHKK 25 1 P42345;B1AKP8;B1AKQ2 P42345 MTOR Serine/threonine-protein kinase mTOR 1 T(0.181)DS(0.785)Y(0.015)S(0.019)AGQSVEILDGVELGEPAHKK;T(0.034)DS(0.952)Y(0.005)S(0.009)AGQSVEILDGVELGEPAHKK;T(0.161)DS(0.807)YS(0.033)AGQSVEILDGVELGEPAHKK 201.8 2.82E-25 220422000 498350 409691 443137 515690 240874 506020 527710 560860 247584 TRUE FALSE 474793.9831 451438.9787 463455.2698 463851.8615 282882.3493 488496.4005 447198.1474 511748.1251 285978.0622 1.660246172 1.578579053 1.62059728 1.62198407 0.989174999 1.708160398 1.563749834 1.789466371 1 18.12554495 TDSEKPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDSEKPFR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 92.062 0.012148 0 479850 414080 447350 483260 308310 500360 560900 531840 335370 FALSE TRUE 457168.4415 456275.2228 467861.44 434681.7867 362079.1664 483032.4077 475324.4034 485269.2701 387377.4668 1.180162711 1.177856902 1.207766275 1.122114279 0.934693413 1.246929543 1.227031627 1.252703917 1 18.56338051 3.240103992 24.99837358 1.146503871 1.185089554 0.051458005 0.10293537 192.8414614 3123419.868 0.029388747 0.037805182 1738.216995 -3.240103992 0.038585684 TDSREDEIS(ph)PPPPNPVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 TDS(0.005)REDEIS(0.994)PPPPNPVVK;TDS(0.002)REDEIS(0.998)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.003)REDEIS(0.997)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.016)REDEIS(0.984)PPPPNPVVK;TDS(0.001)REDEIS(0.999)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.004)REDEIS(0.996)PPPPNPVVK;TDS(0.018)REDEIS(0.982)PPPPNPVVK 180.66 4.69E-14 10830150000 5501988 4622884 4866198 5706490 3648471 5222447 6102710 5615279 4356236 TRUE FALSE 5241919.931 5093961.135 5089317.992 5132862.784 4284763.187 5041592.351 5171629.506 5123575.402 5031778.83 1.041762786 1.012357917 1.011435153 1.020089109 0.851540446 1.001950308 1.027793486 1.018243364 1 22.26263708 -0.386058762 9.332464939 1 1.000877525 0 0.053346569 0 0 0.050959848 0.012011351 0.411094094 0.386058762 0.000877525 TDSS(ph)PNQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.002)S(0.998)PNQAR;TDS(0.001)S(0.999)PNQAR;TDS(0.02)S(0.98)PNQAR;TDS(0.019)S(0.981)PNQAR 244.06 1.64E-10 3239360000 3011960 3072120 2753590 3399920 2132970 2976500 3023450 3118040 2560400 TRUE FALSE 2869590.62 3385172.521 2879844.825 3058153.582 2504959.293 2873423.059 2562167.173 2845007.888 2957453.755 0.970290952 1.144623991 0.973758193 1.034049502 0.846998635 0.97158681 0.866342261 0.961978825 1 21.49592418 2.827093469 8.240910742 0.920329467 1.040309544 0.359607271 0.066031271 0.283498982 24.04231963 0.018601703 0.019743885 671.573373 -2.827093469 0.119980077 TDSTESSGTQS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDSTESSGTQSPK 13 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 TDSTES(0.014)S(0.014)GT(0.03)QS(0.942)PK 80.469 0.01077 0 20640 18279 20490 20557 12437 20107 23097 21435 14447 TRUE FALSE 19664.3881 20141.65088 21429.48677 18490.5713 14606.00886 19410.68955 19573.12844 19558.03777 16687.36697 1.178399692 1.206999937 1.284174238 1.10805805 0.875273426 1.163196661 1.172930905 1.172026587 1 14.02646872 7.999999986 0.017146468 1.13E-08 2.552465912 0.178762675 0.104209218 7770.140151 10.28247628 592.2857209 984.3324583 99999996.7 -7.999999986 2.5524659 TDSTSDGRPAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 162.31 3.71E-05 848270000 731940 729540 691330 833840 630070 773460 843810 827890 751540 FALSE TRUE 697342.6468 803880.9554 723028.1643 750020.819 739954.0085 746674.8863 715071.2869 755395.5627 868084.9849 0.803311495 0.926039466 0.832900208 0.863994692 0.852398119 0.860140308 0.823734196 0.870186187 1 19.72747676 -2.26093742 1.498648915 1.356685559 0.855046377 0.665007147 0.032539804 101530.6788 14120.99155 121944.3782 0.008452603 0.00548356 2.26093742 -0.501639181 TDTESELDLISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 209.85 1.17E-07 36373000 185681 145898 160335 187105 162450 160532 195100 186472 158204 FALSE TRUE 176904.2271 160765.1721 167686.5183 168296.8499 190781.2286 154972.7366 165333.9117 170143.5231 182737.4683 0.968078571 0.879760312 0.917636213 0.920976149 1.044018122 0.848062185 0.904761969 0.931081757 1 17.47941295 4.749816907 10.79506238 0.923731128 0.968166691 0.028652528 0.056178013 0.215208772 999.6099398 0.012394596 0.071417863 56210.42999 -4.749816907 0.044435563 TDTGEPMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TDTGEPMGR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 155.88 0.00016812 102450000 736390 652000 684360 780590 622470 723640 789430 736130 669740 FALSE TRUE 701582.3041 718439.5413 715738.5829 702123.6102 731028.5709 698580.1654 668987.9546 671670.5547 773599.8586 0.906905936 0.928696578 0.925205162 0.90760566 0.944969887 0.903025198 0.864772592 0.868240276 1 19.56122801 2.011057234 24.27651817 0.892958988 0.921702388 0 0.039276065 318.9858293 700339.6358 0.013004211 0.009594939 102.5787101 -2.011057234 0.0287434 TDTS(ph)PVLETAGTVAAMAATPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 T(0.023)DT(0.135)S(0.842)PVLETAGTVAAMAATPSAR 136.61 1.12E-05 30559000 46235 39959 38550 55024 34618 42786 48580 44946 40240 TRUE FALSE 44049.56318 44030.86753 40317.55563 49492.88298 40655.36824 41304.31009 41168.22877 41010.28997 46480.21368 0.947705694 0.947303466 0.867413302 1.064816167 0.874681182 0.888642862 0.885715136 0.882317156 1 15.50432908 TDVSNFDEEFTGEAPTLS(ph)PPRDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.025)LS(0.975)PPRDAR;TDVSNFDEEFTGEAPT(0.289)LS(0.711)PPRDAR 122.89 7.08E-05 236830000 153752 115542 151919 141182 139814 129721 168734 140038 154257 TRUE FALSE 146484.4477 127315.8612 158884.6364 126990.1171 164197.5173 125228.7292 142990.5293 127775.5303 178178.3877 0.822122422 0.714541549 0.891716658 0.712713359 0.921534421 0.702827828 0.802513319 0.717121375 1 17.44296283 -1.159973845 4.602301396 1.000026942 0.784156438 0.433850975 0.076940591 1.96E-05 3.58E-06 0.063075628 0.014865046 0.069187264 1.159973845 -0.215870505 TDWDAGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDWDAGFK 8 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 107.66 0.0092114 45342000 204400 178020 164580 211860 124040 177110 191390 198230 134220 FALSE TRUE 194738.4171 196160.4404 172126.1558 190563.4303 145672.5367 170976.6363 162189.9404 180871.9303 155034.1521 1.25610012 1.265272443 1.1102467 1.229170655 0.939615786 1.102832079 1.046156206 1.166658622 1 17.24222653 3.374368808 1.2308654 1.062317161 1.265601803 0.492558783 0.077438967 0.325574611 1.027384853 0.025009491 0.044187838 2367.929717 -3.374368808 0.203284642 TDWDAGFKEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDWDAGFKEGR 11 1 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 71.555 0.039446 0 171540 71167 181560 135700 185930 149010 279180 189400 255350 FALSE TRUE 163431.6442 78418.99821 189884.7056 122059.1782 218356.1331 143849.7463 236585.9635 172815.1319 294948.3739 0.554102544 0.265873641 0.643789634 0.413832348 0.740319841 0.48771161 0.802126692 0.585916544 1 18.17010293 0.983341629 0.255665431 1.099771854 0.356256511 0.545805587 0.138972474 1.68265964 0.368939414 0.461416564 0.276933602 9.623690086 -0.983341629 -0.743515344 TDWLDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TDWLDGK 7 0 P30405;Q9UNP9-2;Q9UNP9;Q9UNP9-3;E9PKY5;E9PEQ6 P30405;Q9UNP9-2 PPIF;PPIE "Peptidyl-prolyl cis-trans isomerase F, mitochondrial;Peptidyl-prolyl cis-trans isomerase E;Peptidyl-prolyl cis-trans isomerase" 0 ; 111.65 0.015195 228840000 1333690 730630 926280 1077220 829580 957610 1253550 1206230 868250 FALSE TRUE 1270649.117 805082.0277 968750.8542 968935.799 974258.4893 924447.7256 1062297.924 1100606.107 1002893.776 1.266982753 0.802759023 0.965955595 0.966140007 0.971447339 0.9217803 1.059232743 1.097430389 1 19.93573738 -0.510175139 6.684464629 1.000017259 1.000881174 0 0.121261489 0 0 0.112009038 0.026400783 0.308904945 0.510175139 0.000863915 TDYNASVSVPDSSGPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TDYNASVSVPDSSGPER 17 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 194.85 1.19E-10 105610000 62251 51681 57428 64344 47178 59047 60685 57173 54155 FALSE TRUE 59308.5186 56947.35266 60061.1306 57876.01887 55405.82826 57002.18758 51426.38869 52166.62903 62553.08081 0.948131056 0.910384459 0.96016263 0.92523051 0.885740999 0.911261074 0.822123995 0.83395779 1 15.93279332 2.569867597 1.783791101 0.871118807 0.93536029 0.11857471 0.05083991 0.484177127 3.093345968 0.019266768 0.016526873 371.4219765 -2.569867597 0.064241483 TDYYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TDYYAR 6 0 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ;;; 149.11 0.024845 3622850000 1633210 1373210 1290320 1618300 1399330 1456640 1730860 1614010 1468140 FALSE TRUE 1556011.4 1513141.66 1349482.448 1455625.409 1643372.709 1406196.192 1466785.518 1472678.728 1695811.653 0.91756145 0.892281674 0.795773779 0.858365024 0.969077377 0.829217201 0.864946007 0.868421163 1 20.69354451 -2.150003385 2.279626059 1.273035029 0.875786275 0.414543502 0.046864377 4181429.631 1077377.949 5893217.944 0.011942003 0.007079403 2.150003385 -0.397248754 TEADAEKTFEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEADAEKTFEEK 12 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 77.279 0.026313 811030000 1020740 675410 963960 951470 659460 1017510 1216190 1138350 767090 FALSE TRUE 972491.6431 744235.0469 1008158.519 855826.4279 774469.6152 982273.3736 1030637.879 1038670.039 886046.3994 1.097562886 0.839950422 1.137816846 0.965893466 0.87407343 1.108602635 1.163187254 1.172252424 1 19.75702272 2.091316704 8.371672257 1.131385808 0.980418913 0.281715089 0.099839641 0.272982394 22.14141981 0.034892349 0.025742778 123.4004388 -2.091316704 -0.150966894 TEAHQDVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEAHQDVVGR 10 0 Q9H0A0;Q9H0A0-2;A0A087WV29;E9PMU0 Q9H0A0 NAT10 N-acetyltransferase 10 0 80.014 0.025277 35709000 35058 52609 32977 47215 32904 26928 39424 38488 31970 FALSE TRUE 33400.87782 57969.91691 34489.02807 42468.8585 38642.44718 25995.47661 33409.14473 35117.78668 36927.74432 0.904492772 1.569820144 0.933959783 1.150052874 1.046434 0.703955172 0.904716639 0.95098651 1 15.17241752 2.739568655 1.635472094 0.880114041 1.196406967 0.233298624 0.197735214 0.427935507 2.28856241 0.075592149 0.073333274 548.9953359 -2.739568655 0.316292926 TEAQDLCRAS(ph)PEPPGPESSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TEAQDLCRASPEPPGPESSSR 21 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR;TEAQDLCRAS(1)PEPPGPESSSR 209.18 1.65E-22 11633580000 5896130 3274640 6286950 5119100 6046590 5469330 8287170 6114830 8017730 TRUE FALSE 5617431.62 3608329.539 6575212.876 4604518.342 7101113.382 5279925.731 7022810.012 5579383.068 9261078.62 0.606563431 0.389623033 0.709983485 0.497190288 0.766769582 0.570119956 0.758314479 0.602454994 1 23.1427488 -4.999999997 0.1148209 2.337099706 0.383898066 0.569972011 0.109915632 98.29708067 0.741536991 30.42815803 1.06030742 1.00E-05 4.999999997 -1.95320164 TEARSS(ph)DEENGPPS(ph)SPDLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEARSSDEENGPPSSPDLDR 20 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 T(0.245)EARS(0.354)S(0.401)DEENGPPS(0.531)S(0.469)PDLDR 86.551 0.000981 0 28214 19498 25297 23133 23552 25990 29657 28484 26289 TRUE FALSE 26880.38013 21484.86837 26456.89247 20807.62689 27659.46134 25089.95978 25132.27996 25989.78996 30365.76385 0.885219956 0.70753591 0.871273734 0.685233113 0.910876521 0.826258147 0.827651828 0.855891196 1 14.89015804 0.014252647 0.440251001 1.025778583 0.796618022 0.402181497 0.070924103 3.868328655 0.981120383 0.239903325 0.037879418 1.033362379 -0.014252647 -0.229160561 TECAEPPRDEPPADGALKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TECAEPPRDEPPADGALKR 19 2 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 49.34 0.085773 85235000 98792 89244 82204 108790 62616 98390 104290 104970 73709 FALSE TRUE 94122.29795 98338.06506 85973.13471 97854.22251 73536.21058 94982.72963 88378.64508 95778.27032 85139.41527 1.105507921 1.155023966 1.009792403 1.149341022 0.863715241 1.115614071 1.038046183 1.124958047 1 16.37753956 3.743152994 24.86160262 1.045615143 1.130265945 0.164856188 0.081437775 561.3402984 3038900.569 0.01890388 0.032829336 5535.45078 -3.743152994 0.084650802 TECYGYALGDATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TECYGYALGDATR 13 0 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 152.85 2.99E-06 0 72309 68307 63957 72863 64022 64489 79993 70535 84712 FALSE TRUE 68891.09687 75267.56096 66889.49171 65538.67281 75187.41653 62255.72976 67788.59868 64358.58147 97848.70431 0.704057324 0.76922389 0.6836012 0.669796021 0.768404825 0.636244805 0.692789947 0.657735653 1 16.57826513 -0.781978498 5.571812044 1.000000049 0.701930318 0.829436972 0.04303962 2.52E-08 5.68E-09 0.040825327 0.00962262 0.165204359 0.781978498 -0.298069731 TEDEEFLIQHLLQAPS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR 277.1 1.10E-39 738324000 858627 981726 745096 1033050 649784 874029 793347 874940 575086 TRUE FALSE 818041.4033 1081764.996 779259.3886 929205.8513 763106.1239 843761.1566 672307.3443 798325.6153 664267.3997 1.23149413 1.628508333 1.173110992 1.398843074 1.148793579 1.270213105 1.012103476 1.20181363 1 19.34140459 2.459589093 0.751498307 1.054407456 1.411444184 0.411464392 0.140049157 0.5570523 0.632519024 0.099022142 0.073293875 288.1304074 -2.459589093 0.357036727 TEDFIIDTLELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEDFIIDTLELR 12 0 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 121.9 0.00085632 4371800 14764 15543 11449 15420 12355 11991 14319 14088 11470 FALSE TRUE 14066.13498 17126.84937 11973.94797 13869.9523 14509.70809 11575.74866 12134.37356 12854.38003 13248.70902 1.061698537 1.292718358 0.903782245 1.046890854 1.095179015 0.873726538 0.915891016 0.970236422 1 13.69356417 3.729818004 24.98899705 0.967673285 1.17720845 0.49749814 0.085543544 448.0801865 1280746.784 0.022684619 0.035724178 5368.067942 -3.729818004 0.209535165 TEDGDWEWS(ph)DDEMDEKSEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEDGDWEWSDDEMDEKSEEGK 21 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 T(0.001)EDGDWEWS(0.997)DDEMDEKS(0.003)EEGK 60.521 0.034006 45482000 48188 43859 48786 47599 30095 50944 53951 51739 35571 TRUE FALSE 45910.24874 48328.28196 51022.88636 42814.25809 35343.55847 49179.79651 45719.78407 47208.45887 41087.16901 1.117386519 1.176237817 1.241820441 1.042034755 0.860209144 1.196962402 1.112750895 1.148983004 1 15.32640031 1.00594828 0.013898102 3.60E-07 2.16261988 0.094559801 0.104741825 1903.635843 17.9181412 1416.803345 1367.491283 10.13790646 -1.00594828 2.16261952 TEDGGWEWS(ph)DDEFDEESEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEDGGWEWSDDEFDEESEEGK 21 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGK 215.48 4.22E-25 37989000 73589 88002 54375 89705 50703 100730 69510 80566 33419 TRUE FALSE 70110.59381 96969.50385 56868.14753 80687.68297 59545.58715 97241.69484 58904.97286 73511.21393 38601.44784 1.816268501 2.512069087 1.473212812 2.090276077 1.542573931 2.519120403 1.525978329 1.904364164 1 15.23636734 -1.894713273 0.260559478 2.18E-12 2.080393397 0.378475215 0.372010321 27.76009263 1.138581375 17.51721388 0.477563369 0.012743441 1.894713273 2.080393397 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;T(0.009)EDGGWEWS(0.991)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR 267.83 1.60E-54 906725000 549798 382004 392136 509957 318357 491129 563200 537346 306647 TRUE FALSE 523810.1381 420930.6419 410115.8235 458695.1535 373878.36 474121.0796 477273.4961 490293.1356 354200.2506 1.478853099 1.188397358 1.157864295 1.295016457 1.055556452 1.338567883 1.34746798 1.384225829 1 18.43420571 4.608140385 3.02788667 1.239903233 1.487254293 0.275882602 0.127595794 0.401521362 6.144209125 0.029810284 0.202620136 40563.96369 -4.608140385 0.247351061 TEDGKVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TEDGKVEK 8 1 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;; 92.062 0.010984 938880000 1460490 1209920 1237200 1559760 1387640 1483540 1543270 1612440 1165930 FALSE TRUE 1391455.532 1333212.224 1293926.844 1402969.961 1629643.977 1432164.638 1307815.817 1471246.206 1346736.47 1.033205503 0.989957764 0.960786964 1.041755379 1.210068943 1.063433471 0.971100024 1.092452932 1 20.36103614 3.011547557 23.70569326 1.064294525 0.999417296 0.207014755 0.06462391 213.8530498 439007.4096 0.019343838 0.023098094 1026.945879 -3.011547557 -0.06487723 TEDLFENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEDLFENR 8 0 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 0 95.909 0.02114 0 220030 191320 189840 214450 197520 194370 219810 222180 217620 FALSE TRUE 209629.618 210815.7255 198544.3518 192893.0786 231967.4255 187638.9182 186273.9474 202724.7413 251367.3982 0.833957066 0.838675688 0.78985721 0.767375085 0.92282224 0.746472771 0.741042589 0.806487806 1 17.93943802 TEDPDLPAFYFDPLINPISHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TEDPDLPAFYFDPLINPISHR 21 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 250.79 4.19E-31 337704000 326853 286966 269872 354917 280807 298810 341406 331620 266424 FALSE TRUE 311403.3065 316208.1617 282245.8981 319240.0689 329779.6519 288462.1348 289318.2443 302581.5948 307739.6732 1.011904975 1.027518351 0.917157984 1.037370533 1.071618906 0.937357643 0.940139571 0.983238825 1 18.23135092 2.205929357 24.9999997 0.957231121 1.01170943 0.225508747 0.042986101 254.3509568 194865.985 0.01566871 0.011573031 160.6679886 -2.205929357 0.054478309 TEDQRNEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEDQRNEEK 9 1 P63092-4;P63092;P63092-3;A0A0A0MR13;Q5JWD1;P63092-2 P63092-4;P63092-2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short 0 ;; 117.7 0.0010118 309099000 725740 447770 683400 627320 547190 655400 861410 796220 756950 FALSE TRUE 691435.7085 493398.2721 714734.566 564260.6018 642619.7628 632703.3337 729986.0836 726498.7558 874333.94 0.790814215 0.564313301 0.817461765 0.645360515 0.734982063 0.723640367 0.834905349 0.830916796 1 19.73782488 1.127865387 0.708105459 0.998449605 0.69135754 0.619796063 0.072583415 0.395744469 0.465880382 0.063772905 0.02582034 13.42348824 -1.127865387 -0.307092065 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH 31 1 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 0 ; 167.06 1.11E-12 327530000 138204 76030 139081 126098 140517 124758 174737 133282 271280 FALSE TRUE 131671.3708 83777.54344 145458.0014 113422.3895 165023.1203 120437.5992 148077.6614 121611.1215 313348.7169 0.420207149 0.267362012 0.464204873 0.361968578 0.526643677 0.384356446 0.47256508 0.388101546 1 18.25740956 -5 0.281695222 5.408125605 0.36662714 0.871832538 0.070907653 70.26486061 0.670883528 181.1993511 0.073132596 1.00E-05 5 -5.041498465 TEDTEHVIIPVCLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEDTEHVIIPVCLR 14 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 ; 98.531 0.0025409 126324000 131844 130398 163379 180675 112005 156410 141196 168764 141403 FALSE TRUE 125611.9954 143685.7045 170870.0888 162513.2057 131538.6365 150993.4825 119653.957 153986.1295 163331.0551 0.769063761 0.879720666 1.046157993 0.994992689 0.805349825 0.924462788 0.732585465 0.942785372 1 17.3174396 2.701261272 24.9571536 0.857428254 0.905180846 0 0.10409444 2103.412627 1407400.782 0.034456645 0.032486829 502.6448898 -2.701261272 0.047752593 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.997)PT(0.003)GTPTR;TEEARPSPAPGPGT(0.989)PT(0.011)GTPTR;TEEARPSPAPGPGT(0.997)PT(0.003)GTPTR 285.53 3.74E-45 666910000 217465 204030 197020 208003 173404 205284 248630 218512 213191 TRUE FALSE 207185.8604 224820.889 206053.5619 187094.1433 203645.6027 198174.9636 210696.9271 199377.9309 246251.5715 0.841358531 0.912972403 0.836760394 0.759768322 0.826981942 0.80476629 0.855616579 0.809651405 1 17.90977341 -1.524085072 5.584455467 1.000358296 0.837082317 0.641937257 0.039436962 0.000187948 1.60E-05 0.040794307 0.009594414 0.029916786 1.524085072 -0.16327598 TEEDSEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEEDSEEVR 9 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 131.22 0.00078905 151916000 268547 334300 203485 330310 181791 232279 215664 260677 179042 FALSE TRUE 255853.3155 368365.5501 212814.9885 297106.6113 213495.2928 224235.12 182760.4959 237850.7399 206806.9189 1.237160327 1.781205155 1.029051589 1.436637675 1.032341152 1.084272814 0.883725249 1.150110166 1 17.65792493 2.963751807 1.100220481 0.99511904 1.472426539 0.390221137 0.202524957 0.392224495 1.014390321 0.085384728 0.09974749 919.9236993 -2.963751807 0.477307499 TEEEFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TEEEFKK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 107.66 0.011908 1813200000 3614690 3959890 3057780 5304920 2470450 5415680 5205220 5421070 2538170 FALSE TRUE 3443830.767 4363407.293 3197982.238 4771659.363 2901295.698 5228133.644 4411068.089 4946372.372 2931776.44 1.174656676 1.48831515 1.090800169 1.627565901 0.98960332 1.783264771 1.504571777 1.687158783 1 21.48334367 2.228011122 24.99982181 1.541289036 1.302065813 0.122734374 0.273518378 361.1482974 855830.1903 0.08804461 0.065702828 169.0484223 -2.228011122 -0.239223223 TEEGSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TEEGSVR 7 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 0 ;;; 104.11 0.019134 2749990000 2105580 1995840 1824610 2116210 1647840 1975280 2082040 2050770 1755820 FALSE TRUE 2006053.406 2199218.365 1908270.173 1903484.55 1935222.774 1906875.558 1764386.559 1871193.707 2028103.598 0.98912768 1.084371808 0.940913558 0.938553904 0.954203117 0.940225914 0.869968655 0.922632211 1 20.95169992 3.63954807 6.315680084 0.92912296 1.036351884 0.511537349 0.039444836 0.152931894 8.184464224 0.010402975 0.016219807 4360.618267 -3.63954807 0.107228924 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 TEELIES(0.997)PKLES(0.003)SEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(0.999)PKLESSEGEIIQTVDR 229.65 3.04E-33 436664000 253524 233940 233030 264216 153465 266082 269875 284274 165907 TRUE FALSE 241540.423 257778.752 243714.656 237656.5057 180229.2474 256867.5136 228700.6122 259381.4615 191635.0102 1.260419078 1.34515479 1.271764777 1.240151815 0.940481842 1.340399718 1.193417695 1.353518134 1 17.54800163 -4.500891164 0.237617226 4.74E-18 1.27122039 0.265466305 0.121140965 176.761623 2.195242493 85.96919317 0.186680986 3.16E-05 4.500891164 1.27122039 TEEPDRDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TEEPDRDER 9 1 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 143.37 9.31E-05 694350000 1100400 1084810 983900 1252800 895820 1044280 1114250 1089310 895700 FALSE TRUE 1048386.273 1195353.372 1029012.788 1126866.164 1052050.724 1008116.322 944250.6979 993924.2416 1034600.581 1.013324651 1.155376668 0.994599082 1.089179906 1.016866551 0.974401465 0.912671726 0.960684016 1 19.98064248 2.367949415 2.253011284 0.947617683 1.069419273 0.484556322 0.048392314 0.211119283 2.196928406 0.019049315 0.0145334 233.3186288 -2.367949415 0.12180159 TEEPLGS(ph)PHPSGTVESPGEGPQDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEEPLGSPHPSGTVESPGEGPQDTR 25 0 A0A0A0MR84;M0R202;A0A0B4J2G2;Q9NWS9-2;Q9NWS9 A0A0A0MR84 ZNF446 Zinc finger protein 446 1 T(0.001)EEPLGS(0.999)PHPSGTVESPGEGPQDTR 114.03 0.0012269 85814000 16616 12797 16911 15732 18985 15223 15818 18394 13636 TRUE FALSE 15830.59461 14101.02885 17686.38608 14150.58947 22295.97799 14695.82369 13404.67358 16783.32385 15750.60124 1.00507875 0.895269243 1.122902282 0.898415829 1.415563613 0.933032554 0.851057898 1.065567187 1 13.94311928 3.759954644 24.2161903 1.026953523 0.950174016 0.048457243 0.158027041 1986.660235 2248717.201 0.04003081 0.072059046 5753.79844 -3.759954644 -0.076779506 TEERAELAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEERAELAESR 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 122.34 0.00035817 434830000 393990 226029 438070 296132 463960 380730 612350 440330 597140 FALSE TRUE 375366.8735 249061.6121 458155.9428 266364.2487 544874.4771 367545.2246 518924.7609 401772.3709 689741.4214 0.544213907 0.361094179 0.664243046 0.386179865 0.789969197 0.532873934 0.752346814 0.58249709 1 19.39569608 -4.058667944 0.104603942 2.207444499 0.256280826 0.558414231 0.127068938 85.4972573 0.741544989 23.52551505 1.706988668 8.74E-05 4.058667944 -1.951163672 TEESPAS(ph)DEAGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEES(0.002)PAS(0.998)DEAGEK;TEES(0.001)PAS(0.999)DEAGEK 225.36 1.32E-11 182340000 460979 671030 335514 595910 254968 557430 362877 464220 180406 TRUE FALSE 439189.4362 739408.7199 350897.6488 536007.9946 299434.3385 538126.0593 307513.449 423570.4358 208382.4411 2.107612493 3.548325454 1.683911787 2.572232055 1.436946112 2.582396369 1.475716703 2.032658959 1 17.66887419 1.84504318 0.26021739 0.859665136 3.01092112 0.344701998 0.587900693 1.833134764 0.46612946 1.235311722 1.504603778 69.99115813 -1.84504318 2.151255984 TEESPASDEAGEKEAKS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEESPASDEAGEKEAKSD 18 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D 171.5 1.03E-11 975010000 1743120 1761100 1466170 2006200 604640 2028450 1671590 1938300 507310 TRUE FALSE 1660726.172 1940558.092 1533395.345 1804532.964 710089.0246 1958204.268 1416558.245 1768572.176 585981.0438 2.834095385 3.311639707 2.616800255 3.079507406 1.211795214 3.341753609 2.417413088 3.018138889 1 19.16049447 TEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 TEFLDLDNSPLS(0.039)PPS(0.961)PR;TEFLDLDNSPLS(0.011)PPS(0.989)PR;TEFLDLDNSPLS(0.015)PPS(0.985)PR;TEFLDLDNSPLS(0.004)PPS(0.996)PR;TEFLDLDNSPLS(0.25)PPS(0.75)PR 166.6 2.44E-09 150519000 179759 171265 159068 200231 155548 183616 196747 194268 174561 TRUE FALSE 171262.1483 188717.0982 166361.4251 180103.3995 182675.522 177257.3319 166729.6316 177256.864 201631.0283 0.849383896 0.935952664 0.825078494 0.893232559 0.90598914 0.879117333 0.826904634 0.879115013 1 17.62135814 -1.950785247 5.955509728 1.063635098 0.87503291 0.571877665 0.03416256 0.024315725 0.000200939 0.027864796 0.007641734 0.011199916 1.950785247 -0.188602188 TEFLHSQNS(ph)LS(ph)PRS(ph)SLS(ph)DEAPVLPNTTPDLLLATTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEFLHSQNSLSPRSSLSDEAPVLPNTTPDLLLATTAK 37 1 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 4 T(0.567)EFLHS(0.578)QNS(0.591)LS(0.592)PRS(0.613)S(0.072)LS(0.411)DEAPVLPNT(0.292)T(0.282)PDLLLAT(0.001)T(0.001)AK 43.062 0.065352 66922000 12243 6841.1 15592 12321 14897 9990.3 22897 19323 11881 TRUE FALSE 11664.29765 7538.215868 16306.90862 11082.46967 17495.03208 9644.333406 19403.64212 17630.97568 13723.4448 0.849954062 0.549294727 1.188251846 0.80755742 1.274828029 0.702763304 1.413904628 1.284733967 1 13.74435505 3.182757314 0.741905446 1.1881444 0.694940692 0.251152162 0.243709397 0.7751212 0.942508375 0.130878247 0.217276603 1523.201344 -3.182757314 -0.493203708 TEFLHSQNSLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEFLHSQNSLSPR 13 0 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 TEFLHSQNSLS(1)PR;TEFLHSQNSLS(1)PR 211.12 1.58E-08 358280000 728400 585010 656850 704980 630420 614440 763970 677820 572180 TRUE FALSE 693969.9755 644623.1841 686967.2222 634114.071 740365.0484 593161.7887 647412.3452 618466.4875 660910.7521 1.050020708 0.975355874 1.039425096 0.959454917 1.120219403 0.89749151 0.979576052 0.935779128 1 19.33409594 2.211694222 24.99999653 0.952587607 1.020837246 0.348315765 0.050777071 249.076643 231771.6826 0.016785244 0.012400372 162.8149281 -2.211694222 0.068249639 TEGT(ph)PPPPGQPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEGTPPPPGQPAK 13 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;A0A494C150;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 T(0.033)EGT(0.967)PPPPGQPAK;TEGT(1)PPPPGQPAK;T(0.003)EGT(0.997)PPPPGQPAK 126.32 0.0021231 354289000 1051820 784600 840525 1078610 718583 953620 1136390 1040040 774770 TRUE FALSE 1002102.553 864551.632 879063.9026 970186.0736 843903.6477 920595.9003 963012.8343 948968.584 894917.3746 1.119771033 0.966068663 0.982284988 1.08410687 0.94299616 1.028693739 1.076091337 1.060397989 1 19.77139496 1.982523552 24.00670045 1.053561421 1.019229715 0.038690585 0.055521096 1229.030912 1688268.135 0.021580772 0.014281224 96.05579088 -1.982523552 -0.034331706 TEHAEFLHCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEHAEFLHCK 10 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 163.64 3.70E-06 287190000 410070 465570 370270 422650 278590 409800 438280 413780 42719 FALSE TRUE 390686.8038 513012.1123 387247.2457 380164.419 327176.0078 395608.5232 371412.3364 377547.2296 49343.64434 7.917672255 10.39672118 7.847966053 7.704425242 6.630560271 8.017415992 7.527055235 7.651385192 1 15.59057665 -0.365181468 0.430940211 2.00E-13 8.627169094 0.846464676 0.934128944 2.788432917 0.52413113 6.945518349 0.578414444 0.431338806 0.365181468 8.627169094 TEKYEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEKYEHK 7 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 ; 122.52 0.0026036 267950000 1161760 923990 972810 1181440 641060 1176630 1211650 1211530 637870 FALSE TRUE 1106845.907 1018145.631 1017414.301 1062679.407 752860.661 1135883.008 1026790.539 1105442.01 736787.6218 1.502259097 1.381871249 1.380878656 1.442314413 1.021815023 1.541669505 1.393604491 1.500353667 1 19.4908893 -1.959826464 2.559111511 0.686823582 1.396832052 0.427854013 0.143760854 20036761.27 12326232.77 37332477.97 0.035132274 0.010969164 1.959826464 0.71000847 TELDAHFENLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TELDAHFENLLAR 13 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9 B7ZC38 SH3GLB2 Endophilin-B2 0 84.566 0.0096853 155890000 306500 306890 270980 339950 261780 280610 307180 282200 220620 FALSE TRUE 292012.3524 338162.4399 283404.701 305777.5801 307434.3491 270892.4053 260314.0493 257489.072 254832.6228 1.145898626 1.326998232 1.11212096 1.199915367 1.206416768 1.063020905 1.021509909 1.01042429 1 17.95919045 2.144113013 2.758246322 1.01527573 1.209034083 0.710529375 0.055793608 0.142257833 2.169265376 0.024460709 0.016206893 139.3519379 -2.144113013 0.193758352 TELNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TELNKK 6 1 Q92901 Q92901 RPL3L 60S ribosomal protein L3-like 0 ;;;; 97.071 0.066524 2126890000 4238590 3584480 4137860 5461490 2649572 5068970 5627430 5963300 3957180 FALSE TRUE 4038240.251 3949742.587 4327584.974 4912490.649 3111656.518 4893430.298 4768862.199 5441121.839 4570839.264 0.883478945 0.864117585 0.946781264 1.074745876 0.680762621 1.070575887 1.043323102 1.190398858 1 22.12402766 2.059452913 24.99999952 1.076281424 0.895076072 0.429956985 0.106408927 67.10322347 28216.49374 0.036542662 0.026988542 114.6708185 -2.059452913 -0.181205352 TELPQFVSYFQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TELPQFVSYFQQR 13 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 89.356 0.010931 0 111117 78672 100224 93236 127957 88003 121027 105110 143088 FALSE TRUE 105864.7196 86688.76624 104819.3695 83863.74014 150272.6603 84955.43404 102562.1083 95906.01118 165277.3562 0.640527668 0.524504797 0.634202845 0.507412159 0.909215053 0.514017382 0.620545431 0.580273144 1 17.33452956 -2.109819714 2.331922227 1.700410981 0.611663466 0.523486682 0.114959938 4965253.104 1355509.135 18436244.1 0.0254922 0.007765694 2.109819714 -1.088747515 TEMDWVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEMDWVLK 8 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 105.57 0.01015 201320000 599800 440160 434120 605960 455270 519680 622440 589580 489330 FALSE TRUE 571448.6427 485012.8044 454024.8314 545047.7496 534668.9439 501683.3513 527475.3461 537953.2496 565212.7972 1.011032739 0.858106552 0.803281231 0.964323087 0.945960436 0.887600836 0.933233198 0.951771178 1 19.10843461 0.989157479 1.459542469 0.999703946 0.911955971 0.198016278 0.056939574 0.7511995 3.26673827 0.053497223 0.01589831 9.753432406 -0.989157479 -0.087747975 TEMEDLMSSKDDVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TEMEDLMSSKDDVGK 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 254.2 9.92E-25 753590000 2257210 1714074 2074510 2270060 1218737 2453650 2631470 2660710 1318969 FALSE TRUE 2150516.157 1888740.089 2169628.335 2041869.256 1431284.347 2368679.485 2229990.921 2427724.127 1523507.976 1.411555561 1.239731015 1.424100411 1.340241921 0.939466264 1.554753583 1.463721199 1.593509299 1 20.53896562 TEMSEVLTEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEMSEVLTEILR 12 0 O43615;M0QXM9;M0QXU7 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 ; 90.15 0.020989 14229600 22457 18067.3 21051 20573 21483 17510.8 24882 21497 18569.4 FALSE TRUE 21395.50212 19908.37841 22016.20917 18504.96295 25229.6284 16904.39661 21085.79391 19614.60872 21449.04771 0.997503591 0.928170736 1.026442268 0.862740538 1.176258673 0.788118747 0.983064339 0.914474572 1 14.38862598 TENDHINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TENDHINLK 9 0 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ; 138.08 0.00014665 654420000 1604570 1501620 1407160 1677470 1084910 1541090 1701230 1639450 937490 FALSE TRUE 1528725.156 1654636.785 1471679.678 1508847.529 1274117.961 1487721.667 1441676.118 1495891.067 1082871.161 1.411733188 1.528008912 1.359053349 1.393376777 1.176610853 1.373867659 1.331345935 1.381411862 1 20.04643017 -4.20596897 0.140352855 2.56E-15 1.523114948 0.671831055 0.082734309 61.81056514 0.654980737 18.08347555 0.514438142 6.22E-05 4.20596897 1.523114948 TENNDHINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TENNDHINLK 10 0 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;;;;;;;; 180.66 1.97E-06 11034420000 32234680 28425270 27834750 33083210 20821320 31124350 33390790 32416640 20096810 FALSE TRUE 30711010.56 31321837.33 29111000.82 29757622.88 24452551.62 30046505.96 28296411.72 29578067.15 23213320.65 1.322990839 1.34930447 1.254064477 1.281920123 1.053384476 1.294364835 1.218973026 1.274185094 1 24.46844958 -5 0.094924247 0.200366755 1.452940143 0.535281481 0.077532274 148.5970771 0.97030621 24.10007516 1.471128946 1.00E-05 5 1.252573388 TENPLILIDEVDKIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TENPLILIDEVDKIGR 16 1 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 179.14 2.44E-09 52530000 87226 62424 76645 67996 55293 65228 77598 80369 62603 FALSE TRUE 83102.99985 68785.07657 80159.24906 61160.9129 64936.08169 62969.138 65758.99991 73331.4643 72311.15351 1.149241795 0.95123744 1.108532297 0.845801926 0.898009208 0.870808097 0.909389447 1.014110006 1 16.14193057 4.908337954 0.692999355 0.922179566 1.327904646 0.410743636 0.076165562 3.220801183 0.995359757 0.028820087 1.082821368 80972.57559 -4.908337954 0.40572508 TEPAAEAEAASGPSESPS(ph)PPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 TEPAAEAEAASGPS(0.014)ES(0.042)PS(0.944)PPAAEELPGSHAEPPVPAQGEAPGEQAR;TEPAAEAEAAS(0.004)GPS(0.082)ES(0.393)PS(0.522)PPAAEELPGSHAEPPVPAQGEAPGEQAR 209.16 1.47E-38 435480000 71329 65436 68089 77942 67317 68153 78249 76584 56625 TRUE FALSE 67957.41953 72104.00279 71210.948 70107.12208 79057.06349 65792.84452 66310.67791 69877.89896 65406.1158 1.039007113 1.102404598 1.088750603 1.071874109 1.20871057 1.00591273 1.013829932 1.068369496 1 15.99713792 TEPS(ph)SPLSDPSDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.769)S(0.231)PLSDPSDIIR 178.67 7.37E-07 114190000 329080 330440 253640 347430 228260 294190 295010 320700 229760 TRUE FALSE 313525.0406 364112.2117 265269.6449 312505.6763 268068.4717 284002.1265 250000.8063 292617.8079 265390.0073 1.181374701 1.371989154 0.999546469 1.177533696 1.010092559 1.070131198 0.942012884 1.102595425 1 18.01775452 3.730421382 24.99859731 1.040522762 1.27668193 0.603909125 0.078612953 330.2759707 1014399.704 0.019805 0.031269882 5375.531136 -3.730421382 0.236159167 TEPSS(ph)PLSDPSDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.24)S(0.76)PLSDPSDIIR;TEPS(0.038)S(0.962)PLSDPSDIIR;TEPS(0.432)S(0.568)PLS(0.001)DPSDIIR;TEPS(0.056)S(0.944)PLSDPSDIIR 206.49 1.93E-11 282652000 743674 804980 608113 862120 551152 690710 706310 716620 539319 TRUE FALSE 708522.0038 887008.3772 635995.5826 775458.0597 647272.7343 666790.5395 598549.4372 653868.9538 622953.8361 1.137358762 1.423874974 1.020935334 1.244808226 1.039038042 1.070369104 0.960824707 1.049626659 1 19.24876573 2.875249829 0.966686193 0.999967689 1.260971889 0.414928207 0.105054036 0.424928017 0.85810053 0.051354693 0.054995268 750.3257121 -2.875249829 0.2610042 TEPTS(ph)PTPSAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 TEPT(0.003)S(0.991)PT(0.006)PSAFK 144.57 6.63E-05 71915000 209400 254750 200080 271770 147980 236150 214200 232280 164650 TRUE FALSE 199502.077 280709.3146 209253.8659 244451.1633 173787.6651 227972.0663 181519.8559 211940.3318 190183.0811 1.049000131 1.475995199 1.100275927 1.28534653 0.913791406 1.198697934 0.954447971 1.11440161 1 17.53702938 2.753938938 24.85766661 1.040454641 1.242117517 0.321840302 0.137261831 803.1747425 1298258.209 0.038598096 0.040793174 567.4648144 -2.753938938 0.201662877 TEQELPRPQS(ph)PSDLDS(ph)LDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 2 TEQELPRPQS(0.99)PS(0.01)DLDS(1)LDGR 103.86 0.00015885 97368000 78625 71729 72686 89447 60907 78473 84889 78853 72755 TRUE FALSE 74908.55207 79038.26665 76018.725 80455.61762 71529.16152 75755.46033 71937.62396 71948.21329 84037.47382 0.891370821 0.940512167 0.904581272 0.957377869 0.851157921 0.901448567 0.856018401 0.856144408 1 16.35874517 2.734757797 24.99896102 0.88258482 0.9216881 0.072656264 0.046397525 602.6234397 3961509.1 0.012974783 0.012643535 542.9474488 -2.734757797 0.03910328 TEQELPRPQS(ph)PSDLDSLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 1 TEQELPRPQS(0.906)PS(0.094)DLDSLDGR 148.09 6.93E-08 144790000 149620 146320 134140 159450 138810 142970 146780 166980 131850 TRUE FALSE 142547.7591 161230.1744 140290.4517 143421.7831 163018.4201 138018.9131 124386.0152 152358.346 152296.6246 0.935987646 1.058658882 0.921165863 0.941726604 1.070400742 0.906250637 0.816735207 1.000405271 1 17.21652444 2.065272284 24.99821846 0.904385609 0.986305093 0.075702986 0.072352406 81.55347666 31232.73144 0.025580756 0.018892638 116.217702 -2.065272284 0.081919484 TES(ph)PATAAETASEELDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;T(0.001)ES(0.998)PATAAETASEELDNR;T(0.003)ES(0.997)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR 470.24 7.08E-195 2430950000 525309 479920 536966 593639 429962 557228 611139 587929 496513 TRUE FALSE 500478.6846 528824.3936 561586.4222 533965.2799 504947.2367 537931.0546 517898.5212 536446.82 573509.7002 0.872659494 0.92208448 0.97920998 0.931048385 0.880451083 0.937963306 0.903033586 0.935375321 1 19.12945836 -5 0.308184026 1.718262904 0.914042004 0.410012214 0.030230064 300.3790767 2.731037035 139.9385412 0.028788343 1.00E-05 5 -0.8042209 TESDDLHTFLLEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TESDDLHTFLLEIK 14 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ;; 189.5 7.11E-07 98631000 397266 313958 336596 403756 255143 383482 418825 413254 238562 FALSE TRUE 378488.0235 345950.6771 352029.2595 363169.6798 299639.8584 370201.9222 354925.554 377067.289 275556.9766 1.373538163 1.255459693 1.277518951 1.317947687 1.087397104 1.34346779 1.288029643 1.368382299 1 18.07199113 -1.045131671 4.077011998 0.999964654 1.287967192 0.556432846 0.081077737 4139981.782 2123666.053 1259.797055 0.017567234 0.090129784 1.045131671 0.288002538 TESSTEGKEQEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TESSTEGKEQEEK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 170.56 2.43E-05 366590000 439360 401003 476290 641320 280056 622860 609960 681370 284394 FALSE TRUE 418592.3235 441865.6616 498128.3676 576853.2952 328897.6777 601290.202 516899.3993 621705.6306 328496.369 1.274267733 1.345115816 1.516389265 1.756041617 1.001221653 1.830431806 1.573531546 1.892579916 1 18.3255179 3.773173012 3.596522296 1.545543461 1.301028223 0.062223551 0.305814976 0.499217648 13.7182962 0.073579981 0.134501208 5931.615785 -3.773173012 -0.244515238 TET(ph)PPPLASLNVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 T(0.001)ET(0.999)PPPLASLNVSK;TET(1)PPPLASLNVSK 144.18 9.97E-05 148537000 301700 321730 234260 328590 141155 278150 250620 279600 136837 TRUE FALSE 287439.2389 354514.6528 245001.0527 295559.5089 165772.3873 268517.5958 212383.316 255116.7417 158056.9831 1.818579814 2.242954698 1.550080534 1.869955399 1.048814067 1.698865754 1.343713589 1.6140808 1 17.27008525 3.561199785 0.192520091 0.932992013 2.636913712 0.461677147 0.275718427 6.996167249 0.40810543 0.747604682 3.071551477 3640.82484 -3.561199785 1.703921699 TETGQELECLQDHLDDLVVECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TETGQELECLQDHLDDLVVECR 22 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 106.03 0.00049997 6719400 8385.7 8215.6 7647.8 9365.3 8615.4 6612.1 8941.5 8786 9225.6 FALSE TRUE 7989.32458 9052.77898 7998.459195 8423.882251 10117.92303 6383.121319 7577.309953 8016.651262 10656.25893 0.749730711 0.849526934 0.750587917 0.790510282 0.949481718 0.599002085 0.711066614 0.752295089 1 13.37941342 2.236983493 24.99999995 0.733161388 0.811756944 0.014116482 0.114741689 95.10634523 1507549.158 0.037395995 0.029100946 172.5772294 -2.236983493 0.078595556 TETVDRLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TETVDRLER 9 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 106.18 0.0027159 91812000 339080 205200 307470 279530 249750 311400 424640 394650 120740 FALSE TRUE 323052.3604 226110.1133 321567.8036 251431.1133 293306.3209 300616.1399 359853.369 360092.3538 139463.7425 2.316389583 1.621282415 2.305744832 1.802842149 2.103100889 2.155514648 2.580264679 2.581978278 1 17.08953058 2.283101257 3.292655746 2.253787701 1.995445019 0 0.491264347 0.745458031 16.65234122 0.170156972 0.131130062 191.9116134 -2.283101257 -0.258342682 TETVVDDWDEEFDRGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TETVVDDWDEEFDRGK 16 1 Q9P275;K7EKN3;K7EKL7;K7EIH0 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36 0 ;; 140.96 1.51E-06 135838000 197584 156768 199399 207677 146315 185033 231035 208438 177840 FALSE TRUE 188244.5959 172742.8374 208541.6414 186800.9134 171832.2897 178625.2608 195786.3675 190186.0637 205418.5189 0.916395449 0.84093118 1.015203705 0.909367444 0.836498533 0.869567465 0.953109625 0.925846729 1 17.64820672 1.031264103 1.242025966 0.996419499 0.897681798 0.251991943 0.051947722 0.641804999 2.042744898 0.047936198 0.014886572 10.74642726 -1.031264103 -0.0987377 TEVLS(ph)PNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEVLSPNSK 9 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TEVLS(1)PNSK 96.82 0.0074575 72618000 212810 246920 174780 264590 136310 241470 237960 229580 130730 TRUE FALSE 202750.893 272081.4287 182793.8359 237992.9105 160082.4208 233107.8334 201654.8316 209476.7581 151002.9407 1.342694997 1.801828676 1.210531629 1.576081296 1.060127836 1.543730422 1.335436453 1.387236282 1 17.20421712 -3.686863022 0.135194917 7.51E-13 1.618858198 0.289331944 0.202466021 103.7287714 1.227077269 30.29427578 1.339352238 0.000205654 3.686863022 1.618858198 TEVNYTQLVDLHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TEVNYTQLVDLHAR 14 0 A0A087X2I2;A0A087WT12;P36969-2;P36969;K7ERP4;K7EKX7;K7ENB4;K7EJ20;A0A087X247;R4GNE4 A0A087X2I2 GPX4 "Glutathione peroxidase;Phospholipid hydroperoxide glutathione peroxidase, mitochondrial" 0 130.06 6.43E-05 63989000 74396 66359 62187 77630 62704 71217 69062 76493 60641 FALSE TRUE 70879.44852 73121.05754 65038.33546 69826.48491 73639.55775 68750.73743 58525.32349 69794.86741 70044.89657 1.011914529 1.043916989 0.928523542 0.996881833 1.051319387 0.981523863 0.835540151 0.996430444 1 16.09599232 1.986103473 24.67635499 0.921420656 1.0088124 0.166999684 0.05658237 594.1947443 1055123.499 0.02116279 0.014285483 96.85085818 -1.986103473 0.087391744 TEWLDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 173.59 0.0019951 54784360000 58100060 39760915 47311140 54080150 34383118 52473530 59858710 53312340 36614880 FALSE TRUE 55353785.31 43812597.44 49480402.57 48643910.58 40379522.89 50656358.5 50726164.41 48644028.88 42292928.59 1.308818924 1.035931985 1.169945053 1.150166522 0.95475826 1.197750078 1.199400611 1.150169319 1 25.33391313 4.682510454 3.57331088 1.120703052 1.319901023 0.344511864 0.085447963 0.291410991 6.265418844 0.019851911 0.139843356 48140.48414 -4.682510454 0.199197971 TEYGDLELCIEVVDNVQDAIDHIHK ddPTM_SK-BR-3_Trastuzumab_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 0 115.11 0.00093918 14997000 36923 33691 33087 34204 24700 29831 36854 28177 2211.6 FALSE TRUE 35177.72296 37124.1512 34604.07168 30765.74894 29007.67218 28797.94499 31231.24543 25709.6725 2554.563633 13.77054089 14.53248247 13.54598149 12.04344591 11.35523571 11.27313668 12.22566744 10.06421299 1 11.31886116 0.03459696 0.409593052 7.27E-17 13.88556692 0.952251336 0.831220618 0.938032825 0.214618382 3.624314444 0.611311835 1.08292146 -0.03459696 13.88556692 TEYLSNADER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TEYLSNADER 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 89.029 0.027432 192608000 193452 171560 182000 203041 229790 176451 211605 199362 269290 FALSE TRUE 184307.9073 189042.159 190344.88 182630.9329 269865.3032 170340.4576 179320.7709 181904.8064 311050.1179 0.59253444 0.607754661 0.6119428 0.587143108 0.867594281 0.547630262 0.576501215 0.584808672 1 18.24678753 -1.133171312 4.279295768 1.000073924 0.618484439 0.638726922 0.089309872 11946443.78 3163459.672 8298.081473 0.019812065 0.073591675 1.133171312 -0.381589485 TFAYTNHTVLPEALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFAYTNHTVLPEALER 16 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 113.69 0.0006419 63214000 75906 65040 57541 80607 62176 69815 77845 80576 71061 FALSE TRUE 72318.07381 71667.64994 60179.31177 72504.23122 73019.47471 67397.28904 65968.31553 73520.33828 82080.77695 0.881059811 0.873135618 0.73317181 0.883327789 0.889605063 0.821109297 0.80369994 0.895707144 1 16.32475677 0.95094666 6.06076846 0.999984672 0.843338774 0.534175909 0.047446616 0.274281059 31.16948965 0.045280031 0.011384386 8.931957744 -0.95094666 -0.156645899 TFCGT(ph)PDYIAPEIIAYQPYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFCGTPDYIAPEIIAYQPYGK 21 0 P05771;P05771-2;P05129-2;P05129;P17252 P05771;P17252 PRKCB;PRKCG;PRKCA Protein kinase C beta type;Protein kinase C gamma type;Protein kinase C alpha type 1 T(0.414)FCGT(0.562)PDY(0.024)IAPEIIAYQPYGK 141.6 5.68E-07 74294000 173060 132870 193230 244990 198870 265300 262730 209030 161340 TRUE FALSE 164879.7968 146409.6041 202089.7866 220363.1397 233552.865 256112.5945 222645.7131 190726.2251 186359.7832 0.884739153 0.785628753 1.084406642 1.182460808 1.253236407 1.374291116 1.194709016 1.023430173 1 17.50773103 3.568383468 3.166622171 1.197809804 0.835121122 0.596764453 0.110846021 0.140877142 2.69948367 0.029887195 0.047947615 3701.548707 -3.568383468 -0.362688681 TFCPAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 99.139 0.010748 19805960000 28931930 24905360 24574270 30038990 21034180 27399020 32225530 29409660 22269100 FALSE TRUE 27564375.01 27443244.5 25701024.59 27019413.65 24702534.33 26450185.07 27308933.54 26834394.26 25722478.29 1.071606503 1.066897372 0.999165955 1.050420311 0.960348146 1.028290694 1.061675832 1.043227404 1 24.61652631 3.819721534 8.217535967 1.024519783 1.069561388 0.315615345 0.029414312 0.39465671 36.5678003 0.007554902 0.013658122 6602.699532 -3.819721534 0.045041605 TFCQLILDPIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFCQLILDPIFK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 165.7 0.0001254 141680000 511990 468180 457110 545210 379300 441820 606480 543140 405240 FALSE TRUE 487789.2474 515888.0743 478068.9456 490404.455 445449.7999 426519.6626 513950.3372 495579.7822 468082.5495 1.042100903 1.102130543 1.02133469 1.047687968 0.951647953 0.911206075 1.097990809 1.058744409 1 18.83640346 3.608266568 5.785084154 1.013797813 1.071898283 0.17175354 0.054422362 0.400396215 17.1341618 0.015063729 0.023499 4057.575112 -3.608266568 0.05810047 TFDFWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFDFWK 6 0 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 113.25 0.061181 104130000 377710 338830 213410 282310 299090 232300 393320 316480 271150 FALSE TRUE 359856.3968 373357.1622 223195.0596 253931.6624 351251.2013 224255.3928 333311.8102 288767.3334 313198.5572 1.148972077 1.192078168 0.712631187 0.810768941 1.121496869 0.716016685 1.064218856 0.921994456 1 18.25671804 3.767959546 24.87632499 0.911854566 1.170525194 0.396865316 0.135083116 581.2322752 491816.0448 0.032134588 0.057919984 5860.835685 -3.767959546 0.258670629 TFDFWKDIVAAIQHNYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFDFWKDIVAAIQHNYK 17 1 Q5TFE4;Q5TFE4-2;Q5QPD0 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 141.93 3.64E-07 14574000 74722 33488 64990 72080 73283 70667 127750 87063 78210 FALSE TRUE 71190.03914 36900.46527 67969.85578 64834.38146 86063.532 68219.78407 108259.3912 79439.30217 90338.40736 0.78803735 0.408469292 0.752391566 0.717683468 0.952679315 0.755158144 1.198376132 0.879352476 1 16.46305186 2.72191885 1.079142091 1.016538788 0.604762645 0.500354969 0.146337884 0.340768671 0.828940696 0.07195198 0.065338845 527.1313557 -2.72191885 -0.411776143 TFDHYCEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFDHYCEYR 9 0 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 176.38 5.32E-05 1489520000 2441070 2156630 1874880 2305180 2305320 2077180 2622930 2329910 2103630 FALSE TRUE 2325685.459 2376393.049 1960845.103 2073458.927 2707367.078 2005246.736 2222753.855 2125890.729 2429850.197 0.95713121 0.977999818 0.806981889 0.853327884 1.114211519 0.825255293 0.914769914 0.874906088 1 21.21243594 TFDHYCEYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFDHYCEYRR 10 1 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 101.38 0.0021881 158280000 54315 38371 54451 44377 62288 53528 80038 71379 60434 FALSE TRUE 51747.63759 42281.04852 56947.63221 39916.13965 73151.00748 51674.31194 67826.7331 65128.67636 69805.79607 0.741308609 0.605695385 0.815800914 0.571816982 1.047921686 0.740258186 0.971649017 0.932998118 1 16.09105921 2.740323594 25 0.923221713 0.684409442 0.596857741 0.10367452 105.7922375 1500201.208 0.028775526 0.029121952 549.9504909 -2.740323594 -0.238812271 TFDQLTPEESKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 203.32 7.92E-08 5315150000 7192630 5095440 6028320 6544820 4822010 6747410 8170820 7152290 5489170 FALSE TRUE 6852648.634 5614671.129 6304724.435 5886922.259 5662967.017 6513745.5 6924211.342 6525997.571 6340402.449 1.0807908 0.885538603 0.99437291 0.928477696 0.893155768 1.02733944 1.092077577 1.02927182 1 22.59614299 2.038955417 11.03221145 1.052940257 0.958639288 0.308471261 0.059286676 0.610731771 170.4188675 0.021498531 0.015858397 109.384407 -2.038955417 -0.09430097 TFEEKQGTEIDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFEEKQGTEIDGR 13 1 P19338;H7BY16 P19338 NCL Nucleolin 0 64.65 0.055387 112300000 101180 37706 131480 66931 131380 106310 215640 122430 230060 FALSE TRUE 96397.42192 41548.28427 137508.4881 60202.96872 154292.6304 102628.458 182740.1575 111709.3802 265736.5298 0.362755629 0.156351422 0.517461744 0.226551347 0.580622583 0.386203802 0.687674207 0.420376454 1 18.01963704 -1.066715293 0.157073072 1.625998257 0.107390861 0.667482051 0.138621811 13.4228299 0.435814373 4.191853708 0.727355205 0.085759987 1.066715293 -1.518607396 TFEGIDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TFEGIDPK 8 0 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 117.39 0.004859 404004000 2200840 1945640 1966950 2348290 1512450 2210020 2460870 2413430 1617640 FALSE TRUE 2096810.655 2143902.928 2057136.603 2112235.428 1776220.801 2133486.453 2085419.085 2202097.275 1868495.349 1.122192065 1.147395378 1.10095891 1.130447249 0.950615586 1.141820585 1.116095411 1.17854041 1 20.83344554 -1.712923498 2.538295846 0.979091017 1.112104395 0.247920104 0.060735546 5301971.108 4061956.354 704508.2884 0.013958743 0.019367631 1.712923498 0.133013378 TFEHVTSEIGAEEAEEVGVEHLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFEHVTSEIGAEEAEEVGVEHLLR 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;;;; 344.81 1.15E-88 290707000 89733.9 74667.3 85622.6 96519.2 101523.5 80229.4 105245 88791.1 70277.3 FALSE TRUE 85492.35638 82275.98276 89548.4809 86816.90664 119229.1663 77451.03576 89187.94229 81016.08057 81175.54476 1.053178721 1.013556275 1.103146042 1.06949583 1.468781843 0.954117844 1.098704574 0.998035564 1 16.30875754 TFEINPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFEINPR 7 0 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;; 173.59 0.0019951 1503610000 2090820 1824740 1871420 2082800 1929470 1841580 2303550 2024520 2089780 FALSE TRUE 1991991.082 2010683.081 1957226.458 1873432.987 2265968.957 1777805.623 1952101.14 1847242.296 2413852.409 0.825233173 0.83297681 0.810831039 0.776117454 0.938735504 0.736501377 0.808707746 0.765267292 1 21.20290604 -1.686078955 7.50954701 1.000819138 0.813464261 0.548652882 0.053627011 0.00066208 2.77E-05 0.046743777 0.010971642 0.020602553 1.686078955 -0.187354878 TFESLVDFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFESLVDFSK 10 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 122.26 0.0011477 94695000 456490 324700 379740 370920 317520 339510 397580 382660 363560 FALSE TRUE 434912.6224 357787.2992 397151.4546 333634.4169 372895.3875 327752.6836 336921.8689 349152.2618 419939.028 1.035656592 0.851998208 0.945735995 0.794482996 0.887975069 0.780476835 0.802311399 0.83143561 1 18.67982035 5.836529294 0.655297507 0.837602418 1.73757175 0.354007898 0.070577764 10.13212526 1.105939955 0.024966001 9.45918433 686324.1702 -5.836529294 0.899969332 TFGETHPFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFGETHPFTK 10 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 77.662 0.032326 600720000 1593800 1378000 1470000 1646600 1137300 1561900 1621200 1677700 1191400 FALSE TRUE 1518464.233 1518419.767 1537400.954 1481080.64 1335644.76 1507811.011 1373856.165 1530791.694 1376156.227 1.103409775 1.103377463 1.117170365 1.07624455 0.970561869 1.095668487 0.998328633 1.112367669 1 20.39221283 2.993162907 21.28038563 1.035845529 1.105140065 0.377327577 0.042868829 41.9953508 130715.0438 0.010995243 0.012633624 984.380284 -2.993162907 0.069294536 TFHHVYSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFHHVYSGK 9 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 150.35 4.94E-05 1161360000 2040490 2163770 1883310 2463000 2031010 2116700 2674000 2026850 710920 FALSE TRUE 1944040.082 2384260.623 1969661.626 2215414.561 2385217.501 2043398.148 2266032.189 1849368.269 821165.8427 2.367414693 2.903506818 2.398616119 2.697889324 2.904672086 2.488411039 2.7595305 2.252125177 1 19.64731409 0.844573654 3.124634948 1.000308116 2.651242972 0.883322722 0.187564294 0.198932526 3.400432073 0.162112813 0.042289124 6.991552993 -0.844573654 1.650934855 TFHIEEPR ddPTM_SK-BR-3_Trastuzumab_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 81.594 0.025474 0 62159 62195 60005 69962 75923 53636 71527 54952 53547 FALSE TRUE 59220.86726 68532.74121 62756.2886 62929.28684 89163.94716 51778.57187 60614.24247 50140.11156 61850.79528 0.957479479 1.108033307 1.014639962 1.017436988 1.441597424 0.837152888 0.980007487 0.810662358 1 15.91650453 TFHIFYYLLSGAGEHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFHIFYYLLSGAGEHLK 17 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 257.35 2.30E-27 211740000 1478870 1254410 495830 642420 951850 763160 1651290 1112740 295980 FALSE TRUE 1408966.746 1382235.805 518564.2959 577842.7211 1117852.339 736731.5778 1399355.382 1015302.587 341879.0667 4.121243103 4.04305481 1.516806223 1.690196263 3.269730286 2.154947903 4.09312976 2.969771142 1 18.38312656 0.947601684 21.54212765 0.99999999 3.116197668 0.287307898 0.963943473 3935.913533 1618146.635 0.984777367 0.246194342 8.863427237 -0.947601684 2.116197678 TFIAIKPDGVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 144.27 5.74E-05 14872882000 7583630 6636880 6796810 7840230 5778410 7158900 8647440 7569380 6256500 FALSE TRUE 7225166.839 7313185.618 7108450.461 7052115.185 6786162.874 6910985.498 7328114.207 6906564.959 7226726.066 0.999784242 1.011963862 0.983633584 0.975838176 0.93903696 0.956309321 1.014029609 0.955697628 1 22.78491078 3.572375797 3.635071377 0.974384602 1.005762285 0.269103298 0.021706734 0.312807623 7.621794111 0.006074199 0.009627823 3735.732728 -3.572375797 0.031377682 TFIGPGGNMPGYLRPETAQGIFLNFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFIGPGGNMPGYLRPETAQGIFLNFKR 27 2 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 127.14 3.66E-05 164473000 98512 64228 96790 86789 101893 91320 127962 109752 124732 FALSE TRUE 93855.53299 70772.90622 101227.9172 78064.80483 119663.1069 88157.5655 108439.0467 100141.533 144074.8015 0.651436143 0.491223347 0.702606675 0.541835241 0.830562358 0.611887468 0.752657964 0.695066257 1 17.13645851 -4.999993949 0.124544491 2.211890776 0.483149206 0.617557203 0.089503451 84.42059193 0.673417931 25.37505916 0.674203428 1.00E-05 4.999993949 -1.72874157 TFLDKDAQRLS(ph)PIPEEVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TFLDKDAQRLSPIPEEVPK 19 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 T(0.021)FLDKDAQRLS(0.979)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK 169.6 7.21E-12 1666560000 3597880 2441211 3120980 3434710 2063736 3598260 4148220 3866660 2339600 TRUE FALSE 3427815.343 2689973.176 3264080.02 3089446.425 2423650.905 3473651.354 3515332.852 3528074.752 2702413.219 1.268427537 0.995396691 1.207838978 1.143217626 0.896846895 1.285388678 1.300812484 1.305527492 1 21.36581686 TFLEGDWTS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TFLEGDWT(0.017)S(0.982)PSK;TFLEGDWT(0.002)S(0.998)PSK;TFLEGDWTS(1)PSK;TFLEGDWT(0.001)S(0.999)PSK;TFLEGDWT(0.014)S(0.985)PS(0.002)K 386.35 1.00E-102 477222000 2340910 2316550 2253890 2630290 1590080 2658850 2798840 2855340 1851680 TRUE FALSE 2230259.824 2552609.079 2357233.086 2365888.252 1867389.449 2566773.358 2371825.554 2605311.292 2138829.077 1.042748038 1.193460995 1.102113821 1.106160505 0.873089612 1.200083441 1.108936464 1.21810168 1 21.02838976 -0.412627282 7.147628253 1.000007937 1.107049805 0.101726544 0.098519865 0 0 0.0883301 0.020819604 0.386698706 0.412627282 0.107041868 TFLVGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFLVGER 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;; 126.67 0.0091423 1309459000 1706740 1951660 1564700 1942680 1521180 1615860 1651250 1761530 1434190 FALSE TRUE 1626065.783 2150536.373 1636443.043 1747398.116 1786473.31 1559902.363 1399321.485 1607281.095 1656596.86 0.981570001 1.298165187 0.987834205 1.05481192 1.078399551 0.941630641 0.844696449 0.970230678 1 20.65979113 2.232968387 3.764925538 0.914494397 1.097711435 0.332376703 0.095986493 0.206618686 6.384256215 0.036608318 0.027657923 170.9890843 -2.232968387 0.183217038 TFLVWVNEEDHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TFLVWVNEEDHLR 13 0 P12277;H0YJG0 P12277 CKB Creatine kinase B-type 0 ;;; 184.21 9.70E-06 207611000 389006 404422 360208 410576 396193 344172 452487 385518 331956 FALSE TRUE 370618.4573 445633.0616 376723.8931 369304.1204 465288.9338 332253.2373 383451.7977 351760.0002 383434.0411 0.966576823 1.162215698 0.982499864 0.963149019 1.213478418 0.866519927 1.000046309 0.917393769 1 18.5486189 2.208221603 24.99999963 0.948946903 1.055873389 0.279780168 0.088888746 269.6590694 222203.196 0.030727707 0.022696615 161.5182508 -2.208221603 0.106926486 TFNGS(ph)IELCR ddPTM_SK-BR-3_Trastuzumab_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 104.24 0.00284 44706000 112170 91831 98763 136480 92877 147880 131540 128360 101840 TRUE FALSE 106867.9464 101188.6833 103291.3812 122760.7711 109074.7194 142758.8785 111471.1571 117120.1179 117632.8271 0.908487444 0.860207867 0.878082962 1.043592798 0.927247284 1.213597276 0.947619469 0.995641445 1 16.84393119 3.242926452 24.99652289 1.022717583 0.881280922 0.416788137 0.077509028 96.4794587 552387.2929 0.020004002 0.026179444 1749.550376 -3.242926452 -0.14143666 TFNMDEYVGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFNMDEYVGLPR 12 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13;Q8TDQ7-3;Q8TDQ7;Q8TDQ7-2 D6RAY7;Q8TDQ7-3 GNPDA1;GNPDA2 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1;Glucosamine-6-phosphate isomerase 2 0 ; 132.32 0.00042575 84930000 258480 171678 187030 180956 159092 181808 189432 286290 168118 FALSE TRUE 246262.1627 189172.1834 195605.5105 162765.9591 186837.5944 175511.9434 160530.6692 261220.9299 194188.8808 1.268157897 0.974165887 1.007295112 0.838183723 0.962143629 0.903820768 0.826672818 1.345189945 1 17.56710107 4.564548797 1.663594916 0.956394681 1.322926635 0.263084651 0.145045807 0.764370367 2.710069487 0.035585152 0.405555775 36690.0917 -4.564548797 0.366531953 TFNQVEIKPEMIGHYLGEFSITYKPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TFNQVEIKPEMIGHYLGEFSITYKPVK 27 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841 K7EM56 RPS15 40S ribosomal protein S15 0 ;; 279.57 2.98E-61 1282070000 2632561 2355323 2512084 2825301 1627962 2873786 3259373 3176335 1609670 FALSE TRUE 2508125.059 2595333.091 2627265.536 2541296.376 1911878.057 2774266.07 2762095.786 2898198.269 1859289.403 1.348969695 1.395873654 1.413048196 1.366810553 1.028284276 1.492110946 1.485565282 1.558766626 1 20.82631992 TFNTSTGGLLLPSDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFNTSTGGLLLPSDTKR 17 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 221.81 5.71E-15 1039620000 1027450 771270 876610 1001950 686270 883790 1135360 1042770 795880 FALSE TRUE 978884.4747 849863.2899 916803.4356 901232.0824 805955.2707 853184.1307 962139.9797 951459.5307 919301.0056 1.064813884 0.924466834 0.997283186 0.980344933 0.876704437 0.928079188 1.046599507 1.034981497 1 19.81017779 1.702068161 8.900519806 1.029844579 0.964388447 0.265943384 0.050829742 0.163642215 26.25489745 0.024889009 0.013290779 50.35796371 -1.702068161 -0.065456132 TFNVDMYEEIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 103.76 0.0022111 66152000 62923 63483 60438 69239 52870 61662 63485 62784 50021 FALSE TRUE 59948.75449 69951.98987 63209.14208 62278.96417 62090.51126 59526.62948 53799.19727 57286.30012 57778.00121 1.037570585 1.210702835 1.094000152 1.077900981 1.074639308 1.030264603 0.931136352 0.991489822 1 15.81823268 2.28145682 1.457835752 0.966142047 1.117583621 0.586672521 0.047795734 0.252319444 1.062211718 0.026572131 0.016418466 191.1863227 -2.28145682 0.151441574 TFQARPLS(ph)ADLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFQARPLSADLTK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 T(0.03)FQARPLS(0.967)ADLT(0.003)K;TFQARPLS(1)ADLTK 127.97 0.00010343 368460000 473730 365320 398360 475660 388370 424600 534920 465780 359920 TRUE FALSE 451337.7217 402546.5233 416625.2 427845.7531 456101.605 409895.9955 453308.1295 424993.8339 415734.5554 1.08563918 0.968277758 1.00214234 1.029132045 1.097098134 0.985956039 1.090378761 1.022272093 1 18.66530314 2.994001589 24.81504007 1.04591131 1.017222737 0.029585405 0.044922872 629.7339844 2605188.141 0.01229264 0.014238092 986.2830951 -2.994001589 -0.028688573 TFQEDSSPVVHQS(ph)LQEVSEPLTATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFQEDSSPVVHQSLQEVSEPLTATK 25 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 TFQEDSSPVVHQS(1)LQEVSEPLTATK 176.11 5.58E-13 139740000 82231 74292 79416 82677 69097 99009 100840 100360 71470 TRUE FALSE 78344.1036 81862.43926 83057.30215 74366.15088 81147.49492 95580.2935 85455.00595 91571.94636 82553.20258 0.949013499 0.991632507 1.00610636 0.900826964 0.9829721 1.157802369 1.035150706 1.109247655 1 16.33303656 2.395080635 8.994980717 1.076424037 0.965307895 0.549912696 0.049475118 0.20237225 20.1618137 0.015365808 0.012843536 248.3594186 -2.395080635 -0.111116142 TFQQIQEEEDDDYPGSYS(ph)PQDPSAGPLLTEELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIK 34 0 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 TFQQIQEEEDDDYPGS(0.003)YS(0.985)PQDPS(0.012)AGPLLTEELIK;TFQQIQEEEDDDYPGS(0.001)YS(0.997)PQDPS(0.002)AGPLLTEELIK 213.55 2.82E-28 83658000 90462 78247 84485 90830 66231 89832 100189 97516 71849 TRUE FALSE 86186.04054 86220.45826 88358.72082 81699.59583 77781.66543 86721.09532 84903.32795 88976.98208 82990.97597 1.03849894 1.038913656 1.064678657 0.984439511 0.937230398 1.044946084 1.023042891 1.072128398 1 16.34066685 -3.082354572 9.663420717 1.000443174 1.024124142 0 0.040161522 0 0 0 0.008722721 0.000827266 3.082354572 0.023680968 TFS(ph)ATVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 T(0.001)FS(0.891)AT(0.109)VR;TFS(0.999)AT(0.001)VR;TFS(0.978)AT(0.022)VR;TFS(0.814)AT(0.186)VR;T(0.178)FS(0.795)AT(0.027)VR;TFS(0.964)AT(0.036)VR;TFS(0.982)AT(0.018)VR;TFS(0.982)AT(0.018)VR;TFS(0.988)AT(0.012)VR;T(0.001)FS(0.996)AT(0.003)VR;TFS(0.923)AT(0.077)VR;T(0.002)FS(0.998)ATVR;T(0.009)FS(0.986)AT(0.005)VR 195.45 0.00049012 79246905900 27792948 22754125 22592565 28103048 23565211 26059700 29391020 26059066 24509472 TRUE FALSE 26479230.43 25072796.21 23628456.45 25278076.22 27674976.34 25157246.05 24906880.1 23777196.03 28310275.74 0.935322237 0.885642953 0.834624737 0.892894031 0.977559406 0.888625963 0.879782321 0.839878645 1 24.75482247 4.60001502 3.25401245 0.894581454 0.935826183 0.034127203 0.052635441 0.865429313 15.67871242 0.011943971 0.073690446 39812.09392 -4.60001502 0.041244729 TFS(ph)LDAVPPDHS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFSLDAVPPDHSPR 14 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 2 T(0.36)FS(0.64)LDAVPPDHS(1)PR 99.963 0.001042 94433000 64389 62212 62905 75741 67152 73423 79539 79173 63766 TRUE FALSE 61345.45958 68551.47353 65789.25647 68127.37078 78863.28754 70880.3431 67403.86472 72240.1924 73654.50561 0.832881289 0.930716634 0.893214284 0.924958632 1.070719121 0.962335468 0.915135662 0.980798008 1 16.16848616 4.644817931 0.596339394 0.972284484 0.757988769 0.494759985 0.045672728 3.038070605 0.883598502 0.023223951 0.442708633 44138.5367 -4.644817931 -0.214295715 TFS(ph)LTEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.007)FS(0.993)LTEVR;T(0.094)FS(0.905)LTEVR;T(0.001)FS(0.998)LTEVR 232.63 1.44E-07 229115000 508910 454400 496820 604140 540520 561240 662460 610120 601790 TRUE FALSE 484854.8329 500703.8766 519599.6884 543410.6994 634786.5169 541804.1181 561389.5601 556694.6584 695112.5197 0.697519925 0.720320613 0.747504431 0.781759333 0.913214046 0.779448079 0.807624009 0.800869849 1 19.406887 -4.999999947 0.045860266 1.954454245 0.265042077 0.73226052 0.04659454 331.1848059 1.12783821 40.61812891 10.27002087 1.00E-05 4.999999947 -1.689412168 TFS(ph)YIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFSYIK 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 TFS(1)YIK;TFS(1)YIK 114.28 0.065877 0 306910 225540 265150 375350 260970 352420 385900 293740 231540 TRUE FALSE 292402.9725 248522.7824 277307.3898 337619.1049 306483.0854 340215.607 327023.8675 268018.5684 267446.0407 1.093315765 0.929244575 1.036872294 1.262382139 1.145962321 1.272090648 1.222765784 1.002140722 1 18.02888832 3.372993258 6.86335962 1.173518361 1.006862661 0.25183864 0.102126145 0.216532265 12.59363459 0.026306886 0.035695131 2360.44159 -3.372993258 -0.1666557 TFSHELSDFGLESTAGEIPVVAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TFSHELSDFGLESTAGEIPVVAIR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 246.22 7.33E-38 1308551000 893496 906344 767793 1014538 794412 798398 893796 856587 730277 FALSE TRUE 851262.2148 998701.484 802997.0685 912554.7127 932957.2013 770749.2771 757431.0045 781579.7012 843524.6274 1.009172924 1.183962449 0.951954504 1.081835293 1.106022481 0.913724688 0.897935851 0.926564176 1 19.68607066 2.232887544 24.9707695 0.922598264 1.072857547 0.494010877 0.065736708 97.50880458 429192.7927 0.022914727 0.017391095 170.9572583 -2.232887544 0.150259283 TFSVVAGDLVLPGSCQDPACSDKAPGMEGT(ph)AALHGDSPARPQQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFSVVAGDLVLPGSCQDPACSDKAPGMEGTAALHGDSPARPQQAK 45 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TFSVVAGDLVLPGS(0.002)CQDPACS(0.077)DKAPGMEGT(0.488)AALHGDS(0.433)PARPQQAK 64.273 0.0017672 88170000 28581 29137 28687 33571 18756 30399 35595 34861 22427 TRUE FALSE 27230.03277 32106.09343 30002.32733 30196.3793 22027.04046 29346.27501 30164.329 31808.38603 25904.86462 1.051155185 1.239384722 1.158173485 1.165664432 0.850305176 1.132848036 1.164427201 1.227892386 1 14.66093542 -2.469079512 1.910008054 7.92E-05 1.127069435 0.110318701 0.110064378 2441308.639 158487.4551 10575489.6 0.026295029 0.003395631 2.469079512 1.126990213 TFTAWCNSHLR ddPTM_SK-BR-3_Trastuzumab_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 ; 158.06 3.03E-05 1268940000 1552600 1212000 778860 879980 1549780 820220 1395630 1076940 1187430 FALSE TRUE 1479211.675 1335504.178 814571.5014 791522.7385 1820061.141 791815.5757 1182701.011 982637.4244 1371570.58 1.078480172 0.973704305 0.59389689 0.57709224 1.326990509 0.577305745 0.862296865 0.71643227 1 20.38739743 3.980782204 21.7844251 0.801979513 1.039189443 0.141733572 0.228934707 231.2385291 262124.0712 0.054110904 0.098477991 9567.141641 -3.980782204 0.23720993 TFTEMDSHEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFTEMDSHEEK 11 0 B0YIW6;P48444;P48444-2;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 155.48 3.15E-05 437360000 1400100 1212600 1316700 1459400 1089400 1448100 1738900 1479700 1038900 FALSE TRUE 1333920.048 1336165.319 1377071.997 1312698.339 1279391.015 1397951.934 1473598.868 1350129.624 1200007.306 1.111593272 1.11346432 1.147553011 1.093908623 1.066152688 1.164952852 1.22799158 1.12510117 1 20.19461176 2.205636674 24.99481496 1.157613761 1.109229831 0 0.061903719 384.6013856 291975.2229 0.021293729 0.015727408 160.5597467 -2.205636674 -0.048383931 TFTTQETITNAETAKEWFLQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFTTQETITNAETAKEWFLQAAK 23 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 244.78 1.65E-37 269470000 313640 207010 282960 258290 212940 305360 384250 320300 260460 FALSE TRUE 298814.8588 228104.5544 295933.9959 232326.1985 250076.6686 294785.3066 325625.6053 292252.834 300850.8066 0.9932327 0.758198248 0.98365698 0.772230599 0.831231505 0.979838844 1.082349118 0.971421142 1 18.1986887 2.098100203 4.827047186 1.027989677 0.865681794 0.4306692 0.080856385 0.173719721 6.820996161 0.029281488 0.02114054 125.343034 -2.098100203 -0.162307884 TFVEESIYNEFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TFVEESIYNEFLER 14 0 P30837 P30837 ALDH1B1 "Aldehyde dehydrogenase X, mitochondrial" 0 ; 122.42 0.00025316 13691400 12750.9 14566.6 13383.5 12694.6 13226.2 14663.2 18224 14285.6 13712.6 FALSE TRUE 12148.19023 16050.9531 13997.14671 11418.51469 15532.84509 14155.40971 15443.59409 13034.67713 15839.07997 0.766975749 1.013376606 0.88370958 0.720907698 0.980665867 0.893701511 0.975031007 0.822944082 1 13.95120092 TFVLEVMGR ddPTM_SK-BR-3_Trastuzumab_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" 0 101.64 0.0097633 0 195790 190690 179870 173460 159050 178570 209420 188880 149490 FALSE TRUE 186535.3947 210121.5278 188117.2174 156023.4712 186788.2696 172386.0761 177469.1327 172340.6659 172672.1457 1.080286539 1.216881431 1.089447384 0.903582165 1.081751019 0.998343279 1.027780897 0.998080294 1 17.39767585 3.471588135 24.9824406 1.007098348 1.149347397 0.568207624 0.054011316 87.16635834 393560.1543 0.013528908 0.018376316 2962.021012 -3.471588135 0.142249049 TFVNITPAEVGVLVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFVNITPAEVGVLVGK 16 0 P07737;I3L3D5 P07737 PFN1 Profilin-1 0 171.76 1.12E-08 34629000 107650 96339 121170 112030 119260 98961 133400 115320 133230 FALSE TRUE 102561.5978 106156.0536 126725.7644 100768.5316 140058.9062 95533.95576 113047.3799 105221.9695 153890.628 0.666457725 0.689814936 0.823479415 0.654806163 0.910119792 0.620791253 0.734595611 0.683745143 1 17.23154585 -1.588459748 2.98681148 1.016530214 0.719718657 0.506937808 0.085806972 17148481.26 18570952.43 2239081.866 0.018411088 0.02579528 1.588459748 -0.296811557 TFVQEDIYDEFVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TFVQEDIYDEFVER 14 0 P05091;P05091-2;S4R3S4 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ;;;;;;;;; 267.67 1.15E-24 921914000 1151812 960978 1053201 1015910 1070447 815851 1083609 1049750 1150699 FALSE TRUE 1097368.129 1058902.751 1101491.308 913788.7967 1257132.618 787597.8753 918284.5452 957828.3249 1329143.524 0.825620491 0.796680518 0.828722623 0.687501974 0.945821572 0.592560443 0.690884414 0.720635738 1 20.34206547 2.234049572 24.99998069 0.716838113 0.809570388 0.03471525 0.120447918 225.2413989 1248261.195 0.038897737 0.029703911 171.4152954 -2.234049572 0.092732275 TFWS(ph)PELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFWSPELKK 9 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EPP6;O15083 G8JLD3 ERC1;ERC2 ELKS/Rab6-interacting/CAST family member 1;ERC protein 2 1 T(0.017)FWS(0.983)PELKK 54.023 0.084381 166820000 510950 546910 545230 644660 330590 604960 656560 698610 430200 TRUE FALSE 486798.4061 602640.7508 570229.3348 579857.552 388244.7913 584010.0835 556389.7134 637436.0048 496913.2188 0.97964471 1.212768604 1.147543098 1.166919152 0.781313068 1.175275805 1.119691915 1.282791402 1 18.9226344 -0.709779179 6.005329717 0.999999998 1.107037703 0.056281982 0.139218829 3.73E-09 6.21E-10 0.12514153 0.029496141 0.195083627 0.709779179 0.107037705 TFYEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TFYEKR 6 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 86.086 0.086548 144030000 332860 199120 275710 217740 323030 272740 461440 364500 410770 FALSE TRUE 317126.3675 219410.5544 288351.5762 195852.3615 379366.3297 263294.9454 391038.8531 332582.4477 474470.1137 0.668380069 0.462432824 0.607733908 0.412781239 0.799557904 0.554924194 0.824159081 0.700955525 1 18.85595769 1.17659554 0.544523498 0.997162867 0.545124197 0.574332591 0.114413771 0.533855821 0.404534157 0.107184328 0.052954098 15.01742737 -1.17659554 -0.45203867 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGADTTAAGPLFQQRPYPSPGAVLR 25 1 O60828-2;O60828;O60828-5;O60828-4;H7C053 O60828-2 PQBP1 Polyglutamine-binding protein 1 1 TGADTTAAGPLFQQRPYPS(1)PGAVLR 120.52 0.00012973 150160000 100030 120310 115550 143600 117550 126640 135550 133480 141380 TRUE FALSE 95301.78014 132569.7258 120848.0818 129165.0552 138050.6828 122254.425 114869.358 121791.7836 163304.4883 0.583583349 0.811794747 0.740016904 0.790946143 0.845357554 0.748628689 0.703406006 0.74579569 1 17.31720492 TGAIVDVPVGEELLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TGAIVDVPVGEELLGR 16 0 P25705;P25705-2;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 137.88 2.24E-05 127351000 409559 379938 366634 405378 397444 348902 420465 408089 401877 FALSE TRUE 390199.9577 418654.1142 383444.5316 364628.6333 466758.1078 336819.4363 356315.3419 372354.5637 464198.0327 0.840589426 0.901886877 0.826036529 0.785502324 1.005515049 0.725594278 0.767593391 0.802145932 1 18.82438088 TGASSLLNKSS(ph)PVKKPSLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGASSLLNKSSPVKKPSLLK 20 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 TGASSLLNKS(0.179)S(0.821)PVKKPSLLK 98.766 0.0041611 136070000 246710 204700 233430 246370 107330 297370 324240 317930 155220 TRUE FALSE 235048.5072 225559.1627 244132.9964 221604.4195 126048.318 287072.0023 274771.2329 290090.3637 179290.7248 1.310990892 1.258063756 1.361659933 1.236006044 0.703038699 1.601153671 1.53254572 1.617988683 1 17.45194133 TGCTFPEKPDFH ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TGCTFPEKPDFH 12 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ;;; 136.38 0.00010127 1844150000 4219130 3976430 3783330 4481190 3037450 4160130 4701860 4399820 3054750 FALSE TRUE 4019700.086 4381632.738 3956799.423 4030732.267 3567180.318 4016063.655 3984504.901 4014548.436 3528465.028 1.139220611 1.241795711 1.121393975 1.142347235 1.010972275 1.138190013 1.129245967 1.137760585 1 21.75060928 -4.999999997 0.061807506 0.514787141 1.341393011 0.389444608 0.053810962 371.2942127 1.671983672 27.24779458 4.312636485 1.00E-05 4.999999997 0.82660587 TGDEKDVS(ph)V ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGDEKDVSV 9 1 Q16543;K7EL68 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 TGDEKDVS(1)V 77.64 0.084256 173110000 623880 531410 553350 662080 337070 680940 675080 642780 337780 TRUE FALSE 594390.4288 585561.2832 578721.6448 595526.4605 395854.9013 657358.8771 572084.1473 586494.7756 390161.1973 1.523448341 1.50081886 1.483288571 1.52636004 1.014593209 1.684839194 1.466276378 1.503211441 1 18.57371078 -1.593869478 2.893468776 0.968732985 1.468751471 0.420830855 0.170521224 24630200.49 25332740.88 5879454.524 0.03841103 0.025475958 1.593869478 0.500018486 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.998)PS(0.992)PEPIY(0.008)NS(0.002)EGK;TGDLGIPPNPEDRS(1)PS(0.998)PEPIY(0.002)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(0.999)PEPIY(0.001)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK 205.03 2.02E-25 5978803000 5109604 4785942 4429709 5503585 3091361 5194790 5368359 5182549 3242933 TRUE FALSE 4868083.145 5273634.931 4632815.539 4950354.18 3630493.38 5014893.12 4549317.238 4728737.535 3745830.487 1.299600492 1.407868015 1.23679263 1.321563855 0.969209203 1.338793396 1.214501632 1.262400301 1 21.83685418 -5 0.070855318 0.122641746 1.580995905 0.359525562 0.112835148 307.7307521 1.567610812 44.40675397 5.403371158 1.00E-05 5 1.458354159 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.999)PS(0.987)PEPIY(0.012)NS(0.001)EGKR;TGDLGIPPNPEDRS(0.977)PS(0.942)PEPIY(0.012)NS(0.068)EGKR;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(0.955)PS(0.882)PEPIY(0.119)NS(0.044)EGKR 160.27 6.93E-11 2543330000 1423030 955855 1380890 1295510 986536 1330220 1750460 1476040 1279150 TRUE FALSE 1355766.192 1053257.711 1444205.172 1165282.873 1158587.566 1284154.148 1483395.178 1346790.113 1477514.049 0.917599527 0.712858001 0.977456135 0.788678033 0.784146565 0.869131599 1.003980421 0.911524404 1 20.49474042 1.895265441 4.792518631 0.968318528 0.83065348 0.396057067 0.07642062 0.21410571 7.48968726 0.032734546 0.019150506 78.57157185 -1.895265441 -0.137665048 TGDLGIPPNPEDRS(ph)PSPEPIYNS(ph)EGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.945)PS(0.367)PEPIY(0.002)NS(0.686)EGKR 86.628 0.0043376 604330000 336120 228360 312270 312880 218420 313660 425230 308020 301350 TRUE FALSE 320232.2737 251630.1436 326587.8884 281428.708 256512.3788 302797.8756 360353.3536 281048.1359 348081.8189 0.919991382 0.722905162 0.93825035 0.808513093 0.736931276 0.869904313 1.035254742 0.807419752 1 18.40906694 1.990311408 24.55958323 0.951751416 0.822586291 0.283833565 0.088486942 410.8777125 1041532.882 0.031727042 0.022099895 97.79381928 -1.990311408 -0.129165124 TGDLGIPPNPEDRSPS(ph)PEPIY(ph)NSEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.603)PS(0.538)PEPIY(0.532)NS(0.327)EGKR 133.94 4.74E-05 68073000 124780 81548 114090 108170 87879 113010 151320 130000 103860 TRUE FALSE 118881.8967 89857.83391 119321.1394 97296.54609 103205.0698 109096.4354 128233.3548 118616.5108 119966.0784 0.990962598 0.749027018 0.994623989 0.811033814 0.860285434 0.909394029 1.068913451 0.988750424 1 16.872267 1.885397761 5.049036944 1.022612661 0.875829055 0.409318037 0.075880048 0.197541996 7.187779877 0.031981368 0.018811815 76.80646219 -1.885397761 -0.146783607 TGEAIVDAALSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGEAIVDAALSALR 14 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 113.22 0.0012747 58878000 260890 220950 247560 240460 214870 250230 292890 275050 222390 FALSE TRUE 248558.2467 243465.0562 258910.8709 216288.504 252343.26 241564.4724 248204.2512 250965.1639 256877.1054 0.967615414 0.947788071 1.00791727 0.841992141 0.982350138 0.940389265 0.966237341 0.976985331 1 17.97071879 1.155587391 1.427593588 0.999185512 0.948820624 0.140840203 0.042847856 0.752114792 3.005346591 0.036122538 0.010980657 14.3082787 -1.155587391 -0.050364888 TGEEDEEEFFCNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGEEDEEEFFCNR 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 ; 225.93 2.70E-11 160332000 305610 251560 291010 312940 214760 291590 322130 311940 227750 FALSE TRUE 291164.421 277194.25 304353.0963 281482.6767 252214.076 281492.1652 272983.1522 284624.8799 263068.3068 1.106801593 1.053696864 1.156935626 1.069998435 0.958739877 1.070034504 1.037689243 1.081942874 1 18.00507792 2.994918647 24.99768302 1.033661632 1.097120633 0.400791754 0.042129218 245.0708379 1205632.482 0.011547146 0.013427422 988.3679347 -2.994918647 0.063459001 TGENFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGENFR 6 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ;; 137.44 0.029627 1074981000 1294240 1257240 1171060 1359940 969510 1278160 1331170 1282340 962640 FALSE TRUE 1233063.84 1385354.185 1224754.259 1223236.247 1138592.237 1233896.999 1128075.568 1170051.511 1111921.295 1.108948849 1.245910292 1.101475676 1.10011046 1.023986358 1.109698146 1.014528252 1.052279075 1 20.08462324 3.273999781 1.949187484 1.045738557 1.175837573 0.554267589 0.046973552 0.208090869 1.625066292 0.013720571 0.019498889 1879.31587 -3.273999781 0.130099015 TGEPSPPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TGEPSPPHDILHEPPDVVS(1)DDEKDHGK 95.244 0.0024778 136890000 96284 90273 88827 113680 47206 105380 101950 113120 19277 TRUE FALSE 91732.84614 99471.92133 92899.80581 102252.6704 55438.71145 101730.6642 86395.65506 103214.6131 22266.37871 4.119791877 4.46735963 4.172200924 4.592245186 2.489794689 4.568801488 3.880094568 4.635446764 1 14.44257932 TGFINLDKPSNPSSHEVVAWIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGFINLDKPSNPSSHEVVAWIR 22 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 181.69 2.93E-17 209570000 186730 159010 166210 202040 160670 187090 226090 192060 156280 FALSE TRUE 177903.643 175213.2998 173830.8929 181730.5553 188690.7971 180611.0264 191595.8181 175242.2082 180515.1042 0.985533281 0.97062958 0.962971457 1.006733238 1.045290908 1.00053138 1.06138386 0.970789724 1 17.46176003 3.082598193 4.974312812 1.021988454 0.974611397 0.350489702 0.025710282 0.180457971 7.868021697 0.006852767 0.008234119 1209.478612 -3.082598193 -0.047377057 TGFLEIDEHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGFLEIDEHMR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5 P35813 PPM1A Protein phosphatase 1A 0 133.07 0.00016936 44632000 82758 64447 67921 78797 72239 70458 82870 73907 63431 FALSE TRUE 78846.19335 71014.22257 71035.24503 70876.17586 84837.45873 68018.02179 70226.65949 67435.31127 73267.55552 1.07614063 0.969245146 0.969532074 0.967361001 1.157913051 0.928351182 0.958496008 0.920397996 1 16.16088686 TGGIGDSRPPSFHPHAGGGS(ph)QENLDNDTETDSLVSAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR 162.51 5.25E-18 61457000 53155 42150 49809 58444 49053 46355 74019 59416 18631 TRUE FALSE 50642.46849 46445.13292 52092.79192 52569.09808 57607.82767 44749.71473 62726.0421 54213.22006 21520.20033 2.353252652 2.158210993 2.420646236 2.442779216 2.676918746 2.079428353 2.914751775 2.519178225 1 14.39340389 3.713130285 21.89776506 2.411031888 2.255731824 0 0.522517204 801.9798171 690574.3301 0.121850541 0.188924458 5165.713134 -3.713130285 -0.155300065 TGGMAFHSYFMEAIAPPLLQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 175.33 1.65E-12 1106230000 2401419 2351305 2160426 2787330 1466449 2412148 2510520 2598774 1396496 FALSE TRUE 2287908.683 2590905.653 2259483.669 2507142.293 1722197.241 2328614.71 2127494.065 2371211.572 1613057.467 1.418367745 1.606207903 1.400745922 1.554279586 1.06766019 1.443603069 1.318920192 1.470010598 1 20.62136641 -3.87194008 0.138732286 2.82E-12 1.586652849 0.448565031 0.144140873 81.86812716 0.940816565 24.25446718 0.884581841 0.000134295 3.87194008 1.586652849 TGGMAFHSYFMEAIAPPLLQELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 205.02 6.63E-25 906692000 2141232 1665988 2075051 2233726 1394903 2279533 2760347 2478609 1306647 FALSE TRUE 2040020.207 1835754.071 2170194.141 2009187.619 1638173.642 2200592.201 2339205.368 2261568.856 1509275.143 1.351655605 1.21631505 1.437904911 1.331226866 1.085404241 1.458045745 1.549886631 1.49844703 1 20.5254244 TGHSGTLDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGHSGTLDPK 10 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 90.142 0.011032 59803000 120710 131270 125560 142270 84190 137940 128930 136150 67355 FALSE TRUE 115004.2775 144646.5622 131317.0502 127968.7493 98872.70934 133163.1032 109259.3605 124227.9842 77800.0694 1.478202763 1.859208653 1.687878317 1.644841069 1.270856313 1.711606484 1.404360708 1.596759298 1 16.24748382 -2.74268114 0.205280964 5.10E-10 1.713786156 0.56654771 0.162598403 33.73493919 0.770048432 15.25346875 0.369610105 0.001808501 2.74268114 1.713786156 TGHSLLHTLYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGHSLLHTLYGR 12 0 P31040;D6RFM5;P31040-2;A0A494C1T6 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 ; 185.3 7.64E-06 755370000 702090 542720 577440 669480 560960 557960 746790 522230 293600 FALSE TRUE 668903.5971 598023.785 603916.1952 602182.5985 658791.2464 538637.7053 632853.4698 476500.7727 339129.9885 1.972410638 1.763405789 1.780780868 1.775668973 1.942592129 1.58829276 1.866108841 1.40506823 1 18.37147884 1.00571941 2.751436968 1.000503647 1.814681618 0.861678616 0.108196007 0.079750091 1.390442484 0.09445335 0.025210525 10.13256527 -1.00571941 0.814177971 TGKPEEASLDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TGKPEEASLDSR 12 1 Q9BY42;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ;;; 104.17 0.0019758 802410000 2662090 2510830 2451110 2893690 1667940 2788610 2958080 2983750 1932780 FALSE TRUE 2536258.281 2766686.432 2563495.818 2602810.784 1958828.208 2692039.736 2506770.567 2722477.032 2232505.651 1.136059064 1.2392741 1.148259498 1.16586974 0.87741243 1.205837815 1.122850715 1.219471508 1 21.0902324 -5 0.15624261 0.533955296 1.180297439 0.131572971 0.10197516 267.8171235 2.434573695 39.69663586 0.44062114 1.00E-05 5 0.646342143 TGNAWHSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGNAWHSK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 82.645 0.019736 1585390000 3582010 2952860 2740980 3504470 2763380 3181750 4173340 3635500 2599630 FALSE TRUE 3412695.486 3253759.791 2866656.644 3152194.018 3245312.597 3071565.2 3536620.334 3317156.347 3002767.343 1.136516785 1.083587045 0.95467158 1.049762988 1.080773908 1.022911484 1.177786998 1.104699755 1 21.51786127 1.758807941 25 1.112556747 1.061295071 0.047952379 0.063679113 20.31263006 25103.03241 0.029126808 0.016152683 57.3862625 -1.758807941 -0.051261676 TGPFAEHSNQLWNISAVPSWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 109.08 0.00040137 72480000 177690 182120 162070 211400 120090 177150 194420 181090 126960 FALSE TRUE 169290.9458 200678.2351 169501.0698 190149.6704 141033.658 171015.2511 164757.6582 165232.7996 146648.3084 1.154400945 1.36843198 1.155833788 1.296637326 0.9617135 1.166159044 1.123488297 1.126728303 1 17.1620009 2.760039592 24.91906571 1.094012583 1.249769102 0.474209597 0.08671929 678.8127617 787530.9976 0.024443088 0.025904256 575.4923986 -2.760039592 0.155756519 TGPPPIS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.999)PS(0.001)K;TGPPPIS(0.991)PS(0.009)K;TGPPPIS(0.995)PS(0.005)K;TGPPPIS(0.993)PS(0.007)K 151.13 2.13E-05 1089328000 1553610 1355260 1326210 1597360 793487 1582300 1577680 1610540 943400 TRUE FALSE 1480173.934 1493362.535 1387018.04 1436790.338 931870.8816 1527504.554 1336975.94 1469512.58 1089697.654 1.358334515 1.370437506 1.27284668 1.318522007 0.855164621 1.40176915 1.226923758 1.348550742 1 20.05549647 -4.999996784 0.044707333 3.99E-09 1.836607312 0.217300085 0.156624752 1026.011858 3.410152191 134.7556435 35.25419887 1.00E-05 4.999996784 1.836607308 TGPPPIS(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.978)PS(0.022)KR 64.121 0.033359 0 97924 78841 87183 102330 59585 97159 111530 106180 73383 TRUE FALSE 93295.32659 86874.98753 91180.42679 92043.59399 69976.60513 93794.35947 94514.05011 96882.3163 84762.86085 1.100662786 1.024918067 1.075712003 1.085895321 0.825557378 1.106550186 1.115040823 1.142980727 1 16.37114466 TGQAGS(ph)LSGS(ph)PKPFSPQLSAPITTK ddPTM_SK-BR-3_Trastuzumab_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 2 TGQAGS(0.824)LS(0.352)GS(0.824)PKPFSPQLSAPITTK;TGQAGS(0.649)LS(0.418)GS(0.932)PKPFSPQLSAPITTK 146.39 1.48E-07 645350000 1569840 1467130 1436410 1764090 756980 1842220 1758770 1868350 777330 TRUE FALSE 1495636.774 1616632.215 1502270.819 1586760.322 888997.0723 1778423.459 1490437.334 1704747.369 897874.3663 1.665752838 1.80051049 1.67314145 1.76724092 0.990112989 1.980704123 1.659962006 1.898647999 1 19.77615407 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_SK-BR-3_Trastuzumab_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 TGQAGSLS(0.016)GS(0.984)PKPFSPQLSAPITTK;TGQAGSLS(0.386)GS(0.609)PKPFS(0.004)PQLSAPITTK 196.84 5.09E-25 1715370000 2056600 1641060 1840800 2174200 929330 2203600 2196100 2236900 989980 TRUE FALSE 1959388.594 1808285.88 1925202.501 1955645.285 1091404.858 2127288.779 1861044.611 2041025.177 1143501.042 1.713499613 1.581359188 1.683603626 1.710226063 0.954441507 1.86032955 1.627497083 1.784891401 1 20.12502625 -1.938623361 2.565698072 0.572332643 1.614614699 0.378910965 0.24724026 4793352.731 2685904.048 12259713.61 0.056628933 0.011517988 1.938623361 1.042282056 TGQEIPVNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGQEIPVNVR 10 0 Q96KP4;J3QKT2;J3QRH4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 101.97 0.0069992 87697000 65272 68665 65740 82662 70862 67094 74055 70761 76669 FALSE TRUE 62186.72192 75662.04157 68754.24403 74352.65871 83220.31036 64770.51796 62756.54964 64564.79171 88558.43695 0.702211151 0.854374176 0.776371472 0.839588652 0.939721987 0.731387321 0.708645633 0.729064265 1 16.43434214 -0.16921286 7.902274431 0.999999999 0.784333778 0.44820391 0.074906252 0 0 0.073966456 0.017434061 0.677309458 0.16921286 -0.215666222 TGQLEGAPAPGPAAS(ph)PQTLDHSGATATGGASELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.999)PQT(0.001)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.995)PQT(0.005)LDHSGATATGGASELK 179.18 5.73E-20 1306320000 1474930 1807770 1415240 1780710 803600 1641510 1438620 1619840 752910 TRUE FALSE 1405212.982 1991983.818 1480130.154 1601709.648 943747.5856 1584664.097 1219132.097 1477998.222 869667.4375 1.615804986 2.290512134 1.701949608 1.841749591 1.085182157 1.822149512 1.401837121 1.699498174 1 19.73010429 2.919160865 9.53564696 1.458726009 1.90471106 0.356462324 0.301236787 0.481014037 54.20892983 0.083536325 0.088692607 830.1582064 -2.919160865 0.445985051 TGQLEGAPAPGPAASPQT(ph)LDHSGATATGGASELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.223)PQT(0.777)LDHSGATATGGASELK 241.74 1.47E-46 745510000 831620 976160 736190 1022900 453840 894090 808730 906620 473720 TRUE FALSE 792310.9707 1075631.814 769945.0397 920076.1486 532989.5523 863127.4391 685343.3852 827231.5465 547182.0782 1.44798414 1.965765797 1.407109389 1.681480782 0.974062517 1.577404439 1.252496038 1.511803072 1 19.06166145 2.78311986 24.81427484 1.302480101 1.650410984 0.35057973 0.240794196 437.4515436 243608.3462 0.066564558 0.070602012 606.9038049 -2.78311986 0.347930883 TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_SK-BR-3_Trastuzumab_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 265.84 1.51E-60 811290000 237996 219236 237779 256683 182784 243214 266004 238627 213823 TRUE FALSE 226746.4007 241576.3977 248681.4023 230880.7372 214661.4717 234791.4382 225420.2043 217731.5548 246981.5788 0.918070092 0.978115043 1.00688239 0.934809545 0.869139605 0.950643523 0.912700475 0.881570018 1 17.91404392 3.009189819 24.95406485 0.917691322 0.963836245 0.187446858 0.041765068 288.9863134 784708.2838 0.011175833 0.013338732 1021.385808 -3.009189819 0.046144923 TGRDT(ph)PENGETAIGAENSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGRDTPENGETAIGAENSEK 20 1 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 T(0.005)GRDT(0.995)PENGETAIGAENSEK 267.27 1.23E-36 334990000 291860 326800 248690 350850 168810 320790 282590 306030 135280 TRUE FALSE 278064.3562 360101.2915 260092.6825 315581.8914 198250.4106 309680.9619 239475.7054 279232.3908 156258.5315 1.779514716 2.304522435 1.664502284 2.019613831 1.268733353 1.981849944 1.532560834 1.786989729 1 17.25357544 -1.644955166 0.151937937 6.01E-10 2.200418424 0.478993224 0.270723822 28.17596085 0.702594253 12.11368566 1.499474674 0.022648781 1.644955166 2.200418423 TGRPAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGRPAGK 7 1 O75131;A0A087WYQ3;H0YB26;E5RHZ0;A0A087WXR6;A0A087WUS8 O75131 CPNE3 Copine-3 0 ; 67.032 0.060432 281810000 655710 498930 408930 758510 510140 435790 577520 573430 532600 FALSE TRUE 624715.8878 549771.5342 427679.845 682263.1337 599108.2545 420698.483 489408.7171 523217.4293 615192.8879 1.015479698 0.893657168 0.695196342 1.109023116 0.973854325 0.683848093 0.795537021 0.8504933 1 19.2306793 2.267400078 24.99599205 0.808599987 0.935353763 0.127663821 0.129786341 344.669699 298734.0162 0.042923865 0.035907018 185.0972975 -2.267400078 0.126753776 TGS(ph)CSELDACPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSCSELDACPSK 13 0 A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9;H0Y9Z7 A0A1B0GUA8 KIF13A Kinesin-like protein KIF13A 1 T(0.014)GS(0.986)CSELDACPSK 180.3 4.61E-07 0 136200 98860 119900 133790 71486 132080 131910 125620 89435 TRUE FALSE 129762.0959 108933.9464 125397.5336 120341.175 83953.13577 127506.0365 111784.7068 114620.0468 103304.123 1.256117298 1.054497567 1.213867655 1.164921317 0.812679429 1.234278292 1.082093372 1.109539905 1 16.65653831 7.999999981 0.619124009 1.081330115 13.27623096 0.174113614 0.119082565 341.4016505 2.460605046 0.045534929 5663.284702 99999995.55 -7.999999981 12.19490085 TGS(ph)EPALSPAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 T(0.029)GS(0.971)EPALSPAVVR;TGS(1)EPALSPAVVR;TGS(1)EPALSPAVVR 191.95 3.28E-06 288569000 429700 308921 343248 380600 270208 389267 421600 407800 326550 TRUE FALSE 409388.9326 340400.4011 358986.2603 342341.3649 317332.1896 375786.5862 357277.1768 372090.8701 377189.7062 1.085366132 0.902464716 0.951739282 0.907610572 0.841306601 0.996280068 0.947208184 0.986482038 1 18.52493078 -3.049056918 9.442729193 0.999800205 0.955173585 0 0.066425285 0 0 0 0.014278093 0.000893188 3.049056918 -0.044626621 TGS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.49)ES(0.49)S(0.019)QTGTSTTSSR;T(0.016)GS(0.98)ES(0.002)S(0.001)QTGTSTTSSR;T(0.005)GS(0.994)ES(0.001)SQTGTSTTSSR;T(0.006)GS(0.96)ES(0.034)SQTGTSTTSSR;T(0.064)GS(0.837)ES(0.077)S(0.016)QT(0.006)GT(0.001)STTSSR;T(0.005)GS(0.405)ES(0.405)S(0.185)QTGTSTTSSR 333.13 1.34E-71 1156636000 948711 835769 862772 1017336 580356 916641 897260 866700 507235 TRUE FALSE 903867.3112 920934.8113 902330.9496 915071.4525 681569.9027 884897.4923 760366.5077 790807.1533 585894.4132 1.542713654 1.57184433 1.540091404 1.561836795 1.163298177 1.510336116 1.297787606 1.349743461 1 19.16028117 -0.471127357 0.140472778 0.540856016 1.765227956 0.692880731 0.107151268 11.71487312 0.436894715 3.013556017 0.889304711 0.337965713 0.471127357 1.22437194 TGS(ph)NAAQYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TGSNAAQYK 9 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 T(0.001)GS(0.999)NAAQYK;T(0.007)GS(0.993)NAAQYK;TGS(1)NAAQYK;T(0.001)GS(0.999)NAAQYK;T(0.004)GS(0.996)NAAQYK 148.1 9.53E-05 885160000 1396373 1184413 1144881 1312498 712645 1304408 1338641 1355216 715311 TRUE FALSE 1330369.216 1305106.031 1197374.926 1180563.207 836930.0624 1259236.024 1134406.73 1236546.103 826237.7766 1.610152977 1.57957681 1.449189277 1.428841964 1.012940931 1.524060095 1.372978532 1.496598361 1 19.6561975 6.060322222 0.03916413 4.95E-14 3.348691959 0.438177939 0.160600064 519.1412135 2.242044115 63.26060981 141.7853635 1149005.803 -6.060322222 3.348691959 TGS(ph)PGPELLFHEGQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGSPGPELLFHEGQQK 16 0 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 T(0.07)GS(0.93)PGPELLFHEGQQK;T(0.067)GS(0.933)PGPELLFHEGQQK;T(0.025)GS(0.975)PGPELLFHEGQQK 232.84 2.80E-17 174104000 564080 566040 506020 689790 308070 602880 579210 599910 293844 TRUE FALSE 537417.0563 623720.1195 529221.5175 620450.9987 361797.3105 582002.1144 490840.8766 547378.7001 339411.8268 1.583377519 1.837649929 1.559231222 1.828018206 1.065953753 1.714737285 1.446151365 1.612727244 1 18.37267731 -2.803215218 0.172325004 4.59E-15 1.769723653 0.427158246 0.21551782 47.94468687 0.913415777 18.81713435 0.748473066 0.001573203 2.803215218 1.769723653 TGS(ph)QEGTSMEGSRPAAPAEPGTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.189)GS(0.802)QEGT(0.004)S(0.004)MEGS(0.001)RPAAPAEPGTLK;T(0.07)GS(0.924)QEGT(0.002)S(0.002)MEGS(0.001)RPAAPAEPGTLK;T(0.058)GS(0.94)QEGT(0.001)S(0.001)MEGSRPAAPAEPGTLK;T(0.102)GS(0.867)QEGT(0.014)S(0.014)MEGS(0.003)RPAAPAEPGTLK;T(0.033)GS(0.933)QEGT(0.014)S(0.02)MEGSRPAAPAEPGTLK;TGS(0.875)QEGT(0.062)S(0.062)MEGSRPAAPAEPGTLK 229.7 1.56E-33 4361910000 4998220 4226150 4547390 5558060 2799730 5696740 5521100 4933320 2493530 TRUE FALSE 4761964.046 4656799.49 4755892.329 4999353.249 3288002.026 5499460.465 4678754.793 4501332.348 2880213.897 1.653336945 1.616824186 1.651228867 1.73575763 1.141582585 1.909393073 1.624446989 1.562846548 1 21.45774453 0.731857468 3.543059312 1.00001763 1.623522366 0.505368285 0.190993802 2.425623153 31.24857588 0.164104302 0.042278703 5.393335888 -0.731857468 0.623504735 TGS(ph)TSSKEDDYESDAATIVQK ddPTM_SK-BR-3_Trastuzumab_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(0.021)GS(0.935)T(0.021)S(0.021)SKEDDYESDAATIVQK;T(0.025)GS(0.953)T(0.018)S(0.003)SKEDDYESDAATIVQK 308.86 1.08E-66 166738000 321960 239890 292580 349280 125210 294220 271340 238930 102722 TRUE FALSE 306741.5889 264335.0637 305995.0824 314169.7108 147046.5844 284031.0876 229942.0995 218008.0226 118651.6031 2.585229199 2.227825472 2.578937615 2.647833679 1.239313928 2.393824273 1.937960326 1.837379494 1 16.85637207 -0.514690432 0.164695963 2.39E-14 2.830821799 0.582929873 0.36601955 12.65246239 0.559662773 8.014456577 1.920366916 0.305709946 0.514690432 2.830821799 TGS(ph)YGALAEITASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TGSYGALAEITASK 14 0 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 T(0.005)GS(0.995)YGALAEITASK;T(0.26)GS(0.74)YGALAEITASK;T(0.061)GS(0.939)YGALAEITASK;TGS(1)YGALAEITASK;T(0.002)GS(0.998)YGALAEITASK;T(0.001)GS(0.999)YGALAEITASK;TGS(1)YGALAEITASK;TGS(1)YGALAEITASK;T(0.005)GS(0.995)YGALAEITASK 328.88 2.42E-68 1773838000 4805806 4067891 4026530 4730036 2462723 4497026 4605294 4614738 2551489 TRUE FALSE 4578645.075 4482413.718 4211150.383 4254563.795 2892221.111 4341292.862 3902671.818 4210647.076 2947160.883 1.553578259 1.520926036 1.42888378 1.443614368 0.981358408 1.473042373 1.32421404 1.428713003 1 21.49089439 7.999978269 0.03632164 2.75E-08 3.537461623 0.441990356 0.150648325 835.7170509 2.318280922 65.37813482 190.955848 99994996.29 -7.999978269 3.537461595 TGSDHTNPT(ph)SPLLVKPSDLLEENKINSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSDHTNPTSPLLVKPSDLLEENKINSSVK 30 2 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3;H0YE73 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 TGSDHT(0.011)NPT(0.494)S(0.494)PLLVKPSDLLEENKINSSVK 105.75 0.015176 106980000 236090 169190 225120 271700 142230 248900 299620 271010 120710 TRUE FALSE 224930.4936 186430.6534 235441.9747 244388.1998 167034.867 240280.5306 253907.4661 247278.9277 139429.0903 1.613224996 1.33710012 1.688614436 1.752777697 1.197991514 1.723317064 1.821050869 1.773510299 1 17.08917207 3.721231394 24.6984538 1.613852213 1.475162532 0 0.277523048 2204.257577 3141615.27 0.06863055 0.106601744 5262.976052 -3.721231394 -0.138689681 TGSDHTNPTS(ph)PLLVKPSDLLEENKINSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSDHTNPTSPLLVKPSDLLEENKINSSVK 30 2 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3;H0YE73 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 TGSDHTNPT(0.129)S(0.871)PLLVKPSDLLEENKINSSVK 178.15 3.91E-18 325570000 776260 586680 722010 842530 419020 795100 1022300 969910 464650 TRUE FALSE 739567.7282 646463.359 755114.8727 757837.2837 492096.9553 767565.4876 866329.3592 884979.5386 536705.5489 1.377976676 1.204502842 1.406944412 1.41201686 0.916884419 1.430142634 1.614161361 1.64891073 1 19.03377128 2.015005894 24.99143356 1.497486239 1.270434412 0.077456819 0.226966835 366.1458723 609791.9782 0.077008627 0.056854542 103.5156216 -2.015005894 -0.227051827 TGSES(ph)SQTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.003)ES(0.982)S(0.015)QTGTSTTSSR;TGS(0.034)ES(0.965)S(0.001)QTGTSTTSSR 353 2.85E-87 2315620000 639000 560500 584930 667070 384610 589440 585770 527670 348760 TRUE FALSE 608795.7364 617615.5872 611749.6191 600014.8562 451685.8622 569027.545 496400.0281 481464.4174 402843.9196 1.511244695 1.53313866 1.518577269 1.489447469 1.121242844 1.412526086 1.232239098 1.19516367 1 18.61986145 1.939834707 0.337788893 0.982082893 1.606455073 0.750593889 0.094450489 0.644671962 0.214008789 0.12393594 0.14067167 87.0632164 -1.939834707 0.62437218 TGSESS(ph)QTGTSTTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.158)ES(0.095)S(0.746)QT(0.001)GTSTTSSR 158.17 1.00E-08 1621600000 245050 219910 225520 290750 189950 246180 267080 253650 196150 TRUE FALSE 233466.9721 242319.079 235860.3151 261523.2576 223077.2199 237654.7249 226332.0407 231439.0613 226567.9402 1.030450168 1.069520599 1.041013635 1.154281834 0.984593053 1.048933599 0.998958814 1.021499605 1 17.78958421 TGSGGVASSSESNRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSGGVASSSESNRDR 16 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 67.136 0.047995 39921000 47023 32635 46142 44064 53632 54988 69497 45024 51860 FALSE TRUE 44800.31598 35960.5436 48257.65634 39634.603 62985.40382 53083.75177 58893.95625 41081.45987 59902.18394 0.747891196 0.600321077 0.805607628 0.661655392 1.051470909 0.886173897 0.983168766 0.68580905 1 15.87032098 2.753925803 24.90251738 0.922613926 0.697154384 0.491233717 0.109867222 583.9055028 946340.6898 0.030567562 0.032310281 567.4476521 -2.753925803 -0.225459542 TGSGS(ph)PFAGNS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 TGS(0.002)GS(0.998)PFAGNS(1)PAR;TGS(0.004)GS(0.996)PFAGNS(1)PAR 163.51 6.24E-06 339370000 1053750 1130200 910800 1145620 740400 1020010 1006700 1019350 725850 TRUE FALSE 1003941.326 1245368.665 952561.0809 1030460.101 869525.5256 984686.7979 853109.4257 930090.3101 838411.1109 1.197433232 1.485391413 1.136150355 1.229063031 1.037111167 1.174467734 1.017531155 1.109348741 1 19.67729831 3.221925946 1.483570914 1.073332605 1.332871167 0.494407242 0.099455365 0.271597881 1.245474161 0.031731012 0.045633354 1666.962944 -3.221925946 0.259538562 TGSGS(ph)PFAGNS(ph)PAREGEQDAASLKDVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSGSPFAGNSPAREGEQDAASLKDVFK 28 2 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 T(0.081)GS(0.102)GS(0.823)PFAGNS(0.994)PAREGEQDAASLKDVFK 94.949 0.0012213 83091000 154210 97073 161820 147740 99696 155270 184390 176560 116710 TRUE FALSE 146920.7989 106964.8491 169239.6071 132888.8945 117082.9508 149892.961 156257.9189 161099.4704 134808.7907 1.089845834 0.793456039 1.25540483 0.985758375 0.868511246 1.111893076 1.159107786 1.195021998 1 17.04055505 2.0456687 15.54311872 1.135666931 0.990011001 0.159337222 0.13177971 4.403169791 1497.261882 0.046945943 0.03467033 111.088397 -2.0456687 -0.14565593 TGSGS(ph)PFAGNSPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGS(0.012)GS(0.988)PFAGNSPAR;TGS(0.002)GS(0.998)PFAGNSPAR;T(0.001)GS(0.003)GS(0.997)PFAGNSPAR 207.91 9.21E-09 569011000 518790 456823 475839 520050 437054 470251 546930 496107 444496 TRUE FALSE 494267.8248 503373.7831 497656.6888 467773.586 513276.0792 453966.09 463485.7834 452665.2411 513426.1695 0.962685298 0.98042097 0.969285787 0.911082476 0.999707669 0.88418962 0.902731125 0.881655957 1 18.96979731 2.23110216 24.99999288 0.907475194 0.964388563 0.246660782 0.039672414 182.3125092 611088.0059 0.0130351 0.00981799 170.2558959 -2.23110216 0.056913369 TGSGSPFAGNS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 248.41 6.38E-18 457773000 626160 609710 524700 696710 449689 568090 590020 601190 481687 TRUE FALSE 596562.6577 671840.1422 548758.014 626675.3871 528114.6192 548416.9009 500001.6125 548546.6165 556384.5598 1.07221282 1.2075104 0.986292672 1.126334971 0.949189926 0.985679583 0.898661912 0.985912723 1 19.08572286 2.904160076 1.211376832 0.947983924 1.126564311 0.477290151 0.064976873 0.302384605 0.92906861 0.025970055 0.028477164 801.9736081 -2.904160076 0.178580387 TGSGSPFAGNS(ph)PAREGEQDAASLKDVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGSGSPFAGNSPAREGEQDAASLKDVFK 28 2 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGS(0.011)PFAGNS(0.989)PAREGEQDAASLKDVFK;TGSGSPFAGNS(0.999)PAREGEQDAASLKDVFK 155.71 9.19E-09 169142000 302690 159496 316850 266840 178189 294490 394990 311280 233855 TRUE FALSE 288382.4436 175748.8237 331377.8859 240016.7362 209265.1052 284291.7375 334727.021 284022.673 270120.039 1.067608477 0.650632305 1.22678009 0.888555833 0.774711517 1.052464447 1.239178782 1.051468355 1 18.04324115 2.018763126 14.27766117 1.129050717 0.910590034 0.189800876 0.165314099 2.239441138 1702.011403 0.058711939 0.04323342 104.4150561 -2.018763126 -0.218460684 TGSQGQCTQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 87.363 0.032059 28208000 14107 10090 10876 13310 13800 12327 14409 12571 14940 FALSE TRUE 13440.19007 11118.18247 11374.67536 11972.05351 16206.71563 11900.1129 12210.64241 11470.2166 17256.8189 0.778833582 0.644277635 0.659140913 0.693757846 0.939148503 0.689589024 0.707583621 0.664677347 1 14.07487892 -2.129713871 2.310955939 1.558548498 0.719914312 0.510565841 0.08547669 7841092.345 2057427.268 22963689.38 0.01987721 0.007417988 2.129713871 -0.838634186 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 TGS(0.013)S(0.107)S(0.879)PPGGPPKPGSQLDSMLGSLQSDLNK;TGS(0.001)S(0.133)S(0.866)PPGGPPKPGSQLDSMLGSLQSDLNK 357.31 1.16E-120 606550000 1522740 1374180 1385490 1579040 744320 1584190 1627840 1704650 776290 TRUE FALSE 1450763.098 1514210.504 1449016.087 1420311.899 874129.1723 1529329.103 1379483.111 1555381.809 896673.0885 1.617939823 1.688698505 1.615991497 1.583979621 0.974858266 1.705559275 1.538445983 1.73461413 1 19.77422257 -1.821386989 2.859590564 0.826378282 1.562819993 0.397550063 0.215597194 101766762.4 99052695.64 123406319.7 0.049667318 0.015087352 1.821386989 0.736441711 TGSSSPPGGPPKPGSQLDSMLGS(ph)LQSDLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 TGSSSPPGGPPKPGSQLDSMLGS(0.994)LQS(0.006)DLNK;TGSSSPPGGPPKPGSQLDSMLGS(0.999)LQSDLNK 225.73 4.55E-35 93825000 244530 225930 219810 262420 132056 281990 285050 306380 138583 TRUE FALSE 232971.5515 248952.5239 229888.5059 236041.043 155086.5246 272224.6156 241560.3872 279551.743 160073.7439 1.455401404 1.555236467 1.436141246 1.474576888 0.968844239 1.700620033 1.509056897 1.746393482 1 17.28837716 3.647571312 9.230512214 1.433462214 1.505241466 0.016784928 0.255049406 2.259104965 213.9481045 0.06349117 0.098439856 4441.925923 -3.647571312 0.071779252 TGTITTFEHAHNMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TGTITTFEHAHNMR 14 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;; 191.06 3.07E-07 7210240000 4417530 4564730 4288150 4591850 3738610 4614780 4722240 4257850 510219 FALSE TRUE 4208722.112 5029881.177 4484765.919 4130268.514 4390622.4 4454969.011 4001775.558 3885010.082 589341.1567 7.141401994 8.534752952 7.609795902 7.008281141 7.450052233 7.55923621 6.790253002 6.592124167 1 19.16874349 -0.383923029 0.503277401 1.06E-17 7.746727269 0.960396387 0.410276838 1.33396933 0.315492776 2.866097711 0.195809231 0.413120714 0.383923029 7.746727269 TGTIVVEGHELHDEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TGTIVVEGHELHDEDIR 17 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 208.43 3.00E-12 452629000 856930 821930 821590 933350 751680 781160 920130 829590 91427.3 FALSE TRUE 816424.6172 905685.6015 859260.7142 839527.8848 882772.754 754108.2333 779747.2692 756946.7017 105605.3787 7.73089995 8.57613137 8.136524147 7.94966975 8.359164699 7.140812735 7.383594268 7.167690801 1 16.68832379 -0.392498532 0.513778065 3.66E-17 8.184977906 0.976186008 0.338220318 1.013880456 0.246155584 2.288353011 0.150374158 0.405043314 0.392498532 8.184977906 TGTLQDLIQHGS(ph)PINNECHPSLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGTLQDLIQHGSPINNECHPSLER 24 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER 231.22 2.26E-33 176047000 150925 117447 128281 152158 134005 133325 169134 147507 82965 TRUE FALSE 143791.0744 129414.9828 134162.8107 136862.7888 157375.4296 128707.9218 143329.5019 134590.5051 95830.78847 1.500468447 1.350453073 1.399996941 1.428171373 1.642222005 1.34307485 1.495651911 1.404459957 1 16.54820162 0.94978087 19.69860933 0.999999999 1.445911937 0.72941732 0.085699019 399.2322857 156601.1035 0.076240369 0.019060092 8.908013567 -0.94978087 0.445911937 TGTRFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGTRFER 7 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 106.36 0.0070411 138793000 76639 57225 82411 73102 144644 67385 96779 93076 148479 FALSE TRUE 73016.42635 63056.29256 86189.62587 65753.64808 169869.8678 65051.44055 82013.58608 84925.77201 171504.365 0.425740921 0.367665817 0.502550625 0.383393438 0.990469647 0.379299037 0.478201159 0.495181403 1 17.38788577 -5 0.220376166 3.555632374 0.425470537 0.430080257 0.180047961 144.2117561 1.442183623 164.0210179 0.325836201 1.00E-05 5 -3.130161837 TGVCICFYQHKEEYQLVQVEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGVCICFYQHKEEYQLVQVEQK 22 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 99.686 0.00058284 15530000 51908 48017 46883 47338 36052 55285 58063 62152 40425 FALSE TRUE 49454.41171 52909.98689 49032.63192 42579.4943 42339.45739 53370.46659 49204.42295 56709.64139 46693.90254 1.059119264 1.133124113 1.050086398 0.911885535 0.906744887 1.142985779 1.053765487 1.214497789 1 15.51094655 -0.311598401 7.714473596 0.999999987 1.059773551 0.036487206 0.095255897 0 0 0.091167685 0.021488429 0.487979524 0.311598401 0.059773564 TGVELGKPTHFTVNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGVELGKPTHFTVNAK 16 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 127.75 3.88E-05 501130000 979780 774040 810350 960110 584060 983520 1182300 1092200 709160 FALSE TRUE 933467.7411 852915.556 847505.349 863597.9187 685919.8791 949460.4558 1001918.421 996561.1779 819132.9109 1.139580316 1.041241958 1.034637161 1.05428302 0.837373117 1.159104271 1.223145118 1.216604979 1 19.64373803 2.034493257 24.99998542 1.176314466 1.033734572 0.281038176 0.097264692 197.5462402 143176.5808 0.034669406 0.025604932 108.2662906 -2.034493257 -0.142579893 TGVHHYSGNNIELGTACGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TGVHHYSGNNIELGTACGK 19 0 E5RI99;P62888;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 ; 128.79 1.20E-05 137809000 157416 143334 149724 176255 158163 145911 198668 175567 72987 FALSE TRUE 149975.2576 157939.8976 156588.9935 158537.5125 185746.5771 140858.0655 168357.5478 160193.4227 84305.45119 1.778950893 1.873424498 1.857400575 1.880513185 2.203257019 1.67080614 1.996994802 1.900154978 1 16.3633383 -1.135557916 11.19936684 1.000000005 1.891737459 0.806057288 0.137988014 1.58E-09 0 0.120642119 0.02843562 0.073188371 1.135557916 0.891737454 TGVIHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGVIHEK 7 0 Q96M27;Q96M27-3;Q96M27-2;Q96M27-5 Q96M27 PRRC1 Protein PRRC1 0 ;; 75.38 0.043628 523950000 1879320 1550430 1679770 1996780 1288240 1826050 2004160 1927370 1317320 FALSE TRUE 1790488.268 1708420.58 1756789.116 1796059.881 1512908.648 1762813.431 1698388.583 1758599.265 1521603.258 1.176711642 1.122776631 1.154564508 1.180373315 0.994285889 1.158523696 1.116183588 1.15575414 1 20.53716081 -5 0.20037827 0.413474511 1.153400707 0.379947136 0.053145438 146.4712937 1.449294039 34.55087154 0.116654153 1.00E-05 5 0.739926196 TGVNSGVMLMNMTRMRRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGVNSGVMLMNMTRMRRK 18 3 Q4G148-2;Q4G148 Q4G148-2 GXYLT1 Glucoside xylosyltransferase 1 0 41.412 0.066725 35618000 35434 44345 50982 39463 153440 18532 42299 17610 164970 FALSE TRUE 33759.10504 48863.80592 53319.57513 35496.10427 180199.8874 17890.23219 35845.51068 16067.97504 190552.705 0.177164134 0.256431972 0.279815367 0.186279719 0.945669532 0.093886005 0.188113366 0.084322996 1 17.53983056 -1.050870458 4.453800838 1.00004177 0.271709736 0.460718678 0.245963299 28857277.7 10213277.59 11808.88046 0.054264237 0.088946639 1.050870458 -0.728332034 TGVPSTAS(ph)VGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TGVPSTASVGK 11 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TGVPS(0.364)T(0.257)AS(0.379)VGK 86.288 0.010414 0 168110 130630 148100 162830 105090 178330 183720 190020 135720 TRUE FALSE 160163.7735 143941.3455 154890.5315 146462.019 123417.6627 172154.3874 155690.1398 173380.8414 156766.7644 1.021669191 0.918187895 0.988031692 0.934267028 0.787269312 1.098156156 0.993132315 1.105979587 1 17.25826021 2.178997006 24.99999999 1.044550913 0.939471169 0.414282207 0.069949302 81.07991957 34030.01527 0.024870143 0.018367825 151.0069745 -2.178997006 -0.105079744 TGVTSTS(ph)DS(ph)EEEGDDQEGEKKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TGVTSTSDSEEEGDDQEGEKKR 22 2 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 2 TGVT(0.008)S(0.067)T(0.081)S(0.843)DS(1)EEEGDDQEGEKKR;TGVT(0.003)S(0.03)T(0.308)S(0.658)DS(1)EEEGDDQEGEKKR;TGVT(0.002)S(0.015)T(0.095)S(0.889)DS(1)EEEGDDQEGEKKR;TGVTS(0.004)T(0.03)S(0.966)DS(1)EEEGDDQEGEKKR 190.5 8.64E-17 1245270000 2832830 1826630 2806430 2698780 1406864 3093860 3610770 3316710 1676720 TRUE FALSE 2698927.74 2012765.674 2935107.591 2427493.507 1652220.636 2986718.852 3059880.72 3026281.289 1936737.174 1.393543624 1.039255972 1.515490915 1.253393356 0.853094916 1.542139477 1.579915314 1.562566842 1 20.88519675 TGYTLDVTTGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TGYTLDVTTGQR 12 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;F6UXX1;O43390;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;; 139.15 0.00014363 130000000 321938 280553 316453 340868 277236 341625 377531 330365 332946 FALSE TRUE 306720.6288 309141.6697 330962.6831 306603.301 325585.8706 329794.4406 319931.7121 301436.4892 384577.5652 0.797552058 0.803847384 0.860587598 0.797246976 0.846606511 0.857549869 0.831904253 0.783811945 1 18.55291508 -1.881624095 2.85205344 1.081504839 0.822624793 0.812899985 0.026778662 27125743.57 31410526.18 15217066.87 0.006407458 0.013133362 1.881624095 -0.258880045 THEAQIQEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 THEAQIQEMR 10 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;; 183.08 1.71E-06 4797280000 1800665 1850052 1910312 2168808 1842001 1944890 2084738 1780807 1035793 FALSE TRUE 1715551.134 2038574.402 1997901.695 1950795.299 2163245.391 1877537.972 1766672.929 1624870.098 1196418.488 1.43390557 1.703897442 1.669902057 1.630529216 1.808100938 1.569298694 1.476634594 1.358111826 1 20.19029068 0.993934543 1.161407476 1.005289693 1.63702926 0.819714563 0.095965646 0.212521114 0.593973704 0.091217017 0.028788138 9.861308448 -0.993934543 0.631739567 THETLSHAGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THETLSHAGQK 11 0 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 ; 204.69 1.87E-08 192240000 173480 181287 185535 248540 169762 211987 288390 177809 52738 FALSE TRUE 165279.9442 199760.3514 194041.9633 223556.287 199368.4391 204645.837 244390.8089 162239.1013 60916.33969 2.713228422 3.279257296 3.185384484 3.669890347 3.27282368 3.359457217 4.011908957 2.663310077 1 15.89454164 4.565989827 2.270780979 3.251837404 2.670317341 0 0.829270861 1.474303678 11.73858901 0.182947971 1.485110409 36812.03504 -4.565989827 -0.581520063 THFDYQFGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THFDYQFGYR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 0 152.54 1.79E-05 147290000 327680 394340 300850 346110 273980 339350 333140 344400 191770 FALSE TRUE 312191.2158 434523.6943 314644.2701 311318.3652 321762.0253 327598.2244 282313.3745 314242.5102 221508.7122 1.40938572 1.961655097 1.420460022 1.40544524 1.452593093 1.478940585 1.274502351 1.418646279 1 17.75700392 1.167742336 0.257610087 0.904232748 1.730024893 0.496961931 0.166440118 1.666336698 0.417105325 0.534364816 0.376543078 14.71439249 -1.167742336 0.825792145 THFGGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 4352630000 18830100 19877400 19729000 23973400 15414600 21722600 24568900 19062400 8368400 FALSE TRUE 17940038.49 21902929.66 20633594.16 21563548.29 18102901.36 20970340.92 20820463.07 17393195.2 9666128.732 1.855969332 2.265946406 2.13462853 2.230836034 1.872818153 2.169466339 2.153960871 1.799396189 1 23.20450678 0.867128322 3.049980144 1.000473251 2.101549076 0.865752554 0.13611222 0.176294071 3.171899912 0.123339379 0.032272925 7.364246578 -0.867128322 1.101075826 THILLFLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 98.033 0.0062881 516640000 953540 803460 546040 780530 703570 731130 1183000 725150 295550 FALSE TRUE 908468.0539 885333.4875 571076.4741 702069.6415 826272.3852 705810.7848 1002511.623 661652.0217 341382.3845 2.661145083 2.593377771 1.672835213 2.056549117 2.42037206 2.067507923 2.936623763 1.938155135 1 18.38102909 0.986005307 23.49353573 0.999999967 2.378187991 0.587912815 0.355511771 242.5801783 407232.0473 0.348397496 0.087099374 9.682896878 -0.986005307 1.378188024 THINIVVIGHVDSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 191.44 1.01E-07 3049650000 8884550 10374740 10862660 13392980 7511390 12009270 13144510 9265950 2238132 FALSE TRUE 8464594.929 11431937.8 11360723.71 12046692.21 8821374.038 11593385.97 11139073.58 8454574.296 2585210.08 3.274238715 4.422053701 4.394506967 4.659850393 3.412246497 4.484504397 4.308769206 3.270362576 1 21.30185009 0.875724936 3.254671271 1.001373635 4.131073877 0.825772217 0.454040304 0.20378995 4.267697224 0.423186586 0.110003045 7.511469977 -0.875724936 3.129700242 THKHS(ph)PEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 THKHSPEKR 9 2 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 THKHS(1)PEKR;THKHS(1)PEKR;THKHS(1)PEKR;THKHS(1)PEKR;THKHS(1)PEKR;T(0.004)HKHS(0.996)PEKR;THKHS(1)PEKR 151.7 3.91E-05 451788000 480595 507338 487492 592416 281559 592221 633247 443781 62888.5 TRUE FALSE 457878.2268 559036.319 509843.9904 532865.2182 330662.8005 571712.2383 536633.5398 404921.183 72640.92739 6.303309212 7.695886315 7.018687794 7.335605936 4.552017882 7.870387381 7.387481948 5.574284326 1 16.148495 THKNPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THKNPALK 8 1 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ; 95.502 0.0057711 1758250000 3244700 3234600 3517500 4230500 2416600 3929300 4516200 3519300 1176600 FALSE TRUE 3091329.461 3564209.417 3678780.854 3805242.103 2838054.275 3793227.356 3827170.744 3211131.435 1359061.119 2.274606652 2.622552708 2.70685461 2.799905059 2.088246243 2.791064584 2.8160402 2.362757194 1 20.37417891 0.955260641 17.59171716 0.999999992 2.58526983 0.814424495 0.236030049 64.68273937 25434.13787 0.223064148 0.055766632 9.021123768 -0.955260641 1.585269837 THLENNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THLENNR 7 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 140.98 0.0025876 112285000 90676 99474 101119 119730 104436 110628 129325 101390 58459 FALSE TRUE 86389.92518 109610.5137 105755.4062 107694.5129 122649.6053 106796.9246 109594.096 92511.7541 67524.52315 1.279385935 1.623269719 1.566177756 1.594894831 1.816371292 1.581602056 1.623026582 1.370046759 1 16.04312393 0.929317931 3.324510961 1.000544588 1.57632871 0.674615018 0.129770366 0.196249491 5.284917042 0.128728136 0.033433882 8.498023568 -0.929317931 0.575784122 THLMSEEEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THLMSEEEWR 10 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 167.09 5.35E-06 53925000 37983 50683 44614 63690 44694 51271 57343 38553 17357 FALSE TRUE 36187.61887 55847.65532 46659.59603 57287.7602 52488.61945 49495.47241 48594.27217 35177.09494 20048.63491 1.804991663 2.785608874 2.32732035 2.857439444 2.618064506 2.4687702 2.423819496 1.754588035 1 14.29121639 1.0043156 2.303912883 1.003111377 2.478271974 0.743516042 0.286311816 0.145277522 1.692451888 0.264788498 0.072572347 10.09986572 -1.0043156 1.475160596 THLPGCGARARLCGTGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THLPGCGARARLCGTGAR 18 2 Q9NYQ6;Q9NYQ6-2 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 0 ; 50.653 0.088117 1001060000 127305 178803 195424 110452 1733860 0 70108 30324 685060 FALSE TRUE 121287.5449 197023.229 204384.3837 99349.15511 2036244.635 0 59411.73698 27668.6698 791295.606 0.153277162 0.24898815 0.258290811 0.125552517 2.573304615 0 0.075081596 0.034966288 1 19.59385722 THLPGFVEQAEALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 THLPGFVEQAEALK 14 0 P30044-2;P30044 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;; 173.44 2.70E-06 2514320000 2599750 2701340 2708360 3222880 1954730 2905370 3347170 2443470 671740 FALSE TRUE 2476864.97 2976609.617 2832540.985 2898909.979 2295634.293 2804756.308 2836497.742 2229506.813 775910.0084 3.192206497 3.836282023 3.650605037 3.736142011 2.958634723 3.614795889 3.655704541 2.873409015 1 19.56552981 0.855737126 3.041106282 1.000848404 3.53139434 0.900488013 0.263324804 0.168465596 2.882172383 0.242296968 0.063403151 7.173599495 -0.855737126 2.530545935 THLTELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THLTELQR 8 0 Q02218;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 98.629 0.0073866 60022000 103680 89144 82711 97069 117280 99729 121760 94263 62254 FALSE TRUE 98779.25187 98227.87495 86503.38116 87311.4397 137733.5949 96275.35972 103183.2757 86008.832 71908.03237 1.373688705 1.366020898 1.20297244 1.214209829 1.915413207 1.338867948 1.434933933 1.196094917 1 16.13386531 1.016094468 3.217617438 1.001195446 1.402571016 0.324093659 0.196243698 0.259413733 6.327263399 0.178649441 0.046756054 10.37754125 -1.016094468 0.40137557 THMEET(ph)KHT(ph)S(ph)LLPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THMEETKHTSLLPDR 15 1 Q9NRM2 Q9NRM2 ZNF277 Zinc finger protein 277 3 THMEET(1)KHT(1)S(1)LLPDR 45.257 0.089531 2856000000 211550 191280 352030 262640 713120 169920 325320 120430 150980 TRUE FALSE 201550.4508 210771.6495 368170.9237 236238.9282 837487.9022 164035.6278 275686.4591 109884.5108 174393.2073 1.155724204 1.20860011 2.111154037 1.354633772 4.802296576 0.940607896 1.580832553 0.630096278 1 17.41198432 3.760733252 19.34612842 1.837645162 1.182158799 0.040893099 1.160895999 140.2309048 122346.582 0.284831811 0.511907287 5764.12316 -3.760733252 -0.655486363 THMQDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 107.29 0.0075096 604790000 988600 1110430 980660 1326000 780190 1228200 1340270 1072120 397170 FALSE TRUE 941870.8372 1223584.079 1025624.231 1192707.961 916254.889 1185667.126 1135787.196 978239.4891 458761.0951 2.053074786 2.667148746 2.235639076 2.599845483 1.997237557 2.584497985 2.475770522 2.132350584 1 18.80738352 0.832486365 3.841166806 1.000113972 2.38453068 0.783210894 0.225455197 0.459857047 9.992021312 0.194202194 0.049761807 6.799646968 -0.832486365 1.384416708 THNDIIHNENMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 THNDIIHNENMR 12 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;;;;; 237.32 2.44E-16 9902270000 1321854 1671605 1593025 2046874 1592079 1589402 2035783 1037482 497873 FALSE TRUE 1259372.581 1841943.45 1666066.772 1841118.337 1869737.074 1534360.61 1725186.914 946634.576 575080.6021 2.189906209 3.202930934 2.897101321 3.201496156 3.251260896 2.66807923 2.999904548 1.646090257 1 19.13340465 1.103336815 3.347453915 1.013856572 2.913990964 0.820801518 0.316383839 0.086624326 1.804194786 0.296070062 0.077977183 12.68635369 -1.103336815 1.900134392 THPQYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 THPQYSR 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;; 116.73 0.0083084 702982000 1949425 1318410 1211132 1695521 1711558 1318757 1913836 1413226 1427190 FALSE TRUE 1857279.544 1452757.478 1266663.6 1525084.008 2010053.173 1273088.114 1621845.168 1289476.439 1648511.336 1.126640444 0.881254163 0.768368147 0.925128008 1.219314135 0.772265308 0.983824092 0.782206595 1 20.65273238 4.588685752 3.038539274 0.918072916 1.130914391 0.190079983 0.135669909 0.468135047 7.411828111 0.031178776 0.199279264 38786.96088 -4.588685752 0.212841475 THPVEIFYTPEPERDYLEAAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 THPVEIFYTPEPERDYLEAAIR 22 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;; 174.2 1.73E-12 223004000 78554 75872 75807 84254 69941 76408 92222 81194 69857 FALSE TRUE 74840.9081 83603.44306 79282.82593 75784.62785 82138.68826 73761.9718 78151.84013 74084.22292 80690.06678 0.927510796 1.036105761 0.982559925 0.939206409 1.01795291 0.914139432 0.968543505 0.918133122 1 16.30010346 2.236595668 24.99991551 0.948634054 0.981596025 0.126272917 0.039680939 100.7336271 1281594.037 0.013333703 0.010344092 172.4231869 -2.236595668 0.032961971 THPYS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 88.496 0.011958 776670000 3694800 3470600 3618900 4181900 2329620 4166200 4217300 3961700 1759910 TRUE FALSE 3520154.126 3824258.086 3784830.145 3761527.467 2735904.99 4021923.449 3573873.429 3614792.546 2032827.854 1.731653823 1.881250337 1.861854724 1.850391541 1.345861621 1.978486983 1.758079722 1.778208882 1 20.95505662 0.213898784 2.897096273 0.999999734 1.780441394 0.677618422 0.167545435 86.18743817 314.8695776 0.147797422 0.038744189 1.636435091 -0.213898784 0.78044166 THS(ph)EGSLLQEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 THSEGSLLQEPR 12 0 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 T(0.185)HS(0.815)EGSLLQEPR;T(0.112)HS(0.888)EGSLLQEPR;T(0.032)HS(0.968)EGSLLQEPR 207.4 5.08E-08 1188260000 1209160 1126670 1145440 1398180 1089090 1195390 1440080 982510 703850 TRUE FALSE 1152005.403 1241478.954 1197959.557 1257632.29 1279026.951 1153993.345 1220369.347 896476.2158 812999.4632 1.416981751 1.527035392 1.473505963 1.546904207 1.573219921 1.419426945 1.501070299 1.1026775 1 19.63289487 1.174814875 3.830070809 1.005522164 1.49487721 0.928849284 0.051249918 0.049226888 1.304821013 0.045638239 0.012188814 14.95597997 -1.174814875 0.489355046 THS(ph)FENVSCHLPDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THSFENVSCHLPDSR 15 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 T(0.058)HS(0.942)FENVSCHLPDSR;T(0.011)HS(0.989)FENVSCHLPDSR 192.09 2.48E-07 842920000 280145 241786 295935 411380 388620 325824 458600 219076 106230 TRUE FALSE 266903.101 266424.2683 309503.9125 370027.3008 456395.205 314540.6332 388632.1472 199892.544 122703.6059 2.175185474 2.171283121 2.522370148 3.015618802 3.719493016 2.56341801 3.167243086 1.629068214 1 16.90481812 3.606019739 3.772420094 2.71955178 2.173689669 0 0.779203851 0.568688997 14.27117838 0.192817848 0.308745007 4036.637394 -3.606019739 -0.545862111 THS(ph)TSS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 T(0.09)HS(0.597)T(0.292)S(0.14)S(0.866)S(0.016)LGSGESPFSR 120.49 3.64E-05 116540000 56415 60931 73598 85996 74667 75741 99491 51838 35421 TRUE FALSE 53748.37475 67139.93817 76972.5411 77351.5187 87688.90116 73118.07018 84311.82067 47298.78991 40913.90777 1.313694479 1.641005268 1.881329486 1.890592293 2.143254114 1.787120179 2.060712977 1.156056522 1 15.32030372 4.264327782 2.028393799 1.792062201 1.331322551 0.053692924 0.372799312 0.626329029 4.749174452 0.088512377 0.371117244 18379.24986 -4.264327782 -0.46073965 THS(ph)TSSSLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.171)HS(0.65)T(0.171)S(0.008)SSLGSGESPFSR;T(0.157)HS(0.645)T(0.157)S(0.039)S(0.002)SLGSGESPFSR;T(0.179)HS(0.746)T(0.075)S(0.001)SSLGSGESPFSR;T(0.134)HS(0.732)T(0.134)S(0.001)SSLGSGESPFSR;THS(0.591)T(0.193)S(0.072)S(0.072)S(0.072)LGSGESPFSR;THS(0.976)T(0.012)S(0.012)SSLGSGESPFSR;T(0.084)HS(0.395)T(0.395)S(0.123)S(0.002)S(0.001)LGSGESPFSR 324.6 5.11E-59 4791235000 1433525 1217533 1589685 1825174 1733578 1496924 2113069 1246686 860717 TRUE FALSE 1365765.114 1341600.997 1662573.63 1641704.042 2035913.454 1445085.147 1790681.515 1137519.565 994192.5964 1.373742994 1.349437726 1.672285265 1.651293771 2.04780589 1.453526361 1.80114147 1.144164188 1 19.92316583 1.104252163 5.506840672 1.007355544 1.595511877 0.549080632 0.207664624 0.164522681 6.81435915 0.211084086 0.053300889 12.7131205 -1.104252163 0.588156333 THSDQFLVAFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THSDQFLVAFK 11 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 ; 98.156 0.0057307 348280000 1459740 1681610 1274340 1280310 1056210 1194020 1366700 1290800 598300 FALSE TRUE 1390740.983 1852967.971 1332769.749 1151610.806 1240412.69 1152670.788 1158184.814 1177770.709 691081.3083 2.012412963 2.68125899 1.928528139 1.666389747 1.794886759 1.667923548 1.675902386 1.704243328 1 19.39849593 2.368932968 0.154281464 0.620272154 3.018394197 0.661046064 0.240643755 4.049522234 0.371356614 1.900221657 3.191478 233.8476273 -2.368932968 2.398122043 THSDSKPYGPMSVGLDFSLPGMEHVYGIPEHADNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THSDSKPYGPMSVGLDFSLPGMEHVYGIPEHADNLR 36 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 40.864 0.048233 179930000 162870 137580 141930 171090 119550 155720 161860 157930 103820 FALSE TRUE 155171.4579 151599.5584 148437.6309 153891.7082 140399.4821 150327.3774 137165.2842 144100.812 119919.8754 1.293959466 1.264173749 1.237806748 1.283287759 1.170777419 1.253565157 1.143807762 1.201642443 1 16.87171126 -5 0.109359003 0.200977296 1.377767999 0.849336543 0.033721841 50.92704935 0.370862696 9.000860979 0.36553821 1.00E-05 5 1.176790703 THSEGS(ph)LLQEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THSEGSLLQEPR 12 0 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 THS(0.037)EGS(0.963)LLQEPR 193.62 2.70E-06 107200000 66622 59106 67014 84058 68313 68897 85844 72443 52220 TRUE FALSE 63472.91009 65128.9686 70086.65819 75608.33014 80226.76557 66511.07961 72746.92117 66099.50688 60318.0109 1.05230443 1.079759886 1.161952411 1.253495084 1.330063183 1.102673623 1.206056368 1.095850243 1 15.88030123 3.739437539 3.593128282 1.181980473 1.06283303 0.151934265 0.091091411 0.308955529 8.751703377 0.02274468 0.040241979 5488.296159 -3.739437539 -0.119147443 THSLCNGDS(ph)PGPVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THSLCNGDSPGPVQK 15 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 THSLCNGDS(1)PGPVQK;THSLCNGDS(1)PGPVQK 221.37 2.32E-12 0 282780 310320 313800 357920 199581 328150 360130 285740 106181 TRUE FALSE 269413.5498 341941.9608 328188.0404 321941.2016 234387.8632 316786.0832 305185.5543 260719.0908 122647.0072 2.196658166 2.788017161 2.675874837 2.624941358 1.911076908 2.5829092 2.488324512 2.125768062 1 16.9041525 0.799483749 2.396728874 1.000416026 2.481843133 0.768951123 0.251935764 0.371054788 3.520821879 0.233217398 0.062805925 6.302077637 -0.799483749 1.481427107 THSQGGYGSQGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THSQGGYGSQGYK 13 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 183.06 1.07E-05 222106000 198679 186281 216302 240740 149802 212871 247520 201933 104655 FALSE TRUE 189287.8374 205263.2457 226219.6607 216540.3578 175927.4214 205499.2239 209756.278 184250.676 120884.3629 1.56585875 1.698013215 1.871372403 1.791301643 1.455336465 1.699965314 1.735181234 1.524189495 1 16.88326811 0.856720604 3.506309238 1.000133213 1.684896187 0.782699537 0.113714788 0.323121861 6.994821359 0.108709513 0.028057088 7.189862818 -0.856720604 0.684762974 THST(ph)SS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 T(0.042)HS(0.394)T(0.537)S(0.039)S(0.951)S(0.036)LGSGESPFSR 152 4.06E-07 106880000 47213 49846 61029 74525 66566 64276 87361 48894 38458 TRUE FALSE 44981.33506 54925.36407 63827.24002 67033.60541 78175.08932 62050.106 74032.47496 44612.58216 44421.87022 1.012594356 1.236448709 1.436842701 1.509022584 1.759833364 1.396836866 1.666577174 1.004293199 1 15.43898251 4.028328498 1.848773971 1.457933774 1.04295866 0.164829943 0.249374596 0.439199911 2.883562485 0.062843607 0.190763553 10674.03195 -4.028328498 -0.414975114 THSTSS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.001)HS(0.025)T(0.018)S(0.165)S(0.779)S(0.013)LGSGESPFSR;THSTS(0.01)S(0.835)S(0.155)LGSGESPFSR;T(0.001)HS(0.002)T(0.015)S(0.1)S(0.878)S(0.003)LGSGESPFSR 216.99 5.37E-15 6524570000 300344 289613 306042 400317 351176 309248 423950 328544 215041 TRUE FALSE 286147.3343 319124.894 320074.3284 360076.3746 412420.9832 298538.6642 359268.6411 299774.9456 248388.46 1.152015413 1.284781483 1.28860386 1.449650175 1.660387053 1.201902311 1.446398279 1.206879521 1 17.92223862 0.970313956 6.086086146 1.000056831 1.342673342 0.389830299 0.14362198 0.219373291 34.48350458 0.139800359 0.035146774 9.339292041 -0.970313956 0.342616511 THT(ph)GEKPYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.017)HT(0.983)GEKPYK;T(0.017)HT(0.983)GEKPYK;THT(1)GEKPYK 131.17 0.00049925 177438000 283788 417860 340090 491970 219378 427600 456900 303882 127128 TRUE FALSE 270373.9037 460440.4091 355683.4629 442516.2409 257637.4537 412792.1048 387191.5135 277272.4811 146842.361 1.841252769 3.135610229 2.422212913 3.013546214 1.754517239 2.811124134 2.636783493 1.888232246 1 17.16390869 0.967623798 3.293708328 1.003297065 2.538471141 0.548371438 0.445790599 0.168542175 4.698825527 0.387674924 0.100920245 9.281620291 -0.967623798 1.535174076 THTGEKPYVCDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THTGEKPYVCDK 12 1 Q49AA0 Q49AA0 ZFP69 Zinc finger protein ZFP69 0 ; 52.344 0.089716 581400000 1987630 2911800 1802960 2075700 772360 2565800 1362410 1805740 418570 FALSE TRUE 1893678.669 3208515.73 1885627.499 1867046.692 907059.3395 2476945.703 1154549.332 1647619.833 483479.6978 3.916769778 6.636298783 3.900117229 3.861685818 1.876106367 5.123163834 2.387999615 3.407836648 1 18.88309578 1.698329546 0.202788542 0.191591398 6.260122575 0.435325133 1.201961839 2.29585476 0.475035878 5.196580947 5.790953726 49.92631881 -1.698329546 6.068531176 THTRVS(ph)VQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 THTRVSVQR 9 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 THTRVS(1)VQR;THTRVS(1)VQR;THT(0.004)RVS(0.996)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THT(0.005)RVS(0.995)VQR;THTRVS(1)VQR;THT(0.001)RVS(0.999)VQR;THTRVS(1)VQR;THTRVS(1)VQR;T(0.002)HT(0.007)RVS(0.991)VQR 146.16 5.78E-05 8783295000 2139237 2195939 2409986 2628386 2270648 2462185 3024263 1977140 1045263 TRUE FALSE 2038119.507 2419707.681 2520486.242 2364175.646 2666648.292 2376918.916 2562856.135 1804011.14 1207357.048 1.688083497 2.004135964 2.087606352 1.958141256 2.20866586 1.968695939 2.122699445 1.494181977 1 20.20342095 1.0092599 3.708375209 1.003051112 1.995057058 0.854601706 0.138232918 0.071792526 2.497618173 0.13826946 0.035642322 10.21550638 -1.0092599 0.992005946 THTTALAGRS(ph)PS(ph)PASGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(1)PS(1)PASGR;THTTALAGRS(1)PS(1)PASGR;THTTALAGRS(0.998)PS(0.999)PAS(0.003)GR;THTTALAGRS(0.999)PS(0.998)PAS(0.003)GR;THTTALAGRS(0.999)PS(0.989)PAS(0.012)GR;THTTALAGRS(0.998)PS(0.996)PAS(0.005)GR;THTTALAGRS(1)PS(1)PASGR;T(0.029)HT(0.032)T(0.034)ALAGRS(0.913)PS(0.99)PAS(0.002)GR;T(0.035)HT(0.04)T(0.043)ALAGRS(0.888)PS(0.994)PASGR;T(0.013)HT(0.014)T(0.015)ALAGRS(0.961)PS(0.994)PAS(0.002)GR 173.43 1.96E-09 14978855000 5417852 5167216 6218422 7472791 7289143 6158967 9093678 4989970 2417650 TRUE FALSE 5161760.873 5693761.185 6503542.8 6721611.851 8560367.231 5945680.428 7706270.404 4553021.773 2792566.814 1.848392972 2.038898821 2.328876346 2.406965454 3.065411788 2.129109462 2.759565273 1.630407462 1 21.41316037 1.010383779 5.349657623 1.001703128 2.330607695 0.636292856 0.348278982 0.097620343 9.52224999 0.355398667 0.089677108 10.24197659 -1.010383779 1.328904566 THTTALAGRS(ph)PS(ph)PASGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 THTTALAGRSPSPASGRR 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(1)PS(0.967)PAS(0.034)GRR;THTTALAGRS(1)PS(0.985)PAS(0.015)GRR;THTTALAGRS(0.999)PS(0.619)PAS(0.382)GRR;THTTALAGRS(1)PS(0.899)PAS(0.101)GRR;THTTALAGRS(1)PS(0.974)PAS(0.026)GRR;THTTALAGRS(0.996)PS(0.946)PAS(0.058)GRR;THTTALAGRS(1)PS(0.945)PAS(0.055)GRR;THTTALAGRS(1)PS(0.98)PAS(0.02)GRR;THT(0.001)T(0.001)ALAGRS(0.996)PS(0.867)PAS(0.135)GRR;THTTALAGRS(0.999)PS(0.869)PAS(0.131)GRR 141.08 6.57E-08 4520581000 1144470 935092 1447972 1403165 1593746 1243993 1954588 1167950 892442 TRUE FALSE 1090373.171 1030378.938 1514362.948 1262116.188 1871694.798 1200913.21 1656379.702 1065678.106 1030837.347 1.057754818 0.999555304 1.469061004 1.224360169 1.815703324 1.164988069 1.606829347 1.033798503 1 19.97538528 3.745242046 24.69547813 1.374955394 1.028655031 0.180396724 0.254365992 520.7523737 1924765.538 0.057588332 0.100785514 5562.141668 -3.745242046 -0.346300363 THTYECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THTYECR 7 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 100.19 0.0099773 11973000 14736 20262 16923 19393 29889 17245 24575 17013 25029 FALSE TRUE 14039.45848 22326.72084 17698.93629 17443.5788 35101.63214 16647.80133 20825.6324 15523.25153 28910.36949 0.485620168 0.772273798 0.61220028 0.60336755 1.214153702 0.575841873 0.720351651 0.536944072 1 14.81929943 5.314052415 0.873360643 0.749693243 1.68E-09 0.139407131 0.2096334 11.15757514 3.271671354 0.062963843 10.15553762 206087.8624 -5.314052415 -0.749693241 THVADFAPEVAWVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 169.09 1.22E-06 741910000 761170 717990 719870 848860 731390 803400 991180 759180 390670 FALSE TRUE 725191.0026 791153.9973 752876.7515 763530.9801 858944.1844 775578.0566 839957.2867 692702.1745 451253.1083 1.607060404 1.753237779 1.668413442 1.692023758 1.903464305 1.718720696 1.861388368 1.535063497 1 18.78357734 0.914937309 4.84563418 1.000101084 1.740076588 0.879984906 0.086616393 0.157896615 8.256397864 0.083334935 0.021094419 8.221239667 -0.914937309 0.739975504 THVGSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 THVGSYK 7 0 H0Y8R1;F5H5I6;H0YAK1;Q12849;Q12849-5 H0Y8R1 GRSF1 G-rich sequence factor 1 0 ; 128.57 0.0037452 67149000 236052 232494 237272 261560 235130 218620 298540 222620 166871 FALSE TRUE 224894.2898 256185.4029 248151.1559 235267.4919 276136.5976 211049.1346 252992.2399 203126.2126 192748.5024 1.166775809 1.329117475 1.287434936 1.220593099 1.432626423 1.094945652 1.312551002 1.053840679 1 17.55636013 1.147433814 4.911008195 1.004898128 1.262609112 0.53511151 0.092028798 0.143881357 5.47517236 0.077044292 0.019717649 14.04215665 -1.147433814 0.257710984 THYDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 THYDAK 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 118.06 0.022193 412209000 953980 945480 828310 1070770 593270 909820 958670 936540 463880 FALSE TRUE 908887.256 1041825.487 866288.8328 963134.1653 696736.1002 878312.7053 812407.2843 854531.5927 535816.1412 1.696267033 1.944371225 1.616765092 1.797508681 1.300326822 1.639205387 1.516205321 1.594822416 1 19.03137852 -2.162662819 0.136839343 1.67E-11 2.001612692 0.669995007 0.150277614 28.51399473 0.53242263 10.20011494 1.110717557 0.006876021 2.162662819 2.001612692 THYDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 101.64 0.0089085 3202539000 1894852 1741055 1889608 2175819 1959460 1940801 2344370 1817902 1325916 FALSE TRUE 1805286.101 1918470.484 1976248.396 1957101.54 2301189.204 1873590.575 1986693.299 1658716.864 1531532.281 1.178745054 1.252647761 1.290373321 1.277871557 1.50254045 1.223343835 1.297193225 1.08304401 1 20.54654435 1.12580358 3.503205026 1.00229333 1.283269935 0.602512667 0.084655856 0.155793817 3.405656527 0.08016452 0.021112745 13.35991145 -1.12580358 0.280976605 THYDPPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 88.948 0.0092525 989470000 1405690 1226580 1262960 1510710 1109670 1342960 1514780 1436240 1281890 FALSE TRUE 1339245.82 1351569.897 1320867.965 1358850.561 1303196.097 1296452.958 1283672.49 1310475.212 1480678.954 0.904480891 0.912804152 0.892069116 0.917721263 0.880134139 0.875580054 0.866948562 0.885050205 1 20.49782743 -0.838191769 5.57092481 1.000000036 0.892289038 0.816401423 0.016117036 8.36E-09 1.74E-09 0.018088428 0.004263482 0.145147056 0.838191769 -0.107710998 THYSNIEANESEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 THYSNIEANESEEVR 15 0 A0A0C4DGQ5;K7ELJ7;P04632;U3KQE2;K7EIV0;A0A075B7C0;K7EM73 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 166.92 1.34E-06 111650000 266170 293690 280090 289880 245400 313510 351850 348110 279910 FALSE TRUE 253588.6716 323617.3449 292932.4035 260740.7117 288197.6823 302653.0701 298168.8203 317627.643 323317.0132 0.78433445 1.000928908 0.906022237 0.806455278 0.89137803 0.936087672 0.922218158 0.982403121 1 18.3025899 1.433986332 1.138121763 1.000636692 0.885852558 0.35366343 0.059405257 0.552603297 1.398503865 0.053847826 0.018557956 27.16353781 -1.433986332 -0.114784134 TIADLELHYQEFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TIADLELHYQEFIR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 214.45 6.87E-12 152223000 209123 199219 192844 215649 202001 190796 233335 226231 197352 FALSE TRUE 199238.1702 219519.6426 201686.0881 193971.5528 237229.9104 184188.6867 197735.4603 206421.0143 227956.3402 0.87401899 0.962989853 0.884757528 0.850915367 1.040681344 0.807999841 0.867426894 0.905528726 1 17.79839801 TIAHS(ph)PTSFTESSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIAHSPTSFTESSSK 15 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 T(0.072)IAHS(0.634)PT(0.285)S(0.009)FTESSSK 118.05 0.00020743 232910000 153730 147540 151070 168190 126670 139580 187160 169730 131980 TRUE FALSE 146463.4876 162574.4937 157996.7089 151283.2217 148761.2079 134746.3096 158605.3046 154867.5414 152446.7843 0.960751571 1.066434392 1.036405652 0.992367417 0.975823849 0.883890796 1.040397836 1.015879358 1 17.21794619 4.760584508 23.34623971 1.002124674 0.960751463 0.063124499 0.049143388 1130.759421 2493885.1 0.01185092 0.160095668 57621.4931 -4.760584508 -0.041373211 TIAPTGHLHTVEFHQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIAPTGHLHTVEFHQQR 17 0 Q96FX7;H0Y2Q1 Q96FX7 TRMT61A tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 0 91.657 0.0012172 48159000 43832 43495 47267 43968 67474 33555 59665 33419 35854 FALSE TRUE 41760.14823 47927.18995 49434.2387 39548.25311 79241.44424 32392.98194 50562.00843 30492.65519 41414.0552 1.008356898 1.157268703 1.193658493 0.954947612 1.913394954 0.782173631 1.220890062 0.736287597 1 15.33783286 1.450904962 2.055492151 0.89154181 1.179545066 0.123382983 0.305869676 0.651085427 5.162333293 0.237036306 0.075841037 28.24261862 -1.450904962 0.288003255 TIAQDYGVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TIAQDYGVLK 10 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 158.79 1.83E-05 205130000 536928 429464 374464 406394 459489 429290 570947 472584 497999 FALSE TRUE 511548.4775 473226.8699 391633.5448 365542.503 539623.7361 414423.5797 483838.549 431202.0396 575226.1415 0.889299774 0.822679701 0.680834052 0.635476166 0.938107115 0.720453314 0.841127539 0.749621772 1 19.13376972 -1.323088736 6.073514755 1.000016089 0.792148697 0.343329816 0.093070618 1.95E-05 2.17E-06 0.0865043 0.020387682 0.047523811 1.323088736 -0.207867391 TIAQDYGVLKADEGISFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TIAQDYGVLKADEGISFR 18 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 217.42 7.69E-19 352275000 457617 191362 525453 328437 512241 442730 838309 537883 865680 FALSE TRUE 435986.3513 210862.0054 549545.5398 295421.8888 601575.6682 427398.1491 710409.5654 490783.113 999925.2331 0.436018951 0.210877772 0.549586631 0.295443978 0.60162065 0.427430107 0.710462685 0.49081981 1 19.9314607 0.151807052 0.230881921 1.22774302 0.259729592 0.676054033 0.125340782 3.370732739 0.343351124 0.921092063 0.269911216 1.418427205 -0.151807052 -0.968013427 TIAS(ph)DS(ph)EEEAGKELSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIASDSEEEAGKELSDK 17 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 T(0.005)IAS(0.995)DS(1)EEEAGKELSDK;TIAS(1)DS(1)EEEAGKELSDK 159.59 1.82E-09 840890000 2753490 2656140 2227650 2996500 1253520 2819640 2457230 2854000 1107920 TRUE FALSE 2623337.985 2926803.686 2329789.956 2695286.127 1472133.491 2721995.16 2082334.433 2604088.63 1279730.575 2.049914283 2.287046776 1.820531603 2.106135603 1.150346424 2.127006428 1.627166275 2.034872559 1 20.28740868 -1.512985184 0.141262518 8.11E-15 2.383415181 0.446645511 0.318300102 32.87846631 0.794075565 14.65647981 2.248760894 0.030691267 1.512985184 2.383415181 TICTFDSSGFESMS(ph)PIKETVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TICTFDSSGFESMSPIKETVSSR 23 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 TICTFDSSGFES(0.005)MS(0.995)PIKETVSSR;TICTFDSSGFES(0.016)MS(0.984)PIKETVSSR 266.17 2.54E-44 201135000 119688 125293 132824 155172 96598 145101 153208 157731 113141 TRUE FALSE 114030.5854 138060.4991 138914.1118 139573.8158 113444.6606 140076.116 129833.3057 143919.2375 130686.3284 0.872551757 1.056426489 1.062958256 1.068006251 0.868068313 1.071849808 0.993472747 1.101257026 1 16.9957487 4.605696076 2.984101596 1.024993579 0.866931754 0.353489664 0.065588386 0.319412714 4.743339789 0.014916853 0.102226078 40336.30168 -4.605696076 -0.158061824 TIDDLEDKLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TIDDLEDKLK 10 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 192.5 6.17E-07 6035710000 14142586 11752524 12423261 15291350 9070256 16422269 18595490 18298455 10529495 FALSE TRUE 13474093.99 12950119.56 12992879.81 13754234.45 10652105.77 15853561.71 15758406.47 16696145.27 12162355.31 1.107852356 1.064770699 1.068286485 1.130885762 0.875825899 1.303494373 1.295670622 1.372772366 1 23.53591931 2.206138193 24.99309299 1.271909845 1.061456828 0.383532405 0.11886494 165.8517705 127847.2447 0.039355687 0.029068232 160.7452665 -2.206138193 -0.210453017 TIDDLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIDDLEEK 8 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 133.58 0.0021246 120020000 214930 183490 207770 253350 138220 200660 230730 238020 161840 FALSE TRUE 204770.6849 202187.8396 217296.46 227882.7767 162325.5242 193711.0939 195527.9009 217177.707 186937.3206 1.09539756 1.081580922 1.162402774 1.219033074 0.868341986 1.036235532 1.045954335 1.161767518 1 17.5121951 2.767548338 24.99996225 1.028118658 1.126287963 0.340328069 0.079877794 970.7435347 837199.5138 0.024007537 0.025460091 585.5289041 -2.767548338 0.098169305 TIDLGAAAHY(ph)TGDKASPDQNASTHTPQSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHY(0.171)T(0.171)GDKAS(0.162)PDQNAS(0.162)T(0.162)HT(0.162)PQS(0.005)S(0.006)VK 42.355 0.052763 138460000 27160 27563 31248 28663 29569 21753 30489 26169 15119 TRUE FALSE 25876.20063 30371.70104 32680.75171 25781.74078 34725.82424 20999.68816 25837.34308 23877.50363 17463.5773 1.481723943 1.739145452 1.871366395 1.47631498 1.988471413 1.202484909 1.479498881 1.367274483 1 14.0920615 1.219938371 0.700345006 1.019546863 1.683433226 0.515347389 0.20624333 0.499632109 0.574648869 0.181525124 0.075732939 16.59351418 -1.219938371 0.663886364 TIDLGAAAHYTGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIDLGAAAHYTGDK 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 113.25 0.00054627 121210000 157990 155800 148240 179580 122650 168960 177040 190080 129300 FALSE TRUE 150522.1258 171676.1971 155036.9506 161528.2772 144040.1212 163108.8728 150029.2964 173435.5875 149351.1836 1.007840193 1.14947999 1.038069782 1.081533292 0.9644391 1.092116372 1.004540391 1.161260214 1 17.18834915 TIDLGAAAHYTGDKAS(ph)PDQNAS(ph)THTPQSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 2 TIDLGAAAHY(0.002)T(0.005)GDKAS(0.993)PDQNAS(0.545)T(0.38)HT(0.073)PQS(0.002)SVK 88.582 0.00080056 98397000 54955 42573 45152 61292 32093 58264 65893 66283 39883 TRUE FALSE 52357.38606 46911.2371 47222.26386 55130.81171 37690.00904 56246.30307 55839.81264 60478.90913 46067.85195 1.136527618 1.018307456 1.025058948 1.196730678 0.81814123 1.220944774 1.212121041 1.312822426 1 15.49147271 TIDLGAAAHYTGDKAS(ph)PDQNASTHTPQSSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYT(0.002)GDKAS(0.998)PDQNASTHTPQSSVK;T(0.018)IDLGAAAHY(0.023)T(0.06)GDKAS(0.846)PDQNAS(0.025)T(0.025)HT(0.003)PQS(0.001)S(0.001)VK;TIDLGAAAHYT(0.006)GDKAS(0.994)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK 294.93 1.56E-81 3473240000 2602600 1867800 2369610 2787210 1694720 2581690 3240020 2998360 1446390 TRUE FALSE 2479580.256 2058130.944 2478258.962 2507034.355 1990278.631 2492285.428 2745695.442 2735807.703 1670688.774 1.484166467 1.231905652 1.4833756 1.50059927 1.191292276 1.491771218 1.643451183 1.637532822 1 20.67201157 2.027480493 24.97471233 1.515769885 1.375212724 0 0.208380758 477.2029284 433687.5884 0.070070814 0.051749572 106.5321011 -2.027480493 -0.14055716 TIDQIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 107.59 0.0074425 1210550000 2080630 1921390 1749130 2250870 1575670 2092730 2413890 2273180 1714810 FALSE TRUE 1982282.743 2117181.825 1829329.341 2024608.271 1850466.349 2020258.235 2045606.746 2074128.308 1980733.977 1.000781915 1.068887519 0.923561348 1.022150523 0.934232649 1.01995435 1.032751884 1.047151376 1 20.9176037 2.014685218 24.99687417 1.02929344 0.998206968 0.127359644 0.042725635 551.255101 938331.192 0.015867645 0.011714933 103.4392154 -2.014685218 -0.031086472 TIEAEAAHGTVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIEAEAAHGTVTR 13 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 325.68 6.87E-52 1502070000 1760380 1391100 1428990 1434060 1701400 1194950 1603170 1523640 1704980 FALSE TRUE 1677170.326 1532854.672 1494510.605 1289905.564 1998123.621 1153568.582 1358576.972 1390222.004 1969379.591 0.851623696 0.778343941 0.758873816 0.65498067 1.014595475 0.585752278 0.689850234 0.705918763 1 20.90930978 TIEDAIAVLSVAEEAADRHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;;;;;;;; 216.82 7.89E-26 526816000 431912 382472 392742 448234 420838 399416 458560 429759 375002 FALSE TRUE 411496.3757 421446.3316 410749.6092 403176.6667 494232.014 385584.1238 388598.25 392127.0237 433155.3949 0.949997115 0.972967985 0.9482731 0.9307899 1.141003944 0.890175046 0.89713358 0.905280249 1 18.72452516 -0.850199368 4.797686427 1.00000011 0.953442345 0.038698233 0.071184692 8809164.682 1836127.555 13.09317765 0.016142025 0.141188925 0.850199368 -0.046557766 TIEDAIAVLSVAEEAADRHPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TIEDAIAVLSVAEEAADRHPERR 23 2 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;; 122.53 3.92E-05 65665300 43151.8 15774.6 41743.2 27517.7 56528 32026.3 65418 43402.7 69107 FALSE TRUE 41112.09993 17382.04967 43657.16701 24751.56852 66386.4653 30917.2212 55437.28262 39602.1295 79823.76061 0.515035869 0.217755334 0.546919447 0.310077705 0.831662963 0.387318525 0.694496002 0.496119566 1 16.28453063 -4.999991867 0.115946154 2.743378658 0.207988472 0.488954976 0.168664465 115.1411879 0.874626145 46.77421042 1.579414751 1.00E-05 4.999991867 -2.535390186 TIEELEKEMLNGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIEELEKEMLNGQK 14 1 Q8N335 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein 0 77.527 0.022273 26502000 71084 53022 67669 67921 58696 73711 83194 79092 75766 FALSE TRUE 67724.00019 58425.00208 70771.69058 61093.45204 68932.56382 71158.36959 70501.22734 72166.28519 87515.40432 0.773852337 0.667596779 0.808676954 0.698087982 0.787662062 0.813095365 0.805586489 0.824612372 1 16.41724936 0.236892181 0.322110476 1.052647033 0.715750444 0.777258328 0.041499906 1.65076027 0.295709507 0.164425922 0.041586297 1.725409484 -0.236892181 -0.33689659 TIEELSNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TIEELSNAR 9 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;;; 76.221 0.036044 2988302000 1769907 1733395 1706100 1740060 4649140 1030449 1886854 1103486 4306370 FALSE TRUE 1686247.004 1910029.921 1784326.373 1565145.863 5459948.544 994764.2928 1598979.768 1006858.916 4974179.866 0.339000006 0.383988913 0.358717702 0.314654055 1.097658044 0.19998559 0.321455961 0.20241707 1 22.24602725 -0.935470082 4.225692182 1.000018154 0.398840191 0.351837307 0.254941918 128162685.1 269879651.6 36406.94251 0.05774867 0.116019214 0.935470082 -0.601177963 TIEEVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIEEVVGR 8 0 P05091;P05091-2 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 93.374 0.025856 346110000 567030 452390 548630 519480 478010 516690 579050 563400 494810 FALSE TRUE 540227.6156 498489.0553 573785.2282 467260.8835 561374.7927 498796.8957 490705.2875 514065.7092 571542.6077 0.945209698 0.872181791 1.003923803 0.817543394 0.982209874 0.872720404 0.858562915 0.899435497 1 19.12450153 TIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIEGQSPEPVFGDADVDVSAVQAK 24 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.166)IEGQS(0.834)PEPVFGDADVDVSAVQAK 132.76 3.02E-05 26701000 20907 25133 25914 25186 22219 29217 30028 31112 25194 TRUE FALSE 19918.76754 27694.08127 27102.18253 22654.25543 26093.98657 28205.20796 25446.6771 28387.66834 29100.95685 0.684471224 0.95165535 0.931315856 0.778471153 0.896671086 0.969219264 0.874427505 0.975489174 1 14.82877897 4.598503331 2.807906367 0.912331894 0.673800979 0.570660601 0.064000326 0.22716639 2.952882039 0.014884574 0.106502205 39673.7572 -4.598503331 -0.238530915 TIEKFEK ddPTM_SK-BR-3_Trastuzumab_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 ;;; 103.56 0.0076133 3730160000 3502250 2249420 2959780 2700290 2232150 3311980 4000370 3497060 2890710 FALSE TRUE 3336705.583 2478638.455 3095488.841 2428851.719 2621436.253 3197285.302 3390040.085 3190838.887 3338986.543 0.999316871 0.742332568 0.927074368 0.727421835 0.785099377 0.957561602 1.015290131 0.955630952 1 21.67097885 2.112727474 5.556968241 0.990494532 0.837903917 0.443042679 0.081802054 0.191106303 8.598223357 0.03018407 0.0220829 129.6365528 -2.112727474 -0.152590614 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK 31 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;; 124.28 2.46E-06 428712000 338084 292560 339513 343974 379382 319869 434210 352973 130497 FALSE TRUE 322103.4393 322372.1966 355080.0069 309397.08 445546.1007 308791.8563 367963.2897 322064.8129 150733.8083 2.136902418 2.13868541 2.355675949 2.05260574 2.95584717 2.048590557 2.441146375 2.136646162 1 17.20164351 0.948673053 17.11787945 0.999999996 2.286905177 0.70158795 0.265028965 92.91822007 30989.63956 0.231775917 0.057944713 8.885319589 -0.948673053 1.286905181 TIGDMFQNQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIGDMFQNQDR 11 0 Q96AY3;H0Y827;Q96AY3-2 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 ; 167.09 4.57E-05 159568000 111130 102000 91478 117896 105336 108504 120004 105033 118716 FALSE TRUE 105877.1051 112393.916 95672.35678 106044.8701 123706.565 104746.4793 101695.1858 95835.75371 137125.871 0.772116191 0.819640489 0.69769735 0.773339628 0.902138774 0.763871023 0.741619251 0.698888933 1 17.06514126 -1.17264371 3.869958286 1.000124192 0.774558866 0.598615114 0.058830565 4135859058 9100024522 7675146.326 0.013868232 0.067197991 1.17264371 -0.225565326 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(0.999)FNT(0.001)FFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(0.996)FNT(0.004)FFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(0.999)FNT(0.001)FFSETGAGK 378.84 1.30E-112 2531957000 2173724 2068002 2151011 2498885 1593677 2348518 2557397 2490905 1795602 TRUE FALSE 2070976.374 2278733.755 2249636.982 2247692.332 1871613.764 2267188.233 2167219.118 2272788.153 2074054.787 0.998515751 1.09868542 1.084656488 1.08371888 0.902393599 1.093118777 1.044918934 1.095818764 1 20.98402257 -1.280031488 3.691181322 0.999888689 1.050592002 0.063367473 0.060673652 5.14E-05 1.00E-05 0.054333165 0.012778345 0.052476941 1.280031488 0.050703313 TIGGGDDSFNTFFSETGAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 423.25 3.49E-173 722390000 1362060 1206990 1232660 1459780 1002114 1339430 1468090 1471920 1192610 FALSE TRUE 1297678.123 1329983.653 1289178.68 1313040.141 1176882.364 1293045.203 1244105.907 1343030.882 1377553.868 0.942016246 0.965467619 0.935846293 0.95316791 0.854327654 0.938653096 0.903126866 0.974938921 1 20.3936773 1.047669197 5.648790447 0.999788989 0.930303476 0.406477275 0.030772171 0.171881474 11.72942002 0.029597085 0.007457641 11.16012856 -1.047669197 -0.069485513 TIHLSSIRPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIHLSSIRPPR 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 166.14 1.25E-05 586010000 234317 262580 245300 278180 510790 208603 354300 267240 506580 FALSE TRUE 223241.2998 289337.2005 256547.2476 250216.8179 599871.6143 201379.0258 300245.0278 243839.0489 585137.8391 0.381519165 0.494476995 0.438438998 0.427620299 1.025180007 0.34415656 0.513118462 0.416720698 1 19.15841699 -1.572628491 2.853530384 1.030045085 0.501678698 0.397197514 0.191540441 40686779.84 41425454.38 9260752.17 0.042440341 0.02675294 1.572628491 -0.528366388 TIHT(ph)FPCLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIHTFPCLK 9 0 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 TIHT(1)FPCLK 126.19 0.0017674 72911000 193450 131340 187590 200650 172400 194560 243810 207920 145630 TRUE FALSE 184306.0019 144723.6953 196191.1871 180480.2808 202466.5054 187822.3384 206612.3066 189713.4225 168213.5566 1.095666756 0.860356907 1.166322091 1.072923517 1.203627754 1.116570758 1.228273813 1.12781292 1 17.35993445 3.715578512 24.85281498 1.144949415 0.978011821 0.346520091 0.085521498 581.1388184 628442.6843 0.020890277 0.032388017 5194.915786 -3.715578512 -0.166937594 TIISYIDEQFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TIISYIDEQFER 12 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310;C9IZU3;C9JQJ4 Q15019-2 2-Sep Septin-2 0 ;;; 270.63 2.50E-27 228238000 224226 236822 214139 242766 217317 216255 233806 241321 214327 FALSE TRUE 213627.2814 260954.431 223957.485 218362.7005 255217.016 208766.0351 198134.6006 220189.6539 247563.7365 0.862918311 1.054089887 0.904645762 0.882046391 1.03091438 0.843281969 0.800337737 0.889426121 1 17.91744048 2.20584547 24.99319879 0.858687285 0.949029269 0.104694101 0.079001251 269.2357754 205684.9619 0.0276681 0.020435617 160.6369575 -2.20584547 0.090341983 TILHYMGTSTFSEYTVVADISVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TILHYMGTSTFSEYTVVADISVAK 24 0 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 119.87 0.00026599 102803000 116020 119299 107568 127156 93629 113929 112308 117124 76908 FALSE TRUE 110535.9645 131455.7037 112500.0992 114374.0373 109957.868 109983.6102 95173.35192 106868.0016 88834.49985 1.244290954 1.479782111 1.266400997 1.287495708 1.237783385 1.238073162 1.071355747 1.203001107 1 16.43883245 1.943138819 0.545299401 1.021735887 1.364520334 0.637454481 0.076677651 0.464260137 0.294474023 0.069695441 0.047583197 87.72811923 -1.943138819 0.342784447 TILMMGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TILMMGR 7 0 P13639 P13639 EEF2 Elongation factor 2 0 124.89 0.0095448 154160000 216440 174550 128920 139010 260530 123570 237190 157850 255740 FALSE TRUE 206209.3101 192336.8434 134831.1095 125036.4507 305966.3495 119290.7399 201002.3092 144027.8172 295398.8531 0.698070788 0.651108972 0.456437485 0.423280082 1.035773654 0.403829394 0.68044377 0.487570672 1 18.1723047 -1.449424229 3.324020445 1.005662589 0.613371047 0.307231569 0.186194961 40509563.09 52896173.46 2149398.269 0.039755781 0.03552841 1.449424229 -0.392291543 TINLYPLTNYTFGTKEPLYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TINLYPLTNYTFGTKEPLYEK 21 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 112.85 0.00019606 39728000 168810 117660 162430 162620 157590 160190 229400 176310 200190 FALSE TRUE 160830.6858 129649.6878 169877.5762 146273.1286 185073.6461 154642.5801 194400.8168 160871.3617 231234.4428 0.695530838 0.560685018 0.734655158 0.632575004 0.800372314 0.668769662 0.840708739 0.695706746 1 17.81899678 -2.261127366 0.144301034 1.480500321 0.55339173 0.645447496 0.072660336 27.31352516 0.52179843 4.715574547 0.431723516 0.005481162 2.261127366 -0.927108591 TIPWLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TIPWLEDR 8 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;; 155.88 0.0009351 154958000 319624 257701 215035 360554 314148 222179 304902 253599 318719 FALSE TRUE 304516.007 283961.0249 224894.5674 324310.4269 368935.3117 214484.8855 258383.6 231392.5271 368144.3147 0.827164769 0.771330735 0.610886977 0.880932868 1.002148606 0.582610886 0.701854109 0.628537554 1 18.4899119 TIPWLEDRVPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 203.61 1.12E-07 1552480000 1819350 1148550 1038290 1605720 1480930 1228870 2136180 1662610 1767790 FALSE TRUE 1733352.931 1265588.551 1085896.624 1444309.975 1739203.723 1186313.924 1810266.507 1517023.054 2041929.845 0.848879767 0.619800212 0.531799183 0.707325954 0.851745092 0.580976828 0.886546867 0.742935933 1 20.96150187 0.793315366 0.627432147 1.000789834 0.689001974 0.393057407 0.115037337 1.086674949 0.914088104 0.117890138 0.046063123 6.21320047 -0.793315366 -0.311787861 TIQEVLEEQS(ph)EDEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 368.13 1.83E-97 298041000 340210 397410 325684 413140 292245 375860 375400 386214 302349 TRUE FALSE 324128.9475 437906.5308 340616.9335 371610.3823 343212.4355 362843.874 318125.8353 352395.0547 349235.7387 0.92810933 1.253899536 0.975320953 1.064067451 0.982752901 1.038965471 0.910920046 1.009046371 1 18.41384168 2.86103183 1.304963748 0.97502575 1.080977144 0.102047567 0.090022167 0.692635019 2.43365328 0.036657805 0.038667463 726.1591762 -2.86103183 0.105951394 TIQEVLEEQS(ph)EDEDREAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK 297.5 1.33E-49 2114735000 2150880 2184050 2061900 2463570 1498054 2361710 2425460 2563810 1658502 TRUE FALSE 2049212.165 2406607.178 2156440.154 2215927.263 1759314.143 2279923.391 2055411.53 2339309.205 1915694.02 1.06969701 1.256258647 1.125670453 1.156722963 0.918369074 1.1901292 1.072933104 1.221128834 1 20.86943572 -5 0.218549541 0.385579853 1.144111757 0.124388592 0.095815206 304.3361856 3.042391517 82.91974174 0.172862438 1.00E-05 5 0.758531904 TIQEVLEEQS(ph)EDEDREAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;TIQEVLEEQS(1)EDEDREAKR 201.97 3.00E-16 1860660000 1336840 1164940 1258940 1363730 903286 1442620 1629200 1700780 1235080 TRUE FALSE 1273650.223 1283648.71 1316663.644 1226645.269 1060818.792 1392661.708 1380635.618 1551850.687 1426609.898 0.892781008 0.899789572 0.922931802 0.859832299 0.743594162 0.976203592 0.967773755 1.087789092 1 20.44415946 1.787847036 2.292024127 1.031349884 0.875071225 0.579999972 0.059293228 0.205800537 2.119256945 0.035966069 0.016258672 61.35458681 -1.787847036 -0.156278659 TIQFVDWCPTGFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TIQFVDWCPTGFK 13 0 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ; 208.95 9.72E-08 112282000 1169850 1106650 1051020 1167450 944690 1149490 1271110 1243000 942770 FALSE TRUE 1114553.509 1219418.893 1099210.307 1050095.708 1109443.637 1109682.873 1077178.824 1134156.33 1088969.957 1.02349335 1.119791125 1.009403703 0.964301817 1.01880096 1.01902065 0.989172215 1.041494601 1 20.05453272 3.615244746 8.255734927 1.003912117 1.071478252 0.446144662 0.030378861 0.217561423 13.66249957 0.007586059 0.011766653 4123.298219 -3.615244746 0.067566135 TIRYPDPLIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIRYPDPLIK 10 1 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 71.153 0.047276 594280000 3289700 2440000 3065800 3169900 2858300 2906700 3779700 3436900 3271600 FALSE TRUE 3134202.401 2688638.774 3206369.962 2851255.63 3356786.615 2806040.25 3203037.346 3135946.816 3778943.019 0.829385991 0.711479046 0.848483279 0.754511411 0.888287174 0.742546325 0.847601387 0.829847606 1 21.84955133 -2.722728087 0.238544362 1.337866316 0.772645247 0.574139825 0.053419351 31.07059888 0.816183888 5.42961057 0.079081139 0.001893529 2.722728087 -0.565221069 TIS(ph)AQDTLAYATALLNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.023)IS(0.977)AQDTLAYATALLNEK;T(0.002)IS(0.998)AQDTLAYATALLNEK;T(0.108)IS(0.892)AQDTLAYATALLNEK;T(0.116)IS(0.884)AQDTLAYATALLNEK 384.06 2.07E-126 731408000 640311 580469 538264 716396 413089 702067 686028 710128 445058 TRUE FALSE 610044.768 639619.451 562943.9368 644382.513 485131.5908 677754.2438 581361.8288 647945.4277 514075.3216 1.186683629 1.244213492 1.095061197 1.253478792 0.94369749 1.318394825 1.130888421 1.260409517 1 18.97162023 -2.382629342 1.942554384 4.24E-05 1.180598367 0.220626727 0.105758064 1400654.192 133365.0749 6152531.514 0.022293795 0.004143532 2.382629342 1.180555952 TIS(ph)DGTISASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TISDGTISASK 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 TIS(1)DGTISASK;TIS(1)DGTISASK;T(0.002)IS(0.998)DGTISASK;TIS(0.999)DGT(0.001)ISASK;T(0.001)IS(0.999)DGTISASK;TIS(1)DGTISASK;TIS(1)DGTISASK;TIS(1)DGTISASK;T(0.003)IS(0.983)DGT(0.014)ISASK;T(0.014)IS(0.984)DGT(0.002)ISASK 300.89 8.20E-36 11761700000 35303790 34451430 31025960 38627030 21792420 33853700 35858800 36542120 22401340 TRUE FALSE 33635049.81 37962069.89 32448530.95 34744167.56 25593011.15 32681337.88 30387881.47 33342298.25 25875225.4 1.299893983 1.467120356 1.254038582 1.342758064 0.989093264 1.263035872 1.174400648 1.288580012 1 24.62506809 2.910382114 13.41256661 1.165294111 1.353828355 0.435555204 0.110003422 1.184156182 175.1709194 0.030783822 0.032654364 813.545999 -2.910382114 0.188534244 TIS(ph)DGTISASKQESGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TISDGTISASKQESGK 16 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 TIS(0.998)DGT(0.002)ISASKQESGK;T(0.003)IS(0.994)DGT(0.003)ISASKQESGK;T(0.003)IS(0.997)DGT(0.001)ISASKQESGK;TIS(0.994)DGT(0.006)ISASKQESGK 239.56 4.77E-20 2683290000 1610210 696710 1858260 1133520 1148570 1654960 2477800 1966320 1706810 TRUE FALSE 1534098.564 767705.5411 1943463.059 1019576.416 1348880.244 1597648.32 2099766.102 1794138.597 1971493.378 0.778140359 0.389403053 0.98578219 0.517159442 0.684192125 0.810374683 1.065063736 0.910040387 1 20.91085743 2.028640216 2.898119345 0.994153588 0.648969357 0.452433001 0.159676441 0.213774441 3.509143686 0.071426716 0.042801128 106.8169605 -2.028640216 -0.345184232 TIS(ph)EPDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TISEPDEQR 9 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.007)IS(0.993)EPDEQR;T(0.004)IS(0.996)EPDEQR;TIS(1)EPDEQR;TIS(1)EPDEQR 252.82 7.29E-15 1516270000 2841760 2874890 2356490 3133940 2129080 2628530 2584160 2862000 2082790 TRUE FALSE 2707435.637 3167844.559 2464537.397 2818910.397 2500390.878 2537503.347 2189898.931 2611388.108 2405778.436 1.125388605 1.316764883 1.024424095 1.171724858 1.039327164 1.054753551 0.910266256 1.085464924 1 21.19807235 2.917515164 0.95946939 0.990179795 1.208169493 0.414334721 0.083500033 0.412255996 0.824838356 0.040607338 0.045623556 827.0183845 -2.917515164 0.217989698 TIS(ph)EPDEQRSELPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.044)IS(0.956)EPDEQRSELPR;T(0.011)IS(0.989)EPDEQRSELPR;T(0.009)IS(0.991)EPDEQRSELPR 178 1.23E-06 1120950000 977250 675050 978470 921210 1077070 945730 1282810 1054770 1295380 TRUE FALSE 931057.3292 743838.3625 1023333.817 828608.2206 1264910.667 912979.133 1087093.774 962408.7471 1496260.915 0.622255998 0.497131453 0.683927387 0.553785916 0.845381079 0.61017375 0.726540247 0.643209174 1 20.51293034 -5 0.13562003 2.23935341 0.4989086 0.615730977 0.090171408 82.87826409 0.697690419 27.74451337 0.542371614 1.00E-05 5 -1.74044481 TIS(ph)NPEVVMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.015)IS(0.985)NPEVVMK;TIS(1)NPEVVMK;T(0.039)IS(0.961)NPEVVMK;T(0.003)IS(0.997)NPEVVMK;T(0.001)IS(0.999)NPEVVMK;TIS(1)NPEVVMK;T(0.001)IS(0.999)NPEVVMK 159.52 8.03E-06 1652119000 3768090 2692350 2770130 4081940 2521560 3770950 4175810 3389960 2464020 TRUE FALSE 3589979.853 2966703.526 2897143.201 3671615.636 2961319.266 3640361.056 3538713.49 3093117.131 2846127.637 1.261355888 1.042364892 1.017924552 1.290038995 1.040473107 1.279057555 1.243343216 1.086780892 1 21.44056893 2.240658519 24.99983578 1.183959399 1.132465576 0 0.118788949 205.9548692 2454312.296 0.039839327 0.031824226 174.0437847 -2.240658519 -0.051493823 TIS(ph)PAESTALLQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TISPAESTALLQGR 14 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 TIS(1)PAESTALLQGR;T(0.005)IS(0.995)PAESTALLQGR 183.96 1.41E-06 89556000 95220 99028 99247 114481 96120 90923 109557 95421 111530 TRUE FALSE 90719.13931 109119.0658 103797.5731 102973.1524 112883.2976 87774.31371 92842.0675 87065.43138 128825.5028 0.70420171 0.847030001 0.805722243 0.799322728 0.876249618 0.681342683 0.720680808 0.675840028 1 16.9750587 2.230423882 24.99915517 0.741140301 0.80236897 0 0.101312019 464.0895811 1425848.868 0.033535962 0.025191201 169.9901987 -2.230423882 0.06122867 TIS(ph)QSSSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TISQSSSLK 9 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 TIS(0.999)QS(0.001)SSLK;TIS(0.999)QS(0.001)SSLK;T(0.001)IS(0.86)QS(0.025)S(0.091)S(0.022)LK;T(0.002)IS(0.991)QS(0.004)S(0.002)SLK 178.65 5.32E-05 1076490000 1755610 1304200 1494460 1802350 1460370 1741480 2124310 1920840 1693890 TRUE FALSE 1672625.795 1437099.463 1562982.469 1621174.354 1715058.066 1681172.111 1800207.494 1752641.067 1956569.81 0.854876624 0.734499457 0.798838079 0.828579867 0.876563697 0.859244634 0.920083446 0.895772314 1 20.89989516 1.703571191 0.498558505 0.99370112 0.785335012 0.753309472 0.035190428 0.396450043 0.236594355 0.035425101 0.023698147 50.53254733 -1.703571191 -0.208366108 TISIDENMEPSPTGDFYPSPS(ph)SPAAGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TISIDENMEPSPTGDFYPSPSSPAAGSR 28 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 TISIDENMEPSPTGDFYPS(0.001)PS(0.573)S(0.424)PAAGS(0.002)R 130.23 8.34E-05 80746000 38540 33562 42728 38046 30150 32540 40523 40542 41699 TRUE FALSE 36718.29058 36982.00596 44687.12106 34221.5438 35408.15045 31413.13164 34340.47209 36991.92755 48165.46795 0.762336424 0.76781162 0.927783388 0.71049956 0.735135606 0.652191974 0.712968721 0.768017609 1 15.55571156 0.945727765 20.92772201 1.000000001 0.751071632 0.545477622 0.070524414 1807.366905 696934.4342 0.06883898 0.017209745 8.825265204 -0.945727765 -0.248928369 TISINS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 TIS(0.008)INS(0.992)PK;TIS(0.002)INS(0.998)PK;TISINS(1)PK;TIS(0.015)INS(0.985)PK;TIS(0.003)INS(0.997)PK 136.96 0.00080639 1542683000 4354420 3805090 3667580 4479740 2413590 4497350 4546690 4617360 2879430 TRUE FALSE 4148595.196 4192832.997 3835742.171 4029428.024 2834519.332 4341605.642 3853008.935 4213039.48 3325957.298 1.247338683 1.260639455 1.153274629 1.211509248 0.852241649 1.30537023 1.158466147 1.266714844 1 21.66533822 3.659263938 2.704327463 1.141807397 1.255822823 0.123539884 0.129897716 0.56332705 8.043528564 0.033898306 0.059276483 4563.141515 -3.659263938 0.114015426 TISLCCWDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TISLCCWDSR 10 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 108.43 0.0069983 0 82082 69501 72917 71058 68164 72766 101650 81586 69207 FALSE TRUE 78202.14653 76583.23092 76260.31657 63915.11484 80051.78002 70246.09517 86141.42557 74441.89733 79939.2681 0.978269484 0.958017664 0.953978169 0.79954591 1.001407467 0.878743287 1.077585868 0.931230659 1 16.28661674 1.745102498 25 1.008220428 0.934438442 0.215339644 0.066205326 2.014085237 7721.497576 0.028376478 0.015735993 55.60354723 -1.745102498 -0.073781986 TITEYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TITEYAR 7 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;; 139.27 0.015154 398770000 525910 438276 432674 524480 526870 466946 599920 544760 615320 FALSE TRUE 501051.2766 482936.8227 452512.5309 471758.274 618755.9612 450775.5429 508391.1857 497057.9264 710740.683 0.704970587 0.67948386 0.636677401 0.663755833 0.870579068 0.634233489 0.715297714 0.699352012 1 19.43896376 -5 0.375141735 5.109190211 0.691498561 0.670261782 0.066066438 322.6082493 2.449122586 1076.62852 0.041796572 1.00E-05 5 -4.41769165 TITGFQTHTTPVLLAHGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TITGFQTHTTPVLLAHGER 19 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 160.3 1.84E-11 259560000 417230 364970 332890 403330 310650 361390 412050 417280 283700 FALSE TRUE 397508.3648 402160.8579 348153.3358 362786.5021 364827.2616 348874.9737 349184.2047 380740.7511 327694.7471 1.213044665 1.227242309 1.062431848 1.107086718 1.113314342 1.064634013 1.065577669 1.161876272 1 18.32199302 8 0.22004559 1.035090774 2.169819109 0.518332828 0.049291407 33.26884147 0.425670478 0.072652993 13.41560322 100000000 -8 1.134728335 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_SK-BR-3_Trastuzumab_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(0.994)PIS(0.005)VPGGSALISNLGK;TITLVKS(0.997)PIS(0.002)VPGGSALISNLGK 226.28 6.20E-33 498680000 1375350 1081180 1299470 1412240 912270 1417750 1709230 1664910 1166280 TRUE FALSE 1310339.931 1191353.471 1359051.985 1270278.952 1071369.599 1368652.962 1448455.571 1519121.654 1347140.746 0.972682279 0.884357091 1.008841867 0.942944496 0.795291511 1.015968796 1.075207305 1.127663653 1 20.36146916 2.009786296 24.99647159 1.068382044 0.923909745 0.535140254 0.063507311 147.9859226 377988.825 0.022519243 0.016612529 102.2789582 -2.009786296 -0.1444723 SESSEKPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 SESSEKPAR 9 1 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 64.04 0.065773 34357000 63592 46876 72594 83930 83041 86015 121870 96850 108900 FALSE TRUE 60586.13219 51652.71769 75922.50671 75493.19694 97523.32411 83036.27898 103276.4932 88369.30057 125787.6558 0.481654037 0.410634234 0.603576768 0.600163796 0.775301229 0.660130586 0.82103838 0.702527605 1 16.94063082 3.115290034 0.194970161 1.067614624 0.138285713 0.823930713 0.070757632 2.43761659 0.182872374 0.20596157 0.626056751 1304.037361 -3.115290034 -0.929328912 down TIVEELLADSEFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TIVEELLADSEFRR 14 1 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ;;; 216.46 9.81E-12 137764000 171819 143261 169518 180027 185901 142619 200066 182447 202403 FALSE TRUE 163697.4564 157859.4588 177290.568 161930.3439 218322.0755 137680.0683 169542.2572 166470.9735 233790.6235 0.700188288 0.675217237 0.758330532 0.692629762 0.933835892 0.588903294 0.725188439 0.71205154 1 17.83485754 -1.870731664 2.200508455 1.146206593 0.718505136 0.500592395 0.086740505 3616489.671 1784244.143 2756934.901 0.020197012 0.013466922 1.870731664 -0.427701457 TIVMGAS(ph)FR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TIVMGASFR 9 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 1 TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR 136.96 0.00018691 573945000 974166 855070 815035 920490 839344 881736 986536 960270 843128 TRUE FALSE 928119.1038 942202.6051 852405.1609 827960.5964 985725.3279 851201.2612 836021.8142 876183.6681 973875.9841 0.953015701 0.967476989 0.875270748 0.850170463 1.0121672 0.874034554 0.858447921 0.899687108 1 19.89337854 3.750071768 24.57572638 0.901109357 0.960246351 0.107673395 0.055812424 950.9528299 2030229.136 0.013518697 0.02410115 5624.342608 -3.750071768 0.059136995 TIYENR ddPTM_SK-BR-3_Trastuzumab_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 ;; 132.96 0.034132 928520000 1504480 1414870 1239120 1595510 1471020 1463280 1606810 1451350 1467620 FALSE TRUE 1433366.212 1559046.862 1295934.878 1435126.304 1727565.422 1412606.247 1361661.623 1324262.1 1695211.014 0.84553852 0.919677166 0.764468179 0.846576793 1.01908577 0.833292277 0.803240194 0.781178325 1 20.69303344 -0.897343591 6.379179743 1.000000013 0.854929163 0.288423746 0.073075244 1.34E-08 2.43E-09 0.069295415 0.016333084 0.126664936 0.897343591 -0.145070851 TIYFFGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TIYFFGDK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 112.84 0.0068939 96287000 413360 324590 310060 373460 301020 355030 451570 395160 353010 FALSE TRUE 393821.292 357666.09 324276.5577 335919.0913 353517.7927 342735.2221 382674.7028 360557.6955 407752.9879 0.965833001 0.877163628 0.795276963 0.823829871 0.866990073 0.840546194 0.938496379 0.884255189 1 18.63733592 0.733475376 0.936232322 0.998343733 0.870533577 0.40599014 0.049210856 1.109830978 1.787531088 0.050835724 0.016834536 5.413465532 -0.733475376 -0.127810156 TKADVTPPPDGS(ph)TTHNLEVSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.004)KADVT(0.032)PPPDGS(0.287)T(0.287)T(0.287)HNLEVS(0.103)PK 63.291 0.020023 265560000 145220 103900 124660 138140 68851 157960 161270 149440 77229 TRUE FALSE 138355.7384 114487.5281 130375.7843 124253.9048 80858.5926 152489.8056 136665.2996 136354.2414 89205.27889 1.550981513 1.283416515 1.461525438 1.392898563 0.906432821 1.709425804 1.532031526 1.528544533 1 16.44484147 TKADVTPPPDGSTTHNLEVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 TKADVTPPPDGSTTHNLEVS(1)PK 174.06 1.84E-12 382400000 193140 154950 178910 201050 109820 194770 223710 215710 107790 TRUE FALSE 184010.655 170739.5812 187113.2005 180840.072 128972.5732 188025.0661 189578.9308 196821.2888 124505.5227 1.477931669 1.371341427 1.502850608 1.452466269 1.035878333 1.510174505 1.522654792 1.580823763 1 16.92585021 TKDEYLINSQTTEHIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKDEYLINSQTTEHIVK 17 1 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ; 199.76 7.81E-12 266830000 597000 506180 525220 546550 409730 485770 556210 571860 369510 FALSE TRUE 568780.9931 557760.3175 549301.8565 491609.7556 481186.7823 468947.6631 471349.949 521784.9068 426811.7236 1.33262739 1.30680646 1.286988679 1.151818773 1.127398231 1.098722545 1.104350989 1.222517747 1 18.70324028 3.23038805 2.276764307 1.114630699 1.320274668 0.74528574 0.053439483 0.129885284 1.380360539 0.014888328 0.020083997 1699.761742 -3.23038805 0.205643969 TKDGVVEITGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 164.68 2.05E-05 12439470000 33928330 25096930 23866870 32871280 17546900 28840250 30477360 30288470 16422740 FALSE TRUE 32324605.08 27654335.7 24961189.6 29566996.48 20607073.8 27841504.91 25827478.98 27636251 18969494.64 1.704030903 1.457831968 1.315859493 1.558660209 1.086326979 1.46769882 1.361526992 1.45687861 1 24.17717791 8 0.037327203 2.59E-11 3.636348756 0.490045502 0.148970069 730.3340037 2.080485602 57.79966277 173.8502544 100000000 -8 3.636348756 TKDGVVEITGKHEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TKDGVVEITGKHEER 15 2 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 203.9 3.11E-09 1316304000 2504660 862554 2307090 1718340 1835870 2213710 3382730 2526370 2090300 FALSE TRUE 2386269.686 950449.2332 2412872.359 1545609.199 2156045.147 2137048.668 2866632.41 2305147.65 2414453.048 0.988327227 0.393649913 0.999345322 0.640148791 0.892974559 0.885106741 1.187280247 0.954728712 1 21.20326498 2.25015802 1.82947902 1.06080776 0.735096483 0.290977043 0.185033113 0.35623981 2.395874861 0.087082806 0.055995858 177.8926563 -2.25015802 -0.325711276 TKDIEDVFYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TKDIEDVFYK 10 1 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 156.01 1.07E-05 2695640000 12836900 9759600 10962500 12419700 7387610 11590900 13311400 12864600 7979220 FALSE TRUE 12230125.18 10754114.34 11465141.47 11171248.16 8676006.845 11189504.23 11280501.45 11738107.42 9216596.685 1.326967599 1.166820542 1.243966928 1.212079528 0.941346046 1.21406031 1.223933501 1.273583713 1 23.13580269 5.569135131 0.749308133 1.162427041 1.770566942 0.200797483 0.106640506 13.92394973 2.39352929 0.03651646 9.503566133 370796.0772 -5.569135131 0.6081399 TKDQPDGSSLS(ph)PAQS(ph)PSQSQPPAASSLREPGLESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKDQPDGSSLSPAQSPSQSQPPAASSLREPGLESK 35 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 2 TKDQPDGS(0.001)S(0.003)LS(0.997)PAQS(1)PSQSQPPAASSLREPGLESK 183.1 1.69E-20 157900000 63664 59143 51298 66218 36872 64358 62829 69149 33724 TRUE FALSE 60654.72889 65169.73894 53650.06404 59561.64083 43302.46513 62129.26632 53243.28212 63093.94698 38953.74568 1.557096188 1.673003143 1.377276128 1.529035008 1.11163803 1.594949734 1.366833438 1.619714507 1 15.24947444 -3.512922945 0.178276749 8.89E-19 1.600294391 0.426488426 0.167647021 67.12502363 1.042545944 25.90763628 0.526953881 0.000306957 3.512922945 1.600294391 TKDSGS(ph)ISLQETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKDSGSISLQETR 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 T(0.005)KDS(0.29)GS(0.686)IS(0.019)LQETR 71.872 0.024884 236040000 249030 171090 198780 245540 189460 203350 274240 274310 231470 TRUE FALSE 237258.8454 188524.2655 207894.2596 220857.8527 222501.764 196307.9385 232399.6512 250289.9622 267365.1854 0.887396185 0.705118975 0.77756668 0.826053147 0.832201708 0.73423149 0.869221813 0.936135203 1 18.02845209 1.276400876 2.043566838 0.993138065 0.792868712 0.659259292 0.052017307 0.180209691 1.287313722 0.045789866 0.013459357 18.89734864 -1.276400876 -0.200269354 TKECS(ph)VEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TKECSVEK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.001)KECS(0.999)VEK;TKECS(1)VEK;T(0.002)KECS(0.998)VEK;T(0.002)KECS(0.998)VEK 98.407 0.0045688 1402889000 4499020 3934160 3372440 4626160 1754800 4521450 4233220 4586370 1884970 TRUE FALSE 4286360.241 4335055.377 3527069.71 4161129.608 2060836.564 4364871.053 3587364.541 4184763.129 2177281.521 1.96867525 1.991040357 1.619941967 1.911158281 0.94651819 2.00473435 1.64763468 1.922012881 1 21.05409653 -2.528108642 0.164566743 4.62E-26 2.002633721 0.335935549 0.32154878 57.96403965 1.157807077 24.3263825 1.353036279 0.00296409 2.528108642 2.002633721 TKECS(ph)VEKGTGDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKECSVEKGTGDSLR 15 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.002)KECS(0.998)VEKGTGDSLR 117.03 0.00020996 754770000 1241200 653820 1084500 973620 616540 1177100 1494500 1335900 790400 TRUE FALSE 1182530.936 720445.0013 1134225.398 875749.8678 724064.3808 1136336.732 1266486.577 1218921.514 912971.1952 1.295255471 0.789121283 1.242345217 0.959230557 0.79308568 1.244657814 1.387214168 1.335114974 1 19.80020982 2.042873179 15.89607763 1.291833994 1.018078483 0.242564497 0.191417695 3.951936849 1464.308183 0.066627655 0.049205067 110.3756259 -2.042873179 -0.273755512 TKEDEKDDKPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TKEDEKDDKPIR 12 3 P35998;C9JLS9 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 96.591 0.0023647 358530000 596750 556360 556900 675300 239346 676070 642610 723910 212721 FALSE TRUE 568542.8101 613053.7165 582434.4158 607417.561 281087.8666 652657.5264 544568.0422 660520.6027 245708.6863 2.313889748 2.495042914 2.370426641 2.472104549 1.143988318 2.656224883 2.216315794 2.688226504 1 17.90658933 TKEEALELINGYIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEEALELINGYIQK 15 1 K7EN45;Q13526;K7EMU7 K7EN45 PIN1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 0 90.412 0.0054091 0 121140 103010 103310 136620 99397 127510 149130 133780 102160 FALSE TRUE 115413.9523 113506.8361 108046.8657 122886.698 116731.8053 123094.2967 126377.4795 122065.514 118002.451 0.978064025 0.96190236 0.915632385 1.041391064 0.98923204 1.043150338 1.070973344 1.034432022 1 16.8484573 3.221179357 24.99905848 1.034951259 0.957759388 0.632367665 0.027733907 150.0278389 215781.1118 0.008219899 0.009846099 1664.099756 -3.221179357 -0.077191871 TKEELEAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TKEELEAEKR 10 2 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 98.353 0.0030566 1086390000 810120 741530 704730 870520 422430 832110 954250 936810 527530 FALSE TRUE 771827.2331 817092.75 737042.5676 783013.6757 496101.6583 803293.8221 808661.6365 854777.9501 609336.6582 1.266667979 1.340954527 1.209581859 1.285026373 0.814166769 1.318308707 1.327117983 1.402800798 1 19.21688001 -2.292223665 2.051341093 4.86E-05 1.251502992 0.184665922 0.161743092 2270546.374 300056.8351 10533481.22 0.038147678 0.005102422 2.292223665 1.251454394 TKEEVNEWFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEEVNEWFTK 11 1 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 82.705 0.016606 485850000 445100 392940 420690 466520 366840 435430 522880 444250 384380 FALSE TRUE 424061.0051 432981.0327 439979.0526 419624.5233 430816.7799 420350.9499 443105.0526 405349.1149 443987.6873 0.955118841 0.97520955 0.990971293 0.945126487 0.970334971 0.946762629 0.998012029 0.912973775 1 18.76016014 -1.824499118 2.913402199 1.010775015 0.965027828 0.182653514 0.024563631 39944360.88 2406207.657 2897761.786 0.005034566 0.014979623 1.824499118 -0.045747187 TKEGVGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKEGVGSPK 9 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 TKEGVGS(1)PK;TKEGVGS(1)PK 75.462 0.026471 160910000 638860 501260 557450 672820 353898 666810 716070 717340 382776 TRUE FALSE 608662.3539 552338.9639 583009.6339 605186.8553 415617.6992 643718.2025 606820.37 654525.9067 442134.9471 1.376643846 1.249254255 1.318623732 1.368783127 0.940024537 1.455931513 1.372477733 1.480375869 1 18.75412725 TKENILEEFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKENILEEFSK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 134.21 0.00013285 916740000 3482800 2989100 2863300 3554600 2008160 3380200 3440400 3429600 1939670 FALSE TRUE 3318174.946 3293692.688 2994585.137 3197284.855 2358382.468 3263142.826 2915503.793 3129286.043 2240464.117 1.481021241 1.470093925 1.33659143 1.427063629 1.052631216 1.456458419 1.301294571 1.396713305 1 21.09536619 -4.527979518 0.105038258 6.44E-14 1.603444509 0.481520355 0.122089181 128.8544918 1.009000794 29.42292183 1.689836887 2.96E-05 4.527979518 1.603444509 TKEPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEPSR 6 1 Q9NYU2-2;Q9NYU2;H7BZG0 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 82.671 0.053469 69216000 139850 139050 134170 151820 117300 156890 170560 168360 162060 FALSE TRUE 133239.5677 153219.3531 140321.8272 136558.7652 137757.0829 151456.86 144537.9395 153617.5059 187191.4371 0.711782386 0.818516891 0.749616699 0.729513952 0.735915515 0.809101433 0.772139697 0.820643873 1 17.51415492 0.361947581 0.751962882 1.004028957 0.756419729 0.848269111 0.031993542 0.813657716 0.649976081 0.036854586 0.010872566 2.301164055 -0.361947581 -0.247609228 TKEQILEEFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEQILEEFSK 11 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 162.93 2.24E-05 313520000 1382200 1183100 1214500 1468700 824710 1383400 1421800 1534600 954720 FALSE TRUE 1316866.145 1303659.235 1270186.026 1321063.486 968539.1629 1335492.511 1204878.297 1400222.289 1102773.102 1.194140611 1.182164521 1.151810853 1.19794678 0.878276013 1.21103109 1.092589487 1.269728366 1 20.07270455 -4.999839693 0.018004238 6.91E-06 1.966779082 0.11533165 0.108460563 8389.633912 11.44050233 817.7455237 475.0226489 1.00E-05 4.999839693 1.966772176 TKEVYELLDS(ph)PGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 TKEVYELLDS(1)PGK 176.94 9.61E-06 292940000 1145700 1478500 1038200 1617600 573620 1410300 1266800 1521100 620600 TRUE FALSE 1091545.032 1629160.831 1085802.497 1454995.775 673659.1464 1361460.957 1073526.394 1387904.42 716839.4784 1.522718913 2.272699649 1.514708006 2.029737226 0.939762899 1.899254991 1.497582689 1.936143951 1 19.45129057 TKEVYELLDS(ph)PGKVLLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKEVYELLDSPGKVLLQSK 19 2 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 TKEVYELLDS(1)PGKVLLQSK;TKEVYELLDS(1)PGKVLLQSK 192.18 4.19E-15 332322000 1327460 1104950 1427070 1517520 805820 1745170 1940170 1859350 1048600 TRUE FALSE 1264713.597 1217545.661 1492502.571 1364976.007 946354.7529 1684734.325 1644161.433 1696535.457 1211211.532 1.044172354 1.005229581 1.232239399 1.126950966 0.781329047 1.390949706 1.35745193 1.400692952 1 20.20801942 2.207231963 24.999618 1.324027871 1.046953779 0.365658784 0.159688245 180.776891 144255.1701 0.054752233 0.040441095 161.1506133 -2.207231963 -0.277074092 TKEVYELLDSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 88.768 0.0070745 455770000 1663700 1416500 1447800 1634800 978160 1767100 1879300 1851600 1071600 FALSE TRUE 1585060.198 1560842.96 1514183.062 1470466.798 1148750.794 1705904.884 1592578.269 1689464.088 1237778.255 1.280568787 1.261003701 1.223307209 1.187988876 0.92807479 1.378199106 1.28664263 1.364916601 1 20.23932145 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 400.96 1.36E-156 2811650000 2068865 1650273 1881882 2009542 998345 2251625 2268730 2336400 1190208 TRUE FALSE 1971073.852 1818437.695 1968168.151 1807539.02 1172456.052 2173650.662 1922593.57 2131812.43 1374779.378 1.433738302 1.322712374 1.431624727 1.314784793 0.852832149 1.581090535 1.398474258 1.550657847 1 20.39076869 3.160877076 9.600386568 1.309528801 1.385616049 0.044375827 0.224248366 1.63407693 187.8076489 0.062847337 0.075207224 1448.361846 -3.160877076 0.076087248 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.162)KFAS(0.838)DDEHDEHDENGATGPVK;T(0.163)KFAS(0.837)DDEHDEHDENGATGPVK 290.05 1.40E-55 1479760000 1606010 1622490 1420880 1930520 836740 1823930 1733910 1705730 211942 TRUE FALSE 1530097.09 1787823.576 1486028.753 1736460.462 982667.1911 1760766.847 1469370.184 1556367.239 244808.8829 6.250169814 7.302935884 6.070158631 7.093126856 4.014017708 7.192414041 6.002111388 6.357478618 1 17.90129638 2.784453523 24.99370658 5.471773247 6.701582363 0.164485868 1.740547515 906.2664992 493559.5078 0.470668685 0.499217778 608.7703936 -2.784453523 1.229809116 TKFAS(ph)DDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.166)KFAS(0.834)DDEHDEHDENGATGPVKR;TKFAS(1)DDEHDEHDENGATGPVKR;T(0.172)KFAS(0.828)DDEHDEHDENGATGPVKR;T(0.151)KFAS(0.849)DDEHDEHDENGATGPVKR;T(0.167)KFAS(0.833)DDEHDEHDENGATGPVKR;T(0.1)KFAS(0.9)DDEHDEHDENGATGPVKR 222.95 7.31E-33 10373830000 4432672 2671740 4437209 3838657 2714418 4563390 5544100 4794250 996544 TRUE FALSE 4223148.379 2943993.344 4640659.422 3452787.905 3187811.64 4405358.66 4698245.721 4374440.054 1151082.954 3.668847988 2.557585736 4.031559503 2.999599546 2.769402178 3.827142644 4.081587435 3.800282195 1 20.13456038 3.749075745 24.84364271 3.393938664 3.113217019 0 0.950213166 3638.665134 8596889.882 0.22238142 0.395443027 5611.45836 -3.749075745 -0.280721645 TKFEECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TKFEECR 7 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 133.23 0.0030018 3467300000 5200190 4452370 4183630 5217780 3466720 4806270 5260610 5008510 3710010 FALSE TRUE 4954387.324 4906071.565 4375453.574 4693278.841 4071314.87 4639827.665 4458007.327 4569938.313 4285339.403 1.156124838 1.144850175 1.021028479 1.095194196 0.950056574 1.082721164 1.040292707 1.066412222 1 22.03097804 3.747370349 22.20785687 1.03989155 1.150487571 0.562078465 0.041736341 85.45674945 215418.3539 0.009575598 0.016873053 5589.466392 -3.747370349 0.110596022 TKFENLCK ddPTM_SK-BR-3_Trastuzumab_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 ; 107.21 0.0036916 4340200000 4720800 3543100 2761300 3245400 2928400 3585200 5182000 4212900 3208000 FALSE TRUE 4497657.14 3904145.918 2887908.336 2919166.226 3439112.033 3461043.625 4391390.726 3843996.142 3705480.256 1.213785213 1.053614012 0.779361415 0.787796999 0.928115061 0.934033752 1.185107037 1.037381359 1 21.82122911 4.186339949 3.002709858 0.961169883 1.185210771 0.326192827 0.11824198 0.320583325 5.720797068 0.03430472 0.095996366 15358.18691 -4.186339949 0.224040888 TKFFEDLILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKFFEDLILK 10 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 87.216 0.013842 0 554450 468710 472700 510430 449790 450690 613960 587230 429580 FALSE TRUE 528242.2473 516472.0819 494373.7626 459120.6066 528233.2336 435082.4923 520289.1259 535809.0281 496197.0724 1.064581548 1.0408608 0.996325432 0.925278749 1.064563382 0.876834057 1.048553397 1.079831095 1 18.9205537 3.851116799 3.469144348 0.996175121 1.056412653 0.121572605 0.061271647 0.445314384 9.934721308 0.015119278 0.029277257 7097.68627 -3.851116799 0.060237532 TKFPAEQYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKFPAEQYYR 10 1 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ; 132.03 0.00021386 668750000 1087660 857230 647150 775700 896900 829440 1273010 1018200 1018460 FALSE TRUE 1036248.467 944582.7116 676822.4676 697725.1623 1053319.076 800716.2848 1078788.944 929041.0102 1176397.575 0.880865865 0.802945136 0.575334803 0.593103197 0.895376783 0.680651084 0.917027514 0.78973387 1 20.16594429 1.69743581 8.323728919 0.888685992 0.750899455 0.295801283 0.117516975 0.185604988 25.41855608 0.058175636 0.030804391 49.82368101 -1.69743581 -0.137786538 TKGDFILVGDLMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKGDFILVGDLMR 13 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 76.85 0.025123 138940000 661510 405460 441770 525920 460210 530930 892070 659760 563750 FALSE TRUE 630241.7333 446776.835 462025.5915 473053.5224 540470.4783 512543.761 755968.3375 601987.9168 651173.4708 0.967855359 0.686110315 0.709527664 0.726463137 0.829994621 0.787107866 1.160932334 0.924466281 1 19.3126824 1.7571894 25 1.039119081 0.783892305 0.585909118 0.096541146 5.085817438 6831.973427 0.0433292 0.024028444 57.17279181 -1.7571894 -0.255226776 TKGTSSFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKGTSSFGK 9 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 104.07 0.0030277 1148310000 2848770 1872400 2723510 2637250 2172330 2987430 3979100 3331720 2709890 FALSE TRUE 2714114.288 2063199.689 2848385.627 2372148.62 2551183.664 2883974.55 3372015.214 3039976.934 3130125.901 0.867094287 0.659142716 0.909990754 0.757844475 0.815041869 0.921360559 1.077277822 0.971199572 1 21.57778926 2.097397687 2.858138704 1.022181773 0.789535309 0.654418819 0.071178982 0.142154663 2.299575465 0.03042256 0.019507281 125.1404427 -2.097397687 -0.232646464 TKIDWNK ddPTM_SK-BR-3_Trastuzumab_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 3205000000 13850800 10977400 10063900 11649000 9520600 12604300 16770300 14690100 10735000 FALSE TRUE 13196100.13 12096009.54 10525339.77 10478020.39 11180989.63 12167809.93 14211682.73 13403756.97 12399728.97 1.064224884 0.975505962 0.848836276 0.845020114 0.90171242 0.981296443 1.146128497 1.080971769 1 23.56380525 1.923968403 5.659796274 1.087550157 0.938952853 0.463542771 0.071929242 0.222661271 12.34850773 0.035589744 0.021589179 83.9398914 -1.923968403 -0.148597304 TKKDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 T(0.019)KKDDS(0.453)HS(0.53)AEDS(0.997)EDEKEDHK 42.106 0.097549 78340000 19986 30804 23838 24818 8187 30405 22500 28066 8980.2 TRUE FALSE 19041.30139 33942.96262 24930.99588 22323.24749 9614.810208 29352.06723 19067.21176 25608.39225 10372.80355 1.835694785 3.272303621 2.403496389 2.152093923 0.92692493 2.82971398 1.838192699 2.468801431 1 13.34051826 3.212454744 3.741065179 1.916225793 2.584983334 0.169322259 0.669668347 0.370621398 11.0460094 0.181855095 0.232466619 1631.002941 -3.212454744 0.66875754 TKKPGISDVTDYSDRGDS(ph)DMDEATYSSSQDHQTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKKPGISDVTDYSDRGDSDMDEATYSSSQDHQTPK 35 3 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 T(0.001)KKPGIS(0.003)DVT(0.012)DY(0.008)S(0.051)DRGDS(0.924)DMDEAT(0.001)YS(0.001)S(0.001)SQDHQTPK;T(0.001)KKPGIS(0.001)DVT(0.004)DY(0.007)S(0.014)DRGDS(0.893)DMDEAT(0.016)Y(0.013)S(0.016)S(0.016)S(0.016)QDHQTPK 83.436 0.0052111 107640000 86780 61656 84711 87032 51403 84852 101433 104936 51669 TRUE FALSE 82678.08138 67938.8165 88595.08314 78283.37801 60367.66693 81913.55396 85957.53291 95747.24754 59681.56463 1.385320273 1.138355151 1.484463145 1.311684412 1.011496051 1.372510162 1.440269427 1.6043019 1 15.86499774 2.024087375 24.96610138 1.399429623 1.264992383 0.027286165 0.196725501 508.4971826 527045.2557 0.067295801 0.049699074 105.7030149 -2.024087375 -0.134437241 TKKPRPPS(ph)LK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKKPRPPSLK 10 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TKKPRPPS(1)LK;TKKPRPPS(1)LK 88.706 0.066375 4674000000 6398200 5751400 5687300 7184500 3004100 7450400 7382500 6858200 3099800 TRUE FALSE 6095769.766 6337474.199 5948068.331 6462300.41 3528014.089 7192390.78 6256164.036 6257659.65 3580501.152 1.702490659 1.769996414 1.661239049 1.80485919 0.985340861 2.008766503 1.747287257 1.747704968 1 21.7717301 TKLDDLALLEDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKLDDLALLEDLEK 14 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 157.8 4.74E-06 46040000 327840 278220 300320 318320 178890 337450 343980 352480 177220 FALSE TRUE 312343.6529 306570.9343 314089.9691 286321.8688 210088.3594 325764.0219 291499.5334 321614.9826 204702.3725 1.525842857 1.497642312 1.534373858 1.398722767 1.026311307 1.591403255 1.424016389 1.571134612 1 17.6431683 -1.949500246 2.639074765 0.669776999 1.448875237 0.432024145 0.160750793 7647707.639 4202313.961 15493981.59 0.036975981 0.011233103 1.949500246 0.779098238 TKMIMVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKMIMVEER 9 1 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 64.04 0.096996 72927000 53647 54258 54334 65575 197210 25210 72693 28738 95497 FALSE TRUE 51111.21263 59786.95189 56825.26764 58983.27642 231603.3616 24336.97138 61602.34775 26221.54837 110306.187 0.463357623 0.542009052 0.515159387 0.534723192 2.099640716 0.220631064 0.55846684 0.237716026 1 16.75115419 2.959580835 24.9998752 0.785541825 0.510260649 0.07774211 0.521416914 1610.484845 996109.3404 0.155753504 0.16522215 911.131024 -2.959580835 -0.275281176 TKNETDEDGWTTVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKNETDEDGWTTVR 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 160.47 2.41E-07 0 155360 148260 127440 169450 102980 142950 166170 155210 107910 FALSE TRUE 148016.4407 163367.8626 133283.2501 152416.5641 120939.6794 137999.6057 140817.7146 141618.9896 124644.1317 1.18751231 1.31067432 1.06931027 1.222813798 0.97027977 1.107148839 1.129758078 1.136186579 1 16.92745544 3.731129863 24.95565123 1.09941169 1.249093316 0.422337063 0.076455884 451.9448318 1517824.431 0.01853347 0.029341388 5384.307607 -3.731129863 0.149681626 TKNFDKLSFLYLITGNLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKNFDKLSFLYLITGNLEK 19 2 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 123.19 1.78E-05 75465000 168750 85304 150690 121550 118690 143510 228520 187530 145650 FALSE TRUE 160773.5219 93996.57458 157599.2856 109331.5631 139389.4984 138540.2127 193655.0769 171108.879 168236.6581 0.955639061 0.558716368 0.936771375 0.649867658 0.828532259 0.823484098 1.151087278 1.017072503 1 17.36013257 1.854774871 5.100003221 1.064858251 0.77539371 0.500901551 0.12408503 0.161997155 5.851511931 0.052610368 0.030634642 71.5772273 -1.854774871 -0.289464541 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE 29 1 P12074 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 106.51 0.00030411 177980000 210530 184700 201320 228460 201250 151300 207610 181910 19090 FALSE TRUE 200578.6641 203521.14 210550.7211 205494.7668 236347.9363 146060.4431 175935.2815 165980.996 22050.3797 9.096381416 9.229824735 9.548621111 9.319330077 10.7185427 6.62394231 7.978786935 7.527353192 1 14.42851588 0.068603343 0.474808703 0.136517766 9.500473997 0.886241251 0.90822359 1.126456049 0.336616081 2.733485534 0.461417761 1.171125244 -0.068603343 9.363956231 TKPIVKPQTS(ph)PEYGQGINPISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 TKPIVKPQT(0.021)S(0.979)PEYGQGINPISR 166.58 6.02E-12 818970000 701660 648300 697030 816480 439900 769310 832200 800700 553430 TRUE FALSE 668493.9224 714362.5071 728989.515 734405.8792 516618.4207 742668.6018 705232.6056 730586.4632 639253.0979 1.045742171 1.117495573 1.140376976 1.148849934 0.808159432 1.161775523 1.103213434 1.142875124 1 19.28602772 -0.395541493 5.944783288 1.000000001 1.084653299 0.060668146 0.103252647 6209428.036 1044517.051 0.092502225 0.022426096 0.402215226 0.395541493 0.084653299 TKPIWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 86.67 0.018154 294280000 352370 299060 325690 405750 328710 407160 457140 445710 387730 FALSE TRUE 335714.1684 329534.554 340623.2087 364963.2391 386036.9199 393059.9471 387394.897 406681.2695 447857.1881 0.749600938 0.735802757 0.760562111 0.814909861 0.861964327 0.877645726 0.864996493 0.908060159 1 18.77267924 2.199050738 0.291754606 1.012779802 0.684337103 0.943562437 0.019186741 0.425713269 0.101947184 0.033501129 0.050450918 158.1432784 -2.199050738 -0.328442699 TKPPRPDS(ph)PATTPNISVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 T(0.033)KPPRPDS(0.949)PAT(0.018)T(0.001)PNISVK;TKPPRPDS(0.999)PAT(0.001)TPNISVK 119.02 4.48E-05 797190000 747140 606810 665290 796210 486366 753900 864780 774170 549429 TRUE FALSE 711824.1729 668644.6289 695794.2046 716173.4581 571188.0764 727792.254 732841.9282 706379.5707 634631.6432 1.121633597 1.053594847 1.0963749 1.128486841 0.90003088 1.146794777 1.154751636 1.113054444 1 19.27555993 TKPQMQEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKPQMQEER 9 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 91.549 0.0097381 271710000 331680 237380 173890 229810 341400 286770 472580 372290 398230 FALSE TRUE 316002.1437 261569.2919 181863.0285 206709.0622 400940.0519 276839.083 400479.2415 339690.314 459985.4745 0.686982875 0.568646852 0.395366894 0.449381717 0.871636332 0.601843098 0.870634539 0.738480523 1 18.81122878 1.663491678 0.710879273 0.959406679 0.557023413 0.524041571 0.132345858 0.522316615 0.53854368 0.120204323 0.056917126 46.07779389 -1.663491678 -0.402383266 TKPSDEEMLFIYGHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKPSDEEMLFIYGHYK 16 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5;P07108-6 P07108 DBI Acyl-CoA-binding protein 0 ; 215.23 9.79E-15 1248020000 5692400 4388100 3545900 5831300 2910900 4567300 5687200 5791200 2713500 FALSE TRUE 5423331.533 4835252.379 3708483.022 5245126.645 3418560.038 4409133.256 4819513.187 5284091.827 3134295.721 1.73031903 1.542691823 1.183194999 1.673462593 1.090694798 1.406738115 1.537670219 1.685894471 1 21.57970987 4.117795507 3.062261633 1.40015548 1.690603706 0.193992874 0.231936892 0.37961558 6.924593524 0.054438424 0.139701037 13115.82178 -4.117795507 0.290448226 TKPTHGIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKPTHGIGK 9 1 F5H8D0;Q96GC5-3;Q96GC5 F5H8D0 MRPL48 "39S ribosomal protein L48, mitochondrial" 0 69.276 0.033467 121010000 721130 519820 482480 534500 385110 456440 594320 571190 437640 FALSE TRUE 687043.614 572790.249 504602.1852 480771.0445 452273.0621 440633.3684 503645.5686 521173.5755 505506.976 1.359117968 1.133100582 0.998210132 0.951067082 0.894692029 0.871666246 0.996317741 1.030991856 1 18.94737148 4.137733948 1.295930938 0.950016665 1.370622544 0.874220097 0.048952593 0.179542429 0.49724157 0.015158538 0.075295082 13732.00484 -4.137733948 0.420605879 TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 2 TKPTQAAGPS(0.005)S(0.995)PQKPPT(1)PEETK;TKPTQAAGPS(0.024)S(0.976)PQKPPT(0.972)PEET(0.028)K 143.09 2.08E-07 1306240000 2204660 2485000 1841980 2585300 704190 2601400 2084120 2523100 633150 TRUE FALSE 2100450.091 2738224.325 1926436.605 2325420.732 827000.513 2511312.866 1766149.217 2302163.988 731335.6683 2.872073908 3.744141635 2.634134623 3.179690029 1.130808395 3.433871715 2.414963871 3.14788966 1 19.4801742 3.25334138 2.113020055 2.4283456 3.268572378 0.169988511 0.829773411 0.519431097 4.760613714 0.232368423 0.321350948 1792.013926 -3.25334138 0.840226778 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 1 TKPTQAAGPS(0.157)S(0.839)PQKPPT(0.004)PEETK;TKPTQAAGPS(0.217)S(0.782)PQKPPTPEETK;TKPTQAAGPS(0.024)S(0.975)PQKPPT(0.001)PEETK 136.53 2.29E-06 1028050000 823380 792520 780100 878750 336450 974970 854730 964300 343458 TRUE FALSE 784460.4592 873278.689 815868.3566 790416.3805 395126.7735 941206.5444 724325.2403 879860.7799 396719.7125 1.977366978 2.201248543 2.056535965 1.992379898 0.995984724 2.372472339 1.825785857 2.21783983 1 18.59776056 2.983714945 24.53086869 1.76738934 2.082053248 0.136202353 0.4449982 1260.312883 1898466.465 0.123024433 0.133954852 963.1966096 -2.983714945 0.314663908 TKPTQNSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKPTQNSVR 9 1 Q9NRF8;P17812;B4E1E0;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 Q9NRF8;P17812 CTPS2;CTPS1 CTP synthase 2;CTP synthase 1;CTP synthase 0 ; 79.311 0.0249 116964000 196110 125774 87842 98153 177573 123100 237990 173376 185896 FALSE TRUE 186840.269 138590.5136 91869.64259 88286.47396 208541.675 118837.0161 201680.2545 158194.2783 214723.8023 0.870142327 0.645436194 0.427850297 0.411162959 0.971208933 0.553441281 0.9392543 0.736733779 1 17.7121226 1.503025419 0.887660749 0.958931716 0.645578244 0.261567508 0.18691314 0.771215369 1.224943128 0.168243104 0.065611636 31.84383894 -1.503025419 -0.313353471 TKPVTGNLRPEEALQALTIYEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKPVTGNLRPEEALQALTIYEGK 23 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 93.572 0.0025448 45876000 146630 127460 150880 151850 105980 160650 204820 180250 112960 FALSE TRUE 139699.0905 140448.3189 157797.9972 136585.7495 124462.8784 155086.6502 173570.9472 164466.3544 130477.2599 1.070677685 1.076419899 1.209390796 1.046816508 0.953904754 1.18861057 1.330277378 1.260498225 1 16.99343886 2.013772405 24.48970758 1.240078018 1.076706904 0.220109734 0.105306757 186.4465128 331532.2895 0.036399883 0.026868992 103.2220323 -2.013772405 -0.163371114 TKS(ph)DES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.129)KS(0.872)DES(0.999)GEEKNGDEDCQR;T(0.291)KS(0.71)DES(1)GEEKNGDEDCQR;T(0.373)KS(0.627)DES(1)GEEKNGDEDCQR 158.05 2.49E-11 897930000 2788270 2577060 2455950 2878410 851209 3280410 2871180 3642760 730842 TRUE FALSE 2656474.003 2839665.344 2568557.737 2589066.758 999659.5801 3166808.579 2433128.758 3323780.623 844177.2447 3.146820196 3.363825976 3.042675875 3.066970561 1.184182097 3.751355061 2.88224869 3.937301845 1 19.68718642 2.982589815 24.63130497 2.717453604 3.197170959 0.079132628 0.939200937 1903.008999 2692313.448 0.261187553 0.282916437 960.704478 -2.982589815 0.479717355 TKS(ph)INGSLYIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKSINGSLYIFR 12 1 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 T(0.001)KS(0.999)INGSLYIFR 80.538 0.012156 279780000 466400 419650 430440 440760 478900 415760 563980 478700 529760 TRUE FALSE 444354.1963 462412.8121 450176.0998 396453.9674 562420.0084 401362.127 477934.4928 436782.4903 611912.4752 0.726172801 0.755684564 0.735687076 0.647893258 0.919118389 0.655914274 0.781050415 0.713798963 1 19.22296579 -2.089167893 2.431051763 1.422662004 0.743459852 0.539826081 0.074873705 9020812.172 2612006.656 21117846.4 0.015559862 0.008143894 2.089167893 -0.679202152 TKS(ph)PKPAESPQSATK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKSPKPAESPQSATK 15 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 T(0.205)KS(0.795)PKPAESPQSATK;T(0.2)KS(0.8)PKPAESPQSATK 216.04 1.18E-12 241710000 465830 432060 447420 525700 233060 534090 485460 554000 242460 TRUE FALSE 443811.1391 476087.4052 467934.6496 472855.6372 273705.5902 515594.3294 411394.1609 505488.8231 280059.4585 1.584703268 1.699951174 1.670840371 1.688411596 0.977312431 1.841017376 1.468952926 1.804933944 1 18.09537363 -1.838710885 2.841531968 0.794629116 1.590225059 0.371252595 0.242114586 31337918.01 16151221.77 43295953.56 0.053311366 0.014497366 1.838710885 0.795595943 TKS(ph)PTDDEVTPSAVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.057)KS(0.93)PT(0.013)DDEVTPSAVVR;T(0.02)KS(0.952)PT(0.028)DDEVTPSAVVR;T(0.002)KS(0.864)PT(0.134)DDEVTPSAVVR;T(0.328)KS(0.67)PT(0.002)DDEVTPSAVVR;T(0.065)KS(0.929)PT(0.006)DDEVTPSAVVR 213.72 7.16E-13 2271500000 1499930 1280470 1256890 1464830 789150 1405720 1487420 1466060 960250 TRUE FALSE 1429031.281 1410951.349 1314519.65 1317582.505 926777.5101 1357039.564 1260486.761 1337684.014 1109160.666 1.288389794 1.27208924 1.185148095 1.187909512 0.835566513 1.223483311 1.13643298 1.206032684 1 20.08103693 3.422285071 2.069865913 1.101839417 1.280285274 0.318187326 0.112410167 0.367749335 3.184502712 0.032508812 0.050858368 2644.143807 -3.422285071 0.178445857 TKSDES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 TKSDES(1)GEEKNGDEDCQR;TKSDES(1)GEEKNGDEDCQR;T(0.002)KS(0.002)DES(0.995)GEEKNGDEDCQR;T(0.003)KS(0.003)DES(0.995)GEEKNGDEDCQR 169.36 9.61E-12 483776000 548500 494220 566396 638278 285513.8 624631 623356 748564 325804.4 TRUE FALSE 522573.492 544581.5799 592365.8168 574117.0828 335307.3163 602999.8718 528251.5935 683015.7678 376328.4824 1.388609995 1.447091053 1.574065862 1.525574358 0.890996382 1.602323236 1.403698147 1.814945718 1 18.52163296 TKTPGPGAQSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKTPGPGAQSALR 13 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 134.02 9.16E-05 601970000 559120 284010 363730 419900 521380 414880 720740 532860 619730 FALSE TRUE 532691.5057 312950.9419 380407.3803 377690.8542 612308.5069 400512.6016 610777.8757 486199.9535 715834.5633 0.744154492 0.437183335 0.531418012 0.527623104 0.85537712 0.559504419 0.853238873 0.67920715 1 19.44926668 1.179699183 0.469063679 0.999153986 0.559071585 0.474751726 0.129092918 0.791188545 0.472142125 0.142278125 0.078369399 15.12513232 -1.179699183 -0.440082401 TKVEAFQTTISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TKVEAFQTTISK 12 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 104.18 0.0010338 0 630290 537340 551880 570120 369750 531020 584020 661510 406560 FALSE TRUE 600497.4408 592095.5569 577184.2439 512810.4544 434234.2829 512630.6442 494917.0227 603584.6775 469607.2484 1.278722683 1.260831384 1.229078652 1.091998593 0.924675427 1.091615698 1.053895621 1.285296766 1 18.84109515 3.270877107 3.653414964 1.068330796 1.265823132 0.477837587 0.090350151 0.177605929 4.976563248 0.024882617 0.033104085 1865.851632 -3.270877107 0.197492336 TKVENGEGTIPVESSDIVPTWDGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKVENGEGTIPVESSDIVPTWDGIR 25 1 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 180.42 2.34E-17 203556000 218902 189380 213320 240451 177520 222029 278560 263880 210363 FALSE TRUE 208554.9363 208678.0373 223100.933 216280.4087 208479.4318 214340.0801 236060.5559 240773.2683 242985.0197 0.858303679 0.858810299 0.918167438 0.890097706 0.857992942 0.882112323 0.971502508 0.990897581 1 17.89050785 1.688149749 3.157601296 0.99261416 0.87433736 0.890438657 0.018298627 0.068806248 1.5696069 0.011847552 0.005324162 48.76966239 -1.688149749 -0.1182768 TKYWELIYEDSMDLIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TKYWELIYEDSMDLIAK 17 1 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VRI6;F8VR34 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 219.01 4.07E-15 851830000 1617070 1309250 1364990 1337450 952730 1261930 1392780 1523020 829600 FALSE TRUE 1540634.306 1442664.063 1427576.142 1203006.985 1118885.81 1218229.048 1180285.831 1389656.295 958250.131 1.607757991 1.505519297 1.489774011 1.255420632 1.167634393 1.271305903 1.231709543 1.45020204 1 19.87004276 8 0.16191526 1.04447965 3.389094375 0.641281309 0.109686728 36.16212682 0.376851928 0.305644789 20.30209936 100000000 -8 2.344614725 TLADLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLADLIR 7 0 Q16878 Q16878 CDO1 Cysteine dioxygenase type 1 0 94.407 0.033089 43478000 122850 82903 63251 64371 154040 64212 113760 110400 248180 FALSE TRUE 117043.124 91350.90995 66151.12091 57900.30478 180904.5272 61988.32234 96403.82265 100732.7907 286666.4869 0.408290223 0.318666165 0.230759869 0.201977934 0.6310627 0.216238469 0.336292616 0.351393676 1 18.12901373 0.561754601 3.580381571 0.999999648 0.334570107 0.742074189 0.122908477 9.890574861 80.14204618 0.108299635 0.027869051 3.645479004 -0.561754601 -0.665429542 TLAGDVHIVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;; 140.78 3.87E-05 2127304000 2837450 2415498 2351877 2846660 2690120 2465183 3024520 2792030 2655100 FALSE TRUE 2703329.362 2661639.992 2459712.887 2560508.328 3159276.076 2379813.095 2563073.925 2547545.052 3066839.348 0.881470809 0.867877215 0.802035127 0.834901356 1.030140714 0.775982314 0.835737916 0.830674438 1 21.54832116 -1.009011992 4.85340535 1.000002212 0.857317455 0.30145783 0.068241663 1.53E-06 3.11E-07 0.061731211 0.01454996 0.097946294 1.009011992 -0.142684756 TLALELAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLALELAPK 9 0 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 112.84 0.0044133 104723000 606740 458090 467380 462320 481040 459470 608990 559070 528100 FALSE TRUE 578060.6026 504769.8918 488809.8353 415846.7152 564933.2237 443558.4387 516077.3906 510114.867 609995.0508 0.947648021 0.82749834 0.8013341 0.681721458 0.926127553 0.727150881 0.846035373 0.836260665 1 19.21843801 0.51333958 2.20286969 0.999988104 0.825929831 0.328355651 0.079159947 6.589947635 28.30851465 0.072637688 0.019703584 3.260915765 -0.51333958 -0.174058273 TLAPTWEELSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLAPTWEELSKK 12 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 146.67 0.00010412 342530000 1193100 980660 1057800 1143200 777990 1132700 1302800 1329700 978320 FALSE TRUE 1136704.527 1080590.369 1106301.176 1028283.364 913671.2097 1093474.315 1104033.932 1213264.419 1130032.869 1.005903951 0.956246848 0.978999113 0.909958809 0.808535074 0.967648238 0.976992761 1.073654096 1 20.10793331 1.509864245 3.039315284 1.035550473 0.941084854 0.338714063 0.055968544 0.290032867 5.600157715 0.042172841 0.015389341 32.34925213 -1.509864245 -0.094465619 TLAYIITELDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLAYIITELDER 12 0 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 85.958 0.026477 10983000 15127 16788 15677 20452 16149 13423 15512 15567 16396 FALSE TRUE 14411.97669 18498.71629 16395.80596 18396.1261 18965.38049 12958.15814 13145.3595 14203.87095 18938.60794 0.760983951 0.976772757 0.865734483 0.97135577 1.001413649 0.684219146 0.694103788 0.749995512 1 14.20904267 2.232428026 24.99991319 0.747308879 0.909916286 0.236076895 0.111265653 162.3284511 661736.3125 0.038222366 0.028945819 170.7764676 -2.232428026 0.162607408 TLAYIITELDERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLAYIITELDERER 14 1 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 ; 179.5 1.70E-06 38421000 33829 27735 35228 34034 37670 34943 40341 39439 39049 FALSE TRUE 32229.97021 30561.22803 36843.23865 30612.83766 44239.63607 33732.91515 34186.23954 35985.51208 45104.51949 0.714561879 0.677564652 0.816841396 0.678708875 0.980824906 0.747883262 0.757933793 0.797824974 1 15.46098438 -5 0.112897947 1.74529938 0.633686093 0.450544726 0.083566749 142.999798 1.065808884 24.7239767 0.909192703 1.00E-05 5 -1.111613288 TLAYIITELDEREREEFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLAYIITELDEREREEFYR 19 2 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 ;;; 284.88 3.34E-40 161317800 117490.4 60715.8 116120.2 105369.9 146073 92096.1 164104.6 121091 182883.3 FALSE TRUE 111936.8616 66902.80905 121444.426 94777.91746 171548.085 88906.78896 139067.4293 110487.6301 211243.9081 0.529893916 0.316708821 0.574901436 0.448665802 0.812085359 0.420872676 0.658326342 0.52303345 1 17.68855021 -5 0.150650044 2.721358667 0.375568759 0.562508872 0.131107072 88.51098783 0.790170957 45.46480827 0.58797675 1.00E-05 5 -2.345789908 TLAYLLPAIVHINHQPYLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLAYLLPAIVHINHQPYLER 20 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 173.09 3.12E-12 653090000 522810 395990 409730 464470 470310 419920 533680 433120 41819 FALSE TRUE 498097.8074 436341.8312 428516.5258 417780.5932 552331.9151 405378.0651 452257.3143 395193.7167 48304.07694 10.31171361 9.033229882 8.871228951 8.648971674 11.43447821 8.392212227 9.362715178 8.181373949 1 15.55985734 0.324809843 1.103129321 0.976955965 9.499381684 0.900046217 0.877089047 0.871244562 1.182795111 0.794929841 0.237868093 2.112563844 -0.324809843 8.522425719 TLCGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLCGCR 6 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 154.34 0.023304 411931000 427357 339024 305814 328745 401216 316932 462639 340132 422994 FALSE TRUE 407156.6815 373570.931 319835.8744 295698.928 471187.9434 305956.5654 392054.9236 310348.2389 488589.7492 0.83333038 0.764590194 0.654610284 0.60520903 0.964383604 0.626203407 0.802421509 0.635191875 1 18.89826407 -1.285407404 4.202458164 1.000254106 0.744105944 0.351741899 0.112234212 0.000240505 4.09E-05 0.0978119 0.023031758 0.051831359 1.285407404 -0.256148162 TLDFDPLLSPAS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLDFDPLLSPASPK 14 0 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLSPAS(1)PK 157.35 5.58E-06 41952000 105280 97855 102340 114670 58797 109550 114790 122470 71369 TRUE FALSE 100303.623 107826.5358 107032.3902 103143.1537 69051.17818 105756.256 97276.67724 111745.8775 82436.54002 1.21673742 1.307994437 1.298361021 1.25118247 0.837628292 1.28288082 1.180018924 1.355538182 1 16.33099633 -4.991052721 0.217565763 2.18E-12 1.243583033 0.159865512 0.145398721 285.3675881 2.862316272 126.5677825 0.273222086 1.02E-05 4.991052721 1.243583033 TLDFDPLLSPAS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLDFDPLLSPASPKR 15 1 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLS(0.009)PAS(0.991)PKR;TLDFDPLLS(0.002)PAS(0.998)PKR 138.55 6.07E-06 76355000 193565 168979 185752 201262 135255 199942 233390 229073 172322 TRUE FALSE 184415.5661 186198.1522 194268.9129 181030.7614 158843.4292 193017.9584 197782.069 209014.1537 199044.8157 0.926502735 0.935458437 0.976005892 0.909497496 0.798028467 0.969721104 0.993655968 1.050085897 1 17.60273377 1.809259252 3.003584251 1.018714311 0.916168847 0.489436744 0.048215063 0.22256945 3.712445266 0.026718138 0.013303718 64.45539176 -1.809259252 -0.102545464 TLDGFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 108.46 0.011621 8598700000 10721500 8810800 9944300 11334200 7589100 11716900 13356300 11801400 8517000 FALSE TRUE 10214715.94 9708630.537 10400255.99 10194864.68 8912636.637 11311140.82 11318551.13 10768006.85 9837772.861 1.038315896 0.986872809 1.057175861 1.036298035 0.905960807 1.149766413 1.150519664 1.094557376 1 23.22990032 2.211338247 24.99998714 1.11683665 1.00929968 0.366041548 0.059077156 189.930734 174424.0704 0.020288998 0.014988066 162.6815297 -2.211338247 -0.10753697 TLDGIFSEQVAMGYSHSLVIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLDGIFSEQVAMGYSHSLVIAR 22 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 228.15 3.87E-26 201611000 276079 238805 249890 292866 304107 238023 316546 276529 300312 FALSE TRUE 263029.2928 263139.501 261347.7037 263426.5533 357143.1645 229780.2038 268251.0939 252314.6548 346882.8512 0.758265483 0.758583193 0.753417769 0.759410713 1.029578612 0.662414423 0.773318984 0.727377136 1 18.40408899 -2.179681358 2.381037364 1.60058145 0.77579738 0.351300234 0.094859159 8129240.223 1654443.304 26377942.32 0.021359204 0.006611784 2.179681358 -0.824784069 TLDS(ph)DEERPRPAPPDWSHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 T(0.002)LDS(0.998)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;T(0.031)LDS(0.969)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;T(0.009)LDS(0.991)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;T(0.002)LDS(0.998)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR 247.89 1.83E-30 6541440000 2973216 2713134 2823232 3189727 2664538 2915880 3420962 3092912 2637071 TRUE FALSE 2832677.972 2989605.439 2952679.98 2869089.582 3129232.584 2814902.344 2899031.417 2822080.229 3046014.502 0.929962077 0.981481026 0.969358477 0.94191593 1.027320317 0.924126376 0.95174577 0.92648286 1 21.53849138 3.939568116 0.001880993 1.913927302 6.51E-07 0.043400278 0.033202406 873130.4724 338.2680187 170324.949 173874.3531 8700.978911 -3.939568116 -1.913926651 TLDSGTSEIVKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLDSGTSEIVKSPR 14 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDS(0.002)GTSEIVKS(0.997)PR 186.98 6.06E-07 2322270000 3016370 2618860 2770440 3126430 2085020 3030770 3332780 3175080 2380770 TRUE FALSE 2873792.168 2885724.811 2897467.414 2812155.317 2448646.828 2925813.675 2824303.2 2897053.163 2749967.652 1.045027626 1.04936682 1.053636908 1.022613962 0.890427502 1.06394476 1.027031426 1.053486269 1 21.39098322 3.112425367 5.767325574 1.009499913 1.048375556 0.143998761 0.046614053 0.433459312 20.34937795 0.013384216 0.016103376 1295.464053 -3.112425367 0.038875643 TLEAEFNSPSPPT(ph)PEPGEGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 TLEAEFNSPS(0.001)PPT(0.999)PEPGEGPR 143.57 1.52E-06 43732000 40037 44179 48565 47996 43203 49032 53804 50919 51314 TRUE FALSE 38144.53036 48680.89033 50791.75329 43171.35089 50737.58952 47334.00955 45595.21162 46460.26242 59271.51304 0.643555874 0.82132019 0.856933638 0.728365933 0.856019813 0.798596275 0.769260126 0.783854841 1 15.85505127 -5 0.197582005 1.961263429 0.743562922 0.561881955 0.06133311 107.6519192 1.062301117 40.9980689 0.149142293 1.00E-05 5 -1.217700507 TLEDEEEQERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLEDEEEQERER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 ; 209.67 4.78E-08 1195680000 1057080 926490 916540 1033410 912300 890240 1043910 1132190 921590 FALSE TRUE 1007113.923 1020900.384 958564.2656 929529.6634 1071404.831 859410.7656 884642.3568 1033049.441 1064505.47 0.946086189 0.959037236 0.900478478 0.873203275 1.006481283 0.807333348 0.831035989 0.970450101 1 20.02175193 3.73047625 18.58174404 0.897508443 0.952561702 0.020395813 0.067440218 38.02728996 87410.56731 0.017254616 0.027509918 5376.210323 -3.73047625 0.055053259 TLEEDEEELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLEEDEEELFK 11 0 P43487;F6WQW2;P43487-2;C9JJ34;C9JDM3 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 198.61 1.23E-07 234850000 995160 860220 908280 1063540 818250 911720 1080470 1034120 830330 FALSE TRUE 948120.759 947877.396 949925.5364 956630.9386 960952.5409 880146.9078 915624.4573 943566.9706 959093.3357 0.988559428 0.988305685 0.990441181 0.997432578 1.001938503 0.917686397 0.954677114 0.983811414 1 19.87131169 2.290100756 24.99995141 0.958146636 0.992270109 0.294910508 0.021634405 100.6532382 48822.14006 0.006962568 0.005825296 195.0297013 -2.290100756 0.034123473 TLEGELHDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 256.91 3.50E-17 23003560000 22345670 16863650 15542130 20071970 18871410 17237080 21255930 19137290 16462490 FALSE TRUE 21289434.46 18582075.11 16254752.03 18054297.44 22162577.93 16640155.6 18012947.49 17461527.43 19015408.87 1.119588572 0.977211441 0.854820012 0.949456179 1.165506252 0.875087973 0.947281629 0.918283038 1 24.18066562 TLEGELHDLRGQVAKLEAALGEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLEGELHDLRGQVAKLEAALGEAK 24 2 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 140.45 1.77E-07 27759000 58262 37679 97707 45601 63186 66392 96428 68838 70925 FALSE TRUE 55508.07072 41518.53294 102186.9626 41017.10084 74205.61839 64092.82839 81716.13758 62810.17979 81923.68677 0.677558261 0.506795221 1.24734331 0.500674499 0.905789538 0.78234795 0.997466555 0.766691323 1 16.32199302 5.944673511 0.220763063 0.980026787 5.21E-10 0.127167768 0.215417127 31.68823003 0.879954781 0.324311992 9.25397809 880386.7773 -5.944673511 -0.980026786 TLEGGRKPLHYAADCGQLEILEFLLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLEGGRKPLHYAADCGQLEILEFLLLK 27 2 P58546 P58546 MTPN Myotrophin 0 ; 114.41 0.00054006 527220000 1064060 479350 1294360 672080 1238200 1116670 2275790 1237880 1496670 FALSE TRUE 1013763.993 528196.31 1353707.686 604521.2415 1454141.688 1077999.438 1928576.438 1129484.665 1728765.94 0.58640905 0.305533732 0.783048564 0.349683683 0.841144342 0.62356587 1.115579844 0.653347361 1 20.72131112 2.408204572 1.216546603 0.922634955 0.486960051 0.406544925 0.197004004 0.379321016 1.121081687 0.10215629 0.068614681 255.9791381 -2.408204572 -0.435674904 TLEPVKPPTVPNDYMT(ph)SPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 TLEPVKPPTVPNDY(0.038)MT(0.481)S(0.481)PAR 75.71 0.019638 129050000 88346 108420 108730 124730 93251 105530 120240 122440 108340 TRUE FALSE 84170.05966 119468.1213 113715.378 112191.9034 109513.9449 101875.4696 101895.1796 111718.5045 125140.8139 0.672602783 0.954669524 0.908699365 0.896525282 0.87512572 0.81408668 0.814244182 0.892742352 1 16.93319287 -4.877648695 0.016885338 2.00944427 3.17E-07 0.28214987 0.075788707 7739.777401 10.0912696 769.2561072 466.5614271 1.33E-05 4.877648695 -2.009443953 TLEPVKPPTVPNDYMTS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.235)S(0.765)PAR 108.49 0.00012794 75516000 85428 76992 81564 94004 68628 98763 87851 89853 92370 TRUE FALSE 81389.98774 84837.57233 85303.79008 84554.53932 80596.70147 95342.81255 74447.71646 81984.99498 106694.2678 0.762833743 0.795146488 0.799516148 0.79249374 0.755398609 0.893607637 0.697766787 0.768410493 1 16.70312314 -0.994756811 4.683268652 1.000003872 0.781635133 0.661205318 0.048772347 1.98E-06 4.26E-07 0.042960223 0.010125623 0.101214606 0.994756811 -0.218368739 TLEQHDNIVTHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLEQHDNIVTHYK 13 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 183.58 5.92E-06 1087330000 1202950 1074530 1065810 1295260 1039930 1150760 1362840 1288880 279177 FALSE TRUE 1146088.938 1184025.829 1114678.443 1165058.004 1221293.463 1110908.893 1154913.728 1176018.834 322470.3433 3.554090977 3.671735566 3.456685137 3.612915197 3.787304749 3.444995534 3.581457184 3.646905394 1 18.29880696 -1.035548614 5.154773394 0.999972307 3.593602756 0.985282431 0.099654167 2.91E-05 5.44E-06 0.08847882 0.020854438 0.092140674 1.035548614 2.593630449 TLETVPLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLETVPLER 9 0 P22626;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 169.09 0.00013663 163800000 259290 203800 201550 259540 238960 209690 265530 252520 250660 FALSE TRUE 247033.8756 224567.4517 210791.2669 233450.5461 280634.5483 202428.3827 225018.5217 230408.0101 289531.0726 0.8532206 0.775624701 0.728043678 0.806305672 0.969272644 0.69915944 0.777182634 0.795797177 1 18.14335866 -1.246375288 5.271170971 1.000021478 0.798401463 0.423660204 0.073059773 1.75E-05 2.50E-06 0.06704285 0.015800469 0.056705438 1.246375288 -0.201620015 TLGDFAAEYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLGDFAAEYAK 11 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 93.477 0.00883 0 82296 66199 80879 85963 83265 74294 89174 89380 89978 FALSE TRUE 78406.03117 72944.75336 84587.38215 77321.83592 97786.38964 71721.18015 75568.86851 81553.41337 103931.3287 0.754402278 0.701855295 0.813877617 0.743970436 0.940875007 0.690082394 0.727103843 0.784685565 1 16.66527108 TLGEDDPWLDDTAAWIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLGEDDPWLDDTAAWIER 18 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 143.86 2.38E-07 17843500 48680 47047 41648 47054 44126 43931 49174 51701 47569 FALSE TRUE 46378.99287 51841.14279 43557.602 42324.04252 51821.56043 42409.65845 41671.60316 47173.78636 54945.75757 0.844086876 0.943496733 0.792738219 0.770287724 0.943140339 0.771845914 0.758413479 0.858551933 1 15.74572047 3.729498874 24.75323519 0.82508321 0.893791806 0.033007513 0.082947436 1092.01671 2982976.583 0.020330648 0.032018114 5364.124805 -3.729498874 0.068708596 TLGLGEEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLGLGEEWR 9 0 O60568;H7C2A8;C9JU11 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 107.69 0.0063561 146580000 100530 75659 81715 97005 98317 80031 101710 94328 100770 FALSE TRUE 95778.14613 83368.73812 85461.71358 87253.8731 115463.4537 77259.5064 86192.27147 86068.14026 116396.8969 0.822858243 0.716245367 0.734226735 0.749623705 0.991980514 0.663759159 0.740503173 0.739436725 1 16.82869307 -1.338814229 3.024486414 1.002334972 0.766474473 0.402287489 0.088087657 11030886.69 13922357.89 228968.6159 0.020079959 0.04583379 1.338814229 -0.235860499 TLGTMIAGDTSGDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TLGTMIAGDTSGDYRR 16 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;;;;; 289.22 2.80E-45 2881920000 1905813 1742261 1688718 2045131 1898112 1870522 2006977 1948299 1838121 FALSE TRUE 1815728.996 1919799.377 1766147.391 1839550.546 2229142.132 1805745.354 1700775.798 1777695.611 2123167.417 0.85519822 0.904214788 0.831845561 0.866418037 1.049913499 0.850495981 0.801055906 0.837284708 1 21.01778671 -0.32188622 8.217029306 1 0.873302154 0.252938961 0.067723169 0 0 0.065423962 0.015420576 0.476555823 0.32188622 -0.126697846 TLHCEGTEINS(ph)DDEQESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLHCEGTEINSDDEQESK 18 0 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK 340.41 1.45E-75 1476560000 1233020 1502620 1123770 1518160 742500 1402970 1242990 1544270 616211 TRUE FALSE 1174737.588 1655738.686 1175295.966 1365551.672 871991.7649 1354384.797 1053349.046 1409045.532 711769.8547 1.650445829 2.326227608 1.651230322 1.918529794 1.225103535 1.902840909 1.479901178 1.979636427 1 19.44105131 3.184388639 1.986977063 1.579515093 1.968674506 0.180009729 0.347448529 0.485605061 3.940290828 0.099514861 0.132400779 1528.93365 -3.184388639 0.389159413 TLHCEGTEINS(ph)DDEQESKEVEETATAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TLHCEGTEINSDDEQESKEVEETATAK 27 1 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 T(0.001)LHCEGT(0.003)EINS(0.993)DDEQES(0.003)KEVEETATAK;TLHCEGTEINS(1)DDEQESKEVEETATAK;TLHCEGT(0.004)EINS(0.996)DDEQESKEVEETATAK;TLHCEGT(0.031)EINS(0.969)DDEQESKEVEETATAK;TLHCEGT(0.002)EINS(0.928)DDEQES(0.07)KEVEETATAK 225.57 9.88E-35 1687397000 642589 548084 616777 684681 341709 703962 787954 751823 340125 TRUE FALSE 612215.0915 603934.3827 645056.8355 615855.5651 401302.9414 679583.6194 667737.1455 685989.3925 392869.8479 1.558315291 1.537237805 1.641909755 1.567581652 1.021465362 1.729793271 1.699639586 1.746098348 1 18.58369192 TLHEWCDGCEAVLLGIEQQVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLHEWCDGCEAVLLGIEQQVLR 22 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2;J3QT95;J3KQ41;Q9H9Q2-3 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 164.35 1.41E-11 42603000 72863 61680 67271 75554 77986 65026 84479 73636 75341 FALSE TRUE 69418.91039 67965.26212 70355.44189 67959.16838 91586.73371 62774.13332 71590.17699 67188.04147 87024.49749 0.797693895 0.780989998 0.808455595 0.780919975 1.052424735 0.721338647 0.822643957 0.772058942 1 16.40913396 -2.560575251 2.211722176 4.219611515 0.814676476 0.29874744 0.088013453 3018561.249 250464.7206 49439065.41 0.019569377 0.002750583 2.560575251 -3.404935039 TLHEWLQQHGIPGLQGVDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLHEWLQQHGIPGLQGVDTR 20 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 183.54 2.51E-17 316680000 173752 147948 169234 208841 176831 170275 210828 188459 122255 FALSE TRUE 165539.0873 163024.0694 176993.5463 187847.9059 207670.2704 164378.3341 178662.3165 171956.5309 141213.681 1.172259558 1.154449542 1.25337393 1.330238717 1.470610134 1.164039723 1.26519127 1.217704472 1 17.10752034 0.766282153 3.661867567 1.000000658 1.247951723 0.424822958 0.093219075 2.568204238 39.05854683 0.094096915 0.024185174 5.838242806 -0.766282153 0.247951064 TLHGQETYTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLHGQETYTPR 11 0 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-4 Q9BUK6-2 MSTO1 Protein misato homolog 1 0 108.56 0.0020461 103000000 93218 82696 84688 83107 78724 80159 99636 75247 82145 FALSE TRUE 88811.76988 91122.81642 88571.02857 74752.92647 92453.44068 77383.07373 84434.69826 68657.97377 94883.62706 0.936007324 0.960363966 0.933470097 0.787837995 0.974387716 0.815557711 0.889876377 0.72360191 1 16.53387154 3.448593709 24.01477478 0.863229459 0.947974231 0.171380818 0.081323381 193.0517818 162511.9727 0.019740254 0.026729046 2809.27147 -3.448593709 0.084744772 TLHPDLGTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLHPDLGTDK 10 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 162.36 6.79E-06 2837590000 7012700 8197200 5194160 7282900 3982830 6364100 6293200 6944200 3554260 FALSE TRUE 6681223.569 9032503.999 5432317.374 6550809.055 4677434.291 6143709.621 5333056.757 6336129.034 4105436.488 1.627408824 2.20013244 1.323200929 1.595642528 1.139326916 1.496481468 1.299023081 1.543350884 1 21.96910419 3.721749442 24.94131021 1.362243308 1.913770631 0.525653799 0.225026989 488.8084461 725203.6246 0.053353779 0.082897509 5269.257742 -3.721749442 0.551527323 TLHPDLGTDKDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLHPDLGTDKDK 12 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 208.95 3.66E-08 3398010000 9369120 10827930 7590030 11531080 4122870 10039090 8358610 10446970 3438060 FALSE TRUE 8926260.265 11931308.38 7938040.383 10371953.93 4841897.223 9691433.796 7083350.528 9532177.924 3971216.786 2.247739357 3.004446501 1.998893743 2.611782356 1.219247773 2.440419226 1.78367259 2.400316688 1 21.92114969 3.101919967 1.850154834 1.88105178 2.570189864 0.239609548 0.535941279 0.442314302 3.101159064 0.15872817 0.200917865 1264.503299 -3.101919967 0.689138084 TLHPDLGTDKDKEQWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 236.81 5.44E-20 3377980000 3656430 3275360 3249850 3671040 1498760 3870930 3561050 3952680 1212570 FALSE TRUE 3483597.8 3609122.908 3398858.837 3302020.085 1760143.269 3736878.723 3017746.419 3606562.385 1400609.163 2.487201921 2.576823716 2.426700416 2.357559962 1.256698383 2.668038182 2.154595657 2.574995567 1 20.417623 2.986033913 24.64012034 2.048289426 2.497582222 0.192019858 0.517445348 987.8643603 1742875.387 0.14119698 0.155502099 968.3534704 -2.986033913 0.449292796 TLHS(ph)PPLQLQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 T(0.005)LHS(0.995)PPLQLQQR;T(0.001)LHS(0.999)PPLQLQQR;TLHS(1)PPLQLQQR 132.65 0.00011417 1404760000 364370 390185 403004 489520 367171 403141 396330 412700 328957 TRUE FALSE 347146.9522 429945.2951 421482.132 440312.5196 431205.5061 389180.1261 335862.5794 376561.8001 379969.9715 0.913616807 1.131524403 1.109251161 1.158808729 1.13484101 1.024239164 0.883918743 0.991030419 1 18.53552588 1.984888789 7.694603144 0.947260281 1.083173696 0.395493579 0.073689597 0.171696074 58.92016157 0.031218751 0.02084594 96.58035304 -1.984888789 0.135913415 TLHSCSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLHSCSVR 8 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 79.906 0.026824 127490000 128700 100050 74388 77663 110520 86210 135430 103640 105170 FALSE TRUE 122616.6061 110245.2087 77798.76338 69856.16769 129794.653 83224.52608 114767.6662 94564.73217 121479.2265 1.00936275 0.907523138 0.640428538 0.575046201 1.068451428 0.685092657 0.944751374 0.778443648 1 16.8903501 -0.339615337 8.58197342 0.999999996 0.840056596 0.097550655 0.161325534 0 0 0.150615637 0.035500446 0.457493221 0.339615337 -0.159943399 TLHSDDEGTVLDDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLHSDDEGTVLDDSR 15 0 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ; 225.32 1.02E-12 692780000 283258 248572 297648 297665 313535 296146 326669 288729 266922 FALSE TRUE 269868.9557 273901.7694 311295.4552 267743.1487 368215.4047 285890.3898 276829.6444 263446.3581 308314.9005 0.875302995 0.888383172 1.009667242 0.868408073 1.19428352 0.927267509 0.897879551 0.854471703 1 18.23404509 3.861583569 7.220165577 0.959681353 0.880337618 0.111966763 0.096304876 0.548590476 29.95858871 0.02396149 0.04347194 7270.822939 -3.861583569 -0.079343735 TLIGHVPDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLIGHVPDQR 10 0 Q16822;Q16822-3;H0YML5;H0YM31;Q16822-2;H0YNG4;H0YMA5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 67.726 0.062111 113290000 52624 39925 46207 46267 49052 37257 46716 44122 58349 FALSE TRUE 50136.56781 43993.40289 48325.63665 41616.15326 57606.65327 35966.78075 39588.6162 40258.44377 67397.46491 0.743893971 0.652745663 0.717024546 0.61747357 0.854730268 0.533651834 0.587390286 0.597328755 1 16.04040671 -0.934754688 8.749163148 0.999996528 0.661581209 0.573078985 0.091395393 6.38E-10 3.34E-26 0.085689635 0.020197241 0.116210485 0.934754688 -0.33841532 TLIPS(ph)PPPRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLIPSPPPRPK 11 1 J3KSG3;J3KSS7;Q9NZ52-3;Q9NZ52-4;Q9NZ52-2;Q9NZ52 J3KSG3 GGA3 ADP-ribosylation factor-binding protein GGA3 1 T(0.002)LIPS(0.998)PPPRPK;TLIPS(1)PPPRPK;TLIPS(1)PPPRPK 96.464 0.0042349 452410000 1456710 1180460 1225630 1467760 1072360 1340950 1538830 1450460 1161100 TRUE FALSE 1387854.205 1300750.216 1281826.348 1320217.976 1259379.244 1294512.565 1304053.221 1323450.033 1341157.458 1.034818244 0.969871366 0.955761264 0.984387007 0.939024152 0.96522042 0.972334168 0.986796908 1 20.3550472 4.524390563 2.283996911 0.969115062 1.038105425 0.568779744 0.017097876 0.240945054 2.039417686 0.003957079 0.027839083 33449.57181 -4.524390563 0.068990364 TLLEEEYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLLEEEYFR 9 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ;;; 182.53 0.00010752 136104000 163083 146162 138045 167419 165508 132061 181056 164847 189991 FALSE TRUE 155374.3898 161056.074 144374.4998 150589.724 194372.5428 127487.6945 153432.5819 150412.1228 219453.8339 0.7080049 0.733895011 0.657880964 0.686202293 0.885710399 0.580931726 0.699156534 0.685393005 1 17.74355795 -0.891782455 4.48747154 1.000002879 0.704952831 0.599111718 0.075927615 6374046.961 4261228.425 172.6452891 0.016196326 0.128297308 0.891782455 -0.295050048 TLLEFLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLLEFLKR 8 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 110.87 0.0053593 85740000 129470 90582 75886 80014 115490 85960 148580 121360 123620 FALSE TRUE 123350.2097 99812.40878 79365.44816 71970.8407 135631.4194 82983.18365 125911.3921 110733.075 142790.3582 0.863855314 0.699013645 0.555817978 0.504031516 0.94986399 0.581153971 0.881791976 0.775494063 1 17.12353904 0.975228918 0.815566128 0.994334765 0.700538017 0.303059488 0.14252805 0.880607721 1.291302081 0.130959532 0.047482699 9.445586252 -0.975228918 -0.293796749 TLLEGSGLESIISIIHSSLAEPR ddPTM_SK-BR-3_Trastuzumab_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 ; 264.66 5.73E-44 2073250000 284190 226752 243197 236710 561800 255843 474790 366010 705690 FALSE TRUE 270756.9019 249858.2866 254347.823 212915.4611 659777.7421 246983.0928 402352.0654 333960.2241 815124.801 0.332166193 0.306527646 0.312035436 0.261205966 0.809419295 0.303000341 0.49360793 0.409704408 1 19.63666144 -4.999999999 0.179454773 3.474308032 0.267922086 0.613665874 0.152595751 84.18412769 0.80962183 74.15992535 0.438680734 1.00E-05 4.999999999 -3.206385946 TLLEQLDDDQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLLEQLDDDQ 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 141.95 8.52E-05 16491000 36690 33919 38733 36738 35475 34449 41682 39865 43470 FALSE TRUE 34955.73641 37375.38466 40508.94636 33045.02644 41661.82877 33256.02249 35322.64536 36374.20926 50211.10559 0.696175398 0.744364901 0.806772643 0.658121865 0.829733348 0.662324044 0.703482724 0.72442558 1 15.61571887 -1.397064657 2.816036529 1.005482957 0.726346323 0.703484539 0.055449764 5065566.388 5776244.954 224196.2732 0.012005695 0.040080704 1.397064657 -0.279136635 TLLISSLS(ph)PALPAEHLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 T(0.009)LLIS(0.134)S(0.134)LS(0.723)PALPAEHLEDR;T(0.002)LLIS(0.034)S(0.034)LS(0.93)PALPAEHLEDR 95.122 0.00095776 59964000 32277 30641 31829 35806 39096 33426 42796 34618 43431 TRUE FALSE 30751.33018 33763.35274 33288.39113 32206.71285 45914.33002 32268.44924 36266.6842 31586.6644 50166.05767 0.612990767 0.673031813 0.663564025 0.64200207 0.915246925 0.64323271 0.722932714 0.62964215 1 15.61442395 -5 0.248566335 2.854884111 0.658489641 0.553577507 0.08724576 132.6041586 1.315376308 125.1234117 0.118750657 1.00E-05 5 -2.19639447 TLLIVSHDQGFLDDVCTDIIHLDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TLLIVSHDQGFLDDVCTDIIHLDAQR 26 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;;;;; 320.78 2.01E-82 548656600 357404.6 387427 354840.3 402366.6 295846.4 340800.2 352739.4 375310.1 174132.4 FALSE TRUE 340510.7929 426906.2518 371110.0787 361919.9449 347441.9185 328998.2036 298922.526 342445.958 201135.9632 1.692938385 2.122475985 1.845070731 1.799379579 1.727398288 1.63570054 1.486171449 1.702559565 1 17.61781153 0.520307815 0.312645168 0.858149741 1.961779612 0.778694167 0.134969712 1.321877572 0.277981928 0.459261235 0.163029808 3.313659002 -0.520307815 1.103629871 TLLPWDS(ph)DESPEASPGPPGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLLPWDSDESPEASPGPPGPR 21 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 TLLPWDS(1)DESPEASPGPPGPR 221.79 4.38E-25 11267000 7503.7 7013.1 9233.3 5779.3 4990.8 6394.4 7249.4 6672.1 11481 TRUE FALSE 7149.014972 7727.742863 9656.655938 5198.353784 5861.19394 6172.960325 6143.370886 6087.855553 13261.41484 0.53908388 0.582723861 0.728176899 0.391990888 0.441973501 0.465482786 0.463251543 0.459065313 1 13.69494708 -1.078331498 4.55052095 1.000029428 0.512779991 0.730168893 0.093783909 1.258658937 58283508.86 3854.572964 0.02249254 0.083496544 1.078331498 -0.487249436 TLLSESSSQSSKS(ph)PSLSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TLLSESSSQSS(0.042)KS(0.957)PSLSSK;TLLSESSSQSS(0.008)KS(0.887)PS(0.105)LSSK;TLLSES(0.001)S(0.001)SQS(0.034)S(0.117)KS(0.838)PS(0.008)LS(0.001)SK;TLLSESSSQSS(0.053)KS(0.865)PS(0.082)LSSK 260.03 2.61E-31 1606760000 1460120 1279950 1507600 1702160 991030 1622600 1844600 1884550 1236310 TRUE FALSE 1391103.021 1410378.36 1576724.951 1531055.643 1163865.318 1566408.955 1563172.392 1719528.811 1428030.641 0.974140877 0.987638724 1.104125434 1.072144812 0.815014248 1.096901502 1.09463505 1.204125992 1 20.4455955 2.041144421 24.99998943 1.106519373 0.994107311 0.265047465 0.089270707 185.6755174 112818.5365 0.031601955 0.023339562 109.9371366 -2.041144421 -0.112412063 TLLTGDGGGEATGS(ph)PLAQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLLTGDGGGEATGSPLAQGK 20 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 TLLTGDGGGEATGS(1)PLAQGK;TLLTGDGGGEATGS(1)PLAQGK 254.54 4.12E-36 156075000 276320 241230 230150 286570 193173 288100 290300 270180 207805 TRUE FALSE 263258.9012 265811.6113 240702.6051 257763.4392 226862.31 278123.0248 246009.4033 246521.6069 240030.3381 1.096773447 1.107408394 1.002800759 1.073878582 0.945140151 1.158699467 1.024909623 1.027043535 1 17.87285724 7.999999913 0.29857186 1.029049761 1.752144636 0.13082922 0.057913461 96.06114934 1.371313859 0.053915971 37.03723245 99999980.01 -7.999999913 0.723094874 TLLWTELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLLWTELFR 9 0 O00217;E9PPW7;E9PN51;F8W9K7;E9PKH6 O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" 0 ; 197.3 6.57E-05 91772000 200866 136167 89981 87628 227070 71964 195449 126436 177254 FALSE TRUE 191371.4623 150042.5721 94106.71785 78819.46696 266670.9361 69471.86864 165629.6654 115364.5936 204741.645 0.934697297 0.732838559 0.459636425 0.384970371 1.302475303 0.339314792 0.808969105 0.563464231 1 17.64344505 4.34860486 2.763260589 0.680341383 0.91727492 0.058031006 0.293148601 0.716020638 10.33700555 0.066906152 0.255058518 22315.40944 -4.34860486 0.236933536 TLMELLNQMDGFDTLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLMELLNQMDGFDTLHR 17 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 300 2.55E-46 839560000 964360 884950 882040 999530 968320 788210 1084940 971480 922540 FALSE TRUE 918776.614 975127.4111 922482.4065 899055.3454 1137194.701 760914.0901 919412.4767 886412.0611 1065602.792 0.862213032 0.915094648 0.865690681 0.843705884 1.067184424 0.71406916 0.862809749 0.831840971 1 20.02323834 TLMLPLTEGS(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLMLPLTEGSLR 12 0 Q7L4E1;Q7L4E1-3 Q7L4E1 FAM73B Protein FAM73B 1 TLMLPLTEGS(1)LR;TLMLPLT(0.001)EGS(0.999)LR;TLMLPLTEGS(1)LR;TLMLPLT(0.001)EGS(0.999)LR 138.02 8.59E-05 103898000 223395 182318 197801 261528 256595 181012 255370 215599 277161 TRUE FALSE 212835.5611 200896.4115 206870.3715 235238.7086 301345.0868 174743.5091 216408.6163 196720.0086 320141.7123 0.664816714 0.627523386 0.646183748 0.734795559 0.941286546 0.545831744 0.675977569 0.614477905 1 18.28835114 -1.957617659 2.403891934 1.254922922 0.677662233 0.479604695 0.1042466 17427472.15 7924046.597 24788473.88 0.024030155 0.011025095 1.957617659 -0.577260689 TLNAET(ph)PKS(ph)SPLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 T(0.239)LNAET(0.761)PKS(0.512)S(0.488)PLPAK 111.95 0.0018377 284260000 823150 651990 741690 850260 384710 818420 823860 904590 456130 TRUE FALSE 784241.3308 718428.5223 775697.2201 764790.2494 451803.3022 790077.9102 698165.0258 825379.3041 526864.3108 1.48850722 1.363593068 1.472290311 1.451588642 0.857532562 1.499585176 1.325132508 1.566587995 1 19.00707193 -1.808764425 2.720326564 0.887029269 1.374607407 0.265739945 0.197442735 16733109.2 11885809.43 12428688.07 0.044819812 0.015532293 1.808764425 0.487578138 TLNAET(ph)PKSS(ph)PLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 T(0.043)LNAET(0.957)PKS(0.255)S(0.745)PLPAK;T(0.032)LNAET(0.967)PKS(0.185)S(0.815)PLPAK 104.86 0.0031181 595170000 1038060 923750 971940 1101470 551340 1136240 1117080 1270530 664130 TRUE FALSE 988992.961 1017881.175 1016504.41 990748.1429 647493.5214 1096891.724 946648.9294 1159275.658 767119.8885 1.28922868 1.326886697 1.325091978 1.291516695 0.844057795 1.429883047 1.234029965 1.511205321 1 19.54909254 2.978931519 24.98059415 1.221150146 1.312459334 0.06724737 0.188526669 2521.31978 2989496.903 0.053527041 0.057336847 952.6459366 -2.978931519 0.091309188 TLNAETPKSS(ph)PLPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.254)S(0.746)PLPAK;TLNAETPKS(0.053)S(0.947)PLPAK;TLNAETPKS(0.111)S(0.888)PLPAK;TLNAETPKS(0.008)S(0.992)PLPAK 199.97 4.33E-09 2883490000 2938660 2199970 2570490 3070180 1627660 3100290 3447990 3065140 1924670 TRUE FALSE 2799755.366 2424149.444 2688349.509 2761559.673 1911523.389 2992926.18 2921935.799 2796740.092 2223137.994 1.259370931 1.090417892 1.209258947 1.24218995 0.859831191 1.34626199 1.314329478 1.258014617 1 21.08416607 TLNDELEIIEGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLNDELEIIEGMK 13 0 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 192.86 5.48E-06 57774000 203559 191765 162351 190202 116320 159134 164312 193560 123889 FALSE TRUE 193937.1695 211306.0715 169794.9539 171082.5336 136606.1712 153623.1497 139243.1866 176610.8603 143101.0734 1.355246085 1.47662115 1.186538647 1.195536341 0.954613183 1.073528982 0.973040826 1.234168662 1 17.12667497 3.389750693 1.731476765 1.046393582 1.416464045 0.69322593 0.093421043 0.159269593 0.974302718 0.026756534 0.042717804 2453.300193 -3.389750693 0.370070464 TLNDELEIIEGMKFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 17 TLNDELEIIEGMKFDR 16 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;;;;;;;;;;;;;; 300.87 5.91E-46 3375664300 5394936.6 2770507.2 4804463.7 3767260.7 4196757.1 3951157.6 5864633 5190658.9 5089372.7 FALSE TRUE 5139928.639 3052825.033 5024753.113 3388568.497 4928670.209 3814328.022 4969875.524 4736137.289 5878606.625 0.874344716 0.519310991 0.854752399 0.576423754 0.838407896 0.648848999 0.845417263 0.805656441 1 22.48704281 0.920214023 0.75607204 0.999193703 0.706275919 0.338581267 0.120470415 0.787668216 0.987859475 0.103378354 0.038533404 8.321737705 -0.920214023 -0.292917784 TLNMTT(ph)SPEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.004)T(0.498)S(0.498)PEEK;TLNMT(0.003)T(0.692)S(0.305)PEEK;TLNMT(0.02)T(0.759)S(0.22)PEEK;TLNMT(0.104)T(0.448)S(0.448)PEEK;TLNMT(0.182)T(0.409)S(0.409)PEEK;TLNMT(0.018)T(0.491)S(0.491)PEEK 246.47 5.66E-15 1220236000 4423840 3860860 4027530 4719310 2780640 4667310 4793180 4919930 3101220 TRUE FALSE 4214733.85 4254286.023 4212196.234 4244915.993 3265582.736 4505679.884 4061892.358 4489114.847 3582141.359 1.176596183 1.187637672 1.175887776 1.185021909 0.911628662 1.257817443 1.13392855 1.253193104 1 21.77239084 -1.850494091 2.734967292 0.93769611 1.159870144 0.216558016 0.095765699 34217445.19 27818194.91 14025032.18 0.020965104 0.014109314 1.850494091 0.222174034 TLNMTTS(ph)PEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.002)T(0.244)S(0.753)PEEK;TLNMTT(0.028)S(0.972)PEEK;TLNMT(0.004)T(0.185)S(0.811)PEEK;TLNMTT(0.245)S(0.755)PEEK;TLNMT(0.038)T(0.235)S(0.727)PEEK 297.72 1.20E-35 1323434000 4176090 3711670 3881160 4560750 2703180 4433770 4629530 4730400 2989260 TRUE FALSE 3978694.502 4089893.393 4059115.025 4102294.745 3174613.736 4280227.433 3923210.171 4316181.099 3452819.174 1.152303177 1.184508423 1.175594441 1.188100082 0.919426583 1.239632665 1.136233893 1.250045508 1 21.71934335 -2.404732713 2.000715921 3.35E-05 1.15496725 0.224520425 0.090946583 913917.1798 104737.7717 4132859.451 0.020083162 0.003937924 2.404732713 1.154933789 TLNPS(ph)PAGWFVQQHPELELMSSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLNPSPAGWFVQQHPELELMSSFR 24 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 TLNPS(1)PAGWFVQQHPELELMSSFR;T(0.001)LNPS(0.999)PAGWFVQQHPELELMSSFR 190.15 8.05E-18 202454000 126621 137697 123026 127837 115796 131225 151913 130851 129346 TRUE FALSE 120635.8763 151728.4808 128666.8638 114986.5819 135990.7857 126680.6453 128735.8818 119392.9928 149404.3171 0.807445719 1.015556202 0.861199103 0.769633597 0.910219921 0.847904852 0.861661057 0.799126793 1 17.18886231 -1.059329571 4.813555024 1.000003915 0.867968453 0.287737132 0.068416539 2.82E-06 5.52E-07 0.065084276 0.015340056 0.087230915 1.059329571 -0.132035461 TLPAHSDPVSAVHFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLPAHSDPVSAVHFNR 16 0 P61964 P61964 WDR5 WD repeat-containing protein 5 0 ; 85.493 0.0041232 161687000 132165 166505 179851 149047 460883 103442 227853 133308 332850 FALSE TRUE 125917.8224 183472.0488 188097.3462 134064.5124 541260.8493 99859.7776 193089.84 121634.8448 384466.678 0.327512967 0.477211835 0.489242259 0.348702554 1.407822525 0.259735845 0.502227764 0.316372918 1 18.55249904 TLPFYKDYFNVPYPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLPFYKDYFNVPYPLPK 17 1 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 71.558 0.027596 79183000 169320 186200 196160 193530 160040 183020 250580 188340 195500 FALSE TRUE 161316.5792 205173.9917 205154.13 174075.9967 187950.9253 176681.9715 212349.4188 171847.9511 225817.1415 0.714368174 0.908584664 0.90849671 0.770871492 0.832314695 0.782411691 0.940360051 0.7610049 1 17.78479548 -5 0.240556054 1.940746088 0.817728663 0.335503842 0.074347904 203.8225171 2.031562994 93.94252139 0.109864995 1.00E-05 5 -1.123017426 TLPLTGSTFHDQIAMLSHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLPLTGSTFHDQIAMLSHR 19 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 277.6 9.46E-40 546940000 651870 525640 640350 665560 721100 617860 804230 675380 383080 FALSE TRUE 621057.397 579203.3136 669710.6809 598656.6443 846859.6117 596463.3533 681529.9428 616240.1468 442486.0899 1.403563663 1.30897519 1.513518043 1.352938901 1.913867195 1.347982156 1.540229079 1.392676879 1 18.75527258 0.918673192 8.791451503 1.000000174 1.468361446 0.436054236 0.170976459 3.743178423 404.9384648 0.155183169 0.038838383 8.292265372 -0.918673192 0.468361272 TLPLTTAPEAGEVTPSDSGGQEDS(ph)PAKGLSVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLPLTTAPEAGEVTPSDSGGQEDSPAKGLSVR 32 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TLPLTTAPEAGEVTPSDSGGQEDS(0.999)PAKGLS(0.001)VR 169.13 2.14E-14 196160000 44579 26908 44887 39259 41163 43145 52319 45769 55493 TRUE FALSE 42471.83902 29649.95579 46945.11335 35312.61073 48341.81417 41650.87783 44336.77565 41761.22372 64098.57102 0.662601964 0.462568125 0.73238939 0.550911045 0.75417928 0.649794171 0.691696787 0.651515674 1 15.96800457 -5 0.17432765 2.471749746 0.55176341 0.653255926 0.082487976 72.81203546 0.693266426 36.96014267 0.251070243 1.00E-05 5 -1.919986336 TLPQQES(ph)LEIELAEEKPVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;TLPQQES(1)LEIELAEEKPVKR 241.29 5.09E-30 2149249000 2907920 1975680 2241220 3555060 2233390 3507760 3871900 2601060 2182320 TRUE FALSE 2770468.385 2177004.038 2343982.154 3197698.615 2622892.509 3386285.392 3281170.543 2373297.397 2520743.04 1.099068148 0.863635842 0.929877467 1.26855398 1.040523555 1.343367943 1.301667997 0.941507071 1 21.26541763 3.247420525 24.99988815 1.181663962 0.961913402 0.248393346 0.144604064 208.7738359 589091.066 0.038512995 0.051382248 1767.748694 -3.247420525 -0.219750559 TLPS(ph)GSPRPGQLERPTSLALDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.099)LPS(0.45)GS(0.45)PRPGQLERPT(0.001)S(0.001)LALDSR 43.936 0.094686 95475000 75400 75075 75306 82437 82519 81168 87322 92054 85029 TRUE FALSE 71835.99143 82725.22785 78758.85459 74150.27614 96910.28747 78357.13181 73999.42512 83993.26375 98214.86305 0.731416704 0.842288278 0.801903624 0.754980192 0.986717127 0.797813379 0.753444263 0.855199113 1 16.58365375 -5 0.282173379 2.397027798 0.7984334 0.406496503 0.071238865 236.5503053 2.256874033 193.8853213 0.077300671 1.00E-05 5 -1.598594398 TLPSGS(ph)PRPGQLERPTSLALDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.05)LPS(0.228)GS(0.723)PRPGQLERPTSLALDSR;T(0.001)LPS(0.029)GS(0.97)PRPGQLERPTSLALDSR 85.489 0.0036993 933450000 642490 593080 604910 687710 675120 629560 709650 686000 674210 TRUE FALSE 612120.771 653515.5263 632645.7218 618580.0842 792860.7142 607758.1793 601379.8589 625930.2033 778763.0434 0.786016717 0.839171211 0.812372553 0.794311042 1.018102645 0.780414767 0.772224445 0.803749239 1 19.5708249 -2.139010577 2.309486647 1.370356353 0.823183455 0.372320352 0.071012228 6007644.954 1321600.156 11679155.83 0.016514574 0.007260883 2.139010577 -0.547172898 TLQALEFHTVPFQLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLQALEFHTVPFQLLAR 17 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 252.3 5.53E-27 1303920000 2948000 2459600 1193010 1373550 2684600 1354700 2667900 1449600 1335790 FALSE TRUE 2808653.882 2710236.036 1247710.689 1235478.144 3152793.39 1307786.399 2260862.856 1322665.339 1542937.491 1.820329015 1.756542992 0.808659259 0.800731171 2.043370784 0.847595192 1.465297764 0.857238447 1 20.55724818 3.817685844 8.389962862 1.163726892 1.792320295 0.33761424 0.386574332 0.360455181 35.27836491 0.091893938 0.166076738 6571.822785 -3.817685844 0.628593403 TLQEVTEMDSVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLQEVTEMDSVKR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 92.939 0.0061315 2773490000 780266 628452 661015 744971 631170 766531 889056 822795 709211 FALSE TRUE 743384.3725 692491.9733 691323.1916 670085.0997 741245.8482 739985.8393 753414.1786 750746.7079 819191.8197 0.907460688 0.845335557 0.843908807 0.817983143 0.904850159 0.903312047 0.919704226 0.916448004 1 19.64384178 1.183966587 0.640072904 0.996750968 0.859872157 0.706777512 0.027624994 0.408197449 0.404511484 0.027984118 0.012308848 15.27448536 -1.183966587 -0.13687881 TLQRLS(ph)SGFDDIDLPSAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 TLQRLS(0.964)S(0.036)GFDDIDLPSAVK;TLQRLS(0.816)S(0.184)GFDDIDLPSAVK;TLQRLS(0.889)S(0.11)GFDDIDLPSAVK;TLQRLS(0.637)S(0.363)GFDDIDLPSAVK;TLQRLS(0.875)S(0.125)GFDDIDLPSAVK 259.56 2.73E-31 6485010000 10039710 7414550 9382830 9727890 8052220 9802590 12803590 10964700 9269850 TRUE FALSE 9565152.805 8170101.075 9813042.036 8750024.015 9456524.619 9463123.85 10850167.19 10004572.74 10707370.99 0.893324123 0.76303521 0.916475393 0.817196305 0.883178945 0.883795271 1.013336252 0.934363136 1 23.35210096 1.96176879 2.517181752 0.982949048 0.846018539 0.594772057 0.047684548 0.177577411 2.076274697 0.023722504 0.012741575 91.57328422 -1.96176879 -0.136930509 TLQTDSIDSFETQRT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR 276.69 1.49E-35 4350970000 5084360 5239580 5408550 5872960 5168480 5391030 6078840 5996760 6425630 TRUE FALSE 4844032.379 5773499.159 5656537.367 5282598.903 6069861.276 5204337.279 5151401.312 5471651.904 7422083.883 0.652651257 0.777881152 0.762122533 0.711740663 0.817810924 0.701196236 0.694064011 0.73721235 1 22.82339288 -1.504819662 2.331068363 1.018906201 0.730044741 0.765964276 0.046575173 749906.6144 639786.9905 89961.85114 0.011693362 0.031273777 1.504819662 -0.28886146 TLQVVPPSDPDPLLASWHGGTGT(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.027)GT(0.486)S(0.486)PPR 148.66 4.36E-07 70625000 102180 81239 92289 100830 112130 84862 125090 108350 123740 TRUE FALSE 97350.1539 89517.34646 96520.54194 90694.37684 131685.4365 81923.20766 106005.2231 98862.2996 142928.9672 0.681108636 0.626306537 0.67530427 0.634541609 0.921334835 0.573174278 0.741663675 0.691688337 1 17.12493881 -5 0.243641745 2.817904681 0.658471842 0.52568991 0.092080511 129.0235972 1.28392713 116.3998585 0.125593657 1.00E-05 5 -2.159432839 TLQVVPPSDPDPLLASWHGGTGTS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.026)GT(0.053)S(0.922)PPR 155.9 1.74E-08 81165000 110450 92480 95422 113940 125920 98623 141540 118350 121250 TRUE FALSE 105229.2474 101903.8171 99797.19309 102486.5347 147880.4081 95207.66078 119945.4734 107986.6466 140052.8307 0.751353949 0.727609836 0.712568197 0.731770534 1.055890176 0.67979819 0.856430197 0.771042228 1 17.09561162 -4.999999997 0.108982367 1.694334133 0.654772232 0.31587862 0.104268747 192.7921276 1.40038792 29.98785125 1.230803917 1.00E-05 4.999999997 -1.0395619 TLRDS(ph)PNVEAAHLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 T(0.026)LRDS(0.974)PNVEAAHLAR;T(0.001)LRDS(0.999)PNVEAAHLAR;T(0.294)LRDS(0.706)PNVEAAHLAR 220.82 9.80E-13 851930000 323547 298979 286006 362288 324777 294997 358493 322213 311643 TRUE FALSE 308253.5745 329445.3 299119.658 325870.1219 381418.006 284781.1799 303798.3087 293998.3216 359971.0048 0.8563289 0.915199546 0.830954866 0.905267695 1.059579802 0.791122552 0.843952165 0.816727785 1 18.45752118 -0.385544413 7.395349046 1 0.878000638 0.210048165 0.07471626 0 0 0.069419248 0.016362274 0.411581255 0.385544413 -0.121999362 TLREQDDELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLREQDDELRK 11 2 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 134.99 7.28E-05 348470000 280770 161600 308080 240840 222810 271530 365610 326960 291450 FALSE TRUE 267498.5585 178067.2237 322205.7727 216630.3056 261667.9935 262126.848 309829.4796 298329.6491 336646.5775 0.794597588 0.528944108 0.957103961 0.643494751 0.777278045 0.77864106 0.920340501 0.88618055 1 18.36087527 1.711282833 0.657857348 0.99829583 0.698898068 0.397368631 0.111215906 0.601453694 0.539239965 0.09605351 0.04928089 51.43785297 -1.711282833 -0.299397762 TLS(ph)ADASVNTLPVVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLSADASVNTLPVVVSR 17 0 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 1 T(0.001)LS(0.999)ADASVNTLPVVVSR;T(0.003)LS(0.997)ADASVNTLPVVVSR;T(0.005)LS(0.995)ADASVNTLPVVVSR 172.2 1.71E-09 193139000 247886 214796 212597 262917 224229 242356 288700 246612 206682 TRUE FALSE 236168.92 236683.9566 222344.7827 236488.0837 263334.4666 233963.151 244653.5127 225017.3459 238733.189 0.98925885 0.991416223 0.931352627 0.990595755 1.103049257 0.980019376 1.024798913 0.942547397 1 17.86503962 2.992288842 24.98044215 1.013845808 0.975674864 0.141555192 0.043324869 677.9301999 2196179.746 0.012012467 0.013789447 982.4011049 -2.992288842 -0.038170944 TLS(ph)DESIYNSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(0.998)DES(0.002)IYNSQR;TLS(1)DESIYNSQR;T(0.005)LS(0.993)DES(0.002)IYNSQR;TLS(0.998)DES(0.002)IYNSQR 364.99 2.42E-86 1559460000 1462777 1324440 1302696 1601581 1108634 1415336 1546285 1475266 1204216 TRUE FALSE 1393634.43 1459401.942 1362425.9 1440587.035 1301979.419 1366322.559 1310370.824 1346083.888 1390959.667 1.001922962 1.049205075 0.979486273 1.03567851 0.936029598 0.982287691 0.942062416 0.967737541 1 20.40764916 2.743794109 24.99862224 0.961829962 1.018323661 0.486538223 0.02581766 308.1960642 1472151.059 0.00715396 0.007385328 554.3628371 -2.743794109 0.056493699 TLS(ph)DESLCSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSDESLCSGR 11 0 O60292;M0R2Q7 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.001)LS(0.998)DES(0.001)LCSGR;TLS(1)DESLCSGR 215.72 0.00045377 320230000 437080 384070 387570 454540 335150 410210 455190 474350 349180 TRUE FALSE 416420.0946 423207.1697 405340.4679 408848.7756 393600.0539 396004.3248 385742.4054 432813.3993 403329.051 1.032457477 1.049285115 1.004987037 1.013685413 0.975878263 0.981839329 0.956396283 1.073102466 1 18.6215978 3.459018097 1.812666516 0.991561752 1.041012271 0.184947997 0.031559858 0.411143137 2.722861634 0.009190716 0.015333672 2877.518321 -3.459018097 0.04945052 TLS(ph)INEEEPEGGFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLSINEEEPEGGFSK 15 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.001)LS(0.999)INEEEPEGGFSK 164.53 3.53E-09 0 55997 46473 47426 71105 48142 56430 63223 47799 53460 TRUE FALSE 53350.13279 51208.65154 49600.52901 63957.39031 56537.94956 54475.81495 53577.17018 43613.46616 61750.30376 0.863965512 0.829285824 0.803243482 1.035742116 0.915589821 0.882195093 0.867642212 0.706287476 1 15.91415861 2.586993063 0.00907464 1.747299158 1.68E-06 0.053946963 0.091097507 10869.51701 43.36534673 4083.598477 4262.708425 386.3608055 -2.586993063 -1.74729748 TLS(ph)LVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSLVK 6 0 F8VRW9;F8W0R1;F8VR88;F8VUZ2;F8VPA6;A0A087WU02;Q96RQ1 F8VRW9 ERGIC2 Endoplasmic reticulum-Golgi intermediate compartment protein 2 1 TLS(1)LVK;TLS(1)LVK 94.114 0.047046 46732000 196665 187691 156671 205000 170864 194382 224340 199237 164457 TRUE FALSE 187369.0352 206816.9263 163854.5203 184393.0105 200662.6275 187650.5026 190112.8127 181790.7521 189960.1516 0.986359684 1.088738478 0.862573118 0.970693111 1.056340637 0.987841402 1.000803648 0.956994141 1 17.53533729 TLS(ph)MDKGF ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 133.23 0.0024424 1330780000 3549060 2330010 2974540 4604410 2353050 4979300 4794300 3042900 2483900 TRUE FALSE 3381302.967 2567440.668 3110925.601 4141565.959 2763421.175 4806865.592 4062841.482 2776447.545 2869090.526 1.178527808 0.894862203 1.084289803 1.443511775 0.96316974 1.675396976 1.416072949 0.967709983 1 21.45216206 3.393903477 7.262858985 1.290858548 1.029070476 0.105557327 0.241229909 0.341822132 25.17167591 0.063232267 0.085807019 2476.871506 -3.393903477 -0.261788072 TLS(ph)MIEEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLSMIEEEIR 10 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 TLS(1)MIEEEIR;TLS(1)MIEEEIR;T(0.102)LS(0.898)MIEEEIR 205.12 1.83E-07 57547300 103269 80379.1 95608 103111 153317 82189.5 108026 89587 145163 TRUE FALSE 98387.67903 88569.82167 99991.72137 92746.08638 180055.4363 79343.25701 91544.64967 81742.28735 167674.1367 0.5867791 0.5282259 0.596345527 0.553132929 1.073841439 0.473199138 0.545967622 0.487506833 1 17.35530065 -1.504222053 2.740111138 1.017524754 0.59975747 0.343467661 0.171184397 16944246.13 17614963.03 2226715.44 0.039363748 0.031316841 1.504222053 -0.417767284 TLS(ph)PGKNGVVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 T(0.003)LS(0.997)PGKNGVVK;T(0.002)LS(0.998)PGKNGVVK 97.69 0.0036814 622120000 1628450 1025380 1475890 1974410 1195750 1465910 1889160 1535810 1027790 TRUE FALSE 1551476.396 1129867.388 1543561.016 1775938.556 1404288.421 1415145.169 1600933.945 1401326.335 1187174.424 1.306864741 0.951728209 1.30019733 1.495937345 1.182882981 1.192028013 1.348524625 1.180387908 1 20.17910049 5.11238668 13.45741204 1.218586982 4.180090601 0.033745118 0.157374451 311581.9958 490346.7251 0.037191333 27376078.27 129534.8661 -5.11238668 2.961503619 TLS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSPGR 6 0 Q13523 Q13523;REV__F5H6U2 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.001)LS(0.999)PGR;T(0.001)LS(0.999)PGR 122.74 0.020023 783830000 891940 853490 795710 985840 835500 809460 993210 875720 891800 TRUE FALSE 849779.7639 940461.6013 832194.0906 886741.4902 981210.9355 781428.1972 841677.5729 799037.3143 1030095.789 0.824952177 0.912984609 0.807880295 0.860834011 0.95254339 0.758597604 0.817086704 0.775692244 1 19.97434707 2.222486389 24.99871073 0.819724695 0.869779841 0.022822555 0.076608022 566.8002258 881484.4854 0.025415332 0.018830377 166.9115494 -2.222486389 0.050055146 TLS(ph)PGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TLSPGRR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.001)LS(0.999)PGRR;T(0.003)LS(0.997)PGRR;T(0.002)LS(0.998)PGRR;T(0.001)LS(0.999)PGRR;T(0.001)LS(0.999)PGRR;T(0.006)LS(0.994)PGRR;T(0.084)LS(0.916)PGRR 75.387 0.02671 4732430000 2884068 2496800 2585145 2912905 2573640 2670713 3073470 2776625 2899945 TRUE FALSE 2747743.821 2751226.759 2703676.455 2620094.255 3022482.001 2578225.539 2604555.703 2533488.995 3349653.66 0.820306844 0.821346634 0.807151046 0.782198556 0.90232672 0.769699139 0.777559703 0.756343566 1 21.6755805 -1.861258265 7.742201631 1.016378837 0.805710403 0.69519639 0.040652321 0.011032549 0.000197705 0.037784401 0.008912443 0.013763907 1.861258265 -0.210668434 TLS(ph)PSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSPSLSR 8 0 A0A1B0GV45 A0A1B0GV45 1 T(0.005)LS(0.993)PS(0.002)LSR;T(0.023)LS(0.975)PS(0.002)LSR 142.55 0.00064583 141050000 1160550 994900 1038180 1188660 995240 1116200 1309760 1257710 1114310 TRUE FALSE 1105693.101 1096281.441 1085781.58 1069173.638 1168809.541 1077545.714 1109932.057 1147578.245 1287111.504 0.859049972 0.851737738 0.843580045 0.830676779 0.908087246 0.837181325 0.862343358 0.891591942 1 20.29570561 0.75431868 1.816211615 0.999952283 0.855039461 0.825033019 0.020832239 0.325699151 1.736195233 0.018045322 0.005071134 5.679612161 -0.75431868 -0.144912822 TLS(ph)PTPSAEGYQDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;T(0.006)LS(0.994)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR 382.24 4.42E-99 6147430000 1663760 1417780 1486750 1688870 1481310 1552180 1752310 1659670 1568990 TRUE FALSE 1585117.362 1562253.394 1554918.958 1519101.579 1739649.995 1498427.617 1484962.926 1514340.496 1812300.956 0.874643561 0.862027573 0.857980543 0.83821706 0.959912309 0.826809484 0.819379872 0.835589967 1 20.78939112 -1.244783217 3.494077968 1.000324736 0.858439577 0.556240601 0.03948213 16135994.7 27830322.27 57861.61129 0.009334964 0.056913695 1.244783217 -0.14188516 TLS(ph)SSAQEDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.986)S(0.013)SAQEDIIR;TLS(0.934)S(0.059)S(0.007)AQEDIIR;TLS(0.984)S(0.014)S(0.002)AQEDIIR;TLS(0.474)S(0.474)S(0.053)AQEDIIR 272.06 1.04E-27 985900000 1419490 1155460 1149740 1410580 1494940 1274320 1848800 1318800 1520340 TRUE FALSE 1352393.521 1273202.688 1202456.716 1268785.818 1755657.063 1230189.979 1566731.604 1203318.881 1756106.562 0.77010903 0.725014481 0.684728787 0.722499332 0.999744036 0.700521258 0.892162035 0.685219739 1 20.74394896 TLSAS(ph)AAEVAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TLSASAAEVAPR 12 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 T(0.002)LS(0.012)AS(0.986)AAEVAPR;TLS(0.001)AS(0.999)AAEVAPR;TLS(0.001)AS(0.999)AAEVAPR 203.97 1.25E-07 662750000 937100 885840 775990 896040 846530 871940 906590 868440 908480 TRUE FALSE 892805.1402 976108.1031 811569.9091 805968.3568 994164.564 841744.4992 768273.0448 792394.7897 1049362.439 0.850807221 0.930191579 0.773393328 0.768055276 0.947398656 0.802148493 0.732133166 0.755120215 1 20.00108162 2.028439424 24.99754761 0.791276236 0.858030143 0 0.092421626 457.1356632 401808.9325 0.032207083 0.023786172 106.7675861 -2.028439424 0.066753907 TLSASTQDLS(ph)PH ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH;TLSASTQDLS(1)PH 252.13 4.96E-21 1882049000 3005830 2436010 2614040 2953540 2874190 2653900 3168750 2715970 2556270 TRUE FALSE 2863750.373 2684242.189 2733896.32 2656644.548 3375447.826 2561994.778 2685298.989 2478145.269 2952683.296 0.969880643 0.909085709 0.925902322 0.899739079 1.143179775 0.867683568 0.909443621 0.839285836 1 21.49359519 TLSDDLDEAAKEFQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 ; 179.14 2.44E-09 76480000 155708 126768 147706 162767 93201 177648 175290 177326 105006 FALSE TRUE 148347.9914 139685.8033 154478.4662 146405.3519 109455.2249 171496.0052 148546.2911 161798.3954 121289.7942 1.223087173 1.151669885 1.273631201 1.20707066 0.902427328 1.41393599 1.224722097 1.333981944 1 16.88809864 TLSDPPS(ph)PLPHGPPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLSDPPSPLPHGPPNK 16 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 TLSDPPS(0.999)PLPHGPPNK 66.779 0.034538 160040000 403610 320490 347280 387410 301540 362850 394900 409460 300580 TRUE FALSE 384532.1552 353148.2954 363203.1315 348466.8108 354128.4805 350284.4135 334650.7522 373605.5117 347192.4113 1.107547696 1.017154419 1.046114834 1.003670586 1.019977595 1.008905731 0.96387692 1.076076261 1 18.40537589 8 0.557234617 1.0063712 5.899315432 0.475032427 0.029572793 101.898291 0.908959701 0.012606182 598.4476907 99999999.99 -8 4.892944232 TLSDVEDQKELAS(ph)PVSPELR ddPTM_SK-BR-3_Trastuzumab_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(1)PVSPELR 202.44 7.03E-22 67963000 157510 113110 134110 153830 107790 155010 178830 165170 126090 TRUE FALSE 150064.8145 124636.0376 140259.0762 138366.7161 126588.5419 149641.9648 151546.1991 150706.8392 145643.3932 1.030357857 0.855761699 0.963030818 0.950037713 0.86916776 1.027454535 1.04052917 1.034766053 1 17.15208073 2.171905632 11.52244445 1.030385005 0.93393732 0.462533805 0.049173141 0.505816471 85.48022402 0.017529817 0.012948356 148.5612797 -2.171905632 -0.096447685 TLSDVEDQKELASPVS(ph)PELR ddPTM_SK-BR-3_Trastuzumab_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(0.001)PVS(0.999)PELR 104.87 0.00016005 57949000 56162 48954 54360 68525 45686 62325 65487 75970 66793 TRUE FALSE 53507.33356 53942.46826 56852.45977 61636.73681 53653.62394 60166.66962 55495.7554 69317.66406 77150.91731 0.69354112 0.699181165 0.736899336 0.798911263 0.695437278 0.779856828 0.719314265 0.898468437 1 16.23539569 1.085090086 2.981992124 0.999141236 0.727937161 0.871389137 0.03576065 0.074486902 1.310075685 0.033712543 0.008986664 12.16438302 -1.085090086 -0.271204075 TLSGGRPGAGPELELGTAGS(ph)PGGAPPEAAPGDCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLSGGRPGAGPELELGTAGSPGGAPPEAAPGDCTR 35 1 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 TLSGGRPGAGPELELGT(0.006)AGS(0.994)PGGAPPEAAPGDCTR;TLSGGRPGAGPELELGT(0.001)AGS(0.999)PGGAPPEAAPGDCTR 226.85 4.24E-37 155087000 67976 52312 64687 66649 69316 70644 73792 65685 77871 TRUE FALSE 64762.9092 57642.65227 67652.96293 59949.3159 81404.68845 68197.58057 62533.67512 59933.27318 89946.83697 0.720013192 0.640852466 0.75214388 0.66649721 0.905031141 0.758198763 0.695229285 0.666318852 1 16.45678493 -2.098773417 2.401003946 1.480804099 0.72151338 0.575800849 0.073963443 9302666.279 2793564.733 24424722.38 0.017793505 0.007965748 2.098773417 -0.759290718 TLSKEEETKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLSKEEETKK 10 2 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 124.21 0.00024842 5054410000 7737480 6062810 7009380 8746090 4383940 9654210 9760010 10211030 4468070 FALSE TRUE 7371744.655 6680617.232 7330767.006 7866916.417 5148497.748 9319882.287 8270941.22 9316898.081 5160955.476 1.428368194 1.294453568 1.42042826 1.524313948 0.997586159 1.80584435 1.602598832 1.805266123 1 22.29920675 2.214596735 24.99998966 1.610753263 1.349103818 0.131494566 0.261958911 350.0978178 365232.3951 0.085775239 0.063382297 163.9067107 -2.214596735 -0.261649445 TLSNAEDYLDDEDS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 1 TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D 446.15 3.54E-175 889561000 2187120 2247420 2064840 2205780 1924820 2226510 2618890 2712540 2607210 TRUE FALSE 2083739.172 2476434.653 2159514.956 1984050.804 2260507.999 2149405.4 2219330.231 2475015.618 3011522.811 0.691922095 0.822319739 0.717084044 0.658819783 0.750619584 0.713727086 0.73694618 0.821848537 1 21.52206176 0.881847529 2.25711447 0.99974546 0.731267179 0.809392507 0.042225075 0.200868097 2.081214217 0.040407415 0.01101518 7.618115081 -0.881847529 -0.268478282 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_SK-BR-3_Trastuzumab_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 TLS(0.029)S(0.965)PS(0.005)NRPSGETSVPPPPAVGR;TLS(0.009)S(0.927)PS(0.065)NRPSGETSVPPPPAVGR;TLS(0.01)S(0.948)PS(0.042)NRPSGETSVPPPPAVGR;TLS(0.061)S(0.936)PS(0.002)NRPSGETSVPPPPAVGR 197 1.84E-24 1933000000 730400 627770 706030 752710 694250 660370 787720 738950 771640 TRUE FALSE 695875.4395 691740.4767 738402.1739 677046.1607 815326.9802 637501.2213 667538.8465 674243.6206 891301.9902 0.780740363 0.776101124 0.828453411 0.759614775 0.914759519 0.715247165 0.748948004 0.756470453 1 19.7655548 -1.496195021 2.922033622 1.007324272 0.782746027 0.607687105 0.054251235 11629962.63 13345420.25 686461.3671 0.012208554 0.03190105 1.496195021 -0.224578245 TLSS(ph)SAQEDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.411)S(0.54)S(0.048)AQEDIIR 226.54 1.58E-11 457510000 422990 300950 338240 412200 436830 364770 502940 343240 423410 TRUE FALSE 402996.101 331617.1472 353748.6386 370764.8729 513013.0137 352137.9234 426207.2659 313184.086 489070.2603 0.824004512 0.678056251 0.723308423 0.758101449 1.048955652 0.720015 0.871464287 0.640366245 1 18.89968221 2.972580927 24.90361382 0.845407189 0.739980891 0.164883464 0.12245066 1238.612217 1124981.229 0.033853394 0.035998277 938.8169598 -2.972580927 -0.105426298 TLSSFFT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLSSFFTPR 9 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 TLSSFFT(1)PR;TLSSFFT(1)PR;TLSSFFT(1)PR;TLSSFFT(1)PR 127.17 0.0050646 304712000 508346 474254 514962 557848 536611 496448 608039 544436 638141 TRUE FALSE 484317.492 522581.0218 538573.5171 501772.0592 630195.7885 479255.8813 515271.4831 496762.2976 737100.6471 0.657057478 0.708968339 0.730664827 0.68073751 0.854965724 0.650190558 0.699051731 0.673940933 1 19.4915021 -1.10483601 4.299987593 1.000041658 0.705473181 0.717547301 0.057775884 1.085465993 30616394.69 2630.327496 0.012503763 0.07855322 1.10483601 -0.294568478 TLSSS(ph)SMDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLS(0.016)S(0.088)S(0.845)S(0.051)MDLSR;TLS(0.001)S(0.028)S(0.914)S(0.057)MDLSR;TLSS(0.001)S(0.999)SMDLSR;TLSS(0.007)S(0.946)S(0.047)MDLSR;TLSS(0.018)S(0.865)S(0.117)MDLSR;TLSS(0.025)S(0.931)S(0.044)MDLSR;TLS(0.004)S(0.248)S(0.693)S(0.055)MDLSR 277.1 3.46E-27 2622220000 3796540 3105090 3180980 3944630 4026350 3720020 4468110 3758300 4152170 TRUE FALSE 3617085.078 3421502.201 3326831.079 3548108.298 4728544.165 3591194.775 3786417.757 3429203.328 4796067.317 0.754177295 0.713397451 0.693658128 0.73979535 0.985921142 0.748779059 0.789483864 0.715003168 1 22.19342048 2.971432995 24.91217238 0.827007825 0.722856151 0.289758905 0.092601638 949.4192512 827951.9691 0.026123947 0.027762759 936.3387455 -2.971432995 -0.104151675 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TLSVAAAFNEDEDSEPEEMPPEAK 24 0 Q8WW12 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;T(0.001)LS(0.001)VAAAFNEDEDS(0.998)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;T(0.116)LS(0.116)VAAAFNEDEDS(0.768)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK 200.48 9.83E-25 1493110000 1677794 1369306 1464798 1652349 1093392 1629127 1766106 1793082 1251554 TRUE FALSE 1598488.003 1508839.838 1531960.437 1486251.739 1284079.219 1572709.923 1496654.093 1636070.234 1445638.602 1.105731405 1.043718559 1.059711905 1.028093562 0.888243588 1.087899784 1.035289242 1.131728381 1 20.4632755 -1.691791546 7.888419364 0.999827127 1.046666378 0.04986862 0.065128471 0.000188921 7.38E-06 0.060165746 0.014128997 0.020333327 1.691791546 0.04683925 TLT(ph)EPSVDFNHSDDFTPISTVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.009)LT(0.496)EPS(0.496)VDFNHSDDFTPISTVQK 239.15 1.22E-36 90694000 100570 79884 82210 104300 80282 86526 109700 98947 70920 TRUE FALSE 95816.25541 88024.27042 85979.40982 93815.56584 94283.15538 83529.58292 92963.25022 90282.67613 81917.91139 1.169661845 1.074542416 1.049580102 1.145238743 1.150946768 1.019674226 1.134834234 1.102111548 1 16.32189131 -5 0.272610671 0.263361475 1.1135875 0.336357243 0.04706343 253.0169706 2.447908083 105.1283683 0.053568197 1.00E-05 5 0.850226025 TLT(ph)PPLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.354)LT(0.646)PPLRR;T(0.446)LT(0.554)PPLRR 90.827 0.0075714 503550000 456810 395190 413680 470950 364850 438350 496130 477560 369170 TRUE FALSE 435217.4966 435460.3103 432647.6372 423609.2113 428479.7245 423169.8296 420436.2564 435742.3147 426418.9981 1.020633458 1.021202883 1.014606852 0.993410737 1.004832633 0.992380338 0.985969805 1.021864215 1 18.70191219 3.369145145 4.245164808 0.997923364 1.020540772 0.468675948 0.009576608 0.158493665 5.111538597 0.002588666 0.003565441 2339.619029 -3.369145145 0.022617408 TLTAEEAEEEWERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTAEEAEEEWERR 14 1 P35269;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 205.61 1.93E-08 92895000 45132 42441 40731 48814 51773 43208 53840 46315 59661 FALSE TRUE 42998.6998 46765.78615 42598.55664 43907.12398 60802.19481 41711.69613 45625.71916 42259.41307 68912.92317 0.623956985 0.678621425 0.618150481 0.637139189 0.882304683 0.60528119 0.662077838 0.613229147 1 16.07248694 -2.168527397 2.491121196 1.880317795 0.665188105 0.6309397 0.080496787 9727462.593 855229.9298 48949794.45 0.019219612 0.006783793 2.168527397 -1.21512969 TLTAIAVILTNFHDGRPLPIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTAIAVILTNFHDGRPLPIER 22 1 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 132.48 6.33E-06 30807000 45561 45157 50331 53321 39394 52112 59543 48526 37682 FALSE TRUE 43407.42182 49758.54964 52638.72613 47961.07178 46264.30113 50307.34837 50458.62177 44276.80619 43525.53211 0.997286414 1.143203707 1.209375821 1.101906616 1.062923275 1.155812369 1.159287878 1.017260538 1 15.40957431 1.16067188 6.914903952 1.004121282 1.117389193 0.384856493 0.057825738 0.261736428 18.62890608 0.05696581 0.014353844 14.47677684 -1.16067188 0.11326791 TLTAVHDAILEDLVFPSEIVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGK 22 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 214.26 1.52E-25 2605200000 5055700 4768300 4446900 5677300 3940600 5108500 5645200 5519300 3823200 FALSE TRUE 4816727.08 5254195.191 4650794.764 5106607.018 4627839.392 4931591.364 4783921.059 5036000.832 4416082.33 1.090724022 1.189786512 1.05314947 1.1563659 1.047951339 1.116734471 1.083295261 1.140377479 1 22.07433564 -5 0.198112879 0.502224843 1.130670403 0.349719213 0.045272113 139.908164 1.381347981 27.5993047 0.098987723 1.00E-05 5 0.62844556 TLTAVHDAILEDLVFPSEIVGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGKR 23 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 166.34 7.84E-12 206428000 704030 284780 784680 459460 796570 637310 1243270 854850 1319590 FALSE TRUE 670751.8972 313799.4058 820658.3542 413274.2079 935491.5558 615239.7949 1053586.327 779994.8022 1524225.278 0.440060867 0.205874689 0.538410146 0.271137222 0.613748879 0.403640987 0.691227434 0.511731969 1 20.53964472 0.371246561 0.274535644 1.153073639 0.284736682 0.677804815 0.126846656 2.136984051 0.328057025 0.563094072 0.18164431 2.350967152 -0.371246561 -0.868336957 TLTDEELADWK ddPTM_SK-BR-3_Trastuzumab_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 0 106.29 0.00547 14626000 58261 50786 50101 63450 42925 53644 63871 64067 50798 FALSE TRUE 55507.11799 55961.15114 52398.18041 57071.88545 50411.10641 51786.29483 54126.30588 58456.95384 58675.4944 0.946001709 0.953739746 0.893016428 0.972669869 0.859150944 0.882588129 0.92246868 0.996275437 1 15.84047047 1.236737585 7.668169582 0.99875696 0.921006464 0.484438732 0.034082016 0.107415069 44.55315649 0.027647872 0.00842154 17.24795398 -1.236737585 -0.077750497 TLTDEELADWKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTDEELADWKR 12 1 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 206.03 1.52E-07 352220000 616780 511760 561120 632460 515040 641110 695870 661280 588690 FALSE TRUE 587626.0317 563908.9258 586847.907 568883.9192 604862.8129 618908.1999 589702.251 603374.8175 679981.0386 0.864180026 0.829300957 0.863035693 0.836617327 0.889528941 0.910184498 0.867233375 0.887340651 1 19.37513499 -5 0.162166903 1.520673394 0.828852308 0.826507595 0.019891537 50.09805126 0.463290523 8.337149991 0.078748515 1.00E-05 5 -0.691821086 TLTDEVNS(ph)PDSDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR 233.37 2.13E-17 3677400000 2399830 2393260 2321030 2655270 2378670 2444570 2739060 2647430 2709010 TRUE FALSE 2286394.792 2637135.915 2427451.521 2388357.215 2793509.295 2359913.928 2321166.091 2415606.994 3129109.435 0.730685468 0.842775227 0.775764342 0.763270593 0.892748992 0.754180695 0.741797671 0.771979071 1 21.57732068 -0.990481517 5.118023849 1.000001471 0.784079221 0.658941423 0.048802817 7.87E-07 1.55E-07 0.04541112 0.010703431 0.102215906 0.990481517 -0.21592225 TLTDEVNSPDS(ph)DRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.279)PDS(0.721)DRR;TLTDEVNS(0.102)PDS(0.898)DRR 242.93 1.75E-17 932120000 1585960 1417110 1508060 1608910 1474770 1510390 1685340 1615700 1661910 TRUE FALSE 1510994.814 1561515.12 1577206.043 1447179.31 1731969.421 1458084.816 1428210.43 1474220.743 1919630.515 0.787127941 0.813445665 0.821619593 0.753884302 0.902241034 0.759565346 0.744002775 0.767971092 1 20.87239722 -0.95879607 4.953581885 1.000001441 0.792812945 0.666941578 0.04580484 7.04E-07 1.48E-07 0.042836637 0.010096622 0.109952202 0.95879607 -0.207188496 TLTEPS(ph)VDFNHSDDFTPISTVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.032)LT(0.199)EPS(0.769)VDFNHSDDFTPISTVQK;T(0.005)LT(0.124)EPS(0.871)VDFNHSDDFTPISTVQK 206.4 8.88E-25 279790000 321350 248490 277190 321820 241620 327720 364780 321220 220379 TRUE FALSE 306160.4224 273811.4135 289899.4357 289470.0422 283758.4515 316370.9742 309126.1114 293092.2739 254554.2498 1.20273153 1.075650529 1.13885129 1.137164445 1.114726828 1.242843027 1.214382049 1.151394149 1 17.95761363 TLTGDVKT(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLT(0.001)GDVKT(0.5)S(0.5)PPR 87.863 0.06566 26638000 127620 104060 118910 132260 101200 129940 145560 145950 99748 TRUE FALSE 121587.6555 114663.8323 124362.1411 118964.9735 118849.248 125440.1452 123352.1486 133169.8443 115216.4104 1.05529807 0.995203998 1.079378716 1.032534976 1.031530557 1.088735058 1.070612669 1.155823583 1 16.81398669 2.239325361 24.99214448 1.083315228 1.035907304 0.173590915 0.042612821 28.52079384 932103.8459 0.0137735 0.010883888 173.51034 -2.239325361 -0.047407924 TLTLVDTGIGMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTLVDTGIGMTK 13 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 101.89 0.0026507 0 39849 40347 42902 47664 26929 45505 47507 36040 31871 FALSE TRUE 37965.41674 44458.40517 44869.09914 42872.72416 31625.40907 43929.15044 40258.93462 32884.14654 36813.39191 1.031293635 1.207669353 1.218825455 1.16459587 0.85907349 1.193292662 1.093594818 0.89326587 1 15.16794306 TLTPDQWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TLTPDQWAR 9 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;;;; 171.73 0.00014702 1195720000 2850340 2310770 2404610 2615350 2753210 2488190 3087370 2648180 2957070 FALSE TRUE 2715610.077 2546240.09 2514863.747 2352450.049 3233368.952 2402023.356 2616335.003 2416291.32 3415637.313 0.795052234 0.745465592 0.736279504 0.688729462 0.946637086 0.703243095 0.765987359 0.707420343 1 21.70372336 -1.424510956 5.506571623 1.00016124 0.762067343 0.514131995 0.072980227 0.000129316 1.35E-05 0.063251671 0.014898528 0.037626086 1.424510956 -0.238093897 TLTPGGHAEHDGQPYCHKPCYGILFGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLTPGGHAEHDGQPYCHKPCYGILFGPK 28 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 176.44 1.18E-13 422140000 181870 139840 145350 199110 140350 166370 234060 178540 6370.9 FALSE TRUE 173273.3655 154089.855 152014.4413 179095.0845 164826.9956 160608.5652 198349.8482 162906.0911 7358.866634 23.54620272 20.93934605 20.65731706 24.33731897 22.39842136 21.82517678 26.95385826 22.1373887 1 12.84526787 0.941267634 23.77153745 1.00000023 22.98635943 0.935724253 1.800872677 4485.592316 1815515.527 1.811899272 0.452974825 8.735095021 -0.941267634 21.9863592 TLTPIIQEYFEHGDTNEVAEMLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLTPIIQEYFEHGDTNEVAEMLR 23 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 ; 202.73 2.03E-24 59256000 52878 49751 44553 49364 48900 44592 55704 46858 48194 FALSE TRUE 50378.56173 54820.68346 46595.79912 44401.83693 57428.14452 43047.76786 47205.33173 42754.86511 55667.67938 0.904987639 0.984784781 0.837035056 0.797623279 1.031624547 0.773299127 0.847984544 0.768037497 1 15.76455232 3.730394394 24.77936432 0.856768076 0.944886211 0.114199238 0.0901103 864.516847 2623267.792 0.021774627 0.034381896 5375.197104 -3.730394394 0.088118135 TLTTGSSAYLWKPPS(ph)R ddPTM_SK-BR-3_Trastuzumab_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 89.483 0.0034974 388670000 187150 167960 154940 184410 105030 170810 209340 218280 132030 TRUE FALSE 178303.7904 185075.315 162044.1523 165872.7564 123347.1987 164894.8069 177401.3382 199166.246 152504.5381 1.169170391 1.213572509 1.062552986 1.08765784 0.808810022 1.081245246 1.163252848 1.305969308 1 17.21849265 3.735612059 24.29060392 1.075189712 1.191371453 0.135792224 0.124259387 331.9176763 2734394.567 0.033314159 0.054125862 5440.164837 -3.735612059 0.11618174 TLVLLMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TLVLLMGK 8 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 112.17 0.0071941 27130000 120740 88505 73698 83663 107960 89580 140570 94510 109760 FALSE TRUE 115032.8595 97523.76012 77077.1262 75253.03629 126788.1898 86477.82214 119123.4648 86234.20337 126781.0202 0.90733502 0.769229968 0.607954772 0.593567051 1.000056551 0.682103851 0.939600143 0.68018228 1 16.95197926 2.739335461 24.99982931 0.848776917 0.742476404 0.188062937 0.140779998 154.7409007 4992679.096 0.042877362 0.043132481 548.7006332 -2.739335461 -0.106300513 TLVS(ph)PNKAETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TLVSPNKAETK 11 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 TLVS(1)PNKAETK;TLVS(1)PNKAETK;TLVS(1)PNKAETK;TLVS(1)PNKAETK 149.35 2.08E-05 4029830000 1902470 2116390 1946070 2444500 1058410 2381570 2350970 2646790 1302500 TRUE FALSE 1812544.013 2332052.547 2035299.234 2198774.216 1242996.369 2299095.634 1992286.348 2415023.036 1504485.048 1.204760404 1.550066949 1.352821178 1.461479607 0.8261939 1.528161172 1.324231405 1.605215711 1 20.52083834 TLVVHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TLVVHEK 7 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;;; 117.4 0.0052398 10176853000 26792220 21912820 21368120 24471390 18779610 23838400 27942620 26012950 19238770 FALSE TRUE 25525804.86 24145761.27 22347869.44 22011479.38 22054768.04 23012870.23 23679460.12 23735118.19 22222220.19 1.148661323 1.086559356 1.005654217 0.990516663 0.992464652 1.035579255 1.065575803 1.068080416 1 24.40549963 4.041227368 2.501594799 1.02614675 1.135891907 0.674005353 0.028739803 0.175161977 2.179533749 0.008509397 0.021922521 10995.81358 -4.041227368 0.109745157 TLYDHVDEVTCLAFHPTEQILASGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TLYDHVDEVTCLAFHPTEQILASGSR 26 0 Q05048;A0A0A0MSZ9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ; 166.79 6.45E-12 68284000 35173 31295.4 35806 34508.3 38566 32917.3 42288 35958.9 25847.4 FALSE TRUE 33510.442 34484.43684 37447.74052 31039.46012 45291.89819 31777.36565 35836.18893 32810.14809 29855.68278 1.12241419 1.155037622 1.254291881 1.039649984 1.517027714 1.064365732 1.200313829 1.098958223 1 14.86571794 0.951172341 1.699043039 0.999620441 1.189938932 0.189872888 0.131587687 0.694213415 4.126346913 0.111522749 0.032044698 8.93660045 -0.951172341 0.190318492 TMAQHEELMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TMAQHEELMK 10 0 P12270 P12270 TPR Nucleoprotein TPR 0 64.439 0.087259 0 156740 132370 128100 169770 130190 152490 161730 160680 137630 FALSE TRUE 149331.2108 145858.6535 133973.5117 152704.3971 152895.0948 147209.2331 137055.1181 146610.0074 158972.9575 0.939349769 0.91750607 0.842744035 0.960568385 0.961767946 0.926001726 0.862128505 0.92223237 1 17.27842185 0.956268658 22.92453266 1.000000001 0.914501582 0.323453978 0.038016162 4532.470699 2375983.971 0.036767391 0.009191848 9.042086511 -0.956268658 -0.085498419 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;T(0.002)MFAQVES(0.998)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;T(0.161)MFAQVES(0.839)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK 180.83 3.22E-17 996500000 1521906.3 1368440.8 1306219.5 1615129.6 656824 1686860.2 1637293.6 1734109.5 681072.1 TRUE FALSE 1449968.805 1507886.473 1366110.956 1452773.704 771373.8976 1628443.808 1387494.39 1582261.679 786689.2828 1.843127696 1.916749734 1.7365318 1.846693143 0.98053185 2.069996177 1.76371335 2.011291769 1 19.5854344 TMGYSVTAPEDTRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TMGYSVTAPEDTRR 14 1 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;; 227.63 3.14E-12 1009510000 485103 423656 418577 468111 478778 461257 549622 499424 510172 FALSE TRUE 462173.1426 466827.0281 437769.1695 421055.5929 562276.7316 445283.5544 465767.0694 455691.7869 589286.8682 0.784292282 0.792189769 0.74287956 0.714517183 0.954164707 0.755631219 0.790391055 0.773293639 1 19.16861059 -1.857444996 2.536604015 1.091924876 0.788561611 0.522629159 0.06354882 9803537.21 6154873.668 5450003.813 0.014702942 0.013885292 1.857444996 -0.303363265 TMHHLLLEVEVIEGTLQCPESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TMHHLLLEVEVIEGTLQCPESGR 23 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;;; 271.05 7.63E-52 295022000 107624.1 96096.5 100794.5 113003 113624.5 101831 130429.5 116701.5 30598.7 FALSE TRUE 102536.9221 105888.8426 105416.0275 101643.7237 133440.5768 98304.56694 110530.0843 106482.498 35343.79012 2.901129781 2.995967389 2.982589789 2.875858062 3.775502751 2.781381584 3.127284423 3.012763986 1 15.10916914 0.909240784 18.91823065 1 3.051361827 0.849896841 0.271662173 1774.136892 369810.3827 0.238397628 0.059599407 8.114108005 -0.909240784 2.051361828 TMIIS(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PER;TMIIS(1)PER 99.34 0.0072193 172693000 241010 286680 205215 294400 209440 239220 211610 239280 175936 TRUE FALSE 229617.9349 315893.0179 214624.3107 264806.3527 245966.2697 230935.7514 179325.008 218327.3747 203219.2563 1.129902447 1.554444316 1.056121918 1.303057385 1.210349226 1.136387149 0.882421338 1.074343931 1 17.63267759 2.105563884 2.361839976 0.975656942 1.280170065 0.422702627 0.138689346 0.246578354 2.696950586 0.065487835 0.039738938 127.5157661 -2.105563884 0.304513124 TMIIS(ph)PERLDPFADGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.009)MIIS(0.991)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.207)MIIS(0.793)PERLDPFADGGK;T(0.004)MIIS(0.996)PERLDPFADGGK;T(0.331)MIIS(0.669)PERLDPFADGGK 241.76 1.36E-20 717334000 2318650 2554970 1909250 2939880 1441240 2554410 2363310 2363590 1393434 TRUE FALSE 2209052.01 2815324.348 1996791.001 2644357.677 1692591.8 2465950.141 2002743.654 2156621.529 1609520.628 1.372490648 1.749169472 1.240612246 1.642947366 1.051612368 1.532102229 1.244310647 1.339915433 1 20.61819964 0.400883875 0.18577495 0.780610236 1.642079719 0.32856909 0.19573311 7.662078988 0.686378779 1.907881365 0.808149342 2.517003823 -0.400883875 0.861469484 TMIIS(ph)PERLDPFADGGKT(ph)PDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 T(0.47)MIIS(0.53)PERLDPFADGGKT(1)PDPK;T(0.475)MIIS(0.525)PERLDPFADGGKT(1)PDPK 103.95 0.0010716 149175000 253184 212438 220106 254171 127468 255602 250737 286060 128269 TRUE FALSE 241216.4941 234085.6737 230198.0778 228621.2482 149698.3788 246750.4386 212482.4655 261011.0699 148160.3014 1.628077776 1.579948687 1.553709567 1.54306684 1.010381171 1.665428838 1.434138994 1.761680203 1 17.17679941 -1.843148702 2.720480933 0.805478229 1.519887394 0.399829403 0.20099453 45054681.47 33994343.31 57305202.11 0.045958676 0.01434998 1.843148702 0.714409164 TMIIS(ph)PERLDPFADGGKTPDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.189)MIIS(0.811)PERLDPFADGGKTPDPK;TMIIS(1)PERLDPFADGGKTPDPK;T(0.001)MIIS(0.999)PERLDPFADGGKTPDPK 163.16 8.04E-12 368308000 864386 636628 855868 908910 505563 1010740 1101400 1002480 584829 TRUE FALSE 823528.1868 701501.117 895110.3944 817544.64 593733.0271 975737.8204 933361.2014 914697.5367 675521.2944 1.219100262 1.038458925 1.32506614 1.210242589 0.878925701 1.444422002 1.381690273 1.354061736 1 19.36564172 2.201354455 24.99999609 1.336925581 1.141102299 0.166286384 0.167116474 225.8768892 151772.5544 0.057083671 0.042160163 158.984379 -2.201354455 -0.195823282 TMKDDETFEISIPFDEAPHLDPQIFYS(ph)LSPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TMKDDETFEISIPFDEAPHLDPQIFYSLSPSRR 33 2 K7EMP7;Q9BWC9;K7ES29 K7EMP7 CCDC106 Coiled-coil domain-containing protein 106 1 TMKDDETFEISIPFDEAPHLDPQIFY(0.014)S(0.436)LS(0.436)PS(0.113)RR 72.231 0.0017496 62007000 62848 51492 60580 52202 46360 69101 77484 67528 48385 TRUE FALSE 59877.29959 56739.09334 63357.65292 46954.55578 54445.16932 66708.01504 65662.39271 61614.89033 55888.29868 1.071374527 1.015223127 1.133647909 0.840150029 0.974178327 1.193595379 1.174886233 1.102464949 1 15.77025864 2.24313593 24.99973137 1.139060929 1.012088091 0.254474734 0.09082097 135.0286989 737806.7745 0.030977024 0.025111551 175.0394461 -2.24313593 -0.126972838 TMKEDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TMKEDEKR 8 2 O95831-3;O95831;O95831-4 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 90.629 0.0073459 28298000 68757 45042 53675 79149 43726 48381 69589 61928 44425 FALSE TRUE 65506.99287 49631.83101 56136.05184 71192.79215 51351.80056 46705.55384 58971.91996 56505.25602 51314.20211 1.276586017 0.967214318 1.093967158 1.387389635 1.00073271 0.910187666 1.149231938 1.101162129 1 15.64707055 TMLITHMQDLQEVTQDLHYENFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TMLITHMQDLQEVTQDLHYENFR 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ;; 313.16 1.78E-73 462109000 345182.4 267513.7 300181.5 328841.1 324930.5 285716.5 391863.7 339327.4 189328 FALSE TRUE 328866.312 294773.6502 313945.1187 295785.3679 381598.2763 275822.066 332077.6955 309614.094 218688.0193 1.503814947 1.347918606 1.435584445 1.352544912 1.744943676 1.261258238 1.518499717 1.415779863 1 17.73851466 0.947575674 21.57334644 0.999999999 1.446531441 0.543191694 0.129320725 2114.404529 870109.2436 0.108912115 0.027228029 8.862896423 -0.947575674 0.446531442 TMLLLSRS(ph)PEAQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TMLLLSRSPEAQPK 14 1 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TMLLLS(0.091)RS(0.909)PEAQPK 157.54 3.19E-06 181940000 379390 111340 437730 259320 432190 381340 717790 459850 622690 TRUE FALSE 361456.9866 122685.6726 457800.3535 233252.6609 507563.7992 368134.1002 608277.9524 419583.0962 719253.5849 0.502544574 0.170573599 0.636493669 0.324298225 0.705681292 0.511827967 0.845707224 0.583359061 1 19.45614098 1.801587977 0.378836435 0.998035727 0.307288365 0.543843088 0.160658051 0.741042242 0.299773413 0.178465089 0.167480074 63.3268633 -1.801587977 -0.690747362 TMPGGNDHEIFTDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TMPGGNDHEIFTDPR 15 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;; 78.285 0.023368 417660000 696740 625120 640660 759590 729760 665320 775150 703500 672430 FALSE TRUE 663806.481 688820.4387 670034.8947 683234.5701 857029.9129 642279.8016 656886.6309 641897.8105 776707.0101 0.854642062 0.886847202 0.862661063 0.87965547 1.103414675 0.826926747 0.845732847 0.826434939 1 19.56701096 TMPLRWS(ph)FGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TMPLRWSFGSK 11 1 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 TMPLRWS(0.999)FGS(0.001)K;TMPLRWS(1)FGSK 183.96 3.10E-06 453950000 1016850 819720 940580 1081010 849620 976690 1232660 1145650 1006290 TRUE FALSE 968785.5157 903250.3999 983706.5234 972344.821 997793.459 942866.9804 1044595.078 1045330.813 1162340.314 0.833478375 0.777096337 0.846315414 0.836540563 0.858434872 0.811179798 0.89869986 0.899332837 1 20.1486011 0.90361558 0.479555507 1.008236789 0.809624412 0.836148121 0.024620437 0.419672641 0.235914684 0.029916493 0.013777614 8.009687635 -0.90361558 -0.198612377 TMS(ph)EVGGSVEDLIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TMSEVGGSVEDLIAK 15 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 1 T(0.024)MS(0.976)EVGGSVEDLIAK;T(0.01)MS(0.99)EVGGSVEDLIAK 151.9 3.07E-06 40120000 68961 52872 61821 65318 44598 67669 62803 70874 50355 TRUE FALSE 65701.3502 58259.71691 64655.554 58752.11054 52375.87708 65325.60556 53221.24889 64667.89683 58163.79622 1.12959185 1.001649148 1.111611659 1.010114785 0.900489316 1.123131738 0.915023646 1.111823867 1 15.82783381 7.999999966 0.555772673 1.008038268 6.593556677 0.155469362 0.077444145 221.7985624 1.988031 0.031951545 1482.276672 99999992.07 -7.999999966 5.585518408 TMYLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 77.674 0.087024 121020000 60371 58660 65519 83267 62780 71704 74937 73795 69438 FALSE TRUE 57517.38247 64637.52069 68523.11096 74896.84296 73728.81212 69220.8725 63503.98434 67333.11859 80206.0904 0.717119887 0.805892924 0.854338001 0.933804934 0.919242064 0.863037609 0.791760127 0.839501318 1 16.29142417 4.095078913 1.688224279 0.874864366 0.724736224 0.47467154 0.057676412 0.370265512 1.960168416 0.016467817 0.059575548 12447.40766 -4.095078913 -0.150128142 TNEGVIEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TNEGVIEFR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 159.79 0.00015304 623080000 1136310 961730 1046040 1176910 1107310 1081490 1222460 1227290 1140970 FALSE TRUE 1082598.878 1059731.38 1094001.969 1058604.771 1300424.513 1044037.73 1035951.275 1119821.981 1317905.8 0.821453914 0.804102524 0.830106346 0.803247676 0.986735557 0.792194503 0.786058666 0.849698044 1 20.32981582 -2.466612134 1.641569137 1.996751097 0.829153516 0.448172354 0.057577104 877919.4057 68178.33842 3234681.924 0.014606462 0.003414978 2.466612134 -1.16759758 TNFFGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNFFGTR 7 0 P16152;E9PQ63;A8MTM1;P16152-2 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ; 121.09 0.010403 339380000 312500 245330 262800 298260 378510 239420 365430 268380 322950 FALSE TRUE 297728.7443 270329.4059 274849.6399 268278.3381 444522.0242 231128.8254 309676.9419 244879.2244 373031.4366 0.79813312 0.724682639 0.736800208 0.719184261 1.191647621 0.619596106 0.830163122 0.65645734 1 18.50893769 TNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.204)NHRLS(0.796)LPMPASGTSLSAAIHR;T(0.146)NHRLS(0.854)LPMPASGTSLSAAIHR;T(0.03)NHRLS(0.97)LPMPASGTSLSAAIHR;T(0.102)NHRLS(0.898)LPMPASGTSLSAAIHR 355.25 1.99E-96 7356430000 1256965 1319553 1250042 1628918 1274565 1388154 1509597 1173842 400756 TRUE FALSE 1197550.756 1454016.951 1307357.662 1465176.068 1496848.732 1340081.879 1279280.252 1071054.172 462903.1937 2.587043623 3.141082133 2.824257166 3.165188938 3.233610726 2.894950601 2.76360213 2.313775723 1 18.82035099 0.802923632 1.35425578 1.001810243 2.975993742 0.917622995 0.186236556 0.184592832 0.616534387 0.17465814 0.052179378 6.352192231 -0.802923632 1.974183499 TNHSNIMDDPFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNHSNIMDDPFIR 13 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 100.45 0.0014181 0 83451 83013 87019 96537 77827 99546 101060 81768 40874 FALSE TRUE 79506.43661 91472.11908 91008.90722 86832.91735 91400.00416 96098.69706 85641.44091 74607.96044 47212.53116 1.684011313 1.937454248 1.927643043 1.839192164 1.935926795 2.035448952 1.813955719 1.580257584 1 15.52688221 0.886555406 2.045112451 1.001701418 1.885303843 0.90564753 0.091032083 0.133831661 1.133748798 0.08842074 0.024493289 7.701146864 -0.886555406 0.883602425 TNIIPVLEDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNIIPVLEDAR 11 0 A6NHQ2 A6NHQ2 FBLL1 rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 75.739 0.086692 30868000 96632 79819 73709 89630 90851 73522 95436 80666 83104 FALSE TRUE 92064.39687 87952.64685 77088.63056 80620.22211 106695.3856 70975.9147 80875.4854 73602.4574 95991.34388 0.959090613 0.916256022 0.80307898 0.83986971 1.11151049 0.739399115 0.842528942 0.766761402 1 16.55061669 TNILQYASTRPPTLS(ph)PIPHIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNILQYASTRPPTLSPIPHIPR 22 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TNILQYASTRPPT(0.014)LS(0.986)PIPHIPR;TNILQYASTRPPT(0.025)LS(0.975)PIPHIPR 202.49 8.46E-23 449780000 504570 673670 505100 645510 408720 597620 521020 616970 406990 TRUE FALSE 480719.9761 742317.7389 528259.3346 580622.1084 480000.6386 576924.2695 441528.8298 562944.836 470103.9306 1.022582337 1.579050271 1.123707547 1.235093073 1.02105217 1.22722707 0.939215354 1.197490171 1 18.84262022 3.065460703 1.748742116 1.073863946 1.292211157 0.177662156 0.165570705 0.477604791 2.987401046 0.053497134 0.06628154 1162.68134 -3.065460703 0.218347212 TNKDEKDILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNKDEKDILR 10 2 P46087-2;P46087;P46087-4;P46087-3 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 0 75.416 0.021969 81622000 170160 139330 150690 161530 136520 154180 178050 167160 133730 FALSE TRUE 162116.874 153527.8854 157599.2856 145292.6975 160329.0448 148840.7079 150885.2024 152522.5842 154468.1654 1.049516407 0.993912791 1.020270327 0.940599619 1.037942312 0.96356882 0.976804521 0.987404646 1 17.23695002 5.53188042 0.654646063 0.983965566 1.197008683 0.32643564 0.027070805 7.999055623 1.208953154 0.009696172 1.611028651 340314.4733 -5.53188042 0.213043117 TNKS(ph)PEAKPLPGKLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNKSPEAKPLPGKLPK 16 3 P46087-2;P46087;P46087-4;P46087-3;F5H359;F5GWB7;F5H709;F5H5X6 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 T(0.156)NKS(0.844)PEAKPLPGKLPK;TNKS(1)PEAKPLPGKLPK 126.22 5.20E-05 1735590000 3226500 3079700 3029300 3367900 1396080 3899400 3612400 3802400 1329590 TRUE FALSE 3073989.739 3393524.931 3168196.401 3029352.293 1639555.91 3764362.8 3061262.034 3469441.698 1535776.027 2.001587267 2.209648329 2.062928674 1.972522191 1.067574882 2.451114443 1.993299792 2.259080516 1 20.5505364 3.129440589 4.77262983 1.855654995 2.102911648 0.078868645 0.461565985 0.652273096 24.58310892 0.126310262 0.153178142 1347.226414 -3.129440589 0.247256654 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK 30 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 187.72 2.21E-18 269820000 743280 561550 687150 717240 527750 779260 917180 808420 533630 FALSE TRUE 708146.6274 618772.5834 718656.5072 645141.6725 619789.4329 752274.0308 777247.3458 737630.4591 616382.615 1.148875082 1.003877411 1.165925984 1.046657801 1.005527116 1.22046601 1.26098194 1.196708734 1 19.23346665 2.22452744 24.99974089 1.199797022 1.074298014 0.194554903 0.087247485 257.8975045 459434.6319 0.029677094 0.022028129 167.6978291 -2.22452744 -0.125499008 TNLSGRQS(ph)PSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TNLSGRQSPSFK 12 1 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 TNLSGRQS(0.998)PS(0.002)FK;TNLSGRQS(0.999)PS(0.001)FK;TNLSGRQS(0.994)PS(0.006)FK;TNLSGRQS(0.971)PS(0.029)FK 169.64 2.62E-05 4473180000 6565100 2635400 6498300 4927200 5368600 6096100 9595800 7399900 7683100 TRUE FALSE 6254780.734 2903950.256 6796253.483 4431908.495 6304882.14 5884990.528 8131784.471 6751925.527 8874555.908 0.704799293 0.327222036 0.76581336 0.49939496 0.710444805 0.663130706 0.916303256 0.760818411 1 23.0812435 1.876693746 0.666796919 0.970648883 0.536041324 0.511151748 0.132917058 0.487854428 0.429270365 0.110934989 0.060531885 75.28245028 -1.876693746 -0.434607559 TNNVSEHEDTDKYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TNNVSEHEDTDKYR 14 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;;;;; 211.57 2.19E-09 3035018000 4268390 3549420 3640900 4623660 2791993 4257120 4604780 4644840 2786645 FALSE TRUE 4066631.664 3911109.933 3807838.866 4158880.912 3278915.695 4109694.867 3902236.238 4238113.186 3218783.674 1.263406328 1.215089403 1.183005524 1.292065989 1.018681597 1.276785048 1.212332556 1.316681584 1 21.61808419 -2.317105401 2.069184297 2.77E-05 1.22072187 0.416027253 0.08273668 1234981.914 116174.5594 5811683.808 0.018510084 0.004818308 2.317105401 1.220694143 TNPPTQKPPS(ph)PPMSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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(0.863)PPMS(0.137)GR;TNPPTQKPPS(0.9)PPMS(0.1)GR;TNPPTQKPPS(1)PPMSGR;TNPPTQKPPS(0.987)PPMS(0.013)GR;TNPPTQKPPS(1)PPMSGR;TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPT(0.003)QKPPS(0.972)PPMS(0.025)GR;TNPPT(0.008)QKPPS(0.636)PPMS(0.355)GR;TNPPT(0.017)QKPPS(0.928)PPMS(0.055)GR;TNPPTQKPPS(0.998)PPMS(0.002)GR;TNPPTQKPPS(0.726)PPMS(0.274)GR;TNPPT(0.001)QKPPS(0.98)PPMS(0.019)GR;TNPPT(0.012)QKPPS(0.982)PPMS(0.006)GR;TNPPT(0.004)QKPPS(0.94)PPMS(0.056)GR 181.87 1.35E-09 11257180000 5063580 4624870 4795240 5291340 2691310 5275610 5461950 5510900 3181530 TRUE FALSE 4824234.608 5096149.511 5015106.497 4759444.45 3160673.612 5092914.303 4628629.212 5028336.381 3674905.423 1.312750684 1.386743038 1.36468995 1.295120255 0.860069375 1.385862687 1.259523356 1.368290011 1 21.80927569 -4.999999997 0.163739161 3.55E-08 1.354187999 0.226282729 0.156495637 202.2612409 1.878350982 66.71388225 0.603780736 1.00E-05 4.999999997 1.354187964 TNPS(ph)PTNPFSSDLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.988)PT(0.012)NPFSSDLQK;TNPS(0.987)PT(0.013)NPFSSDLQK;TNPS(0.831)PT(0.169)NPFSSDLQK;TNPS(0.994)PT(0.006)NPFSSDLQK;TNPS(1)PTNPFSSDLQK;TNPS(0.998)PT(0.002)NPFSSDLQK 313.04 3.37E-56 1232200000 1255511 1033311 1125432 1319020 828462 1263922 1420531 1354877 894643 TRUE FALSE 1196165.483 1138606.566 1177034.17 1186429.604 972945.5105 1220152.064 1203802.906 1236236.787 1033379.667 1.157527597 1.101827916 1.139014254 1.148106201 0.941517954 1.180739377 1.16491832 1.19630454 1 19.97893897 TNRGS(ph)QLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNRGSQLHK 9 1 P42356;P42356-2 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 T(0.181)NRGS(0.819)QLHK 57.567 0.069364 55188000 32525 32847 36252 41492 25893 33974 41334 39633 26881 TRUE FALSE 30987.60771 36194.14664 37914.19006 37321.14533 30408.731 32797.47186 35027.73915 36162.52441 31049.56819 0.998004466 1.165689211 1.221085904 1.20198597 0.979360834 1.056293977 1.12812323 1.164670767 1 14.92228558 2.760294205 24.92033719 1.077227503 1.137469941 0.190677592 0.080012351 1840.94524 2110876.347 0.025637198 0.02716866 575.8298905 -2.760294205 0.060242437 TNRPPLSLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNRPPLSLSR 10 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;F8VUA6;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 109.16 0.0018751 905530000 849390 635560 454210 514100 681880 510040 818780 676030 707220 FALSE TRUE 809241.018 700324.2866 475035.9778 462421.6913 800799.6561 492377.1869 693860.0731 616833.2293 816892.0656 0.990633955 0.857303328 0.58151621 0.566074407 0.980300446 0.602744484 0.849390149 0.755097589 1 19.63978594 -0.497129557 7.359030902 1 0.784940077 0.173260552 0.153924641 0 0 0.147484485 0.034762427 0.318324777 0.497129557 -0.215059923 TNRTS(ph)PNNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNRTSPNNAR 10 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 T(0.002)NRT(0.005)S(0.993)PNNAR 68.171 0.036806 84074000 20521 11559 16152 16419 17734 14326 19136 15066 19840 TRUE FALSE 19551.013 12736.87524 16892.58518 14768.53093 20826.80399 13829.88703 16216.45174 13746.74117 22916.68587 0.853134398 0.555790454 0.737130372 0.644444446 0.90880523 0.603485474 0.707626392 0.599857294 1 14.4841108 -1.077282743 4.234221995 1.000035332 0.699142683 0.415042142 0.111423376 13463196.75 3425345.393 4620.936182 0.0233675 0.08369842 1.077282743 -0.300892649 TNS(ph)MQQLEQWIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TNSMQQLEQWIK 12 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;Q9HAU0-3 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 T(0.109)NS(0.891)MQQLEQWIK 91.207 0.0088402 27964000 19562 17736 18590 22851 15856 19948 22624 20460 18256 TRUE FALSE 18637.34303 19543.31856 19442.36989 20553.97407 18621.28138 19257.19576 19172.29328 18668.41393 21087.04724 0.88382896 0.926792563 0.922005327 0.97472035 0.883067277 0.913223911 0.909197626 0.885302419 1 14.36406947 -2.613585171 2.317922171 3.302448501 0.912918716 0.50855187 0.027097385 1453686.282 365291.5247 17647894.64 0.006429366 0.002434528 2.613585171 -2.389529785 TNS(ph)PGFQK ddPTM_SK-BR-3_Trastuzumab_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;TNS(1)PGFQK 126.03 0.0012974 251030000 909290 827590 793120 961900 615600 906790 917270 886930 677430 TRUE FALSE 866309.6637 911922.3619 829485.3365 865207.9845 722960.4451 875387.6349 777323.6147 809265.7073 782482.3846 1.107129925 1.165422225 1.060069022 1.105721997 0.923931911 1.118731427 0.993407174 1.034228659 1 19.57769875 3.25764894 1.751890673 1.022078856 1.133085075 0.392363723 0.055716053 0.300158656 1.901470881 0.016063967 0.0230004 1809.876494 -3.25764894 0.111006219 TNS(ph)SSSSPVVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.001)NS(0.741)S(0.193)S(0.064)S(0.001)SPVVLK;T(0.007)NS(0.981)S(0.012)SSSPVVLK;TNS(0.902)S(0.096)S(0.001)SSPVVLK 179.27 2.20E-05 349060000 762050 649120 682780 784060 506780 762300 821830 809070 560130 TRUE FALSE 726029.4067 715266.066 714086.1384 705244.7992 595162.2715 735901.3599 696444.7396 738223.5417 646992.0997 1.122161163 1.105525193 1.103701481 1.090036184 0.919891096 1.137419391 1.076434689 1.141008587 1 19.30338857 2.993194917 24.91623094 1.061570226 1.109299957 0.136257155 0.063560446 669.015729 2449555.15 0.017814628 0.02056887 984.4528426 -2.993194917 0.047729732 TNS(ph)TGGSSGSSVGGGSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.968)T(0.032)GGSSGSSVGGGSGK;T(0.002)NS(0.993)T(0.004)GGSSGSSVGGGSGK;TNS(0.887)T(0.113)GGSSGSSVGGGSGK;TNS(0.937)T(0.042)GGS(0.01)S(0.01)GS(0.001)SVGGGSGK;TNS(0.958)T(0.042)GGSSGSSVGGGSGK;T(0.001)NS(0.981)T(0.018)GGSSGSSVGGGSGK 256.53 1.42E-30 462966000 830469 737116 760416 916415 520988 858268 892458 847439 563552 TRUE FALSE 791214.3762 812228.9584 795281.8258 824295.2231 611848.1422 828545.964 756297.141 773232.7486 650944.7659 1.215486194 1.247769398 1.221734727 1.266305939 0.939938647 1.272836049 1.161845337 1.187862303 1 19.31217561 -5 0.136730094 0.346690632 1.267221147 0.304650386 0.093366089 166.1633503 1.405643375 29.71198809 0.563307527 1.00E-05 5 0.920530516 TNSGISSASGGSTEPTT(ph)PDSERPAQALLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSASGGST(0.002)EPT(0.034)T(0.963)PDSERPAQALLR;TNSGISSASGGSTEPT(0.069)T(0.931)PDSERPAQALLR;TNSGISSAS(0.002)GGS(0.002)T(0.001)EPT(0.214)T(0.78)PDSERPAQALLR;TNSGISSAS(0.001)GGS(0.004)T(0.008)EPT(0.249)T(0.734)PDS(0.004)ERPAQALLR 182.83 1.51E-17 1629990000 301246 242768 329920 334379 275038 310733 354277 343740 310255 TRUE FALSE 287006.6986 267506.3352 345047.1583 300766.5876 323004.5401 299972.2383 300225.5369 313640.3033 358367.7608 0.800871981 0.74645759 0.962829797 0.839267983 0.901321423 0.837051407 0.837758219 0.87519118 1 18.45108133 -5 0.076191026 1.489504466 0.679084091 0.427786526 0.056123076 254.7844874 1.383556017 21.73909152 2.267399935 1.00E-05 5 -0.810420375 TNSMSSSGLGS(ph)PNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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(0.999)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMS(0.004)S(0.002)S(0.002)GLGS(0.992)PNR;TNSMSSSGLGS(1)PNR 254.39 3.12E-24 2536730000 3525869 3297571 3336847 3796665 2931375 3525927 3889967 3668824 3063741 TRUE FALSE 3359208.16 3633597.234 3489844.736 3415017.021 3442605.872 3403823.264 3296481.09 3347562.321 3538850.307 0.949237144 1.026773364 0.986152121 0.965007481 0.972803474 0.961844376 0.931511877 0.945946291 1 21.75484931 2.776659091 1.441044997 0.952835294 0.989366218 0.123493565 0.026044282 0.541671615 2.27929917 0.010514446 0.010372024 597.9420429 -2.776659091 0.036530924 TNT(ph)PVKEDWNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 T(0.005)NT(0.995)PVKEDWNVR;T(0.007)NT(0.993)PVKEDWNVR;TNT(1)PVKEDWNVR;T(0.01)NT(0.99)PVKEDWNVR;TNT(1)PVKEDWNVR;T(0.002)NT(0.998)PVKEDWNVR 138.19 0.00012758 2539653000 5980310 6311770 5436883 6447150 2872226 6648370 6128100 6640040 3013145 TRUE FALSE 5697632.598 6954946.539 5686169.463 5799070.233 3373141.305 6418135.28 5193145.795 6058602.897 3480408.138 1.637058751 1.998313492 1.633765133 1.666204078 0.969179812 1.844075472 1.492108279 1.740773684 1 21.73082507 -2.738851534 0.145896274 4.61E-12 1.89504358 0.332711666 0.271617993 68.9644869 1.146344707 24.69075958 1.615430874 0.001824519 2.738851534 1.89504358 TNTMNGSKS(ph)PVISR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TNTMNGSKSPVISR 14 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 TNTMNGS(0.003)KS(0.997)PVISR;TNTMNGSKS(1)PVISR;TNTMNGS(0.005)KS(0.936)PVIS(0.059)R;T(0.014)NT(0.011)MNGS(0.152)KS(0.823)PVISR;T(0.003)NT(0.012)MNGS(0.035)KS(0.951)PVISR;TNTMNGS(0.035)KS(0.965)PVISR;TNTMNGS(0.068)KS(0.931)PVISR;TNTMNGS(0.004)KS(0.996)PVISR 219.53 1.31E-11 7980020000 8548690 7905720 7904570 9324330 4975990 8863490 9428600 9377600 5967390 TRUE FALSE 8144610.366 8711321.856 8267002.353 8387030.633 5843801.081 8556545.119 7990093.902 8556447.63 6892782.364 1.181614323 1.263832426 1.199370866 1.216784484 0.847814536 1.241377526 1.159197183 1.241363383 1 22.71665503 -5 0.118066428 0.511185767 1.251979148 0.146583672 0.119838796 300.4889097 2.31168361 36.40255186 1.158492294 1.00E-05 5 0.740793381 TNTMNGSKS(ph)PVISRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNTMNGSKSPVISRPK 16 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 TNTMNGS(0.006)KS(0.992)PVIS(0.003)RPK;TNTMNGS(0.001)KS(0.997)PVIS(0.001)RPK 117.48 0.00027319 1057410000 619780 538660 586970 650630 331760 631110 696660 673070 367050 TRUE FALSE 590484.2277 593550.0664 613883.1551 585227.4363 389618.839 609254.5025 590371.722 614132.4226 423970.2394 1.392749238 1.399980497 1.447939261 1.380350274 0.918976859 1.437021861 1.392483875 1.448527197 1 18.69360347 -1.799179334 2.646279697 0.895286886 1.356209335 0.333890343 0.156272405 35212872.85 25533772.59 23714144.95 0.037374477 0.015878909 1.799179334 0.460922449 TNTNVNCPIECFMPLDVQADREDS(ph)RE ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE 213.73 1.34E-26 637858000 582899 498668 593042 537731 582096 592409 706001 599777 671130 TRUE FALSE 555346.5195 549482.8361 620233.5623 483677.2583 683613.3581 571893.7278 598287.5809 547257.3463 775205.4127 0.716386277 0.708822239 0.800089308 0.623934315 0.88184802 0.737731856 0.771779416 0.7059514 1 19.56421912 -5 0.282568014 2.906482097 0.726163037 0.580900027 0.068029232 151.4783389 1.444322873 169.6671272 0.066965176 1.00E-05 5 -2.18031906 TNTPVKEDWNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 151.99 6.33E-05 1186880000 2150640 1899180 1931990 2270920 1492940 2208670 2448370 2267280 1644420 FALSE TRUE 2048983.509 2092708.601 2020573.652 2042642.807 1753308.263 2132183.204 2074826.189 2068744.944 1899428.255 1.078736985 1.101757119 1.063779928 1.075398769 0.923071592 1.122539479 1.09234249 1.089140871 1 20.85713379 -2.660346882 1.73345172 5.93E-05 1.071665661 0.133258256 0.054193991 826991.526 36663.68899 3249542.918 0.01314475 0.002186015 2.660346882 1.071606383 TNVLGHLQQGGAPTPFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TNVLGHLQQGGAPTPFDR 18 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 197.86 1.80E-15 1012390000 1052900 1019110 1018590 1120200 777690 1067920 1144740 1076850 846460 FALSE TRUE 1003131.504 1122958.468 1065293.359 1007595.368 913318.8898 1030937.663 970088.8884 982555.3053 977724.6937 1.025985648 1.148542606 1.089563725 1.030551212 0.934126852 1.054425309 0.99219023 1.004940666 1 19.89906876 3.134772438 4.022763786 0.999633792 1.092254107 0.503339801 0.040925293 0.166693544 4.983658459 0.011502291 0.014085003 1363.868308 -3.134772438 0.092620315 TNYNDRYDEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;;;; 188.91 2.68E-06 7571066000 7688137 7539564 6850386 8918108 6506506 7834187 8342165 8130812 6656812 FALSE TRUE 7324734 8307854.143 7164482.974 8021642.841 7641238.586 7562887.14 7069414.515 7418834.997 7689116.407 0.952610627 1.08046929 0.931769347 1.043246378 0.9937733 0.983583385 0.919405318 0.964848834 1 22.87438639 2.032531514 3.909268532 0.952111134 1.005405024 0.111444056 0.045964917 0.316927759 10.47080674 0.01806973 0.011897078 107.7783458 -2.032531514 0.05329389 TNYNDRYDEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;;;;; 194.98 4.70E-07 14811144000 5031530 3402730 4372900 4619380 4663990 4847280 6754990 5096180 5632100 FALSE TRUE 4793699.548 3749472.056 4573401.79 4155031.146 5477388.379 4679417.478 5724392.212 4649931.463 6505497.303 0.736869039 0.576354409 0.703005716 0.638695391 0.841963054 0.71930204 0.879931532 0.714769563 1 22.63322792 1.061681529 0.305092355 1.032400555 0.625142486 0.585737904 0.078692143 1.149652959 0.342054504 0.174315594 0.106863476 11.52607734 -1.061681529 -0.407258069 TPAAAAAMNLAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;TPAAAAAMNLAS(1)PR 145.33 5.01E-06 1675897000 973320 850514 924663 995379 1069298 986749 1164273 1020635 1233201 TRUE FALSE 927313.0925 937182.3436 967059.7132 895321.6118 1255783.233 952577.6347 986641.7705 931262.7887 1424439.513 0.651002085 0.6579306 0.678905425 0.628543089 0.881598145 0.668738564 0.692652627 0.653774892 1 20.44196293 -1.77630235 2.699110583 1.07788507 0.687194953 0.656359077 0.070675322 20159394.63 16359879.31 10414394.77 0.015954586 0.016737772 1.77630235 -0.390690118 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR 364.43 1.55E-118 4385940000 2059350 1815220 2003140 2104970 2056890 1986120 2387480 2047460 2221500 TRUE FALSE 1962008.607 2000192.982 2094985.95 1893374.416 2415610.965 1917340.166 2023226.077 1868173.548 2565998.874 0.764617875 0.779498776 0.816440713 0.737870322 0.941392059 0.747210058 0.788475045 0.728049247 1 21.29108911 -1.694737904 2.790416477 1.029819147 0.787947226 0.54981573 0.060303023 16082364.62 14845941.2 3392539.272 0.012896252 0.020195848 1.694737904 -0.241871921 TPADTGFAFPDWAYKPESS(ph)PGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.207)S(0.792)PGS(0.001)R;TPADTGFAFPDWAYKPES(0.032)S(0.951)PGS(0.017)R;TPADTGFAFPDWAYKPES(0.369)S(0.627)PGS(0.003)R 226.72 5.79E-33 378410000 624853 619436 548423 711342 436740 569964 604600 584149 403300 TRUE FALSE 595317.437 682557.2326 573568.737 639836.5507 512907.3177 550226.0038 512357.1658 532997.8168 465841.7042 1.277939334 1.46521281 1.231252444 1.373506375 1.101033491 1.181143721 1.099852506 1.1441608 1 18.82948028 2.736744356 24.97317814 1.116662126 1.345916807 0.695544561 0.075874532 84.12689792 1156719.683 0.022098768 0.021822208 545.4366997 -2.736744356 0.229254681 TPAEGRDS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPAEGRDSPTREPGALPCACGQLPDLEDELSLLDPLPR 38 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 T(0.039)PAEGRDS(0.797)PT(0.164)REPGALPCACGQLPDLEDELSLLDPLPR 193.22 2.67E-24 22384000 12758 8234 8171.2 9485 9866 9285.1 10214 10641 8038.5 TRUE FALSE 12154.95462 9073.053961 8545.857602 8531.54978 11586.62728 8963.554659 8655.666707 9709.217629 9285.069525 1.309086011 0.977165969 0.920387034 0.918846085 1.247877277 0.965372918 0.932213451 1.04568066 1 13.180697 4.551123541 2.573987635 0.996461199 1.320384849 0.499230928 0.096442679 0.272415112 3.030067365 0.023733361 0.159707553 35573.2497 -4.551123541 0.32392365 TPALAALAALGAPGPAPTAAS(ph)SP ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPALAALAALGAPGPAPTAASSP 23 0 Q86V15 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 TPALAALAALGAPGPAPT(0.006)AAS(0.497)S(0.497)P;TPALAALAALGAPGPAPT(0.068)AAS(0.466)S(0.466)P 174.39 2.87E-12 120432000 421050 414820 406830 444210 452860 357920 463970 401460 444590 TRUE FALSE 401147.8009 457090.6296 425483.5579 399557.1669 531838.6406 345525.1407 393182.8551 366306.0341 513534.7465 0.78115026 0.890087054 0.828538985 0.778052838 1.035642952 0.672836927 0.765640218 0.713303309 1 18.97010237 TPALVFEHVNNTDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPALVFEHVNNTDFK 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YF43;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 166.9 1.34E-06 743990000 1552810 1574570 1413050 1603720 1067100 1638810 1646160 1656540 1053570 FALSE TRUE 1479411.749 1735020.473 1477839.74 1442511.019 1253201.902 1582057.599 1395008.058 1511484.576 1216952.255 1.215669508 1.425709568 1.214377749 1.185347258 1.029787239 1.300016161 1.146312892 1.242024549 1 20.21484114 -4.999999925 0.050480237 0.067618479 1.691846676 0.336374396 0.099790576 555.7461376 2.07297681 69.5559474 15.34504643 1.00E-05 4.999999925 1.624228197 TPAPPEPGS(ph)PAPGEGPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPAPPEPGSPAPGEGPSGR 19 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR 236.67 3.56E-24 794820000 579463 617732 554675 678894 568363 580658 640043 596332 619955 TRUE FALSE 552072.9324 680679.5931 580107.3974 610650.2853 667485.3272 560549.6679 542392.6852 544114.0087 716094.4551 0.770949877 0.950544426 0.810098994 0.852751032 0.932119112 0.782787332 0.757431762 0.759835528 1 19.44979037 2.200243537 24.99839833 0.79893831 0.863898916 0.007828548 0.086767999 338.4623089 220813.8996 0.029372857 0.02169373 158.5782194 -2.200243537 0.064960606 TPARPFGS(ph)VGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPARPFGSVGR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 TPARPFGS(1)VGR;TPARPFGS(1)VGR 95.854 0.0045106 332362000 127894 111687 116034 145975 140601 121224 116099 110129 130593 TRUE FALSE 121848.7041 123068.0323 121354.2737 131301.3157 165121.7699 117025.9825 98385.96525 100485.5209 150844.6955 0.807775863 0.815859198 0.804498118 0.870440391 1.094647507 0.775804427 0.65223351 0.666152168 1 17.20270444 -1.180920756 5.234451055 1.000009904 0.808034425 0.194218936 0.120903375 1.46E-05 2.29E-06 0.122673026 0.028912818 0.065929418 1.180920756 -0.191975479 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 TPASTPVS(0.004)GT(0.996)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVS(0.013)GT(0.987)PQAS(1)PMIER;TPASTPVS(0.007)GT(0.993)PQAS(1)PMIER;TPASTPVS(0.036)GT(0.964)PQAS(1)PMIER;TPASTPVS(0.014)GT(0.986)PQAS(1)PMIER 372.31 2.50E-107 1697630000 1735855 1727072 1532309 1852926 1608285 1589322 1742786 1745741 1620149 TRUE FALSE 1653804.574 1903062.6 1602566.883 1666666.358 1888769.395 1534283.381 1476891.987 1592874.663 1871393.432 0.883728961 1.016922774 0.856349528 0.890601799 1.00928504 0.819861475 0.789193743 0.851170382 1 20.83568146 2.214752169 24.99984504 0.840256535 0.933447381 0.12376634 0.07574204 301.4675217 316551.2183 0.026269295 0.019411449 163.9653833 -2.214752169 0.093190846 TPASTPVSGT(ph)PQASPMIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.01)GT(0.989)PQAS(0.001)PMIER;TPASTPVS(0.002)GT(0.996)PQAS(0.002)PMIER 223.18 2.36E-18 322870000 323680 313230 297820 355660 295830 295500 324700 326510 315130 TRUE FALSE 308380.2879 345148.4931 311475.3416 319908.3811 347422.6583 285266.7609 275161.0515 297919.0535 363998.7509 0.8472015 0.9482134 0.855704424 0.878872195 0.954461128 0.783702582 0.755939549 0.818461747 1 18.47357397 2.225668275 24.98133044 0.811143692 0.896680812 0.075674974 0.074505311 308.9136338 598573.9763 0.025103415 0.018657277 168.1389285 -2.225668275 0.08553712 TPASTPVSGTPQAS(ph)PMIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.003)GT(0.028)PQAS(0.969)PMIER;TPASTPVSGT(0.37)PQAS(0.63)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGT(0.006)PQAS(0.993)PMIER 353.22 8.04E-91 1321385000 667126 665883 579235 732169 567847 614431 641268 654688 557727 TRUE FALSE 635592.2761 733737.2347 605793.4977 658569.9811 666879.337 593153.1004 543430.7889 597360.048 644216.4547 0.986612918 1.138960716 0.94035707 1.022280596 1.035178987 0.920735719 0.843553102 0.927266051 1 19.29718599 2.201077318 4.964768194 0.901080854 1.033227446 0.368818692 0.063239068 0.158046315 9.121382831 0.023060667 0.017246997 158.8829585 -2.201077318 0.132146592 TPDS(ph)TFSETFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(0.209)PDS(0.791)TFSETFK 226.24 5.12E-12 242520000 535370 551150 437040 601980 334440 518560 462840 538300 348530 TRUE FALSE 510064.1211 607312.8116 457078.7163 541467.8267 392766.2301 500602.1372 392225.2574 491163.5983 402578.2524 1.266993729 1.508558418 1.13537856 1.345000192 0.975627043 1.243490264 0.974283273 1.220045036 1 18.61890971 3.124408402 1.273107989 1.083956503 1.374568611 0.386539836 0.13480024 0.359552316 1.230051287 0.04603186 0.062260894 1331.706141 -3.124408402 0.290612107 TPDTIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 132.09 0.0054554 595770000 1293480 815850 1185640 1032720 1690410 1154320 1713700 1327350 1959090 FALSE TRUE 1232339.764 898986.0425 1240002.767 928909.0236 1985216.969 1114345.609 1452243.591 1211120.197 2262895.672 0.54458532 0.397272421 0.547971691 0.410495736 0.877290541 0.492442326 0.641763387 0.535208146 1 21.10973864 -4.999999999 0.161649712 2.704728771 0.426674685 0.539800564 0.131259311 93.65829799 0.864894736 51.11190898 0.489616533 1.00E-05 4.999999999 -2.278054086 TPDVLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPDVLKK 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 69.198 0.096831 623890000 1579600 1313900 1270400 1601600 915260 1476300 1572100 1592900 1138200 FALSE TRUE 1504935.438 1447787.904 1328649.097 1440604.125 1074881.054 1425175.361 1332247.271 1453417.232 1314706.243 1.144693308 1.101225397 1.0106053 1.095761226 0.817582681 1.084025704 1.013342166 1.105507211 1 20.32630905 3.88902344 1.702709495 1.014834411 1.139813146 0.229727655 0.081007513 0.494607309 2.757601436 0.021659424 0.057540552 7745.035993 -3.88902344 0.124978736 TPEAVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPEAVQK 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 85.265 0.048711 118520000 238590 211780 213460 254630 187370 230520 287370 250210 236820 FALSE TRUE 227312.3235 233360.6228 223247.3521 229034.1086 220047.2687 222537.0346 243526.4286 228300.286 273544.8361 0.830987442 0.853098257 0.816127094 0.837281785 0.804428524 0.813530381 0.890261473 0.834599144 1 18.0614178 -0.012473192 0.650003216 1.008311231 0.830929728 0.83250395 0.023368657 1.808421627 0.839428415 0.061528564 0.008796344 0.97168793 0.012473192 -0.177381503 TPEEIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPEEIRK 7 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 71.342 0.087507 310910000 116490 91080 98671 120480 101180 108360 132850 123230 119170 FALSE TRUE 110983.7486 100361.1555 103195.1629 108369.1215 118825.76 104607.466 112581.2925 112439.3279 137650.275 0.806273352 0.729102471 0.749690932 0.787278642 0.863243898 0.759951014 0.817879169 0.816847826 1 17.07064797 -4.99995333 0.205261736 2.012314792 0.754368238 0.784201661 0.035337825 62.16748394 0.617600116 25.76570548 0.076390245 1.00E-05 4.99995333 -1.257946553 TPEEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPEEIRR 7 1 P09525;Q6P452;P09525-2;B4E1S2 P09525 ANXA4 Annexin A4;Annexin 0 ;;; 114.6 0.024808 962120000 1199760 918980 804204 1409270 1565010 868964 1066660 900449 1319360 FALSE TRUE 1143049.722 1012625.107 841077.5489 1267607.502 1837947.248 838871.5588 903921.4264 821600.912 1523959.61 0.750052504 0.66446978 0.551902782 0.831785497 1.206034094 0.550455244 0.593140015 0.539122498 1 20.53939324 4.772303415 18.61628496 0.720448221 0.75005399 0 0.220066653 1740.130635 1451186.407 0.051217748 1.441347663 59197.50667 -4.772303415 0.029605769 TPEELDDS(ph)DFETEDFDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 469.98 1.44E-214 11660090000 3166460 2998958 3160330 3380580 3258870 3108970 3559480 3251280 3284065 TRUE FALSE 3016787.711 3304555.23 3305234.256 3040757.676 3827215.896 3001305.589 3016415.952 2966580.687 3793341.028 0.79528513 0.87114636 0.871325365 0.801604088 1.008930088 0.791203735 0.795187127 0.782049561 1 21.85503765 -2.396577859 2.258373423 2.264717116 0.839189908 0.354141231 0.068076669 2475952.328 315371.5718 16162692.86 0.015611964 0.004012566 2.396577859 -1.425527208 TPEEREWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TPEEREWR 8 1 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2;E9PJG2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 0 ;;;;; 79.906 0.024464 4569640000 3844820 3159280 3337350 3743500 3432780 3324380 3992940 3477450 3615760 FALSE TRUE 3663082.978 3481214.224 3490370.799 3367196.268 4031455.745 3209255.887 3383743.668 3172946.043 4176473.594 0.877075575 0.833529566 0.835721984 0.806229512 0.965277441 0.768412828 0.810191563 0.759718928 1 21.99385389 TPEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TPEFLR 6 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;; 107.55 0.072514 3328773000 2436460 2011110 2095670 2414540 2432690 2067050 2664040 2282120 2416750 FALSE TRUE 2321293.364 2216044.395 2191758.542 2171825.852 2856950.366 1995467.54 2257591.77 2082285.475 2791527.247 0.8315496 0.793846593 0.785146749 0.778006324 1.023436317 0.714830042 0.808729978 0.745930557 1 21.41262321 -1.316410586 3.458718695 1.000819199 0.810270191 0.343957815 0.082384783 32967398.75 53183083.05 283488.5453 0.018055917 0.048260233 1.316410586 -0.190549008 TPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(0.017)PAS(0.983)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.007)PAS(0.993)PPRS(1)PAEPNDIPIAK;T(0.026)PEKLDNT(0.145)PAS(0.834)PPRS(0.995)PAEPNDIPIAK;TPEKLDNT(0.005)PAS(0.995)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.008)PAS(0.992)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.004)PAS(0.996)PPRS(1)PAEPNDIPIAK;T(0.028)PEKLDNT(0.057)PAS(0.929)PPRS(0.987)PAEPNDIPIAK;TPEKLDNT(0.006)PAS(0.994)PPRS(1)PAEPNDIPIAK 149.49 8.23E-08 4781830000 3631420 2845568 3401750 3609430 2345124 3722530 4256120 3843630 2564920 TRUE FALSE 3459769.973 3135534.614 3557723.602 3246603.239 2754112.883 3593617.853 3606770.725 3507061.381 2962674.694 1.167785981 1.0583459 1.200848547 1.095835208 0.92960354 1.212964036 1.217403562 1.183748384 1 21.49846879 TPEKLDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Trastuzumab_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 1 TPEKLDNT(0.001)PAS(0.998)PPRSPAEPNDIPIAK 107.91 0.0014143 491170000 382230 411770 409280 418830 259920 559380 596440 702140 486320 TRUE FALSE 364162.7454 453729.8311 428045.8928 376728.4127 305249.9657 540008.5303 505442.1236 640656.8993 561736.0218 0.648280921 0.807727854 0.762005419 0.670650266 0.543404649 0.961320815 0.89978585 1.1404946 1 19.09953279 2.14830455 8.030688137 0.983635644 0.702552898 0.740485732 0.09190794 0.141070858 11.02108266 0.0344431 0.025425568 140.7033864 -2.14830455 -0.281082745 TPELNLDQFHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPELNLDQFHDK 12 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 159.12 7.06E-05 482910000 878020 956020 730840 1256290 796340 974510 1011540 923600 531180 FALSE TRUE 836517.7347 1053439.525 764349.7369 1130005.342 935221.4439 940762.4743 857210.9948 842724.6877 613552.6815 1.363400014 1.716950405 1.245776866 1.841741348 1.524272442 1.533303501 1.397126963 1.373516428 1 19.2268277 0.806371629 0.950427673 1.002270349 1.546455614 0.503762335 0.165574309 0.6122293 1.074459672 0.140520133 0.046651375 6.40282496 -0.806371629 0.544185265 TPELNLDQFHDKTPYTIMFGPDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPELNLDQFHDKTPYTIMFGPDK 23 1 P27824;P27824-2;P27824-3;H0Y9Q7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 235.95 2.50E-37 327410000 930280 532840 870070 1124610 1055480 1039440 1542730 1004100 929920 FALSE TRUE 886307.508 587137.0018 909963.5701 1011562.066 1239555.378 1003443.932 1307358.204 916175.6809 1074127.244 0.825142005 0.546617735 0.847165524 0.941752545 1.154011673 0.934194657 1.217135317 0.852948927 1 20.03473348 3.30613187 2.411150881 1.048918613 0.687416779 0.542233908 0.125197493 0.169828061 2.014597824 0.034484111 0.048458474 2023.633545 -3.30613187 -0.361501833 TPELTWER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 147.04 0.0012649 561104000 276610 245923 178700 216855 296664 206389 313747 247098 303041 FALSE TRUE 263535.1935 270982.8333 186893.5718 195056.3234 348402.1077 199241.6972 265879.1328 225460.7892 350035.0506 0.752882299 0.774159139 0.533928164 0.557247976 0.995334916 0.569204989 0.759578598 0.644109179 1 18.41713987 -1.370381443 3.232208983 1.002700756 0.706301189 0.323988544 0.136522694 32834145.2 42769460.62 829592.3004 0.030262169 0.042620502 1.370381443 -0.296399567 TPEPVVPTAPELRPS(ph)TSTDRPVTPKPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.303)T(0.303)S(0.069)T(0.023)DRPVT(0.169)PKPT(0.067)S(0.067)R 96.903 0.0057601 462940000 89830 79992 89094 77453 54539 77709 99025 84065 83318 TRUE FALSE 85583.91393 88143.27574 93179.04803 69667.27729 64050.58433 75017.91784 83916.91753 76703.82294 96238.52991 0.889289498 0.915883439 0.968209387 0.723902135 0.665539929 0.779499831 0.87196799 0.797017816 1 16.55432698 3.245027161 24.99982168 0.796749669 0.917598308 0.271204654 0.0901571 191.1755514 739084.5118 0.0242774 0.032110312 1758.03356 -3.245027161 0.120848638 TPEPVVPTAPELRPSTSTDRPVT(ph)PKPTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.003)T(0.003)S(0.003)T(0.003)DRPVT(0.915)PKPT(0.036)S(0.036)R;TPEPVVPT(0.003)APELRPS(0.091)T(0.091)S(0.091)T(0.091)DRPVT(0.609)PKPT(0.011)S(0.011)R;TPEPVVPTAPELRPS(0.031)T(0.031)S(0.031)T(0.135)DRPVT(0.723)PKPT(0.024)S(0.024)R;TPEPVVPTAPELRPS(0.106)T(0.106)S(0.14)T(0.14)DRPVT(0.487)PKPT(0.01)S(0.012)R;TPEPVVPTAPELRPS(0.131)T(0.131)S(0.032)T(0.032)DRPVT(0.666)PKPT(0.004)S(0.005)R;TPEPVVPTAPELRPS(0.087)T(0.087)S(0.087)T(0.087)DRPVT(0.441)PKPT(0.105)S(0.105)R 123.56 2.58E-05 3851700000 1583351 1405119 1449673 1566064 1121534 1506712 1644110 1741635 1295709 TRUE FALSE 1508509.136 1548302.224 1516141.941 1408640.271 1317129.175 1454534.186 1393270.823 1589128.206 1496640.934 1.007929893 1.034518159 1.01302985 0.941201219 0.880056896 0.971865831 0.930931923 1.061796567 1 20.51329671 3.29798477 6.331475017 0.955631254 1.021166869 0.209906106 0.047638554 0.245423327 19.41992439 0.0125127 0.01687841 1986.025267 -3.29798477 0.065535615 TPESNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPESNIK 7 0 E9PPJ9;A0A1W2PQA7;A0A1W2PNY5;A0A1W2PQZ6;A0A1W2PRF0;A0A1W2PRJ0;A0A1W2PPP6;A0A1X7SBS0;A0A1W2PS93;A0A1W2PR08;A0A1W2PRF5;G5E9D4;Q96EB1;Q96EB1-3;Q96EB1-2 E9PPJ9 ELP4 Elongator complex protein 4 0 77.741 0.086604 217250000 202790 176040 187690 225320 161440 190190 240830 219890 204760 FALSE TRUE 193204.5186 193978.6761 196295.7722 202670.4055 189595.0849 183603.6726 204086.9604 200635.2659 236513.135 0.816887056 0.820160268 0.82995717 0.856909725 0.801626027 0.776293767 0.862899053 0.848304961 1 17.85156078 0.531715333 1.143032552 0.99994406 0.820477798 0.844780897 0.023757501 0.612994193 1.109019928 0.021968677 0.006748521 3.401851354 -0.531715333 -0.179466262 TPESQPDT(ph)PPGT(ph)PLVSQDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 2 TPESQPDT(1)PPGT(1)PLVSQDEKR;TPESQPDT(1)PPGT(0.997)PLVS(0.003)QDEKR 114.83 0.00010426 196851000 350290 303240 298610 361410 259010 322550 356850 358520 284470 TRUE FALSE 333732.4859 334140.5008 312301.5639 325080.3802 304181.262 311380.0126 302405.9785 327126.0882 328584.1547 1.015668227 1.016909963 0.950446208 0.989336751 0.925733203 0.947641595 0.920330375 0.995562578 1 18.32590339 3.740744532 24.09623972 0.954788861 1.016289102 0.38635464 0.027893511 88.54679664 976971.5494 0.006821573 0.011581096 5504.83786 -3.740744532 0.061500242 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(1)PPGTPLVSQDEKR;TPESQPDT(0.999)PPGT(0.001)PLVSQDEKR;TPESQPDT(0.999)PPGT(0.001)PLVSQDEKR;TPESQPDT(0.997)PPGT(0.003)PLVSQDEKR;TPESQPDT(0.999)PPGT(0.001)PLVSQDEKR;TPESQPDT(1)PPGTPLVSQDEKR;TPESQPDT(0.998)PPGT(0.002)PLVSQDEKR;TPESQPDT(1)PPGTPLVSQDEKR;T(0.001)PES(0.012)QPDT(0.987)PPGTPLVSQDEKR 194.11 2.83E-18 12581820000 12848970 11819350 11365990 13928970 8707050 12737700 13468260 13767470 9668200 TRUE FALSE 12241624.65 13023755.2 11887131.88 12528803.47 10225556.76 12296590.26 11413429.58 12561917.34 11167495.08 1.096183573 1.166219919 1.064440307 1.121899171 0.915653572 1.1011055 1.022022351 1.124864372 1 23.41280228 LVLVNMVY(ph)FK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 LVLVNMVYFK 10 0 A0A0A0MQW3;Q9UIV8-2;Q9UIV8 A0A0A0MQW3 SERPINB13 Serpin B13 1 LVLVNMVY(1)FK 43.512 0.068247 0 236500 213010 351280 495650 460850 639450 603730 676110 457320 TRUE FALSE 225321.1137 234715.9612 367386.5355 445826.3203 541222.0941 617305.6862 511619.9002 616906.2241 528238.8499 0.426551576 0.444336802 0.695493214 0.843986239 1.024578359 1.168610916 0.968538948 1.167854701 1 19.01083088 3.295123336 1.288316939 1.072160484 0.413811474 0.934967222 0.067815429 0.08417131 0.292971835 0.022472272 0.035939913 1972.982968 -3.295123336 -0.65834901 down TPFLLSGTSYKDLMPHDLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPFLLSGTSYKDLMPHDLAR 20 1 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 184.78 2.33E-17 64627000 88397 28958 90429 49873 116450 63721 135280 95246 137860 FALSE TRUE 84218.649 31908.85312 94575.2591 44859.67129 136758.8431 61514.32579 114640.5514 86905.75531 159238.6247 0.528883298 0.200383878 0.593921602 0.281713506 0.858829592 0.386302795 0.719929299 0.545758012 1 17.28083079 -0.091204647 0.194462946 1.295522101 0.279647347 0.446370183 0.183451577 8.39029646 0.578419252 2.185934617 0.6040082 0.81057901 0.091204647 -1.015874753 TPGRQS(ph)PGPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPGRQSPGPGHR 12 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 TPGRQS(1)PGPGHR 95.067 0.0037884 36734000 39520 37297 38731 43706 36129 38392 38390 38633 36108 TRUE FALSE 37651.96792 41097.6067 40506.85466 39312.58984 42429.88616 37062.47541 32532.90042 35250.08971 41707.44423 0.90276373 0.985378209 0.971214022 0.94257969 1.017321654 0.888629742 0.780026228 0.845175013 1 15.34801729 2.028026459 8.534787798 0.846536715 0.9601346 0.279725355 0.062901101 0.204123649 55.19850991 0.021511386 0.015733817 106.6661105 -2.028026459 0.113597885 TPHDILEDINAS(ph)PEMR ddPTM_SK-BR-3_Trastuzumab_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 232.49 2.38E-16 385224000 284724 236529 254607 277303 283716 239469 316693 269504 282239 TRUE FALSE 271265.6608 260631.574 266280.9828 249427.9756 333195.9806 231176.1285 268375.6664 245904.801 326007.1826 0.832084921 0.799465742 0.816794834 0.765099632 1.022051042 0.709113605 0.823220103 0.754292587 1 18.31454422 -0.932780947 4.223505946 1.000005468 0.815405573 0.332633915 0.08223347 30150654.93 40995887.4 2237.801716 0.017540133 0.116739829 0.932780947 -0.184599894 TPHYGSQTPLHDGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 106.6 0.00070766 135195000 73929 51398 71176 72428 95945 82600 87463 73252 88328 FALSE TRUE 70434.52268 56635.51463 74439.49 65147.39984 112677.7776 79739.54129 74118.91298 66837.66655 102025.4551 0.690362249 0.55511161 0.729616838 0.638540644 1.104408478 0.781565161 0.726474711 0.655107752 1 16.63856962 TPIS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TPISPLK 7 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.001)PIS(0.999)PLK;TPIS(1)PLK;T(0.007)PIS(0.993)PLK;T(0.002)PIS(0.998)PLK;TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK 135.71 0.0032 5236400000 9309820 9027200 7558960 10275580 5224140 9476780 8954660 9622440 5144280 TRUE FALSE 8869763.259 9947081.943 7905545.793 9242659.176 6135228.362 9148596.732 7588462.153 8779848.142 5942028.669 1.492716335 1.674021197 1.330445582 1.555471993 1.032514096 1.539641971 1.277082723 1.477584278 1 22.50252414 -2.715632117 0.077233074 9.10E-11 1.961282209 0.385006425 0.173979514 140.6535432 1.259797592 32.10575182 7.24230858 0.001924721 2.715632117 1.961282209 TPIS(ph)PLKTGVSKPIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPISPLKTGVSKPIVK 16 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.16)PIS(0.84)PLKTGVSKPIVK;TPIS(1)PLKTGVSKPIVK 168.27 4.75E-09 1272820000 2235210 1265930 2340400 1939250 1521330 2462900 3300600 2751300 1908420 TRUE FALSE 2129556.053 1394929.706 2447709.655 1744312.906 1786649.47 2377609.155 2797032.85 2510381.586 2204368.027 0.96606194 0.632802549 1.110390654 0.791298406 0.810504167 1.07858993 1.26885929 1.138821447 1 21.07193368 2.123018971 4.433582908 1.16727267 0.848873723 0.45812039 0.138979706 0.15852 5.409539933 0.051062311 0.03679854 132.7452443 -2.123018971 -0.318398947 TPKDS(ph)PGIPPSAGAHQLFR ddPTM_SK-BR-3_Trastuzumab_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(0.001)PKDS(0.999)PGIPPSAGAHQLFR;T(0.005)PKDS(0.995)PGIPPSAGAHQLFR 155.97 1.25E-08 877550000 1461120 1036060 1243780 1448600 1128660 1249390 1663430 1493370 1152010 TRUE FALSE 1392055.753 1141635.692 1300808.543 1302983.976 1325497.947 1206123.311 1409643.203 1362602.606 1330657.827 1.046141033 0.857948354 0.977568024 0.979202879 0.996122309 0.906411315 1.059358141 1.024006757 1 20.34370821 1.709611354 10.68723962 1.030471114 0.958080456 0.267386197 0.052226271 0.137065325 34.81092106 0.023669462 0.01285399 51.24026344 -1.709611354 -0.072390659 TPKDS(ph)PGIPPSANAHQLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPKDSPGIPPSANAHQLFR 19 1 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 T(0.186)PKDS(0.814)PGIPPSANAHQLFR;T(0.003)PKDS(0.997)PGIPPSANAHQLFR 93.633 0.0010419 386310000 494040 438950 456410 498350 319150 563350 618000 634630 383030 TRUE FALSE 470687.7083 483679.504 477336.85 448254.9112 374809.659 543841.0482 523712.7497 579058.4328 442428.3362 1.063873332 1.093238078 1.078902075 1.013169534 0.847164678 1.229218393 1.183723344 1.308818594 1 18.75508426 2.166661475 24.99999145 1.195657936 1.035831341 0.369928793 0.102416619 45.7600285 15910.04037 0.035971949 0.02656705 146.778172 -2.166661475 -0.159826595 TPLAVELEVLDGHDPDPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TPLAVELEVLDGHDPDPGR 19 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;;;;;; 167.05 1.87E-11 404326900 549800 451900 485807 530669 555432 446843 550269 501573 497727 FALSE TRUE 523812.0436 497949.1238 508081.7315 477325.1439 652299.1649 431368.7149 466315.3577 457652.6091 574911.9611 0.911116969 0.86613109 0.883755715 0.830257807 1.134607051 0.750321343 0.81110742 0.796039464 1 19.13298152 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.011)APS(0.87)PT(0.12)R;TPLDLFAHFGPEPGDHSDPLPPS(0.012)APS(0.804)PT(0.184)R;TPLDLFAHFGPEPGDHSDPLPPS(0.039)APS(0.928)PT(0.034)R;TPLDLFAHFGPEPGDHS(0.011)DPLPPS(0.244)APS(0.578)PT(0.167)R;TPLDLFAHFGPEPGDHSDPLPPS(0.003)APS(0.991)PT(0.006)R;TPLDLFAHFGPEPGDHSDPLPPS(0.193)APS(0.773)PT(0.034)R;TPLDLFAHFGPEPGDHSDPLPPS(0.002)APS(0.967)PT(0.032)R;TPLDLFAHFGPEPGDHSDPLPPS(0.009)APS(0.975)PT(0.016)R 242.82 2.76E-45 1616876000 901324 964138 767722 977476 781962 862022 827359 841898 256882.2 TRUE FALSE 858720.2008 1062384.758 802922.8131 879218.2554 918335.9252 832169.962 701130.1891 768176.9479 296718.1796 2.894059953 3.580450513 2.706011523 2.963142523 3.094976946 2.804580303 2.362949887 2.588910962 1 18.1787338 0.078446022 0.341806645 0.569601922 3.244663595 0.860990151 0.250253595 1.468395771 0.258633395 1.135523092 0.226965955 1.19797022 -0.078446022 2.675061673 TPLEQEIFNLLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 165.73 3.48E-05 103869000 256720 232800 237510 267020 234180 251050 293190 270350 221830 FALSE TRUE 244585.3544 256522.5847 248400.0684 240178.6423 275020.9179 242356.0756 248458.4807 246676.7208 256230.2634 0.954552952 1.001140854 0.969440788 0.937354702 1.073335031 0.945852657 0.969668756 0.962715011 1 17.96708136 4.738130177 5.172999971 0.980578521 0.953445947 0.048407182 0.03806472 0.552890761 44.59585029 0.008314625 0.052555136 54717.99514 -4.738130177 -0.027132574 TPLGAS(ph)LDEQSSSTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK 229.93 5.82E-14 110830000 257054 182131 193185 324195 306900 282183 344532 215225 278015 TRUE FALSE 244903.5669 200690.356 202042.7233 291606.3027 360423.2628 272410.932 291967.3156 196378.758 321128.1463 0.762635009 0.624954113 0.629165415 0.90806834 1.122365844 0.84829354 0.909192542 0.611527704 1 18.29278959 3.232274169 24.99691342 0.903006006 0.675028274 0.396223472 0.132425791 142.2150593 565492.0327 0.036567044 0.044734454 1707.159775 -3.232274169 -0.227977732 TPLRPLDPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 122.69 0.00043945 1435710000 2552470 2380090 1807600 2321700 2579500 2127500 2692120 2510310 2698520 FALSE TRUE 2431819.802 2622623.877 1890480.248 2088318.305 3029363.983 2053824.142 2281387.65 2290493.948 3116992.699 0.780181424 0.841395579 0.606507756 0.669978568 0.971886775 0.65891208 0.731919472 0.734840973 1 21.57172335 -1.487502965 6.383330989 1.000131763 0.753832149 0.370620703 0.102467343 0.000182245 1.46E-05 0.094102134 0.022168303 0.032545956 1.487502965 -0.246299614 TPLS(ph)PSPMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPLSPSPMK 9 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 T(0.001)PLS(0.996)PS(0.002)PMK;T(0.001)PLS(0.997)PS(0.003)PMK 119.34 0.00088511 265220000 628230 534730 513420 607470 515320 539390 609010 549600 423280 TRUE FALSE 598534.8129 589219.5949 536960.8148 546405.9615 605191.6448 520710.7891 516094.3393 501474.1104 488920.1006 1.224197598 1.20514496 1.098258824 1.117577209 1.237812976 1.065022257 1.055580122 1.025677017 1 18.89923919 2.259866116 0.387779141 0.981506096 1.233369169 0.653476657 0.049113481 0.75696613 0.26718175 0.055090669 0.066910925 181.9139969 -2.259866116 0.251863073 TPLSEAEFEEIMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ;;; 193.22 1.93E-07 30065000 49811.2 43520.8 36822.8 45131.8 44403.4 40174.2 48043 40994.5 50954.8 FALSE TRUE 47456.72329 47955.619 38511.1618 40595.06572 52147.3389 38782.95738 40713.15798 37404.80425 58856.61014 0.806310849 0.814787309 0.654321778 0.689728233 0.886006496 0.658939706 0.691734673 0.635524271 1 15.84491683 3.785039334 23.71006044 0.728547907 0.810549193 0.037658691 0.115655511 532.6138704 271697.9046 0.026613106 0.047977167 6095.92106 -3.785039334 0.082001286 TPLSFTNPLHS(ph)DDS(ph)DSDERNSDGAVTQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TPLSFTNPLHS(1)DDS(0.903)DS(0.091)DERNS(0.006)DGAVTQNK;TPLS(0.002)FT(0.002)NPLHS(0.985)DDS(0.876)DS(0.132)DERNS(0.001)DGAVTQNK 172.67 2.27E-12 131532000 106185 82825 93952 103275 83920 86772 113776 80403 89772 TRUE FALSE 101165.8455 91264.96166 98259.79213 92893.60079 98555.62143 83767.06388 96417.38156 73362.48708 103693.3833 0.975624888 0.880142578 0.947599442 0.895848875 0.950452366 0.807834225 0.929831572 0.707494391 1 16.66196431 2.255945271 24.9949128 0.861712598 0.926551379 0.154538324 0.079560358 438.4316565 630356.9976 0.024260359 0.020254264 180.2790542 -2.255945271 0.064838781 TPLSQS(ph)MSVLPTSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPLSQSMSVLPTSKPEK 17 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 TPLSQS(1)MSVLPTSKPEK;TPLSQS(0.999)MS(0.001)VLPTSKPEK 211.98 1.20E-12 1815020000 2786200 1694890 2503000 3138700 2182400 3344200 3581200 2867900 2229100 TRUE FALSE 2654501.848 1867601.218 2617765.026 2823191.913 2563009.869 3228389.515 3034822.167 2616771.472 2574777.443 1.03096361 0.725344718 1.01669565 1.096479977 0.995429673 1.253851871 1.178673588 1.01630977 1 21.2960163 3.494155021 5.02572827 1.108280868 0.875583539 0.381002314 0.108668332 0.154135001 11.02283191 0.029276147 0.043433959 3120.003068 -3.494155021 -0.232697329 TPLYLQPDAYGS(ph)LDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPLYLQPDAYGSLDR 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR 195.17 2.25E-08 315900000 307370 250890 271680 412660 334480 353760 398370 309700 332070 TRUE FALSE 292841.2292 276455.9762 284136.7967 371178.6328 392813.2061 341509.2025 337591.3399 282581.0262 383565.7196 0.763470806 0.720752565 0.740777348 0.967705438 1.024109262 0.890353817 0.880139498 0.736721275 1 18.54911426 3.250471087 24.97284196 0.911685297 0.740300049 0.518855555 0.079273574 174.7594084 366418.2137 0.021847546 0.029352562 1780.209387 -3.250471087 -0.171385249 TPPGALLGAPPPLVPAPRPS(ph)SPPRGPGPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPPGALLGAPPPLVPAPRPSSPPRGPGPAR 30 2 J3KNZ9;Q9HAH7 J3KNZ9 FBRS Probable fibrosin-1 1 TPPGALLGAPPPLVPAPRPS(0.5)S(0.5)PPRGPGPAR 43.554 0.069042 226660000 52975 39144 59248 52605 58031 53551 68969 57320 73991 TRUE FALSE 50470.97674 43132.8181 61964.5794 47317.04546 68151.58803 51696.51544 58446.51235 52300.75693 85465.14639 0.590544554 0.504683136 0.725027476 0.553641425 0.797419661 0.604884185 0.683863713 0.611954219 1 16.38304857 -5 0.181898295 2.530456994 0.550708403 0.653437012 0.083933948 75.34829019 0.727791927 41.72905102 0.231121372 1.00E-05 5 -1.97974859 TPPSTTVGSHS(ph)PPETPVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 265.53 7.68E-37 4065490000 769600 643160 725260 754300 818450 678160 878400 814370 809100 TRUE FALSE 733222.5332 708698.7352 758513.8884 678476.3309 961187.4209 654675.1492 744383.9471 743059.4456 934571.0957 0.784555115 0.758314417 0.811617106 0.725976155 1.028479722 0.700508663 0.796497934 0.795080705 1 19.83394489 -1.673892429 2.175001929 1.039832445 0.795978408 0.336113163 0.088107486 1685985.754 1118461.573 369880.6277 0.020912319 0.021188859 1.673892429 -0.243854037 TPQEAIMDGTEIAVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 TPQEAIMDGTEIAVS(1)PR 140.2 7.03E-07 44423000 76092 79511 73148 77467 78172 73941 84726 85385 91846 TRUE FALSE 72495.28196 87613.2613 76501.90815 69679.86998 91805.17205 71380.40463 71799.4926 77908.23675 106089.0086 0.683343948 0.825846734 0.721110595 0.656805742 0.865359883 0.672835062 0.676785405 0.734366715 1 16.69491567 0.913693614 20.99839712 1 0.730274991 0.611992733 0.067681121 11767.8885 2863141.218 0.062302226 0.015575557 8.197730063 -0.913693614 -0.269725009 TPQEAITDGLEIVVS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPQEAITDGLEIVVSPR 17 0 X6RFN3;Q99496-2;Q99496 X6RFN3 RNF2 E3 ubiquitin-protein ligase RING2 1 TPQEAITDGLEIVVS(1)PR 144.72 5.26E-07 11274000 29578 26376 29288 30677 31372 26152 34752 32246 34598 TRUE FALSE 28179.90656 29063.74439 30630.88377 27593.28968 36843.26687 25246.34968 29449.94414 29422.36929 39963.28114 0.705144967 0.727261215 0.766475697 0.69046607 0.921927975 0.63173866 0.73692508 0.736235075 1 15.28638742 -1.239109832 2.941509776 1.001521225 0.736371891 0.549139917 0.074125424 6158467.24 7966946.03 84805.05211 0.017183573 0.057662062 1.239109832 -0.265149334 TPQPS(ph)SPMDQMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPQPSSPMDQMGK 13 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 TPQPS(0.5)S(0.5)PMDQMGK 77.527 0.017118 26974000 75222 67113 73011 84521 53421 80614 88922 80286 60757 TRUE FALSE 71666.40514 73951.891 76358.62657 76024.7885 62737.60549 77822.31697 75355.31574 73255.73222 70178.88526 1.021196117 1.053762691 1.088056989 1.08330003 0.893966971 1.108913553 1.073760512 1.043842916 1 16.09874941 TPRT(ph)PQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.403)PRT(0.597)PQLK;T(0.086)PRT(0.914)PQLK 88.596 0.023446 3901200000 2031350 1548610 2089390 2038320 1970860 2266200 2674700 2364100 2372180 TRUE FALSE 1935332.111 1706415.12 2185190.598 1833424.201 2314577.36 2187720.926 2266625.391 2157086.871 2740045.559 0.706313844 0.622768886 0.797501557 0.669121794 0.844722217 0.798425018 0.82722179 0.787244892 1 21.38576845 -2.600482172 0.061554994 1.775088648 0.279338665 0.711360202 0.056016106 102.2684675 0.751830751 15.84904871 4.954021269 0.002509099 2.600482172 -1.495749984 TPRT(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.441)PRT(0.559)PRT(1)PQLK;T(0.303)PRT(0.699)PRT(0.999)PQLK;T(0.262)PRT(0.738)PRT(1)PQLK;T(0.373)PRT(0.628)PRT(1)PQLK;T(0.316)PRT(0.688)PRT(0.996)PQLK 121.99 0.0004636 2633630000 2452100 1853820 2420020 2456980 2187790 2592370 3207560 2738820 2496130 TRUE FALSE 2336194.093 2042726.366 2530980.311 2209999.702 2569339.883 2502595.577 2718187.811 2498994.401 2883217.092 0.810273392 0.708488574 0.877832029 0.766504787 0.891136464 0.867987216 0.942762104 0.866738203 1 21.45924804 2.221019288 0.408107637 0.98985998 0.744786878 0.610174467 0.051824987 0.671048142 0.259294769 0.050877513 0.056850232 166.3486529 -2.221019288 -0.245073102 TPS(ph)EADRWLEEVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSEADRWLEEVSK 14 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 T(0.057)PS(0.943)EADRWLEEVSK;T(0.132)PS(0.868)EADRWLEEVSK 166.6 2.29E-06 61295000 73264 60845 62071 71747 54499 69131 82342 75851 62973 TRUE FALSE 69800.95592 67045.17468 64917.01675 64534.85525 64003.60834 66736.97614 69779.21559 69209.08433 72738.53122 0.959614591 0.921728464 0.892470822 0.887216915 0.8799134 0.91749139 0.959315708 0.951477617 1 16.15043217 1.36146267 1.3852069 0.990747213 0.912449477 0.593169459 0.024306586 0.327972625 1.190054673 0.025179972 0.0080451 22.98596122 -1.36146267 -0.078297736 TPS(ph)FHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSFHIK 7 0 O60890 O60890 OPHN1 Oligophrenin-1 1 T(0.296)PS(0.704)FHIK;T(0.344)PS(0.656)FHIK 78.816 0.0221 241130000 446520 349660 370000 434610 340720 384370 421870 406590 290390 TRUE FALSE 425413.8845 385290.7515 386964.866 390922.1771 400141.4601 371059.1705 357505.9833 370986.8241 335422.1981 1.268293771 1.148673981 1.153665047 1.165463047 1.192948655 1.106245122 1.065838771 1.106029435 1 18.35561864 8 0.081364774 0.865936115 1.881672787 0.813506952 0.031292447 77.13206082 0.456554367 0.842598108 8.797157859 100000000 -8 1.015736672 TPS(ph)FLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSFLK 6 0 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 T(0.015)PS(0.985)FLK;T(0.015)PS(0.985)FLK 81.548 0.064604 85394000 711010 696760 585190 795900 484570 687060 692310 772760 511010 TRUE FALSE 677401.9664 767760.6362 612021.5403 715894.6199 569078.8546 663266.9399 586685.3944 705093.0377 590254.8209 1.147643259 1.30072743 1.036876818 1.212856879 0.964124026 1.12369593 0.993952736 1.194557016 1 19.17097839 3.409486326 1.502645 1.062858458 1.217935029 0.234798483 0.095770715 0.43280805 2.000649952 0.02783883 0.047312519 2567.357375 -3.409486326 0.155076571 TPS(ph)GEFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSGEFLER 9 0 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 T(0.021)PS(0.979)GEFLER 75.416 0.0402 77753000 82908 73715 78105 85162 71797 77932 78753 87121 76702 TRUE FALSE 78989.10315 81226.64231 81686.19151 76601.35396 84318.37407 75233.1953 66737.78345 79492.22338 88596.55442 0.891559538 0.916814913 0.9220019 0.864608725 0.951711662 0.849166153 0.753277415 0.897238317 1 16.43496297 2.119039833 8.645355169 0.842529099 0.907187228 0 0.066761324 0.419116914 29.87454891 0.022864312 0.016876909 131.5345468 -2.119039833 0.064658129 TPS(ph)IQPSLLPHAAPFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSIQPSLLPHAAPFAK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 T(0.117)PS(0.812)IQPS(0.07)LLPHAAPFAK 103.9 0.00091079 0 140490 103920 121490 159790 136280 149560 179100 123080 146340 TRUE FALSE 133849.3161 114509.5661 127060.4367 143727.6056 160047.1889 144380.6997 151775.0056 112302.4627 169033.6598 0.791850075 0.677436472 0.75168719 0.850289852 0.946836204 0.854153545 0.897898121 0.664379289 1 17.36695103 3.239259161 4.137444729 0.870131174 0.732038115 0.315326034 0.089930774 0.222004782 8.683118679 0.023902724 0.030963783 1734.838938 -3.239259161 -0.138093058 TPS(ph)PAAEDAREPEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.058)PS(0.942)PAAEDAREPEAK;T(0.248)PS(0.752)PAAEDAREPEAK 100.97 0.0011828 854730000 486640 545810 419070 577530 444490 505520 497010 529910 430000 TRUE FALSE 463637.4916 601428.6595 438284.774 519475.5872 522008.9153 488013.7156 421181.9963 483508.2712 496682.2039 0.933469104 1.210892307 0.88242496 1.045891282 1.050991783 0.982547214 0.847990915 0.973476133 1 18.92196353 1.994705232 7.096657624 0.921335846 1.034954712 0.129449414 0.093802585 0.190148088 58.41622826 0.035685935 0.024344049 98.78823636 -1.994705232 0.113618866 TPS(ph)PAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.137)PS(0.863)PAPK;T(0.377)PS(0.623)PAPK;T(0.366)PS(0.634)PAPK;T(0.377)PS(0.623)PAPK 108.74 0.0075361 2777910000 6075270 5465010 5353850 6396730 3976770 6165340 6577640 6421840 4524030 TRUE FALSE 5788104.027 6021900.732 5599329.318 5753718.547 4670317.429 5951832.73 5574100.211 5859509.645 5225593.467 1.107645297 1.152385996 1.071520269 1.101065091 0.893739143 1.138977375 1.06669228 1.121309892 1 22.31716346 3.511017352 2.592498867 1.05621135 1.129482647 0.161091932 0.069941749 0.476950688 6.373075348 0.018937142 0.03015305 3243.525763 -3.511017352 0.073271296 TPS(ph)PSQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.042)PS(0.956)PS(0.002)QPK;T(0.005)PS(0.992)PS(0.003)QPK 118.67 0.0019322 677880000 1106230 1023850 1022520 1297970 776590 1219900 1195540 1227390 862780 TRUE FALSE 1053940.7 1128181.479 1069403.553 1167495.59 912027.0501 1177654.557 1013138.415 1119913.225 996575.5159 1.057562306 1.132058194 1.073078293 1.171507398 0.915161004 1.181701274 1.016619814 1.123761528 1 19.9266196 TPS(ph)PSQPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.001)PS(0.999)PSQPKK;T(0.018)PS(0.973)PS(0.009)QPKK 110.08 0.0014366 364690000 913420 811300 891420 1000620 648230 1040620 1155240 1087710 753130 TRUE FALSE 870244.4468 893972.3924 932292.4887 900035.7765 761281.1068 1004583.068 978986.9206 992464.3461 869921.5539 1.000371175 1.027647135 1.071697194 1.03461717 0.875114662 1.154797308 1.125373795 1.140866486 1 19.73052578 2.186154596 24.9999986 1.118139098 1.009923055 0.369262791 0.065721848 95.52754949 45570.19044 0.02270994 0.016772421 153.5163359 -2.186154596 -0.108216043 TPS(ph)SEEISPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.004)PS(0.945)S(0.051)EEISPTK 98.368 0.0058456 73119000 241580 222390 228840 284050 289810 199300 243910 223180 300860 TRUE FALSE 230160.9922 245051.7938 239332.5404 255496.7543 340352.7722 192398.191 206697.0498 203637.176 347515.8322 0.662303616 0.705152891 0.688695358 0.735208962 0.979387817 0.553638635 0.594784555 0.585979565 1 18.40671918 TPS(ph)SEEISPTKFPGLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.108)PS(0.826)S(0.066)EEISPTKFPGLYR;T(0.003)PS(0.986)S(0.011)EEISPTKFPGLYR;T(0.026)PS(0.966)S(0.008)EEISPTKFPGLYR;T(0.004)PS(0.995)S(0.001)EEISPTKFPGLYR;T(0.005)PS(0.981)S(0.014)EEISPTKFPGLYR 289.14 3.70E-46 4508250000 4449290 3751670 4082660 4358100 3011440 4456660 4901800 4636040 3785910 TRUE FALSE 4238980.879 4133969.438 4269853.999 3920015.508 3536634.183 4302324.747 4153940.382 4230083.76 4373009.587 0.969350923 0.945337383 0.976410848 0.896411368 0.808741466 0.983836111 0.949904248 0.96731637 1 22.06019508 -0.548767468 5.949683148 0.999998824 0.938853295 0.126538604 0.051713793 0 6.17E-11 0.049308445 0.011622112 0.282639289 0.548767468 -0.06114553 TPS(ph)SPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSSPSK 7 0 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(0.001)PS(0.961)S(0.039)PSK 121.85 0.0046134 225030000 1074600 1589100 987690 1501100 616980 1046300 950300 1478300 729480 TRUE FALSE 1023805.788 1751031.097 1032976.563 1350206.576 724581.1167 1010066.369 805314.2815 1348852.215 842604.0327 1.215049712 2.078118581 1.225933562 1.602421213 0.859930749 1.19874381 0.955744632 1.600813861 1 19.6844953 2.757229191 24.47517119 1.112954248 1.569719935 0.298594348 0.307386822 672.2342485 881321.737 0.087729477 0.092887331 571.7803037 -2.757229191 0.456765687 TPS(ph)SPSKSPASFEIPASAMEANGVDGDGLNKPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSSPSKSPASFEIPASAMEANGVDGDGLNKPAK 34 2 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(0.293)PS(0.336)S(0.336)PS(0.013)KS(0.021)PASFEIPASAMEANGVDGDGLNKPAK 146.37 1.08E-10 1258900000 1093500 901550 987280 1061800 496580 1134500 1163400 1193400 520660 TRUE FALSE 1041812.422 993418.97 1032547.765 955065.8467 583183.3948 1095211.981 985901.9627 1088899.569 601401.2936 1.732308249 1.651840427 1.716903132 1.588067496 0.969707583 1.821100141 1.639341274 1.810603969 1 19.19796845 3.003701748 23.87241169 1.505501917 1.689266598 0.121035605 0.290062696 164.1547652 1058595.928 0.079925509 0.095052131 1008.560019 -3.003701748 0.183764681 TPS(ph)SPSKSPASFEIPASAMEANGVDGDGLNKPAKK ddPTM_SK-BR-3_Trastuzumab_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(0.018)PS(0.454)S(0.454)PS(0.072)KS(0.001)PASFEIPASAMEANGVDGDGLNKPAKK 257.96 4.91E-60 764980000 1754300 1535500 1685500 1673700 814040 2007000 2093600 2143300 797470 TRUE FALSE 1671377.716 1691969.196 1762781.842 1505456.496 956008.3183 1937497.087 1774182.868 1955621.29 921137.5747 1.814471325 1.836825727 1.91370094 1.634344899 1.037856173 2.103374284 1.926078055 2.123050176 1 19.81305712 -1.994387267 2.752014688 0.226220511 1.801796754 0.40437075 0.304622566 27886626.1 6583861.72 136686715.5 0.07178678 0.010130077 1.994387267 1.575576243 TPS(ph)TKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSTKPK 7 1 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.057)PS(0.917)T(0.026)KPK;T(0.004)PS(0.979)T(0.018)KPK 55.549 0.076888 188543000 469790 411340 310050 555360 277910 397210 468530 463100 299090 TRUE FALSE 447583.9577 453256.0137 324266.0992 499534.1577 326377.416 383454.5181 397047.1434 422548.509 345471.3497 1.295574751 1.311993061 0.938619366 1.445949594 0.944730775 1.109945929 1.149291088 1.22310724 1 18.39820655 3.862270021 21.99030278 1.129062091 1.303813473 0.214060477 0.147978148 8.681927714 1511.717236 0.033530612 0.060448175 7282.324398 -3.862270021 0.174751382 TPSNELYKPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TPSNELYKPLR 11 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 82.362 0.017461 1684890000 1476740 1253890 1154530 1405500 1101640 1379550 1537580 1395750 1279880 FALSE TRUE 1406937.427 1381662.817 1207466.342 1264216.47 1293765.667 1331775.838 1302993.931 1273530.731 1478357.254 0.951689738 0.934593322 0.816762213 0.855149502 0.875137362 0.900848448 0.881379604 0.861449915 1 20.49556352 -0.179317732 10.24289597 1.000000001 0.889997367 0.460339817 0.038873438 0 0 0.041807207 0.009854053 0.661732201 0.179317732 -0.110002634 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;TPSNTPSAEADWS(1)PGLELHPDYK;TPSNTPSAEADWS(1)PGLELHPDYK 251.07 8.98E-39 2175560000 1937120 1913100 1891660 2185470 1419160 2130070 2183750 2208160 1332180 TRUE FALSE 1845556.177 2108047.065 1978394.482 1965782.403 1666661.055 2056305.142 1850578.83 2014801.804 1538767.671 1.199372857 1.36995799 1.285700577 1.277504357 1.083114161 1.336332431 1.202636932 1.309360628 1 20.55334399 -3.701348738 0.336151724 2.02E-11 1.271034068 0.486232795 0.082320159 118.2771648 2.320100464 82.92135595 0.062543101 0.000198908 3.701348738 1.271034068 TPSPKEEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;TPSPKEEDEEPES(1)PPEKK 151.42 2.50E-08 17415600000 10568850 9017160 9782600 11012450 4584300 12531390 11775040 12724040 5001500 TRUE FALSE 10069281.41 9936018.856 10231141.89 9905457.604 5383800.469 12097424.82 9978541.385 11609855.6 5777107.076 1.742962572 1.719895222 1.770980138 1.71460516 0.9319198 2.094028146 1.727255745 2.009631369 1 22.4619158 -1.864639477 2.659780389 0.689037379 1.712670332 0.348265895 0.306916091 27527176.74 16143608.33 53993605.44 0.070830089 0.013657164 1.864639477 1.023632953 TPSRHS(ph)CSGS(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSRHSCSGSSPPR 14 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 T(0.172)PS(0.028)RHS(0.793)CS(0.364)GS(0.443)S(0.2)PPR 59.792 0.055808 67262000 95084 83918 101240 110480 126000 92896 114070 100090 124660 TRUE FALSE 90589.56776 92469.33961 105881.9541 99374.3405 147974.3601 89678.98823 96666.52646 91325.58899 143991.6361 0.629130762 0.642185491 0.735334058 0.690139672 1.027659412 0.622806926 0.671334315 0.634242317 1 17.13562549 -2.500916312 2.221431341 4.88647342 0.700249892 0.372869772 0.119326838 5490888.348 373463.1475 107843474.6 0.028071832 0.003155613 2.500916312 -4.186223528 TPSS(ph)PLQSCTPSLSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPS(0.001)S(0.999)PLQSCTPSLSPR;TPS(0.005)S(0.995)PLQSCTPSLSPR 216.13 1.62E-14 366510000 332800 284380 292320 330990 323030 306400 348950 319450 363990 TRUE FALSE 317069.2035 313358.6453 305723.1611 297718.2564 379366.3297 295789.2912 295711.2686 291477.2645 420435.7102 0.754144322 0.745318815 0.727157931 0.708118386 0.902317098 0.703530371 0.703344795 0.693274281 1 18.68152569 -1.764082756 2.774694189 1.057158169 0.741864279 0.644646781 0.060163786 15260097.32 12153899.21 5949988.292 0.013934307 0.017215405 1.764082756 -0.31529389 TPSS(ph)PSKSPASFEIPASAMEANGVDGDGLNKPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPSSPSKSPASFEIPASAMEANGVDGDGLNKPAK 34 2 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(0.004)PS(0.134)S(0.847)PS(0.011)KS(0.004)PASFEIPASAMEANGVDGDGLNKPAK;T(0.126)PS(0.126)S(0.68)PS(0.027)KS(0.034)PAS(0.007)FEIPASAMEANGVDGDGLNKPAK 364.16 1.78E-148 1319790000 1399471 1233575 1222347 1514197 670002 1496291 1512343 1664450 700630 TRUE FALSE 1333320.779 1359277.695 1278392.819 1361987.041 786850.1367 1444474.067 1281607.299 1518701.934 809280.1221 1.647539267 1.679613348 1.57966665 1.682961194 0.972284028 1.784887616 1.583638674 1.876608473 1 19.62627963 TPSSDVLVFDYTKHPSKPDPSGECNPDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPSSDVLVFDYTKHPSKPDPSGECNPDLR 29 2 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 85.982 0.0011862 79051000 141390 72120 144860 118080 144950 131230 223090 173140 187370 FALSE TRUE 134706.7749 79469.10999 151501.9743 106210.3741 170229.2341 126685.4722 189053.5232 157978.9437 216426.3826 0.622413835 0.36718772 0.700016202 0.490745965 0.78654567 0.585351336 0.873523463 0.729943096 1 17.72351685 1.723612281 0.424142588 0.999301196 0.484352233 0.580149827 0.118280691 0.606206078 0.290155682 0.119180077 0.095549601 52.91907953 -1.723612281 -0.514948962 TPST(ph)PVACSTPAQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TPSTPVACSTPAQLK 15 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 TPS(0.002)T(0.998)PVACSTPAQLK;TPS(0.045)T(0.955)PVACSTPAQLK;TPST(1)PVACSTPAQLK;T(0.001)PS(0.043)T(0.955)PVACSTPAQLK 347.04 3.38E-81 541594000 799960 842270 671810 915010 541200 774500 791670 835500 579950 TRUE FALSE 762147.4762 928098.2706 702613.153 823031.4564 635585.1086 747678.8708 670886.2015 762339.1907 669885.684 1.137727667 1.385457687 1.048855304 1.228614786 0.948796375 1.116129048 1.001493564 1.138013857 1 19.3535554 3.260621069 1.514330222 1.049044799 1.250401378 0.324973552 0.104325293 0.354070102 1.687495348 0.031875215 0.047211225 1822.305011 -3.260621069 0.201356578 TPTHQPPKPGS(ph)PGRPACPLSNLLLQSYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPTHQPPKPGSPGRPACPLSNLLLQSYEER 30 2 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 1 TPTHQPPKPGS(1)PGRPACPLSNLLLQSYEER;T(0.005)PT(0.005)HQPPKPGS(0.989)PGRPACPLSNLLLQSYEER 109.05 0.00013148 801830000 362970 343860 353510 426560 315380 423350 460140 392330 311370 TRUE FALSE 345813.1274 378899.7249 369718.7832 383681.3784 370382.1721 408689.2833 389937.1919 357975.5053 359655.6693 0.961511682 1.053506888 1.027979856 1.066801975 1.029824367 1.136334884 1.084195872 0.995328409 1 18.45625682 5.25556826 0.801345419 1.06179888 0.798122712 0.267143465 0.042456063 5.60636446 1.547177718 0.013899924 1.594605327 180122.6221 -5.25556826 -0.263676168 TPTS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TPTSPLK 7 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 TPT(0.004)S(0.996)PLK;T(0.001)PT(0.041)S(0.957)PLK;T(0.001)PT(0.032)S(0.967)PLK;TPT(0.032)S(0.968)PLK;TPT(0.002)S(0.998)PLK;T(0.005)PT(0.029)S(0.967)PLK;T(0.013)PT(0.034)S(0.953)PLK;TPT(0.018)S(0.982)PLK;T(0.06)PT(0.016)S(0.924)PLK 152.79 0.0018773 19308250000 34396600 32937700 32182000 39047200 22500700 36265500 38943200 38588500 26618300 TRUE FALSE 32770740.89 36294089.08 33657576.53 35122101.27 26424814.96 35009616.64 33001699.6 35209486.37 30746130.02 1.065849291 1.180444142 1.094693105 1.14232592 0.85945174 1.138667423 1.073361089 1.14516807 1 24.8739015 TPTSS(ph)PASSPLVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPTS(0.002)S(0.575)PAS(0.136)S(0.287)PLVAK 97.297 0.003179 64879000 224390 228050 233460 289360 197670 240360 261510 256860 239090 TRUE FALSE 213783.5294 251288.5543 244164.3719 260272.9831 232143.5854 232036.2729 221611.8465 234367.9767 276166.8561 0.774110016 0.909915686 0.884119026 0.942448296 0.840591766 0.840203188 0.802456347 0.848646286 1 18.07518066 -2.446579613 2.192556904 2.393111803 0.853862323 0.466082863 0.048645903 2084821.283 208407.5575 14475043.84 0.012855779 0.003576188 2.446579613 -1.53924948 TPTVPDS(ph)PGYMGPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TPTVPDSPGYMGPTR 15 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR;T(0.004)PT(0.006)VPDS(0.99)PGYMGPTR;TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR 285.62 4.34E-34 1511590000 849236 665563 723834 903084 876271 698938 766050 637265 684761 TRUE FALSE 809094.2973 733384.6264 757022.5049 812304.2806 1029092.385 674733.6018 649175.003 581462.6982 790950.2386 1.02293957 0.927219679 0.957105097 1.026997959 1.301083601 0.853067069 0.82075328 0.735144475 1 19.59322741 2.037839887 24.99999682 0.833264061 1.027992974 0.390145118 0.118963212 163.7643342 108194.9028 0.043408291 0.032059075 109.1038026 -2.037839887 0.194728912 TPVEPEVAIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;;;;;; 212.72 4.96E-09 7512520000 5978900 5994880 4880540 6248580 5503940 5359770 6061840 5839690 5163160 FALSE TRUE 5696289.246 6605765.088 5104317.587 5620460.867 6463825.393 5174159.821 5136994.975 5328335.785 5963836.483 0.955138402 1.107636855 0.855878192 0.942423704 1.083836791 0.867589149 0.861357448 0.893440959 1 22.50780927 2.211566047 24.99897925 0.889596449 0.993919634 0.198636581 0.08007876 281.0630462 260283.5197 0.02902071 0.021438926 162.7668831 -2.211566047 0.104323185 TPVQYSQQQNS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TPVQYSQQQNSPQK 14 0 P46013 P46013 MKI67 Antigen KI-67 1 TPVQYS(0.001)QQQNS(0.999)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK 363.25 3.29E-83 213330000 186352 229234 175883 218437 121902 202128 191188 183686 121374 TRUE FALSE 177543.5103 252593.2052 183947.4095 196479.2978 143161.6702 195128.2567 162018.7592 167601.4801 140196.06 1.266394435 1.801714008 1.312072604 1.401460909 1.021153306 1.391824111 1.155658434 1.195479245 1 17.09708628 3.181499757 2.007939134 1.184699317 1.525391024 0.381506134 0.179449623 0.294343933 2.438020384 0.053129869 0.070456673 1518.797092 -3.181499757 0.340691707 TPVS(ph)PVKFSPGDFWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.005)PVS(0.995)PVKFSPGDFWGR;T(0.148)PVS(0.852)PVKFSPGDFWGR 195.18 5.64E-11 674360000 2256590 1701080 2086670 2355650 1675340 2098970 2521100 2278810 1892760 TRUE FALSE 2149925.463 1874421.986 2182345.883 2118855.587 1967518.766 2026282.143 2136459.892 2079265.316 2186279.554 0.98337171 0.857356957 0.998200747 0.969160409 0.899939242 0.926817496 0.977212584 0.951051896 1 21.06004646 1.06095705 0.924786343 0.998003801 0.935779223 0.143946934 0.042121323 1.008197572 1.884673305 0.038556006 0.013352675 11.50686586 -1.06095705 -0.062224577 TPVSGSLKS(ph)PVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPVSGSLKSPVPR 13 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 T(0.002)PVS(0.046)GS(0.033)LKS(0.919)PVPR;TPVSGSLKS(1)PVPR 100.58 0.0014157 320250000 638440 586060 648130 769150 554280 744340 829880 799590 652780 TRUE FALSE 608262.2065 645780.1803 677847.4016 691833.5807 650946.2565 718563.3192 703266.5642 729573.6607 754009.7885 0.806703329 0.856461269 0.898990188 0.917539257 0.86331274 0.952989378 0.932702168 0.967591763 1 19.52422373 8 0.142082173 1.028406256 0.226971985 0.854630849 0.021891496 22.51470117 0.212421092 0.082063242 3.678739291 99999999.98 -8 -0.80143427 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK 31 0 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 164.83 8.64E-13 545680000 540490 580470 494380 639160 385700 546120 607710 551930 156917 FALSE TRUE 514942.1088 639620.5529 517047.812 574910.4225 452965.9579 527207.7275 514992.6781 503600.0832 181250.8869 2.841046008 3.528923713 2.852663624 3.171904051 2.499110297 2.908718056 2.84132501 2.778469622 1 17.46762853 -1.12542665 0.350283577 1.75E-18 3.126891124 0.854631644 0.252632482 5.557743033 0.483823471 5.741025425 0.1946506 0.074915788 1.12542665 3.126891124 TQADLDSLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQADLDSLVR 10 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 176.48 5.77E-06 173486000 281750 258596 270070 280666 275552 245310 306190 271008 307189 FALSE TRUE 268432.2359 284947.2264 282452.9766 252452.9204 323608.1816 236814.8532 259475.0919 247277.1028 354826.3012 0.756517301 0.803061175 0.79603168 0.71148311 0.912018586 0.667410652 0.731273558 0.696896205 1 18.43675343 TQAPTKAS(ph)E ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQAPTKASE 9 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 TQAPT(0.115)KAS(0.885)E;TQAPT(0.014)KAS(0.986)E 122.7 0.0015217 248540000 677050 538780 647070 693220 435390 714930 753880 758260 509370 TRUE FALSE 645047.1883 593682.2945 676738.7995 623536.2086 511321.8782 690171.7948 638861.76 691862.7346 588360.4981 1.096346866 1.009045129 1.15021114 1.059785983 0.869062216 1.173042373 1.085833876 1.175916359 1 19.16634086 TQAVFNHTEDYVLLPDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TQAVFNHTEDYVLLPDER 18 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ;;;; 214.69 9.92E-19 786697000 657961 668587 663834 786438 637755 674424 813998 738241 703660 FALSE TRUE 626860.4875 736716.7754 694271.4455 707383.7581 748979.2701 651068.5278 689807.655 673596.7044 812779.999 0.771254815 0.906415975 0.854193566 0.870326237 0.921503077 0.801039062 0.848701562 0.828756496 1 19.63250537 -2.457435249 2.125168912 2.397089483 0.851046255 0.528391775 0.044448873 1180986.878 127680.2044 7931999.586 0.010621401 0.003487906 2.457435249 -1.546043228 TQAYQDQKPGTSGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQAYQDQKPGTSGLR 15 1 A0A3B3ITK7;P36871 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ; 114.52 0.00054702 475730000 365904 304055 323383 390640 260404 355530 420390 372930 292789 FALSE TRUE 348608.4431 335038.5502 338210.4304 351372.125 305818.3752 343217.907 356251.7845 340274.2722 338193.2228 1.030796656 0.990671982 1.000050881 1.038968558 0.904271152 1.014857436 1.053397172 1.006153433 1 18.36748822 2.007121667 24.9993317 1.027869257 0.995251466 0.0860593 0.038580385 337.1234966 1183407.281 0.013780129 0.01015282 101.6533434 -2.007121667 -0.032617791 TQDECILHFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 196.24 6.12E-08 442373000 988706 838915 710840 842028 815167 760250 970321 888044 782465 FALSE TRUE 941971.8268 924401.3923 743432.7171 757385.7457 957331.8667 733922.3519 822280.7103 810282.1595 903805.6759 1.042228271 1.022787771 0.822558142 0.837996226 1.059223119 0.812035564 0.909798126 0.896522539 1 19.78565309 3.843859046 7.26751361 0.900314593 1.034451782 0.320040737 0.07683175 0.252535046 15.35429051 0.018083037 0.032787426 6980.058231 -3.843859046 0.134137188 TQDPAKAPNTPDILEIEFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQDPAKAPNTPDILEIEFKK 20 2 P00966 P00966 ASS1 Argininosuccinate synthase 0 ; 182.15 2.72E-17 762180000 1709820 1097220 1524410 1503860 911270 1799270 2110810 1970710 1092750 FALSE TRUE 1629000.197 1209027.965 1594305.706 1352689.136 1070195.199 1736960.829 1788767.167 1798144.185 1262208.089 1.290595593 0.957867388 1.263108453 1.07168473 0.847875409 1.376128741 1.417172955 1.424602013 1 20.26751834 2.19312693 24.99959151 1.348908125 1.094680486 0.258619724 0.176313418 140.5402429 77330.4745 0.060625915 0.044775377 156.0008377 -2.19312693 -0.254227639 TQDPSS(ph)PGTTPPQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 TQDPS(0.007)S(0.971)PGT(0.022)TPPQAR;TQDPS(0.02)S(0.966)PGT(0.014)TPPQAR;TQDPS(0.341)S(0.642)PGT(0.012)T(0.004)PPQAR 182.34 5.78E-07 919120000 766190 736070 790820 898970 788580 824150 916700 843910 864370 TRUE FALSE 729973.7171 811076.3698 827079.8792 808603.8277 926108.1023 795609.4788 776840.5786 770012.7666 998412.085 0.731134697 0.812366339 0.828395301 0.809889864 0.927581022 0.796874848 0.778076097 0.771237426 1 19.92927587 -2.498388 2.25564232 3.598482773 0.804788996 0.589482511 0.05060243 1347178.071 223983.2748 17881177.01 0.01272423 0.003174037 2.498388 -2.793693778 TQEDEEEISTS(ph)PGVSEFVSDAFDACNLNQEDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TQEDEEEISTSPGVSEFVSDAFDACNLNQEDLRK 34 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 TQEDEEEIST(0.003)S(0.996)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.001)S(0.999)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.005)S(0.995)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIS(0.008)T(0.387)S(0.581)PGVS(0.019)EFVS(0.004)DAFDACNLNQEDLRK;TQEDEEEIS(0.005)T(0.15)S(0.813)PGVS(0.031)EFVS(0.001)DAFDACNLNQEDLRK 208.68 6.99E-28 203745000 237882 186888 233388 244923 170359 234641 288215 274542 190960 TRUE FALSE 226637.7893 205932.0997 244089.0707 220302.8747 200069.5557 226515.3233 244242.5083 250501.647 220573.1015 1.027495138 0.933622904 1.106613041 0.998774888 0.907044215 1.026939921 1.107308673 1.135685382 1 17.75089734 1.910065308 4.982847092 1.089507809 0.992646575 0.276114763 0.062928825 0.25318776 10.1306945 0.027143657 0.016083137 81.29527562 -1.910065308 -0.096861234 TQEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQEELRR 7 1 P15924 P15924 DSP Desmoplakin 0 78.192 0.076069 0 166010 142990 147060 195180 140430 168410 176750 162370 164370 FALSE TRUE 158163.0363 157560.8436 153802.8465 175560.1356 164920.9475 162577.9195 149783.5413 148152.022 189859.6601 0.833052351 0.829880573 0.810087021 0.924683714 0.868646596 0.856305754 0.788917146 0.780323856 1 17.53457388 TQES(ph)GDQDPQEAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQESGDQDPQEAQK 14 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 T(0.003)QES(0.997)GDQDPQEAQK;TQES(1)GDQDPQEAQK 230.82 2.43E-09 83856000 263780 157337 176938 374510 215524 312340 347230 184681 166441 TRUE FALSE 251311.6422 173369.8192 185050.7823 336863.5433 253111.3174 301523.5875 294253.6862 168509.3526 192251.8202 1.307200327 0.90178506 0.962543721 1.7521995 1.316561357 1.568378324 1.53056385 0.876503288 1 17.55263773 3.275838962 24.99999196 1.392189635 1.05959577 0.171267282 0.279064648 225.7459083 151390.608 0.071717881 0.097104113 1887.291407 -3.275838962 -0.332593865 TQHIQQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TQHIQQPR 8 0 P51397 P51397 DAP Death-associated protein 1 0 ;;; 121.96 0.0037293 0 808012 543352 460130 565208 800739 505501 927440 613791 710752 FALSE TRUE 769818.8741 598720.1865 481227.4156 508392.218 940387.6281 487995.3736 785941.9944 560044.2061 820971.7901 0.937692237 0.729282289 0.586168028 0.619256623 1.145456688 0.594411866 0.957331304 0.68217229 1 19.64697312 TQHLSNDHICYFLYQILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQHLSNDHICYFLYQILR 18 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 212.55 1.04E-16 71033000 80992 88059 75025 92070 106778 78355 122077 92368 45322 FALSE TRUE 77163.66867 97032.31221 78464.97046 82814.94868 125400.0494 75641.5467 103451.9116 84279.76825 52350.30429 1.473987013 1.853519546 1.498844592 1.581938249 2.395402493 1.444911309 1.976147282 1.609919358 1 15.6759103 0.970251385 21.85853074 0.999999985 1.746371327 0.398301008 0.286530639 623.2161371 457925.1918 0.248530386 0.062132597 9.337946572 -0.970251385 0.746371342 TQIAICPNNHEVHIYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQIAICPNNHEVHIYEK 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 139.11 8.15E-07 635500000 875450 709450 833240 944630 645130 847680 984740 852840 27171 FALSE TRUE 834069.2135 781743.7616 871444.8782 849673.9977 757640.4677 818324.629 834499.827 778160.8084 31384.53991 26.57579865 24.90856211 27.7666928 27.07301111 24.14056315 26.07413177 26.58951922 24.79439911 1 14.93776644 0.648102119 3.573345229 1.000040241 26.09184444 0.983245989 1.026637661 0.908935263 9.110711619 0.947746341 0.243951592 4.447358292 -0.648102119 25.0918042 TQIDHYVGIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQIDHYVGIAR 11 0 O95197-3;O95197-4;O95197-7;O95197-2;O95197 O95197-3;O95197-7 RTN3 Reticulon-3 0 ; 99.752 0.0045408 237120000 329010 266570 261370 343920 300820 290200 319480 309250 289850 FALSE TRUE 313458.3493 293733.7861 273354.073 309348.5082 353282.9128 280150.3012 270737.4583 282170.4306 334798.4577 0.936259837 0.877345099 0.816473513 0.923984269 1.055210694 0.836772974 0.808658021 0.842806841 1 18.35293336 -0.756393618 5.380071078 1.000000023 0.885265603 0.190968023 0.072876585 2.10E-08 4.80E-09 0.072199923 0.017017682 0.175229161 0.756393618 -0.11473442 TQLEWTEAILEDEQTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQLEWTEAILEDEQTQR 17 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 231.19 1.27E-15 12564000 20021 15533 16732 21919 17476 19116 22477 17153 19073 FALSE TRUE 19074.64701 17115.83036 17499.17875 19715.66048 20523.80887 18454.00813 19047.72083 15650.99239 22030.74343 0.865819489 0.776906618 0.794307228 0.894915804 0.931598561 0.837647998 0.864597279 0.710415989 1 14.42723056 -1.952048969 2.879483031 1.118632797 0.836938125 0.407298654 0.062672608 11507183.41 11703997.01 9018850.441 0.014568985 0.011167373 1.952048969 -0.281694671 TQLGEDHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQLGEDHEK 9 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 80.245 0.024659 224690000 790300 690280 796660 799880 776850 734140 910900 898940 693410 FALSE TRUE 752944.0852 760620.3168 833187.649 719474.5427 912332.394 708716.5477 771925.4752 820224.048 800940.4814 0.940074953 0.949658975 1.040261628 0.898287151 1.139076392 0.884855447 0.96377383 1.024076154 1 19.61133551 3.966462616 23.43145099 0.986249782 0.943668887 0.06659579 0.071825 759.7756264 530830.2914 0.016670608 0.03006336 9256.836985 -3.966462616 -0.042580894 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_SK-BR-3_Trastuzumab_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 TQLWAS(0.003)EPGT(0.997)PPLPTSLPSQNPILK;T(0.001)QLWAS(0.004)EPGT(0.995)PPLPTSLPSQNPILK 147.73 8.45E-07 703048000 802030 675746 733515 873190 589565 784650 960020 872360 723287 TRUE FALSE 764119.6314 744605.2857 767147.3883 785415.2822 692384.9493 757477.3738 813551.317 795971.5337 835450.6539 0.914619706 0.891261838 0.918243806 0.940109722 0.828756248 0.906669197 0.973787396 0.95274512 1 19.67219509 1.752653383 4.889474118 0.972689062 0.899238799 0.574049215 0.03068429 0.132461841 7.226557469 0.01484332 0.007716782 56.57875446 -1.752653383 -0.073450263 TQLWFHGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQLWFHGR 8 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 124.92 0.0012841 2023120000 1471650 1145220 738860 806760 1347190 842170 1376290 1043730 944770 FALSE TRUE 1402088.021 1261919.22 772737.4618 725662.9521 1582139.509 813005.4417 1166311.683 952335.468 1091280.106 1.284810392 1.156366008 0.70810185 0.664964886 1.449801476 0.745001615 1.068755562 0.872677384 1 20.05759002 3.960797622 10.95794047 0.939089841 1.236750164 0.231444066 0.224658008 1.09408571 304.5035567 0.053762766 0.097507028 9136.873709 -3.960797622 0.297660323 TQMAEVLPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR 199.87 5.12E-08 8444225000 4266981 3854904 4136390 4661960 4038740 4246700 4969450 4411935 4654770 TRUE FALSE 4065289.264 4247723.1 4326047.573 4193330.924 4743094.977 4099635.714 4211269.132 4025602.582 5376607.958 0.756106693 0.790037721 0.804605358 0.779921273 0.882172369 0.762494819 0.783257616 0.748725333 1 22.35826485 -1.135464325 4.683956693 1.000018906 0.788135427 0.761757107 0.037186505 6.91E-06 1.27E-06 0.033872418 0.007983093 0.073204145 1.135464325 -0.21188348 TQPDGTSVPGEPAS(ph)PISQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(0.999)PIS(0.001)QR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(0.999)PIS(0.001)QR 444.53 4.82E-191 14638550000 4818094 4261679 4490239 5056350 4109959 4495989 5073720 4744698 4181855 TRUE FALSE 4590352.245 4695948.935 4696120.9 4548076.092 4826734.548 4340291.774 4299630.829 4329227.09 4830355.715 0.9503135 0.972174559 0.972210159 0.941561318 0.999250331 0.898544958 0.890127163 0.896254302 1 22.203698 2.223264134 24.99833995 0.909240677 0.965338718 0.27223372 0.034834043 226.9932455 370962.0758 0.011494567 0.008521183 167.2107267 -2.223264134 0.056098041 TQPSSGVDSAVGTLPATS(ph)PQSTSVQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQPSSGVDSAVGTLPATSPQSTSVQAK 27 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0 Q13428-4;Q13428-3 TCOF1 Treacle protein 1 TQPSSGVDSAVGTLPAT(0.235)S(0.71)PQS(0.048)T(0.006)S(0.001)VQAK 193.6 1.45E-18 221990000 291560 276620 252240 314690 201760 294530 355970 309350 223910 TRUE FALSE 277778.5366 304807.8925 263805.4535 283056.7633 236946.8801 284330.3522 301660.2387 282261.674 258632.8192 1.074026635 1.178535243 1.019999915 1.094434821 0.916151635 1.099359134 1.166364886 1.09136062 1 17.98054583 -1.689414935 2.364189171 0.983617675 1.088885974 0.093709177 0.07377881 7338610.121 5360500.654 717454.5589 0.018696982 0.020444904 1.689414935 0.105268299 TQQHYYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQQHYYDK 8 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 61.65 0.084625 79759000 270750 259550 208430 263740 172860 234000 240470 272510 170260 FALSE TRUE 257952.1841 285998.4401 217986.7217 237228.3541 203006.7293 225896.5213 203781.885 248647.5797 196663.0512 1.311645388 1.454256091 1.108427436 1.206268044 1.032256583 1.148647496 1.036198125 1.26433297 1 17.58536641 3.729680134 24.66338296 1.113091647 1.38295074 0.622918695 0.08708062 266.4026973 739869.1812 0.02066482 0.032558957 5366.36408 -3.729680134 0.269859093 TQQYHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQQYHK 6 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 69.344 0.093749 344300000 571300 461480 411430 491740 363450 446510 591800 579910 444680 FALSE TRUE 544295.7812 508505.3367 430294.4725 442309.361 426835.5649 431047.2467 501510.0408 529130.0061 513638.7033 1.059686075 0.99000588 0.837737635 0.861129347 0.831003509 0.839203206 0.976386782 1.030159921 1 18.97039439 1.515657484 6.544002759 1.011564795 0.917628048 0.282223466 0.073892591 0.229019498 21.00531552 0.049380714 0.022440799 32.78366357 -1.515657484 -0.093936748 TQS(ph)APLPQNAQALQHLVIQQQHQQFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQSAPLPQNAQALQHLVIQQQHQQFLEK 28 0 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 T(0.019)QS(0.981)APLPQNAQALQHLVIQQQHQQFLEK 275.86 2.50E-61 135100000 127720 107450 119730 132800 87338 145350 133450 147050 68461 TRUE FALSE 121682.9287 118399.2772 125219.7389 119450.6917 102569.7195 140316.4931 113089.7515 134173.5224 79077.58223 1.538779073 1.497254643 1.5835049 1.510550631 1.297077081 1.774415569 1.430111396 1.696732736 1 16.27098114 -1.055827768 4.498074879 0.999969825 1.532850962 0.625125679 0.131538251 3.42E-05 7.18E-06 0.109411692 0.025787125 0.087937119 1.055827768 0.532881137 TQS(ph)ASPPPKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 T(0.002)QS(0.6)AS(0.398)PPPKER 75.669 0.022684 214970000 272910 235980 282940 295660 219590 293370 357000 303020 258880 TRUE FALSE 260010.0852 260026.6303 295913.0789 265939.6951 257886.4265 283210.5233 302533.0932 276485.9624 299025.7882 0.869523952 0.869579282 0.989590499 0.889353713 0.862422027 0.947110699 1.011729106 0.924622468 1 18.18991038 2.03897282 5.888938072 0.980107339 0.894386354 0.453423575 0.041948591 0.15574403 14.12127969 0.016047199 0.011533035 109.3887905 -2.03897282 -0.085720985 TQS(ph)GNFYTDTLGMAEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TQSGNFYTDTLGMAEFR 17 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.041)QS(0.959)GNFYTDTLGMAEFR;T(0.043)QS(0.957)GNFYTDTLGMAEFR;T(0.01)QS(0.99)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR 327.04 7.06E-72 531108000 588172 567733 495586 632946 469504 516378 594584 558356 483211 TRUE FALSE 560370.2752 625585.6382 518309.1083 569321.0656 551385.3489 498495.7004 503869.2905 509463.3886 558144.894 1.003987103 1.120830173 0.928628236 1.020023782 0.987889265 0.893129554 0.902757144 0.912779807 1 19.09028017 2.975796251 0.99563668 0.918561716 1.052837083 0.346063782 0.055808641 0.435942462 0.938782853 0.025858768 0.030891426 945.7933382 -2.975796251 0.134275367 TQS(ph)GNFYTDTLGMAEFRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQSGNFYTDTLGMAEFRR 18 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.358)QS(0.642)GNFYTDTLGMAEFRR;T(0.02)QS(0.98)GNFYTDTLGMAEFRR 118.08 6.92E-05 111391000 53479 25738 43952 39141 52250 47979 59502 49045 55512 TRUE FALSE 50951.15366 28360.73146 45967.24267 35206.47232 61362.38346 46317.4752 50423.87707 44750.3598 64120.51744 0.794615447 0.442303534 0.716888205 0.54906719 0.956985157 0.722350303 0.786392236 0.697910148 1 15.96849845 2.754109101 24.99721182 0.807801095 0.618980711 0.371461678 0.13147399 884.6388941 1422227.642 0.036820591 0.038930072 567.6871991 -2.754109101 -0.188820384 TQS(ph)LPVTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQSLPVTEK 9 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 TQS(1)LPVTEK;TQS(0.999)LPVT(0.001)EK 125.36 0.00052847 112128000 462950 412060 393010 534370 359190 463580 532410 471270 379600 TRUE FALSE 441067.271 454049.3825 411029.8972 480654.1124 421832.6223 447526.1084 451181.0761 430003.1004 438466.4293 1.005931678 1.035539672 0.937426151 1.09621645 0.96206367 1.020662196 1.028997994 0.980697886 1 18.74210686 0.263378874 0.003070709 0.50865386 1.505036437 0.002118199 0.043471578 270272.9979 302.6755562 49552.34001 48656.40107 1.833913612 -0.263378874 0.996382577 TQS(ph)PEFEAQSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQSPEFEAQSSK 12 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK 302.15 7.43E-30 161830000 449270 467750 416050 512270 265835 447200 448670 467530 301070 TRUE FALSE 428033.8975 515414.2568 435126.304 460775.6464 312196.5398 431713.3519 380217.1511 426590.5947 347758.3979 1.230836983 1.482104415 1.251231621 1.324987834 0.897739757 1.241417474 1.093337079 1.22668668 1 18.40772583 2.900474673 12.92488817 1.109605697 1.33605484 0.47529548 0.119184328 0.772936123 97.91219166 0.033128259 0.035141947 795.1968906 -2.900474673 0.226449143 TQS(ph)PGGCSAEAVLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TQSPGGCSAEAVLAR 15 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7 Q96MH2 HEXIM2 Protein HEXIM2 1 TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;T(0.001)QS(0.999)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR 216.34 2.33E-12 904710000 523730 487383 521180 564520 514132 523395 603120 555970 533530 TRUE FALSE 498974.3208 537047.8818 545076.6185 507773.3771 603796.458 505269.6999 511102.9669 507286.3194 616267.1075 0.809672161 0.871453101 0.884481115 0.823950152 0.979764214 0.819887503 0.829352988 0.823159817 1 19.23319627 -2.382696611 2.335013827 2.141455564 0.854174332 0.451376821 0.050152442 1796941.204 421381.0372 10946287.08 0.011812088 0.00414289 2.382696611 -1.287281231 TQS(ph)SLTVSEVLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQSSLTVSEVLTR 13 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 TQS(0.887)S(0.112)LT(0.001)VSEVLTR;TQS(0.897)S(0.101)LT(0.002)VSEVLTR;TQS(0.994)S(0.006)LTVSEVLTR 209.93 3.56E-08 332441000 458300 449490 374823 541960 331024 414289 428284 456790 341636 TRUE FALSE 436637.0673 495293.542 392009.0053 487481.1511 388754.4808 399942.068 362941.4098 416791.046 394615.166 1.106488308 1.255130529 0.99339569 1.235333036 0.985148353 1.013498979 0.919735076 1.056196218 1 18.59008688 2.71909277 24.1679312 0.985740087 1.152378139 0.4819924 0.078255882 392.4378798 487182.5673 0.02323922 0.021945206 523.7122953 -2.71909277 0.166638052 TQSAS(ph)PPPKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 T(0.001)QS(0.186)AS(0.813)PPPKER;TQS(0.02)AS(0.979)PPPKER 75.669 0.022684 333800000 544750 497450 543390 606710 420780 601680 678280 642860 517300 TRUE FALSE 519000.7471 548140.7206 568304.969 545722.3581 494163.8988 580843.6707 574795.9285 586567.7704 597520.242 0.868591071 0.917359249 0.951105802 0.913311918 0.827024532 0.972090366 0.961968965 0.981670125 1 19.18862806 2.086681664 17.07545201 0.974497966 0.899357828 0.599648279 0.033721229 1.561753529 305.230241 0.012456295 0.009199609 122.0904416 -2.086681664 -0.075140138 TQSSSCERDS(ph)PSTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQSSSCERDSPSTSR 15 1 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;Q5JS79 A0A2U3TZM1 CASK Peripheral plasma membrane protein CASK 1 TQSSSCERDS(0.961)PS(0.037)T(0.002)SR;TQSSSCERDS(0.885)PS(0.095)T(0.018)S(0.001)R;T(0.003)QS(0.003)S(0.002)S(0.002)CERDS(0.979)PS(0.007)T(0.002)S(0.001)R 199.31 4.53E-09 369483000 240843 257098 258638 280586 230437 241366 278832 255908 249000 TRUE FALSE 229458.8287 283296.5785 270496.8081 252380.9622 270625.1398 233007.4349 236291.0573 233499.3389 287613.6483 0.797802295 0.984990038 0.94048669 0.877499951 0.940932885 0.810140396 0.821557178 0.81185069 1 18.13377261 2.238480386 25 0.842114852 0.908804406 0.069079436 0.073356305 3.793461984 1181326.232 0.024550164 0.019306146 173.1730819 -2.238480386 0.066689554 TQT(ph)PPLGQTPQLGLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQTPPLGQTPQLGLK 15 0 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 T(0.122)QT(0.878)PPLGQTPQLGLK;T(0.064)QT(0.936)PPLGQTPQLGLK;T(0.18)QT(0.82)PPLGQTPQLGLK 101.04 0.021523 897190000 3994200 3778480 3709540 4396690 2872230 4046550 4261710 4543510 3398510 TRUE FALSE 3805402.082 4163511.408 3879626.078 3954726.368 3373146.003 3906416.959 3611507.868 4145656.178 3925533.574 0.969397411 1.060623054 0.988305413 1.007436644 0.859283442 0.995130187 0.920004326 1.056074569 1 21.90445733 2.952698093 24.99993176 0.957545186 1.010711686 0.100030036 0.056458268 658.4502182 348002.604 0.015616725 0.016564421 896.8051493 -2.952698093 0.0531665 TQT(ph)PPVS(ph)PAPQPTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(1)PAPQPTEER 264.01 2.95E-26 367630000 194960 226000 157420 219930 145350 173450 140540 153250 92828 TRUE FALSE 185744.6272 249029.6569 164637.8627 197822.2186 170698.994 167443.383 119098.0418 139830.6176 107223.2921 1.732316024 2.322533211 1.535467336 1.844955649 1.591995457 1.561632549 1.110747856 1.304106736 1 16.71025881 2.204641905 0.656966374 1.023896512 1.996207222 0.691676255 0.208974421 0.36457701 0.307431339 0.17107788 0.11371918 160.192399 -2.204641905 0.97231071 TQT(ph)PPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 T(0.471)QT(0.577)PPVS(0.951)PAPQPT(0.037)EERLPS(0.457)S(0.411)PVY(0.097)EDAASFK 95.603 0.00074932 34475000 31531 23446 29453 32839 19132 27977 31817 29501 21029 TRUE FALSE 30040.59212 25835.17406 30803.44918 29537.96133 22468.61474 27008.14947 26962.73229 26917.73605 24290.06992 1.236743748 1.063610527 1.268149877 1.216050898 0.925012354 1.111900854 1.11003107 1.108178615 1 14.56807902 2.799190615 24.99999602 1.067126486 1.182563056 0.445274184 0.078715438 273.0950709 112606.6359 0.023478207 0.024902389 629.782538 -2.799190615 0.11543657 TQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.113)QT(0.856)PPVS(0.032)PAPQPT(0.471)EERLPS(0.295)S(0.233)PVY(0.001)EDAASFK 264.99 1.63E-58 92716000 53195 40900 47456 55765 31173 51271 50436 48186 28682 TRUE FALSE 50680.57777 45067.7565 49631.90454 50159.39625 36609.56133 49495.47241 42741.06188 43966.57839 33129.85807 1.529755354 1.36033654 1.498101937 1.51402388 1.105032242 1.493983835 1.290107002 1.327098302 1 15.0158444 -3.915240891 0.134481217 2.74E-17 1.567880609 0.566792153 0.117841589 70.19691543 0.77784055 19.91499016 0.77832005 0.000121551 3.915240891 1.567880609 TQT(ph)PPVSPAPQPTEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 T(0.006)QT(0.994)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;T(0.006)QT(0.994)PPVSPAPQPTEER;TQT(0.998)PPVS(0.002)PAPQPTEER;T(0.033)QT(0.967)PPVSPAPQPTEER;T(0.001)QT(0.999)PPVSPAPQPTEER 278.88 2.42E-34 2347220000 523774 639567 418903 624316 344223 489938 471822 456794 303690 TRUE FALSE 499016.241 704739.6044 438110.1169 561558.5696 404255.3822 472971.3242 399836.8883 416794.6957 350784.6942 1.422571308 2.009037498 1.248943082 1.600863946 1.152431645 1.348323721 1.139835617 1.188178112 1 18.42022627 2.898911483 0.884647511 1.13535425 1.692149437 0.47671891 0.208049289 0.435305143 0.746596231 0.108168798 0.12035464 792.3398212 -2.898911483 0.556795187 TQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(0.004)PAPQPT(0.046)EERLPS(0.799)S(0.151)PVYEDAASFK;T(0.038)QT(0.956)PPVS(0.034)PAPQPT(0.006)EERLPS(0.514)S(0.45)PVY(0.002)EDAASFK;T(0.038)QT(0.962)PPVSPAPQPTEERLPS(0.934)S(0.066)PVYEDAASFK 208.35 2.16E-25 912990000 993420 727700 859430 991320 569430 891130 982210 878010 535410 TRUE FALSE 946463.0054 801853.4573 898835.7156 891670.6302 668738.4117 860269.9447 832355.825 801126.7898 618438.6483 1.530407273 1.29657721 1.453395123 1.441809358 1.081333473 1.391035226 1.345898784 1.295402207 1 19.23827096 -4.440922208 0.12754928 1.01E-14 1.521270935 0.548590155 0.110381091 97.15332004 0.903084298 25.78531716 0.871043732 3.62E-05 4.440922208 1.521270935 TQT(ph)PPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.099)QT(0.772)PPVS(0.13)PAPQPT(0.176)EERLPS(0.094)S(0.719)PVY(0.011)EDAASFK 180.06 1.12E-16 83159000 52656 44718 47049 64253 26579 49284 46883 48764 27834 TRUE FALSE 50167.05523 49274.81504 49206.24319 57794.16637 31214.36918 47577.28272 39730.13728 44493.96565 32150.35456 1.560388864 1.532636753 1.530503904 1.797621431 0.970887246 1.479836953 1.235760471 1.383933902 1 14.97254703 2.745613051 24.9999018 1.251134016 1.584035812 0.557111924 0.171097554 437.4591931 1550731.955 0.04718596 0.04908594 556.6895274 -2.745613051 0.332901796 TQT(ph)PPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 T(0.035)QT(0.889)PPVS(0.071)PAPQPT(0.006)EERLPSSPVYEDAASFK;T(0.035)QT(0.959)PPVS(0.006)PAPQPTEERLPSSPVYEDAASFK 159.49 7.52E-12 686520000 299760 254080 277000 302000 167376 281120 337070 309570 204322 TRUE FALSE 285590.9389 279971.0409 289700.724 271642.3862 196566.3214 271384.7439 285643.7808 282462.4097 236007.2122 1.210094116 1.186281717 1.227507928 1.150991886 0.832882688 1.149900214 1.210318016 1.196838042 1 17.84847142 2.998387471 24.98971552 1.095216849 1.201824053 0.224970051 0.108228408 113.8231575 1763987.525 0.032472279 0.038271504 996.2938994 -2.998387471 0.106607204 TQTGDSSS(ph)ISSFSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDS(0.01)S(0.467)S(0.473)IS(0.05)SFSYR;TQTGDS(0.001)S(0.225)S(0.693)IS(0.073)S(0.008)FSYR 220.93 1.68E-12 242300000 547090 536600 547240 589950 496180 565370 645250 650090 608990 TRUE FALSE 521230.1399 591280.1501 572331.4953 530647.1052 582713.6349 545791.0951 546805.2617 593164.6733 703429.0589 0.740984657 0.840568274 0.813630725 0.754371885 0.828390052 0.775900694 0.777342441 0.843247326 1 19.42404541 0.864014014 3.455559007 0.999945351 0.791677978 0.818239652 0.03106549 0.247050533 5.419997775 0.028153505 0.007276033 7.311626771 -0.864014014 -0.208267373 TQTPNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPNRK 7 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 86.953 0.031584 152800000 65920 46427 55675 54495 41180 50658 70448 66540 54582 FALSE TRUE 62804.09224 51157.96408 58227.75382 49017.05907 48361.77896 48903.70076 59699.86373 60713.40485 63046.29779 0.996158291 0.811434864 0.923571341 0.7774772 0.767083566 0.775679183 0.946921006 0.962997146 1 15.94412403 1.584878842 5.948829543 0.972740796 0.848102556 0.41534728 0.072005533 0.152877922 11.29622778 0.041242621 0.019255269 38.44845051 -1.584878842 -0.12463824 TQTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 T(0.005)QT(0.15)PPVS(0.845)PAPQPTEERLPSSPVYEDAASFK 178.32 4.94E-18 158370000 140540 106190 121100 130910 78108 127740 140970 141760 82609 TRUE FALSE 133896.9527 117010.8817 126652.5548 117750.6781 91730.01047 123316.3318 119462.4374 129346.7429 95419.58181 1.403243969 1.226277453 1.327322468 1.23403054 0.961333185 1.292358753 1.251969828 1.355557637 1 16.54199774 -5 0.157867782 0.15647677 1.322264893 0.294755135 0.120303758 180.3769108 1.647769273 48.86487405 0.518870747 1.00E-05 5 1.165788122 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVY(0.001)EDAASFK;TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK;TQTPPVSPAPQPT(0.083)EERLPS(0.427)S(0.427)PVY(0.063)EDAASFK;TQTPPVSPAPQPT(0.004)EERLPS(0.457)S(0.457)PVY(0.081)EDAASFK;TQTPPVSPAPQPTEERLPS(0.651)S(0.349)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.633)S(0.367)PVYEDAASFK 328.72 1.73E-105 5815307000 2794949 2247955 2571408 2690389 1949947 2832038 3159008 3204230 2218883 TRUE FALSE 2662837.3 2477024.17 2689309.6 2419945.986 2290017.139 2733963.814 2677043.31 2923650.635 2562976.043 1.038963008 0.966464036 1.049291743 0.94419376 0.893499237 1.066714541 1.044505788 1.140724917 1 21.28938856 2.115818495 22.04179713 1.064348494 0.983665189 0.361939519 0.055500751 3.879801412 722.7394185 0.019866412 0.014672329 130.5625114 -2.115818495 -0.080683305 TQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPT(0.003)EERLPS(0.201)S(0.78)PVY(0.017)EDAASFK;TQTPPVSPAPQPTEERLPS(0.204)S(0.796)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.209)S(0.791)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.087)S(0.9)PVY(0.013)EDAASFK 340.9 4.49E-106 2748700000 1432480 1172667 1277630 1489570 902999 1499080 1646340 1540920 1107105 TRUE FALSE 1364769.509 1292163.101 1336210.599 1339835.594 1060481.74 1447166.484 1395160.596 1405988.876 1278789.189 1.067235727 1.010458261 1.044902952 1.047737661 0.829285819 1.131669313 1.091001244 1.099468847 1 20.28634702 TQVLS(ph)PDSLFTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TQVLSPDSLFTAK 13 0 P55196-5;P55196;J3KN01;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQVLS(1)PDSLFTAK;TQVLS(1)PDSLFTAK;TQVLS(0.999)PDS(0.001)LFTAK 254.56 8.61E-24 156340000 446786 441110 452471 545260 362103 506510 569730 531680 449270 TRUE FALSE 425667.3112 486059.6105 473217.2429 490449.4289 425253.6486 488969.4317 482807.2247 485123.2806 518940.497 0.820262272 0.936638426 0.911891143 0.94509762 0.819465143 0.942245661 0.930371068 0.934834116 1 18.9852096 -4.999999999 0.014793184 2.091445339 2.29E-10 0.425041099 0.042353477 5700.889775 6.394678144 564.1199982 360.9548812 1.00E-05 4.999999999 -2.091445339 TQVYRPPPPYPPPRPANS(ph)TPDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TQVYRPPPPYPPPRPANSTPDLSR 24 2 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 TQVYRPPPPYPPPRPANS(0.944)T(0.052)PDLS(0.004)R;TQVYRPPPPYPPPRPANS(0.95)T(0.05)PDLS(0.001)R;TQVYRPPPPYPPPRPANS(0.937)T(0.063)PDLSR;TQVYRPPPPYPPPRPANS(0.965)T(0.035)PDLSR 160.07 1.10E-11 551230000 199901 153949 177148 181361 151983 172333 214010 190878 183240 TRUE FALSE 190452.0759 169636.5781 185270.411 163130.2477 178488.7871 166365.065 181358.8439 174163.7104 211655.9233 0.899819258 0.801473332 0.875337709 0.770733203 0.843296914 0.78601658 0.856856926 0.822862444 1 17.69136134 -1.033540177 4.710289485 1.000004685 0.832882851 0.639811389 0.039598119 89376103907 18334042351 4732873.178 0.008309821 0.092567775 1.033540177 -0.167121834 TRAS(ph)LPVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRASLPVVR 9 1 Q5T5P2;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P1;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 T(0.042)RAS(0.958)LPVVR;T(0.472)RAS(0.528)LPVVR;TRAS(1)LPVVR;T(0.011)RAS(0.989)LPVVR 155.86 4.38E-05 1716970000 537338 394829 472808 541570 513812 458187 595703 508528 527549 TRUE FALSE 511939.0976 435062.524 494486.7145 487130.3547 603420.6501 442319.8693 504817.5665 463998.5924 609358.6046 0.84012779 0.713967967 0.811487211 0.799414911 0.990255402 0.725877777 0.82844086 0.761454075 1 19.21693197 -2.392165456 2.18344027 2.397456477 0.805453159 0.381025249 0.076444032 3460160.068 275312.7192 24025908.87 0.017812912 0.004053541 2.392165456 -1.592003318 TRDDEPVCGRPLGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRDDEPVCGRPLGIR 15 2 Q9HDC9;H0Y512;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 ; 116.58 0.00024626 199540000 99755 64714 77345 73353 105420 85589 123135 77710 64079 FALSE TRUE 95039.77885 71308.43017 80891.34475 65979.41708 123805.2146 82625.03147 104348.4942 70905.30043 74016.04405 1.28404294 0.963418555 1.09288933 0.891420474 1.672680784 1.11631245 1.409809124 0.957972036 1 16.17555041 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 2 TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.999)HS(0.999)EEELEHS(0.001)QDTDADDGALQ 189.3 1.09E-18 3083410000 1258890 1051070 1148230 1344270 1050690 1174630 1271180 1124700 715750 TRUE FALSE 1199384.765 1158175.228 1200877.481 1209141.426 1233930.003 1133952.269 1077238.144 1026215.306 826744.8545 1.450731454 1.400885922 1.452536989 1.46253275 1.492516097 1.371586726 1.302987419 1.241272081 1 19.65708264 1.044630376 0.907499735 1.003569399 1.446392671 0.955409307 0.030935081 0.117479803 0.21191567 0.030961685 0.010787542 11.08231207 -1.044630376 0.442823272 TRDDGDEEGLLT(ph)HSEEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.793)HS(0.207)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.839)HS(0.161)EEELEHSQDTDADDGALQ 300.14 1.55E-89 9165100000 1948980 1629450 1863690 2168480 1700620 1732390 2141180 1873540 1043630 TRUE FALSE 1856855.578 1795492.808 1949142.03 1950500.271 1997207.59 1672396.9 1814503.666 1709482.905 1205470.81 1.540357147 1.489453575 1.616913502 1.618040233 1.656786355 1.387339192 1.505224059 1.41810394 1 20.20116529 0.390521962 0.700738133 0.989172642 1.561027517 0.856424174 0.070931447 0.756587892 0.554216581 0.087543211 0.026116391 2.45766091 -0.390521962 0.571854874 TRDDGDEEGLLTHS(ph)EEELEHS(ph)QDTDADDGALQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 2 TRDDGDEEGLLT(0.116)HS(0.883)EEELEHS(0.5)QDT(0.5)DADDGALQ 73.492 0.0035298 229850000 67538 56119 64581 68293 65875 60926 70882 63510 45883 TRUE FALSE 64345.61259 61837.5899 67542.10273 61428.05789 77363.57914 58816.11734 60067.64906 57948.72771 52998.3013 1.214107075 1.166784376 1.274420143 1.159057109 1.459736958 1.109773632 1.133388195 1.093407266 1 15.6936585 2.042016239 24.99999944 1.098208746 1.239744719 0.463021202 0.090058973 143.2464878 85232.24401 0.031618229 0.023351584 110.1580499 -2.042016239 0.141535973 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.021)HS(0.974)EEELEHS(0.003)QDT(0.002)DADDGALQ;TRDDGDEEGLLT(0.024)HS(0.976)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.055)HS(0.945)EEELEHSQDTDADDGALQ;T(0.001)RDDGDEEGLLT(0.172)HS(0.827)EEELEHS(0.001)QDTDADDGALQ;TRDDGDEEGLLT(0.168)HS(0.832)EEELEHSQDTDADDGALQ;T(0.009)RDDGDEEGLLT(0.248)HS(0.726)EEELEHS(0.014)QDT(0.003)DADDGALQ;TRDDGDEEGLLT(0.143)HS(0.857)EEELEHSQDTDADDGALQ 332.55 2.99E-117 11075560000 2759025 2201967 2682011 2906493 2471667 2469347 2801698 2630759 1383844 TRUE FALSE 2628611.356 2426349.941 2804983.857 2614326.802 2902724.942 2383832.894 2374247.513 2400395.795 1598443.46 1.644481911 1.517945427 1.754822068 1.635545371 1.815969733 1.491346397 1.4853497 1.50170829 1 20.60823628 0.540227538 0.706150232 0.993083355 1.644673483 0.809867289 0.096548446 0.657208564 0.555941989 0.105279305 0.035379122 3.469185626 -0.540227538 0.651590129 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLTHSEEELEHS(0.067)QDT(0.933)DADDGALQ;TRDDGDEEGLLT(0.001)HS(0.001)EEELEHS(0.205)QDT(0.793)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.149)QDT(0.85)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.19)QDT(0.81)DADDGALQ 198.65 1.30E-26 934170000 733306 578018 679130 764185 659915 650184 725977 705435 425944 TRUE FALSE 698644.0787 636918.6914 710268.7823 687367.6719 775003.9671 627667.965 615215.8752 643663.3717 491997.2201 1.420016313 1.2945575 1.443643893 1.397096658 1.575220215 1.275755105 1.250445836 1.308266277 1 18.90829064 0.817978485 0.744880032 1.003496297 1.400860261 0.674871866 0.086171701 0.557451792 0.643014368 0.085057778 0.031229486 6.576252572 -0.817978485 0.397363964 TRDELDQFLDKMDDPDYWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRDELDQFLDKMDDPDYWR 19 2 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 177.02 2.31E-14 245410000 176323 113447 150137 162464 126634 157916 196712 173879 152935 FALSE TRUE 167988.5612 125007.3783 157020.93 146132.8101 148718.9295 152447.3293 166699.9715 158653.233 176651.3787 0.95096094 0.707650171 0.888874636 0.827238435 0.841878114 0.86298409 0.943666405 0.898114887 1 17.43054548 1.467656977 0.793563353 0.989433044 0.831219465 0.372728845 0.063649352 0.555028732 0.735346588 0.055881692 0.022966492 29.35330298 -1.467656977 -0.158213579 TRDELEVIHLIEEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;;;;; 193.69 5.33E-08 566100900 399985.7 398190.2 364767.6 412253 344839.3 385391.4 392629.1 385801.8 16710.64 FALSE TRUE 381079.1687 438766.2341 381492.5553 370812.5452 404979.1647 372045.1992 332726.3197 352018.9491 19302.04071 19.7429471 22.73159822 19.76436384 19.21105394 20.98115795 19.27491527 17.23788302 18.23739544 1 14.23646576 -0.07064543 0.558067715 3.31E-17 20.80554671 0.962291193 1.173251336 0.817232188 0.285462072 3.958166807 0.496589508 0.849874052 0.07064543 20.80554671 TREEECHFYAGGQVYPGEASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TREEECHFYAGGQVYPGEASR 21 1 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 ;;; 131.7 7.67E-06 1519460000 679710 621170 682740 687040 662280 701950 786780 716230 678590 FALSE TRUE 647581.4554 684467.9292 714044.3043 617977.4339 777781.4223 677641.2955 666742.2608 653513.1042 783822.2714 0.826184046 0.873243788 0.91097731 0.788415252 0.992293088 0.864534372 0.85062939 0.83375164 1 19.58016704 -2.564648509 2.262799606 3.523684118 0.866867967 0.367136129 0.054664214 1748260.741 324700.9405 22600429.26 0.011971465 0.002724906 2.564648509 -2.656816151 TREEIQEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 164.64 5.66E-05 1422330000 1219380 935430 1073700 1086530 1167460 911940 1184930 1104170 1210360 FALSE TRUE 1161742.324 1030751.38 1122930.207 977309.9401 1371064.654 880359.2891 1004147.166 1007483.021 1398056.447 0.830969541 0.737274509 0.80320806 0.699048985 0.980693346 0.629702249 0.718245081 0.720631147 1 20.41499118 TREGNDLYHEMIESGVINLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TREGNDLYHEMIESGVINLK 20 1 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 162.33 1.28E-11 162920000 304000 223880 292340 253070 274870 249530 368890 300040 307560 FALSE TRUE 289630.5225 246693.6265 305744.0782 227630.9228 322807.241 240888.7135 312609.0554 273766.907 355254.834 0.815275388 0.694413145 0.860633126 0.640753907 0.908663894 0.678073007 0.879957218 0.770621201 1 18.43849475 -0.696391981 0.367484326 1.079387507 0.758699846 0.376654113 0.088892019 9.730080197 1.163085183 0.960122481 0.057486036 0.201190754 0.696391981 -0.320687661 TRETVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRETVQK 7 1 P53675;P53675-2;A0A087WX41 P53675 CLTCL1 Clathrin heavy chain 2 0 98.458 0.010258 97209000 174320 109830 134170 150760 146220 146000 210600 169060 171010 FALSE TRUE 166080.2391 121021.8019 140321.8272 135605.3184 171720.7217 140943.9834 178469.1021 154256.2102 197529.3574 0.840787624 0.612677546 0.710384669 0.686507161 0.869342785 0.713534359 0.903506721 0.780928021 1 17.59170756 1.130140758 0.493382754 0.998790419 0.709944482 0.488484542 0.082678707 0.742639992 0.476471858 0.088173274 0.045731302 13.49400162 -1.130140758 -0.288845938 TRGTS(ph)KTDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRGTSKTDSK 10 2 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 T(0.021)RGT(0.139)S(0.836)KT(0.004)DSK 65.219 0.054833 61853000 86952 56770 75462 70577 41286 83637 102050 99691 56449 TRUE FALSE 82841.95128 62554.92754 78922.00734 63482.46587 48486.26533 80740.62972 86480.39822 90961.52754 65202.82262 1.270527072 0.95938987 1.210407835 0.973615303 0.743622184 1.238299608 1.326329057 1.395055059 1 15.9926468 2.027542471 24.98607776 1.278118935 1.04407726 0.249819974 0.174707338 256.4303472 232628.2497 0.0624134 0.046094528 106.5473056 -2.027542471 -0.234041675 TRHGS(ph)ASQVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRHGSASQVQK 11 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 T(0.035)RHGS(0.963)AS(0.002)QVQK 111.64 0.00098872 39552000 61104 42917 60688 58062 49487 56768 74922 66887 61549 TRUE FALSE 58215.73502 47290.29109 63470.60483 52225.49745 58117.51713 54802.10993 63491.27286 61030.01969 71093.70457 0.818859214 0.665182542 0.892773913 0.734600873 0.817477686 0.770843357 0.893064629 0.858444782 1 16.11743419 1.050726121 0.512745218 1.005440751 0.758836747 0.542837583 0.062797143 0.653722802 0.438293362 0.064868409 0.031539097 11.23895988 -1.050726121 -0.246604004 TRHS(ph)PT(ph)PQQSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(0.002)RHS(0.998)PT(1)PQQSNR;T(0.007)RHS(0.993)PT(0.994)PQQS(0.006)NR;T(0.012)RHS(0.988)PT(0.986)PQQS(0.014)NR;T(0.009)RHS(0.991)PT(0.997)PQQS(0.003)NR 120.54 0.00091265 2974890000 980240 741020 831430 839830 754041 743600 880030 672654 566970 TRUE FALSE 933905.9978 816530.7805 869551.8879 755408.6928 885545.5117 717848.9455 745765.2606 613752.8498 654892.8119 1.42604405 1.246815915 1.32777742 1.153484477 1.352199162 1.096131966 1.13875927 0.937180617 1 19.32089927 1.993994073 0.60285054 0.960329071 1.343354317 0.706213042 0.084146811 0.388496951 0.285181322 0.070083024 0.044391652 98.62660256 -1.993994073 0.383025246 TRHS(ph)PTPQQSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TRHS(0.981)PT(0.019)PQQSNR;T(0.001)RHS(0.973)PT(0.026)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;TRHS(1)PTPQQSNR;T(0.018)RHS(0.981)PT(0.001)PQQSNR;TRHS(0.958)PT(0.042)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;T(0.012)RHS(0.988)PTPQQSNR;TRHS(0.999)PT(0.001)PQQSNR 179.92 1.22E-05 39995489000 6013069.8 5261155.8 5902311 5988878.3 5117377.6 5656160.5 7161478.3 5508480.1 4489797.3 TRUE FALSE 5728843.907 5797273.557 6172937.798 5386864.875 6009846.633 5460286.244 6068863.256 5026128.38 5186052.135 1.104663771 1.117858712 1.190296132 1.038721697 1.158848094 1.052879165 1.170227969 0.969162718 1 22.30620528 1.228831218 25 0.98458126 1.118309905 0.574940355 0.048071957 142.0462339 364979.4218 0.037807871 0.009919818 16.9367945 -1.228831218 0.133728645 TRKS(ph)PSSDSWTCADTSTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TRKSPSSDSWTCADTSTER 19 2 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 T(0.134)RKS(0.773)PS(0.09)S(0.002)DSWTCADTSTER;T(0.189)RKS(0.751)PS(0.036)S(0.024)DS(0.001)WTCADTSTER;T(0.002)RKS(0.95)PS(0.008)S(0.036)DS(0.003)WTCADTSTER 203.79 3.85E-16 965420000 471486 339360 453079 467857 364729 445926 602750 525560 410432 TRUE FALSE 449199.7912 373941.1698 473853.1203 420827.1255 428337.6221 430483.4708 510789.4172 479539.1802 474079.6984 0.947519568 0.788772797 0.999522068 0.887671687 0.903513953 0.908040298 1.077433645 1.011515958 1 18.85477009 1.753058416 24.99999871 1.033707992 0.898353302 0.515640906 0.056209472 3.352538743 5788.881495 0.024693971 0.01369418 56.63154578 -1.753058416 -0.135354691 TRLGIGNMFY(ph)VFY(ph)EDGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRLGIGNMFYVFYEDGIK 18 1 Q8N475-3 Q8N475-3 2 T(0.221)RLGIGNMFY(0.889)VFY(0.889)EDGIK 50.387 0.081374 7481300 14592 21095 17522 21390 13358 25811 16408 19080 9831.5 TRUE FALSE 13902.26508 23244.60448 18325.40103 19239.83656 15687.63097 24917.1586 13904.65825 17409.25405 11356.11881 1.224209196 2.046879297 1.613702828 1.694226424 1.3814254 2.194161493 1.224419934 1.533028524 1 13.47118223 0.939429157 1.133735541 1.014955741 1.669909422 0.29612401 0.31014027 0.662972698 1.741341157 0.264666386 0.083736643 8.698195355 -0.939429157 0.654953681 TRLQQELDDLLVDLDHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;; 246.69 1.57E-24 583225000 481482 265279 535668 370843 509282 442713 683185 558107 649114 FALSE TRUE 458723.3001 292311.2317 560228.9076 333565.1571 598100.6196 427381.7378 578952.5807 509236.1924 749775.2839 0.611814379 0.389865121 0.747195753 0.44488684 0.797706503 0.570013105 0.772168132 0.679185088 1 19.51609874 0.230538836 0.210460951 1.181846134 0.448023914 0.526693296 0.122252119 4.859417689 0.457888704 1.005141442 0.33985436 1.700351999 -0.230538836 -0.73382222 TRLS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 T(0.015)RLS(0.985)PPR;T(0.005)RLS(0.995)PPR;T(0.021)RLS(0.979)PPR;T(0.002)RLS(0.998)PPR;T(0.003)RLS(0.997)PPR;T(0.035)RLS(0.965)PPR;T(0.003)RLS(0.997)PPR;T(0.003)RLS(0.997)PPR;T(0.034)RLS(0.966)PPR 107.21 0.0045601 16928890000 947341 741383 817591 920860 754133 871812 947819 902978 859040 TRUE FALSE 902562.0684 816930.7706 855078.3561 828293.4033 885653.5564 841620.9318 803211.8037 823908.4593 992255.5358 0.909606483 0.823306841 0.861752165 0.834758158 0.892566002 0.848189707 0.809480799 0.83033899 1 19.92035218 -0.970562977 4.803644757 1.000001701 0.850116495 0.698696487 0.030690509 5.58E-07 1.20E-07 0.029651545 0.006988857 0.107013119 0.970562977 -0.149885206 TRLS(ph)TASEETVQNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRLSTASEETVQNR 14 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 T(0.031)RLS(0.766)T(0.203)ASEETVQNR 125.51 5.50E-05 202780000 137670 111220 106600 144770 125870 125220 146780 138060 105480 TRUE FALSE 131162.6119 122553.4444 111487.7154 130217.4446 147821.6881 120883.6 124386.0152 125970.7345 121837.2997 1.076539059 1.005877878 0.915054058 1.06878144 1.213271211 0.99217235 1.020919009 1.033925857 1 16.89459635 TRNEELAQTWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRNEELAQTWK 11 1 Q8TAT6;Q8TAT6-2;I3L283;I3L281;I3L3I1 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 92.19 0.0052355 0 101920 90529 92991 103060 69849 106440 104050 108730 87321 FALSE TRUE 97102.44359 99754.00802 97254.72933 92700.213 82030.64348 102753.9561 88175.26149 99209.02479 100862.2947 0.962722927 0.989011883 0.964232765 0.919076978 0.813293448 1.018754892 0.874214311 0.983608643 1 16.62202743 3.334286956 4.828306143 0.925269463 0.975778786 0.064058529 0.06081264 0.406262409 15.97116073 0.015403336 0.020943539 2159.17059 -3.334286956 0.050509323 TRNEMTAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRNEMTAEEK 10 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 95.162 0.0079862 151478000 162302 130212 149539 162950 117592 157990 175513 179656 142449 FALSE TRUE 154630.3061 143480.7508 156395.5111 146569.9564 138100.0076 152518.7667 148735.2683 163924.3682 164539.2634 0.939777552 0.872015274 0.95050572 0.890790158 0.839313394 0.926944509 0.903950007 0.996262927 1 17.32807236 1.234085176 5.666966751 1.000323427 0.902593629 0.599046421 0.03224313 0.102647806 10.75014876 0.025214374 0.007459032 17.14293489 -1.234085176 -0.097729797 TRNS(ph)GIWESPELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.086)RNS(0.914)GIWESPELDR;T(0.071)RNS(0.929)GIWESPELDR;T(0.266)RNS(0.734)GIWESPELDR 190.25 3.78E-07 490899000 265354 269993 242492 295179 233888 241773 270373 266982 221080 TRUE FALSE 252811.2423 297505.5937 253610.4981 265507.0461 274677.9931 233400.3404 229122.6331 243603.6407 255363.9573 0.990003621 1.165025781 0.99313349 1.039720127 1.075633367 0.913990928 0.897239515 0.953946842 1 17.96219539 2.237937989 24.9999972 0.928258991 1.059022162 0.488477322 0.055740048 11.78462597 473151.4627 0.019376336 0.015178954 172.9569383 -2.237937989 0.130763171 TRNSGIWES(ph)PELDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.003)RNS(0.178)GIWES(0.819)PELDR 82.59 0.012311 0 74472 62640 61929 80998 62318 65203 74238 76023 69073 TRUE FALSE 70951.85615 69023.08722 64768.50591 72855.92715 73186.23947 62945.00376 62911.62963 69366.0231 79784.48806 0.88929387 0.865119134 0.811793213 0.913159048 0.917299105 0.788937866 0.788519563 0.869417412 1 16.28382066 2.244350041 24.99439936 0.836170884 0.876767743 0 0.066606912 361.3934764 1560229.627 0.021670103 0.017672757 175.5294699 -2.244350041 0.040596858 TRPASQPT(ph)PFALHHAASCEVDPSSGDSISLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.212)RPAS(0.342)QPT(0.447)PFALHHAASCEVDPSSGDSISLAR 111.73 4.84E-06 74443000 33213 28555 34008 32807 34147 27649 38264 33738 12681 TRUE FALSE 31643.08731 31464.78696 35567.30044 29509.17803 40102.22599 26691.5082 32426.12403 30783.72186 14647.50471 2.160305658 2.148132913 2.428215668 2.014621508 2.737819633 1.822256331 2.213764369 2.101635908 1 13.83836729 -0.372412036 0.646793319 0.891453299 2.229868279 0.71761867 0.238935935 4.573388594 1.604530077 1.415627368 0.07962352 0.424216898 0.372412036 1.33841498 TRPDGNCFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRPDGNCFYR 10 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 206.97 1.28E-07 2218090000 555330 497290 388567 439106 494795 463390 620720 515278 481807 FALSE TRUE 529080.6515 547964.4164 406383.1813 394966.2306 581087.0913 447342.6881 526017.7637 470157.5267 556523.1688 0.950689353 0.984621031 0.730217903 0.709703122 1.044138185 0.803816828 0.945185741 0.844812135 1 19.08608222 -0.138343286 8.58901727 0.999999999 0.887431764 0.105797425 0.10875623 0 0 0.102314141 0.024115674 0.727204762 0.138343286 -0.112568235 TRPKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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 77.677 0.029452 1797300000 713010 585730 604330 668870 379660 683520 718200 713080 506490 TRUE FALSE 679307.4303 645416.5529 632039.1283 601633.9168 445872.5838 659849.531 608625.3994 650638.9349 585033.8824 1.161142031 1.103212262 1.080346194 1.028374484 0.762131215 1.127882591 1.040325044 1.112138894 1 19.15816066 3.554769785 2.163739567 1.013433983 1.136310174 0.207806753 0.099214023 0.484555614 4.475189586 0.028660285 0.049037211 3587.317244 -3.554769785 0.122876191 TRQDAELDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRQDAELDSK 10 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 112.7 0.0014461 385740000 772960 695310 715010 797630 647250 773150 855190 933800 1171080 FALSE TRUE 736423.7127 766162.8795 747793.9157 717450.717 760130.1951 746375.6216 724715.0589 852031.5216 1352685.105 0.544416221 0.566401505 0.552821875 0.530390047 0.56194172 0.551773372 0.53576036 0.629881647 1 20.3673946 0.768050452 2.816807414 0.999959218 0.550039954 0.993353538 0.011512996 0.093887139 1.031726462 0.01130956 0.002980326 5.862062598 -0.768050452 -0.449919264 TRS(ph)EREWDRDK ddPTM_SK-BR-3_Trastuzumab_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(0.136)RS(0.864)EREWDRDK 99.481 0.026211 187330000 77585 54528 79372 77575 60774 83380 92332 85771 78851 TRUE FALSE 73917.71081 60084.46519 83011.28471 69777.01362 71372.96636 80492.52969 78245.05761 78260.43654 91078.81036 0.811579669 0.659697519 0.911422584 0.766116875 0.783639642 0.883767908 0.859091783 0.859260636 1 16.47482783 0.98735951 0.240295898 1.050896163 0.717547277 0.506160764 0.064250117 2.097031872 0.422979408 0.259155604 0.158900007 9.713136902 -0.98735951 -0.333348886 TRS(ph)LSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRSLSSLR 8 1 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 T(0.018)RS(0.982)LSSLR;T(0.026)RS(0.973)LSSLR;T(0.014)RS(0.986)LSSLR;T(0.001)RS(0.999)LSSLR 143.24 0.00036618 828230000 287533 182908 259392 263828 289020 273061 340438 264708 325080 TRUE FALSE 273941.8849 201546.5331 271285.3798 237307.5082 339424.9965 263604.8291 288497.9305 241528.7642 375491.7461 0.729555011 0.536753564 0.722480274 0.631991277 0.903947956 0.702025629 0.768320299 0.643233218 1 18.51842167 -5 0.151888078 2.072039497 0.607994601 0.472518383 0.096663256 108.7001774 0.974464554 35.2091687 0.440179139 1.00E-05 5 -1.464044897 TRS(ph)NPEGAEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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(0.424)RS(0.576)NPEGAEDR;T(0.456)RS(0.544)NPEGAEDR;T(0.197)RS(0.803)NPEGAEDR;T(0.194)RS(0.806)NPEGAEDR;T(0.004)RS(0.996)NPEGAEDR;T(0.083)RS(0.917)NPEGAEDR 142.32 2.28E-05 1545254000 1152156 991769 1093359 1214191 956425 1150744 1352514 1180966 970957 TRUE FALSE 1097695.869 1092831.389 1143490.592 1092138.214 1123225.217 1110893.447 1146163.149 1077554.356 1121528.053 0.978750257 0.974412888 1.019582693 0.973794825 1.001513261 0.990517753 1.021965653 0.960791265 1 20.09703428 3.842668268 23.44648619 0.996951288 0.976580914 0.149463897 0.018446888 30.59315907 6877.073652 0.004275099 0.00770705 6960.946058 -3.842668268 -0.020370374 TRS(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.156)RS(0.797)PDVIS(0.023)S(0.023)AS(0.001)TALSQDIPEIASEALSR;T(0.176)RS(0.822)PDVIS(0.001)S(0.001)AS(0.001)T(0.001)ALSQDIPEIASEALSR;T(0.177)RS(0.823)PDVISSASTALSQDIPEIASEALSR;T(0.215)RS(0.784)PDVIS(0.001)SASTALSQDIPEIASEALSR;T(0.231)RS(0.768)PDVISSASTALSQDIPEIASEALSR 255.73 9.44E-54 2948714000 232815 193704 222173 247698 209399 218170 260559 246803 255948 TRUE FALSE 221810.2963 213442.6578 232359.8518 222798.9264 245918.1193 210614.7182 220805.9391 225191.6209 295639.1086 0.750273864 0.721970306 0.785957761 0.753617908 0.831818633 0.712404794 0.746876623 0.761711202 1 18.1734776 0.858451283 10.6220114 1 0.754237568 0.840147491 0.033143508 33.73889473 2532.500301 0.030412218 0.007605964 7.218571848 -0.858451283 -0.245762432 TRS(ph)WDSSSPVDRPEPEAASPTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRSWDSSSPVDRPEPEAASPTTR 23 2 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 T(0.2)RS(0.791)WDS(0.009)SSPVDRPEPEAASPTTR 172.94 2.31E-12 681040000 50806 32321 38752 41355 41303 44029 48948 39094 40729 TRUE FALSE 48404.50107 35614.54665 40528.81753 37197.91683 48506.23012 42504.26469 41480.08361 35670.72211 47045.04531 1.028896896 0.757030765 0.861489606 0.790687236 1.031059271 0.903480152 0.88170993 0.758224843 1 15.52175517 4.730464197 4.680383551 0.870582348 1.037051987 0.22161526 0.091716102 0.252482193 13.54585174 0.020414447 0.132750464 53760.61117 -4.730464197 0.16646964 TRS(ph)YDNLTTACDNTVPLASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.217)RS(0.783)YDNLTTACDNTVPLASR;T(0.272)RS(0.728)YDNLTTACDNTVPLASR;T(0.458)RS(0.542)YDNLTTACDNTVPLASR;T(0.208)RS(0.792)YDNLTTACDNTVPLASR 279.46 6.98E-45 2409710000 964120 678530 854050 1051950 925090 1035910 1167530 940030 1001610 TRUE FALSE 918547.9583 747672.9784 893209.0373 946205.9874 1086425.403 1000036.177 989401.8553 857715.9898 1156934.563 0.793949794 0.646253472 0.772048019 0.817856098 0.939055187 0.86438439 0.855192581 0.741369492 1 20.14187584 3.242017203 2.717146949 0.868556478 0.71997255 0.425422509 0.075317954 0.231902237 3.507975699 0.021017955 0.028029662 1745.891307 -3.242017203 -0.148583928 TRSDIVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TRSDIVSR 8 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;; 135.43 0.00076077 965610000 192763 164731 185154 169906 219784 174044 206592 203416 233986 FALSE TRUE 183651.475 181517.2762 193643.494 152826.7261 258114.26 168016.8126 175072.5961 185603.8167 270271.3538 0.679507733 0.671611229 0.716478055 0.565456619 0.955018933 0.621659714 0.647766008 0.686731368 1 18.04404908 -1.02578242 5.174066277 1.000002834 0.688761009 0.472275871 0.101889112 2.98E-06 5.61E-07 0.088296655 0.020811532 0.09423616 1.02578242 -0.311241825 TRT(ph)PAS(ph)INATPANINLADLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 2 T(0.426)RT(0.574)PAS(0.999)INATPANINLADLTR 87.739 0.0058666 57168000 34113 30296 29700 34571 28082 30345 37986 29288 27920 TRUE FALSE 32500.5461 33383.19684 31061.77438 31095.8574 32979.49191 29294.14504 32190.53804 26723.38745 32249.691 1.007778527 1.035147805 0.963165023 0.964221871 1.022629702 0.908354286 0.998165782 0.828640109 1 14.97699772 2.954861835 0.66570815 0.93746822 1.02263903 0.205668674 0.054777342 1.079109575 1.057300772 0.034656058 0.045359922 901.2843599 -2.954861835 0.085170811 TRT(ph)PASINATPANINLADLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.036)RT(0.961)PAS(0.003)INATPANINLADLTR;T(0.347)RT(0.652)PASINATPANINLADLTR 172.17 9.62E-12 281800000 214182 192799 206583 222194 170747 183551 225854 204926 188543 TRUE FALSE 204058.0413 212445.4373 216055.0349 199858.637 200525.2227 177194.5828 191395.8242 186981.5931 217781.2855 0.936986118 0.975499051 0.992073467 0.91770345 0.920764253 0.81363549 0.878844221 0.858575119 1 17.73252046 2.799039789 2.198671323 0.87672552 0.963912118 0.277055076 0.050483326 0.299855882 2.853983501 0.015825286 0.016323297 629.5638589 -2.799039789 0.087186598 TRT(ph)SQEELLAEVVQGQSR ddPTM_SK-BR-3_Trastuzumab_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(0.125)RT(0.437)S(0.437)QEELLAEVVQGQSR;T(0.115)RT(0.443)S(0.443)QEELLAEVVQGQSR;T(0.276)RT(0.362)S(0.362)QEELLAEVVQGQSR 212.65 2.72E-16 371140000 439900 382436 425020 447690 399650 365002 374940 337906 329454 TRUE FALSE 419106.7988 421406.6632 444507.5874 402687.3506 469348.8335 352361.8892 317736.0168 308317.1593 380544.0437 1.101335853 1.107379475 1.168084469 1.058188552 1.233362711 0.925942463 0.834952017 0.810200986 1 18.53770391 2.09685405 5.821405694 0.867512514 1.124531215 0.757862589 0.067683717 0.085640161 4.273487768 0.022910004 0.016767586 124.9838935 -2.09685405 0.2570187 TRTDS(ph)TSDGRPAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.009)RT(0.038)DS(0.75)T(0.166)S(0.038)DGRPAWMR;TRTDS(0.913)T(0.069)S(0.018)DGRPAWMR 101.17 0.0014765 743220000 293760 212360 268330 279020 279810 271300 344470 283090 282860 TRUE FALSE 279874.547 233999.7254 280633.1959 250972.3795 328608.7754 261904.813 291914.7749 258301.1388 326724.4842 0.856607204 0.716198928 0.858929188 0.768146838 1.005767218 0.801607549 0.893458523 0.790577846 1 18.31771505 TRTDS(ph)YSAGQSVEILDGVELGEPAHKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRTDSYSAGQSVEILDGVELGEPAHKK 27 2 P42345;B1AKP8;B1AKQ2 P42345 MTOR Serine/threonine-protein kinase mTOR 1 T(0.009)RT(0.058)DS(0.917)YS(0.015)AGQSVEILDGVELGEPAHKK 206.63 1.40E-25 267730000 311380 219210 304640 344310 220780 328750 435310 355570 212700 TRUE FALSE 296661.6845 241547.7482 318608.0453 309699.3047 259283.9621 317365.3051 368895.4645 324434.4058 245684.4297 1.207490784 0.983162623 1.296818222 1.260557314 1.05535366 1.291759944 1.501501194 1.320533036 1 17.9064469 2.062347485 7.252647071 1.346177722 1.152371716 0.064427843 0.155752097 0.290745461 28.12462248 0.055027852 0.040442434 115.437652 -2.062347485 -0.193806006 TRTDST(ph)SDGRPAWMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.001)RT(0.001)DS(0.415)T(0.566)S(0.019)DGRPAWMR 68.129 0.086097 179670000 110340 63049 93479 92789 93078 95603 109390 104380 123720 TRUE FALSE 105124.4469 69473.76478 97765.10461 83461.67343 109310.7737 92292.24414 92700.54641 95239.93385 142905.8657 0.735620237 0.486150547 0.684122405 0.584032524 0.764914534 0.645825444 0.648682585 0.666452237 1 17.12470561 -5 0.288089944 3.754569403 0.622447619 0.669307036 0.076870994 135.792385 1.283073174 224.44923 0.076926964 1.00E-05 5 -3.132121784 TRTFS(ph)ATVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 TRTFSATVR 9 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 T(0.002)RT(0.012)FS(0.841)AT(0.146)VR;TRTFS(0.849)AT(0.151)VR;TRTFS(1)ATVR;TRTFS(0.997)AT(0.003)VR;TRT(0.001)FS(0.971)AT(0.029)VR;TRTFS(1)ATVR;TRTFS(1)ATVR;TRTFS(0.997)AT(0.003)VR;TRTFS(0.999)AT(0.001)VR;T(0.002)RT(0.006)FS(0.984)AT(0.009)VR 162.93 3.84E-05 12983350000 3356508 1894309 3464870 2374421 3089422 3068265 4373860 3820261 5113850 TRUE FALSE 3197852.519 2087341.241 3623737.717 2135739.69 3628216.219 2962010.214 3706547.326 3485738.694 5906879.74 0.541377624 0.353374596 0.613477483 0.361568169 0.614235667 0.501450909 0.627496663 0.59011506 1 22.49396481 -0.360590933 0.332490388 1.156399146 0.446409756 0.753944868 0.088696099 3.151265 0.398262789 0.646921834 0.073505341 0.435922281 0.360590933 -0.70998939 TRWDSELQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRWDSELQR 9 1 Q969N2;Q969N2-5;Q969N2-6;Q969N2-4;A0A1W2PP53;Q969N2-2;A0A1W2PNP0;A0A1W2PR92;A0A1W2PPC3;A0A1W2PP57;A0A1W2PRZ8;A0A1W2PPQ7;A0A1W2PP13;A0A1W2PRV7;A0A1W2PQ52;A0A1W2PR70;A0A1W2PPI8;A0A1W2PQ29;A0A1W2PRH2;A0A1W2PPS0;A0A1W2PRB4;A0A1W2PPU8;A0A1W2PRL6;A0A1W2PQL3;B7Z7C5;A0A1W2PRG1;H7C2Y2;A0A1W2PRH8;A0A1W2PP98;A0A1W2PNS2;A0A1W2PQI9;A0A1W2PNW9;A0A1W2PNZ5;A0A1W2PP03;A0A1W2PR22 Q969N2 PIGT GPI transamidase component PIG-T 0 85.533 0.015209 0 75235 44611 34668 37142 71892 42591 83016 49729 58437 FALSE TRUE 71678.79065 49156.91162 36257.56209 33408.41559 84429.94204 41116.06299 70350.38451 45374.46513 67499.11151 1.061921988 0.728260129 0.537156139 0.494946005 1.250830421 0.609134877 1.042241638 0.672223147 1 16.04258089 2.764781001 24.99118049 0.902366632 0.739590795 0.156833658 0.23436248 1784.253712 1700605.313 0.06949807 0.073693911 581.8097587 -2.764781001 -0.162775837 TRYDSGQDLDEEGMNMGDFDPNNIFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TRYDSGQDLDEEGMNMGDFDPNNIFK 26 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PRZ0;Q99615-2;K7ER44 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 176.53 2.27E-13 60465000 134850 105540 119980 135820 92141 124200 147590 148710 112470 FALSE TRUE 128475.9077 116294.646 125481.2017 122167.1156 108210.3612 119898.9229 125072.4348 135688.164 129911.2732 0.988951186 0.895185176 0.965899253 0.940388871 0.832955898 0.922929319 0.962752745 1.044467972 1 16.9871671 1.459051775 3.482547114 1.020982259 0.925205424 0.464658007 0.042861311 0.201117115 4.642763261 0.030681962 0.010977626 28.77741471 -1.459051775 -0.095776835 TS(ph)LMAFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSLMAFLR 8 0 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 T(0.091)S(0.909)LMAFLR;T(0.217)S(0.783)LMAFLR;T(0.156)S(0.844)LMAFLR;T(0.11)S(0.89)LMAFLR 195.79 0.00016507 92195000 396956 285792 242093 261020 326063.3 265488 390562 321055 284287 TRUE FALSE 378192.6766 314914.5297 253193.2035 234781.7737 382928.6363 256294.084 330974.5937 292941.7222 328372.776 1.151717512 0.959015341 0.771054186 0.714985501 1.166140022 0.780497358 1.007923366 0.892101123 1 18.324975 4.345837719 2.495305762 0.905092662 1.139001543 0.2480462 0.132906188 0.380567637 4.42848461 0.031656192 0.13016677 22173.67711 -4.345837719 0.23390888 TS(ph)PADGKPR ddPTM_SK-BR-3_Trastuzumab_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(0.2)S(0.8)PADGKPR;T(0.02)S(0.98)PADGKPR 96.113 0.0045951 259470000 443360 412890 425220 490460 282720 465580 498160 470740 338220 TRUE FALSE 422403.2515 454963.9604 444716.7576 441158.029 332026.2785 449456.8479 422156.5427 429519.5101 390669.4302 1.081229343 1.164575278 1.138345423 1.129236113 0.849890605 1.150478674 1.080597841 1.099444893 1 18.57558884 6.556902891 0.012241869 4.19E-07 2.298930939 0.098389633 0.088171131 14403.99557 17.55148011 1429.89234 1894.878774 3604980.262 -6.556902891 2.29893052 TS(ph)PDSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPDSLRR 8 1 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 T(0.423)S(0.577)PDSLRR 74.841 0.02446 147340000 275000 245660 238250 310940 249690 289500 281250 303170 262220 TRUE FALSE 262001.295 270693.0333 249173.9982 279683.7205 293235.8569 279474.5424 238340.147 276622.8276 302883.7384 0.865022653 0.893719269 0.82267209 0.923402894 0.968146585 0.922712272 0.786903081 0.913297059 1 18.2084046 -2.571521663 1.839369884 2.324111334 0.882343814 0.311313277 0.05242427 2236404.477 113653.1305 12346264.04 0.013432457 0.002682121 2.571521663 -1.44176752 TS(ph)PDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.047)S(0.953)PDTLR;T(0.07)S(0.93)PDTLR;T(0.055)S(0.945)PDTLR;T(0.131)S(0.869)PDTLR;T(0.286)S(0.713)PDTLR;T(0.093)S(0.907)PDTLR 218.82 3.36E-05 8304360000 14321680 14165640 10459210 15277290 8184690 12320270 11380400 12176830 7927910 TRUE FALSE 13644722.57 15609134.82 10938775.12 13741587.78 9612097.345 11893615.96 9644110.965 11110562.21 9157329.793 1.490032889 1.704550909 1.194537641 1.500610778 1.049661589 1.298808302 1.053157545 1.213297158 1 23.12649555 3.172763178 0.84474135 1.109109111 1.605846662 0.560326495 0.151208522 0.378721028 0.597447965 0.069140805 0.108517768 1488.549147 -3.172763178 0.496737551 TS(ph)PDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.399)S(0.601)PDTLRR 94.309 0.0064012 117780000 105200 113760 94806 118830 82634 108990 102380 123000 79680 TRUE FALSE 100227.4045 125352.2733 99152.94888 106884.9826 97045.34344 105215.649 86760.05066 112229.4679 92036.36745 1.088997831 1.361986319 1.07732358 1.161334216 1.054423877 1.143196455 0.942671392 1.219403493 1 16.48991642 3.241227036 1.610947128 1.065539135 1.218054474 0.182184838 0.105938783 0.464453335 2.498294476 0.032932862 0.047324864 1742.717674 -3.241227036 0.152515339 TS(ph)PGGRT(ph)SPEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.436)S(0.564)PGGRT(0.474)S(0.526)PEAR;T(0.429)S(0.571)PGGRT(0.7)S(0.3)PEAR 114.27 0.0024642 324398000 695920 623158 639856 710180 492372 599290 709690 607140 520797 TRUE FALSE 663025.2408 686658.5087 669194.0305 638791.3571 578241.5209 578536.437 601413.7561 553975.6029 601559.5389 1.102177254 1.141463919 1.112431916 1.061892158 0.96123739 0.961727642 0.999757659 0.920899042 1 19.19834801 2.951007089 2.552950232 0.970245993 1.121596289 0.888616976 0.024510984 0.07927219 1.026819762 0.007476742 0.008445101 893.3200648 -2.951007089 0.151350296 TS(ph)PGGRTS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.451)S(0.549)PGGRT(0.451)S(0.549)PEAR 88.992 0.0055046 66258000 146870 119480 128920 139250 110680 126630 151930 126060 124150 TRUE FALSE 139927.7462 131655.1478 134831.1095 125252.3254 129982.557 122244.7713 128750.2881 115021.5181 143402.5479 0.975768898 0.918080953 0.94022813 0.87343166 0.906417346 0.852458852 0.897824271 0.802088385 1 17.12971113 3.969355002 0.797795025 0.881461551 0.979667432 0.204445773 0.05132105 1.347985228 1.29809477 0.018450309 0.097268737 9318.692952 -3.969355002 0.098205881 TS(ph)PITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPITR 6 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.292)S(0.708)PITR 71.922 0.091213 531900000 781140 762990 641380 804890 591990 676930 812380 801080 671130 TRUE FALSE 744217.0603 840739.5484 670787.9074 723980.928 695232.8686 653487.7444 688436.5106 730933.1884 775205.4127 0.960025624 1.084537768 0.865303436 0.933921405 0.896836964 0.84298656 0.888069793 0.942889686 1 19.56421912 3.730819152 24.99134956 0.900978315 1.022281697 0.430213578 0.052934204 407.3530163 1315035.846 0.012925758 0.020456579 5380.456839 -3.730819152 0.121303383 TS(ph)PKPAVVETVTTAKPQQIQALMDEVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPKPAVVETVTTAKPQQIQALMDEVTK 28 2 P56192;H0YIP0;H0YI94 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 T(0.447)S(0.553)PKPAVVETVTTAKPQQIQALMDEVTK 209.27 8.28E-26 1712400000 1432000 1158000 1286600 1529500 486470 1613000 1526800 1670700 553130 TRUE FALSE 1364312.198 1276001.517 1345591.883 1375751.754 571310.214 1557141.406 1293858.618 1524404.651 638906.5754 2.135386065 1.997164477 2.106085513 2.153290962 0.894199928 2.437197339 2.02511395 2.38595862 1 19.28524546 TS(ph)PLKDNPS(ph)PEPQLDDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.444)S(0.556)PLKDNPS(1)PEPQLDDIKR;T(0.453)S(0.547)PLKDNPS(1)PEPQLDDIKR 143.29 7.87E-08 327000000 405020 358450 358720 411130 154432 454290 432040 415800 156783 TRUE FALSE 385875.5073 394976.4625 375167.6668 369802.4313 181364.8919 438557.8234 366124.363 379390.3477 181096.1069 2.130777485 2.181032322 2.071649541 2.042023087 1.001484212 2.42168554 2.021713052 2.094966889 1 17.46639601 2.98354866 24.94596167 1.817493399 2.129294023 0.140542681 0.450174502 1649.395209 2501061.869 0.127603599 0.138745411 962.8278859 -2.98354866 0.311800625 TS(ph)PLKDNPSPEPQLDDIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.004)S(0.994)PLKDNPS(0.003)PEPQLDDIKR 191.41 5.07E-15 410050000 479770 388690 388930 477150 204720 439890 484050 539080 255780 TRUE FALSE 457092.2229 428297.9529 406762.8252 429185.9755 240423.1032 424656.499 410199.2823 491875.2974 295445.0561 1.547131061 1.449670401 1.376779935 1.452676112 0.81376587 1.437345084 1.388411395 1.664862171 1 18.17253033 3.70363267 1.547334786 1.307634875 1.521121524 0.118637283 0.237976268 0.90145788 4.20440801 0.069463375 0.156931913 5053.970117 -3.70363267 0.213486649 TS(ph)PPCS(ph)PANLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.031)S(0.969)PPCS(1)PANLSR;T(0.226)S(0.774)PPCS(1)PANLSR;T(0.002)S(0.998)PPCS(1)PANLSR;T(0.116)S(0.884)PPCS(1)PANLSR 227.91 1.73E-11 1965620000 1063310 1028650 956730 1111750 742801 959680 1055430 1002170 828510 TRUE FALSE 1013049.444 1133470.604 1000597.017 999994.7778 872345.2592 926446.041 894404.7692 914414.682 956991.0994 1.058577707 1.184410811 1.045565646 1.044936341 0.911550024 0.968082192 0.934600928 0.955510122 1 19.86814598 3.135646357 1.907611141 0.950487629 1.118002134 0.698932104 0.043068153 0.147771122 1.103490104 0.012954904 0.016741483 1366.615548 -3.135646357 0.167514505 TS(ph)PPCSPANLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.2)S(0.799)PPCS(0.001)PANLSR;T(0.164)S(0.836)PPCSPANLSR;T(0.484)S(0.516)PPCSPANLSR;T(0.192)S(0.808)PPCSPANLSR 145.41 6.70E-05 2839260000 1592610 1426630 1343840 1613200 1199920 1467610 1646420 1451950 1272740 TRUE FALSE 1517330.482 1572005.219 1405456.393 1451038.071 1409185.668 1416786.298 1395228.39 1324809.561 1470110.019 1.03212036 1.069311275 0.956021233 0.987026857 0.958557965 0.963728074 0.949063929 0.901163548 1 20.4874927 3.732229475 24.73448061 0.95809698 1.050715819 0.661266784 0.027169481 207.8807466 812148.5263 0.006761858 0.010772902 5397.957679 -3.732229475 0.092618839 TS(ph)PPLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.011)S(0.989)PPLLDR;T(0.136)S(0.864)PPLLDR;T(0.141)S(0.859)PPLLDR;T(0.184)S(0.816)PPLLDR;T(0.01)S(0.99)PPLLDR 192.64 0.00018341 11723250000 7580990 7398010 6107100 7963300 4845700 6902890 6780520 6939510 4631270 TRUE FALSE 7222651.627 8151875.63 6387116.576 7162813.955 5690788.546 6663841.188 5746027.141 6331849.716 5349463.698 1.350163686 1.523867829 1.193973253 1.338977953 1.063805433 1.245702666 1.074131439 1.183641964 1 22.35096283 3.193686535 1.051908217 1.116282185 1.43556674 0.5733543 0.102161256 0.30595593 0.730741285 0.038514563 0.058397301 1562.019802 -3.193686535 0.319284555 TS(ph)PQVLGSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.162)S(0.838)PQVLGSILK;T(0.115)S(0.885)PQVLGSILK;T(0.161)S(0.839)PQVLGSILK 181.9 6.32E-06 315689000 1598250 1560810 1336530 1492570 1030327 1504240 1739030 1652510 1106757 TRUE FALSE 1522703.89 1719858.313 1397811.223 1342534.028 1210015.703 1452147.792 1473709.034 1507807.464 1278387.223 1.191113195 1.345334405 1.093417704 1.050177915 0.946517362 1.135921703 1.152787675 1.17946068 1 20.28589346 3.719947207 23.29134744 1.086822894 1.268223778 0.495749185 0.078772599 253.695624 317454.6019 0.021378511 0.033201944 5247.436685 -3.719947207 0.181400884 TS(ph)PSGGTWSSVVSGVPR ddPTM_SK-BR-3_Trastuzumab_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(0.141)S(0.858)PS(0.001)GGTWSSVVSGVPR 106.36 0.00079403 374010000 196120 200250 191190 209990 155030 193860 213740 216030 193120 TRUE FALSE 186849.7963 220655.7027 199956.2506 188881.4062 182067.1829 187146.5796 181130.0374 197113.268 223068.0633 0.837635803 0.98918554 0.896391208 0.846743382 0.81619565 0.838966264 0.811994486 0.883646296 1 17.76712445 4.815350489 20.49838048 0.8772515 0.837629909 0.037538741 0.065308196 27008.61751 8466199.754 0.015947533 31.67870391 65365.78614 -4.815350489 -0.039621592 TS(ph)PSKSPFLHSGMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPSKSPFLHSGMK 14 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;H0YEW5 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 T(0.092)S(0.902)PS(0.006)KSPFLHSGMK 122.49 6.57E-05 228590000 125830 111680 109270 144790 62956 126770 136830 149650 63451 TRUE FALSE 119882.2653 123060.319 114280.1376 130235.4341 73935.50647 122379.9231 115954.0704 136545.8527 73290.65702 1.635710064 1.679072394 1.559272931 1.776971846 1.008798522 1.669788867 1.58211258 1.863073115 1 16.16134168 TS(ph)PSSDKVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPSSDKVQK 10 1 F8WDU9;P38435 F8WDU9 GGCX Vitamin K-dependent gamma-carboxylase 1 T(0.111)S(0.885)PS(0.002)S(0.001)DKVQK 81.494 0.012622 88844000 240280 212700 228900 328420 175910 306840 339300 300510 186190 TRUE FALSE 228922.4406 234374.3718 239395.2914 295406.5976 206588.6483 296214.0539 287533.5533 274195.7513 215063.3943 1.064441679 1.089792024 1.113138255 1.373579166 0.960594196 1.377333669 1.336971149 1.274953147 1 17.71440246 3.443026205 17.81365786 1.242754277 1.081174474 0.149840805 0.142999049 12.07334883 6306.917149 0.036821049 0.049860391 2773.487451 -3.443026205 -0.161579803 TS(ph)PTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 T(0.299)S(0.7)PTFR;T(0.362)S(0.638)PT(0.001)FR 143 0.012015 571800000 1536580 1273040 1304920 1615410 1207570 1410630 1578060 1489410 1264100 TRUE FALSE 1463948.909 1402764.223 1364751.873 1453025.918 1418169.826 1361779.529 1337297.964 1358989.365 1460130.172 1.00261534 0.960711757 0.934678222 0.995134506 0.971262599 0.932642552 0.915875851 0.93073165 1 20.47766556 2.249440543 9.974203453 0.935256857 0.973220734 0.154406846 0.029029884 0.250376963 203.6165495 0.009646521 0.007800699 177.599011 -2.249440543 0.037963878 TS(ph)PTPPESATTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.004)S(0.996)PTPPESATTVK;T(0.015)S(0.985)PTPPESATTVK;T(0.003)S(0.997)PTPPESATTVK 225.79 1.24E-11 350508000 1519320 1260160 1355320 1535150 923130 1465750 1688300 1591450 1124470 TRUE FALSE 1447504.755 1388571.737 1417462.763 1380833.805 1084123.58 1414990.71 1430718.827 1452094.201 1298847.065 1.114453575 1.069080244 1.091323837 1.063122706 0.834681472 1.08942057 1.101529862 1.117987052 1 20.30880014 2.998697953 24.93645083 1.035830837 1.088447979 0.113133872 0.079402247 129.7625882 2485302.613 0.023684486 0.027961 997.0064157 -2.998697953 0.052617141 TS(ph)PTVATQTGASATSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.001)S(0.999)PT(0.001)VATQTGASATSTR 216.34 5.59E-15 196920000 184310 155770 187310 184680 132840 176390 199410 183040 147730 TRUE FALSE 175598.0316 171643.1401 195898.3488 166115.6155 156007.2539 170281.5701 168986.3421 167012.0472 170639.2139 1.029060247 1.005883326 1.148026554 0.973490277 0.914252067 0.997904094 0.990313646 0.978743651 1 17.3805897 3.100041299 22.53421318 0.975011502 1.046641454 0.444881591 0.043895368 6.386315608 1426.592046 0.012425789 0.014851659 1259.045134 -3.100041299 0.071629952 TS(ph)PYILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.037)S(0.963)PYILR;T(0.086)S(0.914)PYILR 158.07 0.0015043 148736000 347530 404800 360890 440540 297250 369630 377690 417830 293280 TRUE FALSE 331102.9456 446049.5802 377437.1635 396256.0822 349090.3059 356829.6204 320066.4537 381242.5901 338760.3645 0.977395765 1.316711242 1.114171559 1.169723863 1.030493359 1.053339345 0.944816712 1.125404947 1 18.36990556 2.720531919 9.531436567 1.022373052 1.152961112 0.265767359 0.092843187 0.417797051 211.2797231 0.028591134 0.027503608 525.4506329 -2.720531919 0.13058806 TS(ph)QETADVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSQETADVK 9 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 T(0.404)S(0.596)QETADVK 96.23 0.0078767 199120000 372130 407740 312820 421910 221170 411770 409340 423540 208310 TRUE FALSE 354540.1524 449289.1696 327163.1064 379498.8052 259741.978 397510.3017 346887.665 386452.5923 240613.6509 1.473483117 1.867263839 1.359703014 1.577212281 1.079498096 1.652068784 1.441679072 1.6061125 1 17.87635897 -3.193747562 0.206367755 1.62E-17 1.617518831 0.35060268 0.208768605 66.03808 1.281521116 29.59450481 0.463332108 0.000640107 3.193747562 1.617518831 TS(ph)SPHKEES(ph)PKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 2 T(0.393)S(0.517)S(0.09)PHKEES(1)PKK;T(0.379)S(0.47)S(0.151)PHKEES(1)PKK 78.441 0.013794 171578000 431610 493810 342710 539360 128534 564020 417120 507900 106307 TRUE FALSE 411208.6507 544129.8004 358423.5925 485142.5081 150950.2889 544487.846 353480.6831 463425.5835 122792.5466 3.348807904 4.431293392 2.918936062 3.950911692 1.229311494 4.434209249 2.878681914 3.774053037 1 16.90586347 3.383264743 1.947683204 2.961212399 3.850771042 0.104469635 1.127831018 0.715971823 5.527030067 0.309717217 0.477239667 2416.933734 -3.383264743 0.889558643 TS(ph)SPHKEESPKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.009)S(0.914)S(0.077)PHKEESPKK;T(0.008)S(0.678)S(0.314)PHKEESPKK;T(0.016)S(0.845)S(0.139)PHKEESPKK 127.71 0.0001382 484840000 647503 461572 545423 613612 252124 656827 681818 692460 233113 TRUE FALSE 616896.8164 508606.7116 570431.184 551930.556 296094.3458 634080.9163 577794.1417 631824.5314 269262.9735 2.291056986 1.888884703 2.118490993 2.049782593 1.099647463 2.354876009 2.14583585 2.346496153 1 18.03865633 5.049278168 1.152723325 1.932495304 2.712674351 0.058671895 0.472690401 9.724149498 6.769898007 0.124772493 10.83548492 112015.512 -5.049278168 0.780179046 TS(ph)SPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSPPR 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.009)S(0.682)S(0.309)PPR 111.04 0.029573 350750000 732390 564150 579320 688060 469920 576540 701480 760670 671370 TRUE FALSE 697771.3762 621637.5264 605882.395 618894.9016 551873.8992 556574.2752 594456.3424 694061.7022 775482.6307 0.899789819 0.801613733 0.781297183 0.798077065 0.711652173 0.7177134 0.766563065 0.895006122 1 19.56473494 1.014674403 3.67033392 0.999053195 0.786437075 0.663282113 0.051814198 0.136382462 4.528245232 0.056168385 0.01449593 10.34366396 -1.014674403 -0.212616121 TSAAACAVTDLS(ph)DDS(ph)DFDEKAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSAAACAVTDLSDDSDFDEKAK 22 1 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 2 TSAAACAVTDLS(1)DDS(1)DFDEKAK;TSAAACAVTDLS(1)DDS(1)DFDEKAK 207.13 4.81E-23 374590000 1139350 780040 996850 982500 425940 1164600 1213540 1133480 532900 TRUE FALSE 1085495.183 859526.9628 1042556.559 883737.2334 500223.8011 1124269.61 1028392.185 1034226.482 615539.4103 1.763486083 1.396380067 1.693728364 1.435711863 0.812659259 1.826478681 1.670717045 1.680195394 1 19.2314917 TSADAQEPAS(ph)PVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_SK-BR-3_Trastuzumab_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 3 TSADAQEPAS(0.999)PVVS(0.002)PQQS(0.993)PPT(0.14)S(0.849)PHT(0.017)WR;TSADAQEPAS(1)PVVS(0.024)PQQS(0.971)PPT(0.247)S(0.734)PHT(0.025)WR 125.36 3.52E-05 362180000 251660 198879 219181 250965 208096 241031 278330 240053 201576 TRUE FALSE 239764.5305 219144.9962 229230.6656 225737.5214 244387.8765 232684.036 235865.6466 219032.6867 232835.3766 1.029759885 0.941201459 0.984518199 0.969515564 1.049616601 0.999350011 1.013014646 0.940719104 1 17.82895075 4.753146121 24.0404962 0.989019476 1.029759934 0.142787253 0.032481147 210.2234516 1606133.004 0.007511411 0.052752486 56642.98355 -4.753146121 0.040740459 TSADAQEPASPVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.998)PPT(0.624)S(0.365)PHT(0.013)WR 143.47 3.27E-07 149630000 101000 82325 94784 107210 85089 93575 123190 108330 91126 TRUE FALSE 96225.93016 90714.0111 99129.94015 96433.04711 99928.49466 90334.47429 104395.103 98844.05091 105257.3547 0.914196737 0.861830619 0.941786353 0.916164456 0.949373039 0.85822482 0.991808157 0.939070255 1 16.68356152 1.370236165 0.366163414 1.007100072 0.889019 0.388959468 0.036437924 1.090811703 0.462518136 0.049681958 0.03631397 23.45503932 -1.370236165 -0.118081072 TSADAQEPASPVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_SK-BR-3_Trastuzumab_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(0.98)PPT(0.353)S(0.666)PHT(0.002)WR;TSADAQEPASPVVSPQQS(0.999)PPT(0.338)S(0.662)PHT(0.002)WR 207.92 1.18E-25 658870000 397340 321670 368880 415090 328270 357640 432540 372580 325580 TRUE FALSE 378558.5257 354448.5387 385793.5129 373364.3646 385520.1841 345254.8371 366548.0789 339954.92 376069.2836 1.006619105 0.942508613 1.025857547 0.992807392 1.025130743 0.918061783 0.974682312 0.903968856 1 18.52063895 2.237321733 24.99992541 0.948991113 0.992645416 0.320761103 0.035139261 42.78008854 863246.2718 0.011841675 0.00922559 172.7116896 -2.237321733 0.043654303 TSAVSS(ph)PLLDQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 TSAVS(0.001)S(0.999)PLLDQQR;TSAVSS(1)PLLDQQR;TSAVS(0.001)S(0.999)PLLDQQR;TSAVS(0.002)S(0.998)PLLDQQR;TSAVS(0.018)S(0.982)PLLDQQR;TSAVSS(1)PLLDQQR 361.92 9.33E-77 1693950000 3153230 2783890 2763180 3149300 2759450 2926370 3472210 3204570 2978050 TRUE FALSE 3004183.067 3067571.556 2889874.536 2832726.381 3240697.206 2825029.073 2942460.593 2923960.862 3439870.784 0.873341836 0.891769415 0.840111364 0.823497904 0.942098529 0.82126023 0.855398583 0.850020552 1 21.71392294 -0.698134908 5.920373455 1.000000003 0.863627271 0.599752186 0.035363628 9.46E-10 2.40E-10 0.031753416 0.007484352 0.200384946 0.698134908 -0.136372732 TSCSGSGERES(ph)PER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSCSGSGERESPER 14 1 Q9H8Y5;C9JQZ3;C9K022 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 TSCSGSGERES(1)PER;TSCSGSGERES(1)PER 177.67 1.25E-06 220793000 237435 245090 239464 262190 212188 255604 266170 254920 235550 TRUE FALSE 226211.9181 270064.9496 250443.6613 235834.1631 249193.52 246752.3694 225560.878 232597.8534 272077.891 0.831423374 0.992601599 0.920485161 0.866789147 0.915890369 0.90691812 0.829030529 0.854894356 1 18.0536602 3.258291559 24.14362939 0.884973249 0.919584449 0 0.059757175 462.7793988 566271.173 0.015799081 0.021357911 1812.556525 -3.258291559 0.0346112 TSCSGSGERES(ph)PERK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSCSGSGERESPERK 15 2 Q9H8Y5;C9JQZ3;C9K022 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 TSCSGSGERES(1)PERK;TSCSGSGERES(1)PERK;TSCSGSGERES(1)PERK;TSCS(0.012)GS(0.009)GERES(0.978)PERK;TS(0.007)CS(0.008)GS(0.008)GERES(0.977)PERK;TSCS(0.192)GS(0.192)GERES(0.616)PERK 201.48 3.34E-09 2960780000 1692010 1325588 1525904 1625660 932289 1741820 1761171 1891791 1047846 TRUE FALSE 1612032.041 1460666.924 1595868.208 1462245.568 1094879.906 1681500.337 1492472.018 1726135.751 1210340.606 1.33188297 1.206823036 1.318528189 1.208127333 0.904604787 1.389278628 1.23310084 1.426157019 1 20.20698167 3.207345324 21.36660859 1.207048898 1.275423988 0.064525701 0.1584611 151.2040891 103495.7034 0.04355776 0.052075234 1611.926828 -3.207345324 0.068375089 TSDANETEDHLESLICK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 90.793 0.0035409 0 46066 40630 45134 50972 32938 45401 49363 52220 41110 FALSE TRUE 43888.55147 44770.24319 47203.43854 45848.19772 38682.37677 43828.75199 41831.76774 47647.33996 47485.12884 0.924258869 0.942826613 0.994067821 0.9655275 0.814620866 0.922999538 0.880944598 1.003416041 1 15.53518815 1.219831453 24.68694939 1.001708165 0.921652108 0.329400845 0.048010048 296.8834936 391310.6309 0.045795154 0.011533668 16.58942958 -1.219831453 -0.080056057 TSDDEVGS(ph)PKEESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSDDEVGSPKEESR 14 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 TSDDEVGS(1)PKEESR 132.13 2.15E-05 0 245050 198300 200870 240250 116610 223960 227890 243770 120030 TRUE FALSE 233466.9721 218506.9954 210080.0882 216099.6136 136946.7471 216204.209 193121.195 222424.2065 138643.6394 1.683935687 1.576033321 1.515252262 1.558669511 0.987760763 1.55942393 1.392932239 1.604287131 1 17.08102191 -1.821678467 0.065627652 8.18E-13 2.214079749 0.398697723 0.189696309 160.9230552 1.563446237 42.12303298 15.41307492 0.015077229 1.821678467 2.214079749 TSDIFGS(ph)PVTATSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(0.5)PVT(0.5)ATSR;TSDIFGS(0.992)PVT(0.008)ATSR;TSDIFGS(1)PVTATSR 384.18 7.86E-114 6247010000 5341480 5043730 5405240 6269360 5081120 5773550 6842680 6318230 6136590 TRUE FALSE 5088998.826 5557691.821 5653075.601 5639152.022 5967265.719 5573610.516 5798703.492 5764972.286 7088221.036 0.717951486 0.784074282 0.797530942 0.795566616 0.841856608 0.786320078 0.818075997 0.813317228 1 22.75699216 -5 0.149479929 1.744111895 0.725031812 0.882126615 0.024756508 42.92175214 0.381636903 9.484561493 0.126653029 1.00E-05 5 -1.019080083 TSEEFVHINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSEEFVHINR 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3;A0A3B3IU76 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 103.7 0.0027796 362030000 140953 132874 165721 160269 176473 138561 178849 152372 216970 FALSE TRUE 134290.431 146414.0117 173319.4718 144158.4556 207249.8353 133762.5978 151562.3003 139029.4999 250616.5995 0.535840129 0.58421514 0.691572195 0.575215113 0.82695973 0.533733991 0.604757628 0.554749766 1 17.93512245 -1.617923203 2.96027475 1.0288301 0.609769412 0.654736894 0.088197729 24376165.31 24484644.75 5414745.964 0.019669919 0.024103316 1.617923203 -0.419060688 TSEIEPKNS(ph)PEDLGLSLTGDSCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSEIEPKNSPEDLGLSLTGDSCK 23 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 TSEIEPKNS(1)PEDLGLSLTGDSCK 197.96 1.74E-24 258540000 430110 199320 431250 337110 254710 467440 597460 520980 304320 TRUE FALSE 409779.5527 219630.9346 451023.2391 303223.0623 299131.3434 451252.4356 506306.5039 475360.2293 351512.3913 1.16576133 0.624817048 1.283093428 0.862624106 0.85098378 1.283745457 1.440366019 1.352328512 1 18.42321602 2.18983682 7.151656515 1.322118451 0.941707092 0.336645939 0.21119255 0.192849699 22.62660021 0.073428316 0.054481401 154.8234782 -2.18983682 -0.380411359 TSES(ph)PSKPGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;TSES(0.996)PS(0.004)KPGEK;TS(0.001)ES(0.998)PSKPGEK;T(0.008)S(0.1)ES(0.836)PS(0.056)KPGEK;T(0.005)S(0.05)ES(0.935)PS(0.01)KPGEK 176.4 5.27E-06 5374200000 6684120 5934560 5733800 7237660 3010812 7463540 7103140 7707920 3258477 TRUE FALSE 6368174.894 6539298.411 5996700.402 6510116.666 3535896.66 7205075.738 6019425.535 7032973.663 3763784.971 1.691960339 1.737426144 1.593263283 1.729672847 0.939452356 1.914316517 1.599301124 1.868590718 1 21.84375278 TSEVNCYR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 142.36 0.0014394 529865000 504669 554632 403826 538138 399866 484319 497131 518924 377551 FALSE TRUE 480814.2965 611149.6314 422341.8215 484043.3458 469602.5038 467546.9116 421284.5355 473484.2636 436099.6808 1.102533016 1.401398942 0.968452489 1.1099374 1.076823773 1.07211019 0.966028076 1.085724857 1 18.73429841 3.725201334 24.9994393 1.040277959 1.251965988 0.513784365 0.08577843 512.6346679 959301.5465 0.021610983 0.033686795 5311.306135 -3.725201334 0.211688028 TSFDDRLEDDDFDLIEENLGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TSFDDRLEDDDFDLIEENLGVK 22 1 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;;; 177.47 5.81E-17 87394000 141892 125367 116089 141267 85708.9 134911 146711 150427 100799 FALSE TRUE 135185.0464 138142.0398 121411.7955 127066.5728 100656.505 130238.9982 124327.5424 137254.8144 116430.3941 1.161080381 1.186477473 1.042784373 1.091352252 0.864520865 1.118599651 1.067827206 1.178857252 1 16.8291082 3.738033248 24.98045592 1.053660206 1.173778931 0.275554357 0.082061444 54.39653424 2576698.374 0.020424457 0.033814901 5470.578422 -3.738033248 0.120118726 TSFLDDAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSFLDDAFR 9 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 169.09 0.00013663 51009000 139910 134780 109480 144660 114680 115610 129610 133750 115820 FALSE TRUE 133296.7316 148514.2352 114499.7663 130118.502 134680.1557 111606.3967 109835.614 122038.1409 133780.7741 0.996381823 1.110131379 0.855876093 0.972624825 1.006722802 0.8342484 0.821011949 0.912224808 1 17.02951127 3.353335494 0.896506486 0.884283688 1.052058249 0.200180668 0.081182269 0.661640127 1.133288771 0.036022572 0.070215168 2255.981295 -3.353335494 0.167774561 TSFSVGS(ph)DDELGPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;TSFSVGS(1)DDELGPIR 426.26 2.95E-153 2689532000 2397363 2090809 2156805 2422619 2062036 2228951 2685959 2368441 2293340 TRUE FALSE 2284044.402 2303864.814 2255696.643 2179092.735 2421654.426 2151761.868 2276166.624 2161047.75 2648979.454 0.862235605 0.869717887 0.851534216 0.822615944 0.914183921 0.812298436 0.859261713 0.815803893 1 21.33700522 -2.190957249 2.433037866 1.428214966 0.853097659 0.708314518 0.030030064 4518299.262 1285156.501 10607548.55 0.006421846 0.006442327 2.190957249 -0.575117307 TSFSVGS(ph)DDELGPIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSFSVGSDDELGPIRK 16 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFS(0.019)VGS(0.981)DDELGPIRK 88.574 0.0037264 88796000 61808 58124 64471 62587 46923 57697 77124 72334 54160 TRUE FALSE 58886.45833 64046.90168 67427.05912 56295.63585 55106.35634 55698.93842 65357.31732 66000.05149 62558.85619 0.941296915 1.023786328 1.077817966 0.899882755 0.880872185 0.890344578 1.044733253 1.055007325 1 15.93292651 1.625043837 11.5754705 1.037560703 0.960046914 0.266588533 0.062201767 0.145968439 58.45483525 0.032120704 0.017015656 42.17390707 -1.625043837 -0.077513789 TSGHDHPDVATMLNILALVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 181.41 2.91E-17 97153000 175646 149140 158837 185815 177237 165434 232660 169077 43629 FALSE TRUE 167343.5617 164337.5356 166119.8336 167136.5232 208147.0767 159704.9791 197163.4439 154271.7215 50394.76249 3.320653842 3.261004268 3.296370998 3.316545508 4.130331534 3.169078912 3.912379663 3.061264979 1 15.62098618 0.967038917 21.31151454 0.999999993 3.470073608 0.865547427 0.30585994 200.7451605 129795.566 0.279248814 0.069812204 9.269128809 -0.967038917 2.470073615 TSGHVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSGHVDK 7 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 66.258 0.068362 183267000 754110 807100 670900 945420 430330 684860 789970 1167040 582130 FALSE TRUE 718464.7148 889344.4076 701661.4286 850384.5854 505379.4158 661143.1265 669445.5677 1064847.791 672403.7473 1.068501949 1.32263452 1.043512074 1.264693406 0.751601129 0.983253186 0.99560059 1.583643451 1 19.35896824 TSGNVEDDLIIFPDDCEFKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSGNVEDDLIIFPDDCEFKR 20 1 Q16186 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 64.2 0.045124 33378000 21718 23940 19954 24886 18516 22587 27340 23449 21846 FALSE TRUE 20691.43318 26379.51322 20868.91064 22384.412 21745.18454 21804.80653 23168.78087 21395.68125 25233.76611 0.819989893 1.045405316 0.827023226 0.887081695 0.861749469 0.864112255 0.918165793 0.847898849 1 14.62306792 -1.158826213 4.297492358 1.000025902 0.893275346 0.231357345 0.064519521 1.53E-05 2.99E-06 0.059540361 0.014030393 0.069370334 1.158826213 -0.106750555 TSGQTSANAHSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSGQTSANAHSSR 13 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 78.401 0.023329 4734200 3580.3 1869.5 2488.3 2499.1 2433.1 1401.9 2784.4 2417 4506.5 FALSE TRUE 3411.066314 2060.004175 2602.391016 2247.88572 2857.43187 1353.351851 2359.588641 2205.354667 5205.345004 0.655300717 0.395747866 0.499945924 0.431841831 0.548941879 0.259992729 0.453301105 0.423671181 1 12.34577807 -1.068783043 4.725323647 1.0000201 0.458556839 0.735039515 0.102155471 1.333202109 123163493.2 5688.618815 0.022886245 0.08535264 1.068783043 -0.541463261 TSIDAYDNFDNISLAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 142.57 1.35E-06 60967000 23870 26030 24553 26874 28458 26251 30443 24553 29837 FALSE TRUE 22741.71241 28682.48659 25678.77934 24172.57446 33421.06619 25341.92129 25798.36123 22403.00916 34463.96957 0.659869211 0.832245587 0.745090587 0.701386833 0.969739313 0.735316378 0.748560353 0.650041462 1 15.07280126 -2.083896133 2.240015208 1.371057289 0.759272679 0.412375117 0.091696562 8612447.466 2435343.416 16308914.08 0.02052367 0.008243352 2.083896133 -0.611784611 TSIFWNDVKDPVSIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSIFWNDVKDPVSIEER 17 1 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 276.8 8.31E-36 889240000 1624140 1741880 1502420 1862990 1006360 1722690 1657430 1922890 1060658 FALSE TRUE 1547370.121 1919379.552 1571307.443 1675718.706 1181868.865 1663032.813 1404558.613 1754511.558 1225139.426 1.26301553 1.566662138 1.282553977 1.367777961 0.964681114 1.357423309 1.146447974 1.432091337 1 20.22451451 2.963168827 24.9867709 1.196832228 1.388315364 0.248719262 0.161591073 737.4545111 500299.1158 0.044529672 0.047243445 918.6896563 -2.963168827 0.191483136 TSILAAANPISGHYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSILAAANPISGHYDR 16 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 75.97 0.028012 301120000 358100 336630 373710 415370 234210 386150 437970 467300 268830 FALSE TRUE 341173.3227 370932.9797 390844.9731 373616.2184 275056.1498 372777.5287 371149.6326 426380.7347 310518.7834 1.098720402 1.194558911 1.258683835 1.203200059 0.885795528 1.200499128 1.195256624 1.373123809 1 18.24432101 2.037865286 24.99999327 1.207837272 1.135507277 0.047846949 0.132340196 477.6744776 315375.7122 0.047072601 0.034765339 109.1101835 -2.037865286 -0.072329995 TSKEPPSS(ph)PLQPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 TSKEPPS(0.154)S(0.846)PLQPQK;TSKEPPS(0.155)S(0.845)PLQPQK 158.45 3.07E-06 817560000 1399560 1093790 1269240 1506900 811750 1288510 1435520 1276870 767830 TRUE FALSE 1333405.572 1205248.445 1327435.909 1355423.549 953318.943 1243888.576 1216505.059 1165060.494 886901.1549 1.50344327 1.35894337 1.496712347 1.528269009 1.074887475 1.402510944 1.371635443 1.313630597 1 19.7584138 -3.986009538 0.152170961 1.15E-09 1.51749855 0.543706373 0.118838066 72.88600044 0.870836023 23.00306427 0.57472645 0.000103274 3.986009538 1.517498549 TSKEPVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSKEPVSR 8 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 72.607 0.041694 242130000 255980 198208 213466 223920 321610 230680 286170 228550 313800 FALSE TRUE 243880.3327 218405.6205 223253.6272 201411.1362 377698.6822 222691.4938 242509.5106 208536.9504 362462.5013 0.672842934 0.602560595 0.61593579 0.555674409 1.042035192 0.614384917 0.669060964 0.575333861 1 18.46747222 TSLAEDSCLGRHS(ph)PVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSLAEDSCLGRHSPVPR 17 1 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 TSLAEDSCLGRHS(1)PVPR 115.39 0.00019146 88833000 262470 174370 208990 230410 418310 178540 318160 216140 484720 TRUE FALSE 250063.5633 192138.5012 218572.3982 207248.749 491263.1316 172357.115 269618.8486 197213.6358 559887.902 0.446631482 0.343173161 0.390385999 0.370161149 0.877431232 0.307842185 0.481558626 0.352237716 1 19.09477848 -1.211253825 3.384031584 1.001140608 0.442630148 0.537198062 0.161518802 79322776.72 122240881.7 1002953.141 0.037618406 0.061481744 1.211253825 -0.55851046 TSLDIEEYS(ph)DTEVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK;TSLDIEEYS(0.999)DT(0.001)EVQK;TSLDIEEYS(1)DTEVQK 417.68 1.07E-133 383741000 1333210 1136870 1208200 1386190 819020 1336310 1395620 1406920 892700 TRUE FALSE 1270191.805 1252718.346 1263597.165 1246847.548 961856.8287 1290033.25 1182692.537 1283722.626 1031135.357 1.231838087 1.214892242 1.225442573 1.209198714 0.932813352 1.251080415 1.146980878 1.244960342 1 19.9758023 -5 0.144280802 0.409870543 1.241864444 0.258853385 0.094193752 187.5635087 1.636355962 32.37635054 0.498609213 1.00E-05 5 0.831993901 TSLS(ph)PTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSLSPTSK 8 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 TS(0.001)LS(0.916)PT(0.028)S(0.056)K 68.786 0.058329 148980000 367280 310020 340490 460800 315880 367810 415430 358300 318030 TRUE FALSE 349919.4023 341611.3905 356101.8033 414479.5085 370969.372 355072.6475 352048.5236 326925.3525 367348.4681 0.952554407 0.929938247 0.969384207 1.128300631 1.009856864 0.966582627 0.958350324 0.889959755 1 18.48678973 -0.086507791 6.72257532 0.99999999 0.973972117 0.014324434 0.062254385 8783055.089 57030225.47 0.061318995 0.015329748 0.819392923 0.086507791 -0.026027873 TSNRYS(ph)PESQAQSVHHQRPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.055)S(0.055)NRYS(0.889)PESQAQSVHHQRPGSR;T(0.01)S(0.01)NRY(0.002)S(0.965)PES(0.015)QAQSVHHQRPGSR;T(0.017)S(0.017)NRYS(0.965)PES(0.001)QAQSVHHQRPGSR;T(0.046)S(0.046)NRYS(0.907)PES(0.001)QAQSVHHQRPGSR;T(0.137)S(0.137)NRY(0.073)S(0.653)PES(0.001)QAQSVHHQRPGSR 166.29 5.64E-12 1171582000 268603 221061 267213 292324 268756 225553 326352 285934 94980 TRUE FALSE 255906.6685 243587.3672 279464.9804 262939.0361 315626.9613 217742.0431 276561.0085 260896.1031 109709.0133 2.33259475 2.220304056 2.547329266 2.396694932 2.876946495 1.984723374 2.520859501 2.378073553 1 16.74332253 0.907004131 20.43970299 0.999999999 2.395374575 0.787771233 0.229486227 7287.456403 1601725.022 0.201141852 0.050285463 8.072427089 -0.907004131 1.395374576 TSNTLEKDLDLLASVPS(ph)PSSSGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSNTLEKDLDLLASVPSPSSSGSR 24 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 TSNTLEKDLDLLASVPS(0.579)PS(0.105)S(0.105)S(0.105)GS(0.105)R;TSNTLEKDLDLLASVPS(0.953)PS(0.036)S(0.007)S(0.001)GS(0.001)R;TSNTLEKDLDLLAS(0.028)VPS(0.837)PS(0.034)S(0.034)S(0.034)GS(0.034)R;TSNTLEKDLDLLAS(0.001)VPS(0.963)PS(0.022)S(0.004)S(0.005)GS(0.005)R 145.29 1.30E-07 93047000 287934 112017 326188 201647 296402 270484 488780 314322 442323 TRUE FALSE 274323.9305 123431.6597 341144.0424 181377.0605 348094.415 261117.0713 414207.6339 286798.2994 510916.1918 0.536925498 0.241588859 0.667710376 0.355003547 0.681314119 0.511076132 0.810715418 0.561341183 1 18.96272713 1.16276716 0.299459601 1.059374331 0.355585985 0.538816315 0.14623622 1.147405384 0.350957714 0.307629393 0.207409161 14.5467897 -1.16276716 -0.703788346 TSPADGKPRLS(ph)LHEEEGSSGSEQK ddPTM_SK-BR-3_Trastuzumab_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 T(0.002)S(0.001)PADGKPRLS(0.617)LHEEEGS(0.366)S(0.008)GS(0.006)EQK 152.53 4.82E-08 801990000 398440 280770 351930 410370 187610 366080 453050 425070 190490 TRUE FALSE 379606.5308 309380.7822 368066.3386 369118.8279 220329.1246 353402.5578 383928.9017 387848.6174 220030.2163 1.725247274 1.406083162 1.672799058 1.677582444 1.001358487 1.606154662 1.744891716 1.762706159 1 17.74734213 TSPADGKPRLSLHEEEGS(ph)SGSEQK ddPTM_SK-BR-3_Trastuzumab_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(0.163)LHEEEGS(0.812)S(0.025)GS(0.001)EQK 174.86 1.24E-12 507580000 1324800 924290 1177300 1257900 696320 1310700 1384400 1368100 675040 TRUE FALSE 1262179.33 1018476.202 1231280.37 1131453.502 817757.9875 1265310.13 1173184.354 1248301.911 779721.7556 1.618756076 1.306204674 1.579127889 1.451099054 1.048781802 1.622771356 1.504619238 1.600958165 1 19.57259986 4.707259659 3.935203875 1.418799527 1.631143605 0.083913748 0.219586434 0.587400386 16.88429393 0.047977094 0.33158475 50963.54848 -4.707259659 0.212344078 TSPDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 168.27 0.00049359 1655840000 2436515 1784793 1998928 1956621 2302135 2114744 2894115 2344066 2481688 FALSE TRUE 2321345.765 1966665.436 2090580.826 1759937.74 2703626.615 2041509.885 2452564.603 2138807.154 2866535.5 0.809808832 0.686077474 0.729305751 0.613959862 0.943168719 0.712187198 0.85558494 0.746129659 1 21.45087672 -0.591493659 0.307597918 1.098350595 0.725721489 0.416416059 0.090276536 8.94474917 0.877490721 0.962717366 0.089533994 0.256157067 0.591493659 -0.372629106 TSPGGRTS(ph)PEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 T(0.008)S(0.008)PGGRT(0.215)S(0.768)PEAR 80.411 0.012362 22315000 38303 25299 31998 38461 31776 34781 37242 35706 35708 TRUE FALSE 36492.4931 27876.99686 33465.13995 34594.82721 37317.72434 33576.52525 31560.0489 32579.39335 41245.41427 0.884764858 0.675881122 0.811366319 0.838755722 0.904772688 0.814066869 0.765177159 0.789891287 1 15.33194611 -1.109605981 4.430821661 1.000020646 0.803892752 0.465733056 0.063398009 1.40E-05 2.80E-06 0.06146968 0.0144869 0.07769517 1.109605981 -0.196127894 TSPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSPGSPR 7 0 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 TSPGS(1)PR;TSPGS(1)PR;TS(0.002)PGS(0.998)PR;TSPGS(1)PR;T(0.003)S(0.012)PGS(0.985)PR;TS(0.001)PGS(0.999)PR 117.89 0.0053818 2126119000 3366040 3118050 2912520 3408060 2482490 2935398 3243980 3426870 3071180 TRUE FALSE 3206933.96 3435782.84 3046061.923 3065475.334 2915435.47 2833744.431 2749051.271 3126795.096 3547442.909 0.904012846 0.968523787 0.858664114 0.864136623 0.821841407 0.798813259 0.774938834 0.881422246 1 21.75834804 3.581227056 4.003372354 0.836862203 0.93588952 0.162704677 0.064184202 0.25695795 7.206736431 0.016196633 0.025577103 3812.651023 -3.581227056 0.099027317 TSPYDHMLPGAEHFAEYAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSPYDHMLPGAEHFAEYAGR 20 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 122.22 1.79E-05 68548000 72876 55572 64015 68591 69799 64944 90256 65196 47739 FALSE TRUE 69431.29591 61234.84998 66950.15107 61696.10237 81971.9235 62694.973 76485.78953 59487.09261 55142.1203 1.25913359 1.110491393 1.214138134 1.118856185 1.486557337 1.136970661 1.387066531 1.078795888 1 15.75086712 1.031989017 9.497632296 1.000018839 1.237236856 0.351953083 0.118208181 0.280809061 77.8144229 0.105027918 0.02627636 10.76437991 -1.031989017 0.237218017 TSQEELLAEVVQGQSRT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSQEELLAEVVQGQSRTPR 19 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 TSQEELLAEVVQGQS(0.004)RT(0.996)PR 112.26 0.00032349 28765000 46575 39068 47589 43113 37992 44005 45429 51850 51306 TRUE FALSE 44373.49205 43049.07362 49771.00272 38779.19933 44617.79277 42481.09582 38497.97169 47309.73913 59262.27245 0.748764606 0.726416181 0.839842967 0.654365716 0.752886971 0.716832043 0.649620241 0.798311256 1 15.85482633 0.97913706 21.3832184 1.000000002 0.726107883 0.724672278 0.052967023 114.4515326 117306.5806 0.048571294 0.012142824 9.530969077 -0.97913706 -0.27389212 TSQLGDS(ph)PFYPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSQLGDSPFYPGK 13 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 TSQLGDS(1)PFYPGK;TSQLGDS(1)PFYPGK;TSQLGDS(1)PFYPGK;TSQLGDS(1)PFYPGK 238.37 9.41E-17 550310000 1156030 1146640 1183620 1359210 808240 1268520 1438310 1370310 1001600 TRUE FALSE 1101386.753 1263483.92 1237890.148 1222579.628 949196.8001 1224590.834 1218869.393 1250318.392 1156923.013 0.951996581 1.092107172 1.069984895 1.056751067 0.820449407 1.058489477 1.053544082 1.080727394 1 20.14186143 -0.850881963 5.742635503 0.999999994 1.025034575 0.00727021 0.08147839 6.74E-09 1.17E-09 0.075385851 0.017768611 0.140967188 0.850881963 0.025034581 TSQTWHGGIATIFQSPGDEVWGVVWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSQTWHGGIATIFQSPGDEVWGVVWK 26 0 O75223;B8ZZK2;H7BZK5;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;; 293.2 2.68E-70 493353000 796665 623486.1 601919.5 862622 604493.3 690845 930198 810114 572366.9 FALSE TRUE 759008.2243 687020.0424 629518.1045 775909.5977 709916.7401 666920.8644 788279.2108 739176.1235 661126.6356 1.148052708 1.039165578 0.952189899 1.17361721 1.073798425 1.008764174 1.19232711 1.118055277 1 19.33456711 1.744860466 25 1.122399777 1.0692292 0.02941986 0.078371859 3.181694573 12667.94144 0.034018201 0.018864893 55.57256796 -1.744860466 -0.053170578 TSQVGAASAPAKES(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR 239.73 4.70E-20 88090600000 25042610 22979670 23039320 26580550 14267030 26703660 27785430 27266360 16359310 TRUE FALSE 23858895.45 25321324.5 24095695.61 23908622.61 16755195.51 25778905.56 23546252.34 24878772.97 18896228.24 1.262627396 1.340020039 1.275159005 1.265258987 0.886695234 1.364235509 1.24608213 1.31659994 1 24.17159496 -2.099290421 2.569178348 0.549939501 1.250111707 0.250191181 0.132761129 24348249 19753701.91 62806355.17 0.031283165 0.007956271 2.099290421 0.700172206 TSQVGAASAPAKES(ph)PRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK 179.17 4.86E-10 2250410000 2610340 2407940 2448280 2953120 1288911 2907670 2882570 3190820 1476734 TRUE FALSE 2486954.401 2653311.824 2560536.06 2656266.767 1513696.67 2806976.659 2442781.004 2911414.885 1705738.367 1.457992885 1.555520985 1.501130601 1.557253339 0.88741433 1.645607975 1.432095949 1.706835551 1 20.70196495 TSRPENAIIYNNNEDFQVGQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 285.46 4.67E-46 3245920000 3069540 2286184 2367496 2589253 2011719 2313556 3283120 2495960 2043335 FALSE TRUE 2924448.927 2519148.749 2476048.033 2328976.369 2362562.157 2233436.976 2782219.745 2277400.51 2360204.956 1.239065667 1.067343216 1.049081787 0.986768697 1.000998727 0.946289419 1.178804298 0.964916417 1 21.17048072 4.477029699 1.429858299 1.02771595 1.272364775 0.535567631 0.064051183 0.588625394 1.568095821 0.01786375 0.180250121 29993.67623 -4.477029699 0.244648825 TSS(ph)DDES(ph)EEDEDDLLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSDDESEEDEDDLLQR 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 TS(0.017)S(0.983)DDES(1)EEDEDDLLQR;T(0.213)S(0.316)S(0.471)DDES(1)EEDEDDLLQR 474.98 4.43E-207 178166000 271710 253440 264920 304080 192221 263610 267870 273100 167406 TRUE FALSE 258866.8068 279265.8241 277066.844 273513.3007 225744.2815 254481.1196 227001.5117 249185.9162 193366.4675 1.338736804 1.444230883 1.432858797 1.41448155 1.167442755 1.316056103 1.173944556 1.288671813 1 17.56097811 1.228349438 0.345372333 0.979604489 1.436669646 0.695103152 0.077043546 0.72988725 0.279282575 0.127500123 0.086351176 16.91801624 -1.228349438 0.457065157 TSS(ph)DPVLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSSDPVLLK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 TSS(1)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.002)S(0.998)DPVLLK;TSS(1)DPVLLK 197.79 2.88E-05 1409290000 8382290 7565010 7296480 8937400 5147350 8356770 8906250 8768180 5361990 TRUE FALSE 7986075.764 8335893.12 7631030.825 8038995.572 6045046.21 8067372.959 7547437.988 8000391.676 6193500.024 1.289428551 1.34590992 1.23210314 1.297972962 0.976030708 1.302554764 1.218606274 1.291739993 1 22.56232349 -5 0.128818117 0.219730657 1.3521187 0.353067884 0.102692896 156.6953022 1.277667524 32.09549402 0.757350322 1.00E-05 5 1.132388043 TSS(ph)DSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.118)S(0.118)S(0.763)DS(0.001)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.148)S(0.148)S(0.584)DS(0.121)ALHTSVMNPSPQDTYPGPTPPSILPSR 309.8 3.55E-104 514230000 103017 59746 96533 101772 141707 70627 145528 119095 223749 TRUE FALSE 98147.59057 65834.18533 100959.1335 91541.68521 166420.6559 68181.16928 123325.0308 108666.4104 258446.8522 0.37975928 0.254730072 0.390637892 0.354199265 0.643926032 0.263811181 0.477177531 0.420459408 1 17.97950811 -5 0.234995311 4.404652027 0.322852378 0.762581805 0.106521657 72.91557159 0.728379282 118.2340509 0.159924564 1.00E-05 5 -4.081799648 TSS(ph)EDNLYLAVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 TSS(1)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.013)S(0.987)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;TS(0.005)S(0.995)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;T(0.005)S(0.084)S(0.911)EDNLYLAVLR 356.94 3.31E-76 1445251000 2453478 2298693 2104277 2489044 1726862 2323112 2517944 2501611 1781860 TRUE FALSE 2337506.957 2532932.43 2200760.182 2238840.568 2028026.186 2242662.049 2133785.398 2282556.679 2058181.748 1.13571455 1.230665092 1.069273976 1.087775931 0.985348445 1.089632658 1.036733223 1.109016092 1 20.97293895 3.642606512 5.738476935 1.053987855 1.182710124 0.591974463 0.044703871 0.12743657 6.156132089 0.010819106 0.01693481 4391.435536 -3.642606512 0.128722269 TSS(ph)FTEQLDEGTPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TSSFTEQLDEGTPNR 15 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TSS(0.989)FT(0.011)EQLDEGTPNR;TS(0.001)S(0.5)FT(0.5)EQLDEGTPNR;TSS(0.997)FT(0.003)EQLDEGTPNR;TSS(0.996)FT(0.004)EQLDEGTPNR;TS(0.022)S(0.963)FT(0.014)EQLDEGTPNR;T(0.001)S(0.056)S(0.93)FT(0.013)EQLDEGTPNR 378.74 4.88E-98 2059630000 2304680 2138260 1982280 2708900 1805310 2252470 2237590 2154130 1688470 TRUE FALSE 2195742.344 2356151.125 2073169.499 2436596.225 2120155.492 2174466.399 1896204.549 1965502.957 1950309.304 1.125843136 1.208091004 1.062995236 1.249338359 1.087086796 1.114934126 0.972258372 1.007790381 1 20.89527151 1.967598435 1.880377546 0.988557041 1.15705229 0.618048866 0.054761741 0.194823835 1.279056317 0.029552982 0.014634918 92.81078272 -1.967598435 0.168495249 TSS(ph)IADEGTYTLDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSIADEGTYTLDSILR 17 0 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;E7ERV5 A0A087WY00 MYO5A Unconventional myosin-Va 1 T(0.166)S(0.166)S(0.667)IADEGTYTLDSILR;T(0.001)S(0.033)S(0.967)IADEGTYTLDSILR 205.52 8.19E-12 122121000 189336 175772 166551 237926 149861 182267 167696 168921 124257 TRUE FALSE 180386.4625 193683.3666 174187.5281 214009.2265 175996.711 175955.0481 142110.8953 154129.3817 143526.1409 1.256819568 1.349464044 1.213629287 1.491081869 1.226234537 1.225944256 0.990139457 1.073876722 1 17.130954 1.950323977 2.171580975 1.017785072 1.314950675 0.722160099 0.080843826 0.149450778 1.298877926 0.042088285 0.021438571 89.19160466 -1.950323977 0.297165603 TSS(ph)LTQFPPSQSEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSLTQFPPSQSEER 15 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 T(0.117)S(0.117)S(0.751)LT(0.015)QFPPSQSEER 64.675 0.066937 99363000 63389 54916 63644 71241 55267 63568 77571 74595 70254 TRUE FALSE 60392.72759 60512.00283 66562.14035 64079.71933 64905.5473 61366.62422 65736.11926 68063.06635 81148.63151 0.744223611 0.745693448 0.820249696 0.789658656 0.79983539 0.756225004 0.810070583 0.838745707 1 16.30827914 -5 0.180761637 1.913078381 0.73656635 0.895442333 0.023829432 39.99120333 0.385512231 13.0521649 0.074537198 1.00E-05 5 -1.17651203 TSS(ph)PHKEES(ph)PKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 2 T(0.272)S(0.329)S(0.4)PHKEES(1)PKK 83.106 0.0070546 135680000 500070 560390 388160 603760 137560 645890 494680 597760 115340 TRUE FALSE 476432.6821 617494.3781 405957.5199 543068.8977 161550.4204 623522.6673 419207.4806 545416.9655 133226.3381 3.57611482 4.634927198 3.047126609 4.076287807 1.212601222 4.680175678 3.146581123 4.093912459 1 17.0235198 3.722197052 23.89218663 3.190217638 4.105521037 0.109481643 1.207048799 902.9789877 1318425.742 0.284270056 0.442045137 5274.691347 -3.722197052 0.915303399 TSS(ph)RESLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSRESLNR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TS(0.01)S(0.75)RES(0.241)LNR 81.002 0.05923 99770000 213850 163980 200810 198180 157890 194010 221530 211530 163810 TRUE FALSE 203741.7343 180689.7484 210017.3371 178258.5699 185425.966 187291.3851 187731.5298 193007.3118 189212.8182 1.076786109 0.954955114 1.10995301 0.942106204 0.979986281 0.989845122 0.992171311 1.020054105 1 17.5296503 4.705035745 3.865958058 0.998179634 1.081774024 0.226976845 0.045262117 0.313797057 8.545898226 0.00983103 0.068758786 50703.24379 -4.705035745 0.08359439 TSS(ph)TCS(ph)NESLSVGGTSVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSTCSNESLSVGGTSVTPR 20 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 2 TS(0.001)S(0.999)TCS(1)NESLSVGGTSVTPR;TS(0.001)S(0.998)T(0.001)CS(1)NESLSVGGTSVTPR 313.64 3.46E-66 164408000 263120 187290 218960 238550 164518 207558 230350 207450 170283 TRUE FALSE 250682.8391 206375.0639 228999.5326 214570.5008 193209.8871 200370.2144 195205.8768 189284.5782 196689.618 1.274509767 1.049242284 1.164268531 1.090909134 0.982308518 1.018712713 0.992456434 0.962351649 1 17.58556128 7.999999985 0.285538541 0.96820303 3.279168961 0.778376259 0.045315838 22.69203498 0.321860151 0.047699546 26.33837449 99999996.63 -7.999999985 2.310965931 TSS(ph)VPEYVYNLHLVENDFVGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.117)S(0.117)S(0.765)VPEYVYNLHLVENDFVGGR;T(0.001)S(0.028)S(0.972)VPEYVYNLHLVENDFVGGR;T(0.03)S(0.03)S(0.939)VPEYVYNLHLVENDFVGGR 364.83 4.51E-113 397572000 114774 73459 87364 103331 76802 82322 100717 84628 74231 TRUE FALSE 109348.8605 80944.55562 91369.72581 92943.97156 90196.24448 79471.1685 85350.77186 77217.52368 85742.36436 1.275318931 0.944043895 1.065631051 1.083991237 1.051944918 0.926860008 0.995432917 0.900576095 1 16.38772058 7.99999955 0.854003416 0.992436754 106.3463737 0.655919468 0.062337249 415.8904302 1.128362181 0.019994927 85152.2965 99999896.48 -7.99999955 105.353937 TSS(ph)VSNPQDSVGSPCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 T(0.002)S(0.002)S(0.996)VSNPQDSVGSPCSR;TS(0.044)S(0.956)VSNPQDSVGSPCSR;TS(0.001)S(0.999)VSNPQDSVGSPCSR;T(0.134)S(0.134)S(0.731)VSNPQDSVGSPCSR 297.55 3.52E-46 271422000 347207 308782 328764 372931 325317 338179 427439 369976 349360 TRUE FALSE 330795.2132 340247.2369 343838.1546 335443.2674 382052.1818 326467.7764 362225.3301 337578.9401 403536.9645 0.819739559 0.843162503 0.852061112 0.831257845 0.946758824 0.809015791 0.897626146 0.836550229 1 18.62234131 -5 0.187208355 1.61312495 0.826454678 0.567521011 0.040096923 90.32654643 0.879880537 20.65924388 0.099206348 1.00E-05 5 -0.786670272 TSS(ph)VVTLEVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;TS(0.001)S(0.999)VVTLEVAK;TSS(1)VVTLEVAK;TSS(1)VVTLEVAK;TSS(1)VVTLEVAK;TSS(1)VVTLEVAK 285.32 1.08E-27 1821340000 6263070 5116070 4856650 6086570 3820900 5663760 6793240 6450640 4154640 TRUE FALSE 5967027.093 5637403.349 5079332.206 5474736.42 4487263.75 5467622.571 5756806.472 5885787.765 4798920.352 1.243410321 1.174723258 1.058432279 1.14082669 0.935056934 1.139344304 1.199604505 1.226481653 1 22.19427844 4.056590456 2.953826471 1.110864381 1.227462334 0.216686577 0.087983742 0.399604539 6.998664212 0.023040518 0.056356165 11391.75026 -4.056590456 0.116597953 TSSAFVGKT(ph)PEAS(ph)PEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSAFVGKTPEASPEPK 17 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 2 T(0.216)S(0.237)S(0.26)AFVGKT(0.286)PEAS(1)PEPK;TSSAFVGKT(1)PEAS(1)PEPK 144.5 1.17E-06 558490000 1369370 1241810 1164370 1479770 584160 1603590 1426560 1647870 590810 TRUE FALSE 1304642.594 1368351.851 1217757.516 1331020.708 686037.319 1548057.276 1208912.071 1503573.767 682429.7974 1.911760886 2.005117385 1.784443647 1.950414113 1.00528629 2.268449124 1.771481955 2.203265116 1 19.38032112 3.460358154 2.26014748 1.746206648 1.954715805 0.050240229 0.426274129 1.075765576 11.03110744 0.11499747 0.18142262 2886.410885 -3.460358154 0.208509157 TSSKDDKGSTS(ph)STSGSSGSSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 TSSKDDKGS(0.248)T(0.048)S(0.349)S(0.349)T(0.002)S(0.003)GSSGSSTK;T(0.001)S(0.001)S(0.001)KDDKGS(0.343)T(0.063)S(0.501)S(0.091)TSGSSGSSTK 151.31 2.59E-08 98226000 160325 112704 145648 150988 70321 186913 202208 194900 81122 TRUE FALSE 152746.755 124188.6657 152326.1049 135810.3994 82584.96014 180440.1559 171357.4558 177833.5228 93701.98545 1.630133601 1.32535789 1.625644368 1.449386571 0.881357633 1.925681244 1.828749465 1.89786291 1 16.515792 2.148214951 21.17750825 1.749397789 1.410265914 0.123345908 0.334051197 9.487546855 2216.856489 0.113047019 0.083490807 140.6743611 -2.148214951 -0.339131874 TSSNASTISGRLS(ph)PIMTEQDDLGEGDVHSMVYPPSAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAK 38 1 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 T(0.005)S(0.005)S(0.005)NAS(0.003)T(0.002)IS(0.019)GRLS(0.96)PIMTEQDDLGEGDVHSMVYPPSAAK;T(0.11)S(0.11)S(0.11)NAS(0.11)T(0.086)IS(0.066)GRLS(0.407)PIMTEQDDLGEGDVHSMVYPPSAAK 193.81 4.75E-24 218002000 145979 120680 123305 148646 96999 114171 156580 141916 90788 TRUE FALSE 139078.862 132977.4292 128958.6562 133703.8217 113915.5949 110217.2296 132690.8452 129489.0827 104866.9394 1.326241262 1.268058647 1.229736054 1.274985448 1.086287018 1.0510198 1.265325812 1.234794145 1 16.6782004 8 0.03701137 0.436806805 2.427513342 0.495967661 0.077493995 778.3669648 2.199065328 33.89291818 101.0084071 100000000 -8 1.990706538 TSSS(ph)ETEEKKPEKPLILQSLGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSSETEEKKPEKPLILQSLGPK 23 3 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 T(0.118)S(0.267)S(0.267)S(0.303)ET(0.044)EEKKPEKPLILQSLGPK 101.49 0.0014346 312420000 405660 340280 334650 463670 142650 452840 403560 428640 118400 TRUE FALSE 386485.2557 374954.9189 349994.0335 417061.0107 167528.1148 437158.0373 341989.5101 391106.0092 136760.8673 2.825993015 2.741682809 2.559167987 3.04956395 1.224971135 3.196514075 2.500638647 2.859780118 1 17.06129595 TSSTCS(ph)NESLSVGGTSVTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSSTCSNESLSVGGTSVTPR 20 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 TSS(0.001)T(0.003)CS(0.996)NESLSVGGTSVTPR 149.94 9.77E-08 94519000 167630 144760 153940 171360 114880 150290 170390 169240 144850 TRUE FALSE 159706.4621 159511.2086 160998.3013 154134.5672 134915.0356 145085.4196 144393.8761 154420.4484 167312.5982 0.95453937 0.953372372 0.962260481 0.921237067 0.806365074 0.867151794 0.863018551 0.922945732 1 17.35218656 2.992265564 15.32682339 0.87821568 0.953953383 0.236488807 0.049908538 2.400099051 4757.861959 0.013236338 0.015048001 982.3484489 -2.992265564 0.075737702 TSSVSNPQDSVGS(ph)PCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR 305.1 9.11E-47 213820000 356930 316450 327650 420890 313770 334270 396380 345950 326380 TRUE FALSE 340058.6263 348696.6148 342673.0766 378581.3376 368491.3887 322694.1461 335904.951 315656.784 376993.3435 0.902028198 0.924941039 0.908963202 1.00421226 0.977447997 0.855967756 0.891010297 0.837300683 1 18.52417952 -0.117280138 9.870918409 0.999999999 0.913516518 0.233350876 0.049691749 0 0 0.048414802 0.011411478 0.763343237 0.117280138 -0.086483482 TST(ph)SPPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 T(0.001)S(0.043)T(0.478)S(0.478)PPPEK 109.42 0.027412 95955000 446490 480800 381530 515010 251710 438310 432880 446500 253900 TRUE FALSE 425385.3026 529794.0666 399023.5279 463240.2163 295608.1443 423131.2148 366836.2056 407402.093 293273.5153 1.450472956 1.806484524 1.360584939 1.57955012 1.007960586 1.442786998 1.25083305 1.389154055 1 18.16188727 3.088012683 1.898865751 1.25763276 1.60501559 0.380905893 0.190693133 0.31019976 2.285328129 0.057006653 0.071293205 1224.651964 -3.088012683 0.34738283 TSTS(ph)PPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 T(0.001)S(0.005)T(0.427)S(0.566)PPPEK;TST(0.001)S(0.999)PPPEK;TST(0.001)S(0.999)PPPEK;TSTS(1)PPPEK;TS(0.002)T(0.011)S(0.987)PPPEK;TST(0.073)S(0.927)PPPEK;TST(0.002)S(0.998)PPPEK 182.28 4.88E-05 7198039000 12350150 13621140 10413390 13989330 6479790 12348590 11293590 12217670 6572570 TRUE FALSE 11766382.89 15009149.65 10890854.23 12583095.97 7609863.324 11920955.23 9570545.424 11147826.04 7591810.588 1.549878352 1.977018457 1.434552944 1.657456522 1.002377922 1.570238759 1.260640701 1.468401499 1 22.85601257 3.189466523 1.775570182 1.306577145 1.744468898 0.381544344 0.231909756 0.313159244 2.037172566 0.068180099 0.092452649 1546.915256 -3.189466523 0.437891753 TSVDTGQVSRPENPSQPAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSVDTGQVSRPENPSQPASPR 21 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 TSVDTGQVSRPENPSQPAS(1)PR 246.21 1.70E-30 238050000 249310 201350 251910 250560 211270 234690 266500 257030 212120 TRUE FALSE 237525.6104 221867.7939 263460.3227 225373.2328 248115.4211 226562.6265 225840.5304 234523.0906 245014.4862 0.969434967 0.905529291 1.075284677 0.919836358 1.012656129 0.924690739 0.921743583 0.957180509 1 17.90250752 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TSVLGGGEDGIEPVSPPEGMTEPGHSR 27 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(0.999)PPEGMT(0.001)EPGHSR 152.31 4.67E-08 362518000 231498 252330 201292 255971 196104 234411 230552 227535 148142 TRUE FALSE 220555.5483 278042.7139 210521.4373 230240.3088 230304.4755 226293.2883 195377.058 207610.8292 171115.1048 1.288930914 1.624887027 1.230291374 1.345528842 1.345903834 1.322462378 1.141787327 1.213281723 1 17.38460759 1.55115999 0.464912123 0.995972896 1.439799716 0.5593043 0.10701659 0.60185326 0.34206558 0.111839337 0.074786074 35.57623538 -1.55115999 0.44382682 TSVPENHAQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSVPENHAQSR 11 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 144.57 3.67E-05 241840000 338220 253990 294890 335480 304480 287450 384610 329330 328730 FALSE TRUE 322233.0109 279871.8698 308410.9982 301756.913 357581.2156 277495.5344 325930.6807 300492.1193 379707.7695 0.848634231 0.737071749 0.812232519 0.794708292 0.941727413 0.730813422 0.85837243 0.791377326 1 18.53452999 -5 0.310975278 2.676230354 0.803257028 0.471976303 0.061198823 244.1269957 2.206337898 268.179927 0.051413662 1.00E-05 5 -1.872973326 TSVS(ph)PAPDKTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSVSPAPDKTK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.039)S(0.039)VS(0.923)PAPDKTK 73.386 0.026465 274060000 256990 212300 210240 243870 132140 266030 255800 275380 127720 TRUE FALSE 244842.592 233933.6114 219879.712 219355.7243 155185.1742 256817.3144 216773.0119 251266.2673 147526.1653 1.659655367 1.585709294 1.490445519 1.48689369 1.051916274 1.740825527 1.469386881 1.703197984 1 17.17061133 -2.087179364 2.45051083 0.138897517 1.526513646 0.42480083 0.191414204 5855393.915 1815649.736 28158326.1 0.044581817 0.008181268 2.087179364 1.387616129 TSYAQHQQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSYAQHQQVR 10 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ; 217.45 7.24E-09 891860000 1024570 747880 364250 466890 874580 544740 1100120 822880 807360 FALSE TRUE 976140.6066 824089.8223 380951.2228 419957.3302 1027106.475 525875.5172 932276.4889 750824.2648 932561.2654 1.046730808 0.883684379 0.408499942 0.4503268 1.101382304 0.563904525 0.99969463 0.805120578 1 19.83083898 1.639899309 16.93867711 0.926583934 0.772314261 0.120305892 0.235936165 0.494491152 245.6460514 0.112629645 0.062160242 43.6414638 -1.639899309 -0.154269673 TSYAQLLEECPRDETSGLHLLPLPESAPALPTEEQVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TSYAQLLEECPRDETSGLHLLPLPESAPALPTEEQVQR 38 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 198.52 1.51E-30 226360000 147706 97355 146206 141328 160830 137870 196388 151702 173307 FALSE TRUE 140724.2301 107275.5852 152909.6897 127121.4409 188878.7011 133095.5273 166425.4037 138418.1687 200182.5644 0.702979455 0.535888755 0.763851188 0.635027537 0.943532228 0.664870728 0.831368127 0.691459664 1 17.6109568 -4.999999738 0.072665094 1.998057062 0.370583406 0.42607599 0.106742472 237.236845 1.235813955 39.0228118 4.506084374 1.00E-05 4.999999738 -1.627473656 TSYEEFTHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TSYEEFTHK 9 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 80.688 0.023403 134600000 108860 106790 111840 139520 79492 121540 109610 108010 87868 FALSE TRUE 103714.4035 117672.0224 116967.9746 125495.1845 93355.37963 117331.0393 92886.98137 98552.0718 101494.1207 1.021875975 1.159397427 1.152460594 1.236477381 0.919810714 1.156037794 0.915195686 0.971012618 1 16.63103663 2.151762486 1.28721531 0.964566763 1.122921707 0.318863239 0.092224567 0.502534791 1.58323142 0.056984444 0.030219095 141.8281656 -2.151762486 0.158354944 TT(ph)PDQELAPASEPVWERPWSVEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.196)T(0.804)PDQELAPASEPVWERPWSVEEIR 73.107 0.056146 19797000 5486.1 5508.6 4938.2 5054.4 6540.3 5857.5 5896.8 7510.2 7171.6 TRUE FALSE 5226.782925 6069.932603 5164.621355 4546.322109 7680.926249 5654.653306 4997.134858 6852.567074 8283.735101 0.630969347 0.732753103 0.623465296 0.548825144 0.927229825 0.682621213 0.603246579 0.827231556 1 13.0160657 -4.999999998 0.242197196 2.826032707 0.657394772 0.46530067 0.107233117 155.8604388 1.552220693 140.0438864 0.156909629 1.00E-05 4.999999998 -2.168637935 TT(ph)PDQELVPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.447)T(0.553)PDQELVPASEPVWERPWSVEEIRR 131.68 0.0029356 143110000 48663 38335 42026 56386 30495 45730 51707 47248 41051 TRUE FALSE 46362.79643 42241.38008 43952.93367 50717.97215 35813.31834 44146.35863 43818.14749 43110.71464 47416.97942 0.977767816 0.89084924 0.926945035 1.069616259 0.755284685 0.93102427 0.924102463 0.909183064 1 15.53311614 -1.005322054 4.075845388 1.000006237 0.923362234 0.088810832 0.077409808 9784.229842 37808436.98 586.4075413 0.016291241 0.09878203 1.005322054 -0.076644003 TT(ph)PPPGRPPAPSSEEEDGEAVAH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.461)T(0.539)PPPGRPPAPSSEEEDGEAVAH 107.87 0.0021091 388150000 90326 102140 104410 99434 77401 89570 109750 97903 74191 TRUE FALSE 86056.46899 112548.1821 109197.3018 89438.70541 90899.70989 86468.16844 93005.6218 89330.0943 85696.16136 1.004204478 1.313339831 1.274237959 1.043672248 1.060720906 1.009008654 1.085295074 1.042404851 1 16.38694296 3.218263727 24.71637318 1.045944345 1.194555364 0.442261888 0.082967318 199.8970976 243422.4495 0.024277531 0.029050559 1652.965264 -3.218263727 0.148611019 TT(ph)PTLGLEEVLSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPTLGLEEVLSSR 14 0 O43474-4;O43474-1;O43474 O43474-4 KLF4 Krueppel-like factor 4 1 T(0.103)T(0.897)PTLGLEEVLSSR 96.591 0.037006 14904000 35303 22619 30794 32918 26072 28877 29955 29592 23530 TRUE FALSE 33634.29715 24923.90182 32205.93536 29609.0201 30618.94855 27876.98225 25384.81459 27000.7676 27178.91223 1.23751447 0.917030881 1.184960424 1.089411521 1.126570051 1.025684252 0.933989351 0.993445484 1 14.7302001 2.032836189 4.634313197 0.970311129 1.097934619 0.350910197 0.084001745 0.223011529 11.39931093 0.032790239 0.022525086 107.8539832 -2.032836189 0.127623489 TT(ph)PTQPSEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTPTQPSEQK 10 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 1 T(0.122)T(0.877)PT(0.001)QPSEQK;T(0.094)T(0.905)PT(0.001)QPSEQK;T(0.147)T(0.853)PTQPSEQK 99.215 0.013899 53876000 433680 432585 395481 511990 244752 467570 430827 473510 279020 TRUE FALSE 413180.8059 476665.9033 413614.195 460523.7925 287436.6713 451377.9337 365096.4285 432046.9542 322288.9966 1.282019586 1.479001481 1.283364308 1.428915655 0.891860021 1.400537836 1.132823126 1.34055757 1 18.29799541 -4.03819723 0.058954906 3.28E-07 1.78666636 0.239875359 0.16489406 418.2328428 2.148904067 67.07409866 14.94574419 9.16E-05 4.03819723 1.786666032 TT(ph)SPSSDTDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 1 T(0.003)T(0.498)S(0.498)PSSDTDLLDR 231.74 2.13E-11 122120000 287330 235160 253230 272730 249190 261780 307150 266420 276860 TRUE FALSE 273748.4803 259123.0714 264840.846 245314.6622 292648.6571 252714.493 260288.6263 243090.8524 319794.0348 0.856014968 0.810281128 0.828160682 0.767102058 0.91511606 0.790241422 0.813925833 0.760148177 1 18.2867835 -0.921051853 5.003223259 1.000000722 0.81934444 0.624186809 0.044455485 3.19E-07 6.90E-08 0.038424382 0.009056678 0.11993561 0.921051853 -0.180656283 TTAGS(ph)VDWTDQLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 T(0.001)T(0.004)AGS(0.995)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(0.995)VDWT(0.005)DQLGLR;TTAGS(1)VDWTDQLGLR;T(0.002)T(0.013)AGS(0.984)VDWTDQLGLR;TT(0.001)AGS(0.999)VDWTDQLGLR 347.39 3.11E-82 755259000 435039 353439 377612 556353 425201 481774 529164 385705 416940 TRUE FALSE 414475.5686 389454.8359 394925.8837 500427.3394 499355.9198 465090.0456 448430.313 351930.6254 481596.9258 0.860627522 0.808673841 0.820034063 1.039099946 1.036875223 0.965724698 0.931132009 0.730757625 1 18.87746666 3.265304683 24.92487913 0.951093684 0.829662985 0.299906668 0.087017238 260.7068857 242971.1707 0.023799339 0.032215699 1842.063863 -3.265304683 -0.121430698 TTAPTEGKS(ph)PLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTAPTEGKSPLKK 13 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TT(0.003)APT(0.016)EGKS(0.98)PLKK;TTAPTEGKS(1)PLKK 127.83 8.99E-05 1143430000 2988100 3629800 2547100 3777800 1101690 3557500 2918700 3725200 1020170 TRUE FALSE 2846858.435 3999680.747 2663887.054 3398048.367 1293824.387 3434302.883 2473398.709 3399001.739 1178372.753 2.415923507 3.39424069 2.260648888 2.883678664 1.097975478 2.914445258 2.098995163 2.884487723 1 20.16836455 TTAPTEGKS(ph)PLKKEDR ddPTM_SK-BR-3_Trastuzumab_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 139.44 1.28E-06 1682530000 2470460 2044480 2213280 2682340 962620 2935410 2788910 3075100 1022910 TRUE FALSE 2353686.252 2252814.836 2314761.077 2412706.087 1130500.623 2833756.016 2363410.558 2805827.942 1181537.658 1.99205352 1.906680519 1.959109014 2.042005238 0.956804563 2.398362841 2.000283733 2.374725784 1 20.17223418 TTDEELS(ph)ELEDR ddPTM_SK-BR-3_Trastuzumab_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 213.18 1.22E-08 863420000 721100 675400 675970 785950 600660 682770 741430 794300 637390 TRUE FALSE 687015.0321 744224.0279 706963.8931 706944.8128 705414.9138 659125.5037 628311.2362 724746.8812 736233.1859 0.933148689 1.010853684 0.960244535 0.960218619 0.95814061 0.89526731 0.853413359 0.984398551 1 19.48980326 2.351911459 5.432940578 0.913110021 0.968555841 0.026980879 0.046809625 0.295193571 12.93344606 0.015710113 0.013018677 224.8596129 -2.351911459 0.05544582 TTDEELSELEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 0 151.07 0.00015972 77467000 108640 99690 100610 110230 78986 91560 130100 104340 100820 FALSE TRUE 103504.8025 109848.5243 105223.068 99149.47098 92761.13339 88389.25424 110250.8555 95203.43646 116454.6507 0.888799218 0.943272971 0.903554022 0.85139984 0.796542971 0.759001497 0.946727803 0.817515109 1 16.82940873 -1.694017767 2.933200112 1.016218027 0.871796562 0.321856338 0.061254956 69545381.92 78562618.25 8519876.635 0.01514998 0.020229364 1.694017767 -0.144421465 TTDGVYEGVAIGGDRYPGSTFMDHVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TTDGVYEGVAIGGDRYPGSTFMDHVLR 27 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 274.88 4.46E-61 1686720000 1343915 1070167 1193536 1279523 1244115 1258040 1518986 1332048 1184743 FALSE TRUE 1280390.801 1179218.234 1248260.806 1150902.917 1461088.262 1214473.759 1287236.788 1215406.815 1368466.894 0.935638858 0.861707535 0.912160033 0.841016266 1.067682579 0.887470325 0.940641526 0.888152151 1 20.3841291 TTDGYLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TTDGYLLR 8 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 158.03 0.0008548 787338000 587617 563726 366834 444793 594606 405994 652787 503003 601617 FALSE TRUE 559841.509 621170.3203 383653.7017 400081.5626 698305.0981 391934.326 553192.3539 458957.3907 694912.6917 0.805628557 0.893882538 0.55208907 0.57572925 1.004881774 0.564005134 0.796060225 0.660453315 1 19.4064722 -1.975782192 8.121793895 1.162125144 0.744998685 0.236797855 0.149726317 0.066410842 0.000198026 0.021903874 0.032035462 0.010573477 1.975782192 -0.417126459 TTEYHDRDEQFYWIIEALGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTEYHDRDEQFYWIIEALGIR 21 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 197 5.61E-22 1880500000 2096417 2310816 2191360 2295018 1822051 2252009 2653542 2105822 1255931 FALSE TRUE 1997323.523 2546290.778 2291836.024 2064318.43 2139816.118 2174021.364 2248695.432 1921425.062 1450694.365 1.376805185 1.755222078 1.579820036 1.422986454 1.475028903 1.498607437 1.550082144 1.324486472 1 20.46831217 0.933620926 2.592696333 1.000467493 1.53377432 0.728893929 0.102217844 0.174165096 2.658956048 0.097981928 0.026238384 8.58264058 -0.933620926 0.533306826 TTFDEAMADLHTLSEDSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTFDEAMADLHTLSEDSYK 19 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 279.54 1.36E-39 341858000 695490 739920 587060 824200 398570 710580 676170 763670 338165 FALSE TRUE 662615.566 815318.6892 613977.2817 741349.8501 468080.4818 685972.4364 573007.8478 696799.0063 390605.9011 1.69637879 2.0873179 1.571858694 1.897948413 1.198344624 1.756175302 1.466971815 1.783892676 1 18.57535422 -2.122559632 0.136915723 1.83E-12 2.05479366 0.454139666 0.237904042 42.00271476 0.794984863 15.44249391 1.721356219 0.007541198 2.122559632 2.05479366 TTFTVAQNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTFTVAQNER 10 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;P50225;H3BRY5;P50225-2;E9PKW4;P50226 A0A0A6YYL2;P50225;P50226 SULT1A4;SULT1A3;SULT1A1;SULT1A2 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A1;Sulfotransferase 1A2 0 102.06 0.0069722 55284000 37997 40091 39801 42120 40831 43234 50275 42663 47102 FALSE TRUE 36200.95711 44176.31848 41625.91522 37886.01758 47951.91347 41736.79574 42604.62539 38927.20155 54406.3376 0.665381254 0.811970083 0.765093132 0.696353022 0.881366319 0.767131139 0.783082032 0.715490203 1 15.7314871 -5 0.310975535 3.099003859 0.751915725 0.597753492 0.061238885 201.4338603 1.820492221 277.2944646 0.053160754 1.00E-05 5 -2.347088134 TTFVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTFVKR 6 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 124.32 0.029511 2569300000 6003600 4184800 4225900 4250300 5227900 4529000 7147300 5554500 5818700 FALSE TRUE 5719821.726 4611235.878 4419661.695 3823051.769 6139644.105 4372159.594 6056848.116 5068118.534 6721034.278 0.851032964 0.686090219 0.657586543 0.568818966 0.913496919 0.650518866 0.901177983 0.754068247 1 22.68025183 0.822837662 0.625546859 0.998264883 0.720451606 0.362302639 0.11027858 1.092525771 0.931435612 0.109272188 0.043282151 6.650245248 -0.822837662 -0.277813277 TTGFGMIYDSLDYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTGFGMIYDSLDYAK 15 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 185.59 2.58E-11 0 159620 147910 158470 174830 114300 177430 187040 174700 128340 FALSE TRUE 152075.0789 162982.1972 165736.0062 157255.7562 134233.8838 171285.5546 158503.6128 159402.3419 148242.3117 1.025854745 1.099431028 1.118007432 1.060802104 0.905503174 1.155443089 1.069219786 1.075282354 1 17.17759776 -1.729605401 2.306176947 0.98435536 1.065810017 0.083259171 0.066089308 6546111.01 4257285.306 585615.2928 0.015122228 0.018637798 1.729605401 0.081454657 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 345.29 3.78E-120 22238492000 10250493 10531763 10575385 11024641 8657050 10392396 10729755 11708300 5032267 FALSE TRUE 9765972.51 11604961.62 11060276.86 9916423.141 10166836.78 10032504.72 9092733.809 10683059.18 5812645.265 1.680125324 1.996502641 1.902795777 1.706008657 1.749089496 1.725979182 1.564302206 1.837899733 1 22.47076344 -2.264011424 0.260013591 7.71E-21 1.86893404 0.804622512 0.119506943 15.3490328 0.532117792 9.13366299 0.163189421 0.005444883 2.264011424 1.86893404 TTGT(ph)PPDSSLVTYELHSRPEQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.139)T(0.139)GT(0.723)PPDSSLVTYELHSRPEQDK 226.03 1.56E-32 69997000 122140 130790 94566 148220 68433 123120 104970 119180 62531 TRUE FALSE 116366.6843 144117.6497 98901.94464 133320.644 80367.69353 118856.3235 88954.89859 108743.9674 72227.98812 1.61110239 1.995315853 1.369302222 1.845830785 1.112694616 1.645571566 1.231584887 1.505565505 1 16.14027036 2.081150559 0.218654601 0.902295095 2.000466046 0.408328445 0.241059449 2.430009171 0.431701598 0.679484195 1.009603281 120.5453769 -2.081150559 1.098170951 TTGT(ph)PPDSSLVTYELHSRPEQDKFSQAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.006)T(0.006)GT(0.988)PPDS(0.001)SLVTYELHSRPEQDKFSQAAK;T(0.01)T(0.01)GT(0.98)PPDSSLVTYELHSRPEQDKFSQAAK 255.56 6.15E-58 591400000 834040 638150 739330 774650 487460 817230 963440 924990 494710 TRUE FALSE 794616.5821 703178.2105 773229.0118 696780.7103 572472.8697 788929.1202 816449.5332 843992.9719 571427.1002 1.390582599 1.230565037 1.353154255 1.219369382 1.001830101 1.380629515 1.428790362 1.476991504 1 19.12420993 TTHFVEGGDAGNREDQINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TTHFVEGGDAGNREDQINR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;;; 177.64 2.39E-14 18267400000 2749860 2394400 2596990 2935890 2458700 2759170 2853330 2489890 2112860 FALSE TRUE 2619879.567 2638392.082 2716064.56 2640768.759 2887496.502 2663619.251 2418002.103 2271862.032 2440511.538 1.073496079 1.081081585 1.112907896 1.082055429 1.183152162 1.091418422 0.990776756 0.930895837 1 21.21875214 1.6854383 3.726705482 0.964785631 1.102118485 0.759970542 0.034690018 0.090431596 2.928208971 0.019678303 0.009146583 48.46612517 -1.6854383 0.137332854 TTHLAGALS(ph)PGEAWPFESV ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTHLAGALSPGEAWPFESV 19 0 Q9Y3X0 Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV 199.68 7.16E-16 266250000 220581 201748 211286 252519 210939 216698 262710 226188 163330 TRUE FALSE 210154.5733 222306.3506 220973.6721 227135.3104 247726.6948 209193.6939 222628.7645 206381.7796 188658.3822 1.113942412 1.178353954 1.171289977 1.203950271 1.313096677 1.108849188 1.180062936 1.093944394 1 17.52541668 0.957376669 1.597984138 0.999678635 1.181339087 0.536862615 0.055699079 0.34729991 1.813835189 0.051602369 0.015010473 9.065184948 -0.957376669 0.181660452 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 T(0.001)T(0.001)HLAGALS(0.997)PGGGQSAPAFPESGPSLR 136.12 1.11E-05 110890000 62307 59728 65675 72929 58189 65364 79383 60219 57098 TRUE FALSE 59361.87159 65814.35111 68686.26371 65598.03836 68337.14318 63100.42829 67271.66538 54945.90512 65952.46622 0.900070535 0.997905838 1.041451027 0.994626011 1.03615751 0.956756159 1.020002272 0.83311373 1 16.00913899 -2.919108832 9.75003151 1.001019192 0.978723218 0 0.064877602 0 0 0 0.013255392 0.001204734 2.919108832 -0.022295973 TTHS(ph)PYEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TTHS(1)PYEER;T(0.001)T(0.001)HS(0.98)PY(0.018)EER;T(0.063)T(0.074)HS(0.862)PY(0.001)EER;TTHS(1)PYEER;TTHS(0.999)PYEER;TTHS(1)PYEER 151.1 5.92E-05 1609740000 941029 828644 894783 977767 841134 893950 995992 857695 680112 TRUE FALSE 896548.4241 913083.7657 935809.6856 879480.0035 987827.5033 862992.2873 844035.1278 782590.6789 785580.2954 1.141256253 1.162304822 1.191233654 1.119529103 1.257449441 1.098541158 1.074409749 0.996194384 1 19.58339922 1.638193144 1.847901422 0.999901689 1.167259772 0.750232409 0.040225477 0.146832174 1.037745192 0.028228832 0.010453923 43.47035073 -1.638193144 0.167358082 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR 227.25 2.18E-34 711338000 330123.3 322625.8 303364 342746 325958.3 298551.3 361889 315183.4 319281.2 TRUE FALSE 314519.0259 355501.7358 317273.5395 308292.5209 382805.3243 288212.3936 306676.1865 287584.2706 368793.6978 0.852831889 0.963958272 0.860300871 0.835948452 1.037993129 0.781500322 0.831565692 0.779797139 1 18.49245448 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 ;;;;; 289.66 8.01E-81 394327000 177869.8 154570.7 145197 174724.1 170633.4 155201.3 168059.1 171581 167005.8 FALSE TRUE 169462.2471 170321.6301 151854.4261 157160.5015 200391.8109 149826.6401 142418.5977 156556.458 192904.2065 0.878478754 0.882933727 0.787201217 0.814707488 1.038815143 0.776689336 0.738286636 0.811576175 1 17.55752508 TTIYKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTIYKR 6 1 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 153.67 0.016197 1998620000 3337300 2481300 2766900 2611600 2004800 2505400 2942800 2484400 2362000 FALSE TRUE 3179552.443 2734147.291 2893765.102 2349077.006 2354436.485 2418637.37 2493821.812 2266852.765 2728286.897 1.165402527 1.002148013 1.060652787 0.861008059 0.862972471 0.886504045 0.914061426 0.830870378 1 21.37956393 3.901216243 0.914099936 0.887687726 1.162540286 0.668709141 0.060289304 0.423795111 0.586543466 0.020736196 0.089922518 7965.558713 -3.901216243 0.274852559 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR 43 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 187.06 1.91E-28 247234000 269827 276999 272198 324678 311728 276195 417550 274832 81535 FALSE TRUE 257072.8125 305225.513 284678.5475 292040.7506 366093.2645 266630.2979 353845.0787 250766.2531 94179.03138 2.729618352 3.240907329 3.022738112 3.100910535 3.887205667 2.831100448 3.757153514 2.662654833 1 16.52311826 0.961221234 12.40403945 1.000000063 3.211926863 0.788517563 0.362074526 2.388790808 764.4260094 0.326811254 0.081714399 9.145790189 -0.961221234 2.2119268 TTLLHMLKDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTLLHMLKDDR 11 1 Q9Y6B6;D6RD69;D6RDB2;D6RAA2;Q9NR31;Q5SQT8;X1WI22 Q9Y6B6;Q9NR31 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ; 143.17 2.24E-05 651660000 1448090 841990 801790 796660 1107260 965590 1721780 1120920 1035030 FALSE TRUE 1379641.656 927789.7383 838552.8646 716578.2232 1300365.793 932151.3762 1459090.838 1022766.302 1195537.166 1.153993113 0.776044246 0.70140259 0.599377622 1.087683286 0.779692512 1.220447912 0.855486832 1 20.18922755 1.758604903 25 1.044827084 0.858429058 0.160878065 0.186597957 15.94599726 19906.43876 0.084986693 0.047130046 57.35944007 -1.758604903 -0.186398026 TTMRPQSFYDGSHSCAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTMRPQSFYDGSHSCAR 17 1 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ;; 190.46 1.79E-10 228634000 345537 265448 303870 356868 320124 309562 375912 340367 307732 FALSE TRUE 329204.1508 292497.453 317802.7401 320994.9506 375953.5242 298841.7903 318559.7203 310562.6611 355453.5069 0.926152491 0.822885264 0.894076817 0.903057487 1.057672852 0.840733836 0.896206435 0.873708249 1 18.43930134 TTNESLLTS(ph)FPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTNESLLTSFPK 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 TTNESLLT(0.019)S(0.981)FPK 140.1 6.23E-05 31256000 145650 121360 121490 163550 89898 149240 163260 158030 99373 TRUE FALSE 138765.4132 133726.722 127060.4367 147109.6433 105576.1827 144071.7814 138351.6885 144192.0554 114783.2573 1.208934268 1.165036828 1.10695967 1.281629801 0.919787304 1.25516373 1.205329869 1.256211566 1 16.8085527 TTPATGEQS(ph)PGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;TTPATGEQS(1)PGAR 146.48 4.09E-05 286439000 374508 345861 370831 408481 323247 379481 458839 413064 401248 TRUE FALSE 356805.749 381104.6291 387833.9682 367419.7138 379621.1745 366339.4778 388834.6834 376893.9264 463471.4905 0.769854794 0.822282787 0.836802211 0.792755803 0.819082041 0.790425054 0.838961385 0.813197649 1 18.82212107 -5 0.300262532 2.583876752 0.800480744 0.894687184 0.020535397 76.89771444 0.710548455 76.64027212 0.019269844 1.00E-05 5 -1.783396008 TTPDVIFVFGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTPDVIFVFGFR 12 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 172.59 8.22E-05 220290000 323520 289300 320570 348440 313620 295930 396280 328120 279920 FALSE TRUE 308227.8508 318779.9989 335268.4516 313414.1492 368315.2287 285681.8699 335820.2078 299388.0733 323328.564 0.953296074 0.985932065 1.036928032 0.969336409 1.139136067 0.883565208 1.03863452 0.925956153 1 18.30264144 4.24960311 2.734124026 1.000874432 0.957564976 0.039925992 0.068566681 0.843532569 12.44145644 0.015529315 0.050422922 17766.55031 -4.24960311 -0.043309456 TTPPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 TTPPESAPQNGPSPMAALMS(0.001)VADT(0.007)LGT(0.019)AHS(0.973)PK;TTPPESAPQNGPSPMAALMSVADT(0.007)LGT(0.434)AHS(0.559)PK 225.69 2.44E-36 186236000 232690 220380 200906 252430 132493 235629 239580 256760 112325 TRUE FALSE 221691.2048 242836.9726 210117.7388 227055.2568 155599.7373 227469.1086 203027.6708 234276.7332 129743.7873 1.70868455 1.871665515 1.619482082 1.75002797 1.199284686 1.753217733 1.564835396 1.805687487 1 16.98530593 -2.61062298 0.269377533 2.33E-17 1.733572126 0.531272852 0.190156947 36.865608 1.129892896 22.23775982 0.230864798 0.00245119 2.61062298 1.733572126 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTRPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(0.93)PQRPS(0.016)RPGALPEQT(0.054)RPLR;T(0.004)T(0.004)PPPGAQCEVPAS(0.921)PQRPS(0.039)RPGALPEQT(0.031)RPLR 187.87 6.27E-20 1634620000 30744.2 22075 21857.1 24072.8 22832.4 22450.7 22983.3 26971.7 23256.7 TRUE FALSE 29290.9826 24324.4676 22859.26965 21652.95641 26814.36333 21673.22663 19476.77547 24609.91496 26863.23026 1.09037455 0.905493024 0.850950144 0.806044403 0.998180899 0.806798975 0.725034751 0.916118975 1 14.71334518 4.438354504 1.437796909 0.8505289 1.122341176 0.359670905 0.087130868 0.638860806 1.802240888 0.023756883 0.213784274 27438.12965 -4.438354504 0.271812276 TTPQQGASGPGRS(ph)PVGQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTPQQGASGPGRSPVGQAR 19 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 TTPQQGAS(0.001)GPGRS(0.999)PVGQAR 69.148 0.014129 111200000 7213.8 6729.9 8437.5 6554.4 5787.2 7286.3 8374.8 6650.1 8629.9 TRUE FALSE 6872.81797 7415.684461 8824.367721 5895.539259 6796.485848 7033.973604 7097.070446 6067.78199 9968.180817 0.689475652 0.743935588 0.885253577 0.591435826 0.681818074 0.705642658 0.711972483 0.608715081 1 13.28311452 -1.868003939 4.53821491 1.073690653 0.707289099 0.578992541 0.079682617 0.04357211 0.001267315 0.056584229 0.016958807 0.013551771 1.868003939 -0.366401554 TTPSYVAFTDTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 239.55 1.90E-16 4129550000 1248961 1032267 1131365 1260451 1095150 1136449 1377093 1168199 1253589 FALSE TRUE 1189925.089 1137456.181 1183239.204 1133748.071 1286143.813 1097093.486 1166992.171 1065905.303 1447989.18 0.821777611 0.785541907 0.817160253 0.782981038 0.888227503 0.757666909 0.805939842 0.736127947 1 20.46561939 -1.486228564 3.342954217 1.003817925 0.800726909 0.704833795 0.040783174 2470823.792 1649310.377 65179.59521 0.008438265 0.0326416 1.486228564 -0.203091016 TTQETIDKTANQASDTFSGIGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTQETIDKTANQASDTFSGIGKK 23 2 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 225.88 6.11E-33 526040000 858340 474320 913150 688930 580510 877660 1183160 1145250 808350 FALSE TRUE 817767.9693 522653.7473 955018.8307 619677.4475 681750.7602 847266.4141 1002647.212 1044965.839 933704.7895 0.875831396 0.559763378 1.022827388 0.663675987 0.730156649 0.907424299 1.073837494 1.119160842 1 19.83260696 1.961578455 2.803821313 1.071234258 0.758344803 0.531295557 0.125414442 0.192442275 2.809774325 0.060418394 0.033412289 91.53315993 -1.961578455 -0.312889455 TTQLIEMLHADMNVPFPEGFVIANDVDNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTQLIEMLHADMNVPFPEGFVIANDVDNKR 30 1 Q08J23;Q08J23-2 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 113.68 0.00010306 104830000 123170 108230 119410 127330 83231 129460 140000 133410 76044 FALSE TRUE 117347.9982 119258.76 124885.0666 114530.5465 97746.46005 124976.7677 118640.4287 121727.9131 87836.51514 1.335981943 1.35773556 1.421789861 1.303905856 1.11282261 1.422833858 1.350695989 1.385846341 1 16.4225332 -1.183437913 4.867208484 0.999964142 1.338042103 0.593409666 0.087514998 3.26E-05 5.46E-06 0.08103878 0.019099001 0.065548399 1.183437913 0.338077961 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 TTQSMQDFPVVDS(1)EEEAEEEFQK 184.75 2.09E-17 81968000 234710 250470 219770 273940 155890 246310 246660 273310 158130 TRUE FALSE 223615.7235 275993.1778 229846.6719 246403.0307 183077.1666 237780.2229 209027.4868 249377.5275 182651.9928 1.224272016 1.511032941 1.258385788 1.349030071 1.002327781 1.301821126 1.144402991 1.36531512 1 17.47873797 2.883058105 24.38027551 1.18033015 1.348258777 0.281012201 0.135162609 19.28918464 3975.288593 0.037253706 0.039513526 763.9379848 -2.883058105 0.167928627 TTQVPQFILDDFIQNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTQVPQFILDDFIQNDR 17 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 290.34 1.33E-45 131608000 101127 91105 97995 103224 82516 102222 108368 99581 96832 FALSE TRUE 96346.92712 100388.7031 102488.1677 92847.72741 96906.76427 98682.02651 91834.47129 90861.15973 111848.212 0.861407844 0.897544103 0.916314761 0.83012259 0.866413173 0.882285239 0.821063383 0.812361307 1 16.77118267 3.238982323 24.99999976 0.858147119 0.888660576 0.013510637 0.054381901 30.96303314 1835441.268 0.013800183 0.017596939 1733.73343 -3.238982323 0.030513457 TTS(ph)FFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TTSFFSR 7 0 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 T(0.102)T(0.048)S(0.85)FFSR;TT(0.017)S(0.983)FFSR;T(0.002)T(0.02)S(0.978)FFSR;T(0.019)T(0.02)S(0.962)FFSR 151.44 0.0019731 447467000 1904270 1614140 1584300 2184280 1705630 1907140 2103980 1820590 1696370 TRUE FALSE 1814258.931 1778622.701 1656941.722 1964712.025 2003091.332 1841095.264 1782979.209 1661169.488 1959434.396 0.925909505 0.907722507 0.845622454 1.002693445 1.022280377 0.939605463 0.909945856 0.8477801 1 20.90200584 4.426693923 0.006170075 1.8366205 9.39E-08 0.059177226 0.059156503 57331.54696 60.84191189 8691.36464 9428.692092 26711.23223 -4.426693923 -1.836620406 TTS(ph)GDDACNLTSFRPATLTVTNFFK ddPTM_SK-BR-3_Trastuzumab_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(0.229)T(0.229)S(0.542)GDDACNLTSFRPATLTVTNFFK 79.497 0.015032 264520000 321990 347320 395060 396470 274680 390920 410070 291490 224010 TRUE FALSE 306770.1708 382712.3029 413173.8918 356616.0824 322584.105 377382.3424 347506.29 265965.5903 258748.3267 1.185592868 1.479090929 1.596817637 1.378235318 1.246709917 1.458491914 1.343028164 1.027892987 1 17.98119001 1.249384335 4.173014992 0.998244443 1.387800238 0.64590797 0.114497326 0.128268193 4.592157967 0.097700735 0.029007037 17.75760271 -1.249384335 0.389555795 TTS(ph)PEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TT(0.001)S(0.999)PEPR;T(0.344)T(0.088)S(0.567)PEPR 106.93 0.0079642 2628740000 2568580 2169220 2135800 2581760 2045010 2283020 2646430 2408660 2449720 TRUE FALSE 2447168.314 2390265.984 2233728.543 2322236.58 2401659.097 2203958.445 2242668.498 2197744.961 2829610.066 0.864842949 0.844733348 0.789412142 0.820691376 0.848759737 0.778891223 0.792571572 0.776695343 1 21.43217183 -0.985459737 4.864359159 1.000002122 0.817286334 0.7815346 0.030780121 7.79E-07 1.62E-07 0.032778197 0.007725805 0.103404696 0.985459737 -0.182715787 TTS(ph)PGGRPSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSPGGRPSAR 11 1 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 T(0.173)T(0.025)S(0.706)PGGRPS(0.096)AR 86.288 0.013302 0 150950 126890 138210 161090 130760 131320 145380 145920 126290 TRUE FALSE 143814.8927 139820.2353 144547.0652 144896.9271 153564.5026 126772.3555 123199.6109 133142.4712 145874.4082 0.985881584 0.958497361 0.990900782 0.99329916 1.052717228 0.869051378 0.844559457 0.912719872 1 17.15436728 2.22237352 24.99999144 0.887494008 0.989788347 0.44213421 0.047662541 182.4926121 281847.0167 0.016697004 0.012368737 166.8681765 -2.22237352 0.102294339 TTS(ph)PLEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TTSPLEEEER 10 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.009)T(0.001)S(0.99)PLEEEER;TT(0.001)S(0.999)PLEEEER;TT(0.006)S(0.994)PLEEEER;TTS(1)PLEEEER 346.55 7.38E-66 2027450000 2124070 1857310 1652270 2121180 1594130 1866760 1883300 1875370 1442390 TRUE FALSE 2023669.421 2046572.001 1728028.214 1907954.956 1872145.767 1802113.633 1595967.996 1711152.661 1666068.474 1.214637604 1.228384086 1.037189191 1.145183998 1.12369077 1.081656403 0.957924611 1.027060224 1 20.66801627 3.140409365 0.434654356 0.976888628 1.266839386 0.662498968 0.051681304 0.813513314 0.287338772 0.047953497 0.104198108 1381.686024 -3.140409365 0.289950758 TTS(ph)PLEEEEREIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TTSPLEEEEREIK 13 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.104)T(0.104)S(0.792)PLEEEEREIK;TT(0.004)S(0.996)PLEEEEREIK;T(0.001)T(0.001)S(0.998)PLEEEEREIK;T(0.003)T(0.163)S(0.834)PLEEEEREIK;T(0.001)T(0.11)S(0.889)PLEEEEREIK 208.39 2.80E-08 1308910000 2319840 1628140 2085530 2218120 1628470 2352870 2786490 2573800 1897020 TRUE FALSE 2210185.761 1794049.317 2181153.613 1995150.363 1912474.652 2271389.522 2361359.773 2348424.427 2191200.173 1.00866447 0.818751906 0.995415043 0.910528572 0.872797783 1.036596086 1.07765589 1.071752575 1 21.06328985 2.147277716 6.024739508 1.057587567 0.918356972 0.53388245 0.057954203 0.144346642 7.755343071 0.020607079 0.015168452 140.3711041 -2.147277716 -0.139230595 TTS(ph)PS(ph)SDTDLLDR ddPTM_SK-BR-3_Trastuzumab_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(0.999)PS(0.919)S(0.081)DTDLLDR 197.25 1.98E-07 120570000 226440 182460 204980 216600 213560 219190 234610 204650 212030 TRUE FALSE 215736.63 201052.8814 214378.5358 194826.9565 250804.7964 211599.3953 198815.9356 186729.7611 244910.5295 0.880879358 0.820923796 0.875334091 0.795502573 1.024067021 0.863986517 0.811790069 0.762440723 1 17.90189528 -2.267980503 2.432369671 1.654286801 0.854157255 0.295805201 0.070616499 4987833.555 1071589.935 18186025.34 0.017012564 0.005395348 2.267980503 -0.800129545 TTS(ph)PSS(ph)DTDLLDR ddPTM_SK-BR-3_Trastuzumab_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(0.08)T(0.117)S(0.802)PS(0.175)S(0.824)DT(0.001)DLLDR 118.58 0.00060892 108950000 120960 105160 117370 128110 109560 120530 148860 121630 126980 TRUE FALSE 115242.4605 115875.9236 122751.5306 115232.1394 128667.2293 116356.0159 126148.673 110979.4324 146671.4099 0.785718639 0.790037565 0.836915188 0.78564827 0.877248193 0.793310816 0.860076774 0.756653478 1 17.16222815 -5 0.315394016 2.716518139 0.803589038 0.697259973 0.0386062 160.1399937 1.433194487 183.1856705 0.031415111 1.00E-05 5 -1.912929101 TTS(ph)PSSDTDLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 1 TT(0.001)S(0.999)PSSDTDLLDR;TT(0.002)S(0.998)PSSDTDLLDR;TTS(0.994)PS(0.006)SDTDLLDR;TTS(1)PSSDTDLLDR;TT(0.003)S(0.994)PS(0.002)S(0.001)DTDLLDR 320.48 5.56E-51 594730000 1437380 1174330 1269820 1436590 1252460 1253470 1454260 1282840 1330350 TRUE FALSE 1369437.896 1293995.562 1328042.503 1292181.244 1470888.627 1210062.02 1232385.928 1170507.729 1536653.884 0.891181749 0.842086547 0.864243092 0.840905852 0.957202297 0.787465566 0.801993175 0.761725032 1 20.55136082 TTSQAHSLPLS(ph)PASTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTSQAHSLPLSPASTR 16 0 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 TTSQAHSLPLS(1)PASTR;TTSQAHSLPLS(0.99)PAS(0.007)T(0.002)R 122.47 6.00E-05 1266850000 662870 549690 590140 716210 641300 558260 739390 585220 587120 TRUE FALSE 631537.4488 605704.0359 617198.5027 644215.2101 753142.517 538927.3162 626582.4757 533975.0344 678167.571 0.931241003 0.893148039 0.91009734 0.949935145 1.110555192 0.794681638 0.923934589 0.787379192 1 19.37128227 -0.50932956 5.958780846 0.999999993 0.914369143 0.086904274 0.088850807 0 0 0.078968195 0.018612982 0.309506975 0.50932956 -0.08563085 TTSSANNPNLMYQDECDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TTSSANNPNLMYQDECDRR 19 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 179.58 5.69E-14 1305200000 432153 370464 365368 413897 396970 433361 481194 436317 478199 FALSE TRUE 411725.9841 408214.7028 382120.4842 372291.2872 466201.4423 418353.5999 407779.0176 398110.7704 552355.6586 0.745400138 0.739043217 0.69180152 0.674006469 0.844024018 0.757398957 0.73825444 0.720750778 1 19.07523798 -2.093843032 2.410851505 1.438162615 0.739764862 0.769082739 0.044971196 3696123.267 1288657.978 8870286.169 0.010690647 0.008056696 2.093843032 -0.698397753 TTSSYQNLVWS(ph)DHSQELHSPTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWS(0.5)DHS(0.5)QELHSPTLK 129.57 6.34E-05 72593000 84156 69574 77039 86797 71713 87085 101880 90029 34772 TRUE FALSE 80178.11266 76663.6697 80571.31435 78072.00066 84219.72449 84069.22461 86336.33485 82145.58349 40164.26417 1.996254987 1.908753248 2.006044827 1.943817527 2.096882048 2.093134939 2.149580893 2.045240593 1 15.29362483 -1.231964393 7.440134879 0.999998016 2.027730443 0.952644632 0.072166282 2.81E-06 2.90E-07 0.082603643 0.019469828 0.058618622 1.231964393 1.027732427 TTSSYQNLVWSDHSQELHS(ph)PTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWSDHS(0.001)QELHS(0.944)PT(0.055)LK;TTSSYQNLVWSDHSQELHS(0.997)PT(0.003)LK;TTSSYQNLVWSDHSQELHS(0.751)PT(0.249)LK;TTSSYQNLVWSDHS(0.119)QELHS(0.689)PT(0.191)LK 189.24 3.15E-17 912930000 479714 358737 479813 528617 395594 379275 533231 438685 69780 TRUE FALSE 457038.8699 395292.7082 501812.9006 475479.4149 464585.4684 366140.6116 451876.8175 400271.4158 80601.12601 5.670378226 4.904307517 6.225879531 5.89916591 5.764007171 4.542624027 5.606333805 4.96607722 1 16.29851237 -0.719726048 0.555849678 0.114512264 5.561281908 0.899708498 0.471049228 4.157645856 0.909036204 7.123167944 0.197624492 0.190666306 0.719726048 5.446769643 TTYLVLDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TTYLVLDEADR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 211.78 1.90E-08 241170000 312780 310400 265950 319630 284750 285630 356890 309070 341100 FALSE TRUE 297995.5093 342030.1129 278144.0706 287500.1851 334410.3098 275738.5615 302439.8758 282006.1923 393996.0459 0.75634137 0.868105445 0.705956502 0.729703225 0.84876565 0.699851088 0.767621602 0.71575894 1 18.58782163 -1.346384271 5.529055799 1.000056453 0.767960182 0.631037236 0.057121292 3.82E-05 4.51E-06 0.053138117 0.012521735 0.045041799 1.346384271 -0.232096271 TVAEGHGDTLYVGTTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAEGHGDTLYVGTTR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8;K7EKG3;K7EII6 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 129.05 5.75E-05 127630000 120160 115610 103280 128660 107500 138780 145240 126070 108030 FALSE TRUE 114480.2749 127390.7904 108015.4902 115726.8524 126247.966 133974.0138 123080.9705 115030.6425 124782.7407 0.917436773 1.020900725 0.865628448 0.927426756 1.011742211 1.073658209 0.986362135 0.921847379 1 16.92905888 2.735054092 24.75167124 1.003179027 0.942076793 0.270432704 0.052522705 394.0505522 2781493.404 0.016812602 0.016454973 543.3179985 -2.735054092 -0.061102234 TVAISDAAQLPHDYCT(ph)TPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.629)T(0.365)PGGT(0.006)LFS(0.073)T(0.152)T(0.775)PGGT(0.001)R;TVAISDAAQLPHDY(0.002)CT(0.868)T(0.127)PGGT(0.005)LFS(0.094)T(0.154)T(0.751)PGGTR 205.35 1.15E-25 2591330000 622200 658990 565630 769970 623440 663570 752090 662200 656710 TRUE FALSE 592789.8391 726141.8302 591564.695 692571.1528 732167.7386 640590.4045 637344.8574 604214.2575 758549.2328 0.781478398 0.957277127 0.779863283 0.913020702 0.965221118 0.84449417 0.840215546 0.796539277 1 19.53288329 4.738911747 5.24843708 0.879197913 0.777460926 0.162096794 0.073529581 0.281085918 24.09977643 0.016157816 0.101682646 54816.55606 -4.738911747 -0.101736987 TVAISDAAQLPHDYCT(ph)TPGGTLFSTT(ph)PGGTRIIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.044)CT(0.508)T(0.438)PGGT(0.01)LFS(0.283)T(0.183)T(0.498)PGGT(0.035)RIIYDR 122.77 2.75E-08 386650000 48592 30922 55104 45812 58104 44442 76764 49234 72471 TRUE FALSE 46295.15246 34072.98696 57630.57291 41206.89072 68237.3192 42902.9624 65052.24193 44922.80995 83709.43255 0.553045828 0.4070388 0.688459725 0.492261021 0.815168818 0.512522437 0.777119614 0.536651708 1 16.35310258 -4.999999969 0.108595397 2.32298392 0.347607031 0.511525889 0.1258833 116.6696198 0.845228502 34.35067968 1.425281773 1.00E-05 4.999999969 -1.975376889 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTRIIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.03)CT(0.456)T(0.511)PGGT(0.395)LFS(0.223)T(0.2)T(0.179)PGGT(0.005)RIIYDR 139.7 6.80E-13 162870000 25087 19427 30958 19906 28965 19805 37393 27176 85540 TRUE FALSE 23901.18723 21406.63339 32377.45492 17905.01106 34016.48683 19119.14788 31688.01108 24796.32537 98805.10632 0.241902348 0.216655132 0.327690097 0.181215442 0.344278632 0.193503642 0.320712282 0.250961983 1 16.59229798 -4.553256889 0.421849468 9.999999989 0.245954764 0.944999798 0.056130086 111.5486752 1.066892124 919.3483042 0.027269669 2.80E-05 4.553256889 -9.754045224 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.441)T(0.519)PGGT(0.576)LFS(0.09)T(0.083)T(0.29)PGGT(0.001)RIIYDRK 188.69 2.56E-23 270710000 60471 33460 70329 45728 55398 57463 85924 72454 80170 TRUE FALSE 57612.65567 36869.61204 73553.65421 41131.33456 65059.39366 55473.0419 72814.7157 66109.54366 92602.35415 0.622151091 0.398149835 0.794295727 0.444171587 0.702567384 0.599045698 0.786316032 0.713907808 1 16.49876125 0.942057868 0.37098094 1.035887494 0.518792249 0.552690553 0.116480925 1.014054974 0.37977457 0.187248356 0.097084554 8.751003705 -0.942057868 -0.517095246 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.105)T(0.894)PGGT(0.001)LFS(0.553)T(0.292)T(0.156)PGGTR 218.79 1.27E-34 416020000 173160 177190 172350 214680 169860 185090 215730 206430 179710 TRUE FALSE 164975.07 195245.8624 180252.418 193099.9585 199483.5302 178680.2869 182816.4263 188353.8948 207578.509 0.794759876 0.940588038 0.868357803 0.930250244 0.961002809 0.860784133 0.880709796 0.907386298 1 17.66329756 -4.646299545 0.013467565 2.022375212 3.60E-07 0.385389242 0.045346657 8336.18564 9.002305716 818.0615809 556.8591368 2.26E-05 4.646299545 -2.022374852 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.033)CT(0.459)T(0.503)PGGT(0.092)LFS(0.331)T(0.303)T(0.278)PGGTRIIY(0.001)DRK;TVAISDAAQLPHDYCT(0.409)T(0.554)PGGT(0.039)LFS(0.416)T(0.356)T(0.225)PGGTRIIYDRK 208.08 2.65E-30 396315000 216306 109154 264293 180796 208047 220377 334500 275654 330670 TRUE FALSE 206081.6441 120276.9167 276411.0955 162622.0426 244330.3309 212745.2892 283465.8815 251516.2744 381948.6148 0.539553322 0.314903398 0.723686603 0.425769426 0.639694245 0.556999766 0.742157114 0.658508147 1 18.54301903 0.681032368 0.257939035 1.119419433 0.394959898 0.641089388 0.111749056 1.881809368 0.331677358 0.451851957 0.204560476 4.797692048 -0.681032368 -0.724459536 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.001)CT(0.073)T(0.925)PGGT(0.009)LFS(0.031)T(0.07)T(0.816)PGGT(0.075)R;TVAISDAAQLPHDYCT(0.146)T(0.853)PGGTLFS(0.003)T(0.061)T(0.934)PGGT(0.002)R;TVAISDAAQLPHDYCT(0.467)T(0.531)PGGT(0.011)LFS(0.049)T(0.309)T(0.627)PGGT(0.005)R;TVAISDAAQLPHDYCT(0.17)T(0.829)PGGT(0.001)LFST(0.004)T(0.996)PGGTR;TVAISDAAQLPHDYCT(0.035)T(0.965)PGGTLFS(0.196)T(0.132)T(0.67)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.026)T(0.974)PGGTLFS(0.003)T(0.035)T(0.961)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.127)T(0.873)PGGT(0.004)LFS(0.024)T(0.061)T(0.91)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.184)T(0.812)PGGT(0.006)LFS(0.01)T(0.109)T(0.854)PGGT(0.026)R;TVAISDAAQLPHDYCT(0.222)T(0.778)PGGTLFS(0.026)T(0.063)T(0.911)PGGT(0.001)R 224.28 7.41E-35 5768970000 1733201 1603324 1486578 1836683 1519062 1682626 1885088 1882113 1677575 TRUE FALSE 1651276.024 1766704.538 1554739.072 1652056.135 1783985.932 1624356.24 1597483.204 1717305.208 1937724.763 0.852172638 0.911741735 0.802352894 0.85257523 0.92066013 0.838280168 0.824411823 0.886248264 1 20.88593223 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTRIIYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.073)CT(0.436)T(0.485)PGGT(0.009)LFS(0.182)T(0.165)T(0.58)PGGT(0.068)RIIY(0.001)DR;TVAISDAAQLPHDY(0.057)CT(0.441)T(0.503)PGGT(0.197)LFS(0.138)T(0.157)T(0.499)PGGT(0.009)RIIYDR 162.05 1.85E-17 617120000 79891 51607 86112 66283 86232 73171 115767 92326 177735 TRUE FALSE 76114.71076 56865.81197 90060.32038 59620.10691 101270.8335 70637.06992 98104.61794 84241.44599 205297.2361 0.370753704 0.276992584 0.438682576 0.290408717 0.493288831 0.344072192 0.477866238 0.410338919 1 17.64735468 -5 0.242189242 4.608558983 0.320383302 0.895942922 0.066235483 43.66944914 0.434907572 77.58390455 0.086945447 1.00E-05 5 -4.288175681 TVAISDAAQLPHDYCTTPGGT(ph)LFSTT(ph)PGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.002)CT(0.06)T(0.283)PGGT(0.542)LFS(0.23)T(0.234)T(0.616)PGGT(0.031)RIIY(0.002)DRK 186.91 3.24E-23 1029700000 465970 231360 518770 384450 442130 484320 718010 582380 649840 TRUE FALSE 443944.5216 254935.847 542556.1176 345804.3556 519237.332 467547.877 608464.3873 531383.7198 750613.8683 0.591441939 0.339636473 0.722816538 0.460695399 0.691750251 0.622887342 0.810622363 0.70793219 1 19.51771142 1.494381998 0.374195422 1.016901621 0.454749367 0.62975813 0.109968671 0.632053447 0.273772646 0.135629857 0.106251707 31.21634116 -1.494381998 -0.562152255 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFST(0.001)T(0.896)PGGT(0.103)R;TVAISDAAQLPHDYCTTPGGTLFS(0.005)T(0.063)T(0.926)PGGT(0.006)R;TVAISDAAQLPHDYCTTPGGTLFS(0.001)T(0.014)T(0.983)PGGT(0.002)R;TVAISDAAQLPHDYCTTPGGTLFSTT(1)PGGTR;TVAISDAAQLPHDYCTTPGGTLFST(0.005)T(0.995)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.021)T(0.051)T(0.927)PGGT(0.001)R 349.72 6.89E-120 6765740000 2479540 2268370 2337450 2649620 2275720 2313780 2783680 2530880 2302330 TRUE FALSE 2362337.058 2499519.482 2444624.395 2383275.164 2672604.847 2233653.218 2358978.49 2309262.73 2659363.578 0.888309172 0.939893854 0.919251664 0.896182524 1.004979112 0.839920211 0.88704625 0.868351642 1 21.3426496 TVALWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 167.24 0.00073 1065929000 3654098 2248172 1337187 1624589 3873049 1787876 3978289 2818396 3570158 FALSE TRUE 3481376.029 2477263.283 1398498.347 1461282.227 4548507.519 1725961.406 3371327.947 2571602.305 4123799.869 0.844215563 0.60072345 0.339128569 0.354353333 1.102989394 0.418536656 0.817529476 0.623600171 1 21.97554289 0.076544511 0.532292252 1.027394008 0.619663226 0.192043684 0.237293492 6.406085424 2.321421112 0.620794185 0.104852379 1.192736505 -0.076544511 -0.407730782 TVANLLSGKS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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;TVANLLS(0.182)GKS(0.818)PR;TVANLLS(0.004)GKS(0.996)PR;TVANLLS(0.001)GKS(0.999)PR 180.27 5.17E-05 9699914000 7986510 6944800 7288140 8097850 5359660 8191940 9063020 8470950 6810740 TRUE FALSE 7609003.5 7652483.016 7622308.428 7283838.733 6294383.007 7908251.064 7680289.845 7729188.711 7866914.775 0.967215702 0.972742585 0.968906954 0.925882502 0.800108198 1.005254447 0.97627724 0.982493002 1 22.90736652 TVAPMPPAQDHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVAPMPPAQDHKR 13 1 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;H7C366 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 56.122 0.059442 50697000 63709 48182 48318 71506 43930 60238 69192 55954 64565 FALSE TRUE 60697.60183 53091.80058 50533.42809 64318.08103 51591.37809 58151.94296 58635.4896 51054.37113 74577.41045 0.813887228 0.711901905 0.67759698 0.862433821 0.691782911 0.779752778 0.7862366 0.684582246 1 16.18645108 -1.437219601 4.518840641 1.000703523 0.75430661 0.622510786 0.060883862 0.000386763 4.82E-05 0.052835232 0.012418499 0.036540998 1.437219601 -0.246396914 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK 34 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;; 223.61 1.50E-36 359770000 81212 61428.8 79888 87541 76056.8 82588 109592 89399 82621 FALSE TRUE 77373.26971 67688.46456 83550.94382 78741.21236 89321.08184 79727.95685 92871.7276 81570.74963 95433.44271 0.81075635 0.709274051 0.875489152 0.825090347 0.935951584 0.835429956 0.97315705 0.854739673 1 16.5422073 2.872834606 0.367152047 0.979855424 0.721737259 0.516041468 0.058982843 1.190571042 0.310382463 0.058713176 0.117738406 746.1645398 -2.872834606 -0.258118165 TVART(ph)PLGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVARTPLGQR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.19)VART(0.81)PLGQR;T(0.159)VART(0.841)PLGQR;T(0.303)VART(0.697)PLGQR;T(0.037)VART(0.963)PLGQR 94.551 0.012976 3238160000 3143710 2733080 3177410 3477090 2753760 3216180 3942760 3472350 3350460 TRUE FALSE 2995113.059 3011583.959 3323097.391 3127566.307 3234014.872 3104802.88 3341219.548 3168292.626 3870032.225 0.773924579 0.77818059 0.858674346 0.808149939 0.835655799 0.802267966 0.863357035 0.818673448 1 21.88391415 -5 0.159935129 1.694792186 0.763816581 0.828521331 0.026745765 48.25475602 0.443475577 10.61511009 0.106543032 1.00E-05 5 -0.930975605 TVAS(ph)DLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 164.48 0.00034602 948930000 2890690 2654080 2510730 3078810 1679850 2878140 2973150 3100190 1828150 TRUE FALSE 2754052.812 2924533.769 2625849.454 2769322.169 1972815.308 2778469.29 2519541.362 2828720.928 2111650.165 1.304218311 1.384951834 1.243505907 1.311449318 0.934252908 1.315781059 1.193162297 1.33957839 1 21.00993941 -4.999999986 0.047999247 0.044477106 1.762474111 0.27681939 0.125885285 727.9355142 2.588809393 93.34203499 22.15560493 1.00E-05 4.999999986 1.717997005 TVATPLNQVANPNSAIFGGARPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 269.11 1.11E-44 802480000 247960 189801 233960 232370 227600 194255 258930 203320 242380 FALSE TRUE 236239.4222 209141.9377 244687.2974 209011.7261 267293.3679 187527.9006 219425.4729 185516.2229 279967.0525 0.843811513 0.747023394 0.873986047 0.746558298 0.954731514 0.66982132 0.783754627 0.662635911 1 18.09489753 TVCIYGHLDVQPAALEDGWDSEPFTLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVCIYGHLDVQPAALEDGWDSEPFTLVER 29 0 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3KRD5 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 330.25 4.06E-105 317790000 377780 323900 341060 371830 387670 340850 409290 378750 349260 FALSE TRUE 359923.0881 356905.7782 356697.9384 334452.942 455279.5253 329046.279 346845.2934 345584.6421 403421.457 0.892176363 0.884697063 0.88418187 0.829041034 1.128545637 0.815639013 0.859759161 0.856634262 1 18.62192829 TVDGPS(ph)GK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 TVDGPS(1)GK 79.974 0.027954 43171000 205560 216960 197110 249800 185540 203770 259090 251140 210020 TRUE FALSE 195843.5862 239068.4707 206147.6885 224689.6294 217898.1173 196713.3938 219561.062 229148.8502 242588.829 0.807306697 0.985488374 0.849782281 0.926215895 0.898219915 0.810892219 0.905074908 0.944597701 1 17.88815359 1.056167065 2.593602255 0.998370876 0.885912552 0.357965805 0.052734557 0.282232766 3.986162976 0.046896954 0.012698347 11.38064993 -1.056167065 -0.112458323 TVDGPSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 146.27 0.0012937 4338510000 8994000 7624140 7824290 9171500 6284490 8528850 9909700 9033600 7742990 FALSE TRUE 8568871.444 8401048.534 8183041.436 8249563.395 7380503.066 8233493.786 8397793.261 8242570.094 8943733.343 0.958086642 0.93932234 0.914946938 0.922384767 0.825215017 0.920588022 0.938958368 0.921602845 1 23.09244574 -1.0495248 4.261603418 1.000006964 0.92078555 0.346225033 0.03533383 2.43E-06 5.42E-07 0.035140404 0.008281936 0.089222667 1.0495248 -0.079221414 TVDLKPDWGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVDLKPDWGK 10 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 152.69 1.60E-05 7088700000 13648000 11279100 11148100 13437000 8048500 12921200 14275200 13607700 8389700 FALSE TRUE 13002886.09 12428453.11 11659251.41 12086287.23 9452155.852 12473735.6 12097256.06 12416137.65 9690731.827 1.341785772 1.28250924 1.203134254 1.24720067 0.975381016 1.287182003 1.248332559 1.28123839 1 23.20817419 -5 0.130256498 0.296161459 1.330015795 0.339032217 0.099808711 174.4950983 1.432867751 33.06301779 0.749691271 1.00E-05 5 1.033854337 TVDS(ph)PK ddPTM_SK-BR-3_Trastuzumab_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 86.744 0.055835 635530000 3117840 3082520 2922590 3657500 2214710 3124260 3393870 4317700 3166500 TRUE FALSE 2970465.882 3396632.293 3056593.642 3289841.151 2600954.723 3016066.093 2876072.799 3939619.298 3657544.648 0.812147538 0.928664615 0.835695511 0.89946712 0.71112043 0.824614976 0.786339765 1.077121314 1 21.80244404 1.237129488 24.99999999 1.038560733 0.833348554 0.667877544 0.061564339 23.08675723 403225.4473 0.049107965 0.01481553 17.26352539 -1.237129488 -0.205212179 TVEAEAAHGTVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TVEAEAAHGTVTR 13 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;;; 234.82 1.14E-16 2603923000 1681424 1354428 1445553 1737652 2019194 1468873 2153451 1699417 2182562 FALSE TRUE 1601946.42 1492445.753 1511833.035 1562979.92 2371340.794 1418005.56 1824902.499 1550607.038 2521022.568 0.635435176 0.592000156 0.599690401 0.619978551 0.940626563 0.562472378 0.723873924 0.615070669 1 21.2655776 -5 0.217439424 2.691776221 0.613639556 0.489470508 0.108330675 123.5011909 1.234273888 91.5415297 0.19651627 1.00E-05 5 -2.078136665 TVEDEDQDS(ph)EEEKDNDSYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVEDEDQDSEEEKDNDSYIK 20 1 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 TVEDEDQDS(1)EEEKDNDSYIK;TVEDEDQDS(1)EEEKDNDSYIK 133.95 5.96E-06 457630000 602620 611340 519670 640060 236402 669800 550830 667060 203350 TRUE FALSE 574135.3469 673636.241 543497.3835 575719.9528 277630.434 646604.6581 466790.7668 608648.6901 234884.4794 2.444330712 2.867947012 2.313892279 2.451077032 1.181987139 2.752862427 1.987320609 2.591268233 1 17.84159186 3.207117369 2.453297737 2.030190891 2.630723824 0.198609632 0.562810934 0.442415043 5.450718387 0.154911901 0.204298338 1611.080975 -3.207117369 0.600532934 TVEIVHIDIADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVEIVHIDIADR 12 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;; 142.57 6.15E-05 670450000 1143450 967870 1096640 1192770 1123410 1027220 1239580 1123980 1029800 FALSE TRUE 1089401.385 1066497.053 1146922.029 1072870.493 1319332.348 991647.1138 1050459.305 1025558.353 1189496.125 0.915851142 0.896595652 0.964208294 0.901953753 1.109152288 0.833669899 0.883112843 0.86217881 1 20.18191914 -2.117232736 9.413854554 2.038380663 0.918201627 0.097867067 0.075152066 0.042466154 0.00052884 0.001886702 0.016106485 0.007634266 2.117232736 -1.120179036 TVEMHNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 TVEMHNK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;;; 101.69 0.0088735 921248000 2506089 2021891 1831810 2464288 1845909 1911550 2283866 2024753 1671310 FALSE TRUE 2387631.14 2227923.992 1915800.3 2216573.088 2167834.945 1845352.544 1935420.296 1847454.893 1930488.219 1.236801715 1.154072825 0.992391604 1.148193015 1.122946477 0.955899407 1.002554834 0.956988432 1 20.88053432 5.088391326 0.309449254 0.963101702 1.528009139 0.62755852 0.059192942 5.41335633 0.358157123 0.062306662 1.203998774 122572.015 -5.088391326 0.564907437 TVENIKDPLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVENIKDPLFR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 93.623 0.0083099 448540000 3382400 2890100 3087100 3651000 2810700 3562200 4069100 3770600 3437500 FALSE TRUE 3222520.655 3184604.476 3228646.589 3283994.544 3300885.19 3438840.121 3448284.061 3440426.275 3970569.944 0.811601534 0.80205223 0.813144368 0.827083917 0.831337878 0.866082242 0.868460727 0.86648172 1 21.92091468 -0.508807015 0.232556044 1.095340207 0.785947163 0.974113935 0.009169137 1.575288335 0.109262803 0.126993816 0.019561035 0.309879599 0.508807015 -0.309393043 TVEVPFKGDVEHTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVEVPFKGDVEHTIR 15 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YK13;H0YK71;H0YMW6;H0YN22 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 171.46 6.50E-07 136870000 447460 380560 424770 501060 369840 454370 513910 487280 383940 FALSE TRUE 426309.4526 419339.4967 444246.1247 450692.4968 434339.9789 438635.053 435503.5909 444611.18 443479.4543 0.961283434 0.945566909 1.001728762 1.01626466 0.979391434 0.989076379 0.982015258 1.002551924 1 18.75850774 3.73833867 24.99999831 0.994130541 0.95342517 0.704516984 0.011382702 10.30331568 1160566.989 0.003032696 0.005037646 5474.427011 -3.73833867 -0.040705372 TVFAEHISDECK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVFAEHISDECK 12 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;; 197.07 1.99E-07 2922930000 3596930 2878350 3204590 3932960 3069380 3664100 4802400 4477300 3147260 FALSE TRUE 3426910.247 3171657.137 3351523.621 3537611.389 3604678.9 3537211.298 4069705.678 4085243.876 3635321.007 0.942670603 0.872455866 0.921933335 0.973122149 0.991571004 0.973012092 1.119490045 1.123764275 1 21.79365133 2.340801472 1.07480873 1.088611772 0.911464099 0.647968467 0.046809884 0.270882351 0.612352061 0.029457133 0.01822961 219.1802774 -2.340801472 -0.177147673 TVFDEAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 85.064 0.039567 41860000 79722 70188 57903 73000 59811 64109 75058 67161 55514 FALSE TRUE 75953.69905 77340.237 60557.90982 65661.90131 70242.01946 61888.88926 63606.52357 61280.0268 64122.82759 1.184503271 1.206126428 0.944404857 1.024001963 1.095429227 0.965161575 0.991948202 0.955666322 1 15.96855042 3.746467818 24.99774188 0.999110788 1.195314866 0.790936425 0.04244657 229.8609397 726677.8633 0.010785348 0.019021141 5577.862679 -3.746467818 0.196204079 TVFPGAVPVLPAS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 111.22 0.00054556 21348000 120270 161440 106960 145210 78177 128720 118760 129060 79443 TRUE FALSE 114585.0755 177890.9195 111864.2218 130613.2149 91811.04405 124262.3941 100640.9808 117758.8222 91762.6147 1.248711971 1.93859907 1.219060967 1.423381574 1.000527768 1.354172334 1.096753631 1.283298461 1 16.48561888 3.605604701 10.77251643 1.203754003 1.593506171 0.374304905 0.213292245 0.390007485 31.93749171 0.051983138 0.080546819 4032.781587 -3.605604701 0.389752167 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 232.7 4.33E-27 2251644000 1427810 1092400 1192120 1351720 1056920 1248710 1483900 1363180 1157730 TRUE FALSE 1360320.251 1203716.802 1246779.881 1215842.537 1241246.513 1205466.86 1257503.801 1243812.733 1337264.856 1.01724071 0.900133431 0.932335787 0.909200995 0.928197962 0.901442115 0.940355081 0.930116968 1 20.3508538 -1.064930052 3.640055139 1.000026257 0.932909346 0.292544053 0.033038823 11600456.61 15721858.76 3458.00333 0.007810922 0.086113244 1.064930052 -0.06711691 TVFRPPLDIYDVLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVFRPPLDIYDVLIR 15 1 Q9H6R4-4;Q9H6R4;A0A0C4DFX0 Q9H6R4-4 NOL6 Nucleolar protein 6 0 163.7 1.39E-06 30790000 89681 77321 80845 90814 81347 82084 102750 88600 95111 FALSE TRUE 85441.95686 85200.09781 84551.82322 81685.20418 95533.89104 79241.4105 87073.60037 80841.7143 109860.3281 0.777732584 0.77553107 0.769630172 0.743536867 0.869594081 0.721292316 0.792584565 0.735859028 1 16.74531098 -1.104363069 4.487506552 1.000021567 0.774597262 0.756744613 0.040400948 7.48E-06 1.49E-06 0.033576757 0.007913361 0.07863881 1.104363069 -0.225424305 TVFS(ph)PTLPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TVFSPTLPAAR 11 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 TVFS(0.997)PT(0.003)LPAAR;TVFS(0.988)PT(0.012)LPAAR;TVFS(0.995)PT(0.005)LPAAR;T(0.001)VFS(0.999)PTLPAAR;TVFS(0.995)PT(0.005)LPAAR;T(0.002)VFS(0.982)PT(0.016)LPAAR 205.02 3.27E-08 1711083000 1548381 1472976 1514589 1720170 1575135 1533054 1856910 1731060 1738260 TRUE FALSE 1475192.099 1623073.929 1584034.404 1547255.243 1849838.045 1479963.956 1573604.275 1579479.209 2007820.483 0.734723105 0.808376019 0.788932286 0.770614334 0.921316453 0.73709974 0.783737534 0.78666356 1 20.93719885 -0.953650662 3.771598212 1.000022669 0.789856107 0.618219212 0.051495869 9129542.275 16359352.77 2820.442241 0.011279937 0.111262634 0.953650662 -0.210166562 TVHTEWTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TVHTEWTQR 9 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;;;; 161.79 6.43E-05 1958490000 588406 473320 238519 404812 671849 409768 543250 479712 582382 FALSE TRUE 560593.2145 521551.8461 249455.3321 364119.5287 789019.2529 395577.6314 460367.235 437705.8742 672694.8262 0.833354432 0.775317166 0.370829866 0.541284866 1.172923029 0.588049166 0.684362681 0.65067525 1 19.35959264 3.986239107 24.83679305 0.695632509 0.811590522 0.022652131 0.227049131 2208.465949 3986033.97 0.055390296 0.101960501 9688.111013 -3.986239107 0.115958013 TVIDKCS(ph)PPLEFLDDSDSHLEIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVIDKCSPPLEFLDDSDSHLEIQK 24 1 Q93075;H7C1W4 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 T(0.04)VIDKCS(0.96)PPLEFLDDSDSHLEIQK;T(0.04)VIDKCS(0.96)PPLEFLDDSDSHLEIQK;TVIDKCS(1)PPLEFLDDSDSHLEIQK 158.77 1.37E-11 164253000 397000 346279 374420 431270 243635 438250 502110 489450 245679 TRUE FALSE 378234.5968 381565.2238 391587.5274 387917.9202 286124.8669 423073.2926 425503.8976 446591.1633 283777.6446 1.332855509 1.344592258 1.37990971 1.366978434 1.008271343 1.49086195 1.499427125 1.57373624 1 18.11440142 TVIDYNGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TVIDYNGER 9 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 220.1 1.09E-06 5331980000 6004550 4712190 4332150 4836530 5707680 4498390 5977720 5114280 5880480 FALSE TRUE 5720726.821 5192367.518 4530783.363 4350352.816 6703097.585 4342609.626 5065709.026 4666446.531 6792394.805 0.84222531 0.764438415 0.667037693 0.64047408 0.986853352 0.639334101 0.745791311 0.687010497 1 22.69548889 -2.266478138 2.18403873 1.953462636 0.750419573 0.362943012 0.105382072 6656378.97 1017592.638 31326739.45 0.023599017 0.005414045 2.266478138 -1.203043063 TVIIEQSWGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TVIIEQSWGSPK 12 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JCQ4;C9JL25;C9JL19 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 1 TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK 235.22 5.08E-16 814120000 2491820 1960540 2125780 2121230 1324553 2014370 2240480 2368550 1523800 TRUE FALSE 2374036.607 2160321.255 2223249.116 1907999.93 1555554.624 1944611.862 1898653.627 2161147.206 1760103.122 1.348805407 1.227383344 1.263135715 1.084027354 0.883786072 1.104828369 1.078717266 1.227852607 1 20.74722853 3.236145891 4.624780602 1.060937886 1.28095355 0.565212048 0.089900157 0.136399762 7.313283487 0.025352769 0.032598999 1722.447094 -3.236145891 0.220015664 TVIIHDRPDITHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVIIHDRPDITHPR 14 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 144.68 5.67E-06 271600000 260430 221680 245790 269880 250400 255340 287930 258150 116225 FALSE TRUE 248119.99 244269.444 257059.7146 242751.1497 294069.6807 246497.5118 244000.9903 235545.0175 134248.5794 1.848213151 1.819530941 1.914803983 1.808221366 2.19048635 1.836127525 1.817531265 1.754543836 1 17.0345473 0.436979529 1.172632454 0.999179084 1.89217359 0.865313365 0.109907662 0.801572591 1.345686629 0.101702658 0.030824421 2.735139802 -0.436979529 0.892994506 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR 31 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;; 264.48 5.27E-59 256135000 78807 67588 72739 82778 58618 71290 84702 87411 68599 FALSE TRUE 75081.94929 74475.29404 76074.1551 74456.99817 68840.96064 68821.20942 71779.15424 79756.82945 79236.98256 0.947561945 0.939905731 0.960083949 0.939674831 0.868798362 0.868549094 0.905879451 1.00656066 1 16.27388632 1.234066138 24.99950169 1.003280387 0.919887533 0.563137589 0.030979167 101.0657045 562119.7988 0.02980353 0.008435658 17.14218342 -1.234066138 -0.083392854 TVIRLPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVIRLPSGSGAASPTGSAVDIR 22 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 T(0.004)VIRLPS(0.734)GS(0.265)GAAS(0.764)PT(0.198)GS(0.034)AVDIR 60.197 0.032467 86263000 102010 36320 118590 75824 141530 89565 155620 94192 185900 TRUE FALSE 97188.18946 40021.04929 124027.4688 68202.02746 166212.7872 86463.34159 131877.3108 85944.04914 214728.4226 0.452609805 0.186379841 0.577601546 0.317619934 0.774060486 0.402663702 0.614158616 0.400245334 1 17.71215364 -5 0.136851982 2.862130216 0.24689554 0.521393688 0.161721513 98.38842734 0.832748262 50.03593531 0.945441382 1.00E-05 5 -2.615234675 TVIRLPSGSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TVIRLPSGSGAASPTGSAVDIR 22 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 TVIRLPSGSGAAS(0.994)PT(0.006)GSAVDIR;TVIRLPSGSGAAS(0.952)PT(0.045)GS(0.002)AVDIR;TVIRLPS(0.052)GS(0.038)GAAS(0.805)PT(0.104)GSAVDIR;TVIRLPSGSGAAS(0.996)PT(0.004)GSAVDIR;TVIRLPSGSGAAS(0.977)PT(0.023)GSAVDIR;TVIRLPSGSGAAS(0.988)PT(0.012)GSAVDIR 250.02 1.08E-31 3241462000 2127629 753278 2522158 1373234 2985795 1771640 3666991 2313363 4515757 TRUE FALSE 2027060.194 830037.8846 2637801.439 1235193.909 3506516.703 1710287.663 3107524.174 2110792.672 5216037.532 0.388620707 0.159131885 0.505709827 0.236806944 0.6722568 0.327890214 0.595763385 0.404673597 1 22.31452282 -4.999999994 0.141051643 3.131223764 0.181046239 0.629300331 0.146432774 76.11320752 0.65565441 45.30512054 0.762500854 1.00E-05 4.999999994 -2.950177526 TVKEEAEKPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;;; 110.15 0.001031 4054900000 6170060 4737500 5304710 6249850 3531130 6353380 6969890 6809090 3803570 FALSE TRUE 5878413.492 5220256.636 5547936.201 5621603.204 4146957.954 6133360.858 5906505.27 6212849.982 4393408.21 1.338007581 1.188202049 1.262786415 1.279554035 0.94390454 1.3960371 1.344401655 1.414129916 1 22.06690912 TVKPVENKDDDDSIADFLNS(ph)DEEEDRVSLQNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVKPVENKDDDDSIADFLNSDEEEDRVSLQNLK 33 3 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 1 TVKPVENKDDDDSIADFLNS(0.99)DEEEDRVS(0.01)LQNLK;TVKPVENKDDDDS(0.001)IADFLNS(0.998)DEEEDRVSLQNLK 142.91 2.98E-10 215718000 167843 151657 134912 167171 94011 194916 180485 205252 90293 TRUE FALSE 159909.394 167111.0207 141097.8486 150366.6535 110406.4886 188166.01 152948.6984 187279.0468 104295.1773 1.533238623 1.602289052 1.352870308 1.441741194 1.058596299 1.804167891 1.466498283 1.795663535 1 16.67031292 TVLELQYVLDKLGDDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVLELQYVLDKLGDDEVR 18 1 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;; 193.06 1.30E-14 749812400 1129354 953768 1016784 1190747 793671 1081511 1256585 1193193 880416 FALSE TRUE 1075971.675 1050958.044 1063404.552 1071050.849 932086.9711 1044058.003 1064869.879 1088710.695 1016946.417 1.05804166 1.033444856 1.045683956 1.053202835 0.916554654 1.026659798 1.047124865 1.070568397 1 19.95581223 -0.604979302 6.002057321 1.000000009 1.031764007 0.050740757 0.042671501 0 1.88E-19 0.04008723 0.009448651 0.248325145 0.604979302 0.031763998 TVLPTVPES(ph)PEEEVK ddPTM_SK-BR-3_Trastuzumab_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 316.46 2.51E-56 303903000 1255290 1171330 978920 1386790 715860 1273950 1186450 1294190 702550 TRUE FALSE 1195954.929 1290689.859 1023804.45 1247387.234 840705.7574 1229832.792 1005435.262 1180863.863 811497.8659 1.473762261 1.590503084 1.261623096 1.537141731 1.035992567 1.515509583 1.238986945 1.455165703 1 19.63022778 -3.536990143 0.079071691 9.68E-12 1.829745592 0.361608703 0.165828296 174.1116207 1.314004585 35.8752574 5.826111795 0.000290409 3.536990143 1.829745592 TVLSANADHMAQIEGLMDDVDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVLSANADHMAQIEGLMDDVDFK 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 190.8 1.41E-17 207501000 402903 345883 357805 412847 307449 393742 454150 404719 287968 FALSE TRUE 383858.5737 381128.8709 374210.7132 371346.8352 361068.0083 380106.6158 384861.0765 369279.6588 332624.6067 1.154029395 1.145822838 1.125024143 1.116414203 1.085512019 1.142749539 1.157043312 1.11019946 1 18.34353537 0.921615235 8.396661141 1.000000117 1.134405723 0.797201988 0.020816536 1.291848151 138.45953 0.021529072 0.005389701 8.348630396 -0.921615235 0.134405606 TVLSSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 148.28 0.0048727 4317827000 2499220 1964500 1702510 1700020 2679710 2080620 2886760 2333300 2765430 FALSE TRUE 2381086.824 2164684.783 1780571.768 1529130.76 3147050.576 2008567.608 2446331.743 2128983.882 3194278.761 0.745422364 0.677675602 0.557425291 0.478709241 0.985214758 0.628801604 0.765847919 0.666499089 1 21.60705879 2.75137099 24.97437908 0.777606252 0.636610813 0.309678073 0.138209066 1217.704851 2373966.851 0.040211773 0.042403166 564.1193405 -2.75137099 -0.140995439 TVMDGGLES(ph)DGPNMTENGLEDESRPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVMDGGLESDGPNMTENGLEDESRPQR 27 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TVMDGGLES(1)DGPNMTENGLEDESRPQR 225.53 9.96E-35 114680000 91842 90808 76095 110620 77073 90008 88055 92345 64740 TRUE FALSE 87500.81067 100061.4384 79584.03102 99500.26744 90514.5068 86891.00039 74620.59251 84258.78225 74779.54855 1.170116862 1.338085618 1.064248616 1.33058128 1.210417936 1.161962088 0.997874338 1.126762382 1 16.19035614 1.970179937 3.302613918 1.044409235 1.230555965 0.484457487 0.084767795 0.191030528 4.040289106 0.037228984 0.021632256 93.36410481 -1.970179937 0.18614673 TVNSTRET(ph)PPKSK ddPTM_SK-BR-3_Trastuzumab_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 131.82 0.006002 303890000 216180 190520 239290 213180 148440 258610 267520 241460 206460 TRUE FALSE 205961.5998 209934.2046 250261.6832 191750.7414 174327.889 249654.2709 226704.9107 220316.4823 238476.7623 0.863654797 0.880313044 1.049417481 0.804064679 0.731005769 1.04687043 0.950637322 0.923848849 1 17.86348917 2.20901318 24.99999183 0.97600698 0.873049725 0.307034488 0.085077419 293.1752988 248052.9349 0.031558536 0.023310808 161.8129144 -2.20901318 -0.102957255 TVPFCSTFAAFFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVPFCSTFAAFFTR 14 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 130.1 0.00014902 121120000 22907 24015 36218 22071 59975 24068 36945 30650 59367 FALSE TRUE 21824.23151 26462.1558 37878.63112 19852.38115 70434.62101 23234.51913 31308.36171 27966.12351 68573.33116 0.318261212 0.385895732 0.552381378 0.289505859 1.027143057 0.338827336 0.456567607 0.407827986 1 16.06535999 -5 0.255278407 4.31113223 0.416436045 0.374248271 0.212398683 196.9384769 1.942967273 342.0035412 0.272649664 1.00E-05 5 -3.894696185 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPTSPVR ddPTM_SK-BR-3_Trastuzumab_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(0.997)PPT(0.001)S(0.002)PVR;TVPLFPHPPVPSLSTSESKPPPQPS(0.907)PPT(0.04)S(0.053)PVR 175.3 4.07E-15 1006520000 1160470 932090 987560 1149940 843330 1078520 1294290 1251270 919970 TRUE FALSE 1105616.883 1027071.031 1032840.603 1034345.846 990406.485 1041170.582 1096822.289 1141702.165 1062634.249 1.040449133 0.966532964 0.971962464 0.973378985 0.932029516 0.979801454 1.032172914 1.074407461 1 20.01921369 1.686372073 4.412091062 1.041655488 0.97876632 0.426380928 0.031688691 0.161269493 7.339924603 0.017520085 0.008393311 48.57044397 -1.686372073 -0.062889168 TVPPAVTGITFLS(ph)GGQSEEEASINLNAINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVPPAVTGITFLSGGQSEEEASINLNAINK 30 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 TVPPAVT(0.004)GIT(0.13)FLS(0.725)GGQS(0.13)EEEAS(0.01)INLNAINK;TVPPAVT(0.001)GIT(0.018)FLS(0.803)GGQS(0.133)EEEAS(0.046)INLNAINK 96.338 3.50E-11 0 77247 58909 63554 77150 64914 66844 80799 82171 67906 TRUE FALSE 73595.6874 64911.89407 66468.01376 69394.73542 76234.98105 64529.17552 68471.62857 74975.67162 78436.51566 0.938283487 0.827572382 0.847411607 0.884724861 0.971932274 0.82269304 0.87295602 0.955877132 1 16.25923783 1.090450788 3.719475386 0.998315131 0.878282315 0.447633122 0.046124109 0.182446782 4.619884041 0.042239679 0.010957876 12.31546424 -1.090450788 -0.120032817 TVPS(ph)TPTLVVPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.069)VPS(0.658)T(0.273)PTLVVPHR 131.53 8.33E-05 64386000 54065 62523 51319 72109 55057 47667 48058 47630 53100 TRUE FALSE 51509.4546 68894.16478 53672.02691 64860.46632 64658.92337 46016.27984 40725.86945 43459.2647 61334.4768 0.839812407 1.123253484 0.875071081 1.057487888 1.054201923 0.750251445 0.663996362 0.708561758 1 15.90441064 2.228650581 24.91776534 0.7431103 0.992337479 0.403037923 0.122801572 152.8165581 384238.5729 0.041696822 0.031166622 169.2975142 -2.228650581 0.249227179 TVPST(ph)PTLVVPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 TVPS(0.02)T(0.979)PTLVVPHR;T(0.004)VPS(0.148)T(0.848)PTLVVPHR 160.78 0.00014341 303566000 207065 218810 187469 256338 219632 174999 180224 181282 155514 TRUE FALSE 197277.4478 241106.9878 196064.6391 230570.4172 257935.7513 168938.7407 152727.5188 165407.987 179630.3169 1.098241384 1.342239951 1.091489691 1.283582979 1.435925493 0.940480113 0.850232419 0.920824446 1 17.45467133 2.134139865 7.633945065 0.904925454 1.242753114 0.685532984 0.10815768 0.123723317 8.107394768 0.03864254 0.02850867 136.1883207 -2.134139865 0.337827659 TVPSTPTLVVPHRT(ph)DGFAEAIHSPQVAGVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVPSTPTLVVPHRTDGFAEAIHSPQVAGVPR 31 1 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.001)VPS(0.003)T(0.019)PT(0.108)LVVPHRT(0.524)DGFAEAIHS(0.345)PQVAGVPR 114.2 3.80E-05 53708000 16102 7631.2 17346 14006 22182 12914 21689 14113 13305 TRUE FALSE 15340.89037 8408.827956 18141.33126 12598.09027 26050.53378 12466.78494 18379.9447 12877.1909 15368.27145 0.998218337 0.547155091 1.18044058 0.81974673 1.69508548 0.811202807 1.195966948 0.837907565 1 13.90766729 3.722690718 24.89649645 1.090100164 0.772686696 0.167772099 0.280812185 1036.114352 1625443.353 0.067054638 0.104262761 5280.690546 -3.722690718 -0.317413468 TVQGPPTSDDIFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVQGPPTSDDIFER 14 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 187.62 2.16E-06 152474000 207341 145902 174261 160279 176819 139503 179717 171162 191255 FALSE TRUE 197540.4018 160769.5797 182251.0392 144167.4504 207656.1776 134671.9761 152297.8709 156174.1479 220913.8486 0.894196553 0.727747856 0.824986937 0.652595803 0.939987144 0.6096131 0.689399383 0.706945938 1 17.75312434 4.626810634 2.3047996 0.750028907 0.912367105 0.072181945 0.124571385 0.932582417 7.116761551 0.027991068 0.278799475 42345.82847 -4.626810634 0.162338198 TVQGSGHQEHINIHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 116.96 0.00014165 390435000 638710 480140 581500 689300 559550 613610 745510 562440 87086 FALSE TRUE 608519.4441 529066.8119 608162.3502 620010.2544 657135.3428 592360.5318 631768.7573 513189.7719 100590.8521 6.049451132 5.25959171 6.045901167 6.163684286 6.532754511 5.888811154 6.280578642 5.101753899 1 16.61813958 0.811338171 3.501202212 1.000348176 5.980126982 0.957696104 0.330083375 0.242877182 4.22897121 0.342748474 0.088430268 6.476467207 -0.811338171 4.979778806 TVQS(ph)LEIDLDSMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 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;T(0.001)VQS(0.999)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR 360.07 1.82E-76 2188853000 2299166 2014426 2019217 2303092 2179266 2043874 2499972 2250362 2356132 TRUE FALSE 2190488.98 2219698.3 2111800.097 2071580.817 2559329.3 1973094.131 2118555.356 2053308.373 2721508.917 0.804880324 0.815613091 0.775966628 0.761188326 0.940408199 0.725000061 0.778448802 0.754474241 1 21.37597533 -0.906131774 4.301017934 1.000003825 0.795436783 0.55582396 0.057728168 3159851.243 1102050.963 115.1263462 0.012447858 0.124127562 0.906131774 -0.204567042 TVQSLEIDLDSMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;;;; 351.39 1.32E-75 8333410000 8332594 7419454 7105325 8105140 7931168 7006792 8703673 8189873 8351511 FALSE TRUE 7938728.795 8175504.798 7431111.179 7290395.928 9314361.188 6764145.036 7375767.83 7472724.303 9646620.672 0.822954386 0.847499355 0.770333097 0.755746098 0.965556904 0.701193223 0.764596026 0.774646849 1 23.20159221 TVQTDHNAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVQTDHNAVQR 11 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ;; 106.26 0.0023557 198113000 167302 144949 172939 178067 160685 183849 200342 188045 187708 FALSE TRUE 159393.966 159719.4679 180868.4242 160167.3669 188708.4131 177482.263 169776.1484 171578.7829 216816.798 0.73515506 0.736656336 0.834199314 0.73872213 0.870358823 0.8185817 0.783039644 0.791353735 1 17.72611701 -5 0.162775878 1.803848501 0.727195914 0.718566768 0.04240422 68.8023928 0.637312528 17.90549171 0.166348615 1.00E-05 5 -1.076652587 TVQVVPHITDAIQEWVMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVQVVPHITDAIQEWVMR 18 0 P17812;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 P17812 CTPS1 CTP synthase 1 0 ; 224.89 4.36E-19 292540000 360370 275220 302270 367080 368090 311380 417720 350100 353270 FALSE TRUE 343336.0243 303265.2309 316129.3785 330180.421 432284.7795 300596.8325 353989.142 319443.388 408053.3073 0.84139993 0.743200032 0.774725686 0.809160017 1.059383104 0.736660694 0.867507102 0.782847197 1 18.63839811 -5 0.189028553 1.733884735 0.791706812 0.247737428 0.092641849 188.4430116 1.840434206 52.29715277 0.239164918 1.00E-05 5 -0.942177923 TVS(ph)ASS(ph)TGDLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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)ASS(0.884)T(0.116)GDLPK;TVS(1)ASS(0.851)T(0.149)GDLPK;TVS(1)AS(0.076)S(0.746)T(0.178)GDLPK;TVS(0.997)AS(0.033)S(0.773)T(0.196)GDLPK 258.02 4.51E-16 1162100000 5250900 4249880 4747800 5628700 3171550 5339800 5738800 5278000 3217630 TRUE FALSE 5002700.363 4682947.604 4965491.326 5062892.382 3724667.316 5154881.387 4863240.66 4815830.34 3716603.627 1.346040866 1.260007274 1.336029296 1.362236302 1.002169639 1.386987127 1.308517439 1.295761083 1 21.8255534 -1.169134606 3.922909416 0.999843098 1.289376671 0.413438388 0.107487051 5646834.576 3373515.791 7094.630174 0.022979646 0.067743151 1.169134606 0.289533573 TVS(ph)DNS(ph)LSNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSDNSLSNSR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 2 T(0.002)VS(0.998)DNS(1)LSNSR 104.09 0.0038692 314210000 570710 554670 501770 607260 438000 501120 528640 514850 360500 TRUE FALSE 543733.6693 611191.5036 524776.6508 546217.0711 514387.0613 483766.0887 447986.2589 469767.0046 416404.4988 1.305782408 1.467783142 1.260256919 1.311746325 1.235306205 1.161769602 1.075843945 1.128150647 1 18.66762613 2.316174135 0.673567584 1.02679206 1.38667516 0.824790657 0.055795299 0.25705812 0.229731281 0.044370036 0.031275312 207.0971562 -2.316174135 0.3598831 TVS(ph)DNS(ph)LSNSRGEGKPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSDNSLSNSRGEGKPDLK 19 2 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 2 T(0.466)VS(0.534)DNS(0.96)LS(0.038)NS(0.002)RGEGKPDLK;T(0.133)VS(0.867)DNS(0.999)LSNSRGEGKPDLK 89.511 0.0012791 529300000 547230 365379 509530 505210 360707 581450 678280 609540 391110 TRUE FALSE 521363.5224 402611.5355 532892.4545 454425.331 423614.1866 561314.2407 574795.9285 556165.4462 451761.3413 1.154068475 0.891204047 1.179588437 1.005896896 0.937694636 1.242501714 1.272344214 1.231104558 1 18.78520129 2.225390854 24.9997937 1.217140247 1.030572357 0.290965085 0.114091274 224.7598471 426652.4989 0.039081344 0.029033829 168.0315578 -2.225390854 -0.186567891 TVS(ph)DNSLSNSR ddPTM_SK-BR-3_Trastuzumab_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;TVS(1)DNSLSNSR;TVS(1)DNSLSNSR;TVS(0.997)DNS(0.003)LSNSR;TVS(0.996)DNS(0.004)LSNSR 311.32 1.33E-45 3396380000 2848660 2457420 2391970 2839300 2224170 2471970 2754670 2601310 2286240 TRUE FALSE 2714009.487 2707833.892 2501644.19 2553888.17 2612064.544 2386365.059 2334394.499 2373525.506 2640778.423 1.027730863 1.025392312 0.947313174 0.967096727 0.989126737 0.903659708 0.883979693 0.898797675 1 21.33253183 3.305434842 0.752778153 0.913414498 1.037135957 0.428195924 0.039228433 0.542852726 0.662012117 0.020727824 0.040364593 2020.388288 -3.305434842 0.123721459 TVS(ph)DNSLSNSRGEGKPDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSDNSLSNSRGEGKPDLK 19 2 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 T(0.002)VS(0.998)DNSLSNSRGEGKPDLK;T(0.039)VS(0.943)DNS(0.018)LSNSRGEGKPDLK 141.69 8.49E-08 651540000 651650 261740 673430 418150 479770 628930 997550 789020 707970 TRUE FALSE 620847.7959 288411.6036 704307.4316 376116.7676 563441.7361 607149.9964 845355.4262 719929.2259 817758.3718 0.759206897 0.352685602 0.861265939 0.459936309 0.689007604 0.742456473 1.033747199 0.88036913 1 19.6413151 2.013981118 2.247463475 0.973933043 0.598775485 0.529328704 0.147878868 0.214330557 2.033941511 0.073492427 0.040071052 103.2716505 -2.013981118 -0.375157558 TVS(ph)FEALPIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.002)VS(0.998)FEALPIMR;T(0.003)VS(0.997)FEALPIMR;T(0.001)VS(0.999)FEALPIMR;T(0.006)VS(0.994)FEALPIMR;T(0.001)VS(0.999)FEALPIMR 225.15 5.96E-12 288459000 322219 214365 238629 360997 364152 276092 354071 216630 309815 TRUE FALSE 306988.3464 236209.0372 249570.3757 324708.8957 427659.9935 266530.8648 300050.966 197660.7288 357859.5279 0.857845949 0.660060775 0.697397599 0.90736412 1.195049901 0.744791864 0.838460185 0.552341669 1 18.44903387 5.101730675 17.42835223 0.815368483 3.378717836 0.001117482 0.18240522 908.0913335 158710.1999 0.040929597 1852.103533 126395.2273 -5.101730675 2.563349353 TVS(ph)LCDITITQMLEEDSNQGHLIGDFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSLCDITITQMLEEDSNQGHLIGDFSK 28 0 P30307-4;P30307-3;P30307-2;P30307;H0Y999 P30307-4 CDC25C M-phase inducer phosphatase 3 1 T(0.05)VS(0.95)LCDITITQMLEEDSNQGHLIGDFSK;T(0.021)VS(0.979)LCDITITQMLEEDSNQGHLIGDFSK 138.7 1.19E-06 52768000 54919 55414 58002 68695 48465 65766 74534 71131 52908 TRUE FALSE 52323.08771 61060.7496 60661.44907 61789.64809 56917.28066 63488.50693 63162.46939 64902.39255 61112.70242 0.856173686 0.999149885 0.992616047 1.011077004 0.931349431 1.038875789 1.033540768 1.062011496 1 15.89918466 6.26200659 0.573659578 1.020944074 2.04E-14 0.665983295 0.034153569 10.71204185 0.673247018 0.015336295 10.67739565 1828127.956 -6.26200659 -1.020944074 TVS(ph)PGS(ph)VSPIHGQGQVVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.061)VS(0.939)PGS(0.922)VS(0.078)PIHGQGQVVENLK 206.94 2.08E-22 306200000 452420 357550 364520 435780 311490 408300 471730 440480 323280 TRUE FALSE 431035.0032 393984.7515 381233.6026 391974.5665 365813.7574 394160.4686 399758.9246 401909.2361 373412.6113 1.154312924 1.055092248 1.020944636 1.049708967 0.979650248 1.055562819 1.070555499 1.076314039 1 18.51041113 4.458160359 1.956145487 1.039993238 1.160261982 0.593465593 0.03030375 0.305924811 1.86554827 0.007910432 0.0542706 28718.40784 -4.458160359 0.120268744 TVS(ph)PGSVS(ph)PIHGQGQVVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.084)VS(0.916)PGS(0.032)VS(0.968)PIHGQGQVVENLK;TVS(1)PGS(0.215)VS(0.785)PIHGQGQVVENLK;TVS(1)PGS(0.083)VS(0.917)PIHGQGQVVENLK;T(0.088)VS(0.912)PGS(0.205)VS(0.795)PIHGQGQVVENLK 278.16 3.80E-45 1847840000 2236810 1872540 1898630 2343480 1550490 2227460 2488470 2323010 1886450 TRUE FALSE 2131080.424 2063353.955 1985684.064 2107908.938 1820894.965 2150322.502 2108808.198 2119594.929 2178991.031 0.978012481 0.946930908 0.91128602 0.967378437 0.835659688 0.986843209 0.967791132 0.972741466 1 21.05522883 TVS(ph)PGSVSPIHGQGQVVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 T(0.028)VS(0.805)PGS(0.132)VS(0.035)PIHGQGQVVENLK;T(0.044)VS(0.956)PGSVSPIHGQGQVVENLK 228.19 1.14E-25 244300000 392070 287880 325870 375950 304630 338740 440030 399370 344470 TRUE FALSE 373537.6281 317215.2993 340811.4618 338158.7917 357757.3756 327009.3489 372895.3418 364399.0456 397888.6483 0.93879941 0.797246417 0.85654985 0.849882984 0.899139438 0.821861469 0.937185173 0.915831721 1 18.60200521 1.138897372 1.007619399 0.996814715 0.859332566 0.51714691 0.042349033 0.381886683 0.830834501 0.037062073 0.012523078 13.76884061 -1.138897372 -0.137482148 TVS(ph)PPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSPPIR 7 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 T(0.01)VS(0.99)PPIR;TVS(1)PPIR;T(0.004)VS(0.996)PPIR 99.305 0.011146 816210000 382592 385166 378206 457060 327963 395559 412545 399394 388085 TRUE FALSE 364507.6344 424414.8533 395547.1192 411115.4604 385159.6434 381860.6926 349603.6833 364420.944 448267.2397 0.813148056 0.946789807 0.882391315 0.91712136 0.859218808 0.851859469 0.779900141 0.812954666 1 18.77399954 2.424276746 3.131222804 0.836411305 0.890365273 0 0.067278651 0.520363206 10.47853698 0.022899666 0.019049494 265.6297699 -2.424276746 0.053953968 TVS(ph)PPIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.151)VS(0.849)PPIRK;T(0.135)VS(0.865)PPIRK;T(0.016)VS(0.984)PPIRK;T(0.028)VS(0.972)PPIRK 85.355 0.010291 3521440000 6882920 6196190 6371120 7111320 5171180 6893410 7468930 7151590 6394140 TRUE FALSE 6557578.012 6827588.805 6663242.154 6396476.603 6073032.155 6654689.483 6329407.552 6525358.867 7385710.574 0.887873678 0.924432218 0.902180242 0.866061097 0.822267823 0.90102224 0.856980177 0.883511316 1 22.8163053 -1.671001345 7.382116055 1.000438216 0.882403426 0.641770197 0.028017965 0.000212708 9.48E-06 0.028556061 0.00670611 0.021330383 1.671001345 -0.11803479 TVS(ph)PPTVCTIPTVVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSPPTVCTIPTVVGR 16 0 A0A0C4DH56;Q9BWT3-2;Q9BWT3 A0A0C4DH56 PAPOLG Poly(A) polymerase gamma 1 T(0.286)VS(0.713)PPT(0.001)VCTIPTVVGR 120.54 0.00011379 42065000 31047 26545 27069 28507 32307 28045 34211 29562 40776 TRUE FALSE 29579.46984 29249.96568 28310.14042 25641.4222 37941.33057 27073.79462 28991.48362 26973.39456 47099.33383 0.628023104 0.621027163 0.601073054 0.544411568 0.805559813 0.574823303 0.615539144 0.572691636 1 15.52341903 -1.316439551 3.57188364 1.001369312 0.621130592 0.740561621 0.070609828 15121811.69 24985101.49 223160.4605 0.015297168 0.048257014 1.316439551 -0.38023872 TVS(ph)PSTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSPSTIR 8 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 T(0.005)VS(0.96)PS(0.035)TIR 117.01 0.0022663 323360000 541390 514530 565220 617540 542960 519950 614570 584020 560390 TRUE FALSE 515799.5676 566961.192 591135.8961 555463.706 637652.0521 501944.0011 520806.0591 532880.1127 647292.4191 0.796857112 0.875896543 0.913243966 0.858134113 0.985106628 0.775451691 0.804591625 0.823244792 1 19.30405808 -2.412961023 2.184302755 2.186122086 0.851392348 0.35644961 0.061531121 5143628.356 509095.7578 30148281.44 0.015625719 0.003864017 2.412961023 -1.334729737 TVS(ph)SPIPY(ph)TPSPSSS(ph)RPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.321)VS(0.441)S(0.089)PIPY(0.31)T(0.306)PS(0.287)PS(0.183)S(0.177)S(0.237)RPIS(0.204)PGLS(0.095)Y(0.149)AS(0.087)HT(0.082)VGFT(0.017)PPT(0.005)S(0.005)LT(0.006)R 42.83 0.088785 77540000 18007 19669 24117 23415 25938 19906 31510 28358 32068 TRUE FALSE 17155.8448 21673.29346 25222.7883 21061.27971 30461.57899 19216.65023 26702.57078 25874.82318 37040.94166 0.463158981 0.585117238 0.680943496 0.568594608 0.822375934 0.518794862 0.720893411 0.698546582 1 15.17683315 -5 0.091863366 2.211790075 0.322464991 0.671355157 0.089362318 113.3278526 0.720681207 26.83246742 1.786771307 1.00E-05 5 -1.889325084 TVS(ph)SPIPYTPS(ph)PSSS(ph)RPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.083)VS(0.395)S(0.523)PIPY(0.049)T(0.174)PS(0.761)PS(0.064)S(0.166)S(0.539)RPIS(0.185)PGLS(0.034)Y(0.011)AS(0.01)HT(0.006)VGFTPPTSLTR 103.37 7.55E-05 166740000 41406 43885 39426 39730 46893 38190 47970 49282 51957 TRUE FALSE 39448.82044 48356.93139 41233.7211 35736.26492 55071.12435 36867.47072 40651.29547 44966.60682 60014.2262 0.657324487 0.805757809 0.687065779 0.595463229 0.917634498 0.61431219 0.677360987 0.749265794 1 15.87301691 0.884281048 7.008962797 0.999999542 0.710558358 0.486036737 0.093655892 2.69070213 162.9408774 0.082008239 0.020566415 7.660922136 -0.884281048 -0.289441184 TVS(ph)SPIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.144)VS(0.539)S(0.317)PIPY(0.078)T(0.238)PS(0.597)PS(0.082)S(0.062)S(0.059)RPIS(0.592)PGLS(0.138)Y(0.046)AS(0.037)HT(0.032)VGFT(0.03)PPT(0.004)S(0.003)LT(0.003)R 78.707 0.0028283 2281600000 119090 74437 111230 109610 115180 118210 166440 140710 121710 TRUE FALSE 113460.8517 82022.21493 116330.0055 98591.79455 135267.3555 114116.3581 141046.5211 128388.6864 140584.1652 0.80706708 0.583438503 0.827475878 0.70130085 0.962180594 0.811729813 1.003288819 0.913251405 1 17.10107458 2.667578848 1.05009505 0.960568735 0.70188965 0.556218856 0.088651435 0.326562638 0.748564925 0.044223128 0.037896332 465.1348158 -2.667578848 -0.258679086 TVS(ph)SSGCEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSSSGCEGK 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 TVS(0.754)S(0.178)S(0.068)GCEGK;T(0.003)VS(0.979)S(0.017)SGCEGK 134.13 0.00018757 152490000 345940 300583 289255 368360 246498 329873 337248 301128 240834 TRUE FALSE 329588.1018 331212.7494 302517.6279 331331.753 289487.1732 318449.4153 285794.6236 274759.6359 278181.3067 1.184796008 1.190636256 1.087483668 1.191064047 1.040642078 1.144754905 1.027368183 0.987699854 1 18.08566595 2.223142219 0.516879717 0.982438466 1.19201438 0.66822517 0.045854205 0.477130959 0.267365089 0.039025756 0.033164257 167.1637939 -2.223142219 0.209575914 TVS(ph)SSGCEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSSGCEGKR 11 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 T(0.016)VS(0.961)S(0.01)S(0.013)GCEGKR 72.681 0.027948 228300000 372020 199690 319770 385540 309580 337650 435350 330130 319100 TRUE FALSE 354435.3519 220038.638 334431.7708 346784.7867 363570.654 325957.0958 368929.3617 301222.0671 368584.3983 0.961612465 0.596983049 0.907341093 0.940855848 0.986397297 0.884348598 1.000935915 0.817240416 1 18.49163548 3.50214831 24.47091677 0.939699652 0.774775113 0.287219592 0.102277529 587.4903392 574433.7658 0.025228887 0.038880422 3177.959146 -3.50214831 -0.164924539 TVSASS(ph)TGDLPK ddPTM_SK-BR-3_Trastuzumab_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 TVSASS(0.996)T(0.004)GDLPK;TVSASS(0.996)T(0.004)GDLPK;TVSASS(0.996)T(0.004)GDLPK;TVSAS(0.005)S(0.75)T(0.245)GDLPK;TVSAS(0.004)S(0.965)T(0.031)GDLPK 293.43 3.62E-36 1071730000 3854310 3492050 3562450 4211170 2587210 4071990 4361870 4344490 2957240 TRUE FALSE 3672124.405 3847893.865 3725791.856 3787855.191 3038418.605 3930975.965 3696386.62 3964063.424 3415833.676 1.075030213 1.126487479 1.09074159 1.108910899 0.889510115 1.150810121 1.082133081 1.160496617 1 21.7038063 TVSGPGTPEPRPAT(ph)PGASSVEQLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSGPGTPEPRPATPGASSVEQLRK 25 2 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 TVSGPGTPEPRPAT(0.998)PGAS(0.001)SVEQLRK 157.64 4.25E-07 558390000 312900 217570 330500 307710 307660 338270 459440 379680 436790 TRUE FALSE 298109.8371 239740.6304 345653.7519 276778.4062 361315.8066 326555.6251 389343.9898 346433.2064 504525.1624 0.59087209 0.475180721 0.685107062 0.548591878 0.716150221 0.647253397 0.77170381 0.686651989 1 18.9445667 -0.248388309 0.171560484 1.276082121 0.438252504 0.785213272 0.065618576 5.478763677 0.29328069 1.09212977 0.303193514 0.564432083 0.248388309 -0.837829617 TVSLEHLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSLEHLQR 9 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 0 ; 60.436 0.095735 1203810000 655360 241413 381980 269653 5882600 171651 888500 207653 5180800 FALSE TRUE 624382.4316 266013.2592 399494.1608 242546.9681 6908523.577 165706.6828 752943.0066 189469.8025 5984212.004 0.104338287 0.044452513 0.066758023 0.040531146 1.15445836 0.027690644 0.12582158 0.031661613 1 22.51272986 -2.285577945 2.166088733 4.376488467 0.187416877 0.350768217 0.341924346 25255586.53 3413943.472 417743596.5 0.083447582 0.005181101 2.285577945 -4.18907159 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNY(0.006)EGS(0.994)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.002)EGS(0.998)PIK 205.81 1.63E-25 381651000 545423 571197 433751 636073 269197 576268 541767 629944 241895 TRUE FALSE 519641.9357 629402.6237 453638.9124 572133.7336 316144.8716 556311.6947 459110.4939 574782.7638 279406.8412 1.85980391 2.252638558 1.623578401 2.047672602 1.131485794 1.99104536 1.643161248 2.057153509 1 18.09200782 -2.269681856 0.205046283 2.88E-21 2.016511317 0.378060691 0.31936349 38.46474926 1.048208796 19.64141306 0.737606819 0.005374253 2.269681856 2.016511317 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 21 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;T(0.001)VS(0.001)LGAGAKDELHIVEAEAMNY(0.464)EGS(0.5)PIKVT(0.033)LAT(0.001)LK;TVSLGAGAKDELHIVEAEAMNY(0.013)EGS(0.987)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.094)EGS(0.888)PIKVT(0.017)LATLK;T(0.001)VS(0.001)LGAGAKDELHIVEAEAMNY(0.13)EGS(0.868)PIKVT(0.001)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.019)EGS(0.963)PIKVT(0.018)LATLK;T(0.098)VS(0.098)LGAGAKDELHIVEAEAMNY(0.384)EGS(0.414)PIKVT(0.007)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.01)EGS(0.988)PIKVT(0.002)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.002)EGS(0.997)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.023)EGS(0.977)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.004)EGS(0.996)PIKVTLATLK;T(0.004)VS(0.004)LGAGAKDELHIVEAEAMNY(0.173)EGS(0.765)PIKVT(0.054)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK 378.46 1.85E-149 11795372600 9428640 7018555.1 8870730 8944598 5057346.4 10089478.7 11600511 11158940 5004051.7 TRUE FALSE 8982966.873 7733753.844 9277461.745 8045470.015 5939346.011 9740077.523 9830639.989 10181804.06 5780054.48 1.554131869 1.338007085 1.605082059 1.39193671 1.027558829 1.685118636 1.700786735 1.761541191 1 22.46265166 TVSLGAGAKDELHIVEAEAMNYEGSPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;; 212.77 2.73E-26 1483958000 3281197 2492573 2917238 3277290 2050629 3200647 3731881 3576466 2023566 FALSE TRUE 3126101.321 2746569.023 3050996.248 2947850.583 2408258.048 3089807.792 3162514.013 3263291.677 2337370.28 1.33744377 1.175068001 1.305311475 1.261182538 1.030328001 1.321916265 1.353022257 1.396138089 1 21.15645487 TVSLPLS(ph)SPNIK ddPTM_SK-BR-3_Trastuzumab_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 TVS(0.003)LPLS(0.606)S(0.391)PNIK;TVSLPLS(0.863)S(0.137)PNIK 159.66 7.36E-05 139772000 538640 606010 552880 633300 597400 562770 627810 616400 627710 TRUE FALSE 513179.5547 667763.108 578230.0949 569639.4808 701586.3709 543281.1338 532026.054 562424.7483 725052.0609 0.707783044 0.920986428 0.797501484 0.785653212 0.967635855 0.749299482 0.733776349 0.775702572 1 19.46772506 2.67542716 0.012501046 1.631278049 3.03E-06 0.144182481 0.093882908 5097.330531 26.18218268 1652.250093 1761.785748 473.6168661 -2.67542716 -1.631275019 TVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 T(0.003)VS(0.011)LT(0.31)PS(0.602)PT(0.034)T(0.039)QVETPDLVDHDNT(0.593)S(0.407)PLFR 102.08 0.0020272 35328000 27087 25288 28313 31399 28423 23749 29024 24664 24740 TRUE FALSE 25806.65119 27864.87595 29611.17906 28242.71287 33379.9622 22926.56618 24595.85574 22504.28941 28576.55285 0.903070826 0.975095775 1.036205424 0.988317696 1.168089181 0.802285926 0.860700585 0.78750889 1 14.80254428 2.19841943 24.99999977 0.850312827 0.998559046 0.417334482 0.087366636 148.5976935 92546.03603 0.031197533 0.02304119 157.9135621 -2.19841943 0.148246218 TVSPDRLELEAAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSPDRLELEAAQK 14 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 194.23 1.53E-07 308110000 454900 435040 447710 477700 340810 491470 517730 546630 374560 FALSE TRUE 433397.7785 479371.0706 468237.9463 429680.6884 400247.1561 474450.2707 438740.7797 498764.1793 432644.8518 1.001740288 1.108001329 1.082268619 0.993148738 0.925117113 1.096627566 1.014089912 1.152825874 1 18.72282371 -0.62430486 6.806784353 0.999996341 1.045267874 0.046407934 0.066274185 0 0 0.060020055 0.014146863 0.237517241 0.62430486 0.045271533 TVSPGS(ph)VSPIHGQGQVVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.5)VS(0.5)PIHGQGQVVENLK;TVSPGS(0.5)VS(0.5)PIHGQGQVVENLK;TVSPGS(0.5)VS(0.5)PIHGQGQVVENLK 332.56 2.47E-80 1732140000 1790090 1480060 1497660 1768330 1308550 1724540 1919920 1841970 1362480 TRUE FALSE 1705475.993 1630879.797 1566329.192 1590574.109 1536760.706 1664818.747 1627000.942 1680677.342 1573766.44 1.083690661 1.036290872 0.995274237 1.0106799 0.976485879 1.057856303 1.033826177 1.067933144 1 20.58579002 -0.176759664 7.266412814 0.999999999 1.033782094 0.090126329 0.032561814 0 0 0.032169527 0.00758243 0.665641416 0.176759664 0.033782095 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.158)VS(0.842)PIHGQGQVVENLK;TVSPGS(0.153)VS(0.847)PIHGQGQVVENLK;TVSPGS(0.336)VS(0.664)PIHGQGQVVENLK 386.84 2.92E-131 2126230000 1363470 1188190 1180900 1366110 945700 1288180 1435350 1415960 1015110 TRUE FALSE 1299021.475 1309267.912 1235045.433 1228786.027 1110629.781 1243570.004 1216360.995 1291971.036 1172528.074 1.107880914 1.11661967 1.053318432 1.047980048 0.947209542 1.060588681 1.037383259 1.101867891 1 20.16119104 3.608587423 2.785883256 1.033013227 1.113057696 0.398732534 0.039852348 0.246378091 3.685022803 0.010702344 0.017948852 4060.573937 -3.608587423 0.080044469 TVSS(ph)PIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 4 T(0.095)VS(0.437)S(0.469)PIPY(0.292)T(0.313)PS(0.38)PS(0.057)S(0.056)S(0.056)RPIS(0.701)PGLS(0.098)Y(0.125)AS(0.094)HT(0.086)VGFT(0.656)PPT(0.031)S(0.03)LT(0.026)R 84.588 0.00031802 42285000 19624 22112 21393 26142 18210 22920 30675 19911 26794 TRUE FALSE 18696.41241 24365.23794 22373.89021 23514.15649 21385.81823 22126.27465 25994.96536 18167.48729 30949.07668 0.60410243 0.787268654 0.722925936 0.759769241 0.691000202 0.714925194 0.839927008 0.587012255 1 14.91760875 -2.350736758 2.425527092 2.962661728 0.723241785 0.577257964 0.076674345 6778082.538 743808.6597 73607888.65 0.017318673 0.004459265 2.350736758 -2.239419942 TVSS(ph)PIPYTPS(ph)PS(ph)SSRPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.014)VS(0.117)S(0.869)PIPY(0.006)T(0.021)PS(0.973)PS(0.486)S(0.054)S(0.191)RPIS(0.269)PGLSYASHTVGFTPPTSLTR 228.98 2.12E-39 1889900000 280200 236090 277320 279460 287680 242310 309430 285970 298610 TRUE FALSE 266955.5013 260147.8394 290035.3963 251368.1499 337851.3009 233918.7439 262220.7704 260928.9508 344916.9137 0.773970457 0.75423335 0.840884818 0.728778845 0.97951503 0.678188673 0.760243293 0.756497987 1 18.39588935 -2.194842936 2.342788646 1.628239513 0.780406894 0.415710391 0.080360534 4571523.152 1026599.054 15222249.13 0.018524117 0.006384944 2.194842936 -0.847832618 TVSS(ph)PIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.014)VS(0.121)S(0.865)PIPYT(0.003)PS(0.997)PS(0.235)S(0.172)S(0.147)RPIS(0.445)PGLS(0.001)YAS(0.001)HTVGFTPPTSLTR 197.75 3.37E-24 187690000 58392 52535 61199 62773 62927 55967 73945 70570 67856 TRUE FALSE 55631.92588 57888.37623 64005.03468 56462.93878 73901.44888 54028.84876 62663.33216 64390.51668 78378.76192 0.709783167 0.73857222 0.816611964 0.720385694 0.942875941 0.689330214 0.799493774 0.821530158 1 16.25817516 -5 0.156905083 1.834937503 0.70821207 0.520356403 0.069825935 100.2318243 0.912991638 26.03889296 0.28384751 1.00E-05 5 -1.126725432 TVSS(ph)PIPYTPSPSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.021)S(0.979)PIPYTPSPSSSR;TVS(0.029)S(0.971)PIPYTPSPSSSR;TVS(0.004)S(0.995)PIPYTPSPSSSR 227.29 5.42E-15 245240000 372137 415470 318510 432380 267923 338104 341380 339153 270573 TRUE FALSE 354546.8215 457806.8654 333113.9985 388916.3409 314648.6864 326395.3737 289296.2111 309454.9654 312532.0789 1.134433376 1.4648316 1.065855383 1.24440455 1.006772449 1.04435799 0.925652855 0.990154247 1 18.25364475 2.839093544 1.16468568 0.968097382 1.280363266 0.529151082 0.107403654 0.302481382 0.85919163 0.046441012 0.047720327 690.3884919 -2.839093544 0.312265884 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.014)VS(0.12)S(0.865)PIPYT(0.006)PS(0.003)PS(0.044)S(0.024)S(0.02)RPIS(0.903)PGLSYASHTVGFTPPTSLTR;T(0.013)VS(0.115)S(0.872)PIPYTPS(0.001)PS(0.002)S(0.003)S(0.002)RPIS(0.993)PGLSYASHTVGFTPPTSLTR;T(0.017)VS(0.129)S(0.854)PIPYTPSPSSSRPIS(0.998)PGLSYASHTVGFTPPTSLTR;TVS(0.005)S(0.995)PIPYTPSPSSSRPIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR 250.3 4.84E-51 2472640000 1083700 956900 1032370 1128760 1108190 1052170 1284590 1091510 1170680 TRUE FALSE 1032475.649 1054409.198 1079705.186 1015294.9 1301457.985 1015733.089 1088602.202 995931.5979 1352223.075 0.763539439 0.779759802 0.798466766 0.750833881 0.962458051 0.751157932 0.805046314 0.736514275 1 20.36690174 -1.948927033 2.73223816 1.14985237 0.793355529 0.508465017 0.063815673 13325589.2 8786775.956 12711060.7 0.014030256 0.011247939 1.948927033 -0.356496841 TVSS(ph)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.042)S(0.957)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR;TVS(0.164)S(0.836)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 238.14 2.29E-50 1122100000 217811 172396 190582 199966 211255 175120 227511 199576 211903 TRUE FALSE 207515.5057 189963.3484 199320.3732 179865.0378 248097.8051 169055.5505 192800.0184 182100.0674 244763.835 0.84781931 0.776108727 0.814337515 0.734851363 1.013621171 0.690688436 0.787698144 0.743982735 1 17.90103088 -2.109081383 2.45595427 1.36970553 0.800538197 0.340191883 0.087032687 7995644.628 2605071.63 16485834.26 0.019385999 0.007778908 2.109081383 -0.569167333 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.013)VS(0.11)S(0.877)PPT(0.54)S(0.46)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.157)S(0.842)PPT(0.54)S(0.454)PRPGS(0.006)AATVSASTSNIIPPR;T(0.025)VS(0.148)S(0.827)PPT(0.536)S(0.465)PRPGSAATVSASTSNIIPPR;T(0.006)VS(0.16)S(0.832)PPT(0.53)S(0.471)PRPGSAATVSASTSNIIPPR 140.24 3.08E-07 1168654000 599385 462491 528132 626737 517787 607051 660886 557965 526067 TRUE FALSE 571053.2589 509619.3587 552347.3746 563736.206 608088.8889 586028.6717 560055.7027 509106.6266 607646.7836 0.939778296 0.838676962 0.908994155 0.927736674 1.00072757 0.964423227 0.921679696 0.837833163 1 19.21287342 3.299996184 3.455487645 0.941797747 0.887645505 0.158144164 0.051570657 0.397297079 9.570993905 0.014589409 0.019771984 1995.244783 -3.299996184 -0.054152242 TVSS(ph)PPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.004)VS(0.121)S(0.876)PPT(0.061)S(0.939)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.124)S(0.874)PPT(0.055)S(0.945)PRPGSAATVSASTSNIIPPR;TVS(0.113)S(0.886)PPT(0.146)S(0.854)PRPGSAATVSASTSNIIPPR 162.29 4.93E-12 2796190000 741500 570700 666990 712630 646960 652940 762730 660900 761530 TRUE FALSE 706450.7645 628854.9788 697572.1512 640995.0785 759789.6192 630328.5241 646361.53 603028.0923 879624.183 0.803127947 0.714913245 0.793034303 0.728714707 0.863766179 0.716588443 0.734815552 0.685551971 1 19.74652774 -1.093939529 4.552197414 1.000018412 0.754721372 0.684339476 0.052278792 8.92E-06 1.78E-06 0.04624151 0.010898411 0.080549059 1.093939529 -0.245297039 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.069)S(0.716)PPT(0.162)S(0.051)PRPGS(0.001)AATVSASTSNIIPPR;TVS(0.047)S(0.937)PPT(0.003)S(0.013)PRPGSAATVSASTSNIIPPR;T(0.007)VS(0.151)S(0.818)PPT(0.023)S(0.001)PRPGSAATVSASTSNIIPPR;TVS(0.033)S(0.916)PPT(0.04)S(0.011)PRPGSAATVSASTSNIIPPR 168.87 2.86E-12 1249500000 212347 191311 194727 225077 187974 202648 241182 227567 226127 TRUE FALSE 202309.7781 210805.8084 203655.4256 202451.8323 220756.6061 195630.2489 204385.2563 207640.0271 261193.6203 0.774558651 0.807086361 0.779710566 0.775102516 0.84518376 0.748985556 0.78250478 0.794965922 1 17.99476013 0.756267055 5.962186123 0.999999983 0.787760441 0.876636359 0.024947649 5.951444086 145.5984785 0.021847819 0.005494441 5.705149834 -0.756267055 -0.212239542 TVSS(ph)SGCEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSSSGCEGK 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 TVS(0.053)S(0.857)S(0.09)GCEGK;TVS(0.078)S(0.461)S(0.461)GCEGK 137.55 9.26E-05 200510000 875310 760870 715010 983040 652990 855390 841850 771980 681010 TRUE FALSE 833935.831 838403.518 747793.9157 884222.9515 766871.2493 825767.6298 713410.3209 704381.3387 786617.5527 1.060154109 1.065833727 0.950644838 1.124082406 0.9748972 1.049770155 0.906934149 0.895455913 1 19.58530285 1.74550163 7.991699462 0.927180982 1.040177847 0.437154909 0.055015282 0.096081432 21.45886318 0.02386244 0.012776561 55.65467228 -1.74550163 0.112996865 TVSSDGCS(ph)TPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 TVSSDGCS(0.495)T(0.495)PS(0.009)REEGGCSLASTPATTLHLLQLSGQR;TVSSDGCS(0.499)T(0.499)PS(0.001)REEGGCSLASTPATTLHLLQLSGQR 346.87 4.98E-145 921040000 350760 252590 308100 302330 329210 320660 377090 315690 353820 TRUE FALSE 334180.2699 278329.2082 322226.6898 271939.214 386624.1198 309555.4638 319557.9948 288046.51 408688.5985 0.817689241 0.681030029 0.788440614 0.665394667 0.946011514 0.757436016 0.781910716 0.704806816 1 18.64064247 -1.937544663 2.366225943 1.166060505 0.766594581 0.456709732 0.079566367 12396172.59 6029170.573 11360500.42 0.017320776 0.011546632 1.937544663 -0.399465924 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYTPSPSSSRPIS(0.995)PGLS(0.005)YASHTVGFTPPTSLTR;TVSSPIPYTPSPS(0.004)S(0.003)S(0.002)RPIS(0.99)PGLS(0.001)YASHTVGFTPPTSLTR 275.54 7.05E-77 5704300000 1189330 919490 1161100 1128830 1154590 1103350 1306940 1153720 1213740 TRUE FALSE 1133112.728 1013187.076 1214337.583 1015357.864 1355950.13 1065140.713 1107542.299 1052694.161 1401960.6 0.80823436 0.722692975 0.866170977 0.724241369 0.967181339 0.759750818 0.78999531 0.750872856 1 20.41901437 -2.348992491 2.253094641 2.252754166 0.795115995 0.426488443 0.073280335 2518493.19 456476.601 15965061.07 0.01587529 0.00447721 2.348992491 -1.457638172 TVSTLHHVLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVSTLHHVLQR 11 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 141.1 2.21E-05 384790000 130660 108890 133630 123700 136870 98160 144030 135460 33096 FALSE TRUE 124483.9607 119986.0148 139757.0677 111265.441 160740.0847 94760.69459 122055.5782 123598.4043 38228.35865 3.25632502 3.138665092 3.655847978 2.910547168 4.204734138 2.478806256 3.192801954 3.233160111 1 15.22235564 -1.252991224 0.481501446 5.80E-14 3.306158085 0.719026444 0.444790866 12.69568172 1.581700093 16.94317728 0.195145247 0.055848148 1.252991224 3.306158085 TVTAMDVVYALKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVTAMDVVYALKR 13 1 P62805 P62805 HIST1H4A Histone H4 0 132.06 0.00019758 129110000 228990 201380 203810 257260 272680 223530 293470 259020 267450 FALSE TRUE 218166.0965 221900.851 213154.8901 231399.736 320235.3057 215789.1001 248695.7616 236338.8356 308924.7801 0.70621106 0.718300587 0.689989615 0.749048801 1.036612555 0.698516642 0.805036623 0.765036834 1 18.23689607 -5 0.08956099 1.720501379 0.577944764 0.383120663 0.097112974 223.4045106 1.391489656 31.20257621 2.218570622 1.00E-05 5 -1.142556615 TVTCVTVVEPEAPPS(ph)PDVLQAATHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR 224.06 5.63E-34 3073016000 1899872 1619228 1839079 1892380 1731560 1742864 2053979 1863737 1850457 TRUE FALSE 1810068.816 1784229.174 1923402.591 1702154.367 2033543.516 1682508.183 1740606.78 1700538.308 2137416.421 0.846848933 0.834759739 0.899872656 0.796360667 0.951402589 0.78716911 0.814350803 0.795604587 1 21.02743658 -2.299173317 2.309643573 1.785324308 0.840037525 0.490543612 0.050983117 1769099.896 473891.9829 7182290.689 0.012435725 0.005021422 2.299173317 -0.945286782 TVTIWEIINSEYFTAEQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVTIWEIINSEYFTAEQRR 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 0 149.73 1.32E-07 47576000 67524 78235 83549 82784 76048 83749 97678 113910 75762 FALSE TRUE 64332.27434 86207.23545 87379.80429 74462.39504 89310.74712 80848.75113 82775.42712 103935.4365 87510.78402 0.73513539 0.985104138 0.998503273 0.850893931 1.020568472 0.923871864 0.945888304 1.187687183 1 16.41717319 5.515315868 0.880183869 0.98501901 1.25E-10 0.455060458 0.086365153 6.549827725 1.468326989 0.025784592 8.605659073 327578.8607 -5.515315868 -0.98501901 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR 32 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;; 164.6 3.39E-14 210851000 145893 143221 138965 167819 127996 149157 181018 143748 148226 FALSE TRUE 138996.927 157815.3827 145336.6827 150949.5153 150318.4619 143991.6557 153400.3795 131160.6631 171212.131 0.811840412 0.92175351 0.848869071 0.881651986 0.877966187 0.841013162 0.895966767 0.766071085 1 17.3854254 -1.33500057 4.537909036 1.000132426 0.862062828 0.506839615 0.044350843 5.25E-05 7.70E-06 0.037952262 0.008936871 0.046238041 1.33500057 -0.138069599 TVTNAVVTVPAYFNDSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVTNAVVTVPAYFNDSQR 18 0 P11142;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 222.55 1.31E-18 131856000 448880 386176 432472 471141 454471 413553 518147 466548 532975 FALSE TRUE 427662.332 425527.7734 452301.269 423781.0116 533730.5985 399231.5559 439094.1587 425694.5838 615626.0409 0.694678756 0.691211458 0.734701327 0.688374083 0.866972095 0.648496862 0.713248189 0.691482419 1 19.23169473 -1.127829452 4.378315476 1.000043456 0.713788909 0.703379954 0.057911996 1.17886662 30833400.59 2690.871484 0.01236711 0.074502449 1.127829452 -0.286254547 TVVLT(ph)PTYSGEADALLPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVVLTPTYSGEADALLPSLR 20 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 TVVLT(0.998)PT(0.002)YSGEADALLPSLR;TVVLT(0.999)PT(0.001)YSGEADALLPSLR;TVVLT(0.988)PT(0.012)YSGEADALLPSLR 295.16 1.54E-53 132019000 62925 48246.4 55511 58976 64692 56970 68227 59646 65190 TRUE FALSE 59950.65996 53162.76301 58056.23426 53047.62043 75974.26432 54997.11462 57817.71808 54423.08004 75299.33226 0.796164563 0.70601905 0.771005964 0.704489918 1.008963321 0.730379845 0.76783839 0.722756476 1 16.20034945 -1.704246878 2.610846565 1.038304908 0.773135104 0.389761874 0.088040798 13970565.63 11252658.43 3512727.112 0.019471105 0.019758461 1.704246878 -0.265169803 TVVLTPTYS(ph)GEADALLPSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVVLTPTYSGEADALLPSLR 20 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 TVVLT(0.01)PT(0.305)Y(0.26)S(0.425)GEADALLPSLR 60.628 0.059758 13151000 14897 10884 12201 13182 16828 12691 15277 13457 10816 TRUE FALSE 14192.84833 11993.09197 12760.42792 11856.92032 19762.79787 12251.50749 12946.21307 12278.63374 12493.29004 1.136037688 0.959962663 1.021382508 0.949063079 1.581872974 0.980647007 1.036253303 0.982818273 1 13.60886583 TVVNKDVFRDPALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVVNKDVFRDPALK 14 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 181.26 9.32E-07 1469030000 3472900 1741350 3667900 2965700 3085000 3806400 5727400 4450300 4412900 FALSE TRUE 3308742.9 1918795.545 3836076.843 2667582.202 3623023.023 3674583.414 4853579.939 4060608.139 5097229.994 0.649125683 0.376438879 0.752580685 0.523339579 0.710782725 0.720898099 0.952199517 0.796630355 1 22.28128202 2.132441497 0.777817896 0.96363032 0.534677259 0.63523239 0.110463667 0.356262672 0.406579513 0.084804622 0.04794208 135.6567776 -2.132441497 -0.428953061 TVVTGIEMFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVVTGIEMFHK 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 199.7 4.94E-08 1282060000 4743000 3508800 3786300 3709900 3534800 3358200 4507300 4152400 3297500 FALSE TRUE 4518807.79 3866350.709 3959905.6 3336973.804 4151268.001 3241904.692 3819628.603 3788793.843 3808859.459 1.186393943 1.015094086 1.039656528 0.87610841 1.08989792 0.851148415 1.002827393 0.994731857 1 21.86092762 4.633759264 0.993010206 0.97023904 1.278102575 0.467886581 0.069552066 1.218504544 1.08452853 0.019137592 0.386787805 43028.80291 -4.633759264 0.307863535 TVWDWELMNDIKPIWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVWDWELMNDIKPIWQR 17 1 P14625 P14625 HSP90B1 Endoplasmin 0 198.07 1.33E-11 88367000 289150 314430 239240 298920 184440 229990 237450 286260 181290 FALSE TRUE 275482.4525 346470.7745 250209.3906 268871.9937 216606.2776 222025.3886 201222.6414 261193.5568 209403.5273 1.315557842 1.654560355 1.194867125 1.283989803 1.034396509 1.060275304 0.960932435 1.247321667 1 17.67592622 3.228957676 1.510895346 1.051646894 1.475330082 0.589055292 0.130529229 0.217692338 1.03403901 0.04175816 0.060190179 1694.172686 -3.228957676 0.423683188 TVWDWELMNDIKPIWQRPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVWDWELMNDIKPIWQRPSK 20 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 269.01 1.82E-37 3848900000 3192800 2798260 2763800 3209700 2066270 2920200 3419000 3267300 2329640 FALSE TRUE 3041882.672 3083405.875 2890522.964 2887054.858 2426626.834 2819072.742 2897368.756 2981197.891 2690908.673 1.130429547 1.145860469 1.074180998 1.072892175 0.901787139 1.047628546 1.076725043 1.107877767 1 21.359662 3.486143301 2.295094403 1.035357078 1.138313126 0.372080833 0.055420153 0.312906813 3.292295541 0.016485449 0.026412552 3062.973931 -3.486143301 0.102956048 TVWIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TVWIAR 6 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;; 126.04 0.041095 1681172000 2138518 1701170 1741033 2018391 2217392 1664205 2349912 1940190 2305417 FALSE TRUE 2037434.492 1874521.157 1820861.085 1815498.502 2604104.463 1606573.164 1991389.765 1770296.678 2662929.294 0.765110248 0.703932005 0.683781236 0.681767445 0.977909728 0.603310485 0.747819242 0.664792971 1 21.34458269 -0.914314223 4.213434919 1.000006948 0.729034968 0.425473397 0.099128917 23792776.49 49919361.7 2558.948851 0.021409104 0.121810795 0.914314223 -0.27097198 TVYCNVHKHEPLVLFCESCDTLTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TVYCNVHKHEPLVLFCESCDTLTCR 25 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 153.77 6.13E-08 252320000 222810 147730 224890 189230 208300 217290 358880 215410 17653 FALSE TRUE 212278.2129 162783.855 235201.4289 170208.2409 244627.454 209765.1928 304126.2647 196547.5584 20390.53708 10.41062391 7.983303937 11.53483246 8.347413323 11.99710695 10.28737948 14.91506886 9.639155539 1 14.31561216 0.962688491 23.89450419 0.999999894 10.74810567 0.71559933 1.922849171 2310.025496 1479355.336 1.969422409 0.492355602 9.176741356 -0.962688491 9.748105779 TVYFAEEVQCEGNSFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TVYFAEEVQCEGNSFHK 17 0 P21291;E9PS42 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;; 324.46 5.24E-59 2069350000 1588490 1246900 1384290 1654640 1452690 1328210 1768880 1593100 1561850 FALSE TRUE 1513405.226 1373960.528 1447761.066 1488312.444 1706038.676 1282213.755 1499004.868 1453599.718 1804053.721 0.838891441 0.761596238 0.802504409 0.824982331 0.945669553 0.71074034 0.830909219 0.805740817 1 20.78281087 -1.080069802 5.080726281 1.000003977 0.812283736 0.486271588 0.059653293 0.014485165 36952390.39 311.2651485 0.012772346 0.08316301 1.080069802 -0.187720242 TVYFAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TVYFAEK 7 0 P52943;H0YHD8 P52943 CRIP2 Cysteine-rich protein 2 0 ;; 86.011 0.047436 260985000 495316 399252 424140 410112 428572 460650 566760 448298 452111 FALSE TRUE 471903.3943 439936.2327 443587.2385 368886.7626 503314.8211 444697.575 480290.3527 409042.6505 522222.0648 0.90364507 0.842431338 0.849422628 0.70637912 0.963794629 0.851548805 0.919705208 0.783273397 1 18.99430389 TVYGGGCSEMLMAHAVTQLANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVYGGGCSEMLMAHAVTQLANR 22 0 P78371;P78371-2;F5GWF6 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 318.79 1.69E-67 869730000 389740 294820 306560 416360 391060 365410 450550 358540 376120 FALSE TRUE 371317.7626 324862.4932 320616.0792 374506.7018 459260.7402 352755.7601 381810.3226 327144.3369 434446.7686 0.854691045 0.747761329 0.737987027 0.862031275 1.057116253 0.811965436 0.878842588 0.753013627 1 18.72881989 3.071672523 7.032858798 0.891600935 0.784877725 0.266094273 0.090271376 0.310731462 25.13889888 0.024965122 0.029891266 1179.430958 -3.071672523 -0.10672321 TVYGNHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TVYGNHER 8 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 109.29 0.0036467 72005000 225320 195749 170278 225060 218780 183046 230260 223990 254300 FALSE TRUE 214669.5701 215696.0456 178085.4147 202436.5412 256935.1627 176707.0711 195129.608 204376.2482 293735.5452 0.730825988 0.734320545 0.606278054 0.689179585 0.874715937 0.601585589 0.664303695 0.695783168 1 18.16415833 -1.383111997 5.551303163 1.000112987 0.699691736 0.604231375 0.076398804 0.000102186 1.14E-05 0.070753374 0.016670493 0.041389293 1.383111997 -0.300421252 TWDHFWLNEGHTVYLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TWDHFWLNEGHTVYLER 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 254.05 2.89E-27 554157000 851430 857660 807140 919880 820070 830120 911880 868800 268226 FALSE TRUE 811184.5913 945056.5291 844148.1674 827411.9147 963089.9484 801372.7363 772755.9582 792723.2662 309821.1182 2.61823531 3.050329605 2.72463082 2.670611738 3.108535512 2.58656589 2.494200404 2.558648264 1 18.24107596 -0.17215215 0.521332078 0.796733787 2.841232455 0.906969566 0.176592075 1.457616069 0.423715354 0.754455992 0.078247951 0.672740929 0.17215215 2.044498668 TWEQQQEVVSR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 234.9 9.53E-08 288490000 225620 191302 215493 229694 204664 205487 256425 216989 237219 FALSE TRUE 214955.3897 210795.8913 225373.5672 206604.7227 240357.3368 198370.9337 217302.6567 197988.2928 274005.711 0.784492371 0.769312036 0.822514124 0.754016119 0.877198274 0.72396642 0.79305886 0.72256995 1 18.06384644 -1.129707343 4.866614983 1.000012697 0.781684183 0.695608471 0.045548167 5.41E-06 9.67E-07 0.038005969 0.008957572 0.074180995 1.129707343 -0.218328514 TWESVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWESVKR 7 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;C9JYY9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ; 111.82 0.010413 1062040000 1902010 1445280 1471140 1458750 1466850 1411000 1986570 1754100 1594290 FALSE TRUE 1812105.757 1592555.675 1538593.224 1312113.679 1722668.176 1362136.716 1683482.261 1600501.705 1841524.351 0.984024868 0.864802941 0.835499799 0.712514976 0.935457723 0.739678906 0.914178659 0.869117861 1 20.81246904 0.554877587 1.423931969 0.999746203 0.858185464 0.233755242 0.082048239 2.965501608 7.69276038 0.075765371 0.022174586 3.588207812 -0.554877587 -0.141560739 TWFQEYMNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWFQEYMNSK 10 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BPA9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 109.16 0.0066597 0 265550 246350 226220 274440 228950 255870 303340 282220 253280 FALSE TRUE 252997.9778 271453.3451 236592.4108 246852.7698 268878.8075 247009.1577 257059.9118 257507.3207 292557.3688 0.86478074 0.92786364 0.808704329 0.843775601 0.919063528 0.844310156 0.87866497 0.880194273 1 18.15836003 0.44997777 2.092809972 0.999998176 0.872891821 0.573535936 0.035012229 5.238180551 18.96958832 0.032337906 0.008832687 2.818238674 -0.44997777 -0.127106355 TWHAWMDNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWHAWMDNIR 10 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 66.664 0.065292 314580000 2085680 2118530 1019640 1583760 1186030 1596900 1684150 1842830 919310 FALSE TRUE 1987094.04 2334410.616 1066391.503 1424557.436 1392873.256 1541598.953 1427201.986 1681462.036 1061871.9 1.871312388 2.198391931 1.00425626 1.341553003 1.31171496 1.451774883 1.344043464 1.583488589 1 20.0181783 3.746029595 24.99876054 1.319289706 2.034852192 0.713606963 0.195278105 261.3663689 874793.8626 0.046275635 0.081397489 5572.237195 -3.746029595 0.715562486 TWNDPSVQQDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TWNDPSVQQDIK 12 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 176.78 5.61E-05 56450000 202870 173820 177430 203280 156900 189100 223510 201680 155960 FALSE TRUE 193280.7371 191532.4556 185565.341 182845.9082 184263.3103 182551.4196 189409.4445 184019.83 180145.4803 1.072914718 1.063209886 1.030086021 1.014990262 1.022858359 1.013355535 1.051424905 1.021506783 1 17.45880293 3.751035167 3.252939491 1.024504008 1.069596406 0.679270885 0.013191512 0.136333863 3.008483451 0.003538259 0.006429356 5636.832986 -3.751035167 0.045092397 TWPDHGVPSDPGGVLDFLEEVHHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TWPDHGVPSDPGGVLDFLEEVHHK 24 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 165.66 4.86E-12 164420000 190420 189400 174870 219120 141740 188650 210840 190140 17217 FALSE TRUE 181419.224 208700.0753 182887.9625 197093.6413 166459.4111 182117.0032 178672.4857 173490.3336 19886.92443 9.122538009 10.49433642 9.196392491 9.910715054 8.370294347 9.157625346 8.984420206 8.723839336 1 14.27953256 -0.481279926 0.578728814 1.86E-13 9.586644586 0.959789236 0.532897838 1.738367824 0.476521966 4.503542544 0.212101877 0.330156669 0.481279926 9.586644586 TWS(ph)EKDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TWSEKDLR 8 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2;F5H0D8;E9PKU1;F5H4Y5;E9PQK4;E9PSH0;E9PKA1 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 T(0.156)WS(0.844)EKDLR 115.18 0.0015227 122140000 880300 683520 724710 843930 515120 808300 851240 865710 477150 TRUE FALSE 838689.9636 753171.4651 757938.6703 759096.553 604956.7649 780308.3683 721367.7039 789903.843 551143.9851 1.521725695 1.366560256 1.37520991 1.377310782 1.097638333 1.415797667 1.30885526 1.433207772 1 19.07206974 -4.515058086 0.145102214 8.19E-20 1.483220077 0.517997001 0.109314818 94.54130833 0.943149992 28.4611379 0.589898415 3.05E-05 4.515058086 1.483220077 TWSTDDFFAGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TWSTDDFFAGLR 12 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 121.83 0.00047378 0 104800 98491 87074 113900 90208 84300 101470 105680 92258 FALSE TRUE 99846.31169 108527.3449 91066.42903 102450.5556 105940.2466 81380.66986 85988.88788 96426.09896 106564.8995 0.936953089 1.018415495 0.854563083 0.961391191 0.994138287 0.763672375 0.806915676 0.904857973 1 16.70137279 2.252762457 24.99987443 0.844675947 0.956431387 0.205227774 0.075850642 251.8946015 443416.158 0.024598961 0.020490585 178.9626725 -2.252762457 0.11175544 TWTDFEHMETIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWTDFEHMETIEK 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-4;H7C5K1;Q7Z2W4-5 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 ; 146.5 5.69E-06 45939000 274770 277670 241960 284710 211063 266580 301480 291360 171884 FALSE TRUE 261782.1666 305964.8887 253054.1053 256090.4099 247872.3204 257348.2678 255483.6889 265846.9738 198538.8929 1.3185435 1.541082879 1.274582031 1.289875279 1.248482435 1.296210853 1.286819349 1.339017106 1 17.59906213 -4.607956746 0.13433981 5.48E-11 1.470770613 0.619263948 0.080279231 80.02294159 0.73998446 21.93771455 0.564310626 2.47E-05 4.607956746 1.470770613 TWTLCGT(ph)PEYLAPEIILSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWTLCGTPEYLAPEIILSK 19 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;P22612;P17612-2;P17612;Q15136;K7ERP6 P22694-2;P17612-2 PRKACB;PRKACG;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit gamma;cAMP-dependent protein kinase catalytic subunit alpha 1 T(0.293)WT(0.293)LCGT(0.382)PEY(0.032)LAPEIILSK;T(0.3)WT(0.3)LCGT(0.397)PEY(0.002)LAPEIILSK 101.74 0.0015731 254020000 298830 281360 321790 389820 260700 445740 482450 411400 278040 TRUE FALSE 284704.8981 310030.9039 336544.3898 350634.553 306165.9975 430303.912 408843.3917 375375.635 321157.0232 0.8864975 0.965356139 1.047912284 1.091785412 0.953321819 1.339855214 1.273032698 1.16882275 1 18.29291932 2.250513425 25 1.228402956 0.983789991 0.482859233 0.103623151 154.074205 322254.9586 0.034916646 0.028998755 178.0382946 -2.250513425 -0.244612965 TWTTADFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TWTTADFR 8 0 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 82.241 0.048351 103760000 505820 421830 377700 459090 446050 397320 515540 469370 430350 FALSE TRUE 481910.891 464814.9566 395017.9186 412941.401 523840.9788 383560.7088 436884.9045 428269.4745 497086.4801 0.969470928 0.935078654 0.79466639 0.830723461 1.053822624 0.771617664 0.878891143 0.861559289 1 18.92313734 3.981451134 23.45959088 0.876528107 0.956573862 0.09640698 0.086204051 606.4682361 767031.2801 0.020247411 0.036825342 9581.888967 -3.981451134 0.080045754 TWYVQATCATQGTGLYDGLDWLSHELSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TWYVQATCATQGTGLYDGLDWLSHELSK 28 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 355.86 4.55E-111 604580000 1045400 1088690 926840 1147850 804360 1056240 1064490 1124610 674100 FALSE TRUE 995986.0138 1199628.749 969336.5308 1032465.937 944640.1293 1019662.144 902082.4998 1026133.186 778635.9852 1.279142029 1.540679819 1.244916173 1.325993092 1.213198654 1.309549216 1.158542011 1.317859958 1 19.5705895 -0.557181643 0.138883271 0.685699938 1.516948332 0.517113474 0.095319552 17.08968816 0.603001446 2.92318243 0.828554606 0.277216041 0.557181643 0.831248393 TYDATTHFETTCDDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 TYDATTHFETTCDDIK 16 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 271.43 3.76E-35 8112330000 7790920 7293600 6750280 8596990 4770560 7754800 8121560 8286870 4569650 FALSE TRUE 7422658.652 8036826.132 7059787.015 7732804.232 5602544.154 7486249.332 6882466.859 7561227.731 5278287.983 1.406262537 1.522619864 1.337514557 1.465021283 1.061432073 1.418310133 1.303920302 1.432515193 1 22.33163864 -4.263753029 0.147950701 6.95E-12 1.500701936 0.455594201 0.125689519 90.01751646 0.974817688 27.64561367 0.631214968 5.45E-05 4.263753029 1.500701936 TYDATTHFETTCDDIKNIYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYDATTHFETTCDDIKNIYK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 169.28 6.61E-12 418230000 248790 127460 223730 185260 164040 230690 301750 245450 179020 FALSE TRUE 237030.1898 140448.3189 233988.2418 166637.3128 192648.5241 222701.1475 255712.4955 223957.0968 206781.5073 1.146283306 0.679211215 1.131572377 0.805861777 0.931652577 1.076987736 1.236631355 1.083061535 1 17.65774764 2.157364336 4.07619428 1.13737623 0.924576482 0.211883098 0.148512806 0.256310652 8.130752156 0.054124921 0.039168757 143.6694193 -2.157364336 -0.212799748 TYDRDNSGMIDKNELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYDRDNSGMIDKNELK 16 2 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 87.02 0.031751 104740000 92712 57185 87391 80418 58496 95348 102580 103790 74886 FALSE TRUE 88329.6875 63012.21651 91397.96379 72334.22986 68697.68388 92046.07485 86929.53699 94701.59737 86498.93842 1.021164989 0.728473871 1.056636827 0.836244134 0.794202624 1.064129532 1.004978079 1.094829591 1 16.40039481 2.223521482 24.98326843 1.03830872 0.883218172 0.368706851 0.099788291 246.9423585 410222.2647 0.034838321 0.025830843 167.3098393 -2.223521482 -0.155090548 TYEDIDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TYEDIDKR 8 1 G5E9W7;G5E9V5;P82650;H7C5L9 G5E9W7 MRPS22 "28S ribosomal protein S22, mitochondrial" 0 ;;; 111.17 0.0052681 767330000 1113870 893450 925020 925600 739720 871420 1049690 954620 846490 FALSE TRUE 1061219.573 984493.5708 967433.082 832556.9295 868726.9338 841242.5069 889540.5116 871028.412 977759.3459 1.085358659 1.006887405 0.989438849 0.851494729 0.888487476 0.860377874 0.909774491 0.890841305 1 19.8991199 3.634001148 1.746787538 0.893962067 1.059617288 0.646813875 0.045063217 0.178371089 1.069474853 0.012055066 0.023827391 4305.277485 -3.634001148 0.165655221 TYEDIKENLESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYEDIKENLESR 12 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 107.99 0.0015995 300160000 704500 562070 614320 676850 604610 645250 729570 683610 563810 FALSE TRUE 671199.6812 619345.572 642487.1796 608811.7521 710053.7926 622904.8307 618260.697 623749.4844 651242.7753 1.030644341 0.951021026 0.986555558 0.934846075 1.090305827 0.956486359 0.949355172 0.957783346 1 19.31283594 TYEDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TYEDLKR 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;; 112.17 0.010285 1135280000 2237150 1924850 1980720 2221480 1610960 2157690 2472790 2290690 1851810 FALSE TRUE 2131404.353 2120994.403 2071537.971 1998172.61 1891910.914 2082968.654 2095520.47 2090105.04 2138979.237 0.996458645 0.991591861 0.96847035 0.934171111 0.884492416 0.97381434 0.979682473 0.977150691 1 21.02849105 -1.246596305 6.777077929 1.000000265 0.966173614 0.105267231 0.032703873 1.41E-07 1.56E-08 0.034036371 0.008022387 0.056676588 1.246596305 -0.033826651 TYEDMTLEELEDHEDEFNEEDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 254.73 1.58E-43 89542000 76343 76580 70754 82020 73701 74845 85838 87291 61877 FALSE TRUE 72734.41769 84383.58906 73998.14089 73775.19377 86554.43107 72253.09888 72741.83658 79647.33728 71472.56914 1.017655005 1.180643009 1.035336238 1.0322169 1.211016088 1.01092069 1.017758805 1.114376302 1 16.12510203 1.068632507 0.505905841 1.003914127 1.092084208 0.078037174 0.07197791 2.203010298 1.451763871 0.07844444 0.038802329 11.71203893 -1.068632507 0.088170081 TYEEGLKHEANNPQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 TYEEGLKHEANNPQLK 16 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 233.02 7.30E-20 5782500000 7348950 6046180 6197460 7431990 4171800 7040900 7746110 7747070 4484190 FALSE TRUE 7001579.698 6662292.616 6481619.671 6684912.245 4899360.599 6797071.868 6564298.652 7068695.481 5179575.283 1.351767146 1.286262338 1.251380532 1.29062942 0.945900065 1.312283633 1.267343034 1.364724923 1 22.30440237 -2.164446508 2.566307969 0.310032294 1.261052433 0.326760317 0.116698211 6735853.608 2632024.008 27817170.04 0.027026233 0.006847838 2.164446508 0.951020139 TYEQGPDT(ph)PVSADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TYEQGPDTPVSADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR 43 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4 A0A5F9UK94 AMPD2 AMP deaminase 2 1 T(0.009)YEQGPDT(0.731)PVS(0.255)ADAPVHPPALEQHPY(0.002)EHCEPS(0.001)T(0.001)MPGDLGLGLR;T(0.136)YEQGPDT(0.838)PVS(0.026)ADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR;T(0.003)YEQGPDT(0.981)PVS(0.015)ADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR 95.149 5.86E-05 267868000 68811 68189 67851 73352 67950 65896 76026 63821 43369.2 TRUE FALSE 65558.4404 75137.53662 70962.03546 65978.5176 79800.45849 63614.005 64426.83739 58232.4949 50094.67404 1.308690827 1.499910681 1.416558483 1.317076493 1.592992868 1.269875615 1.286101539 1.162448824 1 15.61236961 1.250491544 1.075019489 1.006412188 1.41812983 0.698637381 0.090972959 0.238063737 0.567839694 0.077414467 0.02600507 17.80293243 -1.250491544 0.411717642 TYEVSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYEVSLR 7 0 Q16531;F5GY55;F5H2L3 Q16531 DDB1 DNA damage-binding protein 1 0 143 0.005702 147000000 197750 180760 171650 201000 200900 189490 245320 187750 205320 FALSE TRUE 188402.7494 199179.6495 179520.3223 180795.0981 235936.8964 182927.9138 207891.9284 171309.6147 237159.977 0.794412075 0.839853554 0.756958761 0.762333934 0.994842804 0.771327085 0.876589427 0.722337794 1 17.85550104 TYFTDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYFTDKK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 124.08 0.0067044 1486070000 2043940 1527180 1690050 2416000 1740120 2039450 2607800 2109600 1634010 FALSE TRUE 1947327.007 1682801.378 1767540.464 2173139.09 2043596.377 1968823.335 2209932.214 1924872.24 1887403.925 1.031748944 0.891595782 0.936492947 1.151390574 1.08275518 1.043138307 1.170884613 1.019851773 1 20.84797178 3.250728708 24.99785893 1.089942524 0.951271269 0.457747582 0.063094625 165.6247714 340253.7803 0.01641219 0.022061901 1781.265712 -3.250728708 -0.138671254 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR 38 1 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ;; 270.68 1.64E-76 366101000 266880 314134 246952 305126 238427 275427 253697 305436 195083 FALSE TRUE 254265.1113 346144.6117 258274.9935 274454.1548 280008.5933 265888.8939 214990.8632 278690.4046 225335.4753 1.128384738 1.536130125 1.146179904 1.217980233 1.242629874 1.179969082 0.954092394 1.23677998 1 17.78171493 2.374731314 0.908849232 1.048753333 1.306669572 0.270412369 0.134333782 0.63399599 1.027112172 0.092443147 0.05960845 236.9907054 -2.374731314 0.257916238 TYHTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYHTEK 6 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 ; 87.989 0.051813 104418000 163764 160958 121156 182818 137253 152023 180616 141931 136312 FALSE TRUE 156023.2003 177359.8032 126711.1224 164440.7873 161189.8797 146758.4054 153059.712 129502.7692 157450.5688 0.990934498 1.126447523 0.804767639 1.044396274 1.023749111 0.932091935 0.972112792 0.822497945 1 17.26453944 3.492313329 0.56489836 0.936158862 1.056210532 0.069592421 0.093584978 2.54911893 1.508442102 0.061109587 0.172208378 3106.800236 -3.492313329 0.12005167 TYIPPKGETK ddPTM_SK-BR-3_Trastuzumab_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 ; 113.47 0.001353 1132940000 1435240 1128770 1229290 1490200 937840 1494190 1716520 1646110 1101940 FALSE TRUE 1367399.05 1243792.946 1285654.162 1340402.265 1101398.999 1442445.826 1454633.348 1501967.882 1272823.227 1.074303973 0.977192213 1.010080689 1.053093812 0.865319689 1.133264852 1.14284004 1.180028656 1 20.27960064 TYLGEEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 117.7 0.0017788 1288300000 656705 564530 634831 778236 601345 705596 911430 798790 689340 FALSE TRUE 625663.8561 622056.2488 663938.6293 700006.2387 706219.3776 681161.0336 772374.6139 728843.7129 796239.3265 0.785773618 0.78124281 0.833843051 0.879140499 0.886943604 0.855472734 0.970028217 0.915357592 1 19.6028426 2.75131901 0.326076733 1.004446002 0.728446286 0.852668457 0.02718703 0.660733484 0.142722224 0.032200731 0.065844232 564.0518265 -2.75131901 -0.275999716 TYLPDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYLPDFR 7 0 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 86.113 0.047262 91893000 198120 174790 164970 183730 207060 177720 237880 191980 226210 FALSE TRUE 188755.2602 192601.2997 172534.0377 165261.1113 243171.1984 171565.5118 201587.037 175169.2135 261289.4915 0.722398973 0.73711843 0.660317553 0.632482808 0.930658164 0.656610838 0.771508398 0.670402826 1 17.99528958 -1.987820907 2.405137252 1.256065896 0.726049803 0.51202455 0.085023382 7841296.51 3227567.535 11143188.65 0.018970359 0.010284403 1.987820907 -0.530016093 TYQEHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 TYQEHK 6 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 106.43 0.03213 1318500000 2966550 2348950 2184550 2723390 1889020 2502660 3111450 2935600 2362630 FALSE TRUE 2826327.061 2588310.676 2284713.778 2449629.663 2218464.49 2415992.257 2636741.157 2678543.301 2729014.594 1.035658463 0.948441493 0.837193683 0.897624245 0.812917782 0.885298401 0.966188002 0.981505672 1 21.37994868 1.579112978 4.618516252 0.985936546 0.912301004 0.272926685 0.060781692 0.288662037 13.54644612 0.040563032 0.01813084 37.94136735 -1.579112978 -0.073635542 TYQLVYFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYQLVYFLDK 10 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 161.62 1.63E-05 36052000 211830 163170 121260 146330 164030 137060 226230 197450 154830 FALSE TRUE 201817.2157 179797.2085 126819.8909 131620.6304 192636.7801 132313.5778 191714.4585 180160.2313 178840.2456 1.128477625 1.005350937 0.709123891 0.735967623 1.077144461 0.739842295 1.071987224 1.007380809 1 17.44831191 1.616635411 24.99999998 1.029764979 0.921237684 0.134207899 0.145191293 1.679924721 4775.783968 0.071815945 0.039060615 41.36522695 -1.616635411 -0.108527296 TYS(ph)APAINAIQVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYSAPAINAIQVPK 14 0 Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 T(0.008)YS(0.992)APAINAIQVPK 179.56 1.94E-06 26979000 45315 55509 40822 59453 28613 40880 43651 48605 29840 TRUE FALSE 43173.04976 61165.43021 42693.72908 53476.67149 33603.09814 39464.31535 36991.23824 44348.88853 34467.4348 1.252575076 1.774586086 1.238668596 1.551512951 0.974923093 1.144973961 1.073222839 1.28668956 1 15.07294631 2.743187274 24.98339364 1.102219242 1.473311405 0.5180299 0.171274592 287.9434356 1554861.417 0.049321757 0.050750258 553.5887738 -2.743187274 0.371092164 TYS(ph)APAINAIQVPKPFSGPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSAPAINAIQVPKPFSGPVR 21 1 Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 T(0.046)YS(0.954)APAINAIQVPKPFSGPVR;T(0.005)YS(0.995)APAINAIQVPKPFSGPVR 182.66 2.78E-17 944830000 750330 589820 716960 799050 589620 692850 873280 800830 649600 TRUE FALSE 714863.3879 649923.3286 749833.3252 718727.9759 692449.5413 668856.4308 740045.0971 730705.0797 750336.6503 0.952723538 0.86617564 0.999329201 0.95787401 0.922851817 0.89140845 0.986284086 0.973836317 1 19.5171785 1.634848679 8.120971985 0.985510044 0.92917825 0.330981237 0.036664431 0.134748831 18.64071971 0.018431279 0.00941918 43.13687489 -1.634848679 -0.056331794 TYS(ph)FEQPWPNAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.033)YS(0.967)FEQPWPNAR;T(0.002)YS(0.998)FEQPWPNAR;TYS(1)FEQPWPNAR 207.8 7.79E-08 393937000 499810 419390 393828 549490 443960 450740 503280 437650 444090 TRUE FALSE 476184.9718 462126.3178 411885.4033 494254.2212 521386.4834 435130.7608 426495.3926 399327.0459 512957.2091 0.928313246 0.900906176 0.802962501 0.963538893 1.016432705 0.848278868 0.831444388 0.77848023 1 18.96847896 TYS(ph)GPMNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSGPMNK 8 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 T(0.005)YS(0.995)GPMNK;TYS(1)GPMNK 91.549 0.013016 385590000 886160 737370 706980 906620 587650 826730 885580 871020 611600 TRUE FALSE 844272.973 812508.8413 739395.7323 815484.8351 690135.9739 798100.1328 750468.5062 794748.8712 706443.8044 1.195102806 1.150139383 1.046644797 1.154352024 0.976915601 1.129743269 1.06231876 1.124999421 1 19.43021528 3.920516697 3.438362945 1.075647513 1.181423677 0.368586503 0.056213738 0.215976007 4.921884252 0.012869055 0.026076768 8327.539423 -3.920516697 0.105776164 TYS(ph)MICLAIDDDDKTDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSMICLAIDDDDKTDK 17 1 Q8IUC4;Q8IUC4-2 Q8IUC4 RHPN2 Rhophilin-2 1 T(0.021)YS(0.979)MICLAIDDDDKTDK;T(0.017)YS(0.983)MICLAIDDDDKTDK 159.74 1.92E-09 137439000 218790 200519 211780 260920 101231 293630 245360 273360 83970 TRUE FALSE 208448.2303 220952.1141 221490.3225 234691.8259 118885.6543 283461.5195 207925.8257 249423.1492 96991.63874 2.14913608 2.278053211 2.28360223 2.419711935 1.225730959 2.922535624 2.143750001 2.57159434 1 16.56557276 -1.410174549 10.27748232 0.999998921 2.244083292 0.455620836 0.429113478 9.29E-06 5.33E-07 0.363943976 0.085782344 0.038888881 1.410174549 1.24408437 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR 33 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 75.261 0.0014775 148253000 925060 579140 924710 852340 666730 968910 1266310 1110220 767890 FALSE TRUE 881334.2471 638155.0244 967108.8682 766661.1639 783007.5009 935356.4038 1073111.152 1013003.251 886970.4594 0.993645547 0.719477202 1.090350708 0.864359298 0.882788702 1.054551923 1.209861209 1.142093562 1 19.75852653 2.098189326 3.923290236 1.139354037 0.898073792 0.438835207 0.107702123 0.170842119 4.961238783 0.041126688 0.028763237 125.3687588 -2.098189326 -0.241280246 TYSS(ph)PGSFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSSPGSFK 9 0 Q8N3Z6 Q8N3Z6 ZCCHC7 Zinc finger CCHC domain-containing protein 7 1 TYS(0.012)S(0.987)PGSFK;TYS(0.001)S(0.998)PGSFK 112.13 0.0021336 81743000 569270 539110 556010 629630 406840 565260 636210 652890 506040 TRUE FALSE 542361.7353 594045.9219 581503.6085 566338.3962 477792.7672 545684.9045 539144.4797 595719.4904 584514.0987 0.927884779 1.01630726 0.994849585 0.968904595 0.817418721 0.933570132 0.922380625 1.019170439 1 19.1568783 1.231994495 24.99499916 1.009585256 0.944179295 0.224544799 0.053214983 289.1358101 1100590.656 0.048809216 0.013348483 17.06060761 -1.231994495 -0.065405961 TYSSS(ph)LKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSSSLKR 8 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 TYS(0.003)S(0.104)S(0.894)LKR;TYS(0.002)S(0.019)S(0.979)LKR 107.21 0.0024793 1121230000 1145860 946030 909950 1306870 760540 1217070 1441820 1156500 931030 TRUE FALSE 1091697.469 1042431.533 951672.1076 1175500.945 893177.9352 1174922.561 1221843.878 1055230.729 1075409.377 1.015145945 0.969334613 0.88493938 1.093072991 0.83054691 1.092535164 1.136166286 0.98123631 1 20.03645453 TYSYLTPDLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYSYLTPDLWK 11 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ; 182.71 1.32E-05 486450000 2363400 2006980 1431100 1613190 2007610 1641390 2737600 2123330 1988930 FALSE TRUE 2251686.766 2211493.544 1496717.351 1451029.076 2357736.548 1584548.253 2319928.841 1937399.969 2297363.106 0.980117927 0.962622555 0.651493596 0.631606328 1.026279451 0.689724775 1.00982245 0.843314652 1 21.13154747 -0.3538283 7.884744813 1.000002534 0.863932538 0.084257223 0.149353557 0 0 0.140910225 0.033212859 0.442763386 0.3538283 -0.136069996 TYT(ph)HEVVTLWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.024)YT(0.976)HEVVTLWYR;T(0.039)YT(0.961)HEVVTLWYR 185.32 4.85E-05 397130000 640896 585362 519335 599898 513164 612039 691320 649348 419046 TRUE FALSE 610602.1162 645011.0533 543147.0234 539595.1133 602659.6391 590843.936 585846.437 592487.6467 484029.5135 1.261497696 1.332586207 1.122136168 1.114797958 1.24508862 1.220677499 1.210352718 1.224073388 1 18.88473549 -5 0.184685988 0.083650934 1.267657989 0.518970938 0.06427874 114.1239669 1.10741353 38.57675441 0.198230209 1.00E-05 5 1.184007055 TYTAYVDLEKDFAAEVVHPGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYTAYVDLEKDFAAEVVHPGDLK 23 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 74.579 0.010955 56551000 212070 173780 196250 219560 125880 226380 229820 243510 122480 FALSE TRUE 202045.8714 191488.3796 205248.2566 197489.4117 147833.4321 218540.4038 194756.7381 222186.9735 141473.5729 1.428152745 1.353527558 1.45078867 1.395945601 1.044954398 1.544743654 1.376629812 1.570519278 1 17.11017306 -2.138006547 2.559473589 0.118940931 1.390640333 0.432623203 0.142294624 1695810.173 1530506.75 8807617.808 0.031654513 0.007277688 2.138006547 1.271699402 TYWNDSCGEDMEAS(ph)DYELEDETRPAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 TYWNDSCGEDMEASDYELEDETRPAKR 27 2 P30291;P30291-2 P30291 WEE1 Wee1-like protein kinase 1 TYWNDSCGEDMEAS(1)DYELEDETRPAKR 179.85 9.84E-18 58987000 58159 41233 48946 48904 42636 53317 63069 55268 54117 TRUE FALSE 55409.93933 45434.68958 51190.22251 43988.07701 50071.7049 51470.61892 53446.66571 50428.44093 62509.18797 0.886428718 0.726848181 0.818923172 0.703705782 0.801029521 0.823408855 0.855020957 0.806736459 1 15.93178064 0.204127582 0.577065892 1.01005856 0.788876591 0.584352362 0.052899402 2.070112092 0.946476469 0.101255495 0.021756966 1.600027996 -0.204127582 -0.221181969 TYYYNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TYYYNNR 7 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 138.25 0.006524 322220000 317790 244790 238540 260170 287500 245160 331110 268000 299400 FALSE TRUE 302768.6965 269734.3793 249477.2949 234017.2173 337639.909 236670.0477 280593.0882 244532.4992 345829.4229 0.875485648 0.779963651 0.721388287 0.676683943 0.97631921 0.684354864 0.811362683 0.707089921 1 18.39970109 -0.965356981 4.979678309 1.000001523 0.783837148 0.358246313 0.092730183 1.41E-06 2.94E-07 0.081035644 0.01910015 0.108303631 0.965356981 -0.216164374 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 344.52 2.59E-96 216040000 191570 136620 166350 192980 162150 158120 181430 172820 192720 FALSE TRUE 182514.8658 150541.7333 173977.312 173581.2838 190428.9087 152644.2648 153749.5213 157686.9646 222606.0333 0.819900804 0.676269781 0.781548054 0.779768999 0.855452594 0.685714859 0.690679938 0.708367883 1 17.76413317 -1.343741715 3.273840527 1.00178961 0.745382263 0.628265878 0.060422629 22441492.73 31885411.24 392972.2357 0.015093899 0.045316701 1.343741715 -0.256407347 VAALFPALRPGGFQAHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAALFPALRPGGFQAHYR 18 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 0 134.9 5.74E-06 112870000 127600 109400 95383 112980 106790 99264 111660 103690 88881 FALSE TRUE 121568.6009 120547.9844 99756.4049 101623.0358 125414.1422 95826.46279 94624.21622 94610.3539 102664.2115 1.184138066 1.174196758 0.971676531 0.989858435 1.221595533 0.933396958 0.921686485 0.921551459 1 16.64757382 3.88052492 0.429908367 0.937548492 1.286297239 0.395561351 0.089676033 2.295074547 0.566132613 0.075434798 0.384228713 7594.950017 -3.88052492 0.348748747 VAAQSPPS(ph)PASAEALLPALPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQS(0.001)PPS(0.998)PAS(0.001)AEALLPALPLR;VAAQSPPS(0.663)PAS(0.337)AEALLPALPLR 204.21 1.25E-22 67995000 88228 72169 76479 88883 94724 82343 86747 86259 98537 TRUE FALSE 84057.63729 79523.10315 79985.6378 79948.31197 111243.8356 79491.44126 73512.15193 78705.70467 113817.6147 0.738529247 0.698688892 0.702752715 0.702424771 0.977386812 0.698410711 0.645876758 0.691507241 1 16.79636432 -2.230105455 2.228128638 1.887798556 0.727353577 0.464451464 0.090339455 5375818.088 766564.5396 24133963.69 0.023023134 0.005887007 2.230105455 -1.160444979 VAAYDKLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VAAYDKLEK 9 1 P35579 P35579 MYH9 Myosin-9 0 ;; 97.456 0.0060909 2673210000 5309340 3923810 3635470 4206830 3152300 4387300 5471940 4939680 3567820 FALSE TRUE 5058378.02 4323650.7 3802159.895 3783951.456 3702060.122 4235366.701 4637095.054 4507135.432 4121099.304 1.22743415 1.049149846 0.922608172 0.918189827 0.898318592 1.027727407 1.125208279 1.093673095 1 21.9745978 4.371689948 2.276095928 1.004412633 1.221928467 0.47909766 0.074049337 0.326692936 3.057299502 0.021976585 0.103553165 23533.68564 -4.371689948 0.217515833 VACAEEWQESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VACAEEWQESR 11 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 171.7 3.31E-05 303860000 127334 116063 110401 149123 121605 144606 143210 140052 148941 FALSE TRUE 121315.1742 127889.9517 115462.9951 134132.8727 142812.8735 139598.258 121360.6843 127788.3044 172038.0096 0.705164948 0.743381954 0.671148168 0.779669987 0.830123958 0.811438462 0.705429484 0.742791112 1 17.39236782 -5 0.297464329 3.063542087 0.73241251 0.725143524 0.048659476 146.6096215 1.362045262 188.5400464 0.050895998 1.00E-05 5 -2.331129577 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR 230.32 2.26E-33 9093340000 6802690 5173764 5535889 6361980 3449147 6525600 7230390 8068410 4376343 TRUE FALSE 6481140.325 5700976.434 5789714.986 5722461.683 4050677.145 6299616.836 6127261.21 7361897.247 5055003.921 1.282123699 1.127788726 1.145343323 1.13203902 0.801320277 1.246214035 1.212117994 1.456358365 1 22.26928078 -0.221973821 7.502172757 1.000001226 1.170440238 0.100930544 0.163935719 0 0 0.151967383 0.035819056 0.599827233 0.221973821 0.170439012 VADEISFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADEISFR 8 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 0 83.313 0.042456 34755000 117420 103740 98739 113790 140440 104930 134240 126950 135400 FALSE TRUE 111869.7893 114311.2239 103266.2808 102351.613 164932.6915 101296.2478 113759.2225 115833.585 156397.1405 0.715293061 0.730903542 0.66028241 0.654434043 1.054576133 0.647686061 0.727374057 0.740637486 1 17.25485461 -2.253938362 1.989691022 1.837958188 0.738225357 0.327184568 0.116463792 4749447.321 735691.8223 17873080.77 0.026271923 0.005572648 2.253938362 -1.099732831 VADIGLAAWGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VADIGLAAWGR 11 0 P23526 P23526 AHCY Adenosylhomocysteinase 0 ; 128.36 0.00062212 339600000 639750 484720 437610 496920 579090 467990 672520 543360 626120 FALSE TRUE 609510.2854 534113.5191 457674.8514 446968.6575 680083.1127 451783.389 569914.7223 495780.5179 723215.4918 0.842778248 0.738526103 0.632833307 0.618029706 0.940360267 0.624687101 0.788028919 0.685522536 1 19.46406606 -1.729005129 2.436055881 1.057023889 0.73921554 0.396296279 0.103048291 7843024.09 5598949.377 2708110.62 0.023800032 0.018663577 1.729005129 -0.317808349 VADKIQLINNMLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADKIQLINNMLDK 14 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 147.24 7.38E-06 140830000 596290 614290 490960 664370 364020 629820 598930 598360 385260 FALSE TRUE 568104.5534 676886.8494 513471.0016 597586.2654 427504.9727 608009.1755 507552.2284 545964.4263 445004.1532 1.276627531 1.521079847 1.15385665 1.342877951 0.960676366 1.366300002 1.140556161 1.226874901 1 18.76345928 7.999999986 0.064299938 0.680158313 2.488160925 0.285849179 0.142729494 308.7438935 1.475850376 7.880579812 51.40513213 99999996.69 -7.999999986 1.808002612 VADMALHYANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VADMALHYANK 11 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 114.83 0.0012043 2129670000 5263600 6050100 3782700 4763300 3615000 4576900 4775200 4878200 3092600 FALSE TRUE 5014800.059 6666612.068 3956140.537 4284484.034 4245454.855 4418400.805 4046655.537 4451038.947 3572184.613 1.403846834 1.866256308 1.107484905 1.199401626 1.188475769 1.236890386 1.132823741 1.246027132 1 21.76837521 3.725332534 24.99913108 1.169560869 1.635051574 0.69779367 0.130168205 339.9354394 642427.963 0.031807669 0.049601615 5312.910922 -3.725332534 0.465490706 VADMALHYANKYNIMLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADMALHYANKYNIMLVR 18 1 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 76.85 0.0087424 7785400 23061 15185 26223 17283 24320 22202 30558 27629 24267 FALSE TRUE 21970.95223 16732.36876 27425.35049 15545.68 28561.4003 21433.13917 25895.81586 25209.65829 28030.20242 0.78383138 0.596940704 0.978421421 0.554604629 1.018950911 0.764644466 0.923854044 0.899374821 1 14.77469454 2.217502204 0.422471031 0.995484589 0.688166438 0.257230991 0.1397169 1.319160305 0.537921189 0.129979741 0.139176316 165.0069374 -2.217502204 -0.307318152 VADNS(ph)FDAKR ddPTM_SK-BR-3_Trastuzumab_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 164.88 3.69E-06 426360000 541550 537520 618420 639340 405040 598270 682500 693050 535670 TRUE FALSE 515952.0047 592293.8991 646775.1687 575072.3285 475678.8478 577551.7599 578372.09 632362.8679 618738.9678 0.833876694 0.957259733 1.04531184 0.929426395 0.768787603 0.933433629 0.934759438 1.022018817 1 19.23897137 1.370556062 3.000560496 1.011801589 0.911894011 0.234997932 0.072791715 0.404490509 6.06840839 0.061111177 0.019340804 23.47232241 -1.370556062 -0.099907578 VADNSFDAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADNSFDAKR 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 100.69 0.0061633 228860000 200660 145700 165840 145020 154600 140990 189000 150760 180200 FALSE TRUE 191175.1995 160546.9956 173443.928 130442.3141 181562.1911 136107.4809 160164.5788 137558.6552 208144.4957 0.918473481 0.771324724 0.833286162 0.626691153 0.872289178 0.653908625 0.769487458 0.660880581 1 17.66722588 4.717065362 1.089005587 0.754679091 0.998375554 0.126247299 0.113152555 2.614225821 2.610781171 0.028901492 0.731450344 52127.31579 -4.717065362 0.243696462 VADPDHDHTGFLT(ph)EY(ph)VATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 2 VADPDHDHTGFLT(1)EY(1)VATR 178.22 4.12E-14 35557000 83756 50171 84330 91374 111160 76162 89945 61250 40635 TRUE FALSE 79797.01987 55283.48194 88196.61391 82188.91192 130546.2688 73524.49084 76222.2383 55886.62529 46936.46827 1.700107034 1.177836424 1.879063704 1.75106724 2.781339833 1.566468325 1.623944901 1.190686632 1 15.51842167 1.228705484 2.071366027 1.00299971 1.760549303 0.349016256 0.399418453 0.395025523 2.936527564 0.38429272 0.111222003 16.93189176 -1.228705484 0.757549593 VADPDHDHTGFLT(ph)EYVATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.691)EY(0.308)VAT(0.001)R 204.17 1.73E-15 480030000 489740 366220 468530 487890 468490 379490 418850 309870 59385 TRUE FALSE 466590.9608 403538.2344 490012.5639 438846.3703 550194.5077 366348.1661 354946.7398 282736.1401 68594.1225 6.802200301 5.882985592 7.143652343 6.397725552 8.021015323 5.340809865 5.174594074 4.12187123 1 16.06579734 0.998611533 0.926732765 1.036567663 6.682978907 0.88198516 0.667407743 0.186303326 0.345455076 0.603047873 0.206834782 9.968080415 -0.998611533 5.646411244 VADPDHDHTGFLTEY(ph)VATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.038)EY(0.962)VATR;VADPDHDHTGFLT(0.018)EY(0.981)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLT(0.005)EY(0.995)VATR 239.75 1.56E-23 3322370000 1698870 1440790 1625910 1848750 1785790 1302210 1659220 1236238 175418 TRUE FALSE 1618567.782 1587608.139 1700459.582 1662910.138 2097231.211 1257114.141 1406075.515 1127986.447 202620.9275 7.988157007 7.835361127 8.392319601 8.207000915 10.35051629 6.204266047 6.939438746 5.566978993 1 17.62842366 0.8100453 0.854479781 1.00386254 8.303170678 0.856524441 0.936002804 0.289526964 0.422386306 0.853966853 0.295517517 6.457215785 -0.8100453 7.299308138 VADPDHDHTGFLTEYVATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;; 176.49 3.10E-13 1271485000 762116 727790 707605 824131 834080 763855 902256 756497 113388 FALSE TRUE 726092.287 801952.6284 740049.3892 741287.7861 979543.2879 737402.5098 764600.2761 690254.1122 130971.6319 5.543889744 6.123101748 5.650455585 5.659911045 7.479049268 5.630246023 5.837907529 5.270256635 1 16.99889484 0.464581774 1.370851259 0.998565534 6.00585696 0.886833148 0.556164237 0.771192862 1.670338333 0.500543341 0.147231693 2.914618884 -0.464581774 5.007291426 VADSSKGPDEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VADSSKGPDEAK 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 68.171 0.04869 130610000 241700 182200 207460 254500 148830 237230 309370 281010 172610 FALSE TRUE 230275.32 200766.3871 216972.2462 228917.1765 174785.9049 229014.6656 262169.9245 256403.2747 199377.4772 1.154971581 1.006966233 1.088248528 1.14815966 0.876658223 1.148648628 1.314942531 1.286019255 1 17.60514292 2.000752339 24.99999611 1.23443457 1.059065395 0.240476313 0.114540734 26.48903464 880196.9181 0.039130669 0.028644695 100.1733827 -2.000752339 -0.175369174 VADWTGATYQDKR ddPTM_SK-BR-3_Trastuzumab_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 ; 149.32 7.01E-05 767160000 893500 739160 836560 894470 723930 919790 1086600 1018140 936010 FALSE TRUE 851266.0257 814481.2444 874917.1035 804556.1762 850183.1628 887937.4417 920819.2132 928986.2641 1081161.65 0.787362394 0.753339007 0.809238011 0.744159003 0.786360821 0.821280926 0.851694298 0.859248257 1 20.04415081 0.879004046 0.578279631 1.003427765 0.768388466 0.920674929 0.02042585 0.238276264 0.182858204 0.020806993 0.008736904 7.568399461 -0.879004046 -0.235039299 VAEAHVPNFIFDEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAEAHVPNFIFDEFR 15 0 Q12768;E7EQI7 Q12768 KIAA0196 WASH complex subunit strumpellin 0 111.43 0.00084286 48619000 34107 31686 34645 39549 34152 37298 38422 37690 35197 FALSE TRUE 32494.8297 34914.83942 36233.50752 35573.45938 40108.09799 36006.36091 32560.01823 34389.66379 40655.171 0.79927913 0.858804392 0.891239826 0.875004545 0.986543581 0.885652674 0.80088258 0.845886586 1 15.31115124 VAEEHAPSIVFIDEIDAIGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTK 21 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 229.62 1.23E-25 89697000 111290 96037 93467 119031 81545 113517 126217 121381 83128 FALSE TRUE 106029.5423 105823.2795 97752.5544 107065.7777 95766.42218 109585.8778 106960.2785 110752.2362 96019.06568 1.104255093 1.102106949 1.018053589 1.115047069 0.997368819 1.141292899 1.113948337 1.153440052 1 16.55103328 VAEEHAPSIVFIDEIDAIGTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTKR 22 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 134.06 5.27E-06 50096000 82124 70244 90211 85250 68047 94023 111658 103355 88412 FALSE TRUE 78242.16127 77401.94346 94347.26358 76680.50804 79914.37526 90766.95993 94622.52136 94304.68828 102122.4814 0.766160009 0.757932459 0.923863798 0.750868046 0.782534601 0.888804881 0.926559167 0.923446894 1 16.63994097 1.766971114 0.881617019 0.988301403 0.785578734 0.646384983 0.05246414 0.336873173 0.492732212 0.045321686 0.019629897 58.47511902 -1.766971114 -0.202722669 VAEFHTELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VAEFHTELER 10 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;; 178.08 2.26E-06 617580000 1164450 1198400 1097350 1249470 1076650 1142870 1152300 1232960 889140 FALSE TRUE 1109408.756 1320518.322 1147664.583 1123870.902 1264417.419 1103292.125 976495.4716 1124995.486 1027023.29 1.080217719 1.285772519 1.117466949 1.094299333 1.231147756 1.074262031 0.950801682 1.095394327 1 19.97003747 2.025400919 6.562022723 1.010274117 1.165625768 0.480051011 0.070194537 0.12699127 19.31302481 0.025806457 0.018518052 106.0232028 -2.025400919 0.155351651 VAEIEHAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VAEIEHAEK 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 163.88 6.27E-05 2729790000 10533000 10162800 8829300 11858000 6525400 10130100 10600900 10566500 5879500 FALSE TRUE 10035125.96 11198400.87 9234132.138 10666011.31 7663427.694 9779292.097 8983538.006 9641241.243 6791262.832 1.477652421 1.648942347 1.359707667 1.570549039 1.128424548 1.439981391 1.322808177 1.419653676 1 22.69524844 -3.216328017 0.095508938 4.09E-18 1.809377067 0.537903058 0.131035119 85.31676958 0.830761734 20.29296685 2.636961894 0.000607676 3.216328017 1.809377067 VAEKLDEIYVAGLVAHSDLDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;;; 229.99 1.42E-26 926821700 2499985 2044401 2360605 2664871 1900105 2539542 3010512 2824348 1802873 FALSE TRUE 2381815.664 2252727.786 2468841.074 2396993.104 2231482.71 2451597.024 2551203.103 2577033.116 2082453.337 1.143754638 1.081766274 1.185544488 1.151042888 1.071564328 1.177263846 1.225094967 1.237498613 1 20.98985274 2.034783371 24.14362772 1.184701183 1.125801675 0.00119055 0.072986446 232.4290131 161330.9289 0.024554906 0.01813488 108.3386378 -2.034783371 -0.058899508 VAELALSLSST(ph)SDDEPPSSVSHGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLSS(0.005)T(0.945)S(0.05)DDEPPSSVSHGAK;VAELALSLSS(0.002)T(0.58)S(0.418)DDEPPSSVSHGAK 247.04 2.14E-38 215420000 175538 149863 171030 198501 169951 193185 239850 230780 189961 TRUE FALSE 167240.6666 165134.2101 178871.8947 178547.3024 199590.4006 186494.955 203256.4774 210571.6798 219419.1817 0.762197112 0.752596964 0.815206279 0.813726954 0.909630594 0.849948275 0.92633869 0.959677628 1 17.74333013 2.421427396 0.403753477 1.005305331 0.72440266 0.910248224 0.024760717 0.310894517 0.111588125 0.024434913 0.031554457 263.8927121 -2.421427396 -0.280902671 VAELALSLSSTS(ph)DDEPPSSVSHGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLS(0.001)S(0.016)T(0.132)S(0.851)DDEPPSSVSHGAK;VAELALS(0.001)LS(0.006)S(0.026)T(0.133)S(0.834)DDEPPSSVSHGAK;VAELALSLSS(0.012)T(0.112)S(0.876)DDEPPSSVSHGAK 210.91 1.02E-25 191970000 204021 179191 208869 239324 187620 208330 263515 263263 217463 TRUE FALSE 194377.3317 197450.7666 218445.8502 215266.6968 220340.8686 201115.4799 223310.947 240210.2961 251186.0514 0.77383808 0.786073771 0.869657567 0.857000998 0.877201848 0.800663408 0.889026065 0.95630428 1 17.93839683 5.822676416 0.039775048 1.490066678 5.86E-10 0.762539837 0.034831994 233.2017679 1.080633162 13.56139509 29.47247285 664777.6592 -5.822676416 -1.490066677 VAEYAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAEYAR 6 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 118.42 0.050903 115200000 214280 149830 161190 183300 220350 173630 221280 199160 257010 FALSE TRUE 204151.4091 165097.8473 168580.7209 164874.3358 258778.9702 167617.1496 187519.6719 181720.4946 296865.7982 0.68768922 0.556136303 0.567868451 0.555383398 0.87170355 0.564622636 0.63166479 0.612130113 1 18.17945136 -1.817725374 2.356984358 1.138316516 0.627956493 0.598202897 0.09503894 6165209.508 3703834.602 4843753.576 0.022225024 0.015215094 1.817725374 -0.510360022 VAGGPQMIQLSLDGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAGGPQMIQLSLDGKR 16 1 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 139.21 3.88E-06 551270000 428690 321150 407170 353020 955800 294440 469080 396370 852410 FALSE TRUE 408426.6733 353875.5501 425839.1472 317533.7589 1122491.217 284243.469 397513.2308 361661.7415 984597.3893 0.414815921 0.359411424 0.432500789 0.322501118 1.140050979 0.288690049 0.403731754 0.36731942 1 19.90917439 -1.621902408 2.835590463 1.045951427 0.456454105 0.320380418 0.244004166 77057816.81 76224290.35 26212918.84 0.055292412 0.023883479 1.621902408 -0.589497321 VAGHPLAQNER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VAGHPLAQNER 11 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;; 129.89 0.0002356 1088890000 929170 678500 562540 677890 1275550 637244 1072870 865250 1317900 FALSE TRUE 885249.9755 747639.9214 588333.0154 609747.2093 1498005.516 615176.0805 909183.9769 789484.123 1522273.201 0.581531603 0.491133865 0.386483198 0.400550446 0.984058259 0.404116738 0.597254143 0.518621836 1 20.53779587 -5 0.297283849 4.724890799 0.51899348 0.409238398 0.171850687 256.7324696 2.385936583 595.1817267 0.161406311 1.00E-05 5 -4.20589732 VAGHPNIVINNAAGNFISPTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAGHPNIVINNAAGNFISPTER 22 0 Q16698-2;Q16698;E5RJD2;E5RJG7;E5RFV2 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ; 305.83 2.49E-56 2148500000 1060330 814190 949930 915230 1036720 735310 955380 977340 981920 FALSE TRUE 1010210.302 897156.8867 993485.2301 823229.3416 1217523.64 709846.0303 809619.2342 891758.9284 1134191.139 0.890687881 0.791010312 0.875941626 0.72582946 1.073473067 0.625861027 0.713829624 0.78625101 1 20.11323236 2.189874908 24.99999432 0.748238196 0.855776211 0.075397304 0.12956669 210.2909764 107982.5214 0.043174438 0.031886492 154.8370571 -2.189874908 0.107538015 VAHALAEGLGVIACIGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAHALAEGLGVIACIGEK 18 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 276.22 4.29E-39 2353400000 2842070 1882890 2286730 2536810 2172290 2594290 3602500 2916930 2601780 FALSE TRUE 2707730.984 2074758.632 2391578.832 2281805.039 2551136.688 2504449.087 3052872.461 2661508.146 3005250.754 0.901000018 0.690377876 0.795800094 0.759272761 0.84889312 0.833357777 1.015846167 0.885619325 1 21.51905394 1.974825115 2.419150558 0.967075377 0.78992777 0.57538445 0.065194047 0.196277548 2.129820636 0.033270523 0.017880805 94.36807903 -1.974825115 -0.177147608 VAHFLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAHFLEK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 134.44 0.0031745 1535930000 3164900 2703000 2415200 2969700 2548900 2815100 3618200 3150700 2530800 FALSE TRUE 3015301.449 2978438.773 2525939.309 2671180.114 2993427.353 2717612.381 3066177.137 2874808.005 2923263.538 1.031484644 1.018874533 0.864081967 0.913766439 1.024001878 0.929650148 1.048888373 0.983424165 1 21.47914847 1.732888642 25 1.01351348 0.971808093 0.127155522 0.055368605 1.477228083 6460.33217 0.027092784 0.015024467 54.06156855 -1.732888642 -0.041705387 VAHLALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAHLALK 7 0 Q5VWC4;P55036-2;P55036;A6PVX3 Q5VWC4 PSMD4 26S proteasome non-ATPase regulatory subunit 4 0 88.591 0.018495 215850000 519830 364220 228490 266580 481960 306960 578200 420070 449850 FALSE TRUE 495258.6661 401334.4321 238966.4925 239782.8719 566013.6714 296329.8982 489984.9706 383286.4439 519610.4405 0.953134555 0.772375612 0.459895479 0.461466617 1.089303885 0.570292425 0.94298523 0.737641922 1 18.98707089 1.664032494 12.10758303 0.879414242 0.736897947 0.130831616 0.208524354 0.304327726 56.77456636 0.096913041 0.052897381 46.13520919 -1.664032494 -0.142516294 VAHSFNCTPIEGMLSHQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAHSFNCTPIEGMLSHQLK 19 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 270 7.53E-33 1596830000 2026100 1611840 1674980 2062870 1521630 2003150 2249000 1988510 1120090 FALSE TRUE 1930330.268 1776088.329 1751779.49 1855506.388 1787001.79 1933780.413 1905873.744 1814385.523 1293787.837 1.491999085 1.372781749 1.353992857 1.434165893 1.381217028 1.494665786 1.473096044 1.402382579 1 20.30316962 0.946433138 21.85367208 1 1.429546945 0.883403501 0.048677031 1247.479815 508935.4454 0.048113533 0.012028383 8.839610676 -0.946433138 0.429546945 VAIEHLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VAIEHLDK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;;;; 174.52 0.00027147 6355190000 20786100 17763600 17429900 21392500 14351940 19855400 21730800 20951000 14075920 FALSE TRUE 19803582.25 19573731.04 18229078.16 19242085.26 16854913.79 19167802.52 18415367.35 19116419.37 16258741.78 1.21802674 1.203889655 1.121186276 1.183491657 1.036667783 1.17892287 1.132644063 1.17576253 1 23.95471228 -5 0.068754688 0.502709322 1.347362502 0.498397153 0.050374856 254.610795 1.262655721 20.75842052 2.684372669 1.00E-05 5 0.84465318 VAIHNADLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAIHNADLSR 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2 Q8TDM6-4 DLG5 Disks large homolog 5 0 91.855 0.0091777 0 49695 40306 38054 47539 53851 36009 47132 43095 56201 FALSE TRUE 47346.01584 44413.22722 39798.81354 42760.2894 63242.59735 34761.9993 39941.14776 39321.37334 64916.36405 0.729338689 0.684160733 0.613078291 0.658698158 0.974216567 0.535489007 0.61527087 0.605723594 1 15.98629458 -1.994368075 2.691040921 1.312556599 0.676291417 0.426947104 0.117600738 16412681.44 5372118.715 31807633.58 0.027042171 0.010130524 1.994368075 -0.636265182 VAILVDDMADTCGTICHAADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 173.87 3.74E-12 134743000 111208 111175 107034 122625 81975 110585 103191 117085 85826 FALSE TRUE 105951.4182 122503.8589 111941.6148 110298.502 96271.41405 106755.4137 87447.31772 106832.4167 99135.45774 1.068754012 1.235721927 1.129178372 1.112603952 0.971109795 1.076864082 0.882099298 1.077640827 1 16.59711354 2.876285849 2.58846616 0.989837322 1.153166945 0.484151531 0.068652983 0.206329328 2.698609677 0.02136749 0.023124957 752.1177687 -2.876285849 0.163329623 VAKPVVEMDGDEMTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VAKPVVEMDGDEMTR 15 1 P48735;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;; 223.06 1.20E-12 3343630000 4318860 3747160 3515270 3864760 3119917 3254010 3756760 3799400 3305531 FALSE TRUE 4114716.047 4128999.864 3676448.607 3476266.982 3664029.537 3141322.818 3183597.264 3466704.394 3818135.865 1.077676697 1.081417742 0.962890986 0.910461834 0.959638333 0.822737307 0.833809319 0.907957316 1 21.86443701 3.496004818 1.351192751 0.882164286 1.090195003 0.61372018 0.054558547 0.226398033 0.837604095 0.01745156 0.033789116 3133.320488 -3.496004818 0.208030717 VALENDDRS(ph)EEEKYTAVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 198.47 3.86E-16 250990000 356110 315470 331570 379660 248260 353430 396410 406110 271900 TRUE FALSE 339277.386 347616.7517 346772.8125 341495.8555 291556.4654 341190.6305 335930.3739 370548.8555 314064.8633 1.080278075 1.106831079 1.10414393 1.087341805 0.928332009 1.086369952 1.069621002 1.179848174 1 18.26070302 -0.36973142 0.006222737 2.00E-08 2.103502922 0.05513862 0.064976711 34705.66494 54.19906202 9414.591351 8907.937752 0.42684341 0.36973142 2.103502902 VALS(ph)DDETKETENMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VALSDDETKETENMR 15 1 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR 303.14 1.09E-44 3766510000 4260870 4209450 3933530 4824500 2680340 4667140 4798680 5008130 3208420 TRUE FALSE 4059467.119 4638397.741 4113886.241 4339532.094 3147790.447 4505515.772 4066553.232 4569591.587 3705965.387 1.095387219 1.251603093 1.110071415 1.170958614 0.84938474 1.215746857 1.097299302 1.233036769 1 21.82141798 -2.248948346 2.313525473 0.506782118 1.130925862 0.111059043 0.113470951 5483739.791 1500130.352 14044841.71 0.026620996 0.005637047 2.248948346 0.624143744 VALS(ph)DDETKETENMRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VALSDDETKETENMRK 16 2 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(1)DDETKETENMRK 86.727 0.0059495 103010000 112600 89918 110180 103160 58912 125860 143260 136900 83896 TRUE FALSE 107277.6212 99080.74643 115231.862 92790.16081 69186.23415 121501.4366 121403.0558 124912.3102 96906.1632 1.107025783 1.022440092 1.189107671 0.957525897 0.713950815 1.253805048 1.252789831 1.289002744 1 16.5643008 VALSEPQPERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VALSEPQPERR 11 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1;H7C1K0 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 117.25 0.0014107 700630000 963020 787320 925160 929310 1084940 914690 1172380 986620 1244800 FALSE TRUE 917499.9531 867548.8031 967579.5011 835893.9932 1274153.192 883014.0559 993511.8988 900226.3224 1437837.226 0.638111141 0.603370665 0.672940917 0.581355092 0.886159552 0.614126578 0.690976614 0.626097521 1 20.45546893 -5 0.284651114 3.539718319 0.6401465 0.598519892 0.085930777 153.7771473 1.461352852 231.4124601 0.086596057 1.00E-05 5 -2.89957182 VALTGLTVAEYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VALTGLTVAEYFR 13 0 P06576;H0YH81;F8W0P7 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 145.99 9.79E-05 151190000 90057 76256 65777 67115 99580 68342 107660 71629 89665 FALSE TRUE 85800.18409 84026.5731 68792.94051 60368.47269 116946.7205 65975.2994 91234.48969 65356.78503 103569.7903 0.828428675 0.811303884 0.664218208 0.582877232 1.129158611 0.637012967 0.880898662 0.63104101 1 16.66024373 VALVLSGCGVYDGTEIHEASAILVHLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VALVLSGCGVYDGTEIHEASAILVHLSR 28 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A2R8Y6K9;F2Z2Q0;A0A096LP12 P0DPI2-2 C21orf33 0 ; 83.881 0.0023524 8006700 9717.4 8558.5 9262.9 10899 13671.7 7648.3 12261.5 11184.4 10262.9 FALSE TRUE 9258.07776 9430.62088 9687.613127 9803.411813 16056.04015 7383.437453 10390.78298 10205.03464 11854.41812 0.780981206 0.79553638 0.817215407 0.826983806 1.354435114 0.622842672 0.876532519 0.860863397 1 13.53313723 2.978972339 24.90817474 0.922551738 0.798373024 0.123539119 0.179175825 1731.078666 2050539.76 0.051946318 0.055648157 952.73548 -2.978972339 -0.124178714 VALVTFNSAAHNKPSLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VALVTFNSAAHNKPSLIR 18 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 209.73 2.95E-16 647260000 1773990 1513670 1452240 1734940 1622700 1582170 1977320 1812310 1735990 FALSE TRUE 1690137.008 1667914.694 1518826.64 1560540.535 1905698.366 1527379.056 1675643.518 1653614.529 2005198.463 0.84287767 0.831795318 0.757444547 0.778247422 0.950378928 0.761709668 0.835649712 0.824663772 1 20.9353136 0.136363278 2.015100914 1.00000845 0.823260947 0.508988708 0.054685153 31.87047211 72.39454346 0.04841232 0.01322416 1.36887338 -0.136363278 -0.176747503 VAMHILNNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAMHILNNGR 10 0 P49748;P49748-3;P49748-2;J3KSR4 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ; 109.48 0.0020133 2192200000 1606730 1417220 1359120 1377510 1579410 1141840 1530990 1425340 1378880 FALSE TRUE 1530783.057 1561636.329 1421436.996 1239040.078 1854858.604 1102297.794 1297409.357 1300529.673 1592709.668 0.961118707 0.980490268 0.8924646 0.777944721 1.164593046 0.692089598 0.814592504 0.816551629 1 20.60305187 2.207828302 24.99965128 0.810873485 0.948361813 0.20054125 0.120204524 274.9350406 223648.3532 0.040703199 0.030064582 161.3720447 -2.207828302 0.137488329 VAMSHFEPNEYIHYDLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VAMSHFEPNEYIHYDLLEK 19 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;; 238.65 1.70E-24 656218000 1227300 966500 1008990 1120170 818260 980660 1108520 1135220 395600 FALSE TRUE 1169287.961 1064987.449 1055253.19 1007568.383 960964.2849 946699.4983 939394.9146 1035814.119 456947.6276 2.558910236 2.330655385 2.309352595 2.204997515 2.103007494 2.071789941 2.055804337 2.26681146 1 18.8016693 -1.467861852 0.232908751 1.14E-19 2.489929892 0.907570151 0.126543837 6.223186343 0.271559436 4.112482361 0.240549518 0.034051649 1.467861852 2.489929892 VANILHDDCAFLSAFGDVSKPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VANILHDDCAFLSAFGDVSKPER 23 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 269.57 4.55E-45 462130000 1174970 1008600 990870 1153680 933750 1082450 1339290 1147200 857810 FALSE TRUE 1119431.497 1111377.487 1036302.37 1037709.895 1096595.704 1044964.485 1134956.713 1046745.086 990834.7937 1.12978622 1.121657711 1.04588815 1.047308695 1.106739197 1.05463039 1.145455045 1.056427462 1 19.918285 -5 0.230927491 0.497711389 1.104909797 0.369757586 0.036503733 180.1172871 1.801067022 42.40367975 0.06381159 1.00E-05 5 0.607198408 VANS(ph)PTMVNLLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VANSPTMVNLLLGK 14 0 Q6UB99;A0A087WTN8;A0A2R8Y438 Q6UB99 ANKRD11 Ankyrin repeat domain-containing protein 11 1 VANS(0.998)PT(0.002)MVNLLLGK;VANS(0.797)PT(0.203)MVNLLLGK 146.76 8.62E-06 45280000 172215 152965 163657 181003 149903 178616 196542 194184 177414 TRUE FALSE 164074.7382 168552.3074 171160.8353 162808.2346 176046.0357 172430.4831 166555.9082 177180.2195 204926.457 0.800651808 0.822501447 0.83523054 0.794471524 0.859069338 0.841426166 0.812759419 0.864603927 1 17.64474673 -4.999999984 0.24785126 2.053022275 0.809459447 0.891187694 0.019268159 51.52338369 0.511347746 27.41553831 0.026507986 1.00E-05 4.999999984 -1.243562828 VAPEEHPVLLTEAPLNPK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;;; 334.04 5.26E-75 16078362000 13003542 11493217 11802490 13079899 9285208 12421051 14386105 13524347 9888045 FALSE TRUE 12388890.34 12664388.88 12343645.84 11765082.7 10904545.34 11990906.89 12191240.46 12340083.48 11421432.52 1.084705471 1.108826661 1.080744103 1.030088186 0.954744102 1.049860153 1.067400297 1.080432202 1 23.44524027 3.335202154 4.313861671 1.033927536 1.096327295 0.399042488 0.035434625 0.230403089 7.705876014 0.010484092 0.014297297 2163.725451 -3.335202154 0.062399759 VAPGPSSGSTPGQVPGSSALSS(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VAPGPSSGSTPGQVPGSSALSSPRR 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 VAPGPSSGSTPGQVPGSS(0.002)ALS(0.22)S(0.778)PRR;VAPGPSSGSTPGQVPGS(0.001)S(0.006)ALS(0.372)S(0.621)PRR;VAPGPSSGSTPGQVPGS(0.001)S(0.005)ALS(0.18)S(0.815)PRR 167.34 7.80E-12 663830000 155868 119500 154695 156172 150640 138218 205070 159717 196162 TRUE FALSE 148500.4285 131677.1859 161787.9188 140473.2939 176911.5683 133431.476 173782.8051 145731.3328 226581.8011 0.655394334 0.581146346 0.71403757 0.61996724 0.780784544 0.58888876 0.766976007 0.643173159 1 17.78967246 -5 0.214655639 2.652202972 0.620491622 0.702449072 0.067795838 71.81700256 0.717101526 51.12513769 0.118137401 1.00E-05 5 -2.03171135 VAPPYPHLFSSCSPPGMVLDGS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAPPYPHLFSSCSPPGMVLDGSPK 24 0 Q9BUK6-2;Q9BUK6;Q9BUK6-5;V9GYF2;Q9BUK6-6 Q9BUK6-2 MSTO1 Protein misato homolog 1 1 VAPPYPHLFSSCSPPGMVLDGS(1)PK 82.684 0.0091935 117830000 134530 108200 105930 140800 108130 119370 166410 147420 122320 TRUE FALSE 128171.0335 119225.703 110786.9953 126646.5165 126987.8378 115236.187 141021.0982 134511.1233 141288.7609 0.907156611 0.843844211 0.784117538 0.896366531 0.898782302 0.815607599 0.998105563 0.952029889 1 17.10828718 1.703351249 7.665100871 0.980218678 0.860228967 0.681295612 0.040403999 0.072095439 9.236472849 0.019348789 0.010152225 50.50696231 -1.703351249 -0.119989711 VAPVINNGS(ph)PTILGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.916)PT(0.084)ILGK;VAPVINNGS(0.975)PT(0.025)ILGK;VAPVINNGS(0.985)PT(0.015)ILGK 213.7 2.53E-10 54064000 206660 220322 201261 231668 179372 223277 242072 252012 213990 TRUE FALSE 196891.5914 242773.0623 210489.0159 208380.2925 210654.42 215544.8615 205139.4704 229944.4933 247174.4763 0.796569267 0.982193089 0.85158071 0.843049394 0.852249889 0.872035271 0.829937919 0.930292224 1 17.91517025 0.994113532 5.076890518 0.999861678 0.866644652 0.479308936 0.047917051 0.133355236 12.57749764 0.045296546 0.011449691 9.865373496 -0.994113532 -0.133217025 VAQEQGGHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAQEQGGHPK 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 104.22 0.0027105 118800000 96671 88422 82550 92442 72721 78299 104905 94341 85758 FALSE TRUE 92101.55341 97432.30233 86334.99915 83149.55453 85403.51938 75587.486 88899.81554 86080.00191 99056.91265 0.929784211 0.983599223 0.871569655 0.839411933 0.862166174 0.763071289 0.897462006 0.868995405 1 16.59597004 3.671298541 6.233708994 0.860958086 0.956500119 0.243977341 0.059905411 0.22696374 16.69264145 0.014329083 0.022450034 4691.357628 -3.671298541 0.095542033 VAQGATEKS(ph)PEDKVQIAANEETQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VAQGATEKSPEDKVQIAANEETQER 25 2 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGAT(0.002)EKS(0.998)PEDKVQIAANEETQER;VAQGAT(0.21)EKS(0.79)PEDKVQIAANEETQER;VAQGAT(0.271)EKS(0.729)PEDKVQIAANEETQER;VAQGAT(0.002)EKS(0.998)PEDKVQIAANEETQER;VAQGAT(0.026)EKS(0.974)PEDKVQIAANEETQER 274.91 2.60E-53 573151000 724939 749302 591297 778419 286021 793572 655404 821897 282427 TRUE FALSE 690672.5702 825656.7257 618408.5523 700170.8432 335902.9718 766090.4027 555410.0825 749927.3415 326224.3367 2.117170586 2.530947672 1.895654256 2.146286357 1.029668648 2.348354541 1.702540307 2.298808694 1 18.31550489 -1.612572801 0.153834177 8.73E-17 2.448754382 0.337357887 0.426652947 39.41135157 1.008227179 19.03898848 2.354013581 0.0244021 1.612572801 2.448754382 VAQWMIQQPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAQWMIQQPHK 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ; 143.5 3.72E-05 1385180000 2318890 1952460 1238720 1675350 2148980 1747930 2804400 2187080 2139350 FALSE TRUE 2209280.665 2151417.894 1295516.537 1506940.635 2523761.432 1687398.746 2376537.274 1995567.681 2471109.472 0.894044028 0.870628322 0.524265134 0.609823503 1.021307012 0.682850665 0.961728851 0.807559399 1 21.23672749 1.699787182 10.34441873 0.91212118 0.783327203 0.185264463 0.150933032 0.241059103 47.16201357 0.071910927 0.038933043 50.09416966 -1.699787182 -0.128793977 VARPTSSEVDRFS(ph)PSGSVVPLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VARPTSSEVDRFSPSGSVVPLTER 24 2 Q5TC79;Q5TC79-2 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 VARPTSSEVDRFS(0.813)PS(0.183)GS(0.003)VVPLTER;VARPT(0.004)S(0.004)S(0.004)EVDRFS(0.987)PS(0.001)GSVVPLTER 95.878 0.003521 189833000 227712 207895 219171 242653 194695 234367 252590 233040 231232 TRUE FALSE 216948.505 229079.7369 229220.2071 218261.0594 228649.7464 226250.812 214052.7564 212633.7822 267090.2776 0.812266575 0.857686543 0.858212471 0.817180848 0.856076636 0.8470949 0.80142474 0.796112027 1 18.02696794 -1.596326161 7.248598461 1.000199525 0.831706421 0.836334276 0.023525615 7.66E-05 4.26E-06 0.02299255 0.005413039 0.025332254 1.596326161 -0.168493104 VAS(ph)EEEEVPLVVYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VASEEEEVPLVVYLK 15 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK 228.48 6.20E-13 43848800 203661 147547 154188 223926 142069 195216 235545 181370 136064 TRUE FALSE 194034.3481 162582.207 161257.6723 201416.533 166845.7886 188455.621 199608.2842 165488.2813 157164.1102 1.234597058 1.034474136 1.026046418 1.281568246 1.061602349 1.199100868 1.270062764 1.052964835 1 17.26191228 3.264358737 24.99070995 1.165059581 1.104140747 0.014156161 0.107622335 643.7709047 623618.1353 0.028201304 0.03817073 1838.055992 -3.264358737 -0.060918833 VAS(ph)FRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VASFRK 6 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 VAS(1)FRK;VAS(1)FRK 73.26 0.051102 271170000 495830 284800 387140 454930 319750 425030 496730 451250 373340 TRUE FALSE 472393.0985 313821.4438 404890.7519 409199.5721 375514.2988 410311.1045 420944.7154 411736.1578 431235.6604 1.095440711 0.727726096 0.938908326 0.948900125 0.870786749 0.951477677 0.976136146 0.954782258 1 18.71811696 2.040484723 7.581059902 0.971787568 0.90940466 0.084468586 0.089842283 0.525187792 81.89156792 0.033106769 0.024245599 109.7702677 -2.040484723 -0.062382909 VAS(ph)FSIPGSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VASFSIPGSSSR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 VAS(0.99)FS(0.01)IPGSSSR;VAS(0.999)FS(0.001)IPGSSSR;VAS(0.985)FS(0.015)IPGSSSR;VAS(0.999)FS(0.001)IPGSSSR;VAS(0.999)FS(0.001)IPGSSSR;VAS(0.998)FS(0.002)IPGSSSR 205.8 1.02E-07 695633000 815107 650819 702974 958051 1032506 833182 1053557 805369 959871 TRUE FALSE 776578.5075 717138.196 735206.0532 861745.8933 1212574.719 804328.6984 892817.5297 734846.6208 1108722.892 0.700426151 0.646814638 0.663110736 0.777241905 1.093667974 0.72545512 0.805266614 0.66278655 1 20.0804674 3.109502917 4.801996285 0.840254995 0.670461175 0.316027462 0.123761965 0.259382302 9.868671304 0.034534501 0.041723764 1286.775895 -3.109502917 -0.169793821 VAS(ph)RSPARTPPASLY(ph)HGYLPENGVLRPEPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VASRSPARTPPASLYHGYLPENGVLRPEPTK 31 3 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 2 VAS(0.35)RS(0.374)PART(0.426)PPAS(0.278)LY(0.571)HGY(0.001)LPENGVLRPEPTK 63.282 0.016449 121710000 41672 37415 40578 47717 38268 41551 52301 51862 42068 TRUE FALSE 39702.24715 41227.63104 42438.54144 42920.3965 44941.92708 40112.07845 44321.52188 47320.68834 48591.69059 0.817058363 0.84845023 0.873370342 0.883286751 0.924889143 0.825492548 0.912121421 0.973843218 1 15.56842201 2.575834653 0.025252269 1.770249057 8.15E-09 0.703963648 0.03249632 176.5205115 1.984088362 65.23082245 73.39490737 376.5604055 -2.575834653 -1.770249049 VASEAPLEHKPQVEAS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.843)S(0.157)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR 144.5 8.13E-08 332093000 430490 366281 383490 438650 326149 422990 446370 443033 360704 TRUE FALSE 410141.5908 403605.4503 401073.3958 394556.0686 383029.2823 408341.7502 378268.0584 404238.6819 416640.1341 0.984402503 0.968714767 0.962637449 0.946994868 0.919328819 0.98008261 0.907901154 0.970234619 1 18.66844229 3.713050374 1.585329585 0.947177624 0.980276499 0.070793049 0.027498513 0.614940083 3.008643341 0.007444878 0.016764402 5164.762717 -3.713050374 0.033098875 VASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 32 0 Q14764 Q14764 MVP Major vault protein 1 VAS(0.016)GPS(0.016)PGEGIS(0.953)PQS(0.016)AQAPQAPGDNHVVPVLR 74.631 0.001528 209260000 12342 10424 11671 13302 8618.7 11673 12793 12324 11954 TRUE FALSE 11758.61812 11486.21745 12206.12689 11964.85769 10121.79855 11268.76108 10841.19289 11244.84523 13807.76527 0.851594584 0.831866506 0.884004519 0.866531076 0.733051175 0.81611766 0.785151882 0.814385602 1 13.75319222 -1.422531463 3.216914307 1.002451344 0.822709463 0.633253692 0.042370769 18769001.73 24232406.7 420947.0947 0.010416071 0.037797975 1.422531463 -0.179741881 VASGS(ph)DLHLTDIDSDSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.15)GS(0.85)DLHLTDIDSDSNR 187.57 2.72E-14 586070000 587690 468400 503930 581380 501780 498460 598740 567000 483340 TRUE FALSE 559911.0584 516130.4925 527035.689 522938.5779 589290.2731 481198.2052 507391.2164 517350.4741 558293.8986 1.00289661 0.924478118 0.944011192 0.936672565 1.055519816 0.861908408 0.908824577 0.926663314 1 19.09066526 2.206881017 24.99999699 0.913943239 0.965938652 0.166239711 0.05027524 302.8921634 239026.0244 0.017388887 0.012843663 161.020443 -2.206881017 0.051995412 VASGSDLHLTDIDS(ph)DSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(0.996)DS(0.004)NR;VASGSDLHLTDIDS(1)DSNR;VASGSDLHLT(0.001)DIDS(0.994)DS(0.005)NR 211.98 1.56E-16 496913000 725207 718830 701718 846386 752971 720975 816407 769636 715086 TRUE FALSE 690927.9023 792079.5942 733892.4644 761305.6713 884288.904 696007.455 691849.1178 702242.5917 825977.8847 0.836496854 0.958959809 0.888513455 0.921702246 1.070596344 0.842646598 0.837612157 0.850195392 1 19.65574363 -0.531433318 7.353930985 0.999992929 0.900245946 0.157112854 0.07216823 0 0 0.069413928 0.01636102 0.29414853 0.531433318 -0.099746984 VASGSDLHLTDIDSDSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 130.56 1.88E-05 149770000 161890 122680 130760 158480 167690 128330 168370 140580 160610 FALSE TRUE 154237.7805 135181.2315 136755.4753 142549.2893 196935.0829 123885.8999 142682.0642 128270.0699 185516.5785 0.831396211 0.728674669 0.737160401 0.768391108 1.061549779 0.667788835 0.769106811 0.691421063 1 17.50118859 -1.01924295 4.486377307 1.000007722 0.780745407 0.283013723 0.109063552 8.84E-06 1.93E-06 0.098085365 0.023118022 0.095665876 1.01924295 -0.219262315 VASPSQGQVGSS(ph)SPKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.122)S(0.439)S(0.439)PKR 100.39 0.0012676 102790000 68062 56703 54696 65442 39311 63130 68335 65768 45903 TRUE FALSE 64844.84415 62481.10017 57203.8657 58863.64583 46166.82595 60943.79227 57909.24069 60009.00526 53021.4028 1.222993748 1.178412808 1.07888254 1.110186504 0.870720568 1.149418707 1.092186129 1.131788336 1 15.69428722 3.798174089 2.00345048 1.063511716 1.213823826 0.355637539 0.079119215 0.344639151 2.698174441 0.021588751 0.047215411 6283.101693 -3.798174089 0.150312111 VASPSQGQVGSSS(ph)PKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.004)S(0.103)S(0.893)PKR;VASPSQGQVGS(0.004)S(0.163)S(0.833)PKR;VASPSQGQVGS(0.001)S(0.04)S(0.959)PKR 160.02 5.47E-09 701620000 393664 351235 358637 396490 260822 391419 408224 428252 288199 TRUE FALSE 375056.2829 387026.2458 375080.8612 356634.0719 306309.2742 377864.0619 345941.9313 390751.9846 332891.429 1.12666248 1.162620038 1.126736313 1.071322482 0.920147674 1.135096998 1.039203479 1.173812092 1 18.3446922 3.254178996 4.084710203 1.055639723 1.143907939 0.243604495 0.068955396 0.273239499 10.22030757 0.018479223 0.02422593 1795.473485 -3.254178996 0.088268216 VASRS(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VASRSPAR 8 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 VAS(0.038)RS(0.962)PAR;VAS(0.044)RS(0.956)PAR 54.784 0.077559 125837000 110752 74063 72164 83316 109379 100464 132585 103333 137090 TRUE FALSE 105516.9724 81610.1039 75472.79078 74940.91739 128454.663 96984.90649 112356.7232 94284.61472 158349.217 0.666356136 0.515380533 0.476622444 0.47326358 0.811211229 0.612474809 0.709550229 0.595422046 1 17.27275021 -1.264072064 0.268292527 1.28438986 0.544819814 0.608902912 0.101289694 12.32897051 0.703774285 2.623321408 0.138215278 0.054441231 1.264072064 -0.739570046 VASS(ph)PVMVSNPATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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(0.002)S(0.998)PVMVSNPATR;VAS(0.028)S(0.972)PVMVSNPATR;VAS(0.075)S(0.924)PVMVS(0.001)NPATR 261.79 1.67E-24 217910000 513633 414341 540787 558150 526075 502110 635500 558220 638820 TRUE FALSE 489354.586 456562.819 565582.6189 502043.7016 617822.3134 484721.8048 538542.8032 509339.2975 737884.943 0.663185488 0.618745271 0.766491611 0.680382093 0.837288143 0.656907028 0.729846582 0.690269265 1 19.49303635 -5 0.228254409 2.58759361 0.664852651 0.686970923 0.06223885 87.76594776 0.877937431 64.37775671 0.103926669 1.00E-05 5 -1.922740959 VASSTLLDDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VASSTLLDDRR 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;;; 217.83 1.77E-11 1960120000 1155010 958537 908945 977835 1207910 986837 1258220 1100699 1303490 FALSE TRUE 1100414.966 1056213.01 950621.0273 879541.168 1418569.122 952662.5872 1066255.43 1004315.96 1505628.572 0.730867484 0.701509675 0.63137818 0.584168755 0.942177339 0.632734132 0.708179594 0.667040982 1 20.52193448 -1.89347895 2.360376921 1.167542663 0.701047408 0.489894659 0.096275951 12273536.63 6393622.81 11439577.4 0.021084901 0.012779712 1.89347895 -0.466495254 VATLNS(ph)EEESDPPTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 349.02 3.89E-87 537280000 1724680 2066160 1676510 2194450 1202940 1995890 1916810 2062850 1296940 TRUE FALSE 1643157.794 2276704.053 1753379.642 1973859.717 1412732.355 1926771.829 1624365.43 1882215.918 1498062.831 1.096855058 1.519765397 1.17043131 1.317608097 0.943039454 1.286175579 1.084310615 1.256433227 1 20.5146667 2.837383194 24.9982477 1.130474537 1.290968642 0.219676568 0.148945446 62.89635339 15901.16365 0.041536948 0.044056585 687.6749326 -2.837383194 0.160494106 VATPVDWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VATPVDWK 8 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 110.03 0.0081545 367368000 2049170 1987910 1752400 2354690 1514640 1987560 2011560 2120160 1570470 FALSE TRUE 1952309.795 2190480.289 1832749.273 2117992.088 1778792.736 1918730.299 1704659.577 1934507.551 1814010.467 1.076239543 1.207534537 1.010330043 1.167574348 0.980585707 1.057728351 0.939718711 1.066425793 1 20.79075135 2.731389154 24.97046535 1.003848052 1.120580453 0.413905425 0.062697058 463.3823456 1613457.944 0.018440068 0.01769371 538.7523208 -2.731389154 0.116732402 VATTPGS(ph)PSLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VATT(0.055)PGS(0.945)PSLGR;VATT(0.01)PGS(0.989)PSLGR;VATT(0.023)PGS(0.976)PSLGR 236.57 4.66E-16 459760000 954420 996220 887870 1090290 940540 925700 963700 1030800 991150 TRUE FALSE 909306.4581 1097735.951 928579.7177 980691.9778 1104569.878 893642.7769 816669.8654 940537.6874 1144852.48 0.794256443 0.95884489 0.811091153 0.856609908 0.964814155 0.780574609 0.713340697 0.82153614 1 20.12673028 2.187347705 24.99931823 0.794285081 0.876800406 0.005152209 0.091783472 181.8112449 88748.90884 0.031506536 0.023269143 153.9386611 -2.187347705 0.082515325 VATWFNQPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VATWFNQPAR 10 0 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ; 115.86 0.0027144 247190000 233800 141321 152938 150907 193982 174964 256270 206223 244930 FALSE TRUE 222748.7373 155721.7706 159950.3586 135737.5417 227812.3994 168904.9528 217171.3048 188165.0209 282912.4935 0.787341466 0.550423803 0.565370432 0.479786311 0.805239799 0.597021894 0.767627128 0.665099722 1 18.10999636 0.219249526 0.534123345 1.022171837 0.624168303 0.527132253 0.105873721 2.291612981 0.934188784 0.217662901 0.047246803 1.656721568 -0.219249526 -0.398003535 VATWFNQPARK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VATWFNQPARK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 70.488 0.0739 0 190820 110510 140860 125870 152620 138500 189750 161610 193920 FALSE TRUE 181800.3168 121771.0946 147318.5703 113217.3085 179236.8797 133703.7103 160800.1525 147458.5717 223992.1232 0.811637098 0.543640075 0.657695316 0.505452187 0.80019278 0.596912554 0.717883068 0.658320344 1 17.77308847 -0.76424701 0.574614983 1.067681989 0.652095203 0.538869476 0.09847492 11.97563956 2.669314237 1.594754879 0.03722996 0.172088952 0.76424701 -0.415586786 VAVAT(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VAVATPAK 8 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAK;VAVAT(1)PAK;VAVAT(1)PAK;VAVAT(1)PAK 125.74 0.013964 616910000 2150090 2291230 2101430 2620820 1589220 2348310 2602470 2526520 1909560 TRUE FALSE 2048459.507 2524708.942 2197782.644 2357370.194 1866379.465 2266987.436 2205415.404 2305284.515 2205684.812 0.928718145 1.144637225 0.996417363 1.068770198 0.8461678 1.027793012 0.999877857 1.045155909 1 21.07279522 VAVAT(ph)PAKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VAVATPAKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK 118.9 0.0005354 11512000000 21073600 21088200 21858000 24094800 12765000 24899700 26583600 25655500 16239900 TRUE FALSE 20077492.69 23237111.56 22860210.92 21672744.93 14991211.96 24037417.15 22527783.58 23408968.41 18758300.75 1.07032577 1.238764207 1.218671735 1.15536824 0.799177503 1.281428284 1.200950122 1.24792585 1 24.16102581 -0.19768898 8.484731476 0.99995924 1.155347625 0.105824945 0.138082419 0 0 0.127264307 0.029996485 0.634323819 0.19768898 0.155388385 VAVEEVDEEGKFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 242.43 1.60E-17 9173470000 6919340 5318780 5805210 6398510 4395584 6393850 7059840 6991250 4651213 FALSE TRUE 6592276.511 5860769.729 6071384.621 5755319.618 5162172.458 6172429.371 5982731.745 6379059.087 5372499.357 1.227040912 1.090883282 1.130085686 1.071255525 0.960851201 1.148893459 1.113584451 1.18735409 1 22.35716197 4.6587253 1.511547066 1.090843987 1.268661796 0.297022636 0.066971554 1.184878349 2.863458312 0.017343451 0.302080636 45574.85548 -4.6587253 0.177817809 VAVTASEVQQAESEVS(ph)DIESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VAVTASEVQQAESEVSDIESR 21 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 VAVTASEVQQAESEVS(1)DIESR 237.76 7.55E-30 19290000 28420 23430 27432 30630 28692 25668 32533 28966 41007 TRUE FALSE 27076.64292 25817.54364 28689.78433 27551.01421 33695.87572 24779.11072 27569.49334 26429.58348 47366.15613 0.571645351 0.545063095 0.605702187 0.581660334 0.711391391 0.523139574 0.582050468 0.557984554 1 15.53156898 -1.820292371 2.436924525 1.152476754 0.582027225 0.870341556 0.050349518 3159533.019 1976835.332 2827886.053 0.011898725 0.015125426 1.820292371 -0.570449529 VAYEGS(ph)DSEKGEGAEPLKVPVWEPQDWQQQLVNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIR 35 2 P78549-3;P78549-2;P78549;H3BRL9;A0A494C106;H3BPD5 P78549-3 NTHL1 Endonuclease III-like protein 1 1 VAYEGS(1)DSEKGEGAEPLKVPVWEPQDWQQQLVNIR;VAYEGS(0.994)DS(0.006)EKGEGAEPLKVPVWEPQDWQQQLVNIR 242.24 9.23E-48 74823000 92115 91548 98000 109365 57295 127682 111876 122370 61515 TRUE FALSE 87760.9065 100876.8453 102493.3969 98371.42242 67287.22986 123260.3403 94807.26146 111654.6341 71054.43202 1.235122201 1.419712218 1.442463109 1.384451604 0.946981461 1.734731203 1.33429061 1.571395772 1 16.11663702 4.646343865 3.322612839 1.373841535 1.229136439 0.018533774 0.23566287 1.094369823 19.79493495 0.050975809 0.349229009 44293.89428 -4.646343865 -0.144705096 VAYTEADYYHTELWMEQALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VAYTEADYYHTELWMEQALR 20 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;;;; 348.04 5.06E-95 484417000 569657 459582 481679 562763 578483 474968 607320 534556 504062 FALSE TRUE 542730.4426 506413.9283 503764.4586 506192.9941 679370.252 458519.7391 514662.1798 487747.4428 582229.3606 0.932159179 0.869784251 0.865233691 0.869404788 1.166842997 0.787524248 0.883950922 0.837723887 1 19.15122807 -1.171001532 3.83316644 1.000065301 0.900116337 0.085359049 0.101149507 106997.3051 47697115.61 6102.983505 0.021862584 0.067452565 1.171001532 -0.099948963 VAYVSFGPHAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 211.46 3.16E-08 1737930000 3856300 3266900 2721400 3339900 3411200 3401900 4800000 4282400 3717400 FALSE TRUE 3674020.341 3599800.824 2846178.882 3004166.907 4006112.2 3284091.35 4067671.842 3907410.354 4293875.406 0.855642047 0.838357075 0.662846173 0.699639981 0.93298287 0.764831542 0.947319486 0.909996212 1 22.0338489 1.588252535 1.096870087 0.985747489 0.791546937 0.463285452 0.080010884 0.451769674 1.038640882 0.071304509 0.026318602 38.74828943 -1.588252535 -0.194200552 VCADLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VCADLIR 7 0 P60866;P60866-2;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 ;;; 104.11 0.019134 286305000 1065540 803746 516532 562020 1212920 601137 1153630 841070 1170860 FALSE TRUE 1015174.036 885648.6312 540215.5031 505524.6818 1424452.864 580319.475 977622.5556 767421.452 1352430.989 0.750629085 0.654856801 0.399440347 0.373789632 1.053253642 0.429093595 0.722863173 0.56743853 1 20.36712355 -1.622355585 2.648736363 1.037147493 0.627700135 0.259996328 0.201563308 20082310.86 18355255.64 5149802.039 0.048221726 0.02385857 1.622355585 -0.409447358 VCASEKPPKDLGYIYFYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VCASEKPPKDLGYIYFYQR 19 2 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 105.32 0.00018887 211510000 305770 223420 445760 272510 303010 366770 429650 368430 372900 FALSE TRUE 291316.8581 246186.752 466198.5369 245116.7771 355854.8481 354068.6629 364099.0014 336168.316 430727.4275 0.676336912 0.571560426 1.082351639 0.569076315 0.826171786 0.822024882 0.845311857 0.780466473 1 18.71641567 6.119648526 0.08596903 1.170943724 1.05E-13 0.243706378 0.143206995 136.4993758 1.272814078 3.432158641 19.72710674 1317190.305 -6.119648526 -1.170943724 VCDTAFTCNSQLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCDTAFTCNSQLAR 14 0 Q8N4W9-2;Q8N4W9 Q8N4W9-2 ZNF808 Zinc finger protein 808 0 ; 78.655 0.026659 25022000 31906 24762 20321.8 33108 20875 30536 33322 31418 24288 FALSE TRUE 30397.86661 27285.27595 21253.57463 29779.92094 24515.59339 29478.53066 28238.1169 28666.87336 28054.45899 1.083530665 0.972582503 0.757582766 1.061504018 0.873857286 1.050760974 1.006546478 1.021829484 1 14.77594247 VCEALEHGHVEWSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCEALEHGHVEWSSR 15 0 A0A0A0MTR2;Q8N543;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 162.46 9.22E-07 90559000 87145 89120 96337 100174 119135 81237 122653 93749 59622 FALSE TRUE 83025.82855 98201.42932 100754.1467 90104.3192 139912.1063 78423.74232 103940.0322 85539.84057 68867.87525 1.205581387 1.425939583 1.463006465 1.308365023 2.031601901 1.138756525 1.5092673 1.242086245 1 16.07154355 -0.365176341 7.635829742 1.000014779 1.415196422 0.217299532 0.247867308 0 0 0.215111311 0.050702222 0.431343898 0.365176341 0.415181643 VCEDFGVIATFDPKPIPGNWNGAGCHTNFSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VCEDFGVIATFDPKPIPGNWNGAGCHTNFSTK 32 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 202.14 4.14E-27 82080000 423810 350330 339650 427010 305000 393100 506100 472750 334390 FALSE TRUE 403777.3412 386029.0253 355223.2885 384086.1435 358191.9034 379486.8484 428885.1498 431353.5038 386245.4934 1.045390427 0.999439558 0.919682675 0.994409385 0.927368499 0.982501686 1.110395221 1.116785856 1 18.55915857 1.761355638 9.820895465 1.084523539 0.982156312 0.480690787 0.04739325 0.145034231 51.65980424 0.022181617 0.012160877 57.72389638 -1.761355638 -0.102367227 VCEEIAIIPSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCEEIAIIPSKK 12 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 133.71 0.00025391 929890000 2126300 1788120 1885700 2060720 1412080 2042400 2313000 2165830 1706450 FALSE TRUE 2025794.013 1970331.461 1972161.21 1853572.51 1658346.305 1971671.176 1960109.369 1976178.443 1971077.551 1.02775967 0.999621481 1.00054978 0.940385379 0.841339959 1.000301168 0.994435439 1.00258787 1 20.91055311 -3.150309234 10.82467063 0.999947817 0.980108987 0 0.05314329 0 0 0 0.012104519 0.000707442 3.150309234 -0.01983883 VCEKAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VCEKAFR 7 1 A6NHJ4 A6NHJ4 ZNF860 Zinc finger protein 860 0 60.799 0.086944 635900000 292750 257450 247040 272070 1010500 136440 335240 184260 968800 FALSE TRUE 278912.2877 283684.4477 258367.0284 244721.0067 1186730.88 131715.0486 284092.9809 168125.2176 1119036.556 0.249243232 0.253507757 0.230883457 0.218689019 1.060493398 0.117703973 0.253872833 0.150241041 1 20.09382574 -1.403754372 5.714637968 1.000269829 0.310672716 0.389309443 0.2688042 0.000867273 9.05E-05 0.244260688 0.057551001 0.039468046 1.403754372 -0.689597112 VCENIPIVLCGNKVDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCENIPIVLCGNKVDIK 17 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 103.88 0.00080029 494820000 692940 532930 722890 725770 446940 789130 866060 750450 420660 FALSE TRUE 660186.0995 587236.1729 756035.2215 652814.2207 524886.1945 761802.2302 733926.6407 684736.6196 485893.8044 1.358704502 1.208568966 1.555968022 1.343532712 1.080248791 1.567836888 1.510467172 1.409231016 1 18.89028151 2.199441653 24.99998475 1.430192003 1.312893598 0 0.193799692 414.2822469 264755.3881 0.066570927 0.049166627 158.2856899 -2.199441653 -0.117298405 VCEVCSAYLGLHDNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 157.91 2.20E-08 1064910000 566097 478976 448886 584910 496675 484870 502430 510057 452350 FALSE TRUE 539338.7167 527784.199 469467.8671 526113.7355 583294.9627 468078.8303 425775.0757 465393.7051 522498.1277 1.032230908 1.010116919 0.898506315 1.006919848 1.116357996 0.895847861 0.814883448 0.890708847 1 18.99506634 2.065980634 11.09546695 0.874821197 1.008671006 0.371134524 0.069768237 0.446341047 73.04604073 0.024885821 0.018375956 116.407412 -2.065980634 0.13384981 VCEVCSAYLGLHDNDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 186.85 3.25E-10 3457870000 1756060 1287060 1519460 1657860 1777540 1469720 1957100 1632190 1802270 FALSE TRUE 1673054.524 1418212.877 1589128.744 1491208.763 2087542.413 1418823.228 1658508.45 1489266.791 2081756.827 0.80367433 0.681257705 0.763359449 0.716322264 1.002779185 0.681550895 0.796686928 0.715389411 1 20.98937012 -1.7619571 2.693203328 1.0531156 0.767519078 0.376504755 0.092911401 15673494.96 12218421.92 5517384.968 0.020742387 0.017299872 1.7619571 -0.285596522 VCGTLLEYLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCGTLLEYLGK 11 0 F8VWW7;Q8NCJ5 F8VWW7 SPRYD3 SPRY domain-containing protein 3 0 ; 70.17 0.052499 324150000 692000 665120 759890 662780 2568600 365040 804590 366810 2721700 FALSE TRUE 659290.5314 732896.4842 794731.7081 596156.0952 3016563.027 352398.5733 681835.0182 334690.1718 3143767.335 0.209713526 0.233126821 0.252795968 0.189631112 0.95953762 0.112094355 0.216884695 0.106461495 1 21.58406302 -1.191593074 4.813693364 1.00009248 0.279773952 0.456771462 0.244977396 0.000228137 3.83E-05 0.222565119 0.052452423 0.064329019 1.191593074 -0.720318528 VCHAHPTLSEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VCHAHPTLSEAFR 13 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;; 204.49 4.48E-08 1705190000 1066320 767580 901260 864400 1218370 781880 1144960 968140 246233 FALSE TRUE 1015917.167 845797.2747 942583.6625 777508.8697 1430853.342 754803.2995 970275.3234 883364.5292 284417.5561 3.571921442 2.973787154 3.314083967 2.733688034 5.030819342 2.653856218 3.411446666 3.105872019 1 18.11765099 0.240852558 1.17564955 0.994700733 3.369953573 0.56163666 0.656608249 3.362001607 4.545861748 0.591888564 0.17117306 1.741215635 -0.240852558 2.37525284 VCHANPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VCHANPSER 9 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 91.087 0.01099 542226000 317766 303200 308401 346491 338428 306295 333867 293041 342637 FALSE TRUE 302745.8309 334096.4247 322541.4909 311661.0664 397449.736 295687.9273 282929.4573 267380.7765 395771.396 0.764951267 0.844165162 0.814969182 0.787477492 1.00424068 0.747117984 0.714881015 0.67559399 1 18.59430782 -1.433100157 7.613469575 1.000009878 0.795476534 0.347975918 0.088527963 1.47E-05 1.10E-06 0.085146185 0.02006818 0.036889251 1.433100157 -0.204533344 VCIESEHSMDTLLATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCIESEHSMDTLLATLK 17 0 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 317.83 2.27E-58 317230000 1137500 949350 916220 1076020 920150 964020 1249620 1128580 924440 FALSE TRUE 1083732.629 1046089.844 958229.5933 967856.4253 1080623.869 930635.7457 1058967.518 1029755.552 1067797.434 1.014923426 0.979670686 0.897388927 0.906404525 1.012012049 0.87154709 0.99173072 0.964373503 1 20.02620656 -1.275925151 6.699815358 1.000000593 0.957929573 0.074472202 0.049003248 4.18E-07 4.52E-08 0.045684566 0.010767804 0.052975474 1.275925151 -0.04207102 VCIESEHSMDTLLATLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VCIESEHSMDTLLATLKK 18 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 232.74 5.24E-21 442080000 1307069.2 1084253.8 1248914 1421899 1085811.5 1354446 1777781 1588471 1179912 FALSE TRUE 1245286.629 1194740.495 1306177.942 1278967.011 1275176.682 1307541.195 1506547.857 1449376.058 1362886.727 0.913712493 0.87662494 0.958390684 0.938425025 0.935643922 0.959390953 1.105409443 1.063460396 1 20.37823423 1.910798868 4.244522548 1.064422059 0.920730148 0.76444412 0.03324699 0.098552944 3.008865982 0.015806334 0.009123514 81.43270617 -1.910798868 -0.143691911 VCS(ph)LCYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VCSLCYR 7 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 VCS(1)LCYR;VCS(1)LCYR;VCS(1)LCYR;VCS(1)LCYR 118.5 0.005238 449290000 693080 552890 628910 658900 639290 631460 756940 697480 684830 TRUE FALSE 660319.482 609230.1196 657746.1456 592666.1202 750781.9736 609592.3819 641454.9008 636404.9536 791029.9388 0.834759153 0.770173276 0.831506007 0.749233488 0.949119543 0.770631239 0.810911028 0.804527013 1 19.59337277 -1.643791354 2.680148359 1.020791328 0.812658439 0.527932224 0.054902416 15788424.1 14262412.5 2269183.831 0.011736688 0.022709556 1.643791354 -0.208132889 VCSTLLGLEEHLNALDR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 253.02 5.31E-27 578320000 805170 678687 719704 853130 782630 763070 922020 801630 759930 FALSE TRUE 767111.2098 747845.9769 752703.1403 767371.7516 919120.4242 736644.6946 781348.9149 731435.0275 877776.0632 0.87392587 0.851978094 0.857511582 0.87422269 1.047101263 0.839217114 0.890146072 0.833282039 1 19.7434934 VCTFSPQRVS(ph)PTTSPRPAS(ph)PVPGSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VCTFSPQRVSPTTSPRPASPVPGSER 26 2 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 2 VCT(0.055)FS(0.059)PQRVS(0.866)PT(0.055)T(0.049)S(0.041)PRPAS(0.856)PVPGS(0.019)ER 45.192 0.084191 311110000 108370 82726 91578 105910 116500 93403 109390 99419 118590 TRUE FALSE 103247.5649 91155.87345 95776.94188 95263.72558 136817.5631 90168.43069 92700.54641 90713.34531 136980.3315 0.753740071 0.665466877 0.699202147 0.695455505 0.998811739 0.658258231 0.676743481 0.662236281 1 17.06360923 -1.482157428 3.164795454 1.006347942 0.722398311 0.42032722 0.100945331 26905947.78 31534186.23 1487679.101 0.024919762 0.032949025 1.482157428 -0.283949631 VCTLAIIDPGDSDIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VCTLAIIDPGDSDIIR 16 0 E5RI99;P62888;A0A0C4DH44;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 190.3 2.05E-09 119125000 569860 553119 527563 594383 518488 555760 584140 601190 536455 FALSE TRUE 542923.8472 609482.4549 551752.2854 534634.4916 608912.143 536513.8918 495018.7145 548546.6165 619645.7016 0.876184319 0.983598294 0.890431877 0.862806746 0.98267791 0.86583977 0.798873797 0.885258487 1 19.24108403 2.047858285 24.99395902 0.86236158 0.920500791 0 0.064586964 200.285154 104597.831 0.022351965 0.016508017 111.6498862 -2.047858285 0.058139211 VDATEESDLAQQYGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VDATEESDLAQQYGVR 16 0 P07237;H7BZ94;I3L3U6;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 366.59 8.06E-104 394748000 430127 379380 403417 458932 397699 431000 483848 439003 436468 FALSE TRUE 409795.7491 418039.2533 421914.0685 412799.2834 467057.5797 416074.3619 410028.1011 400561.57 504153.2283 0.812839681 0.829190869 0.836876657 0.818797263 0.926419893 0.82529346 0.813300557 0.794523465 1 18.94350276 -1.22232415 3.587774604 1.000261888 0.831618414 0.689242076 0.035417305 11431247.94 16446452.14 33631.18056 0.008283478 0.059934357 1.22232415 -0.168643474 VDCDQHSDIAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDCDQHSDIAQR 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;; 170.95 3.98E-05 2597400000 2257250 1976060 2040590 2308200 2031340 2062440 2429660 2251980 1827980 FALSE TRUE 2150554.266 2177422.761 2134153.07 2076175.351 2385605.053 1991017.186 2058970.743 2054784.693 2111453.802 1.018518266 1.031243382 1.01075054 0.983291867 1.129840042 0.942960335 0.975143638 0.973161094 1 21.00980525 VDCTAHSDVCSAQGVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDCTAHSDVCSAQGVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 268.56 1.54E-27 2945950000 2218420 2136770 1957260 2322070 1952820 2233880 2370010 2172470 1964720 FALSE TRUE 2113559.683 2354509.292 2047002.307 2088651.112 2293391.19 2156520.175 2008421.446 1982237.01 2269398.743 0.931330243 1.037503568 0.902002045 0.920354397 1.01057216 0.950260584 0.885001568 0.873463518 1 21.11387869 1.917560665 6.468070279 0.90863147 0.965069607 0.098340146 0.052265289 0.390341642 25.23286432 0.021582685 0.013267519 82.71050348 -1.917560665 0.056438137 VDCTQHYELCSGNQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDCTQHYELCSGNQVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 270.17 1.26E-28 1665750000 1289010 1136390 1099900 1350150 1169040 1132880 1400700 1310590 1051520 FALSE TRUE 1228081.052 1252189.433 1150331.503 1214430.357 1372920.206 1093648.082 1186997.489 1195827.792 1214584.351 1.011112197 1.030961276 0.9470989 0.999873212 1.130362172 0.900429913 0.977286994 0.98455722 1 20.21203126 VDDDS(ph)LGEFPVTNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDDDSLGEFPVTNSR 15 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 VDDDS(1)LGEFPVTNSR;VDDDS(1)LGEFPVTNSR 226.06 9.60E-13 476910000 774230 644470 717640 721750 615430 821160 879150 897600 732360 TRUE FALSE 737633.6823 710142.2257 750544.5038 649198.3188 722760.7971 792723.0233 745019.5208 819001.3855 845930.6484 0.871978907 0.839480431 0.887241177 0.767436811 0.854397223 0.93710167 0.880709928 0.96816611 1 19.69017987 1.388084933 0.90877968 0.999605129 0.846435469 0.644702313 0.039582298 0.32049224 0.550535109 0.034805486 0.012974892 24.43908447 -1.388084933 -0.15316966 VDDFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDDFLR 6 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 98.415 0.092966 47063000 103233 96514 80969 101269 91120 81349 100452 97599 90925 FALSE TRUE 98353.38068 106348.8863 84681.50874 91089.24772 107011.2992 78531.86373 85126.20247 89052.71416 105025.1846 0.936474247 1.01260366 0.806297166 0.867308618 1.018910841 0.747743163 0.810531329 0.847917711 1 16.6803758 2.237029175 24.99985955 0.829912621 0.932234033 0.13662835 0.088472796 58.22651148 950483.5472 0.030656048 0.023862362 172.5953835 -2.237029175 0.102321413 VDDHLMGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDDHLMGK 8 0 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 93.429 0.011075 336800000 527910 463140 446460 561470 392750 546740 573530 575620 436330 FALSE TRUE 502956.7405 510334.4925 466930.6326 505029.9689 461245.4757 527806.2567 486027.4649 525215.6612 503993.8279 0.997942262 1.012580838 0.926461013 1.00205586 0.915180802 1.047247461 0.964352018 1.042107328 1 18.94304654 VDDKPS(ph)SPGDSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.5)S(0.5)PGDSSK;VDDKPS(0.497)S(0.497)PGDS(0.005)SK 173.87 1.27E-05 2066340000 3880500 3545000 3394800 4003100 1568660 4299200 3829000 4160600 1494900 TRUE FALSE 3697076.455 3906239.53 3550454.938 3600700.783 1842233.807 4150317.626 3244815.726 3796275.807 1726721.457 2.141096029 2.262229101 2.056182787 2.085281774 1.066896922 2.403582586 1.879177277 2.198545568 1 20.71960395 2.977402007 24.94735027 1.805005166 2.161804392 0.172815591 0.438833993 1438.128872 1587643.101 0.121819583 0.130139456 949.2967775 -2.977402007 0.356799226 VDDKPSS(ph)PGDSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.238)S(0.661)PGDS(0.082)S(0.02)K;VDDKPS(0.148)S(0.851)PGDSSK;VDDKPS(0.094)S(0.645)PGDS(0.199)S(0.062)K;VDDKPS(0.025)S(0.975)PGDSSK;VDDKPS(0.4)S(0.6)PGDSSK;VDDKPS(0.149)S(0.851)PGDSSK;VDDKPS(0.032)S(0.952)PGDS(0.016)SK 185.71 5.10E-06 1559318000 4075710 3776670 3672330 4302530 1821570 4671580 4366480 4750140 1840554 TRUE FALSE 3883059.266 4161516.967 3840709.963 3870031.51 2139251.231 4509802.013 3700293.28 4334192.56 2125977.714 1.826481642 1.957460297 1.806561723 1.820353753 1.006243488 2.121283767 1.740513673 2.038682029 1 21.01969504 2.979068271 24.98958674 1.653998831 1.870235784 0.100869098 0.370390121 2084.559565 2488678.232 0.104015163 0.111448588 952.9459557 -2.979068271 0.216236953 VDDKPSS(ph)PGDSSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDDKPSSPGDSSKK 14 2 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.007)S(0.605)PGDS(0.323)S(0.065)KK 116.6 0.00018356 401740000 1107900 915520 955280 1130700 458710 1276200 1204100 1365400 448370 TRUE FALSE 1055531.763 1008812.529 999080.5329 1017039.888 538708.8788 1232004.874 1020392.43 1245838.338 517900.9296 2.038095903 1.947887079 1.929095848 1.963773049 1.04017747 2.378842754 1.970246377 2.405553391 1 18.98231662 2.954311487 24.99798445 1.844114772 1.972374873 0.030555979 0.469360491 2465.144049 1348776.87 0.133372132 0.141467709 900.1429552 -2.954311487 0.128260101 VDDKWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDDKWEK 7 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 112.84 0.0057124 831620000 1910700 2164250 1701770 2306430 950940 2154920 1751580 2080150 847440 FALSE TRUE 1820384.998 2384789.536 1779797.838 2074583.274 1116783.635 2080294.58 1484344.301 1898001.038 978856.6671 1.859705367 2.43630106 1.818241524 2.119394334 1.140906194 2.125229004 1.516406182 1.938997917 1 19.9007381 -1.177947064 0.139745651 5.25E-12 2.412814868 0.407279394 0.34277392 29.39120957 0.797151759 13.49956226 2.594641174 0.066382398 1.177947064 2.412814868 VDDQIYSEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDDQIYSEFR 10 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 152.54 4.15E-05 58927000 91010 93006 76032 102240 78731 89356 96995 94774 82594 FALSE TRUE 86708.13766 102483.4171 79518.14241 91962.64096 92461.66147 86261.57931 82196.63131 86475.08613 95402.25569 0.908868842 1.074224256 0.833503797 0.963946191 0.96917689 0.904188048 0.861579537 0.906426012 1 16.54173576 2.229568961 22.91142216 0.901615923 0.958500925 0.018617703 0.069069397 138.661655 353312.8451 0.024435876 0.018350891 169.6558974 -2.229568961 0.056885002 VDDQIYSEFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDDQIYSEFRK 11 1 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 179.6 1.13E-05 138470000 231950 181930 207390 260480 222870 249460 309330 278520 267140 FALSE TRUE 220986.1832 200468.8738 216899.0366 234296.0555 261738.4574 240821.1376 262136.0273 254131.3123 308566.7068 0.716169886 0.649677588 0.702924301 0.759304391 0.848239462 0.780450814 0.849527903 0.8235863 1 18.23522288 1.572741514 0.232465287 1.050303985 0.609593222 0.847286071 0.038172881 0.755618236 0.186764326 0.128161969 0.128614265 37.38879892 -1.572741514 -0.440710764 VDDSSGSIGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDDSSGSIGRR 11 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 159.94 0.0015431 266870000 680080 407828 662480 582310 815310 609080 901970 706310 987620 FALSE TRUE 647933.9662 449386.1369 692855.3633 523775.0925 957499.8059 587987.4069 764357.9107 644461.752 1140775.066 0.567976971 0.393930539 0.607354933 0.459139675 0.839341457 0.515427997 0.670033851 0.564933238 1 20.12158292 -5 0.150309116 2.561544269 0.431849275 0.574161806 0.116869652 86.83102289 0.774270049 40.37783781 0.527085061 1.00E-05 5 -2.129694994 VDDSTGTVIS(ph)DVEEDAGELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDDSTGTVISDVEEDAGELSR 21 0 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 VDDSTGTVIS(1)DVEEDAGELSR;VDDS(0.008)T(0.008)GT(0.005)VIS(0.977)DVEEDAGELS(0.002)R 183.6 4.46E-17 33700000 85969 79508 79318 89541 73932 85076 87608 90754 98256 TRUE FALSE 81905.41574 87609.95559 82954.80876 80540.16856 86825.71739 82129.79679 74241.79057 82807.09864 113493.0387 0.721677882 0.771941228 0.730924202 0.709648535 0.765031216 0.723654929 0.654152814 0.729622712 1 16.79224428 0.920593041 22.12720276 1 0.724893038 0.880045991 0.031814436 9056.743089 2523717.15 0.034017045 0.008504261 8.329003439 -0.920593041 -0.275106962 VDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 VDEFPLCGHMVSDEYEQLSSEALEAAR 27 0 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;;;;;;; 317.17 3.14E-82 1754573000 918732 824710 834246 958591 841502.2 907191 1055226 969655 844505 FALSE TRUE 875305.3591 908748.8866 872497.0043 862231.6115 988259.9173 875774.7482 894231.8931 884746.8677 975466.5223 0.897319733 0.931604382 0.894440746 0.883917174 1.013115155 0.897800927 0.916722279 0.9069987 1 19.89573284 -1.591827355 2.943251424 1.005162483 0.917921946 0.335611707 0.036372625 18611134.77 19890914.57 746968.8848 0.007967906 0.025596032 1.591827355 -0.087240537 VDEFVTHNLSFDEINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDEFVTHNLSFDEINK 16 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 215.79 1.58E-14 477020000 566610 592280 498900 655030 356300 577260 551090 615340 350320 FALSE TRUE 539827.4682 652634.0054 521775.0585 589185.1399 418438.6072 557269.3415 467011.099 561457.5675 404645.8364 1.334073947 1.612852392 1.289461083 1.456051408 1.034086032 1.377177994 1.15412308 1.387528344 1 18.62630023 2.769257879 24.76316135 1.211656708 1.437415742 0.367383378 0.149689898 614.6877526 495861.0426 0.040926763 0.043405207 587.8383006 -2.769257879 0.225759034 VDFPQDQLTALTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDFPQDQLTALTGR 14 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 87.18 0.01639 133570000 88209 75407 79990 80904 87831 72816 96557 77939 91617 FALSE TRUE 84039.53538 83091.05903 83657.62062 72771.37621 103148.6986 70294.36366 81825.45626 71114.24798 105824.4964 0.794140659 0.78517793 0.790531715 0.687660973 0.974714759 0.664254176 0.77321848 0.672001761 1 16.6913141 -1.573107608 2.734873917 1.015555585 0.770868093 0.403598277 0.088667004 14356605.78 14232526.47 1626274.47 0.021023562 0.026723442 1.573107608 -0.244687492 VDGAEWGVDLPSVEAQLGSHR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 231.39 5.64E-26 458974000 747613 707171 694464 796674 671395 736521 818301 748003 631582 FALSE TRUE 712274.8151 779232.5289 726305.8613 716590.8159 788486.0754 711015.0931 693454.1533 682503.8919 729524.5109 0.976354878 1.068137557 0.995588017 0.982271062 1.08082191 0.974628107 0.950556346 0.935546211 1 19.47659693 2.01785769 24.93164945 0.95805338 1.020831337 0.360247064 0.036910281 218.0875464 304477.2456 0.012855623 0.009492657 104.1975938 -2.01785769 0.062777957 VDGETAS(ph)DSESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDGETASDSESR 12 0 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VDGET(0.026)AS(0.974)DSESR 146.79 6.82E-05 84962000 86010 121360 65051 165460 90289 108110 95007 90339 74147 TRUE FALSE 81944.47776 133726.722 68033.65269 148827.6464 106035.373 104366.1236 80511.93723 82428.43824 85645.33807 0.956788538 1.561401064 0.794364927 1.737720345 1.238075246 1.218584992 0.94006211 0.962439289 1 16.3860871 1.810456277 3.830599505 0.961799535 1.269569486 0.20259905 0.264947888 0.329199595 8.495277694 0.123322059 0.065330547 64.63329201 -1.810456277 0.30776995 VDGPRS(ph)PS(ph)YGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VDGPRS(0.919)PS(0.846)Y(0.234)GR 95.755 0.089928 1256100000 1673200 1406200 1299000 1597400 1160700 1257100 1506100 1403600 1129600 TRUE FALSE 1594111.152 1549493.379 1358560.435 1436826.317 1363125.713 1213566.312 1276316.784 1280693.343 1304772.599 1.221754008 1.187558185 1.041223916 1.101208225 1.044722823 0.930097944 0.978190977 0.981545247 1 20.31536696 3.51805676 0.695017896 0.967425901 1.250516233 0.835228143 0.037721668 0.305117332 0.287394341 0.019928914 0.054117441 3296.527936 -3.51805676 0.283090333 VDGPRS(ph)PS(ph)YGRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDGPRSPSYGRSR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 VDGPRS(0.977)PS(0.75)Y(0.276)GRS(0.997)R 62.739 0.0491 700350000 813860 601950 760760 780840 748080 761620 882420 729260 789140 TRUE FALSE 775390.4507 663289.3894 795641.5985 702348.4797 878544.9151 735244.9084 747790.6222 665402.1283 911515.8008 0.85066046 0.727677336 0.872877462 0.770528036 0.963828509 0.806617842 0.820381415 0.729995166 1 19.79790814 -2.251858091 2.354144677 1.720293493 0.81611572 0.403054086 0.069649158 8846288.517 1685472.555 33860433.06 0.016619166 0.005599405 2.251858091 -0.904177773 VDGPRS(ph)PSYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VDGPRS(0.947)PS(0.053)YGR;VDGPRS(0.907)PS(0.093)YGR;VDGPRS(0.997)PS(0.003)YGR;VDGPRS(0.974)PS(0.026)YGR;VDGPRS(0.5)PS(0.5)YGR;VDGPRS(0.906)PS(0.094)YGR 178.68 4.50E-06 10399870000 12051050 6082790 10831580 10294360 12735580 10570810 15885170 11670320 14818940 TRUE FALSE 11481420.75 6702633.217 11328218.66 9259551.375 14956661.12 10204740.2 13461595.57 10648404.91 17116985.53 0.670761842 0.391577898 0.661811546 0.540956897 0.873790604 0.596176247 0.786446629 0.622095806 1 24.02892532 -2.692286943 0.117311214 1.719658862 0.389412366 0.471844999 0.12459617 59.8572592 0.815972215 12.48310973 1.379344999 0.002031015 2.692286943 -1.330246497 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK 30 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 286.71 1.45E-72 8361410000 2066270 1882730 1856690 2159320 1607420 1979450 2299390 2042830 387736 FALSE TRUE 1968601.512 2074582.327 1941821.073 1942261.051 1887753.539 1910901.15 1948575.824 1863948.975 447864.1186 4.395532998 4.632169092 4.335737096 4.336719488 4.21501402 4.266698471 4.35081924 4.161862713 1 18.77270156 -1.059162856 0.563108304 6.80E-16 4.426230486 0.990264915 0.104203415 2.421078974 0.42826579 4.110308556 0.047635303 0.087264407 1.059162856 4.426230486 VDIDAPDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;;; 267.38 1.67E-31 8542950000 14199000 12504950 12259200 15116700 9861460 13033130 14725800 13805300 714344 FALSE TRUE 13527841.41 13779218.62 12821296.45 13597140.6 11581295.5 12581789.44 12479108.75 12596434.75 825120.8192 16.39498252 16.69963756 15.53868979 16.47896924 14.03587842 15.24842077 15.12397756 15.26617006 1 19.65424586 -0.45089203 0.687764908 7.78E-15 15.956969 0.973286564 0.760701564 1.799530317 0.653748675 6.597964951 0.280326783 0.354085359 0.45089203 15.956969 VDIDAPDVEVHDPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;; 290.2 2.18E-49 2304492000 3143874 2724687 2760392 3347172 2026996 2869653 3296010 3144022 681287 FALSE TRUE 2995269.307 3002335.703 2886958.704 3010707.911 2380503.461 2770276.197 2793143.139 2868714.766 786937.5084 3.806235279 3.815214894 3.668599695 3.825853869 3.025022235 3.520325524 3.549383667 3.645416231 1 19.58588955 -1.176552915 0.500199584 4.42E-20 3.690568758 0.924148907 0.234540899 6.25435577 0.86372333 9.138968226 0.111402962 0.066595838 1.176552915 3.690568758 VDIDT(ph)PDIDIHGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK 212.79 1.32E-11 142769000 430309 430268 375594 576334 321420 453231 467081 514735 273801 TRUE FALSE 409969.1464 474112.7984 392815.3564 518399.8114 377475.5462 437535.4968 395819.2149 469662.0746 316260.6607 1.296301429 1.499120369 1.242062024 1.639153634 1.193558331 1.383464816 1.251560071 1.485047409 1 18.27075459 -3.266432379 0.327557653 1.22E-17 1.389271119 0.40838612 0.138916013 89.29649936 2.244026261 61.29133159 0.104286876 0.000541462 3.266432379 1.389271119 VDIDT(ph)PDINIEGSEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDIDTPDINIEGSEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK 308.73 1.50E-56 205828000 760607 681616 659460 859347 491102 790811 821734 919934 617528 TRUE FALSE 724654.6145 751073.4453 689696.8933 772963.8069 576750.0333 763425.0168 696363.3861 839379.7021 713291.0883 1.01593112 1.052969058 0.966922067 1.083658298 0.80857597 1.070285371 0.976268171 1.176770208 1 19.44413142 -0.698863173 5.563623297 0.999999999 1.015282362 0.00258866 0.095328665 1.20E-09 2.16E-10 0.080739104 0.019030388 0.200049203 0.698863173 0.015282362 VDIDTPDIDIHGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 295.03 1.20E-45 637070000 780000 814960 632489 912780 472035 702550 711930 799680 409189 FALSE TRUE 743130.9458 898005.3505 661489.2463 821025.6202 554357.7545 678220.5173 603312.003 729655.7798 472643.9403 1.572284933 1.899961629 1.399550888 1.737091181 1.172886622 1.434950202 1.276461944 1.543774748 1 18.85039423 2.946068972 1.51669203 1.310336618 1.702869545 0.400789952 0.203302204 0.345972841 1.62359353 0.068490326 0.077948255 883.220156 -2.946068972 0.392532927 VDIDVPDVDVQGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;; 293.83 2.98E-49 1880500000 6337650 5787440 5635120 6735500 4595480 5824830 6665300 6922000 4443570 FALSE TRUE 6038081.845 6377186.716 5893495.826 6058434.743 5396930.257 5623114.677 5648386.068 6315872.984 5132656.141 1.176404902 1.242473008 1.148235078 1.180370276 1.051488763 1.095556476 1.100480124 1.230527199 1 22.29127418 3.112219421 1.974541506 1.102809558 1.204217557 0.321197052 0.062960825 0.349106099 2.784468027 0.01895493 0.024021093 1294.84988 -3.112219421 0.101407999 VDIGDTIIYLVH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDIGDTIIYLVH 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 87.639 0.024276 9538700 22362 26136 21454 29693 28984 20979 26286 27849 23545 FALSE TRUE 21304.99258 28799.28811 22437.68712 26708.20323 34038.80042 20252.49197 22275.58792 25410.39392 27196.23835 0.783380124 1.058943805 0.825029066 0.982055051 1.251599577 0.744679897 0.819068712 0.934334874 1 14.7311195 0.969732517 22.28573876 1.000000014 0.920457978 0.024429366 0.149704158 4391.592501 3233508.311 0.139536665 0.034884166 9.326796835 -0.969732517 -0.079542036 VDIIENQVMDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VDIIENQVMDFR 12 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;; 166.11 0.00012284 623217000 840237 1042293 689606 909968 660468 735026 717105 818428 573247 FALSE TRUE 800520.6622 1148503.842 721225.1172 818496.2878 775653.4101 709571.8653 607697.4617 746762.1056 662143.217 1.208984162 1.734524816 1.08922828 1.236131802 1.171428462 1.071628988 0.917773446 1.127795447 1 19.33678377 3.123485158 1.095931834 1.021605661 1.451584885 0.423278408 0.166957686 0.380526738 0.983579971 0.068346115 0.094853439 1328.878142 -3.123485158 0.429979224 VDIIPGFEFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDIIPGFEFDR 11 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 128.27 0.00062657 151090000 184000 175750 183560 220290 149260 166010 163490 193710 153230 FALSE TRUE 175302.6847 193659.1248 191976.4076 198146.0307 175290.8967 160261.0321 138546.5978 176747.7255 176992.1258 0.99045471 1.094168025 1.084660725 1.119518904 0.990388109 0.905469841 0.782783964 0.998619146 1 17.43332565 2.397192727 3.29123193 0.890527381 1.067033697 0.474860966 0.071041801 0.171832311 3.75459864 0.025470469 0.020929025 249.5702 -2.397192727 0.176506316 VDIKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDIKDR 6 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 79.597 0.060858 771080000 3323500 2931380 2904270 3672200 2486320 3402500 3361800 3484600 2542550 FALSE TRUE 3166404.742 3230090.955 3037433.652 3303063.479 2919933.421 3284670.572 2848895.666 3179469.951 2936835.668 1.078168852 1.099854169 1.034253869 1.124701499 0.994244742 1.118438668 0.970056206 1.082617589 1 21.48583111 2.106355832 0.435540341 1.004423472 1.09273559 0.172896462 0.049396146 1.488735505 0.65452187 0.045221692 0.043642996 127.7485066 -2.106355832 0.088312118 VDINAPDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VDINAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 265.29 2.85E-31 1121930000 2483010 2160790 2236850 2701510 1940420 2309170 2843970 2607410 275358 FALSE TRUE 2365643.038 2380976.958 2339411.785 2429949.082 2278828.634 2229202.864 2410070.143 2379091.358 318059.1123 7.437746465 7.485957376 7.355273578 7.639929146 7.164795931 7.008769055 7.577428378 7.480028918 1 18.27893539 -0.644281827 7.51684504 0.99995624 7.399996522 0.991415278 0.186978202 0 0 0.175825629 0.041442498 0.226839234 0.644281827 6.400040281 VDINAPDVDVQGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDINAPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 304.09 7.82E-50 1842490000 2525960 2144310 2266560 2670120 1928630 2243160 2675620 2641710 1965610 FALSE TRUE 2406562.877 2362817.627 2370484.018 2401714.465 2264982.461 2165478.807 2267405.028 2410387.868 2270426.76 1.059960585 1.040693172 1.044069802 1.057825122 0.997602081 0.953776112 0.998669091 1.061645286 1 21.11453207 2.733072396 24.23889121 0.997911919 1.049650919 0.446518774 0.026456333 260.2036324 1149195.381 0.008321964 0.008048746 540.8444728 -2.733072396 0.051739 VDINAPDVEVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDINAPDVEVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 257.2 7.45E-31 889720000 1775910 1610090 1608770 1803580 1310903 1598900 1861390 1802350 200038 FALSE TRUE 1691966.254 1774160.002 1682533.696 1622280.712 1539524.068 1543529.692 1577400.769 1644526.679 231058.8714 7.322663024 7.678389455 7.281839843 7.021070873 6.662908284 6.680244229 6.826834907 7.117349225 1 17.81790096 -0.723049494 0.586324613 1.24E-17 7.243354678 0.973050442 0.317445331 2.52555826 0.596828402 5.682503574 0.141975371 0.189212797 0.723049494 7.243354678 VDINT(ph)PDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDINT(1)PDVDVHGPDWHLK;VDINT(1)PDVDVHGPDWHLK;VDINT(1)PDVDVHGPDWHLK 247.64 3.93E-24 772760000 1449560 1151680 1272930 1566070 1089290 1409320 1644240 1576310 203528 TRUE FALSE 1381042.172 1269037.501 1331295.1 1408645.668 1279261.831 1360514.895 1393380.989 1438279.94 235090.0828 5.874523312 5.398090325 5.66291476 5.99193999 5.44158144 5.78720667 5.927008801 6.117994953 1 17.84285415 -1.026389878 12.30340875 1.000005685 5.753941608 0.977462051 0.227855151 0 0 0.218353575 0.051466433 0.094104442 1.026389878 4.753935923 VDINTPDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 275.49 2.62E-39 618610000 1374910 1228730 1282660 1508900 1053690 1262860 1565230 1422490 87715 FALSE TRUE 1309920.729 1353938.984 1341471.23 1357222.505 1237453.202 1219126.842 1326425.416 1297929.235 101317.3942 12.92888294 13.36334195 13.24028554 13.39575021 12.21363036 12.03274967 13.09178376 12.8105272 1 16.62852235 -0.805445948 0.893229602 3.82E-15 12.95985141 0.98549725 0.453082912 5.879603908 2.411513037 19.13907319 0.149398122 0.156514311 0.805445948 12.95985141 VDISAPDVDVHGPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDISAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 280.15 1.72E-39 946460000 2187030 1874690 1909630 2191830 1554630 1887180 2307210 2090070 100783 FALSE TRUE 2083653.426 2065723.042 1997188.424 1971503.084 1825756.98 1821826.483 1955202.74 1907052.391 116411.9129 17.89897077 17.74494543 17.15622031 16.93557845 15.68359229 15.64982859 16.79555546 16.381935 1 16.82887918 -0.478398288 0.724911249 8.09E-18 17.11558118 0.979161193 0.723946491 2.026029942 0.779525836 7.69028146 0.283975557 0.332354614 0.478398288 17.11558118 VDIVAINDPFIDLNYMVYMFQYDSTHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VDIVAINDPFIDLNYMVYMFQYDSTHGK 28 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 216.69 3.35E-34 2303409000 1658738 1345825 1418440 1725392 1522276 1383658 2298134 1589655 1252498 FALSE TRUE 1580332.742 1482966.098 1483476.877 1551952.318 1787760.452 1335741.577 1947511.45 1450456.381 1446728.993 1.092348843 1.025047611 1.025400669 1.072731884 1.235725876 0.923283893 1.346148076 1.002576424 1 20.46436327 2.984396747 24.25028161 1.129097831 1.049147762 0.012441461 0.123164171 1149.554204 1786620.294 0.033525811 0.036615605 964.7099258 -2.984396747 -0.07995007 VDKDAELVAQWNYCTLSQEILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDKDAELVAQWNYCTLSQEILR 22 1 Q9BY42;A2A2L6 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ;; 193.4 6.65E-18 282846000 549635 517559 472055 562507 395434 530895 555746 555278 426074 FALSE TRUE 523654.8428 570298.8505 493699.1887 505962.7277 464397.5644 512509.973 470956.7407 506654.9146 492147.3798 1.064020381 1.158796885 1.003153138 1.028071566 0.943614826 1.041374991 0.956942493 1.029478029 1 18.90873089 3.717816493 21.13364713 0.99746185 1.111408578 0.595946984 0.037949969 57.05975074 58131.16796 0.009114758 0.014155204 5221.755017 -3.717816493 0.113946728 VDKGVVPLAGTDGETTTQGLDGLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDKGVVPLAGTDGETTTQGLDGLSER 26 1 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 ; 227.41 1.20E-34 500330000 483140 318930 388760 420850 383850 392620 542050 478240 411130 FALSE TRUE 460302.9297 351429.3296 406585.0305 378545.3584 450793.3185 379023.471 459350.3171 436362.7703 474885.9406 0.96929155 0.74002892 0.856174074 0.797129007 0.949266508 0.798135802 0.967285569 0.91887911 1 18.85722152 1.468230195 0.951805524 0.993050038 0.844727586 0.309497376 0.072961635 0.563720963 1.024315411 0.061658122 0.023002378 29.39207148 -1.468230195 -0.148322452 VDKGVVPLAGTNGETTTQGLDGLSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDKGVVPLAGTNGETTTQGLDGLSER 26 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 358.45 2.35E-110 3942670000 2638610 1882140 2455220 2643280 2203830 2515810 3324120 2811540 2797640 FALSE TRUE 2513888.135 2073932.206 2567794.266 2377572.472 2588177.254 2428686.869 2816964.442 2565346.653 3231483.723 0.77793619 0.641789464 0.794617732 0.735752576 0.800925357 0.7515702 0.871724782 0.793860305 1 21.62376529 0.527953277 0.299328787 1.04953085 0.700179803 0.703371076 0.050406265 1.575881631 0.310945133 0.174043397 0.063422022 3.372510243 -0.527953277 -0.349351046 VDKITEYLCEPLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 96.096 0.0019726 293410000 468300 382920 433850 470640 333770 459810 560400 526690 398660 FALSE TRUE 446164.3871 421939.9833 453742.4516 423330.373 391979.3823 443886.6644 474900.6875 480570.2314 460482.1567 0.968907004 0.916300398 0.985363808 0.919319819 0.851236854 0.963960618 1.031311812 1.043624002 1 18.81278573 1.857448338 4.068813164 1.027172098 0.930974135 0.582337938 0.037083142 0.162525525 4.245485353 0.017864262 0.009922428 72.01920755 -1.857448338 -0.096197963 VDKWWGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDKWWGNR 8 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 63.283 0.092426 0 320140 378290 275380 332600 259670 296330 350090 336760 285160 FALSE TRUE 305007.6167 416838.1811 288006.4454 299166.4161 304956.3658 286068.0178 296677.3407 307271.5091 329381.1564 0.926002021 1.265519211 0.874386527 0.908268158 0.925846424 0.868501468 0.900711334 0.932875191 1 18.3293985 3.706695086 24.99080944 0.908477385 1.095760684 0.417624077 0.088021417 485.3172449 380614.1682 0.021797024 0.033770981 5089.733998 -3.706695086 0.187283299 VDKWWGNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDKWWGNRK 9 2 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 94.692 0.0048088 1524600000 1696670 1382370 1067880 1139420 1529020 1269150 2050740 1579320 1620670 FALSE TRUE 1616471.772 1523235.075 1116843.354 1024883.337 1795680.604 1225199.017 1737861.949 1441026.368 1871995.226 0.86350208 0.813696025 0.596605877 0.547481811 0.959233538 0.654488323 0.928347425 0.769781006 1 20.83614533 1.6923742 9.658527438 0.885440613 0.753078177 0.232486077 0.134703941 0.207773729 33.05738031 0.063204844 0.033990916 49.24636731 -1.6923742 -0.132362437 VDLFYLHMPDHSTPVEETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDLFYLHMPDHSTPVEETLR 20 0 O95154 O95154 AKR7A3 Aflatoxin B1 aldehyde reductase member 3 0 ;;; 228.49 1.74E-25 297709000 225658 178205 201591 224567 241255 193597 250315 214217 43095.4 FALSE TRUE 214991.5936 196364.2921 210834.1468 201993.0985 283329.7956 186892.6873 212124.8494 195459.0238 49778.41453 4.318972301 3.944767907 4.235453233 4.057845161 5.691820406 3.754492567 4.261382195 3.926581947 1 15.60323266 0.288672031 1.195990981 0.99427235 4.312300379 0.800248053 0.517948187 1.714895271 2.496861281 0.474940203 0.139884656 1.943891545 -0.288672031 3.31802803 VDLHFIALVHVDGHLYELDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDLHFIALVHVDGHLYELDGR 21 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ; 118.52 2.80E-05 14411700 20149.9 17501.3 19945.5 23113 17763.3 20020.3 23344 16905.5 9777.2 FALSE TRUE 19197.45416 19284.70237 20860.0209 20789.63733 20861.2139 19326.99199 19782.44406 15425.1648 11293.39824 1.699882865 1.707608459 1.847098673 1.840866397 1.847204309 1.711353091 1.751682145 1.365856801 1 13.46319205 1.026756601 2.328595072 1.000965325 1.770903966 0.951803666 0.058388834 0.061124893 0.714099856 0.061153474 0.016771621 10.63546789 -1.026756601 0.76993864 VDLNSNGFICDYELHELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 ;; 321.05 5.57E-62 977310000 1770084 1562798 1416466 1899347 1241754 1664294 1846977 1897637 1150381 FALSE TRUE 1686415.637 1722048.893 1481412.367 1708421.031 1458315.504 1606659.081 1565186.737 1731469.844 1328776.21 1.269149481 1.295966078 1.114869724 1.285710128 1.097487668 1.209126916 1.177915984 1.303056023 1 20.34166672 -5 0.183728233 0.121189996 1.26348301 0.432019128 0.075382234 120.4518554 1.167017477 39.00856626 0.20567671 1.00E-05 5 1.142293013 VDLTLLS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VDLTLLSPK 9 0 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VDLTLLS(1)PK;VDLT(0.002)LLS(0.998)PK;VDLTLLS(1)PK;VDLTLLS(1)PK 126.48 0.00049546 219101000 945250 755418 739012 921030 612744 911880 1049360 1001810 663230 TRUE FALSE 900569.9058 832395.953 772896.4312 828446.3146 719606.3596 880301.367 889260.8592 914086.2055 766080.3211 1.175555462 1.086564855 1.008897383 1.08140921 0.939335393 1.149098003 1.160793242 1.193198912 1 19.54713614 VDLVDENFTELRGEIAGPPDTPYEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDLVDENFTELRGEIAGPPDTPYEGGR 27 1 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 128.36 5.34E-05 93338000 59928 53144 59000 61925 59788 60298 70330 68143 60948 FALSE TRUE 57095.32221 58559.43402 61705.20836 55700.18135 70215.00827 58209.86514 59599.8668 62176.03767 70399.50456 0.811018807 0.831815996 0.876500605 0.791201326 0.997379296 0.826850494 0.846594975 0.883188569 1 16.10327766 -5 0.148450778 1.513838003 0.806536359 0.425107919 0.054655167 126.2853611 1.118806217 19.20114894 0.263736952 1.00E-05 5 -0.707301645 VDNDENEHQLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VDNDENEHQLSLR 13 0 P06748;P06748-3;P06748-2;E5RGW4 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;; 323.88 2.28E-51 89722080000 43174630 43063930 36347670 47103800 31925780 40474520 40521500 41217420 26861510 FALSE TRUE 41133850.8 47452193.43 38014246.62 42368836.53 37493625.92 39072877.22 34339200.95 37608204.2 31027055.78 1.32574135 1.529381123 1.225196709 1.36554486 1.208417137 1.259316304 1.106750224 1.212109988 1 24.88702347 2.149561443 0.384924283 1.006825935 1.453921017 0.644904127 0.085202768 0.665257845 0.241353246 0.089908205 0.102636201 141.1111865 -2.149561443 0.447095082 VDNEFDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDNEFDQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 99.802 0.015249 726050000 1398980 1179100 1289840 1564320 1322700 1367380 1598470 1505970 1483860 FALSE TRUE 1332852.988 1299251.631 1348980.44 1407071.582 1553378.461 1320027.288 1354594.044 1374099.283 1713969.43 0.77764105 0.758036641 0.787050467 0.820943219 0.906304648 0.770158011 0.790325673 0.801705829 1 20.70890995 -5 0.295543444 2.629517967 0.78612964 0.695120253 0.041218558 152.8308378 1.42498803 154.0314482 0.043661188 1.00E-05 5 -1.843388326 VDNLTYRT(ph)SPDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.764)S(0.236)PDTLR 155.79 9.29E-06 721240000 263530 195920 242630 220440 223130 237530 274800 234850 265390 TRUE FALSE 251073.4592 215884.4707 253754.8255 198280.9524 262043.8014 229304.2765 232874.213 214285.289 306545.3258 0.819041878 0.704249756 0.827788924 0.646824256 0.854828893 0.748027314 0.759673019 0.699032968 1 18.22574088 -1.787036204 2.693499105 1.064645877 0.757774989 0.586985565 0.063943816 23175388.09 17634013.83 9851251.492 0.013112527 0.016329158 1.787036204 -0.306870888 VDNLTYRT(ph)SPDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.017)YRT(0.491)S(0.491)PDTLRR;VDNLTYRT(0.5)S(0.5)PDTLRR 122.49 0.0051749 457550000 290440 163254 294470 267420 324250 269450 389790 298170 411120 TRUE FALSE 276711.4768 179889.7682 307971.7408 240538.4335 380799.0973 260118.8789 330320.3765 272060.6541 474874.3899 0.582704569 0.378815476 0.648533059 0.50653065 0.801894365 0.547763544 0.695595264 0.572910774 1 18.85718643 -4.999999999 0.132402711 2.424634478 0.410264304 0.592034786 0.108817295 88.08870939 0.730767823 33.15968486 0.708512851 1.00E-05 4.999999999 -2.014370174 VDNLTYRTS(ph)PDSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDNLTYRTSPDSLRR 15 2 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 VDNLTYRT(0.174)S(0.825)PDSLRR 125.28 4.77E-05 116670000 91032 27648 105550 56565 133110 78783 172340 96040 203670 TRUE FALSE 86729.09777 30465.36263 110389.5719 50878.97873 156324.3419 76054.72496 146046.3678 87630.22846 235254.1034 0.36866136 0.129499814 0.469235479 0.216272439 0.664491457 0.32328756 0.620802637 0.372491817 1 17.84386036 -5 0.125414165 3.103736963 0.099419914 0.623014726 0.153513606 82.43259081 0.660581674 43.4101876 1.125839802 1.00E-05 5 -3.004317049 VDNLTYRTS(ph)PDTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.3)S(0.7)PDTLR;VDNLTYRT(0.014)S(0.981)PDT(0.004)LR;VDNLT(0.001)YRT(0.17)S(0.812)PDT(0.017)LR;VDNLTYRT(0.386)S(0.612)PDT(0.002)LR;VDNLT(0.06)YRT(0.253)S(0.654)PDT(0.032)LR;VDNLTYRT(0.058)S(0.942)PDTLR;VDNLTYRT(0.044)S(0.956)PDT(0.001)LR;VDNLTYRT(0.299)S(0.693)PDT(0.008)LR;VDNLTYRT(0.431)S(0.569)PDTLR 199.19 5.52E-08 14953730000 6150080 3558270 5193290 5368300 5407060 5134000 6501140 5682440 5902680 TRUE FALSE 5859377.907 3920861.758 5431407.483 4828668.285 6350049.552 4956208.293 5509271.691 5184855.429 6818037.468 0.859393621 0.5750719 0.796623297 0.708219676 0.931360319 0.72692594 0.808043622 0.760461563 1 22.7009251 -4.999999985 0.188282162 2.025157318 0.717390515 0.362703629 0.094700803 136.4241657 1.330990908 52.27226889 0.243884292 1.00E-05 4.999999985 -1.307766803 VDNLTYRTS(ph)PDTLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.119)S(0.881)PDTLRR;VDNLT(0.002)YRT(0.395)S(0.603)PDTLRR;VDNLTYRT(0.088)S(0.911)PDTLRR;VDNLTYRT(0.096)S(0.904)PDTLRR;VDNLTYRT(0.156)S(0.844)PDTLRR;VDNLTYRT(0.022)S(0.978)PDTLRR;VDNLTYRT(0.041)S(0.959)PDTLRR;VDNLTYRT(0.217)S(0.783)PDTLRR 225.08 5.46E-13 9413680000 5679580 2611549 5606050 4471560 6279930 4909400 7454940 5642520 7697160 TRUE FALSE 5411117.509 2877668.812 5863092.938 4022070.293 7375147.804 4739386.247 6317551.984 5148431.036 8890796.261 0.608620122 0.323668289 0.65945645 0.452385835 0.829526129 0.533066568 0.710572124 0.579074234 1 23.0838812 -4.999999991 0.120704294 2.436291329 0.36256805 0.503212225 0.133282895 109.4513192 0.854916553 38.06342608 1.125417302 1.00E-05 4.999999991 -2.073723278 VDNLTYRTSPDT(ph)LR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.005)S(0.099)PDT(0.896)LR 176.11 3.68E-06 1419100000 495410 330940 475230 440930 453030 480450 567870 484300 541740 TRUE FALSE 471992.9511 364663.1622 497019.7656 396606.8787 532038.2886 463811.896 481231.0019 441892.1246 625750.2724 0.754283253 0.582761492 0.794278145 0.633810157 0.850240602 0.74120926 0.769046412 0.706179676 1 19.25522749 -5 0.178660168 2.130604792 0.663615458 0.553084818 0.076421939 90.34045952 0.867552317 36.19668042 0.218750374 1.00E-05 5 -1.466989334 VDNLTYRTSPDT(ph)LRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.005)Y(0.001)RT(0.026)S(0.065)PDT(0.903)LRR 67.164 0.090705 587350000 183670 92942 176000 159790 201740 154640 224860 162060 242900 TRUE FALSE 174988.2831 102412.8955 184069.7741 143727.6056 236923.3921 149284.778 190553.4772 147869.1673 280567.6914 0.623693634 0.365020274 0.656061905 0.512274257 0.84444289 0.532081143 0.679171134 0.52703562 1 18.09798936 -5 0.178643284 2.676840938 0.495675552 0.494530172 0.127565797 103.0243123 0.989326038 61.36676705 0.371031791 1.00E-05 5 -2.181165385 VDPSLMEDS(ph)DDGPSLPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDPSLMEDSDDGPSLPTK 18 0 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 1 VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK 240.63 2.53E-20 42594000 142784 146918 101920 179228 86159 134676 137366 149171 94416 TRUE FALSE 136034.8833 161889.1112 106593.1328 161211.6609 101185.1023 130012.1364 116408.2938 136108.7964 109057.5511 1.247367853 1.484437434 0.977402589 1.478225573 0.927813813 1.192142452 1.067402419 1.248045597 1 16.73473014 3.263214271 1.036229364 1.107474464 1.347560223 0.16942893 0.177307129 0.732219539 1.688577214 0.065721382 0.108609829 1833.218666 -3.263214271 0.240085759 VDRTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDRTPK 6 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 73.039 0.07662 90718000 105080 62907 96283 100680 94627 100080 135220 115760 123560 FALSE TRUE 100113.0766 69317.29482 100697.6708 90559.45512 111129.9188 96614.20451 114589.7055 105623.4407 142721.0537 0.701459764 0.485683738 0.705555825 0.634520645 0.778651194 0.676944305 0.802892793 0.740069092 1 17.12283865 0.717518183 0.269435753 1.074487149 0.566234791 0.680525329 0.073815653 1.604726402 0.310637942 0.273802032 0.126148563 5.218169514 -0.717518183 -0.508252358 VDS(ph)PSHGLVTSSLCIPSPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.899)PS(0.101)HGLVTSSLCIPSPAR;VDS(0.999)PS(0.001)HGLVTSSLCIPSPAR 274.6 1.12E-44 740870000 582950 596210 492170 664940 423590 574500 564920 599240 375140 TRUE FALSE 555395.1088 656964.4768 514736.4813 598098.9679 497463.9619 554604.9209 478731.0785 546767.3688 433314.7953 1.281735853 1.51613673 1.187904237 1.380287436 1.148042872 1.279912265 1.104811291 1.261824832 1 18.72505597 1.906617033 0.287308338 0.983823522 1.44175298 0.467578384 0.105119322 1.265908542 0.350162825 0.173549493 0.213718708 80.65235131 -1.906617033 0.457929458 VDS(ph)TTCLFPVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.991)T(0.009)TCLFPVEEK;VDS(0.5)T(0.5)TCLFPVEEK;VDS(0.804)T(0.139)T(0.058)CLFPVEEK;VDS(0.993)T(0.007)TCLFPVEEK;VDS(0.993)T(0.007)TCLFPVEEK 315.21 1.05E-50 2990450000 4506300 4395270 4321420 5138590 2594630 5420700 5109870 5295690 2981440 TRUE FALSE 4293296.13 4843153.01 4519561.381 4622049.171 3047132.651 5232979.8 4330265.482 4831971.309 3443786.488 1.246678952 1.40634532 1.312381414 1.342141618 0.884820433 1.519542462 1.25741404 1.403098399 1 21.71556427 -1.776497392 2.641889227 0.923083343 1.299773724 0.238677142 0.166361528 17679719.71 13530216.15 8810511.037 0.035892643 0.016730257 1.776497392 0.37669038 VDSEGDFS(ph)ENDDAAGDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 VDSEGDFS(1)ENDDAAGDFR 236.66 8.33E-24 123050000 137720 118280 122900 142790 110090 119140 133550 133080 105950 TRUE FALSE 131210.2485 130332.8665 128535.0866 128436.4779 129289.6611 115014.1519 113174.4947 121426.8097 122380.1849 1.072152724 1.064983409 1.050293286 1.04948753 1.05645911 0.939810248 0.924777935 0.992209726 1 16.90101046 2.244338123 24.8843869 0.953731686 1.059962048 0.793592263 0.023670754 48.16818561 207466.4944 0.008024553 0.006545042 175.5246529 -2.244338123 0.106230362 VDSEVMILMQLNLT(ph)VNS(ph)S(ph)KNFTVLNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDSEVMILMQLNLTVNSSKNFTVLNFK 27 1 H0Y8A4;P34925;P34925-2 H0Y8A4 RYK Tyrosine-protein kinase RYK 3 VDS(0.095)EVMILMQLNLT(0.72)VNS(0.773)S(0.772)KNFT(0.639)VLNFK 42.319 0.068553 303850000 139720 88881 164410 123660 283290 78319 145390 82966 296280 TRUE FALSE 133115.7125 97938.07495 171948.3611 111229.4619 332695.6863 75606.79339 123208.0852 75701.05721 342225.5892 0.388970658 0.286179871 0.502441566 0.325017957 0.972153155 0.220926768 0.360020084 0.221202212 1 18.38458811 -1.124801916 4.57760726 1.000058865 0.402729744 0.423162632 0.216493895 0.000120455 2.30E-05 0.194142305 0.045755289 0.075023632 1.124801916 -0.597329121 VDSLVS(ph)LSEEDLESDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDSLVSLSEEDLESDQR 17 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 VDSLVS(1)LSEEDLESDQR 153.95 1.64E-07 12957000 15373 16729 11054 16155 12832 15082 17407 15435 13439 TRUE FALSE 14646.34876 18433.70412 11560.83683 14531.06871 15069.89674 14559.70656 14751.24245 14083.42957 15523.05148 0.943522527 1.187505185 0.74475285 0.936096149 0.970807625 0.937941008 0.950279812 0.907259091 1 13.92212457 3.753580457 24.99949511 0.924266314 1.065513836 0.312817973 0.088934094 861.9913285 1434721.713 0.021315179 0.038246339 5669.966025 -3.753580457 0.141247521 VDSSTNSSPSPQQSESLS(ph)PAHTSDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 1 VDSSTNSSPSPQQS(0.001)ES(0.054)LS(0.941)PAHT(0.003)S(0.001)DFR 124.32 2.10E-10 0 32138 28718 35735 33909 41536 37893 42690 42035 42087 TRUE FALSE 30618.90043 31644.39685 37373.4851 30500.4029 48779.86525 36580.75591 36176.85644 38354.19256 48613.63701 0.629841796 0.650936626 0.768786032 0.627404259 1.003419375 0.752479307 0.74417095 0.788959537 1 15.56907345 2.507740331 0.056594685 1.51504598 1.07E-14 0.489488169 0.096076012 50.91862669 1.375572811 15.88879961 20.29313963 321.9143456 -2.507740331 -1.51504598 VDST(ph)TCLFPVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.001)T(0.574)T(0.426)CLFPVEEK;VDS(0.013)T(0.493)T(0.493)CLFPVEEK;VDS(0.246)T(0.719)T(0.036)CLFPVEEK;VDS(0.436)T(0.533)T(0.031)CLFPVEEK;VDS(0.358)T(0.642)T(0.001)CLFPVEEK 368.67 3.84E-90 13570350000 12530160 12054990 11682000 13889100 6925240 14890400 14201600 13921200 7186050 TRUE FALSE 11937884.17 13283407.19 12217631.26 12492941.28 8132999.663 14374741.71 12034885.09 12702185.93 8300425.933 1.438225492 1.60032838 1.47192823 1.505096411 0.979829195 1.731807721 1.44991175 1.530305316 1 22.98475394 -1.852802037 2.512184977 0.798713764 1.47164107 0.364235735 0.192144516 14587269.58 8375155.523 17555014.45 0.042220457 0.014034533 1.852802037 0.672927305 VDSTT(ph)CLFPVEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.097)T(0.257)T(0.646)CLFPVEEK 330.24 2.34E-61 3150500000 2004400 1804900 1753800 2137400 1039700 2336300 2143400 2147200 1102600 TRUE FALSE 1909655.984 1988821.362 1834213.465 1922544.491 1221023.351 2255393.345 1816384.964 1959179.785 1273585.577 1.499432798 1.561592247 1.44019648 1.509552657 0.958728941 1.770900508 1.426197813 1.538318132 1 20.28046447 -1.748324937 2.648497436 0.898668881 1.470242347 0.339409121 0.202830108 17470433.48 13428280.04 11583171.66 0.045149777 0.017851514 1.748324937 0.571573466 VDTPHYPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDTPHYPR 8 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 ;; 126.41 0.0012203 403840000 745525 770232 688495 864021 787087 778794 777100 792046 773478 FALSE TRUE 710285.5107 848719.5165 720063.1768 777167.9675 924354.7236 751824.1685 658539.1226 722690.2533 893425.0179 0.795014127 0.949961664 0.805958152 0.869874866 1.034619252 0.841507853 0.73709501 0.808898608 1 19.76898713 -1.381734869 7.19422077 1.000005165 0.855115373 0.225908984 0.084138679 7.13E-06 6.13E-07 0.083380306 0.019652226 0.041520744 1.381734869 -0.144889792 VDVADQAQDKDRDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VDVADQAQDKDRDDR 15 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;;;; 232.26 4.76E-14 4547120000 8671410 9424240 7094730 9876590 4794730 8660020 8363580 9260210 4935170 FALSE TRUE 8261529.634 10384580.77 7420030.388 8883776.409 5630929.394 8360121.336 7087562.263 8449336.921 5700490.958 1.449266334 1.821699367 1.301647602 1.558423033 0.987797268 1.466561634 1.243324885 1.482212143 1 22.44265475 3.375998411 1.834359939 1.28131162 1.623918823 0.286800317 0.212790011 0.36603283 2.512924316 0.059149595 0.09196021 2376.831588 -3.375998411 0.342607202 VDVEVPDVS(ph)LEGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVEVPDVS(1)LEGPEGK 151.8 6.39E-07 22666000 62532 59985 60228 93625 56731 81650 85072 78566 54293 TRUE FALSE 59576.23629 66097.5397 62989.51337 84213.63712 66624.86844 78822.44003 72092.70395 71686.34454 62712.48115 0.949990101 1.05397743 1.004417497 1.342852899 1.062386103 1.256886007 1.149575055 1.143095333 1 15.93646498 3.367088576 22.00588244 1.168073108 1.006134276 0.364667768 0.096762391 3.388012107 660.4503309 0.02326115 0.031495735 2328.566128 -3.367088576 -0.161938831 VDVFREDLCTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VDVFREDLCTK 11 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 204.85 2.90E-08 2890070000 5753460 4037070 5394210 5240800 4535240 5587140 7116280 6246830 5480050 FALSE TRUE 5481505.348 4448452.023 5641539.864 4713984.827 5326184.42 5393655.941 6030560.787 5699824.449 6329868.166 0.865974647 0.70277167 0.891257087 0.744720854 0.841436864 0.852096094 0.952715069 0.900464954 1 22.59374402 1.859819927 1.057627692 0.972317649 0.794089994 0.552787025 0.058659982 0.336812267 0.69370647 0.044087523 0.018850511 72.41356472 -1.859819927 -0.178227656 VDVGKDQEFTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VDVGKDQEFTVK 12 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 150.12 6.19E-05 229480000 341260 293530 280900 356140 219010 341220 397530 409870 241530 FALSE TRUE 325129.3161 323441.0407 293779.5428 320340.1306 257205.2747 329403.4658 336879.4974 373979.6099 278985.2388 1.165399709 1.159348222 1.053028985 1.148233261 0.921931482 1.180720052 1.207517282 1.340499632 1 18.08982927 2.021984159 24.99741152 1.202827122 1.102357624 0.140158063 0.107717879 398.013929 452565.515 0.037645399 0.027801034 105.1923503 -2.021984159 -0.100469498 VDVKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDVKSPK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVKS(1)PK;VDVKS(1)PK 111.65 0.0039551 1252100000 1385360 1469450 1221410 1824400 616720 1375670 1309880 1519580 517640 TRUE FALSE 1319876.778 1619188.626 1277412.857 1641007.846 724275.7727 1328030.203 1110033.748 1386517.519 597912.9675 2.207473077 2.708067417 2.136452839 2.744559719 1.211339797 2.221109551 1.856513922 2.318928665 1 19.18957597 2.757746143 24.98304227 1.822034655 2.448070015 0.389246938 0.443037468 871.0011953 1134200.518 0.120068512 0.127179311 572.4613139 -2.757746143 0.62603536 VDVNAPDVQAPDWHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VDVNAPDVQAPDWHLK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 244.36 4.73E-20 709250000 973710 847400 847970 960270 747270 845770 1001540 938410 722370 FALSE TRUE 927684.658 933751.0234 886850.2633 863741.8352 877593.6514 816480.7728 848736.6785 856237.8456 834391.4502 1.11180988 1.119080287 1.062870746 1.035175798 1.051776898 0.978534443 1.017192444 1.02618243 1 19.67036485 3.357023251 1.092448828 1.009856795 1.121379608 0.829744036 0.018444073 0.168376393 0.423354411 0.006733726 0.012217336 2275.219237 -3.357023251 0.111522812 VDVSAPDVEAHGPEWNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VDVSAPDVEAHGPEWNLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 314.42 2.90E-61 819250000 2380300 2093010 2105390 2385200 1721910 2146900 2530700 2490100 1667230 FALSE TRUE 2267787.936 2306290.099 2201924.214 2145435.164 2022210.559 2072552.315 2144595.236 2272053.643 1925775.513 1.177597244 1.197590312 1.143396101 1.114062958 1.050075954 1.076216984 1.113626807 1.179812303 1 20.87700811 8 0.074505554 0.913998815 1.649506848 0.484300569 0.044564742 184.2563441 1.007811609 1.624851058 14.07474853 100000000 -8 0.735508033 VEADIPGHGQEVLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEADIPGHGQEVLIR 15 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 134.14 3.02E-05 0 248620 138530 190080 253120 232700 199970 271690 238990 229300 FALSE TRUE 236868.2253 152646.3645 198795.356 227675.8967 273282.8063 193044.9888 230238.7006 218062.7686 264858.6729 0.894319309 0.57633138 0.750571442 0.859612767 1.031806145 0.728860364 0.869288885 0.823317455 1 18.01486323 3.255712153 4.780614886 0.875199554 0.725140027 0.264261331 0.113165909 0.242370827 13.96426929 0.030837974 0.040357157 1801.82311 -3.255712153 -0.150059527 VEAEAGGSGART(ph)PPLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VEAEAGGSGARTPPLSR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.001)GART(0.999)PPLSR 199.75 2.10E-11 8624490000 1681420 1256552 1553280 1617170 1770480 1656860 1906900 1758960 2001800 TRUE FALSE 1601942.609 1384596.077 1624499.424 1454608.999 2079251.151 1599482.523 1615967.382 1604936.138 2312228.92 0.692813153 0.598814445 0.702568595 0.629093852 0.899241045 0.691749207 0.698878631 0.694107804 1 21.14085281 -4.999999999 0.208771019 2.44695679 0.649660267 0.594972185 0.077839572 98.10717695 0.976862739 59.46235551 0.16059416 1.00E-05 4.999999999 -1.797296523 VEAFEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEAFEHR 7 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 130.04 0.003602 153270000 388770 389880 363450 427760 900210 351330 398530 354130 577470 FALSE TRUE 370393.6126 429609.2153 380114.542 384760.7521 1057206.339 339163.354 337726.929 323120.4998 667021.0983 0.555295198 0.644071404 0.569868844 0.576834456 1.584966865 0.508474702 0.506321209 0.484423207 1 19.34737287 VEAKEES(ph)EES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEAKEESEESDEDMGFGLFD 20 1 F8VWS0;P05388;P05388-2;Q8NHW5;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 2 VEAKEES(1)EES(1)DEDMGFGLFD;VEAKEES(1)EES(1)DEDMGFGLFD 84.762 0.0017998 35311000 174243 143477 143721 174944 94769 183721 166968 194246 113731 TRUE FALSE 166006.8787 158097.4694 150310.75 157358.2967 111296.6836 177358.6957 141493.965 177236.7905 131367.8226 1.263679913 1.203471796 1.14419762 1.197845055 0.847214191 1.350092375 1.077082365 1.349164407 1 17.00325242 4.007068658 1.638617489 1.139128709 1.257380676 0.073722229 0.149287163 1.043784762 5.275505308 0.038313942 0.123354145 10164.09365 -4.007068658 0.118251967 VEAMNKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VEAMNKR 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 129.68 0.0058311 1395690000 1992911 1419640 1311080 1403612 1552735 1471025 2149107 1789664 1729929 FALSE TRUE 1898710.047 1564302.93 1371194.315 1262518.255 1823531.492 1420083.035 1821221.256 1632951.533 1998197.554 0.950211376 0.782856994 0.686215591 0.631828546 0.912588192 0.710682001 0.911432032 0.817212257 1 20.93026779 0.778400314 0.858753939 0.997141757 0.790712385 0.288444118 0.102494766 1.249998308 1.797527684 0.098500788 0.033861045 6.003441926 -0.778400314 -0.206429372 VEAPS(ph)LDVHMDSPDINIEGPDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VEAPS(1)LDVHMDSPDINIEGPDVK 118.63 0.00016983 46560000 52526 43226 48659 66518 58221 62807 77505 50859 68067 TRUE FALSE 50043.20008 47630.77854 50890.06328 59831.48426 68374.72397 60631.97784 65680.18877 46405.51634 78622.48272 0.636499871 0.605816261 0.647271131 0.760997137 0.869658673 0.771178621 0.835386858 0.590232141 1 16.2626543 3.208017195 3.262842478 0.803502596 0.621984759 0.408600049 0.100696355 0.216752384 4.764548216 0.026699576 0.034384809 1614.422477 -3.208017195 -0.181517837 VEAPSLDVHMDS(ph)PDINIEGPDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VEAPSLDVHMDS(1)PDINIEGPDVK 93.278 0.0029744 111630000 61795 56250 49784 60616 41403 57993 64408 58519 47344 TRUE FALSE 58874.07282 61981.93895 52066.64564 54522.76452 48623.67009 55984.68787 54581.37667 53394.76613 54685.86572 1.076586647 1.133417898 0.952104259 0.997017489 0.88914511 1.0237506 0.998089286 0.976390616 1 15.73888038 3.737855748 24.99979914 0.977942452 1.105002276 0.654478219 0.03876505 32.68692083 1159318.659 0.009697759 0.016059516 5468.342999 -3.737855748 0.127059824 VEAVNMAEGIIHDTETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEAVNMAEGIIHDTETK 17 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 272.76 1.21E-35 374860000 804336 711777 576566 754419 467069 601220 687030 743212 431977 FALSE TRUE 766316.6313 784307.8855 603002.1214 678583.3688 548525.6857 580399.6006 582210.9553 678132.4173 498965.7869 1.535809972 1.571867062 1.208503944 1.359979755 1.099325245 1.163205205 1.166835424 1.359075983 1 18.92858137 3.735747532 23.445328 1.199691437 1.553838552 0.659011598 0.107591978 50.78534677 423269.1479 0.02585957 0.042163931 5441.862101 -3.735747532 0.354147115 VECYDYDNDGSHDLIGTFQTTMTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VECYDYDNDGSHDLIGTFQTTMTK 24 0 O75131;H0YB26 O75131 CPNE3 Copine-3 0 165.85 1.37E-11 94295000 112430 96241 73130 162660 110690 89122 101340 97720 73953 FALSE TRUE 107115.6567 106048.0673 76483.08284 146309.1078 129994.301 86035.68279 85878.72176 89163.11875 85421.25354 1.253969619 1.241471682 0.89536362 1.712795138 1.521802778 1.007192932 1.005355438 1.04380485 1 16.38230745 2.206733901 24.79858646 1.013288613 1.305305524 0.353850224 0.207869969 221.9712354 172953.1081 0.078350185 0.057870721 160.9659071 -2.206733901 0.292016911 VEDLAWHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEDLAWHR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 103.56 0.0047486 52844000 91930 92341 76274 90928 96803 76082 95990 89578 79252 FALSE TRUE 87584.65109 101750.6529 79771.23835 81787.74469 113685.4126 73447.26126 81344.96252 81734.07544 91541.9954 0.956770176 1.111518844 0.871416862 0.893445072 1.241893538 0.802334065 0.888608143 0.892858792 1 16.48214612 VEDMAELTCLNEASVLHNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 273.78 1.84E-44 515798000 1383470 1365560 1360280 1662350 999450 1410900 1503560 1617760 936480 FALSE TRUE 1318076.115 1504712.117 1422650.184 1495247.42 1173753.764 1362040.179 1274164.307 1476100.358 1081704.536 1.218517693 1.391056492 1.315192954 1.382306693 1.085096461 1.259161013 1.177922682 1.364605869 1 20.04487505 2.753095299 24.90009636 1.1941059 1.324812183 0.320415009 0.106567377 956.6062653 1638808.857 0.02932314 0.030969909 566.3635548 -2.753095299 0.130706283 VEDVEALDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VEDVEALDR 9 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 172.25 0.00013106 681287000 929450 846550 823650 956900 861710 827060 1038450 932090 940920 FALSE TRUE 885516.7405 932814.4074 861415.1672 860710.594 1011991.951 798418.7048 880015.3801 850471.2583 1086833.068 0.81476794 0.858286737 0.792591974 0.791943693 0.931138351 0.734628646 0.809706114 0.782522434 1 20.05169894 -2.059667395 3.080459631 1.280222433 0.816473223 0.560532166 0.051605734 0.046877049 0.000907992 0.023584482 0.010785434 0.008716309 2.059667395 -0.46374921 VEDVEALDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VEDVEALDRK 10 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 101.95 0.0048283 344521000 723240 625340 669900 741250 541120 719990 787500 782950 590190 FALSE TRUE 689053.8785 689062.857 700615.5776 666738.1417 635491.1567 695056.5658 667352.4116 714390.7473 681713.6509 1.010767318 1.010780488 1.027727077 0.978032552 0.932196613 1.019572609 0.978933619 1.047933757 1 19.37880635 -0.579815669 6.290279406 0.999999997 0.999621117 0 0.031991301 0 1.15E-18 0.029241767 0.006892351 0.263138462 0.579815669 -0.00037888 VEEAS(ph)PGRPSSVDTLLS(ph)PTALIDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VEEAS(0.595)PGRPS(0.374)S(0.373)VDT(0.046)LLS(0.592)PT(0.019)ALIDSILR 104.52 0.001237 284710000 78015 86671 71930 90333 63135 71948 92167 78015 62578 TRUE FALSE 74327.38556 95502.87344 75228.06165 81252.55522 74145.72401 69456.42272 78105.23139 71183.59302 72282.27664 1.028293366 1.32124883 1.040753905 1.124100665 1.025780142 0.9609053 1.080558541 0.984800097 1 16.14135433 3.095518796 1.583345919 1.017039978 1.165898816 0.314091318 0.084786822 0.392601448 2.03177725 0.028448185 0.036408468 1246.002164 -3.095518796 0.148858838 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VEEAS(0.996)PGRPS(0.002)S(0.002)VDTLLSPTALIDSILR;VEEAS(0.444)PGRPS(0.272)S(0.272)VDT(0.012)LLSPTALIDSILR 193.75 1.25E-18 1933260000 103095 108442 103451 121103 84442 105007 117092 116877 87322 TRUE FALSE 98221.90366 119492.3631 108194.3307 108929.4964 99168.65806 101370.5813 99227.46486 106642.6303 100863.4498 0.973810671 1.18469439 1.072681243 1.079969965 0.983197167 1.005027901 0.983780201 1.057297073 1 16.62204395 2.750334531 22.26609857 1.003049969 1.083769727 0.302123813 0.053888358 191.7232048 362573.187 0.016062215 0.016876366 562.7746562 -2.750334531 0.080719758 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR 34 1 O75607 O75607 NPM3 Nucleoplasmin-3 0 53.123 0.035222 402510000 56512 59648 45708 58217 45843 71350 60509 72328 38459 FALSE TRUE 53840.78976 65726.19901 47803.75701 52364.91655 53838.00469 68879.13161 51277.24073 65994.57689 44423.0253 1.212001871 1.47955252 1.07610314 1.178778712 1.211939176 1.550527708 1.154294206 1.485593933 1 15.43902003 -1.036995852 4.291826153 0.999980235 1.294093978 0.249337898 0.160095624 0.429532314 41825282.77 2007.770046 0.034227935 0.091834137 1.036995852 0.294113743 VEEEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 5458810000 4719560 3745430 4092690 4564260 3838380 4200050 4868720 4476450 4272290 FALSE TRUE 4496475.752 4127093.575 4280343.885 4105451.913 4507792.257 4054601.215 4125907.344 4084468.307 4934814.913 0.911174144 0.836321858 0.867376783 0.831936351 0.913467341 0.821631872 0.836081477 0.827684195 1 22.23456454 -1.083510123 4.778725635 1.00000595 0.855660219 0.65329468 0.033034401 0.016860414 20023595.33 254.4461075 0.007358409 0.082506825 1.083510123 -0.14434573 VEEEHTNAIGTLHGGLTATLVDNISTMALLCTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEEEHTNAIGTLHGGLTATLVDNISTMALLCTER 34 0 Q9NPJ3-2;Q9NPJ3 Q9NPJ3-2 ACOT13 "Acyl-coenzyme A thioesterase 13;Acyl-coenzyme A thioesterase 13, N-terminally processed" 0 106.09 8.98E-06 10230000 12973 10951 10747 12614 10435 9556.2 13031 11599 2968.4 FALSE TRUE 12359.792 12066.91935 11239.76058 11346.01675 12254.8607 9225.266398 11042.88162 10583.33007 3428.724312 3.604778593 3.519361212 3.278117329 3.309107331 3.574174994 2.690582724 3.220696859 3.086666967 1 11.74345619 -0.902847275 0.338961064 5.87E-17 3.541057053 0.915053756 0.223260973 3.234934324 0.305128217 3.56534317 0.18148791 0.125069878 0.902847275 3.541057053 VEEGGRHPS(ph)PCQFTIATPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEEGGRHPSPCQFTIATPK 19 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VEEGGRHPS(0.983)PCQFT(0.017)IATPK 69.27 0.013985 176980000 232450 161850 195090 203560 145340 186120 219720 202880 148080 TRUE FALSE 221462.5492 178342.699 204035.0695 183097.7621 170687.25 179674.6177 186197.6786 185114.7517 171043.4901 1.294773329 1.042674579 1.192884157 1.070474895 0.997917254 1.050461597 1.088598452 1.082267156 1 17.38400367 8 0.63475671 1.058150752 19.98931409 0.643726972 0.053878407 123.3396763 0.839153017 0.020663566 3269.556801 99999999.91 -8 18.93116334 VEELARSLRADIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEELARSLRADIER 14 2 Q9BX97 Q9BX97 PLVAP Plasmalemma vesicle-associated protein 0 62.162 0.047585 155610000 449470 420640 390990 483120 300330 449600 466630 425010 222480 FALSE TRUE 428224.4439 463503.6942 408917.2782 434555.8597 352707.4569 434030.2393 395437.0233 387793.8713 256981.0621 1.666365764 1.803649228 1.591235069 1.691003439 1.372503693 1.688958072 1.53877885 1.509036767 1 17.97130252 -2.636921637 0.194570536 7.34E-13 1.772789396 0.792016953 0.102395713 19.25200435 0.434892408 8.449045443 0.267300404 0.002307163 2.636921637 1.772789396 VEELDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEELDRK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 86.953 0.055891 0 76821 63237 71757 85394 92688 72502 86996 75011 93821 FALSE TRUE 73189.82357 69680.92219 75047.12943 76810.03288 108852.7579 69991.23756 73723.16241 68442.63918 108370.2815 0.67536803 0.642989215 0.692506547 0.708773954 1.004452109 0.645852688 0.68028948 0.631562807 1 16.72560965 -1.793242143 2.394918039 1.094142639 0.705564538 0.417203583 0.107508498 8567340.298 5453924.237 4692314.824 0.026320867 0.016097479 1.793242143 -0.388578101 VEEPSKYGVVVCEADTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEEPSKYGVVVCEADTGR 18 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 ; 177.61 8.48E-14 425850000 403761 253268 373914 372626 335019 364945 485750 421788 431460 FALSE TRUE 384676.0177 279076.2971 391058.3268 335168.9265 393446.2075 352306.8631 411639.9161 384854.0067 498368.6132 0.771870474 0.559979681 0.784676876 0.672532173 0.789468271 0.706920247 0.825974801 0.772227617 1 18.92685369 0.351089295 0.32351877 1.055461995 0.666032746 0.617227897 0.069626185 2.083014045 0.408184905 0.244698054 0.070695289 2.244343335 -0.351089295 -0.389429249 VEERDPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEERDPPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 82.287 0.018845 298660000 296110 330320 277210 358310 271220 316870 348570 321120 265760 FALSE TRUE 282113.4671 363979.9835 289920.3527 322291.9981 318520.6821 305896.7124 295389.2446 293001.0304 306972.7035 0.919018088 1.185707978 0.944449944 1.049904419 1.03761891 0.996494832 0.962265508 0.954485617 1 18.22775085 2.06511213 3.077700918 0.969243515 1.036457448 0.103381236 0.071466722 0.479117327 9.011618544 0.030876616 0.01962859 116.1748525 -2.06511213 0.067213933 VEESGEHVILGTGELYLDCVMHDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VEESGEHVILGTGELYLDCVMHDLR 25 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;;; 252.47 5.04E-45 352002000 177724.4 178755.5 168555.9 194907 163956 176676.5 185579 192876 89600.3 FALSE TRUE 169323.7198 196970.8887 176284.3547 175314.5781 192549.8745 170558.1485 157265.5152 175986.7549 103495.0569 1.636056106 1.903191269 1.70331183 1.693941559 1.860474116 1.647983523 1.519546149 1.700436332 1 16.65920234 -0.534757478 0.378545583 0.785195991 1.779393124 0.828204348 0.102614834 3.286939257 0.45349329 0.980364129 0.07234776 0.291905664 0.534757478 0.994197133 VEESGEHVILGTGELYLDCVMHDLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEESGEHVILGTGELYLDCVMHDLRK 26 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 212.01 3.42E-26 57282000 76134 57143 77249 79565 71586 80235 105051 86043 44000 FALSE TRUE 72535.2967 62965.93667 80790.94306 71566.97504 84070.57574 77456.44183 89023.54056 78508.61878 50823.29528 1.4272057 1.238918813 1.589643934 1.408152987 1.654174041 1.524034233 1.751628659 1.544736884 1 15.6332023 3.730236166 24.43563879 1.54402163 1.333062254 0.060754336 0.208129622 691.5907887 2030101.452 0.049265159 0.077799199 5373.239097 -3.730236166 -0.210959376 VEETVKHDWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 204.32 2.02E-08 4899540000 3787800 2760620 3203890 3503840 2581310 3446740 4044460 3738380 2516390 FALSE TRUE 3608758.201 3041930.317 3350791.526 3151627.346 3031489.647 3327378.53 3427403.345 3411027.629 2906618.909 1.241565652 1.046552855 1.152814191 1.084293278 1.042960822 1.144759129 1.179171901 1.173537961 1 21.4709105 VEFATLQEALAHALTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEFATLQEALAHALTEK 17 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 312.21 3.75E-58 456740000 1528130 1531240 1264570 1750820 976540 1484280 1568870 1587690 925630 FALSE TRUE 1455898.323 1687275.097 1322551.785 1574824.247 1146848.267 1432879.011 1329510.067 1448663.447 1069171.973 1.361706405 1.578113848 1.236986957 1.472938206 1.072650889 1.340176368 1.243495061 1.354939601 1 20.02806249 -3.283700357 0.066641062 2.01E-11 1.863886507 0.41862307 0.130683177 192.8353726 1.305094195 36.60330385 8.472668852 0.000520355 3.283700357 1.863886507 VEFEELCADLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VEFEELCADLFER 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;;; 226.4 2.52E-11 229415000 255893 225970 209945 262943 228735 208983 259153 230642 241353 FALSE TRUE 243797.445 248996.5999 219571.1859 236511.4701 268626.3116 201745.8663 219614.4502 210445.7638 278780.7906 0.87451307 0.893162687 0.787612322 0.84837793 0.963575399 0.72367205 0.787767513 0.754878998 1 18.08877163 2.228708918 24.99991269 0.79501506 0.871192219 0.075078989 0.085183842 352.634517 894847.5584 0.028368757 0.021204633 169.3202567 -2.228708918 0.076177159 VEFMDDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VEFMDDTSR 9 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;;;;; 230.56 1.99E-07 5004808000 6475560 5712550 5554590 6667550 6308990 5825860 7064320 6407980 6340420 FALSE TRUE 6169473.112 6294665.34 5809273.446 5997315.206 7409275.858 5624109.007 5986528.239 5846863.3 7323659.951 0.842403 0.859497216 0.793219986 0.818895914 1.011690317 0.767936939 0.817423021 0.798352646 1 22.80413338 -0.924223152 4.299349713 1.000003649 0.839189554 0.366848611 0.066602172 18170528.11 35787284 998.2895163 0.01504152 0.119063007 0.924223152 -0.160814095 VEFNIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEFNIR 6 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 101.21 0.08557 286180000 947860 966080 893590 957200 989780 971980 998870 1008600 963870 FALSE TRUE 903056.5363 1064524.65 934561.9854 860980.4374 1162397.319 938320.0889 846474.036 920281.6371 1113342.037 0.811122284 0.956152391 0.839420371 0.773329677 1.044061286 0.842795886 0.760300077 0.826593811 1 20.08646545 2.017617267 24.98032411 0.827135394 0.885940271 0 0.097024854 618.8298285 877463.6106 0.033601909 0.024811532 104.1399265 -2.017617267 0.058804877 VEGDLKGPEVDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEGDLKGPEVDIR 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 77.527 0.023445 244540000 1483900 1124800 1294300 1462500 970950 1337900 1518900 1588600 997210 FALSE TRUE 1413758.988 1239418.399 1353644.935 1315486.721 1140283.373 1291568.188 1287163.908 1449493.762 1151852.234 1.227378779 1.076022047 1.175189747 1.142062048 0.989956297 1.121296769 1.117473119 1.258402528 1 20.13552422 VEGDLKGPEVDIRDPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEGDLKGPEVDIRDPK 16 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 132.47 2.19E-05 246260000 1227500 827140 1095100 1149900 617190 1170400 1305600 1297500 632320 FALSE TRUE 1169478.508 911426.5064 1145311.418 1034309.867 724827.7406 1129868.755 1106406.741 1183884.022 730376.9562 1.601198529 1.24788508 1.568110013 1.416131572 0.992402258 1.546966597 1.51484344 1.620921925 1 19.47828172 2.996913919 24.83438665 1.377074768 1.448867171 0.05122333 0.229802015 635.1931187 5111604.185 0.064779722 0.07603704 992.9192225 -2.996913919 0.071792404 VEGDLKGPEVDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEGDLKGPEVDLK 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 128.76 0.00014731 471390000 2341100 2229000 1974100 2639600 1135570 2381000 2235080 2646800 1087450 FALSE TRUE 2230440.843 2456137.634 2064614.438 2374262.393 1333613.048 2298545.373 1894077.496 2415032.16 1256086.192 1.77570684 1.955389407 1.643688507 1.890206586 1.061720969 1.829926471 1.507920004 1.922664365 1 20.26050403 -2.619739973 0.179844165 6.90E-16 1.889128322 0.382541404 0.268985321 48.72957505 1.028166641 21.06508615 0.855314835 0.00240027 2.619739973 1.889128322 VEGDLKGPEVDLKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEGDLKGPEVDLKGPK 16 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 160.25 4.98E-09 587000000 1865270 1159150 1806710 1712020 992700 1980630 2424200 2366600 1136350 FALSE TRUE 1777102.384 1277268.703 1889549.441 1539924.497 1165826.566 1912040.286 2054343.767 2159367.958 1312569.354 1.353911226 0.973105687 1.439580647 1.173213813 0.888201878 1.456715624 1.565131595 1.645145798 1 20.32396222 2.085311182 13.41253093 1.47738812 1.169312597 0.204837073 0.232951835 0.911692168 139.9540144 0.07939072 0.058633695 121.7057737 -2.085311182 -0.308075523 VEGQKEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEGQKEEK 8 1 A0A1W2PNT1 A0A1W2PNT1 0 58.676 0.062152 213710000 71067 70787 62644 80973 164440 45836 76830 52518 200730 FALSE TRUE 67707.80375 78000.27578 65516.28936 72833.4402 193118.2839 44248.68783 65108.17242 47919.2455 231858.1832 0.292022489 0.336413728 0.282570528 0.314129263 0.83291554 0.190843762 0.280810328 0.206674808 1 17.82288312 -1.565795513 3.096545684 1.029808197 0.33945373 0.567857516 0.180368379 106452551.2 123119863.6 26352625.67 0.040714274 0.027177186 1.565795513 -0.690354466 VEHES(ph)FEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;VEHES(1)FEK;VEHES(1)FEK 95.62 0.0099869 15537420000 6137960 5191237 6037399 6035127 4744977 7173660 7671260 7519190 5472820 TRUE FALSE 5847830.795 5720229.952 6314219.716 5428464.568 5572499.486 6925234.355 6500868.395 6860769.862 6321516.974 0.925067641 0.904882479 0.998845648 0.858728149 0.881513015 1.095501979 1.028371579 1.085304349 1 22.59183937 2.24075836 24.99999912 1.053300983 0.914975779 0.705466635 0.044458545 29.83258122 339359.1746 0.014754892 0.011788866 174.0838009 -2.24075836 -0.138325204 VEHTNTGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEHTNTGTK 9 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 102.06 0.0036456 58408000 92474 83406 82460 101740 67976 90217 107730 106930 88151 FALSE TRUE 88102.93729 91905.16622 86240.87256 91512.90191 79830.99288 87092.76267 91293.8099 97566.64233 101821.0069 0.865272698 0.902614981 0.846985069 0.898762492 0.784032641 0.855351615 0.896610756 0.958217222 1 16.63567571 1.216935138 2.10478043 0.997820411 0.863051173 0.700903684 0.032571893 0.170574037 1.314300587 0.029856793 0.008599244 16.47916258 -1.216935138 -0.134769238 VEHTPDGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VEHTPDGVK 9 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 111.46 0.002122 1490540000 2346470 1852960 1827690 2202590 1692020 2043620 2517070 2330290 1850030 FALSE TRUE 2235557.013 2041778.731 1911491.394 1981181.469 1987107.752 1972848.927 2133044.742 2126237.454 2136923.204 1.046156928 0.955475951 0.894506359 0.927118703 0.929891982 0.923219385 0.998185025 0.994999469 1 21.02710363 1.639583354 7.703287291 0.997841949 0.9516263 0.266932156 0.039607021 0.20913687 25.13874801 0.022679085 0.01154566 43.60972558 -1.639583354 -0.046215648 VEIAGPGFINVHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEIAGPGFINVHLR 14 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 193 3.09E-07 645710000 2533000 2046300 1488770 1775230 2267200 1973820 3117700 2508700 1945000 FALSE TRUE 2413270.11 2254820.296 1557031.577 1596780.508 2662598.962 1905466.118 2642037.605 2289024.929 2246620.666 1.074177829 1.003649762 0.693054952 0.710747716 1.185157335 0.848147686 1.176005208 1.018874687 1 21.09932512 2.723374098 24.96481125 1.049821612 0.905402798 0.240744354 0.148873569 1460.1888 2400371.649 0.050332477 0.047616134 528.9006469 -2.723374098 -0.144418814 VEIFYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VEIFYR 6 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EQT9;K7ES75;K7EN99;K7ERZ6;K7EJD3 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;;; 168.62 0.01465 1359180000 2338922 1268796 1318644 1725608 2043865 1575805 2518589 2033859 2505276 FALSE TRUE 2228365.792 1398087.755 1379105.132 1552146.605 2400314.409 1521234.478 2134331.991 1855763.524 2893781.407 0.770053255 0.483135233 0.476575435 0.536373135 0.829473299 0.525690874 0.737558126 0.64129361 1 21.46452452 -0.116874033 0.445494935 1.05772528 0.58925231 0.500070673 0.120325366 4.171647181 0.981227517 0.53298348 0.066953881 0.764057365 0.116874033 -0.46847297 VEILANDQGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;; 152.54 7.65E-05 1813895000 2052340 1646070 1803090 2046210 1884160 1780920 2153030 1955530 2115510 FALSE TRUE 1955329.956 1813806.404 1885763.46 1840521.083 2212756.907 1719246.294 1824545.73 1784293.426 2443572.486 0.800193146 0.742276488 0.77172397 0.75320912 0.905541751 0.703579003 0.746671417 0.730198689 1 21.22056047 -1.38931165 5.742121648 1.00007232 0.767775511 0.637796911 0.054657522 4.71E-05 5.01E-06 0.049229256 0.011599845 0.040802648 1.38931165 -0.232296809 VEKIPGGIIEDSCVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEKIPGGIIEDSCVLR 16 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 156.13 1.76E-07 1052770000 1209880 851000 1098850 1081810 1057740 1084810 1371820 1247240 1260290 FALSE TRUE 1152691.37 937717.8675 1149233.359 973064.4035 1242209.521 1047242.758 1162523.664 1138025.054 1455729.337 0.791830831 0.644156743 0.789455382 0.668437723 0.853324509 0.719393868 0.798585035 0.781755938 1 20.47331071 -1.395232321 0.281215994 1.19085303 0.716471476 0.625559501 0.060798088 11.61751226 0.659647659 1.662551088 0.066784508 0.040250166 1.395232321 -0.474381554 VEKPDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEKPDTK 7 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 101.64 0.0081244 5470040000 9793200 9096200 8105000 10702600 5258380 9909400 10211500 10337400 5633590 FALSE TRUE 9330294.844 10023113.12 8476622.267 9626754.314 6175439.807 9566234.993 8653548.128 9432202.454 6507218.365 1.433837674 1.540306865 1.302649119 1.47939623 0.949013766 1.470095893 1.329838288 1.449498376 1 22.63360954 -4.466878866 0.135265609 9.06E-15 1.522365584 0.314942789 0.166912318 139.2164647 1.341291244 39.54436099 1.082954111 3.41E-05 4.466878866 1.522365584 VEKPGGQDKGSQEDDPAATQRPPS(ph)NGGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEKPGGQDKGSQEDDPAATQRPPSNGGAK 29 3 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 VEKPGGQDKGSQEDDPAAT(0.159)QRPPS(0.841)NGGAK 136.12 3.70E-06 93680000 99831 68547 82187 89009 42121 86754 105260 110370 49893 TRUE FALSE 95112.18648 75532.01723 85955.35524 80061.64621 49466.88906 83749.68723 89200.65377 100705.4177 57630.15162 1.650389315 1.310633672 1.491499724 1.38923192 0.85835084 1.453226911 1.547812235 1.74744322 1 15.81453619 4.624527686 2.794957246 1.372805673 1.669387455 0.111669357 0.258195064 0.810714061 10.09079522 0.061827002 0.48519752 42123.81399 -4.624527686 0.296581782 VELAQLQEEWNEHNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VELAQLQEEWNEHNAK 16 0 Q9H307 Q9H307 PNN Pinin 0 ;; 315.82 8.02E-58 359993000 320858 297240 302715 372021 262084 307337 372559 369155 284338 FALSE TRUE 305691.6782 327529.0939 316594.7822 334624.7423 307791.3666 296693.8426 315718.282 336829.8312 328431.6848 0.930761837 0.997251815 0.963959316 1.018856455 0.937154912 0.903365468 0.961290572 1.025570451 1 18.32523379 1.248489384 24.38718496 1.012785222 0.959629833 0.315474977 0.032957541 164.9292457 405110.7925 0.022668654 0.008051014 17.72104729 -1.248489384 -0.053155389 VELS(ph)PGPPKPAGR ddPTM_SK-BR-3_Trastuzumab_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 160.8 2.62E-05 1442830000 3271910 3275700 2875420 3676070 2012930 3379530 3452820 3604790 2248760 TRUE FALSE 3117253.299 3609497.554 3007260.851 3306544.46 2363984.355 3262496.029 2926028.894 3289135.477 2597486.216 1.200103885 1.389611823 1.157758156 1.272978636 0.910104678 1.256020536 1.126484859 1.266276393 1 21.30868466 7.99999998 0.023637886 4.55E-08 2.788598872 0.198898373 0.124674819 2966.244679 5.396581216 223.3715788 449.6326555 99999995.38 -7.99999998 2.788598826 VELSNGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VELSNGEKR 9 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 72.325 0.075473 130180000 71475 60497 78034 91209 57431 85785 90863 99990 79679 FALSE TRUE 68096.5184 66661.71308 81611.93609 82040.49803 67446.94822 82814.24394 77000.18054 91234.34552 92035.21238 0.739896358 0.724306614 0.886746865 0.891403365 0.732838513 0.899810429 0.836638266 0.991298256 1 16.48989832 7.672199261 0.083900775 1.158339593 1.18E-15 0.569101369 0.065469945 109.8991051 0.71270427 1.49106506 14.73829824 47010975.27 -7.672199261 -1.158339593 VEMYS(ph)GS(ph)DDDDDFNKLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEMYSGSDDDDDFNKLPK 18 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 VEMY(0.016)S(0.992)GS(0.992)DDDDDFNKLPK;VEMY(0.152)S(0.931)GS(0.917)DDDDDFNKLPK;VEMY(0.081)S(0.936)GS(0.984)DDDDDFNKLPK;VEMY(0.006)S(0.998)GS(0.996)DDDDDFNKLPK 128.88 1.47E-05 474810000 2004220 1910440 1763400 2147800 878700 2329320 2040910 2483500 986240 TRUE FALSE 1909484.493 2105116.008 1844253.634 1931899.063 1031945.002 2248655.064 1729531.696 2266031.574 1139181.062 1.676190516 1.847920474 1.61892933 1.695866555 0.905865657 1.973922442 1.518223707 1.989175952 1 20.11956564 3.337907764 2.639823083 1.538691233 1.755795043 0.074317593 0.353251302 0.754761718 10.6629464 0.095616487 0.135413993 2177.247315 -3.337907764 0.21710381 VENMSSNQDGNDS(ph)DEFM ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VENMSSNQDGNDSDEFM 17 0 Q86WR0;Q86WR0-2 Q86WR0 CCDC25 Coiled-coil domain-containing protein 25 1 VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM;VENMSSNQDGNDS(1)DEFM 285.34 1.83E-36 404418000 632108 598091 661528 728096 590785 677152 718624 688265 674946 TRUE FALSE 602229.5076 659037.1529 691859.7131 654906.4068 693817.717 653702.0564 608984.7104 627996.8679 779613.1785 0.7724722 0.845338651 0.887439736 0.840040195 0.889951243 0.83849539 0.781137014 0.805523669 1 19.57239895 4.479695098 2.459113947 0.849856588 0.77198323 0.154982401 0.060099693 0.627216886 6.625771984 0.014226259 0.080922992 30178.32271 -4.479695098 -0.077873358 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 VENS(0.012)PQVDGS(0.988)PPGLEGLLGGIGEK;VENS(0.007)PQVDGS(0.993)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENS(0.002)PQVDGS(0.998)PPGLEGLLGGIGEK 210 3.00E-25 114954500 214340.5 206465.4 220002 252383 165475 247020 271589 288452 214627.2 TRUE FALSE 204209.0493 227504.459 230089.3093 227012.9813 194333.7876 238465.6355 230153.11 263193.6137 247910.49 0.823720889 0.917687908 0.928114455 0.915705428 0.783886909 0.961902159 0.928371809 1.061647749 1 17.91945979 1.550758667 1.854675688 1.026819376 0.882393867 0.531990498 0.053958159 0.243104413 1.688273654 0.041569919 0.014260528 35.54337528 -1.550758667 -0.144425509 VEPSSQSPGRS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 VEPSSQS(0.319)PGRS(0.681)PR;VEPS(0.001)S(0.002)QS(0.244)PGRS(0.753)PR;VEPSSQS(0.032)PGRS(0.968)PR;VEPSSQS(0.017)PGRS(0.983)PR;VEPSSQS(0.045)PGRS(0.955)PR;VEPSSQS(0.038)PGRS(0.961)PR 134.76 5.56E-05 1974080000 1352810 1302920 1279860 1507580 1354830 1281020 1418240 1333190 1349130 TRUE FALSE 1288865.352 1435689.029 1338542.847 1356035.194 1591111.923 1236657.956 1201861.44 1216448.816 1558346.19 0.827072547 0.921290172 0.85895089 0.870175833 1.021025965 0.793570751 0.77124162 0.780602426 1 20.57158434 VEQATKPS(ph)FESGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 VEQAT(0.001)KPS(0.999)FESGR;VEQATKPS(1)FESGR;VEQATKPS(1)FESGR 120.9 0.00015316 688220000 766630 730390 593320 827720 438780 692260 704450 727480 481850 TRUE FALSE 730392.9192 804817.5714 620524.3089 744516.013 515303.0931 668286.8626 596973.2144 663777.9946 556572.8371 1.312304285 1.446023805 1.114902251 1.33767939 0.925850237 1.20071771 1.072587763 1.192616582 1 19.08621098 3.384090076 1.350668831 1.100073649 1.376282501 0.42490898 0.120293187 0.333306053 1.256991118 0.036420992 0.062762829 2421.531237 -3.384090076 0.276208851 VEQATKPSFESGR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 184.76 8.42E-06 2999150000 3535930 3385880 2614370 3988770 2470680 3243280 3389760 3326630 2533970 FALSE TRUE 3368793.596 3730905.021 2734241.45 3587811.261 2901565.81 3130964.4 2872589.855 3035332.642 2926925.126 1.150966783 1.274684135 0.934168567 1.225795368 0.991335851 1.069711136 0.981436057 1.037038022 1 21.48095441 3.332135811 0.692088323 1.006374848 1.218248611 0.295893232 0.093210816 0.8228812 0.832204914 0.049602689 0.103444056 2148.502241 -3.332135811 0.211873764 VEQHVVDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VEQHVVDGK 9 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 121.6 0.00060923 1747080000 7114160 4642970 5658400 7003990 4781830 6218490 7566040 6845240 4914840 FALSE TRUE 6777887.756 5116093.922 5917843.237 6299935.618 5615779.638 6003142.132 6411701.638 6245834.497 5677008.286 1.193918947 0.90119543 1.042422864 1.1097281 0.989214628 1.057448189 1.129415586 1.100198235 1 22.43669942 1.985915991 23.72948313 1.091546071 1.041653247 0.012614747 0.081777117 941.1899343 1585765.502 0.031394978 0.021193009 96.80905739 -1.985915991 -0.049892824 VEQIAAIAQELNELDYYDSHNVNTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VEQIAAIAQELNELDYYDSHNVNTR 25 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;;; 320.72 6.37E-75 1201847000 1056041 681352 494018 944647 945328 664848 1063904 810825 843764 FALSE TRUE 1006124.035 750782.5434 516669.214 849689.2888 1110192.904 641824.1471 901585.9049 739824.8645 974610.6118 1.032334373 0.770341031 0.530128861 0.871824376 1.13911432 0.658544181 0.925072941 0.759097896 1 19.89446641 4.623226811 3.32597496 0.827070851 1.037318033 0.118181213 0.171126075 0.565361068 10.4118948 0.039544301 0.253669398 41997.82613 -4.623226811 0.210247182 VEQMPQAS(ph)PGLAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VEQMPQASPGLAPR 14 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 VEQMPQAS(1)PGLAPR;VEQMPQAS(1)PGLAPR;VEQMPQAS(1)PGLAPR 202.52 6.38E-08 294630000 792840 675790 704450 751020 754950 699070 843700 780960 857000 TRUE FALSE 755364.0245 744653.7693 736749.7293 675526.0428 886613.041 674861.0306 714978.0694 712575.0023 989899.1831 0.763071672 0.75225213 0.744267438 0.682419032 0.895659938 0.681747235 0.722273623 0.719846035 1 19.91692207 -1.086050153 5.386565448 1.000003045 0.744948955 0.642268109 0.059763246 1.97E-06 3.35E-07 0.052284036 0.012323318 0.082025682 1.086050153 -0.25505409 VEQNSRPVS(ph)CSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEQNSRPVSCSGR 13 1 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VEQNSRPVS(0.994)CS(0.006)GR;VEQNSRPVS(0.992)CS(0.008)GR 123.63 0.00013393 534500000 197809 193837 186463 206902 215424 197303 246863 222730 219310 TRUE FALSE 188458.9606 213589.2107 195012.513 186103.8179 252993.8774 190470.3476 209199.5154 203226.5804 253319.4747 0.743957648 0.84316143 0.769828349 0.734660523 0.998714677 0.751897768 0.825832738 0.802254073 1 17.95059847 -5 0.239449116 2.080327621 0.789230813 0.393083916 0.075504086 171.3439617 1.708718406 90.21082623 0.108596915 1.00E-05 5 -1.291096807 VEQVLSLEPQHELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEQVLSLEPQHELK 14 0 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 157.8 5.20E-06 266380000 440820 385630 391940 573850 525320 452410 531460 449780 461700 FALSE TRUE 419983.3122 424926.1354 409910.8367 516165.5078 616935.6417 436742.9283 450376.0161 410394.8788 533298.078 0.787520769 0.796789175 0.768633628 0.967874307 1.156830799 0.818947126 0.844510856 0.769541267 1 19.0245826 3.247414069 24.99418437 0.916801897 0.787445675 0.276340796 0.10753431 283.8160401 801236.4496 0.030923942 0.041255051 1767.722414 -3.247414069 -0.129356222 VERLS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.942)S(0.058)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.96)S(0.04)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.809)S(0.19)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.965)S(0.035)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.97)S(0.03)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 402.16 3.63E-199 1808450000 748039 690593 692406 882567 624595 753211 908271 919196 343326 TRUE FALSE 712680.6789 760965.2118 724153.5 793849.6884 733524.1702 727127.1142 769697.5774 838706.3253 396567.2426 1.797124428 1.918880659 1.826054757 2.001803485 1.849684219 1.833553143 1.940900545 2.114915795 1 18.59720599 -1.609098456 6.34627178 0.99701776 1.902215707 0.900596904 0.095015825 0.003743561 0.000230586 0.085902841 0.020219252 0.024598099 1.609098456 0.905197947 VERPPS(ph)PFSMAPQASLPPVPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VERPPSPFSMAPQASLPPVPPR 22 1 P22681;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 VERPPS(0.985)PFS(0.015)MAPQASLPPVPPR;VERPPS(0.986)PFS(0.014)MAPQASLPPVPPR;VERPPS(0.999)PFS(0.001)MAPQASLPPVPPR;VERPPS(0.997)PFS(0.003)MAPQASLPPVPPR;VERPPS(0.997)PFS(0.003)MAPQASLPPVPPR;VERPPS(1)PFSMAPQASLPPVPPR 161.2 1.07E-11 916090000 1485314 1274037 1573961 1516480 1136017 1756763 1852955 1669490 1126594 TRUE FALSE 1415106.151 1403862.819 1646128.669 1364040.549 1334138.005 1695925.857 1570252.683 1523300.605 1301300.444 1.087455366 1.078815292 1.264987403 1.04821339 1.02523442 1.303254652 1.206679588 1.170598698 1 20.31152266 2.251704434 24.99939033 1.193566107 1.101757974 0.089081482 0.09792093 385.7946286 733776.423 0.03169287 0.026364192 178.5272168 -2.251704434 -0.091808133 VES(ph)MEALPILSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VESMEALPILSR 12 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VES(1)MEALPILSR 80.318 0.021674 8184400 18334 13694 16394 14111 14568 15036 19948 16339 15364 TRUE FALSE 17467.38815 15089.43417 17145.68112 12692.53547 17108.65459 14515.29955 16904.56623 14908.27054 17746.57065 0.984268369 0.850273242 0.966140527 0.715210602 0.964054122 0.81792138 0.952553964 0.840064869 1 14.11525264 -1.156469326 3.438069147 1.000136869 0.89012472 0.151073197 0.084265979 24197927.69 40065525.8 37219.08811 0.017686832 0.069747826 1.156469326 -0.110012149 VESEIKVPDVELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VESEIKVPDVELK 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 148.91 3.97E-05 143260000 217020 195980 200050 221250 119640 194890 221720 244510 130860 FALSE TRUE 206761.8947 215950.5848 209222.4904 199009.5297 140505.1781 188140.9104 187892.5418 223099.4082 151153.1005 1.367897146 1.428687762 1.384175976 1.316608982 0.929555383 1.244704276 1.243061117 1.47598301 1 17.20565105 2.991234026 23.95477783 1.195039255 1.391557897 0.312261292 0.146900214 300.0276334 819891.128 0.041347031 0.047092089 980.0179404 -2.991234026 0.196518642 VESGDPSLHPPPSPGTPSAT(ph)PASPPASATPSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.074)AT(0.655)PAS(0.271)PPASATPSQR 178.41 5.32E-19 118990000 59300 48551 59165 59915 67011 54483 70194 62586 62654 TRUE FALSE 56497.00652 53498.4021 61877.77377 53892.23037 78697.69718 52596.24005 59484.6161 57105.63805 72370.06233 0.780668203 0.739233882 0.855018937 0.744675749 1.087434426 0.726767925 0.821950599 0.789078194 1 16.14310539 -5 0.176063201 1.714788847 0.772376212 0.224323201 0.104012148 194.1967309 1.855562884 49.0235525 0.317767784 1.00E-05 5 -0.942412635 VESLESLYFT(ph)PIPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VESLESLYFTPIPAR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VESLESLYFT(1)PIPAR;VESLESLYFT(1)PIPAR 130.98 0.00063039 25749000 45730 49822 48055 50027 39574 45959 45949 50530 44445 TRUE FALSE 43568.43353 54898.91844 50258.36928 44998.19091 46475.69307 44367.42831 38938.63614 46105.32532 51337.30361 0.848670079 1.069376741 0.978983424 0.876520342 0.905300626 0.864233709 0.758486196 0.898086227 1 15.6477199 3.190753323 5.019332085 0.862734068 0.971393731 0.157616192 0.079981962 0.250421495 13.77092248 0.022999981 0.02834815 1551.505513 -3.190753323 0.108659663 VESTDVSDLLHQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VESTDVSDLLHQYR 14 0 Q5JNW7;A0A140T998;X5D2R7;P28062-2;P28062 Q5JNW7 PSMB8;PSM8 Proteasome subunit beta type;Proteasome subunit beta type-8 0 ; 187.74 9.13E-07 165018000 161530 126447 138919 163318 162626 143183 173704 152583 158696 FALSE TRUE 153894.797 139332.0931 145288.5736 146900.9644 190987.9229 138224.5368 147202.2645 139222.0236 183305.7652 0.839552411 0.760107534 0.792602314 0.801398495 1.04190898 0.754065409 0.803042198 0.759507065 1 17.48389264 -2.204135879 2.288520104 1.5383987 0.816405389 0.316854302 0.083434051 11357465.6 1847178.373 31760908.22 0.019109165 0.006249771 2.204135879 -0.721993311 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_SK-BR-3_Trastuzumab_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 ; 245.04 8.16E-38 381050000 1738670 1507800 1569260 1854620 1091450 1809710 1961680 1890010 1312560 FALSE TRUE 1656486.515 1661446.534 1641212.123 1668190.074 1281798.534 1747039.289 1662389.687 1724510.705 1516105.101 1.092593458 1.095865012 1.0825187 1.100312948 0.845454931 1.152320698 1.096487101 1.137461185 1 20.53193834 -0.820976894 8.20837516 1 1.077216929 0.072252418 0.084656583 0 0 0.076440583 0.018017218 0.15101605 0.820976894 0.077216928 VEVGKDQEFTVDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 188.59 7.44E-07 2198650000 7514280 6869020 6445810 7886090 4878290 7414270 7727390 8210370 5647220 FALSE TRUE 7159094.876 7568980.947 6741356.764 7093365.251 5729062.231 7157511.971 6548434.732 7491426.477 6522962.036 1.097522082 1.160359497 1.033480914 1.087445429 0.878291519 1.097279416 1.003905081 1.148470041 1 22.6370958 3.725944649 23.58740597 1.033385989 1.128940787 0.219006504 0.073228301 424.5343801 793730.3097 0.017649294 0.027564855 5320.40446 -3.725944649 0.095554799 VEVRPMMYVALTYDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VEVRPMMYVALTYDHR 16 1 P36957-2;P36957 P36957-2 DLST "Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial" 0 117.26 0.00021867 146740000 198700 138620 161900 158350 200160 138530 204420 156010 170000 FALSE TRUE 189307.8448 152745.5356 169323.2751 142432.3572 235067.8406 133732.6714 173231.9746 142348.9373 196362.7318 0.964072169 0.777874367 0.862298429 0.725353309 1.197110259 0.681049149 0.882203935 0.724928483 1 17.58316162 -0.950594795 4.163657018 1.000005998 0.853285647 0.088960583 0.148922438 14093515.82 6770398.61 744.3654724 0.030459724 0.112048283 0.950594795 -0.146720351 VEVTEFEDIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VEVTEFEDIK 10 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;; 167.12 1.24E-05 892610000 2108333 1931596 1772040 2224834 1378270 2046564 2293621 2203213 1498320 FALSE TRUE 2008676.277 2128427.828 1853289.787 2001189.459 1618639.852 1975690.976 1943686.991 2010287.99 1730671.813 1.160633843 1.229827523 1.070849928 1.156307882 0.935266779 1.141574596 1.123082364 1.161565107 1 20.72290074 3.733826271 24.90069992 1.091445476 1.195230684 0.280934726 0.07318913 438.42347 2305929.382 0.018060007 0.029031861 5417.841189 -3.733826271 0.103785208 VEVTEFEDIKSGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEVTEFEDIKSGYR 14 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;; 220.85 4.09E-12 534855000 693070 327183 873650 529550 783822 740640 1167150 828100 1219910 FALSE TRUE 660309.9546 360523.3197 913707.7167 476318.6279 920520.3086 714991.4511 989079.8313 755587.174 1409087.412 0.468608227 0.255855894 0.648439344 0.338033413 0.653274098 0.507414547 0.701929364 0.536224486 1 20.42632968 -4.781044288 0.098154106 2.632545878 0.121829744 0.636159493 0.124461731 95.55136933 0.670603125 32.03400082 1.967292105 1.66E-05 4.781044288 -2.510716134 VEWSAFLEAADNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEWSAFLEAADNLR 14 0 F5GYQ2;Q9UI30;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ; 199.82 4.68E-08 101838000 178963 158892 176259 169561 182107 157180 212006 186822 189114 FALSE TRUE 170503.7737 175083.2754 184340.6495 152516.4061 213866.4031 151736.8172 179660.5909 170462.8753 218440.8333 0.780548999 0.801513494 0.843892814 0.698204653 0.979058722 0.694635774 0.82246798 0.78036177 1 17.73688304 -1.121373187 4.870927422 1.000010522 0.79963808 0.385084511 0.07939015 7.65E-06 1.38E-06 0.064826888 0.015279042 0.075618283 1.121373187 -0.200372441 VEYEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VEYEKR 6 1 P63279 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ;;; 115.3 0.039363 1046220000 1780610 1361110 1436140 1546080 1506700 1651580 2278000 1785870 1873290 FALSE TRUE 1696444.094 1499808.656 1501988.44 1390665.101 1769468.003 1594385.37 1930449.262 1629489.755 2163790.246 0.784015039 0.693139577 0.694146968 0.642698664 0.817763185 0.736848395 0.892160996 0.753071957 1 21.04512922 0.909382082 0.506284167 1.001654015 0.711060301 0.627444219 0.063942872 0.691788025 0.428165674 0.073364768 0.03318453 8.116748353 -0.909382082 -0.290593714 VEYFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEYFLK 6 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ; 118.06 0.05163 465240000 2009670 1854660 1284160 1818570 1386660 1587460 1878010 1906010 1388270 FALSE TRUE 1914676.882 2043651.963 1343040.006 1635763.889 1628493.065 1532485.862 1591485.082 1739109.66 1603555.821 1.194019476 1.274450153 0.837538668 1.020085404 1.015551216 0.955679772 0.992472517 1.084533283 1 20.61284315 3.755105739 24.99997374 0.987227696 1.234234839 0.71424648 0.065130224 359.9078397 543825.593 0.015400843 0.027665515 5689.914477 -3.755105739 0.247007143 VEYHAGGSTQNSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VEYHAGGSTQNSIK 14 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 ; 189.86 6.70E-07 319310000 263840 255830 219277 277730 203169 240110 264910 274330 225550 FALSE TRUE 251368.8061 281899.3679 229331.0673 249812.0527 238601.6093 231794.9305 224493.1141 250308.2109 260527.1421 0.964846903 1.082034546 0.880257871 0.958871505 0.915841656 0.889715093 0.861688008 0.960775944 1 17.99107416 3.730539113 24.99502385 0.91403677 1.023440726 0.391349074 0.050472288 451.2522006 1406103.476 0.012607063 0.019917646 5376.988565 -3.730539113 0.109403955 VEYSEEELKTHISK ddPTM_SK-BR-3_Trastuzumab_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 2244150000 3777907 2569987 3485493 3663262 2875185 3600540 5032426 4386563 3252906 FALSE TRUE 3599332.823 2831871.597 3645306.302 3295023.944 3376616.354 3475852.397 4264636.987 4002452.289 3757350.049 0.957944502 0.75368852 0.970180115 0.87695421 0.898669623 0.925080802 1.135011892 1.06523274 1 21.8412841 1.881211741 4.828975038 1.076387339 0.883783648 0.591742013 0.066500253 0.13697224 4.639628435 0.029362433 0.017103575 76.06970648 -1.881211741 -0.19260369 VFDAIMNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFDAIMNFK 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 122.52 0.0013577 97154000 815290 758040 589660 624350 641620 660690 865340 770260 607520 FALSE TRUE 776752.8574 835285.1378 616696.4943 561589.1518 753518.3249 637810.1396 733316.4899 702811.951 701731.0988 1.106909554 1.190320821 0.878821667 0.800291098 1.073799246 0.90890961 1.045010676 1.001540265 1 19.42055877 3.746103421 24.91062703 0.960580736 1.148615197 0.477029115 0.082801207 434.0922793 1433615.106 0.021083603 0.0370887 5573.184503 -3.746103421 0.188034461 VFDAIMNFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFDAIMNFKK 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 151.15 3.26E-05 225202000 1114320 669650 736980 718950 1092670 848830 1636630 1176300 1331510 FALSE TRUE 1061648.302 737888.0963 770771.262 646679.7801 1283231.302 819434.8043 1386932.035 1073296.936 1537993.77 0.690281276 0.479773137 0.501153696 0.420469701 0.834354031 0.532794619 0.901780008 0.697855191 1 20.55261823 1.559591971 0.68879675 0.967944759 0.541124855 0.51396208 0.134808611 0.482571638 0.489507723 0.116224527 0.054279355 36.27370951 -1.559591971 -0.426819904 VFDDES(ph)DEKEDEEYADEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK 283.64 1.09E-39 2191490000 3130500 4234620 2349590 3895280 1223120 3826460 2533260 4084630 902981 TRUE FALSE 2982527.469 4666132.592 2457321.026 3503719.054 1436431.741 3693948.731 2146764.66 3726958.143 1043010.682 2.85953684 4.473715058 2.35598836 3.359236023 1.377197536 3.541621189 2.058238423 3.573269391 1 19.9923225 3.716299213 24.34020012 2.538119693 3.666626062 0.215347993 0.944726826 704.0583518 769804.0712 0.219203215 0.339915003 5203.543781 -3.716299213 1.128506369 VFDDES(ph)DEKEDEEYADEKGLEAADKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VFDDESDEKEDEEYADEKGLEAADKK 26 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEKGLEAADKK;VFDDES(1)DEKEDEEYADEKGLEAADKK;VFDDES(0.994)DEKEDEEY(0.006)ADEKGLEAADKK 129.03 5.91E-05 352460000 598260 605520 494100 641260 182540 701950 519260 846020 167069 TRUE FALSE 569981.4354 667223.1764 516754.9737 576799.3265 214374.9182 677641.2955 440037.3501 771938.0038 192977.2072 2.9536205 3.457523227 2.677803151 2.988950533 1.110882064 3.511509495 2.280255562 4.000151182 1 17.55807093 3.45188111 2.413783671 2.529446815 3.195854934 0.0863915 0.937126199 0.691556152 8.106242368 0.246005381 0.380705075 2830.616998 -3.45188111 0.666408119 VFDFTFSPEEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFDFTFSPEEMK 12 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 183.33 0.00026716 0 89614 70826 75267 84881 74256 80325 99092 89515 76176 FALSE TRUE 85378.12382 78043.24992 78718.0664 76348.60062 87206.22289 77543.32511 83973.69545 81676.59205 87988.98503 0.970327409 0.886966134 0.894635463 0.867706345 0.991103862 0.881284459 0.954365997 0.928259282 1 16.42503531 0.467384434 0.634892405 1.001771246 0.915316052 0.286782214 0.040020196 2.29773782 1.530393592 0.046939051 0.014821412 2.933488796 -0.467384434 -0.086455194 VFDGIPPPYDKK ddPTM_SK-BR-3_Trastuzumab_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 0 101.39 0.0043275 222790000 609290 479500 524800 547910 385240 599280 625280 670890 402600 FALSE TRUE 580490.0692 528361.5951 548862.5991 492833.0458 452425.734 578526.7833 529882.0519 612143.315 465033.1518 1.248276745 1.136180492 1.180265529 1.059780456 0.972889206 1.244054926 1.139450058 1.316343389 1 18.82697404 -0.859674479 0.010827017 4.66E-05 2.204721343 0.091456034 0.104941512 12729.78033 27.92862969 3017.41388 2674.617442 0.13814193 0.859674479 2.204674758 VFDKDGNGYISAAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;;; 276.38 2.46E-35 16652319000 17639298 15576067 7837485 19573053 11860789 12267613 13861066 12754055 9584894 FALSE TRUE 16805523.34 17163285.94 8196841.44 17605532.53 13929306.85 11842782.49 11746305.81 11637242.33 11071270.41 1.517939922 1.550254424 0.740370449 1.590199848 1.258148914 1.069685957 1.06097181 1.051120775 1 23.40031744 7.3857077 0.215298241 0.958140093 3.590869227 0.301519033 0.231236356 39.75315975 0.632414713 0.353005334 34.22867508 24305675.78 -7.3857077 2.632729134 VFDKEGNGTVMGAELR ddPTM_SK-BR-3_Trastuzumab_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 ; 252.05 1.47E-26 1313930000 2009000 1476500 1582460 1822440 1695660 1757400 2277800 2058060 2035010 FALSE TRUE 1914038.551 1626957.029 1655017.356 1639244.869 1991382.567 1696540.797 1930279.775 1877845.356 2350588.957 0.814280415 0.692148673 0.704086247 0.697376231 0.847184516 0.721751369 0.821189842 0.798882914 1 21.16459085 0.324363092 0.518499166 1.015468935 0.736142145 0.695571532 0.051753984 1.348253611 0.568920457 0.094369925 0.023995896 2.110391808 -0.324363092 -0.279326789 VFDKYMTISGFQIEETIDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFDKYMTISGFQIEETIDR 19 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 118.96 6.29E-05 43332000 60412 39354 62236 55987 73526 57814 72606 78610 80560 FALSE TRUE 57556.44449 43364.21734 65089.58216 50359.08039 86348.91112 55811.88668 61528.6212 71726.49166 93052.83336 0.61853511 0.466017162 0.699490599 0.541188039 0.927955743 0.599787074 0.661222437 0.770814698 1 16.50576246 -5 0.101351253 2.190406837 0.394338384 0.515722236 0.114842568 136.1101253 0.935829162 33.85348293 1.722672325 1.00E-05 5 -1.796068453 VFDMLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 128.48 0.0087314 590699000 1804930 1874050 1341210 1579870 1688530 1400600 1827310 1622110 1440380 FALSE TRUE 1719614.536 2065017.826 1402705.805 1421058.466 1983009.097 1352096.871 1548520.299 1480069.449 1663746.774 1.033579486 1.241185172 0.843100541 0.854131463 1.191893579 0.812681889 0.930742781 0.889600192 1 20.66600444 3.735593484 24.99566746 0.929167544 1.13738233 0.346896427 0.117268541 241.1570527 2031552.85 0.02893099 0.047027767 5439.932169 -3.735593484 0.208214785 VFDMLNRR ddPTM_SK-BR-3_Trastuzumab_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 ; 115.49 0.0039332 3741300000 4030500 2568500 2015130 1857810 6004700 2135710 4949700 3103700 4973600 FALSE TRUE 3839986.253 2830233.07 2107525.704 1671059.409 7051917.779 2061749.827 4194532.358 2831923.574 5744880.486 0.668418823 0.492653081 0.366852837 0.290878011 1.2275134 0.35888472 0.730133963 0.492947343 1 22.45384545 VFDYSEYWEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFDYSEYWEGAR 12 0 P11498 P11498 PC "Pyruvate carboxylase, mitochondrial" 0 ; 163.38 0.0001399 121660000 95618 77319 79409 79800 115464 62986 88864 82278 105602 FALSE TRUE 91098.32664 85197.894 83049.9812 71778.35239 135600.885 60804.77903 75306.1647 75073.30214 121978.2188 0.746840932 0.698468094 0.680859107 0.58845221 1.111681137 0.498488825 0.617373867 0.615464817 1 16.89626403 VFEEDALSWEDKLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 250.31 8.11E-19 355570000 329923 338083 298999 398610 242480 355464 323342 373812 249515 FALSE TRUE 314328.1936 372534.0421 312708.3999 358540.9655 284768.4352 343154.1925 274010.2393 341079.0396 288208.5119 1.090627725 1.292585148 1.08500751 1.244033229 0.988063931 1.190645586 0.95073611 1.183445407 1 18.13675342 2.741830886 24.99838078 1.061193431 1.182265513 0.253935795 0.098228233 359.2621511 2746260.081 0.027208959 0.02776951 551.8625032 -2.741830886 0.121072082 VFELMTSLHTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFELMTSLHTK 11 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 220.1 9.40E-12 682610000 2072980 1782970 1754060 2097590 1842070 1922670 2457800 2359400 1791020 FALSE TRUE 1974994.344 1964656.67 1834485.386 1886736.268 2163326.425 1856087.456 2082817.469 2152798.428 2068762.234 0.954674399 0.949677366 0.886755063 0.912012138 1.045710517 0.89719709 1.006794031 1.040621485 1 20.98033641 1.591712904 6.504080395 1.021061158 0.94393916 0.386600639 0.044507925 0.129872814 11.55923821 0.022705506 0.010741031 39.0582611 -1.591712904 -0.077121997 VFEVSLADLQNDEVAFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VFEVSLADLQNDEVAFRK 18 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 ;; 252.76 2.76E-30 333482000 381623 301907 409905 371642 404216 396117 512260 453096 525711 FALSE TRUE 363584.4371 332671.6665 428699.5497 334283.8401 474711.1424 382399.369 434105.3287 413420.5122 607235.5769 0.598753517 0.547846139 0.705985561 0.550501079 0.78175779 0.629738084 0.714887838 0.680823931 1 19.21189679 -4.999999999 0.1471385 2.286889493 0.525089795 0.752275111 0.065759241 57.17607183 0.50416146 21.41509089 0.304921111 1.00E-05 4.999999999 -1.761799698 VFFQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFFQSPR 7 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 VFFQS(1)PR;VFFQS(1)PR 102.01 0.0091225 116816000 211690 183381 184061 194141 243230 196859 246560 210870 288050 TRUE FALSE 201683.8332 202067.7324 192500.3789 174625.5778 285649.235 190041.7235 208942.7436 192405.1049 332719.3228 0.60616808 0.607321903 0.578566875 0.524843512 0.858529143 0.571177297 0.627984999 0.578280526 1 18.34394613 -1.867740201 2.594469014 1.172917566 0.618932967 0.641073206 0.089567789 6574907.981 3954738.75 6998076.093 0.021353602 0.013560003 1.867740201 -0.5539846 VFFRPGK ddPTM_SK-BR-3_Trastuzumab_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 ; 71.715 0.048852 1342940000 2109520 1717980 1749800 2189460 2141480 2068800 2652500 2381280 2194940 FALSE TRUE 2009807.17 1893044.115 1830030.061 1969371.321 2514953.434 1997156.937 2247812.408 2172762.499 2535320.085 0.792723247 0.746668685 0.721814209 0.776774236 0.991966832 0.787733647 0.886599062 0.856997313 1 21.27373647 2.925781369 10.01252474 0.887010529 0.756727916 0.551239722 0.064253013 0.417642108 54.69796684 0.017613041 0.01869885 842.9103169 -2.925781369 -0.130282613 VFGNEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFGNEIK 7 0 P19338 P19338 NCL Nucleolin 0 ; 91.065 0.0388 90574000 160904 135144 148113 169304 134079 136950 177730 184017 183646 FALSE TRUE 153298.3868 148915.3272 154904.1276 152285.2403 157462.3351 132207.3872 150614.0243 167903.4959 212124.8837 0.722679886 0.702017249 0.730249676 0.717903706 0.742309588 0.623252609 0.710025253 0.791531352 1 17.69455434 0.869283028 2.706637447 0.99971034 0.706013721 0.892850216 0.032073254 0.148547842 2.155976447 0.029873875 0.007930237 7.400874303 -0.869283028 -0.29369662 VFGNEIKLEKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFGNEIKLEKPK 12 2 P19338 P19338 NCL Nucleolin 0 63.709 0.038673 208090000 435510 257240 396280 292860 383750 419120 680780 519610 587780 FALSE TRUE 414924.3054 283453.0485 414449.83 263421.1564 450675.8785 404605.7693 576914.5076 474110.1938 678929.9204 0.611144527 0.417499715 0.61044567 0.38799462 0.663803236 0.595946293 0.849740879 0.698319782 1 19.37290314 1.53022408 0.684938557 0.972641899 0.501725968 0.692696107 0.100123868 0.318634734 0.323646999 0.084453854 0.039217557 33.90190323 -1.53022408 -0.470915931 VFGS(ph)LER ddPTM_SK-BR-3_Trastuzumab_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 114.99 0.0060646 1607630000 1521030 1519800 1504950 1683320 1494420 1571190 1886050 1639170 1725200 TRUE FALSE 1449133.926 1674669.348 1573953.446 1514109.476 1755046.375 1516779.296 1598298.433 1495635.585 1992735.205 0.727208473 0.840387295 0.789845757 0.759814687 0.880722321 0.761154464 0.802062627 0.750544067 1 20.92631859 -1.124790844 4.293713372 1.00003342 0.791335248 0.684873246 0.044961757 5672193.275 1485900.836 1934.210131 0.009463638 0.075025545 1.124790844 -0.208698172 VFGWVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFGWVHR 7 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 149.94 0.0019825 699540000 1033140 1289430 741100 971240 826970 769610 864690 1013530 653090 FALSE TRUE 984305.5197 1420824.383 775080.168 873609.11 971193.3062 742958.2127 732765.6594 924779.9401 754367.8617 1.304808396 1.883463566 1.027456507 1.158067773 1.287426673 0.984875219 0.971363835 1.225900502 1 19.52490869 3.721674239 24.98530307 1.089095685 1.594135988 0.593644832 0.172139799 454.0567958 671828.3906 0.044323984 0.068867204 5268.345382 -3.721674239 0.505040303 VFHGNESLWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VFHGNESLWK 10 0 Q13268;H0YJG9 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 152.54 1.79E-05 16674240000 18389010 13441260 11269130 10584930 13957820 9731640 16549070 13264160 12254650 FALSE TRUE 17519797.94 14810939.68 11785830.76 9520912.726 16392059.39 9394630.867 14024205.43 12102679.83 14155038.53 1.237707541 1.046336938 0.832624421 0.672616518 1.158037073 0.663695181 0.990757135 0.855008611 1 23.75481234 4.069589789 2.372734759 0.878767687 1.202641407 0.372385511 0.149439601 0.261712901 2.908441095 0.035502351 0.097343294 11737.88335 -4.069589789 0.32387372 VFIDQNLS(ph)PGKGVVSLVAVHPSTVNPLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFIDQNLSPGKGVVSLVAVHPSTVNPLGK 29 1 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGKGVVSLVAVHPSTVNPLGK 233.72 2.03E-45 126980000 293130 222420 284570 322150 253940 280230 449440 426800 349990 TRUE FALSE 279274.3258 245084.8509 297617.816 289766.87 298227.0556 270525.5648 380869.6735 389427.1294 404264.6617 0.690820525 0.606248515 0.736195478 0.716775166 0.73770251 0.669179353 0.942129524 0.963297479 1 18.62494057 1.685225333 4.234132567 0.973391473 0.686399889 0.914748464 0.039679238 0.048975462 2.054387977 0.023797893 0.011314306 48.44236443 -1.685225333 -0.286991584 VFIEDVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VFIEDVSR 8 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;; 154.92 0.00097083 205277000 569685 478369 434659 474065 563003 445965 567918 489413 573863 FALSE TRUE 542757.1191 527115.345 454588.5451 426411.0855 661190.5449 430521.1202 481271.6786 446557.4032 662854.7432 0.818817584 0.795219994 0.685804167 0.643294915 0.997489347 0.649495421 0.72605904 0.673688176 1 19.33833323 VFIGEFAYTYAAMYDKGPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFIGEFAYTYAAMYDKGPFR 20 1 P15559-2;P15559;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 125.88 2.22E-05 58655000 147250 151050 118840 148160 114260 125620 143290 146860 101370 FALSE TRUE 140289.7843 166442.1667 124288.9315 133266.6753 134186.9078 121269.7479 121428.4788 134000.1598 117089.9419 1.198136937 1.421489874 1.061482563 1.138156473 1.146015667 1.035697396 1.037053028 1.144420756 1 16.83725763 3.723747438 24.94444737 1.081493392 1.309813406 0.633338735 0.072564751 403.9586828 680240.6726 0.018516777 0.028815251 5293.555103 -3.723747438 0.228320014 VFIPHGLIMDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFIPHGLIMDR 11 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 157.78 3.04E-05 342260000 576830 577930 512860 556510 563590 557440 615930 565210 508450 FALSE TRUE 549564.3891 636821.7241 536375.1383 500568.5575 661879.9176 538135.713 521958.5662 515717.216 587297.8292 0.935750758 1.084325009 0.913293242 0.85232489 1.126991936 0.916290996 0.888745948 0.878118717 1 19.16373278 2.037212502 24.9997437 0.908074147 0.986309799 0.107481041 0.084957051 289.6753879 194605.7926 0.030245132 0.022337445 108.9463041 -2.037212502 0.078235652 VFITDDFHDMMPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VFITDDFHDMMPK 13 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 167.14 3.24E-05 1277480000 3509790 3839920 3197700 3725470 2668815 3436800 3714430 3603060 2372970 FALSE TRUE 3343889.182 4231212.214 3344317.708 3350978.678 3134255.491 3317782.754 3147725.483 3287556.965 2740958.068 1.219970937 1.543698265 1.220127278 1.22255744 1.143489033 1.210446374 1.14840337 1.19941892 1 21.38624883 2.381290959 0.314185826 1.013007424 1.422634916 0.446981789 0.100418338 1.538262851 0.37185587 0.138591634 0.224934968 240.597416 -2.381290959 0.409627492 VFLAQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFLAQK 6 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 ; 131.72 0.03538 392570000 1710860 1171070 1000450 1152620 1551620 1194390 1902370 1478610 1651480 FALSE TRUE 1629991.038 1290403.364 1046321.622 1036756.448 1822222.037 1153027.975 1612128.517 1349135.07 1907583.084 0.854479709 0.676459849 0.548506448 0.543492159 0.955251728 0.604444433 0.845115754 0.707248393 1 20.86331446 0.105840085 0.537803933 1.020088161 0.701531057 0.310019329 0.134576161 4.439165752 1.673531178 0.332669283 0.05932175 1.275968887 -0.105840085 -0.318557103 VFLENVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFLENVIR 8 0 P62805 P62805 HIST1H4A Histone H4 0 95.815 0.021828 25925000 91217 82415 74456 87537 112690 82537 111630 92924 92392 FALSE TRUE 86905.35318 90813.1822 77869.88125 78737.61445 132343.1003 79678.72299 94598.79327 84787.08194 106719.6795 0.814332967 0.850950665 0.729667495 0.737798453 1.240100242 0.746616963 0.886423139 0.794484038 1 16.70346671 VFLGRHHEPGPGQLTKSAGPTPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFLGRHHEPGPGQLTKSAGPTPEK 24 2 A0A087WYA1;Q9UKN7 A0A087WYA1 MYO15A Unconventional myosin-XV 0 52.909 0.066538 601150000 1735200 1558700 1797200 1643300 1463900 2053900 2259400 2300100 1457100 FALSE TRUE 1653180.535 1717533.302 1879603.398 1478112.362 1719203.697 1982772.928 1914687.033 2098691.05 1683059.626 0.982247158 1.020482742 1.116777664 0.87822935 1.021475217 1.178076461 1.137622817 1.246949911 1 20.68265486 2.289838356 6.386310621 1.151430321 1.002615017 0.398048642 0.083272906 0.173944673 15.65850141 0.026555408 0.021902024 194.9119003 -2.289838356 -0.148815304 VFLKNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFLKNEK 7 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 85.064 0.01923 4559700000 9203700 5656400 7445000 7571800 7102000 8433400 11626200 9769900 8850200 FALSE TRUE 8768659.341 6232793.591 7786360.614 6810668.279 8340586.551 8141349.243 9852409.66 8914395.763 10222643.82 0.857768254 0.609704662 0.761677777 0.66623355 0.815893296 0.796403493 0.963782935 0.87202449 1 23.28526502 2.005779766 1.368086615 0.953595274 0.723283153 0.606164137 0.075104482 0.26897485 0.936915028 0.048899392 0.023125709 101.3397353 -2.005779766 -0.230312121 VFLLDR ddPTM_SK-BR-3_Trastuzumab_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 ; 106.76 0.074087 80728000 156869 136329 131692 151763 174645 121349 176580 163896 179001 FALSE TRUE 149454.1133 150221.0801 137730.2085 136507.4949 205103.0327 117146.6537 149639.4779 149544.3974 206759.5609 0.722840156 0.726549619 0.666137072 0.660223374 0.991988142 0.566583974 0.723736679 0.723276818 1 17.65759452 0.567433574 4.59384742 0.999999987 0.720574878 0.396461478 0.1075148 71.24159422 755.4885408 0.092934705 0.023568437 3.693461483 -0.567433574 -0.279425109 VFLWGSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFLWGSFR 8 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ; 172.97 0.00065247 116531000 241860 129446 62413 55582 302810 63587 238460 138661 203406 FALSE TRUE 230427.7571 142636.6946 65274.69778 49994.79176 355619.9681 61384.96625 202078.5474 126519.1078 234949.1636 0.980755809 0.607095988 0.277824772 0.212789826 1.51360389 0.261269141 0.860094772 0.538495672 1 17.84198911 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 295.73 6.68E-62 308653000 580139 351940 482672 608566 487019 505897 659267 537262 173216 FALSE TRUE 552716.9792 387803.0861 504802.9886 547391.7895 571954.9594 488377.66 558683.7109 490216.4911 200077.4526 2.762515076 1.938264812 2.523037864 2.735899435 2.858667741 2.440943013 2.792337185 2.450133609 1 17.61019907 VFNYNTLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFNYNTLER 9 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 117.84 0.0025282 73161000 103720 78422 82217 85310 83344 85898 105960 100640 106320 FALSE TRUE 98817.36115 86413.29096 85986.73077 76734.47672 97879.16721 82923.33072 89793.85591 91827.42807 122807.5626 0.804652084 0.703647961 0.700174557 0.624835109 0.797012539 0.675229839 0.731175296 0.74773431 1 16.90603988 0.534520742 1.988440389 0.999986979 0.720585591 0.734398 0.052616838 1.819726105 7.180717448 0.04765582 0.013128446 3.423897399 -0.534520742 -0.279401389 VFPEPT(ph)ESGDEGEELGLPLLSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.534)ES(0.466)GDEGEELGLPLLSTR 107.3 6.64E-05 0 5345.4 5747.7 5178.1 6367.9 6081.8 7014 6460.7 6130.2 7032 TRUE FALSE 5092.733536 6333.397165 5415.521007 5727.786594 7142.463994 6771.103421 5475.001556 5593.40719 8122.486646 0.626991925 0.779736236 0.666731907 0.705176486 0.879344504 0.833624445 0.674054855 0.688632365 1 12.98770575 -2.730691225 2.08798438 9.999592027 0.731747145 0.535079351 0.078571167 2565273.011 79270.18948 110513216.2 0.019394512 0.001859126 2.730691225 -9.267844882 VFPEPTES(ph)GDEGEELGLPLLSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.121)ES(0.879)GDEGEELGLPLLSTR 80.156 0.0073973 10646000 15669 17033 13002 15564 18523 12441 15513 15569 20661 TRUE FALSE 14928.35742 18768.68206 13598.15456 13999.47715 21753.40534 12010.16505 13146.20693 14205.69582 23865.00236 0.625533457 0.786452135 0.569794813 0.586611178 0.911519094 0.5032543 0.55085714 0.595252228 1 14.54260886 -1.33720023 5.085249426 1.000151516 0.644394326 0.464457896 0.121051152 0.000203364 2.65E-05 0.114625416 0.027006049 0.046004442 1.33720023 -0.35575719 VFPGSTTEDYNLIVIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFPGSTTEDYNLIVIER 17 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 97.69 0.004682 23185000 22498 16533 19329 20615 28078 18254 20831 19780 30857 FALSE TRUE 21434.56413 18217.7315 20215.25377 18542.74103 32974.79431 17621.8594 17652.84836 18047.95834 35642.14596 0.601382536 0.511128918 0.567172745 0.520247604 0.925162989 0.49441073 0.495280177 0.506365648 1 15.12129658 -1.459104006 3.013661214 1.009987043 0.572000159 0.516477206 0.128326067 43626598.82 51596866.91 3680995.349 0.029280939 0.034745294 1.459104006 -0.437986884 VFPHAEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFPHAEFR 8 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ; 128.69 0.0011229 364190000 141773 109239 62680 75880 159911 83228 160453 129310 169786 FALSE TRUE 135071.6713 120370.5783 65553.94 68252.39824 187799.4278 80345.79349 135972.9479 117986.9309 196115.5457 0.688735157 0.613773772 0.334261824 0.348021356 0.957595825 0.409686 0.693330799 0.601619471 1 17.58134437 -0.262957849 0.561807079 1.045093509 0.568320011 0.343242523 0.184840626 7.828559896 2.396070262 0.923381401 0.075386823 0.545810833 0.262957849 -0.476773498 VFPLS(ph)PASNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFPLSPASNLR 11 0 A0A2R8YH03;Q5VWN6;J3KPH3 A0A2R8YH03 FAM208B Protein FAM208B 1 VFPLS(0.994)PAS(0.006)NLR;VFPLS(0.98)PAS(0.02)NLR 118.61 0.0007319 71138000 124824 139294 129831 148062 119310 149666 166331 159191 131100 TRUE FALSE 118923.8169 153488.217 135783.8798 133178.5265 140117.6262 144483.0289 140954.1511 145251.3921 151430.3184 0.7853369 1.013589739 0.896675654 0.879470689 0.925294404 0.954122202 0.930818561 0.95919624 1 17.20829456 4.691342516 3.689430856 0.938743125 0.776096409 0.587805115 0.041642721 0.163302634 3.837761511 0.009439392 0.066021836 49129.51942 -4.691342516 -0.162646715 VFQGTDEQLNDLYHNHQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFQGTDEQLNDLYHNHQR 18 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;E7ESD9 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 171.72 7.27E-12 333840000 90688 77544 77024 83615 99132 84571 98814 86796 90534 FALSE TRUE 86401.35797 85445.82176 80555.62659 75209.86134 116420.5894 81642.28506 83738.10946 79195.68211 104573.5503 0.82622573 0.817088274 0.770325061 0.719205393 1.113289059 0.780716393 0.800758023 0.757320392 1 16.67415847 VFQSWWDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFQSWWDR 8 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 ; 151.5 0.0010986 572460000 535180 438290 446870 502700 558620 412470 572280 511030 559670 FALSE TRUE 509883.102 482952.2493 467359.4315 452167.6409 656043.1511 398186.0605 484968.1754 466281.5041 646460.7652 0.788730159 0.747071246 0.722950961 0.699451019 1.014822842 0.61594776 0.75018965 0.721283532 1 19.30220329 -1.11460987 4.335743432 1.000035281 0.756573226 0.359009329 0.10180169 3.12E-05 6.36E-06 0.088482096 0.020852411 0.076805113 1.11460987 -0.243462054 VFS(ph)LSEADSHGGHWV ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 VFS(0.854)LS(0.146)EADSHGGHWV 140.93 3.13E-06 18197000 27820 19097 22748 25752 28748 23291 26088 25673 9921.6 TRUE FALSE 26505.00373 21043.00601 23791.0183 23163.36003 33761.6421 22484.42683 22107.79646 23424.93602 11460.19106 2.312788993 1.836182827 2.075970478 2.021201909 2.945992954 1.961959161 1.92909493 2.044026658 1 13.48434348 0.32375661 0.905436133 0.993151562 2.158655841 0.582161801 0.307176955 1.967573008 2.012468616 0.320122949 0.094976482 2.10744675 -0.32375661 1.165504279 VFS(ph)QENVCDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFSQENVCDR 10 0 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 VFS(1)QENVCDR 122.97 0.0030046 0 108000 77194 84487 93716 58451 80283 101910 87535 61545 TRUE FALSE 102895.054 85060.15636 88360.81252 84295.48963 68644.83589 77502.77958 86361.75779 79869.97135 71089.08427 1.447410036 1.196529077 1.242958936 1.185772619 0.965617107 1.090220536 1.214838518 1.123519485 1 16.11734043 7.999999995 0.413646823 1.09361091 7.638098085 0.667221222 0.077870798 46.38720499 0.601197827 0.053249817 250.0126908 99999998.83 -7.999999995 6.544487175 VFSWGFGGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFSWGFGGYGR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 254.15 4.62E-20 1575670000 338750 273570 232440 314290 332850 253930 379320 309180 367570 FALSE TRUE 322737.9588 301447.094 243097.6039 282696.9721 390898.9346 245136.3404 321447.7673 282106.5601 424570.8783 0.760150956 0.71000417 0.572572487 0.665841645 0.92069182 0.577374363 0.757112142 0.664451036 1 18.69564589 -1.11477474 4.143158427 1.000052487 0.707023839 0.466086904 0.099659858 18521222.27 50172245.51 16236.77034 0.021882534 0.076775961 1.11477474 -0.293028648 VFSWLQQEGHLSEEEMAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VFSWLQQEGHLSEEEMAR 18 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;; 266.29 3.95E-31 140239000 133071 117217 121431 135439 165742 120827 157972 140500 170834 FALSE TRUE 126780.9976 129161.5456 126998.7315 121824.4144 194647.3523 116642.7307 133870.47 128197.0752 197326.0642 0.642494939 0.654558971 0.643598361 0.617376193 0.986424946 0.591116694 0.678422643 0.649671272 1 17.590222 -2.052377082 2.516693894 1.433899717 0.679716388 0.447890731 0.11057103 5477311.605 2207130.949 13666882.85 0.02527159 0.008863861 2.052377082 -0.754183329 VFTTQELVQAFTHAPATLEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VFTTQELVQAFTHAPATLEADR 22 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;; 239.19 1.40E-30 1022606000 1453122 1360844 1320466 1677287 1345401 1422014 1581112 1458949 1351499 FALSE TRUE 1384435.803 1499515.551 1381010.672 1508682.924 1580038.508 1372769.299 1339884.325 1331195.691 1561082.562 0.886843423 0.960561335 0.884649349 0.966433782 1.012142821 0.879370081 0.858304588 0.852738813 1 20.57411541 -1.461947161 7.749897169 1.000005849 0.913515166 0.218870935 0.051847654 5.39E-06 3.74E-07 0.051673182 0.012178662 0.034518573 1.461947161 -0.086490683 VFTTVGSAEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 237.84 2.18E-15 5790450000 3498530 2839930 2885710 2963660 2845560 3178080 4091240 3684360 3345040 FALSE TRUE 3333161.42 3129322.096 3018022.658 2665747.266 3341824.763 3068022.293 3467046.197 3361737.906 3863771.719 0.862670381 0.809913816 0.781107911 0.689933945 0.864912579 0.79404854 0.897321697 0.870066389 1 21.88157843 1.070452497 0.871111105 0.995267703 0.800994786 0.598595459 0.051695045 0.421174261 0.709064579 0.048375109 0.017249363 11.76122335 -1.070452497 -0.194272917 VFVDGHQLFDFYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VFVDGHQLFDFYHR 14 0 Q3ZCW2 Q3ZCW2 LGALSL Galectin-related protein 0 ; 175.15 1.40E-06 115219000 168311 111967 107723 133204 167385 116238 181258 140287 45628 FALSE TRUE 160355.2726 123376.5646 112662.2061 119814.0808 196576.891 112212.6489 153603.7631 128002.7266 52703.7572 3.042577628 2.340944387 2.13765037 2.273349894 3.729845867 2.129120481 2.914474626 2.428721089 1 15.68561819 0.960061 20.62756832 0.999999991 2.642979925 0.524971534 0.49011638 532.1849667 274862.6109 0.433343083 0.108335771 9.121389463 -0.960061 1.642979935 VFVHYTGWLLDGTK ddPTM_SK-BR-3_Trastuzumab_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 ; 247.32 8.16E-18 497490000 1235000 1130420 927150 1205650 974380 1045290 1288140 1364360 865830 FALSE TRUE 1176623.998 1245611.083 969660.7446 1084455.771 1144311.563 1009091.345 1091610.585 1244889.405 1000098.494 1.176508118 1.24548841 0.969565248 1.084348969 1.144198866 1.008991965 1.091503078 1.244766803 1 19.93171066 3.762086547 24.99101202 1.08080454 1.210998275 0.324442494 0.079909142 814.7387574 865473.8225 0.019053473 0.034323241 5782.112633 -3.762086547 0.130193736 VFVHYTGWLLDGTKFDSSLDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFVHYTGWLLDGTKFDSSLDRK 22 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" 0 228.63 2.09E-26 396700000 1093600 719700 1040700 949330 1003300 1035600 1711000 1360600 1122400 FALSE TRUE 1041907.695 793038.2482 1088417.124 853901.5448 1178275.202 999736.9123 1449955.525 1241458.651 1296456.06 0.803658317 0.611696974 0.839532598 0.658642874 0.908843145 0.771130579 1.118399281 0.957578656 1 20.30614188 2.108499115 1.373863116 1.033863958 0.726650973 0.578821179 0.099467219 0.25352805 0.90532219 0.058360986 0.030130937 128.3805154 -2.108499115 -0.307212985 VFVLDEADVMIATQGHQDQSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 130.09 1.19E-06 0 8170.3 7965.9 7576 7173.2 8295.8 8129.6 8829.9 9291.7 7714.7 FALSE TRUE 7784.106111 8777.634266 7923.367094 6452.136308 9742.584893 7848.069914 7482.736583 8478.06949 8911.056275 0.873533493 0.985027363 0.88916138 0.724059652 1.09331426 0.88071152 0.839713761 0.951410162 1 13.12138074 VFYELQHSDKPVGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VFYELQHSDKPVGTK 15 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 130.06 3.73E-05 483950000 609720 541220 536140 609530 390730 547570 606360 593520 375340 FALSE TRUE 580899.7439 596370.9333 560722.5493 548258.8864 458873.1883 528607.5136 513848.6454 541548.2424 433545.8102 1.339880885 1.375566132 1.293340948 1.264592745 1.058419151 1.219265649 1.185223414 1.249114233 1 18.72582492 7.999999976 0.072351625 0.770648475 2.370181502 0.638536353 0.070142834 138.8982178 0.739792588 2.756838513 22.50490954 99999994.39 -7.999999976 1.599533027 VGCYDANDAS(ph)DEEEFDREGDCISLPGALPGPIRPLSEDDPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGCYDANDASDEEEFDREGDCISLPGALPGPIRPLSEDDPRR 42 3 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 VGCY(0.17)DANDAS(0.828)DEEEFDREGDCIS(0.002)LPGALPGPIRPLSEDDPRR 48.173 0.023344 15163000 7658.1 4102.9 5630.6 5872.6 7275.4 7745.9 7543.1 5731.7 6812.4 TRUE FALSE 7296.11679 4520.990175 5888.768579 5282.275091 8544.227457 7477.657541 6392.261556 5229.801962 7868.832199 0.927217229 0.574543981 0.748366267 0.671290854 1.085831702 0.950288093 0.812351998 0.664622377 1 12.94193383 2.785606645 24.9977566 0.888644556 0.727260405 0.267307829 0.140622579 595.4663926 316397.9844 0.042244907 0.044807398 610.3889252 -2.785606645 -0.161384151 VGDAIPAVEVFEGEPGNKVNLAELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGDAIPAVEVFEGEPGNKVNLAELFK 26 1 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 311.34 8.46E-82 761680000 1256820 919900 1006800 1123960 675010 1162660 1320770 1332940 818490 FALSE TRUE 1197412.609 1013638.856 1052962.776 1010977.405 792731.5303 1122396.793 1119262.279 1216220.707 945417.2489 1.266544069 1.072160315 1.113754564 1.069345209 0.838499119 1.187197287 1.183881805 1.286438034 1 19.85059166 -0.258633714 7.447650515 1.000000002 1.126809156 0.092294869 0.125385157 0 0 0.119848153 0.028248481 0.551272446 0.258633714 0.126809154 VGDFGDAINWPTPGEIAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGDFGDAINWPTPGEIAHK 19 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;H0YAX9 Q6PKG0 LARP1 La-related protein 1 0 150.45 7.55E-08 168130000 217070 208800 209610 241470 182700 222950 229320 242830 171520 FALSE TRUE 206809.5313 230076.9574 219220.8258 217196.9768 214562.8222 215229.1856 194333.0222 221566.5179 198118.4456 1.04386813 1.161310128 1.10651396 1.096298612 1.083002754 1.086366214 0.98089313 1.118353807 1 17.59600368 1.936911941 9.08796286 1.031440725 1.100729189 0.304723551 0.04517682 0.487054225 67.16666833 0.017683865 0.011202715 86.47925534 -1.936911941 0.069288464 VGDGDLS(ph)AEEIPENEVSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGDGDLSAEEIPENEVSLR 19 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 VGDGDLS(1)AEEIPENEVSLR 187.31 4.64E-17 0 40402 45596 38641 43598 31594 42287 41369 41641 32245 TRUE FALSE 38492.27753 50242.28424 40412.72807 39215.44621 37103.9836 40822.59059 35057.39926 37994.69329 37245.38992 1.033477636 1.348953101 1.085039737 1.052893963 0.996203387 1.096044119 0.941254725 1.020118017 1 15.18477425 3.499444897 6.402931763 1.018092717 1.195886016 0.416033269 0.084254815 0.142912778 22.38401834 0.02195752 0.032710324 3158.238304 -3.499444897 0.177793299 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 177.99 1.28E-17 571801000 59386 60940 52660 70897 50822 62230 58404 62267 51346 TRUE FALSE 56578.94147 67149.85528 55074.51309 63770.29886 59685.34071 60074.9595 49493.39714 56814.57138 59308.47544 0.953977337 1.132213478 0.928611175 1.075230789 1.006354324 1.012923685 0.834507999 0.957950292 1 15.85595067 1.896084735 8.696906153 0.914410423 1.02568895 0.243724232 0.070199885 0.343204404 26.27157643 0.027000725 0.017011019 78.71993646 -1.896084735 0.111278528 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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(0.999)PEPQRENASPAPGTTAEEAMSR;VGDPPQPLPEEPMEVQGAERAS(0.998)PEPQRENAS(0.001)PAPGTTAEEAMSR;VGDPPQPLPEEPMEVQGAERAS(0.899)PEPQRENAS(0.042)PAPGT(0.019)T(0.019)AEEAMS(0.019)R;VGDPPQPLPEEPMEVQGAERAS(0.991)PEPQRENAS(0.004)PAPGT(0.002)T(0.002)AEEAMS(0.002)R 94.695 3.26E-05 293643000 13031.6 9495 14130.8 17783.2 12378.7 13997.3 16758.3 10402.3 17874.8 TRUE FALSE 12415.62209 10462.55129 14778.71116 15995.59895 14537.54136 13512.56999 14201.51355 9491.419466 20646.73269 0.601335925 0.506741258 0.71578934 0.774727856 0.704108567 0.654465294 0.687833458 0.45970564 1 14.33362588 -2.251390735 2.46290518 2.510273568 0.637025694 0.58601705 0.095592584 4158366.205 1202507.138 34789261.51 0.024280353 0.005605434 2.251390735 -1.873247874 VGDPQELNGITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 196.67 4.74E-07 1296660000 1147800 1010770 1102560 1279410 1059640 1113160 1317250 1171770 1247930 FALSE TRUE 1093545.769 1113768.612 1153113.467 1150801.276 1244440.881 1074610.99 1116279.32 1069163.607 1441452.611 0.758641499 0.772670987 0.799966269 0.798362199 0.863324171 0.745505598 0.774412777 0.741726505 1 20.45909198 -2.113011464 2.622757024 1.433422797 0.780974137 0.795824873 0.034727045 4093025.359 1109227.999 10727480.47 0.008463181 0.007708831 2.113011464 -0.65244866 VGDQVWLFIDEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGDQVWLFIDEPR 13 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 162.32 9.46E-05 106748000 111670 115076 108075 118640 103108 103126 112358 113212 109538 FALSE TRUE 106391.5804 126802.3752 113030.3457 106714.0818 121090.0026 99554.72076 95215.7235 103298.5571 126524.5936 0.840876682 1.002195475 0.893346838 0.843425604 0.957047157 0.786840866 0.752547159 0.816430657 1 16.94905831 2.230466845 24.99907148 0.8101603 0.910717615 0.104646239 0.08176107 234.2567864 723538.2967 0.027946329 0.020999605 170.007016 -2.230466845 0.100557315 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANAS(0.001)ES(0.999)P 233.6 1.49E-37 248320000 848340 790850 837440 987770 651050 934390 1034810 950240 746550 TRUE FALSE 808240.6494 871438.5141 875837.4523 888477.483 764592.9139 902031.84 876930.7289 867031.9481 862321.1612 0.937284954 1.010573036 1.015674312 1.03033246 0.886668388 1.046050915 1.016942142 1.005462915 1 19.71786576 VGDTEKPEPERS(ph)PPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VGDTEKPEPERSPPNR 16 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDT(0.006)EKPEPERS(0.994)PPNR;VGDT(0.014)EKPEPERS(0.986)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDT(0.001)EKPEPERS(0.999)PPNR 173.03 3.44E-09 4981140000 2445541 2194330 2149970 2518220 1459138 2469570 2638260 2584830 1712234 TRUE FALSE 2329945.124 2417934.722 2248548.251 2265083.741 1713611.205 2384048.172 2235744.982 2358488.582 1977758.504 1.178073622 1.222563178 1.136917499 1.145278221 0.866441076 1.205429362 1.130443873 1.192505848 1 20.91543484 3.427306777 2.595365505 1.096144619 1.199046607 0.173056845 0.098769583 0.48110834 6.550808338 0.027785592 0.041743919 2674.895235 -3.427306777 0.102901989 VGDVT(ph)PQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VGDVT(1)PQVK 171.67 0.00063467 898870000 3187340 2847030 2902990 3266790 2010840 3071710 3339450 3466340 2435090 TRUE FALSE 3036680.755 3137145.594 3036094.963 2938406.063 2361529.859 2965335.912 2829955.569 3162808.893 2812711.32 1.079627594 1.115345742 1.079419328 1.044688106 0.839591977 1.054262445 1.006130828 1.124469785 1 21.42353006 3.144267487 4.049617023 1.004152069 1.095308037 0.230875681 0.07103265 0.29444289 8.994216442 0.02008195 0.024659064 1394.015128 -3.144267487 0.091155969 VGDVYIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 153.73 0.0010153 1980900000 2789960 2362800 2428280 2760700 2626040 2443150 3018660 2652140 2735170 FALSE TRUE 2658084.12 2603572.006 2539619.04 2483189.191 3084020.545 2358543.103 2558107.976 2419904.562 3159326.194 0.841345261 0.824090912 0.803848316 0.78598696 0.976164016 0.746533583 0.809700493 0.765955907 1 21.59118547 -1.1552037 4.290403691 1.000042693 0.820163625 0.455643619 0.0620965 17228026899 3392232143 7547932.447 0.013254623 0.069951382 1.1552037 -0.179879068 VGDYGSLSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGDYGSLSGR 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 150.62 4.94E-05 165510000 328410 318530 297730 368690 273570 320390 400670 384750 286300 FALSE TRUE 312886.7101 350988.5691 311381.215 331628.5807 321280.5214 309294.814 339540.4327 351059.2503 330697.9418 0.946140482 1.061356981 0.941588004 1.002814166 0.971522591 0.93527892 1.026738875 1.061570714 1 18.33515454 1.581187768 8.728252879 1.034717494 0.983149719 0.275912141 0.039383837 0.150253098 24.24280567 0.020157936 0.009530997 38.12306136 -1.581187768 -0.051567775 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK 307.81 1.03E-103 2532925000 1831467 1615593 1627921 1878671 920671 1969378 1939460 1948701 426094 TRUE FALSE 1744897.185 1780223.763 1702562.788 1689823.422 1081235.731 1901177.946 1643559.756 1778062.41 492170.4813 3.545310519 3.617087637 3.459294803 3.433410751 2.196872368 3.862844315 3.339411482 3.612696164 1 18.90879861 2.977516468 24.53473211 3.040427582 3.543729495 0.124424365 0.815182 1510.968789 1648818.1 0.222654517 0.237963035 949.5470037 -2.977516468 0.503301912 VGEEEHVY(ph)SFPNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGEEEHVYSFPNK 13 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 VGEEEHVY(0.993)S(0.007)FPNK 92.781 0.034339 465030000 396530 391970 371880 467850 275330 416450 425370 487200 272730 TRUE FALSE 377786.8127 431912.1886 388931.0658 420820.8291 323347.4648 402028.2321 360471.994 444538.1852 315023.5755 1.199233461 1.371047192 1.234609395 1.335839162 1.026423068 1.276184589 1.144269896 1.411126721 1 18.26510027 VGEEFEEQTVDGRPCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VGEEFEEQTVDGRPCK 16 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;; 271.19 3.48E-35 2680620000 1844600 1462920 1527330 1714790 1108110 1685800 1862650 1750170 1087900 FALSE TRUE 1757409.414 1611993.211 1597359.591 1542416.051 1301364.033 1627420.323 1578468.533 1596915.837 1256605.976 1.398536572 1.282815172 1.271169819 1.227446058 1.035618211 1.295091982 1.256136421 1.270816682 1 20.26110092 -2.056691628 0.034352652 1.65E-16 2.106663774 0.485673069 0.086209002 557.5931763 2.630688587 106.2255908 60.10532265 0.008776238 2.056691628 2.106663774 VGEFCHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VGEFCHNR 8 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 198.07 0.00013893 5948440000 6391580 5192280 4511880 5010110 5365720 4888700 6584170 5754610 4945540 FALSE TRUE 6089462.68 5721379.235 4718754.161 4506484.224 6301499.869 4719403.093 5579633.94 5250705.841 5712469.085 1.06599486 1.001559772 0.826044586 0.788885534 1.103113168 0.826158185 0.976746457 0.919165734 1 22.44568302 3.964679777 8.474264341 0.91852017 1.04208154 0.215778975 0.093432089 0.400727264 91.10080316 0.022167837 0.040718372 9218.914281 -3.964679777 0.12356137 VGEFSGANK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGEFSGANK 9 0 P10599;P10599-2 P10599 TXN Thioredoxin 0 128.38 0.00097451 63882000 103430 91094 86154 111550 75540 93749 119070 105600 96300 FALSE TRUE 98541.06888 100376.5822 90104.24612 100336.7821 88714.15208 90502.44862 100903.6846 96353.10418 111233.7122 0.885892118 0.90239353 0.810044404 0.902035724 0.797547347 0.813624277 0.907132223 0.86622214 1 16.76323457 0.3453502 1.172842587 1.000078697 0.862080731 0.536415582 0.040794656 2.730737054 4.124969358 0.039254322 0.011743132 2.214879991 -0.3453502 -0.137997967 VGEGDKEDATRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGEGDKEDATRR 12 2 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 151.66 3.89E-05 209290000 548230 483480 479260 583010 310040 546670 605840 600090 328090 FALSE TRUE 522316.2544 532747.1617 501234.5451 524404.7272 364110.8778 527738.6808 513407.981 547542.9383 378968.5215 1.378257625 1.405782094 1.322628442 1.383768565 0.960794518 1.392566007 1.354750993 1.444824325 1 18.53171849 -2.073648449 2.512917227 0.48756037 1.334636035 0.369744231 0.135475389 13129896.92 6100807.278 38410571.11 0.031575989 0.008440177 2.073648449 0.847075666 VGELKDDDFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGELKDDDFER 11 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ; 100.55 0.0035971 632920000 807190 699820 655410 834380 501490 766890 813610 868310 578620 FALSE TRUE 769035.7284 771132.4536 685461.1968 750506.5372 588949.6972 740332.407 689478.8515 792276.1732 668349.4344 1.15064918 1.153786349 1.025603018 1.122925372 0.881200263 1.107702601 1.031614326 1.185422075 1 19.35024306 3.747321012 22.91116571 1.050312243 1.152217798 0.214097358 0.080908901 265.6268712 694689.8933 0.01888933 0.033316934 5588.831445 -3.747321012 0.101905555 VGEVCHITCKPEYAYGSAGSPPK ddPTM_SK-BR-3_Trastuzumab_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 ; 147.26 7.16E-08 749444000 1263320 1375770 1134500 1422810 708116 1287330 1186650 1475570 755404 FALSE TRUE 1203605.367 1515962.527 1186517.947 1279786.436 831611.2062 1242749.439 1005604.748 1346361.268 872548.1943 1.379414198 1.737396899 1.359830844 1.46672292 0.953083408 1.424275986 1.152491925 1.543022239 1 19.73487529 2.970267871 23.28727132 1.23280345 1.514218801 0.30676128 0.200998757 326.1704568 255468.4272 0.055452537 0.058929462 933.8301062 -2.970267871 0.281415351 VGEVIVTKDDAMLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGEVIVTKDDAMLLK 15 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 173.03 9.05E-07 548650000 1956680 1265780 2053200 1976820 1802760 2309230 2922230 2836430 1999170 FALSE TRUE 1864191.614 1394764.421 2147341.251 1778106.298 2117160.773 2229260.786 2476390.143 2588057.152 2309191.073 0.807292058 0.604005635 0.929910598 0.770012633 0.916840879 0.965386023 1.072405905 1.120763536 1 21.13895612 2.540540981 0.897432741 1.081146852 0.726751184 0.686064054 0.084806126 0.282982374 0.465534872 0.053011779 0.040067769 347.1690338 -2.540540981 -0.354395668 VGFQYEGTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGFQYEGTYK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 111.06 0.0057702 0 62420 54308 53875 62302 54203 48690 70979 65966 58638 FALSE TRUE 59469.5303 59842.04694 56345.22204 56039.28459 63655.98604 47003.85309 60149.84993 60189.66733 67731.28156 0.878021631 0.883521551 0.831893635 0.827376705 0.939831413 0.693975546 0.888066024 0.888653897 1 16.04753467 0.85095048 2.215668099 0.999407566 0.850234746 0.360612045 0.0636081 0.596539795 5.592838852 0.055503907 0.015152092 7.094968641 -0.85095048 -0.149172821 VGGS(ph)DEEASGIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR 275.25 4.83E-33 8267850000 4658840 4409340 4338820 4853130 3495350 4509900 4450080 4265120 3329640 TRUE FALSE 4438625.866 4858656.759 4537759.189 4365284.152 4104937.933 4353721.032 3771138.565 3891643.482 3845983.566 1.15409382 1.263306688 1.179869625 1.13502413 1.067331117 1.132017586 0.980539438 1.011872104 1 21.87492117 2.463070258 0.791678086 0.99187024 1.212393335 0.773049883 0.042392271 0.270448789 0.340466166 0.030563366 0.022181939 290.4492488 -2.463070258 0.220523095 VGGSSVDLHR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 185.61 1.43E-06 885310000 1201270 919650 972800 1141940 1181710 1020190 1361340 1167150 1193010 FALSE TRUE 1144488.348 1013363.381 1017403.842 1027150.022 1387799.85 984860.5645 1153642.58 1064948.159 1378015.898 0.830533486 0.735378585 0.738310671 0.745383289 1.007100028 0.714694632 0.837176539 0.77281268 1 20.3941611 -4.999999997 0.265717076 2.361163384 0.780450314 0.35854054 0.084646776 217.356317 2.121257231 162.0124383 0.098594381 1.00E-05 4.999999997 -1.58071307 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKTQES(ph)L ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKTQESL 37 2 P55327-2;P55327-4;P55327-3 P55327-2 1 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKT(0.016)QES(0.984)L;VGGTKPAGGDFGEVLNSAANASATTTEPLPEKT(0.01)QES(0.99)L 231.05 2.84E-40 329516000 574282 428036 532520 576702 333665 620996 671615 643660 376642 TRUE FALSE 547136.828 471653.355 556936.5687 518730.8193 391856.0704 599490.7528 569147.7967 587297.7181 435049.7177 1.257642071 1.084136676 1.280167636 1.192348364 0.900715606 1.377982167 1.308236216 1.349955406 1 18.73082076 VGGTNPNGGS(ph)FEEVLSSTAHASAQSLAGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGGTNPNGGSFEEVLSSTAHASAQSLAGGSR 31 0 Q16890-5;E9PPQ1;J3KNE7;Q16890 Q16890-5 TPD52L1 Tumor protein D53 1 VGGT(0.029)NPNGGS(0.971)FEEVLSSTAHASAQSLAGGSR;VGGT(0.002)NPNGGS(0.998)FEEVLSSTAHASAQSLAGGSR 127.35 3.64E-06 237490000 121393 120696 117158 156131 117754 140477 166216 134872 131453 TRUE FALSE 115654.9935 132995.0596 122529.8102 140436.4153 138290.2603 135612.2463 140856.6964 123061.8927 151838.0599 0.761699626 0.875900678 0.806976922 0.924909179 0.91077468 0.893137375 0.927677135 0.810481198 1 17.21217394 8 0.214246721 0.945065504 0.07366584 0.474220852 0.050687593 41.67394363 0.525090699 0.074411057 12.46084332 100000000 -8 -0.871399664 VGGTSDVEVNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGGTSDVEVNEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 149.23 0.00073747 0 166050 127170 145930 169580 114700 134250 157830 161950 126690 FALSE TRUE 158201.1456 140128.7676 152621.0348 152533.4962 134703.6437 129600.8888 133750.1348 147768.7994 146336.4382 1.081078285 0.957579461 1.042946219 1.042348018 0.920506508 0.885636486 0.91399064 1.009788138 1 17.15892952 2.736902646 24.9918763 0.933510922 1.024983175 0.414310275 0.048757064 131.4659874 1981678.546 0.01489396 0.014740323 545.635534 -2.736902646 0.091472252 VGGVS(ph)PEEHPAPEVSTPFPPLPPEPEGGGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGGVSPEEHPAPEVSTPFPPLPPEPEGGGEEK 32 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK 158.99 5.30E-14 49158000 101810 107770 88473 111010 48958 109000 96983 112500 46055 TRUE FALSE 96997.64307 118751.8855 92529.57456 99851.06389 57496.2597 105225.3027 82186.46214 102648.9036 53196.97418 1.823367674 2.232305264 1.739376647 1.877006454 1.080818234 1.978031726 1.544946182 1.929600418 1 15.69905657 -1.814169634 0.131063896 7.19E-12 2.233656001 0.388822953 0.303666302 46.98436331 0.940589797 18.37636223 2.673651411 0.015340177 1.814169634 2.233656001 VGHFDPVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGHFDPVTR 9 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 126.24 0.00047898 1085360000 535260 469841 456354 584019 563576 469358 565470 535491 489823 FALSE TRUE 509959.3206 517718.3321 477278.2823 525312.3006 661863.476 453104.0148 479197.1659 488600.5692 565782.2492 0.901334959 0.915048736 0.843572387 0.928470805 1.169820151 0.800845229 0.846963945 0.863584126 1 19.10988739 -0.389761759 6.417079359 0.999999999 0.906035505 0.075171326 0.100248147 0 0 0.094047759 0.022167269 0.407603816 0.389761759 -0.093964494 VGHSELVGEIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VGHSELVGEIIR 12 0 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 184.03 1.48E-05 1076470000 574346 551516 508469 566257 572063 527612 616253 557694 546671 FALSE TRUE 547197.8028 607716.1074 531782.8066 509335.7705 671830.6061 509340.6641 522232.2866 508859.3568 631445.9467 0.866579009 0.962419841 0.842166791 0.806618165 1.063955845 0.806625914 0.827041949 0.805863684 1 19.26829972 VGIDT(ph)PDIDIHGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VGIDT(1)PDIDIHGPEGK 122.57 0.00034074 69548000 121300 103670 114180 141660 96010 124810 138160 127610 90544 TRUE FALSE 115566.3894 114234.0909 119415.2659 127420.0677 112754.1136 120487.7984 117081.1545 116435.7919 104585.1011 1.104998592 1.092259697 1.141799976 1.218338619 1.07810876 1.152055093 1.119482157 1.113311463 1 16.67431782 0.521089864 1.814461902 1.000008634 1.126798811 0.523823793 0.038470474 2.689111681 9.228832089 0.035936246 0.010045602 3.319631403 -0.521089864 0.126790177 VGIDTPDIDIHGPEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 201.3 3.33E-11 915025000 2173346 1937193 1897779 2319738 1524477 2034915 2411126 2316673 1484039 FALSE TRUE 2070616.242 2134595.169 1984794.044 2086553.529 1790345.306 1964445.383 2043264.445 2113812.831 1714176.189 1.207936649 1.245260075 1.157870502 1.217233994 1.044434824 1.145999691 1.191980415 1.23313627 1 20.70908397 -5 0.206577405 0.170360761 1.210280459 0.464932151 0.058907901 131.55141 1.308065833 45.46931112 0.130169142 1.00E-05 5 1.039919698 VGIIAWHPTAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGIIAWHPTAR 11 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 113.63 0.001366 672900000 684710 612460 606440 698040 779890 607180 792680 664430 708630 FALSE TRUE 652345.1153 674870.3703 634245.8739 627871.693 915902.5691 586153.2044 671742.1074 606248.9868 818520.7212 0.796980575 0.824500044 0.774868439 0.767081 1.118972978 0.716112847 0.820678194 0.74066419 1 19.64265941 -2.366204918 2.252764143 2.200615078 0.820383981 0.204772694 0.111485291 6924282.366 703958.5933 42529865.4 0.025314693 0.004303235 2.366204918 -1.380231097 VGILS(ph)GHDNRVS(ph)CLGVT(ph)ADGMAVATGSWDSFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGILSGHDNRVSCLGVTADGMAVATGSWDSFLK 33 1 E9PCP0;P16520-2;P16520 E9PCP0 GNB3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 3 VGILS(0.594)GHDNRVS(0.594)CLGVT(0.594)ADGMAVAT(0.594)GS(0.594)WDS(0.031)FLK 42.355 0.067065 327310000 85259 74562 85406 94766 65410 98450 91563 90042 55719 TRUE FALSE 81228.97604 82159.95257 89321.94958 85239.94164 76817.48329 95040.65181 77593.38268 82157.44514 64359.61795 1.262110911 1.276576139 1.387857051 1.324432064 1.19356649 1.476712492 1.205622177 1.276537179 1 15.97386814 0.455839974 1.159065576 0.999999508 1.305154037 0.575118223 0.082031443 1.520158047 2.566102629 0.071133585 0.021649394 2.856537794 -0.455839974 0.305154529 VGKFPFAANSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGKFPFAANSR 11 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 135.6 0.00010641 896750000 1770590 1073470 1084720 933980 1694610 1060170 1870440 1436900 1772860 FALSE TRUE 1686897.72 1182857.813 1134455.485 840094.556 1990149.447 1023456.047 1585070.025 1311077.419 2047786.074 0.823766574 0.577627628 0.55399121 0.410245272 0.971854176 0.499786604 0.774040826 0.640241398 1 20.96563358 -0.549204671 0.525687113 1.060631996 0.645819147 0.30268279 0.164286954 12.54017002 2.830581623 1.521535119 0.068829278 0.2823549 0.549204671 -0.414812849 VGLKAPGIIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGLKAPGIIPR 11 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 81.865 0.014984 0 705420 328970 570350 476590 712900 508380 792940 578750 834490 FALSE TRUE 672076.1946 362492.417 596501.1117 428682.2677 837229.5343 490774.6731 671962.4397 528071.5819 963898.4472 0.697247927 0.376069095 0.618842279 0.444738 0.868586869 0.509155995 0.697129912 0.547849811 1 19.87852163 -5 0.215056359 3.044198453 0.532547367 0.446582417 0.140764937 125.6543905 1.254856891 110.8663878 0.253482322 1.00E-05 5 -2.511651086 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 VGLSPDSPAGDRNS(0.985)VGS(0.015)EGSVGSIR;VGLSPDSPAGDRNS(1)VGSEGSVGSIR 283.7 1.14E-53 599850000 450560 384520 417080 433610 465200 359150 455420 451340 481590 TRUE FALSE 429262.9217 423703.0252 436203.5305 390022.699 546330.7327 346712.5454 385937.3146 411818.2769 556272.5176 0.771677385 0.76168247 0.784154379 0.70113602 0.982127852 0.623278222 0.693791806 0.740317495 1 19.08543231 -1.301328504 3.70551119 1.000631832 0.753880949 0.404313313 0.092510947 10049474.73 7058723.449 47175.219 0.020252131 0.049965645 1.301328504 -0.246750883 VGLVEDSPSTAGDGDDSPVVSLTVPSTS(ph)PPSSSGLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLT(0.007)VPS(0.171)T(0.171)S(0.275)PPS(0.094)S(0.094)S(0.094)GLS(0.094)R 83.562 0.00061072 50540000 40556 31792 36654 36992 39470 33889 41014 37379 40823 TRUE FALSE 38638.99825 35031.64094 38334.62216 33273.49388 46353.5555 32715.41543 34756.56103 34105.8966 47153.62235 0.819427996 0.742925765 0.812973007 0.70564025 0.98303276 0.693804925 0.737092068 0.723293247 1 15.52508098 -1.217563195 5.020523965 1.000026518 0.775202414 0.410670139 0.083818031 2.25E-05 3.51E-06 0.073536276 0.017330624 0.060595002 1.217563195 -0.224824104 VGNES(ph)PVQELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;VGNES(1)PVQELK;VGNES(1)PVQELK 263.27 9.08E-21 1446880000 4255840 4239110 3388860 4574660 2036860 4162940 3773680 4228210 1990230 TRUE FALSE 4054674.877 4671080.128 3544242.583 4114806.486 2392087.739 4018776.344 3197935.808 3857965.517 2298864.704 1.763772731 2.031907368 1.541736048 1.78992982 1.040551771 1.748156965 1.391093526 1.678204686 1 21.13249013 5.248523756 0.057353492 8.04E-13 3.859143574 0.425469369 0.249918346 173.2270521 1.343445221 27.24316928 71.29633349 177224.4986 -5.248523756 3.859143574 VGNES(ph)PVQELKQDVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGNESPVQELKQDVSK 16 1 Q5JSH3-2;Q5JSH3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VGNES(1)PVQELKQDVSK 115.54 0.00030157 36779000 111480 62744 109250 97546 63843 110170 148290 130300 72392 TRUE FALSE 106210.5613 69137.68493 114259.2206 87740.49075 74977.19899 106354.7853 125665.637 118890.2412 83618.18163 1.270185015 0.82682598 1.36643991 1.049299196 0.896661438 1.271909807 1.50285063 1.421822849 1 16.35152905 2.030517861 9.906498629 1.369951478 1.076169863 0.201243165 0.203916514 0.411639479 128.8758089 0.070534507 0.051869473 107.2797767 -2.030517861 -0.293781615 VGNHTAEGTGTNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGNHTAEGTGTNKK 14 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 109.84 0.00048324 61684000 195110 179740 184080 223740 132880 204260 241620 228750 152540 FALSE TRUE 185887.537 198055.7103 192520.2501 201249.2301 156054.2299 197186.425 204756.4313 208719.4373 176195.1241 1.055009541 1.124070324 1.092653676 1.142195229 0.885689832 1.119136673 1.16210044 1.184592584 1 17.42681448 2.020125627 24.99997739 1.135336386 1.067531744 0.081018329 0.084382772 473.6264576 588334.5501 0.029654387 0.021898658 104.7431493 -2.020125627 -0.067804642 VGPCS(ph)SPPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.79)S(0.21)PPAAR;VGPCS(0.614)S(0.386)PPAAR;VGPCS(0.642)S(0.358)PPAAR;VGPCS(0.74)S(0.26)PPAAR 131.83 0.00020481 808172000 1288400 1067390 1176910 1347740 1166560 1172380 1389000 1276560 1280390 TRUE FALSE 1227499.885 1176158.255 1230872.488 1212262.615 1370007.695 1131780.187 1177082.539 1164777.639 1478946.342 0.829982705 0.795267699 0.832263114 0.819679917 0.926340365 0.765261156 0.795892661 0.787572616 1 20.49613828 -1.397040159 5.59373745 1.000077486 0.817179333 0.633586772 0.043229526 3.98E-05 4.29E-06 0.039918643 0.009404938 0.040082965 1.397040159 -0.182898153 VGPCSS(ph)PPAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.263)S(0.737)PPAAR;VGPCS(0.191)S(0.809)PPAAR 94.791 0.0086438 411060000 616280 523640 542510 629880 496680 562610 653780 613820 529060 TRUE FALSE 587149.6657 576999.5113 567384.6201 566563.2657 583300.8347 543126.6746 554033.8535 560070.6667 611103.9227 0.960801664 0.944192125 0.928458481 0.927114431 0.954503503 0.888763195 0.906611515 0.916490053 1 19.22105822 4.053734554 0.893477141 0.922742919 0.965312345 0.037617337 0.030555376 1.739315866 2.054975044 0.010283854 0.059126591 11317.08437 -4.053734554 0.042569426 VGPDTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGPDTER 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 90.986 0.038936 248700000 186190 147200 172580 196890 177850 166820 202180 190790 198320 FALSE TRUE 177389.1677 162199.8474 180492.9637 177098.2431 208866.9837 161042.9816 171333.7277 174083.4162 229074.4527 0.774373421 0.708066069 0.787922711 0.773103421 0.911786457 0.703015896 0.747939046 0.759942517 1 17.80545705 -1.438872723 6.030629902 1.000096748 0.765793825 0.611435562 0.057307328 7.17E-05 6.67E-06 0.053357553 0.012571326 0.03640217 1.438872723 -0.234302923 VGPGNHGTEGSGGERHS(ph)DTDSDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGPGNHGTEGSGGERHSDTDSDRR 24 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 VGPGNHGT(0.042)EGS(0.042)GGERHS(0.916)DT(0.001)DSDRR;VGPGNHGT(0.18)EGS(0.18)GGERHS(0.627)DT(0.013)DS(0.001)DRR 102.57 0.0016086 105410000 34495 49076 37956 60346 44304 41117 48125 39953.5 21999.2 TRUE FALSE 32864.48971 54076.90019 39696.32014 54279.90543 52030.60357 39693.10798 40782.64737 36454.95973 25410.72358 1.293331518 2.128113354 1.562187713 2.136102314 2.047584494 1.562061303 1.604938452 1.434628952 1 14.63314984 1.056672122 1.051983869 1.011987939 1.810815475 0.480655801 0.267042904 0.442983348 1.041689578 0.240432455 0.078992579 11.39389261 -1.056672122 0.798827536 VGQEIEVRPGIVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VGQEIEVRPGIVSK 14 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;; 113.47 0.00048654 806000000 1130430 1061100 1065950 1205600 947370 1191230 1359730 1320040 1101900 FALSE TRUE 1076996.814 1169227.296 1114824.862 1084410.798 1112591.028 1149977.406 1152278.215 1204450.3 1272777.024 0.846178705 0.91864268 0.875899581 0.85200375 0.874144494 0.903518357 0.905326065 0.946316815 1 20.27954827 1.090401145 1.022239759 0.999955021 0.876794369 0.806979389 0.020148752 0.223226346 0.49929702 0.018872394 0.006295683 12.31405659 -1.090401145 -0.123160652 VGQGYPHDPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGQGYPHDPPK 11 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 102.4 0.0028735 650370000 851380 744460 741820 941000 594080 840860 882670 854640 570120 FALSE TRUE 811136.9547 820321.3204 775833.1808 846408.8922 697687.3639 811740.8074 748002.4802 779803.1909 658531.2978 1.231736377 1.245683118 1.178126512 1.285297897 1.059459689 1.232653345 1.135864738 1.184155094 1 19.32889248 -5 0.118705046 0.336507196 1.299388053 0.552451411 0.058682722 101.5245227 0.78396145 16.08448671 0.502837062 1.00E-05 5 0.962880857 VGQQAIVLCIS(ph)PSKPNPVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGQQAIVLCISPSKPNPVFK 20 1 Q16656-2;Q16656;Q16656-4;C9JP85 Q16656-2 NRF1 Nuclear respiratory factor 1 1 VGQQAIVLCIS(0.988)PS(0.012)KPNPVFK 231.12 7.32E-26 159590000 237510 202660 205260 258390 150210 249600 268760 288280 190440 TRUE FALSE 226283.373 223311.2844 214671.374 232416.1463 176406.5764 240956.2894 227755.7259 263036.6749 219972.4626 1.028689548 1.015178363 0.975901127 1.05656928 0.801948455 1.095392971 1.035382899 1.195770925 1 17.7469634 VGQTIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VGQTIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 93.561 0.034535 464656000 563783 414242 524732 548742 559323 480784 657127 588332 653584 FALSE TRUE 537134.0949 456453.7308 548791.4812 493581.4116 656868.7541 464134.3295 556870.2072 536814.5311 754938.4687 0.711493873 0.604623754 0.726935378 0.653803498 0.870095751 0.614797561 0.73763655 0.711070575 1 19.52599954 -5 0.249008039 2.827533086 0.670041145 0.614938585 0.073912052 110.788144 1.098620954 102.941346 0.096582148 1.00E-05 5 -2.157491941 VGRPSNIGQAQPIIDQLAEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 168.75 8.27E-12 223410000 227230 167994 195802 212790 207470 208030 254260 240530 266060 FALSE TRUE 216489.2882 185112.7796 204779.7154 191399.9449 243652.7023 200825.8689 215467.9672 219467.9181 307319.226 0.704444337 0.602346889 0.666342025 0.622804982 0.792832604 0.653476424 0.701121014 0.714136636 1 18.2293785 -5 0.245660923 2.928609036 0.645991509 0.804675395 0.04993093 69.23716591 0.68814878 66.79085866 0.068370849 1.00E-05 5 -2.282617527 VGRPTASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGRPTASK 8 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 92.051 0.010992 3933670000 4780620 3904020 3681940 4108900 3527320 4321990 5508640 4765330 4303080 FALSE TRUE 4554649.567 4301844.077 3850760.591 3695865.566 4142483.491 4172318.403 4668195.795 4348052.443 4970379.669 0.916358482 0.865496071 0.774741739 0.743578119 0.833434016 0.839436558 0.93920306 0.874792819 1 22.24492463 1.249521827 1.009844158 0.985909006 0.834516929 0.485691955 0.053987518 0.48887786 1.047320657 0.055528063 0.019113338 17.7632254 -1.249521827 -0.151392077 VGS(ph)LDNVGHLPAGGAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK 175.77 7.65E-10 7278735000 13034470 10492080 10455110 12086440 5645716 12231500 12154700 12257440 5326103 TRUE FALSE 12418356.43 11561234.88 10934487.14 10871488.09 6630327.083 11807920.09 10300277.28 11184113.57 6152047.851 2.018572796 1.87924983 1.777373551 1.767133213 1.077743094 1.919347894 1.674284324 1.817949704 1 22.55263529 -2.350399174 0.137002576 3.53E-22 2.097924425 0.464187896 0.252266281 52.84358092 0.930733622 19.78676797 1.916028157 0.004462732 2.350399174 2.097924425 VGS(ph)PLTLTDAQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VGS(0.937)PLT(0.063)LTDAQTR;VGS(1)PLTLTDAQTR;VGS(0.995)PLT(0.005)LTDAQTR;VGS(0.993)PLT(0.007)LTDAQTR 197.06 1.44E-07 352501000 472770 385259 380077 452863 288870 413842 427091 420581 299387 TRUE FALSE 450423.099 424517.3301 397503.9064 407340.3509 339248.8365 399510.5478 361930.4239 383752.698 345814.4069 1.30249952 1.227587173 1.149471793 1.177916081 0.981014179 1.155274447 1.046603081 1.109707087 1 18.39963845 3.792845725 0.668315754 1.059597111 1.338131987 0.684958971 0.055819816 0.602904215 0.439166167 0.025899717 0.108610211 6206.485208 -3.792845725 0.278534876 VGS(ph)PSGDAASSTPPSTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VGSPSGDAASSTPPSTR 17 0 Q9NP87 Q9NP87 POLM DNA-directed DNA/RNA polymerase mu 1 VGS(0.969)PS(0.031)GDAASSTPPSTR;VGS(0.999)PS(0.001)GDAASSTPPSTR;VGS(0.865)PS(0.135)GDAASSTPPSTR;VGS(0.843)PS(0.157)GDAASSTPPSTR;VGS(0.875)PS(0.125)GDAASSTPPSTR;VGS(0.974)PS(0.025)GDAASSTPPSTR 299.1 9.40E-36 605544000 627942 566380 556988 666222 407532 592289 601818 578080 420109 TRUE FALSE 598260.4261 624094.7659 582526.4507 599252.0988 478605.4518 571777.8834 509999.611 527460.2506 485257.3581 1.232872446 1.286110876 1.200448465 1.234916048 0.986292003 1.178298224 1.050987898 1.086970124 1 18.88839056 2.80215982 8.863721048 1.072455355 1.244118452 0.710161314 0.056196791 0.210123417 27.90897587 0.015466759 0.016402249 634.1030179 -2.80215982 0.171663096 VGS(ph)TENIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.981)T(0.019)ENIK;VGS(0.93)T(0.07)ENIK;VGS(0.676)T(0.324)ENIK;VGS(0.872)T(0.128)ENIK;VGS(0.979)T(0.021)ENIK 188.49 0.00020635 2775330000 5119800 4682980 3709900 5189550 1996080 4771580 4103720 4622490 1891060 TRUE FALSE 4877797.2 5160180.986 3880002.585 4667886.574 2344195.72 4606338.988 3477622.144 4217720.27 2184315.927 2.233100597 2.362378502 1.776301009 2.137001575 1.073194446 2.108824521 1.592087528 1.930911284 1 21.0587501 8 0.062422347 2.62E-12 5.881988659 0.47344763 0.337067975 241.1068448 1.121316895 20.63502268 127.6740041 99999999.99 -8 5.881988659 VGS(ph)TENIKHQPGGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGSTENIKHQPGGGR 15 1 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(0.938)T(0.062)ENIKHQPGGGR;VGS(0.896)T(0.104)ENIKHQPGGGR 123.58 6.15E-05 375760000 268646 144160 261659 211569 141955 256747 292540 269078 161468 TRUE FALSE 255947.636 158850.0679 273656.324 190301.6822 166711.9071 247855.787 247907.6501 245516.1038 186507.6328 1.372317219 0.851708134 1.467266084 1.020342596 0.893861042 1.328931065 1.32920914 1.31638636 1 17.50887515 VGSEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VGSEIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 147.69 0.0049651 849540000 1882350 1549130 1617830 1873150 1820100 1648920 2111340 1780920 2036170 FALSE TRUE 1793375.046 1706988.108 1692009.106 1684857.403 2137524.864 1591817.487 1789216.306 1624973.204 2351928.844 0.762512459 0.725782207 0.719413391 0.716372609 0.908839087 0.676813625 0.760744233 0.69091087 1 21.16541298 -1.149805934 4.723014117 1.000024531 0.74578453 0.610534277 0.063961013 1.48E-05 2.66E-06 0.055474994 0.013074321 0.07082622 1.149805934 -0.254240001 VGSGS(ph)LDNLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.006)GS(0.994)LDNLGR 111.53 0.00089604 0 394590 350380 374900 374030 366360 359460 458100 380150 368070 TRUE FALSE 375938.5127 386084.1203 392089.5358 336431.7938 430253.068 347011.8101 388208.4314 346862.0507 425148.4158 0.884252413 0.908116098 0.922241554 0.791327878 1.012006754 0.816213344 0.913112732 0.815861092 1 18.69760704 -1.897390953 2.69469767 1.060016102 0.886525743 0.245208973 0.064290351 25747953.69 19256483.24 9860428.17 0.013018557 0.012665112 1.897390953 -0.173490359 VGSLT(ph)PPS(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.606)S(0.394)PK 135.02 0.00068318 337710000 499890 450150 432260 541350 264860 540370 535510 538620 288130 TRUE FALSE 476261.1904 496020.7968 452079.5486 486932.4695 311051.5001 521656.8514 453808.1142 491455.5774 332811.7288 1.431022855 1.49039458 1.358364232 1.463086867 0.934617002 1.567423279 1.363558057 1.476677457 1 18.34434675 -1.357735674 3.120704408 0.996149149 1.391798906 0.332045334 0.171697605 17543757.18 23067945.42 621039.3405 0.04042045 0.043879768 1.357735674 0.395649757 VGSLT(ph)PPSS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.078)S(0.922)PK;VGSLT(0.999)PPS(0.006)S(0.995)PK;VGSLT(1)PPS(0.007)S(0.993)PK;VGS(0.001)LT(0.999)PPS(0.433)S(0.567)PK 174.72 5.66E-05 827930000 2176300 1951510 1815360 2286270 1095790 2200140 2196160 2277590 1206200 TRUE FALSE 2073430.612 2150371.088 1898596.052 2056449.796 1286895.429 2123948.6 1861095.457 2078152.145 1393251.336 1.488195675 1.543419362 1.362708941 1.476007769 0.923663517 1.524454738 1.335793054 1.491584535 1 20.41002411 -4.417172945 0.120477746 6.35E-17 1.589201842 0.305493139 0.181627232 157.1799847 1.407584755 40.91907109 1.674282924 3.83E-05 4.417172945 1.589201842 VGTEGLVDS(ph)FSQGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.999)FS(0.001)QGLER 155.79 2.36E-07 21193000 37000 45994 38770 50555 35553 44199 38021 38820 34138 TRUE FALSE 35251.08333 50680.84089 40547.64285 45473.11535 41753.43194 42668.37755 32220.19815 35420.715 39431.94669 0.893972687 1.285273621 1.02829422 1.153204931 1.058873209 1.082076365 0.81710899 0.898274571 1 15.26707732 1.754061385 25 0.891277939 1.091893287 0.378665569 0.106942169 4.796764559 7745.9207 0.046226773 0.025635287 56.76248297 -1.754061385 0.200615348 VGTLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGTLWR 6 0 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 0 112.56 0.06256 104390000 231770 199130 181990 207410 237840 200760 249630 233780 243900 FALSE TRUE 220814.6914 219421.5734 190334.4215 186560.7527 279319.2207 193807.6309 211544.3587 213308.9839 281722.7663 0.783801374 0.778856378 0.675608947 0.662213974 0.991468401 0.687937412 0.750895504 0.757159198 1 18.10391663 -0.913964909 4.931215747 1.000001053 0.761289768 0.399071061 0.092171608 9.78E-07 2.15E-07 0.081770992 0.019273522 0.12190881 0.913964909 -0.238711285 VGVEASEETPQTSSSSARPGT(ph)PSDHQSQEASQFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.958)PS(0.041)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.5)PS(0.5)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.95)PS(0.05)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.792)PS(0.207)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.891)PS(0.109)DHQSQEASQFER 360.92 9.13E-133 5619900000 1210374 1053590 1210470 1385913 1653867 1076370 1636816 1444525 1832196 TRUE FALSE 1153162.02 1160952.019 1265971.247 1246598.392 1942300.881 1039095.037 1387089.657 1318034.733 2116323.598 0.54488927 0.548570181 0.598193607 0.589039594 0.917771216 0.490990621 0.655424179 0.622794517 1 21.01312881 -5 0.199809491 2.734209052 0.550785345 0.529607152 0.113494795 107.5277858 1.063399577 74.55773381 0.255576345 1.00E-05 5 -2.183423707 VGVEASEETPQTSSSSARPGTPS(ph)DHQSQEASQFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 VGVEASEETPQTSS(0.001)S(0.001)S(0.004)ARPGT(0.312)PS(0.682)DHQSQEASQFER 275.08 2.56E-74 915840000 514610 419360 520210 563460 664540 436600 704950 597490 737120 TRUE FALSE 490285.4052 462093.2608 544062.1431 506819.9303 780435.5656 421480.4325 597396.9302 545170.6081 851428.8049 0.575838405 0.542726835 0.638998986 0.595258144 0.916618702 0.495027218 0.701640497 0.640300874 1 19.69952637 -5 0.175272479 2.465192506 0.548689986 0.515472075 0.112043475 101.2055689 0.965486161 51.64740411 0.341999666 1.00E-05 5 -1.91650252 VGVNGFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 174.64 0.00062991 5155600000 2742100 2357720 2296830 2623690 2620100 2477530 3239200 2623000 2918400 FALSE TRUE 2612486.367 2597974.349 2402141.927 2359951.697 3077044.61 2391732.515 2745000.548 2393316.215 3370970.567 0.774995306 0.770690309 0.71259653 0.700080778 0.912806727 0.709508573 0.8143057 0.709978378 1 21.6847326 -1.902975106 2.777657348 1.125411161 0.766734988 0.569961937 0.064595954 11494970.29 7523161.578 9418528.898 0.013843858 0.012503307 1.902975106 -0.358676173 VGVSSKPDSS(ph)PVLSPGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VGVSSKPDSSPVLSPGNK 18 1 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 VGVSSKPDS(0.203)S(0.797)PVLSPGNK;VGVSSKPDS(0.285)S(0.714)PVLSPGNK;VGVSSKPDS(0.099)S(0.901)PVLSPGNK;VGVSSKPDS(0.027)S(0.973)PVLSPGNK;VGVSSKPDS(0.032)S(0.968)PVLSPGNK 243.04 2.75E-24 2796960000 6406730 6195230 6146650 7084410 3781530 6653930 7263430 7906060 4508560 TRUE FALSE 6103896.57 6826530.98 6428479.982 6372271.647 4441027.635 6423502.736 6155260.351 7213763.474 5207724.458 1.172085163 1.310847192 1.234412464 1.223619202 0.852776999 1.233456721 1.181948162 1.385204523 1 22.31222169 -1.790444788 2.538359295 0.941488976 1.199322981 0.171035008 0.137886506 21162090.88 15417055.8 7676981.213 0.031796863 0.016201499 1.790444788 0.257834005 VGWEQLLTTIAR ddPTM_SK-BR-3_Trastuzumab_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 ; 178.1 5.22E-05 227470000 253366 152692 142873 204844 262251 155098 299560 193123 293020 FALSE TRUE 241389.8913 168251.4884 149423.8684 184252.6919 307987.4914 149726.9174 253856.6202 176212.1263 338460.0451 0.713200553 0.497108864 0.441481559 0.544385355 0.909967058 0.442376935 0.750034233 0.520629034 1 18.36862601 -4.999999982 0.285583539 3.997481442 0.580876802 0.403942746 0.150462957 232.7837998 2.208781164 414.6502055 0.151510269 1.00E-05 4.999999982 -3.41660464 VGWSVDFSRPQLGEDEFSYGFDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VGWSVDFSRPQLGEDEFSYGFDGR 24 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 257.51 6.09E-44 764220000 594390 507690 489710 579560 679770 514120 738770 567710 727120 FALSE TRUE 566294.3627 559424.1882 512163.6879 521301.5277 798321.6728 496315.8955 626057.0681 517998.3028 839878.056 0.674257839 0.666077872 0.609807203 0.620687163 0.950520932 0.590938044 0.745414246 0.616754181 1 19.67982035 -2.258067918 2.378632892 2.290044848 0.686141102 0.474849116 0.104319487 4282298.014 939246.4334 29627574.52 0.022726746 0.005519911 2.258067918 -1.603903746 VGYELKDEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VGYELKDEIER 11 1 Q8WWY3-4;Q8WWY3;Q8WWY3-3;Q8WWY3-2 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 61.375 0.07999 159360000 310650 258910 258200 330420 215700 299300 339580 316330 222790 FALSE TRUE 295966.1901 285293.2234 270038.7254 297205.5538 253318.0117 288935.166 287770.8342 288630.4682 257339.1353 1.150101751 1.108627426 1.049349626 1.154917823 0.984374224 1.122779734 1.118255231 1.121595702 1 17.97331135 -2.560863453 1.756606819 5.68E-05 1.103459481 0.283954386 0.050420982 585958.1475 26019.70801 2339077.191 0.011770038 0.002748758 2.560863453 1.103402698 VGYTPDWIFLLR ddPTM_SK-BR-3_Trastuzumab_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 ; 146.88 0.00015149 374220000 614130 642800 540250 531770 503290 539280 649920 633730 421610 FALSE TRUE 585101.292 708302.0508 565020.9969 478315.4693 591063.6167 520604.5984 550762.7674 578237.2416 486991.1255 1.201461919 1.4544455 1.160228528 0.982185186 1.213705108 1.069022763 1.130950316 1.187367102 1 18.89353596 3.549774029 7.112828485 1.105768159 1.326270328 0.501851001 0.093577125 0.184988069 15.6501704 0.022787138 0.035279887 3546.288214 -3.549774029 0.220502169 VHACGVNPVETYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHACGVNPVETYIR 14 0 A6NP24;Q08257;C9JH92;Q08257-3 A6NP24 CRYZ Quinone oxidoreductase 0 ; 171.26 3.04E-06 223780000 348020 291984 381370 323370 664070 267228 404330 297120 554270 FALSE TRUE 331569.7843 321737.5016 398856.1917 290864.2332 779883.5977 257973.8274 342642.0325 271102.5977 640223.3608 0.517897041 0.502539459 0.622995373 0.454316807 1.218142988 0.402943477 0.535191393 0.423450024 1 19.28821579 VHAEEKLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHAEEKLDR 9 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;A0A0U1RRM9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 137.98 8.99E-05 196552000 251797 202919 246706 267410 200356 252033 319608 267111 171415 FALSE TRUE 239895.0548 223596.6768 258017.7141 240529.4388 235298.023 243305.034 270845.9296 243721.3448 197997.1627 1.211608548 1.129292328 1.303138442 1.214812553 1.188390883 1.228830912 1.367928337 1.230933522 1 17.59512023 3.749169202 24.95638853 1.241091331 1.170450441 0.003722819 0.097280748 1598.703187 3760888.421 0.02319236 0.041283093 5612.666044 -3.749169202 -0.070640891 VHAELADVLTEAVVDSILAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 87.16 0.0026454 740550000 62916 77429 81223 89674 55440 67924 80411 77010 43586 FALSE TRUE 59942.08537 85319.10313 84947.15489 80659.79915 65108.71845 65571.77485 68142.8251 70266.59614 50345.09427 1.190624156 1.694685537 1.687297563 1.602138209 1.293248516 1.302446163 1.353514699 1.395698968 1 15.61956359 2.729318923 23.81220598 1.298454475 1.53760216 0.373932071 0.174244012 431.1342548 1110860.189 0.055579669 0.053120576 536.1902623 -2.729318923 0.239147685 VHAIQCDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHAIQCDVR 9 0 Q16698-2;Q16698;E5RJD2;E5RJG7;E5RFV2 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;; 91.584 0.010654 1557160000 1225620 1036840 860630 1002180 951300 940280 1157330 1054200 926550 FALSE TRUE 1167687.372 1142495.175 900090.7368 901438.9624 1117206.419 907717.8678 980758.0527 961888.6593 1070234.642 1.091057349 1.067518402 0.841021867 0.842281615 1.043889232 0.848148464 0.916395353 0.898764273 1 20.0294957 3.799156219 7.769922619 0.908584133 1.080334731 0.519661975 0.066408283 0.200230069 23.23160285 0.015668108 0.02829447 6297.326613 -3.799156219 0.171750598 VHAIQCDVRDPDMVQNTVSELIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VHAIQCDVRDPDMVQNTVSELIK 23 1 Q16698-2;Q16698;E5RJD2;E5RJG7;E5RFV2 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;; 114.46 0.00040102 212208000 268221 197168 236776 228432 201609 232509 251889 238724 178872 FALSE TRUE 255542.7249 217259.6434 247632.4138 205469.5814 236769.5458 224457.155 213458.7068 217820.061 206610.5562 1.236832859 1.051541835 1.198546765 0.994477655 1.145970226 1.086377962 1.033145211 1.054254269 1 17.65655444 8 0.235528883 1.023095949 2.07583771 0.456818054 0.060022436 44.27007297 0.587070383 0.075675006 18.11471011 100000000 -8 1.052741762 VHATSTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHATSTYR 8 0 Q9H074;Q9H074-3;Q9H074-2;D6REB4 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 71.501 0.048579 29023000 20061 16655 19825 23958 24396 19444 24603 22495 31630 FALSE TRUE 19112.75629 18352.16344 20733.99586 21549.69632 28650.65468 18770.6494 20849.36048 20525.21855 36535.01886 0.523135252 0.502317065 0.5675102 0.589836737 0.784197068 0.513771444 0.570667845 0.561795756 1 15.15699233 -5 0.32251547 5.124652637 0.551964844 0.735204462 0.079578639 173.0939544 1.523721469 488.0011245 0.069962794 1.00E-05 5 -4.572687793 VHAYFAPVT(ph)PPPSVGGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHAYFAPVTPPPSVGGSR 18 0 J3KTA1;Q96IG2-2;Q96IG2 J3KTA1 FBXL20 F-box/LRR-repeat protein 20 1 VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR 181.85 2.63E-13 1595080000 526871 446349 435228 607514 610782 502108 605176 484886 425371 TRUE FALSE 501966.852 491832.4706 455183.6343 546445.5385 717302.1874 484719.8741 512845.2864 442426.8113 491335.3622 1.02163795 1.00101175 0.926421482 1.112164075 1.459903444 0.986535697 1.043778498 0.900457906 1 18.90634855 3.220855518 24.90199349 1.093530566 0.99239461 0.088848505 0.148999024 575.5908105 809559.4405 0.043222081 0.051764373 1662.859353 -3.220855518 -0.101135956 VHDAES(ph)S(ph)DEDGYDWGPATDL ddPTM_SK-BR-3_Trastuzumab_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 154.46 6.02E-08 72801000 169937 144818 162421 193895 139959 170460 199524 155537 132870 TRUE FALSE 161904.4148 159575.1188 169868.1635 174404.3062 164367.8053 164556.9275 169082.9493 141917.3557 153474.801 1.054925067 1.03974801 1.106814685 1.136370955 1.070975849 1.072208118 1.101698443 0.924694835 1 17.22764227 1.243238845 24.9998399 0.9623474 1.079760596 0.702231804 0.032669042 62.2553767 332698.631 0.024397882 0.008258438 17.50809299 -1.243238845 0.117413196 VHDFDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHDFDVK 7 0 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 0 ; 91.9 0.016065 335880000 661930 586290 609800 752300 463670 677880 727120 677500 381970 FALSE TRUE 630641.8807 646033.6176 637759.9332 676677.3747 544533.9012 654404.8456 616184.4895 618174.5083 441203.9568 1.429365877 1.464251641 1.445499124 1.533706496 1.23419995 1.483225242 1.396597832 1.40110826 1 18.7510862 -3.08691847 0.32063187 1.03E-09 1.450541898 0.754880948 0.076410053 36.51873059 1.003276985 24.63060206 0.061290248 0.000818618 3.08691847 1.450541897 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR 359.63 4.51E-96 11527670000 1464227 1378361 1467351 1590044 1350108 1495079 1645264 1225386 844233 TRUE FALSE 1395015.892 1518817.553 1534630.495 1430209.756 1585566.408 1443304.039 1394248.759 1118084.706 975152.3419 1.430562007 1.557518234 1.573734102 1.46665264 1.625967902 1.480080575 1.429775328 1.146574394 1 19.89526809 1.19591496 1.941323639 0.998150921 1.523710002 0.918646598 0.055567445 0.075975337 0.512633982 0.049005851 0.014184202 15.70055338 -1.19591496 0.525559082 VHDRS(ph)EEEEEEEEEEEEEQPRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHDRSEEEEEEEEEEEEEQPRR 22 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPRR;VHDRS(1)EEEEEEEEEEEEEQPRR 408.65 1.34E-152 1410140000 294779 274745 217330 308264 254812 254232 302515 230727 166783 TRUE FALSE 280845.3809 302741.8279 227294.7955 277276.7171 299251.1321 245427.8821 256360.7807 210523.3207 192646.8558 1.457824887 1.571485953 1.17985209 1.439300506 1.553366292 1.273978135 1.330729119 1.092793961 1 17.55559911 1.308881055 1.122576594 0.99231207 1.445357443 0.634462419 0.115206887 0.274916092 0.696639274 0.10346913 0.034640032 20.36484248 -1.308881055 0.453045373 VHEDST(ph)SPAVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHEDSTSPAVAK 12 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VHEDS(0.11)T(0.829)S(0.06)PAVAK 78.486 0.05614 0 231990 240040 261740 310750 255760 254280 345110 291930 217180 TRUE FALSE 221024.2925 264500.3489 273741.0379 279512.8196 300364.463 245474.2198 292457.1311 266367.0616 250859.1652 0.881069234 1.054377857 1.091214019 1.114222075 1.19734299 0.97853399 1.16582199 1.061819134 1 17.93651812 4.447310721 1.522891008 1.097350536 0.855521963 0.476168516 0.066623436 0.456333125 1.479913023 0.016227848 0.141314228 28009.84601 -4.447310721 -0.241828573 VHELNEEIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 164.31 6.20E-06 2798920000 6809750 6511260 6054120 7399900 4375800 7092810 7375960 6814620 2793460 FALSE TRUE 6487866.613 7174764.797 6331707.39 6656047.993 5138938.135 6847184.211 6250621.833 6217895.746 3226655.51 2.010709415 2.22359182 1.962312795 2.062831924 1.592651623 2.12206856 1.937182886 1.927040469 1 21.62160813 -1.948595347 0.327121295 9.05E-13 2.06876741 0.787674305 0.160774204 14.4604395 0.741459173 11.26491719 0.135954666 0.011256533 1.948595347 2.06876741 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGSSPR 40 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.5)S(0.5)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPES(0.004)DAPQQPGS(0.498)S(0.498)PR;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.5)S(0.5)PR 101.7 9.93E-06 357110000 76614 72407.1 73485.2 84315 57978.6 79694 90626 87744 56559.5 TRUE FALSE 72992.60805 79785.46581 76854.56911 75839.49601 68090.04948 76934.1768 76799.33924 80060.6702 65330.45839 1.117282962 1.22125985 1.176397212 1.160859695 1.042240498 1.177615751 1.17555182 1.225472347 1 15.99546814 2.990371802 24.63926464 1.138552236 1.173776415 0.07301248 0.070218517 1285.180134 3288882.738 0.01968841 0.022285873 978.0741966 -2.990371802 0.035224179 VHFEESSKLEDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHFEESSKLEDLLR 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 263.83 7.27E-25 585742000 1985800 2102940 1613430 2139020 1270780 1910090 1941850 2105590 945180 FALSE TRUE 1891935.169 2317231.977 1687407.361 1924001.646 1492403.63 1843943.104 1645585.118 1921213.377 1091753.687 1.732932246 2.122486055 1.545593462 1.762303776 1.366978328 1.688973553 1.507286064 1.759749841 1 20.05821597 -1.889058087 0.123432326 5.12E-12 2.148264647 0.558111268 0.195127021 37.11704068 0.680012931 13.34718953 2.065696545 0.012910466 1.889058087 2.148264647 VHFTAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VHFTAER 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;; 138.85 0.0027458 5579580000 3899401 3192053 2787248 3170024 4450662 2946284 4363574 3493349 3265965 FALSE TRUE 3715084.043 3517326.83 2915046.078 2851367.165 5226856.044 2844253.446 3697830.644 3187452.842 3772434.172 0.98479758 0.932375933 0.772722848 0.755842789 1.385539364 0.753957078 0.980224034 0.844932661 1 21.8470643 4.416618897 3.317436937 0.925915219 0.980362457 0.008970354 0.185073494 1.739950198 35.94329656 0.042591158 0.159043329 26098.70128 -4.416618897 0.054447237 VHGEPTS(ph)DLS(ph)DID ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.068)S(0.932)DLS(1)DID;VHGEPT(0.076)S(0.924)DLS(1)DID 174.9 2.80E-05 834690000 1407160 1417730 1533930 1692370 1269390 1504940 1689790 1316000 721350 TRUE FALSE 1340646.336 1562198.299 1604262.208 1522249.752 1490771.214 1452823.55 1431981.5 1200764.063 833213.2739 1.609007415 1.874908079 1.925392043 1.826962916 1.789183227 1.743639469 1.718625405 1.441124501 1 19.6683263 0.930900196 1.426556999 0.999352579 1.799907043 0.907456482 0.082237245 0.141858006 0.58059825 0.080268036 0.023873379 8.529040884 -0.930900196 0.800554464 VHHEPQLSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 102.52 0.0016977 428110000 263300 270471 231025 305520 176778 277710 296880 268054 64055 FALSE TRUE 250854.3308 298032.3024 241617.7248 274808.5491 207608.0272 268092.8331 251585.5034 244581.7707 73988.32225 3.390458429 4.02809921 3.265619728 3.714215173 2.805956682 3.623447929 3.400340699 3.305680725 1 16.17500996 -1.13145959 0.456607923 2.82E-14 3.57333671 0.858172571 0.312795988 6.771779021 0.847165932 9.06979344 0.156309878 0.073882301 1.13145959 3.57333671 VHIDIGADGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VHIDIGADGR 10 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;; 172.88 3.58E-06 2986920000 1517946 1144219 1012055 1279481 1488236 1119869 1466043 1317658 1015914 FALSE TRUE 1446195.701 1260816.217 1058458.723 1150865.139 1747783.887 1081087.656 1242371.215 1202276.88 1173456.755 1.232423517 1.074446256 0.902000622 0.980747807 1.489431869 0.921284616 1.058727737 1.024560024 1 20.16233324 2.002331664 0.017638474 1.27E-06 2.13689637 0.051405366 0.167881145 1293.240674 17.31441022 1027.594517 1065.173405 100.5383293 -2.002331664 2.136895099 VHIEIGPDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 182.28 1.79E-06 15581650000 6463614 5381830 4743315 6323445 6018679 5255652 6740986 5913032 4312285 FALSE TRUE 6158091.776 5930244.596 4960800.685 5687800.295 7068334.712 5073647.453 5712524.779 5395255.571 4981012.134 1.236313346 1.190570197 0.995942301 1.141896495 1.419055911 1.01859769 1.146860242 1.083164511 1 22.24800749 1.204839585 0.999714129 1.005754195 1.180029641 0.193928573 0.115129457 0.813012925 1.728150062 0.103422719 0.035448243 16.0265331 -1.204839585 0.174275447 VHKPPKVQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHKPPKVQEK 10 2 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 140.07 2.40E-05 282240000 452840 414180 368840 534090 316700 466700 635780 540330 340920 FALSE TRUE 431435.1506 456385.4129 385751.6788 480402.2585 371932.3797 450538.062 538780.0841 493015.8407 393788.1324 1.095602216 1.158961826 0.979591936 1.219951083 0.944498701 1.144112849 1.36819787 1.251982475 1 18.58706011 1.988374407 24.76752219 1.2497671 1.089669241 0.156823169 0.12083776 592.4267942 1262124.088 0.042445887 0.02912278 97.3586194 -1.988374407 -0.160097859 VHLFDIITQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHLFDIITQYR 11 0 B4DYU2;Q96MW5;H3BQV3 B4DYU2 COG8 Conserved oligomeric Golgi complex subunit 8 0 109.24 0.0019558 51243000 55058 60723 48165 54810 57465 56308 60459 55470 36395 FALSE TRUE 52455.51745 66910.74274 50373.41289 49300.39467 67486.87781 54358.03984 51234.86914 50612.75274 42038.95072 1.2477837 1.591636841 1.198255714 1.172731332 1.605341633 1.293039881 1.218747573 1.203949001 1 15.35943904 1.148803447 1.010250497 1.008512289 1.370327873 0.362179968 0.148288103 0.520553783 1.136542464 0.134178514 0.04536108 14.08651126 -1.148803447 0.361815584 VHLVGIDIFTGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 192.3 4.26E-06 3101789300 8332314 7979900 7750200 9153880 6685711 8542951 10084634 8760022 4707801 FALSE TRUE 7938462.03 8793060.882 8105554.336 8233714.591 7851696.882 8247106.465 8546037.866 7992948.034 5437862.735 1.459849654 1.617006775 1.490577223 1.514145353 1.443893909 1.516608062 1.571580285 1.4698694 1 22.3746083 0.899165116 9.502081578 1.000000019 1.521608252 0.912049583 0.049995017 3.01673642 284.454989 0.04703225 0.011766628 7.92802691 -0.899165116 0.521608233 VHMFEAHSDYIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHMFEAHSDYIR 12 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 186.46 6.78E-06 173480000 45023 56144 37545 48884 54534 46053 57895 46762 6565.2 FALSE TRUE 42894.85202 61865.13743 39266.47539 43970.08745 64044.71233 44458.17306 49062.05444 42667.27138 7583.297686 5.656490592 8.15807845 5.178021095 5.798280546 8.445496272 5.862643787 6.469751877 5.626479818 1 12.88860964 3.718128135 24.83733567 5.89823632 6.907284951 0.053401064 1.95904383 2187.39035 2658950.198 0.464354012 0.720300866 5225.503399 -3.718128135 1.009048632 VHNDAQS(ph)FDYDHDAFLGAEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 1 VHNDAQS(1)FDYDHDAFLGAEEAK 140.04 2.22E-07 82440000 100350 40494 49567 120150 108170 90212 58831 37230 24020 TRUE FALSE 95606.65437 44620.38464 51839.69598 108072.2937 127034.8138 87087.93582 49855.25044 33969.94383 27744.89892 3.44591828 1.608237419 1.868440614 3.8952131 4.57867279 3.138880991 1.796915915 1.224367186 1 14.75993493 1.574229644 3.291467614 1.183014816 2.98446223 0.481249693 0.870132385 0.215559615 5.367836786 0.628596942 0.253811513 37.51713307 -1.574229644 1.801447414 VHNDAQSFDYDHDAFLGAEEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 217.86 7.10E-26 1946290000 1489453 1956552 1466504 2087899 925993 1767465 1646975 1567671 191781 FALSE TRUE 1419049.509 2155926.873 1533744.659 1878019.426 1087485.886 1706257.244 1395698.715 1430397.416 221521.418 6.405924634 9.732363095 6.923685632 8.47782324 4.909168133 7.702448184 6.300513637 6.457151771 1 17.75708667 -0.164700924 0.394822878 9.53E-15 7.9230705 0.712127183 1.249079465 2.82967908 0.530615473 6.367727654 0.806670125 0.684382784 0.164700924 7.9230705 VHNNS(ph)PDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.999)PDT(0.001)SR;VHNNS(0.955)PDT(0.034)S(0.011)R;VHNNS(0.974)PDT(0.022)S(0.004)R;VHNNS(0.937)PDT(0.051)S(0.012)R 167.22 5.57E-06 256806000 251425 311512 241896 333667 231659 259009 271557 231320 116296.2 TRUE FALSE 239540.6385 343255.427 252987.1709 300126.1592 272060.2563 250039.4534 230125.9922 211064.3945 134330.8207 1.783214286 2.555299112 1.883314413 2.23423156 2.025300335 1.861370697 1.713128759 1.571228355 1 17.03543083 1.138700775 0.657813448 1.000536161 2.157969526 0.738719507 0.208706361 0.330060665 0.342543261 0.190595575 0.081208146 13.76260912 -1.138700775 1.157433365 VHNNSPDT(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.274)PDT(0.7)S(0.026)R 132.69 0.0024257 112320000 112190 125550 111150 150920 105360 125190 119890 106390 57468 TRUE FALSE 106887.001 138343.6877 116246.3374 135749.2349 123734.7506 120854.6389 101598.5786 97073.92759 66379.84393 1.610232786 2.084121919 1.751229448 2.045036969 1.864041 1.820652652 1.530563685 1.46240066 1 16.01845762 1.139837455 0.973061334 1.014101733 1.885238025 0.801101095 0.140402024 0.205496225 0.420558575 0.122838602 0.042116803 13.79867718 -1.139837455 0.871136292 VHPETYEWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VHPETYEWAR 10 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 135.86 0.00013302 334191000 116960.7 74302.6 109000.1 97441.6 226644 74934.7 174319.7 105574 167021 FALSE TRUE 111432.1995 81874.11942 113997.8624 87646.58524 266170.6418 72339.69255 147724.0282 96329.38088 192921.7637 0.577603052 0.42439027 0.590902033 0.454311549 1.379681778 0.374969061 0.765719872 0.499318372 1 17.55765638 VHPVSTMIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHPVSTMIK 9 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 138.98 0.00012151 2920900000 6272100 3788200 1602830 1862730 5488100 2949400 6784900 4642200 4790300 FALSE TRUE 5975630.263 4174221.887 1676321.341 1675484.841 6445222.902 2847261.538 5749738.892 4235704.358 5533155.259 1.079967936 0.754401728 0.30295939 0.30280821 1.164836807 0.514581899 1.03914288 0.765513375 1 22.39967098 1.708812364 12.81417749 0.92519167 0.713599129 0.134863702 0.29071448 0.303208078 104.9438178 0.138028922 0.075728618 51.14608123 -1.708812364 -0.211592541 VHQLYETIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VHQLYETIQR 10 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ;; 141.1 3.81E-05 629270000 324555 260129 208843 292002 285914 276362 301403 244943 245252 FALSE TRUE 309213.9284 286636.4408 218418.6581 262649.4042 335777.3111 266791.5146 255418.4367 223494.4924 283284.4276 1.091531684 1.011832677 0.771022467 0.927157933 1.185300985 0.94177967 0.901632465 0.788940269 1 18.11189177 1.857036254 3.902993555 0.886379844 0.998432468 0.125078609 0.117529389 0.458055798 11.22803377 0.058589746 0.03222796 71.9509039 -1.857036254 0.112052624 VHRPRS(ph)PILEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHRPRSPILEEK 12 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 VHRPRS(1)PILEEK;VHRPRS(1)PILEEK;VHRPRS(1)PILEEK;VHRPRS(1)PILEEK 141.57 3.16E-05 1678720000 1845170 955190 1953130 1742500 1528230 1855670 2539920 1817870 1322250 TRUE FALSE 1757952.471 1052524.947 2042682.942 1567340.589 1794752.828 1791407.683 2152408.555 1658687.666 1527297.777 1.15102143 0.689141936 1.337449038 1.026218078 1.175116507 1.172926269 1.409292011 1.086027683 1 20.54254994 3.726832112 24.98973505 1.196347796 0.92008167 0.273429241 0.167526992 730.9556214 1557435.352 0.042362291 0.066220481 5331.287605 -3.726832112 -0.276266126 VHSDFTAAATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHSDFTAAATR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;; 167.6 1.91E-05 503970000 274166 270479 207929 253386 294158 236078 322153 278622 272781 FALSE TRUE 261206.7165 298041.1176 217462.7503 227915.1579 345459.0621 227902.5597 273002.6431 254224.3806 315082.4843 0.829010591 0.945914586 0.690177211 0.723350771 1.096408335 0.723310787 0.866448174 0.806850248 1 18.26537003 VHSFPTLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VHSFPTLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 145.63 0.00056623 6140500000 9133000 7768300 7241200 8806900 7358900 8104100 10167800 8774700 6126500 FALSE TRUE 8701301.19 8559898.602 7573216.183 7921613.68 8642289.83 7823452.985 8616515.366 8006340.75 7076566.33 1.229593674 1.209611866 1.070182321 1.119414884 1.221254691 1.105543652 1.217612464 1.131387791 1 22.75461808 -5 0.229784609 0.095054319 1.189448211 0.464229937 0.055336012 146.668012 1.466872497 61.80599858 0.095843084 1.00E-05 5 1.094393892 VHSPSGAVEECHVSELEPDKYAVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHSPSGAVEECHVSELEPDKYAVR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 338.24 2.49E-87 958360000 683088 556675 676729 793632 765415 666185 1010885 795154 275294 FALSE TRUE 650799.784 613400.8154 707757.694 713854.6036 898903.1337 643114.8464 856655.9271 725526.1004 317985.1875 2.046635534 1.929023236 2.225756802 2.244930367 2.82687109 2.022467938 2.694012051 2.281634896 1 18.27860004 -0.078995604 9.134953342 1 2.271128522 0.670386754 0.282803586 0 0 0.28453099 0.067064597 0.833689623 0.078995604 1.271128522 VHTVEDYQAIVDAEWNILYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VHTVEDYQAIVDAEWNILYDK 21 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 120.52 3.32E-05 15384000 26656 41206 22557 35630 16605 29972 26334 31475 12666 FALSE TRUE 25396.02371 45404.93825 23591.26076 32048.40471 19500.90674 28934.06212 22316.26464 28718.88214 14630.17859 1.735865598 3.103512234 1.612506684 2.19056825 1.332923356 1.977697124 1.52535832 1.962989171 1 13.83665976 3.697329344 24.98960268 1.696521476 2.41968944 0.310523993 0.469405905 488.8231682 296267.7005 0.112386476 0.174109997 4981.146829 -3.697329344 0.723167964 VHTVEDYQAIVDAEWNILYDKLEK ddPTM_SK-BR-3_Trastuzumab_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 2145800000 3067900 3284900 3076600 3578500 1795530 3404700 3518700 3456400 1188920 FALSE TRUE 2922886.447 3619635.045 3217665.153 3218782.381 2108669.864 3286794.385 2981857.69 3153739.292 1373291.641 2.128379988 2.635736602 2.343031193 2.343844733 1.535485836 2.393369541 2.171321517 2.296481823 1 20.38920661 2.963460086 24.85590737 2.004383185 2.385768275 0.21349895 0.424749608 920.7818803 626352.4793 0.117164011 0.124309256 919.305981 -2.963460086 0.38138509 VHVGDEDFVHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 ;;;;; 211.46 1.83E-08 1734455000 1234490 862742 845886 1328491 1055054 1002897 1404096 1113789 263278.8 FALSE TRUE 1176138.104 950656.3907 884670.7098 1194948.561 1239055.084 968166.4254 1189875.367 1016259.731 304106.7317 3.867517492 3.126061648 2.909079667 3.929372277 4.074408602 3.183640231 3.912689998 3.341786369 1 18.21421823 0.950905629 21.12105894 0.999999994 3.556863665 0.808270136 0.390760487 741.2555948 318899.1326 0.36532909 0.091332273 8.93111393 -0.950905629 2.55686367 VHVQFFDDS(ph)PTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 1 VHVQFFDDS(0.999)PT(0.001)R;VHVQFFDDS(0.999)PT(0.001)R;VHVQFFDDS(0.996)PT(0.004)R;VHVQFFDDS(0.995)PT(0.005)R 205.3 8.55E-06 290102000 377636 425639 406924 472187 440669 426746 494143 433855 281939 TRUE FALSE 359785.8947 469012.098 425581.8679 424721.8657 517521.5341 411967.679 418752.4098 395864.3562 325660.6602 1.104787709 1.440186536 1.306826154 1.304185361 1.589143539 1.265021322 1.285855066 1.215573155 1 18.31300993 0.867123344 1.334935653 1.001589954 1.334215003 0.426308899 0.122660849 0.583330616 2.011199458 0.111900221 0.033665838 7.364162171 -0.867123344 0.332625049 VIADNVKDWSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIADNVKDWSK 11 1 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 153.75 2.95E-05 1712220000 2271410 784540 2083100 1467030 2272650 1888100 4210100 2600890 3970700 FALSE TRUE 2164044.951 864485.5179 2178612.195 1319561.357 2668999.44 1822714.624 3567771.921 2373142.283 4586455.876 0.47183381 0.18848661 0.475009954 0.287708286 0.581930692 0.397412441 0.777893 0.517423986 1 22.12894833 1.165831408 0.431546099 1.014304207 0.312734196 0.665086686 0.134197518 0.560166607 0.292813277 0.154656018 0.089158854 14.64979028 -1.165831408 -0.701570011 VIAHTQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VIAHTQMR 8 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;; 201.39 0.00011215 1659325000 958434 645138 341093 443692 1026799 459731 958990 675004 970152 FALSE TRUE 913130.7243 710878.2957 356732.4514 399091.2372 1205872.421 443810.4002 812678.4624 615897.0713 1120598.217 0.814860054 0.634373931 0.318341084 0.356141239 1.076097036 0.396047748 0.725218414 0.549614538 1 20.09583767 -1.538045271 2.59793539 1.023907483 0.619517247 0.222191703 0.229229726 15378009.63 14566639.33 2578937.86 0.053653853 0.028970416 1.538045271 -0.404390236 VIAINVDDPDAANYNDINDVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VIAINVDDPDAANYNDINDVKR 22 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 294.33 2.81E-55 10096120000 7988100 6925151 7008952 8653630 6056312 8048716 9162970 8797480 7215490 FALSE TRUE 7610518.344 7630831.76 7330319.382 7783750.672 7112530.895 7769986.947 7764990.637 8027126.013 8334431.338 0.913141885 0.915579174 0.87952244 0.933927026 0.853391264 0.932275597 0.931676118 0.963128219 1 22.99065234 1.224135616 1.257281529 0.998498249 0.903930808 0.666974719 0.023307254 0.232810151 0.730946003 0.019537737 0.006203494 16.75465989 -1.224135616 -0.094567441 VIAPWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VIAPWR 6 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;; 170.59 0.013239 1847760000 1543210 1278540 1343260 1375610 1628000 1255360 1655520 1370040 1747960 FALSE TRUE 1470265.522 1408824.68 1404849.8 1237331.069 1911922.685 1211886.568 1402940.018 1250072.035 2019024.709 0.728205809 0.697774858 0.695806145 0.612836021 0.946953584 0.600233649 0.694860252 0.619146476 1 20.94522714 -1.220208942 4.972568808 1.000039658 0.700841206 0.482950116 0.097713568 3.82E-05 5.98E-06 0.084016424 0.01980024 0.060226976 1.220208942 -0.299198452 VICILSHPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VICILSHPIK 10 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 90.15 0.011027 265870000 457390 362560 196790 212850 393430 256340 456270 421320 340460 FALSE TRUE 435770.0812 399505.2762 205813.0162 191453.9136 462044.0674 247462.8815 386657.6315 384426.9872 393256.798 1.108105654 1.015889053 0.523355266 0.486841968 1.174916924 0.629265362 0.983219193 0.97754696 1 18.58511218 1.594444651 25 0.985328674 0.852737148 0.090209791 0.23290971 2.915626673 5416.479511 0.128534618 0.060031454 39.30471497 -1.594444651 -0.132591526 VICILSHPIKNTNDANSCQIIIPQNQVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VICILSHPIKNTNDANSCQIIIPQNQVNR 29 1 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 190.37 2.26E-18 1101430000 476500 278890 544320 413870 519130 473490 696890 537920 603620 FALSE TRUE 453976.7893 307309.2081 569277.6104 372267.0013 609666.1076 457092.9226 590566.6312 490816.8731 697226.3067 0.651118274 0.440759629 0.816489001 0.533925639 0.874416386 0.655587602 0.847022876 0.703956331 1 19.41126748 1.634965175 0.14530808 1.179481172 0.351464563 0.442856461 0.124211977 3.676527777 0.548157852 1.308485824 1.379347679 43.14844758 -1.634965175 -0.828016608 VIDFDENTALDDAEEESFRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 129.15 2.96E-05 72337000 75756 65183 62922 77795 53312 71030 84312 73789 70609 FALSE TRUE 72175.16401 71825.22181 65807.03594 69974.8988 62609.59592 68570.21329 71448.6559 67327.64398 81558.6831 0.884947639 0.880656959 0.806867319 0.857969944 0.767663154 0.840746941 0.876039843 0.825511661 1 16.31555086 -1.236723261 3.784468483 1.000196105 0.847688805 0.645322395 0.036507407 5580463.358 1829911.454 8939.373134 0.008757574 0.057979803 1.236723261 -0.1525073 VIDGLETLDELEKLPVNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIDGLETLDELEKLPVNEK 19 1 B8ZZ77;H7BZ14;Q9H2H8;Q9H2H8-2 B8ZZ77 PPIL3 Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase-like 3 0 ; 220.34 2.66E-19 35054000 146604 127727 125914 152593 91855 147857 153572 166184 97591 FALSE TRUE 139674.3195 140742.5265 131687.2814 137254.0617 107874.4829 142736.675 130141.7709 151632.048 112724.9139 1.239072311 1.248548539 1.168218071 1.217601833 0.956971083 1.266238936 1.15450761 1.345151154 1 16.78244688 -2.345154892 2.035393462 4.71E-05 1.198364928 0.278187792 0.100996128 1467527.78 188192.9861 6738347.519 0.022812819 0.004516948 2.345154892 1.198317835 VIDGPHSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIDGPHSGR 9 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 114.97 0.0015521 223620000 445240 408930 414040 470950 514410 441910 477580 415970 495930 FALSE TRUE 424194.3876 450600.4319 433024.1435 423609.2113 604122.9411 426606.5459 404716.3996 379545.4616 572836.2915 0.74051591 0.786612927 0.75593001 0.739494368 1.054617087 0.744726813 0.706513197 0.662572304 1 19.12776337 -2.352411829 2.28056944 2.441371964 0.773534255 0.313839261 0.10507759 5076673.235 457088.1073 38125829.31 0.026436601 0.004442098 2.352411829 -1.66783771 VIDPATATSVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIDPATATSVDLR 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 121.6 0.00056935 87883000 126328 108181 111792 128087 140136 115518 130018 115720 153927 FALSE TRUE 120356.7258 119204.7669 116917.7738 115211.4514 164575.674 111517.5827 110181.3662 105586.9433 177797.213 0.676932578 0.670453518 0.657590588 0.647993573 0.925636973 0.627217833 0.619702437 0.593861633 1 17.43987318 -1.42838092 3.000672239 1.00622696 0.676241585 0.549683798 0.091751059 22641875.39 26896661.46 1196380.532 0.023643872 0.037292292 1.42838092 -0.329985375 VIDRELYQQLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIDRELYQQLQR 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 ; 240.6 2.96E-16 406920000 224970 115557 206056 143777 319240 198921 344550 246350 413870 FALSE TRUE 214336.1139 127332.3897 215503.8714 129324.2628 374915.3549 192032.3159 291982.5694 224778.288 478050.8458 0.44835422 0.266357419 0.450796967 0.270524075 0.784258324 0.401698517 0.610777226 0.470197449 1 18.86680455 -5 0.139035622 2.939101844 0.247048613 0.606878667 0.14196253 83.02031033 0.709246756 44.30535045 0.788243377 1.00E-05 5 -2.692053231 VIDTLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIDTLHR 7 0 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 146.21 0.0022347 92178000 224300 201740 221870 247920 265230 210800 262680 234030 268440 FALSE TRUE 213697.7835 222297.5354 232042.959 222998.6106 311486.028 203499.9431 222603.3416 213537.0925 310068.3042 0.689195834 0.716930858 0.748360783 0.719191893 1.004572295 0.656306821 0.717917112 0.68867759 1 18.24222653 -1.945167915 2.581233955 1.18836998 0.739000605 0.412230769 0.09648897 26404489.61 13816070.37 29893115.93 0.024155165 0.011345721 1.945167915 -0.449369375 VIEEEWQQVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ; 183.78 1.21E-05 469950000 246660 213093 255726 239920 268230 255530 339070 316360 308950 FALSE TRUE 235000.8706 234807.419 267451.29 215802.7858 315009.2271 246680.932 287338.6441 288657.8413 356860.3881 0.658523273 0.657981179 0.749456367 0.604726086 0.882723994 0.691253331 0.805185035 0.808881711 1 18.44500024 -3.267782498 0.102019402 1.673004651 0.499301771 0.671713947 0.067983487 58.11347438 0.594847705 9.443335654 1.050025574 0.000539781 3.267782498 -1.17370288 VIEETEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VIEETEER 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 183.9 0.00051381 5353000000 5350910 4890910 4541290 6033710 4608000 4770720 5024610 5252240 4588620 FALSE TRUE 5097983.089 5389299.29 4749512.638 5427190.008 5411633.741 4605508.77 4258013.461 4792326.022 5300199.754 0.96184735 1.016810599 0.896100687 1.023959522 1.021024488 0.868931169 0.803368488 0.904178379 1 22.3376153 2.227087602 24.75851136 0.869451453 0.984246118 0.307637035 0.062251896 169.4879165 365748.1652 0.021485164 0.016007906 168.6893258 -2.227087602 0.114794665 VIEHIMEDLDTNADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VIEHIMEDLDTNADK 15 0 P06702 P06702 S100A9 Protein S100-A9 0 ;;;;;;;;; 331.42 6.98E-69 476130700 1161460 997201.8 807668.5 1226309 716309.1 1086528.6 1109864 1169095.2 609952.1 FALSE TRUE 1106560.088 1098817.797 844700.8996 1103038.089 841233.1802 1048901.842 940533.8627 1066723.027 704540.3565 1.57061278 1.559623643 1.198938985 1.565613778 1.194017025 1.488774678 1.334960949 1.514069445 1 19.42632282 -3.909567286 0.149256128 3.03E-21 1.5793608 0.451565627 0.145341207 79.38351283 0.955506449 25.40422918 0.714122897 0.00012315 3.909567286 1.5793608 VIENPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIENPR 6 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 118.01 0.05172 44691000 88773 70789 79804 79211 197390 67751 86353 91236 236150 FALSE TRUE 84576.87622 78002.47958 83463.09234 71248.55979 231814.7535 65404.76588 73178.26387 83246.89217 272770.9359 0.310065572 0.28596331 0.305982351 0.261202901 0.84985137 0.239779087 0.26827735 0.305189744 1 18.05733041 -1.16224161 4.499080232 1.000101153 0.34456541 0.564167226 0.178489586 50.59834278 203565286.7 43794.45507 0.039728653 0.068826929 1.16224161 -0.655535743 VIEPLKDFHKDEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIEPLKDFHKDEVR 14 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 226.24 1.49E-12 1569950000 5581400 4773900 4830200 5653300 3768300 5489400 6405500 6271600 3675300 FALSE TRUE 5317578.283 5260365.837 5051669.448 5085019.543 4425490.327 5299300.702 5428223.33 5722425.456 4245246.753 1.252595807 1.239118983 1.189958969 1.197814836 1.042457738 1.248290384 1.278659085 1.347960623 1 22.01741698 VIET(ph)PENDFK ddPTM_SK-BR-3_Trastuzumab_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 154.36 0.00016353 237079000 1105150 1072050 982290 1241310 762840 1150460 1125410 1227530 853410 TRUE FALSE 1052911.75 1181293.114 1027328.968 1116531.16 895879.0545 1110619.282 953708.0349 1120040.966 985752.4642 1.06812997 1.198366889 1.042177428 1.132668901 0.908827608 1.126671575 0.967492418 1.136229435 1 19.91086589 3.152462317 2.016285086 1.031045267 1.125694794 0.152102035 0.081146542 0.457005588 3.81067088 0.023149241 0.030085184 1420.568947 -3.152462317 0.094649526 VIFGLFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIFGLFGK 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 153.52 0.001023 82143000 485210 402530 342810 443360 469070 357360 578100 474340 543100 FALSE TRUE 462275.0849 443548.2646 358528.1776 398792.6105 550875.6595 344984.5336 489900.2275 432804.275 627321.1742 0.736903366 0.707051321 0.571522519 0.635707237 0.878139751 0.54993287 0.780940047 0.689924544 1 19.25884473 -0.885874072 0.549608703 1.075693446 0.689615619 0.50465066 0.095586794 14.90940191 2.863629991 1.992314982 0.037684782 0.130054663 0.885874072 -0.386077827 VIFLEDDDVAAVVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VIFLEDDDVAAVVDGR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 198.49 9.44E-11 57113000 55741 57302 62548 64929 66401 53335.6 66864 60266 62981.5 FALSE TRUE 53106.2334 63141.13895 65415.88767 58402.21356 77981.31338 51488.5748 56662.66876 54988.78955 72748.34936 0.729999153 0.867939129 0.899207862 0.802797783 1.071932409 0.707762791 0.778885971 0.7558768 1 16.15062689 0.014676497 7.942928607 0.999999997 0.824717182 0.212816983 0.104616846 2160529.287 317341.0714 0.095886971 0.023256006 1.034371383 -0.014676497 -0.175282815 VIFWSALAGAIPLNGDS(ph)EEEANRDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIFWSALAGAIPLNGDSEEEANRDDR 26 1 Q9H089 Q9H089 LSG1 Large subunit GTPase 1 homolog 1 VIFWSALAGAIPLNGDS(1)EEEANRDDR;VIFWSALAGAIPLNGDS(1)EEEANRDDR 200.14 3.31E-25 206012000 156138 203815 166568 196305 164076 177498 167291 157623 142943 TRUE FALSE 148757.6662 224583.9802 174205.3076 176572.0484 192690.8025 171351.1998 141767.6854 143820.6945 165109.8704 0.90096168 1.360209294 1.05508718 1.069421519 1.167045931 1.037801068 0.85862635 0.87106055 1 17.33306684 1.934235351 4.027520689 0.899703743 1.12060368 0.367622842 0.119125676 0.220320045 6.669649041 0.054198147 0.031542723 85.94791602 -1.934235351 0.220899937 VIGELVGHTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIGELVGHTER 11 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 134.75 0.0013576 0 38374 40022 40989 40402 43713 39428 41014 39179 44373 FALSE TRUE 36560.13707 44100.2873 42868.38619 36340.7142 51336.53336 38062.59847 34756.56103 35748.27906 51254.13821 0.713310931 0.860423935 0.836388781 0.709029855 1.00160758 0.742624885 0.678122045 0.697471079 1 15.64538087 -0.457991748 8.997829975 0.999997077 0.780030545 0.331575502 0.098222495 0 0 0.092832923 0.02188093 0.348343934 0.457991748 -0.219966532 VIGIDHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIGIDHIK 8 0 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8;C9J0F2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 123.98 0.0013243 680270000 1036100 728810 893610 1025500 816260 922690 1202500 1031300 819100 FALSE TRUE 987125.6064 803076.5676 934582.9024 922414.7917 958615.4856 890737.0139 1019036.54 940993.9047 946121.8446 1.043338775 0.848808821 0.987803958 0.974942918 1.013205108 0.941461207 1.077066918 0.994580043 1 19.85166646 2.663040957 1.101330681 1.01977093 0.949055458 0.106860306 0.057671522 0.792248583 1.988474993 0.029706664 0.025433441 460.2999811 -2.663040957 -0.070715472 VIGMHYFSPVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIGMHYFSPVDK 12 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 97.911 0.0046552 401850000 1000500 589290 832500 662570 1073500 714420 1194700 918970 1266200 FALSE TRUE 953208.3478 649339.321 870670.9485 595967.2048 1260718.06 689679.4563 1012426.573 838500.115 1462555.829 0.651741512 0.44397575 0.595307838 0.407483388 0.861996537 0.471557695 0.692231061 0.573311527 1 20.48006027 -5 0.226656306 3.226366263 0.533036501 0.496880126 0.131349535 119.3373728 1.193886299 121.427502 0.204436288 1.00E-05 5 -2.693329762 VIGQDSSEIHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIGQDSSEIHFK 12 0 B8ZZN6;P63165;B8ZZJ0;B9A032;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 ; 148.68 6.66E-05 860820000 2037350 1656450 1666730 2139740 1683230 1763750 2209000 2044410 1778350 FALSE TRUE 1941048.503 1825244.138 1743151.219 1924649.27 1976784.779 1702670.895 1871976.479 1865390.622 2054127.435 0.944950381 0.888573954 0.848609093 0.936966829 0.962347683 0.828902271 0.911324413 0.908118255 1 20.97009426 0.591848366 2.816028486 0.999996732 0.902716377 0.352766711 0.041042297 6.923554082 46.38213717 0.037337183 0.009823579 3.907044576 -0.591848366 -0.097280355 VIGSGCNLDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 306.79 5.32E-37 4807600000 1746104 1336824 1158832 1455369 1711084 1392531 1874952 1579707 1737147 FALSE TRUE 1663569.124 1473047.885 1211965.593 1309072.543 2009496.508 1344307.302 1588893.637 1441379.481 2006534.885 0.829075605 0.734125231 0.604009231 0.652404577 1.001475989 0.669964581 0.791859463 0.718342597 1 20.93627481 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR 34 0 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ; 210.51 5.73E-28 325490000 148179 133484 150120 160045 160517 148245 186532 159556 67888 FALSE TRUE 141174.8723 147086.1714 157003.1505 143956.9725 188511.114 143111.2385 158073.1175 145584.4308 78415.72432 1.800338817 1.87572292 2.002189636 1.835817673 2.403996336 1.825032412 2.015834437 1.856571906 1 16.25885536 0.804168177 4.836856724 1.000003454 1.952866818 0.751609126 0.172961244 1.608755248 39.43434625 0.156259665 0.03954696 6.370421633 -0.804168177 0.952863363 VIHCSGYLK ddPTM_SK-BR-3_Trastuzumab_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 9603800000 857970 873370 1026500 813260 3164100 535340 1140810 511480 1675160 FALSE TRUE 817415.4584 962367.3959 1073566.04 731509.5597 3715918.038 516801.0416 966758.4821 466692.0997 1934935.257 0.422451064 0.497364133 0.554833055 0.378053765 1.920435335 0.267089578 0.499633504 0.241192618 1 20.88385386 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_SK-BR-3_Trastuzumab_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;VIHDNFGIVEGLMTTVHAITAT(1)QK 336.04 9.50E-87 944516000 914430 1359461 1421444 1167520 673602 1476073 1059254 1156736 395228 TRUE FALSE 871206.7061 1497991.621 1486618.613 1050158.671 791077.9755 1424956.222 897645.3478 1055446.064 456517.9397 1.908373429 3.28134229 3.256429779 2.300366711 1.732851892 3.121358654 1.966287126 2.311948714 1 18.80031203 3.031859869 16.07024219 2.151417413 2.784788252 0.225161628 0.644541466 7.061564503 3559.562829 0.174688032 0.208747097 1076.117933 -3.031859869 0.63337084 VIHDNFGIVEGLMTTVHAITATQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 18 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;; 396.92 6.65E-138 50126741400 27896409.6 22202823.6 23424821.9 27409619.3 22661299.1 25900483.3 31209209.1 26253390.2 13756309.1 FALSE TRUE 26577801.6 24465316.57 24498873.15 24654352.29 26613422.49 25003543.07 26447671.06 23954504.18 15889567.26 1.672657359 1.539709431 1.541821294 1.551606277 1.674899137 1.57358238 1.664467674 1.507561772 1 23.9215765 0.859903511 5.234185119 1.000007636 1.600943381 0.926809186 0.05283155 0.409962159 15.14631556 0.049493027 0.012491238 7.242750263 -0.859903511 0.600935745 VIHLVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 145.04 0.0023131 189290000 164996 148634 150769 161915 190179 158085 207348 175082 186426 FALSE TRUE 157196.9661 163779.9736 157681.9078 145638.9966 223346.1574 152610.4768 175713.2544 159750.8919 215335.9919 0.730007857 0.760578722 0.732259881 0.676333739 1.037198451 0.708708634 0.815995751 0.741868048 1 17.71622995 -5 0.183072754 1.918944576 0.729610962 0.33754252 0.099523614 149.9479535 1.451227526 50.31943286 0.27003159 1.00E-05 5 -1.189333614 VIISAPSADAPMFVMGVNHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VIISAPSADAPMFVMGVNHEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 343.5 5.08E-81 11673837000 13929841 13637578 11896110 15872486 10803620 13784103 14692330 14347982 10134920 FALSE TRUE 13271405.02 15027262.7 12441558.41 14276953.55 12687767.91 13306756.06 12450745.22 13091596.63 11706591.63 1.133669427 1.283658231 1.062782303 1.219565353 1.083814 1.136689181 1.063567058 1.118309842 1 23.48081776 1.786312955 0.331962547 0.995460949 1.215068305 0.392293104 0.063267089 1.157953915 0.401464826 0.084648442 0.087878064 61.13824319 -1.786312955 0.219607356 VIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIISAPSADAPMFVMGVNHEKYDNSLK 27 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 254.11 1.08E-52 2520800000 2130400 1020860 2091770 1608870 1868710 2011650 3228500 2467700 2610500 FALSE TRUE 2029700.214 1124886.795 2187679.724 1447143.331 2194612.432 1941986.056 2735933.03 2251615.106 3015323.007 0.67312862 0.373056814 0.725520854 0.479929788 0.727820014 0.644039146 0.907343267 0.746724348 1 21.52388112 1.808036944 0.637471821 0.972728523 0.532899418 0.571352259 0.118677798 0.441188793 0.366510073 0.099235708 0.0545171 64.27423906 -1.808036944 -0.439829105 VIKDEALS(ph)DGDDLRDFPSDLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VIKDEALSDGDDLRDFPSDLKK 22 3 Q01831-2;Q01831;E7EUB5;Q01831-3 Q01831-2 XPC DNA repair protein complementing XP-C cells 1 VIKDEALS(1)DGDDLRDFPSDLKK 154.63 1.79E-08 93522000 587060 611850 506890 647280 319630 675570 610490 660320 314020 TRUE FALSE 559310.8372 674198.2106 530131.4079 582214.1846 375373.3708 652174.8415 517348.5381 602498.8802 362716.6178 1.542004997 1.858746408 1.461558092 1.605148913 1.034894329 1.79802857 1.426316062 1.661073275 1 18.46848332 -3.002961423 0.22185421 7.69E-15 1.648913086 0.345141329 0.230172211 60.84951246 1.344034584 29.57903313 0.423383548 0.000993204 3.002961423 1.648913086 VIKDFMIQGGDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VIKDFMIQGGDFTR 14 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 153.95 5.70E-06 2582720000 4046490 2960240 3291320 3703910 3636970 3522510 4715250 4101260 4549960 FALSE TRUE 3855220.437 3261891.822 3442230.278 3331585.93 4271256.416 3400524.595 3995852.011 3742131.932 5255544.559 0.733552992 0.620657248 0.654971191 0.633918311 0.812714338 0.647035632 0.760311699 0.71203505 1 22.32540883 -1.685421496 0.300266904 1.270223519 0.663010992 0.736918714 0.057901755 12.10257237 0.644320614 2.437483117 0.056285397 0.020633766 1.685421496 -0.607212527 VILEDVAMLHIKPDQFTYTSDHFETIMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VILEDVAMLHIKPDQFTYTSDHFETIMK 28 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 261.94 5.77E-54 877160000 1262830 1007340 1162390 1304480 946610 1193930 1511320 1395800 528110 FALSE TRUE 1203138.529 1109989.091 1215686.731 1173351.192 1111698.484 1152583.905 1280740.377 1273576.352 610006.6016 1.972336898 1.819634555 1.9929075 1.923505728 1.822436809 1.889461363 2.099551666 2.087807491 1 19.21846533 -0.521541166 7.398186163 0.999996178 1.945789565 0.907884272 0.095182375 0 0 0.0971175 0.022890814 0.300925391 0.521541166 0.945793387 VILGSEAAQQHPEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VILGSEAAQQHPEEVR 16 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQ14;E9PNX5 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 240.92 6.98E-20 427070000 270030 232920 243960 293790 304440 257550 287530 274230 297220 FALSE TRUE 257266.217 256654.8128 255145.8073 264257.671 357534.2396 248630.9789 243662.0176 250216.9674 343311.3596 0.749367039 0.747586136 0.743190693 0.769731801 1.041428516 0.72421425 0.709740621 0.72883393 1 18.38915807 -2.218835439 2.355229651 1.746584749 0.772188761 0.348378606 0.095768273 8440935.702 1744925.075 33547123.78 0.022848357 0.006041775 2.218835439 -0.974395988 VILHLK ddPTM_SK-BR-3_Trastuzumab_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 ; 104.03 0.034176 6309200000 11731000 13649900 9682500 13523800 8881900 10815000 11182000 11428800 7960900 FALSE TRUE 11176498.88 15040840.33 10126452.2 12164361.93 10430900.55 10440473.84 9475980.528 10428033.68 9195435.713 1.215439836 1.635685442 1.101247675 1.322869553 1.134356313 1.135397404 1.030509138 1.134044542 1 23.13248651 2.938264369 0.951928699 1.060333653 1.403768267 0.423691819 0.137571652 0.436996865 0.863335969 0.066909205 0.077032725 867.4897831 -2.938264369 0.343434614 VILHLKEDQTEYLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 28 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 339.3 3.75E-72 9145106100 9985115.6 7325061.7 9200920.7 9174500.3 8277897.1 9377908.3 11522509.6 9982468.4 8964528.1 FALSE TRUE 9513138.974 8071493.815 9622792.015 8252262.099 9721559.733 9053148.984 9764539.135 9108350.547 10354701.33 0.918726544 0.779500398 0.929316231 0.796958003 0.938854673 0.874303246 0.943005387 0.879634308 1 23.30378261 0.907452849 0.377015367 1.00792672 0.849632275 0.329493153 0.055002317 1.585358189 0.596910447 0.088481481 0.04425098 8.080771921 -0.907452849 -0.158294446 VILHLKEDQTEYLEERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VILHLKEDQTEYLEERR 17 2 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 ;; 246.69 6.72E-21 1468785000 1038038 562629 1143509 934323 1255163 1009813 1713985 1355430 1528799 FALSE TRUE 988972.0009 619961.5348 1195940.019 840403.0769 1474063.03 974842.9226 1452485.109 1236741.364 1765877.341 0.560045694 0.351078481 0.677249768 0.475912487 0.834748256 0.552044528 0.822528878 0.700355192 1 20.75195371 1.75072847 0.262844751 1.05232165 0.373386978 0.579355957 0.123307403 1.117303073 0.300378413 0.254841353 0.287984884 56.32853677 -1.75072847 -0.678934672 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHRSEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(0.934)DQEDHRS(0.066)EEK;VILSNMVSISSEPFGHLVDDDDIS(0.72)DQEDHRS(0.28)EEK 280.03 3.53E-74 257637000 81652 64070 78469 87394 83456 73190 123629 100498 79778 TRUE FALSE 77792.47178 70598.80584 82066.88127 78608.98908 98010.69998 70655.41195 104767.1254 91697.86235 92149.56479 0.844197929 0.766132819 0.890583493 0.853058712 1.063604589 0.766747104 1.136924799 0.99509816 1 16.49168973 2.716934729 0.726391818 1.032357754 0.799848959 0.369948493 0.098227177 0.613631422 0.694055006 0.06385795 0.06153748 521.1163858 -2.716934729 -0.232508795 VILSNMVSISSEPFGHLVDDDDISDQEDHRS(ph)EEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISS(0.009)EPFGHLVDDDDIS(0.494)DQEDHRS(0.496)EEK 101.77 1.24E-05 40414000 33452 35202 34831 40008 62191 26950 36347 24510 23735 TRUE FALSE 31870.79026 38789.12382 36428.0358 35986.31983 73037.09071 26016.71474 30801.59759 22363.77446 27415.70258 1.162501313 1.414850621 1.328728881 1.312617093 2.664060514 0.948971294 1.123502033 0.815728665 1 14.74271483 VINAAHSFYNGTTTLPISDEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VINAAHSFYNGTTTLPISDEDR 22 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 116.2 0.00017101 325290000 135210 131350 119610 115680 107570 131460 116920 137880 116290 FALSE TRUE 128818.8913 144734.7143 125094.2368 104051.6266 126330.1739 126907.5072 99081.70662 125806.4963 134323.6593 0.959018627 1.077507232 0.931289674 0.774633651 0.940490861 0.944788937 0.737634064 0.936592235 1 17.03535391 3.483187194 24.60881425 0.871254245 1.015952201 0.262559033 0.085157324 217.4786138 882286.1476 0.022004466 0.03082897 3042.196021 -3.483187194 0.144697957 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGTTTLPIS(0.002)DEDRT(0.998)PR;VINAAHSFYNGT(0.013)T(0.009)T(0.007)LPIS(0.003)DEDRT(0.967)PR;VINAAHSFYNGTTTLPISDEDRT(1)PR;VINAAHSFYNGTTTLPIS(0.002)DEDRT(0.998)PR 241.57 1.88E-38 1964200000 760637 785147 850023 857381 1050226 772980 1031251 895036 1262577 TRUE FALSE 724683.1964 865154.3719 888997.3953 771195.433 1233385.082 746211.5088 873914.7197 816661.903 1458370.993 0.496912788 0.593233393 0.609582472 0.52880607 0.845727931 0.511674678 0.599240333 0.559982273 1 20.47592634 -1.708489247 2.532538019 1.074799444 0.590520409 0.632940111 0.09735269 10507893.47 8071965.454 4989227.333 0.021794964 0.019566392 1.708489247 -0.484279035 VINAAHSFYNGTTTLPISDEDRTPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 259.77 3.09E-45 844402000 367027 247649 342585 324836 431136 326508 459437 392223 472560 FALSE TRUE 349678.3611 272884.7147 358292.8611 292182.8681 506325.9819 315200.9461 389341.4475 357877.8748 545842.1913 0.640621716 0.499933349 0.65640375 0.535288171 0.927605066 0.577458011 0.713285733 0.655643482 1 19.05812439 -5 0.146648059 2.27685393 0.522814139 0.499463028 0.113239794 103.0067277 0.906658262 38.25125777 0.552020828 1.00E-05 5 -1.754039791 VINIDFRDPEESKWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VINIDFRDPEESKWK 15 2 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 124.09 5.55E-05 375300000 1250700 864560 1189730 1242990 955330 1383660 1603970 1559900 1149060 FALSE TRUE 1191581.89 952659.6469 1244280.297 1118042.284 1121939.25 1335743.507 1359254.918 1423306.886 1327250.356 0.897782309 0.717769366 0.937487258 0.842374823 0.845310942 1.006399057 1.024113432 1.072372578 1 20.3400091 2.213020986 3.964701478 1.030687359 0.837262486 0.694437678 0.058492578 0.114856382 3.946563262 0.022137771 0.016540135 163.3130861 -2.213020986 -0.193424873 VIPAKS(ph)PPPPTHSTQLGAPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.985)PPPPT(0.015)HSTQLGAPSR;VIPAKS(0.995)PPPPT(0.005)HSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR 274.34 5.87E-45 5818404000 2298614 1722903 2132002 2270402 1993570 2087507 2792539 2496168 2364645 TRUE FALSE 2189963.072 1898468.774 2229756.401 2042176.877 2341247.977 2015216.109 2366485.887 2277590.297 2731342.07 0.801790115 0.695068112 0.816359264 0.747682577 0.857178602 0.73781169 0.866418715 0.833872228 1 21.38117858 0.284700855 0.347304238 1.039886049 0.748372939 0.674970969 0.048077631 1.818114531 0.380797349 0.15666219 0.040407488 1.926197678 -0.284700855 -0.29151311 VIPELNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIPELNGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 107.29 0.0093769 1564920000 5135900 4549300 4220500 4921800 4331300 4553200 5635800 5143000 4724900 FALSE TRUE 4893136.185 5012878.842 4414014.1 4427051.313 5086677.349 4395521.542 4775955.201 4692651.655 5457613.361 0.896570692 0.918511172 0.80878102 0.811169832 0.932033292 0.805392623 0.875099588 0.859835856 1 22.37983876 -1.545297716 6.245633364 1.000192018 0.867185533 0.475187748 0.044952939 0.000117882 8.58E-06 0.04268869 0.010047371 0.028490645 1.545297716 -0.133006485 VIPEYCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VIPEYCR 7 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 124.12 0.0097174 526050000 599600 532070 477350 575990 660120 550940 667200 610080 689030 FALSE TRUE 571258.0963 586288.5379 499236.9697 518090.3909 775244.719 531860.8097 565406.386 556658.161 795881.2533 0.717768001 0.736653283 0.627275699 0.650964436 0.974070838 0.668266538 0.710415509 0.699423637 1 19.60219367 -1.095171604 4.209942069 1.000036541 0.723076645 0.455974418 0.095051156 12119139.16 3152665.974 4764.910265 0.020748252 0.080320868 1.095171604 -0.276959895 VIQLMPS(ph)PIMHPLILNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR 184.02 3.89E-14 203679000 264837 213190 230294 252603 284720 229655 307570 247270 258620 TRUE FALSE 252318.6799 234914.3034 240853.2077 227210.8665 334375.0779 221701.9898 260644.5476 225617.7279 298725.4688 0.844650712 0.786388601 0.806269411 0.760600921 1.119339035 0.742159651 0.872522014 0.755267801 1 18.18846072 VIQPMGMS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIQPMGMSPR 10 0 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35 Q9NPQ8-4 RIC8A Synembryn-A 1 VIQPMGMS(1)PR;VIQPMGMS(1)PR 136.27 0.00012797 295760000 344480 296740 340360 363320 356760 334660 411760 354630 348680 TRUE FALSE 328197.1131 326978.1434 355965.8427 326798.3833 418978.831 323070.6403 348938.4495 323576.7172 402751.5136 0.814887349 0.811860744 0.883834897 0.811414414 1.04029114 0.802158724 0.866386439 0.803415273 1 18.61953049 VIQYLAYVASSHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VIQYLAYVASSHK 13 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 218.31 2.44E-11 584750000 2219900 1584680 1361530 1668160 2216490 1723960 2898000 2287100 2183820 FALSE TRUE 2114969.726 1746160.694 1423957.497 1500473.388 2603045.154 1664258.833 2455856.875 2086829.399 2522475.652 0.838450006 0.692240852 0.564507925 0.594841574 1.031940646 0.659772011 0.973589922 0.827294169 1 21.26640891 2.748670882 24.94661336 0.883412396 0.688236199 0.436887821 0.126298179 724.4243957 1787483.366 0.037294136 0.039149544 560.6229629 -2.748670882 -0.195176196 VIREPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 103.02 0.031961 699860000 1867380 2218970 1576840 2361780 1276920 1836240 1826720 1969800 1330480 FALSE TRUE 1779112.648 2445085.566 1649139.674 2124369.387 1499614.444 1772650.548 1548020.314 1797313.869 1536804.043 1.157670463 1.591019738 1.073096912 1.382329385 0.975800689 1.153465568 1.007298439 1.169514017 1 20.55150179 2.94090448 1.498073127 1.063078089 1.344691158 0.312609144 0.157599598 0.386374424 1.770365287 0.054750688 0.062057902 872.7793855 -2.94090448 0.281613069 VIREPKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 159.28 0.00020254 17944237000 9053128 6677757 8016575 8842289 8024915 8009445 11023582 9571390 9653304 FALSE TRUE 8625204.581 7358228.03 8384142.893 7953445.31 9424457.635 7732075.911 9341732.104 8733268.35 11150289.08 0.773540894 0.659913656 0.751921572 0.713294987 0.845220923 0.693441744 0.837801786 0.78323246 1 23.41057778 -0.467910338 0.292825381 1.102659499 0.708436645 0.688238647 0.053631384 4.542524575 0.445780992 0.506418828 0.059179737 0.340478475 0.467910338 -0.394222854 VISAFVEIIFDNSDNRLPIDKEEVSLRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VISAFVEIIFDNSDNRLPIDKEEVSLRR 28 3 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 170.55 1.63E-12 235100000 351390 245894 311930 299150 335880 366180 464060 374520 347220 FALSE TRUE 334780.4911 270950.8782 326232.299 269078.8737 394457.3657 353499.0948 393259.124 341725.0433 401065.1042 0.834728545 0.675578292 0.813414819 0.67091071 0.983524524 0.881400778 0.980536875 0.85204382 1 18.61347692 2.732529204 24.99949722 0.936997856 0.749639104 0.661876096 0.067764791 272.2691673 1128521.159 0.019258521 0.018585032 540.1684368 -2.732529204 -0.187358753 VISFIENTST(ph)PVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VISFIENTSTPVDR 14 0 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 VISFIENTS(0.025)T(0.974)PVDR 164.53 4.59E-05 11803000 31483 30145 31971 38974 37415 32457 35230 32967 40753 TRUE FALSE 29994.86098 33216.80977 33436.90197 35056.25947 43940.16415 31333.00595 29855.01646 30080.23471 47072.7671 0.637201992 0.705648123 0.710323697 0.744724851 0.933451906 0.66562915 0.634231176 0.639015647 1 15.52260504 -1.739946291 2.822271234 1.054430208 0.704848614 0.520569994 0.087759286 19246094.59 16888348.09 7358028.018 0.021724397 0.018199259 1.739946291 -0.349581595 VISGVLQLGNIVFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VISGVLQLGNIVFKK 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 105.31 0.0021242 37413000 98720 65487 93484 78392 85116 88148 125780 101830 120260 FALSE TRUE 94053.70124 72160.19975 97770.33387 70511.88722 99960.20345 85095.41266 106589.9509 92913.22537 138909.3066 0.677087112 0.519477071 0.703842934 0.507610965 0.719607677 0.612596915 0.767334842 0.668876893 1 17.08378373 0.053761973 0.386101197 1.063125281 0.59455063 0.688736847 0.07712073 2.120791714 0.446833743 0.281310523 0.050392596 1.131779889 -0.053761973 -0.468574651 VITEEEKNFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VITEEEKNFK 10 1 P26373;P26373-2;J3KS98;H3BUK8 P26373 RPL13 60S ribosomal protein L13 0 ;; 161.62 6.40E-06 1402230000 2083850 1175790 2090040 1736850 1681570 2149790 3010960 2570140 2228670 FALSE TRUE 1985350.54 1295604.338 2185870.401 1562258.538 1974835.276 2075342.233 2551582.752 2345084.916 2574280.761 0.771225334 0.503287892 0.849118882 0.606871854 0.767140595 0.806183329 0.991182776 0.910967037 1 21.29573798 2.081253214 1.469743217 0.976545776 0.670025193 0.615337666 0.096649517 0.241096584 0.983170813 0.057506262 0.029407821 120.5738736 -2.081253214 -0.306520583 VITLWYRPPELLLGEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 119.4 0.00011108 59914000 104440 104110 118400 90628 78280 122720 128240 113230 97643 FALSE TRUE 99503.32818 114718.9274 123828.7571 81517.90126 91932.00722 118470.1756 108674.6327 103314.9809 112784.9777 0.882239197 1.017147227 1.097918886 0.722772686 0.815108617 1.050407403 0.963555917 0.916034945 1 16.7832154 2.21557924 24.99948391 0.980291963 0.920098619 0.103416554 0.106534251 735.6297572 800223.9654 0.04098033 0.030285171 164.2779368 -2.21557924 -0.060193344 VIY(ph)DFIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VIYDFIEK 8 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VIY(1)DFIEK;VIY(1)DFIEK;VIY(1)DFIEK;VIY(1)DFIEK 194.44 0.001704 267601000 399470 335595 354192 430834 333521 436352 485872 508922 469231 TRUE FALSE 380587.8448 369792.512 370432.0535 387525.7478 391686.9568 421241.0208 411743.3027 464358.0917 541996.947 0.702195551 0.682277851 0.683457823 0.714996182 0.722673733 0.777201833 0.759678269 0.856754073 1 19.0479252 0.890796041 0.555289458 1.008547446 0.687024159 0.968711977 0.017243249 0.152115816 0.10944183 0.018101397 0.007784546 7.776712449 -0.890796041 -0.321523287 VKADRDESSPYAAMLAAQDVAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VKADRDESSPYAAMLAAQDVAQR 23 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;; 158 1.93E-09 2565990000 2561329 1549648 2247515 2442039 2306263 2344693 3368580 2560487 2823620 FALSE TRUE 2440260.054 1707558.893 2350565.786 2196560.6 2708474.537 2263495.693 2854641.253 2336277.184 3261492.569 0.748203469 0.523551367 0.720702481 0.673483245 0.830440199 0.694006086 0.875256096 0.71632148 1 21.63710091 0.978188283 0.271075194 1.051288371 0.604753968 0.542594889 0.086379111 1.603193129 0.380690877 0.262555925 0.154239854 9.510170054 -0.978188283 -0.446534403 VKAEGPGLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKAEGPGLSR 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 90.614 0.0099698 0 165210 123060 141640 147680 139140 149880 175230 156250 165440 FALSE TRUE 157400.8507 135599.9539 148134.3341 132834.9258 163405.9719 144689.618 148495.4452 142567.9217 191095.5902 0.823675996 0.709592271 0.775184471 0.695122926 0.855100695 0.75715833 0.77707416 0.746055529 1 17.54393496 -1.390795545 3.056883639 1.003192198 0.766579247 0.704819733 0.047309592 12548259.22 15673125.05 353508.0158 0.010231404 0.040663472 1.390795545 -0.236612951 VKAEPAKIEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKAEPAKIEAFR 12 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 178.58 1.23E-05 2293900000 4873900 3230300 4191600 3928900 4120200 4542100 6470100 5626100 5253700 FALSE TRUE 4643520.406 3559471.243 4383789.006 3533959.508 4838761.575 4384805.938 5482967.413 5133448.858 6068416.964 0.765194685 0.586556801 0.722394165 0.582352783 0.797368013 0.722561743 0.903525161 0.845928829 1 22.53288879 1.675035432 0.841627412 0.977787556 0.665531271 0.693579288 0.071616594 0.28420931 0.389980203 0.057928139 0.024703781 47.31898622 -1.675035432 -0.312256285 VKANLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKANLEK 7 1 P35579 P35579 MYH9 Myosin-9 0 67.897 0.058292 531980000 1519400 1067200 1072100 1339500 1141900 1382800 1702200 1537800 1430000 FALSE TRUE 1447580.973 1175948.893 1121256.845 1204850.915 1341046.998 1334913.289 1442498.127 1403142.08 1651757.097 0.87638853 0.711938151 0.678826716 0.729435894 0.811891168 0.808177723 0.873311294 0.849484517 1 20.65557011 1.19292105 0.711497887 0.992681589 0.756492481 0.641092971 0.056172181 0.43698588 0.517758413 0.056492534 0.023164882 15.59269021 -1.19292105 -0.236189108 VKAQT(ph)PPGPSLSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKAQTPPGPSLSGSK 15 1 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKAQT(1)PPGPSLSGSK;VKAQT(1)PPGPSLSGSK 152.04 4.69E-06 1425610000 2814500 2632300 2537000 2933900 1611540 3097800 3160100 3239300 1817710 TRUE FALSE 2681464.163 2900534.363 2653323.959 2638978.798 1892592.066 2990522.409 2677968.706 2955649.719 2099591.183 1.277136323 1.381475778 1.263733617 1.256901257 0.901409799 1.424335572 1.275471495 1.407726296 1 21.00167701 -1.456068737 3.359426196 0.995907083 1.278069365 0.257351723 0.145842862 5711232.687 2559839.742 169541.9648 0.03230964 0.034988978 1.456068737 0.282162282 VKAQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKAQTPPGPSLSGSKSPCPQEK 22 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKAQT(1)PPGPS(0.04)LS(0.126)GS(0.37)KS(0.464)PCPQEK;VKAQT(1)PPGPS(0.007)LS(0.075)GS(0.054)KS(0.864)PCPQEK;VKAQT(1)PPGPS(0.004)LS(0.305)GS(0.23)KS(0.461)PCPQEK 110.17 0.00069191 1114200000 2896390 2390820 2558350 2882790 1232880 3149290 3176560 3371290 1331350 TRUE FALSE 2759483.385 2634447.276 2675652.878 2593006.472 1447893.882 3040229.298 2691917.43 3076081.975 1537808.958 1.794425354 1.713117395 1.739912402 1.686169441 0.941530399 1.976987636 1.750488847 2.000301766 1 20.55244486 -1.89861522 2.681922244 0.625043903 1.701286623 0.365895272 0.289752148 31363270.27 19514729.04 74319975.94 0.066090034 0.01262946 1.89861522 1.07624272 VKAQTPPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKAQTPPGPSLSGSKSPCPQEK 22 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKAQTPPGPSLS(0.007)GS(0.215)KS(0.778)PCPQEK;VKAQTPPGPS(0.001)LS(0.209)GS(0.209)KS(0.582)PCPQEK 115.66 9.84E-05 743470000 962610 738600 1050950 945400 536540 1064420 1249070 1157120 691440 TRUE FALSE 917109.333 813864.1797 1099137.097 850366.5959 630112.4061 1027558.869 1058501.431 1055796.439 798664.9838 1.14830292 1.019030753 1.376217963 1.064735043 0.788957096 1.286595618 1.325338474 1.321951582 1 19.60723094 VKAS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VKAS(0.944)PIT(0.056)NDGEDEFVPSDGLDKDEYTFSPGK;VKAS(0.977)PIT(0.023)NDGEDEFVPSDGLDKDEYTFSPGK 146.78 8.49E-09 816930000 621690 522290 514460 603660 246613 602780 615570 667840 235672 TRUE FALSE 592303.9458 575511.9448 538048.4999 542978.9499 289622.2291 581905.5775 521653.4908 609360.3892 272218.8101 2.175837686 2.114152011 1.976529468 1.994641552 1.063931728 2.137639119 1.916302149 2.238494794 1 18.05440723 2.984120294 24.61457574 1.756244565 2.091553878 0.176153574 0.404927082 1135.241149 1759700.881 0.114020442 0.124362238 964.0960289 -2.984120294 0.335309312 VKASPIT(ph)NDGEDEFVPSDGLDKDEYTFSPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VKAS(0.344)PIT(0.656)NDGEDEFVPSDGLDKDEYTFSPGK 140.01 1.24E-06 350970000 388010 327190 295090 399320 171990 382160 394920 423530 159520 TRUE FALSE 369669.5363 360531.033 308620.1684 359179.5949 201985.0015 368925.7034 334667.7008 386443.4679 184257.5469 2.006265374 1.956669016 1.674939093 1.94933451 1.096210196 2.002228455 1.816303899 2.097300623 1 17.49136419 3.790690014 4.98689969 1.711241879 1.986764827 0.106715685 0.363301364 0.463332874 25.77100636 0.085701854 0.155376963 6175.754365 -3.790690014 0.275522948 VKDATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKDATR 6 1 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 70.67 0.082315 57353000 230500 184800 198420 201630 193180 154640 209640 244500 291920 FALSE TRUE 219604.7218 203631.3301 207517.7533 181361.7693 226870.5308 149284.778 177655.5677 223090.2838 337189.4627 0.651279907 0.603907751 0.615433684 0.537863099 0.672828056 0.442732631 0.526871647 0.661617009 1 18.36319993 0.884294282 5.321074921 0.999986865 0.580111247 0.800078095 0.065827425 0.504530158 22.78765001 0.064680034 0.01631616 7.66115559 -0.884294282 -0.419875618 VKDDIESLHDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKDDIESLHDK 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 142.91 2.25E-05 259500000 775900 787330 622810 931800 433030 785670 750370 865150 398640 FALSE TRUE 739224.7447 867559.8221 651366.4545 838133.6937 508550.2949 758462.0509 635887.275 789392.8796 460459.0552 1.605408204 1.884119364 1.414602335 1.820213294 1.104441946 1.647186742 1.380985492 1.714360638 1 18.81271335 -2.82911878 0.133031894 7.91E-14 1.861231582 0.373399396 0.229447452 66.39012556 0.983355497 21.52256236 1.667144989 0.001482113 2.82911878 1.861231582 VKDEPQR ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 109.21 0.0064555 1082884000 2051015 2119417 1640877 2260678 1546371 1852106 1853814 1816216 1480927 FALSE TRUE 1954067.586 2335388.002 1716112.833 2033430.352 1816057.613 1787967.105 1570980.627 1657178.499 1710581.596 1.142341056 1.365259633 1.003233542 1.188736251 1.06166091 1.045239297 0.918389763 0.968780737 1 20.70605549 2.760516389 0.807572769 0.951667453 1.237120857 0.508715398 0.090286024 0.418724694 0.589414954 0.055342421 0.053753786 576.1245595 -2.760516389 0.285453405 VKDEPQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 VKDEPQRR 8 2 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;;;;;; 131.44 0.00056525 8382913000 9882180 8401170 8715030 9461220 8022490 9413390 11187750 9900360 8611350 FALSE TRUE 9415068.936 9257258.774 9114622.746 8510160.19 9421609.716 9087401.944 9480853.26 9033431.993 9946754.177 0.94654686 0.930681367 0.91634141 0.85557158 0.94720444 0.913604758 0.953160508 0.908178872 1 23.24579439 -1.015878689 0.552929698 1.022056771 0.9225179 0.431951244 0.028063184 23.39000016 4.150339859 0.868465204 0.011766508 0.096409829 1.015878689 -0.099538871 VKDGPGGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKDGPGGK 8 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 61.78 0.076431 611550000 1520700 1383400 1158000 1496500 821520 1357200 1553400 1614100 1059000 FALSE TRUE 1448819.525 1524370.033 1211095.445 1346068.977 964792.8279 1310199.824 1316400.3 1472760.847 1223224.311 1.184426692 1.246190105 0.990084512 1.100426933 0.788729278 1.071103486 1.076172447 1.203999 1 20.22225755 3.74101616 24.9710405 1.033761134 1.215308407 0.337369763 0.106256435 216.7883493 2204563.983 0.026800745 0.045590307 5508.281919 -3.74101616 0.181547273 VKDLESLFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKDLESLFHR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 174.1 1.93E-06 856720000 2584600 1723080 1987080 2229200 2366700 2060270 3042400 2457300 2430900 FALSE TRUE 2462431.08 1898663.811 2078189.583 2005116.581 2779451.731 1988922.333 2578226.002 2242125.785 2807871.557 0.87697426 0.676193256 0.74012986 0.714105521 0.989878516 0.708338075 0.918213654 0.798514369 1 21.42104551 0.691692745 0.384593255 1.016734288 0.758475253 0.304822462 0.098321892 2.229131762 0.749539742 0.186387124 0.075118993 4.916915501 -0.691692745 -0.258259035 VKDSS(ph)PGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.104)S(0.896)PGEK;VKDS(0.05)S(0.95)PGEK;VKDS(0.036)S(0.964)PGEK;VKDS(0.098)S(0.902)PGEK;VKDS(0.063)S(0.937)PGEK 128.21 0.00025657 2961310000 8724120 8233670 7212050 9597500 3846190 9362780 9198490 10486910 4663390 TRUE FALSE 8311748.137 9072690.334 7542729.626 8632741.066 4516964.318 9038544.581 7795091.409 9568620.566 5386564.704 1.543051758 1.684318454 1.400285718 1.602643158 0.838561229 1.677979395 1.447135946 1.776386453 1 22.36093405 3.727868174 23.29930766 1.415576485 1.6136851 0.088169366 0.288846643 651.9824258 1420700.513 0.070164108 0.11010764 5344.02122 -3.727868174 0.198108615 VKEDPDGEHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VKEDPDGEHAR 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;; 136.7 5.63E-05 5850700000 14164170 13359910 12499730 15469560 10558440 13982020 15394080 14663800 10018040 FALSE TRUE 13494657.75 14721300.02 13072854.98 13914530.44 12399828.59 13497819.14 13045430.36 13379759.93 11571586.48 1.166189077 1.272193752 1.129737483 1.202473876 1.071575502 1.16646228 1.127367487 1.156259771 1 23.46408334 -4.999999998 0.094443454 0.446239886 1.298228085 0.5445005 0.049010136 133.7748596 0.86997041 14.68239442 0.908567523 1.00E-05 4.999999998 0.851988199 VKEDPDGEHARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKEDPDGEHARR 12 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 95.417 0.0036386 439730000 723917 470025 705476 674770 645330 714129 980492 799025 740054 FALSE TRUE 689698.8781 517921.0819 737822.7724 606940.8376 757875.3477 689398.5337 830899.9374 729058.1351 854817.7946 0.806837296 0.605884769 0.86313455 0.710023635 0.886592853 0.806485941 0.972019935 0.852881327 1 19.70525742 2.268680143 0.613688354 0.972788996 0.711954576 0.491983576 0.082122345 0.556969954 0.418017276 0.065419269 0.048117045 185.6436689 -2.268680143 -0.26083442 VKEEIIEAFVQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 165.45 3.61E-06 352100000 642760 531740 577300 660260 526830 620490 770190 629500 558920 FALSE TRUE 612378.0086 585924.9105 603769.776 593889.4104 618708.9852 599002.2757 652683.37 574377.6428 645594.459 0.948549047 0.907574256 0.935215239 0.919910947 0.958355476 0.927830571 1.01098044 0.889688 1 19.30026867 2.352857785 1.590808571 0.965667683 0.927438302 0.137731178 0.035351571 0.619043908 3.162751791 0.016142992 0.011004097 225.3501157 -2.352857785 -0.038229381 VKEEPPS(ph)PPQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 78.794 0.012666 1666240000 2264000 2250890 1909290 2492810 1437060 2207730 2178290 2230620 1541860 TRUE FALSE 2156985.207 2480258.25 1996832.835 2242228.003 1687682.809 2131275.757 1845951.853 2035295.088 1780963.774 1.211133678 1.392649467 1.121209125 1.258996974 0.947623323 1.196697983 1.036490399 1.142805439 1 20.76422674 3.22196918 1.545570881 1.078712744 1.293033094 0.409633219 0.100409553 0.308368707 1.530804501 0.030341058 0.043266183 1667.128899 -3.22196918 0.21432035 VKEEPPS(ph)PPQSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VKEEPPS(0.999)PPQS(0.001)PR;VKEEPPS(0.999)PPQS(0.001)PR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR;VKEEPPS(0.999)PPQS(0.001)PR 108.49 0.00073411 2496920000 4428250 3785520 4019570 4398470 3144710 4418070 5004660 4787640 3801070 TRUE FALSE 4218935.398 4171268.792 4203871.26 3956327.439 3693146.428 4265071.128 4241107.2 4368408.861 4390520.522 0.960919184 0.950062474 0.957488124 0.901106695 0.841163687 0.971427216 0.96596911 0.994963772 1 22.06596056 1.780552276 2.604213373 0.98904557 0.929808618 0.378109017 0.036840578 0.334208847 4.450124524 0.02324994 0.010854615 60.33263257 -1.780552276 -0.059236952 VKEFCENLSADCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEFCENLSADCR 13 1 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 112.17 0.00084057 829360000 809340 624480 725400 773180 723480 769340 1043590 828740 910810 FALSE TRUE 771084.1022 688115.222 758660.3075 695458.4775 849654.6829 742697.5629 884371.1787 756171.1322 1052053.763 0.732932222 0.654068496 0.721123135 0.66104842 0.807615269 0.705950199 0.840614054 0.718757119 1 20.004777 -1.527487001 0.220656 1.259047511 0.666696902 0.727475956 0.053420699 11.04471232 0.440491122 1.674954691 0.104667733 0.029683356 1.527487001 -0.592350609 VKEFLHNQGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEFLHNQGK 10 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 160.36 4.45E-06 1392550000 4325800 3464500 3529900 4064000 2961500 3880700 4811500 4639100 3375300 FALSE TRUE 4121328.007 3817536.489 3691749.407 3655478.999 3477984.662 3746310.386 4077417.306 4232875.811 3898724.285 1.057096554 0.979175805 0.946912153 0.937609005 0.892082745 0.960906725 1.045833716 1.085707914 1 21.8945707 1.698865457 5.361205706 1.05004045 0.967288382 0.406575805 0.045955516 0.169779597 11.42508937 0.026487777 0.013183112 49.987965 -1.698865457 -0.082752068 VKEGMNIVEAMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 30 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 220.46 1.89E-11 82257990000 86944760 59737760 66966560 76108100 71390190 74114200 96585480 81214010 77984360 FALSE TRUE 82835053.5 65825105.66 70037043.01 68457569.19 83840616.53 71547606.67 81849591.11 74102480.74 90077776.26 0.919594787 0.730758555 0.777517451 0.759982895 0.930758063 0.794287 0.908654659 0.822649979 1 26.42466788 0.366256743 0.439330272 1.014673041 0.806854782 0.386156858 0.068466504 2.597402468 0.85615274 0.150887931 0.040558205 2.324110338 -0.366256743 -0.207818259 VKELEEQLENETLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKELEEQLENETLHK 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 226.25 5.35E-13 151299000 346030 316035 295820 385460 205335 352422 368950 380650 170446 FALSE TRUE 329673.8477 348239.3258 309383.6396 346712.8285 241145.359 340217.5378 312659.9013 347318.268 196877.8952 1.674509205 1.768808659 1.571449346 1.761055136 1.224847303 1.728063669 1.58809043 1.76413034 1 17.58694161 -1.669638103 2.623605103 0.913181968 1.639388337 0.603677979 0.161692871 11311958.03 9570045.911 6570054.418 0.037838933 0.021397444 1.669638103 0.72620637 VKELLVDCYKPTEAFISGLLDK ddPTM_SK-BR-3_Trastuzumab_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 ; 163.62 8.37E-12 377550000 794410 669040 712450 843370 466920 829940 884800 897460 505580 FALSE TRUE 756859.8137 737215.9366 745116.5372 758592.8453 548350.7002 801198.9697 749807.5095 818873.6447 583982.7643 1.296031082 1.262393313 1.275922138 1.298998689 0.938984391 1.371956535 1.283954862 1.402222283 1 19.15556626 VKELQAEQEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VKELQAEQEDR 11 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;; 188.09 3.01E-06 1546120000 2451110 2131810 2384040 2590550 2058630 2561130 2958970 2760230 2558170 FALSE TRUE 2335250.888 2349043.863 2493350.592 2330142.992 2417654.42 2472437.426 2507524.781 2518529.628 2954877.938 0.790303673 0.794971539 0.843808321 0.788575041 0.818190961 0.836730815 0.848605199 0.852329497 1 21.49466711 -5 0.1679174 1.72269302 0.773090788 0.936978395 0.01530422 27.26717238 0.255908746 6.516941736 0.052656723 1.00E-05 5 -0.949602232 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQRDDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 44 3 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.559)S(0.441)PQRDDLK 183.47 2.16E-28 207430000 151040 127590 157200 150800 112420 168650 208620 160640 13842 TRUE FALSE 143900.6385 140591.5661 164407.7755 135641.2975 132026.0124 162809.6082 176791.1874 146573.51 15988.54666 9.000232576 8.793267394 10.28284677 8.483653977 8.257536796 10.18288977 11.05736445 9.167406711 1 13.96475119 VKELVEFAQDDDRLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKELVEFAQDDDRLR 15 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 271.68 1.19E-33 257480000 326250 220868 294640 312850 284630 302960 391740 345020 365560 FALSE TRUE 310828.8091 243374.7003 308149.5354 281401.7236 334269.3819 292468.4192 331972.8682 314808.2197 422249.1778 0.736126499 0.576376967 0.729781256 0.66643522 0.791640101 0.692644141 0.786201337 0.745550818 1 18.68773509 -1.425112368 0.218105615 1.269301701 0.637436299 0.73632965 0.055861105 10.35456825 0.42579343 1.65230343 0.116996164 0.037574017 1.425112368 -0.631865402 VKENDQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKENDQK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 ;; 126.41 0.0036066 693370000 909370 827830 914000 1193920 565485 962200 1035770 1469880 788640 FALSE TRUE 866385.8823 912186.8182 955907.8041 1073904.893 664105.405 928878.7727 877744.2633 1341169.515 910938.2634 0.951091767 1.001370625 1.049366178 1.178899753 0.729034482 1.019694539 0.963560648 1.472294632 1 19.79699376 1.282832821 24.99703141 1.236149103 0.984922714 0.307105043 0.157010471 124.0125135 70019.92295 0.092019901 0.033602502 19.17930302 -1.282832821 -0.251226389 VKENFDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKENFDK 7 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 ;; 95.358 0.012335 1499430000 2393200 1757070 2234590 2154910 1687240 2649940 3233470 2926630 2087670 FALSE TRUE 2280078.179 1936117.431 2337048.162 1938294.353 1981494.122 2558171.913 2740144.765 2670358.762 2411415.201 0.945535293 0.802896751 0.969160417 0.803799508 0.821714204 1.060859164 1.136322257 1.107382404 1 21.20144865 2.165119754 5.61823188 1.095771996 0.868501511 0.712910631 0.065152745 0.095936651 5.328047453 0.022923799 0.016898523 146.2580415 -2.165119754 -0.227270485 VKENLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKENLNK 7 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 83.265 0.039082 0 312940 281270 296020 305150 202430 315320 281950 280240 189050 FALSE TRUE 298147.9464 309931.7328 309592.8098 274475.7423 237733.7279 304400.3893 238933.3491 255700.7 218366.9085 1.36535315 1.419316393 1.417764312 1.256947512 1.088689351 1.39398589 1.094182955 1.170968173 1 17.73639472 2.124348716 0.332826719 0.989649203 1.46146824 0.613325124 0.094928044 0.941065278 0.281244528 0.121322883 0.157551885 133.1523133 -2.124348716 0.471819038 VKEPS(ph)VQEATSTSDILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKEPSVQEATSTSDILK 17 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VKEPS(0.846)VQEAT(0.118)S(0.026)T(0.008)S(0.003)DILK 70.917 0.019148 107830000 79022 84029 76133 92223 59944 80215 82295 95396 61236 TRUE FALSE 75286.78667 92591.65063 79623.77336 82952.56883 70398.21462 77437.13444 69739.3863 87042.62051 70732.16613 1.064392493 1.30904588 1.125708114 1.17277009 0.995278647 1.094793765 0.985964238 1.230594583 1 16.11007882 2.767554433 18.6373357 1.057055505 1.177632938 0.24497012 0.092182346 38.03041645 24445.00373 0.026054734 0.027612901 585.5371205 -2.767554433 0.120577434 VKESITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKESITR 7 1 Q60FE5;P21333-2;P21333;O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-5;O75369-4;A0A0C4DGA1 Q60FE5;O75369-8 FLNA;FLNB Filamin-A;Filamin-B 0 ; 87.639 0.017505 499030000 828420 705320 797360 866340 746460 811510 1034720 875960 831900 FALSE TRUE 789262.2284 777192.9099 833919.7447 779253.8573 876642.3877 783407.2052 876854.4601 799256.2986 960906.8032 0.821372297 0.808811955 0.867846644 0.810956749 0.9123074 0.81527907 0.912528101 0.831772963 1 19.87403699 -4.999999998 0.136814595 1.530481233 0.787641557 0.630970522 0.037494224 76.56858495 0.647962429 11.05679402 0.209136486 1.00E-05 4.999999998 -0.742839675 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKESSIIAPAPAEDVDTPPR 20 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 VKESSIIAPAPAEDVDT(1)PPR 127.16 3.56E-05 153900000 427830 390250 397870 479180 354390 432070 531360 479380 474210 TRUE FALSE 407607.3238 430016.9187 416112.733 431011.916 416195.5038 417107.3076 450291.2729 437402.9458 547748.0649 0.744151098 0.785063328 0.759679056 0.786879852 0.759830167 0.761494808 0.822077341 0.798547679 1 19.06315296 -0.677889751 0.408409118 1.068853368 0.761034528 0.944344648 0.017352281 2.102279893 0.297235077 0.202266507 0.010431377 0.209947278 0.677889751 -0.30781884 VKEVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 VKEVHDELEDLPS(1)PPPPLS(0.878)PPPT(0.043)T(0.041)S(0.038)PHK;VKEVHDELEDLPS(1)PPPPLS(0.906)PPPT(0.034)T(0.031)S(0.029)PHK 70.249 0.0059135 143432000 440360 311681 382470 403770 288650 352850 423080 362830 216768 TRUE FALSE 419545.0555 343441.6483 400006.6278 363182.2725 338990.4686 340630.716 358531.3756 331058.6817 250383.2743 1.675611347 1.371663699 1.59757727 1.450505324 1.353886235 1.360437181 1.431930214 1.322207654 1 17.93377867 -3.35437465 0.115301452 8.48E-12 1.732491132 0.796709963 0.080790973 43.57360984 0.489051156 11.60628609 0.942060712 0.000442207 3.35437465 1.732491132 VKEVHDELEDLPSPPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 VKEVHDELEDLPSPPPPLS(1)PPPTTSPHK;VKEVHDELEDLPSPPPPLS(0.983)PPPT(0.007)T(0.008)S(0.002)PHK 151.49 2.99E-08 195162000 653460 634320 639770 743910 480750 721890 884480 870420 415300 TRUE FALSE 622572.2408 698957.9292 669104.0873 669130.7535 564592.6478 696890.7683 749536.3314 794201.4104 479702.6029 1.297829607 1.457065117 1.394831054 1.394886643 1.176963903 1.452755862 1.562502114 1.655612051 1 18.87178074 2.023076349 24.99792748 1.478311071 1.356292532 0 0.187383077 538.6849805 583538.8704 0.0627811 0.046364556 105.4572273 -2.023076349 -0.122018539 VKEYQVETIVDTLCTNMLSDKEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKEYQVETIVDTLCTNMLSDKEQLR 25 2 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 249.96 1.18E-39 575200000 378770 300405 363711 374906 303399 376342 496169 441834 367891 FALSE TRUE 360866.2927 331016.611 380387.5091 337219.7366 356311.6895 363309.1822 420469.3063 403144.6727 424941.6574 0.849213737 0.778969549 0.895152317 0.793567142 0.838495552 0.854962501 0.989475376 0.948705936 1 18.69690525 1.821233659 3.596676858 0.978069394 0.827876993 0.80143258 0.033942918 0.090787595 2.043418523 0.016181437 0.008515881 66.25728859 -1.821233659 -0.150192401 VKFEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKFEER 6 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 102.71 0.032198 1304100000 3953300 3360200 3423100 3929200 3047100 3962000 4604300 3966000 3395600 FALSE TRUE 3766435.344 3702608.2 3580052.521 3534229.351 3578513.275 3824794.947 3901829.471 3618716.015 3922172.306 0.960293187 0.944019771 0.912772882 0.901089773 0.912380435 0.975172595 0.994813376 0.922630556 1 21.90322149 2.224225697 24.77688812 0.975176398 0.929917115 0.433255182 0.026493091 222.8475938 385173.4546 0.010237317 0.007597224 167.5813546 -2.224225697 -0.045259284 VKFQGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKFQGGR 7 1 Q9UK45;K7ENY5;K7EML7 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 94.887 0.01265 222430000 326120 244260 270680 323690 349190 308460 369920 319240 429670 FALSE TRUE 310704.9539 269150.3717 283090.9457 291152.0662 410088.6254 297777.9529 313481.91 291285.6532 496301.0291 0.626041325 0.542312741 0.57040169 0.586644091 0.826290097 0.599994631 0.631636631 0.586913256 1 18.92085592 -5 0.307330255 4.321199856 0.599040678 0.696716357 0.078165333 160.9794392 1.466261224 345.7791433 0.072686708 1.00E-05 5 -3.722159178 VKFSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKFSDAGQPMSFVLEFHFEPNEYFTNEVLTK 31 1 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 79.071 0.0012232 80483000 23164 15388 23528 21039 21882 21247 29784 25965 26736 FALSE TRUE 22069.08363 16956.05469 24606.78207 18924.11975 25698.21387 20511.21106 25239.90378 23691.36695 30882.08233 0.714624208 0.549058011 0.796798021 0.61278639 0.832139931 0.664178369 0.817299284 0.767155747 1 14.91448241 -0.179483808 0.214078625 1.159280604 0.603088483 0.574136524 0.082568989 6.080944995 0.45307109 0.88227046 0.20486513 0.6614792 0.179483808 -0.556192121 VKGDLDIAGPNLEGDFKGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKGDLDIAGPNLEGDFKGPK 20 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 125.73 1.38E-05 131380000 132960 88070 114590 128930 81935 128830 146770 162910 91036 FALSE TRUE 126675.2443 97044.43313 119844.0648 115969.7114 96224.43806 124368.5848 124377.5409 148644.7368 105153.3979 1.204670955 0.922884424 1.139707011 1.102862235 0.91508634 1.182734816 1.182819988 1.413598987 1 16.68213594 2.026903922 24.62178939 1.210034139 1.057250702 0.212932763 0.131305744 243.5183107 222860.5802 0.044927618 0.033180425 106.3907627 -2.026903922 -0.152783437 VKGDVDVSLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKGDVDVSLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 103.75 0.0021399 0 512240 478970 439680 571170 343230 488100 568520 567160 398610 FALSE TRUE 488027.4304 527777.5875 459839.7629 513754.9064 403089.2033 471196.9746 481781.8324 517496.4637 460424.403 1.059951269 1.146285002 0.998730215 1.115829011 0.875473152 1.023397048 1.046386398 1.123955334 1 18.81260477 3.731532811 24.93582991 1.026679892 1.103118136 0.166830627 0.071408403 809.4891741 2872201.912 0.017906124 0.028406408 5389.305602 -3.731532811 0.076438244 VKGEEIYSMDEGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKGEEIYSMDEGIR 14 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 153.95 5.70E-06 882740000 600590 531610 536720 632660 479320 591360 659050 630320 557410 FALSE TRUE 572201.301 585781.6634 561329.1429 569063.8148 562913.2562 570881.0549 558499.8182 575125.8393 643850.2959 0.888717928 0.90981035 0.87183177 0.883844922 0.874292145 0.88666738 0.867437387 0.893260192 1 19.29636576 -1.440310296 3.805693356 1.000851871 0.885083792 0.901275731 0.012013775 9.42E-05 1.38E-05 0.012615151 0.002951704 0.036281873 1.440310296 -0.115768079 VKGGGHVAQIYAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKGGGHVAQIYAIR 14 1 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ; 112.51 0.00035425 1026530000 780910 607230 706990 705460 758930 736540 885170 818190 759480 FALSE TRUE 743997.9319 669107.4274 739406.1908 634545.8205 891287.1517 711033.4351 750121.0592 746544.9461 877256.2795 0.848096445 0.76272743 0.842862238 0.723330041 1.01599404 0.81051963 0.855076306 0.850999832 1 19.74263884 2.76413455 24.99546273 0.886180021 0.79768256 0.34540444 0.073838554 984.8681917 962589.2358 0.020527583 0.021764629 580.9443731 -2.76413455 -0.088497461 VKGNNVYCLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKGNNVYCLDR 11 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 117.2 0.0008086 958560000 1352870 864130 932950 925790 1272800 1077130 1601350 1255680 1528670 FALSE TRUE 1288922.516 952185.8294 975726.6803 832727.8303 1494775.917 1039828.718 1357034.647 1145726.002 1765728.336 0.72996649 0.539259528 0.552591619 0.47160586 0.846549204 0.588895073 0.768541014 0.648868786 1 20.75183197 0.049928131 0.402717016 1.056481988 0.598313694 0.524675762 0.110007072 3.198657577 0.719813185 0.410006628 0.071400736 1.121832792 -0.049928131 -0.458168294 VKGNVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKGNVFK 7 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 91.065 0.01521 2729700000 4337900 3466400 3653100 4507400 3415900 4306800 5136000 4503800 4023000 FALSE TRUE 4132856.064 3819630.101 3820598.248 4054307.588 4011631.878 4157654.436 4352408.871 4109423.396 4646866.293 0.889385621 0.821979773 0.822188117 0.872482084 0.863298323 0.894722201 0.936633119 0.884342939 1 22.1478267 1.190506874 0.495166042 0.998388779 0.843750787 0.721149399 0.027554527 0.469752848 0.305754523 0.030626158 0.016327067 15.50625328 -1.190506874 -0.154637992 VKGPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKGPVR 6 1 P60866;P60866-2;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 ; 99.511 0.035309 2567600000 8589900 5674100 2895300 3397500 7998000 4322200 9780000 6456100 8451900 FALSE TRUE 8183872.451 6252297.241 3028052.369 3055976.845 9392848.668 4172521.13 8287881.378 5890769.658 9762577.486 0.83829014 0.640435095 0.310169356 0.313029715 0.96212795 0.42739954 0.848943979 0.603403114 1 23.21883066 0.484918003 0.656704521 1.004264692 0.603382251 0.2333289 0.221284701 2.752348247 1.968145201 0.260501 0.083928333 3.054344384 -0.484918003 -0.400882441 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 39 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 458.91 3.19E-269 879310000 286858 200764 234322 275589 99450 349624 328897 410828 109040.2 FALSE TRUE 273298.7908 221222.0798 245065.8955 247886.2701 116794.0485 337516.4332 278717.722 374853.7224 125949.5973 2.169906031 1.756433403 1.945745764 1.968138648 0.927307836 2.679773818 2.212930632 2.976220094 1 16.94248698 VKLDGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VKLDGSR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;;;; 123.92 0.0038278 3998285000 11549100 9356690 9309990 10800700 8855200 10214490 12049940 11208800 9911270 FALSE TRUE 11003196.93 10310147.35 9736862.25 9714993.116 10399544.08 9860759.65 10211500.34 10227298.05 11448259.13 0.961124028 0.900586476 0.850510295 0.848600036 0.908395238 0.861332674 0.891969707 0.893349629 1 23.4486249 0.579642971 4.200809956 0.999999985 0.891582397 0.528702221 0.032743747 34.47312592 343.3797133 0.033912645 0.008638041 3.798769754 -0.579642971 -0.108417588 VKLEAEIATYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VKLEAEIATYR 11 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 187.44 3.27E-06 21268741000 21446730 20729590 18487100 23111340 16131950 20982780 24131730 22917730 18039000 FALSE TRUE 20432985.58 22841958.79 19334751.82 20788144.19 18945356.97 20256141.07 20449991.38 20910932.07 20836395.99 0.980639146 1.096252864 0.927931675 0.997684254 0.909243469 0.972151858 0.981455305 1.003577206 1 24.31260242 3.730029819 24.99133004 0.969035581 1.038446007 0.323533118 0.04093969 589.0005249 1725504.124 0.010110039 0.015940143 5370.686712 -3.730029819 0.069410426 VKLEAEIATYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKLEAEIATYRR 12 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 145.71 3.61E-05 6370110000 4365560 2316227 4486660 3568160 4837180 4311680 6949860 4822720 6398060 FALSE TRUE 4159208.631 2552253.165 4692377.799 3209481.778 5680782.66 4162365.44 5889531.214 4400417.07 7390238.468 0.562797621 0.345354643 0.634942677 0.434286633 0.768687328 0.563224781 0.796933853 0.595436411 1 22.81718949 0.885613831 0.224588396 1.128321229 0.373122348 0.58977884 0.119521099 2.109476029 0.357998843 0.568949185 0.326342497 7.684468443 -0.885613831 -0.755198881 VKLPSGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKLPSGSK 8 1 P62917;E9PKZ0;G3V1A1 P62917 RPL8 60S ribosomal protein L8 0 ; 91.584 0.012678 0 1173110 1145340 937870 1209750 761270 1122160 1237990 1204570 866560 FALSE TRUE 1117659.415 1262051.448 980872.2672 1088143.632 894035.247 1083299.318 1049111.888 1099091.465 1000941.699 1.116607907 1.260864094 0.97994945 1.087119892 0.893194127 1.082280136 1.04812487 1.098057425 1 19.93292651 3.733772498 24.99956376 1.030393233 1.188736002 0.482933213 0.069522076 283.5092031 1480250.363 0.017058121 0.027372303 5417.17042 -3.733772498 0.158342769 VKLWEVS(ph)VADRRS(ph)LLEPFVY(ph)LASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKLWEVSVADRRSLLEPFVYLASK 24 3 K7ERG2;H7BXP1;Q9NYR9-3;Q9NYR9-2;Q9NYR9 K7ERG2 NKIRAS2 NF-kappa-B inhibitor-interacting Ras-like protein 2 3 VKLWEVS(1)VADRRS(1)LLEPFVY(1)LASK 70.453 0.071 631550000 814730 617500 755460 818930 493340 832810 962060 980150 385000 TRUE FALSE 776219.3275 680423.952 790098.5883 736609.6005 579378.3398 803969.5809 815280.0776 894322.8699 444703.8337 1.745474783 1.530060909 1.776684904 1.656404881 1.302840893 1.807876434 1.833310207 2.011052755 1 18.76248532 VKNELFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKNELFK 7 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 90.657 0.015484 1723220000 3845600 2965600 2755300 2952100 2746100 2579700 3811600 3018000 3012900 FALSE TRUE 3663826.109 3267798.012 2881633.23 2655349.299 3225018.971 2490364.342 3230070.415 2753727.921 3480125.144 1.052785735 0.93898865 0.828025749 0.763003969 0.926696264 0.715596204 0.928147777 0.791272672 1 21.73070776 4.091102367 2.10566241 0.844242133 1.036436668 0.366082529 0.085364088 0.280347675 2.417427956 0.020102741 0.061070714 12333.9552 -4.091102367 0.192194535 VKNQYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKNQYEK 7 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 95.099 0.012508 309850000 532650 468950 476780 583570 399700 561910 637870 651070 490250 FALSE TRUE 507472.6901 516736.5382 498640.8346 524908.4349 469407.5535 542450.9158 540551.2162 594058.8593 566275.4661 0.896158708 0.912517969 0.880562314 0.926948926 0.828938532 0.957927631 0.954572904 1.049063388 1 19.1111445 1.647955509 1.865954184 1.020474221 0.895598064 0.70021785 0.033863925 0.159010674 1.148712383 0.02283125 0.008546755 44.45857199 -1.647955509 -0.124876157 VKPAPDETSFSEALLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKPAPDETSFSEALLKR 17 2 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 195.77 9.34E-12 1868050000 1712560 1194410 1592960 1632420 1300840 1624790 2221160 2011340 1762110 FALSE TRUE 1631610.683 1316121.737 1665998.792 1468326.04 1527706.084 1568523.115 1882281.248 1835216.407 2035369.019 0.801628927 0.646625612 0.818524197 0.721405321 0.750579413 0.770633286 0.924786233 0.90166274 1 20.95685895 1.725714613 1.84759631 0.957896598 0.738888358 0.752803972 0.051671402 0.146720076 1.011448902 0.034864888 0.013993263 53.17587107 -1.725714613 -0.21900824 VKPAPLEIKPLPEWEELQAPVRS(ph)PITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKPAPLEIKPLPEWEELQAPVRSPITR 27 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VKPAPLEIKPLPEWEELQAPVRS(0.997)PIT(0.003)R 190.14 3.55E-17 392750000 302580 264420 264130 340770 233980 281110 293790 267880 206780 TRUE FALSE 288277.6431 291364.6986 276240.6218 306515.1522 274786.0379 271375.0902 248966.9397 244423.0071 238846.3863 1.206958361 1.219883219 1.156561864 1.283315008 1.150471825 1.136190898 1.042372646 1.023348148 1 17.86572352 1.90031032 1.33566391 1.005627737 1.212530486 0.860951207 0.033893651 0.133591604 0.442657765 0.022812317 0.009915313 79.48960147 -1.90031032 0.206902749 VKPAS(ph)PVAQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VKPASPVAQPK 11 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK 97.823 0.0036213 2916640000 7845700 6933930 6667760 8073500 4001140 8076600 8419800 8593800 4342580 TRUE FALSE 7474849.31 7640505.35 6973483.391 7261936.441 4698937.549 7796905.317 7135204.87 7841281.313 5016005.128 1.490199695 1.523225187 1.390246464 1.447752994 0.936788825 1.554405372 1.422487555 1.563252252 1 22.25810739 -2.174178303 2.150197654 2.79E-05 1.422160155 0.346593108 0.179350145 4015494.4 840284.8303 19546294.96 0.041441336 0.006696096 2.174178303 1.422132207 VKPET(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VKPETPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR;VKPET(1)PPR 87.298 0.024935 8793470000 4774500 5100730 3694080 5342870 2546900 4721040 4173010 4789410 2643720 TRUE FALSE 4548818.847 5620500.186 3863457.222 4805794.557 2991078.554 4557549.201 3536340.682 4370023.87 3053694.595 1.489611585 1.8405574 1.265174726 1.573763979 0.979494989 1.492470533 1.158053162 1.431061206 1 21.54212435 3.387593592 1.624521528 1.252947022 1.65333739 0.330606577 0.218207153 0.351348394 1.897354843 0.061660073 0.100124079 2441.145086 -3.387593592 0.400390367 VKPET(ph)PPRQSHSGSIS(ph)PYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKPET(0.993)PPRQS(0.007)HS(0.001)GS(0.012)IS(0.987)PY(0.001)PK;VKPET(0.958)PPRQS(0.038)HS(0.005)GS(0.006)IS(0.992)PYPK;VKPET(0.977)PPRQS(0.016)HS(0.007)GSIS(0.999)PYPK;VKPET(1)PPRQS(0.001)HS(0.11)GS(0.041)IS(0.838)PY(0.011)PK 106.81 0.00044603 3252320000 3251870 2025390 3059300 2856430 1771560 3247470 4127820 3559700 2027460 TRUE FALSE 3098160.55 2231779.544 3199571.931 2569296.23 2080519.503 3135009.3 3498045.246 3247993.797 2341868.142 1.322944061 0.95299112 1.366247687 1.097113959 0.888401642 1.338678828 1.493698635 1.386924284 1 21.15922842 2.036051226 24.88360161 1.365344648 1.12826647 0.146702329 0.19269395 207.1361219 142970.5346 0.066504897 0.049116965 108.6553778 -2.036051226 -0.237078178 VKPET(ph)PPRQSHSGSISPYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(0.999)PPRQS(0.001)HSGSISPYPK;VKPET(0.798)PPRQS(0.146)HS(0.028)GS(0.028)ISPYPK;VKPET(0.696)PPRQS(0.122)HS(0.18)GS(0.002)ISPYPK 184.76 1.85E-15 1720720000 2619550 1662870 2562850 2512180 1815150 2792550 3697000 3159710 2336290 TRUE FALSE 2495729.063 1832318.344 2680359.208 2259650.894 2131711.585 2695843.293 3132954.75 2883029.042 2698589.921 0.92482709 0.678991028 0.993244356 0.837345043 0.789935354 0.998982199 1.160959924 1.068346479 1 21.36377433 2.069827078 4.397531806 1.091978362 0.836794299 0.582931141 0.09046888 0.127983061 4.842477391 0.034486669 0.024248254 117.4429842 -2.069827078 -0.255184063 VKPFVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKPFVVR 7 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 111.04 0.0060824 1336730000 3284900 2702200 2661900 3175600 3063000 3126000 3845700 3339600 3434500 FALSE TRUE 3129629.287 2977557.252 2783950.748 2856382.655 3597186.23 3017745.836 3258967.834 3047166.92 3967104.719 0.788895053 0.750561798 0.701758825 0.720016954 0.906753536 0.760692255 0.821497809 0.768108516 1 21.91965505 -4.999999998 0.214476305 2.107292943 0.746529844 0.621733537 0.05539082 96.33355208 0.96183802 45.87800118 0.106516946 1.00E-05 4.999999998 -1.360763099 VKPLLQVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKPLLQVSR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 104.42 0.0038537 0 2421710 1562700 913040 1090660 2227900 1235590 2548400 1806990 1823050 FALSE TRUE 2307240.568 1721940.907 954903.7871 981024.7847 2616445.055 1192801.208 2159594.775 1648760.376 2105759.283 1.095681062 0.817729225 0.453472434 0.465876984 1.24251859 0.566447085 1.025565834 0.782976663 1 21.0059091 1.640434676 25 0.928198645 0.797239664 0.075394536 0.259214646 2.341201331 1787.313691 0.118794378 0.065868804 43.69529505 -1.640434676 -0.130958981 VKPPGGHS(ph)PQVNHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKPPGGHSPQVNHLK 15 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 VKPPGGHS(1)PQVNHLK;VKPPGGHS(1)PQVNHLK 138.28 6.96E-06 481440000 1011960 888430 828660 1084390 605750 1013110 1045190 1081070 308820 TRUE FALSE 964126.6563 978962.0271 866654.8807 975385.057 711392.6082 978025.7467 885727.0693 986405.7797 356710.2284 2.702828738 2.744418156 2.429576759 2.734390492 1.994315138 2.741793391 2.483043655 2.765285941 1 18.44439306 -1.2299743 4.896917832 0.999732027 2.580679177 0.814554885 0.236075084 0.000633492 9.96E-05 0.209657118 0.049408743 0.05888785 1.2299743 1.58094715 VKQEEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKQEEQR 7 1 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 0 ; 105.57 0.0072026 91322000 299790 239993 241008 281180 197384 262850 311010 287750 264190 FALSE TRUE 285619.5208 264448.5595 252058.4552 252915.2522 231807.7071 253747.4386 263559.7124 262553.0845 305159.2359 0.93596879 0.866592023 0.825989928 0.828797632 0.759628679 0.831524689 0.863679291 0.860380594 1 18.21920273 -2.100672398 5.612246672 1.5498705 0.850286112 0.543092098 0.044110342 0.030640913 0.000549636 0.004312101 0.011016067 0.007930994 2.100672398 -0.699584388 VKQIESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKQIESK 7 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 101.64 0.0081244 4340700000 8978600 6193300 7900800 8607300 6092600 8849300 11483800 10011300 8626400 FALSE TRUE 8554199.372 6824404.311 8263059.495 7742077.851 7155147.511 8542846.522 9731735.396 9134657.499 9964138.054 0.85849868 0.684896604 0.829279909 0.776994238 0.718089961 0.857359309 0.97667609 0.916753406 1 23.24831358 1.95600229 3.663796415 0.957944016 0.772044845 0.726443713 0.053292191 0.117350646 3.08059508 0.023727842 0.013874847 90.36542385 -1.95600229 -0.185899171 GLEWLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 GLEWLGR 7 0 A0A0B4J1U7 A0A0B4J1U7 IGHV6-1 0 ;;;; 126.24 0.0092382 1480469000 9488970 824943 224758 195094 332336 132417 139986 119130 116957 FALSE TRUE 9040445.193 909005.6296 235063.3766 175482.7805 390295.2932 127831.3661 118628.5647 108698.3457 135094.0942 66.9196181 6.728685179 1.739997429 1.298967075 2.889062586 0.946239485 0.878118065 0.804612121 1 17.04360508 4.537992978 1.693974514 1.139556669 76.72990568 0.996955112 1.129464368 0.032075139 0.123423785 0.340917245 3.491771728 34513.81585 -4.537992978 75.59034901 up VKS(ph)PGGPGSHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VKSPGGPGSHVR 12 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 VKS(0.999)PGGPGS(0.001)HVR;VKS(1)PGGPGSHVR;VKS(1)PGGPGSHVR;VKS(0.997)PGGPGS(0.003)HVR;VKS(0.999)PGGPGS(0.001)HVR;VKS(0.992)PGGPGS(0.008)HVR;VKS(0.987)PGGPGS(0.013)HVR;VKS(1)PGGPGSHVR;VKS(0.992)PGGPGS(0.008)HVR 123.42 0.0002066 7110590000 2801810 2485413 2501357 2829940 1957875 2611100 2954310 2863470 2038254 TRUE FALSE 2669373.994 2738679.41 2616046.693 2545469.055 2299327.78 2520676.952 2503575.75 2612729.387 2354336.02 1.133811814 1.163249165 1.111161138 1.081183413 0.976635349 1.070653012 1.063389307 1.109752119 1 21.16688881 3.298193111 2.576002232 1.050378164 1.147234125 0.550859324 0.038120982 0.192558644 2.604767396 0.010878029 0.015086045 1986.978239 -3.298193111 0.096855962 VKS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 60.59 0.077708 99559000 200790 229790 211130 301030 120160 227040 238880 360880 170240 TRUE FALSE 191299.0546 253205.8622 220810.5193 270769.8925 141115.866 219177.5479 202434.4687 329279.4341 196639.9497 0.972839216 1.287662363 1.1229179 1.376983125 0.717635791 1.114613527 1.029467659 1.67452969 1 17.58519693 -1.220952808 4.550803489 0.999959149 1.143381655 0.034107412 0.254312109 9.43E-05 1.62E-05 0.220400952 0.051934216 0.060123907 1.220952808 0.143422506 VKSGT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VKSGTPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKS(0.047)GT(0.953)PPR;VKS(0.017)GT(0.983)PPR;VKS(0.044)GT(0.956)PPR;VKS(0.019)GT(0.981)PPR;VKS(0.05)GT(0.95)PPR 86.095 0.026314 2521000000 2500860 2302560 2113730 2561850 1721850 2491670 2580310 2569580 1974870 TRUE FALSE 2382649.304 2537193.482 2210646.611 2304327.971 2022140.095 2405382.843 2186636.319 2344573.953 2281122.753 1.044507272 1.112256444 0.969104625 1.010172718 0.886467022 1.054473215 0.958578979 1.027815776 1 21.12131265 3.731579334 24.91372317 0.984408998 1.078381859 0.389128377 0.04771328 409.2873693 1460602.481 0.011276647 0.017898101 5389.882956 -3.731579334 0.09397286 VKSGT(ph)PPRQGS(ph)ITSPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKSGTPPRQGSITSPQANEQSVTPQRR 27 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.433)GT(0.568)PPRQGS(0.333)IT(0.333)S(0.333)PQANEQS(0.061)VT(0.939)PQRR 125.36 6.46E-05 175860000 191020 81328 232410 141590 178020 186030 299960 185580 301530 TRUE FALSE 181990.8632 89615.41566 243066.2284 127357.1042 209066.6316 179587.7345 254195.5929 169329.6314 348289.7324 0.522527213 0.257301342 0.697885139 0.365664251 0.600266422 0.515627415 0.729839468 0.486174629 1 18.40992842 -5 0.124615028 2.677259831 0.282853366 0.563392266 0.135641934 93.83984272 0.748833985 39.09306285 1.036645968 1.00E-05 5 -2.394406465 VKSGT(ph)PPRQGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKSGTPPRQGSITSPQANEQSVTPQRR 27 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.45)GT(0.552)PPRQGS(0.145)IT(0.427)S(0.427)PQANEQS(0.143)VT(0.857)PQRR;VKS(0.438)GT(0.561)PPRQGS(0.388)IT(0.496)S(0.117)PQANEQS(0.083)VT(0.917)PQRR 107.04 0.0031302 361520000 261955 115762 292820 202469 254558 259312 410050 267998 396890 TRUE FALSE 249572.9063 127558.2794 306246.0866 182116.4315 298952.8346 250331.9604 347489.3414 244530.6744 458437.6742 0.544398771 0.27824563 0.668021203 0.397254505 0.652112275 0.546054512 0.757986006 0.533400041 1 18.80636608 -0.446854862 0.180269128 1.342729934 0.32784258 0.584827208 0.126576963 9.198459919 0.471577264 2.195213485 0.496360597 0.357392256 0.446854862 -1.014887353 VKT(ph)PEMIIQKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKTPEMIIQKPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VKT(1)PEMIIQKPK;VKT(1)PEMIIQKPK 148.33 0.00010666 610300000 620470 633060 607340 756860 307340 707160 687170 762810 335350 TRUE FALSE 591141.6128 697569.5337 635187.1397 680778.9949 360939.9987 682670.8719 582329.5958 696014.3125 387354.3653 1.526100299 1.800856261 1.639808911 1.757509547 0.931808264 1.762393645 1.50335106 1.796841277 1 18.56329447 -1.835993975 2.502290696 0.769681764 1.59282978 0.342934865 0.256554698 24768609.87 15550765.76 34232541.31 0.061850105 0.014588345 1.835993975 0.823148016 VKTDDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKTDDIAR 8 1 Q52LJ0;Q52LJ0-1 Q52LJ0 FAM98B Protein FAM98B 0 ; 73.067 0.040609 172142000 258580 207239 155151 210195 241360 187829 321640 272840 271130 FALSE TRUE 246357.4359 228356.8897 162264.8268 189065.7993 283453.1076 181324.4346 272567.9107 248948.6832 313175.4557 0.786643498 0.729165985 0.518127535 0.603705673 0.905093622 0.578986735 0.870336119 0.794917605 1 18.25661162 1.027866306 0.832292721 0.995780643 0.693617788 0.411475816 0.116930341 0.646168502 0.996837615 0.106654743 0.038621236 10.66267829 -1.027866306 -0.302162856 VKTPEMIIQKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKTPEMIIQKPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 55.899 0.069807 185420000 360670 311540 287630 348030 232300 347410 414580 385860 237710 FALSE TRUE 343621.8439 343286.2802 300818.12 313045.3632 272813.0465 335379.1046 351328.2067 352072.0528 274572.8527 1.251477852 1.250255722 1.095585805 1.140117678 0.993590749 1.221457625 1.279544584 1.282253687 1 18.06682947 3.778849432 20.82617649 1.161631059 1.250867234 0.145489943 0.10067568 155.6177485 80439.31345 0.026589563 0.047931555 6009.653497 -3.778849432 0.089236175 VKTSEDADELHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKTSEDADELHK 12 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 64.121 0.039558 105250000 262790 193790 255220 249980 227680 261710 309380 274270 128990 FALSE TRUE 250368.4375 213537.4213 266922.0894 224851.5355 267387.3199 252646.9171 262178.3988 250253.4648 148993.1104 1.680402784 1.433203326 1.791506256 1.509140489 1.794628753 1.6956953 1.759667934 1.679631119 1 17.1848861 -1.795530945 10.22955544 0.994662133 1.659167548 0.764870763 0.116302058 0.013895213 0.000277738 0.110515786 0.026248167 0.016012865 1.795530945 0.664505414 VKVDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VKVDGPR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 95.099 0.012508 1584290000 4303060 3831970 2442060 3567300 3151510 3386020 4221800 4338070 3340890 FALSE TRUE 4099662.882 4222452.1 2554030.867 3208708.227 3701132.346 3268761.278 3577686.871 3958205.593 3858978.158 1.062370066 1.094189168 0.661841234 0.831491679 0.959096474 0.847053584 0.927107313 1.025713396 1 21.87978745 VKVDGPRS(ph)PS(ph)YGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VKVDGPRS(0.976)PS(0.939)Y(0.084)GR 80.361 0.088533 5856600000 1532300 1263000 1201200 1438900 915160 1364000 1486200 1375100 1004300 TRUE FALSE 1459871.216 1391701.136 1256276.208 1294259.038 1074763.614 1316764.338 1259452.894 1254688.954 1160041.715 1.258464413 1.199699216 1.082957787 1.115700429 0.92648704 1.135100851 1.085696211 1.081589514 1 20.14574525 3.816026108 1.698652692 1.061919596 1.25021087 0.593966665 0.059110306 0.236795855 1.32097174 0.016267679 0.039578523 6546.755299 -3.816026108 0.188291275 VKVDGPRS(ph)PSY(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VKVDGPRS(0.985)PS(0.438)Y(0.577)GR 66.335 0.092131 378190000 942000 796120 843020 1031400 621530 899490 1000300 926460 765490 TRUE FALSE 897473.5269 877245.5331 881673.3009 927721.7125 729924.6352 868340.4358 847685.8632 845334.2509 884198.2796 1.01501388 0.992136666 0.99714433 1.049223612 0.825521438 0.982065285 0.958705624 0.956046025 1 19.7540104 VKVDGPRS(ph)PSYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.999)PS(0.001)YGR;VKVDGPRS(0.998)PS(0.002)YGR;VKVDGPRS(0.99)PS(0.01)YGR;VKVDGPRS(0.995)PS(0.005)YGR;VKVDGPRS(0.948)PS(0.052)YGR;VKVDGPRS(0.998)PS(0.002)YGR;VKVDGPRS(0.977)PS(0.023)YGR;VKVDGPRS(0.826)PS(0.174)YGR;VKVDGPRS(0.993)PS(0.007)YGR 156.67 2.28E-05 51544810000 20553830 9997090 20184370 17120320 19572010 19121760 29117900 21397550 24817700 TRUE FALSE 19582291.19 11015804.84 21109843.33 15399352.91 22985362.35 18459568.66 24675429.57 19523867.09 28666302.16 0.683111867 0.384277148 0.736399247 0.53719356 0.801825161 0.643946629 0.860781744 0.681073791 1 24.77285248 1.502684794 0.320536743 1.020652867 0.508476767 0.490370335 0.120734599 0.993595894 0.355602573 0.189865505 0.164476162 31.81887303 -1.502684794 -0.5121761 VKVDPSHDASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 107.09 0.0013484 1516000000 4495080 3425820 3057110 4835390 2760470 4162490 5172880 4602520 3100310 FALSE TRUE 4282606.477 3774914.953 3197281.517 4349327.411 3241895.094 4018341.928 4383662.15 4199498.949 3581090.241 1.195894599 1.054124498 0.892823499 1.214526057 0.905281598 1.122100159 1.224113847 1.172687273 1 21.77196744 2.007623198 24.99734908 1.161153208 1.061535202 0.07719439 0.117596215 345.0301037 1131388.417 0.041161995 0.030345435 101.7708023 -2.007623198 -0.099618005 VKVEPAVDTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VKVEPAVDTSR 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 ;; 151.7 3.04E-05 1537250000 3516450 2261210 2417060 3367420 2500590 2886590 3945110 3524980 3352420 FALSE TRUE 3350234.377 2491629.87 2527884.592 3028920.544 2936692.104 2786626.665 3343211.013 3216314.064 3872296.172 0.865180304 0.643450232 0.652812822 0.782202706 0.758385199 0.719631593 0.863366557 0.830596091 1 21.88475787 1.059199912 0.788886637 0.996567508 0.729614417 0.601833082 0.067533035 0.441379328 0.623192702 0.063718718 0.023859516 11.46040358 -1.059199912 -0.266953091 VKVETYNDESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 172.33 1.23E-05 311650000 387510 437240 384570 467490 309810 461180 415730 446690 332170 FALSE TRUE 369193.1703 481795.2531 402202.9149 420497.017 363840.7659 445209.221 352302.7531 407575.4555 383681.2271 0.962239339 1.255717557 1.048273636 1.095954108 0.948289205 1.160362273 0.918217333 1.062276251 1 18.54954865 2.87724375 8.826499424 1.016904954 1.102198806 0.11870446 0.096286462 0.583515485 39.52851937 0.027491577 0.029185438 753.7785073 -2.87724375 0.085293853 VKVGVNGFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VKVGVNGFGR 10 1 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 163.94 5.75E-06 4199800000 2301300 2028280 2340090 2506800 2363740 2385800 3058400 2694900 2861100 FALSE TRUE 2192522.11 2234964.038 2447385.441 2254811.701 2775975.508 2303179.148 2591784.909 2458920.269 3304784.776 0.663438698 0.676281268 0.740558193 0.682287003 0.839986776 0.696922585 0.784252254 0.744048535 1 21.65612489 -5 0.141237997 1.966538976 0.624543574 0.785550389 0.046706502 54.64808491 0.471103783 14.82071141 0.248161719 1.00E-05 5 -1.341995402 VKVNKDDIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKVNKDDIQK 10 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 75.479 0.021863 2098800000 6160700 4143300 5930000 6144700 3886000 7127400 8370600 7758400 5134800 FALSE TRUE 5869495.92 4565506.981 6201896.366 5527023.082 4563717.17 6880576.351 7093511.233 7079033.366 5931078.559 0.989616958 0.769759991 1.045660802 0.931874873 0.769458223 1.160088554 1.195990099 1.193549081 1 22.49986305 2.219680879 24.96220157 1.158493174 0.899325563 0.570218812 0.10112498 150.1346385 198502.0834 0.03527172 0.026092636 165.8367886 -2.219680879 -0.259167612 VKVPEVDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VKVPEVDVR 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 105.86 0.0027624 1566910000 5522130 4554010 4645970 5457090 4544100 4756510 5993800 5433320 5084590 FALSE TRUE 5261109.859 5018068.796 4858992.32 4908532.945 5336589.601 4591790.866 5079335.726 4957549.697 5873082.249 0.895800473 0.854418274 0.827332585 0.835767786 0.908652284 0.781836636 0.864850093 0.844113787 1 22.48568641 -1.629759854 4.468589003 1.003262409 0.852772343 0.636664315 0.035222705 0.001078287 8.93E-05 0.032122535 0.007415525 0.023455254 1.629759854 -0.150490065 VKWGDIEFPPPFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKWGDIEFPPPFGR 14 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 136.81 1.58E-05 0 339950 238050 302680 315500 294700 315960 412740 366560 335820 FALSE TRUE 323881.2372 262307.5656 316558.1774 283785.3406 346095.5867 305018.226 349768.9325 334462.0631 387897.2505 0.834966571 0.676229505 0.816087706 0.731599258 0.892235215 0.786337685 0.901705109 0.862243965 1 18.56531502 1.345912928 0.460602284 1.001508165 0.751662496 0.585575831 0.058490958 0.577463673 0.336761386 0.060415062 0.036810388 22.17751736 -1.345912928 -0.24984567 VKYETELAMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VKYETELAMR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 77.124 0.030955 299720000 907970 582820 663680 855080 852500 810090 1200200 950830 1046000 FALSE TRUE 865052.0575 642210.0206 694110.3845 769125.7339 1001175.73 782036.3802 1017087.447 867570.2845 1208208.338 0.715979215 0.53153914 0.574495609 0.6365837 0.828644944 0.647269478 0.841814623 0.718063481 1 20.20443782 1.072548952 0.373356065 1.018655525 0.592108859 0.627208103 0.084890136 0.841359598 0.340751849 0.133707519 0.077341076 11.81813514 -1.072548952 -0.426546667 VLAAVYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLAAVYK 7 0 H3BPS8;A0A087WXX2;A0A3B3IS80;P05062;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOB;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase B;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ; 142.42 0.0057936 372230000 2291100 1487830 850010 941420 2229900 1119350 2587100 1581890 2121500 FALSE TRUE 2182804.244 1639441.569 888983.7993 846786.673 2618793.854 1080586.629 2192390.38 1443371.325 2450491.385 0.890761852 0.669025641 0.36277777 0.345557907 1.06868111 0.440967324 0.894673776 0.589013018 1 21.22463964 1.667627425 13.69322444 0.8056411 0.650123179 0.120275901 0.246131965 0.340929333 70.79864111 0.111031341 0.061011839 46.51868455 -1.667627425 -0.155517921 VLADPSDDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 182.98 4.00E-06 400105000 2459170 2214730 2129670 2691160 1647370 2489070 2539310 2655660 1829800 FALSE TRUE 2342929.908 2440413.505 2227317.476 2420639.484 1934670.806 2402872.882 2151891.622 2423116.332 2113556.039 1.108525095 1.154648119 1.053824661 1.145292313 0.91536291 1.136886289 1.018137954 1.146464199 1 21.01124093 3.343741977 1.693115076 1.053141731 1.128274837 0.13080376 0.073629685 0.609628777 3.589333832 0.020949044 0.032390164 2206.693303 -3.343741977 0.075133106 VLADPSDDTKGFFDPNTHENLTYLQLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLADPSDDTKGFFDPNTHENLTYLQLLER 29 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 98.29 0.00055513 29790000 113110 46982 99282 64727 100460 87994 159000 108600 149040 FALSE TRUE 107763.5145 51769.51921 103834.1779 58220.51899 117980.1922 84946.74572 134741.6298 99090.40828 172152.362 0.625977554 0.300719192 0.603152793 0.33819181 0.685324272 0.493439327 0.782688243 0.575597146 1 17.39332645 0.863072713 0.439559147 1.019761641 0.453131993 0.551821133 0.135995824 0.903041351 0.427523932 0.17745006 0.081608974 7.295796524 -0.863072713 -0.566629648 VLADPSDDTKGFFDPNTHENLTYVQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLADPSDDTKGFFDPNTHENLTYVQLLR 28 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 45.489 0.07437 561880000 271390 117210 294360 180980 328200 241740 472880 292500 431200 FALSE TRUE 258561.9325 129153.8323 307856.6972 162787.5466 385437.9761 233368.4832 400733.471 266887.1494 498068.2937 0.519129476 0.259309484 0.618101375 0.326837802 0.773865715 0.468547157 0.804575348 0.535844487 1 18.92598405 0.970435794 0.246782256 1.111651819 0.318929635 0.508693484 0.156742712 1.926661 0.39816217 0.561964891 0.336863308 9.341912464 -0.970435794 -0.792722184 VLAEDEELYGDFEDLETGDVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLAEDEELYGDFEDLETGDVHK 22 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ;;; 168.79 9.03E-12 59920800 152696.6 130848 120906.9 139890.8 100093 138920 134537 146040 82548.5 FALSE TRUE 145478.9343 144181.56 126450.601 125828.711 117549.1875 134109.1656 114010.9097 133251.9634 95349.69978 1.525740875 1.512134388 1.326177232 1.319655031 1.232821789 1.406498037 1.195713358 1.397507949 1 16.54094078 8 0.043728991 0.209912056 3.296337191 0.683092622 0.087628763 321.6189575 1.067798206 19.50590368 70.67830294 100000000 -8 3.086425135 VLAELYVSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLAELYVSDR 10 0 O43776;K7EIU7;O43776-2;K7EJ19;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 116.3 0.0025776 37191000 42262 44339 35380 41351 42546 36658 44445 41177 38923 FALSE TRUE 40264.35902 48857.19451 37002.208 37194.31892 49966.00893 35388.52427 37664.09896 37571.32359 44958.98005 0.895579904 1.086706025 0.823021518 0.827294544 1.111368827 0.787129162 0.837743626 0.83568007 1 15.45632169 2.173585326 24.99990673 0.847827423 0.951533519 0.118988745 0.108520857 101.6077213 39093.25214 0.038507657 0.028439796 149.1369738 -2.173585326 0.103706096 VLAFFETDMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLAFFETDMER 11 0 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 ; 102.61 0.0050901 0 18037 17020.5 17740.9 20625.9 24278 14532.6 21226 16602.8 28431 FALSE TRUE 17184.42676 18754.9083 18554.33781 18552.54535 28512.07551 14029.33242 17987.58386 15148.97082 32839.93427 0.523278354 0.571100665 0.564993147 0.564938565 0.868213538 0.427203426 0.547735075 0.461297233 1 15.00316362 -1.33375953 5.193212925 1.000150714 0.565400744 0.574887238 0.117260805 0.000190076 2.44E-05 0.105466245 0.024850097 0.04637036 1.33375953 -0.43474997 VLAGDKNFITAEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VLAGDKNFITAEELR 15 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 238.83 8.01E-18 3198652000 5613910 3983025 3575687 5172310 4721881 4229079 6282150 4928275 5539820 FALSE TRUE 5348551.6 4388899.776 3739635.786 4652379.572 5545375.551 4082624.934 5323692.638 4496729.115 6398906.992 0.835853937 0.685882727 0.5844179 0.727058477 0.866612932 0.638019108 0.83196906 0.702733939 1 22.60939407 -1.769000168 0.403891456 1.219649184 0.727185836 0.461624407 0.089980382 33.33383233 2.399011397 7.134514993 0.053528885 0.017021578 1.769000168 -0.492463348 VLAGDKNFITAEELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 201.04 1.91E-11 1355110000 1929160 1163560 1780120 1670130 1803650 1730580 2574000 2049390 2532500 FALSE TRUE 1837972.43 1282128.087 1861740.263 1502245.359 2118205.989 1670649.581 2181289.025 1869934.547 2925227.166 0.628317845 0.438300349 0.636442969 0.513548273 0.72411675 0.571117895 0.745681925 0.639244216 1 21.48011723 -0.509400553 0.250333398 1.204398666 0.508627695 0.711553064 0.081516589 4.99526098 0.383251852 0.932340387 0.129507579 0.309456385 0.509400553 -0.695770971 VLAGETLSVNDPPDVLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 98.105 0.002986 13163000 45285 42569 44515 48741 50467 39765 43485 46531 55645 FALSE TRUE 43144.4678 46906.8295 46556.05678 43841.46208 59268.42882 38387.92808 36850.56459 42456.49896 64274.1424 0.671256997 0.72979316 0.724335713 0.682101082 0.922119325 0.597253058 0.573334209 0.660553333 1 15.97195084 -0.965306909 4.489086089 1.000006257 0.690886259 0.507464953 0.094321895 18634.40792 57358327.2 958.4929112 0.022440111 0.108316119 0.965306909 -0.309119997 VLAPILPDNFS(ph)TPTGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.491)T(0.491)PT(0.009)GS(0.009)R 82.908 0.0064818 12213000 26632 28950 32796 32374 31364 28157 33180 33102 35942 TRUE FALSE 25373.15814 31900.03791 34299.72904 29119.70401 36833.87167 27181.91603 28117.78161 30203.4134 41515.70179 0.611170161 0.768384889 0.826186902 0.70141423 0.887227485 0.654738204 0.677280653 0.727517833 1 15.34136947 -2.185000243 2.256507499 1.713369829 0.727205373 0.51966732 0.080948263 7492429.635 1564489.339 27297914.59 0.019308003 0.006531302 2.185000243 -0.986164455 VLAPILPDNFST(ph)PTGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.322)T(0.672)PT(0.003)GS(0.003)R;VLAPILPDNFS(0.057)T(0.925)PT(0.018)GS(0.001)R;VLAPILPDNFS(0.048)T(0.935)PT(0.017)GSR;VLAPILPDNFS(0.007)T(0.959)PT(0.028)GS(0.006)R;VLAPILPDNFS(0.056)T(0.889)PT(0.045)GS(0.01)R 278.72 8.59E-35 497823000 396513 399214 383559 443510 428499 393460 437594 433756 523510 TRUE FALSE 377770.6163 439894.3605 401145.5595 398927.5322 503229.0899 379834.3815 370830.9983 395774.0252 604693.2571 0.624730989 0.727466952 0.663386857 0.659718837 0.832205559 0.628143901 0.613254727 0.654503784 1 19.20584397 -1.579231543 2.721043065 1.023327779 0.674243375 0.717862045 0.063944014 11484904.03 11239850.84 1932948.433 0.015020941 0.026349262 1.579231543 -0.349084404 VLATVTKPVGGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLATVTKPVGGDK 13 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 160.65 1.05E-06 0 1561900 1563900 1326200 1792900 958130 1629000 1706100 1692900 1157100 FALSE TRUE 1488072.082 1723263.188 1387007.582 1612674.286 1125227.569 1572587.322 1445803.11 1544660.701 1336537.158 1.113378759 1.289349254 1.03776208 1.206606397 0.841897707 1.176613244 1.081753022 1.155718486 1 20.35006852 3.724144646 24.72433585 1.077648435 1.201364013 0.189338857 0.11116424 956.2442796 1640022.147 0.026811449 0.041756925 5298.398831 -3.724144646 0.123715579 VLCQGLKDSPCQLEALKLESCGVTSDNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLCQGLKDSPCQLEALKLESCGVTSDNCR 29 2 P13489 P13489 RNH1 Ribonuclease inhibitor 0 100.66 0.00040575 39102000 129150 61909 141000 91248 125410 123200 193710 146550 191190 FALSE TRUE 123045.3355 68217.59748 147464.9895 82075.57768 147281.4643 118933.5531 164155.9818 133717.3051 220838.7687 0.557172711 0.308902272 0.667749555 0.371653846 0.666918518 0.538553777 0.743329546 0.605497422 1 17.75263394 0.630242673 0.301677453 1.087632603 0.414550392 0.621015873 0.11819101 1.621416108 0.349900639 0.355338306 0.143745967 4.268179475 -0.630242673 -0.673082211 VLDEEGS(ph)ER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLDEEGSER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VLDEEGS(1)ER;VLDEEGS(1)ER 161.27 6.78E-05 445540000 763710 1655310 763550 1121220 648210 1131640 627880 887340 413100 TRUE FALSE 727610.9418 1823987.971 798559.5228 1008512.835 761257.6188 1092451.023 532085.3742 809639.8055 477161.4382 1.52487373 3.82258042 1.67356257 2.113567348 1.595387971 2.289478855 1.115105563 1.696783815 1 18.86411793 2.334611498 0.596381795 1.150147113 2.588418998 0.27009651 0.676182515 0.916759235 0.657126045 0.570640557 0.451186078 216.0784709 -2.334611498 1.438271885 VLDFEHFLPMLQTVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 182.18 1.66E-09 490980000 1343000 1113920 939390 1098680 1080350 1017560 1525400 1342120 1075530 FALSE TRUE 1279519.052 1227429.714 982461.9607 988238.599 1268762.698 982321.6421 1292672.214 1224596.858 1242317.699 1.02994512 0.98801596 0.790829883 0.795479771 1.021286824 0.790716934 1.040532719 0.98573566 1 20.24460273 -0.401290625 6.825142528 1 0.937404734 0.039864063 0.102348466 0 0 0.097525479 0.022986976 0.396925842 0.401290625 -0.062595266 VLDLDLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLDLDLFR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 143.12 0.0014111 243014000 1156627 961925 616297 678794 1278720 643133 1257990 935972 1172360 FALSE TRUE 1101955.534 1059946.251 644554.8271 610560.3375 1501728.363 620861.1429 1066060.521 854013.3298 1354163.601 0.813753621 0.782731311 0.475980027 0.450876347 1.108971148 0.458483113 0.787246474 0.630657425 1 20.36897062 -1.477760144 2.731440495 1.011197361 0.699818552 0.18715567 0.20276072 22502689.7 23644243.65 1910642.684 0.049616002 0.033284333 1.477760144 -0.31137881 VLDPFTIKPLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 190.78 5.66E-06 7892409000 15472420 12558400 11244200 13080560 12097250 11440160 16023010 11960100 11688980 FALSE TRUE 14741069.37 13838115.24 11759757.69 11765677.26 14207006.57 11043984.39 13578405.54 10912810.24 13501647.32 1.091797839 1.024920509 0.870986881 0.871425314 1.052242459 0.817973106 1.005685101 0.808257687 1 23.6866321 3.926661257 4.150957266 0.921247066 1.06951358 0.349502042 0.08141521 0.203212726 6.68525598 0.018724204 0.036423921 8446.197969 -3.926661257 0.148266514 VLDPFTIKPLDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLDPFTIKPLDRK 13 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 202.13 5.42E-08 3410700000 6332700 4086700 5058800 4891400 4746600 4894800 7753500 5602400 5501600 FALSE TRUE 6033365.821 4503139.376 5290750.984 4399707.179 5574405.537 4725291.849 6570561.172 5111824.156 6354760.03 0.949424651 0.708624614 0.832565031 0.69234828 0.87720158 0.743583051 1.033958976 0.804408684 1 22.59940622 1.746595417 25 0.943788671 0.801464312 0.337181516 0.096141446 1.976184287 6164.830592 0.040107519 0.022241597 55.7950173 -1.746595417 -0.142324359 VLDSGAPIKIPVGPETLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLDSGAPIKIPVGPETLGR 19 1 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 172.3 7.85E-12 880180000 1976410 1408020 1813230 1651600 1708790 1491410 1828520 1764400 1976260 FALSE TRUE 1882989.016 1551498.839 1896368.389 1485578.03 2006802.435 1439762.098 1549545.691 1609899.782 2282728.307 0.824885296 0.679668638 0.830746429 0.650790559 0.879124523 0.630719868 0.678813018 0.705252472 1 21.12232773 -0.945969707 9.003311962 1.00000967 0.731459799 0.496550006 0.083790692 0 0 0.073514508 0.017327535 0.113247935 0.945969707 -0.268549871 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 2 VLDTSSLT(0.011)QS(0.989)APAS(1)PTNK;VLDTSSLT(0.002)QS(0.998)APAS(0.996)PT(0.004)NK 261.16 1.31E-30 159169000 529350 490270 494850 634580 431020 616540 641870 638180 529250 TRUE FALSE 504328.6746 540229.0704 517539.362 570790.8128 506189.7515 595189.0652 543940.9427 582297.576 611323.387 0.824978539 0.883704242 0.846588521 0.933697001 0.82802288 0.97360755 0.889776106 0.952519711 1 19.22157623 8 0.040662941 1.307589902 0.215397215 0.575034405 0.039607547 461.3301119 1.427906087 10.39832353 34.46823274 100000000 -8 -1.092192687 VLDTSSLTQSAPAS(ph)PTNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 VLDTSSLTQSAPAS(0.997)PT(0.003)NK;VLDTSSLTQSAPAS(0.974)PT(0.026)NK;VLDTSSLTQSAPAS(0.998)PT(0.002)NK 399.65 1.97E-127 1099720000 1265980 1238240 1251610 1449850 886510 1392200 1462330 1507700 1022200 TRUE FALSE 1206139.634 1364418.064 1308997.557 1304108.323 1041117.063 1343987.765 1239224.701 1375677.795 1180717.555 1.021531042 1.155583787 1.108645798 1.104504898 0.881766396 1.138280496 1.049552194 1.165120133 1 20.17123246 -2.547075386 2.023994786 0.000338219 1.078082945 0.081194979 0.082590103 1236530.816 156681.3775 5826765.222 0.01900887 0.002837426 2.547075386 1.077744726 VLDWICR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLDWICR 7 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 114.72 0.01359 203290000 369710 345120 366040 390530 376160 347980 406750 370860 363320 FALSE TRUE 352234.541 380288.1204 382823.2961 351273.1824 441762.1849 335929.3653 344692.817 338385.5323 419661.81 0.839329509 0.906177573 0.91221857 0.837038716 1.052662345 0.800476377 0.821358553 0.806329107 1 18.67886766 -0.268201867 7.551984277 0.99998206 0.871666516 0.226727771 0.07431737 0 0 0.068398202 0.016121611 0.539259907 0.268201867 -0.128315544 VLEALLPLKGLEER ddPTM_SK-BR-3_Trastuzumab_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 ; 135.47 2.99E-05 3609000000 2948800 1843010 3072100 2765600 2683300 3087400 3806400 3356300 3194400 FALSE TRUE 2809416.068 2030814.814 3212958.824 2487596.634 3151266.67 2980482.564 3225663.771 3062404.579 3689771.237 0.761406572 0.55039044 0.870774532 0.674187226 0.854054755 0.80776893 0.874217821 0.829971394 1 21.81509994 2.028531523 0.310949217 1.008000497 0.627660752 0.50085576 0.086195585 1.133507252 0.324604487 0.12086488 0.155104676 106.7902304 -2.028531523 -0.380339744 VLECLASGIVMPDGSGIYDPCEKEATDAIGHLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLECLASGIVMPDGSGIYDPCEKEATDAIGHLDR 34 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 64.984 0.0034291 49866000 107560 47307 107490 84659 110850 87550 151190 114020 139210 FALSE TRUE 102475.852 52127.63708 112418.5228 76148.91648 130182.2049 84518.12155 128123.1887 104035.8043 160797.9758 0.637295659 0.324180928 0.699128968 0.473568875 0.809601018 0.525616825 0.79679603 0.646996978 1 17.29488972 0.654286488 0.244400847 1.116628145 0.442361167 0.48350948 0.136446754 2.837732355 0.452294892 0.627119223 0.283406392 4.511141899 -0.654286488 -0.674266978 VLEDSDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLEDSDLK 8 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 134.81 0.0020022 209322000 636480 515090 528360 668590 418740 619640 658430 647750 465850 FALSE TRUE 606394.8518 567578.2566 552585.8286 601382.063 491768.1234 598181.7114 557974.4106 591029.5761 538091.6388 1.126936024 1.054798506 1.026936285 1.117620159 0.913911475 1.111672563 1.036950531 1.098380896 1 19.03749236 4.492733111 1.868368321 1.045867703 1.134013221 0.157137665 0.059833487 0.850350383 4.453290387 0.013875993 0.110801148 31098.04669 -4.492733111 0.088145518 VLEFNCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VLEFNCR 7 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;;;; 179.16 0.0016406 677671000 635783 552915 521255 599362 712519 550936 677072 636428 724776 FALSE TRUE 605730.7976 609257.6671 545155.0573 539112.993 836782.088 531856.9482 573772.2311 580698.9904 837170.5604 0.723545268 0.727758113 0.651187563 0.643970319 0.99953597 0.635302976 0.685370769 0.693644781 1 19.67516205 -1.441974466 5.808015331 1.000161501 0.718677428 0.415933149 0.104249154 0.000201648 1.94E-05 0.093361186 0.02199292 0.036143111 1.441974466 -0.281484073 VLEGMEVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLEGMEVVR 9 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 111.74 0.0048295 47460000 338140 189120 231690 313520 337100 325820 478370 346900 424670 FALSE TRUE 322156.7923 208391.543 242313.2157 282004.374 395890.1333 314536.7717 405385.8706 316523.597 490525.6547 0.656758294 0.424833117 0.493986835 0.574902396 0.807073248 0.641223897 0.826431537 0.645274297 1 18.90396907 1.440684035 0.357383134 1.006711939 0.492114651 0.607629011 0.105173804 0.773942256 0.317889513 0.151905862 0.118387512 27.58570164 -1.440684035 -0.514597287 VLELEERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLELEERER 9 1 A0A1B0GUE0;Q96N16-5;Q96N16-2 A0A1B0GUE0 0 66.692 0.057466 103920000 56077 39946 51823 47504 183590 38526 62599 38320 179370 FALSE TRUE 53426.35134 44016.54281 54199.13581 42728.80767 215608.0379 37191.83496 53048.37284 34964.49765 207185.7835 0.257866879 0.212449629 0.26159679 0.206234264 1.040650735 0.17950959 0.256042533 0.168759155 1 17.66056549 -1.611885537 2.979761083 1.047797581 0.314451774 0.404825996 0.257837863 111577429.2 117597864.7 41625780.92 0.059009256 0.024440746 1.611885537 -0.733345807 VLELVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLELVLR 7 0 K7EIG1;A0A494C0R8;O75153;Q9Y5I4-2;Q9Y5I4 K7EIG1 CLUH;PCDHAC2 Clustered mitochondria protein homolog;Protocadherin alpha-C2 0 93.262 0.035045 11858000 57602 53490 51463 56889 65960 53000 67118 60296 59346 FALSE TRUE 54879.26762 58940.69181 53822.62945 51170.40964 77463.40312 51164.59671 56877.91639 55016.16259 68549.07458 0.80058364 0.859832057 0.785169308 0.746478489 1.130043018 0.74639369 0.829740106 0.802580676 1 16.06484957 -2.456900366 2.069392269 2.436403485 0.83718772 0.178275241 0.109568654 4927853.019 325737.7799 33271641.68 0.024158962 0.003492204 2.456900366 -1.599215765 VLENAEGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLENAEGAR 9 0 P38646;D6RJI2;A0A3B3ITI4;D6RA73 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 132.13 0.00072948 564490000 897800 694320 833590 778670 863430 711810 934540 843540 892920 FALSE TRUE 855362.7733 765071.9974 871810.926 700396.6122 1014011.919 687159.8412 791958.759 769675.1657 1031389.473 0.829330525 0.741787673 0.845278092 0.679080629 0.983151317 0.666246708 0.767856159 0.746250748 1 19.9761578 -1.920345962 2.334560096 1.143214597 0.780208055 0.36294354 0.090571541 12209671.88 5726978.523 9550890.93 0.020110076 0.012013071 1.920345962 -0.363006542 VLEQLEDLDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLEQLEDLDSR 11 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 101.35 0.0077926 12308000 35235 29580 29255 32932 31816 31467 34954 33609 34903 FALSE TRUE 33569.51138 32594.23563 30596.37069 29621.61279 37364.70033 30377.2899 29621.12533 30666.01779 40315.57898 0.832668468 0.808477429 0.758921773 0.734743579 0.9268055 0.753487626 0.734731488 0.760649321 1 15.29904982 -1.437138578 5.204594942 1.00024802 0.789159883 0.568132172 0.057865524 0.000163973 1.77E-05 0.055167472 0.012987935 0.036547815 1.437138578 -0.211088138 VLFICTANVTDTIPEPLRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLFICTANVTDTIPEPLRDR 20 1 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 182.7 4.23E-17 201809000 102304 90318 104509 94476 124571 85830 115020 116600 124055 FALSE TRUE 97468.29267 99521.50688 109300.841 84979.09299 146296.143 82857.68558 97471.58651 106389.8859 143292.8158 0.680203624 0.694532425 0.76277963 0.593045035 1.02095937 0.578240333 0.680226611 0.742464898 1 17.12860675 0.900041831 9.079500344 0.999999973 0.710607222 0.347642041 0.121329733 8.813461189 801.1187889 0.104078362 0.026043772 7.944047479 -0.900041831 -0.289392751 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR 33 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 284.38 4.68E-74 317140000 167483 142223 164376 142979 180471 127874 171193 162321 178613 FALSE TRUE 159566.4105 156715.6854 171912.8022 128606.4793 211945.0853 123445.6913 145074.3637 148107.3127 206311.3918 0.773425108 0.759607523 0.833268588 0.623361018 1.027306749 0.598346462 0.703181547 0.717882379 1 17.65446396 -0.969574332 4.721303872 1.000003384 0.75206169 0.297041769 0.11861116 0.019666737 66600400.58 534.6538199 0.024772435 0.107257006 0.969574332 -0.247941694 VLGEKPELPDGGDDDDIIADISNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VLGEKPELPDGGDDDDIIADISNR 24 1 Q9Y6U3;Q9Y6U3-2;E5RHN8;E5RHX6 Q9Y6U3 SCIN Adseverin 0 ;;;;;; 282.35 2.30E-52 1731504000 1914393 1599769 1299984 2033111 1227636 1689936 1799057 1958102 1347600 FALSE TRUE 1823903.437 1762787.28 1359589.552 1828738.82 1441735.33 1631413.093 1524577.813 1786640.208 1556578.925 1.171738488 1.132475361 0.873447231 1.174844905 0.926220512 1.048076051 0.979441381 1.147799305 1 20.5699473 3.973223609 24.60395267 1.020614049 1.15701486 0.269226569 0.090444908 589.6267139 541789.8425 0.02008518 0.036253492 9402.072783 -3.973223609 0.136400811 VLGEKPELPDGGDDDDIIADISNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLGEKPELPDGGDDDDIIADISNRK 25 2 Q9Y6U3;Q9Y6U3-2;E5RHN8;E5RHX6 Q9Y6U3 SCIN Adseverin 0 194.19 1.22E-18 86866000 236490 187760 171270 234260 133140 223080 246240 251380 150870 FALSE TRUE 225311.5864 206892.9575 179122.8989 210711.7397 156359.5738 215354.6837 208671.5655 229367.8346 174266.1491 1.292916539 1.187224017 1.027869726 1.209137523 0.89724582 1.235780356 1.19743029 1.316192707 1 17.41093283 7.992536546 0.011915898 1.03E-06 2.510765949 0.078312047 0.129523292 27450.7594 25.31391094 2233.07971 3177.813944 98296158.68 -7.992536546 2.510764923 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 271.91 1.72E-26 121770000 593510 660860 585660 715840 492610 711490 702300 700110 532990 TRUE FALSE 565455.9585 728202.3853 612513.0903 643882.4032 578521.028 686850.9229 595151.2364 638804.6569 615643.3671 0.918479738 1.182831529 0.994915438 1.045869147 0.939701553 1.115663645 0.966714283 1.037621277 1 19.23173534 VLGS(ph)EGEEEDEALSPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK 349.09 1.35E-87 961928000 1601392 1510119 1567248 1789464 1353959 1640641 1860958 1793484 1380801 TRUE FALSE 1525697.374 1664001.843 1639107.871 1609583.679 1590089.021 1583825.191 1577034.678 1636437.033 1594928.567 0.956592919 1.043308069 1.027699864 1.00918857 0.996965666 0.993038324 0.988780759 1.026025282 1 20.60506038 2.761435594 9.041791052 0.998662673 1.010076109 0.022957865 0.02394168 1.239206549 463.8238493 0.007451128 0.007783206 577.3452456 -2.761435594 0.011413436 VLGSEGEEEDEALS(ph)PAK ddPTM_SK-BR-3_Trastuzumab_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 242.45 2.19E-20 342170000 484768 538441 421546 567277 272936 540644 509576 584452 311619 TRUE FALSE 461853.9774 593308.7501 440874.3011 510253.2382 320535.952 521921.3627 431830.8222 533274.2845 359943.283 1.283129868 1.648339553 1.224843807 1.417593444 0.890517943 1.450010008 1.199719074 1.481550871 1 18.45741007 3.705395795 24.37991112 1.24904341 1.465734782 0.172669972 0.206324216 680.0363814 499903.7321 0.049133236 0.076123383 5074.529661 -3.705395795 0.216691373 VLGTEDLYDYIDKYNIELDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLGTEDLYDYIDKYNIELDPR 21 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;;; 192.94 8.26E-18 697876000 2438639 2215235 2321191 2578921 2040552 2438118 2792028 2688387 2375968 FALSE TRUE 2323369.367 2440969.965 2427619.903 2319682.961 2396423.623 2353685.362 2366052.849 2452977.582 2744420.983 0.846579072 0.889429858 0.884565422 0.845235835 0.873198259 0.85762548 0.86213189 0.893805141 1 21.38807037 0.805290502 2.937939124 0.99997608 0.866372917 0.895495744 0.014366134 0.279535861 3.721601725 0.013363589 0.003506856 6.386905674 -0.805290502 -0.133603163 VLGTLAAVFVSHLHADHHTGLPSILLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLGTLAAVFVSHLHADHHTGLPSILLQR 28 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 176.44 6.34E-14 18208000 10847 8753.5 8135 7028.7 10045 10168 14844 10480 4410.6 FALSE TRUE 10334.28381 9645.491602 8507.997797 6322.161722 11796.84482 9815.87961 12579.27517 9562.315642 5094.573322 2.028488581 1.893287424 1.670011846 1.240960003 2.315570721 1.926732425 2.469151856 1.87696104 1 12.31474561 VLGTPVETIELTEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLGTPVETIELTEDRR 16 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 221.73 1.65E-14 557550000 176203 128568 132168 174403 189594 149582 198355 143105 184448 FALSE TRUE 167874.2334 141669.2254 138228.0335 156871.6791 222659.1336 144401.9378 168092.3017 130573.9676 213051.2538 0.787952337 0.664953728 0.648801784 0.736309579 1.045096565 0.677780277 0.788975886 0.612875847 1 17.70084102 2.986394836 24.91296923 0.807235092 0.703812528 0.153140479 0.133424781 1288.237834 2358949.521 0.03734857 0.04122814 969.1585607 -2.986394836 -0.103422564 VLHEAEGHIVTCETNTGEVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VLHEAEGHIVTCETNTGEVYR 21 0 P62318;P62318-2;H3BT13 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 ;;;; 249.5 6.31E-31 1227800000 617299 547182 527027 655575 573825 572099 699303 598970 250253 FALSE TRUE 588120.4996 602940.4679 551191.7093 589675.3555 673899.8983 552287.0682 592611.4838 546521.0115 289060.9571 2.034589885 2.085859238 1.90683555 2.039968875 2.331341822 1.91062492 2.050126346 1.890677374 1 18.14101423 0.42321977 1.262284621 0.999100526 2.058592097 0.888984982 0.115878147 0.786037852 1.439913054 0.10285991 0.030694536 2.649840723 -0.42321977 1.059491572 VLHEEHVELLMEEFAFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLHEEHVELLMEEFAFLK 18 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 138.5 1.09E-06 88429000 183099 238755 150417 229283 132430 174018 169127 172713 22427.7 FALSE TRUE 174444.2731 263084.4059 157313.7682 206235.0372 155525.7501 167991.713 143323.5699 157589.3341 25905.67317 6.733825135 10.1554746 6.072560523 7.960998962 6.003540192 6.484746099 5.532516718 6.083197803 1 14.66098045 0.400315307 0.305086117 2.43E-13 8.513972035 0.742855334 1.154637484 1.677688943 0.310286608 4.369182534 1.373746151 2.513710777 -0.400315307 8.513972035 VLHEEHVELLMEEFAFLKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLHEEHVELLMEEFAFLKK 19 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 161.32 1.21E-11 391830000 1669705 1540960 1583297 1728234 1139507 1701267 1757928 1689783 62094.7 FALSE TRUE 1590781.354 1697985.576 1655892.734 1554508.635 1338236.66 1642351.697 1489723.797 1541816.642 71724.02894 22.17919681 23.67387333 23.08700108 21.67347063 18.65813563 22.8982075 20.77021912 21.4965147 1 16.13016891 -0.428297095 0.768409295 9.66E-15 22.19688615 0.956905545 1.387912301 2.633944208 1.1432131 11.4737125 0.470871841 0.37299491 0.428297095 22.19688615 VLHMVGDKPVFSFQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLHMVGDKPVFSFQPR 16 1 M0QWZ7;Q9NP81;Q9NP81-2;M0R2C6 M0QWZ7 SARS2 "Serine--tRNA ligase, mitochondrial" 0 100.41 0.0012401 145510000 115740 104100 107060 101580 117350 91211 129100 133950 123100 FALSE TRUE 110269.1996 114707.9084 111968.8069 91368.98541 137815.8028 88052.3402 109403.4239 122220.6279 142189.7193 0.775507541 0.806724346 0.787460637 0.642585033 0.96923887 0.61925954 0.769418664 0.85956023 1 17.11745763 0.955013058 3.160639056 0.99930673 0.76810737 0.387831262 0.094494232 0.25521104 6.383196902 0.079690776 0.020827923 9.015982462 -0.955013058 -0.231199361 VLHNDSDILFPVSGVGSYSPADAPLGS(ph)LENGTGPEDHVLPDPGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVSGVGSYSPADAPLGS(0.844)LENGT(0.156)GPEDHVLPDPGLR 146.32 5.44E-14 84483000 33726 24547 31944 34746 39697 29633 34712 29461 33129 TRUE FALSE 32131.83882 27048.36721 33408.664 31253.26607 46620.14423 28606.80178 29416.04687 26881.23866 38266.47612 0.83968638 0.706842384 0.873053058 0.816727048 1.218302518 0.747568229 0.768715854 0.702474891 1 15.22379343 5.136334498 18.00602194 0.835885153 1.932073057 0 0.156945546 14111.90235 2136907.399 0.035080497 93653.62149 136878.267 -5.136334498 1.096187904 VLIAAHGNSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ; 196.48 6.03E-08 5436500000 3706900 2620700 2118360 2591900 3873500 2385900 3801000 2823000 3616800 FALSE TRUE 3531682.183 2887752.309 2215488.901 2331357.288 4549037.174 2303275.685 3221087.64 2575803.154 4177674.872 0.845370282 0.691234334 0.530316257 0.558051394 1.088892102 0.551329569 0.771024012 0.616563814 1 21.99426879 -0.532877784 10.14785451 0.999999784 0.712627861 0.229834605 0.168470231 0 0 0.14906574 0.035135132 0.293171815 0.532877784 -0.287371923 VLIDPVSVQDKDTLSIHYLMLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLIDPVSVQDKDTLSIHYLMLPR 23 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 182.77 2.31E-17 116090000 209080 182420 198980 261420 218240 212800 273130 226280 201710 FALSE TRUE 199197.2028 201008.8054 208103.4298 235141.5649 256300.9869 205430.6826 231459.0021 206465.7236 232990.1566 0.854959736 0.862735183 0.893185501 1.009233902 1.100050709 0.881713999 0.993428244 0.886156422 1 17.82990948 3.384933822 4.683081776 0.977742426 0.861482783 0.410895524 0.061881756 0.191147866 7.312287885 0.016625096 0.022858096 2426.240353 -3.384933822 -0.116259643 VLIEILCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLIEILCTR 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 123.92 0.0034425 0 119280 110850 114610 124790 108360 116390 142440 135400 77324 FALSE TRUE 113641.8708 122145.741 119864.9819 112245.8721 127257.9497 112359.3851 120708.1619 123543.6582 89315.011 1.272371458 1.367583564 1.34204744 1.256741402 1.424821519 1.25801233 1.351487959 1.3832351 1 16.44661505 -1.288259844 4.432761675 0.999768538 1.33071513 0.779636647 0.055473083 0.000110847 1.78E-05 0.046919629 0.011051391 0.051492047 1.288259844 0.330946592 VLISTDVWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLISTDVWAR 10 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 121.09 0.0012195 154430000 193470 186480 166660 214600 297590 187840 266950 207570 301560 FALSE TRUE 184325.0565 205482.524 174301.5258 193028.0003 349489.6018 181335.0537 226221.8746 189394.0704 348324.3846 0.529176436 0.589917138 0.500400011 0.554161606 1.003345207 0.520592476 0.649457473 0.543729003 1 18.41007195 -5 0.222105646 2.965350306 0.561519296 0.408311819 0.146168772 153.9677679 1.540116326 135.946379 0.25802142 1.00E-05 5 -2.40383101 VLISVGS(ph)YK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLISVGSYK 9 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 VLISVGS(1)YK;VLISVGS(1)YK;VLISVGS(1)YK 158.05 7.04E-05 181357000 1002744 897994 898314 1076120 773327 1025903 1168670 1164360 938705 TRUE FALSE 955346.2784 989500.6095 939502.5855 967946.3731 908194.984 990375.7219 990367.9274 1062402.466 1084274.577 0.881092574 0.912592281 0.866480323 0.892713334 0.837606085 0.913399376 0.913392187 0.979827885 1 20.04829871 1.303577066 1.688959906 1.001524179 0.884219165 0.806806311 0.021367465 0.141826659 0.725792078 0.018655754 0.00564999 20.11764155 -1.303577066 -0.117305014 VLKEYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLKEYK 6 1 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 66.682 0.091899 320590000 528690 347530 515310 439510 362910 472380 605730 525250 468670 FALSE TRUE 503699.8715 382943.7021 538937.4732 395329.6198 426201.3891 456021.3622 513314.7635 479256.3255 541348.95 0.930453216 0.70738791 0.99554543 0.730267639 0.787295125 0.842379693 0.948214204 0.885300185 1 19.04619932 1.795836068 4.530672204 0.937788713 0.824904053 0.259073739 0.089009918 0.280509928 10.54903067 0.040386626 0.021911113 62.4936755 -1.795836068 -0.11288466 TPEVTCVVVDVSHEDPEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 TPEVTCVVVDVSHEDPEVK 19 0 A0A0A0MS08;P01857;A0A0A0MS07 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 185.28 2.31E-14 91714000 1793000 136724 130689 127682 73473 81569 61557 73647 47698 FALSE TRUE 1708248.443 150656.331 136681.2199 114847.1628 86286.66794 78744.24508 52165.34908 67198.07825 55094.76223 31.00564145 2.734494622 2.480838729 2.084538677 1.56615011 1.429251019 0.946829553 1.219681791 1 15.74962755 4.559401208 1.772503307 1.397404453 35.48999372 0.99386912 0.723068806 0.040518641 0.170737108 0.197921711 2.073520813 36257.77985 -4.559401208 34.09258927 up VLKPNFAAAWEEVGDTFEKEETFALSSTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLKPNFAAAWEEVGDTFEKEETFALSSTK 29 2 Q9UBF2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 287.53 3.73E-81 96962000 223510 213720 229900 246970 133870 249570 269930 280810 169250 FALSE TRUE 212945.1253 235498.311 240441.1424 222144.1064 157216.8856 240927.3283 228747.2209 256220.7877 195496.4256 1.089253293 1.204616966 1.229900453 1.136307765 0.804193146 1.232387383 1.170083904 1.310616227 1 17.5767827 -0.321767372 8.150620678 1.000000007 1.146350748 0.104035847 0.135710895 0 0 0.125061216 0.029477211 0.476686254 0.321767372 0.146350741 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR 38 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 282.06 6.69E-77 730880000 333160 263780 278120 299090 363930 289910 431030 321500 199163 FALSE TRUE 317412.1871 290659.4819 290872.0771 269024.905 427399.2768 279870.344 365268.4571 293347.7556 230048.1809 1.379763952 1.263472203 1.264396337 1.169428526 1.857868535 1.216572733 1.587791113 1.275157902 1 17.81157652 0.983585733 24.02076233 0.999999985 1.386147445 0.272040355 0.202434331 792.162013 1159258.666 0.178850648 0.044712662 9.629100797 -0.983585733 0.38614746 VLLMELEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLLMELEEAR 10 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;;; 93.649 0.020105 38573500 43729.7 35447.3 30732.8 33938.9 40728.9 30615.7 43545.2 31830.6 43608.6 FALSE TRUE 41662.68374 39059.42017 32141.92928 30527.29729 47832.00726 29555.47063 36901.57998 29043.34392 50371.19897 0.827113204 0.775431615 0.638101334 0.606046668 0.949590406 0.586753368 0.732592845 0.576586314 1 15.62031145 -1.003781561 4.58542314 1.000007538 0.721181086 0.368283501 0.118134772 8.46E-06 1.84E-06 0.106295285 0.025053362 0.099133043 1.003781561 -0.278826451 VLLPEYGGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLLPEYGGTK 10 0 P61604;B8ZZL8;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ; 106.2 0.0080439 66240000 641620 465190 481710 517940 477060 461210 587760 550100 559920 FALSE TRUE 611291.8942 512593.3899 503796.88 465875.6872 560259.113 445238.1821 498086.417 501930.3277 646749.5339 0.945175624 0.792568627 0.778967519 0.720334013 0.866269063 0.688424434 0.770138038 0.776081468 1 19.30284758 4.512382735 1.979966042 0.782248765 0.958433438 0.198881022 0.086526893 0.565506114 3.36551421 0.019377033 0.154050308 32537.39165 -4.512382735 0.176184674 VLLS(ph)DSNLHDA ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLLSDSNLHDA 11 0 Q6FI81-3;Q6FI81;H3BV90;Q6FI81-2 Q6FI81-3 CIAPIN1 Anamorsin 1 VLLS(0.997)DS(0.003)NLHDA;VLLS(1)DSNLHDA 160.84 2.83E-05 43107000 93487 90033 85799 120576 103168 102466 121610 105826 95354 TRUE FALSE 89068.05478 99207.46506 89732.96902 108455.4714 121160.4665 98917.57673 103056.161 96559.31442 110141.0113 0.808672934 0.900731379 0.81470987 0.984696528 1.100048611 0.898099405 0.93567473 0.876688104 1 16.74899223 3.234737641 24.99987711 0.962363948 0.849420177 0.443549806 0.065449621 97.16566715 635403.4596 0.018735119 0.023215008 1716.870906 -3.234737641 -0.112943771 VLLSLEHGLWAPNLHFHS(ph)PNPEIPALLDGR ddPTM_SK-BR-3_Trastuzumab_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 VLLSLEHGLWAPNLHFHS(1)PNPEIPALLDGR 140.49 2.49E-08 141740000 73647 79506 79439 84653 102970 83425 103010 75738 13709 TRUE FALSE 70165.85226 87607.75179 83081.35673 76143.51961 120927.9354 80535.97133 87293.93259 69105.97921 15834.9217 4.431082993 5.532566149 5.246717242 4.808582008 7.636787706 5.085972185 5.512747977 4.364150357 1 13.95082211 0.79182856 2.310088805 1.000938489 5.438690856 0.732703536 0.846377853 0.420146521 3.671309634 0.770028486 0.208432032 6.191965954 -0.79182856 4.437752366 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR ddPTM_SK-BR-3_Trastuzumab_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 ;; 259.47 1.72E-58 6710480000 884480 787570 944880 1079960 1324860 959060 1409510 923580 108020 FALSE TRUE 842672.3833 867824.2784 988203.6826 971400.369 1555915.165 925847.5117 1194463.362 842706.439 124771.1899 6.75374166 6.955325817 7.920127101 7.785454076 12.47014768 7.420362925 9.57323051 6.754014605 1 16.92892532 3.673625725 2.526813452 8.235018982 6.809449276 0 2.889146989 0.997997046 12.48472115 0.719299424 1.293857838 4716.563921 -3.673625725 -1.425569706 VLMATNRPDTLDPALMRPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLMATNRPDTLDPALMRPGR 20 2 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 116.73 5.10E-05 614060000 647250 613740 537810 692320 639570 613050 655550 631310 610510 FALSE TRUE 616655.7752 676280.8038 562469.1205 622726.6783 751110.8055 591819.9248 555533.8075 576029.1496 705184.7727 0.874459857 0.959012205 0.797619492 0.88306881 1.06512624 0.83924093 0.787784747 0.816848537 1 19.4276418 2.059586804 24.99997768 0.836845433 0.91453632 0.058416001 0.08841037 131.7312525 55267.61757 0.030927155 0.022841216 114.7061765 -2.059586804 0.077690888 VLNEECDQNWYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLNEECDQNWYK 12 0 P62993;J3KT38;P62993-2;J3QRL5 P62993 GRB2 Growth factor receptor-bound protein 2 0 141.73 0.00014136 37719000 42899 40891 39790 43843 29828 43138 44072 48011 33388 FALSE TRUE 40871.24929 45057.83939 41614.41086 39435.81834 35029.99376 41644.12024 37348.00696 43806.90232 38565.64052 1.059784013 1.168341528 1.079054057 1.022563552 0.908321327 1.079824416 0.968426985 1.135904959 1 15.23502845 3.342986414 3.694108342 1.013166242 1.115130784 0.269953618 0.065634618 0.245376256 6.396832956 0.017180281 0.023654285 2202.85755 -3.342986414 0.101964543 VLNNMEIGTSLFDEEGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLNNMEIGTSLFDEEGAK 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 176.25 4.72E-14 0 66417 48720 64749 67281 48544 57891 72972 66494 45871 FALSE TRUE 63277.60004 53684.62339 67717.8057 60517.78605 57010.05823 55886.22015 61838.78118 60671.43285 52984.4404 1.194267592 1.013214879 1.278069659 1.142180338 1.075977359 1.05476664 1.167112094 1.145080186 1 15.69328113 2.79901087 11.16034227 1.101603857 1.143886794 0.134478285 0.079565784 2.8711726 524.7948364 0.023748438 0.025188008 629.5219391 -2.79901087 0.042282937 VLNSYWVGEDSTYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLNSYWVGEDSTYK 14 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 202.13 3.93E-08 71230000 249460 246760 191760 257280 166940 223440 247990 259620 181710 FALSE TRUE 237668.5202 271905.1245 200552.3857 231417.7256 196054.2831 215702.2168 210154.5709 236886.2965 209888.6588 1.132355229 1.295473163 0.955517973 1.10257375 0.934087074 1.027698295 1.00126692 1.128628378 1 17.67926469 3.735560827 24.99961571 1.020411258 1.213914198 0.565657413 0.07013051 151.6234666 1263600.449 0.016704618 0.027138803 5439.523114 -3.735560827 0.19350294 VLNT(ph)GSDVEEAVADALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.5)GS(0.5)DVEEAVADALK 84.14 0.059882 12471000 26815 29461 20648 33284 18132 29970 27544 30697 15792 TRUE FALSE 25547.50809 32463.10939 21594.73122 29938.22908 21294.21506 28932.13139 23341.65692 28009.00794 18240.94271 1.40055854 1.779683754 1.183860482 1.641265453 1.167385667 1.586109438 1.279629967 1.535502216 1 14.15489267 -3.493803379 0.175742347 1.32E-16 1.575980135 0.314797983 0.200989891 76.43780134 1.18160663 28.54594056 0.620379118 0.000320772 3.493803379 1.575980135 VLNTGS(ph)DVEEAVADALKKPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLNTGSDVEEAVADALKKPAR 21 2 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.145)GS(0.855)DVEEAVADALKKPAR;VLNT(0.052)GS(0.948)DVEEAVADALKKPAR;VLNT(0.212)GS(0.788)DVEEAVADALKKPAR 196.22 5.10E-22 311314000 704304 499157 721661 690761 534269 712175 946427 816917 639822 TRUE FALSE 671012.9457 550021.6658 754749.8707 621324.3919 627445.3444 687512.2012 802032.1788 745383.4167 739042.328 0.907949275 0.744235675 1.021253915 0.84071557 0.848997846 0.930274458 1.085231723 1.008580143 1 19.49529747 1.957054903 4.280067892 1.036645939 0.864664711 0.50110658 0.071797527 0.160247209 6.194011709 0.031467086 0.018928112 90.58471099 -1.957054903 -0.171981228 VLPAFRES(ph)PSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLPAFRESPSGR 12 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VLPAFRES(0.957)PS(0.043)GR 78.985 0.014304 0 81252 76453 79405 81879 80421 80618 90820 86321 84696 TRUE FALSE 77411.37899 84243.64762 83045.79779 73648.36736 94446.39694 77826.17845 76963.74098 78762.27562 97830.22311 0.791282863 0.861120878 0.848876709 0.752818148 0.965411239 0.795522856 0.786707201 0.805091444 1 16.57799261 -1.908290893 2.439121063 1.104313352 0.825377242 0.467811747 0.0583712 7781829.244 3951205.033 4646195.006 0.013560295 0.012351199 1.908290893 -0.27893611 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR 32 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 248.12 2.72E-47 633090000 118611 84222 107053 117771 140809 103464 151162 129327 158309 FALSE TRUE 113004.4931 92804.31755 111961.4859 105932.4353 165366.045 99881.01574 128099.4606 118002.4423 182858.7512 0.617987886 0.507519148 0.612283991 0.57931291 0.904337605 0.546219501 0.700537764 0.64532018 1 17.48037015 -4.999999994 0.158984212 2.374950776 0.528033143 0.552069934 0.10477317 93.64051757 0.858231125 40.55369401 0.417714044 1.00E-05 4.999999994 -1.846917633 VLPCLHTFCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLPCLHTFCER 11 0 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5;Q9C040;Q9C040-2;A0A0J9YX34;A0A0J9YW70;C9JVI3 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 155 3.17E-05 132350000 214420 164900 154970 191810 221290 168650 221230 201520 231790 FALSE TRUE 204284.7915 181703.4975 162075.5278 172528.8944 259882.9059 162809.6082 187477.3003 183873.8405 267734.8094 0.763011698 0.67866968 0.605358445 0.644402178 0.970672833 0.608100264 0.70023506 0.686775996 1 18.0304452 -1.044868405 4.478710601 1.000011243 0.706024513 0.437597224 0.104327854 0.315442383 57831139.28 1972.408247 0.022675805 0.090184436 1.044868405 -0.29398673 VLPGDYEILATHPTWALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLPGDYEILATHPTWALK 18 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 83.792 0.0039386 414550000 770470 541730 626800 703030 627330 678040 861470 732360 718800 FALSE TRUE 734051.41 596932.9029 655539.4 632360.0887 736736.1534 654559.3048 730036.9295 668230.6759 830267.8329 0.884113994 0.718964266 0.789551725 0.761633853 0.887347581 0.788371269 0.879278831 0.804837487 1 19.66321728 -0.437064048 0.361624975 1.055242838 0.791539083 0.533335422 0.054997585 5.824044949 0.797065214 0.451690527 0.041314515 0.365540879 0.437064048 -0.263703755 VLPITVPKS(ph)PAFALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLPITVPKSPAFALK 15 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 VLPITVPKS(1)PAFALK;VLPITVPKS(1)PAFALK 180.88 3.70E-07 313230000 918340 543390 1037200 939020 892610 1052690 1463150 1180810 1204250 TRUE FALSE 874931.8882 598762.0588 1084756.646 844627.9256 1048280.901 1016235.081 1239919.595 1077412.017 1390998.94 0.628995367 0.43045472 0.779840024 0.607209611 0.753617326 0.730579336 0.891387879 0.774559912 1 20.40768989 2.252415096 0.367137267 0.996808774 0.492232148 0.65095629 0.092138939 0.724709074 0.235948755 0.100546315 0.129056712 178.8195906 -2.252415096 -0.504576626 VLPPPAGYVPIRT(ph)PAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLPPPAGYVPIRTPAR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR 194.19 4.10E-10 631970000 310465 251632 277354 317069 317989 279250 319284 287280 330996 TRUE FALSE 295789.9347 277273.5869 290070.9552 285196.6217 373446.1809 269579.5025 270571.3617 262124.2402 382325.1692 0.773660639 0.72522975 0.758702222 0.745953039 0.976776344 0.705105298 0.70769958 0.685605504 1 18.54444065 -2.343587466 2.397539699 2.616661621 0.757431837 0.460881926 0.08159257 8039746.389 652503.9389 71974762.52 0.020969254 0.00453328 2.343587466 -1.859229783 VLPYIFEDPDWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLPYIFEDPDWR 12 0 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 ;; 163.94 0.00013641 214369000 413362 320015 365132 404109 433968 330665 448290 419623 483760 FALSE TRUE 393823.1975 352624.8923 381873.6634 363487.1956 509651.8818 319213.9881 379895.1271 382878.5856 558779.0301 0.704792371 0.631063217 0.683407291 0.650502571 0.91208126 0.571270522 0.679866471 0.685205716 1 19.09191835 -0.892504214 4.67996709 1.000002067 0.684997381 0.552932897 0.087572454 0.005835926 49712644.36 261.9660679 0.018654257 0.128084267 0.892504214 -0.315004685 VLQGDLVMNVYR ddPTM_SK-BR-3_Trastuzumab_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 ; 196.88 4.69E-07 453260000 833440 543380 455470 512680 919050 480000 926360 636210 842340 FALSE TRUE 794044.9429 598751.0398 476353.75 461144.4324 1079332.029 463377.4796 785026.7682 580500.0796 972965.7851 0.816107776 0.615387559 0.489589415 0.473957501 1.109321669 0.476252595 0.806839028 0.596629489 1 19.89202955 VLQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLQLLR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5;H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5;A0A2R8YFJ4 P18124;H0Y4W2 RPL7;TRRAP 60S ribosomal protein L7;Transformation/transcription domain-associated protein 0 126.52 0.040604 81259000 130040 113900 75882 86704 143230 92513 148350 110740 117260 FALSE TRUE 123893.2669 125506.5395 79361.26476 77988.34919 168209.2667 89309.25161 125716.4829 101043.0185 135444.0819 0.914718939 0.926629925 0.585933794 0.575797392 1.241909312 0.659380981 0.928179962 0.746012798 1 17.04733783 VLRPPGGGSNFSLGFDEPTEQPVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 122.04 9.93E-05 323200000 233313 206326 221738 252819 202145 245196 279032 277030 269550 FALSE TRUE 222284.7569 227350.854 231904.9066 227405.1538 237399.024 236704.801 236460.5436 252771.7846 311350.4373 0.713937513 0.730208879 0.744835654 0.73038328 0.762481743 0.760252027 0.759467517 0.811856205 1 18.24817978 -3.321668891 0.223056323 1.575845626 0.708222447 0.982831547 0.01079342 7.213336664 0.14121552 1.92505593 0.019577457 0.000476794 3.321668891 -0.867623179 VLS(ph)AMIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSAMIR 7 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 VLS(1)AMIR 62.969 0.086285 5296800 35857 28222 37564 32752 37554 39017 46042 36858 21684 TRUE FALSE 34162.11067 31097.85389 39286.34656 29459.70674 44103.40571 37665.83151 39017.44728 33630.51812 25046.64397 1.363939644 1.241597634 1.568527368 1.176193775 1.760850905 1.503827481 1.557791428 1.342715541 1 14.61232969 0.974539744 21.42036647 0.999999992 1.440275465 0.418121776 0.16736693 361.3373434 304004.0773 0.157767013 0.039441753 9.430609108 -0.974539744 0.440275473 VLS(ph)PLIIK ddPTM_SK-BR-3_Trastuzumab_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 445587300 835045 699512 725050 859137 624419 816209 959946 833555 661325 TRUE FALSE 795574.0777 770793.0681 758294.2597 772774.9165 733317.4759 787943.4777 813488.6071 760564.5052 763879.9034 1.041491044 1.009050067 0.992687799 1.011644518 0.959990533 1.031501777 1.064943067 0.995659791 1 19.54298631 2.054045243 24.99980863 1.032619207 1.006272857 0.062554609 0.028044288 162.6119058 75218.6919 0.010376808 0.007663777 113.2518337 -2.054045243 -0.02634635 VLS(ph)PPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 69.825 0.097012 208110000 421950 473340 374380 548770 265350 439080 415860 445970 269540 TRUE FALSE 402005.2597 521573.8841 391545.6933 493606.597 311626.956 423874.5495 352412.9192 406918.5026 311338.8866 1.29121442 1.675260967 1.257618981 1.585431882 1.00092526 1.361457138 1.131927088 1.306995432 1 18.24812626 2.745692817 24.99808408 1.181995453 1.460800526 0.430049778 0.165936931 506.164641 1774088.159 0.045584265 0.047439083 556.7917822 -2.745692817 0.278805073 VLS(ph)PPKLNEVSSDANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VLSPPKLNEVSSDANR 16 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0 Q9H6Z4 RANBP3 Ran-binding protein 3 1 VLS(1)PPKLNEVSSDANR;VLS(0.999)PPKLNEVS(0.001)S(0.001)DANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR 172.24 2.81E-09 5900016000 3161500 2973990 2794520 3486710 1735720 3329940 3122120 3527000 1862567 TRUE FALSE 3012062.16 3277042.962 2922651.506 3136219.286 2038429.018 3214623.343 2645783.252 3218157.182 2151404.378 1.400044637 1.523211069 1.358485432 1.457754441 0.947487622 1.49419764 1.229793562 1.495840213 1 21.03684729 -4.59146789 0.122433762 9.23E-13 1.535934729 0.288946778 0.172960477 159.3575263 1.38522876 41.05258701 1.451491359 2.56E-05 4.59146789 1.535934729 VLS(ph)SPQLAQQGQGLMGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSSPQLAQQGQGLMGHR 18 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VLS(0.5)S(0.5)PQLAQQGQGLMGHR 138.28 1.31E-06 0 38671 32979 35192 36204 36803 39866 47787 36917 41861 TRUE FALSE 36843.09847 36339.59759 36805.58801 32564.70514 43221.43155 38485.43042 40496.21548 33684.35177 48352.59008 0.761967423 0.751554312 0.761191654 0.673484194 0.893880379 0.795933172 0.837519054 0.696640071 1 15.56130555 2.735654908 24.99978023 0.831089744 0.743576789 0.300560521 0.079897498 360.0312868 3097578.734 0.022538711 0.02211747 544.0701611 -2.735654908 -0.087512955 VLSAPPHFHFGQT(ph)NRTPEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.5)NRT(0.5)PEFLR 222.72 5.61E-25 242020000 182520 188820 182930 211360 234770 194430 246290 205060 48413 TRUE FALSE 173892.6413 208060.9727 191317.5214 190113.6912 275713.8137 187696.8403 208713.9371 187103.8593 55920.64078 3.109632488 3.720647149 3.421232639 3.399705164 4.930448039 3.356485865 3.732323775 3.345881891 1 15.77109327 0.666808996 2.646894893 1.000026557 3.649557995 0.743322063 0.488500164 1.343422599 10.07408979 0.442999195 0.117457216 4.643110247 -0.666808996 2.649531438 VLSAPPHFHFGQTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSAPPHFHFGQTNR 15 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 114.27 0.000358 1067500000 960090 830050 953490 901150 764840 1150100 1149400 1106800 617750 FALSE TRUE 914708.4484 914633.0387 997208.4596 810564.6899 898227.8538 1110271.749 974037.9198 1009882.724 713547.515 1.281916662 1.281810979 1.397536168 1.135964561 1.258819959 1.55598853 1.365063853 1.415298496 1 19.44464998 VLSAPPHFHFGQTNRT(ph)PEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.214)NRT(0.786)PEFLR 157.31 1.00E-08 179570000 145930 142430 138960 168510 163650 142020 189350 155900 38044 TRUE FALSE 139032.1781 156943.7789 145331.4535 151571.0547 192190.5082 137101.8118 160461.1798 142248.5695 43943.66922 3.163872762 3.571476432 3.307221633 3.449212534 4.37356533 3.119944561 3.651519837 3.237066273 1 15.42336772 0.773567011 4.047925127 1.000016819 3.506082503 0.83617833 0.347686537 1.021554292 17.93506383 0.308184759 0.078682116 5.936999477 -0.773567011 2.506065684 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 376.56 4.91E-119 570013000 645019 560896 509162 687870 493795 592261 729789 732264 529130 FALSE TRUE 614530.2302 618051.9401 532507.5813 618724.0007 579912.6917 571750.8531 618446.2846 668143.0822 611184.778 1.005473716 1.01123582 0.871271014 1.012335423 0.948833663 0.935479537 1.011881033 1.093193264 1 19.22124909 1.504517346 5.54073007 1.048842154 0.97058621 0.339118159 0.047814983 0.166749936 11.46212985 0.026956521 0.01177936 31.95341983 -1.504517346 -0.078255944 VLSIGDGIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLSIGDGIAR 10 0 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 96.034 0.016322 154741000 398280 319318 328130 333520 452430 290095 398200 339704 452020 FALSE TRUE 379454.0937 351856.8672 343175.0851 299993.936 531333.6488 280048.9374 337447.2766 309957.7169 522116.953 0.726760722 0.673904314 0.657276273 0.574572295 1.01765255 0.536372044 0.646305918 0.593655722 1 18.99401348 -1.024924064 4.604447823 1.000008286 0.678459941 0.369347892 0.132103219 1.28E-05 2.71E-06 0.115774586 0.027287448 0.094422596 1.024924064 -0.321548345 VLSNRGDS(ph)LSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSNRGDSLSR 11 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3 Q15642 TRIP10 Cdc42-interacting protein 4 1 VLS(0.033)NRGDS(0.928)LS(0.039)R 62.104 0.050321 190950000 159950 117440 138060 172380 179030 153490 211650 171000 205210 TRUE FALSE 152389.4805 129407.2695 144390.1876 155052.0349 210252.7753 148174.6028 179358.9053 156026.3335 237032.9187 0.642904291 0.545946404 0.609156687 0.654137137 0.887019307 0.625122467 0.756683528 0.658247531 1 17.85472791 -5 0.118225889 2.096116191 0.495687376 0.601494935 0.087317225 99.98458021 0.769910157 26.20836483 0.830363556 1.00E-05 5 -1.600428815 VLSNRPIMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLSNRPIMFR 10 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 184.71 1.40E-06 1947990000 1285320 840630 511590 635190 1219800 785510 1358380 964390 1210360 FALSE TRUE 1224565.471 926291.1527 535046.9075 571339.4944 1432532.734 758307.5917 1151134.183 879942.899 1398056.447 0.8759056 0.662556333 0.382707657 0.408666972 1.024660154 0.542401269 0.823381763 0.629404414 1 20.41499118 -0.292294139 0.514033596 1.04313206 0.66192269 0.212853252 0.200157423 11.25471998 2.934425752 1.139255555 0.092688018 0.510159362 0.292294139 -0.381209369 VLSPT(ph)AAKPSPFEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.481)PT(0.519)AAKPSPFEGK 164.53 2.39E-06 167600000 634290 536200 513990 671900 377710 620750 682030 683070 481990 TRUE FALSE 604308.3687 590839.3896 537556.9499 604359.3355 443582.5044 599253.2719 577973.7972 623256.7696 556734.5475 1.085451534 1.061258713 0.965553426 1.08554308 0.79675764 1.076371629 1.038149689 1.119486427 1 19.08663009 -0.185162459 7.030478969 1.000000001 1.03050504 0.009079396 0.091851645 0 0 0.082455617 0.019434975 0.652886277 0.185162459 0.030505039 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSS(0.003)AAS(0.994)LPGS(0.003)ELPSSRPEGSQGGELSR;VLSS(0.002)AAS(0.998)LPGSELPSSRPEGSQGGELSR 147.5 4.82E-08 242606000 58553 56227 57848 61201 60475 55890 74913 63373 70612 TRUE FALSE 55785.31573 61956.59522 60500.38802 55048.95921 71021.82085 53954.51529 63483.64598 57823.72416 81562.14832 0.683960843 0.759624366 0.741770408 0.674932678 0.870769374 0.661514151 0.778346908 0.708952932 1 16.31561216 -5 0.45521601 7.182109594 0.733237113 0.650123752 0.060990201 790.868235 4.478959118 4935.386592 0.02765192 1.00E-05 5 -6.448872481 VLSSIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLSSIEQK 8 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 111.95 0.0092114 173880000 285320 259738 222939 290200 262900 262692 300840 299340 287320 FALSE TRUE 271833.489 286205.5975 233160.9737 261028.5447 308749.6768 253594.9102 254941.3327 273128.2027 331876.1182 0.8190812 0.862386842 0.702554239 0.786524038 0.930316042 0.764125215 0.768182218 0.822982395 1 18.34028529 -2.106677671 1.926711599 1.308572609 0.807772654 0.498084669 0.06087667 2110878.578 508169.3883 2851190.327 0.015974199 0.007822081 2.106677671 -0.500799956 VLSTNTDDNIGGAHFTETLAQYLASEFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLSTNTDDNIGGAHFTETLAQYLASEFQR 29 0 Q0VDF9 Q0VDF9 HSPA14 Heat shock 70 kDa protein 14 0 ; 204.05 2.53E-25 111766000 48412 38534 48668 48504 59721 43011 56223 51415 62786 FALSE TRUE 46123.6607 42460.65841 50899.47594 43628.28577 70136.32349 41521.51829 47645.14874 46912.83003 72522.53221 0.635990764 0.585482292 0.701843612 0.601582494 0.967097002 0.57253266 0.656970286 0.646872477 1 16.14614168 -2.454629659 2.025585503 3.800385515 0.664035839 0.459125187 0.111977403 2881831.517 187006.3268 37108335.4 0.025322713 0.003510511 2.454629659 -3.136349676 VLSTS(ph)TDLEAAVADALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.015)T(0.191)S(0.776)T(0.018)DLEAAVADALK;VLST(0.007)S(0.972)T(0.021)DLEAAVADALK;VLS(0.017)T(0.117)S(0.844)T(0.022)DLEAAVADALK 309.81 4.60E-58 183929000 524950 560820 442160 633090 402150 534030 504550 542950 406264 TRUE FALSE 500136.6539 617968.1956 462433.4734 569450.5904 472284.8327 515536.4072 427571.6308 495406.4196 469265.3462 1.065786464 1.316884361 0.985441344 1.213493805 1.006434497 1.098603192 0.911151088 1.055706379 1 18.8400444 2.583983401 1.070631272 0.986140983 1.167853925 0.262322678 0.10075139 0.529563939 1.244303849 0.052704214 0.041499928 383.6925803 -2.583983401 0.181712942 VLSTS(ph)TDLEAAVADALKKPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.013)T(0.095)S(0.726)T(0.166)DLEAAVADALKKPVR 172.75 2.71E-12 521890000 487070 319950 403330 450100 340940 422940 534760 477070 444910 TRUE FALSE 464047.1664 352553.2688 421823.0794 404855.0929 400399.8281 408293.4818 453172.5405 435295.2217 513904.3705 0.902983498 0.686028936 0.820820183 0.787802393 0.77913295 0.79449311 0.881822702 0.847035454 1 18.9711404 0.86964146 0.750815791 0.998620386 0.788531505 0.55472713 0.056069095 0.59514978 0.718314441 0.052041421 0.019259815 7.406984906 -0.86964146 -0.210088881 VLT(ph)IDPTEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLTIDPTEFK 10 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 VLT(1)IDPTEFK 101.95 0.012324 0 35487 37347 33494 36971 26895 39338 41884 39741 31416 TRUE FALSE 33809.59984 41152.70176 35029.73303 33254.60484 31585.47948 37975.7152 35493.82655 36261.06736 36287.83283 0.931706228 1.134063364 0.965329983 0.916411983 0.870415151 1.046513727 0.978119215 0.999262412 1 15.14719828 3.585550413 22.21693188 0.966520705 1.035689492 0.137223511 0.06746647 19.84491004 4046.559547 0.017604369 0.027272551 3850.795121 -3.585550413 0.069168787 VLT(ph)PEEQLADKLR ddPTM_SK-BR-3_Trastuzumab_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 168.64 4.83E-05 508450000 1276160 1123150 1041900 1307650 670540 1189080 1196210 1282230 689400 TRUE FALSE 1215838.446 1237600.262 1089672.146 1176202.538 787481.9637 1147901.861 1013706.195 1169951.144 796308.631 1.526843235 1.554171603 1.368404288 1.477068679 0.98891552 1.441528845 1.273006665 1.469218213 1 19.60296817 8 0.037007414 9.83E-11 3.534169396 0.412754214 0.155495133 795.0982695 2.246102917 61.46859211 183.1687567 100000000 -8 3.534169396 VLT(ph)PELYAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTPELYAELR 11 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 1 VLT(1)PELYAELR;VLT(1)PELYAELR 141.58 0.00042544 22887100 47993 40509 43936 45554 39341 42362 48838 46636 39106 TRUE FALSE 45724.466 44636.91315 45950.50906 40974.82537 46202.05794 40894.99332 41386.86613 42552.30461 45170.35875 1.012267054 0.988190362 1.017271289 0.907117555 1.022840181 0.9053502 0.916239482 0.942040439 1 15.46308875 3.251929377 24.9997621 0.943283078 1.003020817 0.316823442 0.038779158 244.0343585 456344.9463 0.010076832 0.013565951 1786.197089 -3.251929377 0.059737739 VLT(ph)PPHDVDSLPHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 VLT(1)PPHDVDSLPHLR;VLT(1)PPHDVDSLPHLR 88.264 0.01279 142368000 75293 72412 72821 88054 68232 81976 90207 79737 24271 TRUE FALSE 71734.04911 79790.86513 76159.91488 79202.64463 80131.6392 79137.15056 76444.26538 72754.80557 28034.82272 2.558748091 2.846134107 2.716618387 2.825152326 2.858289492 2.822816158 2.726761148 2.595158396 1 14.77493233 0.455021082 1.721377277 0.999956458 2.766771316 0.975757804 0.086790447 0.569715256 1.643456447 0.083025732 0.023395314 2.851156668 -0.455021082 1.766814858 VLTANSNPSS(ph)PSAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.232)S(0.768)PSAAK;VLTANSNPS(0.07)S(0.93)PSAAK;VLTANSNPS(0.064)S(0.935)PS(0.001)AAK 317.31 2.30E-56 586930000 1301180 1375560 1177580 1523470 936200 1383190 1423700 1516290 1050130 TRUE FALSE 1239675.8 1515731.128 1231573.208 1370327.901 1099472.984 1335289.783 1206488.417 1383515.609 1212978.797 1.022009456 1.249594083 1.015329543 1.129721232 0.90642391 1.100835222 0.994649222 1.140593399 1 20.2101229 3.68088484 24.9999779 1.039872226 1.135802858 0.166382509 0.08811433 378.0486144 163867.6637 0.021132821 0.032738833 4796.062567 -3.68088484 0.095930632 VLTANSNPSS(ph)PSAAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTANSNPSSPSAAKR 16 1 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.052)S(0.677)PS(0.271)AAKR;VLTANSNPS(0.036)S(0.934)PS(0.03)AAKR 105.71 0.00077311 587400000 246490 234420 238700 279130 216927 243570 316350 288580 251470 TRUE FALSE 234838.9062 258307.6645 249644.6311 251071.3221 254759.0001 235135.1098 268084.9973 263310.4053 290466.6833 0.80848827 0.889285 0.859460467 0.864372186 0.877067887 0.809508021 0.922945772 0.906508114 1 18.14801317 0.99589571 1.039367034 0.998246491 0.854366534 0.692670897 0.03078664 0.299006659 0.681395115 0.026852659 0.008798005 9.905940375 -0.99589571 -0.143879956 VLTEFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTEFTR 7 0 Q96P70 Q96P70 IPO9 Importin-9 0 ; 101.69 0.020643 34863000 83325 74986 81265 79390 91211 78375 95212 82834 78252 FALSE TRUE 79386.39238 82627.15865 84991.08063 71409.56637 107118.1695 75660.8541 80685.66071 75580.61583 90386.9205 0.878295133 0.914149505 0.940302869 0.790043139 1.18510697 0.837077463 0.89266965 0.836189743 1 16.4638264 4.648915119 1.206753274 0.920671411 0.861984329 0.016451252 0.109839806 8.064417198 11.2546351 0.029213533 0.571247897 44556.9155 -4.648915119 -0.058687082 VLTEIIASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTEIIASR 9 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 91.265 0.025288 181255000 341440 284960 311030 330160 362010 318660 375100 322570 361000 FALSE TRUE 325300.8079 313997.748 325291.0332 296971.6895 425144.4294 307624.7243 317871.6058 294324.0607 416982.0363 0.780131467 0.753024641 0.780108026 0.712193005 1.019574927 0.737740952 0.762314868 0.705843502 1 18.66962571 -1.536280054 2.968649609 1.009197025 0.78045571 0.376641019 0.088387474 109991727 127100614.8 8185487.679 0.019339475 0.029088407 1.536280054 -0.228741314 VLTELLEQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 160.16 1.74E-05 181100900 254147 210664 220608 242953 278308 216771 272348 245345 295688 FALSE TRUE 242133.975 232130.9011 230723.095 218530.9029 326844.8271 209264.1659 230796.3106 223861.2911 341541.7849 0.708943929 0.679655935 0.67553402 0.639836508 0.956968786 0.612704434 0.675748388 0.655443349 1 18.38170257 -1.381785888 3.006758878 1.004141991 0.698670239 0.495897044 0.09484843 28436807.97 35588844.62 1032298.626 0.020735168 0.041515867 1.381785888 -0.305471752 VLTLSDDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;; 237.08 8.52E-12 216223000 293647 277366 264658 300604 329471 275077 338084 292852 355410 FALSE TRUE 279766.8883 305629.9107 276792.8311 270386.7148 386930.6381 265551.0145 286503.0765 267208.3264 410525.1676 0.681485352 0.744485198 0.674240833 0.658636147 0.942525985 0.646856845 0.697894061 0.650893898 1 18.64711114 -1.184162982 4.09186478 1.000125912 0.713275129 0.521463997 0.086659674 13.30161157 43413260.66 10730.14681 0.018631811 0.065439055 1.184162982 -0.286850783 VLTLSERPLDFLDLERPPT(ph)TPQNEEIR ddPTM_SK-BR-3_Trastuzumab_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;VLTLS(0.001)ERPLDFLDLERPPT(0.804)T(0.194)PQNEEIR 140.94 1.03E-05 138725000 37999 30805 35507 54586 58378 37296 44475 39605 46560 TRUE FALSE 36202.86258 33944.06452 37135.03107 49098.91157 68559.10472 36004.43017 37689.52191 36136.97624 53780.287 0.673162316 0.631161833 0.690495219 0.912953692 1.274799904 0.66947263 0.700805518 0.671937214 1 15.71478983 3.346519784 5.685196056 0.850416541 0.65409025 0.220704373 0.18091254 0.354595905 16.48919131 0.052668724 0.07154096 2220.852848 -3.346519784 -0.196326292 VLTLSERPLDFLDLERPPTT(ph)PQNEEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.035)T(0.965)PQNEEIR;VLTLSERPLDFLDLERPPT(0.17)T(0.83)PQNEEIR;VLTLSERPLDFLDLERPPT(0.046)T(0.954)PQNEEIR 230.88 2.13E-33 436875000 219088 161845 178020 297901 300293 195952 259496 202710 288393 TRUE FALSE 208732.1444 178337.1895 186182.3931 267955.4255 352664.0041 189166.1331 219905.1192 184959.6378 333115.5135 0.626605895 0.535361405 0.558912406 0.804391914 1.058683819 0.567869479 0.660146737 0.555241741 1 18.34566302 3.246684617 24.78734554 0.749993454 0.572995324 0.239661096 0.164793059 259.6657065 792267.2259 0.045363382 0.060363861 1764.755795 -3.246684617 -0.176998131 VLTPEEQLADKLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 197.25 1.23E-07 895090000 911030 684050 788890 839770 825350 823650 1081380 937690 989300 FALSE TRUE 867967.4174 753755.4727 825061.3868 755354.7241 969290.7787 795126.794 916395.6201 855580.8926 1142715.591 0.759565568 0.659617737 0.722018141 0.661017256 0.848234492 0.695822128 0.801945495 0.748726016 1 20.12403495 -2.014719804 0.252170794 1.306125487 0.695057545 0.697133912 0.055746321 15.87134715 0.595404191 2.900607237 0.07615424 0.009666744 2.014719804 -0.611067942 VLTPELYAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VLTPELYAELR 11 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 0 ;;; 89.08 0.029081 94686000 127875 112275 105470 125015 152324 98259 142247 116824 131189 FALSE TRUE 121830.6022 123715.9501 110305.9038 112448.2547 178889.2574 94856.26619 120544.6076 106594.2712 151533.1201 0.803986627 0.816428449 0.727932638 0.742070477 1.180529097 0.625977121 0.79550007 0.703438767 1 17.20927363 -2.364077108 2.300329461 2.371745248 0.800641571 0.156019008 0.14654336 8964356.631 863328.7284 64485650.33 0.032181949 0.00432437 2.364077108 -1.571103677 VLVALYEEPEKPNSALDFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLVALYEEPEKPNSALDFLK 20 1 A0A087WV05;Q99417 A0A087WV05 MYCBP C-Myc-binding protein 0 185.13 3.43E-17 44814000 167220 134690 151130 187350 102160 189000 199300 191020 100380 FALSE TRUE 159315.842 148415.0641 158059.46 168517.2221 119976.6717 182454.8826 168893.1246 174293.2761 115946.4177 1.374047126 1.280031475 1.363211241 1.453406025 1.034759624 1.573613797 1.456648061 1.503222605 1 16.82309872 VLVDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLVDVER 7 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 84.097 0.050705 50193000 132360 105630 111600 134500 146560 118780 139530 130070 152230 FALSE TRUE 126103.6051 116393.8171 116716.9704 120979.8045 172120.0176 114666.6188 118242.1359 118680.3813 175837.0509 0.717161738 0.661941363 0.663779162 0.688022256 0.978860921 0.652118642 0.672452906 0.674945244 1 17.42387957 -1.441401764 3.217281988 1.004610499 0.709387967 0.466160519 0.096202459 102298611.7 133743830.1 4310194.379 0.022365048 0.036190804 1.441401764 -0.295222531 VLVPEHEKDVLEWIACVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLVPEHEKDVLEWIACVR 18 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 151.57 2.81E-08 146098000 251480 274620 245550 292780 227760 249130 273800 275670 208122 FALSE TRUE 239593.0388 302604.0902 256808.7104 263349.1982 267481.2719 240502.5656 232026.7813 251530.8734 240396.4968 0.99665778 1.258770798 1.068271434 1.095478518 1.112667096 1.000441224 0.965183704 1.046316717 1 17.87505635 2.235958654 6.394915961 0.995821833 1.115254923 0.362459667 0.067303776 0.141348219 24.48230122 0.02398516 0.018685451 172.1704658 -2.235958654 0.11943309 VLVTVEEDDTIMEELVDNHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VLVTVEEDDTIMEELVDNHGK 21 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;;; 348.17 2.76E-95 225477600 312824 319020 268724 341995 230998 280273 324364 328534 228206 FALSE TRUE 298037.4295 351528.5007 281045.2612 307617.0129 271283.9781 270567.0757 274876.3144 299765.8213 263595.021 1.130664109 1.333593098 1.066200948 1.167006159 1.029169584 1.026449873 1.042797825 1.137221106 1 18.00796359 3.320855972 1.61035368 1.052175153 1.22553581 0.4167248 0.074699627 0.292149852 1.562975222 0.022768439 0.034987724 2093.418086 -3.320855972 0.173360657 VLVTVEEDDTIMEELVDNHGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VLVTVEEDDTIMEELVDNHGKK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;; 356.18 1.90E-96 653981900 902115.2 682518.2 781744.2 868839.4 590737.8 885894.3 1082953 1014395 606242.2 FALSE TRUE 859474.0023 752067.5805 817587.9448 781502.0128 693762.2853 855215.5583 917728.6301 925569.1962 700255.1441 1.227372636 1.073990797 1.167557214 1.116024665 0.990727867 1.221291361 1.310563211 1.321759938 1 19.41752115 2.021514616 24.98005081 1.250442909 1.120805733 0.137967074 0.107548012 299.618564 347877.7985 0.036655253 0.027069597 105.0786817 -2.021514616 -0.129637177 VLVVHDGFEGLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VLVVHDGFEGLAK 13 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0;F8VP00 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 212.9 3.83E-07 0 541680 505230 469690 595620 444690 527200 556930 595040 427940 FALSE TRUE 516075.8599 556713.5114 491225.7511 535747.146 522243.7952 508942.9318 471960.0998 542935.1431 494302.7496 1.044048127 1.126260196 0.993775073 1.083844155 1.056526179 1.029617845 0.954799665 1.098385845 1 18.91503541 2.179540901 3.730229003 1.00868837 1.066726893 0.133583993 0.048149729 0.319744239 9.02604572 0.017932906 0.013011341 151.1962088 -2.179540901 0.058038523 VLVWDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VLVWDLR 7 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 119.89 0.01089 214609000 910340 762690 595340 664450 1131970 599370 1186650 800720 1150290 FALSE TRUE 867310.0323 840408.9781 622636.9279 597658.2236 1329385.21 578613.6666 1005604.748 730604.7119 1328671.098 0.652765032 0.632518446 0.468616295 0.44981653 1.000537463 0.435482993 0.756850021 0.549876273 1 20.34155259 -4.999999939 0.318956714 4.531233672 0.608429734 0.33322307 0.168907657 360.793967 3.202741473 859.4748407 0.134749293 1.00E-05 4.999999939 -3.922803939 VLWLADCDVSDSSCSSLAATLLANHSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VLWLADCDVSDSSCSSLAATLLANHSLR 28 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;; 363.88 2.49E-127 553330000 536653 415087 477517 518131 516805 445478 564020 553148 534195 FALSE TRUE 511286.4762 457384.8372 499411.6268 466047.4875 606935.6284 430050.9852 477968.3901 504711.4287 617035.2323 0.828617961 0.741262108 0.809372951 0.755301258 0.983632047 0.696963419 0.774620905 0.817962091 1 19.23499334 0.866161734 6.579592021 0.999999634 0.794030669 0.407530399 0.075619217 3.493754519 171.6622023 0.066275176 0.016636265 7.347874566 -0.866161734 -0.205968965 VLYIDIDIHHGDGVEEAFYTTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VLYIDIDIHHGDGVEEAFYTTDR 23 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;;; 89.483 0.0033669 42342500 36154.1 36548.4 32686.5 43039.7 40435.6 38274.4 36778.6 33797.3 25076.5 FALSE TRUE 34445.16734 40272.72351 34185.20836 38713.26759 47487.55584 36948.94793 31167.34908 30837.82924 28965.23555 1.189189961 1.390381357 1.1802151 1.336542474 1.639467277 1.275630846 1.076026088 1.064649697 1 14.82203478 1.750805613 3.747413038 1.046467937 1.338907753 0.540079396 0.12670611 0.16938857 4.986835837 0.068552488 0.034102054 56.33854327 -1.750805613 0.292439816 VMALELGPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMALELGPHK 10 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ; 120.09 0.00060585 621370000 2602500 2180170 2041160 2521210 2320310 2583570 3321200 2941960 2544010 FALSE TRUE 2479484.983 2402331.802 2134749.205 2267773.181 2724971.329 2494100.323 2814489.942 2684346.386 2938522.078 0.843786406 0.817530629 0.726470365 0.771739371 0.927327159 0.84876011 0.95779098 0.913502201 1 21.48665931 2.108884945 1.042605867 0.964068322 0.800545183 0.65225143 0.049679102 0.343234494 0.695177901 0.037350803 0.018942227 128.4946202 -2.108884945 -0.163523139 VMDQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VMDQHK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 106.84 0.03178 1451690000 3267270 2379020 1699445 2152640 2350720 2124170 3349080 2841940 2479460 FALSE TRUE 3112832.622 2621444.843 1777366.234 1936252.537 2760684.824 2050609.46 2838116.336 2593084.668 2863961.993 1.086897322 0.9153211 0.620597005 0.676074802 0.963939057 0.716004425 0.990975558 0.905418673 1 21.44958092 1.618416371 25 0.961146366 0.85084318 0.159308649 0.141388082 1.82717018 4318.710892 0.071569097 0.039160597 41.5352062 -1.618416371 -0.110303186 VMDS(ph)DEDDDY ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VMDSDEDDDY 10 0 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 VMDS(1)DEDDDY;VMDS(1)DEDDDY;VMDS(1)DEDDDY;VMDS(1)DEDDDY 265.58 1.29E-17 952170000 1286040 1184760 1131640 1367420 1166640 1246810 1256760 1220780 1169230 TRUE FALSE 1225251.438 1305488.391 1183526.813 1229964.344 1370101.647 1203632.657 1065018.18 1113882.031 1350548.217 0.907225246 0.9666359 0.876330662 0.91071487 1.014478143 0.891217834 0.788582123 0.824762876 1 20.36511372 1.999209881 24.99454684 0.845693081 0.934718926 0.133054048 0.066359185 34.24244998 1083245.374 0.022706971 0.016565891 99.81823387 -1.999209881 0.089025845 VMEGLDAFDDLMQHTHIQPWYLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMEGLDAFDDLMQHTHIQPWYLR 23 0 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 274.8 6.03E-52 533930000 631160 529410 562020 647770 698420 494840 642260 501790 28837.4 FALSE TRUE 601326.3176 583357.4809 587789.1729 582654.9289 820224.2269 477703.5667 544271.4411 457850.6074 33309.35671 18.05277487 17.51332174 17.6463682 17.49223001 24.62443913 14.34142277 16.3398965 13.74540528 1 15.02363987 0.581197033 0.904608421 0.949936386 18.41679659 0.825363069 2.482496998 0.515994786 0.680103883 2.262451555 0.740981766 3.812387463 -0.581197033 17.4668602 VMEHFIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VMEHFIK 7 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 105.39 0.0079373 3828990000 11325290 9073810 9488880 11310520 9514580 9818050 12282040 10679040 9208510 FALSE TRUE 10789965.99 9998441.555 9923954.534 10173565.04 11173919.74 9478048.467 10408189.22 9743926.644 10636518.7 1.014426458 0.940010716 0.933007764 0.956475077 1.050524147 0.891085583 0.978533439 0.916082312 1 23.3425227 2.201615597 24.99987267 0.94635586 0.973714031 0.10646251 0.045377185 451.855099 305757.5854 0.015850515 0.011706732 159.0800054 -2.201615597 0.027358171 VMEIVDADEKVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VMEIVDADEKVR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 121.04 0.00034958 433320000 375300 293663 356085 383450 345057 370590 458370 435200 406830 FALSE TRUE 357560.3128 323587.5936 372411.8495 344904.8775 405234.8316 357756.3754 388437.238 397091.5809 469919.1186 0.760897564 0.688602742 0.792502017 0.733966472 0.862350169 0.761314791 0.826604457 0.845021122 1 18.84205294 -0.879319479 0.182306418 1.195477071 0.685400523 0.780261955 0.040114892 7.840182834 0.330320463 0.906516633 0.143864311 0.132032401 0.879319479 -0.510076547 VMEKPSPLLVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 62.042 0.073486 315670000 371010 299280 290960 353650 333430 344130 421420 421280 392030 FALSE TRUE 353473.0926 329776.9723 304300.8038 318100.4301 391580.0864 332212.6918 357124.6391 384390.4899 452824.0102 0.780597063 0.728267417 0.672006777 0.702481368 0.864751156 0.733646371 0.788661005 0.848873914 1 18.78859093 0.645067976 0.627361742 1.00618555 0.735900722 0.727247662 0.049790645 0.707003269 0.534029618 0.055448575 0.020079369 4.416395674 -0.645067976 -0.270284828 VMES(ph)MLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMESMLK 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 VMES(1)MLK;VMES(1)MLK 74.335 0.030938 482580000 684080 525890 561080 622100 1101970 451870 729460 486520 1135250 TRUE FALSE 651744.8941 579478.7889 586806.073 559565.3261 1294153.219 436221.6286 618167.4795 443917.7296 1311298.772 0.497022424 0.441912096 0.447499903 0.426726035 0.986924755 0.332663797 0.471416197 0.338532865 1 20.322565 -1.896569453 2.433496627 1.284825745 0.491293393 0.429956126 0.183515925 29635504.69 15599374.93 48368965.5 0.041604232 0.012689092 1.896569453 -0.793532352 VMEYINR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VMEYINR 7 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 157.99 0.003347 154760000 180430 187790 160660 206630 197490 179110 200210 179340 204160 FALSE TRUE 171901.4315 206926.0145 168026.4199 185859.1598 231932.1935 172907.3758 169664.2874 163636.0389 235820.0901 0.728951598 0.877474071 0.712519531 0.788139635 0.983513293 0.733217326 0.719464942 0.693902028 1 17.8473271 -0.295734245 7.522768165 1.00000501 0.782903708 0.375974317 0.089128153 0 0 0.083901922 0.019775873 0.506134283 0.295734245 -0.217101302 VMFEVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMFEVWR 7 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 95.62 0.031016 89945000 251040 224629 156703 197376 262290 180028 266810 226656 225140 FALSE TRUE 239173.8367 247518.9505 163887.9876 177535.3895 308033.293 173793.5852 226103.2342 206808.7991 260053.5613 0.919709907 0.951799888 0.630208587 0.682687784 1.184499421 0.668299193 0.869448713 0.795254631 1 17.98844927 3.877421307 19.70640745 0.825582516 0.935813952 0.061304105 0.165308903 8.735143153 1363.480718 0.039289982 0.070831356 7540.867456 -3.877421307 0.110231436 VMHETVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VMHETVK 7 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 108.24 0.0072977 59527000 187160 151900 148150 184610 211260 150230 196920 158130 176640 FALSE TRUE 178313.3177 167378.7827 154942.824 166052.6521 248103.6771 145027.4974 166876.2373 144283.2989 204032.429 0.873945963 0.820353821 0.759402928 0.813854213 1.216001193 0.710806111 0.817890754 0.707158659 1 17.63843895 -1.14266242 4.195736374 1.000032172 0.840760797 0.109634516 0.143343764 5.03E-05 1.03E-05 0.129319707 0.030473247 0.072000843 1.14266242 -0.159271375 VMLGET(ph)NPADSKPGTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 1 VMLGET(0.999)NPADS(0.001)KPGTIR;VMLGET(1)NPADSKPGTIR;VMLGET(1)NPADSKPGTIR 152.81 3.21E-07 707850000 345797 325629 316881 350071 294399 384871 407824 360389 330901 TRUE FALSE 329451.8611 358810.9653 331410.3073 314881.198 345742.0924 371542.8208 345602.9586 328831.4286 382215.4371 0.86195331 0.938766283 0.867077243 0.823831712 0.904573858 0.972076962 0.904209838 0.860330057 1 18.54402652 2.47828077 24.9997467 0.927066531 0.880528695 0.266557691 0.046492014 74.18486729 1599525.792 0.015526283 0.013157868 300.8020349 -2.47828077 -0.046537836 VMLGETNPADSKPGTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 211.78 1.98E-12 5441350000 2667760 2345940 2213590 2667630 1968520 2481870 2879020 2565140 2328290 FALSE TRUE 2541660.272 2584993.953 2315085.291 2399474.764 2311829.265 2395922.22 2439772.622 2340522.743 2689349.322 0.945083724 0.961196797 0.860834728 0.892213869 0.859624016 0.890892901 0.90719811 0.870293317 1 21.35882573 3.752919942 24.50764144 0.892282436 0.953140268 0.243880955 0.040133604 640.555387 1093257.742 0.008934477 0.016009105 5661.349185 -3.752919942 0.060857832 VMPNS(ph)PQNGVLVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VMPNSPQNGVLVK 13 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 VMPNS(1)PQNGVLVK 150.39 1.40E-06 0 150350 130180 135690 156110 114100 136180 170000 156530 152910 TRUE FALSE 143243.2535 143445.49 141911.5207 140417.5262 133999.0039 131464.0525 144063.3777 142823.4034 176622.5018 0.811013614 0.812158635 0.803473619 0.795014932 0.758674588 0.744322219 0.815656987 0.808636509 1 17.43030963 0.425072239 1.62994319 0.999989483 0.792751363 0.888538738 0.023068292 1.432983728 3.691256648 0.023691551 0.006736651 2.661167673 -0.425072239 -0.207238119 VMQEQGTHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VMQEQGTHPK 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 147.28 2.72E-05 3355280000 7031510 5656380 5937620 7091930 5532070 6566590 7908240 7085940 5775570 FALSE TRUE 6699144.457 6232771.553 6209865.75 6379035.723 6496861.256 6339187.342 6701692.743 6465457.529 6671215.898 1.004186427 0.934278196 0.930844668 0.95620286 0.973864638 0.950229679 1.004568409 0.969157291 1 22.6695183 1.74517548 25 0.990316628 0.958497641 0.325846518 0.022343536 1.728368455 6552.795201 0.010342256 0.005735322 55.61289196 -1.74517548 -0.031818987 VMS(ph)KSAADLISQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VMSKSAADLISQAR 14 1 Q14195-2;Q14195 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 VMS(0.5)KS(0.5)AADLISQAR 55.196 0.081535 475410000 108080 124930 136920 102010 497340 52824 135640 54467 413890 TRUE FALSE 102971.2726 137660.509 143197.9174 91755.76099 584075.9385 50994.69163 114945.6268 49697.58073 478073.9473 0.215387752 0.287948151 0.299530895 0.191927967 1.221727186 0.106666954 0.240434827 0.103953752 1 18.86687426 -2.227885485 2.228504006 3.16708737 0.326989606 0.295818634 0.323059859 28955478.49 4809672.433 316520748.1 0.082212077 0.005917176 2.227885485 -2.840097763 VMS(ph)PENFPTASVEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMSPENFPTASVEGK 15 0 H3BRU9;H3BSP3;H3BTW3;Q3L8U1-2;Q3L8U1-3;Q3L8U1 H3BRU9 CHD9 Chromodomain-helicase-DNA-binding protein 9 1 VMS(1)PENFPTASVEGK;VMS(0.998)PENFPT(0.001)ASVEGK 160.64 1.78E-06 64345000 140462 128762 121845 155872 94412 136186 152100 153684 101192 TRUE FALSE 133822.6396 141882.9942 127431.7138 140203.4504 110877.4229 131469.8447 128894.3515 140226.6142 116884.3385 1.144915061 1.213875152 1.090237712 1.199505872 0.948608037 1.124785804 1.102751259 1.199704049 1 16.83472211 -4.999879509 0.018995801 5.45E-06 1.927321555 0.18571336 0.077709946 5299.701213 7.621608919 513.4409906 289.4819361 1.00E-05 4.999879509 1.927316102 VMTIPYQPMPAS(ph)SPVICAGGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.651)S(0.349)PVICAGGQDR;VMTIPYQPMPAS(0.718)S(0.282)PVICAGGQDR 138.71 8.66E-06 349050000 421460 369280 409420 435330 444590 424760 478350 434850 540490 TRUE FALSE 401538.4211 406910.0518 428192.312 391569.8013 522126.3552 410050.4547 405368.922 396772.2287 624306.4288 0.643175214 0.651779372 0.685868817 0.627207703 0.836330256 0.656809598 0.649310825 0.635540834 1 19.2518948 -2.018831028 2.431578233 1.365510296 0.67104596 0.744564297 0.060133273 4399500.093 1778182.43 8975754.339 0.014034276 0.009575666 2.018831028 -0.694464336 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.086)S(0.914)PVICAGGQDR;VMTIPYQPMPAS(0.002)S(0.998)PVICAGGQDR;VMTIPYQPMPAS(0.034)S(0.966)PVICAGGQDR;VMTIPYQPMPAS(0.186)S(0.814)PVICAGGQDR;VMTIPYQPMPAS(0.252)S(0.748)PVICAGGQDR;VMTIPYQPMPAS(0.413)S(0.587)PVICAGGQDR;VMTIPYQPMPAS(0.049)S(0.951)PVICAGGQDR;VMTIPYQPMPAS(0.085)S(0.915)PVICAGGQDR;VMTIPYQPMPAS(0.031)S(0.969)PVICAGGQDR 234.71 2.89E-37 2104900000 2008509 1729263 1876885 2125845 2135950 1886047 2244180 2090330 2413850 TRUE FALSE 1913570.76 1905476.866 1962942.034 1912151.022 2508459.004 1820732.719 1901789.124 1907289.624 2788177.53 0.686315968 0.683413034 0.704023332 0.685806769 0.899676931 0.653018934 0.682090399 0.684063193 1 21.41089099 -1.325784967 4.061402666 1.000536311 0.706454393 0.636747995 0.068842786 0.000317085 5.26E-05 0.063221864 0.014874744 0.047229683 1.325784967 -0.294081918 VMWS(ph)GLIPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VMWSGLIPK 9 0 H7BXX0;Q7Z407-5;Q7Z407-3;Q7Z407-4;Q7Z407-2;Q7Z407 H7BXX0 CSMD3 CUB and sushi domain-containing protein 3 1 VMWS(1)GLIPK 70.594 0.04316 0 48974 28786 41179 41868 42903 42690 65945 52216 65172 TRUE FALSE 46659.09608 31719.32613 43067.09788 37659.3491 50385.26962 41211.6346 55883.87909 47643.69023 75278.54091 0.619819347 0.42135947 0.57210325 0.500266725 0.66931783 0.547455279 0.742361348 0.632898694 1 16.19995104 0.409704195 0.377843549 1.056667217 0.506768546 0.767709012 0.075622322 1.168764998 0.308825249 0.191334669 0.055958447 2.568645643 -0.409704195 -0.549898671 VNCLDKFWHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNCLDKFWHK 10 1 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 124.42 0.00026195 258670000 528900 344130 381630 416090 407950 441230 658270 535960 415010 FALSE TRUE 503899.9452 379197.2382 399128.113 374263.8427 479096.3508 425950.0945 557838.8215 489028.5011 479367.6312 1.051176409 0.791036385 0.832613817 0.78074492 0.999434087 0.888566659 1.163697307 1.020153363 1 18.87077297 1.756778958 25 1.074141298 0.889191098 0.421054331 0.093939087 6.549988384 8997.328289 0.042335678 0.023477701 57.11878457 -1.756778958 -0.1849502 VNDAEPGS(ph)PEAPQGK ddPTM_SK-BR-3_Trastuzumab_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 289.77 7.36E-44 1713090000 4052270 3869510 3863720 4620230 2705600 4494990 4640400 4650900 3232450 TRUE FALSE 3860727.228 4263817.468 4040875.384 4155795.703 3177455.783 4339327.369 3932421.753 4243642.54 3733721.837 1.034015761 1.141975127 1.082264711 1.113043736 0.851015668 1.162198889 1.053217654 1.13657169 1 21.83218302 -2.565250373 2.007275999 0.000329541 1.073320368 0.061482103 0.087964579 1374668.116 149166.4532 6377044.076 0.019993985 0.002721132 2.565250373 1.072990827 VNDDIIVNWVNETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNDDIIVNWVNETLR 15 0 P13796;P13796-2 P13796 LCP1 Plastin-2 0 151.54 6.95E-06 29970000 90818 74545 53351 71722 72102 70467 107680 83907 83951 FALSE TRUE 86525.21312 82141.22025 55797.19612 64512.3683 84676.56597 68026.71012 91251.43832 76559.65826 96969.69232 0.892291303 0.847081374 0.575408613 0.66528383 0.873227128 0.701525482 0.941030503 0.789521514 1 16.56524629 0.938141932 0.819568238 0.992067506 0.775663811 0.28730696 0.110277686 1.037752216 1.513083301 0.108678534 0.039069596 8.672452538 -0.938141932 -0.216403695 VNFDDYTVNLGGLKDHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNFDDYTVNLGGLKDHIK 18 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 216.96 5.22E-19 191670000 680530 708150 625610 791550 422360 730160 728580 824490 426190 FALSE TRUE 648362.6956 780311.2901 654294.8373 711981.8902 496019.4503 704874.3761 617421.7397 752293.2847 492281.3685 1.317057149 1.585092063 1.329107456 1.446290548 1.007593385 1.431852638 1.254204971 1.528177446 1 18.90912361 -4.052705757 0.193553278 5.53E-16 1.433782649 0.298524533 0.164325318 108.609578 1.485815758 43.40636852 0.40508529 8.86E-05 4.052705757 1.433782649 VNFEDDSR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 156.01 0.00093025 619250000 1235990 1011280 1031960 1295600 1143710 1044970 1332400 1210920 1298810 FALSE TRUE 1177567.202 1114330.582 1079276.387 1165363.827 1343172.662 1008782.427 1129117.909 1104885.425 1500222.821 0.784928202 0.742776717 0.719410724 0.776793827 0.895315444 0.672421731 0.752633471 0.736480881 1 20.51674536 -0.993087065 4.646743108 1.000005049 0.758950162 0.634644952 0.057199098 2.80E-06 6.06E-07 0.05180654 0.012210663 0.101604498 0.993087065 -0.241054888 VNFPENGFLS(ph)PDKLSLLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNFPENGFLSPDKLSLLEK 19 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 VNFPENGFLS(1)PDKLSLLEK;VNFPENGFLS(1)PDKLSLLEK 245.09 8.96E-25 404530000 789090 840080 753380 937080 425850 932370 977340 1041510 489420 TRUE FALSE 751791.2795 925685.1071 787923.2182 842882.9381 500118.1052 900081.7931 828228.8329 950309.863 565316.754 1.329858481 1.637462715 1.393772982 1.490992319 0.884668819 1.592172506 1.465070382 1.681021934 1 19.10869993 VNFTVDQIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNFTVDQIR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 119.75 0.0018078 300330000 779660 566280 401520 430450 833820 500160 910570 646880 763530 FALSE TRUE 742807.0169 623984.5758 419930.0892 387180.3482 979237.944 482839.3338 771645.8227 590235.7579 881934.3328 0.842247534 0.707518182 0.476146663 0.439012672 1.110329769 0.547477648 0.874947027 0.669251367 1 19.75031171 2.759717355 24.99686011 0.811922369 0.648776226 0.236706367 0.192458324 1576.428895 1862561.175 0.056825478 0.060217242 575.0655544 -2.759717355 -0.163146144 VNGDAS(ph)PAAAESGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK 214.46 2.59E-12 240160000 760210 1001780 774090 1056540 479140 943270 818250 914490 520060 TRUE FALSE 724276.3799 1103862.521 809582.7922 950334.5919 562701.8643 910604.3234 693410.9343 834412.4076 600708.2487 1.205704069 1.837601736 1.347713793 1.582023543 0.93673071 1.5158845 1.154322312 1.389047694 1 19.19630495 2.776095521 24.99854462 1.2304214 1.51061429 0.277985312 0.231736869 718.2021312 478326.9558 0.064136071 0.068025116 597.1666165 -2.776095521 0.280192889 VNGDDHHEEDMDMS(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 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;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D 358.74 9.67E-83 13690479000 7386472 6392190 6890576 7607921 6528897 6920655 7859364 7017236 2186810 TRUE FALSE 7037328.107 7043561.428 7206515.725 6843158.327 7667534.57 6680990.982 6660273.675 6402769.615 2525929.326 2.786035236 2.78850297 2.853015582 2.709164606 3.035530128 2.644963544 2.636761688 2.534817403 1 21.26838284 0.030110273 0.70894525 0.934465736 2.817051823 0.969641868 0.098641306 0.63575586 0.348699857 0.199018019 0.032274378 1.071791412 -0.030110273 1.882586088 VNGRPLEMIEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VNGRPLEMIEPR 12 1 P62249;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;;;;; 156.81 5.84E-05 4904180000 5681840 5021170 4990490 5653380 5403910 5146810 6199320 5689790 5716900 FALSE TRUE 5413270.684 5532832.932 5219308.903 5085091.502 6346350.193 4968574.679 5253499.876 5191561.824 6603447.654 0.819764306 0.83787034 0.790391501 0.770066148 0.961066177 0.752421302 0.795569247 0.786189593 1 22.65478802 -1.093634395 4.137377807 1.000028772 0.814784289 0.508842395 0.057374882 7191959.716 1901053.366 2126.062065 0.012355496 0.080605672 1.093634395 -0.185244483 VNHEPEPAGGATPGATLPKS(ph)PSQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNHEPEPAGGATPGATLPKSPSQLR 25 1 O00499-6;O00499-11;O00499-2;O00499 O00499-6 BIN1 Myc box-dependent-interacting protein 1 1 VNHEPEPAGGATPGAT(0.002)LPKS(0.994)PS(0.004)QLR 201.1 3.83E-25 134470000 232950 154670 210230 214770 185790 212930 253910 224240 190060 TRUE FALSE 221938.9152 170431.0488 219869.2534 193180.9116 218191.7172 205556.1807 215171.3661 204604.3568 219533.5341 1.010956782 0.776332643 1.001529239 0.879960833 0.993887873 0.936331579 0.980129833 0.931995914 1 17.74408181 2.930342412 1.547882514 0.965418271 0.904153941 0.076944189 0.069513145 0.780931411 3.802656184 0.024431449 0.027453277 851.8093675 -2.930342412 -0.06126433 VNHPGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNHPGSK 7 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 86.953 0.019698 123134000 178821 153743 150325 190988 150791 152093 210683 173206 175454 FALSE TRUE 170368.4857 169409.5865 157217.5499 171789.5234 177088.9027 146825.9813 178539.4389 158039.1644 202662.5102 0.840651216 0.835919709 0.7757604 0.847663059 0.873811848 0.724485161 0.880969246 0.779814502 1 17.62871971 -2.119572449 2.168226166 1.32028481 0.823685359 0.57917628 0.048153341 2670800.567 690561.5679 4210136.764 0.010377856 0.007593247 2.119572449 -0.49659945 VNIAFNYDMPEDSDTYLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VNIAFNYDMPEDSDTYLHR 19 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;; 218.37 2.57E-19 1769566000 1866380 1551031 1662708 1890123 1843647 1727337 2093760 1832561 1881244 FALSE TRUE 1778159.916 1709082.822 1738944.806 1700124.245 2165178.453 1667518.887 1774318.457 1672092.244 2172977.711 0.81830564 0.786516499 0.800258925 0.78239378 0.996410797 0.767388859 0.816537808 0.769493509 1 21.05124195 -2.299136654 2.363674715 1.936851755 0.816099153 0.43033206 0.066101125 3152545.081 611047.0391 15830954.5 0.014704853 0.005021845 2.299136654 -1.120752602 VNIKPQVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VNIKPQVDR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 125.97 0.00044384 6060430000 12902640 12821360 11721660 13315500 9143430 13365350 13021300 13995300 9628260 FALSE TRUE 12292757.78 14127871.16 12259109.71 11977000.64 10738041.3 12902504.58 11034661.53 12769797.34 11121361.39 1.105328507 1.270336488 1.102302972 1.076936557 0.965532989 1.16015514 0.992204205 1.148222497 1 23.40683007 3.51162191 4.961329439 1.057189453 1.188733143 0.34368009 0.07372403 0.18099698 11.16446615 0.018074713 0.027346342 3248.044043 -3.51162191 0.13154369 VNIVDLQQVINVDLIHIENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNIVDLQQVINVDLIHIENR 20 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 138.3 2.05E-06 76799100 73124 83962 78787 71441 76232 75183 81218 72326 65810 FALSE TRUE 69667.57344 92517.82326 82399.46188 64259.61495 89526.83666 72579.39386 68826.70243 65992.75202 76015.47869 0.916491939 1.217091898 1.083982674 0.84534908 1.177744825 0.954797564 0.905430099 0.868148871 1 16.2140056 2.017198994 24.77331323 0.918042351 1.052838151 0.209563639 0.11282161 294.8383861 424681.2208 0.040388613 0.029822266 104.0396767 -2.017198994 0.1347958 VNIVFNYDMPEDSDTYLHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VNIVFNYDMPEDSDTYLHR 19 0 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 177.73 3.95E-14 618150000 590066 485965 540908 625134 665224 519683 614307 557606 583673 FALSE TRUE 562174.7496 535485.386 565709.1668 562294.3426 781238.855 501686.2474 520583.1846 508779.0626 674186.0279 0.833857016 0.79426948 0.839099512 0.834034405 1.158788261 0.744136228 0.77216549 0.754656788 1 19.3627872 -0.5497776 5.872456269 1 0.836724563 0.150748899 0.117862516 8.22E-10 1.40E-10 0.110301804 0.025998384 0.281982658 0.5497776 -0.163275437 VNKDDIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VNKDDIQK 8 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;;;;; 121.73 0.0012956 6436870000 15135420 12763270 12987760 16101380 8795710 15573190 16432170 16406290 10046250 FALSE TRUE 14419998.69 14063861.72 13583261.64 14482838.69 10329679.04 15033886.53 13925140.67 14969668.27 11604171.14 1.2426565 1.211966073 1.170549924 1.248071794 0.890169484 1.295558842 1.20001166 1.290024776 1 23.46814014 3.850573418 1.551088991 1.165414514 1.237716381 0.05211529 0.126264033 1.470412553 6.759238278 0.035128343 0.094551381 7088.811332 -3.850573418 0.072301867 VNKNDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNKNDIR 7 1 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 0 83.801 0.020076 115310000 763640 610410 650270 763330 613910 687880 853360 746030 689990 FALSE TRUE 727544.2506 672611.473 680085.5227 686598.6182 720975.7096 664058.5431 723164.259 680703.6582 796990.1252 0.912864824 0.843939532 0.853317376 0.861489492 0.90462314 0.833207994 0.907369158 0.854092964 1 19.60420232 -4.999977212 0.51524769 5.513014337 0.871524963 0.673052119 0.028117656 1648.162593 7.213576939 8601.344153 0.011679407 1.00E-05 4.999977212 -4.641489374 VNKPPYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNKPPYPK 8 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2;P13796 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 ; 94.302 0.0095355 901110000 3303700 2121030 1963750 2748300 2358250 2491400 3723700 3239500 2933000 FALSE TRUE 3147540.648 2337165.368 2053789.88 2472035.663 2769528.053 2405122.193 3155581.175 2955832.206 3387834.66 0.929071506 0.689869962 0.606224945 0.729680138 0.817492095 0.709929036 0.931444858 0.872484198 1 21.69193204 1.693811019 6.190692833 0.926842688 0.751228557 0.493498861 0.089208016 0.130617078 11.14125034 0.046799659 0.023724344 49.40956367 -1.693811019 -0.175614131 VNLEESSGVENS(ph)PAGARPK ddPTM_SK-BR-3_Trastuzumab_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 231.25 2.30E-20 714820000 293213 298345 273013 346620 201007 298214 275898 286879 222333 TRUE FALSE 279353.4026 328746.6947 285530.9161 311777.0991 236062.5572 287886.7744 233804.6929 261758.3539 256811.2661 1.087777054 1.280110097 1.111831737 1.214032016 0.919206391 1.121005238 0.910414471 1.019263515 1 17.97034897 2.745718914 24.96041838 0.992622937 1.178276052 0.571206054 0.077206769 355.3889676 1239213.766 0.021619417 0.02249847 556.8252414 -2.745718914 0.185653116 VNLFPGLS(ph)PSALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VNLFPGLS(0.959)PS(0.041)ALK;VNLFPGLS(0.914)PS(0.086)ALK 210.08 3.44E-08 535250000 1213130 1352700 1291580 1419540 981130 1330140 1533290 1480950 1197360 TRUE FALSE 1155787.749 1490541.668 1350800.221 1276845.142 1152238.761 1284076.918 1299358.45 1351270.167 1383040.474 0.835686136 1.077728162 0.976688858 0.923216035 0.833120059 0.928444932 0.939494161 0.97702865 1 20.39941195 1.108502768 3.011139075 0.999277609 0.936627473 0.10901845 0.068859909 0.629825766 10.80959272 0.066148873 0.017695927 12.83815954 -1.108502768 -0.062650136 VNLLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNLLYSR 7 0 Q13011;M0R248 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 89.296 0.041823 59541000 106280 88657 64476 77906 93334 72768 116940 97606 98215 FALSE TRUE 101256.355 97691.24909 67432.28838 70074.74087 109611.42 70248.02591 99098.65525 89059.1012 113445.6806 0.892553639 0.861127974 0.59440155 0.617694217 0.966201794 0.619221689 0.873533966 0.785037392 1 16.79164215 0.302647367 1.030640912 1.000614035 0.780539131 0.230715457 0.128683942 5.21719702 6.295046597 0.12789235 0.037932638 2.007462157 -0.302647367 -0.220074904 VNMEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 113.14 0.014418 125947000 620770 527810 466820 593140 676080 510940 737960 600650 749440 FALSE TRUE 591427.4323 581594.4391 488224.1587 533516.4403 793988.1379 493246.0197 625370.6484 548053.9018 865659.3276 0.683210373 0.671851409 0.563991103 0.616312241 0.917206241 0.5697923 0.722421198 0.633105755 1 19.72343985 -1.894271833 2.409317622 1.181167313 0.674274937 0.515961349 0.099751425 7198632.747 3767363.602 7401261.957 0.022590633 0.012756401 1.894271833 -0.506892376 VNNVVWDLDRPLEEDCTLELLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNNVVWDLDRPLEEDCTLELLK 22 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 167.24 9.84E-12 149709000 74647 90362 64404 92360 47166 76642 71203 80092 47330 FALSE TRUE 71118.58425 99569.99053 67356.9871 83075.79733 55391.73547 73987.86832 60339.67462 73078.71989 54669.69467 1.300877656 1.821301383 1.232071763 1.519595049 1.013207332 1.353361652 1.103713401 1.33673181 1 15.7384537 3.07810487 1.586458912 1.180697321 1.536285861 0.32144984 0.201686184 0.369752627 1.917765242 0.064438628 0.081313547 1197.029547 -3.07810487 0.35558854 VNPALAELNLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNPALAELNLR 11 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 ; 131.09 0.00049003 71901000 116131 99905 108884 116091 126616 97304 145026 129195 143123 FALSE TRUE 110641.7178 110085.4331 113876.4391 104421.3121 148697.7903 93934.33808 122899.6201 117882.0009 165317.7839 0.669266882 0.665901941 0.688833569 0.631639922 0.89946639 0.568204678 0.743414394 0.713063036 1 17.3348824 -5 0.267649252 3.078120411 0.671128551 0.561878797 0.084713552 140.0422131 1.363558154 160.5633922 0.092962989 1.00E-05 5 -2.40699186 VNPCIGGVILFHETLYQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VNPCIGGVILFHETLYQK 18 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;; 267.39 2.87E-31 3569220000 4994870 4627690 3979270 5807190 4053200 4426830 5283540 5215240 3991100 FALSE TRUE 4758772.394 5099256.872 4161723.466 5223440.228 4760076.797 4273527.767 4477438.934 4758565.938 4610019.404 1.032267324 1.106124818 0.902756171 1.133062525 1.032550273 0.927008629 0.9712408 1.03222254 1 22.13634139 2.432879749 12.08870302 0.977619188 1.048690591 0.165636071 0.065037154 1.256723769 340.3727044 0.020885851 0.017476243 270.9441317 -2.432879749 0.071071403 VNPFRPGDSEPPPAPGAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNPFRPGDSEPPPAPGAQR 19 1 Q15942;H0Y2Y8;C9IZ41 Q15942 ZYX Zyxin 0 123.42 2.85E-05 228050000 133520 104930 109530 144450 125530 118880 145680 129890 160160 FALSE TRUE 127208.7742 115622.4863 114552.0588 129929.6116 147422.3923 114763.1558 123453.8404 118516.143 184996.7948 0.687626909 0.624997241 0.619211046 0.702334393 0.796891602 0.62035213 0.667329618 0.640638899 1 17.49714075 -1.056126785 4.588650327 1.000014745 0.667935565 0.791985147 0.053153995 0.175167229 31783645.71 1070.121657 0.012163895 0.087876594 1.056126785 -0.33207918 VNPHKVS(ph)PASSVDSNIPSSQGYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNPHKVSPASSVDSNIPSSQGYK 23 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 VNPHKVS(0.647)PAS(0.157)S(0.157)VDS(0.039)NIPSSQGYK 69.952 0.014392 61594000 235560 229540 191210 256480 125990 224550 213400 233390 113060 TRUE FALSE 224425.5456 252930.387 199977.1676 230698.1431 147962.6161 216773.7772 180841.9106 212953.1343 130592.7674 1.718514357 1.936787098 1.531303545 1.766546094 1.133007739 1.659921767 1.384777383 1.630665607 1 16.99471547 0.549099237 0.074522813 4.06E-17 2.680822642 0.506070639 0.202009216 27.60879862 0.948345952 19.33672244 13.79053478 3.540782393 -0.549099237 2.680822642 VNPLGGAVALGHPLGCTGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNPLGGAVALGHPLGCTGAR 20 0 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 217.42 1.06E-24 1244580000 1007900 796920 885930 1055900 942810 892900 1109230 1014620 984090 FALSE TRUE 960258.5645 878127.054 926550.7668 949758.9259 1107235.765 861978.6491 939996.5911 925774.494 1136697.651 0.844779228 0.772524737 0.815125083 0.835542261 0.974081159 0.758318316 0.826953931 0.814442163 1 20.11641713 -2.103757938 2.317039803 1.301455367 0.826723446 0.459528726 0.057754506 3996300.722 1118992.241 6348405.834 0.01318578 0.007874846 2.103757938 -0.474731922 VNPTVFFDIAVDGEPLGR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 271.73 1.35E-38 1149429000 696513 498914 597447 672881 732373 625847 774802 714920 782185 FALSE TRUE 663590.2108 549753.9038 624840.5359 605241.7235 860098.6193 604173.7615 656591.7247 652317.8148 903482.255 0.734480625 0.608483344 0.691591376 0.66989885 0.951981751 0.668716799 0.7267345 0.722004014 1 19.78513674 -5 0.20854028 2.352261422 0.672715477 0.492430452 0.089255987 120.2326661 1.197004986 67.99485746 0.184766677 1.00E-05 5 -1.679545945 VNQAIWLLCTGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNQAIWLLCTGAR 13 0 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 270.1 2.53E-25 360560000 178090 163860 148760 162120 181810 148050 212040 149770 190000 FALSE TRUE 169672.0386 180557.5203 155580.7931 145823.3896 213517.6064 142922.9914 179689.4036 136655.3448 219464.2296 0.773119332 0.822719587 0.708911851 0.664451742 0.972903907 0.651235929 0.818763969 0.622677076 1 17.74362629 -2.126265543 2.480779341 1.486382513 0.763577192 0.35614762 0.103139436 19286036.91 3970209.87 53038033.5 0.023128882 0.007477122 2.126265543 -0.72280532 VNQIGSVTESLQACK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNQIGSVTESLQACK 15 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 293.13 1.33E-43 170136000 482410 442190 446290 468440 396280 488000 596090 548460 202314 FALSE TRUE 459607.4353 487249.6637 466752.8379 421351.5212 465391.1065 471100.4376 505145.5226 500433.9348 233687.8218 1.966758181 2.085045168 1.997334881 1.80305297 1.991507743 2.015939187 2.161625362 2.141463474 1 17.83422303 -1.15839945 4.494206591 0.999830816 2.024908348 0.91094763 0.100250059 9.052075313 15770433.72 5170.394015 0.024649291 0.069438535 1.15839945 1.025077532 VNQSALEAVTPS(ph)PSFQQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 VNQSALEAVT(0.03)PS(0.956)PS(0.014)FQQR;VNQSALEAVT(0.005)PS(0.995)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR 421.24 1.23E-168 1905900000 1387387 1318982 1406295 1498780 1387338 1301435 1537198 1440369 1512302 TRUE FALSE 1321807.966 1453387.765 1470775.017 1348119.787 1629289.308 1256365.98 1302670.213 1314242.654 1746822.07 0.756692962 0.832018206 0.841971854 0.771755641 0.932716237 0.719229509 0.745737207 0.752362062 1 20.73630123 VNS(ph)GDTEVGSSLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 VNS(0.998)GDT(0.002)EVGSSLLR;VNS(0.931)GDT(0.069)EVGSSLLR;VNS(0.998)GDT(0.002)EVGSSLLR;VNS(0.997)GDT(0.003)EVGSSLLR;VNS(0.887)GDT(0.113)EVGSSLLR;VNS(0.972)GDT(0.028)EVGSSLLR 318.02 5.77E-56 967931000 1729510 1676635 1539610 1962840 1118861 1733240 1608246 1764490 1119508 TRUE FALSE 1647759.49 1847486.013 1610202.641 1765531.594 1313990.004 1673217.464 1362878.535 1609981.901 1293115.583 1.274255381 1.428709109 1.245211691 1.36533162 1.016142734 1.293942696 1.05394951 1.245040987 1 20.3024198 2.754562119 24.98948718 1.133500865 1.334465188 0.490741143 0.104100745 631.1085095 985599.0189 0.027928388 0.029537553 568.2796688 -2.754562119 0.200964323 VNS(ph)KEDTEAQGIFIDLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNSKEDTEAQGIFIDLSK 18 1 Q9H2U2-2;A0A0C4DGB9 Q9H2U2-2;A0A0C4DGB9 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 VNS(0.5)KEDT(0.5)EAQGIFIDLSK 49.049 0.080074 273070000 138400 103140 144930 132410 449200 73220 183200 75179 481250 TRUE FALSE 131858.1063 113650.0833 151575.1839 119099.8952 527540.3378 70684.37304 155249.4753 68595.92821 555879.7921 0.237206152 0.204450827 0.27267619 0.214254767 0.949018736 0.127157659 0.279286057 0.123400651 1 19.08441341 -1.259866704 4.693792873 1.000236537 0.295417201 0.4627136 0.236672312 0.000547673 8.64E-05 0.214231505 0.050478242 0.054970957 1.259866704 -0.704819337 VNSKFDTIYQILLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNSKFDTIYQILLK 14 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 113.63 0.00047828 37555000 169370 132960 149700 156120 143040 151590 222630 174180 170980 FALSE TRUE 161364.2158 146508.7752 156563.8931 140426.521 167986.1307 146340.4003 188663.7046 158927.8758 197494.7052 0.817055909 0.741836471 0.792749826 0.711039422 0.850585491 0.740983917 0.955284874 0.804719679 1 17.59145445 1.201525085 0.624164171 0.992200477 0.767017429 0.532571041 0.063122357 0.500589568 0.475246204 0.05582898 0.025138824 15.90468548 -1.201525085 -0.225183048 VNSSLSDELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNSSLSDELRR 11 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 160.22 4.45E-05 144350000 124410 92836 108750 117960 123390 113100 146060 115770 139390 FALSE TRUE 118529.3859 102296.0939 113736.2951 106102.4367 144909.1769 109183.3186 123775.8644 105632.5651 161005.8893 0.736180436 0.635356225 0.706410775 0.65899724 0.900024077 0.678132453 0.768766068 0.65607889 1 17.29675393 -5 0.280119823 3.063595046 0.697990164 0.562009482 0.077321209 159.8489772 1.529937953 191.9210832 0.080649329 1.00E-05 5 -2.365604882 VNTLIRPDGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VNTLIRPDGEK 11 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ;; 161.23 2.42E-05 705530000 938240 891450 1002920 1397490 960140 1276010 1347320 1370640 1010810 FALSE TRUE 893891.2546 982289.7685 1048904.874 1257011.65 1127588.112 1231821.454 1141761.589 1250619.495 1167561.252 0.765605447 0.841317547 0.89837246 1.076613024 0.96576356 1.05503797 0.977902946 1.071138232 1 20.15506681 3.582044788 2.028743535 1.019936973 0.79310903 0.824502039 0.042491821 0.105816271 0.857651948 0.011005191 0.0196168 3819.836622 -3.582044788 -0.226827944 VNTLIRPDGEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VNTLIRPDGEKK 12 2 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 120.53 0.00022497 3129000000 4449100 3726800 3918100 4915300 2781000 4847200 5061400 5255100 3103900 FALSE TRUE 4238799.86 4106565.157 4097748.761 4421204.706 3266005.52 4679340.249 4289190.471 4794935.585 3585236.959 1.182292805 1.145409691 1.142950607 1.233169454 0.910959459 1.305169031 1.196347834 1.337411066 1 21.77363704 VNVEHMTEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNVEHMTEK 9 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 65.719 0.049883 146470000 243280 157270 222970 188140 240740 206860 339130 247210 306690 FALSE TRUE 231780.6365 173295.9918 233193.395 169227.8098 282724.9798 199696.3863 287389.49 225562.9819 354249.9188 0.654285645 0.489191338 0.658273672 0.477707406 0.798094692 0.56371611 0.811261978 0.63673404 1 18.434408 0.150404664 0.303268366 1.095207612 0.550037927 0.569254598 0.104307612 2.996529345 0.459141603 0.477458844 0.113272569 1.413854321 -0.150404664 -0.545169685 VNVPVIGGHAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VNVPVIGGHAGK 12 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;; 137.16 9.72E-05 9304250000 5348270 3998881 4066270 4552410 3783584 3938479 5016940 4695300 4066457 FALSE TRUE 5095467.876 4406371.52 4252712.502 4094793.098 4443439.852 3802088.485 4251513.661 4284154.641 4697062.383 1.084820141 0.938112199 0.905398344 0.871777457 0.94600401 0.80946093 0.905143112 0.912092344 1 22.16332732 4.456457963 1.393433077 0.897061642 1.113741668 0.554190198 0.049092065 0.451255077 1.150722471 0.012214735 0.119151663 28606.05455 -4.456457963 0.216680026 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 VNVTVDYIRPAS(0.944)PAT(0.053)ET(0.003)VPAFSER;VNVTVDYIRPAS(0.997)PAT(0.003)ETVPAFSER;VNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;VNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;VNVTVDYIRPAS(1)PATETVPAFSER;VNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER;VNVTVDYIRPAS(0.992)PAT(0.008)ETVPAFSER 301.72 1.80E-62 5037639000 2722764 2298435 2453605 2725398 2488854 2483514 2620887 2532098 2573328 TRUE FALSE 2594064.342 2532648.14 2566105.216 2451435.815 2922909.35 2397509.287 2221022.552 2310374.076 2972386.564 0.872721056 0.852058804 0.863314768 0.824736542 0.983354381 0.80659404 0.747218609 0.777279141 1 21.50319032 2.058350672 24.99999908 0.804282714 0.873674022 0.023877498 0.07978503 134.2604359 57522.15514 0.026778085 0.019776924 114.3801527 -2.058350672 0.069391308 VNVTVDYIRPASPATETVPAFSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 235.76 1.97E-37 771940000 410043 369721 433181 412695 429423 449192 516444 490174 462468 FALSE TRUE 390661.08 407395.9902 453042.7773 371210.1145 504314.2352 433636.3684 437650.9827 447251.766 534185.1755 0.731321455 0.762649375 0.848100618 0.694909053 0.944081301 0.811771626 0.819287024 0.837259787 1 19.02698041 -4.999999998 0.083256891 1.654028388 0.612002417 0.549757383 0.061342628 165.2881222 0.968644815 19.64368669 1.6723991 1.00E-05 4.999999998 -1.04202597 VNVVS(ph)PSLEVAPGAGQGASSSRPDPEPLEEGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VNVVSPSLEVAPGAGQGASSSRPDPEPLEEGTR 33 1 Q32MK0 Q32MK0 MYLK3 Myosin light chain kinase 3 1 VNVVS(0.781)PS(0.218)LEVAPGAGQGASSSRPDPEPLEEGTR 156.52 2.53E-11 117240000 102240 99841 94114 116020 104500 98760 122360 115600 100700 TRUE FALSE 97407.31782 110014.9114 98429.21999 104357.4492 122724.7669 95339.91644 103691.7347 105477.4512 116316.0417 0.837436663 0.945827504 0.846222228 0.897188794 1.055097518 0.819662663 0.891465469 0.90681775 1 16.82769055 VNVVSPS(ph)LEVAPGAGQGASSSRPDPEPLEEGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VNVVSPSLEVAPGAGQGASSSRPDPEPLEEGTR 33 1 Q32MK0 Q32MK0 MYLK3 Myosin light chain kinase 3 1 VNVVS(0.213)PS(0.787)LEVAPGAGQGASSSRPDPEPLEEGTR;VNVVS(0.345)PS(0.655)LEVAPGAGQGASSSRPDPEPLEEGTR;VNVVS(0.441)PS(0.559)LEVAPGAGQGASSSRPDPEPLEEGTR 176 1.54E-15 544530000 415170 338576 370476 426371 385212 386324 450971 425685 431537 TRUE FALSE 395545.7369 373077.2793 387462.6911 383511.377 452392.8508 372945.503 382167.0913 388409.7647 498457.554 0.793539457 0.748463488 0.777323341 0.769396258 0.907585505 0.74819912 0.766699367 0.779223349 1 18.92711113 -1.035066121 5.09081552 1.000002652 0.78325309 0.686291381 0.045363831 1.29E-06 2.45E-07 0.041635228 0.009813397 0.092243098 1.035066121 -0.216749563 VPAAFPTKVPVPGPGS(ph)GGNGPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPAAFPTKVPVPGPGSGGNGPER 23 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPAAFPT(0.002)KVPVPGPGS(0.998)GGNGPER;VPAAFPTKVPVPGPGS(1)GGNGPER 117.04 1.63E-06 0 396760 323860 371020 401560 348600 387260 454350 416810 409100 TRUE FALSE 378005.9411 356861.7022 388031.634 361194.4259 409395.7296 373849.0891 385030.5628 380311.9068 472541.1386 0.799942926 0.75519711 0.821159476 0.764366097 0.866370557 0.791146122 0.814808556 0.804822852 1 18.85008041 -5 0.258719759 2.287650778 0.782892625 0.811503152 0.03007246 72.50086462 0.712954389 49.56281038 0.036141223 1.00E-05 5 -1.504758153 VPADTEVVCAPPTAYIDFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPADTEVVCAPPTAYIDFAR 20 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 157.75 7.65E-09 166772000 62656 47430 49555 59650 67127 50335 85888 62465 85972 FALSE TRUE 59694.37505 52263.17092 51827.14577 53653.86867 78833.92755 48591.88633 72784.20816 56995.23345 99304.09868 0.601127001 0.526294198 0.52190339 0.540298632 0.793863784 0.489324076 0.732942639 0.573946435 1 16.59956564 -4.999999999 0.202263455 2.877078592 0.532309582 0.649360017 0.094096553 79.81264907 0.79103051 60.42878561 0.194031411 1.00E-05 4.999999999 -2.34476901 VPAHPDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPAHPDSR 8 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ;;; 90.657 0.013041 241509000 400188 349035 356617 390606 458320 370515 451780 421062 458060 FALSE TRUE 381271.9063 384602.0633 372968.2422 351341.5428 538250.8629 357683.9726 382852.6635 384191.5791 529093.6054 0.720613333 0.726907412 0.704919202 0.664044205 1.017307443 0.676031555 0.723601003 0.726131587 1 19.01316346 -1.920358546 2.484042693 1.163595843 0.741942688 0.393871045 0.099373789 23768505.86 12917027.78 22631426.09 0.023167477 0.012012723 1.920358546 -0.421653156 VPAPVTMDSFFFGCELSGHTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPAPVTMDSFFFGCELSGHTR 21 0 O75607 O75607 NPM3 Nucleoplasmin-3 0 179.87 5.59E-17 42029000 67119 60103 66039 70448 67826 65579 84523 70023 62356 FALSE TRUE 63946.41789 66227.56403 69066.95347 63366.4332 79654.83293 63307.98279 71627.46398 63891.4149 72025.85001 0.887825939 0.919497153 0.958918964 0.879773487 1.105920068 0.878961967 0.994468847 0.887062282 1 16.13622716 3.913294703 1.044935222 0.962242365 0.886437749 0.111915279 0.068424011 1.342399531 2.51355382 0.020774705 0.083423115 8190.203686 -3.913294703 -0.075804616 VPAS(ph)PLPGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;VPAS(1)PLPGLER;VPAS(1)PLPGLER 159.77 2.97E-05 8115960000 2364970 2147830 2171850 2301480 2387420 2006600 2399790 2302920 2571970 TRUE FALSE 2253182.555 2366696.319 2271431.471 2070130.858 2803785.292 1937110.939 2033657.96 2101264.116 2970817.972 0.758438442 0.796648041 0.764581167 0.696821844 0.943775525 0.652046324 0.684544789 0.707301537 1 21.50242878 VPCNVEGIS(ph)PELEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPCNVEGISPELEK 14 0 Q86VQ1;H7C2L5;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK 184.22 1.38E-06 819600000 1464520 1189960 1223380 1390700 917330 1357810 1489090 1503350 1020900 TRUE FALSE 1395295.042 1311218.277 1279473.183 1250904.194 1077312.062 1310788.699 1261901.971 1371708.704 1179215.958 1.18323962 1.11194075 1.085020241 1.060793136 0.913583347 1.111576459 1.070119483 1.163237908 1 20.16939652 4.075473045 1.409225253 1.056923424 1.180153402 0.285795034 0.065548795 0.623409274 2.182641063 0.018692467 0.076559506 11897.97481 -4.075473045 0.123229977 VPDEEENEES(ph)DNEKETEK ddPTM_SK-BR-3_Trastuzumab_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 248.45 1.01E-24 4236010000 4276950 6452560 4320640 6206950 1667320 6048000 3520170 5096880 1185594 TRUE FALSE 4074787.05 7110083.2 4518745.618 5583015.594 1958100.08 5838556.243 2983103.414 4650570.167 1369449.862 2.975491956 5.191926624 3.299679486 4.076830958 1.4298443 4.263431911 2.178322475 3.395940439 1 20.38516502 2.781383156 24.70344728 2.646864571 3.969902166 0.292092712 1.081668795 513.6226093 296297.371 0.294774124 0.312652848 604.4816976 -2.781383156 1.323037595 VPDGKPENEFAFNAEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPDGKPENEFAFNAEFK 17 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 166.76 2.10E-09 277560000 520010 527260 385640 579170 282950 519050 487540 528260 244400 FALSE TRUE 495430.1579 580988.3934 403321.9755 520950.7312 332296.3904 501075.1684 413156.8187 482002.7539 282300.3038 1.754975646 2.058050897 1.42869834 1.845377863 1.17710249 1.774972119 1.463536571 1.707411389 1 18.10687116 -1.544026089 0.102443229 1.22E-10 2.258947002 0.434866282 0.240220824 54.05521311 0.911982687 18.73337081 4.571222433 0.028574189 1.544026089 2.258947002 VPDHHPC ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPDHHPC 7 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 74.717 0.045424 159509000 321070 301147 301193 337530 326690 299144 332930 332420 145410 FALSE TRUE 305893.6574 331834.2217 315002.997 303600.8431 383664.6326 288784.5683 282135.4138 303311.5425 167959.4401 1.821235276 1.975680684 1.87547063 1.807584277 2.284269537 1.719370867 1.679783009 1.805861833 1 17.35775336 0.222134568 0.609052294 0.962170493 1.925519246 0.755234383 0.158749868 1.358225296 0.68780974 0.274046295 0.061700767 1.667763897 -0.222134568 0.963348753 VPDS(ph)PENELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPDSPENELK 10 0 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 VPDS(1)PENELK 100.38 0.0042541 41844000 80995 71691 72189 82850 65712 80063 95927 87714 82843 TRUE FALSE 77166.52687 78996.39441 75498.93705 74521.7606 77172.15199 77290.39823 81291.57433 80033.29716 95689.86934 0.806423161 0.825546058 0.788996135 0.778784224 0.806481946 0.807717669 0.849531668 0.836382134 1 16.54607857 0.284446238 0.680324862 1.005100772 0.802973916 0.937994925 0.015562249 0.62106613 0.395687582 0.023770637 0.00616367 1.925068724 -0.284446238 -0.202126855 VPEASSEPFDTSS(ph)PQAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPEASSEPFDTSSPQAGR 18 0 H0Y6F5;Q9H4I2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 VPEASSEPFDT(0.002)S(0.099)S(0.9)PQAGR 159.88 4.40E-11 112240000 60965 49687 55754 70071 51082 51011 67409 60292 57203 TRUE FALSE 58083.30527 54750.16179 58310.37605 63027.32995 59990.68463 49244.47628 57124.519 55012.51285 66073.74909 0.8790678 0.828621995 0.882504427 0.953893654 0.907935231 0.745295627 0.86455695 0.832592574 1 16.01178959 -1.062050927 4.919855635 1.000003407 0.859752097 0.386376557 0.054675919 2.01E-06 3.83E-07 0.052078083 0.012274624 0.086686022 1.062050927 -0.14025131 VPEEDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VPEEDLKR 8 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 161.37 0.00055786 4051530000 5627940 4475170 4995450 5730360 4120610 5534540 6014100 5826960 4526490 FALSE TRUE 5361918.43 4931194.911 5224496.324 5154333.326 4839243.079 5342877.492 5096538.588 5316720.492 5228434.951 1.025530293 0.943149328 0.999246691 0.985827188 0.925562453 1.021888489 0.974773261 1.016885653 1 22.31794773 VPELFANR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPELFANR 8 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 95.531 0.022298 46721000 41021 31742 27400 29497 48911 31836 42304 31453 48044 FALSE TRUE 39082.01863 34976.54589 28656.3171 26531.90552 57441.06291 30733.51134 35849.74783 28698.80858 55494.41815 0.704251345 0.630271423 0.516381972 0.478100436 1.035078208 0.55381266 0.646006374 0.517147662 1 15.76005505 VPEWCLDDWHPSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPEWCLDDWHPSEK 14 0 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 169.04 3.39E-06 148078000 357740 350140 346370 388660 329630 291400 414320 399620 303580 FALSE TRUE 340830.3392 385819.6641 362251.4071 349591.1584 387117.3676 281308.7449 351107.8745 364627.1543 350657.6359 0.971974668 1.100274526 1.033062937 0.996958636 1.103975297 0.80223191 1.001283983 1.039838055 1 18.41970362 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR 31 1 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 128.49 3.30E-06 315420000 109235 88671 98774 97425 108090 102282 102865 99083 61697 FALSE TRUE 104071.678 97706.67571 103302.8856 87631.6539 126940.8618 98739.94869 87171.055 90406.76725 71264.65566 1.460354745 1.371039751 1.449566895 1.229665016 1.781259737 1.385538845 1.223201799 1.268605965 1 16.12089912 1.210556926 1.19199404 1.025358587 1.439827939 0.486345714 0.1452035 0.362838265 1.043227128 0.127155518 0.040928774 16.23891192 -1.210556926 0.414469352 VPHNAAVQVYDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPHNAAVQVYDYR 13 0 Q14764 Q14764 MVP Major vault protein 0 ; 178.15 5.64E-07 160850000 304130 242940 243120 279460 284460 253130 280500 282830 275150 FALSE TRUE 289754.3776 267695.8622 254267.2925 251368.1499 334069.7339 244364.0446 237704.5733 258063.9058 317818.8567 0.911696621 0.842290684 0.800038409 0.790916412 1.051132514 0.76887837 0.747924701 0.811984249 1 18.2778452 VPKDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPKDER 6 1 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 75.311 0.07116 87898000 426720 324610 313960 384520 333990 370140 479050 433460 400730 FALSE TRUE 406549.7913 357688.1281 328355.3765 345867.3191 392237.7503 357321.959 405962.1241 395503.9445 462873.1618 0.878317917 0.772756249 0.709385213 0.747218348 0.847397911 0.77196517 0.87704831 0.854454259 1 18.82025739 0.901160506 0.8086647 0.99822697 0.787967766 0.632003713 0.050503652 0.519486084 0.72689308 0.049721636 0.017877816 7.964536492 -0.901160506 -0.210259204 VPKPEPIPEPKEPS(ph)PEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 185.9 2.89E-10 2624980000 3645200 3527070 2860690 4083190 1265230 4114960 3335270 4334460 1125000 TRUE FALSE 3472898.62 3886482.443 2991855.466 3672739.984 1485885.711 3972457.903 2826413.305 3954911.704 1299459.254 2.672572155 2.990845946 2.302384978 2.826360251 1.143464642 3.057008437 2.175068819 3.043505744 1 20.30947997 3.41957462 1.84907066 2.251817758 2.818361214 0.11001811 0.705487123 0.737411027 5.111054385 0.194342402 0.312155872 2627.692973 -3.41957462 0.566543456 VPLAPITDPQQLQLS(ph)PLK ddPTM_SK-BR-3_Trastuzumab_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 239.43 6.78E-24 967679000 1379730 1914730 1338270 1748150 764972 1732960 1542290 1811160 1009439 TRUE FALSE 1314512.897 2109843.164 1399631.003 1572422.641 898382.8746 1672947.161 1306985.334 1652565.229 1165977.645 1.127391167 1.809505674 1.200392657 1.348587298 0.770497512 1.434802089 1.120935157 1.417321538 1 20.1531087 3.533307207 24.99991087 1.189601568 1.474532152 0.175923435 0.255230246 417.0885565 185581.9999 0.061975543 0.096011759 3414.343467 -3.533307207 0.284930585 VPLAPITDPQQLQLS(ph)PLKGLSLVDKENTPPALSGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPLAPITDPQQLQLSPLKGLSLVDKENTPPALSGTR 36 2 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(1)PLKGLSLVDKENTPPALSGTR;VPLAPITDPQQLQLS(0.999)PLKGLS(0.001)LVDKENTPPALSGTR 272.13 2.45E-76 892140000 717790 456320 845240 664390 501750 883530 1170420 1015630 810350 TRUE FALSE 683861.4892 502819.5268 883995.0901 597604.2549 589255.0411 852933.1346 991850.9328 926696.053 936014.9393 0.730609588 0.537191775 0.944424125 0.638455894 0.629535936 0.911238805 1.059652887 0.990044084 1 19.83617203 2.087480248 4.132229821 1.016264253 0.686873484 0.665264826 0.105515264 0.122465306 3.939439368 0.041106796 0.028868193 122.3151487 -2.087480248 -0.329390769 VPLS(ph)PLSLLAGPADAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPLSPLSLLAGPADAR 16 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(0.986)PLS(0.014)LLAGPADAR;VPLS(0.983)PLS(0.017)LLAGPADAR;VPLS(0.985)PLS(0.015)LLAGPADAR;VPLS(0.958)PLS(0.042)LLAGPADAR 145.46 1.28E-06 438519000 146903 148909 137285 158630 133184 134658 148343 127935 128679 TRUE FALSE 139959.1863 164082.9964 143579.653 142684.211 156411.2474 129994.7597 125710.5508 116732.3332 148633.8821 0.941637158 1.10394073 0.965995445 0.959970963 1.052325656 0.874597083 0.845773178 0.785368259 1 17.1814035 2.186065445 7.509687941 0.861129461 1.008665708 0.441462082 0.070768687 0.177999433 21.37200371 0.024536495 0.018176853 153.4848257 -2.186065445 0.147536248 VPLS(ph)PLSLLAGPADARR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPLSPLSLLAGPADARR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(0.999)PLS(0.001)LLAGPADARR 135.18 8.88E-06 22547000 40630 32877 39296 46417 43141 34325 46211 37875 40583 TRUE FALSE 38709.50042 36227.20368 41097.76047 41751.07497 50664.77674 33136.31664 39160.66323 34558.46421 46876.40437 0.825777935 0.772823858 0.876725957 0.890662915 1.080816189 0.70688691 0.835402454 0.737225149 1 15.51657429 -2.414502113 2.185397111 2.309381667 0.837389811 0.1910467 0.102747415 4747450.954 422695.2868 30873811.29 0.023810306 0.003850329 2.414502113 -1.471991856 VPLVAEKPLKEPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 95.264 0.0026861 641380000 1217230 1357760 1009110 1634580 731630 1350750 1347210 1645810 779170 FALSE TRUE 1159693.95 1496117.288 1055378.692 1470268.913 859226.0404 1303973.189 1141668.371 1501694.151 899999.7042 1.288549257 1.662353088 1.172643376 1.633632662 0.954695914 1.448859575 1.26852083 1.668549606 1 19.779565 VPLVAPEDLRDDIIENAPTTHTEEYSGEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPLVAPEDLRDDIIENAPTTHTEEYSGEEK 30 1 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" 0 199.03 1.47E-25 33747000 48662 45287 54464 57942 33236 56011 64215 60980 38807 FALSE TRUE 46361.8437 49901.79679 56961.22827 52117.56008 39032.34788 54071.32503 54417.82236 55640.26792 44824.99136 1.034285614 1.113258369 1.270747111 1.162689796 0.870772011 1.206276307 1.21400631 1.241277828 1 15.45201568 VPPELLGGS(ph)PPWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPPELLGGSPPWK 13 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK 106.42 0.0014424 669798000 752503 595550 632485 736259 521045 712567 776617 689716 584818 TRUE FALSE 716933.6745 656237.2221 661485.0629 662248.8465 611915.083 687890.6261 658129.8131 629320.8106 675508.5886 1.061324292 0.971471323 0.979240048 0.980370728 0.905858332 1.018329948 0.97427305 0.93162518 1 19.36561459 4.595121056 1.694688298 0.969513582 1.079524415 0.447759571 0.031746956 0.586840961 2.093768005 0.007752602 0.096384139 39365.97894 -4.595121056 0.110010833 VPPS(ph)PDDLPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPPSPDDLPSR 11 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 VPPS(1)PDDLPSR 65.395 0.068771 40749000 29250 26055 30606 31649 42610 23262 35456 26090 50507 TRUE FALSE 27867.41047 28710.03412 32009.31537 28467.58239 50041.17051 22456.43111 30046.53601 23805.42129 58339.36761 0.477677623 0.492121106 0.548674363 0.487965221 0.857759907 0.384927572 0.515030197 0.408050726 1 15.83218213 -1.050967757 4.564884007 1.000022353 0.519658474 0.576764615 0.128802082 15772184.23 3631211.416 3528.287269 0.027751526 0.088926714 1.050967757 -0.480363879 VPQIEVETHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPQIEVETHK 10 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 155.97 1.18E-05 484150000 301620 246506 263010 307160 227657 308070 324170 330790 256780 FALSE TRUE 287363.0204 271625.2417 275069.2687 276283.6932 267360.3087 297401.4587 274711.9127 301824.274 296600.1309 0.968856687 0.915796095 0.927407779 0.931502263 0.901416691 1.002701711 0.926202938 1.017613421 1 18.17815971 1.364944798 1.222463255 1.007514817 0.934376718 0.419574923 0.031063649 0.394321861 1.146771995 0.025789741 0.008519171 23.17100111 -1.364944798 -0.073138099 VPS(ph)GIFDVNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPSGIFDVNSR 11 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 VPS(1)GIFDVNSR;VPS(1)GIFDVNSR;VPS(1)GIFDVNSR;VPS(1)GIFDVNSR 180.61 6.91E-06 267686000 200130 209842 198598 213654 357992 174973 203680 179592 302461 TRUE FALSE 190670.2515 231225.1384 207703.9147 192177.094 420425.6915 168913.6411 172604.8752 163865.9724 349365.1071 0.545762149 0.661843824 0.5945182 0.550075237 1.203399203 0.48348744 0.494052988 0.46903932 1 18.414376 4.87395087 1.08335386 0.659240068 0.463194973 0.02335088 0.240957711 12.24451926 9.786554016 0.068838449 2.949882213 74808.48674 -4.87395087 -0.196045095 VPS(ph)PDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VPSPDHR 7 0 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHR;VPS(1)PDHR;VPS(1)PDHR;VPS(1)PDHR;VPS(1)PDHR 85.29 0.013475 1990840000 1972150 1994980 1807430 2191650 1753370 1925130 2078930 2086960 1757310 TRUE FALSE 1878930.378 2198270.73 1890302.453 1971341.178 2059157.173 1858462.265 1761751.046 1904214.719 2029824.66 0.925661421 1.082985528 0.931263912 0.971187915 1.014450762 0.915577735 0.867932626 0.938117837 1 20.95292368 2.225724116 24.35172436 0.913750321 0.989971808 0.165585477 0.055097322 198.8942122 377312.4613 0.019524191 0.014518476 168.1605486 -2.225724116 0.076221488 VPS(ph)PDHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VPSPDHRR 8 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHRR;VPS(1)PDHRR;VPS(1)PDHRR;VPS(1)PDHRR;VPS(1)PDHRR;VPS(1)PDHRR 84.17 0.010806 817798000 511099 320164 428052 440293 494973 465847 596343 504456 580890 TRUE FALSE 486940.3632 352789.0756 447678.6076 396033.9111 581296.1345 449714.6016 505359.9228 460283.1584 670971.4544 0.72572441 0.525788502 0.667209618 0.590239583 0.866350022 0.670244015 0.753176487 0.685995142 1 19.35589186 -5 0.153750962 2.200398542 0.58056166 0.574109897 0.087535275 88.3615744 0.796981047 32.15929427 0.38208797 1.00E-05 5 -1.619836883 VPS(ph)PGMEEAGCSR ddPTM_SK-BR-3_Trastuzumab_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 237.59 9.96E-17 2296670000 288887 297974 245254 300342 197702 257919 264594 273217 202402 TRUE FALSE 275231.884 328337.8894 256499.1385 270151.0515 232181.1662 248987.2004 224225.3257 249292.6711 233789.4684 1.177263826 1.404416938 1.097137267 1.155531314 0.993120724 1.065006059 0.959090789 1.066312665 1 17.83485042 3.270853783 1.547143758 1.015237284 1.285231293 0.624224507 0.077897988 0.199473958 0.990625069 0.024232563 0.036029402 1865.751429 -3.270853783 0.269994009 VPS(ph)S(ph)DEEVVEEPQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR 203.2 8.08E-09 4966330000 1292637 1279396 1170484 1440313 1036296 1275160 1328173 1293393 1130641 TRUE FALSE 1231536.611 1409767.907 1224151.849 1295530.001 1217025.694 1231000.889 1125535.815 1180136.652 1305975.032 0.943001651 1.07947539 0.937347054 0.99200212 0.931890476 0.942591443 0.861835631 0.903644115 1 20.31669588 2.753298345 1.313029214 0.909230781 1.003153814 0.213808666 0.052329452 0.444665548 1.568995208 0.021952574 0.020982469 566.6284089 -2.753298345 0.093923033 VPS(ph)TPPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPSTPPPK 8 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 VPS(0.687)T(0.313)PPPK 66.621 0.064205 636570000 544230 485460 472610 587170 426740 545320 609130 588950 487080 TRUE FALSE 518505.3265 534928.9259 494279.636 528146.556 501163.3209 526435.4317 516196.0311 537378.4158 562613.8787 0.921600668 0.950792268 0.878541491 0.938737162 0.890776676 0.935695779 0.917496085 0.955146035 1 19.10178562 0.959864615 2.640169441 0.999936592 0.921180671 0.599583736 0.021559658 0.196981802 3.198825422 0.018797641 0.005028947 9.117265784 -0.959864615 -0.078755921 VPS(ph)VESLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 143.5 0.00010677 2340551900 277679 241184 234542 267227.1 264819 251896 303525 261194 274970 TRUE FALSE 264553.664 265760.9238 245295.9827 240364.9242 311003.3498 243172.7784 257216.6866 238322.4687 317610.9432 0.832948831 0.836749896 0.772315904 0.756790436 0.979195951 0.765630982 0.809848313 0.750359752 1 18.2769011 -1.076375185 4.653947285 1.000008993 0.815806586 0.439057995 0.066365394 0.073842288 37757709.07 743.8369518 0.014247477 0.083873509 1.076375185 -0.184202407 VPS(ph)WGLEDNVVCSQPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR 223.86 3.05E-15 366920000 67418.5 50792.5 61220.3 64346 51016.2 63298 77795.2 66667.8 54183.8 TRUE FALSE 64231.76112 55968.3135 64027.31131 57877.81783 59913.40913 61105.97439 65926.11343 60830.014 62586.34697 1.026290305 0.894257553 1.023023621 0.924767471 0.957291998 0.976346717 1.05336254 0.971937442 1 15.93356035 1.965904185 12.64970583 1.014496824 0.962234077 0.163092859 0.043943845 2.557366125 946.3420475 0.016586819 0.010724581 92.44941873 -1.965904185 -0.052262747 VPSS(ph)DEEVVEEPQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.469)S(0.531)DEEVVEEPQSR;VPS(0.235)S(0.765)DEEVVEEPQSR;VPS(0.009)S(0.991)DEEVVEEPQSR;VPS(0.054)S(0.946)DEEVVEEPQSR 302.13 2.30E-44 872110000 550330 460510 486043 563969 505943 497934 556959 544947 564510 TRUE FALSE 524316.9915 507436.4926 508328.5523 507277.7646 594179.299 480690.4207 471984.6753 497228.5517 652051.3277 0.804103863 0.778215565 0.779583647 0.777972137 0.911246207 0.737197212 0.723845893 0.762560447 1 19.31462601 -2.237268438 2.350745584 1.787558625 0.78197894 0.64230896 0.050549675 3807580.285 694983.7932 15959095.98 0.013214491 0.005790707 2.237268438 -1.005579686 VPST(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPSTPPPK 8 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 VPS(0.008)T(0.992)PPPK;VPS(0.056)T(0.944)PPPK 98.033 0.087299 376180000 1009120 881740 900420 1053420 774060 945210 1096630 1054250 936810 TRUE FALSE 961420.8975 971590.3085 941705.1476 947528.2202 909055.8189 912477.1407 929318.9525 961934.2811 1082085.71 0.888488674 0.897886645 0.870268537 0.875649878 0.840095946 0.843257731 0.858821943 0.888963113 1 20.04538335 -1.58129294 5.340093401 1.000748832 0.871080292 0.821251441 0.018995202 0.000194341 1.52E-05 0.021106458 0.004946528 0.026224491 1.58129294 -0.12966854 VPT(ph)ANVSVVDLTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPT(1)ANVSVVDLTCR;VPT(1)ANVSVVDLTCR 209.33 7.59E-08 311110000 118212 87943 86084 112080 101022 79377 108818 92218 107349 TRUE FALSE 112624.353 96904.49168 90031.03655 100813.5055 118640.2048 76628.15459 92215.81552 84142.90304 123996.1347 0.908289225 0.781512198 0.72607938 0.813037485 0.956805671 0.617988253 0.743699114 0.678592952 1 16.91993562 2.234896257 24.99999989 0.734934522 0.829881982 0.078123132 0.11682991 181.7510006 1239974.461 0.038820156 0.02979164 171.7498068 -2.234896257 0.09494746 VPTANVS(ph)VVDLTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPTANVS(1)VVDLTCR 162.59 2.13E-07 0 21717 16561 14869 18371 18188 14978 22707 18374 44411 TRUE FALSE 20690.48045 18248.58473 15550.75836 16524.31218 21359.98144 14459.3081 19242.63011 16765.07515 51298.03106 0.403338686 0.355736553 0.303145326 0.322123712 0.416389889 0.281868676 0.375114399 0.326817127 1 15.64661583 -1.456300244 3.049116337 1.014268299 0.350826056 0.959121913 0.042294018 9384028.652 11368649.67 1143536.089 0.00996638 0.034970332 1.456300244 -0.663442243 VPTANVSVVDLTCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 228.62 3.70E-12 2880220000 931673 826330 928742 1011778 957398 865487 1099144 854930 1059238 FALSE TRUE 887634.6637 910533.9665 971325.7394 910072.1532 1124367.908 835514.9682 931449.3956 780067.7969 1223499.219 0.725488541 0.744204779 0.793891589 0.743827326 0.918977218 0.682889662 0.761299542 0.637571144 1 20.22258175 -2.102318264 2.700877974 1.467558753 0.752564453 0.532118564 0.073359698 4448166.169 3642414.767 12808113.85 0.016267788 0.007900994 2.102318264 -0.714994301 VPTANVSVVDLTCRLEKPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPTANVSVVDLTCRLEKPAK 20 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 231.06 7.04E-26 497240000 549210 166511 695240 310360 671420 515590 1184790 730640 1364730 FALSE TRUE 523249.9317 183478.6602 727117.4417 279162.0232 788515.4354 497734.989 1004028.525 666661.2882 1576365.358 0.331934427 0.116393487 0.461262002 0.177092209 0.500211091 0.315748495 0.636926281 0.42291039 1 20.58817052 0.11884917 0.264754852 1.219438868 0.179071283 0.727999661 0.129827454 2.560812974 0.311903366 0.765956424 0.194466018 1.314768136 -0.11884917 -1.040367585 VPVASPS(ph)AHNISSSGGAPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 VPVASPS(1)AHNISSSGGAPDR;VPVAS(0.005)PS(0.995)AHNISSSGGAPDR;VPVAS(0.001)PS(0.999)AHNISSSGGAPDR;VPVAS(0.009)PS(0.991)AHNISSSGGAPDR;VPVAS(0.001)PS(0.999)AHNISSSGGAPDR;VPVAS(0.007)PS(0.993)AHNISSSGGAPDR 287.48 1.20E-45 2186410000 1188319 1014695 1106890 1246439 1201628 1024005 1251769 1190189 1092086 TRUE FALSE 1132149.516 1118093.574 1157642.001 1121144.584 1411191.543 988543.4501 1060788.649 1085969.742 1261441.119 0.897504845 0.88636208 0.917713862 0.88878075 1.118713764 0.783661984 0.840933939 0.860896101 1 20.26664144 -0.487135184 7.380289654 1.000000317 0.895578725 0.117038252 0.086363812 0 0 0.079901395 0.018832939 0.325735292 0.487135184 -0.104421592 VPVDVAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VPVDVAYR 8 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 ;;;; 139.68 0.0015395 3730160000 1318850 1194020 983480 1263450 1168820 1108670 1180750 1168440 1113460 FALSE TRUE 1256510.574 1315691.995 1028573.531 1136445.606 1372661.838 1070276.48 1000604.902 1066125.199 1286129.69 0.976970351 1.022985478 0.799743244 0.883616648 1.067281044 0.832168395 0.777996892 0.828940664 1 20.2946047 2.174638569 24.99526429 0.834170315 0.952638816 0.166494196 0.092802627 81.41027929 31832.61307 0.033770529 0.024941195 149.4990968 -2.174638569 0.118468501 VPVDVAYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VPVDVAYRR 9 1 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 ;;;; 174.02 8.82E-05 4987460000 3549130 1507950 2501370 1914120 4549980 2374360 4788590 2931050 5042850 FALSE TRUE 3381369.659 1661611.819 2616060.289 1721709.021 5343495.071 2292135.318 4058002.647 2674391.724 5824869.423 0.580505658 0.285261643 0.44911913 0.29557899 0.917358774 0.393508447 0.696668432 0.459133335 1 22.47379428 -4.999892359 0.152033314 2.841797756 0.348756317 0.415164959 0.186600332 118.7518625 1.065121152 65.57861564 0.816662888 1.00E-05 4.999892359 -2.493041438 VPVPDERFDFLCQYHKPASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VPVPDERFDFLCQYHKPASK 20 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 104.63 0.00016085 486940000 992750 681530 884850 929940 749880 925640 1153520 1032210 777460 FALSE TRUE 945824.6749 750978.6818 925421.2477 836460.6644 880658.8346 893584.8547 977529.3382 941824.2203 898024.5261 1.053228111 0.836256316 1.030507765 0.931445234 0.980662342 0.99505618 1.088533007 1.048773383 1 19.77639532 2.038800183 2.899756689 1.054012183 0.957481463 0.239482209 0.062177366 0.299870051 4.9458781 0.027821536 0.016862883 109.3453158 -2.038800183 -0.096530721 VPVPGPGS(ph)GGNGPER ddPTM_SK-BR-3_Trastuzumab_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 177.3 7.96E-07 1767930000 640813 572620 564359 677244 561630 585476 646908 603284 552506 TRUE FALSE 610523.0395 630970.629 590235.4184 609166.1464 659578.0942 565200.8193 548210.3033 550457.2548 638185.8087 0.956654051 0.988694234 0.924864531 0.954527879 1.033520466 0.885636772 0.859013622 0.862534465 1 19.283617 2.204092838 24.88821723 0.88656469 0.969707575 0.319817759 0.048361189 157.8320683 113965.1757 0.016386396 0.012102736 159.99 -2.204092838 0.083142884 VQAGPGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQAGPGSPR 9 0 Q6PK04;I3L0U5;I3L4F6 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 VQAGPGS(1)PR;VQAGPGS(1)PR 117.21 0.0012471 1017650000 1085380 1086510 1043440 1242400 1074720 1150480 1189080 1102690 1160200 TRUE FALSE 1034076.238 1197226.604 1091282.756 1117511.592 1262150.828 1110638.589 1007664.007 1006132.618 1340117.891 0.771630799 0.893374092 0.814318474 0.83389051 0.941820743 0.828761855 0.751921912 0.750779185 1 20.35392849 -0.687814128 8.816470693 1 0.82488483 0.462523422 0.059836624 0 0 0.058988178 0.013903647 0.205204023 0.687814128 -0.17511517 VQAGPGS(ph)PRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQAGPGSPRR 10 1 Q6PK04;I3L0U5;I3L4F6 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 VQAGPGS(1)PRR 79.466 0.016489 65828000 52396 37714 46833 45394 58292 46565 65576 48051 67716 TRUE FALSE 49919.34492 41557.09948 48980.33937 40830.90888 68458.10634 44952.44237 55571.17681 43843.39971 78217.05143 0.638215632 0.531304859 0.626210506 0.522020559 0.875232511 0.574714101 0.710473941 0.560535061 1 16.25519553 -5 0.235058216 3.049778752 0.58859598 0.547583091 0.104628806 116.7639831 1.166373326 114.2050326 0.154220414 1.00E-05 5 -2.461182772 VQAHAAAALINFTEDCPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQAHAAAALINFTEDCPK 18 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 106.94 0.00065151 0 207160 169090 170570 207950 171550 187850 227750 208750 160180 FALSE TRUE 197367.9574 186320.4632 178390.8032 187046.4709 201468.2657 181344.7074 193002.5546 190470.7433 185019.8963 1.066739098 1.007029336 0.964170918 1.010953279 1.088900544 0.98013625 1.043144864 1.02946087 1 17.4973209 4.597259946 3.168761889 1.017231523 1.067558916 0.177782174 0.034330497 0.492907567 8.466767467 0.008066901 0.050697546 39560.33371 -4.597259946 0.050327393 VQAMQISSEKEEDDNEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ;; 149.36 3.53E-08 335720000 334858 371783 301559 418178 188947 348440 330502 393261 208237 FALSE TRUE 319029.926 409668.1104 315385.7784 376141.953 221899.297 336373.4354 280077.8498 358824.982 240529.3304 1.326366 1.703193992 1.311215467 1.563809088 0.922545689 1.398471591 1.164422856 1.491813832 1 17.8758533 2.778730421 24.99992647 1.218917896 1.488182429 0.326128444 0.198576688 582.2456695 362363.1706 0.054226074 0.057514785 600.8006879 -2.778730421 0.269264534 VQAYEEPSVAS(ph)SPNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVAS(0.709)S(0.291)PNGK 237.89 9.40E-20 240240000 240200 264300 251290 284680 187020 266220 269400 263550 179090 TRUE FALSE 228846.222 291232.4705 262811.8951 256063.4255 219636.2288 257000.7346 228298.0821 240472.1648 206862.3625 1.106272882 1.407856252 1.270467435 1.237844441 1.061750558 1.242375517 1.103623102 1.162474226 1 17.65831165 2.902821049 5.519485526 1.130014418 1.268955274 0.346846733 0.095326944 0.257945769 11.74976409 0.027616667 0.029528637 799.5047506 -2.902821049 0.138940856 VQAYEEPSVASS(ph)PNGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVAS(0.027)S(0.973)PNGK;VQAYEEPSVAS(0.06)S(0.94)PNGK;VQAYEEPSVAS(0.001)S(0.999)PNGK;VQAYEEPSVAS(0.021)S(0.979)PNGK;VQAYEEPSVAS(0.181)S(0.819)PNGK 331.19 1.56E-71 1173736000 3645350 3690570 3384900 4166590 2448525 3915530 4037590 3884930 2773230 TRUE FALSE 3473041.53 4066643.279 3540101.013 3747756.457 2875546.985 3779934.214 3421581.49 3544744.934 3203288.345 1.084211334 1.269521455 1.10514591 1.169971621 0.897685964 1.180016848 1.06814658 1.106595646 1 21.61112224 VQCCLYFIAPSGHGLKPLDIEFMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQCCLYFIAPSGHGLKPLDIEFMK 24 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1 E7EPK1 7-Sep Septin-7 0 ; 194.37 1.55E-18 180624000 560640 466130 460520 592650 412570 535870 664520 650230 437830 FALSE TRUE 534139.6583 513629.1769 481635.2975 533075.696 484522.0774 517312.6875 563135.2693 593292.4141 505726.4403 1.056182979 1.015626505 0.952363292 1.054079149 0.958071477 1.022910108 1.113517555 1.173148894 1 18.94799768 1.772132102 5.173210808 1.107194746 1.011055103 0.354212194 0.053874518 0.177704006 10.27887721 0.024217461 0.01304095 59.17416009 -1.772132102 -0.096139643 VQDLSAGGQGSLTDSGPERRPEGPGAQAPS(ph)SPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQDLSAGGQGSLTDSGPERRPEGPGAQAPSSPR 33 2 P40222 P40222 TXLNA Alpha-taxilin 1 VQDLSAGGQGSLTDSGPERRPEGPGAQAPS(0.5)S(0.5)PR;VQDLSAGGQGSLTDSGPERRPEGPGAQAPS(0.852)S(0.148)PR;VQDLSAGGQGSLTDS(0.002)GPERRPEGPGAQAPS(0.499)S(0.499)PR 177.58 7.91E-20 1168270000 535900 237509 618900 381430 763370 437268 830850 521962 961590 TRUE FALSE 510569.0691 261711.4371 647277.1772 343087.9317 896501.4863 422125.2995 704088.5729 476256.2402 1110708.466 0.459678741 0.23562568 0.582760641 0.308891075 0.807143831 0.380050492 0.633909432 0.428786 1 20.08304876 -4.999999996 0.143470891 2.859876833 0.285693341 0.507720975 0.162709451 97.88677546 0.851332742 51.91567202 0.817514487 1.00E-05 4.999999996 -2.574183491 VQDLSAGGQGSLTDSGPERRPEGPGAQAPSS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQDLSAGGQGSLTDSGPERRPEGPGAQAPSSPR 33 2 P40222 P40222 TXLNA Alpha-taxilin 1 VQDLSAGGQGSLTDSGPERRPEGPGAQAPS(0.42)S(0.58)PR 213.61 1.24E-28 391190000 229850 81111 272360 168390 311860 186300 349430 231010 435470 TRUE FALSE 218985.446 89376.30312 284847.9754 151463.1173 366248.2853 179848.3843 296118.0358 210781.5397 503000.4635 0.435358338 0.177686324 0.56629764 0.30111924 0.728127133 0.35755113 0.588703306 0.419048401 1 18.9402002 -4.999999998 0.151752948 3.05463857 0.25953515 0.571452208 0.152461565 85.21521275 0.763584613 52.63783886 0.660506233 1.00E-05 4.999999998 -2.795103419 VQDNFDKIEFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQDNFDKIEFNR 12 1 Q9UH65 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 121.56 0.0003412 601680000 1144930 1062530 1049880 1215460 842980 1073480 1116230 1131310 913750 FALSE TRUE 1090811.428 1170803.015 1098018.036 1093279.652 989995.4451 1036305.118 945928.6125 1032246.499 1055449.683 1.033503961 1.109293066 1.040331959 1.035842512 0.937984502 0.981861225 0.896232788 0.978015831 1 20.00942637 2.911627518 2.162550673 0.948461197 1.068710017 0.636124192 0.035622269 0.160609899 1.488223344 0.011270357 0.012478195 815.8823119 -2.911627518 0.12024882 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.551)S(0.395)NT(0.054)GLGEDIIHQLSK;VQDT(0.658)S(0.337)NT(0.005)GLGEDIIHQLSK;VQDT(0.626)S(0.365)NT(0.008)GLGEDIIHQLSK;VQDT(0.649)S(0.344)NT(0.007)GLGEDIIHQLSK 305.7 6.89E-50 490628000 470252 541034 485347 619276 416481 583350 612905 594127 482658 TRUE FALSE 448024.1199 596165.9797 507600.64 557025.1999 489115.1545 563148.4432 519395.0855 542102.0902 557506.1376 0.803621861 1.069344245 0.910484398 0.999137341 0.877326942 1.010120616 0.931640121 0.972369726 1 19.08862816 4.718555315 4.225641936 0.966640947 0.794046688 0.478351805 0.054801697 0.158030823 5.781313496 0.01154738 0.077689975 52306.45832 -4.718555315 -0.172594259 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.201)S(0.792)NT(0.007)GLGEDIIHQLSK;VQDT(0.249)S(0.746)NT(0.005)GLGEDIIHQLSK;VQDT(0.173)S(0.819)NT(0.008)GLGEDIIHQLSK;VQDT(0.293)S(0.7)NT(0.007)GLGEDIIHQLSK 303.6 2.44E-50 654618000 853161 965209 817610 1141413 758682 1066907 1140396 1106601 860793 TRUE FALSE 812833.7703 1063564.894 855098.2272 1026675.997 890995.9006 1029959.743 966407.6454 1009701.15 994280.3821 0.817509613 1.069683073 0.860017197 1.032581971 0.896121372 1.035884607 0.971966925 1.015509476 1 19.92329322 4.701750841 3.831984682 0.981803744 0.807300522 0.401543881 0.064141753 0.204860651 5.409472135 0.013288119 0.092556251 50321.18286 -4.701750841 -0.174503223 VQEFDSGLLHWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQEFDSGLLHWR 12 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 0 114.56 0.0010442 31753000 42524 36253 37032 37993 47344 35864 49496 42858 46428 FALSE TRUE 40513.97479 39947.22192 38729.95383 34173.87146 55600.77861 34622.02069 41944.47614 39105.12632 53627.81712 0.75546567 0.744897407 0.722198961 0.637241516 1.03678989 0.645598172 0.782140285 0.729194817 1 15.71069391 -1.24704377 3.413558934 1.00065345 0.756282834 0.328014213 0.109443295 35002858.75 55719249.86 243593.2589 0.023129413 0.056618222 1.24704377 -0.244370615 VQEFEHVNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 124.1 0.00044442 95598000 70630 87262 66413 84803 77256 75607 63638 70685 68689 FALSE TRUE 67291.45988 96154.09701 69458.10174 76278.44132 90729.42194 72988.71063 53928.85431 64495.44668 79340.93931 0.848130366 1.211910243 0.875438359 0.961400785 1.143538541 0.919937567 0.679710308 0.812889881 1 16.27577786 1.995274199 24.3212836 0.796415199 1.014731747 0.256651306 0.133671083 142.9682053 735785.9992 0.047523664 0.034149968 98.9177431 -1.995274199 0.218316548 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VQEHEDS(1)GDS(1)EVENEAK;VQEHEDS(1)GDS(1)EVENEAK 262.17 3.66E-27 2260480000 3036340 2616850 2748970 3006530 1862660 2877400 3171050 2898500 1949630 TRUE FALSE 2892818.226 2883509.99 2875012.994 2704307.892 2187507.314 2777754.917 2687248.082 2644691.974 2251968.663 1.284573037 1.28043966 1.276666519 1.200863909 0.971375557 1.233478495 1.1932884 1.174391108 1 21.10275532 7.999999902 0.039599084 0.487568927 2.352185144 0.46317925 0.080924563 703.4066569 2.122021865 27.53084235 88.47687944 99999977.44 -7.999999902 1.864616217 VQEKPDS(ph)PGGSTQIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VQEKPDSPGGSTQIQR 16 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 VQEKPDS(0.986)PGGS(0.013)T(0.001)QIQR;VQEKPDS(1)PGGSTQIQR;VQEKPDS(1)PGGSTQIQR;VQEKPDS(1)PGGSTQIQR;VQEKPDS(0.508)PGGS(0.184)T(0.308)QIQR;VQEKPDS(0.994)PGGS(0.006)T(0.001)QIQR;VQEKPDS(0.992)PGGS(0.006)T(0.002)QIQR 208.44 8.99E-12 3033783000 3851110 3402290 3510250 4091570 2436390 3957950 4316620 4322770 2877030 TRUE FALSE 3669075.662 3748987.219 3671198.435 3680277.61 2861295.645 3820885.199 3658040.339 3944245.342 3323185.119 1.104084043 1.12813072 1.10472282 1.10745489 0.861010008 1.149765981 1.100763336 1.186887038 1 21.66413523 2.966891613 24.98703325 1.067015093 1.113472065 0.074637628 0.087980184 1971.69721 1488048.266 0.026080974 0.027681792 926.5985438 -2.966891613 0.046456972 VQENSPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQENSPGHR 9 0 Q9H8Y8;F8WEG2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;; 102.06 0.0036456 148977100 139548 133595 132299 144336 146400 139943 163912 147430 155755 FALSE TRUE 132951.8426 147208.4824 138365.04 129827.0711 171932.1136 135096.7388 138904.2139 134520.2476 179908.6899 0.738996224 0.818239977 0.769084807 0.721627572 0.955663196 0.750918362 0.772081738 0.747714008 1 17.45690535 -1.151761514 3.711179729 1.000143813 0.784962431 0.512529336 0.066110008 18635322.72 30937667.47 33510.41424 0.014569428 0.070508015 1.151761514 -0.215181382 VQESTKGPDEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQESTKGPDEAK 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 145.43 5.42E-05 506840000 911150 714120 795560 1023170 532560 1075670 1117710 1099000 575800 FALSE TRUE 868081.7452 786889.6399 832037.2129 920319.0077 625438.2954 1038419.278 947182.8113 1002765.734 665092.1232 1.305205271 1.183128791 1.251010475 1.383746665 0.940378443 1.561316458 1.424137767 1.507709532 1 19.34319466 2.205273903 24.99994688 1.415749436 1.226588596 0.133896077 0.187925953 283.6903226 213063.6679 0.0617677 0.045621282 160.4256852 -2.205273903 -0.18916084 VQGGHS(ph)PDDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQGGHSPDDHR 11 0 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 1 VQGGHS(1)PDDHR 86.497 0.0092924 69305000 136910 110450 118130 146890 128070 111490 134870 120080 27135 TRUE FALSE 130438.5356 121704.9806 123546.3773 132124.3381 150405.3675 107629.0733 114293.1044 109565.1586 31342.95721 4.161653757 3.88300886 3.941758798 4.215439444 4.798697405 3.433915715 3.646532255 3.495686698 1 14.93585368 0.254401159 0.667553797 0.907503591 4.114032892 0.894160247 0.327584376 0.808637601 0.487248128 0.493254376 0.121283837 1.796392192 -0.254401159 3.206529301 VQGGVPAGS(ph)DEYEDECPHLIALSSLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQGGVPAGSDEYEDECPHLIALSSLNR 27 0 Q9BVS4-2;Q9BVS4;H0Y919;H0Y8R4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 VQGGVPAGS(1)DEYEDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR 232.27 8.86E-36 770810000 344685 352099 319520 353012 325389 335308 387711 366573 363435 TRUE FALSE 328392.4231 387978.2884 334170.308 317526.5631 382136.7386 323696.1999 328558.5661 334473.9248 419794.6436 0.782269207 0.924209716 0.796032806 0.756385456 0.91029446 0.771082254 0.782664979 0.796756056 1 18.67932423 -1.167872276 4.004950265 1.000074743 0.818673637 0.508660841 0.057049579 10363859.23 29970363.9 12247.49339 0.013938788 0.067940341 1.167872276 -0.181401106 VQHQDALQISDVVMASLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQHQDALQISDVVMASLLR 19 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 144.01 1.40E-07 91695000 79698 86169 81285 95164 72508 79109 91036 94353 79721 FALSE TRUE 75930.83349 94949.71907 85011.99765 85597.93392 85153.37224 76369.43549 77146.78621 86090.95112 92083.72552 0.824584725 1.031123779 0.923203282 0.929566364 0.924738565 0.829347803 0.837789585 0.934920374 1 16.49065858 2.445063928 24.32598729 0.879337915 0.932274189 0 0.069387718 309.0943262 234547.1265 0.022856409 0.019123234 278.6531313 -2.445063928 0.052936273 VQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(1)DNEEDS(0.942)Y(0.058)DEEIHDPR;VQIPVS(0.002)RPDPEPVS(0.994)DNEEDS(0.527)Y(0.477)DEEIHDPR;VQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.923)Y(0.077)DEEIHDPR;VQIPVSRPDPEPVS(1)DNEEDS(0.653)Y(0.347)DEEIHDPR 181.32 1.38E-17 2999210000 1382780 1307930 1332990 1426160 1418050 1322790 1494570 1369230 1390550 TRUE FALSE 1317418.73 1441209.554 1394108.91 1282799.687 1665357.471 1276981.451 1266545.897 1249332.962 1606189.392 0.820213816 0.897284941 0.867960476 0.798660291 1.036837548 0.795037906 0.788540818 0.77782419 1 20.61521059 -0.30449003 8.286679962 1.000000435 0.848520268 0.279917947 0.076711884 0 0 0.071013426 0.016738025 0.496032315 0.30449003 -0.151480168 VQIS(ph)PDSGGLPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.885)PDS(0.115)GGLPER;VQIS(0.961)PDS(0.039)GGLPER;VQIS(0.931)PDS(0.069)GGLPER;VQIS(0.995)PDS(0.005)GGLPER;VQIS(0.986)PDS(0.014)GGLPER;VQIS(0.63)PDS(0.37)GGLPER 228.84 7.09E-12 3810680000 3957610 3258560 3466030 3804180 3689000 3491320 4228710 3641320 4003150 TRUE FALSE 3770541.619 3590610.969 3624950.904 3421776.599 4332360.432 3370414.713 3583542.624 3322466.717 4623938.057 0.815439474 0.776526615 0.783953171 0.740013503 0.93694171 0.72890568 0.774997974 0.718536165 1 22.14069064 -1.020606897 4.258240106 1.00001417 0.785504542 0.550098713 0.061264766 6140088.304 2943289.427 775.9126815 0.012992665 0.095365898 1.020606897 -0.214509628 VQKDDIEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQKDDIEVR 9 1 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 ; 91.937 0.0081877 0 608920 477950 482790 591910 495320 551660 650210 596600 550480 FALSE TRUE 580137.5584 526653.6484 504926.399 532410.0822 581703.6512 532555.8759 551008.5226 544358.5412 635845.6269 0.912387431 0.828272817 0.794102181 0.837326011 0.914850439 0.837555302 0.866575941 0.856117457 1 19.27831702 -2.041104974 0.504473978 1.153141469 0.853978388 0.606259567 0.036529712 57.88637045 4.445799914 10.2474886 0.016963184 0.009096934 2.041104974 -0.29916308 VQLEELRDDLELYYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQLEELRDDLELYYK 15 1 Q14746-2;Q14746;V9GY21 Q14746-2 COG2 Conserved oligomeric Golgi complex subunit 2 0 129.38 6.04E-05 39928000 37693 30985 34653 41450 31648 34837 45370 43419 38721 FALSE TRUE 35911.32659 34142.40673 36241.87433 37283.36725 37167.40118 33630.58595 38447.97322 39617.00218 44725.65492 0.802924555 0.763374103 0.810315118 0.833601371 0.83100854 0.751930542 0.859640251 0.885778023 1 15.44881499 0.996024898 1.276291954 0.998781685 0.797708042 0.833735519 0.028522056 0.177753815 0.5940955 0.026286244 0.008075702 9.908887496 -0.996024898 -0.201073643 VQLS(ph)ESPASLPSCPPVETALINQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQLSESPASLPSCPPVETALINQR 24 0 H7C3T2;Q2TAZ0-3 H7C3T2 ATG2A Autophagy-related protein 2 homolog A 1 VQLS(0.4)ES(0.306)PAS(0.293)LPSCPPVETALINQR 73.389 0.017478 31192000 14833 13986 15139 12835 17988 14877 16258 16477 19123 TRUE FALSE 14131.87349 15411.1893 15833.13812 11544.80142 21125.1015 14361.80576 13777.5435 15034.18653 22088.49717 0.63978429 0.697702029 0.716804679 0.522661244 0.956384735 0.650193884 0.62374291 0.680634197 1 14.43100765 -2.146730535 2.253316908 1.680094537 0.68241381 0.447015879 0.109695667 6202032.174 1515631.604 21537492.67 0.024040052 0.007132955 2.146730535 -0.997680727 VQLVVGDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQLVVGDGR 9 0 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 83.647 0.037287 102280000 148150 102340 136400 150340 151660 132130 165510 159780 130100 FALSE TRUE 141147.2431 112768.5624 142654.0749 135227.5376 178109.456 127554.305 140258.4097 145788.8162 150275.2435 0.939258122 0.750413439 0.949285269 0.899865702 1.185221543 0.848804513 0.93334342 0.970145266 1 17.19724783 3.574446221 8.221414565 0.964796593 0.844823131 0.219328259 0.097953154 0.43040427 32.88564888 0.024723243 0.038329923 3753.584703 -3.574446221 -0.119973462 VQMTS(ph)PSSTGSPMFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 VQMT(0.038)S(0.854)PS(0.026)S(0.038)T(0.038)GS(0.005)PMFK;VQMT(0.001)S(0.982)PS(0.011)S(0.002)T(0.005)GSPMFK;VQMT(0.001)S(0.891)PS(0.106)S(0.001)TGSPMFK 197.75 8.67E-09 216690000 668392 536287 629824 708900 578981 628414 762161 692969 849620 TRUE FALSE 636798.4348 590935.255 658702.0534 637640.0252 679955.1031 606651.8656 645879.3414 632288.9607 981374.7303 0.648884076 0.60215047 0.671203398 0.649741638 0.692859804 0.618165362 0.658137327 0.644289017 1 19.9044446 -4.842666853 0.492958351 10 0.64263448 0.94981468 0.025398703 361.482351 2.067046752 3571.976583 0.011694795 1.44E-05 4.842666853 -9.35736552 VQNGSVHQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQNGSVHQK 9 0 Q9Y5A9;S4R3J8;S4R3V3 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 74.165 0.033859 0 65296 55582 63840 68459 58824 61244 76883 76887 64000 FALSE TRUE 62209.58748 61245.86899 66767.12715 61577.37126 69082.88698 59123.10492 65153.0863 70154.36668 73924.79313 0.841525351 0.828488879 0.903176381 0.832973197 0.93450227 0.799773695 0.881342829 0.948996456 1 16.17377068 1.150661929 2.566777996 0.997497356 0.85518248 0.622482918 0.038406252 0.153000421 1.831126431 0.032550478 0.009000583 14.14692103 -1.150661929 -0.142314876 VQNS(ph)PPVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 VQNSPPVGR 9 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR 158.02 7.04E-05 17971310000 11563510 10941890 10606010 12359850 10780700 10836810 12483440 12037680 11562410 TRUE FALSE 11016925.8 12056881.03 11092306.05 11117414.4 12660850.67 10461528.55 10578861.95 10983596.92 13355449.49 0.824901162 0.902768644 0.830545318 0.832425326 0.947991356 0.783315347 0.79210078 0.822405635 1 23.6709252 VQNS(ph)PPVGRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQNSPPVGRK 10 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VQNS(1)PPVGRK;VQNS(1)PPVGRK;VQNS(1)PPVGRK;VQNS(1)PPVGRK 89.46 0.0070424 3442800000 4729110 1982080 4923150 3497180 4455110 4635430 7395650 5623930 6926100 TRUE FALSE 4505574.342 2184056.205 5148881.297 3145636.822 5232079.773 4474903.897 6267307.762 5131468.875 8000164.214 0.563185232 0.273001422 0.643596951 0.393196532 0.653996547 0.559351505 0.78339739 0.641420443 1 22.93159818 1.310770521 0.393305249 1.017245606 0.408752908 0.640602929 0.118475087 0.610727479 0.284464369 0.145619875 0.097743109 20.45363593 -1.310770521 -0.608492698 VQPQWS(ph)PPAGTQPCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQPQWSPPAGTQPCR 15 0 P49589-3;P49589;B4DKY1;P49589-2;E9PLP0;C9JLN0;E9PRS8 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR 184 5.06E-07 196259000 289870 274770 258230 316440 292880 265080 323230 285340 333490 TRUE FALSE 276168.4196 302769.3754 270070.1009 284630.85 343958.1793 255900.2131 273915.327 260354.1169 385205.926 0.7169371 0.785993556 0.701105779 0.738905689 0.89292027 0.664320551 0.71108804 0.675882948 1 18.55527037 -1.430347378 3.309258301 1.00340176 0.737790259 0.619190564 0.065076066 13303615.3 16037308.03 415728.0225 0.015044358 0.037123817 1.430347378 -0.265611501 VQQGERDFEQISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQQGERDFEQISK 13 1 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 205.61 6.25E-08 147930000 183590 84370 154200 140290 179750 168640 245620 183270 234750 FALSE TRUE 174912.0645 92967.39892 161270.2225 126187.7827 211098.3431 162799.9545 208146.1579 167221.9072 271153.8311 0.645065806 0.342858512 0.594755464 0.465373409 0.778518755 0.600397029 0.767631263 0.61670494 1 18.04875203 0.794392935 0.290300972 1.071208514 0.457243356 0.576617371 0.11634761 1.642865769 0.37781804 0.346833454 0.167737253 6.228635758 -0.794392935 -0.613965159 VQQLLHICSEHFDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQQLLHICSEHFDSK 15 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 210.9 9.53E-10 510120000 1157670 1016740 1021250 1213710 824710 1065220 1125950 1160810 197017 FALSE TRUE 1102949.233 1120346.962 1068075.323 1091705.565 968539.1629 1028331.164 954165.648 1059163.323 227569.3901 4.846650214 4.923100428 4.69340504 4.797242565 4.256016867 4.518758712 4.192855847 4.654243358 1 17.79594699 -0.815283481 0.454729736 7.52E-16 4.790931359 0.960755836 0.229618797 2.285544445 0.34751041 3.626331332 0.119000475 0.153008839 0.815283481 4.790931359 VQQTVQDLFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQQTVQDLFGR 11 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 138.76 0.00011814 922549000 1466377 1299604 879721 1445566 977447 1047051 1296631 1334291 1006798 FALSE TRUE 1397064.265 1432035.125 920057.078 1300254.959 1147913.447 1010791.361 1098806.127 1217453.407 1162927.092 1.201334353 1.231405765 0.791156285 1.118088114 0.98708978 0.869178617 0.944862438 1.046887131 1 20.14932922 3.763809336 24.946189 0.963188037 1.216370116 0.575989177 0.089533773 440.0325835 434758.5108 0.02114551 0.038101313 5805.095059 -3.763809336 0.253182079 VQRAVCMLSNTTAVAEAWARLDHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQRAVCMLSNTTAVAEAWARLDHK 24 2 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 46.982 0.089267 93931000 244690 127860 238860 196300 172940 258550 336750 270910 203800 FALSE TRUE 233123.9886 140889.0794 249811.9673 176567.5511 203100.6812 249596.3487 285372.6027 247187.6842 235404.2631 0.990313368 0.598498419 1.061204092 0.750060975 0.862774015 1.060288142 1.212266077 1.050056107 1 17.84478092 2.210433688 3.893160877 1.115904543 0.832942283 0.402954617 0.135910795 0.176135092 5.770705244 0.049202377 0.036630799 162.3430452 -2.210433688 -0.282962261 VQRPHSS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQRPHSSPPR 10 1 R4GNF5;E9PP52;E9PMB0;E9PJ55;Q9NUJ3 R4GNF5 TCP11L1 T-complex protein 11-like protein 1 1 VQRPHS(0.177)S(0.823)PPR;VQRPHS(0.093)S(0.907)PPR;VQRPHS(0.069)S(0.931)PPR;VQRPHS(0.219)S(0.781)PPR 116.98 0.00061665 1712520000 897640 858370 804950 1048660 835910 859420 943100 943100 824010 TRUE FALSE 855210.3362 945838.8789 841857.7537 943246.7045 981692.4393 829658.0699 799212.7738 860517.1643 951793.2623 0.89852531 0.993744037 0.884496442 0.991020573 1.03141352 0.871678864 0.839691565 0.90410092 1 19.86028872 2.194574061 24.99994144 0.88439151 0.956881982 0.141983426 0.060219855 180.4438988 102554.9689 0.021102462 0.015585289 156.5215214 -2.194574061 0.072490472 VQS(ph)LPSVPLSCAAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(0.806)LPS(0.194)VPLSCAAYR;VQS(1)LPSVPLSCAAYR 218.83 1.98E-12 151221000 265053 244067 222871 268549 241333 251705 292160 242670 254940 TRUE FALSE 252524.47 268937.7048 233089.8558 241553.9443 283421.3988 242988.3927 247585.6261 221420.5283 294474.7931 0.857541888 0.913279204 0.79154434 0.820287338 0.962464039 0.825158548 0.840770184 0.751916746 1 18.16778462 VQS(ph)PSQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQSPSQTR 8 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;J3KSK9 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 VQS(0.943)PS(0.057)QTR 88.576 0.015228 338780000 501740 570080 673750 660440 392800 635650 490090 558300 370230 TRUE FALSE 478023.7446 628171.8001 704642.1039 594051.3164 461304.1956 613637.2811 415317.7694 509412.2923 427643.3775 1.1178093 1.468915066 1.647732997 1.389127829 1.078712357 1.43492759 0.971177835 1.191208187 1 18.70604867 1.974629449 1.095817695 1.041168811 1.381292862 0.353147758 0.179822284 0.570785706 1.261486345 0.139660747 0.063932451 94.3255724 -1.974629449 0.340124051 VQSCPDPAVYGVVQSGDHIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQSCPDPAVYGVVQSGDHIGR 21 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 176.61 1.77E-13 89548000 146550 122680 137570 148550 135070 134970 153850 152840 158620 FALSE TRUE 139622.8719 135181.2315 143877.7206 133617.4718 158626.1652 130295.9551 130377.3569 139456.5193 183217.9795 0.762058791 0.737816408 0.785281668 0.729281439 0.865778379 0.711152669 0.711596958 0.761150842 1 17.48320156 -1.451098001 3.102077585 1.004870874 0.754332809 0.74184508 0.044814883 13220596.4 16700130.68 562578.0746 0.010260749 0.035391747 1.451098001 -0.250538065 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 VQSGMGLILQGY(0.001)ES(0.999)GS(1)EEEGEIHEK;VQSGMGLILQGYES(1)GS(1)EEEGEIHEK 164.17 1.60E-11 169747000 243770 205985 226550 243740 188494 243500 287010 259450 165514 TRUE FALSE 232247.4752 226975.1057 236937.5416 219238.7921 221367.2939 235067.5339 243221.3532 236731.1826 191181.0658 1.214803748 1.187225862 1.239335813 1.146759964 1.157893398 1.22955447 1.272204191 1.238256422 1 17.54458012 -1.214633236 3.736103951 0.999760914 1.211617168 0.749863399 0.038251068 3016555.229 980709.7239 5952.907383 0.009644627 0.061005187 1.214633236 0.211856254 VQT(ph)TPPPAVQGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.713)T(0.287)PPPAVQGQK;VQT(0.608)T(0.392)PPPAVQGQK 106.32 0.01546 562885000 740840 650350 692210 795140 588980 771590 887130 816800 704870 TRUE FALSE 705821.9614 716621.4044 723948.5132 715211.0165 691697.9255 744869.6448 751782.0252 745276.6619 814177.6396 0.86691396 0.880178194 0.889177592 0.878445909 0.84956635 0.91487362 0.923363635 0.915373532 1 19.63498407 0.884211876 0.556912341 1.001879127 0.871854941 0.851026979 0.01605928 0.372724048 0.268592249 0.017849983 0.007640722 7.65970204 -0.884211876 -0.130024186 VQT(ph)TPSKPGGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.86)T(0.139)PS(0.001)KPGGDR;VQT(0.598)T(0.342)PS(0.06)KPGGDR;VQT(0.499)T(0.499)PS(0.002)KPGGDR 125.39 0.00049493 2695800000 3220230 3028390 3061010 3456080 2391020 3421910 3579360 3784220 2893690 TRUE FALSE 3068016.11 3336986.384 3201360.336 3108668.272 2808013.131 3303408.399 3033262.893 3452853.635 3342428.666 0.91790025 0.998371758 0.957794662 0.930062713 0.840111611 0.988325774 0.907502656 1.033037345 1 21.67246534 1.232193178 24.99976741 1.016518707 0.938213614 0.365042333 0.044852381 183.3194505 719713.1404 0.037841948 0.010377074 17.06841439 -1.232193178 -0.078305093 VQTEKEEKEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQTEKEEKEEAR 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 91.307 0.0047086 111940000 245770 201480 222200 268920 169400 251100 303670 308100 202700 FALSE TRUE 234152.9392 222011.0411 232388.0898 241887.6507 198943.3064 242404.344 257339.5642 281121.1307 234133.6808 1.000082254 0.948223427 0.992544469 1.033117704 0.849699649 1.035324535 1.09911382 1.200686419 1 17.83697296 1.886267568 3.590450846 1.109840403 0.968607293 0.4446336 0.068015341 0.196560152 4.258761208 0.030748134 0.016905849 76.96044464 -1.886267568 -0.14123311 VQTT(ph)PPPAVQGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.169)T(0.831)PPPAVQGQK;VQT(0.089)T(0.911)PPPAVQGQK;VQT(0.177)T(0.823)PPPAVQGQK 146.77 0.00047455 961561000 980890 855490 900460 1027800 704930 975560 1142590 1014400 845140 TRUE FALSE 934525.2736 942665.4036 941746.9817 924483.5913 827869.5688 941776.1126 968266.9104 925573.7583 976199.9948 0.957309238 0.965647827 0.964707014 0.947022737 0.84805324 0.964736855 0.991873505 0.948139483 1 19.89681722 2.008959481 24.99544719 0.978902353 0.941012591 0.233895197 0.036011078 331.5113512 924856.91 0.013734411 0.01013087 102.0844237 -2.008959481 -0.037889763 VQTT(ph)PSKPGGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.189)T(0.784)PS(0.027)KPGGDR;VQT(0.336)T(0.662)PS(0.002)KPGGDR 131.96 0.00030634 1651640000 2749200 2789400 2707900 3060300 2055540 3019000 3208900 3319100 2466000 TRUE FALSE 2619250.764 3073643.031 2832059.893 2752672.83 2414025.525 2914451.273 2719323.37 3028462.008 2848414.685 0.919546855 1.079071473 0.994258283 0.96638767 0.847497921 1.023183628 0.954679592 1.06320966 1 21.44172777 -0.887282743 5.058542193 1.000000042 0.981928657 0.007638131 0.067366713 3.02E-08 6.70E-09 0.061430348 0.014479238 0.129633503 0.887282743 -0.018071385 VQVAALQAS(ph)PPLDQDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 230.29 8.75E-16 106938000 148470 153840 127510 172156 147743 139447 144273 145764 139511 TRUE FALSE 141452.1173 169516.4709 133356.4596 154850.5518 173509.3324 134617.9154 122261.5041 133000.1314 161145.6534 0.877790461 1.051945661 0.827552322 0.960935331 1.076723627 0.835380369 0.758701842 0.825341104 1 17.29800575 2.088495524 12.25239602 0.825172549 0.958361612 0.202622866 0.095079217 0.625763846 83.21153446 0.032925639 0.024316585 122.6014266 -2.088495524 0.133189063 VQVEYK ddPTM_SK-BR-3_Trastuzumab_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 0 107.43 0.072758 430620000 463490 502390 371980 495190 334770 444930 469740 461860 374190 FALSE TRUE 441581.7462 553584.1122 389035.6509 445412.5604 393153.782 429521.9625 398072.5356 421417.0899 432217.4741 1.021665649 1.280799934 0.900092371 1.030528813 0.909620285 0.993763529 0.92100056 0.97501169 1 18.72139787 3.725108865 24.99971662 0.958590287 1.151232798 0.532213207 0.073940742 468.2135408 870162.2171 0.017973732 0.028010623 5310.175377 -3.725108865 0.192642511 VQVEYKGETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 149.38 2.14E-05 4882300000 7813540 4904310 6395180 6253040 5193600 7232590 10064750 8552570 6511480 FALSE TRUE 7444209.449 5404064.765 6688405.329 5624472.539 6099362.196 6982123.595 8529187.536 7803661.631 7521247.062 0.989757335 0.718506482 0.889268132 0.747811166 0.810950916 0.928319936 1.134012414 1.037548902 1 22.84254046 1.973511373 4.193745261 1.066870511 0.830561111 0.618212222 0.080819542 0.128288968 5.025321718 0.034679765 0.021252072 94.08304678 -1.973511373 -0.2363094 VQVNHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VQVNHEK 7 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 94.114 0.014438 1053680000 2454110 1974980 1930610 2574250 1748350 1946260 2298680 1947440 1796380 FALSE TRUE 2338109.084 2176232.707 2019130.378 2315481.499 2053261.686 1878860.528 1947974.148 1776911.83 2074953.436 1.126824845 1.048810383 0.973096718 1.11591974 0.98954591 0.905495273 0.938803789 0.856362268 1 20.98464753 2.476806702 4.139218939 0.922585999 1.064675396 0.601499623 0.053984443 0.135177702 5.474124069 0.01789413 0.015583716 299.7827933 -2.476806702 0.142089397 VQVSYKGETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VQVSYKGETK 10 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 62.088 0.079676 479650000 374880 218780 316510 307090 300140 353170 502250 390950 375020 FALSE TRUE 357160.1653 241073.9307 331022.2966 276220.7298 352484.321 340939.6343 425622.538 356716.3454 433176.1863 0.824514774 0.556526278 0.764174733 0.6376637 0.813720449 0.7870692 0.98256218 0.823490203 1 18.72459441 2.168915894 1.385406893 0.93689217 0.690683815 0.549518763 0.089976213 0.288428061 1.062727332 0.051705548 0.028255427 147.5420774 -2.168915894 -0.246208355 VRDALTAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VRDALTAEK 9 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 143.28 9.33E-05 1522390000 2488300 1843450 1484180 1678690 2102970 2023870 2998680 2573040 2493850 FALSE TRUE 2370682.99 2031299.651 1552231.121 1509944.892 2469727.302 1953782.874 2541176.291 2347730.977 2880583.521 0.822987069 0.705169503 0.53885996 0.524180216 0.857370489 0.678259408 0.88217414 0.815019235 1 21.45792966 1.392715971 0.894621296 0.979522256 0.683451618 0.474843507 0.10888266 0.496201998 0.828273476 0.102875989 0.038700714 24.70108161 -1.392715971 -0.296070638 VRDVFEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VRDVFEAK 8 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;; 132.01 0.00089427 1278590000 1394230 1177290 1239870 1488880 1205530 1383910 1841200 1715120 1468610 FALSE TRUE 1328327.511 1297257.189 1296719.266 1339214.954 1415774.05 1335984.85 1560291.124 1564935 1696354.538 0.783048284 0.764732348 0.764415243 0.789466426 0.834597968 0.787562281 0.919790698 0.92252826 1 20.69400629 1.521224733 0.846453661 0.998971566 0.772401156 0.916596996 0.023328707 0.12794504 0.185871883 0.019399506 0.007804738 33.2066246 -1.521224733 -0.22657041 VRDVLDFYNVPIQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRDVLDFYNVPIQDR 15 1 Q8N5N7 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 209.66 2.07E-09 178990000 275680 204880 259290 264100 285220 206490 313700 275600 310560 FALSE TRUE 262649.1527 225757.5049 271178.703 237552.1662 334962.2777 199339.1995 265839.3035 251467.003 358720.0587 0.732184182 0.629341737 0.755961916 0.662221586 0.933770693 0.555695715 0.741077331 0.701011825 1 18.45249889 -1.20136697 4.794479735 1.000043137 0.709010545 0.456496467 0.09797539 3.96E-05 6.59E-06 0.08311648 0.019587843 0.062897449 1.20136697 -0.291032591 VRDVVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VRDVVTK 7 1 Q12931-2;Q12931;I3L0K7;I3L239;I3L2D5 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 72.038 0.048052 180300000 866920 672390 810920 750230 867660 754300 1023650 902660 1041250 FALSE TRUE 825942.4097 740907.3054 848101.4841 674815.4551 1018979.629 728178.4019 867473.3919 823618.3051 1202721.732 0.686727767 0.616025541 0.705151875 0.561073636 0.847228085 0.605442126 0.721258599 0.684795396 1 20.19787146 -5 0.273824864 3.296707612 0.652428062 0.636199978 0.076833565 122.3646488 1.181908903 159.1068846 0.0785815 1.00E-05 5 -2.64427955 VREAAEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VREAAEK 7 1 P38646;H0YBG6;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 108.74 0.0065522 4842725000 3168192 2364324 2713915 2673031 2166259 2488660 3127719 2912292 2763089 FALSE TRUE 3018437.843 2605251.304 2838350.687 2404332.845 2544053.884 2402477.08 2650528.022 2657276.273 3191574.73 0.945751893 0.81629024 0.889326094 0.753337474 0.797115562 0.752756016 0.830476566 0.832590962 1 21.605837 -1.436474595 1.898069677 1.014549088 0.828844429 0.469227853 0.057732273 80406.39466 56186.8059 6185.157191 0.015714711 0.036603735 1.436474595 -0.185704659 VREEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VREEAER 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;;;; 102.46 0.0078384 264865000 356545 283258 298758 338332 335225 334167 424887 330004 364234 FALSE TRUE 339691.8245 312122.3122 312456.3498 304322.2246 393688.1339 322594.713 360062.6846 301107.1003 420717.5485 0.807410639 0.741880897 0.742674868 0.723340934 0.935754012 0.766772658 0.855829964 0.715698932 1 18.68249247 2.772946212 24.99444593 0.83955009 0.757170046 0.263335097 0.081658144 925.2068571 672519.393 0.022133992 0.023475504 592.8518948 -2.772946212 -0.082380044 VREEEIEVDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ;;;;; 182.71 5.17E-06 2181170000 3818210 3436230 3648740 4018510 3720310 3628290 4266910 3907920 4044410 FALSE TRUE 3637730.78 3786385.744 3816038.338 3614561.74 4369130.886 3502641.408 3615914.512 3565721.808 4671596.447 0.778691144 0.810512164 0.816859586 0.773731589 0.935254347 0.749773969 0.774021162 0.763276933 1 22.15548422 -1.300261802 3.914205283 1.000365818 0.799467801 0.592522658 0.052050454 1905623938 340667069.3 6483714.231 0.011382038 0.05008852 1.300261802 -0.200898017 VREEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VREEFK 6 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 85.265 0.050079 26143540000 35848160 30060910 29254950 37102890 25302760 34363930 39522860 35963270 27960900 FALSE TRUE 34153688.52 33124150.91 30596318.39 33373237.01 29715553.33 33173898.49 33492921.82 32814135.43 32296933.57 1.057490131 1.025612875 0.947344377 1.033325252 0.920073519 1.027153195 1.037031016 1.016013962 1 24.94489386 -3.150381491 8.726128019 1.000107853 1.011000062 0 0.042527941 0 0 0 0.009185886 0.000707324 3.150381491 0.010892209 VREEILAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VREEILAK 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 128.36 0.0010368 183260000 169310 155670 148130 183730 155860 167780 223290 200210 163530 FALSE TRUE 161307.0518 171532.95 154921.907 165261.1113 183041.9347 161969.7365 189223.0095 182678.551 188889.3972 0.853976212 0.908113174 0.820172595 0.874909411 0.969042929 0.857484533 1.001766178 0.967119138 1 17.5271822 1.916905932 0.84333285 1.002095742 0.868948195 0.574102087 0.042425082 0.409447965 0.541311706 0.033774278 0.016099418 82.58590501 -1.916905932 -0.133147548 VREELIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VREELIDK 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 121.73 0.0012956 832680000 716460 635850 600395 725880 568483 650680 756220 729760 614890 FALSE TRUE 682594.3557 700643.8379 627923.7046 652913.1633 667626.2552 628146.7884 640844.7501 665858.3457 710244.0008 0.961070217 0.986483289 0.884095753 0.919280082 0.939995628 0.884409848 0.902288156 0.93750647 1 19.43795521 3.751732656 24.692637 0.917089949 0.973776757 0.251541586 0.034187377 653.1748945 1224454.807 0.007848737 0.01404632 5645.893162 -3.751732656 0.056686808 VREEVPLELVEAHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VREEVPLELVEAHVK 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 164.41 8.91E-07 16058000 61644 64669 60878 68073 54521 61783 67108 67937 53526 FALSE TRUE 58730.21029 71258.84462 63669.31652 61230.17271 64029.44514 59643.43922 56869.44208 61988.07612 61826.53871 0.949919105 1.152560795 1.029805612 0.990354207 1.035630434 0.964689929 0.919822511 1.002612752 1 15.91593862 2.619247089 1.339371924 0.961268971 1.049535076 0.177657471 0.056942862 0.537838122 1.961306604 0.026796929 0.022658716 416.1473075 -2.619247089 0.088266105 VREFTMAEIEHFVDPSEKDHPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VREFTMAEIEHFVDPSEKDHPK 22 2 P41250 P41250 GARS Glycine--tRNA ligase 0 102.48 0.00019772 27992000 106840 93832 95212 106820 63170 111190 112720 120030 19076 FALSE TRUE 101789.8849 103393.5875 99577.56438 96082.25066 74186.828 107339.4624 95522.49376 109519.5369 22034.20865 4.61962971 4.692412108 4.519225807 4.360594572 3.366893233 4.871491602 4.335190578 4.97043205 1 14.42745746 3.048639819 4.212188156 4.028213787 4.622506971 0.087706686 1.121911549 0.631544389 23.92471297 0.296854417 0.352388866 1118.509866 -3.048639819 0.594293184 VREITENLMATGDLDQDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VREITENLMATGDLDQDGR 19 1 P13796;Q5TBN3 P13796 LCP1 Plastin-2 0 ; 139.11 5.48E-07 159040000 110083 85854 104213 105829 119745 98137 120605 109945 136678 FALSE TRUE 104879.5948 94602.62021 108991.2691 95190.86786 140628.4901 94738.49108 102204.4922 100317.6329 157873.3262 0.664327517 0.599231184 0.690371653 0.602957258 0.890767893 0.600091816 0.647382903 0.635431174 1 17.26840791 -1.358434461 3.5722223 1.001712591 0.661686793 0.601902129 0.085209354 43066699.72 78747805.93 811269.1413 0.018915533 0.043809222 1.358434461 -0.340025797 VREYELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VREYELR 7 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 151.04 0.0017405 2752400000 3728400 4368300 6700700 4861600 3428800 5704700 4157100 5221200 4098500 FALSE TRUE 3552165.921 4813434.736 7007933.723 4372902.732 4026781.634 5507144.809 3522858.045 4764004.049 4734074.448 0.750340106 1.016763633 1.4803176 0.923708062 0.850595334 1.163299156 0.74414927 1.006322165 1 22.17465096 1.739013251 25 0.894930931 1.01387349 0.055265502 0.208254263 0.227557933 11482.92721 0.096568944 0.053552427 54.8293694 -1.739013251 0.118942559 VRGEVAPDAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VRGEVAPDAK 10 1 P09382;F8WEI7 P09382 LGALS1 Galectin-1 0 ;; 88.83 0.010878 1524080000 3359850 2731510 2990470 3276220 2223260 2871200 3525440 3204220 2607680 FALSE TRUE 3201036.549 3009853.974 3127586.007 2946888.141 2610995.84 2771769.624 2987569.379 2923641.51 3012065.696 1.062737959 0.999265713 1.03835252 0.978361177 0.866845582 0.920222168 0.99186727 0.970643341 1 21.52232181 3.09076929 4.74512859 0.948063638 1.029756753 0.46805104 0.040405929 0.1867637 7.337225123 0.01203689 0.014495847 1232.449945 -3.09076929 0.081693116 VRGGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.601)S(0.399)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.6)S(0.4)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.597)S(0.403)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.696)S(0.304)PDAR 226.07 8.55E-35 2832660000 1663370 1306280 1633350 1447880 1663490 1308060 1907010 1757120 2185440 TRUE FALSE 1584745.797 1439391.417 1708240.713 1302336.352 1953602.129 1262761.554 1616060.6 1603257.258 2524346.874 0.627784483 0.570203498 0.676706015 0.51591022 0.773903995 0.500232978 0.640189594 0.635117651 1 21.26747874 0.404892297 1.826153874 0.999998716 0.611235136 0.703966623 0.078060655 2.9789141 8.56240418 0.063243104 0.017634786 2.540342634 -0.404892297 -0.38876358 VRGQTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VRGQTPK 7 1 P62861;E9PR30;E9PM49 P62861 FAU 40S ribosomal protein S30 0 ; 62.546 0.077342 785350000 898580 817000 865940 996780 1029940 930980 1196200 1094150 1255820 FALSE TRUE 856105.9042 900253.2289 905644.2055 896581.7806 1209561.21 898739.9292 1013697.72 998340.4255 1450566.152 0.590187427 0.620621974 0.624338438 0.618090929 0.833854567 0.619578727 0.698829019 0.688241915 1 20.46818466 -4.999999999 0.169746474 2.345175424 0.573431104 0.753957208 0.063028477 61.29006725 0.577714332 27.72098521 0.213153647 1.00E-05 4.999999999 -1.77174432 VRGSEYDDFLDEFMEAVSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRGSEYDDFLDEFMEAVSSK 20 1 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 112.93 0.00013339 68550000 113150 97166 115760 128640 102250 117070 150780 126030 121610 FALSE TRUE 107801.6237 107067.3259 121067.7105 115708.8628 120082.3676 113015.8365 127775.7417 114994.1451 140468.6577 0.767442542 0.762215057 0.861884156 0.823734381 0.854869475 0.804562658 0.909638804 0.818646287 1 17.09988874 -5 0.058680215 1.675690421 0.530132762 0.717904596 0.037235989 190.8764882 0.819465429 18.68041478 3.239484877 1.00E-05 5 -1.145557659 VRHFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRHFSQSEETGNEVFGALNEEQPLPR 26 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 VRHFS(0.738)QS(0.193)EET(0.069)GNEVFGALNEEQPLPR 106.37 0.001829 84775000 18177 10948 24654 17409 32673 14405 28641 23251 46537 TRUE FALSE 17317.80923 12063.61365 25784.41029 15659.01425 38371.16086 13906.15124 24271.28942 21215.01918 53753.72028 0.322169501 0.22442379 0.479676758 0.291310335 0.713832655 0.258701187 0.451527621 0.394670714 1 15.71407699 -5 0.218275382 4.109700778 0.298861845 0.658229995 0.138375387 85.70558528 0.856726978 117.1133449 0.245920313 1.00E-05 5 -3.810838933 VRLDDDDEGVPSSALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VRLDDDDEGVPSSALR 16 1 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 ; 227.4 4.62E-15 254890000 443330 319550 393290 417020 453470 369670 525140 440940 512750 FALSE TRUE 422374.6695 352112.5083 411322.7355 375100.3573 532555.0244 356868.2352 445020.2481 402328.956 592264.6512 0.713151914 0.594518865 0.694491448 0.63333234 0.899184213 0.602548598 0.751387487 0.679306042 1 19.17588246 -5 0.237966088 2.741645067 0.659512984 0.546833807 0.086917817 118.4237253 1.181719833 99.68218187 0.12474323 1.00E-05 5 -2.082132082 VRPDYTAQNLDHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRPDYTAQNLDHGK 14 1 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 141.85 5.74E-06 197070000 311220 227340 259480 253040 200280 234210 247570 228470 201930 FALSE TRUE 296509.2474 250506.2045 271377.4147 227603.9385 235208.7686 226099.249 209798.6496 208463.9556 233244.2731 1.271239133 1.074007954 1.163490152 0.975817907 1.008422481 0.969366776 0.899480389 0.893758088 1 17.83148213 3.88316836 0.520139514 0.916942386 1.322419234 0.787174555 0.053602693 0.766788325 0.294783901 0.034436596 0.172971432 7641.319518 -3.88316836 0.405476848 VRPGETLLIHSGSGGVGQAAIAIALSLGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 165.3 1.85E-12 583401000 471178.8 496160.5 485702.6 553771.4 507070.4 491593.4 580602.4 565469.6 467611.9 FALSE TRUE 448907.1119 546719.819 507972.5446 498105.2468 595503.3172 474569.3973 492020.8404 515954.0841 540126.7652 0.831114362 1.012206493 0.940469122 0.922200637 1.102525103 0.878625959 0.910935862 0.955246282 1 19.04293852 4.676448393 3.511225457 0.957991217 0.823857238 0.30247723 0.063040778 0.325063793 6.672242934 0.014630837 0.103117488 47473.18758 -4.676448393 -0.134133979 VRPS(ph)SDLNNSTGQSPHHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRPSSDLNNSTGQSPHHK 18 1 J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 VRPS(0.642)S(0.358)DLNNSTGQSPHHK 202.43 7.82E-16 128850000 132490 91389 130940 154400 145510 111690 193250 156300 15276 TRUE FALSE 126227.4603 100701.643 136943.7285 138879.4187 170886.8979 107822.1473 163766.1632 142613.5434 17644.92406 7.153754804 5.707116826 7.761083473 7.870785852 9.684762447 6.110660886 9.281205329 8.082411854 1 14.1069656 -0.074291815 10.10708179 1.000000001 7.613051137 0.747458923 1.224022584 0 0 1.214039688 0.286151899 0.842768287 0.074291815 6.613051135 VRPSS(ph)DLNNSTGQSPHHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRPSSDLNNSTGQSPHHK 18 1 J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 VRPS(0.434)S(0.566)DLNNSTGQSPHHK 79.568 0.0060663 47337000 18618 15048 20248 23263 24827 21862 30489 23862 7362.2 TRUE FALSE 17737.96404 16581.40831 21176.39083 20924.55904 29156.82094 21104.91346 25837.34308 21772.51678 8503.892375 2.085864126 1.949861026 2.490199769 2.460586061 3.428644161 2.481794516 3.038296105 2.560300133 1 13.05390762 3.565439633 2.548931744 2.664598612 2.013918127 0.046290753 0.63204345 0.46373977 5.89192137 0.158475189 0.262833647 3676.542862 -3.565439633 -0.650680485 VRS(ph)LETENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRSLETENR 9 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 VRS(1)LETENR 136.27 0.0001195 214630000 245220 253790 223090 305690 177590 234760 273720 286250 228780 TRUE FALSE 233628.9366 279651.4895 233318.8972 274961.4604 208561.6398 226630.2023 231958.9868 261184.4325 264258.034 0.884093978 1.058251609 0.882920733 1.040503694 0.789234812 0.857609507 0.877774588 0.988368938 1 18.01158781 4.803333959 21.1689525 0.93086091 0.884091035 0.031666529 0.086202252 20624.12348 8183154.422 0.020128366 15.13030123 63581.96698 -4.803333959 -0.046769875 VRTDITYPAGFMDVISIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VRTDITYPAGFMDVISIDK 19 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 201.61 5.39E-16 345500000 1013380 1079120 936250 1021470 789800 1031770 1152370 1150780 924580 FALSE TRUE 965479.5357 1189083.555 979177.9886 918789.8949 927540.8699 996039.5462 976554.7918 1050011.603 1067959.144 0.904041639 1.113416708 0.916868397 0.860323075 0.868517185 0.932656976 0.914412126 0.983194543 1 20.02642503 3.583140297 24.34601139 0.916972725 1.009800316 0.210483731 0.065836419 29.91249094 6854.528549 0.01656931 0.025669062 3829.48433 -3.583140297 0.09282759 VRTELADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VRTELADK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 137.28 0.00068859 2113830000 2652380 2698960 1929560 2669800 1676370 2431410 2505970 2630990 1819130 FALSE TRUE 2527007.254 2973987.092 2018032.235 2401426.632 1968728.397 2347209.662 2123638.251 2400606.568 2101231.39 1.202631593 1.4153544 0.960404573 1.142866342 0.936940314 1.117063867 1.010663681 1.142476064 1 21.00280361 3.735893238 24.99997332 1.04666562 1.308993 0.612268929 0.087540524 121.8728258 1142254.085 0.020341489 0.033162106 5443.688148 -3.735893238 0.262327379 VRVDS(ph)TAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 1 VRVDS(0.863)T(0.137)AK 58.132 0.064728 197490000 359000 244380 307880 402140 265860 343280 393490 382230 290880 TRUE FALSE 342030.7815 269282.5998 321996.6025 361716.1232 312225.8998 331392.1275 333455.8736 348759.9149 335988.1848 1.017984551 0.801464492 0.958356922 1.076573938 0.929276427 0.986320777 0.992463094 1.038012438 1 18.35805098 3.481635225 24.98406372 0.999699429 0.904755549 0.273075222 0.063296716 211.8181766 1172380.086 0.016410032 0.02279283 3031.344015 -3.481635225 -0.09494388 VRVDSTAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;; 117.3 0.0019203 2335169000 3580430 2751900 2300720 2632010 2897210 2677680 3869550 3343580 3320540 FALSE TRUE 3411190.17 3032321.739 2406210.288 2367435.354 3402482.507 2584951.27 3279179.078 3050798.41 3835472.384 0.889379411 0.790599289 0.627356958 0.617247399 0.887109114 0.673959036 0.854960941 0.795416602 1 21.87097284 0.572499743 0.915286105 0.999823249 0.761244384 0.37284641 0.097829133 1.640353212 2.184775673 0.0960061 0.03130069 3.736799042 -0.572499743 -0.238578865 VRVELSNGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VRVELSNGEK 10 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;; 193.3 5.36E-07 4530670000 2861550 2553300 2557000 3356910 2065880 2961120 3149540 3016710 2295310 FALSE TRUE 2726290.203 2813484.173 2674240.979 3019467.029 2426168.818 2858575.672 2669019.828 2752550.88 2651254.952 1.028301786 1.061189597 1.008669867 1.138882184 0.915102041 1.078197202 1.006700554 1.038206785 1 21.33824398 2.750594549 24.99389291 1.013814824 1.053331796 0.184384423 0.052416645 1532.754677 3183460.843 0.014231631 0.014991681 563.111698 -2.750594549 0.039516972 VRVELSNGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VRVELSNGEKR 11 2 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 174.42 6.20E-06 1160300000 1009130 632900 901500 803450 862300 926590 1280840 1062470 1176310 FALSE TRUE 961430.4248 697393.2295 942834.6667 722685.6795 1012684.847 894501.956 1085424.334 969434.4943 1358726.147 0.707596911 0.513269897 0.69391074 0.531884722 0.745319319 0.658338664 0.79885438 0.713487774 1 20.37382328 0.754053144 0.435608742 1.019925266 0.602030131 0.676117852 0.077414516 0.8103385 0.352031594 0.110918396 0.046448744 5.676140596 -0.754053144 -0.417895136 VRVELSTGMPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VRVELSTGMPR 11 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 162.93 2.24E-05 1223970000 772350 603730 669900 905210 974550 842320 1209680 1012630 1081510 FALSE TRUE 735842.5462 665250.7734 700615.5776 814216.571 1144511.211 813150.2472 1025121.099 923958.7489 1249225.047 0.589039219 0.532530768 0.560840162 0.651777334 0.916176964 0.650923746 0.820605623 0.739625539 1 20.25260197 2.252364691 0.191712849 1.08052857 0.368042478 0.661198273 0.089840321 2.409121049 0.318021063 0.367965764 0.609848635 178.7988375 -2.252364691 -0.712486092 VRVPTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VRVPTER 7 1 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 86.833 0.018045 26506000 43993 37403 35316 44017 45630 37420 44256 38953 48134 FALSE TRUE 41913.53808 41214.40822 36935.27353 39592.32753 53587.85755 36124.13602 37503.93438 35542.06882 55598.37489 0.753862647 0.741288002 0.664322898 0.712113036 0.963838559 0.649733667 0.67455091 0.639264527 1 15.76275509 -2.230897276 2.423409364 1.994612973 0.725826787 0.464510614 0.092830709 10908557.67 2053800.708 59512693.07 0.022219448 0.005876283 2.230897276 -1.268786186 VRYDS(ph)SNQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VRYDSSNQVK 10 1 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 VRYDS(0.91)S(0.09)NQVK;VRYDS(0.967)S(0.033)NQVK;VRYDS(0.533)S(0.467)NQVK;VRYDS(0.986)S(0.014)NQVK 196.42 2.02E-07 3676500000 2900970 2456070 2715110 3172510 2247130 3050430 3377960 3223620 2645850 TRUE FALSE 2763846.897 2706346.325 2839600.479 2853603.267 2639028.761 2944792.844 2862590.162 2941342.743 3056154.905 0.904354322 0.885539644 0.929141541 0.933723373 0.863512761 0.963561382 0.936663962 0.96243248 1 21.54328624 1.344869797 0.570312 1.001177582 0.89947616 0.600417256 0.025094101 0.47731934 0.384198627 0.023404226 0.01187172 22.12431318 -1.344869797 -0.101701422 VVSVLTVLHQDWLNGK ddPTM_SK-BR-3_Trastuzumab_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 ; 278.84 2.18E-35 576970000 7316300 543320 392810 335480 218430 101107 96544 69390 45833 FALSE TRUE 6970472.999 598684.9257 410820.727 301756.913 256524.1228 97605.63924 81814.43965 63313.84374 52940.54756 131.6660541 11.30862738 7.760039252 5.699920514 4.845513216 1.843683976 1.545402219 1.195942367 1 15.6920855 4.560811269 1.67121976 2.851321653 153.8804257 0.994549372 2.962804904 0.042101387 0.151818528 0.822214813 9.209925782 36375.69246 -4.560811269 151.0291041 up VS(ph)GSPEQAVEENLSSYSLDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSGSPEQAVEENLSSYSLDRR 21 1 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 VS(0.543)GS(0.457)PEQAVEENLSSYSLDRR 76.162 0.0069762 36206000 22448 13970 18005 16309 19704 19948 24860 20584 26353 TRUE FALSE 21386.92753 15393.55888 18830.54706 14669.58833 23140.37136 19257.19576 21067.15041 18781.55584 30439.68865 0.702600075 0.505706844 0.618618255 0.481923074 0.760203944 0.632634452 0.692094806 0.617008802 1 14.89366598 -2.711265517 0.273460212 1.644697262 0.58664477 0.669735664 0.083005473 28.85811649 0.855304434 10.97691157 0.094808281 0.001944171 2.711265517 -1.058052492 VS(ph)LDVNHFAPDELTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VS(1)LDVNHFAPDELTVK 228.57 2.56E-15 102020000 388660 280720 280890 373140 235170 336680 388850 365620 234770 TRUE FALSE 370288.812 309325.6872 293769.0843 335631.2583 276183.5735 325020.6872 329523.7908 333604.3745 271176.9326 1.36548787 1.140678465 1.083311481 1.23768366 1.018462636 1.198555807 1.215161584 1.230209264 1 18.04887494 4.545957412 2.563313695 1.151693389 1.372754589 0.399087175 0.085439847 0.331032488 3.664345338 0.019789089 0.131554117 35152.59675 -4.545957412 0.2210612 VS(ph)LERLDLDLTADSQPPVFK ddPTM_SK-BR-3_Trastuzumab_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 275.17 1.01E-44 341962000 912545 877020 936066 1076522 696197 1075393 1177170 1213440 886486 TRUE FALSE 869410.8063 966389.3351 978985.552 968307.9633 817613.5364 1038151.871 997571.0963 1107184.761 1023957.721 0.849069047 0.943778552 0.956080053 0.945652289 0.798483687 1.013862046 0.974230748 1.081279762 1 19.96572472 2.160721366 24.99993713 1.010760331 0.905015654 0.537092587 0.054440001 28.95395875 9297.806759 0.019578354 0.014459576 144.7842652 -2.160721366 -0.105744678 VS(ph)LGQWSY(ph)GKSKEQQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSLGQWSYGKSKEQQK 16 2 O00559-2 O00559-2 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 2 VS(0.405)LGQWS(0.481)Y(0.689)GKS(0.426)KEQQK 72.359 0.090022 131650000 255810 176250 243050 237490 225560 211620 340210 281700 311750 TRUE FALSE 243718.3683 194210.0754 254194.0829 213617.054 264897.5926 204291.5463 288304.7161 257032.8546 360094.5978 0.676817619 0.539330711 0.705909182 0.593224823 0.735633342 0.56732744 0.800636049 0.713792587 1 18.45801643 0.420515209 0.445506911 1.031137938 0.613867422 0.701805876 0.072091299 1.143264546 0.402425105 0.134505194 0.03880312 2.633390161 -0.420515209 -0.417270516 VS(ph)PAAAQLADTLFSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPAAAQLADTLFSK 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VS(1)PAAAQLADTLFSK;VS(1)PAAAQLADTLFSK 159.95 1.82E-06 65089000 278730 303874 226304 326755 180961 277445 259324 283112 170756 TRUE FALSE 265554.9853 334839.1061 236680.2622 293908.9666 212520.5411 267837.0101 219759.361 258321.2124 197235.9684 1.34638214 1.697657424 1.199985298 1.490138787 1.077493841 1.357952164 1.114195158 1.309706412 1 17.58956314 2.544083585 0.349111972 1.033265025 1.573655882 0.367990309 0.163926497 1.489566358 0.398018044 0.177290506 0.292457654 350.0125244 -2.544083585 0.540390857 VS(ph)PAHS(ph)PPENGLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 162.76 6.88E-08 369650000 899000 1028480 733410 1056690 492276 948270 830700 879090 445271 TRUE FALSE 856506.0516 1133283.281 767037.5739 950469.5136 578128.7785 915431.1721 703961.4581 802112.2193 514321.3526 1.665313033 2.203453688 1.491358603 1.848007105 1.124061398 1.779881717 1.368719099 1.559554577 1 18.97231052 1.636992757 0.146130834 0.640909463 2.326133753 0.419760969 0.266469374 3.942247209 0.590885042 2.848152044 3.006869183 43.35036484 -1.636992757 1.68522429 VS(ph)PENLVDK ddPTM_SK-BR-3_Trastuzumab_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 198.33 2.79E-05 623590000 2328210 2332840 1961330 2518770 1649050 2291820 2201870 2503680 1614570 TRUE FALSE 2218160.127 2570559.048 2051258.921 2265578.454 1936643.798 2212453.699 1865934.291 2284444.506 1864949.27 1.189394352 1.378353337 1.099900654 1.21482042 1.038443152 1.186334521 1.000528176 1.22493654 1 20.83070496 3.719459512 24.30471141 1.108806761 1.283873842 0.380553137 0.092605407 460.3266036 585730.7127 0.022151804 0.034384268 5241.547327 -3.719459512 0.175067081 VS(ph)PGLPS(ph)PNLENGAPAVGPVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 2 VS(1)PGLPS(1)PNLENGAPAVGPVQPR 122.34 3.48E-05 37991000 49571 57905 55238 68829 58780 58938 55731 53779 55910 TRUE FALSE 47227.87707 63805.58533 57770.71694 61910.17815 69031.21339 56896.96228 47228.21238 49069.82566 64580.23725 0.731305413 0.988004815 0.894557211 0.958655167 1.068921644 0.881027458 0.731310605 0.759827275 1 15.97880512 -1.430422738 6.948336709 1.000013661 0.876094604 0.107360188 0.111719897 2.46E-05 2.02E-06 0.112667852 0.026553141 0.037117376 1.430422738 -0.123919056 VS(ph)PGLPSPNLENGAPAVGPVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VS(1)PGLPSPNLENGAPAVGPVQPR;VS(0.996)PGLPS(0.004)PNLENGAPAVGPVQPR 238.49 3.65E-37 325140000 74619 69702 57622 72607 53625 72787 68002 68398 55375 TRUE FALSE 71091.90775 76804.71304 60264.0257 65308.40642 62977.18302 70266.36794 57627.04596 62408.70852 63962.27218 1.111466265 1.200781499 0.942180814 1.021045754 0.984598903 1.098559597 0.900953703 0.97571125 1 15.96493357 3.738697086 25 0.987500705 1.156123886 0.614048181 0.055071552 6.855708565 1255836.146 0.013771969 0.022990187 5478.946826 -3.738697086 0.168623182 VS(ph)PPAADVLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSPPAADVLK 10 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VS(1)PPAADVLK 129.74 0.0003095 135890000 306400 414190 235140 390580 148470 281910 241680 291010 142710 TRUE FALSE 291917.0792 456396.4319 245921.4016 351318.1563 174363.121 272147.386 204807.2772 265527.6217 164840.7379 1.770903739 2.76871141 1.491872729 2.13125809 1.057767171 1.650971656 1.242455474 1.61081311 1 17.3307133 3.096925242 1.414128325 1.34840209 2.217826542 0.415044524 0.400011906 0.329918441 1.375123402 0.133215758 0.172983044 1250.043833 -3.096925242 0.869424452 VS(ph)PPAADVLKDFSLAGNFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPPAADVLKDFSLAGNFSR 20 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VS(1)PPAADVLKDFSLAGNFSR;VS(1)PPAADVLKDFSLAGNFSR 104.54 0.00016303 308290000 527470 477260 491290 584300 362680 541520 579720 559760 375380 TRUE FALSE 502537.5384 525893.3366 513816.1325 525565.0539 425931.2772 522767.0266 491273.0667 510744.4469 433592.0132 1.159010137 1.212875977 1.185022133 1.212118853 0.982331925 1.20566572 1.13303071 1.177937857 1 18.72597866 -5 0.180559052 0.347550208 1.194285899 0.354846567 0.067282962 142.4665308 1.372873249 33.41435414 0.191863701 1.00E-05 5 0.846735691 VS(ph)PSDTTPLVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VSPSDTTPLVSR 12 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 VS(0.975)PS(0.025)DTTPLVSR;VS(0.926)PS(0.073)DT(0.001)TPLVSR;VS(0.997)PS(0.003)DTTPLVSR;VS(0.999)PS(0.001)DTTPLVSR;VS(0.998)PS(0.002)DTTPLVSR;VS(0.963)PS(0.037)DTTPLVSR 255.54 4.03E-21 1085400000 1275130 1345830 1119760 1423930 1011409 1262520 1176410 1212410 1005449 TRUE FALSE 1214857.132 1482971.607 1171102.104 1280793.851 1187798.409 1218798.616 996927.0482 1106244.953 1161368.896 1.046056198 1.276916932 1.008380806 1.102831198 1.022757208 1.049450024 0.858406878 0.952535372 1 20.14739487 2.549823905 0.982296232 0.929029303 1.143260704 0.417204744 0.081876251 0.418043827 0.823928154 0.048657786 0.036868268 354.6695506 -2.549823905 0.214231401 VS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.672)PS(0.328)PSQESLSSSK 304.86 3.23E-44 111830000 139740 157250 121170 165550 72483 135440 116850 151320 75708 TRUE FALSE 133134.7671 173273.9538 126725.7644 148908.5995 85124.01225 130749.6788 99022.3864 138069.6186 87448.40998 1.522437826 1.981442016 1.449148868 1.702816547 0.973419783 1.495163593 1.132352051 1.5788694 1 16.41614453 2.764836227 24.07035631 1.256280004 1.689216006 0.449342492 0.234095193 392.3075596 359381.1554 0.06439515 0.068277619 581.8837469 -2.764836227 0.432936001 VS(ph)PSSTEADGELYVFNTPSGTSSVETQMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPSSTEADGELYVFNTPSGTSSVETQMR 29 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VS(0.25)PS(0.25)S(0.25)T(0.25)EADGELY(0.001)VFNTPSGTSSVETQMR;VS(0.25)PS(0.25)S(0.25)T(0.25)EADGELYVFNTPSGTSSVETQMR 82.342 0.0056737 63047000 35558 29255.2 30365 38131 31717 31284 39244 36236 32959 TRUE FALSE 33877.24381 32236.33814 31757.26529 34297.99944 37248.43476 30200.62724 33256.60703 33062.98374 38070.11339 0.889864537 0.846762336 0.834178374 0.900916661 0.978416701 0.793289658 0.873562069 0.868476104 1 15.21637125 -1.725410488 2.447412013 1.027384566 0.871215742 0.407073311 0.048047649 9778219.555 7023321.354 1631552.015 0.011496306 0.018818695 1.725410488 -0.156168824 VS(ph)PSTSYTPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VS(0.845)PS(0.1)T(0.027)S(0.027)YT(0.002)PSR;VS(0.906)PS(0.066)T(0.014)S(0.014)YT(0.001)PSR 68.536 0.058389 134800000 188414 195649 175514 207366 158375 188654 200634 206744 194724 TRUE FALSE 179508.0436 215585.8555 183561.4905 186521.1757 185995.5499 182120.8647 170023.5984 188640.3993 224920.8034 0.798094444 0.958496734 0.816116107 0.829274895 0.826937958 0.809711071 0.755926512 0.838696983 1 17.77905758 4.790694271 21.77720361 0.843399286 0.798093269 0.037270923 0.072873212 10560.67588 5650374.339 0.016971782 4.078286158 61758.14894 -4.790694271 -0.045306017 VS(ph)SGVYEPVVIESH ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSSGVYEPVVIESH 14 0 Q5T9C2-3;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 VS(0.5)S(0.5)GVYEPVVIESH 90.731 0.005912 72060000 34653 31024 27939 30566 29107 31544 35373 28621 40478 TRUE FALSE 33015.02137 34185.38087 29220.03079 27493.44761 34183.25158 30451.62337 29976.19918 26114.79351 46755.12151 0.706126309 0.731157994 0.624958932 0.588030717 0.731112453 0.651300272 0.641131885 0.55854402 1 15.51283678 -0.93873523 5.089224232 1.000001343 0.661852682 0.781637073 0.05733383 8.90E-07 1.86E-07 0.056540902 0.013326766 0.115150219 0.93873523 -0.338148661 VS(ph)SGYVPPPVATPFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSGYVPPPVATPFSSK 17 0 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 VS(0.967)S(0.033)GYVPPPVATPFSSK;VS(0.967)S(0.033)GYVPPPVATPFSSK 139.49 1.30E-05 30135000 351680 335180 334550 382440 261330 364470 432660 415230 307920 TRUE FALSE 335056.7834 369335.2231 349889.4484 343996.4046 306905.8693 351848.3125 366649.7707 378870.2599 355670.661 0.942042232 1.038419143 0.983745602 0.96717678 0.862893409 0.989253124 1.030868753 1.065227756 1 18.44018245 1.792964073 4.054585668 1.03611062 0.966941362 0.330619773 0.046191836 0.275802145 8.383526771 0.024253087 0.012812531 62.08176743 -1.792964073 -0.069169258 VS(ph)SPTKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.896)S(0.104)PTKPK 94.692 0.0061645 1222000000 3737300 3620800 3740300 4359000 2080200 4509300 4415700 4555000 2161700 TRUE FALSE 3560645.236 3989763.637 3911796.455 3920825.038 2442986.221 4353141.81 3742003.865 4156140.052 2496925.396 1.426011863 1.597870583 1.566645308 1.570261188 0.978397763 1.743400831 1.498644642 1.664503096 1 21.25172129 -1.819641824 2.766990027 0.839254802 1.50721829 0.372721613 0.206172437 15768435.8 11302899.51 16884574.62 0.046421362 0.0151481 1.819641824 0.667963488 VS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.25)S(0.25)S(0.25)S(0.25)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 56.22 0.039832 14336000 8742.5 9106.1 8004.7 12993 9038.4 8115.6 10144 9259.2 8517.3 TRUE FALSE 8329.259351 10034.02194 8371.723413 11686.91895 10614.6941 7834.554737 8596.346493 8448.415362 9838.119384 0.846631254 1.019912602 0.850947532 1.187922051 1.078935281 0.796346785 0.873779445 0.858742919 1 13.26416685 2.233378104 24.99972136 0.869230685 0.988405275 0.203145088 0.110821802 202.7455998 978005.3987 0.040056677 0.03047482 171.150473 -2.233378104 0.11917459 VS(ph)VS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_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 82.749 0.034567 814110000 2346700 2385500 1892630 2543100 1668000 2350800 2279300 2112700 1536560 TRUE FALSE 2235776.142 2628585.162 1979408.958 2287462.756 1958898.672 2269391.207 1931550.923 1927700.788 1774841.877 1.259704411 1.481024984 1.115259327 1.288826225 1.103703207 1.278644163 1.088294652 1.086125369 1 20.75925907 2.433839217 0.351627836 0.992934173 1.400565056 0.487820521 0.100487758 1.160697894 0.328320661 0.112362046 0.170395034 271.5433784 -2.433839217 0.407630883 VSAGEPGSHPS(ph)PAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSAGEPGSHPSPAPR 15 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 VSAGEPGSHPS(1)PAPR;VSAGEPGS(0.002)HPS(0.998)PAPR 151.95 1.88E-06 583450000 871400 636220 750880 1028860 1013940 651150 827170 855850 782600 TRUE FALSE 830210.6489 701051.5413 785308.5907 925437.0381 1190770.815 628600.5122 700970.0245 780907.2369 903961.611 0.918413613 0.775532426 0.868741085 1.023757012 1.317280292 0.695384079 0.775442249 0.863872124 1 19.78590198 -0.718836579 4.213688113 1.000000408 0.890837592 0.023809346 0.172017512 50379966.9 121359751.5 369.2760601 0.041656639 0.191057205 0.718836579 -0.109162816 VSALEEDMDDVES(ph)S(ph)EEEEEEDEKLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSALEEDMDDVESSEEEEEEDEKLER 26 1 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 2 VSALEEDMDDVES(1)S(1)EEEEEEDEKLER 86.304 0.0084671 122330000 149140 128860 125140 149380 81255 148840 138750 153560 78087 TRUE FALSE 142090.4478 141990.9805 130877.7928 134364.0386 95425.84627 143685.6335 117581.1392 140113.4723 90196.33315 1.575346168 1.574243382 1.4510323 1.489684047 1.057979221 1.593031872 1.303613296 1.553427589 1 16.46078116 -3.766652568 0.1112269 7.57E-14 1.721425242 0.428273013 0.16311315 106.1579229 1.040698145 27.2457963 1.955092638 0.000171138 3.766652568 1.721425242 VSAWELINSEYFSEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSAWELINSEYFSEGR 16 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 179.41 6.12E-09 62370000 88214 82962 82261 89306 76075 68840 93764 96556 70645 FALSE TRUE 84044.29904 91415.92212 86032.74822 80328.79121 89342.45591 66456.05354 79458.57971 88101.04476 81600.2658 1.02995129 1.120289514 1.054319461 0.984418254 1.094879472 0.814409768 0.973753932 1.079666149 1 16.31628623 2.940319854 1.459069032 0.969607675 1.074149838 0.156226683 0.078950163 0.560049648 2.441404937 0.029214633 0.033104635 871.6052836 -2.940319854 0.104542163 VSDILHSIFSSYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSDILHSIFSSYK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 182.02 1.16E-05 210897000 1792140 1627640 1149230 1479480 1555250 1359980 2041090 1890850 1416950 FALSE TRUE 1707429.094 1793498.366 1201923.332 1330759.86 1826485.108 1312883.552 1729684.233 1725277.15 1636683.369 1.043225053 1.095812666 0.734365214 0.813083266 1.115967292 0.80216099 1.056822759 1.054130067 1 20.64234382 1.604166681 25 1.041616934 0.953932091 0.112706823 0.128046326 0.964165339 6471.39589 0.067270422 0.033014596 40.19450462 -1.604166681 -0.087684843 VSDQNS(ph)PVLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK 286.26 8.03E-28 4816450000 8085360 7793020 7550430 9091090 5209010 8928390 8750460 8874600 6014240 TRUE FALSE 7703181.056 8587137.598 7896624.684 8177236.361 6117459.695 8619197.616 7415416.614 8097492.977 6946897.623 1.108866357 1.236111148 1.136712402 1.177106214 0.880603116 1.240726161 1.06744291 1.165627222 1 22.72793741 -4.999999992 0.089721911 0.596391464 1.235796538 0.125341403 0.102345151 399.4093138 2.491422721 31.27326289 2.213422758 1.00E-05 4.999999992 0.639405074 VSDS(ph)LTDLALK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSDSLTDLALK 11 0 Q8N3C0 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 1 VS(0.004)DS(0.996)LTDLALK 129.71 0.0010714 0 52947 45781 44000 54360 34463 47121 53630 52361 38848 TRUE FALSE 50444.30024 50446.13595 46017.44352 48895.62952 40473.33629 45489.18795 45447.75852 47775.99326 44872.34943 1.124173369 1.124214279 1.025518924 1.089660563 0.901966062 1.013746517 1.012823244 1.064708977 1 15.4535391 3.563522473 1.488728812 1.005974058 1.129458651 0.467389575 0.048375119 0.306343043 1.353539817 0.01436751 0.028515934 3660.348808 -3.563522473 0.123484593 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 223.34 6.65E-40 88871000 43804.6 29451.2 38383.8 41039.8 47599.3 35580.9 51071 46409 53011 FALSE TRUE 41734.04337 32452.31076 40143.7352 36914.40133 55900.60285 34348.72451 43279.18097 42345.18193 61231.67514 0.681576052 0.529992209 0.655604066 0.602864469 0.912936037 0.560963332 0.706810337 0.69155681 1 15.90199053 -5 0.193744843 2.509424864 0.598262358 0.520689642 0.101969843 103.4528431 1.01653679 60.21065364 0.242683527 1.00E-05 5 -1.911162505 VSDYEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSDYEMK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 87.616 0.044693 108130000 140600 136320 131730 145240 128560 155460 155720 152800 137190 FALSE TRUE 133954.1166 150211.163 137769.9508 130640.1993 150980.8233 150076.3812 131962.054 139420.022 158464.7245 0.845324516 0.947915465 0.869404539 0.824411866 0.952772447 0.947064917 0.8327535 0.8798174 1 17.2738022 2.721531977 24.9552895 0.907761433 0.881387166 0.133764278 0.055379566 2845.885212 4170609.059 0.017882842 0.016893843 526.6619912 -2.721531977 -0.026374267 VSEHVGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSEHVGSR 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 120.15 0.0040714 0 105570 113950 95234 141360 107790 95363 97246 117120 114810 FALSE TRUE 100579.9153 125561.6346 99600.5731 127150.2242 126588.5419 92060.5554 82409.33665 106864.3519 132614.1484 0.758440306 0.946819295 0.751055406 0.958798331 0.954562868 0.694198594 0.621421904 0.805829191 1 17.01687518 2.227149022 24.99962142 0.733214494 0.871646407 0.070980045 0.123803891 314.1529762 688216.8364 0.042771338 0.031861331 168.7131841 -2.227149022 0.138431914 VSELKEELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSELKEELK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 76.143 0.033075 483410000 773510 757630 580740 685340 497240 681860 779090 835910 572960 FALSE TRUE 736947.7152 834833.3584 607367.5034 616448.3211 583958.4986 658247.0172 660225.5115 762713.289 661811.7105 1.113530788 1.261436365 0.917734597 0.931455747 0.882363502 0.994613735 0.997603247 1.152462667 1 19.33606129 3.736289774 24.99768958 0.978017246 1.187483579 0.532100067 0.079904914 134.4702905 1480265.456 0.020777286 0.03395247 5448.660826 -3.736289774 0.209466333 VSELKEELKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSELKEELKK 10 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 69.03 0.032735 2497200000 4247600 3944400 3756600 4713000 2139770 4743400 4728500 5068300 2360800 FALSE TRUE 4046824.366 4346338.844 3928843.826 4239240.286 2512945.211 4579134.869 4007080.48 4624492.783 2726900.807 1.48403798 1.593874934 1.440772549 1.554600107 0.921538915 1.679245119 1.469463235 1.695878622 1 21.37883079 -1.678499556 2.77049371 0.937974024 1.482704792 0.328470374 0.215623515 29196722.2 25684701.29 12740410.15 0.047574626 0.020965269 1.678499556 0.544730767 VSELYDVTWEEMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSELYDVTWEEMR 13 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 87.363 0.013986 0 3808.9 4623.6 6014.6 8701.8 6946.1 5710.4 6747.2 5564.5 6776.3 FALSE TRUE 3628.860846 5094.750097 6290.375359 7827.078532 8157.497641 5512.647416 5717.790719 5077.242881 7827.133995 0.463625747 0.650908762 0.803662664 0.999992914 1.042207486 0.704299609 0.730508858 0.648672028 1 12.93426843 4.008109366 2.028294395 0.835791949 0.496704101 0.472054298 0.134465572 0.301423933 2.417673528 0.038866458 0.10780207 10188.47927 -4.008109366 -0.339087848 VSEQGLIEILKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSEQGLIEILKK 12 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 0 116.51 0.0013369 153260000 234810 182230 206710 235700 168270 199900 239530 247710 181450 FALSE TRUE 223710.9966 200799.4442 216187.858 212006.9882 197616.2347 192977.4129 202985.2992 226019.1992 209588.3393 1.067382839 0.958065916 1.031488005 1.011539998 0.942878003 0.920744988 0.968495194 1.078395869 1 17.67719893 4.64759314 3.101002804 0.984043512 1.072468529 0.217384719 0.045737897 0.431814841 6.698317542 0.011023943 0.082500063 44421.49186 -4.64759314 0.088425017 VSFELFADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSFELFADK 9 0 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 ; 149.94 0.00020109 655800000 1316680 1086040 714400 1099160 841200 960600 1208210 1126280 761880 FALSE TRUE 1254443.146 1196708.711 747155.9466 988670.3485 987905.0137 927334.1811 1023875.374 1027656.952 880028.4593 1.425457475 1.359852284 0.849013391 1.1234527 1.122583029 1.053754764 1.163457117 1.167754226 1 19.74719065 3.895619994 7.964805888 1.08392526 1.400931285 0.670465755 0.094408998 0.144250005 9.795434786 0.022905938 0.041484806 7863.574287 -3.895619994 0.317006024 VSFELFADKVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 155.66 6.61E-05 30642743000 29678468 21211991 23501711 27397227 18761011 27663072 33705636 30336335 21612555 FALSE TRUE 28275625.63 23373517 24579287.7 24643205.69 22032925.38 26705092.88 28563222.18 27679924.68 24964119.65 1.132650622 0.936284449 0.984584598 0.987144992 0.882583712 1.06973902 1.144171018 1.108788336 1 24.5733527 2.015684651 24.94639262 1.101992863 0.990331317 0.293533466 0.072308207 251.5701961 400120.0644 0.02648268 0.019552453 103.6775322 -2.015684651 -0.111661546 VSFPSYLAS(ph)PAGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSFPSYLASPAGSR 14 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 VSFPS(0.003)YLAS(0.996)PAGS(0.001)R 82.663 0.010578 37745000 71023 53644 49976 34208 39314 33020 39163 40980 46283 TRUE FALSE 67665.88354 59110.38459 52267.44903 30769.34685 46170.34915 31876.50912 33187.96507 37391.57395 53460.33126 1.265721367 1.105686837 0.977686591 0.575554736 0.863637543 0.596264714 0.620796099 0.699426529 1 15.70618116 3.563116967 2.037633322 0.697718546 1.206737581 0.654920183 0.137314809 0.154197772 1.263803942 0.036359213 0.063726374 3656.93269 -3.563116967 0.509019034 VSGAGFS(ph)PSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(0.962)PS(0.038)SK;VSGAGFS(0.96)PS(0.039)SK;VSGAGFS(0.996)PS(0.002)S(0.002)K;VSGAGFS(0.998)PS(0.002)SK;VSGAGFS(0.974)PS(0.023)S(0.003)K;VSGAGFS(0.997)PS(0.003)SK;VSGAGFS(0.986)PS(0.014)SK 255.93 1.85E-20 4585809000 4463680 3978400 4160660 4663230 2936070 4271610 4705340 4263670 3153560 TRUE FALSE 4252690.693 4383803.483 4351430.376 4194473.261 3448119.678 4123683.075 3987453.964 3890320.452 3642597.979 1.167488347 1.203482654 1.194595287 1.151505954 0.946610002 1.132071971 1.094673084 1.068007086 1 21.79653635 2.983387461 24.10458248 1.062849642 1.18676407 0.613406313 0.051645356 309.4622539 449027.0441 0.014711735 0.016004068 962.4705759 -2.983387461 0.123914428 VSGRRS(ph)PESCSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSGRRSPESCSKPEK 15 3 Q03111 Q03111 MLLT1 Protein ENL 1 VS(0.033)GRRS(0.761)PES(0.103)CS(0.103)KPEK 82.482 0.06022 166840000 143840 39401 167170 92540 137540 135650 278760 179430 227680 TRUE FALSE 137040.9683 43416.0067 174834.9099 83237.70339 161526.9325 130952.4065 236230.0422 163718.158 262987.4516 0.521093183 0.16508775 0.66480324 0.31650827 0.614200151 0.497941654 0.898255946 0.622532204 1 18.00463444 1.783016394 0.555911693 0.974560865 0.358144005 0.54811975 0.164495271 0.507414235 0.344762713 0.143865541 0.089078191 60.6759233 -1.783016394 -0.616416859 VSGRRSPES(ph)CSKPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSGRRSPESCSKPEK 15 3 Q03111 Q03111 MLLT1 Protein ENL 1 VSGRRS(0.048)PES(0.901)CS(0.051)KPEK;VS(0.009)GRRS(0.09)PES(0.875)CS(0.026)KPEK 116.39 0.0025008 584030000 341590 69612 397970 210851 327270 336230 712460 431430 534900 TRUE FALSE 325443.7177 76705.54194 416217.3181 189655.8569 384345.7844 324586.2708 603761.1418 393651.702 617849.5601 0.526736181 0.124149222 0.673654794 0.306961223 0.622070176 0.525348389 0.977197656 0.637131961 1 19.23689607 2.070099505 0.771991899 0.937288203 0.358345524 0.523796449 0.182983421 0.435394098 0.487857619 0.14128519 0.077094718 117.5166776 -2.070099505 -0.578942679 VSGRT(ph)SPPLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.205)GRT(0.56)S(0.236)PPLLDR;VS(0.048)GRT(0.565)S(0.387)PPLLDR;VS(0.013)GRT(0.537)S(0.45)PPLLDR;VS(0.015)GRT(0.657)S(0.327)PPLLDR 96.208 0.0090757 11637540000 2713430 1472420 2497890 2143360 2756170 2476710 3520810 2720400 3220180 TRUE FALSE 2585171.541 1622461.272 2612420.727 1927905.381 3236845.175 2390940.912 2983645.77 2482187.354 3719549.068 0.695022836 0.436198378 0.702348774 0.518316964 0.870225158 0.642803971 0.80215255 0.667335558 1 21.8266963 0.342698611 0.217244935 1.139838137 0.514271562 0.478715394 0.116977163 4.723075702 0.503011021 0.864394766 0.314962728 2.201398219 -0.342698611 -0.625566575 VSGRTS(ph)PPLLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.019)GRT(0.311)S(0.67)PPLLDR;VS(0.039)GRT(0.251)S(0.71)PPLLDR 90.422 0.0053714 9178000000 1754870 936890 1680080 1386840 1844490 1585070 2327000 1730510 2189800 TRUE FALSE 1671920.773 1032360.156 1757113.33 1247432.208 2166168.472 1530178.628 1971973.412 1578977.37 2529383 0.66099945 0.408147029 0.694680612 0.493176482 0.856401926 0.604961221 0.779626261 0.624253966 1 21.27035408 -3.012539469 0.124327801 1.763443834 0.418236943 0.482313761 0.122659579 59.70734034 0.787333406 13.19254024 1.078095181 0.00097154 3.012539469 -1.345206891 VSGTLDT(ph)PEKTVDSQGPTPVCTPTFLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 VSGTLDT(0.973)PEKT(0.027)VDSQGPTPVCTPTFLER 301.77 2.12E-71 134410000 111430 151380 122180 136830 73526 150370 154660 174900 99359 TRUE FALSE 106162.9247 166805.7941 127782.0739 123075.5884 86348.91112 145162.6492 131063.7765 159584.8288 114767.0863 0.925029363 1.453428849 1.113403485 1.072394468 0.752383928 1.264845645 1.141997943 1.390510415 1 16.80834943 -0.270805967 7.432930498 1.000062084 1.145632577 0.042750187 0.205112837 0 0 0.188468928 0.044422552 0.536036092 0.270805967 0.145570492 VSHEQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSHEQFR 7 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 109.01 0.0187 247940000 511440 442370 420810 503440 496520 436540 591770 479410 540470 FALSE TRUE 487265.2448 487448.0059 440104.5547 452833.2547 583112.9308 421422.5103 501484.6179 437430.3189 624283.3273 0.780519395 0.780812148 0.704975667 0.725364966 0.934051744 0.675050081 0.80329651 0.700691977 1 19.25184141 -1.554721929 3.327031268 1.007696752 0.766749208 0.509033679 0.073040432 32519241.6 28675149.71 2121990.765 0.015574513 0.027879056 1.554721929 -0.240947544 VSHLLGINVTDFTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 206.55 1.07E-08 3521500000 1750210 1542500 1423560 1783660 1749480 1666230 1947550 1787710 1605520 FALSE TRUE 1667481.042 1699682.504 1488831.634 1604363.108 2054588.758 1608528.037 1650415.478 1631168.635 1854495.842 0.899155989 0.916519986 0.802822848 0.865120898 1.107896126 0.867366753 0.889953723 0.879575245 1 20.8225956 VSHS(ph)PPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VSHSPPPK 8 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.038)HS(0.962)PPPK;VS(0.015)HS(0.985)PPPK;VSHS(1)PPPK;VS(0.18)HS(0.82)PPPK 94.087 0.011127 1923360000 2209290 1908010 1754290 2303770 1451520 2047240 2150930 2083900 1331100 TRUE FALSE 2104861.24 2102438.388 1834725.932 2072190.663 1704664.628 1976343.565 1822766.124 1901422.669 1537520.19 1.368997464 1.367421646 1.193302009 1.347748587 1.108710403 1.28540983 1.185523375 1.236681431 1 20.55217392 3.589171737 0.03363503 1.60E-15 2.601991276 0.634759002 0.071524257 190.179591 1.54189367 50.54240729 69.12545272 3883.038864 -3.589171737 2.601991276 VSHS(ph)PPPKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSHSPPPKQR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.018)HS(0.982)PPPKQR;VS(0.006)HS(0.994)PPPKQR;VS(0.002)HS(0.998)PPPKQR 69.864 0.033734 182639000 299269 109509 319803 198847 337697 268130 502840 321770 424180 TRUE FALSE 285123.1475 120668.0916 334466.2839 178858.5218 396591.2499 258844.5909 426122.5227 293594.113 489959.668 0.581931873 0.246281683 0.682640441 0.365047439 0.809436523 0.528297751 0.869709387 0.599220981 1 18.90230347 1.739299469 0.355521465 1.002551126 0.383560518 0.447229756 0.168149766 0.94426841 0.361419102 0.203336989 0.19415266 54.86551618 -1.739299469 -0.618990608 VSIGNITLSPAIS(ph)RHSPVQMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSIGNITLSPAISRHSPVQMNR 22 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 VSIGNITLSPAIS(0.5)RHS(0.5)PVQMNR;VSIGNITLSPAIS(0.5)RHS(0.5)PVQMNR 143.25 6.58E-08 639200000 366260 245390 405480 386340 499600 345370 514090 408530 581580 TRUE FALSE 348947.6157 270395.52 424071.6591 347504.3692 586730.0818 333409.7503 435656.1286 372756.9474 671768.4561 0.519446265 0.402512975 0.631276529 0.517297837 0.873411183 0.496316472 0.648521264 0.554889031 1 19.35760453 -5 0.138317017 2.445916689 0.412029315 0.540440572 0.123065968 100.1333338 0.852859624 40.11906779 0.728041834 1.00E-05 5 -2.033887374 VSISEGDDKIEYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VSISEGDDKIEYR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;;;;; 229.97 4.44E-12 3942840000 7355480 6285900 6519440 7616710 4619090 7192810 7650650 7406590 5200150 FALSE TRUE 7007801.038 6926440.356 6818362.773 6851063.84 5424657.834 6943721.186 6483402.829 6758029.715 6006562.703 1.166690732 1.153145434 1.135152184 1.140596407 0.903121819 1.156022426 1.079386523 1.125107661 1 22.5181082 8 0.162298471 1.021192261 1.650377604 0.234476833 0.073159836 87.35314761 0.911920522 0.197276824 13.1995304 100000000 -8 0.629185342 VSITEAMHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 179.37 4.99E-05 579250000 637820 433780 270200 291500 609490 312320 619960 473520 541910 FALSE TRUE 607671.5126 477982.6752 282588.9373 262197.8662 715784.863 301504.2801 525373.7157 432056.0785 625946.6351 0.970804025 0.763615696 0.451458513 0.41888214 1.143523781 0.481677292 0.839326687 0.69024427 1 19.25568014 -1.355704062 2.737752667 1.004603586 0.731826368 0.125022807 0.230943914 15042843.72 17040924.57 554660.6249 0.055069299 0.044085517 1.355704062 -0.272777218 VSIYDNVPGSHLYAS(ph)TGDLLDLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSIYDNVPGSHLYASTGDLLDLEK 24 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 VSIYDNVPGSHLYAS(0.832)T(0.168)GDLLDLEK 134.77 2.10E-05 41219000 31136 35926 29496 35936 19661 34998 35145 36514 22673 TRUE FALSE 29664.26299 39586.90024 30848.42078 32323.64501 23089.87218 33786.01048 29782.98477 33316.64059 26189.01304 1.132698775 1.511584273 1.177914598 1.234244488 0.881662556 1.290083381 1.137232042 1.272160983 1 14.67667407 3.505408742 23.83936706 1.146590672 1.325909571 0.198244375 0.151880829 555.5975139 468229.5047 0.03728526 0.057600525 3201.907213 -3.505408742 0.179318898 VSKEEEEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSKEEEEKER 10 2 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;; 66.262 0.0374 625220000 1635280 1511280 1476190 1725560 1050890 1781090 1732770 1801720 1111430 FALSE TRUE 1557983.555 1665281.15 1543874.772 1552103.43 1234164.883 1719410.407 1468404.112 1643951.845 1283784.888 1.213586147 1.297165254 1.202596156 1.209005843 0.961348661 1.33932906 1.143808535 1.280550862 1 20.29197205 -4.392918747 0.2787632 9.64E-32 1.222755629 0.265555469 0.104234258 204.1900238 2.695945953 117.4977821 0.110971655 4.05E-05 4.392918747 1.222755629 VSLDVNHFAPDELTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 214.54 1.69E-14 8635090000 18597800 12755510 13958470 17083960 12441680 15741500 18596260 16738090 11801650 FALSE TRUE 17718718.85 14055310.97 14598479.66 15366647.88 14611505.05 15196367.91 15759058.99 15272414.11 13631789.61 1.299808709 1.031068655 1.07091439 1.127265629 1.071869907 1.114774241 1.156052099 1.120352833 1 23.70047164 4.646166543 3.259486783 1.096891567 1.309457414 0.656778645 0.047789654 0.170053029 2.951367485 0.011308688 0.079240999 44275.8128 -4.646166543 0.212565847 VSLEPHQGPGT(ph)PESK ddPTM_SK-BR-3_Trastuzumab_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(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(0.999)PES(0.001)K 237.16 3.66E-17 4840710000 1997600 1911510 1878780 2257250 1467830 2132570 2399160 2404740 1637000 TRUE FALSE 1903177.407 2106295.042 1964923.921 2030346.942 1723819.087 2058718.566 2033124.078 2194168.217 1890857.599 1.00651546 1.113936366 1.039170756 1.073770411 0.91165992 1.088775044 1.075239129 1.160409022 1 20.85060929 VSLEPHQGPGT(ph)PESKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSLEPHQGPGTPESKK 16 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VSLEPHQGPGT(0.954)PES(0.046)KK 99.86 0.0017155 236000000 338730 273070 323320 355990 224770 379140 436390 443460 260420 TRUE FALSE 322718.9042 300896.1435 338144.5418 320205.2089 263969.8168 366010.2867 369810.6906 404628.2915 300804.6036 1.072852278 1.000304317 1.124133533 1.064495706 0.877545801 1.216770895 1.229405023 1.345153255 1 18.19846712 2.162370574 14.78551561 1.218382757 1.034247004 0.383689419 0.105450173 1.226830899 236.2142511 0.035587323 0.026283337 145.3351201 -2.162370574 -0.184135753 VSLQVHPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VSLQVHPDR 9 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;; 142.83 0.0001034 2414800000 1860400 1761900 1574390 1885380 1933920 1734960 2035300 1904870 1888670 FALSE TRUE 1772462.579 1941439.613 1646577.339 1695858.02 2271195.036 1674877.9 1724777.604 1738069.484 2181555.298 0.812476576 0.889933716 0.754772222 0.777361923 1.041089831 0.767744875 0.790618329 0.796711175 1 21.05692561 -1.468271941 2.754489295 1.00580439 0.830229647 0.290941453 0.083949375 12189707.13 12765478.39 541178.8401 0.019133731 0.03401951 1.468271941 -0.175574743 VSMPDVELNLKS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSMPDVELNLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSMPDVELNLKS(1)PK 154.74 3.66E-06 722850000 794070 787650 840900 1034300 480630 919900 861280 1028100 477600 TRUE FALSE 756535.8848 867912.4305 879456.0968 930330.199 564451.7198 888043.6323 729875.9175 938074.1137 551663.7688 1.371371345 1.573263425 1.59418861 1.686408011 1.023180698 1.609755222 1.323044867 1.700445392 1 19.07342971 VSNEEVTEELLHVNDDLNNVFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSNEEVTEELLHVNDDLNNVFLR 23 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;; 175.77 1.14E-12 51554000 48340.2 38016.5 43260.7 49062 43098.3 38842.2 50294 46244 37522.6 FALSE TRUE 46055.25455 41890.42457 45244.24589 44130.19455 50614.62987 37497.08487 42620.72659 42194.63021 43341.41317 1.062615434 0.96652189 1.043903338 1.018199254 1.167812173 0.865156028 0.983371872 0.973540711 1 15.40345857 2.221065785 24.99998858 0.954086731 1.039275292 0.367631145 0.061534088 286.6934175 409680.2033 0.02174214 0.01609508 166.3664637 -2.221065785 0.085188561 VSNLQVS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 155.88 7.58E-05 293480000 783420 580980 674620 794030 490920 683580 747140 686000 442530 TRUE FALSE 746389.2892 640182.5225 705551.9943 714212.5958 576536.2926 659907.4532 633150.0708 625930.2033 511155.2923 1.460200648 1.252422761 1.380308499 1.39725169 1.127908292 1.291011681 1.238664806 1.224540199 1 18.96340213 -4.485657339 0.071396011 3.97E-11 1.686054982 0.685238723 0.075051335 152.4644831 0.860386785 25.90944196 3.66855177 3.27E-05 4.485657339 1.686054982 VSNQDSKS(ph)PLGFYCDQNPVESSMCQSNSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSNQDSKSPLGFYCDQNPVESSMCQSNSR 29 1 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VSNQDS(0.25)KS(0.75)PLGFYCDQNPVESSMCQSNSR;VSNQDS(0.25)KS(0.75)PLGFYCDQNPVESSMCQSNSR 310.63 2.97E-92 527680000 466300 350380 431740 460300 299940 466600 541650 512570 356870 TRUE FALSE 444258.9231 386084.1203 451535.706 414029.7695 352249.441 450441.525 459011.3444 467686.6535 412211.577 1.077744896 0.936616393 1.095397925 1.004410824 0.854535536 1.092743509 1.113533365 1.134579133 1 18.6530255 2.053014279 24.99998547 1.09727571 0.996605876 0.259629426 0.075502367 113.1712583 53367.65275 0.026511217 0.019579828 112.983306 -2.053014279 -0.100669834 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 2 VS(0.048)PAS(0.953)PAGS(0.955)PS(0.044)ADFAVHGESLGDR 88.395 0.0056918 143270000 127130 102350 129180 135660 120710 131140 147590 143000 162010 TRUE FALSE 121120.8168 112779.5814 135103.0308 122023.1991 141761.7858 126598.5889 125072.4348 130478.1619 187133.6834 0.6472422 0.602668527 0.721959983 0.652064326 0.75754286 0.676514172 0.668358751 0.697245731 1 17.51370974 -5 0.256562433 3.077397208 0.643598678 0.861059459 0.040872296 65.56557878 0.646098174 71.65216307 0.055251776 1.00E-05 5 -2.43379853 VSPGLPS(ph)PNLENGAPAVGPVQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VS(0.38)PGLPS(0.62)PNLENGAPAVGPVQPR;VSPGLPS(1)PNLENGAPAVGPVQPR 231.63 2.04E-33 470910000 180240 134979 135789 167666 142151 142007 171152 154574 103911 TRUE FALSE 171720.4124 148733.5136 142015.06 150811.8951 166942.0894 137089.262 145039.619 141038.6811 120024.9872 1.430705526 1.239187915 1.183212457 1.256504155 1.390894457 1.142172686 1.208411868 1.17507766 1 16.87297526 -2.797984506 0.044939528 1.35E-09 1.951942752 0.619256228 0.075018309 286.9556033 1.468754525 49.09679942 20.06254468 0.001592266 2.797984506 1.95194275 VSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSPNELILGWYATGHDITEHSVLIHEYYSR 30 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ;; 204.53 5.43E-26 474889000 206394.1 264311 194962.2 257070 203352.2 207080.1 230353 217455.1 44731.9 FALSE TRUE 196638.2599 291244.5914 203901.4097 231228.8352 238816.7593 199908.8642 195208.4191 198413.5786 51668.69459 3.805752429 5.636770847 3.946324004 4.475221157 4.62207844 3.869051962 3.778079177 3.840112087 1 15.65700281 -0.317560463 0.373753528 0.142021395 4.689121792 0.805145868 0.5161965 2.664655479 0.414054948 3.515950689 0.370522852 0.481326238 0.317560463 4.547100397 VSPS(ph)PSQESLSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.062)PS(0.938)PSQESLSSSK;VS(0.375)PS(0.625)PSQESLSSSK 352.77 5.85E-82 397250000 406160 483920 339680 505350 213856 387590 331550 404390 208491 TRUE FALSE 386961.6217 533231.9982 355254.664 454551.2579 251152.4187 374167.6611 280965.9582 368979.4678 240822.7195 1.606831875 2.214209687 1.475170884 1.887493252 1.042893375 1.553705821 1.166692075 1.532162201 1 17.87761198 2.750705083 24.94920988 1.28520274 1.826810071 0.508112717 0.260977565 555.3014845 1140793.11 0.07288247 0.076782223 563.2550356 -2.750705083 0.541607331 VSPTTSPRPAS(ph)PVPGSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSPTTSPRPASPVPGSER 18 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VSPTTSPRPAS(0.996)PVPGS(0.004)ER;VSPT(0.002)T(0.003)S(0.003)PRPAS(0.981)PVPGS(0.011)ER 73.981 0.011692 328210000 124107 115406 153404 139123 134643 128206 157114 136717 161424 TRUE FALSE 118240.7081 127166.0026 160437.7251 125138.0917 158124.6966 123766.1941 133143.3737 124745.3347 186456.8095 0.634145293 0.682013186 0.860455167 0.67113715 0.848049996 0.663779427 0.714070857 0.669030726 1 17.50848196 -2.175049542 2.288214414 1.719494149 0.713968446 0.570442557 0.076885173 3563070.461 880989.0353 13256825.63 0.018091991 0.006682677 2.175049542 -1.005525703 VSQEHPVVLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VSQEHPVVLTK 11 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;;; 153.38 3.25E-05 691366000 2264960 1522420 1872480 1846760 2042130 1690780 2251870 1935170 2176890 FALSE TRUE 2157899.83 1677556.329 1958335.06 1661120.176 2398276.825 1632227.865 1908305.873 1765716.256 2514470.983 0.858192377 0.667160743 0.778825874 0.660624118 0.95378982 0.649133705 0.758929368 0.702221767 1 21.26182347 -2.188561828 2.282240034 1.668367316 0.751910111 0.398631237 0.095086265 4706000.258 943391.5352 16263482.03 0.020086078 0.006477959 2.188561828 -0.916457205 VSQGKEPVHLLSLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSQGKEPVHLLSLFK 15 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ; 185.67 2.48E-07 908310000 4390900 2803900 3148300 3499400 3360700 3559100 5364900 4478800 3798800 FALSE TRUE 4183350.859 3089620.598 3292652.669 3147633.664 3946805.016 3435847.475 4546385.972 4086612.528 4387898.502 0.953383688 0.704123078 0.750393991 0.717344228 0.899475002 0.78302802 1.03611922 0.931337069 1 22.06509872 1.752581166 10.4576507 0.986080042 0.800349564 0.548983239 0.080226143 0.095991326 49.80689212 0.037129728 0.020260355 56.56934703 -1.752581166 -0.185730478 VSQGSAESLS(ph)PSFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 VSQGSAESLS(1)PSFR 273.52 5.44E-33 97964000 107610 99067 102320 115420 119920 103670 121550 94364 115910 TRUE FALSE 102523.4886 109162.0399 107011.4732 103817.7623 140834.01 100079.8819 103005.3151 86100.9879 133884.7308 0.765759381 0.815343462 0.799280639 0.775426456 1.051904942 0.74750781 0.769358197 0.64309789 1 17.03063191 -1.669528694 7.571155519 1.000633687 0.798662631 0.28278734 0.102039643 0.001028463 4.49E-05 0.093097103 0.021877019 0.021402835 1.669528694 -0.201971056 VSQGSKDPAEGDGAQPEETPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSQGSKDPAEGDGAQPEETPR 21 1 Q14697;F5H6X6 Q14697 GANAB Neutral alpha-glucosidase AB 0 174.37 2.82E-12 395790000 581120 543540 502640 689350 362330 630700 611340 623210 414280 FALSE TRUE 553651.6093 598927.344 525686.5412 620055.2283 425520.2373 608858.7009 518068.855 568638.4286 478524.4266 1.156997592 1.251612897 1.098557382 1.295765052 0.889234099 1.272367025 1.082638265 1.18831641 1 18.86823304 -4.999999973 0.11174495 0.499969181 1.246086181 0.146083386 0.117004744 277.926874 2.056133281 31.8890941 1.211194119 1.00E-05 4.999999973 0.746117 VSQGVEDGPDTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 107.46 0.0015226 606770000 827850 676200 784740 866540 616900 842210 948750 899450 729260 FALSE TRUE 788719.1711 745105.5488 820721.1052 779433.7529 724487.1647 813044.0565 804000.7625 820689.3897 842349.9163 0.936331987 0.884555853 0.974323247 0.925308756 0.860078633 0.965209399 0.954473607 0.974285595 1 19.68406013 1.64976654 1.503394813 0.988064521 0.917779564 0.41035005 0.032844825 0.364859052 1.615311306 0.025671636 0.009393805 44.64435372 -1.64976654 -0.070284956 VSQPIEGHAASFAQFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSQPIEGHAASFAQFK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 147.09 1.06E-06 631690000 655170 613050 574710 720120 545040 660180 745520 772160 624580 FALSE TRUE 624201.4125 675520.492 601061.022 647732.1695 640094.8034 637317.8011 631777.2316 704545.5769 721436.6765 0.86521996 0.936354519 0.833144532 0.897836485 0.887250156 0.883400889 0.875720978 0.976586858 1 19.46051324 1.169212427 4.708532555 0.996856146 0.885307273 0.740683617 0.02605238 0.099088439 3.914713823 0.022829765 0.005935131 14.76428523 -1.169212427 -0.111548873 VSRPENEQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSRPENEQLR 10 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 118.77 0.00071269 798680000 533260 446680 400593 469464 430360 417897 554110 491280 493670 FALSE TRUE 508053.8566 492197.1998 418960.5853 422272.5868 505414.6477 403425.1221 469570.3426 448260.9188 570225.8223 0.890969572 0.863161892 0.734727487 0.740535715 0.886341214 0.707483082 0.823481372 0.786111223 1 19.12117385 -1.105813661 3.714086772 1.000088755 0.809760888 0.478208792 0.064067246 16701384.87 31976733.9 18910.60501 0.015591784 0.078376585 1.105813661 -0.190327867 VSRS(ph)PGASR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSRSPGASR 9 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 VS(0.072)RS(0.928)PGASR 59.116 0.063217 50484000 21506 13630 20524 17602 26504 15449 24877 18365 27348 TRUE FALSE 20489.454 15018.9125 21465.0457 15832.61352 31126.28921 14913.99726 21081.55675 16756.86324 31588.98817 0.648626474 0.475447723 0.679510391 0.501206732 0.985352524 0.472126463 0.667370434 0.530465337 1 14.94713411 -1.681487435 2.583230607 1.057861634 0.615183324 0.384490398 0.150983538 14346441.46 11904027.49 5443256.403 0.033002126 0.020821526 1.681487435 -0.44267831 VSS(ph)GFGLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSGFGLSK 9 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 VS(0.001)S(0.999)GFGLSK;VSS(1)GFGLSK 168.59 6.20E-05 109752000 463380 332410 382950 497090 322170 421830 490810 453050 374240 TRUE FALSE 441476.9457 366282.9569 400508.6363 447121.5688 378356.346 407221.9213 415927.9202 413378.5402 432275.2278 1.021286711 0.847337375 0.926513042 1.034344649 0.875267241 0.942043159 0.962183103 0.956285518 1 18.72159064 0.912978913 0.996136219 0.999203841 0.937663057 0.086924951 0.056618428 1.558952373 3.186367025 0.050980008 0.016816646 8.18425049 -0.912978913 -0.061540784 VSS(ph)GVYEPVVIESH ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSGVYEPVVIESH 14 0 Q5T9C2-3;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 VS(0.132)S(0.868)GVYEPVVIESH;VS(0.023)S(0.977)GVYEPVVIESH 273.15 5.57E-33 190025000 269560 182800 213701 230909 232454 230514 256080 258490 202592 TRUE FALSE 256818.433 201427.5278 223499.4022 207697.5886 272993.904 222531.2424 217010.2928 235855.2453 234008.9327 1.097472776 0.860768542 0.955089191 0.887562651 1.166596082 0.950951914 0.927359013 1.007889924 1 17.83620408 4.737540575 5.131846497 0.964795522 1.103205569 0.187401402 0.083198962 0.247979174 19.33293347 0.018836642 0.119207473 54643.75998 -4.737540575 0.138410047 VSS(ph)PPNAMMSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSPPNAMMSSR 12 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VS(0.14)S(0.86)PPNAMMSSR;VS(0.001)S(0.999)PPNAMMSSR 129.37 0.0001568 304930000 356260 287770 292970 315480 303870 308800 388050 329190 307680 TRUE FALSE 339420.2958 317094.0902 306402.9643 283767.351 356864.8318 298106.1786 328845.8455 300364.3785 355393.443 0.955055031 0.892233935 0.862151428 0.798459726 1.004140169 0.838806074 0.925300824 0.845160158 1 18.43905754 -1.665793453 6.565592213 1.000677184 0.894081844 0.246408064 0.060018966 0.000538636 2.74E-05 0.052613791 0.012323688 0.021587709 1.665793453 -0.106595339 VSS(ph)PSPELGTTPASIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VS(0.085)S(0.837)PS(0.078)PELGTTPASIFR;VS(0.157)S(0.842)PS(0.001)PELGTTPASIFR;VS(0.024)S(0.973)PS(0.002)PELGTTPASIFR;VS(0.002)S(0.987)PS(0.012)PELGTTPASIFR;VSS(0.689)PS(0.311)PELGTTPASIFR 340.97 1.63E-72 510614000 729334 586361 635045 696748 632163 667711 747068 716747 721483 TRUE FALSE 694859.8272 646111.8525 664162.4414 626709.5673 742412.027 644588.0006 633089.0558 653984.833 833366.8988 0.833798208 0.775302995 0.796962829 0.75202119 0.89085855 0.773474446 0.759676268 0.784750191 1 19.66859227 -0.956024406 4.615991804 1.000002551 0.794257899 0.714915823 0.040502269 1.45914E+11 32994886674 5088665.861 0.008938218 0.11065616 0.956024406 -0.205744653 VSS(ph)PTKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.247)S(0.753)PT(0.001)KPK;VS(0.023)S(0.975)PT(0.002)KPK;VS(0.216)S(0.783)PTKPK 110.53 0.0020636 2174670000 4990500 4782050 4562470 5657210 2536620 5745700 5737670 5884600 2915840 TRUE FALSE 4754608.955 5269346.332 4771663.762 5088536.503 2979005.725 5546724.968 4862283.062 5369313.228 3368013.575 1.411695306 1.564526453 1.416759065 1.510842041 0.884499322 1.646883198 1.443664924 1.594207716 1 21.68346652 -1.964334235 2.500360547 0.641962343 1.439660878 0.296451832 0.210029349 10909736.32 5769548.229 22656467.77 0.047039055 0.010855898 1.964334235 0.797698535 VSS(ph)PVFGATSSIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSPVFGATSSIK 13 0 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 VSS(1)PVFGATSSIK;VSS(1)PVFGATSSIK 233.52 1.29E-16 262320000 1131210 1048290 998320 1155790 788850 1132550 1261560 1242100 875510 TRUE FALSE 1077739.945 1155111.943 1044093.959 1039607.793 926425.1902 1093329.51 1069085.852 1133335.139 1011279.619 1.06571904 1.142228045 1.032448335 1.028012207 0.916092021 1.081134721 1.057161473 1.120694136 1 19.94775053 3.717634707 23.70506313 1.035205324 1.10397354 0.213287018 0.05608869 566.0321146 641206.3092 0.014755703 0.022890502 5219.569763 -3.717634707 0.068768216 VSS(ph)SPQKEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSSPQKEGR 10 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 VS(0.114)S(0.443)S(0.443)PQKEGR;VS(0.103)S(0.449)S(0.449)PQKEGR 63.966 0.045513 312980000 403760 318780 409440 438950 297670 417390 527380 468230 426540 TRUE FALSE 384675.065 351264.0444 428213.229 394825.912 349583.5538 402935.6796 446918.495 427229.299 492685.6447 0.780771815 0.712957741 0.869140868 0.801374906 0.709546863 0.817835234 0.907106793 0.867143793 1 18.91030791 1.336139244 0.79188038 0.992810596 0.767200967 0.651699196 0.051807348 0.340449796 0.469601781 0.048259151 0.019151449 21.68399229 -1.336139244 -0.225609629 VSSFEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VSSFEEK 7 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;;; 152.31 0.0042389 2162680000 3335060 2451530 2560770 2751800 2128620 2450260 2982170 2845290 2324730 FALSE TRUE 3177418.323 2701343.694 2678183.837 2475183.836 2499850.654 2365406.882 2527185.195 2596141.324 2685237.255 1.183291464 1.005998144 0.997373261 0.921774726 0.930960811 0.880893067 0.941140374 0.96682009 1 21.35661813 4.527325831 0.921114516 0.933619798 1.270317607 0.829542334 0.033709902 0.518126482 0.433457996 0.010474752 0.16349873 33676.41328 -4.527325831 0.336697809 VSSPLSPLSPGIKS(ph)PTIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 VSSPLSPLSPGIKS(0.999)PTIPR;VSSPLSPLSPGIKS(0.996)PT(0.004)IPR 211.87 6.58E-17 490800000 556200 437650 484920 537770 382770 522530 569390 580660 430870 TRUE FALSE 529909.5283 482247.0326 507154.0617 483712.3379 449524.9668 504434.6551 482519.0979 529814.3321 497687.119 1.06474431 0.968976319 1.019021876 0.971920549 0.903228052 1.013557787 0.969522978 1.064553033 1 18.92487952 -0.384045138 6.330459196 1.000000001 0.994480747 0 0.048215577 0 0 0.043837268 0.010332543 0.413004575 0.384045138 -0.005519253 VSSQS(ph)FSEIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 VS(0.002)S(0.015)QS(0.975)FS(0.008)EIER;VSS(0.008)QS(0.862)FS(0.13)EIER 125.93 0.00033365 362940000 578860 512980 495990 637320 476760 586450 698960 596380 514000 TRUE FALSE 551498.435 565253.2452 518731.6321 573255.3828 559906.7931 566141.0895 592320.8147 544157.8056 593708.4949 0.928904403 0.952072019 0.873714351 0.965550245 0.943066838 0.95356744 0.997662691 0.916540373 1 19.17939523 2.488856527 1.442705081 0.970878542 0.929180262 0.245008117 0.032282098 0.572510667 2.412237447 0.01470412 0.011155025 308.2169561 -2.488856527 -0.04169828 VSSS(ph)PGVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSSPGVK 8 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 VSSS(1)PGVK;VSSS(1)PGVK 180.09 0.00025271 317660000 1269020 1188970 1059120 1380450 785110 1288580 1303850 1368590 885890 TRUE FALSE 1209035.94 1310127.395 1107681.7 1241684.543 922032.9354 1243956.151 1104923.736 1248749.004 1023269.297 1.181542282 1.280334902 1.082492852 1.213448451 0.901065769 1.215668403 1.079797605 1.220352265 1 19.96475444 3.73141758 24.94436806 1.106768723 1.230938593 0.211463133 0.103306957 688.9852773 2406022.81 0.024283365 0.038529281 5387.87585 -3.73141758 0.12416987 VSSS(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.013)S(0.079)S(0.504)S(0.404)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.003)S(0.04)S(0.478)S(0.478)ELDLPSGDHCEAGLLQLDVPLLR 333.67 3.57E-96 174138000 117088 121815 95280 112815 98336 103716 122941 120662 88718 TRUE FALSE 111553.4823 134228.087 99648.68224 101474.6219 115485.7673 100124.2889 104184.0925 110096.1956 102475.9343 1.088582241 1.309849848 0.972410575 0.990228804 1.126955007 0.97705173 1.016668871 1.074361472 1 16.64492562 3.72619919 24.94579645 1.022979342 1.199216049 0.523300975 0.070109257 469.8246762 948122.6305 0.017550695 0.027409466 5323.523671 -3.72619919 0.176236708 VSSSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.003)S(0.016)S(0.105)S(0.876)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.004)S(0.022)S(0.136)S(0.838)ELDLPSGDHCEAGLLQLDVPLLR 256.12 9.77E-54 159951000 94283 86171 78841 90348 75667 78346 94774 88862 70703 TRUE FALSE 89826.42944 94951.92287 82455.93783 81266.04739 88863.30084 75632.85838 80314.48566 81080.77219 81667.26014 1.09990747 1.162668157 1.009657208 0.995087227 1.088114144 0.926109903 0.983435535 0.992818567 1 16.31747021 3.68348594 6.29195943 0.996204796 1.13114378 0.633543993 0.041709185 0.117720421 10.46882214 0.010818364 0.017005895 4824.873601 -3.68348594 0.134938984 VSTEVDAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VSTEVDAR 8 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;;;;; 150.35 0.0011413 2344450000 4775630 4085940 4060390 4714510 4687460 4265000 5154750 4751850 5028680 FALSE TRUE 4549895.434 4502301.931 4246562.898 4240598.498 5504951.54 4117301.981 4368298.214 4335752.823 5808502.011 0.783316495 0.775122729 0.731094332 0.730067492 0.947740317 0.708840588 0.752052458 0.746449397 1 22.46973472 -0.963150445 4.220430001 1.000009014 0.771342966 0.539508215 0.066245046 12716954.47 23706274.5 1689.485017 0.014798267 0.108855294 0.963150445 -0.228666048 VSTTTDSPVS(ph)PAQAASPFIPLDELSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSTTTDSPVSPAQAASPFIPLDELSSK 27 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 VS(0.012)T(0.012)T(0.012)T(0.012)DS(0.204)PVS(0.746)PAQAASPFIPLDELSSK 94.185 0.0034319 16929000 18294 17336 20968 21037 13998 17719 21832 16574 18090 TRUE FALSE 17429.27888 19102.55811 21929.40354 18922.32079 16439.24677 17105.38659 18501.12743 15122.6927 20895.30481 0.834124175 0.914203372 1.049489526 0.905577639 0.786743573 0.818623454 0.885420318 0.723736401 1 14.35089118 2.918167369 8.16504096 0.838555468 0.922290941 0.183596239 0.08727384 0.553678671 50.51246931 0.025347833 0.026943901 828.2612988 -2.918167369 0.083735473 VSVGAPDLSLEASEGS(ph)IKLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSVGAPDLSLEASEGSIKLPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSVGAPDLSLEAS(0.001)EGS(0.999)IKLPK;VSVGAPDLSLEASEGS(1)IKLPK 215.51 3.96E-25 366360000 374110 288574 296124 430097 201159 347338 421770 348774 167684 TRUE FALSE 356426.5617 317980.0187 309701.5783 386862.8324 236241.0659 335309.598 357421.2402 318233.4996 193687.5783 1.840213837 1.641716115 1.598974911 1.997354894 1.219701686 1.731187931 1.845349316 1.643024826 1 17.56337191 0.953200031 22.03018507 0.999999997 1.702890698 0.531472319 0.20403552 1967.372439 926104.6989 0.179340927 0.044835232 8.978422351 -0.953200031 0.702890701 VSVHVIEGDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 208.74 1.07E-08 36294505000 13981220 10742976 13239942 14894388 18124874 12443547 18577177.9 15026130.7 3319077 FALSE TRUE 13320355.44 11837697.47 13847006.44 13397175.82 21285846.29 12012623.85 15742888.22 13710363.04 3833782.51 3.474468206 3.087733182 3.611839326 3.494505958 5.552178882 3.133360804 4.106359236 3.576197398 1 21.87033706 2.98764589 24.67934831 3.755845488 3.365037414 0 1.131071392 2230.647635 4456093.276 0.29895529 0.332501417 971.9544005 -2.98764589 -0.390808074 VSVQPEESYSHWQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSVQPEESYSHWQR 14 0 P51687 P51687 SUOX "Sulfite oxidase, mitochondrial" 0 ; 123.72 0.00057232 0 107628 94730 103071 112005 97801 109859 155763 131643 105953 FALSE TRUE 102540.6377 104383.0947 107796.9073 100746.0446 114857.4634 106054.5553 131998.4936 120115.641 122383.6501 0.837862228 0.852916992 0.880811344 0.823198561 0.938503332 0.86657454 1.078563137 0.981468039 1 16.90105131 1.751759965 25 1.023130036 0.864484187 0.775005652 0.038930654 1.632565827 3096.773199 0.016684537 0.009252447 56.46248205 -1.751759965 -0.158645849 VSVS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VSVS(1)PGR;VSVS(1)PGR;VSVS(1)PGR;VSVS(1)PGR;VSVS(1)PGR 125.31 0.0042601 5813660000 5601390 5046190 4961100 5574770 5152470 5088480 5593860 5517590 5513970 TRUE FALSE 5336623.396 5560402.498 5188571.342 5014383.528 6051059.137 4912264.662 4740413.919 5034440.569 6369048.306 0.837899658 0.873035064 0.814654104 0.787304992 0.950072734 0.771271378 0.744289208 0.790454135 1 22.60264638 VSVT(ph)PPEESQNSDTPPRPDRLPLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.034)VT(0.962)PPEES(0.002)QNS(0.002)DTPPRPDRLPLDEK;VS(0.028)VT(0.955)PPEES(0.014)QNS(0.003)DTPPRPDRLPLDEK 131.81 0.0028838 348300000 489480 405310 427940 481970 338230 480840 536520 538420 373330 TRUE FALSE 466343.2505 446611.5498 447561.4723 433521.4599 397217.2049 464188.3902 454664.0201 491273.0905 431224.1097 1.081440578 1.035683163 1.037886014 1.005327509 0.921138675 1.076443501 1.054356679 1.139252373 1 18.71807832 VSVTPPEES(ph)QNSDTPPRPDRLPLDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.028)VT(0.273)PPEES(0.343)QNS(0.343)DT(0.013)PPRPDRLPLDEK 43.696 0.088591 228450000 175310 125300 170840 165780 109520 173400 176200 164170 122510 TRUE FALSE 167023.4437 138068.2125 178673.183 149115.4794 128620.2533 167395.1145 149317.4539 149794.4045 141508.2251 1.180309085 0.97569037 1.262634613 1.05375839 0.908924221 1.182935581 1.055185688 1.058556168 1 17.11052639 3.046989677 24.99999271 1.049591741 1.116248989 0.163524452 0.097426951 286.4568552 152402.2828 0.026805223 0.032038355 1114.268047 -3.046989677 0.066657248 VSYDEWNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VSYDEWNR 8 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 85.212 0.039324 64700000 142820 114130 123190 162900 146580 132330 163310 140640 157990 FALSE TRUE 136069.1816 125759.9768 128838.3834 146524.9825 172143.5056 127747.3789 138394.0601 128324.816 182490.2823 0.74562426 0.689132458 0.706001337 0.80291937 0.943302314 0.700022913 0.758363998 0.70318712 1 17.47746012 -1.91065587 2.684068444 1.142239225 0.752846516 0.511795393 0.074813581 10117768.79 6220553.485 9070150.952 0.018982934 0.012284122 1.91065587 -0.389392709 VSYLVFDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VSYLVFDEADR 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;;;; 213.8 3.02E-09 327397000 474555 512724 423949 543593 439094 442625 458664 471792 474720 FALSE TRUE 452123.7256 564971.1585 443387.481 488949.9989 515671.8546 427296.7853 388686.3829 430479.3914 548337.1531 0.824536005 1.030335361 0.808603755 0.891695914 0.940428442 0.779259226 0.708845608 0.78506333 1 19.0647037 2.229875275 24.82390267 0.784374834 0.905780737 0.102182179 0.09728669 221.6194663 633413.4911 0.033300413 0.024978531 169.7756004 -2.229875275 0.121405903 VT(ph)KSPGETSKPRPFAGGGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.644)KS(0.356)PGETSKPRPFAGGGYR 107.9 0.00022619 1677100000 1035100 844270 979150 1007900 800300 1048500 1290500 1201800 934170 TRUE FALSE 986172.8744 930302.0729 1024044.996 906583.9771 939872.0666 1012190.182 1093610.523 1096564.021 1079036.313 0.913938542 0.862160116 0.94903664 0.840179303 0.871029136 0.938050157 1.013506692 1.016243854 1 20.04131199 1.918324802 2.945352129 1.011276207 0.887242683 0.778053155 0.02980179 0.112650853 1.753536634 0.014609484 0.007867455 82.85616 -1.918324802 -0.124033524 VTAEADSSS(ph)PTGILATSESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTAEADSSSPTGILATSESK 20 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 VTAEADSSS(0.998)PT(0.002)GILATSESK;VTAEADS(0.001)S(0.009)S(0.989)PT(0.002)GILATSESK;VTAEADS(0.025)S(0.193)S(0.779)PT(0.002)GILATSESK 302.64 5.87E-55 305130000 1201630 1119860 1054940 1241960 812940 1170080 1285780 1191430 996550 TRUE FALSE 1144831.331 1233975.007 1103310.042 1117115.821 954716.4786 1129559.836 1089610.646 1087102.073 1151089.884 0.994562933 1.072005778 0.95849165 0.970485308 0.829402197 0.981295945 0.94659041 0.944411108 1 20.13456906 3.594936771 5.009977101 0.941919286 1.032865809 0.349111904 0.048867631 0.206016967 7.607047687 0.012304465 0.019264979 3934.927829 -3.594936771 0.090946523 VTAEDKGTGNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTAEDKGTGNK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 126.76 0.0002742 154110000 472870 231050 302520 520800 284670 415080 576690 477300 385910 FALSE TRUE 450518.3722 254594.2577 316390.8412 468448.1945 334316.3579 400705.6755 488705.3489 435505.0817 445754.9518 1.010686186 0.571152954 0.709786487 1.050909682 0.750000323 0.898937126 1.096354279 0.977005594 1 18.7658913 1.965727653 4.956186964 1.029304295 0.808428684 0.307452064 0.14040713 0.229980619 13.9993491 0.061215472 0.037998923 92.41184754 -1.965727653 -0.220875612 VTAGWPSEPGQGDLNPES(ph)PAALGQDLLEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VTAGWPS(0.001)EPGQGDLNPES(0.999)PAALGQDLLEPR;VTAGWPSEPGQGDLNPES(1)PAALGQDLLEPR;VTAGWPSEPGQGDLNPES(1)PAALGQDLLEPR 129.73 6.33E-06 109021000 112927 110228 104959 115629 122434 105248 120198 109190 118744 TRUE FALSE 107589.1645 121460.3585 109771.474 104005.7532 143786.4508 101603.2354 101859.5875 99628.74475 137158.2131 0.784416493 0.885549292 0.800327385 0.758290378 1.048325489 0.74077398 0.742643005 0.726378264 1 17.06548149 -1.208350379 6.984788739 1.000000553 0.812786263 0.278612104 0.095612204 7.90E-07 8.94E-08 0.088734353 0.020914826 0.061894152 1.208350379 -0.18721429 VTAIHIDPATHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 204.49 6.53E-08 73701378100 48007511.7 44074892 44912789.7 52603394 48743762.8 45190843 53332188 49703295.2 11225067 FALSE TRUE 45738291.76 48566173.6 46972085.53 47315600.9 57244659.6 43625872.78 45195383.21 45351011.18 12965793.06 3.527612353 3.745715621 3.622769954 3.649263927 4.415052695 3.364689886 3.485739977 3.497742943 1 23.62820712 -0.178154785 0.746243513 0.881927595 3.720447442 0.904071467 0.274058201 2.056730995 1.031880166 0.971469095 0.090349633 0.663506551 0.178154785 2.838519847 VTANNDKNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTANNDKNR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ;; 98.943 0.0050198 156470000 242690 156070 154375 220598 178900 175279 296760 243132 290173 FALSE TRUE 231218.5247 171973.7104 161453.2464 198423.0699 210100.1034 169209.0443 251483.8116 221842.0732 335171.5468 0.689851292 0.513091615 0.481703319 0.592004518 0.626843494 0.504843105 0.750313724 0.66187621 1 18.35454016 0.653091869 0.712372221 1.002740332 0.567807151 0.749116979 0.075821764 0.595042752 0.562009775 0.07566604 0.026838892 4.498750097 -0.653091869 -0.434933182 VTAPDVDLHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTAPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 136.96 8.84E-05 250210000 713490 725550 601560 851450 521960 644150 672360 778020 490550 FALSE TRUE 679764.7417 799484.3699 629142.121 765860.6284 612989.6587 621842.924 569779.1333 709892.4443 566621.9886 1.199679425 1.410966016 1.110338345 1.351625323 1.081831752 1.097456393 1.005571871 1.252850151 1 19.11202706 2.723720002 24.27134596 1.081846909 1.275579029 0.420968002 0.10497644 464.3742531 759467.6128 0.030987886 0.029339901 529.3220695 -2.723720002 0.19373212 VTDALPEPEPPGAMAAS(ph)EDEEEEEEALEAMQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 203.46 2.89E-27 170770000 241360 233730 221700 269940 270050 246050 300610 263360 277890 TRUE FALSE 229951.3911 257547.3527 231865.1643 242805.1183 317146.6345 237529.2268 254746.4234 240298.8022 320983.7619 0.716395713 0.80236879 0.722357925 0.756440503 0.988045727 0.740003872 0.793642712 0.74863227 1 18.29214079 -5 0.276564021 2.530233481 0.768747298 0.428818478 0.078074931 213.3323137 2.052625039 187.3628105 0.086250604 1.00E-05 5 -1.761486183 VTDKLTPIHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VTDKLTPIHDR 11 1 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;;; 202.81 2.33E-08 3055550000 7598600 5196340 6829400 6790320 6547470 7003420 9257880 7688270 7719070 FALSE TRUE 7239429.237 5725852.954 7142534.745 6107744.133 7689346.695 6760889.809 7845420.373 7015044.321 8916103.952 0.811949847 0.642192261 0.801082489 0.685023881 0.862411064 0.758278486 0.879915759 0.786783595 1 23.08798201 0.663479856 0.341987137 1.029676924 0.718696161 0.546238414 0.067503483 1.555289495 0.421290467 0.157512067 0.06337108 4.607653965 -0.663479856 -0.310980762 VTEGGEPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTEGGEPYR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 92.439 0.016774 58384000 197162 210631 170375 226604 184692 202365 200533 203716 218001 FALSE TRUE 187842.543 232094.5384 178186.8623 203825.3354 216902.2263 195357.0493 169938.0078 185877.5471 251807.4817 0.745976814 0.921714227 0.707631326 0.809449084 0.861381182 0.775819082 0.674872751 0.73817325 1 17.94196162 2.013721588 23.72213804 0.757504039 0.814576471 0 0.103195902 356.6633392 616601.5525 0.035187535 0.025971549 103.2099548 -2.013721588 0.057072432 VTEGLTDVILYHQPDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VTEGLTDVILYHQPDDK 17 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;; 256.45 4.26E-27 1727022000 4266060 4348200 3613810 4951100 2563636 4286430 4047320 4539960 2273277 FALSE TRUE 4064411.798 4791286.523 3779506.763 4453406.022 3010733.307 4137989.854 3429827 4142417.035 2625805.187 1.547872561 1.824692307 1.439370591 1.696015395 1.146594318 1.575893701 1.306200101 1.577579729 1 21.32432845 -2.337607018 0.101145657 1.50E-13 1.979020607 0.461634815 0.182618142 67.16112879 0.872865517 18.92524287 3.274232494 0.004596137 2.337607018 1.979020607 VTEGLVDVILYHQPDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VTEGLVDVILYHQPDDK 17 0 O43390;O43390-3;B4DT28 O43390 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;;;; 274.81 1.06E-35 1382790000 4248864 4319559 3636251 4826739 2611888 4382447 4173073 4588503 2189049 FALSE TRUE 4048028.619 4759726.973 3802976.705 4341546.026 3067400.44 4230681.762 3536394.07 4186709.352 2528515.539 1.600950659 1.882419507 1.504035331 1.717033555 1.213123033 1.673187962 1.39860484 1.655797359 1 21.26985921 -2.75732657 0.148016798 1.15E-14 1.832598053 0.509695471 0.180502976 44.50671981 0.745849731 15.61996539 0.973408453 0.001748531 2.75732657 1.832598053 VTEGQQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTEGQQER 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 147.36 0.0012528 195430000 249082 231267 224122 278177 272549 239895 259360 248759 283954 FALSE TRUE 237308.3875 254833.3702 234398.2154 250214.1195 320081.4593 231587.376 219789.8685 226976.3432 327988.1361 0.723527352 0.77695911 0.714654555 0.762875519 0.975893406 0.706084613 0.670115301 0.692026077 1 18.32328411 5.216849142 0.884617235 0.771512674 0.650414061 0.013984918 0.114570391 29.47194238 10.03220605 0.035564639 4.214648109 164758.9978 -5.216849142 -0.121098613 VTEHGT(ph)PKPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VTEHGTPKPFR 11 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VT(0.003)EHGT(0.997)PKPFR 203.87 5.15E-08 3176520000 2592940 2078530 1732730 2488830 1631830 2052560 2543910 2548100 1618210 TRUE FALSE 2470376.865 2290334.57 1812177.384 2238648.08 1916420.635 1981479.333 2155789.807 2324974.856 1869153.742 1.321655255 1.225332362 0.969517565 1.197680014 1.025287857 1.060094356 1.153350716 1.243864966 1 20.83395381 3.96083042 7.301853525 1.101192751 1.286266819 0.438552714 0.08736005 0.185205389 29.70805407 0.020804122 0.038437024 9137.563762 -3.96083042 0.185074068 VTEKIPVR ddPTM_SK-BR-3_Trastuzumab_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 ; 81.972 0.019589 932700000 1144120 1102880 1112890 1093070 1087790 1130390 1305360 1268650 1201270 FALSE TRUE 1090039.715 1215264.726 1163917.107 983192.5269 1277500.232 1091244.311 1106203.357 1157560.28 1387556.816 0.78558204 0.875830605 0.838824828 0.708578211 0.920683187 0.786450182 0.797231035 0.834243518 1 20.40411542 0.947570865 19.25818505 1.000000001 0.818037589 0.506796412 0.056542664 555.2367819 203950.2484 0.04919382 0.012298455 8.86279829 -0.947570865 -0.181962412 VTENGGSPQGIKS(ph)PSKPPGPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTENGGSPQGIKSPSKPPGPNR 22 2 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6;C9JPJ6;C9JE09 Q92766 RREB1 Ras-responsive element-binding protein 1 1 VTENGGSPQGIKS(0.996)PS(0.004)KPPGPNR 100.95 0.00040611 85497000 80828 86049 84829 93473 51306 94333 95153 100320 82198 TRUE FALSE 77007.42063 94817.49093 88718.49356 84076.91645 60253.75016 91066.22456 80635.66225 91535.44897 94944.84603 0.811075312 0.998658641 0.934421375 0.885534286 0.634618441 0.959148689 0.849289515 0.964090762 1 16.53480207 1.102919467 4.400243239 0.998862472 0.875201959 0.187516958 0.099286762 0.35674636 11.17530423 0.091377388 0.023373035 12.67416821 -1.102919467 -0.123660514 VTEQEWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VTEQEWR 7 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;;; 165.52 0.002693 1906770000 3871410 3275940 3303420 4243740 3864450 3317000 4721900 3666730 4091260 FALSE TRUE 3688416.122 3609762.01 3454885.075 3817151.193 4538408.856 3202131.458 4001487.431 3345651.683 4725711.706 0.780499605 0.76385574 0.731082489 0.80774102 0.960365155 0.677597716 0.846748105 0.707967792 1 22.17210019 -2.302978738 2.394989304 2.135353695 0.786460966 0.424391472 0.078849889 11051150.82 2601838.073 67184257.24 0.01709651 0.004977615 2.302978738 -1.348892729 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VTFFEPGS(1)GDENGTSNKEDEFR 220.53 6.11E-26 538097000 717320 696030 690370 817750 489550 833700 854370 801450 569370 TRUE FALSE 683413.7052 766956.2483 722024.1474 735548.2164 574927.365 804828.76 724020.1649 731270.7892 657664.9917 1.039151717 1.166180743 1.097860091 1.118423857 0.874194875 1.22376707 1.100895097 1.111919896 1 19.32699335 -2.555320837 1.83349115 3.16E-05 1.095899825 0.089274446 0.090955212 1737322.041 65485.27297 7262941.249 0.020608153 0.002784064 2.555320837 1.09586826 VTFFEPGSGDENGTSNKEDEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;; 155.87 1.45E-08 252970000 213571 185580 192918 233293 151008 214540 247338 237803 391825 FALSE TRUE 203475.9221 204490.813 201763.4811 209841.9444 177343.7474 207110.426 209602.0454 216979.7086 452587.2198 0.449583888 0.451826309 0.445800218 0.463649735 0.391844355 0.457614393 0.463119673 0.479420759 1 18.78783632 -0.109970321 1.006886263 1.006932988 0.444410058 0.987273712 0.019655714 1.020417944 0.816927447 0.044814058 0.005600401 0.776300166 0.109970321 -0.56252293 VTGGLLDRLDDS(ph)PDQCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 165.38 1.50E-09 151480000 97053 90243 91772 108050 103510 99260 105520 98486 98528 TRUE FALSE 92465.49703 99438.8643 95979.83697 97188.60872 121562.1112 95822.60131 89420.98599 89862.04373 113807.219 0.812474796 0.873748301 0.843354559 0.853975781 1.0681406 0.841972962 0.78572332 0.789598801 1 16.79623255 -2.494478305 2.29631146 2.956308401 0.856830573 0.237705856 0.079507114 9065097.995 1842410.155 89846871.62 0.019667807 0.00320274 2.494478305 -2.099477827 VTGQHQGYGFVEFLSEEDADYAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTGQHQGYGFVEFLSEEDADYAIK 24 0 Q5SZ64;Q15427 Q5SZ64 SF3B4 Splicing factor 3B subunit 4 0 ; 256.12 7.40E-44 102354000 104977 95986 99523 103099 80488 104019 114965 101728 77760 FALSE TRUE 100014.9453 105767.0825 104086.228 92735.29264 94525.08172 100416.7959 97424.97777 92820.15703 89818.62366 1.113521241 1.17756294 1.158849064 1.032472876 1.052399579 1.117995265 1.084685712 1.033417717 1 16.45472699 2.164508594 0.221966949 0.980490483 1.189118178 0.510398698 0.040146536 2.559096606 0.435585968 0.124393408 0.196641198 146.0523649 -2.164508594 0.208627695 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYT(0.001)S(0.003)T(0.016)S(0.075)S(0.285)T(0.193)GGS(0.428)PVRK;VTGTEGSSSTLVDYTSTS(0.001)STGGS(0.998)PVRK 298.2 5.93E-71 911620000 496900 457650 403930 526270 314880 471200 471600 461010 349440 TRUE FALSE 473412.5218 504285.0553 422450.59 473368.3398 369794.9723 454882.2258 399648.7585 420641.5204 403629.3705 1.172889181 1.249376513 1.046629955 1.172779719 0.916174588 1.126979995 0.990137952 1.042147949 1 18.62267163 3.373477208 1.300045089 1.025196979 1.210767915 0.460736119 0.074242561 0.315584529 1.107042495 0.022819094 0.039451532 2363.073381 -3.373477208 0.185570936 VTHAVVTVPAYFNDAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 186.68 5.10E-10 2761700000 2783500 2243400 2383000 2766000 2768300 2333100 2973800 2560800 2587900 FALSE TRUE 2651929.471 2472005.011 2492262.907 2487956.425 3251090.644 2252304.162 2520092.192 2336562.776 2989218.315 0.887164868 0.826973727 0.833750715 0.832310043 1.087605622 0.753475968 0.843060602 0.781663475 1 21.51133684 -2.362269536 2.281902776 1.972123853 0.855133274 0.202747699 0.089887746 5572940.224 568040.7611 28236735.3 0.020031948 0.004342406 2.362269536 -1.116990578 VTHTGQVYDDKDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTHTGQVYDDKDYR 14 1 D6RBT3;O75380 D6RBT3 NDUFS6 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial" 0 ; 200.55 1.15E-08 634160000 957680 863920 803280 882730 610510 753710 842620 846890 539880 FALSE TRUE 912412.3643 951954.4302 840111.1826 793996.3033 716982.7507 727608.8337 714062.8432 772731.822 623601.8331 1.463132909 1.526542065 1.34719165 1.273242414 1.149744457 1.166784309 1.14506213 1.239142961 1 19.25026564 3.264920288 1.458973208 1.147915671 1.499171629 0.833745562 0.064050447 0.127372266 0.564665562 0.019596659 0.029402448 1840.434169 -3.264920288 0.351255958 VTHTGQVYDDKDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTHTGQVYDDKDYRR 15 2 D6RBT3;O75380 D6RBT3 NDUFS6 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial" 0 118.19 0.00018655 240890000 279620 192500 263290 203510 198030 211610 261580 274400 224410 FALSE TRUE 266402.9168 212115.9689 275362.1069 183052.7882 232566.3693 204281.8926 221671.1668 250372.0813 259210.3567 1.027747966 0.818315948 1.062311362 0.70619396 0.897210946 0.788093097 0.855178665 0.965903078 1 17.98376384 4.666589935 3.221330363 0.875160278 1.038215053 0.14267008 0.104997576 0.470365695 7.888726084 0.022697333 0.172821005 46407.68826 -4.666589935 0.163054775 VTIAQGGVLPNIQAVLLPK ddPTM_SK-BR-3_Trastuzumab_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 ; 234.22 9.18E-24 119418000 260060 217390 207880 247510 190105 246150 269510 255790 218880 FALSE TRUE 247767.4792 239542.2882 217411.5036 222629.8246 223259.2518 237625.7638 228391.2996 233391.6716 252822.7925 0.980004519 0.947471095 0.859936327 0.880576559 0.883066157 0.939890591 0.903365149 0.923143318 1 17.94776701 -1.031410567 7.080582708 1.000000011 0.917961424 0.358519972 0.035626422 7.15E-09 9.61E-10 0.038065352 0.008972088 0.093022805 1.031410567 -0.082038587 VTKEQWDTIEELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTKEQWDTIEELIR 14 1 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 188.06 8.00E-07 88671000 271710 146510 306860 188700 279100 213550 357010 293740 348370 FALSE TRUE 258866.8068 161439.5356 320929.8345 169731.5175 327774.9516 206154.71 302541.5676 268018.5684 402393.4404 0.643317661 0.401198229 0.797552351 0.421804882 0.814563357 0.512321249 0.751855118 0.666060978 1 18.61824726 -2.05515942 0.188297762 1.507944507 0.501705 0.431856502 0.14037785 29.20668901 0.790196637 6.806393602 0.388100103 0.008807255 2.05515942 -1.006239507 VTKNEEPS(ph)EEEIDAPKPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VTKNEEPSEEEIDAPKPK 18 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 VT(0.001)KNEEPS(0.999)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VT(0.001)KNEEPS(0.999)EEEIDAPKPK 217.94 4.25E-19 4730400000 4617890 4533769 4677100 5021260 2102146 6258320 5681170 6026270 2406573 TRUE FALSE 4399611.491 4995765.216 4891549.661 4516513.405 2468759.597 6041592.809 4814403.175 5498577.852 2779772.05 1.582723839 1.79718521 1.759694527 1.624778336 0.888115843 2.173413036 1.731941716 1.978067897 1 21.40653515 VTKS(ph)PGETSKPRPFAGGGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.241)KS(0.759)PGETSKPRPFAGGGYR 123.2 0.00016089 2384800000 1160900 860190 1270000 1059100 750980 1246100 1502000 1220300 1010000 TRUE FALSE 1106026.558 947844.339 1328230.756 952637.2558 881950.6742 1202947.245 1272842.314 1113444.063 1166625.642 0.948056101 0.812466575 1.138523541 0.816574934 0.755984304 1.031133897 1.091046063 0.954414187 1 20.15391026 2.065716257 24.98265732 1.034225413 0.895438834 0.242767189 0.1081049 71.35505036 27125.43962 0.038850747 0.028693175 116.3365706 -2.065716257 -0.138786579 VTKS(ph)PQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VTKS(1)PQK;VT(0.155)KS(0.845)PQK 100.48 0.0059139 627680000 2919800 3336200 2440000 3257400 1492050 3042000 3046700 3775100 2132800 TRUE FALSE 2781786.84 3676162.573 2551876.413 2929959.963 1752263.048 2936654.777 2581869.959 3444532.231 2463543.731 1.129181027 1.492225418 1.035855942 1.189327361 0.711277427 1.192044915 1.048030902 1.398202186 1 21.23230365 3.714098825 24.53553328 1.078190969 1.310703259 0.194099973 0.193523788 798.6456268 801053.0485 0.047712727 0.073956453 5177.246281 -3.714098825 0.23251229 VTLATLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTLATLK 7 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ; 96.19 0.030042 81647000 676890 498950 401070 530100 691780 578080 990330 605980 717380 FALSE TRUE 644894.7512 549793.5723 419459.4562 476813.3409 812426.213 558060.9446 839236.9698 552917.1787 828627.6265 0.778268465 0.663498965 0.506209838 0.575425349 0.980447896 0.673476151 1.012803511 0.667268579 1 19.6603644 2.746134063 24.89830659 0.863567302 0.645747303 0.417201818 0.138044728 564.6160018 1856220.381 0.039925863 0.041610418 557.3577745 -2.746134063 -0.217819999 VTLEYRPVIDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTLEYRPVIDK 11 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 ;; 151.78 3.03E-05 1851910000 4097710 3065500 3225340 3130460 3272580 2907500 3884020 3556950 3570260 FALSE TRUE 3904019.369 3377877.935 3373225.029 2815780.213 3843316.916 2806812.546 3291441.414 3245484.601 4123917.686 0.946677326 0.819094413 0.817966139 0.682792535 0.931957718 0.680617985 0.798134605 0.786990636 1 21.97558411 4.475298269 1.658513788 0.797593731 0.962757953 0.136049353 0.097986224 0.871379267 3.418874746 0.022810089 0.196894024 29874.33653 -4.475298269 0.165164222 VTLLEGDHVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 141.93 3.66E-05 258530000 193850 197100 165690 215040 181930 181410 202580 223300 179030 FALSE TRUE 184687.0947 217184.7141 173287.0504 193423.7707 213658.5344 175127.7262 171672.7004 203746.6682 206793.058 0.893101037 1.050251474 0.837973247 0.935349438 1.033199743 0.8468743 0.830166651 0.985268413 1 17.65782823 2.215373618 24.99842688 0.891841586 0.952722964 0.005670888 0.0811481 512.9517786 553021.3064 0.028908108 0.021363024 164.2001757 -2.215373618 0.060881377 VTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLQDYRLPDSDDDEDEETAIQR 23 1 H3BRF9;Q96K21-2;Q96K21;Q96K21-4 H3BRF9 ZFYVE19 Abscission/NoCut checkpoint regulator 1 VTLQDYRLPDS(0.999)DDDEDEET(0.001)AIQR 56.914 0.05191 67307000 20402 8809.9 16353 13557 41807 15286 49565 20565 62832 TRUE FALSE 19437.63789 9707.638826 17102.80123 12194.2246 49098.12756 14756.64199 42002.94893 18764.21958 72575.66566 0.26782583 0.133758867 0.235654762 0.168020844 0.676509504 0.203327684 0.578747002 0.258546986 1 16.14719828 -5 0.141634873 3.445794311 0.062267834 0.636763405 0.167554126 77.27714022 0.667244388 53.02260429 0.878180972 1.00E-05 5 -3.383526478 VTLT(ph)SEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 1 VTLT(0.627)S(0.373)EEEAR 155.99 0.00013121 114820000 234030 175360 197950 231620 229600 198810 251190 203950 236400 TRUE FALSE 222967.8657 193229.3834 207026.2033 208337.1176 269642.1673 191925.1598 212866.3521 186091.0568 273059.7046 0.81655353 0.707645178 0.75817193 0.762972764 0.987484285 0.702868847 0.779559739 0.681503179 1 18.05885691 -1.824835349 2.650030654 1.077627564 0.773837571 0.406946088 0.085511147 17011884.93 12340094.25 8445868.976 0.019153948 0.01496803 1.824835349 -0.303789993 VTLTS(ph)EEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 1 VTLT(0.191)S(0.809)EEEAR 208.33 1.21E-07 96533000 296450 227370 243840 280650 295570 247260 295260 265050 288490 TRUE FALSE 282437.396 250539.2615 255020.3052 252438.5288 347117.3144 238697.3242 250212.6642 241840.8169 333227.5558 0.847581153 0.751856373 0.765303771 0.757555984 1.041682503 0.716319284 0.75087627 0.725752756 1 18.34614818 -1.027165437 4.216740544 1.000014714 0.792714656 0.317005337 0.094705866 9908362.308 4827201.345 1398.883799 0.020960782 0.093936541 1.027165437 -0.207300058 VTLTSEEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 226.64 6.83E-09 1966900000 592100 470630 506300 557130 503960 529740 625680 528590 560570 FALSE TRUE 564112.6064 518587.7321 529514.3558 501126.2339 591850.4644 511394.971 530221.0246 482303.8574 647500.3326 0.871215933 0.800907283 0.817782369 0.773939732 0.914054302 0.789798777 0.818873749 0.74487044 1 19.30452141 -2.186659798 2.491027169 1.528622153 0.818809456 0.593775267 0.047681184 5408623.573 2018263.811 15971934.01 0.010520306 0.006506392 2.186659798 -0.709812698 VTLVFEHVDQDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTLVFEHVDQDLR 13 0 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VXD2;F8VZZ0;F8VZ51 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 98.942 0.0030881 27285000 34629 36044 33403 36273 34546 34565 35803 36115 30188 FALSE TRUE 32992.1558 39716.92458 34934.56059 32626.76913 40570.81146 33368.00538 30340.59478 32952.57914 34869.40086 0.946163541 1.139019415 1.001868679 0.935684822 1.163507559 0.956942321 0.870120909 0.945028544 1 15.08967395 2.014459171 24.93485951 0.921346986 1.038588379 0.255973929 0.078558009 244.0601182 420880.2444 0.027462738 0.020274387 103.3853902 -2.014459171 0.117241392 VTLYNTDQDGSDS(ph)PR ddPTM_SK-BR-3_Trastuzumab_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;VTLYNTDQDGS(0.035)DS(0.965)PR 200.67 1.25E-11 0 352070 306980 301340 350010 300910 327190 346180 342780 312720 TRUE FALSE 335428.3488 338261.611 315156.7371 314826.3298 353388.6087 315859.3283 293363.883 312764.366 361215.0204 0.928611298 0.936454997 0.872490675 0.871575964 0.978333094 0.874435753 0.812158594 0.865867553 1 18.46249836 2.025901663 24.98521057 0.864677348 0.917742562 0 0.057145469 368.3882636 355352.3449 0.019700273 0.014549173 106.1455185 -2.025901663 0.053065213 VTMLFLGLHNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTMLFLGLHNVR 12 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 106.01 0.0019685 22700000 119650 101140 87143 99383 123400 96161 132590 112740 121580 FALSE TRUE 113994.3816 111446.281 91138.59275 89392.83202 144920.9209 92830.92046 112360.9603 102867.8879 140434.0055 0.811729191 0.793584721 0.648978091 0.636546909 1.031950349 0.661028788 0.800097953 0.73249985 1 17.09953279 VTNDIS(ph)PESS(ph)PGVGR ddPTM_SK-BR-3_Trastuzumab_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 2 VTNDIS(1)PES(0.189)S(0.811)PGVGR 191.61 1.60E-11 0 166090 150120 172600 184110 185240 164150 191860 175470 205280 TRUE FALSE 158239.2549 165417.3987 180513.8807 165602.913 217545.7974 158465.4443 162588.2332 160104.9166 237113.774 0.667355811 0.697628805 0.761296477 0.69841119 0.917474315 0.668309739 0.685697126 0.675224024 1 17.85521995 -2.075917862 2.401287488 1.429683378 0.717657774 0.577469697 0.074825874 8164219.058 2567875.116 19204138.16 0.017392268 0.008396188 2.075917862 -0.712025604 VTNDIS(ph)PESSPGVGR ddPTM_SK-BR-3_Trastuzumab_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 VTNDIS(0.731)PES(0.212)S(0.057)PGVGR;VTNDIS(0.958)PES(0.042)SPGVGR;VTNDIS(0.775)PES(0.213)S(0.012)PGVGR 250.26 9.71E-19 1099810000 1429180 1328720 1335970 1582050 1348210 1333160 1596270 1466650 1449710 TRUE FALSE 1361625.494 1464118.079 1397225.546 1423019.328 1583337.397 1286992.335 1352729.694 1338222.351 1674523.623 0.813142004 0.874349014 0.834401813 0.849805466 0.945544975 0.768572218 0.807829568 0.799166003 1 20.6753193 -2.42642234 2.306483324 2.57008225 0.83694302 0.531945486 0.048167816 6128932.098 853517.8315 49875068.2 0.012062398 0.003746085 2.42642234 -1.733139229 VTNGAFTGEIS(ph)PGMIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTNGAFTGEISPGMIK 16 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 VTNGAFTGEIS(1)PGMIK 200.4 3.74E-11 72504000 104930 89339 98446 116690 71159 100780 104340 112640 78817 TRUE FALSE 99970.16685 98442.74567 102959.8465 104960.0995 83569.10707 97289.96333 88421.01666 102776.6445 91039.53782 1.09809616 1.081318601 1.130935514 1.15290677 0.917943007 1.068656165 0.971237539 1.128923179 1 16.47420561 2.761912923 24.93025028 1.016186525 1.108936375 0.410203935 0.05839943 737.108455 786914.2873 0.01611791 0.017083836 577.9801488 -2.761912923 0.09274985 VTNLSEDTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTNLSEDTR 9 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 93.178 0.014996 0 418020 407180 369680 446710 411450 398310 430430 416800 451700 FALSE TRUE 398261.023 448672.1049 386630.1937 401805.8621 483206.7497 384516.4248 364759.9981 380302.7824 521747.329 0.763321633 0.859941355 0.74102956 0.770115801 0.926131717 0.736978233 0.699112344 0.728902212 1 18.99299178 VTPDTDWAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VTPDTDWAR 9 0 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ;;;;; 206.75 2.98E-05 3482720000 4008300 3550050 3118070 3507720 3892680 3304830 4321060 3632120 3776510 FALSE TRUE 3818835.603 3911804.131 3261036.594 3155117.321 4571562.16 3190382.908 3661802.935 3314072.318 4362151.883 0.875447647 0.896760185 0.747575206 0.723293779 1.048006186 0.731378227 0.839448748 0.759733362 1 22.05660857 VTPQEEADS(ph)DVGEEPDSENTPQKADKDAGLAQHSGPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTPQEEADSDVGEEPDSENTPQKADKDAGLAQHSGPQK 38 2 Q5JSP0-2;Q5JSP0-3;Q5JSP0 Q5JSP0-2 FGD3 "FYVE, RhoGEF and PH domain-containing protein 3" 1 VTPQEEADS(1)DVGEEPDSENTPQKADKDAGLAQHSGPQK;VTPQEEADS(1)DVGEEPDSENTPQKADKDAGLAQHSGPQK;VTPQEEADS(1)DVGEEPDSENTPQKADKDAGLAQHSGPQK 197.04 1.31E-30 322284000 246227 151882 245604 216377 149933 255729 370363 311063 187360 TRUE FALSE 234588.3377 167358.9485 256865.1863 194626.3729 176081.2677 246873.0406 313857.3222 283824.6747 216414.8319 1.083975325 0.773324762 1.186911193 0.899320861 0.813628466 1.140739932 1.450257912 1.311484394 1 17.72343985 2.01269137 6.662776362 1.30267137 0.948975835 0.413718728 0.163318251 0.110744584 22.51698455 0.058535429 0.041313564 102.9654141 -2.01269137 -0.353695535 VTPTEEHVEGPLPS(ph)PVTNGTSPAQLNGGSACSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;VTPTEEHVEGPLPS(0.995)PVT(0.005)NGTSPAQLNGGSACSSR 416.04 4.14E-187 461900000 188611 170830 192642 198858 186502 161871 204501 161837 137789 TRUE FALSE 179695.7318 188237.7712 201474.8262 178868.416 219027.8898 156265.3667 173300.6165 147665.6943 159156.6144 1.129049726 1.182720379 1.265890375 1.123851602 1.376178367 0.981833946 1.088868453 0.927801178 1 17.28008759 2.203901524 24.99971865 1.014899784 1.201321699 0.626167799 0.08211633 127.568069 92014.54628 0.028454378 0.021015876 159.9195371 -2.203901524 0.186421914 VTPTEEHVEGPLPSPVTNGT(ph)SPAQLNGGSACSSR ddPTM_SK-BR-3_Trastuzumab_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 VTPTEEHVEGPLPSPVTNGT(0.573)S(0.427)PAQLNGGSACSSR 115.92 1.87E-05 100600000 25127 29359 25440 29610 27649 25400 28947 29679 29546 TRUE FALSE 23939.29651 32350.71548 26606.44916 26633.54654 32470.97685 24520.39163 24530.6035 27080.14942 34127.84278 0.701459411 0.947927347 0.779611221 0.780405217 0.951451196 0.718486421 0.718785645 0.79349139 1 15.0586616 VTQDELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTQDELK 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 114.28 0.013819 287860000 423220 397920 356300 434490 293650 429710 452230 463220 334960 FALSE TRUE 403215.2293 438468.5004 372636.7074 390814.2397 344862.467 414829.035 383234.0077 422658.0011 386903.8861 1.042158644 1.133274997 0.963124747 1.010106783 0.891338856 1.072175933 0.990514755 1.092410845 1 18.56161569 3.73574549 24.99921625 1.001731238 1.087716821 0.264179403 0.058889955 277.7476123 2466493.713 0.014351548 0.02340721 5441.836509 -3.73574549 0.085985583 VTQDELKEVFEDAAEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VTQDELKEVFEDAAEIR 17 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 197.45 1.38E-11 242236600 385551 48874.2 525846 159251.6 719253 338721.3 1158256 448343 1214738 FALSE TRUE 367326.7683 53854.53655 549956.5592 143243.3266 844690.4955 326991.2964 981542.7744 409083.7101 1403113.365 0.261794077 0.038382171 0.391954473 0.102089632 0.602011581 0.233046954 0.699546308 0.291554282 1 20.42020015 -0.172913664 0.183977727 1.444469738 6.05E-18 0.599990726 0.184851387 7.114658661 0.434697378 2.545700959 0.696396088 0.671562343 0.172913664 -1.444469738 VTQHES(ph)DNENEIQIQNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 VT(0.016)QHES(0.984)DNENEIQIQNK;VT(0.028)QHES(0.972)DNENEIQIQNK;VT(0.034)QHES(0.966)DNENEIQIQNK 309.66 2.85E-58 1088620000 1181850 1155560 1283060 1309060 950040 1316600 1423480 1392240 992700 TRUE FALSE 1125986.293 1273312.878 1341889.57 1177470.802 1115726.675 1271005.812 1206301.982 1270328.085 1146642.846 0.98198519 1.110470346 1.170276843 1.026885404 0.973037663 1.108458328 1.052029397 1.107867275 1 20.12898466 -1.039779961 4.179137988 0.999993659 1.065315935 0.103510764 0.061319134 3.49E-06 8.02E-07 0.057189223 0.013478321 0.091247303 1.039779961 0.065322275 VTQSNLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTQSNLK 7 0 A0A087WV20;A0A087WTU9;Q8TCU4-3;Q8TCU4-2;Q8TCU4 A0A087WV20 ALMS1 Alstrom syndrome protein 1 0 91.626 0.037841 246890000 234240 177510 153600 190770 210210 204700 294850 248630 238590 FALSE TRUE 223167.9394 195598.4708 160642.7119 171593.4372 246870.5574 197611.1877 249865.2172 226858.6391 275589.3187 0.80978443 0.709746197 0.582906162 0.622641828 0.895791458 0.717049516 0.906657843 0.823176458 1 18.07216045 1.510416539 0.743881624 0.979157938 0.706007633 0.509698624 0.09125325 0.512875638 0.600450276 0.084447405 0.036683647 32.390417 -1.510416539 -0.273150305 VTRS(ph)PPTQVAISSDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.01)RS(0.988)PPT(0.002)QVAISSDSAR;VT(0.019)RS(0.981)PPTQVAISSDSAR;VTRS(1)PPTQVAISSDSAR;VT(0.013)RS(0.986)PPT(0.001)QVAISSDSAR;VT(0.005)RS(0.995)PPTQVAISSDSAR;VT(0.032)RS(0.967)PPTQVAISSDSAR;VT(0.019)RS(0.98)PPT(0.001)QVAISSDSAR;VT(0.12)RS(0.879)PPT(0.001)QVAISSDSAR 171.42 1.05E-09 3922100000 772887 576693 705643 750135 802498 690903 824948 742855 876423 TRUE FALSE 736354.1632 635458.6723 737997.4295 674730.0046 942453.3971 666976.8559 699087.0314 677806.6781 1012334.203 0.72738248 0.627716292 0.729005725 0.666509146 0.930970617 0.658850461 0.690569408 0.669548333 1 19.94925422 -1.353945371 3.229869791 1.002385763 0.707798775 0.537975349 0.083608114 26200002.81 36145552.72 594877.0561 0.018761635 0.044264405 1.353945371 -0.294586988 VTRSPPTQVAIS(ph)SDSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.009)RS(0.069)PPT(0.06)QVAIS(0.327)S(0.209)DS(0.327)AR 99.044 0.0044148 43882000 54643 37475 48918 48308 51435 44190 57564 53807 62982 TRUE FALSE 52060.13368 41293.74511 51160.93869 43451.98806 60405.24772 42659.68922 48781.55456 49095.37383 72748.92689 0.715613768 0.567619989 0.703253517 0.597286997 0.830324931 0.58639613 0.670546723 0.674860454 1 16.15063835 -4.999999861 0.459968706 9.179515081 0.658785761 0.652749374 0.07594488 836.5811814 4.646856855 6987.075571 0.034957852 1.00E-05 4.999999861 -8.52072932 VTRVEFEELCADLFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VTRVEFEELCADLFER 16 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 194.37 2.04E-10 292066000 256194 139843 256571 191419 308512 226171 359710 255617 414088 FALSE TRUE 244084.2173 154093.1607 268335.0341 172177.1984 362316.3951 218338.6416 304829.633 233233.8204 478302.6522 0.510313326 0.322166645 0.56101515 0.359975421 0.757504466 0.45648637 0.637315373 0.487628114 1 18.86756427 -5 0.163940936 2.907105678 0.373718997 0.619774052 0.122168064 76.53276394 0.711118419 47.30061143 0.425743382 1.00E-05 5 -2.533386681 VTS(ph)TQQQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VTSTQQQTR 9 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 VT(0.001)S(0.996)T(0.003)QQQTR;VTS(0.999)T(0.001)QQQTR;VTS(0.997)T(0.002)QQQTR;VT(0.001)S(0.997)T(0.003)QQQTR;VT(0.013)S(0.982)T(0.004)QQQTR;VT(0.023)S(0.967)T(0.01)QQQTR 209.84 8.14E-06 1822214000 2672500 2227680 2361620 2683600 2583050 2459560 2996560 2706950 2800560 TRUE FALSE 2546176.221 2454683.125 2469902.613 2413839.429 3033533.102 2374384.82 2539379.736 2469915.108 3234856.542 0.78710638 0.75882287 0.763527712 0.746196747 0.937764338 0.734000037 0.785005364 0.763531574 1 21.6252703 -1.089751229 4.202103864 1.000029446 0.783043019 0.586694763 0.056833157 10373221.04 29150713.96 4838.788664 0.012543305 0.081329625 1.089751229 -0.216986426 VTSAHKGPDETLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VTSAHKGPDETLR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 204.31 4.74E-08 3815680000 2210730 1492970 2057490 2080540 2046280 2084470 2871890 2603760 2464270 FALSE TRUE 2106233.174 1645105.34 2151827.952 1871400.166 2403150.584 2012284.281 2433730.435 2375760.971 2846416.406 0.73995961 0.577956668 0.755977919 0.657458326 0.844272321 0.706953585 0.855015601 0.834649831 1 21.4407153 1.350530619 0.409070178 1.011023816 0.652148299 0.676871672 0.066789258 0.540599238 0.266305022 0.077061541 0.051646005 22.41458071 -1.350530619 -0.358875516 VTSLANLIS(ph)PVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTSLANLISPVR 12 0 Q7Z628-2;Q7Z628 Q7Z628-2 NET1 Neuroepithelial cell-transforming gene 1 protein 1 VTSLANLIS(1)PVR 60.55 0.095613 11909000 94466 96148 88420 99269 82628 89872 99242 91990 82987 TRUE FALSE 90000.77939 105945.5905 92474.14446 89290.29152 97038.29704 86759.71011 84100.8102 83934.86793 95856.20012 0.938914533 1.10525548 0.964717403 0.931502515 1.012331982 0.905102748 0.877364324 0.875633165 1 16.54858413 2.671062704 1.070424601 0.902481449 1.014006612 0.213146346 0.061727786 0.551715808 1.312662808 0.032295995 0.027810767 468.8810745 -2.671062704 0.111525163 VTSSMSS(ph)PSMQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.009)S(0.854)PS(0.136)MQPK;VTSSMS(0.02)S(0.979)PSMQPK;VTSSMS(0.021)S(0.979)PSMQPK;VTSSMS(0.001)S(0.998)PS(0.002)MQPK;VTSSMS(0.138)S(0.847)PS(0.015)MQPK;VTSSMS(0.003)S(0.991)PS(0.006)MQPK;VTSSMS(0.01)S(0.951)PS(0.039)MQPK;VTSSMS(0.252)S(0.718)PS(0.03)MQPK;VTSS(0.001)MS(0.254)S(0.717)PS(0.028)MQPK 309.29 1.60E-50 1302239000 3209230 2723160 2862970 3271720 2205840 2987770 3360440 3423100 2619830 TRUE FALSE 3057536.058 3000653.1 2994240.006 2942840.49 2590537.798 2884302.776 2847743.159 3123355.217 3026099.856 1.010388356 0.991590907 0.989471646 0.972486246 0.856064876 0.953141969 0.941060538 1.032138847 1 21.52902816 3.120070639 4.180640746 0.94865527 0.997844055 0.124478342 0.045538315 0.345466315 10.85706829 0.012823791 0.015605335 1318.471174 -3.120070639 0.049188785 VTSSVPLPSGSTS(ph)SPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPS(0.081)GS(0.051)T(0.051)S(0.409)S(0.409)PGR 105.46 0.00083979 205400000 143840 187190 164490 176400 155250 179900 157890 192210 170260 TRUE FALSE 137040.9683 206264.8738 172032.0292 158667.9369 182325.5508 173670.0179 133800.9807 175379.0734 196663.0512 0.696831293 1.048823724 0.874755213 0.806800952 0.927096115 0.883084122 0.680356477 0.891774394 1 17.58536641 VTSSVPLPSGSTSS(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPS(0.001)GS(0.005)T(0.005)S(0.307)S(0.681)PGR;VTSSVPLPSGSTS(0.004)S(0.996)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR 209.9 4.05E-12 509660000 728060 931430 795270 880470 664720 811770 805520 877150 733050 TRUE FALSE 693646.0467 1026343.776 831733.9161 791963.4828 780646.9575 783658.2014 682623.1296 800342.0959 846727.6501 0.819207979 1.212129751 0.982292141 0.935322571 0.921957559 0.92551389 0.806189723 0.945217858 1 19.69153848 3.228178643 3.10007589 0.902932744 1.025579813 0.106294882 0.10530215 0.380788712 7.556997897 0.030698946 0.040167287 1691.136421 -3.228178643 0.122647069 VTTHPLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VTTHPLAK 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 106.04 0.0042717 3234260000 9972710 7797570 7769660 9405940 7767810 8864650 10887740 9486360 8341330 FALSE TRUE 9501319.762 8592151.248 8125906.596 8460437.041 9122513.605 8557664.948 9226615.296 8655684.028 9634860.855 0.986139801 0.891777409 0.843385983 0.878106822 0.946823596 0.888198084 0.957628287 0.898371462 1 23.1998324 -0.076973768 0.603848414 1.00576656 0.910199646 0.30125448 0.042071546 6.885951334 2.710669505 0.141317155 0.017314907 0.837579871 0.076973768 -0.095566914 VTTVTEIGKDVIGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTTVTEIGKDVIGLR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 204.52 4.44E-09 550470000 965320 760770 933790 1034200 931630 1012650 1299090 1155960 1067370 FALSE TRUE 919691.2367 838293.3279 976605.1951 930240.2511 1094105.977 977581.6766 1100889.961 1054738.014 1232892.288 0.745962357 0.679940442 0.792125317 0.754518671 0.887430303 0.792917342 0.892932798 0.855498914 1 20.23361533 1.974747143 0.25606085 1.026935083 0.652083928 0.774991234 0.0431205 0.839167533 0.194410868 0.088274249 0.119077359 94.3511381 -1.974747143 -0.374851156 VTVAGGVHISGLHTESAPR ddPTM_SK-BR-3_Trastuzumab_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 ; 263.47 1.66E-31 627322000 420259 310739 383964 483998 714930 358948 544357 471796 186520 FALSE TRUE 400394.1899 342403.6574 401569.1292 435345.6015 839613.5656 346517.5408 461305.3418 430483.0411 215444.569 1.858455712 1.589288878 1.863909269 2.020684966 3.897121053 1.608383736 2.141178791 1.998115075 1 17.71695721 0.397258931 1.703281433 0.999935216 2.09157214 0.224819903 0.654928145 8.991928065 23.50068007 0.615216239 0.17352588 2.496082473 -0.397258931 1.091636924 VTVAGLAGKDPVQCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTVAGLAGKDPVQCSR 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 218.28 1.23E-14 4301000000 1500920 1187140 1251750 1475730 1324180 1491350 1885010 1630330 1628850 FALSE TRUE 1429974.486 1308110.916 1309143.976 1327386.817 1555116.573 1439704.176 1597417.104 1487569.662 1881443.739 0.760041056 0.695269749 0.695818827 0.70551502 0.826554917 0.765212451 0.849037933 0.790653279 1 20.84340872 0.671693782 0.368090453 1.026486077 0.705057741 0.808738099 0.040019399 0.838450988 0.258115663 0.087179998 0.034728571 4.695629063 -0.671693782 -0.321428337 VTVLFAGQHISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTVLFAGQHISK 12 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 95.631 0.0059382 154010000 551960 420050 403600 450580 619490 457820 666450 598970 673750 FALSE TRUE 525869.9447 462853.5726 422105.4592 405286.8424 727528.8599 441965.5786 564770.8123 546521.0115 778231.709 0.67572413 0.594750339 0.542390466 0.520779143 0.934848647 0.567910011 0.725710358 0.702260015 1 19.56984024 -1.231020488 0.267976101 1.248121272 0.597990569 0.493401959 0.114215365 14.62573883 0.847224307 2.724405708 0.14961481 0.058746164 1.231020488 -0.650130704 VTVLGHVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTVLGHVQR 9 0 P17858;P17858-2;A0A2R8Y891;P08237;P08237-3 P17858;A0A2R8Y891 PFKL;PFKM "ATP-dependent 6-phosphofructokinase, liver type;ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 152.86 7.95E-05 1045590000 1581320 1187840 806650 1006660 1563020 965750 1596870 1288510 1556280 FALSE TRUE 1506574.137 1308882.246 843635.7004 905468.6243 1835610.193 932305.8353 1353238.153 1175681.234 1797619.954 0.8380938 0.728119558 0.46930704 0.503704146 1.021133632 0.518633448 0.752794355 0.654021019 1 20.77765661 -1.268148802 3.111499589 1.001615546 0.693668002 0.25772045 0.167135498 24792683.04 33689761.71 379269.8655 0.037810969 0.05393258 1.268148802 -0.307947544 VTYLVHNFEEGGGVAMGMYNQDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VTYLVHNFEEGGGVAMGMYNQDK 23 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 248.45 8.35E-38 415210000 675120 565470 569710 723750 558070 619970 722570 724890 559090 FALSE TRUE 643208.4156 623092.0359 595831.767 650997.275 655397.2313 598500.2834 612328.6756 661414.7887 645790.8218 0.996001172 0.964851179 0.922638952 1.008062136 1.01487542 0.92677112 0.948184234 1.024193541 1 19.30070741 1.232031776 24.99981382 1.012096785 0.968397439 0.244183855 0.031685718 247.538811 947815.4739 0.027931637 0.007621915 17.06207223 -1.232031776 -0.043699346 VTYS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTYSPR 6 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 VT(0.012)YS(0.988)PR 77.741 0.075128 126730000 194020 176510 166570 210820 186490 180080 216770 204000 242520 TRUE FALSE 184849.0591 194496.5697 174207.3993 189627.9731 219013.797 173843.7844 183697.7552 186136.6785 280128.763 0.659871757 0.694311315 0.621883299 0.676931462 0.781832592 0.620585272 0.655761848 0.664468284 1 18.0957306 -0.795660585 5.510884152 1.000000076 0.671681801 0.840085058 0.044979691 3.94E-08 8.53E-09 0.040982805 0.009659738 0.160080862 0.795660585 -0.328318275 VTYVVLDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VTYVVLDEADR 11 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 93.096 0.022113 20460000 52730 48611 41613 51190 54786 46278 61596 56487 60427 FALSE TRUE 50237.5574 53564.51617 43520.99721 46044.28395 64340.66105 44675.38126 52198.39891 51540.69882 69797.71054 0.719759388 0.767425117 0.623530441 0.659681866 0.921816211 0.640069437 0.747852594 0.738429648 1 16.09089209 -4.999975792 0.406290495 5.575003872 0.723464851 0.515401879 0.083371728 629.4081479 4.29903891 2559.514471 0.046479463 1.00E-05 4.999975792 -4.851539021 VVAEPVELAQEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVAEPVELAQEFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;; 94.692 0.011722 75598000 69213 66837 74950 75872 87005 65660 88178 73071 83169 FALSE TRUE 65941.43866 73647.76629 78386.53164 68245.20241 102178.6445 63386.17774 74724.8266 66672.51587 96066.42375 0.686415046 0.766633787 0.815961796 0.710395992 1.063624943 0.659816149 0.777845408 0.694025168 1 16.55174466 -2.46589847 2.20824417 3.457842805 0.770033523 0.283551498 0.113945282 6154904.051 571748.894 75553330.92 0.025195881 0.003420594 2.46589847 -2.687809282 VVDLMAHMASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VVDLMAHMASK 11 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 122.7 0.00038533 14236760000 18911000 19720300 14120700 19626700 14931700 16636200 18933900 17988600 13084330 FALSE TRUE 18017114.51 21729820.99 14768148.06 17653786.83 17535783.75 16060084.22 16045185.81 16413422.82 15113381.07 1.192129969 1.437786878 0.977157129 1.168089837 1.160281983 1.062640064 1.061654287 1.086019253 1 23.84932311 3.735830331 24.99999783 1.081692126 1.314958424 0.591599864 0.08313243 141.4904049 1295566.856 0.020612152 0.033555978 5442.89969 -3.735830331 0.233266298 VVDLMAHMASKE ddPTM_SK-BR-3_Trastuzumab_2h_R1 22 VVDLMAHMASKE 12 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;; 181.98 2.80E-05 49153255000 52579800 34701951 42773320 44530650 47417720 46901340 66182800 53204190 51819160 FALSE TRUE 50094457.06 38238119.26 44734519.03 40054344.46 55687355.35 45277134.84 56085398.33 48545349.07 59855010.68 0.83693005 0.638845751 0.747381356 0.669189497 0.93037082 0.756446859 0.937020939 0.811049042 1 25.83496869 1.74284173 0.566603376 0.976318975 0.721297456 0.442543713 0.087357529 0.645546952 0.456417506 0.07745675 0.046207858 55.31484883 -1.74284173 -0.25502152 VVDPFSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVDPFSKK 8 1 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 90.629 0.020942 827650000 2995400 2678600 2628200 3061300 2117630 3050000 3354600 3186300 2432900 FALSE TRUE 2853813.378 2951552.385 2748705.57 2753572.308 2486944.002 2944377.735 2842794.159 2907290.68 2810181.706 1.015526281 1.050306597 0.978123786 0.979855609 0.884976226 1.047753506 1.011605104 1.034556119 1 21.42223199 -0.73615827 7.464700397 0.99999961 1.003713351 0 0.047826178 0 0 0.046066219 0.010857912 0.183586918 0.73615827 0.003713741 VVDRDSEEAEIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;;; 232.5 5.86E-13 4143820000 2612860 2252410 2226400 2722070 2756730 2285480 2860200 2456060 2759450 FALSE TRUE 2489355.286 2481933.14 2328482.642 2448442.352 3237502.839 2206333.255 2423823.959 2240994.366 3187371.413 0.781005714 0.778677104 0.730533829 0.768169766 1.015728141 0.692210906 0.760446037 0.703085419 1 21.60393571 -2.312563631 2.348613671 2.198669686 0.778929909 0.376238647 0.08953582 4941059.672 633488.5331 31697396.07 0.020328895 0.004868962 2.312563631 -1.419739778 VVDRDSEEAEIIRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVDRDSEEAEIIRK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 206.43 6.10E-09 2642850000 1352780 1056590 1366320 1376230 1451610 1333210 1873780 1669150 1852780 FALSE TRUE 1288836.77 1164257.722 1428967.123 1237888.746 1704770.324 1287040.603 1587900.447 1522990.377 2140099.66 0.602232127 0.54402033 0.667710551 0.578425748 0.79658455 0.601392836 0.741975001 0.711644605 1 21.02924655 -4.999999995 0.123782797 2.216767323 0.476901189 0.768235555 0.06425177 60.06899609 0.477219953 18.04275106 0.489647967 1.00E-05 4.999999995 -1.739866134 VVDYSQFQES(ph)DDADEDYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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;VVDYS(0.028)QFQES(0.972)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.003)QFQES(0.997)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR 392.6 4.46E-127 16080596000 3009179.2 3215944.2 2774303.3 3364144 2759923 2844890.6 2956843 2902633 2560206 TRUE FALSE 2866941.263 3543652.57 2901507.85 3025973.854 3241252.697 2746371.325 2505722.294 2648463.067 2957229.671 0.969468584 1.198301439 0.981157426 1.023246143 1.096043615 0.928697339 0.847320828 0.895589238 1 21.49581486 2.142948521 5.185933683 0.895618185 1.060777239 0.442641406 0.074352935 0.159635693 6.918010073 0.027248706 0.019955941 138.9787884 -2.142948521 0.165159054 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK 341.99 7.76E-96 16504016000 7038064 4933170 6112531 6393868 5414632 6468557 8158109 7143559 6681796 TRUE FALSE 6705388.663 5435865.632 6392796.592 5751144.241 6358942.106 6244549.249 6913439.638 6518031.104 7717974.798 0.868801575 0.704312436 0.82829975 0.74516235 0.823913303 0.809091687 0.895758255 0.844526093 1 22.8797909 0.989847528 0.591612424 0.999211241 0.781842893 0.617476966 0.049708574 0.532309255 0.446762152 0.048080379 0.020906425 9.768941939 -0.989847528 -0.217368348 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VVDYSQFQESDDADEDYGRDSGPPTKK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK 212.24 3.58E-26 17537190000 1982120 1109950 2130692 1705049 1572290 2062173 2926380 2374547 2262045 TRUE FALSE 1888429.116 1223055.167 2228386.336 1533654.235 1846496.878 1990759.432 2479906.984 2166619.076 2612831.386 0.722752002 0.468095712 0.852862664 0.586970228 0.706703421 0.761916533 0.9491263 0.829222692 1 21.3171826 2.01377535 1.438083 0.93691298 0.640544845 0.546231773 0.106746914 0.28503215 1.099688792 0.067702885 0.032519176 103.2227321 -2.01377535 -0.296368135 VVEEAPSIFLDAETRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVEEAPSIFLDAETRR 16 1 A0A1B0GWA1;A0A1B0GUX9;A0A1B0GWI4;A0A1B0GU58;P05165-3;P05165-2;P05165 A0A1B0GWA1 PCCA "Propionyl-CoA carboxylase alpha chain, mitochondrial" 0 118.16 0.00047075 16938000 16101 10393 16417 14905 23461 14864 16499 14112 19265 FALSE TRUE 15339.93764 11452.05852 17169.73569 13406.72108 27552.59097 14349.25595 13981.77453 12876.27847 22252.51781 0.689357392 0.514641022 0.771586201 0.602481085 1.238178583 0.64483741 0.62832326 0.578643665 1 14.44168096 VVEHPEFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVEHPEFLK 9 0 P06396-2;Q5T0I0 P06396-2 GSN Gelsolin 0 ;;; 94.309 0.008809 1399320000 4015500 3248750 3000530 3818170 3064820 3326350 4072780 4038770 2794240 FALSE TRUE 3825695.273 3579801.319 3138107.268 3434360.298 3599323.638 3211157.665 3451402.609 3685113.888 3227556.468 1.185322491 1.109136696 0.972285783 1.064074426 1.115185334 0.994919128 1.069354678 1.141765891 1 21.62201091 4.127928381 3.036452872 1.053962768 1.169597092 0.387338752 0.053527523 0.227592531 4.08180263 0.012883068 0.033519572 13425.43546 -4.127928381 0.115634324 VVELRPPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;VVELRPPS(1)R;VVELRPPS(1)R;VVELRPPS(1)R 113.77 0.001058 1242820000 1489680 1283610 1308910 1518580 1432470 1298070 1578280 1374500 1562430 TRUE FALSE 1419265.779 1414411.318 1368924.818 1365929.453 1682292.314 1253117.51 1337484.399 1254141.493 1804723.665 0.786417226 0.783727363 0.758523227 0.756863491 0.932160611 0.69435423 0.741102045 0.69492162 1 20.78334652 -1.28723851 3.632437341 1.000573975 0.769723883 0.548208874 0.066035742 1229413067 2313445044 8351055.251 0.015081971 0.051613284 1.28723851 -0.230850093 VVENLQDDFDFNYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVENLQDDFDFNYK 14 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 252.99 7.52E-24 94913000 197095 184533 181624 212133 145923 182520 217230 216560 180893 FALSE TRUE 187778.71 203337.1225 189951.6401 190808.9878 171371.925 176199.2866 184087.5738 197596.8583 208944.9626 0.898699388 0.973161162 0.909098921 0.913202144 0.820177347 0.843280855 0.881033797 0.945688548 1 17.67276345 0.997201838 4.099149603 0.99970529 0.895994188 0.433362909 0.041120508 0.20585852 9.796648944 0.044550939 0.011389063 9.935777048 -0.997201838 -0.103711102 VVESLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVESLR 6 0 Q12905;B4DY09;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;;; 129.96 0.037149 579980000 633260 535655 548852 654716 668412 578554 683951 637403 692268 FALSE TRUE 603327.0548 590238.8535 574017.4071 588902.7038 784982.8412 558518.5299 579601.7133 581588.6142 799621.3858 0.754515907 0.738147908 0.7178615 0.736476931 0.981693155 0.69847873 0.724845187 0.72732999 1 19.60895753 -1.901855723 2.620793625 1.134261249 0.757149614 0.468161218 0.080369825 24903231.9 14734652.79 20627843.11 0.01948329 0.012535576 1.901855723 -0.377111635 VVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR 46 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 93.059 1.25E-05 93510000 69494 33890 51256 53836 46109 55608 79284 61985 50566 FALSE TRUE 66209.15634 37343.42953 53606.1383 48424.303 54150.395 53682.28102 67187.76965 56557.2648 58407.51702 1.133572521 0.63935999 0.917795192 0.829076555 0.927113457 0.919098838 1.150327442 0.968321676 1 15.83386643 1.923323325 6.476256808 1.052854074 0.879644907 0.220514372 0.128221735 0.31513956 21.803593 0.053496586 0.032938061 83.81530407 -1.923323325 -0.173209168 VVEVGSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVEVGSK 7 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 112.17 0.014922 551490000 1315280 1089890 1151260 1468870 1176400 1235980 1651770 1373950 1465840 FALSE TRUE 1253109.321 1200951.03 1204046.41 1321216.397 1381563.788 1193177.703 1399762.15 1253639.654 1693154.981 0.740103142 0.709297757 0.71112593 0.780328093 0.81597007 0.704706726 0.826718266 0.740416364 1 20.6912826 -5 0.201313744 2.140474023 0.712666446 0.780963911 0.041403892 58.81310247 0.58242761 26.94158666 0.088723351 1.00E-05 5 -1.427807577 VVEVLAGHGHLYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 191.49 2.79E-07 12661335000 2125435 1970455 2038833 2351950 2517419 1970993 2534015 2156616 349010 FALSE TRUE 2024969.9 2171246.605 2132315.51 2115527.518 2956456.077 1902737.018 2147404.471 1967771.27 403132.6883 5.023085348 5.38593537 5.289363953 5.247720115 7.333704664 4.719877781 5.326793221 4.88119998 1 18.62089524 0.322556758 1.126048297 0.990156094 5.482983395 0.803210823 0.691524357 1.38643901 1.931539984 0.641898826 0.191699674 2.101632415 -0.322556758 4.492827301 VVFQEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VVFQEFR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 140.12 0.0061558 1858591000 5128090 3512320 1833037 2179160 5248430 2578264 5335250 3932560 5193920 FALSE TRUE 4885695.349 3870229.401 1917083.56 1960106.697 6163754.53 2488978.071 4521259.624 3588204.199 5999366.587 0.81436853 0.645106337 0.319547661 0.326718941 1.027400883 0.414873476 0.75362283 0.598097174 1 22.51637876 -0.423301897 0.615600207 1.041082266 0.61221493 0.233297032 0.221153997 15.21647034 4.775225928 1.631475092 0.083513877 0.377309816 0.423301897 -0.428867336 VVGS(ph)SPGHPAVQVESHSGGQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVGSSPGHPAVQVESHSGGQK 21 0 Q6AI39 Q6AI39 GLTSCR1L GLTSCR1-like protein 1 VVGS(0.5)S(0.5)PGHPAVQVESHSGGQK;VVGS(0.5)S(0.5)PGHPAVQVESHSGGQK 124.31 4.18E-05 154793000 231374 207480 222723 269640 196549 239326 259352 247961 151528 TRUE FALSE 220437.4096 228622.4479 232935.0699 242535.2749 230827.0834 231038.0806 219783.0891 226248.2203 175026.1883 1.259453866 1.306218515 1.330858382 1.385708489 1.318814547 1.320020066 1.255715451 1.292653531 1 17.41721128 -0.000113132 0.759282143 0.990719422 1.314715038 0.886819928 0.034898042 1.732578022 1.027015514 0.083008997 0.012842533 0.999739537 0.000113132 0.323995615 VVGSVGQHTGEPVEELALSHCGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVGSVGQHTGEPVEELALSHCGR 23 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ; 284.99 1.71E-52 679770000 281347 232813 250702 268330 295249 235323 292270 273218 206269 FALSE TRUE 268048.2849 256536.9094 262196.9347 241356.9586 346740.3321 227173.7055 247678.8436 249293.5835 238256.143 1.125042492 1.076727366 1.100483418 1.01301463 1.455325885 0.953485197 1.039548615 1.046325943 1 17.86215389 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR 33 0 Q9P0R6 Q9P0R6 GSKIP GSK3-beta interaction protein 0 125.47 6.02E-08 66149000 42574 32944 45783 41414 46211 46133 66597 46304 40427 FALSE TRUE 40561.61139 36301.03105 47882.19584 37250.98604 54270.18377 44535.40264 56436.40451 42249.37629 46696.21269 0.868627434 0.777387051 1.025397844 0.797730349 1.162196689 0.953726225 1.208586334 0.904770941 1 15.51101792 2.74470393 24.99850423 1.063327542 0.861235658 0.385892581 0.110607233 427.9242292 1741319.116 0.031000314 0.03214947 555.5254114 -2.74470393 -0.202091884 VVHIMDFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVHIMDFQR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;P43243-2;B3KM87;H0Y8T4;D6RBI2;D6RE02;D6RIA2;D6RAY2;D6RAM9;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 138.26 0.00014162 1070700000 1548990 890760 592450 491000 1872310 827230 1890170 1179450 1657940 FALSE TRUE 1475772.313 981529.4567 619614.4185 441643.7472 2198840.271 798582.8177 1601789.851 1076171.105 1915044.868 0.770620228 0.512536011 0.323550862 0.230617963 1.148192561 0.417004756 0.836424189 0.561956079 1 20.86894676 2.757192718 24.95527376 0.755961188 0.495243064 0.300179954 0.246765871 1236.523093 1656159.945 0.071832556 0.076066377 571.7322858 -2.757192718 -0.260718123 VVHVNGYGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VVHVNGYGK 9 0 E9PEX6;P09622-2;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;; 148.99 8.87E-05 2640350000 4991520 3983280 4327120 4392750 4404950 3540200 5041220 4660060 4503890 FALSE TRUE 4755580.742 4389180.761 4525522.732 3951182.424 5173171.885 3417601.986 4272089.301 4252000.442 5202330.259 0.914125114 0.843695141 0.869903006 0.759502421 0.994395132 0.65693676 0.821187639 0.817326127 1 22.31072656 4.826555483 0.790987307 0.826161512 0.97663803 0.021258913 0.10173715 7.953695806 3.467141922 0.03263093 1.091001598 67074.19708 -4.826555483 0.150476517 VVIGMDVAASEFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVIGMDVAASEFFR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 205.56 2.81E-08 333460000 250085 274552 223615 256203 271155 210266 274368 249349 264450 FALSE TRUE 238263.9777 302529.1609 233867.9689 230448.9877 318444.3461 202984.4357 232508.1225 227514.6797 305459.5554 0.780018086 0.990406604 0.765626627 0.754433717 1.042509034 0.66452148 0.761174821 0.744827509 1 18.22062185 2.204961824 24.99988563 0.767626506 0.865923129 0.06377464 0.125493397 375.290806 279240.8856 0.042810527 0.031619399 160.3104466 -2.204961824 0.098296624 VVKPESNDKETEAAYES(ph)DIPEELCGHHLPQQSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVKPESNDKETEAAYESDIPEELCGHHLPQQSLK 34 2 Q8IYB7;Q8IYB7-3;Q8IYB7-2;Q8IYB7-4;Q8IYB7-5 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 VVKPESNDKETEAAYES(1)DIPEELCGHHLPQQSLK 138.84 1.38E-09 113600000 157280 141770 144540 162570 98803 171120 176460 185030 35074 TRUE FALSE 149845.6861 156216.5242 151167.302 146228.1547 116034.2119 165194.0715 149537.7861 168827.7923 40513.09679 3.698697409 3.8559512 3.73131935 3.609404522 2.864116079 4.077547376 3.691097397 4.167239873 1 15.30610075 2.994670065 22.37218403 3.41087945 3.760242642 0.053639719 0.895676263 237.0515913 995044.0744 0.23280569 0.269844825 987.8023736 -2.994670065 0.349363192 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(1)PEPEATLTFPFLDK 123.32 1.51E-05 303890000 307700 254410 247170 299620 135930 288330 311420 355120 146660 TRUE FALSE 293155.6308 280334.6682 258502.989 269501.6284 159636.149 278345.0598 263907.1594 324023.8102 169403.2838 1.730519175 1.654836093 1.52596209 1.590887865 0.942343887 1.643091289 1.557863304 1.9127363 1 17.37010232 3.708493668 1.814647214 1.467796199 1.711336637 0.112788019 0.287902538 0.809398355 5.202188241 0.079750441 0.166673473 5110.856276 -3.708493668 0.243540438 VVLASAS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVLASASPR 9 0 O95671;O95671-2 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 VVLASAS(1)PR;VVLAS(0.005)AS(0.995)PR 122.74 0.0006056 131914000 284190 268840 240670 292370 322510 299980 342950 308950 352000 TRUE FALSE 270756.9019 296235.1016 251704.9576 262980.4121 378755.6419 289591.6174 290626.6788 281896.7002 406586.3622 0.665927161 0.728590846 0.619068864 0.646800868 0.931550286 0.712251183 0.714796918 0.693325518 1 18.6332023 -5 0.253648467 2.763896045 0.688853757 0.536993074 0.083798544 147.7192947 1.459467396 135.4585918 0.112653849 1.00E-05 5 -2.075042288 VVLDDKDYFLFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;;;; 184.31 1.32E-05 11199875000 9789220 7435000 7477970 7480880 6448010 6448010 8791200 8577720 7025390 FALSE TRUE 9326502.971 8192634.953 7820842.321 6728887.73 7572540.902 6224713.797 7449940.979 7826609.363 8114851.6 1.149312819 1.009585308 0.963768989 0.829206504 0.933170596 0.767076726 0.918062504 0.964479666 1 22.95213328 4.061044189 1.283122628 0.892173276 1.14851082 0.564866536 0.067951892 0.338552074 0.954028429 0.019048381 0.082740596 11509.17489 -4.061044189 0.256337544 VVLEHEEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLEHEEVR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 196.79 2.91E-05 142900000 154140 155610 142800 176840 182860 147430 168670 165960 154720 FALSE TRUE 146854.1077 171466.8359 149347.5212 159063.7072 214750.7261 142324.4621 142936.2937 151427.6626 178713.1874 0.821730673 0.95945262 0.835682713 0.890050195 1.201650137 0.796384778 0.799808317 0.847322264 1 17.44728657 -2.032556472 8.55311341 1.20571783 0.891654036 0.071966236 0.11934825 0.076538938 0.000291337 0.018891682 0.026437912 0.009277768 2.032556472 -0.314063794 VVLFEMEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLFEMEAR 9 0 O75131;A0A087WYQ3;H0YB26;E5RHZ0 O75131 CPNE3 Copine-3 0 77.318 0.076637 26958000 223020 187020 184240 168750 216960 205930 286550 255750 254860 FALSE TRUE 212478.2866 206077.5506 192687.5862 151786.9294 254797.7553 198798.5925 242831.5346 233355.1742 294382.3872 0.721776492 0.70003356 0.654548623 0.51561145 0.865533287 0.675307359 0.824884726 0.792694075 1 18.16733183 0.978876028 0.630070839 0.999439935 0.676343809 0.574715132 0.085912955 0.590797448 0.551071859 0.081505269 0.034041465 9.525242223 -0.978876028 -0.323096127 VVLGDGVQLPPGDYS(ph)TTPGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.043)S(0.306)T(0.306)T(0.306)PGGT(0.094)LFS(0.341)T(0.3)T(0.265)PGGT(0.04)R 52.971 0.010552 0 22566 22707 20799 25961 22681 21097 25958 26868 23022 TRUE FALSE 21499.3499 25020.86912 21752.65472 23351.35096 26636.55922 20366.4056 21997.63035 24515.29548 26592.13418 0.808485312 0.940912412 0.818010867 0.878130006 1.001670608 0.765880823 0.827223201 0.921900263 1 14.69871195 0.977091695 5.525743288 0.999931915 0.864311257 0.303381136 0.067715285 0.201782676 25.77968831 0.062046216 0.015637386 9.486187302 -0.977091695 -0.135620658 VVLGDGVQLPPGDYST(ph)TPGGTLFST(ph)TPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.107)T(0.481)T(0.411)PGGT(0.003)LFS(0.164)T(0.512)T(0.321)PGGT(0.001)RIIYDRK 190.7 1.80E-23 250260000 152570 69023 174580 120320 156310 157340 236660 172960 232380 TRUE FALSE 145358.3185 76056.52217 182584.6657 108225.205 183570.4145 151891.2763 200553.1704 157814.7055 268416.3036 0.541540572 0.283352841 0.680229417 0.403199074 0.68390188 0.565879473 0.74717209 0.58794754 1 18.03411278 0.358232229 0.196983085 1.221244843 0.326896668 0.60264168 0.1221405 4.209713969 0.395763279 1.08580048 0.428075938 2.281561761 -0.358232229 -0.894348175 VVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.001)S(0.037)T(0.169)T(0.792)PGGT(0.02)LFS(0.404)T(0.302)T(0.227)PGGT(0.049)R 98.967 0.00048939 37248000 107540 94533 98939 118760 108610 106740 112350 110230 107910 TRUE FALSE 102456.7973 104166.0202 103475.451 106822.0192 127551.5496 103043.567 95208.94405 100577.6768 124644.1317 0.821994553 0.835707376 0.830167049 0.857016032 1.023325751 0.826702113 0.763846182 0.806918669 1 16.92745544 3.205639291 5.998229186 0.864143286 0.829537128 0.058622943 0.080729166 0.745217076 74.77908018 0.024001729 0.029511971 1605.607142 -3.205639291 -0.034606158 VVLGDGVQLPPGDYSTT(ph)PGGTLFST(ph)TPGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.002)S(0.018)T(0.098)T(0.879)PGGT(0.015)LFS(0.171)T(0.435)T(0.366)PGGT(0.015)RIIY(0.001)DRK;VVLGDGVQLPPGDY(0.001)S(0.03)T(0.153)T(0.816)PGGT(0.008)LFS(0.136)T(0.55)T(0.271)PGGT(0.035)RIIYDRK 162.68 1.41E-17 582670000 281870 129449 313210 214425 249470 251450 407210 300890 381970 TRUE FALSE 268546.5637 142640.0003 327570.9883 192870.5916 292977.489 242742.2235 345082.6356 274542.4765 441203.9568 0.608667623 0.323297192 0.742447984 0.437146106 0.664040937 0.550181429 0.782138579 0.622257512 1 18.7510862 0.528693374 0.293448426 1.092527522 0.459454182 0.544242195 0.125614337 2.196339448 0.420233378 0.43988974 0.161803713 3.378262355 -0.528693374 -0.63307334 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.048)T(0.048)T(0.902)PGGT(0.002)LFS(0.047)T(0.032)T(0.888)PGGT(0.032)R;VVLGDGVQLPPGDY(0.003)S(0.039)T(0.148)T(0.58)PGGT(0.227)LFS(0.199)T(0.163)T(0.631)PGGT(0.01)R;VVLGDGVQLPPGDYS(0.001)T(0.006)T(0.993)PGGT(0.001)LFS(0.002)T(0.016)T(0.894)PGGT(0.088)R;VVLGDGVQLPPGDYS(0.005)T(0.024)T(0.971)PGGT(0.013)LFS(0.144)T(0.11)T(0.716)PGGT(0.017)R;VVLGDGVQLPPGDYS(0.003)T(0.011)T(0.981)PGGT(0.011)LFS(0.335)T(0.153)T(0.505)PGGT(0.001)R;VVLGDGVQLPPGDYS(0.001)T(0.035)T(0.958)PGGT(0.006)LFS(0.044)T(0.033)T(0.879)PGGT(0.044)R;VVLGDGVQLPPGDY(0.004)S(0.056)T(0.056)T(0.81)PGGT(0.072)LFS(0.021)T(0.045)T(0.89)PGGT(0.044)R;VVLGDGVQLPPGDYS(0.008)T(0.038)T(0.945)PGGT(0.009)LFS(0.182)T(0.132)T(0.665)PGGT(0.02)R 155.61 5.95E-09 933303000 1971272 1775032 1708732 2085857 1856777 1806155 2031568 1991392 1873167 TRUE FALSE 1878093.879 1955909.779 1787079.052 1876182.691 2180598.321 1743607.399 1721614.989 1817015.159 2163648.172 0.868021846 0.903986981 0.825956399 0.867138528 1.00783406 0.805864568 0.795700064 0.839792339 1 21.04503449 -1.493966961 8.658984654 1.000005663 0.863607361 0.335668734 0.059994622 6.65E-06 3.89E-07 0.058883452 0.013878387 0.032065133 1.493966961 -0.136398302 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTRIIYDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.006)T(0.23)T(0.76)PGGT(0.018)LFS(0.206)T(0.175)T(0.588)PGGT(0.015)RIIYDRK 171.89 4.88E-18 320670000 175100 90634 209610 130970 174500 165090 245830 202450 252700 TRUE FALSE 166823.37 99869.70764 219220.8258 117804.6468 204932.7448 159372.8919 208324.1185 184722.4047 291887.4254 0.571533254 0.342151456 0.751045803 0.403596169 0.702095147 0.546008077 0.71371392 0.632854959 1 18.15505253 -2.150905087 0.157143057 1.639986673 0.389963293 0.566099348 0.121925676 27.76304849 0.600672014 6.92509964 0.56507592 0.007064719 2.150905087 -1.25002338 VVLIGGKPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VVLIGGKPDR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;; 130.98 0.00023912 10476730000 9480280 8185470 7869460 9126100 6983740 8586200 9478310 8813240 7351000 FALSE TRUE 9032165.953 9019578.699 8230282.525 8208727.09 8201702.045 8288857.741 8032219.728 8041505.984 8490955.536 1.063739636 1.062257205 0.96929992 0.966761286 0.965933929 0.976198463 0.945973594 0.947067259 1 23.01749549 3.730926686 5.414394084 0.964103221 1.063651782 0.872735285 0.015163394 0.043908554 4.619698324 0.003760716 0.006298509 5381.789242 -3.730926686 0.099548561 VVLLGEFLHPCEDDIVCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVLLGEFLHPCEDDIVCK 18 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 ; 210.9 2.21E-18 58470000 483060 358030 417370 463760 372610 411090 535670 441680 349310 FALSE TRUE 460226.7111 394513.664 436506.8273 417141.9637 437593.066 396853.8502 453943.7032 403004.1577 403479.2108 1.140645413 0.977779408 1.081857047 1.033862347 1.084549227 0.983579425 1.12507334 0.998822608 1 18.62213482 1.068338367 0.00666298 9.16E-07 2.078965387 0.133668993 0.054630734 8133.079279 39.09953698 6143.798868 6051.9483 11.70410924 -1.068338367 2.078964472 VVLQELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVLQELR 7 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;G3V2F7;Q13404-6;A0A0A0MSL3;G3V113;H0YBP9 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ; 89.55 0.041389 172142000 427790 349530 194592 254080 395840 256850 420620 345530 365170 FALSE TRUE 407569.2145 385147.5044 203514.2357 228539.3957 464874.3707 247955.2201 356446.6938 315273.5614 421798.6986 0.966264751 0.91310738 0.482491379 0.541821007 1.102123767 0.587852027 0.845063522 0.747450294 1 18.68619512 3.972172758 24.98760996 0.748370933 0.946330838 0.132750297 0.193599543 1107.811906 994766.7977 0.046140738 0.083256078 9379.35033 -3.972172758 0.197959905 VVLQELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVLQELRR 8 1 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;G3V2F7;Q13404-6;A0A0A0MSL3;G3V113;H0YBP9 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ; 163.15 0.00054128 1175150000 1046230 560060 687160 606900 1148350 738970 1134730 886640 1200420 FALSE TRUE 996776.7813 617130.7507 718666.9657 545893.259 1348621.876 713379.2836 961606.0978 809001.1012 1386575.003 0.71887693 0.445075636 0.518303708 0.393699048 0.972628148 0.514490224 0.69351178 0.583452824 1 20.40309423 -4.568461469 0.220068146 2.656727779 0.54720224 0.370148305 0.163297738 127.459575 1.516411479 93.34663309 0.288426384 2.70E-05 4.568461469 -2.109525539 VVNGAAASQPPS(ph)KR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VVNGAAAS(0.06)QPPS(0.94)KR 127.75 8.23E-05 12796000 43216 37628 43448 49926 40883 50244 65769 47763 49226 TRUE FALSE 41173.26533 41462.33598 45440.13378 44907.34363 48012.98226 48504.03768 55734.73112 43580.61851 56859.71667 0.724120128 0.729204055 0.799162156 0.789791899 0.844411212 0.853047474 0.980214718 0.766458594 1 15.79511929 3.165564444 0.229843894 1.01062649 0.590885999 0.615609412 0.058507837 2.954275301 0.277498588 0.113418704 0.369987338 1464.078772 -3.165564444 -0.419740492 VVNGGVPWPS(ph)PCPS(ph)PSSRPPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVNGGVPWPSPCPSPSSRPPSR 22 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 VVNGGVPWPS(0.997)PCPS(0.343)PS(0.343)S(0.309)RPPS(0.008)R 72.881 0.0084223 158770000 85301 70279 86194 74592 75596 76254 91804 75179 97719 TRUE FALSE 81268.99078 77440.51 90146.08016 67093.87044 88779.91847 73613.30486 77797.6137 68595.92821 112872.7634 0.720005325 0.686086773 0.798652194 0.594420376 0.786548639 0.652179522 0.689250545 0.607727906 1 16.78433788 -2.283451739 2.42835906 2.493033134 0.693997268 0.681726483 0.066153545 7584525.663 510760.8335 63037557.29 0.015093885 0.005206529 2.283451739 -1.799035866 VVNGKVEYFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVNGKVEYFLK 11 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 136.38 0.0013228 0 1482600 648630 1104200 896110 1397300 1137000 2091000 1406200 1751400 FALSE TRUE 1412520.436 714726.1344 1154828.662 806031.3203 1640988.678 1097625.405 1771979.546 1283065.673 2022998.167 0.698231199 0.353300436 0.570850078 0.398434034 0.811166666 0.542573603 0.875917524 0.634239662 1 20.94806358 1.459554029 0.527202216 0.97876553 0.500984888 0.46515417 0.148499202 0.63108458 0.43888859 0.13833087 0.078663614 28.81071454 -1.459554029 -0.477780642 VVNSCHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VVNSCHR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;; 129.68 0.0036367 407293000 316858 194917 174115 210766 434833 180246 416724 300036 490828 FALSE TRUE 301880.7503 214779.2639 182098.345 189579.4013 510667.7375 174004.0358 353145.1001 273763.2572 566943.0994 0.532470984 0.378837425 0.321193335 0.334388762 0.90073896 0.306916225 0.622893374 0.482876073 1 19.11284442 -5 0.207910882 3.492555165 0.404290403 0.468507062 0.175630793 121.8792805 1.212934355 126.2126692 0.348745039 1.00E-05 5 -3.088264762 VVNTDHGS(ph)PEQLQIPVTDSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VVNTDHGSPEQLQIPVTDSGR 21 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 1 VVNT(0.257)DHGS(0.743)PEQLQIPVTDSGR;VVNT(0.012)DHGS(0.988)PEQLQIPVTDSGR;VVNTDHGS(1)PEQLQIPVTDSGR;VVNT(0.004)DHGS(0.996)PEQLQIPVTDSGR;VVNT(0.025)DHGS(0.975)PEQLQIPVTDSGR 246.44 1.73E-30 989813000 574036 477520 520399 602850 546218 528638 608202 550403 572017 TRUE FALSE 546902.4559 526179.8309 544259.8089 542250.3727 641478.2463 510331.1335 515409.6145 502206.7955 660722.4749 0.827733998 0.796370414 0.823734366 0.820693095 0.970873961 0.772383494 0.780069748 0.760087351 1 19.33368489 2.982459188 24.88625716 0.837528004 0.814532666 0.02755669 0.080491146 4049.20016 5744856.846 0.023365842 0.025274358 960.4155619 -2.982459188 -0.022995338 VVPEDGS(ph)PEKR ddPTM_SK-BR-3_Trastuzumab_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 126.95 0.00018182 3112660000 4523330 3790100 4034820 4564730 3128680 4888710 5346840 4921860 4036190 TRUE FALSE 4309521.155 4176315.499 4219820.488 4105874.668 3674320.801 4719412.747 4531081.357 4490875.846 4662101.731 0.924373041 0.895801023 0.905132649 0.880691779 0.788125402 1.012292957 0.971896715 0.963272812 1 22.15254906 2.207004104 24.99999158 0.984162587 0.886561054 0.65966891 0.038316038 132.7858983 105196.1272 0.014247659 0.010523544 161.0660855 -2.207004104 -0.097601532 VVPGQFDDADS(ph)SDSENRDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.819)S(0.18)DSENRDLK 222.17 4.45E-25 184070000 273170 212980 255860 269340 190630 269080 338470 323110 240970 TRUE FALSE 260257.7955 234682.9041 267591.4341 242265.4315 223875.8116 259761.6921 286830.1851 294816.7755 278338.3969 0.935040937 0.843156772 0.96138886 0.870398889 0.804329601 0.933258562 1.030508864 1.059202678 1 18.08648042 1.836039251 3.507938569 1.033959136 0.884348635 0.677527837 0.046017308 0.131047994 2.75897075 0.022719473 0.012014459 68.55501826 -1.836039251 -0.149610501 VVPGQFDDADSS(ph)DSENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.034)S(0.966)DSENR;VVPGQFDDADS(0.057)S(0.943)DSENR 242.98 2.06E-20 192623000 221904 258800 187894 246690 194437 209775 204367 214551 188047 TRUE FALSE 211415.0377 285172.0142 196509.1258 221892.2525 228346.7512 202510.4392 173187.0607 195763.777 217208.3683 0.973328235 1.312896075 0.904703291 1.021564013 1.051279713 0.932332583 0.797331438 0.9012718 1 17.72872016 2.745558403 0.935774113 0.879448028 1.116496789 0.237364772 0.118229768 0.577316863 1.0758496 0.067061203 0.062461584 556.6194824 -2.745558403 0.237048761 VVPGQFDDADSS(ph)DSENRDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.142)S(0.857)DS(0.001)ENRDLK 252.66 2.66E-36 211720000 180000 140560 175040 174880 131020 175880 219620 199430 160760 TRUE FALSE 171491.7567 154883.2238 183065.7571 157300.7301 153869.8465 169789.2315 186112.9354 181966.852 185689.8398 0.923538719 0.834096384 0.985868464 0.847115439 0.828639018 0.914370069 1.002278507 0.979950503 1 17.50253535 1.850728522 4.015730513 0.992959985 0.882909403 0.539434917 0.046383896 0.171285639 4.407763485 0.021682205 0.011958325 70.91343488 -1.850728522 -0.110050582 VVPGYGHAVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VVPGYGHAVLR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;;;; 211.02 1.08E-08 3274980000 2635447 2020879 1913583 2083672 2650530 1774277 2288398 2093377 2404056 FALSE TRUE 2510874.643 2226808.868 2001322.673 1874217.332 3112781.593 1712833.343 1939260.856 1910069.812 2776864.726 0.904212085 0.801914781 0.72071306 0.674940091 1.120969835 0.616822752 0.698363459 0.687851228 1 21.40502547 VVPSFLPVDQGGS(ph)LVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVPSFLPVDQGGSLVGR 17 0 Q14126 Q14126 DSG2 Desmoglein-2 1 VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR 239.43 2.91E-20 360281000 256636 257200 232923 347481 301278 257702 301972 310552 355240 TRUE FALSE 244505.3249 283408.9724 243602.7499 312551.5497 353820.7878 248777.7151 255900.6253 283358.4205 410328.8049 0.59587658 0.69068749 0.593676942 0.76170999 0.86228601 0.606288694 0.623647724 0.690564292 1 18.64642091 -1.937855666 2.046773841 1.244059525 0.6728959 0.591535499 0.083967439 1783334.571 700341.3301 2075661.722 0.022163089 0.011538367 1.937855666 -0.571163625 VVQVSAGDSHTAALTDDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VVQVSAGDSHTAALTDDGR 19 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ;; 264.03 2.64E-31 507766000 502280 429350 466940 517430 541170 432280 553330 490350 543220 FALSE TRUE 478538.2198 473101.2531 488349.6609 465416.9533 635549.8767 417310.0352 468909.3459 447412.3545 627459.7832 0.762659588 0.753994544 0.778296353 0.741747863 1.012893406 0.665078538 0.747313786 0.713053436 1 19.25916347 -1.701319514 2.57672154 1.039127526 0.769757088 0.381457128 0.09125553 17550350.97 14214012.97 4457371.14 0.022330303 0.019892093 1.701319514 -0.269370437 VVS(ph)ETNDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 VVS(0.998)ET(0.002)NDTK 61.375 0.093947 0 207270 159070 196370 230880 168070 217160 233030 215320 209030 TRUE FALSE 197472.7579 175279.4138 205373.7587 207671.5038 197381.3548 209639.6947 197476.9936 196465.4393 241445.3048 0.817877813 0.72595909 0.850601584 0.860118211 0.817499247 0.868269917 0.817895356 0.813705777 1 17.88133688 -5 0.179035985 1.740199801 0.777515985 0.664457997 0.039609369 79.98673684 0.768661348 21.08991071 0.126169767 1.00E-05 5 -0.962683817 VVS(ph)QSQPGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 2 VVS(0.668)QS(0.332)QPGS(1)R 87.498 0.018764 80089000 224750 208160 211010 254220 220530 224560 245280 212370 236130 TRUE FALSE 214126.5129 229371.7407 220685.0172 228665.3226 258990.3622 216783.4309 207858.0311 193773.757 272747.8344 0.785071359 0.840966313 0.809117395 0.838376309 0.949559738 0.794812657 0.762088658 0.710450213 1 18.05720822 -0.252202922 7.540065841 0.999999998 0.812746213 0.479755411 0.061736496 0 0 0.059958174 0.014132277 0.559496118 0.252202922 -0.187253785 VVSAPVGKET(ph)PSKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VVSAPVGKETPSKR 14 2 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 1 VVSAPVGKET(0.956)PS(0.044)KR;VVSAPVGKET(0.999)PS(0.001)KR;VVSAPVGKET(0.973)PS(0.027)KR 110.12 0.03469 834000000 1203200 1170240 1115920 1238910 759310 1291640 1410310 1507670 950390 TRUE FALSE 1146327.121 1289488.786 1167086.036 1114372.413 891733.4236 1246910.183 1195141.307 1375650.422 1097771.627 1.04423096 1.174642115 1.063141009 1.015122258 0.812312326 1.135855721 1.088697574 1.253129875 1 20.06614653 -0.181662174 7.325473929 1.000021563 1.07471908 0.038499527 0.115094539 0 0 0.108184165 0.025499252 0.658169611 0.181662174 0.074697518 VVSETNDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 99.688 0.012023 60764000 107240 89918 102660 117040 71111 111220 115310 107970 86481 FALSE TRUE 102170.9777 99080.74643 107367.0625 105274.9168 83512.73589 107368.4235 97717.34169 98515.57442 99892.0318 1.022814091 0.991878378 1.074831101 1.053887031 0.836030005 1.074844726 0.978229594 0.986220549 1 16.60808198 VVSHLIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSHLIEK 8 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 99.139 0.0070255 334580000 681120 601010 554140 698240 614250 633160 737020 756280 630060 FALSE TRUE 648924.8074 662253.6023 579547.8671 628051.5886 721375.0055 611233.5104 624574.0627 690056.1139 727766.4869 0.891666241 0.909980899 0.796337668 0.862985037 0.991217676 0.839875869 0.858206683 0.948183416 1 19.47311609 1.035434845 4.307075297 0.999406906 0.880387814 0.402971355 0.0503978 0.17626384 7.521437223 0.046680055 0.011906606 10.85012758 -1.035434845 -0.119019092 VVSHPTLPVTITAHEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSHPTLPVTITAHEDR 17 0 Q13033-2;Q13033 Q13033-2 STRN3 Striatin-3 0 149.09 1.95E-07 153170000 63747 46451 47090 64610 89850 45402 69985 53346 68921 FALSE TRUE 60733.80564 51184.40971 49249.12308 58115.28005 105519.8116 43829.71736 59307.50289 48674.74144 79608.91668 0.762902049 0.6429482 0.618638277 0.730009683 1.325477295 0.550562917 0.744985679 0.611423236 1 16.28064241 5.109456319 16.78824104 0.757003443 1.170120053 0 0.230710916 747.0250716 959166.6897 0.050108407 86676.99447 128663.7839 -5.109456319 0.41311661 VVSISSEHLEPIT(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSISSEHLEPITPTK 16 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 VVSISSEHLEPIT(0.997)PT(0.003)K 96.487 0.012496 115240000 109320 106810 86901 130810 87983 98286 120340 127280 92308 TRUE FALSE 104152.6603 117694.0604 90885.49681 117660.7303 103327.2073 94882.33118 101979.9228 116134.6884 106622.6532 0.976834257 1.103837289 0.852403257 1.10352469 0.969092442 0.889889046 0.956456435 1.089212142 1 16.70215446 VVSQS(ph)QPGS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 2 VVS(0.009)QS(0.991)QPGS(1)R;VVS(0.014)QS(0.986)QPGS(1)R;VVS(0.051)QS(0.949)QPGS(1)R;VVS(0.198)QS(0.802)QPGS(1)R 103.76 0.0040518 492317000 932720 823820 861630 1039460 953420 873920 972270 941240 1014080 TRUE FALSE 888632.1741 907768.1946 901136.5878 934971.506 1119696.146 843655.9313 823932.3545 858820.0358 1171338.347 0.758646873 0.774983758 0.769322195 0.798207886 0.955911799 0.720249562 0.703411065 0.733195526 1 20.15972644 3.247354231 10.23525206 0.796721208 0.767915053 0.026510249 0.097407558 1.109723743 1118.57577 0.026830556 0.034953845 1767.478873 -3.247354231 -0.028806156 VVSQS(ph)QPGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VVS(0.072)QS(0.928)QPGSR 92.781 0.0096855 45683000 65039 59327 62140 70732 60658 59490 68389 65007 70135 TRUE FALSE 61964.73536 65372.48875 64989.18046 63621.88498 71236.73599 57429.84638 57955.002 59314.64246 81011.1776 0.764891182 0.806956406 0.802224858 0.785346996 0.879344531 0.708912623 0.715395131 0.732178499 1 16.30583336 2.213129543 24.99916668 0.758028822 0.802478052 0 0.088871422 692.7041194 680935.2937 0.029495634 0.021792186 163.3539135 -2.213129543 0.04444923 VVSSIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVSSIEQK 8 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 143.01 0.0026299 0 205319 182727 178123 204418 155318 184857 217736 213568 190446 FALSE TRUE 195613.9778 201347.089 186290.1157 183869.5143 182405.41 178455.3557 184516.3742 194866.8537 219979.393 0.889237738 0.915299776 0.846852576 0.835848812 0.829193169 0.811236695 0.83878936 0.885841401 1 17.74700886 0.88469902 5.125165768 0.999993747 0.856774244 0.700572735 0.030144236 0.719526494 31.20847844 0.035464649 0.00895737 7.668298679 -0.88469902 -0.143219503 NVS(ph)PEFVPCEGEGGFGLHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 NVSPEFVPCEGEGGFGLHK 19 0 O94986-3;O94986 O94986-3 CEP152 Centrosomal protein of 152 kDa 1 NVS(1)PEFVPCEGEGGFGLHK;NVS(1)PEFVPCEGEGGFGLHK 106.88 0.00019673 176204000 1412800 496530 472000 520930 321250 462200 512320 521350 314570 TRUE FALSE 1346019.744 547126.9715 493641.6669 468565.1267 377275.8983 446193.8981 434156.1746 475697.8301 363351.909 3.704452104 1.505777066 1.358577331 1.289562859 1.038320947 1.227993818 1.194864163 1.30919315 1 18.47100796 4.599635195 1.326626243 1.188775755 4.438520481 0.981474934 0.107254466 0.105002701 0.198070299 0.027504339 0.431572714 39777.29034 -4.599635195 3.249744726 up VVTDTDETELAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 96.171 0.013108 55411000 185380 204250 142360 201920 83029 206360 171380 193280 88592 FALSE TRUE 176617.4548 225063.3072 148887.3468 181622.618 97509.23131 199213.7015 145232.8334 176355.3786 102330.3949 1.725953027 2.199378859 1.454966992 1.774864821 0.952886299 1.946769595 1.419254109 1.723391948 1 16.6428752 1.619461208 0.069167783 4.57E-11 3.03122608 0.291124508 0.328380323 22.09506294 1.55621571 32.52538881 33.17958541 41.63525296 -1.619461208 3.03122608 VVTTPAFMCETALHYIHDGIGAMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVTTPAFMCETALHYIHDGIGAMVR 25 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A096LNH5;A0A096LPI6 P0DPI2-2 0 ; 223.97 5.11E-34 159527000 132751 106157 117618 116945 129167 105959 128819 100221 32577 FALSE TRUE 126476.1233 116974.519 123010.9016 105189.4664 151693.6839 102289.6133 109165.2956 91445.11794 37628.87478 3.361145505 3.108637175 3.269056074 2.79544544 4.031310657 2.718380867 2.901104438 2.430184758 1 15.19955253 0.769647842 0.918161953 0.998171345 3.250814806 0.805351319 0.345545319 0.339099822 0.544234288 0.294164919 0.098499577 5.883663716 -0.769647842 2.252643461 VVTTSAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 0 ;;;; 137.44 0.0067063 3768100000 2018760 1633050 1561320 1456390 2225620 1744810 2386690 1943660 2417670 FALSE TRUE 1923337.216 1799459.652 1632908.066 1309990.91 2613767.423 1684386.792 2022556.606 1773462.826 2792589.916 0.688728841 0.644369458 0.584728913 0.469095338 0.935965359 0.603162957 0.724258365 0.635060242 1 21.4131723 -5 0.272846581 3.369463894 0.638586622 0.449100902 0.118566577 191.5452335 1.852586947 255.9369721 0.129624132 1.00E-05 5 -2.730877272 VVTVFSVADGYSENNVFYGHHAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVTVFSVADGYSENNVFYGHHAK 23 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 273.46 6.60E-52 511180000 481430 501480 549620 478000 657410 491100 536800 490300 375965 FALSE TRUE 458673.758 552581.3821 574820.6206 429950.5319 772062.0959 474093.0839 454901.301 447366.7328 434267.732 1.056200413 1.272444028 1.323654921 0.990058667 1.777848177 1.09170691 1.047513475 1.030163422 1 18.72822523 2.02133061 24.99789126 1.04078086 1.265567456 0.252249591 0.207475237 348.0526123 407890.0012 0.073085817 0.053973014 105.0341705 -2.02133061 0.224786596 VVTVHLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVTVHLEK 8 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 92.439 0.011777 187920000 581650 679170 456250 685320 417030 513350 571670 532900 388940 FALSE TRUE 554156.5572 748378.1952 477169.5138 616430.3316 489759.9 495572.5608 484451.2421 486236.4509 449254.8288 1.233501616 1.665821149 1.062135526 1.37211732 1.090160569 1.103099019 1.078343984 1.082317695 1 18.77717448 3.048169793 1.024929173 1.062671078 1.425306089 0.414796269 0.152025186 0.420733231 0.9594681 0.065194025 0.084160205 1117.299986 -3.048169793 0.362635011 VVVDALSGLKGDLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVVDALSGLKGDLAGR 16 1 P12532;P12532-2;F8WCN3;C9JSQ1 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 76.391 0.024479 146050000 125670 138430 122660 139170 108510 117200 133410 141020 129490 FALSE TRUE 119729.8282 152536.1744 128284.0823 125180.3672 127434.1096 113141.3346 113055.8543 128671.5412 149570.6479 0.800490135 1.019826928 0.8576822 0.83693137 0.85199945 0.75644076 0.755869256 0.860272674 1 17.19046756 3.487914954 20.32507271 0.823145163 0.914924545 0.057884174 0.086122641 68.69240467 129349.7462 0.022098378 0.03202312 3075.494497 -3.487914954 0.091779382 VVVHPLVLLSVVDHFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VVVHPLVLLSVVDHFNR 17 0 P51665;H3BNT7;H3BTM8;H3BQV2 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 301.91 1.11E-46 492760000 451730 385850 368360 436550 480100 393190 529410 447200 315540 FALSE TRUE 430377.6181 425168.5537 385249.6704 392667.1646 563829.288 379573.7317 448638.7812 408040.7972 364472.3316 1.18082384 1.166531769 1.057006628 1.077357952 1.546974184 1.041433598 1.230926856 1.119538472 1 18.47544977 0.953386407 5.900736841 1.000018235 1.182730363 0.148612727 0.142263986 0.569597492 64.24487119 0.124410893 0.031298732 8.982276237 -0.953386407 0.182712128 VVVLMGSTSDLGHCEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVVLMGSTSDLGHCEK 16 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 197.47 4.32E-11 241390000 260860 257450 255310 302740 245230 265560 272540 306780 234670 FALSE TRUE 248529.6648 283684.4477 267016.216 272308 287998.0344 256363.5906 230959.0175 279916.7169 271061.4251 0.916875814 1.046568864 0.985076412 1.004598865 1.062482551 0.945776739 0.85205417 1.032668949 1 18.04826029 2.026369167 24.80159423 0.933580812 1.000758373 0.065990961 0.061537697 296.2351128 278623.3613 0.021928008 0.01619444 106.2598423 -2.026369167 0.067177561 VVVS(ph)PTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 VVVSPTK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.999)PT(0.001)K;VVVS(1)PTK;VVVS(1)PTK;VVVS(0.85)PT(0.15)K;VVVS(0.987)PT(0.013)K;VVVS(0.999)PT(0.001)K;VVVS(0.999)PT(0.001)K 155.84 0.0016611 4933840000 8135610 8223840 7492590 9046190 5321810 8957280 9192580 9288250 6471150 TRUE FALSE 7751055.839 9061858.646 7836132.663 8136849.795 6249931.979 8647087.148 7790083.088 8474921.59 7474662.892 1.036977313 1.212343456 1.048359341 1.088590872 0.83614901 1.156853128 1.042198585 1.133819908 1 22.83357708 3.533333688 24.88959325 1.045279488 1.125608976 0.108893732 0.096227555 541.6507326 239828.7845 0.023853917 0.036954187 3414.551659 -3.533333688 0.080329488 VVVS(ph)PTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VVVSPTKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.987)PT(0.013)KK;VVVS(0.893)PT(0.107)KK;VVVS(0.999)PT(0.001)KK 130.98 0.00062755 15717290000 10409160 10351800 10153340 12219600 6026310 12458200 12085900 13750000 7248280 TRUE FALSE 9917139.636 11406660.19 10618880.68 10991262.59 7077296.556 12026769.41 10241973.98 12545977.11 8372306.243 1.184517067 1.362427491 1.268334002 1.312811819 0.845322227 1.436494206 1.223315737 1.498509102 1 22.99719365 VVVSGLPPSGSWQDLKDHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VVVSGLPPSGSWQDLKDHMR 20 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 61.648 0.029282 133070000 438630 262110 407240 361670 441030 405390 578830 478530 513460 FALSE TRUE 417896.8292 288819.307 425912.3568 325314.2445 517945.4924 391351.2427 490518.8526 436627.3764 593084.7544 0.7046157 0.486978134 0.718130678 0.548512235 0.873307716 0.659857195 0.827063668 0.736197269 1 19.17787876 1.120438639 0.305131156 1.038647972 0.568349799 0.529901636 0.102355175 1.203381974 0.369930998 0.213562228 0.137964792 13.19588856 -1.120438639 -0.470298173 VVWVEESDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 208.6 1.78E-07 1487470000 1414403 1415122 1221649 1340356 1046310 1290332 1419830 1559709 1081246 FALSE TRUE 1347546.973 1559324.541 1277662.815 1205620.868 1228786.133 1245647.479 1203208.857 1423132.611 1248920.107 1.078969716 1.248538262 1.023014048 0.965330657 0.983878893 0.997379634 0.963399379 1.139490511 1 20.25224976 3.615171438 6.47217393 1.001224584 1.16300758 0.498335177 0.063800179 0.157387058 7.644876925 0.015888218 0.024723982 4122.602271 -3.615171438 0.161782997 VVYAFS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VVYAFSPK 8 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK 153.12 0.00046801 1468242000 4734300 4089460 3811130 4256320 3033750 4379650 4936730 5017240 3340800 TRUE FALSE 4510519.021 4506180.623 3985874.08 3828466.627 3562835.039 4227981.622 4183541.169 4577903.868 3858874.202 1.168869154 1.167744888 1.032911122 0.992120092 0.923283542 1.095651582 1.084135152 1.186331461 1 21.87974858 3.742894765 23.63675491 1.046635295 1.168307043 0.350355727 0.069821402 184.3419439 1005318.843 0.018592213 0.032026919 5532.160424 -3.742894765 0.121671748 VWAALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWAALR 6 0 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 0 ; 142.14 0.026902 244650000 570290 327240 156221 168254 734070 214780 579340 340700 588110 FALSE TRUE 543333.5219 360586.128 163383.8874 151340.7883 862091.5756 207342.1147 490951.0427 310866.5018 679311.0952 0.799830189 0.53081148 0.240514086 0.222785686 1.269067415 0.305224096 0.722719011 0.457620233 1 19.37371289 VWAHYEEQPVEEVMPVLEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VWAHYEEQPVEEVMPVLEEK 20 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 225.69 4.93E-25 351615000 624028 650288 527052 732695 408687 664385 679310 686155 342226 FALSE TRUE 594531.4331 716553.0865 551217.8555 659043.1066 479961.8834 641377.1809 575668.7831 626071.6307 395296.6602 1.504013297 1.812697041 1.394440963 1.667211421 1.214181479 1.622521122 1.45629559 1.583801974 1 18.59257624 -2.976736356 0.232126179 4.39E-20 1.62209221 0.504405976 0.163569954 42.78339832 0.99001925 21.47301725 0.265121107 0.001055027 2.976736356 1.62209221 VWAHYEEQPVEEVMPVLEEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VWAHYEEQPVEEVMPVLEEKER 22 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 152.32 2.53E-08 140022000 178277 77048 190069 136134 186384 174050 277249 193007 229434 FALSE TRUE 169850.1995 84899.2788 198783.8517 122449.5517 218889.3106 168022.6049 234949.573 176106.2839 265013.4529 0.640911613 0.320358374 0.750089663 0.462050324 0.825955468 0.634015379 0.886557156 0.66451828 1 18.01570607 1.993549968 0.37332538 0.986709345 0.455057174 0.445063627 0.147228368 0.950588691 0.350836212 0.160494357 0.171804747 98.52579952 -1.993549968 -0.531652171 VWCDGCYDMVHYGHSNQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWCDGCYDMVHYGHSNQLR 19 0 Q99447-3;Q99447;I3L1L9;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 172.97 4.24E-12 310600000 129342 101720 119819 145486 136533 143264 165882 142565 67488 FALSE TRUE 123228.26 112085.3836 125312.8197 130861.4709 160344.312 138302.7318 140573.6543 130081.2528 77953.69436 1.580787941 1.437845692 1.60752894 1.67870775 2.056917421 1.7741652 1.803296886 1.668699013 1 16.25032978 3.351495794 3.056852366 1.736316026 1.511233038 0.006552925 0.272611717 0.497843686 9.294559728 0.070270398 0.09863257 2246.445019 -3.351495794 -0.225082988 VWDAVSGDELMTLAHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWDAVSGDELMTLAHK 16 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 150.76 7.08E-07 254760000 796920 659540 679790 767070 635340 684400 845140 767070 568940 FALSE TRUE 759251.1709 726747.8758 710959.0439 689962.6663 746143.0948 660699.0564 716198.3709 699901.2843 657168.3095 1.155337468 1.105877848 1.081852295 1.049902523 1.135391169 1.005372668 1.089824875 1.065025921 1 19.32590339 8 0.136532118 0.997394568 1.513033626 0.520247598 0.034634543 56.71051307 0.518623943 0.142485213 5.683485728 100000000 -8 0.515639058 VWDDGIIDPADTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VWDDGIIDPADTR 13 0 Q9HCC0-2;Q9HCC0 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ;; 156.58 0.00010992 234201000 681900 499910 580780 577820 631040 467690 612420 585640 652110 FALSE TRUE 649667.9384 550851.3974 607409.3375 519736.4358 741093.1762 451493.778 518984.0811 534358.2569 753235.8883 0.862502635 0.731313266 0.80639989 0.690004876 0.98387927 0.599405558 0.689006046 0.709416884 1 19.52274221 2.203412472 24.99999658 0.715407572 0.801711982 0.026037937 0.128892407 408.5125401 290562.3863 0.042769392 0.031588517 159.7395555 -2.203412472 0.08630441 VWDEANLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWDEANLR 8 0 Q96GA7;F8VYZ3 Q96GA7 SDSL Serine dehydratase-like 0 ; 126.52 0.0028279 105239000 251860 210350 188182 211900 328920 185182 252910 224330 314940 FALSE TRUE 239955.0769 231784.9041 196810.3308 190599.4094 386283.5439 178769.1009 214323.9345 204686.476 363779.2867 0.659617207 0.637158059 0.54101577 0.523942446 1.061862393 0.49142188 0.589159258 0.562666659 1 18.47270387 -1.165858124 3.600270563 1.000333206 0.632446978 0.340019003 0.160527641 158206307.1 278457187.5 673666.6638 0.035856595 0.068256164 1.165858124 -0.367886228 VWDISGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VWDISGLR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 166.45 0.00098513 37005000 672660 603140 541220 636540 685760 550770 698120 643650 669940 FALSE TRUE 640864.6949 664600.6517 566035.4723 572553.7899 805356.3269 531696.6968 591608.9721 587288.5938 773830.8736 0.828171525 0.858844839 0.731471813 0.739895253 1.040739462 0.687096774 0.764519732 0.758936628 1 19.56165876 VWDLSDIDKDGHLDRDEFAVAMHLVYR ddPTM_SK-BR-3_Trastuzumab_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 ; 180.83 5.69E-18 144452000 285930 265230 234390 336560 198643 281930 325000 328950 107907 FALSE TRUE 272414.6556 292257.2385 245137.0133 302728.3494 233286.2763 272166.6934 275415.281 300145.3941 124640.6664 2.18560012 2.344798426 1.96674986 2.428808815 1.871670643 2.183610704 2.209674329 2.408085601 1 16.92741533 -1.296795518 3.654231443 0.996803805 2.201928395 0.820778877 0.176203369 2630704.916 1401626.919 64312.63359 0.036582955 0.050489897 1.296795518 1.205124591 VWDPDNPLTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VWDPDNPLTDR 11 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 ;;; 188.87 6.88E-06 259733000 630600 654600 609470 682870 708110 602902 694120 629360 743630 FALSE TRUE 600792.7877 721304.4842 637414.8023 614226.6102 831604.1598 582023.3526 588219.2456 574249.902 858948.3425 0.699451594 0.839753043 0.74208747 0.715091444 0.96816551 0.677599948 0.684813296 0.668549986 1 19.71221184 VWDVGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VWDVGTR 7 0 H3BQA8;H0YL19;H0YN81;Q9GZS3 H3BQA8 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 ;; 122.5 0.010084 273933000 934270 780840 825790 929520 953820 843020 1067680 907290 987010 FALSE TRUE 890108.9086 860408.4837 863653.2883 836082.8836 1120165.906 813826.006 904785.8067 827842.8778 1140070.47 0.780749026 0.754697632 0.757543776 0.733360705 0.982540936 0.713838335 0.793622702 0.726133077 1 20.12069157 -1.214183266 3.274088583 1.000585401 0.780036366 0.452974405 0.07587089 24937870.48 38323282.71 151354.6293 0.017000629 0.061068427 1.214183266 -0.220549035 VWDVIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWDVIGR 7 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 110.63 0.015726 27425000 151480 126260 127290 142380 161900 124740 153670 142190 168470 FALSE TRUE 144319.8406 139126.0375 133126.3724 128067.6919 190135.3087 120420.2225 130224.8192 129739.0898 194595.4672 0.7416403 0.714950043 0.684118568 0.658122688 0.977079844 0.618823369 0.669207875 0.666711777 1 17.57011858 -1.203605102 5.165864612 1.000021915 0.71501861 0.450403332 0.098467404 2.31E-05 3.57E-06 0.08874445 0.02091566 0.062574141 1.203605102 -0.285003305 VWDVRPFAPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWDVRPFAPK 10 1 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 136.63 0.00010257 304650000 1073100 773380 579530 802110 895890 731020 1345200 932550 1071500 FALSE TRUE 1022376.69 852188.3013 606102.0237 721480.3789 1052132.932 705704.5941 1139965.034 850890.9782 1237662.748 0.826054345 0.688546458 0.489715009 0.582937784 0.850096631 0.570191351 0.921062734 0.687498254 1 20.23918682 0.828898321 0.659929156 0.995116734 0.678033076 0.347302113 0.132271142 1.127374291 1.059430924 0.132275306 0.051346861 6.743701233 -0.828898321 -0.317083658 VWDYETGDFER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VWDYETGDFER 11 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 231.16 2.95E-12 1007076000 1504740 1627250 1304250 1668550 1313660 1425460 1372040 1495340 1223150 FALSE TRUE 1433613.922 1793068.625 1364051.153 1500824.184 1542761.888 1376095.963 1162710.099 1364400.102 1412829.855 1.014710949 1.26913274 0.965474468 1.062282326 1.091965804 0.973999776 0.822965408 0.965721454 1 20.4301563 2.122562112 3.770036913 0.9075083 1.09468672 0.362460409 0.090765326 0.197742772 5.321016758 0.036097344 0.02539876 132.6056755 -2.122562112 0.18717842 VWEDRPS(ph)SAGSTPFPYNPLIMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.736)S(0.264)AGSTPFPYNPLIMR 178.95 3.54E-17 42642000 54422 54691 51100 59944 59047 47379 59870 58190 63839 TRUE FALSE 51849.57991 60264.07508 53442.98554 53918.31523 69344.77811 45738.25335 50735.73191 53094.57512 73738.82608 0.703151686 0.817263825 0.724760461 0.731206586 0.94041066 0.620273685 0.688046374 0.720035535 1 16.17013683 -0.887302444 4.345509647 1.000003669 0.742790152 0.473699521 0.085085309 13616049.52 44649593.89 934.2074641 0.019826282 0.129627623 0.887302444 -0.257213517 VWLDPNETNEIANANSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWLDPNETNEIANANSR 17 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 255.08 1.09E-26 368320000 444670 461350 382930 482270 429730 413520 460580 443160 465020 FALSE TRUE 423651.3304 508362.0895 400487.7193 433791.3033 504674.7759 399199.6987 390310.0619 404354.5611 537132.9266 0.788727165 0.946436281 0.745602624 0.807605123 0.939571475 0.743204669 0.726654507 0.752801664 1 19.03491964 2.198345449 24.99381673 0.77544436 0.847900272 0 0.09891677 328.1100423 203919.2198 0.033827641 0.024983689 157.8866642 -2.198345449 0.072455913 VWNWQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWNWQSR 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 147.83 0.0049434 485850000 726900 642880 386640 451180 721390 487880 771430 608010 613140 FALSE TRUE 692540.8776 708390.2029 404367.8264 405826.5292 847200.1876 470984.5933 653734.1852 554769.4211 708222.6197 0.977857609 1.000236625 0.570961468 0.573021135 1.196234297 0.66502337 0.923063126 0.783326324 1 19.4338434 VWQLGSSSPNFTLEGHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWQLGSSSPNFTLEGHEK 18 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 248.94 1.42E-24 928320000 1043620 914460 919580 1111790 753600 1090160 1235910 1201610 837080 FALSE TRUE 994290.1509 1007644.514 961743.6526 1000030.757 885027.6014 1052407.486 1047349.23 1096390.658 966890.0912 1.02833834 1.042150005 0.994677328 1.034275525 0.915334234 1.088445828 1.083214359 1.133935148 1 19.88299238 VWQVTIGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWQVTIGTR 9 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6RAC2;H0Y8R5;D6RF23;D6RHJ5 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 136.21 0.0004634 438980000 495190 494890 402850 444120 463810 492850 547870 540370 529750 FALSE TRUE 471783.3501 545319.8536 421321.071 399476.2138 544698.3172 475782.4809 464282.3692 493052.3381 611900.9244 0.771012645 0.891189786 0.68854459 0.652844599 0.890174039 0.77754823 0.758754156 0.80577152 1 19.22293855 0.939451697 15.22589125 1.000000001 0.782539103 0.467480052 0.074363503 86.65926269 21793.23435 0.070493222 0.017623722 8.698646798 -0.939451697 -0.217460899 VWS(ph)PLVTEEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWSPLVTEEGK 11 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(0.999)PLVT(0.001)EEGK 109.22 0.0012425 0 52606 57644 49364 62259 43806 57086 54917 59593 41623 TRUE FALSE 50119.41864 63517.98914 51627.38823 56000.60704 51445.75253 55109.09751 46538.40303 54374.721 48077.68226 1.042467446 1.321153312 1.073832718 1.164794233 1.070054755 1.146251128 0.967983498 1.130976338 1 15.55307973 2.403483022 0.94644913 1.032275446 1.170483869 0.200237506 0.088676804 0.725851131 1.284751612 0.057121507 0.03759892 253.2112645 -2.403483022 0.138208422 VWS(ph)PLVTEEGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(0.999)PLVT(0.001)EEGKR 154.65 4.39E-05 123380000 225820 269570 203320 294640 138950 240600 218520 276190 140160 TRUE FALSE 215145.9361 297039.4895 212642.4231 265022.2274 163182.836 232267.9617 185180.7606 252005.3394 161895.297 1.328920235 1.83476293 1.313456457 1.636997692 1.007952912 1.434680105 1.14383039 1.556594565 1 17.30470155 2.757328346 24.97735393 1.246709431 1.545444323 0.303385295 0.224252951 933.392218 1242219.357 0.061415881 0.065042898 571.9108635 -2.757328346 0.298734893 VWWMFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VWWMFR 6 0 P25325-2;P25325;B1AH49;Q16762;B1AH48 P25325-2;Q16762 MPST;TST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase;Thiosulfate sulfurtransferase 0 159.55 0.021132 70160000 88310 84337 40954 44807 82302 41459 89668 60645 67804 FALSE TRUE 84135.76131 92931.03618 42831.78141 40302.91523 96655.44274 40023.26443 75987.49973 55334.6023 78318.69803 1.074274259 1.186575346 0.546890876 0.514601446 1.234129846 0.511030768 0.970234461 0.706531182 1 16.25706916 3.759021498 24.67415911 0.784273812 1.130424853 0.272771522 0.235602054 775.9945478 935782.9456 0.055088966 0.099157007 5741.448824 -3.759021498 0.34615104 VWYHVCSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VWYHVCSSR 9 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 92.051 0.010338 540520000 459540 334750 186944 228020 541870 235034 578420 352500 543550 FALSE TRUE 437818.4549 368861.4056 195515.5673 205098.9964 636371.9564 226894.7136 490171.4056 321633.2313 627840.9579 0.697339747 0.587507713 0.311409386 0.326673489 1.013587834 0.361388837 0.780725436 0.512284564 1 19.26003962 -1.09263553 0.395234001 1.191336413 0.559295651 0.272386913 0.218756073 22.80475947 2.388177945 5.01230022 0.133996992 0.080791277 1.09263553 -0.632040762 VWYVSNIDGTHIAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VWYVSNIDGTHIAK 14 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7EPY4;K7ENA0 P06744 GPI Glucose-6-phosphate isomerase 0 ;; 279.86 3.07E-33 6575317000 8534875 7234063 7027000 8411954 7646850 7604755 9301162 8593592 7526780 FALSE TRUE 8131448.373 7971222.244 7349194.901 7566368.402 8980458.219 7341400.427 7882098.909 7841091.527 8693994.601 0.93529485 0.916865332 0.845318549 0.870298263 1.032949597 0.844422014 0.906614194 0.901897446 1 23.05158777 -1.104938314 4.917006443 1.000003681 0.907330593 0.230221671 0.053600843 1.99E-06 3.63E-07 0.047839489 0.011275428 0.078534718 1.104938314 -0.092673088 VY(ph)VMEDIT(ph)FNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYVMEDITFNVK 12 0 Q9H706-2;Q9H706-3;Q9H706 Q9H706-2 GAREM GRB2-associated and regulator of MAPK protein 2 VY(1)VMEDIT(1)FNVK 60.401 0.076741 159820000 208620 238250 230370 279880 295500 256260 295590 305210 442130 TRUE FALSE 198758.946 262527.9459 240932.6924 251745.9307 347035.1064 247385.6519 250492.3166 278484.1944 510693.2623 0.389194377 0.514061894 0.471775741 0.492949387 0.679537272 0.484411427 0.490494657 0.545306185 1 18.9620975 -5 0.263821861 4.284568581 0.463798523 0.83734223 0.068829277 77.09580366 0.754048532 137.5202297 0.087885531 1.00E-05 5 -3.820770058 VYADGIFDLFHSGHAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 114.63 0.00032882 158613000 248960 187550 199591 234580 284520 207273 297620 221110 14218.2 FALSE TRUE 237192.1542 206661.5582 208742.4448 210999.5727 334140.1979 200095.084 252212.6028 201748.4362 16423.08584 14.44260576 12.58360093 12.7103059 12.84774218 20.34576213 12.18376899 15.35719933 12.28444144 1 14.00343761 0.83097684 4.517190161 1.000220911 14.21607307 0.75764399 2.354614802 0.81315641 21.30847685 2.106638321 0.534765538 6.776053718 -0.83097684 13.21585216 VYAILTHGIFSGPAISR ddPTM_SK-BR-3_Trastuzumab_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 ; 169.92 1.91E-09 215630000 391790 386760 318470 366130 402420 335550 409700 406180 342810 FALSE TRUE 373270.8632 426171.2837 333072.1645 329325.9168 472601.9206 323929.8194 347192.7403 370612.7259 395971.224 0.942671691 1.076268319 0.841152448 0.831691539 1.193525923 0.81806404 0.876813059 0.935958735 1 18.59503606 VYASQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYASQR 6 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 99.279 0.090682 87910000 117930 93112 60287 75150 138300 79021 141500 100270 146120 FALSE TRUE 112355.6826 102600.2187 63051.21858 67595.77922 162419.4762 76284.48296 119911.5762 91489.82724 168779.5433 0.665694908 0.607894871 0.373571449 0.400497465 0.962317311 0.451977067 0.710462736 0.542067039 1 17.36478053 -4.999971762 0.314323289 4.695934329 0.57791138 0.362855164 0.171032932 336.8116072 3.021652821 825.5458771 0.145453967 1.00E-05 4.999971762 -4.118022948 VYEDSGIPLPAES(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 199.58 7.71E-09 38023000 207940 228830 181490 256870 104480 219510 190300 216210 107470 TRUE FALSE 198111.0883 252148.0372 189811.496 231048.9396 122701.2789 211908.3137 161266.2399 197277.5062 124135.8987 1.595921005 2.031225776 1.529062084 1.86125804 0.988443151 1.70706714 1.299110423 1.589205929 1 16.92156086 1.512842196 0.165317754 0.747066145 2.097412312 0.361067645 0.269687697 3.587805341 0.617701888 2.111721811 2.06179535 32.57183274 -1.512842196 1.350346167 VYEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYEELR 6 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 98.133 0.093712 184320000 338210 290850 301750 312670 331700 288570 345960 342310 360190 FALSE TRUE 322223.4836 320487.9457 315585.536 281239.8176 389548.375 278576.7485 293177.448 312335.5217 416046.4256 0.774489249 0.770317748 0.758534424 0.675981814 0.936309871 0.66958092 0.704674839 0.750722762 1 18.666385 -1.540490095 2.665951276 1.014692953 0.753295864 0.517879765 0.074249394 8595909.264 8341915.929 905000.9451 0.017322524 0.028807788 1.540490095 -0.261397089 VYEFLDKLDVVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYEFLDKLDVVR 12 1 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 180.28 1.79E-05 343510000 1395810 1363810 1277860 1433900 1128210 1418010 1610450 1519400 1200590 FALSE TRUE 1329832.828 1502783.79 1336451.145 1289761.648 1324969.467 1368903.958 1364746.275 1386353.281 1386771.365 0.958941654 1.083656489 0.963714119 0.930046351 0.955434688 0.987115823 0.98411772 0.99969852 1 20.40329852 VYEGERPLTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VYEGERPLTK 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 172.61 3.34E-06 8552930000 12973330 7863560 9204280 12242860 9980220 10430360 13850600 11626710 11880380 FALSE TRUE 12360106.4 8664865.704 9626305.342 11012184.45 11720767.21 10069154.02 11737436.59 10608613.64 13722728.65 0.900703258 0.6314244 0.701486241 0.802477753 0.854113457 0.733757423 0.855328185 0.773068819 1 23.71006404 -0.494832809 0.36691307 1.067204934 0.754836354 0.430555999 0.079171962 7.897220593 1.0656208 0.732569199 0.060167592 0.320012683 0.494832809 -0.312368581 VYEHT(ph)SRFSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.38)S(0.31)RFS(0.31)PK 80.522 0.035445 80744000 127950 98269 109250 134860 93435 120210 158380 142030 110040 TRUE FALSE 121902.0571 108282.7228 114259.2206 121303.6166 109730.0344 116047.0976 134216.2222 129593.1003 127104.4412 0.959070005 0.851919271 0.89893964 0.954361747 0.863306061 0.913005844 1.055952262 1.019579639 1 16.95565492 1.775009142 7.669040617 1.027963348 0.904115459 0.705521073 0.036019771 0.098924083 15.45462556 0.015891334 0.008903066 59.56746821 -1.775009142 -0.123847889 VYEHTS(ph)RFSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.004)S(0.776)RFS(0.219)PK 107.99 0.0012818 248740000 190640 130710 208280 210790 195800 213400 311020 270670 281050 TRUE FALSE 181628.825 144029.4976 217829.844 189600.9887 229947.458 206009.9045 263568.1867 246968.6999 324633.7986 0.55948834 0.443667598 0.671001741 0.584045745 0.708328766 0.63459167 0.811893857 0.760760897 1 18.30845369 1.601420119 0.28768214 1.04729056 0.443053366 0.829329069 0.062883726 0.536307241 0.167031924 0.117334689 0.11483029 39.94110895 -1.601420119 -0.604237194 VYEIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYEIGR 6 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 97.596 0.095131 121560000 307690 265590 254980 294950 288110 271880 319770 315760 296310 FALSE TRUE 293146.1035 292653.923 266671.0852 265301.0656 338356.2928 262464.7274 270983.2135 288110.3805 342260.2415 0.856500604 0.855062574 0.779147131 0.775144272 0.988593625 0.766857191 0.791746106 0.841787463 1 18.38473419 -2.129378955 2.105440768 1.316478101 0.830978932 0.400270141 0.064674784 5687589.45 1330170.921 8601042.042 0.015255053 0.007423711 2.129378955 -0.485499169 VYENYPTYDLTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYENYPTYDLTER 13 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ; 173.6 4.98E-05 293610000 235035 243027 221588 264714 238101 247827 270910 251540 264971 FALSE TRUE 223925.3613 267791.7276 231748.029 238104.4458 279625.739 239244.6888 229577.7039 229513.8241 306061.3494 0.731635542 0.874960945 0.757194691 0.777963131 0.913626433 0.781688669 0.750103547 0.749894832 1 18.22346134 -1.459231556 2.90047437 1.005553344 0.794331483 0.557933128 0.058119426 10587911.54 12179034.25 476955.6483 0.013605588 0.034735091 1.459231556 -0.211221861 VYFDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYFDLR 6 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;; 132.8 0.034289 1155586000 4410790 3679530 3047980 3876690 4870680 3188800 5222250 4035880 5533250 FALSE TRUE 4202300.698 4054478.29 3187732.898 3486997.756 5720125.05 3078371.056 4425499.849 3682476.952 6391318.15 0.65750141 0.634372784 0.498759853 0.545583505 0.894983619 0.481648853 0.692423651 0.576168619 1 22.60768207 -1.511774315 2.907914409 1.014177674 0.626536317 0.505189444 0.117300568 45952020.63 51016916.48 5185850.033 0.025372948 0.030776958 1.511774315 -0.387641358 VYFQS(ph)PPGAAGEGPGGADDEGPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 1 VYFQS(1)PPGAAGEGPGGADDEGPVRR;VYFQS(1)PPGAAGEGPGGADDEGPVRR;VY(0.008)FQS(0.992)PPGAAGEGPGGADDEGPVRR 130.81 5.34E-05 383191000 419738 413444 458745 479280 483641 454430 561410 490770 615670 TRUE FALSE 399897.8166 455574.4136 479778.912 431101.8638 567987.8373 438692.9752 475756.5935 447795.5771 711144.9592 0.562329538 0.640621026 0.674656982 0.606208141 0.798694879 0.616882633 0.669000866 0.629682558 1 19.43978414 -5 0.278476481 3.542996367 0.623940412 0.759281635 0.061913398 104.0869013 0.998697382 152.9512154 0.067038547 1.00E-05 5 -2.919055955 VYFQSPPGAAGEGPGGADDEGPVRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ;;; 234.3 3.54E-38 1004480000 448601 365142 393869 445011 440622 395262 454199 467752 490352 FALSE TRUE 427396.5198 402350.3849 411928.2832 400277.6488 517466.3373 381573.9778 384902.6006 426793.1552 566393.2838 0.754593199 0.710372804 0.727283135 0.706713268 0.913616655 0.673690859 0.679567734 0.753527924 1 19.11144463 -1.321609204 2.902604672 1.002839478 0.734874169 0.594104863 0.067444507 8691822.234 10784529.03 213314.9016 0.01596635 0.047685989 1.321609204 -0.267965308 VYIVHGVQEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYIVHGVQEDLR 12 0 Q15024 Q15024 EXOSC7 Exosome complex component RRP42 0 125.28 0.00023483 0 76869 65119 72064 79295 76120 70064 88696 80080 78550 FALSE TRUE 73235.55471 71754.70013 75368.20568 71324.11595 89395.3039 67637.66611 75163.79619 73067.77067 90731.13282 0.807171171 0.790849821 0.830676344 0.786104105 0.985277061 0.745473621 0.828423429 0.805321926 1 16.46931005 -1.866831992 2.251446425 1.090301713 0.819891958 0.441217268 0.06275046 4455996.519 2309177.86 2149969.22 0.015660679 0.01358839 1.866831992 -0.270409754 VYLLYRPGHYDILYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYLLYRPGHYDILYK 15 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 138.87 4.76E-06 1688820000 4311400 3637000 3357900 4143400 4002300 3902000 5379200 4511300 3430900 FALSE TRUE 4107608.666 4007614.435 3511863.036 3726897.56 4700299.853 3766872.762 4558504.244 4116266.656 3962946.449 1.036503702 1.011271408 0.886174739 0.940436013 1.186061914 0.950523256 1.150281565 1.038688438 1 21.91814204 2.780055626 24.99802916 1.071008717 0.978675215 0.269450146 0.077853317 669.5956436 403386.4222 0.022406495 0.023765458 602.6367694 -2.780055626 -0.092333501 VYMGHGGKPWVSDFSHPHYLAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VYMGHGGKPWVSDFSHPHYLAGR 23 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;;;; 258.5 4.03E-44 5947580000 6304260 5362880 5234870 6257280 6838240 5667260 7731910 5986030 1292232 FALSE TRUE 6006270.124 5909363.569 5474893.967 5628286.326 8030826.891 5471001.365 6552265.123 5461861.479 1492624.739 4.023965279 3.959041691 3.667964107 3.770730968 5.380338864 3.665356217 4.389760502 3.659232852 1 20.50942007 0.841004344 4.871307485 1.00003657 4.103782105 0.792551297 0.498129419 0.780299408 23.58518313 0.441254861 0.111649244 6.93432742 -0.841004344 3.103745535 VYNLLT(ph)PDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VYNLLTPDSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 VYNLLT(0.972)PDS(0.028)K;VYNLLT(0.988)PDS(0.012)K;VYNLLT(0.997)PDS(0.003)K;VYNLLT(0.998)PDS(0.002)K;VYNLLT(0.998)PDS(0.002)K;VYNLLT(0.98)PDS(0.02)K 156.08 0.00012931 799669000 1547360 1577530 1576480 1770280 1208540 1666600 1896480 1943660 1536880 TRUE FALSE 1474219.359 1738282.101 1648763.167 1592328.091 1419308.993 1608885.224 1607137.145 1773462.826 1775211.501 0.830447166 0.979197183 0.92876999 0.896979368 0.799515434 0.906306219 0.905321503 0.999014949 1 20.75955949 1.257764297 4.039805543 1.003352986 0.895126986 0.451765906 0.049090823 0.203090362 6.515337261 0.04167831 0.012490516 18.10357298 -1.257764297 -0.108226 VYNWDVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYNWDVK 7 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;; 86.011 0.047436 213085000 370602 303997 315453 368131 313672 348925 390693 353115 324097 FALSE TRUE 353084.3779 334974.6399 329916.8321 331125.7725 368376.2975 336841.6398 331085.6073 322194.3786 374356.3075 0.943177318 0.894801645 0.881290967 0.884520351 0.984025887 0.899788872 0.88441306 0.860662348 1 18.51405254 4.635363229 3.280782941 0.905984686 0.944552777 0.035338757 0.045571706 0.82277276 14.57613802 0.010188373 0.068608621 43188.01351 -4.635363229 0.03856809 VYNYNHLMPTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYNYNHLMPTR 11 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 130.01 0.00023316 2845600000 3073200 2356500 2035550 2679000 2625000 2483700 3413100 3030900 2782400 FALSE TRUE 2927935.926 2596630.029 2128881.981 2409701.83 3082799.169 2397688.846 2892368.909 2765498.328 3213880.381 0.911028283 0.807942338 0.66240237 0.749779564 0.959214035 0.74604172 0.899961593 0.860485768 1 21.6158848 0.807983845 0.737498538 0.999631412 0.809029746 0.32732073 0.085697059 1.171888211 1.31976791 0.084098591 0.030935134 6.426638111 -0.807983845 -0.190601666 VYQSLCPTSWVTDWDEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYQSLCPTSWVTDWDEQR 18 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;; 271.08 1.40E-38 182806000 152187 165708 121589.6 174443 129408 133436.5 137254 133379 139384 FALSE TRUE 144993.4221 182593.8336 127164.6034 156907.6582 151976.7142 128815.5605 116313.3815 121699.6277 160998.9588 0.900586085 1.134130524 0.789847365 0.974588031 0.943960851 0.800101823 0.722448035 0.755903197 1 17.29669183 2.252884784 4.440640186 0.786864766 0.965257041 0.21848786 0.11260823 0.210709825 9.914960737 0.039490183 0.030831539 179.0130877 -2.252884784 0.178392275 VYQWDDPDPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 160.59 1.71E-05 56498820000 32335850 29128850 30205550 34632360 33739690 30766060 36145870 32555760 36259060 FALSE TRUE 30807398.45 32097112.93 31590504.34 31151049.38 39623881.25 29700623.63 30631153.67 29705005.07 41881929.84 0.735577338 0.766371393 0.75427528 0.743782569 0.946085374 0.709151267 0.731369203 0.709255881 1 25.31982458 -2.113732838 2.517671586 1.462281703 0.760949081 0.548062359 0.067919866 4703881.943 2236317.42 12356648.06 0.015915997 0.007696037 2.113732838 -0.701332622 VYRDDIGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYRDDIGR 8 1 A0A087WY71;Q96CW1-2;Q96CW1;C9JJ47;C9JJD3;C9JGT8 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 140.35 0.00059677 332630000 512860 518740 435160 524130 377880 480580 527590 486320 380640 FALSE TRUE 488618.1242 571600.1958 455112.5164 471443.4566 443782.1524 463937.3941 447096.4556 443735.2427 439667.7072 1.111335029 1.300073184 1.035128369 1.072272193 1.009358079 1.055200067 1.01689628 1.009251386 1 18.74605405 3.715320084 23.88515325 1.030807286 1.205704088 0.687707529 0.049678294 201.1150964 206693.399 0.01239185 0.019213419 5191.825459 -3.715320084 0.174896803 VYSEDGACR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYSEDGACR 9 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 84.498 0.035898 0 168030 124820 135560 166470 188970 131740 192850 159930 201050 FALSE TRUE 160087.5549 137539.2999 141775.5601 149736.1193 221926.3082 127177.8108 163427.1906 145925.6814 232227.8072 0.689355667 0.592260253 0.610502083 0.644781179 0.955640545 0.547642474 0.703736527 0.628372989 1 17.82518121 -2.164182377 2.248065315 1.775703467 0.668447108 0.465372829 0.110596575 5137502.048 1157006.586 20292314.2 0.024730839 0.006852004 2.164182377 -1.107256359 VYSGHQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 VYSGHQGR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;; 164.72 0.00032843 675193000 641282 699696 598410 716523 708159 611907 688043 681701 619338 FALSE TRUE 610969.8708 770995.8179 625847.6904 644496.7467 831661.7054 590716.5072 583069.4036 622007.6465 715381.7739 0.854047298 1.07774037 0.874844332 0.900913009 1.162542485 0.825736032 0.81504649 0.869476508 1 19.44835384 VYSLDDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYSLDDIR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 87.323 0.038216 0 73305 109420 77061 98830 85252 76047 69397 87723 68757 FALSE TRUE 69840.01793 120570.0224 80594.32307 88895.42064 100119.9218 73413.47332 58809.21309 80041.50907 79419.4844 0.879381407 1.518141591 1.014792827 1.119315006 1.260646837 0.924376101 0.740488478 1.007832142 1 16.27720537 2.149212269 5.950566345 0.875267322 1.173259647 0.292953248 0.18045676 0.21373921 11.4442299 0.065522407 0.048228124 140.9977781 -2.149212269 0.297992325 VYSLDDIRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYSLDDIRR 9 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 193.38 5.40E-05 836860000 460143 354204 374054 380397 556590 381517 547414 482121 593215 FALSE TRUE 438392.9523 390297.7903 391204.7459 342158.7709 653659.1198 368304.9706 463895.9404 439903.9294 685207.7525 0.639795669 0.569605042 0.570928663 0.499350408 0.953957566 0.53750847 0.67701502 0.642000806 1 19.38618195 -5 0.229194559 2.979150957 0.589398702 0.468808893 0.123266817 135.2002752 1.35228878 123.9652591 0.195236975 1.00E-05 5 -2.389752255 VYSLFLDESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYSLFLDESR 10 0 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ;; 270.57 2.38E-23 180067000 332536 289216 224496 263943 353771 261343 377810 305087 357640 FALSE TRUE 316817.6823 318687.4392 234789.3637 237410.9482 415468.5504 252292.6264 320168.1455 278371.9649 413100.9846 0.766925508 0.771451657 0.568358277 0.574704387 1.005731203 0.610728698 0.775036026 0.67385936 1 18.65613497 -1.382383703 2.863430574 1.004681973 0.724751895 0.321673766 0.128236721 35105557.86 41163497.35 1360201.035 0.029777761 0.041458759 1.382383703 -0.279930078 VYSTSVTGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYSTSVTGSR 10 0 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ; 118.67 0.0018479 50134000 94262 70731 80101 92115 84623 75180 93082 86927 94965 FALSE TRUE 89806.42207 77938.56931 83773.71008 82855.42519 99381.22441 72576.49775 78880.63133 79315.21105 109691.6872 0.818716754 0.710523936 0.76371977 0.755348261 0.906005067 0.661640819 0.719112208 0.723074037 1 16.74309467 -1.025670044 4.482074619 1.000010036 0.75440952 0.566885126 0.066636644 74301080781 16154202303 8470546.235 0.014877298 0.094260547 1.025670044 -0.245600516 VYSVLSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYSVLSDR 8 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 153.71 0.0010159 147590000 116590 105520 77908 95968 125980 88359 122200 108460 123650 FALSE TRUE 111079.0218 116272.608 81480.15886 86321.11431 147950.8721 85299.10567 103556.1456 98962.66742 142825.0105 0.777728084 0.814091367 0.57048943 0.604383742 1.035889104 0.597228072 0.725056104 0.692894522 1 17.12388911 -1.301598139 3.392433739 1.001140998 0.732507116 0.287536463 0.134714505 1357034864 1758714586 15348128.94 0.030100283 0.049934633 1.301598139 -0.268633882 VYT(ph)HEVVTLWYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VYTHEVVTLWYR 12 0 P06493;A0A087WZZ9;E5RIU6 P06493 CDK1 Cyclin-dependent kinase 1 1 VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR 223.06 8.58E-11 1336550000 1824469 1573631 1312713 1554970 1510286 1613668 2041770 1733392 1233847 TRUE FALSE 1738229.966 1733985.788 1372902.19 1398661.461 1773679.4 1557786.273 1730260.487 1581607.007 1425185.691 1.21965157 1.216673588 0.963314604 0.981388931 1.244525125 1.093040915 1.214059682 1.109755042 1 20.44271847 3.928819793 24.99946945 1.103530809 1.218538433 0.243238175 0.09282235 210.1350278 73801.73316 0.023926928 0.043134894 8488.281872 -3.928819793 0.115007624 VYTDVNTHRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 170.52 9.38E-06 909740000 847600 864870 863250 1010050 843890 965090 998240 944650 845600 FALSE TRUE 807535.6278 953001.2363 902830.8664 908517.855 991064.1488 931668.6913 845940.1541 861931.4381 976731.3293 0.826773549 0.975704585 0.924339006 0.930161476 1.01467427 0.953863835 0.866092987 0.882465231 1 19.89760225 4.655198472 3.300021366 0.937030243 0.820994712 0.368451397 0.047207037 0.321824723 5.719120542 0.011736212 0.083330883 45206.24887 -4.655198472 -0.116035532 VYTDVQQVASSLTHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 VYTDVQQVASSLTHPR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;; 206.28 2.04E-11 525539000 646441 499323 565933 658050 802268 586273 793711 691993 872943 FALSE TRUE 615885.0151 550204.5814 591881.5878 591901.5638 942183.2852 565970.219 672615.8094 631398.4244 1008314.542 0.610806439 0.545667605 0.587000944 0.587020755 0.93441406 0.56130324 0.667069433 0.626191925 1 19.94351432 -4.999999999 0.19953338 2.64491174 0.573660679 0.52075016 0.109314009 110.0381443 1.087942586 72.24221562 0.249468924 1.00E-05 4.999999999 -2.07125106 VYTVGPDYAHAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYTVGPDYAHAEAR 14 0 A0A087WZV0;O43314-2;O43314;D6RBU4;Q6PFW1-6;B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;F8W9A8;Q6PFW1;Q6PFW1-5 A0A087WZV0;B7WPL9 PPIP5K2;PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2;Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 0 141.46 1.11E-05 0 56776 51482 55605 61625 56302 53234 63808 55877 63779 FALSE TRUE 54092.311 56728.07433 58154.54425 55430.33792 66121.05097 51390.49323 54072.91769 50984.11366 73669.52158 0.734256309 0.770034515 0.78939761 0.752418866 0.897536044 0.697581471 0.733993062 0.69206522 1 16.16878025 -1.063006443 4.365521916 1.000019617 0.758365912 0.635407526 0.057511984 1.04E-05 2.23E-06 0.052679414 0.012415649 0.086495509 1.063006443 -0.241653705 VYVGNLGNNGNKTELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 VYVGNLGNNGNKTELER 17 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;; 325.17 3.08E-59 3748820000 1771910 1336470 1789690 1954200 1714340 2013270 2530540 2182490 2243410 FALSE TRUE 1688155.326 1472657.812 1871749.057 1757760.103 2013320.353 1943549.955 2144459.646 1991379.605 2591306.565 0.65146878 0.568307059 0.722318649 0.678329661 0.776951821 0.750027025 0.827559223 0.768484761 1 21.30524827 1.405936808 0.172955994 1.128008155 0.475577609 0.846821417 0.044852934 1.16653409 0.205458588 0.331239889 0.299924789 25.46459705 -1.405936808 -0.652430547 VYVGNLGTGAGKGELER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYVGNLGTGAGKGELER 17 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 211.09 2.54E-12 573890000 569490 291200 625360 541740 724240 650750 949370 744380 974280 FALSE TRUE 542571.3363 320873.6111 654033.3746 487283.266 850547.2267 628214.3643 804526.1701 679198.141 1125366.366 0.482128623 0.285128133 0.581173735 0.432999671 0.755795848 0.558230975 0.714901559 0.603535134 1 20.10196332 0.592479965 0.129128373 1.401711533 0.09997006 0.689078954 0.108456904 6.217713385 0.408505659 2.369885783 1.390503074 3.912730768 -0.592479965 -1.301741473 VYWNDGLDQYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 VYWNDGLDQYR 11 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 208.11 4.81E-08 194809000 307480 284740 247460 265160 338680 262060 360300 307260 350060 FALSE TRUE 292946.0298 313755.3297 258806.2858 238505.613 397745.6848 252984.7965 305329.6176 280354.6855 404345.5169 0.724494319 0.775958473 0.640062211 0.58985596 0.983677741 0.625664898 0.755120571 0.693354257 1 18.62522909 -1.944414486 2.578358715 1.196018285 0.727259 0.38830329 0.10896477 16170996.21 7931471.117 19019058.1 0.023720609 0.011365421 1.944414486 -0.468759284 VYYS(ph)PPVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;VYYS(1)PPVAR;VYYS(1)PPVAR;VYYS(1)PPVAR;VYYS(1)PPVAR 117.02 0.0012787 1167273000 1871290 1875050 1899530 2079380 1943200 1847020 2123280 2040310 2300400 TRUE FALSE 1782837.83 2066119.727 1986625.329 1870356.772 2282093.465 1783057.234 1799334.639 1861649.64 2657134.283 0.670962639 0.777574449 0.747657106 0.703899981 0.858855151 0.67104521 0.677171135 0.700623093 1 21.34143971 -0.940425888 4.555970628 1.00000384 0.725220078 0.687413196 0.058070626 6681.312153 34190889.52 341.3663117 0.013179628 0.114702824 0.940425888 -0.274783762 VYYTAGYNS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 VYYTAGYNS(1)PVK 163.8 6.19E-05 71883000 107320 107710 104980 133950 88477 117470 126470 142190 100870 TRUE FALSE 102247.1963 118685.7715 109793.4368 120485.0915 103907.3608 113401.9844 107174.6787 129739.0898 116512.4044 0.877564898 1.018653525 0.942332599 1.034096688 0.89181372 0.973303959 0.919856381 1.113521693 1 16.83012403 1.246644185 24.99997128 1.056760858 0.952873096 0.379321715 0.056160625 154.193836 476884.3559 0.034851262 0.012244854 17.6459151 -1.246644185 -0.103887762 WAASLENLLEDPEGVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAASLENLLEDPEGVKR 17 1 O43665;O43665-2;O43665-1 O43665 RGS10 Regulator of G-protein signaling 10 0 144.33 8.27E-07 28330000 35063 34757 30565 39141 28005 37897 41631 37587 30973 FALSE TRUE 33405.64148 38298.77782 31966.43548 35206.47232 32889.06313 36584.61739 35279.42634 34295.68302 35776.13465 0.933740937 1.070511898 0.893512835 0.98407703 0.919301748 1.022598381 0.986116211 0.958619017 1 15.1267099 WAEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAEALR 6 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 105.42 0.076756 366590000 442100 326890 235350 262840 443010 299370 465350 409510 445440 FALSE TRUE 421202.8092 360200.4626 246141.0303 236418.8238 520270.8037 289002.7418 394352.3108 373651.1335 514516.5602 0.818638003 0.700075548 0.478392824 0.459497015 1.011183787 0.561697648 0.766452125 0.726217895 1 18.97285799 0.16036612 0.662968047 1.011344336 0.678855838 0.275307692 0.162169654 4.597348526 2.531825995 0.283292573 0.058989188 1.446658823 -0.16036612 -0.332488498 WAEKLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WAEKLDR 7 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 86.011 0.018596 1135010000 2459800 1525120 2445700 2529200 2589300 2536100 3626200 2989200 3383400 FALSE TRUE 2343530.129 1680531.462 2557837.764 2274960.011 3040873.1 2448274.221 3072956.59 2727449.801 3908080.392 0.599662723 0.430014558 0.654499782 0.582116994 0.778098912 0.626464652 0.786308438 0.697900127 1 21.89802871 0.881624129 0.180988406 1.173505152 0.393508002 0.719703619 0.080010915 2.397477676 0.304430534 0.663111518 0.408575237 7.614197345 -0.881624129 -0.77999715 WAEQYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WAEQYLK 7 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 103.92 0.019235 87293000 211520 146849 122128 134120 182419 138119 221708 176851 181653 FALSE TRUE 201521.8688 161813.0801 127727.6896 120638.0028 214232.8158 133335.9044 187882.3727 161364.9889 209822.8195 0.960438284 0.771189142 0.608740698 0.574951776 1.021017716 0.635469034 0.895433457 0.769053572 1 17.67881206 0.130348897 0.721228638 1.005693844 0.778445455 0.181005289 0.147670873 6.732024421 4.11812475 0.247936769 0.050623673 1.350047027 -0.130348897 -0.227248389 WAEYHADIYDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WAEYHADIYDK 11 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;; 142.08 3.78E-05 1256530000 3771650 2934590 2542750 3435030 2508740 2922180 3900620 3614240 2134930 FALSE TRUE 3593371.579 3233628.057 2659337.603 3089734.258 2946263.462 2820984.174 3305508.779 3297757.985 2466004.041 1.457163703 1.311282546 1.078399532 1.252931547 1.194752082 1.143949534 1.34043121 1.337288152 1 21.23374373 4.153597214 2.787259597 1.213098733 1.431159532 0.370913404 0.107955983 0.265339062 4.04735966 0.026395032 0.073708557 14242.86027 -4.153597214 0.218060799 WAEYHADIYDKVSGDMQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAEYHADIYDKVSGDMQK 18 1 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 158.15 2.78E-11 106600000 131900 94222 114220 113840 97192 128450 157700 142720 97938 FALSE TRUE 125665.3484 103823.3289 119457.1 102396.5869 114142.254 124001.7443 133639.9686 130222.6802 113125.7248 1.110846791 0.917769403 1.055967598 0.9051574 1.008985836 1.096140992 1.18134022 1.151132339 1 16.78756751 2.178084895 3.836499378 1.132108408 0.996212199 0.320301393 0.075727933 0.20858991 6.205898933 0.027678149 0.020127298 150.6901605 -2.178084895 -0.135896209 WAFQGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAFQGER 7 0 F5H8H2;Q03426;F5H092;A0A1B0GWC2;A0A1B0GWF3 F5H8H2 MVK Mevalonate kinase 0 82.716 0.055217 104600000 208520 158360 141640 163390 203750 159870 221880 175160 191730 FALSE TRUE 198663.6728 174497.064 148134.3341 146965.7268 239283.9355 154333.6618 188028.1309 159822.0618 221462.5092 0.897053292 0.787930493 0.668891248 0.663614475 1.080471527 0.696883921 0.849029172 0.721666446 1 17.75670296 WAGVLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WAGVLSR 7 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 101.21 0.021463 151146000 550240 449580 379930 384470 564360 387920 612830 449260 523290 FALSE TRUE 524231.2457 495392.7131 397350.1663 345822.3452 662784.2053 374486.2331 519331.5281 409920.4127 604439.1406 0.867301951 0.819590724 0.657386558 0.572137577 1.096527608 0.619559866 0.859195729 0.678183104 1 19.20523756 WAHDKFS(ph)GEEGEIEDDES(ph)GTENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.861)GT(0.139)ENR;WAHDKFS(1)GEEGEIEDDES(0.922)GT(0.078)ENR 211.37 2.83E-25 438000000 776040 952380 654680 930350 465343 920430 715720 791980 324703 TRUE FALSE 739358.1272 1049428.605 684697.7256 836829.4505 546498.6719 888555.2783 606523.7689 722630.0326 375056.2829 1.971325801 2.798056326 1.825586603 2.231210324 1.457111097 2.369125166 1.617154002 1.926724243 1 18.51674758 -0.847948499 0.162597268 9.10E-10 2.590013608 0.474958581 0.360906816 17.1413787 0.637595515 9.48478134 1.823163955 0.141922581 0.847948499 2.590013607 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.951)GT(0.049)ENREEK 150.31 7.43E-08 319360000 225260 275090 211510 278840 122670 292120 246880 324920 100280 TRUE FALSE 214612.4062 303121.9838 221207.9427 250810.4734 144063.6092 282003.8112 209213.9217 296468.2823 115830.9102 1.852807733 2.616935178 1.909748808 2.16531557 1.243740629 2.434616205 1.806201137 2.55949195 1 16.82166077 3.59952258 18.12132037 1.92039557 2.239752002 0.074037089 0.510232422 6.060068787 873.0495493 0.120055017 0.185988287 3976.697718 -3.59952258 0.319356432 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.98)GT(0.02)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.971)GT(0.029)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.978)GT(0.022)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.845)GT(0.155)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.523)GT(0.461)ENREEKDNIQPT(0.008)T(0.008)E 267.36 5.07E-60 4199360000 2217530 1799525 2056040 2250560 1142411 2370410 2590180 2536260 1076405 TRUE FALSE 2112711.752 1982898.643 2150311.468 2024329.433 1341647.117 2288322.107 2195000.469 2314171.629 1243328.39 1.699238728 1.594830987 1.729479907 1.628153471 1.079077038 1.840480862 1.765422946 1.861271445 1 20.24577596 2.993064293 24.86769681 1.576013327 1.663203315 0.038902286 0.293691867 1710.316327 6132304.971 0.082745287 0.095336659 984.1567907 -2.993064293 0.087189988 WAHDKFS(ph)GEEGEIEDDESGT(ph)ENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.293)GT(0.707)ENR 162.81 3.71E-11 200460000 437850 581870 394020 527610 304740 555710 465650 481130 191830 TRUE FALSE 417153.6982 641163.2145 412086.2067 474573.6404 357886.5595 536465.6234 394606.5403 438999.7066 221578.0167 1.882649301 2.893622861 1.859779291 2.141790271 1.61517178 2.421113933 1.780892104 1.981242152 1 17.75745523 -1.419476834 0.216084445 2.74E-15 2.38664316 0.482738731 0.356065951 18.01763487 0.734551599 10.78563747 0.783627699 0.038064766 1.419476834 2.38664316 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;WAHDKFS(1)GEEGEIEDDESGTENR 287.53 6.60E-53 1780088000 1734037 1951113 1394205 2023254 1066615 1913434 1618981 1711945 768804 TRUE FALSE 1652072.508 2149933.633 1458130.678 1819872.664 1252632.318 1847171.301 1371975.714 1562038.02 888026.1978 1.860387128 2.421025008 1.64199061 2.049345693 1.410580365 2.080086494 1.544972116 1.75899993 1 19.76024271 -1.265961549 0.149419035 9.32E-12 2.338392248 0.521266673 0.272157382 21.91910338 0.619452237 10.08528913 1.654008224 0.054204888 1.265961549 2.338392248 WAHDKFS(ph)GEEGEIEDDESGTENREEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEK 163.19 7.92E-12 37146000 34345 38589 31365 37671 20553 42289 36001 37437 20388 TRUE FALSE 32721.57992 42521.26297 32803.11627 33884.23951 24137.43669 40824.52133 30508.38625 34158.81781 23549.66691 1.389471029 1.805599337 1.392933344 1.438841561 1.02495873 1.733549841 1.2954912 1.450501102 1 14.52341903 -3.521305953 0.143986113 1.55E-17 1.640481485 0.294331317 0.215272117 96.45501086 1.259158553 30.27293971 1.233020092 0.000301088 3.521305953 1.640481485 WAHDKFS(ph)GEEGEIEDDESGTENREEKDNIQPTTE ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(0.996)GEEGEIEDDES(0.003)GT(0.001)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE 210.21 5.92E-27 962567000 301614 231642 267806 299243 164667 295932 338403 305254 145717 TRUE FALSE 287357.304 255246.5832 280085.17 269162.5251 193384.8727 285683.8006 286773.4072 278524.3415 168314.0481 1.707268687 1.516490073 1.664062941 1.599168507 1.148952656 1.697325944 1.703799596 1.65478963 1 17.36079607 -1.094194032 4.251127971 0.999929191 1.590479269 0.55209215 0.165979754 9911514902 38476528850 14761566.1 0.038884602 0.08050187 1.094194032 0.590550078 WAHDKFSGEEGEIEDDES(ph)GTENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.959)GT(0.041)ENR;WAHDKFSGEEGEIEDDES(0.999)GT(0.001)ENR 153.27 3.18E-08 212705000 312690 286860 270690 336080 201390 307670 281090 307350 169396 TRUE FALSE 297909.7634 316091.3601 283101.4042 302296.5999 236512.3522 297015.3108 238204.5579 280436.8046 195665.0665 1.522549573 1.61547161 1.446867391 1.544969704 1.208761259 1.517978227 1.217409741 1.433249223 1 17.57802668 -2.472129906 0.089544724 2.96E-16 1.924748427 0.640997293 0.114495222 58.7437322 0.650230326 14.71566247 2.919492455 0.003371864 2.472129906 1.924748427 WAHDKFSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.934)GT(0.066)ENREEKDNIQPTTE;WAHDKFSGEEGEIEDDES(0.833)GT(0.167)ENREEKDNIQPTTE;WAHDKFSGEEGEIEDDES(0.681)GT(0.319)ENREEKDNIQPTTE;WAHDKFSGEEGEIEDDES(0.975)GT(0.025)ENREEKDNIQPTTE 278.02 3.95E-73 1342750000 1437740 847720 1340060 1254920 867070 1411630 1806020 1527880 772650 TRUE FALSE 1369780.88 934103.6318 1401503.077 1128773.057 1018286.733 1362744.899 1530478.479 1394090.727 892468.6159 1.534822463 1.046651518 1.570366791 1.264776192 1.140977638 1.526938735 1.714882128 1.562061346 1 19.76744191 2.163245747 11.40405064 1.533480095 1.305402647 0.028604109 0.244229838 0.901409496 132.1871426 0.083503517 0.061674989 145.6282892 -2.163245747 -0.228077448 WALHILAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WALHILAR 8 0 O95373 O95373 IPO7 Importin-7 0 117.93 0.0044931 0 121430 89572 48800 66576 116550 64750 128450 99003 96526 FALSE TRUE 115690.2446 98699.48863 51037.52827 59883.65399 136876.2831 62507.69126 108852.5934 90333.77247 111494.7591 1.037629441 0.885238817 0.457757196 0.537098376 1.227647687 0.560633448 0.976302332 0.810206446 1 16.76661637 1.61323663 25 0.919942947 0.807442431 0.069432308 0.238868575 1.771690794 8211.051559 0.112795203 0.06025015 41.04276679 -1.61323663 -0.112500516 WANFHLENSGWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WANFHLENSGWQK 13 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 ; 131.13 0.00013401 519540000 652980 427410 396660 753020 487060 539330 712870 700520 466760 FALSE TRUE 622114.9295 470963.5649 414847.2534 677324.999 572003.1098 520652.8669 604108.5887 639178.7551 539142.7569 1.15389648 0.873541486 0.769457158 1.256299914 1.060949261 0.96570502 1.120498386 1.185546401 1 19.0403078 3.233659699 24.99999977 1.094443139 0.951364495 0.275017803 0.125590675 182.4246126 930563.4251 0.035875755 0.044174541 1712.614823 -3.233659699 -0.143078644 WASLADSYS(ph)DPGLTEDGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 WASLADS(0.114)Y(0.007)S(0.878)DPGLT(0.002)EDGLGR 93.754 0.0015371 13176000 49934 40190 42322 47485 45342 46929 50837 46360 61214 TRUE FALSE 47573.71878 44285.40669 44262.50556 42711.71758 53249.63044 45303.83696 43080.88196 42300.47263 70706.75448 0.672831318 0.626324981 0.626001093 0.604068422 0.753105284 0.64072856 0.609289484 0.598252217 1 16.10956042 -1.193820511 4.131527757 1.000167252 0.641220361 0.862583982 0.04499054 3499694652 682886825.5 5789770.395 0.010165809 0.063999929 1.193820511 -0.358946891 WATHGEPSPVNSHPQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WATHGEPSPVNSHPQR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 176.25 1.87E-09 686220000 334043 275302 319292 374182 387462 323062 375332 332871 288579 FALSE TRUE 318253.4494 303355.5868 333931.854 336568.5145 455035.2501 311874.2819 318068.21 303723.0506 333330.3575 0.954768872 0.910074885 1.001804506 1.009714558 1.365117938 0.935631199 0.954213149 0.911177286 1 18.34659319 3.560593091 3.579764544 1.029858947 0.932847825 0.088753917 0.126268499 0.58854208 14.23505555 0.035355954 0.05579789 3635.742282 -3.560593091 -0.097011122 WCDKSDEDDWSKPLPPSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 179.95 1.95E-14 673560000 845320 766370 750320 908880 524930 963880 1010150 945030 546730 FALSE TRUE 805363.3989 844463.9743 784722.9142 817517.6556 616477.6258 930500.5939 856033.0648 862278.1633 631514.0961 1.275289663 1.337205265 1.24260554 1.294535879 0.976189811 1.473443902 1.355524873 1.365413961 1 19.26845541 3.734060506 23.92304278 1.268955605 1.306247459 0.00749824 0.15632171 1471.330934 7821769.104 0.03928544 0.063334408 5420.764075 -3.734060506 0.037291853 WCNEHLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 99.799 0.010263 903910000 1782580 1341180 910380 999090 1425270 988490 1902320 1356090 1318010 FALSE TRUE 1698320.976 1477847.767 952121.8235 898659.5751 1673836.637 954258.3434 1612086.145 1237343.571 1522400.259 1.115554839 0.970735362 0.625408343 0.590291265 1.099472117 0.626811732 1.058910845 0.812758381 1 20.53791628 3.988974642 16.61939294 0.832655113 1.061253024 0.207202246 0.181901929 10.01063397 15096.36394 0.043692666 0.082681746 9749.327112 -3.988974642 0.228597911 WCNVQSTQDEFEELTMS(ph)QK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WCNVQSTQDEFEELTMSQK 19 0 D6RCP9;D6RFG8;P27707 D6RCP9 DCK Deoxycytidine kinase 1 WCNVQSTQDEFEELT(0.001)MS(0.999)QK 166.59 1.26E-11 52869000 62876 55241 58543 67094 44427 65092 69977 70725 51625 TRUE FALSE 59903.97609 60870.1207 61227.25446 60349.58365 52175.05473 62837.84772 59300.72343 64531.94406 59630.74134 1.004582112 1.020784235 1.026773323 1.012054895 0.874969077 1.053782769 0.994465641 1.082192551 1 15.86376865 -1.260524417 6.247176995 0.999999826 1.007249064 0.001933192 0.053787575 1.19E-07 1.40E-08 0.047425462 0.01117802 0.05488777 1.260524417 0.007249238 WDAADDIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDAADDIHR 9 0 Q9HD15;R4GMW4 Q9HD15 SRA1 Steroid receptor RNA activator 1 0 ; 125.48 0.0005004 132330000 170748 168703 149916 184119 159705 166129 186295 166562 153049 FALSE TRUE 162677.0804 185894.0275 156789.7969 165611.0083 187557.5014 160375.9111 157872.2762 151976.9483 176783.0573 0.920207417 1.051537576 0.88690511 0.936803622 1.060947267 0.907190505 0.893028318 0.859680507 1 17.43162049 2.054231346 24.9998905 0.904289231 0.973169972 0.152037612 0.063851218 132.6879716 61166.55365 0.022297246 0.016467605 113.3003747 -2.054231346 0.068880741 WDDPYYDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 WDDPYYDIAR 10 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;; 179.37 4.92E-06 1213050000 2900430 2649810 2345280 2801370 2635400 2288930 3042460 2769050 2674350 FALSE TRUE 2763332.422 2919828.652 2452813.408 2519770.965 3095012.926 2209663.78 2578276.848 2526577.302 3089074.539 0.894550257 0.945211459 0.79402856 0.815704164 1.001922384 0.715315785 0.834643779 0.817907522 1 21.55874325 2.237503382 24.99999203 0.824847784 0.890396263 0.052039727 0.090151353 61.60856343 1456774.21 0.030067263 0.023488461 172.7839436 -2.237503382 0.065548479 WDEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WDEAFR 6 0 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;; 150.07 0.024564 427902000 1096230 1145080 865930 1099380 960320 910040 1073880 986190 901570 FALSE TRUE 1044413.38 1261764.954 905633.747 988868.2337 1127799.504 878525.0866 910039.8828 899833.9755 1041380.871 1.002912008 1.211626782 0.869646997 0.949574033 1.082984656 0.843615541 0.873878048 0.864077688 1 19.99006638 3.728308692 24.95600779 0.920538767 1.107269398 0.423056431 0.087685662 540.9523948 1316827.15 0.022929259 0.03595042 5349.444576 -3.728308692 0.186730631 WDEMNILATYHPADKDYGLMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDEMNILATYHPADKDYGLMK 21 1 P41236;E7EMN6;E7EUI7 P41236 PPP1R2 Protein phosphatase inhibitor 2 0 141.08 9.56E-08 188010000 437510 390800 393250 445940 340100 412420 499030 450430 323790 FALSE TRUE 416829.7694 430622.9643 411280.9015 401113.264 399413.3323 398137.792 422893.8082 410987.9613 374001.6995 1.114513035 1.151393068 1.099676558 1.072490485 1.067945234 1.064534713 1.130726969 1.098893299 1 18.5126853 -5 0.159016447 0.629961619 1.132242052 0.562170546 0.027664663 107.2226662 0.982805666 12.63179186 0.129996564 1.00E-05 5 0.502280433 WDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDEQTSNTKGDDDEESDEEAVKK 23 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 WDEQTSNTKGDDDEES(1)DEEAVKK;WDEQTSNTKGDDDEES(1)DEEAVKK 187.45 1.27E-17 246810000 283790 261830 207055 279160 102949 285940 249740 304190 92444 TRUE FALSE 270375.8091 288510.7747 216548.6766 251098.3064 120903.273 276037.8261 211637.5762 277553.511 106779.7434 2.532088958 2.701924218 2.027993978 2.351553754 1.132267874 2.585114155 1.982001169 2.599308653 1 16.70427846 -1.549682185 0.178580817 2.13E-29 2.638767558 0.377145918 0.475170537 31.15637119 0.964810785 18.0427083 1.748935972 0.028204462 1.549682185 2.638767558 WDET(ph)PGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDET(1)PGR;WDET(1)PGR;WDET(1)PGR;WDET(1)PGR;WDET(1)PGR 143.37 0.027119 3325140000 5206480 4503650 4829510 5395210 4784080 4817560 5438870 4926250 4622720 TRUE FALSE 4960380.009 4962577.055 5050947.811 4852873.241 5618422.037 4650726.689 4609070.49 4494881.434 5339587.808 0.928981822 0.929393285 0.945943393 0.908847914 1.052220179 0.870989832 0.863188444 0.841803075 1 22.34829695 WDET(ph)PKTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDETPKTER 9 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDET(1)PKTER 105.17 0.0050786 100900000 325930 338730 287870 336970 294730 306380 343550 313890 314570 TRUE FALSE 310523.9348 373246.9721 301069.1242 303097.1354 346130.8187 295769.9838 291135.1378 286404.1276 363351.909 0.854609339 1.027232726 0.828588255 0.834169652 0.952604927 0.81400421 0.801248406 0.788227942 1 18.47100796 3.707031867 24.87260244 0.848747381 0.940921076 0.142629767 0.079097628 850.9255952 671283.7786 0.019732804 0.030573291 5093.682458 -3.707031867 0.092173695 WDETPASQMGGST(ph)PVLTPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDETPASQMGGSTPVLTPGK 20 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDETPASQMGGS(0.037)T(0.963)PVLTPGK 135.09 5.13E-07 0 39510 44180 35477 52866 33084 42695 42199 42260 42030 TRUE FALSE 37642.4406 48681.99223 37103.65554 47551.80924 38853.83913 41216.46144 35760.76751 38559.49037 48547.79774 0.775368654 1.002764173 0.764270621 0.979484373 0.800321352 0.848987253 0.736609469 0.794258281 1 15.56711823 WDETPGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 120.52 0.010558 178303000 564330 487050 426410 599500 540040 478530 579070 535060 568650 FALSE TRUE 537655.2393 536680.9487 445961.3203 539237.121 634222.805 461958.3861 490722.2361 488207.3099 656833.3377 0.818556563 0.817073248 0.678956586 0.820964909 0.965576454 0.703311418 0.74710312 0.743274255 1 19.32516783 2.620187371 0.011765493 1.598732879 2.97E-06 0.117260444 0.097794717 6121.387375 30.86803391 2035.609147 2155.919725 417.0492752 -2.620187371 -1.598729913 WDGS(ph)EEDEDNSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK 375.07 1.03E-86 8554120000 12238489 10345865 10882509 12134292 6517642 12935231 12854520 11975257 6615274 TRUE FALSE 11659999.88 11400120.41 11381482.8 10914529.91 7654316.701 12487280.71 10893326.88 10926640.01 7641136.906 1.525950918 1.491940342 1.489501228 1.428390834 1.001724847 1.634217638 1.425615981 1.429975689 1 22.86535588 -3.131052883 0.305363972 5.20E-24 1.46530853 0.401521549 0.164079038 79.6486812 2.078046843 51.4272195 0.154452675 0.000739515 3.131052883 1.46530853 WDGS(ph)EEDEDNSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WDGSEEDEDNSKK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK 198.95 7.46E-08 1122070000 1073170 977940 940400 1109720 428555 1191780 1086620 1151860 393924 TRUE FALSE 1022443.381 1077593.198 983518.2702 998168.8373 503294.8563 1150508.36 920836.1619 1050997.032 455011.722 2.247070419 2.368275685 2.161522929 2.193721148 1.106114045 2.52852466 2.023763603 2.309824079 1 18.79554419 2.976150142 24.90462147 1.902835552 2.267801394 0.160732476 0.476497322 1484.4767 1550129.409 0.133030803 0.141848238 946.5643467 -2.976150142 0.364965843 WDGVPFILR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDGVPFILR 9 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 141.52 0.00024782 694360000 2172900 1853470 1158260 1515150 2010320 1234450 2107310 1593710 1663660 FALSE TRUE 2070191.323 2042340.7 1211367.367 1362844.243 2360919.172 1191700.687 1785801.156 1454156.304 1921651.896 1.077297781 1.062804717 0.63037815 0.709204537 1.22858837 0.620143893 0.929305229 0.75672202 1 20.87391559 3.873908478 11.14009127 0.839050278 1.071821466 0.216138768 0.182855844 0.604405938 51.3300765 0.042859968 0.077316593 7480.118501 -3.873908478 0.232771188 WDHSLAWDVPAAEDFPNGS(ph)GSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 WDHS(0.001)LAWDVPAAEDFPNGS(0.468)GS(0.468)PS(0.052)AAIY(0.007)NIDT(0.003)S(0.001)S(0.001)ES(0.001)PDHY(0.001)LVDHTLDGR;WDHS(0.001)LAWDVPAAEDFPNGS(0.39)GS(0.39)PS(0.17)AAIY(0.034)NIDT(0.002)S(0.002)S(0.002)ES(0.002)PDHY(0.002)LVDHT(0.002)LDGR;WDHSLAWDVPAAEDFPNGS(0.202)GS(0.202)PS(0.199)AAIY(0.054)NIDT(0.057)S(0.057)S(0.057)ES(0.057)PDHY(0.054)LVDHT(0.06)LDGR 47.018 0.0077152 508768000 40215.2 35415.8 36647.8 42355 44439.9 36053.3 50310.6 43152.9 18066.1 TRUE FALSE 38314.30719 39024.71028 38328.13788 38097.39493 52190.20449 34804.76518 42634.79395 39374.20331 20867.69852 1.836058114 1.870101307 1.836720894 1.825663472 2.501004337 1.667877516 2.043099957 1.886849346 1 14.34898388 0.937658284 20.76177627 0.999999999 1.93187651 0.638664042 0.220933813 2062.08638 686742.4187 0.192951462 0.048237865 8.662799923 -0.937658284 0.931876511 WDHSLAWDVPAAEDFPNGSGS(ph)PSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Trastuzumab_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(0.061)GS(0.914)PS(0.025)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.102)GS(0.898)PS(0.001)AAIYNIDTSSESPDHYLVDHTLDGR 305.72 2.85E-103 551100000 173608 138451 171477 199729 213229 164807 223608 179466 25280 TRUE FALSE 165401.8939 152559.3143 179339.3901 179651.8615 250416.0701 159099.6923 189492.4928 163751.0056 29200.29329 5.664391527 5.224581575 6.141698246 6.152399214 8.575806675 5.448564872 6.48940375 5.607854826 1 14.83369524 0.801302062 4.668988496 1.00002398 6.149246079 0.759678382 0.91817828 1.539754402 35.83337113 0.878688248 0.222707417 6.328518623 -0.801302062 5.149222099 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 365.66 3.77E-182 17567078000 1583000 1293092.1 1589161 1803835 1934901 1472911.5 2044179.6 1710719.6 113400 FALSE TRUE 1508174.727 1424859.655 1662025.604 1622510.079 2272347.122 1421904.205 1732302.458 1560919.923 130985.4928 11.51405926 10.87799591 12.68862351 12.38694487 17.34808239 10.85543273 13.22514746 11.91673894 1 16.99904751 0.929391653 17.69957365 0.999999987 12.53051301 0.798337534 1.83505942 331.4556202 83087.88475 1.72126431 0.430324563 8.499466242 -0.929391653 11.53051302 WDKYTIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDKYTIR 7 1 Q14320;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 97.798 0.02251 0 438650 328980 303330 318330 375160 341870 469600 402030 385820 FALSE TRUE 417915.8838 362503.436 317237.9805 286330.8636 440587.7852 330030.9562 397953.8952 366826.1219 445650.9951 0.937764952 0.813424496 0.711852961 0.642500223 0.988638621 0.740559226 0.892972078 0.823124207 1 18.7655548 0.266168053 0.706471146 1.003837958 0.81448178 0.237707801 0.103451436 4.193813701 2.791192925 0.141658224 0.036330785 1.8457295 -0.266168053 -0.189356178 WDLDRFHGTSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WDLDRFHGTSSR 12 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;; 131.13 0.00012267 296818000 553500 182959 540680 291825 830150 374812 785770 465080 942950 FALSE TRUE 527337.1519 201602.7301 565470.7128 262490.1966 974927.8972 361832.1665 665886.3548 424355.1297 1089177.87 0.484160729 0.185096242 0.519172055 0.240998467 0.895104394 0.332206682 0.611366034 0.389610496 1 20.05480814 -4.999999992 0.15613203 3.034058334 0.286964941 0.422856311 0.199870049 114.5068939 1.040563266 72.0718765 0.80239342 1.00E-05 4.999999992 -2.747093393 WDNGPDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDNGPDGR 8 0 Q14166;V9GY16 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 76.221 0.065228 0 392970 378330 322200 360250 372140 313310 359150 346070 413180 FALSE TRUE 374395.0869 416882.2571 336973.1887 324036.9856 437041.0982 302459.9961 304355.0713 315766.2762 477253.8442 0.784477886 0.873502146 0.706066997 0.678961499 0.915741389 0.63375078 0.637721571 0.661631708 1 18.86439729 3.729487874 24.28762889 0.724663644 0.828990017 0.045261627 0.124058722 838.7509733 2245328.611 0.030574663 0.048154484 5363.988943 -3.729487874 0.104326373 WDNGPDGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDNGPDGRR 9 1 Q14166;V9GY16 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 134.26 0.0004071 600610000 428950 226069 313470 289790 451030 320210 517740 395350 536780 FALSE TRUE 408674.3836 249105.6881 327842.9096 260659.7586 529689.4892 309121.0474 438749.2541 360731.0581 620021.1009 0.659129799 0.401769694 0.528760891 0.420404658 0.85430881 0.498565366 0.707636004 0.581804486 1 19.24195779 -1.376992598 0.248866836 1.346411898 0.498335373 0.511613 0.131759847 15.38413215 0.757929952 3.605280892 0.198906979 0.041976614 1.376992598 -0.848076525 WDPTANEDPEWILVEKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDPTANEDPEWILVEKDR 18 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 141.86 1.07E-07 78280000 158040 89070 150170 131040 128100 137350 197010 158610 153360 FALSE TRUE 150569.7624 98146.33426 157055.443 117867.6102 150440.5994 132593.5351 166952.5062 144721.2676 177142.2855 0.849993337 0.554053675 0.886606168 0.665383818 0.849264189 0.748514307 0.942476866 0.816977534 1 17.43454911 1.592163246 0.544371391 0.989787826 0.71600612 0.344566897 0.105506028 0.745505212 0.52189812 0.095141626 0.055395246 39.09878361 -1.592163246 -0.273781706 WDQSTFLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDQSTFLGR 9 0 S4R3N9;A0A1P0AYU5;Q9BWM7 S4R3N9 SFXN3 Sideroflexin-3 0 ; 102.62 0.0082699 137144000 222610 139889 174682 253230 256240 143109 236460 177854 295650 FALSE TRUE 212087.6665 154143.8481 182691.3425 227774.8393 300928.1749 138153.0994 200383.6841 162280.1609 341497.892 0.621051173 0.451375694 0.53497063 0.666987541 0.881200681 0.404550373 0.586778685 0.475201062 1 18.38151715 -1.417230631 4.041213015 1.001886134 0.572764113 0.496481195 0.133548629 21553012.5 7561639.476 359137.2735 0.029992695 0.03826215 1.417230631 -0.429122021 WDQTADQTPGAT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDQTADQTPGAT(1)PK;WDQTADQT(0.006)PGAT(0.994)PK;WDQTADQTPGAT(1)PK 283.88 1.93E-32 357810000 1227110 1235040 1164420 1341320 679641 1339890 1282010 1309010 771910 TRUE FALSE 1169106.942 1360891.98 1217809.809 1206487.965 798170.1752 1293489.273 1086415.829 1194386.145 891613.8604 1.311225626 1.526324388 1.365848898 1.353150751 0.895197137 1.450728091 1.218482436 1.339577813 1 19.76605952 -4.58792237 0.07381687 5.04E-12 1.687845837 0.270723051 0.165233276 321.2335432 1.832471615 55.97345866 7.180330411 2.58E-05 4.58792237 1.687845837 WDS(ph)CDSLNGLDPSEKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDSCDSLNGLDPSEKEK 17 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 WDS(0.997)CDS(0.003)LNGLDPSEKEK 71.434 0.018484 157030000 113650 102830 111180 127880 89250 120540 138600 129400 79903 TRUE FALSE 108277.9897 113308.4939 116277.713 115025.2594 104815.1717 116365.6696 117454.0244 118069.05 92293.94915 1.173186224 1.227691468 1.259862798 1.246292531 1.135666777 1.260815803 1.272608069 1.279271838 1 16.49394845 -1.784400114 6.499614067 0.990837947 1.230838871 0.721394514 0.045291279 0.006231531 0.000206707 0.045446303 0.01049637 0.016428575 1.784400114 0.240000924 WDS(ph)YDNFSGHRDDGMEEVVGHTQGPLDGSLYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDSYDNFSGHRDDGMEEVVGHTQGPLDGSLYAK 33 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1 E9PGF5 TNS1 Tensin-1 1 WDS(0.944)YDNFS(0.055)GHRDDGMEEVVGHTQGPLDGSLYAK 94.138 0.00012196 63490000 57963 56001 58785 67516 103810 55943 72929 64691 111990 TRUE FALSE 55223.20386 61707.56557 61480.3504 60729.16341 121914.4311 54005.67988 61802.34162 59026.31309 129356.8372 0.426905953 0.47703366 0.475277161 0.46947007 0.942466079 0.417493818 0.477766332 0.456306094 1 16.98099678 -2.233110258 2.170945129 2.565979719 0.511692773 0.49542428 0.152809507 9461827.282 1594597.449 72728697.39 0.037402276 0.005846416 2.233110258 -2.054286945 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 WDS(0.997)YENLS(0.003)ADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(0.994)YENLS(0.006)ADGEVLHTQGPVDGSLYAK 262.43 2.51E-53 745480000 601050 587140 474152 663538 353766 599364 563565 606351 291362 TRUE FALSE 572639.5577 646970.2335 495892.3382 596837.8996 415462.6784 578607.8744 477582.8087 553255.692 336544.9309 1.701524834 1.922388882 1.473480337 1.773427096 1.234493942 1.71925892 1.419075924 1.643928169 1 18.3604396 -2.258966326 0.121717452 3.29E-12 2.015208674 0.530649594 0.187429756 44.38151678 0.712833867 14.58829192 1.890521352 0.005508504 2.258966326 2.015208674 WDSNVIETFDIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WDSNVIETFDIAR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 158.4 2.51E-06 0 128006 134535 98457 120385 107862 101026 118343 120714 107906 FALSE TRUE 121955.4101 148244.2695 102971.3508 108283.6711 126673.0986 97527.44429 100287.6018 110143.6422 124639.5114 0.978465085 1.189384232 0.826153358 0.868774836 1.016315751 0.782476144 0.804621269 0.883697641 1 16.92740196 3.728245013 24.99845855 0.869864417 1.08392466 0.451678943 0.091057555 492.4458978 1193376.056 0.023306537 0.036543202 5348.660263 -3.728245013 0.214060243 WDVLIQQATQCLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDVLIQQATQCLNR 14 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 115.14 0.0010166 32350000 82841 68887 76513 68437 90121 64269 93646 63892 86679 FALSE TRUE 78925.27011 75906.66362 80021.19673 61557.58274 105838.0739 62043.34841 79358.58277 58297.27777 100120.7366 0.788300933 0.75815127 0.799246983 0.614833498 1.057104426 0.619685297 0.792628834 0.582269765 1 16.61138129 4.696735797 3.729269505 0.768338664 0.789557804 0 0.155986521 4.275429396 104.1551237 0.032503982 0.22934337 49743.43791 -4.696735797 0.02121914 WDYLTQVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WDYLTQVEK 9 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 182.65 0.00010721 117730000 255760 230420 194200 255910 179760 239980 289410 270870 208540 FALSE TRUE 243670.7317 253900.06 203104.2621 230185.4406 211110.0871 231669.4324 245255.1891 247151.1868 240879.3181 1.011588432 1.054055043 0.8431785 0.955604833 0.876414334 0.961765561 1.018166238 1.02603739 1 17.877951 -0.694184859 7.532062324 1 0.974695406 0.01412416 0.066392985 0 0 0.066464841 0.015665913 0.202215826 0.694184859 -0.025304594 WEAERDDWLHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WEAERDDWLHNR 12 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ;;;; 138.42 4.49E-05 716369000 792441 685405 804889 831161 1104771 738198 969661 769256 832669 FALSE TRUE 754983.8844 755248.5487 841793.9568 747611.1172 1297442.713 712634.0182 821721.4054 701895.8666 961795.0558 0.784973763 0.785248941 0.875232152 0.777308131 1.348980435 0.740941653 0.854362268 0.729776954 1 19.87536998 3.404513045 2.154343379 0.907828941 0.788355488 0.078009258 0.17688506 0.841671002 7.91137125 0.051305233 0.078533062 2538.125224 -3.404513045 -0.119473452 WEEEGFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WEEEGFR 7 0 Q3KQV9 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 138.24 0.0065249 498740000 808350 851230 675960 815820 763810 703320 786700 784360 801650 FALSE TRUE 770140.8975 937971.3048 706953.4346 733812.2236 897018.2222 678963.852 666674.4663 715677.2802 925965.7877 0.831716363 1.0129654 0.763476841 0.792483085 0.968737975 0.733249393 0.719977428 0.772898189 1 19.82059936 2.221917196 24.99365085 0.774638803 0.880292192 0.052555738 0.107823103 401.672423 603193.1169 0.037990534 0.028134235 166.6929362 -2.221917196 0.105653388 WEETRTPESQPDT(ph)PPGTPLVSQDEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WEETRTPESQPDTPPGTPLVSQDEKR 26 2 A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60;A0A0D9SEV0;M0R000;M0QYI1 A0A0D9SFD6 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 1 WEETRTPESQPDT(0.999)PPGT(0.001)PLVSQDEKR 120.37 0.0094893 827190000 284140 132640 274830 221620 247640 263550 414570 299240 323040 TRUE FALSE 270709.2653 146156.1668 287431.2273 199342.3365 290828.3376 254423.1974 351319.7324 273036.9592 373135.3933 0.72549876 0.391697409 0.770313491 0.534235937 0.77941772 0.681852223 0.941534196 0.731736962 1 18.50933969 1.972362404 0.602767172 0.961974951 0.567662557 0.462236431 0.12860647 0.578210289 0.425643171 0.107853708 0.067550816 93.83446969 -1.972362404 -0.394312394 WEFGTCQPLSDEKDLTQLFMFAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WEFGTCQPLSDEKDLTQLFMFAR 23 1 Q9UHL4;R4GMR2 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 175.77 1.04E-12 47474000 46203 49807 38435 49792 35701 38377 48800 48975 40929 FALSE TRUE 44019.07576 54882.38993 40197.28277 44786.81356 41927.2431 37047.99487 41354.66373 44686.48937 47276.06028 0.931107108 1.160891783 0.850267187 0.94734657 0.886859921 0.783652332 0.874748519 0.945224477 1 15.52882219 3.719840951 24.97764905 0.886955891 1.045999456 0.361332778 0.080545681 655.8893077 875153.3054 0.020238734 0.03141819 5246.152987 -3.719840951 0.159043565 WEFKHPQPFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WEFKHPQPFLR 11 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 103.43 0.0016433 474300000 899570 468600 627960 603630 941290 691200 1234850 851460 1060410 FALSE TRUE 857049.1089 516350.8728 656752.5871 542951.9656 1105450.678 667263.5707 1046450.953 776901.6485 1224852.967 0.69971591 0.421561515 0.536188918 0.4432793 0.902517043 0.544770343 0.854348221 0.634281558 1 20.22417715 1.208276932 0.414202446 1.003316873 0.523698265 0.42821937 0.148222749 0.963305511 0.477208604 0.181336558 0.110140431 16.15388295 -1.208276932 -0.479618608 WEGGDS(ph)NSDDYDLESDMSNGWDPNEMFK ddPTM_SK-BR-3_Trastuzumab_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(0.34)NS(0.34)DDY(0.317)DLES(0.002)DMS(0.002)NGWDPNEMFK 54.441 0.038427 23051000 14610 11050 12232 16864 9398.5 12435 16686 17647 12494 TRUE FALSE 13919.41425 12176.00756 12792.8493 15168.79868 11037.59542 12004.37283 14140.24424 16101.73513 14431.50571 0.964515729 0.84371013 0.886452845 1.051089123 0.764826321 0.831817073 0.979817666 1.115734938 1 13.81693421 1.505981945 4.763778262 1.056707015 0.892336626 0.423531965 0.081414912 0.152220724 7.565287984 0.047389024 0.019920192 32.06136033 -1.505981945 -0.164370389 WENPGLGAESHTDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WENPGLGAESHTDSLR 16 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 145.8 1.19E-06 141910000 154160 142360 157160 189800 275990 126240 178390 113460 287120 FALSE TRUE 146873.1623 156866.6458 164365.9415 170720.9434 324122.5686 121868.2771 151173.3291 103524.8409 331645.1032 0.442862448 0.472995513 0.495607925 0.514769981 0.977317517 0.367465933 0.455828618 0.312155494 1 18.3392807 -1.273414677 3.476397554 1.00142634 0.502782989 0.431789849 0.178484428 42319272.19 61977392.74 654901.5847 0.040750822 0.05328259 1.273414677 -0.498643352 WES(ph)QQDVSQTTVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WESQQDVSQTTVSR 14 0 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(0.997)QQDVS(0.003)QTTVSR;WES(1)QQDVSQTTVSR 328.56 2.47E-68 958610000 1148230 912560 1000030 1112810 847020 1006680 1159540 1053320 865540 TRUE FALSE 1093955.443 1005550.901 1045882.365 1000948.225 994740.0198 971818.4192 982630.8766 961085.7168 999763.5226 1.0942142 1.005788748 1.046129751 1.001184982 0.994975309 0.972048287 0.982863302 0.961313046 1 19.93122736 7.73026024 0.343523965 0.97454704 2.082506344 0.775812262 0.018171229 20.20575922 0.341741573 0.014489914 13.98606818 53735369.51 -7.73026024 1.107959304 WESGSLLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WESGSLLER 9 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 121.67 0.0014129 249610000 347220 309410 261410 358980 317880 306720 341840 319060 325760 FALSE TRUE 330807.5987 340939.2308 273395.9071 322894.6484 373318.1714 296098.2095 289686.0297 291121.415 376277.197 0.879159304 0.906085284 0.726581119 0.858129727 0.992136048 0.786915104 0.769873997 0.773688699 1 18.52143634 WEWLVNQHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 168.8 5.90E-05 666570000 826040 769570 528400 778400 684810 630670 753920 691530 518970 FALSE TRUE 786994.7263 847990.0579 552627.6627 700153.7531 804240.6472 608829.7398 638895.6573 630975.9672 599449.2171 1.312863048 1.41461534 0.921892375 1.167995108 1.341632659 1.015648569 1.065804474 1.052592862 1 19.19327801 5.209538062 0.257363754 0.990566857 1.806867353 0.331610911 0.134169268 11.86748656 0.548347941 0.177580597 3.205334713 162008.5974 -5.209538062 0.816300496 WFCHIQHYPGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WFCHIQHYPGIR 12 0 O43324 O43324 EEF1E1 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 94.363 0.0038467 532780000 443790 439810 358540 456620 466990 403080 460900 419220 164838 FALSE TRUE 422812.9262 484627.139 374979.4136 410719.6901 548432.9081 389121.2385 390581.24 382510.8744 190400.2352 2.220653382 2.54530746 1.969427261 2.157138565 2.88042138 2.04370146 2.051369525 2.008983203 1 17.53867573 0.537933668 0.751132542 0.987563219 2.334869713 0.704838837 0.260298806 0.80885182 0.756090166 0.261586303 0.087417631 3.450910275 -0.537933668 1.347306494 WFDFPFTR ddPTM_SK-BR-3_Trastuzumab_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 ; 119.21 0.0040428 61076000 345720 342890 299340 381270 335420 268920 366530 354590 320170 FALSE TRUE 329378.5008 377830.8808 313065.0351 342944.0152 393917.1418 259607.233 310609.1167 323540.2198 369820.3284 0.89064466 1.02166066 0.846532792 0.927326025 1.065158163 0.701982052 0.83989195 0.874857857 1 18.496465 2.243970733 24.99994681 0.835779753 0.948822571 0.193992588 0.09402335 172.7068051 798074.0494 0.030411411 0.024756453 175.3762311 -2.243970733 0.113042818 WFHPNITGVEAENLLLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WFHPNITGVEAENLLLTR 18 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 242.98 4.58E-24 286750000 589820 524340 509040 630080 644230 562450 655360 609050 584540 FALSE TRUE 561940.3775 577770.8421 532379.9875 566743.1613 756583.508 542972.2155 555372.7955 555718.3532 675187.4778 0.832273103 0.855719132 0.788492093 0.839386363 1.120553228 0.804179925 0.822546054 0.823057849 1 19.36492862 WFLTCINQPQFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WFLTCINQPQFR 12 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 222 6.02E-11 1084170000 606100 502790 481730 561300 596810 498130 677720 587280 573430 FALSE TRUE 577450.8542 554024.8726 503817.797 504877.0576 700893.475 480879.6332 574321.3668 535854.6498 662354.5957 0.871815275 0.836447541 0.760646639 0.762245874 1.058184664 0.726015395 0.867090484 0.809014768 1 19.33724425 -1.188905159 4.748912379 1.000022798 0.83792171 0.239221543 0.091636017 1.97E-05 3.37E-06 0.079101013 0.018641666 0.064728395 1.188905159 -0.162101088 WFNGQPIHAELSPVTDFR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 223.71 5.00E-19 1696000000 2703040 2112190 2335220 2593100 2770310 2443570 2964310 2473350 2632890 FALSE TRUE 2575272.656 2327424.562 2442292.147 2332436.661 3253451.187 2358948.558 2512050.066 2256770.362 3041185.134 0.846799041 0.765301835 0.803072499 0.766949909 1.069797149 0.775667529 0.826010241 0.742069378 1 21.53620221 WFQQKYDGIILPGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WFQQKYDGIILPGK 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 131.53 5.08E-05 340790000 867040 320650 971860 578110 960880 831830 1616190 1050910 1980650 FALSE TRUE 826056.7375 353324.5995 1016420.742 519997.2845 1128457.168 803023.5185 1369610.532 958886.7492 2287799.086 0.36107049 0.154438649 0.444278848 0.227291499 0.493250117 0.35100264 0.598658571 0.419130664 1 21.12552893 -0.896822138 0.225146861 1.44343013 0.205075999 0.780935128 0.108328493 6.108559626 0.332901025 1.923512114 0.213094258 0.126817113 0.896822138 -1.23835413 WFSNPS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;WFSNPS(1)R 110.88 0.0070319 595395000 721797 621182 632729 762007 798965 652502 820989 710416 815111 TRUE FALSE 687679.0863 684481.152 661740.2505 685408.6086 938304.243 629905.6921 695732.0496 648208.2089 941514.2509 0.730396896 0.72700031 0.70284677 0.727985379 0.99659059 0.669034687 0.7389501 0.688474134 1 19.84462341 -2.319584946 2.305743662 2.384733937 0.746221703 0.430466808 0.091204235 5718497.364 777373.491 41322692.84 0.021852683 0.004790877 2.319584946 -1.638512234 WGDAGAEYVVESTGVFTTMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WGDAGAEYVVESTGVFTTMEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 162.76 1.82E-11 29287000 65259 61215 62230 69375 46368 57580 73957 65311 61020 FALSE TRUE 62174.3364 67452.8781 65083.30705 62401.2932 54454.56452 55585.99016 62673.50134 59592.0226 70482.66995 0.882122321 0.957013662 0.923394461 0.885342358 0.772595087 0.788647624 0.889204415 0.84548475 1 16.10498096 3.008291176 6.506816079 0.847618842 0.921214751 0.148871243 0.064021767 0.207320165 40.52161607 0.017476548 0.020258363 1019.274539 -3.008291176 0.073595909 WGDEHIPGSPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WGDEHIPGSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 105.65 0.0020072 1161900000 2765080 1931380 1711620 1999300 2634540 1915110 3054310 2219520 2210340 FALSE TRUE 2634380.148 2128189.818 1790099.47 1798326.566 3094002.942 1848789.26 2588318.913 2025167.062 2553108.238 1.031832536 0.833568192 0.701145154 0.704367539 1.211857334 0.724132739 1.013791297 0.793216297 1 21.28382327 WGDIEFPPPFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 144.65 0.0001471 326909000 514378 541958 537126 550912 482823 510069 555212 678454 470679 FALSE TRUE 490064.3713 597184.1364 561753.7584 495533.2791 567027.1783 492405.1826 470504.2122 619044.971 543669.4954 0.901401266 1.098432304 1.033263339 0.911460516 1.042963019 0.905706844 0.865423233 1.138642091 1 19.05237036 3.262498749 24.77841892 0.961712176 1.014099303 0.010210409 0.090973386 607.805993 629136.822 0.024360998 0.032966978 1830.200834 -3.262498749 0.052387127 WGDKPGVSPSIGLSVGSGWPSS(ph)PGSDPPLPKPCGDHPLNHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WGDKPGVSPSIGLSVGSGWPSSPGSDPPLPKPCGDHPLNHR 41 2 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 WGDKPGVSPSIGLSVGSGWPS(0.049)S(0.902)PGS(0.049)DPPLPKPCGDHPLNHR 147.06 1.03E-13 142560000 126730 102720 122480 144880 88921 140440 145330 117750 8824.6 TRUE FALSE 120739.7241 113187.2848 128095.8291 130316.3871 104428.7942 135576.5276 123157.2393 107439.1858 10193.0739 11.84527114 11.1043328 12.56694795 12.78479764 10.24507379 13.3008481 12.08244349 10.54041076 1 13.31530157 0.721790687 2.934311095 1.000616544 11.94239207 0.941302755 0.855537661 0.44168671 4.402741749 0.773248949 0.20272105 5.269758179 -0.721790687 10.94177553 WGEDNHWICKPWNLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WGEDNHWICKPWNLAR 16 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 191.86 3.77E-10 1181340000 4190600 3145700 2090300 2472800 3631200 2557600 4527800 3208900 2810500 FALSE TRUE 3992518.643 3466250.406 2186142.323 2224229.446 4264480.13 2469029.671 3837000.951 2927911.705 3246337.986 1.229853041 1.06774169 0.673417966 0.6851503 1.313627894 0.760558414 1.181947464 0.90191216 1 21.63038178 4.089004515 3.870051942 0.94375187 1.186726891 0.177044107 0.204598097 0.361667454 10.16709858 0.049832501 0.116161458 12274.51992 -4.089004515 0.242975021 WGEEHIPGSPFHVTVP ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WGEEHIPGSPFHVTVP 16 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 116.84 0.00039666 325431000 497125 362210 450244 506401 539971 413813 667281 523169 35908.1 FALSE TRUE 473626.8865 399119.6108 470888.1328 455496.6094 634141.7714 399482.552 565475.028 477357.5489 41476.54475 11.41915001 9.622778685 11.35311862 10.98202881 15.28916585 9.631529203 13.63360982 11.50909633 1 15.34000809 0.90931935 21.68989532 0.999999925 11.62251455 0.796030669 1.698887067 15891.12764 3801002.638 1.558349904 0.389587476 8.115576007 -0.90931935 10.62251462 WGEEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WGEEKR 6 1 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 101.52 0.05841 163080000 243670 187080 204960 229500 151270 218320 247960 238840 171830 FALSE TRUE 232152.202 206143.6647 214357.6187 206430.224 177651.4401 210759.5237 210129.1479 217925.9034 198476.5188 1.169670868 1.03862999 1.080015006 1.040073784 0.895075353 1.061886438 1.058710366 1.097993378 1 17.59860881 4.834393142 1.077964228 1.031855893 1.262363699 0.372075139 0.05569826 2.218683974 1.852789492 0.016454843 0.61403907 68295.66562 -4.834393142 0.230507805 WGQPPS(ph)PTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_SK-BR-3_Trastuzumab_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(1)PTPVPRPPDADPNT(0.883)PS(0.117)PKPLEGRPER 163.18 3.90E-14 711080000 690350 586460 596570 696030 375360 681480 679430 695080 409800 TRUE FALSE 657718.5236 646220.9407 623923.3246 626063.742 440822.6652 657880.1767 575770.4749 634215.1103 473349.691 1.389498158 1.365208329 1.318102317 1.32262417 0.931283306 1.389839667 1.21637446 1.339844775 1 18.85254685 -3.417959195 0.045058181 1.49E-10 1.9542621 0.326731927 0.132708728 561.5024375 2.513386986 89.52408902 32.11910385 0.00038198 3.417959195 1.9542621 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_SK-BR-3_Trastuzumab_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(0.992)PT(0.008)PVPRPPDADPNT(0.219)PS(0.781)PKPLEGRPER;WGQPPS(0.946)PT(0.054)PVPRPPDADPNT(0.014)PS(0.986)PKPLEGRPER 184.45 1.83E-19 1213890000 886470 857940 844590 947440 520250 1007700 929070 941380 635750 TRUE FALSE 844568.3199 945365.0614 883315.2869 852201.5312 610981.4353 972803.0963 787323.308 858947.7766 734338.863 1.150107072 1.287368964 1.202871496 1.160501744 0.832015662 1.324733233 1.072152582 1.169688573 1 19.48608643 7.9634677 0.019536087 1.88E-08 2.605010588 0.126603746 0.132111493 5908.331141 8.951411859 446.2636002 793.3048762 91932209.8 -7.9634677 2.605010569 WGQPPS(ph)PTPVPRPPDADPNTPSPK ddPTM_SK-BR-3_Trastuzumab_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(0.892)PT(0.108)PVPRPPDADPNTPSPK;WGQPPS(0.89)PT(0.11)PVPRPPDADPNTPSPK 220.38 6.13E-33 610790000 1328320 1593370 1151440 1637310 796990 1403380 1181310 1376650 816190 TRUE FALSE 1265532.946 1755736.215 1204234.663 1472724.488 935984.8037 1354780.599 1001079.463 1256103.228 942760.5767 1.342369396 1.862335208 1.277349406 1.56214051 0.992812838 1.437035693 1.0618597 1.332367156 1 19.84653191 3.022271026 1.635323832 1.182301703 1.575904977 0.34623844 0.216455642 0.348294724 1.903603337 0.069285561 0.083497577 1052.618567 -3.022271026 0.393603274 WGQPPS(ph)PTPVPRPPDADPNTPSPKPLEGRPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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(0.902)PT(0.098)PVPRPPDADPNTPSPKPLEGRPER;WGQPPS(0.494)PT(0.494)PVPRPPDADPNT(0.01)PS(0.003)PKPLEGRPER;WGQPPS(0.975)PT(0.025)PVPRPPDADPNTPSPKPLEGRPER;WGQPPS(0.779)PT(0.218)PVPRPPDADPNT(0.002)PSPKPLEGRPER;WGQPPS(0.969)PT(0.031)PVPRPPDADPNTPSPKPLEGRPER 166.28 2.68E-13 5854360000 961870 897550 887650 1005730 742966 1000180 1053640 983890 782867 TRUE FALSE 916404.3113 989011.3654 928349.6305 904632.1096 872539.0352 965543.5158 892887.8666 897735.3757 904270.016 1.013418885 1.09371244 1.026628788 1.000400426 0.964909839 1.067760181 0.987412886 0.992773574 1 19.7863941 3.484394952 6.511420348 1.004073876 1.054749194 0.304270031 0.032068394 0.156999044 31.98508889 0.008257929 0.011977112 3050.668036 -3.484394952 0.050675318 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_SK-BR-3_Trastuzumab_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(0.155)PT(0.802)PVPRPPDADPNT(0.037)PS(0.005)PKPLEGRPER 124.29 7.73E-08 796120000 418750 370970 382400 430220 310540 431860 474720 427160 325850 TRUE FALSE 398956.5174 408772.2648 399933.4182 386973.4682 364698.0777 416904.5799 402292.7452 389755.6059 376381.1538 1.059980058 1.086059333 1.062575568 1.028142521 0.968959455 1.107665928 1.068844019 1.03553433 1 18.52183487 3.432171004 6.524340814 1.042382802 1.073263512 0.143623147 0.037625062 0.416446328 43.62270711 0.010566346 0.014460877 2705.023263 -3.432171004 0.03088071 WGQPPSPTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_SK-BR-3_Trastuzumab_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(0.014)PT(0.065)PVPRPPDADPNT(0.137)PS(0.784)PKPLEGRPER 167.32 3.12E-14 888070000 571250 527720 553780 610440 422380 623060 572810 628810 457880 TRUE FALSE 544248.1446 581495.268 579171.3608 549077.4114 496042.9383 601483.276 485417.3141 573748.0629 528885.6919 1.02904683 1.099472489 1.09507852 1.038177852 0.937901981 1.137265169 0.917811394 1.084824323 1 19.01259642 3.004994425 18.79654072 1.010495781 1.072535492 0.141568557 0.065566489 10.61878779 39949.74317 0.017035125 0.020199763 1011.566468 -3.004994425 0.062039711 WGRDDIENIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;; 212.9 3.97E-09 796380000 586490 438350 508170 588000 576510 464860 593970 546330 644790 FALSE TRUE 558767.78 483018.3634 531470.0971 528893.1229 677053.1615 448761.7816 503348.9675 498490.4489 744780.7401 0.750244669 0.648537667 0.713592697 0.710132653 0.909063735 0.602542141 0.675835102 0.669311681 1 19.50645624 -1.872467537 2.749431596 1.131201124 0.705835373 0.556372452 0.081335458 25165182.22 17895031.21 21587551.18 0.018344804 0.013413202 1.872467537 -0.425365751 WGTDEAQFIYILGNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WGTDEAQFIYILGNR 15 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 181.98 1.32E-06 107930000 135940 129440 136280 165630 127940 135180 143120 134710 124580 FALSE TRUE 129514.3856 142630.0832 142528.5728 148980.5577 150252.6955 130498.6827 121284.4154 122914.0783 143899.2301 0.900035292 0.991180307 0.990474881 1.035311708 1.044152185 0.906875475 0.842842698 0.854167727 1 17.13469935 2.067927593 7.101958455 0.879874768 0.985291233 0.366126667 0.057518861 0.206428272 17.80391689 0.02146541 0.015777218 116.9304424 -2.067927593 0.105416464 WGTDEEKFITIFGTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WGTDEEKFITIFGTR 15 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 162.59 1.45E-06 1130430000 2137500 1317920 2145800 2355800 2032020 2463700 3252600 2769500 2318600 FALSE TRUE 2036464.611 1452217.546 2244187.052 2118990.508 2386403.645 2378381.451 2756356.132 2526987.898 2678156.646 0.760397871 0.542245185 0.837959593 0.791212311 0.89106201 0.888066594 1.029198996 0.943554927 1 21.35280892 2.890111516 0.870365107 0.990509905 0.654748195 0.70962507 0.074649172 0.272752201 0.453115149 0.040858744 0.045137399 776.4464633 -2.890111516 -0.335761709 WGTIEVENTTHCEFAYLR ddPTM_SK-BR-3_Trastuzumab_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 0 151.62 4.64E-08 72929000 24658 31437 27800 31274 27986 25769 33241 23441 32271 FALSE TRUE 23492.46521 34640.46604 29074.6575 28130.2781 32866.74954 24876.61307 28169.47494 21388.38177 37275.42186 0.630240089 0.929311174 0.779995398 0.754660221 0.881727098 0.667373079 0.755711767 0.573793151 1 15.18593706 2.225644899 24.99890885 0.729542881 0.795948708 0.019691314 0.131874108 710.9522676 1376068.223 0.044278981 0.032910166 168.1298784 -2.225644899 0.066405826 WGTLTDCVVMRDPQTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WGTLTDCVVMRDPQTK 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 188.9 1.01E-09 732620000 1240520 928640 1054830 1206390 985740 1066180 1427750 1323450 1069980 FALSE TRUE 1181883.078 1023269.472 1103194.999 1085121.385 1157652.744 1029257.919 1209920.515 1207561.702 1235907.034 0.95628801 0.827950197 0.892619727 0.877995962 0.936682705 0.832795583 0.978973727 0.977065159 1 20.2371388 1.627807727 6.973833778 0.985362494 0.887769307 0.576259466 0.039608588 0.085430987 8.810898136 0.019140229 0.009469197 42.44316155 -1.627807727 -0.097593187 WHFYDTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WHFYDTVK 8 0 P31040;D6RFM5;A0A494C1T6 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 155.75 0.00040391 337280000 664080 313830 103530 125050 688820 152890 670370 363610 352130 FALSE TRUE 632690.2545 345809.6338 108276.9529 112479.7364 808949.9899 147595.381 568092.7443 331770.3808 406736.522 1.555528506 0.850205514 0.266209074 0.276542013 1.988879646 0.362877128 1.396709451 0.81568869 1 18.63373501 WHLVYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WHLVYR 6 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58 Q99829 CPNE1 Copine-1 0 142.14 0.011563 624160000 460150 457750 333120 456930 521390 383820 553370 397690 185010 FALSE TRUE 438399.6214 504395.2454 348393.8815 410998.5283 612320.2509 370528.2172 468943.2432 362866.1553 213700.4059 2.051468361 2.360291471 1.630291155 1.923246362 2.865320954 1.733867634 2.19439566 1.698013412 1 17.70523012 0.902823591 2.286430363 0.999421216 2.122944585 0.516382834 0.343112276 0.317027855 3.498332009 0.300520606 0.081849935 7.995094307 -0.902823591 1.123523369 WHPDKNPENKEEAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 94.09 0.0027658 115160000 139360 119130 107820 152780 76841 129220 129390 140070 62300 FALSE TRUE 132772.729 131269.4824 112763.6536 137422.2641 90242.04607 124745.079 109649.1791 127804.7282 71961.16582 1.845060839 1.824171148 1.567007043 1.909672565 1.254038134 1.733505532 1.523727108 1.776023593 1 16.13493094 -2.56242182 0.171526478 2.17E-14 1.892125777 0.558514436 0.190716571 33.91661442 0.697308304 13.9947157 0.679006976 0.002738913 2.56242182 1.892125777 WHPHS(ph)PNVRPSFQDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WHPHSPNVRPSFQDDR 16 1 Q9H329-2 Q9H329-2 EPB41L4B Band 4.1-like protein 4B 1 WHPHS(0.999)PNVRPS(0.001)FQDDR;WHPHS(1)PNVRPSFQDDR 96.391 0.0020707 426890000 729550 576690 631520 701360 554220 685480 804110 702560 416590 TRUE FALSE 695065.6173 635455.3666 660475.8167 630857.9603 650875.7925 661741.6557 681428.251 641040.1219 481192.6496 1.444464328 1.32058411 1.372580851 1.311029919 1.352630372 1.37521148 1.416123566 1.332190179 1 18.87625508 0.956841965 21.70859617 1 1.370591553 0.896081984 0.03933699 493.6798302 248322.8277 0.037516179 0.009379045 9.054030743 -0.956841965 0.370591554 WHQPPPS(ph)PLPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WHQPPPSPLPLR 12 0 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 WHQPPPS(1)PLPLR 86.772 0.0040694 0 153020 148400 159710 154840 167110 154690 186980 149850 77554 TRUE FALSE 145787.0479 163522.1287 167032.8615 139275.189 196253.9311 149333.0465 158452.7669 136728.3396 89580.67823 1.627438536 1.8254174 1.864608136 1.554745865 2.190806488 1.66702295 1.768827497 1.526315075 1 16.45089997 0.829654102 1.726942978 1.000216091 1.788173277 0.680090598 0.171523419 0.334137478 1.844689153 0.14629684 0.041614927 6.755447177 -0.829654102 0.787957185 WIDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 117.7 0.05234 347154000 1897820 1640820 1762560 2387450 2243610 1891360 2278850 1911150 2206090 FALSE TRUE 1808113.81 1808021.423 1843375.119 2147458.99 2634894.874 1825861.729 1931169.579 1743799.574 2548199.17 0.70956534 0.709529084 0.723403077 0.842735927 1.034022342 0.716530227 0.757856608 0.684326247 1 21.28104661 3.281712097 6.810821555 0.82315043 0.711666734 0.211186667 0.111124723 0.342859339 40.13077822 0.030529645 0.040989458 1912.987344 -3.281712097 -0.111483696 WIDFDNDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WIDFDNDYK 9 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 161.79 0.00014952 299695000 1055290 1440100 1025470 1413050 708340 1171640 1001580 1298010 615400 FALSE TRUE 1005408.533 1586847.827 1072488.814 1271007.529 831874.2717 1131065.813 848770.5757 1184349.363 710833.089 1.414408739 2.232377547 1.508777279 1.788053411 1.170280738 1.591183402 1.194050458 1.666142702 1 19.43915131 2.752596483 24.31743337 1.346492956 1.770309949 0.331296594 0.287765829 589.8881645 1021992.356 0.080735415 0.085212648 565.7134217 -2.752596483 0.423816993 WIDFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WIDFVR 6 0 P05455 P05455 SSB Lupus La protein 0 ; 140.72 0.027321 819310000 1746460 1593120 1453030 1703770 1916630 1352320 2001900 1624830 1908530 FALSE TRUE 1663908.297 1755460.739 1519652.863 1532503.803 2250889.665 1305488.819 1696473.388 1482551.271 2204495.085 0.754779772 0.796309663 0.689342822 0.695172247 1.021045445 0.592194026 0.769551903 0.67251285 1 21.07201683 -1.463064291 3.683395845 1.002600609 0.752470723 0.32982415 0.112398824 606450316.3 49263283.92 13409201.92 0.024167998 0.034429896 1.463064291 -0.250129886 WIDNPTVDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WIDNPTVDDR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;;; 172.27 8.76E-06 1220600000 1955620 1890200 1489110 2240800 1974990 1618720 2068190 1751950 1917470 FALSE TRUE 1863181.718 2082813.529 1557387.166 2015550.527 2319427.631 1562663.321 1752649.631 1598539.97 2214821.455 0.841233371 0.940397938 0.703166011 0.910028446 1.047230072 0.705548214 0.791327728 0.721746652 1 21.07875897 WIGLDLSNGKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WIGLDLSNGKPR 12 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 205.46 9.25E-08 2268400000 4351900 3662600 3445700 3967500 3641700 3842700 4678500 4036400 3932000 FALSE TRUE 4146194.312 4035823.104 3603688.753 3568679.362 4276811.327 3709626.335 3964708.898 3682951.418 4541754.478 0.912905867 0.88860442 0.793457412 0.785749071 0.941665021 0.816782667 0.872946549 0.810909404 1 22.11481829 -1.515581215 6.21078515 1.000139179 0.858030503 0.43734596 0.05215294 9.75E-05 7.60E-06 0.04897999 0.011533433 0.030508355 1.515581215 -0.142108676 WINEAQEAASSDNIMVQYHALGVLYHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WINEAQEAASSDNIMVQYHALGVLYHLR 28 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 73.805 0.0056005 62838000 29024 27237 29223 26180 32652 29209 34517 26983 22261 FALSE TRUE 27652.09304 30012.48127 30562.90346 23548.33666 38346.49846 28197.48501 29250.7977 24620.22547 25713.12219 1.075407834 1.167204863 1.188611139 0.915810087 1.491320198 1.096618481 1.137582495 0.957496538 1 14.65021718 1.285307331 5.034250869 0.977735687 1.152010884 0.20558194 0.142447957 0.279206996 14.53919686 0.097597069 0.032309832 19.28889422 -1.285307331 0.174275196 WISIMTER ddPTM_SK-BR-3_Trastuzumab_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 ; 198.07 0.00032321 476310000 792520 639850 445770 743440 932390 545320 730870 574290 698350 FALSE TRUE 755059.1502 705051.4424 466208.9954 668707.9988 1094998.521 526435.4317 619362.3582 524002.1231 806646.5513 0.936047082 0.874052509 0.577959448 0.82899753 1.357470033 0.652622181 0.767823723 0.649605608 1 19.62157714 WIVEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WIVEER 6 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;; 129.16 0.037954 1404620000 3022280 2632460 2713160 3057380 3102380 2659040 3330240 2889200 3352420 FALSE TRUE 2879422.814 2900710.667 2837561.07 2750046.354 3643434.09 2566956.778 2822150.724 2636206.331 3872296.172 0.743595708 0.749093184 0.732785134 0.710184922 0.940897578 0.662903007 0.728805494 0.680786338 1 21.88475787 -1.046387059 4.418663577 1.000015655 0.743940582 0.534560296 0.075179218 0.222059805 40560562.91 1394.180835 0.016120071 0.089869627 1.046387059 -0.256075073 WIVNLIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WIVNLIR 7 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 99.384 0.024586 37510000 125838 129309 114662 124840 135706 95523 140395 121512 122210 FALSE TRUE 119889.8871 142485.7341 119919.3661 112290.846 159373.0834 92215.01456 118975.1642 110871.7651 141161.7026 0.849308877 1.009379537 0.849517708 0.795476705 1.129010776 0.653258021 0.842828912 0.78542383 1 17.10698921 2.220486876 24.99994599 0.805588216 0.921356071 0.146651391 0.124659447 407.0967744 563100.5821 0.041884071 0.030994503 166.1448468 -2.220486876 0.115767855 WIYEDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 WIYEDVER 8 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;;;;; 221.25 1.30E-05 4531977000 6133296 4973851 4798092 5403973 6826950 4448898 6438060 5237426 6563530 FALSE TRUE 5843387.253 5480692.072 5018089.264 4860755.367 8017567.919 4294831.547 5455815.704 4778809.214 7581368.711 0.770756242 0.722915911 0.661897535 0.641144832 1.057535681 0.566498176 0.719634661 0.630335945 1 22.8540269 -1.001905348 4.048598992 1.000024353 0.723106365 0.304332712 0.132380872 26902749.72 64688145.96 10020.4573 0.02887258 0.099562238 1.001905348 -0.276917988 WKAGLYGLPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WKAGLYGLPR 10 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 ; 136.63 0.00010257 2057300000 3408300 1246310 1505520 1426750 4123400 1894930 5348000 2695800 5974900 FALSE TRUE 3247196.414 1373310.406 1574549.581 1283330.379 4842519.654 1829308.099 4532064.377 2459741.461 6901456.976 0.470508825 0.198988476 0.228147417 0.185950645 0.701666282 0.265061147 0.656682262 0.356409012 1 22.71846953 -0.170130699 0.319552419 1.180265257 0.276338291 0.56703658 0.174623265 4.296157677 0.576467474 1.112131692 0.170231311 0.675879542 0.170130699 -0.903926966 WKDSDEADLVLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WKDSDEADLVLAK 13 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;; 178.23 1.35E-05 5761450000 19915600 17563720 17090110 20316800 11903960 20693600 22495800 22005900 13669180 FALSE TRUE 18974229.06 19353483.04 17873708.45 18274516.66 13980006.86 19976975.44 19063652.55 20078946.74 15788926.62 1.201742811 1.225763062 1.132040757 1.157426157 0.885431112 1.265252282 1.207406495 1.271710688 1 23.91240976 -2.122871961 2.430402183 0.656733525 1.172566322 0.188790289 0.109358467 6574190.603 1577466.241 12517349.51 0.025480996 0.007535777 2.122871961 0.515832797 WKDTDEADLVLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WKDTDEADLVLAK 13 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ; 134.9 8.22E-05 331080000 751970 644490 620110 801430 438400 722290 810640 829990 525520 FALSE TRUE 716425.8684 710164.2637 648542.6569 720868.7338 514856.8212 697276.9162 686961.9796 757311.6755 607014.9576 1.180244176 1.169928772 1.068412975 1.187563378 0.848178146 1.14869808 1.131705193 1.247599694 1 19.21137254 3.781407716 9.064816031 1.095573329 1.175278953 0.093252307 0.108950021 1.050166787 213.2176492 0.026453774 0.047560831 6045.158831 -3.781407716 0.079705624 WKEEKGDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WKEEKGDR 8 2 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 77.662 0.018354 356690000 1518260 1059630 1409970 1540030 1086320 1456140 1799180 1806360 1369970 FALSE TRUE 1446494.859 1167607.502 1474618.519 1385223.259 1275773.864 1405713.507 1524682.047 1648185.542 1582417.951 0.914104177 0.737862902 0.931876764 0.875383939 0.806218018 0.888332634 0.963514125 1.041561454 1 20.59369927 1.676381318 2.275944888 1.019123815 0.847582581 0.608544148 0.055465164 0.171167617 1.92963716 0.037007773 0.014973644 47.46585604 -1.676381318 -0.171541234 WKEPGSGGPQNLS(ph)GPGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR 249.35 7.22E-25 2379600000 959750 859414 908459 1120500 806995 1015360 1166200 1118010 1029370 TRUE FALSE 914384.5195 946989.2637 950112.7437 1007865.211 947734.6725 980197.8286 988274.7713 1020111.117 1188999.442 0.769036963 0.796458964 0.799085946 0.847658271 0.797085885 0.824388804 0.831181863 0.857957608 1 20.18131661 -5 0.161917464 1.727165265 0.760310688 0.936146966 0.016113464 28.57543614 0.264076281 6.632749803 0.063076081 1.00E-05 5 -0.966854577 WKGELWDTCNIGVPWYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WKGELWDTCNIGVPWYDR 18 1 P13807 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 130 1.82E-05 130840000 103330 131050 95462 126290 73476 101210 96180 115750 76473 FALSE TRUE 98445.79568 144404.144 99839.02712 113595.0893 86290.19114 97705.07232 81505.97453 105614.3164 88332.04227 1.114496995 1.634787788 1.130269657 1.286000939 0.976884366 1.106111325 0.922722632 1.195651246 1 16.43064925 3.039870901 1.647522587 1.030530798 1.357723396 0.354143062 0.161458262 0.322943112 1.794205024 0.053266293 0.0650328 1096.152303 -3.039870901 0.327192598 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WKGYDSEDDTWEPEQHLVNCEEYIHDFNR 29 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(1)EDDTWEPEQHLVNCEEYIHDFNR 277.43 1.97E-71 40116000 37655 31423 25148 33871 23319 34608 36890 38863 17099 TRUE FALSE 35875.12278 34625.03942 26301.06067 30466.22273 27385.82622 33409.51628 31261.75297 35459.94969 19750.62559 1.816404377 1.753111023 1.331657094 1.542544695 1.386580192 1.691567496 1.582823431 1.795383621 1 14.26961073 -1.992268532 3.15857107 0.413220163 1.620765262 0.583878703 0.16237091 82071.985 35370478.68 19234.52631 0.03933092 0.010179618 1.992268532 1.207545099 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WKGYDSEDDTWEPEQHLVNCEEYIHDFNRR 30 2 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(0.996)EDDT(0.004)WEPEQHLVNCEEYIHDFNRR;WKGYDS(0.943)EDDT(0.057)WEPEQHLVNCEEYIHDFNRR 232.14 3.74E-36 650730000 348380 188370 281010 271300 227910 315170 423720 321800 168345 TRUE FALSE 331912.7678 207565.1172 293894.5865 244028.4086 267657.4318 304255.5839 359073.7318 293621.486 194451.0828 1.706921674 1.067441303 1.511406274 1.254960399 1.376476942 1.564689584 1.846601863 1.510001805 1 17.56904774 2.2289035 6.118870842 1.584376155 1.369174052 0 0.269632725 0.316621962 44.12725635 0.091611729 0.070570586 169.396136 -2.2289035 -0.215202102 WKGYT(ph)SDDDTWEPEIHLEDCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WKGYTSDDDTWEPEIHLEDCK 21 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 WKGYT(0.5)S(0.5)DDDTWEPEIHLEDCK;WKGYT(0.605)S(0.395)DDDTWEPEIHLEDCK;WKGYT(0.5)S(0.5)DDDTWEPEIHLEDCK;WKGYT(0.714)S(0.286)DDDTWEPEIHLEDCK 198.09 1.28E-21 287443000 603810 479108 520200 607430 332106 602220 643690 621200 305649 TRUE FALSE 575269.0979 527929.6499 544051.6845 546369.9824 390025.1813 581364.9704 545483.2683 566804.4348 353047.4859 1.629438308 1.49535026 1.541015604 1.547582136 1.104738589 1.646704746 1.545070536 1.605462317 1 18.42950272 -1.163257114 4.359802535 0.999883702 1.517141241 0.528235582 0.152761768 0.000161824 3.11E-05 0.1386077 0.032662849 0.06866618 1.163257114 0.517257539 WKPPMIDNPSYQGIWKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WKPPMIDNPSYQGIWKPR 18 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 90.718 0.0014926 338290000 258020 236120 230720 311490 272470 270360 350780 270050 287800 FALSE TRUE 245823.9059 260180.8964 241298.7402 280178.4334 319988.6817 260997.3654 297262.0685 246402.9904 332430.5541 0.739474464 0.782662403 0.7258621 0.842817936 0.962573018 0.785118462 0.894208023 0.741216435 1 18.34269346 -4.56308516 0.027435307 2.114658669 1.96E-06 0.423033266 0.072476501 1444.072852 3.204044853 180.4995473 83.45900679 2.73E-05 4.56308516 -2.114656705 WKS(ph)DVALNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WKSDVALNGR 10 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 WKS(1)DVALNGR;WKS(1)DVALNGR;WKS(1)DVALNGR 137.8 4.95E-05 431255000 1445520 1283090 1286740 1334640 858430 1189340 1389560 1505010 907120 TRUE FALSE 1377193.134 1413838.33 1345738.302 1200479.452 1008139.92 1148152.858 1177557.101 1373223.346 1047791.537 1.314377036 1.349350782 1.284356911 1.145723562 0.962156961 1.095783672 1.123846738 1.310588316 1 19.99892028 3.252077348 3.382060193 1.102962746 1.329193884 0.546631844 0.091397684 0.167013063 3.995811551 0.025899509 0.034184556 1786.805778 -3.252077348 0.226231138 WKSEEEVES(ph)DDEYLALPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WKSEEEVESDDEYLALPAR 19 1 Q5HYA6;Q76N32-2;Q76N32 Q5HYA6 DKFZp686H16130;CEP68 Centrosomal protein of 68 kDa 1 WKSEEEVES(1)DDEYLALPAR;WKSEEEVES(1)DDEYLALPAR 209.76 1.26E-16 88439000 123654 88628 99839 111222 73779 105613 132650 127873 98109 TRUE FALSE 117809.1205 97659.29396 104416.7169 100041.7533 86646.03424 101955.5953 112411.8062 116675.7622 113323.2426 1.039584799 0.861776381 0.92140601 0.882799953 0.764591907 0.899688298 0.991957198 1.029583689 1 16.79008426 1.672417775 4.113197664 1.012700416 0.897676654 0.386082893 0.067020281 0.201684436 7.980548665 0.03940552 0.018443238 47.03463468 -1.672417775 -0.115023763 WLAVDYENVRPDIVLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WLAVDYENVRPDIVLLGK 18 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 236.16 7.48E-24 856950000 1125360 936150 923400 916470 859770 789330 1013640 946130 875620 FALSE TRUE 1072166.463 1031544.749 965738.8034 824344.6944 1009713.616 761995.3042 858990.6012 863281.8414 1011406.678 1.060074535 1.019910954 0.95484717 0.815047708 0.998326033 0.753401496 0.849302877 0.853545721 1 19.94793178 3.573970506 2.203219453 0.865714977 1.04585036 0.423118149 0.076570594 0.232672161 2.220161577 0.020234325 0.034964449 3749.47538 -3.573970506 0.180135382 WLDAIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLDAIIR 7 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 77.674 0.087024 16614000 83928 74266 62592 61997 100120 61070 96054 75475 86673 FALSE TRUE 79960.88977 81833.78983 65461.90511 55764.94377 117580.8963 58955.13059 81399.19815 68866.00888 100113.8062 0.798699928 0.817407638 0.653874901 0.55701552 1.174472341 0.588881123 0.813066661 0.687877242 1 16.61128142 WLDDLLAS(ph)PPPSGGGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WLDDLLAS(0.997)PPPS(0.003)GGGAR;WLDDLLAS(0.996)PPPS(0.004)GGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR 254.71 5.03E-27 1331611000 1009465 991631 1019973 1177414 1118558 973259 1128715 1010026 1097574 TRUE FALSE 961749.59 1092679.326 1066739.771 1059058.108 1313634.161 939554.7968 956508.7965 921582.769 1267780.17 0.758609113 0.861883907 0.841423297 0.835364153 1.036168724 0.741102297 0.754475278 0.726926316 1 20.27387318 -0.358885069 7.43175406 0.999998379 0.818931306 0.286478415 0.089522542 0 0 0.085410666 0.020131487 0.437637905 0.358885069 -0.181067074 WLDES(ph)DAEMELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 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;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR 276.71 7.55E-28 2101661000 2590195 1385365 1514825 2930257 3212390 2185660 3106727 2451834 2839344 TRUE FALSE 2467761.616 1526535.269 1584281.225 2635701.999 3772629.799 2109970.046 2632738.737 2237138.417 3279654.966 0.752445498 0.465456057 0.483063383 0.803652221 1.150313017 0.643351227 0.802748693 0.68212615 1 21.64511261 3.166205041 6.959027647 0.836732114 0.572290248 0.395069487 0.163249253 0.22638431 17.81888742 0.045927954 0.055240362 1466.239925 -3.166205041 -0.264441867 WLEASEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WLEASEEER 9 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;; 205.36 3.51E-05 606770000 630390 516550 583360 578980 574690 534990 679800 605040 640020 FALSE TRUE 600592.714 569187.0323 610107.633 520779.8304 674915.754 516463.1622 576084.0246 552059.4901 739271.0328 0.812412075 0.769930116 0.825282753 0.704450475 0.912947653 0.698611388 0.779259567 0.746761966 1 19.49574386 -1.072855775 5.763356099 1.000000992 0.781175816 0.553662329 0.061736948 6.74E-07 1.08E-07 0.051204956 0.012069069 0.08455596 1.072855775 -0.218825176 WLFTEIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLFTEIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 99.919 0.02367 9455900 59345 49472 59657 54643 107080 50402 75144 53495 53912 FALSE TRUE 56539.87946 54513.25304 62392.33246 49150.18183 125754.7181 48656.5661 63679.40269 48810.69421 62272.39762 0.907944477 0.875399939 1.001925971 0.789277171 2.019429521 0.781350453 1.022594362 0.783825516 1 15.92630521 WLHNEDQMAVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 WLHNEDQMAVEK 12 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;; 212.1 2.42E-08 8620850000 14112325 11572642 11100375 13014054 10907329 12208933 15179720 13141521 9919420 FALSE TRUE 13445263.37 12751907.38 11609338.17 11705856.57 12809563.72 11786134.59 12863774.92 11990779.75 11457672.99 1.17347243 1.112957874 1.013236997 1.021660906 1.117989991 1.028667391 1.122721422 1.046528362 1 23.44981073 4.063970411 3.03877624 1.059325233 1.159206397 0.465977713 0.042434021 0.209775836 3.876923538 0.010518569 0.025670653 11586.98411 -4.063970411 0.099881164 WLIKEELEEMLVEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WLIKEELEEMLVEK 14 1 P82933;H7BZC4 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 169.09 3.09E-06 81414000 302960 345090 316300 282930 196030 273020 281220 324220 183449 FALSE TRUE 288639.6812 380255.0633 330802.6679 254489.3389 230217.5699 263565.2489 238314.724 295829.578 211897.334 1.362167592 1.794525 1.561145965 1.201003024 1.086458077 1.243834663 1.124670705 1.396098631 1 17.69300591 3.242131103 5.266508861 1.176180121 1.593621438 0.625947593 0.144817323 0.099428791 8.11494799 0.038692371 0.049857691 1746.349255 -3.242131103 0.417441317 WLIS(ph)PVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 107.57 0.0078114 361992000 1042510 827341 858899 1057707 730958 985432 1135737 1045973 788843 TRUE FALSE 993232.6184 911647.9885 898280.3687 951384.2828 858436.8438 951306.2427 962459.4614 954382.0591 911172.7436 1.090059624 1.000521575 0.98585079 1.044131631 0.942123049 1.044045983 1.056286493 1.047421651 1 19.79736507 WLKEDKLECSEELGDLVK ddPTM_SK-BR-3_Trastuzumab_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 ; 190.23 1.61E-14 1138250000 1957960 1555410 1720790 2002440 1026670 2207500 2261400 2355800 1158380 FALSE TRUE 1865411.111 1713908.047 1799689.924 1801150.927 1205720.923 2131053.721 1916381.897 2149513.663 1338015.654 1.394162397 1.280932732 1.345043997 1.346135915 0.901126171 1.592697152 1.432256708 1.606493658 1 20.35166356 WLLAHCGRPQTECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WLLAHCGRPQTECR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 164.33 2.49E-06 433210000 234470 182045 165757 223620 297860 190007 329180 249580 339770 FALSE TRUE 223387.0678 200595.5925 173357.1224 201141.2927 349806.6897 183427.0099 278957.5452 227725.4521 392459.7963 0.569197329 0.511123927 0.441719442 0.512514389 0.891318532 0.467377835 0.710792667 0.58025167 1 18.58218535 -5 0.164520606 2.616764989 0.473593571 0.531106877 0.126612075 98.04949209 0.912425271 51.50014359 0.456300259 1.00E-05 5 -2.143171418 WLPSS(ph)PSGVAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLPSSPSGVAK 11 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 WLPS(0.032)S(0.719)PS(0.249)GVAK 116.74 0.00099527 92717000 512790 466710 488450 554430 392670 535010 599270 557590 480120 TRUE FALSE 488551.433 514268.2796 510845.9156 498697.6431 461151.5237 516482.4695 507840.3552 508764.4636 554574.5575 0.880948155 0.927320362 0.92114921 0.899243639 0.831541075 0.931312954 0.915729631 0.917395969 1 19.08102191 0.470169416 0.880144713 1.000365436 0.899783395 0.546916416 0.028423774 1.421881786 1.60825956 0.028058021 0.008972108 2.952360699 -0.470169416 -0.100582041 WLREAEEES(ph)DHN ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLREAEEESDHN 12 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 WLREAEEES(1)DHN 124.69 0.00019294 719970000 556640 256700 748710 399530 1023500 522310 1175400 603530 1431400 TRUE FALSE 530328.7304 282858.0218 783039.0941 359368.4853 1201998.076 504222.2737 996071.1423 550681.7137 1653374.201 0.320755416 0.171079252 0.473600649 0.217354598 0.726996995 0.304965611 0.602447493 0.333065384 1 20.65698185 -5 0.127966419 3.062020709 0.116266371 0.585472343 0.164180999 88.90586193 0.721847953 47.0028253 1.135625582 1.00E-05 5 -2.945754339 WLSTSIPEAQWHSS(ph)LAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 1 WLSTSIPEAQWHS(0.12)S(0.88)LAR;WLSTSIPEAQWHS(0.037)S(0.963)LAR;WLSTSIPEAQWHS(0.004)S(0.996)LAR;WLSTSIPEAQWHS(0.033)S(0.967)LAR;WLSTSIPEAQWHS(0.159)S(0.841)LAR;WLSTSIPEAQWHS(0.059)S(0.941)LAR 262.8 1.49E-27 1369050000 1021450 921130 1069450 1214000 1277060 1143950 1352540 1171000 1255900 TRUE FALSE 973168.0828 1014994.194 1118485.34 1091966.414 1499778.86 1104334.725 1146185.182 1068461.032 1450658.558 0.670845719 0.699678218 0.771019021 0.752738408 1.033860692 0.761264406 0.790113687 0.736535159 1 20.46827656 6.687985653 0.063041446 1.22323554 2.73E-20 0.388999005 0.093983157 251.6433314 1.519392133 6.877172971 29.77048833 4875123.85 -6.687985653 -1.22323554 WLSTSIPEAQWHSSLAR ddPTM_SK-BR-3_Trastuzumab_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 ; 302.96 1.57E-46 8289100000 1868210 1285280 1668300 1929800 4218810 1458890 3396960 2226730 5258300 FALSE TRUE 1779903.416 1416251.493 1744793.205 1735812.838 4954569.128 1408368.273 2878691.363 2031745.717 6073730.308 0.293049465 0.233176552 0.287268798 0.285790239 0.815737426 0.231878632 0.473957719 0.334513654 1 22.53415142 -5 0.182274203 3.626429066 0.231564667 0.581813049 0.169983391 90.91950313 0.878758679 86.5829548 0.47472377 1.00E-05 5 -3.394864399 WLVFDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLVFDEADR 9 0 F8WAJ0;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 114.89 0.0036389 7473800 28261 27826 25427 26159 31416 20407 29818 29536 28940 FALSE TRUE 26925.15854 30661.50104 26592.8531 23529.44762 36894.94045 19700.30047 25268.71645 26949.67126 33427.86739 0.805470424 0.917243708 0.795529454 0.703887189 1.103718045 0.58933764 0.755917695 0.806203726 1 15.0287637 WLVLFCDEINLPDMDKYGTQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WLVLFCDEINLPDMDKYGTQR 21 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 56.081 0.083179 31445000 34155 34813 32536 37762 28209 33842 43989 41415 30540 FALSE TRUE 32540.56084 38360.48428 34027.80778 33966.09202 33128.64067 32670.04305 37277.67014 37788.48305 35275.98722 0.922456419 1.087439 0.96461674 0.962867228 0.939127244 0.926126967 1.056743498 1.071223969 1 15.10639884 1.654954481 8.599888488 1.047905389 0.976395429 0.324210866 0.049936327 0.150504549 19.64667747 0.025102297 0.013170276 45.18085869 -1.654954481 -0.07150996 WLYDETLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WLYDETLEDR 10 0 Q9H5Q4 Q9H5Q4 TFB2M "Dimethyladenosine transferase 2, mitochondrial" 0 ; 171.36 9.41E-06 67272000 115364 91108 101478 96735 119342 79713 113531 97661 114741 FALSE TRUE 109910.9723 100392.0088 106130.8667 87011.01402 140155.207 76952.51882 96209.76081 89109.28511 132534.4483 0.829301165 0.757478603 0.800779481 0.656516213 1.057500211 0.580622773 0.725922672 0.672348105 1 17.01600787 WMDEAQALDTADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WMDEAQALDTADR 13 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 146.07 5.63E-06 87504000 127637 142242 118763 149107 125815 125459 138462 134018 140544 FALSE TRUE 121603.852 156736.6215 124208.401 134118.4811 147757.0962 121114.3234 117337.0789 122282.6734 162338.8457 0.749074268 0.96549055 0.765118173 0.826163821 0.910177078 0.746058793 0.722791137 0.753255777 1 17.30864874 2.220500202 24.9908319 0.774737452 0.846998826 0 0.099713544 526.4537482 728468.0332 0.033983461 0.025147661 166.1499451 -2.220500202 0.072261374 WMGGAELSDDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WMGGAELSDDGR 12 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 166.34 0.00012139 158512000 270990 252490 235354 276830 322400 264300 312320 286380 277580 FALSE TRUE 258180.8398 278219.0181 246145.2137 249002.5225 378626.4579 255147.2247 264669.8478 261303.049 320625.6887 0.805240655 0.867737764 0.767702721 0.776614386 1.180898697 0.795779108 0.825479234 0.814978519 1 18.29053049 -2.673586227 1.937344332 3.971599204 0.852765842 0.127831328 0.119540183 3595532.908 163721.0351 46969618.76 0.02939699 0.00212038 2.673586227 -3.118833362 WMGIAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WMGIAFR 7 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 136.19 0.0069881 373250000 429590 282000 189144 188421 507230 182673 449020 292580 440420 FALSE TRUE 409284.1321 310736.1206 197816.4395 169480.5631 595690.7514 176346.9882 380513.7522 266960.1441 508718.0842 0.804540166 0.610821849 0.388852776 0.333152228 1.170964371 0.346649733 0.747985503 0.524770305 1 18.95650686 -1.711967547 2.704202379 1.062338694 0.625212899 0.185098882 0.252572289 67530002.52 56354643.32 28548737.79 0.058610495 0.019410309 1.711967547 -0.437125794 WMHPQVTPTDDSNPWWAAFSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WMHPQVTPTDDSNPWWAAFSR 21 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 187.86 2.73E-17 285370000 335650 308010 294740 334420 349650 298040 406280 329240 308550 FALSE TRUE 319784.4897 339396.5692 308254.1205 300803.4662 410628.8493 287718.8001 344294.5242 300410.0002 356398.3581 0.897267011 0.952295546 0.864914536 0.844009125 1.152162573 0.807295526 0.966038469 0.842905118 1 18.44313117 4.744671005 6.047999828 0.926609079 0.896444625 0.009247621 0.100192133 1.033646705 166.7046694 0.021107309 0.128521948 55548.32971 -4.744671005 -0.030164453 WMIDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WMIDSR 6 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ;; 114.54 0.058621 293900000 1443830 1046380 1142000 1153990 1444130 892930 1245780 1117510 1350450 FALSE TRUE 1375583.017 1153007.312 1194361.83 1037988.733 1695985.815 862007.6102 1055713.381 1019654.9 1559870.889 0.881856971 0.739168427 0.765679928 0.665432466 1.08726038 0.552614717 0.676795361 0.653679037 1 20.57299519 WNDFAEDSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WNDFAEDSLR 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" 0 123.51 0.0010703 40446000 64906 60234 47571 59210 59757 48901 61981 49727 49151 FALSE TRUE 61838.02201 66371.91308 49752.1774 53258.09831 70178.60188 47207.54611 52524.66009 45372.64026 56773.08605 1.08921368 1.169073547 0.876333856 0.938087076 1.236124487 0.831512771 0.92516831 0.799192776 1 15.79291954 2.211376765 24.99998598 0.885449864 1.064844051 0.360671679 0.114235126 235.7000851 216763.2347 0.041976348 0.031008876 162.6959587 -2.211376765 0.179394186 WNDNCPSWNTIDPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WNDNCPSWNTIDPEER 16 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;; 183.79 4.48E-09 559060000 453690 433152 390047 480590 418435 449780 500550 450769 453140 FALSE TRUE 432244.9728 477290.6813 407931.0408 432280.1801 491409.9315 434204.0058 424181.9043 411297.2767 523410.6369 0.825823822 0.911885712 0.779370941 0.825891088 0.938861186 0.829566645 0.810418961 0.785802289 1 18.99758372 3.785060511 24.99888311 0.844033754 0.868854711 0 0.071695061 1995.072021 1072566.398 0.016871197 0.030414908 6096.218306 -3.785060511 0.024820957 WNGHTDMIDQDGLYEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNGHTDMIDQDGLYEK 16 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ; 152.9 5.03E-07 293980000 271312 228318 233467 290936 233170 212079 268127 256495 240130 FALSE TRUE 258487.6194 251583.8638 244171.6929 261690.5605 273834.7742 204734.6511 227219.3017 234034.938 277368.134 0.931929763 0.907039537 0.880316312 0.943477381 0.987261118 0.738133282 0.819197571 0.8437701 1 18.08144252 2.249886234 24.99892577 0.830025945 0.925401998 0.218778461 0.070085196 244.6784362 540076.2621 0.022112537 0.018344571 177.7813639 -2.249886234 0.095376053 WNLDELPKFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WNLDELPKFEK 11 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 121.4 0.0003761 75559000 190680 134210 187120 189620 148490 204280 258130 231240 191680 FALSE TRUE 181666.9343 147886.1516 195699.6371 170559.0373 174386.609 197205.7324 218747.5276 210991.3997 221404.7554 0.820519568 0.667944784 0.883899881 0.770349476 0.787637143 0.890702334 0.987998325 0.952966883 1 17.75632668 2.057160346 2.198138083 0.980460725 0.774409255 0.72459099 0.054707376 0.155166488 1.431997444 0.028242716 0.015940567 114.0670856 -2.057160346 -0.20605147 WNNNKKS(ph)PIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNNNKKSPIK 10 2 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 WNNNKKS(1)PIK;WNNNKKS(1)PIK 58.32 0.058369 1814670000 4256500 3799900 3377000 4338700 2062350 4633300 4963700 5407900 2245200 TRUE FALSE 4055303.681 4187114.13 3531838.79 3902565.633 2422023.187 4472847.659 4206396.4 4934355.607 2593374.149 1.563717168 1.61454302 1.36187013 1.504821676 0.933927404 1.72472131 1.621978225 1.902677872 1 21.30639893 WNS(ph)FQLSHQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNSFQLSHQPR 11 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 WNS(1)FQLSHQPR;WNS(1)FQLSHQPR 183 2.38E-05 453110000 667000 554740 465620 658110 456650 555770 579590 535050 396030 TRUE FALSE 635472.2319 611268.6367 486969.1376 591955.5325 536289.6154 536523.5455 491162.9006 488198.1855 457444.3098 1.389179444 1.33626897 1.064542999 1.294049395 1.172360447 1.172871832 1.073710811 1.06722977 1 18.80323659 8 0.162169316 0.957500451 2.755312384 0.703757903 0.070444636 29.11613476 0.303777623 0.18816027 12.55874385 100000000 -8 1.797811933 WNSIEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WNSIEER 7 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 81.642 0.061992 85275000 209500 207100 192210 201050 271890 175190 249520 195410 289170 FALSE TRUE 199597.3502 228203.7255 201023.0186 180840.072 319307.5299 169123.1264 211451.1413 178298.8645 334013.0067 0.597573586 0.683218081 0.601841888 0.541416257 0.955973341 0.506336948 0.633062596 0.533808148 1 18.34954476 -0.971370759 4.248481486 1.000015138 0.634607982 0.456707645 0.126220684 30696928.57 64154919.96 6998.699156 0.027287387 0.106814261 0.971370759 -0.365407156 WNTEDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WNTEDK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;; 143.23 0.026582 4437560000 3827150 4090260 2995210 4517750 2231880 3758590 3421610 3685410 2095280 FALSE TRUE 3646248.204 4507062.144 3132543.341 4063617.187 2621119.165 3628429.086 2899580.552 3362695.963 2420205.321 1.50658631 1.862264373 1.294329582 1.6790382 1.083015206 1.499223663 1.198072133 1.389425903 1 21.20669801 2.455513419 0.255529507 0.975089276 1.833252908 0.416438592 0.20121626 2.279782175 0.38494442 0.352219885 0.676573224 285.4390707 -2.455513419 0.858163633 WNTEDKVSHVSTGGGASLELLEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNTEDKVSHVSTGGGASLELLEGK 24 1 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 174.7 1.55E-12 814503000 1292210 725632 1277960 1251220 1234440 1271680 2020660 1619220 1577030 FALSE TRUE 1231129.794 799574.7258 1336555.73 1125444.988 1449725.945 1227641.403 1712371.205 1477432.513 1821587.758 0.675855329 0.43894384 0.733731177 0.617837369 0.795858415 0.673940301 0.940043211 0.811068534 1 20.79676507 2.085668603 0.529661697 0.986248302 0.555924833 0.63692389 0.096279837 0.47191321 0.279245846 0.083916562 0.06388666 121.8059781 -2.085668603 -0.430323469 WNTTLYEGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNTTLYEGTWR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 196.11 1.43E-07 425580000 493310 501700 405820 472150 457670 446170 459780 476220 480810 FALSE TRUE 469992.2139 552823.8004 424427.2484 424688.585 537487.5031 430719.021 389632.1166 434519.6522 555371.5592 0.846266263 0.995412515 0.764222153 0.764692714 0.967798034 0.775551095 0.701570165 0.782394498 1 19.08309377 3.727950735 24.83971452 0.804554953 0.920839391 0.123926839 0.100622115 926.651292 2169463.452 0.025668315 0.040215985 5345.037241 -3.727950735 0.116284439 WNWLTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNWLTR 6 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 114.54 0.058621 258320000 370640 366980 278190 314880 352720 283390 359820 317990 329260 FALSE TRUE 353120.5817 404375.6792 290945.2867 283227.6642 414234.2563 273576.1332 304922.8505 290145.1098 380319.9592 0.928482908 1.063251269 0.765001362 0.744708915 1.089173067 0.719331517 0.801753479 0.762897405 1 18.53685413 3.737948963 24.99995184 0.82945616 0.995867091 0.214889339 0.122147816 66.59187542 2721814.13 0.029751473 0.049265085 5469.516828 -3.737948963 0.16641093 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 36 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 147.5 2.26E-13 43494000 39677 35653.6 30276.7 36793 22817.1 35764 37207 35962 13509.1 FALSE TRUE 37801.54684 39286.74237 31664.91664 33094.49774 26796.39502 34525.48371 31530.3888 32812.97663 15604.02223 2.42255146 2.517731761 2.029279129 2.120895321 1.717274855 2.212601546 2.020657772 2.102853748 1 13.92963034 -1.363351762 0.183086544 2.02E-20 2.553931379 0.767656335 0.202977611 12.53919472 0.430663985 7.156660332 0.766130672 0.043315989 1.363351762 2.553931379 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 37 2 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 311.88 3.50E-110 1162517000 1009521 825632 1017051 1039767 912163 1066823 1454250 1049748 528549 FALSE TRUE 961802.943 909764.8395 1063683.794 935247.6457 1071243.938 1029878.652 1232377.453 957826.5001 610513.6795 1.575399496 1.490162907 1.742276758 1.53190285 1.754660009 1.68690512 2.018591057 1.568886222 1 19.2196641 3.742304315 24.83246188 1.683579394 1.532781198 0 0.264116019 849.6820014 5636031.826 0.062376905 0.107155169 5524.644222 -3.742304315 -0.150798197 WPAS(ph)PGSHSNDDFDNWSTFRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WPASPGSHSNDDFDNWSTFRPR 22 1 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 WPAS(0.998)PGS(0.002)HSNDDFDNWSTFRPR 169.44 5.01E-12 92132000 82396 75432 67761 95179 79729 79805 84761 67266 70518 TRUE FALSE 78501.30437 83118.60656 70867.90887 85611.42609 93633.71236 77041.33284 71829.15271 61375.83244 81453.57128 0.963755218 1.020441526 0.870040537 1.051045703 1.14953477 0.945831246 0.881841662 0.753506955 1 16.31369033 1.829387714 3.534985816 0.863774229 1.005536074 0.294105059 0.091403742 0.271331559 5.842941532 0.045011735 0.023733135 67.51304783 -1.829387714 0.141761844 WPFSGKTS(ph)PPCS(ph)PANLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 WPFS(0.001)GKT(0.297)S(0.702)PPCS(1)PANLSR;WPFS(0.002)GKT(0.267)S(0.731)PPCS(1)PANLSR;WPFS(0.034)GKT(0.108)S(0.859)PPCS(0.994)PANLS(0.005)R;WPFS(0.006)GKT(0.061)S(0.934)PPCS(0.997)PANLS(0.003)R 162.11 2.07E-11 1702510000 2772070 1811990 2629920 2410070 2184270 2784200 3505300 2904890 3013650 TRUE FALSE 2641039.745 1996633.841 2750504.433 2167805.185 2565205.996 2687782.456 2970502.106 2650522.432 3480991.45 0.758703313 0.573581943 0.790149724 0.622755102 0.736918212 0.772131301 0.85334944 0.761427447 1 21.73106684 1.070606809 0.43894659 1.007183642 0.664428124 0.625232911 0.071100188 0.656079768 0.342774127 0.086113025 0.046218484 11.76540304 -1.070606809 -0.342755519 WPFSGKTS(ph)PPCSPANLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.017)GKT(0.079)S(0.902)PPCS(0.002)PANLSR;WPFS(0.001)GKT(0.2)S(0.799)PPCSPANLSR 127.35 1.55E-05 6150800000 3083700 2090790 2737400 2780100 2476100 2900400 3884500 3035800 2846400 TRUE FALSE 2937939.612 2303843.878 2862912.498 2500639.066 2907931.056 2799958.421 3291848.181 2769969.258 3287805.175 0.893586893 0.700723965 0.870767076 0.760580063 0.884459663 0.851619324 1.001229698 0.842497992 1 21.64869338 2.221973151 1.521089596 0.946106671 0.802471605 0.383083263 0.072433752 0.360892403 1.637968744 0.037707871 0.022223455 166.7144144 -2.221973151 -0.143635066 WPFWLSPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WPFWLSPR 8 0 P26639;P26639-2;B7ZLP8;A2RTX5-2;A2RTX5 P26639;B7ZLP8 TARS;TARSL2 "Threonine--tRNA ligase, cytoplasmic;Probable threonine--tRNA ligase 2, cytoplasmic" 0 86.472 0.037244 6511100 49750 60528 48976 43164 97781 26534 58580 33378 51738 FALSE TRUE 47398.4161 66695.87201 51221.59804 38825.07271 114833.9754 25615.12093 49642.5451 30455.24537 59761.2648 0.7931294 1.116038495 0.857103648 0.649669528 1.921545266 0.428624143 0.830680965 0.509615141 1 15.86692306 WPS(ph)DSWIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WPSDSWIR 8 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 WPS(1)DSWIR;WPS(1)DSWIR;WPS(0.999)DS(0.001)WIR;WPS(1)DSWIR 123.88 0.0013936 178330000 378457 317396 332785 380211 342197 315670 420308 369872 354841 TRUE FALSE 360568.0876 349739.0132 348043.5214 341991.4679 401876.0485 304738.2687 356182.2951 337484.0469 409867.93 0.879717736 0.853296849 0.849160171 0.834394308 0.980501325 0.743503569 0.869017235 0.823397056 1 18.64479959 -0.696063242 6.963876142 1.000010093 0.85472625 0.383162671 0.058163172 0 1.06E-10 0.049447709 0.011654937 0.201343103 0.696063242 -0.145283843 WPT(ph)GDNIHAEHQVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WPTGDNIHAEHQVR 14 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 WPT(1)GDNIHAEHQVR 115.98 0.00072446 29292000 31848 35495 31271 36136 33110 31308 34062 33187 19400 TRUE FALSE 30342.60816 39111.98085 32704.80628 32503.54063 38884.37352 30223.79611 28865.21631 30280.97034 22408.45292 1.354069746 1.745411921 1.45948524 1.450503555 1.735254712 1.348767638 1.288139633 1.351319096 1 14.45175543 1.177143265 0.719152269 1.014544179 1.552934234 0.586005141 0.138240118 0.428615067 0.51781964 0.126355351 0.051257105 15.03637904 -1.177143265 0.538390055 WQDEDGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 WQDEDGKK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;; 125.56 0.0020149 4312400000 8291750 7145650 7138590 9166290 4250720 9242100 9295090 9113220 4848570 FALSE TRUE 7899815.41 7873799.859 7465901.413 8244877.114 4992044.222 8922043.76 7876953.304 8315218.145 5600461.473 1.410565084 1.405919833 1.333086827 1.472178169 0.891363015 1.59309082 1.406482902 1.484738032 1 22.41711428 3.572209744 1.840943669 1.33447325 1.409345049 0.025183759 0.216489829 1.869505723 12.53146164 0.060739739 0.111032824 3734.304638 -3.572209744 0.074871799 WQFDIECDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WQFDIECDK 9 0 Q13257 Q13257 MAD2L1 Mitotic spindle assembly checkpoint protein MAD2A 0 93.821 0.021263 28234000 83245 90188 75567 97489 65913 89049 86334 90933 73703 FALSE TRUE 79310.17383 99378.25974 79031.8217 87689.2205 77408.20633 85965.2108 73162.16267 82970.42445 85132.48482 0.931608821 1.167336534 0.928339186 1.030032433 0.909267555 1.00978153 0.859391839 0.97460358 1 16.37742212 3.169017654 1.555539237 0.941343729 1.041279663 0.100256059 0.079652908 0.547606298 2.750857507 0.025734183 0.035056002 1475.766521 -3.169017654 0.099935934 WQFLTLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WQFLTLR 7 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 155.51 0.0037367 95774000 302230 229835 122032 138842 309990 135541 309790 223835 259987 FALSE TRUE 287944.1869 253255.4478 127627.2879 124885.3384 364052.1579 130847.1812 262525.8458 204234.8208 300304.4561 0.958840873 0.84332897 0.424992987 0.415862422 1.212276909 0.435715084 0.874198969 0.680092541 1 18.19606636 -0.361798158 7.549570958 1.000022347 0.746549925 0.094087527 0.258503708 0 0 0.232941014 0.054904723 0.434712214 0.361798158 -0.253472423 WQGGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WQGGER 6 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;;; 114.94 0.057818 690530000 646156 560277 543232 615253 792760 561780 673038 579745 789650 FALSE TRUE 615613.4864 617369.8633 568139.7245 553406.5995 931017.093 542325.4177 570353.6919 528979.4544 912104.889 0.674937163 0.676862794 0.622888586 0.606735701 1.020734681 0.59458668 0.625315903 0.579954631 1 19.79884021 -2.195485807 2.388233154 1.953035719 0.674778886 0.392843978 0.126877579 4341306.368 806674.3177 22503798.66 0.028805558 0.006375499 2.195485807 -1.278256834 WQMNPYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WQMNPYDR 8 0 F1T0B3;A0A087X2G1;Q92499;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 110.31 0.0080274 327550000 451310 295360 179102 223710 492010 274050 514000 365170 532450 FALSE TRUE 429977.4707 325457.5198 187314.0039 201222.2458 577816.3882 264559.5798 435579.8597 333193.7789 615019.6266 0.699128047 0.529182331 0.304565896 0.327180202 0.93950886 0.430164451 0.708237332 0.541761213 1 19.23027293 -0.599867364 0.417929198 1.118957592 0.534751503 0.355753254 0.188250358 10.88998125 1.674696601 1.951744602 0.111313724 0.251265369 0.599867364 -0.584206089 WQPDTEEEYEDSSGNVVNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WQPDTEEEYEDSSGNVVNKK 20 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 209.67 7.15E-22 177190000 116587 102315 127215 136368 81608 135471 149616 132332 108329 FALSE TRUE 111076.1636 112741.0148 133047.9336 122660.0296 95840.40936 130779.6053 126789.3313 120744.3085 125128.1081 0.887699537 0.901004711 1.063293737 0.980275587 0.765938292 1.045165689 1.01327618 0.96496551 1 16.93304638 WQQHQGLLPPGMTIDLFR ddPTM_SK-BR-3_Trastuzumab_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 80.596 0.0083421 128380000 241150 200520 228010 231040 237510 255580 308660 268360 217950 FALSE TRUE 229751.3174 220953.216 238464.484 207815.4203 278931.6688 246729.2005 261568.2481 244860.9757 251748.5729 0.912622125 0.877674155 0.947232714 0.825487977 1.10797716 0.980061963 1.039005882 0.972640969 1 17.94162407 2.743817072 24.99999899 1.02037031 0.894141687 0.643885063 0.04770832 250.8304461 1192965.283 0.012931372 0.013346512 554.3921503 -2.743817072 -0.126228623 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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(0.602)S(0.398)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR 173.9 2.34E-12 2485357000 1288617 1508653 1116088 1616381 1176624 1258312 1288723 1346075 1200039 TRUE FALSE 1227706.628 1662386.456 1167261.739 1453899.311 1381826.853 1214736.34 1092104.637 1228205.537 1386134.919 0.885705 1.199296283 0.842098213 1.048887299 0.99689203 0.876347838 0.787877588 0.886064928 1 20.40263626 2.231955143 4.8040604 0.859615386 1.009043947 0.168952106 0.10876729 0.227049659 13.66364282 0.038111951 0.02929398 170.5906183 -2.231955143 0.149428561 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.393)S(0.607)PPPFLPAASEEAEPAEGLR 190.15 5.49E-18 240950000 152700 196530 133740 194750 153390 151870 150220 149680 138260 TRUE FALSE 145482.1736 216556.6304 139872.1113 175173.36 180141.1674 146610.7038 127301.18 136573.2257 159700.6547 0.910967923 1.356015922 0.875839311 1.096885673 1.127992667 0.918034457 0.797123721 0.855182629 1 17.2850107 2.126213136 4.697642786 0.860936266 1.088955414 0.287676565 0.139047345 0.220116714 8.112549744 0.051244899 0.037170548 133.7251629 -2.126213136 0.228019148 WQRPSS(ph)PPPFLPAASEEAEPAEGLRVPGLAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.406)S(0.594)PPPFLPAASEEAEPAEGLRVPGLAK;WQRPS(0.406)S(0.594)PPPFLPAASEEAEPAEGLRVPGLAK 180.97 1.69E-18 1042240000 743620 520900 810510 667490 658460 733790 996600 828260 869460 TRUE FALSE 708470.5563 573980.3022 847672.6852 600392.6371 773295.2155 708378.6683 844550.3662 755733.1635 1004291.416 0.705443206 0.571527639 0.844050513 0.597827112 0.769990864 0.705351711 0.840941536 0.752503856 1 19.93774653 0.16333911 0.241528929 1.111480862 0.620827408 0.5691099 0.08153391 3.935637887 0.431199156 0.551307126 0.1575451 1.456595991 -0.16333911 -0.490653454 WQS(ph)PVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(1)PVTK;WQS(1)PVTK;WQS(1)PVTK;WQS(1)PVTK;WQS(1)PVTK;WQS(0.999)PVT(0.001)K;WQS(0.965)PVT(0.035)K;WQS(1)PVTK;WQS(0.981)PVT(0.019)K;WQS(0.988)PVT(0.012)K;WQS(0.999)PVT(0.001)K 169.93 0.0010421 31719030000 24565200 20875770 21118260 24426500 16895930 24056000 26297200 23695400 18015450 TRUE FALSE 23404051.68 23003034.7 22086553.11 21971101.81 19842574.84 23222934.69 22285079.16 21620505.16 20809193.98 1.124697656 1.105426511 1.061384364 1.055836273 0.953548459 1.115993955 1.070924668 1.038988112 1 24.31071775 3.734782994 2.182699122 1.046256602 1.119630408 0.341920947 0.042650078 0.356323001 3.324420171 0.011835302 0.023494979 5429.789507 -3.734782994 0.073373806 WQSPVT(ph)K ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(0.419)PVT(0.581)K 137.69 0.031949 5049700000 2731900 2397200 2422700 2704200 1816400 2632500 3013900 2617500 1950400 TRUE FALSE 2602768.501 2641477.405 2533783.191 2432368.678 2133179.585 2541335.865 2554074.201 2388297.824 2252858.071 1.155318453 1.172500585 1.124697212 1.079681277 0.946877041 1.128049697 1.133703998 1.060119079 1 21.103325 8 0.168607096 1.023982154 1.653063138 0.322957528 0.058317523 75.988967 0.815837236 0.159946895 12.04469548 100000000 -8 0.629080984 WQVVDTPGILDHPLEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WQVVDTPGILDHPLEDR 17 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 122.49 5.67E-05 86077000 190703 205828 159869 214383 189514 167840 190504 196218 163146 FALSE TRUE 181688.8471 226802.1072 167199.1518 192832.8135 222565.1816 162027.6587 161439.116 179036.1117 188445.8484 0.964143538 1.203539951 0.887253039 1.023279712 1.181056433 0.859810179 0.856687039 0.950066628 1 17.52379049 2.216974181 24.99995513 0.897950977 1.055784471 0.299286588 0.100923373 251.2410513 290968.6046 0.036006134 0.026616173 164.806441 -2.216974181 0.157833495 WRCPVPT(ph)LPGCQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WRCPVPTLPGCQK 13 1 E5RJ64 E5RJ64 C8orf58 1 WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK 74.76 0.053727 795600000 506460 582280 509220 344440 4330000 385660 607060 574940 3406030 TRUE FALSE 482520.6395 641614.994 532568.2407 309816.2368 5085150.629 372304.4975 514441.8476 524595.2057 3934219.737 0.122647099 0.163085704 0.135368199 0.078749093 1.292543622 0.09463236 0.130760832 0.133341613 1 21.90764611 -2.251088063 2.229672002 3.706107529 0.25454023 0.282274809 0.365740694 15694040.88 2473909.599 214181275.9 0.08442624 0.005609342 2.251088063 -3.451567299 WREEQMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WREEQMER 8 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ; 182.39 0.00020867 940720000 699800 577120 464220 499140 748300 489460 726120 595090 719570 FALSE TRUE 666721.8409 635929.1841 485504.9462 448965.4989 878803.2831 472509.8775 615337.0579 542980.7648 831157.2405 0.802160901 0.765112969 0.584131284 0.540169149 1.057324944 0.568496374 0.740337722 0.653282843 1 19.66476191 -1.621675429 3.991075836 1.008656163 0.71994232 0.2648374 0.149512423 0.01074235 0.001018296 0.135041785 0.031071701 0.023895965 1.621675429 -0.288713843 WREEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 172.52 0.00465 3835921000 3755040 3214758 3307682 3605380 3680960 3470280 4206800 3719540 3916620 FALSE TRUE 3577546.701 3542345.495 3459342.491 3242960.353 4322918.259 3350103.333 3564975.397 3393837.359 4523989.426 0.790794665 0.783013655 0.764666352 0.716836413 0.955554457 0.740519709 0.788015855 0.750186846 1 22.10916413 -1.35492883 5.32446352 1.000078442 0.786590849 0.520866781 0.064442365 5.37E-05 6.51E-06 0.055875475 0.013165149 0.044164282 1.35492883 -0.213487593 WRELPDSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WRELPDSK 8 1 Q00059;Q00059-2;H7BYN3 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ; 156.35 0.0003597 462900000 1076640 667190 892610 777440 828600 781800 1105740 964680 989190 FALSE TRUE 1025749.361 735177.4195 933537.0514 699290.2542 973107.5777 754726.07 937039.0547 880207.5051 1142588.533 0.89774169 0.64343147 0.817036951 0.612022818 0.851669301 0.66054056 0.820101924 0.770362628 1 20.12387453 0.268075902 0.937806967 1.001608328 0.750458288 0.396922417 0.093798607 3.014075337 3.073792499 0.090088997 0.025727318 1.853855593 -0.268075902 -0.25115004 WRPHS(ph)PDGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR;WRPHS(1)PDGPR 127.71 0.00021062 11052400000 6651850 5920700 5997760 6750700 6832600 6128610 7223930 6180150 5997130 TRUE FALSE 6337430.233 6524026.061 6272763.229 6072106.811 8024203.277 5916374.699 6121786.802 5638983.303 6927134.291 0.914870416 0.94180736 0.905535098 0.876568369 1.158372704 0.854086907 0.883740165 0.814042729 1 22.72382721 WRPHS(ph)PGWR ddPTM_SK-BR-3_Trastuzumab_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 115.92 0.00084649 610020000 574100 499300 500550 582580 582840 551810 634250 537650 530120 TRUE FALSE 546963.4308 550179.2377 523500.7126 524017.9516 684487.1115 532700.6813 537483.5137 490570.5157 612328.3021 0.893251919 0.898503688 0.854934699 0.855779407 1.117843335 0.869959268 0.877770163 0.801156037 1 19.22394584 WRS(ph)LPGSPEFLHQEACPFVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WRSLPGSPEFLHQEACPFVGR 21 1 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 WRS(1)LPGSPEFLHQEACPFVGR 165.48 8.85E-12 69874000 17122 15337 22639 22328 17430 20478 18835 20285 20118 TRUE FALSE 16312.67699 16899.85774 23677.02054 20083.54702 20469.78648 19768.84173 15961.37482 18508.73786 23237.79669 0.701988971 0.72725732 1.018901269 0.864262102 0.880883276 0.850719282 0.686871266 0.796492805 1 14.50418566 -4.993127822 0.02002319 1.971252698 2.91E-07 0.164631129 0.104193259 6923.792017 10.50209194 696.7347372 381.109869 1.02E-05 4.993127822 -1.971252407 WRS(ph)LQQLAEER ddPTM_SK-BR-3_Trastuzumab_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 231.13 7.83E-13 772688000 849792 657956 718964 750624 831121 678488 1006951 816522 877181 TRUE FALSE 809624.0163 725002.4644 751929.2106 675169.8494 976068.2393 654991.7904 853322.131 745023.005 1013209.749 0.799068521 0.715550225 0.742125913 0.666367304 0.963342723 0.646452317 0.842196921 0.735309747 1 19.95050143 -5 0.29615259 2.918160708 0.751162054 0.398457277 0.090917223 243.1416746 2.264462002 288.8931543 0.080629866 1.00E-05 5 -2.166998654 WRVS(ph)LDVNHFAPDELTVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WRVSLDVNHFAPDELTVK 18 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 WRVS(1)LDVNHFAPDELTVK 198.05 1.07E-15 265300000 530510 323500 373120 451870 376390 465240 494820 459370 371390 TRUE FALSE 505433.8437 356465.0178 390227.9211 406447.1691 442032.2968 449128.6221 419326.121 419145.1275 428983.2644 1.178213431 0.830953203 0.90965768 0.94746626 1.030418512 1.046960708 0.977488298 0.977066385 1 18.71056184 2.744948268 24.51216804 1.006109084 0.964323104 0.047151268 0.088674697 1430.623035 5489918.337 0.027945893 0.028955776 555.838043 -2.744948268 -0.04178598 WRYPSLSLHGIEGAFSGSGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WRYPSLSLHGIEGAFSGSGAK 21 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 243.06 2.67E-30 656220000 551100 354790 436190 462480 579990 433630 761020 610160 658400 FALSE TRUE 525050.5952 390943.5044 456189.743 415990.6317 681140.0724 418613.2844 644912.4219 556731.1557 760501.3094 0.690400646 0.514060265 0.599853988 0.546995287 0.895646153 0.550443871 0.848009614 0.732058116 1 19.53659121 1.090807523 0.409185404 1.015617731 0.57832631 0.516039025 0.113843518 0.881317533 0.414748353 0.146170579 0.08240268 12.3255845 -1.090807523 -0.437291422 WS(ph)DQGPAQTSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WSDQGPAQTSR 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WS(0.999)DQGPAQT(0.001)SR 97.273 0.0067025 150930000 381610 345070 355460 421230 313410 377160 437840 408190 356130 TRUE FALSE 363572.0516 380233.0253 371758.1926 378887.1601 368068.6048 364098.8546 371039.4665 372446.7196 411356.8215 0.883836204 0.924338689 0.903736545 0.921066919 0.894767232 0.885116851 0.901989336 0.90541034 1 18.65003084 WS(ph)GNEPTDEFSDLPLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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;WS(1)GNEPTDEFSDLPLR 260.96 8.64E-27 380596000 395909 404848 269007 429043 271242 349333 364605 389516 253937 TRUE FALSE 377195.1662 446102.4715 281341.237 385914.7825 318546.5189 337235.5106 308977.8108 355407.9141 293316.253 1.285967492 1.520892439 0.959173705 1.315695187 1.086017279 1.149733461 1.053394783 1.211688443 1 18.16209749 3.743735557 24.99778752 1.118727237 1.403429968 0.523395134 0.115895649 284.6745835 1375128.994 0.026797031 0.046541733 5542.881032 -3.743735557 0.28470273 WS(ph)PPQNYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK 120.45 0.0015724 6390290000 3321340 3372710 2726200 3638950 2064960 3160790 3291220 3340720 2258370 TRUE FALSE 3164346.84 3716392.983 2851198.967 3273155.832 2425088.37 3051331.05 2789083.942 3048188.847 2608586.485 1.213050385 1.424676929 1.093005343 1.254762244 0.929656112 1.169725852 1.069193587 1.168521291 1 21.31483683 3.721704862 24.65531882 1.102560924 1.318863654 0.441227902 0.103300829 497.7746804 728107.0224 0.024731314 0.038425282 5268.716883 -3.721704862 0.21630273 WS(ph)PPQNYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WSPPQNYKK 9 1 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 WS(1)PPQNYKK 59.57 0.049142 0 1807900 1480600 1561300 1809500 992350 1697800 1827100 1807600 1079300 TRUE FALSE 1722444.15 1631474.823 1632887.149 1627605.622 1165415.526 1639004.76 1548342.338 1649316.961 1246672.332 1.381633414 1.308663698 1.309796574 1.305560074 0.93482104 1.314703727 1.241980189 1.322975508 1 20.24965089 -4.695721953 0.04403385 1.07E-14 1.852759017 0.333130414 0.120809455 784.4487214 2.702926512 105.0915365 29.82157648 2.02E-05 4.695721953 1.852759017 WS(ph)TTAGFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WSTTAGFLK 9 0 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 WS(0.851)T(0.147)T(0.003)AGFLK;WS(0.843)T(0.144)T(0.013)AGFLK 135.56 0.0002281 312651000 631615 592318 364274 547613 401743 477978 578010 554482 364351 TRUE FALSE 601759.8107 652675.8776 380976.3232 492565.9008 471806.852 461425.502 489823.9586 505928.6166 420852.6922 1.429858527 1.550841636 0.90524863 1.170399786 1.121073622 1.096406202 1.163884579 1.202151313 1 18.68295582 3.752242311 24.96723504 1.108587943 1.490350114 0.760596923 0.09213127 312.5616324 570380.8465 0.021774759 0.038990363 5652.522642 -3.752242311 0.381762171 WSAEASGKPSPSDPGSGTATMMNS(ph)SSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGS(0.001)GT(0.004)AT(0.011)MMNS(0.328)S(0.328)S(0.328)R 80.554 8.12E-06 0 196190 207020 205620 264640 181010 195540 217180 207170 162360 TRUE FALSE 186916.4875 228115.5734 215047.8804 238037.8844 212578.0867 188768.4008 184045.2022 189029.0965 187537.9596 0.996686153 1.216370136 1.14668988 1.269278417 1.133520313 1.006561025 0.981375731 1.007951121 1 17.51682312 2.248982369 4.701454515 0.994459869 1.153362113 0.554165102 0.068681103 0.148861819 8.32995102 0.025900915 0.020238125 177.4117457 -2.248982369 0.158902245 WSDSSKQDDS(ph)PSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WSDSSKQDDSPSGASYGQDYDLSPSR 26 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 WSDSS(0.001)KQDDS(0.999)PSGASYGQDYDLS(0.999)PS(0.001)R;WSDSSKQDDS(1)PSGASYGQDYDLS(0.898)PS(0.102)R;WSDSSKQDDS(0.984)PS(0.012)GAS(0.002)Y(0.002)GQDYDLS(0.851)PS(0.147)R 280.98 4.35E-61 793460000 1165476 861715 1163947 1115014 823820 1194056 1541762 1363318 1182520 TRUE FALSE 1110386.259 949524.7382 1217315.121 1002930.674 967493.9472 1152705.541 1306537.89 1243938.649 1365899.162 0.812934285 0.695164595 0.89121888 0.734264067 0.708320185 0.843917013 0.956540517 0.910710456 1 20.38141955 1.916159659 3.325116855 0.949350848 0.766534377 0.670800048 0.059579136 0.143047998 2.807604824 0.028122 0.015540956 82.44411474 -1.916159659 -0.18281647 WSEPWVPVEALPPS(ph)PLELSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 WSEPWVPVEALPPSPLELSR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 WSEPWVPVEALPPS(0.972)PLELS(0.028)R;WSEPWVPVEALPPS(0.97)PLELS(0.03)R;WSEPWVPVEALPPS(0.993)PLELS(0.007)R;WSEPWVPVEALPPS(0.98)PLELS(0.02)R;WSEPWVPVEALPPS(0.972)PLELS(0.028)R;WSEPWVPVEALPPS(0.894)PLELS(0.106)R;WSEPWVPVEALPPS(0.975)PLELS(0.025)R 172.66 2.40E-15 14325000 258831 218027 231146 268454 249770 237914 268904 237077 252832 TRUE FALSE 246596.5716 240244.1992 241744.2727 241468.4939 293329.8089 229674.9785 227877.756 216317.2811 292039.8953 0.844393439 0.822641711 0.827778248 0.826833929 1.004416909 0.786450695 0.780296664 0.740711405 1 18.15580594 -0.231318563 7.292016822 0.999999999 0.829075772 0.376041874 0.069147035 0 65826610.25 0.065363031 0.015852863 0.587058577 0.231318563 -0.170924227 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK 32 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;; 298 7.84E-90 1146450000 990270 381910 671410 863900 804060 757470 1210900 893250 60559 FALSE TRUE 943461.8996 420827.0632 702194.8126 777059.1307 944287.8094 731238.624 1026154.965 815032.2946 69950.18043 13.48762639 6.016096894 10.03849895 11.10875091 13.49943351 10.45370604 14.66979726 11.65161104 1 16.09404016 -0.692205866 9.028372203 0.999972065 11.24449561 0.649625671 2.390935912 0 0 2.430364807 0.572842479 0.203139385 0.692205866 10.24452355 WSHDGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 WSHDGK 6 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 137.83 0.012566 2117940000 7157560 7161060 6664170 7942580 5142000 7534600 7616940 7400170 4485460 FALSE TRUE 6819236.324 7890780.155 6969728.786 7144176.768 6038763.172 7273674.913 6454835.908 6752171.884 5181042.228 1.316190068 1.523010199 1.345236823 1.378907265 1.165549885 1.403901878 1.245856649 1.30324587 1 22.30481091 -4.292589277 0.138082807 9.59E-10 1.487372945 0.614187988 0.087853468 66.85665976 0.684143584 18.83325618 0.535844513 5.10E-05 4.292589277 1.487372944 WSLELEDQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WSLELEDQER 10 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ;;; 282.72 8.12E-24 331486000 734924 672936 641791 754884 703970 677460 763568 714586 732355 FALSE TRUE 700185.599 741508.9435 671217.7522 679001.6261 826742.1451 653999.3903 647071.6777 652013.0616 845924.873 0.827716055 0.876565954 0.793472061 0.802673674 0.977323367 0.77311758 0.764928067 0.770769465 1 19.69017002 WSMPELAEVEENKKMS(ph)QPGS(ph)PSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WSMPELAEVEENKKMSQPGSPSPK 24 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 2 WS(0.002)MPELAEVEENKKMS(0.989)QPGS(0.812)PS(0.197)PK 52.556 0.064738 56414000 107860 94009 97328 105860 53123 119590 117690 122210 58975 TRUE FALSE 102761.6716 103588.624 101790.5851 95218.75168 62387.63438 115448.5683 99734.22897 111508.6445 68120.5418 1.508526927 1.520666472 1.494271513 1.397797921 0.915841723 1.694768792 1.464084494 1.636931263 1 16.05580229 3.249170919 5.396314192 1.383477111 1.511986088 0.074552185 0.243506964 0.549517293 47.9093629 0.06623043 0.086015391 1774.887861 -3.249170919 0.128508976 WSPAYSFSSDS(ph)PLDSSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WSPAYSFSSDSPLDSSPK 18 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 1 WSPAYSFSS(0.002)DS(0.998)PLDSSPK;WSPAYSFS(0.001)S(0.014)DS(0.985)PLDSSPK 349.02 2.62E-90 168913000 291460 248602 239220 320300 206192 274330 285400 292230 222715 TRUE FALSE 277683.2634 273934.8264 250188.4736 288102.8355 242151.8195 264829.8833 241856.9883 266640.792 257252.5047 1.079419086 1.064848044 0.972540477 1.119922373 0.941300143 1.029455024 0.940154066 1.036494445 1 17.9728256 2.729562843 24.99513698 0.985376598 1.057561819 0.344019313 0.047616405 665.632346 1849073.044 0.013831605 0.013210983 536.4914967 -2.729562843 0.072185221 WSTELVPEGLQS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WSTELVPEGLQSPR 14 0 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44;H3BMM1 H3BRD5 MYO9A Unconventional myosin-IXa 1 WSTELVPEGLQS(1)PR 111.74 0.00066508 23281000 48555 58758 42509 54467 48454 50717 46520 50188 51473 TRUE FALSE 46259.90138 64745.507 44458.0797 48991.87368 56904.36226 48960.65757 39422.5196 45793.27266 59455.16995 0.778063563 1.08898027 0.747758012 0.824013685 0.957096957 0.823488649 0.663062937 0.77021515 1 15.85951465 2.002679224 24.1083074 0.766060381 0.8901318 0.018864476 0.127619102 89.45915408 804964.2085 0.045280928 0.03323106 100.6188209 -2.002679224 0.124071419 WT(ph)SQDSLLGMEFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.699)S(0.301)QDSLLGMEFSGR 130.29 0.00067752 36705000 65114 80040 61365 80472 60613 78249 70752 72297 58814 TRUE FALSE 62036.19026 88196.167 64178.64595 72382.80167 71183.88801 75539.21751 59957.48295 65966.29141 67934.57474 0.913175515 1.298251551 0.944712559 1.065478101 1.047830038 1.111940684 0.88257685 0.971026781 1 16.05185839 1.744921836 25 0.944056011 1.073972843 0.192281358 0.106822257 1.819045027 7172.44605 0.046900409 0.026008705 55.58042155 -1.744921836 0.129916833 WTDLFDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WTDLFDNK 8 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0A3 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 96.711 0.02035 44978000 240720 227430 204890 215710 172340 220600 215230 236210 162450 FALSE TRUE 229341.6427 250605.3756 214284.4092 194026.421 202396.0414 212960.5667 182392.7105 215526.2002 187641.9163 1.222230337 1.335551142 1.141985828 1.034024938 1.078629154 1.134930675 0.972025409 1.148603704 1 17.51762261 3.530784957 4.040878548 1.060759249 1.277445539 0.685513574 0.060231453 0.105608526 3.519818231 0.015311787 0.023611514 3394.571473 -3.530784957 0.21668629 WTETYVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WTETYVR 7 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 155.53 0.0037329 276250000 472720 432270 275150 358590 502710 344920 489520 411730 489640 FALSE TRUE 450375.4624 476318.8045 287765.8997 322543.8519 590382.4648 332975.3339 414834.7333 375676.7385 565570.8705 0.796320118 0.84219119 0.508806084 0.570297851 1.043870001 0.588742015 0.733479666 0.664243436 1 19.10934829 -2.071081518 2.480129836 1.408582161 0.727856974 0.245905103 0.15415115 24191852.9 6941298.756 55980150.86 0.037255593 0.008490211 2.071081518 -0.680725187 WTKPSSFS(ph)DSER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WTKPSSFSDSER 12 1 Q8NC56;H0Y9B7;Q8NC56-2 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WTKPSS(0.001)FS(0.999)DSER;WTKPSS(0.004)FS(0.995)DS(0.001)ER;WTKPSS(0.001)FS(0.999)DSER;WTKPSSFS(0.999)DSER 188.47 5.55E-06 3379140000 3898440 3072520 3559710 5157000 4711100 4462900 5077600 3719820 4140440 TRUE FALSE 3714168.467 3385613.281 3722926.225 4638608.562 5532714.348 4308348.654 4302918.863 3394092.841 4782518.289 0.776613542 0.707914341 0.778444744 0.969909216 1.156862141 0.900853566 0.899718225 0.709687373 1 22.18933905 3.316802809 5.182186749 0.93928541 0.743328302 0.384661661 0.110793303 0.207287017 9.771326874 0.031262639 0.042318882 2073.971617 -3.316802809 -0.195957108 WTLGFCDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WTLGFCDER 9 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 ;;; 204.36 3.89E-05 648700000 1113600 659263 801144 972180 1201600 843431 1253750 998240 1234350 FALSE TRUE 1060962.335 726442.6492 837877.2448 874454.6194 1411158.66 814222.773 1062467.411 910828.8136 1425766.694 0.744134605 0.509510183 0.587667848 0.613322378 0.98975426 0.571077145 0.74519023 0.638834402 1 20.44330649 2.939653474 24.99970049 0.757861858 0.608856328 0.249923272 0.14538853 367.1839804 152112.5589 0.040519623 0.042977621 870.2689208 -2.939653474 -0.149005531 WTPKS(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WTPKSPLDPDSGLLSCTLPNGFGGQSGPEGER 32 1 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 WTPKS(1)PLDPDSGLLSCTLPNGFGGQSGPEGER;WT(0.008)PKS(0.992)PLDPDSGLLSCTLPNGFGGQSGPEGER;WT(0.007)PKS(0.981)PLDPDS(0.012)GLLSCTLPNGFGGQSGPEGER 274.5 1.21E-73 443410000 594000 480250 534700 622840 430460 583980 685670 607190 476810 TRUE FALSE 565922.7972 529188.021 559216.5239 560230.9399 505532.0877 563756.6262 581058.4483 554021.2247 550751.2596 1.027546987 0.960847591 1.015370395 1.017212272 0.917895473 1.023613866 1.055028814 1.005937281 1 19.07104136 2.030473818 24.99998018 1.029657702 0.98868112 0.16892451 0.03481402 270.4858257 221898.6124 0.012241538 0.009040909 107.2688978 -2.030473818 -0.040976582 WTS(ph)QDSLLGMEFSGR ddPTM_SK-BR-3_Trastuzumab_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(0.122)S(0.877)QDSLLGMEFSGR;WT(0.174)S(0.826)QDSLLGMEFSGR 84.842 0.0085724 55968000 136935 144104 123027 166635 119247 137476 127683 136262 116918 TRUE FALSE 130462.3539 158788.3614 128667.9096 149884.5332 140043.639 132715.1716 108202.6133 124330.1769 135049.0463 0.96603684 1.175782916 0.952749487 1.109852586 1.036983547 0.982718318 0.801209755 0.920629803 1 17.04312393 2.013799948 4.138888518 0.885572202 1.055224801 0.377948378 0.080394592 0.166533263 6.586690383 0.031706645 0.020638035 103.2285788 -2.013799948 0.169652599 WTSQDSLLGMEFSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 367.81 4.15E-97 4210119000 3882233 3740271 3570018 4287733 3895585 3532829 4090831 3912387 3938646 FALSE TRUE 3698727.54 4121408.867 3733706.857 3856721.933 4574973.791 3410486.246 3466699.598 3569797.653 4549431.106 0.813008803 0.905917415 0.820697527 0.847737188 1.005614479 0.749651147 0.762007275 0.784669021 1 22.11725472 WTTLNSLQLHGLQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WTTLNSLQLHGLQLR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 77.191 0.026619 113210000 148660 155530 159080 167810 276140 143940 210890 177900 364200 FALSE TRUE 141633.1364 171378.6838 166373.9754 150941.42 324298.7286 138955.3217 178714.8572 162322.1329 420678.2759 0.336678038 0.407386579 0.395489819 0.358804884 0.770894879 0.330312568 0.424825496 0.38585813 1 18.68235779 -1.461048402 2.835002546 1.01711112 0.422471917 0.670679058 0.126318689 13131685.16 14585722.25 1777901.945 0.029540461 0.034590083 1.461048402 -0.594639202 WVAIQSVSAWPEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WVAIQSVSAWPEKR 14 1 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 249.3 7.05E-18 1184600000 1840620 1479100 1263110 1399350 1817110 1447050 2030450 1788500 1854310 FALSE TRUE 1753617.54 1629821.972 1321024.843 1258684.679 2134013.409 1396938.296 1720667.561 1631889.459 2141866.924 0.81873319 0.760935216 0.616763268 0.587657742 0.996333332 0.652205924 0.803349424 0.76190049 1 21.03043742 -0.5244674 0.535192894 1.041518075 0.742855501 0.320432536 0.115885341 12.21132502 2.88165936 1.047516475 0.048957845 0.298904601 0.5244674 -0.298662575 WVCSSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 WVCSSLR 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 ;;;;; 187.69 0.0013506 3192550000 3592810 1768950 518220 644898 4555480 990966 3803300 1837860 3718740 FALSE TRUE 3422984.992 1949208.016 541980.8996 580071.6278 5349954.27 956648.5989 3223036.733 1676927.235 4295423.207 0.796891209 0.453787188 0.126176368 0.135044116 1.245501086 0.222713468 0.750342068 0.390398607 1 22.03436885 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR 39 1 Q99447-3;Q99447;Q99447-4;I3L1R7;Q99447-2;I3L2Q1;I3L1C4 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 193.77 1.35E-24 95258000 46988 34370 41880 50141 41527 49297 59417 42800 42378 FALSE TRUE 44766.97036 37872.34208 43800.23942 45100.73142 48769.29565 47589.83253 50351.84538 39052.2051 48949.7638 0.914549262 0.773698158 0.894799812 0.921367703 0.996313197 0.972217817 1.028643276 0.797801707 1 15.57901428 3.239701075 2.423936392 0.966400675 0.84417036 0.283714471 0.071210428 0.290159183 3.491781369 0.020377012 0.027451329 1736.605112 -3.239701075 -0.122230315 WVDWTVSEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WVDWTVSEPR 10 0 X6RLT1;H0UI80;Q8IXH7-4;Q8IXH7 X6RLT1 NELFCD;TH1L Negative elongation factor C/D 0 83.647 0.035968 26192000 35637 41069 50045 45576 51997 45554 39066 39345 51685 FALSE TRUE 33952.50964 45253.97779 52339.61275 40994.61389 61065.26034 43976.45356 33105.7642 35899.74322 59700.04583 0.568718318 0.758022497 0.876709758 0.686676422 1.022867897 0.736623447 0.554534988 0.601335271 1 15.86544442 -2.451402087 2.316467184 4.115652078 0.719597134 0.266262191 0.142791036 7220183.642 603529.9848 120033988.4 0.036399927 0.003536697 2.451402087 -3.396054944 WVEQHLGPQFVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 WVEQHLGPQFVER 13 0 Q8TCD5;J3KSY6;J3KRC4 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ;;; 157.09 4.75E-05 334890000 491168 381704 422590 461204 607765 422470 590337 460579 582367 FALSE TRUE 467951.462 420600.0716 441966.1695 414842.8977 713759.0236 407839.758 500270.2484 420248.2611 672677.5 0.695654994 0.625262584 0.657025349 0.616703989 1.061071648 0.606293146 0.743699987 0.624739583 1 19.35955548 WVESLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 145.87 0.025802 4123470000 15685560 13555280 14051440 16665620 12511490 15333830 17806690 16242880 14490250 FALSE TRUE 14944134.66 14936578.44 14695712.42 14990360.21 14693489.89 14802815.62 15089952.4 14820567.32 16737323.96 0.892862843 0.892411384 0.878020432 0.895624668 0.877887644 0.884419496 0.901574973 0.885480101 1 23.99656555 -1.894774158 0.592976103 1.0965041 0.888580071 0.955462943 0.007559551 20.35760852 2.085249031 2.732710684 0.002897493 0.012741655 1.894774158 -0.207924029 WVGESER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WVGESER 7 0 Q6PL18;Q6PL18-2;Q9ULI0-2;Q9ULI0 Q6PL18;Q9ULI0-2 ATAD2;ATAD2B ATPase family AAA domain-containing protein 2;ATPase family AAA domain-containing protein 2B 0 ; 128.48 0.0087314 190945000 560000 494000 471680 542860 635330 483600 615340 537700 667260 FALSE TRUE 533529.9098 544339.1616 493306.9946 488290.6814 746131.3508 466852.8107 521458.5815 490616.1375 770735.2729 0.692234972 0.706259569 0.640047253 0.633538776 0.968077337 0.605723946 0.676572878 0.636555968 1 19.55587589 -0.973473293 4.134881098 1.000016847 0.695054506 0.470244921 0.101777836 3578893.613 1442690.608 532.4887158 0.021917565 0.106298395 0.973473293 -0.304962341 WVNDPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WVNDPHR 7 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 122.13 0.0043709 130153000 228999 260713 169308 256817 213645 200798 196591 216395 166268 FALSE TRUE 218174.6711 287279.9511 177070.9393 231001.2672 250904.6204 193844.3149 166597.4323 197446.3066 192051.9923 1.136018786 1.495844681 0.921994806 1.202805889 1.306441123 1.009332487 0.867460058 1.028087781 1 17.5511374 2.125429559 5.303402243 0.948148109 1.229918491 0.383192046 0.148048535 0.191810178 8.176795641 0.055783573 0.040784008 133.4841064 -2.125429559 0.281770383 WVNPHKL ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WVNPHKL 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 97.473 0.019196 2595900000 6793500 3985600 1775060 2044490 6567900 2697800 7365100 4045700 5645300 FALSE TRUE 6472384.718 4391737.171 1856448.257 1838973.981 7713339.681 2604374.51 6241418.726 3691437.06 6520744.292 0.992583734 0.673502437 0.284698828 0.28201903 1.182892525 0.39939835 0.957163546 0.566106704 1 22.63660522 1.693138162 20.5447689 0.821083244 0.661563827 0.084944546 0.30765353 0.881264095 381.2905693 0.138858892 0.076944334 49.33307221 -1.693138162 -0.159519417 WVPFDGDDIQLEFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WVPFDGDDIQLEFVR 15 0 A0A0C4DGS1;P39656-2;P39656-3;P39656 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 151.26 7.07E-06 36046000 42320 33559 32893 48729 50804 34516 46374 40033 41298 FALSE TRUE 40319.61747 36978.70025 34401.17659 43830.66834 59664.20151 33320.70227 39298.79458 36527.49829 47702.28292 0.845234547 0.775197705 0.721164156 0.91883796 1.250761973 0.698513786 0.823834672 0.765738997 1 15.54177069 3.222972173 24.97093225 0.896871901 0.788632237 0.13491594 0.151352635 559.4075021 896105.9821 0.043987047 0.052748531 1670.983542 -3.222972173 -0.108239664 WVTYFNKPDIDAWELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WVTYFNKPDIDAWELR 16 1 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 155.92 1.94E-07 126950000 221680 199610 173320 240640 199630 140400 206390 192000 185280 FALSE TRUE 211201.6257 219950.4859 181266.8934 216450.41 234445.4088 135537.9128 174901.4149 175187.4621 214012.2761 0.986866873 1.027747052 0.84699297 1.011392496 1.095476451 0.633318402 0.81724945 0.818586042 1 17.70733403 2.249800381 24.99959459 0.7976603 0.991853987 0.398127643 0.106556517 184.1875095 409671.5846 0.034012324 0.028216481 177.746223 -2.249800381 0.194193687 WVTYFNKPDIDAWELRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WVTYFNKPDIDAWELRK 17 2 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 ; 203.19 5.57E-12 930940000 1196030 840306 1064615 1215128 1110569 1038043 1499312 1270777 1243399 FALSE TRUE 1139496.032 925934.1367 1113428.651 1092981.025 1304251.882 1002095.311 1270564.418 1159501.029 1436218.967 0.793399933 0.644702624 0.775249928 0.761012805 0.908114927 0.697731567 0.884659267 0.807328866 1 20.45384429 -0.009719928 0.206129239 1.118541839 0.68580645 0.512943132 0.071733084 6.590624455 0.516411735 0.75682862 0.211801285 0.977867634 0.009719928 -0.43273539 WVVIGDENYGEGSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 WVVIGDENYGEGSSR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;;;; 278.38 3.01E-33 485930000 571376 430814 540733 528041 572709 408600 541625 498898 584465 FALSE TRUE 544368.1888 474714.4364 565526.1429 474961.3155 672589.2683 394450.0795 458990.1586 455211.8463 675100.8472 0.806350919 0.70317559 0.837691354 0.703541282 0.996279698 0.584283194 0.679883843 0.67428718 1 19.3647435 WWDNLNHLNQFVDHEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 WWDNLNHLNQFVDHEK 16 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 199.49 2.20E-11 193440000 174960 182830 126520 154570 107570 152890 157470 158320 45408 FALSE TRUE 166689.9875 201460.5849 132321.0671 139032.3299 126330.1739 147595.381 133445.0594 144456.6615 52449.64073 3.178095888 3.841028881 2.52282123 2.650777546 2.408599414 2.814039885 2.544251162 2.75419735 1 15.67864527 0.00486824 0.165146651 2.50E-14 3.888017428 0.716317 0.378341676 7.020244951 0.41455798 6.779318898 2.341764119 1.0112726 -0.00486824 3.888017428 WWGNRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WWGNRK 6 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 112.95 0.04258 2270300000 2271400 1858010 1835210 2532250 2822230 2533990 3466300 2851780 2923610 FALSE TRUE 2164035.423 2047343.331 1919356.194 2277703.419 3314426.018 2446237.291 2937452.272 2602063.025 3376988.507 0.640818119 0.606263044 0.568363259 0.674477693 0.981473882 0.724384251 0.869843728 0.770527652 1 21.68730584 2.927672309 6.202121075 0.849367267 0.611507679 0.676909569 0.085150353 0.12757801 8.703655257 0.022938222 0.024544286 846.588392 -2.927672309 -0.237859588 WYFDVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WYFDVER 7 0 K7EM91;O43291-2;O43291 K7EM91 SPINT2 Kunitz-type protease inhibitor 2 0 ; 91.906 0.037363 55387000 165509 107462 60417 87167 219010 78814 173652 102429 168674 FALSE TRUE 157685.7176 118412.5 63187.17921 78404.80755 257205.2747 76084.65142 147158.1981 93459.77375 194831.1025 0.809345713 0.607770004 0.324317721 0.402424493 1.32014484 0.390515942 0.755311633 0.479696376 1 17.57186448 WYHPGCFVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WYHPGCFVK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 114.93 0.001558 1579500000 5817400 4054900 2908100 3303600 5521200 3558900 6432900 4632200 5021700 FALSE TRUE 5542423.031 4468098.92 3041439.262 2971515.852 6484095.532 3435654.401 5451442.957 4226580.011 5800439.589 0.955517758 0.770303501 0.524346339 0.512291492 1.117862781 0.592309315 0.939832727 0.728665465 1 22.46773081 2.753265532 24.99012223 0.854114283 0.724092786 0.176754827 0.189421411 1971.823005 3350992.456 0.057299437 0.060538145 566.5855997 -2.753265532 -0.130021497 WYNHIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 WYNHIK 6 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 97.306 0.041221 2525100000 5548800 4449200 3607800 4735300 4277300 4557400 6077500 5010400 4030300 FALSE TRUE 5286519.221 4902578.538 3773221.199 4259298.648 5023259.766 4399576.095 5150265.754 4571662.814 4655298.34 1.135591929 1.053118013 0.810521888 0.9149357 1.079041427 0.945068559 1.106323457 0.982034336 1 22.1504422 3.994836468 24.54597428 0.984100168 1.104664254 0.276610238 0.082732889 340.720348 1619708.337 0.021504537 0.042326426 9881.809282 -3.994836468 0.120564086 WYQMGAYQPFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 WYQMGAYQPFFR 12 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 196.88 4.69E-07 502581000 624576 428761 354555 381959 617437 349283 631514 512477 617139 FALSE TRUE 595053.5303 472452.2334 370811.6975 343563.7556 725117.8173 337187.2421 535164.9407 467601.7971 712841.7642 0.83476244 0.662772942 0.520187952 0.481963562 1.017221288 0.47301836 0.750748578 0.655968576 1 19.44322234 -1.500527898 2.560832171 1.016858377 0.679265173 0.272299978 0.167029465 7701236.258 7399549.676 909503.1172 0.03882864 0.031584362 1.500527898 -0.337593204 WYVVQTNYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 125.97 0.00091895 74687000 82338 65397 79085 49791 76314 56083 77882 65960 69975 FALSE TRUE 78446.04592 72061.02865 82711.12548 44785.91408 89623.13744 54140.83165 65999.6705 60184.19272 80826.36562 0.970550207 0.891553494 1.023318627 0.554100308 1.108835425 0.669841224 0.816561155 0.744610898 1 16.30253836 Y(ph)LRAFLPESGFTILPCT(ph)RY(ph)S(ph)METNGAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLRAFLPESGFTILPCTRYSMETNGAK 27 2 Q86Y97 Q86Y97 SUV420H2 Histone-lysine N-methyltransferase SUV420H2 4 Y(0.821)LRAFLPES(0.438)GFT(0.497)ILPCT(0.758)RY(0.774)S(0.711)METNGAK 51.758 0.076057 259850000 81167 100060 76250 89082 43690 91208 72040 85094 8807.3 TRUE FALSE 77330.39677 110256.2278 79746.13792 80127.30812 51309.52217 88049.44409 61048.97489 77642.71825 10173.0911 7.60146508 10.83802619 7.838928907 7.876397381 5.043651104 8.655131779 6.001025085 7.632165825 1 13.31247049 3.146154043 1.987696153 6.219602467 9.177200187 0.283150168 2.195166751 0.40174716 3.255562132 0.632533914 0.819782457 1400.083839 -3.146154043 2.95759772 Y(ph)QDEDTPPQEHISPQITNEVIGPELVHVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 Y(0.551)QDEDT(0.44)PPQEHIS(0.008)PQITNEVIGPELVHVSEK 75.275 0.0039493 14915000 41035 34794 43785 46759 64712 35692 76015 57475 58589 TRUE FALSE 39095.35687 38339.54816 45792.58556 42058.69648 75997.75231 34455.97709 64417.51564 52442.18431 67674.68289 0.577695457 0.566527193 0.676657556 0.621483466 1.122986456 0.509141316 0.951870225 0.774915848 1 16.0463286 4.235823963 0.188561911 1.035358892 0.17576479 0.348864199 0.167103287 12.62398948 0.530479753 0.409071457 2.637309575 17211.70775 -4.235823963 -0.859594101 Y(ph)RY(ph)QRRS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRYQRRSR 8 3 Q9Y698 Q9Y698 CACNG2 Voltage-dependent calcium channel gamma-2 subunit 3 Y(1)RY(1)QRRS(1)R 46.813 0.047125 224400000 27328 22639 28111 29213 27942 16879 33403 28222 27189 TRUE FALSE 26036.2596 24945.93984 29399.91716 26276.45374 32815.07595 16294.476 28306.75886 25750.73207 31405.33126 0.829039483 0.794321819 0.936144151 0.83668768 1.044888706 0.518844264 0.901336102 0.819947793 1 14.93872187 -0.920827774 3.797622192 1.000011473 0.831500058 0.130196268 0.133609906 25753744.55 51735145.16 4751.305796 0.029575451 0.119997508 0.920827774 -0.168511415 Y(ph)SPSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.626)S(0.35)PS(0.024)QNS(1)PIHHIPSR 168.05 2.30E-05 604120000 502700 646430 411600 655590 383690 522100 412120 372060 114200 TRUE FALSE 478938.3673 712301.9519 430472.2671 589688.8477 450605.4145 504019.5461 349243.5249 339480.454 131909.5527 3.630808818 5.399926973 3.263389635 4.470402904 3.41601806 3.820948033 2.647598431 2.573585058 1 17.00918952 1.269901611 0.535089324 0.953975115 4.417604294 0.739704178 0.598569892 0.36434212 0.268212983 0.571960345 0.297381383 18.61665329 -1.269901611 3.463629179 Y(ph)T(ph)T(ph)T(ph)QQVVKLIGSHTISKVTVKIGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTTTQQVVKLIGSHTISKVTVKIGDLK 27 3 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 4 Y(0.851)T(0.499)T(0.499)T(0.499)QQVVKLIGS(0.499)HT(0.499)IS(0.499)KVT(0.157)VKIGDLK 42.806 0.053969 64330000 56239 38009 57949 55487 97383 28967 75963 36333 124910 TRUE FALSE 53580.69392 41882.16031 60606.01897 49909.34134 114366.5644 27963.86553 64373.44919 33151.48991 144280.4048 0.37136501 0.29028308 0.420057173 0.345919055 0.792668724 0.193816101 0.446169036 0.229771256 1 17.13851585 -1.15884791 3.568464346 1.000609635 0.38468109 0.579943558 0.164148796 81415624.06 138302281.5 574282.6759 0.035921994 0.069366869 1.15884791 -0.615928545 Y(ph)Y(ph)S(ph)QPRSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYSQPRSYR 9 1 A0A1W2PNU3 A0A1W2PNU3 3 Y(1)Y(1)S(1)QPRSYR 63.473 0.097971 866370000 25046 12975 19360 16259 20347 13669 18539 16399 25299 TRUE FALSE 23862.12522 14297.16725 20247.67515 14624.61443 23895.51036 13195.6391 15710.53506 14963.01662 29222.23971 0.816574138 0.489256381 0.692885807 0.500461791 0.817716595 0.451561524 0.537622551 0.512042088 1 14.83477914 -1.035768309 5.305198955 1.000003069 0.599659525 0.469570317 0.132823793 4.43E-06 8.05E-07 0.118079258 0.027831335 0.092094075 1.035768309 -0.400343544 YAALSVDGEDENEGEDYAE ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 380.89 1.81E-108 363932000 457290 427552 469315 474676 459604 414097 502952 477695 523463 FALSE TRUE 435674.808 471120.0349 490833.557 426960.6667 539758.7921 399756.7171 426217.4351 435865.4934 604638.9686 0.720553637 0.779175772 0.811779562 0.706141497 0.892696006 0.661149443 0.704912282 0.720869008 1 19.20571444 -1.707453283 2.482919728 1.047278516 0.748196889 0.590543154 0.065500534 8826277.992 6617671.102 2596552.911 0.016011831 0.019613121 1.707453283 -0.299081627 YADEEIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YADEEIPR 8 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 ; 145.34 0.0013282 788980000 783880 638400 604870 753350 661380 663680 846120 775370 834460 FALSE TRUE 746827.5459 703453.6858 632603.8878 677621.8267 776724.4626 640696.5952 717028.8539 707474.4923 963863.795 0.774826848 0.729826859 0.656320832 0.703026538 0.805844629 0.664716943 0.743910973 0.733998409 1 19.87846977 0.19385337 1.737645837 1.000039658 0.726738898 0.785028895 0.044994186 7.171614851 14.76774323 0.041256879 0.011518236 1.562619968 -0.19385337 -0.27330076 YADEEIPRS(ph)PFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YADEEIPRSPFK 12 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 YADEEIPRS(1)PFK;YADEEIPRS(1)PFK;YADEEIPRS(1)PFK;YADEEIPRS(1)PFK 175.27 1.70E-05 1031230000 2289240 2118850 2121810 2553910 1517070 2408360 2577040 2607660 1610370 TRUE FALSE 2181032.162 2334763.224 2219097.087 2297186.115 1781646.528 2324957.889 2183865.217 2379319.466 1860097.955 1.172536186 1.255182942 1.193000122 1.234981259 0.957824034 1.249911535 1.174059254 1.27913665 1 20.82694717 -1.766964469 2.577903056 0.952255845 1.190453834 0.306456136 0.089619779 14366961.14 10350322.01 4337188.469 0.020826937 0.017101552 1.766964469 0.238197989 YADEEIPRSPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YADEEIPRSPFK 12 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 71.241 0.041148 84473000 148590 121860 141970 151580 132620 148040 186900 175880 166820 FALSE TRUE 141566.4452 134277.6725 148479.4649 136342.8904 155748.886 142913.3377 158384.9723 160479.0148 192689.5936 0.734686511 0.696860012 0.770562967 0.707577861 0.808289037 0.74167647 0.821969518 0.832836957 1 17.55591913 0.46606443 0.367886908 1.035790058 0.710722033 0.885677203 0.029504389 0.710492437 0.187332035 0.070144652 0.022135365 2.924586224 -0.46606443 -0.325068025 YADLSHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YADLSHNR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;; 179.68 0.00024309 1739930000 3789280 2881430 2243810 2524140 3701580 2538820 3931860 3224440 3319080 FALSE TRUE 3610168.244 3175050.993 2346690.908 2270408.652 4347134.38 2450900.027 3331982.543 2942090.94 3833785.975 0.941671827 0.828176381 0.612107959 0.592210589 1.133901164 0.639289737 0.869110213 0.767411368 1 21.87033837 YADLTEDQLPSCESLKDTIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YADLTEDQLPSCESLKDTIAR 21 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;; 257.73 1.57E-36 5343450000 4540520 3877500 4104010 4645760 3474560 4517100 5269910 4738560 4023160 FALSE TRUE 4325898.618 4272621.658 4292182.918 4178759.378 4080522.164 4360671.694 4465888.441 4323626.566 4647051.105 0.930891122 0.919426441 0.923635833 0.899228195 0.878088506 0.938373948 0.961015564 0.930402199 1 22.14788408 1.037681149 0.806849154 0.996610253 0.914874731 0.615813411 0.020362766 0.459456682 0.672370188 0.020236164 0.007457609 10.90639315 -1.037681149 -0.081735522 YADSPGAS(ph)SPEQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.5)S(0.5)PEQPK 184.98 1.29E-06 182990000 262450 203110 220140 265210 188170 267070 289810 269570 206090 TRUE FALSE 250044.5086 223807.1399 230233.6367 238550.5869 220986.7884 257821.2989 245594.1618 245965.0217 238049.3846 1.050389225 0.94017105 0.967167536 1.002105455 0.928323292 1.083058036 1.031694168 1.03325208 1 17.86090137 2.233515285 24.99999993 1.040341227 0.979774285 0.366247566 0.038639189 132.1105706 654611.0342 0.01348325 0.010264571 171.2045429 -2.233515285 -0.060566942 YADSPGASS(ph)PEQPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADSPGAS(0.488)S(0.512)PEQPK 228.38 1.76E-12 177850000 479740 417090 407470 501500 356560 484770 576480 556140 403700 TRUE FALSE 457063.641 459591.9452 426152.9025 451088.2672 418743.9511 467982.2933 488527.3882 507441.4333 466303.7342 0.980184389 0.985606401 0.913895539 0.967370051 0.898006858 1.003599712 1.047659181 1.088220823 1 18.83091046 1.965338986 4.208772622 1.047225668 0.955524787 0.615974132 0.034606597 0.14753603 5.660654973 0.0154417 0.009361687 92.32918168 -1.965338986 -0.091700882 YAEAVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YAEAVTR 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 147.69 0.0049651 2205690000 2901240 2403080 2379090 2851690 2605750 2558110 3075410 2704230 2838290 FALSE TRUE 2764104.135 2647956.584 2488173.63 2565032.703 3060191.975 2469522.009 2606199.721 2467433.285 3278437.517 0.843116308 0.807688593 0.75895106 0.782394873 0.933430013 0.75326188 0.794951774 0.752624771 1 21.64457697 -1.422176322 3.009749634 1.003537018 0.805016789 0.568295164 0.053859148 11772913.09 14898182.33 360427.5975 0.012809665 0.037828897 1.422176322 -0.198520229 YAEEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YAEEDR 6 0 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 126.24 0.040887 525370000 1076980 919340 894900 958290 906680 753640 924060 907990 902970 FALSE TRUE 1026073.29 1013021.791 935932.0502 861960.8686 1064804.705 727541.2578 783077.6755 828481.582 1042997.976 0.98377304 0.971259595 0.897347907 0.826426214 1.020907739 0.697548101 0.75079501 0.794327124 1 19.99230493 2.239668479 24.99999643 0.782412306 0.94110193 0.298249473 0.094193784 27.98486064 631524.3976 0.031282324 0.024804668 173.6474777 -2.239668479 0.158689623 YAEEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YAEEDRR 7 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 144.35 0.0037842 2439800000 1935710 1523528 1532155 1530946 1553535 1256000 1705976 1488551 1718362 FALSE TRUE 1844212.825 1678777.235 1602405.822 1377052.399 1824471.012 1212504.405 1445698.029 1358205.583 1984836.803 0.929150861 0.845801142 0.807323715 0.693786208 0.919204546 0.610883677 0.728371233 0.68429081 1 20.92058896 4.013616615 1.012270307 0.749276323 0.940242257 0.135386268 0.115377283 1.071414481 1.754726694 0.035181971 0.171982151 10318.50111 -4.013616615 0.190965933 YAEERDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YAEERDR 7 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;; 88.942 0.016632 2215012000 318223 160057 327597 253819 434850 298869 474190 338847 549440 FALSE TRUE 303181.2294 176366.9903 342617.6465 228304.6319 510687.7023 288519.0916 401843.6064 309175.7603 634644.349 0.477718316 0.277898937 0.539857712 0.359736335 0.804683289 0.454615395 0.633179208 0.487163812 1 19.27558881 -4.999999995 0.12551736 2.702974058 0.26156567 0.581825882 0.136685374 93.04329017 0.746014221 39.85557338 1.030691399 1.00E-05 4.999999995 -2.441408389 YAELLEEHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 111.65 0.0020901 58861000 120340 111520 109720 131730 136460 113010 135320 122520 112860 FALSE TRUE 114651.7667 122884.0148 114750.7705 118488.2501 160258.5808 109096.4354 114674.4487 111791.4993 130361.7524 0.879489303 0.942638562 0.880248757 0.90891882 1.229337423 0.836874569 0.879663295 0.857548301 1 16.99216113 -0.988670279 3.975950073 1.000006957 0.925111847 0.040680035 0.111371718 11278902.92 5674679.689 642.5108689 0.024817681 0.102643091 0.988670279 -0.07489511 YAETFLEPWFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAETFLEPWFK 11 0 Q9NXG2 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 0 132.78 0.0026271 0 112640 107040 100270 118480 94567 100690 123940 108410 101270 FALSE TRUE 107315.7304 117947.4977 104867.4787 106570.1653 111059.4549 97203.08005 105030.6767 98917.04568 116974.4344 0.917428932 1.008318598 0.89649913 0.911055188 0.94943357 0.830977132 0.89789429 0.845629613 1 16.83583373 3.708359303 23.72396365 0.897929098 0.962873764 0.16891911 0.05227469 455.5063554 357812.5993 0.012659951 0.019616641 5109.275288 -3.708359303 0.064944666 YAGGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAGGPR 6 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;E9PK49 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 0 118.11 0.051516 93112000 137440 121310 118690 140210 152500 116000 154130 134870 166820 FALSE TRUE 130943.4836 133671.6269 124132.0539 126115.8244 179095.9517 111982.8909 130614.6377 123060.0678 192689.5936 0.679556592 0.693714821 0.644207357 0.654502519 0.92945316 0.581156921 0.677849983 0.638644078 1 17.55591913 -1.149386577 4.810593518 1.000025327 0.687001037 0.535349191 0.09152783 12143690.72 2901470.752 3262.868938 0.019613227 0.070894644 1.149386577 -0.313024291 YAGKDGYNYTLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YAGKDGYNYTLSK 13 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 154.07 4.09E-05 8398300000 7706600 3238280 6433200 4598100 6709000 5840400 10601400 7337000 9279300 FALSE TRUE 7342324.291 3568264.414 6728168.583 4135890.252 7879047.476 5638145.484 8983961.722 6694533.384 10718286.45 0.68502781 0.332913701 0.627728006 0.385872338 0.735103275 0.526030491 0.838190112 0.624589893 1 23.35357094 1.161765646 0.503777348 0.997120959 0.498208902 0.497486625 0.140233855 0.665909895 0.444142424 0.139906424 0.072658875 14.51328241 -1.161765646 -0.498912057 YAHQSGFHVDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YAHQSGFHVDR 11 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 201 2.60E-08 360348000 166997 143543 146187 187884 297629 135629 216075 177762 57563 FALSE TRUE 159103.3828 158170.1949 152889.8185 168997.5434 349535.4034 130932.1337 183108.7903 162196.2169 66489.57605 2.392907163 2.378872062 2.299455458 2.541714858 5.256995519 1.969212943 2.753947327 2.439423238 1 16.02084056 2.989731768 24.92111699 2.844806619 2.373581358 0.006875618 1.062863964 1755.619586 4260924.438 0.293374185 0.331072377 976.6338393 -2.989731768 -0.471225262 YAHVVLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;;; 154.29 0.0016884 3687190000 4933060 5218770 4324120 5267130 4749120 4467480 5093940 4940820 4268620 FALSE TRUE 4699884.03 5750568.596 4522385.179 4737668.086 5577365.024 4312770.047 4316765.896 4508175.608 4930575.789 0.953212004 1.166307718 0.917212385 0.960875218 1.13117925 0.874699068 0.87550949 0.914330456 1 22.2333247 2.215873416 24.99876482 0.901409982 1.030445229 0.28832339 0.083999912 253.8381751 279699.5375 0.030153976 0.022285237 164.3892507 -2.215873416 0.129035247 YAIAVNDLGTEYVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAIAVNDLGTEYVHR 15 0 H7BZD1;O94925-3;O94925 H7BZD1 GLS "Glutaminase kidney isoform, mitochondrial" 0 151.22 3.04E-06 88248000 119040 98463 105640 100990 109450 92949 114040 117230 107390 FALSE TRUE 113413.2151 108496.4916 110483.6985 90838.29333 128538.0453 89730.15282 96641.10351 106964.7197 124043.4927 0.914302013 0.87466492 0.890685163 0.732310026 1.036233683 0.723376542 0.779090474 0.862316252 1 16.92048653 3.418758873 24.99997691 0.837166692 0.89251925 0.008466717 0.102677535 222.3880578 95260.39057 0.026137759 0.0353907 2622.761943 -3.418758873 0.055352558 YAILNEPFKGEMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAILNEPFKGEMNR 14 1 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 0 120.66 0.0001086 213600000 187800 151810 160850 176450 155510 183240 202480 200830 178520 FALSE TRUE 178923.0662 167279.6116 168225.1316 158712.9108 182630.8948 176894.3529 171587.9572 183244.2605 206203.9698 0.867699426 0.811233711 0.815819073 0.76968892 0.885680789 0.857861044 0.832127322 0.888655348 1 17.65371258 0.411708346 0.689877144 1.003883721 0.827712075 0.7276531 0.032261046 1.041351754 0.757779016 0.038525519 0.011697446 2.580526637 -0.411708346 -0.176171646 YALGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YALGER 6 0 P09960-4;P09960;P09960-3;P09960-2;B4DEH5 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 116.87 0.053984 128750000 323220 235300 262340 292650 346790 270970 295270 330020 359100 FALSE TRUE 307942.0312 259277.3375 274368.5485 263232.266 407270.0662 261586.241 250221.1385 301121.6993 414787.394 0.74240933 0.625084902 0.661467905 0.634619735 0.981876673 0.630651376 0.60325155 0.725966371 1 18.66201252 -1.687140931 1.907199748 1.077983382 0.69189216 0.422369213 0.109585324 279741.0284 153570.8947 104426.3567 0.027977423 0.020552236 1.687140931 -0.386091222 YALPLVGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YALPLVGHR 9 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 143.85 0.00010096 891680000 1228000 1068330 1022620 1184780 1110820 1035630 1374180 1154460 1128670 FALSE TRUE 1169954.874 1177194.042 1069508.139 1065683.663 1304546.656 999765.8734 1164523.602 1053369.362 1303698.379 0.897412233 0.902965027 0.820364707 0.817431149 1.00065067 0.766869001 0.893246184 0.807985481 1 20.3141787 -1.093727171 4.815363872 1.000005711 0.8679544 0.296503763 0.065805597 3.59E-06 6.76E-07 0.056721 0.01336869 0.080588455 1.093727171 -0.13205131 YALQMEQLNGILLHLESELAQTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YALQMEQLNGILLHLESELAQTR 23 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 228.71 4.91E-33 3838380000 854194 784621 793079 945620 825988 779274 912265 862513 782202 FALSE TRUE 813817.9425 864574.7719 829442.4566 850564.481 970040.0457 752287.546 773082.2194 786986.7893 903501.8912 0.900737398 0.956915287 0.918030681 0.941408634 1.073644732 0.832635275 0.855650914 0.871040556 1 19.7851681 YALTGDEVKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 152.07 3.00E-05 1492980000 4165010 4534730 3832790 4933190 2656010 4725190 4747530 5147110 3024480 FALSE TRUE 3968138.232 4996824.143 4008527.213 4437296.369 3119217.303 4561555.485 4023207.104 4696401.762 3493500.911 1.135862944 1.430319977 1.147424121 1.270157496 0.892862885 1.305726147 1.151626178 1.344325329 1 21.73624209 -4.590924631 0.253223975 1.03E-16 1.233853882 0.144468336 0.148467348 276.1019717 3.310989908 143.7013838 0.194097526 2.56E-05 4.590924631 1.233853882 YALYDASFETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YALYDASFETK 11 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 208.11 4.81E-08 2457050000 4190780 3902310 3912000 3991110 3059950 4592950 4658060 4764110 3234690 FALSE TRUE 3992690.135 4299959.826 4091369.069 3589916.04 3593604.311 4433894.99 3947387.396 4346939.272 3736309.205 1.068618767 1.150857595 1.095029572 0.960818777 0.96180592 1.186704512 1.05649377 1.163431353 1 21.83318242 3.464126712 24.86430619 1.059446191 1.11193911 0.08592473 0.076885521 532.6205456 1019134.337 0.020931197 0.028360155 2911.566487 -3.464126712 0.052492918 YALYDATYETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YALYDATYETK 11 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;;;;;; 295.96 3.12E-35 3003280000 4026580 3471550 3514850 4054260 2908710 3869370 4423020 4172880 3248150 FALSE TRUE 3836251.543 3825304.892 3676009.349 3646718.082 3415988.103 3735372.747 3748207.065 3807480.505 3751856.513 1.022494205 1.019576543 0.979784098 0.971976959 0.91047941 0.995606504 0.999027295 1.014825725 1 21.83917322 -0.233213709 8.062506469 1 0.991618064 0.006026316 0.032410063 0 0 0.033367187 0.007864721 0.58450239 0.233213709 -0.008381936 YAQGFLPEKLPQQDHT(ph)TTTDSEMEEPYLQESK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YAQGFLPEKLPQQDHTTTTDSEMEEPYLQESK 32 1 B3KPJ4;A0A0A0MSI2;Q8IXK0-3;Q8IXK0-2;Q8IXK0-4;Q8IXK0;Q8IXK0-5 B3KPJ4 PHC2 Polyhomeotic-like protein 2 1 YAQGFLPEKLPQQDHT(0.237)T(0.237)T(0.237)T(0.237)DS(0.05)EMEEPYLQESK 80.048 0.0014765 27546000 19760 18744 14452 20894 13670 19246 20349 19401 13028 TRUE FALSE 18825.98396 20654.03491 15114.63849 18793.69542 16054.04367 18579.50619 17244.38631 17702.14559 15048.3157 1.251035952 1.372514726 1.004407323 1.248890294 1.066833258 1.234656859 1.145934645 1.176353948 1 13.8773144 7.999999999 0.066176104 0.807429126 2.038017891 0.293906695 0.099216019 301.3690102 1.479344187 5.080241929 34.92861135 99999999.68 -7.999999999 1.230588765 YASICQQNGIVPIVEPEILPDGDHDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 261.58 4.32E-53 2384970000 1981831 2853248 1807654 2483257 1182108 2059717 1858664 2261611 1010671 FALSE TRUE 1888153.776 3143997.215 1890536.724 2233635.288 1388267.261 1988388.484 1575090.67 2063572.351 1167400.697 1.617399905 2.693160303 1.619441147 1.913340719 1.189195162 1.703261347 1.349228825 1.767664142 1 20.1548684 3.206272835 1.831172311 1.451751208 2.130151724 0.33968465 0.373511654 0.325902861 2.253131958 0.111003094 0.151705992 1607.951093 -3.206272835 0.678400516 YASICQQNGIVPIVEPEILPDGDHDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 238.2 2.22E-45 11713221000 8051665 6220828 7015348 8382532 6067190 7935229 9484223 8405253 6123401 FALSE TRUE 7671078.752 6854737.446 7337008.645 7539903.958 7125306.015 7660430.03 8037230.592 7669244.488 7072986.753 1.084560034 0.969143261 1.037328204 1.066014149 1.007397054 1.083054486 1.136327675 1.0843007 1 22.75388813 2.137173425 6.306705812 1.09358611 1.030751353 0.13203317 0.04621796 0.257258879 13.80121901 0.016362992 0.012044977 137.1429303 -2.137173425 -0.062834758 YASS(ph)PKPNNSYMFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YASSPKPNNSYMFK 14 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 YAS(0.058)S(0.942)PKPNNSYMFK;YAS(0.025)S(0.975)PKPNNSYMFK 164.93 2.45E-06 1582430000 2069660 1596800 1358860 1645790 1106390 1650510 1978280 1854400 1101190 TRUE FALSE 1971831.273 1759515.735 1421165.075 1480352.062 1299344.066 1593352.425 1676457.052 1692018.905 1271956.921 1.550234321 1.383313936 1.117305981 1.163838207 1.021531503 1.252677979 1.318014018 1.330248593 1 20.27861838 3.995168992 2.806880808 1.191547965 1.50904224 0.552023168 0.113168928 0.196666546 3.125531566 0.030623101 0.071288019 9889.378334 -3.995168992 0.317494275 YATDTFAGLCHQLTNALVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YATDTFAGLCHQLTNALVER 20 0 Q9UNS2-2;Q9UNS2;H7C3P9;J3QKR0;K7ES36;C9JLV5 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 132.14 1.31E-05 93426000 181090 165100 166850 173480 183590 169610 177720 230800 173800 FALSE TRUE 172530.2346 181923.8777 174500.2375 156041.4608 215608.0379 163736.3632 150605.5499 210589.9285 200752.0164 0.859419685 0.906211957 0.869232801 0.77728465 1.074001855 0.815615037 0.75020691 1.049005297 1 17.61505495 1.216534094 24.99891244 1.024502853 0.86445768 0.362618958 0.088153367 297.77655 337951.4644 0.081372845 0.020409648 16.46395209 -1.216534094 -0.160045173 YATS(ph)PKPNNSYMFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YATSPKPNNSYMFK 14 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 YAT(0.165)S(0.835)PKPNNSYMFK;YAT(0.252)S(0.748)PKPNNSYMFK 117.18 0.00019298 458600000 1384570 1213690 1019960 1232690 779930 1259580 1530920 1436640 851110 TRUE FALSE 1319124.12 1337366.391 1066726.175 1108777.659 915949.5451 1215960.429 1297350.037 1310840.185 983095.7919 1.341806293 1.360362237 1.085068397 1.127842951 0.931699182 1.236868715 1.319657807 1.333379917 1 19.90697247 3.753422316 23.90079779 1.166059256 1.351084308 0.2960749 0.127930188 593.0615352 953765.0034 0.034563887 0.061942972 5667.901782 -3.753422316 0.185025051 YAVTTGDHGIIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YAVTTGDHGIIR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 257.13 3.43E-21 1410360000 878648 798625 671107 756629 825610 688081 877486 808851 786906 FALSE TRUE 837116.0504 880005.7955 701877.9198 680571.2154 969596.1226 664252.5824 743609.3946 738023.7185 908935.3635 0.920985236 0.968172029 0.772197835 0.748756449 1.066738254 0.730802881 0.818110313 0.811965018 1 19.79381818 3.753802189 24.37879528 0.838564885 0.944578643 0.111383541 0.107727237 987.3266742 1579216.37 0.025426494 0.04560012 5672.86161 -3.753802189 0.106013758 YAWQGVALLPFVDER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YAWQGVALLPFVDER 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 188.48 6.92E-07 110298000 269420 227092 229173 240935 288520 225383 312240 258020 276300 FALSE TRUE 256685.0505 250232.933 239680.8087 216715.7561 338837.7967 217577.9302 264602.0533 235426.4009 319147.1929 0.804284218 0.784067473 0.75100397 0.679046412 1.061697562 0.681747905 0.829090963 0.737673419 1 18.28386243 -2.204928307 2.29538419 1.612736268 0.792602884 0.271829566 0.107436933 9171445.242 1450669.584 29294568.66 0.022833886 0.006238378 2.204928307 -0.820133384 YAYDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YAYDKR 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 110.24 0.046296 2784910000 6171820 4979350 4191670 4666650 5290940 4880390 6827330 5960900 5560280 FALSE TRUE 5880090.3 5486751.426 4383862.216 4197549.476 6213678.261 4711380.871 5785695.416 5438931.995 6422539.824 0.915539718 0.854296209 0.682574548 0.653565348 0.967479911 0.73356974 0.90084228 0.846850645 1 22.6147125 0.716792075 0.875526298 0.998945647 0.812694911 0.262033744 0.100171483 1.518805938 2.148780384 0.096052532 0.032487449 5.209452406 -0.716792075 -0.186250736 YAYYDTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YAYYDTER 8 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 113.1 0.0067774 356680000 701870 620740 546580 594020 808820 561400 718450 647610 936550 FALSE TRUE 668693.9961 683994.1117 571641.2336 534307.981 949877.9519 541958.5772 608837.2573 590901.8352 1081785.391 0.618139237 0.63228263 0.52842388 0.493913105 0.878065058 0.500985299 0.562807801 0.546228337 1 20.04498289 -1.298374916 3.975939853 1.000654224 0.596515608 0.572122422 0.110036245 2190278094 386513494.6 13541888.39 0.023765596 0.050306614 1.298374916 -0.404138616 YCDPDSYHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YCDPDSYHR 9 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;;;; 155.84 7.23E-05 2374060000 4632420 4022400 3710280 4934410 4204680 4221500 4838710 4675110 3749700 FALSE TRUE 4413454.687 4432287.133 3880400.008 4438393.732 4937974.861 4075308.396 4100475.92 4265732.584 4331184.325 1.018994888 1.023342994 0.895921235 1.024752908 1.140098063 0.940922411 0.946733183 0.984888258 1 22.04633014 YCDPDSYHRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YCDPDSYHRR 10 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 68.893 0.038048 87511000 83212 58133 71927 65707 93328 72280 103000 88037 116060 FALSE TRUE 79278.73367 64056.81879 75224.9241 59102.00752 109604.3737 69776.92548 87285.45828 80328.01357 134057.992 0.591376407 0.477829168 0.561137184 0.44086896 0.817589254 0.520498065 0.651102235 0.599203467 1 17.0324977 -5 0.2018932 2.967936745 0.508666808 0.64453411 0.099491905 80.6604324 0.799182514 63.89271779 0.207186731 1.00E-05 5 -2.459269937 YCFPNYVGRPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YCFPNYVGRPK 11 1 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 167.67 1.73E-05 738990000 976760 731980 676970 816350 1017940 830100 1135060 928500 1218810 FALSE TRUE 930590.4906 806569.5942 708009.7441 734288.947 1195468.414 801353.4289 961885.7502 847195.6177 1407816.83 0.661016739 0.572922256 0.502913255 0.52157989 0.849164741 0.569217111 0.683246378 0.60177972 1 20.42502821 -5 0.262284988 3.497059439 0.59020244 0.602622454 0.097413828 132.9389764 1.302445701 178.9449894 0.118990859 1.00E-05 5 -2.906856999 YCLS(ph)ILTSHVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YCLSILTSHVK 11 0 O95163;F5H2T0 O95163 IKBKAP Elongator complex protein 1 1 Y(0.22)CLS(0.26)ILT(0.26)S(0.26)HVK 58.223 0.069361 279020000 291430 301550 753750 692770 250570 753380 423110 522590 434190 TRUE FALSE 277654.6815 332278.2878 788310.1831 623131.4434 294269.3287 727290.2617 358556.7986 476829.2492 501521.9677 0.553624167 0.662539847 1.5718358 1.242480855 0.58675262 1.450166311 0.714937374 0.950764433 1 18.93595337 3.969175579 24.72948372 1.056321982 0.594467343 0.295764589 0.299730349 615.4724657 493775.2672 0.072824682 0.1313501 9314.843844 -3.969175579 -0.461854638 YCPEGVHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YCPEGVHK 8 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 ; 67.563 0.058772 128301000 1102570 815490 780960 1151780 767450 925910 1232920 1133350 932850 FALSE TRUE 1050453.701 898589.3581 816767.7885 1036000.886 901293.037 893845.5045 1044815.41 1034107.866 1077511.614 0.974888519 0.833948652 0.758012979 0.961475378 0.83645784 0.829546051 0.969655822 0.959718534 1 20.03927199 1.653406361 6.107660521 0.975217873 0.869084538 0.398457697 0.063992327 0.148028279 11.46851222 0.032851719 0.016244421 45.02009026 -1.653406361 -0.106133335 YCQVIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YCQVIR 6 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 136.44 0.030638 1008990000 780960 654850 566820 681320 743690 623940 841000 734020 773670 FALSE TRUE 744045.5685 721579.9595 592809.2577 612832.4192 873389.3005 602332.8014 712690.004 669745.3175 893646.7922 0.832594684 0.807455435 0.663359688 0.685765813 0.977331657 0.674016632 0.797507483 0.749451935 1 19.7693452 -2.037503026 2.539261944 1.277375013 0.777257124 0.37091336 0.092609751 15529889.52 3977637.908 25094733.63 0.021247331 0.009172695 2.037503026 -0.500117889 YCRPESQEHPEADPGSAAPYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YCRPESQEHPEADPGSAAPYLK 22 1 P40763;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;;; 169.84 4.71E-12 931813000 870064 673999 691803 845598 663352 791686 968769 874720 722365 FALSE TRUE 828937.799 742680.2644 723522.8518 760596.8825 779040.3788 764269.7153 820965.4964 798124.8796 834385.6749 0.993470794 0.8900923 0.867132399 0.911565126 0.933669408 0.915966966 0.983916097 0.956541925 1 19.67035486 1.740076512 6.76239936 0.977203124 0.919387586 0.420240445 0.033939499 0.150264224 19.87106422 0.017330028 0.009125614 54.96376978 -1.740076512 -0.057815538 YCVEEEEKAAEMHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YCVEEEEKAAEMHK 14 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5;C9J6M0 A0A494C1K3 GTF2I General transcription factor II-I 0 145.52 5.14E-06 171960000 192580 135150 135550 157040 113940 148330 222440 190310 111940 FALSE TRUE 183477.1251 148921.9387 141765.1016 141254.0408 133811.0999 143193.2949 188502.6926 173645.4475 129299.0835 1.419013346 1.151763297 1.09641227 1.092459722 1.034895966 1.107457927 1.45788112 1.342975084 1 16.98035252 1.761788125 25 1.314307052 1.162426457 0.08362806 0.154457341 22.80943329 24568.49668 0.071165572 0.039466287 57.78140855 -1.761788125 -0.151880595 YCYYNETHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YCYYNETHK 9 0 Q9H0A0;Q9H0A0-2;E9PMU0;E9PJN6 Q9H0A0 NAT10 N-acetyltransferase 10 0 114.5 0.0016287 120980000 127640 125490 107890 120130 91556 117060 124720 129980 105980 FALSE TRUE 121606.7102 138277.5737 112836.8632 108054.3042 107523.3374 113006.1828 105691.6734 118598.2621 122414.8371 0.993398456 1.129581813 0.921758064 0.882689604 0.878352167 0.923141226 0.863389405 0.968822611 1 16.9014189 3.655372507 6.958669485 0.907697815 1.061081016 0.544818345 0.053056084 0.141764637 10.14616408 0.012876096 0.020045458 4522.436809 -3.655372507 0.153383201 YDAVQHCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YDAVQHCR 8 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ;; 107.66 0.0039594 302149000 453080 339576 325858 374220 454960 353967 482440 431420 425950 FALSE TRUE 431663.8063 374179.1805 340798.9116 336602.6946 534304.88 341709.034 408834.9174 393642.5777 492004.1505 0.877358059 0.760520374 0.692674871 0.684146047 1.085976367 0.694524698 0.830958269 0.800079791 1 18.90831096 YDCGEEILITVLSAMTEEAAVAIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDCGEEILITVLSAMTEEAAVAIK 24 0 P63241;P63241-2;Q6IS14 P63241 EIF5A;EIF5AL1 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-1-like 0 ;;; 266.45 2.01E-44 1272748000 1098627 1077362 937765 1276716 776094 981225 1132473 1216882 792213 FALSE TRUE 1046697.079 1187146.413 980762.4528 1148378.082 911444.5479 947244.9322 959693.4446 1110325.361 915065.346 1.143849544 1.297335122 1.071794989 1.254968388 0.996043126 1.035166435 1.048770395 1.213383684 1 19.80351525 2.739838159 24.99921797 1.058598142 1.197519088 0.381241924 0.084262623 112.2230984 2196018.095 0.024557328 0.024782406 549.3361239 -2.739838159 0.138920946 YDDAER ddPTM_SK-BR-3_Trastuzumab_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 0 123.1 0.044052 229100000 830210 788720 691230 939420 677910 727100 766030 803350 703000 FALSE TRUE 790967.6186 869091.4647 722923.5792 844987.7168 796137.2894 701920.3447 649158.0544 733004.4152 812017.6496 0.97407688 1.070286422 0.890280623 1.040602649 0.980443331 0.864415133 0.799438355 0.902695176 1 19.63115156 2.274373376 5.093574106 0.86596035 0.999278461 0.309067595 0.069211104 0.160101869 9.989069231 0.023129776 0.018617263 188.0933217 -2.274373376 0.133318112 YDDAERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 138.26 0.0044941 7485740000 11447940 9279280 11236490 11452220 10926410 11539880 13591690 11941630 11829610 FALSE TRUE 10906818.56 10224849.18 11751694.18 10301021.09 12831972.44 11140251.06 11518028.06 10895957.57 13664085.5 0.79821065 0.748301025 0.860042495 0.753875632 0.939102177 0.815294303 0.842941744 0.797415793 1 23.70388557 -5 0.155056697 1.660109619 0.762572454 0.519676105 0.054583482 97.91469851 0.886817461 19.95895386 0.228826439 1.00E-05 5 -0.897537165 YDDEVKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDDEVKR 7 1 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;; 106.04 0.013952 498120000 2385940 1974570 2123990 2218110 1705110 1962930 2363510 2372570 1842410 FALSE TRUE 2273161.345 2175780.928 2221377.042 1995141.369 2002480.644 1894953.242 2002913.141 2164815.193 2128121.533 1.068153914 1.022395053 1.043820575 0.93751289 0.940961601 0.890434692 0.94116483 1.017242277 1 21.02114911 3.241413446 24.98619675 0.945976111 1.043328705 0.563726563 0.036903731 46.91082842 410859.2373 0.009994383 0.012957886 1743.465855 -3.241413446 0.097352594 YDDIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDDIKK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 88.254 0.082597 1610400000 5252700 5818300 4172800 6241000 2629000 5635500 5039400 5920100 2562900 FALSE TRUE 5004415.281 6411191.385 4364127.007 5613642.823 3087496.768 5440341.222 4270546.975 5401704.66 2960341.443 1.690485837 2.165693218 1.47419718 1.896282213 1.042952925 1.837741128 1.442585951 1.824689741 1 21.49733215 -1.826685821 0.111685097 1.60E-10 2.195479834 0.31724813 0.305940061 66.13410794 1.112778005 22.84174204 4.300953456 0.014904389 1.826685821 2.195479834 YDDMAACMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDDMAACMK 9 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 68.227 0.020202 0 24361 21552 19298 31794 20722 21776 28817 31469 24014 FALSE TRUE 23209.50381 23748.1733 20182.83239 28598.00672 24335.91024 21021.89166 24420.43739 28713.40753 27737.96847 0.8367413 0.856161233 0.72762475 1.031005812 0.87735013 0.757874236 0.880397474 1.035166204 1 14.75957451 1.303551788 5.143694317 1.017762632 0.849454331 0.425171901 0.080359324 0.173045847 8.174752969 0.055478196 0.018871748 20.11647064 -1.303551788 -0.168308301 YDDPPDWQEILTYFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDDPPDWQEILTYFR 15 0 P61221;D6R9I9;D6RGF4;H0Y990 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 154.28 5.83E-06 331770000 134855 141336 108893 150138 110244 134729 127939 119858 103874 FALSE TRUE 128480.6714 155738.2991 113885.8518 135045.843 129470.5187 130063.3009 108419.5558 109362.5981 119982.2494 1.070830661 1.298011163 0.94918917 1.125548518 1.079080608 1.084021191 0.903629965 0.911489813 1 16.87246146 1.847559337 3.741191014 0.930110619 1.119505485 0.419914351 0.088979707 0.20464925 4.72537952 0.04457433 0.02413138 70.39784055 -1.847559337 0.189394866 YDDRGS(ph)RDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDDRGSRDYDR 11 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 YDDRGS(1)RDYDR 71.879 0.037664 135440000 226740 231750 199880 272950 216740 248240 228020 236520 234440 TRUE FALSE 216022.4496 255365.5885 209044.6957 245512.5474 254539.3874 239643.3866 193231.3611 215809.0549 270795.7578 0.79773203 0.943019161 0.771964441 0.906633654 0.939968149 0.884959899 0.713568642 0.796944002 1 18.04684561 -1.092730468 6.697581014 1.00000013 0.844967199 0.296155184 0.075405502 1.51E-07 2.04E-08 0.075103649 0.017702085 0.080773617 1.092730468 -0.155032931 YDDYDR ddPTM_SK-BR-3_Trastuzumab_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 ; 130.05 0.037058 809580000 1521480 1306620 1237350 1586860 1319600 1401950 1634140 1499500 1443690 FALSE TRUE 1449562.656 1439766.064 1294083.721 1427345.818 1549737.822 1353400.12 1384821.93 1368195.831 1667570.072 0.869266414 0.863391643 0.776029591 0.855943532 0.929338952 0.81160015 0.830443022 0.820472767 1 20.66931595 -1.438237239 3.200900694 1.002437017 0.845916273 0.590897796 0.040632561 25268868.73 36239958.36 571406.3072 0.009558524 0.036455475 1.438237239 -0.156520744 YDDYRDYDS(ph)PERER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;YDDYRDYDS(1)PERER;YDDYRDYDS(1)PERER;YDDYRDYDS(1)PERER;YDDYRDY(0.001)DS(0.999)PERER;YDDY(0.002)RDY(0.092)DS(0.906)PERER 180.88 1.34E-06 1976993000 1821283 1578391 1675583 1901945 1591695 1634450 1908390 1790929 1845427 TRUE FALSE 1735194.562 1739230.837 1752410.138 1710757.875 1869286.104 1577848.587 1617230.056 1634105.762 2131606.394 0.814031412 0.815924949 0.822107751 0.802567435 0.876937745 0.740215732 0.758690751 0.766607647 1 21.02350964 2.233791205 24.99943779 0.790241241 0.82251003 0 0.075667967 427.8739349 2242722.079 0.024439605 0.01863711 171.3133488 -2.233791205 0.03226879 YDDYSSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 253.18 1.36E-12 3731560000 5262200 4529700 4385300 5165100 4953500 4674500 5673700 5010500 5110100 FALSE TRUE 5013466.235 4991281.58 4586370.343 4645894.335 5817388.832 4512620.893 4808072.86 4571754.058 5902548.209 0.849373196 0.845614708 0.777015313 0.78709977 0.985572438 0.764520802 0.814575788 0.774539046 1 22.49290649 -1.121498314 4.535439725 1.000017958 0.826761997 0.424946095 0.064018208 1.08E-05 2.08E-06 0.057350426 0.013516224 0.0755965 1.121498314 -0.173255961 YDEEFQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDEEFQR 7 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ; 110.14 0.015986 713410000 776910 1128410 706370 1369950 972400 1322370 1267630 1297810 1021060 FALSE TRUE 740187.004 1243396.262 738757.7632 1232240.023 1141986.252 1276575.995 1074229.762 1184166.876 1179400.77 0.627595829 1.054261023 0.626383993 1.04480178 0.968276672 1.082393727 0.910826743 1.004041125 1 20.16962261 5.565821011 0.617024818 0.980741731 1.17E-31 0.393650882 0.129103062 9.248942034 1.251199098 0.051647708 8.085376494 367977.2849 -5.565821011 -0.980741731 YDEGS(ph)GGS(ph)GDEGRDEAHKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDEGSGGSGDEGRDEAHKR 19 2 O94762-4;O94762 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 2 YDEGS(1)GGS(1)GDEGRDEAHKR;Y(0.01)DEGS(0.99)GGS(1)GDEGRDEAHKR;Y(0.005)DEGS(0.995)GGS(1)GDEGRDEAHKR;Y(0.001)DEGS(0.999)GGS(1)GDEGRDEAHKR 115.11 7.74E-05 681700000 517342 447920 467902 507540 332601 513780 571420 527140 364615 TRUE FALSE 492888.2689 493563.5572 489355.7695 456521.1149 390606.5091 495987.6698 484239.3842 480980.8271 421157.632 1.17031779 1.171921199 1.161930195 1.083967333 0.927459173 1.177677031 1.149781809 1.142044666 1 18.68400078 -4.999999039 0.016732126 1.52E-10 1.957151404 0.201339059 0.075040032 8113.326812 10.28666572 772.6522967 466.3405742 1.00E-05 4.999999039 1.957151404 YDEMVESMKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDEMVESMKK 10 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 161.62 1.13E-05 407970000 1355400 1162600 1045100 1334600 757930 1344700 1304600 1460800 822320 FALSE TRUE 1291332.928 1281070.262 1093018.869 1200443.472 890112.752 1298132.702 1105559.309 1332884.608 949841.1858 1.359525095 1.348720482 1.15073855 1.263835987 0.937117452 1.366683948 1.163941221 1.403271018 1 19.85732679 3.750362246 22.42621577 1.192984503 1.35412288 0.194390607 0.143298222 271.0191744 515001.4465 0.032878498 0.058498915 5628.105704 -3.750362246 0.161138377 YDERPGPS(ph)PLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR 142.94 2.37E-05 16174880000 9198870 8308390 8108740 9932520 8475590 8906130 9722240 9349130 7396570 TRUE FALSE 8764057.646 9155024.387 8480533.75 8934084.219 9953730.213 8597708.485 8238933.727 8530470.614 8543592.299 1.02580476 1.071566159 0.9926192 1.045705823 1.165052107 1.006334125 0.964340694 0.998464149 1 23.02641137 2.014425322 24.99994658 0.984063926 1.057427643 0.367094926 0.044685066 238.9197407 414060.4597 0.016252758 0.011998559 103.3773326 -2.014425322 0.073363717 YDERPGPS(ph)PLPHRDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YDERPGPSPLPHRDR 15 2 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 YDERPGPS(1)PLPHRDR;YDERPGPS(1)PLPHRDR;YDERPGPS(1)PLPHRDR;YDERPGPS(1)PLPHRDR;YDERPGPS(1)PLPHRDR 126.84 4.27E-05 1240830000 635055 434710 647134 575399 809467 554055 831675 675926 905444 TRUE FALSE 605037.2087 479007.4432 676805.734 517558.7993 950637.7885 534867.9364 704787.704 616738.3361 1045855.631 0.5785093 0.45800532 0.647131128 0.494866389 0.908956992 0.511416605 0.673886226 0.58969739 1 19.99625229 -5 0.168695278 2.543902681 0.502045833 0.499517925 0.124559291 101.0529636 0.950171647 52.2468238 0.413344829 1.00E-05 5 -2.041856848 YDERPGPSPLPHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 109.22 0.00069367 1151700000 1469540 1130790 1212430 1463740 1549110 1259180 1715520 1428600 1490680 FALSE TRUE 1400077.757 1246018.787 1268021.115 1316602.074 1819274.294 1215574.281 1453785.916 1303504.211 1721847.041 0.813125512 0.723652425 0.736430754 0.7646452 1.056582989 0.705971118 0.84431769 0.757038331 1 20.71552556 -5 0.202775396 1.91531965 0.766219389 0.275146854 0.100438779 183.816745 1.822597549 68.44094543 0.216782388 1.00E-05 5 -1.149100261 YDEYVNVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDEYVNVK 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 155.01 0.00096741 83513000 122780 111100 109470 132970 80862 124640 133260 145680 101620 FALSE TRUE 116976.4327 122421.2163 114489.3078 119603.603 94964.3072 120323.6855 112928.7395 132923.4869 117378.7106 0.996572821 1.042959287 0.975383928 1.01895482 0.809042004 1.025089515 0.962088772 1.132432672 1 16.84081124 -0.854571447 5.873070427 1.000000001 0.993217553 0 0.08079621 2.13E-09 1.81E-10 0.071478635 0.016847673 0.139774695 0.854571447 -0.006782448 YDFGIYDDDPEIITLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDFGIYDDDPEIITLER 17 0 Q8IXB1-2;Q8IXB1;Q71S60;A0A087WXH7;E7EP04;A0A494C1G5;Q8IXB1-3 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 112.43 0.002294 0 20647 17621 20460 21707 16068 22491 22712 20599 20291 FALSE TRUE 19671.05723 19416.59993 21398.11124 19524.97112 18870.25411 21712.13103 19246.86727 18795.24236 23437.62465 0.839293978 0.828437191 0.912981224 0.833061004 0.80512656 0.926379331 0.821195303 0.801926076 1 14.51653874 -1.456918884 4.769928492 1.000394937 0.846189655 0.573038048 0.041762183 0.00016103 1.83E-05 0.03712377 0.008727911 0.034920553 1.456918884 -0.154205282 YDGHLPIEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDGHLPIEIK 10 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 120.06 0.00060965 1232510000 5318990 4448020 4555430 5466910 3751590 4919850 5805530 5610430 3851880 FALSE TRUE 5067571.884 4901278.295 4764300.971 4917365.82 4405866.108 4749474.361 4919789.773 5119151.006 4449209.878 1.138982431 1.101606449 1.070819562 1.105222265 0.990258097 1.067487147 1.105767071 1.150575304 1 22.08511772 1.664300577 0.009370858 1.37E-07 2.151028966 0.21396245 0.046641623 1873.661274 17.5640127 2009.927156 2018.975717 46.1636965 -1.664300577 2.151028829 YDGNVYENLFEWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDGNVYENLFEWAK 14 0 Q15067-2;Q15067;Q15067-3;K7ENF1;K7ESC7 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 183.58 3.24E-06 66918000 150836 137184 143570 150318 118952 137601 170115 166336 137912 FALSE TRUE 143706.2812 151163.2056 150152.8265 135207.7491 139697.1911 132835.8429 144160.8324 151770.738 159298.6886 0.90211842 0.948929378 0.942586708 0.848768752 0.876951294 0.833879074 0.904971872 0.952743173 1 17.28137486 1.056337461 2.985851917 0.998769231 0.896766368 0.501589533 0.035827674 0.218283 4.101425286 0.037014137 0.009820899 11.38511603 -1.056337461 -0.102002863 YDGSTIVPGEQGAEYQHFIQQCTDDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDGSTIVPGEQGAEYQHFIQQCTDDVR 27 0 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 255.68 7.23E-53 481080000 408850 468250 376170 452650 400840 416600 428420 412230 325220 FALSE TRUE 389524.4708 515965.2074 393417.7666 407148.762 470746.3691 402173.0375 363056.6605 376132.9558 375653.4566 1.036925027 1.373513802 1.04728909 1.083841383 1.253139991 1.070595866 0.966466977 1.00127644 1 18.51904285 2.01082473 5.453871781 0.992231208 1.168765717 0.376435658 0.099615446 0.167037025 16.12541376 0.03942615 0.027012526 102.5238083 -2.01082473 0.176534509 YDIDLPNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDIDLPNKK 9 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ;;; 107.24 0.0044977 4203970000 20449200 20250600 16287760 23008200 11084980 19839300 19585200 20736200 11056610 FALSE TRUE 19482606.84 22314159.16 17034569.91 20695372.02 13018197 19152260.07 16597118.03 18920428.4 12771212.61 1.525509553 1.747223216 1.333825568 1.620470401 1.01933915 1.499643037 1.299572604 1.481490363 1 23.60639218 3.130641897 0.050255039 3.46E-14 2.939579823 0.390385449 0.18772438 107.0242263 1.659558197 39.73762548 56.98237198 1350.958155 -3.130641897 2.939579823 YDLDFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YDLDFK 6 0 P06733;A0A2R8Y6G6;P06733-2;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;U3KQP4 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Beta-enolase;Enolase;Gamma-enolase 0 ;; 101.21 0.08557 1918820000 8866500 10510900 6042490 10203100 4835190 8343900 7381490 8765600 3933820 FALSE TRUE 8447398.117 11581972.66 6319544.143 9177465.003 5678445.605 8054948.651 6255308.13 7998037.595 4543856.714 1.859081095 2.548929992 1.390788605 2.01975229 1.24969733 1.772711852 1.376651713 1.760187017 1 22.11548591 3.757795535 0.143826689 0.749298133 3.119827571 0.386770761 0.344177875 15.58266517 0.559432494 2.107364931 7.824546023 5725.264226 -3.757795535 2.370529437 YDLDFKSPDDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;;; 140.82 3.61E-05 7414465000 19519620 10673370 15356650 15534200 13205420 17767100 22852800 20224300 15258440 FALSE TRUE 18596966.25 11760998.54 16060767.59 13972672.7 15508441.07 17151820.87 19366185.64 18453353.08 17624640.95 1.055168517 0.667304291 0.911267789 0.792791907 0.879929476 0.973172783 1.098813059 1.047020086 1 24.07109053 2.119641897 2.777493694 1.056877644 0.849656991 0.429434951 0.099119809 0.22982952 3.527249124 0.042914294 0.027854852 131.7170202 -2.119641897 -0.207220653 YDNGSGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDNGSGYR 8 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 136.39 0.0018447 439720000 552210 473550 554780 618730 574220 571140 677760 567790 619930 FALSE TRUE 526108.1277 521805.2834 580217.2118 556534.0849 674363.7862 551361.2786 574355.2641 518071.2976 716065.5782 0.734720595 0.728711586 0.810285021 0.777211057 0.941762608 0.769987129 0.802098693 0.723497 1 19.44973219 -5 0.215634524 2.034828666 0.755023018 0.504466526 0.064669563 125.2075878 1.250644432 56.49982533 0.127219063 1.00E-05 5 -1.279805648 YDNQIHIIDFDDENNIINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDNQIHIIDFDDENNIINK 19 0 A8MUM1;Q53HC9;F8WDS8;C9J0U9;D3YTH5 A8MUM1 TSSC1 Protein TSSC1 0 ; 290.94 1.54E-49 187171000 414290 325710 325810 412880 331390 366390 523100 416790 338870 FALSE TRUE 394707.3327 358900.2193 340748.7108 371376.518 389184.3111 353701.8224 443291.4876 380293.6581 391420.2289 1.00839789 0.916917913 0.870544457 0.948792348 0.994287679 0.903637054 1.132520639 0.971573848 1 18.57835879 1.75567203 25 1.046287009 0.942650063 0.36964386 0.057320847 6.047797135 8845.622197 0.024855867 0.013784013 56.97338589 -1.75567203 -0.103636946 YDNSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YDNSLK 6 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;; 134.66 0.032419 18932080000 9510870 8632410 7885620 10119970 6258110 9165300 9639040 9321330 6826440 FALSE TRUE 9061310.024 9512062.393 8247183.477 9102691.389 7349522.403 8847903.363 8168427.415 8505104.93 7885049.451 1.149176055 1.206341501 1.045926665 1.154424135 0.932083235 1.122111335 1.035938641 1.078636854 1 22.91068837 3.546645732 1.716432568 1.049600325 1.178097393 0.36375803 0.064823599 0.324068691 1.900031054 0.017499522 0.032110567 3520.835481 -3.546645732 0.128497069 YDPQKEAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDPQKEAELR 10 1 B4DDF4;B4DUT8;Q99439;H3BVI6;Q99439-2;A0A087X271;K7ES69 B4DDF4 CNN2 Calponin;Calponin-2 0 68.069 0.055708 109140000 495380 301900 476830 452260 449510 484530 620110 508200 532790 FALSE TRUE 471964.3691 332663.9532 498693.1271 406797.9656 527904.4017 467750.6046 525500.8304 463699.3139 615412.3521 0.766907534 0.54055456 0.810339808 0.661016901 0.85780599 0.760060475 0.853900362 0.753477424 1 19.23119388 0.903914251 0.213576114 1.084111848 0.607381289 0.487717521 0.087194553 2.779616965 0.44700505 0.476830585 0.282480838 8.01519792 -0.903914251 -0.476730559 YDPSIGIYGLDFYVVLGRPGFSIADKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDPSIGIYGLDFYVVLGRPGFSIADKK 27 2 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 219.38 1.70E-34 345110000 489690 418200 421970 523930 331530 495550 587090 505930 359250 FALSE TRUE 466543.3242 460815.0555 441317.7419 471263.561 389348.727 478388.9792 497518.6379 461628.0871 414960.6552 1.124307373 1.110503007 1.063517074 1.135682516 0.938278659 1.152853827 1.19895376 1.112462305 1 18.66261503 YDS(ph)DGDKSDDLVVDVSNEDPATPR ddPTM_SK-BR-3_Trastuzumab_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(1)DGDKSDDLVVDVSNEDPATPR;Y(0.023)DS(0.954)DGDKS(0.024)DDLVVDVSNEDPATPR 156.03 2.04E-08 94868000 171604 178589 157450 197274 78434 183582 160972 189694 78717 TRUE FALSE 163492.619 196787.4221 164669.2382 177443.6427 92112.86477 177224.5093 136412.7649 173083.3877 90924.03033 1.798123317 2.164305975 1.811064002 1.951559363 1.01307503 1.949149292 1.500293866 1.903604439 1 16.47237401 -1.728384878 0.130285799 2.14E-12 2.226254994 0.378628249 0.311038164 46.15269334 0.945351294 17.99711287 2.781056787 0.01869025 1.728384878 2.226254994 YDS(ph)SNQVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YDSSNQVK 8 0 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YDS(0.915)S(0.085)NQVK;YDS(0.5)S(0.5)NQVK;YDS(0.929)S(0.071)NQVK;YDS(0.923)S(0.077)NQVK;YDS(0.5)S(0.5)NQVK;YDS(0.5)S(0.5)NQVK;YDS(0.983)S(0.017)NQVK 163.84 0.00034991 2131630000 3911236 3405680 3551347 4198786 2540255 4171225 4399742 4200693 2983612 TRUE FALSE 3726359.626 3752722.664 3714179.773 3776716.054 2983274.668 4026774.432 3728480.551 3832858.052 3446295.311 1.081265327 1.088915002 1.07773114 1.095877084 0.865646846 1.168435688 1.081880749 1.112167619 1 21.7166149 -1.481323007 6.860234008 0.99997971 1.073379014 0.076374926 0.077884476 2.21E-05 1.67E-06 0.068911375 0.016238078 0.033012392 1.481323007 0.073399304 YDSDGVWDPEKWHASLYPAS(ph)GR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDSDGVWDPEKWHASLYPASGR 22 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 YDSDGVWDPEKWHASLYPAS(1)GR 197.73 1.19E-22 36161000 67337 73585 54853 85453 63501 70268 73106 87530 54285 TRUE FALSE 64154.11346 81083.39516 57368.06431 76863.10209 74575.55429 67834.60154 61952.33702 79865.40917 62703.24055 1.023138723 1.293129262 0.914913867 1.225823441 1.189341311 1.081835659 0.988024486 1.273704652 1 15.93625238 2.062039823 12.94460541 1.073172633 1.136553621 0.021797197 0.129132255 3.091598065 639.5444776 0.044688404 0.033003041 115.3559031 -2.062039823 0.063380987 YDSWHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YDSWHK 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 106.29 0.032252 107500000 200610 177570 157040 240020 168890 195190 225980 231660 177120 FALSE TRUE 191127.5629 195664.5849 164240.4393 215892.7336 198344.3625 188430.5214 191502.6006 211374.6223 204586.865 0.934212286 0.956388793 0.802790733 1.055261948 0.969487276 0.921029419 0.936045433 1.033177874 1 17.642354 1.244398058 24.96002321 1.016588949 0.939887207 0.213499187 0.061651538 186.0424987 795516.8889 0.040416777 0.013863159 17.55488779 -1.244398058 -0.076701742 YDSYESCDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YDSYESCDSR 10 0 Q9ULX6;V9GZ50;M0R1Y5;M0R010;M0QYT7 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 ; 192.32 1.62E-06 93680000 196728 172305 167782 203319 175338 171936 188794 195710 195125 FALSE TRUE 187429.0573 189863.0754 175474.9707 182880.9878 205916.8917 165981.8132 159990.0079 178572.5949 225383.9884 0.831598813 0.842398241 0.778560056 0.811419609 0.913626976 0.736440128 0.709855252 0.792303819 1 17.7820255 2.205544397 24.99998884 0.775618299 0.832417577 0 0.085972924 448.7044613 339757.8804 0.029103778 0.021495896 160.5256353 -2.205544397 0.056799278 YDVDTLDMVFLDHWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YDVDTLDMVFLDHWK 15 0 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 264.87 3.68E-25 564492000 2010561 2369557 1691112 2355266 1248908 1811931 1912699 2076910 997786 FALSE TRUE 1915525.766 2611017.552 1768651.158 2118510.187 1466717.16 1749183.375 1620881.638 1895044.75 1152517.557 1.662036083 2.265490479 1.534598017 1.838158711 1.272620231 1.517706489 1.406383468 1.644265407 1 20.1363573 3.100421785 1.467888596 1.406014766 1.936476982 0.414271527 0.256848817 0.337590766 1.511224821 0.084307285 0.109297535 1260.148669 -3.100421785 0.530462215 YDVDTLDMVFLDHWKDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YDVDTLDMVFLDHWKDR 17 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;; 155.92 4.95E-08 125107000 212057 142599 205988 160362.6 349339 158214 250314 207471 284951 FALSE TRUE 202033.4859 157130.0002 215432.7535 144242.6468 410263.611 152735.0095 212124.002 189303.7394 329139.7458 0.613822817 0.477396007 0.654532782 0.438241351 1.246472407 0.464043044 0.644480057 0.575147006 1 18.32834073 YDWDLLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YDWDLLAAR 9 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 178.83 0.0001175 211267000 916401 746868 559856 654669 894819 580731 989022 783681 815950 FALSE TRUE 873084.5409 822974.6983 585525.9514 588860.4283 1050875.15 560620.1399 838128.5293 715057.7371 942483.3587 0.926366002 0.873198121 0.621258663 0.624796632 1.115006584 0.594832932 0.889276741 0.758695345 1 19.84610762 -1.028177364 4.545255661 1.000006215 0.809975627 0.128245987 0.161829043 0.111675721 90183137.23 1467.39836 0.034843435 0.093717919 1.028177364 -0.190030588 YEAANWK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEAANWK 7 0 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;P60900-3 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 114.78 0.013557 318570000 555190 475320 378500 412100 448350 442040 587150 478330 510000 FALSE TRUE 528947.269 523755.6484 395854.5994 370674.9251 526542.098 426732.044 497569.4838 436444.8894 589088.1953 0.897908451 0.889095474 0.671978496 0.629235025 0.89382558 0.724394152 0.844643447 0.740882083 1 19.16812412 -1.107680109 7.726417687 1.000000028 0.798117511 0.322892371 0.0958606 4.32E-08 4.92E-09 0.094523443 0.022279386 0.078040473 1.107680109 -0.201882516 YEAQKLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YEAQKLER 8 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ;;;; 123.63 0.0012217 2047559000 3078520 2206330 2402840 2439990 2582430 2586340 3625030 3073410 2891670 FALSE TRUE 2933004.461 2431157.535 2513012.591 2194717.57 3032804.974 2496774.397 3071965.095 2804285.927 3340095.415 0.878119963 0.727870684 0.752377486 0.657082298 0.907999502 0.74751589 0.919723754 0.83958258 1 21.67145789 1.207908684 0.728434023 0.991473541 0.771364182 0.441878255 0.078126488 0.563003278 0.693284371 0.069655422 0.028231838 16.14019152 -1.207908684 -0.220109359 YEAWLAEAESR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEAWLAEAESR 11 0 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3 Q15642 TRIP10 Cdc42-interacting protein 4 0 ; 117.67 0.0019149 49030000 60040 61958 51574 57095 58128 52179 67115 64408 59822 FALSE TRUE 57202.02819 68271.59064 53938.71891 51355.70213 68265.5048 50372.02815 56875.3741 58768.09407 69098.89023 0.827828464 0.98802731 0.780601812 0.743220361 0.987939236 0.728984619 0.823101122 0.850492589 1 16.07637492 YEDFKEEGSENAVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YEDFKEEGSENAVK 14 1 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 201.24 1.65E-08 937465000 1595890 1447370 1454310 1697640 794600 1705210 1731710 1835450 875330 FALSE TRUE 1520455.442 1594858.649 1520991.552 1526990.002 933177.9884 1646158.15 1467505.834 1674728.268 1011071.706 1.503805748 1.577394204 1.504335986 1.510268751 0.922959255 1.628131952 1.451435962 1.656389214 1 19.94745389 -2.017665758 2.810199916 0.470276471 1.472564142 0.342996144 0.204097308 25819554.56 26211159.43 87974357.26 0.047671592 0.009601393 2.017665758 1.00228767 YEDHTIFHDISLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YEDHTIFHDISLR 13 0 P82675 P82675 MRPS5 "28S ribosomal protein S5, mitochondrial" 0 ;; 199.8 6.65E-08 183653000 291469 264759 240978 252011 265817 212944 247643 245399 33934 FALSE TRUE 277691.838 291738.2431 252027.0797 226678.3755 312175.4006 205569.6959 209860.5121 223910.5626 39196.31141 7.084642101 7.443002482 6.429867266 5.783155796 7.964407604 5.244618396 5.354088294 5.71254168 1 15.25843027 0.02166491 0.351967161 6.69E-15 7.282027796 0.852515163 0.735182303 1.603054803 0.284445046 3.354482942 0.609227777 1.051150521 -0.02166491 7.282027796 YEDICPSTHNMDVPNIK ddPTM_SK-BR-3_Trastuzumab_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 ; 256.45 4.26E-27 291650000 648500 577470 553110 808680 538850 646350 683070 700920 515290 FALSE TRUE 617846.6902 636314.8495 578470.6406 727389.95 632825.2694 623966.7374 578855.1261 639543.729 595198.5415 1.038051418 1.069079988 0.971895259 1.222096325 1.063217104 1.048333781 0.972541237 1.074504866 1 19.18301147 -1.099312777 6.087567732 0.999999824 1.053432366 0.061664422 0.068868969 1.56E-07 2.31E-08 0.063422852 0.01494886 0.079558617 1.099312777 0.053432542 YEDKDGKQPVGR ddPTM_SK-BR-3_Trastuzumab_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 54.7 0.07459 120680000 234790 193390 193230 281900 140010 263480 254280 295180 169760 FALSE TRUE 223691.942 213096.6609 202089.7866 253562.8764 164427.6997 254355.6215 215484.9158 269332.4744 196085.5138 1.140787699 1.086753717 1.030620685 1.293123962 0.83855098 1.297166816 1.098933377 1.373546006 1 17.58112343 YEDRYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YEDRYDR 7 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 170.66 0.00088133 1542748000 3115411 3584900 2497686 3545128 2472837 2826454 2791407 2963541 2354804 FALSE TRUE 2968151.696 3950205.386 2612207.374 3188764.998 2904098.99 2728573.189 2365526.594 2704037.639 2719974.978 1.09124228 1.452294752 0.960379193 1.172350858 1.067693274 1.003161136 0.869686896 0.994140631 1 21.37516195 2.880167636 0.916419984 0.940579137 1.246965001 0.361576144 0.126140082 0.476413173 0.871223132 0.066478053 0.072007016 758.8704404 -2.880167636 0.306385863 YEDYDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEDYDYR 7 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 83.843 0.051139 814400000 2078480 2194120 1814210 2387300 1873310 1929750 1982060 1969130 1719000 FALSE TRUE 1980234.37 2417703.323 1897393.323 2147324.068 2200014.671 1862922.274 1679660.344 1796702.538 1985573.741 0.997310918 1.217634618 0.955589452 1.081462765 1.107999479 0.938228702 0.845931989 0.904878273 1 20.92112451 2.144240502 4.826822613 0.898493431 1.080021415 0.46607599 0.078539708 0.15385782 6.087122658 0.028673775 0.020929335 139.3928514 -2.144240502 0.181527985 YEECKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEECKEK 7 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 85.161 0.019165 372780000 918560 728470 772750 884250 536680 971960 1164000 1109000 696590 FALSE TRUE 875141.4892 802701.9212 808181.3519 795363.51 630276.8221 938300.7815 986410.4217 1011890.081 804613.6195 1.087654332 0.997624079 1.004434094 0.988503663 0.783328553 1.166150757 1.225942984 1.257609934 1 19.61793663 2.035952356 24.999197 1.188728674 0.987301214 0.450558984 0.102102989 139.9404765 97305.99541 0.036224377 0.026753386 108.6306444 -2.035952356 -0.20142746 YEEEEEQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 247.07 2.19E-10 1495450000 808490 784550 759070 858740 722670 795270 849260 811190 784420 FALSE TRUE 770274.28 864496.537 793874.1103 772417.8237 848703.4192 767729.6005 719689.7893 740157.9032 906063.8473 0.850132452 0.954123199 0.876178994 0.852498227 0.936692731 0.847323953 0.794303615 0.81689376 1 19.78925319 2.097365956 9.272652558 0.84090742 0.895393616 0 0.064526551 0.531890507 45.84890537 0.021913797 0.016177393 125.1312997 -2.097365956 0.054486196 YEEIDNAPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YEEIDNAPEER 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;; 248.11 8.01E-16 898510000 1410010 1072590 1161180 1164720 1301970 1048400 1261640 1175610 1216280 FALSE TRUE 1343361.622 1181888.14 1214421.252 1047640.133 1529033.156 1012093.645 1069153.646 1072667.356 1404894.491 0.956201075 0.841264699 0.864421677 0.745707339 1.088361557 0.720405448 0.761020599 0.763521648 1 20.42203036 YEEIVK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;;; 132.22 0.034881 2997484000 6244750 6040580 5559550 6524780 4380540 6072220 6393810 6292230 4855880 FALSE TRUE 5949573.043 6656121.97 5814460.867 5868896.718 5144504.789 5861937.499 5418316.854 5741248.984 5608905.07 1.060736983 1.186706119 1.036648115 1.046353369 0.917203041 1.045112625 0.966020424 1.023595321 1 22.41928774 3.401955144 2.430250688 0.993236276 1.122538749 0.505102134 0.04906649 0.185778723 2.220614801 0.013118526 0.019591402 2523.220149 -3.401955144 0.129302473 YEEIVKEVSTYIKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEEIVKEVSTYIKK 14 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 89.506 0.0034432 40429000 195350 91352 233540 142780 175340 188440 323050 247480 278790 FALSE TRUE 186116.1926 100660.8727 244248.04 128427.4831 205919.2405 181914.2755 273762.7893 225809.3392 322023.3293 0.577958724 0.312588758 0.758479333 0.398814221 0.639454418 0.564910238 0.850133404 0.701220435 1 18.29680568 1.498598784 0.517729508 0.997485135 0.466130989 0.56504437 0.133030967 0.514586559 0.344872943 0.123696326 0.072730855 31.5209127 -1.498598784 -0.531354145 YEELFPAFSDSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YEELFPAFSDSR 12 0 P54920;M0R0Y2;M0R2M1;M0R213;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;;; 181.53 4.20E-05 419538000 531738 555841 472883 571475 476205 482461 520974 533538 477727 FALSE TRUE 506603.7985 612481.8298 494565.1533 514029.2473 559255.0012 465753.2546 441489.848 486818.5843 551810.4633 0.918075738 1.109949649 0.896259107 0.931532259 1.013491114 0.844045711 0.800075166 0.882220648 1 19.07381329 2.233392066 24.99955595 0.857231075 0.981896158 0.225326722 0.07873113 134.3945422 650040.4891 0.027837497 0.021183556 171.1559756 -2.233392066 0.124665083 YEEVAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEEVAR 6 0 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 97.596 0.095131 243760000 487770 422320 400220 505270 484400 443170 499790 482170 494230 FALSE TRUE 464714.0788 465354.8881 418570.4829 454479.2996 568879.2066 427822.9118 423537.8562 439948.6387 570872.6642 0.814041568 0.815164077 0.733211641 0.796113263 0.996508052 0.749419159 0.741913009 0.770659845 1 19.12280946 -1.142168943 3.840860318 1.000093167 0.800816984 0.408905474 0.074750844 6229993.843 5565002.325 4455.721732 0.01720427 0.072082702 1.142168943 -0.199276183 YEEVSVSGFEEFHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YEEVSVSGFEEFHR 14 0 Q9BRA2;I3L2R6;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;; 203.7 1.47E-08 1097369000 1290540 1119303 1228561 1365459 1361056 1189174 1536609 1326446 1246727 FALSE TRUE 1229538.732 1233361.248 1284891.737 1228200.467 1598423.735 1147992.606 1302171.075 1210295.356 1440063.056 0.853808954 0.856463363 0.892246858 0.852879645 1.109967879 0.79718218 0.904245873 0.840446084 1 20.45770055 YEFTDALLCHDDELEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YEFTDALLCHDDELEGR 17 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ;;; 236.81 3.37E-20 129106000 188135 214329 183852 224604 188923 184991 204825 218021 175339 FALSE TRUE 179242.2314 236169.3688 192281.7961 202026.3792 221871.1114 178584.7153 173575.1844 198929.9254 202529.6766 0.885017121 1.166097595 0.949400598 0.997514945 1.095499263 0.881770604 0.857035805 0.982226056 1 17.6277738 2.224049019 24.99897093 0.910469426 1.022537785 0.188766524 0.086707334 301.9832825 520219.8096 0.030796912 0.022842722 167.513194 -2.224049019 0.112068359 YEFTDALLCHDDELEGRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEFTDALLCHDDELEGRR 18 1 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 170.11 1.08E-11 59880000 36281.3 28569.8 35546.4 31696.5 37604 34437.5 41641 38480 59180 FALSE TRUE 34566.35485 31481.0951 37176.2376 28510.3076 44162.12569 33244.92074 35287.90066 35110.4872 68357.33215 0.505671502 0.460537211 0.5438515 0.417077535 0.646048117 0.486340231 0.516227002 0.513631619 1 16.06080847 -5 0.393347172 8.598442969 0.49736276 0.871705504 0.058946969 204.4743271 1.461384933 1331.474275 0.033117243 1.00E-05 5 -8.101080209 YEHANDDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEHANDDK 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 146.81 0.00054736 607180000 1412920 1410740 1182200 1611340 734030 1367940 1330190 1408200 623030 FALSE TRUE 1346134.072 1554496.01 1236405.039 1449365.042 862044.5996 1320567.895 1127245.085 1284890.543 719646.3104 1.870549536 2.160083346 1.7180732 2.013996349 1.197872604 1.835023505 1.566387639 1.785447273 1 19.4569285 -1.265313473 0.121609995 2.54E-13 2.352145132 0.529297781 0.242307704 30.78519061 0.691085091 12.61849333 2.808889049 0.054285836 1.265313473 2.352145132 YEHANDDKSSLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEHANDDKSSLK 12 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 166.48 3.11E-05 123190000 327470 260210 279820 347040 244430 322010 365280 333150 215510 FALSE TRUE 311991.1421 286725.6948 292650.0238 312154.8799 287058.5146 310858.713 309549.8272 303977.6199 248930.1901 1.253327858 1.151831743 1.175630901 1.253985624 1.153168744 1.248778675 1.243520631 1.221136013 1 17.92538168 -0.924265574 7.483733534 0.999999998 1.21197351 0.737550457 0.039867573 1.67E-09 1.49E-10 0.037457772 0.008828882 0.119051378 0.924265574 0.211973512 YEIDLDTSDHAHLEHITR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEIDLDTSDHAHLEHITR 18 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 134.37 3.71E-06 98919000 117390 103250 126300 136464 150300 119476 167132 115141 4086.95 FALSE TRUE 111841.2073 113771.2924 132090.9799 122746.3795 176512.2724 115338.5162 141632.9438 105058.6436 4720.733333 23.69149017 24.10034297 27.98102977 26.00154908 37.39085857 24.43233033 30.00231825 22.25472956 1 12.20479527 0.858623755 4.407924615 1.001291993 27.26657364 0.813399522 3.988976627 0.442435291 13.27581563 3.777066599 0.960031993 7.221439124 -0.858623755 26.26528165 YEKDIAAYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YEKDIAAYR 9 1 P26583;P09429 P26583;P09429 HMGB2;HMGB1 High mobility group protein B2;High mobility group protein B1 0 ;;;; 131.82 0.00029406 4373570000 5867250 3673510 4147510 3985230 5588410 4457710 7159860 5319320 6545330 FALSE TRUE 5589916.72 4047844.845 4337677.436 3584627.109 6563026.935 4303338.385 6067491.857 4853532.141 7560346.347 0.739373101 0.535404684 0.573740572 0.474135303 0.868085486 0.569198577 0.802541521 0.641972195 1 22.8500209 0.119496749 0.396698293 1.052982991 0.603582866 0.469763244 0.119854683 3.209297385 0.741028199 0.406166969 0.078978663 1.316730056 -0.119496749 -0.449400125 YEKDVADYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YEKDVADYK 9 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 ;;; 135.66 0.00019564 1353580000 2741280 2296130 2498800 2944230 1957560 2920160 3201380 3196880 2122690 FALSE TRUE 2611705.127 2530108.257 2613372.452 2648270.407 2298957.844 2819034.127 2712950.684 2916944.239 2451865.924 1.065190842 1.031911343 1.065870864 1.080104088 0.937636035 1.149750522 1.10648411 1.189683421 1 21.22544866 2.176845394 24.99999993 1.119917217 1.041552339 0.264652826 0.061324336 81.25504751 32914.41939 0.020305733 0.014996783 150.2606953 -2.176845394 -0.078364879 YELGRPAANTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YELGRPAANTK 11 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 184.65 2.29E-05 791250000 3110200 2343310 2565120 2857510 2413900 2701340 3375080 3108260 2937860 FALSE TRUE 2963187.01 2582095.953 2682733.289 2570267.666 2834883.396 2607791.918 2860149.558 2836084.276 3393448.324 0.873208231 0.760906225 0.790562588 0.7574206 0.835399017 0.768478453 0.842844589 0.8357529 1 21.69432061 0.467867726 0.931303049 1.000723307 0.799156316 0.739289689 0.036651325 0.901026997 1.109991088 0.034261693 0.010871866 2.936755064 -0.467867726 -0.20156699 YELHLK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 114.67 0.025089 5443860000 15345200 15161000 10264400 14543200 10987900 12116600 14873200 14174900 9948780 FALSE TRUE 14619862.81 16705923.14 10735032.89 13081289.91 12904186.28 11696999.1 12604020.17 12933670.61 11491585.99 1.272223244 1.453752611 0.934164605 1.138336337 1.122924746 1.017875088 1.096804234 1.125490478 1 23.45407459 3.744041853 24.98791662 1.070648875 1.362987935 0.722376779 0.077378471 198.113396 903158.4503 0.018391807 0.032013027 5546.791651 -3.744041853 0.29233906 YELISETGGSHDKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 ;;;; 207.97 5.64E-09 1396042000 2433996 2481400 1833807 2810602 1581849 2263496 2343581 2428310 1546600 FALSE TRUE 2318945.833 2734257.481 1917888.865 2528074.947 1857722.965 2185110.566 1986024.676 2215674.303 1786438.829 1.298082977 1.530563172 1.073582164 1.415147782 1.039902926 1.223165624 1.111722743 1.240274376 1 20.76865508 3.308788853 1.063651306 1.13940767 1.40337051 0.300307469 0.140743592 0.520863259 1.25439163 0.050362535 0.087125416 2036.05194 -3.308788853 0.26396284 YELYSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YELYSR 6 0 A0A0G2JQD6;Q8IXL6 A0A0G2JQD6 FAM20C Extracellular serine/threonine protein kinase FAM20C 0 ;;;;; 114.67 0.058367 2205748000 1105620 1283390 1859810 1612470 1169940 1710990 1405550 1504510 1565630 FALSE TRUE 1053359.534 1414168.9 1945084.128 1450381.452 1373977.166 1651737.987 1191107.533 1372767.128 1808419.904 0.582475083 0.781991448 1.075571068 0.802015864 0.759766668 0.91335977 0.658645445 0.759097555 1 20.78629827 4.357484828 2.762661729 0.831407871 0.598714352 0.305091541 0.123564946 0.337618725 4.852307048 0.030740888 0.119055172 22776.38674 -4.357484828 -0.232693519 YEMACAIADAFNLPSSHLRPITDS(ph)PVLGAQRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPS(0.001)S(0.001)HLRPIT(0.032)DS(0.965)PVLGAQRPR;YEMACAIADAFNLPS(0.001)S(0.007)HLRPIT(0.385)DS(0.607)PVLGAQRPR 217.1 3.18E-36 884220000 277899 215945 241125 263405 291249 219607 305755 281065 331543 TRUE FALSE 264763.265 237950.041 252180.8198 236927.029 342042.7334 212001.9545 259106.4592 256453.4586 382956.9952 0.691365528 0.621349248 0.658509501 0.618677898 0.893162255 0.553592067 0.676594141 0.669666469 1 18.54682287 0.312312121 3.645017915 0.999999996 0.669037936 0.579166189 0.087582467 190.3400357 1005.291527 0.075661948 0.019443119 2.05263685 -0.312312121 -0.33096206 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 103.68 7.33E-06 77934000 33422 30374 40641 42274 39069 33293 47633 39959 46444 FALSE TRUE 31842.2083 33469.14513 42504.43005 38024.5372 45882.62123 32140.05506 40365.71101 36459.97812 53646.29832 0.59355835 0.623885453 0.792308722 0.708800763 0.855280283 0.599110397 0.752441683 0.67963642 1 15.71119101 -5 0.162750001 2.11491109 0.615474222 0.55628279 0.083918171 97.83912877 0.906215009 35.45345668 0.329607603 1.00E-05 5 -1.499436868 YENGAFQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YENGAFQER 9 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 109.88 0.0059157 0 162410 148210 132370 156030 159090 157810 171910 165500 175560 FALSE TRUE 154733.2012 163312.7675 138439.2954 140345.568 186835.2456 152345.0001 145681.9722 151007.9426 202784.9482 0.76304086 0.805349554 0.682690193 0.692090657 0.921346714 0.751263846 0.71840624 0.744670371 1 17.62959105 -0.936876012 4.791211571 1.000001205 0.761048462 0.557125895 0.067280196 1.33E-06 2.95E-07 0.062599118 0.014754635 0.115644235 0.936876012 -0.238952743 YEPFSFADDIGSNNCGYYDLQAVLTHQGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEPFSFADDIGSNNCGYYDLQAVLTHQGR 29 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 186.54 6.58E-18 27898000 14285 14716 13011 14493 13559 13976 15775 14570 14076 FALSE TRUE 13609.77636 16215.57713 13607.56722 13036.13611 15923.68531 13492.00762 13368.23402 13294.17356 16258.83419 0.837069633 0.997339474 0.836933759 0.801787874 0.97938666 0.829826263 0.822213565 0.817658474 1 13.98893619 3.647342396 21.72793514 0.859417792 0.917291222 0.048151138 0.078052708 41.78767997 9948.048909 0.019232435 0.02979478 4439.585211 -3.647342396 0.05787343 YEPQS(ph)PGYEPR ddPTM_SK-BR-3_Trastuzumab_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(0.997)PGY(0.003)EPR 168.43 1.90E-05 2903000000 1574260 1556790 1395230 1617260 1254860 1490390 1573580 1581030 1310320 TRUE FALSE 1499847.85 1715428.671 1459202.676 1454689.952 1473707.187 1438777.421 1333501.47 1442586.632 1513517.733 0.990968138 1.133405069 0.964113365 0.961131753 0.973696676 0.950618145 0.881061015 0.953134938 1 20.52947415 3.585265436 6.520939308 0.945181282 1.061776862 0.488244422 0.045281614 0.168602647 8.827960104 0.012063021 0.018745034 3848.269122 -3.585265436 0.116595581 YEPSDKDRQS(ph)PPPAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YEPSDKDRQSPPPAK 15 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPSDKDRQS(1)PPPAK;YEPS(0.001)DKDRQS(0.999)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK 149.34 1.76E-06 2310430000 4896660 4826970 3938370 5423240 2487530 5106920 4780730 5271400 2590900 TRUE FALSE 4665204.586 5318843.731 4118948.16 4878085.612 2921354.444 4930066.08 4051341.834 4809808.271 2992683.54 1.558869999 1.777282382 1.376339364 1.630003823 0.976165507 1.647373006 1.353748828 1.607189069 1 21.5130083 -3.196945462 0.101866827 7.12E-14 1.864984836 0.316170722 0.223096668 123.9723956 1.289756012 32.01508356 3.689236934 0.000635411 3.196945462 1.864984836 YEQGTGCWQGPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YEQGTGCWQGPNR 13 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 326.41 8.36E-53 1361990000 508867 400828 367323 439159 487367 366747 551842 456760 514020 FALSE TRUE 484813.8654 441672.8289 384165.1229 395013.903 572363.6505 354046.4594 467648.3676 416763.673 593731.5963 0.816553925 0.743893085 0.647034999 0.665307195 0.964010765 0.596307257 0.787642717 0.701939522 1 19.17945136 -1.046549417 4.655426911 1.000009334 0.743688226 0.387145685 0.102595759 8.89E-06 1.82E-06 0.08886258 0.020944348 0.089836037 1.046549417 -0.256321107 YESLTDPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 0 127.68 0.0010205 122940000 470470 529200 380780 552550 275320 470380 435460 473870 262610 FALSE TRUE 448231.8155 583126.0817 398239.1396 497006.6242 323335.7208 454090.6227 369022.5792 432375.4307 303334.2176 1.477682996 1.922388072 1.312872457 1.6384786 1.06593883 1.496997689 1.216554407 1.425409352 1 18.21054872 2.553026041 0.245080456 0.980114511 1.863381007 0.37777015 0.213365888 2.847100883 0.424191899 0.406386951 0.846414235 357.2942611 -2.553026041 0.883266496 YESLTDPSKLDSGK ddPTM_SK-BR-3_Trastuzumab_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 ;;;;; 193.96 1.81E-07 14584180000 30718800 26562600 26655700 31068200 16678400 32683500 33736100 34893300 18735700 FALSE TRUE 29266783.2 29269359.14 27877890.21 27945165.51 19587107.68 31551662.2 28589038.34 31837857.67 21641136.67 1.352368115 1.352487145 1.28818974 1.291298417 0.905086825 1.457948475 1.321050681 1.471173079 1 24.36727294 3.603514004 2.769484832 1.261863348 1.353394946 0.054734168 0.177159666 0.958704831 14.18216156 0.047540891 0.079560035 4013.414391 -3.603514004 0.091531598 YESQEPLAGQES(ph)PLPLATR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YESQEPLAGQESPLPLATR 19 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(0.799)PLPLAT(0.201)R;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(0.997)PLPLAT(0.003)R;YESQEPLAGQES(0.997)PLPLAT(0.003)R 406.05 1.50E-147 3369452000 2670781 2550345 2321407 2907006 2448087 2445066 2695058 2643920 2435427 TRUE FALSE 2544538.475 2810228.055 2427845.807 2614788.234 2875032.598 2360392.751 2283877.404 2412404.348 2813100.581 0.904531638 0.998978876 0.863049769 0.929503997 1.022015572 0.839071581 0.811871932 0.857560645 1 21.42372971 2.207750546 24.99805933 0.855337673 0.94330883 0.163599113 0.067095019 242.8450664 197033.421 0.023073904 0.017043056 161.3431555 -2.207750546 0.087971157 YESQLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YESQLR 6 0 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ; 144.9 0.026088 227294000 373110 330170 318110 355570 387900 340190 428390 387470 418490 FALSE TRUE 355473.8297 363814.6984 332695.6582 319827.4281 455549.6372 328409.135 363031.2376 353541.0727 483387.2918 0.735380999 0.752636043 0.688259008 0.661638056 0.942411282 0.67939133 0.75101527 0.731382638 1 18.88282002 -1.446905808 2.634187389 1.008974593 0.742887424 0.522384546 0.0772996 4155295.287 4301408.467 275433.5686 0.017940512 0.035735033 1.446905808 -0.266087168 YETSSTSAGDRYDSLLGR ddPTM_SK-BR-3_Trastuzumab_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 ;; 270.32 5.71E-39 584510000 267654 212590 247391 252654 242569 246353 298178 265796 281859 FALSE TRUE 255002.5259 234253.1627 258734.1221 227256.7399 284872.9568 237821.7338 252685.4697 242521.4932 325568.2542 0.783253658 0.719520898 0.794715451 0.698031018 0.875002256 0.730481952 0.776136698 0.74491751 1 18.31260051 -1.895724596 2.332275487 1.134938539 0.76375171 0.693829435 0.048996974 3390976.084 1708785.009 2512695.968 0.010611531 0.012713801 1.895724596 -0.371186829 YEWDVAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 YEWDVAEAR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;; 199.29 5.81E-05 6944320000 8286980 8827880 6299317 8811240 7137940 6993394 7936490 7738320 7077360 FALSE TRUE 7895270.879 9727451.008 6588146.915 7925517.415 8382794.476 6751211.012 6725632.687 7060711.677 8174880.843 0.965796448 1.189919608 0.805901278 0.969496384 1.025433231 0.825848247 0.822719354 0.863708207 1 22.96276627 3.733915526 24.99986064 0.893454634 1.077858028 0.38000768 0.092971186 342.199754 1841719.387 0.024297593 0.039041217 5418.954763 -3.733915526 0.184403394 YEWVVIKHPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEWVVIKHPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 45 3 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 YEWVVIKHPELTKPPPLMAAEPTAPLSHSAS(0.004)S(0.098)DPADRLS(0.898)PFLAAR 196.08 1.87E-36 326800000 443450 198370 328130 314350 367450 325560 523250 408570 304170 TRUE FALSE 422488.9973 218584.1285 343175.0851 282750.9408 431533.1637 314285.7756 443418.6024 372793.4448 351339.1301 1.202510512 0.622145699 0.976763064 0.804780671 1.228252496 0.894536784 1.26208146 1.061064404 1 18.42250474 2.745033909 24.96072502 1.101934127 0.892601167 0.215519509 0.176592346 687.9859821 2652844.522 0.050997239 0.052904211 555.9476634 -2.745033909 -0.209332959 YEYDPDIS(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YEYDPDISPPR 11 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR 126.65 0.0003179 682980000 866520 909680 746900 1013720 796110 816150 842220 825550 748820 TRUE FALSE 825561.3169 1002377.426 781146.1038 911818.9397 934951.3319 787886.5209 713723.8706 753260.4655 864943.1812 0.954468842 1.158893957 0.903118402 1.054195188 1.080939595 0.910911304 0.825168504 0.870878552 1 19.72224584 2.125636315 5.427386123 0.876941949 1.035842451 0.369423603 0.081539167 0.176902585 7.745192597 0.02901683 0.021238829 133.5476698 -2.125636315 0.158900501 YEYHWADGTNIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEYHWADGTNIK 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 164.11 5.82E-05 348330000 230530 204970 208160 250190 165340 228240 276730 220640 181620 FALSE TRUE 219633.3038 225856.676 217704.3419 225040.4259 194175.2437 220335.9916 234509.756 201319.5919 209784.702 1.046946234 1.076611754 1.037751275 1.07272086 0.925592962 1.050295801 1.117859185 0.959648582 1 17.67854995 YEYQPFAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YEYQPFAGK 9 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 96.331 0.017309 52238000 63899 58249 52759 68439 65550 60450 76900 66925 74433 FALSE TRUE 60878.62091 64184.63932 55178.05234 61559.38169 76981.89925 58356.60134 65167.49263 61064.69221 85975.68949 0.708091104 0.746544049 0.64178668 0.716009166 0.895391473 0.678757003 0.757975807 0.710255336 1 16.39164116 -5 0.363967549 4.3794281 0.725358426 0.614364779 0.066681366 327.7187576 2.576270187 869.1242971 0.044417347 1.00E-05 5 -3.654069673 YFAEALGPLQSFQARPDDLLISTYPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFAEALGPLQSFQARPDDLLISTYPK 26 1 P50225;H3BRY5;H3BQX5;E9PKW4;E9PM76;P50226;E9PKR8 P50225;P50226 SULT1A1;SULT1A2 Sulfotransferase 1A1;Sulfotransferase;Sulfotransferase 1A2 0 ; 233.91 6.47E-45 121701000 238550 219710 222190 264770 203217 242340 274050 264610 248660 FALSE TRUE 227274.2143 242098.6988 232377.6313 238154.8166 238657.9805 233947.705 232238.6392 241439.3456 287220.9228 0.791287111 0.842900637 0.809055374 0.829169457 0.830921293 0.814521807 0.808571454 0.840605006 1 18.13180132 0.789849269 4.080092226 0.999997222 0.818735322 0.941001069 0.014202588 0.486357091 9.246788981 0.012889278 0.003289334 6.163810369 -0.789849269 -0.1812619 YFDDEFTAQSITIT(ph)PPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSIT(0.374)IT(0.626)PPDR;YFDDEFTAQSIT(0.003)IT(0.997)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSITIT(1)PPDR 199.76 1.77E-14 99318000 176740 230204 163249 222184 178882 182082 183287 195605 168300 TRUE FALSE 168385.8505 253662.0493 170734.1281 199849.6422 210078.9642 175776.4547 155323.2019 178476.7892 194399.1044 0.866186349 1.304851944 0.878266022 1.028037875 1.080658086 0.904204035 0.798991345 0.918094709 1 17.56866205 2.165397328 5.68890313 0.876609765 1.046523674 0.171245682 0.130106438 0.264885323 15.04572182 0.047287429 0.034867195 146.3515507 -2.165397328 0.16991391 YFDDEFTAQSITIT(ph)PPDRYDSLGLLELDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSITIT(1)PPDRYDSLGLLELDQR;YFDDEFT(0.039)AQS(0.026)IT(0.374)IT(0.561)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.007)IT(0.993)PPDRYDS(0.001)LGLLELDQR;YFDDEFTAQSIT(0.002)IT(0.782)PPDRY(0.1)DS(0.115)LGLLELDQR;YFDDEFT(0.016)AQS(0.013)IT(0.041)IT(0.929)PPDRYDSLGLLELDQR;YFDDEFT(0.053)AQS(0.055)IT(0.213)IT(0.678)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.005)IT(0.995)PPDRYDSLGLLELDQR;YFDDEFTAQS(0.001)IT(0.257)IT(0.743)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.007)IT(0.992)PPDRYDS(0.001)LGLLELDQR;YFDDEFTAQS(0.001)IT(0.004)IT(0.994)PPDRYDSLGLLELDQR 182.26 1.02E-17 1359030000 619599 548481.4 580392.2 640368 641913 580657.5 737077 665626 746487 TRUE FALSE 590311.7832 604372.2782 607003.7565 575996.992 753862.424 560549.1852 624622.3663 607340.2587 862248.3914 0.684619176 0.700925956 0.703977836 0.668017474 0.874298441 0.650101746 0.72441117 0.704368097 1 19.71774401 -1.738186678 2.466320433 1.065062812 0.712129168 0.686354021 0.060783728 5941084.783 4305122.456 2364594.41 0.013279154 0.018273146 1.738186678 -0.352933644 YFDGSGGNNHAVEHYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YFDGSGGNNHAVEHYR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;; 186.85 8.29E-10 1714840000 1031643 907103 923354 1100159 1033468 914763 1066975 988263 112572 FALSE TRUE 982879.2799 999537.827 965690.6942 989568.9272 1213704.492 883084.5279 904188.3674 901725.4526 130029.0908 7.558918344 7.687032345 7.426728035 7.610365657 9.334099657 6.791438149 6.953739057 6.934797797 1 16.9884749 -0.032587851 0.687482997 0.703721186 7.768166609 0.913396381 0.639612015 1.29998331 0.647092813 1.629473177 0.224494915 0.927709809 0.032587851 7.064445422 YFDLGLPNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YFDLGLPNR 9 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;; 159.2 0.00015409 734860000 1027250 924980 858800 980490 940660 782620 938830 953920 918510 FALSE TRUE 978693.9283 1019236.514 898176.8295 881929.2824 1104710.806 755517.6732 795594.2407 870389.7078 1060947.84 0.922471296 0.960684848 0.84657963 0.831265449 1.041248933 0.712115756 0.749890061 0.820388784 1 20.0169223 2.226243723 24.99999748 0.791283363 0.918708773 0.185669162 0.095470719 268.495654 544970.6935 0.032682121 0.024309516 168.361863 -2.226243723 0.12742541 YFDLGLPNRDQTDDQVTIDSALATQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFDLGLPNRDQTDDQVTIDSALATQK 26 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 249.91 6.16E-46 226900000 229560 133600 200070 160420 197880 174730 247810 212550 248650 FALSE TRUE 218709.1537 147213.9919 209243.4074 144294.2768 232390.2093 168679.0563 210002.0332 193937.9952 287209.3721 0.761497273 0.512566811 0.728539622 0.502401004 0.809131707 0.587303454 0.731180991 0.675249536 1 18.1317433 -0.726281579 0.432194198 1.101453814 0.638010607 0.522393311 0.101715708 8.151860434 1.216470593 1.20585489 0.051654745 0.187809874 0.726281579 -0.463443207 YFDNKDDDS(ph)DTETSNDLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFDNKDDDSDTETSNDLPK 19 1 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 YFDNKDDDS(0.987)DT(0.013)ET(0.001)SNDLPK;YFDNKDDDS(0.922)DT(0.036)ET(0.036)S(0.007)NDLPK 195.03 1.10E-15 175500000 449870 388446 398529 498710 243761 507310 501350 513850 287027 TRUE FALSE 428605.5367 428029.089 416801.9488 448578.7233 286272.8412 489741.7275 424859.8496 468854.5699 331537.6812 1.292780763 1.291042054 1.257178211 1.353024856 0.863469999 1.477182701 1.281482841 1.414181846 1 18.33881332 YFDPANGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFDPANGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 122.18 0.0032608 310680000 1307560 1161060 1166780 1421170 1097550 1266740 1452230 1384240 1305800 FALSE TRUE 1245754.23 1279373.334 1220278.017 1278311.292 1288962.373 1222872.476 1230665.641 1263028.607 1508296.795 0.825934414 0.848223863 0.809043698 0.847519729 0.854581391 0.810763823 0.815930688 0.837387318 1 20.52448891 0.938357992 22.27172473 1 0.830501112 0.918009327 0.015870035 2264.827259 818300.5187 0.015176008 0.003794002 8.676768129 -0.938357992 -0.169498888 YFDS(ph)GDYNMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 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(0.98)GDY(0.02)NMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK 262.43 1.02E-20 11971900000 26152590 24003930 23854430 29538170 21143020 25892940 28569780 28202300 25112420 TRUE FALSE 24916408.9 26449957.76 24948179.21 26568937.03 24830355.99 24996261 24210935.34 25732757.1 29006725.84 0.858987293 0.911856026 0.860082567 0.915957809 0.856020639 0.861740175 0.834666259 0.887130704 1 24.78988412 0.962489888 23.30953744 1.000000001 0.872057135 0.721617549 0.024915676 1576.238055 979507.5486 0.024385367 0.006096342 9.172545789 -0.962489888 -0.127942866 YFEADPPGQVAAS(ph)PDPTT ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YFEADPPGQVAASPDPTT 18 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 YFEADPPGQVAAS(1)PDPTT;YFEADPPGQVAAS(1)PDPTT;YFEADPPGQVAAS(1)PDPTT 199.01 1.99E-18 142688000 632560 545570 580990 672040 640810 596880 659320 594870 629160 TRUE FALSE 602660.1424 601164.2033 607628.9662 604485.2624 752567.0611 576209.8959 558728.6248 542780.0292 726726.9195 0.829280059 0.827221597 0.836117323 0.831791483 1.03555688 0.792883655 0.768828854 0.746883065 1 19.47105382 -0.700747544 7.173913253 1 0.832243804 0.312076178 0.077633437 0 0 0.074283946 0.017508894 0.199183086 0.700747544 -0.167756195 YFEITEEPPYIHFLNTFTSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFEITEEPPYIHFLNTFTSK 20 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 203.81 1.03E-21 97162000 334870 335590 298330 371110 277790 299020 364810 336430 244330 FALSE TRUE 319041.3587 369787.0025 312008.7256 333805.3177 326236.488 288664.8624 309151.5343 306970.4057 282219.4485 1.130472618 1.310281784 1.105553594 1.182786372 1.155967421 1.022838305 1.095429588 1.087701104 1 18.10645789 2.572136488 0.936410599 1.050720364 1.20962636 0.480614843 0.062290467 0.445945212 0.803667558 0.037547742 0.029158752 373.3674793 -2.572136488 0.158905995 YFEITSEAPFLHYLSMFSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFEITSEAPFLHYLSMFSSK 20 0 P31146;H3BRY3 P31146 CORO1A Coronin-1A;Coronin 0 211.49 1.02E-25 0 125150 126110 106040 129850 130860 117440 163040 145700 141580 FALSE TRUE 119234.4075 138960.7524 110902.0389 116797.2313 153681.9426 113373.0234 138165.2536 132941.7356 163535.5033 0.72910411 0.849728344 0.678152674 0.714201069 0.939746657 0.693262448 0.844863964 0.812922778 1 17.31924435 -0.92130737 0.3308251 1.104848938 0.761208244 0.448934555 0.07917586 12.04709636 1.08697268 1.279178943 0.066592228 0.119865066 0.92130737 -0.343640694 YFEYIMAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFEYIMAK 8 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 114.93 0.0059582 53204000 276300 233600 179666 194504 321850 203790 313610 241970 254160 FALSE TRUE 263239.8466 257404.1056 187903.8638 174952.0884 377980.5381 196732.7012 265763.0347 220781.824 293573.8347 0.896673393 0.87679512 0.640056577 0.595938969 1.287514395 0.670130229 0.905268124 0.752048711 1 18.16336387 YFGTDAVPDGS(ph)DEEEVAYTG ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFGTDAVPDGSDEEEVAYTG 20 0 Q9NWZ5;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 YFGTDAVPDGS(1)DEEEVAYTG;YFGTDAVPDGS(1)DEEEVAYTG 110.35 0.00019311 54042000 212050 210890 202745 234360 203006 214232 221580 215169 223590 TRUE FALSE 202026.8167 232379.9308 212041.0588 210801.6875 238410.1821 206813.0921 187773.9014 196327.6617 258263.1953 0.782251674 0.899779508 0.821027009 0.81622814 0.923128756 0.800784223 0.727064115 0.760184437 1 17.97848254 2.025740898 24.99256602 0.790048475 0.848010647 0 0.083880713 486.9340996 472776.178 0.028226118 0.020845676 106.1062333 -2.025740898 0.057962172 YFHVVIAGPQDSPFEGGTFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFHVVIAGPQDSPFEGGTFK 20 0 P61088;F8VSD4;F8VV71;F8VZ29 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 278.82 1.23E-44 1379780000 1523790 1543640 1293980 1768720 1065430 1480660 1488740 1609170 1038330 FALSE TRUE 1451763.467 1700938.671 1353310.263 1590924.905 1251240.655 1429384.373 1261605.37 1468262.544 1199348.913 1.210459651 1.418218378 1.128370775 1.326490471 1.043266593 1.191800282 1.051908545 1.224216346 1 20.19382 2.918731643 1.361991825 1.105224916 1.297157245 0.337276066 0.105561176 0.401802958 1.53634645 0.038008357 0.042278617 829.3381481 -2.918731643 0.191932329 YFIRDEFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFIRDEFLR 9 1 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 0 ; 204.79 1.46E-05 749380000 1176790 949500 818390 980300 1389240 796730 1186630 1056350 1341490 FALSE TRUE 1121165.469 1046255.129 855913.991 881758.3816 1631523.016 769139.0403 1005587.8 963850.3939 1549521.418 0.723555968 0.67521179 0.552373127 0.569052077 1.052920597 0.496371997 0.648966699 0.622031024 1 20.56339127 -1.052319275 4.570247766 1.000012862 0.667653269 0.322478803 0.151434883 2.19E-05 4.53E-06 0.134001427 0.031582967 0.088650405 1.052319275 -0.332359593 YFLHDDRDDGVDYWAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFLHDDRDDGVDYWAK 16 1 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 52.522 0.095548 262070000 175800 160930 153500 186460 158720 161080 210640 176170 143330 FALSE TRUE 167490.2824 177328.95 160538.1268 167716.6865 186400.7177 155501.7592 178502.9993 160743.6209 165556.8844 1.011678149 1.071105866 0.9696856 1.01304568 1.125901339 0.939264832 1.078197382 0.97092683 1 17.33696748 1.207735265 24.999341 0.985463371 1.031191793 0.104507356 0.053891694 490.1340346 397487.559 0.045234449 0.011313893 16.13374783 -1.207735265 0.045728422 YFLNLVLVDEEDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFLNLVLVDEEDRR 14 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 296.97 1.85E-43 471160000 706410 708790 651610 764370 678400 611410 712700 716380 630260 FALSE TRUE 673019.3993 781016.5068 681486.963 687534.0754 796712.7452 590236.7184 603964.5254 653649.9694 727997.5019 0.924480369 1.072828553 0.936111678 0.944418179 1.094389394 0.810767505 0.829624448 0.897873918 1 19.47357397 2.225268391 24.99998989 0.86387446 0.993848228 0.331643217 0.0749924 213.6006327 401736.9747 0.025838715 0.019193664 167.9841828 -2.225268391 0.129973768 YFQFQEEGKEGENR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YFQFQEEGKEGENR 14 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;; 230.16 9.26E-13 1167410000 1288670 1099300 1198580 1321890 912440 1281190 1427890 1448830 1078810 FALSE TRUE 1227757.123 1211319.92 1253536.079 1189011.106 1071569.247 1236822.069 1210039.156 1321962.764 1246106.345 0.985274754 0.972083903 1.005962359 0.954181086 0.859934027 0.992549371 0.97105609 1.060874756 1 20.24899577 1.349918725 5.861279223 1.029793926 0.96408611 0.307440698 0.042059675 0.254908047 11.40115808 0.028799637 0.010278107 22.38302219 -1.349918725 -0.065707815 YFQHLLGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFQHLLGK 8 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 86.794 0.015781 957040000 4943100 4025800 3942300 4591500 4146400 4088300 5380100 4837500 4061500 FALSE TRUE 4709449.459 4436033.597 4123058.354 4129953.697 4869530.847 3946721.146 4559266.933 4413902.855 4691336.677 1.0038609 0.945579885 0.878866438 0.880336241 1.037983667 0.841278599 0.971848163 0.940862521 1 22.16156761 0.546288572 1.592086911 0.99990415 0.938832234 0.098689001 0.05936004 5.743970294 17.2525223 0.052866456 0.015131872 3.517941165 -0.546288572 -0.061071916 YFQINQDEEEEEDED ddPTM_SK-BR-3_Trastuzumab_2h_R1 20 YFQINQDEEEEEDED 15 0 P35268;K7ERI7 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;;;;;;; 351.94 4.99E-82 9402202300 12543967 11996311 12002116 12771272 13076744 11780559 13415774 12142998 13148750 FALSE TRUE 11951038.54 13218748.73 12552424.89 11487479.47 15357324.01 11372595.29 11368951.28 11079692.72 15187791 0.78688458 0.870353611 0.826481277 0.756362757 1.011162454 0.748798511 0.748558581 0.729513115 1 23.85640871 -1.588257997 8.672960516 1.000050662 0.811327093 0.342160928 0.082871857 7.77E-05 3.69E-06 0.076785522 0.018093681 0.025807266 1.588257997 -0.188723569 YFQS(ph)PS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 YFQS(1)PS(1)R 73.499 0.071235 198060000 626420 762540 604550 644940 549910 627970 629140 624100 553260 TRUE FALSE 596810.368 840243.6929 632269.2155 580109.4059 645814.1299 606223.2414 533153.1381 569450.4954 639056.7351 0.933892619 1.314818617 0.989378847 0.907758848 1.010574014 0.948621942 0.834281385 0.891079718 1 19.28558449 3.491669336 22.9732561 0.924720608 1.128979515 0.365477957 0.103173425 201.7649878 318611.3411 0.027062953 0.040203359 3102.19673 -3.491669336 0.204258907 YFSEGDKVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFSEGDKVK 9 1 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 77.662 0.029153 168860000 499810 381040 379200 394070 552920 360350 593870 459560 649760 FALSE TRUE 476184.9718 419868.4092 396586.6951 354457.3349 649349.0729 347870.9891 503264.2243 419318.4901 750521.4623 0.634472158 0.55943558 0.528414862 0.472281411 0.865197207 0.463505718 0.670552742 0.558702864 1 19.5175338 -5 0.388335024 7.036450722 0.58646209 0.548615987 0.115525091 462.100553 3.359371048 2356.073732 0.06622235 1.00E-05 5 -6.449988632 YFSERGDAVTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YFSERGDAVTK 11 1 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 66.953 0.055905 413510000 642670 358740 584820 510900 438500 561500 771550 718310 486820 FALSE TRUE 612292.2627 395296.0139 611634.5755 459543.3614 514974.2612 542055.1142 653835.877 655410.9684 562313.5593 1.088880488 0.702981472 1.087710878 0.817236849 0.915813344 0.963973045 1.16276029 1.16556138 1 19.10101531 1.876881871 4.06498564 1.122985816 0.912139711 0.326114134 0.121912873 0.229305182 6.009149751 0.05440141 0.030545431 75.31506774 -1.876881871 -0.210846105 YFTWDPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YFTWDPSR 8 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 161.6 0.00080627 877510000 4257970 3662480 2174160 2625450 4270350 2564670 3963320 3329870 3560980 FALSE TRUE 4056704.197 4035690.876 2273847.387 2361534.778 5015097.688 2475854.835 3358642.743 3038288.93 4113198.591 0.986265094 0.98115634 0.552817311 0.574135852 1.219269524 0.601929321 0.816552536 0.738668183 1 21.9718293 3.927935754 24.99879673 0.777920205 0.984352555 0.139862283 0.20284577 226.8307515 78686.055 0.048202752 0.086898777 8471.020907 -3.927935754 0.20643235 YFTWDPSRFPQPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFTWDPSRFPQPR 13 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 120.84 0.00023131 2252800000 2429100 1422520 2064570 1971360 2893800 2041130 3294100 2489200 3584800 FALSE TRUE 2314281.257 1567476.405 2159232.577 1773195.147 3398477.804 1970445.156 2791524.545 2271232.452 4140712.475 0.558908949 0.378552342 0.521464021 0.428234309 0.820747112 0.475871041 0.67416527 0.548512476 1 21.9814476 -5 0.152286526 2.689444934 0.40132634 0.599397646 0.119100872 82.48561351 0.740437369 41.89531284 0.518091689 1.00E-05 5 -2.288118594 YFVAFDGDLVQEFDMTSATHVLGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YFVAFDGDLVQEFDMTSATHVLGSR 25 0 P49916-3;P49916 P49916-3 LIG3 DNA ligase 3 0 ; 143.31 3.28E-07 15189000 16336.7 11386.8 14509.5 14355 15382.4 11928.9 17518.3 14411.6 13654.6 FALSE TRUE 15564.49657 12547.12787 15174.77493 12912.00813 18065.08569 11515.7992 14845.56159 13149.6439 15772.08563 0.986838198 0.795527501 0.962128617 0.818662061 1.14538344 0.730138009 0.941255452 0.833728919 1 13.94508583 4.75269277 23.82876973 0.897766699 0.986838285 0.044820559 0.118654512 232.6378864 2058218.337 0.024398615 0.16683578 56583.88597 -4.75269277 0.089071586 YGADALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGADALR 7 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 108.98 0.016588 199680000 723790 600910 484870 581120 740170 588300 847880 689240 804730 FALSE TRUE 689577.8811 662143.4122 507101.7691 522704.7135 869255.4137 567927.0235 718520.3336 628886.4917 929523.4184 0.741861762 0.712347208 0.545550289 0.56233625 0.935162468 0.610987321 0.772998635 0.676568744 1 19.82613169 -2.986905543 0.332377718 1.671652939 0.683995133 0.425247639 0.112000747 78.3721594 2.32444818 36.94724646 0.088452084 0.00103061 2.986905543 -0.987657807 YGAFGLPITVAHVDGQTHMLFGSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGAFGLPITVAHVDGQTHMLFGSDR 25 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ;; 251.32 2.06E-40 923327000 623674 457332 520639 588236 614222 496577 639901 539777 81075.7 FALSE TRUE 594194.166 503934.6507 544510.8131 529105.3997 721342.1223 479380.414 542272.3499 492511.2643 93648.50548 6.344940189 5.381128595 5.814410068 5.649907567 7.702654929 5.118932881 5.790507249 5.259147082 1 16.51496835 0.266167415 0.991481055 0.972917194 5.992419025 0.834915219 0.690704805 1.248823926 1.375580643 0.679555415 0.196043392 1.845726784 -0.266167415 5.019501831 YGAHNYHPLPVALER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YGAHNYHPLPVALER 15 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;; 134.9 1.87E-05 1308860000 1872490 1312290 1382200 1412930 1800040 1216780 1635620 1420630 120701 FALSE TRUE 1783981.109 1446013.843 1445575.237 1270899.592 2113966.406 1174642.603 1386076.129 1296232.106 139418.6946 12.7958529 10.37173563 10.36858967 9.115704285 15.1627184 8.425287632 9.941824032 9.297405269 1 17.0890645 -0.094635646 0.513895131 2.47E-19 11.36390827 0.741613546 1.841560692 2.330160374 0.700821032 6.63924727 0.810783163 0.804200528 0.094635646 11.36390827 YGASLRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGASLRK 7 1 Q6P4E4;E9PEL3;P61513;G5E9R3 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 107.32 0.012033 535590000 1416810 888190 1061920 925740 1304460 1060910 1791480 1271870 1628260 FALSE TRUE 1349840.199 978697.5708 1110610.082 832682.8564 1531957.411 1024170.421 1518156.823 1160498.32 1880762.245 0.717709111 0.520372829 0.590510622 0.442736906 0.814540708 0.544550713 0.807202945 0.617036164 1 20.84288605 0.195307718 0.430666404 1.042558178 0.588308125 0.503264682 0.117400733 2.535994066 0.709479123 0.315965188 0.066787948 1.567861582 -0.195307718 -0.454250053 YGDAFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGDAFIR 7 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ;; 138.85 0.0063879 240560000 641990 483170 477800 604650 585720 489950 669070 570960 604160 FALSE TRUE 611644.405 532405.5723 499707.6026 543869.4332 687869.3826 472982.9086 566991.0832 520963.7156 697850.0472 0.876469676 0.7629226 0.716067305 0.779349999 0.985697981 0.677771551 0.812482689 0.746526733 1 19.41255754 -1.037526719 4.796060885 1.000004947 0.795626447 0.358981803 0.086224274 4.18E-06 8.38E-07 0.076446255 0.018018119 0.09172195 1.037526719 -0.2043785 YGDFFIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGDFFIR 7 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 135.87 0.0070624 94950000 185472 170337 114889 129504 213310 118405 187627 152519 195634 FALSE TRUE 176705.1061 187694.534 120156.7743 116486.0119 250511.1965 114304.6052 159001.0551 139163.6278 225971.9216 0.781978154 0.830609983 0.531733206 0.515488876 1.108594354 0.505835435 0.703631912 0.615844778 1 17.78578399 -1.422289979 5.789359926 1.000131788 0.708627381 0.210709419 0.182143363 0.000286671 2.86E-05 0.163177514 0.03844404 0.037818998 1.422289979 -0.291504407 YGDGGSSFQSTTGHCVHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGDGGSSFQSTTGHCVHMR 19 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ; 186.94 1.12E-14 333570000 174902 112163 159575 177797 202466 151166 218478 165760 39878 FALSE TRUE 166634.7291 123592.5372 166891.6716 159924.5078 237776.0063 145931.0835 185145.1685 151245.1757 46062.07657 3.617612177 2.68317337 3.623190356 3.471934391 5.16207744 3.168139484 4.019470729 3.283507538 1 15.49129183 3.651449225 24.99786036 3.600765121 3.150362555 0 1.060319457 262.419686 75298.71491 0.248405615 0.384828339 4481.766491 -3.651449225 -0.450402566 YGDGGSTFQSTTGHCVHMR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGDGGSTFQSTTGHCVHMR 19 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;D6RIT2;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 82.482 0.0030758 143830000 42407 30181 33456 44608 43323 37810 52925 46431 23044 FALSE TRUE 40402.50515 33256.47821 34989.99069 40123.91909 50878.51748 36500.63022 44850.31922 42365.25549 26617.54583 1.517889944 1.249419403 1.314546086 1.507423688 1.911465385 1.37129961 1.684990777 1.591628912 1 14.70008994 5.109843283 18.06912094 1.477697513 5.399287735 0 0.25016301 1976.692246 326775.5083 0.054843048 1581.129828 128778.4764 -5.109843283 3.921590222 YGDGPRPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGDGPRPPK 9 1 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 73.233 0.040584 707670000 1087400 934820 1038290 1213480 887180 1177830 1289290 1223730 1046500 FALSE TRUE 1036000.757 1030079.221 1085896.624 1091498.685 1041903.911 1137041.452 1092585.131 1116573.714 1208785.875 0.857058953 0.852160206 0.898336625 0.902971078 0.861942493 0.940647533 0.903869869 0.923715057 1 20.20512728 -5 0.060211394 1.443081259 0.70373791 0.797784783 0.019907251 149.2343611 0.656080837 9.605818545 1.59287943 1.00E-05 5 -0.739343349 YGDSLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGDSLYR 7 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 100.07 0.023419 307910000 501090 477100 456830 546560 483630 473420 542340 500500 489700 FALSE TRUE 477404.4688 525717.0324 477776.1074 491618.7504 567974.9189 457025.3467 459596.0722 456673.5667 565640.175 0.844007356 0.929419542 0.844664379 0.869136904 1.004127613 0.807978936 0.812523743 0.807357021 1 19.10952507 YGEAGEGPGWGGAHPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YGEAGEGPGWGGAHPR 16 0 P26640;A0A140T954;A2ABF4;A0A0G2JJT9 P26640 VARS Valine--tRNA ligase 0 ;;; 257.04 1.17E-26 2151680000 1817850 1583980 1670530 1900520 1527550 1700460 2008940 1779610 1560110 FALSE TRUE 1731923.833 1745389.363 1747125.453 1709476.119 1793954.236 1641572.644 1702439.306 1623777.914 1802043.891 0.961088596 0.968560961 0.969524362 0.948631788 0.995510845 0.910950423 0.944726882 0.901075674 1 20.78120272 2.233631719 24.99998062 0.934825101 0.967089358 0.202660726 0.028377235 161.9987373 821668.9421 0.008997922 0.006850814 171.250449 -2.233631719 0.032264257 YGEIPAELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGEIPAELR 9 0 F8WAU4;C9IZ01;Q96RP9;Q96RP9-2 F8WAU4 GFM1 "Elongation factor G, mitochondrial" 0 ;; 122.44 0.001363 321551000 732270 560596 608475 607069 572577 545792 697680 674102 588665 FALSE TRUE 697657.0483 617721.3697 636374.1806 546045.2708 672434.2475 526891.0862 591236.1022 615074.0552 679952.1617 1.02603843 0.908477691 0.935910225 0.803064247 0.988943466 0.774894347 0.869526028 0.904584307 1 19.37507372 4.656064187 0.983242887 0.880810241 1.09116922 0.226080871 0.071695085 1.994883813 1.690972059 0.020066384 0.432928604 45296.45213 -4.656064187 0.210358979 YGEPGEVFINK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGEPGEVFINK 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 101.97 0.0068182 95868000 256510 203736 246379 283800 267830 229824 280600 249398 292240 FALSE TRUE 244385.2807 224496.93 257675.7209 255271.8848 314539.4672 221865.1373 237789.3164 227559.389 337559.0866 0.723977787 0.665059656 0.763349976 0.756228746 0.931805659 0.657263116 0.704437611 0.67413202 1 18.36478053 -1.467370875 3.162275174 1.005564793 0.729729759 0.527863479 0.078785721 27994186.72 32116452.19 1358932.579 0.019103093 0.034090167 1.467370875 -0.275835034 YGEYFPGTGDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YGEYFPGTGDLR 12 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;;;; 168.46 0.00010809 1391651000 1734540 1729500 1577580 1841840 1437424 1622630 1755320 1830070 1445751 FALSE TRUE 1652551.732 1905738.016 1649913.603 1656694.744 1688110.29 1566437.916 1487513.695 1669819.369 1669950.681 0.98958116 1.141194191 0.988001395 0.992062079 1.010874339 0.938014478 0.89075307 0.999921368 1 20.67137407 3.043884937 1.233469501 0.947313335 1.060629187 0.274871188 0.053761617 0.418602246 1.344683002 0.021475073 0.026961193 1106.330631 -3.043884937 0.113315851 YGGDEIPFS(ph)PYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGGDEIPFSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR 103.14 0.0023902 123851000 299800 256920 243340 338660 281250 294430 328550 294230 269550 TRUE FALSE 285629.0481 283100.4401 254497.3797 304617.2534 330299.911 284233.8153 278423.6633 268465.6614 311350.4373 0.917387657 0.909266236 0.817398498 0.978374259 1.060862203 0.912906427 0.894245294 0.862262034 1 18.24817978 3.200931425 24.99976886 0.945081154 0.892480417 0.210496789 0.061956732 340.4457224 226181.5158 0.018678355 0.022325382 1588.295936 -3.200931425 -0.052600737 YGGDPQNPHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGGDPQNPHK 10 0 B8ZZV5;Q8TCC3-3;Q8TCC3;Q8TCC3-2 B8ZZV5 MRPL30 "39S ribosomal protein L30, mitochondrial" 0 71.349 0.05125 49745000 322920 297070 277820 335310 179690 306770 336810 337920 206880 FALSE TRUE 307656.2116 327341.7707 290558.3218 301604.0018 211027.8791 296146.478 285423.4486 308329.9334 238961.8938 1.287469758 1.369849249 1.215919062 1.262142666 0.883102639 1.239304197 1.194430811 1.290289127 1 17.86642105 3.341012749 2.20909654 1.14768729 1.324496819 0.275017757 0.123844099 0.38112749 3.792214442 0.035688473 0.052004016 2192.869309 -3.341012749 0.176809528 YGGELVPHFPAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YGGELVPHFPAR 12 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 ;;;; 149.31 6.43E-05 1373570000 2925420 1820000 1659810 2390290 3050080 1978470 3598940 2613820 3166230 FALSE TRUE 2787141.194 2005460.069 1735913.93 2150013.508 3582012.986 1909955.088 3049855.604 2384940.064 3657232.778 0.762090182 0.548354505 0.474652295 0.587879864 0.979432594 0.522240504 0.833924387 0.652116015 1 21.80232102 -0.104504692 0.318662939 1.091485093 0.610462632 0.333382614 0.151457497 6.66131957 0.928702144 0.91864091 0.153367264 0.786131698 0.104504692 -0.481022461 YGGGGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YGGGGYGR 8 0 Q01130;J3KP15 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;; 118.42 0.0043963 1476276000 2845760 2793580 2360520 3037830 2166430 2608580 2708340 2689240 1984630 FALSE TRUE 2711246.565 3078248.978 2468752.177 2732461.557 2544254.706 2518244.221 2295132.991 2453755.889 2292396.284 1.18271286 1.342808396 1.076930805 1.191967364 1.109866878 1.09852046 1.001193819 1.070389054 1 21.12842503 2.764433089 0.658103508 1.011527308 1.25985904 0.584980144 0.065186076 0.453443464 0.423742878 0.046329328 0.049450719 581.3438591 -2.764433089 0.248331732 YGGPNHIVGS(ph)PFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGGPNHIVGSPFK 13 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 YGGPNHIVGS(1)PFK 74.12 0.022528 109350000 185520 167970 152030 188400 139780 179620 219140 219070 139940 TRUE FALSE 176750.8373 185086.334 159000.7259 169461.6741 164157.5877 173399.7144 185706.1682 199887.0694 161641.1805 1.093476531 1.145044434 0.983664716 1.048381814 1.01556786 1.072744667 1.148879064 1.23660981 1 17.30243527 1.755742461 5.730461759 1.144123585 1.06692777 0.154142309 0.071570236 0.275127072 22.56042041 0.034303355 0.01820313 56.98262626 -1.755742461 -0.077195815 YGGQPLFSEKFPTLWSGAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGGQPLFSEKFPTLWSGAR 19 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 72.883 0.01644 149210000 213690 118460 193790 165830 273460 157340 278980 188040 404980 FALSE TRUE 203589.2972 130531.2087 202675.4632 149160.4533 321151.3374 151891.2763 236416.4772 171574.2207 467782.23 0.435222384 0.279042683 0.433268838 0.318867293 0.686540268 0.324705101 0.505398585 0.366782254 1 18.83547753 -5 0.281669196 5.327922954 0.376731834 0.707284008 0.117026004 115.1937808 1.099906011 291.7035577 0.117810854 1.00E-05 5 -4.95119112 YGGSVGSQPPPVAPEPGPVPS(ph)SPSQEPPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.466)S(0.466)PS(0.049)QEPPT(0.02)KR 290.18 2.17E-81 410310000 262140 267510 283940 303880 220130 293780 315860 270000 249940 TRUE FALSE 249749.1617 294769.5731 296958.9299 273333.4051 258520.6023 283606.3249 267669.7558 246357.3686 288699.4187 0.865083701 1.021025863 1.028609379 0.946775045 0.895466307 0.98235849 0.927157239 0.853335174 1 18.13920868 3.005763493 24.99902514 0.930431187 0.969549139 0.085416303 0.059408486 401.6621487 1742178.632 0.016907918 0.020152709 1013.359382 -3.005763493 0.039117952 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.114)S(0.77)PS(0.114)QEPPT(0.001)KR;YGGSVGSQPPPVAPEPGPVPS(0.093)S(0.774)PS(0.132)QEPPT(0.001)KR;YGGSVGSQPPPVAPEPGPVPS(0.104)S(0.791)PS(0.104)QEPPT(0.002)KR 241.09 3.93E-46 966240000 477480 420374 443013 533230 419002 474670 541900 513060 449218 TRUE FALSE 454910.4667 463210.5885 463325.5842 479628.7073 492075.8161 458232.0589 459223.2023 468133.7465 518880.4332 0.8767154 0.892711613 0.892933236 0.924353043 0.948341438 0.88311686 0.885027018 0.902199653 1 18.98504261 YGIDKDKVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGIDKDKVDK 10 2 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 74.962 0.022735 1357000000 2357800 2029400 2101200 2184100 947380 2722000 2497800 2532400 1182900 FALSE TRUE 2246351.467 2236198.167 2197542.098 1964550.118 1112602.772 2627736.457 2116714.735 2310649.631 1366338.091 1.644067074 1.636636044 1.608344314 1.43782138 0.814295363 1.923196371 1.549188118 1.691125825 1 20.38188308 3.279347057 5.646281053 1.446205791 1.635628073 0.093078071 0.315694706 0.531201888 41.22004291 0.085435255 0.114123701 1902.598093 -3.279347057 0.189422282 YGIICMEDLIHEIYTVGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGIICMEDLIHEIYTVGK 18 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 146.16 6.51E-08 136410000 296810 262900 269790 323200 250290 275150 332710 301010 246810 FALSE TRUE 282780.3795 289689.8089 282160.1384 290711.322 293940.4968 265621.4865 281948.9789 274651.9686 285084.0343 0.991919384 1.016155849 0.98974374 1.019739049 1.031066147 0.931730488 0.989003048 0.963407051 1 18.12102772 2.25484233 24.99999233 0.97077103 1.00853007 0.448232346 0.021306355 209.8520107 322219.7625 0.006705117 0.00559357 179.8217956 -2.25484233 0.037759039 YGIICMEDLIHEIYTVGKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGIICMEDLIHEIYTVGKR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 243.86 1.14E-24 3775200000 1658050 981860 1584630 1387540 1771360 1545340 2331150 1857790 1843230 FALSE TRUE 1579677.262 1081912.65 1657286.853 1248061.843 2080284.623 1491824.488 1975490.253 1695112.059 2129068.694 0.741956925 0.508162397 0.778409291 0.586200833 0.977086662 0.70069345 0.927865906 0.796175372 1 21.02179107 2.746927212 24.99771359 0.86534273 0.646166588 0.493671414 0.113395539 493.8155704 1475422.026 0.031102671 0.032500363 558.3766032 -2.746927212 -0.219176141 YGIKPEWMMIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGIKPEWMMIHR 12 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F2Z2R5 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 110.98 0.00086011 219340000 330760 274610 205590 230670 352700 241950 393680 330670 308380 FALSE TRUE 315125.6303 302593.0712 215016.5049 207482.6134 414210.7683 233571.2108 333616.8856 301714.7818 356201.9954 0.884682383 0.849498529 0.603636441 0.582485826 1.162853588 0.655726846 0.936594657 0.847032823 1 18.44233607 2.765741662 24.99987456 0.896205712 0.760133725 0.24885567 0.157516261 1426.914717 1312407.976 0.046981594 0.049819502 583.0981474 -2.765741662 -0.136071987 YGINTTDIFQTVDLWEGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGINTTDIFQTVDLWEGK 18 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 321.81 2.60E-61 120324000 803390 526540 588410 757950 586180 638230 957000 858400 757200 FALSE TRUE 765415.3469 580195.0246 615389.1805 681759.426 688409.6064 616127.9351 810992.0735 783233.9453 874622.7088 0.875137747 0.663366065 0.703605308 0.779489738 0.787093223 0.704449963 0.927247904 0.895510644 1 19.73830128 1.669688553 5.631100266 0.936371243 0.752164148 0.666054861 0.062887715 0.088326689 6.083043939 0.032375073 0.015949189 46.73998334 -1.669688553 -0.184207095 YGISSMIQSQEKPDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGISSMIQSQEKPDR 15 1 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 217.48 1.88E-12 223310000 277700 248000 250940 308300 207770 274720 295980 292120 215670 FALSE TRUE 264573.6713 273271.482 262445.8472 277309.0983 244005.0222 265206.3775 250822.815 266540.4242 249115.0021 1.062054349 1.096969189 1.053512815 1.11317703 0.979487466 1.064594164 1.00685552 1.069949308 1 17.92645238 2.747904273 24.99094526 1.026482745 1.080314956 0.444968716 0.031703538 584.4453602 1563182.73 0.008452378 0.008845522 559.6342341 -2.747904273 0.053832211 YGKIETIEVMEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGKIETIEVMEDR 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 130.72 0.0001266 388290000 869970 627990 898180 679170 993880 819120 1232500 942290 1237300 FALSE TRUE 828848.2422 691982.895 939362.4414 610898.5413 1167212.357 790753.669 1044459.489 859778.0922 1429174.165 0.57994908 0.484183742 0.657276394 0.427448632 0.81670407 0.553294125 0.730813301 0.601590844 1 20.44675031 -5 0.148710827 2.458310638 0.470736558 0.589078908 0.106945449 81.17396325 0.719810606 34.75855802 0.474034876 1.00E-05 5 -1.98757408 YGLFQHICTAYELVLADGSFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGLFQHICTAYELVLADGSFVR 22 0 A0A0A0MTI1;Q15392-2;Q15392;A0A3B3IT58;A0A3B3ITT9 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 165.66 1.26E-11 20628000 23456 21234 18241 26942 23979 18616 27074 20703 16804 FALSE TRUE 22347.28137 23397.76874 19077.36789 24233.73897 28160.93001 17971.32325 22943.36405 18890.13557 19409.8785 1.151335459 1.205456734 0.982869001 1.248526052 1.450855553 0.925885407 1.182045733 0.973222762 1 14.24450347 1.549667448 1.378432752 0.998525402 1.181283625 0.197497864 0.14332208 0.663103335 2.423497306 0.117345477 0.040540751 35.45418025 -1.549667448 0.182758222 YGLLVGGAASHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGLLVGGAASHR 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 180.97 1.88E-05 1656180000 1913450 1424420 1178950 1507690 2089700 1305400 2078500 1530370 1881890 FALSE TRUE 1823005.011 1569570.017 1233006.024 1356134.137 2454143.018 1260193.671 1761386.651 1396362.69 2173723.89 0.838655277 0.722065035 0.567232126 0.623875987 1.129004024 0.579739532 0.810308365 0.642382731 1 21.05173727 YGLQDS(ph)DEEEEEHPSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK 273.87 2.09E-35 3789420000 3074585 2634703 2612486 3345302 2159894 3158394 3378581 3161004 1999008 TRUE FALSE 2929255.46 2903182.231 2732271.067 3009025.887 2536578.83 3049018.024 2863116.417 2884209.732 2309003.951 1.268622974 1.257330993 1.18331156 1.303170523 1.098559761 1.320490605 1.239979003 1.249114247 1 21.13883921 -1.076304732 5.837767687 0.999999017 1.2426862 0.594231558 0.062312378 6.93E-07 1.10E-07 0.052448644 0.012362214 0.083887117 1.076304732 0.242687183 YGMGTS(ph)VER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 YGMGTSVER 9 0 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 1 YGMGT(0.02)S(0.98)VER;YGMGT(0.021)S(0.979)VER;YGMGT(0.006)S(0.994)VER;YGMGT(0.049)S(0.951)VER;YGMGT(0.188)S(0.812)VER;YGMGT(0.034)S(0.966)VER;YGMGT(0.029)S(0.971)VER;YGMGT(0.028)S(0.972)VER;YGMGT(0.036)S(0.964)VER;YGMGT(0.04)S(0.96)VER;YGMGT(0.057)S(0.943)VER;YGMGT(0.074)S(0.926)VER 134.84 0.00024911 10017290000 16393820 12700530 14781830 13674930 16512060 13336530 14979440 13194510 15806400 TRUE FALSE 15618916.62 13994728.45 15459591.53 12300300.06 19391758.04 12874682.62 12694051.31 12039128.76 18257575.78 0.85547593 0.766516246 0.84674941 0.67370938 1.062121185 0.705169338 0.695275838 0.659404562 1 24.12199188 YGNANAWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGNANAWR 8 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 85.359 0.03908 123030000 217650 227630 188050 198270 232440 194320 276400 229050 231330 FALSE TRUE 207362.1158 250825.7558 196672.2785 178339.5229 272977.4624 187590.6497 234230.1036 208993.1677 267203.4749 0.77604573 0.938706938 0.736039374 0.667429654 1.021608954 0.702051684 0.876598269 0.782149887 1 18.02757924 -1.359364704 2.971781028 1.002236035 0.820548747 0.225307213 0.108326641 26887921.88 33406762.8 522314.179 0.023707865 0.043715484 1.359364704 -0.181687288 YGNPWEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 126.28 0.0092303 312800000 429910 396700 374630 436480 336770 397160 457690 431830 345840 FALSE TRUE 409589.0063 437124.181 391807.1561 392604.2011 395502.5814 383406.2496 387860.9844 394016.6759 399471.1009 1.025328254 1.094257332 0.98081477 0.982810021 0.990065565 0.959784697 0.970936279 0.986345883 1 18.60773161 3.721223599 24.25360217 0.978929414 1.059792789 0.733285683 0.019572149 217.248936 303920.0229 0.004953273 0.00769714 5262.881588 -3.721223599 0.080863374 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 284.8 1.91E-77 23179466000 2397946 2034313 1952305 2454553 962360 2616442 2480844 2868548 1008389 TRUE FALSE 2284599.845 2241611.808 2041820.115 2207816.669 1130195.279 2525833.957 2102345.684 2617362.73 1164764.816 1.961425872 1.924518819 1.752989176 1.895504259 0.970320586 2.16853559 1.804952944 2.247116924 1 20.15160725 3.714018387 2.137215536 1.730013711 1.954482248 0.052857346 0.421973381 1.099137494 9.823561822 0.111057193 0.217956741 5176.287469 -3.714018387 0.224468537 YGPIVDVYVPLDFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGPIVDVYVPLDFYTR 16 0 O75494-2;O75494;O75494-5;Q6IQ42;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10;FUSIP1 Serine/arginine-rich splicing factor 10 0 138.94 9.08E-06 41567000 71973 60810 67028 73784 68647 65403 81134 66472 72907 FALSE TRUE 68570.97893 67006.60814 70101.3001 66367.09214 80619.01507 63138.07771 68755.51817 60651.35929 84213.0452 0.814256019 0.795679671 0.832428039 0.788085646 0.957322169 0.749742247 0.816447357 0.720213349 1 16.36175611 -2.231960255 2.4317823 1.694214829 0.810601171 0.482581833 0.06205228 2993188.319 919051.8026 11387257.03 0.013630791 0.005861918 2.231960255 -0.883613657 YGQFSGLNPGGRPIT(ph)PPRNSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGQFSGLNPGGRPITPPRNSAK 22 2 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 YGQFSGLNPGGRPIT(1)PPRNSAK 111.4 0.01554 284760000 179730 74965 211360 137220 187340 186000 280580 228240 267660 TRUE FALSE 171234.5191 82604.01873 221051.0651 123426.3849 220012.0367 179558.7734 237772.3678 208254.0956 309167.3458 0.553857066 0.267182223 0.714988397 0.399221931 0.711627666 0.580781819 0.769073355 0.673596673 1 18.23802842 1.412016271 0.300637787 1.048548772 0.375156736 0.582796907 0.130102112 0.926125518 0.306735758 0.238256774 0.197633537 25.82356935 -1.412016271 -0.673392037 YGQFSGLNPGGRPITPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 157.22 5.43E-09 668040000 374210 312850 326830 392350 335890 348200 396760 387150 396410 FALSE TRUE 356521.8349 344729.7707 341815.4788 352910.2326 394469.1097 336141.7467 336226.975 353249.0936 457883.2382 0.778630457 0.752877026 0.746512321 0.770742851 0.861505897 0.7341211 0.734307236 0.771482911 1 18.80462023 0.924211702 21.22664365 1 0.765858133 0.799883282 0.036333265 4638.021343 1299010.661 0.03463433 0.008658059 8.398692904 -0.924211702 -0.234141867 YGQNCHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YGQNCHK 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;; 108.98 0.0071304 965770000 1080160 975950 878800 1123060 767850 1008950 1092950 1076350 793620 FALSE TRUE 1029102.977 1075400.415 919093.8493 1010167.875 901762.7969 974009.8085 926200.4041 982099.0879 916690.5364 1.122628561 1.173133541 1.002621728 1.101972623 0.983715617 1.062528487 1.010374131 1.071352926 1 19.80607525 3.740669984 24.99994767 1.034735108 1.147881055 0.604950875 0.038505184 99.60821371 1180541.014 0.008725585 0.014790708 5503.893016 -3.740669984 0.113145947 YGREDLDVLGLTFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGREDLDVLGLTFR 14 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 240.2 1.98E-17 68065000 94816 92859 74413 105260 81696 82574 85715 96516 72531 FALSE TRUE 90334.23559 102321.4377 77824.90965 94679.06482 95943.75653 79714.44168 72637.60249 88064.54738 83778.73704 1.07824776 1.221329436 0.928933909 1.130108523 1.14520414 0.951487746 0.867017158 1.051156302 1 16.35429652 2.229200213 24.24908168 0.946590669 1.108681707 0.355723264 0.08683347 122.4569987 317233.8198 0.031131816 0.023317346 169.5119082 -2.229200213 0.162091038 YGRPPDSHHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGRPPDSHHSR 11 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;; 74.46 0.024492 51688500 47939.1 27923.2 33835.6 37357 73058 30567.7 68246 51221 31950.9 FALSE TRUE 45673.11375 30768.60583 35386.99573 33601.80339 85799.29207 29509.13288 57833.81928 46735.8177 36905.68239 1.237563182 0.83370917 0.958849517 0.91047777 2.324826057 0.799582367 1.567070856 1.266358313 1 15.17155535 YGS(ph)FEEAEASYPILNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR 209.13 1.37E-11 36994000 67536 49128 51144 69980 58183 60646 75233 53580 49443 TRUE FALSE 64343.70712 54134.19905 53489.00299 62945.47745 68330.09678 58545.81381 63754.8241 48888.25115 57110.36792 1.126655447 0.947887416 0.936590061 1.102172508 1.196456953 1.025134594 1.116344132 0.856031101 1 15.80146506 1.24253585 24.99846365 0.928015547 1.059316691 0.299072277 0.086564679 123.9887439 779750.1896 0.062723832 0.020990591 17.47977548 -1.24253585 0.131301144 YGS(ph)PPQRDPNWNGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YGSPPQRDPNWNGER 15 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;Y(0.001)GS(0.999)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER 153.25 1.63E-06 3044816000 3736740 3120310 3438580 3739260 2663670 3623090 3916200 3906890 2689180 TRUE FALSE 3560111.706 3438273.136 3596242.294 3363382.481 3128213.205 3497621.485 3318711.764 3564782 3106204.3 1.146129283 1.106905021 1.157761031 1.082794999 1.007085466 1.12601141 1.068413872 1.14763282 1 21.56672129 -5 0.074585027 0.692878494 1.209997351 0.345183491 0.045151411 314.7476262 1.677641378 16.82154144 1.837664189 1.00E-05 5 0.517118858 YGSGQQCCYTADGTQLLTADSSGGSTPDRGHDWGAPPFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGSGQQCCYTADGTQLLTADSSGGSTPDRGHDWGAPPFR 39 1 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 174.16 5.58E-19 51349000 23090 11886 18720 18361 28195 18424 35357 23835 35229 FALSE TRUE 21998.58146 13097.19691 19578.33052 16515.3174 33112.19907 17785.97226 29962.64027 21747.88104 40692.1334 0.540610178 0.32186066 0.481133057 0.4058602 0.813724824 0.437086257 0.736325127 0.534449271 1 15.3124623 -0.780909789 0.18777616 1.378147012 0.342127333 0.565927569 0.136436864 11.55895304 0.528835756 2.775884932 0.455959507 0.165611393 0.780909789 -1.036019679 YGTCPHGGYGLGLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGTCPHGGYGLGLER 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 233.02 1.28E-17 846850000 878450 831450 702510 882910 819610 744490 897510 838910 781500 FALSE TRUE 836927.4094 916175.7003 734720.7784 794158.2094 962549.7245 718708.1246 760578.3656 765450.5931 902691.0287 0.927147144 1.014938302 0.813922765 0.879767478 1.066311389 0.796183968 0.842567768 0.847965216 1 19.78387274 2.202520165 24.99992196 0.85461878 0.940866747 0.12390931 0.085634228 281.0355396 194942.3112 0.030212911 0.022314434 159.4116898 -2.202520165 0.086247967 YGVIILDEAHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;; 202.65 1.34E-07 1398297000 2345230 2188530 2219420 2471410 2335230 2247360 2386110 2316440 1991940 FALSE TRUE 2234375.626 2411543.695 2321182.602 2222979.171 2742493.373 2169533.36 2022065.096 2113600.233 2300839.882 0.971113046 1.048114523 1.008841433 0.966159875 1.191953162 0.942931047 0.878837816 0.918621174 1 21.13372916 2.021322263 24.99995164 0.916988929 1.031458397 0.343320113 0.06896214 223.5759545 262137.5161 0.023884532 0.017638496 105.0321518 -2.021322263 0.114469468 YGVQADRVDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGVQADRVDK 10 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 150.04 2.03E-05 597800000 724460 573710 613410 673290 556620 659810 815730 798010 798860 FALSE TRUE 690216.2115 632171.7013 641535.4552 605609.61 653694.3518 636960.6143 691275.4066 728132.0139 922743.1288 0.748004716 0.685100416 0.695248152 0.656314408 0.708425055 0.690290282 0.749152592 0.789095027 1 19.81556956 0.72326385 1.092492216 0.999837116 0.697826171 0.939684984 0.023898617 0.208172847 0.433991511 0.0227433 0.007161196 5.287663999 -0.72326385 -0.302010945 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK 121.77 1.88E-05 637862000 455655 404678 421069 469091 327273 460473 496776 482732 353852 TRUE FALSE 434117.0912 445915.1483 440375.4301 421937.0815 384349.3076 444526.7045 420983.6973 440461.427 408725.5609 1.062123666 1.09098914 1.077435503 1.032323695 0.94036034 1.087592133 1.029991118 1.077645905 1 18.64077294 3.231831382 7.134944252 1.029462424 1.077890624 0.241876352 0.040731976 0.189334952 51.77874944 0.011067596 0.01393932 1705.420121 -3.231831382 0.0484282 YGYIHLYDLETGTCIYMNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGYIHLYDLETGTCIYMNR 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 268.92 5.84E-32 454230000 491691 575206 496846 589533 528841 545191 528955 565734 438643 FALSE TRUE 468449.7409 633820.1454 519626.8805 530272.0228 621070.703 526310.899 448253.1998 516195.3318 506665.5162 0.924573956 1.250963654 1.025581698 1.046591895 1.225800224 1.03877387 0.884712272 1.018808889 1 18.95067412 1.994402466 24.90609336 0.956708733 1.098305036 0.251658296 0.099229896 277.0283663 1232633.957 0.035982103 0.025749879 98.71939068 -1.994402466 0.141596303 YGYTHLSAGELLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YGYTHLSAGELLR 13 0 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;; 220.66 2.04E-11 649900000 1873840 1241060 1376560 1451630 2319640 1333140 2289790 1823320 2345320 FALSE TRUE 1785267.297 1367525.425 1439676.638 1305709.394 2724184.482 1286973.028 1940440.481 1663660.435 2709020.247 0.659008473 0.504804431 0.531438124 0.481985838 1.005597682 0.475069549 0.716288659 0.614118863 1 21.36933975 -5 0.191055205 2.668712743 0.548405549 0.376323674 0.154968875 137.1630915 1.343270271 86.90653599 0.376430482 1.00E-05 5 -2.120307194 YGYTHLSTGDLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YGYTHLSTGDLLR 13 0 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 155.02 4.65E-05 146890000 107150 68929 58384 62952 172670 62932 146590 94844 188780 FALSE TRUE 102085.2319 75952.94347 61060.96415 56623.94536 202783.5933 60752.64906 124225.0032 86538.95656 218055.0382 0.468162683 0.348320058 0.280025468 0.259677308 0.929965182 0.278611536 0.569695634 0.396867494 1 17.7343328 -5 0.222594364 3.897420909 0.369970426 0.44680243 0.196694967 136.9757119 1.370214466 178.0168645 0.333544564 1.00E-05 5 -3.527450483 YHDEKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHDEKK 6 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 109.68 0.019053 72613000 337630 298600 329560 395100 190712 365850 369120 380210 150424 FALSE TRUE 321670.899 329027.6795 344670.652 355383.7974 223972.1124 353180.5228 312803.9646 346916.7968 173750.9857 1.851332801 1.893673744 1.983704729 2.04536277 1.289040816 2.032682125 1.800300375 1.996632108 1 17.40666164 YHDGNRNPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YHDGNRNPK 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;;; 173.37 3.33E-05 454097000 772542 419255 664098 640732 728237 717260 1187785 738284 458009 FALSE TRUE 736025.4707 461977.5612 694547.5502 576324.402 855241.3022 692421.1064 1006566.583 673635.9391 529034.6965 1.391261245 0.873246243 1.31285822 1.089388665 1.616607205 1.308838741 1.902647576 1.273330357 1 19.01300282 2.743955692 24.90984166 1.501341597 1.150854576 0.138283262 0.274794378 529.2485204 2443618.908 0.078236037 0.080826646 554.5691313 -2.743955692 -0.35048702 YHEAWQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YHEAWQK 7 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;; 117.93 0.0051196 610360000 1873930 1806090 1650530 2138910 1552810 1950440 2271160 1837450 870200 FALSE TRUE 1785353.043 1990132.624 1726208.433 1923902.703 1823619.572 1882895.774 1924652.829 1676553.137 1005146.172 1.776212349 1.979943495 1.717370549 1.91405266 1.814282961 1.873255679 1.914798945 1.66796948 1 19.93897389 0.842193084 3.339780646 1.000154408 1.861121514 0.927082914 0.075109378 0.170852873 3.205001167 0.065075483 0.016864717 6.953333887 -0.842193084 0.860967106 YHEDFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 170.06 0.00098884 658590000 1760210 1635170 1663900 2029080 1330300 1843210 2024790 1760650 655350 FALSE TRUE 1677008.362 1801795.682 1740191.461 1825113.023 1562303.899 1779379.176 1715871.098 1606478.152 756978.3309 2.215398107 2.380247371 2.298865621 2.411050553 2.06386872 2.350634229 2.266737405 2.122224754 1 19.52989248 0.521455574 1.683653865 0.999957342 2.291718836 0.945183439 0.09639886 0.531753464 1.655869187 0.083570585 0.023665354 3.322427971 -0.521455574 1.291761495 YHEEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YHEEFEK 7 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;; 154.35 0.0016845 1930060000 5901670 5650520 5824020 6954440 4553560 6518530 7214350 6077730 2124160 FALSE TRUE 5622709.755 6226314.412 6091057.078 6255366.479 5347699.422 6292791.672 6113668.407 5545531.741 2453563.884 2.291650033 2.537661421 2.482534536 2.549502183 2.179563963 2.564755584 2.491750244 2.260194559 1 21.22644741 0.753079461 3.332817375 1.000050463 2.444993148 0.932376277 0.121108269 0.461296661 5.970188695 0.108372995 0.028066369 5.663429009 -0.753079461 1.444942686 YHEEKER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YHEEKER 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 154.31 0.0010139 132247000 269440 216674 286815 276249 261547 289283 359626 276292 142177 FALSE TRUE 256704.1052 238753.3269 299965.7514 248479.9257 307160.714 279265.0572 304758.4487 252098.4078 164225.083 1.563123613 1.453817666 1.826552594 1.513044908 1.870364188 1.700501848 1.855736305 1.535078583 1 17.32531497 0.9738599 22.91718663 0.999999994 1.669772302 0.691894821 0.142563009 536.193403 470085.2362 0.144048789 0.036012197 9.415857985 -0.9738599 0.669772308 YHFFLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YHFFLYK 7 0 Q12792;Q12792-3;Q12792-4;F8VS81;Q6IBS0;H0Y858;D6RG15 Q12792;Q6IBS0 TWF1;TWF2 Twinfilin-1;Twinfilin-2 0 88.591 0.018495 218640000 910460 633430 277830 311980 940130 363750 1003700 513340 343840 FALSE TRUE 867424.3602 697977.2372 290568.7803 280619.1777 1104088.374 351153.2463 850567.1308 468389.2282 397160.9511 2.184062551 1.757416572 0.731614675 0.70656286 2.779951985 0.884158539 2.141618224 1.179343606 1 18.59936426 1.016611424 23.83565353 0.999999479 1.625714495 0.090972524 0.676730562 248.6829509 356831.7554 0.609906589 0.152476647 10.38990135 -1.016611424 0.625715016 YHFLEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YHFLEER 7 0 H0YE96;Q96I59-2;Q96I59 H0YE96 NARS2 "Probable asparagine--tRNA ligase, mitochondrial" 0 121.52 0.0044301 67434000 34263 30936 37752 38692 38326 30490 40767 36218 14820 FALSE TRUE 32643.45589 34088.41357 39482.96654 34802.60665 45010.04227 29434.12365 34547.24541 33046.55992 17118.20991 1.906943312 1.991353871 2.306489215 2.033075119 2.629366184 1.719462713 2.018157599 1.93049157 1 14.06324422 0.227059785 0.813828227 0.984463206 2.093947968 0.67030949 0.239032968 1.874879784 1.496257852 0.292302946 0.075477336 1.686785211 -0.227059785 1.109484762 YHGHS(ph)MSDPGVS(ph)YR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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" 2 YHGHS(1)MSDPGVS(1)YR;YHGHS(0.999)MS(0.001)DPGVS(0.993)Y(0.007)R;YHGHS(1)MSDPGVS(1)YR;YHGHS(1)MSDPGVS(1)YR;YHGHS(0.965)MS(0.035)DPGVS(0.999)Y(0.001)R;YHGHS(1)MSDPGVS(0.997)Y(0.003)R;YHGHS(0.999)MS(0.001)DPGVS(0.995)Y(0.005)R;YHGHS(0.974)MS(0.027)DPGVS(0.998)Y(0.001)R;YHGHS(0.999)MS(0.001)DPGVS(1)YR;YHGHS(1)MSDPGVS(1)YR 180.62 9.14E-07 6990500000 4661580 3867430 5318540 4833470 5752390 5007300 5810070 3286240 1208366 TRUE FALSE 4441236.352 4261525.514 5562400.32 4347600.413 6755604.995 4833895.945 4923637.112 2998479.404 1395753.228 3.181963877 3.053208425 3.985231923 3.114877563 4.840114184 3.463288387 3.527584256 2.148287637 1 20.41261246 1.047195176 2.657513602 1.009419655 3.558868279 0.740365704 0.521635285 0.127813447 1.929554461 0.488028112 0.131508067 11.1479542 -1.047195176 2.549448624 YHGHS(ph)MSDPGVSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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(1)MSDPGVSYR;YHGHS(0.882)MS(0.118)DPGVSYR;YHGHS(0.996)MS(0.004)DPGVSYR;YHGHS(0.92)MS(0.08)DPGVSYR;YHGHS(0.951)MS(0.049)DPGVSYR;YHGHS(0.683)MS(0.317)DPGVSYR;YHGHS(0.907)MS(0.093)DPGVSYR;Y(0.301)HGHS(0.408)MS(0.29)DPGVSYR;YHGHS(0.979)MS(0.021)DPGVSYR;Y(0.42)HGHS(0.508)MS(0.071)DPGVSYR;YHGHS(1)MSDPGVSYR;YHGHS(1)MSDPGVSYR;YHGHS(0.92)MS(0.08)DPGVSYR;YHGHS(0.998)MS(0.002)DPGVSYR 174.52 1.73E-06 13695820000 8585740 8073720 9076290 9593760 9319130 8147640 10033610 6370469 796813 TRUE FALSE 8179909.085 8896441.247 9492446.874 8629377.018 10944383.32 7865485.184 8502798.515 5812636.962 920378.6905 8.887547235 9.666066087 10.31363174 9.37589832 11.89117418 8.545922744 9.2383696 6.315484075 1 19.81186806 0.873252654 1.472330534 0.998743338 9.799850957 0.908783477 0.891730237 0.144813657 0.60933691 0.786937905 0.231584409 7.468831371 -0.873252654 8.801107618 YHGNVMLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 209.87 7.71E-06 8278074000 1691864 1326925 932526 862794 1857042 917402 1919346 1295507 1117941 FALSE TRUE 1611892.942 1462140.166 975283.2395 776064.3079 2180909.537 885632.1387 1626514.516 1182065.539 1291305.581 1.24826607 1.132296017 0.755269128 0.600991988 1.688918231 0.685842416 1.259589164 0.915403416 1 20.30039902 3.988960299 22.8742711 1.002616251 1.204777475 0.072129222 0.310801469 523.2190097 1084123.746 0.073068999 0.136898611 9749.005132 -3.988960299 0.202161224 YHIDLDPHFNDILGQHSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHIDLDPHFNDILGQHSR 18 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 76.713 0.0051367 80448000 131729 163287 152757 188588 147064 159938 194652 128971 20197.7 FALSE TRUE 125502.4312 179926.1309 159761.0595 169630.7759 172711.915 154399.307 164954.2624 117677.6155 23329.85616 5.379477283 7.712269193 6.847923041 7.270973931 7.40304243 6.618099396 7.070522049 5.044078057 1 14.50988979 0.874041968 2.534103942 1.002912033 6.909441342 0.898536797 0.628588701 0.136803637 1.767737812 0.580403476 0.155478955 7.482418026 -0.874041968 5.906529309 YHIEVNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YHIEVNR 7 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 81.635 0.026668 96687000 86068 102960 74418 92215 76142 79823 80953 89233 78495 FALSE TRUE 81999.73621 113451.7411 77830.13891 82945.373 89421.14069 77058.70949 68602.13305 81419.28547 90667.6037 0.904399508 1.251293035 0.858411778 0.914829218 0.986252388 0.849903453 0.756633354 0.897997544 1 16.46829954 3.702869935 24.74008027 0.879215484 1.077846343 0.325980064 0.107575738 473.6117144 328298.2597 0.028299923 0.043843859 5045.101809 -3.702869935 0.198630859 YHNEMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YHNEMK 6 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ;; 117.7 0.022498 484210000 1211120 1057300 1108920 1119050 908550 1126090 1276390 1088160 665500 FALSE TRUE 1153872.758 1165040.072 1159765.079 1006560.968 1067000.832 1087093.221 1081653.263 992874.9417 768702.3411 1.501065752 1.51559324 1.508731035 1.309428779 1.388054615 1.414192676 1.407115869 1.291624714 1 19.55206554 -3.588285216 0.15460548 1.77E-13 1.579539975 0.8753725 0.053666471 26.7998581 0.363819456 8.760793273 0.27349082 0.000258056 3.588285216 1.579539975 YHNTICGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHNTICGR 8 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ; 109.11 0.0036814 179155000 77092 65717 67542 77379 86615 70638 94313 67822 63231 FALSE TRUE 73448.01394 72413.63701 70638.86751 69600.71591 101720.6286 68191.78835 79923.81967 61883.14613 73036.54054 1.005633802 0.991471344 0.967171596 0.952957457 1.392736127 0.933666735 1.094299088 0.847290215 1 16.15633081 1.24580067 24.99877695 0.923645097 1.042322 0.125575201 0.136024195 317.9556425 1097878.839 0.088548755 0.030879121 17.61167532 -1.24580067 0.118676903 YHNVGLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHNVGLSK 8 0 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 101.64 0.0052489 1299180000 3647500 3398600 3372600 4177800 3045700 3865700 4565100 3578000 1801630 FALSE TRUE 3475089.904 3744921.204 3527237.046 3757839.607 3576869.116 3731829.84 3868610.151 3264691.352 2081017.579 1.669899351 1.799562503 1.694957833 1.805770237 1.718807737 1.793271656 1.858999266 1.568795663 1 20.98885772 0.894396977 4.356290001 1.000118149 1.763083924 0.946987429 0.056746235 0.119951768 4.522409572 0.054789728 0.013936981 7.841460824 -0.894396977 0.762965775 YHPDKNKEPGAEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHPDKNKEPGAEEK 14 2 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 153.24 3.87E-06 144034000 315520 258410 251530 339830 138000 313090 334140 362890 129451 FALSE TRUE 300605.9949 284742.2728 263062.8993 305669.6428 162067.1563 302247.6148 283160.8061 331113.4278 149525.5999 2.010398186 1.9043045 1.759316795 2.044262942 1.083875647 2.021377041 1.893727938 2.214426345 1 17.19003298 3.918292826 1.290647747 1.757429194 2.005481103 0.057487604 0.395128442 1.750352217 5.301860488 0.112554927 0.38369612 8285.005982 -3.918292826 0.248051909 YHPDKNPEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YHPDKNPEGR 10 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 107.06 0.0014028 60030000 91312 69506 72563 82447 68048 78472 102590 86640 95634 FALSE TRUE 86995.86272 76588.74042 75890.08532 74159.27092 79915.54966 75754.49496 86938.01131 79053.34229 110464.4323 0.787546371 0.693333943 0.687009237 0.671340715 0.723450508 0.68578178 0.78702266 0.715645214 1 16.7532224 -0.305925114 0.65391609 1.022099851 0.713800793 0.832248576 0.03972277 3.296784773 1.234559694 0.22243676 0.014914922 0.494395929 0.305925114 -0.308299058 YHPGYFGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHPGYFGK 8 0 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 140.53 0.00064813 4459800000 12295000 12625200 9576700 13422000 9138100 10751300 11724800 11606000 7803000 FALSE TRUE 11713839.72 13911722.23 10015801.17 12072795.06 10731781.75 10378979.79 9935966.419 10589717.11 9013049.388 1.299653337 1.543508932 1.111255551 1.339479519 1.190693769 1.151550307 1.102397867 1.174931664 1 23.10358387 2.780551847 0.454110104 1.038422191 1.444144637 0.504766527 0.106575338 0.847444627 0.357121085 0.094089936 0.140239925 603.3257302 -2.780551847 0.405722446 YHQIGSGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHQIGSGK 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ; 144.09 0.000591 832650000 2443200 2391300 2449400 2909800 2186000 2721900 3179200 2517900 1123710 FALSE TRUE 2327714.778 2634976.189 2561707.413 2617301.376 2567237.708 2627639.92 2694154.65 2297419.328 1297969.208 1.793351309 2.03007604 1.973627261 2.016458757 1.97788799 2.024423927 2.075669156 1.770010655 1 20.30782473 0.86443703 4.080860522 1.000104862 1.981932421 0.944379283 0.074795178 0.182094797 5.124777425 0.075557391 0.019288261 7.318751989 -0.86443703 0.981827559 YHSDDYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YHSDDYIK 8 0 Q13547;Q5TEE2 Q13547 HDAC1 Histone deacetylase 1 0 ;; 150.4 0.0004898 1207590000 1922400 1770230 1452160 1834750 1607090 1675610 2397400 1905740 1067300 FALSE TRUE 1831531.962 1950618.45 1518742.972 1650317.444 1887365.987 1617583.206 2031632.599 1738863.303 1232811.433 1.485654588 1.582252076 1.231934529 1.338661696 1.530944585 1.312109186 1.647967032 1.410486029 1 20.23352072 0.96165825 23.51687969 0.999999998 1.461963075 0.545054662 0.126911694 2568.231019 1575224.215 0.119312051 0.029828013 9.154997929 -0.96165825 0.461963077 YHSDEYIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHSDEYIK 8 0 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19 Q92769 HDAC2 Histone deacetylase 2 0 ; 167.24 0.00031378 614060000 993710 924720 781780 961390 721280 948740 1149190 943710 435680 FALSE TRUE 946739.2976 1018950.019 817625.3863 864749.2507 847071.0036 915884.8959 973859.9592 861073.7495 503243.0293 1.881276526 2.02476728 1.62471279 1.718353162 1.683224515 1.81996539 1.935168304 1.711049532 1 18.94089576 -2.164335601 0.48072019 5.51E-14 1.836941759 0.8053536 0.123336336 37.99047556 2.540534607 41.23049133 0.065806677 0.006849587 2.164335601 1.836941759 YHSDFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YHSDFNR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 144.83 0.0023274 1515440000 622500 507042 439196 541407 638449 523846 658755 528022 524587 FALSE TRUE 593075.6587 558710.1563 459333.571 486983.7398 749794.3035 505705.0817 558249.8259 481785.5945 605937.2727 0.978774017 0.922059397 0.758054656 0.803686721 1.237412414 0.834583222 0.921299697 0.795108035 1 19.20880893 -2.218901841 2.349752868 1.287931311 0.911970521 0.043550042 0.135656865 9189596.67 2425875.946 14066456.21 0.033123165 0.006040851 2.218901841 -0.37596079 YHSDFNRQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YHSDFNRQDR 10 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 145.34 1.84E-05 307621000 97872 67588 84965 75649 146990 83799 144825 94494 132510 FALSE TRUE 93245.78452 74475.29404 88860.72929 68044.6188 172625.0095 80897.01962 122729.2864 86219.60442 153058.974 0.609214749 0.486579075 0.580565301 0.444564713 1.127833311 0.528534966 0.801843127 0.563309698 1 17.22372811 YHTINGHNAEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;; 308.37 1.85E-46 19410750000 3224628 3434096 3331082 4230599 3586554 3632283 4535180 2868943 280846.3 FALSE TRUE 3072206.225 3784034.287 3483815.405 3805331.151 4212047.882 3506496.129 3843254.997 2617723.142 324398.5098 9.470469598 11.66477087 10.73930767 11.73042118 12.98417765 10.80922391 11.8473263 8.069467221 1 18.30740767 0.889296722 2.945149706 1.005609763 11.28093448 0.926765497 0.919825634 0.107906877 1.97038927 0.88093896 0.231565462 7.749911122 -0.889296722 10.27532471 YHTINGHNCEVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YHTINGHNCEVK 12 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 196.11 1.22E-07 655700000 545320 698740 573780 821640 454840 690750 751420 526430 71424 FALSE TRUE 519543.8043 769942.4004 600088.3805 739047.1862 534163.952 666829.1543 636777.0782 480332.9984 82500.06914 6.297495381 9.332627335 7.273792456 8.958140204 6.474709144 8.082770854 7.718503571 5.822213284 1 16.33210771 0.829792775 2.135632227 1.002932853 7.815874144 0.833465439 0.949607885 0.217109874 1.810752012 0.81604166 0.223860876 6.757604565 -0.829792775 6.812941291 YHTSQSGDEMTSLSEYVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 YHTSQSGDEMTSLSEYVSR 19 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 311.87 1.50E-61 4164493000 1127718 1082282 1181156 1318863 2016041 1062901 1839752 1336751 1135957 FALSE TRUE 1074413.005 1192567.766 1235313.171 1186288.386 2367637.912 1026092.472 1559064.043 1219697.996 1312115.41 0.818840322 0.908889384 0.941466857 0.904103691 1.80444334 0.782013887 1.188206488 0.929566094 1 20.32346319 2.952140196 24.99961787 1.148238598 0.888592435 0.174344199 0.267537746 631.538638 329884.5809 0.074604604 0.07913196 895.6538471 -2.952140196 -0.259646163 YHTVNGHNCEVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 242.48 1.56E-16 11901970000 1682854 2010446 1831807 2319987 1915097 1983695 2454709 1619629 232575 FALSE TRUE 1603308.827 2215312.733 1915797.163 2086777.499 2249089.31 1914999.145 2080198.058 1477805.699 268641.5432 5.968208817 8.246352023 7.131425543 7.767888296 8.372083051 7.128454974 7.743396772 5.5010319 1 18.0353229 0.874712771 2.714447261 1.003066893 7.481634827 0.900912628 0.680152216 0.13416614 1.990619588 0.621337965 0.164907945 7.493984155 -0.874712771 6.478567934 YHYLGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ;;;;;;; 142.63 0.0024763 2055944000 2783802 2467812 2338632 2839318 2950658 2466569 3254026 2572717 1652266 FALSE TRUE 2652217.196 2719284.848 2445860.59 2553904.36 3465251.821 2381151.097 2757564.569 2347436.261 1908490.973 1.389693341 1.424835059 1.281567807 1.338179953 1.815702495 1.247661703 1.444892645 1.229995999 1 20.86400093 0.956309255 2.219014181 0.999448112 1.420328229 0.441172749 0.154653756 0.306669058 3.316972566 0.135169632 0.037116165 9.042931782 -0.956309255 0.420880118 YIAIVSTTVETKEPEKEIRPALELLEPIEQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIAIVSTTVETKEPEKEIRPALELLEPIEQK 31 3 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 130.87 1.75E-06 543950000 1802030 1451720 1795830 1812520 881950 2099980 2161900 2193700 913180 FALSE TRUE 1716851.613 1599651.918 1878170.582 1630322.046 1035761.801 2027257.166 1832062.449 2001607.998 1054791.291 1.627669501 1.516557762 1.780608732 1.545634725 0.981959 1.921950991 1.736895692 1.897634173 1 20.00852613 YIASTQRPDGTWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIASTQRPDGTWR 13 1 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 0 ; 151.08 4.06E-05 509120000 463010 371800 361340 420880 503140 391540 479100 376580 472660 FALSE TRUE 441124.4349 409686.8427 377907.7964 378572.3428 590887.4567 377980.8716 406004.4957 343604.6588 545957.6988 0.807982809 0.75040034 0.692192449 0.693409661 1.08229531 0.692326296 0.743655592 0.629361322 1 19.05842965 4.723508641 4.439189688 0.77342293 0.809859927 0 0.144717137 1.918038313 83.53966351 0.031760869 0.208161001 52906.45234 -4.723508641 0.036436997 YICPHAPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YICPHAPR 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 164.89 0.00032745 346830000 651780 476160 386280 439000 750080 444070 708500 556390 678540 FALSE TRUE 620971.6511 524681.2453 403991.3201 394870.886 880893.7145 428691.7446 600405.3125 507669.542 783764.5177 0.792293651 0.669437355 0.515449872 0.50381317 1.123926504 0.546964981 0.766053194 0.647732234 1 19.58006074 YIDENQDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 231.73 1.33E-06 8292640000 3987950 3479240 3504600 3949580 4110940 3623190 4200910 3825200 4272840 FALSE TRUE 3799447.507 3833778.512 3665289.377 3552560.715 4827886.634 3497718.022 3559984.024 3490245.209 4935450.205 0.769827949 0.776783951 0.742645397 0.719804793 0.978205925 0.708692799 0.721308873 0.70717869 1 22.23475026 -0.926249628 7.922363692 1.000000001 0.765286677 0.463363342 0.079289973 1.08E-09 1.36E-10 0.072316889 0.017045254 0.118508738 0.926249628 -0.234713323 YIDQEELNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 214.96 1.53E-06 4741680000 10237780 8846940 9001440 10393950 6814530 9697360 10702340 10515120 7664410 FALSE TRUE 9753860.429 9748453.244 9414164.928 9349130.399 8002981.874 9361537.992 9069501.471 9594360.349 8852967.558 1.101761682 1.101150906 1.063390876 1.056044805 0.903988614 1.057446323 1.024458907 1.083745115 1 23.0777297 3.333264392 2.350600996 1.018186908 1.09986139 0.342616213 0.047433802 0.305005627 3.433003245 0.013681006 0.019633665 2154.092715 -3.333264392 0.081674482 YIDTEHGGSQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIDTEHGGSQAR 12 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 112.73 0.0012425 287030000 487840 437280 468080 568890 629820 451300 593410 545630 696850 FALSE TRUE 464780.77 481839.3291 489541.931 511704.0964 739660.4086 435671.3678 502874.4058 497851.7446 804913.939 0.577429148 0.59862217 0.608191643 0.635725227 0.918931047 0.541264534 0.624755494 0.618515497 1 19.61847501 -1.85974092 2.621662002 1.15650894 0.634935069 0.546565592 0.102817262 37145914.07 23616118.15 36294641.54 0.02433851 0.01381208 1.85974092 -0.521573871 YIEIDS(ph)DEEPRGELLSLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 YIEIDSDEEPRGELLSLR 18 1 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(0.994)DEEPRGELLS(0.006)LR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR 310.88 2.27E-61 3721668000 1847137 1677858 1587345 1893571 1902545 1683133 1922535 1730083 2079796 TRUE FALSE 1759826.495 1848833.638 1660126.338 1703225.646 2234348.246 1624845.682 1629216.976 1578587.761 2402320.142 0.732552862 0.769603354 0.691051251 0.708991952 0.930079304 0.676365175 0.678184788 0.657109656 1 21.19599699 -1.610271309 3.050780714 1.017355007 0.731829529 0.542426837 0.077783099 26381853.38 29700269.65 3675679.684 0.018687069 0.024531759 1.610271309 -0.285525478 YIELFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 ;;;;;; 162.47 0.019043 2946191000 3991881 3272079 3324471 3903853 4108259 3088775 4207770 3704553 4074157 FALSE TRUE 3803192.696 3605507.57 3476901.284 3511430.28 4824738.069 2981809.947 3565797.406 3380162.7 4705956.46 0.808165721 0.766158293 0.738829888 0.746167184 1.025240694 0.633624636 0.757720016 0.718273263 1 22.16605654 -2.419443852 2.238659175 2.966982978 0.773675561 0.336146304 0.099688566 2597714.111 302914.445 26060428.12 0.022107898 0.003806766 2.419443852 -2.193307417 YIEVFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YIEVFK 6 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;; 118.03 0.051687 628046000 2640860 2345860 2273940 2884670 2307700 2472750 2905510 2769770 2395780 FALSE TRUE 2516031.781 2584905.801 2378202.398 2594697.491 2710162.149 2387118.047 2462221.086 2527234.255 2767305.326 0.909199197 0.934087676 0.859392845 0.937626024 0.979350606 0.862614625 0.889754037 0.91324735 1 21.4000504 -1.233557407 3.039866136 1.000419625 0.91030986 0.384040238 0.035555847 8053257.099 10780293.35 31632.17891 0.008412553 0.058404 1.233557407 -0.090109765 YIHLENLLAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 108.47 0.002147 439080000 102460 74063 99470 88836 95648 90225 103810 92930 93297 FALSE TRUE 97616.91886 81610.1039 104030.7979 79906.0365 112328.9809 87100.48563 87971.8779 84792.55655 107765.0223 0.905831195 0.757296776 0.965348456 0.74148397 1.04235102 0.808244492 0.816330531 0.786828182 1 16.71752947 -2.304137871 2.244006794 1.727956393 0.848807587 0.19116218 0.094708142 4769852.058 663141.3457 17650730.56 0.021856389 0.004964347 2.304137871 -0.879148806 YIHSANVLHR ddPTM_SK-BR-3_Trastuzumab_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 ; 150.61 1.23E-05 215097000 286406 335670 211220 298925 295390 278360 310615 278206 73472 FALSE TRUE 272868.156 369875.1546 220904.6459 268876.4911 346905.9225 268720.3234 263224.9769 253844.8078 84865.66252 3.215295184 4.358360539 2.602992063 3.168260084 4.087706526 3.166419909 3.101666435 2.991136818 1 16.37289332 -0.713295903 0.370896801 0.128272648 3.613724187 0.694228604 0.496146607 5.789995957 0.694451612 6.244532993 0.358243852 0.193510305 0.713295903 3.485451539 YIIEELNVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIIEELNVR 9 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 95.502 0.018616 54026000 82911 70368 68591 73270 92030 67806 95278 82927 101590 FALSE TRUE 78991.96134 77538.5792 71735.9652 65904.7604 108080.0029 65457.86122 80741.5912 75665.47226 117344.0584 0.673165412 0.660779764 0.611330188 0.561636962 0.921052198 0.55782851 0.688075667 0.644817244 1 16.84038527 -1.835300967 2.376945816 1.136044144 0.664879972 0.521453941 0.100905313 11893960.62 6965051.94 9215938.569 0.024498251 0.014611642 1.835300967 -0.471164172 YIKDYMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIKDYMK 7 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 ; 86.011 0.018596 1593960000 2769800 1650430 1081380 1182440 2297800 1546010 3300500 2066960 2394100 FALSE TRUE 2638877.043 1818610.693 1130962.343 1063578.885 2698535.592 1492471.286 2796948.107 1885966.025 2765364.801 0.95426001 0.657638621 0.408974014 0.384607081 0.975833493 0.539701411 1.011421027 0.681995382 1 21.39903838 1.737702724 24.99999939 0.886745432 0.669764854 0.222075285 0.213775345 0.220691238 5947.962309 0.098394406 0.054564746 54.66416574 -1.737702724 -0.216980578 YIKNPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIKNPR 6 1 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 84.609 0.050758 2491100000 3008100 2478700 2362100 2883500 2753900 2781300 3479000 3125700 3142300 FALSE TRUE 2865913.074 2731282.348 2470404.621 2593645.102 3234179.288 2684982.884 2948214.654 2851997.138 3629591.835 0.789596518 0.752503993 0.680628769 0.714583132 0.891058674 0.739747885 0.812271679 0.785762495 1 21.79137589 -1.423883133 0.315082666 1.165294821 0.747755105 0.64475957 0.054791271 13.08305821 0.843856484 1.7936359 0.051539271 0.037680518 1.423883133 -0.417539717 YIMIFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIMIFR 6 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 159.55 0.021132 217334000 538570 459520 304100 367580 627170 339990 623350 474790 582260 FALSE TRUE 513112.8634 506345.6104 318043.2858 330630.16 736548.2494 328216.061 528246.5089 433214.8706 672553.907 0.76293195 0.752869926 0.472888913 0.491603954 1.095151246 0.488014504 0.785433708 0.644134048 1 19.35929038 -1.662212895 2.280372918 1.051758519 0.694966883 0.217309975 0.18630685 4630013.441 3311524.378 1391806.373 0.043756223 0.021766425 1.662212895 -0.356791636 YINENLIVNTDELGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YINENLIVNTDELGR 15 0 P17987;E7ERF2;F5H136;F5H7Y1 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 279.56 2.68E-33 234030000 166361 161516 142264 155633 153197 142152 160562 161872 146595 FALSE TRUE 158497.4452 177974.664 148786.9451 139988.4752 179914.5083 137229.2406 136065.318 147697.6295 169328.2039 0.936036889 1.051063319 0.878689679 0.826728637 1.06251944 0.810433451 0.803559684 0.872256518 1 17.36946277 3.718632241 23.68418042 0.879859971 0.993550097 0.17379818 0.086882774 518.2350584 615904.3453 0.022395688 0.034758793 5231.572418 -3.718632241 0.113690125 YINTEHGGSQAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YINTEHGGSQAR 12 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;; 175.48 2.76E-05 2363693000 1330974 1079048 1166661 1366150 1312305 1211241 1426430 1277984 1458940 FALSE TRUE 1268061.497 1189004.218 1220153.561 1228822.006 1541170.577 1169295.42 1208801.905 1166076.946 1685184.964 0.752476152 0.705563035 0.724047263 0.729191176 0.914540902 0.693867703 0.717311115 0.691957839 1 20.68447552 -2.049667654 2.587983559 1.350699536 0.739176823 0.615800892 0.064246569 7847250.948 3473972.598 16266690.25 0.014692126 0.008919332 2.049667654 -0.611522712 YIPPHLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YIPPHLR 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8Y770;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 91.584 0.016296 69372000 79958 77540 73016 87760 100850 72201 83287 80987 97507 FALSE TRUE 76178.5438 85441.41416 76363.85582 78938.19807 118438.2081 69700.66127 70580.03848 73895.34894 112627.8876 0.676373725 0.758616858 0.678019072 0.700876131 1.051588649 0.618857929 0.62666574 0.656101704 1 16.78120457 5.487298855 1.067916558 0.741339676 0.456027464 0.015056036 0.150779992 45.21773159 13.24243255 0.042010493 21.49856791 307113.4628 -5.487298855 -0.285312212 YIQELWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YIQELWR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 180.7 0.001588 8364050000 6914610 6173040 5028310 6040640 7325790 5436930 7476570 6480780 7365660 FALSE TRUE 6587770.089 6802079.794 5258862.987 5433423.391 8603405.457 5248647.751 6335881.93 5913288.546 8507888.934 0.774313127 0.799502655 0.618116084 0.638633559 1.011226818 0.616915405 0.744706704 0.695035936 1 23.02036977 -1.39313092 3.931531659 1.001062594 0.741600039 0.336430311 0.115804417 0.000991293 0.000153015 0.103052212 0.024192445 0.040445395 1.39313092 -0.259462554 YIQHTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YIQHTYR 7 0 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;;;; 176.41 0.00075288 11594950000 5213740 4088790 2862911 3498660 5522160 3181291 5590610 4003240 4849330 FALSE TRUE 4967296.843 4505442.35 2994178.301 3146968.05 6485222.956 3071122.095 4737659.766 3652695.083 5601339.329 0.8868052 0.804350903 0.534546851 0.561824211 1.157798622 0.548283529 0.845808384 0.652111016 1 22.4173404 YIQHTYRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIQHTYRK 8 1 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 92.062 0.0078185 876840000 660760 318760 479990 377760 835180 435630 1000900 591890 1041740 FALSE TRUE 629527.1843 351242.0064 501998.0163 339786.8471 980835.1276 420544.0239 848194.3222 540060.9738 1203287.719 0.523172617 0.291901929 0.417188681 0.282382045 0.815129343 0.349495817 0.704897348 0.448821147 1 20.19855022 -1.439922284 0.216797411 1.485669703 0.346886491 0.50962612 0.165433228 16.93695443 0.687084659 4.853310328 0.343341883 0.036314303 1.439922284 -1.138783212 YIQPWESEFIDSQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YIQPWESEFIDSQR 14 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 173.19 6.37E-06 133352000 61806 52614 56949.1 66598 76154 64636 76243 65183 89704 FALSE TRUE 58884.55287 57975.42642 59560.27257 59903.44251 89435.23349 62397.63911 64610.73005 59475.23096 103614.8382 0.568302319 0.559528224 0.574823776 0.578135753 0.863150829 0.602207562 0.623566385 0.574003029 1 16.66087109 -5 0.256179406 3.406969989 0.581651083 0.636857665 0.090144162 122.2033365 1.204649181 154.7082215 0.120487613 1.00E-05 5 -2.825318907 YIQQTKPLTLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YIQQTKPLTLER 12 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 214.42 4.00E-11 1682370000 1829450 1563840 1415550 1732000 1865180 1685580 2139080 1922150 2050910 FALSE TRUE 1742975.524 1723197.074 1480454.368 1557896.069 2190466.801 1627207.942 1812724.059 1753836.356 2368954.648 0.735757236 0.727408216 0.624939937 0.657630179 0.92465544 0.6868886 0.765199984 0.740341888 1 21.17581915 -4.999999989 0.243012793 2.567377787 0.706038541 0.542856942 0.078326332 132.8378999 1.322352635 102.9260256 0.112892823 1.00E-05 4.999999989 -1.861339246 YIS(ph)PDQLADLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 YIS(1)PDQLADLYK;YIS(1)PDQLADLYK;YIS(1)PDQLADLYK;YIS(1)PDQLADLYK 231.17 4.28E-12 112249000 454885 349216 328534 371763 325596 385674 472343 437757 361648 TRUE FALSE 433383.4875 384801.5074 343597.6089 334392.6769 382379.8393 372318.0127 400278.4002 399424.6764 417730.5248 1.037471436 0.921171628 0.822534118 0.800498544 0.915374426 0.891287542 0.958221572 0.956177853 1 18.67221304 -0.462709169 7.695956337 0.999996403 0.917154485 0.13890996 0.067441765 0 0 0.069944491 0.016486075 0.344580607 0.462709169 -0.082841918 YISKPENLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YISKPENLK 9 1 Q9H9S4;Q5TAW7;B7ZBJ4;Q9Y376;A0A087X0K1 Q9H9S4;Q9Y376 CAB39L;CAB39 Calcium-binding protein 39-like;Calcium-binding protein 39 0 84.17 0.014294 478480000 473690 417560 416600 476830 332080 458200 505350 504220 388850 FALSE TRUE 451299.6125 460109.8387 435701.5221 428898.1425 389994.6469 442332.4191 428249.5761 460067.8238 449150.872 1.004784006 1.0243993 0.970056053 0.95490885 0.868293198 0.984819237 0.953464866 1.024305757 1 18.77684061 3.633341493 4.37413102 0.958795404 1.014463006 0.193162813 0.040995493 0.291919292 9.340670135 0.010604198 0.016880229 4298.743116 -3.633341493 0.055667603 YISPDQLADLYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 251.34 1.78E-17 2836036000 2755306 2114141 1832327 2021089 1951010 2134543 2811997 2544989 2071470 FALSE TRUE 2625068.146 2329574.371 1916341.005 1817925.294 2291265.526 2060623.241 2382975.212 2322136.271 2392702.988 1.097114084 0.973616192 0.800910525 0.759778921 0.957605494 0.861211463 0.995934399 0.970507532 1 21.19020989 1.625602581 12.67919686 0.987463091 0.922707847 0.127587035 0.094234183 0.288891781 145.6332769 0.05090758 0.027261163 42.22820105 -1.625602581 -0.064755244 YISSQIERPIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YISSQIERPIR 11 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 92.866 0.0045969 0 54306 44981 49662 56910 49579 59601 63439 50916 62291 FALSE TRUE 51739.063 49564.61504 51939.05182 51189.29868 58225.5619 57537.00243 53760.21541 46457.52512 71950.77014 0.719089773 0.688868444 0.721869296 0.711448933 0.809241677 0.799671808 0.747180542 0.64568489 1 16.13472251 -2.165583527 2.519662479 1.7010255 0.731776942 0.756682107 0.048042926 4493383.311 1603266.742 17884206.97 0.012063924 0.006829933 2.165583527 -0.969248558 YITDWQNVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YITDWQNVFR 10 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 247.07 2.66E-12 1730820000 593870 507420 487110 577450 624350 485380 640040 563200 628920 FALSE TRUE 565798.942 559126.6749 509444.4753 519403.6289 733236.4423 468571.1689 542390.1429 513883.2223 726449.7015 0.778854945 0.769670183 0.701279764 0.714989115 1.009342341 0.645015296 0.74663138 0.707389956 1 19.47050339 -1.214664149 4.972348088 1.000029919 0.759609777 0.379637937 0.096757761 2.93E-05 4.63E-06 0.085580633 0.020169041 0.061000845 1.214664149 -0.240420142 YIYFYEKENDAVTIQVLNQLIQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YIYFYEKENDAVTIQVLNQLIQK 23 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 346.9 1.49E-101 583045000 1362334 1373240 1420970 1625760 1154514 1649670 1679480 1771080 1209248 FALSE TRUE 1297939.172 1513174.717 1486122.88 1462335.516 1355860.876 1592541.514 1423244.48 1615994.846 1396772.004 0.929241972 1.083336946 1.06396955 1.046939309 0.970710232 1.14015853 1.018952611 1.156949625 1 20.41366512 4.602798857 2.843124031 1.059258302 0.923154152 0.334783012 0.05769815 0.332960193 4.434001686 0.012560887 0.089902402 40068.10996 -4.602798857 -0.13610415 YKAEDEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YKAEDEK 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;; 112.84 0.0057124 14052160000 16073030 14787770 10852550 18730470 6923070 15898150 15530340 16831960 6822010 FALSE TRUE 15313289.73 16294660.58 11350150.15 16847647.57 8130451.216 15347593.08 13160901.4 15358064.35 7879932.469 1.943327533 2.067868048 1.440386729 2.138044664 1.031791992 1.947680788 1.670179465 1.949009641 1 22.90975184 -2.434662258 0.205533474 3.32E-27 1.946757197 0.328751766 0.335942302 46.89385708 1.20293883 23.47675384 0.752495332 0.00367568 2.434662258 1.946757197 YKAEDEKQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YKAEDEKQR 9 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;; 135.86 0.00011755 5683570000 9191750 5826290 7978650 7471290 6020220 8883610 11914670 10243240 7882440 FALSE TRUE 8757274.194 6419995.575 8344478.994 6720261.735 7070144.462 8575968.358 10096868.26 9346287.603 9104808.537 0.961829582 0.705121426 0.91649143 0.73810028 0.776528626 0.941916387 1.108959977 1.026522146 1 23.11819725 2.017308129 4.257861888 1.05249521 0.818621308 0.622797206 0.080423878 0.120932049 5.156332286 0.032082516 0.021140903 104.0658244 -2.017308129 -0.233873902 YKAEDEVQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 192.12 3.20E-05 12675700000 14974230 12343670 11613480 14609390 9371720 13237420 14348650 13936840 10409230 FALSE TRUE 14266427.82 13601504.01 12145969.55 13140826.36 11006145 12779004.83 12159499.91 12716456.41 12023440.23 1.186551233 1.13124894 1.01019087 1.092933979 0.91539067 1.062840966 1.011316203 1.05763876 1 23.51934641 3.902983356 1.784274361 1.019727715 1.180226608 0.588868374 0.048257325 0.211027072 1.297127786 0.012256638 0.032161727 7998.036031 -3.902983356 0.160498893 YKCEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 76.592 0.068081 314600000 418330 313370 355090 391910 340290 400340 492760 435630 432190 FALSE TRUE 398556.37 345302.7593 371371.2277 352514.4622 399636.4683 386476.1254 417580.4118 397483.9278 499211.8179 0.798371264 0.691695883 0.743915137 0.706142062 0.800534871 0.774172629 0.83647942 0.796222993 1 18.92929256 0.426907452 0.44148025 1.020437192 0.733039062 0.812407495 0.036919401 0.920090458 0.320481139 0.074999523 0.02182844 2.672436855 -0.426907452 -0.287398131 YKDAIHFYNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKDAIHFYNK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 128.01 0.00020477 3665700000 6035300 4615000 3022300 3480700 4626100 3742200 6889500 4984200 4535700 FALSE TRUE 5750023.33 5085273.747 3160875.444 3130813.423 5432890.375 3612606.676 5838380.241 4547757.025 5239073.191 1.097526818 0.970643769 0.603327216 0.597589174 1.036994556 0.689550717 1.114391807 0.868046095 1 22.32088019 -0.242607552 8.773594026 0.999999992 0.891650331 0.033628793 0.191591984 0 0 0.185997309 0.043839986 0.571995284 0.242607552 -0.108349661 YKDDDDDQLFYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YKDDDDDQLFYTR 13 1 O60568;H7C2V1 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ;;; 192.32 2.57E-06 1056870000 2273140 2102560 1888450 2301210 1398860 2140420 2218250 2384020 1495450 FALSE TRUE 2165693.177 2316813.254 1975037.3 2069887.999 1642820.741 2066296.719 1879815.222 2175262.57 1727356.748 1.253761378 1.341247693 1.143387029 1.19829792 0.951060482 1.196218859 1.088261139 1.259301284 1 20.72013464 3.641224521 4.532445052 1.119679785 1.297099346 0.383803101 0.093961851 0.194389195 6.717559264 0.02279764 0.036251659 4377.483534 -3.641224521 0.177419561 YKDDPVDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YKDDPVDLR 9 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;;; 98.249 0.0056016 3058290000 8681300 7419090 7617960 9094350 6440760 8399310 9434210 8797200 6860270 FALSE TRUE 8270952.154 8175103.706 7967251.001 8180168.66 7564026.505 8108439.789 7994847.993 8026870.531 7924125.634 1.043768428 1.031672652 1.005442287 1.032311833 0.95455661 1.023259873 1.008924942 1.012966086 1 22.91782032 3.844362146 1.363725415 1.004532033 1.043478115 0.314045576 0.020343654 0.50793494 1.774987284 0.005809252 0.017016687 6988.148829 -3.844362146 0.038946082 YKDEDGDLITIFDSSDLSFAIQCSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKDEDGDLITIFDSSDLSFAIQCSR 25 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 153.87 8.47E-08 44116000 78169 51379 70230 81179 52672 74558 90686 83321 58222 FALSE TRUE 74474.10629 56614.57851 73450.11497 73018.73269 61857.98012 71976.03776 76850.18514 76024.97153 67250.7704 1.107408969 0.841842825 1.092182506 1.085767973 0.919810729 1.070263394 1.142740591 1.130469898 1 16.03726317 2.011067565 24.46806911 1.10682318 1.002058731 0.146081844 0.089394565 237.9364584 526024.9079 0.032172646 0.023738503 102.5811503 -2.011067565 -0.104764448 YKDIIRQPS(ph)EEEIIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YKDIIRQPSEEEIIK 15 2 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK 221.92 7.67E-13 1948950000 1181400 427160 1107310 975130 986000 1304390 1888050 1040330 1219590 TRUE FALSE 1125557.563 470688.0896 1158081.259 877108.0798 1157958.088 1259218.647 1599993.296 949233.1901 1408717.788 0.798994357 0.334125184 0.822081803 0.622628668 0.821994368 0.893875734 1.135779863 0.673827787 1 20.42595119 2.612686533 1.495051811 0.963431162 0.601880281 0.357310991 0.174397388 0.350772289 1.583221072 0.073544929 0.063208939 409.9081309 -2.612686533 -0.361550882 YKDLDEDELLGNLS(ph)ETELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 YKDLDEDELLGNLS(0.92)ET(0.08)ELK;YKDLDEDELLGNLS(0.971)ET(0.029)ELK;YKDLDEDELLGNLS(0.996)ET(0.004)ELK;YKDLDEDELLGNLS(0.5)ET(0.5)ELK 207.07 2.03E-16 180953000 416824 443372 372387 479601 202194 482368 426055 507641 233557 TRUE FALSE 397121.5556 488552.1109 389461.3123 431390.5963 237456.5696 465663.4752 361052.4847 463189.2629 269775.8267 1.472042771 1.810955847 1.443647924 1.599070612 0.880199581 1.72611268 1.338342612 1.716941316 1 18.04140156 -3.405675541 0.18779796 5.68E-16 1.613125728 0.230029047 0.268032492 96.92902444 1.623132088 39.6661099 0.730054104 0.000392938 3.405675541 1.613125728 YKDLDEDELLGNLSETELK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 184.6 2.24E-14 154250000 354060 302410 312750 370000 190800 363600 378720 394740 216320 FALSE TRUE 337324.2855 333225.9228 327089.8969 332806.897 224075.4596 351008.4408 320939.3083 360174.473 249865.8008 1.350021829 1.333619574 1.309062288 1.331942571 0.896783229 1.404787849 1.28444672 1.441471669 1 17.93079393 -1.421377025 3.670007307 0.997811449 1.294816562 0.279291219 0.148426581 1872.50721 33819412.07 99904.03029 0.03236555 0.037898583 1.421377025 0.297005113 YKDNPFSLGES(ph)FGSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YKDNPFSLGESFGSR 15 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 YKDNPFS(0.008)LGES(0.982)FGS(0.011)R;YKDNPFSLGES(0.999)FGS(0.001)R;YKDNPFSLGES(1)FGSR 190.31 1.34E-07 522279000 776350 563750 662360 1044070 749470 984000 980070 732200 656418 TRUE FALSE 739653.4741 621196.7659 692729.8612 939118.1 880177.3307 949923.8333 830542.3213 668084.6864 758211.9509 0.975523365 0.81929171 0.913636168 1.23859575 1.160859216 1.25284735 1.095395978 0.881131833 1 19.53224167 3.324735064 7.813898312 1.120839662 0.893188813 0.403938318 0.11452481 0.207012901 16.31218846 0.030858499 0.041785352 2112.200125 -3.324735064 -0.227650848 YKDPQDENK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 93.096 0.0087833 713160000 2174100 1883010 1913820 2306160 1187830 2444090 2444750 2588040 1360910 FALSE TRUE 2071334.602 2074890.86 2001570.54 2074340.415 1394987.176 2359450.55 2071758.487 2361417.498 1571952.972 1.317682296 1.319944614 1.273301794 1.319594448 0.88742297 1.500967645 1.317951951 1.502218921 1 20.58412663 YKDQTGGYTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKDQTGGYTR 10 1 E9PKV2;Q9NRX2 E9PKV2 MRPL17 "39S ribosomal protein L17, mitochondrial" 0 71.555 0.046177 107050000 200030 147800 181820 186400 191710 166500 208330 195010 202430 FALSE TRUE 190574.9783 162860.988 190156.6268 167662.7179 225144.1633 160734.0633 176545.4323 177933.8906 233821.8105 0.815043635 0.696517522 0.813254445 0.717053373 0.962887777 0.687421173 0.755042619 0.760980724 1 17.83504998 -1.216349851 5.365475113 1.000014295 0.771004932 0.440660801 0.079123058 1.21E-05 1.77E-06 0.068563 0.016159446 0.060764531 1.216349851 -0.229009363 YKDSAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKDSAQR 7 1 P05026-2;P05026;V9GYR2 P05026-2;V9GYR2 ATP1B1 Sodium/potassium-transporting ATPase subunit beta-1 0 ; 60.973 0.085988 121180000 197358 150121 123672 202900 178191 154259 217000 183816 190070 FALSE TRUE 188029.2785 165418.5006 129342.4835 182504.1065 209267.454 148916.9722 183892.6645 167720.0966 219545.0849 0.856449501 0.753460278 0.589138598 0.831283044 0.953186696 0.67829791 0.83760775 0.763943755 1 17.74415771 -5 0.365124846 3.753852586 0.77857352 0.318375999 0.099735272 628.2443761 4.921347567 1362.362096 0.067666401 1.00E-05 5 -2.975279065 YKDSSSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKDSSSGR 8 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8Y6N0;A0A2R8YGG3;A0A2R8YFK5;K7EQF0 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 65.224 0.05912 48224000 29373 26799 24252 31490 24920 29869 31190 30203 29460 FALSE TRUE 27984.5965 29529.84857 25363.97819 28324.56537 29266.04011 28834.62904 26431.39266 27558.2652 34028.50634 0.822386861 0.867797378 0.74537442 0.832377569 0.860044805 0.847366874 0.776742664 0.809858209 1 15.05445621 -1.181764244 4.169777622 1.000068943 0.821797665 0.699033249 0.037055363 5352865.717 1517066.45 3350.517615 0.008593354 0.065801494 1.181764244 -0.178271277 YKEALLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKEALLGR 8 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 156.92 0.00035135 4057600000 4260900 3043600 3307900 3603600 3633100 3627500 4858800 3882100 3919200 FALSE TRUE 4059495.701 3353746.3 3459570.487 3241359.282 4266711.49 3501878.765 4117500.822 3542162.744 4526969.52 0.896735815 0.740836952 0.764213338 0.716010847 0.942509436 0.773559166 0.909549049 0.782457829 1 22.11011416 -0.327433847 0.371991333 1.046225448 0.79667667 0.361718872 0.076588776 7.266592011 1.113745722 0.526828382 0.054977345 0.47050707 0.327433847 -0.249548778 YKEEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YKEEAR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 84.244 0.051138 1446460000 3212500 2716700 2798380 3452300 2554160 3144290 3557300 3502940 3099520 FALSE TRUE 3060651.492 2993534.819 2926688.491 3105268.245 2999604.695 3035402.449 3014568.551 3196204.003 3580177.731 0.854888143 0.836141399 0.817470168 0.867350304 0.837836812 0.847835688 0.842016452 0.892750093 1 21.77159978 0.860716149 2.267367531 0.999931258 0.84286978 0.935565681 0.013037353 0.110671161 1.109296059 0.011495391 0.003128348 7.256315355 -0.860716149 -0.157061478 YKEEFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YKEEFEK 7 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 95.099 0.012508 3365240000 8015790 7443770 7063800 8710400 4956170 8401300 9379700 9397600 5513670 FALSE TRUE 7636899.492 8202298.626 7387682.217 7834814.043 5820524.479 8110360.874 7948654.495 8574696.324 6368701.784 1.199129705 1.287907474 1.159998139 1.230205827 0.913926366 1.273471604 1.248080812 1.346380568 1 22.60256789 -2.302995183 2.2336942 0.000146634 1.210383975 0.23997745 0.115879005 1944271.355 349735.7177 9876740.747 0.026985707 0.004977426 2.302995183 1.210237341 YKEETIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YKEETIEK 8 1 P61254 P61254 RPL26 60S ribosomal protein L26 0 ;;;; 129.85 0.00097858 3373690000 6328370 5710780 5062950 6195390 4098590 5972930 6606830 6313750 4720800 FALSE TRUE 6029240.492 6292714.975 5295091.265 5572617.627 4813382.798 5766085.936 5598836.741 5760884.579 5452877.553 1.105698859 1.15401729 0.971063666 1.021959061 0.882723434 1.057439101 1.026767369 1.056485227 1 22.37858633 3.741022701 24.99928038 1.004118197 1.12985808 0.518882669 0.051023193 155.3943241 1577822.58 0.012892783 0.021957213 5508.364884 -3.741022701 0.125739883 YKELGEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YKELGEK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 98.033 0.010543 6633950000 11761070 9806760 10085700 12212270 6901460 11309160 12360870 12052660 7793730 FALSE TRUE 11205147.53 10806079.99 10548139.32 10984669.42 8105072.439 10917520.95 10474992.26 10997265.2 9002341.844 1.244692517 1.200363215 1.171710595 1.220201322 0.900329334 1.212742322 1.163585258 1.221600489 1 23.10186892 2.681213167 0.019029042 6.27E-07 2.323153395 0.21604465 0.098312992 1022.339972 7.968570317 461.7875702 509.4139094 479.9689765 -2.681213167 2.323152768 YKETDLLILFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKETDLLILFK 11 1 P05455 P05455 SSB Lupus La protein 0 ; 146.5 3.26E-05 185940000 1387220 1182970 980110 1409740 855500 1174680 1314370 1378340 787580 FALSE TRUE 1321648.86 1303515.988 1025049.013 1268030.257 1004698.929 1134000.537 1113838.716 1257645.243 909713.884 1.45281817 1.43288567 1.126781762 1.393878096 1.104411999 1.246546367 1.224383552 1.382462403 1 19.79505335 8 0.106594015 0.963442233 2.430622244 0.406217718 0.117966726 102.4541808 0.766045044 1.100733001 22.06746702 100000000 -8 1.467180011 YKETDLLILFKDDYFAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKETDLLILFKDDYFAK 17 2 P05455 P05455 SSB Lupus La protein 0 222.25 1.92E-15 536620000 1539400 1119900 1392300 1385900 969620 1639400 2002600 1725200 1042100 FALSE TRUE 1466635.613 1234019.083 1456138.332 1246586.699 1138721.421 1582627.167 1697066.59 1574132.342 1203703.546 1.2184359 1.025185219 1.209715081 1.035626009 0.946014843 1.314798127 1.40987089 1.307740887 1 20.19904869 2.211268953 24.90255276 1.305664865 1.093759073 0.254649076 0.134692225 211.277123 192780.5777 0.046517566 0.034363973 162.6555748 -2.211268953 -0.211905792 YKHDYVS(ph)H ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YKHDYVSH 8 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 YKHDYVS(1)H;YKHDYVS(1)H;YKHDYVS(1)H 73.327 0.026558 342273000 736710 669500 699880 799230 559320 720880 824790 774820 330487 TRUE FALSE 701887.1783 737722.8112 731970.1903 718889.882 656865.2309 695915.7448 698953.1372 706972.6532 381737.2361 1.838665742 1.932540872 1.917471289 1.883206075 1.720726114 1.823022957 1.830979719 1.851987667 1 18.54222039 -2.140546157 0.430446967 6.78E-13 1.875715884 0.955539659 0.057632288 11.87526321 0.724828384 11.60441803 0.033147827 0.007235255 2.140546157 1.875715884 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNK 270.58 2.70E-71 101730000 201160 251470 202720 262130 66949 282440 172530 259190 51970 TRUE FALSE 191651.5655 277095.0789 212014.9125 235780.1944 78624.8844 272659.032 146207.3798 236493.9495 60029.24217 3.192636764 4.616001616 3.531860554 3.927755638 1.309776395 4.542103517 2.435602624 3.939645762 1 15.87337783 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNKK 30 3 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLS(0.001)KYNLDAS(0.999)EEEDSNKK 108.71 0.0014303 83106000 123300 125920 106080 139290 54676 136040 114520 150250 47183 TRUE FALSE 117471.8534 138751.3912 110943.8729 125288.3046 64211.47709 131328.9007 97047.8707 137093.3135 54499.89866 2.155450858 2.545901819 2.035671178 2.298872248 1.178194431 2.40970908 1.780698186 2.515478319 1 15.73396593 YKPESEELTAER ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;;;;; 171.36 3.53E-05 16000180000 22104310 17622410 17618430 22331140 18264300 19113930 24082730 21992030 21548470 FALSE TRUE 21059483.07 19418153.61 18426252.44 20086371.38 21449588.14 18452009.81 20408467.23 20066291.27 24890096.67 0.846098886 0.780155813 0.740304575 0.807002546 0.86177199 0.741339419 0.819943269 0.806195795 1 24.5690685 0.129026932 1.387412604 1.00021692 0.799005283 0.720892553 0.03908281 5.568314245 8.233738271 0.037737895 0.010353616 1.345943819 -0.129026932 -0.201211637 YKQDVYLLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKQDVYLLPK 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 97.214 0.0055769 0 1267900 1150400 1067000 1247900 872990 1183700 1376600 1326700 1144200 FALSE TRUE 1207968.88 1267627.068 1115923.005 1122458.721 1025239.18 1142708.172 1166574.387 1210527.115 1321636.692 0.91399466 0.959134288 0.844349292 0.84929446 0.775734501 0.864615956 0.882674031 0.915930317 1 20.33389421 -0.572249148 6.109317125 1.000000154 0.880432277 0.380455932 0.049518686 7118265.23 1165148.738 0.052921873 0.01283544 0.267763177 0.572249148 -0.119567877 YKQENTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKQENTR 7 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 84.476 0.019624 120067000 172795 154966 138991 191446 144775 164069 193470 198835 193120 FALSE TRUE 164627.3228 170757.2116 145363.8748 172201.4844 170023.7142 158387.2494 163952.5982 181423.9533 223068.0633 0.738013862 0.765493765 0.651657044 0.771968348 0.762205542 0.710040008 0.734989114 0.813312092 1 17.76712445 0.859176407 2.502833021 0.999818038 0.735056525 0.856741942 0.034476779 0.180677698 2.190706863 0.030926065 0.008294103 7.230634466 -0.859176407 -0.264761512 YKSTTS(ph)VSEEDVSSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKSTTSVSEEDVSSR 15 1 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 Y(0.001)KS(0.024)T(0.024)T(0.115)S(0.831)VS(0.006)EEDVSSR;YKST(0.002)T(0.05)S(0.935)VS(0.013)EEDVSSR 152.13 1.75E-06 478060000 268420 150543 271730 319930 319840 391360 488570 259140 369400 TRUE FALSE 255732.3186 165883.5029 284189.0893 287770.0286 375619.9947 377807.1051 414029.6733 236448.3278 426684.6654 0.599347338 0.38877306 0.666040081 0.674432554 0.880322227 0.88544805 0.970341113 0.554152392 1 18.70281074 3.142845662 1.63878348 0.868687245 0.500220667 0.527947723 0.135251202 0.240063849 1.332619351 0.043008761 0.056913447 1389.458762 -3.142845662 -0.368466578 YKVPDGKPENEFAFNAEFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YKVPDGKPENEFAFNAEFK 19 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 237.39 1.81E-24 2340100000 4213500 4171600 3359700 4603300 1907230 4629000 4141600 4635200 1785390 FALSE TRUE 4014336.205 4596690.783 3513745.568 4140567.538 2239850.308 4468696.569 3509722.854 4229317.315 2062259.163 1.946572127 2.228958836 1.703833171 2.007782345 1.086114853 2.166893788 1.701882536 2.050817565 1 20.97579422 -2.21389063 0.252200168 2.02E-18 1.991840278 0.386780049 0.33061096 36.31842893 1.248468594 22.19736561 0.465498037 0.006110959 2.21389063 1.991840278 YKYGYEIPVDMLCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YKYGYEIPVDMLCK 14 1 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;P60900-3 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 103.39 0.0010203 242900000 401230 365980 330280 391990 311710 378450 454560 422480 399750 FALSE TRUE 382264.6531 403273.7781 345423.6647 352586.4205 366072.1253 365344.1816 385208.5234 385485.4115 461741.1884 0.827876444 0.873376229 0.748089348 0.763601839 0.792808037 0.791231518 0.834252029 0.83485169 1 18.8167249 0.461425505 1.210949278 1.000061674 0.807894297 0.750745286 0.035235945 1.311770516 2.375031398 0.037648162 0.011360115 2.893513445 -0.461425505 -0.192167377 YLADPSNLFVVSSDFCHWGQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLADPSNLFVVSSDFCHWGQR 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ; 198.24 8.66E-22 278840000 520140 547260 517000 573760 511080 504520 560800 548920 493360 FALSE TRUE 495554.013 603026.4162 540704.9614 516084.5547 600212.1902 487048.3459 475239.6602 500853.6548 569867.7491 0.869594768 1.058186601 0.948825341 0.905621621 1.053248216 0.854669082 0.833947282 0.878894543 1 19.12026762 2.206770931 24.9996793 0.87248105 0.967028511 0.189154728 0.072605088 240.9341732 189471.3431 0.025198321 0.018611845 160.9796323 -2.206770931 0.094547461 YLAEFATGNDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLAEFATGNDR 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 226.09 1.16E-11 1296155000 808189 837811 694865 911520 684425 782419 762430 763112 647754 FALSE TRUE 769987.5076 923184.8934 726725.2476 819892.2778 803788.5033 755323.6338 646107.3005 696289.8678 748204.3821 1.029113871 1.233867263 0.971292424 1.095813253 1.074290024 1.009515116 0.86354386 0.930614528 1 19.51307289 2.052238693 3.112420576 0.918460729 1.093138141 0.449825672 0.074083251 0.192261588 3.708350067 0.032616393 0.020523847 112.7817146 -2.052238693 0.174677411 YLAEFATGNDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 211.26 5.44E-08 6526730000 7974930 7836950 7377100 8515720 5932580 8270020 8822120 8735470 6409590 FALSE TRUE 7597970.864 8635544.115 7715347.332 7659703.647 6967220.074 7983627.134 7476143.565 7970545.937 7403556.482 1.026259593 1.16640484 1.042113659 1.034597854 0.941063946 1.07835027 1.009804353 1.07658339 1 22.81978704 3.498627181 22.85372479 1.024208777 1.097653416 0.254807443 0.050895084 291.9230092 310216.5047 0.012598159 0.019268382 3152.297383 -3.498627181 0.073444639 YLAEKYEWDVAEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 217.48 5.24E-12 6848008000 10862050 8422140 10717130 10896620 9869190 11043550 13694750 11793310 11865970 FALSE TRUE 10348622.42 9280365.641 11208521.01 9801271.055 11590373.61 10661109.09 11605364.37 10760625.26 13706084.02 0.755038595 0.67709826 0.817777054 0.715103675 0.845637134 0.777837716 0.846730864 0.785098445 1 23.7083131 -4.999999998 0.111599235 1.765904244 0.639518465 0.71159083 0.047221179 75.13555455 0.555334803 12.99610617 0.495632316 1.00E-05 4.999999998 -1.126385779 YLAEVAAGDDKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLAEVAAGDDKK 12 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 182.08 2.78E-05 5964770000 7039090 7742210 6448030 8053130 3645340 8443980 7482090 8835850 3869770 FALSE TRUE 6706366.166 8531150.001 6743678.553 7243614.072 4281086.142 8151562.855 6340559.752 8062136.132 4469874.168 1.500347865 1.908588403 1.508695391 1.620540937 0.957764353 1.823667188 1.418509675 1.803660647 1 22.09180279 -2.103217825 2.322327647 0.000153275 1.575571113 0.307865608 0.267287556 9598418.042 2912674.646 50625787.86 0.065017117 0.007884646 2.103217825 1.575417838 YLAEVACGDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 YLAEVACGDDR 11 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;;;; 216.45 2.81E-11 4436220000 2744793 2639410 2407389 2797300 2647016 2610448 2841323 2740198 2783831 FALSE TRUE 2615052.075 2908368.88 2517770.167 2516110.089 3108654.752 2520047.531 2407826.992 2500251.736 3215533.294 0.813256103 0.904474815 0.783002363 0.782486095 0.966761799 0.783710601 0.74881109 0.777554299 1 21.6166266 YLAEVACGDDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YLAEVACGDDRK 12 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;;; 259.23 4.62E-21 8177300000 3987890 4215660 3946030 4954470 3218848 5142730 5035950 5411570 3644330 FALSE TRUE 3799390.343 4645240.547 4126959.379 4456437.263 3780214.072 4964635.971 4267623.336 4937704.242 4209474.084 0.902580766 1.103520405 0.980397859 1.058668417 0.898025263 1.17939578 1.0138139 1.172997896 1 22.00520857 2.234911464 24.99987522 1.087346789 0.999289422 0.265953521 0.08379841 139.7813175 957612.8634 0.027664125 0.021231588 171.7558206 -2.234911464 -0.088057367 YLAEVATGDDKKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLAEVATGDDKKR 13 2 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 108.97 0.00066043 135810000 176410 140710 197080 197320 168870 204850 237490 222190 230720 FALSE TRUE 168071.4489 155048.509 206116.3129 177485.0187 198320.8745 197755.9931 201256.5387 202733.8657 266498.8792 0.630664749 0.581797978 0.773422813 0.665987862 0.744171514 0.742051875 0.755187186 0.76073065 1 18.02376994 -5 0.085752073 2.026134935 0.415898302 0.836874941 0.045026354 77.31443582 0.464495432 14.59728539 1.157113602 1.00E-05 5 -1.610236634 YLAEVATGEKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 208.56 3.07E-08 3761320000 4010870 3309310 3771950 3944650 3729040 4013540 4700210 4546890 4498190 FALSE TRUE 3821284.124 3646532.451 3944897.638 3548126.288 4379383.395 3874550.103 3983106.639 4148740.207 5195746.332 0.735463951 0.701830347 0.759255242 0.682890592 0.8428786 0.745715794 0.766609142 0.798487829 1 22.30889957 -5 0.189535738 2.101551971 0.701319908 0.808993247 0.039086427 51.00047675 0.498446525 21.11099133 0.095240733 1.00E-05 5 -1.400232063 YLAFLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLAFLR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 161.85 0.019487 645020000 1454860 853880 227257 292649 1683490 365620 1422590 696670 1168830 FALSE TRUE 1386091.651 940891.3428 237676.9582 263231.3665 1977090.123 352958.4877 1205547.768 635665.8815 1350086.187 1.026669012 0.696912058 0.176045767 0.19497375 1.464417711 0.261434041 0.892941339 0.470833557 1 20.36462008 4.378773474 2.880857584 0.630095869 1.000522537 0.081081292 0.403073138 0.631994146 9.819711654 0.09385741 0.365441792 23920.67737 -4.378773474 0.370426667 YLDEDTIYHLQPSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;; 222.45 1.40E-12 1379210000 1495230 1475480 1509650 1584230 2028930 1385850 1871270 1573710 2178020 FALSE TRUE 1424553.441 1625833.089 1578868.946 1424980.191 2382774.75 1337857.667 1585773.393 1435907.61 2515776.218 0.566248075 0.646255052 0.627587197 0.566417705 0.947133029 0.53178723 0.630331657 0.570761262 1 21.26257217 -1.626730279 2.914430476 1.02980507 0.634596468 0.491730493 0.116355234 19136509.49 19455476.88 4329415.976 0.025776064 0.023619447 1.626730279 -0.395208602 YLDESSGGWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLDESSGGWR 10 0 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 ;;; 236.82 8.68E-12 626930000 826090 692520 609810 734000 819790 637050 856770 740930 835360 FALSE TRUE 787042.3629 763088.5753 637770.3917 660216.9255 962761.1164 614988.7988 726054.0008 676050.2413 964903.3624 0.815669624 0.79084456 0.660968151 0.684231138 0.997779834 0.637357919 0.752462919 0.700640362 1 19.88002493 -2.023862547 2.532348862 1.277611597 0.758441937 0.360086679 0.102553 31168197 11173968.41 50284345.67 0.023104199 0.009465367 2.023862547 -0.51916966 YLDIHER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLDIHER 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 ; 107.66 0.0074265 596330000 1035790 923820 907850 1063370 1084500 862030 1113700 1055790 972670 FALSE TRUE 986830.2594 1017958.308 949475.8205 956478.0273 1273636.457 832177.685 943784.6105 963339.4305 1123506.696 0.878348356 0.90605451 0.845100278 0.851332734 1.133626049 0.740696685 0.8400347 0.857439866 1 20.09957729 -0.128978034 7.350034605 0.999999996 0.879831965 0.12317182 0.099198796 12090913.61 1645013.926 0.089166764 0.021626117 0.743056719 0.128978034 -0.120168031 YLDKELAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLDKELAGR 9 1 Q9HD26-2;Q9HD26;F5H1Y4;Q9HD26-3 Q9HD26-2 GOPC Golgi-associated PDZ and coiled-coil motif-containing protein 0 73.067 0.041014 287920000 223300 155680 211100 244570 262570 235490 332380 285400 315540 FALSE TRUE 212745.0515 171543.969 220779.1438 219985.3589 308362.1249 227334.9223 281669.3264 260408.863 364472.3316 0.583707001 0.4706639 0.605750079 0.603572178 0.846050847 0.623737119 0.772814016 0.714481842 1 18.47544977 0.683961785 0.118994426 1.345328786 0.256816957 0.717681562 0.080437313 6.551337247 0.421804025 2.168426483 1.383861706 4.83016298 -0.683961785 -1.088511829 YLDLHDCYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLDLHDCYLK 10 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 157.66 8.77E-06 417300000 2074400 1875110 1500670 1705280 1734970 1693040 2293000 1927940 1647840 FALSE TRUE 1976347.223 2066185.841 1569477.204 1533862.015 2037548.219 1634409.6 1943160.736 1759119.353 1903378.611 1.038336362 1.085535914 0.824574362 0.805862799 1.070490236 0.858688645 1.020900794 0.924208848 1 20.86013113 3.765212324 24.96146133 0.931954416 1.061936159 0.293809949 0.085443406 832.2202688 779438.1444 0.020851491 0.03757808 5823.878744 -3.765212324 0.129981744 YLDQMEDLYEDFHIVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLDQMEDLYEDFHIVK 16 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ; 204.43 2.52E-11 51580000 76893 63509 70531 84811 65301 66117 81457 76383 59832 FALSE TRUE 73258.42028 69980.6393 73764.91611 76285.63715 76689.47372 63827.35171 69029.23859 69694.49959 69110.44098 1.060019575 1.012591416 1.067348364 1.103822173 1.109665524 0.923555845 0.998825034 1.008451091 1 16.07661606 2.243825403 24.99996802 0.982238316 1.063151138 0.603315506 0.035154876 101.0616657 479896.1728 0.01311049 0.010666652 175.3175539 -2.243825403 0.080912822 YLEEDNS(ph)DES(ph)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLEEDNSDESDAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 40 1 Q9H1C4 Q9H1C4 UNC93B1 Protein unc-93 homolog B1 2 YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 216.5 7.84E-40 703050000 197530 185453 221584 279205 292735 237186 305120 230617 278237 TRUE FALSE 188193.1484 204350.8715 231743.8456 251138.7829 343787.8913 228972.1893 258568.3401 210422.9529 321384.5729 0.58556995 0.635845304 0.721079557 0.781427623 1.069708755 0.712455446 0.804544965 0.65473881 1 18.29394115 3.51403717 2.050769505 0.828400225 0.605425525 0.376612896 0.122007889 0.32494076 2.71900757 0.034376527 0.057828916 3266.15785 -3.51403717 -0.222974701 YLEES(ph)DEDDLF ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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;YLEES(1)DEDDLF;YLEES(1)DEDDLF 217.02 1.22E-11 3083710000 2967740 2783120 2815970 3145980 2931030 2737440 3247230 3038960 3098660 TRUE FALSE 2827460.812 3066723.092 2945085.01 2829740.113 3442200.704 2642641.766 2751805.424 2772852.552 3579184.367 0.789973503 0.856821772 0.822836911 0.790610324 0.961727687 0.738336307 0.768835897 0.774716323 1 21.77119943 -2.275106652 2.260332947 1.783091976 0.812965489 0.476475317 0.061607479 2464933.876 358290.9723 9904520.47 0.014431515 0.005307541 2.275106652 -0.970126487 YLEGTSCIAGVLVPAKDQPGRQEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLEGTSCIAGVLVPAKDQPGRQEK 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 157.15 8.36E-09 636780000 344060 154110 363850 253650 305360 339810 526150 375380 425550 FALSE TRUE 327796.9657 169813.9842 380532.8824 228152.6201 358614.6873 328042.2945 445876.1541 342509.7372 491542.1206 0.666874622 0.345471888 0.77416129 0.464156805 0.729570615 0.667373722 0.907096534 0.696806485 1 18.90695552 1.851897942 0.519010384 0.973711585 0.514039434 0.480284418 0.136463716 0.618409394 0.373273406 0.121960145 0.083873918 71.10463997 -1.851897942 -0.45967215 YLEKPMEIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLEKPMEIAR 10 1 P40763;P40763-2;P40763-3 P40763 STAT3 Signal transducer and activator of transcription 3 0 91.937 0.0089456 212890000 619960 537820 460680 512120 559830 521260 685500 619980 558160 FALSE TRUE 590655.7194 592624.4695 481802.6337 460640.7246 657464.1748 503208.6355 580914.3849 565691.2645 644716.6021 0.916147835 0.919201503 0.747309178 0.714485594 1.019772366 0.780511366 0.901038352 0.877426241 1 19.29830561 0.409696111 1.014107124 1.000345118 0.860165735 0.197792905 0.090512735 4.057644744 5.350267919 0.086221721 0.026637744 2.568597825 -0.409696111 -0.140179383 YLELLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLELLER 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;;; 140.98 0.0060195 356597000 885577 961875 972268 1194110 909228 970720 1041447 1093770 1021310 FALSE TRUE 843717.5303 1059891.156 1016847.45 1074075.794 1067797.075 937103.723 882555.1327 997993.7004 1179689.539 0.715203028 0.898449229 0.861961911 0.910473272 0.905150923 0.794364697 0.748124912 0.845979953 1 20.1699758 -2.594411648 2.051497107 3.806609021 0.830675629 0.380445375 0.065986171 2170023.666 135338.4985 28339204.88 0.016807914 0.002544417 2.594411648 -2.975933392 YLEMIYS(ph)MCKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLEMIYSMCKK 11 1 O95373 O95373 IPO7 Importin-7 1 YLEMIY(0.45)S(0.55)MCKK 40.496 0.094173 371080000 35723 35247 45877 31056 954350 0 0 9834.3 364700 TRUE FALSE 34034.44459 38838.70937 47980.50583 27934.19188 1120788.338 0 0 8973.156557 421255.8134 0.080792819 0.092197444 0.113898739 0.066311707 2.660588417 0 0 0.021300968 1 18.68433707 YLENYDAIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLENYDAIR 9 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ; 177.91 0.00011997 202754000 308220 236915 175190 197182 358100 202153 360210 241706 329924 FALSE TRUE 293651.0514 261056.9078 183222.6348 177360.8907 420552.5266 195152.3909 305253.3488 220540.9413 381086.9289 0.770561857 0.685032438 0.480789607 0.465407962 1.103560618 0.51209416 0.801007134 0.578715575 1 18.5397606 YLEPLYNDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLEPLYNDYR 10 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 83.783 0.035752 45411000 76115 73788 62948 67769 81323 66176 63820 69359 77343 FALSE TRUE 72517.1948 81307.08109 65834.22806 60956.73137 95505.70545 63884.30853 54083.08687 63285.55826 89336.95743 0.811726713 0.910116971 0.736920419 0.68232379 1.069050348 0.715093847 0.605383129 0.70839169 1 16.4469695 2.057778664 24.9999991 0.71061145 0.841150379 0.037346463 0.144711963 136.0019967 58845.21417 0.049858718 0.036823099 114.2296021 -2.057778664 0.130538929 YLEQLHQLYSDSFPMELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLEQLHQLYSDSFPMELR 18 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 257.83 1.23E-30 686910000 891730 757710 760950 921800 891150 808710 923400 817190 816410 FALSE TRUE 849579.6901 834921.5104 795840.3102 829138.9127 1046566.278 780704.1699 782518.3706 745632.5114 943014.6932 0.900918826 0.885374869 0.843932036 0.879242835 1.109809089 0.827881236 0.829805067 0.790690237 1 19.84692072 -1.029292761 4.716658354 1.000003071 0.88361787 0.151347445 0.086728772 11064840.32 2414624.866 352.4989748 0.019777198 0.093477532 1.029292761 -0.116385201 YLESEEYQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLESEEYQER 10 0 Q9Y676;A0A0G2JIC6 Q9Y676 MRPS18B "28S ribosomal protein S18b, mitochondrial" 0 152.37 4.22E-05 84002000 114820 77015 95348 86960 107780 80670 102990 98633 115760 FALSE TRUE 109392.6862 84862.91606 99719.80011 78218.61559 126576.7979 77876.37767 87276.98396 89996.17163 133711.4696 0.818124926 0.634671927 0.745783443 0.584980599 0.946641289 0.582421074 0.652726234 0.673062467 1 17.0287637 -0.945594721 5.386575463 1.000000625 0.70106539 0.410466604 0.111101177 7.48E-07 1.47E-07 0.096473618 0.022739002 0.11334576 0.945594721 -0.298935235 YLGEGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLGEGPR 7 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 102.98 0.019726 102560000 134520 114420 120450 154510 172110 141150 182770 147520 180230 FALSE TRUE 128161.5062 126079.5281 125972.7516 138978.3613 202125.9295 136261.9401 154885.0797 134602.3667 208179.1479 0.615630852 0.605629955 0.605117049 0.667590211 0.970923032 0.654541732 0.743999009 0.64656988 1 17.66746604 -4.999999999 0.09701742 1.965721645 0.462575115 0.481902324 0.104976817 163.810488 1.088395033 32.59435679 1.874963175 1.00E-05 4.999999999 -1.50314653 YLGGS(ph)MDLSTFDFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YLGGSMDLSTFDFR 14 0 O95983-2;O95983 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(0.941)MDLS(0.059)TFDFR;YLGGS(1)MDLSTFDFR 293.8 1.56E-43 275009500 239732.5 130267.2 138290 297865.8 342909 208056.2 263094.1 144466.1 277262 TRUE FALSE 228400.8198 143541.5758 144630.7333 267923.7639 402712.221 200851.1616 222954.263 131815.8824 320258.3749 0.713176728 0.448205534 0.451606405 0.836586284 1.25746039 0.627153503 0.696169969 0.411592304 1 18.28887677 3.231836379 24.9665534 0.792068337 0.543566855 0.224536711 0.233162005 247.4526456 918771.1584 0.067065323 0.081892948 1705.439742 -3.231836379 -0.248501482 YLGS(ph)PITTVPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLGSPITTVPK 11 0 P30307-4;P30307-3;P30307-2;P30307;D6RJC2;A0A3B3IT42 P30307-4 CDC25C M-phase inducer phosphatase 3 1 YLGS(0.998)PIT(0.002)TVPK 124.12 0.00037308 35827000 162460 158150 161230 212940 153640 176690 211500 205590 189210 TRUE FALSE 154780.8378 174265.6648 168622.555 191534.8666 180434.7674 170571.181 179231.7905 187587.4497 218551.7204 0.708211482 0.797365788 0.77154531 0.876382333 0.825592985 0.780461397 0.820088674 0.858320627 1 17.73761521 -5 0.105770589 1.640370217 0.674893522 0.776660665 0.036479342 83.57726507 0.593678494 11.69021311 0.525164389 1.00E-05 5 -0.965476695 YLHDESGLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLHDESGLNR 10 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 87.485 0.012844 60737000 68846 64993 60668 70313 87095 64056 75335 59119 97077 FALSE TRUE 65591.78602 71615.86059 63449.68781 63245.00365 102284.3404 61837.72466 63841.26213 53942.22695 112131.2054 0.584955685 0.638679129 0.565852187 0.564026789 0.912184437 0.5514765 0.569344296 0.481063472 1 16.7748283 -1.002534724 4.351625343 1.000016686 0.610592643 0.53472236 0.114769214 11939490.12 5501279.603 1901.954682 0.025354284 0.099418058 1.002534724 -0.389424043 YLHDESGLNRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLHDESGLNRR 11 1 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;; 167.12 1.27E-05 488383000 393580 367250 422530 440430 399910 384560 458320 416660 383870 FALSE TRUE 374976.2534 404673.1925 441903.4184 396157.1396 469654.1774 371242.5908 388394.8664 380175.0415 443398.5991 0.845686599 0.912662316 0.996627909 0.893456002 1.059214392 0.837266044 0.875949692 0.857411463 1 18.75824469 -0.186047798 7.534188138 0.999999998 0.907201528 0.141820577 0.069485837 0 0 0.064495255 0.015201677 0.651556681 0.186047798 -0.092798469 YLIATSEQPIAALHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLIATSEQPIAALHR 15 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 185.27 4.30E-07 225760000 379750 347000 314110 344320 353720 359900 348540 337850 357200 FALSE TRUE 361799.9701 382359.6945 328512.2542 309708.2994 415408.656 347436.5728 295363.8216 308266.0629 412592.7517 0.876893665 0.926724216 0.796214313 0.750639215 1.0068249 0.842081135 0.715872541 0.747143671 1 18.65435895 1.991018244 24.94814161 0.786820965 0.875067014 0.013665657 0.102081251 794.3232823 2206350.261 0.036892285 0.025854382 97.95311324 -1.991018244 0.088246049 YLIDVEGVRPDDAIELFNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLIDVEGVRPDDAIELFNR 19 1 O75319 O75319 DUSP11 RNA/RNP complex-1-interacting phosphatase 0 60.034 0.060104 12924000 16385 15583 16808 16158 20029 15116 18250 17373 19825 FALSE TRUE 15610.51352 17170.92542 17578.66343 14533.76714 23522.05126 14592.52913 15465.62732 15851.72802 22899.35975 0.681700873 0.749843035 0.767648686 0.634680065 1.027192529 0.637246163 0.675373787 0.692234551 1 14.48301964 -1.604628865 2.59200293 1.025482643 0.730125411 0.355449655 0.112822585 16856051.42 15014988.34 2912567.876 0.02702446 0.02485256 1.604628865 -0.295357232 YLKDVTLQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLKDVTLQK 9 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81;J3KSJ0 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 120.06 0.0017565 0 2535700 1668130 2095400 2071780 2496900 2566700 4163300 3021200 3301300 FALSE TRUE 2415842.486 1838114.344 2191476.163 1863520.738 2932358.569 2477814.535 3528112.121 2756647.712 3813248.743 0.633539181 0.482033685 0.574700553 0.488696349 0.768992208 0.649790953 0.925224751 0.722913163 1 21.86258921 1.98922691 0.784275084 0.93524924 0.538770302 0.679434936 0.096322102 0.325581928 0.375241155 0.074598336 0.038461178 97.54991834 -1.98922691 -0.396478938 YLLGDAPVS(ph)PSSQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.998)PS(0.002)SQK;YLLGDAPVS(0.969)PS(0.031)SQK;YLLGDAPVS(0.994)PS(0.006)SQK;YLLGDAPVS(0.94)PS(0.06)SQK;YLLGDAPVS(0.851)PS(0.135)S(0.014)QK;YLLGDAPVS(0.994)PS(0.005)S(0.001)QK 291.2 1.86E-43 1400740000 3759840 3417110 3528150 4066510 2708520 3801970 4306020 4195230 3258580 TRUE FALSE 3582119.814 3765317.394 3689919.167 3657736.689 3180885.03 3670306.826 3649057.564 3827873.421 3763903.944 0.951703303 1.000375528 0.980343607 0.971793314 0.845102606 0.975132968 0.969487431 1.016995513 1 21.84379838 1.404846175 2.895790059 1.008298763 0.957207837 0.213949533 0.041859012 0.452832236 6.594039483 0.034300044 0.011090312 25.40072868 -1.404846175 -0.051090925 YLLGDAPVSPS(ph)SQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.074)PS(0.925)S(0.001)QK;YLLGDAPVS(0.344)PS(0.656)SQK 287.48 5.41E-34 969120000 1880720 1736920 1745260 2028850 1414870 1995680 2233520 2173880 1694730 TRUE FALSE 1791822.093 1913914.123 1825281.897 1824906.143 1661622.88 1926569.101 1892755.503 1983523.543 1957540.073 0.915343761 0.977713892 0.932436542 0.93224459 0.848832115 0.984178627 0.966905112 1.013273531 1 20.90061041 2.057767137 24.99999934 0.986173885 0.928384656 0.505213498 0.033764215 77.95861507 33737.79582 0.012643625 0.009337934 114.2265703 -2.057767137 -0.057789229 YLLGDMEGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLLGDMEGR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;; 122.52 0.0013577 220797000 527736 511673 472763 526575 537297 474877 561982 524464 532090 FALSE TRUE 502790.9652 563813.0604 494439.6512 473642.6806 631001.4267 458431.8904 476241.3244 478539.1518 614603.7997 0.818073311 0.917360193 0.804485185 0.770647173 1.026679996 0.745898237 0.774875334 0.778614047 1 19.22929716 YLLGTSLARPCIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLLGTSLARPCIAR 14 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ; 243.4 1.43E-17 1767590000 653690 382950 414690 419910 783480 490640 871370 644320 933110 FALSE TRUE 622791.3692 421973.0404 433703.9467 377699.849 920118.6639 473649.0138 738426.5027 587899.925 1077811.933 0.57782935 0.391508971 0.402392972 0.350432054 0.853691294 0.439454231 0.68511628 0.545456871 1 20.03967403 -0.586074531 0.272816351 1.227487177 0.433274713 0.530727316 0.14495993 7.787997405 0.645879323 1.713907518 0.192894751 0.25937342 0.586074531 -0.794212464 YLLHGLECVVAMHQAQLISK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLLHGLECVVAMHQAQLISK 20 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 231.77 4.44E-26 62319000 88058 89414 85955 104930 83949 83770 107630 89180 60737 FALSE TRUE 83895.67285 98525.38826 89896.12177 94382.23705 98589.67902 80869.0239 91209.06674 81370.92643 70155.78376 1.195848273 1.404380123 1.281378626 1.345323678 1.405296524 1.152706442 1.300093333 1.159860557 1 16.09827443 0.876663602 0.849832334 0.999061918 1.316186904 0.608643736 0.079007568 0.486883316 0.734084497 0.069771187 0.02443715 7.527722515 -0.876663602 0.317124986 YLLLMDLQDRNEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLLLMDLQDRNEK 13 1 P48163 P48163 ME1 NADP-dependent malic enzyme 0 147.68 3.91E-05 135840000 152330 111280 143630 151670 139920 153050 191590 174300 160070 FALSE TRUE 145129.6628 122619.5585 150215.5776 136423.8434 164322.0037 147749.8401 162359.4267 159037.368 184892.8381 0.784939343 0.663192581 0.812446708 0.737853585 0.888741854 0.799110672 0.878127181 0.860159699 1 17.49632982 1.534176014 0.307290608 1.018752066 0.699685669 0.681945893 0.051467269 0.737158621 0.250239346 0.086992263 0.078715792 34.21180706 -1.534176014 -0.319066397 YLLSQSS(ph)PAPLTAAEEELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLSQS(0.017)S(0.983)PAPLTAAEEELR;YLLSQS(0.024)S(0.976)PAPLTAAEEELR;YLLS(0.001)QS(0.046)S(0.953)PAPLTAAEEELR;YLLSQS(0.006)S(0.994)PAPLTAAEEELR;YLLSQS(0.02)S(0.98)PAPLTAAEEELR 198.42 7.78E-16 212517000 365461 332966 357586 408092 401854 364024 426208 379044 436151 TRUE FALSE 348186.3828 366895.614 373981.6718 367069.8168 471937.2104 351417.7576 361182.1418 345852.8979 503787.0695 0.69113799 0.72827517 0.742340752 0.728620957 0.936779125 0.697552158 0.716934125 0.686506103 1 18.94245457 -1.385975807 3.520529569 1.001795971 0.738831806 0.561087412 0.071962456 40863321.32 32708477.39 675565.1584 0.016810543 0.041117263 1.385975807 -0.262964165 YLMAS(ph)DPNLQVLGAAYIQHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YLMASDPNLQVLGAAYIQHK 20 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK 308.61 2.12E-66 2859389000 4891773 4659616 4699525 5429734 4233182 5011484 5809852 5374811 4424051 TRUE FALSE 4660548.585 5134436.168 4915002.87 4883926.822 4971447.601 4837935.052 4923452.372 4904164.055 5110110.234 0.912025058 1.004760354 0.961819343 0.955738056 0.972865041 0.946737904 0.963472831 0.95969829 1 22.28492298 YLMEEDEDAYKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 12 YLMEEDEDAYKK 12 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;;;;;; 215.85 6.49E-11 10792932000 7143290 6472760 6173660 7523180 3870480 7668360 7711530 8085790 4107980 FALSE TRUE 6805640.838 7132341.603 6456728.418 6766935.653 4545490.487 7402802.77 6534994.467 7377755.362 4745024.558 1.434268834 1.503120061 1.360736565 1.42611183 0.95794878 1.560118958 1.377230905 1.554840291 1 22.17798412 -2.12577294 2.421337145 0.191861647 1.400807762 0.350048606 0.169842895 5243197.121 1409003.4 23335912.17 0.039804581 0.007485608 2.12577294 1.208946115 YLMGER ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLMGER 6 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 140.72 0.027321 7908000000 5105800 3801850 2914530 3651830 5608500 3433460 5226400 4082590 5544600 FALSE TRUE 4864458.953 4189262.837 3048164.083 3284741.11 6586620.624 3314558.419 4429016.691 3725096.776 6404428.25 0.759546171 0.654119724 0.475946324 0.512885926 1.028447875 0.517541659 0.691555361 0.581643924 1 22.61063835 -0.867244211 4.096570246 1.000007567 0.65747204 0.319075355 0.159304828 2.54029E+11 5.20304E+11 29423660.05 0.035467009 0.135754986 0.867244211 -0.342535527 YLNFFTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLNFFTK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 98.299 0.026439 147750000 189310 164410 156240 162930 183560 155410 229320 180780 192620 FALSE TRUE 180361.6915 181163.5659 163403.7585 146551.9669 215572.8059 150028.1127 194333.0222 164949.9448 222490.5258 0.810648862 0.814252945 0.734430187 0.658688572 0.9689078 0.674312365 0.873444033 0.741379635 1 17.76338438 -4.99998902 0.493071294 7.373420477 0.788433157 0.348789187 0.092048613 2405.277456 11.61406724 16897.28587 0.038613785 1.00E-05 4.99998902 -6.584987319 YLNQDYEALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YLNQDYEALR 10 0 P17655 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;; 236.89 8.64E-12 1419121000 1759240 1694170 1059081 1503090 1672020 1332300 1713220 1594590 1518180 FALSE TRUE 1676084.212 1866807.849 1107640.911 1351996.538 1963619.759 1286162.117 1451836.824 1454959.246 1753611.601 0.955789875 1.064550353 0.631634115 0.770978327 1.11975751 0.733436136 0.82791242 0.829692987 1 20.74189782 3.787658428 24.99865012 0.83849602 1.010170171 0.199461211 0.137308916 516.0955099 262773.4605 0.033110077 0.05968992 6132.794718 -3.787658428 0.171674151 YLPDTLLLEECGLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLPDTLLLEECGLLR 15 0 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 220.23 3.95E-12 220606000 117178 84444 97343.2 106358 114941 92696.3 135811 114723 116514 FALSE TRUE 111639.2282 93048.9396 101806.482 95666.69177 134986.674 89486.20389 115090.5376 104677.2459 134582.396 0.829523262 0.691390125 0.756462101 0.71084105 1.003003944 0.664917601 0.855167845 0.777793003 1 17.03813019 -4.999999987 0.209055555 2.048727975 0.750733087 0.330787132 0.096263914 157.0510903 1.564031332 68.87291265 0.184610254 1.00E-05 4.999999987 -1.297994887 YLPEFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLPEFR 6 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C007;A0A494C0P4;A0A494C1D8;A0A494C0S8;A0A494C1T3 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ; 111.69 0.064292 166662000 377650 330370 349320 392610 413470 316660 419990 397590 441360 FALSE TRUE 359799.2329 364035.0786 365336.6675 353144.0969 485579.0371 305693.9848 355912.8119 362774.9118 509803.8546 0.705760126 0.714068902 0.716622019 0.692705819 0.952482082 0.599630587 0.698136761 0.711597036 1 18.95958276 -1.927340844 2.475705803 1.184751712 0.720370406 0.491349433 0.088228108 18022614.21 9170402.34 19267202.72 0.020974333 0.011821134 1.927340844 -0.464381307 YLPELMAEKDSLDPSFTHAMQLLTAEIEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLPELMAEKDSLDPSFTHAMQLLTAEIEK 29 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 80.359 0.0046683 45406000 110500 75531 100590 101870 85392 96497 134310 114870 89726 FALSE TRUE 105276.884 83227.69477 105202.151 91629.83406 100284.3378 93155.28469 113818.5427 104811.3738 103640.2498 1.015791492 0.803044135 1.015070411 0.884114369 0.967619607 0.898833077 1.098207916 1.011299896 1 16.66122487 1.747380007 25 1.042531394 0.925420642 0.348707986 0.067706923 1.961723593 5573.945378 0.028520961 0.015816426 55.89590697 -1.747380007 -0.117110752 YLPENDLKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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" 0 112.71 0.0030758 138970000 133860 121020 113540 129200 106810 127440 142430 143000 126830 FALSE TRUE 127532.7031 133352.0756 118745.9213 116212.5705 125437.6302 123026.7208 120699.6876 130478.1619 146498.1486 0.870541398 0.910264579 0.810562607 0.793269892 0.856240378 0.839783451 0.823899064 0.890647173 1 17.16052291 0.915461111 4.831851004 0.999977522 0.848418677 0.696760869 0.032558157 0.32083316 16.78329446 0.03522833 0.008918347 8.231161282 -0.915461111 -0.151558845 YLPHSAGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;;;;; 187.55 0.00020166 10627280000 8352810 6841750 6684110 7554770 8428000 7075850 9388620 7765810 8573720 FALSE TRUE 7957989.225 7538932.103 6990583.055 6795350.166 9897840.532 6830811.54 7956213.585 7085794.507 9903288.709 0.803570355 0.76125541 0.705885011 0.686171066 0.999449862 0.689751833 0.803391057 0.715499135 1 23.23947627 -1.829740937 2.689703907 1.07911907 0.772789985 0.382164782 0.091620166 44938830.47 29300131.58 22935527.89 0.020313466 0.01479991 1.829740937 -0.306329086 YLQAHTQSVYNYHLS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLQAHTQSVYNYHLSPR 17 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR 162.65 4.71E-09 222511000 164792 157898 164289 168209 182077 157747 190662 160120 98862 TRUE FALSE 157002.6087 173987.9857 171821.8132 151300.3117 213831.1712 152284.1818 161573.0102 146099.044 114193.014 1.374888036 1.523630733 1.504661337 1.324952433 1.872541617 1.333568284 1.414911512 1.279404394 1 16.80111487 0.953343639 1.214165191 1.003061214 1.492239405 0.515717265 0.152973251 0.40841079 1.227715767 0.131372283 0.040771078 8.981391726 -0.953343639 0.489178191 YLQDLLAWVEENQHR ddPTM_SK-BR-3_Trastuzumab_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 ; 260.49 6.63E-25 2488400000 2635900 2438800 2392100 2759200 2648800 2321700 2785800 2744700 2402400 FALSE TRUE 2511306.231 2687316.493 2501780.151 2481839.974 3110749.881 2241298.947 2360775.045 2504359.517 2774951.922 0.904990898 0.968419118 0.901558017 0.894372243 1.12101037 0.80768929 0.850744485 0.902487534 1 21.40403135 YLQEAFHVEPEEHQQTLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLQEAFHVEPEEHQQTLQR 19 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 ;;; 183.54 1.55E-14 604330000 495529 489572 471790 585887 495352 463705 571887 510226 241920 FALSE TRUE 472106.3262 539459.9434 493422.0382 526992.5256 581741.232 447646.7796 484635.1347 465547.9066 279435.718 1.689498857 1.930533245 1.765780129 1.885916837 2.08184278 1.601966931 1.734334959 1.66602863 1 18.09215692 0.339157074 0.705673467 0.982879314 1.844353819 0.802153861 0.127504565 0.950363172 0.672929846 0.155761368 0.043999889 2.183519497 -0.339157074 0.861474505 YLQLAEELIRPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 173.44 1.98E-05 82523000 61548 62855 67534 77875 71730 66291 68631 73438 76849 FALSE TRUE 58638.74802 69259.99596 70630.5007 70046.85705 84239.68929 63995.32605 58160.08046 67007.3794 88766.35043 0.660596586 0.780250575 0.795690037 0.789114982 0.949004762 0.720941277 0.655204142 0.754873655 1 16.43772526 -2.49220917 2.164467515 3.831565161 0.756450136 0.448027664 0.08229522 2921993.294 251771.1074 40564781.48 0.021858715 0.003219518 2.49220917 -3.075115025 YLQSLLAEVER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLQSLLAEVER 11 0 O95232;J3KPP4;D6RDI2;D6RHH0;U3KQT3 O95232 LUC7L3 Luc7-like protein 3 0 ; 126.19 0.00072714 28701000 43446 48248 36981 42431 45440 36880 48586 42247 43278 FALSE TRUE 41392.39368 53164.52605 38676.61543 38165.75527 53364.72161 35602.83635 41173.31336 38547.62871 49989.33121 0.828024554 1.06351745 0.773697397 0.763478013 1.067522216 0.712208695 0.823642012 0.771117112 1 15.60933261 3.718883286 24.98052385 0.834362104 0.945771028 0.099829513 0.123499475 1398.620915 1775560.413 0.030307943 0.047024299 5234.597405 -3.718883286 0.111408924 YLQSLLAEVERR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLQSLLAEVERR 12 1 O95232;J3KPP4;D6RDI2;D6RHH0;U3KQT3 O95232 LUC7L3 Luc7-like protein 3 0 ; 215.51 6.62E-11 186722000 185043 111479 162281 141369 205109 149377 232350 178021 238550 FALSE TRUE 176296.3841 122838.8368 169721.7444 127158.3195 240879.9447 144204.037 196900.7401 162432.5375 275543.1157 0.639814149 0.445806227 0.615953492 0.461482477 0.874200555 0.523344728 0.714591398 0.589499531 1 18.07191856 -5 0.175257726 2.615669143 0.512013504 0.510249625 0.122354921 97.06545815 0.925962075 54.36579255 0.360143573 1.00E-05 5 -2.103655639 YLS(ph)FHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLSFHFK 7 0 P53004 P53004 BLVRA Biliverdin reductase A 1 YLS(1)FHFK 73.233 0.031851 88497000 565750 371350 468360 553380 438200 508880 655620 547620 385390 TRUE FALSE 539008.1187 409190.9872 489834.7693 497753.191 514621.9413 491257.358 555593.1277 499667.4897 445154.3129 1.210834318 0.919211553 1.100370714 1.118158752 1.156052915 1.103566435 1.248091081 1.122459056 1 18.76394601 3.26476639 3.11015407 1.146173938 1.058998403 0.028752434 0.09303148 0.461801425 9.191116998 0.026228936 0.035066962 1839.782102 -3.26476639 -0.087175535 YLS(ph)FTPPEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.995)FT(0.005)PPEK;YLS(0.999)FT(0.001)PPEK;YLS(0.981)FT(0.019)PPEK;YLS(0.992)FT(0.008)PPEK;YLS(0.999)FT(0.001)PPEK 205.53 1.55E-05 2019640000 4127610 4583400 3489090 4858980 2661070 4197200 3911150 4383680 2357730 TRUE FALSE 3932506.055 5050453.671 3649068.228 4370546.099 3125159.765 4051849.912 3314432.234 3999821.74 2723354.727 1.443993328 1.854497184 1.339916608 1.604839082 1.147540471 1.487815697 1.217040219 1.468711255 1 21.37695348 1.638333837 0.181660469 0.846708787 1.827550157 0.409472623 0.18534794 2.705848929 0.508293058 1.067310187 1.136658657 43.48443557 -1.638333837 0.980841371 YLS(ph)FTPPEKDGFPS(ph)GTPALNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 2 Y(0.001)LS(0.983)FT(0.018)PPEKDGFPS(0.499)GT(0.499)PALNAK;YLS(0.998)FT(0.002)PPEKDGFPS(0.881)GT(0.119)PALNAK;YLS(0.977)FT(0.023)PPEKDGFPS(0.5)GT(0.5)PALNAK 168.26 5.48E-12 310575000 1221440 990000 1081630 1241540 717450 1268630 1392230 1325880 717140 TRUE FALSE 1163704.952 1090882.126 1131223.805 1116738.04 842573.0528 1224697.025 1179819.743 1209778.918 828350.4086 1.404846234 1.316933165 1.365634391 1.348146906 1.01716984 1.478476998 1.42430031 1.460467582 1 19.65988166 2.97930874 24.82169292 1.314251394 1.358532235 0.031068766 0.167131779 4403.919599 5283046.442 0.048842411 0.052360115 953.4737484 -2.97930874 0.044280841 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.896)FT(0.104)PPEKDGFPSGTPALNAK;YLS(0.962)FT(0.038)PPEKDGFPSGTPALNAK;YLS(0.999)FT(0.001)PPEKDGFPSGTPALNAK;YLS(1)FTPPEKDGFPSGTPALNAK 271.44 1.53E-45 7712020000 4058530 3446850 3566440 4150400 2622960 4342450 4771160 4539970 2956920 TRUE FALSE 3866691.33 3798087.934 3729964.802 3733193.907 3080403.394 4192069.868 4043231.914 4142426.159 3415464.052 1.132113022 1.112026909 1.092081411 1.093026848 0.901898936 1.227379297 1.183801631 1.212844315 1 21.70365018 YLSEVASGDNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 209.39 0.0017232 0 480880 455400 409030 499200 330100 470410 484870 517280 373060 FALSE TRUE 458149.7554 501805.7777 427784.4301 449019.4676 387669.3355 454119.5837 410894.1763 471984.2209 430912.2395 1.063208963 1.164519667 0.992741424 1.042020686 0.899648002 1.053856313 0.953544918 1.095314028 1 18.71703455 3.724535356 24.58814752 1.000680439 1.113864315 0.368827315 0.058799981 506.7215263 888350.3783 0.013965324 0.021760889 5303.167637 -3.724535356 0.113183876 YLSVPPS(ph)PNIS(ph)TSESRSPPEGDTTLFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 YLS(0.011)VPPS(0.974)PNIS(0.253)T(0.231)S(0.21)ES(0.175)RS(0.145)PPEGDTTLFLSR 61.099 0.016511 26698000 45879 35734 49440 49751 42419 43439 45948 44762 51170 TRUE FALSE 43710.39059 39375.33523 51706.8729 44749.93496 49816.86017 41934.69654 38937.78871 40842.40198 59105.18226 0.739535671 0.666190911 0.874828076 0.757123711 0.842850969 0.70949272 0.658788066 0.691012199 1 15.85099701 YLSVPPSPNISTSESRS(ph)PPEGDTTLFLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPSPNIS(0.002)T(0.002)S(0.002)ES(0.22)RS(0.774)PPEGDTTLFLSR;YLSVPPS(0.011)PNIS(0.067)T(0.067)S(0.067)ES(0.371)RS(0.416)PPEGDTTLFLSR;YLSVPPS(0.003)PNIS(0.003)T(0.003)S(0.003)ES(0.272)RS(0.716)PPEGDTTLFLSR 117.6 7.51E-05 441300000 183072 166399 210377 219873 183552 203331 206373 198796 234443 TRUE FALSE 174418.5494 183355.2473 220022.9935 197770.9483 215563.4107 196289.5965 174887.0085 181388.3684 270799.2231 0.644088072 0.677089266 0.812494922 0.730323175 0.796026696 0.724852879 0.645817985 0.669826029 1 18.04686407 -2.052951853 2.414649386 1.392908755 0.707268612 0.710224416 0.057611723 4996943.781 1748275.721 10833939.37 0.015555295 0.008852137 2.052951853 -0.685640143 YLTVAAVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLTVAAVFR 9 0 Q5JP53;P07437;Q5ST81;P68371;P04350 Q5JP53;P68371;P04350 TUBB;TUBB4B;TUBB4A Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-4A chain 0 ; 189.53 8.87E-05 408270000 696050 415790 149517 163530 803140 245260 762270 428390 649320 FALSE TRUE 663149.0959 458159.4737 156372.5023 147091.6537 943207.3617 236766.5847 645971.7115 390877.9006 750013.2293 0.884183198 0.610868523 0.208492992 0.196118746 1.257587633 0.315683211 0.861280423 0.521161341 1 19.51655652 2.776153701 24.99740204 0.749659915 0.52824766 0.180252676 0.319676329 1347.136361 895771.61 0.09525886 0.101034951 597.2466204 -2.776153701 -0.221412255 YLVIDEAHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 138.98 0.00012151 539650000 549090 544426 467605 533258 608320 426428 510288 516925 539870 FALSE TRUE 523135.6039 599903.6284 489045.1518 479653.8927 714410.8154 411660.6914 432434.1935 471660.3066 623590.2823 0.838909166 0.962015678 0.784241137 0.769181154 1.145641354 0.660146098 0.69345884 0.756362503 1 19.25023892 YLVLDEADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 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 ;;; 160.88 0.00015112 966330000 1801110 1544280 1581680 1809810 1972550 1491400 1918500 1650630 1970210 FALSE TRUE 1715975.1 1701643.888 1654201.592 1627884.46 2316562.095 1439752.444 1625797.589 1506092.087 2275740.104 0.754029468 0.747732083 0.726885108 0.7153209 1.017937897 0.632652402 0.714403893 0.661803201 1 21.11790438 -2.058362058 2.62579548 1.361465292 0.746074508 0.372701211 0.103418785 6507489.588 4300212.089 14042466.11 0.023961264 0.008742546 2.058362058 -0.615390783 YLWNNIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YLWNNIKR 8 1 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 97.093 0.013591 298120000 583150 466330 408370 392690 508360 441430 723830 546210 557660 FALSE TRUE 555585.6552 513849.5572 427094.1684 353216.0551 597017.823 426143.1684 613396.4395 498380.9568 644139.0647 0.862524392 0.797730778 0.663046525 0.548353724 0.926846167 0.661570136 0.95227331 0.773716398 1 19.29701266 1.715046993 10.91499037 0.895725419 0.755308334 0.287611775 0.121045053 0.159783308 48.82227908 0.055117846 0.029983505 51.88561786 -1.715046993 -0.140417085 YLYRPES(ph)D ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLYRPESD 8 1 A0A1B0GV45 A0A1B0GV45 1 YLYRPES(1)D;YLYRPES(1)D 109.79 0.0093404 317750000 552060 444460 463280 552760 522750 500860 597210 497200 608610 TRUE FALSE 525965.2179 489750.9793 484521.8462 497195.5146 613917.4345 483515.0926 506094.646 453662.5322 702990.1305 0.748182933 0.696668357 0.689229941 0.707258172 0.873294528 0.687797839 0.719917143 0.645332719 1 19.42314491 -0.989502435 4.257623319 1.000013348 0.721963558 0.680043883 0.060147849 6154078.46 2891442.994 742.9362642 0.013191223 0.102446604 0.989502435 -0.278049789 YLYTLVITDKEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLYTLVITDKEK 12 1 J3KT73;J3QL01;P63173 J3KT73 RPL38 60S ribosomal protein L38 0 ; 182.08 1.58E-05 1457420000 3521200 2701200 2385220 2656300 2331960 2840400 4048100 3466500 2488540 FALSE TRUE 3354759.854 2976455.351 2494584.696 2389283.677 2738653.086 2742036.236 3430487.997 3162954.883 2874450.073 1.167096234 1.035486884 0.867847634 0.831214186 0.952757229 0.953934202 1.193441496 1.100368697 1 21.45485454 -0.101268511 8.109103793 1.000000005 1.022594913 0 0.11853225 0 0 0.125008682 0.029464829 0.792011502 0.101268511 0.022594909 YLYVDKNFINNPLAQADWAAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YLYVDKNFINNPLAQADWAAK 21 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 299.51 4.52E-55 241870000 718810 575600 612870 724690 528030 706610 781470 788770 620890 FALSE TRUE 684833.2758 634254.2944 640970.6957 651842.7844 620118.2648 682139.9185 662242.3988 719701.1173 717174.4501 0.954904732 0.884379378 0.893744466 0.908904081 0.864668652 0.95114922 0.923404896 1.003523086 1 19.45196457 1.350945125 1.706415398 1.006708181 0.906518638 0.639777865 0.027938286 0.211621888 1.109307468 0.023968833 0.00735731 22.43598418 -1.350945125 -0.100189544 YLYYTGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YLYYTGR 7 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 158.38 0.0033101 931831000 811690 794530 744020 861170 883370 750110 936960 792170 879380 FALSE TRUE 773323.0223 875493.5103 778134.0529 774603.5555 1037429.448 724133.5026 794009.5435 722803.3952 1015749.759 0.761332223 0.861918502 0.766068656 0.762592901 1.021343534 0.712905414 0.781697989 0.711595931 1 19.95411359 -2.281561803 2.364815635 1.924083559 0.800566489 0.333815102 0.089835803 7098606.567 766202.0517 35435841 0.021021617 0.005229235 2.281561803 -1.12351707 YMACCLLYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YMACCLLYR 9 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 ;;;; 175.93 0.00012455 3432243000 1675131 821393 282215 416444 1894048 534924 1662967 881528 1497092 FALSE TRUE 1595950.877 905093.8805 295154.8369 374582.2579 2224369.372 516399.4478 1409250.842 804336.735 1729253.381 0.922913261 0.523401539 0.170683394 0.216615021 1.286317781 0.298625669 0.81494757 0.465135268 1 20.72171785 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 1 YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.035)DS(0.964)DGNPIAPT(0.001)KK 305.15 1.13E-90 428000000 218587 197044 229332 229735 300846 202375 287715 251640 375920 TRUE FALSE 208254.8257 217123.0076 239847.099 206641.6013 353313.4471 195366.703 243818.7925 229605.0676 434215.7537 0.4796114 0.500034846 0.552368487 0.475896141 0.81368178 0.449930021 0.561515308 0.528781062 1 18.72805254 -5 0.323643303 5.446861106 0.52125473 0.662323286 0.101895903 192.2018132 1.687356141 586.4827118 0.081733674 1.00E-05 5 -4.925606377 YMDLLWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YMDLLWR 7 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 119.89 0.01089 95473000 519450 398160 259890 274050 570490 248530 542810 389790 486070 FALSE TRUE 494896.628 438732.9567 271806.2136 246501.9733 669983.2754 239923.3438 459994.3651 355657.9212 561447.2531 0.881465935 0.78143219 0.484117096 0.43904743 1.193314727 0.427330159 0.819301123 0.633466313 1 19.09879096 -0.429772064 8.936870324 0.999999962 0.719205018 0.132402241 0.233641876 0 0 0.205124503 0.048348309 0.371730278 0.429772064 -0.280794943 YMEHEERPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YMEHEERPK 9 1 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 105.4 0.0041756 167345000 150334 128262 135682 159701 111086 149502 178116 156823 119745 FALSE TRUE 143228.0098 141332.0436 141903.1539 143647.5521 130459.3632 144324.7083 150941.1329 143090.7467 138314.443 1.035524611 1.021816959 1.025946031 1.038557861 0.943208535 1.043453634 1.091289742 1.034532212 1 17.07759229 2.013768771 24.99203678 1.055905909 1.015951176 0.103100667 0.035204638 328.5980371 596443.7851 0.012414793 0.009164087 103.2211684 -2.013768771 -0.039954733 YMHSGPVVAMVWEGLNVVK ddPTM_SK-BR-3_Trastuzumab_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 ; 198.07 7.58E-16 547390000 348000 344040 306760 365670 287520 338720 420300 378170 270180 FALSE TRUE 331550.7297 379098.0671 320825.2494 328912.1569 337663.397 326990.0415 356175.5157 345055.43 312078.1345 1.062396538 1.214753695 1.028028605 1.053941691 1.081983515 1.047782607 1.141302374 1.105669997 1 18.25154775 -1.954728121 2.541577341 0.924014381 1.099042081 0.211463458 0.054321494 11361999.86 5891303.06 5097770.646 0.013090181 0.011098694 1.954728121 0.1750277 YMIGVTYGGDDIPLSPYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YMIGVTYGGDDIPLSPYR 18 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 246.3 3.23E-22 0 73846 55232 66121 93386 78022 62017 89721 87002 91000 FALSE TRUE 70355.44593 60860.20359 69152.71325 83998.66186 91629.0121 59869.33574 76032.41361 79383.64365 105111.8152 0.669339082 0.579004401 0.65789667 0.79913625 0.871728948 0.569577603 0.723347927 0.755230451 1 16.68156532 -5 0.167190733 2.186053321 0.615107967 0.536559803 0.089489406 105.5670574 0.989022389 41.50429222 0.342027494 1.00E-05 5 -1.570945354 YMNNITYYFDNVSSTELYSVDQELLKDYIKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YMNNITYYFDNVSSTELYSVDQELLKDYIKR 31 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 0 224.41 2.42E-35 106820000 162140 82486 153650 115220 132570 153850 241410 184970 177920 FALSE TRUE 154475.9635 90891.41718 160695.0045 103637.8667 155690.166 148522.1359 204578.4707 168773.0462 205510.9249 0.751667891 0.442270489 0.781929255 0.50429371 0.757576105 0.722697034 0.995462751 0.821236371 1 17.64885556 2.069145932 1.545669824 0.943455647 0.615992577 0.553619286 0.118817004 0.258690813 1.166219548 0.067466131 0.034557962 117.2589315 -2.069145932 -0.32746307 YMNSDTTS(ph)PELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YMNSDTTSPELR 12 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 YMNSDTT(0.002)S(0.998)PELR;YMNSDTT(0.002)S(0.998)PELR;YMNSDTTS(1)PELR;YMNSDTTS(1)PELR;YMNS(0.009)DT(0.045)T(0.135)S(0.811)PELR;YMNSDT(0.001)T(0.003)S(0.997)PELR;YMNSDT(0.005)T(0.083)S(0.912)PELR;YMNS(0.004)DT(0.046)T(0.046)S(0.904)PELR 259.68 2.90E-21 1894577000 3541988 3007925 3144776 3618628 3382075 3296217 3824914 3423299 3680485 TRUE FALSE 3374565.247 3314435.977 3288967.09 3254876.638 3971907.809 3182068.179 3241353.12 3123536.792 4251235.816 0.793784535 0.779640585 0.773649647 0.765630696 0.934294869 0.748504274 0.762449617 0.734736186 1 22.01945086 -1.136521683 3.938181725 1.000083588 0.786306048 0.597725061 0.055021467 17260738.08 27369143.79 17539.14842 0.012558308 0.073026135 1.136521683 -0.21377754 YMVENHGEDYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YMVENHGEDYK 11 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 61.038 0.06815 155370000 247760 213170 206750 259180 175900 245970 247070 237620 210560 FALSE TRUE 236048.8758 234892.2654 216229.692 233126.734 206576.9043 237451.9972 209374.9337 216812.7331 243212.5694 0.970545545 0.965789992 0.889056403 0.958530781 0.849367715 0.976314661 0.860872176 0.891453652 1 17.89185826 3.757766763 21.37250676 0.911589896 0.968167854 0.144398221 0.048964285 173.5879847 193163.6995 0.011006089 0.019769919 5724.884943 -3.757766763 0.056577958 YMWDSQSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YMWDSQSGR 9 0 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 78.149 0.071164 73182000 87934 112400 73237 93326 93596 83395 95293 108910 89876 FALSE TRUE 83777.53409 123853.6878 76594.98889 83944.69317 109919.1128 80507.01024 80754.30267 99373.26303 103813.5111 0.807000295 1.193040159 0.737813297 0.808610482 1.05881317 0.775496459 0.777878543 0.957228611 1 16.66363469 3.718869129 24.87295967 0.858572564 1.000020284 0.117261073 0.139378237 1211.511916 1530300.092 0.035203609 0.05461513 5234.426775 -3.718869129 0.141447721 YNADEAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 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 ;;;;;;; 138.83 0.0063917 3509792000 5872480 5084880 5098460 5706410 5653420 5252400 6363800 5797990 6102190 FALSE TRUE 5594899.509 5603035.053 5332229.434 5132790.825 6639374.658 5070508.071 5392885.431 5290287.259 7048486.46 0.79377318 0.794927405 0.756507012 0.728211774 0.941957496 0.719375443 0.765112547 0.75055649 1 22.74888207 -1.137593657 4.949715598 1.000011758 0.781725373 0.551103432 0.062029067 7.33E-06 1.28E-06 0.054684563 0.012888581 0.072846106 1.137593657 -0.218286385 YNAPTSHVT(ph)PSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNAPTSHVTPSVK 13 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 YNAPTSHVT(0.997)PS(0.003)VK 87.429 0.030802 153290000 251830 226570 260220 259870 217870 242990 276480 279100 222040 TRUE FALSE 239926.495 249657.7406 272151.3444 233747.3739 255866.459 234575.1954 234297.8981 254660.5244 256472.8292 0.93548504 0.973427639 1.061131291 0.911392348 0.997635733 0.914620064 0.913538868 0.992933736 1 17.96844647 2.634200772 1.891289386 0.946453337 0.974282784 0 0.048931193 1.084317826 7.716068696 0.018423777 0.016773543 430.7256863 -2.634200772 0.027829447 YNEEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNEEER 6 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 ; 174.21 0.010655 852220000 968810 890540 872160 990570 986090 873340 1077470 972910 1074960 FALSE TRUE 923016.2713 981287.0385 912149.3987 890996.0216 1158063.784 843096.0168 913082.1624 887716.8427 1241659.307 0.743373215 0.790302971 0.73462132 0.717584942 0.932674348 0.679007528 0.735372543 0.714943977 1 20.24383794 -0.99676347 4.682119273 1.000003676 0.756753365 0.554459761 0.068739742 8061567.37 1721777.317 405.0504416 0.014802855 0.100748022 0.99676347 -0.243250312 YNGGVGR ddPTM_SK-BR-3_Trastuzumab_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 ;; 128.82 0.0086565 644650000 464930 454660 411400 506370 597350 427080 502250 429130 585560 FALSE TRUE 442953.6803 500990.3709 430263.0969 455468.7256 701527.6509 412290.1125 425622.538 391553.1022 676365.6542 0.654902681 0.74070936 0.636139778 0.673406053 1.037201766 0.609566896 0.629278757 0.578907429 1 19.36744388 6.174645745 0.854003523 0.72087904 3.05E-06 0.016140608 0.159427462 145.4725557 11.51343132 0.048446711 168.7948798 1495015.669 -6.174645745 -0.720875992 YNGLIHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YNGLIHR 7 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;;;;;;; 132.29 0.0033837 2961730000 4878900 4290060 3993690 4675780 4906980 4180860 5419230 4652650 4515230 FALSE TRUE 4648284.066 4727221.991 4176804.637 4205761.711 5762755.758 4036075.77 4592426.933 4245239.301 5215428.808 0.891256354 0.906391817 0.80085546 0.806407654 1.104943806 0.773872278 0.880546375 0.81397704 1 22.31435444 YNLDAS(ph)EEEDSNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNLDASEEEDSNK 13 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK 315.47 1.02E-50 160166000 442780 694740 391480 624840 240750 515990 346320 501430 176437 TRUE FALSE 421850.6669 765534.7959 409429.7452 562029.8961 282736.7238 498121.1369 293482.5234 457522.131 203797.9488 2.069945597 3.756342005 2.008998361 2.757779945 1.387338417 2.44419112 1.44006613 2.244979076 1 17.63678001 2.996104964 1.47582334 1.752178132 2.847251627 0.314845854 0.645503676 0.408717594 1.831008851 0.2195773 0.260573947 991.0714476 -2.996104964 1.095073495 YNLDAS(ph)EEEDSNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YNLDASEEEDSNKK 14 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK 153.36 1.47E-07 1748290000 1699340 2006420 1377050 2083390 693224 1912100 1470790 1834840 597896 TRUE FALSE 1619015.566 2210876.479 1440189.105 1873963.679 814122.0461 1845883.498 1246393.973 1674171.683 690614.6581 2.344311038 3.201317049 2.085372918 2.713472205 1.178836905 2.67281251 1.80476038 2.424176294 1 19.39752143 -0.178464745 0.14655368 7.66E-15 3.182934461 0.384583596 0.535741132 16.53368563 0.756575217 11.97638172 4.069383738 0.663033169 0.178464745 3.182934461 YNLDAS(ph)EEEDSNKKK ddPTM_SK-BR-3_Trastuzumab_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 177.02 4.02E-07 750550000 1062710 1238860 940980 1240760 343460 1283950 1018590 1325150 341110 TRUE FALSE 1012477.804 1365101.242 984124.8638 1116036.448 403359.3153 1239486.49 863185.3878 1209112.841 394007.5967 2.569691074 3.464657164 2.497730684 2.832525203 1.023734869 3.145844141 2.190783617 3.068755149 1 18.58786392 3.234888923 2.40218396 2.24489401 2.987252215 0.157827726 0.765125313 0.497160406 5.876802246 0.211322108 0.28412162 1717.469062 -3.234888923 0.742358206 YNLDFWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNLDFWR 7 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9;H0YE90 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 119.57 0.011058 222760000 1137240 835410 341810 389930 1230330 449160 1128500 734900 895230 FALSE TRUE 1083484.919 920539.2288 357482.3266 350733.4956 1444899.162 433605.4766 956326.5987 670548.2601 1034057.696 1.047799289 0.890220374 0.345708298 0.339181747 1.397310003 0.419324258 0.924829052 0.648463101 1 19.97988525 -1.341637119 3.265619298 1.001595491 0.773000754 0.048075441 0.335566355 319238176 448154358.5 4949307.871 0.075818373 0.045536839 1.341637119 -0.228594737 YNLGLDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNLGLDLR 8 0 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 87.476 0.035587 30683000 242570 185180 92779 98966 240290 101950 201900 162570 209620 FALSE TRUE 231104.1968 204050.0525 97033.00892 89017.74966 282196.4999 98419.44594 171096.4469 148334.509 242126.799 0.95447591 0.842740471 0.400752867 0.367649306 1.165490566 0.406478945 0.706639858 0.61263152 1 17.88540324 3.979743794 22.03252109 0.647567094 0.912575356 0.126814685 0.257404598 263.1539741 286232.7685 0.060281384 0.109493389 9544.293669 -3.979743794 0.265008263 YNMGLPVDFDQYNELHLPAVILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNMGLPVDFDQYNELHLPAVILK 23 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 213.13 1.85E-25 242970000 635390 588200 559190 648670 478320 562330 664750 641260 497800 FALSE TRUE 605356.3739 648138.2487 584829.4146 583464.4592 561738.8566 542856.3711 563330.1785 585107.8749 574996.2816 1.052800502 1.127204244 1.017101212 1.014727361 0.97694346 0.944104142 0.979710994 1.017585493 1 19.1331931 3.447162623 2.336375992 0.982199398 1.089454601 0.665865528 0.028561114 0.145110029 1.593997383 0.008172675 0.01268514 2800.029601 -3.447162623 0.107255202 YNPENLATLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNPENLATLER 11 0 Q9UBQ5;K7ERF1;Q9UBQ5-2;K7ES31 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 106.62 0.0053676 41408000 25276 23029 26241 32949 25389 24289 38023 34976 36175 FALSE TRUE 24081.25357 25375.68128 27444.17581 29636.90392 29816.83356 23447.86584 32221.89301 31913.31602 41784.83424 0.576315642 0.607294052 0.656797527 0.709274177 0.713580276 0.561157326 0.771138467 0.763753563 1 15.35069179 -5 0.124367465 2.176772333 0.499275915 0.817679709 0.054018049 57.60097319 0.459046427 16.77267669 0.447839294 1.00E-05 5 -1.677496418 YNPTWHCIVGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNPTWHCIVGR 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 199.12 5.13E-08 4370600000 1682220 854490 1220010 1112610 1911500 1136780 1935940 1406400 1849460 FALSE TRUE 1602704.794 941563.5025 1275948.665 1000768.329 2244864.995 1097413.024 1640576.797 1283248.16 2136264.811 0.750236949 0.440752241 0.597280196 0.46846642 1.05083648 0.513706455 0.76796509 0.600697139 1 21.02665906 YNQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YNQLLR 6 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 164.83 0.017359 19085700000 8231500 6157060 5666710 6093140 7275060 6152080 8550300 7178030 7530360 FALSE TRUE 7842413.308 6784471.414 5926534.259 5480645.991 8543828.161 5939031.927 7245794.698 6549483.64 8698129.769 0.901620638 0.779991975 0.681357305 0.63009476 0.982260369 0.682794128 0.833029041 0.752976078 1 23.0522738 -1.43839531 3.146999229 1.00366187 0.785446286 0.296607625 0.105980357 38320462.84 52550997.33 1266494.15 0.023468599 0.036442209 1.43839531 -0.218215584 YNRFEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNRFEK 6 1 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 86.113 0.0492 565790000 1036190 936310 957520 1073000 933630 954580 1119130 989540 1137730 FALSE TRUE 987211.3522 1031721.053 1001423.239 965140.0014 1096454.776 921522.6552 948386.1643 902890.6317 1314163.358 0.751209008 0.785078238 0.762023407 0.734414025 0.834336744 0.701223824 0.721665354 0.687045965 1 20.32571319 -0.913404461 13.02344588 1 0.749317102 0.781842182 0.041965074 0 0 0.039786077 0.009377668 0.122066232 0.913404461 -0.250682898 YNSPELDEEGYSIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNSPELDEEGYSIR 14 0 F6R8P8;Q9BQI5-4;Q9BQI5-5;Q9BQI5;Q9BQI5-2;Q9BQI5-3 F6R8P8 SGIP1 SH3-containing GRB2-like protein 3-interacting protein 1 0 41.227 0.082325 219520000 119050 34682 153990 69421 197460 107500 259140 129280 76558 FALSE TRUE 113422.7424 38216.13523 161050.5938 62442.66919 231896.9615 103777.248 219603.4336 117959.5578 88430.22364 1.282624173 0.432161468 1.821216629 0.706123615 2.622372216 1.173549537 2.483352688 1.333928073 1 16.43225192 2.762861022 24.99301866 1.822684223 1.022740377 0.204751689 0.629566489 923.8623694 950192.9223 0.170715859 0.18099169 579.2433036 -2.762861022 -0.799943846 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.976)PS(0.021)PS(0.004)QESLSSSK;YNTEGRVS(0.777)PS(0.223)PSQESLSSSK;YNTEGRVS(0.794)PS(0.206)PSQESLSSSK;YNTEGRVS(0.881)PS(0.119)PSQESLSSSK;YNTEGRVS(0.982)PS(0.018)PSQESLSSSK;YNTEGRVS(0.981)PS(0.019)PSQESLSSSK 274.97 1.03E-44 2197680000 1789370 1897240 1602941 1997160 1154928 1780610 1743834 1878750 1340157 TRUE FALSE 1704790.026 2090570.913 1676437.43 1796401.682 1356347.078 1718947.029 1477780.096 1714236.69 1547981.703 1.101298564 1.350513969 1.082982717 1.16047992 0.876203559 1.110444023 0.954649588 1.107401132 1 20.56195699 3.199415744 1.985103885 1.0137602 1.218418114 0.373315074 0.100612287 0.270231865 2.189629903 0.028981655 0.038965743 1582.76247 -3.199415744 0.204657913 YNVPFLTFINKLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNVPFLTFINKLDR 14 1 F8WAU4;C9IZ01;Q96RP9;Q96RP9-2 F8WAU4 GFM1 "Elongation factor G, mitochondrial" 0 ; 149.6 6.79E-06 104775000 299990 202222 216300 186762 281580 210448 346030 283840 278340 FALSE TRUE 285810.0672 222828.6517 226217.5689 167988.3289 330687.4628 203160.133 293236.7682 258985.4649 321503.5456 0.888979519 0.69308303 0.70362387 0.52250848 1.028565524 0.631906353 0.912079422 0.805544662 1 18.29447512 0.995113254 0.699169009 0.995803161 0.743639551 0.228817285 0.143018006 1.094340878 1.231282894 0.128117262 0.050633188 9.888109207 -0.995113254 -0.25216361 YNVPLNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNVPLNR 7 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 79.454 0.075798 62699000 79298 67251 66474 77539 81827 73095 94386 71369 95092 FALSE TRUE 75549.74069 74103.95336 69521.89865 69744.63241 96097.60289 70563.70182 79985.68218 65119.55201 109838.3817 0.687826418 0.674663558 0.632947223 0.634975055 0.874900025 0.642432096 0.728212497 0.592867002 1 16.74502275 -2.132705096 2.43177644 1.658061315 0.687031022 0.623679847 0.077197493 4175296.722 1375988.285 15120735.89 0.016912982 0.007367072 2.132705096 -0.971030293 YNVYPTYDFACPIVDSIEGVTHALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNVYPTYDFACPIVDSIEGVTHALR 25 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 214.17 1.72E-28 342570000 561020 626850 491260 600490 515260 532810 553570 579920 460300 FALSE TRUE 534501.6964 690726.7277 513784.7569 540127.6043 605121.1809 514358.6561 469112.7295 529139.1305 531680.9731 1.005305293 1.29913757 0.966340311 1.015886653 1.138128335 0.967419716 0.88231995 0.995219233 1 19.02020131 2.641914374 0.880040929 0.941904081 1.127774277 0.197943763 0.102034415 0.693618947 1.124529826 0.064926821 0.054551834 438.4442446 -2.641914374 0.185870195 YNWSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YNWSAK 6 0 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 107.43 0.072758 773690000 1054900 855820 715840 928120 854830 899600 1083300 951410 933080 FALSE TRUE 1005036.968 943029.031 748661.9721 834823.6143 1003912.081 868446.6264 918022.6888 868099.4967 1077777.281 0.932508957 0.874975793 0.69463514 0.774578968 0.931465247 0.805775592 0.851774022 0.805453513 1 20.03962765 -1.363814388 3.705524815 1.000701658 0.840061799 0.344592634 0.071544409 11656204.09 4290264.935 65436.77386 0.017042376 0.043269872 1.363814388 -0.160639859 YNYHLDSSGSYVFENTVATVMALR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNYHLDSSGSYVFENTVATVMALR 24 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 277.15 4.48E-52 50650100 63198.7 77519.7 59710.4 73703 61978 55718.9 61335.2 72044 48087 FALSE TRUE 60211.4227 85419.04556 62448.1809 66294.23441 72786.94358 53789.34052 51977.38874 65735.44543 55544.08637 1.084029401 1.537860304 1.124299363 1.193542621 1.310435518 0.968408053 0.935786186 1.183482342 1 15.7613457 2.237658434 24.99961735 1.006192772 1.265908348 0.3970787 0.138309295 21.63416957 599458.5659 0.04880331 0.038151808 172.8456419 -2.237658434 0.259715576 YNYIEGTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YNYIEGTK 8 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 104.2 0.010762 348310000 485590 423410 390780 495370 375940 478040 541860 499940 444370 FALSE TRUE 462637.123 466555.9604 408697.6495 445574.4665 441503.817 461485.3549 459189.3051 456162.6033 513280.6301 0.901333688 0.90896857 0.796246002 0.868091333 0.860160682 0.899089753 0.894616469 0.888719692 1 18.96938829 0.113345032 0.710819311 1.003692108 0.875308781 0.605657382 0.031640386 2.848039663 1.679881508 0.060494115 0.011839724 1.298210246 -0.113345032 -0.128383326 YPALHKPENQDIDWGALEGETR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YPALHKPENQDIDWGALEGETR 22 1 P13796 P13796 LCP1 Plastin-2 0 ;; 216.38 8.10E-26 813380000 722570 427930 244965 457390 579740 414883 809790 666380 587990 FALSE TRUE 688415.5481 471536.5535 256196.8876 411412.2882 680846.4724 400515.4977 686241.6627 608028.2345 679172.4862 1.0136093 0.694281001 0.377219179 0.605755234 1.002464744 0.589711017 1.010408514 0.895248625 1 19.37341849 1.686252082 8.453481159 0.962688548 0.728984898 0.282727491 0.189760224 0.179244141 22.77984303 0.094676156 0.050111187 48.55702632 -1.686252082 -0.23370365 YPDLYPQEDEDEEEEREK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPDLYPQEDEDEEEEREK 18 1 Q8N4Q1;Q8N4Q1-2 Q8N4Q1 CHCHD4 Mitochondrial intermembrane space import and assembly protein 40 0 196.31 1.79E-15 304790000 432700 328990 343020 501460 271410 351850 343150 413300 216430 FALSE TRUE 412247.1285 362514.455 358747.8063 451052.2881 318743.8181 339665.3463 290796.1651 377109.261 249992.859 1.649035617 1.450099241 1.435032215 1.804260689 1.275011692 1.358700195 1.163217886 1.508480132 1 17.93152736 2.640248956 11.34430826 1.269673411 1.560979223 0.485118252 0.1646954 0.54925112 60.98768553 0.04806102 0.045302639 436.7661329 -2.640248956 0.291305812 YPEAPPFVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPEAPPFVR 9 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;G3V2F7;Q13404-6;A0A0A0MSL3 I3L0A0 TMEM189-UBE2V1;UBE2V1 Ubiquitin-conjugating enzyme E2 variant 1 0 80.229 0.05747 49624000 48163 45332 41034 45990 48019 43798 42894 40369 42939 FALSE TRUE 45886.43044 49951.38234 42915.44949 41366.99782 56393.4984 42281.26428 36349.7325 36834.07635 49597.76082 0.925171413 1.007129788 0.865269899 0.834049706 1.137017024 0.85248333 0.732890596 0.742656034 1 15.59798737 2.009614497 24.98076489 0.794799253 0.952769409 0.221274516 0.10958171 222.7627872 578788.4734 0.037666763 0.027785185 102.2385065 -2.009614497 0.157970156 YPEPERPS(ph)SR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.639)S(0.361)R;YPEPERPS(0.724)S(0.276)R;YPEPERPS(0.637)S(0.363)R;YPEPERPS(0.59)S(0.41)R 107.17 0.0061032 1642830000 1423630 1386660 1184120 1488100 1150750 1290950 1292422 1298450 1066586 TRUE FALSE 1356337.831 1527962.231 1238413.073 1338513.361 1351440.436 1246244.078 1095239.287 1184750.834 1231986.71 1.100935441 1.240242463 1.005216261 1.086467371 1.096960239 1.011572664 0.889002518 0.961658779 1 20.23255526 2.50238151 0.888557995 0.93462287 1.148897649 0.516931238 0.066202652 0.39223045 0.626803741 0.044905389 0.032746837 317.9666049 -2.50238151 0.214274779 YPEPERPSS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.268)S(0.732)R 53.388 0.087171 370050000 253120 287410 225140 272610 243480 201300 216390 264130 183950 TRUE FALSE 241155.5192 316697.4058 235462.8917 245206.7249 285942.8349 194328.9305 183375.7312 241001.377 212476.0265 1.134977546 1.490508887 1.108185688 1.154044195 1.345765165 0.914592266 0.863041983 1.134252089 1 17.69694055 2.233120355 24.99516447 0.953611387 1.25927983 0.504001386 0.131152998 97.45030627 447728.4811 0.047446946 0.036050101 171.0489275 -2.233120355 0.305668443 YPESNRT(ph)PVKPSSVEEEDSFFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.321)NRT(0.664)PVKPS(0.011)S(0.003)VEEEDSFFR;YPES(0.063)NRT(0.935)PVKPS(0.001)SVEEEDSFFR 198.4 9.01E-21 457600000 443240 392480 353570 439490 306360 418310 440850 462550 348880 TRUE FALSE 422288.9236 432474.1582 369781.5342 395311.6302 359789.087 403823.8198 373590.2357 422046.6699 402982.5286 1.047908764 1.073183395 0.917611827 0.980964688 0.892815597 1.002087662 0.927063109 1.047307612 1 18.62035777 3.749908435 24.96515262 0.961466193 1.060546088 0.414343112 0.045974615 541.1305812 1190482.043 0.01040325 0.01854678 5622.227759 -3.749908435 0.099079895 YPHVEDYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPHVEDYRR 9 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 56.563 0.078623 60607000 69470 61549 52135 50181 75623 59714 86500 63924 71066 FALSE TRUE 66186.29078 67820.91308 54525.44132 45136.71054 88811.62726 57646.08921 73302.83632 58326.47568 82086.55233 0.806298826 0.826212225 0.664243287 0.549867296 1.081926634 0.702259841 0.892994458 0.710548488 1 16.32485827 2.748997081 24.98733395 0.858281351 0.738630161 0.248104881 0.137795591 1315.779892 3150282.676 0.040077972 0.042083296 561.0442047 -2.748997081 -0.11965119 YPHYFPLLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPHYFPLLK 9 0 P52888;K7EP46 P52888 THOP1 Thimet oligopeptidase 0 68.227 0.058667 50916000 169250 187130 146950 179230 551080 119080 231560 149490 684320 FALSE TRUE 161249.8879 206198.7597 153687.8029 161213.4599 647188.1775 114956.2297 196231.2691 136399.8631 790440.8506 0.203999942 0.260865515 0.194433021 0.203953857 0.818768637 0.145433058 0.248255475 0.172561758 1 19.59229798 -2.064440975 2.55980263 2.056472934 0.277537612 0.574478559 0.194441283 12079206.28 4242647.297 74565412.28 0.047651186 0.008621027 2.064440975 -1.778935322 YPIEHGIITNWDDMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 23 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 ;;;;;;;;;;;;;;;;;;;;;; 220.27 8.84E-15 98202814100 69177262 63530480 58471693 72319323 44373293 66195449 68318893 69112518 43905291 FALSE TRUE 65907389.92 70004308.14 61152677.96 65049647.25 52111981.25 63903084 57895591.11 63060659.54 50713899.29 1.299592239 1.380377157 1.205836641 1.282678874 1.027568023 1.260070413 1.141611904 1.243459099 1 25.59587787 7.999999997 0.062807517 0.719009228 2.307333189 0.486491183 0.085383814 225.5098146 1.054784781 5.179479192 32.39648581 99999999.31 -7.999999997 1.588323961 YPIEHGIITNWDDMEKIWHHTFYNELR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YPIEHGIITNWDDMEKIWHHTFYNELR 27 1 P68133;P68032;A6NL76 P68133 ACTA1;ACTC1 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1" 0 ;; 201.16 1.56E-25 2680420000 1810520 652100 2050640 1279430 2639600 1600000 3859790 2078670 377920 FALSE TRUE 1724940.308 718549.7314 2144663.872 1150819.266 3099945.404 1544591.599 3270908.146 1896650.635 436525.9035 3.951518785 1.646064359 4.913027739 2.636313805 7.10140081 3.538373294 7.493044788 4.344875344 1 18.73570774 2.767324339 24.94612866 5.192959016 3.177501664 0.079441868 2.006093257 1049.14232 909895.748 0.544705645 0.57765866 585.2269792 -2.767324339 -2.015457352 YPIEHGIVTNWDDMEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 293.52 1.02E-45 12952190000 17545110 16242080 15345040 18610170 12126750 17182920 18242900 18331450 11479600 FALSE TRUE 16715787.42 17897166.42 16048625.26 16739440.35 14241651.36 16587871.17 15459610.55 16726251.06 13259797.74 1.260636682 1.349731479 1.210322026 1.26242049 1.074047406 1.250989759 1.165900933 1.261425807 1 23.66055543 -5 0.087835408 0.256075097 1.433817287 0.527184487 0.070033087 156.2752434 0.957852908 22.07997695 1.649135829 1.00E-05 5 1.17774219 YPLFEGQETGKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 115.8 0.0014592 1187290000 1677650 1499210 1447070 1857980 1037350 1813220 1943580 1946390 1209750 FALSE TRUE 1598350.809 1651981.203 1513419.591 1671212.32 1218263.512 1750427.737 1647051.175 1775953.773 1397351.851 1.143842768 1.182222789 1.083062644 1.195985334 0.871837333 1.252675004 1.178694667 1.270942441 1 20.4142639 YPPYTT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPPYTTPPR 9 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 YPPYT(0.004)T(0.996)PPR 94.409 0.016149 0 172510 156880 161160 191440 194520 170990 188760 182160 200090 TRUE FALSE 164355.7942 172866.2504 168549.3454 172196.0875 228444.2264 165068.5734 159961.1952 166209.1047 231118.9353 0.711130804 0.747953646 0.729275363 0.745054001 0.988427132 0.71421484 0.692116356 0.719149664 1 17.81827594 -2.0917412 2.564962688 1.426359414 0.752012711 0.451291064 0.084486178 5616302.762 2424756.129 13966251.52 0.020893591 0.008095782 2.0917412 -0.674346703 YPQLLPGIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YPQLLPGIR 9 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 77.282 0.076868 120742000 303770 252140 297290 309300 280820 302080 382710 328420 290230 FALSE TRUE 289411.3941 277833.3527 310921.0406 278208.5764 329794.9191 291618.8939 324320.5605 299661.8037 335237.3861 0.86330286 0.828766015 0.927465293 0.829885293 0.983765334 0.869887745 0.967435537 0.89387943 1 18.35482352 3.217801905 0.1381232 1.047067045 0.725686997 0.412862467 0.047192706 12.4606597 0.557923264 0.353478594 0.927788514 1651.20846 -3.217801905 -0.321380048 YPS(ph)SISSSPQKDLTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPS(0.306)S(0.253)IS(0.174)S(0.145)S(0.121)PQKDLTQAK 92.098 0.0020546 326470000 173130 200380 156140 225820 104510 178610 182620 222160 105360 TRUE FALSE 164946.488 220798.9498 163299.1734 203120.1446 122736.5109 172424.6909 154757.965 202706.4927 121698.6907 1.355367811 1.814308343 1.341831802 1.66904133 1.008527785 1.416816318 1.271648561 1.665642346 1 16.89295412 2.768430186 24.99683432 1.299569394 1.557618909 0.247631887 0.233037185 966.2118719 808588.5157 0.064332584 0.068226929 586.7190453 -2.768430186 0.258049515 YPSSISS(ph)SPQKDLTQAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPS(0.002)S(0.037)IS(0.114)S(0.438)S(0.409)PQKDLTQAK 75.912 0.01273 378430000 649480 760040 510620 736270 312150 657920 626310 730760 332180 TRUE FALSE 618780.3675 837488.9401 534032.4321 662258.7408 366588.8612 635136.0654 530754.9065 666770.7804 383692.7779 1.612697458 2.182707073 1.391822997 1.726013047 0.955422886 1.655324525 1.38328094 1.737772559 1 18.54959208 3.717680281 24.43759827 1.42967442 1.897702272 0.314257889 0.299858168 587.6820431 687801.9813 0.071297692 0.110590804 5220.117531 -3.717680281 0.468027852 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR 44 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;; 159.09 2.08E-20 451346000 387408.7 355485.9 384670.8 422384.9 348795.1 401260 512586 415826.3 81459.2 FALSE TRUE 369096.6585 391710.3174 402308.3367 379925.9674 409624.855 387364.2656 434381.5914 379414.3447 94091.4767 3.922742755 4.163079708 4.275714983 4.037836164 4.353474612 4.116890065 4.616588098 4.032398662 1 16.52177642 0.948881132 24.00951237 1 4.212056876 0.966630512 0.186549916 2118.012813 994789.294 0.187068805 0.046767201 8.889577743 -0.948881132 3.212056876 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YQDEVFGGFVTEPQEESEEEVEEPEER 27 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVT(0.001)EPQEES(0.999)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER 268.23 6.63E-54 7120600000 4701257 4225740 4636442 4894439 4738083 4622945 5277550 4856634 5285013 TRUE FALSE 4479037.899 4656347.71 4849027.452 4402440.693 5564403.175 4462851.255 4472362.819 4431361.38 6104585.824 0.733716918 0.762762265 0.79432538 0.721169432 0.91151199 0.731065364 0.732623465 0.725906967 1 22.54146199 -2.309732435 2.326574462 2.248255733 0.762503596 0.630451309 0.056739053 3033950.525 488672.2954 19914689.05 0.0136149 0.004900807 2.309732435 -1.485752137 YQDILVFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQDILVFR 8 0 P19623;K7EKM4 P19623 SRM Spermidine synthase 0 105.78 0.015296 0 43859 51638 44093 48788 47573 46372 45538 47659 42838 FALSE TRUE 41785.87199 56899.97091 46114.70766 43883.73755 55869.71614 44766.12601 38590.34174 43485.7253 49481.09825 0.844481498 1.149933468 0.93196613 0.88687881 1.12911229 0.904711649 0.779900671 0.878835087 1 15.5945899 2.010553632 24.99350602 0.856918852 0.992439548 0.149175488 0.109066645 276.5210158 654864.7238 0.038315419 0.02827077 102.4598304 -2.010553632 0.135520697 YQDTHPER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQDTHPER 8 0 C9JAH0;F8WD54;A0A087WUI8;Q96IJ6;Q96IJ6-2 C9JAH0 GMPPA Mannose-1-phosphate guanyltransferase alpha 0 73.067 0.044626 0 99207 104370 97179 108770 99621 91400 109800 110980 94810 FALSE TRUE 94517.68172 115005.4217 101634.7533 97836.23295 116994.8709 88234.79508 93047.99338 101262.0029 109512.6506 0.863075464 1.050156498 0.928064043 0.893378367 1.068322885 0.805704132 0.849655203 0.924660323 1 16.74073801 2.221211939 24.9954997 0.876217823 0.959411609 0.122981927 0.080323313 375.8223327 541471.1458 0.027862928 0.020626173 166.4224605 -2.221211939 0.083193786 YQEALHLGSQLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQEALHLGSQLLR 13 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 143.05 4.06E-05 180870000 221570 200420 166230 226330 216070 187990 208020 188510 195610 FALSE TRUE 211096.8252 220843.0259 173851.8099 203578.8784 253752.5396 181479.8592 176282.7285 172003.065 225944.1998 0.934287428 0.97742286 0.769445775 0.901013961 1.123076139 0.803206541 0.780204708 0.761263468 1 17.785607 YQEEFEHFQQELDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQEEFEHFQQELDK 14 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 159.31 4.93E-06 40588000 87109 74471 53383 76693 61926 66734 86638 71057 39643 FALSE TRUE 82991.5302 82059.67957 55830.66335 68983.67393 72725.87479 64422.98485 73419.78188 64834.87238 45790.63397 1.81241278 1.792062534 1.219259454 1.506501831 1.588225986 1.406903099 1.603379895 1.415898116 1 15.48276492 0.940990341 0.061092867 1.68E-18 2.750219715 0.57188963 0.160757875 30.39384441 1.200189842 28.56918203 24.08533123 8.729519539 -0.940990341 2.750219715 YQEGGVESAFHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YQEGGVESAFHK 12 0 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 ;;; 210.41 4.39E-08 1837920000 1934550 1377080 1496330 1873720 1667480 1600600 2188060 1969220 1827570 FALSE TRUE 1843107.655 1517406.018 1564938.211 1685370.106 1958287.984 1545170.821 1854231.261 1796784.657 2110980.222 0.873105127 0.718815838 0.741332484 0.798382708 0.927667613 0.731968403 0.87837453 0.851161294 1 21.00948163 0.461108221 0.463425178 1.014708766 0.785448915 0.46957219 0.065875591 1.864453358 0.724470785 0.120047061 0.036418184 2.891400292 -0.461108221 -0.229259851 YQEISKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQEISKR 7 1 M0R0N0;M0R1K9;O95182 M0R0N0 NDUFA7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 0 91.318 0.026444 98808000 173230 130170 157130 137310 135080 133850 167730 158570 163430 FALSE TRUE 165041.7612 143434.471 164334.5659 123507.3379 158637.9092 129214.7409 142139.7079 144684.7702 188773.8897 0.874282781 0.759821558 0.870536525 0.654260704 0.840359382 0.684494774 0.752962754 0.766444821 1 17.52629971 -1.434157386 3.018753336 1.004394737 0.775328493 0.489245657 0.072121288 13402146.49 16791133.76 505906.397 0.017092349 0.036799559 1.434157386 -0.229066244 YQEQGGEAS(ph)PQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR 255.72 3.98E-21 1390118000 1241050 1603102 1289017 1641466 1232196 1347890 1403078 1446630 1366406 TRUE FALSE 1182388.026 1766459.916 1348119.704 1476462.719 1447090.592 1301212.231 1189012.682 1319955.408 1578301.264 0.749152303 1.11921593 0.854158668 0.935475852 0.91686589 0.82443844 0.753349635 0.836313978 1 20.58994118 2.25613402 5.695928617 0.823726109 0.926488049 0.03710123 0.110611607 0.300218001 30.33533552 0.037744122 0.030111146 180.3574226 -2.25613402 0.10276194 YQEQGGEAS(ph)PQRTWEQQQEVVSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YQEQGGEASPQRTWEQQQEVVSR 23 1 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(0.998)PQRT(0.002)WEQQQEVVSR;YQEQGGEAS(1)PQRTWEQQQEVVSR;YQEQGGEAS(1)PQRTWEQQQEVVSR;YQEQGGEAS(1)PQRTWEQQQEVVSR;YQEQGGEAS(1)PQRTWEQQQEVVSR 270.45 8.25E-52 641200000 301894 198846 348597 283438 379934 290708 442228 336044 508086 TRUE FALSE 287624.0689 219108.6335 364580.5173 254946.2737 446194.3693 280640.7091 374757.9965 306618.2059 586877.3819 0.490092271 0.373346529 0.621220937 0.434411483 0.760285509 0.478193091 0.638562685 0.522457016 1 19.16269958 -4.999999997 0.158275102 2.738228747 0.399317628 0.649858126 0.107784203 72.92881496 0.667018724 39.76879513 0.417621285 1.00E-05 4.999999997 -2.338911119 YQEQGGEAS(ph)PQSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YQEQGGEASPQSR 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4 Q9UJU6-2 DBNL Drebrin-like protein 1 YQEQGGEAS(0.999)PQS(0.001)R;YQEQGGEAS(0.999)PQS(0.001)R;YQEQGGEAS(1)PQSR;YQEQGGEAS(0.999)PQS(0.001)R 226.14 1.18E-11 393929000 540930 552250 596570 671950 649270 585080 722310 641100 762020 TRUE FALSE 515361.3109 608524.9029 623923.3246 604404.3094 762502.4824 564818.5329 612108.3434 584961.8853 880190.1697 0.585511323 0.691356168 0.708850594 0.686674687 0.866292886 0.641700569 0.69542738 0.664585797 1 19.74745573 -5 0.318396403 3.888948345 0.675972087 0.643096294 0.07161891 202.780267 1.802404135 394.6981132 0.062759623 1.00E-05 5 -3.212976257 YQETFNVIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQETFNVIER 10 0 Q13011;M0R248;M0QZW4 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ; 175.15 6.72E-06 525210000 376570 339840 310520 301330 400690 302390 400340 297660 432600 FALSE TRUE 358770.2824 374470.0824 324757.6491 271039.7359 470570.2091 291918.1585 339260.7803 271595.3124 499685.3986 0.717992328 0.749411697 0.649924232 0.542420765 0.941732959 0.5842039 0.678948757 0.543532617 1 18.93066054 -2.098396171 2.553618479 1.564044195 0.683791034 0.43055972 0.116788423 6614409.699 2971243.377 21597287.31 0.026611682 0.007972671 2.098396171 -0.880253161 YQEVDRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQEVDRR 7 1 Q96MU7-2;Q96MU7 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 118.74 0.0079175 100320000 112890 76783 91052 94660 103030 90844 102580 108690 118470 FALSE TRUE 107553.9134 84607.275 95226.82426 85144.59696 120998.3994 87698.0495 86929.53699 99172.5274 136841.7225 0.785973104 0.618285662 0.695890277 0.622212256 0.884221545 0.640872154 0.635256085 0.724724343 1 17.06214864 0.957068451 21.75853651 1.000000001 0.692689208 0.563807409 0.082921132 1191.859034 604058.7325 0.074338211 0.018584553 9.058753695 -0.957068451 -0.307310793 YQHDDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YQHDDGR 7 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;; 93.429 0.014942 114031000 171231 137909 132129 184627 163657 150260 192946 168463 176953 FALSE TRUE 163137.25 151962.0839 138187.2453 166067.9432 192198.729 145056.4585 163508.544 153711.4866 204393.9675 0.798151002 0.743476365 0.676082798 0.812489455 0.940334646 0.709690508 0.799967563 0.752035339 1 17.64099309 -1.846440635 2.287940441 1.098745206 0.778243762 0.489022418 0.070982403 7233661.977 3963632.702 3901506.501 0.017836051 0.014241619 1.846440635 -0.320501444 YQHTGAVLDCAFYDPTHAWSGGLDHQLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQHTGAVLDCAFYDPTHAWSGGLDHQLK 28 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 222.71 7.32E-35 153930000 224210 197320 187340 225970 167330 184120 242160 222680 70279 FALSE TRUE 213612.0376 217427.1323 195929.7243 203255.0663 196512.299 177743.8782 205214.0444 203180.9587 81177.50838 2.631418996 2.678415939 2.413596182 2.503834748 2.420772735 2.189570508 2.527966779 2.502921841 1 16.30879244 -1.560979029 0.40413595 5.56E-19 2.561429957 0.923067209 0.13443548 7.674007109 0.626396859 8.001073123 0.087355808 0.027480268 1.560979029 2.561429957 YQILPLHSQIPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQILPLHSQIPR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 187.44 1.05E-05 1436150000 1223950 1080680 1137260 1274370 1216820 1139600 1437870 1210320 1303620 FALSE TRUE 1166096.309 1190802.521 1189404.496 1146267.906 1429033.023 1100135.366 1218496.523 1104337.964 1505778.732 0.774414119 0.790821716 0.789893276 0.761245914 0.949032546 0.730608916 0.80921353 0.733399896 1 20.52207836 -1.182363493 4.465415946 1.000046174 0.793230613 0.534172448 0.060941602 2.49E-05 4.55E-06 0.052393513 0.012346515 0.065710762 1.182363493 -0.206815561 YQLDKDGVVLFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQLDKDGVVLFK 12 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 ; 187.98 8.93E-06 3601700000 6434300 5201300 4729800 6621400 3644700 5769000 6911600 6284900 4189600 FALSE TRUE 6130163.391 5731318.383 4946666.008 5955804.292 4280334.526 5569218.083 5857108.48 5734560.838 4839301.77 1.266745428 1.184327545 1.022185894 1.230715623 0.884494237 1.150830915 1.210320984 1.18499757 1 22.20636748 4.067110935 3.277335869 1.111618061 1.246396138 0.201724959 0.10753039 0.374737011 8.042349466 0.026541469 0.063436677 11671.07701 -4.067110935 0.134778077 YQLDKDGVVLFKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQLDKDGVVLFKK 13 2 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 136.83 3.81E-05 269150000 3985200 2602500 3211200 3365600 2922300 3504400 4862000 4174000 3465900 FALSE TRUE 3796827.494 2867697.709 3358436.696 3027283.494 3431948.195 3383041.749 4120212.603 3808502.432 4003374.071 0.948406876 0.716320198 0.838901546 0.75618302 0.857263931 0.845047625 1.029185015 0.95132315 1 21.932785 1.826147261 4.824729542 0.993000224 0.820511805 0.604008817 0.063593842 0.141998413 5.189195789 0.028912423 0.016354751 67.01117938 -1.826147261 -0.172488419 YQLLQLRPAQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQLLQLRPAQR 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 100.88 0.0033751 236800000 581850 422090 417450 494400 497850 450590 627170 465920 532490 FALSE TRUE 554347.1036 465101.4509 436590.4954 444701.9727 584674.8824 434985.9553 531483.6977 425121.5748 615065.8296 0.901280931 0.75618158 0.709827265 0.723015247 0.950589115 0.707218536 0.86410864 0.691180609 1 19.2303813 -0.996719975 5.303525084 1.000000984 0.794051206 0.353371179 0.089818666 9.45E-07 1.79E-07 0.078711735 0.018552445 0.100758113 0.996719975 -0.205949778 YQPLASTAS(ph)DNDFVTPEPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLASTAS(1)DNDFVTPEPR;YQPLAST(0.001)AS(0.999)DNDFVTPEPR 282.97 9.09E-40 212760000 166928 154073 171575 194318 160898 176977 189798 189846 191191 TRUE FALSE 159037.6443 169773.2139 179441.8835 174784.7855 188958.5603 170848.2421 160840.8292 173222.0778 220839.9238 0.720148973 0.768761422 0.81254277 0.791454654 0.85563587 0.773629329 0.728314095 0.784378453 1 17.75264148 -2.371988243 2.057912901 2.312697628 0.774778915 0.761305283 0.038751527 2583987.568 231933.8235 15814588.83 0.009999096 0.004246311 2.371988243 -1.537918713 YQQETSVSQLPGRPKS(ph)PLSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YQQETSVSQLPGRPKSPLSK 20 2 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 YQQETSVSQLPGRPKS(0.976)PLS(0.024)K;YQQETSVSQLPGRPKS(0.998)PLS(0.002)K;YQQETSVSQLPGRPKS(0.999)PLS(0.001)K;YQQETSVSQLPGRPKS(1)PLSK 197.08 8.82E-22 2463260000 1326740 879220 1129840 1221380 722279 1167920 1375810 1244990 760398 TRUE FALSE 1264027.63 968813.5176 1181644.282 1098604.562 848244.2289 1127474.638 1165904.916 1135972.075 878316.6383 1.439147996 1.103034459 1.34535113 1.250806957 0.965761312 1.283676738 1.327431208 1.293351425 1 19.74438161 4.695359819 3.731039315 1.215767397 1.452922463 0.232064062 0.134588548 0.361286872 8.791235434 0.030806957 0.21594215 49586.08488 -4.695359819 0.237155066 YQQGDFGYCPR ddPTM_SK-BR-3_Trastuzumab_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 ;;; 245.5 1.40E-15 1210201000 1189460 851090 941400 906310 912770 1029910 1002510 1211670 882010 FALSE TRUE 1133236.583 937817.0386 984564.1212 815205.9969 1071956.799 994243.9585 849558.6871 1105569.751 1018787.606 1.112338407 0.920522622 0.966407635 0.800172668 1.052188692 0.975908965 0.833891855 1.085181783 1 19.95842188 4.589213509 2.576572267 0.942387706 1.122926036 0.228590466 0.088323295 0.45416197 4.84145283 0.02019821 0.154052923 38834.12367 -4.589213509 0.18053833 YQQLFEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQQLFEDIR 9 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 82.426 0.043008 70127000 287570 312330 250940 341730 264660 280160 326300 313460 274390 FALSE TRUE 273977.136 344156.7821 262445.8472 307378.6512 310816.6202 270457.989 276516.9421 286011.7806 316940.9998 0.864442077 1.085870185 0.828059 0.969829247 0.980676594 0.8533386 0.872455575 0.902413322 1 18.27385477 2.245218874 24.99271541 0.892316479 0.95322792 0.037709027 0.078729223 322.370343 1210064.488 0.025857503 0.021175252 175.8809787 -2.245218874 0.060911441 YQQWMER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQQWMER 7 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-2;H7C2I4;J3QQT1 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 134.85 0.0072917 241300000 319200 280910 253870 282180 342940 288050 368310 317480 368890 FALSE TRUE 304112.0486 309535.0484 265510.1906 253814.7303 402748.6274 278074.7563 312117.545 289679.7681 426095.5772 0.713717919 0.72644511 0.623123555 0.595675581 0.945207247 0.652611224 0.732505949 0.679846926 1 18.70081755 -2.119800977 2.335823366 1.550920235 0.710787769 0.482302437 0.094842319 14449409.77 3619329.871 42265207.25 0.021626906 0.007589253 2.119800977 -0.840132466 YQVAGAEYWDNNDHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQVAGAEYWDNNDHR 15 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 153.95 2.56E-06 121860000 122060 155900 120370 136590 104290 129010 98469 127000 87457 FALSE TRUE 116290.4657 171786.3872 125889.0836 122859.7137 122478.143 124542.3514 83445.74554 115879.2067 101019.3849 1.151169806 1.700528937 1.24618739 1.216199384 1.212422181 1.232855966 0.826036959 1.147098716 1 16.62427264 2.519656454 0.937256275 0.981722067 1.40660507 0.399751632 0.171048796 0.473450699 0.844650567 0.10897717 0.080285725 330.8692858 -2.519656454 0.424883003 YQVFFFGTHETAFLGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQVFFFGTHETAFLGPK 17 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 230.33 8.24E-16 980570000 1482490 1211350 1122760 1376630 1132260 1211460 1532390 1424160 985100 FALSE TRUE 1412415.636 1334787.942 1174239.657 1238248.537 1329725.786 1169506.836 1298595.761 1299453 1137864.277 1.241286562 1.173064283 1.031968118 1.088221647 1.16861546 1.027808729 1.141257167 1.142010543 1 20.11789705 3.974600905 4.215750929 1.094198512 1.219295335 0.463295143 0.0556885 0.16085308 6.733720424 0.013220759 0.026869755 9431.937307 -3.974600905 0.125096823 YQYGGLNSGRPVT(ph)PPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 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 178.43 4.51E-09 7096920000 2801730 2756850 2397280 3147720 2591660 2477510 2645380 2753140 2637760 TRUE FALSE 2669297.775 3037776.149 2507197.659 2831305.205 3043644.683 2391713.207 2241778.695 2512060.466 3046810.349 0.876095808 0.997034866 0.82289259 0.929268606 0.99896099 0.784989196 0.735778876 0.824488622 1 21.53886827 2.222134975 24.9982225 0.804836531 0.925828005 0.166911136 0.086369723 274.1839542 417278.6078 0.029635251 0.021950343 166.7765457 -2.222134975 0.120991473 YQYGGLNSGRPVT(ph)PPRTANPPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YQYGGLNSGRPVTPPRTANPPK 22 2 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 1 YQYGGLNS(0.006)GRPVT(0.994)PPRTANPPK 141.78 5.71E-06 603340000 199990 101600 210220 178130 190560 207560 299620 233660 286050 TRUE FALSE 190536.869 111953.1555 219858.7949 160224.034 223793.6037 200372.1452 253907.4661 213199.4917 330409.1731 0.576669429 0.338831863 0.665413714 0.484926107 0.677322611 0.606436387 0.768463732 0.645258997 1 18.33389421 0.936464873 0.260799204 1.092077599 0.411686702 0.68046523 0.097555166 1.3220284 0.288094317 0.326114801 0.186522761 8.639027831 -0.936464873 -0.680390898 YQYGGLNSGRPVTPPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 182.57 1.94E-09 1327290000 881070 726960 786850 956780 724750 884110 932180 924780 769500 FALSE TRUE 839423.5672 801038.0505 822927.8508 860602.6566 851146.1705 853493.049 789958.8203 843801.3606 888830.1299 0.944413942 0.901227381 0.925855035 0.968241993 0.957602743 0.960243156 0.888762423 0.949339286 1 19.7615482 2.392833786 0.006173589 1.876858735 1.51E-07 0.220486272 0.028550376 9261.306974 29.57793738 4441.734215 4548.268696 247.0778343 -2.392833786 -1.876858584 YQYPLFGLPFVHNDFQSEADWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YQYPLFGLPFVHNDFQSEADWLR 23 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 212.36 3.22E-25 220550000 242520 222120 210685 237500 242190 194841 309690 246090 232520 FALSE TRUE 231056.5602 244754.2805 220345.1156 213626.0488 284427.8593 188093.6073 262441.1027 224541.055 268578.0141 0.860295885 0.911296784 0.820413824 0.795396636 1.059013934 0.700331365 0.977150358 0.83603662 1 18.03498168 -4.999999996 0.338037171 2.336985385 0.870434608 0.144230824 0.098480404 730.73939 6.18569816 704.352627 0.068474109 1.00E-05 4.999999996 -1.466550777 YRADTLGELDLER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRADTLGELDLER 13 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ; 192.54 2.40E-06 266110000 257420 181361 225620 207848 292450 188760 266950 230310 307060 FALSE TRUE 245252.2668 199841.8921 235964.9002 186954.7242 343453.1874 182223.1939 226221.8746 210142.8354 354677.2966 0.691480027 0.563447094 0.665294628 0.527112183 0.968354024 0.513771802 0.637824515 0.592490237 1 18.43614746 -1.456407971 5.583273033 1.000331119 0.641072353 0.430872681 0.128162114 0.000467568 4.55E-05 0.109838723 0.025865846 0.034961659 1.456407971 -0.359258766 YRCELLYEGPPDDEAAMGIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRCELLYEGPPDDEAAMGIK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 182.39 4.33E-17 73586000 101810 66333 104550 82775 82150 99496 138220 112930 120930 FALSE TRUE 96997.64307 73092.40811 109343.7209 74454.29974 96476.93399 96050.42857 117132.0004 103041.2505 139683.2068 0.694411628 0.523272695 0.7827979 0.533022555 0.690683843 0.687630466 0.838554635 0.737678157 1 17.09179906 1.096751632 0.52432217 1.001651917 0.615778965 0.625266553 0.084854129 0.523402184 0.368608758 0.084351914 0.041349224 12.49544226 -1.096751632 -0.385872952 YRDELKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRDELKR 7 2 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 86.833 0.011129 28322000 203500 179000 177470 161560 239350 182500 242260 213930 115450 FALSE TRUE 193880.9583 197240.3035 185607.175 145319.6819 281092.5642 176179.9792 205298.7876 195197.1551 133353.3964 1.453888417 1.479079715 1.391844378 1.089733639 2.107877054 1.321151047 1.539509253 1.463758407 1 17.02489504 0.925945505 19.06977001 0.999999999 1.481705276 0.260712633 0.254669169 3022.876328 778425.254 0.21842164 0.05460541 8.432289439 -0.925945505 0.481705277 YRDYYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YRDYYR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 107.49 0.028472 1838910000 1246090 906920 631890 829410 1326180 791380 1417620 1078010 1387450 FALSE TRUE 1187189.795 999336.1791 660862.7815 746036.131 1557465.372 763974.3122 1201336.033 983613.7295 1602608.66 0.740785836 0.623568438 0.41236691 0.465513603 0.971831372 0.476706717 0.749612842 0.613757902 1 20.61199075 -1.218859685 0.417633211 1.178745726 0.619691225 0.336161606 0.163440029 24.0966625 2.523604068 5.004943375 0.092544551 0.060414379 1.218859685 -0.559054502 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR 33 1 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 107.04 8.94E-06 77608000 29910 22635 20170 27444 28238 24248 29524 26854 28507 FALSE TRUE 28496.21358 24941.53223 21094.81445 24685.27698 33162.69826 23408.28568 25019.57155 24502.5214 32927.71997 0.86541715 0.757463082 0.640639998 0.749680725 1.007136185 0.710899075 0.759833101 0.744130521 1 15.007015 YREWHHFLVVNMK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YREWHHFLVVNMK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 69.716 0.030291 938570000 1151430 492310 671480 801870 895360 787830 1345720 900950 564440 FALSE TRUE 1097004.186 542476.9487 702268.0222 721264.5041 1051510.501 760547.2496 1140405.698 822058.0418 651970.4724 1.682597958 0.832057542 1.077146975 1.106284003 1.612819207 1.166536341 1.74916771 1.26088232 1 19.3144471 2.760262849 24.34152854 1.416163385 1.168487481 0.067232532 0.297935551 1123.144369 1259732.382 0.08654045 0.091706137 575.7883178 -2.760262849 -0.247675905 YREYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 Y(0.022)REY(0.019)S(0.959)PPYAPSHQQYPPSHATPLPK;YREYS(0.998)PPYAPS(0.001)HQQYPPSHATPLPK 133.25 3.76E-05 588120000 340720 253610 327580 339640 285660 330400 418430 374630 241790 TRUE FALSE 324614.8408 279453.1473 342599.867 305498.7419 335479.0136 318958.1652 354590.8185 341825.4112 279285.5583 1.162304427 1.000600063 1.226700976 1.093857999 1.2012043 1.142050334 1.269635353 1.223927987 1 18.09138145 3.726211423 24.90029008 1.179013731 1.08145224 0.126194587 0.086109704 992.6172358 2001463.456 0.021062126 0.03289718 5323.673633 -3.726211423 -0.097561491 YRGDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YRGDYDR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;; 147.04 0.0019868 3175743000 2082604 1644348 1756864 2099970 2252760 1781738 2179848 1948297 2366500 FALSE TRUE 1984163.436 1811908.931 1837417.952 1888877.026 2645640.631 1720035.966 1847272.152 1777693.786 2733484.734 0.725873246 0.662856795 0.672188847 0.691014295 0.967863694 0.629246597 0.675793843 0.650339753 1 21.38230989 -1.156082608 4.136876995 1.000082726 0.706396373 0.477452266 0.095497478 12986170.16 3629091.581 11051.96116 0.021266883 0.06980996 1.156082608 -0.293686353 YRGFTIPEAFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRGFTIPEAFR 11 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 155.88 2.86E-05 331930000 220900 121760 177590 143440 271890 166780 316470 236830 391540 FALSE TRUE 210458.4948 134167.4824 185732.6772 129021.1387 319307.5299 161004.3668 268186.6891 216091.9097 452258.0235 0.465350494 0.296661365 0.410678567 0.285282144 0.706029552 0.356001129 0.592994873 0.477806691 1 18.78678657 -3.097930939 0.204789057 2.116642354 0.331818002 0.68806792 0.120369486 29.91494455 0.597689629 14.52790451 0.255765263 0.000798122 3.097930939 -1.784824353 YRIQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRIQEQESSGEEDSDLSPEER 21 1 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 Y(0.001)RIQEQES(0.999)S(0.999)GEEDSDLSPEER;YRIQEQES(1)S(1)GEEDSDLSPEER 136.67 2.59E-06 921190000 1034880 662090 1072750 874130 977840 856450 1247870 1053990 1352670 TRUE FALSE 985963.2733 729557.7237 1121936.649 786260.7917 1148374.986 826790.9217 1057484.513 961697.048 1562435.155 0.631042684 0.466936321 0.718069255 0.503227791 0.734990494 0.529168151 0.676818177 0.615511655 1 20.57536488 -5 0.245648489 3.365701345 0.5645956 0.661355295 0.088084876 93.47815051 0.929087001 110.6505475 0.113304645 1.00E-05 5 -2.801105744 YRLEVGIQAMEHLIHVLQTDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRLEVGIQAMEHLIHVLQTDR 21 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 248.03 1.20E-30 43757000 46414 57761 45512 59855 47062 51236 50885 43995 3452.7 FALSE TRUE 44220.1022 63646.91157 47598.77022 53838.26168 55269.5979 49461.68447 43121.55868 40142.56457 3988.127082 11.08793709 15.95909816 11.93511873 13.49963544 13.85853479 12.40223379 10.8124836 10.06551791 1 11.96149567 0.500529417 0.697935926 0.795966989 13.47957369 0.891455674 1.310855612 0.468190542 0.375275801 1.385604255 0.453806303 3.166134913 -0.500529417 12.68360671 YRPAS(ph)ASVSALIGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YRPASASVSALIGGR 15 1 P46108-2 P46108-2 CRK Adapter molecule crk 1 YRPAS(1)ASVSALIGGR;YRPAS(0.999)AS(0.001)VSALIGGR;YRPAS(1)ASVSALIGGR;YRPAS(1)ASVSALIGGR 218.14 1.20E-12 1334061000 316856 294589 299674 324692 343928 316660 381866 336312 405627 TRUE FALSE 301878.8448 324607.954 313414.3493 292053.3433 403908.9343 305693.9848 323605.3282 306862.7384 468529.5635 0.644311199 0.692822779 0.668931853 0.623340267 0.862077798 0.652453994 0.690682837 0.654948508 1 18.83778056 -2.157127225 2.360540985 1.737707796 0.685987121 0.691136437 0.065926697 2736467.198 676693.5599 10802161.55 0.015060742 0.006964225 2.157127225 -1.051720675 YRPDWTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRPDWTR 7 1 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 0 83.206 0.020475 136730000 53898 53225 42705 58829 55218 58220 51498 50919 55754 FALSE TRUE 51350.34836 58648.68801 44663.06649 52915.39715 64848.00172 56203.8268 43641.03427 46460.26242 64400.04557 0.797365093 0.910693269 0.693525386 0.821667076 1.006955836 0.872729612 0.677655332 0.721432136 1 15.97477409 -1.424361471 5.864118981 1.00007769 0.815507285 0.252491751 0.10115295 0.000104914 1.03E-05 0.100011293 0.023562991 0.037639039 1.424361471 -0.184570405 YRPETK ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YRPETK 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;;; 138.37 0.011249 7657680000 7790710 6317310 6601630 8229900 5991190 7940660 8816850 7976390 7127740 FALSE TRUE 7422458.578 6961051.071 6904321.265 7402614.816 7036051.639 7665672.953 7471677.6 7277935.006 8233073.516 0.901541637 0.845498471 0.838607994 0.899131388 0.854608139 0.931082777 0.907519845 0.883987613 1 22.97299968 -0.133322312 0.326525166 1.032175991 0.862524746 0.655868393 0.027599483 3.529140808 0.501393081 0.171769063 0.027001315 0.735660923 0.133322312 -0.169651246 YRPLFDYFLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRPLFDYFLK 10 1 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 172.27 3.43E-06 275430000 1823680 1280850 801000 1073040 1741990 1034110 2181030 1601630 1818460 FALSE TRUE 1737478.261 1411370.071 837726.6423 965175.9806 2045792.504 998298.5114 1848273.816 1461382.786 2100457.489 0.827190395 0.671934604 0.398830563 0.459507505 0.973974724 0.475276704 0.879938692 0.695744995 1 21.00227216 0.810011281 0.705987493 0.99684511 0.647617173 0.257971659 0.184463741 1.377466737 1.439313754 0.178355105 0.066868114 6.456709998 -0.810011281 -0.349227937 YRPSHSDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRPSHSDK 8 1 E9PGM7;O94988-6;O94988-5;O94988-1;O94988;O94988-3 E9PGM7 FAM13A Protein FAM13A 0 51.346 0.09002 18817000 22988 18508 22438 21037 17159 20201 25635 22895 19104 FALSE TRUE 21901.4028 20393.98624 23466.80449 18922.32079 20151.52417 19501.4343 21723.90993 20890.19243 22066.55075 0.992515915 0.924203627 1.063455941 0.857511489 0.913215862 0.883755442 0.984472389 0.94669043 1 14.42957352 0.73894932 1.429348994 0.999305216 0.944594973 0.078801299 0.058392615 2.480178918 8.458352995 0.052074307 0.015323286 5.48212987 -0.73894932 -0.054710243 YRPSMEGYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRPSMEGYR 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 0 ; 81.865 0.018307 221860000 329280 295780 219975 318650 286220 251260 392850 446380 340590 FALSE TRUE 313715.587 325920.3183 230061.0713 286618.6966 336136.6774 242558.8032 332913.5173 407292.6008 393406.9577 0.797432737 0.828455908 0.584791567 0.72855523 0.854424841 0.616559515 0.8462319 1.035295876 1 18.58566295 1.3900883 3.956870156 1.014814971 0.748201548 0.643736514 0.085671378 0.143758938 3.639297858 0.062641083 0.021460442 24.55208055 -1.3900883 -0.266613423 YRQDDDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 YRQDDDQR 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;; 158.87 0.00033055 6307308000 8051302 7171882 7400416 8078044 7836237 7561874 8757543 7766523 8468908 FALSE TRUE 7670732.911 7902704.93 7739732.394 7266023.67 9202874.252 7300004.407 7421418.972 7086445.073 9782222.999 0.784150281 0.807863911 0.791203839 0.742778372 0.940775349 0.746252095 0.758663851 0.724420725 1 23.22173092 -2.464461491 2.338557932 3.584415478 0.788083691 0.554019415 0.060048281 2630412.648 363104.0859 36453404.23 0.013559335 0.003431931 2.464461491 -2.796331787 YRQENQEAVGGFFSQIGELYVVHHLWAYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YRQENQEAVGGFFSQIGELYVVHHLWAYK 29 1 Q9BPW8 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 176.09 1.79E-13 93812000 166480 115350 131090 130650 139770 141360 175620 147510 67940 FALSE TRUE 158610.8203 127104.2961 137100.6062 117516.8138 164145.8437 136464.6678 148825.9435 134593.2424 78475.78821 2.021143386 1.619662561 1.747043378 1.497491347 2.091674993 1.738939753 1.896456817 1.715092584 1 16.25995999 0.952834516 19.81441202 0.999999998 1.798216712 0.672536414 0.174456292 396.2948746 166486.1813 0.154340875 0.038585219 8.970869027 -0.952834516 0.798216714 YRS(ph)DIHTEAVQAALAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRSDIHTEAVQAALAK 16 1 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 Y(0.002)RS(0.879)DIHT(0.118)EAVQAALAK;Y(0.33)RS(0.386)DIHT(0.284)EAVQAALAK 118.37 0.00016813 477730000 688090 639650 646670 748140 530000 828350 850120 765660 529600 TRUE FALSE 655565.3494 704831.0622 676320.4591 672935.5458 622431.8322 799664.0318 720418.5805 698614.7514 611727.6632 1.071662095 1.152197464 1.105590772 1.100057405 1.017498259 1.307222282 1.177678604 1.142035571 1 19.22252999 2.264343309 24.99998943 1.177044289 1.097571986 0.119432724 0.081414314 350.9503929 340295.0482 0.025688598 0.021485727 183.7990697 -2.264343309 -0.079472303 YRS(ph)PEPDPYLSYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 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 Y(0.169)RS(0.831)PEPDPYLSYR;Y(0.022)RS(0.978)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR 168.91 1.78E-05 6800560000 3937290 3345150 3475200 4153020 4174440 3627970 4377870 3757020 4256880 TRUE FALSE 3751182.105 3686024.588 3634541.357 3735550.539 4902461.014 3502332.489 3709945.526 3428035.412 4917015.209 0.762898211 0.749646774 0.73917635 0.759719135 0.997040035 0.712288317 0.754511704 0.697178118 1 22.22935139 -2.329906141 2.37301582 2.391349081 0.77063222 0.428224581 0.082951565 9126394.733 1205837.621 68242027.12 0.020172275 0.004678362 2.329906141 -1.620716861 YRS(ph)PYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRSPYR 6 1 Q14498-3 Q14498-3 RBM39 RNA-binding protein 39 1 Y(0.001)RS(0.986)PY(0.013)R;Y(0.003)RS(0.993)PY(0.004)R 63.673 0.067259 958840000 408160 311980 396370 376160 619040 310180 502730 361670 746330 TRUE FALSE 388867.0857 343771.1167 414543.9566 338347.6821 727000.38 299438.3888 426029.3052 330000.2575 862067.0447 0.451086825 0.398775384 0.480872061 0.392484186 0.84332232 0.347349305 0.494195095 0.382801152 1 19.71744055 -1.274986766 3.417331915 1.001756556 0.470676362 0.58552879 0.139092786 70756251.9 105228997.1 1290760.601 0.032191977 0.053090062 1.274986766 -0.531080194 YRS(ph)PYSGPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.905)PY(0.001)S(0.094)GPK;Y(0.075)RS(0.91)PY(0.014)S(0.001)GPK;YRS(0.586)PYS(0.414)GPK;Y(0.123)RS(0.869)PY(0.001)S(0.007)GPK;Y(0.005)RS(0.995)PYS(0.001)GPK;Y(0.124)RS(0.871)PY(0.004)S(0.001)GPK;Y(0.092)RS(0.905)PY(0.003)S(0.001)GPK 132.03 0.00083274 42840320000 35711540 29548280 30344170 34287900 23770840 33649650 36521980 34758550 26357670 TRUE FALSE 34023526.28 32559283.33 31735480.21 30841215.15 27916466.97 32484354.18 30949881.18 31714907.1 30445082.85 1.117537648 1.069443085 1.042384426 1.013011372 0.916945016 1.06698196 1.016580619 1.041708681 1 24.8597059 3.863410939 1.524553963 1.011089588 1.109473778 0.462575898 0.038639815 0.353735216 1.56458261 0.011218018 0.031079921 7301.480653 -3.863410939 0.09838419 YRS(ph)QSGEDESMNQPGPIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRSQSGEDESMNQPGPIK 18 1 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 YRS(0.655)QS(0.345)GEDESMNQPGPIK;YRS(0.77)QS(0.23)GEDESMNQPGPIK 215.84 5.63E-19 278330000 422100 303310 394630 387540 358740 393850 498870 465600 467650 TRUE FALSE 402148.1695 334217.6338 412724.1758 348583.7429 421304.1424 380210.8757 422758.2191 424829.5957 540170.7736 0.744483392 0.618725874 0.764062397 0.645321369 0.7799462 0.703871617 0.782638084 0.786472754 1 19.04305606 0.266337838 0.42906262 1.033046057 0.68505117 0.770596797 0.049390791 1.225207652 0.359454921 0.118142181 0.027724655 1.846451217 -0.266337838 -0.347994888 YRSPYS(ph)GPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.115)PYS(0.885)GPK;YRS(0.297)PYS(0.703)GPK 162.1 0.00016844 3077500000 2534820 2095110 2214180 2608280 1753730 2271590 2654650 2493540 1870870 TRUE FALSE 2415004.082 2308604.091 2315702.343 2346090.739 2059579.957 2192924.269 2249634.387 2275192.419 2160994.965 1.11754267 1.068306095 1.071590809 1.085653034 0.953070225 1.014775279 1.041017875 1.05284485 1 21.04326428 2.802820619 23.16978981 1.017212907 1.085604218 0.604301879 0.029379679 71.41561342 25749.40813 0.008997558 0.009543347 635.068569 -2.802820619 0.068391311 YRVPDVLVADPPIAR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YRVPDVLVADPPIAR 15 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 121.82 0.0001028 2667560000 3843390 3298180 3452580 3969430 3933680 3524860 4379590 3979340 4489470 FALSE TRUE 3661720.572 3634268.292 3610884.208 3570415.355 4619712.547 3402793.214 3711403.109 3630887.894 5185674.079 0.70612239 0.70082852 0.696319158 0.688515186 0.890860566 0.656191107 0.715703118 0.700176648 1 22.3061001 -2.142947574 2.380152621 1.618525192 0.71744777 0.661506146 0.063081684 3388287.244 921747.9868 11306259.83 0.01396226 0.007195358 2.142947574 -0.901077422 YS(ph)DGSIALDIFGPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSDGSIALDIFGPQK 15 0 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 YS(1)DGSIALDIFGPQK;Y(0.279)S(0.36)DGS(0.36)IALDIFGPQK 251.87 1.31E-24 77753900 280135 235364 225100 277726 190647 256612 283388 295775 179541 TRUE FALSE 266893.5737 259347.8592 235421.0577 249808.4548 223895.7764 247725.4621 240151.9558 269875.373 207383.3013 1.28695788 1.250572527 1.135197753 1.204573624 1.079622974 1.194529456 1.158010092 1.301336083 1 17.66194021 -5 0.073163754 0.452815927 1.398665624 0.394070534 0.071960605 289.6050662 1.517741219 27.84679878 3.169556432 1.00E-05 5 0.945849697 YS(ph)PRHS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YSPRHSR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 Y(0.016)S(0.984)PRHS(1)R;Y(0.007)S(0.993)PRHS(1)R;Y(0.005)S(0.995)PRHS(1)R;Y(0.019)S(0.981)PRHS(1)R;Y(0.019)S(0.981)PRHS(1)R;Y(0.017)S(0.983)PRHS(1)R;Y(0.017)S(0.983)PRHS(1)R 94.297 0.0081394 21650620000 10579350 11087450 8900980 11302920 7322130 9937380 9342400 8162290 5870410 TRUE FALSE 10079285.09 12217273.76 9309098.737 10166729.01 8599107.154 9593246.039 7917045.295 7447556.617 6780763.201 1.486452895 1.801754965 1.372868874 1.499348776 1.268162137 1.414773788 1.167574366 1.098336042 1 22.69301623 2.195756138 0.495611732 0.991531937 1.65547773 0.736753245 0.117914768 0.429908924 0.225818208 0.107828749 0.09445363 156.9481274 -2.195756138 0.663945792 YS(ph)PRHS(ph)RS(ph)R ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSPRHSRSR 9 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 Y(0.205)S(0.796)PRHS(0.999)RS(1)R 55.841 0.083105 256280000 546180 391660 494400 512350 379080 406800 533030 312570 304120 TRUE FALSE 520363.1538 431570.5993 517068.729 460847.6046 445191.432 392712.414 451706.4837 285199.7138 351281.3764 1.481328612 1.228561001 1.471950305 1.311904461 1.267335708 1.117942596 1.285882242 0.811883957 1 18.42226757 1.70960568 0.80829687 0.941116526 1.371116264 0.631737082 0.123416323 0.380382405 0.481522122 0.102797704 0.045484695 51.23959404 -1.70960568 0.429999738 YS(ph)PSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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(0.078)S(0.907)PS(0.014)QNS(1)PIHHIPSR;Y(0.041)S(0.925)PS(0.034)QNS(1)PIHHIPSR;Y(0.056)S(0.915)PS(0.03)QNS(1)PIHHIPSR;Y(0.039)S(0.647)PS(0.314)QNS(1)PIHHIPSR;Y(0.034)S(0.83)PS(0.137)QNS(1)PIHHIPSR;Y(0.435)S(0.564)PS(0.001)QNS(1)PIHHIPSR;Y(0.45)S(0.55)PS(0.001)QNS(1)PIHHIPSR;Y(0.443)S(0.557)PS(0.072)QNS(0.928)PIHHIPSR;Y(0.304)S(0.638)PS(0.069)QNS(0.989)PIHHIPSR 196.98 4.57E-09 4681300000 3282800 4529100 2806305 4338440 2713605 3458060 2798270 3035340 761579 TRUE FALSE 3127628.55 4990620.439 2934976.86 3902331.769 3186856.853 3338306.515 2371342.518 2769549.538 879680.7817 3.555413071 5.673217539 3.336411254 4.436077097 3.622742385 3.794906726 2.695685261 3.148357445 1 19.74662057 1.029788052 0.416019259 0.843712701 4.582462114 0.682999514 0.670013949 0.639610636 0.301550348 0.890224686 0.47611132 10.709965 -1.029788052 3.738749413 YS(ph)PSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 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;Y(0.001)S(0.999)PSQNS(1)PIHHIPSRR;YS(0.939)PS(0.061)QNS(1)PIHHIPSRR;Y(0.143)S(0.799)PS(0.066)QNS(0.707)PIHHIPS(0.286)RR;Y(0.001)S(0.999)PS(0.001)QNS(1)PIHHIPSRR;YS(0.633)PS(0.367)QNS(1)PIHHIPSRR;YS(0.848)PS(0.152)QNS(1)PIHHIPSRR;YS(0.71)PS(0.289)QNS(1)PIHHIPSRR;Y(0.053)S(0.711)PS(0.236)QNS(1)PIHHIPSRR;Y(0.003)S(0.932)PS(0.065)QNS(1)PIHHIPSRR 224.36 8.03E-15 5346721000 3162458 2735242 2838424 3387327 2764354 2924304 3276191 2756950 1164590 TRUE FALSE 3012974.878 3013966.27 2968568.548 3046826.454 3246456.462 2823034.619 2776347.892 2515536.842 1345188.669 2.239815831 2.240552822 2.206804604 2.26498076 2.41338374 2.098616115 2.063909662 1.870025298 1 20.3593771 0.644493062 0.875895771 0.995532212 2.260329098 0.968187944 0.070655245 0.181702606 0.241211846 0.06679626 0.022326993 4.41055317 -0.644493062 1.264796886 YS(ph)PSQNSPIHHIPSR ddPTM_SK-BR-3_Trastuzumab_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(0.945)PS(0.055)QNSPIHHIPSR;YS(0.995)PS(0.005)QNSPIHHIPSR;YS(0.871)PS(0.129)QNSPIHHIPSR;YS(0.992)PS(0.008)QNSPIHHIPSR 225.39 6.48E-13 976570000 435456 543362 346486 563697 367157 371910 388936 391068 137708 TRUE FALSE 414872.8579 598731.2056 362372.7258 507033.1066 431189.0646 359030.6634 329596.6699 356824.0127 159063.0533 2.608228933 3.764112363 2.278170312 3.187623373 2.710805907 2.257159384 2.07211331 2.243286579 1 17.27923924 1.237611488 0.408643824 0.93596854 3.189952037 0.676827703 0.411608573 0.578127102 0.282118147 0.51213938 0.319743369 17.28269588 -1.237611488 2.253983497 YS(ph)PSQNSPIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_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 YS(0.996)PS(0.004)QNSPIHHIPSRR;YS(0.97)PS(0.03)QNSPIHHIPSRR 194.92 6.39E-11 1057790000 174795 150417 147184 182922 194743 164621 207122 196556 75706 TRUE FALSE 166532.7868 165744.6633 153932.532 164534.333 228706.1175 158920.1335 175521.7348 179344.5146 87446.09983 1.904404966 1.895392289 1.760313293 1.881551417 2.615395289 1.817349588 2.007199123 2.050914963 1 16.41610642 -0.943061777 6.302667869 0.999999786 1.980384216 0.632730781 0.237278221 6.74E-07 1.13E-07 0.217537755 0.051274129 0.11400876 0.943061777 0.98038443 YS(ph)PVSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSPVSK 6 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;A0A590UK70;H7C166;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;Q12959-8;A0A590UJX2;A0A590UJ64;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 YS(0.991)PVS(0.009)K;YS(0.996)PVS(0.003)K;YS(0.982)PVS(0.018)K 84.568 0.05843 1043580000 4115390 5221100 3454630 5330000 2431910 4145890 3846390 4623900 2391470 TRUE FALSE 3920863.671 5753136.026 3613028.203 4794218.274 2856034.334 4002316.79 3259552.562 4219006.803 2762326.954 1.419406079 2.08271364 1.307965445 1.735572347 1.033923349 1.448893218 1.180002446 1.527337956 1 21.39745266 3.041747287 1.630587416 1.265024618 1.712526245 0.295905501 0.272119259 0.387561934 2.111196972 0.08700902 0.106460704 1100.898518 -3.041747287 0.447501626 YSCPESPSQELGGPLPS(ph)PGPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSCPESPSQELGGPLPSPGPR 21 0 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR 351.41 5.67E-78 254655000 223067 145702 194790 222972 238710 174145 210628 183703 196512 TRUE FALSE 212523.065 160549.1994 203721.3142 200558.4309 280340.9484 168114.315 178492.8302 167616.9914 226986.0773 0.936282381 0.707308577 0.89750577 0.883571509 1.235057902 0.740637122 0.786360257 0.738446135 1 17.79224428 -1.064530363 4.186641669 1.000015551 0.857305305 0.0697689 0.151478484 0.510774091 82234642.89 3063.527183 0.03449394 0.086192532 1.064530363 -0.142710246 YSDESGNMDFDNFISCLVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSDESGNMDFDNFISCLVR 19 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EMQ1 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ;; 243.78 4.13E-24 172637000 146398 125872 126248 134540 143948 117462.4 159256 139864 148307 FALSE TRUE 139478.0567 138698.4999 132036.5957 121015.7836 169052.4856 113394.6476 134958.5723 127616.7667 171305.6921 0.814205617 0.80965494 0.770765957 0.706431772 0.986846867 0.661943256 0.787823047 0.744965127 1 17.38621356 -2.102365727 2.437029823 1.378342553 0.786994524 0.385164445 0.085214499 13437682.63 4223536.957 28156210.58 0.019395466 0.007900131 2.102365727 -0.591348029 YSDFEWLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YSDFEWLR 8 0 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 0 ;;;;; 238.7 2.56E-08 808808000 1637868 1247056 800422 909851 1707651 892730 1814783 1238000 1562495 FALSE TRUE 1560449.226 1374132.424 837122.1404 818391.0489 2005464.794 861814.5363 1537904.523 1129594.157 1804798.744 0.86461121 0.761377094 0.463831296 0.453452803 1.111184723 0.477512819 0.852119677 0.625883723 1 20.78340654 -1.411462215 11.36535427 1.000000058 0.714397527 0.164472833 0.209762655 2.85E-07 1.47E-08 0.18588235 0.043812881 0.038773748 1.411462215 -0.285602531 YSDFVVHEIGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSDFVVHEIGK 11 0 Q96PZ0;Q96PZ0-2;E7EUH7;H0Y863 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 ; 113.63 0.00085128 158140000 653680 706080 591770 792110 495970 667560 690100 745330 459110 FALSE TRUE 622781.8419 778030.3547 618903.2398 712485.5979 582467.011 644442.2298 584812.5704 680064.954 530306.434 1.174381078 1.467133538 1.16706719 1.343535647 1.098359314 1.215226119 1.10278234 1.282399968 1 19.01646673 2.739792349 24.99491645 1.148672124 1.298532353 0.299702129 0.111654982 130.2870606 2643861.461 0.03173063 0.032002486 549.2781823 -2.739792349 0.149860229 YSDFVVHEIGKDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSDFVVHEIGKDGR 14 1 Q96PZ0;Q96PZ0-2;E7EUH7;H0Y863 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 133.14 2.78E-05 104470000 198210 123100 199810 187410 181500 189940 267880 217630 201290 FALSE TRUE 188841.0061 135644.03 208971.4861 168571.1907 213153.5425 183362.3302 227009.986 198573.1635 232505.0252 0.812201827 0.583402573 0.898782665 0.725021709 0.916769616 0.788638138 0.976365934 0.854059663 1 17.82690237 2.451143485 0.514238945 0.974871624 0.699164152 0.39541146 0.095657209 0.799409438 0.440046122 0.080202649 0.080188766 282.5813433 -2.451143485 -0.275707472 YSDPGPVYDCLVWHDGEVWR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSDPGPVYDCLVWHDGEVWR 20 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 271.48 2.11E-44 236037000 199637 181134 180898 222752 195027 183369 210011 196483 171652 FALSE TRUE 190200.5547 199591.7605 189192.3522 200360.5458 229039.6471 177018.8856 177969.9648 179277.9069 198270.9155 0.959296295 1.006661819 0.954211321 1.010539268 1.1551853 0.892813175 0.897610042 0.904206784 1 17.59711354 YSDVEVPASVTGYSFASDGDSGTCSPLRHS(ph)FQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSDVEVPASVTGYSFASDGDSGTCSPLRHSFQK 33 1 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 YSDVEVPASVTGYSFASDGDS(0.03)GT(0.217)CS(0.138)PLRHS(0.615)FQK;YSDVEVPASVTGYSFASDGDSGT(0.001)CS(0.013)PLRHS(0.986)FQK 353.16 4.54E-132 370800000 376410 292270 366740 360780 296040 352640 445880 417980 323110 TRUE FALSE 358617.8453 322052.6453 383555.3918 324513.709 347669.2823 340427.9884 377852.8169 381379.4553 373216.2486 0.960884867 0.86291164 1.027702822 0.869505843 0.931549158 0.91214675 1.012423275 1.021872592 1 18.50965227 1.699890205 5.656323298 1.01333849 0.924371482 0.419935362 0.046319724 0.126016528 9.397985386 0.02173915 0.010909686 50.10605437 -1.699890205 -0.088967007 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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;YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR 268.39 8.14E-68 421170000 218598 183920 204162 295474 288676 198923 280635 216271 266026 TRUE FALSE 208265.3058 202661.6571 213523.0296 265772.3922 339021.003 192034.2466 237818.9765 197333.1647 307279.9534 0.677770559 0.659534261 0.694881092 0.864919397 1.103296845 0.624948828 0.773948882 0.642193422 1 18.22919412 3.33645961 5.855373805 0.817996057 0.670548686 0.204666179 0.144217203 0.352287314 17.58293572 0.039300468 0.053314746 2169.999379 -3.33645961 -0.147447372 YSEEGLS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSEEGLSPSK 10 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 YSEEGLS(1)PSK 152.55 1.87E-05 216590000 290350 320810 284880 320190 187960 334310 311270 348580 215540 TRUE FALSE 276625.7309 353500.9037 297942.0298 288003.8929 220740.1645 322732.7609 263780.0446 318056.4873 248964.8424 1.111103593 1.419882825 1.196723308 1.156805476 0.886631873 1.296298537 1.059507206 1.277515669 1 17.9255825 3.335006875 3.458872732 1.113246044 1.269882142 0.168469777 0.140601113 0.355352125 8.321408942 0.037218359 0.051284706 2162.752758 -3.335006875 0.156636098 YSEKEDKYEEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSEKEDKYEEEIK 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 174.17 1.15E-05 934470000 2123200 2176900 1681300 2414400 775490 2576900 2114700 2718600 687170 FALSE TRUE 2022840.544 2398728.585 1758389.268 2171699.925 910735.2105 2487661.307 1792063.676 2480544.972 793732.814 2.548515707 3.022085698 2.215341532 2.736059146 1.147407786 3.134129348 2.257766901 3.125163692 1 19.59829392 3.727465192 24.05524726 2.310641657 2.785300705 0.084184233 0.723990871 1009.33489 2188272.291 0.170469548 0.267080954 5339.0648 -3.727465192 0.474659048 YSEKQER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSEKQER 7 1 B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;A0A087X271 B4DDF4 CNN2 Calponin;Calponin-2 0 60.973 0.085988 63207000 56830 36200 53083 47278 49115 54471 74976 57791 70080 FALSE TRUE 54143.75853 39888.82116 55516.90806 42525.52562 57680.64045 52584.65561 63537.03417 52730.51367 80947.64848 0.668873766 0.492773069 0.685837194 0.525346028 0.712567215 0.649613134 0.784915132 0.651415015 1 16.30470155 0.048766377 0.300899657 1.100686188 0.564615995 0.691595752 0.077448645 2.648783342 0.374071033 0.409873619 0.08680169 1.118835859 -0.048766377 -0.536070193 YSESNFS(ph)VDDQDLSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSESNFSVDDQDLSR 15 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 YSESNFS(1)VDDQDLSR;YSESNFS(1)VDDQDLSR 207.42 3.57E-09 173055000 214752 175510 180169 233034 228277 200512 243448 190177 248516 TRUE FALSE 204601.0986 193394.6685 188429.9269 209608.9796 268088.4365 193568.2192 206305.5364 173524.0937 287054.592 0.712760235 0.673720867 0.656425405 0.73020598 0.933928402 0.674325458 0.718697914 0.604498581 1 18.13096561 -1.611183988 2.882787716 1.021653186 0.713587898 0.521474287 0.086378912 21945409.25 21969511.27 3583836.356 0.020401779 0.024480259 1.611183988 -0.308065287 YSGGNYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;; 125.08 0.0095001 692860000 828000 931280 761750 1018970 827200 900850 939630 894560 776270 FALSE TRUE 788862.0809 1026178.491 796676.991 916541.1997 971463.4181 869653.3386 796272.186 816227.584 896649.987 0.879788203 1.144458268 0.888503878 1.022183921 1.083436605 0.969891654 0.888052415 0.910307919 1 19.7741854 1.996567159 24.82132853 0.922504117 1.008836664 0.125892607 0.083407489 204.8754852 1481368.613 0.029745553 0.021518641 99.21267497 -1.996567159 0.086332547 YSGGNYRDNYDN ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSGGNYRDNYDN 12 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;; 199.68 0.0001783 660700000 677752 387142 723660 566688 894570 663410 1018870 739650 1051640 FALSE TRUE 645716.0061 426592.2099 756840.5268 509723.4456 1050582.725 640435.9454 863422.6687 674882.3249 1214722.96 0.531574711 0.351184775 0.623056081 0.41962115 0.864874345 0.527227991 0.710798015 0.555585386 1 20.21219589 -5 0.093010417 2.444917242 0.212906654 0.524738619 0.135093398 139.0130211 0.892963579 39.36477721 2.537168452 1.00E-05 5 -2.232010588 YSGKEGDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSGKEGDK 8 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 73.721 0.039064 431850000 765710 552330 614410 729350 400740 755900 802990 884360 512360 FALSE TRUE 729516.4058 608613.0549 642581.3062 656034.3523 470628.9291 729722.9935 680479.1276 806920.7501 591814.172 1.232678162 1.028385402 1.085782221 1.108514097 0.795230921 1.233027237 1.149818912 1.363469799 1 19.17478472 YSGKEGDKFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSGKEGDKFK 10 2 P26447 P26447 S100A4 Protein S100-A4 0 ; 65.842 0.03811 8567100000 5747200 2681600 5901800 4095200 3760100 6410000 8798400 6828100 4420200 FALSE TRUE 5475541.246 2954858.089 6172403.368 3683542.716 4415860.25 6188020.093 7456042.486 6230195.366 5105662.041 1.072444906 0.578741418 1.208933008 0.721462307 0.864894741 1.211991715 1.460347831 1.220252206 1 22.28366661 2.188214004 4.699128373 1.289565814 0.86949546 0.378486248 0.20604829 0.163147326 7.635039041 0.072636026 0.053822289 154.2460333 -2.188214004 -0.420070354 YSGKEGDKFKLNK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSGKEGDKFKLNK 13 3 P26447 P26447 S100A4 Protein S100-A4 0 ; 48.467 0.080001 1539080000 2452680 917640 3920400 1864620 2252210 3530200 5348000 4063900 3348000 FALSE TRUE 2336746.677 1011148.559 4100154.218 1677184.855 2644994.711 3407948.289 4532064.377 3708043.372 3867190.741 0.604249139 0.261468499 1.06024101 0.433695922 0.683957655 0.881246496 1.171926776 0.958846775 1 21.88285449 2.18969329 2.443315196 1.058906156 0.562547244 0.481057879 0.20816973 0.219485096 2.651126066 0.091254815 0.060807798 154.7723191 -2.18969329 -0.496358911 YSGREGDKHTLSKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSGREGDKHTLSKK 14 3 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 74.769 0.019257 336610000 639430 333420 669770 582230 577210 673070 1106600 891160 838830 FALSE TRUE 609205.4111 367395.8771 700479.617 523703.1342 677875.2412 649761.4171 937767.8459 813125.3061 968911.4723 0.628752397 0.379184154 0.722955231 0.540506692 0.69962557 0.670609685 0.967857098 0.839215273 1 19.88600533 2.02747605 0.807592872 0.986928635 0.529636107 0.701025169 0.102050311 0.299228914 0.364084508 0.079981436 0.041490776 106.5310112 -2.02747605 -0.457292529 YSGSKS(ph)PGPSR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSGSKSPGPSR 11 1 G5E9L9;A0A0U1RR70;Q8N568-2;Q8N568;Q8N568-3 G5E9L9 DCLK2 Serine/threonine-protein kinase DCLK2 1 YS(0.176)GS(0.148)KS(0.676)PGPSR 64.675 0.040898 67417000 39847 32545 38406 45364 40443 39860 46189 44966 44503 TRUE FALSE 37963.51128 35861.3725 40166.95309 40803.92453 47496.2464 38479.63821 39142.01973 41028.53866 51404.29795 0.73852796 0.697633737 0.781392893 0.793784297 0.923974226 0.7485685 0.761454223 0.798153857 1 15.64960137 -5 0.166712251 1.854565699 0.716401718 0.599847183 0.057335121 95.80108507 0.896470783 27.18666584 0.226966022 1.00E-05 5 -1.138163981 YSGTLNLDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 217.66 1.30E-06 12496170000 10081490 7846250 5194690 5888320 10346720 6169850 10618300 7652380 9744210 FALSE TRUE 9604957.947 8645791.795 5432871.675 5296414.887 12151184.69 5956186.547 8998283.317 6982297.039 11255292.32 0.853372589 0.768153465 0.482694853 0.470571064 1.079597433 0.529189858 0.799471312 0.620356792 1 23.42410019 -0.414002801 14.23346097 0.999997432 0.712409836 0.197892705 0.188173256 0 0 0.168691929 0.039761069 0.385475871 0.414002801 -0.287587596 YSHDFNFHINYGDLGFLGPEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHDFNFHINYGDLGFLGPEDLR 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 69.947 0.013784 27382000 20606 19258 18421 19900 21778 16811 27248 19524 4745.3 FALSE TRUE 19631.99522 21220.41209 19265.62107 17899.61419 25576.0763 16228.83085 23090.81716 17814.37506 5481.176888 3.581711668 3.871506526 3.514869427 3.265651621 4.6661651 2.960829615 4.212748033 3.250100374 1 12.42026998 0.964333546 18.92717897 0.999999991 3.725538953 0.76461638 0.471970036 77.78344016 41278.07758 0.386774453 0.096693579 9.211567643 -0.964333546 2.725538962 YSHS(ph)GS(ph)SSPDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.979)GS(0.548)S(0.366)S(0.107)PDTK;Y(0.054)S(0.113)HS(0.683)GS(0.435)S(0.388)S(0.328)PDTK;Y(0.001)S(0.007)HS(0.924)GS(0.571)S(0.145)S(0.351)PDT(0.002)K 160.84 0.00031498 0 875560 737256 808330 889880 527822 844790 925370 848020 487389 TRUE FALSE 834174.014 812383.2246 845392.73 800427.5717 619873.9897 815534.7105 784187.8109 773762.8732 562970.7969 1.481735853 1.443029068 1.501663558 1.421792349 1.101076633 1.448627025 1.392945807 1.374428083 1 19.10270056 -3.793024551 0.185379868 1.59E-16 1.490892534 0.588103483 0.107129857 59.01785087 0.859134563 22.7255024 0.316892347 0.000161055 3.793024551 1.490892534 YSHSGS(ph)SS(ph)PDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.001)GS(0.788)S(0.272)S(0.936)PDT(0.003)K 195.94 3.11E-07 242450000 285560 236660 266570 288030 175700 292800 316290 275920 186800 TRUE FALSE 272062.1447 260775.9231 278792.4982 259076.6772 206342.0244 282660.2626 268034.1514 251758.9821 215767.99 1.260901326 1.208594116 1.292093875 1.200718778 0.956314347 1.310019446 1.242233157 1.166804131 1 17.71912133 -4.347752513 0.279112139 6.06E-14 1.225450327 0.309695665 0.097409392 191.2006477 2.583849619 109.8383255 0.109022887 4.49E-05 4.347752513 1.225450327 YSHSGSS(ph)S(ph)PDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHSGS(0.496)S(0.551)S(0.953)PDTK 197.25 0.00016638 0 293730 258310 266130 294240 183820 302700 336260 274350 187960 TRUE FALSE 279845.965 284632.0827 278332.3237 264662.4362 215878.1498 292217.4231 284957.3612 250326.4596 217107.8768 1.288971958 1.31101684 1.282000118 1.219036546 0.994335871 1.345954957 1.312515075 1.153004963 1 17.72805254 -4.60075414 0.213813524 6.49E-13 1.286832815 0.371760644 0.100442347 139.0693062 1.622250346 59.95147557 0.209140137 2.51E-05 4.60075414 1.286832815 YSHSGSSS(ph)PDTK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHSGS(0.012)S(0.317)S(0.67)PDTK;YSHSGSS(0.009)S(0.991)PDTK;YSHS(0.003)GS(0.067)S(0.246)S(0.684)PDTK;YS(0.001)HS(0.005)GS(0.004)S(0.309)S(0.682)PDTK;YSHSGS(0.445)S(0.015)S(0.539)PDTK;YSHS(0.004)GS(0.029)S(0.195)S(0.772)PDTK;Y(0.001)S(0.005)HS(0.036)GS(0.027)S(0.223)S(0.707)PDT(0.001)K 246.68 1.52E-16 2661259000 3673210 3044490 3453980 3794360 2587632 3886420 4402110 4223410 2881954 TRUE FALSE 3499584.643 3354726.992 3612348.399 3412943.724 3038914.202 3751832.301 3730487.269 3853585.831 3328872.707 1.051282206 1.007766679 1.085156663 1.025255101 0.912895887 1.127057905 1.120645815 1.157624869 1 21.66660227 YSHSYLS(ph)DS(ph)DTEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 YSHS(0.001)YLS(0.998)DS(0.957)DT(0.043)EAK 83.253 0.0030262 0 112840 120780 95349 135430 72138 120130 105580 109730 75091 TRUE FALSE 107506.2768 133087.6193 99720.84596 121816.3191 84718.84436 115969.868 89471.83189 100121.4595 86735.72877 1.239469344 1.534403656 1.149708977 1.404453745 0.976746787 1.337048407 1.031545283 1.15432776 1 16.40433878 2.601566071 0.595972695 1.049643402 1.386204109 0.328791441 0.148757213 0.821445693 0.609100143 0.111162575 0.108932034 399.5453413 -2.601566071 0.336560708 YSHSYLS(ph)DS(ph)DTEAKLTETNA ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSHSYLSDSDTEAKLTETNA 20 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 YSHS(0.002)Y(0.001)LS(0.998)DS(1)DTEAKLTETNA;YSHSYLS(0.999)DS(0.999)DT(0.001)EAKLTETNA;YSHSYLS(1)DS(0.999)DT(0.001)EAKLTETNA;Y(0.005)S(0.001)HS(0.011)Y(0.208)LS(0.782)DS(0.99)DT(0.003)EAKLTETNA 225.26 2.97E-25 657288000 749601 535047 661698 683494 471041 667102 837482 719149 701297 TRUE FALSE 714168.8463 589568.8976 692037.5078 614787.8846 553190.4013 644000.0905 709708.7395 656176.5011 810050.557 0.881634905 0.727817409 0.854313971 0.758950018 0.682908488 0.795012219 0.876128944 0.810043886 1 19.62765243 0.621706703 0.856843935 0.99903339 0.786818257 0.515902677 0.062345615 1.022769547 1.281674477 0.060015025 0.020099319 4.185108322 -0.621706703 -0.212215133 YSHSYLS(ph)DSDT(ph)EAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 YSHSYLS(0.999)DS(0.206)DT(0.795)EAK 311.08 1.32E-32 0 685380 695930 551300 776860 371450 723890 596310 626680 378010 TRUE FALSE 652983.4457 766846.0582 576577.6503 698768.5569 436230.7624 698821.5078 505331.9575 571804.577 436629.8602 1.495507993 1.756284048 1.320518139 1.600368231 0.999085959 1.600489503 1.15734631 1.309586515 1 18.73605127 2.448745249 0.230837851 0.945047629 1.802104938 0.397423825 0.199766941 2.911599485 0.425879841 0.436568194 0.849278359 281.0251893 -2.448745249 0.857057309 YSHSYLS(ph)DSDTEAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 YSHSYLS(1)DSDTEAK 291.2 1.86E-43 98415000 216230 202130 180320 240530 131570 213370 227930 232780 123680 TRUE FALSE 206009.2364 222727.2768 188587.8504 216351.4674 154515.7663 205980.9434 193155.0923 212396.5492 142859.6627 1.442039219 1.559063437 1.320091667 1.514433559 1.081591286 1.441841171 1.352061797 1.486749619 1 17.12423909 -3.794047299 0.193786689 2.33E-15 1.484757161 0.448504986 0.135932039 71.69517058 1.073795421 29.00899611 0.338057568 0.000160677 3.794047299 1.484757161 YSHSYLSDS(ph)DTEAKLTETNA ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSHSYLSDSDTEAKLTETNA 20 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 YSHSYLSDS(1)DTEAKLTETNA;YSHSYLSDS(1)DTEAKLTETNA;YS(0.001)HS(0.001)YLS(0.022)DS(0.842)DT(0.134)EAKLTETNA 336.46 2.92E-80 457351000 622246 341132 594419 516909 424967 559033 758320 625640 521169 TRUE FALSE 592833.6648 375893.7386 621673.6991 464948.3253 499081.1103 539673.547 642624.3565 570855.6449 601989.2268 0.984791153 0.624419378 1.032699044 0.772353233 0.829053226 0.896483729 1.067501424 0.948282161 1 19.19937814 1.948538147 4.649778475 1.008682833 0.836737545 0.278736411 0.113986633 0.242411898 10.98392125 0.048053567 0.028965786 88.82559935 -1.948538147 -0.171945288 YSHVNKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSHVNKK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 114.6 0.0038093 150340000 401210 323750 364740 419840 340410 392440 463020 419360 345120 FALSE TRUE 382245.5984 356740.4931 381463.6898 377636.8856 399777.3962 378849.7044 392377.7951 382638.6152 398639.447 0.958875498 0.894895113 0.956914055 0.947314393 1.002854583 0.950356788 0.984292443 0.959861394 1 18.60472495 3.219528127 2.089565082 0.976072454 0.927981276 0.404326365 0.023724054 0.263650915 2.364515285 0.0067805 0.009180001 1657.784699 -3.219528127 -0.048091178 YSLS(ph)PSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSLSPSK 7 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;F8W705;Q99666-2;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;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 YSLS(0.994)PS(0.006)K;YSLS(0.999)PS(0.001)K;YSLS(1)PSK;YSLS(1)PSK 204.86 0.00026618 1577210000 5949200 4982760 3985350 5038000 3865190 5362300 6370400 6258900 4460790 TRUE FALSE 5667993.106 5490508.909 4168082.24 4531570.668 4539277.912 5176602.206 5398478.48 5710837.535 5152546.531 1.100037248 1.06559133 0.808936361 0.879481756 0.880977568 1.004668696 1.047730175 1.108352443 1 22.2968542 1.830982354 3.48737665 1.058418152 0.966570048 0.20090077 0.090546613 0.509089811 10.68709982 0.054505687 0.028676714 67.7613975 -1.830982354 -0.091848104 YSNFVSFPLYLNGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSNFVSFPLYLNGR 14 0 Q12931-2;Q12931;I3L0K7;I3L239;I3L2D5 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 205.8 2.73E-08 37517000 157930 134050 122680 116100 153240 112610 189730 145090 173050 FALSE TRUE 150464.9619 147709.8474 128304.9993 104429.4074 179965.0075 108710.2875 160783.2039 132385.1504 199885.7102 0.752754971 0.738971522 0.641891805 0.522445588 0.900339536 0.543862227 0.804375679 0.662304225 1 17.60881581 -2.01569834 0.620534773 1.305261376 0.701491751 0.412317581 0.113739241 151.5612437 14.72550632 65.97270317 0.039168159 0.009644987 2.01569834 -0.603769625 YSPNCK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YSPNCK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 129.96 0.037149 1690140000 2662940 2316170 2296610 2795800 1977960 2604040 2841770 2695650 2266990 FALSE TRUE 2537068.104 2552190.356 2401911.84 2514760.872 2322915.598 2513861.442 2408205.794 2459604.595 2618543.231 0.968885323 0.974660386 0.917270264 0.960366376 0.887102252 0.960022891 0.919673873 0.93930265 1 21.32033299 3.755979357 23.90716174 0.936073175 0.971772863 0.14247553 0.030364693 611.7083332 839562.9613 0.006692459 0.012023123 5701.371715 -3.755979357 0.035699687 YSPPAIS(ph)PLVSEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK 251.91 1.01E-23 146194000 426230 343340 394900 433810 324820 402460 461800 425840 375970 TRUE FALSE 406082.9526 378326.7363 413006.5556 390202.5946 381468.5052 388522.7093 391343.9285 388551.1921 434273.5074 0.935085714 0.871171577 0.951028669 0.898518072 0.878406117 0.894649806 0.901146217 0.894715394 1 18.72824442 -1.530342404 4.208214845 1.001032145 0.90224011 0.619595872 0.023855478 0.000213622 2.38E-05 0.021359536 0.004982382 0.029488834 1.530342404 -0.098792035 YSPS(ph)QNSPIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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(0.423)PS(0.577)QNSPIHHIPSRR 198.24 1.94E-11 692990000 91875 85333 72301 113380 100030 88974 103280 89667 55992 TRUE FALSE 87532.25083 94028.52972 75616.07237 101982.827 117475.2003 85892.80807 87522.73913 81815.28213 64674.95339 1.353418074 1.453863123 1.169170883 1.57685196 1.816394047 1.328069114 1.353271004 1.265022668 1 15.98091949 0.975917819 1.294704637 1.005430902 1.446801103 0.421993439 0.168031219 0.496247536 1.699060427 0.157596494 0.048151378 9.460581237 -0.975917819 0.441370201 YSPSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Trastuzumab_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 YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR 182.34 9.20E-07 793690000 312560 328695 303893 374610 294823 317087 337905 351651 177782 TRUE FALSE 297785.9082 362189.3942 317826.7946 336953.4911 346240.0379 306106.1977 286351.3862 320858.5742 205351.5246 1.450127574 1.76375313 1.547720648 1.640861892 1.686084574 1.490644875 1.3944449 1.5624845 1 17.64773613 0.085814134 0.460882545 0.935670612 1.624258356 0.747965601 0.1050123 1.796974307 0.518009361 0.326286898 0.057103279 1.218468018 -0.085814134 0.688587744 YSPSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Trastuzumab_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 YSPSQNS(1)PIHHIPSRR;YSPSQNS(1)PIHHIPSRR;YSPSQNS(1)PIHHIPSRR;YSPSQNS(1)PIHHIPSRR 182.82 9.79E-10 1990630000 927630 700880 906890 949430 873660 868740 1137020 1049490 371717 TRUE FALSE 883782.7683 772300.4688 948471.8035 853991.4926 1026026.027 838655.316 963546.7162 957591.0919 429360.9739 2.058367719 1.798720694 2.209031238 1.988982568 2.389658329 1.95326396 2.244141351 2.230270449 1 18.71183154 -1.184104516 6.629341442 0.999995746 2.090503553 0.806300621 0.170617478 1.06E-05 1.31E-06 0.163533434 0.03854505 0.065447865 1.184104516 1.090507806 YSPT(ph)SPTYSPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.469)S(0.469)PT(0.007)Y(0.054)SPT(0.193)S(0.807)PK 165.34 2.11E-05 93587000 323950 295500 300330 337750 198100 355770 350350 349950 200080 TRUE FALSE 308637.5255 325611.786 314100.4276 303798.7283 232648.5773 343449.5957 296897.6729 319306.5228 231107.3845 1.335472366 1.408919869 1.359110304 1.314534925 1.00666873 1.486103944 1.284674107 1.38163704 1 17.81820383 -1.321193762 3.582294158 0.998797358 1.326395093 0.395738514 0.125001272 6623612.276 4886262.329 56771.48586 0.027189499 0.047731627 1.321193762 0.327597735 YSPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.132)S(0.868)PK;YSPT(0.028)S(0.972)PK;YSPT(0.164)S(0.836)PK;YSPT(0.012)S(0.988)PK;YSPT(0.238)S(0.762)PK 148.62 0.002173 3061300000 10066700 9129100 9026100 10417500 5581390 10036700 10571600 10571800 5985920 TRUE FALSE 9590867.041 10059365.67 9439955.613 9370313.108 6554782.649 9689126.562 8958708.259 9646077.147 6914185.902 1.387128894 1.454887938 1.365302546 1.355230137 0.94801944 1.401340187 1.295699651 1.395113942 1 22.72112796 -5 0.116269361 0.007489819 1.495876832 0.339629984 0.141030632 180.5126034 1.37388402 43.18298314 1.445028194 1.00E-05 5 1.488387013 YSPTS(ph)PTYS(ph)PTSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.01)S(0.719)PT(0.017)Y(0.254)S(0.999)PT(0.001)SPK;YSPT(0.001)S(0.978)PT(0.018)Y(0.003)S(0.989)PT(0.01)S(0.001)PK;YSPT(0.024)S(0.921)PT(0.018)Y(0.037)S(0.999)PTSPK 206.55 1.56E-08 981810000 765010 689210 728740 800790 522710 802800 864620 831420 615120 TRUE FALSE 728849.4934 759441.2826 762153.4498 720293.0678 613870.4585 774998.8347 732706.3392 758616.4572 710509.668 1.025812211 1.06886833 1.072685544 1.013769552 0.863986074 1.090764658 1.031240491 1.067707438 1 19.43849475 -0.171822003 19.44061147 1 1.031317269 0.019839466 0.063523937 0 0 0.058823638 0.013864864 0.673252535 0.171822003 0.031317269 YSPTS(ph)PTYSPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.018)S(0.957)PT(0.023)Y(0.002)SPT(0.023)S(0.977)PK;Y(0.002)S(0.001)PT(0.388)S(0.536)PT(0.013)Y(0.061)SPT(0.047)S(0.953)PK 243.95 2.14E-17 300870000 951160 830830 929780 964440 539950 1005230 962540 1018500 554450 TRUE FALSE 906200.5518 915492.5216 972411.3327 867492.6589 634117.109 970418.633 815686.8447 929314.7406 640431.2743 1.414984852 1.429493778 1.51836953 1.354544498 0.990140761 1.515258033 1.273652424 1.451076451 1 19.28868424 -3.989607718 0.194195436 1.16E-13 1.43901744 0.357857931 0.153377091 97.9625732 1.372459495 39.2252232 0.38147999 0.000102422 3.989607718 1.43901744 YSPTS(ph)PTYSPTSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.021)S(0.961)PT(0.015)YS(0.002)PTSPK;YSPT(0.019)S(0.962)PT(0.019)YSPTSPK 179.5 1.95E-06 187451000 613860 573360 565670 675830 461880 636260 681550 690560 564610 TRUE FALSE 584844.0544 631786.0359 591606.529 607894.2844 542431.7258 614226.1567 577567.03 630090.9055 652166.8352 0.896770616 0.968749102 0.907139856 0.932114685 0.831737673 0.941823662 0.885612391 0.966149874 1 19.31488155 1.043842327 5.026257756 0.999691154 0.912834965 0.427607782 0.036483076 0.157558226 8.745794454 0.032992477 0.008347806 11.0622209 -1.043842327 -0.086856189 YSPTS(ph)PTYSPTT(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.099)S(0.899)PTY(0.002)SPT(0.025)T(0.975)PK 184.87 6.60E-06 17331000 56208 51454 54756 61999 31764 54072 61551 67231 41419 TRUE FALSE 53551.15923 56697.2211 57266.61676 55766.74273 37303.63154 52199.47308 52160.26449 61343.89723 47842.04698 1.119332525 1.185091874 1.196993448 1.165642907 0.779724822 1.091079424 1.090259882 1.282217236 1 15.5459915 YSPTS(ph)PTYSPTTPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTS(0.999)PTYSPTTPK;YSPT(0.106)S(0.894)PTYSPTTPK;YSPT(0.001)S(0.875)PT(0.123)YSPTTPK;YSPTS(0.998)PT(0.002)YSPTTPK 286.74 8.01E-34 2209620000 4640180 4101010 4269850 4763520 3221020 4486000 5080420 4734880 3778020 TRUE FALSE 4420847.887 4518907.581 4465626.846 4284681.92 3782764.868 4330648.695 4305308.621 4320268.806 4363896.046 1.013050687 1.035521363 1.023311921 0.981847843 0.86683203 0.992381269 0.986574514 0.990002686 1 22.0571853 3.178204723 4.746127291 0.96618864 1.025068823 0.315895208 0.038023737 0.230208059 10.36411108 0.011005858 0.013537055 1507.317438 -3.178204723 0.058880183 YSPTSPTYS(ph)PTSPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.995)PT(0.005)SPK 281.65 2.59E-33 348280000 112260 104440 106420 117230 80975 111000 125650 121140 96260 TRUE FALSE 106953.6923 115082.5547 111299.4623 105445.8177 95097.01436 107156.0422 106479.7848 110532.3394 111187.5092 0.96192183 1.035031323 1.001006886 0.948360283 0.85528505 0.963741728 0.957659593 0.994107524 1 16.7626352 3.238799742 9.169904751 0.947809892 1.001680637 0.197956885 0.042781284 0.139374207 152.254242 0.011883665 0.015128444 1733.004705 -3.238799742 0.053870745 YSPTSPTYSPT(ph)SPK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPT(0.002)YS(0.171)PT(0.816)S(0.011)PK;YSPTSPTYS(0.009)PT(0.815)S(0.176)PK 225.32 3.15E-11 548940000 869650 825980 786480 973660 598700 976680 1005030 1055500 714600 TRUE FALSE 828543.368 910148.3011 822540.8859 875785.847 703113.0904 942857.3267 851694.2149 963074.8244 825416.5183 1.003788208 1.102653365 0.996516144 1.061022923 0.851828228 1.142280662 1.03183568 1.166774353 1 19.65476278 YSPTSPTYSPTS(ph)PK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYSPT(0.204)S(0.796)PK 281.1 2.78E-33 180210000 355240 315760 311200 377660 221180 360570 399370 412020 284720 TRUE FALSE 338448.5092 347936.303 325468.8278 339696.8993 259753.722 348083.3705 338438.7716 375941.3445 328872.9235 1.02911637 1.057965792 0.989649207 1.032912335 0.789830063 1.058412979 1.029086761 1.14312039 1 18.32717071 -0.085515075 8.448400308 1 1.016531661 0.003237284 0.089564471 0 4.28E-18 0.081708482 0.019258874 0.821268045 0.085515075 0.016531661 YSQFINFPIYVWSSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSQFINFPIYVWSSK 15 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 167.55 3.03E-06 52466000 143280 138400 63868 82576 113880 85694 147710 116410 93967 FALSE TRUE 136507.4384 152503.1173 66796.41097 74275.3036 133740.6359 82726.39529 125174.1266 106216.5233 108538.9224 1.257681901 1.405054647 0.615414355 0.684319523 1.232190563 0.762181837 1.153264873 0.978603075 1 16.72785297 3.763032116 24.96426663 0.931571815 1.331368331 0.432519986 0.196371375 660.9218313 674228.0609 0.04901067 0.088303954 5794.715471 -3.763032116 0.399796517 YSQKEDKYEEEIK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 183.41 5.84E-06 7705790000 10300730 9847640 9618080 12180270 4190670 12467950 11226500 13661510 3975980 FALSE TRUE 9813834.907 10851125.71 10059078.48 10955886.12 4921521.521 12036181.77 9513691.236 12465235.76 4592554.672 2.136901051 2.362764624 2.190301303 2.385575546 1.07163047 2.620803153 2.071546648 2.714226972 1 22.13086547 -1.265759462 7.077969983 0.999992449 2.188358998 0.413695557 0.446745787 4.74E-05 4.92E-06 0.385336538 0.090824117 0.054230117 1.265759462 1.188366549 YSS(ph)QDADEQDWEFQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YS(0.18)S(0.82)QDADEQDWEFQKR 115.54 0.000305 216340000 100880 98297 101420 125030 73510 107360 110900 107870 112970 TRUE FALSE 96111.60232 108313.5761 106070.2073 112461.7469 86330.12073 103642.0963 93980.16818 98424.33095 130488.8106 0.736550528 0.83006026 0.812868221 0.861849735 0.661590218 0.79426041 0.720216298 0.754274106 1 16.99356658 -1.253859368 4.819068849 1.000057738 0.772403631 0.606980549 0.057790089 3.42E-05 5.30E-06 0.053446106 0.012594178 0.05573662 1.253859368 -0.227654107 YSSDYFQAPSDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSSDYFQAPSDYR 13 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 210.15 7.49E-08 583770000 385400 351820 288170 369890 406160 303960 426430 354710 319600 FALSE TRUE 367182.9058 387670.858 301382.8795 332707.9545 476994.1754 293433.789 361370.2716 323649.712 369161.9357 0.994639128 1.050137678 0.816397495 0.901252058 1.292100104 0.794864694 0.978893642 0.876714744 1 18.49389428 YSSNLGNFNYER ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSSNLGNFNYER 12 0 Q9BZZ5-2;Q9BZZ5-5 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 211.46 7.35E-08 196525000 128486 104305 80898 89523 130214 82449 146465 120508 148183 FALSE TRUE 122412.7214 114933.7981 84607.25332 80523.97796 152923.2804 79593.77046 124119.0742 109955.6807 171162.4628 0.715184389 0.671489509 0.494309628 0.47045349 0.893439355 0.465018843 0.725153589 0.642405343 1 17.38500682 -0.228389687 0.785486877 1.014798057 0.633410232 0.430799394 0.132388285 8.633367009 4.487500602 0.51906273 0.040997755 0.591031072 0.228389687 -0.381387826 YSSQDADEQDWEFQKR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 163.41 1.24E-08 228370000 137210 140000 137880 154110 120480 155070 155110 168980 137650 FALSE TRUE 130724.3552 154266.1592 144201.9344 138618.57 141491.6739 149699.887 131445.1207 154183.2154 158996.059 0.822186135 0.970251465 0.906952885 0.871836515 0.889906799 0.94153206 0.826719364 0.969729793 1 17.27863148 1.05189396 7.894355695 0.99992014 0.892752239 0.439653585 0.045189714 0.184115561 23.17555922 0.041158047 0.010309173 11.26922266 -1.05189396 -0.107167902 YSSS(ph)GSPANSFHFK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 YS(0.062)S(0.095)S(0.421)GS(0.421)PANSFHFK;YS(0.077)S(0.061)S(0.482)GS(0.38)PANSFHFK 127.22 5.21E-05 273900000 438770 476060 454230 549210 451320 491200 657260 633020 559080 TRUE FALSE 418030.2117 524571.0552 475056.8948 494002.3674 530030.0651 474189.6208 556982.9156 577589.4129 645779.271 0.647326773 0.812307051 0.735633546 0.764970927 0.820760419 0.734290557 0.862497359 0.894406865 1 19.30068161 -4.999999983 0.0533837 1.976028797 0.327283585 0.788343849 0.044924738 211.3886198 0.831064546 27.86638856 5.644355913 1.00E-05 4.999999983 -1.648745212 YSSSFCTHDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YSSSFCTHDR 10 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 ;;;; 170.02 4.45E-06 2370612000 2216380 2106450 1784110 2228540 2164990 1929180 2464460 2291350 2076170 FALSE TRUE 2111616.11 2321099.65 1865913.208 2004522.925 2542563.571 1862372.013 2088461.364 2090707.247 2398131.84 0.880525447 0.967878251 0.778069486 0.835868526 1.060226768 0.776592839 0.87087012 0.871806634 1 21.19347954 YSSSSIPEPFGSRGS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSSSSIPEPFGSRGSPR 17 1 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSSSIPEPFGS(0.111)RGS(0.889)PR;YSSSSIPEPFGS(0.19)RGS(0.81)PR 87.963 0.0026727 776750000 575620 421780 548390 512570 561370 534720 670640 569690 577190 TRUE FALSE 548411.5834 464759.8615 573534.2239 461045.4898 659272.7503 516202.5123 568321.5509 519804.9235 666697.6773 0.822579112 0.697107366 0.86026132 0.691536067 0.988863127 0.774267753 0.852442674 0.779671118 1 19.34667318 -4.999999999 0.155453931 1.714527114 0.746932425 0.329449404 0.085485111 138.3041398 1.254182826 30.49161704 0.345811384 1.00E-05 4.999999999 -0.967594689 YSTVS(ph)LQEDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSTVSLQEDR 10 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 YST(0.027)VS(0.973)LQEDR 76.262 0.038313 93152000 100550 110690 89122 108230 78750 83956 105020 88198 90997 TRUE FALSE 95797.20077 121969.4368 93208.33185 97350.51478 92483.97507 81048.58267 88997.27018 80474.91555 105108.35 0.911413801 1.160416245 0.886783323 0.926192018 0.879891798 0.771095566 0.846719316 0.765637702 1 16.68151776 3.292779805 1.734338486 0.840523189 1.03096077 0.318036267 0.093940508 0.311234397 1.929628474 0.028044676 0.041365029 1962.365073 -3.292779805 0.190437581 YSVDIPLDK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSVDIPLDK 9 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 122.33 0.0013699 174108000 668070 634840 640450 735780 587380 712210 824830 733620 705000 FALSE TRUE 636491.6551 699530.9178 669815.266 661817.9965 689818.886 687545.9891 698987.0345 669380.3436 814327.7994 0.781616022 0.859028659 0.82253764 0.812716939 0.847102219 0.844311087 0.858360767 0.822003552 1 19.63525013 -5 0.239786963 1.957480052 0.815256464 0.851462259 0.022360911 59.30244656 0.591299693 27.67632337 0.033024197 1.00E-05 5 -1.142223589 YSVLNNDDYFADVS(ph)PLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSVLNNDDYFADVSPLR 17 0 Q1ED39;H3BMC9 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 YSVLNNDDYFADVS(1)PLR 104.89 0.0008687 15801000 36293 33462 28905 41450 37379 35357 35023 34871 33443 TRUE FALSE 34577.50182 36871.81584 30230.32284 37283.36725 43897.88577 34132.57822 29679.59811 31817.51038 38629.16964 0.895113774 0.954507078 0.782577599 0.965160981 1.136392166 0.88359596 0.768320893 0.823665398 1 15.23740305 2.003439445 24.99955067 0.835179566 0.942613753 0.102563597 0.104262572 167.623096 1218357.734 0.03795459 0.027892802 100.7951057 -2.003439445 0.107434187 YSYLTEPGMS(ph)PQSPCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.993)PQS(0.007)PCER 168.5 2.19E-09 167160000 82803 74064 73756 77128 81899 63486 86922 70287 79339 TRUE FALSE 78889.06629 81611.2058 77137.78555 69374.94691 96182.15967 61287.4639 73660.45247 64132.29767 91642.48691 0.860835066 0.890538969 0.841725145 0.757017288 1.04953677 0.668766922 0.803780593 0.699809661 1 16.48372899 2.20650729 24.99997874 0.775779165 0.872318093 0.117777848 0.112735048 343.8665835 268196.6703 0.036968892 0.02730544 160.8819385 -2.20650729 0.096538927 YSYLTEPGMSPQS(ph)PCER ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.085)PQS(0.915)PCER;YSYLTEPGMS(0.052)PQS(0.948)PCER;YSYLTEPGMS(0.001)PQS(0.999)PCER;YSYLTEPGMS(0.005)PQS(0.995)PCER 302.9 6.22E-46 921540000 1086866 831841 997728 1150886 1179741 867064 1084678 843847 966672 TRUE FALSE 1035491.998 916606.5436 1043474.816 1035196.753 1385487.457 837037.3563 919190.4496 769955.2832 1116578.557 0.927379441 0.820906454 0.934528797 0.927115022 1.240832943 0.749644843 0.823220582 0.689566604 1 20.09065332 YSYYDESQGEIYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YSYYDESQGEIYR 13 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ; 284.1 2.83E-32 274610000 97507 98464 95560 104666 104418 95566 115417 111155 102165 FALSE TRUE 92898.03735 108497.5935 99941.52052 94144.77483 122628.4661 92256.52546 97808.01687 101421.6789 118008.2264 0.787216622 0.919407035 0.846902996 0.797781457 1.039151844 0.781780459 0.828823717 0.859445837 1 16.84852791 -2.549575379 1.965636806 2.723595209 0.856743057 0.25739649 0.076021304 2526591.476 155783.7159 19387128.59 0.01893555 0.00282114 2.549575379 -1.866852152 YT(ph)LENKEEGSLSDTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 34 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 Y(0.229)T(0.248)LENKEEGS(0.122)LS(0.201)DT(0.201)EADAVSGQLPDPTTNPSAGK 83.26 0.0010393 143170000 159430 140670 140070 169290 86474 159660 164680 179740 96966 TRUE FALSE 151894.0599 155004.4329 146492.348 152272.6476 101555.0382 154130.9342 139555.0414 164001.0127 112002.992 1.356160734 1.38393118 1.307932452 1.359540891 0.90671719 1.376132292 1.245993869 1.464255639 1 16.77317775 -2.247723557 2.107559766 2.84E-05 1.300541157 0.281626946 0.150618085 2332936.351 342668.2645 11135073.28 0.035769501 0.005652967 2.247723557 1.300512774 YT(ph)T(ph)T(ph)QQVVKLIGS(ph)HTISKVTVKIGDLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTTTQQVVKLIGSHTISKVTVKIGDLK 27 3 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 4 Y(0.525)T(0.55)T(0.55)T(0.55)QQVVKLIGS(0.55)HT(0.55)IS(0.55)KVT(0.175)VKIGDLK 49.25 0.066962 155640000 85530 74152 98591 81144 153480 67320 126830 64922 196680 TRUE FALSE 81487.1664 81708.1731 103111.4949 72987.25096 180246.8634 64988.69152 107479.7541 59237.08551 227180.1299 0.358689673 0.359662498 0.453875499 0.321274801 0.793409457 0.286066794 0.473103674 0.260749413 1 17.79347713 -2.052683724 2.658417893 1.809379759 0.413813372 0.60052546 0.150368288 46267176.99 15026029.48 227747769.5 0.033151129 0.008857604 2.052683724 -1.395566387 YTCGEAPDYDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 11 YTCGEAPDYDR 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;;;; 309.63 3.28E-45 19817653000 17120617 16144820 14512722 18028999 15128168 15052080 16425550 16165724 13549552 FALSE TRUE 16311359.36 17789995.51 15178144.66 16216689.77 17766515.71 14530822.7 13919530.67 14750167.51 15650747.32 1.042209616 1.136686648 0.969803189 1.03616073 1.135186413 0.928442738 0.88938441 0.942457712 1 23.89972821 2.218936868 24.68675379 0.926323986 1.06639012 0.547536773 0.055336907 137.8808736 173453.4105 0.019978912 0.01477678 165.5529285 -2.218936868 0.140066134 YTEFYHVPTHSDASK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 194.23 3.48E-08 599530000 1898080 1543620 1548780 1856540 1397810 1751870 2011250 1848350 327970 FALSE TRUE 1808361.52 1700916.633 1619793.095 1669917.072 1641587.621 1691202.303 1704396.873 1686498.675 378829.9126 4.773544697 4.489921668 4.275779291 4.408091908 4.333310457 4.464278682 4.499108483 4.451862483 1 18.53119073 0.811766545 11.50903978 1.000000001 4.475361089 0.985717872 0.130957439 98.73106583 6037.428139 0.136919352 0.034237524 6.482858532 -0.811766545 3.475361088 YTGEDFDEDLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YTGEDFDEDLR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 174.73 2.48E-05 629196000 950360 882310 828270 1027640 857600 935230 967280 944420 908960 FALSE TRUE 905438.3662 972218.3921 866246.9988 924339.6748 1007165.168 902842.7506 819703.6707 861721.5781 1049916.874 0.862390527 0.925995587 0.82506246 0.880393198 0.959280866 0.859918316 0.780731971 0.820752194 1 20.00184368 2.005495413 24.99400876 0.837179985 0.891116273 0 0.067604113 289.0875864 1314809.553 0.0230217 0.016953437 101.2734053 -2.005495413 0.053936289 YTIENPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YTIENPR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 149.99 0.0046034 1456000000 2033370 1792990 1818620 2145250 2035280 1823730 2233510 1988420 2245170 FALSE TRUE 1937256.63 1975697.719 1902005.526 1929605.394 2390232.188 1760573.773 1892747.028 1814303.404 2593339.497 0.747012349 0.761835356 0.733419411 0.744062008 0.921681172 0.678882875 0.729849305 0.699601192 1 21.30637965 -1.515893848 5.932558 1.000333065 0.751963109 0.590471563 0.064896499 0.000267955 2.19E-05 0.05889453 0.013863247 0.030486401 1.515893848 -0.248369955 YTIHSQLEHLQSK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTIHSQLEHLQSK 13 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 162.93 2.29E-05 138320000 283580 309790 224900 337790 234840 322160 350500 343850 64281 FALSE TRUE 270175.7354 341357.9532 235211.8875 303834.7074 275796.0216 311003.5184 297024.7876 313740.6711 74249.36918 3.638761358 4.597452571 3.167863782 4.092084698 3.714456092 4.188635161 4.000367827 4.225499484 1 16.18009115 -1.27410366 10.69287335 0.999999948 3.977875562 0.852194666 0.386389248 4.16E-07 2.90E-08 0.335717366 0.07912934 0.053198127 1.27410366 2.977875613 YTISQEAYDQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTISQEAYDQR 11 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 130.23 0.00053153 252480000 105980 91685 66088 85864 85746 81649 103740 87497 87413 FALSE TRUE 100970.5354 101027.8057 69118.20017 77232.78759 100700.0753 78821.47466 87912.55768 79835.29883 100968.5616 1.000019549 1.000586758 0.684551697 0.764919163 0.997340892 0.780653635 0.870692385 0.790694624 1 16.62354663 3.802617798 23.38497975 0.837558787 1.000303936 0.310546747 0.098396928 107.820452 39360.43689 0.023172975 0.041775664 6347.720532 -3.802617798 0.162745149 YTLENKEEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 34 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 YT(0.005)LENKEEGS(0.037)LS(0.786)DT(0.171)EADAVSGQLPDPTTNPSAGK 236.89 3.60E-47 127240000 335970 312910 288640 368540 183840 380750 352050 392460 200280 TRUE FALSE 320089.3639 344795.8847 301874.4295 331493.659 215901.6378 367564.532 298338.3067 358094.1218 231338.3995 1.3836413 1.490439484 1.304904115 1.432938326 0.933271944 1.588860876 1.289618616 1.5479234 1 17.81964523 -2.072542318 2.692432911 0.414997742 1.373106874 0.290390412 0.18246613 2963987.568 5007040.313 10602236.04 0.039977122 0.008461701 2.072542318 0.958109132 YTLETRPNQEGIDVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YTLETRPNQEGIDVR 15 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ;; 110.97 0.00080181 426240000 824730 818510 771080 911340 809870 807920 872290 871560 858460 FALSE TRUE 785746.6474 901917.0996 806434.7807 819730.3718 951111.0716 779941.5278 739206.1398 795241.586 991585.5924 0.792414345 0.909570597 0.813278034 0.826686449 0.95918202 0.786559964 0.745478903 0.801989856 1 19.91937778 YTLHYK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YTLHYK 6 0 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 118.06 0.022193 1406980000 6471900 4639400 3688500 4076900 5158500 3781900 6302000 5186100 4758900 FALSE TRUE 6165986.113 5112160.135 3857621.373 3667082.266 6058140.767 3650931.855 5340514.156 4731977.591 5496885.907 1.121723503 0.930010231 0.701783053 0.667119953 1.102104149 0.664181851 0.971552666 0.860846972 1 22.3901831 4.266852662 2.576952818 0.849004572 1.100373004 0.243183231 0.146713254 0.347266852 4.481122713 0.034613936 0.12030322 18486.41348 -4.266852662 0.251368432 YTPEEIAMATVTALRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YTPEEIAMATVTALRR 16 1 P09972;A8MVZ9 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 182.57 3.40E-09 92428000 170660 118690 142240 172620 208920 141390 219300 157220 189200 FALSE TRUE 162593.24 130784.6459 148761.8447 155267.9096 245355.5819 136493.6288 185841.7573 143452.9833 218540.1697 0.743997043 0.598446712 0.680707098 0.710477666 1.12270244 0.624569977 0.850378022 0.656414716 1 17.73753896 2.980068376 24.93764857 0.832908776 0.671498177 0.237881211 0.148113183 1065.450899 1333050.981 0.040820449 0.043841212 955.1429528 -2.980068376 -0.161410599 YTQLQYIGEGAYGMVSSAYDHVR ddPTM_SK-BR-3_Trastuzumab_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 0 171.52 6.08E-12 68547000 135710 122830 128590 138160 136800 126890 145580 136700 129950 FALSE TRUE 129295.2573 135346.5166 134485.9787 124271.8943 160657.8767 122495.7675 123369.0972 124729.8233 150101.9823 0.861382743 0.901697063 0.895964041 0.82791641 1.070324817 0.816083609 0.821901852 0.830967196 1 17.1955835 -0.231490262 7.335744084 1 0.877212644 0.208833036 0.074430282 0 0 0.068085553 0.016047919 0.586826527 0.231490262 -0.122787356 YTQVGPDHNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 8 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 129.89 0.00029116 5209810000 3674372 3469408 3336519 4086450 3839963 3695615 3950900 3561709 3615510 FALSE TRUE 3500691.717 3822944.62 3489501.696 3675672.282 4509651.331 3567634.926 3348117.642 3249826.878 4176184.825 0.838251146 0.915415572 0.835571662 0.880150768 1.079849556 0.854280899 0.801716826 0.778180807 1 21.99375413 -0.742794677 5.084058916 1.000000033 0.87373017 0.188739739 0.082780035 4.75E-08 1.19E-08 0.079700424 0.018785563 0.180802871 0.742794677 -0.126269863 YTRPTPVQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 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 ; 111.06 0.0019942 716240000 665860 531660 566680 612990 513530 639680 703110 694680 592780 FALSE TRUE 634386.1174 585836.7584 592662.8385 551371.0806 603089.4694 617527.7212 595837.656 633850.1365 684705.2949 0.926509729 0.855604247 0.865573617 0.805267733 0.880801527 0.901888339 0.870210382 0.925726939 1 19.38512364 0.869100181 1.482060183 1.000366786 0.871275933 0.636217782 0.031297972 0.376741045 1.600742649 0.029745901 0.008739326 7.397759031 -0.869100181 -0.129090853 YTVQDESHSEWVSCVR ddPTM_SK-BR-3_Trastuzumab_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 ;;;; 256.08 1.25E-26 4097800000 2277008 2664383 2528397 2592121 2020849 2320774 2362918 2559073 1699432 FALSE TRUE 2169378.344 2935886.657 2644326.503 2331556.072 2373284.426 2240405.014 2002411.461 2334987.002 1962971.235 1.105150348 1.49563407 1.347104051 1.187768843 1.209026594 1.141333594 1.020092106 1.189516667 1 20.9046076 2.543689191 1.261366083 1.072310906 1.316331423 0.431286379 0.110427123 0.399744251 1.291326397 0.0566132 0.043908713 349.6948133 -2.543689191 0.244020518 YVAQAHDKPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YVAQAHDKPR 10 1 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 134.75 9.76E-05 1124690000 3726900 3178430 2931300 3273000 2607640 2759950 3076010 3165650 2675460 FALSE TRUE 3550736.823 3502315.631 3065703.004 2943991.822 3062411.59 2664372.239 2606708.18 2888448.904 3090356.672 1.148973144 1.133304664 0.992022388 0.952638201 0.990957328 0.862156871 0.843497517 0.934665222 1 21.55934193 3.528550821 1.056892253 0.900761116 1.165330616 0.730079018 0.051338494 0.232646271 0.524948272 0.018881763 0.043054032 3377.153655 -3.528550821 0.264569501 YVASYLLAALGGNSS(ph)PSAK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNS(0.001)S(0.999)PSAK;YVASYLLAALGGNS(0.014)S(0.98)PS(0.006)AK;YVASYLLAALGGNS(0.191)S(0.806)PS(0.002)AK 390.62 5.47E-127 2734050000 1041757 898299 767064 957224 813453 993929 1227690 1141261 916397 TRUE FALSE 992515.2112 989836.6894 802234.6431 861002.0249 955318.9457 959508.9895 1040383.342 1041326.137 1058507.166 0.937655637 0.935125166 0.7578925 0.813411616 0.902515331 0.906473777 0.982877939 0.983768622 1 20.01359961 1.834630264 2.033241197 0.993586164 0.876671714 0.507581019 0.053689751 0.325617734 2.559235664 0.039022971 0.017701153 68.33296478 -1.834630264 -0.11691445 YVATLGVEVHPLVFHTNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 307.21 6.60E-51 4855268000 3179867 3007786 2922315 3449530 3443831 3116613 3420308 3297881 742452.6 FALSE TRUE 3029560.989 3314282.813 3056306.033 3102776.691 4044434.036 3008683.91 2898477.196 3009101.056 857588.3573 3.532651724 3.864654627 3.563838067 3.61802567 4.716055205 3.508307785 3.379800077 3.508794203 1 19.70992579 0.111066593 0.811042491 0.948073009 3.786280226 0.849081135 0.362188553 1.503223161 1.077485199 0.556158543 0.116366742 1.291417279 -0.111066593 2.838207217 YVAVMPPHIGDQPLTGAYTVTLDGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVAVMPPHIGDQPLTGAYTVTLDGR 25 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 174.99 2.39E-12 201120000 613360 437050 500970 605290 589610 508700 638250 584030 570150 FALSE TRUE 584367.6884 481585.8919 523939.97 544445.0992 692437.7973 491083.5914 540873.2402 532889.2371 658565.9501 0.887333589 0.731264487 0.795577072 0.826713102 1.051432734 0.745686277 0.821289409 0.809166093 1 19.3289684 -1.385476007 2.96469182 1.002585873 0.828314576 0.255799918 0.088820317 13433619.42 16637890.52 298090.1561 0.020625608 0.041164609 1.385476007 -0.174271297 YVDEASKK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YVDEASKK 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;; 105.52 0.0070102 2148170000 3150200 3293710 2641750 3219480 2483660 3187980 3112610 3367430 2477080 FALSE TRUE 3001296.289 3629342.794 2762876.851 2895851.754 2916809.518 3077579.453 2637724.177 3072559.977 2861212.915 1.048959437 1.268463026 0.965631336 1.012106348 1.019431131 1.075620565 0.921890211 1.073866248 1 21.44819543 3.721526806 24.99997721 1.00597428 1.158711241 0.447283351 0.068720784 584.4532853 857783.6821 0.017122677 0.026599864 5266.55721 -3.721526806 0.152736961 YVDEENS(ph)DGETSNHR ddPTM_SK-BR-3_Trastuzumab_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 276.89 9.50E-34 5916730000 3336190 2762540 3129470 3348620 3957630 2908970 3772270 3235030 3878020 TRUE FALSE 3178494.91 3044045.967 3272959.295 3012010.356 4647839.419 2808231.639 3196740.929 2951753.623 4479403.535 0.709579944 0.679565023 0.730668552 0.672413265 1.037602302 0.626920887 0.713653258 0.65896131 1 22.09487521 -1.157301281 3.637289359 1.000228029 0.725309644 0.358547892 0.113974541 149983208.8 260686216.9 416551.3294 0.025392892 0.069614341 1.157301281 -0.274918385 YVDKLEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVDKLEK 7 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 72.547 0.046793 12539000000 477770 408520 458010 505000 350190 529540 529520 540190 347910 FALSE TRUE 455186.7589 450148.6524 479010.2115 454236.4406 411263.0251 511201.897 448731.9987 492888.0999 401862.1059 1.132693907 1.120157004 1.191976562 1.13032912 1.023393396 1.27208286 1.11663178 1.226510518 1 18.61634102 2.246421622 24.99999396 1.162378315 1.124718871 0.035086768 0.081318198 575.1880243 1829249.137 0.025220987 0.020733693 176.3687441 -2.246421622 -0.037659444 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVEAAWYPWWEQQGFFKPEYGRPNVSAANPR 31 2 P26640;A0A140T936;P26640-2;A0A140T954 P26640 VARS Valine--tRNA ligase 0 ; 251.59 2.18E-49 463490000 723070 595690 599500 710640 677930 660060 829730 745300 728720 FALSE TRUE 688891.9141 656391.4882 626987.668 639205.1171 796160.7774 637201.9567 703139.4495 680037.5809 841726.1758 0.818427576 0.779815939 0.744883177 0.759397932 0.94586672 0.757018108 0.835354144 0.80790832 1 19.68299146 -5 0.246897924 2.168544018 0.786571503 0.542782952 0.056572911 132.7960366 1.318799873 78.10399961 0.077416213 1.00E-05 5 -1.381972515 YVEQYVGTEGASS(ph)SPTEGFLLKPVFLQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVEQYVGTEGASSSPTEGFLLKPVFLQR 28 1 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 YVEQYVGTEGASS(0.5)S(0.5)PT(0.001)EGFLLKPVFLQR 301.78 7.92E-72 168090000 249920 220890 230200 253810 231180 230190 280840 250570 279810 TRUE FALSE 238106.7769 243398.9421 240754.8977 228296.5366 271497.7188 222218.4626 237992.7 228628.7624 323201.5057 0.73671308 0.753087278 0.744906485 0.706359756 0.840026157 0.687553921 0.736360121 0.707387677 1 18.30207439 -1.021094797 5.399557639 1.000001348 0.739816528 0.799610728 0.041052723 5.90E-07 1.07E-07 0.035210412 0.008299131 0.095258821 1.021094797 -0.26018482 YVGFGNT(ph)PPPQK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 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 120.14 0.0049426 59745000 330130 335600 280090 363850 260050 324740 355420 357060 318620 TRUE FALSE 314525.4092 369798.0215 292932.4035 327275.1067 305402.6377 313494.1724 301194.1513 325793.9335 368029.9623 0.854619029 1.004804118 0.795947161 0.889262126 0.829830908 0.851816984 0.818395734 0.885237526 1 18.4894637 5.122303616 12.63572936 0.878970059 0.000177881 0.012297587 0.070191532 1778038.293 2466969.353 0.016315492 43608716.54 132526.7708 -5.122303616 -0.878792178 YVGSMVADVHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YVGSMVADVHR 11 0 P09467;A0A3B3IUC7;O00757 P09467 FBP1;FBP2 "Fructose-1,6-bisphosphatase 1;Fructose-1,6-bisphosphatase isozyme 2" 0 ;;;; 189.58 2.65E-06 1123000000 1280050 856670 513513 672437 1371480 731368 1273510 944370 1042630 FALSE TRUE 1219544.573 943965.647 537058.079 604842.3552 1610665.678 706040.5428 1079212.66 861675.9564 1204315.735 1.01264522 0.783819076 0.445944583 0.502229056 1.33741147 0.586258671 0.896121032 0.715490075 1 20.19978224 YVIS(ph)DEEEEDDD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVISDEEEEDDD 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 YVIS(1)DEEEEDDD;YVIS(1)DEEEEDDD 274.62 8.83E-28 540310000 590120 547310 559260 608780 605200 556040 661390 589070 618270 TRUE FALSE 562226.1971 603081.5112 584902.6242 547584.2778 710746.6884 536784.1954 560482.8082 537487.9079 714148.1539 0.787268292 0.844476749 0.819021405 0.766765656 0.995237031 0.751642628 0.784827077 0.752628016 1 19.44586387 4.677007005 3.516043846 0.827281889 0.784973815 0.016256096 0.09139041 1.404682467 28.9361098 0.019968613 0.140770438 47534.28931 -4.677007005 -0.042308074 YVIYIER ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 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 ;;;;; 138.85 0.0063879 1587612000 2181530 2162350 1809030 2208220 2156660 1780490 2238540 2104350 2230120 FALSE TRUE 2078413.4 2382695.923 1891975.815 1986245.53 2532780.821 1718831.185 1897009.609 1920081.958 2575955.62 0.806851401 0.924975533 0.734475315 0.771071332 0.983239308 0.667259627 0.736429461 0.745386273 1 21.29667631 2.216047379 24.99926876 0.758709322 0.843455316 0.033830122 0.11150448 487.8409314 541707.5374 0.037963438 0.028058134 164.4551126 -2.216047379 0.084745994 YVLGQLVGLNS(ph)PNSILK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVLGQLVGLNSPNSILK 17 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 YVLGQLVGLNS(1)PNSILK;YVLGQLVGLNS(1)PNSILK 265.43 1.57E-27 121465000 334050 381790 368730 444340 267670 390870 442140 416010 339350 TRUE FALSE 318260.1185 420694.8351 385636.6352 399674.099 314351.5633 377334.0739 374683.4225 379581.959 391974.6648 0.811940534 1.073270476 0.983830512 1.019642683 0.801969085 0.96264914 0.955886837 0.968383911 1 18.58040088 0.965019672 1.760955104 0.99944752 0.947708155 0.045229522 0.083111005 1.628374847 10.48886041 0.07570115 0.021630166 9.226132184 -0.965019672 -0.051739365 YVLHCQGTEEEK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVLHCQGTEEEK 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 167.71 4.85E-05 169260000 189650 217280 180680 218710 108590 194850 160970 204560 109210 FALSE TRUE 180685.6204 239421.079 188964.3567 196724.8553 127528.0616 188102.2956 136411.0701 186647.642 126145.729 1.432356226 1.897972138 1.497984578 1.559504684 1.010958219 1.491150728 1.081376842 1.479619194 1 16.94473184 2.894517885 5.612520658 1.230131779 1.632929581 0.459886888 0.206291103 0.186078008 8.260443739 0.05731391 0.061195073 784.3644205 -2.894517885 0.402797802 YVLSNQYRPDISPTER ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVLSNQYRPDISPTER 16 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y7R8;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 67.326 0.047513 25578000 63492 51439 52743 71097 43197 73003 63565 64541 38844 FALSE TRUE 60490.85899 56680.69258 55161.31872 63950.19448 50730.54312 70474.8878 53866.9918 58889.44789 44867.72913 1.348204158 1.263284184 1.229420784 1.425304907 1.130668837 1.570725534 1.20057317 1.312512334 1 15.45339055 0.22405668 1.325046241 0.999744378 1.31069166 0.386703078 0.122723603 6.22415895 9.626306841 0.103599024 0.029767122 1.675161488 -0.22405668 0.310947281 YVLTS(ph)PR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YVLTSPR 7 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 YVLTS(1)PR;YVLTS(1)PR;YVLT(0.004)S(0.996)PR;YVLT(0.004)S(0.996)PR 132.84 0.0034926 790610000 1842970 1470010 1570630 1802350 1978920 1619380 1968660 1707190 1981910 TRUE FALSE 1755856.461 1619805.69 1642644.939 1621174.354 2324043.021 1563300.465 1668304.76 1557699.393 2289254.481 0.766999246 0.707569082 0.717545801 0.708166946 1.01519645 0.682886275 0.728754612 0.680439596 1 21.12644642 -1.415478867 2.935366252 1.004796776 0.74906958 0.39322256 0.097203713 26617981.19 31227334.33 1071341.434 0.022197128 0.038416795 1.415478867 -0.255727196 YVPAIAHLIHSLNPVR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVPAIAHLIHSLNPVR 16 0 Q9H3G5;C9JLV0 Q9H3G5 CPVL Probable serine carboxypeptidase CPVL 0 198.33 2.37E-11 24839000 33917 23598 22826 23328 35157 23865 34217 27124 6900.4 FALSE TRUE 32313.81063 26002.66303 23872.59468 20983.02512 41288.36967 23038.54907 28996.56821 24748.87877 7970.47879 4.054186891 3.262371523 2.995126806 2.632592806 5.180161789 2.89048496 3.637995781 3.105068017 1 12.96045067 0.648222885 2.031867144 0.999849007 3.520132327 0.547841904 0.714270493 1.358104034 6.905701286 0.624779224 0.17184208 4.448595161 -0.648222885 2.52028332 YVQHTYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YVQHTYR 7 0 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 145.34 0.0022931 499820000 475367 306595 172134 193657 573780 230103 515063 331581 454055 FALSE TRUE 452897.344 337837.3791 180026.5142 174190.2304 673847.0503 222134.4754 436480.6796 302546.0098 524467.5304 0.863537431 0.644153088 0.343255786 0.332127768 1.284821293 0.423542855 0.832235847 0.576863185 1 19.00049393 YVSERPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YVSERPR 7 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 182.95 0.00059261 41486000 34432 33851 28129 38477 53249 28689 39244 39107 45789 FALSE TRUE 32804.4676 37300.45539 29418.74247 34609.21886 62535.60874 27695.49274 33256.60703 35682.58376 52889.72426 0.620242742 0.705249572 0.556227942 0.654365651 1.182377288 0.523646004 0.628791462 0.674660045 1 15.69069983 2.96715409 24.99767252 0.761130707 0.638249032 0.142705068 0.190740608 1648.13849 1254330.78 0.056798868 0.060286197 927.1587265 -2.96715409 -0.122881675 YVSGS(ph)SPDLVTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVS(0.003)GS(0.718)S(0.279)PDLVTR;YVS(0.041)GS(0.937)S(0.022)PDLVTR;YVS(0.005)GS(0.971)S(0.024)PDLVTR;YVSGS(0.923)S(0.077)PDLVTR;YVS(0.001)GS(0.954)S(0.044)PDLVTR;YVS(0.008)GS(0.948)S(0.044)PDLVTR 254.51 4.31E-21 835136000 1341270 1336890 1218690 1479970 1324800 1249481 1396300 1412618 1405270 TRUE FALSE 1277870.825 1473120.611 1274568.142 1331200.604 1555844.701 1206211.16 1183268.79 1288921.679 1623192.094 0.787257916 0.907545457 0.785223232 0.820112794 0.958509289 0.743110544 0.728976437 0.794066016 1 20.63040231 YVSHGATGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YVSHGATGK 9 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;; 186.16 4.20E-05 4198030000 9691950 7753840 7914590 9343100 7244070 8709640 10163410 8889470 8023140 FALSE TRUE 9233830.731 8543965.111 8277481.78 8403913.837 8507433.514 8408022.983 8612795.141 8111060.881 9267327.575 0.99638549 0.921944869 0.893189726 0.9068325 0.918002892 0.907275902 0.929372041 0.875231917 1 23.14372194 4.47324431 2.216731706 0.914866056 0.998639415 0.350171151 0.032768173 0.339551482 2.793407051 0.007199862 0.044933404 29733.38198 -4.47324431 0.083773359 YVTAFNGELEDYMSDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVTAFNGELEDYMSDR 16 0 F5H8D7 F5H8D7 XRCC1 0 ; 167.32 3.70E-09 18318000 32508 27642 27023 28153 32551 27849 32472 30022 37185 FALSE TRUE 30971.41126 30458.75123 28262.03128 25323.00695 38227.88409 26884.58215 27517.80001 27393.11452 42951.45989 0.721079361 0.709143561 0.657999317 0.589572672 0.890025256 0.625929415 0.640672054 0.637769114 1 15.39041955 -1.584217467 3.031279978 1.017260126 0.685120365 0.590875484 0.082625295 34861408.78 36594333.94 4811051.416 0.018645426 0.026048489 1.584217467 -0.332139761 YVWLVYEQDRPLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVWLVYEQDRPLK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 186.16 7.34E-06 1625510000 3113800 1506750 1887470 2891100 2224000 2333100 2946500 2597100 2338600 FALSE TRUE 2966616.845 1660289.538 1974012.366 2600481.135 2611864.896 2252304.162 2496957.309 2369684.156 2701258.144 1.098235225 0.614635644 0.730775165 0.962692566 0.96690681 0.833798194 0.924368267 0.877252017 1 21.36520009 3.225652356 24.99682269 0.919253561 0.812236807 0.145600683 0.127909699 461.2268259 893162.9392 0.037025575 0.044518476 1681.327653 -3.225652356 -0.107016755 YVWLVYEQDRPLKCDEPILSNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YVWLVYEQDRPLKCDEPILSNR 22 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 272.84 1.31E-45 2019130000 1280220 392340 1027260 972050 1237090 1000470 1922640 1180950 1526940 FALSE TRUE 1219706.538 432319.8921 1074360.887 874337.6872 1452838.104 965823.473 1629305.956 1077539.757 1763730.057 0.691549443 0.245116814 0.609141338 0.495732147 0.823730422 0.547602775 0.923784198 0.610943695 1 20.75019834 1.93598154 0.476411395 0.956921174 0.453975444 0.401169122 0.169091618 0.803174518 0.419937468 0.158292772 0.125032286 86.29418663 -1.93598154 -0.50294573 YWCDAEYDAYRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YWCDAEYDAYRR 12 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 182.35 2.72E-05 128930000 120390 85523 93149 109860 126070 106630 132380 110560 148930 FALSE TRUE 114699.4033 94237.89093 97419.97379 98816.66408 148056.5681 102937.3764 112182.9997 100878.7803 172025.3038 0.666758906 0.547814123 0.566311883 0.574430981 0.860667383 0.598385087 0.652130804 0.586418266 1 17.39226127 -5 0.34705511 5.184289377 0.617176243 0.620190628 0.090120841 275.1791218 2.27285894 855.890358 0.066477921 1.00E-05 5 -4.567113134 YWDGWFR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YWDGWFR 7 0 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 97.602 0.02763 339530000 1259510 1153700 1054350 1282720 1318440 970050 1410370 1251230 1308730 FALSE TRUE 1199975.458 1271263.342 1102692.99 1153778.549 1548375.519 936456.9253 1195192.153 1141665.668 1511681.164 0.793801952 0.840959967 0.729448125 0.763241996 1.024273871 0.619480448 0.790637723 0.755229142 1 20.52772246 -1.325324428 3.606526204 1.000768004 0.791235623 0.298982143 0.101206019 6216534.308 3426841.596 35645.42746 0.02148029 0.047279794 1.325324428 -0.20953238 YWGEIISQQYNFDRDNTEVAYLK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YWGEIISQQYNFDRDNTEVAYLK 23 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 111.83 0.00084037 53284000 47017 41466 44190 45898 41458 46462 60200 55357 42046 FALSE TRUE 44794.59959 45691.43254 46216.15521 41284.24584 48688.26207 44853.00929 51015.38435 50509.64761 48566.27894 0.922339544 0.94080571 0.951609969 0.850059892 1.002511684 0.923542225 1.050428105 1.040014774 1 15.56766733 1.744641976 7.908335223 1.032785456 0.932421424 0.582745909 0.039156005 0.077806927 16.75360691 0.017160006 0.009175584 55.54461695 -1.744641976 -0.100364033 YWGPAS(ph)PTHK ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.986)PT(0.014)HK;YWGPAS(0.994)PT(0.006)HK;YWGPAS(0.99)PT(0.01)HK;YWGPAS(0.93)PT(0.07)HK;YWGPAS(0.992)PT(0.008)HK;YWGPAS(0.756)PT(0.244)HK;YWGPAS(0.986)PT(0.014)HK;YWGPAS(0.985)PT(0.015)HK;YWGPAS(0.974)PT(0.026)HK 172.11 4.00E-06 18006720000 12719740 13798920 10431880 14912850 8082930 12338880 10935800 11337410 5152000 TRUE FALSE 12118503.1 15205045.64 10910192.02 13413781.99 9492590.433 11911581.49 9267342.86 10344646.28 5950945.847 2.036399492 2.555063687 1.833354276 2.254058822 1.595139777 2.001628279 1.557289059 1.738319679 1 22.50468756 1.227796982 0.271828762 0.831668961 2.422557095 0.678625905 0.239272446 0.968598756 0.268349329 0.599580201 0.43922631 16.89650891 -1.227796982 1.590888134 YWGPAS(ph)PTHKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YWGPASPTHKLPPSFPGNKDELMQHMDEVNDELIR 35 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.954)PT(0.046)HKLPPSFPGNKDELMQHMDEVNDELIR;YWGPAS(0.875)PT(0.125)HKLPPSFPGNKDELMQHMDEVNDELIR 187.69 1.03E-20 397800000 473947 339815 440622 476695 344600 430732 557873 474992 263651 TRUE FALSE 451544.4646 374442.5348 460824.9545 428776.7129 404698.1309 415815.6428 472759.2278 433399.1824 304536.6505 1.48272618 1.229548346 1.513200312 1.407964237 1.328897951 1.365404269 1.552388611 1.423142934 1 18.21625634 -0.73972638 5.158376734 0.999999872 1.409529343 0.661385175 0.092822171 5990934.648 1161399.225 8.670056167 0.021832359 0.182084769 0.73972638 0.409529471 YWGPASPT(ph)HKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YWGPASPTHKLPPSFPGNKDELMQHMDEVNDELIR 35 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.185)PT(0.815)HKLPPSFPGNKDELMQHMDEVNDELIR;YWGPAS(0.058)PT(0.936)HKLPPS(0.006)FPGNKDELMQHMDEVNDELIR;Y(0.002)WGPAS(0.479)PT(0.518)HKLPPS(0.001)FPGNKDELMQHMDEVNDELIR 187.35 2.07E-20 2153950000 1020220 708240 883620 956970 758310 903850 1093390 906170 572930 TRUE FALSE 971996.2225 780410.4612 924134.851 860773.5575 890559.0239 872549.4479 926573.274 826820.9509 661777.0583 1.468766876 1.179264907 1.396444376 1.300700208 1.345708517 1.318494555 1.400129035 1.249395005 1 19.33598575 0.918784413 5.515616532 1.000020524 1.337850383 0.672679159 0.075610169 0.34396199 22.43305031 0.0671504 0.016922098 8.294389264 -0.918784413 0.33782986 YWLEEAECR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YWLEEAECR 9 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 194.92 7.41E-05 408300000 922330 901920 762010 861260 886170 744190 909780 840860 871510 FALSE TRUE 878733.2888 993826.6734 796948.9122 774684.5085 1040717.767 718418.5137 770976.3517 767229.8407 1006659.32 0.872920234 0.987252245 0.791676883 0.769559764 1.033833142 0.713665984 0.765876138 0.762154411 1 19.94114409 2.21163125 24.99986074 0.78547239 0.892480171 0.100655263 0.108894348 357.841754 332199.9859 0.037827397 0.027944476 162.7913219 -2.21163125 0.10700778 YWPQEAGEYAVHVLCNSEDIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YWPQEAGEYAVHVLCNSEDIR 21 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 214.39 6.96E-25 272670000 235430 134275 177454 214010 273280 176608 296010 227000 278970 FALSE TRUE 224301.6905 147957.7752 185590.4414 192497.3082 320939.9455 170492.0207 250848.2379 207122.6766 322231.2428 0.696089208 0.459166448 0.575954212 0.597388715 0.995992638 0.529098356 0.778472738 0.642776519 1 18.29773686 2.968496907 24.97104078 0.758611593 0.571040583 0.302652904 0.152491823 812.2240029 643812.5188 0.041802504 0.044381801 930.0298909 -2.968496907 -0.18757101 YWPTADGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 4 YWPTADGR 8 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ;;; 104.21 0.010758 784090000 1286630 1009330 1031790 1219680 1501350 1054070 1332150 1116770 1502070 FALSE TRUE 1225813.55 1112181.875 1079098.592 1097075.449 1763184.965 1017567.292 1128906.051 1018979.698 1735003.344 0.706519416 0.641025781 0.621957644 0.632318925 1.016242978 0.586492986 0.650665058 0.587307052 1 20.72650701 -1.307640623 3.520094334 1.001172015 0.678906316 0.394963625 0.124336102 41101749.58 54810013.49 492333.8872 0.028136584 0.049244686 1.307640623 -0.3222657 YWQQVIDMNDYQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YWQQVIDMNDYQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 188.96 1.32E-05 100962000 146188 117048 122215 140406 138851 111263 154520 134816 155854 FALSE TRUE 139277.983 128975.3243 127818.6786 126292.1221 163066.5704 107409.9344 130945.136 123010.7963 180023.0423 0.773667533 0.716437866 0.710012879 0.701533095 0.905809436 0.59664548 0.727379864 0.683305841 1 17.45782205 -1.577355783 5.536718985 1.001247698 0.726994387 0.550738891 0.07753205 0.001078219 8.23E-05 0.067784348 0.015908277 0.026463313 1.577355783 -0.27425331 YWSQFDENIR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YWSQFDENIR 10 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 136.57 0.0096812 0 100110 85672 93721 103330 108880 92954 102770 103030 118680 FALSE TRUE 95377.9987 94402.0742 98018.20055 92943.07209 127868.6375 89734.97967 87090.549 94008.147 137084.2883 0.695761709 0.688642553 0.715021406 0.67799945 0.932773837 0.654597115 0.63530657 0.68576894 1 17.0647037 -1.123842066 4.305772051 1.000043986 0.705861739 0.549761265 0.082163544 3.80E-05 7.72E-06 0.077097654 0.018169028 0.075189628 1.123842066 -0.294182247 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Trastuzumab_2h_R1 16 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR 32 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;; 353.56 1.59E-131 2255611000 697649.9 768325 619646.4 785680 645787 699476.1 651017 675194.5 588076.1 FALSE TRUE 664673.3718 846618.191 648057.8004 706701.9537 758412.0483 675253.0673 551692.3999 616070.8901 679271.9381 0.97850851 1.246361205 0.954047656 1.040381494 1.116507257 0.994083561 0.812181939 0.906957664 1 19.37362973 1.98376112 5.618025353 0.888461352 1.076063782 0.386218821 0.091279239 0.1464449 15.48362646 0.036788304 0.023919685 96.32990234 -1.98376112 0.187602431 YWVSGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YWVSGR 6 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ;;;;; 177.91 0.0083285 1767260000 2820380 2245150 2360180 2626220 3070760 2305210 3629660 2701910 3050310 FALSE TRUE 2687066.227 2473933.338 2468396.588 2362227.376 3606299.572 2225380 3075888.704 2465316.437 3523336.496 0.762648197 0.702156419 0.700584968 0.670451823 1.023546736 0.631611543 0.873004525 0.699710754 1 21.74851084 -4.999999999 0.181373488 1.992408648 0.709123349 0.304348759 0.114389301 153.5384408 1.481689226 54.9060183 0.30842973 1.00E-05 4.999999999 -1.2832853 YYAGWADK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 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 ;; 124.08 0.0030712 588820000 1067760 1094750 907640 1031460 712320 899200 987310 1042470 727310 FALSE TRUE 1017289.101 1206306.27 949256.1918 927775.6812 836548.3825 868060.4785 836677.7263 951185.8003 840097.5202 1.210917871 1.435912189 1.129935715 1.104366647 0.995775326 1.033285372 0.995929289 1.132232601 1 19.68019728 3.49692651 3.125125961 1.037905459 1.32268693 0.714348877 0.071508851 0.110920551 2.206227187 0.019098182 0.029321117 3139.977313 -3.49692651 0.28478147 YYAGWADKYHGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYAGWADKYHGK 12 1 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 165.7 3.24E-05 3023400000 5564400 3861500 4187800 4189200 4274400 4194700 5482300 5041300 3996400 FALSE TRUE 5301381.84 4254991.24 4379814.772 3768093.657 5019854.007 4049436.487 4645874.446 4599857.046 4616141.301 1.148444446 0.921763647 0.948804312 0.816286463 1.087456748 0.877234084 1.006441125 0.996472323 1 22.13825596 4.597519363 2.82381091 0.955170224 1.157063513 0.389282746 0.075041491 0.297410102 3.923285878 0.016667411 0.118150696 39583.97127 -4.597519363 0.201893289 YYDDTYPSVK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYDDTYPSVK 10 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 120.12 0.0014006 38900000 119980 109560 105000 135050 95553 129400 131990 120840 120170 FALSE TRUE 114308.7832 120724.2886 109814.3539 121474.5174 112217.4129 124918.8456 111852.5013 110258.609 138805.3499 0.82351857 0.869738009 0.791139203 0.875142907 0.808451642 0.899956995 0.805822697 0.794339765 1 17.08270365 -1.482968906 3.111654123 1.004022873 0.836105736 0.665826118 0.037026489 11765354.98 13506179.21 404363.2561 0.008078323 0.032887518 1.482968906 -0.167917137 YYDSRPGGYGYGYGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 7 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;;;; 191.19 1.69E-07 7719170000 5959980 5885970 5968700 6826070 7124570 6017320 7639880 6698040 7148520 FALSE TRUE 5678263.557 6485757.035 6242370.799 6139900.475 8367092.752 5808938.7 6474275.99 6111524.109 8257075.972 0.687684548 0.785478668 0.756002587 0.743592586 1.013323939 0.703510385 0.784088219 0.740155974 1 22.97719955 -5 0.287275256 2.698383597 0.761470674 0.373558493 0.090078143 257.9021923 2.440229091 262.5801248 0.09188721 1.00E-05 5 -1.936912923 YYEGYYAAGPGYGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYEGYYAAGPGYGGR 15 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 192.5 3.07E-07 378270000 241870 166292 186418 238620 222310 179167 227660 208566 213920 FALSE TRUE 230437.2844 183237.3439 194965.4497 214633.4643 261080.7936 172962.4019 192926.2857 190302.8554 247093.621 0.932590989 0.741570515 0.789034735 0.868632154 1.056606773 0.699987321 0.780782138 0.770164987 1 17.91469824 -0.465349231 7.416121565 1.000000042 0.825672565 0.210465558 0.103234464 0 0 0.096635602 0.02277723 0.342492266 0.465349231 -0.174327477 YYFSHDTD ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYFSHDTD 8 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 174.64 0.00062991 337950000 845160 740450 710440 862490 927380 722780 912520 859960 789870 FALSE TRUE 805210.9617 815902.6968 743014.3767 775790.8666 1089114.778 697749.9474 773298.3144 784657.3435 912359.0055 0.88255934 0.894278121 0.814388165 0.850313157 1.193734891 0.764775646 0.847581171 0.860031346 1 19.7992421 4.834165364 0.007602934 1.750606853 7.05E-06 0.03408219 0.117682081 69523.88468 79.84693727 8676.486731 9730.220743 68259.85539 -4.834165364 -1.750599802 YYGGGSEGGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYGGGSEGGR 10 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 112.17 0.0038529 63234000 92283 66036 61183 76642 73281 65545 69753 62878 74166 FALSE TRUE 87920.96548 72765.14348 63988.30107 68937.80055 86061.1832 63275.16021 59110.89875 57372.06898 85667.28449 1.02630737 0.849392436 0.746939762 0.804715604 1.004598006 0.73861522 0.690005515 0.669708038 1 16.38645674 2.1973223 24.70046465 0.742093152 0.884013983 0.14791704 0.122721421 186.2910382 111581.299 0.043955829 0.032463888 157.5151389 -2.1973223 0.14192083 YYGTKDPVPGYSVPAAEHSTITAWGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYGTKDPVPGYSVPAAEHSTITAWGK 26 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 114.41 0.00084137 109750000 164440 128270 154220 163290 136240 139360 190530 191600 152130 FALSE TRUE 156667.2471 141340.8588 161291.1395 146875.779 160000.2129 134533.9283 161461.1492 174822.4883 175721.5434 0.891565394 0.804345649 0.917879142 0.835843893 0.910532708 0.765608619 0.918846637 0.994883637 1 17.42293155 1.417956556 3.886991176 0.99482908 0.854523739 0.613623979 0.046690692 0.133390551 3.470299273 0.030406177 0.010664068 26.17921114 -1.417956556 -0.140305341 YYHSPTNTVHMYPPEMAPSSAPPSTPPT(ph)HK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSSAPPS(0.309)T(0.309)PPT(0.383)HK 78.921 0.0024804 44071000 57938 57389 54321 69925 52456 56220 68046 62977 15217 TRUE FALSE 55199.38556 63237.00435 56811.67158 62896.00615 61604.30979 54273.0873 57664.33295 57462.40002 17576.77464 3.140472964 3.597759295 3.232201171 3.578358796 3.50486998 3.087772837 3.280711855 3.269223233 1 14.10138274 -1.283320072 0.526552881 4.32E-14 3.390901409 0.949672038 0.169309989 6.035480172 0.833589534 8.726763458 0.071264457 0.052081074 1.283320072 3.390901409 YYIADR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYIADR 6 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 102.98 0.081604 750490000 942230 765970 759800 861870 1017110 779070 994760 906470 1198400 FALSE TRUE 897692.6552 844023.2138 794637.5815 775233.1902 1194493.662 752090.6106 842991.092 827094.6813 1384241.751 0.648508582 0.609736856 0.574059828 0.560041762 0.862922723 0.543323166 0.608991234 0.597507394 1 20.40066449 -1.262173496 3.932316771 1.000471238 0.624333042 0.63402392 0.089381139 12514953.06 4017090.046 50205.43361 0.019206594 0.054679748 1.262173496 -0.376138196 YYIDADLLR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYIDADLLR 9 0 Q7Z3B4-2;Q7Z3B4-3;Q7Z3B4 Q7Z3B4-2 NUP54 Nucleoporin p54 0 ; 126.41 0.0011033 116289000 346020 264010 203821 207731 396780 223150 384420 278220 366230 FALSE TRUE 329664.3203 290912.9192 213166.3945 186849.4852 465978.3064 215422.2595 325769.6686 253857.5819 423023.078 0.779305758 0.687699878 0.503911974 0.441700453 1.101543463 0.509244698 0.770099046 0.600103387 1 18.69037685 YYITIIDAPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYITIIDAPGHR 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 178.81 2.15E-05 801700000 1535090 1899560 1413410 1753960 1391070 1430680 1313330 1523270 1014710 FALSE TRUE 1462529.338 2093127.324 1478216.247 1577648.608 1633672.168 1381135.193 1112957.388 1389884.403 1172066.044 1.24782161 1.78584418 1.26120559 1.346040708 1.393839686 1.178376594 0.949568834 1.18584137 1 20.16062244 2.279878022 1.180219676 1.020045781 1.46917213 0.5012946 0.162764542 0.349532796 0.946143616 0.102449035 0.060371493 190.4925618 -2.279878022 0.449126349 YYKVDENGK ddPTM_SK-BR-3_Trastuzumab_2h_R1 6 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;; 155.15 6.75E-05 5530620000 17387900 12844500 18078200 19339600 13938700 20828500 25158600 23698800 17693200 FALSE TRUE 16566008.43 14153369.15 18907103.35 17395546.67 16369604.87 20107203.82 21320193.5 21623607.44 20436971.09 0.810590197 0.692537514 0.925142149 0.851180275 0.800979988 0.983864181 1.043216894 1.05806322 1 24.28467806 2.161023538 3.375777926 1.03474988 0.803861633 0.748681543 0.059294402 0.119788059 2.727472454 0.025865553 0.018260723 144.8850377 -2.161023538 -0.230888246 YYLHDDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 125.25 0.011864 365820000 1772460 1652600 1406780 1787730 2229690 1302580 1832200 1628900 2215330 FALSE TRUE 1688679.328 1821001.819 1471282.254 1608023.984 2618547.23 1257471.328 1552664.239 1486264.881 2558872.062 0.659931129 0.711642386 0.574972964 0.628411247 1.023320888 0.491416256 0.606776815 0.580828132 1 21.28707659 -1.001094042 4.638438999 1.000006886 0.660207233 0.363323232 0.141585972 12351769.9 2665828.35 994.1940162 0.032069774 0.099748405 1.001094042 -0.339799653 YYPTEDVPR ddPTM_SK-BR-3_Trastuzumab_2h_R1 5 YYPTEDVPR 9 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;;; 237.81 6.67E-10 2636760000 3604580 3258950 3393560 3909120 4086809 3374190 4161660 3716190 4180160 FALSE TRUE 3434198.647 3591040.71 3549158.083 3516167.831 4799547.196 3257340.954 3526722.333 3390780.703 4828397.864 0.711250138 0.74373339 0.735059161 0.728226615 0.994024795 0.674621489 0.730412537 0.702257933 1 22.20311313 -2.189388347 2.40124078 1.71190554 0.750214799 0.43701535 0.088269212 5042828.737 1168596.784 19528726.64 0.020158909 0.006465642 2.189388347 -0.96169074 YYPTEDVPRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 3 YYPTEDVPRK 10 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;; 146.11 4.69E-05 1574580000 1143250 964890 1158850 1139420 996520 1241570 1332610 1268910 1209000 FALSE TRUE 1089210.838 1063213.388 1211984.419 1024883.337 1170312.772 1198574.12 1129295.869 1157797.513 1396485.545 0.779965709 0.761349368 0.867881822 0.733901858 0.838041451 0.85827893 0.808669931 0.829079483 1 20.41336921 -5 0.174819004 1.785505494 0.761293296 0.713492991 0.0391311 65.43307363 0.623642906 17.78420596 0.119215022 1.00E-05 5 -1.024212198 YYQDCSGGDRK ddPTM_SK-BR-3_Trastuzumab_2h_R1 1 YYQDCSGGDRK 11 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 0 83.182 0.027101 80825000 144970 119070 124740 127100 132770 144010 144120 144730 176850 FALSE TRUE 138117.5554 131203.3684 130459.4524 114323.6665 155925.046 139022.8976 122131.8471 132056.6739 204274.9948 0.6761354 0.642287954 0.638646216 0.559655707 0.763309509 0.680567378 0.597879575 0.646465193 1 17.64015309 -1.234104069 5.225728144 1.00003489 0.649198247 0.809388609 0.053280237 2.05E-05 3.01E-06 0.048848263 0.011512503 0.058330531 1.234104069 -0.350836643 YYS(ph)DS(ph)DDELTVEQR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYSDSDDELTVEQR 14 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 2 YYS(1)DS(1)DDELTVEQR;YYS(1)DS(1)DDELTVEQR 196.22 1.29E-07 0 271700 217133 245030 272840 225370 235210 283550 230670 243430 TRUE FALSE 258857.2795 239259.0996 256264.8679 245413.6048 264674.4566 227064.6187 240289.2397 210471.3119 281179.8811 0.920610957 0.850911163 0.911391195 0.872799305 0.941299412 0.807542196 0.854574797 0.748529059 1 18.10113385 2.229239444 24.96921965 0.840867596 0.89405373 0.092643369 0.067246699 370.4382005 992308.28 0.021809368 0.016326226 169.5272213 -2.229239444 0.053186133 YYSHVDYR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYSHVDYR 8 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8VWU8;F8VPY7;F8VRK2 F8W0Q9 PPHLN1 Periphilin-1 0 ; 126.41 0.0012203 208320000 322640 242880 225610 232420 340510 230280 338080 270270 313780 FALSE TRUE 307389.4466 267629.7481 235954.4417 209056.7 399894.8362 222305.3459 286499.6867 246603.726 362439.3998 0.848112669 0.738412403 0.651017637 0.576804564 1.103342618 0.613358663 0.79047611 0.680399885 1 18.46738027 YYTLFGR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYTLFGR 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 114.19 0.013869 1853010000 1752580 1222310 1032790 1043920 1864310 1031970 2125400 1582500 1570180 FALSE TRUE 1669739.017 1346864.779 1080144.443 938983.1783 2189445.074 996232.6201 1801131.194 1443927.911 1813675.495 0.920638241 0.742616186 0.595555515 0.517723915 1.207186776 0.549289342 0.993083492 0.79613355 1 20.79048492 2.769781782 24.99199265 0.885762578 0.721904619 0.218453972 0.196272793 1289.034964 1031847.602 0.056450871 0.059869823 588.5478562 -2.769781782 -0.16385796 YYTSASGDEMVS(ph)LKDYCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 2 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 YYTSASGDEMVS(1)LKDYCTR;YYTSASGDEMVS(1)LKDYCTR 196.55 5.02E-16 429470000 244080 190093 204760 208680 146063 236750 252680 259710 179513 TRUE FALSE 232542.8221 209463.6928 214148.4485 187703.0899 171536.341 228551.2881 214129.0252 236968.4156 207350.9592 1.121493833 1.010189167 1.032782531 0.905243413 0.827275367 1.102243698 1.032688858 1.142837325 1 17.6617152 -0.005829106 7.534429509 0.999999999 1.02217241 0.00508254 0.095951489 4563482.075 605683.7822 0.092265425 0.023066356 0.98666766 0.005829106 0.02217241 YYTSASGDEMVSLKDYCTR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 313.56 1.21E-61 4521247000 4616160 2631393 4590211 3882862 4702475 4300175 6457051 5095757 6350555 FALSE TRUE 4397963.265 2899534.938 4800676.715 3492549.335 5522585.151 4151258.862 5471909.278 4649545.503 7335366.635 0.599556025 0.395281529 0.654456274 0.476124713 0.752871046 0.565923841 0.745962615 0.633853185 1 22.80643765 -0.689997816 0.192223611 1.308886603 0.437584957 0.648874234 0.098210015 8.675381018 0.427031231 1.784928071 0.305320945 0.204174821 0.689997816 -0.871301646 YYTVFDR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YYTVFDR 7 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;; 189.62 0.0012852 6109565000 12448544 11203840 9680956 13232644 12285649 9940621 12447651 11628417 10961444 FALSE TRUE 11860126 12345524.03 10124837.41 11902473.48 14428262.3 9596374.802 10548533.22 10610171.16 12661288.75 0.936723443 0.975060618 0.799668786 0.940068086 1.139557163 0.757930333 0.833132664 0.838000884 1 23.59392092 YYTVFDRDNNR ddPTM_SK-BR-3_Trastuzumab_2h_R1 10 YYTVFDRDNNR 11 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;; 224.66 5.51E-12 26377190000 9573410 5515840 6627890 6636230 10631710 6691780 10947640 8077070 11263300 FALSE TRUE 9120893.882 6077910.367 6931785.312 5969143.552 12485876.86 6460041.981 9277376.451 7369798.932 13009955.04 0.701070361 0.467173818 0.532806247 0.458813542 0.959717141 0.496546065 0.713098272 0.56647382 1 23.63311264 -5 0.227764809 3.087457098 0.563283015 0.393910169 0.151098194 154.4744196 1.545300649 148.3096481 0.242521413 1.00E-05 5 -2.524174083 YYVTIIDAPGHR ddPTM_SK-BR-3_Trastuzumab_2h_R1 9 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 ;;;;;;;; 202.16 1.40E-07 24527746000 8700514 11028000 8415493 9790879 8203250 8701489 8095652 9077070 6324301 FALSE TRUE 8289257.946 12151765.74 8801351.678 8806681.241 9633894.203 8400154.254 6860511.601 8282233.63 7305041.299 1.134731154 1.663476665 1.204832569 1.205562143 1.318800785 1.149911946 0.939147545 1.133769583 1 22.800461 2.308368218 0.993648664 1.000862428 1.3662509 0.393799605 0.153079035 0.479731133 0.916611602 0.105690622 0.063523542 203.4080884 -2.308368218 0.365388472